Carrel name: keyword-sars-cord Creating study carrel named keyword-sars-cord Initializing database file: cache/cord-015009-3o90pzw7.json key: cord-015009-3o90pzw7 authors: nan title: How and who does SARS kill? date: 2003-06-10 journal: Nature DOI: 10.1038/nature.2003.2 sha: doc_id: 15009 cord_uid: 3o90pzw7 file: cache/cord-007581-nu1shltl.json key: cord-007581-nu1shltl authors: Wang, Jiun-Ling; Wang, Jann-Tay; Yu, Chong-Jen; Chen, Yee-Chun; Hsueh, Po-Ren; Hsiao, Cheng-Hsiang; Kao, Chuan-Liang; Chang, Shan-Chwen; Yang, Pan-Chyr title: Rhabdomyolysis associated with probable SARS date: 2003-10-01 journal: Am J Med DOI: 10.1016/s0002-9343(03)00448-0 sha: doc_id: 7581 cord_uid: nu1shltl file: cache/cord-006890-81wv1s33.json key: cord-006890-81wv1s33 authors: Viret, Jean-Francois; Glück, Reinhard; Moser, Christian title: Development of a SARS vaccine: an industrial perspective on the global race against a global disease date: 2014-01-09 journal: Expert Rev Vaccines DOI: 10.1586/14760584.2.4.465 sha: doc_id: 6890 cord_uid: 81wv1s33 file: cache/cord-000333-4prvgmvt.json key: cord-000333-4prvgmvt authors: Darbyshire, Philip title: Nursing heroism in the 21(st )Century' date: 2011-02-16 journal: BMC Nurs DOI: 10.1186/1472-6955-10-4 sha: doc_id: 333 cord_uid: 4prvgmvt file: cache/cord-004634-pkrxiipo.json key: cord-004634-pkrxiipo authors: Brun-Buisson, Christian title: SARS: The challenge of emerging pathogens to the intensivist date: 2003-05-08 journal: Intensive Care Med DOI: 10.1007/s00134-003-1823-y sha: doc_id: 4634 cord_uid: pkrxiipo file: cache/cord-007567-vst954ef.json key: cord-007567-vst954ef authors: Farquharson, Carolyn; Baguley, Karen title: Responding to the severe acute respiratory syndrome (SARS) outbreak: Lessons learned in a Toronto emergency department() date: 2003-06-04 journal: J Emerg Nurs DOI: 10.1067/men.2003.109 sha: doc_id: 7567 cord_uid: vst954ef file: cache/cord-007049-02p8ug67.json key: cord-007049-02p8ug67 authors: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 journal: Clin Infect Dis DOI: 10.1086/421784 sha: doc_id: 7049 cord_uid: 02p8ug67 file: cache/cord-009153-zxx4m1kz.json key: cord-009153-zxx4m1kz authors: Heymann, David L; Aylward, R Bruce; Wolff, Christopher title: Dangerous pathogens in the laboratory: from smallpox to today's SARS setbacks and tomorrow's polio-free world date: 2004-05-15 journal: Lancet DOI: 10.1016/s0140-6736(04)16234-x sha: doc_id: 9153 cord_uid: zxx4m1kz file: cache/cord-008841-r17qhfsj.json key: cord-008841-r17qhfsj authors: Tomlinson, Brian; Cockram, Clive title: SARS: experience at Prince of Wales Hospital, Hong Kong date: 2003-05-03 journal: Lancet DOI: 10.1016/s0140-6736(03)13218-7 sha: doc_id: 8841 cord_uid: r17qhfsj file: cache/cord-010384-wyp7hrde.json key: cord-010384-wyp7hrde authors: Iwen, Peter C; Stiles, Karen L; Pentella, Michael A title: Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-04-10 journal: Lab Med DOI: 10.1093/labmed/lmaa018 sha: doc_id: 10384 cord_uid: wyp7hrde file: cache/cord-014897-rnrlslfh.json key: cord-014897-rnrlslfh authors: Rong-bing, Wang; Jun-min, Liu; Yu-yong, Jiang; Yun-zhong, Wu; Xiao-jing, Wang; Pin-pin, Chi; Feng-xia, Sun; Lian-yin, Gao title: Therapeutic effects of integrated traditional Chinese medicine and western medicine in treating severe acute respiratory syndrome date: 2003 journal: Chin J Integr Med DOI: 10.1007/bf02838610 sha: doc_id: 14897 cord_uid: rnrlslfh file: cache/cord-011813-lm105z6n.json key: cord-011813-lm105z6n authors: Imperiale, Michael J. title: Recurring Themes date: 2020-07-08 journal: mSphere DOI: 10.1128/msphere.00633-20 sha: doc_id: 11813 cord_uid: lm105z6n file: cache/cord-015516-hx7ktq8j.json key: cord-015516-hx7ktq8j authors: nan title: In the Literature date: 2005-10-15 journal: Clin Infect Dis DOI: 10.1086/497097 sha: doc_id: 15516 cord_uid: hx7ktq8j file: cache/cord-016120-pz2q62i7.json key: cord-016120-pz2q62i7 authors: Zhang, Jie title: Chai Jing: The Power of Vulnerability date: 2019-02-16 journal: Female Celebrities in Contemporary Chinese Society DOI: 10.1007/978-981-13-5980-4_3 sha: doc_id: 16120 cord_uid: pz2q62i7 file: cache/cord-016844-lq2bgu7a.json key: cord-016844-lq2bgu7a authors: Teksam, Ozlem; Bayrakci, Benan title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective date: 2013-05-29 journal: Noninvasive Ventilation in High-Risk Infections and Mass Casualty Events DOI: 10.1007/978-3-7091-1496-4_29 sha: doc_id: 16844 cord_uid: lq2bgu7a file: cache/cord-016451-k8m2xz0e.json key: cord-016451-k8m2xz0e authors: Chertow, Daniel S.; Kindrachuk, Jason title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 journal: Highly Infectious Diseases in Critical Care DOI: 10.1007/978-3-030-33803-9_5 sha: doc_id: 16451 cord_uid: k8m2xz0e file: cache/cord-007560-nck4f5ny.json key: cord-007560-nck4f5ny authors: Ling, Lowell; Joynt, Gavin M.; Lipman, Jeff; Constantin, Jean-Michel; Joannes-Boyau, Olivier title: COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics date: 2020-02-20 journal: Anaesth Crit Care Pain Med DOI: 10.1016/j.accpm.2020.02.002 sha: doc_id: 7560 cord_uid: nck4f5ny file: cache/cord-017668-my2l85bn.json key: cord-017668-my2l85bn authors: Cho, Yeon-Jin; Kim, Hyeoncheol title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction date: 2005 journal: Knowledge-Based Intelligent Information and Engineering Systems DOI: 10.1007/11553939_111 sha: doc_id: 17668 cord_uid: my2l85bn file: cache/cord-018106-5giapmcf.json key: cord-018106-5giapmcf authors: Levin, Jacqueline title: Mental Health Care for Survivors and Healthcare Workers in the Aftermath of an Outbreak date: 2019-05-16 journal: Psychiatry of Pandemics DOI: 10.1007/978-3-030-15346-5_11 sha: doc_id: 18106 cord_uid: 5giapmcf file: cache/cord-012424-z3mkp9y9.json key: cord-012424-z3mkp9y9 authors: Bansal, Poonam; Fory, Elissa K.; Malik, Shaneela; Memon, Anza B. title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) date: 2020-08-13 journal: Radiology DOI: 10.1148/radiol.2020203132 sha: doc_id: 12424 cord_uid: z3mkp9y9 file: cache/cord-015503-j99cgsjt.json key: cord-015503-j99cgsjt authors: Tang, Xiaolu; Wu, Changcheng; Li, Xiang; Song, Yuhe; Yao, Xinmin; Wu, Xinkai; Duan, Yuange; Zhang, Hong; Wang, Yirong; Qian, Zhaohui; Cui, Jie; Lu, Jian title: On the origin and continuing evolution of SARS-CoV-2 date: 2020-03-03 journal: Natl Sci Rev DOI: 10.1093/nsr/nwaa036 sha: doc_id: 15503 cord_uid: j99cgsjt file: cache/cord-016897-t71f10kv.json key: cord-016897-t71f10kv authors: Flores, Marco V.; Cohen, Mark title: Preventing Airborne Disease Transmission: Implications for Patients During Mechanical Ventilation date: 2013-05-29 journal: Noninvasive Ventilation in High-Risk Infections and Mass Casualty Events DOI: 10.1007/978-3-7091-1496-4_34 sha: doc_id: 16897 cord_uid: t71f10kv file: cache/cord-015183-1eytelxn.json key: cord-015183-1eytelxn authors: Walgate, Robert title: Latest SARS evidence date: 2003-04-07 journal: Genome Biol DOI: 10.1186/gb-spotlight-20030407-01 sha: doc_id: 15183 cord_uid: 1eytelxn file: cache/cord-015181-875gf11z.json key: cord-015181-875gf11z authors: Walgate, Robert title: SARS escaped Beijing lab twice date: 2004-04-27 journal: Genome Biol DOI: 10.1186/gb-spotlight-20040427-03 sha: doc_id: 15181 cord_uid: 875gf11z file: cache/cord-010050-utbrf4ad.json key: cord-010050-utbrf4ad authors: Fisher, Dale A; Chew, Madeleine H L; Lim, Yean‐Teng; Tambyah, Paul A title: Preventing local transmission of SARS: lessons from Singapore date: 2003-06-02 journal: Med J Aust DOI: 10.5694/j.1326-5377.2003.tb05358.x sha: doc_id: 10050 cord_uid: utbrf4ad file: cache/cord-017942-og0b2l6b.json key: cord-017942-og0b2l6b authors: Chen, Yi-Da; Tseng, Chunju; King, Chwan-Chuen; Wu, Tsung-Shu Joseph; Chen, Hsinchun title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data date: 2007 journal: Intelligence and Security Informatics: Biosurveillance DOI: 10.1007/978-3-540-72608-1_3 sha: doc_id: 17942 cord_uid: og0b2l6b file: cache/cord-009573-ghv9uezx.json key: cord-009573-ghv9uezx authors: Karlberg, J; Lai, WYY title: Do sensational media reports about severe acute respiratory syndrome affect the mindset of healthcare workers? date: 2007-01-02 journal: Acta Paediatr DOI: 10.1111/j.1651-2227.2003.tb00508.x sha: doc_id: 9573 cord_uid: ghv9uezx file: cache/cord-015552-pm9kdqdw.json key: cord-015552-pm9kdqdw authors: Kreuder-Sonnen, Christian title: China vs the WHO: a behavioural norm conflict in the SARS crisis date: 2019-05-01 journal: Int Aff DOI: 10.1093/ia/iiz022 sha: doc_id: 15552 cord_uid: pm9kdqdw file: cache/cord-017108-vqbl0eov.json key: cord-017108-vqbl0eov authors: Zheng, Xiaolong; Zeng, Daniel; Sun, Aaron; Luo, Yuan; Wang, Quanyi; Wang, Feiyue title: Network-Based Analysis of Beijing SARS Data date: 2008 journal: Biosurveillance and Biosecurity DOI: 10.1007/978-3-540-89746-0_7 sha: doc_id: 17108 cord_uid: vqbl0eov file: cache/cord-017354-cndb031c.json key: cord-017354-cndb031c authors: Janies, D.; Pol, D. title: Large-Scale Phylogenetic Analysis of Emerging Infectious Diseases date: 2008 journal: Tutorials in Mathematical Biosciences IV DOI: 10.1007/978-3-540-74331-6_2 sha: doc_id: 17354 cord_uid: cndb031c file: cache/cord-018265-twp33bb6.json key: cord-018265-twp33bb6 authors: Becker, Pablo D.; Guzmán, Carlos A. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 journal: Community-Acquired Pneumonia DOI: 10.1007/978-3-7643-7563-8_10 sha: doc_id: 18265 cord_uid: twp33bb6 file: cache/cord-009295-4c0zwhdh.json key: cord-009295-4c0zwhdh authors: Bal, A.; Destras, G.; Gaymard, A.; Bouscambert-Duchamp, M.; Valette, M.; Escuret, V.; Frobert, E.; Billaud, G.; Trouillet-Assant, S.; Cheynet, V.; Brengel-Pesce, K.; Morfin, F.; Lina, B.; Josset, L. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.03.020 sha: doc_id: 9295 cord_uid: 4c0zwhdh file: cache/cord-018101-zd4v222b.json key: cord-018101-zd4v222b authors: Kawashima, Kent; Matsumoto, Tomotaka; Akashi, Hiroshi title: Disease Outbreaks: Critical Biological Factors and Control Strategies date: 2016-05-31 journal: Urban Resilience DOI: 10.1007/978-3-319-39812-9_10 sha: doc_id: 18101 cord_uid: zd4v222b file: cache/cord-007713-611sp7uo.json key: cord-007713-611sp7uo authors: Hughes, J. 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Karen title: Infectious disease: Inextricable linkages between human and ecosystem health date: 2006-06-06 journal: Biol Conserv DOI: 10.1016/j.biocon.2006.05.007 sha: doc_id: 15613 cord_uid: ls9qus8y file: cache/cord-013269-u1e0kzmm.json key: cord-013269-u1e0kzmm authors: Cucinotta, Domenico title: Primum non nocere (first do no harm). 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N.; Richardus, Jan Hendrik; Cao, Wu‐Chun title: Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date: 2009-06-05 journal: Trop Med Int Health DOI: 10.1111/j.1365-3156.2009.02255.x sha: doc_id: 23463 cord_uid: vr6uaw3a file: cache/cord-016160-ugc7ce21.json key: cord-016160-ugc7ce21 authors: Ching, Frank title: Bird Flu, SARS and Beyond date: 2018-03-15 journal: 130 Years of Medicine in Hong Kong DOI: 10.1007/978-981-10-6316-9_14 sha: doc_id: 16160 cord_uid: ugc7ce21 file: cache/cord-016990-ot1wi3xi.json key: cord-016990-ot1wi3xi authors: Zaki, Sherif R.; Paddock, Christopher D. title: Viral Infections of the Lung date: 2008 journal: Dail and Hammar’s Pulmonary Pathology DOI: 10.1007/978-0-387-68792-6_11 sha: doc_id: 16990 cord_uid: ot1wi3xi file: cache/cord-023867-ti4b03lh.json key: cord-023867-ti4b03lh authors: Zuo, Wei; Zhao, Xingang; Chen, Ye-Guang title: SARS Coronavirus and Lung Fibrosis date: 2009-07-22 journal: Molecular Biology of the SARS-Coronavirus DOI: 10.1007/978-3-642-03683-5_15 sha: doc_id: 23867 cord_uid: ti4b03lh file: cache/cord-014938-7evmiuv5.json key: cord-014938-7evmiuv5 authors: Wei-ming, Yan; 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Saiful; Rahman, Kazi M.; Sun, Yanni; Qureshi, Mohammed O.; Abdi, Ikram; Chughtai, Abrar A.; Seale, Holly title: Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis date: 2020-05-15 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.237 sha: doc_id: 252714 cord_uid: idlyl4ga file: cache/cord-252725-e3pazjdi.json key: cord-252725-e3pazjdi authors: Khalil, Ayman; Tazeddinova, Diana title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 journal: Nat Prod Bioprospect DOI: 10.1007/s13659-020-00271-z sha: doc_id: 252725 cord_uid: e3pazjdi file: cache/cord-252818-1gms4zw3.json key: cord-252818-1gms4zw3 authors: Bouayed, Jaouad; Bohn, Torsten title: Behavioural manipulation ‐ key to the successful global spread of the new Coronavirus SARS‐Cov‐2? date: 2020-08-19 journal: J Med Virol DOI: 10.1002/jmv.26446 sha: doc_id: 252818 cord_uid: 1gms4zw3 file: cache/cord-252873-4tazhf40.json key: cord-252873-4tazhf40 authors: Kruglikov, Ilja L.; Scherer, Philipp E. title: The role of adipocytes and adipocyte‐like cells in the severity of COVID‐19 infections date: 2020-04-27 journal: Obesity (Silver Spring) DOI: 10.1002/oby.22856 sha: doc_id: 252873 cord_uid: 4tazhf40 file: cache/cord-252933-bu4oihem.json key: cord-252933-bu4oihem authors: Xu, Jieqing Jessica; Samaha, Daniel; Mondhe, Suhas; Massicotte‐Azarniouch, David; Knoll, Gregory; Ruzicka, Marcel title: Renal Infarct in a COVID‐19 Positive Kidney‐Pancreas Transplant Recipient date: 2020-06-01 journal: Am J Transplant DOI: 10.1111/ajt.16089 sha: doc_id: 252933 cord_uid: bu4oihem file: cache/cord-252671-uf96jgig.json key: cord-252671-uf96jgig authors: Wang, Yi; Liu, Li title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism date: 2016-02-09 journal: mBio DOI: 10.1128/mbio.01872-15 sha: doc_id: 252671 cord_uid: uf96jgig file: cache/cord-252980-1e28zj1d.json key: cord-252980-1e28zj1d authors: Zhang, Jiahao; Jia, Weixin; Zhu, Junhai; Li, Bo; Xing, Jinchao; Liao, Ming; Qi, Wenbao title: Insights into the cross-species evolution of 2019 novel coronavirus date: 2020-03-04 journal: J Infect DOI: 10.1016/j.jinf.2020.02.025 sha: doc_id: 252980 cord_uid: 1e28zj1d file: cache/cord-252767-as841xo0.json key: cord-252767-as841xo0 authors: Fischer, Bastian; Knabbe, Cornelius; Vollmer, Tanja title: SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, March to June 2020 date: 2020-07-16 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.28.2001285 sha: doc_id: 252767 cord_uid: as841xo0 file: cache/cord-252804-u7tz6xzz.json key: cord-252804-u7tz6xzz authors: Ciotti, Marco; Angeletti, Silvia; Minieri, Marilena; Giovannetti, Marta; Benvenuto, Domenico; Pascarella, Stefano; Sagnelli, Caterina; Bianchi, Martina; Bernardini, Sergio; Ciccozzi, Massimo title: COVID-19 Outbreak: An Overview date: 2020-04-07 journal: Chemotherapy DOI: 10.1159/000507423 sha: doc_id: 252804 cord_uid: u7tz6xzz file: cache/cord-252857-vaq0kwln.json key: cord-252857-vaq0kwln authors: Rejdak, Konrad; Grieb, Paweł title: Adamantanes might be protective from COVID-19 in patients with neurological diseases: multiple sclerosis, parkinsonism and cognitive impairment date: 2020-04-30 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102163 sha: doc_id: 252857 cord_uid: vaq0kwln file: cache/cord-252910-7qvnj6c8.json key: cord-252910-7qvnj6c8 authors: Li, Xin; Jin, Xiufeng; Chen, Shunmei; Wang, Liangge; Yau, Tung On; Yang, Jianyi; Hong, Zhangyong; Ruan, Jishou; Duan, Guangyou; Gao, Shan title: The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date: 2020-09-21 journal: bioRxiv DOI: 10.1101/2020.07.22.213926 sha: doc_id: 252910 cord_uid: 7qvnj6c8 file: cache/cord-253179-pi5uq90z.json key: cord-253179-pi5uq90z authors: Yu, Jing; Ouyang, Wen; Chua, Melvin L.K.; Xie, Conghua title: SARS-CoV-2 transmission in cancer patients of a tertiary hospital in Wuhan date: 2020-02-25 journal: nan DOI: 10.1101/2020.02.22.20025320 sha: doc_id: 253179 cord_uid: pi5uq90z file: cache/cord-252771-6kwfulqe.json key: cord-252771-6kwfulqe authors: Yue, Jing-Li; Yan, Wei; Sun, Yan-Kun; Yuan, Kai; Su, Si-Zhen; Han, Ying; Ravindran, Arun V.; Kosten, Thomas; Everall, Ian; Davey, Christopher G; Bullmore, Edward; Kawakami, Norito; Barbui, Corrado; Thornicroft, Graham; Lund, Crick; Lin, Xiao; Liu, Lin; Shi, Le; Shi, Jie; Ran, Mao-Sheng; Bao, Yan-Ping; Lu, Lin title: Mental health services for infectious disease outbreaks including COVID-19: a rapid systematic review date: 2020-11-05 journal: Psychological medicine DOI: 10.1017/s0033291720003888 sha: doc_id: 252771 cord_uid: 6kwfulqe file: cache/cord-253035-tijcxtwx.json key: cord-253035-tijcxtwx authors: Wang, Chen; Horby, Peter W; Hayden, Frederick G; Gao, George F title: A novel coronavirus outbreak of global health concern date: 2020-01-24 journal: Lancet DOI: 10.1016/s0140-6736(20)30185-9 sha: doc_id: 253035 cord_uid: tijcxtwx file: cache/cord-253006-r2a2ozrc.json key: cord-253006-r2a2ozrc authors: Yan, Xiquan; Han, Xiaotong; Fan, Yong; Fang, Zhixiong; Long, Da; Zhu, Yimin title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers date: 2020-05-24 journal: Crit Care DOI: 10.1186/s13054-020-02952-0 sha: doc_id: 253006 cord_uid: r2a2ozrc file: cache/cord-253238-ptmxkpae.json key: cord-253238-ptmxkpae authors: Kopel, Jonathan; Perisetti, Abhilash; Gajendran, Mahesh; Boregowda, Umesha; Goyal, Hemant title: Clinical Insights into the Gastrointestinal Manifestations of COVID-19 date: 2020-05-23 journal: Dig Dis Sci DOI: 10.1007/s10620-020-06362-8 sha: doc_id: 253238 cord_uid: ptmxkpae file: cache/cord-252922-cdhnlvxv.json key: cord-252922-cdhnlvxv authors: West, Erin A.; Anker, Daniela; Amati, Rebecca; Richard, Aude; Wisniak, Ania; Butty, Audrey; Albanese, Emiliano; Bochud, Murielle; Chiolero, Arnaud; Crivelli, Luca; Cullati, Stéphane; d’Acremont, Valérie; Epure, Adina Mihaela; Fehr, Jan; Flahault, Antoine; Fornerod, Luc; Frank, Irène; Frei, Anja; Michel, Gisela; Gonseth, Semira; Guessous, Idris; Imboden, Medea; Kahlert, Christian R.; Kaufmann, Laurent; Kohler, Philipp; Mösli, Nicolai; Paris, Daniel; Probst-Hensch, Nicole; Rodondi, Nicolas; Stringhini, Silvia; Vermes, Thomas; Vollrath, Fabian; Puhan, Milo A. title: Corona Immunitas: study protocol of a nationwide program of SARS-CoV-2 seroprevalence and seroepidemiologic studies in Switzerland date: 2020-10-24 journal: Int J Public Health DOI: 10.1007/s00038-020-01494-0 sha: doc_id: 252922 cord_uid: cdhnlvxv file: cache/cord-252919-647zcjgu.json key: cord-252919-647zcjgu authors: Chen, Yun; Guo, Yao; Pan, Yihang; Zhao, Zhizhuang Joe title: Structure analysis of the receptor binding of 2019-nCoV date: 2020-02-17 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.02.071 sha: doc_id: 252919 cord_uid: 647zcjgu file: cache/cord-253201-r6vsa0pw.json key: cord-253201-r6vsa0pw authors: Nazari, S.; Azari Jafari, A.; Mirmoeeni, S.; Sadeghian, S.; Heidari, M. E.; Asarzadegan, F.; Puormand, S. M.; Alikhani, K.; Ebadi, H.; Fathi, D.; Dalvand, S. title: Central Nervous System Manifestations in COVID-19 Patients: A Systematic Review and Meta-analysis date: 2020-07-22 journal: nan DOI: 10.1101/2020.07.21.20158691 sha: doc_id: 253201 cord_uid: r6vsa0pw file: cache/cord-253459-tcn10pho.json key: cord-253459-tcn10pho authors: Moreau, Gregory Brett; Burgess, Stacey L.; Sturek, Jeffrey M.; Donlan, Alexandra N.; Petri, William A.; Mann, Barbara J. title: Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection date: 2020-07-28 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0762 sha: doc_id: 253459 cord_uid: tcn10pho file: cache/cord-253252-s8fm5rfa.json key: cord-253252-s8fm5rfa authors: Jayaweera, Mahesh; Perera, Hasini; Gunawardana, Buddhika; Manatunge, Jagath title: Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy date: 2020-06-13 journal: Environ Res DOI: 10.1016/j.envres.2020.109819 sha: doc_id: 253252 cord_uid: s8fm5rfa file: cache/cord-252965-30pl5tx3.json key: cord-252965-30pl5tx3 authors: Stutt, Richard O. 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Ahmed title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. (Labiatae) date: 2020-11-03 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1840439 sha: doc_id: 253431 cord_uid: fjds5cdr file: cache/cord-253457-gawn4s9g.json key: cord-253457-gawn4s9g authors: Yau, Kevin; Muller, Matthew P.; Lin, Molly; Siddiqui, Naureen; Neskovic, Sanja; Shokar, Gagan; Fattouh, Ramzi; Matukas, Larissa M.; Beaubien-Souligny, William; Thomas, Alison; Weinstein, Jordan J.; Zaltzman, Jeffrey; Wald, Ron title: COVID-19 Outbreak in an Urban Hemodialysis Unit date: 2020-07-15 journal: Am J Kidney Dis DOI: 10.1053/j.ajkd.2020.07.001 sha: doc_id: 253457 cord_uid: gawn4s9g file: cache/cord-253656-2x4y403o.json key: cord-253656-2x4y403o authors: Ren, Wenlin; Sun, Hunter; Gao, George F.; Chen, Jianxin; Sun, Sean; Zhao, Rongqing; Gao, Guang; Hu, Yalin; Zhao, Gan; Chen, Yuxin; Jin, Xia; Fang, Feng; Chen, Jinggong; Wang, Qi; Gong, Sitao; Gao, Wen; Sun, Yufei; Su, Junchi; He, Ailiang; Cheng, Xin; Li, Min; Xia, Chenxi; Li, Maohua; Sun, Le title: Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates date: 2020-06-24 journal: Vaccine DOI: 10.1016/j.vaccine.2020.06.066 sha: doc_id: 253656 cord_uid: 2x4y403o file: cache/cord-253513-zn87f1lk.json key: cord-253513-zn87f1lk authors: Liu, Jia; Cao, Ruiyuan; Xu, Mingyue; Wang, Xi; Zhang, Huanyu; Hu, Hengrui; Li, Yufeng; Hu, Zhihong; Zhong, Wu; Wang, Manli title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro date: 2020-03-18 journal: Cell Discov DOI: 10.1038/s41421-020-0156-0 sha: doc_id: 253513 cord_uid: zn87f1lk file: cache/cord-253704-y0t30xw3.json key: cord-253704-y0t30xw3 authors: Lahiri, Durjoy; Ardila, Alfredo title: COVID-19 Pandemic: A Neurological Perspective date: 2020-04-29 journal: Cureus DOI: 10.7759/cureus.7889 sha: doc_id: 253704 cord_uid: y0t30xw3 file: cache/cord-253331-z443e8lk.json key: cord-253331-z443e8lk authors: Stanhope, Michael J.; Brown, James R.; Amrine-Madsen, Heather title: Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV date: 2004-03-31 journal: Infection, Genetics and Evolution DOI: 10.1016/j.meegid.2003.10.001 sha: doc_id: 253331 cord_uid: z443e8lk file: cache/cord-253422-m18ngwbt.json key: cord-253422-m18ngwbt authors: Trimarchi, Hernán; Coppo, Rosanna title: COVID-19 and acute kidney injury in pediatric subjects: is there a place for eculizumab treatment? date: 2020-09-29 journal: J Nephrol DOI: 10.1007/s40620-020-00859-1 sha: doc_id: 253422 cord_uid: m18ngwbt file: cache/cord-253618-bosb7e63.json key: cord-253618-bosb7e63 authors: Ramteke, Shobhana; Sahu, Bharat Lal title: Novel coronavirus disease 2019 (COVID-19) pandemic: considerations for the biomedical waste sector in India date: 2020-08-01 journal: nan DOI: 10.1016/j.cscee.2020.100029 sha: doc_id: 253618 cord_uid: bosb7e63 file: cache/cord-253665-1dn3ek34.json key: cord-253665-1dn3ek34 authors: Vishnubalaji, Radhakrishnan; Shaath, Hibah; Alajez, Nehad M. title: Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response date: 2020-07-07 journal: Genes (Basel) DOI: 10.3390/genes11070760 sha: doc_id: 253665 cord_uid: 1dn3ek34 file: cache/cord-253851-27nt0op8.json key: cord-253851-27nt0op8 authors: Koh, David; Lim, Meng‐Kin; Chia, Sin‐Eng title: SARS: health care work can be hazardous to health date: 2003-06-17 journal: Occup Med (Lond) DOI: 10.1093/occmed/kqg090 sha: doc_id: 253851 cord_uid: 27nt0op8 file: cache/cord-253844-y6xdcf20.json key: cord-253844-y6xdcf20 authors: Yesudhas, Dhanusha; Srivastava, Ambuj; Gromiha, M. Michael title: COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date: 2020-09-04 journal: Infection DOI: 10.1007/s15010-020-01516-2 sha: doc_id: 253844 cord_uid: y6xdcf20 file: cache/cord-253905-zknmfgsh.json key: cord-253905-zknmfgsh authors: Li, Xingguang; Zai, Junjie; Zhao, Qiang; Nie, Qing; Li, Yi; Foley, Brian T.; Chaillon, Antoine title: Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 date: 2020-03-11 journal: J Med Virol DOI: 10.1002/jmv.25731 sha: doc_id: 253905 cord_uid: zknmfgsh file: cache/cord-253933-29tedkf8.json key: cord-253933-29tedkf8 authors: David, Abel P.; Russell, Marika D.; El‐Sayed, Ivan H.; Russell, Matthew S. title: Tracheostomy guidelines developed at a large academic medical center during the COVID‐19 pandemic date: 2020-04-27 journal: Head Neck DOI: 10.1002/hed.26191 sha: doc_id: 253933 cord_uid: 29tedkf8 file: cache/cord-253777-h8wy0coq.json key: cord-253777-h8wy0coq authors: Afshar, Hale; Yassin, Zeynab; Kalantari, Saeed; Aloosh, Oldooz; Lotfi, Tayebeh; Moghaddasi, Mehdi; Sadeghipour, Alireza; Emamikhah, Maziar title: Evolution and resolution of brain involvement associated with SARS- CoV2 infection: A close Clinical – Paraclinical follow up study of a case date: 2020-05-21 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102216 sha: doc_id: 253777 cord_uid: h8wy0coq file: cache/cord-253869-1ouai07v.json key: cord-253869-1ouai07v authors: Noorimotlagh, Zahra; Mirzaee, Seyyed Abbas; Jaafarzadeh, Neemat; Maleki, Maryam; Kalvandi, Gholamreza; Karami, Chiman title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies date: 2020-10-02 journal: Environ Sci Pollut Res Int DOI: 10.1007/s11356-020-11060-z sha: doc_id: 253869 cord_uid: 1ouai07v file: cache/cord-253606-o8a0jhx2.json key: cord-253606-o8a0jhx2 authors: Mégarbane, Bruno; Scherrmann, Jean-Michel title: Comment on: Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial date: 2020-08-07 journal: J Antimicrob Chemother DOI: 10.1093/jac/dkaa327 sha: doc_id: 253606 cord_uid: o8a0jhx2 file: cache/cord-254079-pvl44u4d.json key: cord-254079-pvl44u4d authors: Marinella, Mark A. title: COVID-19 pandemic and the stethoscope: don't forget to sanitize date: 2020-04-11 journal: Heart Lung DOI: 10.1016/j.hrtlng.2020.03.017 sha: doc_id: 254079 cord_uid: pvl44u4d file: cache/cord-254162-tu81j66h.json key: cord-254162-tu81j66h authors: Bai, Xiyuan; Hippensteel, Joseph; Leavitt, Alida; Maloney, James P.; Beckham, David; Garcia, Cindy; Li, Qing; Freed, Brian M.; Ordway, Diane; Sandhaus, Robert A.; Chan, Edward D. title: Hypothesis: alpha-1-antitrypsin is a promising treatment option for COVID-19 date: 2020-11-12 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110394 sha: doc_id: 254162 cord_uid: tu81j66h file: cache/cord-253245-433mg0ke.json key: cord-253245-433mg0ke authors: Gao, Zhiru; Xu, Yinghui; Guo, Ye; Xu, Dongsheng; Zhang, Li; Wang, Xu; Sun, Chao; Qiu, Shi; Ma, Kewei title: A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date: 2020-08-05 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104494 sha: doc_id: 253245 cord_uid: 433mg0ke file: cache/cord-253990-m75xwrz9.json key: cord-253990-m75xwrz9 authors: Wang, Zhiguo; Hong, Xiaojing; Wang, Hongyan; Liu, Jun; Liu, Jun‐Ping title: Covid‐19: From structure to therapeutic targeting in studying approved drugs and local DNA vaccination date: 2020-10-29 journal: Clin Exp Pharmacol Physiol DOI: 10.1111/1440-1681.13409 sha: doc_id: 253990 cord_uid: m75xwrz9 file: cache/cord-254120-1q8tqeg7.json key: cord-254120-1q8tqeg7 authors: Iannone, Primiano; Castellini, Greta; Coclite, Daniela; Napoletano, Antonello; Fauci, Alice; Iacorossi, Laura; D'Angelo, Daniela; Renzi, Cristina; La Torre, Giuseppe; Mastroianni, Claudio; Gianola, Silvia title: The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness. date: 2020-04-11 journal: nan DOI: 10.1101/2020.04.06.20054841 sha: doc_id: 254120 cord_uid: 1q8tqeg7 file: cache/cord-253671-g3ypisig.json key: cord-253671-g3ypisig authors: Otte, Martin Sylvester; Klußmann, Jens Peter; Luers, Jan Christoffer title: Riechstörungen bei COVID-19 – aktueller Wissensstand date: 2020-06-10 journal: Laryngorhinootologie DOI: 10.1055/a-1183-4835 sha: doc_id: 253671 cord_uid: g3ypisig file: cache/cord-253472-3s142p6u.json key: cord-253472-3s142p6u authors: Saurabh, Suman; Bhardwaj, Pankaj title: Author’s reply to correspondence regarding the article ‘Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals’ date: 2020-09-18 journal: QJM DOI: 10.1093/qjmed/hcaa269 sha: doc_id: 253472 cord_uid: 3s142p6u file: cache/cord-253833-0lajhqn5.json key: cord-253833-0lajhqn5 authors: Misra-Hebert, Anita D; Jehi, Lara; Ji, Xinge; Nowacki, Amy S.; Gordon, Steven; Terpeluk, Paul; Chung, Mina K.; Mehra, Reena; Dell, Katherine M.; Pennell, Nathan; Hamilton, Aaron; Milinovich, Alex; Kattan, Michael W.; Young, James B. title: Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system. date: 2020-08-19 journal: Res Sq DOI: 10.21203/rs.3.rs-61235/v1 sha: doc_id: 253833 cord_uid: 0lajhqn5 file: cache/cord-253987-83h861lp.json key: cord-253987-83h861lp authors: Tada, Takuya; Fan, Chen; Kaur, Ramanjit; Stapleford, Kenneth A.; Gristick, Harry; Nimigean, Crina; Landau, Nathaniel R. title: A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date: 2020-09-17 journal: bioRxiv DOI: 10.1101/2020.09.16.300319 sha: doc_id: 253987 cord_uid: 83h861lp file: cache/cord-253970-sbj869yy.json key: cord-253970-sbj869yy authors: Agarwal, Amit; Pinho, Marco; Raj, Karuna; Yu, Frank F.; Bathla, Girish; Achilleos, Michael; ONeill, Thomas; Still, Michael; Maldjian, Joseph title: Neurological emergencies associated with COVID-19: stroke and beyond date: 2020-08-11 journal: Emerg Radiol DOI: 10.1007/s10140-020-01837-7 sha: doc_id: 253970 cord_uid: sbj869yy file: cache/cord-253968-jtr0p930.json key: cord-253968-jtr0p930 authors: López, Verónica; Vázquez, Teresa; Alonso-Titos, Juana; Cabello, Mercedes; Alonso, Angel; Beneyto, Isabel; Crespo, Marta; Díaz-Corte, Carmen; Franco, Antonio; González-Roncero, Francisco; Gutiérrez, Elena; Guirado, Luis; Jiménez, Carlos; Jironda, Cristina; Lauzurica, Ricardo; Llorente, Santiago; Mazuecos, Auxiliadora; Paul, Javier; Rodríguez-Benot, Alberto; Ruiz, Juan Carlos; Sánchez-Fructuoso, Ana; Sola, Eugenia; Torregrosa, Vicente; Zárraga, Sofía; Hernández, Domingo title: Recomendaciones en el manejo de la pandemia por coronavirus SARS-CoV-2 (Covid-19) en pacientes con trasplante renal date: 2020-04-03 journal: Nefrologia DOI: 10.1016/j.nefro.2020.03.002 sha: doc_id: 253968 cord_uid: jtr0p930 file: cache/cord-254072-evgw0as5.json key: cord-254072-evgw0as5 authors: Hsu, Li-Yang; Lee, Cheng-Chuan; Green, Justin A.; Ang, Brenda; Paton, Nicholas I.; Lee, Lawrence; Villacian, Jorge S.; Lim, Poh-Lian; Earnest, Arul; Leo, Yee-Sin title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts date: 2003-06-17 journal: Emerg Infect Dis DOI: 10.3201/eid0906.030264 sha: doc_id: 254072 cord_uid: evgw0as5 file: cache/cord-254446-yxqbe1dj.json key: cord-254446-yxqbe1dj authors: Ren, Yunzhao R.; Golding, Amit; Sorbello, Alfred; Ji, Ping; Chen, Jianmeng; Bhawana, Saluja; Witzmann, Kimberly; Arya, Vikram; Reynolds, Kellie S.; Choi, Su‐Young; Nikolov, Nikolay; Sahajwalla, Chandrahas title: A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19 date: 2020-05-29 journal: J Clin Pharmacol DOI: 10.1002/jcph.1673 sha: doc_id: 254446 cord_uid: yxqbe1dj file: cache/cord-253862-jl1zhg13.json key: cord-253862-jl1zhg13 authors: Khalaf, Khalil; Papp, Natalia; Chou, Jadzia Tin-Tsen; Hana, Doris; Mackiewicz, Andrzej; Kaczmarek, Mariusz title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 journal: Front Immunol DOI: 10.3389/fimmu.2020.570927 sha: doc_id: 253862 cord_uid: jl1zhg13 file: cache/cord-254395-tu4aqczj.json key: cord-254395-tu4aqczj authors: Froggatt, Heather M.; Heaton, Brook E.; Heaton, Nicholas S. title: Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL(pro) Reporter Assay date: 2020-10-27 journal: J Virol DOI: 10.1128/jvi.01265-20 sha: doc_id: 254395 cord_uid: tu4aqczj file: cache/cord-254469-7q6xi2xx.json key: cord-254469-7q6xi2xx authors: Wang, Fuzhou; Kream, Richard M.; Stefano, George B. title: An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development date: 2020-05-05 journal: Med Sci Monit DOI: 10.12659/msm.924700 sha: doc_id: 254469 cord_uid: 7q6xi2xx file: cache/cord-253993-ynrthadj.json key: cord-253993-ynrthadj authors: Belhassan, Assia; En-nahli, Fatima; Zaki, Hanane; Lakhlifi, Tahar; Bouachrine, Mohammed title: Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach date: 2020-09-18 journal: Life Sci DOI: 10.1016/j.lfs.2020.118469 sha: doc_id: 253993 cord_uid: ynrthadj file: cache/cord-254017-4a6fs57r.json key: cord-254017-4a6fs57r authors: Pan, Xiu-wu; Xu, Da; Zhang, Hao; Zhou, Wang; Wang, Lin-hui; Cui, Xin-gang title: Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis date: 2020-03-31 journal: Intensive Care Med DOI: 10.1007/s00134-020-06026-1 sha: doc_id: 254017 cord_uid: 4a6fs57r file: cache/cord-254094-ed1epul1.json key: cord-254094-ed1epul1 authors: Mayoral, Eduardo Pérez-Campos; Hernández-Huerta, María Teresa; Pérez-Campos Mayoral, Laura; Matias-Cervantes, Carlos Alberto; Mayoral-Andrade, Gabriel; Barrios, Luis Ángel Laguna; Pérez-Campos, Eduardo title: Factors related to asymptomatic or severe COVID-19 infection date: 2020-09-24 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110296 sha: doc_id: 254094 cord_uid: ed1epul1 file: cache/cord-254821-px4fe7mn.json key: cord-254821-px4fe7mn authors: Infantino, Maria; Grossi, Valentina; Lari, Barbara; Bambi, Riccardo; Perri, Alessandro; Manneschi, Matteo; Terenzi, Giovanni; Liotti, Irene; Ciotta, Giovanni; Taddei, Cristina; Benucci, Maurizio; Casprini, Patrizia; Veneziani, Francesca; Fabbri, Sergio; Pompetti, Adolfo; Manfredi, Mariangela title: Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date: 2020-05-10 journal: J Med Virol DOI: 10.1002/jmv.25932 sha: doc_id: 254821 cord_uid: px4fe7mn file: cache/cord-254318-w8wrn9lx.json key: cord-254318-w8wrn9lx authors: Díez, José-María; Romero, Carolina; Gajardo, Rodrigo title: Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens date: 2020-05-13 journal: Immunotherapy DOI: 10.2217/imt-2020-0095 sha: doc_id: 254318 cord_uid: w8wrn9lx file: cache/cord-254478-scc9wee0.json key: cord-254478-scc9wee0 authors: To, Kelvin Kai-Wang; Tsang, Owen Tak-Yin; Leung, Wai-Shing; Tam, Anthony Raymond; Wu, Tak-Chiu; Lung, David Christopher; Yip, Cyril Chik-Yan; Cai, Jian-Piao; Chan, Jacky Man-Chun; Chik, Thomas Shiu-Hong; Lau, Daphne Pui-Ling; Choi, Chris Yau-Chung; Chen, Lin-Lei; Chan, Wan-Mui; Chan, Kwok-Hung; Ip, Jonathan Daniel; Ng, Anthony Chin-Ki; Poon, Rosana Wing-Shan; Luo, Cui-Ting; Cheng, Vincent Chi-Chung; Chan, Jasper Fuk-Woo; Hung, Ivan Fan-Ngai; Chen, Zhiwei; Chen, Honglin; Yuen, Kwok-Yung title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date: 2020-03-23 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30196-1 sha: doc_id: 254478 cord_uid: scc9wee0 file: cache/cord-254855-gmy9zyad.json key: cord-254855-gmy9zyad authors: He, Sijia; Waheed, Abdul A.; Hetrick, Brian; Dabbagh, Deemah; Akhrymuk, Ivan V.; Kehn-Hall, Kylene; Freed, Eric O.; Wu, Yuntao title: PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date: 2020-07-06 journal: bioRxiv DOI: 10.1101/2020.05.01.073387 sha: doc_id: 254855 cord_uid: gmy9zyad file: cache/cord-254419-qw83atrx.json key: cord-254419-qw83atrx authors: Bhattacharyya, Rajat; Iyer, Prasad; Phua, Ghee Chee; Lee, Jan Hau title: The Interplay Between Coagulation and Inflammation Pathways in COVID-19-Associated Respiratory Failure: A Narrative Review date: 2020-08-25 journal: Pulm Ther DOI: 10.1007/s41030-020-00126-5 sha: doc_id: 254419 cord_uid: qw83atrx file: cache/cord-254464-6l7fwylu.json key: cord-254464-6l7fwylu authors: Shingare, Ashay; Bahadur, Madan M.; Raina, Shailesh title: COVID‐19 in recent kidney transplant recipients date: 2020-06-08 journal: Am J Transplant DOI: 10.1111/ajt.16120 sha: doc_id: 254464 cord_uid: 6l7fwylu file: cache/cord-254668-szxhlejx.json key: cord-254668-szxhlejx authors: Brogna, Barbara; Bignardi, Elio; Salvatore, Petronilla; Alberigo, Martino; Brogna, Claudia; Megliola, Antonia; Fontanella, Giovanni; Mazza, Emerico Maria; Musto, Lanfranco title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. date: 2020-06-13 journal: Heart Lung DOI: 10.1016/j.hrtlng.2020.06.005 sha: doc_id: 254668 cord_uid: szxhlejx file: cache/cord-254630-ed5gawoj.json key: cord-254630-ed5gawoj authors: Barron, Sarah P.; Kennedy, Marcus P. title: Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy? date: 2020-09-17 journal: Adv Ther DOI: 10.1007/s12325-020-01495-8 sha: doc_id: 254630 cord_uid: ed5gawoj file: cache/cord-254825-c5d0wul9.json key: cord-254825-c5d0wul9 authors: Kim, Sei Won; Jo, Sung Jin; Lee, Heayon; Oh, Jung Hwan; Lim, Jihyang; Lee, Sang Haak; Choi, Jung Hyun; Lee, Jehoon title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 journal: PLoS One DOI: 10.1371/journal.pone.0237692 sha: doc_id: 254825 cord_uid: c5d0wul9 file: cache/cord-254636-3lr008th.json key: cord-254636-3lr008th authors: Shishir, Tushar Ahmed; Naser, Iftekhar Bin; Faruque, Shah M. title: In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date: 2020-08-16 journal: bioRxiv DOI: 10.1101/2020.07.20.212563 sha: doc_id: 254636 cord_uid: 3lr008th file: cache/cord-255365-fog62qdu.json key: cord-255365-fog62qdu authors: Goldstein, Neal D.; Burstyn, Igor title: On the importance of early testing even when imperfect in a pandemic such as COVID-19 date: 2020-08-03 journal: Glob Epidemiol DOI: 10.1016/j.gloepi.2020.100031 sha: doc_id: 255365 cord_uid: fog62qdu file: cache/cord-254207-uru7bkr4.json key: cord-254207-uru7bkr4 authors: Singanayagam, Anika; Patel, Monika; Charlett, Andre; Lopez Bernal, Jamie; Saliba, Vanessa; Ellis, Joanna; Ladhani, Shamez; Zambon, Maria; Gopal, Robin title: Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020 date: 2020-08-13 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.32.2001483 sha: doc_id: 254207 cord_uid: uru7bkr4 file: cache/cord-254505-mjj8xrer.json key: cord-254505-mjj8xrer authors: Kannan, Saathvik R.; Spratt, Austin N.; Quinn, Thomas P.; Heng, Xiao; Lorson, Christian L.; Sönnerborg, Anders; Byrareddy, Siddappa N.; Singh, Kamal title: Infectivity of SARS-CoV-2: there Is Something More than D614G? date: 2020-09-15 journal: J Neuroimmune Pharmacol DOI: 10.1007/s11481-020-09954-3 sha: doc_id: 254505 cord_uid: mjj8xrer file: cache/cord-254884-5rmnwcfd.json key: cord-254884-5rmnwcfd authors: Ng, S. M.; Chan, Timothy H. Y.; Chan, Cecilia L. W.; Lee, Antoinette M.; Yau, Josephine K. Y.; Chan, Celia H. 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W.; McNally, E.; Zelikovich, A.; D'Aquila, R.; Mustanski, B.; Miller, A.; Vaught, L.; Reiser, N.; Bogdanovic, E.; Fallon, K.; Demonbreun, A. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-06-02 journal: nan DOI: 10.1101/2020.06.01.20119602 sha: doc_id: 255446 cord_uid: wddj6hrv file: cache/cord-254777-h8hw4m9f.json key: cord-254777-h8hw4m9f authors: Tanner, Tamara; Wahezi, Dawn M. title: Hyperinflammation and the utility of immunomodulatory medications in children with COVID-19 date: 2020-07-29 journal: Paediatr Respir Rev DOI: 10.1016/j.prrv.2020.07.003 sha: doc_id: 254777 cord_uid: h8hw4m9f file: cache/cord-255284-ffh1jl40.json key: cord-255284-ffh1jl40 authors: Guery, B; Alfandari, S; Leroy, O; Georges, H; D’escrivan, T; Kipnis, E; Mouton, Y; Yazdanpanah, Y title: Syndrome respiratoire aigu sévère date: 2003-06-30 journal: Médecine et Maladies Infectieuses DOI: 10.1016/s0399-077x(03)00200-2 sha: doc_id: 255284 cord_uid: ffh1jl40 file: cache/cord-255290-p64apuk1.json key: cord-255290-p64apuk1 authors: Matheeussen, Veerle; 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Bonnet-Madin, Lucie; Karpf, Léa; Meertens, Laurent; Poirot, Justine; Legoff, Jérome; Delaugerre, Constance; Amara, Ali; Soumelis, Vassili title: SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date: 2020-07-10 journal: bioRxiv DOI: 10.1101/2020.07.10.197343 sha: doc_id: 255997 cord_uid: oer5lxxr file: cache/cord-256092-bph9ys72.json key: cord-256092-bph9ys72 authors: Hussain, Aneela N.; Hussain, Fazal; Hashmi, Shahrukh K. title: Role of testosterone in COVID-19 patients - a double-edged sword? date: 2020-09-17 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110287 sha: doc_id: 256092 cord_uid: bph9ys72 file: cache/cord-255909-m94j1rh4.json key: cord-255909-m94j1rh4 authors: Shree, Priya; Mishra, Priyanka; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Chaube, Radha; Garg, Neha; Tripathi, Yamini Bhusan title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study date: 2020-08-27 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1810778 sha: doc_id: 255909 cord_uid: m94j1rh4 file: cache/cord-256075-fudeaq7y.json key: cord-256075-fudeaq7y authors: Audo, Andrea; 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date: 2020-04-10 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0008271 sha: doc_id: 256303 cord_uid: bpa571ys file: cache/cord-256572-sqz8yc7b.json key: cord-256572-sqz8yc7b authors: Huo, Jiandong; Zhao, Yuguang; Ren, Jingshan; Zhou, Daming; Duyvesteyn, Helen ME; Ginn, Helen M; Carrique, Loic; Malinauskas, Tomas; Ruza, Reinis R; Shah, Pranav NM; Tan, Tiong Kit; Rijal, Pramila; Coombes, Naomi; Bewley, Kevin; Radecke, Julika; Paterson, Neil G; Supasa, Piyasa; Mongkolsapaya, Juthathip; Screaton, Gavin R; Carroll, Miles; Townsend, Alain; Fry, Elizabeth E; Owens, Raymond J; Stuart, David I title: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date: 2020-05-06 journal: bioRxiv DOI: 10.1101/2020.05.05.079202 sha: doc_id: 256572 cord_uid: sqz8yc7b file: cache/cord-256556-1zea3wa1.json key: cord-256556-1zea3wa1 authors: Lou, Yan; Liu, Lin; Yao, Hangping; Hu, Xingjiang; Su, Junwei; Xu, Kaijin; Luo, Rui; Yang, Xi; He, Lingjuan; Lu, Xiaoyang; Zhao, Qingwei; Liang, Tingbo; Qiu, Yunqing title: Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial date: 2020-10-25 journal: Eur J Pharm Sci DOI: 10.1016/j.ejps.2020.105631 sha: doc_id: 256556 cord_uid: 1zea3wa1 file: cache/cord-257008-7q5s1vu1.json key: cord-257008-7q5s1vu1 authors: Sharma, Virender K.; Jinadatha, Chetan; Lichtfouse, Eric title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 journal: Environ Chem Lett DOI: 10.1007/s10311-020-01017-6 sha: doc_id: 257008 cord_uid: 7q5s1vu1 file: cache/cord-256351-q8lkhklw.json key: cord-256351-q8lkhklw authors: Di Giorgio, Angelo; Nicastro, Emanuele; Speziani, Camilla; De Giorgio, Massimo; Pasulo, Luisa; Magro, Bianca; Fagiuoli, Stefano; Antiga, Lorenzo D' title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy date: 2020-05-12 journal: J Hepatol DOI: 10.1016/j.jhep.2020.05.008 sha: doc_id: 256351 cord_uid: q8lkhklw file: cache/cord-256893-3sh87h2x.json key: cord-256893-3sh87h2x authors: Yang, Li; Liu, Shasha; Liu, Jinyan; Zhang, Zhixin; Wan, Xiaochun; Huang, Bo; Chen, Youhai; Zhang, Yi title: COVID-19: immunopathogenesis and Immunotherapeutics date: 2020-07-25 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00243-2 sha: doc_id: 256893 cord_uid: 3sh87h2x file: cache/cord-257140-ge15qrqg.json key: cord-257140-ge15qrqg authors: Perkmann, T.; Perkmann-Nagele, N.; Ozsvar-Kozma, M.; Koller, T.; Breyer, M.-K.; Breyer-Kohansal, R.; Burghuber, O. 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QI, Yan; BAO, Qi-Yu; TIAN, Wei; XU, Jian-Cheng; FENG, Ming-Guang; YANG, Huan-Ming title: Polymorphism of SARS-CoV Genomes date: 2006-04-30 journal: Acta Genetica Sinica DOI: 10.1016/s0379-4172(06)60061-9 sha: doc_id: 257022 cord_uid: 6vw88jib file: cache/cord-256808-lxlerb13.json key: cord-256808-lxlerb13 authors: Lim, W.S; Anderson, S.R; Read, R.C title: Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004 date: 2004-06-02 journal: J Infect DOI: 10.1016/j.jinf.2004.04.001 sha: doc_id: 256808 cord_uid: lxlerb13 file: cache/cord-257399-p6of5fno.json key: cord-257399-p6of5fno authors: Gentry, Chris A; Humphrey, Mary Beth; Thind, Sharanjeet K; Hendrickson, Sage C; Kurdgelashvili, George; Williams, Riley J title: Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date: 2020-09-21 journal: Lancet Rheumatol DOI: 10.1016/s2665-9913(20)30305-2 sha: doc_id: 257399 cord_uid: p6of5fno file: cache/cord-256940-yuja99jg.json key: cord-256940-yuja99jg authors: Wei, Bo; Hang, Xiaofeng; Xie, Ying; Zhang, Yuanjing; Wang, Jianrong; Cao, Xinghao; Wu, Jinzi J.; Wang, Junxue title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 journal: Revista da Sociedade Brasileira de Medicina Tropical DOI: 10.1590/0037-8682-0372-2020 sha: doc_id: 256940 cord_uid: yuja99jg file: cache/cord-257398-fmkfo5ju.json key: cord-257398-fmkfo5ju authors: Meng, Qing-Bin; Peng, Jing-Jing; Wei, Xin; Yang, Jia-Yao; Li, Peng-Cheng; Qu, Zi-Wei; Xiong, Yong-Fen; Wu, Guang-Jiang; Hu, Zhi-Min; Yu, Jian-Chun; Su, Wen title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i19.4360 sha: doc_id: 257398 cord_uid: fmkfo5ju file: cache/cord-257310-wqu7t44n.json key: cord-257310-wqu7t44n authors: Maideniuc, Catalina; Memon, Anza B. title: Acute necrotizing myelitis and acute motor axonal neuropathy in a COVID-19 patient date: 2020-08-09 journal: J Neurol DOI: 10.1007/s00415-020-10145-6 sha: doc_id: 257310 cord_uid: wqu7t44n file: cache/cord-256904-uq6gy24x.json key: cord-256904-uq6gy24x authors: Bartolini, A.; 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A. title: Three months of COVID‐19: A systematic review and meta‐analysis date: 2020-05-18 journal: Rev Med Virol DOI: 10.1002/rmv.2113 sha: doc_id: 257556 cord_uid: lmws8eed file: cache/cord-257584-v38tjof3.json key: cord-257584-v38tjof3 authors: Fahmi, Muhamad; Kubota, Yukihiko; Ito, Masahiro title: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date: 2020-03-03 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104272 sha: doc_id: 257584 cord_uid: v38tjof3 file: cache/cord-256688-yy7abob9.json key: cord-256688-yy7abob9 authors: Chavez, Summer; Long, Brit; Koyfman, Alex; Liang, Stephen Y. title: Coronavirus Disease (COVID-19): A primer for emergency physicians date: 2020-03-24 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.03.036 sha: doc_id: 256688 cord_uid: yy7abob9 file: cache/cord-257258-hu9oxea1.json key: cord-257258-hu9oxea1 authors: Chabner, Bruce A. title: Taking the Longer View of COVID‐19 date: 2020-04-27 journal: Oncologist DOI: 10.1634/theoncologist.2020-0313 sha: doc_id: 257258 cord_uid: hu9oxea1 file: cache/cord-256699-d2tf2g7f.json key: cord-256699-d2tf2g7f authors: Brochot, Etienne; Demey, Baptiste; Handala, Lynda; François, Catherine; Duverlie, Gilles; Castelain, Sandrine title: Comparison of different serological assays for SARS-CoV-2 in real life date: 2020-08-02 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104569 sha: doc_id: 256699 cord_uid: d2tf2g7f file: cache/cord-257169-1lk737lw.json key: cord-257169-1lk737lw authors: Lau, C. 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C. title: Performance of an automated chemiluminescence SARS-COV-2 IG-G Assay date: 2020-09-08 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.09.005 sha: doc_id: 257169 cord_uid: 1lk737lw file: cache/cord-257468-woyycghi.json key: cord-257468-woyycghi authors: Basso, Trude; Nordbø, Svein Arne; Sundqvist, Erik; Martinsen, Tom Christian; Witsø, Eivind; Wik, Tina S. title: Transmission of infection from non-isolated patients with COVID-19 to health care workers date: 2020-08-20 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.08.015 sha: doc_id: 257468 cord_uid: woyycghi file: cache/cord-256750-5m7psxri.json key: cord-256750-5m7psxri authors: Park, Hye Yoon; Park, Wan Beom; Lee, So Hee; Kim, Jeong Lan; Lee, Jung Jae; Lee, Haewoo; Shin, Hyoung-Shik title: Posttraumatic stress disorder and depression of survivors 12 months after the outbreak of Middle East respiratory syndrome in South Korea date: 2020-05-15 journal: BMC Public Health DOI: 10.1186/s12889-020-08726-1 sha: doc_id: 256750 cord_uid: 5m7psxri file: cache/cord-257600-0plhquk9.json key: cord-257600-0plhquk9 authors: Calles, Antonio; Aparicio, María Inmaculada; Alva, Manuel; Bringas, Marianela; Gutierrez, Natalia; Soto, Javier; Arregui, Marta; Tirado, Victoria Clara; Álvarez, Enrique Luis; del Monte-Millán, María; Massarrah, Tatiana; Galera, Mar; Álvarez, Rosa; Martín, Miguel title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 journal: Front Oncol DOI: 10.3389/fonc.2020.01777 sha: doc_id: 257600 cord_uid: 0plhquk9 file: cache/cord-257663-i7wrqh2g.json key: cord-257663-i7wrqh2g authors: Principi, Nicola; Bosis, Samantha; Esposito, Susanna title: Effects of Coronavirus Infections in Children date: 2010-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1602.090469 sha: doc_id: 257663 cord_uid: i7wrqh2g file: cache/cord-257766-z7vcdtcq.json key: cord-257766-z7vcdtcq authors: Varadhachary, Atul; Chatterjee, Dev; Garza, Javier; Garr, R. Patrick; Foley, Christopher; Letkeman, Andrea; Dean, John; Haug, David; Breeze, Juliet; Traylor, Robbyn; Malek, Andrew; Nath, Rohan; Linbeck, Leo title: Salivary anti-SARS-CoV-2 IgA as an accessible biomarker of mucosal immunity against COVID-19 date: 2020-08-11 journal: medRxiv DOI: 10.1101/2020.08.07.20170258 sha: doc_id: 257766 cord_uid: z7vcdtcq file: cache/cord-256982-t6urqus7.json key: cord-256982-t6urqus7 authors: Wellinghausen, Nele; Voss, Meike; Ivanova, Ralitsa; Deininger, Susanne title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 journal: GMS Infect Dis DOI: 10.3205/id000066 sha: doc_id: 256982 cord_uid: t6urqus7 file: cache/cord-257408-ejhhk1iu.json key: cord-257408-ejhhk1iu authors: Goss, Matthew B.; Galván, N. Thao N.; Ruan, Wenly; Munoz, Flor M.; Brewer, Eileen D.; O’Mahony, Christine A.; Melicoff‐Portillo, Ernestina; Dreyer, William J.; Miloh, Tamir A.; Cigarroa, Francisco G.; Ranch, Daniel; Yoeli, Dor; Adams, Megan A.; Koohmaraie, Sarah; Harter, Diana M.; Rana, Abbas; Cotton, Ronald T.; Carter, Beth; Patel, Shreena; Moreno, Nicolas F.; Leung, Daniel H.; Goss, John A. title: The Pediatric Solid Organ Transplant Experience with COVID‐19: An Initial Multi‐Center, Multi‐Organ Case Series date: 2020-09-18 journal: Pediatr Transplant DOI: 10.1111/petr.13868 sha: doc_id: 257408 cord_uid: ejhhk1iu file: cache/cord-257142-q79yy6o5.json key: cord-257142-q79yy6o5 authors: Wambier, Carlos Gustavo; Goren, Andy; Vaño‐Galván, Sergio; Ramos, Paulo Müller; Ossimetha, Angelina; Nau, Gerard; Herrera, Sabina; McCoy, John title: Androgen sensitivity gateway to COVID‐19 disease severity date: 2020-05-15 journal: Drug Dev Res DOI: 10.1002/ddr.21688 sha: doc_id: 257142 cord_uid: q79yy6o5 file: cache/cord-257533-i85dyg8n.json key: cord-257533-i85dyg8n authors: Henn, Wolfram title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity date: 2020-06-23 journal: Vaccine DOI: 10.1016/j.vaccine.2020.06.058 sha: doc_id: 257533 cord_uid: i85dyg8n file: cache/cord-257719-5s6acr7m.json key: cord-257719-5s6acr7m authors: Poh Ng, Lisa Fong title: The Virus That Changed My World date: 2003-12-22 journal: PLoS Biol DOI: 10.1371/journal.pbio.0000066 sha: doc_id: 257719 cord_uid: 5s6acr7m file: cache/cord-257456-15bm9psj.json key: cord-257456-15bm9psj authors: Arumugam, Arunkumar; Faron, Matthew L.; Yu, Peter; Markham, Cole; Wu, Michelle; Wong, Season title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10100739 sha: doc_id: 257456 cord_uid: 15bm9psj file: cache/cord-257792-m7nij17v.json key: cord-257792-m7nij17v authors: Ng, Oi-Wing; Chia, Adeline; Tan, Anthony T.; Jadi, Ramesh S.; Leong, Hoe Nam; Bertoletti, Antonio; Tan, Yee-Joo title: Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection date: 2016-04-12 journal: Vaccine DOI: 10.1016/j.vaccine.2016.02.063 sha: doc_id: 257792 cord_uid: m7nij17v file: cache/cord-257732-3xuy6tbn.json key: cord-257732-3xuy6tbn authors: Azzi, Lorenzo; Carcano, Giulio; Gianfagna, Francesco; Grossi, Paolo; Gasperina, Daniela Dalla; Genoni, Angelo; Fasano, Mauro; Sessa, Fausto; Tettamanti, Lucia; Carinci, Francesco; Maurino, Vittorio; Rossi, Agostino; Tagliabue, Angelo; Baj, Andreina title: Saliva is a reliable tool to detect SARS-CoV-2 date: 2020-04-14 journal: J Infect DOI: 10.1016/j.jinf.2020.04.005 sha: doc_id: 257732 cord_uid: 3xuy6tbn file: cache/cord-257809-bq9ha4d0.json key: cord-257809-bq9ha4d0 authors: Mukaino, Masahiko; Tatemoto, Tsuyoshi; Kumazawa, Nobuhiro; Tanabe, Shigeo; Katoh, Masaki; Saitoh, Eiichi; Otaka, Yohei title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-04-08 journal: Am J Phys Med Rehabil DOI: 10.1097/phm.0000000000001441 sha: doc_id: 257809 cord_uid: bq9ha4d0 file: cache/cord-257058-wf6oxzrk.json key: cord-257058-wf6oxzrk authors: Kim, Sinae; Lee, Jong Ho; Lee, Siyoung; Shim, Saerok; Nguyen, Tam T.; Hwang, Jihyeong; Kim, Heijun; Choi, Yeo-Ok; Hong, Jaewoo; Bae, Suyoung; Jhun, Hyunjhung; Yum, Hokee; Lee, Youngmin; Chan, Edward D.; Yu, Liping; Azam, Tania; Kim, Yong-Dae; Yeom, Su Cheong; Yoo, Kwang Ha; Kang, Lin-Woo; Shin, Kyeong-Cheol; Kim, Soohyun title: The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene date: 2020-10-26 journal: Immune Netw DOI: 10.4110/in.2020.20.e41 sha: doc_id: 257058 cord_uid: wf6oxzrk file: cache/cord-257729-s0vo7dlk.json key: cord-257729-s0vo7dlk authors: Bauer, Melissa; Bernstein, Kyra; Dinges, Emily; Delgado, Carlos; El-Sharawi, Nadir; Sultan, Pervez; Mhyre, Jill M.; Landau, Ruth title: Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date: 2020-04-20 journal: Anesth Analg DOI: 10.1213/ane.0000000000004856 sha: doc_id: 257729 cord_uid: s0vo7dlk file: cache/cord-258113-mnou31j3.json key: cord-258113-mnou31j3 authors: Wang, Yaping; Liao, Baolin; Guo, Yan; Li, Feng; Lei, Chunliang; Zhang, Fuchun; Cai, Weiping; Hong, Wenxin; Zeng, Yu; Qiu, Shuang; Wang, Jian; Li, Yueping; Deng, Xilong; Li, Jianping; Xiao, Guangming; Guo, Fengxia; Lai, Xunxi; Liang, Zhiwei; Wen, Xueliang; Li, Pinghong; Jiao, Qian; Xiang, Fangfei; Wang, Yong; Ma, Chenghui; Xie, Zhiwei; Lin, Weiyin; Wu, Yanrong; Tang, Xiaoping; Li, Linghua; Guan, Yujuan title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date: 2020-05-19 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa187 sha: doc_id: 258113 cord_uid: mnou31j3 file: cache/cord-257611-z0sng9sx.json key: cord-257611-z0sng9sx authors: Kalantari, Hamidreza; Tabrizi, Aida Haji Hossein; Foroohi, Fatemeh title: Determination of COVID-19 prevalence with regards to age range of patients referring to the hospitals located in western Tehran, Iran date: 2020-10-07 journal: Gene Rep DOI: 10.1016/j.genrep.2020.100910 sha: doc_id: 257611 cord_uid: z0sng9sx file: cache/cord-257802-vgizgq2y.json key: cord-257802-vgizgq2y authors: Uttamchandani, Mahesh; Neo, Jia Ling; Ong, Brandon Ngiap Zhung; Moochhala, Shabbir title: Applications of microarrays in pathogen detection and biodefence date: 2008-11-12 journal: Trends Biotechnol DOI: 10.1016/j.tibtech.2008.09.004 sha: doc_id: 257802 cord_uid: vgizgq2y file: cache/cord-257613-o0q7hvn3.json key: cord-257613-o0q7hvn3 authors: Shafiee, Abbas; Moradi, Lida; Lim, Mayasari; Brown, Jason title: Coronavirus disease 2019: A tissue engineering and regenerative medicine perspective date: 2020-08-21 journal: Stem Cells Transl Med DOI: 10.1002/sctm.20-0197 sha: doc_id: 257613 cord_uid: o0q7hvn3 file: cache/cord-257876-nzjp1hrz.json key: cord-257876-nzjp1hrz authors: Yang, Wenzhong; Jin, Guangxu title: Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality date: 2020-09-14 journal: Brief Bioinform DOI: 10.1093/bib/bbaa208 sha: doc_id: 257876 cord_uid: nzjp1hrz file: cache/cord-257487-xanqvdhn.json key: cord-257487-xanqvdhn authors: Carbajo-Lozoya, Javier; Müller, Marcel A.; Kallies, Stephan; Thiel, Volker; Drosten, Christian; von Brunn, Albrecht title: Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date: 2012-02-10 journal: Virus Res DOI: 10.1016/j.virusres.2012.02.002 sha: doc_id: 257487 cord_uid: xanqvdhn file: cache/cord-257820-4qmajxtb.json key: cord-257820-4qmajxtb authors: Abate, Giulia; Memo, Maurizio; Uberti, Daniela title: Impact of COVID-19 on Alzheimer’s Disease Risk: Viewpoint for Research Action date: 2020-08-21 journal: Healthcare (Basel) DOI: 10.3390/healthcare8030286 sha: doc_id: 257820 cord_uid: 4qmajxtb file: cache/cord-257789-pdybfft6.json key: cord-257789-pdybfft6 authors: Diamond, Betty; Volpe, Bruce T.; VanPatten, Sonya; Al Abed, Yousef title: SARS-CoV-2 and interferon blockade date: 2020-11-09 journal: Mol Med DOI: 10.1186/s10020-020-00231-w sha: doc_id: 257789 cord_uid: pdybfft6 file: cache/cord-258067-par61wwh.json key: cord-258067-par61wwh authors: Di Martino, Marcello; García Septiem, Javier; Maqueda González, Rocío; Muñoz de Nova, Jose Luis; de la Hoz Rodríguez, Ángela; Correa Bonito, Alba; Martín-Pérez, Elena title: Elective Surgery During the SARS-CoV-2 Pandemic (COVID-19): A Morbimortality Analysis and Recommendations on Patient Prioritisation and Security Measures date: 2020-06-20 journal: nan DOI: 10.1016/j.cireng.2020.06.005 sha: doc_id: 258067 cord_uid: par61wwh file: cache/cord-257698-ed2tqn35.json key: cord-257698-ed2tqn35 authors: Wong, Raymond S.M.; Hui, David S. title: Index Patient and SARS Outbreak in Hong Kong date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030645 sha: doc_id: 257698 cord_uid: ed2tqn35 file: cache/cord-257994-i6hut28h.json key: cord-257994-i6hut28h authors: Nogee, Daniel; 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Michael; Ghosh, Preetam title: Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date: 2020-10-10 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.104051 sha: doc_id: 257958 cord_uid: yehnlabq file: cache/cord-258167-jqm3qyfm.json key: cord-258167-jqm3qyfm authors: Zhou, Peng; Han, Zhenggang; Wang, Lin-Fa; Shi, Zhengli title: Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date: 2009-09-18 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2009.07.025 sha: doc_id: 258167 cord_uid: jqm3qyfm file: cache/cord-257805-pcp3qgn0.json key: cord-257805-pcp3qgn0 authors: Mehta, Harsh; Ivanovic, Sasa; Cronin, Amanda; VanBrunt, Lindsey; Mistry, Nirav; Miller, Richard; Yodice, Paul; Rezai, Fariborz title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date: 2020-05-16 journal: Case Rep Womens Health DOI: 10.1016/j.crwh.2020.e00220 sha: doc_id: 257805 cord_uid: pcp3qgn0 file: cache/cord-258255-hzmcrenk.json key: cord-258255-hzmcrenk authors: Jiang, Xuejun; Luo, Mei; Zou, Zhen; Wang, Xu; Chen, Chengzhi; Qiu, Jingfu title: Asymptomatic SARS‐CoV‐2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days date: 2020-04-24 journal: J Med Virol DOI: 10.1002/jmv.25941 sha: doc_id: 258255 cord_uid: hzmcrenk file: cache/cord-258242-xblxjlb5.json key: cord-258242-xblxjlb5 authors: Liu, Tengwen; Guo, Yuhong; Zhao, Jingxia; He, Shasha; Bai, Yunjing; Wang, Ning; Lin, Yan; Liu, Qingquan; Xu, Xiaolong title: Systems Pharmacology and Verification of ShenFuHuang Formula in Zebrafish Model Reveal Multi-Scale Treatment Strategy for Septic Syndrome in COVID-19 date: 2020-09-15 journal: Front Pharmacol DOI: 10.3389/fphar.2020.584057 sha: doc_id: 258242 cord_uid: xblxjlb5 file: cache/cord-258382-ep73us0e.json key: cord-258382-ep73us0e authors: Braga, Cássia L.; Silva‐Aguiar, Rodrigo P.; Battaglini, Denise; Peruchetti, Diogo B.; Robba, Chiara; Pelosi, Paolo; Rocco, Patricia R. M.; Caruso‐Neves, Celso; Silva, Pedro L. title: The renin–angiotensin–aldosterone system: Role in pathogenesis and potential therapeutic target in COVID‐19 date: 2020-07-13 journal: Pharmacol Res Perspect DOI: 10.1002/prp2.623 sha: doc_id: 258382 cord_uid: ep73us0e file: cache/cord-258576-ywbyflas.json key: cord-258576-ywbyflas authors: Bösmüller, Hans; Traxler, Selina; Bitzer, Michael; Häberle, Helene; Raiser, Wolfgang; Nann, Dominik; Frauenfeld, Leonie; Vogelsberg, Antonio; Klingel, Karin; Fend, Falko title: The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation date: 2020-06-30 journal: Virchows Arch DOI: 10.1007/s00428-020-02881-x sha: doc_id: 258576 cord_uid: ywbyflas file: cache/cord-258435-lhn34tc4.json key: cord-258435-lhn34tc4 authors: Tracy, C Shawn; Rea, Elizabeth; Upshur, Ross EG title: Public perceptions of quarantine: community-based telephone survey following an infectious disease outbreak date: 2009-12-16 journal: BMC Public Health DOI: 10.1186/1471-2458-9-470 sha: doc_id: 258435 cord_uid: lhn34tc4 file: cache/cord-258681-66ct8nod.json key: cord-258681-66ct8nod authors: Warnock, David G. title: Clinical Trials during the SARS-CoV-2 Pandemic date: 2020-04-14 journal: Nephron Clin Pract DOI: 10.1159/000507582 sha: doc_id: 258681 cord_uid: 66ct8nod file: cache/cord-258019-njky7v5x.json key: cord-258019-njky7v5x authors: Kinaret, Pia A.S.; Giudice, Giusy del; Greco, Dario title: Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us date: 2020-08-10 journal: Nano Today DOI: 10.1016/j.nantod.2020.100945 sha: doc_id: 258019 cord_uid: njky7v5x file: cache/cord-258548-1u7v1nlr.json key: cord-258548-1u7v1nlr authors: Mansueto, Gelsomina; Niola, Massimo; Napoli, Claudio title: Can COVID 2019 disease induces a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? date: 2020-06-26 journal: Pathol Res Pract DOI: 10.1016/j.prp.2020.153086 sha: doc_id: 258548 cord_uid: 1u7v1nlr file: cache/cord-258221-pn8gh73b.json key: cord-258221-pn8gh73b authors: Rocha, José Lucas Martins; de Oliveira, Waldir César Ferreira; Noronha, Nádia Cássia; dos Santos, Natalia Cristine Dias; Covas, Dimas Tadeu; Picanço-Castro, Virgínia; Swiech, Kamilla; Malmegrim, Kelen Cristina Ribeiro title: Mesenchymal Stromal Cells in Viral Infections: Implications for COVID-19 date: 2020-09-07 journal: Stem Cell Rev Rep DOI: 10.1007/s12015-020-10032-7 sha: doc_id: 258221 cord_uid: pn8gh73b file: cache/cord-258722-1o6zhnnj.json key: cord-258722-1o6zhnnj authors: Gbinigie, Kome; Frie, Kerstin title: Should azithromycin be used to treat COVID-19? A rapid review date: 2020-05-13 journal: BJGP open DOI: 10.3399/bjgpopen20x101094 sha: doc_id: 258722 cord_uid: 1o6zhnnj file: cache/cord-258701-jyzxu9nk.json key: cord-258701-jyzxu9nk authors: Kaushal, Darwin; Nair, Nithin Prakasan; Soni, Kapil; Goyal, Amit; Choudhury, Bikram; Rajan, Nikhil title: Endoscopy in Otorhinolaryngology During Corona Outbreak: A Proposal for Safe Practice date: 2020-08-13 journal: Indian J Otolaryngol Head Neck Surg DOI: 10.1007/s12070-020-02048-9 sha: doc_id: 258701 cord_uid: jyzxu9nk file: cache/cord-258614-7unadw41.json key: cord-258614-7unadw41 authors: Ogidigo, Joyce Oloaigbe; Iwuchukwu, Emmanuel A.; Ibeji, Collins U.; Okpalefe, Okiemute; Soliman, Mahmoud E. S. title: Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach date: 2020-10-25 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1837681 sha: doc_id: 258614 cord_uid: 7unadw41 file: cache/cord-258725-z79gel8h.json key: cord-258725-z79gel8h authors: Wood, R.; Thomson, E. C.; Galbraith, R.; Gribben, C.; Caldwell, D.; Bishop, J.; Reid, M.; Shah, A.; Templeton, K.; Goldberg, D.; Robertson, C.; Hutchinson, S.; Colhoun, H. M.; McKeigue, P. M.; McAllister, D. title: Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland date: 2020-09-22 journal: nan DOI: 10.1101/2020.09.21.20196428 sha: doc_id: 258725 cord_uid: z79gel8h file: cache/cord-258844-b4d79m1f.json key: cord-258844-b4d79m1f authors: Denning, M.; Goh, E. T.; Tan, B.; Kanneganti, A.; Almonte, M.; Scott, A.; Martin, G.; Clarke, J.; Sounderajah, V.; Markar, S.; Przybylowicz, J.; Chan, Y. H.; Sia, C.-H.; Chua, Y. X.; Sim, K.; Lim, L.; Tan, L.; Tan, M.; Sharma, V.; Ooi, S.; Winter Beatty, J.; Flott, K.; Mason, S.; Chidambaram, S.; Yalamanchili, S.; Zbikowska, G.; Fedorowski, J.; Dykowska, G.; Wells, M.; Purkayastha, S.; Kinross, J. title: DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY date: 2020-07-18 journal: nan DOI: 10.1101/2020.07.16.20155622 sha: doc_id: 258844 cord_uid: b4d79m1f file: cache/cord-258624-041cf99j.json key: cord-258624-041cf99j authors: Ahmad, Sajjad; Navid, Afifa; Farid, Rabia; Abbas, Ghulam; Ahmad, Faisal; Zaman, Naila; Parvaiz, Nousheen; Azam, Syed Sikander title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date: 2020-05-23 journal: Eur J Pharm Sci DOI: 10.1016/j.ejps.2020.105387 sha: doc_id: 258624 cord_uid: 041cf99j file: cache/cord-258708-da6x5rxa.json key: cord-258708-da6x5rxa authors: Hafiane, Anouar title: SARS-CoV-2 and the cardiovascular system date: 2020-07-16 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.07.019 sha: doc_id: 258708 cord_uid: da6x5rxa file: cache/cord-258630-mvz2l3yj.json key: cord-258630-mvz2l3yj authors: Liu, Tiantian; Chen, Zhong; Chen, Wanqiu; Chen, Xin; Hosseini, Maryam; Yang, Zhaowei; Li, Jing; Ho, Diana; Turay, David; Gheorghe, Ciprian; Jones, Wendell; Wang, Charles title: A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date: 2020-11-10 journal: bioRxiv DOI: 10.1101/2020.11.10.375022 sha: doc_id: 258630 cord_uid: mvz2l3yj file: cache/cord-258084-nkr3lrov.json key: cord-258084-nkr3lrov authors: Juthani, Prerak; Bhojwani, Rohan; Gupta, Neil title: Coronavirus Disease 2019 (COVID-19) Manifestation as Acute Myocardial Infarction in a Young, Healthy Male date: 2020-07-11 journal: Case Rep Infect Dis DOI: 10.1155/2020/8864985 sha: doc_id: 258084 cord_uid: nkr3lrov file: cache/cord-258250-zueo1xfa.json key: cord-258250-zueo1xfa authors: Hirotsu, Yosuke; Maejima, Makoto; Shibusawa, Masahiro; Nagakubo, Yuki; Hosaka, Kazuhiro; Amemiya, Kenji; Sueki, Hitomi; Hayakawa, Miyoko; Mochizuki, Hitoshi; Tsutsui, Toshiharu; Kakizaki, Yumiko; Miyashita, Yoshihiro; Yagi, Shintaro; Kojima, Satoshi; Omata, Masao title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.029 sha: doc_id: 258250 cord_uid: zueo1xfa file: cache/cord-258859-iaiosjlu.json key: cord-258859-iaiosjlu authors: Wang, Jiao; Pan, Lijun; Tang, Song; Ji, John S.; Shi, Xiaoming title: Mask use during COVID-19: A risk adjusted strategy() date: 2020-06-25 journal: Environ Pollut DOI: 10.1016/j.envpol.2020.115099 sha: doc_id: 258859 cord_uid: iaiosjlu file: cache/cord-258905-0hgdtalg.json key: cord-258905-0hgdtalg authors: Bond, Katherine; Nicholson, Suellen; Lim, Seok Ming; Karapanagiotidis, Theo; Williams, Eloise; Johnson, Douglas; Hoang, Tuyet; Sia, Cheryll; Purcell, Damian; Mordant, Francesca; Lewin, Sharon R; Catton, Mike; Subbarao, Kanta; Howden, Benjamin P; Williamson, Deborah A title: Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date: 2020-08-06 journal: J Infect Dis DOI: 10.1093/infdis/jiaa467 sha: doc_id: 258905 cord_uid: 0hgdtalg file: cache/cord-258128-qtmjgrml.json key: cord-258128-qtmjgrml authors: Mirjalili, Mahtabalsadat; Shafiekhani, Mojtaba; Vazin, Afsaneh title: Coronavirus Disease 2019 (COVID-19) and Transplantation: Pharmacotherapeutic Management of Immunosuppression Regimen date: 2020-07-03 journal: Ther Clin Risk Manag DOI: 10.2147/tcrm.s256246 sha: doc_id: 258128 cord_uid: qtmjgrml file: cache/cord-258223-8dhtwf03.json key: cord-258223-8dhtwf03 authors: Chow, Cristelle; Shahdadpuri, Raveen; Kai-Qian, Kam; Hwee, Chan Yoke title: The Next Pandemic: Supporting COVID-19 Frontline Doctors Through Film Discussion date: 2020-09-05 journal: J Med Humanit DOI: 10.1007/s10912-020-09662-2 sha: doc_id: 258223 cord_uid: 8dhtwf03 file: cache/cord-258792-4lakgpxp.json key: cord-258792-4lakgpxp authors: Yoon, Sung‐Won title: Sovereign Dignity, Nationalism and the Health of a Nation: A Study of China's Response in Combat of Epidemics date: 2008-04-08 journal: Stud Ethn Natl DOI: 10.1111/j.1754-9469.2008.00009.x sha: doc_id: 258792 cord_uid: 4lakgpxp file: cache/cord-258268-7ypq0t3d.json key: cord-258268-7ypq0t3d authors: Zanin, Luca; Saraceno, Giorgio; Panciani, Pier Paolo; Renisi, Giulia; Signorini, Liana; Migliorati, Karol; Fontanella, Marco Maria title: SARS-CoV-2 can induce brain and spine demyelinating lesions date: 2020-05-04 journal: Acta Neurochir (Wien) DOI: 10.1007/s00701-020-04374-x sha: doc_id: 258268 cord_uid: 7ypq0t3d file: cache/cord-258431-8zgwj2fa.json key: cord-258431-8zgwj2fa authors: Strafella, Claudia; Caputo, Valerio; Termine, Andrea; Barati, Shila; Gambardella, Stefano; Borgiani, Paola; Caltagirone, Carlo; Novelli, Giuseppe; Giardina, Emiliano; Cascella, Raffaella title: Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications date: 2020-07-03 journal: Genes (Basel) DOI: 10.3390/genes11070741 sha: doc_id: 258431 cord_uid: 8zgwj2fa file: cache/cord-258312-3v5t4k8d.json key: cord-258312-3v5t4k8d authors: Majachani, Nicole; Francois, Jean Luc M.; Fernando, Ashen K.; Zuberi, Jamshed title: A Case of a Newborn Baby Girl Infected with SARS-CoV-2 Due to Transplacental Viral Transmission date: 2020-10-25 journal: Am J Case Rep DOI: 10.12659/ajcr.925766 sha: doc_id: 258312 cord_uid: 3v5t4k8d file: cache/cord-258595-bk35vxlr.json key: cord-258595-bk35vxlr authors: Westhaus, Sandra; Weber, Frank-Andreas; Schiwy, Sabrina; Linnemann, Volker; Brinkmann, Markus; Widera, Marek; Greve, Carola; Janke, Axel; Hollert, Henner; Wintgens, Thomas; Ciesek, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141750 sha: doc_id: 258595 cord_uid: bk35vxlr file: cache/cord-258172-p54j4zzo.json key: cord-258172-p54j4zzo authors: Barker, Harlan; Parkkila, Seppo title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0240647 sha: doc_id: 258172 cord_uid: p54j4zzo file: cache/cord-259084-lwh3rww4.json key: cord-259084-lwh3rww4 authors: Anderson, Cole; Castillo, Fritz; Koenig, Michael; Managbanag, Jim title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date: 2020-05-22 journal: bioRxiv DOI: 10.1101/2020.05.22.110932 sha: doc_id: 259084 cord_uid: lwh3rww4 file: cache/cord-259185-qg4jwbes.json key: cord-259185-qg4jwbes authors: Vadlamani, B. S.; Uppal, T.; Verma, S. C.; Misra, M. title: Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-09-09 journal: nan DOI: 10.1101/2020.09.07.20190173 sha: doc_id: 259185 cord_uid: qg4jwbes file: cache/cord-258902-h0wrs01h.json key: cord-258902-h0wrs01h authors: Liu, Xianglei; Drelich, Aleksandra; Li, Wei; Chen, Chuan; Sun, Zehua; Shi, Megan; Adams, Cynthia; Mellors, John W.; Tseng, Chien-Te; Dimitrov, Dimiter S. title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date: 2020-09-22 journal: Vaccine DOI: 10.1016/j.vaccine.2020.09.058 sha: doc_id: 258902 cord_uid: h0wrs01h file: cache/cord-258873-l9oxmqdp.json key: cord-258873-l9oxmqdp authors: Baker, D.; Roberts, C. A. K.; Pryce, G.; Kang, A. S.; Marta, M.; Reyes, S.; Schmierer, K.; Giovannoni, G.; Amor, S. title: COVID‐19 vaccine‐readiness for anti‐CD20‐depleting therapy in autoimmune diseases date: 2020-08-01 journal: Clin Exp Immunol DOI: 10.1111/cei.13495 sha: doc_id: 258873 cord_uid: l9oxmqdp file: cache/cord-259200-65b267ic.json key: cord-259200-65b267ic authors: Harypursat, Vijay; Chen, Yao-Kai title: Six weeks into the 2019 coronavirus disease outbreak: it is time to consider strategies to impede the emergence of new zoonotic infections date: 2020-05-05 journal: Chin Med J (Engl) DOI: 10.1097/cm9.0000000000000760 sha: doc_id: 259200 cord_uid: 65b267ic file: cache/cord-258533-gds7sdc9.json key: cord-258533-gds7sdc9 authors: Lytras, Theodore; Dellis, George; Flountzi, Anastasia; Hatzianastasiou, Sophia; Nikolopoulou, Georgia; Tsekou, Katerina; Diamantis, Zafiris; Stathopoulou, Grigoria; Togka, Marianthi; Gerolymatos, Gerasimos; Rigakos, George; Sapounas, Spiridon; Tsiodras, Sotirios title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries date: 2020-04-16 journal: J Travel Med DOI: 10.1093/jtm/taaa054 sha: doc_id: 258533 cord_uid: gds7sdc9 file: cache/cord-259223-6b07qiw2.json key: cord-259223-6b07qiw2 authors: Feitosa, Eduardo L; Júnior, Francisco Tiago Dos S S; Nery Neto, José Arimatéa De O; Matos, Luis F L; Moura, Matheus H De S; Rosales, Thiele Osvaldt; De Freitas, Guilherme Barroso L title: COVID-19: Rational discovery of the therapeutic potential of Melatonin as a SARS-CoV-2 main Protease Inhibitor date: 2020-07-30 journal: Int J Med Sci DOI: 10.7150/ijms.48053 sha: doc_id: 259223 cord_uid: 6b07qiw2 file: cache/cord-258724-1qhen1bj.json key: cord-258724-1qhen1bj authors: Young, Barnaby E; Ong, Sean W X; Ng, Lisa F P; Anderson, Danielle E; Chia, Wan Ni; Chia, Po Ying; Ang, Li Wei; Mak, Tze-Minn; Kalimuddin, Shirin; Chai, Louis Yi Ann; Pada, Surinder; Tan, Seow Yen; Sun, Louisa; Parthasarathy, Purnima; Fong, Siew-Wai; Chan, Yi-Hao; Tan, Chee Wah; Lee, Bernett; Rötzschke, Olaf; Ding, Ying; Tambyah, Paul; Low, Jenny G H; Cui, Lin; Barkham, Timothy; Lin, Raymond Tzer Pin; Leo, Yee-Sin; Renia, Laurent; Wang, Lin-Fa; Lye, David Chien title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1280 sha: doc_id: 258724 cord_uid: 1qhen1bj file: cache/cord-259238-n2uuaof6.json key: cord-259238-n2uuaof6 authors: Zhang, Bao-Zhong; Chu, Hin; Han, Shuo; Shuai, Huiping; Deng, Jian; Hu, Ye-fan; Gong, Hua-rui; Lee, Andrew Chak-Yiu; Zou, Zijiao; Yau, Thomas; Wu, Wutian; Hung, Ivan Fan-Ngai; Chan, Jasper Fuk-Woo; Yuen, Kwok-Yung; Huang, Jian-Dong title: SARS-CoV-2 infects human neural progenitor cells and brain organoids date: 2020-08-04 journal: Cell Res DOI: 10.1038/s41422-020-0390-x sha: doc_id: 259238 cord_uid: n2uuaof6 file: cache/cord-259261-fmuozy3w.json key: cord-259261-fmuozy3w authors: Bickler, Stephen W.; Cauvi, David M.; Fisch, Kathleen M.; Prieto, James M.; Gaidry, Alicia D.; Thangarajah, Hariharan; Lazar, David; Ignacio, Romeo; Gerstmann, Dale R.; Ryan, Allen F.; Bickler, Philip E.; De Maio, Antonio title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.15.134403 sha: doc_id: 259261 cord_uid: fmuozy3w file: cache/cord-259523-92hz534s.json key: cord-259523-92hz534s authors: Pullen, Lara C. title: COVID‐19: transplant works toward adaptation date: 2020-09-29 journal: Am J Transplant DOI: 10.1111/ajt.16298 sha: doc_id: 259523 cord_uid: 92hz534s file: cache/cord-259572-8n12n6ym.json key: cord-259572-8n12n6ym authors: Bogensperger, Christina; Cardini, Benno; Oberhuber, Rupert; Weissenbacher, Annemarie; Gasteiger, Silvia; Berchtold, Valeria; Otarashvili, Giorgi; Öfner, Dietmar; Schneeberger, Stefan title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report date: 2020-07-22 journal: Transplant Proc DOI: 10.1016/j.transproceed.2020.07.011 sha: doc_id: 259572 cord_uid: 8n12n6ym file: cache/cord-259033-op94wuy4.json key: cord-259033-op94wuy4 authors: Wendling, Daniel; Verhoeven, Frank; Chouk, Mickael; Prati, Clément title: Can SARS-CoV-2 trigger reactive arthritis? date: 2020-10-27 journal: Joint Bone Spine DOI: 10.1016/j.jbspin.2020.105086 sha: doc_id: 259033 cord_uid: op94wuy4 file: cache/cord-259585-mjtxiu0t.json key: cord-259585-mjtxiu0t authors: Occhipinti, Vincenzo; Pastorelli, Luca title: Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date: 2020-04-21 journal: Inflamm Bowel Dis DOI: 10.1093/ibd/izaa084 sha: doc_id: 259585 cord_uid: mjtxiu0t file: cache/cord-259267-trpo5w11.json key: cord-259267-trpo5w11 authors: Vilibic-Cavlek, Tatjana; Stevanovic, Vladimir; Tabain, Irena; Betica-Radic, Ljiljana; Sabadi, Dario; Peric, Ljiljana; Bogdanic, Maja; Vilibic, Maja; Kolaric, Branko; Kudumija, Boris; Petrovic, Goranka; Mrzljak, Anna; Karabuva, Svjetlana; Hrstic, Irena; Capak, Krunoslav; Kucinar, Jasmina; Savic, Vladimir; Barbic, Ljubo title: Severe acute respiratory syndrome coronavirus 2 seroprevalence among personnel in the healthcare facilities of Croatia, 2020 date: 2020-08-26 journal: Revista da Sociedade Brasileira de Medicina Tropical DOI: 10.1590/0037-8682-0458-2020 sha: doc_id: 259267 cord_uid: trpo5w11 file: cache/cord-259347-3acsko74.json key: cord-259347-3acsko74 authors: Cheng, Qi; Yang, Yue; Gao, Jianqun title: Infectivity of human coronavirus in the brain date: 2020-05-28 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102799 sha: doc_id: 259347 cord_uid: 3acsko74 file: cache/cord-259852-skhoro95.json key: cord-259852-skhoro95 authors: Oboh, Mary Aigbiremo; Omoleke, Semeeh Akinwale; Imafidon, Christian Eseigbe; Ajibola, Olumide; Oriero, Eniyou Cheryll; Amambua-Ngwa, Alfred title: Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics date: 2020-08-18 journal: J Prev Med Public Health DOI: 10.3961/jpmph.20.259 sha: doc_id: 259852 cord_uid: skhoro95 file: cache/cord-259593-shrd1s7r.json key: cord-259593-shrd1s7r authors: Qin, Zhao-ling; Zhao, Ping; Cao, Ming-mei; Qi, Zhong-tian title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 journal: J Virol Methods DOI: 10.1016/j.jviromet.2007.05.017 sha: doc_id: 259593 cord_uid: shrd1s7r file: cache/cord-259471-lsdodl0a.json key: cord-259471-lsdodl0a authors: Pagliano, Pasquale; Piazza, Ornella; De Caro, Francesco; Ascione, Tiziana; Filippelli, Amelia title: Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? 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H.; Ali, Umi K.; Rashid, Zetti Z.; Kori, Najma title: Aerosolized SARS-CoV-2 transmission risk: Surgical or N95 masks? date: 2020-09-15 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.465 sha: doc_id: 259396 cord_uid: vmc2q1bi file: cache/cord-259668-nwezszhj.json key: cord-259668-nwezszhj authors: Ortiz, Alberto title: Complement and protection from tissue injury in COVID-19 date: 2020-10-04 journal: Clin Kidney J DOI: 10.1093/ckj/sfaa196 sha: doc_id: 259668 cord_uid: nwezszhj file: cache/cord-259907-yqmi0cqy.json key: cord-259907-yqmi0cqy authors: Maxwell, Cynthia; McGeer, Alison; Young Tai, Kin Fan; Sermer, Mathew; Farine, Dan; Basso, Melanie; Delisle, Marie-France; Hudon, Lynda; Menticoglou, Savas; Mundle, William; Ouellet, Annie; Yudin, Mark H.; Boucher, Marc; Castillo, Eliana; Cormier, Beatrice; Gruslin, Andrée; Money, Deborah M.; Murphy, Kellie; Paquet, Caroline; Steenbeek, Audrey; Van Eyk, Nancy; van Schalkwyk, Julie; Wong, Thomas title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 date: 2009-10-31 journal: International Journal of Gynecology & Obstetrics DOI: 10.1016/j.ijgo.2009.05.006 sha: doc_id: 259907 cord_uid: yqmi0cqy file: cache/cord-259340-1ir19s25.json key: cord-259340-1ir19s25 authors: Das, Rohit Pritam; Jagadeb, Manaswini; Rath, Surya Narayan title: Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date: 2020-07-01 journal: bioRxiv DOI: 10.1101/2020.07.01.150805 sha: doc_id: 259340 cord_uid: 1ir19s25 file: cache/cord-259620-qigfstxt.json key: cord-259620-qigfstxt authors: Yang, Chen; Zhang, Yu; Chen, Hong; Chen, Yuchen; Yang, Dong; Shen, Ziwei; Wang, Xiaomu; Liu, Xinran; Xiong, Mingrui; Huang, Kun title: Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date: 2020-10-10 journal: bioRxiv DOI: 10.1101/2020.10.09.334052 sha: doc_id: 259620 cord_uid: qigfstxt file: cache/cord-259558-remrzrq1.json key: cord-259558-remrzrq1 authors: LeBlanc, Jason J.; Heinstein, Charles; MacDonald, Jimmy; Pettipas, Janice; Hatchette, Todd F; Patriquin, Glenn title: A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 date: 2020-05-16 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104442 sha: doc_id: 259558 cord_uid: remrzrq1 file: cache/cord-259935-xyo2pe4g.json key: cord-259935-xyo2pe4g authors: Wang, Ching-Ying; Lu, Chien-Yi; Li, Shih-Wen; Lai, Chien-Chen; Hua, Chun-Hung; Huang, Su-Hua; Lin, Ying-Ju; Hour, Mann-Jen; Lin, Cheng-Wen title: SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date: 2017-05-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.04.008 sha: doc_id: 259935 cord_uid: xyo2pe4g file: cache/cord-259619-sco0d5cc.json key: cord-259619-sco0d5cc authors: Ludvigsson, Johnny; von Herrath, Matthias G.; Mallone, Roberto; Buschard, Karsten; Cilio, Corrado; Craig, Maria; Ilonen, Jorma; Leslie, David; McGeoch, Julie E. M.; Schneider, Darius; Skyler, Jay S.; Flodström Tullberg, Malin; Hober, Didier title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society date: 2020-09-30 journal: Front Public Health DOI: 10.3389/fpubh.2020.562901 sha: doc_id: 259619 cord_uid: sco0d5cc file: cache/cord-259566-qtlq7a6l.json key: cord-259566-qtlq7a6l authors: Guraya, Salman Yousuf title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article date: 2020-06-23 journal: Int J Surg DOI: 10.1016/j.ijsu.2020.06.027 sha: doc_id: 259566 cord_uid: qtlq7a6l file: cache/cord-259660-x9sobzyw.json key: cord-259660-x9sobzyw authors: Mohakud, Nirmal K; Yerru, Hari; Rajguru, Monalisha; Naik, Sushree S title: An Assumed Vertical Transmission of SARS-CoV-2 During Pregnancy: A Case Report and Review of Literature date: 2020-09-26 journal: Cureus DOI: 10.7759/cureus.10659 sha: doc_id: 259660 cord_uid: x9sobzyw file: cache/cord-259863-ndclxrm7.json key: cord-259863-ndclxrm7 authors: Cooke, William R.; Billett, Anne; Gleeson, Suzie; Jacques, Andrew; Place, Kelly; Siddall, Jane; Walden, Andrew; Soulsby, Kim title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases date: 2020-05-15 journal: Eur J Obstet Gynecol Reprod Biol DOI: 10.1016/j.ejogrb.2020.05.025 sha: doc_id: 259863 cord_uid: ndclxrm7 file: cache/cord-258914-g6pv8zz9.json key: cord-258914-g6pv8zz9 authors: Proud, Pamela C.; Tsitoura, Daphne; Watson, Robert J.; Chua, Brendon Y; Aram, Marilyn J.; Bewley, Kevin R.; Cavell, Breeze E.; Cobb, Rebecca; Dowall, Stuart; Fotheringham, Susan A.; Ho, Catherine M. K.; Lucas, Vanessa; Ngabo, Didier; Rayner, Emma; Ryan, Kathryn A.; Slack, Gillian S.; Thomas, Stephen; Wand, Nadina I.; Yeates, Paul; Demaison, Christophe; Jackson, David C.; Bartlett, Nathan W.; Mercuri, Francesca; Carroll, Miles W. title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date: 2020-09-25 journal: bioRxiv DOI: 10.1101/2020.09.25.309914 sha: doc_id: 258914 cord_uid: g6pv8zz9 file: cache/cord-259925-g28sx9qu.json key: cord-259925-g28sx9qu authors: Saleemi, Mansab Ali; Ahmad, Bilal; Benchoula, Khaled; Vohra, Muhammad Sufyan; Mea, Hing Jian; Chong, Pei Pei; Palanisamy, Navindra Kumari; Wong, Eng Hwa title: Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date: 2020-10-06 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104583 sha: doc_id: 259925 cord_uid: g28sx9qu file: cache/cord-259869-kwzsdhrr.json key: cord-259869-kwzsdhrr authors: Baghizadeh Fini, Maryam title: Oral saliva and CVID-19 date: 2020-05-27 journal: Oral Oncol DOI: 10.1016/j.oraloncology.2020.104821 sha: doc_id: 259869 cord_uid: kwzsdhrr file: cache/cord-259747-sl9q63oc.json key: cord-259747-sl9q63oc authors: Remmelink, Myriam; De Mendonça, Ricardo; D’Haene, Nicky; De Clercq, Sarah; Verocq, Camille; Lebrun, Laetitia; Lavis, Philomène; Racu, Marie-Lucie; Trépant, Anne-Laure; Maris, Calliope; Rorive, Sandrine; Goffard, Jean-Christophe; De Witte, Olivier; Peluso, Lorenzo; Vincent, Jean-Louis; Decaestecker, Christine; Taccone, Fabio Silvio; Salmon, Isabelle title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 journal: Crit Care DOI: 10.1186/s13054-020-03218-5 sha: doc_id: 259747 cord_uid: sl9q63oc file: cache/cord-260310-0gkoanrg.json key: cord-260310-0gkoanrg authors: Kim, Jin Yong; Ko, Jae-Hoon; Kim, Yeonjae; Kim, Yae-Jean; Kim, Jeong-Min; Chung, Yoon-Seok; Kim, Heui Man; Han, Myung-Guk; Kim, So Yeon; Chin, Bum Sik title: Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea date: 2020-02-20 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e86 sha: doc_id: 260310 cord_uid: 0gkoanrg file: cache/cord-259229-e8m8m4ut.json key: cord-259229-e8m8m4ut authors: Samidurai, Arun; 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Yakhkind, Aleksandra title: More Than Meets the Eye: The Similarities Between COVID-19 and Smoking date: 2020-08-11 journal: Mayo Clin Proc DOI: 10.1016/j.mayocp.2020.08.008 sha: doc_id: 260402 cord_uid: 9b1ltcf1 file: cache/cord-259933-ggx4v0bz.json key: cord-259933-ggx4v0bz authors: Dalan, Rinkoo; Bornstein, Stefan R.; El-Armouche, Ali; Rodionov, Roman N; Markov, Alexander; Wielockx, Ben; Beuschlein, Felix; Boehm, Bernhard O. title: The ACE-2 in COVID-19: Foe or Friend? date: 2020-04-27 journal: Horm Metab Res DOI: 10.1055/a-1155-0501 sha: doc_id: 259933 cord_uid: ggx4v0bz file: cache/cord-260054-iihgc5nr.json key: cord-260054-iihgc5nr authors: Cavallo, Luigi; Oliva, Romina title: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date: 2020-06-08 journal: bioRxiv DOI: 10.1101/2020.06.08.140152 sha: doc_id: 260054 cord_uid: iihgc5nr file: cache/cord-259699-48jg7ci7.json key: cord-259699-48jg7ci7 authors: González-Calatayud, Dra Mariel; Vargas-Ábrego, Dr Benito; Gutiérrez-Uvalle, Dra Gabriela; López-Romero, Dra Sandra C.; Gabriel González-Pérez, Dr Luis; Alberto Carranco Martínez, Dr José; Raful Zacarías Ezzat, Dr Jed; Gracida Mancilla, Dr Noé I. title: Observational study of the suspected or confirmed cases of sars COV-2 infection needing emergency surgical intervention during the first months of the pandemic in a third level hospital: Case series date: 2020-10-24 journal: Ann Med Surg (Lond) DOI: 10.1016/j.amsu.2020.10.038 sha: doc_id: 259699 cord_uid: 48jg7ci7 file: cache/cord-260132-lqpk3ig7.json key: cord-260132-lqpk3ig7 authors: Quartuccio, Luca; Semerano, Luca; Benucci, Maurizio; Boissier, Marie-Christophe; De Vita, Salvatore title: Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome date: 2020-04-19 journal: Joint Bone Spine DOI: 10.1016/j.jbspin.2020.03.011 sha: doc_id: 260132 cord_uid: lqpk3ig7 file: cache/cord-260238-2p209g2p.json key: cord-260238-2p209g2p authors: Peiris, J S M; Guan, Y; Yuen, K Y title: Severe acute respiratory syndrome date: 2004-11-30 journal: Nat Med DOI: 10.1038/nm1143 sha: doc_id: 260238 cord_uid: 2p209g2p file: cache/cord-260034-a1y0enrg.json key: cord-260034-a1y0enrg authors: Karsulovic, Claudio; Lopez, Mercedes; Tempio, Fabian; Guerrero, Julia; Goecke, Annelise title: mTORC inhibitor Sirolimus deprograms monocytes in “cytokine storm” in SARS-CoV2 secondary hemophagocytic lymphohistiocytosis- like syndrome date: 2020-07-13 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108539 sha: doc_id: 260034 cord_uid: a1y0enrg file: cache/cord-260062-qajk0ov4.json key: cord-260062-qajk0ov4 authors: Mocchegiani, Federico; Baroni, Gianluca Svegliati; Vivarelli, Marco title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area date: 2020-09-10 journal: Updates Surg DOI: 10.1007/s13304-020-00881-9 sha: doc_id: 260062 cord_uid: qajk0ov4 file: cache/cord-260180-kojb8efv.json key: cord-260180-kojb8efv authors: Elsoukkary, Sarah S.; Mostyka, Maria; Dillard, Alicia; Berman, Diana R.; Ma, Lucy X.; Chadburn, Amy; Yantiss, Rhonda K.; Jessurun, Jose; Seshan, Surya V.; Borczuk, Alain C.; Salvatore, Steven P. title: Autopsy Findings in 32 Patients with COVID-19: A Single-Institution Experience date: 2020-09-17 journal: Pathobiology DOI: 10.1159/000511325 sha: doc_id: 260180 cord_uid: kojb8efv file: cache/cord-260550-ld9eieik.json key: cord-260550-ld9eieik authors: Ng, Man Wai; Zhou, Gangqiao; Chong, Wai Po; Lee, Loretta Wing Yan; Law, Helen Ka Wai; Zhang, Hongxing; Wong, Wilfred Hing Sang; Fok, Susanna Fung Shan; Zhai, Yun; Yung, Raymond WH; Chow, Eudora Y; Au, Ka Leung; Chan, Eric YT; Lim, Wilina; Peiris, JS Malik; He, Fuchu; Lau, Yu Lung title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date: 2007-06-01 journal: BMC Infect Dis DOI: 10.1186/1471-2334-7-50 sha: doc_id: 260550 cord_uid: ld9eieik file: cache/cord-260191-0u0pu0br.json key: cord-260191-0u0pu0br authors: Haas, W.; Krause, G.; Marcus, U.; Stark, K.; Ammon, A.; Burger, R. title: „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date: 2004-05-29 journal: Internist (Berl) DOI: 10.1007/s00108-004-1199-2 sha: doc_id: 260191 cord_uid: 0u0pu0br file: cache/cord-259968-cr3zf4oa.json key: cord-259968-cr3zf4oa authors: Harb, Roa; Remaley, Alan T; Sacks, David B title: Evaluation of Three Commercial Automated Assays for the Detection of anti-SARS-CoV-2 Antibodies date: 2020-08-06 journal: Clin Chem DOI: 10.1093/clinchem/hvaa193 sha: doc_id: 259968 cord_uid: cr3zf4oa file: cache/cord-260247-akujsk0s.json key: cord-260247-akujsk0s authors: Hamed, Ehab title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar date: 2020-11-02 journal: J Infect DOI: 10.1016/j.jinf.2020.10.029 sha: doc_id: 260247 cord_uid: akujsk0s file: cache/cord-260048-yis26g81.json key: cord-260048-yis26g81 authors: McNamara, Ryan P.; Caro-Vegas, Carolina; Landis, Justin T.; Moorad, Razia; Pluta, Linda J.; Eason, Anthony B.; Thompson, Cecilia; Bailey, Aubrey; Villamor, Femi Cleola S.; Lange, Philip T.; Wong, Jason P.; Seltzer, Tischan; Seltzer, Jedediah; Zhou, Yijun; Vahrson, Wolfgang; Juarez, Angelica; Meyo, James O.; Calabre, Tiphaine; Broussard, Grant; Rivera-Soto, Ricardo; Chappell, Danielle L.; Baric, Ralph S.; Damania, Blossom; Miller, Melissa B.; Dittmer, Dirk P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-10-20 journal: Cell Rep DOI: 10.1016/j.celrep.2020.108352 sha: doc_id: 260048 cord_uid: yis26g81 file: cache/cord-260508-z11exbyu.json key: cord-260508-z11exbyu authors: Wang, Hongru; Pipes, Lenore; Nielsen, Rasmus title: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.04.20.052019 sha: doc_id: 260508 cord_uid: z11exbyu file: cache/cord-260057-2m6jdvtc.json key: cord-260057-2m6jdvtc authors: Pandey, Preeti; Prasad, Kartikay; Prakash, Amresh; Kumar, Vijay title: Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date: 2020-09-23 journal: J Mol Med (Berl) DOI: 10.1007/s00109-020-01980-1 sha: doc_id: 260057 cord_uid: 2m6jdvtc file: cache/cord-260376-29ih5c9v.json key: cord-260376-29ih5c9v authors: Guo, Jian-Ping; Petric, Martin; Campbell, William; McGeer, Patrick L title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 journal: Virology DOI: 10.1016/j.virol.2004.04.017 sha: doc_id: 260376 cord_uid: 29ih5c9v file: cache/cord-260077-xf4sofyc.json key: cord-260077-xf4sofyc authors: Sawalha, Amr H.; Zhao, Ming; Coit, Patrick; Lu, Qianjin title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients date: 2020-04-08 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108410 sha: doc_id: 260077 cord_uid: xf4sofyc file: cache/cord-260412-yjr83ef6.json key: cord-260412-yjr83ef6 authors: Hotez, Peter J.; Bottazzi, Maria Elena title: Developing a low-cost and accessible COVID-19 vaccine for global health date: 2020-07-29 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0008548 sha: doc_id: 260412 cord_uid: yjr83ef6 file: cache/cord-260225-bc1hr0fr.json key: cord-260225-bc1hr0fr authors: Sirpilla, Olivia; Bauss, Jacob; Gupta, Ruchir; Underwood, Adam; Qutob, Dinah; Freeland, Tom; Bupp, Caleb; Carcillo, Joseph; Hartog, Nicholas; Rajasekaran, Surender; Prokop, Jeremy W. title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00421 sha: doc_id: 260225 cord_uid: bc1hr0fr file: cache/cord-260257-phmd0u6d.json key: cord-260257-phmd0u6d authors: Siegler, Aaron J; Hall, Eric; Luisi, Nicole; Zlotorzynska, Maria; Wilde, Gretchen; Sanchez, Travis; Bradley, Heather; Sullivan, Patrick S title: Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date: 2020-06-30 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa269 sha: doc_id: 260257 cord_uid: phmd0u6d file: cache/cord-260315-uau554jj.json key: cord-260315-uau554jj authors: Ramirez, Santseharay; Fernandez-Antunez, Carlota; Pham, Long V.; Ryberg, Line A.; Feng, Shan; Pedersen, Martin S.; Mikkelsen, Lotte S.; Belouzard, Sandrine; Dubuisson, Jean; Gottwein, Judith M.; Fahnøe, Ulrik; Bukh, Jens title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date: 2020-10-04 journal: bioRxiv DOI: 10.1101/2020.10.04.325316 sha: doc_id: 260315 cord_uid: uau554jj file: cache/cord-260365-neili1bd.json key: cord-260365-neili1bd authors: Silverstein, Jenna S.; Limaye, Meghana A.; Brubaker, Sara G.; Roman, Ashley S.; Bautista, Judita; Chervenak, Judith; Ratner, Adam J.; Sommer, Philip M.; Roselli, Nicole M.; Gibson, Charlisa D.; Ellenberg, David; Penfield, Christina A. title: Acute Respiratory Decompensation Requiring Intubation in Pregnant Women with SARS-CoV-2 (COVID-19) date: 2020-06-04 journal: AJP Rep DOI: 10.1055/s-0040-1712925 sha: doc_id: 260365 cord_uid: neili1bd file: cache/cord-260429-5wsj003j.json key: cord-260429-5wsj003j authors: Kenyon, Chris title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study date: 2020-04-06 journal: nan DOI: 10.1101/2020.03.31.20048652 sha: doc_id: 260429 cord_uid: 5wsj003j file: cache/cord-260503-yq4dtf8n.json key: cord-260503-yq4dtf8n authors: SAMARANAYAKE, LAKSHMAN P.; PEIRIS, MALIK title: Severe acute respiratory syndrome and dentistry A retrospective view date: 2004-09-30 journal: The Journal of the American Dental Association DOI: 10.14219/jada.archive.2004.0405 sha: doc_id: 260503 cord_uid: yq4dtf8n file: cache/cord-260624-rqjeacow.json key: cord-260624-rqjeacow authors: Gu, Jiang; Gong, Encong; Zhang, Bo; Zheng, Jie; Gao, Zifen; Zhong, Yanfeng; Zou, Wanzhong; Zhan, Jun; Wang, Shenglan; Xie, Zhigang; Zhuang, Hui; Wu, Bingquan; Zhong, Haohao; Shao, Hongquan; Fang, Weigang; Gao, Dongshia; Pei, Fei; Li, Xingwang; He, Zhongpin; Xu, Danzhen; Shi, Xeying; Anderson, Virginia M.; Leong, Anthony S.-Y. title: Multiple organ infection and the pathogenesis of SARS date: 2005-08-01 journal: J Exp Med DOI: 10.1084/jem.20050828 sha: doc_id: 260624 cord_uid: rqjeacow file: cache/cord-260729-b12v3c8c.json key: cord-260729-b12v3c8c authors: de Lang, Anna; Baas, Tracey; Teal, Thomas; Leijten, Lonneke M; Rain, Brandon; Osterhaus, Albert D; Haagmans, Bart L; Katze, Michael G title: Functional Genomics Highlights Differential Induction of Antiviral Pathways in the Lungs of SARS-CoV–Infected Macaques date: 2007-08-10 journal: PLoS Pathog DOI: 10.1371/journal.ppat.0030112 sha: doc_id: 260729 cord_uid: b12v3c8c file: cache/cord-260559-n8i52e8q.json key: cord-260559-n8i52e8q authors: Peiris, Malik; Leung, Gabriel M title: What can we expect from first-generation COVID-19 vaccines? date: 2020-09-21 journal: Lancet DOI: 10.1016/s0140-6736(20)31976-0 sha: doc_id: 260559 cord_uid: n8i52e8q file: cache/cord-260673-gf028lf6.json key: cord-260673-gf028lf6 authors: Bottemanne, Hugo; Morlaàs, Orphée; Fossati, Philippe; Schmidt, Liane title: Does the Coronavirus Epidemic Take Advantage of Human Optimism Bias? date: 2020-08-26 journal: Front Psychol DOI: 10.3389/fpsyg.2020.02001 sha: doc_id: 260673 cord_uid: gf028lf6 file: cache/cord-260854-v7wgb6mr.json key: cord-260854-v7wgb6mr authors: Colafrancesco, Serena; Alessandri, Cristiano; Conti, Fabrizio; Priori, Roberta title: COVID-19 gone bad: A new character in the spectrum of the hyperferritinemic syndrome? date: 2020-05-05 journal: Autoimmun Rev DOI: 10.1016/j.autrev.2020.102573 sha: doc_id: 260854 cord_uid: v7wgb6mr file: cache/cord-260871-dtn5t8ka.json key: cord-260871-dtn5t8ka authors: Silva, Marcus Tulius T.; Lima, Marco; Araujo, Abelardo Q.-C. title: SARS-CoV-2: Should We Be Concerned about the Nervous System? date: 2020-07-17 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0447 sha: doc_id: 260871 cord_uid: dtn5t8ka file: cache/cord-260407-jf1dnllj.json key: cord-260407-jf1dnllj authors: Tang, Catherine So-kum; Wong, Chi-yan title: Factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult Chinese in Hong Kong date: 2004-06-11 journal: Prev Med DOI: 10.1016/j.ypmed.2004.04.032 sha: doc_id: 260407 cord_uid: jf1dnllj file: cache/cord-260618-k0y0fz7k.json key: cord-260618-k0y0fz7k authors: Belli, Simone; Mugnaini, Rogério; Baltà, Joan; Abadal, Ernest title: Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? date: 2020-07-01 journal: Scientometrics DOI: 10.1007/s11192-020-03590-7 sha: doc_id: 260618 cord_uid: k0y0fz7k file: cache/cord-260772-n5q2yi7j.json key: cord-260772-n5q2yi7j authors: Ji, Dong; Qin, Enqiang; Xu, Jing; Zhang, Dawei; Cheng, Gregory; Wang, Yudong; Lau, George title: Reply to: ‘No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease’ date: 2020-05-06 journal: J Hepatol DOI: 10.1016/j.jhep.2020.04.039 sha: doc_id: 260772 cord_uid: n5q2yi7j file: cache/cord-260886-v1ei9im8.json key: cord-260886-v1ei9im8 authors: Baggett, Travis P.; Keyes, Harrison; Sporn, Nora; Gaeta, Jessie M. title: COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing date: 2020-04-15 journal: nan DOI: 10.1101/2020.04.12.20059618 sha: doc_id: 260886 cord_uid: v1ei9im8 file: cache/cord-260565-cdthfl5f.json key: cord-260565-cdthfl5f authors: Burkle, Frederick M. title: Declining Public Health Protections within Autocratic Regimes: Impact on Global Public Health Security, Infectious Disease Outbreaks, Epidemics, and Pandemics date: 2020-04-02 journal: Prehospital and disaster medicine DOI: 10.1017/s1049023x20000424 sha: doc_id: 260565 cord_uid: cdthfl5f file: cache/cord-260644-5moccf8c.json key: cord-260644-5moccf8c authors: Hashemi, Seyed Ahmad; Khoshi, Amirhosein; Ghasemzadeh-moghaddam, Hamed; Ghafouri, Majid; Taghavi, Mohammadreza; Namdar-Ahmadabad, Hasan; Azimian, Amir title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date: 2020-11-07 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104625 sha: doc_id: 260644 cord_uid: 5moccf8c file: cache/cord-260925-puuqv6zk.json key: cord-260925-puuqv6zk authors: Wen, Feng; Yu, Hai; Guo, Jinyue; Li, Yong; Luo, Kaijian; Huang, Shujian title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 date: 2020-03-05 journal: J Infect DOI: 10.1016/j.jinf.2020.02.027 sha: doc_id: 260925 cord_uid: puuqv6zk file: cache/cord-260866-bzdd4f5h.json key: cord-260866-bzdd4f5h authors: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 journal: nan DOI: 10.1016/j.cscee.2020.100042 sha: doc_id: 260866 cord_uid: bzdd4f5h file: cache/cord-261025-y49su5uc.json key: cord-261025-y49su5uc authors: Sampathkumar, Priya; Temesgen, Zelalem; Smith, Thomas F.; Thompson, Rodney L. title: SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date: 2003-07-31 journal: Mayo Clinic Proceedings DOI: 10.4065/78.7.882 sha: doc_id: 261025 cord_uid: y49su5uc file: cache/cord-260697-oepk0b1d.json key: cord-260697-oepk0b1d authors: Huang, J.; Zhai, S.; Ye, F.; Wang, S.; Zeng, M.; Way, G.; Madarha, V.; Zhu, T.; Qiu, L.; Xu, Z.; Ye, M.; Liu, L.; Cui, X.; Liao, J. title: COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches date: 2020-08-01 journal: nan DOI: 10.1101/2020.07.29.20164699 sha: doc_id: 260697 cord_uid: oepk0b1d file: cache/cord-261180-w62mynqb.json key: cord-261180-w62mynqb authors: Ling, L.; Wong, W. T.; Wan, W. T. P.; Choi, G.; Joynt, G. 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C.; Cho, William C. S.; Cheng, Wai Wai; Chan, Johnny W. M.; Ma, Victor W. S.; Yip, Tai-Tung; Lau Yip, Christine N. B.; Ngan, Roger K. C.; Law, Stephen C. K. title: Application of ProteinChip Array Profiling in Serum Biomarker Discovery for Patients Suffering From Severe Acute Respiratory Syndrome date: 2007 journal: Microarrays DOI: 10.1007/978-1-59745-304-2_20 sha: doc_id: 261253 cord_uid: btwx2vxo file: cache/cord-261307-qmh3wtqo.json key: cord-261307-qmh3wtqo authors: Evans, Scott E.; Tseng, Chien-Te K.; Scott, Brenton L.; Höök, A. 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A Protective Mechanism from Beta Chain Hemoglobin Defects? date: 2020-07-01 journal: Mediterr J Hematol Infect Dis DOI: 10.4084/mjhid.2020.052 sha: doc_id: 260981 cord_uid: 647wfa8z file: cache/cord-261075-wqtxhiy8.json key: cord-261075-wqtxhiy8 authors: Zhang, Meng; Zhou, Lingyan; Wang, Jing; Wang, Kun; Wang, Yuan; Pan, Xudong; Ma, Aijun title: The nervous system——a new territory being explored of SARS-CoV-2 date: 2020-10-28 journal: J Clin Neurosci DOI: 10.1016/j.jocn.2020.10.056 sha: doc_id: 261075 cord_uid: wqtxhiy8 file: cache/cord-261111-g1qxo01i.json key: cord-261111-g1qxo01i authors: Kowalewski, Joel; Ray, Anandasankar title: Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space date: 2020-08-06 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e04639 sha: doc_id: 261111 cord_uid: g1qxo01i file: cache/cord-261414-vqvctafm.json key: cord-261414-vqvctafm authors: Ian Gallicano, G.; Casey, John L.; Fu, Jiayu; Mahapatra, Samiksha title: Molecular targeting of vulnerable RNA sequences in SARS CoV-2: identifying clinical feasibility date: 2020-11-12 journal: Gene Ther DOI: 10.1038/s41434-020-00210-0 sha: doc_id: 261414 cord_uid: vqvctafm file: cache/cord-261297-kbcsa9zj.json key: cord-261297-kbcsa9zj authors: Chang, Shan-Chwen title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) date: 2005-03-31 journal: Journal of the Chinese Medical Association DOI: 10.1016/s1726-4901(09)70229-1 sha: doc_id: 261297 cord_uid: kbcsa9zj file: cache/cord-261279-6mef38eo.json key: cord-261279-6mef38eo authors: Chu, Daniel K W; Pan, Yang; Cheng, Samuel M S; Hui, Kenrie P Y; Krishnan, Pavithra; Liu, Yingzhi; Ng, Daisy Y M; Wan, Carrie K C; Yang, Peng; Wang, Quanyi; Peiris, Malik; Poon, Leo L M title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 journal: Clin Chem DOI: 10.1093/clinchem/hvaa029 sha: doc_id: 261279 cord_uid: 6mef38eo file: cache/cord-261415-qxl14j2m.json key: cord-261415-qxl14j2m authors: Fu, Yajing; Cheng, Yuanxiong; Wu, Yuntao title: Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools date: 2020-03-03 journal: Virol Sin DOI: 10.1007/s12250-020-00207-4 sha: doc_id: 261415 cord_uid: qxl14j2m file: cache/cord-261470-sqxdwu6j.json key: cord-261470-sqxdwu6j authors: Weichmann, Franziska; Rohdewald, Peter title: Projected supportive effects of Pycnogenol® in patients suffering from multi-dimensional health impairments after a SARS-CoV2 infection date: 2020-10-09 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.106191 sha: doc_id: 261470 cord_uid: sqxdwu6j file: cache/cord-261834-x5ltmj30.json key: cord-261834-x5ltmj30 authors: Guo, Cheng-Xian; He, Li; Yin, Ji-Ye; Meng, Xiang-Guang; Tan, Wei; Yang, Guo-Ping; Bo, Tao; Liu, Jun-Ping; Lin, Xin-Jian; Chen, Xiang title: Epidemiological and clinical features of pediatric COVID-19 date: 2020-08-06 journal: BMC Med DOI: 10.1186/s12916-020-01719-2 sha: doc_id: 261834 cord_uid: x5ltmj30 file: cache/cord-261634-vfe1lawl.json key: cord-261634-vfe1lawl authors: Riddell, Shane; Goldie, Sarah; Hill, Andrew; Eagles, Debbie; Drew, Trevor W. title: The effect of temperature on persistence of SARS-CoV-2 on common surfaces date: 2020-10-07 journal: Virol J DOI: 10.1186/s12985-020-01418-7 sha: doc_id: 261634 cord_uid: vfe1lawl file: cache/cord-261750-6b1y7yxg.json key: cord-261750-6b1y7yxg authors: Kwek, Seow-Khee; Chew, Wuen-Ming; Ong, Kian-Chung; Ng, Alan Wei-Keong; Lee, Lawrence Soon-U; Kaw, Gregory; Leow, Melvin Khee-Shing title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge date: 2006-05-31 journal: Journal of Psychosomatic Research DOI: 10.1016/j.jpsychores.2005.08.020 sha: doc_id: 261750 cord_uid: 6b1y7yxg file: cache/cord-261877-4y37676n.json key: cord-261877-4y37676n authors: Xu, Cong; Wang, Yanxing; Liu, Caixuan; Zhang, Chao; Han, Wenyu; Hong, Xiaoyu; Wang, Yifan; Hong, Qin; Wang, Shutian; Zhao, Qiaoyu; Wang, Yalei; Yang, Yong; Chen, Kaijian; Zheng, Wei; Kong, Liangliang; Wang, Fangfang; Zuo, Qinyu; Huang, Zhong; Cong, Yao title: Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date: 2020-06-30 journal: bioRxiv DOI: 10.1101/2020.06.30.177097 sha: doc_id: 261877 cord_uid: 4y37676n file: cache/cord-261921-c97ygxq2.json key: cord-261921-c97ygxq2 authors: Souders, Colby P.; Zhao, Hanson; Ackerman, A. Lenore title: Considerations for Bedside Urologic Procedures in Patients with Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-04-24 journal: Urology DOI: 10.1016/j.urology.2020.04.066 sha: doc_id: 261921 cord_uid: c97ygxq2 file: cache/cord-261662-d0tg9i90.json key: cord-261662-d0tg9i90 authors: Andres, Cristina; Garcia-Cehic, Damir; Gregori, Josep; Piñana, Maria; Rodriguez-Frias, Francisco; Guerrero-Murillo, Mercedes; Esperalba, Juliana; Rando, Ariadna; Goterris, Lidia; Codina, Maria Gema; Quer, Susanna; Martín, Maria Carmen; Campins, Magda; Ferrer, Ricard; Almirante, Benito; Esteban, Juan Ignacio; Pumarola, Tomás; Antón, Andrés; Quer, Josep title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date: 2020-06-08 journal: bioRxiv DOI: 10.1101/2020.06.03.129585 sha: doc_id: 261662 cord_uid: d0tg9i90 file: cache/cord-261959-pvufajw4.json key: cord-261959-pvufajw4 authors: Karathanou, Konstantina; Lazaratos, Michalis; Bertalan, Éva; Siemers, Malte; Buzar, Krzysztof; Schertler, Gebhard F.X.; del Val, Coral; Bondar, Ana-Nicoleta title: A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2 date: 2020-09-10 journal: J Struct Biol DOI: 10.1016/j.jsb.2020.107617 sha: doc_id: 261959 cord_uid: pvufajw4 file: cache/cord-261718-zqoggwnk.json key: cord-261718-zqoggwnk authors: Pietschmann, Jan; Vöpel, Nadja; Spiegel, Holger; Krause, Hans-Joachim; Schröper, Florian title: Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date: 2020-06-03 journal: bioRxiv DOI: 10.1101/2020.06.02.131102 sha: doc_id: 261718 cord_uid: zqoggwnk file: cache/cord-262104-oig3qrr7.json key: cord-262104-oig3qrr7 authors: Brüssow, Harald title: COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date: 2020-06-08 journal: Environ Microbiol DOI: 10.1111/1462-2920.15118 sha: doc_id: 262104 cord_uid: oig3qrr7 file: cache/cord-261472-qcu73sdu.json key: cord-261472-qcu73sdu authors: Yao, Yong Xiu; Ren, Junyuan; Heinen, Paul; Zambon, Maria; Jones, Ian M. title: Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date: 2004-07-01 journal: J Infect Dis DOI: 10.1086/421280 sha: doc_id: 261472 cord_uid: qcu73sdu file: cache/cord-261941-xf1k5uj1.json key: cord-261941-xf1k5uj1 authors: Stackhouse, Robin A. title: Severe acute respiratory syndrome and tuberculosis date: 2005-03-01 journal: Anesthesiol Clin North Am DOI: 10.1016/j.atc.2004.06.002 sha: doc_id: 261941 cord_uid: xf1k5uj1 file: cache/cord-261435-wcn4bjnw.json key: cord-261435-wcn4bjnw authors: Ren, Xianwen; Wen, Wen; Fan, Xiaoying; Hou, Wenhong; Su, Bin; Cai, Pengfei; Li, Jiesheng; Liu, Yang; Tang, Fei; Zhang, Fan; Yang, Yu; He, Jiangping; Ma, Wenji; He, Jingjing; Wang, Pingping; Cao, Qiqi; Chen, Fangjin; Chen, Yuqing; Cheng, Xuelian; Deng, Guohong; Deng, Xilong; Ding, Wenyu; Feng, Yingmei; Gan, Rui; Guo, Chuang; Guo, Weiqiang; He, Shuai; Jiang, Chen; Liang, Juanran; Li, Yi-min; Lin, Jun; Ling, Yun; Liu, Haofei; Liu, Jianwei; Liu, Nianping; Liu, Yang; Luo, Meng; Ma, Qiang; Song, Qibing; Sun, Wujianan; Wang, GaoXiang; Wang, Feng; Wang, Ying; Wen, Xiaofeng; Wu, Qian; Xu, Gang; Xie, Xiaowei; Xiong, Xinxin; Xing, Xudong; Xu, Hao; Yin, Chonghai; Yu, Dongdong; Yu, Kezhuo; Yuan, Jin; Zhang, Biao; Zhang, Tong; Zhao, Jincun; Zhao, Peidong; Zhou, Jianfeng; Zhou, Wei; Zhong, Sujuan; Zhong, Xiaosong; Zhang, Shuye; Zhu, Lin; Zhu, Ping; Zou, Bin; Zou, Jiahua; Zuo, Zengtao; Bai, Fan; Huang, Xi; Bian, Xiuwu; Zhou, Penghui; Jiang, Qinghua; Huang, Zhiwei; Bei, Jin-Xin; Wei, Lai; Liu, Xindong; Cheng, Tao; Li, Xiangpan; Zhao, Pingsen; Wang, Fu-Sheng; Wang, Hongyang; Su, Bing; Zhang, Zheng; Qu, Kun; Wang, Xiaoqun; Chen, Jiekai; Jin, Ronghua; Zhang, Zemin title: Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date: 2020-10-29 journal: bioRxiv DOI: 10.1101/2020.10.29.360479 sha: doc_id: 261435 cord_uid: wcn4bjnw file: cache/cord-262000-k32cb9ym.json key: cord-262000-k32cb9ym authors: Li, Xue-Ting; Liu, Ying; Song, Juan-Juan; Zhong, Jiu-Chang title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 date: 2020-09-07 journal: Acta Pharm Sin B DOI: 10.1016/j.apsb.2020.09.003 sha: doc_id: 262000 cord_uid: k32cb9ym file: cache/cord-262068-9ixq8hwb.json key: cord-262068-9ixq8hwb authors: Gottardi, Andrea De; Fratila, Corneliu; Bertoli, Raffaela; Cerny, Andreas; Magenta, Lorenzo; Gianella, Pietro; Majno-Hurst, Pietro; Ceschi, Alessandro; Vanini, Gianluca; Bernasconi, Enos title: Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection date: 2020-06-10 journal: Clin Res Hepatol Gastroenterol DOI: 10.1016/j.clinre.2020.05.014 sha: doc_id: 262068 cord_uid: 9ixq8hwb file: cache/cord-261688-njlxrxv6.json key: cord-261688-njlxrxv6 authors: Yang, Ziwei; Zhang, Xiaolin; Wang, Fan; Wang, Peihui; Kuang, Ersheng; Li, Xiaojuan title: Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date: 2020-08-12 journal: bioRxiv DOI: 10.1101/2020.08.12.247767 sha: doc_id: 261688 cord_uid: njlxrxv6 file: cache/cord-261619-31jk1vh6.json key: cord-261619-31jk1vh6 authors: Lindholm, David A; Kiley, John L; Jansen, Nathan K; Hoard, Robert T; Bondaryk, Matthew R; Stanley, Elizabeth M; Alvarado, Gadiel R; Markelz, Ana E; Cybulski, Robert J; Okulicz, Jason F title: Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date: 2020-07-17 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa306 sha: doc_id: 261619 cord_uid: 31jk1vh6 file: cache/cord-262020-ygl8xlhk.json key: cord-262020-ygl8xlhk authors: McDermott, Aoibhinn; O’Kelly, John; de Barra, Eoghan; Fitzpatrick, Fidelma; Little, Dilly M.; Davis, Niall F. title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection date: 2020-05-16 journal: Eur Urol DOI: 10.1016/j.eururo.2020.05.012 sha: doc_id: 262020 cord_uid: ygl8xlhk file: cache/cord-262180-t4akem15.json key: cord-262180-t4akem15 authors: Cheruiyot, Isaac title: Comment on “Encephalopathy in patients with COVID‐19: A review” date: 2020-07-11 journal: J Med Virol DOI: 10.1002/jmv.26238 sha: doc_id: 262180 cord_uid: t4akem15 file: cache/cord-261566-fn08b0y2.json key: cord-261566-fn08b0y2 authors: Mudgal, Rajat; Nehul, Sanketkumar; Tomar, Shailly title: Prospects for mucosal vaccine: shutting the door on SARS-CoV-2 date: 2020-09-15 journal: Human vaccines & immunotherapeutics DOI: 10.1080/21645515.2020.1805992 sha: doc_id: 261566 cord_uid: fn08b0y2 file: cache/cord-262029-zzn74cjr.json key: cord-262029-zzn74cjr authors: Kang, Chang Kyung; Seong, Moon-Woo; Choi, Su-Jin; Kim, Taek Soo; Choe, Pyoeng Gyun; Song, Sang Hoon; Kim, Nam-Joong; Park, Wan Beom; Oh, Myoung-don title: In vitro activity of lopinavir/ritonavir and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2 at concentrations achievable by usual doses date: 2020-05-29 journal: Korean J Intern Med DOI: 10.3904/kjim.2020.157 sha: doc_id: 262029 cord_uid: zzn74cjr file: cache/cord-262149-qrjprsv5.json key: cord-262149-qrjprsv5 authors: Sarode, Gargi S.; Sarode, Sachin C.; Sengupta, Namrata; Gadbail, Amol R.; Gondivkar, Shailesh; Sharma, Nilesh Kumar; Patil, Shankargouda title: Clinical status determines the efficacy of salivary and nasopharyngeal samples for detection of SARS-CoV-2 date: 2020-10-12 journal: Clin Oral Investig DOI: 10.1007/s00784-020-03630-9 sha: doc_id: 262149 cord_uid: qrjprsv5 file: cache/cord-262145-i29e3fge.json key: cord-262145-i29e3fge authors: Huang, Kuan-Ying A.; Tan, Tiong Kit; Chen, Ting-Hua; Huang, Chung-Guei; Harvey, Ruth; Hussain, Saira; Chen, Cheng-Pin; Harding, Adam; Gilbert-Jaramillo, Javier; Liu, Xu; Knight, Michael; Schimanski, Lisa; Shih, Shin-Ru; Lin, Yi-Chun; Cheng, Chien-Yu; Cheng, Shu-Hsing; Huang, Yhu-Chering; Lin, Tzou-Yien; Jan, Jia-Tsrong; Ma, Che; James, William; Daniels, Rodney S.; McCauley, John W.; Rijal, Pramila; Townsend, Alain R. title: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date: 2020-10-19 journal: bioRxiv DOI: 10.1101/2020.08.28.267526 sha: doc_id: 262145 cord_uid: i29e3fge file: cache/cord-261952-xq6qney7.json key: cord-261952-xq6qney7 authors: Mazzulli, Tony; Low, Donald E; Poutanen, Susan M title: Proteomics and Severe Acute Respiratory Syndrome (SARS): Emerging Technology Meets Emerging Pathogen date: 2005-01-01 journal: Clin Chem DOI: 10.1373/clinchem.2004.041574 sha: doc_id: 261952 cord_uid: xq6qney7 file: cache/cord-262184-uxyb4vih.json key: cord-262184-uxyb4vih authors: Jockusch, Steffen; Tao, Chuanjuan; Li, Xiaoxu; Anderson, Thomas K.; Chien, Minchen; Kumar, Shiv; Russo, James J.; Kirchdoerfer, Robert N.; Ju, Jingyue title: A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses that Cause SARS and COVID-19 date: 2020-06-18 journal: Antiviral Res DOI: 10.1016/j.antiviral.2020.104857 sha: doc_id: 262184 cord_uid: uxyb4vih file: cache/cord-262268-gm99cadh.json key: cord-262268-gm99cadh authors: Wang, Jingqiang; Wen, Jie; Li, Jingxiang; Yin, Jianning; Zhu, Qingyu; Wang, Hao; Yang, Yongkui; Qin, E’de; You, Bo; Li, Wei; Li, Xiaolei; Huang, Shengyong; Yang, Ruifu; Zhang, Xumin; Yang, Ling; Zhang, Ting; Yin, Ye; Cui, Xiaodai; Tang, Xiangjun; Wang, Luoping; He, Bo; Ma, Lianhua; Lei, Tingting; Zeng, Changqing; Fang, Jianqiu; Yu, Jun; Wang, Jian; Yang, Huanming; West, Matthew B; Bhatnagar, Aruni; Lu, Youyong; Xu, Ningzhi; Liu, Siqi title: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date: 2003-12-01 journal: Clin Chem DOI: 10.1373/clinchem.2003.023184 sha: doc_id: 262268 cord_uid: gm99cadh file: cache/cord-261876-7rsc803x.json key: cord-261876-7rsc803x authors: Kaslow, David C. title: Certainty of success: three critical parameters in coronavirus vaccine development date: 2020-05-25 journal: NPJ Vaccines DOI: 10.1038/s41541-020-0193-6 sha: doc_id: 261876 cord_uid: 7rsc803x file: cache/cord-262159-8y0q45gr.json key: cord-262159-8y0q45gr authors: Ciorba, Andrea; Corazzi, Virginia; Skarżyński, Piotr Henryk; Skarżyńska, Magdalena B; Bianchini, Chiara; Pelucchi, Stefano; Hatzopoulos, Stavros title: Don’t forget ototoxicity during the SARS-CoV-2 (Covid-19) pandemic! date: 2020-07-10 journal: Int J Immunopathol Pharmacol DOI: 10.1177/2058738420941754 sha: doc_id: 262159 cord_uid: 8y0q45gr file: cache/cord-261615-p81l6zvz.json key: cord-261615-p81l6zvz authors: Grabbe, Stephan; Beissert, Stefan; Enk, Alexander title: Systemische Immunsuppression in Zeiten von COVID‐19: Müssen wir umdenken? date: 2020-08-21 journal: J Dtsch Dermatol Ges DOI: 10.1111/ddg.14194_g sha: doc_id: 261615 cord_uid: p81l6zvz file: cache/cord-262250-o7qhncic.json key: cord-262250-o7qhncic authors: Habel, J. R.; Nguyen, T. H. O.; van de Sandt, C. E.; Juno, J. A.; Chaurasia, P.; Wragg, K.; Koutsakos, M.; Hensen, L.; Chua, B.; Zhang, W.; Tan, H. X.; Flanagan, K. L.; Doolan, D.; Torresi, J.; Chen, W.; Wakim, L.; Cheng, A.; Petersen, J.; Rossjohn, J.; Wheatley, A. K.; Kent, S.; Rowntree, L.; Kedzierska, K. title: Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype date: 2020-08-19 journal: nan DOI: 10.1101/2020.08.17.20176370 sha: doc_id: 262250 cord_uid: o7qhncic file: cache/cord-262043-66qle52a.json key: cord-262043-66qle52a authors: Basit, Abdul; Ali, Tanveer; Rehman, Shafiq Ur title: Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date: 2020-05-20 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1768150 sha: doc_id: 262043 cord_uid: 66qle52a file: cache/cord-262090-nbxzyjvf.json key: cord-262090-nbxzyjvf authors: Acharya, Arpan; Kevadiya, Bhavesh D.; Gendelman, Howard E.; Byrareddy, Siddappa N. title: SARS-CoV-2 Infection Leads to Neurological Dysfunction date: 2020-05-23 journal: J Neuroimmune Pharmacol DOI: 10.1007/s11481-020-09924-9 sha: doc_id: 262090 cord_uid: nbxzyjvf file: cache/cord-262119-s6hc7fxs.json key: cord-262119-s6hc7fxs authors: Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Orta-Resendiz, Aurelio; Singh, Vidisha; Aghamiri, Sara Sadat; Acencio, Marcio Luis; Glaab, Enrico; Ruepp, Andreas; Fobo, Gisela; Montrone, Corinna; Brauner, Barbara; Frischman, Goar; Monraz Gómez, Luis Cristóbal; Somers, Julia; Hoch, Matti; Gupta, Shailendra Kumar; Scheel, Julia; Borlinghaus, Hanna; Czauderna, Tobias; Schreiber, Falk; Montagud, Arnau; de Leon, Miguel Ponce; Funahashi, Akira; Hiki, Yusuke; Hiroi, Noriko; Yamada, Takahiro G.; Dräger, Andreas; Renz, Alina; Naveez, Muhammad; Bocskei, Zsolt; Messina, Francesco; Börnigen, Daniela; Fergusson, Liam; Conti, Marta; Rameil, Marius; Nakonecnij, Vanessa; Vanhoefer, Jakob; Schmiester, Leonard; Wang, Muying; Ackerman, Emily E.; Shoemaker, Jason; Zucker, Jeremy; Oxford, Kristie; Teuton, Jeremy; Kocakaya, Ebru; Summak, Gökçe Yağmur; Hanspers, Kristina; Kutmon, Martina; Coort, Susan; Eijssen, Lars; Ehrhart, Friederike; Rex, D. A. B.; Slenter, Denise; Martens, Marvin; Haw, Robin; Jassal, Bijay; Matthews, Lisa; Orlic-Milacic, Marija; Senff Ribeiro, Andrea; Rothfels, Karen; Shamovsky, Veronica; Stephan, Ralf; Sevilla, Cristoffer; Varusai, Thawfeek; Ravel, Jean-Marie; Fraser, Rupsha; Ortseifen, Vera; Marchesi, Silvia; Gawron, Piotr; Smula, Ewa; Heirendt, Laurent; Satagopam, Venkata; Wu, Guanming; Riutta, Anders; Golebiewski, Martin; Owen, Stuart; Goble, Carole; Hu, Xiaoming; Overall, Rupert W.; Maier, Dieter; Bauch, Angela; Gyori, Benjamin M.; Bachman, John A.; Vega, Carlos; Grouès, Valentin; Vazquez, Miguel; Porras, Pablo; Licata, Luana; Iannuccelli, Marta; Sacco, Francesca; Nesterova, Anastasia; Yuryev, Anton; de Waard, Anita; Turei, Denes; Luna, Augustin; Babur, Ozgun; Soliman, Sylvain; Valdeolivas, Alberto; Esteban-Medina, Marina; Peña-Chilet, Maria; Helikar, Tomáš; Puniya, Bhanwar Lal; Modos, Dezso; Treveil, Agatha; Olbei, Marton; De Meulder, Bertrand; Dugourd, Aurélien; Naldi, Aurelien; Noel, Vincent; Calzone, Laurence; Sander, Chris; Demir, Emek; Korcsmaros, Tamas; Freeman, Tom C.; Augé, Franck; Beckmann, Jacques S.; Hasenauer, Jan; Wolkenhauer, Olaf; Wilighagen, Egon L.; Pico, Alexander R.; Evelo, Chris T.; Gillespie, Marc E.; Stein, Lincoln D.; Hermjakob, Henning; D’Eustachio, Peter; Saez-Rodriguez, Julio; Dopazo, Joaquin; Valencia, Alfonso; Kitano, Hiroaki; Barillot, Emmanuel; Auffray, Charles; Balling, Rudi; Schneider, Reinhard title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date: 2020-10-27 journal: bioRxiv DOI: 10.1101/2020.10.26.356014 sha: doc_id: 262119 cord_uid: s6hc7fxs file: cache/cord-261961-u4d0vvmq.json key: cord-261961-u4d0vvmq authors: St-Germain, Jonathan R.; Astori, Audrey; Samavarchi-Tehrani, Payman; Abdouni, Hala; Macwan, Vinitha; Kim, Dae-Kyum; Knapp, Jennifer J.; Roth, Frederick P.; Gingras, Anne-Claude; Raught, Brian title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.28.269175 sha: doc_id: 261961 cord_uid: u4d0vvmq file: cache/cord-262107-qso8ewi9.json key: cord-262107-qso8ewi9 authors: Kim, In-Cheol; Hwang, Ilseon; Kim, Yun Seok; Kim, Jae-Bum title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned date: 2020-05-22 journal: Korean Circ J DOI: 10.4070/kcj.2020.0177 sha: doc_id: 262107 cord_uid: qso8ewi9 file: cache/cord-262266-m0fjt483.json key: cord-262266-m0fjt483 authors: Peddu, Vikas; Shean, Ryan C; Xie, Hong; Shrestha, Lasata; Perchetti, Garrett A; Minot, Samuel S; Roychoudhury, Pavitra; Huang, Meei-Li; Nalla, Arun; Reddy, Shriya B; Phung, Quynh; Reinhardt, Adam; Jerome, Keith R; Greninger, Alexander L title: Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization date: 2020-05-07 journal: Clin Chem DOI: 10.1093/clinchem/hvaa106 sha: doc_id: 262266 cord_uid: m0fjt483 file: cache/cord-262192-w86qc3fq.json key: cord-262192-w86qc3fq authors: Balkhair, Abdullah A. title: COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases date: 2020-04-21 journal: Oman Med J DOI: 10.5001/omj.2020.41 sha: doc_id: 262192 cord_uid: w86qc3fq file: cache/cord-262328-q7mt0xve.json key: cord-262328-q7mt0xve authors: Wajnberg, Ania; Mansour, Mayce; Leven, Emily; Bouvier, Nicole M; Patel, Gopi; Firpo-Betancourt, Adolfo; Mendu, Rao; Jhang, Jeffrey; Arinsburg, Suzanne; Gitman, Melissa; Houldsworth, Jane; Sordillo, Emilia; Paniz-Mondolfi, Alberto; Baine, Ian; Simon, Viviana; Aberg, Judith; Krammer, Florian; Reich, David; Cordon-Cardo, Carlos title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 journal: Lancet Microbe DOI: 10.1016/s2666-5247(20)30120-8 sha: doc_id: 262328 cord_uid: q7mt0xve file: cache/cord-262412-bs7quwov.json key: cord-262412-bs7quwov authors: Kaya, Gürkan; Kaya, Aysin; Saurat, Jean-Hilaire title: Clinical and Histopathological Features and Potential Pathological Mechanisms of Skin Lesions in COVID-19: Review of the Literature date: 2020-06-30 journal: Dermatopathology (Basel) DOI: 10.3390/dermatopathology7010002 sha: doc_id: 262412 cord_uid: bs7quwov file: cache/cord-262428-erlmyzwn.json key: cord-262428-erlmyzwn authors: CABARKAPA, Sonja; Nadjidai, Sarah E.; Murgier, Jerome; Ng, Chee H. title: The psychological impact of COVID-19 and other viral epidemics on frontline healthcare workers and ways to address it: A rapid systematic review date: 2020-09-17 journal: Brain Behav Immun Health DOI: 10.1016/j.bbih.2020.100144 sha: doc_id: 262428 cord_uid: erlmyzwn file: cache/cord-262282-9xh51cd1.json key: cord-262282-9xh51cd1 authors: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 journal: Antibiotics (Basel) DOI: 10.3390/antibiotics9050255 sha: doc_id: 262282 cord_uid: 9xh51cd1 file: cache/cord-262361-3f09z5pf.json key: cord-262361-3f09z5pf authors: Agbelele, Penance; Vanmaris, François; Sanguina, Mario; Zerkly, Bachar; Djebara, Az-Eddine; Girard, Pierre title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case date: 2020-07-30 journal: Radiol Case Rep DOI: 10.1016/j.radcr.2020.07.071 sha: doc_id: 262361 cord_uid: 3f09z5pf file: cache/cord-262454-bccrvapy.json key: cord-262454-bccrvapy authors: Szente Fonseca, Silvia Nunes; Queiroz de Sousa, Anastasio; Wolkoff, Alexandre Giandoni; Moreira, Marcelo Sampaio; Pinto, Bruno Castro; Valente Takeda, Christianne Fernandes; Rebouças, Eduardo; Vasconcellos Abdon, Ana Paula; Nascimento, Anderson L.A.; Risch, Harvey A. title: Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis date: 2020-10-31 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101906 sha: doc_id: 262454 cord_uid: bccrvapy file: cache/cord-262441-slh52nxm.json key: cord-262441-slh52nxm authors: Sakai, Yusuke; Kawachi, Kengo; Terada, Yutaka; Omori, Hiroko; Matsuura, Yoshiharu; Kamitani, Wataru title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 journal: Virology DOI: 10.1016/j.virol.2017.07.019 sha: doc_id: 262441 cord_uid: slh52nxm file: cache/cord-262415-cj4pjuuc.json key: cord-262415-cj4pjuuc authors: Eiros, R.; Barreiro-Perez, M.; Martin-Garcia, A.; Almeida, J.; Villacorta, E.; Perez-Pons, A.; Merchan, S.; Torres-Valle, A.; Sanchez-Pablo, C.; Gonzalez-Calle, D.; Perez-Escurza, O.; Toranzo, I.; Diaz-Pelaez, E.; Fuentes-Herrero, B.; Macias-Alvarez, L.; Oliva-Ariza, G.; Lecrevisse, Q.; Fluxa, R.; Bravo-Grandez, J. L.; Orfao, A.; Sanchez, P. L. title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers date: 2020-07-14 journal: nan DOI: 10.1101/2020.07.12.20151316 sha: doc_id: 262415 cord_uid: cj4pjuuc file: cache/cord-262420-vw7fnguu.json key: cord-262420-vw7fnguu authors: Moey, Melissa Y.Y.; Sengodan, Prasanna M.; Shah, Neeraj; McCallen, Justin D.; Eboh, Oghenesuvwe; Nekkanti, Rajasekhar; Carabello, Blase A.; Naniwadekar, Aditi R. title: Electrocardiographic Changes and Arrhythmias in Hospitalized Patients With COVID-19 date: 2020-09-15 journal: Circ Arrhythm Electrophysiol DOI: 10.1161/circep.120.009023 sha: doc_id: 262420 cord_uid: vw7fnguu file: cache/cord-262556-gpnp06je.json key: cord-262556-gpnp06je authors: Behrens, Estuardo; Poggi, Luis; Aparicio, Sergio; Martínez Duartez, Pedro; Rodríguez, Nelson; Zundel, Natan; Ramos Cardoso, Almino; Camacho, Diego; López-Corvalá, Juan Antonio; Vilas-Bôas, Marcos Leão; Laynez, Jorge title: COVID-19: IFSO LAC Recommendations for the Resumption of Elective Bariatric Surgery date: 2020-08-22 journal: Obes Surg DOI: 10.1007/s11695-020-04910-9 sha: doc_id: 262556 cord_uid: gpnp06je file: cache/cord-262338-ipvzugo8.json key: cord-262338-ipvzugo8 authors: Choi, Jun-Yong; Joo, Myungsoo title: The pathogenesis and alternative treatment of SARS-CoV2 date: 2020-05-03 journal: Integr Med Res DOI: 10.1016/j.imr.2020.100421 sha: doc_id: 262338 cord_uid: ipvzugo8 file: cache/cord-262470-nkql7h9x.json key: cord-262470-nkql7h9x authors: Muus, Christoph; Luecken, Malte D.; Eraslan, Gokcen; Waghray, Avinash; Heimberg, Graham; Sikkema, Lisa; Kobayashi, Yoshihiko; Vaishnav, Eeshit Dhaval; Subramanian, Ayshwarya; Smilie, Christopher; Jagadeesh, Karthik; Duong, Elizabeth Thu; Fiskin, Evgenij; Triglia, Elena Torlai; Ansari, Meshal; Cai, Peiwen; Lin, Brian; Buchanan, Justin; Chen, Sijia; Shu, Jian; Haber, Adam L; Chung, Hattie; Montoro, Daniel T; Adams, Taylor; Aliee, Hananeh; Samuel, J.; Andrusivova, Allon Zaneta; Angelidis, Ilias; Ashenberg, Orr; Bassler, Kevin; Bécavin, Christophe; Benhar, Inbal; Bergenstråhle, Joseph; Bergenstråhle, Ludvig; Bolt, Liam; Braun, Emelie; Bui, Linh T; Chaffin, Mark; Chichelnitskiy, Evgeny; Chiou, Joshua; Conlon, Thomas M; Cuoco, Michael S; Deprez, Marie; Fischer, David S; Gillich, Astrid; Gould, Joshua; Guo, Minzhe; Gutierrez, Austin J; Habermann, Arun C; Harvey, Tyler; He, Peng; Hou, Xiaomeng; Hu, Lijuan; Jaiswal, Alok; Jiang, Peiyong; Kapellos, Theodoros; Kuo, Christin S; Larsson, Ludvig; Kyungtae Lim, Michael A. Leney-Greene; Litviňuková, Monika; Lu, Ji; Maatz, Henrike; Madissoon, Elo; Mamanova, Lira; Manakongtreecheep, Kasidet; Marquette, Charles-Hugo; Mbano, Ian; McAdams, Alexi Marie; Metzger, Ross J; Nabhan, Ahmad N; Nyquist, Sarah K.; Ordovas-Montanes, Jose; Penland, Lolita; Poirion, Olivier B; Poli, Sergio; Qi, CanCan; Reichart, Daniel; Rosas, Ivan; Schupp, Jonas; Sinha, Rahul; Sit, Rene V; Slowikowski, Kamil; Slyper, Michal; Smith, Neal; Sountoulidis, Alex; Strunz, Maximilian; Sun, Dawei; Talavera-López, Carlos; Tan, Peng; Tantivit, Jessica; Travaglini, Kyle J; Tucker, Nathan R.; Vernon, Katherine; Wadsworth, Marc H.; Waldmann, Julia; Wang, Xiuting; Yan, Wenjun; Zhao, William; Ziegler, Carly G. K. title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date: 2020-04-20 journal: bioRxiv DOI: 10.1101/2020.04.19.049254 sha: doc_id: 262470 cord_uid: nkql7h9x file: cache/cord-262485-sx2q5ol4.json key: cord-262485-sx2q5ol4 authors: Davda, Jayeshkumar Narsibhai; Frank, Keith; Prakash, Sivakumar; Purohit, Gunjan; Vijayashankar, Devi Prasad; Vedagiri, Dhiviya; Tallapaka, Karthik Bharadwaj; Harshan, Krishnan Harinivas; Siva, Archana Bharadwaj; Mishra, Rakesh Kumar; Dhawan, Jyotsna; Siddiqi, Imran title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 journal: bioRxiv DOI: 10.1101/2020.06.08.139477 sha: doc_id: 262485 cord_uid: sx2q5ol4 file: cache/cord-262499-68vmdqky.json key: cord-262499-68vmdqky authors: Bordi, Licia; Sberna, Giuseppe; Lalle, Eleonora; Piselli, Pierluca; Colavita, Francesca; Nicastri, Emanuele; Antinori, Andrea; Boumis, Evangelo; Petrosillo, Nicola; Marchioni, Luisa; Minnucci, Giulia; D’Agostini, Elena; Castilletti, Concetta; Locatelli, Franco; Zumla, Alimuddin; Ippolito, Giuseppe; Capobianchi, Maria Rosaria title: Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay date: 2020-10-20 journal: Viruses DOI: 10.3390/v12101184 sha: doc_id: 262499 cord_uid: 68vmdqky file: cache/cord-262640-4vr4cm1s.json key: cord-262640-4vr4cm1s authors: Nguyen, N. N.; Mutnal, M. B.; Gomez, R. R.; Pham, H. N.; Nguyen, L. T.; Koss, W.; Rao, A.; Arroliga, A. C.; Wang, L.; Wang, D.; Hua, Y.; Powell, P. R.; Chen, L.; McCormack, C.; Linz, W. J.; Mohammad, A. A. title: Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2 date: 2020-07-08 journal: nan DOI: 10.1101/2020.07.06.20145938 sha: doc_id: 262640 cord_uid: 4vr4cm1s file: cache/cord-262760-mf1pn587.json key: cord-262760-mf1pn587 authors: Weber, Stefanie; Ramirez, Christina; Doerfler, Walter title: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date: 2020-09-24 journal: Virus Res DOI: 10.1016/j.virusres.2020.198170 sha: doc_id: 262760 cord_uid: mf1pn587 file: cache/cord-262467-epqqd8n8.json key: cord-262467-epqqd8n8 authors: Chen, Jun; Lu, Hongzhou; Melino, Gerry; Boccia, Stefania; Piacentini, Mauro; Ricciardi, Walter; Wang, Ying; Shi, Yufang; Zhu, Tongyu title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 journal: Cell Death Dis DOI: 10.1038/s41419-020-2603-0 sha: doc_id: 262467 cord_uid: epqqd8n8 file: cache/cord-262276-5nue46dm.json key: cord-262276-5nue46dm authors: Roussel, Yanis; Giraud-Gatineau, Audrey; Jimeno, Marie-Thérèse; Rolain, Jean-Marc; Zandotti, Christine; Colson, Philippe; Raoult, Didier title: SARS-CoV-2: fear versus data date: 2020-03-19 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.105947 sha: doc_id: 262276 cord_uid: 5nue46dm file: cache/cord-262726-lfuxhlki.json key: cord-262726-lfuxhlki authors: Diallo, Aïssatou Bailo; Gay, Laetitia; Coiffard, Benjamin; Leone, Marc; Mezouar, Soraya; Mege, Jean-Louis title: Daytime variation in SARS-CoV-2 infection and cytokine production date: 2020-09-11 journal: bioRxiv DOI: 10.1101/2020.09.09.290718 sha: doc_id: 262726 cord_uid: lfuxhlki file: cache/cord-262783-uhfnv532.json key: cord-262783-uhfnv532 authors: Yamamoto, Fumiichiro; Yamamoto, Miyako; Muñiz‐Diaz, Eduardo title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression date: 2020-09-23 journal: Vox Sang DOI: 10.1111/vox.13004 sha: doc_id: 262783 cord_uid: uhfnv532 file: cache/cord-262550-oip5m9br.json key: cord-262550-oip5m9br authors: Kumar, S. Udhaya; Kumar, D. Thirumal; Christopher, B. Prabhu; Doss, C. George Priya title: The Rise and Impact of COVID-19 in India date: 2020-05-22 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00250 sha: doc_id: 262550 cord_uid: oip5m9br file: cache/cord-262575-06i2nv0t.json key: cord-262575-06i2nv0t authors: Caracciolo, Massimo; Macheda, Sebastiano; Labate, Demetrio; Tescione, Marco; La Scala, Stefano; Vadalà, Eugenio; Squillaci, Rosalba; D’Aleo, Francesco; Morabito, Antonella; Garreffa, Cristina; Marciano, Maria Concetta; Oliva, Esther N. title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome date: 2020-08-25 journal: Front Immunol DOI: 10.3389/fimmu.2020.01942 sha: doc_id: 262575 cord_uid: 06i2nv0t file: cache/cord-262786-otxpc46a.json key: cord-262786-otxpc46a authors: Mohammadi, Soheil; Moosaie, Fatemeh; Aarabi, Mohammad Hadi title: Understanding the Immunologic Characteristics of Neurologic Manifestations of SARS-CoV-2 and Potential Immunological Mechanisms date: 2020-09-01 journal: Mol Neurobiol DOI: 10.1007/s12035-020-02094-y sha: doc_id: 262786 cord_uid: otxpc46a file: cache/cord-262841-nr42rs8f.json key: cord-262841-nr42rs8f authors: Li, Lanjuan; Wo, Jianer; Shao, Junbing; Zhu, Haihong; Wu, Nanping; Li, Minwei; Yao, Hangpin; Hu, Minjun; Dennin, Reinhard H. title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 journal: Journal of Clinical Virology DOI: 10.1016/s1386-6532(03)00195-1 sha: doc_id: 262841 cord_uid: nr42rs8f file: cache/cord-263031-cco2vh0f.json key: cord-263031-cco2vh0f authors: Vultaggio, Alessandra; Agache, Ioana; Akdis, Cezmi A.; Akdis, Mubeccel; Bavbek, Sevim; Bossios, Apostolos; Bousquet, Jean; Boyman, Onur; Chaker, Adam M.; Chan, Susan; Chatzipetrou, Alexia; Feleszko, Wojciech; Firinu, Davide; Jutel, Marek; Kauppi, Paula; Klimek, Ludger; Kolios, Antonios; Kothari, Akash; Kowalski, Marek L.; Matucci, Andrea; Palomares, Oscar; Pfaar, Oliver; Rogala, Barbara; Untersmayr, Eva; Eiwegger, Thomas title: Considerations on Biologicals for Patients with allergic disease in times of the COVID‐19 pandemic: an EAACI Statement date: 2020-06-05 journal: Allergy DOI: 10.1111/all.14407 sha: doc_id: 263031 cord_uid: cco2vh0f file: cache/cord-262766-ndn6iwre.json key: cord-262766-ndn6iwre authors: Easom, Nicholas; Moss, Peter; Barlow, Gavin; Samson, Anda; Taynton, Tom; Adams, Kate; Ivan, Monica; Burns, Phillipa; Gajee, Kavitha; Eastick, Kirstine; Lillie, Patrick title: 68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit date: 2020-03-06 journal: nan DOI: 10.1101/2020.02.29.20029462 sha: doc_id: 262766 cord_uid: ndn6iwre file: cache/cord-262796-syu4wbpi.json key: cord-262796-syu4wbpi authors: Wei, Xiao-Shan; Wang, Xu; Niu, Yi-Ran; Ye, Lin-Lin; Peng, Wen-Bei; Wang, Zi-Hao; Yang, Wei-Bing; Yang, Bo-Han; Zhang, Jian-Chu; Ma, Wan-Li; Wang, Xiao-Rong; Zhou, Qiong title: Diarrhea is associated with prolonged symptoms and viral carriage in COVID-19 date: 2020-04-18 journal: Clin Gastroenterol Hepatol DOI: 10.1016/j.cgh.2020.04.030 sha: doc_id: 262796 cord_uid: syu4wbpi file: cache/cord-262635-fdwd99ah.json key: cord-262635-fdwd99ah authors: Hajra Martínez, Ismael El; Pérez, Lucia Relea; Moya, Marta Calvo title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus date: 2020-08-07 journal: Gastroenterology DOI: 10.1053/j.gastro.2020.05.101 sha: doc_id: 262635 cord_uid: fdwd99ah file: cache/cord-262863-f07v5uk8.json key: cord-262863-f07v5uk8 authors: Bertocchi, Ilaria; Foglietta, Federica; Collotta, Debora; Eva, Carola; Brancaleone, Vincenzo; Thiemermann, Christoph; Collino, Massimo title: The hidden role of NLRP3 inflammasome in obesity‐related COVID‐19 exacerbations: lessons for drug repurposing date: 2020-08-09 journal: Br J Pharmacol DOI: 10.1111/bph.15229 sha: doc_id: 262863 cord_uid: f07v5uk8 file: cache/cord-263292-qjfe2t9v.json key: cord-263292-qjfe2t9v authors: Sansone, A.; Mollaioli, D.; Ciocca, G.; Limoncin, E.; Colonnello, E.; Vena, W.; Jannini, E. A. title: Addressing male sexual and reproductive health in the wake of COVID-19 outbreak date: 2020-07-13 journal: J Endocrinol Invest DOI: 10.1007/s40618-020-01350-1 sha: doc_id: 263292 cord_uid: qjfe2t9v file: cache/cord-262911-e9z00y3b.json key: cord-262911-e9z00y3b authors: Delpino, M. Victoria; Quarleri, Jorge title: SARS-CoV-2 Pathogenesis: Imbalance in the Renin-Angiotensin System Favors Lung Fibrosis date: 2020-06-12 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2020.00340 sha: doc_id: 262911 cord_uid: e9z00y3b file: cache/cord-262936-yo6jf3ng.json key: cord-262936-yo6jf3ng authors: Deng, Jia-gang; Hou, Xiao-tao; Zhang, Tie-jun; Bai, Gang; Hao, Er-wei; Chu, Justin Jang Hann; Wattanathorn, Jintanaporn; Sirisa-ard, Panee; Soo Ee, Ch'ng; Low, John; Liu, Chang-xiao title: Carry forward advantages of traditional medicines in prevention and control of outbreak of COVID-19 pandemic date: 2020-06-02 journal: Chin Herb Med DOI: 10.1016/j.chmed.2020.05.003 sha: doc_id: 262936 cord_uid: yo6jf3ng file: cache/cord-262730-1dxeg8ci.json key: cord-262730-1dxeg8ci authors: Barón-Sánchez, J.; Santiago, C.; Goizueta-San Martín, G.; Arca, R.; Fernández, R. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 journal: nan DOI: 10.1016/j.nrleng.2020.07.007 sha: doc_id: 262730 cord_uid: 1dxeg8ci file: cache/cord-262598-zk192s0x.json key: cord-262598-zk192s0x authors: Tatu, Laurent; Nono, Sandra; Grácio, Simone; Koçer, Serdar title: Guillain–Barré syndrome in the COVID-19 era: another occasional cluster? date: 2020-06-23 journal: J Neurol DOI: 10.1007/s00415-020-10005-3 sha: doc_id: 262598 cord_uid: zk192s0x file: cache/cord-262673-j2ot35lt.json key: cord-262673-j2ot35lt authors: Ahmed-Hassan, Hanaa; Sisson, Brianna; Shukla, Rajni Kant; Wijewantha, Yasasvi; Funderburg, Nicholas T.; Li, Zihai; Hayes, Don; Demberg, Thorsten; Liyanage, Namal P. 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Kaur, Upinder; Banerjee, Anindita; Ganguly, Upasana; Banerjee, Tuhina; Saha, Sarama; Parashar, Gaurav; Prasad, Suvarna; Chakrabarti, Suddhachitta; Mittal, Amit; Agrawal, Bimal Kumar; Rawal, Ravindra Kumar; Zhao, Robert Chunhua; Gambhir, Indrajeet Singh; Khanna, Rahul; Shetty, Ashok K; Jin, Kunlin; Chakrabarti, Sasanka title: COVID-19 in India: Are Biological and Environmental Factors Helping to Stem the Incidence and Severity? date: 2020-05-09 journal: Aging Dis DOI: 10.14336/ad.2020.0402 sha: doc_id: 264266 cord_uid: 6xvj9zey file: cache/cord-264260-8p6pvjkn.json key: cord-264260-8p6pvjkn authors: Peng, Hongbing; Gong, Tiefeng; Huang, Xiaoying; Sun, Xun; Luo, Hong; Wang, Weizhong; Luo, Junbiao; Luo, Baowei; Chen, Yanhui; Wang, Xingxing; Long, Haifeng; Mei, Hua; Li, Chuang; Dai, Yanni; Li, Honghui title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report date: 2020-07-16 journal: Stem Cell Res Ther DOI: 10.1186/s13287-020-01802-8 sha: doc_id: 264260 cord_uid: 8p6pvjkn file: cache/cord-264360-eroqjkoh.json key: cord-264360-eroqjkoh authors: Risku, Minna; Lappalainen, Suvi; Räsänen, Sirpa; Vesikari, Timo title: Detection of human coronaviruses in children with acute gastroenteritis date: 2010-03-15 journal: J Clin Virol DOI: 10.1016/j.jcv.2010.02.013 sha: doc_id: 264360 cord_uid: eroqjkoh file: cache/cord-263803-0n41gylj.json key: cord-263803-0n41gylj authors: Villoutreix, Bruno O.; Beaune, Philippe H.; Tamouza, Ryad; Krishnamoorthy, Rajogapal; Leboyer, Marion title: Prevention of COVID-19 by drug repurposing: rationale from drugs prescribed for mental disorders date: 2020-06-25 journal: Drug Discov Today DOI: 10.1016/j.drudis.2020.06.022 sha: doc_id: 263803 cord_uid: 0n41gylj file: cache/cord-264031-0y7xbgun.json key: cord-264031-0y7xbgun authors: Wierbowski, Shayne D.; Liang, Siqi; Chen, You; Andre, Nicole M.; Lipkin, Steven M.; Whittaker, Gary R.; Yu, Haiyuan title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date: 2020-10-13 journal: bioRxiv DOI: 10.1101/2020.10.13.308676 sha: doc_id: 264031 cord_uid: 0y7xbgun file: cache/cord-264326-teahway7.json key: cord-264326-teahway7 authors: Eleftheriou, Phaedra; Amanatidou, Dionysia; Petrou, Anthi; Geronikaki, Athina title: In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus date: 2020-05-29 journal: Molecules DOI: 10.3390/molecules25112529 sha: doc_id: 264326 cord_uid: teahway7 file: cache/cord-264477-2onwu92a.json key: cord-264477-2onwu92a authors: Brida, Margarita; Chessa, Massimo; Gu, Hong; Gatzoulis, Michael A. title: The globe on the spotlight: Coronavirus disease 2019 (Covid-19) date: 2020-07-01 journal: Int J Cardiol DOI: 10.1016/j.ijcard.2020.04.006 sha: doc_id: 264477 cord_uid: 2onwu92a file: cache/cord-264614-2x7cdul3.json key: cord-264614-2x7cdul3 authors: Díaz-Guio, Diego Andrés; Díaz-Guio, Yimmy; Pinzón-Rodas, Valentina; Díaz-Gomez, Ana Sofía; Guarín-Medina, Jorge Andrés; Chaparro-Zúñiga, Yesid; Ricardo-Zapata, Alejandra; Rodriguez-Morales, Alfonso J. title: COVID-19: Biosafety in the Intensive Care Unit date: 2020-08-27 journal: Curr Trop Med Rep DOI: 10.1007/s40475-020-00208-z sha: doc_id: 264614 cord_uid: 2x7cdul3 file: cache/cord-264261-98h1bmb2.json key: cord-264261-98h1bmb2 authors: Caruana, Giorgia; 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M. B.; Victora, C. G.; Hartwig, F. P.; Silveira, M. F.; Horta, B. L.; Barros, A. J. D.; Whermeister, F. C.; Mesenburg, M. A.; Pellanda, L. C.; Dellagostin, O. A.; Struchiner, C. J.; Burattini, M. N.; Barros, F. C.; Hallal, P. C. title: High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey date: 2020-08-12 journal: nan DOI: 10.1101/2020.08.10.20171942 sha: doc_id: 264709 cord_uid: p835wf4f file: cache/cord-263965-i8yutik6.json key: cord-263965-i8yutik6 authors: Relf, Michael V. title: What's Old is New! Similarities Between SARS-CoV-2 and HIV date: 2020-04-09 journal: J Assoc Nurses AIDS Care DOI: 10.1097/jnc.0000000000000174 sha: doc_id: 263965 cord_uid: i8yutik6 file: cache/cord-264974-hspek930.json key: cord-264974-hspek930 authors: Timmis, Kenneth; Brüssow, Harald title: The COVID‐19 pandemic: some lessons learned about crisis preparedness and management, and the need for international benchmarking to reduce deficits date: 2020-05-03 journal: Environ Microbiol DOI: 10.1111/1462-2920.15029 sha: doc_id: 264974 cord_uid: hspek930 file: cache/cord-264497-7xz97awb.json key: cord-264497-7xz97awb authors: Przedlacki, Jerzy; Wojtaszek, Ewa; Żebrowski, Paweł; Mieczkowski, Mariusz; Głogowski, Tomasz; Pyrża, Michał; Ołdakowska-Jedynak, Urszula title: Patients’ and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic date: 2020-07-27 journal: J Nephrol DOI: 10.1007/s40620-020-00811-3 sha: doc_id: 264497 cord_uid: 7xz97awb file: cache/cord-264828-6w13xo2a.json key: cord-264828-6w13xo2a authors: Albini, Adriana; Di Guardo, Giovanni; Noonan, Douglas McClain; Lombardo, Michele title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies date: 2020-05-19 journal: Intern Emerg Med DOI: 10.1007/s11739-020-02364-6 sha: doc_id: 264828 cord_uid: 6w13xo2a file: cache/cord-265111-d44ireu5.json key: cord-265111-d44ireu5 authors: D’Ardes, Damiano; Pontolillo, Michela; Esposito, Lucia; Masciarelli, Mara; Boccatonda, Andrea; Rossi, Ilaria; Bucci, Marco; Guagnano, Maria Teresa; Ucciferri, Claudio; Santilli, Francesca; Di Nicola, Marta; Falasca, Katia; Vecchiet, Jacopo; Schael, Thomas; Cipollone, Francesco title: Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids date: 2020-08-31 journal: Microorganisms DOI: 10.3390/microorganisms8091327 sha: doc_id: 265111 cord_uid: d44ireu5 file: cache/cord-264915-g5ar0pwb.json key: cord-264915-g5ar0pwb authors: Abrams, Rory M.C.; Kim, Brian D.; Markantone, Desiree M.; Reilly, Kaitlin; Paniz-Mondolfi, Alberto E.; Gitman, Melissa R.; Choo, S. Yoon; Tse, Winona; Robinson-Papp, Jessica title: Severe rapidly progressive Guillain-Barré syndrome in the setting of acute COVID-19 disease date: 2020-07-27 journal: J Neurovirol DOI: 10.1007/s13365-020-00884-7 sha: doc_id: 264915 cord_uid: g5ar0pwb file: cache/cord-264968-ctx39vhi.json key: cord-264968-ctx39vhi authors: Woo, Patrick CY; Lau, Susanna KP; Tsoi, Hoi-wah; Chan, Kwok-hung; Wong, Beatrice HL; Che, Xiao-yan; Tam, Victoria KP; Tam, Sidney CF; Cheng, Vincent CC; Hung, Ivan FN; Wong, Samson SY; Zheng, Bo-jian; Guan, Yi; Yuen, Kwok-yung title: Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia date: 2004-03-13 journal: Lancet DOI: 10.1016/s0140-6736(04)15729-2 sha: doc_id: 264968 cord_uid: ctx39vhi file: cache/cord-265191-unk6rt7u.json key: cord-265191-unk6rt7u authors: Durrani, Muhammad; Kucharski, Kevin; Smith, Zachary; Fien, Stephanie title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report date: 2020-06-22 journal: Clin Pract Cases Emerg Med DOI: 10.5811/cpcem.2020.6.48462 sha: doc_id: 265191 cord_uid: unk6rt7u file: cache/cord-264148-qpcvxwti.json key: cord-264148-qpcvxwti authors: He, Feng; Deng, Yu; Li, Weina title: Coronavirus disease 2019: What we know? date: 2020-03-28 journal: J Med Virol DOI: 10.1002/jmv.25766 sha: doc_id: 264148 cord_uid: qpcvxwti file: cache/cord-264970-232stxxo.json key: cord-264970-232stxxo authors: Testa, Sophie; Paoletti, Oriana; Giorgi-Pierfranceschi, Matteo; Pan, Angelo title: Switch from oral anticoagulants to parenteral heparin in SARS-CoV-2 hospitalized patients date: 2020-04-15 journal: Intern Emerg Med DOI: 10.1007/s11739-020-02331-1 sha: doc_id: 264970 cord_uid: 232stxxo file: cache/cord-264421-799n9wqj.json key: cord-264421-799n9wqj authors: Novelli, Antonio; Biancolella, Michela; Borgiani, Paola; Cocciadiferro, Dario; Colona, Vito Luigi; D’Apice, Maria Rosaria; Rogliani, Paola; Zaffina, Salvatore; Leonardis, Francesca; Campana, Andrea; Raponi, Massimiliano; Andreoni, Massimo; Grelli, Sandro; Novelli, Giuseppe title: Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients date: 2020-09-11 journal: Hum Genomics DOI: 10.1186/s40246-020-00279-z sha: doc_id: 264421 cord_uid: 799n9wqj file: cache/cord-264976-6n9cdex6.json key: cord-264976-6n9cdex6 authors: Corse, Tanner; Dayan, Linda; Kersten, Sydney; Battaglia, Fortunato; Terlecky, Stanley R; Han, Zhiyong title: Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date: 2020-10-18 journal: Int J Med Sci DOI: 10.7150/ijms.50537 sha: doc_id: 264976 cord_uid: 6n9cdex6 file: cache/cord-264772-v3a2qmj5.json key: cord-264772-v3a2qmj5 authors: Harada, Kouji H.; Harada Sassa, Mariko; Yamamoto, Naomichi title: Letter to the Editor on “An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)”, Back to Basics date: 2020-06-18 journal: Environ Sci Technol DOI: 10.1021/acs.est.0c02850 sha: doc_id: 264772 cord_uid: v3a2qmj5 file: cache/cord-265128-i0d4lxko.json key: cord-265128-i0d4lxko authors: Gurung, Arun Bahadur; Ali, Mohammad Ajmal; Lee, Joongku; Farah, Mohammad Abul; Al-Anazi, Khalid Mashay title: Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M(pro) enzyme through in silico approach date: 2020-05-22 journal: Life Sci DOI: 10.1016/j.lfs.2020.117831 sha: doc_id: 265128 cord_uid: i0d4lxko file: cache/cord-265329-bsypo08l.json key: cord-265329-bsypo08l authors: van Dorp, Lucy; 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Koirala, Archana; Macartney, Kristine; Russell, Fiona; Teh, Benjamin W.; Wen, Sophie CH title: Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date: 2020-10-02 journal: Front Immunol DOI: 10.3389/fimmu.2020.579250 sha: doc_id: 264814 cord_uid: v4wnmg03 file: cache/cord-265170-yv04ijsm.json key: cord-265170-yv04ijsm authors: Ceccarelli, Giancarlo; Scagnolari, Carolina; Pugliese, Francesco; Mastroianni, Claudio M; d'Ettorre, Gabriella title: Probiotics and COVID-19 date: 2020-07-13 journal: Lancet Gastroenterol Hepatol DOI: 10.1016/s2468-1253(20)30196-5 sha: doc_id: 265170 cord_uid: yv04ijsm file: cache/cord-265221-qtkwciym.json key: cord-265221-qtkwciym authors: Bahadur, Gulam; Acharya, Santanu; Muneer, Asif; Huirne, Judith; Łukaszuk, Mariusz; Doreski, Pablo Alexis; Homburg, Roy title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 journal: Reprod Biomed Online DOI: 10.1016/j.rbmo.2020.05.014 sha: doc_id: 265221 cord_uid: qtkwciym file: cache/cord-265262-r01u4jr6.json key: cord-265262-r01u4jr6 authors: Cannarella, Rossella; 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Ovsyannikova, Inna G.; Kennedy, Richard B.; Poland, Gregory A. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 journal: bioRxiv DOI: 10.1101/2020.05.14.093757 sha: doc_id: 265277 cord_uid: ymvrserl file: cache/cord-265617-e91s6xo8.json key: cord-265617-e91s6xo8 authors: Jouali, Farah; Marchoudi, Nabila; El Ansari, Fatima Zahra; Kasmi, Yassine; Chenaoui, Mohamed; El Aliani, Aissam; Azami, Nawfel; Loukman, Salma; Ennaji, Moulay Mustapha; Benhida, Rachid; Fekkak, Jamal title: SARS-CoV-2 Genome Sequence from Morocco, Obtained Using Ion AmpliSeq Technology date: 2020-07-30 journal: Microbiol Resour Announc DOI: 10.1128/mra.00690-20 sha: doc_id: 265617 cord_uid: e91s6xo8 file: cache/cord-265022-p5cab562.json key: cord-265022-p5cab562 authors: Kotfis, Katarzyna; Williams Roberson, Shawniqua; Wilson, Jo Ellen; Dabrowski, Wojciech; Pun, Brenda T.; Ely, E. Wesley title: COVID-19: ICU delirium management during SARS-CoV-2 pandemic date: 2020-04-28 journal: Crit Care DOI: 10.1186/s13054-020-02882-x sha: doc_id: 265022 cord_uid: p5cab562 file: cache/cord-265278-wf5pbvvt.json key: cord-265278-wf5pbvvt authors: Fishman, Jay A.; Roberts, Matthew B.; Zhang, Eric W.; Kumar, Deepali; Hirsch, Hans H.; Maggiore, Umberto title: Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation date: 2020-09-17 journal: N Engl J Med DOI: 10.1056/nejmcpc2004982 sha: doc_id: 265278 cord_uid: wf5pbvvt file: cache/cord-265682-yac7kzaf.json key: cord-265682-yac7kzaf authors: Eden, John-Sebastian; Rockett, Rebecca; Carter, Ian; Rahman, Hossinur; de Ligt, Joep; Hadfield, James; Storey, Matthew; Ren, Xiaoyun; Tulloch, Rachel; Basile, Kerri; Wells, Jessica; Byun, Roy; Gilroy, Nicky; O’Sullivan, Matthew V; Sintchenko, Vitali; Chen, Sharon C; Maddocks, Susan; Sorrell, Tania C; Holmes, Edward C; Dwyer, Dominic E; Kok, Jen title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-04-10 journal: Virus Evol DOI: 10.1093/ve/veaa027 sha: doc_id: 265682 cord_uid: yac7kzaf file: cache/cord-265260-n6wm54wz.json key: cord-265260-n6wm54wz authors: Cuong, Hoang Quoc; Hai, Nguyen Duc; Linh, Hoang Thuy; Anh, Nguyen Hoang; Hieu, Nguyen Trung; Thang, Cao Minh; Thao, Nguyen Thi Thanh; Lan, Phan Trong title: Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-09-25 journal: Biomed Res Int DOI: 10.1155/2020/7610678 sha: doc_id: 265260 cord_uid: n6wm54wz file: cache/cord-265595-55s19mr1.json key: cord-265595-55s19mr1 authors: Brug, Johannes; Aro, Arja R.; Richardus, Jan Hendrik title: Risk Perceptions and Behaviour: Towards Pandemic Control of Emerging Infectious Diseases: International Research on Risk Perception in the Control of Emerging Infectious Diseases date: 2009-01-06 journal: Int J Behav Med DOI: 10.1007/s12529-008-9000-x sha: doc_id: 265595 cord_uid: 55s19mr1 file: cache/cord-265599-903w782b.json key: cord-265599-903w782b authors: Woods, R.; Walsh, M.; Nwaokorie, K.; Crowley, J.; Lacy, P.; de Barra, E. title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection date: 2020-10-21 journal: nan DOI: 10.1101/2020.10.19.20213140 sha: doc_id: 265599 cord_uid: 903w782b file: cache/cord-265242-y8t37p0b.json key: cord-265242-y8t37p0b authors: Cui, Wei; Fan, Ying; Wu, Wei; Zhang, Feng; Wang, Jun-ying; Ni, An-ping title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date: 2003-09-15 journal: Clin Infect Dis DOI: 10.1086/378587 sha: doc_id: 265242 cord_uid: y8t37p0b file: cache/cord-265473-ju81kiyw.json key: cord-265473-ju81kiyw authors: Balmeh, Negar; Mahmoudi, Samira; Mohammadi, Niloofar; Karabedianhajiabadi, Anasik title: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date: 2020-08-07 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100407 sha: doc_id: 265473 cord_uid: ju81kiyw file: cache/cord-265418-yqe9vdj1.json key: cord-265418-yqe9vdj1 authors: Kumar, Nilesh; Mishra, Bharat; Mehmood, Adeel; Athar, Mohammad; Mukhtar, M. Shahid title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date: 2020-04-11 journal: bioRxiv DOI: 10.1101/2020.04.09.033910 sha: doc_id: 265418 cord_uid: yqe9vdj1 file: cache/cord-265598-4h3wx81q.json key: cord-265598-4h3wx81q authors: Hasan, Abdulkarim; Nafie, Khalid; Abbadi, Osama title: Histopathology Laboratory Paperwork as a Potential Risk of COVID-19 Transmission among the Lab Personnel date: 2020-08-06 journal: nan DOI: 10.1016/j.infpip.2020.100081 sha: doc_id: 265598 cord_uid: 4h3wx81q file: cache/cord-265723-6k8196p2.json key: cord-265723-6k8196p2 authors: Yu, Chengjun; Kang, Lian; Chen, Jiadong; Zang, Na title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis date: 2020-06-25 journal: Int Immunopharmacol DOI: 10.1016/j.intimp.2020.106740 sha: doc_id: 265723 cord_uid: 6k8196p2 file: cache/cord-265366-vmuqbpkk.json key: cord-265366-vmuqbpkk authors: Leibowitz, Jill; Krief, William; Barone, Stephen; Williamson, Kristy A.; Goenka, Pratichi K.; Rai, Shipra; Moriarty, Shannon; Baodhankar, Prachi; Rubin, Lorry G. title: Comparison of Clinical and Epidemiologic Characteristics of Young Febrile Infants with and without SARS-CoV-2 Infection date: 2020-10-09 journal: J Pediatr DOI: 10.1016/j.jpeds.2020.10.002 sha: doc_id: 265366 cord_uid: vmuqbpkk file: cache/cord-265155-jbvrcjx8.json key: cord-265155-jbvrcjx8 authors: Aroniadis, Olga C.; DiMaio, Christopher J.; Dixon, Rebekah E.; Elmunzer, B. Joseph; Kolb, Jennifer M.; Mendelsohn, Robin; Singal, Amit G.; Ordiah, Collins O.; Rockey, Don C.; Spitzer, Rebecca L.; Tierney, William M.; Wani, Sachin; Yadav, Dhiraj title: Current Knowledge and Research Priorities in the Digestive Manifestations of COVID-19 date: 2020-04-22 journal: Clin Gastroenterol Hepatol DOI: 10.1016/j.cgh.2020.04.039 sha: doc_id: 265155 cord_uid: jbvrcjx8 file: cache/cord-265740-wjdeps3h.json key: cord-265740-wjdeps3h authors: Radbel, Jared; Jagpal, Sugeet; Roy, Jason; Brooks, Andrew; Tischfield, Jay; Sheldon, Michael; Bixby, Christian; Witt, Dana; Gennaro, Maria Laura; Horton, Daniel B.; Barrett, Emily S.; Carson, Jeffrey L.; Panettieri, Reynold A.; Blaser, Martin J. title: Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media date: 2020-05-13 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2020.04.209 sha: doc_id: 265740 cord_uid: wjdeps3h file: cache/cord-265697-bbvlowyo.json key: cord-265697-bbvlowyo authors: Sang, Eric R.; Tian, Yun; Gong, Yuanying; Miller, Laura C.; Sang, Yongming title: Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date: 2020-08-31 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e04818 sha: doc_id: 265697 cord_uid: bbvlowyo file: cache/cord-265353-xwpdq8wo.json key: cord-265353-xwpdq8wo authors: Ramzy, Danny title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. date: 2020-09-15 journal: JTCVS Tech DOI: 10.1016/j.xjtc.2020.09.012 sha: doc_id: 265353 cord_uid: xwpdq8wo file: cache/cord-265724-fdt00qw1.json key: cord-265724-fdt00qw1 authors: Varadarajan, Saranya; Madapusi Balaji, Thodur; Sarode, Sachin C.; Sarode, Gargi S.; Sharma, Nilesh K.; Gondivkar, Shailesh; Gadbail, Amol; Patil, Shankargouda title: EMMPRIN/BASIGIN as a biological modulator of oral cancer and COVID-19 interaction: novel propositions date: 2020-07-09 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110089 sha: doc_id: 265724 cord_uid: fdt00qw1 file: cache/cord-265887-g5zhoyo9.json key: cord-265887-g5zhoyo9 authors: Mukherjee, Shruti; Bhattacharyya, Dipita; Bhunia, Anirban title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 journal: Biophys Chem DOI: 10.1016/j.bpc.2020.106452 sha: doc_id: 265887 cord_uid: g5zhoyo9 file: cache/cord-265228-afbkp3wm.json key: cord-265228-afbkp3wm authors: Fomsgaard, Anna S.; Rosenstierne, Maiken Worsøe title: An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020 date: 2020-04-09 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.14.2000398 sha: doc_id: 265228 cord_uid: afbkp3wm file: cache/cord-265877-dund6unq.json key: cord-265877-dund6unq authors: Yang, Q.; Yang, X. title: Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis date: 2020-06-03 journal: nan DOI: 10.1101/2020.05.28.20116400 sha: doc_id: 265877 cord_uid: dund6unq file: cache/cord-266016-555e3ndo.json key: cord-266016-555e3ndo authors: Hildenwall, Helena; Luthander, Joachim; Rhedin, Samuel; Hertting, Olof; Olsson‐Åkefeldt, Selma; Melén, Erik; Alfvén, Tobias; Herlenius, Eric; Ryd Rinder, Malin title: Paediatric COVID‐19 admissions in a region with open schools during the two first months of the pandemic date: 2020-06-21 journal: Acta Paediatr DOI: 10.1111/apa.15432 sha: doc_id: 266016 cord_uid: 555e3ndo file: cache/cord-265813-2onv9mvl.json key: cord-265813-2onv9mvl authors: Criado, Paulo Ricardo; Abdalla, Beatrice Martinez Zugaib; de Assis, Isabelle Carvalho; van Blarcum de Graaff Mello, Cristina; Caputo, Gabriela Cacciolari; Vieira, Ingrid Campos title: Are the cutaneous manifestations during or due to SARS-CoV-2 infection/COVID-19 frequent or not? Revision of possible pathophysiologic mechanisms date: 2020-06-02 journal: Inflamm Res DOI: 10.1007/s00011-020-01370-w sha: doc_id: 265813 cord_uid: 2onv9mvl file: cache/cord-266033-gbx48scp.json key: cord-266033-gbx48scp authors: Xu, Yu-Huan; Dong, Jing-Hui; An, Wei-Min; Lv, Xiao-Yan; Yin, Xiao-Ping; Zhang, Jian-Zeng; Dong, Li; Ma, Xi; Zhang, Hong-Jie; Gao, Bu-Lang title: Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 date: 2020-02-25 journal: J Infect DOI: 10.1016/j.jinf.2020.02.017 sha: doc_id: 266033 cord_uid: gbx48scp file: cache/cord-265899-skpkuzyu.json key: cord-265899-skpkuzyu authors: Pryzdial, Edward L. G.; Sutherland, Michael R.; Lin, Bryan H.; Horwitz, Marc title: Antiviral anticoagulation date: 2020-07-06 journal: Res Pract Thromb Haemost DOI: 10.1002/rth2.12406 sha: doc_id: 265899 cord_uid: skpkuzyu file: cache/cord-266150-wox7pnkr.json key: cord-266150-wox7pnkr authors: Torres, Juan Pablo; Piñera, Cecilia; De La Maza, Verónica; Lagomarcino, Anne J; Simian, Daniela; Torres, Bárbara; Urquidi, Cinthya; Valenzuela, María Teresa; O’Ryan, Miguel title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa955 sha: doc_id: 266150 cord_uid: wox7pnkr file: cache/cord-266348-tbr2ynx0.json key: cord-266348-tbr2ynx0 authors: Stroemer, A.; Grobe, O.; Rose, R.; Fickenscher, H.; Lorentz, T.; Krumbholz, A. title: Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera date: 2020-06-17 journal: nan DOI: 10.1101/2020.06.15.20131672 sha: doc_id: 266348 cord_uid: tbr2ynx0 file: cache/cord-265529-0n9xxa9h.json key: cord-265529-0n9xxa9h authors: John Hann, Angus; Lembach, Hanns; McKay, Siobhan C.; Perrin, Moira; Isaac, John; Oo, Ye H.; Mutimer, David; Mirza, Darius F.; Hartog, Hermien; Perera, Thamara title: Controversies regarding shielding and susceptibility to COVID‐19 disease in liver transplant recipients in the United Kingdom date: 2020-06-17 journal: Transpl Infect Dis DOI: 10.1111/tid.13352 sha: doc_id: 265529 cord_uid: 0n9xxa9h file: cache/cord-266036-qhlo99l7.json key: cord-266036-qhlo99l7 authors: Axell-House, Dierdre B.; Lavingia, Richa; Rafferty, Megan; Clark, Eva; Amirian, E. Susan; Chiao, Elizabeth Y. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 journal: J Infect DOI: 10.1016/j.jinf.2020.08.043 sha: doc_id: 266036 cord_uid: qhlo99l7 file: cache/cord-266090-f40v4039.json key: cord-266090-f40v4039 authors: Gao, Wei; Baskonus, Haci Mehmet; Shi, Li title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system date: 2020-08-03 journal: Adv Differ Equ DOI: 10.1186/s13662-020-02831-6 sha: doc_id: 266090 cord_uid: f40v4039 file: cache/cord-266175-4jyltfus.json key: cord-266175-4jyltfus authors: Brendish, Nathan J; Poole, Stephen; Naidu, Vasanth V; Mansbridge, Christopher T; Norton, Nicholas J; Wheeler, Helen; Presland, Laura; Kidd, Stephen; Cortes, Nicholas J; Borca, Florina; Phan, Hang; Babbage, Gavin; Visseaux, Benoit; Ewings, Sean; Clark, Tristan W title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30454-9 sha: doc_id: 266175 cord_uid: 4jyltfus file: cache/cord-266113-3fp46sov.json key: cord-266113-3fp46sov authors: Dashti‐Khavidaki, Simin; Khalili, Hossein title: Considerations for Statin Therapy in Patients with COVID‐19 date: 2020-05-04 journal: Pharmacotherapy DOI: 10.1002/phar.2397 sha: doc_id: 266113 cord_uid: 3fp46sov file: cache/cord-266135-jbc9nml0.json key: cord-266135-jbc9nml0 authors: Princiotta Cariddi, Lucia; Tabaee Damavandi, Payam; Carimati, Federico; Banfi, Paola; Clemenzi, Alessandro; Marelli, Margherita; Giorgianni, Andrea; Vinacci, Gabriele; Mauri, Marco; Versino, Maurizio title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient date: 2020-06-24 journal: J Neurol DOI: 10.1007/s00415-020-10001-7 sha: doc_id: 266135 cord_uid: jbc9nml0 file: cache/cord-265233-v5sq5epy.json key: cord-265233-v5sq5epy authors: Cassorla, Lydia title: Decontamination and Reuse of N95 Filtering Facepiece Respirators: Where Do We Stand? date: 2020-10-15 journal: Anesth Analg DOI: 10.1213/ane.0000000000005254 sha: doc_id: 265233 cord_uid: v5sq5epy file: cache/cord-266324-uvsmbrbf.json key: cord-266324-uvsmbrbf authors: Zhang, Hu; Liao, Yu-Sheng; Gong, Jing; Liu, Jing; Xia, Xi; Zhang, Heng title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases date: 2020-05-08 journal: Dig Liver Dis DOI: 10.1016/j.dld.2020.04.034 sha: doc_id: 266324 cord_uid: uvsmbrbf file: cache/cord-266450-g9vihgbk.json key: cord-266450-g9vihgbk authors: Tran, Michael; Sheth, Chirag; Bhandari, Rohan; Cameron, Scott J.; Hornacek, Deborah title: SARS-CoV-2 and pulmonary embolism: who stole the platelets? date: 2020-09-03 journal: Thromb J DOI: 10.1186/s12959-020-00229-8 sha: doc_id: 266450 cord_uid: g9vihgbk file: cache/cord-266350-yybunc6z.json key: cord-266350-yybunc6z authors: Sinha, Saurabh K.; Shakya, Anshul; Prasad, Satyendra K.; Singh, Shashikant; Gurav, Nilambari S.; Prasad, Rupali S.; Gurav, Shailendra S. title: An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets date: 2020-05-13 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1762741 sha: doc_id: 266350 cord_uid: yybunc6z file: cache/cord-266022-aco5kpaj.json key: cord-266022-aco5kpaj authors: Matusiak, Magdalena; Schürch, Christian M. title: Expression of SARS-CoV-2 entry receptors in the respiratory tract of healthy individuals, smokers and asthmatics date: 2020-09-29 journal: Respir Res DOI: 10.1186/s12931-020-01521-x sha: doc_id: 266022 cord_uid: aco5kpaj file: cache/cord-266104-xqvwht7c.json key: cord-266104-xqvwht7c authors: Mu, Chenglin; Sheng, Yifan; Wang, Qian; Amin, Amr; Li, Xugang; Xie, Yingqiu title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology date: 2020-08-14 journal: Journal of functional foods DOI: 10.1016/j.jff.2020.104149 sha: doc_id: 266104 cord_uid: xqvwht7c file: cache/cord-266313-b518n9dx.json key: cord-266313-b518n9dx authors: Cao, Yu-chen; Deng, Qi-xin; Dai, Shi-xue title: Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence date: 2020-04-02 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101647 sha: doc_id: 266313 cord_uid: b518n9dx file: cache/cord-266156-xmf4emln.json key: cord-266156-xmf4emln authors: Miller, Tyler E.; Garcia Beltran, Wilfredo F.; Bard, Adam Z.; Gogakos, Tasos; Anahtar, Melis N.; Astudillo, Michael Gerino; Yang, Diane; Thierauf, Julia; Fisch, Adam S.; Mahowald, Grace K.; Fitzpatrick, Megan J.; Nardi, Valentina; Feldman, Jared; Hauser, Blake M.; Caradonna, Timothy M.; Marble, Hetal D.; Ritterhouse, Lauren L.; Turbett, Sara E.; Batten, Julie; Georgantas, Nicholas Zeke; Alter, Galit; Schmidt, Aaron G.; Harris, Jason B.; Gelfand, Jeffrey A.; Poznansky, Mark C.; Bernstein, Bradley E.; Louis, David N.; Dighe, Anand; Charles, Richelle C.; Ryan, Edward T.; Branda, John A.; Pierce, Virginia M.; Murali, Mandakolathur R.; Iafrate, A. John; Rosenberg, Eric S.; Lennerz, Jochen K. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 journal: FASEB J DOI: 10.1096/fj.202001700rr sha: doc_id: 266156 cord_uid: xmf4emln file: cache/cord-266168-hxu5u5op.json key: cord-266168-hxu5u5op authors: Grimaud, Emilie; Challiol, Marie; Guilbaud, Camille; Delestrain, Céline; Madhi, Fouad; Ngo, Julien; Epaud, Ralph; Nattes, Elodie title: Delayed acute bronchiolitis in infants hospitalized for COVID‐19 date: 2020-07-10 journal: Pediatr Pulmonol DOI: 10.1002/ppul.24946 sha: doc_id: 266168 cord_uid: hxu5u5op file: cache/cord-266480-u8o4eitu.json key: cord-266480-u8o4eitu authors: Colubri, Andrés; Kemball, Molly; Sani, Kian; Boehm, Chloe; Mutch-Jones, Karen; Fry, Ben; Brown, Todd; Sabeti, Pardis C. title: Preventing outbreaks through interactive, experiential real-life simulations date: 2020-09-02 journal: Cell DOI: 10.1016/j.cell.2020.08.042 sha: doc_id: 266480 cord_uid: u8o4eitu file: cache/cord-266307-w56rii2p.json key: cord-266307-w56rii2p authors: Acheampong, Desmond Omane; Barffour, Isaac Kyei; Boye, Alex; Aninagyei, Enoch; Ocansey, Stephen; Morna, Martin Tangnaa title: Male Predisposition to Severe COVID-19: Review of Evidence and Potential Therapeutic Prospects date: 2020-09-09 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110748 sha: doc_id: 266307 cord_uid: w56rii2p file: cache/cord-266648-962r0vm8.json key: cord-266648-962r0vm8 authors: Grossberg, Laurie B; Pellish, Randall S; Cheifetz, Adam S; Feuerstein, Joseph D title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date: 2020-07-03 journal: Inflamm Bowel Dis DOI: 10.1093/ibd/izaa174 sha: doc_id: 266648 cord_uid: 962r0vm8 file: cache/cord-266558-vd41u2t1.json key: cord-266558-vd41u2t1 authors: Verdecchia, Paolo; Cavallini, Claudio; Spanevello, Antonio; Angeli, Fabio title: The pivotal link between ACE2 deficiency and SARS-CoV-2 infection date: 2020-04-20 journal: Eur J Intern Med DOI: 10.1016/j.ejim.2020.04.037 sha: doc_id: 266558 cord_uid: vd41u2t1 file: cache/cord-266512-xh6zed03.json key: cord-266512-xh6zed03 authors: Scala, Enrico; Abeni, Damiano; Tedeschi, Alberto; Manzotti, Giuseppina; Yang, Baoran; Borrelli, Paolo; Marra, Alessandro; Giani, Mauro; Sgadari, Antonio; Saltalamacchia, Francesca; Asero, Riccardo title: Atopic statusprotects from severe complications of COVID‐19 date: 2020-08-16 journal: Allergy DOI: 10.1111/all.14551 sha: doc_id: 266512 cord_uid: xh6zed03 file: cache/cord-266511-g5h4tazp.json key: cord-266511-g5h4tazp authors: Deslandes, A; Berti, V; Tandjaoui-Lambotte, Y; Alloui, Chakib; Carbonnelle, E; Zahar, JR; Brichler, S; Cohen, Yves title: SARS-COV-2 was already spreading in France in late December 2019 date: 2020-05-03 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.106006 sha: doc_id: 266511 cord_uid: g5h4tazp file: cache/cord-265855-zf52vl11.json key: cord-265855-zf52vl11 authors: Mayor-Ibarguren, Ander; Busca-Arenzana, Carmen; Robles-Marhuenda, Ángel title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01736 sha: doc_id: 265855 cord_uid: zf52vl11 file: cache/cord-266616-boeb1xcp.json key: cord-266616-boeb1xcp authors: Liu, Yu; Qi, Guangying; Bellanti, Joseph A.; Moser, René; Ryffel, Bernhard; Zheng, Song Guo title: Regulatory T cells: A potential weapon to combat COVID‐19? date: 2020-08-06 journal: MedComm (Beijing) DOI: 10.1002/mco2.12 sha: doc_id: 266616 cord_uid: boeb1xcp file: cache/cord-266034-811lov8f.json key: cord-266034-811lov8f authors: Benameur, Karima; Agarwal, Ankita; Auld, Sara C.; Butters, Matthew P.; Webster, Andrew S.; Ozturk, Tugba; Howell, J. Christina; Bassit, Leda C.; Velasquez, Alvaro; Schinazi, Raymond F.; Mullins, Mark E.; Hu, William T. title: Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020 date: 2020-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid2609.202122 sha: doc_id: 266034 cord_uid: 811lov8f file: cache/cord-266308-fjpq1ljp.json key: cord-266308-fjpq1ljp authors: Mondal, Priya; Natesh, Jagadish; Abdul Salam, Abdul Ajees; Thiyagarajan, Saravanamuthu; Meeran, Syed Musthapa title: Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation date: 2020-11-05 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1842246 sha: doc_id: 266308 cord_uid: fjpq1ljp file: cache/cord-266444-rw94yls8.json key: cord-266444-rw94yls8 authors: Dominguez Andres, Ana; Feng, Yongmei; Campos, Alexandre Rosa; Yin, Jun; Yang, Chih-Cheng; James, Brian; Murad, Rabi; Kim, Hyungsoo; Deshpande, Aniruddha J.; Gordon, David E.; Krogan, Nevan; Pippa, Raffaella; Ronai, Ze’ev A. title: SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date: 2020-08-19 journal: bioRxiv DOI: 10.1101/2020.08.18.256776 sha: doc_id: 266444 cord_uid: rw94yls8 file: cache/cord-266775-4npowkkz.json key: cord-266775-4npowkkz authors: Xu, Jun; Zhong, Shuqing; Liu, Jinghua; Li, Li; Li, Yong; Wu, Xinwei; Li, Zhijie; Deng, Peng; Zhang, Jingqiang; Zhong, Nanshan; Ding, Yanqing; Jiang, Yong title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 journal: Clin Infect Dis DOI: 10.1086/444461 sha: doc_id: 266775 cord_uid: 4npowkkz file: cache/cord-266052-rcuzi70u.json key: cord-266052-rcuzi70u authors: Liu, Lilong; Hu, Junyi; Hou, Yaxin; Tao, Zhen; Chen, Zhaohui; Chen, Ke title: Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19 date: 2020-10-29 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.143283 sha: doc_id: 266052 cord_uid: rcuzi70u file: cache/cord-266885-a5fdeuvv.json key: cord-266885-a5fdeuvv authors: Dlotko, P.; Rudkin, S. title: Covid-19 clinical data analysis using Ball Mapper date: 2020-04-15 journal: nan DOI: 10.1101/2020.04.10.20061374 sha: doc_id: 266885 cord_uid: a5fdeuvv file: cache/cord-266031-tlrsco40.json key: cord-266031-tlrsco40 authors: Haghani, Milad; Bliemer, Michiel C. J. title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCoV literature date: 2020-09-21 journal: Scientometrics DOI: 10.1007/s11192-020-03706-z sha: doc_id: 266031 cord_uid: tlrsco40 file: cache/cord-266695-ktbgm0p9.json key: cord-266695-ktbgm0p9 authors: Dawson, Liza; Earl, Jake; Livezey, Jeffrey title: SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date: 2020-06-04 journal: J Infect Dis DOI: 10.1093/infdis/jiaa314 sha: doc_id: 266695 cord_uid: ktbgm0p9 file: cache/cord-266696-w9sb038q.json key: cord-266696-w9sb038q authors: Zhou, Yi-Hua; Chen, Zhaochun title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date: 2004-03-15 journal: Clin Infect Dis DOI: 10.1086/382081 sha: doc_id: 266696 cord_uid: w9sb038q file: cache/cord-266536-4frv2vb7.json key: cord-266536-4frv2vb7 authors: Martel, Jan; Ko, Yun-Fei; Young, John D.; Ojcius, David M. title: Could nitric oxide help to prevent or treat COVID-19? date: 2020-05-06 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.05.002 sha: doc_id: 266536 cord_uid: 4frv2vb7 file: cache/cord-266755-y2lf7ssp.json key: cord-266755-y2lf7ssp authors: Yehualashet, Awgichew Shewasinad; Belachew, Teshome Fentik title: ACEIs and ARBs and Their Correlation with COVID-19: A Review date: 2020-09-16 journal: Infect Drug Resist DOI: 10.2147/idr.s264882 sha: doc_id: 266755 cord_uid: y2lf7ssp file: cache/cord-266930-a1mzxmsb.json key: cord-266930-a1mzxmsb authors: Rigatti, S. J.; Stout, R. title: SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population date: 2020-09-11 journal: nan DOI: 10.1101/2020.09.09.20191296 sha: doc_id: 266930 cord_uid: a1mzxmsb file: cache/cord-266948-n7sltd1b.json key: cord-266948-n7sltd1b authors: Ahamed, Jasimuddin title: Severe aortic stenosis patient risk during the COVID-19 pandemic date: 2020-09-14 journal: Open Heart DOI: 10.1136/openhrt-2020-001355 sha: doc_id: 266948 cord_uid: n7sltd1b file: cache/cord-266820-exl36jt3.json key: cord-266820-exl36jt3 authors: Rivera, Frida; Safdar, Nasia; Ledeboer, Nathan; Schaack, Grace; Chen, Derrick J; Munoz-Price, L Silvia title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1225 sha: doc_id: 266820 cord_uid: exl36jt3 file: cache/cord-266888-ryvk6mte.json key: cord-266888-ryvk6mte authors: Cai, Guoshuai; Bossé, Yohan; Xiao, Feifei; Kheradmand, Farrah; Amos, Christopher I. title: Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2 date: 2020-06-15 journal: Am J Respir Crit Care Med DOI: 10.1164/rccm.202003-0693le sha: doc_id: 266888 cord_uid: ryvk6mte file: cache/cord-266903-lxtxqdst.json key: cord-266903-lxtxqdst authors: Lee, Jong-Hwan; Choi, Minsuk; Jung, Yujin; Lee, Sung Kyun; Lee, Chang-Seop; Kim, Jung; Kim, Jongwoo; Kim, Nam Hoon; Kim, Bum-Tae; Kim, Hong Gi title: A novel rapid detection for SARS-CoV-2 spike 1 antigens using human angiotensin converting enzyme 2 (ACE2) date: 2020-10-15 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112715 sha: doc_id: 266903 cord_uid: lxtxqdst file: cache/cord-266914-3eatplc2.json key: cord-266914-3eatplc2 authors: Wang, Yongjin; Shi, Huiling; Rigolet, Pascal; Wu, Nannan; Zhu, Lichen; Xi, Xu-Guang; Vabret, Astrid; Wang, Xiaoming; Wang, Tianhou title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date: 2010-06-02 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2010.05.014 sha: doc_id: 266914 cord_uid: 3eatplc2 file: cache/cord-267013-nbwrl4g3.json key: cord-267013-nbwrl4g3 authors: Ruan, R; Zorzano-Martinez, M; Campos, A; Rius, F; Hernández, M title: Subacute Thyroiditis might be a complication triggered by SARS-CoV-2 date: 2020-10-13 journal: Endocrinol Diabetes Nutr DOI: 10.1016/j.endinu.2020.09.002 sha: doc_id: 267013 cord_uid: nbwrl4g3 file: cache/cord-266866-z98x80zj.json key: cord-266866-z98x80zj authors: Sohpal, Vipan Kumar title: Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA date: 2020-09-24 journal: Genomics Inform DOI: 10.5808/gi.2020.18.3.e30 sha: doc_id: 266866 cord_uid: z98x80zj file: cache/cord-266896-unb9yvjr.json key: cord-266896-unb9yvjr authors: Nihei, Yoshihito; Nagasawa, Hajime; Fukao, Yusuke; Kihara, Masao; Ueda, Seiji; Gohda, Tomohito; Suzuki, Yusuke title: Continuous extracorporeal treatments in a dialysis patient with COVID-19 date: 2020-10-04 journal: CEN Case Rep DOI: 10.1007/s13730-020-00538-x sha: doc_id: 266896 cord_uid: unb9yvjr file: cache/cord-266564-imj1lcy9.json key: cord-266564-imj1lcy9 authors: Liu, Yangli; Chen, Haihong; Tang, Kejing; Guo, Yubiao title: Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy date: 2020-03-05 journal: J Infect DOI: 10.1016/j.jinf.2020.02.028 sha: doc_id: 266564 cord_uid: imj1lcy9 file: cache/cord-266996-knwpkyg6.json key: cord-266996-knwpkyg6 authors: Kipkorir, Vincent; Cheruiyot, Isaac; Ngure, Brian; Misiani, Musa; Munguti, Jeremiah title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test date: 2020-05-13 journal: J Med Virol DOI: 10.1002/jmv.26007 sha: doc_id: 266996 cord_uid: knwpkyg6 file: cache/cord-266710-3wdy16tw.json key: cord-266710-3wdy16tw authors: Fintelman-Rodrigues, Natalia; Sacramento, Carolina Q.; Ribeiro Lima, Carlyle; Souza da Silva, Franklin; Ferreira, André C.; Mattos, Mayara; de Freitas, Caroline S.; Cardoso Soares, Vinicius; da Silva Gomes Dias, Suelen; Temerozo, Jairo R.; Miranda, Milene D.; Matos, Aline R.; Bozza, Fernando A.; Carels, Nicolas; Alves, Carlos Roberto; Siqueira, Marilda M.; Bozza, Patrícia T.; Souza, Thiago Moreno L. title: Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production date: 2020-09-21 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.00825-20 sha: doc_id: 266710 cord_uid: 3wdy16tw file: cache/cord-266869-fs8dn7ir.json key: cord-266869-fs8dn7ir authors: Kim, So Young; Jin, Weihua; Sood, Amika; Montgomery, David W.; Grant, Oliver C.; Fuster, Mark M.; Fu, Li; Dordick, Jonathan S.; Woods, Robert J.; Zhang, Fuming; Linhardt, Robert J. title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date: 2020-04-15 journal: bioRxiv DOI: 10.1101/2020.04.14.041459 sha: doc_id: 266869 cord_uid: fs8dn7ir file: cache/cord-266988-72uvawth.json key: cord-266988-72uvawth authors: Barth, Rolf F.; Buja, L. Maximillian; Parwani, Anil V. title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 date: 2020-07-14 journal: Diagn Pathol DOI: 10.1186/s13000-020-00999-9 sha: doc_id: 266988 cord_uid: 72uvawth file: cache/cord-267115-6jqdi417.json key: cord-267115-6jqdi417 authors: Giobbe, Giovanni Giuseppe; Bonfante, Francesco; Zambaiti, Elisa; Gagliano, Onelia; Jones, Brendan C.; Luni, Camilla; Laterza, Cecilia; Perin, Silvia; Stuart, Hannah T.; Pagliari, Matteo; Bortolami, Alessio; Mazzetto, Eva; Manfredi, Anna; Colantuono, Chiara; Di Filippo, Lucio; Pellegata, Alessandro; Li, Vivian Sze Wing; Eaton, Simon; Thapar, Nikhil; Cacchiarelli, Davide; Elvassore, Nicola; De Coppi, Paolo title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 journal: bioRxiv DOI: 10.1101/2020.06.24.167049 sha: doc_id: 267115 cord_uid: 6jqdi417 file: cache/cord-266702-6oxtlzqo.json key: cord-266702-6oxtlzqo authors: Cristelo, Cecília; Azevedo, Cláudia; Moreira Marques, Joana; Nunes, Rute; Sarmento, Bruno title: SARS-CoV-2 and Diabetes: New Challenges for the Disease date: 2020-05-22 journal: Diabetes Res Clin Pract DOI: 10.1016/j.diabres.2020.108228 sha: doc_id: 266702 cord_uid: 6oxtlzqo file: cache/cord-266923-hd1tjj6b.json key: cord-266923-hd1tjj6b authors: Padroni, Marina; Mastrangelo, Vincenzo; Asioli, Gian Maria; Pavolucci, Lucia; Abu-Rumeileh, Samir; Piscaglia, Maria Grazia; Querzani, Pietro; Callegarini, Claudio; Foschi, Matteo title: Guillain-Barré syndrome following COVID-19: new infection, old complication? date: 2020-04-24 journal: J Neurol DOI: 10.1007/s00415-020-09849-6 sha: doc_id: 266923 cord_uid: hd1tjj6b file: cache/cord-266983-hpwebkbi.json key: cord-266983-hpwebkbi authors: Mallhi, Tauqeer Hussain; Khan, Yusra Habib; Butt, Muhammad Hammad; Liaqat, Aroosa; Abid, Arooj; Ahmad, Abrar; Misbah, Shahzadi title: Risks of Zoonotic Transmission of COVID-19 During Eid-Ul-Adha in Pakistan date: 2020-07-27 journal: Disaster medicine and public health preparedness DOI: 10.1017/dmp.2020.278 sha: doc_id: 266983 cord_uid: hpwebkbi file: cache/cord-266987-ikt8r2o1.json key: cord-266987-ikt8r2o1 authors: Loeffelholz, Michael J.; Tang, Yi-Wei title: Laboratory diagnosis of emerging human coronavirus infections – the state of the art date: 2020-03-30 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1745095 sha: doc_id: 266987 cord_uid: ikt8r2o1 file: cache/cord-267134-5gz2dotn.json key: cord-267134-5gz2dotn authors: Sallenave, Jean-Michel; Guillot, Loïc title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.01229 sha: doc_id: 267134 cord_uid: 5gz2dotn file: cache/cord-267261-8z4aqfff.json key: cord-267261-8z4aqfff authors: Su, John R. title: Emerging viral infections date: 2005-03-01 journal: Clin Lab Med DOI: 10.1016/j.cll.2004.05.002 sha: doc_id: 267261 cord_uid: 8z4aqfff file: cache/cord-267308-rgqjolue.json key: cord-267308-rgqjolue authors: Crovetto, F.; Crispi, F.; Llurba, E.; Figueras, F.; Gomez-Roig, M. D.; Gratacos, E. title: SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY date: 2020-06-19 journal: nan DOI: 10.1101/2020.06.17.20134098 sha: doc_id: 267308 cord_uid: rgqjolue file: cache/cord-267246-hq7g62p5.json key: cord-267246-hq7g62p5 authors: Huang, Su-Hua; Lee, Tzu-Ying; Lin, Ying-Ju; Wan, Lei; Lai, Chih-Ho; Lin, Cheng-Wen title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism date: 2015-07-31 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2015.07.002 sha: doc_id: 267246 cord_uid: hq7g62p5 file: cache/cord-267307-kyh0xsrp.json key: cord-267307-kyh0xsrp authors: Kasting, Monica L.; Head, Katharine J.; Hartsock, Jane A.; Sturm, Lynne; Zimet, Gregory D. title: Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date: 2020-11-04 journal: PLoS One DOI: 10.1371/journal.pone.0241662 sha: doc_id: 267307 cord_uid: kyh0xsrp file: cache/cord-267388-jz5mm91w.json key: cord-267388-jz5mm91w authors: Cheung, Szeya; Fuentes, Alain Delgado; Fetterman, Alan D. title: Recurrent Acute Pancreatitis in a Patient with COVID-19 Infection date: 2020-08-24 journal: Am J Case Rep DOI: 10.12659/ajcr.927076 sha: doc_id: 267388 cord_uid: jz5mm91w file: cache/cord-267476-j59tm40d.json key: cord-267476-j59tm40d authors: Yong, Sarah Ee Fang; Anderson, Danielle Elizabeth; Wei, Wycliffe E; Pang, Junxiong; Chia, Wan Ni; Tan, Chee Wah; Teoh, Yee Leong; Rajendram, Priyanka; Toh, Matthias Paul Han Sim; Poh, Cuiqin; Koh, Valerie T J; Lum, Joshua; Suhaimi, Nur-Afidah Md; Chia, Po Ying; Chen, Mark I-Cheng; Vasoo, Shawn; Ong, Benjamin; Leo, Yee Sin; Wang, Linfa; Lee, Vernon J M title: Connecting clusters of COVID-19: an epidemiological and serological investigation date: 2020-04-21 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30273-5 sha: doc_id: 267476 cord_uid: j59tm40d file: cache/cord-267373-nzxbogga.json key: cord-267373-nzxbogga authors: Antinori, Spinello; Cossu, Maria Vittoria; Ridolfo, Anna Lisa; Rech, Roberto; Bonazzetti, Cecilia; Pagani, Gabriele; Gubertini, Guido; Coen, Massimo; Magni, Carlo; Castelli, Antonio; Borghi, Beatrice; Colombo, Riccardo; Giorgi, Riccardo; Angeli, Elena; Mileto, Davide; Milazzo, Laura; Vimercati, Stefania; Pellicciotta, Martina; Corbellino, Mario; Torre, Alessandro; Rusconi, Stefano; Oreni, Letizia; Gismondo, Maria Rita; Giacomelli, Andrea; Meroni, Luca; Rizzardini, Giuliano; Galli, Massimo title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status date: 2020-05-11 journal: Pharmacol Res DOI: 10.1016/j.phrs.2020.104899 sha: doc_id: 267373 cord_uid: nzxbogga file: cache/cord-267124-8efdzlc0.json key: cord-267124-8efdzlc0 authors: Wichmann, Dominic; Sperhake, Jan-Peter; Lütgehetmann, Marc; Steurer, Stefan; Edler, Carolin; Heinemann, Axel; Heinrich, Fabian; Mushumba, Herbert; Kniep, Inga; Schröder, Ann Sophie; Burdelski, Christoph; de Heer, Geraldine; Nierhaus, Axel; Frings, Daniel; Pfefferle, Susanne; Becker, Heinrich; Bredereke-Wiedling, Hanns; de Weerth, Andreas; Paschen, Hans-Richard; Sheikhzadeh-Eggers, Sara; Stang, Axel; Schmiedel, Stefan; Bokemeyer, Carsten; Addo, Marylyn M.; Aepfelbacher, Martin; Püschel, Klaus; Kluge, Stefan title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 journal: Ann Intern Med DOI: 10.7326/m20-2003 sha: doc_id: 267124 cord_uid: 8efdzlc0 file: cache/cord-267397-b7ogeokm.json key: cord-267397-b7ogeokm authors: Smith, E. R.; He, S.; Oakley, E. M.; Miller, L.; Tielsch, J. 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Asad; Araf, Yusha; Rahman, Mohammad Shahedur title: Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach date: 2020-11-11 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100478 sha: doc_id: 267666 cord_uid: i7uuf3ck file: cache/cord-267588-ruuzr6l1.json key: cord-267588-ruuzr6l1 authors: Garnett, Lauren; Bello, Alexander; Tran, Kaylie N.; Audet, Jonathan; Leung, Anders; Schiffman, Zachary; Griffin, Bryan D.; Tailor, Nikesh; Kobasa, Darwyn; Strong, James E. title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113947 sha: doc_id: 267588 cord_uid: ruuzr6l1 file: cache/cord-267511-tb69dwg8.json key: cord-267511-tb69dwg8 authors: Talebian, Sepehr; Conde, João title: Why Go NANO on COVID-19 Pandemic? date: 2020-09-02 journal: Matter DOI: 10.1016/j.matt.2020.08.005 sha: doc_id: 267511 cord_uid: tb69dwg8 file: cache/cord-267610-bzbr9ios.json key: cord-267610-bzbr9ios authors: Anastassopoulou, Cleo; Spanakis, Nicholas; Tsakris, Athanasios title: SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall date: 2020-09-03 journal: Future microbiology DOI: 10.2217/fmb-2020-0195 sha: doc_id: 267610 cord_uid: bzbr9ios file: cache/cord-267831-uu883ofc.json key: cord-267831-uu883ofc authors: Kang, Yuan-Lin; Chou, Yi-Ying; Rothlauf, Paul W.; Liu, Zhuoming; Soh, Timothy K.; Cureton, David; Case, James Brett; Chen, Rita E.; Diamond, Michael S.; Whelan, Sean P. J.; Kirchhausen, Tom title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 journal: bioRxiv DOI: 10.1101/2020.04.21.053058 sha: doc_id: 267831 cord_uid: uu883ofc file: cache/cord-267845-18hb5ndr.json key: cord-267845-18hb5ndr authors: Resende, Paola Cristina; Motta, Fernando Couto; Roy, Sunando; Appolinario, Luciana; Fabri, Allison; Xavier, Joilson; Harris, Kathryn; Matos, Aline Rocha; Caetano, Braulia; Orgeswalska, Maria; Miranda, Milene; Garcia, Cristiana; Abreu, André; Williams, Rachel; Breuer, Judith; Siqueira, Marilda M title: SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date: 2020-05-01 journal: bioRxiv DOI: 10.1101/2020.04.30.069039 sha: doc_id: 267845 cord_uid: 18hb5ndr file: cache/cord-267762-mzon01fd.json key: cord-267762-mzon01fd authors: Ferreira, A.; Oliveira-e-Silva, A.; Bettencourt, P. title: Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection. date: 2020-06-29 journal: nan DOI: 10.1101/2020.06.26.20056507 sha: doc_id: 267762 cord_uid: mzon01fd file: cache/cord-267533-nmgtan4e.json key: cord-267533-nmgtan4e authors: Hu, Zhigang; Li, Sijia; Yang, Ailan; Li, Wenxin; Xiong, Xiaoqi; Hu, Jianwu; Jiang, Jun; Song, Xinyu title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04085-2 sha: doc_id: 267533 cord_uid: nmgtan4e file: cache/cord-267566-gdjl0qmu.json key: cord-267566-gdjl0qmu authors: Kweon, Oh Joo; Lim, Yong Kwan; Kim, Hye Ryoun; Kim, Min-Chul; Choi, Seong-Ho; Chung, Jin-Won; Lee, Mi-Kyung title: Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date: 2020-10-22 journal: PLoS One DOI: 10.1371/journal.pone.0240395 sha: doc_id: 267566 cord_uid: gdjl0qmu file: cache/cord-267723-loj718vd.json key: cord-267723-loj718vd authors: Kloc, Małgorzata; Ghobrial, Rafik M.; Lewicki, Sławomir; Kubiak, Jacek Z. title: Macrophages in diabetes mellitus (DM) and COVID-19: do they trigger DM? date: 2020-10-17 journal: J Diabetes Metab Disord DOI: 10.1007/s40200-020-00665-3 sha: doc_id: 267723 cord_uid: loj718vd file: cache/cord-267770-ik1ib3zb.json key: cord-267770-ik1ib3zb authors: Koo, Hyun Jung; Choi, Sang-Ho; Sung, Heungsup; Choe, Jooae; Do, Kyung-Hyun title: RadioGraphics Update: Radiographic and CT Features of Viral Pneumonia date: 2020-06-05 journal: Radiographics DOI: 10.1148/rg.2020200097 sha: doc_id: 267770 cord_uid: ik1ib3zb file: cache/cord-267856-t3ksa18w.json key: cord-267856-t3ksa18w authors: Funk, Colin D.; Ardakani, Ali title: A Novel Strategy to Mitigate the Hyperinflammatory Response to COVID-19 by Targeting Leukotrienes date: 2020-08-06 journal: Front Pharmacol DOI: 10.3389/fphar.2020.01214 sha: doc_id: 267856 cord_uid: t3ksa18w file: cache/cord-267887-ntwvquqz.json key: cord-267887-ntwvquqz authors: Yang, Ren; Huang, Baoying; Ruhan, A.; Li, Wenhui; Wang, Wenling; Deng, Yao; Tan, Wenjie title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro date: 2020-08-21 journal: Biosaf Health DOI: 10.1016/j.bsheal.2020.08.004 sha: doc_id: 267887 cord_uid: ntwvquqz file: cache/cord-267482-afqfymbq.json key: cord-267482-afqfymbq authors: Ryu, Seungjin; Shchukina, Irina; Youm, Yun-Hee; Qing, Hua; Hilliard, Brandon K.; Dlugos, Tamara; Zhang, Xinbo; Yasumoto, Yuki; Booth, Carmen J.; Fernández-Hernando, Carlos; Suárez, Yajaira; Khanna, Kamal M.; Horvath, Tamas L.; Dietrich, Marcelo O.; Artyomov, Maxim N.; Wang, Andrew; Dixit, Vishwa Deep title: Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date: 2020-09-12 journal: bioRxiv DOI: 10.1101/2020.09.11.294363 sha: doc_id: 267482 cord_uid: afqfymbq file: cache/cord-267509-w7nfbnbb.json key: cord-267509-w7nfbnbb authors: Tian, Yuan; Rong, Long; Nian, Weidong; He, Yan title: Review article: gastrointestinal features in COVID‐19 and the possibility of faecal transmission date: 2020-03-31 journal: Aliment Pharmacol Ther DOI: 10.1111/apt.15731 sha: doc_id: 267509 cord_uid: w7nfbnbb file: cache/cord-267690-g0kesgjm.json key: cord-267690-g0kesgjm authors: Mueller, Sarina K.; Traxdorf, Maximilian; Mantsopoulos, Konstantinos; Gostian, Antoniu-Oreste; Sievert, Matti; Koch, Michael; Huebner, Matthias J.; Iro, Heinrich title: Considerations for Continuing Semielective and Emergency Otolaryngological Procedures During the COVID-19 Pandemic date: 2020-09-07 journal: Ear Nose Throat J DOI: 10.1177/0145561320952506 sha: doc_id: 267690 cord_uid: g0kesgjm file: cache/cord-268075-kbislbx0.json key: cord-268075-kbislbx0 authors: Song, Limin; Zhao, Shuai; Wang, Li; Yang, Kai; Xiao, Weimin; Clifford, Sean P.; Huang, Jiapeng; Chen, Xiangdong title: Cardiovascular Changes in Patients With COVID-19 From Wuhan, China date: 2020-09-02 journal: Front Cardiovasc Med DOI: 10.3389/fcvm.2020.00150 sha: doc_id: 268075 cord_uid: kbislbx0 file: cache/cord-267735-y3832u9e.json key: cord-267735-y3832u9e authors: Sun, Wuping; Gao, Hong; Luo, Yuhui; Zheng, Hushan; Liao, Xiang; Xiong, Donglin; Xiao, Lizu title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date: 2020-09-24 journal: Front Microbiol DOI: 10.3389/fmicb.2020.572318 sha: doc_id: 267735 cord_uid: y3832u9e file: cache/cord-267613-hsc2x36j.json key: cord-267613-hsc2x36j authors: Dittmar, Mark; Lee, Jae Seung; Whig, Kanupriya; Segrist, Elisha; Li, Minghua; Jurado, Kellie; Samby, Kirandeep; Ramage, Holly; Schultz, David; Cherry, Sara title: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date: 2020-06-19 journal: bioRxiv DOI: 10.1101/2020.06.19.161042 sha: doc_id: 267613 cord_uid: hsc2x36j file: cache/cord-267815-4fw7xgnt.json key: cord-267815-4fw7xgnt authors: Peña, Juan A.; Bianco, Angela T.; Simpson, Lynn L.; Bernstein, Peter S.; Roman, Ashley S.; Goffman, Dena; Schweizer, William E.; Overbey, Jessica; Stone, Joanne L. title: A Survey of Labor and Delivery Practices in New York City during the COVID-19 Pandemic date: 2020-06-09 journal: Am J Perinatol DOI: 10.1055/s-0040-1713120 sha: doc_id: 267815 cord_uid: 4fw7xgnt file: cache/cord-267917-belkwihy.json key: cord-267917-belkwihy authors: Peters, Alexandra; Parneix, Pierre; Otter, Jon; Pittet, Didier title: Putting some context to the aerosolization debate around SARS-CoV-2 date: 2020-04-30 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.04.040 sha: doc_id: 267917 cord_uid: belkwihy file: cache/cord-268034-7id7sfsu.json key: cord-268034-7id7sfsu authors: Auerswald, Heidi; Yann, Sokhoun; Dul, Sokha; In, Saraden; Dussart, Philippe; Martin, Nicholas J.; Karlsson, Erik A.; Garcia-Rivera, Jose A. title: Assessment of Inactivation Procedures for SARS-CoV-2 date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.28.120444 sha: doc_id: 268034 cord_uid: 7id7sfsu file: cache/cord-267971-xgwmda8e.json key: cord-267971-xgwmda8e authors: Tan, Shing Cheng title: Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients date: 2020-04-07 journal: nan DOI: 10.1101/2020.04.02.20050989 sha: doc_id: 267971 cord_uid: xgwmda8e file: cache/cord-267782-4pjfnund.json key: cord-267782-4pjfnund authors: Lan, Fan-Yun; Suharlim, Christian; Kales, Stefanos N; Yang, Justin title: Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA date: 2020-10-30 journal: Occup Environ Med DOI: 10.1136/oemed-2020-106774 sha: doc_id: 267782 cord_uid: 4pjfnund file: cache/cord-268140-s5lailkp.json key: cord-268140-s5lailkp authors: Atal, Shubham; Fatima, Zeenat title: IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising Therapy? date: 2020-06-13 journal: Pharmaceut Med DOI: 10.1007/s40290-020-00342-z sha: doc_id: 268140 cord_uid: s5lailkp file: cache/cord-268065-mxvbbkc4.json key: cord-268065-mxvbbkc4 authors: Wei, Maoti; Yang, Ning; Wang, Fenghua; Zhao, Guoping; Gao, Hongwei; Li, Yuming title: Epidemiology of Coronavirus Disease 2019 (COVID-19) Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-18 journal: Disaster medicine and public health preparedness DOI: 10.1017/dmp.2020.155 sha: doc_id: 268065 cord_uid: mxvbbkc4 file: cache/cord-268169-xry3nhzt.json key: cord-268169-xry3nhzt authors: Couturier, Aymeric; Ferlicot, Sophie; Chevalier, Kévin; Guillet, Matthieu; Essig, Marie; Jauréguiberry, Stéphane; Collarino, Rocco; Dargelos, Mathilde; Michaut, Alice; Geri, Guillaume; Roque-Afonso, Anne-Marie; Zaidan, Mohamad; Massy, Ziad A title: Indirect effects of severe acute respiratory syndrome coronavirus 2 on the kidney in coronavirus disease patients date: 2020-05-22 journal: Clin Kidney J DOI: 10.1093/ckj/sfaa088 sha: doc_id: 268169 cord_uid: xry3nhzt file: cache/cord-268329-apl6n6jl.json key: cord-268329-apl6n6jl authors: Antunes, Douglas Eulálio; Goulart, Isabela Maria Bernardes; Goulart, Luiz Ricardo title: Will cases of leprosy reaction increase with COVID-19 infection? date: 2020-07-17 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0008460 sha: doc_id: 268329 cord_uid: apl6n6jl file: cache/cord-267960-r5m7o9dp.json key: cord-267960-r5m7o9dp authors: Hourdel, Véronique; Kwasiborski, Aurelia; Balière, Charlotte; Matheus, Séverine; Batéjat, Christophe Frédéric; Manuguerra, Jean-Claude; Vanhomwegen, Jessica; Caro, Valérie title: Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date: 2020-09-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.571328 sha: doc_id: 267960 cord_uid: r5m7o9dp file: cache/cord-268211-egy8rgtl.json key: cord-268211-egy8rgtl authors: Barrasa, Helena; Rello, Jordi; Tejada, Sofia; Martín, Alejandro; Balziskueta, Goiatz; Vinuesa, Cristina; Fernández-Miret, Borja; Villagra, Ana; Vallejo, Ana; Sebastián, Ana San; Cabañes, Sara; Iribarren, Sebastián; Fonseca, Fernando; Maynar, Javier title: SARS-Cov-2 in Spanish Intensive Care: Early Experience with 15-day Survival In Vitoria date: 2020-04-09 journal: Anaesth Crit Care Pain Med DOI: 10.1016/j.accpm.2020.04.001 sha: doc_id: 268211 cord_uid: egy8rgtl file: cache/cord-268049-7xqln70d.json key: cord-268049-7xqln70d authors: Montrief, Tim; Ramzy, Mark; Long, Brit; Gottlieb, Michael; Hercz, Dan title: COVID-19 respiratory support in the emergency department setting date: 2020-08-08 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.08.001 sha: doc_id: 268049 cord_uid: 7xqln70d file: cache/cord-268074-9mact9br.json key: cord-268074-9mact9br authors: Bi, Qifang; Wu, Yongsheng; Mei, Shujiang; Ye, Chenfei; Zou, Xuan; Zhang, Zhen; Liu, Xiaojian; Wei, Lan; Truelove, Shaun A; Zhang, Tong; Gao, Wei; Cheng, Cong; Tang, Xiujuan; Wu, Xiaoliang; Wu, Yu; Sun, Binbin; Huang, Suli; Sun, Yu; Zhang, Juncen; Ma, Ting; Lessler, Justin; Feng, Tiejian title: Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study date: 2020-04-27 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30287-5 sha: doc_id: 268074 cord_uid: 9mact9br file: cache/cord-268340-xwj8ge5t.json key: cord-268340-xwj8ge5t authors: Ozaki, Masayuki; Yasuda, Yuma; Jingushi, Naruhiro; Goto, Yukari; Numaguchi, Atsushi title: Reducing Aerosol Generation During Ventilator Weaning in a Coronavirus Disease 2019 Patient Using a Supraglottic Airway: A Case Report date: 2020-05-21 journal: A A Pract DOI: 10.1213/xaa.0000000000001247 sha: doc_id: 268340 cord_uid: xwj8ge5t file: cache/cord-268324-86a0n0dc.json key: cord-268324-86a0n0dc authors: Charitos, Ioannis A; Ballini, Andrea; Bottalico, Lucrezia; Cantore, Stefania; Passarelli, Pier Carmine; Inchingolo, Francesco; D'Addona, Antonio; Santacroce, Luigi title: Special features of SARS-CoV-2 in daily practice date: 2020-09-26 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i18.3920 sha: doc_id: 268324 cord_uid: 86a0n0dc file: cache/cord-268098-71g1w1mc.json key: cord-268098-71g1w1mc authors: Beckman, M. F.; Igba, C. K.; Mougeot, F. B.; Mougeot, J.-L. title: Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date: 2020-09-15 journal: nan DOI: 10.1101/2020.09.14.20192609 sha: doc_id: 268098 cord_uid: 71g1w1mc file: cache/cord-268071-ow2aijmj.json key: cord-268071-ow2aijmj authors: Pachetti, Maria; Marini, Bruna; Benedetti, Francesca; Giudici, Fabiola; Mauro, Elisabetta; Storici, Paola; Masciovecchio, Claudio; Angeletti, Silvia; Ciccozzi, Massimo; Gallo, Robert C.; Zella, Davide; Ippodrino, Rudy title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 journal: J Transl Med DOI: 10.1186/s12967-020-02344-6 sha: doc_id: 268071 cord_uid: ow2aijmj file: cache/cord-268085-vpzrk8u7.json key: cord-268085-vpzrk8u7 authors: Mandal, Amrendra; Konala, Venu Madhav; Adapa, Sreedhar; Naramala, Srikanth; Gayam, Vijay title: Gastrointestinal Manifestations in COVID-19 Infection and Its Practical Applications date: 2020-06-21 journal: Cureus DOI: 10.7759/cureus.8750 sha: doc_id: 268085 cord_uid: vpzrk8u7 file: cache/cord-268193-xwptzgvl.json key: cord-268193-xwptzgvl authors: Wang, Tzong-Luen; 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Mansuy, Jean-Michel; Charpentier, Sandrine; Claudet, Isabelle; Izopet, Jacques title: Children are protected against SARS-CoV-2 infection date: 2020-05-20 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104451 sha: doc_id: 268335 cord_uid: mfcjldu3 file: cache/cord-268468-036i1082.json key: cord-268468-036i1082 authors: Asif, Muhammad; Ajmal, Muhammad; Ashraf, Ghazala; Muhammad, Nadeem; Aziz, Ayesha; Iftikhar, Tayyaba; Wang, Junlei; Liu, Hongfang title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 journal: Curr Opin Electrochem DOI: 10.1016/j.coelec.2020.08.011 sha: doc_id: 268468 cord_uid: 036i1082 file: cache/cord-268406-3v309r41.json key: cord-268406-3v309r41 authors: Grajewski, Rafael S.; Rokohl, Alexander C.; Becker, Martina; Dewald, Felix; Lehmann, Clara; Fätkenheuer, Gerd; Cursiefen, Claus; Klein, Florian; Heindl, Ludwig M. title: A missing link between SARS‐CoV‐2 and the eye?: ACE2 expression on the ocular surface date: 2020-06-12 journal: J Med Virol DOI: 10.1002/jmv.26136 sha: doc_id: 268406 cord_uid: 3v309r41 file: cache/cord-268339-jxm69ndw.json key: cord-268339-jxm69ndw authors: Karamitros, Timokratis; 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Ganguly, Dipyaman; Chattopadhyay, Samit title: Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past date: 2020-08-07 journal: Front Immunol DOI: 10.3389/fimmu.2020.01949 sha: doc_id: 268483 cord_uid: joiajgs4 file: cache/cord-268206-ino9srb6.json key: cord-268206-ino9srb6 authors: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 journal: Bull Natl Res Cent DOI: 10.1186/s42269-020-00341-9 sha: doc_id: 268206 cord_uid: ino9srb6 file: cache/cord-268453-87b298uk.json key: cord-268453-87b298uk authors: Ibáñez, Sebastián; Martínez, Oriela; Valenzuela, Francisca; Silva, Francisco; Valenzuela, Omar title: Hydroxychloroquine and chloroquine in COVID-19: should they be used as standard therapy? date: 2020-06-03 journal: Clin Rheumatol DOI: 10.1007/s10067-020-05202-4 sha: doc_id: 268453 cord_uid: 87b298uk file: cache/cord-268330-mo5myrz4.json key: cord-268330-mo5myrz4 authors: Gentile, Pietro; Sterodimas, Aris title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia date: 2020-04-29 journal: Expert Opin Biol Ther DOI: 10.1080/14712598.2020.1761322 sha: doc_id: 268330 cord_uid: mo5myrz4 file: cache/cord-268501-z4oztgi0.json key: cord-268501-z4oztgi0 authors: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 journal: Front Immunol DOI: 10.3389/fimmu.2020.02173 sha: doc_id: 268501 cord_uid: z4oztgi0 file: cache/cord-268561-vq1uhj5i.json key: cord-268561-vq1uhj5i authors: da Silva, Severino Jefferson Ribeiro; Silva, Caroline Targino Alves da; Guarines, Klarissa Miranda; Mendes, Renata Pessôa Germano; Pardee, Keith; Kohl, Alain; Pena, Lindomar title: Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19 date: 2020-08-04 journal: ACS Infect Dis DOI: 10.1021/acsinfecdis.0c00274 sha: doc_id: 268561 cord_uid: vq1uhj5i file: cache/cord-268661-a56u5e2o.json key: cord-268661-a56u5e2o authors: Nadeau, S. A.; Vaughan, T. G.; Scire, J.; Huisman, J. S.; Stadler, T. title: The origin and early spread of SARS-CoV-2 in Europe date: 2020-06-12 journal: nan DOI: 10.1101/2020.06.10.20127738 sha: doc_id: 268661 cord_uid: a56u5e2o file: cache/cord-268476-3lxsh1zz.json key: cord-268476-3lxsh1zz authors: Skoog, Hunter; Withrow, Kirk; Jeyarajan, Harishanker; Greene, Benjamin; Batra, Hitesh; Cox, Daniel; Pierce, Albert; Grayson, Jessica W.; Carroll, William R. title: Tracheotomy in the SARS‐CoV‐2 pandemic date: 2020-04-29 journal: Head Neck DOI: 10.1002/hed.26214 sha: doc_id: 268476 cord_uid: 3lxsh1zz file: cache/cord-268653-mje0rysp.json key: cord-268653-mje0rysp authors: Chen, Miaomiao; Zeng, Jing; Liu, Xiyao; Sun, Guoqiang; Gao, Ying; Liao, Jiujiang; Yu, Jiaxiao; Luo, Xin; Qi, Hongbo title: Changes in physiology and immune system during pregnancy and coronavirus infection: a review date: 2020-10-16 journal: Eur J Obstet Gynecol Reprod Biol DOI: 10.1016/j.ejogrb.2020.10.035 sha: doc_id: 268653 cord_uid: mje0rysp file: cache/cord-268760-31i0mpvn.json key: cord-268760-31i0mpvn authors: Zhang, Qian; Shan, Khine S; Abdollahi, Shahrzad; Nace, Travis title: Anosmia and Ageusia as the Only Indicators of Coronavirus Disease 2019 (COVID-19) date: 2020-05-01 journal: Cureus DOI: 10.7759/cureus.7918 sha: doc_id: 268760 cord_uid: 31i0mpvn file: cache/cord-268370-kfjujs4z.json key: cord-268370-kfjujs4z authors: Huang, Yu-Tung; Lee, Yue-Chune; Hsiao, Chun-Ju title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study date: 2009-05-31 journal: Journal of the Formosan Medical Association DOI: 10.1016/s0929-6646(09)60082-6 sha: doc_id: 268370 cord_uid: kfjujs4z file: cache/cord-268572-uhak283t.json key: cord-268572-uhak283t authors: Woo, Marcel S.; Steins, David; Häußler, Vivien; Kohsar, Matin; Haag, Friedrich; Elias-Hamp, Birte; Heesen, Christoph; Lütgehetmann, Marc; Schulze zur Wiesch, Julian; Friese, Manuel A. title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients date: 2020-07-11 journal: J Neurol DOI: 10.1007/s00415-020-10046-8 sha: doc_id: 268572 cord_uid: uhak283t file: cache/cord-268894-amfv3z2y.json key: cord-268894-amfv3z2y authors: Nguyen-Contant, Phuong; Embong, A. Karim; Kanagaiah, Preshetha; Chaves, Francisco A.; Yang, Hongmei; Branche, Angela R.; Topham, David J.; Sangster, Mark Y. title: S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date: 2020-07-21 journal: bioRxiv DOI: 10.1101/2020.07.20.213298 sha: doc_id: 268894 cord_uid: amfv3z2y file: cache/cord-268540-wrjzr3ws.json key: cord-268540-wrjzr3ws authors: Park, You Jeong; Farooq, Jeffrey; Cho, Justin; Sadanandan, Nadia; Cozene, Blaise; Gonzales-Portillo, Bella; Saft, Madeline; Borlongan, Maximillian C.; Borlongan, Mia C.; Shytle, R. Douglas; Willing, Alison E.; Garbuzova-Davis, Svitlana; Sanberg, Paul R.; Borlongan, Cesar V. title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 journal: Stem Cell Rev Rep DOI: 10.1007/s12015-020-10026-5 sha: doc_id: 268540 cord_uid: wrjzr3ws file: cache/cord-268484-hf4zflsy.json key: cord-268484-hf4zflsy authors: Davanzo, Riccardo title: Breast feeding at the time of COVID-19: do not forget expressed mother’s milk, please date: 2020-04-06 journal: Arch Dis Child Fetal Neonatal Ed DOI: 10.1136/archdischild-2020-319149 sha: doc_id: 268484 cord_uid: hf4zflsy file: cache/cord-268740-ldz5366v.json key: cord-268740-ldz5366v authors: Sun, Mei; Guo, Dong; Zhang, Jing; Zhang, Jian; Teng, Hai-Feng; Xia, Jun; Liu, Peng; Ge, Quan-Xu; Wang, Ming-Yi title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients date: 2020-08-14 journal: Future microbiology DOI: 10.2217/fmb-2020-0090 sha: doc_id: 268740 cord_uid: ldz5366v file: cache/cord-268750-kox3uah2.json key: cord-268750-kox3uah2 authors: Wong, S. F.; Chow, K. M.; Shek, C. C.; Leung, Y. P.; Chiu, A.; Lam, P. W. Y.; Ho, L. C. title: Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures date: 2004-01-08 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-003-1068-2 sha: doc_id: 268750 cord_uid: kox3uah2 file: cache/cord-268645-5op2m7pu.json key: cord-268645-5op2m7pu authors: Wu, Zhiqiang; Yang, Li; Ren, Xianwen; He, Guimei; Zhang, Junpeng; Yang, Jian; Qian, Zhaohui; Dong, Jie; Sun, Lilian; Zhu, Yafang; Du, Jiang; Yang, Fan; Zhang, Shuyi; Jin, Qi title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 journal: The ISME Journal DOI: 10.1038/ismej.2015.138 sha: doc_id: 268645 cord_uid: 5op2m7pu file: cache/cord-268755-13xmmin1.json key: cord-268755-13xmmin1 authors: Meltzer, Martin I. title: Multiple Contact Dates and SARS Incubation Periods date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030426 sha: doc_id: 268755 cord_uid: 13xmmin1 file: cache/cord-268970-uz7q6z2f.json key: cord-268970-uz7q6z2f authors: Ott, Isabel M.; Strine, Madison S.; Watkins, Anne E.; Boot, Maikel; Kalinich, Chaney C.; Harden, Christina A.; Vogels, Chantal B.F.; Casanovas-Massana, Arnau; Moore, Adam J.; Muenker, M. Catherine; Nakahata, Maura; Tokuyama, Maria; Nelson, Allison; Fournier, John; Bermejo, Santos; Campbell, Melissa; Datta, Rupak; Dela Cruz, Charles S.; Farhadian, Shelli F.; Ko, Albert I.; Iwasaki, Akiko; Grubaugh, Nathan D.; Wilen, Craig B.; Wyllie, Anne L. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 journal: medRxiv DOI: 10.1101/2020.08.03.20165233 sha: doc_id: 268970 cord_uid: uz7q6z2f file: cache/cord-268492-0rbmqarx.json key: cord-268492-0rbmqarx authors: Alberer, Martin; von Both, Ulrich title: Cats and kids: how a feline disease may help us unravel COVID-19 associated paediatric hyperinflammatory syndrome date: 2020-09-02 journal: Infection DOI: 10.1007/s15010-020-01515-3 sha: doc_id: 268492 cord_uid: 0rbmqarx file: cache/cord-268895-m97zsodx.json key: cord-268895-m97zsodx authors: Duan, Ping; Deng, Zhi-Qing; Pan, Zhen-Yu; Wang, Yan-Ping title: Safety considerations during return to work in the context of stable COVID-19 epidemic control: an analysis of health screening results of all returned staff from a hospital date: 2020-09-18 journal: Epidemiology and infection DOI: 10.1017/s0950268820002150 sha: doc_id: 268895 cord_uid: m97zsodx file: cache/cord-269001-m4mpcoab.json key: cord-269001-m4mpcoab authors: Zullo, Fabrizio; Di Mascio, Daniele; Saccone, Gabriele title: COVID-19 Antibody Testing in Pregnancy date: 2020-05-18 journal: Am J Obstet Gynecol MFM DOI: 10.1016/j.ajogmf.2020.100142 sha: doc_id: 269001 cord_uid: m4mpcoab file: cache/cord-268718-tt07cwrf.json key: cord-268718-tt07cwrf authors: Tan, Heng Wee; Xu, Yan‐Ming; Lau, Andy T. Y. title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 journal: Rev Med Virol DOI: 10.1002/rmv.2122 sha: doc_id: 268718 cord_uid: tt07cwrf file: cache/cord-268886-mpceglk1.json key: cord-268886-mpceglk1 authors: Bourne, T.; Leonardi, M.; Kyriacou, C.; Al‐Memar, M.; Landolfo, C.; Cibula, D.; Condous, G.; Metzger, U.; Fischerova, D.; Timmerman, D.; van den Bosch, T. title: ISUOG Consensus Statement on rationalization of gynecological ultrasound services in context of SARS‐CoV‐2 date: 2020-04-08 journal: Ultrasound Obstet Gynecol DOI: 10.1002/uog.22047 sha: doc_id: 268886 cord_uid: mpceglk1 file: cache/cord-269130-zsem29ss.json key: cord-269130-zsem29ss authors: Lingappan, K.; Karmouty-Quintana, H.; Davies, J.; Akkanti, B.; Harting, M. T. title: Understanding the age divide in COVID-19: why are children overwhelmingly spared? date: 2020-07-01 journal: Am J Physiol Lung Cell Mol Physiol DOI: 10.1152/ajplung.00183.2020 sha: doc_id: 269130 cord_uid: zsem29ss file: cache/cord-268939-ws74xprt.json key: cord-268939-ws74xprt authors: Ozoner, Baris; Gungor, Abuzer; Hasanov, Teyyup; Toktas, Zafer Orcun; Kilic, Turker title: Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic date: 2020-05-28 journal: World Neurosurg DOI: 10.1016/j.wneu.2020.05.195 sha: doc_id: 268939 cord_uid: ws74xprt file: cache/cord-269009-0i2bvt77.json key: cord-269009-0i2bvt77 authors: D’Souza, Rohan; Malhamé, Isabelle; Teshler, Lizabeth; Acharya, Ganesh; Hunt, Beverley J.; McLintock, Claire title: A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID‐19 date: 2020-08-05 journal: Acta Obstet Gynecol Scand DOI: 10.1111/aogs.13962 sha: doc_id: 269009 cord_uid: 0i2bvt77 file: cache/cord-269213-tsm6zoe3.json key: cord-269213-tsm6zoe3 authors: Slaughter, Laura; Keselman, Alla; Kushniruk, Andre; Patel, Vimla L. title: A framework for capturing the interactions between laypersons’ understanding of disease, information gathering behaviors, and actions taken during an epidemic date: 2005-01-30 journal: J Biomed Inform DOI: 10.1016/j.jbi.2004.12.006 sha: doc_id: 269213 cord_uid: tsm6zoe3 file: cache/cord-268827-qwcbvtna.json key: cord-268827-qwcbvtna authors: Ibanez, Agustin; Kosik, Kenneth S title: COVID-19 in older people with cognitive impairment in Latin America date: 2020-08-18 journal: Lancet Neurol DOI: 10.1016/s1474-4422(20)30270-2 sha: doc_id: 268827 cord_uid: qwcbvtna file: cache/cord-269071-jbxbknyt.json key: cord-269071-jbxbknyt authors: Giorgianni, Andrea; Vinacci, Gabriele; Agosti, Edoardo; Cariddi, Lucia Princiotta; Mauri, Marco; Baruzzi, Fabio; Versino, Maurizio title: Transient acute-onset tetraparesis in a COVID-19 patient date: 2020-06-02 journal: Spinal Cord DOI: 10.1038/s41393-020-0493-8 sha: doc_id: 269071 cord_uid: jbxbknyt file: cache/cord-269114-mdsiv6tr.json key: cord-269114-mdsiv6tr authors: Pattabiraman, C.; Habib, F.; PK, H.; Rasheed, R.; Reddy, V.; Dinesh, P.; Damodar, T.; Kiran Reddy, N. V.; Hosallimath, K.; George, A. K.; John, B.; Pattanaik, A.; Kumar, N.; Mani, R. S.; Venkataswamy, M. M.; Shahul Hameed, S. K.; Kumar B.G., P.; Desai, A.; Vasanthapuram, R. title: Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka date: 2020-07-11 journal: nan DOI: 10.1101/2020.07.10.20150045 sha: doc_id: 269114 cord_uid: mdsiv6tr file: cache/cord-268817-wx96wwpg.json key: cord-268817-wx96wwpg authors: Karp, Donna Grace; Cuda, Deanne; Tandel, Devangkumar; Danh, Kenneth; Robinson, Peter V.; Seftel, David; Tian, Honglin; Pandori, Mark; Miller, Kevin W. P.; Tsai, Cheng-T. title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 journal: SLAS Technol DOI: 10.1177/2472630320950663 sha: doc_id: 268817 cord_uid: wx96wwpg file: cache/cord-269021-juh2qkm0.json key: cord-269021-juh2qkm0 authors: Bai, Zhihua; Gong, Yue; Tian, Xiaodong; Cao, Ying; Liu, Wenjun; Li, Jing title: The Rapid Assessment and Early Warning Models for COVID-19 date: 2020-04-01 journal: Virol Sin DOI: 10.1007/s12250-020-00219-0 sha: doc_id: 269021 cord_uid: juh2qkm0 file: cache/cord-268809-plgip4h6.json key: cord-268809-plgip4h6 authors: Bielecki, Michel; Züst, Roland; Siegrist, Denise; Meyerhofer, Daniele; Crameri, Giovanni Andrea Gerardo; Stanga, Zeno Giovanni; Stettbacher, Andreas; Buehrer, Thomas Werner; Deuel, Jeremy Werner title: Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date: 2020-06-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa889 sha: doc_id: 268809 cord_uid: plgip4h6 file: cache/cord-268935-4obwu75u.json key: cord-268935-4obwu75u authors: Lepak, Alexander J.; Shirley, Daniel K.; Buys, Ashley; Stevens, Linda; Safdar, Nasia title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) date: 2020-10-12 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.1262 sha: doc_id: 268935 cord_uid: 4obwu75u file: cache/cord-269025-2j37561h.json key: cord-269025-2j37561h authors: Pratelli, Annamaria title: Canine coronavirus inactivation with physical and chemical agents date: 2007-05-21 journal: Vet J DOI: 10.1016/j.tvjl.2007.03.019 sha: doc_id: 269025 cord_uid: 2j37561h file: cache/cord-269202-re2djjrc.json key: cord-269202-re2djjrc authors: Sapino, Anna; Facchetti, Fabio; Bonoldi, Emanuela; Gianatti, Andrea; Barbareschi, Mattia title: The autopsy debate during the COVID-19 emergency: the Italian experience date: 2020-04-29 journal: Virchows Arch DOI: 10.1007/s00428-020-02828-2 sha: doc_id: 269202 cord_uid: re2djjrc file: cache/cord-269143-8j3m03gc.json key: cord-269143-8j3m03gc authors: Brindisi, Giulia; De Vittori, Valentina; De Castro, Giovanna; Duse, Marzia; Zicari, Anna Maria title: Pills to think about in allergic rhinitis children during COVID‐19 era date: 2020-07-05 journal: Acta Paediatr DOI: 10.1111/apa.15462 sha: doc_id: 269143 cord_uid: 8j3m03gc file: cache/cord-268622-3jireyep.json key: cord-268622-3jireyep authors: Babadaei, Mohammad Mahdi Nejadi; Hasan, Anwarul; Bloukh, Samir Haj; Edis, Zehra; Sharifi, Majid; Kachooei, Ehsan; Falahati, Mojtaba title: The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets date: 2020-06-01 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1767211 sha: doc_id: 268622 cord_uid: 3jireyep file: cache/cord-268874-ldja6aa4.json key: cord-268874-ldja6aa4 authors: Park, Sun Hee title: Personal Protective Equipment for Healthcare Workers during the COVID-19 Pandemic date: 2020-06-24 journal: Infect Chemother DOI: 10.3947/ic.2020.52.2.165 sha: doc_id: 268874 cord_uid: ldja6aa4 file: cache/cord-269470-emzr3dzb.json key: cord-269470-emzr3dzb authors: Menéndez, Cintia A.; Byléhn, Fabian; Perez-Lemus, Gustavo R.; Alvarado, Walter; de Pablo, Juan J. title: Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease date: 2020-09-11 journal: Sci Adv DOI: 10.1126/sciadv.abd0345 sha: doc_id: 269470 cord_uid: emzr3dzb file: cache/cord-269283-jm18lj5t.json key: cord-269283-jm18lj5t authors: Uddin, Md Bashir; Hasan, Mahmudul; Harun-Al-Rashid, Ahmed; Ahsan, Md Irtija; Imran, Md Abdus Shukur; Ahmed, Syed Sayeem Uddin title: Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date: 2020-07-01 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104440 sha: doc_id: 269283 cord_uid: jm18lj5t file: cache/cord-269087-f9hyntvf.json key: cord-269087-f9hyntvf authors: Li, X.; Qian, K.; Xie, L.-l.; Li, X.-j.; Cheng, M.; Jiang, L.; Schuller, B. W. title: A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19 date: 2020-04-04 journal: nan DOI: 10.1101/2020.03.30.20044545 sha: doc_id: 269087 cord_uid: f9hyntvf file: cache/cord-269275-b7xxk48t.json key: cord-269275-b7xxk48t authors: Tang, Xiaojia; Luo, Yuhan; Song, Yuxia; Fan, Hongyang; Dong, Sisi; Liu, Peipei; Chen, Yingzhu title: Neurological manifestations in COVID-19 and its possible mechanism date: 2020-09-27 journal: Aging (Albany NY) DOI: 10.18632/aging.103732 sha: doc_id: 269275 cord_uid: b7xxk48t file: cache/cord-269206-160ddfsc.json key: cord-269206-160ddfsc authors: Ceylan, Rahmiye Figen; Ozkan, Burhan; Mulazimogullari, Esra title: Historical evidence for economic effects of COVID-19 date: 2020-06-04 journal: Eur J Health Econ DOI: 10.1007/s10198-020-01206-8 sha: doc_id: 269206 cord_uid: 160ddfsc file: cache/cord-269289-6uog10j4.json key: cord-269289-6uog10j4 authors: Mabillard, Holly; Sayer, John A. title: Electrolyte Disturbances in SARS-CoV-2 Infection date: 2020-07-22 journal: F1000Res DOI: 10.12688/f1000research.24441.2 sha: doc_id: 269289 cord_uid: 6uog10j4 file: cache/cord-269187-lt0uo7q3.json key: cord-269187-lt0uo7q3 authors: Saha, Indrajit; Ghosh, Nimisha; Maity, Debasree; Sharma, Nikhil; Sarkar, Jnanendra Prasad; Mitra, Kaushik title: Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date: 2020-07-11 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104457 sha: doc_id: 269187 cord_uid: lt0uo7q3 file: cache/cord-269101-7altkx5u.json key: cord-269101-7altkx5u authors: Jakhmola Mani, Ruchi; Sehgal, Nikita; Dogra, Nitu; Saxena, Shikha; Pande Katare, Deepshikha title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study date: 2020-10-28 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1839560 sha: doc_id: 269101 cord_uid: 7altkx5u file: cache/cord-269408-6qncy0nd.json key: cord-269408-6qncy0nd authors: Khonyongwa, Kirstin; Taori, Surabhi K.; Soares, Ana; Desai, Nergish; Sudhanva, Malur; Bernal, William; Schelenz, Silke; Curran, Lisa A. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-10-13 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.10.006 sha: doc_id: 269408 cord_uid: 6qncy0nd file: cache/cord-269553-d3hozs14.json key: cord-269553-d3hozs14 authors: Khan, Suliman; Siddique, Rabeea; Ali, Ashaq; Bai, Qian; Li, Zhe; Li, Hongmin; Shereen, Muhammad Adnan; Xue, Mengzhou; Nabi, Ghulam title: The spread of novel coronavirus has created an alarming situation worldwide date: 2020-04-30 journal: Journal of Infection and Public Health DOI: 10.1016/j.jiph.2020.03.005 sha: doc_id: 269553 cord_uid: d3hozs14 file: cache/cord-269568-vwkawh6x.json key: cord-269568-vwkawh6x authors: Ten Hulzen, Richard D.; Fabry, David A. title: Impact of Hearing Loss and Universal Face Masking in the COVID-19 Era. date: 2020-08-03 journal: Mayo Clin Proc DOI: 10.1016/j.mayocp.2020.07.027 sha: doc_id: 269568 cord_uid: vwkawh6x file: cache/cord-269383-1tyorrb0.json key: cord-269383-1tyorrb0 authors: Lai, Christopher K C; Chen, Zigui; Lui, Grace; Ling, Lowell; Li, Timothy; Wong, Martin C S; Ng, Rita W Y; Tso, Eugene Y K; Ho, Tracy; Fung, Kitty S C; Ng, Siu T; Wong, Barry K C; Boon, Siaw S; Hui, David S C; Chan, Paul K S title: Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date: 2020-08-01 journal: J Infect Dis DOI: 10.1093/infdis/jiaa487 sha: doc_id: 269383 cord_uid: 1tyorrb0 file: cache/cord-269377-ylgyvxtd.json key: cord-269377-ylgyvxtd authors: Matos, Ana R.; Quintas-Neves, Miguel; Oliveira, Ana I.; Dias, Luís; Marques, Sofia; Carvalho, Raquel; Alves, José N. title: COVID-19 Associated Central Nervous System Vasculopathy date: 2020-06-02 journal: The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques DOI: 10.1017/cjn.2020.109 sha: doc_id: 269377 cord_uid: ylgyvxtd file: cache/cord-269488-7fy6exsd.json key: cord-269488-7fy6exsd authors: Zhen, Wei; Berry, Gregory J. title: Development of a New Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection date: 2020-09-19 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2020.09.004 sha: doc_id: 269488 cord_uid: 7fy6exsd file: cache/cord-269496-tnw7sxlh.json key: cord-269496-tnw7sxlh authors: Sen Gupta, Parth Sarthi; Biswal, Satyaranjan; Panda, Saroj Kumar; Ray, Abhik Kumar; Rana, Malay Kumar title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1839564 sha: doc_id: 269496 cord_uid: tnw7sxlh file: cache/cord-269555-29t956ik.json key: cord-269555-29t956ik authors: Zaconeta, Alberto; Heinen, Bruna Gabriel; Moreira Salles, Yvina Vilela; Egidio da Costa Matsunaga, Michelle title: Letter to the editor“SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?” date: 2020-09-22 journal: Placenta DOI: 10.1016/j.placenta.2020.09.063 sha: doc_id: 269555 cord_uid: 29t956ik file: cache/cord-269726-z0frgm7s.json key: cord-269726-z0frgm7s authors: Gidari, Anna; Nofri, Marco; Saccarelli, Luca; Bastianelli, Sabrina; Sabbatini, Samuele; Bozza, Silvia; Camilloni, Barbara; Fusco-Moffa, Igino; Monari, Claudia; De Robertis, Edoardo; Mencacci, Antonella; Francisci, Daniela title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04057-6 sha: doc_id: 269726 cord_uid: z0frgm7s file: cache/cord-268795-tjmx6msm.json key: cord-268795-tjmx6msm authors: Sardar, Rahila; Satish, Deepshikha; Birla, Shweta; Gupta, Dinesh title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date: 2020-03-21 journal: bioRxiv DOI: 10.1101/2020.03.21.001586 sha: doc_id: 268795 cord_uid: tjmx6msm file: cache/cord-269521-vq2m4c8q.json key: cord-269521-vq2m4c8q authors: Lucchese, Guglielmo; Flöel, Agnes title: Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons date: 2020-05-01 journal: Autoimmun Rev DOI: 10.1016/j.autrev.2020.102556 sha: doc_id: 269521 cord_uid: vq2m4c8q file: cache/cord-269564-r5mmsnbx.json key: cord-269564-r5mmsnbx authors: Hans, Diana; Kelly, Erin; Wilhelmson, Krista; Katz, Eric D. title: Rapidly Fatal Infections date: 2008-05-31 journal: Emergency Medicine Clinics of North America DOI: 10.1016/j.emc.2008.01.003 sha: doc_id: 269564 cord_uid: r5mmsnbx file: cache/cord-269474-94c1mudi.json key: cord-269474-94c1mudi authors: Nasef, Nehad; O'Brien, Karel; Wylie, Lesley; Unger, Sharon title: Lessons from SARS: A retrospective study of outpatient care during an infectious disease outbreak date: 2010-07-20 journal: BMC Pediatr DOI: 10.1186/1471-2431-10-51 sha: doc_id: 269474 cord_uid: 94c1mudi file: cache/cord-269526-3npk3u5t.json key: cord-269526-3npk3u5t authors: Dehghanbanadaki, Hojat; Seif, Farhad; Vahidi, Yasmin; Razi, Farideh; Hashemi, Ehsan; Khoshmirsafa, Majid; Aazami, Hossein title: Bibliometric analysis of global scientific research on Coronavirus (COVID-19) date: 2020-05-23 journal: Med J Islam Repub Iran DOI: 10.34171/mjiri.34.51 sha: doc_id: 269526 cord_uid: 3npk3u5t file: cache/cord-269045-i7vijtol.json key: cord-269045-i7vijtol authors: Martínez‐Murcia, A.; Bru, G.; Navarro, A.; Ros‐Tárraga, P.; García‐Sirera, A.; Pérez, L. title: Comparative in silico design and validation of GPS™ CoVID‐19 dtec‐RT‐qPCR test date: 2020-07-29 journal: J Appl Microbiol DOI: 10.1111/jam.14781 sha: doc_id: 269045 cord_uid: i7vijtol file: cache/cord-269519-8hr8wyrr.json key: cord-269519-8hr8wyrr authors: Hirotsu, Yosuke; Maejima, Makoto; Shibusawa, Masahiro; Amemiya, Kenji; Nagakubo, Yuki; Hosaka, Kazuhiro; Sueki, Hitomi; Mochizuki, Hitoshi; Tsutsui, Toshiharu; Kakizaki, Yumiko; Miyashita, Yoshihiro; Omata, Masao title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104543 sha: doc_id: 269519 cord_uid: 8hr8wyrr file: cache/cord-269234-8twdx4g2.json key: cord-269234-8twdx4g2 authors: Koyama, Takahiko; Platt, Daniel; Parida, Laxmi title: Variant analysis of SARS-CoV-2 genomes date: 2020-07-01 journal: Bull World Health Organ DOI: 10.2471/blt.20.253591 sha: doc_id: 269234 cord_uid: 8twdx4g2 file: cache/cord-269537-h3lzl1un.json key: cord-269537-h3lzl1un authors: Banerjee, Aditi; Czinn, Steven J.; Reiter, Russel J.; Blanchard, Thomas G. title: Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19 date: 2020-05-23 journal: Life Sci DOI: 10.1016/j.lfs.2020.117842 sha: doc_id: 269537 cord_uid: h3lzl1un file: cache/cord-269465-3fdjqnhb.json key: cord-269465-3fdjqnhb authors: Leth-Larsen, Rikke; Zhong, Fei; Chow, Vincent T.K.; Holmskov, Uffe; Lu, Jinhua title: The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages date: 2007-05-15 journal: Immunobiology DOI: 10.1016/j.imbio.2006.12.001 sha: doc_id: 269465 cord_uid: 3fdjqnhb file: cache/cord-269522-38dhwggn.json key: cord-269522-38dhwggn authors: Hong, Xia; Currier, Glenn W.; Zhao, Xiaohui; Jiang, Yinan; Zhou, Wei; Wei, Jing title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() date: 2009-08-27 journal: Gen Hosp Psychiatry DOI: 10.1016/j.genhosppsych.2009.06.008 sha: doc_id: 269522 cord_uid: 38dhwggn file: cache/cord-269612-pmzdovna.json key: cord-269612-pmzdovna authors: Pennington, Hugh title: Politics, media and microbiologists date: 2004 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro846 sha: doc_id: 269612 cord_uid: pmzdovna file: cache/cord-269902-sbp18486.json key: cord-269902-sbp18486 authors: Springer, Steffen; Menzel, Lisa M.; Zieger, Michael title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin date: 2020-05-06 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.05.005 sha: doc_id: 269902 cord_uid: sbp18486 file: cache/cord-269454-9gthf2jl.json key: cord-269454-9gthf2jl authors: Kulkarni, Rajesh; Rajput, Uday; Dawre, Rahul; Valvi, Chhaya; Nagpal, Rema; Magdum, Nikita; Vankar, Harshali; Sonkawade, Naresh; Das, Aiswarya; Vartak, Sagar; Joshi, Suvarna; Varma, Santosh; Karyakarte, Rajesh; Bhosale, Ramesh; Kinikar, Aarti title: Early-onset symptomatic neonatal COVID-19 infection with high probability of vertical transmission date: 2020-08-02 journal: Infection DOI: 10.1007/s15010-020-01493-6 sha: doc_id: 269454 cord_uid: 9gthf2jl file: cache/cord-269718-e1mxmo3a.json key: cord-269718-e1mxmo3a authors: Wang, Jingquan; Li, Wei; Yang, Bo; Cheng, Xin; Tian, Zixin; Guo, Hongguang title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China date: 2020-11-13 journal: Environ Res DOI: 10.1016/j.envres.2020.110474 sha: doc_id: 269718 cord_uid: e1mxmo3a file: cache/cord-269825-k685efoh.json key: cord-269825-k685efoh authors: Hu, Parker; 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Germoglio Farias de Melo, Cynthia; Lima de Oliveira, Janaína title: The influence of ABO blood groups on COVID-19 susceptibility and severity: a molecular hypothesis based on carbohydrate-carbohydrate interactions date: 2020-08-02 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110155 sha: doc_id: 269563 cord_uid: 2979u47a file: cache/cord-269756-tid8a464.json key: cord-269756-tid8a464 authors: Basso, Luis G. M.; Vicente, Eduardo F.; Crusca Jr., Edson; Cilli, Eduardo M.; Costa-Filho, Antonio J. title: SARS-CoV fusion peptides induce membrane surface ordering and curvature date: 2016-11-28 journal: Sci Rep DOI: 10.1038/srep37131 sha: doc_id: 269756 cord_uid: tid8a464 file: cache/cord-269766-arjoemla.json key: cord-269766-arjoemla authors: Dutescu, R. Michael; Banasik, Peter; Schildgen, Oliver; Schrage, Norbert; Uthoff, Daniel title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 journal: Cornea DOI: 10.1097/ico.0000000000002562 sha: doc_id: 269766 cord_uid: arjoemla file: cache/cord-269946-zb7gcw0m.json key: cord-269946-zb7gcw0m authors: Boscolo-Rizzo, Paolo; Borsetto, Daniele; Spinato, Giacomo; Fabbris, Cristoforo; Menegaldo, Anna; Gaudioso, Piergiorgio; Nicolai, Piero; Tirelli, Giancarlo; Da Mosto, Maria Cristina; Rigoli, Roberto; Polesel, Jerry; Hopkins, Claire title: New onset of loss of smell or taste in household contacts of home-isolated SARS-CoV-2-positive subjects date: 2020-05-24 journal: Eur Arch Otorhinolaryngol DOI: 10.1007/s00405-020-06066-9 sha: doc_id: 269946 cord_uid: zb7gcw0m file: cache/cord-270116-r2rnnsfh.json key: cord-270116-r2rnnsfh authors: Lippi, Giuseppe; Mattiuzzi, Camilla; Bovo, Chiara; Plebani, Mario title: Current laboratory diagnostics of coronavirus disease 2019 (COVID-19) date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9548 sha: doc_id: 270116 cord_uid: r2rnnsfh file: cache/cord-270112-o2exvfy5.json key: cord-270112-o2exvfy5 authors: Ferrarese, Carlo; Silani, Vincenzo; Priori, Alberto; Galimberti, Stefania; Agostoni, Elio; Monaco, Salvatore; Padovani, Alessandro; Tedeschi, Gioacchino title: An Italian multicenter retrospective-prospective observational study on neurological manifestations of COVID-19 (NEUROCOVID) date: 2020-05-19 journal: Neurol Sci DOI: 10.1007/s10072-020-04450-1 sha: doc_id: 270112 cord_uid: o2exvfy5 file: cache/cord-270122-xijsj0d8.json key: cord-270122-xijsj0d8 authors: Hogan, Robert Edward; Grinspan, Zachary; Axeen, Erika; Marquis, Belinda; Day, B. Keith title: COVID-19 in Patients With Seizures and Epilepsy: Interpretation of Relevant Knowledge of Presenting Signs and Symptoms date: 2020-08-24 journal: Epilepsy Curr DOI: 10.1177/1535759720948549 sha: doc_id: 270122 cord_uid: xijsj0d8 file: cache/cord-270218-578lsck9.json key: cord-270218-578lsck9 authors: Gentile, Davide; Patamia, Vincenzo; Scala, Angela; Sciortino, Maria Teresa; Piperno, Anna; Rescifina, Antonio title: Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study date: 2020-04-23 journal: Mar Drugs DOI: 10.3390/md18040225 sha: doc_id: 270218 cord_uid: 578lsck9 file: cache/cord-269723-gm65p1op.json key: cord-269723-gm65p1op authors: Tzeng, Nian-Sheng; Chung, Chi-Hsiang; Chang, Chuan-Chia; Chang, Hsin-An; Kao, Yu-Chen; Chang, Shan-Yueh; Chien, Wu-Chien title: What could we learn from SARS when facing the mental health issues related to the COVID-19 outbreak? A nationwide cohort study in Taiwan date: 2020-10-06 journal: Transl Psychiatry DOI: 10.1038/s41398-020-01021-y sha: doc_id: 269723 cord_uid: gm65p1op file: cache/cord-270019-er70ehk4.json key: cord-270019-er70ehk4 authors: Yang, Kunyu; Sheng, Yuhan; Huang, Chaolin; Jin, Yang; Xiong, Nian; Jiang, Ke; Lu, Hongda; Liu, Jing; Yang, Jiyuan; Dong, Youhong; Pan, Dongfeng; Shu, Chengrong; Li, Jun; Wei, Jielin; Huang, Yu; Peng, Ling; Wu, Mengjiao; Zhang, Ruiguang; Wu, Bian; Li, Yuhui; Cai, Liqiong; Li, Guiling; Zhang, Tao; Wu, Gang title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study date: 2020-05-29 journal: Lancet Oncol DOI: 10.1016/s1470-2045(20)30310-7 sha: doc_id: 270019 cord_uid: er70ehk4 file: cache/cord-269909-1cso5cl4.json key: cord-269909-1cso5cl4 authors: Amatya, Shaili; Corr, Tammy E.; Gandhi, Chintan K.; Glass, Kristen M.; Kresch, Mitchell J.; Mujsce, Dennis J.; Oji-Mmuo, Christiana N.; Mola, Sara J.; Murray, Yuanyi L.; Palmer, Timothy W.; Singh, Meenakshi; Fricchione, Ashley; Arnold, Jill; Prentice, Danielle; Bridgeman, Colin R.; Smith, Brandon M.; Gavigan, Patrick J.; Ericson, Jessica E.; Miller, Jennifer R.; Pauli, Jaimey M.; Williams, Duane C.; McSherry, George D.; Legro, Richard S.; Iriana, Sarah M.; Kaiser, Jeffrey R. title: Management of newborns exposed to mothers with confirmed or suspected COVID-19 date: 2020-05-21 journal: J Perinatol DOI: 10.1038/s41372-020-0695-0 sha: doc_id: 269909 cord_uid: 1cso5cl4 file: cache/cord-270355-5mljrk1h.json key: cord-270355-5mljrk1h authors: Fontanet, Arnaud title: Les enseignements du SRAS date: 2007-02-28 journal: La Presse Médicale DOI: 10.1016/j.lpm.2006.12.005 sha: doc_id: 270355 cord_uid: 5mljrk1h file: cache/cord-269707-titu9lm4.json key: cord-269707-titu9lm4 authors: Hsieh, Ching-Lin; Goldsmith, Jory A.; Schaub, Jeffrey M.; DiVenere, Andrea M.; Kuo, Hung-Che; Javanmardi, Kamyab; Le, Kevin C.; Wrapp, Daniel; Lee, Alison G.; Liu, Yutong; Chou, Chia-Wei; Byrne, Patrick O.; Hjorth, Christy K.; Johnson, Nicole V.; Ludes-Meyers, John; Nguyen, Annalee W.; Park, Juyeon; Wang, Nianshuang; Amengor, Dzifa; Lavinder, Jason J.; Ippolito, Gregory C.; Maynard, Jennifer A.; Finkelstein, Ilya J.; McLellan, Jason S. title: Structure-based design of prefusion-stabilized SARS-CoV-2 spikes date: 2020-07-23 journal: Science DOI: 10.1126/science.abd0826 sha: doc_id: 269707 cord_uid: titu9lm4 file: cache/cord-270257-5f95gve3.json key: cord-270257-5f95gve3 authors: Jeon, Sangeun; Ko, Meehyun; Lee, Jihye; Choi, Inhee; Byun, Soo Young; Park, Soonju; Shum, David; Kim, Seungtaek title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date: 2020-03-28 journal: bioRxiv DOI: 10.1101/2020.03.20.999730 sha: doc_id: 270257 cord_uid: 5f95gve3 file: cache/cord-269862-krcu3hfa.json key: cord-269862-krcu3hfa authors: Wang, Shui-Mei; Wang, Chin-Tien title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date: 2009-05-25 journal: Virology DOI: 10.1016/j.virol.2009.03.010 sha: doc_id: 269862 cord_uid: krcu3hfa file: cache/cord-269939-8nvrt5y7.json key: cord-269939-8nvrt5y7 authors: Tan, Boon Fei; Loong Tuan, Jeffrey Kit; Yap, Swee Peng; Ho, Shaun Zhirui; Chek Wang, Michael Lian title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore date: 2020-04-23 journal: Clin Oncol (R Coll Radiol) DOI: 10.1016/j.clon.2020.04.006 sha: doc_id: 269939 cord_uid: 8nvrt5y7 file: cache/cord-270348-5804ffwx.json key: cord-270348-5804ffwx authors: Angelino, Andrew F.; Lyketsos, Constantine G.; Ahmed, M. Shafeeq; Potash, James B.; Cullen, Bernadette A. title: Design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 positive patients. date: 2020-07-02 journal: Psychosomatics DOI: 10.1016/j.psym.2020.06.018 sha: doc_id: 270348 cord_uid: 5804ffwx file: cache/cord-269835-mz7i66qp.json key: cord-269835-mz7i66qp authors: Furfaro, Federica; Vuitton, Lucine; Fiorino, Gionata; Koch, Stephane; Allocca, Mariangela; Gilardi, Daniela; Zilli, Alessandra; D’Amico, Ferdinando; Radice, Simona; Chevaux, Jean-Baptiste; Schaefer, Marion; Chaussade, Stanislas; Danese, Silvio; Peyrin-Biroulet, Laurent title: SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date: 2020-06-11 journal: Nat Rev Gastroenterol Hepatol DOI: 10.1038/s41575-020-0319-3 sha: doc_id: 269835 cord_uid: mz7i66qp file: cache/cord-270049-54t3w94z.json key: cord-270049-54t3w94z authors: Campione, Elena; Lanna, Caterina; Cosio, Terenzio; Rosa, Luigi; Conte, Maria Pia; Iacovelli, Federico; Romeo, Alice; Falconi, Mattia; Del Vecchio, Claudia; Franchin, Elisa; Lia, Maria Stella; Minieri, Marilena; Chiaramonte, Carlo; Ciotti, Marco; Nuccetelli, Marzia; Terrinoni, Alessandro; Iannuzzi, Ilaria; Coppeda, Luca; Magrini, Andrea; Moricca, Nicola; Sabatini, Stefano; Rosapepe, Felice; Bartoletti, Pier Luigi; Bernardini, Sergio; Andreoni, Massimo; Valenti, Piera; Bianchi, Luca title: Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date: 2020-08-17 journal: bioRxiv DOI: 10.1101/2020.08.11.244996 sha: doc_id: 270049 cord_uid: 54t3w94z file: cache/cord-270035-1e1wzdri.json key: cord-270035-1e1wzdri authors: Cazzaniga, Marco; Baselli, Lucia Augusta; Cimaz, Rolando; Guez, Sophie Suzanne; Pinzani, Raffaella; Dellepiane, Rosa Maria title: SARS-COV-2 Infection and Kawasaki Disease: Case Report of a Hitherto Unrecognized Association date: 2020-07-03 journal: Front Pediatr DOI: 10.3389/fped.2020.00398 sha: doc_id: 270035 cord_uid: 1e1wzdri file: cache/cord-270123-m8utyd1m.json key: cord-270123-m8utyd1m authors: Enmozhi, Sukanth Kumar; Raja, Kavitha; Sebastine, Irudhayasamy; Joseph, Jerrine title: Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach date: 2020-05-05 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1760136 sha: doc_id: 270123 cord_uid: m8utyd1m file: cache/cord-270458-7imgvale.json key: cord-270458-7imgvale authors: Franchini, Massimo; Farrugia, Albert; Velati, Claudio; Zanetti, Alessandro; Romanò, Luisa; Grazzini, Giuliano; Lopez, Nadia; Pati, Ilaria; Marano, Giuseppe; Pupella, Simonetta; Liumbruno, Giancarlo Maria title: The impact of the SARS‐CoV‐2 outbreak on the safety and availability of blood transfusions in Italy date: 2020-04-13 journal: Vox Sang DOI: 10.1111/vox.12928 sha: doc_id: 270458 cord_uid: 7imgvale file: cache/cord-270064-hidirfkv.json key: cord-270064-hidirfkv authors: Tort, Fernando L.; Castells, Matías; Cristina, Juan title: A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date: 2020-04-12 journal: Virus Res DOI: 10.1016/j.virusres.2020.197976 sha: doc_id: 270064 cord_uid: hidirfkv file: cache/cord-270329-t60t639i.json key: cord-270329-t60t639i authors: Schloer, Sebastian; Brunotte, Linda; Mecate-Zambrano, Angeles; Zheng, Shuyu; Tang, Jing; Ludwig, Stephan; Rescher, Ursula title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date: 2020-10-16 journal: bioRxiv DOI: 10.1101/2020.10.16.342410 sha: doc_id: 270329 cord_uid: t60t639i file: cache/cord-270462-d9l3agr0.json key: cord-270462-d9l3agr0 authors: Zeng, Zhi; Xu, Li; Xie, Xiao‐yu; Yan, Hong‐lin; Xie, Bao‐jun; Xu, Wan‐zhou; Liu, Xin‐an; Kang, Gan‐jun; Jiang, Wan‐li; Yuan, Jing‐ping title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion date: 2020-05-06 journal: Histopathology DOI: 10.1111/his.14138 sha: doc_id: 270462 cord_uid: d9l3agr0 file: cache/cord-270533-s2d3q4ob.json key: cord-270533-s2d3q4ob authors: Lau, Yu-Lung title: SARS: future research and vaccine date: 2004-11-05 journal: Paediatr Respir Rev DOI: 10.1016/j.prrv.2004.07.005 sha: doc_id: 270533 cord_uid: s2d3q4ob file: cache/cord-269771-hffxb7bm.json key: cord-269771-hffxb7bm authors: Cheung, Ka Shing; Hung, Ivan FN.; Chan, Pierre PY.; Lung, K. C.; Tso, Eugene; Liu, Raymond; Ng, Y. Y.; Chu, Man Y.; Chung, Tom WH.; Tam, Anthony Raymond; Yip, Cyril CY.; Leung, Kit-Hang; Yim-Fong Fung, Agnes; Zhang, Ricky R.; Lin, Yansheng; Cheng, Ho Ming; Zhang, Anna JX.; To, Kelvin KW.; Chan, Kwok-H.; Yuen, Kwok-Y.; Leung, Wai K. title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 journal: Gastroenterology DOI: 10.1053/j.gastro.2020.03.065 sha: doc_id: 269771 cord_uid: hffxb7bm file: cache/cord-270278-d61n3v90.json key: cord-270278-d61n3v90 authors: Choi, S.M.Y.; Lam, P. Y. title: Enhancing legal preparedness for the prevention and control of infectious diseases: Experience from severe acute respiratory syndrome in Hong Kong date: 2009-03-31 journal: Public Health DOI: 10.1016/j.puhe.2009.01.004 sha: doc_id: 270278 cord_uid: d61n3v90 file: cache/cord-270474-jaurhjvr.json key: cord-270474-jaurhjvr authors: Xiang, Zhen; Liu, Jialin; Shi, Dake; Chen, Wei; Li, Jun; Yan, Ranlin; Bi, Yufang; Hu, Weiguo; Zhu, Zhenggang; Yu, Yingyan; Yang, Zhitao title: Glucocorticoids improve severe or critical COVID-19 by activating ACE2 and reducing IL-6 levels date: 2020-06-27 journal: Int J Biol Sci DOI: 10.7150/ijbs.47652 sha: doc_id: 270474 cord_uid: jaurhjvr file: cache/cord-270645-tzctvs9q.json key: cord-270645-tzctvs9q authors: Martelletti, Luigi; Martelletti, Paolo title: Air Pollution and the Novel Covid-19 Disease: a Putative Disease Risk Factor date: 2020-04-15 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00274-4 sha: doc_id: 270645 cord_uid: tzctvs9q file: cache/cord-270591-0szbkhiz.json key: cord-270591-0szbkhiz authors: Shi, Chen; Tingting, Wu; Li, Jin-Ping; Sullivan, Mitchell A.; Wang, Cong; Wang, Hanxiang; Deng, Bin; Zhang, Yu title: Comprehensive Landscape of Heparin Therapy for COVID-19 date: 2020-10-22 journal: Carbohydr Polym DOI: 10.1016/j.carbpol.2020.117232 sha: doc_id: 270591 cord_uid: 0szbkhiz file: cache/cord-270635-l8380adr.json key: cord-270635-l8380adr authors: Maggi, Enrico; Canonica, Giorgio Walter; Moretta, Lorenzo title: COVID-19: unanswered questions on immune response and pathogenesis date: 2020-05-08 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2020.05.001 sha: doc_id: 270635 cord_uid: l8380adr file: cache/cord-270399-yfko8mpc.json key: cord-270399-yfko8mpc authors: Foster, Allison; Khan, Zohaib; Siddiqui, Aisha; Singh, Sukhdev; Atere, Muhammed; Nfonoyim, Jay M title: It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date: 2020-10-15 journal: SAGE Open Med Case Rep DOI: 10.1177/2050313x20965423 sha: doc_id: 270399 cord_uid: yfko8mpc file: cache/cord-270788-w0pewq52.json key: cord-270788-w0pewq52 authors: Chou, Chih-Fong; Shen, Shuo; Tan, Yee-Joo; Fielding, Burtram C.; Tan, Timothy H.P.; Fu, Jianlin; Xu, Qiurong; Lim, Seng Gee; Hong, Wanjin title: A novel cell-based binding assay system reconstituting interaction between SARS-CoV S protein and its cellular receptor date: 2004-11-05 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.09.008 sha: doc_id: 270788 cord_uid: w0pewq52 file: cache/cord-270515-bfjdvfuq.json key: cord-270515-bfjdvfuq authors: Deng, Chu-Xia title: The global battle against SARS-CoV-2 and COVID-19 date: 2020-03-15 journal: Int J Biol Sci DOI: 10.7150/ijbs.45587 sha: doc_id: 270515 cord_uid: bfjdvfuq file: cache/cord-269871-w41o1krr.json key: cord-269871-w41o1krr authors: Aggarwal, Shyam; Aggarwal, Shreyas; Aggarwal, Anita; Jain, Kriti; Minhas, Sachin title: High Viral Load and Poor Ventilation: Cause of High Mortality From COVID-19 date: 2020-07-25 journal: Asia Pac J Public Health DOI: 10.1177/1010539520944725 sha: doc_id: 269871 cord_uid: w41o1krr file: cache/cord-270550-if748w2n.json key: cord-270550-if748w2n authors: Bailey, Adam L.; Dmytrenko, Oleksandr; Greenberg, Lina; Bredemeyer, Andrea L.; Ma, Pan; Liu, Jing; Penna, Vinay; Lai, Lulu; Winkler, Emma S.; Sviben, Sanja; Brooks, Erin; Nair, Ajith P.; Heck, Kent A.; Rali, Aniket S.; Simpson, Leo; Saririan, Mehrdad; Hobohm, Dan; Stump, W. Tom; Fitzpatrick, James A.; Xie, Xuping; Shi, Pei-Yong; Hinson, J. Travis; Gi, Weng-Tein; Schmidt, Constanze; Leuschner, Florian; Lin, Chieh-Yu; Diamond, Michael S.; Greenberg, Michael J.; Lavine, Kory J. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.04.364315 sha: doc_id: 270550 cord_uid: if748w2n file: cache/cord-270606-r46pbaf0.json key: cord-270606-r46pbaf0 authors: Rashed, Mohamed Z.; Kopechek, Jonathan A.; Priddy, Mariah C.; Hamorsky, Krystal T.; Palmer, Kenneth E.; Mittal, Nikhil; Valdez, Joseph; Flynn, Joseph; Williams, Stuart J. title: Rapid detection of SARS-CoV-2 antibodies using electrochemical impedance-based detector date: 2020-10-07 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112709 sha: doc_id: 270606 cord_uid: r46pbaf0 file: cache/cord-270613-vnjuubt4.json key: cord-270613-vnjuubt4 authors: Poon, Terence C.W.; Pang, Ronald T.K.; Chan, K.C. Allen; Lee, Nelson L.S.; Chiu, Rossa W.K.; Tong, Yu‐Kwan; Chim, Stephen S.C.; Ngai, Sai M.; Sung, Joseph J.Y.; Lo, Y.M. Dennis title: Proteomic analysis reveals platelet factor 4 and beta‐thromboglobulin as prognostic markers in severe acute respiratory syndrome date: 2012-06-28 journal: Electrophoresis DOI: 10.1002/elps.201200002 sha: doc_id: 270613 cord_uid: vnjuubt4 file: cache/cord-270665-z4l3lq39.json key: cord-270665-z4l3lq39 authors: Tian, Qing; Yan, Xiaodong; Shi, Rui; Wang, Guijie; Xu, Xiaomei; Wang, Hongyan; Wang, Qingqing; Yang, Long; Liu, Zirong; Wang, Lanying; Shrestha, Dhan Bahadur; Zhang, Yamin title: Endoscopic mask innovation and protective measures changes during the COVID‐19 pandemic: experience from a Chinese hepato‐biliary‐pancreatic unit date: 2020-07-23 journal: Dig Endosc DOI: 10.1111/den.13799 sha: doc_id: 270665 cord_uid: z4l3lq39 file: cache/cord-270377-lfcoy8n1.json key: cord-270377-lfcoy8n1 authors: Novazzi, Federica; Cassaniti, Irene; Piralla, Antonio; Di Sabatino, Antonio; Bruno, Raffaele; Baldanti, Fausto title: SARS-CoV-2 positivity in rectal swabs implication for possible transmission date: 2020-07-02 journal: J Glob Antimicrob Resist DOI: 10.1016/j.jgar.2020.06.011 sha: doc_id: 270377 cord_uid: lfcoy8n1 file: cache/cord-270510-z6qg48nz.json key: cord-270510-z6qg48nz authors: Lauro, A.; Pagano, N.; Impellizzeri, G.; Cervellera, M.; Tonini, V. title: Emergency Endoscopy During the SARS-CoV-2 Pandemic in the North of Italy: Experience from St. Orsola University Hospital—Bologna date: 2020-04-22 journal: Dig Dis Sci DOI: 10.1007/s10620-020-06270-x sha: doc_id: 270510 cord_uid: z6qg48nz file: cache/cord-270495-2u072mtp.json key: cord-270495-2u072mtp authors: Lokida, Dewi; Lukman, Nurhayati; Salim, Gustiani; Butar-butar, Deni Pepy; Kosasih, Herman; Wulan, Wahyu Nawang; Naysilla, Adhella Menur; Djajady, Yuanita; Sari, Rizki Amalia; Arlinda, Dona; Lau, Chuen-Yen; Karyana, Muhammad title: Diagnosis of COVID-19 in a Dengue-Endemic Area date: 2020-08-05 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0676 sha: doc_id: 270495 cord_uid: 2u072mtp file: cache/cord-270837-xvauo76d.json key: cord-270837-xvauo76d authors: Hui, David S.; Wong, Ka T.; Ko, Fanny W.; Tam, Lai S.; Chan, Doris P.; Woo, Jean; Sung, Joseph J.Y. title: The 1-Year Impact of Severe Acute Respiratory Syndrome on Pulmonary Function, Exercise Capacity, and Quality of Life in a Cohort of Survivors date: 2005-10-31 journal: Chest DOI: 10.1378/chest.128.4.2247 sha: doc_id: 270837 cord_uid: xvauo76d file: cache/cord-270622-aofva2ab.json key: cord-270622-aofva2ab authors: Li, Qizhang; Wang, Zhiying; Zheng, Qiang; Liu, Sen title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 date: 2020-08-26 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.08.016 sha: doc_id: 270622 cord_uid: aofva2ab file: cache/cord-270475-mkpn9tz6.json key: cord-270475-mkpn9tz6 authors: Requena, Manuel; Olivé, Marta; Muchada, Marian; García-Tornel, Álvaro; Deck, Matías; Juega, Jesús; Boned, Sandra; Rodríguez-Villatoro, Noelia; Piñana, Carlos; Pagola, Jorge; Rodríguez-Luna, David; Hernández, David; Rubiera, Marta; Tomasello, Alejandro; Molina, Carlos A.; Ribo, Marc title: COVID-19 and Stroke: incidence and etiological description in a high-volume center. date: 2020-08-05 journal: J Stroke Cerebrovasc Dis DOI: 10.1016/j.jstrokecerebrovasdis.2020.105225 sha: doc_id: 270475 cord_uid: mkpn9tz6 file: cache/cord-270588-c9rxmo44.json key: cord-270588-c9rxmo44 authors: Algarroba, Gabriela N.; Rekawek, Patricia; Vahanian, Sevan A.; Khullar, Poonam; Palaia, Thomas; Peltier, Morgan R.; Chavez, Martin R.; Vintzileos, Anthony M. title: Visualization of SARS-CoV-2 virus invading the human placenta using electron microscopy date: 2020-05-13 journal: Am J Obstet Gynecol DOI: 10.1016/j.ajog.2020.05.023 sha: doc_id: 270588 cord_uid: c9rxmo44 file: cache/cord-270661-e83xe4sp.json key: cord-270661-e83xe4sp authors: Falahi, Shahab; Kenarkoohi, Azra title: Transmission routes for SARS-COV-2 infection: Review of Evidence date: 2020-10-06 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100778 sha: doc_id: 270661 cord_uid: e83xe4sp file: cache/cord-270866-olc5r2yx.json key: cord-270866-olc5r2yx authors: Mallet, Jasmina; Dubertret, Caroline; Le Strat, Yann title: Addictions in the COVID-19 era: Current evidence, future perspectives a comprehensive review date: 2020-08-12 journal: Prog Neuropsychopharmacol Biol Psychiatry DOI: 10.1016/j.pnpbp.2020.110070 sha: doc_id: 270866 cord_uid: olc5r2yx file: cache/cord-270886-m9na7cbm.json key: cord-270886-m9na7cbm authors: Quadeer, Ahmed Abdul title: Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges date: 2020-08-15 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102947 sha: doc_id: 270886 cord_uid: m9na7cbm file: cache/cord-270909-wb7mwklo.json key: cord-270909-wb7mwklo authors: Cheng, Vincent C.C.; Wong, Shuk-Ching; Chuang, Vivien W.M.; So, Simon Y.C.; Chen, Jonathan H.K.; Sridhar, Siddharth; To, Kelvin K.W.; Chan, Jasper F.W.; Hung, Ivan F.N.; Ho, Pak-Leung; Yuen, Kwok-Yung title: Absence of nosocomial transmission of coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in the pre-pandemic phase in Hong Kong date: 2020-05-24 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.05.018 sha: doc_id: 270909 cord_uid: wb7mwklo file: cache/cord-270858-ozvdz9ew.json key: cord-270858-ozvdz9ew authors: Altmann, Daniel M; Douek, Daniel C; Boyton, Rosemary J title: What policy makers need to know about COVID-19 protective immunity date: 2020-04-27 journal: Lancet DOI: 10.1016/s0140-6736(20)30985-5 sha: doc_id: 270858 cord_uid: ozvdz9ew file: cache/cord-270743-yyl50z94.json key: cord-270743-yyl50z94 authors: Haseli, Sara; Karimi-Galougahi, Mahboobeh title: Reply to “MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss” date: 2020-06-10 journal: Acad Radiol DOI: 10.1016/j.acra.2020.05.025 sha: doc_id: 270743 cord_uid: yyl50z94 file: cache/cord-270683-982eqtog.json key: cord-270683-982eqtog authors: Pavel, Shaikh Terkis Islam; Yetiskin, Hazel; Aydin, Gunsu; Holyavkin, Can; Uygut, Muhammet Ali; Dursun, Zehra Bestepe; Celik, İlhami; Cevik, Ceren; Ozdarendeli, Aykut title: Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date: 2020-09-16 journal: PLoS One DOI: 10.1371/journal.pone.0238614 sha: doc_id: 270683 cord_uid: 982eqtog file: cache/cord-270528-3rsv3jlh.json key: cord-270528-3rsv3jlh authors: Yazdanpanah, Fereshteh; Hamblin, Michael R.; Rezaei, Nima title: The immune system and COVID-19: Friend or foe? date: 2020-06-02 journal: Life Sci DOI: 10.1016/j.lfs.2020.117900 sha: doc_id: 270528 cord_uid: 3rsv3jlh file: cache/cord-270951-6nq3jwgr.json key: cord-270951-6nq3jwgr authors: Amerio, Paolo; Prignano, Francesca; Giuliani, Federica; Gualdi, Giulio title: COVID‐19 and psoriasis: Should we fear for patients treated with biologics? date: 2020-05-05 journal: Dermatol Ther DOI: 10.1111/dth.13434 sha: doc_id: 270951 cord_uid: 6nq3jwgr file: cache/cord-270888-8j17ul7k.json key: cord-270888-8j17ul7k authors: Fernández-González, Sara Mª; Varela-Ferreiro, Nerea; Aguiar, Susana Castro; Pardo-Vázquez, Jerónimo José title: ¿Infección Por Sars-Cov-2 Como Desencadenante De Un Síndrome Inflamatorio Sistémico? date: 2020-09-09 journal: Enferm Infecc Microbiol Clin DOI: 10.1016/j.eimc.2020.07.012 sha: doc_id: 270888 cord_uid: 8j17ul7k file: cache/cord-270698-9w3ap3gz.json key: cord-270698-9w3ap3gz authors: Guo, Hua; Hu, Bing-Jie; Yang, Xing-Lou; Zeng, Lei-Ping; Li, Bei; Ouyang, Song-Ying; Shi, Zheng-Li title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date: 2020-05-13 journal: bioRxiv DOI: 10.1101/2020.05.13.093658 sha: doc_id: 270698 cord_uid: 9w3ap3gz file: cache/cord-270935-t9pym9k0.json key: cord-270935-t9pym9k0 authors: Dumyati, Ghinwa; Gaur, Swati; Nace, David A.; Jump, Robin L.P. title: Does Universal Testing for COVID-19 Work for Everyone? date: 2020-08-15 journal: J Am Med Dir Assoc DOI: 10.1016/j.jamda.2020.08.013 sha: doc_id: 270935 cord_uid: t9pym9k0 file: cache/cord-270880-azslipmp.json key: cord-270880-azslipmp authors: Cozzupoli, Grazia Maria; Savastano, Maria Cristina; Falsini, Benedetto; Savastano, Alfonso; Rizzo, Stanislao title: Possible Retinal Impairment Secondary to Ritonavir Use in SARS-CoV-2 Patients: A Narrative Systematic Review date: 2020-08-22 journal: J Ophthalmol DOI: 10.1155/2020/5350494 sha: doc_id: 270880 cord_uid: azslipmp file: cache/cord-271014-xzpvupms.json key: cord-271014-xzpvupms authors: Erikstrup, Christian; Hother, Christoffer Egeberg; Pedersen, Ole Birger Vestager; Mølbak, Kåre; Skov, Robert Leo; Holm, Dorte Kinggaard; Sækmose, Susanne Gjørup; Nilsson, Anna Christine; Brooks, Patrick Terrence; Boldsen, Jens Kjærgaard; Mikkelsen, Christina; Gybel-Brask, Mikkel; Sørensen, Erik; Dinh, Khoa Manh; Mikkelsen, Susan; Møller, Bjarne Kuno; Haunstrup, Thure; Harritshøj, Lene; Jensen, Bitten Aagaard; Hjalgrim, Henrik; Lillevang, Søren Thue; Ullum, Henrik title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa849 sha: doc_id: 271014 cord_uid: xzpvupms file: cache/cord-270776-oulnk1b3.json key: cord-270776-oulnk1b3 authors: Chau, Tai-nin; Lee, Po-oi; Choi, Kin-wing; Lee, Chiu-man; Ma, Ka-fai; Tsang, Tak-yin; Tso, Yuk-keung; Chiu, Ming-chee; Tong, Wing-lok; Yu, Wai-cho; Lai, Sik-to title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome date: 2004-08-15 journal: The American Journal of Medicine DOI: 10.1016/j.amjmed.2004.03.020 sha: doc_id: 270776 cord_uid: oulnk1b3 file: cache/cord-271174-886xc1n3.json key: cord-271174-886xc1n3 authors: Lipworth, Brian; Chan, Rory; Lipworth, Samuel; RuiWen Kuo, Chris title: Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection date: 2020-04-18 journal: J Allergy Clin Immunol Pract DOI: 10.1016/j.jaip.2020.04.014 sha: doc_id: 271174 cord_uid: 886xc1n3 file: cache/cord-270919-0hldozml.json key: cord-270919-0hldozml authors: Cortey, Martí; Li, Yanli; Díaz, Ivan; Clilverd, Hepzibar; Darwich, Laila; Mateu, Enric title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date: 2020-05-17 journal: bioRxiv DOI: 10.1101/2020.05.16.099499 sha: doc_id: 270919 cord_uid: 0hldozml file: cache/cord-271188-ewlxy5po.json key: cord-271188-ewlxy5po authors: Liu, Wei; Zhang, Shuping; Nekhai, Sergei; Liu, Sijin title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 journal: Curr Clin Microbiol Rep DOI: 10.1007/s40588-020-00140-w sha: doc_id: 271188 cord_uid: ewlxy5po file: cache/cord-271338-v2k9zn87.json key: cord-271338-v2k9zn87 authors: Pujadas, E.; Chaudhry, F.; McBride, R.; Richter, F.; Zhao, S.; Wajnberg, A.; Nadkarni, G.; Glicksberg, B. S.; Houldsworth, J.; Cordon-Cardo, C. title: SARS-CoV-2 Viral Load Predicts COVID-19 Mortality date: 2020-06-12 journal: nan DOI: 10.1101/2020.06.11.20128934 sha: doc_id: 271338 cord_uid: v2k9zn87 file: cache/cord-271404-tu8u1b1d.json key: cord-271404-tu8u1b1d authors: Gaunkar, Ridhima B; Nagarsekar, Aradhana; Carvalho, Karla M; Jodalli, Praveen S; Mascarenhas, Kennedy title: COVID-19 in Smokeless Tobacco Habitués: Increased Susceptibility and Transmission date: 2020-06-25 journal: Cureus DOI: 10.7759/cureus.8824 sha: doc_id: 271404 cord_uid: tu8u1b1d file: cache/cord-271495-5906wju4.json key: cord-271495-5906wju4 authors: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.025 sha: doc_id: 271495 cord_uid: 5906wju4 file: cache/cord-271027-4omocd8q.json key: cord-271027-4omocd8q authors: Fronza, R.; Lusic, M.; Schmidt, M.; Lucic, B. title: Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak date: 2020-05-01 journal: nan DOI: 10.1101/2020.04.26.20080846 sha: doc_id: 271027 cord_uid: 4omocd8q file: cache/cord-271701-tx0lqgff.json key: cord-271701-tx0lqgff authors: te Velthuis, Aartjan J.W.; van den Worm, Sjoerd H. E.; Snijder, Eric J. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 journal: Nucleic Acids Res DOI: 10.1093/nar/gkr893 sha: doc_id: 271701 cord_uid: tx0lqgff file: cache/cord-270994-1mmqfp7g.json key: cord-270994-1mmqfp7g authors: ul Qamar, Muhammad Tahir; Alqahtani, Safar M.; Alamri, Mubarak A.; Chen, Ling-Ling title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants date: 2020-03-26 journal: J Pharm Anal DOI: 10.1016/j.jpha.2020.03.009 sha: doc_id: 270994 cord_uid: 1mmqfp7g file: cache/cord-271469-lozvq3y6.json key: cord-271469-lozvq3y6 authors: Shaikh, Faiq; Anderson, Michael; Sohail, M. Rizwan; Mulero, Francisca; Awan, Omer; Dupont-Roettger, Diana; Kubassova, Olga; Dehmsehki, Jamshid; Bisdas, Sotirios title: Current landscape of Imaging and the potential role for Artificial intelligence in the management of COVID-19 date: 2020-06-27 journal: Curr Probl Diagn Radiol DOI: 10.1067/j.cpradiol.2020.06.009 sha: doc_id: 271469 cord_uid: lozvq3y6 file: cache/cord-271211-frkk6w0a.json key: cord-271211-frkk6w0a authors: Han, Yu; Yang, Hailan title: The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID‐19): A Chinese perspective date: 2020-03-12 journal: J Med Virol DOI: 10.1002/jmv.25749 sha: doc_id: 271211 cord_uid: frkk6w0a file: cache/cord-271371-qs7zge3l.json key: cord-271371-qs7zge3l authors: Gao, Jia; Zhang, Liang; Liu, Xiaodan; Li, Fudong; Ma, Rongsheng; Zhu, Zhongliang; Zhang, Jiahai; Wu, Jihui; Shi, Yunyu; Pan, Yueyin; Ge, Yushu; Ruan, Ke title: Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-07-28 journal: J Phys Chem Lett DOI: 10.1021/acs.jpclett.0c01894 sha: doc_id: 271371 cord_uid: qs7zge3l file: cache/cord-271419-v6dfel3l.json key: cord-271419-v6dfel3l authors: Adachi, Shun; Koma, Takaaki; Doi, Naoya; Nomaguchi, Masako; Adachi, Akio title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 journal: Front Immunol DOI: 10.3389/fimmu.2020.00811 sha: doc_id: 271419 cord_uid: v6dfel3l file: cache/cord-271411-h3k7r2ia.json key: cord-271411-h3k7r2ia authors: Pelletier, Jesse S.; Stewart, Kevin; Tessema, Belachew title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination date: 2020-08-26 journal: Ther Adv Ophthalmol DOI: 10.1177/2515841420951392 sha: doc_id: 271411 cord_uid: h3k7r2ia file: cache/cord-271090-91lzr4tz.json key: cord-271090-91lzr4tz authors: Edwards, Kathryn M.; Orenstein, Walter A. title: Anticipating SARS-CoV-2 Vaccine Testing, Licensure, and Recommendations for Use date: 2020-06-19 journal: J Pediatr DOI: 10.1016/j.jpeds.2020.06.048 sha: doc_id: 271090 cord_uid: 91lzr4tz file: cache/cord-271243-8cfyen86.json key: cord-271243-8cfyen86 authors: Xiao, Y.; Meng, Q.; Yin, X.; Guan, Y.; Liu, Y.; Li, C.; Wang, M.; Liu, G.; Tong, T.; Wang, L.-F.; Kong, X.; Wu, D. title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus date: 2008-05-31 journal: Journal of Comparative Pathology DOI: 10.1016/j.jcpa.2007.12.005 sha: doc_id: 271243 cord_uid: 8cfyen86 file: cache/cord-271505-eot38721.json key: cord-271505-eot38721 authors: Wang, Hongliang; Rao, Shuan; Jiang, Chengyu title: Molecular pathogenesis of severe acute respiratory syndrome date: 2006-09-28 journal: Microbes Infect DOI: 10.1016/j.micinf.2006.06.012 sha: doc_id: 271505 cord_uid: eot38721 file: cache/cord-271751-46oo9xv5.json key: cord-271751-46oo9xv5 authors: Ingraham, Nicholas E.; Boulware, David; Sparks, Matthew A.; Schacker, Timothy; Benson, Bradley; Sparks, Jeffrey A.; Murray, Thomas; Connett, John; Chipman, Jeffrey G.; Charles, Anthony; Tignanelli, Christopher J. title: Shining a light on the evidence for hydroxychloroquine in SARS-CoV-2 date: 2020-04-28 journal: Crit Care DOI: 10.1186/s13054-020-02894-7 sha: doc_id: 271751 cord_uid: 46oo9xv5 file: cache/cord-270964-kxze0470.json key: cord-270964-kxze0470 authors: Lau, Kwok-Kwong; Yu, Wai-Cho; Chu, Chung-Ming; Lau, Suet-Ting; Sheng, Bun; Yuen, Kwok-Yung title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030638 sha: doc_id: 270964 cord_uid: kxze0470 file: cache/cord-271920-1dzkgt6w.json key: cord-271920-1dzkgt6w authors: Carpenter, Christopher R.; Mudd, Philip; West, Colin P.; Wilber, Erin; Wilber, Scott T. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 journal: Acad Emerg Med DOI: 10.1111/acem.14048 sha: doc_id: 271920 cord_uid: 1dzkgt6w file: cache/cord-270857-8424oq4x.json key: cord-270857-8424oq4x authors: Hui, David S.; Hall, Stephen D.; Chan, Matthew T.V.; Chow, Benny K.; Ng, Susanna S.; Gin, Tony; Sung, Joseph J.Y. title: Exhaled Air Dispersion During Oxygen Delivery Via a Simple Oxygen Mask date: 2007-08-31 journal: Chest DOI: 10.1378/chest.07-0636 sha: doc_id: 270857 cord_uid: 8424oq4x file: cache/cord-271504-t3y1w9ef.json key: cord-271504-t3y1w9ef authors: Luo, Zichao; Ang, Melgious Jin Yan; Chan, Siew Yin; Yi, Zhigao; Goh, Yi Yiing; Yan, Shuangqian; Tao, Jun; Liu, Kai; Li, Xiaosong; Zhang, Hongjie; Huang, Wei; Liu, Xiaogang title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 journal: Research (Wash D C) DOI: 10.34133/2020/6925296 sha: doc_id: 271504 cord_uid: t3y1w9ef file: cache/cord-271723-8qoozmgk.json key: cord-271723-8qoozmgk authors: Gelman, Ram; Bayatra, Areej; Kessler, Asa; Schwartz, Asaf; Ilan, Yaron title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents date: 2020-06-18 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1776161 sha: doc_id: 271723 cord_uid: 8qoozmgk file: cache/cord-271551-bj2db91j.json key: cord-271551-bj2db91j authors: Tomczyk, Samuel; Rahn, Maxi; Schmidt, Silke title: Social Distancing and Stigma: Association Between Compliance With Behavioral Recommendations, Risk Perception, and Stigmatizing Attitudes During the COVID-19 Outbreak date: 2020-08-11 journal: Front Psychol DOI: 10.3389/fpsyg.2020.01821 sha: doc_id: 271551 cord_uid: bj2db91j file: cache/cord-271871-8grkln6o.json key: cord-271871-8grkln6o authors: Singer, J. S.; Cheng, E. M.; Murad, D.; de St. Maurice, A.; Hines, O. J.; Uslan, D. Z.; Garner, O.; Pregler, J.; Bukata, S. V.; Pfeffer, M. A.; Cherry, R. A. title: Low Prevalence (0.13%) of COVID-19 Infection in Asymptomatic Pre-operative/Pre-procedure Patients at a Large Academic Medical Center Informs Approaches to Perioperative Care date: 2020-08-14 journal: Surgery DOI: 10.1016/j.surg.2020.07.048 sha: doc_id: 271871 cord_uid: 8grkln6o file: cache/cord-272179-wvw5mmy3.json key: cord-272179-wvw5mmy3 authors: Calderaro, Adriana; De Conto, Flora; Buttrini, Mirko; Piccolo, Giovanna; Montecchini, Sara; Maccari, Clara; Martinelli, Monica; Di Maio, Alan; Ferraglia, Francesca; Pinardi, Federica; Montagna, Paolo; Arcangeletti, Maria Cristina; Chezzi, Carlo title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1473 sha: doc_id: 272179 cord_uid: wvw5mmy3 file: cache/cord-271781-cfv0ta10.json key: cord-271781-cfv0ta10 authors: Patel, Kishan P.; Vunnam, Srinivas R.; Patel, Puja A.; Krill, Kaleigh L.; Korbitz, Parker M.; Gallagher, John P.; Suh, Jane E.; Vunnam, Rama R. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-03961-1 sha: doc_id: 271781 cord_uid: cfv0ta10 file: cache/cord-271849-wxmr8eki.json key: cord-271849-wxmr8eki authors: Meysman, Pieter; Postovskaya, Anna; De Neuter, Nicolas; Ogunjimi, Benson; Laukens, Kris title: Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date: 2020-09-09 journal: bioRxiv DOI: 10.1101/2020.09.09.289355 sha: doc_id: 271849 cord_uid: wxmr8eki file: cache/cord-271919-pbs95hy0.json key: cord-271919-pbs95hy0 authors: Desenclos, Jean-Claude; van der Werf, Sylvie; Bonmarin, Isabelle; Levy-Bruhl, Daniel; Yazdanpanah, Yazdan; Hoen, Bruno; Emmanuelli, Julien; Lesens, Olivier; Dupon, Michel; Natali, François; Michelet, Christian; Reynes, Jacques; Guery, Benoit; Larsen, Christine; Semaille, Caroline; Mouton, Yves; Christmann, Daniel; André, Michel; Escriou, Nicolas; Burguière, Anna; Manuguerra, Jean-Claude; Coignard, Bruno; Lepoutre, Agnés; Meffre, Christine; Bitar, Dounia; Decludt, Bénédicte; Capek, Isabelle; Antona, Denise; Che, Didier; Herida, Magid; Infuso, Andréa; Saura, Christine; Brücker, Gilles; Hubert, Bruno; LeGoff, Dominique; Scheidegger, Suzanne title: Introduction of SARS in France, March–April, 2003 date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030351 sha: doc_id: 271919 cord_uid: pbs95hy0 file: cache/cord-271998-hdkmwihu.json key: cord-271998-hdkmwihu authors: Rabenau, H. F.; Biesert, L.; Schmidt, T.; Bauer, G.; Cinatl, J.; Doerr, H. W. title: SARS-coronavirus (SARS-CoV) and the safety of a solvent/detergent (S/D) treated immunoglobulin preparation date: 2005-06-30 journal: Biologicals DOI: 10.1016/j.biologicals.2005.01.003 sha: doc_id: 271998 cord_uid: hdkmwihu file: cache/cord-271930-9a18h2tr.json key: cord-271930-9a18h2tr authors: Licari, Amelia; Votto, Martina; Brambilla, Ilaria; Castagnoli, Riccardo; Piccotti, Emanuela; Olcese, Roberta; Tosca, Maria Angela; Ciprandi, Giorgio; Marseglia, Gian Luigi title: Allergy and asthma in children and adolescents during the COVID outbreak: What we know and how we could prevent allergy and asthma flares date: 2020-05-28 journal: Allergy DOI: 10.1111/all.14369 sha: doc_id: 271930 cord_uid: 9a18h2tr file: cache/cord-271648-m2c5bvuj.json key: cord-271648-m2c5bvuj authors: Ashour, Hossam M.; Elkhatib, Walid F.; Rahman, Md. Masudur; Elshabrawy, Hatem A. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 journal: Pathogens DOI: 10.3390/pathogens9030186 sha: doc_id: 271648 cord_uid: m2c5bvuj file: cache/cord-272414-oo8kcuf3.json key: cord-272414-oo8kcuf3 authors: Chiocchetti, Roberto; Galiazzo, Giorgia; Fracassi, Federico; Giancola, Fiorella; Pietra, Marco title: ACE2 Expression in the Cat and the Tiger Gastrointestinal Tracts date: 2020-08-13 journal: Front Vet Sci DOI: 10.3389/fvets.2020.00514 sha: doc_id: 272414 cord_uid: oo8kcuf3 file: cache/cord-271544-i20105lq.json key: cord-271544-i20105lq authors: Poston, Daniel; Weisblum, Yiska; Wise, Helen; Templeton, Kate; Jenks, Sara; Hatziioannou, Theodora; Bieniasz, Paul title: Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection date: 2020-10-11 journal: medRxiv DOI: 10.1101/2020.10.08.20209650 sha: doc_id: 271544 cord_uid: i20105lq file: cache/cord-272019-4uua0zgp.json key: cord-272019-4uua0zgp authors: Sun, Wei; 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N.; Pöhlmann, Stefan; Blasczyk, Rainer; Schulz, Thomas F.; Förster, Reinhold title: Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID-19 convalescent patients revealed by two different detection methods date: 2020-11-02 journal: Cell Mol Immunol DOI: 10.1038/s41423-020-00573-9 sha: doc_id: 272654 cord_uid: hh29olk7 file: cache/cord-272009-yxjhfg7m.json key: cord-272009-yxjhfg7m authors: Cui, Jie; Han, Naijian; Streicker, Daniel; Li, Gang; Tang, Xianchun; Shi, Zhengli; Hu, Zhihong; Zhao, Guoping; Fontanet, Arnaud; Guan, Yi; Wang, Linfa; Jones, Gareth; Field, Hume E.; Daszak, Peter; Zhang, Shuyi title: Evolutionary Relationships between Bat Coronaviruses and Their Hosts date: 2007-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid1310.070448 sha: doc_id: 272009 cord_uid: yxjhfg7m file: cache/cord-272211-nkv6irr7.json key: cord-272211-nkv6irr7 authors: Hagan, Liesl M.; Williams, Samantha P.; Spaulding, Anne C.; Toblin, Robin L.; Figlenski, Jessica; Ocampo, Jeanne; Ross, Tara; Bauer, Heidi; Hutchinson, Justine; Lucas, Kimberley D.; Zahn, Matthew; Chiang, Chun; Collins, Timothy; Burakoff, Alexis; Bettridge, Juli; Stringer, Ginger; Maul, Randolph; Waters, Kristen; Dewart, Courtney; Clayton, Jennifer; de Fijter, Sietske; Sadacharan, Radha; Garcia, Linda; Lockett, Naomi; Short, Kirstin; Sunder, Laxman; Handanagic, Senad title: Mass Testing for SARS-CoV-2 in 16 Prisons and Jails — Six Jurisdictions, United States, April–May 2020 date: 2020-08-21 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6933a3 sha: doc_id: 272211 cord_uid: nkv6irr7 file: cache/cord-272602-rywg9mek.json key: cord-272602-rywg9mek authors: Allison, James R; Currie, Charlotte C; Edwards, David C; Bowes, Charlotte; Coulter, Jamie; Pickering, Kimberley; Kozhevnikova, Ekaterina; Durham, Justin; Nile, Christopher J; Jakubovics, Nicholas; Rostami, Nadia; Holliday, Richard title: Evaluating aerosol and splatter following dental procedures: addressing new challenges for oral healthcare and rehabilitation date: 2020-09-23 journal: J Oral Rehabil DOI: 10.1111/joor.13098 sha: doc_id: 272602 cord_uid: rywg9mek file: cache/cord-272318-8yfg1j0o.json key: cord-272318-8yfg1j0o authors: Reddy, Sujan T.; Garg, Tanu; Shah, Chintan; Nascimento, Fábio A.; Imran, Rajeel; Kan, Peter; Bowry, Ritvij; Gonzales, Nicole; Barreto, Andrew; Kumar, Abhay; Volpi, John; Misra, Vivek; Chiu, David; Gadhia, Rajan; Savitz, Sean I. title: Cerebrovascular Disease in Patients with COVID-19: A Review of the Literature and Case Series date: 2020-06-11 journal: Case Rep Neurol DOI: 10.1159/000508958 sha: doc_id: 272318 cord_uid: 8yfg1j0o file: cache/cord-271339-wt5o9sgm.json key: cord-271339-wt5o9sgm authors: Chen, Chao-Ju; Hsieh, Li-Ling; Lin, Shu-Kai; Wang, Chu-Feng; Huang, Yi-Hui; Lin, Shang-Yi; Lu, Po-Liang title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10050333 sha: doc_id: 271339 cord_uid: wt5o9sgm file: cache/cord-272241-2fwz8z8n.json key: cord-272241-2fwz8z8n authors: Kumar, Amit; Kumar, Prateek; Saumya, Kumar Udit; Kapuganti, Shivani K.; Bhardwaj, Taniya; Giri, Rajanish title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date: 2020-09-09 journal: Expert review of vaccines DOI: 10.1080/14760584.2020.1813576 sha: doc_id: 272241 cord_uid: 2fwz8z8n file: cache/cord-272734-kawim93f.json key: cord-272734-kawim93f authors: Freire-Paspuel, Byron; Vega-Mariño, Patricio; Velez, Alberto; Castillo, Paulina; Cruz, Marilyn; Garcia-Bereguiain, Miguel Angel title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date: 2020-05-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104454 sha: doc_id: 272734 cord_uid: kawim93f file: cache/cord-272681-u3p0hsla.json key: cord-272681-u3p0hsla authors: Vargas-Gandica, Jair; Winter, Daniel; Schnippe, Rainer; Rodriguez-Morales, Andrea G.; Mondragon, Johana; Escalera-Antezana, Juan Pablo; Trelles-Thorne, María del Pilar; Bonilla-Aldana, D. 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N.; Petric, M.; Henry, B.; Krajden, M. title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 date: 2020-07-15 journal: nan DOI: 10.1101/2020.07.13.20153148 sha: doc_id: 273253 cord_uid: rgqvdzna file: cache/cord-273626-zy8qjaai.json key: cord-273626-zy8qjaai authors: Gong, Shu‐ran; Bao, Lin‐lin title: The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models date: 2018-07-28 journal: Animal Model Exp Med DOI: 10.1002/ame2.12017 sha: doc_id: 273626 cord_uid: zy8qjaai file: cache/cord-273314-p1dlzoh1.json key: cord-273314-p1dlzoh1 authors: Gadiparthi, Chiranjeevi; Perisetti, Abhilash; Sayana, Hari; Tharian, Benjamin; Inamdar, Sumant; Korman, Andrew title: Gastrointestinal Bleeding in Patients with Severe SARS-CoV-2 date: 2020-06-04 journal: Am J Gastroenterol DOI: 10.14309/ajg.0000000000000719 sha: doc_id: 273314 cord_uid: p1dlzoh1 file: cache/cord-273351-vq3budip.json key: cord-273351-vq3budip authors: Farré, Núria; Mojón, Diana; Llagostera, Marc; Belarte-Tornero, Laia C.; Calvo-Fernández, Alicia; Vallés, Ermengol; Negrete, Alejandro; García-Guimaraes, Marcos; Bartolomé, Yolanda; Fernández, Camino; García-Duran, Ana B.; Marrugat, Jaume; Vaquerizo, Beatriz title: Prolonged QT Interval in SARS-CoV-2 Infection: Prevalence and Prognosis date: 2020-08-21 journal: J Clin Med DOI: 10.3390/jcm9092712 sha: doc_id: 273351 cord_uid: vq3budip file: cache/cord-273604-0w5shxmf.json key: cord-273604-0w5shxmf authors: Psevdos, George; Papamanoli, Aikaterini; Barrett, Nancy; Bailey, Lisa; Thorne, Monique; Ford, Florence; Lobo, Zeena title: Halting a SARS-CoV-2 Outbreak in a U.S. Veterans Affairs Nursing Home date: 2020-11-03 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.10.022 sha: doc_id: 273604 cord_uid: 0w5shxmf file: cache/cord-272759-dqkjofw2.json key: cord-272759-dqkjofw2 authors: Small, Michael; Tse, C.K.; Walker, David M. title: Super-spreaders and the rate of transmission of the SARS virus date: 2006-03-15 journal: Physica D DOI: 10.1016/j.physd.2006.01.021 sha: doc_id: 272759 cord_uid: dqkjofw2 file: cache/cord-273064-c58nf9vb.json key: cord-273064-c58nf9vb authors: Hallowell, Benjamin D.; Carlson, Christina M.; Jacobs, Jesica R.; Pomeroy, Mary; Steinberg, Jonathan; Tenforde, Mark W.; McDonald, Emily; Foster, Loretta; Feldstein, Leora R.; Rolfes, Melissa A.; Haynes, Amber; Abedi, Glen R.; Odongo, George S.; Saruwatari, Kim; Rider, Errin C.; Douville, Gina; Bhakta, Neenaben; Maniatis, Panagiotis; Lindstrom, Stephen; Thornburg, Natalie J.; Lu, Xiaoyan; Whitaker, Brett L.; Kamili, Shifaq; Sakthivel, Senthilkumar K.; Wang, Lijuan; Malapati, Lakshmi; Murray, Janna R.; Lynch, Brian; Cetron, Martin; Brown, Clive; Roohi, Shahrokh; Rotz, Lisa; Borntrager, Denise; Ishii, Kenta; Moser, Kathleen; Rasheed, Mohammad; Freeman, Brandi; Lester, Sandra; Corbett, Kizzmekia S.; Abiona, Olubukola M.; Hutchinson, Geoffrey B.; Graham, Barney S.; Pesik, Nicki; Mahon, Barbara; Braden, Christopher; Behravesh, Casey Barton; Stewart, Rebekah; Knight, Nancy; Hall, Aron J.; Killerby, Marie E. title: Severe Acute Respiratory Syndrome Coronavirus 2 Prevalence, Seroprevalence, and Exposure among Evacuees from Wuhan, China, 2020 date: 2020-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid2609.201590 sha: doc_id: 273064 cord_uid: c58nf9vb file: cache/cord-272702-7uc4ozjy.json key: cord-272702-7uc4ozjy authors: Graham, T. 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A.; Darzacq, X.; Tjian, R. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.16.20193466 sha: doc_id: 272702 cord_uid: 7uc4ozjy file: cache/cord-273505-pcsw3vmx.json key: cord-273505-pcsw3vmx authors: Liu, Xiaosheng; Cao, Wei; Li, Taisheng title: High-Dose Intravenous Immunoglobulins in the Treatment of Severe Acute Viral Pneumonia: The Known Mechanisms and Clinical Effects date: 2020-07-14 journal: Front Immunol DOI: 10.3389/fimmu.2020.01660 sha: doc_id: 273505 cord_uid: pcsw3vmx file: cache/cord-273182-djb0ozrt.json key: cord-273182-djb0ozrt authors: Díez, José María; Romero, Carolina; Vergara-Alert, Júlia; Belló-Perez, Melissa; Rodon, Jordi; Honrubia, José Manuel; Segalés, Joaquim; Sola, Isabel; Enjuanes, Luis; Gajardo, Rodrigo title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-09-09 journal: Immunotherapy DOI: 10.2217/imt-2020-0220 sha: doc_id: 273182 cord_uid: djb0ozrt file: cache/cord-272566-rtnhndw3.json key: cord-272566-rtnhndw3 authors: Robertson, M.; Kulkarni, S.; Berry, A.; Mirzayi, C.; Maroko, A. R.; Zimba, R.; Westmoreland, D.; Grov, C.; Parcesepe, A.; Waldron, L.; Nash, D. title: A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort date: 2020-05-04 journal: nan DOI: 10.1101/2020.04.28.20080630 sha: doc_id: 272566 cord_uid: rtnhndw3 file: cache/cord-272603-nbosceoz.json key: cord-272603-nbosceoz authors: Lin, Qiuyuan; Wen, Donghua; Wu, Jing; Liu, Liling; Wu, Wenjuan; Fang, Xueen; Kong, Jilie title: Microfluidic Immunoassays for Sensitive and Simultaneous Detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min date: 2020-07-02 journal: Anal Chem DOI: 10.1021/acs.analchem.0c01635 sha: doc_id: 272603 cord_uid: nbosceoz file: cache/cord-273114-eanwxkvt.json key: cord-273114-eanwxkvt authors: Perrone, Serafina; Deolmi, Michela; Giordano, Maurizio; D’Alvano, Tiziana; Gambini, Lucia; Corradi, Mara; Frusca, Tiziana; Ghi, Tullio; Esposito, Susanna title: Report of a series of healthy term newborns from convalescent mothers with COVID-19 date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9743 sha: doc_id: 273114 cord_uid: eanwxkvt file: cache/cord-273251-k3ltbpnb.json key: cord-273251-k3ltbpnb authors: Phipps, Meaghan M.; Barraza, Luis H.; LaSota, Elijah D.; Sobieszczyk, Magdalena E.; Pereira, Marcus R.; Zheng, Elizabeth X.; Fox, Alyson N.; Zucker, Jason; Verna, Elizabeth C. title: Acute Liver Injury in COVID‐19: Prevalence and Association with Clinical Outcomes in a Large US Cohort date: 2020-05-30 journal: Hepatology DOI: 10.1002/hep.31404 sha: doc_id: 273251 cord_uid: k3ltbpnb file: cache/cord-273373-5elel6qo.json key: cord-273373-5elel6qo authors: Wang, Haofeng; Xue, Song; Yang, Haitao; Chen, Cheng title: Recent progress in the discovery of inhibitors targeting coronavirus proteases date: 2016-02-19 journal: Virol Sin DOI: 10.1007/s12250-015-3711-3 sha: doc_id: 273373 cord_uid: 5elel6qo file: cache/cord-273645-czh3zfb3.json key: cord-273645-czh3zfb3 authors: Lu, Shuaiyao; Zhao, Yuan; Yu, Wenhai; Yang, Yun; Gao, Jiahong; Wang, Junbin; Kuang, Dexuan; Yang, Mengli; Yang, Jing; Ma, Chunxia; Xu, Jingwen; Qian, Xingli; Li, Haiyan; Zhao, Siwen; Li, Jingmei; Wang, Haixuan; Long, Haiting; Zhou, Jingxian; Luo, Fangyu; Ding, Kaiyun; Wu, Daoju; Zhang, Yong; Dong, Yinliang; Liu, Yuqin; Zheng, Yingqiu; Lin, Xiaochen; Jiao, Li; Zheng, Huanying; Dai, Qing; Sun, Qiangmin; Hu, Yunzhang; Ke, Changwen; Liu, Hongqi; Peng, Xiaozhong title: Comparison of SARS-CoV-2 infections among 3 species of non-human primates date: 2020-07-17 journal: bioRxiv DOI: 10.1101/2020.04.08.031807 sha: doc_id: 273645 cord_uid: czh3zfb3 file: cache/cord-273685-oxvfxmtr.json key: cord-273685-oxvfxmtr authors: Fan, Qihong; Pan, Yan; Wu, Qingcui; Liu, Shan; Song, Xu; Xie, Zhongguo; Liu, Yang; Zhao, Liang; Wang, Zhonghong; Zhang, Yifei; Wu, Zuchuang; Guan, Lei; Lv, Xiaolong title: Anal swab findings in an infant with COVID‐19 date: 2020-03-17 journal: Pediatr Investig DOI: 10.1002/ped4.12186 sha: doc_id: 273685 cord_uid: oxvfxmtr file: cache/cord-273492-i483r91m.json key: cord-273492-i483r91m authors: Fulzele, Sadanand; Sahay, Bikash; Yusufu, Ibrahim; Lee, Tae Jin; Sharma, Ashok; Kolhe, Ravindra; Isales, Carlos M title: COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile date: 2020-05-09 journal: Aging Dis DOI: 10.14336/ad.2020.0428 sha: doc_id: 273492 cord_uid: i483r91m file: cache/cord-273553-xp4nfnq3.json key: cord-273553-xp4nfnq3 authors: Ramatillah, D. L.; Isnaini, S. title: TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA date: 2020-10-16 journal: nan DOI: 10.1101/2020.10.14.20212449 sha: doc_id: 273553 cord_uid: xp4nfnq3 file: cache/cord-273613-cpiveo7j.json key: cord-273613-cpiveo7j authors: Cao, Xia; Maruyama, Junki; Zhou, Heyue; Kerwin, Lisa; Sattler, Rachel; Manning, John T.; Johnson, Sachi; Richards, Susan; Li, Yan; Shen, Weiqun; Blair, Benjamin; Du, Na; Morais, Kyndal; Lawrence, Kate; Lu, Lucy; Pai, Chin-I; Li, Donghui; Brunswick, Mark; Zhang, Yanliang; Ji, Henry; Paessler, Slobodan; Allen, Robert D. title: Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date: 2020-09-29 journal: bioRxiv DOI: 10.1101/2020.09.27.316174 sha: doc_id: 273613 cord_uid: cpiveo7j file: cache/cord-273614-qmp2tqtb.json key: cord-273614-qmp2tqtb authors: Tahir, Faryal; Bin Arif, Taha; Ahmed, Jawad; Malik, Farheen; Khalid, Muhammad title: Cardiac Manifestations of Coronavirus Disease 2019 (COVID-19): A Comprehensive Review date: 2020-05-08 journal: Cureus DOI: 10.7759/cureus.8021 sha: doc_id: 273614 cord_uid: qmp2tqtb file: cache/cord-273764-itu39mln.json key: cord-273764-itu39mln authors: Li, Taisheng; Xie, Jing; He, Yuxian; Fan, Hongwei; Baril, Laurence; Qiu, Zhifeng; Han, Yang; Xu, Wenbing; Zhang, Weihong; You, Hui; Zuo, Yanling; Fang, Qing; Yu, Jian; Chen, Zhiwei; Zhang, Linqi title: Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date: 2006-12-20 journal: PLoS One DOI: 10.1371/journal.pone.0000024 sha: doc_id: 273764 cord_uid: itu39mln file: cache/cord-273126-gceffbfp.json key: cord-273126-gceffbfp authors: Yuan, Kehu; Yi, Ling; Chen, Jian; Qu, Xiuxia; Qing, Tingting; Rao, Xi; Jiang, Pengfei; Hu, Jianhe; Xiong, Zikai; Nie, Yuchun; Shi, Xuanling; Wang, Wei; Ling, Chen; Yin, Xiaolei; Fan, Keqiang; Lai, Luhua; Ding, Mingxiao; Deng, Hongkui title: Suppression of SARS-CoV entry by peptides corresponding to heptad regions on spike glycoprotein date: 2004-07-02 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2004.05.046 sha: doc_id: 273126 cord_uid: gceffbfp file: cache/cord-273859-tr4s5i7h.json key: cord-273859-tr4s5i7h authors: Luis García Garmendia, José; Almodóvar, Ana Esmeralda Barrero; Amigo, Víctor Jorge; Arcos, Mercedes Ramírez; Caballero, Mónica Chávez; Martino, María del Carmen Serrano title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 journal: Med Intensiva DOI: 10.1016/j.medin.2020.04.014 sha: doc_id: 273859 cord_uid: tr4s5i7h file: cache/cord-273349-penb65x7.json key: cord-273349-penb65x7 authors: Zhang, Chao; Shi, Lei; Wang, Fu-Sheng title: Liver injury in COVID-19: management and challenges date: 2020-05-31 journal: The Lancet Gastroenterology & Hepatology DOI: 10.1016/s2468-1253(20)30057-1 sha: doc_id: 273349 cord_uid: penb65x7 file: cache/cord-272956-0yumc7em.json key: cord-272956-0yumc7em authors: Gnavi, Roberto; Demaria, Moreno; Picariello, Roberta; Dalmasso, Marco; Ricceri, Fulvio; Costa, Giuseppe title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa634 sha: doc_id: 272956 cord_uid: 0yumc7em file: cache/cord-273426-55vu6b3u.json key: cord-273426-55vu6b3u authors: Iba, Toshiaki; Levy, Jerrold H.; Levi, Marcel; Connors, Jean Marie; Thachil, Jecko title: Coagulopathy of Coronavirus Disease 2019 date: 2020-05-26 journal: Crit Care Med DOI: 10.1097/ccm.0000000000004458 sha: doc_id: 273426 cord_uid: 55vu6b3u file: cache/cord-273675-0oiq44gl.json key: cord-273675-0oiq44gl authors: Wu, Di; Lu, Jianyun; Liu, Qun; Ma, Xiaowei; He, Weiyun title: To alert coinfection of COVID-19 and dengue virus in developing countries in the dengue-endemic area date: 2020-05-04 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.187 sha: doc_id: 273675 cord_uid: 0oiq44gl file: cache/cord-273751-61eeykj1.json key: cord-273751-61eeykj1 authors: Yang, Zhenwei; Liu, Jialong; Zhou, Yunjiao; Zhao, Xixian; Zhao, Qiu; Liu, Jing title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis date: 2020-04-10 journal: J Infect DOI: 10.1016/j.jinf.2020.03.062 sha: doc_id: 273751 cord_uid: 61eeykj1 file: cache/cord-273913-xem3alih.json key: cord-273913-xem3alih authors: Marraha, Farah; Al Faker, Ibtissam; Gallouj, Salim title: A Review of the Dermatological Manifestations of Coronavirus Disease 2019 (COVID-19) date: 2020-08-11 journal: Dermatol Res Pract DOI: 10.1155/2020/9360476 sha: doc_id: 273913 cord_uid: xem3alih file: cache/cord-273083-xrydkiu4.json key: cord-273083-xrydkiu4 authors: Pahmeier, Felix; Neufeldt, Christoper J; Cerikan, Berati; Prasad, Vibhu; Pape, Costantin; Laketa, Vibor; Ruggieri, Alessia; Bartenschlager, Ralf; Cortese, Mirko title: A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date: 2020-09-01 journal: bioRxiv DOI: 10.1101/2020.08.31.276683 sha: doc_id: 273083 cord_uid: xrydkiu4 file: cache/cord-273408-jtpaue0z.json key: cord-273408-jtpaue0z authors: Romeyke, Tobias; Noehammer, Elisabeth; Stummer, Harald title: COVID-19 Case Report: An 84-Year-Old Man with Exacerbation of Multiple Comorbidities Due to COVID-19 Managed by a Multidisciplinary Team Using Patient-Reported Outcomes date: 2020-08-21 journal: Am J Case Rep DOI: 10.12659/ajcr.926694 sha: doc_id: 273408 cord_uid: jtpaue0z file: cache/cord-273311-dl9u85nh.json key: cord-273311-dl9u85nh authors: Boscolo‐Rizzo, Paolo; Borsetto, Daniele; Hopkins, Claire; Polesel, Jerry title: Challenges in interpreting the diagnostic performance of symptoms to predict COVID‐19 status: the case of anosmia date: 2020-06-25 journal: Int Forum Allergy Rhinol DOI: 10.1002/alr.22650 sha: doc_id: 273311 cord_uid: dl9u85nh file: cache/cord-273382-7w8fli6w.json key: cord-273382-7w8fli6w authors: Guderian, Daniela B.; Loth, Andreas G.; Weiß, Roxanne; Diensthuber, Marc; Stöver, Timo; Leinung, Martin title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling date: 2020-09-07 journal: Eur Arch Otorhinolaryngol DOI: 10.1007/s00405-020-06330-y sha: doc_id: 273382 cord_uid: 7w8fli6w file: cache/cord-273784-sr6afv60.json key: cord-273784-sr6afv60 authors: Cazares, Lisa H.; Chaerkady, Raghothama; Samuel Weng, Shao Huan; Boo, Chelsea C.; Cimbro, Raffaello; Hsu, Hsiang-En; Rajan, Sarav; Dall’Acqua, William; Clarke, Lori; Ren, Kuishu; McTamney, Patrick; Kallewaard-LeLay, Nicole; Ghaedi, Mahboobe; Ikeda, Yasuhiro; Hess, Sonja title: Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein date: 2020-09-23 journal: Anal Chem DOI: 10.1021/acs.analchem.0c02288 sha: doc_id: 273784 cord_uid: sr6afv60 file: cache/cord-273882-tqdcb3oo.json key: cord-273882-tqdcb3oo authors: Pratibha,; Shaju, C.; Kamal, title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date: 2020-08-21 journal: bioRxiv DOI: 10.1101/2020.08.21.261289 sha: doc_id: 273882 cord_uid: tqdcb3oo file: cache/cord-273726-24mi50rv.json key: cord-273726-24mi50rv authors: Aaroe, Ashley; Majd, Nazanin; Weathers, Shiao-Pei; de Groot, John title: Potential Neurologic and Oncologic Implications of the Novel Coronavirus date: 2020-04-16 journal: Neuro Oncol DOI: 10.1093/neuonc/noaa096 sha: doc_id: 273726 cord_uid: 24mi50rv file: cache/cord-273891-7w334xgt.json key: cord-273891-7w334xgt authors: Kirchdoerfer, Robert N.; Wang, Nianshuang; Pallesen, Jesper; Wrapp, Daniel; Turner, Hannah L.; Cottrell, Christopher A.; Corbett, Kizzmekia S.; Graham, Barney S.; McLellan, Jason S.; Ward, Andrew B. title: Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date: 2018-03-31 journal: bioRxiv DOI: 10.1101/292672 sha: doc_id: 273891 cord_uid: 7w334xgt file: cache/cord-273893-3nd6ptrg.json key: cord-273893-3nd6ptrg authors: Lu, Guangwen; Hu, Yawei; Wang, Qihui; Qi, Jianxun; Gao, Feng; Li, Yan; Zhang, Yanfang; Zhang, Wei; Yuan, Yuan; Bao, Jinku; Zhang, Buchang; Shi, Yi; Yan, Jinghua; Gao, George F. title: Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 date: 2013-07-07 journal: Nature DOI: 10.1038/nature12328 sha: doc_id: 273893 cord_uid: 3nd6ptrg file: cache/cord-274028-dvsvtsn0.json key: cord-274028-dvsvtsn0 authors: Del Brutto, Oscar H.; Costa, Aldo F.; Mera, Robertino M.; Recalde, Bettsy Y.; Bustos, Javier A.; García, Héctor H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.003 sha: doc_id: 274028 cord_uid: dvsvtsn0 file: cache/cord-273828-557vlq9d.json key: cord-273828-557vlq9d authors: Brito, Carlos Antunes; Barros, Fabio Marinho; Lopes, Edmundo Pessoa title: Mechanisms and consequences of COVID-19 associated liver injury: What can we affirm? date: 2020-08-27 journal: World J Hepatol DOI: 10.4254/wjh.v12.i8.413 sha: doc_id: 273828 cord_uid: 557vlq9d file: cache/cord-273723-srfypn7j.json key: cord-273723-srfypn7j authors: Omar, Sarah; Bartz, Christoph; Becker, Sabine; Basenach, Silke; Pfeifer, Sandra; Trapp, Corinna; Hamm, Hildegard; Schlichting, Hans Christoph; Friederichs, Magdalena; Koch, Ulrich; Jestrabek, Christian; Hilger, Ernst; Vogt, Manfred; Jahn, Klaus; Chen, Simiao; Bärnighausen, Till; Zanger, Philipp title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.30.2001292 sha: doc_id: 273723 cord_uid: srfypn7j file: cache/cord-273906-s7l0yxc0.json key: cord-273906-s7l0yxc0 authors: Ranga, Vipin; Niemelä, Erik; Tamirat, Mahlet Z.; Eriksson, John E.; Airenne, Tomi T.; Johnson, Mark S. title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 journal: Vaccines (Basel) DOI: 10.3390/vaccines8030408 sha: doc_id: 273906 cord_uid: s7l0yxc0 file: cache/cord-274007-zndtddty.json key: cord-274007-zndtddty authors: Rasmussen, Sonja A.; Smulian, John C.; Lednicky, John A.; Wen, Tony S.; Jamieson, Denise J. title: Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date: 2020-02-24 journal: Am J Obstet Gynecol DOI: 10.1016/j.ajog.2020.02.017 sha: doc_id: 274007 cord_uid: zndtddty file: cache/cord-274008-p3st70u3.json key: cord-274008-p3st70u3 authors: Mann, E. R.; Menon, M.; Knight, S. B.; Konkel, J. E.; Jagger, C.; Shaw, T. N.; Krishnan, S.; Rattray, M.; Ustianowski, A.; Bakerly, N. D.; Dark, P.; Lord, G.; Simpson, A.; Felton, T.; Ho, L.-P.; NIHR Respiratory TRC,; Feldmann, M.; CIRCO,; Grainger, J.; Hussell, T. title: Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis date: 2020-06-16 journal: nan DOI: 10.1101/2020.06.13.20127605 sha: doc_id: 274008 cord_uid: p3st70u3 file: cache/cord-274090-eab7i4f6.json key: cord-274090-eab7i4f6 authors: Gaspari, Valeria; Lanzoni, Anna; Patrizi, Annalisa; Orioni, Gionathan; Viviani, Filippo; Bardazzi, Federico title: Can Covid‐19 be a sexually transmitted disease? Posterity will judge date: 2020-05-24 journal: Dermatol Ther DOI: 10.1111/dth.13676 sha: doc_id: 274090 cord_uid: eab7i4f6 file: cache/cord-273918-knlc3bxh.json key: cord-273918-knlc3bxh authors: Holmes, Emily A; O'Connor, Rory C; Perry, V Hugh; Tracey, Irene; Wessely, Simon; Arseneault, Louise; Ballard, Clive; Christensen, Helen; Cohen Silver, Roxane; Everall, Ian; Ford, Tamsin; John, Ann; Kabir, Thomas; King, Kate; Madan, Ira; Michie, Susan; Przybylski, Andrew K; Shafran, Roz; Sweeney, Angela; Worthman, Carol M; Yardley, Lucy; Cowan, Katherine; Cope, Claire; Hotopf, Matthew; Bullmore, Ed title: Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science date: 2020-04-15 journal: Lancet Psychiatry DOI: 10.1016/s2215-0366(20)30168-1 sha: doc_id: 273918 cord_uid: knlc3bxh file: cache/cord-274053-406dfdih.json key: cord-274053-406dfdih authors: Srivastava, Kamna title: Association between COVID-19 and cardiovascular disease date: 2020-07-14 journal: Int J Cardiol Heart Vasc DOI: 10.1016/j.ijcha.2020.100583 sha: doc_id: 274053 cord_uid: 406dfdih file: cache/cord-274122-n9jnu2ah.json key: cord-274122-n9jnu2ah authors: Mielech, Anna M.; Kilianski, Andy; Baez-Santos, Yahira M.; Mesecar, Andrew D.; Baker, Susan C. title: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date: 2014-02-01 journal: Virology DOI: 10.1016/j.virol.2013.11.040 sha: doc_id: 274122 cord_uid: n9jnu2ah file: cache/cord-273961-ja8xggnd.json key: cord-273961-ja8xggnd authors: Nakagawara, Kensuke; Masaki, Katsunori; Uwamino, Yoshifumi; Kabata, Hiroki; Uchida, Sho; Uno, Shunsuke; Asakura, Takanori; Funakoshi, Takeru; Kanzaki, Sho; Ishii, Makoto; Hasegawa, Naoki; Fukunaga, Koichi title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date: 2020-07-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.034 sha: doc_id: 273961 cord_uid: ja8xggnd file: cache/cord-274459-781by93r.json key: cord-274459-781by93r authors: Khalifa, Shaden A. M.; Mohamed, Briksam S.; Elashal, Mohamed H.; Du, Ming; Guo, Zhiming; Zhao, Chao; Musharraf, Syed Ghulam; Boskabady, Mohammad H.; El-Seedi, Haged H. R.; Efferth, Thomas; El-Seedi, Hesham R. title: Comprehensive Overview on Multiple Strategies Fighting COVID-19 date: 2020-08-11 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165813 sha: doc_id: 274459 cord_uid: 781by93r file: cache/cord-273898-i7icvsg1.json key: cord-273898-i7icvsg1 authors: Parcell, B.; Brechin, K.; Allstaff, S.; Park, M.; Third, W.; Bean, S.; Hind, C.; Farmer, R.; Chalmers, J. D. title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland date: 2020-05-11 journal: nan DOI: 10.1101/2020.05.08.20078386 sha: doc_id: 273898 cord_uid: i7icvsg1 file: cache/cord-274141-vujx538o.json key: cord-274141-vujx538o authors: Chinsembu, Kazhila C. title: Coronaviruses and Nature’s Pharmacy for the Relief of Coronavirus Disease 2019 date: 2020-10-06 journal: Rev Bras Farmacogn DOI: 10.1007/s43450-020-00104-7 sha: doc_id: 274141 cord_uid: vujx538o file: cache/cord-274184-hm516x6p.json key: cord-274184-hm516x6p authors: Elli, Luca; Rimondi, Alessandro; Scaramella, Lucia; Topa, Matilde; Vecchi, Maurizio; Mangioni, Davide; Gori, Andrea; Penagini, Roberto title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 journal: Dig Liver Dis DOI: 10.1016/j.dld.2020.04.018 sha: doc_id: 274184 cord_uid: hm516x6p file: cache/cord-274097-11hvriqy.json key: cord-274097-11hvriqy authors: Katz, Louis M. title: Is SARS‐CoV‐2 transfusion transmitted? date: 2020-06-16 journal: Transfusion DOI: 10.1111/trf.15831 sha: doc_id: 274097 cord_uid: 11hvriqy file: cache/cord-274343-y9zqbefu.json key: cord-274343-y9zqbefu authors: Petersen, Irene; Phillips, Andrew title: Three Quarters of People with SARS-CoV-2 Infection are Asymptomatic: Analysis of English Household Survey Data date: 2020-10-08 journal: Clin Epidemiol DOI: 10.2147/clep.s276825 sha: doc_id: 274343 cord_uid: y9zqbefu file: cache/cord-274396-l611eisi.json key: cord-274396-l611eisi authors: Park, Su-Jin; Yu, Kwang-Min; Kim, Young-Il; Kim, Se-Mi; Kim, Eun-Ha; Kim, Seong-Gyu; Kim, Eun Ji; Casel, Mark Anthony B.; Rollon, Rare; Jang, Seung-Gyu; Lee, Min-Hyeok; Chang, Jae-Hyung; Song, Min-Suk; Jeong, Hye Won; Choi, Younho; Chen, Weiqiang; Shin, Woo-Jin; Jung, Jae U.; Choi, Young Ki title: Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets date: 2020-05-22 journal: mBio DOI: 10.1128/mbio.01114-20 sha: doc_id: 274396 cord_uid: l611eisi file: cache/cord-274114-fglyfz8p.json key: cord-274114-fglyfz8p authors: Minervina, Anastasia A.; Komech, Ekaterina A.; Titov, Aleksei; Koraichi, Meriem Bensouda; Rosati, Elisa; Mamedov, Ilgar Z.; Franke, Andre; Efimov, Grigory A.; Chudakov, Dmitriy M.; Mora, Thierry; Walczak, Aleksandra M.; Lebedev, Yuri B.; Pogorelyy, Mikhail V. title: Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date: 2020-10-01 journal: bioRxiv DOI: 10.1101/2020.05.18.100545 sha: doc_id: 274114 cord_uid: fglyfz8p file: cache/cord-274366-t138l6px.json key: cord-274366-t138l6px authors: Benetti, Elisa; Tita, Rossella; Spiga, Ottavia; Ciolfi, Andrea; Birolo, Giovanni; Bruselles, Alessandro; Doddato, Gabriella; Giliberti, Annarita; Marconi, Caterina; Musacchia, Francesco; Pippucci, Tommaso; Torella, Annalaura; Trezza, Alfonso; Valentino, Floriana; Baldassarri, Margherita; Brusco, Alfredo; Asselta, Rosanna; Bruttini, Mirella; Furini, Simone; Seri, Marco; Nigro, Vincenzo; Matullo, Giuseppe; Tartaglia, Marco; Mari, Francesca; Renieri, Alessandra; Pinto, Anna Maria title: ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date: 2020-07-17 journal: Eur J Hum Genet DOI: 10.1038/s41431-020-0691-z sha: doc_id: 274366 cord_uid: t138l6px file: cache/cord-274439-y9jrdg5n.json key: cord-274439-y9jrdg5n authors: Aoyama, Kazuyoshi; Heath, Anna; Yang, Alan; Maynes, Jason T.; Petroz, Guy; Robertson, James; Mc Donnell, Conor; Velummailum, Russanthy; Bond, Elizabeth; Pechlivanoglou, Petros title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model date: 2020-07-27 journal: Can J Anaesth DOI: 10.1007/s12630-020-01771-9 sha: doc_id: 274439 cord_uid: y9jrdg5n file: cache/cord-274286-07arhrv9.json key: cord-274286-07arhrv9 authors: Hosier, H.; Farhadian, S.; Morotti, R.; Deshmukh, U.; Lu-Culligans, A.; Campbell, K.; Yasumoto, Y.; Vogels, C.; Casanovas-Massana, A.; Vijayakumar, P.; Geng, B.; Odio, C.; Fournier, J.; Brito, A.; Fauver, J.; Liu, F.; Alpert, T.; Tal, R.; Szigeti-Buck, K.; Perincheri, S.; Larsen, C.; Gariepy, A.; Aguilar, G.; Fardelmann, K.; Harigopal, M.; Taylor, H.; Pettker, C.; Wyllie, A.; Dela Cruz, C.; Ring, A.; Grubaugh, N.; Ko, A.; Horvath, T.; Iwasaki, A.; Reddy, U.; Lipkind, H. title: First case of placental infection with SARS-CoV-2 date: 2020-05-05 journal: nan DOI: 10.1101/2020.04.30.20083907 sha: doc_id: 274286 cord_uid: 07arhrv9 file: cache/cord-274521-u8p5lz9o.json key: cord-274521-u8p5lz9o authors: Lee, Abby C.; Chakladar, Jaideep; Li, Wei Tse; Chen, Chengyu; Chang, Eric Y.; Wang-Rodriguez, Jessica; Ongkeko, Weg M. title: Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation date: 2020-07-31 journal: Int J Mol Sci DOI: 10.3390/ijms21155513 sha: doc_id: 274521 cord_uid: u8p5lz9o file: cache/cord-274680-6pui91uu.json key: cord-274680-6pui91uu authors: Gao, Chun; Zhu, Li; Jin, Cheng Cheng; Tong, Yi Xin; Xiao, Ai Tang; Zhang, Sheng title: Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date: 2020-10-14 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108611 sha: doc_id: 274680 cord_uid: 6pui91uu file: cache/cord-274156-c0c4rjfa.json key: cord-274156-c0c4rjfa authors: Chau, J.P.C.; Thompson, D. R.; Lee, D.T.F.; Twinn, S. title: Infection control practices among hospital health and support workers in Hong Kong date: 2010-08-31 journal: Journal of Hospital Infection DOI: 10.1016/j.jhin.2009.10.014 sha: doc_id: 274156 cord_uid: c0c4rjfa file: cache/cord-274231-2s7ki6g7.json key: cord-274231-2s7ki6g7 authors: Ziebuhr, John title: SARS – Unprecedented global response to a newly emerging disease date: 2003-12-31 journal: International Journal of Medical Microbiology DOI: 10.1078/1438-4221-00270 sha: doc_id: 274231 cord_uid: 2s7ki6g7 file: cache/cord-274409-4ugdxbmy.json key: cord-274409-4ugdxbmy authors: Laskar, Rezwanuzzaman; Ali, Safdar title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date: 2020-10-19 journal: bioRxiv DOI: 10.1101/2020.10.19.345066 sha: doc_id: 274409 cord_uid: 4ugdxbmy file: cache/cord-274508-nigru1o8.json key: cord-274508-nigru1o8 authors: Lally, Michelle; Tsoukas, Philip; Halladay, Christopher; O’Neill, Emily; Gravenstein, Stefan; Rudolph, James L. title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 date: 2020-10-26 journal: J Am Med Dir Assoc DOI: 10.1016/j.jamda.2020.10.031 sha: doc_id: 274508 cord_uid: nigru1o8 file: cache/cord-274513-0biyfhab.json key: cord-274513-0biyfhab authors: Baumgartner, M. T.; Lansac-Toha, F. M. title: Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19 date: 2020-07-22 journal: nan DOI: 10.1101/2020.07.20.20158576 sha: doc_id: 274513 cord_uid: 0biyfhab file: cache/cord-274205-e2r38v29.json key: cord-274205-e2r38v29 authors: Tsunetsugu-Yokota, Yasuko title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen date: 2007-11-28 journal: SARS- and Other Coronaviruses DOI: 10.1007/978-1-59745-181-9_11 sha: doc_id: 274205 cord_uid: e2r38v29 file: cache/cord-274280-x5s4l0pp.json key: cord-274280-x5s4l0pp authors: Yang, Jinsung; Petitjean, Simon J. L.; Koehler, Melanie; Zhang, Qingrong; Dumitru, Andra C.; Chen, Wenzhang; Derclaye, Sylvie; Vincent, Stéphane P.; Soumillion, Patrice; Alsteens, David title: Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor date: 2020-09-11 journal: Nat Commun DOI: 10.1038/s41467-020-18319-6 sha: doc_id: 274280 cord_uid: x5s4l0pp file: cache/cord-274341-vrwmxwvm.json key: cord-274341-vrwmxwvm authors: Frank, Carlos Henrique Michiles; Almeida, Taynná Vernalha Rocha; Marques, Elyana Almeida; de Sousa Monteiro, Quezia; Feitoza, Pablo Vinícius Silveira; Borba, Mayla Gabriela Silva; Vasconcelos, Heline Lira; de Souza Bastos, Michele; Lacerda, Marcus Vinicius Guimarães title: Guillain–Barré Syndrome Associated with SARS-CoV-2 Infection in a Pediatric Patient date: 2020-07-12 journal: J Trop Pediatr DOI: 10.1093/tropej/fmaa044 sha: doc_id: 274341 cord_uid: vrwmxwvm file: cache/cord-274399-cd7cmpoj.json key: cord-274399-cd7cmpoj authors: Barzin, Amir; Schmitz, John L.; Rosin, Samuel; Sirpal, Rameet; Almond, Martha; Robinette, Carole; Wells, Samantha; Hudgens, Michael; Olshan, Andrew; Deen, Stephanie; Krejci, Patrick; Quackenbush, Eugenia; Chronowski, Kevin; Cornaby, Caleb; Goins, Janette; Butler, Linda; Aucoin, Julia; Boyer, Kim; Faulk, Janet; Alston-Johnson, Devena; Page, Cristen; Zhou, Yijun; Fiscus, Lynne; Damania, Blossom; Dittmer, Dirk P.; Peden, David B. title: SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures date: 2020-09-29 journal: mBio DOI: 10.1128/mbio.02426-20 sha: doc_id: 274399 cord_uid: cd7cmpoj file: cache/cord-274326-msbdrp3e.json key: cord-274326-msbdrp3e authors: Ren, Xiaohan; Wang, Shangqian; Chen, Xinglin; Wei, Xiyi; Li, Guangyao; Ren, Shancheng; Zhang, Tongtong; Zhang, Xu; Lu, Zhongwen; You, Zebing; Wang, Zengjun; Song, Ninghong; Qin, Chao title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 date: 2020-11-04 journal: Infect Drug Resist DOI: 10.2147/idr.s270543 sha: doc_id: 274326 cord_uid: msbdrp3e file: cache/cord-274252-h4occy7h.json key: cord-274252-h4occy7h authors: de Lima Menezes, Gabriela; da Silva, Roosevelt Alves title: Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) date: 2020-07-13 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1792992 sha: doc_id: 274252 cord_uid: h4occy7h file: cache/cord-274279-f99nd3dx.json key: cord-274279-f99nd3dx authors: Fantini, Jacques; Di Scala, Coralie; Chahinian, Henri; Yahi, Nouara title: Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection date: 2020-04-03 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.105960 sha: doc_id: 274279 cord_uid: f99nd3dx file: cache/cord-274313-mrvk9r4w.json key: cord-274313-mrvk9r4w authors: Li, Hui; Liu, Liang; Zhang, Dingyu; Xu, Jiuyang; Dai, Huaping; Tang, Nan; Su, Xiao; Cao, Bin title: SARS-CoV-2 and viral sepsis: observations and hypotheses date: 2020-04-17 journal: Lancet DOI: 10.1016/s0140-6736(20)30920-x sha: doc_id: 274313 cord_uid: mrvk9r4w file: cache/cord-274648-e0daf8w6.json key: cord-274648-e0daf8w6 authors: Madeddu, Paolo title: Cardiovascular complications of COVID-19: evidence, misconceptions, and new opportunities date: 2020-06-08 journal: Vasc Biol DOI: 10.1530/vb-20-0008 sha: doc_id: 274648 cord_uid: e0daf8w6 file: cache/cord-274474-u2fdicgz.json key: cord-274474-u2fdicgz authors: Majumder, Joydeb; Minko, Tamara title: Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus date: 2020-10-13 journal: Adv Ther (Weinh) DOI: 10.1002/adtp.202000203 sha: doc_id: 274474 cord_uid: u2fdicgz file: cache/cord-274708-w6gmscv4.json key: cord-274708-w6gmscv4 authors: Mathewson, Alison C.; Bishop, Alexandra; Yao, Yongxiu; Kemp, Fred; Ren, Junyuan; Chen, Hongying; Xu, Xiaodong; Berkhout, Ben; van der Hoek, Lia; Jones, Ian M. title: Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 date: 2008-11-17 journal: J Gen Virol DOI: 10.1099/vir.0.2008/003962-0 sha: doc_id: 274708 cord_uid: w6gmscv4 file: cache/cord-274284-mi4n7xty.json key: cord-274284-mi4n7xty authors: Pang, Khang Wen; Chee, Jeremy; Subramaniam, Somasundaram; Ng, Chew Lip title: Frequency and Clinical Utility of Olfactory Dysfunction in COVID-19: a Systematic Review and Meta-analysis date: 2020-10-13 journal: Curr Allergy Asthma Rep DOI: 10.1007/s11882-020-00972-y sha: doc_id: 274284 cord_uid: mi4n7xty file: cache/cord-274416-bmvazgj7.json key: cord-274416-bmvazgj7 authors: Trevisanuto, Daniele; Moschino, Laura; Doglioni, Nicoletta; Roehr, Charles Christoph; Gervasi, Maria Teresa; Baraldi, Eugenio title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan date: 2020-04-24 journal: Neonatology DOI: 10.1159/000507935 sha: doc_id: 274416 cord_uid: bmvazgj7 file: cache/cord-274536-fv7mltj7.json key: cord-274536-fv7mltj7 authors: Tong, Yongqing; Bao, Anyu; Chen, Hongbing; Huang, Jingtao; Lv, Zhihua; Feng, Lina; Cheng, Yun; Wang, Youna; Bai, Li; Rao, Wenlong; Zheng, Hongyun; Wu, Zegang; Qiao, Bin; Zhao, Zhijun; Wang, Huiming; Li, Yan title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 journal: J Transl Med DOI: 10.1186/s12967-020-02580-w sha: doc_id: 274536 cord_uid: fv7mltj7 file: cache/cord-274707-mxh38hwd.json key: cord-274707-mxh38hwd authors: Laureano, Ana Flávia Santarine; Riboldi, Márcia title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 journal: JBRA Assist Reprod DOI: 10.5935/1518-0557.20200046 sha: doc_id: 274707 cord_uid: mxh38hwd file: cache/cord-274510-fo7p98np.json key: cord-274510-fo7p98np authors: Spadera, Lucrezia; Spadera, Maria title: Potential Role of GcMAF in suppressing the severity of COVID-19-induced immune responses: lesson learned from HIV date: 2020-09-24 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110293 sha: doc_id: 274510 cord_uid: fo7p98np file: cache/cord-274520-c674wkmt.json key: cord-274520-c674wkmt authors: Moelling, Karin; Broecker, Felix title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection date: 2020-05-28 journal: J Environ Public Health DOI: 10.1155/2020/1646943 sha: doc_id: 274520 cord_uid: c674wkmt file: cache/cord-274602-q9i2k304.json key: cord-274602-q9i2k304 authors: Iqbal, Yousaf; Al Abdulla, Majid Ali; Albrahim, Sultan; Latoo, Javed; Kumar, Rajeev; Haddad, Peter M. title: Psychiatric presentation of patients with acute SARS-CoV-2 infection: a retrospective review of 50 consecutive patients seen by a consultation-liaison psychiatry team date: 2020-09-10 journal: BJPsych Open DOI: 10.1192/bjo.2020.85 sha: doc_id: 274602 cord_uid: q9i2k304 file: cache/cord-274945-6p5de7o2.json key: cord-274945-6p5de7o2 authors: Clevers, Hans title: COVID-19: organoids go viral date: 2020-06-01 journal: Nat Rev Mol Cell Biol DOI: 10.1038/s41580-020-0258-4 sha: doc_id: 274945 cord_uid: 6p5de7o2 file: cache/cord-274542-fpzk5k79.json key: cord-274542-fpzk5k79 authors: Patti, Giuseppe; Lio, Veronica; Cavallari, Ilaria; Gragnano, Felice; Riva, Letizia; Calabrò, Paolo; Di Pasquale, Giuseppe; Pengo, Vittorio; Rubboli, Andrea title: Questions and Answers on Practical Thrombotic Issues in SARS-CoV-2 Infection: A Guidance Document from the Italian Working Group on Atherosclerosis, Thrombosis and Vascular Biology date: 2020-11-03 journal: Am J Cardiovasc Drugs DOI: 10.1007/s40256-020-00446-6 sha: doc_id: 274542 cord_uid: fpzk5k79 file: cache/cord-274834-24v2b509.json key: cord-274834-24v2b509 authors: Lima, Rosiane; Gootkind, Elizabeth F.; De la Flor, Denis; Yockey, Laura J.; Bordt, Evan A.; D’Avino, Paolo; Ning, Shen; Heath, Katerina; Harding, Katherine; Zois, Jaclyn; Park, Grace; Hardcastle, Margot; Grinke, Kathleen A.; Grimmel, Sheila; Davidson, Susan P.; Forde, Pamela J.; Hall, Kathryn E.; Neilan, Anne M.; Matute, Juan D.; Lerou, Paul H.; Fasano, Alessio; Shui, Jessica E.; Edlow, Andrea G.; Yonker, Lael M. title: Establishment of a pediatric COVID-19 biorepository: unique considerations and opportunities for studying the impact of the COVID-19 pandemic on children date: 2020-09-11 journal: BMC Med Res Methodol DOI: 10.1186/s12874-020-01110-y sha: doc_id: 274834 cord_uid: 24v2b509 file: cache/cord-274591-p34kk4up.json key: cord-274591-p34kk4up authors: Horby, Peter W,; Pfeiffer, Dirk; Oshitani, Hitoshi title: Prospects for Emerging Infections in East and Southeast Asia 10 Years after Severe Acute Respiratory Syndrome date: 2013-06-17 journal: Emerg Infect Dis DOI: 10.3201/eid1906.121783 sha: doc_id: 274591 cord_uid: p34kk4up file: cache/cord-274668-lh7c9izt.json key: cord-274668-lh7c9izt authors: Wang, Chaofu; Xie, Jing; Zhao, Lei; Fei, Xiaochun; Zhang, Heng; Tan, Yun; Nie, Xiu; Zhou, Luting; Liu, Zhenhua; Ren, Yong; Yuan, Ling; Zhang, Yu; Zhang, Jinsheng; Liang, Liwei; Chen, Xinwei; Liu, Xin; Wang, Peng; Han, Xiao; Weng, Xiangqin; Chen, Ying; Yu, Ting; Zhang, Xinxin; Cai, Jun; Chen, Rong; Shi, Zhengli; Bian, Xiuwu title: Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients date: 2020-06-20 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102833 sha: doc_id: 274668 cord_uid: lh7c9izt file: cache/cord-275111-38hgg0jz.json key: cord-275111-38hgg0jz authors: Kumar, Abhishek; Kumar, Piyush; Dungdung, Ajit; Kumar Gupta, Anitesh; Anurag, Aditya; Kumar, Abhinav title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients date: 2020-10-06 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.10.001 sha: doc_id: 275111 cord_uid: 38hgg0jz file: cache/cord-274528-mr81o9cu.json key: cord-274528-mr81o9cu authors: Li, Fei; Han, Ming; Dai, Pengfei; Xu, Wei; He, Juan; Tao, Xiaoting; Wu, Yang; Tong, Xinyuan; Xia, Xinyi; Guo, Wangxin; Zhou, Yunjiao; Li, Yunguang; Zhu, Yiqin; Zhang, Xiaoyu; Liu, Zhuang; Aji, Rebiguli; Cai, Xia; Li, Yutang; Qu, Di; Chen, Yu; Jiang, Shibo; Wang, Qiao; Ji, Hongbin; Xie, Youhua; Sun, Yihua; Lu, Lu; Gao, Dong title: Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date: 2020-09-12 journal: bioRxiv DOI: 10.1101/2020.09.11.293035 sha: doc_id: 274528 cord_uid: mr81o9cu file: cache/cord-275128-620wf0pb.json key: cord-275128-620wf0pb authors: White, J. R.; Foote, M. B.; Jee, J.; Argiles, G.; Wan, J. C. M.; Diaz, L. A. title: PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection date: 2020-09-03 journal: nan DOI: 10.1101/2020.09.02.20186783 sha: doc_id: 275128 cord_uid: 620wf0pb file: cache/cord-274841-rcdoewwv.json key: cord-274841-rcdoewwv authors: Tay, Matthew Zirui; Poh, Chek Meng; Rénia, Laurent; MacAry, Paul A.; Ng, Lisa F. P. title: The trinity of COVID-19: immunity, inflammation and intervention date: 2020-04-28 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0311-8 sha: doc_id: 274841 cord_uid: rcdoewwv file: cache/cord-275360-uphdzj5l.json key: cord-275360-uphdzj5l authors: Sahajpal, Nikhil Shri; Mondal, Ashis K.; Njau, Allan; Ananth, Sudha; Jones, Kimya; Ahluwalia, Pankaj K.; Ahluwalia, Meenakshi; Jilani, Yasmeen; Chaubey, Alka; Hegde, Madhuri; Kota, Vamsi; Rojiani, Amyn; Kolhe, Ravindra title: Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date: 2020-07-30 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2020.07.001 sha: doc_id: 275360 cord_uid: uphdzj5l file: cache/cord-274715-dcs1rgd0.json key: cord-274715-dcs1rgd0 authors: Mani Mishra, Pushpendra; Uversky, Vladimir N.; Nandi, Chayan K. title: Serum albumin-mediated strategy for the effective targeting of SARS-CoV-2 date: 2020-04-24 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109790 sha: doc_id: 274715 cord_uid: dcs1rgd0 file: cache/cord-275023-0z219rcy.json key: cord-275023-0z219rcy authors: Cerofolini, Linda; Fragai, Marco; Luchinat, Claudio; Ravera, Enrico title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date: 2020-07-29 journal: Biophys Chem DOI: 10.1016/j.bpc.2020.106441 sha: doc_id: 275023 cord_uid: 0z219rcy file: cache/cord-274750-fynxciwg.json key: cord-274750-fynxciwg authors: Peterson, Danielle; Damsky, William; King, Brett title: Calm before the storm: understanding the role of JAK inhibitors in COVID-19 date: 2020-04-25 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.04.097 sha: doc_id: 274750 cord_uid: fynxciwg file: cache/cord-275004-qzg03dvg.json key: cord-275004-qzg03dvg authors: Veras, Flavio Protasio; Pontelli, Marjorie Cornejo; Silva, Camila Meirelles; Toller-Kawahisa, Juliana E.; de Lima, Mikhael; Nascimento, Daniele Carvalho; Schneider, Ayda Henriques; Caetité, Diego; Tavares, Lucas Alves; Paiva, Isadora M.; Rosales, Roberta; Colón, David; Martins, Ronaldo; Castro, Italo Araujo; Almeida, Glaucia M.; Lopes, Maria Isabel Fernandes; Benatti, Maíra Nilson; Bonjorno, Letícia Pastorelli; Giannini, Marcela Cavichioli; Luppino-Assad, Rodrigo; Almeida, Sérgio Luna; Vilar, Fernando; Santana, Rodrigo; Bollela, Valdes R.; Auxiliadora-Martins, Maria; Borges, Marcos; Miranda, Carlos Henrique; Pazin-Filho, Antônio; da Silva, Luis Lamberti P.; Cunha, Larissa; Zamboni, Dario S.; Dal-Pizzol, Felipe; Leiria, Luiz O.; Siyuan, Li; Batah, Sabrina; Fabro, Alexandre; Mauad, Thais; Dolhnikoff, Marisa; Duarte-Neto, Amaro; Saldiva, Paulo; Cunha, Thiago Mattar; Alves-Filho, José Carlos; Arruda, Eurico; Louzada-Junior, Paulo; Oliveira, Renê Donizeti; Cunha, Fernando Queiroz title: SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology date: 2020-09-14 journal: J Exp Med DOI: 10.1084/jem.20201129 sha: doc_id: 275004 cord_uid: qzg03dvg file: cache/cord-275108-snqbrxgr.json key: cord-275108-snqbrxgr authors: Daverio, Marco; Amigoni, Angela; Cavicchiolo, Maria Elena title: Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date: 2020-05-22 journal: J Infect Dis DOI: 10.1093/infdis/jiaa283 sha: doc_id: 275108 cord_uid: snqbrxgr file: cache/cord-274761-c2hgkbg6.json key: cord-274761-c2hgkbg6 authors: Rosenberg, Eli S.; Tesoriero, James M.; Rosenthal, Elizabeth M.; Chung, Rakkoo; Barranco, Meredith A.; Styer, Linda M.; Parker, Monica M.; John Leung, Shu-Yin; Morne, Johanne E.; Greene, Danielle; Holtgrave, David R.; Hoefer, Dina; Kumar, Jessica; Udo, Tomoko; Hutton, Brad; Zucker, Howard A. title: Cumulative incidence and diagnosis of SARS-CoV-2 infection in New York date: 2020-06-17 journal: Ann Epidemiol DOI: 10.1016/j.annepidem.2020.06.004 sha: doc_id: 274761 cord_uid: c2hgkbg6 file: cache/cord-275420-zkxyxiv5.json key: cord-275420-zkxyxiv5 authors: Crabtree, Scott J.; Cohen, Stuart H. title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States date: 2020-07-23 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.360 sha: doc_id: 275420 cord_uid: zkxyxiv5 file: cache/cord-274824-kaefedl1.json key: cord-274824-kaefedl1 authors: Turski, Waldemar A.; Wnorowski, Artur; Turski, Gabrielle N.; Turski, Christopher A.; Turski, Lechoslaw title: AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date: 2020-09-24 journal: Restorative neurology and neuroscience DOI: 10.3233/rnn-201042 sha: doc_id: 274824 cord_uid: kaefedl1 file: cache/cord-274788-oyk8js16.json key: cord-274788-oyk8js16 authors: Bae, Sanghyuk; Kim, Hwami; Jung, Tae-Young; Lim, Ji-Ae; Jo, Da-Hye; Kang, Gi-Seok; Jeong, Seung-Hee; Choi, Dong-Kwon; Kim, Hye-Jin; Cheon, Young Hee; Chun, Min-kyo; Kim, Miyoung; Choi, Siwon; Chun, Chaemin; Shin, Seung Hwan; Kim, Hee Kyoung; Park, Young Joon; Park, Ok; Kwon, Ho-Jang title: Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea date: 2020-08-05 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e288 sha: doc_id: 274788 cord_uid: oyk8js16 file: cache/cord-274802-7ioiwsd8.json key: cord-274802-7ioiwsd8 authors: Varghese, Praveen Mathews; Tsolaki, Anthony G.; Yasmin, Hadida; Shastri, Abhishek; Ferluga, Janez; Vatish, Manu; Madan, Taruna; Kishore, Uday title: Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies date: 2020-08-19 journal: Immunobiology DOI: 10.1016/j.imbio.2020.152008 sha: doc_id: 274802 cord_uid: 7ioiwsd8 file: cache/cord-274852-84m62t4x.json key: cord-274852-84m62t4x authors: Hogan, Catherine A.; Garamani, Natasha; Sahoo, Malaya K.; Huang, ChunHong; Zehnder, James; Pinsky, Benjamin A. title: Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019 date: 2020-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid2610.202296 sha: doc_id: 274852 cord_uid: 84m62t4x file: cache/cord-275348-jna496x7.json key: cord-275348-jna496x7 authors: Kapadia, Sagar U.; Simon, Ian D.; Rose, John K. title: SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date: 2008-06-20 journal: Virology DOI: 10.1016/j.virol.2008.03.002 sha: doc_id: 275348 cord_uid: jna496x7 file: cache/cord-274839-r4jg6wac.json key: cord-274839-r4jg6wac authors: Azam, Faizul; Taban, Ismail M.; Eid, Eltayeb E. M.; Iqbal, Muzaffar; Alam, Ozair; Khan, Shamshir; Mahmood, Danish; Anwar, Md Jamir; Khalilullah, Habibullah; Khan, M. U. title: An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α date: 2020-11-02 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1841028 sha: doc_id: 274839 cord_uid: r4jg6wac file: cache/cord-274948-ze6scnae.json key: cord-274948-ze6scnae authors: Segondy, Michel title: Les Coronavirus humains date: 2020-10-31 journal: Rev Francoph Lab DOI: 10.1016/s1773-035x(20)30311-7 sha: doc_id: 274948 cord_uid: ze6scnae file: cache/cord-275199-y7b12vml.json key: cord-275199-y7b12vml authors: Suárez-Fariñas, Mayte; Tokuyama, Minami; Wei, Gabrielle; Huang, Ruiqi; Livanos, Alexandra; Jha, Divya; Levescot, Anais; Irizar, Haritz; Kosoy, Roman; Cording, Sascha; Wang, Wenhui; Losic, Bojan; Ungaro, Ryan; Di’Narzo, Antonio; Martinez-Delgado, Gustavo; Suprun, Maria; Corley, Michael J.; Stojmirovic, Aleksandar; Houten, Sander M.; Peters, Lauren; Curran, Mark; Brodmerkel, Carrie; Perrigoue, Jacqueline; Friedman, Joshua R.; Hao, Ke; Schadt, Eric E.; Zhu, Jun; Ko, Huaibin M.; Cho, Judy; Dubinsky, Marla C.; Sands, Bruce E.; Ndhlovu, Lishomwa; Cerf-Bensusan, Nadine; Kasarskis, Andrew; Colombel, Jean Frederic; Harpaz, Noam; Argmann, Carmen; Mehandru, Saurabh title: Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date: 2020-09-25 journal: Gastroenterology DOI: 10.1053/j.gastro.2020.09.029 sha: doc_id: 275199 cord_uid: y7b12vml file: cache/cord-275452-ymimvoq9.json key: cord-275452-ymimvoq9 authors: Ameen, Fuad; Amna, Touseef; AA Alghamdi, Abdullah; Almansob, Abobakr title: Covid-19 pandemic outburst in Saudi Arabia: A Glimpse date: 2020-07-30 journal: Saudi J Biol Sci DOI: 10.1016/j.sjbs.2020.07.026 sha: doc_id: 275452 cord_uid: ymimvoq9 file: cache/cord-275340-q8d7rvnj.json key: cord-275340-q8d7rvnj authors: Sun, JingKang; Chen, YuTing; Fan, XiuDe; Wang, XiaoYun; Han, QunYing; Liu, ZhengWen title: Advances in the use of chloroquine and hydroxychloroquine for the treatment of COVID-19 date: 2020-06-21 journal: Postgraduate medicine DOI: 10.1080/00325481.2020.1778982 sha: doc_id: 275340 cord_uid: q8d7rvnj file: cache/cord-275404-hv3y4x4g.json key: cord-275404-hv3y4x4g authors: Zumla, Alimuddin; Hui, David S title: Infection control and MERS-CoV in health-care workers date: 2014-05-20 journal: Lancet DOI: 10.1016/s0140-6736(14)60852-7 sha: doc_id: 275404 cord_uid: hv3y4x4g file: cache/cord-275173-ely3aen3.json key: cord-275173-ely3aen3 authors: Pickering, Brad S.; Smith, Greg; Pinette, Mathieu M.; Embury-Hyatt, Carissa; Moffat, Estella; Marszal, Peter; Lewis, Charles E. title: Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date: 2020-09-10 journal: bioRxiv DOI: 10.1101/2020.09.10.288548 sha: doc_id: 275173 cord_uid: ely3aen3 file: cache/cord-275250-ilmgy7ce.json key: cord-275250-ilmgy7ce authors: Xia, Yong; Hong, Honghai; Feng, Yao; Liu, Meiling; Pan, Xingfei; Chen, Dexiong title: Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date: 2020-05-17 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.042 sha: doc_id: 275250 cord_uid: ilmgy7ce file: cache/cord-275252-4e3cn50u.json key: cord-275252-4e3cn50u authors: Rad SM, Ali Hosseini; McLellan, Alexander D. title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 journal: bioRxiv DOI: 10.1101/2020.05.15.098947 sha: doc_id: 275252 cord_uid: 4e3cn50u file: cache/cord-275552-ijxxeo27.json key: cord-275552-ijxxeo27 authors: Yen, Zui-Shen; Chang, Chee-Jen; Chen, Shey-Ying; Lee, Chien-Chang; Hsu, Chiung-Yuan; Chen, Shyr-Chyr; Chen, Wen-Jone title: How much would you be willing to pay for preventing a new dangerous infectious disease: A willingness-to-pay study in medical personnel working in the emergency department date: 2007-10-10 journal: Am J Infect Control DOI: 10.1016/j.ajic.2006.09.008 sha: doc_id: 275552 cord_uid: ijxxeo27 file: cache/cord-275216-dnt88ycw.json key: cord-275216-dnt88ycw authors: Zhang, Xue-Yan; Huang, Hao-Jie; Zhuang, Dong-Lin; Nasser, Moussa Ide; Yang, Ming-Hua; Zhu, Ping; Zhao, Ming-Yi title: Biological, clinical and epidemiological features of COVID-19, SARS and MERS and AutoDock simulation of ACE2 date: 2020-07-20 journal: Infect Dis Poverty DOI: 10.1186/s40249-020-00691-6 sha: doc_id: 275216 cord_uid: dnt88ycw file: cache/cord-275438-drywzvx8.json key: cord-275438-drywzvx8 authors: Satış, Hasan; Özger, Hasan Selçuk; Aysert Yıldız, Pınar; Hızel, Kenan; Gulbahar, Özlem; Erbaş, Gonca; Aygencel, Gülbin; Guzel Tunccan, Ozlem; Öztürk, Mehmet Akif; Dizbay, Murat; Tufan, Abdurrahman title: Prognostic value of interleukin-18 and its association with other inflammatory markers and disease severity in COVID-19 date: 2020-09-29 journal: Cytokine DOI: 10.1016/j.cyto.2020.155302 sha: doc_id: 275438 cord_uid: drywzvx8 file: cache/cord-275336-lnhkux0m.json key: cord-275336-lnhkux0m authors: Marino Gammazza, Antonella; Légaré, Sébastien; Lo Bosco, Giosuè; Fucarino, Alberto; Angileri, Francesca; Conway de Macario, Everly; Macario, Alberto JL; Cappello, Francesco title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 date: 2020-08-04 journal: Cell Stress Chaperones DOI: 10.1007/s12192-020-01148-3 sha: doc_id: 275336 cord_uid: lnhkux0m file: cache/cord-275482-ncrhb75f.json key: cord-275482-ncrhb75f authors: Jia, Hong Peng; Look, Dwight C.; Hickey, Melissa; Shi, Lei; Pewe, Lecia; Netland, Jason; Farzan, Michael; Wohlford-Lenane, Christine; Perlman, Stanley; McCray, Paul B. title: Infection of Human Airway Epithelia by Sars Coronavirus is Associated with ACE2 Expression and Localization date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_85 sha: doc_id: 275482 cord_uid: ncrhb75f file: cache/cord-275521-dlp055z8.json key: cord-275521-dlp055z8 authors: Goldman, Emanuel title: Exaggerated risk of transmission of COVID-19 by fomites date: 2020-07-03 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30561-2 sha: doc_id: 275521 cord_uid: dlp055z8 file: cache/cord-275604-5u4kikov.json key: cord-275604-5u4kikov authors: Feehan, Amy K.; Fort, Daniel; Garcia-Diaz, Julia; Price-Haywood, Eboni G.; Velasco, Cruz; Sapp, Eric; Pevey, Dawn; Seoane, Leonardo title: Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 date: 2020-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid2611.203029 sha: doc_id: 275604 cord_uid: 5u4kikov file: cache/cord-275257-upj8mvzn.json key: cord-275257-upj8mvzn authors: Hwang, E. Shelley; Balch, Charles M.; Balch, Glen C.; Feldman, Sheldon M.; Golshan, Mehra; Grobmyer, Stephen R.; Libutti, Steven K.; Margenthaler, Julie A.; Sasidhar, Madhu; Turaga, Kiran K.; Wong, Sandra L.; McMasters, Kelly M.; Tanabe, Kenneth K. title: Surgical Oncologists and the COVID-19 Pandemic: Guiding Cancer Patients Effectively through Turbulence and Change date: 2020-06-14 journal: Ann Surg Oncol DOI: 10.1245/s10434-020-08673-6 sha: doc_id: 275257 cord_uid: upj8mvzn file: cache/cord-275357-yx8lsfdv.json key: cord-275357-yx8lsfdv authors: Lu, J.; Becker, D.; Sandoval, E.; Amin, A.; De Hoff, P.; Diets, A.; Leonetti, N.; Lim, Y. W.; Elliott, C.; Laurent, L.; Grzymski, J. title: Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting date: 2020-05-15 journal: nan DOI: 10.1101/2020.05.11.20092338 sha: doc_id: 275357 cord_uid: yx8lsfdv file: cache/cord-275191-lgze4zex.json key: cord-275191-lgze4zex authors: Al-Sadeq, Duaa W.; Nasrallah, Gheyath K. title: The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date: 2020-07-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.098 sha: doc_id: 275191 cord_uid: lgze4zex file: cache/cord-275185-9br8lwma.json key: cord-275185-9br8lwma authors: Zeng, Hao; Wang, Dongfang; Nie, Jingmin; Liang, Haoyu; Gu, Jiang; Zhao, Anne; Xu, Lixin; Lang, Chunhui; Cui, Xiaoping; Guo, Xiaolan; Zhou, Changlong; Li, Haibo; Guo, Bin; Zhang, Jinyong; Wang, Qiang; Fang, Li; Liu, Wen; Huang, Yishan; Mao, Wei; Chen, Yaokai; Zou, Quanming title: The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date: 2020-10-06 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00329-x sha: doc_id: 275185 cord_uid: 9br8lwma file: cache/cord-275088-wbqznzj7.json key: cord-275088-wbqznzj7 authors: Garrido, Pablo F.; Calvelo, Martín; Blanco-González, Alexandre; Veleiro, Uxía; Suárez, Fabián; Conde, Daniel; Cabezón, Alfonso; Piñeiro, Ángel; Garcia-Fandino, Rebeca title: The Lord of the NanoRings: cyclodextrins and the battle against SARS-CoV-2 date: 2020-07-25 journal: Int J Pharm DOI: 10.1016/j.ijpharm.2020.119689 sha: doc_id: 275088 cord_uid: wbqznzj7 file: cache/cord-275439-cdlcv1c9.json key: cord-275439-cdlcv1c9 authors: Iwasaki, S.; Fujisawa, S.; Nakakubo, S.; Kamada, K.; Yamashita, Y.; Fukumoto, T.; Sato, K.; Oguri, S.; Taki, K.; Senjo, H.; Hayasaka, K.; Konno, S.; Nishida, M.; Teshima, T. title: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date: 2020-05-19 journal: nan DOI: 10.1101/2020.05.13.20100206 sha: doc_id: 275439 cord_uid: cdlcv1c9 file: cache/cord-275495-h60x89zi.json key: cord-275495-h60x89zi authors: Bocksberger, S.; Wagner, W.; Hummel, T.; Guggemos, W.; Seilmaier, M.; Hoelscher, M.; Wendtner, C.-M. title: Temporäre Hyposmie bei COVID-19-Patienten date: 2020-05-25 journal: HNO DOI: 10.1007/s00106-020-00891-4 sha: doc_id: 275495 cord_uid: h60x89zi file: cache/cord-275569-i5y23mmz.json key: cord-275569-i5y23mmz authors: de Bernardis, E.; Busà, L. title: A putative role for the tobacco mosaic virus in smokers’ resistance to COVID-19 date: 2020-07-31 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110153 sha: doc_id: 275569 cord_uid: i5y23mmz file: cache/cord-275708-17cz3agx.json key: cord-275708-17cz3agx authors: Babyn, Paul S.; Chu, Winnie C. W.; Tsou, Ian Y. Y.; Wansaicheong, Gervais K. L.; Allen, Upton; Bitnun, Ari; Chee, Thomas S. G.; Cheng, Frankie W. T.; Chiu, Man-Chun; Fok, Tai-Fai; Hon, Ellis K. L.; Gahunia, Harpal K.; Kaw, Gregory J. L.; Khong, Pek L.; Leung, Chi-Wai; Li, Albert M.; Manson, David; Metreweli, Constantine; Ng, Pak-Cheung; Read, Stanley; Stringer, David A. title: Severe acute respiratory syndrome (SARS): chest radiographic features in children date: 2003-11-18 journal: Pediatr Radiol DOI: 10.1007/s00247-003-1081-8 sha: doc_id: 275708 cord_uid: 17cz3agx file: cache/cord-275746-3sgbpn13.json key: cord-275746-3sgbpn13 authors: Shimamoto, Yasuhiro; Hattori, Yasunao; Kobayashi, Kazuya; Teruya, Kenta; Sanjoh, Akira; Nakagawa, Atsushi; Yamashita, Eiki; Akaji, Kenichi title: Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors date: 2015-02-15 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2014.12.028 sha: doc_id: 275746 cord_uid: 3sgbpn13 file: cache/cord-275454-an8xvow3.json key: cord-275454-an8xvow3 authors: Clark, Andrew E; Lee, Francesca M title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1145 sha: doc_id: 275454 cord_uid: an8xvow3 file: cache/cord-275960-1m6poddy.json key: cord-275960-1m6poddy authors: Thieme, C. 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B.; Li, X. title: Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients date: 2020-09-23 journal: nan DOI: 10.1101/2020.09.21.20198309 sha: doc_id: 276139 cord_uid: l13hbucu file: cache/cord-276013-8dhqa2gj.json key: cord-276013-8dhqa2gj authors: Luo, Yung-Hung; Chiu, Hwa-Yen; Weng, Chia-Sui; Chen, Yuh-Min title: Overview of coronavirus disease 2019: Treatment updates and advances date: 2020-08-17 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000367 sha: doc_id: 276013 cord_uid: 8dhqa2gj file: cache/cord-275858-46jzw94p.json key: cord-275858-46jzw94p authors: Leung, Janice M.; Niikura, Masahiro; Yang, Cheng Wei Tony; Sin, Don D. title: COVID-19 and COPD date: 2020-08-13 journal: Eur Respir J DOI: 10.1183/13993003.02108-2020 sha: doc_id: 275858 cord_uid: 46jzw94p file: cache/cord-276394-s9y11oep.json key: cord-276394-s9y11oep authors: Liang, W.; McLaws, M.-L.; Liu, M.; Mi, J.; Chan, D.K.Y. title: Hindsight: A re-analysis of the severe acute respiratory syndrome outbreak in Beijing date: 2007-10-31 journal: Public Health DOI: 10.1016/j.puhe.2007.02.023 sha: doc_id: 276394 cord_uid: s9y11oep file: cache/cord-275978-pezm1tnw.json key: cord-275978-pezm1tnw authors: Riccardo, Flavia; 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Lu, J.; Koh, D.R.; Chow, Vincent T.K. title: Characterization of cytotoxic T‐lymphocyte epitopes and immune responses to SARS coronavirus spike DNA vaccine expressing the RGD‐integrin‐binding motif date: 2009-05-27 journal: J Med Virol DOI: 10.1002/jmv.21571 sha: doc_id: 276335 cord_uid: e1xlwcvc file: cache/cord-276147-30buoweg.json key: cord-276147-30buoweg authors: Avancini, Joao; Miyamoto, Denise; Arnone, Marcelo; Villas-Boas Gabbi, Tatiana; Ferreira, Paula Silva; Neta, Cyro Festa; Sanches, Jose Antonio title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil date: 2020-09-15 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.09.030 sha: doc_id: 276147 cord_uid: 30buoweg file: cache/cord-276316-7ot9ds34.json key: cord-276316-7ot9ds34 authors: Lei, Chunliang; Lin, Weiyin; Deng, Xilong; Hu, Fengyu; Chen, Fengjuan; Cai, Weiping; Li, Yueping; Wen, Chunyan; Guan, Yujuan; Wang, Jian; Chen, Xiaoting; Cao, Yi; Li, Feng; Tang, Xiaoping; Li, Linghua title: Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China date: 2020-10-14 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104661 sha: doc_id: 276316 cord_uid: 7ot9ds34 file: cache/cord-276132-tv5y1eqc.json key: cord-276132-tv5y1eqc authors: Ray, Upasana; Aziz, Faisal; Shankar, Abhishek; Biswas, Aalekhya Sharma; Chakraborty, Abhijit title: COVID-19: The Impact in Oncology Care date: 2020-10-23 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00592-7 sha: doc_id: 276132 cord_uid: tv5y1eqc file: cache/cord-276234-2nkeq4ud.json key: cord-276234-2nkeq4ud authors: Siedlecki, Jakob; Brantl, Victor; Schworm, Benedikt; Mayer, Wolfgang Johann; Gerhardt, Maximilian; Michalakis, Stylianos; Kreutzer, Thomas; Priglinger, Siegfried title: COVID-19: Ophthalmological Aspects of the SARS-CoV 2 Global Pandemic date: 2020-05-06 journal: Klin Monbl Augenheilkd DOI: 10.1055/a-1164-9381 sha: doc_id: 276234 cord_uid: 2nkeq4ud file: cache/cord-276487-8vkrh70j.json key: cord-276487-8vkrh70j authors: Kang, Sisi; Yang, Mei; Hong, Zhongsi; Zhang, Liping; Huang, Zhaoxia; Chen, Xiaoxue; He, Suhua; Zhou, Ziliang; Zhou, Zhechong; Chen, Qiuyue; Yan, Yan; Zhang, Changsheng; Shan, Hong; Chen, Shoudeng title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites date: 2020-04-20 journal: Acta Pharm Sin B DOI: 10.1016/j.apsb.2020.04.009 sha: doc_id: 276487 cord_uid: 8vkrh70j file: cache/cord-276358-so390gp4.json key: cord-276358-so390gp4 authors: Nieto-Torres, Jose L.; 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Liu, GuanQun; Gack, Michaela U. title: Dysregulation of type I interferon responses in COVID-19 date: 2020-05-26 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0346-x sha: doc_id: 276350 cord_uid: lcl9jn35 file: cache/cord-276784-8lmg97zc.json key: cord-276784-8lmg97zc authors: Boziki, Marina Kleopatra; Mentis, Alexios-Fotios A.; Shumilina, Maria; Makshakov, Gleb; Evdoshenko, Evgeniy; Grigoriadis, Nikolaos title: COVID-19 Immunopathology and the Central Nervous System: Implication for Multiple Sclerosis and Other Autoimmune Diseases with Associated Demyelination date: 2020-06-04 journal: Brain Sci DOI: 10.3390/brainsci10060345 sha: doc_id: 276784 cord_uid: 8lmg97zc file: cache/cord-276980-k8xi2zvh.json key: cord-276980-k8xi2zvh authors: Koh, David; Lim, Meng-Kin; Ong, Choon-Nam; Chia, Sin-Eng title: Occupational Health Response to SARS date: 2005-01-17 journal: Emerg Infect Dis DOI: 10.3201/eid1101.040637 sha: doc_id: 276980 cord_uid: k8xi2zvh file: cache/cord-276995-b003vcdc.json key: cord-276995-b003vcdc authors: Wiese, Andrew D; 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Nabi, Ghulam; Liu, Jianbo title: Coronaviruses disease 2019 (COVID-19): causative agent, mental health concerns, and potential management options date: 2020-07-25 journal: J Infect Public Health DOI: 10.1016/j.jiph.2020.07.010 sha: doc_id: 276769 cord_uid: th7iou21 file: cache/cord-276820-l7bd5y8y.json key: cord-276820-l7bd5y8y authors: So, Winnie K.W.; Chan, Sophia S.C.; Lee, Angel C.K.; Tiwari, Agnes F.Y. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong date: 2004-11-30 journal: International Journal of Nursing Studies DOI: 10.1016/j.ijnurstu.2004.04.004 sha: doc_id: 276820 cord_uid: l7bd5y8y file: cache/cord-276857-i948aq4b.json key: cord-276857-i948aq4b authors: Chung, Grace TY; Chiu, Rossa WK; Cheung, Jo LK; Jin, Yongjie; Chim, Stephen SC; Chan, Paul KS; Lo, YM Dennis title: A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date: 2005-10-18 journal: BMC Infect Dis DOI: 10.1186/1471-2334-5-87 sha: doc_id: 276857 cord_uid: i948aq4b file: cache/cord-276957-pk33dl8q.json key: cord-276957-pk33dl8q authors: Hu, Xuejiao; 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A.; Lee, J.-H.; Brescia, P.; Kumar, D.; Nong, T.; Shih, R.; Woodle, E. S.; Maltzman, J. S.; Gebel, H. M. title: Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins date: 2020-09-03 journal: nan DOI: 10.1101/2020.09.02.20185199 sha: doc_id: 277239 cord_uid: cedoi5jr file: cache/cord-276874-9rjbmsvb.json key: cord-276874-9rjbmsvb authors: Ng, M.L.; Lee, J.W.M.; Leong, M.L.N.; Ling, A.-E.; Tan, H.-C.; Ooi, E.E. title: Topographic Changes in SARS Coronavirus–infected Cells at Late Stages of Infection date: 2004-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid1011.040195 sha: doc_id: 276874 cord_uid: 9rjbmsvb file: cache/cord-276797-86hc3lbi.json key: cord-276797-86hc3lbi authors: Jamieson, Denise J.; Ellis, Jane E.; Jernigan, Daniel B.; Treadwell, Tracee A. title: Emerging infectious disease outbreaks: Old lessons and new challenges for obstetrician-gynecologists date: 2006-06-30 journal: American Journal of Obstetrics and Gynecology DOI: 10.1016/j.ajog.2005.06.062 sha: doc_id: 276797 cord_uid: 86hc3lbi file: cache/cord-277025-gmy51dx4.json key: cord-277025-gmy51dx4 authors: Pfefferle, Susanne; Huang, Jiabin; Nörz, Dominik; Indenbirken, Daniela; Lütgehetmann, Marc; Oestereich, Lisa; Günther, Thomas; Grundhoff, Adam; Aepfelbacher, Martin; Fischer, Nicole title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date: 2020-06-04 journal: Microbiol Resour Announc DOI: 10.1128/mra.00520-20 sha: doc_id: 277025 cord_uid: gmy51dx4 file: cache/cord-277197-njy99jh4.json key: cord-277197-njy99jh4 authors: Song, Fang; Zhang, Xiangyan; Zha, Yan; Liu, Weijia title: COVID‐19: Recommended sampling sites at different stage of the disease date: 2020-04-16 journal: J Med Virol DOI: 10.1002/jmv.25892 sha: doc_id: 277197 cord_uid: njy99jh4 file: cache/cord-277278-lg38l5gh.json key: cord-277278-lg38l5gh authors: Tang, Olive; Bigelow, Benjamin F.; Sheikh, Fatima; Peters, Matthew; Zenilman, Jonathan M.; Bennett, Richard; Katz, Morgan J. title: Outcomes of nursing home COVID-19 patients by initial symptoms and comorbidity: Results of universal testing of 1,970 residents date: 2020-10-14 journal: J Am Med Dir Assoc DOI: 10.1016/j.jamda.2020.10.011 sha: doc_id: 277278 cord_uid: lg38l5gh file: cache/cord-276758-k2imddzr.json key: cord-276758-k2imddzr authors: Siegel, Jane D.; Rhinehart, Emily; Jackson, Marguerite; Chiarello, Linda title: 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date: 2007-12-07 journal: Am J Infect Control DOI: 10.1016/j.ajic.2007.10.007 sha: doc_id: 276758 cord_uid: k2imddzr file: cache/cord-276895-p85obwp2.json key: cord-276895-p85obwp2 authors: Carriazo, Sol; Kanbay, Mehmet; Ortiz, Alberto title: Kidney disease and electrolytes in COVID-19: more than meets the eye date: 2020-07-16 journal: Clin Kidney J DOI: 10.1093/ckj/sfaa112 sha: doc_id: 276895 cord_uid: p85obwp2 file: cache/cord-277210-xaj2623u.json key: cord-277210-xaj2623u authors: Weinkove, Robert; McQuilten, Zoe K; Adler, Jonathan; Agar, Meera R; Blyth, Emily; Cheng, Allen C; Conyers, Rachel; Haeusler, Gabrielle M; Hardie, Claire; Jackson, Christopher; Lane, Steven W; Middlemiss, Tom; Mollee, Peter; Mulligan, Stephen P; Ritchie, David; Ruka, Myra; Solomon, Benjamin; Szer, Jeffrey; Thursky, Karin A; Wood, Erica M; Worth, Leon J; Yong, Michelle K; Slavin, Monica A; Teh, Benjamin W title: Managing haematology and oncology patients during the COVID‐19 pandemic: interim consensus guidance date: 2020-05-13 journal: Med J Aust DOI: 10.5694/mja2.50607 sha: doc_id: 277210 cord_uid: xaj2623u file: cache/cord-277039-yo5ojr0s.json key: cord-277039-yo5ojr0s authors: Mendenhall, Ian H.; Kerimbayev, Aslan A.; Strochkov, Vitaliy M.; Sultankulova, Kulyaisan T.; Kopeyev, Syrym K.; Su, Yvonne C.F.; Smith, Gavin J.D.; Orynbayev, Mukhit B. title: Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date: 2019-04-17 journal: Viruses DOI: 10.3390/v11040356 sha: doc_id: 277039 cord_uid: yo5ojr0s file: cache/cord-277110-e27lm7rr.json key: cord-277110-e27lm7rr authors: Iria, Neri; Annalucia, Virdi; Ilaria, Corsini; Alba, Guglielmo; Tiziana, Lazzarotto; Liliana, Gabrielli; Cosimo, Misciali; Annalisa, Patrizi; Marcello, Lanari title: Major cluster of pediatric “ true ” primary chilblains during the COVID‐19 pandemic: a consequence of lifestyle changes due to lockdown date: 2020-06-13 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16751 sha: doc_id: 277110 cord_uid: e27lm7rr file: cache/cord-277113-pykf7iw1.json key: cord-277113-pykf7iw1 authors: Wang, Xingyu; Xu, Hao; Jiang, Haini; Wang, Liuming; Lu, Chao; Wei, Xiang; Liu, Jihong; Xu, Shuyun title: The Clinical Features and Outcomes of Discharged Coronavirus Disease 2019 Patients：A Prospective Cohort Study date: 2020-05-22 journal: QJM DOI: 10.1093/qjmed/hcaa178 sha: doc_id: 277113 cord_uid: pykf7iw1 file: cache/cord-277357-lpurk7pe.json key: cord-277357-lpurk7pe authors: González-González, Everardo; Trujillo-de Santiago, Grissel; Lara-Mayorga, Itzel Montserrat; Martínez-Chapa, Sergio Omar; Alvarez, Mario Moisés title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237418 sha: doc_id: 277357 cord_uid: lpurk7pe file: cache/cord-276630-qci7khki.json key: cord-276630-qci7khki authors: Lima, William Gustavo; Brito, Júlio César Moreira; Overhage, Joerg; Nizer, Waleska Stephanie da Cruz title: The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date: 2020-06-08 journal: Arch Virol DOI: 10.1007/s00705-020-04693-5 sha: doc_id: 276630 cord_uid: qci7khki file: cache/cord-277186-sj8ngpk8.json key: cord-277186-sj8ngpk8 authors: He, Qigai; Du, Qingyun; Lau, Suelyn; Manopo, Ivanus; Lu, Liqun; Chan, Shzu-Wei; Fenner, Beau J.; Kwang, Jimmy title: Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA date: 2005-04-19 journal: J Virol Methods DOI: 10.1016/j.jviromet.2005.03.004 sha: doc_id: 277186 cord_uid: sj8ngpk8 file: cache/cord-277188-t33nw4zb.json key: cord-277188-t33nw4zb authors: Fang, Jie; Li, Hui; Du, Wei; Yu, Ping; Guan, Ying-Yun; Ma, Shi-Yu; Liu, Dong; Chen, Wei; Shi, Guo-Chao; Bian, Xiao-Lan title: Efficacy of Early Combination Therapy With Lianhuaqingwen and Arbidol in Moderate and Severe COVID-19 Patients: A Retrospective Cohort Study date: 2020-09-18 journal: Front Pharmacol DOI: 10.3389/fphar.2020.560209 sha: doc_id: 277188 cord_uid: t33nw4zb file: cache/cord-277137-k3jj5vom.json key: cord-277137-k3jj5vom authors: Anand, Praveen; Puranik, Arjun; Aravamudan, Murali; Venkatakrishnan, AJ; Soundararajan, Venky title: SARS-CoV-2 strategically mimics proteolytic activation of human ENaC date: 2020-05-26 journal: eLife DOI: 10.7554/elife.58603 sha: doc_id: 277137 cord_uid: k3jj5vom file: cache/cord-277260-7se220oz.json key: cord-277260-7se220oz authors: Gosain, Rohit; Abdou, Yara; Singh, Abhay; Rana, Navpreet; Puzanov, Igor; Ernstoff, Marc S. title: COVID-19 and Cancer: a Comprehensive Review date: 2020-05-08 journal: Curr Oncol Rep DOI: 10.1007/s11912-020-00934-7 sha: doc_id: 277260 cord_uid: 7se220oz file: cache/cord-277309-kelebqr6.json key: cord-277309-kelebqr6 authors: Wang, Lin-Fa; Anderson, Danielle E title: Viruses in bats and potential spillover to animals and humans date: 2019-01-18 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2018.12.007 sha: doc_id: 277309 cord_uid: kelebqr6 file: cache/cord-277342-40d24mvm.json key: cord-277342-40d24mvm authors: Chen, Yu; Li, Lanjuan title: SARS-CoV-2: virus dynamics and host response date: 2020-03-23 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30235-8 sha: doc_id: 277342 cord_uid: 40d24mvm file: cache/cord-277307-wabruzfs.json key: cord-277307-wabruzfs authors: Gu, Wei; Deng, Xianding; Reyes, Kevin; Hsu, Elaine; Wang, Candace; Sotomayor-Gonzalez, Alicia; Federman, Scot; Bushnell, Brian; Miller, Steve; Chiu, Charles title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa599 sha: doc_id: 277307 cord_uid: wabruzfs file: cache/cord-277313-5f5lrn3c.json key: cord-277313-5f5lrn3c authors: Hayakawa, Satoshi; Komine‐Aizawa, Shihoko; Mor, Gil G. title: Covid‐19 pandemic and pregnancy date: 2020-08-10 journal: J Obstet Gynaecol Res DOI: 10.1111/jog.14384 sha: doc_id: 277313 cord_uid: 5f5lrn3c file: cache/cord-277399-0w8is9xm.json key: cord-277399-0w8is9xm authors: Esteves, Sandro C.; Lombardo, Francesco; Garrido, Nicolás; Alvarez, Juan; Zini, Armand; Colpi, Giovanni M.; Kirkman‐Brown, Jackson; Lewis, Sheena E. M.; Björndahl, Lars; Majzoub, Ahmad; Cho, Chak‐Lam; Vendeira, Pedro; Hallak, Jorge; Amar, Edouard; Cocuzza, Marcello; Bento, Fabiola C.; Figueira, Rita C.; Sciorio, Romualdo; Laursen, Rita J.; Metwalley, Ahmad M.; Jindal, Sunil K.; Parekattil, Sijo; Ramasamy, Ranjith; Alviggi, Carlo; Humaidan, Peter; Yovich, John L.; Agarwal, Ashok title: SARS‐CoV‐2 pandemic and repercussions for male infertility patients: A proposal for the individualized provision of andrological services date: 2020-05-22 journal: Andrology DOI: 10.1111/andr.12809 sha: doc_id: 277399 cord_uid: 0w8is9xm file: cache/cord-277486-12uah5qi.json key: cord-277486-12uah5qi authors: Kopp, Kristen; Lichtenauer, Michael; Motloch, Lukas Jaroslaw; Hoppe, Uta C.; Egle, Alexander; Salzer, Helmut J. F.; Lamprecht, Bernd; Tomasits, Josef; Müller, Hannes M.; Dieplinger, Anna title: Interdisciplinary Model for Scheduling Post-discharge Cardiopulmonary Care of Patients Following Severe and Critical SARS-CoV-2 (Coronavirus) Infection date: 2020-08-14 journal: Front Cardiovasc Med DOI: 10.3389/fcvm.2020.00157 sha: doc_id: 277486 cord_uid: 12uah5qi file: cache/cord-277705-6lgt2i7f.json key: cord-277705-6lgt2i7f authors: Luan, Junwen; Lu, Yue; Gao, Shan; Zhang, Leiliang title: A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2 date: 2020-04-10 journal: J Infect DOI: 10.1016/j.jinf.2020.03.046 sha: doc_id: 277705 cord_uid: 6lgt2i7f file: cache/cord-277490-xrgnt6l5.json key: cord-277490-xrgnt6l5 authors: Huang, Zhongwei; Huang, Jianping; Gu, Qianqing; Du, Pengyue; Liang, Hongbin; Dong, Qing title: Optimal temperature zone for the dispersal of COVID-19 date: 2020-05-16 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.139487 sha: doc_id: 277490 cord_uid: xrgnt6l5 file: cache/cord-277731-thazunob.json key: cord-277731-thazunob authors: Smith, Matthew L.; Gandolfi, Stefano; Coshall, Philippa M.; Rahman, Pattanathu K. 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M. title: Biosurfactants: A Covid-19 Perspective date: 2020-06-09 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01341 sha: doc_id: 277731 cord_uid: thazunob file: cache/cord-277440-9nehpbg2.json key: cord-277440-9nehpbg2 authors: Grimm, Christian; Tang, Rachel title: Could an endo-lysosomal ion channel be the Achilles heel of SARS-CoV2? date: 2020-05-06 journal: Cell Calcium DOI: 10.1016/j.ceca.2020.102212 sha: doc_id: 277440 cord_uid: 9nehpbg2 file: cache/cord-277498-hdhq99k2.json key: cord-277498-hdhq99k2 authors: Chua, Melvin L.K.; Ma, Daniel J.; Anderson, Carryn M.; Karam, Sana D.; Margalit, Danielle N.; Kimple, Randall J. title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic date: 2020-05-15 journal: Adv Radiat Oncol DOI: 10.1016/j.adro.2020.04.031 sha: doc_id: 277498 cord_uid: hdhq99k2 file: cache/cord-277487-jgbjxgh1.json key: cord-277487-jgbjxgh1 authors: Graham, Simon P.; McLean, Rebecca K.; Spencer, Alexandra J.; Belij-Rammerstorfer, Sandra; Wright, Daniel; Ulaszewska, Marta; Edwards, Jane C.; Hayes, Jack W. P.; Martini, Veronica; Thakur, Nazia; Conceicao, Carina; Dietrich, Isabelle; Shelton, Holly; Waters, Ryan; Ludi, Anna; Wilsden, Ginette; Browning, Clare; Bialy, Dagmara; Bhat, Sushant; Stevenson-Leggett, Phoebe; Hollinghurst, Philippa; Gilbride, Ciaran; Pulido, David; Moffat, Katy; Sharpe, Hannah; Allen, Elizabeth; Mioulet, Valerie; Chiu, Chris; Newman, Joseph; Asfor, Amin S.; Burman, Alison; Crossley, Sylvia; Huo, Jiandong; Owens, Raymond J.; Carroll, Miles; Hammond, John A.; Tchilian, Elma; Bailey, Dalan; Charleston, Bryan; Gilbert, Sarah C.; Tuthill, Tobias J.; Lambe, Teresa title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.20.159715 sha: doc_id: 277487 cord_uid: jgbjxgh1 file: cache/cord-277735-a9gkath5.json key: cord-277735-a9gkath5 authors: Leung, Danny Tze Ming; Chi Hang, Tam Frankie; Chun Hung, Ma; Sheung Chan, Paul Kay; Cheung, Jo Lai Ken; Niu, Haitao; Tam, John Siu Lun; Lim, Pak Leong title: Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date: 2004-07-15 journal: J Infect Dis DOI: 10.1086/422040 sha: doc_id: 277735 cord_uid: a9gkath5 file: cache/cord-277796-9ddi0mm9.json key: cord-277796-9ddi0mm9 authors: Cheng, Hao; Wang, Yan; Wang, Gui‐Qiang title: Organ‐protective effect of angiotensin‐converting enzyme 2 and its effect on the prognosis of COVID‐19 date: 2020-04-05 journal: J Med Virol DOI: 10.1002/jmv.25785 sha: doc_id: 277796 cord_uid: 9ddi0mm9 file: cache/cord-277253-vy0mvzeb.json key: cord-277253-vy0mvzeb authors: Liu, Hongbo; Ye, Fei; Sun, Qi; Liang, Hao; Li, Chunmei; Lu, Roujian; Huang, Baoying; Tan, Wenjie; Lai, Luhua title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date: 2020-04-11 journal: bioRxiv DOI: 10.1101/2020.04.10.035824 sha: doc_id: 277253 cord_uid: vy0mvzeb file: cache/cord-277345-bbgerem6.json key: cord-277345-bbgerem6 authors: Pan, A.; Khan, O.; Meeks, J.; Boom, M.; Masud, F.; Andrieni, J.; Phillips, R.; Tiruneh, Y.; Kash, B.; Vahidy, F. title: Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area date: 2020-08-22 journal: nan DOI: 10.1101/2020.08.19.20177956 sha: doc_id: 277345 cord_uid: bbgerem6 file: cache/cord-277509-khvuiwl1.json key: cord-277509-khvuiwl1 authors: Hashemi, Seyyed Alireza; Golab Behbahan, Nader Ghaleh; Bahrani, Sonia; Mousavi, Seyyed Mojtaba; Gholami, Ahmad; Ramakrishna, Seeram; Firoozsani, Mohammad; Moghadami, Mohsen; Lankarani, Kamran Bagheri; Omidifar, Navid title: Ultra-sensitive viral glycoprotein detection NanoSystem toward accurate tracing SARS-CoV-2 in biological/non-biological media date: 2021-01-01 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112731 sha: doc_id: 277509 cord_uid: khvuiwl1 file: cache/cord-277549-sg7tzhdm.json key: cord-277549-sg7tzhdm authors: Stanley, Kate E.; Thomas, Elizabeth; Leaver, Megan; Wells, Dagan title: Coronavirus disease (COVID-19) and fertility: viral host entry protein expression in male and female reproductive tissues date: 2020-05-08 journal: Fertil Steril DOI: 10.1016/j.fertnstert.2020.05.001 sha: doc_id: 277549 cord_uid: sg7tzhdm file: cache/cord-277443-mv7sk5aa.json key: cord-277443-mv7sk5aa authors: Kumaki, Yohichi; Salazar, Andres M.; Wandersee, Miles K.; Barnard, Dale L. title: Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol(®) (Poly IC:LC), in a lethal SARS-CoV-infected BALB/c mouse model date: 2016-12-09 journal: Antiviral Res DOI: 10.1016/j.antiviral.2016.12.007 sha: doc_id: 277443 cord_uid: mv7sk5aa file: cache/cord-277760-i4xjk61t.json key: cord-277760-i4xjk61t authors: Castillo, Andrés E.; Parra, Bárbara; Tapia, Paz; Acevedo, Alejandra; Lagos, Jaime; Andrade, Winston; Arata, Loredana; Leal, Gabriel; Barra, Gisselle; Tambley, Carolina; Tognarelli, Javier; Bustos, Patricia; Ulloa, Soledad; Fasce, Rodrigo; Fernández, Jorge title: Phylogenetic analysis of the first four SARS‐CoV‐2 cases in Chile date: 2020-04-08 journal: J Med Virol DOI: 10.1002/jmv.25797 sha: doc_id: 277760 cord_uid: i4xjk61t file: cache/cord-277774-kec1o4ys.json key: cord-277774-kec1o4ys authors: Wang, Shangqian; Zhou, Xiang; Zhang, Tongtong; Wang, Zengjun title: The need for urogenital tract monitoring in COVID-19 date: 2020-04-20 journal: Nat Rev Urol DOI: 10.1038/s41585-020-0319-7 sha: doc_id: 277774 cord_uid: kec1o4ys file: cache/cord-277529-z2r14w2k.json key: cord-277529-z2r14w2k authors: Stella, Alessandro; Lamkanfi, Mohamed; Portincasa, Piero title: Familial Mediterranean Fever and COVID-19: Friends or Foes? date: 2020-09-18 journal: Front Immunol DOI: 10.3389/fimmu.2020.574593 sha: doc_id: 277529 cord_uid: z2r14w2k file: cache/cord-277763-ihg3te63.json key: cord-277763-ihg3te63 authors: Moynan, David; Cagney, Maura; Dhuthaigh, Aoife Ni; Foley, Margaret; Salter, Aisling; Reidy, Niamh; Reidy, Paul; de Barra, Eoghan; Fitzpatrick, Fidelma title: The role of healthcare staff COVID-19 screening in infection prevention & control date: 2020-06-25 journal: J Infect DOI: 10.1016/j.jinf.2020.06.057 sha: doc_id: 277763 cord_uid: ihg3te63 file: cache/cord-277619-83bve5z0.json key: cord-277619-83bve5z0 authors: Huang, Victoria W.; Imam, Sarah A.; Nguyen, Shaun A. title: Head and neck survivorship care in the times of the SARS‐CoV‐2 pandemic date: 2020-05-02 journal: Head Neck DOI: 10.1002/hed.26235 sha: doc_id: 277619 cord_uid: 83bve5z0 file: cache/cord-277640-vy7ex5lv.json key: cord-277640-vy7ex5lv authors: Calderaro, Adriana; Arcangeletti, Maria Cristina; De Conto, Flora; Buttrini, Mirko; Montagna, Paolo; Montecchini, Sara; Ferraglia, Francesca; Pinardi, Federica; Chezzi, Carlo title: SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date: 2020-05-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.035 sha: doc_id: 277640 cord_uid: vy7ex5lv file: cache/cord-277679-sc9hugxr.json key: cord-277679-sc9hugxr authors: Khateb, Mohamed; Bosak, Noam; Muqary, Maryam title: Coronaviruses and Central Nervous System Manifestations date: 2020-06-23 journal: Front Neurol DOI: 10.3389/fneur.2020.00715 sha: doc_id: 277679 cord_uid: sc9hugxr file: cache/cord-277860-vzyrcmu4.json key: cord-277860-vzyrcmu4 authors: Pizzorno, Andrés; Padey, Blandine; Dubois, Julia; Julien, Thomas; Traversier, Aurélien; Dulière, Victoria; Brun, Pauline; Lina, Bruno; Rosa-Calatrava, Manuel; Terrier, Olivier title: In vitro evaluation of antiviral activity of single and combined repurposable drugs against SARS-CoV-2 date: 2020-07-15 journal: Antiviral Res DOI: 10.1016/j.antiviral.2020.104878 sha: doc_id: 277860 cord_uid: vzyrcmu4 file: cache/cord-277564-x5qfxag3.json key: cord-277564-x5qfxag3 authors: Kim, Si-Hyun; Jeong, Yeon Jeong; Kim, Youn Jeong; An, Ye Rin; Kwak, Eunji; Seo, Yeseul; Ahn, Joong Hyun title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea date: 2020-10-24 journal: nan DOI: 10.1016/j.ijso.2020.10.007 sha: doc_id: 277564 cord_uid: x5qfxag3 file: cache/cord-277873-4819g00y.json key: cord-277873-4819g00y authors: Matson, M. Jeremiah; Yinda, Claude Kwe; Seifert, Stephanie N.; Bushmaker, Trenton; Fischer, Robert J.; van Doremalen, Neeltje; Lloyd-Smith, James O.; Munster, Vincent J. title: Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum date: 2020-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid2609.202267 sha: doc_id: 277873 cord_uid: 4819g00y file: cache/cord-277812-4cz2hziz.json key: cord-277812-4cz2hziz authors: Sieni, Elena; Pegoraro, Francesco; Casini, Tommaso; Tondo, Annalisa; Bortone, Barbara; Moriondo, Maria; Azzari, Chiara; Galli, Luisa; Favre, Claudio title: Favourable outcome of coronavirus disease 2019 in a 1‐year‐old girl with acute myeloid leukaemia and severe treatment‐induced immunosuppression date: 2020-05-19 journal: Br J Haematol DOI: 10.1111/bjh.16781 sha: doc_id: 277812 cord_uid: 4cz2hziz file: cache/cord-277496-9ss09g6h.json key: cord-277496-9ss09g6h authors: Thaweerat, Wajana title: Current evidence on pancreatic involvement in SARS-CoV-2 infection date: 2020-05-27 journal: Pancreatology DOI: 10.1016/j.pan.2020.05.015 sha: doc_id: 277496 cord_uid: 9ss09g6h file: cache/cord-277410-lt19mijb.json key: cord-277410-lt19mijb authors: Salvatore, Phillip P; Dawson, Patrick; Wadhwa, Ashutosh; Rabold, Elizabeth M; Buono, Sean; Dietrich, Elizabeth A; Reses, Hannah E; Vuong, Jeni; Pawloski, Lucia; Dasu, Trivikram; Bhattacharyya, Sanjib; Pevzner, Eric; Hall, Aron J; Tate, Jacqueline E; Kirking, Hannah L title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1469 sha: doc_id: 277410 cord_uid: lt19mijb file: cache/cord-277611-3iynrfzq.json key: cord-277611-3iynrfzq authors: Buetti, Niccolò; Patrier, Juliette; Le Hingrat, Quentin; Loiodice, Ambre; Bouadma, Lila; Visseaux, Benoit; Timsit, Jean-François title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1315 sha: doc_id: 277611 cord_uid: 3iynrfzq file: cache/cord-277491-q18b88lm.json key: cord-277491-q18b88lm authors: Cao, Ying-Li; Wang, Ying; Guo, Rong; Yang, Fan; Zhang, Yun; Wang, Shu-Hui; Liu, Li title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date: 2011-02-11 journal: Molecules DOI: 10.3390/molecules16021544 sha: doc_id: 277491 cord_uid: q18b88lm file: cache/cord-278256-dmrtsxik.json key: cord-278256-dmrtsxik authors: Qiu, Haiyan; Wu, Junhua; Hong, Liang; Luo, Yunling; Song, Qifa; Chen, Dong title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study date: 2020-03-25 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30198-5 sha: doc_id: 278256 cord_uid: dmrtsxik file: cache/cord-277683-9cg90zbo.json key: cord-277683-9cg90zbo authors: Panettieri, Reynold A.; Carson, Jeffrey; Horton, Daniel; Barrett, Emily; Roy, Jason; Radbel, Jared title: Asthma and COVID: What are the Important Questions? date: 2020-06-22 journal: J Allergy Clin Immunol Pract DOI: 10.1016/j.jaip.2020.06.008 sha: doc_id: 277683 cord_uid: 9cg90zbo file: cache/cord-277911-x916hsg6.json key: cord-277911-x916hsg6 authors: Wu, Di; Lu, Jianyun; Ma, Xiaowei; Liu, Qun; Wang, Dedong; Gu, Yuzhou; Li, Yongguang; He, Weiyun title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) date: 2020-04-13 journal: Pediatr Infect Dis J DOI: 10.1097/inf.0000000000002688 sha: doc_id: 277911 cord_uid: x916hsg6 file: cache/cord-278106-ev1nx60h.json key: cord-278106-ev1nx60h authors: Cancarevic, Ivan; Tathineni, Praveena; Malik, Bilal Haider title: Coronavirus Disease 2019 (COVID-19) in Cancer Patients date: 2020-04-26 journal: Cureus DOI: 10.7759/cureus.7835 sha: doc_id: 278106 cord_uid: ev1nx60h file: cache/cord-277841-7sp8ftbc.json key: cord-277841-7sp8ftbc authors: Kumari, Pratibha; Singh, Archana; Rinchui Ngasainao, Moses; Shakeel, Ilma; Kumar, Sanjay; Lal, Seema; Singhal, Anchal; Singh Sohal, Sukhwinder; Kumar Singh, Indrakant; Imtaiyaz Hassan, Md. title: Potential diagnostics and therapeutic approaches in COVID-19 date: 2020-08-12 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.08.013 sha: doc_id: 277841 cord_uid: 7sp8ftbc file: cache/cord-277870-o79wph9r.json key: cord-277870-o79wph9r authors: Han, Yanqiang; Wang, Zhilong; Ren, Jiahao; Wei, Zhiyun; Li, Jinjin title: Potential inhibitors for the novel coronavirus (SARS-CoV-2) date: 2020-09-18 journal: Brief Bioinform DOI: 10.1093/bib/bbaa209 sha: doc_id: 277870 cord_uid: o79wph9r file: cache/cord-278249-vvhq9vgp.json key: cord-278249-vvhq9vgp authors: Blot, Mathieu; Jacquier, Marine; Aho Glele, Ludwig-Serge; Beltramo, Guillaume; Nguyen, Maxime; Bonniaud, Philippe; Prin, Sebastien; Andreu, Pascal; Bouhemad, Belaid; Bour, Jean-Baptiste; Binquet, Christine; Piroth, Lionel; Pais de Barros, Jean-Paul; Masson, David; Quenot, Jean-Pierre; Charles, Pierre-Emmanuel title: CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDS date: 2020-11-02 journal: Crit Care DOI: 10.1186/s13054-020-03328-0 sha: doc_id: 278249 cord_uid: vvhq9vgp file: cache/cord-277539-xt2nt11e.json key: cord-277539-xt2nt11e authors: Kochhar, Anuraj Singh; Bhasin, Ritasha; Kochhar, Gulsheen Kaur; Dadlani, Himanshu; Thakkar, Balvinder; Singh, Gurkeerat title: Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date: 2020 journal: Int J Clin Pediatr Dent DOI: 10.5005/jp-journals-10005-1782 sha: doc_id: 277539 cord_uid: xt2nt11e file: cache/cord-277759-zbmzjsvs.json key: cord-277759-zbmzjsvs authors: Wang, Luwen; Li, Xun; Chen, Hui; Yan, Shaonan; Li, Dong; Li, Yan; Gong, Zuojiong title: Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China date: 2020-03-31 journal: Am J Nephrol DOI: 10.1159/000507471 sha: doc_id: 277759 cord_uid: zbmzjsvs file: cache/cord-278050-wl83d6gs.json key: cord-278050-wl83d6gs authors: Morgenstern, Birgit; Michaelis, Martin; Baer, Patrick C.; Doerr, Hans W.; Cinatl, Jindrich title: Ribavirin and interferon-β synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines date: 2005-01-28 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2004.11.128 sha: doc_id: 278050 cord_uid: wl83d6gs file: cache/cord-277830-6fsz9iy7.json key: cord-277830-6fsz9iy7 authors: Saikatendu, Kumar Singh; Joseph, Jeremiah S.; Subramanian, Vanitha; Clayton, Tom; Griffith, Mark; Moy, Kin; Velasquez, Jeffrey; Neuman, Benjamin W.; Buchmeier, Michael J.; Stevens, Raymond C.; Kuhn, Peter title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 journal: Structure DOI: 10.1016/j.str.2005.07.022 sha: doc_id: 277830 cord_uid: 6fsz9iy7 file: cache/cord-277889-8u685f45.json key: cord-277889-8u685f45 authors: Costela-Ruiz, Víctor J.; Illescas-Montes, Rebeca; Puerta-Puerta, Jose M.; Ruiz, Concepción; Melguizo-Rodríguez, Lucia title: SARS-CoV-2 infection: the role of cytokines in COVID-19 disease date: 2020-06-02 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2020.06.001 sha: doc_id: 277889 cord_uid: 8u685f45 file: cache/cord-278182-75u57fw1.json key: cord-278182-75u57fw1 authors: Goh, Gerard Kian-Meng; Dunker, A. Keith; Foster, James A.; Uversky, Vladimir N. title: Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids date: 2020-03-31 journal: Microb Pathog DOI: 10.1016/j.micpath.2020.104177 sha: doc_id: 278182 cord_uid: 75u57fw1 file: cache/cord-278238-w1l8h8g8.json key: cord-278238-w1l8h8g8 authors: Okba, Nisreen MA; Raj, V Stalin; Haagmans, Bart L title: Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches date: 2017-04-13 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2017.03.007 sha: doc_id: 278238 cord_uid: w1l8h8g8 file: cache/cord-278362-pwi48i20.json key: cord-278362-pwi48i20 authors: Khan, Abbas; Ali, Syed Shujait; Khan, Muhammad Tahir; Saleem, Shoaib; Ali, Arif; Suleman, Muhammad; Babar, Zainib; Shafiq, Athar; Khan, Mazhar; Wei, Dong-Qing title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) date: 2020-06-18 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1779128 sha: doc_id: 278362 cord_uid: pwi48i20 file: cache/cord-277659-afysef1e.json key: cord-277659-afysef1e authors: Hamilton, F.; Muir, P.; Attwood, M.; Noel, A.; Vipond, B.; Hopes, R.; Moran, E.; Maskell, N.; Warwick, D.; Albur, M.; Turner, J.; MacGowan, A. P.; Arnold, D. T. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 journal: nan DOI: 10.1101/2020.07.03.20145722 sha: doc_id: 277659 cord_uid: afysef1e file: cache/cord-278522-e4qa19o6.json key: cord-278522-e4qa19o6 authors: Park, Se Yoon; Yun, Soon Gyu; Shin, Jeong Won; Lee, Bo Young; Son, Hyo-Ju; Lee, Seungjae; Lee, Eunjung; Kim, Tae Hyong title: Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs date: 2020-06-19 journal: Korean J Intern Med DOI: 10.3904/kjim.2020.203 sha: doc_id: 278522 cord_uid: e4qa19o6 file: cache/cord-277874-cr53ycrm.json key: cord-277874-cr53ycrm authors: Neault, N.; Baig, A. T.; Graber, T. E.; D'Aoust, P. M.; Mercier, E.; Alexandrov, I.; Crosby, D.; Mayne, J.; Pounds, T.; MacKenzie, M.; Figeys, D.; MacKenzie, A. E.; Delatolla, R. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 journal: nan DOI: 10.1101/2020.09.01.20185280 sha: doc_id: 277874 cord_uid: cr53ycrm file: cache/cord-278129-bpuyrsza.json key: cord-278129-bpuyrsza authors: De Haan, Cornelis A. M.; Rottier, Peter J. M. title: Hosting the severe acute respiratory syndrome coronavirus: specific cell factors required for infection date: 2006-06-27 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2006.00744.x sha: doc_id: 278129 cord_uid: bpuyrsza file: cache/cord-278457-yrm5hi3v.json key: cord-278457-yrm5hi3v authors: Sung, Heungsup; Han, Myung-Guk; Yoo, Cheon-Kwon; Lee, Sang-Won; Chung, Yoon-Seok; Park, Jae-Sun; Kim, Mi-Na; Lee, Hyukmin; Hong, Ki Ho; Seong, Moon-Woo; Lee, Kyunghoon; Chun, Sail; Lee, Wee Gyo; Kwon, Gye-Cheol; Min, Won-Ki title: Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea date: 2020-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid2610.202551 sha: doc_id: 278457 cord_uid: yrm5hi3v file: cache/cord-278406-n5e3a09i.json key: cord-278406-n5e3a09i authors: Macauley, Precious; Martin, Alvaro; Epelbaum, Oleg title: CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date: 2020-08-21 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.051 sha: doc_id: 278406 cord_uid: n5e3a09i file: cache/cord-277669-uujny2dm.json key: cord-277669-uujny2dm authors: Lumpuy-Castillo, Jairo; Lorenzo-Almorós, Ana; Pello-Lázaro, Ana María; Sánchez-Ferrer, Carlos; Egido, Jesús; Tuñón, José; Peiró, Concepción; Lorenzo, Óscar title: Cardiovascular Damage in COVID-19: Therapeutic Approaches Targeting the Renin-Angiotensin-Aldosterone System date: 2020-09-04 journal: Int J Mol Sci DOI: 10.3390/ijms21186471 sha: doc_id: 277669 cord_uid: uujny2dm file: cache/cord-277585-evw3pu87.json key: cord-277585-evw3pu87 authors: Malavolta, Marco; Giacconi, Robertina; Brunetti, Dario; Provinciali, Mauro; Maggi, Fabrizio title: Exploring the Relevance of Senotherapeutics for the Current SARS-CoV-2 Emergency and Similar Future Global Health Threats date: 2020-04-08 journal: Cells DOI: 10.3390/cells9040909 sha: doc_id: 277585 cord_uid: evw3pu87 file: cache/cord-278123-mq56em3z.json key: cord-278123-mq56em3z authors: Hasan, Mohammad Rubayet; Mirza, Faheem; Al-Hail, Hamad; Sundararaju, Sathyavathi; Xaba, Thabisile; Iqbal, Muhammad; Alhussain, Hashim; Yassine, Hadi Mohamad; Perez-Lopez, Andres; Tang, Patrick title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0236564 sha: doc_id: 278123 cord_uid: mq56em3z file: cache/cord-278176-o9glkhyv.json key: cord-278176-o9glkhyv authors: Houng, Huo-Shu H; Norwood, David; Ludwig, George V; Sun, Wellington; Lin, Minta; Vaughn, David W title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.04.008 sha: doc_id: 278176 cord_uid: o9glkhyv file: cache/cord-278271-rpq62xhl.json key: cord-278271-rpq62xhl authors: Lyu, Jinglu; Miao, Tianyu; Dong, Jiajia; Cao, Ranran; Li, Yan; Chen, Qianming title: Reflection on lower rates of COVID-19 in children: does childhood immunizations offer unexpected protection? date: 2020-05-15 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109842 sha: doc_id: 278271 cord_uid: rpq62xhl file: cache/cord-277816-ncdy9qgb.json key: cord-277816-ncdy9qgb authors: Wang, Ji-gan; Cui, Hai-rong; Tang, Hua-bo; Deng, Xiu-li title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis date: 2020-10-20 journal: Sci Rep DOI: 10.1038/s41598-020-74913-0 sha: doc_id: 277816 cord_uid: ncdy9qgb file: cache/cord-278509-k62bsk9b.json key: cord-278509-k62bsk9b authors: Manikandan, Natesan title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? date: 2020-09-12 journal: Vacunas DOI: 10.1016/j.vacun.2020.09.001 sha: doc_id: 278509 cord_uid: k62bsk9b file: cache/cord-277739-eb4z3u66.json key: cord-277739-eb4z3u66 authors: Hu, Ke; Guan, Wei-jie; Bi, Ying; Zhang, Wei; Li, Lanjuan; Zhang, Boli; Liu, Qingquan; Song, Yuanlin; Li, Xingwang; Duan, Zhongping; Zheng, Qingshan; Yang, Zifeng; Liang, Jingyi; Han, Mingfeng; Ruan, Lianguo; Wu, Chaomin; Zhang, Yunting; Jia, Zhen-hua; Zhong, Nan-shan title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial date: 2020-05-16 journal: Phytomedicine DOI: 10.1016/j.phymed.2020.153242 sha: doc_id: 277739 cord_uid: eb4z3u66 file: cache/cord-277907-x6387i7b.json key: cord-277907-x6387i7b authors: Tham, Sai Meng; Lim, Wei Yang; Lee, Chun Kiat; Loh, Jerold; Premkumar, Arthi; Yan, Benedict; Kee, Adrian; Chai, Louis; Tambyah, Paul Anantharajah; Yan, Gabriel title: Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020 date: 2020-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid2611.202752 sha: doc_id: 277907 cord_uid: x6387i7b file: cache/cord-278491-cnqxsno8.json key: cord-278491-cnqxsno8 authors: Wang, K.; Long, Q.-X.; Deng, H.-J.; Hu, J.; Gao, Q.-Z.; Zhang, G.-J.; He, C.-L.; Huang, L.-Y.; Hu, J.-L.; Chen, J.; Tang, N.; Huang, A.-L. title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-07-17 journal: nan DOI: 10.1101/2020.07.14.20151159 sha: doc_id: 278491 cord_uid: cnqxsno8 file: cache/cord-278045-hr3r17mz.json key: cord-278045-hr3r17mz authors: Yokota, Isao; Shane, Peter Y; Okada, Kazufumi; Unoki, Yoko; Yang, Yichi; Inao, Tasuku; Sakamaki, Kentaro; Iwasaki, Sumio; Hayasaka, Kasumi; Sugita, Junichi; Nishida, Mutsumi; Fujisawa, Shinichi; Teshima, Takanori title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-09-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1388 sha: doc_id: 278045 cord_uid: hr3r17mz file: cache/cord-278951-vxrwrzlj.json key: cord-278951-vxrwrzlj authors: Huang, Hsien-Hao; Yen, David Hung-Tsang; Kao, Wei-Fong; Wang, Lee-Min; Huang, Chun-I; Lee, Chen-Hsen title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak date: 2006-12-31 journal: Journal of the Formosan Medical Association DOI: 10.1016/s0929-6646(09)60106-6 sha: doc_id: 278951 cord_uid: vxrwrzlj file: cache/cord-278325-ykcd7d59.json key: cord-278325-ykcd7d59 authors: Cheung, Carmen Ka Man; Law, Man Fai; Lui, Grace Chung Yan; Wong, Sunny Hei; Wong, Raymond Siu Ming title: Coronavirus Disease 2019 (COVID-19): A Haematologist's Perspective date: 2020-07-28 journal: Acta Haematol DOI: 10.1159/000510178 sha: doc_id: 278325 cord_uid: ykcd7d59 file: cache/cord-278370-fuu20ae7.json key: cord-278370-fuu20ae7 authors: Palao, M.; Fernández-Díaz, E.; Gracia-Gil, J.; Romero-Sánchez, C.M.; Díaz-Maroto, I.; Segura, T. title: Multiple Sclerosis following SARS-CoV-2 infection date: 2020-07-07 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102377 sha: doc_id: 278370 cord_uid: fuu20ae7 file: cache/cord-278440-vti6xp9v.json key: cord-278440-vti6xp9v authors: Paraiso, Ines L; Revel, Johana S; Stevens, Jan F title: Potential use of polyphenols in the battle against COVID-19 date: 2020-09-09 journal: Curr Opin Food Sci DOI: 10.1016/j.cofs.2020.08.004 sha: doc_id: 278440 cord_uid: vti6xp9v file: cache/cord-278540-gy65bvot.json key: cord-278540-gy65bvot authors: Chen, I-Yin; Moriyama, Miyu; Chang, Ming-Fu; Ichinohe, Takeshi title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date: 2019-01-29 journal: Front Microbiol DOI: 10.3389/fmicb.2019.00050 sha: doc_id: 278540 cord_uid: gy65bvot file: cache/cord-278055-v2ed3tei.json key: cord-278055-v2ed3tei authors: Sia, Sin Fun; Yan, Li-Meng; Chin, Alex WH; Fung, Kevin; Choy, Ka-Tim; Wong, Alvina YL; Kaewpreedee, Prathanporn; Perera, Ranawaka APM; Poon, Leo LM; Nicholls, John M; Peiris, Malik; Yen, Hui-Ling title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 journal: Nature DOI: 10.1038/s41586-020-2342-5 sha: doc_id: 278055 cord_uid: v2ed3tei file: cache/cord-278093-0twnkv93.json key: cord-278093-0twnkv93 authors: Perveen, Shagufta; Orfali, Raha; Azam, Shafiq; Aati, Hanan Y.; Bukhari, Khulud; Bukhari, Sara I.; Al-Taweel, Areej title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 journal: Saudi Pharm J DOI: 10.1016/j.jsps.2020.06.006 sha: doc_id: 278093 cord_uid: 0twnkv93 file: cache/cord-278260-3o91v72a.json key: cord-278260-3o91v72a authors: Halstead, Scott B; Katzelnick, Leah title: COVID 19 Vaccines: Should we fear ADE? date: 2020-08-12 journal: J Infect Dis DOI: 10.1093/infdis/jiaa518 sha: doc_id: 278260 cord_uid: 3o91v72a file: cache/cord-278169-elhz77ek.json key: cord-278169-elhz77ek authors: Zhou, Dapeng; Tian, Xiaoxu; Qi, Ruibing; Peng, Chao; Zhang, Wen title: Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics date: 2020-06-10 journal: Glycobiology DOI: 10.1093/glycob/cwaa052 sha: doc_id: 278169 cord_uid: elhz77ek file: cache/cord-278649-ge9ike2c.json key: cord-278649-ge9ike2c authors: Makaronidis, Janine; Mok, Jessica; Balogun, Nyaladzi; Magee, Cormac G.; Omar, Rumana Z.; Carnemolla, Alisia; Batterham, Rachel L. title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study date: 2020-10-01 journal: PLoS Med DOI: 10.1371/journal.pmed.1003358 sha: doc_id: 278649 cord_uid: ge9ike2c file: cache/cord-278812-5jps95q9.json key: cord-278812-5jps95q9 authors: Edwards, Sarah J L; Santini, Joanne M title: Anthroponotic risk of SARS-CoV-2, precautionary mitigation, and outbreak management date: 2020-07-02 journal: Lancet Microbe DOI: 10.1016/s2666-5247(20)30086-0 sha: doc_id: 278812 cord_uid: 5jps95q9 file: cache/cord-278467-c0jw9dkw.json key: cord-278467-c0jw9dkw authors: Tulchinsky, Mark; Osmany, Saabry title: The American College of Nuclear Medicine Guidance on Operating Procedures for a Nuclear Medicine Facility During COVID-19 Pandemic date: 2020-05-01 journal: Clin Nucl Med DOI: 10.1097/rlu.0000000000003146 sha: doc_id: 278467 cord_uid: c0jw9dkw file: cache/cord-278678-ivye1qao.json key: cord-278678-ivye1qao authors: Calvez, R. M.; Taylor, A.; Calvo-Bado, L.; Fink, C. G. title: Molecular detection of SARS-CoV-2 using a reagent-free approach date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.28.20083626 sha: doc_id: 278678 cord_uid: ivye1qao file: cache/cord-278945-q5lzf5o4.json key: cord-278945-q5lzf5o4 authors: Hashemi, Seyed Ahmad; Safamanesh, Saghar; Ghasemzadeh‐Moghaddam, Hamed; Ghafouri, Majid; Zadeh‐Heydari, Mina Sadat Mohajer; Abad, Hasan Namdar Ahmad; Amir, Azimian title: Report of death in children with SARS‐CoV‐2 and Human metapneumovirus (hMPV) co‐infection: is hMPV the trigger? date: 2020-08-07 journal: J Med Virol DOI: 10.1002/jmv.26401 sha: doc_id: 278945 cord_uid: q5lzf5o4 file: cache/cord-278618-7tu5c7m1.json key: cord-278618-7tu5c7m1 authors: Romano-Bertrand, Sara; Aho-Glele, Ludwig-Serge; Grandbastien, Bruno; Gehanno, Jean-François; Lepelletier, Didier title: Sustainability of SARS-CoV-2 in aerosols: Should we worry about airborne transmission? date: 2020-06-12 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.06.018 sha: doc_id: 278618 cord_uid: 7tu5c7m1 file: cache/cord-278839-uu2wlpmp.json key: cord-278839-uu2wlpmp authors: Alberca, Ricardo Wesley; Pereira, Nátalli Zanete; Oliveira, Luanda Mara Da Silva; Gozzi-Silva, Sarah Cristina; Sato, Maria Notomi title: Pregnancy, Viral Infection, and COVID-19 date: 2020-07-07 journal: Front Immunol DOI: 10.3389/fimmu.2020.01672 sha: doc_id: 278839 cord_uid: uu2wlpmp file: cache/cord-278225-d0gxb6bx.json key: cord-278225-d0gxb6bx authors: Meng, Yifan; Guo, Ensong; Liu, Jia; Huang, Xiaoyuan; Sun, Chaoyang; Wu, Peng; Chen, Gang title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients date: 2020-04-30 journal: J Infect DOI: 10.1016/j.jinf.2020.04.036 sha: doc_id: 278225 cord_uid: d0gxb6bx file: cache/cord-279105-e2zjxjox.json key: cord-279105-e2zjxjox authors: Lee, Cheryl Yi-Pin; Lin, Raymond T. P.; Renia, Laurent; Ng, Lisa F. 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T. title: The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 date: 2020-05-20 journal: nan DOI: 10.1101/2020.05.15.20103416 sha: doc_id: 278960 cord_uid: 3xw4qjoy file: cache/cord-278987-3s5p9yw6.json key: cord-278987-3s5p9yw6 authors: Hirotsu, Yosuke; Maejima, Makoto; Nakajima, Masumi; Mochizuki, Hitoshi; Omata, Masao title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship date: 2020-04-17 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.144 sha: doc_id: 278987 cord_uid: 3s5p9yw6 file: cache/cord-278759-pykihnup.json key: cord-278759-pykihnup authors: Koh, Yiwen; Hegney, Desley; Drury, Vicki title: Nurses' perceptions of risk from emerging respiratory infectious diseases: A Singapore study date: 2012-03-21 journal: Int J Nurs Pract DOI: 10.1111/j.1440-172x.2012.02018.x sha: doc_id: 278759 cord_uid: pykihnup file: cache/cord-279132-florvm7z.json key: cord-279132-florvm7z authors: K., Branimir; Hackenberger, title: From apparent to true – from frequency to distributions (II) date: 2020-08-17 journal: Croat Med J DOI: 10.3325/cmj.2020.61.381 sha: doc_id: 279132 cord_uid: florvm7z file: cache/cord-278721-g5zqebju.json key: cord-278721-g5zqebju authors: Jakhmola, Shweta; Indari, Omkar; Baral, Budhadev; Kashyap, Dharmendra; Varshney, Nidhi; Das, Ayan; Chatterjee, Sayantani; Jha, Hem Chandra title: Comorbidity Assessment Is Essential During COVID-19 Treatment date: 2020-08-04 journal: Front Physiol DOI: 10.3389/fphys.2020.00984 sha: doc_id: 278721 cord_uid: g5zqebju file: cache/cord-278453-ogbmaw3o.json key: cord-278453-ogbmaw3o authors: Spiller, Tobias R.; Méan, Marie; Ernst, Jutta; Sazpinar, Onur; Gehrke, Samuel; Paolercio, Francesca; Petry, Heidi; Pfaltz, Monique C.; Morina, Naser; Aebischer, Oriane; Gachoud, David; von Känel, Roland; Weilenmann, Sonja title: Development of health care workers' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies date: 2020-08-13 journal: Psychological medicine DOI: 10.1017/s0033291720003128 sha: doc_id: 278453 cord_uid: ogbmaw3o file: cache/cord-279290-wtnnlp4i.json key: cord-279290-wtnnlp4i authors: Solorio-Pineda, Saúl; Almendárez-Sánchez, César Adán; Tafur-Grandett, Abrahan Alfonso; Ramos-Martínez, Gabriel Arturo; Huato-Reyes, Raúl; Ruiz-Flores, Milton Inocencio; Sosa-Najera, Antonio title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? date: 2020-09-25 journal: Surg Neurol Int DOI: 10.25259/sni_305_2020 sha: doc_id: 279290 cord_uid: wtnnlp4i file: cache/cord-279334-j0i9ozsz.json key: cord-279334-j0i9ozsz authors: McCreary, Erin K; Pogue, Jason M title: Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date: 2020-03-23 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa105 sha: doc_id: 279334 cord_uid: j0i9ozsz file: cache/cord-279255-v861kk0i.json key: cord-279255-v861kk0i authors: Dhama, Kuldeep; Khan, Sharun; Tiwari, Ruchi; Sircar, Shubhankar; Bhat, Sudipta; Malik, Yashpal Singh; Singh, Karam Pal; Chaicumpa, Wanpen; Bonilla-Aldana, D. Katterine; Rodriguez-Morales, Alfonso J. title: Coronavirus Disease 2019–COVID-19 date: 2020-06-24 journal: Clin Microbiol Rev DOI: 10.1128/cmr.00028-20 sha: doc_id: 279255 cord_uid: v861kk0i file: cache/cord-279172-d2algx16.json key: cord-279172-d2algx16 authors: Zheng, Kewen; Ma, Guozheng; Zhou, Jinming; Zen, Min; Zhao, Wenna; Jiang, Yongjun; Yu, Qingsen; Feng, Jialiang title: Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme date: 2006-11-02 journal: Proteins DOI: 10.1002/prot.21160 sha: doc_id: 279172 cord_uid: d2algx16 file: cache/cord-279260-tdvb0fhv.json key: cord-279260-tdvb0fhv authors: Lv, Huibin; Wu, Nicholas C.; Mok, Chris K. 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Tian, Honglin; Laverdure, Chris; Morzunov, Sergey; Verma, Subhash C.; VanHooser, Stephanie; Pandori, Mark W. title: High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date: 2020-06-10 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104501 sha: doc_id: 279563 cord_uid: 4lu1n0s7 file: cache/cord-279115-eyk8sxk7.json key: cord-279115-eyk8sxk7 authors: Cecconi, Maurizio; Forni, Guido; Mantovani, Alberto title: Ten things we learned about COVID-19 date: 2020-06-05 journal: Intensive Care Med DOI: 10.1007/s00134-020-06140-0 sha: doc_id: 279115 cord_uid: eyk8sxk7 file: cache/cord-279180-xad53zht.json key: cord-279180-xad53zht authors: Kumaravel, Santhosh Kumar; Subramani, Ranjith Kumar; Jayaraj Sivakumar, Tharun Kumar; Madurai Elavarasan, Rajvikram; Manavalanagar Vetrichelvan, Ajayragavan; Annam, Annapurna; Subramaniam, Umashankar title: Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies date: 2020-08-17 journal: 3 Biotech DOI: 10.1007/s13205-020-02382-3 sha: doc_id: 279180 cord_uid: xad53zht file: cache/cord-279363-4almssg6.json key: cord-279363-4almssg6 authors: Crespo, Roland Mojica; Morales Crespo, Mairim Melissa title: Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión date: 2020-05-16 journal: Semergen DOI: 10.1016/j.semerg.2020.05.010 sha: doc_id: 279363 cord_uid: 4almssg6 file: cache/cord-279435-ffgd2ets.json key: cord-279435-ffgd2ets authors: ALBalawi, Hani B title: COVID-19: Precautionary Guidelines for Ophthalmologists date: 2020-06-25 journal: Cureus DOI: 10.7759/cureus.8815 sha: doc_id: 279435 cord_uid: ffgd2ets file: cache/cord-279629-t1xjy12y.json key: cord-279629-t1xjy12y authors: Nazneen Akhand, Mst Rubaiat; Azim, Kazi Faizul; Hoque, Syeda Farjana; Moli, Mahmuda Akther; Joy, Bijit Das; Akter, Hafsa; Afif, Ibrahim Khalil; Ahmed, Nadim; Hasan, Mahmudul title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date: 2020-04-15 journal: bioRxiv DOI: 10.1101/2020.04.15.036285 sha: doc_id: 279629 cord_uid: t1xjy12y file: cache/cord-279642-0j5828ah.json key: cord-279642-0j5828ah authors: Stafford, Emma G.; Riviere, Jim; Xu, Xuan; Kawakami, Jessica; Wyckoff, Gerald J.; Jaberi-Douraki, Majid title: Pharmacovigilance in Patients with Diabetes: A Data-Driven Analysis Identifying Specific RAS Antagonists with Adverse Pulmonary Safety Profiles That Have Implications for COVID-19 Morbidity and Mortality date: 2020-06-01 journal: J Am Pharm Assoc (2003) DOI: 10.1016/j.japh.2020.05.018 sha: doc_id: 279642 cord_uid: 0j5828ah file: cache/cord-279346-7del8d2p.json key: cord-279346-7del8d2p authors: Callendret, Benoît; Lorin, Valérie; Charneau, Pierre; Marianneau, Philippe; Contamin, Hugues; Betton, Jean-Michel; van der Werf, Sylvie; Escriou, Nicolas title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 journal: Virology DOI: 10.1016/j.virol.2007.01.012 sha: doc_id: 279346 cord_uid: 7del8d2p file: cache/cord-279765-sb1ifyfx.json key: cord-279765-sb1ifyfx authors: Isakova-Sivak, Irina; Rudenko, Larisa title: A promising inactivated whole-virion SARS-CoV-2 vaccine date: 2020-10-15 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30832-x sha: doc_id: 279765 cord_uid: sb1ifyfx file: cache/cord-279443-2e4gz2bo.json key: cord-279443-2e4gz2bo authors: Khan, Suliman; Liu, Jianbo; Xue, Mengzhou title: Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns date: 2020-06-09 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00310 sha: doc_id: 279443 cord_uid: 2e4gz2bo file: cache/cord-279766-s3ms5f56.json key: cord-279766-s3ms5f56 authors: Ye, Zhongde; Wong, Chung Kai; Li, Peng; Xie, Yong title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis date: 2008-07-28 journal: Biochim Biophys Acta Gen Subj DOI: 10.1016/j.bbagen.2008.07.009 sha: doc_id: 279766 cord_uid: s3ms5f56 file: cache/cord-279616-8gtumtxb.json key: cord-279616-8gtumtxb authors: Wu, Kitty K.; Chan, Sumee K.; Ma, Tracy M. title: Posttraumatic Stress after SARS date: 2005-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid1108.041083 sha: doc_id: 279616 cord_uid: 8gtumtxb file: cache/cord-279750-if9vphb2.json key: cord-279750-if9vphb2 authors: Savić, Dragan; Alsheikh, Tarik M.; Alhaj, Ahmad Kh.; Lazovic, Lazar; Alsarraf, Lamya; Bosnjakovic, Petar; Yousef, Waleed title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report date: 2020-07-27 journal: Acta Neurochir (Wien) DOI: 10.1007/s00701-020-04510-7 sha: doc_id: 279750 cord_uid: if9vphb2 file: cache/cord-279131-1unb0z79.json key: cord-279131-1unb0z79 authors: Buijsers, Baranca; Yanginlar, Cansu; Maciej-Hulme, Marissa L.; de Mast, Quirijn; van der Vlag, Johan title: Beneficial non-anticoagulant mechanisms underlying heparin treatment of COVID-19 patients date: 2020-08-25 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102969 sha: doc_id: 279131 cord_uid: 1unb0z79 file: cache/cord-279439-h4ji0ttm.json key: cord-279439-h4ji0ttm authors: Viotti, Manuel; Montano, Mauricio; Victor, Andrea; Griffin, Darren K.; Duong, Tommy; Bolduc, Nathalie; Farmer, Andrew; Gonzalez, Isabel; Barnes, Frank; Zouves, Christo; Greene, Warner C. title: HUMAN PRE-IMPLANTATION EMBRYOS ARE PERMISSIVE TO SARS-COV-2 ENTRY date: 2020-09-30 journal: Fertility and Sterility DOI: 10.1016/j.fertnstert.2020.09.127 sha: doc_id: 279439 cord_uid: h4ji0ttm file: cache/cord-279223-qvih5qas.json key: cord-279223-qvih5qas authors: Hascoët, Jean-Michel; Jellimann, Jean-Marc; Hartard, Cedric; Wittwer, Apolline; Jeulin, Hélène; Franck, Patricia; Morel, Olivier title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 journal: Front Pediatr DOI: 10.3389/fped.2020.568979 sha: doc_id: 279223 cord_uid: qvih5qas file: cache/cord-279861-gk8cow8k.json key: cord-279861-gk8cow8k authors: Glasser, John W.; Hupert, Nathaniel; McCauley, Mary M.; Hatchett, Richard title: Modeling and public health emergency responses: Lessons from SARS date: 2011-01-28 journal: Epidemics DOI: 10.1016/j.epidem.2011.01.001 sha: doc_id: 279861 cord_uid: gk8cow8k file: cache/cord-279584-9x1d1kp1.json key: cord-279584-9x1d1kp1 authors: Anderson, E. 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E. title: Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection date: 2020-11-10 journal: nan DOI: 10.1101/2020.11.06.20227215 sha: doc_id: 279584 cord_uid: 9x1d1kp1 file: cache/cord-279725-d82sj80v.json key: cord-279725-d82sj80v authors: Ströher, Ute; DiCaro, Antonino; Li, Yan; Strong, James E.; Aoki, Fred; Plummer, Frank; Jones, Steven M.; Feldmann, Heinz title: Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date: 2004-04-01 journal: J Infect Dis DOI: 10.1086/382597 sha: doc_id: 279725 cord_uid: d82sj80v file: cache/cord-279576-wt4crton.json key: cord-279576-wt4crton authors: Fajardo, Álvaro; Pereira-Gómez, Marianoel; Echeverría, Natalia; López-Tort, Fernando; Perbolianachis, Paula; Aldunate, Fabián; Moreno, Pilar; Moratorio, Gonzalo title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 journal: bioRxiv DOI: 10.1101/2020.05.13.093609 sha: doc_id: 279576 cord_uid: wt4crton file: cache/cord-280147-xvzi1i0v.json key: cord-280147-xvzi1i0v authors: Consoli, Letizia; Bendotti, Vittorio; Cicchinelli, Sara; Gaioni, Federico; Prandolini, Paola; Bettonagli, Monica; Terragnoli, Paolo title: 2019 novel coronavirus (COVID-19) pneumonia complications: the importance of lung ultrasound date: 2020-06-19 journal: J Ultrasound DOI: 10.1007/s40477-020-00494-3 sha: doc_id: 280147 cord_uid: xvzi1i0v file: cache/cord-279754-95zawygq.json key: cord-279754-95zawygq authors: Hsu, Yu-Chen; Chen, Yu-Ling; Wei, Han-Ning; Yang, Yu-Wen; Chen, Ying-Hwei title: Risk and Outbreak Communication: Lessons from Taiwan's Experiences in the Post-SARS Era date: 2017-04-01 journal: Health Secur DOI: 10.1089/hs.2016.0111 sha: doc_id: 279754 cord_uid: 95zawygq file: cache/cord-279406-wwdqh9qs.json key: cord-279406-wwdqh9qs authors: Guzman, Norberto A.; Guzman, Daniel E. title: A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy date: 2020-07-30 journal: Biomedicines DOI: 10.3390/biomedicines8080255 sha: doc_id: 279406 cord_uid: wwdqh9qs file: cache/cord-280025-4hmecfi0.json key: cord-280025-4hmecfi0 authors: Korber, B; Fischer, WM; Gnanakaran, S; Yoon, H; Theiler, J; Abfalterer, W; Foley, B; Giorgi, EE; Bhattacharya, T; Parker, MD; Partridge, DG; Evans, CM; Freeman, TM; de Silva, TI; LaBranche, CC; Montefiori, DC title: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date: 2020-05-05 journal: bioRxiv DOI: 10.1101/2020.04.29.069054 sha: doc_id: 280025 cord_uid: 4hmecfi0 file: cache/cord-280043-bm0qkrod.json key: cord-280043-bm0qkrod authors: Esagian, Stepan M.; Ziogas, Ioannis A.; Giannis, Dimitrios; Hayat, Muhammad H.; Elias, Nahel; Tsoulfas, Georgios title: Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic date: 2020-06-04 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00287 sha: doc_id: 280043 cord_uid: bm0qkrod file: cache/cord-279932-bilr71ay.json key: cord-279932-bilr71ay authors: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1013 sha: doc_id: 279932 cord_uid: bilr71ay file: cache/cord-279474-c5y2lygj.json key: cord-279474-c5y2lygj authors: Bozzo, Caterina Prelli; Nchioua, Rayhane; Volcic, Meta; Wettstein, Lukas; Weil, Tatjana; Krüger, Jana; Heller, Sandra; Conzelmann, Carina; Müller, Janis; Gross, Rüdiger; Zech, Fabian; Schütz, Desiree; Koepke, Lennart; Stuerzel, Christina M; Schüler, Christiane; Stenzel, Saskia; Braun, Elisabeth; Weiß, Johanna; Sauter, Daniel; Münch, Jan; Stenger, Steffen; Sato, Kei; Kleger, Alexander; Goffinet, Christine; Sparrer, Konstantin M.J.; Kirchhoff, Frank title: IFITM proteins promote SARS-CoV-2 infection of human lung cells date: 2020-08-18 journal: bioRxiv DOI: 10.1101/2020.08.18.255935 sha: doc_id: 279474 cord_uid: c5y2lygj file: cache/cord-279519-4ad8ubrt.json key: cord-279519-4ad8ubrt authors: Poochi, Saravana Prabha; Easwaran, Murugesh; Balasubramanian, Balamuralikrishnan; Anbuselvam, Mohan; Meyyazhagan, Arun; Park, Sungkwon; Bhotla, Haripriya Kuchi; Anbuselvam, Jeeva; Arumugam, Vijaya Anand; Keshavarao, Sasikala; Kanniyappan, Gopalakrishnan Velliyur; Pappusamy, Manikantan; Kaul, Tanushri title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein date: 2020-07-06 journal: Food Front DOI: 10.1002/fft2.29 sha: doc_id: 279519 cord_uid: 4ad8ubrt file: cache/cord-279518-z3k7zaw4.json key: cord-279518-z3k7zaw4 authors: Xue, Xiaotong; Mi, Zihao; Wang, Zhenzhen; Pang, Zheng; Liu, Hong; Zhang, Furen title: High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2 date: 2020-05-23 journal: J Invest Dermatol DOI: 10.1016/j.jid.2020.05.087 sha: doc_id: 279518 cord_uid: z3k7zaw4 file: cache/cord-279520-zccd1mq5.json key: cord-279520-zccd1mq5 authors: Christian, Michael D.; Loutfy, Mona; McDonald, L. Clifford; Martinez, Kenneth F.; Ofner, Mariana; Wong, Tom; Wallington, Tamara; Gold, Wayne L.; Mederski, Barbara; Green, Karen; Low, Donald E. title: Possible SARS Coronavirus Transmission during Cardiopulmonary Resuscitation date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030700 sha: doc_id: 279520 cord_uid: zccd1mq5 file: cache/cord-279989-swsxez0a.json key: cord-279989-swsxez0a authors: Sokolov, Elisaveta; Hadavi, Shahrzad; Mantoan Ritter, Laura; Brunnhuber, Franz title: Non-convulsive status epilepticus: COVID-19 or clozapine induced? date: 2020-10-04 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-239015 sha: doc_id: 279989 cord_uid: swsxez0a file: cache/cord-280029-g1k3zlax.json key: cord-280029-g1k3zlax authors: Gabutti, Giovanni; d’Anchera, Erica; Sandri, Federica; Savio, Marta; Stefanati, Armando title: Coronavirus: Update Related to the Current Outbreak of COVID-19 date: 2020-04-08 journal: Infect Dis Ther DOI: 10.1007/s40121-020-00295-5 sha: doc_id: 280029 cord_uid: g1k3zlax file: cache/cord-280050-fktc778q.json key: cord-280050-fktc778q authors: Tahir, Shumaila; Tahir, Syeda Anjala; Bin Arif, Taha; Majid, Bushra; Majid, Zainab; Malik, Farheen; Ahmed, Ashfaque; Memon, Arslan; Ahmed, Jawad title: Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan date: 2020-06-17 journal: Cureus DOI: 10.7759/cureus.8679 sha: doc_id: 280050 cord_uid: fktc778q file: cache/cord-280003-ndpuezpo.json key: cord-280003-ndpuezpo authors: Lou, Bin; Li, Tigndong; Zheng, Shufa; Su, Yingying; Li, Zhiyong; Liu, Wei; Yu, Fei; Ge, Shengxiang; Zou, Qianda; Yuan, Quan; Lin, Sha; Hong, Congming; Yao, Xiangyang; Zhang, Xuejie; Wu, Dinghui; Zhou, Guoliang; Hou, Wangheng; Li, Tingting; Zhang, Yali; Zhang, Shiyin; Fan, Jian; Zhang, Jun; Xia, Ningshao; Chen, Yu title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date: 2020-03-27 journal: nan DOI: 10.1101/2020.03.23.20041707 sha: doc_id: 280003 cord_uid: ndpuezpo file: cache/cord-279569-289fu2yb.json key: cord-279569-289fu2yb authors: Lei, Yu; lan, yunping; lu, jianli; huang, xiaobo; silang, bamu; zeng, fan title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area date: 2020-03-13 journal: nan DOI: 10.1101/2020.03.09.20033126 sha: doc_id: 279569 cord_uid: 289fu2yb file: cache/cord-279976-juz9jnfk.json key: cord-279976-juz9jnfk authors: Xie, Mingxuan; Chen, Qiong title: Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date: 2020-04-01 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.071 sha: doc_id: 279976 cord_uid: juz9jnfk file: cache/cord-279691-v5kpmk0b.json key: cord-279691-v5kpmk0b authors: Hagemeijer, Marne C.; Rottier, Peter J.M.; de Haan, Cornelis A.M. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 journal: Viruses DOI: 10.3390/v4113245 sha: doc_id: 279691 cord_uid: v5kpmk0b file: cache/cord-280198-bhjw6xc5.json key: cord-280198-bhjw6xc5 authors: Olaleye, Omonike A.; Kaur, Manvir; Onyenaka, Collins; Adebusuyi, Tolu title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date: 2020-08-14 journal: bioRxiv DOI: 10.1101/2020.08.14.250480 sha: doc_id: 280198 cord_uid: bhjw6xc5 file: cache/cord-279940-i2rgjpxf.json key: cord-279940-i2rgjpxf authors: Comentale, Giuseppe; Manzo, Rachele; Pilato, Emanuele title: Sars-Cov-2 interference in HEME production: is it the time for an early predictive biomarker? date: 2020-06-29 journal: J Mol Med (Berl) DOI: 10.1007/s00109-020-01945-4 sha: doc_id: 279940 cord_uid: i2rgjpxf file: cache/cord-280350-ay4cnzn5.json key: cord-280350-ay4cnzn5 authors: Chan, Jasper F.W.; Chan, Kwok-Hung; Kao, Richard Y.T.; To, Kelvin K.W.; Zheng, Bo-Jian; Li, Clara P.Y.; Li, Patrick T.W.; Dai, Jun; Mok, Florence K.Y.; Chen, Honglin; Hayden, Frederick G.; Yuen, Kwok-Yung title: Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus date: 2013-10-03 journal: J Infect DOI: 10.1016/j.jinf.2013.09.029 sha: doc_id: 280350 cord_uid: ay4cnzn5 file: cache/cord-280454-etf32afd.json key: cord-280454-etf32afd authors: Moustaqil, Mehdi; Ollivier, Emma; Chiu, Hsin-Ping; Van Tol, Sarah; Rudolffi-Soto, Paulina; Stevens, Christian; Bhumkar, Akshay; Hunter, Dominic J.B.; Freiberg, Alex; Jacques, David; Lee, Benhur; Sierecki, Emma; Gambin, Yann title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date: 2020-06-05 journal: bioRxiv DOI: 10.1101/2020.06.05.135699 sha: doc_id: 280454 cord_uid: etf32afd file: cache/cord-280001-y7pvj2l1.json key: cord-280001-y7pvj2l1 authors: Patel, Robin; Babady, Esther; Theel, Elitza S.; Storch, Gregory A.; Pinsky, Benjamin A.; St. George, Kirsten; Smith, Tara C.; Bertuzzi, Stefano title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 journal: mBio DOI: 10.1128/mbio.00722-20 sha: doc_id: 280001 cord_uid: y7pvj2l1 file: cache/cord-280392-ij5gtesw.json key: cord-280392-ij5gtesw authors: Gultom, Mitra; Licheri, Matthias; Laloli, Laura; Wider, Manon; Strässle, Marina; Steiner, Silvio; Kratzel, Annika; Thao, Tran Thi Nhu; Stalder, Hanspeter; Portmann, Jasmine; Holwerda, Melle; V’kovski, Philip; Ebert, Nadine; Stokar – Regenscheit, Nadine; Gurtner, Corinne; Zanolari, Patrik; Posthaus, Horst; Schuller, Simone; Vicente – Santos, Amanda; Moreira – Soto, Andres; Corrales – Aguilar, Eugenia; Ruggli, Nicolas; Tekes, Gergely; von Messling, Veronika; Sawatsky, Bevan; Thiel, Volker; Dijkman, Ronald title: Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date: 2020-11-10 journal: bioRxiv DOI: 10.1101/2020.11.10.374587 sha: doc_id: 280392 cord_uid: ij5gtesw file: cache/cord-280231-jo3grxd5.json key: cord-280231-jo3grxd5 authors: Hardenberg, Jan‐Hendrik; Luft, Friedrich C. title: Covid‐19, ACE2 and the kidney date: 2020-08-02 journal: Acta Physiol (Oxf) DOI: 10.1111/apha.13539 sha: doc_id: 280231 cord_uid: jo3grxd5 file: cache/cord-280408-0ze1lfnf.json key: cord-280408-0ze1lfnf authors: Leon, A.; Debry, C.; Renaud, M. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 journal: Eur Ann Otorhinolaryngol Head Neck Dis DOI: 10.1016/j.anorl.2020.05.005 sha: doc_id: 280408 cord_uid: 0ze1lfnf file: cache/cord-280423-v3r7vo0o.json key: cord-280423-v3r7vo0o authors: Desmazes‐Dufeu, Nadine; Coltey, Bérengère; Amari, Lyria; Gouitaa, Marion; Touzery, Camille; Reynaud‐Gaubert, Martine; Chanez, Pascal; Cassir, Nadim title: Discordant courses of COVID‐19 in a cohabiting couple of lung transplant recipients date: 2020-07-31 journal: Transpl Infect Dis DOI: 10.1111/tid.13410 sha: doc_id: 280423 cord_uid: v3r7vo0o file: cache/cord-280518-2tl0mtb8.json key: cord-280518-2tl0mtb8 authors: Xia, Jianhua; Tong, Jianping; Liu, Mengyun; Shen, Ye; Guo, Dongyu title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection date: 2020-03-12 journal: J Med Virol DOI: 10.1002/jmv.25725 sha: doc_id: 280518 cord_uid: 2tl0mtb8 file: cache/cord-280621-tph5n7ak.json key: cord-280621-tph5n7ak authors: Kim, Yunjeong; Liu, Hongwei; Galasiti Kankanamalage, Anushka C.; Weerasekara, Sahani; Hua, Duy H.; Groutas, William C.; Chang, Kyeong-Ok; Pedersen, Niels C. title: Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor date: 2016-03-30 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005531 sha: doc_id: 280621 cord_uid: tph5n7ak file: cache/cord-280062-1qrav1d5.json key: cord-280062-1qrav1d5 authors: McClenaghan, Elliot; Cosgriff, Rebecca; Brownlee, Keith; Ahern, Susannah; Burgel, Pierre-Régis; Byrnes, Catherine A; Colombo, Carla; Corvol, Harriet; Cheng, Stephanie Y; Daneau, Géraldine; Elbert, Alexander; Faro, Albert; Goss, Christopher H; Gulmans, Vincent; Gutierrez, Hector; de Monestrol, Isabelle; Jung, Andreas; Justus, Lutz Nährlich; Kashirskaya, Nataliya; Marshall, Bruce C; McKone, Edward; Middleton, Peter G; Mondejar-Lopez, Pedro; Pastor-Vivero, M Dolores; Padoan, Rita; Rizvi, Samar; Ruseckaite, Rasa; Salvatore, Marco; Stephenson, Anne; Filho, Luiz Vicente R da Silva; Melo, Joel; Zampoli, Marco; Carr, Siobhán B title: The global impact of SARS-CoV-2 in 181 people with cystic fibrosis date: 2020-11-04 journal: J Cyst Fibros DOI: 10.1016/j.jcf.2020.10.003 sha: doc_id: 280062 cord_uid: 1qrav1d5 file: cache/cord-280172-6o1gqe8v.json key: cord-280172-6o1gqe8v authors: Sanami, Samira; Zandi, Milad; Pourhossein, Behzad; Mobini, Gholam-Reza; Safaei, Mohsen; Abed, Atena; Arvejeh, Pooria Mohammadi; Chermahini, Fatemeh Amini; Alizadeh, Morteza title: Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date: 2020-07-15 journal: Int J Biol Macromol DOI: 10.1016/j.ijbiomac.2020.07.117 sha: doc_id: 280172 cord_uid: 6o1gqe8v file: cache/cord-280280-9jr7ekbu.json key: cord-280280-9jr7ekbu authors: Bertoncelli, Deborah; Guidarini, Marta; Della Greca, Anna; Ratti, Chiara; Falcinella, Francesca; Iovane, Brunella; Dutto, Mauro Luigi; Caffarelli, Carlo; Tchana, Bertrand title: COVID19: potential cardiovascular issues in pediatric patients date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9655 sha: doc_id: 280280 cord_uid: 9jr7ekbu file: cache/cord-280528-7ivw72l0.json key: cord-280528-7ivw72l0 authors: TUFAN, Abdurrahman; AVANOĞLU GÜLER, Aslıhan; MATUCCI-CERINIC, Marco title: COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs date: 2020-04-21 journal: Turk J Med Sci DOI: 10.3906/sag-2004-168 sha: doc_id: 280528 cord_uid: 7ivw72l0 file: cache/cord-280068-rszu1c48.json key: cord-280068-rszu1c48 authors: Twomey, Julianne D.; Luo, Shen; Dean, Alexis Q.; Bozza, William P.; Nalli, Ancy; Zhang, Baolin title: COVID-19 update: The race to therapeutic development date: 2020-10-24 journal: Drug Resist Updat DOI: 10.1016/j.drup.2020.100733 sha: doc_id: 280068 cord_uid: rszu1c48 file: cache/cord-280821-kc0ut4oy.json key: cord-280821-kc0ut4oy authors: Venturini, Elisabetta; Montagnani, Carlotta; Garazzino, Silvia; Donà, Daniele; Pierantoni, Luca; Lo Vecchio, Andrea; Nicolini, Giangiacomo; Bianchini, Sonia; Krzysztofiak, Andrzej; Galli, Luisa; Villani, Alberto; Castelli-Gattinara, Guido title: Treatment of children with COVID-19: position paper of the Italian Society of Pediatric Infectious Disease date: 2020-09-24 journal: Ital J Pediatr DOI: 10.1186/s13052-020-00900-w sha: doc_id: 280821 cord_uid: kc0ut4oy file: cache/cord-280628-ok62havd.json key: cord-280628-ok62havd authors: Groß, Sonja; Jahn, Christopher; Cushman, Sarah; Bär, Christian; Thum, Thomas title: SARS-CoV-2 receptor ACE2-dependent implications on the cardiovascular system: From basic science to clinical implications date: 2020-04-30 journal: J Mol Cell Cardiol DOI: 10.1016/j.yjmcc.2020.04.031 sha: doc_id: 280628 cord_uid: ok62havd file: cache/cord-280662-gakayv6e.json key: cord-280662-gakayv6e authors: Bian, Jingwei; Li, Zijian title: Angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 receptor and RAS modulator date: 2020-10-13 journal: Acta Pharm Sin B DOI: 10.1016/j.apsb.2020.10.006 sha: doc_id: 280662 cord_uid: gakayv6e file: cache/cord-280544-1rhu478r.json key: cord-280544-1rhu478r authors: Korte, Wolfgang; Buljan, Marija; Rösslein, Matthias; Wick, Peter; Golubov, Valentina; Jentsch, Jana; Reut, Michael; Peier, Karen; Nohynek, Brigitte; Fischer, Aldo; Stolz, Raphael; Cettuzzi, Michele; Nolte, Oliver title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on date: 2020-08-25 journal: J Infect DOI: 10.1016/j.jinf.2020.08.032 sha: doc_id: 280544 cord_uid: 1rhu478r file: cache/cord-280627-dfnc9g2c.json key: cord-280627-dfnc9g2c authors: Wang, Xiong; Tan, Li; Wang, Xu; Liu, Weiyong; Lu, Yanjun; Cheng, Liming; Sun, Ziyong title: Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.023 sha: doc_id: 280627 cord_uid: dfnc9g2c file: cache/cord-280697-tovty20e.json key: cord-280697-tovty20e authors: Rodríguez‐Martínez, Carlos E.; Fernandes, Ricardo M.; Hawcutt, Daniel B.; Sinha, Ian P.; Pacheco, Rafael Leite title: Efficacy, safety and cost‐effectiveness of hydroxychloroquine in children with COVID‐19: A call for evidence date: 2020-06-03 journal: Acta Paediatr DOI: 10.1111/apa.15373 sha: doc_id: 280697 cord_uid: tovty20e file: cache/cord-280427-smqc23vr.json key: cord-280427-smqc23vr authors: Singla, Rubal; Mishra, Abhishek; Joshi, Rupa; Jha, Sonali; Sharma, Amit Raj; Upadhyay, Sujata; Sarma, Phulen; Prakash, Ajay; Medhi, Bikash title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 journal: Vet Res Commun DOI: 10.1007/s11259-020-09781-0 sha: doc_id: 280427 cord_uid: smqc23vr file: cache/cord-280774-r2xm164s.json key: cord-280774-r2xm164s authors: Gallizzi, Romina; Sutera, Diana; Spagnolo, Alessandra; Bagnato, Anna Maria; Cannavò, Serafinella Patrizia; Grasso, Loredana; Guarneri, Claudio; Nunnari, Giuseppe; Mazza, Francesca; Pajno, Giovanni Battista title: Management of pernio‐like cutaneous manifestations in children during the outbreak of covid‐19. date: 2020-09-19 journal: Dermatol Ther DOI: 10.1111/dth.14312 sha: doc_id: 280774 cord_uid: r2xm164s file: cache/cord-280914-6k8gpp4y.json key: cord-280914-6k8gpp4y authors: Alpaslan Kocamemi, B.; Kurt, H.; Hacioglu, S.; Yarali, C.; Saatci, A. M.; Pakdemirli, B. title: First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey date: 2020-05-06 journal: nan DOI: 10.1101/2020.05.03.20089417 sha: doc_id: 280914 cord_uid: 6k8gpp4y file: cache/cord-280915-yk872yaz.json key: cord-280915-yk872yaz authors: Flaherman, Valerie J; Afshar, Yalda; Boscardin, John; Keller, Roberta L; Mardy, Anne; Prahl, Mary K; Phillips, Carolyn; Asiodu, Ifeyinwa V; Berghella, W Vincenzo; Chambers, Brittany D; Crear-Perry, Joia; Jamieson, Denise J; Jacoby, Vanessa L; Gaw, Stephanie L title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1411 sha: doc_id: 280915 cord_uid: yk872yaz file: cache/cord-280961-fka8c69p.json key: cord-280961-fka8c69p authors: Zhang, Rui; Ouyang, Huangqing; Fu, Lingli; Wang, Shijie; Han, Jianglong; Huang, Kejie; Jia, Mingfang; Song, Qibin; Fu, Zhenming title: CT features of SARS-CoV-2 pneumonia according to clinical presentation: a retrospective analysis of 120 consecutive patients from Wuhan city date: 2020-04-11 journal: Eur Radiol DOI: 10.1007/s00330-020-06854-1 sha: doc_id: 280961 cord_uid: fka8c69p file: cache/cord-280819-z6ucnwk0.json key: cord-280819-z6ucnwk0 authors: Achilonu, Ikechukwu; Iwuchukwu, Emmanuel Amarachi; Achilonu, Okechinyere Juliet; Fernandes, Manuel Antonio; Sayed, Yasien title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach date: 2020-09-02 journal: J Mol Graph Model DOI: 10.1016/j.jmgm.2020.107730 sha: doc_id: 280819 cord_uid: z6ucnwk0 file: cache/cord-280970-gy0kfhy6.json key: cord-280970-gy0kfhy6 authors: Peng, Fujun; Tu, Lei; Yang, Yongshi; Hu, Peng; Wang, Runsheng; Hu, Qinyong; Cao, Feng; Jiang, Taijiao; Sun, Jinlyu; Xu, Guogang; Chang, Christopher title: Management and Treatment of COVID-19: The Chinese Experience date: 2020-04-17 journal: Can J Cardiol DOI: 10.1016/j.cjca.2020.04.010 sha: doc_id: 280970 cord_uid: gy0kfhy6 file: cache/cord-280671-0b1qcdwk.json key: cord-280671-0b1qcdwk authors: Calderone, Alba; Menichetti, Francesco; Santini, Ferruccio; Colangelo, Luciano; Lucenteforte, Ersilia; Calderone, Vincenzo title: Selective Estrogen Receptor Modulators in COVID-19: A Possible Therapeutic Option? date: 2020-07-15 journal: Front Pharmacol DOI: 10.3389/fphar.2020.01085 sha: doc_id: 280671 cord_uid: 0b1qcdwk file: cache/cord-281241-k1adcls8.json key: cord-281241-k1adcls8 authors: Döhla, M.; Boesecke, C.; Schulte, B.; Diegmann, C.; Sib, E.; Richter, E.; Eschbach-Bludau, M.; Aldabbagh, S.; Marx, B.; Eis-Hübinger, A.-M.; Schmithausen, R.M.; Streeck, H. title: Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date: 2020-04-18 journal: Public Health DOI: 10.1016/j.puhe.2020.04.009 sha: doc_id: 281241 cord_uid: k1adcls8 file: cache/cord-281081-rifr5uub.json key: cord-281081-rifr5uub authors: Deng, Junhua; Jin, Yipeng; Liu, Yuxiu; Sun, Jie; Hao, Liying; Bai, Jingjing; Huang, Tian; Lin, Degui; Jin, Yaping; Tian, Kegong title: Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date: 2020-05-07 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13577 sha: doc_id: 281081 cord_uid: rifr5uub file: cache/cord-280922-w6a5ec06.json key: cord-280922-w6a5ec06 authors: Sen, Sanjana; Sanders, Emily C.; Gabriel, Kristin N.; Miller, Brian M.; Isoda, Hariny M.; Salcedo, Gabriela S.; Garrido, Jason E.; Dyer, Rebekah P.; Nakajima, Rie; Jain, Aarti; Santos, Alicia M.; Bhuvan, Keertna; Tifrea, Delia F.; Ricks-Oddie, Joni L.; Felgner, Philip L.; Edwards, Robert A.; Majumdar, Sudipta; Weiss, Gregory A. title: Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date: 2020-10-29 journal: bioRxiv DOI: 10.1101/2020.10.15.341743 sha: doc_id: 280922 cord_uid: w6a5ec06 file: cache/cord-280924-g6062fwk.json key: cord-280924-g6062fwk authors: Hachim, Mahmood Yaseen; Al Heialy, Saba; Hachim, Ibrahim Yaseen; Halwani, Rabih; Senok, Abiola C.; Maghazachi, Azzam A.; Hamid, Qutayba title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date: 2020-06-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01372 sha: doc_id: 280924 cord_uid: g6062fwk file: cache/cord-280958-36ytqapi.json key: cord-280958-36ytqapi authors: Decker, Summer J; Goldstein, Todd A; Ford, Jonathan M; Teng, Michael N; Pugliese, Robert S; Berry, Gregory J; Pettengill, Matthew; Silbert, Suzane; Hazelton, Todd R; Wilson, Jason W; Shine, Kristy; Wang, Zi-Xuan; Hutchinson, Morgan; Castagnaro, Joseph; Bloom, Ona E; Breining, Dwayne A; Goldsmith, Barbara M; Sinnott, John T; O'Donnell, Donna Gentile; Crawford, James M; Lockwood, Charles J; Kim, Kami title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1366 sha: doc_id: 280958 cord_uid: 36ytqapi file: cache/cord-281005-6gi18vka.json key: cord-281005-6gi18vka authors: Singh, Praveen Kumar; Kulsum, Umay; Rufai, Syed Beenish; Mudliar, S. Rashmi; Singh, Sarman title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date: 2020-09-01 journal: J Lab Physicians DOI: 10.1055/s-0040-1715790 sha: doc_id: 281005 cord_uid: 6gi18vka file: cache/cord-280994-w8dtfjel.json key: cord-280994-w8dtfjel authors: Peng, Qi; Peng, Ruchao; Yuan, Bin; Zhao, Jingru; Wang, Min; Wang, Xixi; Wang, Qian; Sun, Yan; Fan, Zheng; Qi, Jianxun; Gao, George F.; Shi, Yi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 journal: bioRxiv DOI: 10.1101/2020.04.23.057265 sha: doc_id: 280994 cord_uid: w8dtfjel file: cache/cord-281248-z2gisufl.json key: cord-281248-z2gisufl authors: Buonsenso, Danilo; Valentini, Piero; Moscato, Umberto; Ricciardi, Walter; Roland, Damian title: A Pediatric Strategy for the Next Phase of the SARS–CoV-2 Pandemic date: 2020-10-09 journal: Front Pediatr DOI: 10.3389/fped.2020.582798 sha: doc_id: 281248 cord_uid: z2gisufl file: cache/cord-281106-vzb5xzza.json key: cord-281106-vzb5xzza authors: Zerwes, S.; Steinbauer, M.; Gosslau, Y.; Warm, T.; Hyhlik-Dürr, A. title: COVID-19-Infektion – Risiko für thrombembolische Komplikationen date: 2020-09-01 journal: Gefasschirurgie DOI: 10.1007/s00772-020-00687-4 sha: doc_id: 281106 cord_uid: vzb5xzza file: cache/cord-281101-gv1sgbk1.json key: cord-281101-gv1sgbk1 authors: Shin, Gu-Choul; Chung, Yoon-Seok; Kim, In-Soo; Cho, Hae-Wol; Kang, Chun title: Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date: 2006-08-30 journal: Virus Res DOI: 10.1016/j.virusres.2006.07.004 sha: doc_id: 281101 cord_uid: gv1sgbk1 file: cache/cord-280996-anq680a1.json key: cord-280996-anq680a1 authors: Agarwal, Arnav; Basmaji, John; Muttalib, Fiona; Granton, David; Chaudhuri, Dipayan; Chetan, Devin; Hu, Malini; Fernando, Shannon M.; Honarmand, Kimia; Bakaa, Layla; Brar, Sonia; Rochwerg, Bram; Adhikari, Neill K.; Lamontagne, Francois; Murthy, Srinivas; Hui, David S. 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A.; Couban, Rachel; Ibrahim, Quazi; Guyatt, Gordon H.; Vandvik, Per O. title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission date: 2020-06-15 journal: Can J Anaesth DOI: 10.1007/s12630-020-01740-2 sha: doc_id: 280996 cord_uid: anq680a1 file: cache/cord-281254-x7ivjvti.json key: cord-281254-x7ivjvti authors: Chang, Zhijie; Babiuk, Lorne A.; Hu, Jim title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 journal: BioDrugs DOI: 10.2165/00063030-200721010-00002 sha: doc_id: 281254 cord_uid: x7ivjvti file: cache/cord-281113-t450ccnq.json key: cord-281113-t450ccnq authors: Mattar, Rejane title: Breath tests for gastrointestinal diseases - will it be safe to conduct breath tests after the COVID-19 pandemic? date: 2020-06-16 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e2092 sha: doc_id: 281113 cord_uid: t450ccnq file: cache/cord-280979-0vaarrji.json key: cord-280979-0vaarrji authors: Gauttier, V.; Morello, A.; Girault, I.; Mary, C.; Belarif, L.; Desselle, A.; Wilhelm, E.; Bourquard, T.; Pengam, S.; Teppaz, G.; Thepenier, V.; Biteau, K.; De Barbeyrac, E.; Kiepferlé, D.; Vasseur, B.; Le Flem, FX.; Debieuvre, D.; Costantini, D.; Poirier, N. title: Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date: 2020-08-14 journal: bioRxiv DOI: 10.1101/2020.08.14.240093 sha: doc_id: 280979 cord_uid: 0vaarrji file: cache/cord-281281-knelqmzx.json key: cord-281281-knelqmzx authors: Villas-Boas, Gustavo R.; Rescia, Vanessa C.; Paes, Marina M.; Lavorato, Stefânia N.; de Magalhães-Filho, Manoel F.; Cunha, Mila S.; Simões, Rafael da C.; de Lacerda, Roseli B.; de Freitas-Júnior, Renilson S.; Ramos, Bruno H. da S.; Mapeli, Ana M.; Henriques, Matheus da S. T.; de Freitas, William R.; Lopes, Luiz A. F.; Oliveira, Luiz G. R.; da Silva, Jonatas G.; Silva-Filho, Saulo E.; da Silveira, Ana P. S.; Leão, Katyuscya V.; Matos, Maria M. de S.; Fernandes, Jamille S.; Cuman, Roberto K. N.; Silva-Comar, Francielli M. de S.; Comar, Jurandir F.; Brasileiro, Luana do A.; dos Santos, Jussileide N.; Oesterreich, Silvia A. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 journal: Molecules DOI: 10.3390/molecules25184086 sha: doc_id: 281281 cord_uid: knelqmzx file: cache/cord-280939-d478p8u6.json key: cord-280939-d478p8u6 authors: Abe, Kento T.; Li, Zhijie; Samson, Reuben; Samavarchi-Tehrani, Payman; Valcourt, Emelissa J.; Wood, Heidi; Budylowski, Patrick; Dupuis, Alan P.; Girardin, Roxie C.; Rathod, Bhavisha; Wang, Jenny H.; Barrios-Rodiles, Miriam; Colwill, Karen; McGeer, Allison J.; Mubareka, Samira; Gommerman, Jennifer L.; Durocher, Yves; Ostrowski, Mario; McDonough, Kathleen A.; Drebot, Michael A.; Drews, Steven J.; Rini, James M.; Gingras, Anne-Claude title: A simple protein-based surrogate neutralization assay for SARS-CoV-2 date: 2020-10-02 journal: JCI insight DOI: 10.1172/jci.insight.142362 sha: doc_id: 280939 cord_uid: d478p8u6 file: cache/cord-281141-ouno4jpl.json key: cord-281141-ouno4jpl authors: Mahajan, Swapnil; Kode, Vasumathi; Bhojak, Keshav; Magdalene, Coral M.; Lee, Kayla; Manoharan, Malini; Ramesh, Athulya; Sudheendra, HV; Srivastava, Ankita; Sathian, Rekha; Khan, Tahira; Kumar, Prasanna; Chakraborty, Papia; Chaudhuri, Amitabha title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.03.367375 sha: doc_id: 281141 cord_uid: ouno4jpl file: cache/cord-281216-7t647fww.json key: cord-281216-7t647fww authors: Goldust, Mohamad; Zalaudek, Iris; Gupta, Atula; Lallas, Aimilios; Rudnicka, Lidia; Navarini, Alexander A. title: Performing dermoscopy in the COVID‐19 pandemic date: 2020-05-05 journal: Dermatol Ther DOI: 10.1111/dth.13506 sha: doc_id: 281216 cord_uid: 7t647fww file: cache/cord-281346-bjhdy8mg.json key: cord-281346-bjhdy8mg authors: Palacios Cruz, M.; Santos, E.; Velázquez Cervantes, M.A.; León Juárez, M. title: COVID-19, a worldwide public health emergency() date: 2020-04-21 journal: Rev Clin Esp (Barc) DOI: 10.1016/j.rceng.2020.03.001 sha: doc_id: 281346 cord_uid: bjhdy8mg file: cache/cord-281500-5mm1nnwv.json key: cord-281500-5mm1nnwv authors: Spadera, Lucrezia; Viola, Pasquale; Pisani, Davide; Scarpa, Alfonso; Malanga, Donatella; Sorrentino, Gerardo; Madini, Enrico; Laria, Carla; Aragona, Teodoro; Leopardi, Gianluca; Maggiore, Giandomenico; Ciriolo, Marco; Boccuto, Luigi; Pizzolato, Raffaella; Abenavoli, Ludovico; Cassandro, Claudia; Ralli, Massimo; Cassandro, Ettore; Chiarella, Giuseppe title: Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey date: 2020-08-04 journal: Eur Arch Otorhinolaryngol DOI: 10.1007/s00405-020-06252-9 sha: doc_id: 281500 cord_uid: 5mm1nnwv file: cache/cord-281501-ca9oxl7f.json key: cord-281501-ca9oxl7f authors: Khan, Shumayila; Gomes, James title: Neuropathogenesis of SARS-CoV-2 infection date: 2020-07-30 journal: eLife DOI: 10.7554/elife.59136 sha: doc_id: 281501 cord_uid: ca9oxl7f file: cache/cord-281528-xy8j5jiv.json key: cord-281528-xy8j5jiv authors: Di Paola, Luisa; Hadi-Alijanvand, Hamid; Song, Xingyu; Hu, Guang; Giuliani, Alessandro title: The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date: 2020-06-17 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00273 sha: doc_id: 281528 cord_uid: xy8j5jiv file: cache/cord-281294-dnaith3a.json key: cord-281294-dnaith3a authors: Röhr, Susanne; Müller, Felix; Jung, Franziska; Apfelbacher, Christian; Seidler, Andreas; Riedel-Heller, Steffi G. title: Psychosoziale Folgen von Quarantänemaßnahmen bei schwerwiegenden Coronavirus-Ausbrüchen: ein Rapid Review date: 2020-04-27 journal: Psychiatr Prax DOI: 10.1055/a-1159-5562 sha: doc_id: 281294 cord_uid: dnaith3a file: cache/cord-281161-u896icp9.json key: cord-281161-u896icp9 authors: Wang, Jing; Tricoche, Nancy; Du, Lanying; Hunter, Meredith; Zhan, Bin; Goud, Gaddam; Didier, Elizabeth S.; Liu, Jing; Lu, Lu; Marx, Preston A.; Jiang, Shibo; Lustigman, Sara title: The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date: 2012-05-17 journal: PLoS One DOI: 10.1371/journal.pone.0037019 sha: doc_id: 281161 cord_uid: u896icp9 file: cache/cord-281508-zl2url8z.json key: cord-281508-zl2url8z authors: Pearce, N.; Moirano, G.; Maule, M.; Kogevinas, M.; Rodo, X.; Lawlor, D.; Vandenbroucke, J.; Vandenbroucke-Grauls, C.; Polack, F. P.; Custovic, A. title: Is death from Covid-19 a multistep process? date: 2020-06-03 journal: nan DOI: 10.1101/2020.06.01.20116608 sha: doc_id: 281508 cord_uid: zl2url8z file: cache/cord-281393-96j70n2z.json key: cord-281393-96j70n2z authors: Capai, L.; Ayhan, N.; Masse, S.; Canarelli, J.; Priet, S.; Simeoni, M.-H.; Charrel, R. N.; de Lamballerie, X.; Falchi, A. title: Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020. date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.29.20201368 sha: doc_id: 281393 cord_uid: 96j70n2z file: cache/cord-281551-0aj2zwx8.json key: cord-281551-0aj2zwx8 authors: Schlagenhauf, Patricia; Grobusch, Martin P.; Maier, Julian D.; Gautret, Philippe title: Repurposing antimalarials and other drugs for COVID-19 date: 2020-04-02 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101658 sha: doc_id: 281551 cord_uid: 0aj2zwx8 file: cache/cord-281699-pxof67pl.json key: cord-281699-pxof67pl authors: Eskier, Doğa; Suner, Aslı; Oktay, Yavuz; Karakülah, Gökhan title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-08-13 journal: bioRxiv DOI: 10.1101/2020.08.12.248732 sha: doc_id: 281699 cord_uid: pxof67pl file: cache/cord-281285-5g1rw202.json key: cord-281285-5g1rw202 authors: Simonis, Alexander; Theobald, Sebastian J; Fätkenheuer, Gerd; Rybniker, Jan; Malin, Jakob J title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 journal: EMBO Mol Med DOI: 10.15252/emmm.202013105 sha: doc_id: 281285 cord_uid: 5g1rw202 file: cache/cord-281487-x0a9qgjs.json key: cord-281487-x0a9qgjs authors: Kim, Min Young; Brennan, Daniel C.; Shah, Pali title: General Approach to the Clinical Care of Solid Organ Transplant Recipients with COVID-19 Infection: Management for Transplant Recipients date: 2020-10-29 journal: Curr Transplant Rep DOI: 10.1007/s40472-020-00305-y sha: doc_id: 281487 cord_uid: x0a9qgjs file: cache/cord-281686-edpyn8fd.json key: cord-281686-edpyn8fd authors: Dalamaga, Maria; Karampela, Irene; Mantzoros, Christos S. title: 19 treatment regimens? date: 2020-05-08 journal: Metabolism DOI: 10.1016/j.metabol.2020.154260 sha: doc_id: 281686 cord_uid: edpyn8fd file: cache/cord-281536-8y7yxcp4.json key: cord-281536-8y7yxcp4 authors: Lim, Hocheol; Baek, Ayoung; Kim, Jongwan; Kim, Min Sung; Liu, Jiaxin; Nam, Ky-Youb; Yoon, JeongHyeok; No, Kyoung Tai title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method date: 2020-10-08 journal: Sci Rep DOI: 10.1038/s41598-020-73820-8 sha: doc_id: 281536 cord_uid: 8y7yxcp4 file: cache/cord-281679-xmbnpawj.json key: cord-281679-xmbnpawj authors: Meekins, David A.; Morozov, Igor; Trujillo, Jessie D.; Gaudreault, Natasha N.; Bold, Dashzeveg; Artiaga, Bianca L.; Indran, Sabarish V.; Kwon, Taeyong; Balaraman, Velmurugan; Madden, Daniel W.; Feldmann, Heinz; Henningson, Jamie; Ma, Wenjun; Balasuriya, Udeni B. R.; Richt, Juergen A. title: Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date: 2020-08-16 journal: bioRxiv DOI: 10.1101/2020.08.15.252395 sha: doc_id: 281679 cord_uid: xmbnpawj file: cache/cord-281677-pspmmrq7.json key: cord-281677-pspmmrq7 authors: Schulze-Koops, Hendrik; Iking-Konert, Christof; Leipe, Jan; Hoyer, Bimba Franziska; Holle, Julia; Moosig, Frank; Aries, Peer; Burmester, Gerd; Fiehn, Christoph; Krause, Andreas; Lorenz, Hanns-Martin; Schneider, Matthias; Sewerin, Philipp; Voormann, Anna; Wagner, Ulf; Krüger, Klaus; Specker, Christof title: Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie e. 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Alonso; Catherina, Richard; Frye, Hailey; Shelley, Louise title: Illicit Wildlife Trade, Wet Markets, and COVID‐19: Preventing Future Pandemics date: 2020-07-05 journal: World Med Health Policy DOI: 10.1002/wmh3.348 sha: doc_id: 281512 cord_uid: 79g22dk6 file: cache/cord-281561-r10y2sgb.json key: cord-281561-r10y2sgb authors: Tiwari, Nidhi; Upadhyay, Jyoti; Nazam Ansari, Mohd; Joshi, Rohit title: Novel β-Coronavirus (SARS-CoV-2): Current and Future Aspects of Pharmacological Treatments date: 2020-08-27 journal: Saudi Pharm J DOI: 10.1016/j.jsps.2020.08.015 sha: doc_id: 281561 cord_uid: r10y2sgb file: cache/cord-281793-tj4m01s4.json key: cord-281793-tj4m01s4 authors: Ho, Mitchell title: Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date: 2020-05-20 journal: Antib Ther DOI: 10.1093/abt/tbaa009 sha: doc_id: 281793 cord_uid: tj4m01s4 file: cache/cord-282133-5dzzm9s8.json key: cord-282133-5dzzm9s8 authors: Watzky, Manon; de Dieuleveult, Maud; Letessier, Anne; Saint-Ruf, Claude; Miotto, Benoit title: Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry date: 2020-10-15 journal: Environ Res DOI: 10.1016/j.envres.2020.110317 sha: doc_id: 282133 cord_uid: 5dzzm9s8 file: cache/cord-281754-auqh3vtr.json key: cord-281754-auqh3vtr authors: nan title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date: 2017-09-12 journal: Dis Mon DOI: 10.1016/j.disamonth.2017.03.019 sha: doc_id: 281754 cord_uid: auqh3vtr file: cache/cord-282043-cs1oyohu.json key: cord-282043-cs1oyohu authors: Giustino, Gennaro; Pinney, Sean P.; Lala, Anuradha; Reddy, Vivek Y.; Johnston-Cox, Hillary A.; Mechanick, Jeffrey I.; Halperin, Jonathan L.; Fuster, Valentin title: Coronavirus and Cardiovascular Disease, Myocardial Injury, and Arrhythmia: JACC Focus Seminar date: 2020-10-27 journal: J Am Coll Cardiol DOI: 10.1016/j.jacc.2020.08.059 sha: doc_id: 282043 cord_uid: cs1oyohu file: cache/cord-282045-pf08iakf.json key: cord-282045-pf08iakf authors: Chen, Haoyan; Zou, Tian-Hui; Xuan, Baoqin; Yan, Yuqing; Yan, Tingting; Shen, Chaoqin; Zhao, Gang; Chen, Ying-Xuan; Xiao, Xiao; Hong, Jie; Fang, Jing-Yuan title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production date: 2020-07-08 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00237-0 sha: doc_id: 282045 cord_uid: pf08iakf file: cache/cord-282058-it0ojdk3.json key: cord-282058-it0ojdk3 authors: Yu, Yuanqiang; Chen, Pingyang title: Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review date: 2020-05-15 journal: Front Pediatr DOI: 10.3389/fped.2020.00287 sha: doc_id: 282058 cord_uid: it0ojdk3 file: cache/cord-281552-zfjy3m3i.json key: cord-281552-zfjy3m3i authors: Alsaadi, Entedar A. 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Zhu, Airu; Li, Heying; Zheng, Kui; Zhuang, Zhen; Chen, Zhao; Shi, Yongxia; Zhang, Zhaoyong; Chen, Si-bei; Liu, Xuesong; Dai, Jun; Li, Xiaobo; Huang, Shuxiang; Huang, Xiaofang; Luo, Ling; Wen, Liyan; Zhuo, Jianfen; Li, Yuming; Wang, Yanqun; Zhang, Lu; Zhang, Yanjun; Li, Fang; Feng, Liqiang; Chen, Xinwen; Zhong, Nanshan; Yang, Zifeng; Huang, Jicheng; Zhao, Jincun; Li, Yi-min title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient date: 2020-05-18 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1760144 sha: doc_id: 281727 cord_uid: elartlro file: cache/cord-282108-hhnnloxp.json key: cord-282108-hhnnloxp authors: Heister, Paula M.; Poston, Robin N. title: Pharmacological hypothesis: TPC2 antagonist tetrandrine as a potential therapeutic agent for COVID‐19 date: 2020-09-15 journal: Pharmacol Res Perspect DOI: 10.1002/prp2.653 sha: doc_id: 282108 cord_uid: hhnnloxp file: cache/cord-282372-nmii30mc.json key: cord-282372-nmii30mc authors: Youk, Jeonghwan; Kim, Taewoo; 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Bryce, Elizabeth; Hoang, Linda; Daly, Patricia; Lysyshyn, Mark; Hayden, Althea S.; Harding, John; Boraston, Suni; Dawar, Meena; Schwandt, Michael title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks date: 2020-07-06 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.07.001 sha: doc_id: 282272 cord_uid: wy8do2z6 file: cache/cord-282371-39qo9afy.json key: cord-282371-39qo9afy authors: Khulood, Daulat; Adil, Mir Shoebulla; Sultana, Ruqiya; Nimra, title: Convalescent plasma appears efficacious and safe in COVID-19 date: 2020-09-28 journal: Ther Adv Infect Dis DOI: 10.1177/2049936120957931 sha: doc_id: 282371 cord_uid: 39qo9afy file: cache/cord-282750-d9sb7o63.json key: cord-282750-d9sb7o63 authors: Benhadou, F.; Del Marmol, V. title: Improvement of SARS‐CoV2 symptoms following Guselkumab injection in a psoriatic patient date: 2020-05-07 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16590 sha: doc_id: 282750 cord_uid: d9sb7o63 file: cache/cord-281684-m3m4mhye.json key: cord-281684-m3m4mhye authors: Fagre, Anna C.; 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Wainstein, Alberto Julius Alves; de Castro Ribeiro, Heber Salvador; Pinheiro, Rodrigo Nascimento; Oliveira, Alexandre Ferreira title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 journal: Ann Surg Oncol DOI: 10.1245/s10434-020-09098-x sha: doc_id: 281887 cord_uid: b511bjdy file: cache/cord-282009-a83mun7u.json key: cord-282009-a83mun7u authors: Pundir, Hemlata; Joshi, Tanuja; Joshi, Tushar; Sharma, Priyanka; Mathpal, Shalini; Chandra, Subhash; Tamta, Sushma title: Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors date: 2020-10-20 journal: Mol Divers DOI: 10.1007/s11030-020-10148-5 sha: doc_id: 282009 cord_uid: a83mun7u file: cache/cord-282560-tofppr3b.json key: cord-282560-tofppr3b authors: Henderson, Jack A.; Verma, Neha; Harris, Robert C.; Liu, Ruibin; Shen, Jana title: Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors date: 2020-09-21 journal: J Chem Phys DOI: 10.1063/5.0020458 sha: doc_id: 282560 cord_uid: tofppr3b file: cache/cord-282965-xguotf4m.json key: cord-282965-xguotf4m authors: O’Callaghan-Gordo, Cristina; 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S.; Wong, Tze Wai; Chiu, Yuk Lan; Lee, Nelson; Li, Yuguo title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date: 2005-05-01 journal: Clin Infect Dis DOI: 10.1086/428735 sha: doc_id: 281726 cord_uid: s1o5l7ns file: cache/cord-281948-xv7vuypd.json key: cord-281948-xv7vuypd authors: Hoang, Ansel; Chorath, Kevin; Moreira, Axel; Evans, Mary; Burmeister-Morton, Finn; Burmeister, Fiona; Naqvi, Rija; Petershack, Matthew; Moreira, Alvaro title: COVID-19 in 7780 pediatric patients: A systematic review date: 2020-06-26 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100433 sha: doc_id: 281948 cord_uid: xv7vuypd file: cache/cord-281937-yztlb0fn.json key: cord-281937-yztlb0fn authors: Sheahan, Timothy P; Frieman, Matthew B title: The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health date: 2020-06-04 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2020.05.010 sha: doc_id: 281937 cord_uid: yztlb0fn file: cache/cord-282732-qym6wji7.json key: cord-282732-qym6wji7 authors: McLaughlin, Katie-May; Bechtel, Marco; Bojkova, Denisa; Münch, Christian; Ciesek, Sandra; Wass, Mark N.; Michaelis, Martin; Cinatl, Jindrich title: COVID-19-Related Coagulopathy—Is Transferrin a Missing Link? date: 2020-07-30 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10080539 sha: doc_id: 282732 cord_uid: qym6wji7 file: cache/cord-282795-kje7rn57.json key: cord-282795-kje7rn57 authors: Zheng, Yue; Larragoite, Erin T.; Lama, Juan; Cisneros, Isabel; Delgado, Julio C.; Slev, Patricia; Rychert, Jenna; Innis, Emily A.; Williams, Elizabeth S.C.P.; Coiras, Mayte; Rondina, Matthew T.; Spivak, Adam M.; Planelles, Vicente title: Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date: 2020-09-21 journal: bioRxiv DOI: 10.1101/2020.07.17.207563 sha: doc_id: 282795 cord_uid: kje7rn57 file: cache/cord-282862-kve6fa49.json key: cord-282862-kve6fa49 authors: Pastick, Katelyn A; Nicol, Melanie R; Smyth, Elizabeth; Zash, Rebecca; Boulware, David R; Rajasingham, Radha; McDonald, Emily G title: A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date: 2020-08-13 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa350 sha: doc_id: 282862 cord_uid: kve6fa49 file: cache/cord-282895-85if4mnu.json key: cord-282895-85if4mnu authors: Xiao, Xiaodong; Chakraborti, Samitabh; Dimitrov, Anthony S; Gramatikoff, Kosi; Dimitrov, Dimiter S title: The SARS-CoV S glycoprotein: expression and functional characterization date: 2003-12-26 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2003.11.054 sha: doc_id: 282895 cord_uid: 85if4mnu file: cache/cord-282738-aqc9gxlw.json key: cord-282738-aqc9gxlw authors: Liu, Anding; Li, Ying; Wan, Zhengce; Wang, Wenjie; Lei, Xiaomei; Lv, Yongman title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 journal: JAMA Netw Open DOI: 10.1001/jamanetworkopen.2020.25717 sha: doc_id: 282738 cord_uid: aqc9gxlw file: cache/cord-283193-8qj41kpp.json key: cord-283193-8qj41kpp authors: Chak-Yiu Lee, Andrew; Zhang, Anna Jinxia; Fuk-Woo Chan, Jasper; Li, Can; Fan, Zhimeng; Liu, Feifei; Chen, Yanxia; Liang, Ronghui; Sridhar, Siddharth; Cai, Jian-Piao; Kwok-Man Poon, Vincent; Chung-Sing Chan, Chris; Kai-Wang To, Kelvin; Yuan, Shuofeng; Zhou, Jie; Chu, Hin; Yuen, Kwok-Yung title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters date: 2020-09-22 journal: Cell Rep Med DOI: 10.1016/j.xcrm.2020.100121 sha: doc_id: 283193 cord_uid: 8qj41kpp file: cache/cord-282142-76jr4p7n.json key: cord-282142-76jr4p7n authors: Wang, Yun; Wang, Yiliang; Han, Xiaoxue; Ye, Jiazhuo; Li, Ruiman title: Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date: 2020-08-07 journal: Front Pediatr DOI: 10.3389/fped.2020.00511 sha: doc_id: 282142 cord_uid: 76jr4p7n file: cache/cord-283116-ib5c3lbi.json key: cord-283116-ib5c3lbi authors: Koh, David; Goh, Hui Poh title: Occupational health responses to COVID‐19: What lessons can we learn from SARS? date: 2020-05-13 journal: J Occup Health DOI: 10.1002/1348-9585.12128 sha: doc_id: 283116 cord_uid: ib5c3lbi file: cache/cord-282964-dmc8mlxu.json key: cord-282964-dmc8mlxu authors: Wathore, Roshan; Gupta, Ankit; Bherwani, Hemant; Labhasetwar, Nitin title: Understanding air and water borne transmission and survival of coronavirus: Insights and way forward for SARS-CoV-2 date: 2020-08-04 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141486 sha: doc_id: 282964 cord_uid: dmc8mlxu file: cache/cord-282384-qbcqbhk4.json key: cord-282384-qbcqbhk4 authors: Savastano, Alfonso; Crincoli, Emanuele; Savastano, Maria Cristina; Younis, Saad; Gambini, Gloria; De Vico, Umberto; Cozzupoli, Grazia Maria; Culiersi, Carola; Rizzo, Stanislao title: Peripapillary Retinal Vascular Involvement in Early Post-COVID-19 Patients date: 2020-09-08 journal: J Clin Med DOI: 10.3390/jcm9092895 sha: doc_id: 282384 cord_uid: qbcqbhk4 file: cache/cord-283152-wav0d0ws.json key: cord-283152-wav0d0ws authors: Patel, Sanjay K. S.; Lee, Jung-Kul; Kalia, Vipin C. title: Deploying Biomolecules as Anti-COVID-19 Agents date: 2020-06-09 journal: Indian J Microbiol DOI: 10.1007/s12088-020-00893-4 sha: doc_id: 283152 cord_uid: wav0d0ws file: cache/cord-282920-s4yixzuy.json key: cord-282920-s4yixzuy authors: Rubin, Elizabeth S.; Sansone, Stephanie A.; Hirshberg, Adi; Clement, Elizabeth G.; Srinivas, Sindhu K. title: Detection of COVID-19 in a Vulvar Lesion date: 2020-07-02 journal: Am J Perinatol DOI: 10.1055/s-0040-1713665 sha: doc_id: 282920 cord_uid: s4yixzuy file: cache/cord-283196-laerx0n2.json key: cord-283196-laerx0n2 authors: Bedford, Juliet; Enria, Delia; Giesecke, Johan; Heymann, David L; Ihekweazu, Chikwe; Kobinger, Gary; Lane, H Clifford; Memish, Ziad A; Oh, Myoung-don; Sall, Amadou Alpha; Ungchusak, Kumnuan; Wieler, Lothar H title: Living with the COVID-19 pandemic: act now with the tools we have date: 2020-10-08 journal: Lancet DOI: 10.1016/s0140-6736(20)32117-6 sha: doc_id: 283196 cord_uid: laerx0n2 file: cache/cord-283138-18q23z8l.json key: cord-283138-18q23z8l authors: Balasubramanian, S.; Rao, Neha Mohan; Goenka, Anu; Roderick, Marion; Ramanan, Athimalaipet V title: Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date: 2020-04-09 journal: Indian Pediatr DOI: 10.1007/s13312-020-1819-5 sha: doc_id: 283138 cord_uid: 18q23z8l file: cache/cord-283197-jjye8t6j.json key: cord-283197-jjye8t6j authors: Ingraham, Nicholas E.; Tignanelli, Christopher J. title: Fact Versus Science Fiction: Fighting Coronavirus Disease 2019 Requires the Wisdom to Know the Difference date: 2020-04-29 journal: Crit Care Explor DOI: 10.1097/cce.0000000000000108 sha: doc_id: 283197 cord_uid: jjye8t6j file: cache/cord-283127-jetmocvk.json key: cord-283127-jetmocvk authors: Wang, Denong; Tang, Jin; Tang, Jiulai; Wang, Lai-Xi title: Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date: 2015-03-12 journal: Molecules DOI: 10.3390/molecules20034610 sha: doc_id: 283127 cord_uid: jetmocvk file: cache/cord-282317-k9mtf6yl.json key: cord-282317-k9mtf6yl authors: Srivastava, Vivek; Yadav, Ankush; Sarkar, Paratpar title: Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2 date: 2020-10-14 journal: Mater Today Proc DOI: 10.1016/j.matpr.2020.10.055 sha: doc_id: 282317 cord_uid: k9mtf6yl file: cache/cord-282571-ilf73g71.json key: cord-282571-ilf73g71 authors: Ni, Wentao; Yang, Xiuwen; Yang, Deqing; Bao, Jing; Li, Ran; Xiao, Yongjiu; Hou, Chang; Wang, Haibin; Liu, Jie; Yang, Donghong; Xu, Yu; Cao, Zhaolong; Gao, Zhancheng title: Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19 date: 2020-07-13 journal: Crit Care DOI: 10.1186/s13054-020-03120-0 sha: doc_id: 282571 cord_uid: ilf73g71 file: cache/cord-282899-kp114q7n.json key: cord-282899-kp114q7n authors: Biswas, Saurav; Thakur, Vikram; Kaur, Parneet; Khan, Azhar; Kulshrestha, Saurabh; Kumar, Pradeep title: Blood clots in COVID-19 patients: Simplifying the curious mystery date: 2020-11-06 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110371 sha: doc_id: 282899 cord_uid: kp114q7n file: cache/cord-283413-xapzer5s.json key: cord-283413-xapzer5s authors: Chan, A. K. M.; Nickson, C. P.; Rudolph, J. W.; Lee, A.; Joynt, G. M. title: Social media for rapid knowledge dissemination: early experience from the COVID‐19 pandemic date: 2020-03-31 journal: Anaesthesia DOI: 10.1111/anae.15057 sha: doc_id: 283413 cord_uid: xapzer5s file: cache/cord-282421-yialyuav.json key: cord-282421-yialyuav authors: Alcoba-Florez, Julia; Gil-Campesino, Helena; de Artola, Diego García-Martínez; González-Montelongo, Rafaela; Valenzuela-Fernández, Agustín; Ciuffreda, Laura; Flores, Carlos title: Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date: 2020-08-01 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.058 sha: doc_id: 282421 cord_uid: yialyuav file: cache/cord-283034-ebely0rx.json key: cord-283034-ebely0rx authors: Brunet, E; Casabella, A; Calzado, S; Villoria, A title: Ileitis as the exclusive manifestation of covid-19. The first reported case date: 2020-10-19 journal: Gastroenterol Hepatol DOI: 10.1016/j.gastrohep.2020.10.001 sha: doc_id: 283034 cord_uid: ebely0rx file: cache/cord-283109-ka3n9pft.json key: cord-283109-ka3n9pft authors: Arumugam, Arunkumar; Wong, Season title: The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date: 2020-04-08 journal: bioRxiv DOI: 10.1101/2020.04.06.028811 sha: doc_id: 283109 cord_uid: ka3n9pft file: cache/cord-283376-6wolrfvk.json key: cord-283376-6wolrfvk authors: Yin, M.; Zhang, L.; Deng, G.; Han, C.; Shen, M.; Sun, H.; Zeng, F.; Zhang, W.; Chen, L.; Luo, Q.; Yao, D.; Wu, M.; Yu, S.; Chen, H.; Baud, D.; Chen, X. title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study date: 2020-04-11 journal: nan DOI: 10.1101/2020.04.07.20053744 sha: doc_id: 283376 cord_uid: 6wolrfvk file: cache/cord-283372-c20i99qa.json key: cord-283372-c20i99qa authors: Sanchis-Gomar, Fabian; Lavie, Carl J.; Morin, Daniel P.; Perez-Quilis, Carme; Laukkanen, Jari A.; Perez, Marco V. title: Amiodarone in the COVID-19 Era: Treatment for Symptomatic Patients Only, or Drug to Prevent Infection? date: 2020-08-01 journal: Am J Cardiovasc Drugs DOI: 10.1007/s40256-020-00429-7 sha: doc_id: 283372 cord_uid: c20i99qa file: cache/cord-283310-5wam14aa.json key: cord-283310-5wam14aa authors: Bevova, M. R.; Netesov, S. V.; Aulchenko, Yu. S. title: The New Coronavirus COVID-19 Infection date: 2020-09-09 journal: Mol DOI: 10.3103/s0891416820020044 sha: doc_id: 283310 cord_uid: 5wam14aa file: cache/cord-283699-c4jjdj5o.json key: cord-283699-c4jjdj5o authors: Eslami, Gholamali; Mousaviasl, Sajedeh; Radmanesh, Esmat; Jelvay, Saeed; Bitaraf, Saeid; Simmons, Bryony; Wentzel, Hannah; Hill, Andrew; Sadeghi, Anahita; Freeman, James; Salmanzadeh, Shokrollah; Esmaeilian, Hani; Mobarak, Morteza; Tabibi, Ramin; Jafari Kashi, Amir Hosein; Lotfi, Zahra; Talebzadeh, Seyed Mehdi; Wickramatillake, Aseni; Momtazan, Mahboobeh; Hajizadeh Farsani, Majid; Marjani, Sedigheh; Mobarak, Sara title: The impact of sofosbuvir/daclatasvir or ribavirin in patients with severe COVID-19 date: 2020-08-19 journal: J Antimicrob Chemother DOI: 10.1093/jac/dkaa331 sha: doc_id: 283699 cord_uid: c4jjdj5o file: cache/cord-283439-hqdq2qrh.json key: cord-283439-hqdq2qrh authors: Rahman, Mohammad Tariqur; Idid, Syed Zahir title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 journal: Biol Trace Elem Res DOI: 10.1007/s12011-020-02194-9 sha: doc_id: 283439 cord_uid: hqdq2qrh file: cache/cord-282853-l0c69uul.json key: cord-282853-l0c69uul authors: Massad, Eduardo; Burattini, Marcelo N.; Lopez, Luis F.; Coutinho, Francisco A.B. title: Forecasting versus projection models in epidemiology: The case of the SARS epidemics date: 2005-03-30 journal: Med Hypotheses DOI: 10.1016/j.mehy.2004.09.029 sha: doc_id: 282853 cord_uid: l0c69uul file: cache/cord-282839-3ii79g6j.json key: cord-282839-3ii79g6j authors: Moreno-Fernández Ayala, Daniel J.; Navas, Plácido; López-Lluch, Guillermo title: Age-related mitochondrial dysfunction as a key factor in COVID-19 disease date: 2020-11-07 journal: Exp Gerontol DOI: 10.1016/j.exger.2020.111147 sha: doc_id: 282839 cord_uid: 3ii79g6j file: cache/cord-283430-k1ex9fes.json key: cord-283430-k1ex9fes authors: Smithgall, Marie C.; Liu‐Jarin, Xiaolin; Hamele‐Bena, Diane; Cimic, Adela; Mourad, Mirella; Debelenko, Larisa; Chen, Xiaowei title: Third Trimester Placentas of SARS‐CoV‐2‐Positive Women: Histomorphology, including Viral Immunohistochemistry and in Situ Hybridization date: 2020-07-21 journal: Histopathology DOI: 10.1111/his.14215 sha: doc_id: 283430 cord_uid: k1ex9fes file: cache/cord-283823-8n1cy0hj.json key: cord-283823-8n1cy0hj authors: Parikh, Bijal A.; Bailey, Thomas C.; Lyons, Patrick G.; Anderson, Neil W. title: The Brief Case: “Not Positive” or “Not Sure”—COVID-19-Negative Results in a Symptomatic Patient date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.01195-20 sha: doc_id: 283823 cord_uid: 8n1cy0hj file: cache/cord-283512-qly8iclf.json key: cord-283512-qly8iclf authors: Na, Ki Ryang; Kim, Hae Ri; Ham, Youngrok; Choi, Dae Eun; Lee, Kang Wook; Moon, Jae Young; Kim, Yeon-Sook; Cheon, Shinhye; Sohn, Kyung Mok; Kim, Jungok; Kim, Sungmin; Jeong, Hyeongseok; Jeon, Jae Wan title: Acute Kidney Injury and Kidney Damage in COVID-19 Patients date: 2020-07-07 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e257 sha: doc_id: 283512 cord_uid: qly8iclf file: cache/cord-282539-skzosh6u.json key: cord-282539-skzosh6u authors: Casadevall, Arturo; Joyner, Michael J; Pirofski, Liise-anne title: Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date: 2020-08-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1213 sha: doc_id: 282539 cord_uid: skzosh6u file: cache/cord-283411-40ojqv1y.json key: cord-283411-40ojqv1y authors: Ben-Shmuel, Amir; Brosh-Nissimov, Tal; Glinert, Itai; Bar-David, Elad; Sittner, Assa; Poni, Reut; Cohen, Regev; Achdout, Hagit; Tamir, Hadas; Yahalom-Ronen, Yfat; Politi, Boaz; Melamed, Sharon; Vitner, Einat; Cherry, Lilach; Israeli, Ofir; Beth-Din, Adi; Paran, Nir; Israely, Tomer; Yitzhaki, Shmuel; Haim levy; Weiss, Shay title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.004 sha: doc_id: 283411 cord_uid: 40ojqv1y file: cache/cord-283705-ia65pade.json key: cord-283705-ia65pade authors: de Gabory, Ludovic; Alharbi, Ahmed; Kérimian, Mélodie; Lafon, Marie-Edith title: Le virus influenza, le SARS-CoV2 et les voies aériennes : mise au point pour l’Otorhinolaryngologiste date: 2020-06-05 journal: nan DOI: 10.1016/j.aforl.2020.05.010 sha: doc_id: 283705 cord_uid: ia65pade file: cache/cord-282771-iwpx02v3.json key: cord-282771-iwpx02v3 authors: Dietzel, Steffen; Ferrando‐May, Elisa; Fried, Hans; Kukat, Christian; Naumann, Angela; Nitschke, Roland; Pasierbek, Pawel; Peychl, Jan; Rasse, Tobias Manuel; Schroth‐Diez, Britta; Stöckl, Martin Thomas; Terjung, Stefan; Thuenauer, Roland; Tulok, Silke; Weidtkamp‐Peters, Stefanie title: A joint action in times of pandemic: the German BioImaging recommendations for operating imaging core facilities during the SARS‐Cov‐2 emergency date: 2020-06-24 journal: Cytometry A DOI: 10.1002/cyto.a.24178 sha: doc_id: 282771 cord_uid: iwpx02v3 file: cache/cord-283590-xvnv17zy.json key: cord-283590-xvnv17zy authors: Chen, Dabiao; Xu, Wenxiong; Lei, Ziying; Huang, Zhanlian; Liu, Jing; Gao, Zhiliang; Peng, Liang title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.003 sha: doc_id: 283590 cord_uid: xvnv17zy file: cache/cord-283779-mudwcypl.json key: cord-283779-mudwcypl authors: Lauretani, Fulvio; Ravazzoni, Giulia; Roberti, Maria Federica; Longobucco, Yari; Adorni, Elisa; Grossi, Margherita; De Iorio, Aurelio; La Porta, Umberto; Fazio, Chiara; Gallini, Elena; Federici, Raffaele; Salvi, Marco; Ciarrocchi, Erika; Rossi, Francesca; Bergamin, Marina; Bussolati, Giacomo; Grieco, Ilaria; Broccoli, Federica; Zucchini, Irene; Ielo, Giuseppe; Morganti, Simonetta; Artoni, Andrea; Arisi, Arianna; Tagliaferri, Sara; Maggio, Marcello title: Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9629 sha: doc_id: 283779 cord_uid: mudwcypl file: cache/cord-282990-qb4wk4yb.json key: cord-282990-qb4wk4yb authors: Chen, Zhuo; Sikorski, Timothy W title: Safety considerations in the bioanalytical laboratories handling specimens from coronavirus disease 2019 patients date: 2020-08-21 journal: Bioanalysis DOI: 10.4155/bio-2020-0185 sha: doc_id: 282990 cord_uid: qb4wk4yb file: cache/cord-282858-zikoui4h.json key: cord-282858-zikoui4h authors: Graudenz, Gustavo Silveira; Degobbi, Cristiane; Saldiva, Paulo Hilario title: SARS-CoV-2. Long Distance Airborne Transmission and its Public Health Implications date: 2020-11-02 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e2343 sha: doc_id: 282858 cord_uid: zikoui4h file: cache/cord-283818-4m9p717r.json key: cord-283818-4m9p717r authors: Yan, Chao; Cui, Jinghua; Huang, Lei; Du, Bing; Chen, Lu; Xue, Guanhua; Li, Shaoli; Zhang, Weiwei; Zhao, Linqing; Sun, Yu; Yao, Hailan; Li, Nannan; Zhao, Hanqing; Feng, Yanling; Liu, Shiyu; Zhang, Qun; Liu, Di; Yuan, Jing title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.04.001 sha: doc_id: 283818 cord_uid: 4m9p717r file: cache/cord-282878-8qgsq2km.json key: cord-282878-8qgsq2km authors: Fignani, Daniela; Licata, Giada; Brusco, Noemi; Nigi, Laura; Grieco, Giuseppina E.; Marselli, Lorella; Overbergh, Lut; Gysemans, Conny; Colli, Maikel L.; Marchetti, Piero; Mathieu, Chantal; Eizirik, Decio L.; Sebastiani, Guido; Dotta, Francesco title: SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date: 2020-10-23 journal: bioRxiv DOI: 10.1101/2020.07.23.208041 sha: doc_id: 282878 cord_uid: 8qgsq2km file: cache/cord-283716-tleh9323.json key: cord-283716-tleh9323 authors: Amatore, F.; Macagno, N.; Mailhe, M.; Demarez, B.; Gaudy‐Marqueste, C.; Grob, J.J.; Raoult, D.; Brouqui, P.; Richard, M.A. title: SARS‐CoV‐2 infection presenting as a febrile rash date: 2020-05-27 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16528 sha: doc_id: 283716 cord_uid: tleh9323 file: cache/cord-283786-d65njv7b.json key: cord-283786-d65njv7b authors: Toptan, Tuna; Hoehl, Sebastian; Westhaus, Sandra; Bojkova, Denisa; Berger, Annemarie; Rotter, Björn; Hoffmeier, Klaus; Cinatl, Jindrich; Ciesek, Sandra; Widera, Marek title: Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date: 2020-06-20 journal: Int J Mol Sci DOI: 10.3390/ijms21124396 sha: doc_id: 283786 cord_uid: d65njv7b file: cache/cord-282635-ffq8kpij.json key: cord-282635-ffq8kpij authors: Tierraseca, Melody Sánchez; Serrano, Elena María Balmaseda; Hernández, Tomás Bertó title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) date: 2020-05-11 journal: An Pediatr (Barc) DOI: 10.1016/j.anpedi.2020.04.021 sha: doc_id: 282635 cord_uid: ffq8kpij file: cache/cord-282867-kbyxdegu.json key: cord-282867-kbyxdegu authors: Shah, Sayed Zulfiqar Ali; Nasb, Mohammad; Lu, Min; Huang, Liangjiang; Wang, Yizhao; Chen, Hong title: Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date: 2020-08-26 journal: Rehabil Res Pract DOI: 10.1155/2020/3642143 sha: doc_id: 282867 cord_uid: kbyxdegu file: cache/cord-282604-xp71rkxc.json key: cord-282604-xp71rkxc authors: Nikolaev, EN; Indeykina, MI; Brzhozovskiy, AG; Bugrova, AE; Kononikhin, AS; Starodubtseva, NL; Petrotchenko, EV; Kovalev, G; Borchers, CH; Sukhikh, GT title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date: 2020-05-25 journal: bioRxiv DOI: 10.1101/2020.05.24.113043 sha: doc_id: 282604 cord_uid: xp71rkxc file: cache/cord-283895-1p5uog38.json key: cord-283895-1p5uog38 authors: Trottier, J.; Darques, R.; Ait Mouheb, N.; Partiot, E.; Bakhache, W.; Deffieu, M. S.; Gaudin, R. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 journal: nan DOI: 10.1101/2020.07.08.20148882 sha: doc_id: 283895 cord_uid: 1p5uog38 file: cache/cord-284028-l0r7f9sr.json key: cord-284028-l0r7f9sr authors: Lee, Chi-Wei; Tsai, Yen-Shuo; Wong, Tai-Wai; Lau, Chor-Chiu title: A loophole in international quarantine procedures disclosed during the SARS crisis date: 2004-12-30 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2004.10.002 sha: doc_id: 284028 cord_uid: l0r7f9sr file: cache/cord-282947-3hgku2e4.json key: cord-282947-3hgku2e4 authors: Wong, Hui Hui; Fung, To Sing; Fang, Shouguo; Huang, Mei; Le, My Tra; Liu, Ding Xiang title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date: 2017-12-30 journal: Virology DOI: 10.1016/j.virol.2017.12.028 sha: doc_id: 282947 cord_uid: 3hgku2e4 file: cache/cord-283984-jch0ja1o.json key: cord-283984-jch0ja1o authors: Loizzo, Monica R.; Saab, Antoine M.; Tundis, Rosa; Statti, Giancarlo A.; Menichini, Francesco; Lampronti, Ilaria; Gambari, Roberto; Cinatl, Jindrich; Doerr, Hans Wilhelm title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species date: 2008-03-20 journal: Chem Biodivers DOI: 10.1002/cbdv.200890045 sha: doc_id: 283984 cord_uid: jch0ja1o file: cache/cord-283948-rb9rrkxb.json key: cord-283948-rb9rrkxb authors: Gavriilidis, Paschalis; Pai, Madhava title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series date: 2020-06-25 journal: J Clin Med Res DOI: 10.14740/jocmr4223 sha: doc_id: 283948 cord_uid: rb9rrkxb file: cache/cord-284008-vlwdtjbe.json key: cord-284008-vlwdtjbe authors: Li, Na; Jie, Zhijun title: The Application of Corticosteroids in COVID-19: A Two-edged Sword date: 2020-06-25 journal: J Transl Int Med DOI: 10.2478/jtim-2020-0011 sha: doc_id: 284008 cord_uid: vlwdtjbe file: cache/cord-284163-3jmqzemf.json key: cord-284163-3jmqzemf authors: Seffer, Malin-Theres; Cottam, Daniel; Forni, Lui G.; Kielstein, Jan T. title: Heparin 2.0: A New Approach to the Infection Crisis date: 2020-07-02 journal: Blood Purif DOI: 10.1159/000508647 sha: doc_id: 284163 cord_uid: 3jmqzemf file: cache/cord-284302-odvv2yn3.json key: cord-284302-odvv2yn3 authors: Minagorre, Pedro J. Alcalá; Pinto, Enrique Villalobos; Miguel Ramos Fernández, José; Rodríguez-Fernández, Rosa; Ronco, Miguel Vázquez; Escosa-García, Luis; Jorge, Juan Ignacio Montiano; García, Juan José García title: CAMBIOS A PARTIR DE LA COVID-19. UNA PERSPECTIVA DESDE LA PEDIATRÍA INTERNA HOSPITALARIA date: 2020-06-19 journal: An Pediatr (Barc) DOI: 10.1016/j.anpedi.2020.06.004 sha: doc_id: 284302 cord_uid: odvv2yn3 file: cache/cord-284045-scd3f8vk.json key: cord-284045-scd3f8vk authors: Pape, Constantin; Remme, Roman; Wolny, Adrian; Olberg, Sylvia; Wolf, Steffen; Cerrone, Lorenzo; Cortese, Mirko; Klaus, Severina; Lucic, Bojana; Ullrich, Stephanie; Anders-Össwein, Maria; Wolf, Stefanie; Cerikan, Berati; Neufeldt, Christopher J.; Ganter, Markus; Schnitzler, Paul; Merle, Uta; Lusic, Marina; Boulant, Steeve; Stanifer, Megan; Bartenschlager, Ralf; Hamprecht, Fred A.; Kreshuk, Anna; Tischer, Christian; Kräusslich, Hans-Georg; Müller, Barbara; Laketa, Vibor title: Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.06.15.152587 sha: doc_id: 284045 cord_uid: scd3f8vk file: cache/cord-284091-1dj4yxkz.json key: cord-284091-1dj4yxkz authors: Duart, Gerard; García-Murria, Mª Jesús; Grau, Brayan; Acosta-Cáceres, José M.; Martínez-Gil, Luis; Mingarro, Ismael title: SARS-CoV-2 envelope protein topology in eukaryotic membranes date: 2020-09-09 journal: Open Biol DOI: 10.1098/rsob.200209 sha: doc_id: 284091 cord_uid: 1dj4yxkz file: cache/cord-284398-rhfwbyav.json key: cord-284398-rhfwbyav authors: Aboubakr, Hamada A.; Sharafeldin, Tamer A.; Goyal, Sagar M. title: Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date: 2020-07-14 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13707 sha: doc_id: 284398 cord_uid: rhfwbyav file: cache/cord-283491-y6t64pux.json key: cord-283491-y6t64pux authors: Brzezinski, Dariusz; Kowiel, Marcin; Cooper, David R.; Cymborowski, Marcin; Grabowski, Marek; Wlodawer, Alexander; Dauter, Zbigniew; Shabalin, Ivan G.; Gilski, Miroslaw; Rupp, Bernhard; Jaskolski, Mariusz; Minor, Wladek title: Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date: 2020-09-27 journal: Protein Sci DOI: 10.1002/pro.3959 sha: doc_id: 283491 cord_uid: y6t64pux file: cache/cord-283120-hyzk59qv.json key: cord-283120-hyzk59qv authors: Sharma, Ashish; Jaiswal, Pragya; Kerakhan, Yasameen; Saravanan, Lakshmi; Murtaza, Zeba; Zergham, Azka; Honganur, Nagaraj-Sanchitha; Akbar, Aelia; Deol, Aran; Francis, Benedict; Patel, Shakumar; Mehta, Deep; Jaiswal, Richa; Singh, Jagmeet; Patel, Urvish; Malik, Preeti title: Liver disease and outcomes among COVID-19 hospitalized patients- a systematic review and meta-analysis date: 2020-10-16 journal: Ann Hepatol DOI: 10.1016/j.aohep.2020.10.001 sha: doc_id: 283120 cord_uid: hyzk59qv file: cache/cord-284464-avriske3.json key: cord-284464-avriske3 authors: Liu, Tao; Wu, Sanyun; Zeng, Guang; Zhou, Fuling; Li, Yirong; Guo, Fangjian; Wang, Xinghuan title: Recurrent positive SARS‐CoV‐2: Immune certificate may not be valid date: 2020-06-09 journal: J Med Virol DOI: 10.1002/jmv.26074 sha: doc_id: 284464 cord_uid: avriske3 file: cache/cord-283249-pk5sc2ca.json key: cord-283249-pk5sc2ca authors: Yoshida, Wataru; Sode, Koji; Ikebukuro, Kazunori title: Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers date: 2006-09-15 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2006.07.069 sha: doc_id: 283249 cord_uid: pk5sc2ca file: cache/cord-284038-93s3ffoy.json key: cord-284038-93s3ffoy authors: Keyhanian, Kiandokht; Umeton, Raffaella Pizzolato; Mohit, Babak; Davoudi, Vahid; Hajighasemi, Fatemeh; Ghasemi, Mehdi title: SARS-CoV-2 and nervous system: From pathogenesis to clinical manifestation date: 2020-11-07 journal: J Neuroimmunol DOI: 10.1016/j.jneuroim.2020.577436 sha: doc_id: 284038 cord_uid: 93s3ffoy file: cache/cord-284444-mgxxbm0u.json key: cord-284444-mgxxbm0u authors: Reychler, G.; Vecellio, L.; Dubus, J.C. title: Nebulization: A potential source of SARS-CoV-2 transmission date: 2020-08-04 journal: Respir Med Res DOI: 10.1016/j.resmer.2020.100778 sha: doc_id: 284444 cord_uid: mgxxbm0u file: cache/cord-283367-azzy2t1a.json key: cord-283367-azzy2t1a authors: Rahman, Asma; Niloofa, Roshan; De Zoysa, Ishan M; Cooray, Akila D; Kariyawasam, Jayani; Seneviratne, Suranjith L title: Neurological manifestations in COVID-19: A narrative review date: 2020-09-10 journal: SAGE Open Med DOI: 10.1177/2050312120957925 sha: doc_id: 283367 cord_uid: azzy2t1a file: cache/cord-283253-qdq4mfz3.json key: cord-283253-qdq4mfz3 authors: Davlantes, Elizabeth; Toro, Mayra; Villalobos, Raúl; Sanchez-Gonzalez, Liliana title: Notes from the Field: COVID-19 Prevention Practices in State Prisons — Puerto Rico, 2020 date: 2020-08-21 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6933a4 sha: doc_id: 283253 cord_uid: qdq4mfz3 file: cache/cord-284625-to6w5hm2.json key: cord-284625-to6w5hm2 authors: Duan, Xiaopei; Guo, Xinyu; Qiang, Jun title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 journal: Jpn J Radiol DOI: 10.1007/s11604-020-00988-4 sha: doc_id: 284625 cord_uid: to6w5hm2 file: cache/cord-283380-l60yyr6l.json key: cord-283380-l60yyr6l authors: Grabbe, Stephan; Beissert, Stefan; Enk, Alexander title: Systemic immunosuppression in times of COVID‐19: Do we need to rethink our standards? date: 2020-08-02 journal: J Dtsch Dermatol Ges DOI: 10.1111/ddg.14194 sha: doc_id: 283380 cord_uid: l60yyr6l file: cache/cord-284449-z7r4n0w7.json key: cord-284449-z7r4n0w7 authors: Ma, L.; Xie, W.; Li, D.; Shi, L.; Mao, Y.; Xiong, Y.; Zhang, Y.; Zhang, M. title: Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study date: 2020-03-24 journal: nan DOI: 10.1101/2020.03.21.20037267 sha: doc_id: 284449 cord_uid: z7r4n0w7 file: cache/cord-284791-bgodmbru.json key: cord-284791-bgodmbru authors: Whitworth, Carrie; Mu, Yi; Houston, Hollis; Martinez-Smith, Marla; Noble-Wang, Judith; Coulliette-Salmond, Angela; Rose, Laura title: Persistence of Bacteriophage Phi 6 on Porous and Nonporous Surfaces and the Potential for Its Use as an Ebola Virus or Coronavirus Surrogate date: 2020-08-18 journal: Appl Environ Microbiol DOI: 10.1128/aem.01482-20 sha: doc_id: 284791 cord_uid: bgodmbru file: cache/cord-284102-rovyvv45.json key: cord-284102-rovyvv45 authors: Wagner, Teresa R.; Kaiser, Philipp D.; Gramlich, Marius; Becker, Matthias; Traenkle, Bjoern; Junker, Daniel; Haering, Julia; Dulovic, Alex; Schweizer, Helen; Nueske, Stefan; Scholz, Armin; Zeck, Anne; Schenke-Layland, Katja; Nelde, Annika; Strengert, Monika; Walz, Juliane S.; Ruetalo, Natalia; Schindler, Michael; Schneiderhan-Marra, Nicole; Rothbauer, Ulrich title: NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date: 2020-09-28 journal: bioRxiv DOI: 10.1101/2020.09.22.308338 sha: doc_id: 284102 cord_uid: rovyvv45 file: cache/cord-283485-xit6najq.json key: cord-283485-xit6najq authors: Van Damme, Wim; Dahake, Ritwik; Delamou, Alexandre; Ingelbeen, Brecht; Wouters, Edwin; Vanham, Guido; van de Pas, Remco; Dossou, Jean-Paul; Ir, Por; Abimbola, Seye; Van der Borght, Stefaan; Narayanan, Devadasan; Bloom, Gerald; Van Engelgem, Ian; Ag Ahmed, Mohamed Ali; Kiendrébéogo, Joël Arthur; Verdonck, Kristien; De Brouwere, Vincent; Bello, Kéfilath; Kloos, Helmut; Aaby, Peter; Kalk, Andreas; Al-Awlaqi, Sameh; Prashanth, NS; Muyembe-Tamfum, Jean-Jacques; Mbala, Placide; Ahuka-Mundeke, Steve; Assefa, Yibeltal title: The COVID-19 pandemic: diverse contexts; different epidemics—how and why? date: 2020-07-27 journal: BMJ Glob Health DOI: 10.1136/bmjgh-2020-003098 sha: doc_id: 283485 cord_uid: xit6najq file: cache/cord-283749-j4600733.json key: cord-283749-j4600733 authors: Itoyama, Satoru; Keicho, Naoto; Quy, Tran; Phi, Nguyen Chi; Long, Hoang Thuy; Ha, Le Dang; Ban, Vo Van; Ohashi, Jun; Hijikata, Minako; Matsushita, Ikumi; Kawana, Akihiko; Yanai, Hideki; Kirikae, Teruo; Kuratsuji, Tadatoshi; Sasazuki, Takehiko title: ACE1 polymorphism and progression of SARS date: 2004-10-22 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2004.08.208 sha: doc_id: 283749 cord_uid: j4600733 file: cache/cord-284498-54j6ys8s.json key: cord-284498-54j6ys8s authors: Ihsanullah, Ihsanullah; Bilal, Muhammad; Naushad, Mu. title: Coronavirus 2 (SARS-CoV-2) in water environments: Current status, challenges and research opportunities date: 2020-10-16 journal: nan DOI: 10.1016/j.jwpe.2020.101735 sha: doc_id: 284498 cord_uid: 54j6ys8s file: cache/cord-284526-a5kgo4ct.json key: cord-284526-a5kgo4ct authors: Gavriilaki, Eleni; Anyfanti, Panagiota; Gavriilaki, Maria; Lazaridis, Antonios; Douma, Stella; Gkaliagkousi, Eugenia title: Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses date: 2020-08-27 journal: Curr Hypertens Rep DOI: 10.1007/s11906-020-01078-6 sha: doc_id: 284526 cord_uid: a5kgo4ct file: cache/cord-283432-od5nnxvg.json key: cord-283432-od5nnxvg authors: Morawska, Lidia; Tang, Julian W.; Bahnfleth, William; Bluyssen, Philomena M.; Boerstra, Atze; Buonanno, Giorgio; Cao, Junji; Dancer, Stephanie; Floto, Andres; Franchimon, Francesco; Haworth, Charles; Hogeling, Jaap; Isaxon, Christina; Jimenez, Jose L.; Kurnitski, Jarek; Li, Yuguo; Loomans, Marcel; Marks, Guy; Marr, Linsey C.; Mazzarella, Livio; Krikor Melikov, Arsen; Miller, Shelly; Milton, Donald K.; Nazaroff, William; Nielsen, Peter V.; Noakes, Catherine; Peccia, Jordan; Querol, Xavier; Sekhar, Chandra; Seppänen, Olli; Tanabe, Shin-ichi; Tellier, Raymond; Wai Tham, Kwok; Wargocki, Pawel; Wierzbicka, Aneta; Yao, Maosheng title: How can airborne transmission of COVID-19 indoors be minimised? date: 2020-05-27 journal: Environ Int DOI: 10.1016/j.envint.2020.105832 sha: doc_id: 283432 cord_uid: od5nnxvg file: cache/cord-283486-ji0e8yoo.json key: cord-283486-ji0e8yoo authors: Radulesco, Thomas; Lechien, Jerome R.; Saussez, Sven; Hopkins, Claire; Michel, Justin title: Safety and Impact of Nasal Lavages During Viral Infections Such as SARS-CoV-2 date: 2020-08-27 journal: Ear Nose Throat J DOI: 10.1177/0145561320950491 sha: doc_id: 283486 cord_uid: ji0e8yoo file: cache/cord-283352-0l1ggmhx.json key: cord-283352-0l1ggmhx authors: Javelot, H; Weiner, L title: Panic and pandemic: narrative review of the literature on the links and risks of panic disorder as a consequence of the SARS-CoV-2 pandemic date: 2020-08-10 journal: Encephale DOI: 10.1016/j.encep.2020.08.001 sha: doc_id: 283352 cord_uid: 0l1ggmhx file: cache/cord-283579-aejbfk3l.json key: cord-283579-aejbfk3l authors: Hilda, Awoyelu Elukunbi; Kolawole, Oladipo Elijah; Olufemi, Adetuyi Babatunde; Senbadejo, Tosin Yetunde; Oyawoye, Olubukola Monisola; Kola, Oloke Julius title: Phyloevolutionary analysis of SARS-CoV-2 in Nigeria date: 2020-06-14 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100717 sha: doc_id: 283579 cord_uid: aejbfk3l file: cache/cord-283850-kt8n6pg2.json key: cord-283850-kt8n6pg2 authors: Steardo, Luca; Steardo, Luca; Verkhratsky, Alexei title: Psychiatric face of COVID-19 date: 2020-07-30 journal: Transl Psychiatry DOI: 10.1038/s41398-020-00949-5 sha: doc_id: 283850 cord_uid: kt8n6pg2 file: cache/cord-284559-g9szoh3g.json key: cord-284559-g9szoh3g authors: Bartoloni, Elena; Perricone, Carlo; Cafaro, Giacomo; Gerli, Roberto title: Hypertension and SARS-Cov-2 infection: is inflammation the missing link? date: 2020-09-23 journal: Cardiovasc Res DOI: 10.1093/cvr/cvaa273 sha: doc_id: 284559 cord_uid: g9szoh3g file: cache/cord-284862-nhihxog0.json key: cord-284862-nhihxog0 authors: Kroemer, Marie; Spehner, Laurie; Vettoretti, Lucie; Bouard, Adeline; Eberst, Guillaume; Floury, Sebastien Pili; Capellier, Gilles; Lepiller, Quentin; Orillard, Emeline; Mansi, Laura; Clairet, Anne-Laure; Westeel, Virginie; Limat, Samuel; Dubois, Maxime; Malinowski, Léa; Bohard, Louis; Borg, Christophe; Chirouze, Catherine; Bouiller, Kevin title: COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity date: 2020-08-25 journal: J Infect DOI: 10.1016/j.jinf.2020.08.036 sha: doc_id: 284862 cord_uid: nhihxog0 file: cache/cord-283956-zgrtux7i.json key: cord-283956-zgrtux7i authors: Amin, Sk. Abdul; Jha, Tarun title: Fight against novel coronavirus: A perspective of medicinal chemists date: 2020-06-12 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2020.112559 sha: doc_id: 283956 cord_uid: zgrtux7i file: cache/cord-284841-flhfagp3.json key: cord-284841-flhfagp3 authors: Nicol, Thomas; Lefeuvre, Caroline; Serri, Orianne; Pivert, Adeline; Joubaud, Françoise; Ducancelle, Alexandra; Lunel-Fabiani, Françoise; Le Guillou-Guillemette, Hélène title: Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech) date: 2020-06-15 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104511 sha: doc_id: 284841 cord_uid: flhfagp3 file: cache/cord-284702-reu77suz.json key: cord-284702-reu77suz authors: Lau, Suet-Ting; Yu, Wai-Cho; Mok, Ngai-Shing; Tsui, Ping-Tim; Tong, Wing-Lok; Cheng, StellaW.C. title: Tachycardia amongst subjects recovering from severe acute respiratory syndrome (SARS) date: 2005-04-08 journal: International Journal of Cardiology DOI: 10.1016/j.ijcard.2004.06.022 sha: doc_id: 284702 cord_uid: reu77suz file: cache/cord-285179-26ey3fm8.json key: cord-285179-26ey3fm8 authors: Chan, Kwok-Hung; Chan, Jasper Fuk-Woo; Tse, Herman; Chen, Honglin; Lau, Candy Choi-Yi; Cai, Jian-Piao; Tsang, Alan Ka-Lun; Xiao, Xincai; To, Kelvin Kai-Wang; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Zheng, Bo-Jiang; Wang, Ming; Yuen, Kwok-Yung title: Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests date: 2013-04-10 journal: J Infect DOI: 10.1016/j.jinf.2013.03.015 sha: doc_id: 285179 cord_uid: 26ey3fm8 file: cache/cord-283440-8du0s33p.json key: cord-283440-8du0s33p authors: Ciuca, Ioana M title: COVID-19 in Children: An Ample Review date: 2020-06-25 journal: Risk Manag Healthc Policy DOI: 10.2147/rmhp.s257180 sha: doc_id: 283440 cord_uid: 8du0s33p file: cache/cord-284829-dge21g0g.json key: cord-284829-dge21g0g authors: Dinakaran, Damodharan; Manjunatha, Narayana; Naveen Kumar, Channaveerachari; Suresh, Bada Math title: Neuropsychiatric aspects of COVID-19 Pandemic: A Selective Review date: 2020-05-30 journal: Asian J Psychiatr DOI: 10.1016/j.ajp.2020.102188 sha: doc_id: 284829 cord_uid: dge21g0g file: cache/cord-285168-qkadqohe.json key: cord-285168-qkadqohe authors: Delatorre, Edson; Mir, Daiana; Graf, Tiago; Bello, Gonzalo title: Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries date: 2020-04-23 journal: nan DOI: 10.1101/2020.04.20.20073007 sha: doc_id: 285168 cord_uid: qkadqohe file: cache/cord-284573-w0sk622m.json key: cord-284573-w0sk622m authors: Caduff, Carlo title: What Went Wrong: Corona and the World after the Full Stop date: 2020-07-21 journal: Med Anthropol Q DOI: 10.1111/maq.12599 sha: doc_id: 284573 cord_uid: w0sk622m file: cache/cord-285362-7dc2gox0.json key: cord-285362-7dc2gox0 authors: Jacot, Damien; Greub, Gilbert; Jaton, Katia; Opota, Onya title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses date: 2020-09-07 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.08.004 sha: doc_id: 285362 cord_uid: 7dc2gox0 file: cache/cord-285557-my16g91c.json key: cord-285557-my16g91c authors: Berger, A.; Drosten, Ch.; Doerr, H. W.; Stürmer, M.; Preiser, W. title: Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date: 2004-01-31 journal: Journal of Clinical Virology DOI: 10.1016/j.jcv.2003.09.011 sha: doc_id: 285557 cord_uid: my16g91c file: cache/cord-284925-vy2li9lz.json key: cord-284925-vy2li9lz authors: Lam, Dennis Shun Chiu; Wong, Raymond Lai Man; Lai, Kenny Ho Wa; Ko, Chung-Nga; Leung, Hiu Ying; Lee, Vincent Yau Wing; Lau, Johnson Yiu Nam; Huang, Suber S. title: COVID-19: Special Precautions in Ophthalmic Practice and FAQs on Personal Protection and Mask Selection date: 2020-04-29 journal: Asia Pac J Ophthalmol (Phila) DOI: 10.1097/apo.0000000000000280 sha: doc_id: 284925 cord_uid: vy2li9lz file: cache/cord-284042-awl5bb0j.json key: cord-284042-awl5bb0j authors: Carrascosa, J.M.; Morillas, V.; Bielsa, I.; Munera-Campos, M. title: Cutaneous Manifestations in the Context of SARS-CoV-2 Infection (COVID-19)() date: 2020-10-15 journal: Actas Dermosifiliogr DOI: 10.1016/j.adengl.2020.10.001 sha: doc_id: 284042 cord_uid: awl5bb0j file: cache/cord-284873-m1ehdydr.json key: cord-284873-m1ehdydr authors: Cadegiani, Flavio A.; Wambier, Carlos G.; Goren, Andy title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 date: 2020-07-28 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00453 sha: doc_id: 284873 cord_uid: m1ehdydr file: cache/cord-284879-sjkni2uc.json key: cord-284879-sjkni2uc authors: Song, Suk-Kyoon; Lee, Duk-Hee; Nam, Jun-Ho; Kim, Kyung-Tae; Do, Jung-Suk; Kang, Dae-Won; Kim, Sang-Gyung; Cho, Myung-Rae title: IgG Seroprevalence of COVID-19 among Individuals without a History of the Coronavirus Disease Infection in Daegu, Korea date: 2020-07-16 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e269 sha: doc_id: 284879 cord_uid: sjkni2uc file: cache/cord-285053-ah9z9luw.json key: cord-285053-ah9z9luw authors: Freedman, David O; Wilder-Smith, Annelies title: In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks date: 2020-09-25 journal: J Travel Med DOI: 10.1093/jtm/taaa178 sha: doc_id: 285053 cord_uid: ah9z9luw file: cache/cord-283912-ha2xwjzy.json key: cord-283912-ha2xwjzy authors: Zheng, Meijuan; Gao, Yong; Liu, Siyu; Sun, Dandan; Yang, Fan; Zong, Lu; Zhang, Min; Tian, Zhigang; Xu, Yuanhong; Sun, Haoyu title: Serum inflammatory factors are positively correlated with the production of specific antibodies in coronavirus disease 2019 patients date: 2020-09-22 journal: Cell Mol Immunol DOI: 10.1038/s41423-020-00551-1 sha: doc_id: 283912 cord_uid: ha2xwjzy file: cache/cord-284037-nj5jo1ev.json key: cord-284037-nj5jo1ev authors: Kwee, Thomas C.; Kwee, Robert M. title: Chest CT in COVID-19: What the Radiologist Needs to Know date: 2020-10-23 journal: Radiographics DOI: 10.1148/rg.2020200159 sha: doc_id: 284037 cord_uid: nj5jo1ev file: cache/cord-284234-9cd2v6bt.json key: cord-284234-9cd2v6bt authors: Sebastian, S; Gonzalez, H A; Peyrin-Biroulet, L title: Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date: 2020-06-10 journal: J Crohns Colitis DOI: 10.1093/ecco-jcc/jjaa120 sha: doc_id: 284234 cord_uid: 9cd2v6bt file: cache/cord-284589-j1609xlu.json key: cord-284589-j1609xlu authors: Sedova, Mayya; Jaroszewski, Lukasz; Alisoltani, Arghavan; Godzik, Adam title: Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence date: 2020-05-29 journal: Bioinformatics DOI: 10.1093/bioinformatics/btaa550 sha: doc_id: 284589 cord_uid: j1609xlu file: cache/cord-284734-qioy7eso.json key: cord-284734-qioy7eso authors: Pourahmad, Ramtin; Moazzami, Bobak; Rezaei, Nima title: Efficacy of Plasmapheresis and Immunoglobulin Replacement Therapy (IVIG) on Patients with COVID-19 date: 2020-07-31 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00438-2 sha: doc_id: 284734 cord_uid: qioy7eso file: cache/cord-284867-p4jgyusp.json key: cord-284867-p4jgyusp authors: Schöler, Lara; Le-Trilling, Vu Thuy Khanh; Eilbrecht, Mareike; Mennerich, Denise; Anastasiou, Olympia E.; Krawczyk, Adalbert; Herrmann, Anke; Dittmer, Ulf; Trilling, Mirko title: A Novel In-Cell ELISA Assay Allows Rapid and Automated Quantification of SARS-CoV-2 to Analyze Neutralizing Antibodies and Antiviral Compounds date: 2020-10-09 journal: Front Immunol DOI: 10.3389/fimmu.2020.573526 sha: doc_id: 284867 cord_uid: p4jgyusp file: cache/cord-285430-o086q2qa.json key: cord-285430-o086q2qa authors: Gribble, Karleen; Mathisen, Roger; Ververs, Mija-tesse; Coutsoudis, Anna title: Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date: 2020-07-25 journal: Int Breastfeed J DOI: 10.1186/s13006-020-00306-8 sha: doc_id: 285430 cord_uid: o086q2qa file: cache/cord-283824-c7y9zf7o.json key: cord-283824-c7y9zf7o authors: Opitz, Sven title: Regulating epidemic space: the nomos of global circulation date: 2015-02-20 journal: J Int Relat Dev (Ljubl) DOI: 10.1057/jird.2014.30 sha: doc_id: 283824 cord_uid: c7y9zf7o file: cache/cord-284950-qqje5s04.json key: cord-284950-qqje5s04 authors: Venkataraman, Thiagarajan; Frieman, Matthew B. title: The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis date: 2017-07-31 journal: Antiviral Research DOI: 10.1016/j.antiviral.2017.03.022 sha: doc_id: 284950 cord_uid: qqje5s04 file: cache/cord-285018-l26px1bc.json key: cord-285018-l26px1bc authors: Ong, David S.Y.; Claas, Eric C.J.; Breijer, Simone; Vaessen, Norbert title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date: 2020-09-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104632 sha: doc_id: 285018 cord_uid: l26px1bc file: cache/cord-283861-kcv1bmyx.json key: cord-283861-kcv1bmyx authors: Zou, J.; Bretin, A.; Gewirtz, A. title: Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents date: 2020-05-06 journal: nan DOI: 10.1101/2020.05.01.20087478 sha: doc_id: 283861 cord_uid: kcv1bmyx file: cache/cord-284478-c1uj3jra.json key: cord-284478-c1uj3jra authors: Schub, David; Klemis, Verena; Schneitler, Sophie; Mihm, Janine; Lepper, Philipp M.; Wilkens, Heinrike; Bals, Robert; Eichler, Hermann; Gärtner, Barbara C.; Becker, Sören L.; Sester, Urban; Sester, Martina; Schmidt, Tina title: High levels of SARS-CoV-2–specific T cells with restricted functionality in severe courses of COVID-19 date: 2020-10-15 journal: JCI insight DOI: 10.1172/jci.insight.142167 sha: doc_id: 284478 cord_uid: c1uj3jra file: cache/cord-284068-sbon3aes.json key: cord-284068-sbon3aes authors: Mok, Chee Keng; Ng, Yan Ling; Ahidjo, Bintou Ahmadou; Hua Lee, Regina Ching; Choy Loe, Marcus Wing; Liu, Jing; Tan, Kai Sen; Kaur, Parveen; Chng, Wee Joo; Wong, John Eu-Li; Wang, De Yun; Hao, Erwei; Hou, Xiaotao; Tan, Yong Wah; Mak, Tze Minn; Lin, Cui; Lin, Raymond; Tambyah, Paul; Deng, JiaGang; Hann Chu, Justin Jang title: Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date: 2020-06-22 journal: bioRxiv DOI: 10.1101/2020.06.21.162396 sha: doc_id: 284068 cord_uid: sbon3aes file: cache/cord-284387-cjziykrz.json key: cord-284387-cjziykrz authors: Garcia-Castrillo, Luis; Petrino, Roberta; Leach, Robert; Dodt, Christoph; Behringer, Wilhelm; Khoury, Abdo; Sabbe, Marc title: European Society For Emergency Medicine position paper on emergency medical systems’ response to COVID-19 date: 2020-05-04 journal: Eur J Emerg Med DOI: 10.1097/mej.0000000000000701 sha: doc_id: 284387 cord_uid: cjziykrz file: cache/cord-284429-d7qxfo6d.json key: cord-284429-d7qxfo6d authors: Trezza, Alfonso; Iovinelli, Daniele; Santucci, Annalisa; Prischi, Filippo; Spiga, Ottavia title: An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors date: 2020-08-17 journal: Sci Rep DOI: 10.1038/s41598-020-70863-9 sha: doc_id: 284429 cord_uid: d7qxfo6d file: cache/cord-285467-uxfk6k3c.json key: cord-285467-uxfk6k3c authors: Ragni, Enrico; Mangiavini, Laura; Viganò, Marco; Brini, Anna Teresa; Peretti, Giuseppe Michele; Banfi, Giuseppe; de Girolamo, Laura title: Management of osteoarthritis during COVID‐19 pandemic date: 2020-05-21 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.1910 sha: doc_id: 285467 cord_uid: uxfk6k3c file: cache/cord-285527-1mceq6v0.json key: cord-285527-1mceq6v0 authors: Kinloch, Natalie N; Ritchie, Gordon; Brumme, Chanson J; Dong, Winnie; Dong, Weiyan; Lawson, Tanya; Jones, R Brad; Montaner, Julio S G; Leung, Victor; Romney, Marc G; Stefanovic, Aleksandra; Matic, Nancy; Lowe, Christopher F; Brumme, Zabrina L title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date: 2020-06-28 journal: J Infect Dis DOI: 10.1093/infdis/jiaa370 sha: doc_id: 285527 cord_uid: 1mceq6v0 file: cache/cord-285449-frft2h85.json key: cord-285449-frft2h85 authors: Guillon, Patrice; Clément, Monique; Sébille, Véronique; Rivain, Jean-Gérard; Chou, Chih-Fong; Ruvoën-Clouet, Nathalie; Le Pendu, Jacques title: Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies date: 2008-09-25 journal: Glycobiology DOI: 10.1093/glycob/cwn093 sha: doc_id: 285449 cord_uid: frft2h85 file: cache/cord-284376-plwyjhl8.json key: cord-266738-8xx1xm2d authors: Feng, Zhan-hui; Cheng, Yong-ran; Chen, Juan; Ye, Lan; Zhou, Meng-Yun; Wang, Ming-Wei title: Chinese medical personnel against the 2019-nCoV date: 2020-05-31 journal: Journal of Infection DOI: 10.1016/j.jinf.2020.02.011 sha: doc_id: 266738 cord_uid: 8xx1xm2d key: cord-284376-plwyjhl8 authors: Fu, Xinmiao; Ying, Qi; Zeng, Tieyong; Long, Tao; Wang, Yan title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 journal: Journal of Infection DOI: 10.1016/j.jinf.2020.02.019 sha: doc_id: 284376 cord_uid: plwyjhl8 key: cord-324559-p92y5er2 authors: Lillie, Patrick J.; 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Dhar, Shrinjana; Bhattacharjee, Sandip; Bhattacharjee, Pritha title: Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date: 2020-04-09 journal: bioRxiv DOI: 10.1101/2020.04.06.027854 sha: doc_id: 284627 cord_uid: qvz63m93 file: cache/cord-284978-vh1x6pg9.json key: cord-284978-vh1x6pg9 authors: Jang, Hongje; Ryoo, Soo‐Ryoon; Kim, Young‐Kwan; Yoon, Soojin; Kim, Henna; Han, Sang Woo; Choi, Byong‐Seok; Kim, Dong‐Eun; Min, Dal‐Hee title: Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date: 2013-02-18 journal: Angew Chem Weinheim Bergstr Ger DOI: 10.1002/ange.201209222 sha: doc_id: 284978 cord_uid: vh1x6pg9 file: cache/cord-284366-snajbvr9.json key: cord-284366-snajbvr9 authors: Han, Zhiyong; Battaglia, Fortunato; Terlecky, Stanley R title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 journal: J Med Virol DOI: 10.1002/jmv.26250 sha: doc_id: 284366 cord_uid: snajbvr9 file: cache/cord-284191-05djnz4p.json key: cord-284191-05djnz4p authors: Bert, Nina Le; 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Kashyap, Rahul; Tosh, Pritish; Sampathkumar, Priya; O’Horo, John C. title: Guide to Understanding the 2019 Novel Coronavirus date: 2020-02-28 journal: Mayo Clin Proc DOI: 10.1016/j.mayocp.2020.02.003 sha: doc_id: 285569 cord_uid: ei9w19i7 file: cache/cord-285469-b61y9ezi.json key: cord-285469-b61y9ezi authors: Hernández-Fernández, Francisco; Valencia, Hernán Sandoval; Barbella-Aponte, Rosa Angélica; Collado-Jiménez, Rosa; Ayo-Martín, Óscar; Barrena, Cristina; Molina-Nuevo, Juan David; García-García, Jorge; Lozano-Setién, Elena; Alcahut-Rodriguez, Cristian; Martínez-Martín, Álvaro; Sánchez-López, Antonio; Segura, Tomás title: Cerebrovascular disease in patients with COVID-19: neuroimaging, histological and clinical description date: 2020-07-09 journal: Brain DOI: 10.1093/brain/awaa239 sha: doc_id: 285469 cord_uid: b61y9ezi file: cache/cord-284954-uuqchon4.json key: cord-284954-uuqchon4 authors: Plebani, Mario title: SARS-CoV-2 antibody-based SURVEILLANCE: New light in the SHADOW date: 2020-11-05 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.103087 sha: doc_id: 284954 cord_uid: uuqchon4 file: cache/cord-285603-f4572w5m.json key: cord-285603-f4572w5m authors: Ortega, Joseph T.; Serrano, Maria Luisa; Jastrzebska, Beata title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 journal: Biomolecules DOI: 10.3390/biom10060954 sha: doc_id: 285603 cord_uid: f4572w5m file: cache/cord-285787-xvi5miqw.json key: cord-285787-xvi5miqw authors: Bell, Jennifer AH; Hyland, Sylvia; DePellegrin, Tania; Upshur, Ross EG; Bernstein, Mark; Martin, Douglas K title: SARS and hospital priority setting: a qualitative case study and evaluation date: 2004-12-19 journal: BMC Health Serv Res DOI: 10.1186/1472-6963-4-36 sha: doc_id: 285787 cord_uid: xvi5miqw file: cache/cord-285162-srkd3wh0.json key: cord-285162-srkd3wh0 authors: Jung, F.; Krieger, V.; Hufert, F.T.; Küpper, J.-H. title: How we should respond to the Coronavirus SARS-CoV-2 outbreak: A German perspective date: 2020-06-05 journal: Clinical hemorheology and microcirculation DOI: 10.3233/ch-209004 sha: doc_id: 285162 cord_uid: srkd3wh0 file: cache/cord-285203-ilxd0ih9.json key: cord-285203-ilxd0ih9 authors: Paradiso, Angelo Virgilio; De Summa, Simona; Loconsole, Daniela; Procacci, Vito; Sallustio, Anna; Centrone, Francesca; Silvestris, Nicola; Cafagna, Vito; De Palma, Giuseppe; Tufaro, Antonio; Garrisi, Vito; Chironna, Maria title: Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date: 2020-04-06 journal: nan DOI: 10.1101/2020.04.03.20052183 sha: doc_id: 285203 cord_uid: ilxd0ih9 file: cache/cord-285574-i0dh1u5i.json key: cord-285574-i0dh1u5i authors: Ferini-Strambi, Luigi; Salsone, Maria title: COVID-19 and neurological disorders: are neurodegenerative or neuroimmunological diseases more vulnerable? date: 2020-07-21 journal: J Neurol DOI: 10.1007/s00415-020-10070-8 sha: doc_id: 285574 cord_uid: i0dh1u5i file: cache/cord-285755-zblitbo0.json key: cord-285755-zblitbo0 authors: Zhang, F.; Yang, D.; Li, J.; Gao, P.; Chen, T.; Cheng, Z.; Cheng, K.; Fang, Q.; Pan, W.; Yi, C.; Fan, H.; Wu, Y.; Li, L.; Fang, Y.; Liu, J.; Tian, G.; He, L. title: Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study date: 2020-03-24 journal: nan DOI: 10.1101/2020.03.21.20040121 sha: doc_id: 285755 cord_uid: zblitbo0 file: cache/cord-285426-iyl12ber.json key: cord-285426-iyl12ber authors: Ghavami, Shaghayegh Baradaran; Shahrokh, Shabnam; Hossein-Khannazer, Nikoo; Shpichka, Anastasia; Asadzadeh Aghdaei, Hamid; Timashev, Peter; Vosough, Massoud title: IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date: 2020-09-08 journal: Cell J DOI: 10.22074/cellj.2020.7603 sha: doc_id: 285426 cord_uid: iyl12ber file: cache/cord-285440-srtkqr13.json key: cord-285440-srtkqr13 authors: Zhang, Jianguo; Sun, Jianyong; Yang, Yuanyuan; Chen, Xiaomeng; Meng, Lili; Lian, Ping title: Web-based electronic patient records for collaborative medical applications date: 2004-12-20 journal: Comput Med Imaging Graph DOI: 10.1016/j.compmedimag.2004.09.005 sha: doc_id: 285440 cord_uid: srtkqr13 file: cache/cord-285580-gq7400tq.json key: cord-285580-gq7400tq authors: Pieretti, Joana C.; Rubilar, Olga; Weller, Richard B.; Tortella, Gonzalo R.; Seabra, Amedea B. title: Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date: 2020-10-18 journal: Virus Res DOI: 10.1016/j.virusres.2020.198202 sha: doc_id: 285580 cord_uid: gq7400tq file: cache/cord-285739-0enn5bzn.json key: cord-285739-0enn5bzn authors: Gutiérrez Rodríguez, José; Muñoz, Javier Montero; Muela, Francisco Jiménez; García-Prendes, Cristina Guirola; Rivera, Marta Martínez; Armas, Laura Gómez title: Variables asociadas a mortalidad en una población de pacientes mayores de 80 años y con algún grado de dependencia funcional hospitalizados por COVID-19 en un Servicio de Geriatría date: 2020-07-16 journal: Rev Esp Geriatr Gerontol DOI: 10.1016/j.regg.2020.07.002 sha: doc_id: 285739 cord_uid: 0enn5bzn file: cache/cord-285159-gytebbua.json key: cord-285159-gytebbua authors: Eydoux, Cecilia; Fattorini, Veronique; Shannon, Ashleigh; Le, Thi-Tuyet-Nhung; Didier, Bruno; Canard, Bruno; Guillemot, Jean-Claude title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 journal: bioRxiv DOI: 10.1101/2020.07.07.192005 sha: doc_id: 285159 cord_uid: gytebbua file: cache/cord-285459-fph03r22.json key: cord-285459-fph03r22 authors: Patel, Ami B; Clifford, Andrea; Creaden, Julie; Kato, Kimberly; Malakooti, Marcelo R; Muller, William J; O’Donnell, Anna; Reynolds, Sally; Richey, Karen; Rippe, Jason; Wheeler, Derek S; Kociolek, Larry K title: SARS-CoV-2 Point Prevalence among Asymptomatic Hospitalized Children and Subsequent Healthcare Worker Evaluation date: 2020-08-28 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa102 sha: doc_id: 285459 cord_uid: fph03r22 file: cache/cord-285636-cs26uuwx.json key: cord-285636-cs26uuwx authors: Singh, N. K.; Ray, P.; Carlin, A. F.; Magallanes, C.; Morgan, S.; Laurent, L. C.; Aronoff-Spencer, E.; Hall, D. A. title: Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer date: 2020-09-25 journal: nan DOI: 10.1101/2020.09.24.20200394 sha: doc_id: 285636 cord_uid: cs26uuwx file: cache/cord-285849-jg43tcfh.json key: cord-285849-jg43tcfh authors: Chan, Ben Chong Pun; Lee, Chin Peng; Tang, Grace Wai King title: Universal SARS preventive measures in an obstetrics unit: Experience of health care staff date: 2004-10-30 journal: Am J Infect Control DOI: 10.1016/j.ajic.2004.01.006 sha: doc_id: 285849 cord_uid: jg43tcfh file: cache/cord-285486-99trkti1.json key: cord-285486-99trkti1 authors: Abd-Elsalam, Sherief; Esmail, Eslam Saber; Khalaf, Mai; Abdo, Ehab Fawzy; Medhat, Mohammed A.; Abd El Ghafar, Mohamed Samir; Ahmed, Ossama Ashraf; Soliman, Shaimaa; Serangawy, Ghada N.; Alboraie, Mohamed title: Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study date: 2020-08-14 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0873 sha: doc_id: 285486 cord_uid: 99trkti1 file: cache/cord-285647-9tegcrc3.json key: cord-285647-9tegcrc3 authors: Estrada, Ernesto title: Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date: 2020-08-17 journal: Chaos DOI: 10.1063/5.0015626 sha: doc_id: 285647 cord_uid: 9tegcrc3 file: cache/cord-285848-37dmv4ep.json key: cord-285848-37dmv4ep authors: Fu, Xiao-Wei; Wu, Li-Na; Shan, Ling title: Review of possible psychological impacts of COVID-19 on frontline medical staff and reduction strategies date: 2020-08-06 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i15.3188 sha: doc_id: 285848 cord_uid: 37dmv4ep file: cache/cord-285711-2utcn0hw.json key: cord-285711-2utcn0hw authors: Elliott, Robert; Ohene Baah, Nana; Grossman, Valerie Aarne; Sharma, Ashwani Kumar title: COVID-19 Related Mortality During Management of a Hepatic Abscess date: 2020-09-22 journal: J Radiol Nurs DOI: 10.1016/j.jradnu.2020.09.001 sha: doc_id: 285711 cord_uid: 2utcn0hw file: cache/cord-285758-c18arb6s.json key: cord-285758-c18arb6s authors: Jiang, Shibo; He, Yuxian; Liu, Shuwen title: SARS Vaccine Development date: 2005-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1107.050219 sha: doc_id: 285758 cord_uid: c18arb6s file: cache/cord-285822-b5itedu3.json key: cord-285822-b5itedu3 authors: Carlos Marín-Gabriel, José; de Santiago, Enrique Rodríguez title: Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 date: 2020-05-27 journal: Gastroenterol Hepatol DOI: 10.1016/j.gastrohep.2020.05.004 sha: doc_id: 285822 cord_uid: b5itedu3 file: cache/cord-286001-pu1fetq7.json key: cord-286001-pu1fetq7 authors: Zang, Ruochen; Castro, Maria F.G.; McCune, Broc T.; Zeng, Qiru; Rothlauf, Paul W.; Sonnek, Naomi M.; Liu, Zhuoming; Brulois, Kevin F.; Wang, Xin; Greenberg, Harry B.; Diamond, Michael S.; Ciorba, Matthew A.; Whelan, Sean P.J.; Ding, Siyuan title: TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date: 2020-04-23 journal: bioRxiv DOI: 10.1101/2020.04.21.054015 sha: doc_id: 286001 cord_uid: pu1fetq7 file: cache/cord-286038-a62k3lma.json key: cord-286038-a62k3lma authors: Klimke, A.; Hefner, G.; Will, B.; Voss, U. title: Hydroxychloroquine as an aerosol might markedly reduce and even prevent severe clinical symptoms after SARS-CoV-2 infection date: 2020-04-27 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109783 sha: doc_id: 286038 cord_uid: a62k3lma file: cache/cord-285806-363ivs67.json key: cord-285806-363ivs67 authors: Magro, Giuseppe title: SARS-CoV-2 and COVID-19: is interleukin-6 (IL-6) the 'culprit lesion' of ARDS onset? What is there besides Tocilizumab? SGP130Fc date: 2020-05-14 journal: Cytokine X DOI: 10.1016/j.cytox.2020.100029 sha: doc_id: 285806 cord_uid: 363ivs67 file: cache/cord-285490-tpsf05ca.json key: cord-285490-tpsf05ca authors: Solís, José Gabriel; Esquivel Pineda, Alejandra; Alberti Minutti, Paolo; Albarrán Sánchez, Alejandra title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm date: 2020-07-29 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0692 sha: doc_id: 285490 cord_uid: tpsf05ca file: cache/cord-285896-lb8toc1m.json key: cord-285896-lb8toc1m authors: Beurton, Alexandra; Haudebourg, Luc; Simon-Tillaux, Noémie; Demoule, Alexandre; Dres, Martin title: Limiting positive end-expiratory pressure to protect renal function in SARS-CoV-2 critically ill patients date: 2020-07-10 journal: J Crit Care DOI: 10.1016/j.jcrc.2020.07.008 sha: doc_id: 285896 cord_uid: lb8toc1m file: cache/cord-285944-8lapwnuw.json key: cord-285944-8lapwnuw authors: Suwanwongse, Kulachanya; Shabarek, Nehad title: Hyperpyrexia in COVID‐19 patients date: 2020-06-10 journal: J Med Virol DOI: 10.1002/jmv.26154 sha: doc_id: 285944 cord_uid: 8lapwnuw file: cache/cord-285852-ocu69od2.json key: cord-285852-ocu69od2 authors: Luqman, Zubair; Iqbal, Nasir; Ali, Hafiz Muhammad; Zahid, Muhammad; Sikandar, Arbab; Kausar, Razia title: Disinfection of corona virus in histopathology laboratories date: 2020-06-25 journal: Clin Anat DOI: 10.1002/ca.23636 sha: doc_id: 285852 cord_uid: ocu69od2 file: cache/cord-285748-us5do6c2.json key: cord-285748-us5do6c2 authors: Cheng, Yongqian; Wang, Wenling; Wu, Liang; Cai, Guangyan title: SARS-CoV-2-Related Kidney Injury: Current Concern and Challenges date: 2020-09-23 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00529-0 sha: doc_id: 285748 cord_uid: us5do6c2 file: cache/cord-285960-1zuhilmu.json key: cord-285960-1zuhilmu authors: Conly, John; Seto, W. H.; Pittet, Didier; Holmes, Alison; Chu, May; Hunter, Paul R. title: Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic date: 2020-08-06 journal: Antimicrob Resist Infect Control DOI: 10.1186/s13756-020-00779-6 sha: doc_id: 285960 cord_uid: 1zuhilmu file: cache/cord-285865-1gsy43a0.json key: cord-285865-1gsy43a0 authors: Wu, Guang; Yan, Shaomin title: Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species date: 2004-12-09 journal: J Mol Model DOI: 10.1007/s00894-004-0210-0 sha: doc_id: 285865 cord_uid: 1gsy43a0 file: cache/cord-285965-mar8zt2t.json key: cord-285965-mar8zt2t authors: Su, Liang; Ma, Xiang; Yu, Huafeng; Zhang, Zhaohua; Bian, Pengfei; Han, Yuling; Sun, Jing; Liu, Yanqin; Yang, Chun; Geng, Jin; Zhang, Zhongfa; Gai, Zhongtao title: The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19 date: 2020-03-25 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1744483 sha: doc_id: 285965 cord_uid: mar8zt2t file: cache/cord-286029-rafcdzhm.json key: cord-286029-rafcdzhm authors: Bogaards, Johannes Antonie; Putter, Hein; Jan Weverling, Gerrit; ter Meulen, Jan; Goudsmit, Jaap title: The potential of targeted antibody prophylaxis in SARS outbreak control: A mathematic analysis() date: 2006-05-05 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2006.01.007 sha: doc_id: 286029 cord_uid: rafcdzhm file: cache/cord-286015-oonfpa0c.json key: cord-286015-oonfpa0c authors: Verbeure, Birgit; van Zimmeren, Esther; Matthijs, Gert; Van Overwalle, Geertrui title: Patent pools and diagnostic testing date: 2006-01-27 journal: Trends Biotechnol DOI: 10.1016/j.tibtech.2006.01.002 sha: doc_id: 286015 cord_uid: oonfpa0c file: cache/cord-285700-9q6vwoct.json key: cord-285700-9q6vwoct authors: Grzelak, Ludivine; Temmam, Sarah; Planchais, Cyril; Demeret, Caroline; Huon, Christele; Guivel, Florence; Staropoli, Isabelle; Chazal, Maxime; Dufloo, Jeremy; Planas, Delphine; Buchrieser, Julian; Rajah, Maaran Michael; Robinot, Remy; Porrot, Francoise; Albert, Melanie; Chen, Kuang-Yu; Crescenzo, Bernadette; Donati, Flora; Anna, Francois; Souque, Philippe; Gransagne, Marion; Bellalou, Jacques; Nowakowski, Mireille; Backovic, Marija; Bouadma, lila; Le Fevre, Lucie; Le Hingrat, Quentin; Descamps, Diane; Pourbaix, Anabelle; Yazdanpanah, Yazdan; Tondeur, Laura; Besombes, Camille; Ungeheuer, Marie-Noelle; Mellon, Guillaume; Morel, Pascal; Rolland, Simon; Rey, Felix; Behillil, Sylvie; Enouf, Vincent; Lemaitre, Audrey; Creach, Marie-Aude; Petres, Stephane; Escriou, Nicolas; Charneau, Pierre; Fontanet, Arnaud; Hoen, Bruno; Bruel, Timothee; Eloit, Marc; Mouquet, Hugo; Schwartz, Olivier; van der Werf, Sylvie title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. date: 2020-04-24 journal: nan DOI: 10.1101/2020.04.21.20068858 sha: doc_id: 285700 cord_uid: 9q6vwoct file: cache/cord-285979-ha5nszxi.json key: cord-285979-ha5nszxi authors: Rojas, Manuel; Rodríguez, Yhojan; Monsalve, Diana M.; Acosta-Ampudia, Yeny; Camacho, Bernardo; Gallo, Juan Esteban; Rojas-Villarraga, Adriana; Ramírez-Santana, Carolina; Díaz-Coronado, Juan C.; Manrique, Rubén; Mantilla, Ruben D.; Shoenfeld, Yehuda; Anaya, Juan-Manuel title: Convalescent plasma in Covid-19: Possible mechanisms of action date: 2020-05-05 journal: Autoimmun Rev DOI: 10.1016/j.autrev.2020.102554 sha: doc_id: 285979 cord_uid: ha5nszxi file: cache/cord-286130-4f7otdx1.json key: cord-286130-4f7otdx1 authors: Xavier, Joilson; Giovanetti, Marta; Adelino, Talita; Fonseca, Vagner; Barbosa da Costa, Alana Vitor; Ribeiro, Adriana Aparecida; Felicio, Katlin Nascimento; Duarte, Clara Guerra; Ferreira Silva, Marcos Vinicius; Salgado, Álvaro; Lima, Mauricio Teixeira; de Jesus, Ronaldo; Fabri, Allison; Soares Zoboli, Cristiane Franco; Souza Santos, Thales Gutemberg; Iani, Felipe; Ciccozzi, Massimo; Bispo de Filippis, Ana Maria; Teixeira de Siqueira, Marilda Agudo Mendonça; de Abreu, André Luiz; de Azevedo, Vasco; Ramalho, Dario Brock; Campelo de Albuquerque, Carlos F.; de Oliveira, Tulio; Holmes, Edward C.; Lourenço, José; Junior Alcantara, Luiz Carlos; Assunção Oliveira, Marluce Aparecida title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing date: 2020-08-11 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1803146 sha: doc_id: 286130 cord_uid: 4f7otdx1 file: cache/cord-286014-cc99e24x.json key: cord-286014-cc99e24x authors: Jang, T.-N; Yeh, D.Y; Shen, S.-H; Huang, C.-H; Jiang, J.-S; Kao, S.-J title: Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases date: 2003-11-05 journal: J Infect DOI: 10.1016/j.jinf.2003.09.004 sha: doc_id: 286014 cord_uid: cc99e24x file: cache/cord-286168-019rcbpg.json key: cord-286168-019rcbpg authors: Vindegaard, Nina; Eriksen Benros, Michael title: COVID-19 pandemic and mental health consequences: systematic review of the current evidence date: 2020-05-30 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.05.048 sha: doc_id: 286168 cord_uid: 019rcbpg file: cache/cord-286217-3uklf2u2.json key: cord-286217-3uklf2u2 authors: Jiang, He-wei; Li, Yang; Zhang, Hai-nan; Wang, Wei; Yang, Xiao; Qi, Huan; Li, Hua; Men, Dong; Zhou, Jie; Tao, Sheng-ce title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date: 2020-07-14 journal: Nat Commun DOI: 10.1038/s41467-020-17488-8 sha: doc_id: 286217 cord_uid: 3uklf2u2 file: cache/cord-286466-scokdxp2.json key: cord-286466-scokdxp2 authors: Tani, Hideki; Tan, Long; Kimura, Miyuki; Yoshida, Yoshihiro; Yamada, Hiroshi; Fukushi, Shuetsu; Saijo, Masayuki; Kawasuji, Hitoshi; Ueno, Akitoshi; Miyajima, Yuki; Fukui, Yasutaka; Sakamaki, Ippei; Yamamoto, Yoshihiro; Morinaga, Yoshitomo title: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date: 2020-08-23 journal: bioRxiv DOI: 10.1101/2020.08.21.262295 sha: doc_id: 286466 cord_uid: scokdxp2 file: cache/cord-285907-xoiju5ub.json key: cord-285907-xoiju5ub authors: Chang, Shang-Miao; Liu, Ching-Lung; Kuo, Hsu-Tah; Chen, Pei-Jan; Lee, Chun Ming; Lin, Fung-J.; Lin, Ching-Chi; Lee, Chao-Hsien; Lu, Yen-Ta title: Comparative study of patients with and without SARS WHO fulfilled the WHO SARS case definition date: 2005-05-31 journal: The Journal of Emergency Medicine DOI: 10.1016/j.jemermed.2004.11.022 sha: doc_id: 285907 cord_uid: xoiju5ub file: cache/cord-286301-7sjw5ci7.json key: cord-286301-7sjw5ci7 authors: Sadasivan, Jibin; Singh, Manmeet; Sarma, Jayasri Das title: Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date: 2017-04-18 journal: J Biosci DOI: 10.1007/s12038-017-9676-7 sha: doc_id: 286301 cord_uid: 7sjw5ci7 file: cache/cord-286365-fy0a8mb4.json key: cord-286365-fy0a8mb4 authors: ElHawary, Hassan; Salimi, Ali; Diab, Nermin; Smith, Lee title: Bibliometric Analysis of Early COVID-19 Research: The Top 50 Cited Papers date: 2020-10-13 journal: Infect Dis (Auckl) DOI: 10.1177/1178633720962935 sha: doc_id: 286365 cord_uid: fy0a8mb4 file: cache/cord-286072-kgpvdb42.json key: cord-286072-kgpvdb42 authors: Sa Ribero, Margarida; Jouvenet, Nolwenn; Dreux, Marlène; Nisole, Sébastien title: Interplay between SARS-CoV-2 and the type I interferon response date: 2020-07-29 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008737 sha: doc_id: 286072 cord_uid: kgpvdb42 file: cache/cord-286084-2275xvxb.json key: cord-286084-2275xvxb authors: Dixit, Alok; Yadav, Ramakant; Singh, Amit Vikram title: Ivermectin: Potential Role as Repurposed Drug for COVID-19 date: 2020-08-19 journal: Malays J Med Sci DOI: 10.21315/mjms2020.27.4.15 sha: doc_id: 286084 cord_uid: 2275xvxb file: cache/cord-286429-voem879q.json key: cord-286429-voem879q authors: Shao, Yi‐Ming; Yang, Wen‐Bin; Peng, Hung‐Pin; Hsu, Min‐Feng; Tsai, Keng‐Chang; Kuo, Tun‐Hsun; Wang, Andrew H.‐J.; Liang, Po‐Huang; Lin, Chun‐Hung; Yang, An‐Suei; Wong, Chi‐Huey title: Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors date: 2007-08-23 journal: Chembiochem DOI: 10.1002/cbic.200700254 sha: doc_id: 286429 cord_uid: voem879q file: cache/cord-286390-ytgw3j4s.json key: cord-286390-ytgw3j4s authors: Case, James Brett; Rothlauf, Paul W.; Chen, Rita E.; Liu, Zhuoming; Zhao, Haiyan; Kim, Arthur S.; Bloyet, Louis-Marie; Zeng, Qiru; Tahan, Stephen; Droit, Lindsay; Ilagan, Ma. Xenia G.; Tartell, Michael A.; Amarasinghe, Gaya; Henderson, Jeffrey P.; Miersch, Shane; Ustav, Mart; Sidhu, Sachdev; Virgin, Herbert W.; Wang, David; Ding, Siyuan; Corti, Davide; Theel, Elitza S.; Fremont, Daved H.; Diamond, Michael S.; Whelan, Sean P.J. title: Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. date: 2020-07-03 journal: Cell Host Microbe DOI: 10.1016/j.chom.2020.06.021 sha: doc_id: 286390 cord_uid: ytgw3j4s file: cache/cord-286121-ltaxmp3u.json key: cord-286121-ltaxmp3u authors: Xu, Ke; Zheng, Bo-Jian; Zeng, Rong; Lu, Wei; Lin, Yong-Ping; Xue, Liang; Li, Li; Yang, Lei-Lei; Xu, Chen; Dai, Jie; Wang, Fei; Li, Qing; Dong, Qing-Xi; Yang, Rui-Fu; Wu, Jia-Rui; Sun, Bing title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date: 2009-06-05 journal: Virology DOI: 10.1016/j.virol.2009.03.032 sha: doc_id: 286121 cord_uid: ltaxmp3u file: cache/cord-286343-s8n1ldol.json key: cord-286343-s8n1ldol authors: Martin, Javier; Klapsa, Dimitra; Wilton, Thomas; Zambon, Maria; Bentley, Emma; Bujaki, Erika; Fritzsche, Martin; Mate, Ryan; Majumdar, Manasi title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 journal: Viruses DOI: 10.3390/v12101144 sha: doc_id: 286343 cord_uid: s8n1ldol file: cache/cord-286269-vrjyj2y1.json key: cord-286269-vrjyj2y1 authors: Sagheb, Setareh; Lamsehchi, Ameneh; Jafary, Mohamadreza; Atef-Yekta, Reza; Sadeghi, Kourosh title: Two seriously ill neonates born to mothers with COVID-19 pneumonia- a case report date: 2020-09-21 journal: Ital J Pediatr DOI: 10.1186/s13052-020-00897-2 sha: doc_id: 286269 cord_uid: vrjyj2y1 file: cache/cord-286006-t5gj0k54.json key: cord-286006-t5gj0k54 authors: Nicholas, David B.; Gearing, Robin E.; Koller, Donna; Salter, Robyn; Selkirk, Enid K. title: Pediatric epidemic crisis: Lessons for policy and practice development date: 2008-12-31 journal: Health Policy DOI: 10.1016/j.healthpol.2007.11.006 sha: doc_id: 286006 cord_uid: t5gj0k54 file: cache/cord-286298-pn9nwl64.json key: cord-286298-pn9nwl64 authors: Helmy, Yosra A.; Fawzy, Mohamed; Elaswad, Ahmed; Sobieh, Ahmed; Kenney, Scott P.; Shehata, Awad A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 journal: J Clin Med DOI: 10.3390/jcm9041225 sha: doc_id: 286298 cord_uid: pn9nwl64 file: cache/cord-286573-k4khwvt7.json key: cord-286573-k4khwvt7 authors: Peng, Michael; Dai, Jiannong; Sugali, Chenna Kesavulu; Rayana, Naga Pradeep; Mao, Weiming title: The Role of the Ocular Tissue in SARS-CoV-2 Transmission date: 2020-10-02 journal: Clin Ophthalmol DOI: 10.2147/opth.s269868 sha: doc_id: 286573 cord_uid: k4khwvt7 file: cache/cord-286555-rz88g3ze.json key: cord-286555-rz88g3ze authors: Petrovan, Vlad; Vrajmasu, Virgil; Bucur, Ana Cristina; Soare, Dan Sebastian; Radu, Eugen; Dimon, Paula; Zaulet, Mihaela title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10070472 sha: doc_id: 286555 cord_uid: rz88g3ze file: cache/cord-286631-3fmg3scx.json key: cord-286631-3fmg3scx authors: Pormohammad, Ali; Ghorbani, Saied; Khatami, Alireza; Farzi, Rana; Baradaran, Behzad; Turner, Diana L.; Turner, Raymond J.; Bahr, Nathan C.; Idrovo, Juan‐Pablo title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis date: 2020-06-05 journal: Rev Med Virol DOI: 10.1002/rmv.2112 sha: doc_id: 286631 cord_uid: 3fmg3scx file: cache/cord-286919-fny060vk.json key: cord-286919-fny060vk authors: Lahfaoui, M; Azizi, M; Elbakkaoui, M; El Amrani, R; kamaoui, I; Benhaddou, H title: Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson date: 2020-04-27 journal: Rev Mal Respir DOI: 10.1016/j.rmr.2020.04.009 sha: doc_id: 286919 cord_uid: fny060vk file: cache/cord-286290-85l99l13.json key: cord-286290-85l99l13 authors: Goddard, N.L.; Delpech, V.C.; Watson, J.M.; Regan, M.; Nicoll, A. title: Lessons learned from SARS: The experience of the Health Protection Agency, England date: 2005-11-16 journal: Public Health DOI: 10.1016/j.puhe.2005.10.003 sha: doc_id: 286290 cord_uid: 85l99l13 file: cache/cord-286341-16tghl48.json key: cord-286341-16tghl48 authors: CONCHA-MEJIA, A.; RINCON-SANCHEZ, R. A. title: CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia date: 2020-07-24 journal: nan DOI: 10.1101/2020.07.24.20161604 sha: doc_id: 286341 cord_uid: 16tghl48 file: cache/cord-286441-nl3kuqw3.json key: cord-286441-nl3kuqw3 authors: Murray, D. D.; Babiker, A. G.; Baker, J. V.; Barkauskas, C. E.; Brown, S. M.; Chang, C.; Davey, V. J.; Gelijns, A. C.; Ginde, A. A.; Grund, B.; Higgs, E.; Hudson, F.; Kan, V. K.; Lane, H. C.; Murray, T. A.; Paredes, R.; Parmar, M. K. B.; Pett, S.; Phillips, A. N.; Polizzotto, M. N.; Reilly, C.; Sandkovsky, U.; Sharma, S.; Teitelbaum, M.; Thompson, B. T.; Young, B. E.; Neaton, J. D.; Lundgren, J. D.; group, TICO study title: Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative date: 2020-11-12 journal: nan DOI: 10.1101/2020.11.08.20227876 sha: doc_id: 286441 cord_uid: nl3kuqw3 file: cache/cord-286638-bqxyb61p.json key: cord-286638-bqxyb61p authors: Singh, Awadhesh Kumar; Gupta, Ritesh; Ghosh, Amerta; Misra, Anoop title: Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations date: 2020-04-09 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.04.004 sha: doc_id: 286638 cord_uid: bqxyb61p file: cache/cord-286854-0s7oq0uv.json key: cord-286854-0s7oq0uv authors: Jin, Xi; Xu, Kangli; Jiang, Penglei; Lian, Jiangshan; Hao, Shaorui; Yao, Hangping; Jia, Hongyu; Zhang, Yimin; Zheng, Lin; Zheng, Nuoheng; Chen, Dong; Yao, Jinmei; Hu, Jianhua; Gao, Jianguo; Wen, Liang; Shen, Jian; Ren, Yue; Yu, Guodong; 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Falzarano, Darryl; Zevenhoven-Dobbe, Jessika C.; Beugeling, Corrine; Fett, Craig; Martellaro, Cynthia; Posthuma, Clara C.; Feldmann, Heinz; Perlman, Stanley; Snijder, Eric J. title: Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date: 2017-01-15 journal: Virus Res DOI: 10.1016/j.virusres.2016.11.011 sha: doc_id: 286703 cord_uid: ipoj13va file: cache/cord-286472-pqtem19t.json key: cord-286472-pqtem19t authors: McFee, R.B. title: MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date: 2020-07-28 journal: Dis Mon DOI: 10.1016/j.disamonth.2020.101053 sha: doc_id: 286472 cord_uid: pqtem19t file: cache/cord-287100-xkp8a9b9.json key: cord-287100-xkp8a9b9 authors: López-Díaz, Álvaro; Ayesa-Arriola, Rosa; Crespo-Facorro, Benedicto; Ruiz-Veguilla, Miguel title: COVID-19 Infection During Pregnancy and Risk of Neurodevelopmental Disorders in Offspring: Time for Collaborative Research date: 2020-10-31 journal: Biol Psychiatry DOI: 10.1016/j.biopsych.2020.09.011 sha: doc_id: 287100 cord_uid: xkp8a9b9 file: cache/cord-286655-5vorrnq3.json key: cord-286655-5vorrnq3 authors: Vivek-Ananth, R.P.; Rana, Abhijit; Rajan, Nithin; Biswal, Himansu S.; Samal, Areejit title: In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection date: 2020-08-22 journal: Molecules DOI: 10.3390/molecules25173822 sha: doc_id: 286655 cord_uid: 5vorrnq3 file: cache/cord-286870-92eckkhk.json key: cord-286870-92eckkhk authors: Gul, Seref; Ozcan, Onur; Asar, Sinan; Okyar, Alper; Barıs, Ibrahim; Kavakli, Ibrahim Halil title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials date: 2020-08-05 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1802346 sha: doc_id: 286870 cord_uid: 92eckkhk file: cache/cord-286713-14i38xtt.json key: cord-286713-14i38xtt authors: Guarner, Jeannette title: Three Emerging Coronaviruses in Two Decades: The Story of SARS, MERS, and Now COVID-19 date: 2020-02-13 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa029 sha: doc_id: 286713 cord_uid: 14i38xtt file: cache/cord-286683-mettlmhz.json key: cord-286683-mettlmhz authors: Ortiz-Prado, Esteban; Simbaña-Rivera, Katherine; Gómez-Barreno, Lenin; Rubio-Neira, Mario; Guaman, Linda P.; Kyriakidis, Nikolaos C; Muslin, Claire; Jaramillo, Ana María Gómez; Barba-Ostria, Carlos; Cevallos-Robalino, Doménica; Sanches-SanMiguel, Hugo; Unigarro, Luis; Zalakeviciute, Rasa; Gadian, Naomi; López-Cortés, Andrés title: Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date: 2020-05-30 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115094 sha: doc_id: 286683 cord_uid: mettlmhz file: cache/cord-286895-i3g4ad4z.json key: cord-286895-i3g4ad4z authors: Panciani, Pier Paolo; Saraceno, Giorgio; Zanin, Luca; Renisi, Giulia; Signorini, Liana; Battaglia, Luigi; Fontanella, Marco Maria title: SARS-CoV-2: “Three-steps” infection model and CSF diagnostic implication date: 2020-05-05 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.05.002 sha: doc_id: 286895 cord_uid: i3g4ad4z file: cache/cord-286923-o4fj8kx0.json key: cord-286923-o4fj8kx0 authors: Berhan, Yifru title: What immunological and hormonal protective factors lower the risk of COVID-19 related deaths in pregnant women? date: 2020-07-18 journal: J Reprod Immunol DOI: 10.1016/j.jri.2020.103180 sha: doc_id: 286923 cord_uid: o4fj8kx0 file: cache/cord-287205-k64svq6n.json key: cord-287205-k64svq6n authors: Pollet, Jeroen; Chen, Wen-Hsiang; Versteeg, Leroy; Keegan, Brian; Zhan, Bin; Wei, Junfei; Liu, Zhuyun; Lee, Jungsoon; Kundu, Rahki; Adhikari, Rakesh; Poveda, Cristina; Mondragon, Maria-Jose Villar; de Araujo Leao, Ana Carolina; Rivera, Joanne Altieri; Gillespie, Portia M.; Strych, Ulrich; Hotez, Peter J.; Bottazzi, Maria Elena title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.04.367359 sha: doc_id: 287205 cord_uid: k64svq6n file: cache/cord-286901-whvq8y1p.json key: cord-286901-whvq8y1p authors: Vidali, Sofia; Morosetti, Daniele; Cossu, Elsa; Luisi, Maria Luisa Eliana; Pancani, Silvia; Semeraro, Vittorio; Consales, Guglielmo title: D-dimer as an indicator of prognosis in SARS-CoV-2 infection: a systematic review date: 2020-07-13 journal: ERJ Open Res DOI: 10.1183/23120541.00260-2020 sha: doc_id: 286901 cord_uid: whvq8y1p file: cache/cord-287043-53oy5w34.json key: cord-287043-53oy5w34 authors: Reyes‐Bueno, José Antonio; 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R.; Laboratory of Clinical Microbiology, Virology and Diagnostic of Bioemergencies Group title: Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase date: 2020-07-24 journal: nan DOI: 10.1101/2020.07.23.20159871 sha: doc_id: 287101 cord_uid: k3zq75zc file: cache/cord-287228-0qm939ve.json key: cord-287228-0qm939ve authors: Hong, Ke; Cao, Wei; Liu, Zhengyin; Lin, Ling; Zhou, Xing; Zeng, Yan; Wei, Yuan; Chen, Li; Liu, Xiaosheng; Han, Yang; Ruan, Lianguo; Li, Taisheng title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1827983 sha: doc_id: 287228 cord_uid: 0qm939ve file: cache/cord-287091-a3nieh5p.json key: cord-287091-a3nieh5p authors: Kumar, Anuj; Choudhir, Gourav; Shukla, Sanjeev Kumar; Sharma, Mansi; Tyagi, Pankaj; Bhushan, Arvind; Rathore, Madhu title: Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches date: 2020-06-04 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1772112 sha: doc_id: 287091 cord_uid: a3nieh5p file: cache/cord-287372-ya5uvoki.json key: cord-287372-ya5uvoki authors: Böszörményi, Kinga P.; Stammes, Marieke A.; Fagrouch, Zahra C.; Kiemenyi-Kayere, Gwendoline; Niphuis, Henk; Mortier, Daniella; van Driel, Nikki; Nieuwenhuis, Ivonne; Zuiderwijk-Sick, Ella; Meijer, Lisette; Mooij, Petra; Remarque, Ed J.; Koopman, Gerrit; Hoste, Alexis C. R.; Sastre, Patricia; Haagmans, Bart L.; Bontrop, Ronald E.; Langermans, Jan A.M.; Bogers, Willy M.; Verschoor, Ernst J.; Verstrepen, Babs E. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.05.369413 sha: doc_id: 287372 cord_uid: ya5uvoki file: cache/cord-287256-hgqz1bcs.json key: cord-287256-hgqz1bcs authors: Magurano, Fabio; Baggieri, Melissa; Marchi, Antonella; Rezza, Giovanni; Nicoletti, Loredana title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date: 2020-11-05 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.034 sha: doc_id: 287256 cord_uid: hgqz1bcs file: cache/cord-287289-zgehbwve.json key: cord-287289-zgehbwve authors: Schmidt, M.; Hoehl, S.; Berger, A.; Zeichhardt, H.; Hourfar, K.; Ciesek, S.; Seifried, E. title: FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity date: 2020-05-01 journal: nan DOI: 10.1101/2020.04.28.20074187 sha: doc_id: 287289 cord_uid: zgehbwve file: cache/cord-287172-h8zoplkm.json key: cord-287172-h8zoplkm authors: Ghobrial, Moheb; Charish, Jason; Takada, Shigeki; Valiante, Taufik; Monnier, Philippe P.; Radovanovic, Ivan; Bader, Gary D.; Wälchli, Thomas title: The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date: 2020-10-21 journal: bioRxiv DOI: 10.1101/2020.10.10.334664 sha: doc_id: 287172 cord_uid: h8zoplkm file: cache/cord-287304-h6wj7m8u.json key: cord-287304-h6wj7m8u authors: Keil, Roger; Ali, Harris title: Governing the Sick City: Urban Governance in the Age of Emerging Infectious Disease date: 2007-12-07 journal: Antipode DOI: 10.1111/j.1467-8330.2007.00555.x sha: doc_id: 287304 cord_uid: h6wj7m8u file: cache/cord-287222-wojyisu0.json key: cord-287222-wojyisu0 authors: Zhou, Min; Zhang, Xinxin; Qu, Jieming title: Coronavirus disease 2019 (COVID-19): a clinical update date: 2020-04-02 journal: Front Med DOI: 10.1007/s11684-020-0767-8 sha: doc_id: 287222 cord_uid: wojyisu0 file: cache/cord-287410-boxxlopy.json key: cord-287410-boxxlopy authors: Devi, Arpita; Chaitanya, Nyshadham S. 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Matthew; Brooks, Erin G.; Akers, Joshua; Armstrong, Danielle; Decker, Lauren; Gonzalez, Adam; Humphrey, William; Mayer, Romana; Miller, Matthew; Perez, Catherine; Arango, Jose Antonio Ruiz; Sathyavagiswaran, Lakshmanan; Stroh, Wendy; Utley, Suzanne title: COVID-19: POSTMORTEM DIAGNOSTIC AND BIOSAFETY CONSIDERATIONS date: 2020-04-24 journal: Am J Forensic Med Pathol DOI: 10.1097/paf.0000000000000567 sha: doc_id: 287653 cord_uid: 69nfi379 file: cache/cord-287220-mpnuhqwg.json key: cord-287220-mpnuhqwg authors: Giuliani, C.; Li Volsi, P.; Brun, E.; Chiambretti, A.; Giandalia, A.; Tonutti, L.; Di Bartolo, P.; Napoli, A. title: Breastfeeding during the COVID-19 pandemic: suggestions on behalf of Woman Study Group of AMD date: 2020-05-30 journal: Diabetes Res Clin Pract DOI: 10.1016/j.diabres.2020.108239 sha: doc_id: 287220 cord_uid: mpnuhqwg file: cache/cord-287247-vv0zc0gd.json key: cord-287247-vv0zc0gd authors: Gutman, Julie R.; Lucchi, Naomi W.; Cantey, Paul T.; Steinhardt, Laura C.; Samuels, Aaron M.; Kamb, Mary L.; Kapella, Bryan K.; McElroy, Peter D.; Udhayakumar, Venkatachalam; Lindblade, Kim A. title: Malaria and Parasitic Neglected Tropical Diseases: Potential Syndemics with COVID-19? date: 2020-06-01 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0516 sha: doc_id: 287247 cord_uid: vv0zc0gd file: cache/cord-287459-k9x3z2h1.json key: cord-287459-k9x3z2h1 authors: Abu-Farha, Mohamed; Thanaraj, Thangavel Alphonse; Qaddoumi, Mohammad G.; Hashem, Anwar; Abubaker, Jehad; Al-Mulla, Fahd title: The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date: 2020-05-17 journal: Int J Mol Sci DOI: 10.3390/ijms21103544 sha: doc_id: 287459 cord_uid: k9x3z2h1 file: cache/cord-287628-lzqsh3jf.json key: cord-287628-lzqsh3jf authors: Gomersall, Charles D.; Joynt, Gavin M.; Ho, Oi Man; Ip, Margaret; Yap, Florence; Derrick, James L.; Leung, Patricia title: Transmission of SARS to healthcare workers. The experience of a Hong Kong ICU date: 2006-02-25 journal: Intensive Care Med DOI: 10.1007/s00134-006-0081-1 sha: doc_id: 287628 cord_uid: lzqsh3jf file: cache/cord-287658-c2lljdi7.json key: cord-287658-c2lljdi7 authors: Lopez-Rincon, Alejandro; Tonda, Alberto; Mendoza-Maldonado, Lucero; Mulders, Daphne G.J.C.; Molenkamp, Richard; Perez-Romero, Carmina A.; Claassen, Eric; Garssen, Johan; Kraneveld, Aletta D. title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 journal: bioRxiv DOI: 10.1101/2020.03.13.990242 sha: doc_id: 287658 cord_uid: c2lljdi7 file: cache/cord-287644-ay0vv27m.json key: cord-287644-ay0vv27m authors: Blackall, Douglas; Wulff, Shephali; Roettger, Timothy; Jacobs, Lauren; Lacasse, Alexandre; Patri, Manokiran; Zinser, Phillip; Pherez, Francisco; Jamkhana, Zafar; Frey, Sharon E.; Smith, Linda; Goel, Ruchika; Katz, Louis title: Rapid Establishment of a COVID‐19 Convalescent Plasma Program in a Regional Healthcare Delivery Network date: 2020-08-04 journal: Transfusion DOI: 10.1111/trf.16026 sha: doc_id: 287644 cord_uid: ay0vv27m file: cache/cord-288051-wp8v2mc5.json key: cord-288051-wp8v2mc5 authors: Sánchez-González, Álvaro; López-Fando Lavalle, Luis; Esteban-Fernández, Alberto; Ruiz, Mercedes; Hevia, Vital; Comeche, Belén; Sánchez Conde, Matilde; Álvarez, Sara; Lorca Álvaro, Javier; Fraile Poblador, Agustín; Hevia Palacios, Manuel; Domínguez Gutiérrez, Ana; Artiles Medina, Alberto; Sanz Mayayo, Enrique; Duque, Gemma; Gómez Dos Santos, Victoria; Moreno-Guillén, Santiago; Burgos Revilla, Javier title: What Should Be Known by a Urologist About the Medical Management of COVID-19’s Patients? date: 2020-09-01 journal: Curr Urol Rep DOI: 10.1007/s11934-020-00995-y sha: doc_id: 288051 cord_uid: wp8v2mc5 file: cache/cord-288146-xqxznv1r.json key: cord-288146-xqxznv1r authors: Kohyama, Shunsuke; Ohno, Satoshi; Suda, Tatsuya; Taneichi, Maiko; Yokoyama, Shoichi; Mori, Masahito; Kobayashi, Akiharu; Hayashi, Hidenori; Uchida, Tetsuya; Matsui, Masanori title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date: 2009-09-11 journal: Antiviral Res DOI: 10.1016/j.antiviral.2009.09.004 sha: doc_id: 288146 cord_uid: xqxznv1r file: cache/cord-287682-97fquq16.json key: cord-287682-97fquq16 authors: Daubin, Cédric; Justet, Aurélien; Vabret, Astrid; Bergot, Emmanuel; Terzi, Nicolas title: Is a COPD patient protected against SARS-CoV-2 virus? date: 2020-10-03 journal: Med Mal Infect DOI: 10.1016/j.medmal.2020.09.015 sha: doc_id: 287682 cord_uid: 97fquq16 file: cache/cord-287847-rmhvc5n5.json key: cord-287847-rmhvc5n5 authors: Miles, Brett A.; Schiff, Bradley; Ganly, Ian; Ow, Thomas; Cohen, Erik; Genden, Eric; Culliney, Bruce; Mehrotra, Bhoomi; Savona, Steven; Wong, Richard J.; Haigentz, Missak; Caruana, Salvatore; Givi, Babak; Patel, Kepal; Hu, Kenneth title: Tracheostomy during SARS‐CoV‐2 pandemic: Recommendations from the New York Head and Neck Society date: 2020-04-20 journal: Head Neck DOI: 10.1002/hed.26166 sha: doc_id: 287847 cord_uid: rmhvc5n5 file: cache/cord-288484-qy619tfg.json key: cord-288484-qy619tfg authors: Bernard‐Valnet, R.; Pizzarotti, B.; Anichini, A.; Demars, Y.; Russo, E.; Schmidhauser, M.; Cerutti‐Sola, J.; Rossetti, A. O.; Du Pasquier, R. title: Two patients with acute meningoencephalitis concomitant with SARS‐CoV‐2 infection date: 2020-05-30 journal: Eur J Neurol DOI: 10.1111/ene.14298 sha: doc_id: 288484 cord_uid: qy619tfg file: cache/cord-287488-h102xn29.json key: cord-287488-h102xn29 authors: Araujo, Danielle Bastos; Machado, Rafael Rahal Guaragna; Amgarten, Deyvid Emanuel; Malta, Fernanda de Mello; de Araujo, Gabriel Guarany; Monteiro, Cairo Oliveira; Candido, Erika Donizetti; Soares, Camila Pereira; de Menezes, Fernando Gatti; Pires, Ana Carolina Cornachioni; Santana, Rúbia Anita Ferraz; Viana, Amanda de Oliveira; Dorlass, Erick; Thomazelli, Luciano; Ferreira, Luis Carlos de Sousa; Botosso, Viviane Fongaro; Carvalho, Cristiane Rodrigues Guzzo; Oliveira, Danielle Bruna Leal; Pinho, João Renato Rebello; Durigon, Edison Luiz title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 journal: Mem Inst Oswaldo Cruz DOI: 10.1590/0074-02760200342 sha: doc_id: 287488 cord_uid: h102xn29 file: cache/cord-287758-da11ypiy.json key: cord-287758-da11ypiy authors: Mônica Vitalino de Almeida, Sinara; Cleberson Santos Soares, José; Lima dos Santos, Keriolaine; Emanuel Ferreira Alves, Josival; Galdino Ribeiro, Amélia; Trindade Tenório Jacob, Íris; Juliane da Silva Ferreira, Cindy; Celerino dos Santos, Jéssica; Ferreira de Oliveira, Jamerson; Bezerra de Carvalho Junior, Luiz; do Carmo Alves de Lima, Maria title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2020.115757 sha: doc_id: 287758 cord_uid: da11ypiy file: cache/cord-288010-i9zrojoo.json key: cord-288010-i9zrojoo authors: Jia, Yuanyuan; Yang, Cuixian; Zhang, Mi; Yang, Xianyao; Li, Jianjian; Liu, Jiafa; Liu, Ying; Yang, XinPing; Feng, Yue; Dong, Xingqi; Xia, Xueshan title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China date: 2020-05-15 journal: J Infect DOI: 10.1016/j.jinf.2020.05.016 sha: doc_id: 288010 cord_uid: i9zrojoo file: cache/cord-288070-qwax5tg9.json key: cord-288070-qwax5tg9 authors: Robilotti, E. 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M.; Taur, Y.; Kamboj, M. title: Determinants of Severity in Cancer Patients with COVID-19 Illness date: 2020-05-08 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.05.04.20086322 sha: doc_id: 288070 cord_uid: qwax5tg9 file: cache/cord-288255-p8uzrsbd.json key: cord-288255-p8uzrsbd authors: Goossens, Gijs H.; Dicker, Dror; Farpour-Lambert, Nathalie J.; Frühbeck, Gema; Mullerova, Dana; Woodward, Euan; Holm, Jens-Christian title: Obesity and COVID-19: A Perspective from the European Association for the Study of Obesity on Immunological Perturbations, Therapeutic Challenges, and Opportunities in Obesity date: 2020-08-13 journal: Obes Facts DOI: 10.1159/000510719 sha: doc_id: 288255 cord_uid: p8uzrsbd file: cache/cord-287448-hwsr1804.json key: cord-287448-hwsr1804 authors: Bigaut, Kévin; Mallaret, Martial; Baloglu, Seyyid; Nemoz, Benjamin; Morand, Patrice; Baicry, Florent; Godon, Alexandre; Voulleminot, Paul; Kremer, Laurent; Chanson, Jean-Baptiste; de Seze, Jérôme title: Guillain-Barré syndrome related to SARS-CoV-2 infection date: 2020-05-27 journal: Neurol Neuroimmunol Neuroinflamm DOI: 10.1212/nxi.0000000000000785 sha: doc_id: 287448 cord_uid: hwsr1804 file: cache/cord-288017-f9b3t0ts.json key: cord-288017-f9b3t0ts authors: Kabeerdoss, Jayakanthan; Danda, Debashish title: Understanding immunopathological fallout of human coronavirus infections including COVID‐19: Will they cross the path of rheumatologists? date: 2020-08-10 journal: Int J Rheum Dis DOI: 10.1111/1756-185x.13909 sha: doc_id: 288017 cord_uid: f9b3t0ts file: cache/cord-287742-y1j9x5ne.json key: cord-287742-y1j9x5ne authors: Lee, Kai Wei; Yusof Khan, Abdul Hanif Khan; Ching, Siew Mooi; Chia, Peck Kee; Loh, Wei Chao; Abdul Rashid, Anna Misya'il; Baharin, Janudin; Inche Mat, Liyana Najwa; Wan Sulaiman, Wan Aliaa; Devaraj, Navin Kumar; Sivaratnam, Dhashani; Basri, Hamidon; Hoo, Fan Kee title: Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis date: 2020-10-06 journal: Front Neurol DOI: 10.3389/fneur.2020.579070 sha: doc_id: 287742 cord_uid: y1j9x5ne file: cache/cord-288231-vg8bwed9.json key: cord-288231-vg8bwed9 authors: Haagmans, Bart L.; Andeweg, Arno C.; Osterhaus, Albert D. 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Jalili, Mahrokh title: The role of environmental factors to transmission of SARS-CoV-2 (COVID-19) date: 2020-05-15 journal: AMB Express DOI: 10.1186/s13568-020-01028-0 sha: doc_id: 288025 cord_uid: skkpkqw6 file: cache/cord-288284-fghu8ouc.json key: cord-288284-fghu8ouc authors: Hawryluck, Laura; Lapinsky, Stephen E; Stewart, Thomas E title: Clinical review: SARS – lessons in disaster management date: 2005-01-13 journal: Crit Care DOI: 10.1186/cc3041 sha: doc_id: 288284 cord_uid: fghu8ouc file: cache/cord-288584-wql253d8.json key: cord-288584-wql253d8 authors: Rivera-Oyola, Ryan; Koschitzky, Merav; Printy, Rachel; Liu, Stephanie; Stanger, Roselyn; Golant, Alexandra; Lebwohl, Mark title: Dermatologic findings in two patients with COVID-19 date: 2020-04-28 journal: JAAD Case Rep DOI: 10.1016/j.jdcr.2020.04.027 sha: doc_id: 288584 cord_uid: wql253d8 file: cache/cord-288500-ko4eda9w.json key: cord-288500-ko4eda9w authors: Zheng, Ruijun; Zhou, Yuhong; Fu, Yan; Xiang, Qiufen; Cheng, Fang; Chen, Huaying; Xu, Huiqiong; fu, Lan; Wu, Xiaoling; Feng, Mei; Ye, Lei; Tian, Yongming; Deng, Rong; Liu, Shanshan; Jiang, Yan; Yu, Chunhua; Li, Junying title: Prevalence and associated factors of depression and anxiety among nurses during the outbreak of COVID-19 in China: A cross-sectional study date: 2020-10-23 journal: Int J Nurs Stud DOI: 10.1016/j.ijnurstu.2020.103809 sha: doc_id: 288500 cord_uid: ko4eda9w file: cache/cord-288660-z0k2ui3y.json key: cord-288660-z0k2ui3y authors: Edler, Alice A. title: Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology date: 2006-02-28 journal: Journal of Clinical Anesthesia DOI: 10.1016/j.jclinane.2005.12.004 sha: doc_id: 288660 cord_uid: z0k2ui3y file: cache/cord-288066-sh6n2c3n.json key: cord-288066-sh6n2c3n authors: Mohamed, Mohamed S.; Moulin, Thiago C.; Schiöth, Helgi B. title: Sex differences in COVID-19: the role of androgens in disease severity and progression date: 2020-11-11 journal: Endocrine DOI: 10.1007/s12020-020-02536-6 sha: doc_id: 288066 cord_uid: sh6n2c3n file: cache/cord-288357-3mqoexcr.json key: cord-288357-3mqoexcr authors: Liu, Pei; Liu, Hongbo; Sun, Qi; Liang, Hao; Li, Chunmei; Deng, Xiaobing; Liu, Ying; Lai, Luhua title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds date: 2020-08-01 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2020.112702 sha: doc_id: 288357 cord_uid: 3mqoexcr file: cache/cord-287991-10jz1dz2.json key: cord-287991-10jz1dz2 authors: Goshen-Lago, Tal; Szwarcwort-Cohen, Moran; Benguigui, Madeleine; Almog, Ronit; Turgeman, Ilit; Zaltzman, Nelly; Halberthal, Michael; Shaked, Yuval; Ben-Aharon, Irit title: The Potential Role of Immune Alteration in the Cancer–COVID19 Equation—A Prospective Longitudinal Study date: 2020-08-26 journal: Cancers (Basel) DOI: 10.3390/cancers12092421 sha: doc_id: 287991 cord_uid: 10jz1dz2 file: cache/cord-288553-fez60jyn.json key: cord-288553-fez60jyn authors: Colaneri, Marta; Seminari, Elena; Piralla, Antonio; Zuccaro, Valentina; Filippo, Alessandro Di; Baldanti, Fausto; Bruno, Raffaele; Mondelli, Mario U. title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. date: 2020-03-19 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.03.018 sha: doc_id: 288553 cord_uid: fez60jyn file: cache/cord-288692-v471648u.json key: cord-288692-v471648u authors: Yip, Shea Ping; To, Shing Shun T; Leung, Polly HM; Cheung, Tsz Shan; Cheng, Peter KC; Lim, Wilina WL title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 journal: Clin Chem DOI: 10.1373/clinchem.2005.054106 sha: doc_id: 288692 cord_uid: v471648u file: cache/cord-288824-sygnmiun.json key: cord-288824-sygnmiun authors: Lam, SD; Bordin, N; Waman, VP; Scholes, HM; Ashford, P; Sen, N; van Dorp, L; Rauer, C; Dawson, NL; Pang, CSM; Abbasian, M; Sillitoe, I; Edwards, SJL; Fraternali, F; Lees, JG; Santini, JM; Orengo, CA title: SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date: 2020-08-19 journal: bioRxiv DOI: 10.1101/2020.05.01.072371 sha: doc_id: 288824 cord_uid: sygnmiun file: cache/cord-288558-rthnj6wd.json key: cord-288558-rthnj6wd authors: Cheng, V. C. C.; Hung, I. F. N.; Tang, B. S. F.; Chu, C. M.; Wong, M. M. L.; Chan, K. H.; Wu, A. K. L.; Tse, D. M. W.; Chan, K. S.; Zheng, B. J.; Peiris, J. S. M.; Sung, J. J. Y.; Yuen, K. Y. title: Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date: 2004-02-15 journal: Clin Infect Dis DOI: 10.1086/382681 sha: doc_id: 288558 cord_uid: rthnj6wd file: cache/cord-287501-7it4kh0e.json key: cord-287501-7it4kh0e authors: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 journal: Int J Nanomedicine DOI: 10.2147/ijn.s31379 sha: doc_id: 287501 cord_uid: 7it4kh0e file: cache/cord-288197-drto66xt.json key: cord-288197-drto66xt authors: Chen, Huijun; Guo, Juanjuan; Wang, Chen; Luo, Fan; Yu, Xuechen; Zhang, Wei; Li, Jiafu; Zhao, Dongchi; Xu, Dan; Gong, Qing; Liao, Jing; Yang, Huixia; Hou, Wei; Zhang, Yuanzhen title: Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records date: 2020-02-12 journal: Lancet DOI: 10.1016/s0140-6736(20)30360-3 sha: doc_id: 288197 cord_uid: drto66xt file: cache/cord-288271-p074ffpt.json key: cord-288271-p074ffpt authors: Mathies, D.; Rauschning, D.; Wagner, U.; Mueller, F.; Maibaum, M.; Binnemann, C.; Waldeck, S.; Thinnes, K.; Braun, M.; Schmidbauer, W.; Hagen, RM.; Bickel, C. title: A Case of SARS‐CoV‐2‐pneumonia with successful antiviral therapy in a 77‐year‐old male with heart transplant date: 2020-04-21 journal: Am J Transplant DOI: 10.1111/ajt.15932 sha: doc_id: 288271 cord_uid: p074ffpt file: cache/cord-288398-vnra553x.json key: cord-288398-vnra553x authors: Yogeswaran, Athiththan; Gall, Henning; Tello, Khodr; Grünig, Ekkehard; Xanthouli, Panagiota; Ewert, Ralf; Kamp, Jan C.; Olsson, Karen M.; Wißmüller, Max; Rosenkranz, Stephan; Klose, Hans; Harbaum, Lars; Lange, Tobias J.; Opitz, Christian F.; Waelde, Andrea; Milger, Katrin; Sommer, Natascha; Seeger, Werner; Ghofrani, Hossein Ardeschir; Richter, Manuel J. title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study date: 2020-07-23 journal: Pulm Circ DOI: 10.1177/2045894020941682 sha: doc_id: 288398 cord_uid: vnra553x file: cache/cord-288403-m6qe57he.json key: cord-288403-m6qe57he authors: Abbas, K. 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R.; van Zandvoort, K.; Clark, A.; Funk, S.; LSHTM CMMID Covid-19 Working Group,; Mengistu, T.; Hogan, D.; Dansereau, E.; Jit, M.; Flasche, S. title: Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.19.20106278 sha: doc_id: 288403 cord_uid: m6qe57he file: cache/cord-288644-ywaefpe8.json key: cord-288644-ywaefpe8 authors: Rodon, Jordi; Muñoz-Basagoiti, Jordana; Perez-Zsolt, Daniel; Noguera-Julian, Marc; Paredes, Roger; Mateu, Lourdes; Quiñones, Carles; Erkizia, Itziar; Blanco, Ignacio; Valencia, Alfonso; Guallar, Víctor; Carrillo, Jorge; Blanco, Julià; Segalés, Joaquim; Clotet, Bonaventura; Vergara-Alert, Júlia; Izquierdo-Useros, Nuria title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 journal: bioRxiv DOI: 10.1101/2020.04.23.055756 sha: doc_id: 288644 cord_uid: ywaefpe8 file: cache/cord-288670-1vlowf2n.json key: cord-288670-1vlowf2n authors: Yang, Naidi; Shen, Han-Ming title: Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19 date: 2020-03-15 journal: Int J Biol Sci DOI: 10.7150/ijbs.45498 sha: doc_id: 288670 cord_uid: 1vlowf2n file: cache/cord-289101-ko1knslk.json key: cord-289101-ko1knslk authors: Fu, Weihui; Liu, Yan; Liu, Li; Hu, Huiliang; Cheng, Xiaobo; Liu, Ping; Song, Zhigang; Zha, Lijun; Bai, Shimeng; Xu, Tingting; Yuan, Songhua; Lu, Fengru; Shang, Zhiying; Zhao, Yihong; Wang, Jing; Zhao, Jun; Ding, Longfei; Chen, Jun; Zhang, Lin; Zhu, Tongyu; Zhang, Xiaoyan; Lu, Hongzhou; Xu, Jianqing title: An open-label, randomized trial of the combination of IFN-κ plus TFF2 with standard care in the treatment of patients with moderate COVID-19 date: 2020-09-20 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100547 sha: doc_id: 289101 cord_uid: ko1knslk file: cache/cord-289255-qwzg7prx.json key: cord-289255-qwzg7prx authors: Seligman, Stephen J. title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date: 2007-02-15 journal: J Infect Dis DOI: 10.1086/510917 sha: doc_id: 289255 cord_uid: qwzg7prx file: cache/cord-288731-x2cwyvb7.json key: cord-288731-x2cwyvb7 authors: Puenpa, Jiratchaya; Suwannakarn, Kamol; Chansaenroj, Jira; Nilyanimit, Pornjarim; Yorsaeng, Ritthideach; Auphimai, Chompoonut; Kitphati, Rungrueng; Mungaomklang, Anek; Kongklieng, Amornmas; Chirathaworn, Chintana; Wanlapakorn, Nasamon; Poovorawan, Yong title: Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020 date: 2020-10-06 journal: Sci Rep DOI: 10.1038/s41598-020-73554-7 sha: doc_id: 288731 cord_uid: x2cwyvb7 file: cache/cord-288758-onis9xmo.json key: cord-288758-onis9xmo authors: Peng, Z.; Jimenez, J. L. title: Exhaled CO2 as COVID-19 infection risk proxy for different indoor environments and activities date: 2020-09-10 journal: nan DOI: 10.1101/2020.09.09.20191676 sha: doc_id: 288758 cord_uid: onis9xmo file: cache/cord-288998-0by0bkgs.json key: cord-288998-0by0bkgs authors: Colarusso, Chiara; Terlizzi, Michela; Pinto, Aldo; Sorrentino, Rosalinda title: A lesson from a saboteur: high molecular weight kininogen (HMWK) impact in COVID‐19 date: 2020-06-04 journal: Br J Pharmacol DOI: 10.1111/bph.15154 sha: doc_id: 288998 cord_uid: 0by0bkgs file: cache/cord-288920-xkfcc2dx.json key: cord-288920-xkfcc2dx authors: Broxmeyer, L title: SARS: Just another viral acronym? date: 2003-08-31 journal: Medical Hypotheses DOI: 10.1016/s0306-9877(03)00195-6 sha: doc_id: 288920 cord_uid: xkfcc2dx file: cache/cord-289003-vov6o1jx.json key: cord-289003-vov6o1jx authors: Burdet, C.; Guégan, J.-F.; Duval, X.; Le Tyrant, M.; Bergeron, H.; Manuguerra, J.-C.; Raude, J.; Leport, C.; Zylberman, P. title: Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals date: 2018-02-28 journal: Revue d'Épidémiologie et de Santé Publique DOI: 10.1016/j.respe.2017.08.001 sha: doc_id: 289003 cord_uid: vov6o1jx file: cache/cord-289038-15yp9uqy.json key: cord-289038-15yp9uqy authors: Chow, Jonathan Tak-Sum; Salmena, Leonardo title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date: 2020-08-26 journal: Genes (Basel) DOI: 10.3390/genes11091002 sha: doc_id: 289038 cord_uid: 15yp9uqy file: cache/cord-288639-wy07nao0.json key: cord-288639-wy07nao0 authors: Earnest, Arul; Chen, Mark I; Ng, Donald; Sin, Leo Yee title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore date: 2005-05-11 journal: BMC Health Serv Res DOI: 10.1186/1472-6963-5-36 sha: doc_id: 288639 cord_uid: wy07nao0 file: cache/cord-289064-435bp4rt.json key: cord-289064-435bp4rt authors: Muniangi-Muhitu, Hermine; Akalestou, Elina; Salem, Victoria; Misra, Shivani; Oliver, Nicholas S.; Rutter, Guy A. title: Covid-19 and Diabetes: A Complex Bidirectional Relationship date: 2020-10-08 journal: Front Endocrinol (Lausanne) DOI: 10.3389/fendo.2020.582936 sha: doc_id: 289064 cord_uid: 435bp4rt file: cache/cord-289079-m417oxpc.json key: cord-289079-m417oxpc authors: Waggershauser, Constanze H.; Tillack‐Schreiber, Cornelia; Berchtold‐Benchieb, Christine; Szokodi, Daniel; Howaldt, Stefanie; Ochsenkühn, Thomas title: Letter: immunotherapy in IBD patients in a SARS‐CoV‐2 endemic area date: 2020-08-14 journal: Aliment Pharmacol Ther DOI: 10.1111/apt.15897 sha: doc_id: 289079 cord_uid: m417oxpc file: cache/cord-289144-d6fgs8qg.json key: cord-289144-d6fgs8qg authors: Sieńko, Jerzy; Kotowski, Maciej; Bogacz, Anna; Lechowicz, Kacper; Drożdżal, Sylwester; Rosik, Jakub; Sietnicki, Marek; Sieńko, Magdalena; Kotfis, Katarzyna title: COVID-19: The Influence of ACE Genotype and ACE-I and ARBs on the Course of SARS-CoV-2 Infection in Elderly Patients date: 2020-07-21 journal: Clin Interv Aging DOI: 10.2147/cia.s261516 sha: doc_id: 289144 cord_uid: d6fgs8qg file: cache/cord-289349-imkgpwn0.json key: cord-289349-imkgpwn0 authors: Qiu, Li; Zhang, Chengdong; Wu, Junbo; Luo, Jie; Netea, Mihai G.; Luo, Zhiguo; Leng, Qibin title: Strong immunity in the early two years of age links to frequent immunization of routine vaccines date: 2020-08-08 journal: Sci Bull (Beijing) DOI: 10.1016/j.scib.2020.08.012 sha: doc_id: 289349 cord_uid: imkgpwn0 file: cache/cord-289076-8iymevqm.json key: cord-289076-8iymevqm authors: Marjanovic, Zdravko; Greenglass, Esther R.; Coffey, Sue title: The relevance of psychosocial variables and working conditions in predicting nurses’ coping strategies during the SARS crisis: An online questionnaire survey date: 2007-08-31 journal: International Journal of Nursing Studies DOI: 10.1016/j.ijnurstu.2006.02.012 sha: doc_id: 289076 cord_uid: 8iymevqm file: cache/cord-289134-ne3tjt5g.json key: cord-289134-ne3tjt5g authors: Xing, Yue; Li, Xiao; Gao, Xiang; Dong, Qunfeng title: Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein date: 2020-07-17 journal: Front Genet DOI: 10.3389/fgene.2020.00783 sha: doc_id: 289134 cord_uid: ne3tjt5g file: cache/cord-288818-6uvb4qsk.json key: cord-288818-6uvb4qsk authors: Tanveer, Faouzia; Khalil, Ali Talha; Ali, Muhammad; Shinwari, Zabta Khan title: Ethics, pandemic and environment; looking at the future of low middle income countries date: 2020-10-15 journal: Int J Equity Health DOI: 10.1186/s12939-020-01296-z sha: doc_id: 288818 cord_uid: 6uvb4qsk file: cache/cord-289282-4oz6r7op.json key: cord-289282-4oz6r7op authors: Hon, Kam Lun; Leung, Karen Ka Yan; Leung, Alexander K. C.; Sridhar, Siddharth; Qian, Suyun; Lee, So Lun; Colin, Andrew A. title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date: 2020-06-01 journal: Pediatr Pulmonol DOI: 10.1002/ppul.24810 sha: doc_id: 289282 cord_uid: 4oz6r7op file: cache/cord-288756-r96izsyq.json key: cord-288756-r96izsyq authors: Wu, Zhiqiang; Yang, Li; Ren, Xianwen; Zhang, Junpeng; Yang, Fan; Zhang, Shuyi; Jin, Qi title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date: 2016-02-15 journal: J Infect Dis DOI: 10.1093/infdis/jiv476 sha: doc_id: 288756 cord_uid: r96izsyq file: cache/cord-289490-u0f0zyad.json key: cord-289490-u0f0zyad authors: Lumba, Rishi; Remon, Juan; Louie, Moi; Quan, Michelle; Verma, Sourabh; Rigaud, Mona; Kunjumon, Bgee title: Neonate Born to a Mother with a Diagnosis of Suspected Intra-Amniotic Infection versus COVID-19 or Both date: 2020-07-18 journal: Case Rep Pediatr DOI: 10.1155/2020/8886800 sha: doc_id: 289490 cord_uid: u0f0zyad file: cache/cord-288862-upcsvjuo.json key: cord-288862-upcsvjuo authors: Wang, Junmei title: Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study date: 2020-04-21 journal: J Chem Inf Model DOI: 10.1021/acs.jcim.0c00179 sha: doc_id: 288862 cord_uid: upcsvjuo file: cache/cord-289216-g4kqi560.json key: cord-289216-g4kqi560 authors: Malecki, M.; Luesebrink, J.; Wendel, A.; Mattner, F. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 journal: nan DOI: 10.1101/2020.09.18.20185744 sha: doc_id: 289216 cord_uid: g4kqi560 file: cache/cord-289332-hvakv08t.json key: cord-289332-hvakv08t authors: Chen, Guoqian; Chen, Da-zhi; Li, Jianhua; Czura, Christopher J.; Tracey, Kevin J.; Sama, Andrew E.; Wang, Haichao title: Pathogenic role of HMGB1 in SARS? date: 2004-04-30 journal: Med Hypotheses DOI: 10.1016/j.mehy.2004.01.037 sha: doc_id: 289332 cord_uid: hvakv08t file: cache/cord-289599-7vsynfgn.json key: cord-289599-7vsynfgn authors: Kostoff, Ronald N.; Briggs, Michael B.; Porter, Alan L.; Spandidos, Demetrios A.; Tsatsakis, Aristidis title: COVID-19 vaccine safety date: 2020-09-18 journal: Int J Mol Med DOI: 10.3892/ijmm.2020.4733 sha: doc_id: 289599 cord_uid: 7vsynfgn file: cache/cord-289476-8wh3hn0n.json key: cord-289476-8wh3hn0n authors: Leiker, Brenna; Wise, Katherine; Perlman, Jane R title: COVID - 19 BRIEF INTRODUCTION IN MENTAL HEALTH CONSIDERATIONS FOR HEALTH CARE WORKERS AND PATIENTS date: 2020-07-28 journal: Dis Mon DOI: 10.1016/j.disamonth.2020.101059 sha: doc_id: 289476 cord_uid: 8wh3hn0n file: cache/cord-289364-p31gt533.json key: cord-289364-p31gt533 authors: AlFehaidi, Alanoud; Ahmed, Syed Ali; Hamed, Ehab title: A case of SARS-CoV-2 re-infection date: 2020-10-25 journal: J Infect DOI: 10.1016/j.jinf.2020.10.019 sha: doc_id: 289364 cord_uid: p31gt533 file: cache/cord-289711-4ab3d00h.json key: cord-289711-4ab3d00h authors: Yarmarkovich, Mark; Warrington, John M.; Farrel, Alvin; Maris, John M. title: Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date: 2020-06-08 journal: Cell Rep Med DOI: 10.1016/j.xcrm.2020.100036 sha: doc_id: 289711 cord_uid: 4ab3d00h file: cache/cord-288733-c51lfwd6.json key: cord-288733-c51lfwd6 authors: Kavanagh, Oisín; Marie Healy, Anne; Dayton, Francis; Robinson, Shane; O'Reilly, Niall J.; Mahoney, Brian; Arthur, Aisling; Walker, Gavin; Farragher, John P. title: Inhaled Hydroxychloroquine to Improve Efficacy and Reduce Harm in the Treatment of COVID-19 date: 2020-07-15 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110110 sha: doc_id: 288733 cord_uid: c51lfwd6 file: cache/cord-289520-i6pv90s9.json key: cord-289520-i6pv90s9 authors: Harris, Carlyn; Carson, Gail; Baillie, J Kenneth; Horby, Peter; Nair, Harish title: An evidence-based framework for priority clinical research questions for COVID-19 date: 2020-03-31 journal: Journal of global health DOI: 10.7189/jogh.10-011001 sha: doc_id: 289520 cord_uid: i6pv90s9 file: cache/cord-289890-sf2uxubd.json key: cord-289890-sf2uxubd authors: Rushworth, S. A.; Johnson, B. B.; Ashurst, K.; Davidson, R.; Paddy, P.; Mistry, J. J.; Moore, J. A.; Hellmich, C.; Edwards, D. R.; Afonso, D. D.; Xydopoulos, G.; Goodwin, R.; Gomez, J.; Prakash, R.; Dervisevic, S.; Fordham, R.; Bowles, K.; Smith, J. title: Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay date: 2020-06-12 journal: nan DOI: 10.1101/2020.06.11.20128306 sha: doc_id: 289890 cord_uid: sf2uxubd file: cache/cord-289114-ifnk41oq.json key: cord-289114-ifnk41oq authors: Singh, Angaraj; Kumar, Manoj; Dubey, Ashutosh Kumar title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 journal: Med Devices Sens DOI: 10.1002/mds3.10140 sha: doc_id: 289114 cord_uid: ifnk41oq file: cache/cord-289377-2vqqabum.json key: cord-289377-2vqqabum authors: Yubero, P.; Lavin, A. A.; Poyatos, J. 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S.; Dunning, J.; Bennett, A. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 journal: nan DOI: 10.1101/2020.09.24.20191411 sha: doc_id: 289407 cord_uid: 8fje16z1 file: cache/cord-289716-nleql08z.json key: cord-289716-nleql08z authors: Tsitsilonis, Ourania E.; Paraskevis, Dimitrios; Lianidou, Evi; Pierros, Vassilios; Akalestos, Athanasios; Kastritis, Efstathios; Moutsatsou, Paraskevi; Scorilas, Andreas; Sphicopoulos, Thomas; Terpos, Evangelos; Thomaidis, Nikolaos; Tsakris, Athanassios; Voulgaris, Nikolaos; Daskalaki, Christina C.; Evangelakou, Zoi; Fouki, Christina; Gianniou, Despoina D.; Gumeni, Sentiljana; Kostaki, Evangelia-Georgia; Kostopoulos, Ioannis V.; Manola, Maria S.; Orologas-Stavrou, Nikolaos; Panteli, Chrysanthi; Papanagnou, Eleni-Dimitra; Rousakis, Pantelis; Sklirou, Aimilia D.; Smilkou, Stavroula; Stergiopoulou, Dimitra; Trougakos, Ioannis P.; Tsiodras, Soritios; Sfikakis, Petros P.; Dimopoulos, Meletios-Athanasios title: Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report date: 2020-09-21 journal: Life (Basel) DOI: 10.3390/life10090214 sha: doc_id: 289716 cord_uid: nleql08z file: cache/cord-289852-4uxb70rh.json key: cord-289852-4uxb70rh authors: Kassem, Dina H.; Kamal, Mohamed M. title: Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis date: 2020-09-30 journal: Front Cell Dev Biol DOI: 10.3389/fcell.2020.587866 sha: doc_id: 289852 cord_uid: 4uxb70rh file: cache/cord-289588-n61gz7pi.json key: cord-289588-n61gz7pi authors: Samudrala, Pavan Kumar; Kumar, Pramod; Choudhary, Kamlesh; Thakur, Nagender; Wadekar, Gaurav Suresh; Dayaramani, Richa; Agrawal, Mukta; Alexander, Amit title: Virology, pathogenesis, diagnosis and in-line treatment of COVID-19 date: 2020-07-17 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173375 sha: doc_id: 289588 cord_uid: n61gz7pi file: cache/cord-287819-qzg4bhoy.json key: cord-287819-qzg4bhoy authors: Priftis, Konstantinos; Algeri, Lorella; Villella, Stella; Spada, Maria Simonetta title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke date: 2020-09-28 journal: Neurol Sci DOI: 10.1007/s10072-020-04768-w sha: doc_id: 287819 cord_uid: qzg4bhoy file: cache/cord-289535-srrfr1es.json key: cord-289535-srrfr1es authors: Tregoning, J. 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M. title: Vaccines for COVID‐19 date: 2020-10-18 journal: Clin Exp Immunol DOI: 10.1111/cei.13517 sha: doc_id: 289535 cord_uid: srrfr1es file: cache/cord-290378-h4cof32m.json key: cord-290378-h4cof32m authors: Guy, Tiphaine; Créac'hcadec, Audrey; Ricordel, Charles; Salé, Alexandre; Arnouat, Baptiste; Bizec, Jean-Louis; Langelot, Marie; Lineau, Christine; Marquette, David; Martin, Françoise; Lederlin, Mathieu; Jouneau, Stéphane title: High-flow nasal oxygen: a safe, efficient treatment for COVID-19 patients not in an ICU date: 2020-08-28 journal: Eur Respir J DOI: 10.1183/13993003.01154-2020 sha: doc_id: 290378 cord_uid: h4cof32m file: cache/cord-290123-scd9u8ix.json key: cord-290123-scd9u8ix authors: Mustafa, Mujahed I.; Abdelmoneim, Abdelrahman H.; Mahmoud, Eiman M.; Makhawi, Abdelrafie M. title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors date: 2020-09-23 journal: Mediators Inflamm DOI: 10.1155/2020/8198963 sha: doc_id: 290123 cord_uid: scd9u8ix file: cache/cord-289905-dvl2pud2.json key: cord-289905-dvl2pud2 authors: Gan, Rosemary; Rosoman, Nicholas P.; Henshaw, David J.E.; Noble, Euan P.; Georgius, Peter; Sommerfeld, Nigel title: COVID-19 as a Viral Functional ACE2 Deficiency Disorder with ACE2 Related Multi-organ Disease date: 2020-06-23 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110024 sha: doc_id: 289905 cord_uid: dvl2pud2 file: cache/cord-290254-m9l8ntur.json key: cord-290254-m9l8ntur authors: Rodriguez-Manzano, J.; Malpartida-Cardenas, K.; Moser, N.; Pennisi, I.; Cavuto, M.; Miglietta, L.; Moniri, A.; Penn, R.; Satta, G.; Randell, P.; Davies, F.; Bolt, F.; Barclay, W.; Holmes, A.; Georgiou, P. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 journal: nan DOI: 10.1101/2020.06.29.20142349 sha: doc_id: 290254 cord_uid: m9l8ntur file: cache/cord-290429-0d34abdo.json key: cord-290429-0d34abdo authors: Elengoe, Asita title: COVID-19 Outbreak in Malaysia date: 2020-06-17 journal: Osong Public Health Res Perspect DOI: 10.24171/j.phrp.2020.11.3.08 sha: doc_id: 290429 cord_uid: 0d34abdo file: cache/cord-289719-64ugdvfe.json key: cord-289719-64ugdvfe authors: Tenforde, Mark W.; Billig Rose, Erica; Lindsell, Christopher J.; Shapiro, Nathan I.; Files, D. 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date: 2020-04-16 journal: J Infect Dis DOI: 10.1093/infdis/jiaa189 sha: doc_id: 290277 cord_uid: ndfoppoq file: cache/cord-290445-vb53bih9.json key: cord-290445-vb53bih9 authors: Ahmed, Shiek SSJ; Paramasivam, Prabu; Raj, Kamal; Kumar, Vishal; murugesan, Ram; Ramakrishnan, title: Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date: 2020-04-23 journal: bioRxiv DOI: 10.1101/2020.04.20.050138 sha: doc_id: 290445 cord_uid: vb53bih9 file: cache/cord-289947-z2dw2eaz.json key: cord-289947-z2dw2eaz authors: Wong, River Chun-Wai; Wong, Ann Han; Ho, Yolanda Iok-Ieng; Leung, Eddie Chi-Man; Lai, Raymond Wai-Man title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay date: 2020-08-16 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104593 sha: doc_id: 289947 cord_uid: z2dw2eaz file: cache/cord-290796-x9xqqcj6.json key: cord-290796-x9xqqcj6 authors: Stefanelli, P.; Bella, A.; Fedele, G.; Fiore, S.; Pancheri, S.; Benedetti, E.; Fabiani, C.; Leone, P.; Vacca, P.; Schiavoni, I.; Neri, A.; Carannante, A.; Simmaco, M.; Santino, I.; Zuccali, M. G.; Bizzarri, G.; Magnoni, R.; Benetollo, P. P.; Brusaferro, S.; Rezza, G.; Ferro, A. title: Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento date: 2020-11-13 journal: nan DOI: 10.1101/2020.11.11.20229062 sha: doc_id: 290796 cord_uid: x9xqqcj6 file: cache/cord-290218-dvyeg5fk.json key: cord-290218-dvyeg5fk authors: Jiang, Yi; Yin, Wanchao; Xu, H. Eric title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.08.116 sha: doc_id: 290218 cord_uid: dvyeg5fk file: cache/cord-290802-761wqgbe.json key: cord-290802-761wqgbe authors: Zhao, Zheng; Bourne, Philip E. title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00623 sha: doc_id: 290802 cord_uid: 761wqgbe file: cache/cord-290428-zrlqzbss.json key: cord-290428-zrlqzbss authors: de Faria Coelho-Ravagnani, Christianne; Corgosinho, Flavia Campos; Sanches, Fabiane La Flor Ziegler; Prado, Carla Marques Maia; Laviano, Alessandro; Mota, João Felipe title: Dietary recommendations during the COVID-19 pandemic date: 2020-07-12 journal: Nutr Rev DOI: 10.1093/nutrit/nuaa067 sha: doc_id: 290428 cord_uid: zrlqzbss file: cache/cord-290195-8uaai9nv.json key: cord-290195-8uaai9nv authors: Stebbing, Justin; Krishnan, Venkatesh; de Bono, Stephanie; Ottaviani, Silvia; Casalini, Giacomo; Richardson, Peter J.; Monteil, Vanessa; Lauschke, Volker M.; Mirazimi, Ali; Youhanna, Sonia; Tan, Yee‐Joo; Baldanti, Fausto; Sarasini, Antonella; Terres, Jorge A. Ross; Nickoloff, Brian J.; Higgs, Richard E.; Rocha, Guilherme; Byers, Nicole L.; Schlichting, Douglas E.; Nirula, Ajay; Cardoso, Anabela; Corbellino, Mario title: Mechanism of baricitinib supports artificial intelligence‐predicted testing in COVID‐19 patients date: 2020-05-30 journal: EMBO Mol Med DOI: 10.15252/emmm.202012697 sha: doc_id: 290195 cord_uid: 8uaai9nv file: cache/cord-289892-yh1lioyz.json key: cord-289892-yh1lioyz authors: Bai, Bingke; Hu, Qinxue; Hu, Hui; Zhou, Peng; Shi, Zhengli; Meng, Jin; Lu, Baojing; Huang, Yi; Mao, Panyong; Wang, Hanzhong title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 journal: PLoS One DOI: 10.1371/journal.pone.0002685 sha: doc_id: 289892 cord_uid: yh1lioyz file: cache/cord-290148-6cxndab8.json key: cord-290148-6cxndab8 authors: Rossi, Gian Paolo; Sanga, Viola; Barton, Matthias title: Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients date: 2020-04-06 journal: eLife DOI: 10.7554/elife.57278 sha: doc_id: 290148 cord_uid: 6cxndab8 file: cache/cord-290414-8i8g0xdc.json key: cord-290414-8i8g0xdc authors: Chuan, Ong Sze; Bin Razali, Muhammad Azri; Shaffiee, Lyana; Xing, Yap Jun; Yin Fei, Terrence Tay; Chee, Loon Seng; Koh, Victor title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? date: 2020-06-21 journal: Ophthalmology DOI: 10.1016/j.ophtha.2020.06.031 sha: doc_id: 290414 cord_uid: 8i8g0xdc file: cache/cord-290851-1e5e033r.json key: cord-290851-1e5e033r authors: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.05.014 sha: doc_id: 290851 cord_uid: 1e5e033r file: cache/cord-290257-2u228xe9.json key: cord-290257-2u228xe9 authors: Hsu, Chih-Cheng; Chen, Ted; Chang, Mei; Chang, Yu-Kang title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan date: 2006-05-05 journal: Am J Infect Control DOI: 10.1016/j.ajic.2005.11.008 sha: doc_id: 290257 cord_uid: 2u228xe9 file: cache/cord-290333-996tmrgo.json key: cord-290333-996tmrgo authors: Chiu, Cheng-Hsun; Tsai, Ming-Chao; Cheng, Hao-Tsai; Le, Puo-Hsien; Kuo, Chia-Jung; Chiu, Cheng-Tang title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic date: 2020-07-23 journal: J Formos Med Assoc DOI: 10.1016/j.jfma.2020.07.028 sha: doc_id: 290333 cord_uid: 996tmrgo file: cache/cord-290792-ggcz1zfw.json key: cord-290792-ggcz1zfw authors: Qutob, N.; Awartani, F.; Salah, Z.; Asia, M.; Abu Khader, I.; Herzallah, K.; Balqis, N.; Sallam, H. title: Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study date: 2020-09-01 journal: nan DOI: 10.1101/2020.08.28.20180083 sha: doc_id: 290792 cord_uid: ggcz1zfw file: cache/cord-290813-6ylwj5je.json key: cord-290813-6ylwj5je authors: Ng, Enders K. O.; Lo, Y. M. Dennis title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 journal: Clinical Applications of PCR DOI: 10.1385/1-59745-074-x:163 sha: doc_id: 290813 cord_uid: 6ylwj5je file: cache/cord-290598-wquwtovs.json key: cord-290598-wquwtovs authors: li, s.; qiu, y.; tang, l.; wang, z.; cao, w.; xu, g.; sun, x. title: Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients date: 2020-09-23 journal: nan DOI: 10.1101/2020.09.22.20198465 sha: doc_id: 290598 cord_uid: wquwtovs file: cache/cord-290690-53t7df81.json key: cord-290690-53t7df81 authors: Roberts, David J. title: Life in Times of COVID‐19 date: 2020-05-13 journal: Transfus Med DOI: 10.1111/tme.12688 sha: doc_id: 290690 cord_uid: 53t7df81 file: cache/cord-290776-l6ajq6vp.json key: cord-290776-l6ajq6vp authors: Frithiof, Robert; Bergqvist, Anders; Järhult, Josef D.; Lipcsey, Miklos; Hultström, Michael title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients date: 2020-09-29 journal: Crit Care DOI: 10.1186/s13054-020-03302-w sha: doc_id: 290776 cord_uid: l6ajq6vp file: cache/cord-290904-ngvhk0qy.json key: cord-290904-ngvhk0qy authors: Zheng, Zhiqiang; Monteil, Vanessa Marthe; Maurer-Stroh, Sebastian; Yew, Chow Wenn; Leong, Carol; Mohd-Ismail, Nur Khairiah; Cheyyatraivendran Arularasu, Suganya; Chow, Vincent Tak Kwong; Lin, Raymond Tzer Pin; Mirazimi, Ali; Hong, Wanjin; Tan, Yee-Joo title: Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date: 2020-07-16 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.28.2000291 sha: doc_id: 290904 cord_uid: ngvhk0qy file: cache/cord-290950-v28kilvn.json key: cord-290950-v28kilvn authors: Peyrony, Olivier; Ellouze, Sami; Fontaine, Jean-Paul; Le Cam, Micheline Thegat; Salmona, Maud; Feghoul, Linda; Mahjoub, Nadia; Mercier-Delarue, Séverine; Gabassi, Audrey; Delaugerre, Constance; Le Goff, Jérôme title: Surfaces and equipment contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Emergency Department at a university hospital date: 2020-08-07 journal: Int J Hyg Environ Health DOI: 10.1016/j.ijheh.2020.113600 sha: doc_id: 290950 cord_uid: v28kilvn file: cache/cord-290845-bf1q4k6t.json key: cord-290845-bf1q4k6t authors: Bouchghoul, Hanane; Vigoureux, Solene title: Do pregnant women have protective immunity against COVID‐19? date: 2020-06-24 journal: BJOG DOI: 10.1111/1471-0528.16342 sha: doc_id: 290845 cord_uid: bf1q4k6t file: cache/cord-290687-kc7t1y5o.json key: cord-290687-kc7t1y5o authors: Ray, Soumi; Roy, Mitu title: Susceptibility and Sustainability of India against CoVid19: a multivariate approach date: 2020-04-21 journal: nan DOI: 10.1101/2020.04.16.20066159 sha: doc_id: 290687 cord_uid: kc7t1y5o file: cache/cord-290863-f0wpsaip.json key: cord-290863-f0wpsaip authors: Tenforde, Mark W.; Kim, Sara S.; Lindsell, Christopher J.; Billig Rose, Erica; Shapiro, Nathan I.; Files, D. Clark; Gibbs, Kevin W.; Erickson, Heidi L.; Steingrub, Jay S.; Smithline, Howard A.; Gong, Michelle N.; Aboodi, Michael S.; Exline, Matthew C.; Henning, Daniel J.; Wilson, Jennifer G.; Khan, Akram; Qadir, Nida; Brown, Samuel M.; Peltan, Ithan D.; Rice, Todd W.; Hager, David N.; Ginde, Adit A.; Stubblefield, William B.; Patel, Manish M.; Self, Wesley H.; Feldstein, Leora R.; Hart, Kimberly W.; McClellan, Robert; Dorough, Layne; Dzuris, Nicole; Griggs, Eric P.; Kassem, Ahmed M.; Marcet, Paula L.; Ogokeh, Constance E.; Sciarratta, Courtney N.; Siddula, Akshita; Smith, Emily R.; Wu, Michael J. title: Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 date: 2020-07-31 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6930e1 sha: doc_id: 290863 cord_uid: f0wpsaip file: cache/cord-291047-mpahl77t.json key: cord-291047-mpahl77t authors: Alm, Erik; Broberg, Eeva K; Connor, Thomas; Hodcroft, Emma B; Komissarov, Andrey B; Maurer-Stroh, Sebastian; Melidou, Angeliki; Neher, Richard A; O’Toole, Áine; Pereyaslov, Dmitriy; Beerenwinkel, Niko; Posada-Céspedes, Susana; Jablonski, Kim Philipp; Ferreira, Pedro Falé; Topolsky, Ivan; Avšič-Županc, Tatjana; Korva, Miša; Poljak, Mario; Zakotnik, Samo; Zorec, Tomaž Mark; Bragstad, Karoline; Hungnes, Olav; Stene-Johansen, Kathrine; Reusken, Chantal; Meijer, Adam; Vennema, Harry; Ruiz-Roldán, Lidia; Bracho, María Alma; García-González, Neris; Chiner-Oms, Álvaro; Cancino-Muñoz, Irving; Comas, Iñaki; Goig, Galo A; Torres-Puente, Manuela; López, Mariana G; Martínez-Priego, Llúcia; D'Auria, Giuseppe; Ferrús-Abad, Loreto; de Marco, Griselda; Galan-Vendrell, Inmaculada; Carbó-Ramirez, Sandra; Ruíz-Hueso, Paula; Coscollá, Mireia; Polackova, Katerina; Kramna, Lenka; Cinek, Ondrej; Richter, Jan; Krashias, George; Tryfonos, Christina; Bashiardes, Stavros; Koptides, Dana; Christodoulou, Christina; Bartolini, Barbara; Gruber, Cesare Em; Di Caro, Antonino; Castilletti, Concetta; Stefani, Fabrizio; Rimoldi, Sara Giordana; Romeri, Francesca; Salerno, Franco; Polesello, Stefano; Nagy, Alexander; Jirincova, Helena; Vecerova, Jaromira; Novakova, Ludmila; Cordey, Samuel; Murtskhvaladze, Marine; Kotaria, Nato; Schär, Tobias; Beisel, Christian; Vugrek, Oliver; Rokić, Filip; Trgovec-Greif, Lovro; Jurak, Igor; Rukavina, Tomislav; Sučić, Neven; Schønning, Kristian; Karst, Søren M; Kirkegaard, Rasmus H; Michaelsen, Thomas Y; Sørensen, Emil Aa; Knutson, Simon; Brandt, Jakob; Le-Quy, Vang; Sørensen, Trine; Petersen, Celine; Pedersen, Martin Schou; Larsen, Sanne Løkkegaard; Skov, Marianne Nielsine; Rasmussen, Morten; Fonager, Jannik; Fomsgaard, Anders; Maksyutov, Rinat Amirovich; Gavrilova, Elena Vasil'Evna; Pyankov, Oleg Victorovich; Bodnev, Sergey Alexandrovich; Tregubchak, Tatyana Vladimirovna; Shvalov, Alexander Nikolayevich; Antonets, Denis Victorovich; Resende, Paola Cristina; Goya, Stephanie; Perrin, Amandine; Lee, Raphael Tc; Yadahalli, Shilpa; Han, Alvin X; Russell, Colin A; Schmutz, Stefan; Zaheri, Maryam; Kufner, Verena; Huber, Michael; Trkola, Alexandra; Antwerpen, Markus; Walter, Mathias C; van der Werf, Sylvie; Gambaro, Fabiana; Behillil, Sylvie; Enouf, Vincent; Donati, Flora; Ustinova, Monta; Rovite, Vita; Klovins, Janis; Savicka, Oksana; Wienecke-Baldacchino, Anke K; Ragimbeau, Catherine; Fournier, Guillaume; Mossong, Joël; Aberle, Stephan W; Haukland, Mattias; Enkirch, Theresa; Advani, Abdolreza; Karlberg, Maria Lind; Lindsjö, Oskar Karlsson; Broddesson, Sandra; Sláviková, Monika; Ličková, Martina; Klempa, Boris; Staroňová, Edita; Tichá, Elena; Szemes, Tomáš; Rusňáková, Diana; Stadler, Tanja; Quer, Josep; Anton, Andres; Andres, Cristina; Piñana, Maria; Garcia-Cehic, Damir; Pumarola, Tomas; Izopet, Jacques; Gioula, Georgia; Exindari, Maria; Papa, Anna; Chatzidimitriou, Dimitrios; Metallidis, Symeon; Pappa, Stella; Macek Jr, Milan; Geryk, Jan; Brož, Petr; Briksí, Aleš; Hubáček, Petr; Dřevínek, Pavel; Zajac, Miroslav; Kvapil, Petr; Holub, Michal; Kvapilová, Kateřina; Novotný, Adam; Kašný, Martin; Klempt, Petr; Vapalahti, Olli; Smura, Teemu; Sironen, Tarja; Selhorst, Philippe; Anthony, Colin; Ariën, Kevin; Simon-Loriere, Etienne; Rabalski, Lukasz; Bienkowska-Szewczyk, Krystyna; Borges, Vítor; Isidro, Joana; Gomes, João Paulo; Guiomar, Raquel; Pechirra, Pedro; Costa, Inês; Duarte, Sílvia; Vieira, Luís; Pyrc, Krzysztof; Zuckerman, Neta S; Turdikulova, Shahlo; Abdullaev, Alisher; Dalimova, Dilbar; Abdurakhimov, Abror; Tagliabracci, Adriano; Alessandrini, Federica; Melchionda, Filomena; Onofri, Valerio; Turchi, Chiara; Bagnarelli, Patrizia; Menzo, Stefano; Caucci, Sara; Di Sante, Laura; Popa, Alexandra; Genger, Jakob-Wendelin; Agerer, Benedikt; Lercher, Alexander; Endler, Lukas; Smyth, Mark; Penz, Thomas; Schuster, Michael; Senekowitsch, Martin; Laine, Jan; Bock, Christoph; Bergthaler, Andreas; Shevtsov, Alexandr; Kalendar, Ruslan; Ramanculov, Yerlan; Graf, Alexander; Muenchhoff, Maximilian; Keppler, Oliver T; Krebs, Stefan; Blum, Helmut; Marcello, Alessandro; Licastro, Danilo; D'Agaro, Pierlanfranco; Laubscher, Florian; Vidanovic, Dejan; Tesovic, Bojana; Volkening, Jeremy; Clementi, Nicola; Mancini, Nicasio; Rupnik, Maja; Mahnic, Aleksander; Walker, Andreas; Houwaart, Torsten; Wienemann, Tobias; Vasconcelos, Malte Kohns; Strelow, Daniel; Jensen, Björn-Erik Ole; Senff, Tina; Hülse, Lisanna; Adams, Ortwin; Andree, Marcel; Hauka, Sandra; Feldt, Torsten; Keitel, Verena; Kindgen-Milles, Detlef; Timm, Jörg; Pfeffer, Klaus; Dilthey, Alexander T; Moore, Catherine; Ozdarendeli, Aykut; Pavel, Shaikh Terkis Islam; Yetiskin, Hazel; Aydin, Gunsu; Holyavkin, Can; Uygut, Muhammet Ali; Cevik, Ceren; Shchetinin, Alexey; Gushchin, Vladimir; Dinler-Doganay, Gizem; Doganay, Levent; Kizilboga-Akgun, Tugba; Karacan, Ilker; Pancer, Katarzyna; Maes, Piet; Martí-Carreras, Joan; Wawina-Bokalanga, Tony; Vanmechelen, Bert; Thürmer, Andrea; Wedde, Marianne; Dürrwald, Ralf; Von Kleist, Max; Drechsel, Oliver; Wolff, Thorsten; Fuchs, Stephan; Kmiecinski, Rene; Michel, Janine; Nitsche, Andreas; Casas, Inmaculada; Caballero, María Iglesias; Zaballos, Ángel; Jiménez, Pilar; Jiménez, Mercedes; Fernández, Sara Monzón; Fernández, Sarai Varona; De La Plaza, Isabel Cuesta; Fadeev, Artem; Ivanova, Anna; Sergeeva, Mariia; Stefanelli, Paola; Torok, M Estee; Hall, Grant; da Silva Filipe, Ana; Turtle, Lance; Afifi, Safiah; Mccluggage, Kathryn; Beer, Robert; Ledesma, Juan; Maksimovic, Joshua; Spellman, Karla; Hamilton, William L; Marchbank, Angela; Southgate, Joel Alexander; Underwood, Anthony; Taylor, Ben; Yeats, Corin; Abudahab, Khalil; Gemmell, Matthew R; Eccles, Richard; Lucaci, Anita; Nelson, Charlotte Abigail; Rainbow, Lucille; Whitehead, Mark; Gregory, Richard; Haldenby, Sam; Paterson, Steve; Hughes, Margaret A; Curran, Martin D; Baker, David; Tucker, Rachel; Green, Luke R; Feltwell, Theresa; Halstead, Fenella D; Wyles, Matthew; Jahun, Aminu S; Ahmad, Shazaad S Y; Georgana, Iliana; Goodfellow, Ian; Yakovleva, Anna; Meredith, Luke W; Gavriil, Artemis; Awan, Ali Raza; Fisher, Chloe; Edgeworth, Jonathan; Lynch, Jessica; Moore, Nathan; Williams, Rebecca; Kidd, Stephen P; Cortes, Nicholas; Brunker, Kirstyn; Mccrone, John T; Quick, Joshua; Duckworth, Nichola; Walsh, Sarah; Sloan, Tim; Ludden, Catherine; George, Ryan P; Eltringham, Gary; Brown, Julianne R; Aranday-Cortes, Elihu; Shepherd, James G; Hughes, Joseph; Li, Kathy K; Williams, Thomas C; Johnson, Natasha; Jesudason, Natasha; Mair, Daniel; Thomson, Emma; Shah, Rajiv; Parr, Yasmin A; Carmichael, Stephen; Robertson, David L; Nomikou, Kyriaki; Broos, Alice; Niebel, Marc; Smollett, Katherine; Tong, Lily; Miah, Shahjahan; Wittner, Anita; Phillips, Nicole; Payne, Brendan; Dewar, Rebecca; Holmes, Alison; Bolt, Frances; Price, James R; Mookerjee, Siddharth; Sethi, Dheeraj K; Potter, Will; Stanley, Rachael; Prakash, Reenesh; Dervisevic, Samir; Graham, Jonathan Clive; Nelson, Andrew; Smith, Darren; Young, Gregory R; Yew, Wen Chyin; Todd, John A; Trebes, Amy; Andersson, Monique; Bull, Matthew; Watkins, Joanne; Birchley, Alec; Gatica-Wilcox, Bree; Gilbert, Lauren; Kumžiene-Summerhayes, Sara; Rey, Sara; Chauhan, Anoop; Butcher, Ethan; Bicknell, Kelly; Elliott, Scott; Glaysher, Sharon; Lackenby, Angie; Bibby, David; Platt, Steven; Mohamed, Hodan; Machin, Nicholas William; Mbisa, Jean Lutamyo; Evans, Jonathan; Perry, Malorie; Pacchiarini, Nicole; Corden, Sally; Adams, Alexander Geraint; Gaskin, Amy; Coombs, Jason; Graham, Lee John; Cottrell, Simon; Morgan, Mari; Gifford, Laura; Kolyva, Anastasia; Rudder, Steven John; Trotter, Alexander J; Mather, Alison E; Aydin, Alp; Page, Andrew J; Kay, Gemma L; de Oliveira Martins, Leonardo; Yasir, Muhammad; Alikhan, Nabil-Fareed; Thomson, Nicholas M; Gilroy, Rachel; Kingsley, Robert A; O'Grady, Justin; Gutierrez, Ana Victoria; Diaz, Maria; Le Viet, Thanh; Tedim, Ana P; Adriaenssens, Evelien M; Mcclure, C Patrick; Moore, Christopher; Sang, Fei; Clark, Gemma; Howson-Wells, Hannah C; Debebe, Johnny; Ball, Jonathan; Chappell, Joseph; Khakh, Manjinder; Carlile, Matthew; Loose, Matthew; Lister, Michelle M; Holmes, Nadine; Tsoleridis, Theocharis; Fleming, Vicki M; Wright, Victoria; Smith, Wendy; Gallagher, Michael D; Parker, Matthew; Partridge, David G; Evans, Cariad; Baker, Paul; Essex, Sarah; Liggett, Steven; Keeley, Alexander J; Bashton, Matthew; Rooke, Stefan; Dervisevic, Samir; Meader, Emma Jane; Balcazar Lopez, Carlos Enrique; Angyal, Adrienn; Kristiansen, Mark; Tutill, Helena J; Findlay, Jacqueline; Mestek-Boukhibar, Lamia; Forrest, Leysa; Dyal, Patricia; Williams, Rachel J; Panchbhaya, Yasmin; Williams, Charlotte A; Roy, Sunando; Pandey, Sarojini; Stockton, Jo; Loman, Nicholas J; Poplawski, Radoslaw; Nicholls, Samuel; Rowe, W P M; Khokhar, Fahad; Pinckert, Malte Lars; Hosmillo, Myra; Chaudhry, Yasmin; Caller, Laura G; Davidson, Rose K; Griffith, Luke; Rambaut, Andrew; Jackson, Ben; Colquhoun, Rachel; Hill, Verity; Nichols, Jenna; Asamaphan, Patawee; Darby, Alistair; Jackson, Kathryn A; Iturriza-Gomara, Miren; Vamos, Ecaterina Edith; Green, Angie; Aanensen, David; Bonsall, David; Buck, David; Macintyre-Cockett, George; de Cesare, Mariateresa; Pybus, Oliver; Golubchik, Tanya; Scarlett, Garry; Loveson, Katie F; Robson, Samuel C; Beckett, Angela; Lindsey, Benjamin; Groves, Danielle C; Parsons, Paul J; Mchugh, Martin P; Barnes, James Daniel; Manso, Carmen F; Grammatopoulos, Dimitris; Menger, Katja Elisabeth; Harrison, Ewan; Gunson, Rory; Peacock, Sharon J; Gonzalez, Gabriel; Carr, Michael; Mihaela, Lazar; Popovici, Odette; Brytting, Mia; Bresner, Catherine; Fuller, William; Workman, Trudy; Mentis, Andreas F; Kossyvakis, Athanasios; Karamitros, Timokratis; Pogka, Vasiliki; Kalliaropoulos, Antonios; Horefti, Elina; Kontou, Aspasia; Martinez-Gonzalez, Beatriz; Labropoulou, Voula; Voulgari-Kokota, Androniki; Evangelidou, Maria; Bizta, Panagiota; Belimezi, Maria; Lambrechts, Laurens; Doymaz, Mehmet Z; Yazici, Merve Kalkan; Cetin, Nesibe S; Karaaslan, Elif; Kallio-Kokko, Hannimari; Virtanen, Jenni; Suvanto, Maija; Nguyen, Phuoc Truong; Ellonen, Pekka; Hannula, Sari; Kangas, Harri; Sreenu, Vattipally B; Burián, Katalin; Terhes, Gabriella; Gombos, Katalin; Gyenesei, Attila; Urbán, Péter; Herczeg, Róbert; Jakab, Ferenc; Kemenesi, Gábor; Tóth, Gábor Endre; Somogyi, Balázs; Zana, Brigitta; Zeghbib, Safia; Kuczmog, Anett; Földes, Fanni; Lanszki, Zsófia; Madai, Mónika; Papp, Henrietta; Nagy, Ágnes; Pereszlényi, Csaba István; Babinszky, Gergely Csaba; Dudás, Gábor; Csoma, Eszter; Abou Tayoun, Ahmad N; Alsheikh-Ali, Alawi A; Loney, Tom; Nowotny, Norbert; Abdul-Wahab, Osama; Gonzalez-Candelas, Fernando; Andersen, Martin H; Taylor, Sarah title: Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 date: 2020-08-13 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.32.2001410 sha: doc_id: 291047 cord_uid: mpahl77t file: cache/cord-290443-naulq6q7.json key: cord-290443-naulq6q7 authors: Battistoni, Allegra; Volpe, Massimo title: Might renin–angiotensin system blockers play a role in the COVID-19 pandemic? date: 2020-04-14 journal: Eur Heart J Cardiovasc Pharmacother DOI: 10.1093/ehjcvp/pvaa030 sha: doc_id: 290443 cord_uid: naulq6q7 file: cache/cord-290671-6p23qxb8.json key: cord-290671-6p23qxb8 authors: Jiang, Shibo; Du, Lanying; Shi, Zhengli title: An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies date: 2020-01-31 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1723441 sha: doc_id: 290671 cord_uid: 6p23qxb8 file: cache/cord-290895-tb0xald0.json key: cord-290895-tb0xald0 authors: Indu, Purushothaman; Rameshkumar, Marimuthu Ragavan; Arunagirinathan, Narasingam; Al-Dhabi, Naif Abdullah; Arasu, Mariadhas Valan; Ignacimuthu, Savarimuthu title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach date: 2020-10-26 journal: J Infect Public Health DOI: 10.1016/j.jiph.2020.10.015 sha: doc_id: 290895 cord_uid: tb0xald0 file: cache/cord-291024-9g4om4sf.json key: cord-291024-9g4om4sf authors: Isakbaeva, Elmira T.; Khetsuriani, Nino; Beard, R. 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K.; Pertinez, H.; Arshad, U.; Box, H.; Tatham, L.; Curley, P.; Neary, M.; Sharp, J.; Liptrott, N. J.; Valentijn, A.; David, C.; Rannard, S. P.; Aljayyoussi, G.; Pennington, S. H.; Hill, A.; Boffito, M.; Ward, S. A.; Khoo, S. H.; Bray, P. G.; O'Neill, P. M.; Hong, W. D.; Biagini, G.; Owen, A. title: Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis date: 2020-05-06 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.05.01.20087130 sha: doc_id: 291923 cord_uid: jvbehgb7 file: cache/cord-291719-1ku6cmwj.json key: cord-291719-1ku6cmwj authors: Hajjo, Rima; Tropsha, Alexander title: A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date: 2020-10-06 journal: Pharm Res DOI: 10.1007/s11095-020-02930-9 sha: doc_id: 291719 cord_uid: 1ku6cmwj file: cache/cord-291590-24psoaer.json key: cord-291590-24psoaer authors: Ogando, Natacha S.; Zevenhoven-Dobbe, Jessika C.; Posthuma, Clara C.; Snijder, Eric J. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.19.162529 sha: doc_id: 291590 cord_uid: 24psoaer file: cache/cord-291624-fod0eyuj.json key: cord-291624-fod0eyuj authors: Malone, Robert W.; Tisdall, Philip; Fremont-Smith, Philip; Liu, Yongfeng; Huang, Xi-Ping; White, Kris M.; Miorin, Lisa; Olmo, Elena Moreno Del; Alon, Assaf; Delaforge, Elise; Hennecker, Christopher D.; Wang, Guanyu; Pottel, Joshua; Bona, Robert; Smith, Nora; Hall, Julie M.; Shapiro, Gideon; Clark, Howard; Mittermaier, Anthony; Kruse, Andrew C.; García-Sastre, Adolfo; Roth, Bryan L.; Glasspool-Malone, Jill; Francone, Victor; Hertzog, Norbert; Fremont-Smith, Maurice; Ricke, Darrell O. title: COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms date: 2020-06-22 journal: Res Sq DOI: 10.21203/rs.3.rs-30934/v2 sha: doc_id: 291624 cord_uid: fod0eyuj file: cache/cord-291644-5y0ioety.json key: cord-291644-5y0ioety authors: Akiyama, Tomohiro; Hirata, Takamichi; Fujimoto, Takahiro; Hatakeyama, Shinnosuke; Yamazaki, Ryuhei; Nomura, Tomohiro title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond date: 2020-08-29 journal: Nanomaterials (Basel) DOI: 10.3390/nano10091699 sha: doc_id: 291644 cord_uid: 5y0ioety file: cache/cord-291655-l7mg5a0z.json key: cord-291655-l7mg5a0z authors: Ku, C. 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Aiuto, Riccardo; Paglia, Luigi; Re, Dino title: COVID-19 and Dentistry: Prevention in Dental Practice, a Literature Review date: 2020-06-26 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17124609 sha: doc_id: 292173 cord_uid: 95t89yee file: cache/cord-292041-a65kfw80.json key: cord-292041-a65kfw80 authors: Orienti, Isabella; Gentilomi, Giovanna Angela; Farruggia, Giovanna title: Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19 date: 2020-05-27 journal: Int J Mol Sci DOI: 10.3390/ijms21113812 sha: doc_id: 292041 cord_uid: a65kfw80 file: cache/cord-292236-eudcs9t2.json key: cord-292236-eudcs9t2 authors: Wang, Yishan; Kang, Hanyujie; Liu, Xuefeng; Tong, Zhaohui title: Asymptomatic cases with SARS‐CoV‐2 infection date: 2020-05-22 journal: J Med Virol DOI: 10.1002/jmv.25990 sha: doc_id: 292236 cord_uid: eudcs9t2 file: cache/cord-292250-jjhpwgfa.json key: cord-292250-jjhpwgfa authors: Heinz, Nicole; Griesemer, Adam; Kinney, Joanna; Vittorio, Jennifer; 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Meurant, Robyn; Ardakani, Ali title: COVID-19 Serological Tests: How Well Do They Actually Perform? date: 2020-07-04 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10070453 sha: doc_id: 292274 cord_uid: upwn9o2m file: cache/cord-292578-co5essuw.json key: cord-292578-co5essuw authors: Johnson, Marina; Wagstaffe, Helen R.; Gilmour, Kimberly C.; Mai, Annabelle Lea; Lewis, Joanna; Hunt, Adam; Sirr, Jake; Bengt, Christopher; Grandjean, Louis; Goldblatt, David title: Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date: 2020-08-02 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104572 sha: doc_id: 292578 cord_uid: co5essuw file: cache/cord-292045-pnid9dmq.json key: cord-292045-pnid9dmq authors: Kumar, Manish; Patel, Arbind Kumar; Shah, Anil V.; Raval, Janvi; Rajpara, Neha; Joshi, Madhvi; Joshi, Chaitanya G. title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141326 sha: doc_id: 292045 cord_uid: pnid9dmq file: cache/cord-292350-cmrtg91a.json key: cord-292350-cmrtg91a authors: Mondal, Samhati; Quintili, Ashley L.; Karamchandani, Kunal; Bose, Somnath title: Thromboembolic disease in COVID-19 patients: A brief narrative review date: 2020-09-14 journal: J Intensive Care DOI: 10.1186/s40560-020-00483-y sha: doc_id: 292350 cord_uid: cmrtg91a file: cache/cord-292367-ocbsmmt6.json key: cord-292367-ocbsmmt6 authors: El-Masri, Maher M.; Oldfield, Margaret title: Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date: 2012-02-29 journal: Intensive and Critical Care Nursing DOI: 10.1016/j.iccn.2011.10.003 sha: doc_id: 292367 cord_uid: ocbsmmt6 file: cache/cord-292423-jupcit75.json key: cord-292423-jupcit75 authors: Narkhede, Rohan R.; Pise, Ashwini V.; Cheke, Rameshwar S.; Shinde, Sachin D. title: Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences date: 2020-06-17 journal: Nat Prod Bioprospect DOI: 10.1007/s13659-020-00253-1 sha: doc_id: 292423 cord_uid: jupcit75 file: cache/cord-292462-zbjig3pt.json key: cord-292462-zbjig3pt authors: Backhaus, Andreas title: Common Pitfalls in the Interpretation of COVID-19 Data and Statistics date: 2020-06-07 journal: Inter Econ DOI: 10.1007/s10272-020-0893-1 sha: doc_id: 292462 cord_uid: zbjig3pt file: cache/cord-292347-d7xq7x5g.json key: cord-292347-d7xq7x5g authors: Carter, Linda J.; Garner, Linda V.; Smoot, Jeffrey W.; Li, Yingzhu; Zhou, Qiongqiong; Saveson, Catherine J.; Sasso, Janet M.; Gregg, Anne C.; Soares, Divya J.; Beskid, Tiffany R.; Jervey, Susan R.; Liu, Cynthia title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 journal: ACS Cent Sci DOI: 10.1021/acscentsci.0c00501 sha: doc_id: 292347 cord_uid: d7xq7x5g file: cache/cord-292544-m7jyydf1.json key: cord-292544-m7jyydf1 authors: Grau-Pujol, Berta; Camprubí, Daniel; Marti-Soler, Helena; Fernández-Pardos, Marc; Guinovart, Caterina; Muñoz, Jose title: Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial date: 2020-07-29 journal: Trials DOI: 10.1186/s13063-020-04621-7 sha: doc_id: 292544 cord_uid: m7jyydf1 file: cache/cord-292561-iy06b9h9.json key: cord-292561-iy06b9h9 authors: Miesbach, Wolfgang; Makris, Michael title: COVID-19: Coagulopathy, Risk of Thrombosis, and the Rationale for Anticoagulation date: 2020-07-17 journal: Clin Appl Thromb Hemost DOI: 10.1177/1076029620938149 sha: doc_id: 292561 cord_uid: iy06b9h9 file: cache/cord-292256-jp80u828.json key: cord-292256-jp80u828 authors: Moriguchi, Takeshi; Harii, Norikazu; Goto, Junko; Harada, Daiki; Sugawara, Hisanori; Takamino, Junichi; Ueno, Masateru; Sakata, Hiroki; Kondo, Kengo; Myose, Natsuhiko; Nakao, Atsuhito; Takeda, Masayuki; Haro, Hirotaka; Inoue, Osamu; Suzuki-Inoue, Katsue; Kubokawa, Kayo; Ogihara, Shinji; Sasaki, Tomoyuki; Kinouchi, Hiroyuki; Kojin, Hiroyuki; Ito, Masami; Onishi, Hiroshi; Shimizu, Tatsuya; Sasaki, Yu; Enomoto, Nobuyuki; Ishihara, Hiroshi; Furuya, Shiomi; Yamamoto, Tomoko; Shimada, Shinji title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.062 sha: doc_id: 292256 cord_uid: jp80u828 file: cache/cord-292650-i95upz10.json key: cord-292650-i95upz10 authors: Marafini, Irene; Salvatori, Silvia; Sena, Giorgia; Calabrese, Emma; Biancone, Livia; Monteleone, Giovanni title: LOW FREQUENCY OF COVID-19 IN INFLAMMATORY BOWEL DISEASES date: 2020-06-13 journal: Dig Liver Dis DOI: 10.1016/j.dld.2020.06.007 sha: doc_id: 292650 cord_uid: i95upz10 file: cache/cord-292386-hfbgigj6.json key: cord-292386-hfbgigj6 authors: Borges, Lysandro Pinto; Martins, Aline Fagundes; de Melo, Mônica Santos; de Oliveira, Makson Gleydson Brito; Neto, José Melquiades de Rezende; Dósea, Marcos Barbosa; Cabral, Bruna Cecília Maia; Menezes, Rafael Fontes; Santos, Aryanne Araujo; Matos, Igor Leonardo Santos; Borges, Pamela Chaves; dos Santos, Kezia Alves; Ribeiro, Anderson Alves; Menendez, Andres Ignacio Martinez; Serafini, Mairim Russo; Walker, Cristiani Banderó; Quintans Junior, Lucindo José; Araújo, Adriano Antunes de Souza; de Souza, Daniela Raguer Valadão title: Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil date: 2020-10-06 journal: Rev Panam Salud Publica DOI: 10.26633/rpsp.2020.108 sha: doc_id: 292386 cord_uid: hfbgigj6 file: cache/cord-292387-2xv3wgaq.json key: cord-292387-2xv3wgaq authors: D′Agostino, Armando; D’Angelo, Simone; Giordano, Barbara; Cigognini, Anna Chiara; Chirico, Margherita Lorenza; Redaelli, Cristiana; Gambini, Orsola title: Brief Psychotic Disorder During the National Lockdown in Italy: An Emerging Clinical Phenomenon of the COVID-19 Pandemic date: 2020-08-06 journal: Schizophr Bull DOI: 10.1093/schbul/sbaa112 sha: doc_id: 292387 cord_uid: 2xv3wgaq file: cache/cord-292416-3hhi4wps.json key: cord-292416-3hhi4wps authors: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 journal: Rambam Maimonides Med J DOI: 10.5041/rmmj.10414 sha: doc_id: 292416 cord_uid: 3hhi4wps file: cache/cord-292580-caxb9ob9.json key: cord-292580-caxb9ob9 authors: Chang, Z; 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D. A.; Hoang, V. T.; Goumballa, N.; Louni, M.; Canard, N.; Dao, T. L.; Medkour, H.; Borg, A.; Bardy, K.; Esteves-Vieira, V.; Filosa, V.; Davoust, B.; Mediannikov, O.; Fournier, P.-E.; Raoult, D.; Gautret, P. title: Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020. date: 2020-05-11 journal: nan DOI: 10.1101/2020.05.05.20091934 sha: doc_id: 292600 cord_uid: mgvrbfzd file: cache/cord-292675-tkyngspy.json key: cord-292675-tkyngspy authors: Qi, Furong; Qian, Shen; Zhang, Shuye; Zhang, Zheng title: Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses date: 2020-03-19 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.03.044 sha: doc_id: 292675 cord_uid: tkyngspy file: cache/cord-292874-6zjqflhz.json key: cord-292874-6zjqflhz authors: SØRENSEN, MORTEN DRÆBY; SØRENSEN, BRIAN; GONZALEZ‐DOSAL, REGINA; MELCHJORSEN, CONNIE JENNING; WEIBEL, JENS; WANG, JING; JUN, CHEN WIE; HUANMING, YANG; KRISTENSEN, PETER title: Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date: 2006-05-10 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1354.072 sha: doc_id: 292874 cord_uid: 6zjqflhz file: cache/cord-292985-w62xaa4f.json key: cord-292985-w62xaa4f authors: Römer, Rudolf A.; Römer, Navodya S.; Wallis, A. Katrine title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 journal: bioRxiv DOI: 10.1101/2020.07.12.199364 sha: doc_id: 292985 cord_uid: w62xaa4f file: cache/cord-293059-2iwzieqm.json key: cord-293059-2iwzieqm authors: Tao, Huaqiang; Ge, Gaoran; Li, Wenming; Liang, Xiaolong; Wang, Hongzhi; Li, Ning; Sun, Houyi; Zhang, Wei; Geng, Dechun title: Dysimmunity and inflammatory storm: Watch out for bone lesions in COVID-19 infection date: 2020-10-06 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110332 sha: doc_id: 293059 cord_uid: 2iwzieqm file: cache/cord-293080-b4pxjrcj.json key: cord-293080-b4pxjrcj authors: Zhang, Chunyan; Zhou, Lei; Liu, Hao; Zhang, Sibing; Tian, Yaping; Huo, Junli; Li, Fei; Zhang, Yao; Wei, Bo; Xu, Dan; Hu, Jinwei; Wang, Jiayi; Cheng, Yuxuan; Shi, Wenjie; Xu, Xiuli; Zhou, Jianping; Sang, Peipei; Tan, Xudong; Wang, Weiwei; Zhang, Minjie; Wang, Bin; Zhou, Yujun; Zhang, Kan; He, Kunlun title: Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method date: 2020-09-18 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1811161 sha: doc_id: 293080 cord_uid: b4pxjrcj file: cache/cord-292880-zegtr19k.json key: cord-292880-zegtr19k authors: Hu, Fuying; Yin, Gang; Chen, Youping; Song, Jiangqin; Ye, Maosong; Liu, Jie; Chen, Cuicui; Song, Yuanlin; Tang, Xinjun; Zhang, Yong title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 date: 2020-08-13 journal: Clin Respir J DOI: 10.1111/crj.13243 sha: doc_id: 292880 cord_uid: zegtr19k file: cache/cord-292673-00s3wgem.json key: cord-292673-00s3wgem authors: Buonaguro, Luigi; Tagliamonte, Maria; Tornesello, Maria Lina; Buonaguro, Franco M. title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 journal: J Transl Med DOI: 10.1186/s12967-020-02355-3 sha: doc_id: 292673 cord_uid: 00s3wgem file: cache/cord-293167-3bd3adip.json key: cord-293167-3bd3adip authors: Nepal, Gaurav; Rehrig, Jessica Holly; Shrestha, Gentle Sunder; Shing, Yow Ka; Yadav, Jayant Kumar; Ojha, Rajeev; Pokhrel, Gaurab; Tu, Zhi Lan; Huang, Dong Ya title: Neurological manifestations of COVID-19: a systematic review date: 2020-07-13 journal: Crit Care DOI: 10.1186/s13054-020-03121-z sha: doc_id: 293167 cord_uid: 3bd3adip file: cache/cord-293367-0fe62h2f.json key: cord-293367-0fe62h2f authors: Henderson, Lauren A.; Canna, Scott W.; Friedman, Kevin G.; Gorelik, Mark; Lapidus, Sivia K.; Bassiri, Hamid; Behrens, Edward M.; Ferris, Anne; Kernan, Kate F.; Schulert, Grant S.; Seo, Philip; F. Son, Mary Beth; Tremoulet, Adriana H.; Yeung, Rae S.M.; Mudano, Amy S.; Turner, Amy S.; Karp, David R.; Mehta, Jay J. title: American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS‐C) Associated with SARS‐CoV‐2 and Hyperinflammation in COVID‐19. Version 1 date: 2020-07-23 journal: Arthritis Rheumatol DOI: 10.1002/art.41454 sha: doc_id: 293367 cord_uid: 0fe62h2f file: cache/cord-292733-dya40tln.json key: cord-292733-dya40tln authors: Lancman, Guido; Mascarenhas, John; Bar-Natan, Michal title: Severe COVID-19 virus reactivation following treatment for B cell acute lymphoblastic leukemia date: 2020-10-02 journal: J Hematol Oncol DOI: 10.1186/s13045-020-00968-1 sha: doc_id: 292733 cord_uid: dya40tln file: cache/cord-292988-q1yz9y8k.json key: cord-292988-q1yz9y8k authors: Zumla, Alimuddin; Wang, Fu-Sheng; Ippolito, Giuseppe; Petrosillo, Nicola; Agrati, Chiara; Azhar, Esam I; El-Kafrawy, Sherif A; Osman, Mohamed; Zitvogel, Laurence; Locatelli, Franco; Gorman, Ellen; O'Kane, Cecilia; Mcauley, Danny; Maeurer, Markus title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.040 sha: doc_id: 292988 cord_uid: q1yz9y8k file: cache/cord-293382-uyat0w58.json key: cord-293382-uyat0w58 authors: Walker, Susanne N.; Chokkalingam, Neethu; Reuschel, Emma L.; Purwar, Mansi; Xu, Ziyang; Gary, Ebony N.; Kim, Kevin Y.; Helble, Michaela; Schultheis, Katherine; Walters, Jewell; Ramos, Stephanie; Muthumani, Kar; Smith, Trevor R. F.; Broderick, Kate E.; Tebas, Pablo; Patel, Ami; Weiner, David B.; Kulp, Daniel W. title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients date: 2020-10-21 journal: J Clin Microbiol DOI: 10.1128/jcm.01533-20 sha: doc_id: 293382 cord_uid: uyat0w58 file: cache/cord-293315-kx4x2g24.json key: cord-293315-kx4x2g24 authors: Colmenero, I.; Santonja, C.; Alonso‐Riaño, M.; Noguera‐Morel, L.; Hernández‐Martín, A.; Andina, D.; Wiesner, T.; Rodríguez‐Peralto, J.L.; Requena, L.; Torrelo, A. title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases date: 2020-06-20 journal: Br J Dermatol DOI: 10.1111/bjd.19327 sha: doc_id: 293315 cord_uid: kx4x2g24 file: cache/cord-292742-mio4przi.json key: cord-292742-mio4przi authors: McAloose, Denise; Laverack, Melissa; Wang, Leyi; Killian, Mary Lea; Caserta, Leonardo C.; Yuan, Fangfeng; Mitchell, Patrick K.; Queen, Krista; Mauldin, Matthew R.; Cronk, Brittany D.; Bartlett, Susan L.; Sykes, John M.; Zec, Stephanie; Stokol, Tracy; Ingerman, Karen; Delaney, Martha A.; Fredrickson, Richard; Ivančić, Marina; Jenkins-Moore, Melinda; Mozingo, Katie; Franzen, Kerrie; Bergeson, Nichole Hines; Goodman, Laura; Wang, Haibin; Fang, Ying; Olmstead, Colleen; McCann, Colleen; Thomas, Patrick; Goodrich, Erin; Elvinger, François; Smith, David C.; Tong, Suxiang; Slavinski, Sally; Calle, Paul P.; Terio, Karen; Torchetti, Mia Kim; Diel, Diego G. title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 journal: mBio DOI: 10.1128/mbio.02220-20 sha: doc_id: 292742 cord_uid: mio4przi file: cache/cord-292883-7hvq9qaj.json key: cord-292883-7hvq9qaj authors: Nguyen-Contant, Phuong; Embong, A. Karim; Kanagaiah, Preshetha; Chaves, Francisco A.; Yang, Hongmei; Branche, Angela R.; Topham, David J.; Sangster, Mark Y. title: S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date: 2020-09-25 journal: mBio DOI: 10.1128/mbio.01991-20 sha: doc_id: 292883 cord_uid: 7hvq9qaj file: cache/cord-293169-rd12xwvl.json key: cord-293169-rd12xwvl authors: Black, Margaret A.; Shen, Guomiao; Feng, Xiaojun; Garcia Beltran, Wilfredo F.; Feng, Yang; Vasudevaraja, Varshini; Allison, Douglas; Lin, Lawrence H.; Gindin, Tatyana; Astudillo, Michael; Yang, Diane; Murali, Mandakolathur; Iafrate, A. John; Jour, George; Cotzia, Paolo; Snuderl, Matija title: Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples date: 2020-11-07 journal: J Immunol Methods DOI: 10.1016/j.jim.2020.112909 sha: doc_id: 293169 cord_uid: rd12xwvl file: cache/cord-293180-f1ulk9ce.json key: cord-293180-f1ulk9ce authors: Li, R W K; Leung, K W C; Sun, F C S; Samaranayake, L P title: Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs date: 2004-08-14 journal: Br Dent J DOI: 10.1038/sj.bdj.4811522 sha: doc_id: 293180 cord_uid: f1ulk9ce file: cache/cord-292836-1o2ynvy3.json key: cord-292836-1o2ynvy3 authors: Ogimi, Chikara; Kim, Yae Jean; Martin, Emily T; Huh, Hee Jae; Chiu, Cheng-Hsun; Englund, Janet A title: What’s New With the Old Coronaviruses? date: 2020-04-21 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa037 sha: doc_id: 292836 cord_uid: 1o2ynvy3 file: cache/cord-293127-c27qh5y7.json key: cord-293127-c27qh5y7 authors: Monteleone, Pedro AA; Nakano, Mayra; Lazar, Victor; Gomes, Alecsandra P; de Martin, Hamilton; Bonetti, Tatiana CS title: A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments date: 2020 journal: JBRA Assist Reprod DOI: 10.5935/1518-0557.20200030 sha: doc_id: 293127 cord_uid: c27qh5y7 file: cache/cord-293544-nemw29r7.json key: cord-293544-nemw29r7 authors: Valdivia, Arantxa; Torres, Ignacio; Huntley, Dixie; Alcaraz, María J.; Albert, Eliseo; Colomina, Javier; Ferrer, Josep; Carratalá, Arturo; Navarro, David title: Qualitative assessment of SARS‐CoV‐2‐specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay date: 2020-08-02 journal: J Med Virol DOI: 10.1002/jmv.26344 sha: doc_id: 293544 cord_uid: nemw29r7 file: cache/cord-293304-kakxmc14.json key: cord-293304-kakxmc14 authors: Achutha, A. 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L.; Suchitra, Surendran title: Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors date: 2020-09-22 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00683 sha: doc_id: 293304 cord_uid: kakxmc14 file: cache/cord-293557-jcgc93it.json key: cord-293557-jcgc93it authors: Recalde, Borja; García-Tobar, Laura; Argueta, Alan; Álvarez, Laura; De Andrea, Carlos Eduardo; Fernández Alonso, Mirian; Ezponda, Ana; Carmona Torre, Francisco; Jordán Iborra, Carlota; Quiroga, Jorge Augusto; Del Pozo, Jose Luis; Zulueta, Javier J; Echarri, Gema; Landecho, Manuel F; Lozano, Maria Dolores title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients date: 2020-08-23 journal: Thorax DOI: 10.1136/thoraxjnl-2020-215577 sha: doc_id: 293557 cord_uid: jcgc93it file: cache/cord-293082-fw7deem8.json key: cord-293082-fw7deem8 authors: Zhang, Guangzhi; Li, Bin; Yoo, Dongwan; Qin, Tong; Zhang, Xiaodon; Jia, Yaxiong; Cui, Shangjin title: Animal coronaviruses and SARS‐CoV‐2 date: 2020-08-16 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13791 sha: doc_id: 293082 cord_uid: fw7deem8 file: cache/cord-293136-lfwqzf8m.json key: cord-293136-lfwqzf8m authors: Escosa‐García, Luis; Aguilera‐Alonso, David; Calvo, Cristina; Mellado, María José; Baquero‐Artigao, Fernando title: Ten key points about COVID‐19 in children: the shadows on the wall date: 2020-08-13 journal: Pediatr Pulmonol DOI: 10.1002/ppul.25025 sha: doc_id: 293136 cord_uid: lfwqzf8m file: cache/cord-293517-8derad2p.json key: cord-293517-8derad2p authors: Fischer, Johannes C.; Zänker, Kurt; van Griensven, Martijn; Schneider, Marion; Kindgen-Milles, Detlef; Knoefel, Wolfram Trudo; Lichtenberg, Artur; Tamaskovics, Balint; Djiepmo-Njanang, Freddy Joel; Budach, Wilfried; Corradini, Stefanie; Ganswindt, Ute; Häussinger, Dieter; Feldt, Torsten; Schelzig, Hubert; Bojar, Hans; Peiper, Matthias; Bölke, Edwin; Haussmann, Jan; Matuschek, Christiane title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update date: 2020-10-30 journal: Eur J Med Res DOI: 10.1186/s40001-020-00449-8 sha: doc_id: 293517 cord_uid: 8derad2p file: cache/cord-293259-o51fnvuw.json key: cord-293259-o51fnvuw authors: Sinaei, Reza; Pezeshki, Sara; Parvaresh, Saeedeh; Sinaei, Roya title: Why COVID-19 is less frequent and severe in children: a narrative review date: 2020-09-25 journal: World J Pediatr DOI: 10.1007/s12519-020-00392-y sha: doc_id: 293259 cord_uid: o51fnvuw file: cache/cord-293265-qqxlwpju.json key: cord-293265-qqxlwpju authors: Zeng, Yong; Zhang, Bo; Zhang, Xufeng; Yi, Cunjian title: Clinical characteristics of 9 cancer patients with SARS-CoV-2 infection date: 2020-05-14 journal: Chin Med DOI: 10.1186/s13020-020-00328-8 sha: doc_id: 293265 cord_uid: qqxlwpju file: cache/cord-293056-kz3w0nfh.json key: cord-293056-kz3w0nfh authors: Indes, Jeffrey E.; Koleilat, Issam; Hatch, Ayesha Nzeribe; Choinski, Krystina; Jones, Davis Brent; Aldailami, Hasan; Billett, Henny; Denesopolis, John M.; Lipsitz, Evan title: Early Experience with Arterial Thromboembolic Complications in Patents with COVID-19 date: 2020-08-28 journal: J Vasc Surg DOI: 10.1016/j.jvs.2020.07.089 sha: doc_id: 293056 cord_uid: kz3w0nfh file: cache/cord-293710-f1tzt6jb.json key: cord-293710-f1tzt6jb authors: Karolyi, M.; Pawelka, E.; Omid, S.; Kelani, H.; Mader, T.; Baumgartner, S.; Laferl, H.; Traugott, M.; Seitz, T.; Zoufaly, A.; Wenisch, C. title: Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients date: 2020-09-23 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04044-x sha: doc_id: 293710 cord_uid: f1tzt6jb file: cache/cord-293579-w5sub348.json key: cord-293579-w5sub348 authors: Che, Xiao-yan; Qiu, Li-wen; Liao, Zhi-yong; Wang, Ya-di; Wen, Kun; Pan, Yu-xian; Hao, Wei; Mei, Ya-bo; Cheng, Vincent C. C.; Yuen, Kwok-yung title: Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date: 2005-06-15 journal: J Infect Dis DOI: 10.1086/430355 sha: doc_id: 293579 cord_uid: w5sub348 file: cache/cord-293890-thfros7x.json key: cord-293890-thfros7x authors: Carbo, Ellen C.; Sidorov, Igor A.; Zevenhoven-Dobbe, Jessica C.; Snijder, Eric J.; Claas, Eric C.; Laros, Jeroen F.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. title: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness date: 2020-08-21 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104594 sha: doc_id: 293890 cord_uid: thfros7x file: cache/cord-293503-e7be12qb.json key: cord-293503-e7be12qb authors: Xiang, Chao; Lu, Ji; Zhou, Jun; Guan, Li; Yang, Cheng; Chai, Changzhu title: CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation date: 2020-08-15 journal: Biomed Res Int DOI: 10.1155/2020/5436025 sha: doc_id: 293503 cord_uid: e7be12qb file: cache/cord-293615-f1e6hs11.json key: cord-293615-f1e6hs11 authors: Dockery, Dominique M.; Rowe, Susannah G.; Murphy, Marjorie A.; Krzystolik, Magdalena G. title: The Ocular Manifestations and Transmission of COVID-19; Recommendations for Prevention date: 2020-05-08 journal: J Emerg Med DOI: 10.1016/j.jemermed.2020.04.060 sha: doc_id: 293615 cord_uid: f1e6hs11 file: cache/cord-293415-u9onutny.json key: cord-293415-u9onutny authors: Amendola, A.; Garoffolo, G.; Songia, P.; Ferrari, S.; Bernava, G.; Canzano, P.; Myasoedova, V.; Colavita, F.; Castilletti, C.; Sberna, G.; Capobianchi, M. R.; Agrifoglio, M.; Colombo, G. I.; Poggio, P.; Pesce, M. title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression date: 2020-11-10 journal: nan DOI: 10.1101/2020.11.06.20226423 sha: doc_id: 293415 cord_uid: u9onutny file: cache/cord-293274-ysr1l557.json key: cord-293274-ysr1l557 authors: Perisé-Barrios, Ana Judith; Tomeo-Martín, Beatriz Davinia; Gómez-Ochoa, Pablo; Delgado-Bonet, Pablo; Plaza, Pedro; Palau-Concejo, Paula; González, Jorge; Ortiz-Diez, Gustavo; Meléndez-Lazo, Antonio; Gentil, Michaela; García-Castro, Javier; Barbero-Fernández, Alicia title: Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.22.308023 sha: doc_id: 293274 cord_uid: ysr1l557 file: cache/cord-293389-3h9vsc1a.json key: cord-293389-3h9vsc1a authors: Risitano, Antonio M.; Mastellos, Dimitrios C.; Huber-Lang, Markus; Yancopoulou, Despina; Garlanda, Cecilia; Ciceri, Fabio; Lambris, John D. title: Complement as a target in COVID-19? date: 2020-04-23 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0320-7 sha: doc_id: 293389 cord_uid: 3h9vsc1a file: cache/cord-293559-c78wcr8m.json key: cord-293559-c78wcr8m authors: Rego, Gabriel N. A.; Nucci, Mariana P.; Alves, Arielly H.; Oliveira, Fernando A.; Marti, Luciana C.; Nucci, Leopoldo P.; Mamani, Javier B.; Gamarra, Lionel F. title: Current Clinical Trials Protocols and the Global Effort for Immunization against SARS-CoV-2 date: 2020-08-25 journal: Vaccines (Basel) DOI: 10.3390/vaccines8030474 sha: doc_id: 293559 cord_uid: c78wcr8m file: cache/cord-293655-2ab7wdsk.json key: cord-293655-2ab7wdsk authors: Mandic-Rajcevic, S.; Masci, F.; Crespi, E.; Franchetti, S.; Longo, A.; Bollina, I.; Veloci, S.; Amorosi, A.; Baldelli, R.; Boselli, L.; Negroni, L.; Za, A.; Orfeo, N. V.; Ortisi, G.; Colosio, C. title: Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy) date: 2020-05-08 journal: nan DOI: 10.1101/2020.05.03.20082818 sha: doc_id: 293655 cord_uid: 2ab7wdsk file: cache/cord-293826-2p7dqacd.json key: cord-293826-2p7dqacd authors: Lee, Cheryl Yi-Pin; Amrun, Siti Naqiah; Chee, Rhonda Sin-Ling; Goh, Yun Shan; Mak, Tze-Minn; Octavia, Sophie; Yeo, Nicholas Kim-Wah; Chang, Zi Wei; Tay, Matthew Zirui; Torres-Ruesta, Anthony; Carissimo, Guillaume; Poh, Chek Meng; Fong, Siew-Wai; Bei, Wang; Lee, Sandy; Young, Barnaby Edward; Tan, Seow-Yen; Leo, Yee-Sin; Lye, David C.; Lin, Raymond T. P.; Maurer-Stroh, Sebastien; Lee, Bernett; Cheng-I, Wang; Renia, Laurent; Ng, Lisa F.P. title: Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date: 2020-10-09 journal: bioRxiv DOI: 10.1101/2020.10.08.332544 sha: doc_id: 293826 cord_uid: 2p7dqacd file: cache/cord-293301-7bmj8qsv.json key: cord-293301-7bmj8qsv authors: Buonanno, Giorgio; Stabile, Luca; Morawska, Lidia title: Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment date: 2020-04-17 journal: nan DOI: 10.1101/2020.04.12.20062828 sha: doc_id: 293301 cord_uid: 7bmj8qsv file: cache/cord-293692-t5rfvyvj.json key: cord-293692-t5rfvyvj authors: Kazi, Sajida; Malinowski, A. Kinga; Othman, Maha title: The delights and perils of publishing, knowledge-sharing and critique during a pandemic: Observations from COVID-19 coagulopathies date: 2020-05-16 journal: Thromb Res DOI: 10.1016/j.thromres.2020.05.023 sha: doc_id: 293692 cord_uid: t5rfvyvj file: cache/cord-293481-bmfj50fb.json key: cord-293481-bmfj50fb authors: Malin, Jakob J.; Suárez, Isabelle; Priesner, Vanessa; Fätkenheuer, Gerd; Rybniker, Jan title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 journal: Clin Microbiol Rev DOI: 10.1128/cmr.00162-20 sha: doc_id: 293481 cord_uid: bmfj50fb file: cache/cord-293543-87ulnpdm.json key: cord-293543-87ulnpdm authors: Shalhoub, Sarah title: Interferon beta-1b for COVID-19 date: 2020-05-10 journal: Lancet DOI: 10.1016/s0140-6736(20)31101-6 sha: doc_id: 293543 cord_uid: 87ulnpdm file: cache/cord-293688-g6kag5ij.json key: cord-293688-g6kag5ij authors: Nora, Holtmann; Philippos, Edimiris; Marcel, Andree; Cornelius, Doehmen; Dunja, Baston-Buest; Ortwin, Adams; Jan-Steffen, Kruessel; Petra, Bielfeld Alexandra title: Assessment of SARS-CoV-2 in human semen - a cohort study date: 2020-05-29 journal: Fertil Steril DOI: 10.1016/j.fertnstert.2020.05.028 sha: doc_id: 293688 cord_uid: g6kag5ij file: cache/cord-293547-29i3u83s.json key: cord-293547-29i3u83s authors: Pfaar, O; Klimek, L; Jutel, M; Akdis, CA; Bousquet, J; Breiteneder, H; Chinthrajah, S; Diamant, Z; Eiwegger, T; Fokkens, WJ; Fritsch, HW; Nadeau, KC; O’Hehir, RE; O’Mahony, L; Rief, W; Sampath, V; Schedlowski, M; Torres, M; Traidl‐Hoffmann, C; Wang, DY; Zhang, L; Bonini, M; Brehler, R; Brough, HA; Chivato, T; Del Giacco, S; Dramburg, S; Gawlik, R; Gelincik, A; Hoffmann‐Sommergruber, K; Hox, V; Knol, E; Lauerma, A; Matricardi, PM; Mortz, CG; Ollert, M; Palomares, O; Riggioni, C; Schwarze, J; Skypala, I; Untersmayr, S; Walusiak‐Skorupa, J; Ansotegui, I; Bachert, C; Bedbrook, A; Bosnic‐Anticevich, S; Brussino, L; Canonica, GW; Cardona, V; Carreiro‐Martins, P; Cruz, AA; Czarlewski, W; Fonseca, JA; Gotua, M; Haatela, T; Ivancevich, JC; Kuna, P; Kvedariene, V; Larenas‐Linnemann, D; Latiff, A; Morais‐Almeida, M; Mullol, J; Naclerio, R; Ohta, K; Okamoto, Y; Onorato, GL; Papadopoulos, NG; Patella, V; Regateiro, FS; Samolinski, B; Suppli Ulrik, C; Toppila‐Salmi, S; Valiulis, A; Ventura, MT; Yorgancioglu, A; Zuberbier, T; Agache, I title: COVID‐19 pandemic: Practical considerations on the organization of an allergy clinic – an EAACI/ARIA Position Paper date: 2020-06-12 journal: Allergy DOI: 10.1111/all.14453 sha: doc_id: 293547 cord_uid: 29i3u83s file: cache/cord-293564-6xtg8uqt.json key: cord-293564-6xtg8uqt authors: Hara, Tasuku; Yamamoto, Chie; Sawada, Ryo; Ohara, Tomoya; Oka, Kohei; Iwai, Naoto; Inada, Yutaka; Tsuji, Toshifumi; Okuda, Takashi; Komaki, Toshiyuki; Kagawa, Keizo title: Infection risk in a gastroenterological ward during a nosocomial COVID‐19 infection event date: 2020-04-22 journal: J Med Virol DOI: 10.1002/jmv.25853 sha: doc_id: 293564 cord_uid: 6xtg8uqt file: cache/cord-293578-yu2i0u2h.json key: cord-293578-yu2i0u2h authors: Kusadasi, Nuray; Sikma, Maaike; Huisman, Albert; Westerink, Jan; Maas, Coen; Schutgens, Roger title: A Pathophysiological Perspective on the SARS-CoV-2 Coagulopathy date: 2020-08-10 journal: Hemasphere DOI: 10.1097/hs9.0000000000000457 sha: doc_id: 293578 cord_uid: yu2i0u2h file: cache/cord-293736-nyvwv31m.json key: cord-293736-nyvwv31m authors: Méry, Geoffroy; Epaulard, Olivier; Borel, Anne-Laure; Toussaint, Bertrand; Le Gouellec, Audrey title: COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella date: 2020-07-21 journal: Front Immunol DOI: 10.3389/fimmu.2020.01714 sha: doc_id: 293736 cord_uid: nyvwv31m file: cache/cord-293946-4bquxdqa.json key: cord-293946-4bquxdqa authors: Huong, Nguyen Quynh; Nga, Nguyen Thi Thanh; Long, Nguyen Van; Luu, Bach Duc; Latinne, Alice; Pruvot, Mathieu; Phuong, Nguyen Thanh; Quang, Le Tin Vinh; Hung, Vo Van; Lan, Nguyen Thi; Hoa, Nguyen Thi; Minh, Phan Quang; Diep, Nguyen Thi; Tung, Nguyen; Ky, Van Dang; Roberton, Scott I.; Thuy, Hoang Bich; Long, Nguyen Van; Gilbert, Martin; Wicker, Leanne; Mazet, Jonna A. K.; Johnson, Christine Kreuder; Goldstein, Tracey; Tremeau-Bravard, Alex; Ontiveros, Victoria; Joly, Damien O.; Walzer, Chris; Fine, Amanda E.; Olson, Sarah H. title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0237129 sha: doc_id: 293946 cord_uid: 4bquxdqa file: cache/cord-294028-pcc6mucj.json key: cord-294028-pcc6mucj authors: Caussy, Cyrielle; Wallet, Florent; Laville, Martine; Disse, Emmanuel title: Obesity is Associated with Severe Forms of COVID‐19 date: 2020-05-21 journal: Obesity (Silver Spring) DOI: 10.1002/oby.22842 sha: doc_id: 294028 cord_uid: pcc6mucj file: cache/cord-293765-xpc4yizb.json key: cord-293765-xpc4yizb authors: Huang, Jia-Ling; Huang, Jian; Duan, Zhao-Hui; Wei, Jing; Min, Jun; Luo, Xiao-Hong; Li, Jian-Guo; Tan, Wei-Ping; Wu, Li-Zhi; Liu, Ran-Yi; Li, Yan; Shao, Jing; Huang, Bi-Jun; Zeng, Yi-Xin; Huang, Wenlin title: Th2 predominance and CD8+ memory T cell depletion in patients with severe acute respiratory syndrome() date: 2005-02-24 journal: Microbes Infect DOI: 10.1016/j.micinf.2004.11.017 sha: doc_id: 293765 cord_uid: xpc4yizb file: cache/cord-293858-dk4snw9r.json key: cord-293858-dk4snw9r authors: Yang, Lin; Chan, King Pan; Wong, Chit Ming; Chiu, Susan Shui Seng; Magalhaes, Ricardo J. Soares; Thach, Thuan Quoc; Peiris, Joseph Syrial Malik; Clements, Archie C. A.; Hu, Wenbiao title: Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date: 2019-02-14 journal: BMC Infect Dis DOI: 10.1186/s12879-019-3735-7 sha: doc_id: 293858 cord_uid: dk4snw9r file: cache/cord-293991-x5zdo8t2.json key: cord-293991-x5zdo8t2 authors: Wheatley, A. K.; Juno, J. A.; Wang, J. J.; Selva, K. J.; Reynaldi, A.; Tan, H.-X.; Lee, W. S.; Wragg, K. M.; Kelly, H. G.; Esterbauer, R.; Davis, S. K.; Kent, H. E.; Mordant, F. L.; Schlub, T. E.; Gordon, D. L.; Khoury, D. S.; Subbarao, K.; Cromer, D.; Gordon, T. P.; Chung, A. W.; Davenport, M. P.; Kent, S. J. title: Evolution of immunity to SARS-CoV-2 date: 2020-09-10 journal: nan DOI: 10.1101/2020.09.09.20191205 sha: doc_id: 293991 cord_uid: x5zdo8t2 file: cache/cord-294073-65h2mkdy.json key: cord-294073-65h2mkdy authors: Ke, Jia; Lan, Nan; Wang, Ting; Wu, Jin-Jie; He, Zhen; He, Xiao-Sheng; Tao, Kai-Xiong; Qian, Qun; Zhou, Ping-Hong; Li, Guo-Xin; Zheng, Min-Hua; Zhang, Zhong-Tao; Ji, Jia-Fu; Lan, Ping title: Strategies and recommendations for the management of gastrointestinal surgery during the COVID-19 pandemic: experience shared by Chinese surgeons date: 2020-07-03 journal: Gastroenterol Rep (Oxf) DOI: 10.1093/gastro/goaa030 sha: doc_id: 294073 cord_uid: 65h2mkdy file: cache/cord-294212-nlekz39f.json key: cord-294212-nlekz39f authors: Wang, Dongliang; Mai, Jinhui; Zhou, Wenfeng; Yu, Wanting; Zhan, Yang; Wang, Naidong; Epstein, Neal D.; Yang, Yi title: Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date: 2020-07-03 journal: Vaccines (Basel) DOI: 10.3390/vaccines8030355 sha: doc_id: 294212 cord_uid: nlekz39f file: cache/cord-293701-u4ntxo0y.json key: cord-293701-u4ntxo0y authors: Su, Shan; Du, Lanying; Jiang, Shibo title: Learning from the past: development of safe and effective COVID-19 vaccines date: 2020-10-16 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-00462-y sha: doc_id: 293701 cord_uid: u4ntxo0y file: cache/cord-293860-6kz0iws6.json key: cord-293860-6kz0iws6 authors: Qutayba Almerie, Muhammad; Daniel Kerrigan, David title: The Association between Obesity and Poor Outcome after COVID-19 Indicates a Potential Therapeutic Role for Montelukast date: 2020-05-27 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109883 sha: doc_id: 293860 cord_uid: 6kz0iws6 file: cache/cord-293831-28ddm9um.json key: cord-293831-28ddm9um authors: Qian, Mengcen; Wu, Qianhui; Wu, Peng; Hou, Zhiyuan; Liang, Yuxia; Cowling, Benjamin J; Yu, Hongjie title: Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey date: 2020-02-20 journal: nan DOI: 10.1101/2020.02.18.20024448 sha: doc_id: 293831 cord_uid: 28ddm9um file: cache/cord-294199-o8w35pdy.json key: cord-294199-o8w35pdy authors: Zhang, Qiangzhe; Honko, Anna; Zhou, Jiarong; Gong, Hua; Downs, Sierra N.; Vasquez, Jhonatan Henao; Fang, Ronnie H.; Gao, Weiwei; Griffiths, Anthony; Zhang, Liangfang title: Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity date: 2020-06-17 journal: Nano Lett DOI: 10.1021/acs.nanolett.0c02278 sha: doc_id: 294199 cord_uid: o8w35pdy file: cache/cord-293852-r72c6584.json key: cord-293852-r72c6584 authors: Greco, S.; Madè, A.; Gaetano, C.; Devaux, Y.; Emanueli, C.; Martelli, F. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 journal: J Transl Med DOI: 10.1186/s12967-020-02582-8 sha: doc_id: 293852 cord_uid: r72c6584 file: cache/cord-293732-rxd1lyi7.json key: cord-293732-rxd1lyi7 authors: Manoj, M.G.; Satheesh Kumar, M.K.; Valsaraj, K.T.; Sivan, C.; Vijayan, Soumya K. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 journal: Environ Res DOI: 10.1016/j.envres.2020.110001 sha: doc_id: 293732 cord_uid: rxd1lyi7 file: cache/cord-294392-a8s66g96.json key: cord-294392-a8s66g96 authors: Zhang, Shuai; Guo, Mengfei; Wu, Feng; Xiong, Nian; Ma, Yanling; Wang, Zhihui; Duan, Limin; Chen, Lan; Ouyang, Haixia; Jin, Yang title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date: 2020-09-07 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.038 sha: doc_id: 294392 cord_uid: a8s66g96 file: cache/cord-294120-8fxrqorg.json key: cord-294120-8fxrqorg authors: Guebre-Xabier, Mimi; Patel, Nita; Tian, Jing-Hui; Zhou, Bin; Maciejewski, Sonia; Lam, Kristal; Portnoff, Alyse D.; Massare, Michael J.; Frieman, Matthew B.; Piedra, Pedro A.; Ellingsworth, Larry; Glenn, Gregory; Smith, Gale title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date: 2020-08-19 journal: bioRxiv DOI: 10.1101/2020.08.18.256578 sha: doc_id: 294120 cord_uid: 8fxrqorg file: cache/cord-294385-6dlgv3tb.json key: cord-294385-6dlgv3tb authors: Tong, Xin; Ning, Mingzhe; Huang, Rui; Jia, Bei; Yan, Xiaomin; Xiong, Yali; Wu, Weihua; Liu, Jiacheng; Chen, Yuxin; Wu, Chao title: Surveillance of SARS‐CoV‐2 infection among frontline health care workers in Wuhan during COVID‐19 outbreak date: 2020-08-20 journal: Immun Inflamm Dis DOI: 10.1002/iid3.340 sha: doc_id: 294385 cord_uid: 6dlgv3tb file: cache/cord-293938-40zyv1h8.json key: cord-293938-40zyv1h8 authors: Jonsdottir, Hulda R.; Dijkman, Ronald title: Coronaviruses and the human airway: a universal system for virus-host interaction studies date: 2016-02-06 journal: Virol J DOI: 10.1186/s12985-016-0479-5 sha: doc_id: 293938 cord_uid: 40zyv1h8 file: cache/cord-293988-f5gvwjyh.json key: cord-293988-f5gvwjyh authors: Musso, Nicolò; Costantino, Angelita; La Spina, Sebastiano; Finocchiaro, Alessandra; Andronico, Francesca; Stracquadanio, Stefano; Liotta, Luigi; Visalli, Rosanna; Emmanuele, Giovanni title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 journal: Pathogens DOI: 10.3390/pathogens9090746 sha: doc_id: 293988 cord_uid: f5gvwjyh file: cache/cord-294335-qnu19ru5.json key: cord-294335-qnu19ru5 authors: Yousaf, Anna R; 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Michael title: Neuropsychiatric Symptoms in an Adolescent Boy with Multisystem Inflammatory Syndrome in Children (MIS-C) date: 2020-06-30 journal: Psychosomatics DOI: 10.1016/j.psym.2020.06.015 sha: doc_id: 293715 cord_uid: lipme817 file: cache/cord-294122-ou3wj4rz.json key: cord-294122-ou3wj4rz authors: Hwang, Stephen W; Cheung, Angela M; Moineddin, Rahim; Bell, Chaim M title: Population mortality during the outbreak of Severe Acute Respiratory Syndrome in Toronto date: 2007-05-29 journal: BMC Public Health DOI: 10.1186/1471-2458-7-93 sha: doc_id: 294122 cord_uid: ou3wj4rz file: cache/cord-294069-7zr77r71.json key: cord-294069-7zr77r71 authors: Hu, Xiaowen; Ni, Wei; Wang, Zhaoguo; Ma, Guangren; Pan, Bei; Dong, Liyan; Gao, Ruqin; Jiang, Fachun title: The distribution of SARS-CoV-2 contamination on the environmental surfaces during incubation period of COVID-19 patients date: 2020-09-30 journal: Ecotoxicol Environ Saf DOI: 10.1016/j.ecoenv.2020.111438 sha: doc_id: 294069 cord_uid: 7zr77r71 file: cache/cord-294262-yvbufnf4.json key: cord-294262-yvbufnf4 authors: Fernandez-Nieto, D.; Ortega-Quijano, D.; Suarez-Valle, A.; Burgos-Blasco, P.; Jimenez-Cauhe, J.; Fernandez-Guarino, M. title: Comment on: “To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out. Characterization of herpetic lesions in hospitalized COVID-19 patients.” date: 2020-06-22 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.06.063 sha: doc_id: 294262 cord_uid: yvbufnf4 file: cache/cord-294115-7t7kubf6.json key: cord-294115-7t7kubf6 authors: Miralles, Oriol; Sanchez-Rodriguez, Dolores; Marco, Esther; Annweiler, Cédric; Baztan, Ainhoa; Betancor, Évora; Cambra, Alicia; Cesari, Matteo; Fontecha, Benito J.; Gąsowski, Jerzy; Gillain, Sophie; Hope, Suzy; Phillips, Katie; Piotrowicz, Karolina; Piro, Niccolò; Sacco, Guillaume; Saporiti, Edoardo; Surquin, Murielle; Vall-llosera, Estel title: Unmet needs, health policies, and actions during the COVID-19 pandemic: a report from six European countries date: 2020-10-15 journal: Eur Geriatr Med DOI: 10.1007/s41999-020-00415-x sha: doc_id: 294115 cord_uid: 7t7kubf6 file: cache/cord-294558-cqa58db8.json key: cord-294558-cqa58db8 authors: Wang, Yubo; Tong, Jin; Qin, Yalan; Xie, Ting; Li, Jianghua; Li, Jianrong; Xiang, Jianhua; Cui, Yong; Higgs, Elizabeth S; Xiang, Jianglin; He, Yong title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa629 sha: doc_id: 294558 cord_uid: cqa58db8 file: cache/cord-294592-zwvr57a0.json key: cord-294592-zwvr57a0 authors: Mukherjee, Moumita; Goswami, Srikanta title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 journal: PLoS One DOI: 10.1371/journal.pone.0237559 sha: doc_id: 294592 cord_uid: zwvr57a0 file: cache/cord-294237-6hovffso.json key: cord-294237-6hovffso authors: Cherry, James D; Krogstad, Paul title: SARS: The First Pandemic of the 21(st) Century date: 2004 journal: Pediatr Res DOI: 10.1203/01.pdr.0000129184.87042.fc sha: doc_id: 294237 cord_uid: 6hovffso file: cache/cord-294363-bv6xa8v8.json key: cord-294363-bv6xa8v8 authors: Zhou, Hong; Fang, Yan; Xu, Tao; Ni, Wei‐Jian; Shen, Ai‐Zong; Meng, Xiao‐Ming title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 journal: Br J Pharmacol DOI: 10.1111/bph.15092 sha: doc_id: 294363 cord_uid: bv6xa8v8 file: cache/cord-294440-zd0arwmr.json key: cord-294440-zd0arwmr authors: Sacco, Guillaume; Foucault, Gonzague; Briere, Olivier; Annweiler, Cédric title: COVID-19 in seniors: Findings and lessons from mass screening in a nursing home date: 2020-06-26 journal: Maturitas DOI: 10.1016/j.maturitas.2020.06.023 sha: doc_id: 294440 cord_uid: zd0arwmr file: cache/cord-294304-9w6zt778.json key: cord-294304-9w6zt778 authors: Doanvo, Anhvinh; Qian, Xiaolu; Ramjee, Divya; Piontkivska, Helen; Desai, Angel; Majumder, Maimuna title: Machine Learning Maps Research Needs in COVID-19 Literature date: 2020-09-16 journal: Patterns (N Y) DOI: 10.1016/j.patter.2020.100123 sha: doc_id: 294304 cord_uid: 9w6zt778 file: cache/cord-294136-e69ao8j0.json key: cord-294136-e69ao8j0 authors: Han, Dongsheng; Li, Rui; Han, Yanxi; Zhang, Rui; Li, Jinming title: COVID-19: Insight into the asymptomatic SARS-COV-2 infection and transmission date: 2020-08-27 journal: Int J Biol Sci DOI: 10.7150/ijbs.48991 sha: doc_id: 294136 cord_uid: e69ao8j0 file: cache/cord-294372-pec1886j.json key: cord-294372-pec1886j authors: Greene, Dina N.; Jackson, Michael L.; Hillyard, David R.; Delgado, Julio C.; Schmidt, Robert L. title: Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240783 sha: doc_id: 294372 cord_uid: pec1886j file: cache/cord-294527-fct2y5vn.json key: cord-294527-fct2y5vn authors: Guadarrama-Ortiz, Parménides; Choreño-Parra, José Alberto; Sánchez-Martínez, Claudia Marisol; Pacheco-Sánchez, Francisco Javier; Rodríguez-Nava, Alberto Iván; García-Quintero, Gabriela title: Neurological Aspects of SARS-CoV-2 Infection: Mechanisms and Manifestations date: 2020-09-04 journal: Front Neurol DOI: 10.3389/fneur.2020.01039 sha: doc_id: 294527 cord_uid: fct2y5vn file: cache/cord-294644-xuafsnxm.json key: cord-294644-xuafsnxm authors: Herrmann, Burkhard L. title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten date: 2020-08-13 journal: MMW Fortschr Med DOI: 10.1007/s15006-020-0750-y sha: doc_id: 294644 cord_uid: xuafsnxm file: cache/cord-294427-6eiligyy.json key: cord-294427-6eiligyy authors: Salimi, Ali; ElHawary, Hassan; Diab, Nermin; Smith, Lee title: The North American Layman's Understanding of COVID-19: Are We Doing Enough? date: 2020-07-03 journal: Front Public Health DOI: 10.3389/fpubh.2020.00358 sha: doc_id: 294427 cord_uid: 6eiligyy file: cache/cord-294498-fv545rfa.json key: cord-294498-fv545rfa authors: Spiegel, Martin; Pichlmair, Andreas; Mühlberger, Elke; Haller, Otto; Weber, Friedemann title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein date: 2004-07-31 journal: Journal of Clinical Virology DOI: 10.1016/j.jcv.2003.11.013 sha: doc_id: 294498 cord_uid: fv545rfa file: cache/cord-294677-l1b4mw9d.json key: cord-294677-l1b4mw9d authors: Prashantha, C.N.; Gouthami, K.; Lavanya, L.; Bhavanam, Sivaramireddy; Jain, Ajay; Shakthiraju, R.G.; Suraj, V.; Sahana, K.V.; Sujana, H.S.; Guruprasad, N.M.; Ramachandra, R. title: Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date: 2020-10-13 journal: J Mol Graph Model DOI: 10.1016/j.jmgm.2020.107769 sha: doc_id: 294677 cord_uid: l1b4mw9d file: cache/cord-294696-pm6pfeeb.json key: cord-294696-pm6pfeeb authors: Kunz, Y.; Horninger, W.; Pinggera, G.-M. title: Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag date: 2020-10-13 journal: Urologe A DOI: 10.1007/s00120-020-01264-z sha: doc_id: 294696 cord_uid: pm6pfeeb file: cache/cord-294134-o9bx1gn7.json key: cord-294134-o9bx1gn7 authors: Brecher, Stephen M.; Dryjowicz-Burek, Jonathan; Yu, Hongbo; Campbell, Sheldon; Ratcliffe, Nora; Gupta, Kalpana title: Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2 date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.01029-20 sha: doc_id: 294134 cord_uid: o9bx1gn7 file: cache/cord-294429-isivkz8b.json key: cord-294429-isivkz8b authors: Grifoni, Alba; Weiskopf, Daniela; Ramirez, Sydney I.; Mateus, Jose; Dan, Jennifer M.; Moderbacher, Carolyn Rydyznski; Rawlings, Stephen A.; Sutherland, Aaron; Premkumar, Lakshmanane; Jadi, Ramesh S.; Marrama, Daniel; de Silva, Aravinda M.; Frazier, April; Carlin, Aaron; Greenbaum, Jason A.; Peters, Bjoern; Krammer, Florian; Smith, Davey M.; Crotty, Shane; Sette, Alessandro title: Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals date: 2020-05-20 journal: Cell DOI: 10.1016/j.cell.2020.05.015 sha: doc_id: 294429 cord_uid: isivkz8b file: cache/cord-294108-uvnh0s9r.json key: cord-294108-uvnh0s9r authors: Dube, Taru; Ghosh, Amrito; Mishra, Jibanananda; Kompella, Uday B.; Panda, Jiban Jyoti title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 journal: Adv Ther (Weinh) DOI: 10.1002/adtp.202000172 sha: doc_id: 294108 cord_uid: uvnh0s9r file: cache/cord-294692-qfz6a1kc.json key: cord-294692-qfz6a1kc authors: Ortega, Karem L.; Rodrigues de Camargo, Alessandra; Bertoldi Franco, Juliana; Mano Azul, Antonio; Pérez Sayáns, Mario; Braz Silva, Paulo Henrique title: SARS-CoV-2 and dentistry date: 2020-06-05 journal: Clin Oral Investig DOI: 10.1007/s00784-020-03381-7 sha: doc_id: 294692 cord_uid: qfz6a1kc file: cache/cord-294349-ps3qlho2.json key: cord-294349-ps3qlho2 authors: Al-Sharif, Eman; Strianese, Diego; AlMadhi, Nada H.; D’Aponte, Antonella; dell’Omo, Roberto; Di Benedetto, Rita; Costagliola, Ciro title: Ocular tropism of coronavirus (CoVs): a comparison of the interaction between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye date: 2020-09-03 journal: Int Ophthalmol DOI: 10.1007/s10792-020-01575-2 sha: doc_id: 294349 cord_uid: ps3qlho2 file: cache/cord-294537-wpq1492g.json key: cord-294537-wpq1492g authors: Ritschl, Paul V.; Nevermann, Nora; Wiering, Leke; Wu, Helen H.; Moroder, Philipp; Brandl, Andreas; Hillebrandt, Karl; Tacke, Frank; Friedersdorff, Frank; Schlomm, Thorsten; Schöning, Wenzel; Öllinger, Robert; Schmelzle, Moritz; Pratschke, Johann title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach date: 2020-05-10 journal: Am J Transplant DOI: 10.1111/ajt.15933 sha: doc_id: 294537 cord_uid: wpq1492g file: cache/cord-294275-pp0vlaye.json key: cord-294275-pp0vlaye authors: Li, Jingjing; Quan, Weipeng; Yan, Shuge; Wu, Shuangju; Qin, Jianhu; Yang, Tingting; Liang, Fan; Wang, Depeng; Liang, Yu title: Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date: 2020-06-03 journal: bioRxiv DOI: 10.1101/2020.06.03.131474 sha: doc_id: 294275 cord_uid: pp0vlaye file: cache/cord-294571-qd0qjo3y.json key: cord-294571-qd0qjo3y authors: Rothan, Hussin A.; Acharya, Arpan; Reid, St Patrick; Kumar, Mukesh; Byrareddy, Siddappa N. title: Molecular Aspects of COVID-19 Differential Pathogenesis date: 2020-07-06 journal: Pathogens DOI: 10.3390/pathogens9070538 sha: doc_id: 294571 cord_uid: qd0qjo3y file: cache/cord-294590-1niaplc2.json key: cord-294590-1niaplc2 authors: Schrag, Stephanie J.; Brooks, John T.; Van Beneden, Chris; Parashar, Umesh D.; Griffin, Patricia M.; Anderson, Larry J.; Bellini, William J.; Benson, Robert F.; Erdman, Dean D.; Klimov, Alexander; Ksiazek, Thomas G.; Peret, Teresa C.T.; Talkington, Deborah F.; Thacker, W. 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E.; McGeer, A.; Dresser, L.; Raboud, J.; Mazzulli, T.; Loeb, M.; Louie, M. title: Early diagnosis of SARS: lessons from the Toronto SARS outbreak date: 2006-04-04 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-006-0127-x sha: doc_id: 294551 cord_uid: s3nsiano file: cache/cord-294700-pb5k21da.json key: cord-294700-pb5k21da authors: Dulek, Daniel E; Fuhlbrigge, Robert C; Tribble, Alison C; Connelly, James A; Loi, Michele M; El Chebib, Hassan; Chandrakasan, Shanmuganathan; Otto, William R; Diorio, Caroline; Keim, Garrett; Walkovich, Kelly; Jaggi, Preeti; Girotto, Jennifer E; Yarbrough, April; Behrens, Edward M; Cron, Randy Q; Bassiri, Hamid title: Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute COVID-19 in Pediatric Patients date: 2020-08-18 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa098 sha: doc_id: 294700 cord_uid: pb5k21da file: cache/cord-294441-nehorqhi.json key: cord-294441-nehorqhi authors: O’Brien, Stephen J.; Troyer, Jennifer L.; Roelke, Melody; Marker, Laurie; Pecon-Slattery, Jill title: Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS date: 2006-08-31 journal: Biological Conservation DOI: 10.1016/j.biocon.2006.05.001 sha: doc_id: 294441 cord_uid: nehorqhi file: cache/cord-294789-07hto8qn.json key: cord-294789-07hto8qn authors: Schoch-Spana, Monica; Brunson, Emily K.; Long, Rex; Ruth, Alexandra; Ravi, Sanjana J.; Trotochaud, Marc; Borio, Luciana; Brewer, Janesse; Buccina, Joseph; Connell, Nancy; Hall, Laura Lee; Kass, Nancy; Kirkland, Anna; Koonin, Lisa; Larson, Heidi; Lu, Brooke Fisher; Omer, Saad B.; Orenstein, Walter A.; Poland, Gregory A.; Privor-Dumm, Lois; Quinn, Sandra Crouse; Salmon, Daniel; White, Alexandre title: The public’s role in COVID-19 vaccination: human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States date: 2020-10-29 journal: Vaccine DOI: 10.1016/j.vaccine.2020.10.059 sha: doc_id: 294789 cord_uid: 07hto8qn file: cache/cord-294666-xlyuhzo9.json key: cord-294666-xlyuhzo9 authors: Arguin, Paul M.; Navin, Ava W.; Steele, Stefanie F.; Weld, Leisa H.; Kozarsky, Phyllis E. title: Health Communication during SARS date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030812 sha: doc_id: 294666 cord_uid: xlyuhzo9 file: cache/cord-294582-flkjekyo.json key: cord-294582-flkjekyo authors: Hijikata, Atsushi; Shionyu‐Mitsuyama, Clara; Nakae, Setsu; Shionyu, Masafumi; Ota, Motonori; Kanaya, Shigehiko; Shirai, Tsuyoshi title: Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs date: 2020-05-25 journal: FEBS Lett DOI: 10.1002/1873-3468.13806 sha: doc_id: 294582 cord_uid: flkjekyo file: cache/cord-294854-rvrgcugn.json key: cord-294854-rvrgcugn authors: Hu, Biying; Huang, Shaoying; Yin, Lianghong title: The cytokine storm and COVID‐19 date: 2020-06-27 journal: J Med Virol DOI: 10.1002/jmv.26232 sha: doc_id: 294854 cord_uid: rvrgcugn file: cache/cord-294921-h44tct43.json key: cord-294921-h44tct43 authors: Greninger, Alexander L.; Jerome, Keith R. title: The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.01416-20 sha: doc_id: 294921 cord_uid: h44tct43 file: cache/cord-294910-gnc04ax1.json key: cord-294910-gnc04ax1 authors: Nogueira, Paulo Jorge; de Araújo Nobre, Miguel; Costa, Andreia; Ribeiro, Ruy M.; Furtado, Cristina; Bacelar Nicolau, Leonor; Camarinha, Catarina; Luís, Márcia; Abrantes, Ricardo; Vaz Carneiro, António title: The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases date: 2020-07-24 journal: J Clin Med DOI: 10.3390/jcm9082368 sha: doc_id: 294910 cord_uid: gnc04ax1 file: cache/cord-294812-nnlzwaf1.json key: cord-294812-nnlzwaf1 authors: Desforges, Marc; Le Coupanec, Alain; Brison, Élodie; Meessen-Pinard, Mathieu; Talbot, Pierre J. title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 journal: Infectious Diseases and Nanomedicine I DOI: 10.1007/978-81-322-1777-0_6 sha: doc_id: 294812 cord_uid: nnlzwaf1 file: cache/cord-294698-mtfrbn87.json key: cord-294698-mtfrbn87 authors: Kim, H. 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G. title: Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date: 2016-05-23 journal: Transbound Emerg Dis DOI: 10.1111/tbed.12515 sha: doc_id: 294698 cord_uid: mtfrbn87 file: cache/cord-294718-n3gx862b.json key: cord-294718-n3gx862b authors: Tam, Patrick C K; Ly, Kathleen M; Kernich, Max L; Spurrier, Nicola; Lawrence, Diana; Gordon, David L; Tucker, Emily C title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa673 sha: doc_id: 294718 cord_uid: n3gx862b file: cache/cord-294931-a77g9rjo.json key: cord-294931-a77g9rjo authors: Zhang, Linqi; Zhang, Fengwen; Yu, Wenjie; He, Tian; Yu, Jian; Yi, Christopher E.; Ba, Lei; Li, Wenhui; Farzan, Michael; Chen, Zhiwei; Yuen, Kwok‐Yung; Ho, David title: Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals date: 2005-11-18 journal: J Med Virol DOI: 10.1002/jmv.20499 sha: doc_id: 294931 cord_uid: a77g9rjo file: cache/cord-295029-zki5ac2g.json key: cord-295029-zki5ac2g authors: Pena, Robert C.F.; Khatri, Deepak; Kwan, Kevin; D'Amico, Randy S. title: In Reply to the Letter to the Editor Regarding “Coronavirus Neurosurgical/Head and Neck Drape to Prevent Aerosolization of Coronavirus Disease 2019 (COVID-19): The Lenox Hill Hospital/Northwell Health Solution” date: 2020-11-03 journal: World Neurosurg DOI: 10.1016/j.wneu.2020.08.116 sha: doc_id: 295029 cord_uid: zki5ac2g file: cache/cord-294912-xl0wzi16.json key: cord-294912-xl0wzi16 authors: Alteri, Claudia; Cento, Valeria; Antonello, Maria; Colagrossi, Luna; Merli, Marco; Ughi, Nicola; Renica, Silvia; Matarazzo, Elisa; Di Ruscio, Federica; Tartaglione, Livia; Colombo, Jacopo; Grimaldi, Chiara; Carta, Stefania; Nava, Alice; Costabile, Valentino; Baiguera, Chiara; Campisi, Daniela; Fanti, Diana; Vismara, Chiara; Fumagalli, Roberto; Scaglione, Francesco; Epis, Oscar Massimiliano; Puoti, Massimo; Perno, Carlo Federico title: Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date: 2020-09-08 journal: PLoS One DOI: 10.1371/journal.pone.0236311 sha: doc_id: 294912 cord_uid: xl0wzi16 file: cache/cord-295034-em6z8mlu.json key: cord-295034-em6z8mlu authors: Daverey, Achlesh; Dutta, Kasturi title: COVID-19: Eco-friendly hand hygiene for human and environmental safety date: 2020-11-11 journal: J Environ Chem Eng DOI: 10.1016/j.jece.2020.104754 sha: doc_id: 295034 cord_uid: em6z8mlu file: cache/cord-294856-eeh2a0t8.json key: cord-294856-eeh2a0t8 authors: Lambert, Paul-Henri; Ambrosino, Donna M.; Andersen, Svein R.; Baric, Ralph S.; Black, Steven B.; Chen, Robert T.; Dekker, Cornelia L.; Didierlaurent, Arnaud M.; Graham, Barney S.; Martin, Samantha D.; Molrine, Deborah C.; Perlman, Stanley; Picard-Fraser, Philip A.; Pollard, Andrew J.; Qin, Chuan; Subbarao, Kanta; Cramer, Jakob P. title: Consensus Summary Report for CEPI/BC March 12-13, 2020 Meeting: Assessment of Risk of Disease Enhancement with COVID-19 Vaccines date: 2020-05-25 journal: Vaccine DOI: 10.1016/j.vaccine.2020.05.064 sha: doc_id: 294856 cord_uid: eeh2a0t8 file: cache/cord-294831-pem059zk.json key: cord-294831-pem059zk authors: Zhang, Ling-Pu; Wang, Meixian; Wang, Yanping; Zhu, Jun; Zhang, Nannan title: Focus on a 2019-novel coronavirus (SARS-CoV-2) date: 2020-06-11 journal: Future microbiology DOI: 10.2217/fmb-2020-0063 sha: doc_id: 294831 cord_uid: pem059zk file: cache/cord-295061-58tj4csz.json key: cord-295061-58tj4csz authors: Wilder‐Smith, Annelies; Paton, Nicholas I.; Goh, Kee Tai title: Short communication: Low risk of transmission of severe acute respiratory syndrome on airplanes: the Singapore experience date: 2003-10-22 journal: Trop Med Int Health DOI: 10.1046/j.1360-2276.2003.01133.x sha: doc_id: 295061 cord_uid: 58tj4csz file: cache/cord-294800-akr4f5p8.json key: cord-294800-akr4f5p8 authors: Kabir, Md. Tanvir; Uddin, Md. Sahab; Hossain, Md. Farhad; Abdulhakim, Jawaher A.; Alam, Md. Asraful; Ashraf, Ghulam Md; Bungau, Simona G.; Bin-Jumah, May N.; Abdel-Daim, Mohamed M.; Aleya, Lotfi title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 journal: Front Cell Dev Biol DOI: 10.3389/fcell.2020.00616 sha: doc_id: 294800 cord_uid: akr4f5p8 file: cache/cord-295302-vwrxentv.json key: cord-295302-vwrxentv authors: Shivarov, Velizar; Petrov, Peter K.; Pashov, Anastas D. title: Potential SARS-CoV-2 Preimmune IgM Epitopes date: 2020-04-30 journal: Front Immunol DOI: 10.3389/fimmu.2020.00932 sha: doc_id: 295302 cord_uid: vwrxentv file: cache/cord-295142-5sqkdpi8.json key: cord-295142-5sqkdpi8 authors: Han, Y.; Jia, Z.; Shi, J.; Wang, W.; He, K. title: The active lung microbiota landscape of COVID-19 patients date: 2020-08-23 journal: nan DOI: 10.1101/2020.08.20.20144014 sha: doc_id: 295142 cord_uid: 5sqkdpi8 file: cache/cord-294933-oc2glu4a.json key: cord-294933-oc2glu4a authors: Cinesi Gómez, César; Peñuelas Rodríguez, Óscar; Luján Torné, Manel; Egea Santaolalla, Carlos; Masa Jiménez, Juan Fernando; García Fernández, Javier; Carratalá Perales, José Manuel; Heili-Frades, Sarah Béatrice; Ferrer Monreal, Miquel; de Andrés Nilsson, José M.; Lista Arias, Eva; Sánchez Rocamora, Juan Luis; Garrote, José Ignacio; Zamorano Serrano, Miguel J.; González Martínez, Mónica; Farrero Muñoz, Eva; Mediano San Andrés, Olga; Rialp Cervera, Gemma; Mas Serra, Arantxa; Hernández Martínez, Gonzalo; de Haro López, Candelaria; Roca Gas, Oriol; Ferrer Roca, Ricard; Romero Berrocal, Antonio; Ferrando Ortola, Carlos title: Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date: 2020-06-19 journal: nan DOI: 10.1016/j.medine.2020.03.002 sha: doc_id: 294933 cord_uid: oc2glu4a file: cache/cord-295559-yc8q62z8.json key: cord-295559-yc8q62z8 authors: Qian, Zhaohui; Dominguez, Samuel R.; Holmes, Kathryn V. title: Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date: 2013-10-03 journal: PLoS One DOI: 10.1371/journal.pone.0076469 sha: doc_id: 295559 cord_uid: yc8q62z8 file: cache/cord-295051-upyar7en.json key: cord-295051-upyar7en authors: Ahmadian, Elham; 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Indari, Omkar; Chatterjee, Sayantani; Jha, Hem Chandra title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00522-7 sha: doc_id: 295041 cord_uid: 5vpawtef file: cache/cord-295455-km0qcmlh.json key: cord-295455-km0qcmlh authors: Fehr, Anthony R.; Jankevicius, Gytis; Ahel, Ivan; Perlman, Stanley title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 journal: Trends in Microbiology DOI: 10.1016/j.tim.2017.11.011 sha: doc_id: 295455 cord_uid: km0qcmlh file: cache/cord-295545-ruxz77i8.json key: cord-295545-ruxz77i8 authors: Hennighausen, Lothar; Lee, Hye Kyung title: Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date: 2020-05-11 journal: bioRxiv DOI: 10.1101/2020.05.11.089045 sha: doc_id: 295545 cord_uid: ruxz77i8 file: cache/cord-295548-o877eog6.json key: cord-295548-o877eog6 authors: Antonio, G.E; Wong, K.T; Chu, W.C.W; Hui, D.S.C; Cheng, F.W.T; Yuen, E.H.Y; Chung, S.S.C; Fok, T.F; Sung, J.J.Y; Ahuja, A.T title: Imaging in Severe Acute Respiratory Syndrome (SARS) date: 2003-10-21 journal: Clin Radiol DOI: 10.1016/s0009-9260(03)00308-8 sha: doc_id: 295548 cord_uid: o877eog6 file: cache/cord-295742-d11ty5ed.json key: cord-295742-d11ty5ed authors: van Dam, Peter A.; Huizing, Manon; Papadimitriou, Kostantinos; Prenen, Hans; Peeters, Marc title: High mortality of cancer patients in times of SARS-Cov-2: do not generalize! date: 2020-08-10 journal: Eur J Cancer DOI: 10.1016/j.ejca.2020.07.021 sha: doc_id: 295742 cord_uid: d11ty5ed file: cache/cord-295800-w0dup04b.json key: cord-295800-w0dup04b authors: So, Loletta K-Y; Lau, Arthur CW; Yam, Loretta YC; Cheung, Thomas MT; Poon, Edwin; Yung, Raymond WH; Yuen, KY title: Development of a standard treatment protocol for severe acute respiratory syndrome date: 2003-05-10 journal: Lancet DOI: 10.1016/s0140-6736(03)13265-5 sha: doc_id: 295800 cord_uid: w0dup04b file: cache/cord-295130-e7j7kac0.json key: cord-295130-e7j7kac0 authors: Moreno-Contreras, Joaquín; 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Penna, Bruno; Yates, Edwin A. title: Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date: 2020-09-29 journal: Front Microbiol DOI: 10.3389/fmicb.2020.581343 sha: doc_id: 295121 cord_uid: 4xemmaqt file: cache/cord-295433-olmein3q.json key: cord-295433-olmein3q authors: Banerjee, Arinjay; Kulcsar, Kirsten; Misra, Vikram; Frieman, Matthew; Mossman, Karen title: Bats and Coronaviruses date: 2019-01-09 journal: Viruses DOI: 10.3390/v11010041 sha: doc_id: 295433 cord_uid: olmein3q file: cache/cord-295973-41jqgsv0.json key: cord-295973-41jqgsv0 authors: Singh, Awadhesh Kumar; Singh, Akriti; Shaikh, Altamash; Singh, Ritu; Misra, Anoop title: Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries date: 2020-03-26 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.03.011 sha: doc_id: 295973 cord_uid: 41jqgsv0 file: cache/cord-295274-gzkfy70s.json key: cord-295274-gzkfy70s authors: Mecham, Jeffrey C.; Thomas, Olivia J.; Pirgousis, Phillip; Janus, Jeffrey R. title: Utility of Tracheostomy in Patients With COVID‐19 and Other Special Considerations date: 2020-05-12 journal: Laryngoscope DOI: 10.1002/lary.28734 sha: doc_id: 295274 cord_uid: gzkfy70s file: cache/cord-295375-nakxfhxk.json key: cord-295375-nakxfhxk authors: Yu, Yang; Shi, Qianling; Zheng, Peng; Gao, Lei; Li, Haiyuan; Tao, Pengxian; Gu, Baohong; Wang, Dengfeng; Chen, Hao title: Assessment of the quality of systematic reviews on COVID‐19: A comparative study of previous coronavirus outbreaks date: 2020-04-28 journal: J Med Virol DOI: 10.1002/jmv.25901 sha: doc_id: 295375 cord_uid: nakxfhxk file: cache/cord-295523-5pv7kw6i.json key: cord-295523-5pv7kw6i authors: Picchianti Diamanti, Andrea; Rosado, Maria Manuela; Pioli, Claudio; Sesti, Giorgio; Laganà, Bruno title: Cytokine Release Syndrome in COVID-19 Patients, A New Scenario for an Old Concern: The Fragile Balance between Infections and Autoimmunity date: 2020-05-08 journal: Int J Mol Sci DOI: 10.3390/ijms21093330 sha: doc_id: 295523 cord_uid: 5pv7kw6i file: cache/cord-295525-emrwcx0m.json key: cord-295525-emrwcx0m authors: To, Kelvin Kai-Wang; 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Debatable immunological and non-immunological evidence date: 2020-07-03 journal: Allergol Immunopathol (Madr) DOI: 10.1016/j.aller.2020.05.003 sha: doc_id: 295792 cord_uid: hajvtzj9 file: cache/cord-296031-r6iqiy1n.json key: cord-296031-r6iqiy1n authors: Tattan-Birch, H.; Perski, O.; Jackson, S. E.; Shahab, L.; West, R.; Brown, J. title: COVID-19, smoking, vaping and quitting: A representative population survey in England date: 2020-06-30 journal: nan DOI: 10.1101/2020.06.29.20142661 sha: doc_id: 296031 cord_uid: r6iqiy1n file: cache/cord-295144-tyyc81uc.json key: cord-295144-tyyc81uc authors: Stradner, Martin H.; Dejaco, Christian; Zwerina, Jochen; Fritsch-Stork, Ruth D. title: Rheumatic Musculoskeletal Diseases and COVID-19 A Review of the First 6 Months of the Pandemic date: 2020-10-09 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.562142 sha: doc_id: 295144 cord_uid: tyyc81uc file: cache/cord-295846-quhnesbr.json key: cord-295846-quhnesbr authors: Li, Huan; Chen, Chongxiang; Hu, Fang; Wang, Jiaojiao; Zhao, Qingyu; Gale, Robert Peter; Liang, Yang title: Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis date: 2020-05-05 journal: Leukemia DOI: 10.1038/s41375-020-0848-3 sha: doc_id: 295846 cord_uid: quhnesbr file: cache/cord-296128-kjoi54ea.json key: cord-296128-kjoi54ea authors: Balestri, Riccardo; Magnano, Michela; Rizzoli, Laura; Rech, Giulia title: Do we have serological evidences that chilblain‐like lesions are related to SARS‐CoV‐2? A review of the literature date: 2020-08-26 journal: Dermatol Ther DOI: 10.1111/dth.14229 sha: doc_id: 296128 cord_uid: kjoi54ea file: cache/cord-295946-p9enjxiq.json key: cord-295946-p9enjxiq authors: Hattori, Shin-ichiro; Higshi-Kuwata, Nobuyo; Raghavaiah, Jakka; Das, Debananda; Bulut, Haydar; Davis, David A.; Takamatsu, Yuki; Matsuda, Kouki; Takamune, Nobutoki; Kishimoto, Naoki; Okamura, Tadashi; Misumi, Shogo; Yarchoan, Robert; Maeda, Kenji; Ghosh, Arun K.; Mitsuya, Hiroaki title: GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection date: 2020-08-20 journal: mBio DOI: 10.1128/mbio.01833-20 sha: doc_id: 295946 cord_uid: p9enjxiq file: cache/cord-295957-s17z2ccf.json key: cord-295957-s17z2ccf authors: Bordi, Licia; Piralla, Antonio; Lalle, Eleonora; Giardina, Federica; Colavita, Francesca; Tallarita, Monica; Sberna, Giuseppe; Novazzi, Federica; Meschi, Silvia; Castilletti, Concetta; Brisci, Angela; Minnucci, Giulia; Tettamanzi, Veronica; Baldanti, Fausto; Capobianchi, Maria Rosaria title: Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay date: 2020-05-04 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104416 sha: doc_id: 295957 cord_uid: s17z2ccf file: cache/cord-296095-onereai5.json key: cord-296095-onereai5 authors: Vardhan, Seshu; Sahoo, Suban K. title: In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 date: 2020-07-28 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.103936 sha: doc_id: 296095 cord_uid: onereai5 file: cache/cord-295514-vhymj0rw.json key: cord-295514-vhymj0rw authors: Lim, Peter A; Ng, Yee Sien; Tay, Boon Keng title: Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: Severe acute respiratory syndrome date: 2004-08-01 journal: Arch Phys Med Rehabil DOI: 10.1016/j.apmr.2004.01.022 sha: doc_id: 295514 cord_uid: vhymj0rw file: cache/cord-295765-c7o2ukm6.json key: cord-295765-c7o2ukm6 authors: Silvas, Jesus A.; Jureka, Alexander S.; Nicolini, Anthony M.; Chvatal, Stacie A.; Basler, Christopher F. title: Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date: 2020-07-20 journal: bioRxiv DOI: 10.1101/2020.07.18.210211 sha: doc_id: 295765 cord_uid: c7o2ukm6 file: cache/cord-295431-p9iy7uaf.json key: cord-295431-p9iy7uaf authors: Atangana, Ernestine; Atangana, Abdon title: Facemasks simple but powerful weapons to protect against COVID-19 spread: Can they have sides effects? date: 2020-09-30 journal: Results Phys DOI: 10.1016/j.rinp.2020.103425 sha: doc_id: 295431 cord_uid: p9iy7uaf file: cache/cord-296020-kje1wiah.json key: cord-296020-kje1wiah authors: Patoulias, Dimitrios; Katsimardou, Alexandra; Papadopoulos, Christodoulos; Doumas, Michael title: Diabetes mellitus and SARS-CoV-2-related mortality: the impact of acute hyperglycemic crises and some further considerations date: 2020-08-20 journal: Acta Diabetol DOI: 10.1007/s00592-020-01593-7 sha: doc_id: 296020 cord_uid: kje1wiah file: cache/cord-296148-za3j19k5.json key: cord-296148-za3j19k5 authors: Rosenzweig, Ivana; Mitrečić, Dinko; Petanjek, Zdravko; Duffy, Bobby; Young, Allan H.; Nesbitt, Alexander D.; Morrell, Mary J. title: Does damage to hypothalamic paraventricular nucleus underlie symptoms of ultradian rhythm disorder and an increased anxiety in coronavirus disease 2019? date: 2020-08-17 journal: Croat Med J DOI: 10.3325/cmj.2020.61.377 sha: doc_id: 296148 cord_uid: za3j19k5 file: cache/cord-296187-nnv2e7gr.json key: cord-296187-nnv2e7gr authors: Mulgaonkar, Nirmitee; Wang, Haoqi; Mallawarachchi, Samavath; Fernando, Sandun; Martina, Byron; Ruzek, Daniel title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 journal: bioRxiv DOI: 10.1101/2020.06.18.158196 sha: doc_id: 296187 cord_uid: nnv2e7gr file: cache/cord-295864-kwdvais7.json key: cord-295864-kwdvais7 authors: Flahault, Antoine title: Has China faced only a herald wave of SARS-CoV-2? date: 2020-03-27 journal: The Lancet DOI: 10.1016/s0140-6736(20)30521-3 sha: doc_id: 295864 cord_uid: kwdvais7 file: cache/cord-296214-xeezt6f7.json key: cord-296214-xeezt6f7 authors: Sabatino, Jolanda; Moscatelli, Sara; Rustamova, Yasmin; Kotlar, Irina; Avesani, Martina; Brida, Margarita; Gök, Gülay; Borrelli, Nunzia; Marchenko, Oksana; Calvieri, Camilla; Czerwińska-Jelonkiewicz, Katarzyna; Moharem-Elgamal, Sarah; Grapsa, Julia; Öz, Tugba Kemaloğlu title: Women's perspective on the COVID-19 pandemic: Walking into a post-peak phase date: 2020-08-13 journal: Int J Cardiol DOI: 10.1016/j.ijcard.2020.08.025 sha: doc_id: 296214 cord_uid: xeezt6f7 file: cache/cord-296007-1gsgd22t.json key: cord-296007-1gsgd22t authors: Mohseni, Amir Hossein; Taghinezhad-S, Sedigheh; Su, Bing; Wang, Feng title: Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date: 2020-09-12 journal: bioRxiv DOI: 10.1101/2020.09.12.294413 sha: doc_id: 296007 cord_uid: 1gsgd22t file: cache/cord-296054-s8pibdeg.json key: cord-296054-s8pibdeg authors: Hanson, K. E.; Barker, A. P.; Hillyard, D. R.; Gilmore, N.; Barrett, J. W.; Orlandi, R. R.; Shakir, S. M. title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 date: 2020-10-21 journal: J Clin Microbiol DOI: 10.1128/jcm.01824-20 sha: doc_id: 296054 cord_uid: s8pibdeg file: cache/cord-296147-yfcp0xf2.json key: cord-296147-yfcp0xf2 authors: Mairesse, Antoine; Favresse, Julien; Eucher, Christine; Elsen, Marc; Tré-Hardy, Marie; Haventith, Caroline; Gruson, Damien; Dogné, Jean-Michel; Douxfils, Jonathan; Göbbels, Paul title: High clinical performance and quantitative assessment of antibody kinetics using a dual recognition assay for the detection of SARS-CoV-2 IgM and IgG antibodies date: 2020-08-25 journal: Clin Biochem DOI: 10.1016/j.clinbiochem.2020.08.009 sha: doc_id: 296147 cord_uid: yfcp0xf2 file: cache/cord-295850-nb6miso7.json key: cord-295850-nb6miso7 authors: Zhang, Chuan-hai; Lu, Jia-hai; Wang, Yi-fei; Zheng, Huan-ying; Xiong, Sheng; Zhang, Mei-ying; Liu, Xin-jian; Li, Jiu-xiang; Wan, Zhuo-yue; Yan, Xin-ge; Qi, Shu-Yuan; Cui, Zhiyong; Zhang, Biliang title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain date: 2005-05-02 journal: Vaccine DOI: 10.1016/j.vaccine.2004.11.073 sha: doc_id: 295850 cord_uid: nb6miso7 file: cache/cord-296195-m2wwlvgx.json key: cord-296195-m2wwlvgx authors: Chen, Chung-Jen; Michaelis, Martin; Hsu, Hseng-Kuang; Tsai, Chin-Chuan; Yang, Kunder D.; Wu, Yang-Chang; Cinatl, Jindrich; Doerr, Hans Wilhelm title: Toona sinensis Roem tender leaf extract inhibits SARS coronavirus replication date: 2008-10-30 journal: J Ethnopharmacol DOI: 10.1016/j.jep.2008.07.048 sha: doc_id: 296195 cord_uid: m2wwlvgx file: cache/cord-296109-kco85lqn.json key: cord-296109-kco85lqn authors: Vanuytsel, Kim; Mithal, Aditya; Giadone, Richard M.; Yeung, Anthony K.; Matte, Taylor M.; Dowrey, Todd W.; Werder, Rhiannon B.; Miller, Gregory J.; Miller, Nancy S.; Andry, Christopher D.; Murphy, George J. title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 journal: Med DOI: 10.1016/j.medj.2020.05.001 sha: doc_id: 296109 cord_uid: kco85lqn file: cache/cord-296219-zzg9hds0.json key: cord-296219-zzg9hds0 authors: Battaglini, Denise; Brunetti, Iole; Anania, Pasquale; Fiaschi, Pietro; Zona, Gianluigi; Ball, Lorenzo; Giacobbe, Daniele Roberto; Vena, Antonio; Bassetti, Matteo; Patroniti, Nicolò; Schenone, Angelo; Pelosi, Paolo; Rocco, Patricia R. M.; Robba, Chiara title: Neurological Manifestations of Severe SARS-CoV-2 Infection: Potential Mechanisms and Implications of Individualized Mechanical Ventilation Settings date: 2020-08-12 journal: Front Neurol DOI: 10.3389/fneur.2020.00845 sha: doc_id: 296219 cord_uid: zzg9hds0 file: cache/cord-295603-mk9oartb.json key: cord-295603-mk9oartb authors: Yu, Xiaoqi; Wei, Dong; Chen, Yongyan; Zhang, Donghua; Zhang, Xinxin title: Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness date: 2020-07-05 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1785952 sha: doc_id: 295603 cord_uid: mk9oartb file: cache/cord-295830-1sbnewog.json key: cord-295830-1sbnewog authors: Kim, Sung-Jae; Nguyen, Van-Giap; Park, Yong-Ho; Park, Bong-Kyun; Chung, Hee-Chun title: A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? date: 2020-05-14 journal: Vaccines (Basel) DOI: 10.3390/vaccines8020220 sha: doc_id: 295830 cord_uid: 1sbnewog file: cache/cord-296043-jc74soom.json key: cord-296043-jc74soom authors: Butterfield, T. R.; Bruce-Mowatt, A.; Phillips, Y. Z. R.; Brown, N.; Francis, K.; Brown, J.; Taylor, D.; Bruce, C. A.; McGrowder, D.; Wharfe, G.; Sandiford, S. L.; Thompson, T. K.; Anzinger, J. J. title: Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica date: 2020-09-29 journal: nan DOI: 10.1101/2020.09.27.20202655 sha: doc_id: 296043 cord_uid: jc74soom file: cache/cord-296227-dm1wkpnv.json key: cord-296227-dm1wkpnv authors: Liao, L.; Xiao, W.; Zhao, M.; Yu, X.; Wang, H.; Wang, Q.; Chu, S.; Cui, Y. title: Can N95 respirators be reused after disinfection? And for how many times? date: 2020-04-07 journal: nan DOI: 10.1101/2020.04.01.20050443 sha: doc_id: 296227 cord_uid: dm1wkpnv file: cache/cord-296259-4kdblf4z.json key: cord-296259-4kdblf4z authors: Oudit, Gavin Y; Pfeffer, Marc A title: Plasma angiotensin-converting enzyme 2: novel biomarker in heart failure with implications for COVID-19 date: 2020-05-14 journal: Eur Heart J DOI: 10.1093/eurheartj/ehaa414 sha: doc_id: 296259 cord_uid: 4kdblf4z file: cache/cord-296306-xcomjvaa.json key: cord-296306-xcomjvaa authors: Rivett, Lucy; Sridhar, Sushmita; Sparkes, Dominic; Routledge, Matthew; Jones, Nick K; Forrest, Sally; Young, Jamie; Pereira-Dias, Joana; Hamilton, William L; Ferris, Mark; Torok, M Estee; Meredith, Luke; Curran, Martin D; Fuller, Stewart; Chaudhry, Afzal; Shaw, Ashley; Samworth, Richard J; Bradley, John R; Dougan, Gordon; Smith, Kenneth GC; Lehner, Paul J; Matheson, Nicholas J; Wright, Giles; Goodfellow, Ian G; Baker, Stephen; Weekes, Michael P title: Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date: 2020-05-11 journal: eLife DOI: 10.7554/elife.58728 sha: doc_id: 296306 cord_uid: xcomjvaa file: cache/cord-296319-fwn97wds.json key: cord-296319-fwn97wds authors: Juno, J. A.; Tan, H.-X.; Lee, W. S.; Reynaldi, A.; Kelly, H. G.; Wragg, K.; Esterbauer, R.; Kent, H. E.; Batten, C. J.; Mordant, F. L.; Gherardin, N. A.; Pymm, P.; Dietrich, M. H.; Scott, N. E.; Tham, W.-H.; Godfrey, D. I.; Subbarao, K.; Davenport, M. P.; Kent, S. J.; Wheatley, A. K. title: Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19 date: 2020-05-21 journal: nan DOI: 10.1101/2020.05.17.20104869 sha: doc_id: 296319 cord_uid: fwn97wds file: cache/cord-296356-qkvafy69.json key: cord-296356-qkvafy69 authors: Garman, Elspeth title: SARS Proteomics Reveals Viral Secrets date: 2005-11-30 journal: Structure DOI: 10.1016/j.str.2005.10.004 sha: doc_id: 296356 cord_uid: qkvafy69 file: cache/cord-296362-9vi8xwu7.json key: cord-296362-9vi8xwu7 authors: Wang, Jian-Min; Wang, Lin-Fa; Shi, Zheng-Li title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function date: 2008-09-12 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2008.06.129 sha: doc_id: 296362 cord_uid: 9vi8xwu7 file: cache/cord-296268-kb7fgfaq.json key: cord-296268-kb7fgfaq authors: Mendonça, Luiza; Howe, Andrew; Gilchrist, James B.; Sun, Dapeng; Knight, Michael L.; Zanetti-Domingues, Laura C.; Bateman, Benji; Krebs, Anna-Sophia; Chen, Long; Radecke, Julika; Sheng, Yuewen; Li, Vivian D.; Ni, Tao; Kounatidis, Ilias; Koronfel, Mohamed A.; Szynkiewicz, Marta; Harkiolaki, Maria; Martin-Fernandez, Marisa L.; James, William; Zhang, Peijun title: SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.05.370239 sha: doc_id: 296268 cord_uid: kb7fgfaq file: cache/cord-296426-upwsdgso.json key: cord-296426-upwsdgso authors: Virmani, Sarthak; Gleeson, Shana E.; Girone, Gianna F.; Malhotra, Divyanshu; Cohen, Elizabeth A.; Klarman, Sharon E.; Asch, William S. title: Identifying a Kidney Transplant Recipient COVID Phenotype to Aid Test Utilization in the Setting of Limited Testing Availability - Does One Exist? date: 2020-06-20 journal: Transplant Proc DOI: 10.1016/j.transproceed.2020.05.033 sha: doc_id: 296426 cord_uid: upwsdgso file: cache/cord-295794-glcg36si.json key: cord-295794-glcg36si authors: Seghers, Victor J.; Desai, Nilesh K.; Masand, Prakash M.; Nasir, Sadia; Foster, Traci L.; Indiero, Dennis A.; Johnson, Trent D.; Huisman, Thierry A. G. M. title: After the initial COVID-19 surge: a phased radiology departmental re-opening plan date: 2020-08-22 journal: Pediatr Radiol DOI: 10.1007/s00247-020-04792-0 sha: doc_id: 295794 cord_uid: glcg36si file: cache/cord-296232-6zj99nuw.json key: cord-296232-6zj99nuw authors: Talukdar, Jayanta; Bhadra, Bhaskar; Dattaroy, Tomal; Nagle, Vinod; Dasgupta, Santanu title: Potential of natural astaxanthin in alleviating the risk of cytokine storm in COVID-19 date: 2020-10-16 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110886 sha: doc_id: 296232 cord_uid: 6zj99nuw file: cache/cord-296331-i4hyzqcv.json key: cord-296331-i4hyzqcv authors: Adapa, Sreedhar; Chenna, Avantika; Balla, Mamtha; Merugu, Ganesh Prasad; Koduri, Narayana Murty; Daggubati, Subba Rao; Gayam, Vijay; Naramala, Srikanth; Konala, Venu Madhav title: COVID-19 Pandemic Causing Acute Kidney Injury and Impact on Patients With Chronic Kidney Disease and Renal Transplantation date: 2020-06-04 journal: J Clin Med Res DOI: 10.14740/jocmr4200 sha: doc_id: 296331 cord_uid: i4hyzqcv file: cache/cord-296339-23yi8so0.json key: cord-296339-23yi8so0 authors: Mok, Wendy; Seto, Kelly; Stone, Jon title: Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens date: 2007-09-26 journal: Evol Bioinform Online DOI: nan sha: doc_id: 296339 cord_uid: 23yi8so0 file: cache/cord-296375-gf0mgz5x.json key: cord-296375-gf0mgz5x authors: Zhang, Xi; Rao, Huaxiang; Wu, Yuwan; Huang, Yubei; Dai, Hongji title: Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date: 2020-10-30 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05537-y sha: doc_id: 296375 cord_uid: gf0mgz5x file: cache/cord-296483-x95lwwnm.json key: cord-296483-x95lwwnm authors: Kranke, Peter; Weibel, Stephanie; Sitter, Magdalena; Meybohm, Patrick; Girard, Thierry title: Geburtshilfliche Anästhesie während der SARS-CoV-2-Pandemie: Übersicht der Handlungsempfehlungen date: 2020-04-09 journal: Anasthesiol Intensivmed Notfallmed Schmerzther DOI: 10.1055/a-1144-5562 sha: doc_id: 296483 cord_uid: x95lwwnm file: cache/cord-296556-fr8x8j3i.json key: cord-296556-fr8x8j3i authors: Chaccour, Carlos; Hammann, Felix; Ramón-García, Santiago; Rabinovich, N. Regina title: Ivermectin and COVID-19: Keeping Rigor in Times of Urgency date: 2020-04-16 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0271 sha: doc_id: 296556 cord_uid: fr8x8j3i file: cache/cord-296388-ayfdsn07.json key: cord-296388-ayfdsn07 authors: Maziarz, Mariusz; Zach, Martin title: Agent‐based modelling for SARS‐CoV‐2 epidemic prediction and intervention assessment: A methodological appraisal date: 2020-08-21 journal: J Eval Clin Pract DOI: 10.1111/jep.13459 sha: doc_id: 296388 cord_uid: ayfdsn07 file: cache/cord-296250-7ln7p715.json key: cord-296250-7ln7p715 authors: Wang, Sheng-Fan; Chen, Kuan-Hsuan; Wang, Szu-Yu; Yarmishyn, Aliaksandr A.; Lai, Wei-Yi; Lin, Yi-Ying; Wang, Mong-Lien; Chou, Shih-Jie; Yang, Yi-Ping; Chang, Yuh-Lih title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date: 2020-05-20 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000353 sha: doc_id: 296250 cord_uid: 7ln7p715 file: cache/cord-296271-85io9yvy.json key: cord-296271-85io9yvy authors: Chong, Woon H.; Saha, Biplab title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) date: 2020-07-28 journal: Am J Med Sci DOI: 10.1016/j.amjms.2020.07.032 sha: doc_id: 296271 cord_uid: 85io9yvy file: cache/cord-296494-6kn4mr04.json key: cord-296494-6kn4mr04 authors: Saban-Ruiz, J.; Ly-Pen, D. title: COVID-19: A Personalized Cardiometabolic Approach for Reducing Complications and Costs. The Role of Aging Beyond Topics date: 2020-05-12 journal: J Nutr Health Aging DOI: 10.1007/s12603-020-1385-5 sha: doc_id: 296494 cord_uid: 6kn4mr04 file: cache/cord-296378-ki93iltt.json key: cord-296378-ki93iltt authors: Smith, Joan C.; Sausville, Erin L.; Girish, Vishruth; Yuan, Monet Lou; Vasudevan, Anand; John, Kristen M.; Sheltzer, Jason M. title: Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract date: 2020-05-16 journal: Dev Cell DOI: 10.1016/j.devcel.2020.05.012 sha: doc_id: 296378 cord_uid: ki93iltt file: cache/cord-296237-i9cti2ok.json key: cord-296237-i9cti2ok authors: Díez, José-María; Romero, Carolina; Vergara-Alert, Júlia; Belló-Perez, Melissa; Rodon, Jordi; Honrubia, José Manuel; Segalés, Joaquim; Sola, Isabel; Enjuanes, Luis; Gajardo, Rodrigo title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-06-19 journal: bioRxiv DOI: 10.1101/2020.06.19.160879 sha: doc_id: 296237 cord_uid: i9cti2ok file: cache/cord-296619-uhhndp0a.json key: cord-296619-uhhndp0a authors: Kondo, Yuki; Miyazaki, Shinichi; Yamashita, Ryo; Ikeda, Takuya title: Coinfection with SARS-CoV-2 and influenza A virus date: 2020-07-01 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-236812 sha: doc_id: 296619 cord_uid: uhhndp0a file: cache/cord-296551-efqt3tw2.json key: cord-296551-efqt3tw2 authors: Fukushi, Shuetsu; Watanabe, Rie; Taguchi, Fumihiro title: Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry Mediated by SARS Coronavirus Spike Proteins date: 2007-11-28 journal: SARS- and Other Coronaviruses DOI: 10.1007/978-1-59745-181-9_23 sha: doc_id: 296551 cord_uid: efqt3tw2 file: cache/cord-296588-q2716lda.json key: cord-296588-q2716lda authors: Hanson, Kimberly E; Caliendo, Angela M; Arias, Cesar A; Englund, Janet A; Lee, Mark J; Loeb, Mark; Patel, Robin; El Alayli, Abdallah; Kalot, Mohamad A; Falck-Ytter, Yngve; Lavergne, Valery; Morgan, Rebecca L; Murad, M Hassan; Sultan, Shahnaz; Bhimraj, Adarsh; Mustafa, Reem A title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa760 sha: doc_id: 296588 cord_uid: q2716lda file: cache/cord-296392-2u9mz6d3.json key: cord-296392-2u9mz6d3 authors: Sarıgül, Figen; Doluca, Osman; Akhan, Sıla; Sayan, Murat title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 journal: Future virology DOI: 10.2217/fvl-2020-0169 sha: doc_id: 296392 cord_uid: 2u9mz6d3 file: cache/cord-296492-knofua00.json key: cord-296492-knofua00 authors: Qiu, L.; Chen, S.; Wang, C.; Liu, C.; Wang, H.; Zhao, X.; Fang, Z.; Chang, S.; Zhao, G.; Zhang, G. title: Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province date: 2020-07-07 journal: nan DOI: 10.1101/2020.07.06.20147264 sha: doc_id: 296492 cord_uid: knofua00 file: cache/cord-296517-414grqif.json key: cord-296517-414grqif authors: Wong, Gary; Liu, Wenjun; Liu, Yingxia; Zhou, Boping; Bi, Yuhai; Gao, George F. title: MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease date: 2015-10-14 journal: Cell Host & Microbe DOI: 10.1016/j.chom.2015.09.013 sha: doc_id: 296517 cord_uid: 414grqif file: cache/cord-296579-oa67njov.json key: cord-296579-oa67njov authors: d’Ettorre, Gabriella; Recchia, Gregorio; Ridolfi, Marco; Siccardi, Guido; Pinacchio, Claudia; Innocenti, Giuseppe Pietro; Santinelli, Letizia; Frasca, Federica; Bitossi, Camilla; Ceccarelli, Giancarlo; Borrazzo, Cristian; Antonelli, Guido; Scagnolari, Carolina; Mastroianni, Claudio Maria title: Analysis of type I IFN response and T cell activation in severe COVID-19/HIV-1 coinfection: A case report date: 2020-09-04 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000021803 sha: doc_id: 296579 cord_uid: oa67njov file: cache/cord-296390-jv86w4j9.json key: cord-296390-jv86w4j9 authors: Shao, Chen; Liu, Hui; Meng, Lingjia; Sun, Lin; Wang, Yankun; Yue, Zhujun; Kong, Heli; Li, Hongjun; Weng, Honglei; Lv, Fudong; Jin, Ronghua title: Evolution of SARS-Co-2 RNA test results in a fatal Covid-19 patient: a case report date: 2020-05-11 journal: Hum Pathol DOI: 10.1016/j.humpath.2020.04.015 sha: doc_id: 296390 cord_uid: jv86w4j9 file: cache/cord-296605-p67twx7a.json key: cord-296605-p67twx7a authors: LAU, Arthur Chun-Wing; YAM, Loretta Yin-Chun; SO, Loletta Kit-Ying title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date: 2004-03-10 journal: Int J Med Sci DOI: nan sha: doc_id: 296605 cord_uid: p67twx7a file: cache/cord-296657-mymndjvd.json key: cord-296657-mymndjvd authors: Higuchi, Yusuke; Suzuki, Tatsuya; Arimori, Takao; Ikemura, Nariko; Kirita, Yuhei; Ohgitani, Eriko; Mazda, Osam; Motooka, Daisuke; Nakamura, Shota; Matsuura, Yoshiharu; Matoba, Satoaki; Okamoto, Toru; Takagi, Junichi; Hoshino, Atsushi title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 journal: bioRxiv DOI: 10.1101/2020.09.16.299891 sha: doc_id: 296657 cord_uid: mymndjvd file: cache/cord-296692-t5p09le8.json key: cord-296692-t5p09le8 authors: Elgin, T.G.; Fricke, E.M.; Hernandez Reyes, M.E.; Tsimis, M.E.; Leslein, N.S.; Thomas, B.A.; Sato, T.S.; McNamara, P.J. title: The changing landscape of SARS-CoV-2: Implications for the maternal-infant dyad date: 2020-09-07 journal: Journal of neonatal-perinatal medicine DOI: 10.3233/npm-200460 sha: doc_id: 296692 cord_uid: t5p09le8 file: cache/cord-296602-19noki6p.json key: cord-296602-19noki6p authors: Law, Helen KW; Cheung, Chung Yan; Sia, Sin Fun; Chan, Yuk On; Peiris, JS Malik; Lau, Yu Lung title: Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells date: 2009-06-08 journal: BMC Immunol DOI: 10.1186/1471-2172-10-35 sha: doc_id: 296602 cord_uid: 19noki6p file: cache/cord-296649-h6oyjz56.json key: cord-296649-h6oyjz56 authors: Scherf-Clavel, Oliver; Kaczmarek, Edith; Kinzig, Martina; Friedl, Bettina; Feja, Malte; Höhl, Rainer; Nau, Roland; Holzgrabe, Ulrike; Gernert, Manuela; Richter, Franziska; Sörgel, Fritz title: Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date: 2020-11-06 journal: bioRxiv DOI: 10.1101/2020.09.16.299537 sha: doc_id: 296649 cord_uid: h6oyjz56 file: cache/cord-296676-2anl2agl.json key: cord-296676-2anl2agl authors: Goldberg, Michael F.; Goldberg, Morton F. title: Neuroradiologic manifestations of COVID-19: what the emergency radiologist needs to know date: 2020-08-21 journal: Emerg Radiol DOI: 10.1007/s10140-020-01840-y sha: doc_id: 296676 cord_uid: 2anl2agl file: cache/cord-296440-18vpg419.json key: cord-296440-18vpg419 authors: Beurnier, Antoine; Jutant, Etienne-Marie; Jevnikar, Mitja; Boucly, Athénaïs; Pichon, Jérémie; Preda, Mariana; Frank, Marie; Laurent, Jérémy; Richard, Christian; Monnet, Xavier; Duranteau, Jacques; Harrois, Anatole; Chaumais, Marie-Camille; Bellin, Marie-France; Noël, Nicolas; Bulifon, Sophie; Jaïs, Xavier; Parent, Florence; Seferian, Andrei; Savale, Laurent; Sitbon, Olivier; Montani, David; Humbert, Marc title: Characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who require hospitalisation date: 2020-07-30 journal: Eur Respir J DOI: 10.1183/13993003.01875-2020 sha: doc_id: 296440 cord_uid: 18vpg419 file: cache/cord-296917-yk574m99.json key: cord-296917-yk574m99 authors: Kumar, Sathish; Kapoor, Lalit; Barman, Dhiraj; Narayan, Pradeep title: Aerosol‐mediated transmission of SARS‐Cov‐2 or COVID‐19 in the cardiac surgical operating room date: 2020-07-11 journal: J Card Surg DOI: 10.1111/jocs.14728 sha: doc_id: 296917 cord_uid: yk574m99 file: cache/cord-296672-i267t23m.json key: cord-296672-i267t23m authors: Wang, Shui-Mei; Chang, Yu-Fen; Chen, Yi-Ming Arthur; Wang, Chin-Tien title: Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain date: 2008-07-01 journal: J Biomed Sci DOI: 10.1007/s11373-008-9265-8 sha: doc_id: 296672 cord_uid: i267t23m file: cache/cord-296977-yzhsdz9c.json key: cord-296977-yzhsdz9c authors: Soares, R. R. G.; Akhtar, A. S.; Pinto, I. F.; Lapins, N.; Barrett, D.; Sandh, G.; Yin, X.; Pelechano, V.; Russom, A. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 journal: nan DOI: 10.1101/2020.11.04.20225888 sha: doc_id: 296977 cord_uid: yzhsdz9c file: cache/cord-296950-9dldbs6o.json key: cord-296950-9dldbs6o authors: El-Zein, Rayan S; Cardinali, Serge; Murphy, Christie; Keeling, Thomas title: COVID-19-associated meningoencephalitis treated with intravenous immunoglobulin date: 2020-09-06 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-237364 sha: doc_id: 296950 cord_uid: 9dldbs6o file: cache/cord-296986-8fuj072z.json key: cord-296986-8fuj072z authors: Kumar, Manish; Taki, Kaling; Gahlot, Rohit; Sharma, Ayushi; Dhangar, Kiran title: A chronicle of SARS-CoV-2: Part-I - Epidemiology, diagnosis, prognosis, transmission and treatment date: 2020-05-15 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.139278 sha: doc_id: 296986 cord_uid: 8fuj072z file: cache/cord-296762-sc6crkkw.json key: cord-296762-sc6crkkw authors: Ali, Fedaa; Elserafy, Menattallah; Alkordi, Mohamed H.; Amin, Muhamed title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-08-20 journal: Biochem Biophys Rep DOI: 10.1016/j.bbrep.2020.100798 sha: doc_id: 296762 cord_uid: sc6crkkw file: cache/cord-296881-2g81sjnl.json key: cord-296881-2g81sjnl authors: Nabil, Ahmed; Uto, Koichiro; Elshemy, Mohamed M.; Soliman, Reham; Hassan, Ayman A.; Ebara, Mitsuhiro; Shiha, Gamal title: Current coronavirus (SARS-CoV-2) epidemiological, diagnostic and therapeutic approaches: An updated review until June 2020 date: 2020-07-20 journal: EXCLI J DOI: 10.17179/excli2020-2554 sha: doc_id: 296881 cord_uid: 2g81sjnl file: cache/cord-296767-mgr32ftl.json key: cord-296767-mgr32ftl authors: Große, Karsten; Kramer, Matthijs; Trautwein, Christian; Bruns, Tony title: SARS‐CoV‐2 as an extrahepatic precipitator of acute‐on‐chronic liver failure date: 2020-05-29 journal: Liver Int DOI: 10.1111/liv.14540 sha: doc_id: 296767 cord_uid: mgr32ftl file: cache/cord-296981-tded20ih.json key: cord-296981-tded20ih authors: Gilmore, Kerry; Zhou, Yuyong; Ramirez, Santseharay; Pham, Long V.; Fahnøe, Ulrik; Feng, Shan; Offersgaard, Anna; Trimpert, Jakob; Bukh, Jens; Osterrieder, Klaus; Gottwein, Judith M.; Seeberger, Peter H. title: In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date: 2020-10-05 journal: bioRxiv DOI: 10.1101/2020.10.05.326637 sha: doc_id: 296981 cord_uid: tded20ih file: cache/cord-297072-f5lmstyn.json key: cord-297072-f5lmstyn authors: Struck, Anna-Winona; Axmann, Marco; Pfefferle, Susanne; Drosten, Christian; Meyer, Bernd title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 date: 2012-01-16 journal: Antiviral Res DOI: 10.1016/j.antiviral.2011.12.012 sha: doc_id: 297072 cord_uid: f5lmstyn file: cache/cord-296997-ba7f2mf3.json key: cord-296997-ba7f2mf3 authors: Sikora, Mateusz; von Bülow, Sören; Blanc, Florian E. C.; Gecht, Michael; Covino, Roberto; Hummer, Gerhard title: Map of SARS-CoV-2 spike epitopes not shielded by glycans date: 2020-07-03 journal: bioRxiv DOI: 10.1101/2020.07.03.186825 sha: doc_id: 296997 cord_uid: ba7f2mf3 file: cache/cord-297023-0qlo0mun.json key: cord-297023-0qlo0mun authors: Park, Sung‐Soo; Oh, Hye-Young; Hong, Duck‐Jin title: Mass screening of healthcare personnel for SARS-CoV-2 in the northern emirates date: 2020-10-17 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.10.008 sha: doc_id: 297023 cord_uid: 0qlo0mun file: cache/cord-297168-t6zf5k99.json key: cord-297168-t6zf5k99 authors: Brüssow, Harald title: The Novel Coronavirus – A Snapshot of Current Knowledge date: 2020-03-06 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13557 sha: doc_id: 297168 cord_uid: t6zf5k99 file: cache/cord-297127-nhgm09db.json key: cord-297127-nhgm09db authors: Hasseli, Rebecca; Mueller-Ladner, Ulf; Schmeiser, Tim; Hoyer, Bimba F; Krause, Andreas; Lorenz, Hanns-Martin; Regierer, Anne Constanze; Richter, Jutta G; Strangfeld, Anja; Voll, Reinhard E; Pfeil, Alexander; Schulze-Koops, Hendrik; Specker, Christof title: National registry for patients with inflammatory rheumatic diseases (IRD) infected with SARS-CoV-2 in Germany (ReCoVery): a valuable mean to gain rapid and reliable knowledge of the clinical course of SARS-CoV-2 infections in patients with IRD date: 2020-09-02 journal: RMD Open DOI: 10.1136/rmdopen-2020-001332 sha: doc_id: 297127 cord_uid: nhgm09db file: cache/cord-297197-klr208kp.json key: cord-297197-klr208kp authors: Weizman, Yehuda; Tan, Adin M.; Konstantin, Franz F. title: Use of Wearable Technology to Enhance Response to the COVID-19 Pandemic date: 2020-07-01 journal: Public Health DOI: 10.1016/j.puhe.2020.06.048 sha: doc_id: 297197 cord_uid: klr208kp file: cache/cord-297202-oup8ptya.json key: cord-297202-oup8ptya authors: Beer, Martin; Doherr, Marcus; Osterrieder, Klaus; Pfeiffer, Dirk; Trimpert, Jakob title: SARS‐CoV‐2 vaccination—A plea for fast and coordinated action date: 2020-07-01 journal: Zoonoses Public Health DOI: 10.1111/zph.12740 sha: doc_id: 297202 cord_uid: oup8ptya file: cache/cord-297217-pe6mehjv.json key: cord-297217-pe6mehjv authors: Simpson, A. Hamish R. W.; Dall, Graham; Haas, Jürgen G. title: COVID-19: potential transmission through aerosols in surgical procedures and blood products date: 2020-07-23 journal: Bone Joint Res DOI: 10.1302/2046-3758.94.bjr-2020-0130 sha: doc_id: 297217 cord_uid: pe6mehjv file: cache/cord-297132-lhfa9fl5.json key: cord-297132-lhfa9fl5 authors: Aghagoli, Ghazal; Gallo Marin, Benjamin; Katchur, Nicole J.; Chaves-Sell, Franz; Asaad, Wael F.; Murphy, Sarah A. title: Neurological Involvement in COVID-19 and Potential Mechanisms: A Review date: 2020-07-13 journal: Neurocrit Care DOI: 10.1007/s12028-020-01049-4 sha: doc_id: 297132 cord_uid: lhfa9fl5 file: cache/cord-297326-n0fpu8s3.json key: cord-297326-n0fpu8s3 authors: ÁLVAREZ, E.; DONADO-CAMPOS, J.; MORILLA, F. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 journal: Epidemiol Infect DOI: 10.1017/s095026881400377x sha: doc_id: 297326 cord_uid: n0fpu8s3 file: cache/cord-296661-6ndn2qxc.json key: cord-296661-6ndn2qxc authors: Lu, Dingnan; Huang, Zhuangrong; Luo, Jiayue; Zhang, Xiaoqi; Sha, Sha title: Primary concentration – The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review date: 2020-07-25 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141245 sha: doc_id: 296661 cord_uid: 6ndn2qxc file: cache/cord-297208-f4ob3ox6.json key: cord-297208-f4ob3ox6 authors: Pisano, Antonio; Landoni, Giovanni; Verniero, Luigi; Zangrillo, Alberto title: Cardiothoracic surgery at the time of COVID-19 pandemic: lessons from the East (and from a previous epidemic) for western battlefields date: 2020-05-06 journal: J Cardiothorac Vasc Anesth DOI: 10.1053/j.jvca.2020.04.051 sha: doc_id: 297208 cord_uid: f4ob3ox6 file: cache/cord-297256-i9468t8v.json key: cord-297256-i9468t8v authors: Cesari, Matteo; Proietti, M. title: Geriatric Medicine in Italy in the Time of Covid-19 date: 2020-04-03 journal: J Nutr Health Aging DOI: 10.1007/s12603-020-1354-z sha: doc_id: 297256 cord_uid: i9468t8v file: cache/cord-297439-xg0pkjrh.json key: cord-297439-xg0pkjrh authors: Gao, Jing; Liu, Jun-Qiang; Wen, Heng-Jun; Liu, Hua; Hu, Wei-Dong; Han, Xia; Li, Chuan-Xing; Wang, Xiao-Jun title: The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China date: 2020-04-22 journal: Respir Res DOI: 10.1186/s12931-020-01363-7 sha: doc_id: 297439 cord_uid: xg0pkjrh file: cache/cord-297324-me5ff1pb.json key: cord-297324-me5ff1pb authors: Zeng, Rong; Yang, Rui-Fu; Shi, Mu-De; Jiang, Man-Rong; Xie, You-Hua; Ruan, Hong-Qiang; Jiang, Xiao-Sheng; Shi, Lv; Zhou, Hu; Zhang, Lei; Wu, Xiao-Dong; Lin, Ying; Ji, Yong-Yong; Xiong, Lei; Jin, Yan; Dai, Er-Hei; Wang, Xiao-Yi; Si, Bin-Ying; Wang, Jin; Wang, Hong-Xia; Wang, Cui-E; Gan, Yong-Hua; Li, Yu-Chuan; Cao, Ju-Tian; Zuo, Jiang-Ping; Shan, Shi-Fang; Xie, En; Chen, Song-Hua; Jiang, Zhi-Qin; Zhang, Xi; Wang, Yuan; Pei, Gang; Sun, Bing; Wu, Jia-Rui title: Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date: 2004-07-30 journal: J Mol Biol DOI: 10.1016/j.jmb.2004.06.016 sha: doc_id: 297324 cord_uid: me5ff1pb file: cache/cord-297178-moxhk2e0.json key: cord-297178-moxhk2e0 authors: Novaes Rocha, Vinicius title: Viral replication of SARS-CoV-2 could be self-limitative - the role of the renin-angiotensin system on COVID-19 pathophysiology date: 2020-10-01 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110330 sha: doc_id: 297178 cord_uid: moxhk2e0 file: cache/cord-297323-l3f12hg4.json key: cord-297323-l3f12hg4 authors: Amor, Sandra; Fernández Blanco, Laura; Baker, David title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 journal: Clin Exp Immunol DOI: 10.1111/cei.13523 sha: doc_id: 297323 cord_uid: l3f12hg4 file: cache/cord-297423-iefq0fh0.json key: cord-297423-iefq0fh0 authors: Bushman, Dena; Alroy, Karen A.; Greene, Sharon K.; Keating, Page; Wahnich, Amanda; Weiss, Don; Pathela, Preeti; Harrison, Christy; Rakeman, Jennifer; Langley, Gayle; Tong, Suxiang; Tao, Ying; Uehara, Anna; Queen, Krista; Paden, Clinton R.; Szymczak, Wendy; Orner, Erika P.; Nori, Priya; Lai, Phi A.; Jacobson, Jessica L.; Singh, Harjot K.; Calfee, David P.; Westblade, Lars F.; Vasovic, Ljiljana V.; Rand, Jacob H.; Liu, Dakai; Singh, Vishnu; Burns, Janice; Prasad, Nishant; Sell, Jessica title: Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020 date: 2020-07-17 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6928a5 sha: doc_id: 297423 cord_uid: iefq0fh0 file: cache/cord-297209-84gs67bn.json key: cord-297209-84gs67bn authors: Livanos, A. E.; Jha, D.; Cossarini, F.; Gonzalez-Reiche, A. S.; Tokuyama, M.; Aydillo, T.; Parigi, T. L.; Ramos, I.; Dunleavy, K.; Lee, B.; Dixon, R.; Chen, S. T.; Martinez-Delgado, G.; Nagula, S.; Ko, H. M.; Reidy, J.; Naymagon, S.; Grinspan, A.; Ahmad, J.; Tankelevich, M.; Gordon, R.; Sharma, K.; Britton, G. J.; Chen-Liaw, A.; Spindler, M. P.; Plitt, T.; Wang, P.; Cerutti, A.; Faith, J. J.; Colombel, J.-F.; Kenigsberg, E.; Argmann, C.; Merad, M.; Gnjatic, S.; Harpaz, N.; Danese, S.; Rahman, A.; Kumta, N. A.; Aghemo, A.; Petralia, F.; van Bakel, H.; Garcia-Sastre, A.; Mehandru, S. title: Gastrointestinal involvement attenuates COVID-19 severity and mortality date: 2020-09-09 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.09.07.20187666 sha: doc_id: 297209 cord_uid: 84gs67bn file: cache/cord-297236-wnuvofwr.json key: cord-297236-wnuvofwr authors: Zhang, Si; Liu, Yangyang; Wang, Xiaofang; Yang, Li; Li, Haishan; Wang, Yuyan; Liu, Mengduan; Zhao, Xiaoyan; Xie, Youhua; Yang, Yan; Zhang, Shenghui; Fan, Zhichao; Dong, Jianzeng; Yuan, Zhenghong; Ding, Zhongren; Zhang, Yi; Hu, Liang title: SARS-CoV-2 binds platelet ACE2 to enhance thrombosis in COVID-19 date: 2020-09-04 journal: J Hematol Oncol DOI: 10.1186/s13045-020-00954-7 sha: doc_id: 297236 cord_uid: wnuvofwr file: cache/cord-297327-19dfgfz6.json key: cord-297327-19dfgfz6 authors: Drożdżal, Sylwester; Rosik, Jakub; Lechowicz, Kacper; Machaj, Filip; Szostak, Bartosz; Majewski, Paweł; Rotter, Iwona; Kotfis, Katarzyna title: COVID-19: Pain Management in Patients with SARS-CoV-2 Infection—Molecular Mechanisms, Challenges, and Perspectives date: 2020-07-20 journal: Brain Sci DOI: 10.3390/brainsci10070465 sha: doc_id: 297327 cord_uid: 19dfgfz6 file: cache/cord-297418-36j840wm.json key: cord-297418-36j840wm authors: Carneiro Leão, Jair; Paula de Lima Gusmão, Teresa; Machado Zarzar, Adriana; Leão Filho, Jair Carneiro; Barkokebas Santos de Faria, Andreza; Morais Silva, Igor Henrique; Gueiros, Luiz Alcino Monteiro; Robinson, Narendran Andrew; Porter, Stephen; de Albuquerque Tavares Carvalho, Alessandra title: Coronaviridae ‐ old friends, new enemy! date: 2020-05-31 journal: Oral Dis DOI: 10.1111/odi.13447 sha: doc_id: 297418 cord_uid: 36j840wm file: cache/cord-297432-2edncbgn.json key: cord-297432-2edncbgn authors: Helleberg, Marie; Niemann, Carsten Utoft; Moestrup, Kasper Sommerlund; Kirk, Ole; Lebech, Anne-Mette; Lane, Clifford; Lundgren, Jens title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 journal: J Infect Dis DOI: 10.1093/infdis/jiaa446 sha: doc_id: 297432 cord_uid: 2edncbgn file: cache/cord-297630-eabtzfd0.json key: cord-297630-eabtzfd0 authors: Manganaro, Marco; Baldovino, Simone title: First considerations on the SARS-CoV-2 epidemic in the Dialysis Units of Piedmont and Aosta Valley, Northern Italy date: 2020-04-10 journal: J Nephrol DOI: 10.1007/s40620-020-00732-1 sha: doc_id: 297630 cord_uid: eabtzfd0 file: cache/cord-297365-11es4w0u.json key: cord-297365-11es4w0u authors: Peng, Hui; Gao, Ping; Xu, Qiong; Liu, Maochang; Peng, Jing; Wang, Yang; Xu, Hua title: Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes date: 2020-05-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104425 sha: doc_id: 297365 cord_uid: 11es4w0u file: cache/cord-297381-1upz6dsy.json key: cord-297381-1upz6dsy authors: Sánchez‐Duque, Jorge A.; Orozco‐Hernández, Juan Pablo; Marín‐Medina, Daniel S.; Cvetkovic‐Vega, Aleksandar; Aveiro‐Róbalo, Telmo Raul; Mondragon‐Cardona, Alvaro; Failoc‐Rojas, Virgilio E.; Gutiérrez‐Ocampo, Estefanía; Villamizar‐Peña, Rhuvi; Henao‐Martínez, Juan F.; Arteaga‐Livias, Kovy; Rodríguez‐Morales, Alfonso J. title: Are we now observing an increasing number of coinfections between SARS‐CoV‐2 and other respiratory pathogens? date: 2020-05-29 journal: J Med Virol DOI: 10.1002/jmv.26089 sha: doc_id: 297381 cord_uid: 1upz6dsy file: cache/cord-297652-ut6e1ysz.json key: cord-297652-ut6e1ysz authors: Vanden Eynde, Jean Jacques title: COVID-19: A Brief Overview of the Discovery Clinical Trial date: 2020-04-10 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph13040065 sha: doc_id: 297652 cord_uid: ut6e1ysz file: cache/cord-297684-9q3oopaz.json key: cord-297684-9q3oopaz authors: Dobaño, Carlota; Vidal, Marta; Santano, Rebeca; Jiménez, Alfons; Chi, Jordi; Barrios, Diana; Ruiz-Olalla, Gemma; Melero, Natalia Rodrigo; Carolis, Carlo; Parras, Daniel; Serra, Pau; de Aguirre, Paula Martínez; Carmona-Torre, Francisco; Reina, Gabriel; Santamaria, Pere; Mayor, Alfredo; García-Basteiro, Alberto; Izquierdo, Luis; Aguilar, Ruth; Moncunill, Gemma title: Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date: 2020-06-12 journal: bioRxiv DOI: 10.1101/2020.06.11.147363 sha: doc_id: 297684 cord_uid: 9q3oopaz file: cache/cord-297332-rzf0cw1x.json key: cord-297332-rzf0cw1x authors: Wang, Qidi; Zhang, Lianfeng; Kuwahara, Kazuhiko; Li, Li; Liu, Zijie; Li, Taisheng; Zhu, Hua; Liu, Jiangning; Xu, Yanfeng; Xie, Jing; Morioka, Hiroshi; Sakaguchi, Nobuo; Qin, Chuan; Liu, Gang title: Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates date: 2016-04-11 journal: ACS Infectious Diseases DOI: 10.1021/acsinfecdis.6b00006 sha: doc_id: 297332 cord_uid: rzf0cw1x file: cache/cord-297599-y4lu8m4k.json key: cord-297599-y4lu8m4k authors: Luo, Hua; Zhao, Mingming; Tan, Dechao; Liu, Chang; Yang, Lin; Qiu, Ling; Gao, Yan; Yu, Hua title: Anti-COVID-19 drug screening: Frontier concepts and core technologies date: 2020-10-28 journal: Chin Med DOI: 10.1186/s13020-020-00393-z sha: doc_id: 297599 cord_uid: y4lu8m4k file: cache/cord-297826-2nruf2g7.json key: cord-297826-2nruf2g7 authors: Tian, Jing-Hui; Patel, Nita; Haupt, Robert; Zhou, Haixia; Weston, Stuart; Hammond, Holly; Lague, James; Portnoff, Alyse D.; Norton, James; Guebre-Xabier, Mimi; Zhou, Bin; Jacobson, Kelsey; Maciejewski, Sonia; Khatoon, Rafia; Wisniewska, Malgorzata; Moffitt, Will; Kluepfel-Stahl, Stefanie; Ekechukwu, Betty; Papin, James; Boddapati, Sarathi; Wong, C. Jason; Piedra, Pedro A.; Frieman, Matthew B.; Massare, Michael J.; Fries, Louis; Lövgren Bengtsson, Karin; Stertman, Linda; Ellingsworth, Larry; Glenn, Gregory; Smith, Gale title: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date: 2020-06-30 journal: bioRxiv DOI: 10.1101/2020.06.29.178509 sha: doc_id: 297826 cord_uid: 2nruf2g7 file: cache/cord-297463-mmmwi8de.json key: cord-297463-mmmwi8de authors: Hsu, You-Ren; Lee, Geng-Yen; Chyi, Jen-Inn; Chang, Chung-ke; Huang, Chih-Cheng; Hsu, Chen-Pin; Huang, Tai-huang; Ren, Fan; Wang, Yu-Lin title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors date: 2013-03-15 journal: ECS Trans DOI: 10.1149/05006.0239ecst sha: doc_id: 297463 cord_uid: mmmwi8de file: cache/cord-297702-vxcj25sn.json key: cord-297702-vxcj25sn authors: Chen, Yuxin; Tong, Xin; Li, Yang; Gu, Bin; Yan, Jiawei; Liu, Yong; Shen, Han; Huang, Rui; Wu, Chao title: A comprehensive, longitudinal analysis of humoral responses specific to four recombinant antigens of SARS-CoV-2 in severe and non-severe COVID-19 patients date: 2020-09-10 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008796 sha: doc_id: 297702 cord_uid: vxcj25sn file: cache/cord-297451-p5rlquym.json key: cord-297451-p5rlquym authors: Luz María Trujillo, G; Salima Valenzuela, F; Astrid von Oetinger, G title: Relación Entre Covid-19 Y Síndrome De Guillain-Barre En Adultos.Revisión Sistemática date: 2020-07-24 journal: Neurologia DOI: 10.1016/j.nrl.2020.07.004 sha: doc_id: 297451 cord_uid: p5rlquym file: cache/cord-297470-lx3xwg92.json key: cord-297470-lx3xwg92 authors: Pan, Yunbao; Li, Xinran; Yang, Gui; Fan, Junli; Tang, Yueting; Hong, Xiaoyue; Guo, Shuang; Li, Jin; Yao, Dongai; Cheng, Zhenshun; Yuan, Yufeng; Li, Yirong; Wang, Xinghuan title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date: 2020-10-07 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.044 sha: doc_id: 297470 cord_uid: lx3xwg92 file: cache/cord-297786-jz1d1m2e.json key: cord-297786-jz1d1m2e authors: Hasan, Md. Mahbub; Das, Rasel; Rasheduzzaman, Md.; Hussain, Md Hamed; Muzahid, Nazmul Hasan; Salauddin, Asma; Rumi, Meheadi Hasan; Rashid, S M Mahbubur; Siddiki, AMAM Zonaed; Mannan, Adnan title: Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date: 2020-08-26 journal: bioRxiv DOI: 10.1101/2020.08.25.267658 sha: doc_id: 297786 cord_uid: jz1d1m2e file: cache/cord-297708-uocs65sl.json key: cord-297708-uocs65sl authors: Alders, N.; Penner, J.; Grant, K.; Patterson, C.; Hassell, J.; MacDermott, N.; Pincott, S.; Bamford, A.; du Pre, P.; Johnson, M.; Moshal, K. title: COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected date: 2020-08-22 journal: nan DOI: 10.1101/2020.08.20.20178541 sha: doc_id: 297708 cord_uid: uocs65sl file: cache/cord-297671-3d3gcn6k.json key: cord-297671-3d3gcn6k authors: Venn, April M.R.; Schmidt, James M.; Mullan, Paul C. title: A case series of pediatric croup with COVID-19 date: 2020-09-15 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.09.034 sha: doc_id: 297671 cord_uid: 3d3gcn6k file: cache/cord-297832-picpuzvo.json key: cord-297832-picpuzvo authors: Salazar, Rafael; Hallo, Alejandro; Vasquez, Sebastian; Reinthaller, Steffy; Echeverria, Juan title: Decreased Mortality in Patients With Severe Bronchospasm Associated With SARS-CoV-2: An Alternative to Invasive Mechanical Ventilation date: 2020-10-06 journal: Cureus DOI: 10.7759/cureus.10822 sha: doc_id: 297832 cord_uid: picpuzvo file: cache/cord-297747-kifqgskc.json key: cord-297747-kifqgskc authors: Lupala, Cecylia S.; Li, Xuanxuan; Lei, Jian; Chen, Hong; Qi, Jianxun; Liu, Haiguang; Su, Xiao-dong title: Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date: 2020-03-27 journal: bioRxiv DOI: 10.1101/2020.03.24.005561 sha: doc_id: 297747 cord_uid: kifqgskc file: cache/cord-297842-hkr1wm3k.json key: cord-297842-hkr1wm3k authors: Tilley, Kimberly; Ayvazyan, Vladimir; Martinez, Lauren; Nanda, Neha; Kawaguchi, Eric S.; O’Gorman, Maurice; Conti, David; Gauderman, W. James; Van Orman, Sarah title: A Cross-Sectional Study Examining the Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in a University Student Population date: 2020-10-15 journal: J Adolesc Health DOI: 10.1016/j.jadohealth.2020.09.001 sha: doc_id: 297842 cord_uid: hkr1wm3k file: cache/cord-297691-w4cdfwv0.json key: cord-297691-w4cdfwv0 authors: Nikaeen, Ghazal; Abbaszadeh, Sepideh; Yousefinejad, Saeed title: Application of nanomaterials in treatment, anti-infection and detection of coronaviruses date: 2020-05-07 journal: Nanomedicine DOI: 10.2217/nnm-2020-0117 sha: doc_id: 297691 cord_uid: w4cdfwv0 file: cache/cord-297884-a6yrtuwf.json key: cord-297884-a6yrtuwf authors: Burke, R. M.; Balter, S.; Barnes, E.; Barry, V.; Bartlett, K.; Beer, K. D.; Benowitz, I.; Biggs, H. M.; Bruce, H.; Bryant-Genevier, J.; Cates, J.; Chatham-Stephens, K.; Chea, N.; Chiou, H.; Christiansen, D.; Chu, V.; Clark, S.; Cody, S. H.; Cohen, M.; Conners, E. E.; Dasari, V.; Dawson, P.; DeSalvo, T.; Donahue, M.; Dratch, A.; Duca, L.; Duchin, J.; Dyal, J. W.; Feldstein, L. R.; Fenstersheib, M.; Fischer, M.; Fisher, R.; Foo, C.; Freeman-Ponder, B.; Fry, A. M.; Gant, J.; Gautom, R.; Ghinai, I.; Gounder, P.; Grigg, C. T.; Gunzenhauser, J.; Hall, A. J.; Han, G. S.; Haupt, T.; Holshue, M.; Hunte, title: Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States date: 2020-05-03 journal: nan DOI: 10.1101/2020.04.27.20081901 sha: doc_id: 297884 cord_uid: a6yrtuwf file: cache/cord-297693-lqyc49t6.json key: cord-297693-lqyc49t6 authors: Samec, Matthew J; Khawaja, Ali; Patel, Ashokakumar M; Dugani, Sagar B title: 80-year-old man with dyspnoea and bilateral groundglass infiltrates: an elusive case of COVID-19 date: 2020-05-27 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-236069 sha: doc_id: 297693 cord_uid: lqyc49t6 file: cache/cord-297878-c4cq92x8.json key: cord-297878-c4cq92x8 authors: Ali, Mohammed; Mujahid, Aisha; Sherani, Khalid; Surani, Salim title: ST-Elevation Myocardial Infarction in a 27-Year-Old Male With COVID-19 date: 2020-09-11 journal: Cureus DOI: 10.7759/cureus.10384 sha: doc_id: 297878 cord_uid: c4cq92x8 file: cache/cord-297641-bgmib6xb.json key: cord-297641-bgmib6xb authors: Meng, Xiujuan; Huang, Xun; Zhou, Pengcheng; Li, Chunhui; Wu, Anhua title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China date: 2020-04-07 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.114 sha: doc_id: 297641 cord_uid: bgmib6xb file: cache/cord-297918-840thddt.json key: cord-297918-840thddt authors: Yilmaz, Umut; Lepper, Philipp M.; Reith, Wolfgang title: COVID-19: neurologische Manifestationen: Was wir bisher wissen date: 2020-09-02 journal: Radiologe DOI: 10.1007/s00117-020-00748-5 sha: doc_id: 297918 cord_uid: 840thddt file: cache/cord-298036-2zurc60t.json key: cord-298036-2zurc60t authors: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 journal: Cell Signal DOI: 10.1016/j.cellsig.2020.109772 sha: doc_id: 298036 cord_uid: 2zurc60t file: cache/cord-297800-hnx213kp.json key: cord-297800-hnx213kp authors: Bi, Qifang; Wu, Yongsheng; Mei, Shujiang; Ye, Chenfei; Zou, Xuan; Zhang, Zhen; Liu, Xiaojian; Wei, Lan; Truelove, Shaun A; Zhang, Tong; Gao, Wei; Cheng, Cong; Tang, Xiujuan; Wu, Xiaoliang; Wu, Yu; Sun, Binbin; Huang, Suli; Sun, Yu; Zhang, Juncen; Ma, Ting; Lessler, Justin; Feng, Teijian title: Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts date: 2020-03-04 journal: nan DOI: 10.1101/2020.03.03.20028423 sha: doc_id: 297800 cord_uid: hnx213kp file: cache/cord-298056-svwtfshi.json key: cord-298056-svwtfshi authors: Fabio, Ciceri; Antonella, Castagna; Patrizia, Rovere-Querini; Francesco, De Cobelli; Annalisa, Ruggeri; Laura, Galli; Caterina, Conte; Rebecca, De Lorenzo; Andrea, Poli; Alberto, Ambrosio; Carlo, Signorelli; Eleonora, Bossi; Maria, Fazio; Cristina, Tresoldi; Sergio, Colombo; Giacomo, Monti; Efgeny, Fominskiy; Stefano, Franchini; Marzia, Spessot; Carlo, Martinenghi; Michele, Carlucci; Luigi, Beretta; Maria, Scandroglio Anna; Massimo, Clementi; Massimo, Locatelli; Moreno, Tresoldi; Paolo, Scarpellini; Gianvito, Martino; Emanuele, Bosi; Lorenzo, Dagna; Adriano, Lazzarin; Giovanni, Landoni; Alberto, Zangrillo title: Early predictors of clinical outcomes of COVID-19 outbreak in Milan, Italy date: 2020-06-12 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108509 sha: doc_id: 298056 cord_uid: svwtfshi file: cache/cord-297942-6wdwrttn.json key: cord-297942-6wdwrttn authors: Li, Taisheng title: Diagnosis and clinical management of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection: an operational recommendation of Peking Union Medical College Hospital (V2.0): Working Group of 2019 Novel Coronavirus, Peking Union Medical College Hospital date: 2020-03-14 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1735265 sha: doc_id: 297942 cord_uid: 6wdwrttn file: cache/cord-297787-t9neub6d.json key: cord-297787-t9neub6d authors: Fu, Ziyang; Huang, Bin; Tang, Jinle; Liu, Shuyan; Liu, Ming; Ye, Yuxin; Liu, Zhihong; Xiong, Yuxian; Cao, Dan; Li, Jihui; Niu, Xiaogang; Zhou, Huan; Zhao, Yong Juan; Zhang, Guoliang; Huang, Hao title: Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date: 2020-07-18 journal: bioRxiv DOI: 10.1101/2020.07.17.208959 sha: doc_id: 297787 cord_uid: t9neub6d file: cache/cord-297974-sduz0j35.json key: cord-297974-sduz0j35 authors: Bokelmann, L.; Nickel, O.; Maricic, T.; Paabo, S.; Meyer, M.; Borte, S.; Riesenberg, S. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 journal: nan DOI: 10.1101/2020.08.04.20168617 sha: doc_id: 297974 cord_uid: sduz0j35 file: cache/cord-297681-m0cckidw.json key: cord-297681-m0cckidw authors: Na, Joo-Young; Noh, Sang Jae; Choi, Min Sung; Park, Jong-Pil title: [Secondary Publication] Standard Operating Procedure for Post-mortem Inspection in a Focus on Coronavirus Disease-19: the Korean Society for Legal Medicine date: 2020-08-13 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e302 sha: doc_id: 297681 cord_uid: m0cckidw file: cache/cord-298067-awo3smgp.json key: cord-298067-awo3smgp authors: Li, Huanjie; Wang, Yangyang; Ji, Mingyu; Pei, Fengyan; Zhao, Qianqian; Zhou, Yunying; Hong, Yatian; Han, Shuyi; Wang, Jun; Wang, Qingxi; Li, Qiang; Wang, Yunshan title: Transmission Routes Analysis of SARS-CoV-2: A Systematic Review and Case Report date: 2020-07-10 journal: Front Cell Dev Biol DOI: 10.3389/fcell.2020.00618 sha: doc_id: 298067 cord_uid: awo3smgp file: cache/cord-298216-iq7fenxm.json key: cord-298216-iq7fenxm authors: Jiang, Chao; Yao, Xingang; Zhao, Yulin; Wu, Jianmin; Huang, Pan; Pan, Chunhua; Liu, Shuwen; Pan, Chungen title: Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season date: 2020-05-13 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.05.005 sha: doc_id: 298216 cord_uid: iq7fenxm file: cache/cord-297859-p57pl45i.json key: cord-297859-p57pl45i authors: Mahlke, Lutz; Flohé, Sascha; Matthes, Gerrit; Paffrath, Thomas; Wagner, Frithjof; Wölfl, Christoph title: Chirurgie in der SARS-CoV-2-Pandemie: Empfehlungen zum operativen Vorgehen date: 2020-06-02 journal: Unfallchirurg DOI: 10.1007/s00113-020-00830-6 sha: doc_id: 297859 cord_uid: p57pl45i file: cache/cord-297941-7yut9vt4.json key: cord-297941-7yut9vt4 authors: Haq, M.; Rehman, A.; Noor, M.; Ahmed, J.; Ahmad, J.; irfan, M.; Anwar, S.; Ahmad, S.; Amin, S.; Rahim, F.; Haq, N. U. title: Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.29.20203125 sha: doc_id: 297941 cord_uid: 7yut9vt4 file: cache/cord-297870-m7n43k4p.json key: cord-297870-m7n43k4p authors: Azevedo, Rafael Bellotti; Botelho, Bruna Gopp; Hollanda, João Victor Gonçalves de; Ferreira, Leonardo Villa Leão; Junqueira de Andrade, Letícia Zarur; Oei, Stephanie Si Min Lilienwald; Mello, Tomás de Souza; Muxfeldt, Elizabeth Silaid title: Covid-19 and the cardiovascular system: a comprehensive review date: 2020-07-27 journal: J Hum Hypertens DOI: 10.1038/s41371-020-0387-4 sha: doc_id: 297870 cord_uid: m7n43k4p file: cache/cord-297879-6xb25uhx.json key: cord-297879-6xb25uhx authors: Moncunill, G.; Mayor, A.; Santano, R.; Jimenez, A.; Vidal, M.; Tortajada, M.; Sanz, S.; Mendez, S.; Llupia, A.; Aguilar, R.; Alonso, S.; Barrios, D.; Carolis, C.; Cistero, P.; Choliz, E.; Cruz, A.; Fochs, S.; Jairoce, C.; Hecht, J.; Lamoglia, M.; Martinez, M.; Moreno, J.; Mitchell, R.; Ortega, N.; Pey, N.; Puyol, L.; Ribes, M.; Rosell, N.; Sotomayor, P.; Torres, S.; Williams, S.; Barroso, S.; Vilella, A.; Trilla, A.; Varela, P.; Dobano, C.; Garcia-Basteiro, A. L. title: SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up date: 2020-08-25 journal: nan DOI: 10.1101/2020.08.23.20180125 sha: doc_id: 297879 cord_uid: 6xb25uhx file: cache/cord-297775-ug4ovsws.json key: cord-297775-ug4ovsws authors: Hosie, Margaret J; Epifano, Ilaria; Herder, Vanessa; Orton, Richard J; Stevenson, Andrew; Johnson, Natasha; MacDonald, Emma; Dunbar, Dawn; McDonald, Michael; Howie, Fiona; Tennant, Bryn; Herrity, Darcy; Da Silva Filipe, Ana; Streicker, Daniel G; Willett, Brian J; Murcia, Pablo R; Jarrett, Ruth F; Robertson, David L; Weir, William title: Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date: 2020-09-23 journal: bioRxiv DOI: 10.1101/2020.09.23.309948 sha: doc_id: 297775 cord_uid: ug4ovsws file: cache/cord-297989-4grwa4ab.json key: cord-297989-4grwa4ab authors: Li, Yunjin; Xu, Qiyue; Ma, Lu; Wu, Duojiao; Gao, Jie; Chen, Geng; Li, Hua title: Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2 date: 2020-07-08 journal: J Cell Mol Med DOI: 10.1111/jcmm.15607 sha: doc_id: 297989 cord_uid: 4grwa4ab file: cache/cord-298372-4pw1y404.json key: cord-298372-4pw1y404 authors: Koch, Lionel; Lopes, Anne-Aurelie; Maiguy, Avelina; Guillier, Sophie; Guillier, Laurent; Tournier, Jean-Nicolas; Biot, Fabrice title: Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? date: 2020-08-18 journal: Journal of global health DOI: 10.7189/jogh.10.020317 sha: doc_id: 298372 cord_uid: 4pw1y404 file: cache/cord-298242-iuskpoug.json key: cord-298242-iuskpoug authors: Yu, Alvin; Pak, Alexander J.; He, Peng; Monje-Galvan, Viviana; Casalino, Lorenzo; Gaieb, Zied; Dommer, Abigail C.; Amaro, Rommie E.; Voth, Gregory A. title: A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date: 2020-10-02 journal: bioRxiv DOI: 10.1101/2020.10.02.323915 sha: doc_id: 298242 cord_uid: iuskpoug file: cache/cord-298227-av1ev8ta.json key: cord-298227-av1ev8ta authors: Kähler, Christian J.; Hain, Rainer title: Fundamental protective mechanisms of face masks against droplet infections date: 2020-06-28 journal: J Aerosol Sci DOI: 10.1016/j.jaerosci.2020.105617 sha: doc_id: 298227 cord_uid: av1ev8ta file: cache/cord-298172-iyxyennq.json key: cord-298172-iyxyennq authors: Guo, Youjia; Kawaguchi, Atsushi; Takeshita, Masaru; Sekiya, Takeshi; Hirohama, Mikako; Yamashita, Akio; Siomi, Haruhiko; Murano, Kensaku title: Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date: 2020-10-02 journal: bioRxiv DOI: 10.1101/2020.10.01.323220 sha: doc_id: 298172 cord_uid: iyxyennq file: cache/cord-298321-8871aifz.json key: cord-298321-8871aifz authors: Laamarti, Meriem; Kartti, Souad; Alouane, Tarek; Laamarti, Rokia; Allam, Loubna; Ouadghiri, Mouna; Chemao-Elfihri, M.W.; Smyej, Imane; Rahoui, Jalila; Benrahma, Houda; Diawara, Idrissa; Essabbar, Abdelomunim; Boumajdi, Nasma; Bendani, Houda; Bouricha, El Mehdi; Aanniz, Tarik; Elattar, Jalil; Hafidi, Naima EL; Jaoudi, Rachid EL; Sbabou, Laila; Nejjari, Chakib; Amzazi, Saaid; Mentag, Rachid; Belyamani, Lahcen; Ibrahimi, Azeddine title: Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date: 2020-07-01 journal: bioRxiv DOI: 10.1101/2020.06.30.181123 sha: doc_id: 298321 cord_uid: 8871aifz file: cache/cord-298343-nvuc1j7t.json key: cord-298343-nvuc1j7t authors: Ma, J.; Qi, X.; Chen, H.; Li, X.; Zhan, Z.; Wang, H.; Sun, L.; Zhang, L.; Guo, J.; Morawska, L.; Grinshpun, S. A.; Biswas, P.; Flagan, R. C.; Yao, M. title: Exhaled breath is a significant source of SARS-CoV-2 emission date: 2020-06-02 journal: nan DOI: 10.1101/2020.05.31.20115154 sha: doc_id: 298343 cord_uid: nvuc1j7t file: cache/cord-298079-hgdyxk98.json key: cord-298079-hgdyxk98 authors: Hsu, Jeffrey J.; Al‐Saffar, Farah; Ardehali, Reza; Baas, Arnold S.; Carlson, Margrit; Cruz, Daniel; Deng, Mario; Fan, Ashley; Fraschilla, Stephanie; Gaynor, Pryce; Kamath, Megan; Kubak, Bernard M.; Schaenman, Joanna; Stimpson, Emily; Vucicevic, Darko; Ardehali, Abbas; Nsair, Ali title: Heart Transplantation in the Early Phase of the COVID‐19 Pandemic: A Single‐Center Case Series date: 2020-07-12 journal: Clin Transplant DOI: 10.1111/ctr.14042 sha: doc_id: 298079 cord_uid: hgdyxk98 file: cache/cord-298083-4h3tg6hg.json key: cord-298083-4h3tg6hg authors: Ho, Tin-Yun; Wu, Shih-Lu; Cheng, Shin-Ei; Wei, Yen-Chiao; Huang, Shan-Ping; Hsiang, Chien-Yun title: Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein date: 2004-01-23 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2003.11.180 sha: doc_id: 298083 cord_uid: 4h3tg6hg file: cache/cord-298156-d0pb1kik.json key: cord-298156-d0pb1kik authors: Cheval, Sorin; Mihai Adamescu, Cristian; Georgiadis, Teodoro; Herrnegger, Mathew; Piticar, Adrian; Legates, David R. title: Observed and Potential Impacts of the COVID-19 Pandemic on the Environment date: 2020-06-10 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17114140 sha: doc_id: 298156 cord_uid: d0pb1kik file: cache/cord-298301-p1zj6jg9.json key: cord-298301-p1zj6jg9 authors: Dey, Lopamudra; Chakraborty, Sanjay; Mukhopadhyay, Anirban title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date: 2020-09-03 journal: Biomed J DOI: 10.1016/j.bj.2020.08.003 sha: doc_id: 298301 cord_uid: p1zj6jg9 file: cache/cord-298406-7wfdwou8.json key: cord-298406-7wfdwou8 authors: Sun, Haifang; Luo, Haibin; Yu, Changying; Sun, Tao; Chen, Jing; Peng, Shuying; Qin, Jun; Shen, Jianhua; Yang, Yiming; Xie, Youhua; Chen, Kaixian; Wang, Yuan; Shen, Xu; Jiang, Hualiang title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus date: 2003-12-31 journal: Protein Expression and Purification DOI: 10.1016/j.pep.2003.08.016 sha: doc_id: 298406 cord_uid: 7wfdwou8 file: cache/cord-298490-p1msabl5.json key: cord-298490-p1msabl5 authors: Obukhov, Alexander G.; Stevens, Bruce R.; Prasad, Ram; Li Calzi, Sergio; Boulton, Michael E.; Raizada, Mohan K.; Oudit, Gavin Y.; Grant, Maria B. title: SARS-CoV-2 Infections and ACE2: Clinical Outcomes Linked With Increased Morbidity and Mortality in Individuals With Diabetes date: 2020-07-15 journal: Diabetes DOI: 10.2337/dbi20-0019 sha: doc_id: 298490 cord_uid: p1msabl5 file: cache/cord-298098-4dfqlebp.json key: cord-298098-4dfqlebp authors: Xu, Ruodan; Shi, Mingfei; Li, Jing; Song, Ping; Li, Ning title: Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System date: 2020-07-30 journal: Front Bioeng Biotechnol DOI: 10.3389/fbioe.2020.00862 sha: doc_id: 298098 cord_uid: 4dfqlebp file: cache/cord-298327-j04nyg5y.json key: cord-298327-j04nyg5y authors: Lv, Zhihua; Cheng, Shaohua; Le, Juan; Huang, Jingtao; Feng, Lina; Zhang, Binghong; Li, Yan title: Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study date: 2020-05-18 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.05.007 sha: doc_id: 298327 cord_uid: j04nyg5y file: cache/cord-298725-da71febn.json key: cord-298725-da71febn authors: Okuhama, Ayako; Ishikane, Masahiro; Katagiri, Daisuke; Kanda, Kohei; Nakamoto, Takato; Kinoshita, Noriko; Nunose, Naoto; Fukaya, Takashi; Kondo, Isao; Katano, Harutaka; Suzuki, Tadaki; Ohmagari, Norio; Hinoshita, Fumihiko title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan date: 2020-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid2611.201956 sha: doc_id: 298725 cord_uid: da71febn file: cache/cord-298679-w0yp4u19.json key: cord-298679-w0yp4u19 authors: Iftimie, Simona; López-Azcona, Ana F.; Vicente-Miralles, Manuel; Descarrega-Reina, Ramon; Hernández-Aguilera, Anna; Riu, Francesc; Simó, Josep M.; Garrido, Pedro; Joven, Jorge; Camps, Jordi; Castro, Antoni title: Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0234452 sha: doc_id: 298679 cord_uid: w0yp4u19 file: cache/cord-298281-wkje5jyt.json key: cord-298281-wkje5jyt authors: Chan, Vinson Wai-Shun; Chiu, Peter Ka-Fung; Yee, Chi-Hang; Yuan, Yuhong; Ng, Chi-Fai; Teoh, Jeremy Yuen-Chun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 journal: World J Urol DOI: 10.1007/s00345-020-03246-4 sha: doc_id: 298281 cord_uid: wkje5jyt file: cache/cord-298696-rsifxvtj.json key: cord-298696-rsifxvtj authors: Lim, Meng-Kin title: Global response to pandemic flu: more research needed on a critical front date: 2006-10-13 journal: Health Res Policy Syst DOI: 10.1186/1478-4505-4-8 sha: doc_id: 298696 cord_uid: rsifxvtj file: cache/cord-298440-0pb8ssj2.json key: cord-298440-0pb8ssj2 authors: Rascón-Ramírez, Fernando J; Carrascosa-Granada, Ángela María; Vargas-Jiménez, Andrés Camilo; Ferrández-Pujante, Borja; Francisco, Ortuño-Andériz title: Supra and infratentorial massive strokes in previously healthy young patients with SARS-CoV-2. The role of neurosurgery date: 2020-09-06 journal: Neurocirugia (Astur) DOI: 10.1016/j.neucir.2020.08.001 sha: doc_id: 298440 cord_uid: 0pb8ssj2 file: cache/cord-298350-pq1dcz3a.json key: cord-298350-pq1dcz3a authors: Ryan, Jeffrey R. title: Category C Diseases and Agents date: 2016-03-25 journal: Biosecurity and Bioterrorism DOI: 10.1016/b978-0-12-802029-6.00005-0 sha: doc_id: 298350 cord_uid: pq1dcz3a file: cache/cord-298639-v9yg80jw.json key: cord-298639-v9yg80jw authors: Chen, Yuxin; Tong, Xin; Wang, Jian; Huang, Weijin; Yin, Shengxia; Huang, Rui; Yang, Hailong; Chen, Yong; Huang, Aijun; Liu, Yong; Chen, Yan; Yuan, Ling; Yan, Xiaomin; Shen, Han; Wu, Chao title: High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients date: 2020-06-04 journal: J Infect DOI: 10.1016/j.jinf.2020.05.067 sha: doc_id: 298639 cord_uid: v9yg80jw file: cache/cord-298505-r7ihqb96.json key: cord-298505-r7ihqb96 authors: Górski, Andrzej; Borysowski, Jan; Międzybrodzki, Ryszard title: Sepsis, Phages, and COVID-19 date: 2020-10-15 journal: Pathogens DOI: 10.3390/pathogens9100844 sha: doc_id: 298505 cord_uid: r7ihqb96 file: cache/cord-298693-x25r0gtt.json key: cord-298693-x25r0gtt authors: Advani, Sonali D.; Yarrington, Michael E.; Smith, Becky A.; Anderson, Deverick J.; Sexton, Daniel J. title: Are we forgetting the “universal” in universal masking? Current challenges and future solutions date: 2020-07-16 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.333 sha: doc_id: 298693 cord_uid: x25r0gtt file: cache/cord-298482-r7lallv0.json key: cord-298482-r7lallv0 authors: De Maio, Flavio; Lo Cascio, Ettore; Babini, Gabriele; Sali, Michela; Della Longa, Stefano; Tilocca, Bruno; Roncada, Paola; Arcovito, Alessandro; Sanguinetti, Maurizio; Scambia, Giovanni; Urbani, Andrea title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis date: 2020-09-04 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.08.006 sha: doc_id: 298482 cord_uid: r7lallv0 file: cache/cord-298669-g2up0cfi.json key: cord-298669-g2up0cfi authors: Pollock, David D; Castoe, Todd A; Perry, Blair W; Lytras, Spyros; Wade, Kristen J; Robertson, David L; Holmes, Edward C; Boni, Maciej F; Kosakovsky Pond, Sergei L; Parry, Rhys; Carlton, Elizabeth J; Wood, James L N; Pennings, Pleuni S; Goldstein, Richard A title: Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2 date: 2020-07-13 journal: Mol Biol Evol DOI: 10.1093/molbev/msaa178 sha: doc_id: 298669 cord_uid: g2up0cfi file: cache/cord-298894-t5hyfum3.json key: cord-298894-t5hyfum3 authors: Rifino, Nicola; Censori, Bruno; Agazzi, Emanuela; Alimonti, Dario; Bonito, Virginio; Camera, Giorgia; Conti, Marta Zaffira; Foresti, Camillo; Frigeni, Barbara; Gerevini, Simonetta; Grimoldi, Maria; La Gioia, Sara; Partziguian, Tania; Quadri, Stefano; Riva, Riccardo; Servalli, Maria Cristina; Sgarzi, Manlio; Storti, Benedetta; Vedovello, Marcella; Venturelli, Elisabetta; Viganò, Martina; Callegaro, Annapaola; Arosio, Marco; Sessa, Maria title: Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital, Bergamo, Italy date: 2020-10-07 journal: J Neurol DOI: 10.1007/s00415-020-10251-5 sha: doc_id: 298894 cord_uid: t5hyfum3 file: cache/cord-298461-tyhtdawb.json key: cord-298461-tyhtdawb authors: Zhao, L.; Qi, Y.; Luzzatto-Fegiz, P.; Cui, Y.; Zhu, Y. title: COVID-19: Effects of weather conditions on the propagation of respiratory droplets date: 2020-05-25 journal: nan DOI: 10.1101/2020.05.24.20111963 sha: doc_id: 298461 cord_uid: tyhtdawb file: cache/cord-298777-hit7rs6q.json key: cord-298777-hit7rs6q authors: Zhang, Linjie; Peres, Tyele G.; Silva, Marcus V. F.; Camargos, Paulo title: What we know so far about Coronavirus Disease 2019 in children: A meta‐analysis of 551 laboratory‐confirmed cases date: 2020-06-10 journal: Pediatr Pulmonol DOI: 10.1002/ppul.24869 sha: doc_id: 298777 cord_uid: hit7rs6q file: cache/cord-298075-lzuxlzb0.json key: cord-298075-lzuxlzb0 authors: Mao, Kang; Zhang, Hua; Yang, Zhugen title: Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology? date: 2020-03-23 journal: Environ Sci Technol DOI: 10.1021/acs.est.0c01174 sha: doc_id: 298075 cord_uid: lzuxlzb0 file: cache/cord-298426-hhly45md.json key: cord-298426-hhly45md authors: Zhang, Shan-Yan; Lian, Jiang-Shan; Hu, Jian-Hua; Zhang, Xiao-Li; Lu, Ying-Feng; Cai, Huan; Gu, Jue-Qing; Ye, Chan-Yuan; Jin, Ci-Liang; Yu, Guo-Dong; Jia, Hong-Yu; Zhang, Yi-Min; Sheng, Ji-Fang; Li, Lan-Juan; Yang, Yi-Da title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China date: 2020-07-08 journal: Infect Dis Poverty DOI: 10.1186/s40249-020-00710-6 sha: doc_id: 298426 cord_uid: hhly45md file: cache/cord-298886-xidaim04.json key: cord-298886-xidaim04 authors: Leszczyński, Piotr title: COVID-19: a short message to rheumatologists date: 2020-06-29 journal: Reumatologia DOI: 10.5114/reum.2020.96685 sha: doc_id: 298886 cord_uid: xidaim04 file: cache/cord-298991-5qae0ege.json key: cord-298991-5qae0ege authors: Aiello, Francesco; Gallo Afflitto, Gabriele; Mancino, Raffaele; Li, Ji-Peng Olivia; Cesareo, Massimo; Giannini, Clarissa; Nucci, Carlo title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 journal: Eye (Lond) DOI: 10.1038/s41433-020-0926-9 sha: doc_id: 298991 cord_uid: 5qae0ege file: cache/cord-298866-dzatps7b.json key: cord-298866-dzatps7b authors: Licskai, Christopher; Yang, Connie L.; Ducharme, Francine M.; Radhakrishnan, Dhenuka; Podgers, Delanya; Ramsey, Clare; Samanta, Tania; Côté, Andréanne; Mahdavian, Masoud; Lougheed, M. Diane title: Key highlights from the Canadian Thoracic Society’s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic date: 2020-05-28 journal: Chest DOI: 10.1016/j.chest.2020.05.551 sha: doc_id: 298866 cord_uid: dzatps7b file: cache/cord-298773-vnmc6nqd.json key: cord-298773-vnmc6nqd authors: Pfeiffer, Julie K. title: Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? date: 2015-01-20 journal: mBio DOI: 10.1128/mbio.02525-14 sha: doc_id: 298773 cord_uid: vnmc6nqd file: cache/cord-298722-rmibv5z7.json key: cord-298722-rmibv5z7 authors: Abdel-latif, Rania G; Mohammed, Shaban; Elgendy, Islam Y title: Statin therapy and SAR-COV-2: an available and potential therapy? date: 2020-05-07 journal: Eur Heart J Cardiovasc Pharmacother DOI: 10.1093/ehjcvp/pvaa050 sha: doc_id: 298722 cord_uid: rmibv5z7 file: cache/cord-298716-pubhq564.json key: cord-298716-pubhq564 authors: Bryche, Bertrand; St Albin, Audrey; Murri, Severine; Lacôte, Sandra; Pulido, Coralie; Gouilh, Meriadeg Ar; Lesellier, Sandrine; Servat, Alexandre; Wasniewski, Marine; Picard-Meyer, Evelyne; Monchatre-Leroy, Elodie; Volmer, Romain; Rampin, Olivier; Le Goffic, Ronan; Marianneau, Philippe; Meunier, Nicolas title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.16.151704 sha: doc_id: 298716 cord_uid: pubhq564 file: cache/cord-298899-lkrmg5qr.json key: cord-298899-lkrmg5qr authors: Xie, Yewei; Wang, Zaisheng; Liao, Huipeng; Marley, Gifty; Wu, Dan; Tang, Weiming title: Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date: 2020-08-31 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05371-2 sha: doc_id: 298899 cord_uid: lkrmg5qr file: cache/cord-298902-afek8kgr.json key: cord-298902-afek8kgr authors: Li, Xingguang; Wang, Wei; Zhao, Xiaofang; Zai, Junjie; Zhao, Qiang; Li, Yi; Chaillon, Antoine title: Transmission dynamics and evolutionary history of 2019‐nCoV date: 2020-02-14 journal: J Med Virol DOI: 10.1002/jmv.25701 sha: doc_id: 298902 cord_uid: afek8kgr file: cache/cord-298850-tgxfki7n.json key: cord-298850-tgxfki7n authors: Figuero-Pérez, Luis; Olivares-Hernández, Alejandro; Escala-Cornejo, Roberto A.; Terán-Brage, Eduardo; López-Gutiérrez, Álvaro; Cruz-Hernández, Juan J. title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab date: 2020-10-15 journal: nan DOI: 10.1016/j.reumae.2020.06.008 sha: doc_id: 298850 cord_uid: tgxfki7n file: cache/cord-298920-1lc2xf7u.json key: cord-298920-1lc2xf7u authors: Bello-Perez, Melissa; Sola, Isabel; Novoa, Beatriz; Klionsky, Daniel J.; Falco, Alberto title: Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date: 2020-07-05 journal: Cells DOI: 10.3390/cells9071619 sha: doc_id: 298920 cord_uid: 1lc2xf7u file: cache/cord-298967-vjyh1xvh.json key: cord-298967-vjyh1xvh authors: Bertossi, Dario; Mohsahebi, Ash; Philippe Dormstrom,; Heidenrich, Izolda; Pirayesh, Ali; D’Souza, Alwyn; Saleh, Hesham; Yavuzer, Rezha; Fakih, Nabil; Vent, Julia; Rahman, Eqram; Kapoor, Krishan Mohan title: Safety guidelines for non‐surgical facial procedures during covid‐19 outbreak date: 2020-06-07 journal: J Cosmet Dermatol DOI: 10.1111/jocd.13530 sha: doc_id: 298967 cord_uid: vjyh1xvh file: cache/cord-298989-qk0k2lmz.json key: cord-298989-qk0k2lmz authors: , Umesh; Kundu, Debanjan; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Dubey, Vikash Kumar title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target date: 2020-05-13 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1763202 sha: doc_id: 298989 cord_uid: qk0k2lmz file: cache/cord-299422-s5evsj96.json key: cord-299422-s5evsj96 authors: Abdollahi, Alireza; Mahmoudi-Aliabadi, Maedeh; Mehrtash, Vahid; Jafarzadeh, Bita; Salehi, Mohammadreza title: The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types date: 2020-05-23 journal: Iran J Pathol DOI: 10.30699/ijp.2020.125135.2367 sha: doc_id: 299422 cord_uid: s5evsj96 file: cache/cord-299156-1dwsm3ie.json key: cord-299156-1dwsm3ie authors: Shemer, Asaf; Einan-Lifshitz, Adi; Itah, Amir; Dubinsky-Pertzov, Biana; Pras, Eran; Hecht, Idan title: Ocular involvement in coronavirus disease 2019 (COVID-19): a clinical and molecular analysis date: 2020-09-14 journal: Int Ophthalmol DOI: 10.1007/s10792-020-01592-1 sha: doc_id: 299156 cord_uid: 1dwsm3ie file: cache/cord-299432-lbv69du4.json key: cord-299432-lbv69du4 authors: Franklin, Alan B.; Bevins, Sarah N. title: Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen date: 2020-05-12 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.139358 sha: doc_id: 299432 cord_uid: lbv69du4 file: cache/cord-299354-rmjohbse.json key: cord-299354-rmjohbse authors: Chen, Fu-Lun; Wang, Cheng-Hui; Hung, Ching-Sheng; Su, Ying-Shih; Lee, Wen-Sen title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.05.007 sha: doc_id: 299354 cord_uid: rmjohbse file: cache/cord-299449-226dd23u.json key: cord-299449-226dd23u authors: Bernhardt, Denise; 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Sveric, Krunoslav; Gerber, Johannes C.; Svitil, Jan; Linke, Axel; Jellinghaus, Stefanie title: Paraneoplastic syndrome and SARS-CoV-2 – incremental effect of two thrombogenic conditions? date: 2020-10-21 journal: CJC Open DOI: 10.1016/j.cjco.2020.10.010 sha: doc_id: 299024 cord_uid: jkqdzt87 file: cache/cord-299082-s8bm40vy.json key: cord-299082-s8bm40vy authors: Wang, Yueying; Wang, Zhaojia; Tse, Gary; Zhang, Lin; Wan, Elaine Y.; Guo, Yutao; Lip, Gregory Y. 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Jacob title: Is Gradual and Controlled Approach to Herd Protection a Valid Strategy to Curb the COVID-19 Pandemic? date: 2020-05-06 journal: Indian Pediatr DOI: 10.1007/s13312-020-1844-4 sha: doc_id: 299308 cord_uid: gza1pwx6 file: cache/cord-299333-qu0bmov5.json key: cord-299333-qu0bmov5 authors: Reddy, Gireesh B.; Greif, Dylan N.; Rodriguez, Jose; Best, Thomas M.; Greditzer, Harry G.; Jose, Jean title: Clinical Characteristics and Multisystem Imaging Findings of COVID-19: An Overview for Orthopedic Surgeons date: 2020-08-17 journal: HSS J DOI: 10.1007/s11420-020-09775-3 sha: doc_id: 299333 cord_uid: qu0bmov5 file: cache/cord-299346-f13xly6q.json key: cord-299346-f13xly6q authors: Awad, Mohamed E.; Rumley, Jacob C.L.; Vazquez, Jose A.; Devine, John G. title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic date: 2020-04-10 journal: J Am Acad Orthop Surg DOI: 10.5435/jaaos-d-20-00227 sha: doc_id: 299346 cord_uid: f13xly6q file: cache/cord-299520-2khjhows.json key: cord-299520-2khjhows authors: Dalla Volta, Alberto; Valcamonico, Francesca; Pedersini, Rebecca; Fornaro, Carla; Tovazzi, Valeria; Monteverdi, Sara; Baggi, Alice; Consoli, Francesca; Ferrari, Vittorio Domenico; Grisanti, Salvatore; Conti, Elisabetta; Amoroso, Vito; Bossi, Paolo; Berruti, Alfredo title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures date: 2020-08-18 journal: Front Oncol DOI: 10.3389/fonc.2020.01574 sha: doc_id: 299520 cord_uid: 2khjhows file: cache/cord-299491-8rfm0jxh.json key: cord-299491-8rfm0jxh authors: Xiao, Shenglan; Li, Yuguo; Wong, Tze-wai; Hui, David S. C. title: Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date: 2017-07-20 journal: PLoS One DOI: 10.1371/journal.pone.0181558 sha: doc_id: 299491 cord_uid: 8rfm0jxh file: cache/cord-298441-77w86l8q.json key: cord-298441-77w86l8q authors: Lombardi, Andrea; Consonni, Dario; Carugno, Michele; Bozzi, Giorgio; Mangioni, Davide; Muscatello, Antonio; Castelli, Valeria; Palomba, Emanuele; Cantù, Anna Paola; Ceriotti, Ferruccio; Tiso, Basilio; Pesatori, Angela Cecilia; Riboldi, Luciano; Bandera, Alessandra; Lunghi, Giovanna; Gori, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.013 sha: doc_id: 298441 cord_uid: 77w86l8q file: cache/cord-299472-pmqqemku.json key: cord-299472-pmqqemku authors: Yang, Naibin; Shen, Yuefei; Shi, Chunwei; Ma, Ada Hoi Yan; Zhang, Xie; Jian, Xiaomin; Wang, Liping; Shi, Jiejun; Wu, Chunyang; Li, Guoxiang; Fu, Yuan; Wang, Keyin; Lu, Mingqin; Qian, Guoqing title: In-flight Transmission Cluster of COVID-19: A Retrospective Case Series date: 2020-03-30 journal: nan DOI: 10.1101/2020.03.28.20040097 sha: doc_id: 299472 cord_uid: pmqqemku file: cache/cord-299116-1agfnjvq.json key: cord-299116-1agfnjvq authors: Bunders, Madeleine; Altfeld, Marcus title: Implications of sex differences in immunity for SARS-CoV-2 pathogenesis and design of therapeutic interventions date: 2020-08-17 journal: Immunity DOI: 10.1016/j.immuni.2020.08.003 sha: doc_id: 299116 cord_uid: 1agfnjvq file: cache/cord-299544-r3cqvf0c.json key: cord-299544-r3cqvf0c authors: de Souza, T. H.; Nadal, J. A.; Nogueira, R. J. N.; Pereira, R. M.; Brandao, M. B. title: Clinical Manifestations of Children with COVID-19: a Systematic Review date: 2020-04-03 journal: nan DOI: 10.1101/2020.04.01.20049833 sha: doc_id: 299544 cord_uid: r3cqvf0c file: cache/cord-299810-e57pwgnx.json key: cord-299810-e57pwgnx authors: Martelloni, Gabriele; Martelloni, Gianluca title: Modelling the downhill of the Sars-Cov-2 in Italy and a universal forecast of the epidemic in the world date: 2020-07-01 journal: Chaos Solitons Fractals DOI: 10.1016/j.chaos.2020.110064 sha: doc_id: 299810 cord_uid: e57pwgnx file: cache/cord-299470-sqqer16k.json key: cord-299470-sqqer16k authors: Chappell, J. G.; Tsoleridis, T.; Clark, G.; Berry, L.; Holmes, N.; Moore, C.; Carlile, M.; Sang, F.; Debebe, J.; Wright, V.; Irving, W.; Thomson, B. J.; Boswell, T. C. J.; Willingham, I.; Joseph, A.; Smith, W.; Khakh, M.; Fleming, V. M.; Lister, M. M.; Howson-Wells, H. C.; Holmes, E. C.; Loose, M. W.; Ball, J. K.; McClure, C. P.; group, The COVID-19 Genomics UK consortium study title: Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom date: 2020-08-21 journal: nan DOI: 10.1101/2020.08.18.20174623 sha: doc_id: 299470 cord_uid: sqqer16k file: cache/cord-299480-mehwd0dk.json key: cord-299480-mehwd0dk authors: Liu, Zheng-Xue; Yi, Guo-Hua; Qi, Yi-Peng; Liu, Ying-Le; Yan, Jun-Peng; Qian, Juan; Du, En-Qi; Ling, Wei-Fang title: Identification of single-chain antibody fragments specific against SARS-associated coronavirus from phage-displayed antibody library date: 2005-04-08 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2005.02.003 sha: doc_id: 299480 cord_uid: mehwd0dk file: cache/cord-299565-shlhreve.json key: cord-299565-shlhreve authors: Sweileh, Waleed M. title: Global research trends of World Health Organization’s top eight emerging pathogens date: 2017-02-08 journal: Global Health DOI: 10.1186/s12992-017-0233-9 sha: doc_id: 299565 cord_uid: shlhreve file: cache/cord-299940-nvlcwcz8.json key: cord-299940-nvlcwcz8 authors: Rastrelli, Giulia; Di Stasi, Vincenza; Inglese, Francesco; Beccaria, Massimiliano; Garuti, Martina; Di Costanzo, Domenica; Spreafico, Fabio; Greco, Graziana Francesca; Cervi, Giulia; Pecoriello, Antonietta; Magini, Angela; Todisco, Tommaso; Cipriani, Sarah; Maseroli, Elisa; Corona, Giovanni; Salonia, Andrea; Lenzi, Andrea; Maggi, Mario; De Donno, Giuseppe; Vignozzi, Linda title: Low testosterone levels predict clinical adverse outcomes in SARS‐CoV‐2 pneumonia patients date: 2020-06-03 journal: Andrology DOI: 10.1111/andr.12821 sha: doc_id: 299940 cord_uid: nvlcwcz8 file: cache/cord-299552-rgrm8dil.json key: cord-299552-rgrm8dil authors: Bianchi, Martina; Benvenuto, Domenico; Giovanetti, Marta; Angeletti, Silvia; Ciccozzi, Massimo; Pascarella, Stefano title: Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? date: 2020-05-30 journal: Biomed Res Int DOI: 10.1155/2020/4389089 sha: doc_id: 299552 cord_uid: rgrm8dil file: cache/cord-299679-6z9e5gi6.json key: cord-299679-6z9e5gi6 authors: Rello, Jordi; Storti, Enrico; Belliato, Mirko; Serrano, Ricardo title: Clinical phenotypes of SARS-CoV-2: implications for clinicians and researchers date: 2020-05-21 journal: Eur Respir J DOI: 10.1183/13993003.01028-2020 sha: doc_id: 299679 cord_uid: 6z9e5gi6 file: cache/cord-300046-orlga9qf.json key: cord-300046-orlga9qf authors: Gomes da Silva, J.; Sofia Silva, C.; Alexandre, B.; Morgado, P. title: Health literacy of inland population in the mitigation phase 3.2. of COVID-19's pandemic in Portugal - a descriptive cohort study date: 2020-05-14 journal: nan DOI: 10.1101/2020.05.11.20098061 sha: doc_id: 300046 cord_uid: orlga9qf file: cache/cord-299560-np6nfvf2.json key: cord-299560-np6nfvf2 authors: Hendaus, Mohamed A. title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date: 2020-05-20 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1767691 sha: doc_id: 299560 cord_uid: np6nfvf2 file: cache/cord-299635-bxdf27sv.json key: cord-299635-bxdf27sv authors: Squire, M. M.; Munsamy, M.; Lin, G.; Telukdarie, A.; Igusa, T. title: Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions date: 2020-08-24 journal: nan DOI: 10.1101/2020.08.21.20178855 sha: doc_id: 299635 cord_uid: bxdf27sv file: cache/cord-299711-m5gb03is.json key: cord-299711-m5gb03is authors: Udrea, Ana-Maria; Avram, Speranta; Nistorescu, Simona; Pascu, Mihail-Lucian; Romanitan, Mihaela Oana title: Laser irradiated phenothiazines: New potential treatment for COVID-19 explored by molecular docking date: 2020-08-15 journal: J Photochem Photobiol B DOI: 10.1016/j.jphotobiol.2020.111997 sha: doc_id: 299711 cord_uid: m5gb03is file: cache/cord-299781-9d5g5xaw.json key: cord-299781-9d5g5xaw authors: Hrusak, Ondrej; Kalina, Tomas; Wolf, Joshua; Balduzzi, Adriana; Provenzi, Massimo; Rizzari, Carmelo; Rives, Susana; del Pozo Carlavilla, María; Valerio Alonso, Maria Eli; Domínguez Pinilla, Nerea; Bourquin, Jean-Pierre; Schmiegelow, Kjeld; Attarbaschi, Andishe; Grillner, Pernilla; Mellgren, Karin; Ten Bosch van der Werff, J.; Pieters, Rob; Brozou, Triantafyllia; Borkhardt, Arndt; Escherich, Gabriele; Lauten, Melchior; Stanulla, Martin; Smith, Owen; Juh Yeoh, Allen Eng; Elitzur, Sarah; Vora, Ajay; Li, Chi-Kong; Ariffin, Hany; Kolenova, Alexandra; Dallapozza, Luciano; Farah, Roula; Lazic, Jelena; Manabe, Atsushi; Styczynski, Jan; Kovacs, Gabor; Ottoffy, Gabor; Felice, Marisa; Buldini, Barbara; Conter, Valentino; Stary, Jan; Schrappe, Martin title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment date: 2020-04-07 journal: Eur J Cancer DOI: 10.1016/j.ejca.2020.03.021 sha: doc_id: 299781 cord_uid: 9d5g5xaw file: cache/cord-299853-pvugij9l.json key: cord-299853-pvugij9l authors: Patil, Uday P.; Maru, Sheela; Krishnan, Parvathy; Carroll-Bennett, Rachel; Sanchez, Joselito; Noble, Lawrence; Wasserman, Randi title: Newborns of COVID-19 mothers: short-term outcomes of colocating and breastfeeding from the pandemic’s epicenter date: 2020-08-10 journal: J Perinatol DOI: 10.1038/s41372-020-0765-3 sha: doc_id: 299853 cord_uid: pvugij9l file: cache/cord-299911-v95pf3eg.json key: cord-299911-v95pf3eg authors: El-Ghiaty, Mahmoud A.; Shoieb, Sherif M.; El-Kadi, Ayman O.S. title: Cytochrome P450-mediated drug interactions in COVID-19 patients: current findings and possible mechanisms date: 2020-06-26 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110033 sha: doc_id: 299911 cord_uid: v95pf3eg file: cache/cord-300024-169g2ih5.json key: cord-300024-169g2ih5 authors: Flemming, S.; Hankir, M.; Hering, I.; Meybohm, P.; Krone, M.; Weissbrich, B.; Germer, C.T.; Wiegering, A. title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-05-26 journal: Br J Surg DOI: 10.1002/bjs.11713 sha: doc_id: 300024 cord_uid: 169g2ih5 file: cache/cord-299783-8ti6r0eh.json key: cord-299783-8ti6r0eh authors: Bruni, M.; Cecatiello, V.; Diaz-Basabe, A.; Lattanzi, G.; Mileti, E.; Monzani, S.; Pirovano, L.; Rizzelli, F.; Visintin, C.; Bonizzi, G.; Giani, M.; Lavitrano, M.; Faravelli, S.; Forneris, F.; Caprioli, F.; Pelicci, P. G.; Natoli, G.; Pasqualato, S.; Mapelli, M.; Facciotti, F. title: Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date: 2020-08-01 journal: nan DOI: 10.1101/2020.07.30.20164368 sha: doc_id: 299783 cord_uid: 8ti6r0eh file: cache/cord-299899-is815pol.json key: cord-299899-is815pol authors: He, Jingjing; Guo, Yifei; Mao, Richeng; Zhang, Jiming title: Proportion of asymptomatic coronavirus disease 2019 (COVID‐19): a systematic review and meta‐analysis date: 2020-07-21 journal: J Med Virol DOI: 10.1002/jmv.26326 sha: doc_id: 299899 cord_uid: is815pol file: cache/cord-300149-djclli8n.json key: cord-300149-djclli8n authors: Ruan, Yijun; Wei, Chia Lin; Ling, Ai Ee; Vega, Vinsensius B; Thoreau, Herve; Se Thoe, Su Yun; Chia, Jer-Ming; Ng, Patrick; Chiu, Kuo Ping; Lim, Landri; Zhang, Tao; Chan, Kwai Peng; Lin Ean, Lynette Oon; Ng, Mah Lee; Leo, Sin Yee; Ng, Lisa FP; Ren, Ee Chee; Stanton, Lawrence W; Long, Philip M; Liu, Edison T title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection date: 2003-05-24 journal: Lancet DOI: 10.1016/s0140-6736(03)13414-9 sha: doc_id: 300149 cord_uid: djclli8n file: cache/cord-299927-ixuvy2g4.json key: cord-299927-ixuvy2g4 authors: Frontera, Jennifer; Mainali, Shraddha; Fink, Ericka L.; Robertson, Courtney L.; Schober, Michelle; Ziai, Wendy; Menon, David; Kochanek, Patrick M.; Suarez, Jose I.; Helbok, Raimund; McNett, Molly; Chou, Sherry H.-Y. title: Global Consortium Study of Neurological Dysfunction in COVID-19 (GCS-NeuroCOVID): Study Design and Rationale date: 2020-05-22 journal: Neurocrit Care DOI: 10.1007/s12028-020-00995-3 sha: doc_id: 299927 cord_uid: ixuvy2g4 file: cache/cord-300040-rvrp5zvv.json key: cord-300040-rvrp5zvv authors: Dutta, Noton Kumar; Mazumdar, Kaushiki; Lee, Byoung-Hee; Baek, Min-Won; Kim, Dong-Jae; Na, Yi-Rang; Park, Sung-Hoon; Lee, Hyun-Kyoung; Kariwa, Hiroaki; Mai, Le Quynh; Park, Jae-Hak title: Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine date: 2008-06-15 journal: Immunol Lett DOI: 10.1016/j.imlet.2008.03.003 sha: doc_id: 300040 cord_uid: rvrp5zvv file: cache/cord-299499-66qh3r75.json key: cord-299499-66qh3r75 authors: Guilamo-Ramos, Vincent; Benzekri, Adam; Thimm-Kaiser, Marco; Hidalgo, Andrew; Perlman, David C title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1348 sha: doc_id: 299499 cord_uid: 66qh3r75 file: cache/cord-299999-jra1yu6a.json key: cord-299999-jra1yu6a authors: Tattar, R.; Roudsari, R. V. title: COVID PDPs date: 2020-05-22 journal: Br Dent J DOI: 10.1038/s41415-020-1696-2 sha: doc_id: 299999 cord_uid: jra1yu6a file: cache/cord-299989-p59u6qa0.json key: cord-299989-p59u6qa0 authors: Zhang, Lei; Han, Xiaohong; Shi, Yuankai title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date: 2020-06-18 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104428 sha: doc_id: 299989 cord_uid: p59u6qa0 file: cache/cord-300018-3uzau7if.json key: cord-300018-3uzau7if authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date: 2020-07-24 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104550 sha: doc_id: 300018 cord_uid: 3uzau7if file: cache/cord-300272-95o8yd7h.json key: cord-300272-95o8yd7h authors: Thépaut, Michel; Luczkowiak, Joanna; Vivès, Corinne; 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Ohashi, Wataru; Yamagishi, Yuka; Mikamo, Hiroshige title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 date: 2020-09-30 journal: J Infect Chemother DOI: 10.1016/j.jiac.2020.09.027 sha: doc_id: 301080 cord_uid: xr7kl573 file: cache/cord-300964-knc0ruou.json key: cord-300964-knc0ruou authors: Hoffman, Tove; Nissen, Karolina; Krambrich, Janina; Rönnberg, Bengt; Akaberi, Dario; Esmaeilzadeh, Mouna; Salaneck, Erik; Lindahl, Johanna; Lundkvist, Åke title: Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 date: 2020-04-14 journal: Infect Ecol Epidemiol DOI: 10.1080/20008686.2020.1754538 sha: doc_id: 300964 cord_uid: knc0ruou file: cache/cord-300991-ipy24zxp.json key: cord-300991-ipy24zxp authors: Khan, Amira Sayed; Hichami, Aziz; Khan, Naim Akhtar title: Obesity and COVID-19: Oro-Naso-Sensory Perception date: 2020-07-08 journal: J Clin Med DOI: 10.3390/jcm9072158 sha: doc_id: 300991 cord_uid: ipy24zxp file: cache/cord-300847-ycuiso0g.json key: cord-300847-ycuiso0g authors: Li, Wei; 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M.; Bosch, Berend-Jan; Drosten, Christian; Koopmans, Marion P.G.; Haagmans, Bart L. title: SARS-CoV-2 specific antibody responses in COVID-19 patients date: 2020-03-20 journal: nan DOI: 10.1101/2020.03.18.20038059 sha: doc_id: 301313 cord_uid: 9595vm0k file: cache/cord-301227-ica5x0r1.json key: cord-301227-ica5x0r1 authors: Sun, Yi-Sheng; Xu, Fang; An, Qi; Chen, Chen; Yang, Zhang-Nv; Lu, Hang-Jing; Chen, Jian-Cai; Yao, Ping-Ping; Jiang, Jian-Min; Zhu, Han-Ping title: A SARS-CoV-2 variant with the 12-bp deletion at E gene date: 2020-10-29 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1837017 sha: doc_id: 301227 cord_uid: ica5x0r1 file: cache/cord-301233-nenw0f81.json key: cord-301233-nenw0f81 authors: Naydenova, Katerina; Muir, Kyle W.; Wu, Long-Fei; Zhang, Ziguo; Coscia, Francesca; Peet, Mathew J.; Castro-Hartmann, Pablo; Qian, Pu; Sader, Kasim; Dent, Kyle; Kimanius, Dari; Sutherland, John D.; Löwe, Jan; Barford, David; Russo, Christopher J. title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 journal: bioRxiv DOI: 10.1101/2020.10.21.347690 sha: doc_id: 301233 cord_uid: nenw0f81 file: cache/cord-301226-hmc2wmst.json key: cord-301226-hmc2wmst authors: Randazzo, Walter; Cuevas-Ferrando, Enric; Sanjuan, Rafael; Domingo-Calap, Pilar; Sanchez, Gloria title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 journal: nan DOI: 10.1101/2020.04.23.20076679 sha: doc_id: 301226 cord_uid: hmc2wmst file: cache/cord-301454-ayf42grs.json key: cord-301454-ayf42grs authors: Phyu Khin, Phyu; Cha, Seon-Heui; Jun, Hee-Sook; Han Lee, Jong title: A potential therapeutic combination for treatment of COVID-19: synergistic effect of DPP4 and RAAS suppression date: 2020-08-14 journal: Medical Hypotheses DOI: 10.1016/j.mehy.2020.110186 sha: doc_id: 301454 cord_uid: ayf42grs file: cache/cord-301388-p3juk2vv.json key: cord-301388-p3juk2vv authors: Yen, Muh-Yong; Schwartz, Jonathan; King, Chwan-Chuen; Lee, Chung-Ming; Hsueh, Po-Ren title: Recommendations for protecting against and mitigating the COVID-19 pandemic in long-term care facilities date: 2020-04-10 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.04.003 sha: doc_id: 301388 cord_uid: p3juk2vv file: cache/cord-301547-d4wt9dqp.json key: cord-301547-d4wt9dqp authors: Seng, J. 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L. title: Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics date: 2020-05-11 journal: nan DOI: 10.1101/2020.05.07.20094227 sha: doc_id: 301547 cord_uid: d4wt9dqp file: cache/cord-301484-y9l2hmqf.json key: cord-301484-y9l2hmqf authors: MASSAROTTI, Claudia; ADRIANO, Marco; CAGNACCI, Angelo; GORLERO, Franco; GUSTAVINO, Claudio; VALLERINO, Gabriele; PAOLUCCI, Roberta; DI LUCA, Martina; ANSERINI, Paola; FERRAIOLO, Antonella title: Asymptomatic SARS‐CoV‐2 infections in pregnant patients in an Italian city during complete lockdown date: 2020-08-25 journal: J Med Virol DOI: 10.1002/jmv.26458 sha: doc_id: 301484 cord_uid: y9l2hmqf file: cache/cord-301590-70qmpccs.json key: cord-301590-70qmpccs authors: Campos, António; Oliveira, Nuno; Martins, Joana; Arruda, Henrique; Sousa, João title: The Paradigm Shift of Ophthalmology in the COVID-19 Era date: 2020-09-14 journal: Clin Ophthalmol DOI: 10.2147/opth.s267427 sha: doc_id: 301590 cord_uid: 70qmpccs file: cache/cord-301556-f3m9gwvo.json key: cord-301556-f3m9gwvo authors: Huang, Jessie; Hume, Adam J.; Abo, Kristine M.; Werder, Rhiannon B.; Villacorta-Martin, Carlos; Alysandratos, Konstantinos-Dionysios; Beermann, Mary Lou; Simone-Roach, Chantelle; Lindstrom-Vautrin, Jonathan; Olejnik, Judith; Suder, Ellen L.; Bullitt, Esther; Hinds, Anne; Sharma, Arjun; Bosmann, Markus; Wang, Ruobing; Hawkins, Finn; Burks, Eric J.; Saeed, Mohsan; Wilson, Andrew A.; Mühlberger, Elke; Kotton, Darrell N. title: SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response date: 2020-09-18 journal: Cell Stem Cell DOI: 10.1016/j.stem.2020.09.013 sha: doc_id: 301556 cord_uid: f3m9gwvo file: cache/cord-301633-t8s4s0wo.json key: cord-301633-t8s4s0wo authors: Gralinski, Lisa E.; Menachery, Vineet D. title: Return of the Coronavirus: 2019-nCoV date: 2020-01-24 journal: Viruses DOI: 10.3390/v12020135 sha: doc_id: 301633 cord_uid: t8s4s0wo file: cache/cord-301535-eui41zyg.json key: cord-301535-eui41zyg authors: Chandler-Brown, Devon; Bueno, Anna M.; Atay, Oguzhan; Tsao, David S. title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 journal: bioRxiv DOI: 10.1101/2020.04.07.029199 sha: doc_id: 301535 cord_uid: eui41zyg file: cache/cord-301622-mn59vszt.json key: cord-301622-mn59vszt authors: Jomah, Shahamah; Asdaq, Syed Mohammed Basheeruddin; Al-Yamani, Mohammed Jaber title: Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review date: 2020-08-03 journal: J Infect Public Health DOI: 10.1016/j.jiph.2020.07.013 sha: doc_id: 301622 cord_uid: mn59vszt file: cache/cord-301638-2f8r37ns.json key: cord-301638-2f8r37ns authors: Bonney, Glenn Kunnath; Yujia, Gao; Chew, Claire Alexandra; Windsor, John Albert title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? 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Katterine; Rodríguez-Morales, Alfonso J. title: Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin date: 2020-04-24 journal: Ann Clin Microbiol Antimicrob DOI: 10.1186/s12941-020-00358-y sha: doc_id: 301947 cord_uid: b6nwaost file: cache/cord-301626-7ow1jja4.json key: cord-301626-7ow1jja4 authors: Li, Shih-Wen; Wang, Ching-Ying; Jou, Yu-Jen; Huang, Su-Hua; Hsiao, Li-Hsin; Wan, Lei; Lin, Ying-Ju; Kung, Szu-Hao; Lin, Cheng-Wen title: SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6 date: 2016-05-05 journal: Int J Mol Sci DOI: 10.3390/ijms17050678 sha: doc_id: 301626 cord_uid: 7ow1jja4 file: cache/cord-301771-43fl2gwp.json key: cord-301771-43fl2gwp authors: Ouassou, Hayat; Kharchoufa, Loubna; Bouhrim, Mohamed; Daoudi, Nour Elhouda; Imtara, Hamada; Bencheikh, Noureddine; ELbouzidi, Amine; Bnouham, Mohamed title: The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention date: 2020-07-10 journal: J Immunol Res DOI: 10.1155/2020/1357983 sha: doc_id: 301771 cord_uid: 43fl2gwp file: cache/cord-301978-9uu318tp.json key: cord-301978-9uu318tp authors: Yin, Xiaoping; Dong, Li; Zhang, Yu; Bian, Weilin; Li, Hongjun title: A mild type of childhood Covid-19 - A case report date: 2020-03-27 journal: Radiol Infect Dis DOI: 10.1016/j.jrid.2020.03.004 sha: doc_id: 301978 cord_uid: 9uu318tp file: cache/cord-301828-qux5hvcw.json key: cord-301828-qux5hvcw authors: Khalifa, Ibrahim; Zhu, Wei; Mohammed, Hammad Hamed Hammad; Dutta, Kunal; Li, Chunmei title: Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date: 2020-08-11 journal: J Food Biochem DOI: 10.1111/jfbc.13432 sha: doc_id: 301828 cord_uid: qux5hvcw file: cache/cord-301779-y07xjnpe.json key: cord-301779-y07xjnpe authors: Fox, Sharon E; Akmatbekov, Aibek; Harbert, Jack L; Li, Guang; Quincy Brown, J; Vander Heide, Richard S title: Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans date: 2020-05-27 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30243-5 sha: doc_id: 301779 cord_uid: y07xjnpe file: cache/cord-302115-r39ser2c.json key: cord-302115-r39ser2c authors: Matricardi, Paolo Maria; Dal Negro, Roberto Walter; Nisini, Roberto title: The first, holistic immunological model of COVID‐19: implications for prevention, diagnosis, and public health measures date: 2020-05-02 journal: Pediatr Allergy Immunol DOI: 10.1111/pai.13271 sha: doc_id: 302115 cord_uid: r39ser2c file: cache/cord-302075-ctd9sutv.json key: cord-302075-ctd9sutv authors: Tetro, Jason A. title: Is COVID-19 receiving ADE from other coronaviruses? date: 2020-02-22 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.02.006 sha: doc_id: 302075 cord_uid: ctd9sutv file: cache/cord-301744-rx7ywew5.json key: cord-301744-rx7ywew5 authors: Kelleni, Mina T. title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality date: 2020-08-15 journal: J Infect DOI: 10.1016/j.jinf.2020.08.018 sha: doc_id: 301744 cord_uid: rx7ywew5 file: cache/cord-301876-d2j9wpqk.json key: cord-301876-d2j9wpqk authors: Kalita, Parismita; Padhi, AdityaK.; Zhang, Kam Y.J.; Tripathi, Timir title: Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2 date: 2020-05-04 journal: Microb Pathog DOI: 10.1016/j.micpath.2020.104236 sha: doc_id: 301876 cord_uid: d2j9wpqk file: cache/cord-301946-erzh30mt.json key: cord-301946-erzh30mt authors: Kwak-Kim, Joanne; Ota, Kuniaki; Sung, Nayoung; Huang, Changsheng; Alsubki, Lujain; Lee, Sungki; Han, Jae Won; Han, Aera; Yang, Xiuhua; Saab, Wael; Derbala, Youssef; Wang, Wen-Juan; He, Qiaohua; Liao, Aihua; Takahashi, Toshifumi; Cavalcante, Marcelo Borges; Barini, Ricardo; Bao, Shihua; Fukui, Atsushi; Coulam, Carolyn title: COVID-19 and immunomodulation treatment for women with reproductive failures date: 2020-06-12 journal: J Reprod Immunol DOI: 10.1016/j.jri.2020.103168 sha: doc_id: 301946 cord_uid: erzh30mt file: cache/cord-302020-ypsh3rjv.json key: cord-302020-ypsh3rjv authors: Kim, Dongwan; Lee, Joo-Yeon; Yang, Jeong-Sun; Kim, Jun Won; Kim, V. Narry; Chang, Hyeshik title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 journal: Cell DOI: 10.1016/j.cell.2020.04.011 sha: doc_id: 302020 cord_uid: ypsh3rjv file: cache/cord-302146-51hof7it.json key: cord-302146-51hof7it authors: Cross, Thomas J.; Takahashi, Gemma R.; Diessner, Elizabeth M.; Crosby, Marquise G.; Farahmand, Vesta; Zhuang, Shannon; Butts, Carter T.; Martin, Rachel W. title: Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date: 2020-05-15 journal: bioRxiv DOI: 10.1101/2020.05.15.097493 sha: doc_id: 302146 cord_uid: 51hof7it file: cache/cord-302160-4yfvspaq.json key: cord-302160-4yfvspaq authors: Ruetalo, Natalia; Businger, Ramona; Schindler, Michael title: Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.09.22.308098 sha: doc_id: 302160 cord_uid: 4yfvspaq file: cache/cord-302125-96w0nh9q.json key: cord-302125-96w0nh9q authors: Péré, Hélène; Wack, Maxime; Védie, Benoit; Guinet, Nathalie Demory; Najiby, Kassis Chikani; Janot, Laurence; Bélec, Laurent; Veyer, David title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date: 2020-09-03 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104617 sha: doc_id: 302125 cord_uid: 96w0nh9q file: cache/cord-302163-0jav84zw.json key: cord-302163-0jav84zw authors: Anastassopoulou, Cleo; Gkizarioti, Zoi; Patrinos, George P.; Tsakris, Athanasios title: Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity date: 2020-10-22 journal: Hum Genomics DOI: 10.1186/s40246-020-00290-4 sha: doc_id: 302163 cord_uid: 0jav84zw file: cache/cord-301974-4wn40ivq.json key: cord-301974-4wn40ivq authors: Berry, Jody D; Jones, Steven; Drebot, Michael A; Andonov, Anton; Sabara, Marta; Yuan, Xin Y; Weingartl, Hana; Fernando, Lisa; Marszal, Peter; Gren, Jason; Nicolas, Brigitte; Andonova, Maya; Ranada, Francesca; Gubbins, Michael J; Ball, T.Blake; Kitching, Paul; Li, Yan; Kabani, Amin; Plummer, Frank title: Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus date: 2004-09-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.04.009 sha: doc_id: 301974 cord_uid: 4wn40ivq file: cache/cord-301921-i1o18nmw.json key: cord-301921-i1o18nmw authors: Sernicola, Alvise; Alaibac, Mauro title: How to Deal With Post-viral Cutaneous Eruptions in the Era of Coronavirus Infection date: 2020-05-12 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00224 sha: doc_id: 301921 cord_uid: i1o18nmw file: cache/cord-301943-qdtfjdxr.json key: cord-301943-qdtfjdxr authors: Javelot, H; Weiner, L title: Panique et pandémie: revue de la littérature sur les liens entre le trouble panique et l'épidémie à SARS-CoV-2 date: 2020-05-21 journal: Encephale DOI: 10.1016/j.encep.2020.05.010 sha: doc_id: 301943 cord_uid: qdtfjdxr file: cache/cord-302166-tah3jdw0.json key: cord-302166-tah3jdw0 authors: Zhang, Shen-Ying; Zhang, Qian; Casanova, Jean-Laurent; Su, Helen C. title: Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity? date: 2020-06-18 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0373-7 sha: doc_id: 302166 cord_uid: tah3jdw0 file: cache/cord-302316-raf5rlkq.json key: cord-302316-raf5rlkq authors: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13611 sha: doc_id: 302316 cord_uid: raf5rlkq file: cache/cord-302393-hrz3bypr.json key: cord-302393-hrz3bypr authors: Omrani, Ali S.; Almaslamani, Muna A.; Daghfal, Joanne; Alattar, Rand A.; Elgara, Mohamed; Shaar, Shahd H.; Ibrahim, Tawheeda B. H.; Zaqout, Ahmed; Bakdach, Dana; Akkari, Abdelrauof M.; Baiou, Anas; Alhariri, Bassem; Elajez, Reem; Husain, Ahmed A. M.; Badawi, Mohamed N.; Abid, Fatma Ben; Abu Jarir, Sulieman H.; Abdalla, Shiema; Kaleeckal, Anvar; Choda, Kris; Chinta, Venkateswara R.; Sherbash, Mohamed A.; Al-Ismail, Khalil; Abukhattab, Mohammed; Ait Hssain, Ali; Coyle, Peter V.; Bertollini, Roberto; Frenneaux, Michael P.; Alkhal, Abdullatif; Al-Kuwari, Hanan M. title: The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date: 2020-10-19 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05511-8 sha: doc_id: 302393 cord_uid: hrz3bypr file: cache/cord-302381-oujsmf8d.json key: cord-302381-oujsmf8d authors: Rankin, John title: Godzilla in the corridor: The Ontario SARS crisis in historical perspective date: 2006-06-30 journal: Intensive and Critical Care Nursing DOI: 10.1016/j.iccn.2005.10.001 sha: doc_id: 302381 cord_uid: oujsmf8d file: cache/cord-302527-n53d5en0.json key: cord-302527-n53d5en0 authors: Dadlani, Shashi title: SARS-CoV-2 Transmission in a Dental Practice in Spain: After the Outbreak date: 2020-06-29 journal: Int J Dent DOI: 10.1155/2020/8828616 sha: doc_id: 302527 cord_uid: n53d5en0 file: cache/cord-302414-g5onwhg1.json key: cord-302414-g5onwhg1 authors: Tahir ul Qamar, Muhammad; Shahid, Farah; Aslam, Sadia; Ashfaq, Usman Ali; Aslam, Sidra; Fatima, Israr; Fareed, Muhammad Mazhar; Zohaib, Ali; Chen, Ling-Ling title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 journal: Infect Dis Poverty DOI: 10.1186/s40249-020-00752-w sha: doc_id: 302414 cord_uid: g5onwhg1 file: cache/cord-302358-vou46eie.json key: cord-302358-vou46eie authors: Fomsgaard, Anna S; Rosenstierne, Maiken W title: An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage date: 2020-03-30 journal: nan DOI: 10.1101/2020.03.27.20044495 sha: doc_id: 302358 cord_uid: vou46eie file: cache/cord-302147-6r67g5zk.json key: cord-302147-6r67g5zk authors: Kayaaslan, Bircan; Korukluoglu, Gulay; Hasanoglu, Imran; Kalem, Ayse Kaya; Eser, Fatma; Akinci, Esragul; Guner, Rahmet title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact date: 2020-10-16 journal: Urol Int DOI: 10.1159/000511618 sha: doc_id: 302147 cord_uid: 6r67g5zk file: cache/cord-302485-hhsa76k8.json key: cord-302485-hhsa76k8 authors: Wu, Yuntao; Ho, Wenzhe; Huang, Yaowei; Jin, Dong-Yan; Li, Shiyue; Liu, Shan-Lu; Liu, Xuefeng; Qiu, Jianming; Sang, Yongming; Wang, Qiuhong; Yuen, Kwok-Yung; Zheng, Zhi-Ming title: SARS-CoV-2 is an appropriate name for the new coronavirus date: 2020-03-06 journal: Lancet DOI: 10.1016/s0140-6736(20)30557-2 sha: doc_id: 302485 cord_uid: hhsa76k8 file: cache/cord-302409-40ktyt5q.json key: cord-302409-40ktyt5q authors: Wang, Jie; Feng, Haiting; Zhang, Sheng; Ni, Zuowei; Ni, Lingmei; Chen, Yu; Zhuo, Lixin; Zhong, Zifeng; Qu, Tingting title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.024 sha: doc_id: 302409 cord_uid: 40ktyt5q file: cache/cord-302195-25gjbyi1.json key: cord-302195-25gjbyi1 authors: Al Huraimel, Khalid; Alhosani, Mohamed; Kunhabdulla, Shabana; Stietiya, Mohammed Hashem title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.140946 sha: doc_id: 302195 cord_uid: 25gjbyi1 file: cache/cord-302228-n5o6jfs2.json key: cord-302228-n5o6jfs2 authors: Lodise, Thomas P.; Rybak, Michael J. title: COVID‐19: Important Therapy Considerations and Approaches in this Hour of Need date: 2020-05-05 journal: Pharmacotherapy DOI: 10.1002/phar.2396 sha: doc_id: 302228 cord_uid: n5o6jfs2 file: cache/cord-302238-l8j1vy0y.json key: cord-302238-l8j1vy0y authors: Shah, Prakesh S.; Diambomba, Yenge; Acharya, Ganesh; Morris, Shaun K.; Bitnun, Ari title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates date: 2020-04-21 journal: Acta Obstet Gynecol Scand DOI: 10.1111/aogs.13870 sha: doc_id: 302238 cord_uid: l8j1vy0y file: cache/cord-302584-fwdpzv85.json key: cord-302584-fwdpzv85 authors: Zhu, Ying; Liu, Mo; Zhao, Weiguang; Zhang, Jianlin; Zhang, Xue; Wang, Ke; Gu, Chunfang; Wu, Kailang; Li, Yan; Zheng, Congyi; Xiao, Gengfu; Yan, Huimin; Zhang, Jiamin; Guo, Deyin; Tien, Po; Wu, Jianguo title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date: 2005-01-01 journal: Virus Genes DOI: 10.1007/s11262-004-4586-9 sha: doc_id: 302584 cord_uid: fwdpzv85 file: cache/cord-302541-0upiu6iq.json key: cord-302541-0upiu6iq authors: Gupta, Abhishek; Singla, Mahima; Bhatia, Himanshu; Sharma, Ved title: Lockdown—the only solution to defeat COVID-19 date: 2020-05-06 journal: Int J Diabetes Dev Ctries DOI: 10.1007/s13410-020-00826-3 sha: doc_id: 302541 cord_uid: 0upiu6iq file: cache/cord-302616-1uwrcvjx.json key: cord-302616-1uwrcvjx authors: Steenblock, Charlotte; Todorov, Vladimir; Kanczkowski, Waldemar; Eisenhofer, Graeme; Schedl, Andreas; Wong, Ma-Li; Licinio, Julio; Bauer, Michael; Young, Allan H.; Gainetdinov, Raul R.; Bornstein, Stefan R. title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis date: 2020-05-07 journal: Mol Psychiatry DOI: 10.1038/s41380-020-0758-9 sha: doc_id: 302616 cord_uid: 1uwrcvjx file: cache/cord-302576-fv2ib5vc.json key: cord-302576-fv2ib5vc authors: Barisione, Emanuela; Grillo, Federica; Ball, Lorenzo; Bianchi, Rita; Grosso, Marco; Morbini, Patrizia; Pelosi, Paolo; Patroniti, Nicolò Antonino; De Lucia, Arduino; Orengo, Giovanni; Gratarola, Angelo; Verda, Marta; Cittadini, Giuseppe; Mastracci, Luca; Fiocca, Roberto title: Fibrotic progression and radiologic correlation in matched lung samples from COVID-19 post-mortems date: 2020-09-28 journal: Virchows Arch DOI: 10.1007/s00428-020-02934-1 sha: doc_id: 302576 cord_uid: fv2ib5vc file: cache/cord-302442-jhio7mrl.json key: cord-302442-jhio7mrl authors: Chrzanowski, Wojciech; Kim, Sally Yunsun; McClements, Lana title: Can Stem Cells Beat COVID-19: Advancing Stem Cells and Extracellular Vesicles Toward Mainstream Medicine for Lung Injuries Associated With SARS-CoV-2 Infections date: 2020-05-26 journal: Front Bioeng Biotechnol DOI: 10.3389/fbioe.2020.00554 sha: doc_id: 302442 cord_uid: jhio7mrl file: cache/cord-302608-fw4pmaoc.json key: cord-302608-fw4pmaoc authors: Huang, Jiao-Mei; Jan, Syed Sajid; Wei, Xiaobin; Wan, Yi; Ouyang, Songying title: Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 journal: bioRxiv DOI: 10.1101/2020.03.16.993816 sha: doc_id: 302608 cord_uid: fw4pmaoc file: cache/cord-302733-rfuyd041.json key: cord-302733-rfuyd041 authors: Dellicour, Simon; Durkin, Keith; Hong, Samuel L.; Vanmechelen, Bert; Martí-Carreras, Joan; Gill, Mandev S.; Meex, Cécile; Bontems, Sébastien; André, Emmanuel; Gilbert, Marius; Walker, Conor; De Maio, Nicola; Faria, Nuno R.; Hadfield, James; Hayette, Marie-Pierre; Bours, Vincent; Wawina-Bokalanga, Tony; Artesi, Maria; Baele, Guy; Maes, Piet title: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date: 2020-10-21 journal: bioRxiv DOI: 10.1101/2020.05.05.078758 sha: doc_id: 302733 cord_uid: rfuyd041 file: cache/cord-302786-ibt7mupq.json key: cord-302786-ibt7mupq authors: Suwanwongse, Kulachanya; Shabarek, Nehad title: Fatal Outcome in a Kidney-Pancreas Transplant Recipient With COVID-19 date: 2020-06-18 journal: Cureus DOI: 10.7759/cureus.8691 sha: doc_id: 302786 cord_uid: ibt7mupq file: cache/cord-303173-q88zdf03.json key: cord-303173-q88zdf03 authors: Panchaud, Alice; Favre, Guillaume; Pomar, Leo; Vouga, Manon; Aebi-Popp, Karoline; Baud, David title: An international registry for emergent pathogens and pregnancy date: 2020-04-27 journal: Lancet DOI: 10.1016/s0140-6736(20)30981-8 sha: doc_id: 303173 cord_uid: q88zdf03 file: cache/cord-302813-963ypqow.json key: cord-302813-963ypqow authors: Tegally, H.; 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J.; Giandhari, J.; Pillay, S.; Msomi, N.; Mlisana, K.; Bhiman, J.; Allam, M.; Ismail, A.; Engelbrecht, S.; Van Zyl, G.; Preiser, W.; Williamson, C.; Pettruccione, F.; Sigal, A.; Gazy, I.; Hardie, D.; Hsiao, M.; Martin, D.; York, D.; Goedhals, D.; San, E. J.; Giovanetti, M.; Lourenco, J.; Alcantara, L. C. J.; de Oliveira, T. title: Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. date: 2020-10-30 journal: nan DOI: 10.1101/2020.10.28.20221143 sha: doc_id: 302813 cord_uid: 963ypqow file: cache/cord-303384-bgvagdft.json key: cord-303384-bgvagdft authors: Bilinska, Katarzyna; Butowt, Rafal title: Anosmia in COVID-19: A Bumpy Road to Establishing a Cellular Mechanism date: 2020-07-16 journal: ACS Chem Neurosci DOI: 10.1021/acschemneuro.0c00406 sha: doc_id: 303384 cord_uid: bgvagdft file: cache/cord-302939-z0071rwa.json key: cord-302939-z0071rwa authors: Erdeve, Ömer; Çetinkaya, Merih; Baş, Ahmet Yağmur; Narlı, Nejat; Duman, Nuray; Vural, Mehmet; Koç, Esin title: The Turkish Neonatal Society proposal for the management of COVID-19 in the neonatal intensive care unit date: 2020-06-19 journal: Turk Pediatri Ars DOI: 10.14744/turkpediatriars.2020.43788 sha: doc_id: 302939 cord_uid: z0071rwa file: cache/cord-303027-r2jgu2be.json key: cord-303027-r2jgu2be authors: Lu, Yen-Ta; Chen, Pei-Jan; Sheu, Chin-Yin; Liu, Ching-Lung title: Viral load and outcome in SARS infection: The role of personal protective equipment in the emergency department date: 2006-01-24 journal: J Emerg Med DOI: 10.1016/j.jemermed.2005.03.011 sha: doc_id: 303027 cord_uid: r2jgu2be file: cache/cord-302902-34vftqt9.json key: cord-302902-34vftqt9 authors: Law, Brenda Hiu Yan; Cheung, Po-Yin; Aziz, Khalid; Schmölzer, Georg M. title: Effect of COVID-19 Precautions on Neonatal Resuscitation Practice: A Balance Between Healthcare Provider Safety, Infection Control, and Effective Neonatal Care date: 2020-08-18 journal: Front Pediatr DOI: 10.3389/fped.2020.00478 sha: doc_id: 302902 cord_uid: 34vftqt9 file: cache/cord-302983-3v5bc80z.json key: cord-302983-3v5bc80z authors: Matterne, Uwe; Egger, Nina; Tempes, Jana; Tischer, Christina; Lander, Jonas; Dierks, Marie-Luise; Bitzer, Eva-Maria; Apfelbacher, Christian title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review date: 2020-10-10 journal: Patient Educ Couns DOI: 10.1016/j.pec.2020.10.012 sha: doc_id: 302983 cord_uid: 3v5bc80z file: cache/cord-302707-cap2rgf7.json key: cord-302707-cap2rgf7 authors: Ng, Dianna L.; Goldgof, Gregory M.; Shy, Brian R.; Levine, Andrew G.; Balcerek, Joanna; Bapat, Sagar P.; Prostko, John; Rodgers, Mary; Coller, Kelly; Pearce, Sandra; Franz, Sergej; Du, Li; Stone, Mars; Pillai, Satish K.; Sotomayor-Gonzalez, Alicia; Servellita, Venice; Martin, Claudia Sanchez San; Granados, Andrea; Glasner, Dustin R.; Han, Lucy M.; Truong, Kent; Akagi, Naomi; Nguyen, David N.; Neumann, Neil M.; Qazi, Daniel; Hsu, Elaine; Gu, Wei; Santos, Yale A.; Custer, Brian; Green, Valerie; Williamson, Phillip; Hills, Nancy K.; Lu, Chuanyi M.; Whitman, Jeffrey D.; Stramer, Susan L.; Wang, Candace; Reyes, Kevin; Hakim, Jill M. C.; Sujishi, Kirk; Alazzeh, Fariba; Pham, Lori; Thornborrow, Edward; Oon, Ching-Ying; Miller, Steve; Kurtz, Theodore; Simmons, Graham; Hackett, John; Busch, Michael P.; Chiu, Charles Y. title: SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood date: 2020-09-17 journal: Nat Commun DOI: 10.1038/s41467-020-18468-8 sha: doc_id: 302707 cord_uid: cap2rgf7 file: cache/cord-303017-4zx94rm6.json key: cord-303017-4zx94rm6 authors: Barbieri, Antonio; Robinson, Nirmal; Palma, Giuseppe; Maurea, Nicola; Desiderio, Vincenzo; Botti, Gerardo title: Can Beta-2-Adrenergic Pathway Be a New Target to Combat SARS-CoV-2 Hyperinflammatory Syndrome?—Lessons Learned From Cancer date: 2020-09-30 journal: Front Immunol DOI: 10.3389/fimmu.2020.588724 sha: doc_id: 303017 cord_uid: 4zx94rm6 file: cache/cord-302912-aqutzlx4.json key: cord-302912-aqutzlx4 authors: Liu, Ziteng; Ying, Ying title: The Inhibitory Effect of Curcumin on Virus-Induced Cytokine Storm and Its Potential Use in the Associated Severe Pneumonia date: 2020-06-12 journal: Front Cell Dev Biol DOI: 10.3389/fcell.2020.00479 sha: doc_id: 302912 cord_uid: aqutzlx4 file: cache/cord-302821-b9ikg0xy.json key: cord-302821-b9ikg0xy authors: Gawałko, Monika; Kapłon-Cieślicka, Agnieszka; Hohl, Mathias; Dobrev, Dobromir; Linz, Dominik title: COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications date: 2020-09-01 journal: Int J Cardiol Heart Vasc DOI: 10.1016/j.ijcha.2020.100631 sha: doc_id: 302821 cord_uid: b9ikg0xy file: cache/cord-303022-9hqoq7tf.json key: cord-303022-9hqoq7tf authors: Madapusi Balaji, Thodur; Varadarajan, Saranya; Vishal Rao, U.S.; Thirumal Raj, A.; Patil, Shankaragouda; Arakeri, Gururaj; Brennan, Peter A title: Oral cancer and periodontal disease increase the risk of COVID 19? A mechanism mediated through furin and cathepsin overexpression date: 2020-06-01 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109936 sha: doc_id: 303022 cord_uid: 9hqoq7tf file: cache/cord-303111-iv4lzpev.json key: cord-303111-iv4lzpev authors: Almazán, Fernando; Sola, Isabel; Zuñiga, Sonia; Marquez-Jurado, Silvia; Morales, Lucia; Becares, Martina; Enjuanes, Luis title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 journal: Virus Res DOI: 10.1016/j.virusres.2014.09.006 sha: doc_id: 303111 cord_uid: iv4lzpev file: cache/cord-302735-zal2gr28.json key: cord-302735-zal2gr28 authors: Priyanka; Choudhary, Om Prakash; Singh, Indraj; Patra, Gautam title: Aerosol transmission of SARS-CoV-2: The unresolved paradox date: 2020-09-04 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101869 sha: doc_id: 302735 cord_uid: zal2gr28 file: cache/cord-303056-bdse9o26.json key: cord-303056-bdse9o26 authors: Okada, Masaji; Okuno, Yoshinobu; Hashimoto, Satomi; Kita, Yoko; Kanamaru, Noriko; Nishida, Yasuko; Tsunai, Yoshie; Inoue, Ruriko; Nakatani, Hitoshi; Fukamizu, Reiko; Namie, Yumi; Yamada, Junko; Takao, Kyoko; Asai, Ritsuko; Asaki, Ryoko; Kase, Tetsuo; Takemoto, Yuji; Yoshida, Shigeto; Peiris, J.S.M.; Chen, Pei-Jer; Yamamoto, Naoki; Nomura, Tatsuji; Ishida, Isao; Morikawa, Shigeru; Tashiro, Masato; Sakatani, Mitsunori title: Development of vaccines and passive immunotherapy against SARS corona virus using SCID-PBL/hu mouse models date: 2007-04-20 journal: Vaccine DOI: 10.1016/j.vaccine.2007.01.032 sha: doc_id: 303056 cord_uid: bdse9o26 file: cache/cord-303539-gimz41yb.json key: cord-303539-gimz41yb authors: Goudouris, Ekaterini S. title: Laboratory diagnosis of COVID-19() date: 2020-08-31 journal: J Pediatr (Rio J) DOI: 10.1016/j.jped.2020.08.001 sha: doc_id: 303539 cord_uid: gimz41yb file: cache/cord-303061-vvzkpetn.json key: cord-303061-vvzkpetn authors: Olyaee, Mohammad Hossein; Pirgazi, Jamshid; Khalifeh, Khosrow; Khanteymoori, Alireza title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation date: 2020-08-07 journal: Data Brief DOI: 10.1016/j.dib.2020.106144 sha: doc_id: 303061 cord_uid: vvzkpetn file: cache/cord-303407-n7j56sci.json key: cord-303407-n7j56sci authors: Popofsky, Stephanie; Noor, Asif; Leavens-Maurer, Jill; Quintos-Alagheband, Maria Lyn; Mock, Ann; Vinci, Alexandra; Magri, Eileen; Akerman, Meredith; Noyola, Estela; Rigaud, Mona; Pak, Billy; Lighter, Jennifer; Ratner, Adam J.; Hanna, Nazeeh; Krilov, Leonard title: Impact of Maternal SARS-CoV-2 Detection on Breastfeeding Due to Infant Separation at Birth date: 2020-08-10 journal: J Pediatr DOI: 10.1016/j.jpeds.2020.08.004 sha: doc_id: 303407 cord_uid: n7j56sci file: cache/cord-303135-rx21ajiw.json key: cord-303135-rx21ajiw authors: Jian, Li; Yi, Wei; Zhang, Nan; Wen, Weiping; Krysko, Olga; Song, Woo-Jung; Bachert, Claus title: Perspective: COVID-19, implications of nasal diseases and consequences for their management date: 2020-05-01 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2020.04.030 sha: doc_id: 303135 cord_uid: rx21ajiw file: cache/cord-303143-4sksz6xz.json key: cord-303143-4sksz6xz authors: Wu, Y. P.; Liu, Z. H.; Wei, R.; Pan, S. D.; Mao, N. Y.; Chen, B.; Han, J. J.; Zhang, F. S.; Holmskov, U.; Xia, Z. L.; De Groot, P. G.; Reid, K. B. M.; Xu, W. B.; Sorensen, G. L. title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients date: 2009-03-19 journal: Scand J Immunol DOI: 10.1111/j.1365-3083.2009.02245.x sha: doc_id: 303143 cord_uid: 4sksz6xz file: cache/cord-303069-ss6g3jkg.json key: cord-303069-ss6g3jkg authors: Jakhar, Renu; Gakhar, S.K title: An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date: 2020-05-26 journal: bioRxiv DOI: 10.1101/2020.05.26.115790 sha: doc_id: 303069 cord_uid: ss6g3jkg file: cache/cord-303330-zh8wzza5.json key: cord-303330-zh8wzza5 authors: Magleby, Reed; Westblade, Lars F; Trzebucki, Alex; Simon, Matthew S; Rajan, Mangala; Park, Joel; Goyal, Parag; Safford, Monika M; Satlin, Michael J title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa851 sha: doc_id: 303330 cord_uid: zh8wzza5 file: cache/cord-303054-s1clwunc.json key: cord-303054-s1clwunc authors: Velly, Lionel; Gayat, Etienne; Jong, Audrey De; Quintard, Hervé; Weiss, Emmanuel; Cuvillon, Philippe; Audibert, Gerard; Amour, Julien; Beaussier, Marc; Biais, Matthieu; Bloc, Sébastien; Bonnet, Marie Pierre; Bouzat, Pierre; Brezac, Gilles; Dahyot-Fizelier, Claire; Dahmani, Souhayl; de Queiroz, Mathilde; Maria, Sophie Di; Ecoffey, Claude; Futier, Emmanuel; Geeraerts, Thomas; Jaber, Haithem; Heyer, Laurent; Hoteit, Rim; Joannes-Boyau, Olivier; Kern, Delphine; Langeron, Olivier; Lasocki, Sigismond; Launey, Yoan; Saché, Frederic le; Lukaszewicz, Anne Claire; Maurice-Szamburski, Axel; Mayeur, Nicolas; Michel, Fabrice; Minville, Vincent; Mirek, Sébastien; Montravers, Philippe; Morau, Estelle; Muller, Laurent; Muret, Jane; Nouette-Gaulain, Karine; Orban, Jean Christophe; Orliaguet, Gilles; Perrigault, Pierre François; Plantet, Florence; Pottecher, Julien; Quesnel, Christophe; Reubrecht, Vanessa; Rozec, Bertrand; Tavernier, Benoit; Veber, Benoit; Veyckmans, Francis; Charbonneau, Hélène; Constant, Isabelle; Frasca, Denis; Fischer, Marc-Olivier; Huraux, Catherine; Blet, Alice; Garnier, Marc title: Guidelines: Anaesthesia in the context of COVID-19 pandemic date: 2020-06-05 journal: Anaesth Crit Care Pain Med DOI: 10.1016/j.accpm.2020.05.012 sha: doc_id: 303054 cord_uid: s1clwunc file: cache/cord-302920-jkr438p9.json key: cord-302920-jkr438p9 authors: Gasser, Romain; Cloutier, Marc; Prévost, Jérémie; Fink, Corby; Ducas, Éric; Ding, Shilei; Dussault, Nathalie; Landry, Patricia; Tremblay, Tony; Laforce-Lavoie, Audrey; Lewin, Antoine; Beaudoin-Bussières, Guillaume; Laumaea, Annemarie; Medjahed, Halima; Larochelle, Catherine; Richard, Jonathan; Dekaban, Gregory A.; Dikeakos, Jimmy D.; Bazin, Renée; Finzi, Andrés title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date: 2020-10-09 journal: bioRxiv DOI: 10.1101/2020.10.09.333278 sha: doc_id: 302920 cord_uid: jkr438p9 file: cache/cord-303363-uu9hb1c9.json key: cord-303363-uu9hb1c9 authors: Karimi, Mehran; De Sanctis, Vincenzo title: Implications of SARSr-CoV 2 infection in thalassemias: Do patients fall into the “high clinical risk” category? date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9592 sha: doc_id: 303363 cord_uid: uu9hb1c9 file: cache/cord-302806-1e99cygs.json key: cord-302806-1e99cygs authors: Bozkurt, Banu; Eğrilmez, Sait; Şengör, Tomris; Yıldırım, Özlem; İrkeç, Murat title: The COVID-19 Pandemic: Clinical Information for Ophthalmologists date: 2020-04-29 journal: Turk J Ophthalmol DOI: 10.4274/tjo.galenos.2020.29805 sha: doc_id: 302806 cord_uid: 1e99cygs file: cache/cord-303018-3ka72y3p.json key: cord-303018-3ka72y3p authors: Ng, Siew C; Tilg, Herbert title: COVID-19 and the gastrointestinal tract: more than meets the eye date: 2020-04-09 journal: Gut DOI: 10.1136/gutjnl-2020-321195 sha: doc_id: 303018 cord_uid: 3ka72y3p file: cache/cord-303216-1pbuywz6.json key: cord-303216-1pbuywz6 authors: Das, Gaurav; Mukherjee, Nabanita; Ghosh, Surajit title: Neurological Insights of COVID-19 Pandemic date: 2020-04-22 journal: ACS Chem Neurosci DOI: 10.1021/acschemneuro.0c00201 sha: doc_id: 303216 cord_uid: 1pbuywz6 file: cache/cord-303377-lkewcf8a.json key: cord-303377-lkewcf8a authors: Dimke, H.; Larsen, S. 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M.; Fernandez Soto, D.; Esteso, G.; Caceres-Martell, Y.; Gardeta, S.; Prat, S.; Mateu-Alberoa, T.; Gabrie, L.; Lopez-Granados, E.; Sanchez-Madrid, F.; Rodriguez-Frade, J. M.; Reyburn, H. T.; Vales-Gomez, M. title: SARS-Cov-2 cysteine-like protease (Mpro) is immunogenic and can be detected in serum and saliva of COVID-19-seropositive individuals date: 2020-07-18 journal: nan DOI: 10.1101/2020.07.16.20155853 sha: doc_id: 303745 cord_uid: wx3udkee file: cache/cord-303960-86mukxg1.json key: cord-303960-86mukxg1 authors: Rahimi, Farid; Bezmin Abadi, Amin Talebi title: Tackling the COVID-19 Pandemic date: 2020-04-24 journal: Arch Med Res DOI: 10.1016/j.arcmed.2020.04.012 sha: doc_id: 303960 cord_uid: 86mukxg1 file: cache/cord-303585-8py6joh6.json key: cord-303585-8py6joh6 authors: Verma, Surjeet; Twilley, Danielle; Esmear, Tenille; Oosthuizen, Carel B.; Reid, Anna-Mari; Nel, Marizé; Lall, Namrita title: Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19) date: 2020-09-25 journal: Front Pharmacol DOI: 10.3389/fphar.2020.561334 sha: doc_id: 303585 cord_uid: 8py6joh6 file: cache/cord-303609-9217t0ui.json key: cord-303609-9217t0ui authors: Baselga, María Trinidad; Fernández, María Luisa; Marín, Antonio; Fernández-Capitán, Carmen; Lorenzo, Alicia; Martínez-Alés, Gonzalo; Quintana, Manuel title: Trombosis y COVID-19: revisión de alcance date: 2020-09-24 journal: nan DOI: 10.1016/j.acci.2020.09.002 sha: doc_id: 303609 cord_uid: 9217t0ui file: cache/cord-303880-zv4nbz9p.json key: cord-303880-zv4nbz9p authors: Tsikala Vafea, Maria; Atalla, Eleftheria; Georgakas, Joanna; Shehadeh, Fadi; Mylona, Evangelia K.; Kalligeros, Markos; Mylonakis, Eleftherios title: Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19 date: 2020-06-24 journal: Cell Mol Bioeng DOI: 10.1007/s12195-020-00629-w sha: doc_id: 303880 cord_uid: zv4nbz9p file: cache/cord-303959-e1654g5j.json key: cord-303959-e1654g5j authors: Vitiello, Antonio; Pelliccia, Chiara; Ferrara, Francesco title: COVID-19 Patients with Pulmonary Fibrotic Tissue: Clinical Pharmacological Rational of Antifibrotic Therapy date: 2020-08-27 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00487-7 sha: doc_id: 303959 cord_uid: e1654g5j file: cache/cord-304088-xkg0ylz8.json key: cord-304088-xkg0ylz8 authors: Zhu, Han; Rhee, June-Wha; Cheng, Paul; Waliany, Sarah; Chang, Amy; Witteles, Ronald M.; Maecker, Holden; Davis, Mark M.; Nguyen, Patricia K.; Wu, Sean M. title: Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date: 2020-04-21 journal: Curr Cardiol Rep DOI: 10.1007/s11886-020-01292-3 sha: doc_id: 304088 cord_uid: xkg0ylz8 file: cache/cord-303651-fkdep6cp.json key: cord-303651-fkdep6cp authors: Thompson, Robin N.; Hollingsworth, T. Déirdre; Isham, Valerie; Arribas-Bel, Daniel; Ashby, Ben; Britton, Tom; Challenor, Peter; Chappell, Lauren H. K.; Clapham, Hannah; Cunniffe, Nik J.; Dawid, A. Philip; Donnelly, Christl A.; Eggo, Rosalind M.; Funk, Sebastian; Gilbert, Nigel; Glendinning, Paul; Gog, Julia R.; Hart, William S.; Heesterbeek, Hans; House, Thomas; Keeling, Matt; Kiss, István Z.; Kretzschmar, Mirjam E.; Lloyd, Alun L.; McBryde, Emma S.; McCaw, James M.; McKinley, Trevelyan J.; Miller, Joel C.; Morris, Martina; O'Neill, Philip D.; Parag, Kris V.; Pearson, Carl A. B.; Pellis, Lorenzo; Pulliam, Juliet R. C.; Ross, Joshua V.; Tomba, Gianpaolo Scalia; Silverman, Bernard W.; Struchiner, Claudio J.; Tildesley, Michael J.; Trapman, Pieter; Webb, Cerian R.; Mollison, Denis; Restif, Olivier title: Key questions for modelling COVID-19 exit strategies date: 2020-08-12 journal: Proc Biol Sci DOI: 10.1098/rspb.2020.1405 sha: doc_id: 303651 cord_uid: fkdep6cp file: cache/cord-303941-3lg1bzsi.json key: cord-303941-3lg1bzsi authors: Han, Hui-Ju; Wen, Hong-ling; Zhou, Chuan-Min; Chen, Fang-Fang; Luo, Li-Mei; Liu, Jian-wei; Yu, Xue-Jie title: Bats as reservoirs of severe emerging infectious diseases date: 2015-07-02 journal: Virus Research DOI: 10.1016/j.virusres.2015.05.006 sha: doc_id: 303941 cord_uid: 3lg1bzsi file: cache/cord-303741-1ou0cy5k.json key: cord-303741-1ou0cy5k authors: Stafstrom, Carl E.; Jantzie, Lauren L. title: COVID-19: Neurological Considerations in Neonates and Children date: 2020-09-10 journal: Children (Basel) DOI: 10.3390/children7090133 sha: doc_id: 303741 cord_uid: 1ou0cy5k file: cache/cord-303832-1kcqhgjw.json key: cord-303832-1kcqhgjw authors: Dai, Manman; Li, Huanan; Yan, Nan; Huang, Jinyu; Zhao, Li; Xu, Siqi; Jiang, Shibo; Pan, Chungen; Liao, Ming title: Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.09.06.284695 sha: doc_id: 303832 cord_uid: 1kcqhgjw file: cache/cord-303934-8gh3q7p3.json key: cord-303934-8gh3q7p3 authors: Sungnak, Waradon; Huang, Ni; B'ecavin, Christophe; Berg, Marijn; Network, HCA Lung Biological title: SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways date: 2020-03-13 journal: Nature medicine DOI: 10.1038/s41591-020-0868-6 sha: doc_id: 303934 cord_uid: 8gh3q7p3 file: cache/cord-304073-f3iwclkm.json key: cord-304073-f3iwclkm authors: Mullick, Jhinuk Basu; Simmons, Chelsey S.; Gaire, Janak title: Animal Models to Study Emerging Technologies Against SARS-CoV-2 date: 2020-07-27 journal: Cell Mol Bioeng DOI: 10.1007/s12195-020-00638-9 sha: doc_id: 304073 cord_uid: f3iwclkm file: cache/cord-304016-4o2bpedp.json key: cord-304016-4o2bpedp authors: Hanage, William P.; Testa, Christian; Chen, Jarvis T.; Davis, Letitia; Pechter, Elise; Seminario, Peg; Santillana, Mauricio; Krieger, Nancy title: COVID-19: US federal accountability for entry, spread, and inequities—lessons for the future date: 2020-11-02 journal: Eur J Epidemiol DOI: 10.1007/s10654-020-00689-2 sha: doc_id: 304016 cord_uid: 4o2bpedp file: cache/cord-303917-2tu707ng.json key: cord-303917-2tu707ng authors: Zhang, Lei; Liu, Yunhui title: Potential interventions for novel coronavirus in China: A systematic review date: 2020-03-03 journal: J Med Virol DOI: 10.1002/jmv.25707 sha: doc_id: 303917 cord_uid: 2tu707ng file: cache/cord-303661-etb19d6y.json key: cord-303661-etb19d6y authors: Shin, Hyoung-Shik title: Empirical Treatment and Prevention of COVID-19 date: 2020-06-22 journal: Infect Chemother DOI: 10.3947/ic.2020.52.2.142 sha: doc_id: 303661 cord_uid: etb19d6y file: cache/cord-304101-b9na3yf6.json key: cord-304101-b9na3yf6 authors: Yong, Suh Kuan; Su, Ping‐Chia; Yang, Yuh‐Shyong title: Molecular Targets for the Testing of COVID‐19 date: 2020-05-18 journal: Biotechnol J DOI: 10.1002/biot.202000152 sha: doc_id: 304101 cord_uid: b9na3yf6 file: cache/cord-304013-nzigx0k0.json key: cord-304013-nzigx0k0 authors: Lipinski, Tom; Ahmad, Darem; Serey, Nicolas; Jouhara, Hussam title: Review of ventilation strategies to reduce the risk of disease transmission in high occupancy buildings date: 2020-09-13 journal: nan DOI: 10.1016/j.ijft.2020.100045 sha: doc_id: 304013 cord_uid: nzigx0k0 file: cache/cord-304139-ya3d7u9b.json key: cord-304139-ya3d7u9b authors: Bosmann, Markus title: Complement Activation during Critical Illness: Current Findings and an Outlook in the Era of COVID-19 date: 2020-07-15 journal: Am J Respir Crit Care Med DOI: 10.1164/rccm.202005-1926ed sha: doc_id: 304139 cord_uid: ya3d7u9b file: cache/cord-304058-i8cywew0.json key: cord-304058-i8cywew0 authors: Pfefferle, Susanne; Krähling, Verena; Ditt, Vanessa; Grywna, Klaus; Mühlberger, Elke; Drosten, Christian title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 journal: Virol J DOI: 10.1186/1743-422x-6-131 sha: doc_id: 304058 cord_uid: i8cywew0 file: cache/cord-304115-xs54f295.json key: cord-304115-xs54f295 authors: Zamaniyan, Marzieh; Ebadi, Aghdas; Aghajanpoor Mir, Samaneh; Rahmani, Zahra; Haghshenas, Mohammadreza; Azizi, Setareh title: Preterm delivery in pregnant woman with critical COVID‐19 pneumonia and vertical transmission date: 2020-04-17 journal: Prenat Diagn DOI: 10.1002/pd.5713 sha: doc_id: 304115 cord_uid: xs54f295 file: cache/cord-304201-fziv9a9k.json key: cord-304201-fziv9a9k authors: Chiang, Chi-Huei; Shih, Jen-Fu; Su, Wei-Juin; Perng, Reury-Perng title: Eight-Month Prospective Study of 14 Patients With Hospital-Acquired Severe Acute Respiratory Syndrome date: 2004-11-30 journal: Mayo Clinic Proceedings DOI: 10.4065/79.11.1372 sha: doc_id: 304201 cord_uid: fziv9a9k file: cache/cord-304271-vyayyk50.json key: cord-304271-vyayyk50 authors: Qin, Yuan-Yuan; Zhou, Yi-Hong; Lu, Yan-Qiu; Sun, Feng; Yang, Sen; Harypursat, Vijay; Chen, Yao-Kai title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial date: 2020-03-05 journal: Chin Med J (Engl) DOI: 10.1097/cm9.0000000000000791 sha: doc_id: 304271 cord_uid: vyayyk50 file: cache/cord-304263-5kddk5fa.json key: cord-304263-5kddk5fa authors: C., Selvaa Kumar; Kumar, Senthil Arun; Wei, Haiyan title: Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2 date: 2020-10-08 journal: Toxicol Rep DOI: 10.1016/j.toxrep.2020.10.002 sha: doc_id: 304263 cord_uid: 5kddk5fa file: cache/cord-304372-6eqnr52t.json key: cord-304372-6eqnr52t authors: Stolle, Claudia; Schmidt, Annika; Domhoff, Dominik; Friedrich, Anna Carina; Heinze, Franziska; Preuß, Benedikt; Seibert, Kathrin; Rothgang, Heinz; Wolf-Ostermann, Karin title: Bedarfe der Langzeitpflege in der COVID-19-Pandemie date: 2020-10-28 journal: Z Gerontol Geriatr DOI: 10.1007/s00391-020-01801-7 sha: doc_id: 304372 cord_uid: 6eqnr52t file: cache/cord-304282-om2xc4bs.json key: cord-304282-om2xc4bs authors: Berhan, Yifru title: Will Africa be Devastated by Covid-19 as Many Predicted? Perspective and Prospective date: 2020-05-17 journal: Ethiop J Health Sci DOI: 10.4314/ejhs.v30i3.17 sha: doc_id: 304282 cord_uid: om2xc4bs file: cache/cord-304355-y3fagw3t.json key: cord-304355-y3fagw3t authors: Pan, Boyu; Fang, Senbiao; Zhang, Ju; Pan, Ya; Liu, Han; Wang, Yun; Li, Min; Liu, Liren title: Chinese herbal compounds against SARS-CoV-2: puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor date: 2020-11-11 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.11.010 sha: doc_id: 304355 cord_uid: y3fagw3t file: cache/cord-304176-yloqrblw.json key: cord-304176-yloqrblw authors: Tunesi, S.; Bourgarit, A. title: Prescribing COVID-19 treatments: what we should never forget date: 2020-05-13 journal: J Infect DOI: 10.1016/j.jinf.2020.05.018 sha: doc_id: 304176 cord_uid: yloqrblw file: cache/cord-304321-y177sqee.json key: cord-304321-y177sqee authors: Cho, Ryan H. W.; Yeung, Zenon W. C.; Ho, Osan Y. M.; Lo, Jacky F. W.; Siu, Alice K. Y.; Kwan, Wendy M. Y.; To, Zion W. H.; Chan, Anthony W. H.; Chan, Becky Y. T.; Fung, Kitty S. C.; Abdullah, Victor; Tong, Michael C. F.; Ku, Peter K. M. title: Pearls of experience for safe and efficient hospital practices in otorhinolaryngology—head and neck surgery in Hong Kong during the 2019 novel coronavirus disease (COVID-19) pandemic date: 2020-05-15 journal: J Otolaryngol Head Neck Surg DOI: 10.1186/s40463-020-00427-4 sha: doc_id: 304321 cord_uid: y177sqee file: cache/cord-304295-3mpymd8a.json key: cord-304295-3mpymd8a authors: Khan, Muhammad Muzamil; Noor, Amna; Madni*, Asadullah; Shafiq, Mudassir title: Emergence of novel coronavirus and progress toward treatment and vaccine date: 2020-06-04 journal: Rev Med Virol DOI: 10.1002/rmv.2116 sha: doc_id: 304295 cord_uid: 3mpymd8a file: cache/cord-304280-2a84u4tm.json key: cord-304280-2a84u4tm authors: Masic, Izet; Naser, Nabil; Zildzic, Muharem title: Public Health Aspects of COVID-19 Infection with Focus on Cardiovascular Diseases date: 2020-03-17 journal: Mater Sociomed DOI: 10.5455/msm.2020.32.71-76 sha: doc_id: 304280 cord_uid: 2a84u4tm file: cache/cord-304340-9mrtic2k.json key: cord-304340-9mrtic2k authors: Karacan, Ilker; Akgun, Tugba Kizilboga; Agaoglu, N. Bugra; Irvem, Arzu; Alkurt, Gizem; Yildiz, Jale; Kose, Betsi; Ozel, A. Serra; Altunal, L. Nilsun; Can, Nisan Denizce; Demirkol, Yasemin Kendir; Aydin, Mehtap; Dogan, Ozlem Akgun; Doganay, Levent; Doganay, Gizem Dinler title: The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey date: 2020-05-15 journal: North Clin Istanb DOI: 10.14744/nci.2020.90532 sha: doc_id: 304340 cord_uid: 9mrtic2k file: cache/cord-304232-c0cpx2q3.json key: cord-304232-c0cpx2q3 authors: Opriessnig, Tanja; Huang, Yao‐Wei title: Update on possible animal sources for COVID‐19 in humans date: 2020-06-17 journal: Xenotransplantation DOI: 10.1111/xen.12621 sha: doc_id: 304232 cord_uid: c0cpx2q3 file: cache/cord-304457-8g36h1bz.json key: cord-304457-8g36h1bz authors: Idelsis, E.-M.; Jesus, P.-E.; Yaquelin, D.-R.; Dania, V.-B.; Monica, B.-R.; Lisandra, B.-R.; Jesus, C.-R.; Lisbeth, C. C.; Ernesto, P.-C.; Saily, T.-P.; Claudia, M.-S.; Ivan, C.-L.; Julio Raul, F.-M.; Hamlet, C.-R.; Marisol, D.-G.; Adriana, S.-M.; Maura, G.-S.; Sara Maria, M.-M.; Marel, A.-V.; Francisco, H.-B.; Hugo, N.-C.; Dianela, B.-G.; Abrahan, B.-C.; Mary Tania, V.-C.; Gerardo, G.-N.; Verena, M.-G.; Iraldo, B.-R. title: Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date: 2020-08-01 journal: nan DOI: 10.1101/2020.07.29.20164251 sha: doc_id: 304457 cord_uid: 8g36h1bz file: cache/cord-304487-ycvu5l5f.json key: cord-304487-ycvu5l5f authors: Wertheim, Joel O title: A glimpse into the origins of genetic diversity in SARS-CoV-2 date: 2020-03-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa213 sha: doc_id: 304487 cord_uid: ycvu5l5f file: cache/cord-304306-rxjahqwh.json key: cord-304306-rxjahqwh authors: Vlachakis, Dimitrios; Papakonstantinou, Eleni; Mitsis, Thanasis; Pierouli, Katerina; Diakou, Io; Chrousos, George; Bacopoulou, Flora title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 journal: Food Chem Toxicol DOI: 10.1016/j.fct.2020.111805 sha: doc_id: 304306 cord_uid: rxjahqwh file: cache/cord-304388-pth2d40p.json key: cord-304388-pth2d40p authors: Lai, Chih-Cheng; Liu, Yen Hung; Wang, Cheng-Yi; Wang, Ya-Hui; Hsueh, Shun-Chung; Yen, Muh-Yen; Ko, Wen-Chien; Hsueh, Po-Ren title: Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths date: 2020-03-04 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.02.012 sha: doc_id: 304388 cord_uid: pth2d40p file: cache/cord-304356-jyp9gjh9.json key: cord-304356-jyp9gjh9 authors: Grant, Rogan A.; Morales-Nebreda, Luisa; Markov, Nikolay S.; Swaminathan, Suchitra; Guzman, Estefany R.; Abbott, Darryl A.; Donnelly, Helen K.; Donayre, Alvaro; Goldberg, Isaac A.; Klug, Zasu M.; Borkowski, Nicole; Lu, Ziyan; Kihshen, Hermon; Politanska, Yuliya; Sichizya, Lango; Kang, Mengjia; Shilatifard, Ali; Qi, Chao; Argento, A. Christine; Kruser, Jacqueline M.; Malsin, Elizabeth S.; Pickens, Chiagozie O.; Smith, Sean; Walter, James M.; Pawlowski, Anna E.; Schneider, Daniel; Nannapaneni, Prasanth; Abdala-Valencia, Hiam; Bharat, Ankit; Gottardi, Cara J.; Budinger, GR Scott; Misharin, Alexander V.; Singer, Benjamin D.; Wunderink, Richard G. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 journal: bioRxiv DOI: 10.1101/2020.08.05.238188 sha: doc_id: 304356 cord_uid: jyp9gjh9 file: cache/cord-304379-4mfyxp6h.json key: cord-304379-4mfyxp6h authors: Wang, Jin title: Mathematical models for COVID-19: applications, limitations, and potentials date: 2020-06-25 journal: J Public Health Emerg DOI: 10.21037/jphe-2020-05 sha: doc_id: 304379 cord_uid: 4mfyxp6h file: cache/cord-304574-03s404s5.json key: cord-304574-03s404s5 authors: Luciani, Lorenzo G.; Gallo, Fabrizio; Malossini, Gianni title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. 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Abdullah-Al-Kamran; Islam, Abul Bashar Mir Md. 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Proyecto SANICOVI date: 2020-05-25 journal: Enferm Clin DOI: 10.1016/j.enfcli.2020.05.021 sha: doc_id: 304734 cord_uid: r0k1rfmt file: cache/cord-304787-fohgekp4.json key: cord-304787-fohgekp4 authors: Prazuck, Thierry; Giaché, Susanna; Gubavu, Camelia; Colin, Mathilda; Rzepecki, Vincent; Sève, Aymeric; Pialoux, Gilles; Hocqueloux, Laurent title: Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission date: 2020-06-29 journal: J Infect DOI: 10.1016/j.jinf.2020.06.066 sha: doc_id: 304787 cord_uid: fohgekp4 file: cache/cord-304791-wv4qu9xm.json key: cord-304791-wv4qu9xm authors: Carfora, Vincenzo; Spiniello, Giorgio; Ricciolino, Riccardo; Di Mauro, Marco; Migliaccio, Marco Giuseppe; Mottola, Filiberto Fausto; Verde, Nicoletta; Coppola, Nicola title: Anticoagulant treatment in COVID-19: a narrative review date: 2020-08-18 journal: J Thromb Thrombolysis DOI: 10.1007/s11239-020-02242-0 sha: doc_id: 304791 cord_uid: wv4qu9xm file: cache/cord-304626-ffao7vka.json key: cord-304626-ffao7vka authors: Mellors, Jack; Tipton, Tom; Longet, Stephanie; Carroll, Miles title: Viral Evasion of the Complement System and Its Importance for Vaccines and Therapeutics date: 2020-07-09 journal: Front Immunol DOI: 10.3389/fimmu.2020.01450 sha: doc_id: 304626 cord_uid: ffao7vka file: cache/cord-304742-ytf2ilw4.json key: cord-304742-ytf2ilw4 authors: Albini, Adriana; Noonan, Douglas McClain; Pelosi, Giuseppe; Di Guardo, Giovanni; Lombardo, Michele title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based antihypertensive therapies—reply date: 2020-07-14 journal: Intern Emerg Med DOI: 10.1007/s11739-020-02436-7 sha: doc_id: 304742 cord_uid: ytf2ilw4 file: cache/cord-304617-5ozf18lg.json key: cord-304617-5ozf18lg authors: Al-Khafaji, Khattab; AL-DuhaidahawiL, Dunya; Taskin Tok, Tugba title: Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 date: 2020-05-15 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1764392 sha: doc_id: 304617 cord_uid: 5ozf18lg file: cache/cord-304871-gva617yp.json key: cord-304871-gva617yp authors: Zheng, Ting; Yang, Chao; Wang, Han‐yu; Chen, Xiao; Yu, Li; Wu, Zi‐ling; Sun, Hui title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-06-08 journal: J Med Virol DOI: 10.1002/jmv.26146 sha: doc_id: 304871 cord_uid: gva617yp file: cache/cord-304584-jxha3rz8.json key: cord-304584-jxha3rz8 authors: Giacomo, Di; Gambale, E.; Monterisi, S.; Valente, M.; Maio, M. title: SARS-COV-2 infection in cancer patients undergoing checkpoint blockade: clinical course and outcome date: 2020-05-03 journal: Eur J Cancer DOI: 10.1016/j.ejca.2020.04.026 sha: doc_id: 304584 cord_uid: jxha3rz8 file: cache/cord-304898-he57l0y7.json key: cord-304898-he57l0y7 authors: Belghmaidi, Sarah; Nassih, Houda; Boutgayout, Saloua; Fakiri, Karima El; Qadiri, Rabiy El; Hajji, Ibtissam; Bourahouate, Aicha; Moutaouakil, Abdeljalil title: Third Cranial Nerve Palsy Presenting with Unilateral Diplopia and Strabismus in a 24-Year-Old Woman with COVID-19 date: 2020-10-15 journal: Am J Case Rep DOI: 10.12659/ajcr.925897 sha: doc_id: 304898 cord_uid: he57l0y7 file: cache/cord-305025-pqye1ebh.json key: cord-305025-pqye1ebh authors: Sharifi, Majid; Hasan, Anwarul; Taghizadeh, Akbar; Haghighat, Setareh; Attar, Farnoosh; Bloukh, Samir Haj; Edis, Zehra; Xue, Mengzhou; Khan, Suliman; Falahati, Mojtaba title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 journal: Talanta DOI: 10.1016/j.talanta.2020.121704 sha: doc_id: 305025 cord_uid: pqye1ebh file: cache/cord-304815-3datxv8j.json key: cord-304815-3datxv8j authors: Gronvall, Gigi Kwik; Waldhorn, Richard E; Henderson, D. A title: The Scientific Response to a Pandemic date: 2006-02-24 journal: PLoS Pathog DOI: 10.1371/journal.ppat.0020009 sha: doc_id: 304815 cord_uid: 3datxv8j file: cache/cord-305091-tfn2pyc6.json key: cord-305091-tfn2pyc6 authors: Tripathi, Praveen Kumar; Upadhyay, Saurabh; Singh, Manju; Raghavendhar, Siva; Bhardwaj, Mohit; Sharma, Pradeep; Patel, Ashok Kumar title: Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2 date: 2020-12-01 journal: Int J Biol Macromol DOI: 10.1016/j.ijbiomac.2020.08.166 sha: doc_id: 305091 cord_uid: tfn2pyc6 file: cache/cord-305054-4d84b2g6.json key: cord-305054-4d84b2g6 authors: Liu, Yuan; Yan, Changhui title: The selection of reference genome and the search for the origin of SARS-CoV-2 date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.08.10.245290 sha: doc_id: 305054 cord_uid: 4d84b2g6 file: cache/cord-305059-8z54lw2d.json key: cord-305059-8z54lw2d authors: Qu, Jie-Ming; Cao, Bin; Chen, Rong-Chang title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 journal: COVID-19 DOI: 10.1016/b978-0-12-824003-8.00004-8 sha: doc_id: 305059 cord_uid: 8z54lw2d file: cache/cord-305104-jk6ai1od.json key: cord-305104-jk6ai1od authors: Escribese, María M; Nistal‐Villan, Estanislao; Fernandez, Paloma; Rico, Pilar; Martin‐Antoniano, Isabel A; de la Cuerda, Alicia; Chivato, Tomas; Barber, Domingo title: Cross‐sectional pilot study exploring the feasibility of a rapid SARS‐CoV‐2 immunization test in health and non‐healthcare workers date: 2020-08-05 journal: Allergy DOI: 10.1111/all.14545 sha: doc_id: 305104 cord_uid: jk6ai1od file: cache/cord-305134-s7h6bpof.json key: cord-305134-s7h6bpof authors: Mackman, Nigel; Antoniak, Silvio; Wolberg, Alisa S.; Kasthuri, Raj; Key, Nigel S. title: Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses date: 2020-07-13 journal: Arterioscler Thromb Vasc Biol DOI: 10.1161/atvbaha.120.314514 sha: doc_id: 305134 cord_uid: s7h6bpof file: cache/cord-304899-vruq4r7z.json key: cord-304899-vruq4r7z authors: Guihot, Amélie; Bricaire, François; Li, Taisheng; Bossi, Philippe title: Syndrome respiratoire aigu sévère : une épidémie singulière de pneumonie virale date: 2004-03-31 journal: La Presse Médicale DOI: 10.1016/s0755-4982(04)98581-8 sha: doc_id: 304899 cord_uid: vruq4r7z file: cache/cord-305093-og4k3fc7.json key: cord-305093-og4k3fc7 authors: Konno, Yoriyuki; Kimura, Izumi; Uriu, Keiya; Fukushi, Masaya; Irie, Takashi; Koyanagi, Yoshio; Sauter, Daniel; Gifford, Robert J.; Nakagawa, So; Sato, Kei title: SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant date: 2020-09-04 journal: Cell Rep DOI: 10.1016/j.celrep.2020.108185 sha: doc_id: 305093 cord_uid: og4k3fc7 file: cache/cord-305274-mcsdem7y.json key: cord-305274-mcsdem7y authors: Beniac, Daniel R.; deVarennes, Shauna L.; Andonov, Anton; He, Runtao; Booth, Tim F. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0001082 sha: doc_id: 305274 cord_uid: mcsdem7y file: cache/cord-305139-851v2qr3.json key: cord-305139-851v2qr3 authors: Peys, Elise; Stevens, Dieter; Weygaerde, Yannick Vande; Malfait, Thomas; Hermie, Laurens; Rogiers, Philippe; Depuydt, Pieter; Van Braeckel, Eva title: Haemoptysis as the first presentation of COVID-19: a case report date: 2020-10-22 journal: BMC Pulm Med DOI: 10.1186/s12890-020-01312-6 sha: doc_id: 305139 cord_uid: 851v2qr3 file: cache/cord-305130-vz72ldbo.json key: cord-305130-vz72ldbo authors: Keil, Shawn D.; 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Rakholiya, Kalpna D.; Kaneria, Mital J.; Galvadiya, Bhemji P.; Vyas, Sudhanshu R.; Kanbi, Vaktabhai H.; Patel, Manubhai P. title: High affinity interaction of Solanum tuberosum and Brassica juncea residue smoke water compounds with proteins involved in coronavirus infection date: 2020-08-11 journal: Phytother Res DOI: 10.1002/ptr.6796 sha: doc_id: 305511 cord_uid: gdpxvqkk file: cache/cord-305263-fgwf6wy3.json key: cord-305263-fgwf6wy3 authors: Wang, Ben X.; Fish, Eleanor N. title: The yin and yang of viruses and interferons date: 2012-02-07 journal: Trends Immunol DOI: 10.1016/j.it.2012.01.004 sha: doc_id: 305263 cord_uid: fgwf6wy3 file: cache/cord-305262-23qylbmg.json key: cord-305262-23qylbmg authors: Rowan, Neil J.; Laffey, John G. title: Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic – Implications for efficacy, re-use and sustainable waste management date: 2020-09-10 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142259 sha: doc_id: 305262 cord_uid: 23qylbmg file: cache/cord-304943-thg4fqi2.json key: cord-304943-thg4fqi2 authors: Noor, Aziz Ullah; Maqbool, Farhana; Bhatti, Zulfiqar A.; Khan, Asmat Ullah title: Epidemiology of CoViD-19 Pandemic: Recovery and mortality ratio around the globe date: 2020-05-17 journal: Pak J Med Sci DOI: 10.12669/pjms.36.covid19-s4.2660 sha: doc_id: 304943 cord_uid: thg4fqi2 file: cache/cord-305223-go75cs6r.json key: cord-305223-go75cs6r authors: Wang, Yafei; Zhou, Ying; Yang, Zhen; Xia, Dongping; Hu, Yi; Geng, Shuang title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China date: 2020-08-25 journal: Respiration DOI: 10.1159/000507940 sha: doc_id: 305223 cord_uid: go75cs6r file: cache/cord-305234-nclk7bbo.json key: cord-305234-nclk7bbo authors: Do, Mytrang H.; Minkis, Kira; Petukhova, Tatyana A.; Lipner, Shari R. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.06.983 sha: doc_id: 305234 cord_uid: nclk7bbo file: cache/cord-305496-t8ykkekl.json key: cord-305496-t8ykkekl authors: Stone, E. Taylor; Geerling, Elizabeth; Steffen, Tara L.; Hassert, Mariah; Dickson, Alexandria; Spencer, Jacqueline F.; Toth, Karoly; DiPaolo, Richard J.; Brien, James D.; Pinto, Amelia K. title: Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date: 2020-08-21 journal: bioRxiv DOI: 10.1101/2020.08.20.259838 sha: doc_id: 305496 cord_uid: t8ykkekl file: cache/cord-305591-ir3wz6nr.json key: cord-305591-ir3wz6nr authors: Ji, Danyang; Juhas, Mario; Tsang, Chi Man; Kwok, Chun Kit; Li, Yongshu; Zhang, Yang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 journal: Brief Bioinform DOI: 10.1093/bib/bbaa114 sha: doc_id: 305591 cord_uid: ir3wz6nr file: cache/cord-305581-0bqxwh1o.json key: cord-305581-0bqxwh1o authors: Hassan, Sk. Sarif; Choudhury, Pabitra Pal; Roy, Bidyut title: Molecular phylogeny and missense mutations of envelope proteins across coronaviruses date: 2020-09-12 journal: Genomics DOI: 10.1016/j.ygeno.2020.09.014 sha: doc_id: 305581 cord_uid: 0bqxwh1o file: cache/cord-305534-936peb1n.json key: cord-305534-936peb1n authors: Johnson, Kemmian D.; Harris, Christen; Cain, John K.; Hummer, Cicily; Goyal, Hemant; Perisetti, Abhilash title: Pulmonary and Extra-Pulmonary Clinical Manifestations of COVID-19 date: 2020-08-13 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00526 sha: doc_id: 305534 cord_uid: 936peb1n file: cache/cord-305589-ofpna4k1.json key: cord-305589-ofpna4k1 authors: Schubert, Katharina; Karousis, Evangelos D.; Jomaa, Ahmad; Scaiola, Alain; Echeverria, Blanca; Gurzeler, Lukas-Adrian; Leibundgut, Marc; Thiel, Volker; Mühlemann, Oliver; Ban, Nenad title: SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date: 2020-07-07 journal: bioRxiv DOI: 10.1101/2020.07.07.191676 sha: doc_id: 305589 cord_uid: ofpna4k1 file: cache/cord-305266-fuaq4ujb.json key: cord-305266-fuaq4ujb authors: Gong, Yue; Ma, Ting-can; Xu, Yang-yang; Yang, Rui; Gao, Lan-jun; Wu, Si-hua; Li, Jing; Yue, Ming-liang; Liang, Hui-gang; He, Xiao; Yun, Tao title: Early Research on COVID-19: A Bibliometric Analysis date: 2020-08-05 journal: Innovation DOI: 10.1016/j.xinn.2020.100027 sha: doc_id: 305266 cord_uid: fuaq4ujb file: cache/cord-305582-3hmsknon.json key: cord-305582-3hmsknon authors: Li, Lei; Li, Ranran; Wu, Zhixiong; Yang, Xianghong; Zhao, Mingyan; Liu, Jiao; Chen, Dechang title: Therapeutic strategies for critically ill patients with COVID-19 date: 2020-04-20 journal: Ann Intensive Care DOI: 10.1186/s13613-020-00661-z sha: doc_id: 305582 cord_uid: 3hmsknon file: cache/cord-305587-xtqvtleb.json key: cord-305587-xtqvtleb authors: Ma, Cuiqing; Su, Shan; Wang, Jiachao; Wei, Lin; Du, Lanying; Jiang, Shibo title: From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development date: 2020-05-11 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.05.004 sha: doc_id: 305587 cord_uid: xtqvtleb file: cache/cord-305616-2obemy16.json key: cord-305616-2obemy16 authors: Montes, Maria Teresa; Herranz-Rubia, Nuria title: Neonatal nursing in the COVID-19 pandemic: can we improve the future? date: 2020-07-10 journal: J Neonatal Nurs DOI: 10.1016/j.jnn.2020.07.005 sha: doc_id: 305616 cord_uid: 2obemy16 file: cache/cord-305742-wf6qxplf.json key: cord-305742-wf6qxplf authors: Gomez, Santiago A.; Rojas-Valencia, Natalia; Gomez, Sara; Egidi, Franco; Cappelli, Chiara; Restrepo, Albeiro title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 journal: Chembiochem DOI: 10.1002/cbic.202000618 sha: doc_id: 305742 cord_uid: wf6qxplf file: cache/cord-305610-v1hn934x.json key: cord-305610-v1hn934x authors: Kerslake, Rachel; Hall, Marcia; Randeva, Harpal S.; Spandidos, Demetrios A.; Chatha, Kamaljit; Kyrou, Ioannis; Karteris, Emmanouil title: Co-expression of peripheral olfactory receptors with SARS-CoV-2 infection mediators: Potential implications beyond loss of smell as a COVID-19 symptom date: 2020-06-17 journal: Int J Mol Med DOI: 10.3892/ijmm.2020.4646 sha: doc_id: 305610 cord_uid: v1hn934x file: cache/cord-305422-t8azymo7.json key: cord-305422-t8azymo7 authors: Yi, Ye; Lagniton, Philip N.P.; Ye, Sen; Li, Enqin; Xu, Ren-He title: COVID-19: what has been learned and to be learned about the novel coronavirus disease date: 2020-03-15 journal: Int J Biol Sci DOI: 10.7150/ijbs.45134 sha: doc_id: 305422 cord_uid: t8azymo7 file: cache/cord-305521-lkou3ycu.json key: cord-305521-lkou3ycu authors: Michel, W.; Farber, J.; Dilas, M.; Tammer, I.; Baar, J.; Kaasch, A. J. title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay date: 2020-09-27 journal: nan DOI: 10.1101/2020.09.25.20201541 sha: doc_id: 305521 cord_uid: lkou3ycu file: cache/cord-305330-mklkugj5.json key: cord-305330-mklkugj5 authors: Moiseev, Sergey; Avdeev, Sergey; Brovko, Michail; Akulkina, Larisa; Fomin, Victor title: Cancer in intensive care unit patients with COVID-19 date: 2020-05-28 journal: J Infect DOI: 10.1016/j.jinf.2020.05.053 sha: doc_id: 305330 cord_uid: mklkugj5 file: cache/cord-305632-xbji6g5x.json key: cord-305632-xbji6g5x authors: Uccelli, Matteo; Cesana, Giovanni Carlo; De Carli, Stefano Maria; Ciccarese, Francesca; Oldani, Alberto; Zanoni, Adelinda Angela Giulia; Giorgi, Riccardo; Villa, Roberta; Ismail, Ayman; Targa, Simone; D’Alessio, Andrea; Cesana, Giancarlo; Mantovani, Lorenzo; Olmi, Stefano title: COVID-19 and Obesity: Is Bariatric Surgery Protective? Retrospective Analysis on 2145 Patients Undergone Bariatric-Metabolic Surgery from High Volume Center in Italy (Lombardy) date: 2020-10-31 journal: Obes Surg DOI: 10.1007/s11695-020-05085-z sha: doc_id: 305632 cord_uid: xbji6g5x file: cache/cord-305763-160heazx.json key: cord-305763-160heazx authors: Lai, Chih-Cheng; Wang, Jui-Hsiang; Hsueh, Po-Ren title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.011 sha: doc_id: 305763 cord_uid: 160heazx file: cache/cord-305703-ypeibwje.json key: cord-305703-ypeibwje authors: Veronese, Nicola; Demurtas, Jacopo; Yang, Lin; Tonelli, Roberto; Barbagallo, Mario; Lopalco, Pierluigi; Lagolio, Erik; Celotto, Stefano; Pizzol, Damiano; Zou, Liye; Tully, Mark A.; Ilie, Petre Cristian; Trott, Mike; López-Sánchez, Guillermo F.; Smith, Lee title: Use of Corticosteroids in Coronavirus Disease 2019 Pneumonia: A Systematic Review of the Literature date: 2020-04-24 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00170 sha: doc_id: 305703 cord_uid: ypeibwje file: cache/cord-305788-z75yv88e.json key: cord-305788-z75yv88e authors: Agergaard, Charlotte Nielsen; Lis-Tønder, Joanna; Olsen, Dorte Aalund; Kierkegaard, Helene; Møller, Jens Kjølseth title: Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date: 2020-09-28 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1442 sha: doc_id: 305788 cord_uid: z75yv88e file: cache/cord-305755-6jup93v4.json key: cord-305755-6jup93v4 authors: Gouveia, Duarte; Miotello, Guylaine; Gallais, Fabrice; Gaillard, Jean-Charles; Debroas, Stéphanie; Bellanger, Laurent; Lavigne, Jean-Philippe; Sotto, Albert; Grenga, Lucia; Pible, Olivier; Armengaud, Jean title: Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date: 2020-07-22 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00535 sha: doc_id: 305755 cord_uid: 6jup93v4 file: cache/cord-305704-grzrkff9.json key: cord-305704-grzrkff9 authors: Almutairi, Abdulelah; Alfaleh, Mohammed; Alasheikh, Muath title: Dermatological Manifestations in Patients With SARS-CoV-2: A Systematic Review date: 2020-07-28 journal: Cureus DOI: 10.7759/cureus.9446 sha: doc_id: 305704 cord_uid: grzrkff9 file: cache/cord-305931-0pgu2gvh.json key: cord-305931-0pgu2gvh authors: Janus, Scott E; Hajjari, Jamal; Cunningham, Michael J; Hoit, Brian D title: COVID19: a case report of thrombus in transit date: 2020-06-17 journal: Eur Heart J Case Rep DOI: 10.1093/ehjcr/ytaa189 sha: doc_id: 305931 cord_uid: 0pgu2gvh file: cache/cord-305770-xygg4lxu.json key: cord-305770-xygg4lxu authors: Busetto, Gian Maria; Porreca, Angelo; Del Giudice, Francesco; Maggi, Martina; D'Agostino, Daniele; Romagnoli, Daniele; Musi, Gennaro; Lucarelli, Giuseppe; Palmer, Katie; Colonna di Paliano, Ascanio; Muto, Matteo; Hurle, Rodolfo; Terracciano, Daniela; de Cobelli, Ottavio; Sciarra, Alessandro; De Berardinis, Ettore; Ferro, Matteo title: SARS-CoV-2 Infection and High-Risk Non-Muscle-Invasive Bladder Cancer: Are There Any Common Features? date: 2020-06-09 journal: Urol Int DOI: 10.1159/000509065 sha: doc_id: 305770 cord_uid: xygg4lxu file: cache/cord-305798-7b8rua4z.json key: cord-305798-7b8rua4z authors: Rivas-García, S; Bernal, J; Bachiller-Corral, J title: Rhabdomyolysis as the main manifestation of coronavirus disease 2019 date: 2020-06-25 journal: Rheumatology (Oxford) DOI: 10.1093/rheumatology/keaa351 sha: doc_id: 305798 cord_uid: 7b8rua4z file: cache/cord-305640-tgowzrqo.json key: cord-305640-tgowzrqo authors: Li, Yong-Hua; Li, Jie; Liu, Xue-En; Wang, Ling; Li, Tong; Zhou, Yi-Hua; Zhuang, Hui title: Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: Comparison with results of other viral markers date: 2005-07-15 journal: J Virol Methods DOI: 10.1016/j.jviromet.2005.06.001 sha: doc_id: 305640 cord_uid: tgowzrqo file: cache/cord-305745-9lngdjow.json key: cord-305745-9lngdjow authors: Solnier, Julia; Fladerer, Johannes-Paul title: Flavonoids: A complementary approach to conventional therapy of COVID-19? date: 2020-09-18 journal: Phytochem Rev DOI: 10.1007/s11101-020-09720-6 sha: doc_id: 305745 cord_uid: 9lngdjow file: cache/cord-305956-l02xdq87.json key: cord-305956-l02xdq87 authors: Alqahtani, Saleh A; Schattenberg, Jörn M title: Liver injury in COVID-19: The current evidence date: 2020-05-26 journal: United European Gastroenterol J DOI: 10.1177/2050640620924157 sha: doc_id: 305956 cord_uid: l02xdq87 file: cache/cord-306108-ja0wyr5w.json key: cord-306108-ja0wyr5w authors: B K, Anupama; Chaudhuri, Debanik title: A Review of Acute Myocardial Injury in Coronavirus Disease 2019 date: 2020-06-03 journal: Cureus DOI: 10.7759/cureus.8426 sha: doc_id: 306108 cord_uid: ja0wyr5w file: cache/cord-306373-61snvddh.json key: cord-306373-61snvddh authors: Xu, Xiao-Wei; Wu, Xiao-Xin; Jiang, Xian-Gao; Xu, Kai-Jin; Ying, Ling-Jun; Ma, Chun-Lian; Li, Shi-Bo; Wang, Hua-Ying; Zhang, Sheng; Gao, Hai-Nv; Sheng, Ji-Fang; Cai, Hong-Liu; Qiu, Yun-Qing; Li, Lan-Juan title: Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series date: 2020-02-19 journal: BMJ DOI: 10.1136/bmj.m606 sha: doc_id: 306373 cord_uid: 61snvddh file: cache/cord-305564-dj3vj4tk.json key: cord-305564-dj3vj4tk authors: DeDiego, Marta L.; Pewe, Lecia; Alvarez, Enrique; Rejas, Maria Teresa; Perlman, Stanley; Enjuanes, Luis title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date: 2008-07-01 journal: Virology DOI: 10.1016/j.virol.2008.03.005 sha: doc_id: 305564 cord_uid: dj3vj4tk file: cache/cord-306390-pzzev8hd.json key: cord-306390-pzzev8hd authors: Reisinger, Emil C.; von Possel, Ronald; Warnke, Philipp; Geerdes-Fenge, Hilte F.; Hemmer, Christoph J.; Pfefferle, Susanne; Löbermann, Micha; Littmann, Martina; Emmerich, Petra title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest date: 2020-06-22 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1197-4293 sha: doc_id: 306390 cord_uid: pzzev8hd file: cache/cord-305856-xt3zxajf.json key: cord-305856-xt3zxajf authors: Shanmugam, Chandrakumar; Mohammed, Abdul Rafi; Ravuri, Swarupa; Luthra, Vishwas; Rajagopal, Narasimhamurthy; Karre, Saritha title: COVID-2019 – A comprehensive pathology insight date: 2020-09-18 journal: Pathol Res Pract DOI: 10.1016/j.prp.2020.153222 sha: doc_id: 305856 cord_uid: xt3zxajf file: cache/cord-305858-gp1u4kh7.json key: cord-305858-gp1u4kh7 authors: Song, Xiang; Hu, Wei; Yu, Haibo; Zhao, Laura; Zhao, Yeqian; Zhao, Yong title: High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date: 2020-07-19 journal: bioRxiv DOI: 10.1101/2020.07.18.210120 sha: doc_id: 305858 cord_uid: gp1u4kh7 file: cache/cord-306308-zjq6cscm.json key: cord-306308-zjq6cscm authors: de Moura, Ronald Rodrigues; Agrelli, Almerinda; Santos-Silva, Carlos André; Silva, Natália; Assunção, Bruno Rodrigo; Brandão, Lucas; Benko-Iseppon, Ana Maria; Crovella, Sergio title: Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date: 2020-08-05 journal: J Clin Pathol DOI: 10.1136/jclinpath-2020-206946 sha: doc_id: 306308 cord_uid: zjq6cscm file: cache/cord-305816-06lddk87.json key: cord-305816-06lddk87 authors: Musarrat, Farhana; Chouljenko, Vladimir; Dahal, Achyut; Nabi, Rafiq; Chouljenko, Tamara; Jois, Seetharama D.; Kousoulas, Konstantin G. title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections date: 2020-05-17 journal: J Med Virol DOI: 10.1002/jmv.25985 sha: doc_id: 305816 cord_uid: 06lddk87 file: cache/cord-306085-gnrnsxej.json key: cord-306085-gnrnsxej authors: Hassan, Sk. Sarif; Choudhury, Pabitra Pal; Roy, Bidyut title: SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences date: 2020-07-05 journal: Genomics DOI: 10.1016/j.ygeno.2020.07.001 sha: doc_id: 306085 cord_uid: gnrnsxej file: cache/cord-306351-ka6asw3m.json key: cord-306351-ka6asw3m authors: Alsuliman, Tamim; Alasadi, Lugien; Alkharat, Banan; Srour, Micha; Alrstom, Ali title: A review of potential treatments to date in COVID-19 patients according to the stage of the disease date: 2020-05-30 journal: Curr Res Transl Med DOI: 10.1016/j.retram.2020.05.004 sha: doc_id: 306351 cord_uid: ka6asw3m file: cache/cord-306438-db2rqz4d.json key: cord-306438-db2rqz4d authors: Kalathiya, Umesh; Padariya, Monikaben; Mayordomo, Marcos; Lisowska, Małgorzata; Nicholson, Judith; Singh, Ashita; Baginski, Maciej; Fahraeus, Robin; Carragher, Neil; Ball, Kathryn; Haas, Juergen; Daniels, Alison; Hupp, Ted R.; Alfaro, Javier Antonio title: Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date: 2020-05-14 journal: J Clin Med DOI: 10.3390/jcm9051473 sha: doc_id: 306438 cord_uid: db2rqz4d file: cache/cord-306017-4wf4yhyz.json key: cord-306017-4wf4yhyz authors: d'Aloja, Ernesto; Finco, Gabriele; Demontis, Roberto; Napoli, Pietro Emanuele; Fossarello, Maurizio; Nioi, Matteo title: COVID-19 and medical liability: Italy denies the shield to its heroes date: 2020-07-24 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100470 sha: doc_id: 306017 cord_uid: 4wf4yhyz file: cache/cord-306465-7kevsl1z.json key: cord-306465-7kevsl1z authors: Agarwal, Krishna Mohan; Mohapatra, Swati; Sharma, Prairit; Sharma, Shreya; Bhatia, Dinesh; Mishra, Animesh title: Study and Overview of the Novel Corona Virus Disease (COVID-19) date: 2020-09-06 journal: nan DOI: 10.1016/j.sintl.2020.100037 sha: doc_id: 306465 cord_uid: 7kevsl1z file: cache/cord-306332-ug6pare2.json key: cord-306332-ug6pare2 authors: Chen, Ze-Liang; Zhang, Wen-Jun; Lu, Yi; Guo, Cheng; Guo, Zhong-Min; Liao, Cong-Hui; Zhang, Xi; Zhang, Yi; Han, Xiao-Hu; Li, Qian-Lin; Lu, Jia-Hai title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends date: 2020-05-05 journal: Chin Med J (Engl) DOI: 10.1097/cm9.0000000000000776 sha: doc_id: 306332 cord_uid: ug6pare2 file: cache/cord-306365-7cydmgn2.json key: cord-306365-7cydmgn2 authors: Ami, Yasushi; Nagata, Noriyo; Shirato, Kazuya; Watanabe, Rie; Iwata, Naoko; Nakagaki, Keiko; Fukushi, Shuetsu; Saijo, Masayuki; Morikawa, Shigeru; Taguchi, Fumihiro title: Co‐infection of respiratory bacterium with severe acute respiratory syndrome coronavirus induces an exacerbated pneumonia in mice date: 2008-04-01 journal: Microbiol Immunol DOI: 10.1111/j.1348-0421.2008.00011.x sha: doc_id: 306365 cord_uid: 7cydmgn2 file: cache/cord-306177-5wefp31y.json key: cord-306177-5wefp31y authors: Iheagwam, Franklyn Nonso; Rotimi, Solomon Oladapo title: Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants date: 2020-09-12 journal: Scientifica (Cairo) DOI: 10.1155/2020/1878410 sha: doc_id: 306177 cord_uid: 5wefp31y file: cache/cord-306414-2dv3qced.json key: cord-306414-2dv3qced authors: Gutierrez, Lucas; Beckford, John; Alachkar, Houda title: Deciphering the TCR Repertoire to Solve the COVID-19 Mystery date: 2020-06-20 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2020.06.001 sha: doc_id: 306414 cord_uid: 2dv3qced file: cache/cord-305959-x061q8t7.json key: cord-305959-x061q8t7 authors: Davoudi-Monfared, Effat; Rahmani, Hamid; Khalili, Hossein; Hajiabdolbaghi, Mahboubeh; Salehi, Mohamadreza; Abbasian, Ladan; Kazemzadeh, Hossein; Yekaninejad, Mir Saeed title: A Randomized Clinical Trial of the Efficacy and Safety of Interferon β-1a in Treatment of Severe COVID-19 date: 2020-08-20 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.01061-20 sha: doc_id: 305959 cord_uid: x061q8t7 file: cache/cord-306486-y6a4u0vh.json key: cord-306486-y6a4u0vh authors: Wang, Bin; Wang, Li; Kong, Xianggen; Geng, Jin; Xiao, Di; Ma, Chunhong; Jiang, Xue‐Mei; Wang, Pei‐Hui title: Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients date: 2020-05-05 journal: J Med Virol DOI: 10.1002/jmv.25946 sha: doc_id: 306486 cord_uid: y6a4u0vh file: cache/cord-306675-kwrm8whn.json key: cord-306675-kwrm8whn authors: Crespo Sabarís, R; Isaula Jiménez, O F; Azofra Andrés, B title: “SARS-CoV-2: una presentación peculiar” date: 2020-05-08 journal: Semergen DOI: 10.1016/j.semerg.2020.05.001 sha: doc_id: 306675 cord_uid: kwrm8whn file: cache/cord-306748-i9ndb71n.json key: cord-306748-i9ndb71n authors: Kobia, Francis; Gitaka, Jesse title: COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness? date: 2020-04-17 journal: AAS Open Res DOI: 10.12688/aasopenres.13061.1 sha: doc_id: 306748 cord_uid: i9ndb71n file: cache/cord-306581-g3d0lqxp.json key: cord-306581-g3d0lqxp authors: Khattab, Mohamed H.; Sherry, Alexander D.; Jessop, Aaron C.; Ciombor, Kristen K.; Chakravarthy, Bapsi title: Early detection of SARS-CoV-2 from staging PET-CT date: 2020-09-29 journal: J Radiat Oncol DOI: 10.1007/s13566-020-00436-w sha: doc_id: 306581 cord_uid: g3d0lqxp file: cache/cord-306034-1u29o2id.json key: cord-306034-1u29o2id authors: Cazzolla, Angela P.; Lovero, Roberto; Lo Muzio, Lorenzo; Testa, Nunzio F.; Schirinzi, Annalisa; Palmieri, Giuseppe; Pozzessere, Pietro; Procacci, Vito; Di Comite, Mariasevera; Ciavarella, Domenico; Pepe, Maria; De Ruvo, Caterina; Crincoli, Vito; Di Serio, Francesca; Santacroce, Luigi title: Taste and Smell Disorders in COVID-19 Patients: Role of Interleukin-6 date: 2020-08-04 journal: ACS Chem Neurosci DOI: 10.1021/acschemneuro.0c00447 sha: doc_id: 306034 cord_uid: 1u29o2id file: cache/cord-306749-qetf3uur.json key: cord-306749-qetf3uur authors: Caves, N.D.; Irwin, M.G. title: Attitudes to basic life support among medical students following the 2003 SARS outbreak in Hong Kong() date: 2005-10-10 journal: Resuscitation DOI: 10.1016/j.resuscitation.2005.05.014 sha: doc_id: 306749 cord_uid: qetf3uur file: cache/cord-306733-df36w6l7.json key: cord-306733-df36w6l7 authors: Rosales-Mendoza, Sergio; Márquez-Escobar, Verónica A.; González-Ortega, Omar; Nieto-Gómez, Ricardo; Arévalo-Villalobos, Jaime I. title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 journal: Vaccines (Basel) DOI: 10.3390/vaccines8020183 sha: doc_id: 306733 cord_uid: df36w6l7 file: cache/cord-306431-r83n27la.json key: cord-306431-r83n27la authors: Chan, Chak-Ming; Tsoi, Ho; Chan, Wing-Man; Zhai, Shenyu; Wong, Ching-On; Yao, Xiaoqiang; Chan, Wood-Yee; Tsui, Stephen Kwok-Wing; Chan, Ho Yin Edwin title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function date: 2009-05-04 journal: Int J Biochem Cell Biol DOI: 10.1016/j.biocel.2009.04.019 sha: doc_id: 306431 cord_uid: r83n27la file: cache/cord-306508-xpwluph5.json key: cord-306508-xpwluph5 authors: Nkengasong, John title: China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response date: 2020-01-27 journal: Nat Med DOI: 10.1038/s41591-020-0771-1 sha: doc_id: 306508 cord_uid: xpwluph5 file: cache/cord-307109-nz8qvuw6.json key: cord-307109-nz8qvuw6 authors: Martinez, Miguel Angel title: Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus date: 2020-04-21 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.00399-20 sha: doc_id: 307109 cord_uid: nz8qvuw6 file: cache/cord-306826-vbfdxoc2.json key: cord-306826-vbfdxoc2 authors: Solerte, Sebastiano Bruno; Di Sabatino, Antonio; Galli, Massimo; Fiorina, Paolo title: Dipeptidyl peptidase-4 (DPP4) inhibition in COVID-19 date: 2020-06-06 journal: Acta Diabetol DOI: 10.1007/s00592-020-01539-z sha: doc_id: 306826 cord_uid: vbfdxoc2 file: cache/cord-306832-w8s282nq.json key: cord-306832-w8s282nq authors: Tarragón, Blanca; Valdenebro, María; Serrano, Maria Luisa; Maroto, Alba; Llópez-Carratalá, MR; Ramos, Antonio; Rubio, Esther; Huerta, Ana; Marques, María; Portolés, Jose title: FRACASO RENAL AGUDO EN PACIENTES HOSPITALIZADOS POR COVID-19 date: 2020-10-09 journal: Nefrologia DOI: 10.1016/j.nefro.2020.08.005 sha: doc_id: 306832 cord_uid: w8s282nq file: cache/cord-306424-gf0bglm0.json key: cord-306424-gf0bglm0 authors: Scutigliani, Enzo Maxim; Kikkert, Marjolein title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2017.05.007 sha: doc_id: 306424 cord_uid: gf0bglm0 file: cache/cord-307070-tqxvu3pu.json key: cord-307070-tqxvu3pu authors: Iqbal, Phool; Ata, Fateen; Rose, Samman; Chaudhry, Hammad S; Rahil, Ali title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? 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E.; Albornoz Almada, M. Clara; Mangas Losada, María; Garrastachu, Puy; Cañete Sánchez, Francisco M.; Ramírez Lasanta, Rafael; Delgado Bolton, Roberto C. title: [(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2 date: 2020-09-16 journal: Eur J Nucl Med Mol Imaging DOI: 10.1007/s00259-020-04979-5 sha: doc_id: 307208 cord_uid: tw6mwa5v file: cache/cord-307113-mu3ow7m4.json key: cord-307113-mu3ow7m4 authors: Colmenero, I.; Santonja, C.; Alonso‐Riaño, M.; Andina, D.; Rodríguez Peralto, J.L.; Requena, L.; Torrelo, A. title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors date: 2020-09-30 journal: Br J Dermatol DOI: 10.1111/bjd.19579 sha: doc_id: 307113 cord_uid: mu3ow7m4 file: cache/cord-307036-n44yml79.json key: cord-307036-n44yml79 authors: Ng, Oi-Wing; Keng, Choong-Tat; Leung, Cynthia Sau-Wai; Peiris, J. S. Malik; Poon, Leo Lit Man; Tan, Yee-Joo title: Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date: 2014-07-14 journal: PLoS One DOI: 10.1371/journal.pone.0102415 sha: doc_id: 307036 cord_uid: n44yml79 file: cache/cord-306760-05my504t.json key: cord-306760-05my504t authors: Turner, Dan; Huang, Ying; Martín-de-Carpi, Javier; Aloi, Marina; Focht, Gili; Kang, Ben; Zhou, Ying; Sanchez, Cesar; Kappelman, Michael D.; Uhlig, Holm H.; Pujol-Muncunill, Gemma; Ledder, Oren; Lionetti, Paolo; Dias, Jorge Amil; Ruemmele, Frank M.; Russell, Richard K. title: Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date: 2020-03-31 journal: J Pediatr Gastroenterol Nutr DOI: 10.1097/mpg.0000000000002729 sha: doc_id: 306760 cord_uid: 05my504t file: cache/cord-307148-k1uo3fxm.json key: cord-307148-k1uo3fxm authors: Bradshaw, Patrick C.; Seeds, William A.; Miller, Alexandra C.; Mahajan, Vikrant R.; Curtis, William M. title: COVID-19: Proposing a Ketone-Based Metabolic Therapy as a Treatment to Blunt the Cytokine Storm date: 2020-09-09 journal: Oxid Med Cell Longev DOI: 10.1155/2020/6401341 sha: doc_id: 307148 cord_uid: k1uo3fxm file: cache/cord-307229-wjx90xki.json key: cord-307229-wjx90xki authors: da Silveira, Matheus Pelinski; da Silva Fagundes, Kimberly Kamila; Bizuti, Matheus Ribeiro; Starck, Édina; Rossi, Renata Calciolari; de Resende e Silva, Débora Tavares title: Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date: 2020-07-29 journal: Clin Exp Med DOI: 10.1007/s10238-020-00650-3 sha: doc_id: 307229 cord_uid: wjx90xki file: cache/cord-307536-qeo5dfxg.json key: cord-307536-qeo5dfxg authors: Feng, Ye; Qiu, Min; Liu, Liang; Zou, Shengmei; Li, Yun; Luo, Kai; Guo, Qianpeng; Han, Ning; Sun, Yingqiang; Wang, Kui; Zhuang, Xinlei; Zhang, Shanshan; Chen, Shuqing; Mo, Fan title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date: 2020-06-30 journal: bioRxiv DOI: 10.1101/2020.03.03.962332 sha: doc_id: 307536 cord_uid: qeo5dfxg file: cache/cord-306770-hjzlj8k3.json key: cord-306770-hjzlj8k3 authors: Mick, Paul; Murphy, Russell title: Aerosol-generating otolaryngology procedures and the need for enhanced PPE during the COVID-19 pandemic: a literature review date: 2020-05-11 journal: J Otolaryngol Head Neck Surg DOI: 10.1186/s40463-020-00424-7 sha: doc_id: 306770 cord_uid: hjzlj8k3 file: cache/cord-307160-1vz0gw1w.json key: cord-307160-1vz0gw1w authors: Morais-Almeida, Mário; Aguiar, Rita; Martin, Bryan; Ansotegui, Ignacio J.; Ebisawa, Motohiro; Arruda, L. 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V.; Nguyen, H. T.; Levine, H.; Nguyen, H.; Nguyen, T. A.; Nguyen, T. P.; Nguyen, T.; Do, T. T. T.; Tuan, N. P.; Bui, H. M. title: Estimation of the incubation period of SARS-CoV-2 in Vietnam date: 2020-05-15 journal: nan DOI: 10.1101/2020.05.09.20096800 sha: doc_id: 307436 cord_uid: qcdlcxyb file: cache/cord-307490-b4un4703.json key: cord-307490-b4un4703 authors: Chan, Sophia S.C.; So, Winnie K.W.; Wong, David C.N.; Lee, Angel C.K.; Tiwari, Agnes title: Improving older adults’ knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study date: 2007-09-30 journal: International Journal of Nursing Studies DOI: 10.1016/j.ijnurstu.2006.04.019 sha: doc_id: 307490 cord_uid: b4un4703 file: cache/cord-306881-wrd2rhjz.json key: cord-306881-wrd2rhjz authors: Gehrie, Eric; Tormey, Christopher A; Sanford, Kimberly W title: Transfusion Service Response to the COVID-19 Pandemic date: 2020-06-25 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa111 sha: doc_id: 306881 cord_uid: wrd2rhjz file: cache/cord-307285-bxy0zsc7.json key: cord-307285-bxy0zsc7 authors: Dar Odeh, Najla; Babkair, Hamzah; Abu-Hammad, Shaden; Borzangy, Sary; Abu-Hammad, Abdalla; Abu-Hammad, Osama title: COVID-19: Present and Future Challenges for Dental Practice date: 2020-04-30 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17093151 sha: doc_id: 307285 cord_uid: bxy0zsc7 file: cache/cord-307406-59yh48tt.json key: cord-307406-59yh48tt authors: de Loyola, Mariana Braccialli; dos Reis, Thaís Tereza Aguiar; de Oliveira, Guilherme Xavier Lyra Malcher; da Fonseca Palmeira, Julys; Argañaraz, Gustavo A.; Argañaraz, Enrique R. title: Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19 date: 2020-08-26 journal: Rev Med Virol DOI: 10.1002/rmv.2157 sha: doc_id: 307406 cord_uid: 59yh48tt file: cache/cord-307242-e20gtx0z.json key: cord-307242-e20gtx0z authors: Jegouic, Sophie M.; Loureiro, Silvia; Thom, Michelle; Paliwal, Deepa; Jones, Ian M. title: Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date: 2020-05-22 journal: bioRxiv DOI: 10.1101/2020.05.21.109298 sha: doc_id: 307242 cord_uid: e20gtx0z file: cache/cord-307287-zpq6byml.json key: cord-307287-zpq6byml authors: Poulsen, Nadia Nicholine; von Brunn, Albrecht; Hornum, Mads; Blomberg Jensen, Martin title: Cyclosporine and COVID‐19: Risk or Favorable? date: 2020-08-10 journal: Am J Transplant DOI: 10.1111/ajt.16250 sha: doc_id: 307287 cord_uid: zpq6byml file: cache/cord-307671-f9l2l8fi.json key: cord-307671-f9l2l8fi authors: Said, Mohammed; Hamed, Hosam title: The Forgotten Element in the Resumption of Elective Bariatric Surgery During the COVID-19 Pandemic: the Patient Consent! date: 2020-09-19 journal: Obes Surg DOI: 10.1007/s11695-020-04976-5 sha: doc_id: 307671 cord_uid: f9l2l8fi file: cache/cord-307702-n74wvika.json key: cord-307702-n74wvika authors: Durant, Thomas J S; Peaper, David R; Ferguson, David; Schulz, Wade L title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 journal: J Appl Lab Med DOI: 10.1093/jalm/jfaa121 sha: doc_id: 307702 cord_uid: n74wvika file: cache/cord-307853-m1q1sjr4.json key: cord-307853-m1q1sjr4 authors: Majumder, Satyabrata; Chaudhuri, Dwaipayan; Datta, Joyeeta; Giri, Kalyan title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model date: 2020-10-16 journal: J Mol Graph Model DOI: 10.1016/j.jmgm.2020.107778 sha: doc_id: 307853 cord_uid: m1q1sjr4 file: cache/cord-307460-v6xgkg1p.json key: cord-307460-v6xgkg1p authors: Hsu, Yu-Lung; Lin, Hsiao-Chuan; Wei, Hsiu-Mei; Lai, Huan-Cheng; Hwang, Kao-Pin title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan date: 2020-06-13 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101790 sha: doc_id: 307460 cord_uid: v6xgkg1p file: cache/cord-307653-nyr6mtj1.json key: cord-307653-nyr6mtj1 authors: Palmeira, Patricia; Barbuto, José Alexandre M; Silva, Clovis Artur A; Carneiro-Sampaio, Magda title: Why is SARS-CoV-2 infection milder among children? date: 2020-05-11 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e1947 sha: doc_id: 307653 cord_uid: nyr6mtj1 file: cache/cord-307701-fujejfwb.json key: cord-307701-fujejfwb authors: Gaurav, Shubham; Pandey, Shambhavi; Puvar, Apurvasinh; Shah, Tejas; Joshi, Madhvi; Joshi, Chaitanya; Kumar, Sachin title: Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date: 2020-06-07 journal: bioRxiv DOI: 10.1101/2020.06.06.137604 sha: doc_id: 307701 cord_uid: fujejfwb file: cache/cord-307815-reg04lpt.json key: cord-307815-reg04lpt authors: Brancatella, Alessandro; Ricci, Debora; Cappellani, Daniele; Viola, Nicola; Sgrò, Daniele; Santini, Ferruccio; Latrofa, Francesco title: Is subacute thyroiditis an underestimated manifestation of SARS-CoV-2 infection? Insights from a case series date: 2020-08-11 journal: J Clin Endocrinol Metab DOI: 10.1210/clinem/dgaa537 sha: doc_id: 307815 cord_uid: reg04lpt file: cache/cord-307463-bheq9p5w.json key: cord-307463-bheq9p5w authors: Rödel, Franz; Arenas, Meritxell; Ott, Oliver J.; Fournier, Claudia; Georgakilas, Alexandros G.; Tapio, Soile; Trott, Klaus-Rüdiger; Gaipl, Udo S. title: Low-dose radiation therapy for COVID-19 pneumopathy: what is the evidence? date: 2020-05-09 journal: Strahlenther Onkol DOI: 10.1007/s00066-020-01635-7 sha: doc_id: 307463 cord_uid: bheq9p5w file: cache/cord-307605-8zgyar7e.json key: cord-307605-8zgyar7e authors: Klimek, Ludger; Worm, Margitta; Lange, Lars; Beyer, Kirsten; Rietschel, Ernst; Vogelberg, Christian; Schnadt, Sabine; Stöcker, Britta; Brockow, Knut; Hagemann, Jan; Bieber, Thomas; Wehrmann, Wolfgang; Becker, Sven; Freudelsperger, Laura; Mülleneisen, Norbert K.; Nemat, Katja; Czech, Wolfgang; Wrede, Holger; Brehler, Randolf; Fuchs, Thomas; Dramburg, Stephanie; Matricardi, Paolo; Hamelmann, Eckard; Werfel, Thomas; Wagenmann, Martin; Taube, Christian; Zuberbier, Torsten; Ring, Johannes title: Management von Anaphylaxie-gefährdeten Patienten während der Covid-19-Pandemie: Ein Positionspapier des Ärzteverbandes Deutscher Allergologen (AeDA)A, der Deutschen Gesellschaft für Allergologie und klinische Immunologie (DGAKI)B, der Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)C und des Deutschen Allergie- und Asthmabundes (DAAB)D date: 2020-11-09 journal: Allergo J DOI: 10.1007/s15007-020-2618-y sha: doc_id: 307605 cord_uid: 8zgyar7e file: cache/cord-307502-vuju89lc.json key: cord-307502-vuju89lc authors: Leipe, J.; Hoyer, B. F.; Iking-Konert, C.; Schulze-Koops, H.; Specker, C.; Krüger, K. title: SARS-CoV-2 & Rheuma: Konsequenzen der SARS-CoV-2-Pandemie für Patienten mit entzündlich rheumatischen Erkrankungen. Ein Vergleich der Handlungsempfehlungen rheumatologischer Fachgesellschaften und Risikobewertung verschiedener antirheumatischer Therapien date: 2020-08-26 journal: Z Rheumatol DOI: 10.1007/s00393-020-00878-0 sha: doc_id: 307502 cord_uid: vuju89lc file: cache/cord-308021-cnf4xljc.json key: cord-308021-cnf4xljc authors: Kohns Vasconcelos, Malte; Renk, Hanna; Popielska, Jolanta; Nyirenda Nyang’wa, Maggie; Burokiene, Sigita; Gkentzi, Despoina; Gowin, Ewelina; Donà, Daniele; Villanueva-Medina, Sara; Riordan, Andrew; Hufnagel, Markus; Eisen, Sarah; Da Dalt, Liviana; Giaquinto, Carlo; Bielicki, Julia A. title: SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date: 2020-10-13 journal: Eur J Pediatr DOI: 10.1007/s00431-020-03843-w sha: doc_id: 308021 cord_uid: cnf4xljc file: cache/cord-307770-1igydu3y.json key: cord-307770-1igydu3y authors: Rawson, Timothy M; Moore, Luke S P; Zhu, Nina; Ranganathan, Nishanthy; Skolimowska, Keira; Gilchrist, Mark; Satta, Giovanni; Cooke, Graham; Holmes, Alison title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date: 2020-05-02 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa530 sha: doc_id: 307770 cord_uid: 1igydu3y file: cache/cord-308080-1heu9vuv.json key: cord-308080-1heu9vuv authors: Simulundu, Edgar; Mupeta, Francis; Chanda-Kapata, Pascalina; Saasa, Ngonda; Changula, Katendi; Muleya, Walter; Chitanga, Simbarashe; Mwanza, Miniva; Simusika, Paul; Chambaro, Herman; Mubemba, Benjamin; Kajihara, Masahiro; Chanda, Duncan; Mulenga, Lloyd; Fwoloshi, Sombo; Shibemba, Aaron Lunda; Kapaya, Fred; Zulu, Paul; Musonda, Kunda; Monze, Mwaka; Sinyange, Nyambe; Liwewe, Mazyanga M.; Kapin’a, Muzala; Chipimo, Peter J.; Hamoonga, Raymond; Simwaba, Davie; Ngosa, William; Morales, Albertina N.; Kayeyi, Nkomba; Tembo, John; Bates, Mathew; Orba, Yasuko; Sawa, Hirofumi; Takada, Ayato; Nalubamba, King S.; Malama, Kennedy; Mukonka, Victor; Zumla, Alimuddin; Kapata, Nathan title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date: 2020-10-06 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1480 sha: doc_id: 308080 cord_uid: 1heu9vuv file: cache/cord-308071-1bk3xuwf.json key: cord-308071-1bk3xuwf authors: Lang, Christian; Jaksch, Peter; Hoda, Mir Alireza; Lang, György; Staudinger, Thomas; Tschernko, Edda; Zapletal, Bernhard; Geleff, Silvana; Prosch, Helmut; Gawish, Riem; Knapp, Sylvia; Robak, Oliver; Thalhammer, Florian; Indra, Alexander; Koestenberger, Markus; Strassl, Robert; Klikovits, Thomas; Ali, Kamran; Fischer, Gottfried; Klepetko, Walter; Hoetzenecker, Konrad; Schellongowski, Peter title: Lung transplantation for COVID-19-associated acute respiratory distress syndrome in a PCR-positive patient date: 2020-08-25 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30361-1 sha: doc_id: 308071 cord_uid: 1bk3xuwf file: cache/cord-307842-7q2jd0mf.json key: cord-307842-7q2jd0mf authors: Fox, Alisa; Marino, Jessica; Amanat, Fatima; Krammer, Florian; Hahn-Holbrook, Jennifer; Zolla-Pazner, Susan; Powell, Rebecca L. title: Robust and specific secretory IgA against SARS-CoV-2 detected in human milk date: 2020-10-26 journal: iScience DOI: 10.1016/j.isci.2020.101735 sha: doc_id: 307842 cord_uid: 7q2jd0mf file: cache/cord-307885-butuv3n1.json key: cord-307885-butuv3n1 authors: Galvani, Alison P. title: Emerging Infections: What Have We Learned from SARS? date: 2004-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1007.040166 sha: doc_id: 307885 cord_uid: butuv3n1 file: cache/cord-308123-eu0azqfu.json key: cord-308123-eu0azqfu authors: Lee, Yun Young; Park, Hee Ho; Park, Wooram; Kim, Hyelim; Jang, Jong Geol; Hong, Kyung Soo; Lee, Jae-Young; Seo, Hee Seung; Na, Dong Hee; Kim, Tae-Hyung; Choy, Young Bin; Ahn, June Hong; Lee, Wonhwa; Park, Chun Gwon title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm date: 2020-10-23 journal: Biomaterials DOI: 10.1016/j.biomaterials.2020.120389 sha: doc_id: 308123 cord_uid: eu0azqfu file: cache/cord-308093-m40czdsr.json key: cord-308093-m40czdsr authors: Matthews, M. M.; Kim, T. G.; Shibata, S.; Shibata, N.; Butcher, C.; Hyun, J.; Kim, K. Y.; Robb, T.; Jheng, S. S.; Narita, M.; Mori, T.; Collins, M.; Wolf, M. title: COVID-19 serological survey using micro blood sampling date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.09.20209858 sha: doc_id: 308093 cord_uid: m40czdsr file: cache/cord-308288-3ewdy5l3.json key: cord-308288-3ewdy5l3 authors: Domingues, Renan Barros; Mendes-Correa, Maria Cássia; de Moura Leite, Fernando Brunale Vilela; Sabino, Ester Cerdeira; Salarini, Diego Zanotti; Claro, Ingra; Santos, Daniel Wagner; de Jesus, Jaqueline Goes; Ferreira, Noely Evangelista; Romano, Camila Malta; Soares, Carlos Augusto Senne title: First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease date: 2020-06-20 journal: J Neurol DOI: 10.1007/s00415-020-09996-w sha: doc_id: 308288 cord_uid: 3ewdy5l3 file: cache/cord-308075-1ftswsm8.json key: cord-308075-1ftswsm8 authors: Segura, Patricia Sanz; Lázaro, Yolanda Arguedas; Tapia, Sonia Mostacero; Chaves, Tomás Cabrera; Domingo, Juan José Sebastián title: Involvement of the digestive system in COVID-19. A review date: 2020-10-09 journal: nan DOI: 10.1016/j.gastre.2020.06.004 sha: doc_id: 308075 cord_uid: 1ftswsm8 file: cache/cord-308356-ojx3tasi.json key: cord-308356-ojx3tasi authors: Schwarz, Silke; Jenetzky, Ekkehart; Krafft, Hanno; Maurer, Tobias; Steuber, Christian; Reckert, Till; Fischbach, Thomas; Martin, David title: Corona bei Kindern: Die Co-Ki Studie: Relevanz von SARS-CoV-2 in der ambulanten pädiatrischen Versorgung in Deutschland date: 2020-11-03 journal: Monatsschr Kinderheilkd DOI: 10.1007/s00112-020-01050-3 sha: doc_id: 308356 cord_uid: ojx3tasi file: cache/cord-307811-6e3j0pn7.json key: cord-307811-6e3j0pn7 authors: Hao, Wei; Ma, Bo; Li, Ziheng; Wang, Xiaoyu; Gao, Xiaopan; Li, Yaohao; Qin, Bo; Shang, Shiying; Cui, Sheng; Tan, Zhongping title: Binding of the SARS-CoV-2 Spike Protein to Glycans date: 2020-07-02 journal: bioRxiv DOI: 10.1101/2020.05.17.100537 sha: doc_id: 307811 cord_uid: 6e3j0pn7 file: cache/cord-307858-274a699i.json key: cord-307858-274a699i authors: Hotez, Peter J.; Corry, David B.; Strych, Ulrich; Bottazzi, Maria Elena title: COVID-19 vaccines: neutralizing antibodies and the alum advantage date: 2020-06-04 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0358-6 sha: doc_id: 307858 cord_uid: 274a699i file: cache/cord-307942-t8165mdx.json key: cord-307942-t8165mdx authors: Zwald, Marissa L.; Lin, Wen; Sondermeyer Cooksey, Gail L.; Weiss, Charles; Suarez, Angela; Fischer, Marc; Bonin, Brandon J.; Jain, Seema; Langley, Gayle E.; Park, Benjamin J.; Moulia, Danielle; Benedict, Rory; Nguyen, Nang; Han, George S. title: Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 date: 2020-04-10 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6914e3 sha: doc_id: 307942 cord_uid: t8165mdx file: cache/cord-308066-lrbi5198.json key: cord-308066-lrbi5198 authors: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_16 sha: doc_id: 308066 cord_uid: lrbi5198 file: cache/cord-308279-gsk4qel5.json key: cord-308279-gsk4qel5 authors: Suzuki, Yuichiro J. title: The viral protein fragment theory of COVID-19 pathogenesis date: 2020-09-11 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110267 sha: doc_id: 308279 cord_uid: gsk4qel5 file: cache/cord-308077-hbxpn5a1.json key: cord-308077-hbxpn5a1 authors: Siepmann, Timo; Kitzler, Hagen H.; Reichmann, Heinz; Barlinn, Kristian title: Variability of symptoms in neuralgic amyotrophy following infection with SARS‐CoV‐2 date: 2020-10-01 journal: Muscle Nerve DOI: 10.1002/mus.27084 sha: doc_id: 308077 cord_uid: hbxpn5a1 file: cache/cord-307932-7t41wvw3.json key: cord-307932-7t41wvw3 authors: Guo, Xiaoqin; Guo, Zhongmin; Duan, Chaohui; chen, Zeliang; Wang, Guoling; Lu, Yi; Li, Mengfeng; Lu, Jiahai title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers date: 2020-02-14 journal: nan DOI: 10.1101/2020.02.12.20021386 sha: doc_id: 307932 cord_uid: 7t41wvw3 file: cache/cord-308234-4obggisp.json key: cord-308234-4obggisp authors: Ford, Nathan; Vitoria, Marco; Rangaraj, Ajay; Norris, Susan L; Calmy, Alexandra; Doherty, Meg title: Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID‐19: initial assessment date: 2020-04-15 journal: J Int AIDS Soc DOI: 10.1002/jia2.25489 sha: doc_id: 308234 cord_uid: 4obggisp file: cache/cord-308142-3x3n6cpt.json key: cord-308142-3x3n6cpt authors: Lee, Nelson; Wong, Chun K.; Lam, Wai Y.; Wong, Ann; Lim, Wilina; Lam, Christopher W.K.; Cockram, Clive S.; Sung, Joseph J.Y.; Chan, Paul K.S.; Tang, Julian W. title: Chikungunya Fever, Hong Kong date: 2006-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid1211.060574 sha: doc_id: 308142 cord_uid: 3x3n6cpt file: cache/cord-308224-cqi1x92w.json key: cord-308224-cqi1x92w authors: Wu, Lianhua; Gao, Chunjin; Wang, Guozhong; Yang, Lin; Hou, Xiaomin; Ge, Huan; Xia, Chengqing; Qi, Man title: Clinical study on the related markers of blood coagulation in the patients with ANFH after SARS date: 2007-10-01 journal: Front Med China DOI: 10.1007/s11684-007-0080-9 sha: doc_id: 308224 cord_uid: cqi1x92w file: cache/cord-308100-tvk47fd7.json key: cord-308100-tvk47fd7 authors: Soetikno, Roy; Teoh, Anthony YB.; Kaltenbach, Tonya; Lau, James YW.; Asokkumar, Ravishankar; Cabral-Prodigalidad, Patricia; Shergill, Amandeep title: Considerations in performing endoscopy during the COVID-19 pandemic date: 2020-03-27 journal: Gastrointest Endosc DOI: 10.1016/j.gie.2020.03.3758 sha: doc_id: 308100 cord_uid: tvk47fd7 file: cache/cord-308358-2bap7iih.json key: cord-308358-2bap7iih authors: Friedland, Robert P; Haribabu, Bodduluri title: The role for the metagenome in the pathogenesis of COVID-19 date: 2020-10-07 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.103019 sha: doc_id: 308358 cord_uid: 2bap7iih file: cache/cord-308302-5yns1hg9.json key: cord-308302-5yns1hg9 authors: Wu, Gang; Zhou, Shuchang; Wang, Yujin; Lv, Wenzhi; Wang, Shili; Wang, Ting; Li, Xiaoming title: A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings date: 2020-08-20 journal: Sci Rep DOI: 10.1038/s41598-020-71114-7 sha: doc_id: 308302 cord_uid: 5yns1hg9 file: cache/cord-307860-iqk1yiw4.json key: cord-307860-iqk1yiw4 authors: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 journal: Protein J DOI: 10.1007/s10930-020-09933-w sha: doc_id: 307860 cord_uid: iqk1yiw4 file: cache/cord-308576-iw8oobbe.json key: cord-308576-iw8oobbe authors: Wuxing, Dai; Mingjun, Lei; Shaoting, Wu; Zhihao, Chen; Liang, Liang; Hujrong, Pan; Li, Qin; Shitong, Gao; Shishan, Yuan; Renli, Zhang title: Expression and purification of SARS coronavirus membrane protein date: 2004 journal: J Huazhong Univ Sci Technolog Med Sci DOI: 10.1007/bf02831095 sha: doc_id: 308576 cord_uid: iw8oobbe file: cache/cord-308256-jy20xtwx.json key: cord-308256-jy20xtwx authors: Wells, P. M.; Doores, K. M.; Couvreur, S.; Martin Martinez, R.; Seow, J.; Graham, C.; Acors, S.; Kouphou, N.; Neil, S.; Tedder, R.; Matos, P.; Poulton, K.; Jose Lista, M.; Dickenson, R.; Sertkaya, H.; Maguire, T.; Scourfield, E.; Bowyer, R.; Hart, D.; O'Byrne, A.; Steele, K.; Hemmings, O.; Rosadas, C.; McClure, M.; Capedevila-Pujol, J.; wolf, J.; Ourseilin, S.; Brown, M.; Malim, M.; Spector, T.; Steves, C. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-07-30 journal: nan DOI: 10.1101/2020.07.29.20162701 sha: doc_id: 308256 cord_uid: jy20xtwx file: cache/cord-308231-1t70vkxm.json key: cord-308231-1t70vkxm authors: Childs, S. J. title: Could Deficiencies in South African Data Be the Explanation for Its Early SARS-CoV-2 Peak? date: 2020-09-02 journal: nan DOI: 10.1101/2020.08.31.20185108 sha: doc_id: 308231 cord_uid: 1t70vkxm file: cache/cord-308110-cco3aq4n.json key: cord-308110-cco3aq4n authors: Okamoto, Mika; Toyama, Masaaki; Baba, Masanori title: The chemokine receptor antagonist cenicriviroc inhibits the replication of SARS-CoV-2 in vitro date: 2020-07-30 journal: Antiviral Res DOI: 10.1016/j.antiviral.2020.104902 sha: doc_id: 308110 cord_uid: cco3aq4n file: cache/cord-308408-aciaj30k.json key: cord-308408-aciaj30k authors: Paneesha, S.; Pratt, G.; Parry, H.; Moss, P. title: Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia date: 2020-04-30 journal: Leuk Res DOI: 10.1016/j.leukres.2020.106366 sha: doc_id: 308408 cord_uid: aciaj30k file: cache/cord-308424-crvnzr44.json key: cord-308424-crvnzr44 authors: Mascarenhas, Victor Hugo Alves; Caroci-Becker, Adriana; Venâncio, Kelly Cristina Máxima Pereira; Baraldi, Nayara Girardi; Durkin, Adelaide Caroci; Riesco, Maria Luiza Gonzalez title: Care recommendations for parturient and postpartum women and newborns during the COVID-19 pandemic: a scoping review date: 2020-08-10 journal: Revista latino-americana de enfermagem DOI: 10.1590/1518-8345.4596.3359 sha: doc_id: 308424 cord_uid: crvnzr44 file: cache/cord-308715-uo6h1h2e.json key: cord-308715-uo6h1h2e authors: Chandra, Aman; Haynes, Richard; Burdon, Michael; Laidlaw, Alistair; Neffendorf, James; Eames, Ian; daCruz, Lyndon; Lee, Richard W.; Charles, Stephen; Wilson, Peter; Dick, Andrew; Flanagan, Declan; Yorston, David; Hingorani, Melanie; Wickham, Louisa title: Personal protective equipment (PPE) for vitreoretinal surgery during COVID-19 date: 2020-05-12 journal: Eye (Lond) DOI: 10.1038/s41433-020-0948-3 sha: doc_id: 308715 cord_uid: uo6h1h2e file: cache/cord-308428-zw26usmh.json key: cord-308428-zw26usmh authors: Walter, Justin D.; Hutter, Cedric A.J.; Garaeva, Alisa A.; Scherer, Melanie; Zimmermann, Iwan; Wyss, Marianne; Rheinberger, Jan; Ruedin, Yelena; Earp, Jennifer C.; Egloff, Pascal; Sorgenfrei, Michèle; Hürlimann, Lea M.; Gonda, Imre; Meier, Gianmarco; Remm, Sille; Thavarasah, Sujani; Zimmer, Gert; Slotboom, Dirk J.; Paulino, Cristina; Plattet, Philippe; Seeger, Markus A. title: Highly potent bispecific sybodies neutralize SARS-CoV-2 date: 2020-11-10 journal: bioRxiv DOI: 10.1101/2020.11.10.376822 sha: doc_id: 308428 cord_uid: zw26usmh file: cache/cord-308501-z3eiac25.json key: cord-308501-z3eiac25 authors: Zhu, Chengliang; Liu, Weiyong; Su, Hanwen; Li, Sitong; Shereen, Muhammad Adnan; Lv, Zhihua; Niu, Zhili; Li, Dong; Liu, Fang; Luo, Zhen; Xia, Yuchen title: nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk date: 2020-06-04 journal: J Infect DOI: 10.1016/j.jinf.2020.06.001 sha: doc_id: 308501 cord_uid: z3eiac25 file: cache/cord-308252-qwoo7b1l.json key: cord-308252-qwoo7b1l authors: Cardinale, Vincenzo; Capurso, Gabriele; Ianiro, Gianluca; Gasbarrini, Antonio; Arcidiacono, Paolo Giorgio; Alvaro, Domenico title: Intestinal permeability changes with bacterial translocation as key events modulating systemic host immune response to SARS-CoV-2: A working hypothesis date: 2020-09-16 journal: Dig Liver Dis DOI: 10.1016/j.dld.2020.09.009 sha: doc_id: 308252 cord_uid: qwoo7b1l file: cache/cord-308310-wtmjt3hf.json key: cord-308310-wtmjt3hf authors: Zha, Lisha; Zhao, Hongxin; Mohsen, Mona O.; Hong, Liang; Zhou, Yuhang; Li, Zehua; Yao, Chuankai; Guo, Lijie; Chen, Hongquan; Liu, Xuelan; Chang, Xinyue; Zhang, Jie; Li, Dong; Wu, Ke; Vogel, Monique; Bachmann, Martin F; Wang, Junfeng title: Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date: 2020-05-14 journal: bioRxiv DOI: 10.1101/2020.05.06.079830 sha: doc_id: 308310 cord_uid: wtmjt3hf file: cache/cord-308342-ycdok8fc.json key: cord-308342-ycdok8fc authors: Shutler, J.; Zaraska, K.; Holding, T. M.; Machnik, M.; Uppuluri, K.; Ashton, I.; Migdal, L.; Dahiya, R. title: Risk of SARS-CoV-2 infection from contaminated water systems date: 2020-06-20 journal: nan DOI: 10.1101/2020.06.17.20133504 sha: doc_id: 308342 cord_uid: ycdok8fc file: cache/cord-308400-8wihm63b.json key: cord-308400-8wihm63b authors: Kanellopoulou, A.; Koskeridis, F.; Markozannes, G.; Bouras, E.; Soutziou, C.; Chaliasos, K.; Doumas, M. T.; Sigounas, D. E.; Tzovaras, V. T.; Panos, A.; Stergiou, Y.; Mellou, K.; Papamichail, D.; Aretouli, E.; Chatzidimitriou, D.; Chatzopoulou, F.; Bairaktari, E.; Tzoulaki, I.; Evangelou, E.; Rizos, E. C.; Ntzani, E.; Vakalis, K.; Tsilidis, K. K. title: Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort date: 2020-11-13 journal: nan DOI: 10.1101/2020.11.10.20229146 sha: doc_id: 308400 cord_uid: 8wihm63b file: cache/cord-308499-xqmguqyi.json key: cord-308499-xqmguqyi authors: Ahmed, Sakir; Anirvan, Prajna title: Reply to Rheumatologists’ perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? date: 2020-05-09 journal: Clin Rheumatol DOI: 10.1007/s10067-020-05145-w sha: doc_id: 308499 cord_uid: xqmguqyi file: cache/cord-308800-b8gtwdxc.json key: cord-308800-b8gtwdxc authors: Goldhaber-Fiebert, Sara N.; Greene, Jeremy A.; Garibaldi, Brian T. title: Low-flow Nasal Cannula and Potential Nosocomial Spread of COVID-19 date: 2020-05-18 journal: Br J Anaesth DOI: 10.1016/j.bja.2020.05.011 sha: doc_id: 308800 cord_uid: b8gtwdxc file: cache/cord-308615-4fobikeh.json key: cord-308615-4fobikeh authors: AKTAS, Busra; ASLIM, Belma title: Gut-lung axis and dysbiosis in COVID-19 date: 2020-06-21 journal: Turk J Biol DOI: 10.3906/biy-2005-102 sha: doc_id: 308615 cord_uid: 4fobikeh file: cache/cord-308786-e6rv5csl.json key: cord-308786-e6rv5csl authors: Alamri, Mubarak A.; Tahir ul Qamar, Muhammad; Mirza, Muhammad Usman; Alqahtani, Safar M.; Froeyen, Matheus; Chen, Ling-Ling title: Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date: 2020-08-28 journal: J Pharm Anal DOI: 10.1016/j.jpha.2020.08.012 sha: doc_id: 308786 cord_uid: e6rv5csl file: cache/cord-308451-pmwmfl3w.json key: cord-308451-pmwmfl3w authors: Chiang, Shu-Fen; Lin, Tze-Yi; Chow, Kuan-Chih; Chiou, Shiow-Her title: SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells date: 2010-07-27 journal: Mol Immunol DOI: 10.1016/j.molimm.2010.06.014 sha: doc_id: 308451 cord_uid: pmwmfl3w file: cache/cord-308740-06jr58kz.json key: cord-308740-06jr58kz authors: Lazaridis, Charalampos; Vlachogiannis, Nikolaos I.; Bakogiannis, Constantinos; Spyridopoulos, Ioakim; Stamatelopoulos, Kimon; Kanakakis, Ioannis; Vassilikos, Vassilios; Stellos, Konstantinos title: Involvement of Cardiovascular System As The Critical Point in Coronavirus Disease 2019 (COVID-19) Prognosis and Recovery date: 2020-06-10 journal: Hellenic J Cardiol DOI: 10.1016/j.hjc.2020.05.004 sha: doc_id: 308740 cord_uid: 06jr58kz file: cache/cord-308994-4nljzm8a.json key: cord-308994-4nljzm8a authors: Tang, Zhongmin; Zhang, Xingcai; Shu, Yiqing; Guo, Ming; Zhang, Han; Tao, Wei title: Insights from nanotechnology in COVID-19 treatment date: 2020-11-04 journal: Nano Today DOI: 10.1016/j.nantod.2020.101019 sha: doc_id: 308994 cord_uid: 4nljzm8a file: cache/cord-308857-otsrexqu.json key: cord-308857-otsrexqu authors: Goel, Saurav; Hawi, Sara; Goel, Gaurav; Thakur, Vijay Kumar; Pearce, Oliver; Hoskins, Clare; Hussain, Tanvir; Agrawal, Anupam; Upadhyaya, Hari M.; Cross, Graham; Barber, Asa H. title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 journal: Mater Today Chem DOI: 10.1016/j.mtchem.2020.100300 sha: doc_id: 308857 cord_uid: otsrexqu file: cache/cord-308667-6jr3z9wx.json key: cord-308667-6jr3z9wx authors: Papachristodoulou, Eleni; Kakoullis, Loukas; Parperis, Konstantinos; Panos, George title: Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge date: 2020-06-08 journal: Pathog Dis DOI: 10.1093/femspd/ftaa025 sha: doc_id: 308667 cord_uid: 6jr3z9wx file: cache/cord-308752-uylvtqlu.json key: cord-308752-uylvtqlu authors: Miao, Y.; Lidove, O.; Mauhin, W. title: First case of acute pancreatitis related to SARS‐CoV‐2 infection date: 2020-06-03 journal: Br J Surg DOI: 10.1002/bjs.11741 sha: doc_id: 308752 cord_uid: uylvtqlu file: cache/cord-308760-xonuu04p.json key: cord-308760-xonuu04p authors: Clerici, Bianca; Birocchi, Simone; Bertinato, Elena; Di Benedetto, Clara; Caberlon, Sabrina; Cattaneo, Marco; Podda, Gian Marco title: A case of newly diagnosed immune thrombocytopenia in the COVID-19 era date: 2020-11-12 journal: Intern Emerg Med DOI: 10.1007/s11739-020-02553-3 sha: doc_id: 308760 cord_uid: xonuu04p file: cache/cord-308583-vtmwv8zl.json key: cord-308583-vtmwv8zl authors: Du, Qishi; Wang, Shuqing; Wei, Dongqing; Sirois, Suzanne; Chou, Kuo-Chen title: Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase date: 2005-02-15 journal: Analytical Biochemistry DOI: 10.1016/j.ab.2004.10.003 sha: doc_id: 308583 cord_uid: vtmwv8zl file: cache/cord-308912-2pd801t1.json key: cord-308912-2pd801t1 authors: Bensimon, Cécile M.; Tracy, C. Shawn; Bernstein, Mark; Shaul, Randi Zlotnik; Upshur, Ross E.G. title: A qualitative study of the duty to care in communicable disease outbreaks date: 2007-12-31 journal: Social Science & Medicine DOI: 10.1016/j.socscimed.2007.07.017 sha: doc_id: 308912 cord_uid: 2pd801t1 file: cache/cord-308736-kpz0o1ag.json key: cord-308736-kpz0o1ag authors: Heßling, Martin; Hönes, Katharina; Vatter, Petra; Lingenfelder, Christian title: Ultraviolet irradiation doses for coronavirus inactivation – review and analysis of coronavirus photoinactivation studies date: 2020-05-14 journal: GMS Hyg Infect Control DOI: 10.3205/dgkh000343 sha: doc_id: 308736 cord_uid: kpz0o1ag file: cache/cord-308370-9av7qw10.json key: cord-308370-9av7qw10 authors: Islam, Rajib; Parves, Md. Rimon; Paul, Archi Sundar; Uddin, Nizam; Rahman, Md. Sajjadur; Mamun, Abdulla Al; Hossain, Md. Nayeem; Ali, Md. Ackas; Halim, Mohammad A. title: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 date: 2020-05-12 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1761883 sha: doc_id: 308370 cord_uid: 9av7qw10 file: cache/cord-308597-ieju8gd8.json key: cord-308597-ieju8gd8 authors: de Carvalho, Renata Cristina; Groner, Matheus Ferreira; Camillo, Jacqueline; Ferreira, Paulo Roberto Abrão; Fraietta, Renato title: The interference of COVID-19 in the male reproductive system: Important questions and the future of assisted reproduction techniques date: 2020-08-21 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e2183 sha: doc_id: 308597 cord_uid: ieju8gd8 file: cache/cord-308833-ei1faruy.json key: cord-308833-ei1faruy authors: Zheng, Xiaohong; Li, Kejun; Wang, Ruzhu; Zhao, Liping; Xu, Lisa X.; Chen, Yazhu; Jin, Xinqiao; Gu, Bo; Bai, Jingfeng; Liu, Hongmin; Ye, Xiaojiang title: Experimental investigation of integrated air purifying technology for bioaerosol removal and inactivation in central air-conditioning system date: 2004 journal: Chin Sci Bull DOI: 10.1007/bf03182817 sha: doc_id: 308833 cord_uid: ei1faruy file: cache/cord-309370-g8d3w7it.json key: cord-309370-g8d3w7it authors: Insausti-García, Alfredo; Reche-Sainz, José Alberto; Ruiz-Arranz, Celia; López Vázquez, Ángel; Ferro-Osuna, Manuel title: Papillophlebitis in a COVID-19 patient: Inflammation and hypercoagulable state date: 2020-07-30 journal: Eur J Ophthalmol DOI: 10.1177/1120672120947591 sha: doc_id: 309370 cord_uid: g8d3w7it file: cache/cord-309043-dlmx12vt.json key: cord-309043-dlmx12vt authors: von Brunn, Albrecht; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph; Haas, Jürgen title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0000459 sha: doc_id: 309043 cord_uid: dlmx12vt file: cache/cord-309304-glcxrh7t.json key: cord-309304-glcxrh7t authors: Flemming, Sven; Hankir, Mohammed; Germer, Christoph‐Thomas; Wiegering, Armin title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-09-19 journal: Br J Surg DOI: 10.1002/bjs.11898 sha: doc_id: 309304 cord_uid: glcxrh7t file: cache/cord-308945-i2agpvhk.json key: cord-308945-i2agpvhk authors: Phipps, William S; SoRelle, Jeffrey A; Li, Quan-Zhen; Mahimainathan, Lenin; Araj, Ellen; Markantonis, John; Lacelle, Chantale; Balani, Jyoti; Parikh, Hiren; Solow, E Blair; Karp, David R; Sarode, Ravi; Muthukumar, Alagarraju title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa123 sha: doc_id: 308945 cord_uid: i2agpvhk file: cache/cord-308831-u5bj1sod.json key: cord-308831-u5bj1sod authors: Chaung, Jenna; Chan, Douglas; Pada, Surinder; Tambyah, Paul A. title: Coinfection with COVID‐19 and Coronavirus HKU1 – the critical need for repeat testing if clinically indicated date: 2020-04-15 journal: J Med Virol DOI: 10.1002/jmv.25890 sha: doc_id: 308831 cord_uid: u5bj1sod file: cache/cord-309317-cgs0sui7.json key: cord-309317-cgs0sui7 authors: Galeotti, Caroline; Bayry, Jagadeesh title: Autoimmune and inflammatory diseases following COVID-19 date: 2020-06-04 journal: Nat Rev Rheumatol DOI: 10.1038/s41584-020-0448-7 sha: doc_id: 309317 cord_uid: cgs0sui7 file: cache/cord-308507-hp6m6qrn.json key: cord-308507-hp6m6qrn authors: Gan, Yi-Ru; Huang, He; Huang, Yong-Dong; Rao, Chun-Ming; Zhao, Yang; Liu, Jin-Sheng; Wu, Lei; Wei, Dong-Qing title: Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase date: 2005-10-19 journal: Peptides DOI: 10.1016/j.peptides.2005.09.006 sha: doc_id: 308507 cord_uid: hp6m6qrn file: cache/cord-309360-cpis1l4u.json key: cord-309360-cpis1l4u authors: Barrios-López, J. 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D. title: Ischaemic stroke and SARS-CoV-2 infection: A causal or incidental association? date: 2020-05-28 journal: nan DOI: 10.1016/j.nrleng.2020.05.008 sha: doc_id: 309360 cord_uid: cpis1l4u file: cache/cord-309138-44qpk2vf.json key: cord-309138-44qpk2vf authors: Khanna, Kanika; Kohli, Sukhmeen Kaur; Kaur, Ravdeep; Bhardwaj, Abhay; Bhardwaj, Vinay; Ohri, Puja; Sharma, Anket; Ahmad, Ajaz; Bhardwaj, Renu; Ahmad, Parvaiz title: Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date: 2020-10-03 journal: Phytomedicine DOI: 10.1016/j.phymed.2020.153361 sha: doc_id: 309138 cord_uid: 44qpk2vf file: cache/cord-309319-si5c14e8.json key: cord-309319-si5c14e8 authors: Cao, Chunxiang; Chen, Wei; Zheng, Sheng; Zhao, Jian; Wang, Jinfeng; Cao, Wuchun title: Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China date: 2016-08-15 journal: Biomed Res Int DOI: 10.1155/2016/7247983 sha: doc_id: 309319 cord_uid: si5c14e8 file: cache/cord-309206-kq77whdx.json key: cord-309206-kq77whdx authors: Yan, Victoria C.; Muller, Florian L. title: Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment date: 2020-06-23 journal: ACS Med Chem Lett DOI: 10.1021/acsmedchemlett.0c00316 sha: doc_id: 309206 cord_uid: kq77whdx file: cache/cord-309091-te15ahvw.json key: cord-309091-te15ahvw authors: Larson, Derek; Brodniak, Sterling L; Voegtly, Logan J; Cer, Regina Z; Glang, Lindsay A; Malagon, Francisco J; Long, Kyle A; Potocki, Ronald; Smith, Darci R; Lanteri, Charlotte; Burgess, Timothy; Bishop-Lilly, Kimberly A title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1436 sha: doc_id: 309091 cord_uid: te15ahvw file: cache/cord-309302-n6cd2fc3.json key: cord-309302-n6cd2fc3 authors: Wang, Li; Jiang, Man; Qu, Jialin; Zhou, Na; Zhang, Xiaochun title: Clinical management of lung cancer patients during the outbreak of COVID-19 epidemic date: 2020-09-23 journal: Infect Agent Cancer DOI: 10.1186/s13027-020-00322-7 sha: doc_id: 309302 cord_uid: n6cd2fc3 file: cache/cord-309074-pys4aa60.json key: cord-309074-pys4aa60 authors: Huang, Victoria W.; Imam, Sarah A.; Nguyen, Shaun A. title: Telehealth in the times of SARS-CoV-2 infection for the Otolaryngologist date: 2020-05-30 journal: World J Otorhinolaryngol Head Neck Surg DOI: 10.1016/j.wjorl.2020.04.008 sha: doc_id: 309074 cord_uid: pys4aa60 file: cache/cord-309200-t2xugb8l.json key: cord-309200-t2xugb8l authors: Asadi, Sima; Bouvier, Nicole; Wexler, Anthony S.; Ristenpart, William D. title: The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? date: 2020-04-03 journal: Aerosol Sci Technol DOI: 10.1080/02786826.2020.1749229 sha: doc_id: 309200 cord_uid: t2xugb8l file: cache/cord-308996-tf0v2ojk.json key: cord-308996-tf0v2ojk authors: Maas, Angela HEM; Oertelt-Prigione, Sabine title: The Coronavirus Disease 2019 Outbreak Highlights the Importance of Sex-sensitive Medicine date: 2020-08-24 journal: Eur Cardiol DOI: 10.15420/ecr.2020.28 sha: doc_id: 308996 cord_uid: tf0v2ojk file: cache/cord-309517-yh4d414y.json key: cord-309517-yh4d414y authors: Yu, Chao; Zhou, Miao; Liu, Yang; Guo, Tinglin; Ou, Chongyang; Yang, Liye; Li, Yan; Li, Dongliang; Hu, Xinyu; Shuai, Li; Wang, Bin; Zou, Zui title: Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study date: 2020-08-12 journal: Virulence DOI: 10.1080/21505594.2020.1802194 sha: doc_id: 309517 cord_uid: yh4d414y file: cache/cord-309289-vm0k7hfx.json key: cord-309289-vm0k7hfx authors: Rothan, Hussin A.; Stone, Shannon; Natekar, Janhavi; Kumari, Pratima; Arora, Komal; Kumar, Mukesh title: The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.14.041228 sha: doc_id: 309289 cord_uid: vm0k7hfx file: cache/cord-309089-ex9nh1yi.json key: cord-309089-ex9nh1yi authors: Coperchini, Francesca; Chiovato, Luca; Croce, Laura; Magri, Flavia; Rotondi, Mario title: The Cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system date: 2020-05-11 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2020.05.003 sha: doc_id: 309089 cord_uid: ex9nh1yi file: cache/cord-309513-dleo9rpl.json key: cord-309513-dleo9rpl authors: Zhang, Huilan; 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Groth, Robert; Spann, Kirsten; Johnson, Graham R. title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 journal: Environ Pollut DOI: 10.1016/j.envpol.2020.115767 sha: doc_id: 309120 cord_uid: 05bg7rfa file: cache/cord-309147-c3ikb81g.json key: cord-309147-c3ikb81g authors: Nadeem, Muhammad Shahid; Zamzami, Mazin A.; Choudhry, Hani; Murtaza, Bibi Nazia; Kazmi, Imran; Ahmad, Habib; Shakoori, Abdul Rauf title: Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19) date: 2020-04-22 journal: Pathogens DOI: 10.3390/pathogens9040307 sha: doc_id: 309147 cord_uid: c3ikb81g file: cache/cord-309394-vroscj3m.json key: cord-309394-vroscj3m authors: Belingheri, Michael; Paladino, Maria Emilia; Riva, Michele Augusto title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers date: 2020-04-07 journal: J Occup Environ Med DOI: 10.1097/jom.0000000000001881 sha: doc_id: 309394 cord_uid: vroscj3m file: cache/cord-309411-2dfiwo65.json key: cord-309411-2dfiwo65 authors: Paris, Kristina A.; Santiago, Ulises; Camacho, Carlos J. title: Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date: 2020-06-23 journal: bioRxiv DOI: 10.1101/2020.06.16.155457 sha: doc_id: 309411 cord_uid: 2dfiwo65 file: cache/cord-309554-ctc84tfy.json key: cord-309554-ctc84tfy authors: Pang, Ronald TK; Poon, Terence CW; Chan, KC Allen; Lee, Nelson LS; Chiu, Rossa WK; Tong, Yu-Kwan; Wong, Ronald MY; Chim, Stephen SC; Ngai, Sai M; Sung, Joseph JY; Lo, YM Dennis title: Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome date: 2006-03-01 journal: Clin Chem DOI: 10.1373/clinchem.2005.061689 sha: doc_id: 309554 cord_uid: ctc84tfy file: cache/cord-309629-7jtnhn65.json key: cord-309629-7jtnhn65 authors: Thomas, Viju; Maillard, Charlotte; Barnard, Annelize; Snyman, Leon; Chrysostomou, Andreas; Shimange-Matsose, Lusandolwethu; Van Herendael, Bruno title: International society for gynecologic endoscopy (ISGE) guidelines and recommendations on gynecological endoscopy during the evolutionary phases of the SARS-CoV-2 pandemic date: 2020-08-26 journal: Eur J Obstet Gynecol Reprod Biol DOI: 10.1016/j.ejogrb.2020.08.039 sha: doc_id: 309629 cord_uid: 7jtnhn65 file: cache/cord-309650-6xz9gjq0.json key: cord-309650-6xz9gjq0 authors: Chou, Roger; Dana, Tracy; Buckley, David I.; Selph, Shelley; Fu, Rongwei; Totten, Annette M. title: Update Alert 4: Epidemiology of and Risk Factors for Coronavirus Infection in Health Care Workers date: 2020-09-11 journal: Ann Intern Med DOI: 10.7326/l20-1134 sha: doc_id: 309650 cord_uid: 6xz9gjq0 file: cache/cord-309193-v8lphej4.json key: cord-309193-v8lphej4 authors: Lemriss, Sanaâ; Souiri, Amal; Amar, Narjis; Lemzaoui, Nabil; Mestoui, Omar; Labioui, Mohamed; Ouaariba, Nabil; Jibjibe, Ayoub; Yartaoui, Mahmoud; Chahmi, Mohamed; El Rhouila, Marouane; Sellak, Samiha; Kandoussi, Nadia; El Kabbaj, Saâd title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco date: 2020-07-02 journal: Microbiol Resour Announc DOI: 10.1128/mra.00633-20 sha: doc_id: 309193 cord_uid: v8lphej4 file: cache/cord-309323-yflng8m3.json key: cord-309323-yflng8m3 authors: Thomas, T.; Stefanoni, D.; Reisz, J. A.; Nemkov, T.; Bertolone, L.; Francis, R. O.; Hudson, K. E.; Zimring, J. C.; Hansen, K. C.; Hod, E. A.; Spitalnik, S. L.; D'Alessandro, A. title: COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status date: 2020-05-16 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.05.14.20102491 sha: doc_id: 309323 cord_uid: yflng8m3 file: cache/cord-309577-438fotfd.json key: cord-309577-438fotfd authors: Xing, Yuhan; Ni, Wei; Wu, Qin; Li, Wenjie; Li, Guoju; Wang, Wendi; Tong, Jianning; Song, Xiufeng; Wong, Gary Wing Kin; Xing, Quansheng title: Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase date: 2020-04-10 journal: J Infect DOI: 10.1016/j.jinf.2020.03.049 sha: doc_id: 309577 cord_uid: 438fotfd file: cache/cord-309582-ihrj84hr.json key: cord-309582-ihrj84hr authors: AlNaamani, Khalid; AlSinani, Siham; Barkun, Alan N title: Medical research during the COVID-19 pandemic date: 2020-08-06 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i15.3156 sha: doc_id: 309582 cord_uid: ihrj84hr file: cache/cord-309418-dx6e0lri.json key: cord-309418-dx6e0lri authors: Segalés, Joaquim; Puig, Mariona; Rodon, Jordi; Avila-Nieto, Carlos; Carrillo, Jorge; Cantero, Guillermo; Terrón, Maria Teresa; Cruz, Sílvia; Parera, Mariona; Noguera-Julián, Marc; Izquierdo-Useros, Nuria; Guallar, Víctor; Vidal, Enric; Valencia, Alfonso; Blanco, Ignacio; Blanco, Julià; Clotet, Bonaventura; Vergara-Alert, Júlia title: Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain date: 2020-10-06 journal: Proc Natl Acad Sci U S A DOI: 10.1073/pnas.2010817117 sha: doc_id: 309418 cord_uid: dx6e0lri file: cache/cord-309182-t9ywnshj.json key: cord-309182-t9ywnshj authors: Premkumar, Lakshmanane; Segovia-Chumbez, Bruno; Jadi, Ramesh; Martinez, David R.; Raut, Rajendra; Markmann, Alena; Cornaby, Caleb; Bartelt, Luther; Weiss, Susan; Park, Yara; Edwards, Caitlin E.; Weimer, Eric; Scherer, Erin M.; Rouphael, Nadine; Edupuganti, Srilatha; Weiskopf, Daniela; Tse, Longping V.; Hou, Yixuan J.; Margolis, David; Sette, Alessandro; Collins, Matthew H.; Schmitz, John; Baric, Ralph S.; de Silva, Aravinda M. title: The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date: 2020-06-11 journal: Sci Immunol DOI: 10.1126/sciimmunol.abc8413 sha: doc_id: 309182 cord_uid: t9ywnshj file: cache/cord-309633-1cd74xdl.json key: cord-309633-1cd74xdl authors: Rogers, Julia H.; Link, Amy C.; McCulloch, Denise; Brandstetter, Elisabeth; Newman, Kira L.; Jackson, Michael L.; Hughes, James P.; Englund, Janet A.; Boeckh, Michael; Sugg, Nancy; Ilcisin, Misja; Sibley, Thomas R.; Fay, Kairsten; Lee, Jover; Han, Peter; Truong, Melissa; Richardson, Matthew; Nickerson, Deborah A.; Starita, Lea M.; Bedford, Trevor; Chu, Helen Y. title: Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study date: 2020-09-15 journal: Ann Intern Med DOI: 10.7326/m20-3799 sha: doc_id: 309633 cord_uid: 1cd74xdl file: cache/cord-309794-scqkyr5g.json key: cord-309794-scqkyr5g authors: Sharif‐Askari, Fatemeh Saheb; Sharif‐Askari, Narjes Saheb; Goel, Swati; Fakhri, Samer; Al‐Muhsen, Saleh; Hamid, Qutayba; Halwani, Rabih title: Are patients with chronic rhinosinusitis with nasal polyps at a decreased risk of COVID‐19 infection? date: 2020-08-05 journal: Int Forum Allergy Rhinol DOI: 10.1002/alr.22672 sha: doc_id: 309794 cord_uid: scqkyr5g file: cache/cord-309540-4pk5tq5w.json key: cord-309540-4pk5tq5w authors: Brandsma, E.; Verhagen, H. J.; van de Laar, T. J. W.; Claas, E. C. J.; Cornelissen, M.; van den Akker, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 journal: nan DOI: 10.1101/2020.07.27.20147249 sha: doc_id: 309540 cord_uid: 4pk5tq5w file: cache/cord-309619-glb2y82u.json key: cord-309619-glb2y82u authors: Domingo, Pere; Mur, Isabel; Pomar, Virginia; Corominas, Héctor; Casademont, Jordi; de Benito, Natividad title: The four horsemen of a viral Apocalypse: The pathogenesis of SARS-CoV-2 infection (COVID-19) date: 2020-07-29 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102887 sha: doc_id: 309619 cord_uid: glb2y82u file: cache/cord-309729-nd48uh8e.json key: cord-309729-nd48uh8e authors: Antunes, Adriane E.C.; Vinderola, Gabriel; Xavier-Santos, Douglas; Sivieri, Katia title: Potential contribution of beneficial microbes to face the COVID- 19 pandemic date: 2020-07-24 journal: Food Res Int DOI: 10.1016/j.foodres.2020.109577 sha: doc_id: 309729 cord_uid: nd48uh8e file: cache/cord-309856-flkjl1dm.json key: cord-309856-flkjl1dm authors: Westblade, Lars F.; Brar, Gagandeep; Pinheiro, Laura C.; Paidoussis, Demetrios; Rajan, Mangala; Martin, Peter; Goyal, Parag; Sepulveda, Jorge L.; Zhang, Lisa; George, Gary; Liu, Dakai; Whittier, Susan; Plate, Markus; Small, Catherine B.; Rand, Jacob H.; Cushing, Melissa M.; Walsh, Thomas J.; Cooke, Joseph; Safford, Monika M.; Loda, Massimo; Satlin, Michael J. title: SARS-CoV-2 Viral Load Predicts Mortality in Patients with and Without Cancer Who Are Hospitalized with COVID-19 date: 2020-09-15 journal: Cancer Cell DOI: 10.1016/j.ccell.2020.09.007 sha: doc_id: 309856 cord_uid: flkjl1dm file: cache/cord-309869-gk0svt2f.json key: cord-309869-gk0svt2f authors: Wiwanitkit, Viroj title: SARS-CoV-2 in Semen date: 2020-10-23 journal: Urol Int DOI: 10.1159/000511616 sha: doc_id: 309869 cord_uid: gk0svt2f file: cache/cord-309737-u960ftdm.json key: cord-309737-u960ftdm authors: Lolachi, Sanaz; Morin, Sarah; Coen, Matteo; Samii, Kaveh; Calmy, Alexandra; Serratrice, Jacques title: Macrophage activation syndrome as an unusual presentation of paucisymptomatic severe acute respiratory syndrome coronavirus 2 infection: A case report date: 2020-08-07 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000021570 sha: doc_id: 309737 cord_uid: u960ftdm file: cache/cord-309588-kw4d32dt.json key: cord-309588-kw4d32dt authors: Chan, Michael H.M.; Chan, Paul K.S.; Griffith, James F.; Chan, Iris H.S.; Lit, Lydia C.W.; Wong, C. K.; Antonio, Gregory E.; Liu, Ester Y.M.; Hui, David S.C.; Suen, Michael W.M; Ahuja, Anil T.; Y. Sung, Joseph J.; K. 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A risk factor for SARS-CoV-2 vulnerability in elderly men? date: 2020-04-24 journal: nan DOI: 10.1101/2020.04.19.20071357 sha: doc_id: 309915 cord_uid: isw1arrp file: cache/cord-309970-jkmjiika.json key: cord-309970-jkmjiika authors: Liu, Qin; Xu, Kaiyuan; Wang, Xiang; Wang, Wenmei title: From SARS to COVID-19: What lessons have we learned? date: 2020-08-21 journal: J Infect Public Health DOI: 10.1016/j.jiph.2020.08.001 sha: doc_id: 309970 cord_uid: jkmjiika file: cache/cord-310017-c8rd714a.json key: cord-310017-c8rd714a authors: Popa, Alexandra; Genger, Jakob-Wendelin; Nicholson, Michael; Penz, Thomas; Schmid, Daniela; Aberle, Stephan W.; Agerer, Benedikt; Lercher, Alexander; Endler, Lukas; Colaço, Henrique; Smyth, Mark; Schuster, Michael; Grau, Miguel; Martinez, Francisco; Pich, Oriol; Borena, Wegene; Pawelka, Erich; Keszei, Zsofia; Senekowitsch, Martin; Laine, Jan; Aberle, Judith H.; Redlberger-Fritz, Monika; Karolyi, Mario; Zoufaly, Alexander; Maritschnik, Sabine; Borkovec, Martin; Hufnagl, Peter; Nairz, Manfred; Weiss, Günter; Wolfinger, Michael T.; von Laer, Dorothee; Superti-Furga, Giulio; Lopez-Bigas, Nuria; Puchhammer-Stöckl, Elisabeth; Allerberger, Franz; Michor, Franziska; Bock, Christoph; Bergthaler, Andreas title: Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date: 2020-07-17 journal: bioRxiv DOI: 10.1101/2020.07.15.204339 sha: doc_id: 310017 cord_uid: c8rd714a file: cache/cord-310051-bl8l4bgo.json key: cord-310051-bl8l4bgo authors: Leitner, Thomas; Kumar, Sudhir title: Where did SARS-CoV-2 come from? date: 2020-07-06 journal: Mol Biol Evol DOI: 10.1093/molbev/msaa162 sha: doc_id: 310051 cord_uid: bl8l4bgo file: cache/cord-309876-l0xginsa.json key: cord-309876-l0xginsa authors: Vena, Antonio; Berruti, Marco; Adessi, Andrea; Blumetti, Pietro; Brignole, Michele; Colognato, Renato; Gaggioli, Germano; Giacobbe, Daniele Roberto; Bracci-Laudiero, Luisa; Magnasco, Laura; Signori, Alessio; Taramasso, Lucia; Varelli, Marco; Vendola, Nicoletta; Ball, Lorenzo; Robba, Chiara; Battaglini, Denise; Brunetti, Iole; Pelosi, Paolo; Bassetti, Matteo title: Prevalence of Antibodies to SARS-CoV-2 in Italian Adults and Associated Risk Factors date: 2020-08-27 journal: J Clin Med DOI: 10.3390/jcm9092780 sha: doc_id: 309876 cord_uid: l0xginsa file: cache/cord-310064-p8u424ch.json key: cord-310064-p8u424ch authors: Katz, Andrew P.; Civantos, Francisco J.; Sargi, Zoukaa; Leibowitz, Jason M.; Nicolli, Elizabeth A.; Weed, Donald; Moskovitz, Alexander E.; Civantos, Alyssa M.; Andrews, David M.; Martinez, Octavio; Thomas, Giovana R. title: False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date: 2020-06-12 journal: Head Neck DOI: 10.1002/hed.26317 sha: doc_id: 310064 cord_uid: p8u424ch file: cache/cord-310091-x31g02xw.json key: cord-310091-x31g02xw authors: Zhang, Zhilan; Li, Lin; Li, Mengyuan; Wang, Xiaosheng title: Pan-cancer analysis reveals that ACE2 is positively associated with immunotherapy response and is a potential protective factor for cancer progression date: 2020-09-02 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.08.024 sha: doc_id: 310091 cord_uid: x31g02xw file: cache/cord-310096-a242g5kg.json key: cord-310096-a242g5kg authors: Yokota, I.; Shane, P. Y.; Okada, K.; Unoki, Y.; Yang, Y.; Inao, T.; Sakamaki, K.; Iwasaki, S.; Hayasaka, K.; Sugita, J.; Nishida, M.; Fujisawa, S.; Teshima, T. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 journal: nan DOI: 10.1101/2020.08.13.20174078 sha: doc_id: 310096 cord_uid: a242g5kg file: cache/cord-310299-isdsestc.json key: cord-310299-isdsestc authors: Hosseini, Akram A.; Shetty, Ashit K.; Sprigg, Nikola; Auer, Dorothee P.; Constantinescu, Cris S. title: Delirium as a presenting feature in COVID-19: neuroinvasive infection or autoimmune encephalopathy? date: 2020-06-09 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.06.012 sha: doc_id: 310299 cord_uid: isdsestc file: cache/cord-310195-am3u7z76.json key: cord-310195-am3u7z76 authors: Waller, J.; Rubin, G. J.; Potts, H. W. W.; Mottershaw, A.; Marteau, T. 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J.; van de Sandt, C. E.; Lemke, M. M.; Lee, C. Y.; Shoffner, S. K.; Chua, B. Y.; Nguyen, T. H. O.; Rowntree, L. C.; Hensen, L.; Koutsakos, M.; Wong, C. Y.; Jackson, D. C.; Flanagan, K. L.; Crowe, J.; Cheng, A. C.; Doolan, D. L.; Amanat, F.; Krammer, F.; Chappell, K.; Modhiran, N.; Watterson, D.; Young, P.; Wines, B.; Hogarth, P. M.; Esterbauer, R.; Kelly, H. G.; Tan, H.-X.; Juno, J. A.; Wheatley, A. K.; Kent, S. J.; Arnold, K. B.; Kedzierska, K.; Chung, A. W. title: Distinct systems serology features in children, elderly and COVID patients date: 2020-05-18 journal: nan DOI: 10.1101/2020.05.11.20098459 sha: doc_id: 310063 cord_uid: 8nbmrjrw file: cache/cord-310419-s3qkscw7.json key: cord-310419-s3qkscw7 authors: Lephart, Paul R.; Bachman, Michael A.; LeBar, William; McClellan, Scott; Barron, Karen; Schroeder, Lee; Newton, Duane W. title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() date: 2020-09-03 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115200 sha: doc_id: 310419 cord_uid: s3qkscw7 file: cache/cord-310692-8fuj9td2.json key: cord-310692-8fuj9td2 authors: Coste, A. 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A.; Russell, C. D.; Um, I. H.; Elshani, M.; Armstrong, S. D.; Penrice-Randal, R.; Millar, T.; Lerpiniere, C. E.; Tagliavini, G.; Hartley, C. S.; Randall, N. P.; Gachanja, N. N.; Potey, P. M.; Anderson, A. M.; Campbell, V. L.; Duguid, A. J.; Al Qsous, W.; BouHaidar, R.; Baillie, J. K.; Dhaliwal, K.; Wallace, W. A.; Bellamy, C. O.; Prost, S.; Smith, C.; Hiscox, J. A.; Harrison, D. J.; Lucas, C. 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H.; Kantele, A.; Amanat, F.; Krammer, F.; Hedman, K.; Vapalahti, O.; Hepojoki, J. title: Rapid homogeneous assay for detecting antibodies against SARS-CoV-2 date: 2020-11-04 journal: nan DOI: 10.1101/2020.11.01.20224113 sha: doc_id: 310411 cord_uid: l0slp1wa file: cache/cord-310606-msmh7d8m.json key: cord-310606-msmh7d8m authors: Westerhuis, B. M.; Aguilar-Bretones, M.; Raadsen, M. P.; de Bruin, E.; Okba, N. M. A.; Haagmans, B. L.; Langerak, T.; Endeman, H.; van den Akker, J. P. C.; Gommers, D. A. M. P. J.; van Gorp, E. C. M.; Rockx, B. H. G.; Koopmans, M. P. G.; van Nierop, G. 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F.; Lam, E. C.; Astudillo, M. G.; Yang, D.; Miller, T. E.; Feldman, J.; Hauser, B. M.; Caradonna, T. M.; Clayton, K. L.; Nitido, A. D.; Murali, M. R.; Alter, G.; Charles, R. C.; Dighe, A.; Branda, J. A.; Lennerz, J. K.; Lingwood, D.; Schmidt, A. G.; Iafrate, A. J.; Balazs, A. B. title: COVID-19 neutralizing antibodies predict disease severity and survival date: 2020-10-20 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.10.15.20213512 sha: doc_id: 310636 cord_uid: y7n22ykt file: cache/cord-310920-itqwhi6a.json key: cord-310920-itqwhi6a authors: Haddad, Christina; Davila-Calderon, Jesse; Tolbert, Blanton S. title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 journal: Methods DOI: 10.1016/j.ymeth.2020.06.013 sha: doc_id: 310920 cord_uid: itqwhi6a file: cache/cord-310507-5h6egve4.json key: cord-310507-5h6egve4 authors: van Doorn, Amarylle S.; Meijer, Berrie; Frampton, Chris M. 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Malik; Lam, Tai-Hing; Hedley, Anthony J. title: SARS-CoV Antibody Prevalence in All Hong Kong Patient Contacts date: 2004-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid1009.040155 sha: doc_id: 310651 cord_uid: pxfwe67t file: cache/cord-310803-iig414jg.json key: cord-310803-iig414jg authors: Khazeei Tabari, Mohammad Amin; Khoshhal, Hooman; Tafazoli, Alireza; Khandan, Mohanna; Bagheri, Abouzar title: Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic date: 2020-10-17 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100458 sha: doc_id: 310803 cord_uid: iig414jg file: cache/cord-310631-ru5f69qg.json key: cord-310631-ru5f69qg authors: Joachim, Denner title: SARS-CoV-2 and enhancing antibodies date: 2020-05-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104424 sha: doc_id: 310631 cord_uid: ru5f69qg file: cache/cord-310304-f28tjmi8.json key: cord-310304-f28tjmi8 authors: Alcendor, Donald J. title: Racial Disparities-Associated COVID-19 Mortality among Minority Populations in the US date: 2020-07-30 journal: J Clin Med DOI: 10.3390/jcm9082442 sha: doc_id: 310304 cord_uid: f28tjmi8 file: cache/cord-310691-6danlh8h.json key: cord-310691-6danlh8h authors: Ma, Simin; Lai, Xiaoquan; Chen, Zhe; Tu, Shenghao; Qin, Kai title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date: 2020-05-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.068 sha: doc_id: 310691 cord_uid: 6danlh8h file: cache/cord-310946-rjwyirld.json key: cord-310946-rjwyirld authors: Wiseman, Jessica; D'Amico, Timothy A.; Zawadzka, Sabina; Anyimadu, Henry title: False negative SARS-CoV-2 PCR - A case report and literature review date: 2020-07-06 journal: Respir Med Case Rep DOI: 10.1016/j.rmcr.2020.101140 sha: doc_id: 310946 cord_uid: rjwyirld file: cache/cord-310774-rpc8hrrx.json key: cord-310774-rpc8hrrx authors: Yang, Chongtu; Wang, Jianwen; Liu, Jiacheng; Huang, Songjiang; Xiong, Bin title: Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia date: 2020-08-28 journal: J Cancer Res Clin Oncol DOI: 10.1007/s00432-020-03350-3 sha: doc_id: 310774 cord_uid: rpc8hrrx file: cache/cord-310928-g553afo9.json key: cord-310928-g553afo9 authors: Murch, Simon H title: Common determinants of severe Covid-19 infection are explicable by SARS-CoV-2 secreted glycoprotein interaction with the CD33-related Siglecs, Siglec-3 and Siglec-5/14 date: 2020-08-07 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110168 sha: doc_id: 310928 cord_uid: g553afo9 file: cache/cord-311035-s3tkbh9r.json key: cord-311035-s3tkbh9r authors: Procko, Erik title: Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community date: 2020-10-21 journal: Expert review of proteomics DOI: 10.1080/14789450.2020.1833721 sha: doc_id: 311035 cord_uid: s3tkbh9r file: cache/cord-310680-klywz85w.json key: cord-310680-klywz85w authors: Li, Qihan; Wang, Lichun; Dong, Chenghong; Che, Yanchun; Jiang, Li; Liu, Longding; Zhao, Hongling; Liao, Yun; Sheng, Yi; Dong, Shaozhong; Ma, Shaohui title: The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date: 2005-04-06 journal: J Clin Virol DOI: 10.1016/j.jcv.2004.12.019 sha: doc_id: 310680 cord_uid: klywz85w file: cache/cord-310857-i9v9antx.json key: cord-310857-i9v9antx authors: Blaisdell, Laura L.; Cohn, Wendy; Pavell, Jeff R.; Rubin, Dana S.; Vergales, Jeffrey E. title: Preventing and Mitigating SARS-CoV-2 Transmission — Four Overnight Camps, Maine, June–August 2020 date: 2020-09-04 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6935e1 sha: doc_id: 310857 cord_uid: i9v9antx file: cache/cord-311026-mpr3xb2a.json key: cord-311026-mpr3xb2a authors: Petersen, Eskild; Wasserman, Sean; Lee, Shui-Shan; GO, Unyeong; Holmes, Allison H.; Abri, Seif Al; McLellan, Susan; Blumberg, Lucille; Tambyah, Paul title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.035 sha: doc_id: 311026 cord_uid: mpr3xb2a file: cache/cord-311044-kjx0z1hc.json key: cord-311044-kjx0z1hc authors: Rubio-Pérez, Inés; Badía, Josep M.; Mora-Rillo, Marta; Quirós, Alejandro Martín; Rodríguez, Julio García; Balibrea, Jose M. title: COVID-19: key concepts for the surgeon date: 2020-05-28 journal: nan DOI: 10.1016/j.cireng.2020.05.009 sha: doc_id: 311044 cord_uid: kjx0z1hc file: cache/cord-310790-3ikgmiof.json key: cord-310790-3ikgmiof authors: Cherrak, Sabri Ahmed; Merzouk, Hafida; Mokhtari-Soulimane, Nassima title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240653 sha: doc_id: 310790 cord_uid: 3ikgmiof file: cache/cord-311105-8edwb59c.json key: cord-311105-8edwb59c authors: Karamese, M.; Ozgur, D.; Tarhan, C.; Dik Altintas, S.; Caliskan, O.; Tuna, A.; Kazci, S.; Karadavut, M.; Gumus, A.; Apaydin, G.; Mumcu, N.; Coruh, O.; Tutuncu, E. E. title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey date: 2020-06-26 journal: nan DOI: 10.1101/2020.06.25.20138131 sha: doc_id: 311105 cord_uid: 8edwb59c file: cache/cord-311207-qkkn0297.json key: cord-311207-qkkn0297 authors: Pegoraro, Manuela; Militello, Valentina; Salvagno, Gian Luca; Gaino, Stefania; Bassi, Antonella; Caloi, Cecilia; Peretti, Angelo; Bizzego, Silvia; Poletto, Laura; Bovo, Chiara; Lippi, Giuseppe; Lo Cascio, Giuliana title: Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness date: 2020-10-20 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04040-1 sha: doc_id: 311207 cord_uid: qkkn0297 file: cache/cord-311066-62edsbfc.json key: cord-311066-62edsbfc authors: Cox, Brian J. title: Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date: 2020-06-24 journal: bioRxiv DOI: 10.1101/2020.06.24.169144 sha: doc_id: 311066 cord_uid: 62edsbfc file: cache/cord-311333-shvtfxog.json key: cord-311333-shvtfxog authors: Fukumoto, Tatsuya; Iwasaki, Sumio; Fujisawa, Shinichi; Hayasaka, Kasumi; Sato, Kaori; Oguri, Satoshi; Taki, Keisuke; Nakakubo, Sho; Kamada, Keisuke; Yamashita, Yu; Konno, Satoshi; Nishida, Mutsumi; Sugita, Junichi; Teshima, Takanori title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.27.120410 sha: doc_id: 311333 cord_uid: shvtfxog file: cache/cord-311123-swiewewq.json key: cord-311123-swiewewq authors: Zhuang, Shu-Fan; Hu, Jia; Qiao, Nan; Lan, Zhi-Hui; Lai, Jun-Yu; Wu, Jian-Guang; Wu, Xiao-Yong title: Low-grade fever during COVID-19 convalescence: A report of 3 cases date: 2020-06-26 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i12.2655 sha: doc_id: 311123 cord_uid: swiewewq file: cache/cord-311114-ggcpsjk8.json key: cord-311114-ggcpsjk8 authors: Radhakrishnan, Chandni; Divakar, Mohit Kumar; Jain, Abhinav; Viswanathan, Prasanth; Bhoyar, Rahul C.; Jolly, Bani; Imran, Mohamed; Sharma, Disha; Rophina, Mercy; Ranjan, Gyan; Jose, Beena Philomina; Raman, Rajendran Vadukkoot; Kesavan, Thulaseedharan Nallaveettil; George, Kalpana; Mathew, Sheela; Poovullathil, Jayesh Kumar; Govindan, Sajeeth Kumar Keeriyatt; Nair, Priyanka Raveendranadhan; Vadekkandiyil, Shameer; Gladson, Vineeth; Mohan, Midhun; Parambath, Fairoz Cheriyalingal; Mangla, Mohit; Shamnath, Afra; Sivasubbu, Sridhar; Scaria, Vinod title: Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date: 2020-09-09 journal: bioRxiv DOI: 10.1101/2020.09.09.289892 sha: doc_id: 311114 cord_uid: ggcpsjk8 file: cache/cord-311144-tumtzad8.json key: cord-311144-tumtzad8 authors: Franco-Muñoz, Carlos; Álvarez-Díaz, Diego A.; Laiton-Donato, Katherine; Wiesner, Magdalena; Escandón, Patricia; Usme-Ciro, José A.; Franco-Sierra, Nicolás D.; Flórez-Sánchez, Astrid C.; Gómez-Rangel, Sergio; Rodríguez-Calderon, Luz D.; Barbosa-Ramirez, Juliana; Ospitia-Baez, Erika; Walteros, Diana M.; Ospina-Martinez, Martha L.; Mercado-Reyes, Marcela title: Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date: 2020-09-17 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104557 sha: doc_id: 311144 cord_uid: tumtzad8 file: cache/cord-311216-mfqlv3nh.json key: cord-311216-mfqlv3nh authors: Buckley, Leo F.; Cheng, Judy W. M.; Desai, Akshay title: Cardiovascular Pharmacology in the Time of COVID-19: A Focus on Angiotensin-Converting Enzyme 2 date: 2020-04-13 journal: J Cardiovasc Pharmacol DOI: 10.1097/fjc.0000000000000840 sha: doc_id: 311216 cord_uid: mfqlv3nh file: cache/cord-311377-ffkwis40.json key: cord-311377-ffkwis40 authors: Forns, Xavier; Navasa, Miquel title: Inmunosupresión en el trasplante hepático en la era Covid-19 date: 2020-06-12 journal: Gastroenterol Hepatol DOI: 10.1016/j.gastrohep.2020.06.003 sha: doc_id: 311377 cord_uid: ffkwis40 file: cache/cord-311012-wyglrpqh.json key: cord-311012-wyglrpqh authors: Meyers, Craig; Kass, Rena; Goldenberg, David; Milici, Janice; Alam, Samina; Robison, Richard title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.09.026 sha: doc_id: 311012 cord_uid: wyglrpqh file: cache/cord-311029-x0lk4110.json key: cord-311029-x0lk4110 authors: Palermo, Sara title: Covid-19 Pandemic: Maximizing Future Vaccination Treatments Considering Aging and Frailty date: 2020-09-18 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.558835 sha: doc_id: 311029 cord_uid: x0lk4110 file: cache/cord-311240-o0zyt2vb.json key: cord-311240-o0zyt2vb authors: Motayo, Babatunde Olarenwaju; Oluwasemowo, Olukunle Oluwapamilerin; Akinduti, Paul Akiniyi; Olusola, Babatunde Adebiyi; Aerege, Olumide T; Faneye, Adedayo Omotayo title: Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date: 2020-07-27 journal: bioRxiv DOI: 10.1101/2020.07.27.222901 sha: doc_id: 311240 cord_uid: o0zyt2vb file: cache/cord-311358-nrj4aysh.json key: cord-311358-nrj4aysh authors: Peng, Yuzhu; Zhou, Yi‐Hua title: Is novel coronavirus disease (COVID‐19) transmitted through conjunctiva? date: 2020-03-16 journal: J Med Virol DOI: 10.1002/jmv.25753 sha: doc_id: 311358 cord_uid: nrj4aysh file: cache/cord-311383-1aqt65cc.json key: cord-311383-1aqt65cc authors: Tan, Jinzhi; Vonrhein, Clemens; Smart, Oliver S.; Bricogne, Gerard; Bollati, Michela; Kusov, Yuri; Hansen, Guido; Mesters, Jeroen R.; Schmidt, Christian L.; Hilgenfeld, Rolf title: The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes date: 2009-05-15 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1000428 sha: doc_id: 311383 cord_uid: 1aqt65cc file: cache/cord-311415-wwwqqvca.json key: cord-311415-wwwqqvca authors: Alamri, Mubarak A.; Tahir ul Qamar, Muhammad; Mirza, Muhammad Usman; Bhadane, Rajendra; Alqahtani, Safar M.; Muneer, Iqra; Froeyen, Matheus; Salo-Ahen, Outi M. H. title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) date: 2020-06-24 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1782768 sha: doc_id: 311415 cord_uid: wwwqqvca file: cache/cord-311125-v9ddes3c.json key: cord-311125-v9ddes3c authors: Cooper, Keiland W.; Brann, David H.; Farruggia, Michael C.; Bhutani, Surabhi; Pellegrino, Robert; Tsukahara, Tatsuya; Weinreb, Caleb; Joseph, Paule V.; Larson, Eric D.; Parma, Valentina; Albers, Mark W.; Barlow, Linda A.; Datta, Sandeep Robert; Di Pizio, Antonella title: COVID-19 and the chemical senses: supporting players take center stage date: 2020-07-01 journal: Neuron DOI: 10.1016/j.neuron.2020.06.032 sha: doc_id: 311125 cord_uid: v9ddes3c file: cache/cord-311446-afhw0450.json key: cord-311446-afhw0450 authors: Suhandynata, Raymond T; Hoffman, Melissa A; Kelner, Michael J; McLawhon, Ronald W; Reed, Sharon L; Fitzgerald, Robert L title: Multi-platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19 date: 2020-08-07 journal: J Appl Lab Med DOI: 10.1093/jalm/jfaa139 sha: doc_id: 311446 cord_uid: afhw0450 file: cache/cord-311429-adcmgd1i.json key: cord-311429-adcmgd1i authors: Salzberger, B.; Buder, F.; Lampl, B. T.; Ehrenstein, B.; Hitzenbichler, F.; Holzmann, T.; Schmidt, B.; Hanses, F. title: Epidemiologie von SARS-CoV-2/COVID 19: Aktueller Stand date: 2020-10-29 journal: Gastroenterologe DOI: 10.1007/s11377-020-00479-y sha: doc_id: 311429 cord_uid: adcmgd1i file: cache/cord-311477-gm0vg53l.json key: cord-311477-gm0vg53l authors: Doboszewska, Urszula; Wlaź, Piotr; Nowak, Gabriel; Młyniec, Katarzyna title: Targeting zinc metalloenzymes in COVID‐19 date: 2020-07-15 journal: Br J Pharmacol DOI: 10.1111/bph.15199 sha: doc_id: 311477 cord_uid: gm0vg53l file: cache/cord-311264-zn7ydrvh.json key: cord-311264-zn7ydrvh authors: Deurenberg-Yap, M.; Foo, L. L.; Low, Y. Y.; Chan, S. P.; Vijaya, K.; Lee, M. title: The Singaporean response to the SARS outbreak: knowledge sufficiency versus public trust date: 2005-06-17 journal: Health Promot Int DOI: 10.1093/heapro/dai010 sha: doc_id: 311264 cord_uid: zn7ydrvh file: cache/cord-311585-h4holhit.json key: cord-311585-h4holhit authors: Ling, R.; Yu, Y.; He, J.; Zhang, J.; Xu, S.; Sun, R.; Li, T.; Ji, H.; Wang, H. title: Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China date: 2020-06-19 journal: nan DOI: 10.1101/2020.06.16.20132423 sha: doc_id: 311585 cord_uid: h4holhit file: cache/cord-311445-b6bc6vwd.json key: cord-311445-b6bc6vwd authors: Bansal, Kanika; Patil, Prabhu B. title: Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.10.12.335521 sha: doc_id: 311445 cord_uid: b6bc6vwd file: cache/cord-311214-eqwxkwqa.json key: cord-311214-eqwxkwqa authors: Kumar, Roshan; Verma, Helianthous; Singhvi, Nirjara; Sood, Utkarsh; Gupta, Vipin; Singh, Mona; Kumari, Rashmi; Hira, Princy; Nagar, Shekhar; Talwar, Chandni; Nayyar, Namita; Anand, Shailly; Rawat, Charu Dogra; Verma, Mansi; Negi, Ram Krishan; Singh, Yogendra; Lal, Rup title: Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date: 2020-04-16 journal: bioRxiv DOI: 10.1101/2020.03.25.006213 sha: doc_id: 311214 cord_uid: eqwxkwqa file: cache/cord-311545-3rll9mca.json key: cord-311545-3rll9mca authors: Bentley, Gillian R title: Don't blame the BAME: Ethnic and structural inequalities in susceptibilities to COVID‐19 date: 2020-07-16 journal: Am J Hum Biol DOI: 10.1002/ajhb.23478 sha: doc_id: 311545 cord_uid: 3rll9mca file: cache/cord-311604-qsc3nks6.json key: cord-311604-qsc3nks6 authors: Wong, River Chun‐Wai; Wong, Ann Han; Ho, Yolanda Iok‐Ieng; Leung, Eddie Chi‐Man; Lai, Raymond Wai‐Man title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date: 2020-09-30 journal: J Med Virol DOI: 10.1002/jmv.26574 sha: doc_id: 311604 cord_uid: qsc3nks6 file: cache/cord-311635-hf6vrbyx.json key: cord-311635-hf6vrbyx authors: Reuken, Philipp Alexander; Rauchfuss, Falk; Albers, Stefanie; Settmacher, Utz; Trautwein, Christian; Bruns, Tony; Stallmach, Andreas title: Between Fear and Courage: Attitudes, Beliefs, and Behavior of Liver Transplantation Recipients and Waiting List Candidates during the COVID‐19 Pandemic date: 2020-06-08 journal: Am J Transplant DOI: 10.1111/ajt.16118 sha: doc_id: 311635 cord_uid: hf6vrbyx file: cache/cord-311332-n8tvglif.json key: cord-311332-n8tvglif authors: Kostoff, Ronald N. title: Literature-related discovery: Potential treatments and preventatives for SARS() date: 2011-04-20 journal: Technol Forecast Soc Change DOI: 10.1016/j.techfore.2011.03.022 sha: doc_id: 311332 cord_uid: n8tvglif file: cache/cord-311696-ccbc1k1m.json key: cord-311696-ccbc1k1m authors: Pelisser, Michel; Thompson, Joe; Majra, Dasha; Youhanna, Sonia; Stebbing, Justin; Davies, Peter title: Sports balls as potential SARS-CoV-2 transmission vectors date: 2020-07-10 journal: nan DOI: 10.1016/j.puhip.2020.100029 sha: doc_id: 311696 cord_uid: ccbc1k1m file: cache/cord-311599-m400cal3.json key: cord-311599-m400cal3 authors: Lehmann, Christian; Wolf, Hans; Xu, Jianguo; Zhao, Quanbi; Shao, Yiming; Motz, Manfred; Lindner, Petra title: A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses date: 2008-05-31 journal: Diagnostic Microbiology and Infectious Disease DOI: 10.1016/j.diagmicrobio.2007.12.002 sha: doc_id: 311599 cord_uid: m400cal3 file: cache/cord-311523-erntrh3p.json key: cord-311523-erntrh3p authors: Gisondi, P; Piaserico, S; Conti, A; Naldi, L title: Dermatologists and SARS‐CoV‐2: The impact of the pandemic on daily practice date: 2020-04-22 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16515 sha: doc_id: 311523 cord_uid: erntrh3p file: cache/cord-311535-ppkwd1kp.json key: cord-311535-ppkwd1kp authors: Korakas, Emmanouil; Ikonomidis, Ignatios; Kousathana, Foteini; Balampanis, Konstantinos; Kountouri, Aikaterini; Raptis, Athanasios; Palaiodimou, Lina; Kokkinos, Alexander; Lambadiari, Vaia title: Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes date: 2020-07-01 journal: Am J Physiol Endocrinol Metab DOI: 10.1152/ajpendo.00198.2020 sha: doc_id: 311535 cord_uid: ppkwd1kp file: cache/cord-311730-189vax2m.json key: cord-311730-189vax2m authors: Becker, Richard C. title: Covid-19 treatment update: follow the scientific evidence date: 2020-04-27 journal: J Thromb Thrombolysis DOI: 10.1007/s11239-020-02120-9 sha: doc_id: 311730 cord_uid: 189vax2m file: cache/cord-311762-f6muhf3d.json key: cord-311762-f6muhf3d authors: Chen, Yu Wai; Yiu, Chin-Pang Bennu; Wong, Kwok-Yin title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates date: 2020-02-21 journal: F1000Res DOI: 10.12688/f1000research.22457.1 sha: doc_id: 311762 cord_uid: f6muhf3d file: cache/cord-311633-i9ret7bw.json key: cord-311633-i9ret7bw authors: Péré, Hélène; Védie, Benoit; Vernet, Raphaël; Demory, Nathalie; Kassis, Najiby; Mirault, Tristan; Lazareth, Hélène; Volle, Geoffroy; Denoix, Elsa; Lebeaux, David; Podglajen, Isabelle; Bélec, Laurent; Veyer, David title: Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology date: 2020-08-04 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104568 sha: doc_id: 311633 cord_uid: i9ret7bw file: cache/cord-311835-dmqfij6j.json key: cord-311835-dmqfij6j authors: Siu, Kam-Leung; Chan, Ching-Ping; Kok, Kin-Hang; Woo, Patrick C-Y; Jin, Dong-Yan title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 date: 2014-01-13 journal: Cell Biosci DOI: 10.1186/2045-3701-4-3 sha: doc_id: 311835 cord_uid: dmqfij6j file: cache/cord-311610-uniz8tuc.json key: cord-311610-uniz8tuc authors: Wang, Shi-Yi; Hsu, Sylvia H; Chen, Li-Kuei title: The impact on neonatal mortality of shifting childbirth services among levels of hospitals: Taiwan's experience date: 2009-06-08 journal: BMC Health Serv Res DOI: 10.1186/1472-6963-9-94 sha: doc_id: 311610 cord_uid: uniz8tuc file: cache/cord-311758-wof4yi39.json key: cord-311758-wof4yi39 authors: Clauw, Daniel J.; Häuser, Winfried; Cohen, Steven P.; Fitzcharles, Mary-Ann title: Considering the potential for an increase in chronic pain after the COVID-19 pandemic date: 2020-06-03 journal: Pain DOI: 10.1097/j.pain.0000000000001950 sha: doc_id: 311758 cord_uid: wof4yi39 file: cache/cord-311766-m9yv4qkm.json key: cord-311766-m9yv4qkm authors: Demey, Baptiste; Daher, Nagib; François, Catherine; Lanoix, Jean-Philippe; Duverlie, Gilles; Castelain, Sandrine; Brochot, Etienne title: Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date: 2020-05-07 journal: J Infect DOI: 10.1016/j.jinf.2020.04.033 sha: doc_id: 311766 cord_uid: m9yv4qkm file: cache/cord-311566-x8n1bbwn.json key: cord-311566-x8n1bbwn authors: Aouidate, Adnane; Ghaleb, Adib; Chtita, Samir; Aarjane, Mohammed; Ousaa, Abdellah; Maghat, Hamid; Sbai, Abdelouahid; Choukrad, M’barek; Bouachrine, Mohammed; Lakhlifi, Tahar title: Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation date: 2020-06-18 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1779130 sha: doc_id: 311566 cord_uid: x8n1bbwn file: cache/cord-312036-5867bc6i.json key: cord-312036-5867bc6i authors: Decker, Annegrit; Welzel, Markus; Laubner, Katharina; Grundmann, Sebastian; Kochs, Georg; Panning, Marcus; Thimme, Robert; Bode, Christoph; Wagner, Dirk; Lother, Achim title: Prolonged SARS‐CoV‐2 shedding and mild course of COVID‐19 in a patient after recent heart transplantation date: 2020-06-09 journal: Am J Transplant DOI: 10.1111/ajt.16133 sha: doc_id: 312036 cord_uid: 5867bc6i file: cache/cord-312065-nqy7m38f.json key: cord-312065-nqy7m38f authors: Peng, Philip W. H.; Wong, David T.; Bevan, David; Gardam, Michael title: Infection control and anesthesia: Lessons learned from the Toronto SARS outbreak date: 2003 journal: Can J Anaesth DOI: 10.1007/bf03018361 sha: doc_id: 312065 cord_uid: nqy7m38f file: cache/cord-311926-n7co0jtu.json key: cord-311926-n7co0jtu authors: Donà, Daniele; Giaquinto, Carlo; Baraldi, Eugenio; Biffi, Alessandra; Gamba, Piergiorgio; Saieva, Anna Maria; Antoniello, Luca; Costenaro, Paola; Masiero, Susanna; Sainati, Laura; Da Dalt, Liviana; Perilongo, Giorgio title: COVID-19 Pandemic: Perspective of an Italian Tertiary Care Pediatric Center date: 2020-09-01 journal: Healthcare (Basel) DOI: 10.3390/healthcare8030311 sha: doc_id: 311926 cord_uid: n7co0jtu file: cache/cord-311782-d2t8bzio.json key: cord-311782-d2t8bzio authors: Fiore, Josè Ramòn; Centra, Michele; De Carlo, Armando; Granato, Tommaso; Rosa, Annamaria; Sarno, Michelina; De Feo, Lucia; Di Stefano, Mariantonietta; D' Errico, Maria; Caputo, Sergio Lo; De Nittis, Rosella; Arena, Fabio; Corso, Gaetano; Margaglione, Maurizio; Santantonio, Teresa Antonia title: Results from a survey in healthy blood donors in South Eastern Italy indicate that we are far away from herd immunity to SARS‐CoV‐2 date: 2020-08-13 journal: J Med Virol DOI: 10.1002/jmv.26425 sha: doc_id: 311782 cord_uid: d2t8bzio file: cache/cord-311848-8n9ee57a.json key: cord-311848-8n9ee57a authors: Giesen, Nicola; Sprute, Rosanne; Rüthrich, Maria; Khodamoradi, Yascha; Mellinghoff, Sibylle C.; Beutel, Gernot; Lueck, Catherina; Koldehoff, Michael; Hentrich, Marcus; Sandherr, Michael; Bergwelt-Baildon, Michael von; Wolf, Hans-Heinrich; Hirsch, Hans H.; Wörmann, Bernhard; Cornely, Oliver A.; Köhler, Philipp; Schalk, Enrico; Lilienfeld-Toal, Marie von title: Evidence-based Management of COVID-19 in Cancer Patients – Guideline by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) date: 2020-09-21 journal: Eur J Cancer DOI: 10.1016/j.ejca.2020.09.009 sha: doc_id: 311848 cord_uid: 8n9ee57a file: cache/cord-311843-un6urdb1.json key: cord-311843-un6urdb1 authors: Baray, Juwel Chandra; Khan, Md. Maksudur Rahman; Mahmud, Asif; Islam, Md. Jikrul; Myti, Sanat; Ali, Md. Rostum; Sarker, Md. Enamul Haq; Kumar, Samir; Chowdhury, Md. Mobarak Hossain; Roy, Rony; Islam, Faqrul; Barman, Uttam; Khan, Habiba; Chakraborty, Sourav; Hossain, Md. Manik; Chowdhury, Md. Mashfiqur Rahman; Ghosh, Polash; Mohiuddin, Mohammad; Sultana, Naznin; Nag, Kakon title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date: 2020-09-30 journal: bioRxiv DOI: 10.1101/2020.09.29.319061 sha: doc_id: 311843 cord_uid: un6urdb1 file: cache/cord-311847-2czqs84q.json key: cord-311847-2czqs84q authors: Pennisi, Manuela; Lanza, Giuseppe; Falzone, Luca; Fisicaro, Francesco; Ferri, Raffaele; Bella, Rita title: SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms date: 2020-07-31 journal: Int J Mol Sci DOI: 10.3390/ijms21155475 sha: doc_id: 311847 cord_uid: 2czqs84q file: cache/cord-311965-3x3tjzhi.json key: cord-311965-3x3tjzhi authors: Alexander, Jan; Tinkov, Alexey; Strand, Tor A.; Alehagen, Urban; Skalny, Anatoly; Aaseth, Jan title: Early Nutritional Interventions with Zinc, Selenium and Vitamin D for Raising Anti-Viral Resistance Against Progressive COVID-19 date: 2020-08-07 journal: Nutrients DOI: 10.3390/nu12082358 sha: doc_id: 311965 cord_uid: 3x3tjzhi file: cache/cord-311673-z4hkw17g.json key: cord-311673-z4hkw17g authors: Uzzan, Mathieu; Corcos, Olivier; Martin, Jerome; Treton, Xavier; Bouhnik, Yoram title: Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis date: 2020-06-23 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110023 sha: doc_id: 311673 cord_uid: z4hkw17g file: cache/cord-311905-4yu29b49.json key: cord-311905-4yu29b49 authors: Kakoulidis, Ioannis; Ilias, Ioannis; Koukkou, Eftychia title: SARS-CoV-2 infection and glucose homeostasis in pregnancy. What about antenatal corticosteroids? date: 2020-05-06 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.04.045 sha: doc_id: 311905 cord_uid: 4yu29b49 file: cache/cord-312027-5tntdjp9.json key: cord-312027-5tntdjp9 authors: Charlton, Carmen L.; Kanji, Jamil N.; Johal, Kam; Bailey, Ashley; Plitt, Sabrina S.; MacDonald, Clayton; Kunst, Andrea; Buss, Emily; Burnes, Laura E.; Fonseca, Kevin; Berenger, Byron M.; Schnabl, Kareena; Hu, Jia; Stokes, William; Zelyas, Nathan; Tipples, Graham title: Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies date: 2020-09-22 journal: J Clin Microbiol DOI: 10.1128/jcm.01361-20 sha: doc_id: 312027 cord_uid: 5tntdjp9 file: cache/cord-312170-p2yrbosz.json key: cord-312170-p2yrbosz authors: Chiu, Man-Chun title: Suggested management of immunocompromized kidney patients suffering from SARS date: 2003-10-24 journal: Pediatr Nephrol DOI: 10.1007/s00467-003-1325-8 sha: doc_id: 312170 cord_uid: p2yrbosz file: cache/cord-312005-9so3orib.json key: cord-312005-9so3orib authors: Klussmeier, Anja; Behrens, Geoffrey A.; Lange, Vinzenz title: Etablierung der PCR-basierten SARS-CoV-2-Testung im Hochdurchsatz date: 2020-09-05 journal: BIOspektrum (Heidelb.) DOI: 10.1007/s12268-020-1431-1 sha: doc_id: 312005 cord_uid: 9so3orib file: cache/cord-312038-g76cpjp7.json key: cord-312038-g76cpjp7 authors: Brunaugh, Ashlee D.; Seo, Hyojong; Warnken, Zachary; Ding, Li; Seo, Sang Heui; Smyth, Hugh D.C. title: Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.09.24.310490 sha: doc_id: 312038 cord_uid: g76cpjp7 file: cache/cord-312178-tojgojjf.json key: cord-312178-tojgojjf authors: Segars, James; Katler, Quinton; McQueen, Dana B.; Kotlyar, Alexander; Glenn, Tanya; Knight, Zac; Feinberg, Eve C.; Taylor, Hugh S.; Toner, James P.; Kawwass, Jennifer F. title: Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known? date: 2020-04-16 journal: Fertil Steril DOI: 10.1016/j.fertnstert.2020.04.025 sha: doc_id: 312178 cord_uid: tojgojjf file: cache/cord-312473-7i7efdp2.json key: cord-312473-7i7efdp2 authors: Sidhom, John-William; Baras, Alexander S. title: Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.20.160499 sha: doc_id: 312473 cord_uid: 7i7efdp2 file: cache/cord-312476-20ifwznd.json key: cord-312476-20ifwznd authors: Kline, Jeffrey A. title: Crash Course in Decision Making date: 2008-01-08 journal: Acad Emerg Med DOI: 10.1111/j.1553-2712.2004.tb01431.x sha: doc_id: 312476 cord_uid: 20ifwznd file: cache/cord-312401-y1tat1bf.json key: cord-312401-y1tat1bf authors: Sakurai, Aki; Sasaki, Toshiharu; Kato, Shigeo; Hayashi, Masamichi; Tsuzuki, Sei-ichiro; Ishihara, Takuma; Iwata, Mitsunaga; Morise, Zenichi; Doi, Yohei title: Natural History of Asymptomatic SARS-CoV-2 Infection date: 2020-06-12 journal: N Engl J Med DOI: 10.1056/nejmc2013020 sha: doc_id: 312401 cord_uid: y1tat1bf file: cache/cord-312275-plqturzi.json key: cord-312275-plqturzi authors: Nielsen, Sandra C.A.; Yang, Fan; Jackson, Katherine J.L.; Hoh, Ramona A.; Röltgen, Katharina; Jean, Grace H.; Stevens, Bryan A.; Lee, Ji-Yeun; Rustagi, Arjun; Rogers, Angela J.; Powell, Abigail E.; Hunter, Molly; Najeeb, Javaria; Otrelo-Cardoso, Ana R.; Yost, Kathryn E.; Daniel, Bence; Nadeau, Kari C.; Chang, Howard Y.; Satpathy, Ansuman T.; Jardetzky, Theodore S.; Kim, Peter S.; Wang, Taia T.; Pinsky, Benjamin A.; Blish, Catherine A.; Boyd, Scott D. title: Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date: 2020-09-03 journal: Cell Host Microbe DOI: 10.1016/j.chom.2020.09.002 sha: doc_id: 312275 cord_uid: plqturzi file: cache/cord-311948-3v311fnd.json key: cord-311948-3v311fnd authors: Ishiguro, Takashi; Takano, Kenji; Kagiyama, Naho; Hosoda, Chiaki; Kobayashi, Yoichi; Takaku, Yotaro; Takata, Naomi; Ueda, Miyuki; Morimoto, Yasuhiro; Kasuga, Keisuke; Ozawa, Ryota; Isono, Taisuke; Nishida, Takashi; Kawate, Eriko; Kobayashi, Yasuhito; Shimizu, Yoshihiko; Kurashima, Kazuyoshi; Yanagisawa, Tsutomu; Takayanagi, Noboru title: Clinical Course and Findings of 14 Patients with COVID-19 Compared with 5 Patients with Conventional Human Coronavirus Pneumonia date: 2020-08-27 journal: Respir Med Case Rep DOI: 10.1016/j.rmcr.2020.101207 sha: doc_id: 311948 cord_uid: 3v311fnd file: cache/cord-312278-rin733w4.json key: cord-312278-rin733w4 authors: Wang, Yung‐Chih; Lee, Yi‐Tzu; Yang, Ting; Sun, Jun‐Ren; Shen, Ching‐Fen; Cheng, Chao‐Min title: Current diagnostic tools for coronaviruses–From laboratory diagnosis to POC diagnosis for COVID‐19 date: 2020-08-13 journal: Bioeng Transl Med DOI: 10.1002/btm2.10177 sha: doc_id: 312278 cord_uid: rin733w4 file: cache/cord-312524-ee5xw1r8.json key: cord-312524-ee5xw1r8 authors: Moustafa, Ahmed M.; Planet, Paul J. title: Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date: 2020-06-08 journal: bioRxiv DOI: 10.1101/2020.06.08.139055 sha: doc_id: 312524 cord_uid: ee5xw1r8 file: cache/cord-312340-hpuoren5.json key: cord-312340-hpuoren5 authors: Holstein, Sarah A.; Vose, Julie M. title: Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button date: 2020-06-02 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.1920 sha: doc_id: 312340 cord_uid: hpuoren5 file: cache/cord-312367-24huwt3y.json key: cord-312367-24huwt3y authors: Coelho, Camila; Gallo, Gloria; Campos, Claudia B.; Hardy, Leon; Würtele, Martin title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 journal: PLoS One DOI: 10.1371/journal.pone.0240079 sha: doc_id: 312367 cord_uid: 24huwt3y file: cache/cord-312559-ygh507x2.json key: cord-312559-ygh507x2 authors: Fiesco-Sepulveda, K. Y.; Serrano-Bermudez, L. M. title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review date: 2020-05-22 journal: nan DOI: 10.1101/2020.05.16.20104422 sha: doc_id: 312559 cord_uid: ygh507x2 file: cache/cord-312434-yx24golq.json key: cord-312434-yx24golq authors: Deng, Ziqin; Chen, Junsheng; Wang, Ting title: Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research date: 2020-09-23 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2020.581404 sha: doc_id: 312434 cord_uid: yx24golq file: cache/cord-311918-gifwg2ho.json key: cord-311918-gifwg2ho authors: BENDER, Whitney R.; HIRSHBERG, Adi; COUTIFARIS, Paulina; ACKER, Alexandra L.; SRINIVAS, Sindhu K. title: Universal Testing for SARS-CoV-2 in Two Philadelphia Hospitals: Carrier Prevalence and Symptom Development Over Two Weeks date: 2020-09-11 journal: Am J Obstet Gynecol MFM DOI: 10.1016/j.ajogmf.2020.100226 sha: doc_id: 311918 cord_uid: gifwg2ho file: cache/cord-312160-2820aftb.json key: cord-312160-2820aftb authors: Ibrahim, Mahmoud A.A.; Abdelrahman, Alaa H.M.; Hussien, Taha A.; Badr, Esraa A.A.; Mohamed, Tarik A.; El−Seedi, Hesham R.; Pare, Paul W.; Efferth, Thomas; Hegazy, Mohamed Elamir F. title: In silico Drug Discovery of Major Metabolites from Spices as SARS-CoV-2 Main Protease Inhibitors date: 2020-10-08 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.104046 sha: doc_id: 312160 cord_uid: 2820aftb file: cache/cord-312444-c1dz5o85.json key: cord-312444-c1dz5o85 authors: Faure‐Bardon, V; Salomon, LJ; Leruez‐Ville, M; Ville, Y title: How should we treat pregnant women infected with SARS‐CoV‐2? date: 2020-05-14 journal: BJOG DOI: 10.1111/1471-0528.16270 sha: doc_id: 312444 cord_uid: c1dz5o85 file: cache/cord-312560-onfabcfv.json key: cord-312560-onfabcfv authors: Klingler, J.; Weiss, S.; Itri, V.; Liu, X.; Oguntuyo, K. Y.; Stevens, C.; Ikegame, S.; Hung, C.-T.; Enyindah-Asonye, G.; Amanat, F.; Baine, I.; Arinsburg, S.; Bandres, J. C.; Kojic, E. M.; Stoever, J.; Jurczyszak, D.; Bermudez-Gonzalez, M.; Simon, V.; Liu, S.; Lee, B.; Krammer, F.; Zolla-Pazner, S.; Hioe, C. E. title: Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2 date: 2020-08-21 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.08.18.20177303 sha: doc_id: 312560 cord_uid: onfabcfv file: cache/cord-312350-klxw65qa.json key: cord-312350-klxw65qa authors: Khan, Zafran; Ghafoor, Dawood; Khan, Asaf; Ualiyeva, Daniya; Khan, Shahzad Akbar; Bilal, Hazrat; Khan, Babar; Khan, Ayub; Sajjad, Wasim title: Diagnostic approaches and potential therapeutic options for coronavirus disease (COVID-19) date: 2020-09-30 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100770 sha: doc_id: 312350 cord_uid: klxw65qa file: cache/cord-312632-g4250q6l.json key: cord-312632-g4250q6l authors: Cai, Xiaofang; Ma, Yaoling; Li, Songbo; Chen, Yan; Rong, Zhihui; Li, Wenbin title: Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children date: 2020-05-12 journal: Front Pediatr DOI: 10.3389/fped.2020.00258 sha: doc_id: 312632 cord_uid: g4250q6l file: cache/cord-312305-ll29frwc.json key: cord-312305-ll29frwc authors: Sun, Shihui; Gu, Hongjing; Cao, Lei; Chen, Qi; Yang, Guan; Li, Rui-Ting; Fan, Hang; Ye, Qing; Deng, Yong-Qiang; Song, Xiaopeng; Qi, Yini; Li, Min; Lan, Jun; Feng, Rui; Guo, Yan; Qin, Si; Wang, Lei; Zhang, Yi-Fei; Zhou, Chao; Zhao, Lingna; Chen, Yuehong; Shen, Meng; Cui, Yujun; Yang, Xiao; Wang, Xinquan; Wang, Hui; Wang, Xiangxi; Qin, Cheng-Feng title: Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date: 2020-11-11 journal: bioRxiv DOI: 10.1101/2020.11.10.377333 sha: doc_id: 312305 cord_uid: ll29frwc file: cache/cord-312414-g5px0b65.json key: cord-312414-g5px0b65 authors: Takagi, Akira; Matsui, Masanori title: An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date: 2020-09-19 journal: bioRxiv DOI: 10.1101/2020.09.18.304493 sha: doc_id: 312414 cord_uid: g5px0b65 file: cache/cord-312509-m3p9fuq0.json key: cord-312509-m3p9fuq0 authors: Tohidinia, Maryam; Sefid, Fatemeh title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 date: 2020-08-21 journal: Microb Pathog DOI: 10.1016/j.micpath.2020.104459 sha: doc_id: 312509 cord_uid: m3p9fuq0 file: cache/cord-312533-4u3bmb0e.json key: cord-312533-4u3bmb0e authors: Shen, Li Wen; Mao, Hui Juan; Wu, Yan Ling; Tanaka, Yoshimasa; Zhang, Wen title: TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections date: 2017-08-01 journal: Biochimie DOI: 10.1016/j.biochi.2017.07.016 sha: doc_id: 312533 cord_uid: 4u3bmb0e file: cache/cord-312663-hhd5f823.json key: cord-312663-hhd5f823 authors: Fiorino, Gionata; Allocca, Mariangela; Furfaro, Federica; Gilardi, Daniela; Zilli, Alessandra; Radice, Simona; Spinelli, Antonino; Danese, Silvio title: Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date: 2020-03-24 journal: J Crohns Colitis DOI: 10.1093/ecco-jcc/jjaa058 sha: doc_id: 312663 cord_uid: hhd5f823 file: cache/cord-312561-9o2fhi6e.json key: cord-312561-9o2fhi6e authors: Hung, I.F.N.; Cheng, V.C.C.; Wu, A.K.L.; Tang, B.S.F.; Chan, K.H.; Chu, C.M.; Wong, M.M.L.; Hui, W.T.; Poon, L.L.M.; Tse, D.M.W.; Chan, K.S.; Woo, P.C.Y.; Lau, S.K.P.; Peiris, J.S.M.; Yuen, K.Y. title: Viral Loads in Clinical Specimens and SARS Manifestations date: 2004-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid1009.040058 sha: doc_id: 312561 cord_uid: 9o2fhi6e file: cache/cord-312646-hfv7ce3f.json key: cord-312646-hfv7ce3f authors: Pfützner, Andreas title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV- 2 in a community screening setting shows low sensitivity date: 2020-06-02 journal: Public Health DOI: 10.1016/j.puhe.2020.05.048 sha: doc_id: 312646 cord_uid: hfv7ce3f file: cache/cord-312115-foy3dsq4.json key: cord-312115-foy3dsq4 authors: Sekine, Takuya; Perez-Potti, André; Rivera-Ballesteros, Olga; Strålin, Kristoffer; Gorin, Jean-Baptiste; Olsson, Annika; Llewellyn-Lacey, Sian; Kamal, Habiba; Bogdanovic, Gordana; Muschiol, Sandra; Wullimann, David J.; Kammann, Tobias; Emgård, Johanna; Parrot, Tiphaine; Folkesson, Elin; Rooyackers, Olav; Eriksson, Lars I.; Henter, Jan-Inge; Sönnerborg, Anders; Allander, Tobias; Albert, Jan; Nielsen, Morten; Klingström, Jonas; Gredmark-Russ, Sara; Björkström, Niklas K.; Sandberg, Johan K.; Price, David A.; Ljunggren, Hans-Gustaf; Aleman, Soo; Buggert, Marcus title: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 date: 2020-08-14 journal: Cell DOI: 10.1016/j.cell.2020.08.017 sha: doc_id: 312115 cord_uid: foy3dsq4 file: cache/cord-312633-cks6aij2.json key: cord-312633-cks6aij2 authors: Cotten, Matthew; Lam, Tommy T.; Watson, Simon J.; Palser, Anne L.; Petrova, Velislava; Grant, Paul; Pybus, Oliver G.; Rambaut, Andrew; Guan, Yi; Pillay, Deenan; Kellam, Paul; Nastouli, Eleni title: Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus date: 2013-05-17 journal: Emerg Infect Dis DOI: 10.3201/eid1905.130057 sha: doc_id: 312633 cord_uid: cks6aij2 file: cache/cord-312477-2y88gzji.json key: cord-312477-2y88gzji authors: Mlcochova, P.; Collier, D.; Ritchie, A. V.; Assennato, S. M.; Hosmillo, M.; Goel, N.; Meng, B.; Chatterji, K.; Mendoza, V.; Temperton, N.; Kiss, L.; Ciazyns, K. A.; Xiong, X.; Briggs, J. A.; Nathan, J.; Mescia, F.; Zhang, H.; Barmpounakis, P.; Demeris, N.; Skells, R.; Lyons, P.; Bradley, J.; Baker, S.; Lee, H. H.; Smith, K. G.; Goodfellow, I.; Gupta, R. K. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 journal: nan DOI: 10.1101/2020.06.16.20133157 sha: doc_id: 312477 cord_uid: 2y88gzji file: cache/cord-312619-7jpf81yz.json key: cord-312619-7jpf81yz authors: Ilyas, Sadia; Srivastava, Rajiv Ranjan; Kim, Hyunjung title: Disinfection technology and strategies for COVID-19 hospital and bio-medical waste management date: 2020-08-12 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141652 sha: doc_id: 312619 cord_uid: 7jpf81yz file: cache/cord-312652-zhccmfgw.json key: cord-312652-zhccmfgw authors: Hu, Xiumei; Zhang, Ruyi; An, Taixue; Li, Qiang; Situ, Bo; Ou, Zihao; Wu, Changmeng; Yang, Biao; Tian, Peifu; Hu, Yuhai; Ping, Baohong; Wang, Qian; Zheng, Lei title: Impact of Heat-Inactivation on the detection of SARS-CoV-2 IgM and IgG Antibody by ELISA date: 2020-06-20 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.06.032 sha: doc_id: 312652 cord_uid: zhccmfgw file: cache/cord-312486-rumqopg0.json key: cord-312486-rumqopg0 authors: Jacob, Chaim Oscar title: On the genetics and immunopathogenesis of COVID-19 date: 2020-09-10 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108591 sha: doc_id: 312486 cord_uid: rumqopg0 file: cache/cord-312684-3i2r2ahr.json key: cord-312684-3i2r2ahr authors: Iba, Toshiaki; Levy, Jerrold H.; Levi, Marcel; Thachil, Jecko title: Coagulopathy in COVID‐19 date: 2020-06-18 journal: J Thromb Haemost DOI: 10.1111/jth.14975 sha: doc_id: 312684 cord_uid: 3i2r2ahr file: cache/cord-312702-fruzsn26.json key: cord-312702-fruzsn26 authors: Finch, Courtney L.; Crozier, Ian; Lee, Ji Hyun; Byrum, Russ; Cooper, Timothy K.; Liang, Janie; Sharer, Kaleb; Solomon, Jeffrey; Sayre, Philip J.; Kocher, Gregory; Bartos, Christopher; Aiosa, Nina M.; Castro, Marcelo; Larson, Peter A.; Adams, Ricky; Beitzel, Brett; Di Paola, Nicholas; Kugelman, Jeffrey R.; Kurtz, Jonathan R.; Burdette, Tracey; Nason, Martha C.; Feuerstein, Irwin M.; Palacios, Gustavo; Claire, Marisa C. St.; Lackemeyer, Matthew G.; Johnson, Reed F.; Braun, Katarina M.; Ramuta, Mitchell D.; Wada, Jiro; Schmaljohn, Connie S.; Friedrich, Thomas C.; O’Connor, David H.; Kuhn, Jens H. title: Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date: 2020-05-14 journal: bioRxiv DOI: 10.1101/2020.05.14.096727 sha: doc_id: 312702 cord_uid: fruzsn26 file: cache/cord-312664-tgpaidhp.json key: cord-312664-tgpaidhp authors: Liang, Julia; Pitsillou, Eleni; Karagiannis, Chris; Darmawan, Kevion K; Ng, Ken; Hung, Andrew; Karagiannis, Tom C. title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex date: 2020-05-28 journal: Comput Biol Chem DOI: 10.1016/j.compbiolchem.2020.107292 sha: doc_id: 312664 cord_uid: tgpaidhp file: cache/cord-312697-ffxcze6c.json key: cord-312697-ffxcze6c authors: Dübel, Stefan; Hust, Michael; Frenzel, André; Schirrmann, Thomas title: Rekombinante, vollständig humane Antikörper zur Behandlung akuter COVID-19 date: 2020-06-26 journal: BIOspektrum (Heidelb.) DOI: 10.1007/s12268-020-1404-4 sha: doc_id: 312697 cord_uid: ffxcze6c file: cache/cord-312730-4ejjmab4.json key: cord-312730-4ejjmab4 authors: Wong, Rebecca S. Y. title: The SARS-CoV-2 Outbreak: an Epidemiological and Clinical Perspective date: 2020-09-29 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00546-z sha: doc_id: 312730 cord_uid: 4ejjmab4 file: cache/cord-312849-vgzvpwz9.json key: cord-312849-vgzvpwz9 authors: Eckbo, Eric J.; Locher, Kerstin; Caza, Melissa; Li, Lisa; Lavergne, Valery; Charles, Marthe title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples date: 2020-11-10 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115260 sha: doc_id: 312849 cord_uid: vgzvpwz9 file: cache/cord-312677-rwznqiib.json key: cord-312677-rwznqiib authors: Razmi, Mahdieh; Hashemi, Farideh; Gheytanchi, Elmira; Dehghan, Masoumeh; Ghods, Roya; Madjd, Zahra title: Immunomodulatory-Based Therapy as a Potential Promising Treatment Strategy against Severe COVID-19 Patients: A Systematic Review date: 2020-08-29 journal: Int Immunopharmacol DOI: 10.1016/j.intimp.2020.106942 sha: doc_id: 312677 cord_uid: rwznqiib file: cache/cord-312670-hi3fjne4.json key: cord-312670-hi3fjne4 authors: Corman, V. M.; Lienau, J.; Witzenrath, M. title: Coronaviren als Ursache respiratorischer Infektionen date: 2019-08-27 journal: Internist (Berl) DOI: 10.1007/s00108-019-00671-5 sha: doc_id: 312670 cord_uid: hi3fjne4 file: cache/cord-312741-0au4nctt.json key: cord-312741-0au4nctt authors: Lin, Panpan; Wang, Manni; Wei, Yuquan; Kim, Taewan; Wei, Xiawei title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 journal: MedComm (Beijing) DOI: 10.1002/mco2.26 sha: doc_id: 312741 cord_uid: 0au4nctt file: cache/cord-312488-uzhj4i1q.json key: cord-312488-uzhj4i1q authors: Petrosillo, Nicola title: SARS-CoV-2, “common cold” coronaviruses’ cross-reactivity and “herd immunity”: The razor of Ockham (1285-1347)? date: 2020-05-29 journal: Infect Dis Rep DOI: 10.4081/idr.2020.8647 sha: doc_id: 312488 cord_uid: uzhj4i1q file: cache/cord-312736-bm6t2bxz.json key: cord-312736-bm6t2bxz authors: Bach, Paxton; Robinson, Samantha; Sutherland, Christy; Brar, Rupinder title: Innovative strategies to support physical distancing among individuals with active addiction date: 2020-05-27 journal: Lancet Psychiatry DOI: 10.1016/s2215-0366(20)30231-5 sha: doc_id: 312736 cord_uid: bm6t2bxz file: cache/cord-312950-ggywr91e.json key: cord-312950-ggywr91e authors: Fuller, Julie; Hanley, Keith; Schultz, Robert; Lewis, Michael; Freed, Nikki E.; Ellis, Michael; Ngauy, Viseth; Stoebner, Richard; Ryan, Margaret; Russell, Kevin title: Surveillance for Febrile Respiratory Infections during Cobra Gold 2003 date: 2006-05-17 journal: Mil Med DOI: 10.7205/milmed.171.5.357 sha: doc_id: 312950 cord_uid: ggywr91e file: cache/cord-312997-wcqdksfg.json key: cord-312997-wcqdksfg authors: Favresse, Julien; Eucher, Christine; Elsen, Marc; Marie, Tré-Hardy; Dogné, Jean-Michel; Douxfils, Jonathan title: Clinical performance of the Elecsys electrochemiluminescent immunoassay for the detection of SARS-CoV-2 total antibodies date: 2020-06-02 journal: Clin Chem DOI: 10.1093/clinchem/hvaa131 sha: doc_id: 312997 cord_uid: wcqdksfg file: cache/cord-313076-531wksez.json key: cord-313076-531wksez authors: Rauch, J. 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Z.; Fitzgibbons, L.; Arias, C. title: CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population date: 2020-08-07 journal: nan DOI: 10.1101/2020.08.06.20169771 sha: doc_id: 313076 cord_uid: 531wksez file: cache/cord-312722-talu4geh.json key: cord-312722-talu4geh authors: Ahmed, Nausheen; de Lima, Marcos; Rohr, Bethany R.; Tomlinson, Benjamin K. title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient date: 2020-06-13 journal: Hematol Transfus Cell Ther DOI: 10.1016/j.htct.2020.06.002 sha: doc_id: 312722 cord_uid: talu4geh file: cache/cord-312708-9ywu6r2t.json key: cord-312708-9ywu6r2t authors: Sharma, Dhruv; Rubel, Kolin E.; Ye, Michael J.; Campiti, Vincent J.; Carroll, Aaron E.; Ting, Jonathan Y.; Illing, Elisa A.; Burgin, Sarah J. title: Cadaveric Simulation of Otologic Procedures: An Analysis of Droplet Splatter Patterns During the COVID-19 Pandemic date: 2020-05-19 journal: Otolaryngol Head Neck Surg DOI: 10.1177/0194599820930245 sha: doc_id: 312708 cord_uid: 9ywu6r2t file: cache/cord-312955-gs65c3fy.json key: cord-312955-gs65c3fy authors: Schreiber, Gideon title: The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date: 2020-09-30 journal: Front Immunol DOI: 10.3389/fimmu.2020.595739 sha: doc_id: 312955 cord_uid: gs65c3fy file: cache/cord-313084-l7odplqg.json key: cord-313084-l7odplqg authors: Sampson, Victoria; Kamona, Nawar; Sampson, Ariane title: Could there be a link between oral hygiene and the severity of SARS-CoV-2 infections? date: 2020-06-26 journal: Br Dent J DOI: 10.1038/s41415-020-1747-8 sha: doc_id: 313084 cord_uid: l7odplqg file: cache/cord-313099-rpdlk1b6.json key: cord-313099-rpdlk1b6 authors: Han, Xiaoyu; Wei, Xiong; Alwalid, Osamah; Cao, Yukun; Li, Yumin; Wang, Li; Shi, Heshui title: Severe Acute Respiratory Syndrome Coronavirus 2 among Asymptomatic Workers Screened for Work Resumption, China date: 2020-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid2609.201848 sha: doc_id: 313099 cord_uid: rpdlk1b6 file: cache/cord-312899-ot5pvtbl.json key: cord-312899-ot5pvtbl authors: Chen, F; Chan, K. H; Jiang, Y; Kao, R.Y.T; Lu, H. T; Fan, K. W; Cheng, V.C.C; Tsui, W.H.W; Hung, I.F.N; Lee, T.S.W; Guan, Y; Peiris, J.S.M; Yuen, K. Y title: In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds date: 2004-09-30 journal: Journal of Clinical Virology DOI: 10.1016/j.jcv.2004.03.003 sha: doc_id: 312899 cord_uid: ot5pvtbl file: cache/cord-313246-2gtiqrnj.json key: cord-313246-2gtiqrnj authors: Hazra, Aniruddha; Collison, Maggie; Pisano, Jennifer; Kumar, Madan; Oehler, Cassandra; Ridgway, Jessica P. title: Coinfections with SARS-CoV-2 and other respiratory pathogens date: 2020-07-03 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.322 sha: doc_id: 313246 cord_uid: 2gtiqrnj file: cache/cord-312884-anlp8lab.json key: cord-312884-anlp8lab authors: Iyer, Gayatri R.; Samajder, Sayani; Zubeda, Syeda; S, Devi Soorya Narayana; Mali, Vishakha; PV, Sharath Krishnan; Sharma, Anuradha; Abbas, Neyha Zainab; Bora, Nandini Shyamali; Narravula, Amulya; Hasan, Qurratulain title: Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants date: 2020-09-04 journal: Front Genet DOI: 10.3389/fgene.2020.00861 sha: doc_id: 312884 cord_uid: anlp8lab file: cache/cord-312971-r9sggqh8.json key: cord-312971-r9sggqh8 authors: Mancino, Enrica; Cristiani, Luca; Pierangeli, Alessandra; Scagnolari, Carolina; Nenna, Raffaella; Petrarca, Laura; Di Mattia, Greta; La Regina, Domenico; Frassanito, Antonella; Oliveto, Giuseppe; Viscido, Agnese; Midulla, Fabio title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 date: 2020-04-29 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104385 sha: doc_id: 312971 cord_uid: r9sggqh8 file: cache/cord-313058-nrrl4kjc.json key: cord-313058-nrrl4kjc authors: Rivas, Magali Noval; Porritt, Rebecca A.; Cheng, Mary Hongying; Bahar, Ivet; Arditi, Moshe title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis date: 2020-10-16 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2020.10.008 sha: doc_id: 313058 cord_uid: nrrl4kjc file: cache/cord-312740-2ro2p77q.json key: cord-312740-2ro2p77q authors: Babadaei, Mohammad Mahdi Nejadi; Hasan, Anwarul; Vahdani, Yasaman; Bloukh, Samir Haj; Sharifi, Majid; Kachooei, Ehsan; Haghighat, Setareh; Falahati, Mojtaba title: Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase date: 2020-05-20 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1767210 sha: doc_id: 312740 cord_uid: 2ro2p77q file: cache/cord-313028-0nhgxoim.json key: cord-313028-0nhgxoim authors: Huang, Chaolin; Wang, Yeming; Li, Xingwang; Ren, Lili; Zhao, Jianping; Hu, Yi; Zhang, Li; Fan, Guohui; Xu, Jiuyang; Gu, Xiaoying; Cheng, Zhenshun; Yu, Ting; Xia, Jiaan; Wei, Yuan; Wu, Wenjuan; Xie, Xuelei; Yin, Wen; Li, Hui; Liu, Min; Xiao, Yan; Gao, Hong; Guo, Li; Xie, Jungang; Wang, Guangfa; Jiang, Rongmeng; Gao, Zhancheng; Jin, Qi; Wang, Jianwei; Cao, Bin title: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China date: 2020-01-24 journal: Lancet DOI: 10.1016/s0140-6736(20)30183-5 sha: doc_id: 313028 cord_uid: 0nhgxoim file: cache/cord-312999-3erodkv9.json key: cord-312999-3erodkv9 authors: Hassan, Sk. Sarif; Attrish, Diksha; Ghosh, Shinjini; Choudhury, Pabitra Pal; Uversky, Vladimir N.; Uhal, Bruce D.; Lundstrom, Kenneth; Rezaei, Nima; Aljabali, Alaa A. A.; Seyran, Murat; Pizzol, Damiano; Adadi, Parise; Abd El-Aziz, Tarek Mohamed; Soares, Antonio; Kandimalla, Ramesh; Tambuwala, Murtaza; Lal, Amos; Azad, Gajendra Kumar; Sherchan, Samendra P.; Baetas-da-Cruz, Wagner; Palù, Giorgio; Brufsky, Adam M. title: Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.09.06.284976 sha: doc_id: 312999 cord_uid: 3erodkv9 file: cache/cord-313215-diqfmitr.json key: cord-313215-diqfmitr authors: Luo, Lei; Liu, Dan; Zhang, Hao; Li, Zhihao; Zhen, Ruonan; Zhang, Xiru; Xie, Huaping; Song, Weiqi; Liu, Jie; Huang, Qingmei; Liu, Jingwen; Yang, Xingfen; Chen, Zongqiu; Mao, Chen title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date: 2020-07-09 journal: bioRxiv DOI: 10.1101/2020.07.09.195008 sha: doc_id: 313215 cord_uid: diqfmitr file: cache/cord-312991-ypgrw78s.json key: cord-312991-ypgrw78s authors: Wang, Zhi-Gang; Zheng, Zhi-Hua; Shang, Lei; Li, Lan-Juan; Cong, Li-Ming; Feng, Ming-Guang; Luo, Yun; Cheng, Su-Yun; Zhang, Yan-Jun; Ru, Miao-Gui; Wang, Zan-Xin; Bao, Qi-Yu title: Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV date: 2005-09-12 journal: FEBS Lett DOI: 10.1016/j.febslet.2005.07.075 sha: doc_id: 312991 cord_uid: ypgrw78s file: cache/cord-312743-9e4yufo5.json key: cord-312743-9e4yufo5 authors: Breiman, Adrien; Ruvën-Clouet, Nathalie; Le Pendu, Jacques title: Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 date: 2020-05-21 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008556 sha: doc_id: 312743 cord_uid: 9e4yufo5 file: cache/cord-313117-0qur0isb.json key: cord-313117-0qur0isb authors: Gardinassi, Luiz G.; Souza, Camila O. S.; Sales-Campos, Helioswilton; Fonseca, Simone G. title: Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse date: 2020-06-26 journal: Front Immunol DOI: 10.3389/fimmu.2020.01636 sha: doc_id: 313117 cord_uid: 0qur0isb file: cache/cord-313193-q5zeoqlb.json key: cord-313193-q5zeoqlb authors: Carrat, F.; de Lamballerie, X.; Rahib, D.; Blanche, H.; Lapidus, N.; Artaud, F.; Kab, S.; Renuy, A.; Szabo de Edelenyi, F.; Meyer, L.; Lydie, N.; Charles, M.-A.; Ancel, P.-Y.; Jusot, F.; Rouquette, A.; Priet, S.; Saba Villaroel, P. M.; Fourie, T.; Lusivika-Nzinga, C.; Nicol, J.; Legot, S.; Druesne-Pecollo, N.; Essedik, Y.; Lai, C.; Gagliolo, J.-M.; Deleuze, J.-F.; Bajos, N.; Severi, G.; Touvier, M.; Zins, M. title: Seroprevalence of SARS-CoV-2 among adults in three regions of France following the lockdown and associated risk factors: a multicohort study. date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.16.20195693 sha: doc_id: 313193 cord_uid: q5zeoqlb file: cache/cord-312996-qzu8pkyt.json key: cord-312996-qzu8pkyt authors: Iles, R. K.; Zmuidinaite, R.; Iles, J. K.; Carnell, G.; Sampson, A.; Heeney, J. L. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 journal: nan DOI: 10.1101/2020.08.22.20176669 sha: doc_id: 312996 cord_uid: qzu8pkyt file: cache/cord-312984-rzryn3on.json key: cord-312984-rzryn3on authors: Pan, Daniel; Sze, Shirley; Rogers, Benedict; Bron, Jan; Bird, Paul W.; Holmes, Christopher W.; Tang, Julian W. title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity date: 2020-09-19 journal: J Infect DOI: 10.1016/j.jinf.2020.09.016 sha: doc_id: 312984 cord_uid: rzryn3on file: cache/cord-312918-iof45k1r.json key: cord-312918-iof45k1r authors: Ortolani, Claudio; Pastorello, Elide A. title: Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost? date: 2020-09-09 journal: Clin Mol Allergy DOI: 10.1186/s12948-020-00132-7 sha: doc_id: 312918 cord_uid: iof45k1r file: cache/cord-313082-n3bo9jw1.json key: cord-313082-n3bo9jw1 authors: Tenenbein, Paul; Riazi, Sheila; Johnstone, Jennie; Keshavjee, Shaf; Karkouti, Keyvan title: The case for routine screening for SARS-CoV-2 before surgery date: 2020-06-03 journal: Can J Anaesth DOI: 10.1007/s12630-020-01730-4 sha: doc_id: 313082 cord_uid: n3bo9jw1 file: cache/cord-313174-ig0h2s6l.json key: cord-313174-ig0h2s6l authors: Hecht, Jonathon L.; Quade, Bradley; Deshpande, Vikram; Mino-Kenudson, Mari; Ting, David T.; Desai, Niyati; Dygulska, Beata; Heyman, Taryn; Salafia, Carolyn; Shen, Dejun; Bates, Sara V.; Roberts, Drucilla J. title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers date: 2020-08-02 journal: Mod Pathol DOI: 10.1038/s41379-020-0639-4 sha: doc_id: 313174 cord_uid: ig0h2s6l file: cache/cord-313316-l147b7jk.json key: cord-313316-l147b7jk authors: Freudenthal, Bernard title: Misuse of SARS-CoV-2 testing in symptomatic health-care staff in the UK date: 2020-10-22 journal: Lancet DOI: 10.1016/s0140-6736(20)32147-4 sha: doc_id: 313316 cord_uid: l147b7jk file: cache/cord-313345-zwe3tmq0.json key: cord-313345-zwe3tmq0 authors: Chou, Roger; Dana, Tracy; Jungbauer, Rebecca; Weeks, Chandler; McDonagh, Marian S. title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings date: 2020-07-20 journal: Ann Intern Med DOI: 10.7326/l20-0948 sha: doc_id: 313345 cord_uid: zwe3tmq0 file: cache/cord-313247-55loucvc.json key: cord-313247-55loucvc authors: Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P.; Nielsen, Rasmus title: Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.06.19.160630 sha: doc_id: 313247 cord_uid: 55loucvc file: cache/cord-313268-j51zyodw.json key: cord-313268-j51zyodw authors: Zeng, Xiangxiang; Song, Xiang; Ma, Tengfei; Pan, Xiaoqin; Zhou, Yadi; Hou, Yuan; Zhang, Zheng; Li, Kenli; Karypis, George; Cheng, Feixiong title: Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning date: 2020-07-12 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00316 sha: doc_id: 313268 cord_uid: j51zyodw file: cache/cord-313275-znrvkmee.json key: cord-313275-znrvkmee authors: Bwire, G. M.; Njiro, B. J. title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM date: 2020-06-12 journal: nan DOI: 10.1101/2020.06.09.20127118 sha: doc_id: 313275 cord_uid: znrvkmee file: cache/cord-313349-ikjivfce.json key: cord-313349-ikjivfce authors: Finsterer, Josef; Stollberger, Claudia title: Causes of hypogeusia/hyposmia in SARS‐CoV2 infected patients date: 2020-04-20 journal: J Med Virol DOI: 10.1002/jmv.25903 sha: doc_id: 313349 cord_uid: ikjivfce file: cache/cord-313356-ninzeazy.json key: cord-313356-ninzeazy authors: Fiorillo, Luca; Cervino, Gabriele; Matarese, Marco; D’Amico, Cesare; Surace, Giovanni; Paduano, Valeria; Fiorillo, Maria Teresa; Moschella, Antonio; La Bruna, Alessia; Romano, Giovanni Luca; Laudicella, Riccardo; Baldari, Sergio; Cicciù, Marco title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17093132 sha: doc_id: 313356 cord_uid: ninzeazy file: cache/cord-313379-6sa6oc6u.json key: cord-313379-6sa6oc6u authors: Bahar, B.; Jacquot, C.; Mo, Y. D.; DeBiasi, R.; Delaney, M. title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children date: 2020-08-07 journal: nan DOI: 10.1101/2020.08.06.20162446 sha: doc_id: 313379 cord_uid: 6sa6oc6u file: cache/cord-313427-6y4zvrmn.json key: cord-313427-6y4zvrmn authors: Mani, Nandita S; Budak, Jehan Z; Lan, Kristine F; Bryson-Cahn, Chloe; Zelikoff, Allison; Barker, Gwendolyn E C; Grant, Carolyn W; Hart, Kristi; Barbee, Carrie J; Sandoval, Marissa D; Dostal, Christine L; Corcorran, Maria; Ungerleider, Hal M; Gates, Jeff O; Olin, Svaya V; Bryan, Andrew; Hoffman, Noah G; Marquis, Sara R; Harvey, Michelle L; Nasenbeny, Keri; Mertens, Kathleen; Chew, Lisa D; Greninger, Alexander L; Jerome, Keith R; Pottinger, Paul S; Dellit, Timothy H; Liu, Catherine; Pergam, Steven A; Neme, Santiago; Lynch, John B; Kim, H Nina; Cohen, Seth A title: Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa761 sha: doc_id: 313427 cord_uid: 6y4zvrmn file: cache/cord-313282-z5cues67.json key: cord-313282-z5cues67 authors: Schaefer, Inga-Marie; Padera, Robert F.; Solomon, Isaac H.; Kanjilal, Sanjat; Hammer, Mark M.; Hornick, Jason L.; Sholl, Lynette M. title: In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19 date: 2020-06-19 journal: Mod Pathol DOI: 10.1038/s41379-020-0595-z sha: doc_id: 313282 cord_uid: z5cues67 file: cache/cord-313227-6zwkfzab.json key: cord-313227-6zwkfzab authors: Scala, Stefania; Pacelli, Roberto title: Fighting the Host Reaction to SARS-COv-2 in Critically Ill Patients: The Possible Contribution of Off-Label Drugs date: 2020-05-27 journal: Front Immunol DOI: 10.3389/fimmu.2020.01201 sha: doc_id: 313227 cord_uid: 6zwkfzab file: cache/cord-313371-fdyfg0kf.json key: cord-313371-fdyfg0kf authors: Brancatella, Alessandro; Ricci, Debora; Viola, Nicola; Sgrò, Daniele; Santini, Ferruccio; Latrofa, Francesco title: Subacute Thyroiditis After Sars-COV-2 Infection date: 2020-05-21 journal: J Clin Endocrinol Metab DOI: 10.1210/clinem/dgaa276 sha: doc_id: 313371 cord_uid: fdyfg0kf file: cache/cord-313265-lff5cajm.json key: cord-313265-lff5cajm authors: Conway, Michael J. title: Identification of coronavirus sequences in carp cDNA from Wuhan, China date: 2020-03-16 journal: J Med Virol DOI: 10.1002/jmv.25751 sha: doc_id: 313265 cord_uid: lff5cajm file: cache/cord-313603-y8p9bmph.json key: cord-313603-y8p9bmph authors: Akter, Shahina; Banu, Tanjina Akhtar; Goswami, Barna; Osman, Eshrar; Uzzaman, Mohammad Samir; Habib, M. Ahashan; Jahan, Iffat; Mahmud, Abu Sayeed Mohammad; Sarker, M. Murshed Hasan; Hossain, M. Saddam; Shamsuzzaman, A. K. Mohammad; Nafisa, Tasnim; Molla, M. Maruf Ahmed; Yeasmin, Mahmuda; Ghosh, Asish Kumar; Al Din, Sheikh M. Selim; Ray, Utpal Chandra; Sajib, Salek Ahmed; Hossain, Maqsud; Khan, M. Salim title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh date: 2020-09-24 journal: Microbiol Resour Announc DOI: 10.1128/mra.00764-20 sha: doc_id: 313603 cord_uid: y8p9bmph file: cache/cord-313627-g1iqhsdk.json key: cord-313627-g1iqhsdk authors: Zou, Xiaojing; Fang, Minghao; Li, Shusheng; Wu, Liang; Gao, Bing; Gao, Hong; Ran, Xiao; YiBian,; Li, Renjie; Yu, Shanshan; Ling, Jianmin; Li, Donghui; Tian, Deying; Huang, Jiao title: Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection date: 2020-06-15 journal: Clin Gastroenterol Hepatol DOI: 10.1016/j.cgh.2020.06.017 sha: doc_id: 313627 cord_uid: g1iqhsdk file: cache/cord-313415-5qrpucr4.json key: cord-313415-5qrpucr4 authors: Lai, Rongtao; Chen, Erzhen; Gao, Weiyi; Cheng, Chengwei; Xie, Qing title: Sentinel surveillance strategies for early detection of coronavirus disease in fever clinics: experience from China date: 2020-08-25 journal: Epidemiol Infect DOI: 10.1017/s0950268820001892 sha: doc_id: 313415 cord_uid: 5qrpucr4 file: cache/cord-313571-umcbulcw.json key: cord-313571-umcbulcw authors: Martínez-Murcia, Antonio; Bru, Gema; Navarro, Aaron; Ros-Tárraga, Patricia; García-Sirera, Adrián; Pérez, Laura title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date: 2020-05-05 journal: bioRxiv DOI: 10.1101/2020.04.27.065383 sha: doc_id: 313571 cord_uid: umcbulcw file: cache/cord-313639-qpt47sx2.json key: cord-313639-qpt47sx2 authors: Zheng, Yi; Sun, Li-jun; Xu, Mi; Pan, Jian; Zhang, Yun-tao; Fang, Xue-ling; Fang, Qiang; Cai, Hong-liu title: Clinical characteristics of 34 COVID-19 patients admitted to intensive care unit in Hangzhou, China date: 2020-05-20 journal: J Zhejiang Univ Sci B DOI: 10.1631/jzus.b2000174 sha: doc_id: 313639 cord_uid: qpt47sx2 file: cache/cord-313305-tih33rys.json key: cord-313305-tih33rys authors: Castro, Rodolfo; Luz, Paula M; Wakimoto, Mayumi D; Veloso, Valdilea G; Grinsztejn, Beatriz; Perazzo, Hugo title: COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil date: 2020-04-18 journal: Braz J Infect Dis DOI: 10.1016/j.bjid.2020.04.003 sha: doc_id: 313305 cord_uid: tih33rys file: cache/cord-313489-i969aqn9.json key: cord-313489-i969aqn9 authors: Galbadage, Thushara; Peterson, Brent M.; Gunasekera, Richard S. title: Does COVID-19 Spread Through Droplets Alone? date: 2020-04-24 journal: Front Public Health DOI: 10.3389/fpubh.2020.00163 sha: doc_id: 313489 cord_uid: i969aqn9 file: cache/cord-313756-2pqpk3v7.json key: cord-313756-2pqpk3v7 authors: De Vriese, An S.; Reynders, Marijke title: In Reply to ‘Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?’ date: 2020-06-27 journal: Am J Kidney Dis DOI: 10.1053/j.ajkd.2020.06.005 sha: doc_id: 313756 cord_uid: 2pqpk3v7 file: cache/cord-313984-7wvfnag1.json key: cord-313984-7wvfnag1 authors: Remy, Kenneth E; Brakenridge, Scott C; Francois, Bruno; Daix, Thomas; Deutschman, Clifford S; Monneret, Guillaume; Jeannet, Robin; Laterre, Pierre-Francois; Hotchkiss, Richard S; Moldawer, Lyle L title: Immunotherapies for COVID-19: lessons learned from sepsis date: 2020-04-28 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30217-4 sha: doc_id: 313984 cord_uid: 7wvfnag1 file: cache/cord-313458-ka02rsla.json key: cord-313458-ka02rsla authors: Zhou, Yitian; Huang, Yongfa; Song, Xiaomin; Guo, Xiaoxiao; Pang, Junling; Wang, Jing; Zhang, Shuyang; Wang, Chen title: Single-cell transcriptional profile of ACE2 in healthy and failing human hearts date: 2020-09-01 journal: Sci China Life Sci DOI: 10.1007/s11427-020-1787-5 sha: doc_id: 313458 cord_uid: ka02rsla file: cache/cord-313537-920tgv1j.json key: cord-313537-920tgv1j authors: Carbonell, Ana Piera; Vargas, Manuel Frías; Vallejo, Olga García; Lerín, Aurora García; Ferriols, María Ángeles Cabrera; Morant, Juan Peiró; Carrasco, Eduardo Carrasco title: Covid-19 y tromboprofilaxis: recomendaciones para nuestra práctica clínica en atención primaria date: 2020-09-18 journal: Semergen DOI: 10.1016/j.semerg.2020.07.007 sha: doc_id: 313537 cord_uid: 920tgv1j file: cache/cord-313541-fpqwzf9k.json key: cord-313541-fpqwzf9k authors: Ulloa, S.; Bravo, C.; Parra, B.; Ramirez, E.; Acevedo, A.; Fasce, R.; Fernandez, J. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113960 sha: doc_id: 313541 cord_uid: fpqwzf9k file: cache/cord-313505-2lr4xara.json key: cord-313505-2lr4xara authors: Resende, Paola Cristina; Delatorre, Edson; Gräf, Tiago; Mir, Daiana; Motta, Fernando do Couto; Appolinario, Luciana Reis; da Paixão, Anna Carolina Dias; Ogrzewalska, Maria; Caetano, Braulia; dos Santos, Mirleide Cordeiro; de Almeida Ferreira, Jessylene; Santos Junior, Edivaldo Costa; da Silva, Sandro Patroca; Fernandes, Sandra Bianchini; Vianna, Lucas A; da Costa Souza, Larissa; Ferro, Jean F G; Nardy, Vanessa B; Croda, Júlio; Oliveira, Wanderson K; Abreu, André; Bello, Gonzalo; Siqueira, Marilda M title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date: 2020-06-18 journal: bioRxiv DOI: 10.1101/2020.06.17.158006 sha: doc_id: 313505 cord_uid: 2lr4xara file: cache/cord-313684-61hkogdh.json key: cord-313684-61hkogdh authors: Samaddar, Arghadip; Grover, Malika; Nag, Vijaya Lakshmi title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 journal: Front Pharmacol DOI: 10.3389/fphar.2020.585888 sha: doc_id: 313684 cord_uid: 61hkogdh file: cache/cord-313755-y7regza1.json key: cord-313755-y7regza1 authors: Mitra, Kartik; Ghanta, Prasanth; Acharya, Sushank; Chakrapani, Gayathri; Ramaiah, Basavaraju; Doble, Mukesh title: Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads date: 2020-07-22 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1796802 sha: doc_id: 313755 cord_uid: y7regza1 file: cache/cord-313460-oao2zppd.json key: cord-313460-oao2zppd authors: D’Ardes, Damiano; Boccatonda, Andrea; Rossi, Ilaria; Pontolillo, Michela; Cocco, Giulio; Schiavone, Cosima; Santilli, Francesca; Guagnano, Maria Teresa; Bucci, Marco; Cipollone, Francesco title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection date: 2020-05-11 journal: Eur J Case Rep Intern Med DOI: 10.12890/2020_001707 sha: doc_id: 313460 cord_uid: oao2zppd file: cache/cord-314025-h9gj814e.json key: cord-314025-h9gj814e authors: Lai, Mary Y. Y.; Cheng, Peter K. C.; Lim, Wilina W. L. title: Survival of Severe Acute Respiratory Syndrome Coronavirus date: 2005-10-01 journal: Clin Infect Dis DOI: 10.1086/433186 sha: doc_id: 314025 cord_uid: h9gj814e file: cache/cord-313957-hviv5zar.json key: cord-313957-hviv5zar authors: Masucci, Maria Grazia title: Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection date: 2020-08-01 journal: Biomolecules DOI: 10.3390/biom10081137 sha: doc_id: 313957 cord_uid: hviv5zar file: cache/cord-313795-jr3n3uo9.json key: cord-313795-jr3n3uo9 authors: McAuley, Julie L.; Deerain, Joshua M.; Hammersla, William; Aktepe, Turgut E.; Purcell, Damian J.F.; Mackenzie, Jason M. title: Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.364661 sha: doc_id: 313795 cord_uid: jr3n3uo9 file: cache/cord-314124-yk4y0kea.json key: cord-314124-yk4y0kea authors: Tsou, Ian Y.; Loh, Lik Eng; Kaw, Gregory J.; Chan, Irene; Chee, Thomas S. title: Severe acute respiratory syndrome (SARS) in a paediatric cluster in Singapore date: 2003-08-20 journal: Pediatr Radiol DOI: 10.1007/s00247-003-1042-2 sha: doc_id: 314124 cord_uid: yk4y0kea file: cache/cord-314229-9k2dd95b.json key: cord-314229-9k2dd95b authors: Spaccaferri, G.; Marie, C.; Danis, K.; Épaulard, O.; Botelho-Nevers, E.; Perpoint, T.; Gaymard, A.; Thabuis, A.; Coignard, B. title: Cas groupés d’infections au nouveau coronavirus (SARS-CoV-2) aux Contamines-Montjoie, Haute-Savoie, janvier–février 2020 date: 2020-09-30 journal: Médecine et Maladies Infectieuses DOI: 10.1016/j.medmal.2020.06.142 sha: doc_id: 314229 cord_uid: 9k2dd95b file: cache/cord-314109-wb45naw2.json key: cord-314109-wb45naw2 authors: Maiese, Kenneth title: The Mechanistic Target of Rapamycin (mTOR): Novel Considerations as an Antiviral Treatment date: 2020-06-17 journal: Curr Neurovasc Res DOI: 10.2174/1567202617666200425205122 sha: doc_id: 314109 cord_uid: wb45naw2 file: cache/cord-314013-g091lv0s.json key: cord-314013-g091lv0s authors: Belladonna, Maria Laura; Orabona, Ciriana title: Potential Benefits of Tryptophan Metabolism to the Efficacy of Tocilizumab in COVID-19 date: 2020-06-19 journal: Front Pharmacol DOI: 10.3389/fphar.2020.00959 sha: doc_id: 314013 cord_uid: g091lv0s file: cache/cord-314070-8qz23nn4.json key: cord-314070-8qz23nn4 authors: Gubbi, Sriram; Nazari, Matthew A; Taieb, David; Klubo-Gwiezdzinska, Joanna; Pacak, Karel title: Catecholamine physiology and its implications in patients with COVID-19 date: 2020-10-28 journal: Lancet Diabetes Endocrinol DOI: 10.1016/s2213-8587(20)30342-9 sha: doc_id: 314070 cord_uid: 8qz23nn4 file: cache/cord-314111-bqmfmcfm.json key: cord-314111-bqmfmcfm authors: Yazdanpanah, Yazdan; Guéry, Benoît title: Les antirétroviraux ont-ils une place dans le traitement du syndrome respiratoire aigu sévère ? date: 2006-01-31 journal: La Presse Médicale DOI: 10.1016/s0755-4982(06)74531-6 sha: doc_id: 314111 cord_uid: bqmfmcfm file: cache/cord-313910-bwe2f7xf.json key: cord-313910-bwe2f7xf authors: Bojadzic, Damir; Alcazar, Oscar; Chen, Jinshui; Buchwald, Peter title: Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date: 2020-10-22 journal: bioRxiv DOI: 10.1101/2020.10.22.351056 sha: doc_id: 313910 cord_uid: bwe2f7xf file: cache/cord-314072-av3r7it7.json key: cord-314072-av3r7it7 authors: Liu, Zhuoming; VanBlargan, Laura A.; Rothlauf, Paul W.; Bloyet, Louis-Marie; Chen, Rita E.; Stumpf, Spencer; Zhao, Haiyan; Errico, John M.; Theel, Elitza S.; Ellebedy, Ali H.; Fremont, Daved H.; Diamond, Michael S.; Whelan, Sean P. J. title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date: 2020-11-08 journal: bioRxiv DOI: 10.1101/2020.11.06.372037 sha: doc_id: 314072 cord_uid: av3r7it7 file: cache/cord-313805-6mnclfeg.json key: cord-313805-6mnclfeg authors: Suzuki, Yuichiro J.; Nikolaienko, Sofia I.; Dibrova, Vyacheslav A.; Dibrova, Yulia V.; Vasylyk, Volodymyr M.; Novikov, Mykhailo Y.; Shults, Nataliia V.; Gychka, Sergiy G. title: SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.10.12.335083 sha: doc_id: 313805 cord_uid: 6mnclfeg file: cache/cord-314135-udce22id.json key: cord-314135-udce22id authors: Geisslinger, Franz; Vollmar, Angelika M.; Bartel, Karin title: Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? date: 2020-07-06 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph13070143 sha: doc_id: 314135 cord_uid: udce22id file: cache/cord-314051-dr27bsvt.json key: cord-314051-dr27bsvt authors: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 journal: Can J Anaesth DOI: 10.1007/s12630-020-01746-w sha: doc_id: 314051 cord_uid: dr27bsvt file: cache/cord-313829-pjscmen8.json key: cord-313829-pjscmen8 authors: Caballero, A.E.; Ceriello, A.; Misra, A.; Aschner, P.; McDonnell, M.E.; Hassanein, M.; Ji, L.; Mbanya, J.C.; Fonseca, V.A. title: COVID-19 in people living with diabetes: An international consensus date: 2020-07-06 journal: J Diabetes Complications DOI: 10.1016/j.jdiacomp.2020.107671 sha: doc_id: 313829 cord_uid: pjscmen8 file: cache/cord-313728-08kwkbmd.json key: cord-313728-08kwkbmd authors: Binda, Barbara; Picchi, Giovanna; Carucci, Anna Cecilia; Sinatti, Gaia; Di Norcia, Monica; Grimaldi, Alessandro; Lancione, Laura; Natili, Andrea; Chiappori, Davide; Montali, Filippo; Lupi, Diana; Martinez, Viviana; Panarese, Alessandra; D’Anselmi, Fabrizio; Pisani, Francesco title: Follow-up and Management of Kidney Transplant Recipients During the COVID-19 Lockdown: the experience of an Italian Transplant Center, Including Two Cases of COVID-19 Pneumonia date: 2020-06-28 journal: Transplant Proc DOI: 10.1016/j.transproceed.2020.06.026 sha: doc_id: 313728 cord_uid: 08kwkbmd file: cache/cord-313754-f4sq45gy.json key: cord-313754-f4sq45gy authors: Wong, Chi-Yan; Tang, Catherine So-Kum title: Practice of habitual and volitional health behaviors to prevent severe acute respiratory syndrome among Chinese adolescents in Hong Kong date: 2005-03-31 journal: Journal of Adolescent Health DOI: 10.1016/j.jadohealth.2004.02.024 sha: doc_id: 313754 cord_uid: f4sq45gy file: cache/cord-314102-8jf3fnqe.json key: cord-314102-8jf3fnqe authors: Wu, Jie; Deng, Wei; Li, Shumin; Yang, Xiuhong title: Advances in research on ACE2 as a receptor for 2019-nCoV date: 2020-08-11 journal: Cell Mol Life Sci DOI: 10.1007/s00018-020-03611-x sha: doc_id: 314102 cord_uid: 8jf3fnqe file: cache/cord-314381-ltil9hwl.json key: cord-314381-ltil9hwl authors: Cheng, Cecilia; Tang, Catherine So‐kum title: The psychology behind the masks: Psychological responses to the severe acute respiratory syndrome outbreak in different regions date: 2004-03-11 journal: Asian J Soc Psychol DOI: 10.1111/j.1467-839x.2004.00130.x sha: doc_id: 314381 cord_uid: ltil9hwl file: cache/cord-314445-4cb4a9r5.json key: cord-314445-4cb4a9r5 authors: McNamara, Ryan P.; Caro-Vegas, Carolina; Landis, Justin T.; Moorad, Razia; Pluta, Linda J.; Eason, Anthony B.; Thompson, Cecilia; Bailey, Aubrey; Villamor, Femi Cleola S.; Lange, Philip T.; Wong, Jason P.; Seltzer, Tischan; Seltzer, Jedediah; Zhou, Yijun; Vahrson, Wolfgang; Juarez, Angelica; Meyo, James O.; Calabre, Tiphaine; Broussard, Grant; Rivera-Soto, Ricardo; Chappell, Danielle L.; Baric, Ralph S.; Damania, Blossom; Miller, Melissa B.; Dittmer, Dirk P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-06-19 journal: bioRxiv DOI: 10.1101/2020.06.19.161141 sha: doc_id: 314445 cord_uid: 4cb4a9r5 file: cache/cord-314679-lmfalzni.json key: cord-314679-lmfalzni authors: Sangith, Nikhil; Diagnotek, Xact title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions date: 2020-06-24 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110030 sha: doc_id: 314679 cord_uid: lmfalzni file: cache/cord-314663-8cf0jci9.json key: cord-314663-8cf0jci9 authors: Ampuero, M.; Valenzuela, S.; Valiente-Echeverria, F.; Soto-Rifo, R.; Barriga, G. 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L.; Investigators, WWAMI Stroke title: SARS-CoV-2 Infection and Stroke: Coincident or Causal? date: 2020-07-29 journal: nan DOI: 10.1101/2020.07.17.20156463 sha: doc_id: 314107 cord_uid: x6e1jhcd file: cache/cord-314024-n6l2804j.json key: cord-314024-n6l2804j authors: Gonçalves, Antonio; Bertrand, Julie; Ke, Ruian; Comets, Emmanuelle; de Lamballerie, Xavier; Malvy, Denis; Pizzorno, Andrés; Terrier, Olivier; Calatrava, Manuel Rosa; Mentré, France; Smith, Patrick; Perelson, Alan S; Guedj, Jérémie title: Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date: 2020-04-07 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.04.04.20047886 sha: doc_id: 314024 cord_uid: n6l2804j file: cache/cord-314311-xbpb9nfi.json key: cord-314311-xbpb9nfi authors: Ge, Huipeng; Wang, Xiufen; Yuan, Xiangning; Xiao, Gong; Wang, Chengzhi; Deng, Tianci; Yuan, Qiongjing; Xiao, Xiangcheng title: The epidemiology and clinical information about COVID-19 date: 2020-04-14 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-03874-z sha: doc_id: 314311 cord_uid: xbpb9nfi file: cache/cord-314386-cxq9v218.json key: cord-314386-cxq9v218 authors: Nitsche, Andreas; Schweiger, Brunhilde; Ellerbrok, Heinz; Niedrig, Matthias; Pauli, Georg title: SARS Coronavirus Detection date: 2004-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1007.030678 sha: doc_id: 314386 cord_uid: cxq9v218 file: cache/cord-314451-mqnqjn0c.json key: cord-314451-mqnqjn0c authors: Roberts, Anjeanette; Deming, Damon; Paddock, Christopher D; Cheng, Aaron; Yount, Boyd; Vogel, Leatrice; Herman, Brian D; Sheahan, Tim; Heise, Mark; Genrich, Gillian L; Zaki, Sherif R; Baric, Ralph; Subbarao, Kanta title: A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice date: 2007-01-12 journal: PLoS Pathog DOI: 10.1371/journal.ppat.0030005 sha: doc_id: 314451 cord_uid: mqnqjn0c file: cache/cord-314369-o4nis91y.json key: cord-314369-o4nis91y authors: Lopez-Lopes, G. 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S.; Di Nisio, A. title: Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome date: 2020-09-16 journal: J Endocrinol Invest DOI: 10.1007/s40618-020-01383-6 sha: doc_id: 315289 cord_uid: 4x229n8n file: cache/cord-314937-jrxu65bl.json key: cord-314937-jrxu65bl authors: Kuwelker, K.; Zhou, F.; Blomberg, B.; Lartey, S.; Brokstad, K. A.; Trieu, M. C.; Madsen, A.; Krammer, F.; Mohn, K. G. I.; Toendel, C.; Linchausen, D. W.; Cox, R. 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E.; Law, A.; Russell, C.; Baillie, J. K.; Clohisey, S. title: Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date: 2020-09-01 journal: nan DOI: 10.1101/2020.08.27.20182238 sha: doc_id: 315498 cord_uid: gpzee1f2 file: cache/cord-315556-84rgd2s9.json key: cord-315556-84rgd2s9 authors: Pilotto, A.; Odolini, S.; Masciocchi, S.; Comelli, A.; Volonghi, I.; Gazzina, S.; Nocivelli, S.; Pezzini, A.; Foca', E.; Caruso, A.; Leonardi, M.; Pasolini, M. 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Kevin; Meng, Xiaoli; Goldring, Christopher E.; Chadwick, Amy E. title: Safety perspectives on presently considered drugs for the treatment of COVID‐19 date: 2020-07-17 journal: Br J Pharmacol DOI: 10.1111/bph.15204 sha: doc_id: 315730 cord_uid: fzgxuak7 file: cache/cord-315462-u2dj79yw.json key: cord-315462-u2dj79yw authors: Hewitt, Judith A.; Lutz, Cathleen; Florence, William C.; Pitt, M. 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A.; Ott, M. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.28.20201947 sha: doc_id: 316179 cord_uid: kmdxltie file: cache/cord-315696-43wmazxa.json key: cord-315696-43wmazxa authors: Marinaki, Smaragdi; Tsiakas, Stathis; Korogiannou, Maria; Grigorakos, Konstantinos; Papalois, Vassilios; Boletis, Ioannis title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients’ Lives and Allografts date: 2020-09-16 journal: J Clin Med DOI: 10.3390/jcm9092986 sha: doc_id: 315696 cord_uid: 43wmazxa file: cache/cord-315951-5gsbtfag.json key: cord-315951-5gsbtfag authors: Kiemer, Lars; Lund, Ole; Brunak, Søren; Blom, Nikolaj title: Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date: 2004-06-06 journal: BMC Bioinformatics DOI: 10.1186/1471-2105-5-72 sha: doc_id: 315951 cord_uid: 5gsbtfag file: cache/cord-315756-g6g34uvh.json key: cord-315756-g6g34uvh authors: Danchin, A.; TURINICI, G. title: Immunity after COVID-19: protection or sensitization ? date: 2020-05-23 journal: nan DOI: 10.1101/2020.05.21.20108860 sha: doc_id: 315756 cord_uid: g6g34uvh file: cache/cord-316180-g3lfecp0.json key: cord-316180-g3lfecp0 authors: Zhang, Jingshu; Lan, Yun; Sanyal, Sumana title: Membrane heist: Coronavirus host membrane remodeling during replication date: 2020-10-25 journal: Biochimie DOI: 10.1016/j.biochi.2020.10.010 sha: doc_id: 316180 cord_uid: g3lfecp0 file: cache/cord-316080-y6ypbdtu.json key: cord-316080-y6ypbdtu authors: Fajnzylber, J. 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D.; Yu, X.; Li, J.; Readiness, Massachusetts Consortium for Pathogen title: SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality date: 2020-07-17 journal: nan DOI: 10.1101/2020.07.15.20131789 sha: doc_id: 316080 cord_uid: y6ypbdtu file: cache/cord-316117-o29773cz.json key: cord-316117-o29773cz authors: Menzella, Francesco; Biava, Mirella; Barbieri, Chiara; Livrieri, Francesco; Facciolongo, Nicola title: Pharmacologicaltreatment of COVID-19: lights and shadows date: 2020-05-19 journal: Drugs Context DOI: 10.7573/dic.2020-4-6 sha: doc_id: 316117 cord_uid: o29773cz file: cache/cord-316083-f1h2j6jx.json key: cord-316083-f1h2j6jx authors: Alamri, Ahmad; Oriez, Constance; Bouilloud, Florence; Dupuy, Olivier; Hamou, Adrien Ben title: nan date: 2020-05-21 journal: Presse Med DOI: 10.1016/j.lpm.2020.104027 sha: doc_id: 316083 cord_uid: f1h2j6jx file: cache/cord-315968-q2rxj90s.json key: cord-315968-q2rxj90s authors: Douglas, Jennifer E.; Kaufman, Adam C.; Rajasekaran, Karthik title: Management of a Unique Sinonasal Undifferentiated Carcinoma Subtype in the Era of SARS-CoV-2 date: 2020-10-05 journal: ORL J Otorhinolaryngol Relat Spec DOI: 10.1159/000511713 sha: doc_id: 315968 cord_uid: q2rxj90s file: cache/cord-316066-pge0vx04.json key: cord-316066-pge0vx04 authors: Zhang, Zheng; Xu, Dongping; Li, Yonggang; Jin, Lei; Shi, Ming; Wang, Min; Zhou, Xianzhi; Wu, Hao; Gao, George F.; Wang, Fu-Sheng title: Longitudinal alteration of circulating dendritic cell subsets and its correlation with steroid treatment in patients with severe acute respiratory syndrome date: 2005-06-16 journal: Clin Immunol DOI: 10.1016/j.clim.2005.04.015 sha: doc_id: 316066 cord_uid: pge0vx04 file: cache/cord-315970-m5o962yw.json key: cord-315970-m5o962yw authors: Di Ciaula, Agostino; Palmieri, Vincenzo O.; Migliore, Giovanni; Portincasa, Piero title: COVID‐19, internists and resilience: the north‐south Italy outbreak. date: 2020-06-01 journal: Eur J Clin Invest DOI: 10.1111/eci.13299 sha: doc_id: 315970 cord_uid: m5o962yw file: cache/cord-316096-3fnwosst.json key: cord-316096-3fnwosst authors: Jin, Huali; Xiao, Chong; Chen, Ze; Kang, Youmin; Ma, Yijie; Zhu, Kaichun; Xie, Qifa; Tu, Yixian; Yu, Yang; Wang, Bin title: Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice date: 2005-03-25 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2005.01.048 sha: doc_id: 316096 cord_uid: 3fnwosst file: cache/cord-316186-254z62e4.json key: cord-316186-254z62e4 authors: Kario, Kazuomi; Morisawa, Yuji; Sukonthasarn, Apichard; Turana, Yuda; Chia, Yook‐Chin; Park, Sungha; Wang, Tzung‐Dau; Chen, Chen‐Huan; Tay, Jam Chin; Li, Yan; Wang, Ji‐Guang title: COVID‐19 and hypertension—evidence and practical management: Guidance from the HOPE Asia Network date: 2020-07-09 journal: J Clin Hypertens (Greenwich) DOI: 10.1111/jch.13917 sha: doc_id: 316186 cord_uid: 254z62e4 file: cache/cord-316003-xt59voyt.json key: cord-316003-xt59voyt authors: Say, Daphne S.; de Lorimier, Arthur; Lammers, Cathleen R.; Natale, JoAnne; Lakshminrusimha, Satyan; Wiedeman, Jean; Partridge, Elizabeth title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol date: 2020-03-31 journal: J Pediatr Gastroenterol Nutr DOI: 10.1097/mpg.0000000000002731 sha: doc_id: 316003 cord_uid: xt59voyt file: cache/cord-316126-j51dik7f.json key: cord-316126-j51dik7f authors: Zhang, X. 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Alfredo title: Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date: 2020-10-19 journal: Int J Genomics DOI: 10.1155/2020/6901217 sha: doc_id: 316330 cord_uid: 55nd3pwe file: cache/cord-316374-mzomj1ab.json key: cord-316374-mzomj1ab authors: Brufsky, Adam; Marti, Juan Luis Gomez; Nasrazadani, Azadeh; Lotze, Michael T. title: Boning up: amino-bisphophonates as immunostimulants and endosomal disruptors of dendritic cell in SARS-CoV-2 infection date: 2020-06-29 journal: J Transl Med DOI: 10.1186/s12967-020-02433-6 sha: doc_id: 316374 cord_uid: mzomj1ab file: cache/cord-316498-f43apjul.json key: cord-316498-f43apjul authors: Karlsson, Jan Olof G; Jynge, Per; Ignarro, Louis J title: May Mangafodipir or Other SOD Mimetics Contribute to Better Care in COVID-19 Patients? date: 2020-10-10 journal: Antioxidants (Basel) DOI: 10.3390/antiox9100971 sha: doc_id: 316498 cord_uid: f43apjul file: cache/cord-315598-qwh72inx.json key: cord-315598-qwh72inx authors: Mendoza, Jose Luis Accini; Estrada, Victor Hugo Nieto; López, Nelly Beltrán; Bolaños, Elisabeth Ramos; Franco, Daniel Molano; Castell, Carmelo Dueñas; Moreno, Albert Alexander Valencia; Amaya, Iván Camilo Alarcón; Flórez, John Serna; Valencia, Bladimir Alejandro Gil; Camilo Pizarro, G; Polo, Yulieth María Zabaleta; Meza, Carmen Lucia Chica title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 journal: nan DOI: 10.1016/j.acci.2020.09.004 sha: doc_id: 315598 cord_uid: qwh72inx file: cache/cord-316095-jzyb4jn5.json key: cord-316095-jzyb4jn5 authors: Falahchai, Mehran; Babaee Hemmati, Yasamin; Hasanzade, Mahya title: Dental care management during the COVID‐19 outbreak date: 2020-09-19 journal: Spec Care Dentist DOI: 10.1111/scd.12523 sha: doc_id: 316095 cord_uid: jzyb4jn5 file: cache/cord-316616-j82q99in.json key: cord-316616-j82q99in authors: Su, Yen-Bo; Kuo, Ming-Jen; Lin, Ting-Yu; Chien, Chian-Shiu; Yang, Yi-Ping; Chou, Shih-Jie; Leu, Hsin-Bang title: Cardiovascular manifestation and treatment in COVID-19 date: 2020-05-19 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000352 sha: doc_id: 316616 cord_uid: j82q99in file: cache/cord-316646-rd3zl9qz.json key: cord-316646-rd3zl9qz authors: Lebedin, Y. S.; Lyang, O. V.; Galstyan, A. G.; Belousov, V. V.; Rebrikov, D. 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M.; Kroidl, I.; Olbrich, L.; Thiel, V.; Diefenbach, M.; Riess, F.; Forster, F.; Theis, F. J.; Wieser, A.; Hoelscher, M.; group, KoCo19 collaboration title: Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19) date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.28.20082743 sha: doc_id: 316232 cord_uid: 7w1vrx96 file: cache/cord-316345-a1cirnya.json key: cord-316345-a1cirnya authors: Comas, Carmina; Carreras, Elena title: COVID‐19 and pregnancy: An opportunity to correct an historic gender bias date: 2020-08-02 journal: J Med Virol DOI: 10.1002/jmv.26350 sha: doc_id: 316345 cord_uid: a1cirnya file: cache/cord-316260-1t3ifsfi.json key: cord-316260-1t3ifsfi authors: Nogueira-de-Almeida, Carlos Alberto; Ciampo, Luiz A. Del; Ferraz, Ivan S.; Ciampo, Ieda R.L. Del; Contini, Andrea A.; Ued, Fábio da V. title: COVID-19 and obesity in childhood and adolescence: A clinical review()() date: 2020-08-04 journal: J Pediatr (Rio J) DOI: 10.1016/j.jped.2020.07.001 sha: doc_id: 316260 cord_uid: 1t3ifsfi file: cache/cord-316432-xemz7zn9.json key: cord-316432-xemz7zn9 authors: Talaie, Haleh; Hosseini, Sayed Masoud; Nazari, Maryam; Fakhri, Yadollah; Mousavizadeh, Atieh; Vatanpour, Hossein; Firoozfar, Ali title: Is there any potential management against COVID-19? 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E.; Bosch, Berend Jan; Haagmans, Bart L. title: Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC date: 2013-03-13 journal: Nature DOI: 10.1038/nature12005 sha: doc_id: 316536 cord_uid: jpbfgwhl file: cache/cord-316930-0s7k9guq.json key: cord-316930-0s7k9guq authors: Caldas, Lucio Ayres; Carneiro, Fabiana Avila; Higa, Luiza Mendonça; Monteiro, Fábio Luiz; da Silva, Gustavo Peixoto; da Costa, Luciana Jesus; Durigon, Edison Luiz; Tanuri, Amilcar; de Souza, Wanderley title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy date: 2020-09-30 journal: Sci Rep DOI: 10.1038/s41598-020-73162-5 sha: doc_id: 316930 cord_uid: 0s7k9guq file: cache/cord-316946-bxfdq8e1.json key: cord-316946-bxfdq8e1 authors: Danion, François; Ruch, Yvon; Fourtage, Marion; Kaeuffer, Charlotte; Greigert, Valentin; Lefebvre, Nicolas; Muller, Joris; Nai, Thierry; Hansmann, Yves title: The Good, the Bad, and the Hoax: When Publication Instantaneously Impacts Treatment Strategies for COVID-19 date: 2020-07-22 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.01127-20 sha: doc_id: 316946 cord_uid: bxfdq8e1 file: cache/cord-316255-93srx4s7.json key: cord-316255-93srx4s7 authors: Cacho, Pedro Muñoz; Hernández, José L.; López-Hoyos, Marcos; Martínez-Taboada, Víctor M. title: Can climatic factors explain the differences in COVID-19 incidence and severity across the Spanish regions?: An ecological study date: 2020-10-13 journal: Environ Health DOI: 10.1186/s12940-020-00660-4 sha: doc_id: 316255 cord_uid: 93srx4s7 file: cache/cord-316617-8cqxz3wi.json key: cord-316617-8cqxz3wi authors: Ward, Michael P. title: SARS‐CoV‐2, where to now? date: 2020-06-19 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13654 sha: doc_id: 316617 cord_uid: 8cqxz3wi file: cache/cord-316670-x9x54fxw.json key: cord-316670-x9x54fxw authors: Flinck, Heini; Rauhio, Anne; Luukinen, Bruno; Lehtimäki, Terho; Haapala, Anna-Maija; Seiskari, Tapio; Aittoniemi, Janne title: Comparison of two fully automated tests detecting antibodies against nucleocapsid N and spike S1/S2 proteins in COVID-19 date: 2020-08-29 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115197 sha: doc_id: 316670 cord_uid: x9x54fxw file: cache/cord-316658-zwxtbena.json key: cord-316658-zwxtbena authors: Butler, S. 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Kodidela, Sunitha; Tadrous, Erene; Cory, Theodore James; Walker, Crystal Martin; Smith, Amber Marie; Mukherjee, Ahona; Kumar, Santosh title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 journal: Viruses DOI: 10.3390/v12080887 sha: doc_id: 317037 cord_uid: 1qydcc5e file: cache/cord-316814-9fv9xrln.json key: cord-316814-9fv9xrln authors: Li, Hong-Ye; Chye, Mee-Len title: Use of GFP to Investigate Expression of Plant-Derived Vaccines date: 2009 journal: Viral Applications of Green Fluorescent Protein DOI: 10.1007/978-1-59745-559-6_19 sha: doc_id: 316814 cord_uid: 9fv9xrln file: cache/cord-316970-n2dly3oa.json key: cord-316970-n2dly3oa authors: Kerbaj, Jad; Cazorla, Cecile; De Greslan, Thierry; Serie, Mathieu; Gourinat, Ann-Claire; Marot, Benoit title: COVID-19: The New Caledonia experience date: 2020-05-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa600 sha: doc_id: 316970 cord_uid: n2dly3oa file: cache/cord-317085-qc8bfb9g.json key: cord-317085-qc8bfb9g authors: Zhang, Nan; 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Nam, Hannah H.; Roberts, Scott C.; Simons, Lacy M.; Jennings, Lawrence J.; Qi, Chao; Achenbach, Chad J.; Hauser, Alan R.; Ison, Michael G.; Hultquist, Judd F.; Ozer, Egon A. title: A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways date: 2020-11-11 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.103112 sha: doc_id: 317233 cord_uid: k3wuqwyu file: cache/cord-316845-k9zvsfvj.json key: cord-316845-k9zvsfvj authors: Robertson, Mary M.; Eapen, Valsamma; Rizzo, Renata; Stern, Jeremy S.; Hartmann, Andreas title: Gilles de la Tourette Syndrome: advice in the times of COVID-19 date: 2020-04-28 journal: F1000Res DOI: 10.12688/f1000research.23275.2 sha: doc_id: 316845 cord_uid: k9zvsfvj file: cache/cord-316859-h8lfmr3e.json key: cord-316859-h8lfmr3e authors: Mu, Jingfang; Xu, Jiuyue; Zhang, Leike; Shu, Ting; Wu, Di; Huang, Muhan; Ren, Yujie; Li, Xufang; Geng, Qing; Xu, Yi; Qiu, Yang; Zhou, Xi title: SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells date: 2020-04-10 journal: Sci China Life Sci DOI: 10.1007/s11427-020-1692-1 sha: doc_id: 316859 cord_uid: h8lfmr3e file: cache/cord-316880-hbw6jbz5.json key: cord-316880-hbw6jbz5 authors: Sutton, Melissa; Cieslak, Paul; Linder, Meghan title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 date: 2020-08-14 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6932a4 sha: doc_id: 316880 cord_uid: hbw6jbz5 file: cache/cord-316788-4x5l2h4d.json key: cord-316788-4x5l2h4d authors: Ryu, Young Bae; Jeong, Hyung Jae; Kim, Jang Hoon; Kim, Young Min; Park, Ji-Young; Kim, Doman; Naguyen, Thi Thanh Hanh; Park, Su-Jin; Chang, Jong Sun; Park, Ki Hun; Rho, Mun-Chual; Lee, Woo Song title: Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition date: 2010-11-15 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2010.09.035 sha: doc_id: 316788 cord_uid: 4x5l2h4d file: cache/cord-317151-cxx5pcln.json key: cord-317151-cxx5pcln authors: Papa, Alfredo; Papa, Valerio; Lopetuso, Loris Riccardo; Gasbarrini, Antonio; Tursi, Antonio title: Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date: 2020-10-24 journal: Therap Adv Gastroenterol DOI: 10.1177/1756284820968747 sha: doc_id: 317151 cord_uid: cxx5pcln file: cache/cord-317129-wa1j2f6b.json key: cord-317129-wa1j2f6b authors: Zhang, Jia; Meng, Bo; Liao, Duanfang; Zhou, Lvyi; Zhang, Xu; Chen, Linling; Guo, Zifen; Peng, Cuiying; Zhu, Bingyang; Lee, Peggy P.; Xu, Xiangmin; Zhou, Tianhong; Deng, Zemin; Hu, Yinghe; Li, Kai title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 journal: Mol Biotechnol DOI: 10.1385/mb:25:2:107 sha: doc_id: 317129 cord_uid: wa1j2f6b file: cache/cord-317355-z5tk3v3b.json key: cord-317355-z5tk3v3b authors: Dunker, Susanne; Hornick, Thomas; Szczepankiewicz, Grit; Maier, Melanie; Bastl, Maximilian; Bumberger, Jan; Treudler, Regina; Liebert, Uwe G.; Simon, Jan-Christoph title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread date: 2020-10-13 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142881 sha: doc_id: 317355 cord_uid: z5tk3v3b file: cache/cord-317092-5qba9jiq.json key: cord-317092-5qba9jiq authors: Singh, Tulika; Heston, Sarah M; Langel, Stephanie N; Blasi, Maria; Hurst, Jillian H; Fouda, Genevieve G; Kelly, Matthew S; Permar, Sallie R title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date: 2020-05-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa547 sha: doc_id: 317092 cord_uid: 5qba9jiq file: cache/cord-317123-0tdfvlqd.json key: cord-317123-0tdfvlqd authors: Tan, Xiaotian; Lin, Cory; Zhang, Jie; Khaing Oo, Maung Kyaw; Fan, Xudong title: Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date: 2020-04-21 journal: bioRxiv DOI: 10.1101/2020.04.20.052233 sha: doc_id: 317123 cord_uid: 0tdfvlqd file: cache/cord-317227-zb434ve3.json key: cord-317227-zb434ve3 authors: Beck, Bo Ram; Shin, Bonggun; Choi, Yoonjung; Park, Sungsoo; Kang, Keunsoo title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model date: 2020-03-30 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.03.025 sha: doc_id: 317227 cord_uid: zb434ve3 file: cache/cord-317067-u90zkjk9.json key: cord-317067-u90zkjk9 authors: Trottein, François; Sokol, Harry title: Potential causes and consequences of gastrointestinal disorders during a SARS-CoV-2 infection date: 2020-07-03 journal: Cell Rep DOI: 10.1016/j.celrep.2020.107915 sha: doc_id: 317067 cord_uid: u90zkjk9 file: cache/cord-317246-8c7d5ynz.json key: cord-317246-8c7d5ynz authors: Cagetti, Maria Grazia; Angelino, Eleonora title: Could SARS‐CoV‐2 burst the use of Non‐Invasive and Minimally Invasive treatments in paediatric dentistry? date: 2020-08-03 journal: Int J Paediatr Dent DOI: 10.1111/ipd.12679 sha: doc_id: 317246 cord_uid: 8c7d5ynz file: cache/cord-317333-unrd76bo.json key: cord-317333-unrd76bo authors: Danesh, Ali; Cameron, Cheryl M.; León, Alberto J.; Ran, Longsi; Xu, Luoling; Fang, Yuan; Kelvin, Alyson A.; Rowe, Thomas; Chen, Honglin; Guan, Yi; Jonsson, Colleen B.; Cameron, Mark J.; Kelvin, David J. title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date: 2011-01-05 journal: Virology DOI: 10.1016/j.virol.2010.10.002 sha: doc_id: 317333 cord_uid: unrd76bo file: cache/cord-317413-w2xfdwea.json key: cord-317413-w2xfdwea authors: Maurya, Vimal K.; Kumar, Swatantra; Bhatt, Madan L. B.; Saxena, Shailendra K. title: Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection date: 2020-10-19 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1832577 sha: doc_id: 317413 cord_uid: w2xfdwea file: cache/cord-317429-pp6hb4q5.json key: cord-317429-pp6hb4q5 authors: Aslam, Saima; Mehra, Mandeep R. title: COVID-19: Yet another coronavirus challenge in transplantation date: 2020-03-14 journal: J Heart Lung Transplant DOI: 10.1016/j.healun.2020.03.007 sha: doc_id: 317429 cord_uid: pp6hb4q5 file: cache/cord-317240-d7ioosi6.json key: cord-317240-d7ioosi6 authors: Shah, Niyati; Davariya, Vipul; Gupta, Sanjeev K.; Gajjar, Pankaj; Parmar, Jitendra; D'Cruz, Lancelot title: Review: An insight into coronaviruses: Challenges, security and scope date: 2020-08-04 journal: Rev Med Virol DOI: 10.1002/rmv.2138 sha: doc_id: 317240 cord_uid: d7ioosi6 file: cache/cord-318018-ybdkp398.json key: cord-318018-ybdkp398 authors: Bruni, Margherita; Cecatiello, Valentina; Diaz-Basabe, Angelica; Lattanzi, Georgia; Mileti, Erika; Monzani, Silvia; Pirovano, Laura; Rizzelli, Francesca; Visintin, Clara; Bonizzi, Giuseppina; Giani, Marco; Lavitrano, Marialuisa; Faravelli, Silvia; Forneris, Federico; Caprioli, Flavio; Pelicci, Pier Giuseppe; Natoli, Gioacchino; Pasqualato, Sebastiano; Mapelli, Marina; Facciotti, Federica title: Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date: 2020-10-01 journal: J Clin Med DOI: 10.3390/jcm9103188 sha: doc_id: 318018 cord_uid: ybdkp398 file: cache/cord-317591-qa6oxy4j.json key: cord-317591-qa6oxy4j authors: Fukushima, Akiko; Fukuda, Noboru; Lai, Yimu; Ueno, Takahiro; Moriyama, Mitsuhiko; Taguchi, Fumihiro; Iguchi, Akifumi; Shimizu, Kazushi; Kuroda, Kazumichi title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 journal: Intervirology DOI: 10.1159/000215946 sha: doc_id: 317591 cord_uid: qa6oxy4j file: cache/cord-317435-4yuw7jo3.json key: cord-317435-4yuw7jo3 authors: Zhou, Yadi; Hou, Yuan; Shen, Jiayu; Huang, Yin; Martin, William; Cheng, Feixiong title: Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 date: 2020-03-16 journal: Cell Discov DOI: 10.1038/s41421-020-0153-3 sha: doc_id: 317435 cord_uid: 4yuw7jo3 file: cache/cord-317423-3nkzp1z2.json key: cord-317423-3nkzp1z2 authors: Turk, Can; Turk, Seyhan; Temirci, Elif Sena; Malkan, Umit Yavuz; Haznedaroglu, İbrahim C. title: In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus date: 2020-06-03 journal: J Renin Angiotensin Aldosterone Syst DOI: 10.1177/1470320320928872 sha: doc_id: 317423 cord_uid: 3nkzp1z2 file: cache/cord-317523-idji1l0a.json key: cord-317523-idji1l0a authors: Xu, Huanzhou; Chitre, Siddhi A.; Akinyemi, Ibukun A.; Loeb, Julia C.; Lednicky, John A.; McIntosh, Michael T.; Bhaduri-McIntosh, Sumita title: SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date: 2020-10-27 journal: bioRxiv DOI: 10.1101/2020.10.27.357731 sha: doc_id: 317523 cord_uid: idji1l0a file: cache/cord-317563-mu47vvma.json key: cord-317563-mu47vvma authors: Yuan, Chunhui; Zhu, Hongmin; Yang, Yuan; Cai, Xiaonan; Xiang, Feiyan; Wu, Huan; Yao, Cong; Xiang, Yun; Xiao, Han title: Viral loads in throat and anal swabs in children infected with SARS-CoV-2 date: 2020-06-09 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1771219 sha: doc_id: 317563 cord_uid: mu47vvma file: cache/cord-317761-tkqmu1va.json key: cord-317761-tkqmu1va authors: Shukla, Ashutosh M; Archibald, Lennox K; Shukla, Aparna Wagle; Mehta, Hiren J; Cherabuddi, Kartikeya title: Chloroquine and hydroxychloroquine in the context of COVID-19 date: 2020-04-28 journal: Drugs Context DOI: 10.7573/dic.2020-4-5 sha: doc_id: 317761 cord_uid: tkqmu1va file: cache/cord-317359-7yuygcew.json key: cord-317359-7yuygcew authors: Straccia, Patrizia; Rossi, Esther Diana; Martini, Maurizio; Mulè, Antonino; Cianfrini, Federica; Curatolo, Mariangela; Cancellieri, Alessandra; Brunelli, Chiara; Zannoni, Gian Franco; Fadda, Guido title: Description of a new biosafe procedure for cytological specimens from patients with COVID‐19 processed by liquid‐based preparations date: 2020-08-07 journal: Cancer Cytopathol DOI: 10.1002/cncy.22341 sha: doc_id: 317359 cord_uid: 7yuygcew file: cache/cord-317379-ljdaj80d.json key: cord-317379-ljdaj80d authors: Faure‐Bardon, V.; Isnard, P.; Roux, N.; Leruez‐Ville, M.; Molina, T.; Bessieres, B.; Ville, Y. title: Anatomical and timely assessment of protein expression of angiotensin‐converting enzyme 2, SARS‐CoV‐2 specific receptor, in fetal and placental tissues: new insight for perinatal counseling date: 2020-08-15 journal: Ultrasound Obstet Gynecol DOI: 10.1002/uog.22178 sha: doc_id: 317379 cord_uid: ljdaj80d file: cache/cord-317573-wp2wr3b5.json key: cord-317573-wp2wr3b5 authors: Peng, Hui; Yang, Li-tao; Li, Jian; Lu, Zhi-qiang; Wang, Ling-yun; Koup, Richard A.; Bailer, Robert T.; Wu, Chang-you title: Human memory T cell responses to SARS-CoV E protein date: 2006-06-30 journal: Microbes Infect DOI: 10.1016/j.micinf.2006.05.008 sha: doc_id: 317573 cord_uid: wp2wr3b5 file: cache/cord-317608-otd81rvy.json key: cord-317608-otd81rvy authors: Corman, Victor M.; Rabenau, Holger F.; Adams, Ortwin; Oberle, Doris; Funk, Markus B.; Keller‐Stanislawski, Brigitte; Timm, Jörg; Drosten, Christian; Ciesek, Sandra title: SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission date: 2020-05-27 journal: Transfusion DOI: 10.1111/trf.15841 sha: doc_id: 317608 cord_uid: otd81rvy file: cache/cord-317820-od9l7p1r.json key: cord-317820-od9l7p1r authors: Goker Bagca, Bakiye; Biray Avci, Cigir title: Overview of the COVID-19 and JAK/STAT Pathway Inhibition: Ruxolitinib Perspective date: 2020-06-20 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2020.06.013 sha: doc_id: 317820 cord_uid: od9l7p1r file: cache/cord-317628-1inxq7t5.json key: cord-317628-1inxq7t5 authors: Cuccarese, Michael F.; Earnshaw, Berton A.; Heiser, Katie; Fogelson, Ben; Davis, Chadwick T.; McLean, Peter F.; Gordon, Hannah B.; Skelly, Kathleen-Rose; Weathersby, Fiona L.; Rodic, Vlad; Quigley, Ian K.; Pastuzyn, Elissa D.; Mendivil, Brandon M.; Lazar, Nathan H.; Brooks, Carl A.; Carpenter, Joseph; Probst, Brandon L.; Jacobson, Pamela; Glazier, Seth W.; Ford, Jes; Jensen, James D.; Campbell, Nicholas D.; Statnick, Michael A.; Low, Adeline S.; Thomas, Kirk R.; Carpenter, Anne E.; Hegde, Sharath S.; Alfa, Ronald W.; Victors, Mason L.; Haque, Imran S.; Chong, Yolanda T.; Gibson, Christopher C. title: Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date: 2020-08-14 journal: bioRxiv DOI: 10.1101/2020.08.02.233064 sha: doc_id: 317628 cord_uid: 1inxq7t5 file: cache/cord-317647-vcktnsv8.json key: cord-317647-vcktnsv8 authors: Wang, Yinhua; Li, Wen; Jiang, Zhiming; Xi, Xiuming; Zhu, Yibing title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis date: 2020-09-18 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000022379 sha: doc_id: 317647 cord_uid: vcktnsv8 file: cache/cord-317952-4oa9hfb4.json key: cord-317952-4oa9hfb4 authors: Bourgonje, Arno R.; Abdulle, Amaal Eman; Timens, Wim; Hillebrands, Jan‐Luuk; Navis, Gerjan J.; Gordijn, Sanne J.; Bolling, Marieke C.; Dijkstra, Gerard; Voors, Adriaan A.; Osterhaus, Albert D. M. E.; van der Voort, Peter H. J.; Mulder, Douwe J.; van Goor, Harry title: Angiotensin‐converting enzyme‐2 (ACE2), SARS‐CoV‐2 and pathophysiology of coronavirus disease 2019 (COVID‐19) date: 2020-05-17 journal: J Pathol DOI: 10.1002/path.5471 sha: doc_id: 317952 cord_uid: 4oa9hfb4 file: cache/cord-317468-pnxni1x5.json key: cord-317468-pnxni1x5 authors: Louie, Philip K.; Barber, Lauren A.; Morse, Kyle W.; Syku, Marie; Qureshi, Sheeraz A.; Lafage, Virginie; Huang, Russel C.; Carli, Alberto V. title: Early Peri-operative Outcomes Were Unchanged in Patients Undergoing Spine Surgery During the COVID-19 Pandemic in New York City date: 2020-09-15 journal: HSS J DOI: 10.1007/s11420-020-09797-x sha: doc_id: 317468 cord_uid: pnxni1x5 file: cache/cord-317971-kuwargnp.json key: cord-317971-kuwargnp authors: Opatz, Till; Senn‐Bilfinger, Joerg; Richert, Clemens title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 journal: Angew Chem Int Ed Engl DOI: 10.1002/anie.202004721 sha: doc_id: 317971 cord_uid: kuwargnp file: cache/cord-317593-tajy3p9e.json key: cord-317593-tajy3p9e authors: Xi, AIqi; Ma, Zhuo; Dai, Jingtao; Ding, Yuehe; Ma, Xiuzhen; Ma, Xiaoli; Wang, Xiaoyi; Shi, Lianmeng; Bai, Huanying; Zheng, Hongying; Nuermberger, Eric; Xu, Jian title: Epidemiological and clinical characteristics of discharged patients infected with SARS-CoV-2 on the Qinghai plateau date: 2020-04-29 journal: nan DOI: 10.1101/2020.04.23.20077644 sha: doc_id: 317593 cord_uid: tajy3p9e file: cache/cord-317622-o10ntfi8.json key: cord-317622-o10ntfi8 authors: Evans, Ronald M.; Lippman, Scott M. title: Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing date: 2020-09-11 journal: Cell Metab DOI: 10.1016/j.cmet.2020.09.007 sha: doc_id: 317622 cord_uid: o10ntfi8 file: cache/cord-317707-r0q7ipa6.json key: cord-317707-r0q7ipa6 authors: Saracco, Margherita; Martini, Silvia; Tandoi, Francesco; Dell’Olio, Dominic; Ottobrelli, Antonio; Scarmozzino, Antonio; Amoroso, Antonio; Fonio, Paolo; Balagna, Roberto; Romagnoli, Renato title: Carrying on with Liver Transplantation during the COVID-19 emergency: Report from Piedmont Region date: 2020-08-07 journal: Clin Res Hepatol Gastroenterol DOI: 10.1016/j.clinre.2020.07.017 sha: doc_id: 317707 cord_uid: r0q7ipa6 file: cache/cord-318204-t024w7h6.json key: cord-318204-t024w7h6 authors: Fang, Ferric C; Naccache, Samia N; Greninger, Alexander L title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date: 2020-06-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa742 sha: doc_id: 318204 cord_uid: t024w7h6 file: cache/cord-317906-u5z5cpfk.json key: cord-317906-u5z5cpfk authors: Gupta, Ishita; Reddy, Mithun K; Hussain, Mir Mehdi; Murthy, Pooja M; Robert, Chris A title: Atypical Neurological Manifestations of COVID-19 date: 2020-06-08 journal: Cureus DOI: 10.7759/cureus.8518 sha: doc_id: 317906 cord_uid: u5z5cpfk file: cache/cord-318262-w8oixzdg.json key: cord-318262-w8oixzdg authors: Chevance, A; Gourion, D; Hoertel, N; Llorca, P-M; Thomas, P; Bocher, R; Moro, M-R; Laprévote, V; Benyamina, A; Fossati, P; Masson, M; Leaune, E; Leboyer, M; Gaillard, R title: Ensuring mental health care during the SARS-CoV-2 epidemic in France: a narrative review date: 2020-04-22 journal: Encephale DOI: 10.1016/j.encep.2020.04.005 sha: doc_id: 318262 cord_uid: w8oixzdg file: cache/cord-317928-doj39520.json key: cord-317928-doj39520 authors: Thum, Thomas title: SARS-CoV-2 receptor ACE2 expression in the human heart: cause of a post-pandemic wave of heart failure? date: 2020-05-14 journal: Eur Heart J DOI: 10.1093/eurheartj/ehaa410 sha: doc_id: 317928 cord_uid: doj39520 file: cache/cord-318048-6nvi63rq.json key: cord-318048-6nvi63rq authors: Arshad, Usman; Pertinez, Henry; Box, Helen; Tatham, Lee; Rajoli, Rajith KR; Curley, Paul; Neary, Megan; Sharp, Joanne; Liptrott, Neill J; Valentijn, Anthony; David, Christopher; Rannard, Steve P; O’Neill, Paul M; Aljayyoussi, Ghaith; Pennington, Shaun; Ward, Stephen A; Hill, Andrew; Back, David J; Khoo, Saye H; Bray, Patrick G; Biagini, Giancarlo A; Owen, Andrew title: Prioritisation of Anti‐SARS‐Cov‐2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics date: 2020-05-21 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.1909 sha: doc_id: 318048 cord_uid: 6nvi63rq file: cache/cord-318253-vp22xd8p.json key: cord-318253-vp22xd8p authors: Parisi, Ortensia Ilaria; Dattilo, Marco; Patitucci, Francesco; Malivindi, Rocco; Pezzi, Vincenzo; Perrotta, Ida; Ruffo, Mariarosa; Amone, Fabio; Puoci, Francesco title: “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.28.120709 sha: doc_id: 318253 cord_uid: vp22xd8p file: cache/cord-317693-l08q2lhp.json key: cord-317693-l08q2lhp authors: Jacob, Michelle Cristine Medeiros; Feitosa, Ivanilda Soares; Albuquerque, Ulysses Paulino title: Animal-based food systems are unsafe: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fosters the debate on meat consumption date: 2020-07-07 journal: Public health nutrition DOI: 10.1017/s1368980020002657 sha: doc_id: 317693 cord_uid: l08q2lhp file: cache/cord-318205-qxkel0ww.json key: cord-318205-qxkel0ww authors: Parkulo, Mark A.; Brinker, Todd M.; Bosch, Wendelyn; Palaj, Arta; DeRuyter, Marie L. title: Risk of SARS-CoV-2 Transmission Among Coworkers in a Surgical Environment date: 2020-10-22 journal: Mayo Clin Proc DOI: 10.1016/j.mayocp.2020.10.016 sha: doc_id: 318205 cord_uid: qxkel0ww file: cache/cord-318316-9unfl966.json key: cord-318316-9unfl966 authors: Ortega, Joseph T.; Zambrano, Jose L.; Jastrzebska, Beata; Liprandi, Ferdinando; Rangel, Hector R.; Pujol, Flor H. title: Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies date: 2020-10-23 journal: Intervirology DOI: 10.1159/000512141 sha: doc_id: 318316 cord_uid: 9unfl966 file: cache/cord-318036-t05ummop.json key: cord-318036-t05ummop authors: Peng, Liang; Liu, Jing; Xu, Wenxiong; Luo, Qiumin; Deng, Keji; Lin, Bingliang; Gao, Zhiliang title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples date: 2020-02-25 journal: nan DOI: 10.1101/2020.02.21.20026179 sha: doc_id: 318036 cord_uid: t05ummop file: cache/cord-318387-s4d442kx.json key: cord-318387-s4d442kx authors: Wang, Ming; Fu, Aisi; Hu, Ben; Tong, Yongqing; Liu, Ran; Gu, Jiashuang; Liu, Jianghao; Jiang, Wen; Shen, Gaigai; Zhao, Wanxu; Men, Dong; Yu, Lilei; Deng, Zixin; Li, Yan; Liu, Tiangang title: Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses date: 2020-03-06 journal: nan DOI: 10.1101/2020.03.04.20029538 sha: doc_id: 318387 cord_uid: s4d442kx file: cache/cord-318164-6rqi17oz.json key: cord-318164-6rqi17oz authors: Paoli, D.; Pallotti, F.; Nigro, G.; Aureli, A.; Perlorca, A.; Mazzuti, L.; Di Carlo, D.; Turriziani, O.; Lenzi, A.; Lombardo, F. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 journal: J Endocrinol Invest DOI: 10.1007/s40618-020-01438-8 sha: doc_id: 318164 cord_uid: 6rqi17oz file: cache/cord-318342-eipscagh.json key: cord-318342-eipscagh authors: Chen, Juan; Wu, Chunhua; Wang, Xiaohang; Yu, Jiangyi; Sun, Zilin title: The Impact of COVID-19 on Blood Glucose: A Systematic Review and Meta-Analysis date: 2020-10-05 journal: Front Endocrinol (Lausanne) DOI: 10.3389/fendo.2020.574541 sha: doc_id: 318342 cord_uid: eipscagh file: cache/cord-317786-iv1br2oj.json key: cord-317786-iv1br2oj authors: Waterfield, T.; Watson, C.; Moore, R.; Ferris, K.; Tonry, C.; Watt, A. 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D.; Ahmad, S.; Ladhani, S.; Corr, M.; McFetridge, L.; Mitchell, H.; Brown, K.; Amirthalingam, G.; Maney, J.-A.; Christie, S. title: Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study. date: 2020-09-02 journal: nan DOI: 10.1101/2020.08.31.20183095 sha: doc_id: 317786 cord_uid: iv1br2oj file: cache/cord-318126-gg68o52z.json key: cord-318126-gg68o52z authors: Zhou, Juan; Tan, Yingzheng; Li, Dan; He, Xiaojin; Yuan, Ting; Long, Yunzhu title: Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection date: 2020-04-03 journal: J Infect DOI: 10.1016/j.jinf.2020.03.028 sha: doc_id: 318126 cord_uid: gg68o52z file: cache/cord-318239-2sraqm6e.json key: cord-318239-2sraqm6e authors: Phan, Lan T.; Nguyen, Thuong V.; Huynh, Loan K.T.; Dao, Manh H.; Vo, Tho A.N.; Vu, Nhung H.P.; Pham, Hang T.T.; Nguyen, Hieu T.; Nguyen, Thuc T.; Le, Hung Q.; Nguyen, Thinh V.; Nguyen, Quan H.; Huynh, Thao P.; Nguyen, Sang N.; Nguyen, Anh H.; Nguyen, Ngoc T.; Nguyen, Thao N.T.; Nguyen, Long T.; Luong, Quang C.; Cao, Thang M.; Pham, Quang D. title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam date: 2020-05-28 journal: J Med Virol DOI: 10.1002/jmv.26075 sha: doc_id: 318239 cord_uid: 2sraqm6e file: cache/cord-318339-j35w1vsw.json key: cord-318339-j35w1vsw authors: Stockman, Lauren J; Bellamy, Richard; Garner, Paul title: SARS: Systematic Review of Treatment Effects date: 2006-09-12 journal: PLoS Med DOI: 10.1371/journal.pmed.0030343 sha: doc_id: 318339 cord_uid: j35w1vsw file: cache/cord-318426-kv7aa0og.json key: cord-318426-kv7aa0og authors: Kritsotakis, Evangelos I. title: On the importance of population-based serological surveys of SARS-CoV-2 without overlooking their inherent uncertainties date: 2020-05-22 journal: nan DOI: 10.1016/j.puhip.2020.100013 sha: doc_id: 318426 cord_uid: kv7aa0og file: cache/cord-318069-logh6rnu.json key: cord-318069-logh6rnu authors: Ordás, Carlos M.; Villacieros-Álvarez, Javier; Pastor-Vivas, Ana-Isabel; Corrales-Benítez, Álvaro title: Concurrent tonic pupil and trochlear nerve palsy in COVID-19 date: 2020-09-10 journal: J Neurovirol DOI: 10.1007/s13365-020-00909-1 sha: doc_id: 318069 cord_uid: logh6rnu file: cache/cord-318499-uihof6k6.json key: cord-318499-uihof6k6 authors: Beddingfield, Brandon; Iwanaga, Naoki; Zheng, Wenshu; Roy, Chad J.; Hu, Tony Y.; Kolls, Jay; Bix, Gregory title: The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.15.153387 sha: doc_id: 318499 cord_uid: uihof6k6 file: cache/cord-317863-xf0bn3cv.json key: cord-317863-xf0bn3cv authors: Pata, Ramakanth; Kiani, Roudabeh; Ahmady, Abolfazl; Awad, Vanessa M title: Probability of COVID-19 Being the Culprit in Neurocognitive Deception: A Case Series of Incidental Strokes in ICU Patients With COVID-19 date: 2020-08-18 journal: Cureus DOI: 10.7759/cureus.9857 sha: doc_id: 317863 cord_uid: xf0bn3cv file: cache/cord-318444-sgm24q1i.json key: cord-318444-sgm24q1i authors: Walter, Justin D.; Hutter, Cedric A.J.; Zimmermann, Iwan; Wyss, Marianne; Earp, Jennifer; Egloff, Pascal; Sorgenfrei, Michèle; Hürlimann, Lea M.; Gonda, Imre; Meier, Gianmarco; Remm, Sille; Thavarasah, Sujani; Plattet, Philippe; Seeger, Markus A. title: Sybodies targeting the SARS-CoV-2 receptor-binding domain date: 2020-05-16 journal: bioRxiv DOI: 10.1101/2020.04.16.045419 sha: doc_id: 318444 cord_uid: sgm24q1i file: cache/cord-318920-njurbf3d.json key: cord-318920-njurbf3d authors: Romana Ponziani, Francesca; Del Zompo, Fabio; Nesci, Antonio; Santopaolo, Francesco; Ianiro, Gianluca; Pompili, Maurizio; Gasbarrini, Antonio title: Liver involvement is not associated with mortality: results from a large cohort of SARS‐CoV‐2 positive patients date: 2020-07-06 journal: Aliment Pharmacol Ther DOI: 10.1111/apt.15996 sha: doc_id: 318920 cord_uid: njurbf3d file: cache/cord-317795-689at1qx.json key: cord-317795-689at1qx authors: Bielicki, Julia A; Duval, Xavier; Gobat, Nina; Goossens, Herman; Koopmans, Marion; Tacconelli, Evelina; van der Werf, Sylvie title: Monitoring approaches for health-care workers during the COVID-19 pandemic date: 2020-07-23 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30458-8 sha: doc_id: 317795 cord_uid: 689at1qx file: cache/cord-318184-atlslk0e.json key: cord-318184-atlslk0e authors: Germain, N.; Herwegh, S.; Hatzfeld, A. 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M.; Marchetti, P. title: Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France date: 2020-09-11 journal: nan DOI: 10.1101/2020.09.11.20192518 sha: doc_id: 318184 cord_uid: atlslk0e file: cache/cord-318738-7dgbc4um.json key: cord-318738-7dgbc4um authors: Schmidt, Marco Florian; Isidro‐Llobet, Albert; Lisurek, Michael; El‐Dahshan, Adeeb; Tan, Jinzhi; Hilgenfeld, Rolf; Rademann, Jörg title: Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening date: 2008-03-17 journal: Angew Chem Int Ed Engl DOI: 10.1002/anie.200704594 sha: doc_id: 318738 cord_uid: 7dgbc4um file: cache/cord-318766-vx0dnnxh.json key: cord-318766-vx0dnnxh authors: Wendt, Ralph; Nagel, Stephan; Nickel, Olaf; Wolf, Johannes; Kalbitz, Sven; Kaiser, Thorsten; Borte, Stephan; Lübbert, Christoph title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany date: 2020-06-03 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.268 sha: doc_id: 318766 cord_uid: vx0dnnxh file: cache/cord-318006-9op556q2.json key: cord-318006-9op556q2 authors: Luo, Y. 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A. title: Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa date: 2020-07-11 journal: nan DOI: 10.1101/2020.07.07.20146332 sha: doc_id: 318483 cord_uid: il5aq8py file: cache/cord-318478-fn0gcxbb.json key: cord-318478-fn0gcxbb authors: Ziv, Omer; Price, Jonathan; Shalamova, Lyudmila; Kamenova, Tsveta; Goodfellow, Ian; Weber, Friedemann; Miska, Eric A. title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.07.19.211110 sha: doc_id: 318478 cord_uid: fn0gcxbb file: cache/cord-319100-3gdawhfn.json key: cord-319100-3gdawhfn authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 journal: bioRxiv DOI: 10.1101/2020.06.09.142323 sha: doc_id: 319100 cord_uid: 3gdawhfn file: cache/cord-318029-xd7nuahh.json key: cord-318029-xd7nuahh authors: Ke, Chunjin; Wang, Yufeng; Zeng, Xing; Yang, Chunguang; Hu, Zhiquan title: 2019 novel coronavirus disease (COVID-19) in hemodialysis patients: a report of two cases date: 2020-04-30 journal: Clin Biochem DOI: 10.1016/j.clinbiochem.2020.04.008 sha: doc_id: 318029 cord_uid: xd7nuahh file: cache/cord-318715-p6agoqu8.json key: cord-318715-p6agoqu8 authors: Belser, Jessica A title: Assessment of SARS-CoV-2 replication in the context of other respiratory viruses date: 2020-05-07 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30227-7 sha: doc_id: 318715 cord_uid: p6agoqu8 file: cache/cord-318944-13zk6cco.json key: cord-318944-13zk6cco authors: Bizzoca, Maria Eleonora; Campisi, Giuseppina; Lo Muzio, Lorenzo title: Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date: 2020-05-27 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17113793 sha: doc_id: 318944 cord_uid: 13zk6cco file: cache/cord-319022-1twsxzcd.json key: cord-319022-1twsxzcd authors: Desai, Antonio; Voza, Giuseppe; Paiardi, Silvia; Teofilo, Francesca Ilaria; Caltagirone, Giuseppe; Pons, Marta Ripoll; Aloise, Monia; Kogan, Maria; Tommasini, Tobia; Savevski, Victor; Stefanini, Giulio; Angelini, Claudio; Ciccarelli, Michele; Badalamenti, Salvatore; De Nalda, Ana Lleo; Aghemo, Alessio; Cecconi, Maurizio; Boneschi, Filippo Martinelli; Voza, Antonio title: The role of anti-hypertensive treatment, comorbidities and early introduction of LMWH in the setting of COVID-19: A retrospective, observational study in Northern Italy() date: 2020-09-25 journal: Int J Cardiol DOI: 10.1016/j.ijcard.2020.09.062 sha: doc_id: 319022 cord_uid: 1twsxzcd file: cache/cord-319236-gxcs77pl.json key: cord-319236-gxcs77pl authors: Chen, Qingyan title: Can we migrate COVID-19 spreading risk? date: 2020-08-28 journal: Front Environ Sci Eng DOI: 10.1007/s11783-020-1328-8 sha: doc_id: 319236 cord_uid: gxcs77pl file: cache/cord-318786-qd0k8174.json key: cord-318786-qd0k8174 authors: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 journal: Sensors (Basel) DOI: 10.3390/s20174745 sha: doc_id: 318786 cord_uid: qd0k8174 file: cache/cord-318789-ylxh8vi2.json key: cord-318789-ylxh8vi2 authors: Byrne, R. 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J.; Milette, S.; Noorah, N.; Guay-Belzile, M.; Spicer, J.; Daneshtalab, N.; Sirois, M.; Tremblay, K.; Emad, A.; Rousseau, S. title: A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date: 2020-07-02 journal: nan DOI: 10.1101/2020.07.01.20144121 sha: doc_id: 319519 cord_uid: mb9ofh12 file: cache/cord-319590-f9qcabcx.json key: cord-319590-f9qcabcx authors: Han, Yanxiao; Král, Petr title: Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date: 2020-04-14 journal: ACS Nano DOI: 10.1021/acsnano.0c02857 sha: doc_id: 319590 cord_uid: f9qcabcx file: cache/cord-319273-ok2p1h9f.json key: cord-319273-ok2p1h9f authors: Lai, Yu-Ju; Chang, Chia-Ming; Lina,, Chi-Kung; Yang, Yi-Ping; Chien, Chian-Shiu; Wang, Peng-Hui; Changa, Cheng-Chang title: Severe acute respiratory syndrome coronavirus-2 and the deduction effect of angiotensin-converting enzyme 2 in pregnancy date: 2020-08-17 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000362 sha: doc_id: 319273 cord_uid: ok2p1h9f file: cache/cord-319540-kivk3h1k.json key: cord-319540-kivk3h1k authors: Uhe, Tobias; Hagendorff, Andreas; Wachter, Rolf; Laufs, Ulrich title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy date: 2020-07-13 journal: Clin Res Cardiol DOI: 10.1007/s00392-020-01706-w sha: doc_id: 319540 cord_uid: kivk3h1k file: cache/cord-319555-pccqo36g.json key: cord-319555-pccqo36g authors: Beggs, Clive B.; Avital, Eldad J. title: Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study date: 2020-10-13 journal: PeerJ DOI: 10.7717/peerj.10196 sha: doc_id: 319555 cord_uid: pccqo36g file: cache/cord-319571-fspmgg4s.json key: cord-319571-fspmgg4s authors: Sehailia, Moussa; Chemat, Smain title: Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 date: 2020-07-22 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1796809 sha: doc_id: 319571 cord_uid: fspmgg4s file: cache/cord-319706-2e9jrv0s.json key: cord-319706-2e9jrv0s authors: Ebinger, Joseph E.; Achamallah, Natalie; Ji, Hongwei; Claggett, Brian L.; Sun, Nancy; Botting, Patrick; Nguyen, Trevor-Trung; Luong, Eric; Kim, Elizabeth H.; Park, Eunice; Liu, Yunxian; Rosenberry, Ryan; Matusov, Yuri; Zhao, Steven; Pedraza, Isabel; Zaman, Tanzira; Thompson, Michael; Raedschelders, Koen; Berg, Anders H.; Grein, Jonathan D.; Noble, Paul W.; Chugh, Sumeet S.; Bairey Merz, C. Noel; Marbán, Eduardo; Van Eyk, Jennifer E.; Solomon, Scott D.; Albert, Christine M.; Chen, Peter; Cheng, Susan title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0236240 sha: doc_id: 319706 cord_uid: 2e9jrv0s file: cache/cord-319749-je0l22l5.json key: cord-319749-je0l22l5 authors: Lippi, Alice; Domingues, Renato; Setz, Cristian; Outeiro, Tiago F.; Krisko, Anita title: SARS‐CoV‐2: At the Crossroad Between Aging and Neurodegeneration date: 2020-04-24 journal: Mov Disord DOI: 10.1002/mds.28084 sha: doc_id: 319749 cord_uid: je0l22l5 file: cache/cord-319469-fkuqs3ie.json key: cord-319469-fkuqs3ie authors: Ray, A.; Singh, K.; Chattopadhyay, S.; Mehdi, F.; Batra, G.; Gupta, A.; Agarwal, A.; M, B.; Sahni, S.; R, C.; Agarwal, S.; Nagpal, C.; B H, G.; Arora, U.; Sharma, K. K.; Singh Jadon, R.; Datt Upadhyay, A.; Nischal, N.; Vikram, N. K.; Soneja, M.; Pandey, R. 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IUPHAR Review 29 date: 2020-05-01 journal: Br J Pharmacol DOI: 10.1111/bph.15094 sha: doc_id: 319780 cord_uid: rfj9t99r file: cache/cord-319876-psilbis0.json key: cord-319876-psilbis0 authors: Zhu, Jian; Wu, Yabin title: COVID-19 Epidemic: Clinical Characteristics of Patients in Pediatric Isolation Ward date: 2020-07-09 journal: Clin Pediatr (Phila) DOI: 10.1177/0009922820941228 sha: doc_id: 319876 cord_uid: psilbis0 file: cache/cord-319900-16osnnga.json key: cord-319900-16osnnga authors: Arcadepani, Felipe B.; Tardelli, Vitor S.; Fidalgo, Thiago M. title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil date: 2020-07-02 journal: Int J Drug Policy DOI: 10.1016/j.drugpo.2020.102835 sha: doc_id: 319900 cord_uid: 16osnnga file: cache/cord-319930-ymqnb54a.json key: cord-319930-ymqnb54a authors: Kremer, Stéphane; Lersy, François; de Sèze, Jérome; Ferré, Jean-Christophe; Maamar, Adel; Carsin-Nicol, Béatrice; Collange, Olivier; Bonneville, Fabrice; Adam, Gilles; Martin-Blondel, Guillaume; Rafiq, Marie; Geeraerts, Thomas; Delamarre, Louis; Grand, Sylvie; Krainik, Alexandre; Caillard, Sophie; Marc Constans, Jean; Metanbou, Serge; Heintz, Adrien; Helms, Julie; Schenck, Maleka; Lefèbvre, Nicolas; Boutet, Claire; Fabre, Xavier; Forestier, Géraud; de Beaurepaire, Isaure; Bornet, Grégoire; Lacalm, Audrey; Oesterlé, Hélène; Bolognini, Federico; Messie, Julien; Hmeydia, Ghazi; Benzakoun, Joseph; Oppenheim, Catherine; Bapst, Blanche; Megdiche, Imen; Henri-Feugeas, Marie-Cécile; Khalil, Antoine; Gaudemer, Augustin; Jager, Lavinia; Nesser, Patrick; Talla Mba, Yannick; Hemmert, Céline; Feuerstein, Philippe; Sebag, Nathan; Carré, Sophie; Alleg, Manel; Lecocq, Claire; Schmitt, Emmanuelle; Anxionnat, René; Zhu, François; Comby, Pierre-Olivier; Ricolfi, Frédéric; Thouant, Pierre; Desal, Hubert; Boulouis, Grégoire; Berge, Jérome; Kazémi, Apolline; Pyatigorskaya, Nadya; Lecler, Augustin; Saleme, Suzana; Edjlali-Goujon, Myriam; Kerleroux, Basile; Zorn, Pierre-Emmanuel; Mathieu, Muriel; Baloglu, Seyyid; Ardellier, François-Daniel; Willaume, Thibault; Brisset, Jean Christophe; Boulay, Clotilde; Mutschler, Véronique; Hansmann, Yves; Mertes, Paul-Michel; Schneider, Francis; Fafi-Kremer, Samira; Ohana, Mickael; Meziani, Ferhat; David, Jean-Stéphane; Meyer, Nicolas; Anheim, Mathieu; Cotton, Pr François title: Brain MRI Findings in Severe COVID-19: A Retrospective Observational Study date: 2020-06-16 journal: Radiology DOI: 10.1148/radiol.2020202222 sha: doc_id: 319930 cord_uid: ymqnb54a file: cache/cord-319864-t6ql9hz2.json key: cord-319864-t6ql9hz2 authors: Lima, Amorce; Healer, Vicki; Vendrone, Elaine; Silbert, Suzane title: Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens date: 2020-11-11 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104688 sha: doc_id: 319864 cord_uid: t6ql9hz2 file: cache/cord-319855-78xmxymu.json key: cord-319855-78xmxymu authors: BR, Bharath; Damle, Hrishikesh; Ganju, Shiban; Damle, Latha title: In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19 date: 2020-07-01 journal: F1000Res DOI: 10.12688/f1000research.24143.1 sha: doc_id: 319855 cord_uid: 78xmxymu file: cache/cord-320087-iu4ulxtu.json key: cord-320087-iu4ulxtu authors: Lampe, Anne; Winschel, Alexander; Lang, Cornelie; Steiner, Thorsten title: Guillain-Barré syndrome and SARS-CoV-2 date: 2020-07-08 journal: Neurol Res Pract DOI: 10.1186/s42466-020-00066-0 sha: doc_id: 320087 cord_uid: iu4ulxtu file: cache/cord-319964-ju9japd8.json key: cord-319964-ju9japd8 authors: Lu, Jing; Plessis, Louis du; Liu, Zhe; Hill, Verity; Kang, Min; Lin, Huifang; Sun, Jiufeng; Francois, Sarah; Kraemer, Moritz U G; Faria, Nuno R; McCrone, John T; Peng, Jinju; Xiong, Qianling; Yuan, Runyu; Zeng, Lilian; Zhou, Pingping; Liang, Chuming; Yi, Lina; Liu, Jun; Xiao, Jianpeng; Hu, Jianxiong; Liu, Tao; Ma, Wenjun; Li, Wei; Su, Juan; Zheng, Huanying; Peng, Bo; Fang, Shisong; Su, Wenzhe; Li, Kuibiao; Sun, Ruilin; Bai, Ru; Tang, Xi; Liang, Minfeng; Quick, Josh; Song, Tie; Rambaut, Andrew; Loman, Nick; Raghwani, Jayna; Pybus, Oliver; Ke, Changwen title: Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China date: 2020-04-04 journal: nan DOI: 10.1101/2020.04.01.20047076 sha: doc_id: 319964 cord_uid: ju9japd8 file: cache/cord-319935-ni6a8vje.json key: cord-319935-ni6a8vje authors: Somsen, G. 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Niederman, Michael S. title: The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security date: 2020-04-09 journal: Curr Opin Pulm Med DOI: 10.1097/mcp.0000000000000676 sha: doc_id: 320646 cord_uid: xk77u4g0 file: cache/cord-320619-r466dc5t.json key: cord-320619-r466dc5t authors: Chand Dakal, Tikam title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 date: 2020-11-05 journal: Immunobiology DOI: 10.1016/j.imbio.2020.152021 sha: doc_id: 320619 cord_uid: r466dc5t file: cache/cord-320587-936cavob.json key: cord-320587-936cavob authors: Ruscio, M.; D'Agnolo, E.; Belgrano, A.; Plebani, M.; Lippi, G. title: Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay date: 2020-11-07 journal: nan DOI: 10.1101/2020.11.05.20226555 sha: doc_id: 320587 cord_uid: 936cavob file: cache/cord-320717-wk4zxmz9.json key: cord-320717-wk4zxmz9 authors: Li, Yang; 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M.; Valdovinos-Diaz, M. A.; Viebig, R.; Defilippi, C.; Bustos-Fernández, L. M.; Sole, L.; Hani-Amador, A. C. title: Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. 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Canales title: No transmission of SARS-CoV-2 in a patient undergoing allogeneic Hematopoietic Cell Transplantation from a matched-related donor with unknown COVID-19 date: 2020-08-24 journal: Transfus Apher Sci DOI: 10.1016/j.transci.2020.102921 sha: doc_id: 321380 cord_uid: e5zq15hz file: cache/cord-321235-h3w8827o.json key: cord-321235-h3w8827o authors: Cabrera Alvargonzalez, Jorge Julio; Rey Cao, Sonia; Pérez Castro, Sonia; Martinez Lamas, Lucía; Cores Calvo, Olaia; Torres Piñon, Julio; Porteiro Fresco, Jacobo; Garcia Comesaña, Julio; Regueiro Garcia, Benito title: Pooling for SARS-CoV-2 control in care institutions date: 2020-10-12 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05446-0 sha: doc_id: 321235 cord_uid: h3w8827o file: cache/cord-321267-ihd30qi0.json key: cord-321267-ihd30qi0 authors: Daughton, Christian G. title: Natural experiment concept to accelerate the Re-purposing of existing therapeutics for Covid-19 date: 2020-05-15 journal: Glob Epidemiol DOI: 10.1016/j.gloepi.2020.100026 sha: doc_id: 321267 cord_uid: ihd30qi0 file: cache/cord-321369-xzu2faol.json key: cord-321369-xzu2faol authors: Andreano, Emanuele; Nicastri, Emanuele; Paciello, Ida; Pileri, Piero; Manganaro, Noemi; Piccini, Giulia; Manenti, Alessandro; Pantano, Elisa; Kabanova, Anna; Troisi, Marco; Vacca, Fabiola; Cardamone, Dario; De Santi, Concetta; Benincasa, Linda; Agrati, Chiara; Capobianchi, Maria Rosaria; Castilletti, Concetta; Emiliozzi, Arianna; Fabbiani, Massimiliano; Montagnani, Francesca; Depau, Lorenzo; Brunetti, Jlenia; Bracci, Luisa; Montomoli, Emanuele; Sala, Claudia; Ippolito, Giuseppe; Rappuoli, Rino title: Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.10.07.328302 sha: doc_id: 321369 cord_uid: xzu2faol file: cache/cord-321549-r7bmtloy.json key: cord-321549-r7bmtloy authors: Jendrny, Paula; Schulz, Claudia; Twele, Friederike; Meller, Sebastian; von Köckritz-Blickwede, Maren; Osterhaus, Albertus Dominicus Marcellinus Erasmus; Ebbers, Janek; Pilchová, Veronika; Pink, Isabell; Welte, Tobias; Manns, Michael Peter; Fathi, Anahita; Ernst, Christiane; Addo, Marylyn Martina; Schalke, Esther; Volk, Holger Andreas title: Scent dog identification of samples from COVID-19 patients – a pilot study date: 2020-07-23 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05281-3 sha: doc_id: 321549 cord_uid: r7bmtloy file: cache/cord-321358-plxz5mkg.json key: cord-321358-plxz5mkg authors: Zheng, Jun title: SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat date: 2020-03-15 journal: Int J Biol Sci DOI: 10.7150/ijbs.45053 sha: doc_id: 321358 cord_uid: plxz5mkg file: cache/cord-320632-369kax2m.json key: cord-320632-369kax2m authors: Song, Yang; Zhang, Min; Yin, Ling; Wang, Kunkun; Zhou, Yiyi; Zhou, Mi; Lu, Yun title: COVID-19 Treatment: Close to a Cure? – A Rapid Review of Pharmacotherapies for the Novel Coronavirus date: 2020-07-04 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.106080 sha: doc_id: 320632 cord_uid: 369kax2m file: cache/cord-321552-lsz1onrj.json key: cord-321552-lsz1onrj authors: Membrilla, Javier A.; de Lorenzo, Íñigo; Sastre, María; Díaz de Terán, Javier title: Headache as a Cardinal Symptom of Coronavirus Disease 2019: A Cross‐Sectional Study date: 2020-09-28 journal: Headache DOI: 10.1111/head.13967 sha: doc_id: 321552 cord_uid: lsz1onrj file: cache/cord-320831-owfnttqr.json key: cord-320831-owfnttqr authors: Klimek, Ludger; Pfaar, Oliver; Worm, Margitta; Bergmann, Karl-Christian; Bieber, Thomas; Buhl, Roland; Buters, Jeroen; Darsow, Ulf; Keil, Thomas; Kleine-Tebbe, Jörg; Lau, Susanne; Maurer, Marcus; Merk, Hans; Mösges, Ralph; Saloga, Joachim; Staubach, Petra; Stute, Petra; Rabe, Klaus; Rabe, Uta; Vogelmeier, Claus; Biedermann, Tilo; Jung, Kirsten; Schlenter, Wolfgang; Ring, Johannes; Chaker, Adam; Wehrmann, Wolfgang; Becker, Sven; Mülleneisen, Norbert; Nemat, Katja; Czech, Wofgang; Wrede, Holger; Brehler, Randolf; Fuchs, Thomas; Tomazic, Peter-Valentin; Aberer, Werner; Fink-Wagner, Antje; Horak, Friedrich; Wöhrl, Stefan; Niederberger-Leppin, Verena; Pali-Schöll, Isabella; Pohl, Wolfgang; Roller-Wirnsberger, Regina; Spranger, Otto; Valenta, Rudolf; Akdis, Mübecell; Akdis, Cezmi; Hoffmann-Sommergruber, Karin; Jutel, Marek; Matricardi, Paolo; Spertin, FranÇois; Khaltaev, Nikolai; Michel, Jean-Pierre; Nicod, Laurent; Schmid-Grendelmeier, Peter; Hamelmann, Eckard; Jakob, Thilo; Werfel, Thomas; Wagenmann, Martin; Taube, Christian; Gerstlauer, Michael; Vogelberg, Christian; Bousquet, Jean; Zuberbier, Torsten title: Allergen immunotherapy in the current COVID-19 pandemic: A position paper of AeDA, ARIA, EAACI, DGAKI and GPA: Position paper of the German ARIA Group(A) in cooperation with the Austrian ARIA Group(B), the Swiss ARIA Group(C), German Society for Applied Allergology (AEDA)(D), German Society for Allergology and Clinical Immunology (DGAKI)(E), Society for Pediatric Allergology (GPA)(F) in cooperation with AG Clinical Immunology, Allergology and Environmental Medicine of the DGHNO-KHC(G) and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-05-28 journal: Allergol Select DOI: 10.5414/alx02147e sha: doc_id: 320831 cord_uid: owfnttqr file: cache/cord-321468-nkl2mls8.json key: cord-321468-nkl2mls8 authors: Yang, Mo; Ng, Margaret H.L.; Li, Chi Kong; Chan, Paul K.S.; Liu, Chang; Ye, Jie Yu; Chong, Beng H. title: Thrombopoietin levels increased in patients with severe acute respiratory syndrome date: 2008-03-07 journal: Thromb Res DOI: 10.1016/j.thromres.2007.12.021 sha: doc_id: 321468 cord_uid: nkl2mls8 file: cache/cord-321564-6950p8i9.json key: cord-321564-6950p8i9 authors: Wang, Shiu‐Mei; Huang, Kuo‐Jung; Wang, Chin‐Tien title: Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date: 2019-07-10 journal: J Med Virol DOI: 10.1002/jmv.25518 sha: doc_id: 321564 cord_uid: 6950p8i9 file: cache/cord-321624-z2mntwef.json key: cord-321624-z2mntwef authors: Kowitdamrong, Ekasit; Puthanakit, Thanyawee; Jantarabenjakul, Watsamon; Prompetchara, Eakachai; Suchartlikitwong, Pintip; Putcharoen, Opass; Hirankarn, Nattiya title: Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date: 2020-10-09 journal: PLoS One DOI: 10.1371/journal.pone.0240502 sha: doc_id: 321624 cord_uid: z2mntwef file: cache/cord-321603-lbbsnriv.json key: cord-321603-lbbsnriv authors: Rao, Mohan; Rashid, Fairuz A; Sabri, Fashihah S A H; Jamil, Nur Nadia; Zain, Rozainanee; Hashim, Rohaidah; Amran, Fairuz; Kok, Huey Tean; Samad, Md Anuar Abd; Ahmad, Norazah title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date: 2020-08-06 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1156 sha: doc_id: 321603 cord_uid: lbbsnriv file: cache/cord-321670-f2d4bykp.json key: cord-321670-f2d4bykp authors: Longardt, Ann Carolin; Winkler, Vincent Patrick; Pecks, Ulrich title: Perinatale Aspekte der SARS-CoV-2 Infektion date: 2020-08-24 journal: Z Geburtshilfe Neonatol DOI: 10.1055/a-1192-7437 sha: doc_id: 321670 cord_uid: f2d4bykp file: cache/cord-321580-3ru92tra.json key: cord-321580-3ru92tra authors: Hadler, James L title: Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? 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Bixby, Billie; Parthasarathy, Sairam; Chaudhary, Sachin; Natt, Bhupinder; Cristan, Elaine; El Aini, Tammer; Rischard, Franz; Campion, Janet; Chopra, Madhav; Insel, Michael; Sam, Afshin; Knepler, James L.; Capaldi, Andrew P.; Spier, Catherine M.; Dake, Michael D.; Edwards, Taylor; Kaplan, Matthew E.; Scott, Serena Jain; Hypes, Cameron; Mosier, Jarrod; Harris, David T.; LaFleur, Bonnie J.; Sprissler, Ryan; Nikolich-Žugich, Janko; Bhattacharya, Deepta title: Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date: 2020-10-14 journal: Immunity DOI: 10.1016/j.immuni.2020.10.004 sha: doc_id: 321854 cord_uid: cy8vyb6j file: cache/cord-321855-7b1c2xdh.json key: cord-321855-7b1c2xdh authors: Alshami, Alanoud; Alattas, Rabab; Anan, Hadeel; Alhalimi, Abdulbary; Alfaraj, Ahmed; Al Qahtani, Hadi title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0241258 sha: doc_id: 321855 cord_uid: 7b1c2xdh file: cache/cord-321858-c5m4dj9m.json key: cord-321858-c5m4dj9m authors: Yoshizawa, Shin-ichiro; 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Richard; McClelland, Ian W.; Silverman, Alexis C.; Burgess, Robert J. title: Loss of Paramedic Availability in an Urban Emergency Medical Services System during a Severe Acute Respiratory Syndrome Outbreak date: 2008-06-28 journal: Acad Emerg Med DOI: 10.1197/j.aem.2004.03.021 sha: doc_id: 322148 cord_uid: sfr9twfa file: cache/cord-322204-kc7dy2za.json key: cord-322204-kc7dy2za authors: Khalil, Asma; Hill, Robert; Wright, Alison; Ladhani, Shamez; O’Brien, Pat title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date: 2020-08-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa893 sha: doc_id: 322204 cord_uid: kc7dy2za file: cache/cord-322141-4a81mapc.json key: cord-322141-4a81mapc authors: Rizzo, Emanuele; Carlà, Simona; Ruggeri, Salvatore title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government date: 2020-09-09 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100516 sha: doc_id: 322141 cord_uid: 4a81mapc file: cache/cord-322087-gj5mfzxz.json key: cord-322087-gj5mfzxz authors: de Sanctis, Vincenzo; Ruggiero, Leopoldo; Soliman, Ashraf T; Daar, Shahina; Di Maio, Salvatore; Kattamis, Christos title: Coronavirus Disease 2019 (COVID-19) in adolescents: An update on current clinical and diagnostic characteristics date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9543 sha: doc_id: 322087 cord_uid: gj5mfzxz file: cache/cord-322388-c2nymio9.json key: cord-322388-c2nymio9 authors: Manopo, Ivanus; Lu, Liqun; He, Qigai; Chee, Li Lian; Chan, Shzu-Wei; Kwang, Jimmy title: Evaluation of a safe and sensitive Spike protein-based immunofluorescence assay for the detection of antibody responses to SARS-CoV date: 2005-01-31 journal: Journal of Immunological Methods DOI: 10.1016/j.jim.2004.10.012 sha: doc_id: 322388 cord_uid: c2nymio9 file: cache/cord-322102-4fi0y96f.json key: cord-322102-4fi0y96f authors: Zimmermann, Matthias; Nkenke, Emeka title: Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic date: 2020-04-04 journal: J Craniomaxillofac Surg DOI: 10.1016/j.jcms.2020.03.011 sha: doc_id: 322102 cord_uid: 4fi0y96f file: cache/cord-322184-kgv9f58a.json key: cord-322184-kgv9f58a authors: Sohn, Yujin; Jeong, Su Jin; Chung, Won Suk; Hyun, Jong Hoon; Baek, Yae Jee; Cho, Yunsuk; Kim, Jung Ho; Ahn, Jin Young; Choi, Jun Yong; Yeom, Joon-Sup title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 journal: J Clin Med DOI: 10.3390/jcm9092924 sha: doc_id: 322184 cord_uid: kgv9f58a file: cache/cord-322329-zqjiiy4l.json key: cord-322329-zqjiiy4l authors: Liu, Chunyu; Li, Xiuhua; Zhang, Chuntao; Xu, Sihong; Shao, Yiming; Zhuang, Hui; Che, Xiaoyan; Qiu, Yan; Yin, Hongzhang; Li, Defu; Wang, Youchun title: Establishment of a reference panel for the detection of anti-SARS-CoV antibodies date: 2007-06-30 journal: Biologicals DOI: 10.1016/j.biologicals.2006.11.001 sha: doc_id: 322329 cord_uid: zqjiiy4l file: cache/cord-322212-8xrehbd1.json key: cord-322212-8xrehbd1 authors: Wang, Hanyin; Das, Subhraleena; Wieruszewski, Patrick M.; Taji, Jamil; Bartlett, Brian; Azad, Nabila; Chowdhury, Arnab; Kolar, Gururaj; Jain, Nitesh; Subla, Mir R.; Khan, Syed Anjum title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock date: 2020-04-23 journal: Chest DOI: 10.1016/j.chest.2020.04.015 sha: doc_id: 322212 cord_uid: 8xrehbd1 file: cache/cord-322051-89wgv100.json key: cord-322051-89wgv100 authors: Tanasa, Ingrid Andrada; Manciuc, Carmen; Carauleanu, Alexandru; Navolan, Dan Bogdan; Bohiltea, Roxana Elena; Nemescu, Dragos title: Anosmia and ageusia associated with coronavirus infection (COVID-19) - what is known? date: 2020-05-28 journal: Exp Ther Med DOI: 10.3892/etm.2020.8808 sha: doc_id: 322051 cord_uid: 89wgv100 file: cache/cord-322417-9e95m4kz.json key: cord-322417-9e95m4kz authors: Segovia-Juarez, Jose; Castagnetto, Jesús M.; Gonzales, Gustavo F. title: High altitude reduces infection rate of COVID-19 but not case-fatality rate date: 2020-07-15 journal: Respir Physiol Neurobiol DOI: 10.1016/j.resp.2020.103494 sha: doc_id: 322417 cord_uid: 9e95m4kz file: cache/cord-322503-fynprt6f.json key: cord-322503-fynprt6f authors: Thakur, Aarzoo; Tan, Shawn Pei Feng; Chan, James Chun Yip title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.2014 sha: doc_id: 322503 cord_uid: fynprt6f file: cache/cord-322473-fmob6k0q.json key: cord-322473-fmob6k0q authors: Charpiat, Bruno; Bleyzac, Nathalie; Tod, Michel title: Proton Pump Inhibitors are Risk Factors for Viral Infections: Even for COVID-19? date: 2020-08-10 journal: Clin Drug Investig DOI: 10.1007/s40261-020-00963-x sha: doc_id: 322473 cord_uid: fmob6k0q file: cache/cord-322007-xy66t0ls.json key: cord-322007-xy66t0ls authors: Humbert, S; Razanamahery, J; Payet-Revest, C; Bouiller, K; Chirouze, C title: COVID-19 as a cause of immune thrombocytopenia date: 2020-05-20 journal: Med Mal Infect DOI: 10.1016/j.medmal.2020.05.003 sha: doc_id: 322007 cord_uid: xy66t0ls file: cache/cord-322345-rq5gh710.json key: cord-322345-rq5gh710 authors: Zheng, Fang; Zhou, Yanwen; Zhou, Zhiguo; Ye, Fei; Huang, Baoying; Huang, Yaxiong; Ma, Jing; Zuo, Qi; Tan, Xin; Xie, Jun; Niu, Peihua; Wang, Wenlong; Xu, Yun; Peng, Feng; Zhou, Ning; Cai, Chunlin; Tang, Wei; Xiao, Xinqiang; Li, Yi; Zhou, Zhiguang; Jiang, Yongfang; Xie, Yuanlin; Tan, Wenjie; Gong, Guozhong title: A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19 date: 2020-04-29 journal: nan DOI: 10.1101/2020.04.24.20077735 sha: doc_id: 322345 cord_uid: rq5gh710 file: cache/cord-322451-cwpz4akv.json key: cord-322451-cwpz4akv authors: Hsin, Dena Hsin-Chen; Macer, Darryl R.J. title: Heroes of SARS: professional roles and ethics of health care workers date: 2004-07-27 journal: J Infect DOI: 10.1016/j.jinf.2004.06.005 sha: doc_id: 322451 cord_uid: cwpz4akv file: cache/cord-322009-0cwljo0c.json key: cord-322009-0cwljo0c authors: Ma, Ling; Wang, Wenjing; Le Grange, Jehane Michael; Wang, Xiaorong; Du, Shuaixian; Li, Chen; Wei, Jia; Zhang, Jin-Nong title: Coinfection of SARS-CoV-2 and Other Respiratory Pathogens date: 2020-08-26 journal: Infect Drug Resist DOI: 10.2147/idr.s267238 sha: doc_id: 322009 cord_uid: 0cwljo0c file: cache/cord-322348-8opy5z9h.json key: cord-322348-8opy5z9h authors: Morelli, Mara; Cattelino, Elena; Baiocco, Roberto; Trumello, Carmen; Babore, Alessandra; Candelori, Carla; Chirumbolo, Antonio title: Parents and Children During the COVID-19 Lockdown: The Influence of Parenting Distress and Parenting Self-Efficacy on Children’s Emotional Well-Being date: 2020-10-06 journal: Front Psychol DOI: 10.3389/fpsyg.2020.584645 sha: doc_id: 322348 cord_uid: 8opy5z9h file: cache/cord-322446-ddv86eoy.json key: cord-322446-ddv86eoy authors: Sharma, Kulbhushan; Åkerström, Sara; Sharma, Anuj Kumar; Chow, Vincent T. K.; Teow, Shumein; Abrenica, Bernard; Booth, Stephanie A.; Booth, Timothy F.; Mirazimi, Ali; Lal, Sunil K. title: SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date: 2011-05-27 journal: PLoS One DOI: 10.1371/journal.pone.0019436 sha: doc_id: 322446 cord_uid: ddv86eoy file: cache/cord-322456-5at1euqm.json key: cord-322456-5at1euqm authors: Rokohl, Alexander C.; Loreck, Niklas; Wawer Matos, Philomena A.; Mor, Joel M.; Zwingelberg, Sarah; Grajewski, Rafael S.; Cursiefen, Claus; Heindl, Ludwig M. title: Die Rolle der Augenheilkunde in der COVID-19-Pandemie date: 2020-06-09 journal: Ophthalmologe DOI: 10.1007/s00347-020-01148-9 sha: doc_id: 322456 cord_uid: 5at1euqm file: cache/cord-322596-vfmzk2el.json key: cord-322596-vfmzk2el authors: Ming, Yi; Qiang, Liu title: Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications date: 2020-07-11 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00400-2 sha: doc_id: 322596 cord_uid: vfmzk2el file: cache/cord-322311-cg5xwx5a.json key: cord-322311-cg5xwx5a authors: Broder, Kari; Babiker, Ahmed; Myers, Charles; White, Terri; Jones, Heather; Cardella, John; Burd, Eileen M.; Hill, Charles E.; Kraft, Colleen S. title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.01187-20 sha: doc_id: 322311 cord_uid: cg5xwx5a file: cache/cord-322562-3gvsn9vf.json key: cord-322562-3gvsn9vf authors: Hatada, Ryo; Okuwaki, Koji; Mochizuki, Yuji; Handa, Yuma; Fukuzawa, Kaori; Komeiji, Yuto; Okiyama, Yoshio; Tanaka, Shigenori title: Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) date: 2020-06-15 journal: J Chem Inf Model DOI: 10.1021/acs.jcim.0c00283 sha: doc_id: 322562 cord_uid: 3gvsn9vf file: cache/cord-322385-sc2vxxnn.json key: cord-322385-sc2vxxnn authors: Ebinger, J.; Botwin, G. 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G.; Cheng, S. title: SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers date: 2020-08-04 journal: nan DOI: 10.1101/2020.07.31.20163055 sha: doc_id: 322385 cord_uid: sc2vxxnn file: cache/cord-322789-9elfpx0e.json key: cord-322789-9elfpx0e authors: Abbaspour Kasgari, Hamideh; Moradi, Siavash; Shabani, Amir Mohammad; Babamahmoodi, Farhang; Davoudi Badabi, Ali Reza; Davoudi, Lotfollah; Alikhani, Ahmad; Hedayatizadeh Omran, Akbar; Saeedi, Majid; Merat, Shahin; Wentzel, Hannah; Garratt, Anna; Levi, Jacob; Simmons, Bryony; Hill, Andrew; Tirgar Fakheri, Hafez title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial date: 2020-08-19 journal: J Antimicrob Chemother DOI: 10.1093/jac/dkaa332 sha: doc_id: 322789 cord_uid: 9elfpx0e file: cache/cord-322603-8ajckhzc.json key: cord-322603-8ajckhzc authors: Wongsawat, Jurai; Moolasart, Visal; Srikirin, Punyavee; Srijareonvijit, Chaisiri; Vaivong, Nutcharin; Uttayamakul, Sumonmal; Disthakumpa, Arom title: Risk of novel coronavirus 2019 transmission from children to caregivers: A case series date: 2020-06-22 journal: J Paediatr Child Health DOI: 10.1111/jpc.14965 sha: doc_id: 322603 cord_uid: 8ajckhzc file: cache/cord-322672-gjph61cq.json key: cord-322672-gjph61cq authors: Ashok, Vishnu; Loke, Wei Ian title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis date: 2020-08-25 journal: Eur Heart J Case Rep DOI: 10.1093/ehjcr/ytaa248 sha: doc_id: 322672 cord_uid: gjph61cq file: cache/cord-322807-b24ujorz.json key: cord-322807-b24ujorz authors: Koyama, Takahiko; Weeraratne, Dilhan; Snowdon, Jane L.; Parida, Laxmi title: Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment date: 2020-04-26 journal: Pathogens DOI: 10.3390/pathogens9050324 sha: doc_id: 322807 cord_uid: b24ujorz file: cache/cord-322885-ob5euspo.json key: cord-322885-ob5euspo authors: Durdagi, Serdar; Dag, Cagdas; Dogan, Berna; Yigin, Merve; Avsar, Timucin; Buyukdag, Cengizhan; Erol, Ismail; Ertem, Betul; Calis, Seyma; Yildirim, Gunseli; Orhan, Muge D.; Guven, Omur; Aksoydan, Busecan; Destan, Ebru; Sahin, Kader; Besler, Sabri O.; Oktay, Lalehan; Shafiei, Alaleh; Tolu, Ilayda; Ayan, Esra; Yuksel, Busra; Peksen, Ayse B.; Gocenler, Oktay; Yucel, Ali D.; Can, Ozgur; Ozabrahamyan, Serena; Olkan, Alpsu; Erdemoglu, Ece; Aksit, Fulya; Tanisali, Gokhan; Yefanov, Oleksandr M.; Barty, Anton; Tolstikova, Alexandra; Ketawala, Gihan K.; Botha, Sabine; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alex; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Sierra, Raymond G.; Snell, Edward; DeMirci, Hasan title: Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date: 2020-09-09 journal: bioRxiv DOI: 10.1101/2020.09.09.287987 sha: doc_id: 322885 cord_uid: ob5euspo file: cache/cord-322812-9u3ptqjs.json key: cord-322812-9u3ptqjs authors: Wells, Philippa M.; Doores, Katie J.; Couvreur, Simon; Nunez, Rocio Martinez; Seow, Jeffrey; Graham, Carl; Acors, Sam; Kouphou, Neophytos; Neil, Stuart J.D.; Tedder, Richard S.; Matos, Pedro M.; Poulton, Kate; Lista, Maria Jose; Dickenson, Ruth E.; Sertkaya, Helin; Maguire, Thomas J.A.; Scourfield, Edward J.; Bowyer, Ruth C.E.; Hart, Deborah; O'Bryne, Aoife; Steel, Kathyrn J.A.; Hemmings, Oliver; Rosadas, Carolina; McClure, Myra O.; Capedevilla-pujol, Joan; Wolf, Jonathan; Ourselin, Sebastien; Brown, Matthew A.; Malim, Michael H.; Spector, Tim; Steves, Claire J. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-10-15 journal: J Infect DOI: 10.1016/j.jinf.2020.10.011 sha: doc_id: 322812 cord_uid: 9u3ptqjs file: cache/cord-322585-5gio6ruj.json key: cord-322585-5gio6ruj authors: Lanari, Marcello; Chiereghin, Angela; Biserni, Giovanni Battista; Rocca, Alessandro; Re, Maria Carla; Lazzarotto, Tiziana title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date: 2020-06-25 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.017 sha: doc_id: 322585 cord_uid: 5gio6ruj file: cache/cord-322834-rl6yum7n.json key: cord-322834-rl6yum7n authors: Wallinga, Jacco; Teunis, Peter title: Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures date: 2004-09-15 journal: Am J Epidemiol DOI: 10.1093/aje/kwh255 sha: doc_id: 322834 cord_uid: rl6yum7n file: cache/cord-322724-7l1668bf.json key: cord-322724-7l1668bf authors: Challener, Douglas; Shah, Aditya; O'Horo, John C.; Berbari, Elie F.; Binnicker, Matthew J.; Tande, Aaron title: In Reply - Repeated testing in SARS-CoV-2 infection date: 2020-08-10 journal: Mayo Clin Proc DOI: 10.1016/j.mayocp.2020.08.006 sha: doc_id: 322724 cord_uid: 7l1668bf file: cache/cord-322811-6lebh7ca.json key: cord-322811-6lebh7ca authors: Baig, Mirza S.; Alagumuthu, Manikandan; Rajpoot, Sajjan; Saqib, Uzma title: Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells date: 2020-06-26 journal: Drugs R D DOI: 10.1007/s40268-020-00312-5 sha: doc_id: 322811 cord_uid: 6lebh7ca file: cache/cord-322908-e3gok0ot.json key: cord-322908-e3gok0ot authors: Huang, Fangfang; Li, Ying; Leung, Elaine Lai-Han; Liu, Xiaohua; Liu, Kaifeng; Wang, Qu; Lan, Yongqi; Li, Xiaoling; Yu, Haibing; Cu, Liao; Luo, Hui; Luo, Lianxiang title: A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19) date: 2020-05-20 journal: Pharmacol Res DOI: 10.1016/j.phrs.2020.104929 sha: doc_id: 322908 cord_uid: e3gok0ot file: cache/cord-323185-n0rubc72.json key: cord-323185-n0rubc72 authors: Varshney, Bhavna; Agnihotram, Sudhakar; Tan, Yee-Joo; Baric, Ralph; Lal, Sunil K. title: SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date: 2012-01-12 journal: PLoS One DOI: 10.1371/journal.pone.0029542 sha: doc_id: 323185 cord_uid: n0rubc72 file: cache/cord-322650-q8inhgtr.json key: cord-322650-q8inhgtr authors: Fung, Yin-Wan Wendy; Lau, Lok Ting; Wong, Freda Pui-Fan; Choi, Kin-Wing; Chau, Tai-Nin; Lai, Sik-To; Wang, Chen G; Dillon, Natalie; Yu, Albert Cheung-Hoi title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date: 2004-08-15 journal: Clin Infect Dis DOI: 10.1086/422887 sha: doc_id: 322650 cord_uid: q8inhgtr file: cache/cord-322641-mz0b91xr.json key: cord-322641-mz0b91xr authors: Farnsworth, Christopher W; Anderson, Neil W title: SARS-CoV-2 Serology: Much Hype, Little Data date: 2020-04-28 journal: Clin Chem DOI: 10.1093/clinchem/hvaa107 sha: doc_id: 322641 cord_uid: mz0b91xr file: cache/cord-322957-clf8f90t.json key: cord-322957-clf8f90t authors: Crespo, Javier; Andrade, Raúl; Parras, Fernando Alberca de las; Balaguer, Francesc; Acosta, Manuel Barreiro-de; Bujanda, Luís; Gutiérrez, Ana; Jorquera, Francisco; Iglesias-García, Julio; Sánchez-Yagüe, Andrés; Calleja, José Luis title: Resumption of activity in gastroenterology departments. 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Pastoris and the diagnostic utility of the expression product date: 2004-12-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.08.015 sha: doc_id: 323072 cord_uid: 4rsgeag7 file: cache/cord-323038-hmi061vn.json key: cord-323038-hmi061vn authors: Lai, Christopher K C; Ng, Rita W Y; Wong, Martin C S; Chong, Ka Chun; Yeoh, Yun Kit; Chen, Zigui; Chan, Paul K S title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy date: 2020-06-30 journal: Int J Epidemiol DOI: 10.1093/ije/dyaa106 sha: doc_id: 323038 cord_uid: hmi061vn file: cache/cord-323093-u3ozc9ry.json key: cord-323093-u3ozc9ry authors: Rathnayake, Athri D.; Zheng, Jian; Kim, Yunjeong; Perera, Krishani Dinali; Mackin, Samantha; Meyerholz, David K.; Kashipathy, Maithri M.; Battaile, Kevin P.; Lovell, Scott; Perlman, Stanley; Groutas, William C.; Chang, Kyeong-Ok title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice date: 2020-08-19 journal: Sci Transl Med DOI: 10.1126/scitranslmed.abc5332 sha: doc_id: 323093 cord_uid: u3ozc9ry file: cache/cord-322837-tqgwgvo0.json key: cord-322837-tqgwgvo0 authors: Gable, Lance; Ram, Natalie; Ram, Jeffrey L title: Legal and Ethical Implications of Wastewater SARS-CoV-2 Monitoring for COVID-19 Surveillance date: 2020-06-24 journal: J Law Biosci DOI: 10.1093/jlb/lsaa039 sha: doc_id: 322837 cord_uid: tqgwgvo0 file: cache/cord-322877-jy1uvwre.json key: cord-322877-jy1uvwre authors: Yuen, Kenneth S.C.; Chan, Wai-Man; Fan, Dorothy S.P.; Chong, Kelvin K.L.; Sung, Joseph J.Y.; Lam, Dennis S.C. title: Ocular screening in severe acute respiratory syndrome date: 2004-03-30 journal: Am J Ophthalmol DOI: 10.1016/j.ajo.2003.09.060 sha: doc_id: 322877 cord_uid: jy1uvwre file: cache/cord-323061-0i5w7vm9.json key: cord-323061-0i5w7vm9 authors: Kharel Sitaula, Ranju; Khatri, Anadi; Janani, M K; Mandage, Rajendra; Sadhu, Soumen; Madhavan, H N; Upadhyay, Madan Prasad; Biswas, Jyotirmay title: Unfolding COVID-19: Lessons-in-Learning in Ophthalmology date: 2020-09-28 journal: Clin Ophthalmol DOI: 10.2147/opth.s259857 sha: doc_id: 323061 cord_uid: 0i5w7vm9 file: cache/cord-323216-rgj8vs9z.json key: cord-323216-rgj8vs9z authors: Plotkin, Stanley A title: Vaccination Against Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-08-03 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa093 sha: doc_id: 323216 cord_uid: rgj8vs9z file: cache/cord-322955-7dw32xby.json key: cord-322955-7dw32xby authors: Kathwate, Gunderao H title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date: 2020-06-12 journal: bioRxiv DOI: 10.1101/2020.06.03.131755 sha: doc_id: 322955 cord_uid: 7dw32xby file: cache/cord-323131-l726qv1g.json key: cord-323131-l726qv1g authors: Atogebania, Julius Wedam; Chen, Hualei title: An Invited Commentary on ‘ Evidence Based Management Guideline for the COVID-19 Pandemic- Review article’ date: 2020-04-23 journal: Int J Surg DOI: 10.1016/j.ijsu.2020.04.050 sha: doc_id: 323131 cord_uid: l726qv1g file: cache/cord-322913-sq9mq6f1.json key: cord-322913-sq9mq6f1 authors: Ciabattini, Annalisa; Garagnani, Paolo; Santoro, Francesco; Rappuoli, Rino; Franceschi, Claudio; Medaglini, Donata title: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date: 2020-11-06 journal: Semin Immunopathol DOI: 10.1007/s00281-020-00821-0 sha: doc_id: 322913 cord_uid: sq9mq6f1 file: cache/cord-323241-1twnqr4k.json key: cord-323241-1twnqr4k authors: Patrì, Angela; Gallo, Lucia; Guarino, Maria; Fabbrocini, Gabriella title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? date: 2020-04-09 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.03.098 sha: doc_id: 323241 cord_uid: 1twnqr4k file: cache/cord-323148-rsjocuh3.json key: cord-323148-rsjocuh3 authors: Assaad, Souad; Fuhrmann, Christine; Avrillon, Virginie; Ray-Coquard, Isabelle; Blay, Jean-Yves title: Risk of death of cancer patients presenting with severe symptoms of infection, with or without documented COVID-19 date: 2020-09-06 journal: Eur J Cancer DOI: 10.1016/j.ejca.2020.08.018 sha: doc_id: 323148 cord_uid: rsjocuh3 file: cache/cord-323327-08p122lw.json key: cord-323327-08p122lw authors: van de Veerdonk, Frank L.; Netea, Mihai G. title: Blocking IL-1 to prevent respiratory failure in COVID-19 date: 2020-07-18 journal: Crit Care DOI: 10.1186/s13054-020-03166-0 sha: doc_id: 323327 cord_uid: 08p122lw file: cache/cord-323394-osx7llte.json key: cord-323394-osx7llte authors: Lanser, Lukas; Bellmann-Weiler, Rosa; Öttl, Karla-Wanda; Huber, Lukas; Griesmacher, Andrea; Theurl, Igor; Weiss, Günter title: Evaluating the clinical utility and sensitivity of SARS-CoV-2 antigen testing in relation to RT-PCR Ct values date: 2020-11-13 journal: Infection DOI: 10.1007/s15010-020-01542-0 sha: doc_id: 323394 cord_uid: osx7llte file: cache/cord-323397-5yop6clu.json key: cord-323397-5yop6clu authors: Albalate, M.; Arribas, P.; Torres, E.; Cintra, M.; Alcázar, R.; Puerta, M.; Ortega, M.; Procaccini, F.; Martin, J.; Jiménez, E.; Fernandez, I.; de Sequera, P. title: Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date: 2020-04-30 journal: Nefrologia DOI: 10.1016/j.nefro.2020.04.005 sha: doc_id: 323397 cord_uid: 5yop6clu file: cache/cord-322942-y4zd2oui.json key: cord-322942-y4zd2oui authors: Olagnier, David; Farahani, Ensieh; Thyrsted, Jacob; Cadanet, Julia B.; Herengt, Angela; Idorn, Manja; Hait, Alon; Hernaez, Bruno; Knudsen, Alice; Iversen, Marie Beck; Schilling, Mirjam; Jørgensen, Sofie E.; Thomsen, Michelle; Reinert, Line; Lappe, Michael; Hoang, Huy-Dung; Gilchrist, Victoria H.; Hansen, Anne Louise; Ottosen, Rasmus; Gunderstofte, Camilla; Møller, Charlotte; van der Horst, Demi; Peri, Suraj; Balachandran, Siddarth; Huang, Jinrong; Jakobsen, Martin; Svenningsen, Esben B.; Poulsen, Thomas B.; Bartsch, Lydia; Thielke, Anne L.; Luo, Yonglun; Alain, Tommy; Rehwinkel, Jan; Alcamí, Antonio; Hiscott, John; Mogensen, Trine; Paludan, Søren R.; Holm, Christian K. title: Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date: 2020-07-17 journal: bioRxiv DOI: 10.1101/2020.07.16.206458 sha: doc_id: 322942 cord_uid: y4zd2oui file: cache/cord-323449-r1gyjxei.json key: cord-323449-r1gyjxei authors: Kim, Uh Jin; Lee, Seung Yeob; Lee, Ji Yeon; Lee, Ahrang; Kim, Seung Eun; Choi, Ok-Ja; Lee, Ji Suk; Kee, Seung-Jung; Jang, Hee-Chang title: Air and Environmental Contamination Caused by COVID-19 Patients: a Multi-Center Study date: 2020-09-08 journal: J Korean Med Sci DOI: 10.3346/jkms.2020.35.e332 sha: doc_id: 323449 cord_uid: r1gyjxei file: cache/cord-323095-q8tj826i.json key: cord-323095-q8tj826i authors: Sokolowska, Milena title: Outsmarting SARS-CoV-2 by empowering a decoy ACE2 date: 2020-11-03 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00370-w sha: doc_id: 323095 cord_uid: q8tj826i file: cache/cord-323024-blc3mnbj.json key: cord-323024-blc3mnbj authors: Bernard-Valnet, R.; Perriot, S.; Canales, M.; Pizzarotti, B.; Caranzano, L.; Castro-Jimenez, M.; Epiney, J.-B.; Vijiala, S.; Salvioni Chiabotti, P.; Anichini, A.; Salerno, A.; Jaton, K.; Vaucher, J.; Perreau, M.; Greub, G.; Pantaleo, G.; Du Pasquier, R. title: CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology date: 2020-11-04 journal: nan DOI: 10.1101/2020.11.01.20217497 sha: doc_id: 323024 cord_uid: blc3mnbj file: cache/cord-323324-h2a25xym.json key: cord-323324-h2a25xym authors: Armijos‐Jaramillo, Vinicio; Yeager, Justin; Muslin, Claire; Perez‐Castillo, Yunierkis title: SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-05-07 journal: Evol Appl DOI: 10.1111/eva.12980 sha: doc_id: 323324 cord_uid: h2a25xym file: cache/cord-323514-jaom3p6s.json key: cord-323514-jaom3p6s authors: He, Yuxian; Li, Jingjing; Jiang, Shibo title: A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date: 2006-05-26 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2006.03.139 sha: doc_id: 323514 cord_uid: jaom3p6s file: cache/cord-321768-oevswvvd.json key: cord-321768-oevswvvd authors: Duan, Ya-qi; Xia, Ming-hui; Ren, Liang; Zhang, Yan-fang; Ao, Qi-lin; Xu, San-peng; Kuang, Dong; Liu, Qian; Yan, Bing; Zhou, Yi-wu; Chu, Qian; Liu, Liang; Yang, Xiang-Ping; Wang, Guo-ping title: Deficiency of Tfh Cells and Germinal Center in Deceased COVID-19 Patients date: 2020-08-07 journal: Curr Med Sci DOI: 10.1007/s11596-020-2225-x sha: doc_id: 321768 cord_uid: oevswvvd file: cache/cord-323092-j2u0ny2u.json key: cord-323092-j2u0ny2u authors: Crosby, James C.; Heimann, Matthew A.; Burleson, Samuel L.; Anzalone, Brendan C.; Swanson, Jonathan F.; Wallace, Douglas W.; Greene, Christopher J. title: COVID‐19: A review of therapeutics under investigation date: 2020-04-19 journal: J Am Coll Emerg Physicians Open DOI: 10.1002/emp2.12081 sha: doc_id: 323092 cord_uid: j2u0ny2u file: cache/cord-323094-zugrtvyo.json key: cord-323094-zugrtvyo authors: Rose, R.; Nolan, D. 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Crespo, Marta; Horcajada, Juan Pablo; Pascual, Julio title: Protection of nephrology health professionals during the COVID-19 pandemic date: 2020-10-06 journal: nan DOI: 10.1016/j.nefroe.2020.06.018 sha: doc_id: 323489 cord_uid: ro7kbnu3 file: cache/cord-323481-uz6usokd.json key: cord-323481-uz6usokd authors: Wang, Yixuan; Wang, Yuyi; Chen, Yan; Qin, Qingsong title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures date: 2020-03-29 journal: J Med Virol DOI: 10.1002/jmv.25748 sha: doc_id: 323481 cord_uid: uz6usokd file: cache/cord-323737-6ajqy0ch.json key: cord-323737-6ajqy0ch authors: Jiang, Yuanyuan; Liu, Lanxin; Manning, Morenci; Bonahoom, Madison; Lotvola, Aaron; Yang, Zhe; Yang, Zeng-Quan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1828172 sha: doc_id: 323737 cord_uid: 6ajqy0ch file: cache/cord-323596-dh7oh54z.json key: cord-323596-dh7oh54z authors: Advani, Sonali D.; Baker, Esther; Cromer, Andrea; Wood, Brittain; Crawford, Kathryn L.; Crane, Linda; Adcock, Linda; Roach, Linda; Padgette, Polly; Anderson, Deverick J.; Sexton, Daniel J. title: Assessing severe acute respiratory coronavirus virus 2 (SARS-CoV-2) preparedness in US community hospitals: A forgotten entity date: 2020-10-07 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.1238 sha: doc_id: 323596 cord_uid: dh7oh54z file: cache/cord-323666-t7cshj05.json key: cord-323666-t7cshj05 authors: Cegolon, L.; Javanbakht, M.; Mastrangelo, G. title: Nasal Disinfection for the Prevention and Control of COVID-19: A Scoping Review on Potential Chemo-preventive Agents. date: 2020-08-18 journal: Int J Hyg Environ Health DOI: 10.1016/j.ijheh.2020.113605 sha: doc_id: 323666 cord_uid: t7cshj05 file: cache/cord-323831-1qadv7r1.json key: cord-323831-1qadv7r1 authors: Coleman, H; Sutherland, J; Calder, N title: Severe acute respiratory syndrome coronavirus-2 in post-laryngectomy patients: case series of four patients date: 2020-06-23 journal: The Journal of laryngology and otology DOI: 10.1017/s0022215120001310 sha: doc_id: 323831 cord_uid: 1qadv7r1 file: cache/cord-323828-ug2duzw1.json key: cord-323828-ug2duzw1 authors: Ni, Dongchun; Lau, Kelvin; Lehmann, Frank; Fränkl, Andri; Hacker, David; Pojer, Florence; Stahlberg, Henning title: Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.10.12.336016 sha: doc_id: 323828 cord_uid: ug2duzw1 file: cache/cord-323839-a4oejky0.json key: cord-323839-a4oejky0 authors: Sasaki, Michihito; Uemura, Kentaro; Sato, Akihiko; Toba, Shinsuke; Sanaki, Takao; Maenaka, Katsumi; Hall, William W.; Orba, Yasuko; Sawa, Hirofumi title: SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.28.271163 sha: doc_id: 323839 cord_uid: a4oejky0 file: cache/cord-323908-8dgngwmw.json key: cord-323908-8dgngwmw authors: He, Zhesheng; Zhao, Wencong; Niu, Wenchao; Gao, Xuejiao; Gao, Xingfa; Gong, Yong; Gao, Xueyun title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date: 2020-05-31 journal: bioRxiv DOI: 10.1101/2020.05.28.120642 sha: doc_id: 323908 cord_uid: 8dgngwmw file: cache/cord-323695-jkik03lb.json key: cord-323695-jkik03lb authors: Paolo, Gisondi; Stefano, Piaserico; Luigi, Naldi; Paolo, Dapavo; Andrea, Conti; Piergiorgio, Malagoli; Valerio, Marzano Angelo; Federico, Bardazzi; Massimo, Gasperini; Simone, Cazzaniga; Antonio, Costanzo; Sacchelli, Lidia; Pezzolo, Elena; Messina, Francesco; Lasagni, Claudia; Bigi, Laura; Cattaneo, Angelo; Carrera, Carlo Giovanni; Arancio, Luisa; Ribero, Simone; Rozzo, Giulia; Damiani, Giovanni; Facheris, Paola title: Incidence rates of hospitalization and death from COVID-19 in patients with psoriasis receiving biological treatment: a Northern Italy experience date: 2020-11-05 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2020.10.032 sha: doc_id: 323695 cord_uid: jkik03lb file: cache/cord-323882-127c5bve.json key: cord-323882-127c5bve authors: Yu, Wen-Bin; Tang, Guang-Da; Zhang, Li; Corlett, Richard T. title: Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data date: 2020-05-17 journal: Zool Res DOI: 10.24272/j.issn.2095-8137.2020.022 sha: doc_id: 323882 cord_uid: 127c5bve file: cache/cord-323622-229kub7c.json key: cord-323622-229kub7c authors: Ou, Xueting; Zhou, Liyang; Huang, Huanliang; Lin, Yuebao; Pan, Xingfei; Chen, Dexiong title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens date: 2020-04-16 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101672 sha: doc_id: 323622 cord_uid: 229kub7c file: cache/cord-323871-2hx4fuk2.json key: cord-323871-2hx4fuk2 authors: Ho, Sheau Ling; Wang, Andrew H.-J. title: Structural bioinformatics analysis of free cysteines in protein environments date: 2009-03-14 journal: J Taiwan Inst Chem Eng DOI: 10.1016/j.jtice.2008.07.015 sha: doc_id: 323871 cord_uid: 2hx4fuk2 file: cache/cord-323824-74xvvwrw.json key: cord-323824-74xvvwrw authors: de Oliveira, Osmair Vital; Rocha, Gerd B.; Paluch, Andrew S.; Costa, Luciano T. title: Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening date: 2020-06-02 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1772885 sha: doc_id: 323824 cord_uid: 74xvvwrw file: cache/cord-323822-jtbfpx88.json key: cord-323822-jtbfpx88 authors: Barnett, Brad P.; Wahlin, Karl; Krawczyk, Michal; Spencer, Doran; Welsbie, Derek; Afshari, Natalie; Chao, Daniel title: Potential of Ocular Transmission of SARS-CoV-2: A Review date: 2020-09-01 journal: Vision (Basel) DOI: 10.3390/vision4030040 sha: doc_id: 323822 cord_uid: jtbfpx88 file: cache/cord-323905-ayufx3wv.json key: cord-323905-ayufx3wv authors: Kort, N. 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C.; Stuyts, B.; Tandogan, R.; Violante, B.; Zagra, L.; Thaler, M. title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members date: 2020-08-18 journal: Knee Surg Sports Traumatol Arthrosc DOI: 10.1007/s00167-020-06212-0 sha: doc_id: 323905 cord_uid: ayufx3wv file: cache/cord-323643-lu3ngt6r.json key: cord-323643-lu3ngt6r authors: Chow, C.B. title: Post-SARS infection control in the hospital and clinic date: 2004-11-05 journal: Paediatr Respir Rev DOI: 10.1016/j.prrv.2004.07.006 sha: doc_id: 323643 cord_uid: lu3ngt6r file: cache/cord-323807-e220ut9u.json key: cord-323807-e220ut9u authors: Bassetti, Matteo; Vena, Antonio; Giacobbe, Daniele Roberto title: The novel Chinese coronavirus (2019‐nCoV) infections: Challenges for fighting the storm date: 2020-02-05 journal: Eur J Clin Invest DOI: 10.1111/eci.13209 sha: doc_id: 323807 cord_uid: e220ut9u file: cache/cord-323930-pl3qlcpo.json key: cord-323930-pl3qlcpo authors: Sohail, Ayesha; Nutini, Alessandro title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 journal: Prog Biophys Mol Biol DOI: 10.1016/j.pbiomolbio.2020.04.002 sha: doc_id: 323930 cord_uid: pl3qlcpo file: cache/cord-323943-9916y6x0.json key: cord-323943-9916y6x0 authors: Platt, Daniel E; Parida, Laxmi E; Zalloua, Pierre title: Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails date: 2020-04-21 journal: nan DOI: 10.1101/2020.04.20.20071928 sha: doc_id: 323943 cord_uid: 9916y6x0 file: cache/cord-324128-css42bsb.json key: cord-324128-css42bsb authors: Boukli, Narjis; Le Mene, Melchior; Schnuriger, Aurélie; Cuervo, Nancy Stella; Laroche, Cécilia; Morand-Joubert, Laurence; Gozlan, Joël title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies date: 2020-10-21 journal: J Clin Microbiol DOI: 10.1128/jcm.01352-20 sha: doc_id: 324128 cord_uid: css42bsb file: cache/cord-324255-ize21we2.json key: cord-324255-ize21we2 authors: Fouchier, Ron A. M.; Kuiken, Thijs; Schutten, Martin; van Amerongen, Geert; van Doornum, Gerard J. J.; van den Hoogen, Bernadette G.; Peiris, Malik; Lim, Wilina; Stöhr, Klaus; Osterhaus, Albert D. M. 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Case report date: 2020-10-06 journal: BMC Pregnancy Childbirth DOI: 10.1186/s12884-020-03275-2 sha: doc_id: 324102 cord_uid: 75v4ebag file: cache/cord-324344-dxuabscn.json key: cord-324344-dxuabscn authors: Zhao, Xuesen; Zheng, Shuangli; Chen, Danying; Zheng, Mei; Li, Xinglin; Li, Guoli; Lin, Hanxin; Chang, Jinhong; Zeng, Hui; Guo, Ju-Tao title: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date: 2020-04-05 journal: bioRxiv DOI: 10.1101/2020.04.02.021469 sha: doc_id: 324344 cord_uid: dxuabscn file: cache/cord-323940-ubazgvov.json key: cord-323940-ubazgvov authors: Cafiero, Concetta; Re, Agnese; Micera, Alessandra; Palmirotta, Raffaele; Monaco, Delio; Romano, Francesca; Fabrizio, Claudia; Di Francia, Raffaele; Cacciamani, Andrea; Surico, Pier Luigi; D’Amato, Gerardo; Pisconti, Salvatore title: Pharmacogenomics and Pharmacogenetics: In Silico Prediction of Drug Effects in Treatments for Novel Coronavirus SARS-CoV2 Disease date: 2020-10-13 journal: Pharmgenomics Pers Med DOI: 10.2147/pgpm.s270069 sha: doc_id: 323940 cord_uid: ubazgvov file: cache/cord-323685-gjocoa60.json key: cord-323685-gjocoa60 authors: Tsai, Shang-Jui; Guo, Chenxu; Atai, Nadia A.; Gould, Stephen J. title: Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date: 2020-11-06 journal: bioRxiv DOI: 10.1101/2020.11.06.371419 sha: doc_id: 323685 cord_uid: gjocoa60 file: cache/cord-324295-9c1zxjng.json key: cord-324295-9c1zxjng authors: Bonilla-Aldana, D. Katterine; Jimenez-Diaz, S. Daniela; Arango-Duque, J. Sebastian; Aguirre-Florez, Mateo; Balbin-Ramon, Graciela J.; Paniz-Mondolfi, Alberto; Suárez, Jose Antonio; Pachar, Monica R.; Perez-Garcia, Luis A.; Delgado-Noguera, Lourdes A.; Sierra, Manuel Antonio; Muñoz-Lara, Fausto; Zambrano, Lysien I.; Rodriguez-Morales, Alfonso J. title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.050 sha: doc_id: 324295 cord_uid: 9c1zxjng file: cache/cord-324166-6ydn2bvy.json key: cord-324166-6ydn2bvy authors: Kumar, Neeraj; Awasthi, Amardeep; Kumari, Anchala; Sood, Damini; Jain, Pallavi; Singh, Taru; Sharma, Neera; Grover, Abhinav; Chandra, Ramesh title: Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis date: 2020-08-20 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1808072 sha: doc_id: 324166 cord_uid: 6ydn2bvy file: cache/cord-324246-liyk6mna.json key: cord-324246-liyk6mna authors: Shakoor, Hira; Feehan, Jack; Mikkelsen, Kathleen; Al Dhaheri, Ayesha S.; Ali, Habiba I.; Platat, Carine; Ismail, Leila Cheikh; Stojanovska, Lily; Apostolopoulos, Vasso title: Be well: A potential role for vitamin B in COVID-19 date: 2020-08-15 journal: Maturitas DOI: 10.1016/j.maturitas.2020.08.007 sha: doc_id: 324246 cord_uid: liyk6mna file: cache/cord-323832-w19ump0o.json key: cord-323832-w19ump0o authors: Mishra, Vijaya Nath; Kumari, Nidhi; Pathak, Abhishek; Chaturvedi, Rajnish Kumar; Gupta, Arun Kumar; Chaurasia, Rameshwar Nath title: Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection date: 2020-09-19 journal: Int J Microbiol DOI: 10.1155/2020/8844963 sha: doc_id: 323832 cord_uid: w19ump0o file: cache/cord-324345-j43rpvwk.json key: cord-324345-j43rpvwk authors: Leong, Hoe Nam; Lim, Hong Huay title: SARS – My personal battle date: 2010-11-19 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2010.10.007 sha: doc_id: 324345 cord_uid: j43rpvwk file: cache/cord-324165-afdmsbw2.json key: cord-324165-afdmsbw2 authors: Joo, Heesoo; Henry, Ronald E.; Lee, Yeon-Kyeng; Berro, Andre D.; Maskery, Brian A. title: The effects of past SARS experience and proximity on declines in numbers of travelers to the Republic of Korea during the 2015 MERS outbreak: A retrospective study date: 2019-08-31 journal: Travel Medicine and Infectious Disease DOI: 10.1016/j.tmaid.2019.05.009 sha: doc_id: 324165 cord_uid: afdmsbw2 file: cache/cord-324325-rmlrhyf2.json key: cord-324325-rmlrhyf2 authors: Chan, Wai S; Wu, Chun; Chow, Sammy C S; Cheung, To; To, Ka-Fai; Leung, Wai-Keung; Chan, Paul K S; Lee, Kam-Cheong; Ng, Ho-Keung; Au, Deborah M Y; Lo, Anthony W I title: Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date: 2005-05-13 journal: Mod Pathol DOI: 10.1038/modpathol.3800439 sha: doc_id: 324325 cord_uid: rmlrhyf2 file: cache/cord-324328-olnwynfu.json key: cord-324328-olnwynfu authors: Nakamichi, K.; Shen, J. Z.; Lee, C. S.; Lee, A. Y.; Roberts, E. A.; Simonson, P. D.; Roychoudhury, P.; Andriesen, J. G.; Randhawa, A. K.; Mathias, P. C.; Greninger, A.; Jerome, K. R.; Van Gelder, R. N. title: Outcomes associated with SARS-CoV-2 viral clades in COVID-19 date: 2020-09-25 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.09.24.20201228 sha: doc_id: 324328 cord_uid: olnwynfu file: cache/cord-324405-6uanhe2p.json key: cord-324405-6uanhe2p authors: Burke, Rachel M.; Balter, Sharon; Barnes, Emily; Barry, Vaughn; Bartlett, Karri; Beer, Karlyn D.; Benowitz, Isaac; Biggs, Holly M.; Bruce, Hollianne; Bryant-Genevier, Jonathan; Cates, Jordan; Chatham-Stephens, Kevin; Chea, Nora; Chiou, Howard; Christiansen, Demian; Chu, Victoria T.; Clark, Shauna; Cody, Sara H.; Cohen, Max; Conners, Erin E.; Dasari, Vishal; Dawson, Patrick; DeSalvo, Traci; Donahue, Matthew; Dratch, Alissa; Duca, Lindsey; Duchin, Jeffrey; Dyal, Jonathan W.; Feldstein, Leora R.; Fenstersheib, Marty; Fischer, Marc; Fisher, Rebecca; Foo, Chelsea; Freeman-Ponder, Brandi; Fry, Alicia M.; Gant, Jessica; Gautom, Romesh; Ghinai, Isaac; Gounder, Prabhu; Grigg, Cheri T.; Gunzenhauser, Jeffrey; Hall, Aron J.; Han, George S.; Haupt, Thomas; Holshue, Michelle; Hunter, Jennifer; Ibrahim, Mireille B.; Jacobs, Max W.; Jarashow, M. Claire; Joshi, Kiran; Kamali, Talar; Kawakami, Vance; Kim, Moon; Kirking, Hannah L.; Kita-Yarbro, Amanda; Klos, Rachel; Kobayashi, Miwako; Kocharian, Anna; Lang, Misty; Layden, Jennifer; Leidman, Eva; Lindquist, Scott; Lindstrom, Stephen; Link-Gelles, Ruth; Marlow, Mariel; Mattison, Claire P.; McClung, Nancy; McPherson, Tristan D.; Mello, Lynn; Midgley, Claire M.; Novosad, Shannon; Patel, Megan T.; Pettrone, Kristen; Pillai, Satish K.; Pray, Ian W.; Reese, Heather E.; Rhodes, Heather; Robinson, Susan; Rolfes, Melissa; Routh, Janell; Rubin, Rachel; Rudman, Sarah L.; Russell, Denny; Scott, Sarah; Shetty, Varun; Smith-Jeffcoat, Sarah E.; Soda, Elizabeth A.; Spitters, Christopher; Stierman, Bryan; Sunenshine, Rebecca; Terashita, Dawn; Traub, Elizabeth; Vahey, Grace M.; Verani, Jennifer R.; Wallace, Megan; Westercamp, Matthew; Wortham, Jonathan; Xie, Amy; Yousaf, Anna; Zahn, Matthew title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 journal: PLoS One DOI: 10.1371/journal.pone.0238342 sha: doc_id: 324405 cord_uid: 6uanhe2p file: cache/cord-323980-rcyjthze.json key: cord-323980-rcyjthze authors: Willems, Laurent M.; Balcik, Yunus; Noda, Anna H.; Siebenbrodt, Kai; Leimeister, Sina; McCoy, Jeannie; Kienitz, Ricardo; Kiyose, Makoto; Reinecke, Raphael; Schäfer, Jan-Hendrik; Zöllner, Johann Philipp; Bauer, Sebastian; Rosenow, Felix; Strzelczyk, Adam title: SARS-CoV-2-related rapid reorganization of an epilepsy outpatient clinic from personal appointments to telemedicine services: A German single-center experience date: 2020-10-06 journal: Epilepsy Behav DOI: 10.1016/j.yebeh.2020.107483 sha: doc_id: 323980 cord_uid: rcyjthze file: cache/cord-324270-8rgkop42.json key: cord-324270-8rgkop42 authors: Renaud-Picard, Benjamin; Gallais, Floriane; Riou, Marianne; Zouzou, Adel; Porzio, Michele; Kessler, Romain title: Delayed pulmonary abscess following COVID-19 pneumonia: a case report date: 2020-06-18 journal: Respir Med Res DOI: 10.1016/j.resmer.2020.100776 sha: doc_id: 324270 cord_uid: 8rgkop42 file: cache/cord-324307-2zbm4iwn.json key: cord-324307-2zbm4iwn authors: Kam, Kai-qian; Yung, Chee Fu; Cui, Lin; Tzer Pin Lin, Raymond; Mak, Tze Minn; Maiwald, Matthias; Li, Jiahui; Chong, Chia Yin; Nadua, Karen; Tan, Natalie Woon Hui; Thoon, Koh Cheng title: A Well Infant With Coronavirus Disease 2019 With High Viral Load date: 2020-02-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa201 sha: doc_id: 324307 cord_uid: 2zbm4iwn file: cache/cord-324480-7u5lh4jx.json key: cord-324480-7u5lh4jx authors: Sharma, A.; Preece, B.; Swann, H; Fan, X.; McKenney, R.J.; Ori-McKenney, K.M.; Saffarian, S.; Vershinin, M.D. title: Structural stability of SARS-CoV-2 degrades with temperature date: 2020-10-14 journal: bioRxiv DOI: 10.1101/2020.10.12.336818 sha: doc_id: 324480 cord_uid: 7u5lh4jx file: cache/cord-324518-a346cjx4.json key: cord-324518-a346cjx4 authors: Zhang, Zhibin; Sheng, Chengfa; Ma, Zufei; Li, Dianmo title: The outbreak pattern of the SARS cases in Asia date: 2004 journal: Chin Sci Bull DOI: 10.1007/bf03183407 sha: doc_id: 324518 cord_uid: a346cjx4 file: cache/cord-324265-j3v3i8vm.json key: cord-324265-j3v3i8vm authors: Marietta, Marco; Coluccio, Valeria; Luppi, Mario title: COVID-19, coagulopathy and venous thromboembolism: more questions than answers date: 2020-07-11 journal: Intern Emerg Med DOI: 10.1007/s11739-020-02432-x sha: doc_id: 324265 cord_uid: j3v3i8vm file: cache/cord-324324-8ybfiz8f.json key: cord-324324-8ybfiz8f authors: Decaro, Nicola; Lorusso, Alessio title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2020.108693 sha: doc_id: 324324 cord_uid: 8ybfiz8f file: cache/cord-324623-x6eom6kh.json key: cord-324623-x6eom6kh authors: Zhang, Jingyi; Yang, Yinmei; Yang, Nan; Ma, Yanfang; Zhou, Qi; Li, Weiguo; Wang, Xia; Huang, Liping; Luo, Xufei; Fukuoka, Toshio; Ahn, Hyeong Sik; Lee, Myeong Soo; Luo, Zhengxiu; Chen, Yaolong; Liu, Enmei; Yang, Kehu; Fu, Zhou title: Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review date: 2020-04-22 journal: nan DOI: 10.1101/2020.04.17.20064444 sha: doc_id: 324623 cord_uid: x6eom6kh file: cache/cord-324557-4u8dja0n.json key: cord-324557-4u8dja0n authors: Leblanc, Jean‐François; Germain, Marc; Delage, Gilles; O’Brien, Sheila; Drews, Steven J.; Lewin, Antoine title: Risk of Transmission of Severe Acute Respiratory Syndrome Coronavirus‐2 by Transfusion: A Literature Review date: 2020-08-15 journal: Transfusion DOI: 10.1111/trf.16056 sha: doc_id: 324557 cord_uid: 4u8dja0n file: cache/cord-324288-qgxswltx.json key: cord-324288-qgxswltx authors: Padhi, Sunali; Suvankar, Subham; Panda, Venketesh K.; Pati, Abhijit; Panda, Aditya K title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study date: 2020-09-14 journal: Int Immunopharmacol DOI: 10.1016/j.intimp.2020.107001 sha: doc_id: 324288 cord_uid: qgxswltx file: cache/cord-324357-ys4tqy5x.json key: cord-324357-ys4tqy5x authors: nan title: Hygiene at home: A bulwark against COVID-19 to be protect from SARS-CoV-2 date: 2020-05-15 journal: Bull Acad Natl Med DOI: 10.1016/j.banm.2020.05.020 sha: doc_id: 324357 cord_uid: ys4tqy5x file: cache/cord-324251-wgtatr8v.json key: cord-324251-wgtatr8v authors: Joshi, Madhvi; 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Yukthamarani; Agho, Kingsley E. title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys date: 2020-07-21 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17145252 sha: doc_id: 324856 cord_uid: hf969tav file: cache/cord-324619-y7gilopu.json key: cord-324619-y7gilopu authors: Alam, S.B.; Willows, Steven; Kulka, Marianna; Sandhu, Jagdeep K. title: Severe acute respiratory syndrome coronavirus‐2 may be an underappreciated pathogen of the central nervous system date: 2020-07-15 journal: Eur J Neurol DOI: 10.1111/ene.14442 sha: doc_id: 324619 cord_uid: y7gilopu file: cache/cord-324644-sz5n7a5z.json key: cord-324644-sz5n7a5z authors: Rehman, Mahin; Gondal, Amlish; Rehman, Najeeb U title: Atypical Manifestation of COVID-19-Induced Myocarditis date: 2020-06-18 journal: Cureus DOI: 10.7759/cureus.8685 sha: doc_id: 324644 cord_uid: sz5n7a5z file: cache/cord-324707-9ld73wv1.json key: cord-324707-9ld73wv1 authors: Mitjà, Oriol; Corbacho-Monné, Marc; Ubals, Maria; Tebe, Cristian; Peñafiel, Judith; Tobias, Aurelio; Ballana, Ester; Alemany, Andrea; Riera-Martí, Núria; Pérez, Carla A; Suñer, Clara; Laporte, Pep; Admella, Pol; Mitjà, Jordi; Clua, Mireia; Bertran, Laia; Sarquella, Maria; Gavilán, Sergi; Ara, Jordi; Argimon, Josep M; Casabona, Jordi; Cuatrecasas, Gabriel; Cañadas, Paz; Elizalde-Torrent, Aleix; Fabregat, Robert; Farré, Magí; Forcada, Anna; Flores-Mateo, Gemma; Muntada, Esteve; Nadal, Núria; Narejos, Silvia; Gil-Ortega, Aroa N; Prat, Nuria; Puig, Jordi; Quiñones, Carles; Reyes-Ureña, Juliana; Ramírez-Viaplana, Ferran; Ruiz, Lidia; Riveira-Muñoz, Eva; Sierra, Alba; Velasco, César; Vivanco-Hidalgo, Rosa Maria; Sentís, Alexis; G-Beiras, Camila; Clotet, Bonaventura; Vall-Mayans, Martí title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date: 2020-07-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1009 sha: doc_id: 324707 cord_uid: 9ld73wv1 file: cache/cord-324727-bj8oei0v.json key: cord-324727-bj8oei0v authors: Zhang, Xiaomei; Tang, Chengwei; Tian, Dean; Hou, Xiaohua; Yang, Yunsheng title: Management of Digestive Disorders and Procedures Associated With COVID-19 date: 2020-06-03 journal: Am J Gastroenterol DOI: 10.14309/ajg.0000000000000728 sha: doc_id: 324727 cord_uid: bj8oei0v file: cache/cord-324638-gwd8qin6.json key: cord-324638-gwd8qin6 authors: Chiu, Rossa WK; Jin, Yongjie; Chung, Grace TY; Lui, Wing-bong; Chan, Anthony TC; Lim, Wilina; Dennis Lo, YM title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 journal: BMC Infect Dis DOI: 10.1186/1471-2334-6-20 sha: doc_id: 324638 cord_uid: gwd8qin6 file: cache/cord-324752-t50bg7pq.json key: cord-324752-t50bg7pq authors: Lavery, Michael Joseph; Bouvier, Charles Alexis; Thompson, Ben title: Cutaneous manifestations of COVID-19 in children (and adults): A virus that does not discriminate date: 2020-11-01 journal: Clin Dermatol DOI: 10.1016/j.clindermatol.2020.10.020 sha: doc_id: 324752 cord_uid: t50bg7pq file: cache/cord-324888-oak27okj.json key: cord-324888-oak27okj authors: Leng, Ling; Ma, Jie; Zhang, Leike; Li, Wei; Zhao, Lei; Zhu, Yunping; Wu, Zhihong; Cao, Ruiyuan; Zhong, Wu title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date: 2020-04-18 journal: bioRxiv DOI: 10.1101/2020.04.16.045799 sha: doc_id: 324888 cord_uid: oak27okj file: cache/cord-324919-ciamusjs.json key: cord-324919-ciamusjs authors: Scialo, Filippo; Daniele, Aurora; Amato, Felice; Pastore, Lucio; Matera, Maria Gabriella; Cazzola, Mario; Castaldo, Giuseppe; Bianco, Andrea title: ACE2: The Major Cell Entry Receptor for SARS-CoV-2 date: 2020-11-10 journal: Lung DOI: 10.1007/s00408-020-00408-4 sha: doc_id: 324919 cord_uid: ciamusjs file: cache/cord-324938-2lu9z5b2.json key: cord-324938-2lu9z5b2 authors: Wu, Li-Ping; Wang, Nai-Chang; Chang, Yi-Hua; Tian, Xiang-Yi; Na, Dan-Yu; Zhang, Li-Yuan; Zheng, Lei; Lan, Tao; Wang, Lin-Fa; Liang, Guo-Dong title: Duration of Antibody Responses after Severe Acute Respiratory Syndrome date: 2007-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid1310.070576 sha: doc_id: 324938 cord_uid: 2lu9z5b2 file: cache/cord-324963-zg3ghl2m.json key: cord-324963-zg3ghl2m authors: Salzberger, B.; Welte, T. title: COVID-19 – eine neue und vielseitige Herausforderung date: 2020-08-03 journal: Internist (Berl) DOI: 10.1007/s00108-020-00851-8 sha: doc_id: 324963 cord_uid: zg3ghl2m file: cache/cord-324651-8teb5jrn.json key: cord-324651-8teb5jrn authors: Filippini, Antonio; D'Amore, Antonella; Palombi, Fioretta; Carpaneto, Armando title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date: 2020-04-30 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00970 sha: doc_id: 324651 cord_uid: 8teb5jrn file: cache/cord-324902-18h0maxi.json key: cord-324902-18h0maxi authors: Liu, Xuemei; Wang, Jing; Xu, Xiaolei; Liao, Guojian; Chen, Yaokai; Hu, Chang-Hua title: Patterns of IgG and IgM antibody response in COVID-19 patients date: 2020-06-09 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1773324 sha: doc_id: 324902 cord_uid: 18h0maxi file: cache/cord-324926-3c5ab73l.json key: cord-324926-3c5ab73l authors: Xia, Shuai; Yan, Lei; Xu, Wei; Agrawal, Anurodh Shankar; Algaissi, Abdullah; Tseng, Chien-Te K.; Wang, Qian; Du, Lanying; Tan, Wenjie; Wilson, Ian A.; Jiang, Shibo; Yang, Bei; Lu, Lu title: A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike date: 2019-04-10 journal: Sci Adv DOI: 10.1126/sciadv.aav4580 sha: doc_id: 324926 cord_uid: 3c5ab73l file: cache/cord-325113-sou8xyld.json key: cord-325113-sou8xyld authors: Kuiper, Johannes W. P.; Baade, Timo; Kremer, Marcel; Kranaster, Ramon; Irmisch, Linda; Schuchmann, Marcus; Zander, Johannes; Marx, Andreas; Hauck, Christof R. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0241740 sha: doc_id: 325113 cord_uid: sou8xyld file: cache/cord-324892-mg2dziuw.json key: cord-324892-mg2dziuw authors: Carneiro, João; Gomes, Catarina; Couto, Cátia; Pereira, Filipe title: CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date: 2020-06-12 journal: bioRxiv DOI: 10.1101/2020.04.19.048991 sha: doc_id: 324892 cord_uid: mg2dziuw file: cache/cord-325055-todb1d4x.json key: cord-325055-todb1d4x authors: Rychter, Anna Maria; Zawada, Agnieszka; Ratajczak, Alicja Ewa; Dobrowolska, Agnieszka; Krela‐Kaźmierczak, Iwona title: Should patients with obesity be more afraid of COVID‐19? date: 2020-06-24 journal: Obes Rev DOI: 10.1111/obr.13083 sha: doc_id: 325055 cord_uid: todb1d4x file: cache/cord-325197-j1uo8qmf.json key: cord-325197-j1uo8qmf authors: Crimi, Ettore; Benincasa, Giuditta; Figueroa-Marrero, Neisaliz; Galdiero, Massimiliano; Napoli, Claudio title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 journal: Br J Anaesth DOI: 10.1016/j.bja.2020.06.060 sha: doc_id: 325197 cord_uid: j1uo8qmf file: cache/cord-325261-bdumhy5b.json key: cord-325261-bdumhy5b authors: Clemente, Valentino; D’Arcy, Padraig; Bazzaro, Martina title: Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19 date: 2020-05-15 journal: Int J Mol Sci DOI: 10.3390/ijms21103492 sha: doc_id: 325261 cord_uid: bdumhy5b file: cache/cord-325014-n7mnhk2v.json key: cord-325014-n7mnhk2v authors: Gujski, Mariusz; Jankowski, Mateusz; Pinkas, Jarosław; Wierzba, Waldemar; Samel-Kowalik, Piotr; Zaczyński, Artur; Jędrusik, Piotr; Pańkowski, Igor; Juszczyk, Grzegorz; Rakocy, Kamil; Raciborski, Filip title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 journal: J Clin Med DOI: 10.3390/jcm9103245 sha: doc_id: 325014 cord_uid: n7mnhk2v file: cache/cord-325134-z9n17z72.json key: cord-325134-z9n17z72 authors: Nolan, Brodie; Chartier, Lucas B.; Verbeek, P. 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C.; Sánchez, J.; Espinosa, J.; Campana B, S.; Quintero, A.; Luo, C.; Ng C, J. title: Pregnancies recovered from SARS‐CoV‐2 infection in the second and third trimesters: obstetric evolution date: 2020-09-30 journal: Ultrasound Obstet Gynecol DOI: 10.1002/uog.23134 sha: doc_id: 325320 cord_uid: v9e2axf4 file: cache/cord-325324-kh2aal5n.json key: cord-325324-kh2aal5n authors: Teng, Shaolei; Tang, Qiyi title: ACE2 Enhance Viral Infection or Viral Infection Aggravate the Underlying Diseases date: 2020-08-06 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.08.002 sha: doc_id: 325324 cord_uid: kh2aal5n file: cache/cord-325124-0hxan9rw.json key: cord-325124-0hxan9rw authors: Li, Chenyu; Debruyne, David N.; Spencer, Julia; Kapoor, Vidushi; Liu, Lily Y.; Zhou, Bo; Pandey, Utsav; Bootwalla, Moiz; Ostrow, Dejerianne; Maglinte, Dennis T; Ruble, David; Ryutov, Alex; Shen, Lishuang; Lee, Lucie; Feigelman, Rounak; Burdon, Grayson; Liu, Jeffrey; Oliva, Alejandra; Borcherding, Adam; Tan, Hongdong; Urban, Alexander E.; Gai, Xiaowu; Bard, Jennifer Dien; Liu, Guoying; Liu, Zhitong title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 journal: bioRxiv DOI: 10.1101/2020.03.12.988246 sha: doc_id: 325124 cord_uid: 0hxan9rw file: cache/cord-325348-yi6yu5l1.json key: cord-325348-yi6yu5l1 authors: Zhang, G.; Pomplun, S.; Loftis, A. R.; Tan, X.; Loas, A.; Pentelute, B. L. title: Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date: 2020-06-17 journal: bioRxiv DOI: 10.1101/2020.03.19.999318 sha: doc_id: 325348 cord_uid: yi6yu5l1 file: cache/cord-325377-g68onkjt.json key: cord-325377-g68onkjt authors: Dey, Anusree; Das, Rituparna; Misra, Hari Sharan; Uppal, Sheetal title: COVID-19: Scientific Overview of the global Pandemic date: 2020-10-28 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100800 sha: doc_id: 325377 cord_uid: g68onkjt file: cache/cord-325282-20l9xcmg.json key: cord-325282-20l9xcmg authors: Helal, Mohamed A.; Shouman, Shaimaa; Abdelwaly, Ahmad; Elmehrath, Ahmed O.; Essawy, Mohamed; Sayed, Shireen M.; Saleh, Amr H.; El-Badri, Nagwa title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date: 2020-09-16 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1822208 sha: doc_id: 325282 cord_uid: 20l9xcmg file: cache/cord-324970-yty7aajj.json key: cord-324970-yty7aajj authors: Ma, Di; Chen, Chong-Bo; Jhanji, Vishal; Xu, Ciyan; Yuan, Xiang-Ling; Liang, Jia-Jian; Huang, Yuqiang; Cen, Ling-Ping; Ng, Tsz Kin title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea date: 2020-05-07 journal: Eye (Lond) DOI: 10.1038/s41433-020-0939-4 sha: doc_id: 324970 cord_uid: yty7aajj file: cache/cord-325136-oyizfh2z.json key: cord-325136-oyizfh2z authors: Pham, Quang Thai; Rabaa, Maia A; Duong, Huy Luong; Dang, Quang Tan; Tran, Dai Quang; Quach, Ha-Linh; Hoang, Ngoc-Anh Thi; Phung, Cong Dinh; Ngu, Duy Nghia; Tran, Anh Tu; La, Ngoc Quang; Tran, My Phuc; Vinh, Chau; Nguyen, Cong Khanh; Dang, Duc Anh; Tran, Nhu Duong; Thwaites, Guy; van Doorn, H Rogier; Choisy, Marc title: The first 100 days of SARS-CoV-2 control in Vietnam date: 2020-08-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1130 sha: doc_id: 325136 cord_uid: oyizfh2z file: cache/cord-325419-15vm22d8.json key: cord-325419-15vm22d8 authors: Dai, C. 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T. title: Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity date: 2020-10-15 journal: nan DOI: 10.1101/2020.10.14.20212803 sha: doc_id: 325419 cord_uid: 15vm22d8 file: cache/cord-325420-e9fjo7tl.json key: cord-325420-e9fjo7tl authors: Xiao, Xia; Wang, Conghui; Chang, De; Wang, Ying; Dong, Xiaojing; Jiao, Tao; Zhao, Zhendong; Ren, Lili; Dela Cruz, Charles S; Sharma, Lokesh; Lei, Xiaobo; Wang, Jianwei title: Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date: 2020-07-06 journal: bioRxiv DOI: 10.1101/2020.07.06.188953 sha: doc_id: 325420 cord_uid: e9fjo7tl file: cache/cord-325449-fl6ob5ja.json key: cord-325449-fl6ob5ja authors: Wang, Jing; Meng, Wen title: COVID-19 and diabetes: the contributions of hyperglycemia date: 2020-10-01 journal: J Mol Cell Biol DOI: 10.1093/jmcb/mjaa054 sha: doc_id: 325449 cord_uid: fl6ob5ja file: cache/cord-325421-1ysn0kyr.json key: cord-325421-1ysn0kyr authors: Christensen, Johanna; Kumar, Dhiren; Moinuddin, Irfan; Bryson, Alexandra; Kashi, Zahra; Kimball, Pamela; Levy, Marlon; Kamal, Layla; King, Anne; Gupta, Gaurav title: Covid-19 Viremia, Serologies and Clinical Course in a Case Series of Transplant Recipients date: 2020-09-03 journal: Transplant Proc DOI: 10.1016/j.transproceed.2020.08.042 sha: doc_id: 325421 cord_uid: 1ysn0kyr file: cache/cord-325473-hrdanbn1.json key: cord-325473-hrdanbn1 authors: Ghahremanpour, Mohammad M.; Tirado-Rives, Julian; Deshmukh, Maya; Ippolito, Joseph A.; Zhang, Chun-Hui; de Vaca, Israel Cabeza; Liosi, Maria-Elena; Anderson, Karen S.; Jorgensen, William L. title: Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.28.271957 sha: doc_id: 325473 cord_uid: hrdanbn1 file: cache/cord-325460-4fhegc0z.json key: cord-325460-4fhegc0z authors: Jacobs, Werner; Lammens, Martin; Kerckhofs, Annelies; Voets, Evy; Van San, Emily; Van Coillie, Samya; Peleman, Cédric; Mergeay, Matthias; Sirimsi, Sabriya; Matheeussen, Veerle; Jansens, Hilde; Baar, Ingrid; Vanden Berghe, Tom; Jorens, Philippe G. title: Fatal lymphocytic cardiac damage in coronavirus disease 2019 (COVID‐19): autopsy reveals a ferroptosis signature date: 2020-09-22 journal: ESC Heart Fail DOI: 10.1002/ehf2.12958 sha: doc_id: 325460 cord_uid: 4fhegc0z file: cache/cord-325234-skshcrh1.json key: cord-325234-skshcrh1 authors: Jin, Tingxu; Li, Jun; Yang, Jun; Li, Jiawei; Hong, Feng; Long, Hai; Deng, Qihong; Qin, Yong; Jiang, Jiajun; Zhou, Xuan; Song, Qian; Pan, Chunliu; Luo, Peng title: SARS-CoV-2 presented in the air of an intensive care unit (ICU) date: 2020-08-15 journal: Sustain Cities Soc DOI: 10.1016/j.scs.2020.102446 sha: doc_id: 325234 cord_uid: skshcrh1 file: cache/cord-325452-2sywbgje.json key: cord-325452-2sywbgje authors: Sun, Pengfei; Lu, Xiaosheng; Xu, Chao; Sun, Wenjuan; Pan, Bo title: Understanding of COVID‐19 based on current evidence date: 2020-03-05 journal: J Med Virol DOI: 10.1002/jmv.25722 sha: doc_id: 325452 cord_uid: 2sywbgje file: cache/cord-325479-2r4oomdp.json key: cord-325479-2r4oomdp authors: Torii, Shotaro; Furumai, Hiroaki; Katayama, Hiroyuki title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.143067 sha: doc_id: 325479 cord_uid: 2r4oomdp file: cache/cord-325112-7ie23c7f.json key: cord-325112-7ie23c7f authors: Heimer, Carol A. title: The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date: 2018-10-04 journal: Br J Sociol DOI: 10.1111/1468-4446.12495 sha: doc_id: 325112 cord_uid: 7ie23c7f file: cache/cord-325498-4yciuh1n.json key: cord-325498-4yciuh1n authors: Del Brutto, Oscar H.; Costa, Aldo F.; García, Héctor H. title: Incident SARS-CoV-2 Infection and a Shared Latrine date: 2020-07-22 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0793 sha: doc_id: 325498 cord_uid: 4yciuh1n file: cache/cord-325529-pid58g2r.json key: cord-325529-pid58g2r authors: Ben-Ami, Roni; Klochendler, Agnes; Seidel, Matan; Sido, Tal; Gurel-Gurevich, Ori; Yassour, Moran; Meshorer, Eran; Benedek, Gil; Fogel, Irit; Oiknine-Djian, Esther; Gertler, Asaf; Rotstein, Zeev; Lavi, Bruno; Dor, Yuval; Wolf, Dana G.; Salton, Maayan; Drier, Yotam title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.009 sha: doc_id: 325529 cord_uid: pid58g2r file: cache/cord-325744-i3r3ff3t.json key: cord-325744-i3r3ff3t authors: Chan, Angelina O. M.; Huak, Chan Yiong title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore date: 2004-05-17 journal: Occup Med (Lond) DOI: 10.1093/occmed/kqh027 sha: doc_id: 325744 cord_uid: i3r3ff3t file: cache/cord-325783-pqonn0as.json key: cord-325783-pqonn0as authors: Nicholls, John M; Poon, Leo LM; Lee, Kam C; Ng, Wai F; Lai, Sik T; Leung, Chung Y; Chu, Chung M; Hui, Pak K; Mak, Kong L; Lim, Wilna; Yan, Kin W; Chan, Kwok H; Tsang, Ngai C; Guan, Yi; Yuen, Kwok Y; Malik Peiris, JS title: Lung pathology of fatal severe acute respiratory syndrome date: 2003-05-24 journal: Lancet DOI: 10.1016/s0140-6736(03)13413-7 sha: doc_id: 325783 cord_uid: pqonn0as file: cache/cord-325559-di8lljoi.json key: cord-325559-di8lljoi authors: Cappello, Francesco; Marino Gammazza, Antonella; Dieli, Francesco; Conway de Macario, Everly; Macario, Alberto JL title: Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date: 2020-06-29 journal: J Clin Med DOI: 10.3390/jcm9072038 sha: doc_id: 325559 cord_uid: di8lljoi file: cache/cord-325657-s2vdazq0.json key: cord-325657-s2vdazq0 authors: Huang, Yan-Jang S.; Vanlandingham, Dana L.; Bilyeu, Ashley N.; Sharp, Haelea M.; Hettenbach, Susan M.; Higgs, Stephen title: SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge date: 2020-07-17 journal: Sci Rep DOI: 10.1038/s41598-020-68882-7 sha: doc_id: 325657 cord_uid: s2vdazq0 file: cache/cord-325593-ww2vq3n4.json key: cord-325593-ww2vq3n4 authors: Hendren, Nicholas S.; Grodin, Justin L.; Drazner, Mark H. title: Unique Patterns of Cardiovascular Involvement in COVID-19 date: 2020-05-14 journal: J Card Fail DOI: 10.1016/j.cardfail.2020.05.006 sha: doc_id: 325593 cord_uid: ww2vq3n4 file: cache/cord-325598-gy809ee0.json key: cord-325598-gy809ee0 authors: Lyne, Cloutier; Natacha, Merindol; Geneviève, Pépin; Caroline, Marcoux-Huard; Pier-Alexandre, Vasil; Claudia, Houle; Shweta, Todkar; Marie-Claude, Lehoux; Nathalie, Houle; Hugo, Germain; Alexis, Danylo title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study date: 2020-08-21 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.08.015 sha: doc_id: 325598 cord_uid: gy809ee0 file: cache/cord-325481-uzch2hwd.json key: cord-325481-uzch2hwd authors: Simmons, Graham; Bertram, Stephanie; Glowacka, Ilona; Steffen, Imke; Chaipan, Chawaree; Agudelo, Juliet; Lu, Kai; Rennekamp, Andrew J.; Hofmann, Heike; Bates, Paul; Pöhlmann, Stefan title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date: 2011-05-01 journal: Virology DOI: 10.1016/j.virol.2011.02.020 sha: doc_id: 325481 cord_uid: uzch2hwd file: cache/cord-325595-y9ae6zbr.json key: cord-325595-y9ae6zbr authors: Montopoli, M.; Zumerle, S.; Rugge, M.; Alimonti, A. title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality date: 2020-10-23 journal: Ann Oncol DOI: 10.1016/j.annonc.2020.07.022 sha: doc_id: 325595 cord_uid: y9ae6zbr file: cache/cord-325614-e9hnhzfg.json key: cord-325614-e9hnhzfg authors: Todorov, German; Uversky, Vladimir N. title: A Possible Path towards Rapid Development of Live-Attenuated SARS-CoV-2 Vaccines: Plunging into the Natural Pool date: 2020-10-14 journal: Biomolecules DOI: 10.3390/biom10101438 sha: doc_id: 325614 cord_uid: e9hnhzfg file: cache/cord-325959-uqg2xkie.json key: cord-325959-uqg2xkie authors: Bundschuh, Christian; Egger, Margot; Wiesinger, Kurt; Gabriel, Christian; Clodi, Martin; Mueller, Thomas; Dieplinger, Benjamin title: Evaluation of the EDI enzyme linked immunosorbent assays for the detection of SARS-CoV-2 IgM and IgG antibodies in human plasma date: 2020-06-08 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.05.047 sha: doc_id: 325959 cord_uid: uqg2xkie file: cache/cord-325863-3t73v4ng.json key: cord-325863-3t73v4ng authors: Foss, Francine M.; Rubinowitz, Ami; Landry, Marie L.; Isufi, Iris; Gowda, Lohith; Seropian, Stuart; Perreault, Sarah; Shenoi, Sheela V. title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib date: 2020-06-25 journal: Clin Lymphoma Myeloma Leuk DOI: 10.1016/j.clml.2020.06.014 sha: doc_id: 325863 cord_uid: 3t73v4ng file: cache/cord-325910-qiay8n43.json key: cord-325910-qiay8n43 authors: Green, D. A.; Zucker, J. E.; Westblade, L. F.; Whittier, S.; Rennert, H.; Velu, P.; Craney, A.; Cushing, M.; Liu, D.; Sobieszczyk, M. E.; Boehme, A. K.; Sepulveda, J. title: Clinical Performance of SARS-CoV-2 Molecular Testing date: 2020-05-08 journal: nan DOI: 10.1101/2020.05.06.20093575 sha: doc_id: 325910 cord_uid: qiay8n43 file: cache/cord-326198-6okk3u49.json key: cord-326198-6okk3u49 authors: Walker, A.; Houwaart, T.; Wienemann, T.; Kohns Vasconcelos, M.; Strelow, D.; Senff, T.; Hülse, L.; Adams, O.; Andree, M.; Hauka, S.; Feldt, T.; Jensen, B.-E.; Keitel, V.; Kindgen-Milles, D.; Timm, J.; Pfeffer, K.; Dilthey, A. T. title: Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events date: 2020-04-30 journal: nan DOI: 10.1101/2020.04.25.20079517 sha: doc_id: 326198 cord_uid: 6okk3u49 file: cache/cord-325830-mrtpihc7.json key: cord-325830-mrtpihc7 authors: Nelson, Philipp P.; Rath, Barbara A.; Fragkou, Paraskevi C.; Antalis, Emmanouil; Tsiodras, Sotirios; Skevaki, Chrysanthi title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2020.00181 sha: doc_id: 325830 cord_uid: mrtpihc7 file: cache/cord-325991-dktffiaa.json key: cord-325991-dktffiaa authors: Gross, Oliver; Moerer, Onnen; Weber, Manfred; Huber, Tobias B; Scheithauer, Simone title: COVID-19-associated nephritis: early warning for disease severity and complications? date: 2020-05-06 journal: Lancet DOI: 10.1016/s0140-6736(20)31041-2 sha: doc_id: 325991 cord_uid: dktffiaa file: cache/cord-325966-0g7a9s5z.json key: cord-325966-0g7a9s5z authors: Shih, Hsin-I.; Wu, Chi-Jung; Tu, Yi-Fang; Chi, Chia-Yu title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 journal: Biomed J DOI: 10.1016/j.bj.2020.05.021 sha: doc_id: 325966 cord_uid: 0g7a9s5z file: cache/cord-326150-cf4rlqe5.json key: cord-326150-cf4rlqe5 authors: Carrascosa, J M; Morillas, V.; Bielsa, I.; Munera-Campos, M. title: Manifestaciones cutáneas en el contexto de la infección por SARS-CoV-2 (COVID-19) date: 2020-08-31 journal: Actas Dermosifiliogr DOI: 10.1016/j.ad.2020.08.002 sha: doc_id: 326150 cord_uid: cf4rlqe5 file: cache/cord-326017-qw4qynqv.json key: cord-326017-qw4qynqv authors: Laskar, Partha; Yallapu, Murali M.; Chauhan, Subhash C. title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 journal: Diseases DOI: 10.3390/diseases8030030 sha: doc_id: 326017 cord_uid: qw4qynqv file: cache/cord-326169-delehk6x.json key: cord-326169-delehk6x authors: CJ Jorgensen, Sarah; LY Tse, Christopher; Burry, Lisa; Dresser, Linda D title: Baricitinib: A review of pharmacology, safety and emerging clinical experience in COVID‐19 date: 2020-06-15 journal: Pharmacotherapy DOI: 10.1002/phar.2438 sha: doc_id: 326169 cord_uid: delehk6x file: cache/cord-325936-rwxg187r.json key: cord-325936-rwxg187r authors: Eyal, Nir; Halkitis, Perry N. title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 journal: AIDS Behav DOI: 10.1007/s10461-020-02953-8 sha: doc_id: 325936 cord_uid: rwxg187r file: cache/cord-325669-6kjlcakt.json key: cord-325669-6kjlcakt authors: Fogacci, Silvia; Fogacci, Federica; Favari, Elda; Toth, Peter P; Borghi, Claudio; Cicero, Arrigo F G title: Management of pregnancy-related hypertensive disorders in patients infected with SARS CoV-2: pharmacological and clinical issues date: 2020-09-10 journal: Eur Heart J Cardiovasc Pharmacother DOI: 10.1093/ehjcvp/pvaa105 sha: doc_id: 325669 cord_uid: 6kjlcakt file: cache/cord-326273-6rp12py3.json key: cord-326273-6rp12py3 authors: Chow, Kuan-Chih; Hsiao, Cheng-Hsiang; Lin, Tze-Yi; Chen, Chi-Long; Chiou, Shiow-Her title: Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date: 2004-04-01 journal: Am J Clin Pathol DOI: 10.1309/c0edu0raqbtxbhce sha: doc_id: 326273 cord_uid: 6rp12py3 file: cache/cord-325609-n6dpac6i.json key: cord-325609-n6dpac6i authors: Dawson, Kathryn L.; Vincent, Logan L.; Krieger, Eric V.; Stout, Karen K.; Buber, Jonathan title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 - single center experience. date: 2020-06-13 journal: JACC Case Rep DOI: 10.1016/j.jaccas.2020.06.013 sha: doc_id: 325609 cord_uid: n6dpac6i file: cache/cord-326254-8dlxsf57.json key: cord-326254-8dlxsf57 authors: Glasbey, T.; Whiteley, G. title: Flawed disinfectant recommendations during a pandemic date: 2020-06-15 journal: nan DOI: 10.1016/j.infpip.2020.100070 sha: doc_id: 326254 cord_uid: 8dlxsf57 file: cache/cord-326282-uxn64olw.json key: cord-326282-uxn64olw authors: Lu, Maolin; Uchil, Pradeep D.; Li, Wenwei; Zheng, Desheng; Terry, Daniel S.; Gorman, Jason; Shi, Wei; Zhang, Baoshan; Zhou, Tongqing; Ding, Shilei; Gasser, Romain; Prévost, Jérémie; Beaudoin-Bussières, Guillaume; Anand, Sai Priya; Laumaea, Annemarie; Grover, Jonathan R.; Liu, Lihong; Ho, David D.; Mascola, John R.; Finzi, Andrés; Kwong, Peter D.; Blanchard, Scott C.; Mothes, Walther title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 journal: bioRxiv DOI: 10.1101/2020.09.10.286948 sha: doc_id: 326282 cord_uid: uxn64olw file: cache/cord-326305-mjd5agvf.json key: cord-326305-mjd5agvf authors: Ashraf, Mohammad Ali; Sherafat, Alireza; Pourdast, Alieh; Nazemi, Pershang; Mohraz, Minoo title: The application of direct viral cytopathic hypothesis to design drug trials in the battle against COVID-19 date: 2020-08-15 journal: Daru DOI: 10.1007/s40199-020-00368-3 sha: doc_id: 326305 cord_uid: mjd5agvf file: cache/cord-326013-5i35zdmv.json key: cord-326013-5i35zdmv authors: Carpinteiro, Alexander; Edwards, Michael J.; Hoffmann, Markus; Kochs, Georg; Gripp, Barbara; Weigang, Sebastian; Adams, Constantin; Carpinteiro, Elisa; Gulbins, Anne; Keitsch, Simone; Sehl, Carolin; Soddemann, Matthias; Wilker, Barbara; Kamler, Markus; Bertsch, Thomas; Lang, Karl S.; Patel, Sameer; Wilson, Gregory C.; Walter, Silke; Hengel, Hartmut; Pöhlmann, Stefan; Lang, Philipp; Kornhuber, Johannes; Becker, Katrin Anne; Ahmad, Syed A.; Fassbender, Klaus; Gulbins, Erich title: Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells date: 2020-10-29 journal: Cell Rep Med DOI: 10.1016/j.xcrm.2020.100142 sha: doc_id: 326013 cord_uid: 5i35zdmv file: cache/cord-326375-8m4110k3.json key: cord-326375-8m4110k3 authors: Seitzman, Gerami D.; Doan, Thuy title: No Time for Tears date: 2020-03-26 journal: Ophthalmology DOI: 10.1016/j.ophtha.2020.03.030 sha: doc_id: 326375 cord_uid: 8m4110k3 file: cache/cord-326503-ljle4vq3.json key: cord-326503-ljle4vq3 authors: Morioka, Shinichiro; Nakamura, Keiji; Iida, Shun; Kutsuna, Satoshi; Kinoshita, Noriko; Suzuki, Tetsuya; Suzuki, Tadaki; Yamamoto, Kei; Hayakawa, Kayoko; Saito, Sho; Ohmagari, Norio title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study date: 2020-07-30 journal: nan DOI: 10.1016/j.infpip.2020.100079 sha: doc_id: 326503 cord_uid: ljle4vq3 file: cache/cord-326148-9wpxm5of.json key: cord-326148-9wpxm5of authors: Van Walle, I.; Leitmeyer, K.; Broberg, E. K.; group, The European COVID-19 microbiological laboratories title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.16.20195917 sha: doc_id: 326148 cord_uid: 9wpxm5of file: cache/cord-326498-8oa5gkrp.json key: cord-326498-8oa5gkrp authors: Gemmati, Donato; Bramanti, Barbara; Serino, Maria Luisa; Secchiero, Paola; Zauli, Giorgio; Tisato, Veronica title: COVID-19 and Individual Genetic Susceptibility/Receptivity: Role of ACE1/ACE2 Genes, Immunity, Inflammation and Coagulation. Might the Double X-Chromosome in Females Be Protective against SARS-CoV-2 Compared to the Single X-Chromosome in Males? date: 2020-05-14 journal: Int J Mol Sci DOI: 10.3390/ijms21103474 sha: doc_id: 326498 cord_uid: 8oa5gkrp file: cache/cord-326337-s0fp5z1q.json key: cord-326337-s0fp5z1q authors: Chan, Kui K.; Tan, Timothy J.C.; Narayanan, Krishna K.; Procko, Erik title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date: 2020-10-19 journal: bioRxiv DOI: 10.1101/2020.10.18.344622 sha: doc_id: 326337 cord_uid: s0fp5z1q file: cache/cord-326045-x8xntne7.json key: cord-326045-x8xntne7 authors: Chng, Shu-Sin; Hoang, Truong-Giang; Wayne Lee, Wei-Woon; Tham, Mun-Pun; Ling, Hui Yvonne; Loh, Teck-Peng title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate date: 2004-12-20 journal: Tetrahedron Lett DOI: 10.1016/j.tetlet.2004.10.146 sha: doc_id: 326045 cord_uid: x8xntne7 file: cache/cord-326257-rcv8sh22.json key: cord-326257-rcv8sh22 authors: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 journal: bioRxiv DOI: 10.1101/2020.05.01.072330 sha: doc_id: 326257 cord_uid: rcv8sh22 file: cache/cord-326393-gxy1w0qk.json key: cord-326393-gxy1w0qk authors: Martino, Marcello Di; Septiem, Javier García; González, Rocío Maqueda; de Nova, Jose Luis Muñoz; de la Hoz Rodríguez, Ángela; Bonito, Alba Correa; Martín-Pérez, Elena title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD date: 2020-04-29 journal: Cir Esp DOI: 10.1016/j.ciresp.2020.04.029 sha: doc_id: 326393 cord_uid: gxy1w0qk file: cache/cord-326730-aprb819p.json key: cord-326730-aprb819p authors: Perkmann, T.; Perkmann-Nagele, N.; Breyer, M.-K.; Breyer-Kohansal, R.; Burghuber, O. C.; Hartl, S.; Aletaha, D.; Sieghart, D.; Quehenberger, P.; Marculescu, R.; Mucher, P.; Strassl, R.; Wagner, O. F.; Binder, C. J.; Haslacher, H. title: Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity date: 2020-06-05 journal: nan DOI: 10.1101/2020.06.04.20117911 sha: doc_id: 326730 cord_uid: aprb819p file: cache/cord-325958-1v1pg2z0.json key: cord-325958-1v1pg2z0 authors: Lange, Clemens; Wolf, Julian; Auw‐Haedrich, Claudia; Schlecht, Anja; Boneva, Stefaniya; Lapp, Thabo; Horres, Ralf; Agostini, Hansjürgen; Martin, Gottfried; Reinhard, Thomas; Schlunck, Günther title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 journal: J Med Virol DOI: 10.1002/jmv.25981 sha: doc_id: 325958 cord_uid: 1v1pg2z0 file: cache/cord-326532-2ehuuvnx.json key: cord-326532-2ehuuvnx authors: Götzinger, Florian; Santiago-García, Begoña; Noguera-Julián, Antoni; Lanaspa, Miguel; Lancella, Laura; Calò Carducci, Francesca I; Gabrovska, Natalia; Velizarova, Svetlana; Prunk, Petra; Osterman, Veronika; Krivec, Uros; Lo Vecchio, Andrea; Shingadia, Delane; Soriano-Arandes, Antoni; Melendo, Susana; Lanari, Marcello; Pierantoni, Luca; Wagner, Noémie; L'Huillier, Arnaud G; Heininger, Ulrich; Ritz, Nicole; Bandi, Srini; Krajcar, Nina; Roglić, Srđan; Santos, Mar; Christiaens, Christelle; Creuven, Marine; Buonsenso, Danilo; Welch, Steven B; Bogyi, Matthias; Brinkmann, Folke; Tebruegge, Marc title: COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study date: 2020-06-25 journal: Lancet Child Adolesc Health DOI: 10.1016/s2352-4642(20)30177-2 sha: doc_id: 326532 cord_uid: 2ehuuvnx file: cache/cord-326706-75mjs6vm.json key: cord-326706-75mjs6vm authors: Waterfield, Thomas; Watson, Chris; Moore, Rebecca; Ferris, Kathryn; Tonry, Claire; Watt, Alison; McGinn, Claire; Foster, Steven; Evans, Jennifer; Lyttle, Mark David; Ahmad, Shazaad; Ladhani, Shamez; Corr, Michael; McFetridge, Lisa; Mitchell, Hannah; Brown, Kevin; Amirthalingam, Gayatri; Maney, Julie-Ann; Christie, Sharon title: Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study date: 2020-11-10 journal: Arch Dis Child DOI: 10.1136/archdischild-2020-320558 sha: doc_id: 326706 cord_uid: 75mjs6vm file: cache/cord-326514-7plamtl8.json key: cord-326514-7plamtl8 authors: Veerus, Piret; Salumets, Andres; Naaber, Paul; Krjutškov, Kaarel; Tilk, Kadi; Laanpere, Made; Uusküla, Anneli title: Seroprevalence of SARS‐CoV‐2 antibodies among pregnant women in Estonia: a call for epidemiological studies date: 2020-09-24 journal: Acta Obstet Gynecol Scand DOI: 10.1111/aogs.13995 sha: doc_id: 326514 cord_uid: 7plamtl8 file: cache/cord-326643-obfvi3ms.json key: cord-326643-obfvi3ms authors: Lo Giudice, Roberto title: The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in Dentistry. Management of Biological Risk in Dental Practice date: 2020-04-28 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17093067 sha: doc_id: 326643 cord_uid: obfvi3ms file: cache/cord-326718-jboiufoq.json key: cord-326718-jboiufoq authors: Deming, Meagan E.; Chen, Wilbur H. title: COVID-19 and Lessons to Be Learned from Prior Coronavirus Outbreaks date: 2020-07-17 journal: Ann Am Thorac Soc DOI: 10.1513/annalsats.202002-149ps sha: doc_id: 326718 cord_uid: jboiufoq file: cache/cord-326721-2v5wkjrq.json key: cord-326721-2v5wkjrq authors: Xiao, Wenlei; Liu, Qiang; Huan, J; Sun, Pengpeng; Wang, Liuquan; Zang, Chenxin; Zhu, Sanying; Gao, Liansheng title: A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks date: 2020-03-17 journal: nan DOI: 10.1101/2020.03.13.20034082 sha: doc_id: 326721 cord_uid: 2v5wkjrq file: cache/cord-326341-egtnqlov.json key: cord-326341-egtnqlov authors: Liotti, Flora Marzia; Menchinelli, Giulia; Lalle, Eleonora; Palucci, Ivana; Marchetti, Simona; Colavita, Francesca; La Sorda, Marilena; Sberna, Giuseppe; Bordi, Licia; Sanguinetti, Maurizio; Cattani, Paola; Capobianchi, Maria Rosaria; Posteraro, Brunella title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.030 sha: doc_id: 326341 cord_uid: egtnqlov file: cache/cord-326427-06djb0sd.json key: cord-326427-06djb0sd authors: Cao, Dongmei; Chen, Miaomiao; Peng, Min; Yin, Heng; Sun, Guoqiang title: Vaginal delivery in women with COVID-19: report of two cases date: 2020-10-02 journal: BMC Pregnancy Childbirth DOI: 10.1186/s12884-020-03281-4 sha: doc_id: 326427 cord_uid: 06djb0sd file: cache/cord-326320-flfrdrbi.json key: cord-326320-flfrdrbi authors: Choudhary, Shalki; Silakari, Om title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date: 2020-08-29 journal: Virus Res DOI: 10.1016/j.virusres.2020.198146 sha: doc_id: 326320 cord_uid: flfrdrbi file: cache/cord-326568-twv2i3fb.json key: cord-326568-twv2i3fb authors: Bruminhent, Jackrapong; Ruangsubvilai, Nattanon; Nabhindhakara, Jeff; Ingsathit, Atiporn; Kiertiburanakul, Sasisopin title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0239250 sha: doc_id: 326568 cord_uid: twv2i3fb file: cache/cord-326581-31trqhi1.json key: cord-326581-31trqhi1 authors: Ihling, Christian; Tänzler, Dirk; Hagemann, Sven; Kehlen, Astrid; Hüttelmaier, Stefan; Arlt, Christian; Sinz, Andrea title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients date: 2020-06-22 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00280 sha: doc_id: 326581 cord_uid: 31trqhi1 file: cache/cord-326911-va3x6au2.json key: cord-326911-va3x6au2 authors: Ramos-Mandujano, G.; Salunke, R.; Mfarrej, S.; Rachmadi, A.; Hala, S.; Xu, J.; Alofi, F. S.; Khogeer, A.; Hashem, A. M.; Almontashiri, N. A.; Alsomali, A.; Hamdan, S.; Hong, P.; Pain, A.; Li, M. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 journal: nan DOI: 10.1101/2020.06.28.20141945 sha: doc_id: 326911 cord_uid: va3x6au2 file: cache/cord-326736-jd6fvaop.json key: cord-326736-jd6fvaop authors: Bosco-Lauth, Angela M.; Hartwig, Airn E.; Porter, Stephanie M.; Gordy, Paul W.; Nehring, Mary; Byas, Alex D.; VandeWoude, Sue; Ragan, Izabela K.; Maison, Rachel M.; Bowen, Richard A. title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date: 2020-05-29 journal: bioRxiv DOI: 10.1101/2020.05.28.120998 sha: doc_id: 326736 cord_uid: jd6fvaop file: cache/cord-326864-i1r3bv4p.json key: cord-326864-i1r3bv4p authors: Hon, Kam Lun; Leung, Karen Ka Yan; Leung, Alexander KC; Qian, Su Yun; Chan, Vivian PY; Ip, Patrick; Wong, Ian CK title: Coronavirus disease 2019 (COVID-19): latest developments in potential treatments date: 2020-06-29 journal: Drugs Context DOI: 10.7573/dic.2020-4-15 sha: doc_id: 326864 cord_uid: i1r3bv4p file: cache/cord-326916-bakwk4tm.json key: cord-326916-bakwk4tm authors: Fauver, Joseph R.; Petrone, Mary E.; Hodcroft, Emma B.; Shioda, Kayoko; Ehrlich, Hanna Y.; Watts, Alexander G.; Vogels, Chantal B.F.; Brito, Anderson F.; Alpert, Tara; Muyombwe, Anthony; Razeq, Jafar; Downing, Randy; Cheemarla, Nagarjuna R.; Wyllie, Anne L.; Kalinich, Chaney C.; Ott, Isabel M.; Quick, Joshua; Loman, Nicholas J.; Neugebauer, Karla M.; Greninger, Alexander L.; Jerome, Keith R.; Roychoudhury, Pavitra; Xie, Hong; Shrestha, Lasata; Huang, Meei-Li; Pitzer, Virginia E.; Iwasaki, Akiko; Omer, Saad B.; Khan, Kamran; Bogoch, Isaac I.; Martinello, Richard A.; Foxman, Ellen F.; Landry, Marie L.; Neher, Richard A.; Ko, Albert I.; Grubaugh, Nathan D. title: Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States date: 2020-05-07 journal: Cell DOI: 10.1016/j.cell.2020.04.021 sha: doc_id: 326916 cord_uid: bakwk4tm file: cache/cord-326406-n0qi6gs8.json key: cord-326406-n0qi6gs8 authors: Creed, Marina; Ballesteros, Enrique; Jr, L. John Greenfield; Imitola, Jaime title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. date: 2020-05-19 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102199 sha: doc_id: 326406 cord_uid: n0qi6gs8 file: cache/cord-326882-bbn1tfq5.json key: cord-326882-bbn1tfq5 authors: Li, Quan; Cao, Zanxia; Rahman, Proton title: Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.14.041434 sha: doc_id: 326882 cord_uid: bbn1tfq5 file: cache/cord-326929-ytix4l1o.json key: cord-326929-ytix4l1o authors: Samillan, V. J.; Flores-Leon, D.; Zutta, B. R.; Rojas, E. title: Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.16.20196170 sha: doc_id: 326929 cord_uid: ytix4l1o file: cache/cord-326888-0p8nctpy.json key: cord-326888-0p8nctpy authors: Gercina, Anne Caroline; de Souza Amorim, Klinger; Pagaduan, Rochelle; de Almeida Souza, Liane Maciel; Groppo, Francisco Carlos title: What is the best mouthrinse against Coronaviruses? date: 2020-08-13 journal: Oral Surg DOI: 10.1111/ors.12549 sha: doc_id: 326888 cord_uid: 0p8nctpy file: cache/cord-326965-xrnhkcsv.json key: cord-326965-xrnhkcsv authors: Lacout, Carole; Rogez, Juliette; Orvain, Corentin; Nicot, Claire; Rony, Louis; Julien, Hélène; Urbanski, Geoffrey title: A new diagnosis of systemic capillary leak syndrome in a patient with COVID-19 date: 2020-09-17 journal: Rheumatology (Oxford) DOI: 10.1093/rheumatology/keaa606 sha: doc_id: 326965 cord_uid: xrnhkcsv file: cache/cord-326883-j7pbe50g.json key: cord-326883-j7pbe50g authors: Stöbe, Stephan; Richter, Sarah; Seige, Markus; Stehr, Sebastian; Laufs, Ulrich; Hagendorff, Andreas title: Echocardiographic characteristics of patients with SARS-CoV-2 infection date: 2020-08-14 journal: Clin Res Cardiol DOI: 10.1007/s00392-020-01727-5 sha: doc_id: 326883 cord_uid: j7pbe50g file: cache/cord-327028-dbvucvy3.json key: cord-327028-dbvucvy3 authors: Zhang, Cantong; Huang, Shaoying; Zheng, Fengping; Dai, Yong title: Controversial treatments: An updated understanding of the coronavirus disease 2019 date: 2020-04-10 journal: J Med Virol DOI: 10.1002/jmv.25788 sha: doc_id: 327028 cord_uid: dbvucvy3 file: cache/cord-327169-sz4ildnd.json key: cord-327169-sz4ildnd authors: Mondoni, Michele; Sferrazza Papa, Giuseppe Francesco; Rinaldo, Rocco; Faverio, Paola; Marruchella, Almerico; D'Arcangelo, Francesca; Pesci, Alberto; Pasini, Simone; Henchi, Sonia; Cipolla, Giuseppe; Tarantini, Francesco; Giuliani, Lisa; Di Marco, Fabiano; Saracino, Laura; Tomaselli, Stefano; Corsico, Angelo; Gasparini, Stefano; Bonifazi, Martina; Zuccatosta, Lina; Saderi, Laura; Pellegrino, Giulia; Davì, Matteo; Carlucci, Paolo; Centanni, Stefano; Sotgiu, Giovanni title: Utility and safety of bronchoscopy during SARS-CoV-2 outbreak in Italy: a retrospective, multicenter study date: 2020-08-28 journal: Eur Respir J DOI: 10.1183/13993003.02767-2020 sha: doc_id: 327169 cord_uid: sz4ildnd file: cache/cord-326983-h6gdck2u.json key: cord-326983-h6gdck2u authors: Ferretti, Andrew P.; Kula, Tomasz; Wang, Yifan; Nguyen, Dalena M.V.; Weinheimer, Adam; Dunlap, Garrett S.; Xu, Qikai; Nabilsi, Nancy; Perullo, Candace R.; Cristofaro, Alexander W.; Whitton, Holly J.; Virbasius, Amy; Olivier, Kenneth J.; Buckner, Lyndsey R.; Alistar, Angela T.; Whitman, Eric D.; Bertino, Sarah A.; Chattopadhyay, Shrikanta; MacBeath, Gavin title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 journal: Immunity DOI: 10.1016/j.immuni.2020.10.006 sha: doc_id: 326983 cord_uid: h6gdck2u file: cache/cord-327000-oyg3oyx1.json key: cord-327000-oyg3oyx1 authors: Li, Shasha; Yang, Jinping; Zhu, Zixiang; Zheng, Haixue title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 journal: Pathogens DOI: 10.3390/pathogens9050367 sha: doc_id: 327000 cord_uid: oyg3oyx1 file: cache/cord-327086-u3l8nr73.json key: cord-327086-u3l8nr73 authors: Mauvais-Jarvis, Franck; Klein, Sabra L; Levin, Ellis R title: Estradiol, Progesterone, Immunomodulation, and COVID-19 Outcomes date: 2020-07-30 journal: Endocrinology DOI: 10.1210/endocr/bqaa127 sha: doc_id: 327086 cord_uid: u3l8nr73 file: cache/cord-326956-oz047qmf.json key: cord-326956-oz047qmf authors: Lu, Yiping; Li, Xuanxuan; Geng, Daoying; Mei, Nan; Wu, Pu-Yeh; Huang, Chu-Chung; Jia, Tianye; Zhao, Yajing; Wang, Dongdong; Xiao, Anling; Yin, Bo title: Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study date: 2020-08-03 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100484 sha: doc_id: 326956 cord_uid: oz047qmf file: cache/cord-326833-boxgt4kb.json key: cord-326833-boxgt4kb authors: Marimuthu, Janakiram; Kumar, Bubby S; Aravind Gandhi, P title: HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date: 2020-07-07 journal: J Med Virol DOI: 10.1002/jmv.26271 sha: doc_id: 326833 cord_uid: boxgt4kb file: cache/cord-327240-nohxk3y6.json key: cord-327240-nohxk3y6 authors: Muller, Matthew P.; Dresser, Linda; Raboud, Janet; McGeer, Allison; Rea, Elizabeth; Richardson, Susan E.; Mazzulli, Tony; Loeb, Mark; Louie, Marie title: Adverse Events Associated with High‐Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome date: 2012-01-06 journal: Pharmacotherapy DOI: 10.1592/phco.27.4.494 sha: doc_id: 327240 cord_uid: nohxk3y6 file: cache/cord-326666-melz5fq4.json key: cord-326666-melz5fq4 authors: Sun, Weitao title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date: 2020-09-03 journal: bioRxiv DOI: 10.1101/2020.09.03.280727 sha: doc_id: 326666 cord_uid: melz5fq4 file: cache/cord-326984-o27rp468.json key: cord-326984-o27rp468 authors: CHIEN, Jung‐Yien; HSUEH, Po‐Ren; CHENG, Wern‐Cherng; YU, Chong‐Jen; YANG, Pan‐Chyr title: Temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome date: 2006-10-16 journal: Respirology DOI: 10.1111/j.1440-1843.2006.00942.x sha: doc_id: 326984 cord_uid: o27rp468 file: cache/cord-327005-7zgolyqf.json key: cord-327005-7zgolyqf authors: Zhang, Lan; Huang, Songming title: Clinical Features of 33 Cases in Children Infected With SARS-CoV-2 in Anhui Province, China–A Multi-Center Retrospective Cohort Study date: 2020-06-16 journal: Front Public Health DOI: 10.3389/fpubh.2020.00255 sha: doc_id: 327005 cord_uid: 7zgolyqf file: cache/cord-327124-kzavc4ez.json key: cord-327124-kzavc4ez authors: Wang, Ming; Yan, Meiying; Xu, Huifang; Liang, Weili; Kan, Biao; Zheng, Bojian; Chen, Honglin; Zheng, Han; Xu, Yanmei; Zhang, Enmin; Wang, Hongxia; Ye, Jingrong; Li, Guichang; Li, Machao; Cui, Zhigang; Liu, Yu-Fei; Guo, Rong-Tong; Liu, Xiao-Ning; Zhan, Liu-Hua; Zhou, Duan-Hua; Zhao, Ailan; Hai, Rong; Yu, Dongzhen; Guan, Yi; Xu, Jianguo title: SARS-CoV Infection in a Restaurant from Palm Civet date: 2005-12-17 journal: Emerg Infect Dis DOI: 10.3201/eid1112.041293 sha: doc_id: 327124 cord_uid: kzavc4ez file: cache/cord-327063-ea7a1xfl.json key: cord-327063-ea7a1xfl authors: Dhama, Kuldeep; Patel, Shailesh Kumar; Sharun, Khan; Pathak, Mamta; Tiwari, Ruchi; Yatoo, Mohd Iqbal; Malik, Yashpal Singh; Sah, Ranjit; Rabaan, Ali A.; Panwar, Parmod Kumar; Singh, Karam Pal; Michalak, Izabela; Chaicumpa, Wanpen; Martinez-Pulgarin, Dayron F.; Bonilla-Aldana, D. Katterine; Rodriguez-Morales, Alfonso J. title: SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus date: 2020-08-02 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101830 sha: doc_id: 327063 cord_uid: ea7a1xfl file: cache/cord-327095-y2zsm8sc.json key: cord-327095-y2zsm8sc authors: Boretti, Alberto title: Favipiravir use for SARS CoV-2 infection date: 2020-10-27 journal: Pharmacol Rep DOI: 10.1007/s43440-020-00175-2 sha: doc_id: 327095 cord_uid: y2zsm8sc file: cache/cord-327084-r12copka.json key: cord-327084-r12copka authors: Zhang, Chenxi; Yang, Lulu; Liu, Shuai; Ma, Simeng; Wang, Ying; Cai, Zhongxiang; Du, Hui; Li, Ruiting; Kang, Lijun; Su, Meilei; Zhang, Jihui; Liu, Zhongchun; Zhang, Bin title: Survey of Insomnia and Related Social Psychological Factors Among Medical Staff Involved in the 2019 Novel Coronavirus Disease Outbreak date: 2020-04-14 journal: Front Psychiatry DOI: 10.3389/fpsyt.2020.00306 sha: doc_id: 327084 cord_uid: r12copka file: cache/cord-327134-egp4t82x.json key: cord-327134-egp4t82x authors: Mukherjee, Prasenjit; Desai, Prashant; Ross, Larry; White, E. Lucile; Avery, Mitchell A. title: Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits date: 2008-04-01 journal: Bioorganic & Medicinal Chemistry DOI: 10.1016/j.bmc.2008.01.011 sha: doc_id: 327134 cord_uid: egp4t82x file: cache/cord-327272-fspxett8.json key: cord-327272-fspxett8 authors: Buonaguro, Luigi; Buonaguro, Franco M. title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 journal: Infect Agent Cancer DOI: 10.1186/s13027-020-00302-x sha: doc_id: 327272 cord_uid: fspxett8 file: cache/cord-327214-kcbxyhhh.json key: cord-327214-kcbxyhhh authors: Eketunde, Adenike O; Mellacheruvu, Sai Priyanka; Oreoluwa, Philip title: A Review of Postmortem Findings in Patients With COVID-19 date: 2020-07-28 journal: Cureus DOI: 10.7759/cureus.9438 sha: doc_id: 327214 cord_uid: kcbxyhhh file: cache/cord-327273-7ntp7x8d.json key: cord-327273-7ntp7x8d authors: Street, Renée; Malema, Shirley; Mahlangeni, Nomfundo; Mathee, Angela title: COVID-19 wastewater surveillance: An African perspective date: 2020-07-03 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.140719 sha: doc_id: 327273 cord_uid: 7ntp7x8d file: cache/cord-327247-dbcacphq.json key: cord-327247-dbcacphq authors: Grace, Sherry L.; Hershenfield, Karen; Robertson, Emma; Stewart, Donna E. title: The Occupational and Psychosocial Impact of SARS on Academic Physicians in Three Affected Hospitals date: 2011-04-12 journal: Psychosomatics DOI: 10.1176/appi.psy.46.5.385 sha: doc_id: 327247 cord_uid: dbcacphq file: cache/cord-327259-7o7fs4yb.json key: cord-327259-7o7fs4yb authors: Correa, I. A.; Rodrigues, T. d. S.; Queiroz, A.; Nascimento, L. d. F.; Wolff, T.; Akamine, R. N.; Kuriyama, S. N.; Costa, L.; Fidalgo-Neto, A. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 journal: nan DOI: 10.1101/2020.08.16.20167536 sha: doc_id: 327259 cord_uid: 7o7fs4yb file: cache/cord-327454-o1mrpgvj.json key: cord-327454-o1mrpgvj authors: Hemmati-Dinarvand, Farshad; Saedi, Samira; Hemmati-Dinarvand, Mohsen; Zarei, Marzie; Seghatoleslam, Atefeh title: Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV date: 2020-05-06 journal: Arch Med Res DOI: 10.1016/j.arcmed.2020.04.022 sha: doc_id: 327454 cord_uid: o1mrpgvj file: cache/cord-327499-4aps0kvp.json key: cord-327499-4aps0kvp authors: Zhang, Wei; Du, Rong-Hui; Li, Bei; Zheng, Xiao-Shuang; Yang, Xing-Lou; Hu, Ben; Wang, Yan-Yi; Xiao, Geng-Fu; Yan, Bing; Shi, Zheng-Li; Zhou, Peng title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes date: 2020-02-17 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1729071 sha: doc_id: 327499 cord_uid: 4aps0kvp file: cache/cord-327138-l2m2g0v8.json key: cord-327138-l2m2g0v8 authors: Ren, Chao; Yao, Ren-Qi; Ren, Di; Li, Ying; Feng, Yong-Wen; Yao, Yong-Ming title: Comparison of clinical laboratory tests between bacterial sepsis and SARS-CoV-2-associated viral sepsis date: 2020-08-04 journal: Mil Med Res DOI: 10.1186/s40779-020-00267-3 sha: doc_id: 327138 cord_uid: l2m2g0v8 file: cache/cord-327263-d5mmeu96.json key: cord-327263-d5mmeu96 authors: Christoff, A. P.; Cruz, G. N. F.; Sereia, A. F. R.; Boberg, D. R.; de Bastiani, D. C.; Yamanaka, L. E.; Fongaro, G.; Stoco, P. H.; Bazzo, M. L.; Grisard, E. C.; Hernandes, C.; de Oliveira, L. F. V. title: Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2 date: 2020-09-05 journal: nan DOI: 10.1101/2020.09.03.20187732 sha: doc_id: 327263 cord_uid: d5mmeu96 file: cache/cord-327349-rxb6zfoc.json key: cord-327349-rxb6zfoc authors: Au, Lewis; Boos, Laura Amanda; Swerdlow, Anthony; Byrne, Fiona; Shepherd, Scott T.C.; Fendler, Annika; Turajlic, Samra title: Cancer, COVID-19, and antiviral immunity: the CAPTURE study date: 2020-09-03 journal: Cell DOI: 10.1016/j.cell.2020.09.005 sha: doc_id: 327349 cord_uid: rxb6zfoc file: cache/cord-327431-dnppshnv.json key: cord-327431-dnppshnv authors: Hognon, Cécilia; Miclot, Tom; Iriepa, Cristina Garcia; Francés-Monerris, Antonio; Grandemange, Stephanie; Terenzi, Alessio; Marazzi, Marco; Barone, Giampaolo; Monari, Antonio title: Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date: 2020-05-27 journal: bioRxiv DOI: 10.1101/2020.04.07.029447 sha: doc_id: 327431 cord_uid: dnppshnv file: cache/cord-326710-vc9wkcro.json key: cord-326710-vc9wkcro authors: Stevens, Bryan; Hogan, Catherine A; Sahoo, Malaya K; Huang, ChunHong; Garamani, Natasha; Zehnder, James; Kurzer, Jason; Pinsky, Benjamin A title: Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA date: 2020-08-06 journal: J Appl Lab Med DOI: 10.1093/jalm/jfaa135 sha: doc_id: 326710 cord_uid: vc9wkcro file: cache/cord-327318-qhrsli0b.json key: cord-327318-qhrsli0b authors: Shen, Qian; Wang, Mo; Che, Ruochen; Li, Qiu; Zhou, Jianhua; Wang, Fang; Shen, Ying; Ding, Jie; Huang, Songming; Yap, Hui-Kim; Warady, Bradley A; Xu, Hong; Zhang, Aihua title: Consensus recommendations for the care of children receiving chronic dialysis in association with the COVID-19 epidemic date: 2020-04-24 journal: Pediatr Nephrol DOI: 10.1007/s00467-020-04555-x sha: doc_id: 327318 cord_uid: qhrsli0b file: cache/cord-327392-9psblokc.json key: cord-327392-9psblokc authors: Srivastava, A.K.; Dwivedi, Neeraj; Dhand, Chetna; Khan, Raju; Sathish, N.; Gupta, Manoj K.; Kumar, Rajeev; Kumar, Surender title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 journal: Mater Today Chem DOI: 10.1016/j.mtchem.2020.100385 sha: doc_id: 327392 cord_uid: 9psblokc file: cache/cord-325971-volbaipv.json key: cord-325971-volbaipv authors: Neupane, Karun; Ahmed, Zahoor; Pervez, Hira; Ashraf, Rabia; Majeed, Aneela title: Potential Treatment Options for COVID-19: A Comprehensive Review of Global Pharmacological Development Efforts date: 2020-06-26 journal: Cureus DOI: 10.7759/cureus.8845 sha: doc_id: 325971 cord_uid: volbaipv file: cache/cord-327459-tyhy784d.json key: cord-327459-tyhy784d authors: Gómez-Rial, J.; Martinón-Torres, F. title: A strategy targeting monocyte-macrophage differentiation to avoid pulmonary complications in SARS-Cov2 infection date: 2020-04-23 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108442 sha: doc_id: 327459 cord_uid: tyhy784d file: cache/cord-327575-5pcnuqgy.json key: cord-327575-5pcnuqgy authors: Morrisette, Taylor; Lodise, Thomas P.; Scheetz, Marc H.; Goswami, Srijib; Pogue, Jason M.; Rybak, Michael J. title: The Pharmacokinetic and Pharmacodynamic Properties of Hydroxychloroquine and Dose Selection for COVID-19: Putting the Cart Before the Horse date: 2020-08-01 journal: Infect Dis Ther DOI: 10.1007/s40121-020-00325-2 sha: doc_id: 327575 cord_uid: 5pcnuqgy file: cache/cord-327622-ezgufe24.json key: cord-327622-ezgufe24 authors: Kaur, Ramandeep; Weiss, Tyler T.; Perez, Andrew; Fink, James B.; Chen, Rongchang; Luo, Fengming; Liang, Zongan; Mirza, Sara; Li, Jie title: Practical strategies to reduce nosocomial transmission to healthcare professionals providing respiratory care to patients with COVID-19 date: 2020-09-23 journal: Crit Care DOI: 10.1186/s13054-020-03231-8 sha: doc_id: 327622 cord_uid: ezgufe24 file: cache/cord-327501-8s6dvanf.json key: cord-327501-8s6dvanf authors: Schwaiger, Julia; Karbiener, Michael; Aberham, Claudia; Farcet, Maria R; Kreil, Thomas R title: No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date: 2020-09-17 journal: J Infect Dis DOI: 10.1093/infdis/jiaa593 sha: doc_id: 327501 cord_uid: 8s6dvanf file: cache/cord-327405-xgtqfwyn.json key: cord-327405-xgtqfwyn authors: Liu, Bing; Han, Junyan; Cheng, Xiaohuan; Yu, Long; Zhang, Li; Wang, Wei; Ni, Lan; Wei, Chaojie; Huang, Yafei; Cheng, Zhenshun title: Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients date: 2020-10-19 journal: Sci Rep DOI: 10.1038/s41598-020-73955-8 sha: doc_id: 327405 cord_uid: xgtqfwyn file: cache/cord-327681-c2kmog0g.json key: cord-327681-c2kmog0g authors: Feng, Zhilan; Yang, Yiding; Xu, Dashun; Zhang, Pei; McCauley, Mary Mason; Glasser, John W. title: Timely identification of optimal control strategies for emerging infectious diseases() date: 2009-07-07 journal: J Theor Biol DOI: 10.1016/j.jtbi.2009.03.006 sha: doc_id: 327681 cord_uid: c2kmog0g file: cache/cord-327511-e3idvknz.json key: cord-327511-e3idvknz authors: Trifan, G.; Goldenberg, F.D.; Caprio, F.C.; Biller, J.; Schneck, M.; Khaja, A.; Terna, T.; Brorson, J.; Lazaridis, C.; Bulwa, Z.; Alvarado-Dyer, R.; Saleh-Velez, F.G.; Prabhakaran, S.; Liotta, E.M.; Batra, A.; Reish, N.J.; Ruland, S.; Teitcher, M.; Taylor, W.; De la Pena, P.; Conners, J.C.; Grewal, P.K.; Pinna, P.; Dafer, R.M.; Osteraas, N.D.; DaSilva, I.; Hall, J.P.; John, S.; Shafi, N.; Miller, K.; Moustafa, B.; Vargas, A.; Gorelick, P.B.; Testai, F.D. title: Characteristics of a Diverse Cohort of Stroke Patients with SARS-CoV-2 and Outcome by Sex date: 2020-09-11 journal: J Stroke Cerebrovasc Dis DOI: 10.1016/j.jstrokecerebrovasdis.2020.105314 sha: doc_id: 327511 cord_uid: e3idvknz file: cache/cord-327685-fymfqvp3.json key: cord-327685-fymfqvp3 authors: Channappanavar, Rudragouda; Perlman, Stanley title: Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date: 2017-05-02 journal: Semin Immunopathol DOI: 10.1007/s00281-017-0629-x sha: doc_id: 327685 cord_uid: fymfqvp3 file: cache/cord-327520-qj7coqfr.json key: cord-327520-qj7coqfr authors: Wei, Yulong; Silke, Jordan R.; Aris, Parisa; Xia, Xuhua title: Coronavirus genomes carry the signatures of their habitats date: 2020-06-13 journal: bioRxiv DOI: 10.1101/2020.06.13.149591 sha: doc_id: 327520 cord_uid: qj7coqfr file: cache/cord-327601-4uqgwlnx.json key: cord-327601-4uqgwlnx authors: Bangash, Mansoor N.; Patel, Jaimin M.; Parekh, Dhruv; Murphy, Nicholas; Brown, Rachel M.; Elsharkawy, Ahmed M.; Mehta, Gautam; Armstrong, Matthew J.; Neil, Desley title: SARS-CoV-2: is the liver merely a bystander to severe disease? date: 2020-06-02 journal: J Hepatol DOI: 10.1016/j.jhep.2020.05.035 sha: doc_id: 327601 cord_uid: 4uqgwlnx file: cache/cord-327661-osx42wdh.json key: cord-327661-osx42wdh authors: Schaefer, E. J.; Geller, A. S.; Diffenderfer, M. R.; Dulipsingh, L.; Wisotzkey, J.; Kleiboeker, S. B. title: Coronavirus Disease-2019 Case, Death, and Testing Rates in the United States and Worldwide: Primary Data and Review date: 2020-10-14 journal: nan DOI: 10.1101/2020.10.13.20172957 sha: doc_id: 327661 cord_uid: osx42wdh file: cache/cord-327933-u0fcs3yg.json key: cord-327933-u0fcs3yg authors: Doná, Daniele; Torres Canizales, Juan; Benetti, Elisa; Cananzi, Mara; De Corti, Federica; Calore, Elisabetta; Hierro, Loreto; Ramos Boluda, Esther; Melgosa Hijosa, Marta; Garcia Guereta, Luis; Pérez‐Martínez, Antonio; Barrios, Maribel; Costa Reis, Patricia; Teixeira, Ana; Lopes, Maria Francelina; Kaliciński, Piotr; Branchereau, Sophie; Boyer, Olivia; Debray, Dominque; Sciveres, Marco; Wennberg, Lars; Fischler, Björn; Barany, Peter; Baker, Alastair; Baumann, Ulrich; Schwerk, Nicolaus; Nicastro, Emanuele; Candusso, Manila; Toporski, Jacek; Sokal, Etienne; Stephenne, Xavier; Lindemans, Caroline; Miglinas, Marius; Rascon, Jelena; Jara, Paloma title: Pediatric transplantation in Europe during the COVID‐19 pandemic: early impact on activity and healthcare date: 2020-08-12 journal: Clin Transplant DOI: 10.1111/ctr.14063 sha: doc_id: 327933 cord_uid: u0fcs3yg file: cache/cord-327654-9g8zcxaa.json key: cord-327654-9g8zcxaa authors: Chi, Xiaojing; Liu, Xiuying; Wang, Conghui; Zhang, Xinhui; Li, Xiang; Hou, Jianhua; Ren, Lili; Jin, Qi; Wang, Jianwei; Yang, Wei title: Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date: 2020-09-10 journal: Nat Commun DOI: 10.1038/s41467-020-18387-8 sha: doc_id: 327654 cord_uid: 9g8zcxaa file: cache/cord-327616-uu9uygic.json key: cord-327616-uu9uygic authors: Wazny, Vanessa; Siau, Anthony; Wu, Kan Xing; Cheung, Christine title: Vascular underpinning of COVID-19 date: 2020-08-27 journal: Open Biol DOI: 10.1098/rsob.200208 sha: doc_id: 327616 cord_uid: uu9uygic file: cache/cord-327653-2gn9h4i2.json key: cord-327653-2gn9h4i2 authors: Vallinoto, Antonio Carlos Rosário; da Silva Torres, Maria Karoliny; Vallinoto, Mariana Cayres; Cayres Vallinoto, Izaura M. V. title: The challenges of COVID-19 in the Brazilian Amazonian communities and the importance of seroepidemiological surveillance studies date: 2020-08-15 journal: Int J Equity Health DOI: 10.1186/s12939-020-01256-7 sha: doc_id: 327653 cord_uid: 2gn9h4i2 file: cache/cord-327690-di7hfghi.json key: cord-327690-di7hfghi authors: Yang, Xiaobo; Yu, Yuan; Xu, Jiqian; Shu, Huaqing; Xia, Jia'an; Liu, Hong; Wu, Yongran; Zhang, Lu; Yu, Zhui; Fang, Minghao; Yu, Ting; Wang, Yaxin; Pan, Shangwen; Zou, Xiaojing; Yuan, Shiying; Shang, You title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study date: 2020-02-24 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30079-5 sha: doc_id: 327690 cord_uid: di7hfghi file: cache/cord-327862-zcg3baym.json key: cord-327862-zcg3baym authors: Luo, Yiqi Ruben; Chakraborty, Indrani; Yun, Cassandra; Wu, Alan H B; Lynch, Kara L title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-09-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1389 sha: doc_id: 327862 cord_uid: zcg3baym file: cache/cord-327799-ngzvdd8c.json key: cord-327799-ngzvdd8c authors: Chaumont, Claire; Kamara, Kimberly; Baring, Elisa; Palacio, Karen; Power, Ana; Lancaster, Warren title: The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date: 2020-09-21 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0008680 sha: doc_id: 327799 cord_uid: ngzvdd8c file: cache/cord-327711-welf0eb1.json key: cord-327711-welf0eb1 authors: Zhou, Daming; Duyvesteyn, Helen ME; Chen, Cheng-Pin; Huang, Chung-Guei; Chen, Ting-Hua; Shih, Shin-Ru; Lin, Yi-Chun; Cheng, Chien-Yu; Cheng, Shu-Hsing; Huang, Yhu-Chering; Lin, Tzou-Yien; Ma, Che; Huo, Jiandong; Carrique, Loic; Malinauskas, Tomas; Ruza, Reinis R; Shah, Pranav NM; Tan, Tiong Kit; Rijal, Pramila; Donat, Robert F.; Godwin, Kerry; Buttigieg, Karen; Tree, Julia; Radecke, Julika; Paterson, Neil G; Supasa, Piyasa; Mongkolsapaya, Juthathip; Screaton, Gavin R; Carroll, Miles W.; Jaramillo, Javier G.; Knight, Michael; James, William; Owens, Raymond J; Naismith, James H.; Townsend, Alain; Fry, Elizabeth E; Zhao, Yuguang; Ren, Jingshan; Stuart, David I; Huang, Kuan-Ying A. title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date: 2020-06-13 journal: bioRxiv DOI: 10.1101/2020.06.12.148387 sha: doc_id: 327711 cord_uid: welf0eb1 file: cache/cord-327808-k3jec87p.json key: cord-327808-k3jec87p authors: Zhu, Yunkai; Feng, Fei; Hu, Gaowei; Wang, Yuyan; Yu, Yin; Zhu, Yuanfei; Xu, Wei; Cai, Xia; Sun, Zhiping; Han, Wendong; Ye, Rong; Chen, Hongjun; Ding, Qiang; Cai, Qiliang; Qu, Di; Xie, Youhua; Yuan, Zhenghong; Zhang, Rong title: The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date: 2020-08-25 journal: bioRxiv DOI: 10.1101/2020.08.25.266775 sha: doc_id: 327808 cord_uid: k3jec87p file: cache/cord-327890-ocisq7e4.json key: cord-327890-ocisq7e4 authors: Pallett, Scott J C; Rayment, Michael; Patel, Aatish; Fitzgerald-Smith, Sophia A M; Denny, Sarah J; Charani, Esmita; Mai, Annabelle L; Gilmour, Kimberly C; Hatcher, James; Scott, Christopher; Randell, Paul; Mughal, Nabeela; Jones, Rachael; Moore, Luke S P; Davies, Gary W title: Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study date: 2020-07-24 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30315-5 sha: doc_id: 327890 cord_uid: ocisq7e4 file: cache/cord-327912-wfjdxgxh.json key: cord-327912-wfjdxgxh authors: Swann, Heather; Sharma, Abhimanyu; Preece, Benjamin; Peterson, Abby; Eldridge, Crystal; Belnap, David M.; Vershinin, Michael; Saffarian, Saveez title: Minimal system for assembly of SARS-CoV-2 virus like particles date: 2020-08-24 journal: bioRxiv DOI: 10.1101/2020.06.01.128058 sha: doc_id: 327912 cord_uid: wfjdxgxh file: cache/cord-327721-y39751g4.json key: cord-327721-y39751g4 authors: Zhang, Yan; Cao, Xiaochen; Wang, Pu; Wang, Guixiang; Lei, Guanghui; Shou, Zhexing; Xie, Simiao; Huang, Fei; Luo, Na; Luo, Mingyan; Bian, Yueran; Zhang, Jingyuan; Xiao, Qiang title: Emotional “inflection point” in public health emergencies with the 2019 New Coronavirus Pneumonia (NCP) in China date: 2020-07-19 journal: J Affect Disord DOI: 10.1016/j.jad.2020.07.097 sha: doc_id: 327721 cord_uid: y39751g4 file: cache/cord-328040-5qd05e4r.json key: cord-328040-5qd05e4r authors: Zhao, Xin-Ying; Xu, Xuan-Xuan; Yin, Hai-Sen; Hu, Qin-Ming; Xiong, Tao; Tang, Yuan-Yan; Yang, Ai-Ying; Yu, Bao-Ping; Huang, Zhi-Ping title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date: 2020-04-29 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05010-w sha: doc_id: 328040 cord_uid: 5qd05e4r file: cache/cord-327920-51s4figy.json key: cord-327920-51s4figy authors: Kohler, Philipp P.; Kahlert, Christian R.; Sumer, Johannes; Flury, Domenica; Güsewell, Sabine; Leal-Neto, Onicio B.; Notter, Julia; Albrich, Werner C.; Babouee Flury, Baharak; McGeer, Allison; Kuster, Stefan; Risch, Lorenz; Schlegel, Matthias; Vernazza, Pietro title: Prevalence of SARS-CoV-2 antibodies among Swiss hospital workers: Results of a prospective cohort study date: 2020-10-08 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.1244 sha: doc_id: 327920 cord_uid: 51s4figy file: cache/cord-327894-b0bsseui.json key: cord-327894-b0bsseui authors: Pecellín, Lidia Gestoso; Flores, Yuneysa García; Quintana, Pino González; Luis Marrero Arencibia, José title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 journal: Enferm Clin DOI: 10.1016/j.enfcli.2020.10.001 sha: doc_id: 327894 cord_uid: b0bsseui file: cache/cord-328073-bqeffvzl.json key: cord-328073-bqeffvzl authors: Limonta, Daniel; Dyna-Dagman, Lovely; Branton, William; Makio, Tadashi; Wozniak, Richard W.; Power, Christopher; Hobman, Tom C. title: Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date: 2020-11-06 journal: bioRxiv DOI: 10.1101/2020.11.05.370767 sha: doc_id: 328073 cord_uid: bqeffvzl file: cache/cord-328011-6lf3no6u.json key: cord-328011-6lf3no6u authors: Zayed, Hatem title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics date: 2020-08-14 journal: Front Immunol DOI: 10.3389/fimmu.2020.02051 sha: doc_id: 328011 cord_uid: 6lf3no6u file: cache/cord-328042-e1is656g.json key: cord-328042-e1is656g authors: Klein, Steffen; 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A.; Pauchard, A.; Ricciardi, A. title: Invasion Science and the Global Spread of SARS-CoV-2 date: 2020-05-19 journal: Trends Ecol Evol DOI: 10.1016/j.tree.2020.05.004 sha: doc_id: 328242 cord_uid: afof417h file: cache/cord-328003-yovp8squ.json key: cord-328003-yovp8squ authors: Duan, Liangwei; Zheng, Qianqian; Zhang, Hongxia; Niu, Yuna; Lou, Yunwei; Wang, Hui title: The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date: 2020-10-07 journal: Front Immunol DOI: 10.3389/fimmu.2020.576622 sha: doc_id: 328003 cord_uid: yovp8squ file: cache/cord-328064-7owd28rr.json key: cord-328064-7owd28rr authors: Callahan, Cody J.; Lee, Rose; Zulauf, Katelyn E.; Tamburello, Lauren; Smith, Kenneth P.; Previtera, Joe; Cheng, Annie; Green, Alex; Abdul Azim, Ahmed; Yano, Amanda; Doraiswami, Nancy; Kirby, James E.; Arnaout, Ramy A. title: Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00876-20 sha: doc_id: 328064 cord_uid: 7owd28rr file: cache/cord-328246-boxsf2sz.json key: cord-328246-boxsf2sz authors: Hadi-Alijanvand, Hamid; Rouhani, Maryam title: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes date: 2020-07-27 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00348 sha: doc_id: 328246 cord_uid: boxsf2sz file: cache/cord-327997-noqbcxua.json key: cord-327997-noqbcxua authors: Wu, Kevin E.; Fazal, Furqan M.; Parker, Kevin R.; Zou, James; Chang, Howard Y. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 journal: Cell Syst DOI: 10.1016/j.cels.2020.06.008 sha: doc_id: 327997 cord_uid: noqbcxua file: cache/cord-328074-pcvdr052.json key: cord-328074-pcvdr052 authors: Fuereder, Thorsten; Gunsilius, Eberhard; Bartsch, Rupert; Hilbe, Wolfgang title: Circumnavigating the challenges of COVID-19 in oncology date: 2020-05-07 journal: Memo DOI: 10.1007/s12254-020-00611-2 sha: doc_id: 328074 cord_uid: pcvdr052 file: cache/cord-328187-9zd79gai.json key: cord-328187-9zd79gai authors: Zhang, Yali; Wang, Shaojuan; Wu, Yangtao; Hou, Wangheng; Yuan, Lunzhi; Sheng, Chenguang; Wang, Juan; Ye, Jianghui; Zheng, Qingbing; Ma, Jian; Xu, Jingjing; Wei, Min; Li, Zonglin; Nian, Sheng; Xiong, Hualong; Zhang, Liang; Shi, Yang; Fu, Baorong; Cao, Jiali; Yang, Chuanlai; Li, Zhiyong; Yang, Ting; Liu, Lei; Yu, Hai; Hu, Jianda; Ge, Shengxiang; Chen, Yixin; Zhang, Tianying; Zhang, Jun; Cheng, Tong; Yuan, Quan; Xia, Ningshao title: Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date: 2020-07-22 journal: bioRxiv DOI: 10.1101/2020.07.22.215236 sha: doc_id: 328187 cord_uid: 9zd79gai file: cache/cord-328113-eczjjc2v.json key: cord-328113-eczjjc2v authors: D’Alessandro, Angelo; Thomas, Tiffany; Dzieciatkowska, Monika; Hill, Ryan C.; Francis, Richard O.; Hudson, Krystalyn E.; Zimring, James C.; Hod, Eldad A.; Spitalnik, Steven L.; Hansen, Kirk C. title: Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level date: 2020-07-30 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00365 sha: doc_id: 328113 cord_uid: eczjjc2v file: cache/cord-328373-cubp1cc1.json key: cord-328373-cubp1cc1 authors: Jiang, Yanfang; Wang, Haifeng; Hao, Sijia; Chen, Yukun; He, Jiaxue; Liu, Yong; Chen, Liguo; Yu, Yuanhua; Hua, Shucheng title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.10.032 sha: doc_id: 328373 cord_uid: cubp1cc1 file: cache/cord-328396-p2gvpe8i.json key: cord-328396-p2gvpe8i authors: Kaur, Savneet; Tripathi, Dinesh M.; Yadav, Angeera title: The Enigma of Endothelium in COVID-19 date: 2020-08-04 journal: Front Physiol DOI: 10.3389/fphys.2020.00989 sha: doc_id: 328396 cord_uid: p2gvpe8i file: cache/cord-328289-3h3kmjlz.json key: cord-328289-3h3kmjlz authors: Iadecola, Costantino; Anrather, Josef; Kamel, Hooman title: Effects of COVID-19 on the nervous system date: 2020-08-19 journal: Cell DOI: 10.1016/j.cell.2020.08.028 sha: doc_id: 328289 cord_uid: 3h3kmjlz file: cache/cord-328325-yonbkrwe.json key: cord-328325-yonbkrwe authors: Nielsen, Sandra C. 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A.; Nitsche, A.; Wendt, S.; Donoso Mantke, O.; Niedrig, M. title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus date: 2005-01-13 journal: Arch Virol DOI: 10.1007/s00705-004-0461-1 sha: doc_id: 328381 cord_uid: bfvdhai8 file: cache/cord-328505-5fkpnbdb.json key: cord-328505-5fkpnbdb authors: Thornton, Jeanine Rempe; Harel, Asaff title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab date: 2020-06-26 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102341 sha: doc_id: 328505 cord_uid: 5fkpnbdb file: cache/cord-328585-1rkrrx8a.json key: cord-328585-1rkrrx8a authors: Lu, Shuai; Xie, Xi-xiu; Zhao, Lei; Wang, Bin; Zhu, Jie; Yang, Ting-rui; Yang, Guang-wen; Ji, Mei; Lv, Cui-ping; Xue, Jian; Dai, Er-hei; Fu, Xi-ming; Liu, Dong-qun; zhang, Lun; Hou, Sheng-jie; Yu, Xiao-lin; Wang, Yu-ling; Gao, Hui-xia; Shi, Xue-han; Ke, Chang-wen; Ke, Bi-xia; Jiang, Chun-guo; Liu, Rui-tian title: The immunodominant and neutralization linear epitopes for SARS-CoV-2 date: 2020-08-27 journal: bioRxiv DOI: 10.1101/2020.08.27.267716 sha: doc_id: 328585 cord_uid: 1rkrrx8a file: cache/cord-328287-3qgzulgj.json key: cord-328287-3qgzulgj authors: Moni, Mohammad Ali; Liò, Pietro title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 journal: BMC Bioinformatics DOI: 10.1186/1471-2105-15-333 sha: doc_id: 328287 cord_uid: 3qgzulgj file: cache/cord-328499-d6cvaxm9.json key: cord-328499-d6cvaxm9 authors: Matzkies, Lucie-Marie; Leitner, Eva; Stelzl, Evelyn; Assig, Karoline; Bozic, Michael; Siebenhofer, David; Mustafa, Maria E.; Steinmetz, Ivo; Kessler, Harald H. title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date: 2020-07-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.036 sha: doc_id: 328499 cord_uid: d6cvaxm9 file: cache/cord-328262-hw8swbt5.json key: cord-328262-hw8swbt5 authors: O’Neill, Luke A. J.; Netea, Mihai G. title: BCG-induced trained immunity: can it offer protection against COVID-19? date: 2020-05-11 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0337-y sha: doc_id: 328262 cord_uid: hw8swbt5 file: cache/cord-328395-2cakgmsj.json key: cord-328395-2cakgmsj authors: Oxford, Alexandra E.; Halla, Fabio; Robertson, Evan B.; Morrison, Brad E. title: Endothelial Cell Contributions to COVID-19 date: 2020-09-25 journal: Pathogens DOI: 10.3390/pathogens9100785 sha: doc_id: 328395 cord_uid: 2cakgmsj file: cache/cord-328659-miujzgtd.json key: cord-328659-miujzgtd authors: Mishra, Akhilesh; Pandey, Ashutosh Kumar; Gupta, Parul; Pradhan, Prashant; Dhamija, Sonam; Gomes, James; Kundu, Bishwajit; Vivekanandan, Perumal; Menon, Manoj B. title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 journal: bioRxiv DOI: 10.1101/2020.05.07.082768 sha: doc_id: 328659 cord_uid: miujzgtd file: cache/cord-328704-m2seavg6.json key: cord-328704-m2seavg6 authors: Malfertheiner, Peter; Bornschein, Jan; Ricciardiello, Luigi title: COVID-19: Don't Neglect the Gastrointestinal Tract! date: 2020-04-29 journal: Dig Dis DOI: 10.1159/000508289 sha: doc_id: 328704 cord_uid: m2seavg6 file: cache/cord-328680-zdwep5b2.json key: cord-328680-zdwep5b2 authors: Burr, Tyler; Barton, Christopher; Doll, Elizabeth; Lakhotia, Arpita; Sweeney, Michael title: NMDA-receptor encephalitis associated with COVID-19 infection in a toddler date: 2020-10-09 journal: Pediatr Neurol DOI: 10.1016/j.pediatrneurol.2020.10.002 sha: doc_id: 328680 cord_uid: zdwep5b2 file: cache/cord-328705-024y5k72.json key: cord-328705-024y5k72 authors: Rahman, Md. Mahbubur; Saha, Titon; Islam, Kazi Jahidul; Suman, Rasel Hosen; Biswas, Sourav; Rahat, Emon Uddin; Hossen, Md. Rubel; Islam, Rajib; Hossain, Md Nayeem; Mamun, Abdulla Al; Khan, Maksud; Ali, Md Ackas; Halim, Mohammad A. title: Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment date: 2020-07-21 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1794974 sha: doc_id: 328705 cord_uid: 024y5k72 file: cache/cord-328471-oz99upzz.json key: cord-328471-oz99upzz authors: Ahmad, Jamshaid; Ikram, Saima; Ahmad, Fawad; Rehman, Irshad Ur; Mushtaq, Maryam title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e04502 sha: doc_id: 328471 cord_uid: oz99upzz file: cache/cord-328687-clr1e9p6.json key: cord-328687-clr1e9p6 authors: Zhou, Fuling; Li, Jingfeng; Lu, Mengxin; Ma, Linlu; Pan, Yunbao; Liu, Xiaoyan; Zhu, Xiaobin; Hu, Chao; Wu, Sanyun; Chen, Liangjun; Wang, Yi; Wei, Yongchang; Li, Yirong; Xu, Haibo; Wang, Xinghuan; Cai, Lin title: Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey date: 2020-09-15 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100510 sha: doc_id: 328687 cord_uid: clr1e9p6 file: cache/cord-328712-7q9mg2tu.json key: cord-328712-7q9mg2tu authors: Moore, Nicholas title: Chloroquine for COVID-19 Infection date: 2020-04-07 journal: Drug Saf DOI: 10.1007/s40264-020-00933-4 sha: doc_id: 328712 cord_uid: 7q9mg2tu file: cache/cord-328644-odtue60a.json key: cord-328644-odtue60a authors: Comandatore, Francesco; Chiodi, Alice; Gabrieli, Paolo; Biffignandi, Gherard Batisti; Perini, Matteo; Ricagno, Stefano; Mascolo, Elia; Petazzoni, Greta; Ramazzotti, Matteo; Rimoldi, Sara Giordana; Gismondo, Maria Rita; Micheli, Valeria; Sassera, Davide; Gaiarsa, Stefano; Bandi, Claudio; Brilli, Matteo title: Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.04.30.071027 sha: doc_id: 328644 cord_uid: odtue60a file: cache/cord-329069-ejdunj41.json key: cord-329069-ejdunj41 authors: Yang, He S; Hou, Yu; Vasovic, Ljiljana V; Steel, Peter; Chadburn, Amy; Racine-Brzostek, Sabrina E; Velu, Priya; Cushing, Melissa M; Loda, Massimo; Kaushal, Rainu; Zhao, Zhen; Wang, Fei title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-08-21 journal: Clin Chem DOI: 10.1093/clinchem/hvaa200 sha: doc_id: 329069 cord_uid: ejdunj41 file: cache/cord-328479-1tzysg7u.json key: cord-328479-1tzysg7u authors: Chen, Jianjun; Huang, Chaolin; Zhang, Yanan; Zhang, Sai; Jin, Meilin title: Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China date: 2020-06-21 journal: J Infect DOI: 10.1016/j.jinf.2020.06.045 sha: doc_id: 328479 cord_uid: 1tzysg7u file: cache/cord-328484-4iptwc3n.json key: cord-328484-4iptwc3n authors: Li, Tao; Lu, Lei; Zhang, Weishuo; Tao, Yu; Wang, Liuming; Bao, Jing; Liu, Bao; Duan, Jun title: Clinical Characteristics of 312 Hospitalized Older Patients with COVID-19 in Wuhan, China date: 2020-07-15 journal: Arch Gerontol Geriatr DOI: 10.1016/j.archger.2020.104185 sha: doc_id: 328484 cord_uid: 4iptwc3n file: cache/cord-328686-5ik5em5a.json key: cord-328686-5ik5em5a authors: Zhao, L.; Atoni, E.; Du, Y.; Zhang, H.; Donde, O.; Huang, D.; Xiao, S.; Ma, T.; Shu, Z.; Yuan, Z.; Tong, L.; Xia, H. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 journal: nan DOI: 10.1101/2020.08.19.20172924 sha: doc_id: 328686 cord_uid: 5ik5em5a file: cache/cord-328695-nptfd6c2.json key: cord-328695-nptfd6c2 authors: Tengs, Torstein; Delwiche, Charles F.; Jonassen, Christine Monceyron title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date: 2020-06-29 journal: bioRxiv DOI: 10.1101/2020.06.29.177030 sha: doc_id: 328695 cord_uid: nptfd6c2 file: cache/cord-328856-1l7x72j7.json key: cord-328856-1l7x72j7 authors: Ucciferri, Claudio; Barone, Mirko; Vecchiet, Jacopo; Falasca, Katia title: Pidotimod in Paucisymptomatic SARS-CoV2 Infected Patients date: 2020-07-01 journal: Mediterr J Hematol Infect Dis DOI: 10.4084/mjhid.2020.048 sha: doc_id: 328856 cord_uid: 1l7x72j7 file: cache/cord-328865-ekgqdjlk.json key: cord-328865-ekgqdjlk authors: Anand, Shuchi; Montez-Rath, Maria; Han, Jialin; Bozeman, Julie; Kerschmann, Russell; Beyer, Paul; Parsonnet, Julie; Chertow, Glenn M title: Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study date: 2020-09-25 journal: Lancet DOI: 10.1016/s0140-6736(20)32009-2 sha: doc_id: 328865 cord_uid: ekgqdjlk file: cache/cord-328683-zvabpty9.json key: cord-328683-zvabpty9 authors: Fontanet, A.; Grant, R.; Tondeur, L.; Madec, Y.; Grzelak, L.; Cailleau, I.; Ungeheuer, M.-N.; Renaudat, C.; Fernandes Pellerin, S.; Kuhmel, L.; Staropoli, I.; Anna, F.; Charneau, P.; Demeret, C.; Bruel, T.; Schwartz, O.; Hoen, B. title: SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission date: 2020-06-29 journal: nan DOI: 10.1101/2020.06.25.20140178 sha: doc_id: 328683 cord_uid: zvabpty9 file: cache/cord-328557-f6o1aynz.json key: cord-328557-f6o1aynz authors: Samad, Abdus; Ahammad, Foysal; Nain, Zulkar; Alam, Rahat; Imon, Raihan Rahman; Hasan, Mahadi; Rahman, Md. Shahedur title: Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach date: 2020-07-17 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1792347 sha: doc_id: 328557 cord_uid: f6o1aynz file: cache/cord-328762-2b1pl8jr.json key: cord-328762-2b1pl8jr authors: Fuest, Matthias; Boor, Peter; Knuechel, Ruth; Walter, Peter; Salla, Sabine title: Postmortem conjunctival and nasopharyngeal swabs in SARS‐CoV‐2 infected and uninfected patients date: 2020-08-06 journal: Acta Ophthalmol DOI: 10.1111/aos.14559 sha: doc_id: 328762 cord_uid: 2b1pl8jr file: cache/cord-328853-0iqdqcp6.json key: cord-328853-0iqdqcp6 authors: Neidleman, Jason; Luo, Xiaoyu; Frouard, Julie; Xie, Guorui; Gill, Gurjot; Stein, Ellen S.; McGregor, Matthew; Ma, Tongcui; George, Ashley F.; Kosters, Astrid; Greene, Warner C.; Vasquez, Joshua; Ghosn, Eliver; Lee, Sulggi; Roan, Nadia R. title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential date: 2020-08-19 journal: Cell Rep Med DOI: 10.1016/j.xcrm.2020.100081 sha: doc_id: 328853 cord_uid: 0iqdqcp6 file: cache/cord-329186-0eoz4npg.json key: cord-329186-0eoz4npg authors: Xia, Shuai; Lan, Qiaoshuai; Su, Shan; Wang, Xinling; Xu, Wei; Liu, Zezhong; Zhu, Yun; Wang, Qian; Lu, Lu; Jiang, Shibo title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin date: 2020-06-12 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-0184-0 sha: doc_id: 329186 cord_uid: 0eoz4npg file: cache/cord-328409-px92ff89.json key: cord-328409-px92ff89 authors: Hornuss, Daniel; Laubner, Katharina; Monasterio, Carmen; Thimme, Robert; Wagner, Dirk title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1170-6061 sha: doc_id: 328409 cord_uid: px92ff89 file: cache/cord-329129-t84pu00z.json key: cord-329129-t84pu00z authors: Zuo, J; Dowell, A; Pearce, H; Verma, K; Long, HM; Begum, J; Aiano, F; Amin-Chowdhury, Z; Hallis, B; Stapley, L; Borrow, R; Linley, E; Ahmad, S; Parker, B; Horsley, A; Amirthalingam, G; Brown, K; Ramsay, ME; Ladhani, S; Moss, P title: Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.01.362319 sha: doc_id: 329129 cord_uid: t84pu00z file: cache/cord-329221-miztel9l.json key: cord-329221-miztel9l authors: rudolf, f.; Kaltenbach, H.-M.; linnik, J.; Ruf, M.-T.; Niederhauser, C.; Nickel, B.; Gygax, D.; Savic, M. title: Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population date: 2020-08-21 journal: nan DOI: 10.1101/2020.08.18.20177204 sha: doc_id: 329221 cord_uid: miztel9l file: cache/cord-329011-spiuqngp.json key: cord-329011-spiuqngp authors: Huang, Yuan; Yang, Chan; Xu, Xin-feng; Xu, Wei; Liu, Shu-wen title: Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date: 2020-08-03 journal: Acta Pharmacol Sin DOI: 10.1038/s41401-020-0485-4 sha: doc_id: 329011 cord_uid: spiuqngp file: cache/cord-328778-mjzsz7rz.json key: cord-328778-mjzsz7rz authors: Steinchen, N.; Müller-Ladner, U.; Lange, U. title: Biologikatherapie nach COVID-19-Infektion: Keine Reaktivierung einer COVID-19-Infektion bei positivem Antikörperstatus SARS-CoV-2 unter Biologikatherapie date: 2020-06-08 journal: Z Rheumatol DOI: 10.1007/s00393-020-00824-0 sha: doc_id: 328778 cord_uid: mjzsz7rz file: cache/cord-329010-n0mz098o.json key: cord-329010-n0mz098o authors: McKee, Dwight L.; Sternberg, Ariane; Stange, Ulrike; Laufer, Stefan; Naujokat, Cord title: Candidate drugs against SARS-CoV-2 and COVID-19 date: 2020-04-29 journal: Pharmacol Res DOI: 10.1016/j.phrs.2020.104859 sha: doc_id: 329010 cord_uid: n0mz098o file: cache/cord-329041-coryaz2s.json key: cord-329041-coryaz2s authors: Brown, Ariane J.; Won, John J.; Graham, Rachel L.; Dinnon, Kenneth H.; Sims, Amy C.; Feng, Joy Y.; Cihlar, Tomas; Denison, Mark R.; Baric, Ralph S.; Sheahan, Timothy P. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 journal: Antiviral Research DOI: 10.1016/j.antiviral.2019.104541 sha: doc_id: 329041 cord_uid: coryaz2s file: cache/cord-329262-ybr1auo2.json key: cord-329262-ybr1auo2 authors: Moriel‐Carretero, María title: The hypothetical role of Phosphatidic Acid in subverting ER membranes during SARS‐CoV infection date: 2020-05-18 journal: Traffic DOI: 10.1111/tra.12738 sha: doc_id: 329262 cord_uid: ybr1auo2 file: cache/cord-328962-1c4vqaqr.json key: cord-328962-1c4vqaqr authors: Benítez-Cardoza, Claudia Guadalupe; 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hre, Peder L My; Jonassen, Christine; Rangberg, Anbjørg; Blomfeldt, Anita; Svensson, My; Omland, Torbjørn; Berdal, Jan-Erik title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1338 sha: doc_id: 329311 cord_uid: p68kr4ga file: cache/cord-329190-kv9n2qj3.json key: cord-329190-kv9n2qj3 authors: Rabaan, Ali A.; Alahmed, Shamsah H.; Bazzi, Ali M.; Alhani, Hatem M. title: A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective date: 2017-09-01 journal: Journal of Medical Microbiology DOI: 10.1099/jmm.0.000565 sha: doc_id: 329190 cord_uid: kv9n2qj3 file: cache/cord-329392-fufattj8.json key: cord-329392-fufattj8 authors: den Hartog, Gerco; Schepp, Rutger M; Kuijer, Marjan; GeurtsvanKessel, Corine; van Beek, Josine; Rots, Nynke; Koopmans, Marion P G; van der Klis, Fiona R M; van Binnendijk, Robert S title: SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date: 2020-08-08 journal: J Infect Dis DOI: 10.1093/infdis/jiaa479 sha: doc_id: 329392 cord_uid: fufattj8 file: cache/cord-329840-f3dsu36p.json key: cord-329840-f3dsu36p authors: Hati, Sanchita; Bhattacharyya, Sudeep title: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date: 2020-05-11 journal: bioRxiv DOI: 10.1101/2020.05.07.083147 sha: doc_id: 329840 cord_uid: f3dsu36p file: cache/cord-329504-91te3nu8.json key: cord-329504-91te3nu8 authors: Croll, Tristan; Diederichs, Kay; Fischer, Florens; Fyfe, Cameron; Gao, Yunyun; Horrell, Sam; Joseph, Agnel Praveen; Kandler, Luise; Kippes, Oliver; Kirsten, Ferdinand; Müller, Konstantin; Nolte, Kristoper; Payne, Alex; Reeves, Matthew G.; Richardson, Jane; Santoni, Gianluca; Stäb, Sabrina; Tronrud, Dale; Williams, Christopher; Thorn, Andrea title: Making the invisible enemy visible date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.10.07.307546 sha: doc_id: 329504 cord_uid: 91te3nu8 file: cache/cord-329473-dtlwjndn.json key: cord-329473-dtlwjndn authors: Guo, Ao-Xiang; Cui, Jia-Jia; OuYang, Qian-Ying; He, Li; Guo, Cheng-Xian; Yin, Ji-Ye title: The clinical characteristics and mortal causes analysis of COVID-19 death patients date: 2020-04-15 journal: nan DOI: 10.1101/2020.04.12.20062380 sha: doc_id: 329473 cord_uid: dtlwjndn file: cache/cord-329493-ueqlhgn0.json key: cord-329493-ueqlhgn0 authors: Stadler, Konrad; Masignani, Vega; Eickmann, Markus; Becker, Stephan; Abrignani, Sergio; Klenk, Hans-Dieter; Rappuoli, Rino title: SARS — beginning to understand a new virus date: 2003 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro775 sha: doc_id: 329493 cord_uid: ueqlhgn0 file: cache/cord-329890-wg23sa1u.json key: cord-329890-wg23sa1u authors: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 journal: Health Policy DOI: 10.1016/j.healthpol.2006.03.002 sha: doc_id: 329890 cord_uid: wg23sa1u file: cache/cord-329328-c6svx4qa.json key: cord-329328-c6svx4qa authors: Reydon, Thomas A. 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Y.; Yuen, Kwok-yung title: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes date: 2007-10-02 journal: Nucleic Acids Res DOI: 10.1093/nar/gkm754 sha: doc_id: 330067 cord_uid: ujhgb3b0 file: cache/cord-329825-e9mepqvn.json key: cord-329825-e9mepqvn authors: Giamarellos-Bourboulis, Evangelos J.; Netea, Mihai G.; Rovina, Nikoletta; Akinosoglou, Karolina; Antoniadou, Anastasia; Antonakos, Nikolaos; Damoraki, Georgia; Gkavogianni, Theologia; Adami, Maria-Evangelia; Katsaounou, Paraskevi; Ntaganou, Maria; Kyriakopoulou, Magdalini; Dimopoulos, George; Koutsodimitropoulos, Ioannis; Velissaris, Dimitrios; Koufargyris, Panagiotis; Karageorgos, Athanassios; Katrini, Konstantina; Lekakis, Vasileios; Lupse, Mihaela; Kotsaki, Antigone; Renieris, George; Theodoulou, Danai; Panou, Vassiliki; Koukaki, Evangelia; Koulouris, Nikolaos; Gogos, Charalambos; Koutsoukou, Antonia title: Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date: 2020-04-21 journal: Cell Host Microbe DOI: 10.1016/j.chom.2020.04.009 sha: doc_id: 329825 cord_uid: e9mepqvn file: cache/cord-330045-4gj9d181.json key: cord-330045-4gj9d181 authors: Sun, Jiufeng; 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Rapparini, Cristiane; Gomes, Bruno Moreno; Pinto, Luiz Alexandre Cabral; Freire, Mário Sérgio da Silva e title: Pneumothorax as a late complication of COVID-19 date: 2020-08-31 journal: Revista do Instituto de Medicina Tropical de Sao Paulo DOI: 10.1590/s1678-9946202062061 sha: doc_id: 330061 cord_uid: q4xi260z file: cache/cord-329853-kf3kh26y.json key: cord-329853-kf3kh26y authors: Trimarchi, Hernán; Gianserra, Raquel; Lampo, Mauro; Monkowski, Matias; Lodolo, Jimena title: Eculizumab, SARS-CoV-2 and atypical hemolytic uremic syndrome date: 2020-09-27 journal: Clin Kidney J DOI: 10.1093/ckj/sfaa166 sha: doc_id: 329853 cord_uid: kf3kh26y file: cache/cord-329844-w969lczb.json key: cord-329844-w969lczb authors: Robson, B. title: Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date: 2020-06-08 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.103849 sha: doc_id: 329844 cord_uid: w969lczb file: cache/cord-330338-i6ozygkp.json key: cord-330338-i6ozygkp authors: Babacic, H.; Lehtiö, J.; Pernemalm, M. title: Global between-countries variance in SARS-CoV-2 mortality is driven by reported prevalence, age distribution, and case detection rate date: 2020-06-02 journal: nan DOI: 10.1101/2020.05.28.20114934 sha: doc_id: 330338 cord_uid: i6ozygkp file: cache/cord-330093-asba80bi.json key: cord-330093-asba80bi authors: Leung, Janice M.; Sin, Don D. title: Smoking, ACE-2 and COVID-19: ongoing controversies date: 2020-07-16 journal: Eur Respir J DOI: 10.1183/13993003.01759-2020 sha: doc_id: 330093 cord_uid: asba80bi file: cache/cord-330337-d41imvo7.json key: cord-330337-d41imvo7 authors: Basu, Souradip; Mukhopadhyay, Suparba; Das, Rajdeep; Mukhopadhyay, Sarmishta; Singh, Pankaj Kumar; Ganguli, Sayak title: Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date: 2020-10-20 journal: bioRxiv DOI: 10.1101/2020.10.20.347021 sha: doc_id: 330337 cord_uid: d41imvo7 file: cache/cord-330121-eadu2ba3.json key: cord-330121-eadu2ba3 authors: Gudmundsdottir, Ágústa; Scheving, Reynir; Lindberg, Fredrik; Stefansson, Bjarki title: Inactivation of SARS‐CoV‐2 and HCoV‐229E in vitro by ColdZyme® a medical device mouth spray against common cold date: 2020-09-25 journal: J Med Virol DOI: 10.1002/jmv.26554 sha: doc_id: 330121 cord_uid: eadu2ba3 file: cache/cord-330198-pwkxgbxk.json key: cord-330198-pwkxgbxk authors: Cai, Xiaofang; Jiang, Hanlan; Zhang, Simin; Xia, Shengying; Du, Wenhui; Ma, Yaoling; Yu, Tao; Li, Wenbin title: Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19 date: 2020-10-27 journal: Front Med DOI: 10.1007/s11684-020-0820-7 sha: doc_id: 330198 cord_uid: pwkxgbxk file: cache/cord-330266-uypjqif7.json key: cord-330266-uypjqif7 authors: Firpo, Mason R.; Mastrodomenico, Vincent; Hawkins, Grant M.; Prot, Matthieu; Levillayer, Laura; Gallagher, Tom; Simon-Loriere, Etienne; Mounce, Bryan C. title: Targeting Polyamines Inhibits Coronavirus Infection by Reducing Cellular Attachment and Entry date: 2020-09-23 journal: ACS Infect Dis DOI: 10.1021/acsinfecdis.0c00491 sha: doc_id: 330266 cord_uid: uypjqif7 file: cache/cord-330287-bkqjkhwu.json key: cord-330287-bkqjkhwu authors: Miller, Danielle; 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Y.; Lv, Huibin; Mok, Chris K. P.; Wilson, Ian A. title: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date: 2020-03-14 journal: bioRxiv DOI: 10.1101/2020.03.13.991570 sha: doc_id: 330473 cord_uid: f03ka7bd file: cache/cord-330583-ltkpt80u.json key: cord-330583-ltkpt80u authors: Lee, Kyu-Myoung; Jung, Kyujin title: Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date: 2019-04-22 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph16081432 sha: doc_id: 330583 cord_uid: ltkpt80u file: cache/cord-330129-izr62c68.json key: cord-330129-izr62c68 authors: Omer, Sumaira; Ali, Salamat; Babar, Zaheer ud Din title: Preventive measures and management of COVID-19 in pregnancy date: 2020-04-09 journal: Drugs Ther Perspect DOI: 10.1007/s40267-020-00725-x sha: doc_id: 330129 cord_uid: izr62c68 file: cache/cord-330369-75cotmn2.json key: cord-330369-75cotmn2 authors: López, Verónica; Vázquez, Teresa; Alonso-Titos, Juana; 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Fuchs, Jonas; Maier, Wolfgang; Weigang, Sebastian; Pedrosa, Núria Díaz i; Weiss, Lisa; Lother, Achim; Nekrutenko, Anton; Ruzsics, Zsolt; Panning, Marcus; Kochs, Georg; Gilsbach, Ralf; Grüning, Björn title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 journal: bioRxiv DOI: 10.1101/2020.07.18.204362 sha: doc_id: 330213 cord_uid: reb9vo7x file: cache/cord-330433-y5dvlcda.json key: cord-330433-y5dvlcda authors: Olivieri, Emily R.; Heller, Lindsey K.; Gillim-Ross, Laura; Wentworth, David E. title: Analysis of SARS-CoV Receptor Activity of ACE2 Orthologs date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_46 sha: doc_id: 330433 cord_uid: y5dvlcda file: cache/cord-330597-nftwj0d5.json key: cord-330597-nftwj0d5 authors: Hopfer, Helmut; Herzig, Martin C.; Gosert, Rainer; Menter, Thomas; Hench, Jürgen; Tzankov, Alexandar; Hirsch, Hans H.; Miller, Sara E. title: Hunting coronavirus by transmission electron microscopy – a guide to SARS‐CoV‐2‐associated ultrastructural pathology in COVID‐19 tissues date: 2020-09-27 journal: Histopathology DOI: 10.1111/his.14264 sha: doc_id: 330597 cord_uid: nftwj0d5 file: cache/cord-330465-16j5vm7h.json key: cord-330465-16j5vm7h authors: Marciniec, Krzysztof; Chrobak, Elwira; Dąbrowska, Aleksandra; Bębenek, Ewa; Kadela-Tomanek, Monika; Pęcak, Paweł; Boryczka, Stanisław title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 journal: Biomolecules DOI: 10.3390/biom10081148 sha: doc_id: 330465 cord_uid: 16j5vm7h file: cache/cord-330692-rqwkkfp0.json key: cord-330692-rqwkkfp0 authors: He, Daihai; Shi, Zhao; Li, Yingke; Cao, Peihua; Gao, Daozhou; Lou, Yijun; Yang, Lin title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date: 2020-06-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.075 sha: doc_id: 330692 cord_uid: rqwkkfp0 file: cache/cord-330324-4hqhty5o.json key: cord-330324-4hqhty5o authors: Yu, Meng; Stevens, Vicky; Berry, Jody D.; Crameri, Gary; McEachern, Jennifer; Tu, Changchun; Shi, Zhengli; Liang, Guodong; Weingartl, Hana; Cardosa, Jane; Eaton, Bryan T.; Wang, Lin-Fa title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date: 2008-02-29 journal: Journal of Immunological Methods DOI: 10.1016/j.jim.2007.11.009 sha: doc_id: 330324 cord_uid: 4hqhty5o file: cache/cord-330701-k68b0wqe.json key: cord-330701-k68b0wqe authors: Gerc, Vjekoslav; Masic, Izet; Salihefendic, Nizama; Zildzic, Muharem title: Cardiovascular Diseases (CVDs) in COVID-19 Pandemic Era date: 2020-06-17 journal: Mater Sociomed DOI: 10.5455/msm.2020.32.158-164 sha: doc_id: 330701 cord_uid: k68b0wqe file: cache/cord-330478-g9n2mfni.json key: cord-330478-g9n2mfni authors: Hattenbach, Lars-Olof; Reinhard, Thomas; Walter, Peter; Roider, Johannes; Feltgen, Nicolas; Hesse, Lutz; Schrecker, Jens; Eter, Nicole title: Krisenstrategien der Kliniken während der Pandemie date: 2020-07-01 journal: Ophthalmologe DOI: 10.1007/s00347-020-01162-x sha: doc_id: 330478 cord_uid: g9n2mfni file: cache/cord-330387-7lci44w5.json key: cord-330387-7lci44w5 authors: Bird, Paul; Badhwar, Vinay; Fallon, Karlie; Kwok, Kin On; Tang, Julian W title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads date: 2020-06-18 journal: J Infect DOI: 10.1016/j.jinf.2020.06.035 sha: doc_id: 330387 cord_uid: 7lci44w5 file: cache/cord-330887-q5i8lpan.json key: cord-330887-q5i8lpan authors: Li, K.; Wu, M.; Huang, B.; Zhong, A.; Li, L.; Cai, Y.; Wu, L.; Zhu, M.; Li, J.; Wang, Z.; Wu, W.; Li, W.; Bosco, B.; Gan, Z.; Qiao, Q.; Wu, J.; wang, q.; Wang, S.; Xia, X. title: The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19 date: 2020-05-21 journal: nan DOI: 10.1101/2020.05.18.20105155 sha: doc_id: 330887 cord_uid: q5i8lpan file: cache/cord-330779-mso2zfom.json key: cord-330779-mso2zfom authors: Sunkari, Emmanuel Daanoba; Korboe, Harriet Mateko; Abu, Mahamuda; Kizildeniz, Tefide title: Sources and routes of SARS-CoV-2 transmission in water systems in Africa: Are there any sustainable remedies? date: 2020-09-09 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142298 sha: doc_id: 330779 cord_uid: mso2zfom file: cache/cord-330743-o11d0aa1.json key: cord-330743-o11d0aa1 authors: Yu, Xi; Zhang, Liming; Tong, Liangqin; Zhang, Nana; Wang, Han; Yang, Yun; Shi, Mingyu; Xiao, Xiaoping; Zhu, Yibin; Wang, Penghua; Ding, Qiang; Zhang, Linqi; Qin, Chengfeng; Cheng, Gong title: Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date: 2020-05-25 journal: bioRxiv DOI: 10.1101/2020.05.22.109900 sha: doc_id: 330743 cord_uid: o11d0aa1 file: cache/cord-330536-q8zr0mkl.json key: cord-330536-q8zr0mkl authors: Lopinto, Julien; Teulier, Marion; Milon, Audrey; Voiriot, Guillaume; Fartoukh, Muriel title: Severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection date: 2020-09-14 journal: BMC Pulm Med DOI: 10.1186/s12890-020-01285-6 sha: doc_id: 330536 cord_uid: q8zr0mkl file: cache/cord-330690-cupy89gl.json key: cord-330690-cupy89gl authors: Vierucci, Francesco; Bacci, Caterina; Mucaria, Cristina; Dini, Francesca; Federico, Giovanni; Maielli, Michela; Vaccaro, Angelina title: How COVID-19 Pandemic Changed Children and Adolescents Use of the Emergency Department: the Experience of a Secondary Care Pediatric Unit in Central Italy date: 2020-09-23 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00532-5 sha: doc_id: 330690 cord_uid: cupy89gl file: cache/cord-330807-abi8pra7.json key: cord-330807-abi8pra7 authors: Garcia-Pachon, Eduardo; Zamora-Molina, Lucia; Soler-Sempere, Maria J.; Baeza-Martinez, Carlos; Grau-Delgado, Justo; Canto-Reig, Vicente; Ramon-Sanchez, Antonio; Padilla-Navas, Isabel; Ruiz-Garcia, Montserrat; Gonzalo-Jimenez, Nieves title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization date: 2020-07-04 journal: Respir Med DOI: 10.1016/j.rmed.2020.106084 sha: doc_id: 330807 cord_uid: abi8pra7 file: cache/cord-330607-zn4urrxc.json key: cord-330607-zn4urrxc authors: Chi, Qiong; Dai, Xinjian; Jiang, Xiangao; Zhu, Lefei; Du, Junyan; Chen, Yuxi; Zheng, Jiyang; Huang, Jianping title: Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date: 2020-09-18 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05383-y sha: doc_id: 330607 cord_uid: zn4urrxc file: cache/cord-330715-olypwdoq.json key: cord-330715-olypwdoq authors: Sun, Zeyu; Ren, Keyi; Zhang, Xing; Chen, Jinghua; Jiang, Zhengyi; Jiang, Jing; Ji, Feiyang; Ouyang, Xiaoxi; Li, Lanjuan title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date: 2020-08-30 journal: Engineering (Beijing) DOI: 10.1016/j.eng.2020.07.014 sha: doc_id: 330715 cord_uid: olypwdoq file: cache/cord-331010-4phhz79k.json key: cord-331010-4phhz79k authors: Knight, M.; Bunch, K.; Vousden, N.; Morris, E.; Simpson, N.; Gale, C.; O'Brien, P.; Quigley, M.; Brocklehurst, P.; Kurinczuk, J. J. title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) date: 2020-05-12 journal: nan DOI: 10.1101/2020.05.08.20089268 sha: doc_id: 331010 cord_uid: 4phhz79k file: cache/cord-330717-uzrxtgrg.json key: cord-330717-uzrxtgrg authors: Gupta, Madhu; Wahl, Brian; Adhikari, Binita; Bar-Zeev, Naor; Bhandari, Sudip; Coria, Alexandra; Erchick, Daniel J.; Gupta, Nidhi; Hariyani, Shreya; Kagucia, E. Wangeci; Killewo, Japhet; Limaye, Rupali Jayant; McCollum, Eric D.; Pandey, Raghukul; Pomat, William S.; Rao, Krishna D.; Santosham, Mathuram; Sauer, Molly; Wanyenze, Rhoda K.; Peters, David H. title: The need for COVID-19 research in low- and middle-income countries date: 2020-07-01 journal: Glob Health Res Policy DOI: 10.1186/s41256-020-00159-y sha: doc_id: 330717 cord_uid: uzrxtgrg file: cache/cord-330626-0aidit63.json key: cord-330626-0aidit63 authors: Sepulveda, Jorge; Westblade, Lars F.; Whittier, Susan; Satlin, Michael J.; Greendyke, William G.; Aaron, Justin G.; Zucker, Jason; Dietz, Donald; Sobieszczyk, Magdalena; Choi, Justin J.; Liu, Dakai; Russell, Sarah; Connelly, Charles; Green, Daniel A. title: Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00875-20 sha: doc_id: 330626 cord_uid: 0aidit63 file: cache/cord-331066-ediowz4s.json key: cord-331066-ediowz4s authors: Chechetkin, Vladimir R.; Lobzin, Vasily V. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1815581 sha: doc_id: 331066 cord_uid: ediowz4s file: cache/cord-330827-gu2mt6zp.json key: cord-330827-gu2mt6zp authors: Shanmugaraj, Balamurugan; Malla, Ashwini; Phoolcharoen, Waranyoo title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 journal: Pathogens DOI: 10.3390/pathogens9020148 sha: doc_id: 330827 cord_uid: gu2mt6zp file: cache/cord-330849-yt44k88m.json key: cord-330849-yt44k88m authors: Han, Rachel H.; Schmidt, Morgan N.; Waits, Wendi M.; Bell, Alexa K. 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Andrew; Yao, Da-Jeng; Ren, Fan; Wang, Yu-Lin title: Investigation of C-terminal domain of SARS nucleocapsid protein–Duplex DNA interaction using transistors and binding-site models date: 2014-03-31 journal: Sens Actuators B Chem DOI: 10.1016/j.snb.2013.11.087 sha: doc_id: 330944 cord_uid: 54xmnum8 file: cache/cord-330873-hwbdreul.json key: cord-330873-hwbdreul authors: Yang, Wan; Cai, Chen; Dai, Xiaohu title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal date: 2020-07-07 journal: Resour Conserv Recycl DOI: 10.1016/j.resconrec.2020.105043 sha: doc_id: 330873 cord_uid: hwbdreul file: cache/cord-331039-qgom2e3n.json key: cord-331039-qgom2e3n authors: Kavitha, Kuppuswamy; Sivakumar, Subramaniam; Ramesh, Balasubramanian title: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates date: 2020-09-22 journal: Biophys Chem DOI: 10.1016/j.bpc.2020.106478 sha: doc_id: 331039 cord_uid: qgom2e3n file: cache/cord-330908-402eb8wg.json key: cord-330908-402eb8wg authors: Tsuji, Motonori title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease date: 2020-05-29 journal: FEBS Open Bio DOI: 10.1002/2211-5463.12875 sha: doc_id: 330908 cord_uid: 402eb8wg file: cache/cord-331060-b3z1zb4t.json key: cord-331060-b3z1zb4t authors: Cruickshank, Marilyn; Shaban, Ramon Z. title: COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic date: 2020-06-04 journal: J Clin Nurs DOI: 10.1111/jocn.15365 sha: doc_id: 331060 cord_uid: b3z1zb4t file: cache/cord-331076-ak481qew.json key: cord-331076-ak481qew authors: Eskier, Doğa; Suner, Aslı; Oktay, Yavuz; Karakülah, Gökhan title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 journal: PeerJ DOI: 10.7717/peerj.10181 sha: doc_id: 331076 cord_uid: ak481qew file: cache/cord-331109-a8e7r80d.json key: cord-331109-a8e7r80d authors: Ibrahim, Yassmin S.; Karuppasamy, Gowri; Parambil, Jessiya V.; Alsoub, Hussam; Al-Shokri, Shaikha D. title: Case Report: Paralytic Ileus: A Potential Extrapulmonary Manifestation of Severe COVID-19 date: 2020-08-31 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0894 sha: doc_id: 331109 cord_uid: a8e7r80d file: cache/cord-331022-tek4u751.json key: cord-331022-tek4u751 authors: Sinderewicz, Emilia; Czelejewska, Wioleta; Jezierska-Wozniak, Katarzyna; Staszkiewicz-Chodor, Joanna; Maksymowicz, Wojciech title: Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience? date: 2020-09-09 journal: Pathogens DOI: 10.3390/pathogens9090739 sha: doc_id: 331022 cord_uid: tek4u751 file: cache/cord-331283-bfyoavon.json key: cord-331283-bfyoavon authors: Meca-Lallana, Dra. Virginia; Aguirre, Dra. Clara; Beatrizdel Río; Cardeñoso, Dra. Laura; Alarcon, Dra. Teresa; Vivancos, Dr. José title: COVID-19 IN 7 MULTIPLE SCLEROSIS PATIENTS IN TREATMENT WITH ANTI-CD20 THERAPIES date: 2020-06-15 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102306 sha: doc_id: 331283 cord_uid: bfyoavon file: cache/cord-331002-7uojryqz.json key: cord-331002-7uojryqz authors: Valent, Francesca; Di Chiara, Antonio title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.041 sha: doc_id: 331002 cord_uid: 7uojryqz file: cache/cord-331147-numz9onx.json key: cord-331147-numz9onx authors: Al‐Kofahi, Mahmoud; Jacobson, Pamala; Boulware, David R.; Matas, Arthur; Kandaswamy, Raja; Jaber, Mutaz M.; Rajasingham, Radha; Young, Jo‐Anne H.; Nicol, Melanie R. title: Finding the Dose for Hydroxychloroquine Prophylaxis for COVID‐19: The Desperate Search for Effectiveness date: 2020-06-01 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.1874 sha: doc_id: 331147 cord_uid: numz9onx file: cache/cord-331428-6pvr2vew.json key: cord-331428-6pvr2vew authors: Heffernan, Kevin S.; Ranadive, Sushant; Jae, Sae Young title: Exercise as medicine for COVID-19: on PPAR with emerging pharmacotherapy date: 2020-08-17 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110197 sha: doc_id: 331428 cord_uid: 6pvr2vew file: cache/cord-331087-kpze9xux.json key: cord-331087-kpze9xux authors: Siddiqui, S.; Naushin, S.; Pradhan, S.; Misra, A.; Tyagi, A.; Loomba, M.; Waghdhare, S.; Pandey, R.; Sengupta, S.; Jha, S. title: SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting date: 2020-09-03 journal: nan DOI: 10.1101/2020.09.02.20186486 sha: doc_id: 331087 cord_uid: kpze9xux file: cache/cord-331300-u5fltc10.json key: cord-331300-u5fltc10 authors: Patel, Jay title: Viability of SARS‐CoV‐2 in faecal bio‐aerosols date: 2020-06-09 journal: Colorectal Dis DOI: 10.1111/codi.15181 sha: doc_id: 331300 cord_uid: u5fltc10 file: cache/cord-331429-mh2hd5fe.json key: cord-331429-mh2hd5fe authors: Srikantiah, Padmini; Charles, Myrna D.; Reagan, Sarah; Clark, Thomas A.; Pletz, Mathias W.R.; Patel, Priti R.; Hoekstra, Robert M.; Lingappa, Jairam; Jernigan, John A.; Fischer, Marc title: SARS Clinical Features, United States, 2003 date: 2005-01-17 journal: Emerg Infect Dis DOI: 10.3201/eid1101.040585 sha: doc_id: 331429 cord_uid: mh2hd5fe file: cache/cord-331055-5ni0jxij.json key: cord-331055-5ni0jxij authors: Bouche, Pierre-Alban; Valteau, Barthelemy; Dumaine, Valerie; Lang, Elena; Michel, Karine; Eyrolle, Luc; Auberger, Guillaume; Anract, Philippe; Hamadouche, Moussa title: Were protective procedures against SARS-CoV-2 effective in an orthopaedic and trauma centre during the lockdown period? A retrospective study date: 2020-07-16 journal: Int Orthop DOI: 10.1007/s00264-020-04729-0 sha: doc_id: 331055 cord_uid: 5ni0jxij file: cache/cord-331094-22366b81.json key: cord-331094-22366b81 authors: Ianevski, Aleksandr; Yao, Rouan; Fenstad, Mona Høysæter; Biza, Svetlana; Zusinaite, Eva; Reisberg, Tuuli; Lysvand, Hilde; Løseth, Kirsti; Landsem, Veslemøy Malm; Malmring, Janne Fossum; Oksenych, Valentyn; Erlandsen, Sten Even; Aas, Per Arne; Hagen, Lars; Pettersen, Caroline H.; Tenson, Tanel; Afset, Jan Egil; Nordbø, Svein Arne; Bjørås, Magnar; Kainov, Denis E. title: Potential Antiviral Options against SARS-CoV-2 Infection date: 2020-06-13 journal: Viruses DOI: 10.3390/v12060642 sha: doc_id: 331094 cord_uid: 22366b81 file: cache/cord-331155-jkm4fuw4.json key: cord-331155-jkm4fuw4 authors: Nakashima, Akiko; Takeya, Mitsue; Kuba, Keiji; Takano, Makoto; Nakashima, Noriyuki title: Virus database annotations assist in tracing information on patients infected with emerging pathogens date: 2020-10-08 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100442 sha: doc_id: 331155 cord_uid: jkm4fuw4 file: cache/cord-331465-humpwwk2.json key: cord-331465-humpwwk2 authors: Canaday, David H; Gravenstein, Stefan title: On setting expectations for a SARS-CoV-2 Vaccine date: 2020-06-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa726 sha: doc_id: 331465 cord_uid: humpwwk2 file: cache/cord-331517-o5ejfq86.json key: cord-331517-o5ejfq86 authors: Hirayama, Takehisa; Hongo, Yu; Kaida, Kenichi; Kano, Osamu title: Guillain-Barré syndrome after COVID-19 in Japan date: 2020-10-29 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-239218 sha: doc_id: 331517 cord_uid: o5ejfq86 file: cache/cord-331193-33cyvidx.json key: cord-331193-33cyvidx authors: Mawhinney, Jamie A; Wilcock, Catherine; Haboubi, Hasan; Roshanzamir, Shahbaz title: Neurotropism of SARS-CoV-2: COVID-19 presenting with an acute manic episode date: 2020-06-14 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-236123 sha: doc_id: 331193 cord_uid: 33cyvidx file: cache/cord-331611-pwj226j0.json key: cord-331611-pwj226j0 authors: Shrimp, Jonathan H.; Kales, Stephen C.; Sanderson, Philip E.; Simeonov, Anton; Shen, Min; Hall, Matthew D. title: An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date: 2020-06-23 journal: bioRxiv DOI: 10.1101/2020.06.23.167544 sha: doc_id: 331611 cord_uid: pwj226j0 file: cache/cord-331423-5wpx0bd0.json key: cord-331423-5wpx0bd0 authors: Pelea, Teodor; Reuter, Ursula; Schmidt, Christine; Laubinger, Raimondo; Siegmund, Robert; Walther, Bjoern Wito title: SARS-CoV-2 associated Guillain–Barré syndrome date: 2020-08-08 journal: J Neurol DOI: 10.1007/s00415-020-10133-w sha: doc_id: 331423 cord_uid: 5wpx0bd0 file: cache/cord-331140-5b0y1xzb.json key: cord-331140-5b0y1xzb authors: Cardona Maya, Walter D.; Carvajal, Alejandro title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health date: 2020-06-01 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109914 sha: doc_id: 331140 cord_uid: 5b0y1xzb file: cache/cord-331666-iwkuwnun.json key: cord-331666-iwkuwnun authors: Schweitzer, Wolf; Ruder, Thomas; Baumeister, Rilana; Bolliger, Stephan; Thali, Michael; Meixner, Eva; Ampanozi, Garyfalia title: Implications for forensic death investigations from first Swiss post-mortem CT in a case of non-hospital treatment with COVID-19 date: 2020-06-30 journal: Forensic Imaging DOI: 10.1016/j.fri.2020.200378 sha: doc_id: 331666 cord_uid: iwkuwnun file: cache/cord-331786-wgt7kg6f.json key: cord-331786-wgt7kg6f authors: Diego-Martin, Borja; González, Beatriz; Vazquez-Vilar, Marta; Selma, Sara; Mateos-Fernández, Rubén; Gianoglio, Silvia; Fernández-del-Carmen, Asun; Orzáez, Diego title: Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date: 2020-10-13 journal: bioRxiv DOI: 10.1101/2020.10.13.331306 sha: doc_id: 331786 cord_uid: wgt7kg6f file: cache/cord-331472-kd4uxcve.json key: cord-331472-kd4uxcve authors: Shahid, Zainab; Kalayanamitra, Ricci; McClafferty, Brendan; Kepko, Douglas; Ramgobin, Devyani; Patel, Ravi; Aggarwal, Chander Shekher; Vunnam, Ramarao; Sahu, Nitasa; Bhatt, Dhirisha; Jones, Kirk; Golamari, Reshma; Jain, Rohit title: COVID‐19 and Older Adults: What We Know date: 2020-04-20 journal: J Am Geriatr Soc DOI: 10.1111/jgs.16472 sha: doc_id: 331472 cord_uid: kd4uxcve file: cache/cord-331496-5xak7z6b.json key: cord-331496-5xak7z6b authors: Garnett, Emily; Jung, Joanna; Tam, Estella; Rajapakshe, Deepthi; Cheney, Stephen; Brown, Cameron; Cao, Jing; Muldrew, Kenneth; Singh, Ila; Versalovic, James; Devaraj, Sridevi title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa157 sha: doc_id: 331496 cord_uid: 5xak7z6b file: cache/cord-331520-o9e4qqn4.json key: cord-331520-o9e4qqn4 authors: Kistler, Christine E.; Jump, Robin L.P.; Sloane, Philip D.; Zimmerman, Sheryl title: The Winter Respiratory Viral Season During the COVID-19 Pandemic date: 2020-10-26 journal: J Am Med Dir Assoc DOI: 10.1016/j.jamda.2020.10.030 sha: doc_id: 331520 cord_uid: o9e4qqn4 file: cache/cord-331375-tbuijeje.json key: cord-331375-tbuijeje authors: Villalobos, Carlos title: SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives date: 2020-09-25 journal: Front Public Health DOI: 10.3389/fpubh.2020.00489 sha: doc_id: 331375 cord_uid: tbuijeje file: cache/cord-331558-6rqd3fmj.json key: cord-331558-6rqd3fmj authors: Sun, Chuan-bin; Wang, Yue-ye; Liu, Geng-hao; Liu, Zhe title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 journal: Front Public Health DOI: 10.3389/fpubh.2020.00155 sha: doc_id: 331558 cord_uid: 6rqd3fmj file: cache/cord-331277-fjsuo3yy.json key: cord-331277-fjsuo3yy authors: Hoste, Alexis C.R.; Venteo, Angel; Fresco-Taboada, Alba; Tapia, Istar; Monedero, Alejandro; López, Lissette; Jebbink, Maarten F.; Pérez-Ramírez, Elisa; Jimenez-Clavero, Miguel Angel; Almonacid, Mercedes; Muñoz, Patricia; Guinea, Jesus; Vela, Carmen; van der Hoek, Lia; Rueda, Paloma; Sastre, Patricia title: Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: A screening tool and a point-of-care test date: 2020-08-11 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115167 sha: doc_id: 331277 cord_uid: fjsuo3yy file: cache/cord-331571-v01kstbr.json key: cord-331571-v01kstbr authors: Rossoff, Jenna; Patel, Ami B.; Muscat, Emily; Kociolek, Larry K.; Muller, William J. title: Benign course of SARS‐CoV‐2 infection in a series of pediatric oncology patients date: 2020-06-23 journal: Pediatr Blood Cancer DOI: 10.1002/pbc.28504 sha: doc_id: 331571 cord_uid: v01kstbr file: cache/cord-331243-0u65qguq.json key: cord-331243-0u65qguq authors: Ucciferri, Claudio; Vecchiet, Jacopo; Falasca, Katia title: Role of monoclonal antibody drugs in the treatment of COVID-19 date: 2020-10-06 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i19.4280 sha: doc_id: 331243 cord_uid: 0u65qguq file: cache/cord-331701-izkz1hz4.json key: cord-331701-izkz1hz4 authors: Eden, John-Sebastian; Rockett, Rebecca; Carter, Ian; Rahman, Hossinur; de Ligt, Joep; Hadfield, James; Storey, Matthew; Ren, Xiaoyun; Tulloch, Rachel; Basile, Kerri; Wells, Jessica; Byun, Roy; Gilroy, Nicky; O’Sullivan, Matthew V; Sintchenko, Vitali; Chen, Sharon C; Maddocks, Susan; Sorrell, Tania C; Holmes, Edward C; Dwyer, Dominic E; Kok, Jen title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-03-17 journal: bioRxiv DOI: 10.1101/2020.03.15.992818 sha: doc_id: 331701 cord_uid: izkz1hz4 file: cache/cord-331547-uqmjhhna.json key: cord-331547-uqmjhhna authors: Bonalumi, Giorgia; Giambuzzi, Ilaria; Barbone, Alessandro; Ranieri, Camilla; Cavallotti, Laura; Trabattoni, Piero; Naliato, Moreno; Polvani, Gianluca; Torracca, Lucia; Pelenghi, Stefano; Ragni, Franco; Russo, Claudio Francesco; Guerra, Francisco; Trimarchi, Santi; Civilini, Efrem; Romani, Federico; Bellosta, Raffaello; Losa, Sergio; Roberto, Maurizio; Alamanni, Francesco title: A call to action becomes practice: cardiac and vascular surgery during the COVID-19 pandemic based on the Lombardy emergency guidelines date: 2020-06-25 journal: Eur J Cardiothorac Surg DOI: 10.1093/ejcts/ezaa204 sha: doc_id: 331547 cord_uid: uqmjhhna file: cache/cord-331790-0w0pjjg1.json key: cord-331790-0w0pjjg1 authors: Abu Jawdeh, Bassam G. title: COVID-19 in Kidney Transplantation: Outcomes, Immunosuppression Management and Operational Challenges date: 2020-07-17 journal: Adv Chronic Kidney Dis DOI: 10.1053/j.ackd.2020.07.004 sha: doc_id: 331790 cord_uid: 0w0pjjg1 file: cache/cord-331617-1ytcd0ax.json key: cord-331617-1ytcd0ax authors: Horvath, Karl; Semlitsch, Thomas; Jeitler, Klaus; Krause, Robert; Siebenhofer, Andrea title: Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date: 2020-05-15 journal: Z Evid Fortbild Qual Gesundhwes DOI: 10.1016/j.zefq.2020.05.005 sha: doc_id: 331617 cord_uid: 1ytcd0ax file: cache/cord-331673-xv1tcugl.json key: cord-331673-xv1tcugl authors: Reina, Giacomo; Peng, Shiyuan; Jacquemin, Lucas; Andrade, Andrés Felipe; Bianco, Alberto title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 journal: ACS Nano DOI: 10.1021/acsnano.0c04117 sha: doc_id: 331673 cord_uid: xv1tcugl file: cache/cord-331825-dwi350c0.json key: cord-331825-dwi350c0 authors: Teherani, Mehgan F; Kao, Carol M; Camacho-Gonzalez, Andres; Banskota, Samridhi; Shane, Andi L; Linam, William M; Jaggi, Preeti title: Burden of illness in households with SARS-CoV-2 infected children date: 2020-08-11 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa097 sha: doc_id: 331825 cord_uid: dwi350c0 file: cache/cord-331831-gw42e6ce.json key: cord-331831-gw42e6ce authors: Moore, Luke S P title: Near-patient SARS-CoV-2 molecular platforms: new-old tools for new-old problems date: 2020-10-08 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30451-3 sha: doc_id: 331831 cord_uid: gw42e6ce file: cache/cord-331835-nuhrd92z.json key: cord-331835-nuhrd92z authors: Hung, Kevin K. 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K.; Tsang, Owen T. Y.; Choi, K. W.; Wong, T. Y.; So, M. K.; Leung, W. S.; Lai, J. Y.; Ng, T. K.; Lai, Thomas S. T. title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date: 2004-05-01 journal: Clin Infect Dis DOI: 10.1086/383580 sha: doc_id: 331930 cord_uid: w2055c42 file: cache/cord-331680-qlzhtxs0.json key: cord-331680-qlzhtxs0 authors: Goryachev, A.N.; Kalantarov, S.A.; Severova, A.G.; Goryacheva, A.S. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 journal: bioRxiv DOI: 10.1101/2020.11.02.363598 sha: doc_id: 331680 cord_uid: qlzhtxs0 file: cache/cord-331541-u0xm9a89.json key: cord-331541-u0xm9a89 authors: Lankes, Heather A; Makhlouf, Hala title: Biospecimen Collection During the COVID-19 Pandemic: Considerations for Biobanking date: 2020-09-25 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa171 sha: doc_id: 331541 cord_uid: u0xm9a89 file: cache/cord-331910-s474ecvk.json key: cord-331910-s474ecvk authors: Thota, Sai Manohar; Balan, Venkatesh; Sivaramakrishnan, Venketesh title: Natural products as home‐based prophylactic and symptom management agents in the setting of COVID‐19 date: 2020-08-17 journal: Phytother Res DOI: 10.1002/ptr.6794 sha: doc_id: 331910 cord_uid: s474ecvk file: cache/cord-331897-4wnoa4l7.json key: cord-331897-4wnoa4l7 authors: Cai, Yi; Xie, Haoran; Lau, Raymond Y.K.; Li, Qing; Wong, Tak-Lam; Wang, Fu Lee title: Temporal event searches based on event maps and relationships() date: 2019-09-25 journal: Appl Soft Comput DOI: 10.1016/j.asoc.2019.105750 sha: doc_id: 331897 cord_uid: 4wnoa4l7 file: cache/cord-332071-bqvn3ceq.json key: cord-332071-bqvn3ceq authors: Lee, Jeong Seok; Park, Seongwan; Jeong, Hye Won; Ahn, Jin Young; Choi, Seong Jin; Lee, Hoyoung; Choi, Baekgyu; Nam, Su Kyung; Sa, Moa; Kwon, Ji-Soo; Jeong, Su Jin; Lee, Heung Kyu; Park, Sung Ho; Park, Su-Hyung; Choi, Jun Yong; Kim, Sung-Han; Jung, Inkyung; Shin, Eui-Cheol title: Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 date: 2020-07-10 journal: Sci Immunol DOI: 10.1126/sciimmunol.abd1554 sha: doc_id: 332071 cord_uid: bqvn3ceq file: cache/cord-332076-b0qtzzac.json key: cord-332076-b0qtzzac authors: Zhen, Wei; Manji, Ryhana; Smith, Elizabeth; Berry, Gregory J. title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00743-20 sha: doc_id: 332076 cord_uid: b0qtzzac file: cache/cord-332013-bl5d4xkc.json key: cord-332013-bl5d4xkc authors: Sánchez-Álvarez, J. Emilio; Fontán, Miguel Pérez; Martín, Carlos Jiménez; Pelícano, Miquel Blasco; Reina, Carlos Jesús Cabezas; Prieto, Ángel M. Sevillano; Melilli, Edoardo; Barrios, Marta Crespo; Heras, Manuel Macía; Pino, María D o lores del Pino y title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) date: 2020-04-27 journal: nan DOI: 10.1016/j.nefroe.2020.04.002 sha: doc_id: 332013 cord_uid: bl5d4xkc file: cache/cord-332268-x30svp5y.json key: cord-332268-x30svp5y authors: Bearden, Donna M.; Aiken, Patricia B.; Cheng, Yu Hsin; Mai, Emily; Peters, Timothy M. title: COVID-19: a primer for healthcare providers date: 2020-05-20 journal: Wien Klin Wochenschr DOI: 10.1007/s00508-020-01678-x sha: doc_id: 332268 cord_uid: x30svp5y file: cache/cord-331871-colmj7uk.json key: cord-331871-colmj7uk authors: Feehan, A. K.; Fort, D.; Garcia-Diaz, J.; Price-Haywood, E.; Velasco, C.; Sapp, E.; Pevey, D.; Seoane, L. title: Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020 date: 2020-06-24 journal: nan DOI: 10.1101/2020.06.23.20138321 sha: doc_id: 331871 cord_uid: colmj7uk file: cache/cord-331878-ww9fu8ey.json key: cord-331878-ww9fu8ey authors: Gao, Xiaopan; Qin, Bo; Chen, Pu; Zhu, Kaixiang; Hou, Pengjiao; Wojdyla, Justyna Aleksandra; Wang, Meitian; Cui, Sheng title: Crystal structure of SARS-CoV-2 papain-like protease date: 2020-09-02 journal: Acta Pharm Sin B DOI: 10.1016/j.apsb.2020.08.014 sha: doc_id: 331878 cord_uid: ww9fu8ey file: cache/cord-331927-b7pfm3i0.json key: cord-331927-b7pfm3i0 authors: Winn, Soe P; Oo, Zin Thawdar; Htun, Nyein Nyein; Soe, May Hnin Pwint; Aung, May M title: Diabetic Ketoacidosis in Coronavirus Disease Patients With Type 2 Diabetes Mellitus date: 2020-08-14 journal: Cureus DOI: 10.7759/cureus.9731 sha: doc_id: 331927 cord_uid: b7pfm3i0 file: cache/cord-332080-923jpec0.json key: cord-332080-923jpec0 authors: Lai, Chih-Cheng; Wang, Cheng-Yi; Ko, Wen-Chien; Hsueh, Po-Ren title: In vitro diagnostics of coronavirus disease 2019: technologies and application date: 2020-06-05 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.05.016 sha: doc_id: 332080 cord_uid: 923jpec0 file: cache/cord-332134-88wfcc3y.json key: cord-332134-88wfcc3y authors: Li, Tingting; Cai, Hongmin; Yao, Hebang; Zhou, Bingjie; Zhang, Ning; Gong, Yuhuan; Zhao, Yapei; Shen, Quan; Qin, Wenming; Hutter, Cedric A.J.; Lai, Yanling; Kuo, Shu-Ming; Bao, Juan; Lan, Jiaming; Seeger, Markus A.; Wong, Gary; Bi, Yuhai; Lavillette, Dimitri; Li, Dianfan title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date: 2020-09-24 journal: bioRxiv DOI: 10.1101/2020.06.09.143438 sha: doc_id: 332134 cord_uid: 88wfcc3y file: cache/cord-332109-ont0tqpn.json key: cord-332109-ont0tqpn authors: Wei, Yufeng; Shah, Rameen title: Substance Use Disorder in the COVID-19 Pandemic: A Systematic Review of Vulnerabilities and Complications date: 2020-07-18 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph13070155 sha: doc_id: 332109 cord_uid: ont0tqpn file: cache/cord-332150-j76726no.json key: cord-332150-j76726no authors: De Stefano, Ludovico; Bobbio-Pallavicini, Francesca; Manzo, Antonio; Montecucco, Carlomaurizio; Bugatti, Serena title: A “Window of Therapeutic Opportunity” for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019 date: 2020-10-06 journal: Front Immunol DOI: 10.3389/fimmu.2020.572635 sha: doc_id: 332150 cord_uid: j76726no file: cache/cord-332245-yfj1kkj7.json key: cord-332245-yfj1kkj7 authors: nan title: SARS-CoV-2 Infektion bei Kindern und Jugendlichen: Ein Literaturüberblick der AG Infektiologie der ÖGKJ1 date: 2020-06-10 journal: Padiatr Padol DOI: 10.1007/s00608-020-00794-1 sha: doc_id: 332245 cord_uid: yfj1kkj7 file: cache/cord-332178-0xyrmk5a.json key: cord-332178-0xyrmk5a authors: Chadchan, Sangappa B.; Maurya, Vineet K.; Popli, Pooja; Kommagani, Ramakrishna title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date: 2020-06-24 journal: bioRxiv DOI: 10.1101/2020.06.23.168252 sha: doc_id: 332178 cord_uid: 0xyrmk5a file: cache/cord-332065-afq26621.json key: cord-332065-afq26621 authors: Ghanchi, Hammad; Patchana, Tye; Wiginton, James; Browne, Jonathan D; Ohno, Ai; Farahmandian, Ronit; Duong, Jason; Cortez, Vladimir; Miulli, Dan E title: Racial Disparity Amongst Stroke Patients During the Coronavirus Disease 2019 Pandemic date: 2020-09-10 journal: Cureus DOI: 10.7759/cureus.10369 sha: doc_id: 332065 cord_uid: afq26621 file: cache/cord-332271-slouuryl.json key: cord-332271-slouuryl authors: Baker, Jeremy D.; Uhrich, Rikki L.; Kraemer, Gerald C.; Love, Jason E.; Kraemer, Brian C. title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date: 2020-08-27 journal: bioRxiv DOI: 10.1101/2020.07.10.197889 sha: doc_id: 332271 cord_uid: slouuryl file: cache/cord-332196-03cklmm3.json key: cord-332196-03cklmm3 authors: Kennedy, Amy J.; Hilmes, Mary K.; Waddell, Linda; Bartow, Alexandrea B.; Baxter, Carla M.; Hadi, Christiane M.; Snyder, Graham M.; Merlin, Jessica S. title: Retesting for severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Patterns of testing from a large US healthcare system date: 2020-08-10 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.413 sha: doc_id: 332196 cord_uid: 03cklmm3 file: cache/cord-332292-n7k4va9k.json key: cord-332292-n7k4va9k authors: Yen, Yung-Feng; Lai, Hsin-Hao; Chan, Shang-Yih; Yi-Fong Su, Vincent; Chiu, Ting-Fang; Huang, Chiao-Yu; Hung, Chia-Chun; Kuo, Tzu-Ling; Lee, Ya-Ling; Chu, Dachen title: Olfactory disorder in patients infected with SARS-CoV-2 date: 2020-08-20 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.08.010 sha: doc_id: 332292 cord_uid: n7k4va9k file: cache/cord-332278-2p64ab2z.json key: cord-332278-2p64ab2z authors: Vivas, David; Roldán, Vanessa; Esteve-Pastor, María Asunción; Roldán, Inmaculada; Tello-Montoliu, Antonio; Ruiz-Nodar, Juan Miguel; Cosín-Sales, Juan; María Gámez, José; Consuegra, Luciano; Luis Ferreiro, José; Marín, Francisco title: Recomendaciones sobre el tratamiento antitrombótico durante la pandemia COVID-19. Posicionamiento del Grupo de Trabajo de Trombosis Cardiovascular de la Sociedad Española de Cardiología date: 2020-06-19 journal: Rev Esp Cardiol (Engl Ed) DOI: 10.1016/j.rec.2020.04.025 sha: doc_id: 332278 cord_uid: 2p64ab2z file: cache/cord-332469-zegawla5.json key: cord-332469-zegawla5 authors: Li, Wei; Zhang, Bo; Lu, Jianhua; Liu, Shihua; Chang, Zhiqiang; Cao, Peng; Liu, Xinhua; Zhang, Peng; Ling, Yan; Tao, Kaixiong; Chen, Jianying title: The characteristics of household transmission of COVID-19 date: 2020-04-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa450 sha: doc_id: 332469 cord_uid: zegawla5 file: cache/cord-332153-fczf3lzc.json key: cord-332153-fczf3lzc authors: Azkur, Ahmet Kursat; Akdis, Mübeccel; Azkur, Dilek; Sokolowska, Milena; van de Veen, Willem; Brüggen, Marie‐Charlotte; O'Mahony, Liam; Gao, Yadong; Nadeau, Kari; Akdis, Cezmi A. title: Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19 date: 2020-05-12 journal: Allergy DOI: 10.1111/all.14364 sha: doc_id: 332153 cord_uid: fczf3lzc file: cache/cord-332276-gs80celr.json key: cord-332276-gs80celr authors: Tan, Yee‐Joo; Lim, Seng Gee; Hong, Wanjin title: Regulation of cell death during infection by the severe acute respiratory syndrome coronavirus and other coronaviruses date: 2007-08-20 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2007.01034.x sha: doc_id: 332276 cord_uid: gs80celr file: cache/cord-332185-a96r1k7a.json key: cord-332185-a96r1k7a authors: Zhang, Shuyuan; Qiao, Shuyuan; Yu, Jinfang; Zeng, Jianwei; Shan, Sisi; Lan, Jun; Tian, Long; Zhang, Linqi; Wang, Xinquan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.21.307439 sha: doc_id: 332185 cord_uid: a96r1k7a file: cache/cord-332480-3uodkrkp.json key: cord-332480-3uodkrkp authors: Bonam, Srinivasa Reddy; Kaveri, Srini V.; Sakuntabhai, Anavaj; Gilardin, Laurent; Bayry, Jagadeesh title: Adjunct immunotherapies for the management of severely ill COVID-19 patients date: 2020-04-30 journal: Cell reports medicine DOI: 10.1016/j.xcrm.2020.100016 sha: doc_id: 332480 cord_uid: 3uodkrkp file: cache/cord-332348-yi85sfks.json key: cord-332348-yi85sfks authors: Liang, Yujie; Xu, Jiabin; Chu, Mei; Mai, Jianbo; Lai, Niangmei; Tang, Wen; Yang, Tuanjie; Zhang, Sien; Guan, Chenyu; Zhong, Fan; Yang, Liuping; Liao, Guiqing title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.086 sha: doc_id: 332348 cord_uid: yi85sfks file: cache/cord-332448-5fz8ef4f.json key: cord-332448-5fz8ef4f authors: Mutnal, M. B.; Arroliga, A. C.; Walker, K.; Mohammad, A. A.; Brigmon, M. M.; Beaver, R. M.; Midturi, J. K.; Rao, A. title: Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.30.20086116 sha: doc_id: 332448 cord_uid: 5fz8ef4f file: cache/cord-332312-od3vjuw5.json key: cord-332312-od3vjuw5 authors: Pagani, G.; Conti, F.; Giacomelli, A.; Bernacchia, D.; Rondanin, R.; Prina, A.; Scolari, V.; Gandolfi, C. E.; Castaldi, S.; Marano, G.; Ottomano, C.; Boracchi, P.; Biganzoli, E. M.; Galli, M. title: Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA). date: 2020-06-24 journal: nan DOI: 10.1101/2020.06.24.20138875 sha: doc_id: 332312 cord_uid: od3vjuw5 file: cache/cord-332207-dmxbk7ad.json key: cord-332207-dmxbk7ad authors: Sastry, Sangeeta R.; Pryor, Rachel; Raybould, Jillian E.; Reznicek, Julie; Cooper, Kaila; Patrick, Amie; Knowlson, Shelley; Bailey, Pamela; Godbout, Emily; Doll, Michelle; Stevens, Michael P.; Bearman, Gonzalo title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence date: 2020-07-23 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.358 sha: doc_id: 332207 cord_uid: dmxbk7ad file: cache/cord-332303-0bbw64p5.json key: cord-332303-0bbw64p5 authors: Schuit, Michael; Ratnesar-Shumate, Shanna; Yolitz, Jason; Williams, Gregory; Weaver, Wade; Green, Brian; Miller, David; Krause, Melissa; Beck, Katie; Wood, Stewart; Holland, Brian; Bohannon, Jordan; Freeburger, Denise; Hooper, Idris; Biryukov, Jennifer; Altamura, Louis A; Wahl, Victoria; Hevey, Michael; Dabisch, Paul title: Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date: 2020-06-11 journal: J Infect Dis DOI: 10.1093/infdis/jiaa334 sha: doc_id: 332303 cord_uid: 0bbw64p5 file: cache/cord-332179-du1zjupf.json key: cord-332179-du1zjupf authors: Sayed, Shomoita title: COVID-19 and Diabetes; possible role of polymorphism and rise of telemedicine date: 2020-08-31 journal: Prim Care Diabetes DOI: 10.1016/j.pcd.2020.08.018 sha: doc_id: 332179 cord_uid: du1zjupf file: cache/cord-332300-5osg046o.json key: cord-332300-5osg046o authors: Yu, Luo; Peel, Garrett K.; Cheema, Faisal H.; Lawrence, William S.; Bukreyeva, Natalya; Jinks, Christopher W.; Peel, Jennifer E.; Peterson, Johnny W.; Paessler, Slobodan; Hourani, Monzer; Ren, Zhifeng title: Catching and killing of airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system date: 2020-07-07 journal: nan DOI: 10.1016/j.mtphys.2020.100249 sha: doc_id: 332300 cord_uid: 5osg046o file: cache/cord-332404-va3rxy5p.json key: cord-332404-va3rxy5p authors: Landeros, A.; Ji, X.; Lange, K. 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S. title: An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic date: 2020-08-06 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.08.05.20169086 sha: doc_id: 332404 cord_uid: va3rxy5p file: cache/cord-332537-rtdu4jae.json key: cord-332537-rtdu4jae authors: Tong, Tommy R. title: Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date: 2005-05-01 journal: J Infect Dis DOI: 10.1086/429637 sha: doc_id: 332537 cord_uid: rtdu4jae file: cache/cord-332610-t99l3zii.json key: cord-332610-t99l3zii authors: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 journal: International Encyclopedia of Public Health DOI: 10.1016/b978-012373960-5.00453-6 sha: doc_id: 332610 cord_uid: t99l3zii file: cache/cord-332458-2kwfcgz9.json key: cord-332458-2kwfcgz9 authors: Ji, Henry; Yan, Ying; Ding, Beibei; Guo, Wenzhong; Brunswick, Mark; Niethammer, Andreas; SooHoo, Williams; Smith, Robin; Nahama, Alexis; Zhang, Yanliang title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus date: 2020-03-25 journal: Med Drug Discov DOI: 10.1016/j.medidd.2020.100026 sha: doc_id: 332458 cord_uid: 2kwfcgz9 file: cache/cord-332374-cbiw6yvb.json key: cord-332374-cbiw6yvb authors: Israeli, Ofir; Beth-Din, Adi; Paran, Nir; Stein, Dana; Lazar, Shirley; Weiss, Shay; Milrot, Elad; Atiya-Nasagi, Yafit; Yitzhaki, Shmuel; Laskar, Orly; Schuster, Ofir title: Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date: 2020-06-10 journal: bioRxiv DOI: 10.1101/2020.06.10.144196 sha: doc_id: 332374 cord_uid: cbiw6yvb file: cache/cord-332457-gan10za0.json key: cord-332457-gan10za0 authors: de Ángel Solá, David E.; Wang, Leyao; Vázquez, Marietta; Méndez Lázaro, Pablo A. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 journal: J Med Virol DOI: 10.1002/jmv.25864 sha: doc_id: 332457 cord_uid: gan10za0 file: cache/cord-332510-x3znuwc0.json key: cord-332510-x3znuwc0 authors: Freire-Álvarez, Eric; Guillén, Lucía; Lambert, Karine; Baidez, Ana; García-Quesada, Miguel; Andreo, María; Alom, Jordi; Masiá, Mar; Gutiérrez, Félix title: COVID-19-associated encephalitis successfully treated with combination therapy date: 2020-11-01 journal: Clin Infect Pract DOI: 10.1016/j.clinpr.2020.100053 sha: doc_id: 332510 cord_uid: x3znuwc0 file: cache/cord-332592-bfqsyiyf.json key: cord-332592-bfqsyiyf authors: Goette, Andreas; Patscheke, Markus; Henschke, Frank; Hammwöhner, Matthias title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation date: 2020-09-26 journal: TH Open DOI: 10.1055/s-0040-1716717 sha: doc_id: 332592 cord_uid: bfqsyiyf file: cache/cord-332654-nav15g8k.json key: cord-332654-nav15g8k authors: Paniri, Alireza; Hosseini, Mohammad Mahdi; Rasoulinejad, Ahmad; Akhavan-Niaki, Haleh title: Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations date: 2020-08-04 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173454 sha: doc_id: 332654 cord_uid: nav15g8k file: cache/cord-332723-rz1iilsv.json key: cord-332723-rz1iilsv authors: Creager, Hannah M.; Cabrera, Barbara; Schnaubelt, Andy; Cox, Jesse L.; Cushman-Vokoun, Allison M.; Shakir, Salika M.; Tardif, Keith D.; Huang, Meei-Li; Jerome, Keith R.; Greninger, Alexander L.; Drobysheva, Daria; Spaulding, Usha; Rogatcheva, Margarita; Bourzac, Kevin M.; Hinrichs, S.H.; Broadhurst, M.J.; Fey, P.D. title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date: 2020-07-06 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104538 sha: doc_id: 332723 cord_uid: rz1iilsv file: cache/cord-332820-6qx6svs5.json key: cord-332820-6qx6svs5 authors: Buck, M. 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B.; Auch, Benjamin; Nelson, Andrew; Yohe, Sophia; Beckman, Kenneth B. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 journal: bioRxiv DOI: 10.1101/2020.05.11.088724 sha: doc_id: 332539 cord_uid: v1bfm57x file: cache/cord-332557-qm3qfvry.json key: cord-332557-qm3qfvry authors: Lau, Susanna K.P.; Che, Xiao-Yan; Woo, Patrick C.Y.; Wong, Beatrice H.L.; Cheng, Vincent C.C.; Woo, Gibson K.S.; Hung, Ivan F.N.; Poon, Rosana W.S.; Chan, Kwok-Hung; Peiris, J.S. Malik; Yuen, Kwok-Yung title: SARS Coronavirus Detection Methods date: 2005-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1107.041045 sha: doc_id: 332557 cord_uid: qm3qfvry file: cache/cord-332595-874tpi09.json key: cord-332595-874tpi09 authors: Salehi, Najmeh; Amiri-Yekta, Amir; Totonchi, Mehdi title: Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients date: 2020-09-08 journal: Cell J DOI: 10.22074/cellj.2020.7524 sha: doc_id: 332595 cord_uid: 874tpi09 file: cache/cord-332672-fbwz8oxp.json key: cord-332672-fbwz8oxp authors: Wang, Manli; Hu, Zhihong title: Bats as animal reservoirs for the SARS coronavirus: Hypothesis proved after 10 years of virus hunting date: 2013-10-30 journal: Virol Sin DOI: 10.1007/s12250-013-3402-x sha: doc_id: 332672 cord_uid: fbwz8oxp file: cache/cord-332948-h297ukuu.json key: cord-332948-h297ukuu authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date: 2020-10-16 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100451 sha: doc_id: 332948 cord_uid: h297ukuu file: cache/cord-332716-1d89j7jh.json key: cord-332716-1d89j7jh authors: Choi, Marcelo; Aiello, Ernesto Alejandro; Ennis, Irene L.; Villa-Abrille, María Celeste title: El SRAA y el SARS-CoV-2: el acertijo a resolver date: 2020-05-27 journal: Hipertens Riesgo Vasc DOI: 10.1016/j.hipert.2020.05.005 sha: doc_id: 332716 cord_uid: 1d89j7jh file: cache/cord-332827-gll4nqdd.json key: cord-332827-gll4nqdd authors: Peixe, Paula; Calinas, Filipe; Tato Marinho, Rui title: Hepatology in the COVID Era: Another C Virus, again Challenging the Liver date: 2020-04-30 journal: GE Port J Gastroenterol DOI: 10.1159/000508116 sha: doc_id: 332827 cord_uid: gll4nqdd file: cache/cord-333121-kt6t41ff.json key: cord-333121-kt6t41ff authors: Kwenandar, Felix; Valeriani Japar, Karunia; Damay, Vika; Ivan Hariyanto, Timotius; Tanaka, Michael; Pratama Hardjito Lugito, Nata; Kurniawan, Andree title: Coronavirus Disease 2019 and Cardiovascular System: A Narrative Review date: 2020-06-03 journal: Int J Cardiol Heart Vasc DOI: 10.1016/j.ijcha.2020.100557 sha: doc_id: 333121 cord_uid: kt6t41ff file: cache/cord-333174-g10kvc0c.json key: cord-333174-g10kvc0c authors: Ahmed, Sinthyia; Mahtarin, Rumana; Ahmed, Sayeda Samina; Akter, Shaila; Islam, Md. Shamiul; Mamun, Abdulla Al; Islam, Rajib; Hossain, Md Nayeem; Ali, Md Ackas; Sultana, Mossammad U. C.; Parves, MD. Rimon; Ullah, M. Obayed; Halim, Mohammad A. title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 date: 2020-07-28 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1796804 sha: doc_id: 333174 cord_uid: g10kvc0c file: cache/cord-333176-6v7ficfk.json key: cord-333176-6v7ficfk authors: Snell, Jonathan title: SARS-CoV-2 infection and its association with thrombosis and ischemic stroke: A review COVID-19, thrombosis, and ischemic stroke date: 2020-09-30 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.09.072 sha: doc_id: 333176 cord_uid: 6v7ficfk file: cache/cord-333018-2h8y118z.json key: cord-333018-2h8y118z authors: Sun, Xingxing; Liu, Yong; Mei, Wei title: Safety Considerations for Neuraxial Anaesthesia in Parturients with COVID-19 date: 2020-05-14 journal: Br J Anaesth DOI: 10.1016/j.bja.2020.05.005 sha: doc_id: 333018 cord_uid: 2h8y118z file: cache/cord-333042-icgsbelo.json key: cord-333042-icgsbelo authors: Fisher, Kiva A.; Tenforde, Mark W.; Feldstein, Leora R.; Lindsell, Christopher J.; Shapiro, Nathan I.; Files, D. 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Keipp; Casey, Jonathan D.; Grijalva, Carlos G.; Flannery, Brendan; Patel, Manish M.; Self, Wesley H.; Hart, Kimberly W.; McClellan, Robert; Tan, Hsi-nien; Baughman, Adrienne; Hennesy, Nora A.; Grear, Brittany; Wu, Michael; Mlynarczyk, Kristin; Marzano, Luc; Plata, Zuwena; Caplan, Alexis; Olson, Samantha M.; Ogokeh, Constance E.; Smith, Emily R.; Kim, Sara S.; Griggs, Eric P.; Richards, Bridget; Robinson, Sonya; Kim, Kaylee; Kassem, Ahmed M.; Sciarratta, Courtney N.; Marcet, Paula L. title: Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities — United States, July 2020 date: 2020-09-11 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6936a5 sha: doc_id: 333042 cord_uid: icgsbelo file: cache/cord-333144-gyuh2fvl.json key: cord-333144-gyuh2fvl authors: Siddiqui, Arif Jamal; Jahan, Sadaf; Ashraf, Syed Amir; Alreshidi, Mousa; Ashraf, Mohammad Saquib; Patel, Mitesh; Snoussi, Mejdi; Singh, Ritu; Adnan, Mohd title: Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 date: 2020-08-05 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1802345 sha: doc_id: 333144 cord_uid: gyuh2fvl file: cache/cord-333092-78vo7i6v.json key: cord-333092-78vo7i6v authors: Taksande, Amar title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age date: 2020-08-11 journal: World J Pediatr DOI: 10.1007/s12519-020-00384-y sha: doc_id: 333092 cord_uid: 78vo7i6v file: cache/cord-332832-kjppd6uz.json key: cord-332832-kjppd6uz authors: Ward, B. J.; Gobeil, P.; Seguin, A.; Atkins, J.; Boulay, I.; Charbonneau, P.-Y.; Couture, M.; D'Aoust, M.-A.; Dhaliwall, J.; Finkle, C.; Hager, K.; Mahmood, A.; Makarkov, A.; Cheng, M.; Pillet, S.; Schimke, P.; St-Martin, S.; Trepanier, S.; Landry, N. title: Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants date: 2020-11-06 journal: nan DOI: 10.1101/2020.11.04.20226282 sha: doc_id: 332832 cord_uid: kjppd6uz file: cache/cord-333140-cdikbi1l.json key: cord-333140-cdikbi1l authors: Zhao, Helong; Mendenhall, Michelle; Deininger, Michael W. title: Imatinib is not a potent anti-SARS-CoV-2 drug date: 2020-09-30 journal: Leukemia DOI: 10.1038/s41375-020-01045-9 sha: doc_id: 333140 cord_uid: cdikbi1l file: cache/cord-333465-cha7ndv5.json key: cord-333465-cha7ndv5 authors: Horspool, A. M.; Kieffer, T.; Russ, B. P.; DeJong, M. A.; Wolf, M. A.; Karakiozis, J. M.; Hickey, B. J.; Fagone, P.; Tacker, D. H.; Bevere, J. R.; Martinez, I.; Barbier, M.; Perrotta, P. L.; Damron, F. H. title: Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date: 2020-08-31 journal: nan DOI: 10.1101/2020.08.24.20180877 sha: doc_id: 333465 cord_uid: cha7ndv5 file: cache/cord-333264-jdvb8px4.json key: cord-333264-jdvb8px4 authors: Hanke, Leo; Vidakovics Perez, Laura; Sheward, Daniel J.; Das, Hrishikesh; Schulte, Tim; Moliner-Morro, Ainhoa; Corcoran, Martin; Achour, Adnane; Karlsson Hedestam, Gunilla B.; Hällberg, B. Martin; Murrell, Ben; McInerney, Gerald M. title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date: 2020-09-04 journal: Nat Commun DOI: 10.1038/s41467-020-18174-5 sha: doc_id: 333264 cord_uid: jdvb8px4 file: cache/cord-333089-ufyzqgqk.json key: cord-333089-ufyzqgqk authors: Aguilar-Pineda, Jorge Alberto; Albaghdadi, Mazen; Jiang, Wanlin; Lopez, Karin J. Vera; Del-Carpio, Gonzalo Davila; Valdez, Badhin Gómez; Lindsay, Mark E.; Malhotra, Rajeev; Lino Cardenas, Christian L. title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date: 2020-07-29 journal: bioRxiv DOI: 10.1101/2020.07.29.227249 sha: doc_id: 333089 cord_uid: ufyzqgqk file: cache/cord-333453-v3gap8kj.json key: cord-333453-v3gap8kj authors: Dima, Mirabela; Enatescu, Ileana; Craina, Marius; Petre, Izabella; Iacob, Emil Radu; Iacob, Daniela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000021284 sha: doc_id: 333453 cord_uid: v3gap8kj file: cache/cord-333320-ndmmbckb.json key: cord-333320-ndmmbckb authors: Samore, M.; Looney, A.; Orleans, B.; Greene, T.; Seegert, N.; Delgado, J. C.; Presson, A.; Zhang, C.; Ying, J.; Zhang, Y.; Shen, J.; Slev, P.; Gaulin, M.; Yang, M.-J.; Pavia, A. T.; Alder, S. C. title: SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample date: 2020-10-27 journal: nan DOI: 10.1101/2020.10.26.20219907 sha: doc_id: 333320 cord_uid: ndmmbckb file: cache/cord-333195-m4gvpsf8.json key: cord-333195-m4gvpsf8 authors: Lu, Renfei; Wu, Xiuming; Wan, Zhenzhou; Li, Yingxue; Zuo, Lulu; Qin, Jianru; Jin, Xia; Zhang, Chiyu title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date: 2020-04-01 journal: Virol Sin DOI: 10.1007/s12250-020-00218-1 sha: doc_id: 333195 cord_uid: m4gvpsf8 file: cache/cord-333239-nj5dma98.json key: cord-333239-nj5dma98 authors: Ducrest, P. J. title: Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2 date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.09.20209866 sha: doc_id: 333239 cord_uid: nj5dma98 file: cache/cord-333080-qytwbsne.json key: cord-333080-qytwbsne authors: Alahari, Suresh K.; Yousefi, Hassan; Poursheikhani, Arash; bahmanpour, Zahra; Vatanmakanian, Mousa; Taheri, Mohammad; Mashouri, Ladan title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110548 sha: doc_id: 333080 cord_uid: qytwbsne file: cache/cord-333234-yvixy77x.json key: cord-333234-yvixy77x authors: Triposkiadis, Filippos; Starling, Randall C.; Xanthopoulos, Andrew; Butler, Javed; Boudoulas, Harisios title: Renin-angiotensin-system inhibition in the context of corona virus disease-19: experimental evidence, observational studies, and clinical implications date: 2020-09-01 journal: Heart Fail Rev DOI: 10.1007/s10741-020-10022-4 sha: doc_id: 333234 cord_uid: yvixy77x file: cache/cord-332680-zfn81hew.json key: cord-332680-zfn81hew authors: Chan, Chieh-Kai; Huang, Yu-Shan; Liao, Hung-Wei; Tsai, I-Jung; Sun, Chiao-Yin; Pan, Heng-Chih; Chueh, Jeff S.; Wang, Jann-Tay; Wu, Vin-Cent; Chu, Tzong-Shinn title: Renin-Angiotensin-Aldosterone System Inhibitors and Risks of Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Systematic Review and Meta-Analysis date: 2020-09-10 journal: Hypertension DOI: 10.1161/hypertensionaha.120.15989 sha: doc_id: 332680 cord_uid: zfn81hew file: cache/cord-333200-yka7wfbi.json key: cord-333200-yka7wfbi authors: Dhampalwar, Swapnil; Saigal, Sanjiv; Soin, Arvinder title: Treatment armamentarium of COVID-19: Evolving strategies & evidence so far date: 2020-07-16 journal: J Clin Exp Hepatol DOI: 10.1016/j.jceh.2020.07.001 sha: doc_id: 333200 cord_uid: yka7wfbi file: cache/cord-333429-bq7kfpby.json key: cord-333429-bq7kfpby authors: Shi, Ding; Wu, Wenrui; Wang, Qing; Xu, Kaijin; Xie, Jiaojiao; Wu, Jingjing; Lv, Longxian; Sheng, Jifang; Guo, Jing; Wang, Kaicen; Fang, Daiqiong; Li, Yating; Li, Lanjuan title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 journal: J Infect Dis DOI: 10.1093/infdis/jiaa388 sha: doc_id: 333429 cord_uid: bq7kfpby file: cache/cord-333487-zem2d4y6.json key: cord-333487-zem2d4y6 authors: Thomaz Ugliara Barone, Mark; Bega Harnik, Simone; Vieira de Luca, Patrícia; Letícia de Souza Lima, Bruna; José Pineda Wieselberg, Ronaldo; Ngongo, Belinda; Cordeiro Pedrosa, Hermelinda; Pimazoni-Netto, Augusto; Reis Franco, Denise; de Fatima Marinho de Souza, Maria; Carvalho Malta, Deborah; Giampaoli, Viviana title: The Impact of COVID-19 on People with Diabetes in Brazil date: 2020-07-03 journal: Diabetes Res Clin Pract DOI: 10.1016/j.diabres.2020.108304 sha: doc_id: 333487 cord_uid: zem2d4y6 file: cache/cord-333099-hy4nmy7l.json key: cord-333099-hy4nmy7l authors: Thoms, Matthias; Buschauer, Robert; Ameismeier, Michael; Koepke, Lennart; Denk, Timo; Hirschenberger, Maximilian; Kratzat, Hanna; Hayn, Manuel; Mackens-Kiani, Timur; Cheng, Jingdong; Straub, Jan H.; Stürzel, Christina M.; Fröhlich, Thomas; Berninghausen, Otto; Becker, Thomas; Kirchhoff, Frank; Sparrer, Konstantin M. J.; Beckmann, Roland title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 date: 2020-07-17 journal: Science DOI: 10.1126/science.abc8665 sha: doc_id: 333099 cord_uid: hy4nmy7l file: cache/cord-333368-kjrk8nn9.json key: cord-333368-kjrk8nn9 authors: Huizinga, Gabrielle P; Singer, Benjamin H; Singer, Kanakadurga title: The Collision of Meta-Inflammation and SARS-CoV-2 Pandemic Infection date: 2020-09-03 journal: Endocrinology DOI: 10.1210/endocr/bqaa154 sha: doc_id: 333368 cord_uid: kjrk8nn9 file: cache/cord-333381-wz70o9tt.json key: cord-333381-wz70o9tt authors: Liu, Shao; Luo, Ping; Tang, Mimi; Hu, Qin; Polidoro, Joseph P.; Sun, Shusen; Gong, Zhicheng title: Providing pharmacy services during the coronavirus pandemic date: 2020-03-28 journal: Int J Clin Pharm DOI: 10.1007/s11096-020-01017-0 sha: doc_id: 333381 cord_uid: wz70o9tt file: cache/cord-333326-n9ifhw5s.json key: cord-333326-n9ifhw5s authors: Wardell, Hanna; Campbell, Jeffrey I; VanderPluym, Christina; Dixit, Avika title: Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Febrile Neonates date: 2020-07-09 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa084 sha: doc_id: 333326 cord_uid: n9ifhw5s file: cache/cord-333524-a6p6ma8r.json key: cord-333524-a6p6ma8r authors: Khan, Pavana; Aufdembrink, Lauren M.; Engelhart, Aaron E. title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 journal: ACS Synth Biol DOI: 10.1021/acssynbio.0c00359 sha: doc_id: 333524 cord_uid: a6p6ma8r file: cache/cord-333515-llqpfhwg.json key: cord-333515-llqpfhwg authors: Zhao, Juanjuan; Yuan, Quan; Wang, Haiyan; Liu, Wei; Liao, Xuejiao; Su, Yingying; Wang, Xin; Yuan, Jing; Li, Tingdong; Li, Jinxiu; Qian, Shen; Hong, Congming; Wang, Fuxiang; Liu, Yingxia; Wang, Zhaoqin; He, Qing; Li, Zhiyong; He, Bin; Zhang, Tianying; Ge, Shengxiang; Liu, Lei; Zhang, Jun; Xia, Ningshao; Zhang, Zheng title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 journal: nan DOI: 10.1101/2020.03.02.20030189 sha: doc_id: 333515 cord_uid: llqpfhwg file: cache/cord-333520-v2sb90rc.json key: cord-333520-v2sb90rc authors: Gardin, Chiara; Ferroni, Letizia; Chachques, Juan Carlos; Zavan, Barbara title: Could Mesenchymal Stem Cell-Derived Exosomes Be a Therapeutic Option for Critically Ill COVID-19 Patients? date: 2020-08-26 journal: J Clin Med DOI: 10.3390/jcm9092762 sha: doc_id: 333520 cord_uid: v2sb90rc file: cache/cord-333606-5z3kumu9.json key: cord-333606-5z3kumu9 authors: Lee, SangJoon; Channappanavar, Rudragouda; Kanneganti, Thirumala-Devi title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines date: 2020-10-15 journal: Trends Immunol DOI: 10.1016/j.it.2020.10.005 sha: doc_id: 333606 cord_uid: 5z3kumu9 file: cache/cord-333262-xvfl7ycj.json key: cord-333262-xvfl7ycj authors: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.103749 sha: doc_id: 333262 cord_uid: xvfl7ycj file: cache/cord-333391-6l0cpvgr.json key: cord-333391-6l0cpvgr authors: Bortolotti, Daria; Gentili, Valentina; Rizzo, Sabrina; Rotola, Antonella; Rizzo, Roberta title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 journal: Cells DOI: 10.3390/cells9091975 sha: doc_id: 333391 cord_uid: 6l0cpvgr file: cache/cord-333498-d25qfq0f.json key: cord-333498-d25qfq0f authors: Chitranshi, Nitin; Gupta, Vivek K.; Rajput, Rashi; Godinez, Angela; Pushpitha, Kanishka; Shen, Ting; Mirzaei, Mehdi; You, Yuyi; Basavarajappa, Devaraj; Gupta, Veer; Graham, Stuart L. title: Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL(pro) targeting repurposed drug candidates date: 2020-07-09 journal: J Transl Med DOI: 10.1186/s12967-020-02448-z sha: doc_id: 333498 cord_uid: d25qfq0f file: cache/cord-333670-qv1orlv5.json key: cord-333670-qv1orlv5 authors: Mutti, Luciano; Pentimalli, Francesca; Baglio, Giovanni; Maiorano, Patrizia; Saladino, Rita Emilena; Correale, Pierpaolo; Giordano, Antonio title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.01208 sha: doc_id: 333670 cord_uid: qv1orlv5 file: cache/cord-333713-nz36i2oa.json key: cord-333713-nz36i2oa authors: Andonegui-Elguera, Sergio; Taniguchi-Ponciano, Keiko; Gonzales-Bonilla, Cesar Raul; Torres, Javier; Mayani, Hector; Herrera, Luis Alonso; Peña-Martínez, Eduardo; Silva-Román, Gloria; Vela-Patiño, Sandra; Ferreira-Hermosillo, Aldo; Ramirez-Renteria, Claudia; Carvente-Garcia, Roberto; Mata-Lozano, Carlos; Marrero-Rodríguez, Daniel; Mercado, Moises title: Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism date: 2020-06-18 journal: Arch Med Res DOI: 10.1016/j.arcmed.2020.06.011 sha: doc_id: 333713 cord_uid: nz36i2oa file: cache/cord-333420-qqyg9um9.json key: cord-333420-qqyg9um9 authors: Zhu, Xun; Chang, Ti-Cheng; Webby, Richard; Wu, Gang title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date: 2020-10-09 journal: bioRxiv DOI: 10.1101/2020.10.08.330456 sha: doc_id: 333420 cord_uid: qqyg9um9 file: cache/cord-333532-vrfduv5a.json key: cord-333532-vrfduv5a authors: Patel, Kishan Pravin; Patel, Puja A.; Vunnam, Srinivas R.; Jain, Rohit; Vunnam, Rama R. title: COVID-19 Patients: Are Current Isolation Guidelines Effective Enough? date: 2020-05-11 journal: Public Health DOI: 10.1016/j.puhe.2020.04.048 sha: doc_id: 333532 cord_uid: vrfduv5a file: cache/cord-333703-1ku3jc9s.json key: cord-333703-1ku3jc9s authors: Kraus, Aurora; Casadei, Elisa; Huertas, Mar; Ye, Chunyan; Bradfute, Steven; Boudinot, Pierre; Levraud, Jean-Pierre; Salinas, Irene title: A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date: 2020-11-08 journal: bioRxiv DOI: 10.1101/2020.11.06.368191 sha: doc_id: 333703 cord_uid: 1ku3jc9s file: cache/cord-333929-oprpgcyr.json key: cord-333929-oprpgcyr authors: Lee, Justin; Holden, Lori; Fung, Kinwah; Danjoux, Cyril; Chow, Edward; Gillies, Carol title: Impact of Severe Acute Respiratory Syndrome on Patient Access to Palliative Radiation Therapy date: 2005-01-31 journal: Supportive Cancer Therapy DOI: 10.3816/sct.2005.n.004 sha: doc_id: 333929 cord_uid: oprpgcyr file: cache/cord-333696-3ci9re9a.json key: cord-333696-3ci9re9a authors: Alomari, Safwan O.; Abou-Mrad, Zaki; Bydon, Ali title: COVID-19 and the Central Nervous System date: 2020-08-04 journal: Clin Neurol Neurosurg DOI: 10.1016/j.clineuro.2020.106116 sha: doc_id: 333696 cord_uid: 3ci9re9a file: cache/cord-333730-qsx0m68e.json key: cord-333730-qsx0m68e authors: Tsai, Y. 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F. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 journal: Ther Adv Musculoskelet Dis DOI: 10.1177/1759720x20947296 sha: doc_id: 333730 cord_uid: qsx0m68e file: cache/cord-333654-8rg99di5.json key: cord-333654-8rg99di5 authors: Pillai, Presaad; Joseph, Joyce Pauline; Fadzillah, Nurul Huda Mohamad; Mahmod, Masliza title: COVID-19 AND MAJOR ORGAN THROMBOEMBOLISM: MANIFESTATIONS IN NEUROVASCULAR AND CARDIOVASCULAR SYSTEMS. date: 2020-10-24 journal: J Stroke Cerebrovasc Dis DOI: 10.1016/j.jstrokecerebrovasdis.2020.105427 sha: doc_id: 333654 cord_uid: 8rg99di5 file: cache/cord-333712-sdtxi8xw.json key: cord-333712-sdtxi8xw authors: Yu, Ping; Hu, Ben; Shi, Zheng-Li; Cui, Jie title: Geographical structure of bat SARS-related coronaviruses date: 2019-02-06 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2019.02.001 sha: doc_id: 333712 cord_uid: sdtxi8xw file: cache/cord-333682-ktbnrkwh.json key: cord-333682-ktbnrkwh authors: Dong, Yunzhu; Chi, Xiangyang; Hai, Huang; Sun, Liangliang; Zhang, Mengyao; Xie, Wei-Fen; Chen, Wei title: Antibodies in the breast milk of a maternal woman with COVID-19 date: 2020-07-03 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1780952 sha: doc_id: 333682 cord_uid: ktbnrkwh file: cache/cord-333763-45dzsn2j.json key: cord-333763-45dzsn2j authors: Bestle, Dorothea; Heindl, Miriam Ruth; Limburg, Hannah; Van Lam van, Thuy; Pilgram, Oliver; Moulton, Hong; Stein, David A; Hardes, Kornelia; Eickmann, Markus; Dolnik, Olga; Rohde, Cornelius; Klenk, Hans-Dieter; Garten, Wolfgang; Steinmetzer, Torsten; Böttcher-Friebertshäuser, Eva title: TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells date: 2020-07-23 journal: Life Sci Alliance DOI: 10.26508/lsa.202000786 sha: doc_id: 333763 cord_uid: 45dzsn2j file: cache/cord-333909-uco4c946.json key: cord-333909-uco4c946 authors: Murray, Meghan T.; Riggs, Margaret A.; Engelthaler, David M.; Johnson, Caroline; Watkins, Sharon; Longenberger, Allison; Brett-Major, David M.; Lowe, John; Broadhurst, M. Jana; Ladva, Chandresh N.; Villanueva, Julie M.; MacNeil, Adam; Qari, Shoukat; Kirking, Hannah L.; Cherry, Michael; Khan, Ali S. title: Mitigating a COVID-19 Outbreak Among Major League Baseball Players — United States, 2020 date: 2020-10-23 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6942a4 sha: doc_id: 333909 cord_uid: uco4c946 file: cache/cord-333632-i2bjap7m.json key: cord-333632-i2bjap7m authors: Senthil Kumar, K. J.; Gokila Vani, M.; Wang, Chung-Shuan; Chen, Chia-Chi; Chen, Yu-Chien; Lu, Li-Ping; Huang, Ching-Hsiang; Lai, Chien-Sing; Wang, Sheng-Yang title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells date: 2020-06-19 journal: Plants (Basel) DOI: 10.3390/plants9060770 sha: doc_id: 333632 cord_uid: i2bjap7m file: cache/cord-333688-bykbyojs.json key: cord-333688-bykbyojs authors: Wang, Junxue; Hang, Xiaofeng; Wei, Bo; Li, Dingchen; Chen, Fangyan; Liu, Wei; Yang, Chaojie; Miao, Xiaohui; Han, Li title: Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report date: 2020-08-21 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000021865 sha: doc_id: 333688 cord_uid: bykbyojs file: cache/cord-333547-88dkh6xd.json key: cord-333547-88dkh6xd authors: Hasan, Shadi W.; Ibrahim, Yazan; Daou, Marianne; Kannout, Hussein; Jan, Nila; Lopes, Alvaro; Alsafar, Habiba; Yousef, Ahmed F. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142929 sha: doc_id: 333547 cord_uid: 88dkh6xd file: cache/cord-334049-r3rlykli.json key: cord-334049-r3rlykli authors: Lobo-Galo, Naún; Terrazas-López, Manuel; Martínez-Martínez, Alejandro; Díaz-Sánchez, Ángel Gabriel title: FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication date: 2020-05-14 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1764393 sha: doc_id: 334049 cord_uid: r3rlykli file: cache/cord-333863-mtljy3s6.json key: cord-333863-mtljy3s6 authors: Hong, Nan; Yu, Wangshu; Xia, Jianhua; Shen, Ye; Yap, Maurice; Han, Wei title: Evaluation of ocular symptoms and tropism of SARS‐CoV‐2 in patients confirmed with COVID‐19 date: 2020-04-26 journal: Acta Ophthalmol DOI: 10.1111/aos.14445 sha: doc_id: 333863 cord_uid: mtljy3s6 file: cache/cord-333738-3xtb8gye.json key: cord-333738-3xtb8gye authors: Rabets, A.; 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Feng, Changyong; Rasubala, Linda; Malmstrom, Hans; Eliav, Eli title: Risk for dental healthcare professionals during the COVID-19 global pandemic: an evidence-based assessment date: 2020-07-18 journal: J Dent DOI: 10.1016/j.jdent.2020.103434 sha: doc_id: 334268 cord_uid: n2hon61o file: cache/cord-334220-sqvfr31q.json key: cord-334220-sqvfr31q authors: Messina, Francesco; Giombini, Emanuela; Montaldo, Chiara; Sharma, Ashish Arunkumar; Piacentini, Mauro; Zoccoli, Antonio; Sekaly, Rafick-Pierre; Locatelli, Franco; Zumla, Alimuddin; Maeurer, Markus; Capobianchi, Maria R.; Lauria, Francesco Nicola; Ippolito, Giuseppe title: Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date: 2020-11-03 journal: bioRxiv DOI: 10.1101/2020.11.03.366666 sha: doc_id: 334220 cord_uid: sqvfr31q file: cache/cord-333897-isodrtly.json key: cord-333897-isodrtly authors: Shenoy, Niraj; Luchtel, Rebecca; Gulani, Perminder title: Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting? date: 2020-08-19 journal: BMC Med DOI: 10.1186/s12916-020-01735-2 sha: doc_id: 333897 cord_uid: isodrtly file: cache/cord-334012-b2akycst.json key: cord-334012-b2akycst authors: Liguori, Claudio; Spanetta, Matteo; Sarmati, Loredana; Cesta, Novella; Pezzuto, Gabriella; Mina, Grazia Genga; Rogliani, Paola; Pierantozzi, Mariangela title: Sleep and wake impairment in patients with SARS-CoV2 infection date: 2020-07-17 journal: Sleep Med DOI: 10.1016/j.sleep.2020.06.036 sha: doc_id: 334012 cord_uid: b2akycst file: cache/cord-334099-rtv6xm90.json key: cord-334099-rtv6xm90 authors: Farrow, Robert; Becherer-Bailey, Graham; Mantuani, Daniel; Nagdev, Arun title: Early Multi-organ Point-of-Care Ultrasound Evaluation of Respiratory Distress During SARS-CoV-2 Outbreak: Case Report date: 2020-04-15 journal: Clin Pract Cases Emerg Med DOI: 10.5811/cpcem.2020.4.47524 sha: doc_id: 334099 cord_uid: rtv6xm90 file: cache/cord-334162-j8m2zqbr.json key: cord-334162-j8m2zqbr authors: Hoechter, D. J.; Groene, P.; Hoffmann, F.; Kreimeier, U. title: Besonderheiten der kardiopulmonalen Reanimation zu Zeiten von SARS-CoV-2 date: 2020-07-15 journal: Anaesthesist DOI: 10.1007/s00101-020-00814-6 sha: doc_id: 334162 cord_uid: j8m2zqbr file: cache/cord-334278-ajdjfzd2.json key: cord-334278-ajdjfzd2 authors: Gilis, M.; Chagrot, N.; Bozon, F.; Koeberlé, S.; Brunel, A.; Tannou, T.; Chirouze, C.; Bouiller, K. title: Caractéristiques de la COVID-19 chez les patients âgés de 75 ans et plus, hospitalisés date: 2020-09-30 journal: Médecine et Maladies Infectieuses DOI: 10.1016/j.medmal.2020.06.131 sha: doc_id: 334278 cord_uid: ajdjfzd2 file: cache/cord-334175-x10bbv7y.json key: cord-334175-x10bbv7y authors: Okur, Hacer Kuzu; Yalcin, Koray; Tastan, Cihan; Demir, Sevda; Yurtsever, Bulut; Sir, Gozde; Kancagi, Derya Dilek; Abanuz, Selen; Seyis, Utku; Zengin, Rehile; Hemsinlioglu, Cansu; Kara, Mujdat; Yildiz, Mehmet Erdem; Deliceo, Elif; Birgen, Nur; Pelit, Nil Banu; Cuhadaroglu, Caglar; Kocagoz, Ayse Sesin; Ovali, Ercument title: Preliminary report of In vitro and In vivo Effectiveness of Dornase alfa on SARS-CoV-2 infection date: 2020-09-07 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100756 sha: doc_id: 334175 cord_uid: x10bbv7y file: cache/cord-334210-lhadzo7o.json key: cord-334210-lhadzo7o authors: Lepak, Alexander J; Chen, Derrick J; Buys, Ashley; Stevens, Linda; Safdar, Nasia title: Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date: 2020-08-27 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa388 sha: doc_id: 334210 cord_uid: lhadzo7o file: cache/cord-334188-bggt1i2e.json key: cord-334188-bggt1i2e authors: Solari, Domenico; Bove, Ilaria; Esposito, Felice; Cappabianca, Paolo; Cavallo, Luigi M. title: The nose lid for the endoscopic endonasal procedures during COVID-19 era: technical note date: 2020-08-11 journal: Acta Neurochir (Wien) DOI: 10.1007/s00701-020-04518-z sha: doc_id: 334188 cord_uid: bggt1i2e file: cache/cord-334300-hnrmaytm.json key: cord-334300-hnrmaytm authors: Ventura Fernandes, Bianca H; Feitosa, Natália Martins; Barbosa, Ana Paula; Bomfim, Camila Gasque; Garnique, Anali M. 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K.-H.; Ho, D. title: IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-08 journal: nan DOI: 10.1101/2020.05.04.20088104 sha: doc_id: 333122 cord_uid: xw8o189s file: cache/cord-334564-bqh9jkds.json key: cord-334564-bqh9jkds authors: Raony, Ícaro; de Figueiredo, Camila Saggioro; Pandolfo, Pablo; Giestal-de-Araujo, Elizabeth; Oliveira-Silva Bomfim, Priscilla; Savino, Wilson title: Psycho-Neuroendocrine-Immune Interactions in COVID-19: Potential Impacts on Mental Health date: 2020-05-27 journal: Front Immunol DOI: 10.3389/fimmu.2020.01170 sha: doc_id: 334564 cord_uid: bqh9jkds file: cache/cord-334582-ccg27nmf.json key: cord-334582-ccg27nmf authors: Bonora, Benedetta Maria; Boscari, Federico; Avogaro, Angelo; Bruttomesso, Daniela; Fadini, Gian Paolo title: Glycaemic Control Among People with Type 1 Diabetes During Lockdown for the SARS-CoV-2 Outbreak in Italy date: 2020-05-11 journal: Diabetes Ther DOI: 10.1007/s13300-020-00829-7 sha: doc_id: 334582 cord_uid: ccg27nmf file: cache/cord-334612-lxqcvqca.json key: cord-334612-lxqcvqca authors: Rao, Nirmala title: Sars, preschool routines and children’s behaviour: Observations from preschools in Hong Kong date: 2006 journal: Int J Early Child DOI: 10.1007/bf03168205 sha: doc_id: 334612 cord_uid: lxqcvqca file: cache/cord-334688-0i1pu8wc.json key: cord-334688-0i1pu8wc authors: Martos Pérez, F.; Luque del Pino, J.; Jiménez García, N.; Mora Ruiz, E.; Asencio Méndez, C.; García Jiménez, J. M.; Navarro Romero, F.; Núñez Rodríguez, M. V. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 journal: Rev Clin Esp (Barc) DOI: 10.1016/j.rceng.2020.05.010 sha: doc_id: 334688 cord_uid: 0i1pu8wc file: cache/cord-334945-lxowaacg.json key: cord-334945-lxowaacg authors: Luo, Yi; Trevathan, Edwin; Qian, Zhengmin; Li, Yirong; Li, Jin; Xiao, Wei; Tu, Ning; Zeng, Zhikun; Mo, Pingzheng; Xiong, Yong; Ye, Guangming title: Asymptomatic SARS-CoV-2 Infection in Household Contacts of a Healthcare Provider, Wuhan, China date: 2020-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid2608.201016 sha: doc_id: 334945 cord_uid: lxowaacg file: cache/cord-334540-ggnkdnky.json key: cord-334540-ggnkdnky authors: Singh, Pankaj; Müller, Michael; Hack, Daniel; Kempf, Volkhard A. 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P.; Bruzzone, Roberto; Altmeyer, Ralf title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date: 2009-11-17 journal: PLoS One DOI: 10.1371/journal.pone.0007870 sha: doc_id: 334695 cord_uid: cjxlw1tu file: cache/cord-334773-yw2qgv13.json key: cord-334773-yw2qgv13 authors: Lisco, Giuseppe; De Tullio, Anna; Giagulli, Vito Angelo; Guastamacchia, Edoardo; De Pergola, Giovanni; Triggiani, Vincenzo title: Hypothesized mechanisms explaining poor prognosis in type 2 diabetes patients with COVID-19: a review date: 2020-08-10 journal: Endocrine DOI: 10.1007/s12020-020-02444-9 sha: doc_id: 334773 cord_uid: yw2qgv13 file: cache/cord-334603-yt2pmxi3.json key: cord-334603-yt2pmxi3 authors: de Sousa, Eric; Ligeiro, Dário; Lérias, Joana R.; Zhang, Chao; Agrati, Chiara; Osman, Mohamed; El-Kafrawy, Sherif A; Azhar, Esam I; Ippolito, Giuseppe; Wang, Fu-Sheng; Zumla, Alimudin; Maeurer, Markus title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.016 sha: doc_id: 334603 cord_uid: yt2pmxi3 file: cache/cord-334735-up81jotp.json key: cord-334735-up81jotp authors: Gillissen, Adrian; 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G.; Yassour, M. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 journal: nan DOI: 10.1101/2020.10.16.20213405 sha: doc_id: 335784 cord_uid: v7nbck0n file: cache/cord-335932-0phqok4g.json key: cord-335932-0phqok4g authors: Vanhems, Philippe; Saadatian-Elahi, Mitra; Chuzeville, Michel; Marion, Elodie; Favrelle, Louise; Hilliquin, Delphine; Martin-Gaujard, Geraldine; Gourmelon, Robin; Noaillon, Mathilde; Khanafer, Nagham title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit date: 2020-03-30 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.99 sha: doc_id: 335932 cord_uid: 0phqok4g file: cache/cord-336022-b2fwktld.json key: cord-336022-b2fwktld authors: Addetia, Amin; Crawford, Katharine HD; Dingens, Adam; Zhu, Haiying; Roychoudhury, Pavitra; Huang, Meei-Li; Jerome, Keith R.; Bloom, Jesse D.; Greninger, Alexander L. title: Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate date: 2020-08-14 journal: medRxiv DOI: 10.1101/2020.08.13.20173161 sha: doc_id: 336022 cord_uid: b2fwktld file: cache/cord-335619-t3yv5y7h.json key: cord-335619-t3yv5y7h authors: Wang, Song-mi; Tao, Fang; Hou, Yan; Zhang, Ai; Xiong, Hao; Sun, Jun-jie; Luo, Xiao-ping; Hao, Yan; Li, Jian-xin; Hu, Qun; Liu, Ai-guo title: Screening of SARS-CoV-2 in 299 Hospitalized Children with Hemato-oncological Diseases: A Multicenter Survey in Hubei, China date: 2020-08-07 journal: Curr Med Sci DOI: 10.1007/s11596-020-2228-7 sha: doc_id: 335619 cord_uid: t3yv5y7h file: cache/cord-336012-8klkojpo.json key: cord-336012-8klkojpo authors: Harilal, Divinlal; Ramaswamy, Sathishkumar; Loney, Tom; Suwaidi, Hanan Al; Khansaheb, Hamda; Alkhaja, Abdulmajeed; Varghese, Rupa; Deesi, Zulfa; Nowotny, Norbert; Alsheikh-Ali, Alawi; Tayoun, Ahmad Abou title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 journal: bioRxiv DOI: 10.1101/2020.06.06.138339 sha: doc_id: 336012 cord_uid: 8klkojpo file: cache/cord-336094-ssr5y4u3.json key: cord-336094-ssr5y4u3 authors: Blumberg, Dean A.; Underwood, Mark A.; Hedriana, Herman L.; Lakshminrusimha, Satyan title: Vertical Transmission of SARS-CoV-2: What is the Optimal Definition? date: 2020-06-05 journal: Am J Perinatol DOI: 10.1055/s-0040-1712457 sha: doc_id: 336094 cord_uid: ssr5y4u3 file: cache/cord-335938-hscgmis5.json key: cord-335938-hscgmis5 authors: Gralinski, Lisa E.; Bankhead, Armand; Jeng, Sophia; Menachery, Vineet D.; Proll, Sean; Belisle, Sarah E.; Matzke, Melissa; Webb-Robertson, Bobbie-Jo M.; Luna, Maria L.; Shukla, Anil K.; Ferris, Martin T.; Bolles, Meagan; Chang, Jean; Aicher, Lauri; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.; Law, G. Lynn; Katze, Michael G.; McWeeney, Shannon; Baric, Ralph S. title: Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury date: 2013-08-06 journal: mBio DOI: 10.1128/mbio.00271-13 sha: doc_id: 335938 cord_uid: hscgmis5 file: cache/cord-335958-dtvlo0kz.json key: cord-335958-dtvlo0kz authors: Satyam, Rohit; Jha, Niraj Kumar; Kar, Rohan; Jha, Saurabh Kumar; Sharma, Ankur; Kumar, Dhruv; Nand, Parma; Ruokolainen, Janne; Kesari, Kavindra Kumar; Kamal, Mohammad Amjad title: Deciphering the SSR incidences across viral members of Coronaviridae family date: 2020-09-21 journal: Chem Biol Interact DOI: 10.1016/j.cbi.2020.109226 sha: doc_id: 335958 cord_uid: dtvlo0kz file: cache/cord-336103-ufvq0ngl.json key: cord-336103-ufvq0ngl authors: Sharma, R.; Goyal, S.; Bist, P. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 journal: nan DOI: 10.1101/2020.07.03.20145953 sha: doc_id: 336103 cord_uid: ufvq0ngl file: cache/cord-336026-x02f7byo.json key: cord-336026-x02f7byo authors: Lommatzsch, Marek; Stoll, Paul; Virchow, Johann Christian title: COVID‐19 in a patient with severe asthma treated with Omalizumab date: 2020-06-27 journal: Allergy DOI: 10.1111/all.14456 sha: doc_id: 336026 cord_uid: x02f7byo file: cache/cord-336066-n9yq8enz.json key: cord-336066-n9yq8enz authors: Lai, Chien‐Chen; Jou, Ming‐Jia; Huang, Shiuan‐Yi; Li, Shih‐Wein; Wan, Lei; Tsai, Fuu‐Jen; Lin, Cheng‐Wen title: Proteomic analysis of up‐regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C‐like protease date: 2007-04-04 journal: Proteomics DOI: 10.1002/pmic.200600459 sha: doc_id: 336066 cord_uid: n9yq8enz file: cache/cord-336049-n3swuykg.json key: cord-336049-n3swuykg authors: Ahmed, Mubbasheer; Advani, Shailesh; Moreira, Axel; Zoretic, Sarah; Martinez, John; Chorath, Kevin; Acosta, Sebastian; Naqvi, Rija; Burmeister-Morton, Finn; Burmeister, Fiona; Tarriela, Aina; Petershack, Matthew; Evans, Mary; Hoang, Ansel; Rajasekaran, Karthik; Ahuja, Sunil; Moreira, Alvaro title: Multisystem inflammatory syndrome in children: A systematic review date: 2020-09-04 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100527 sha: doc_id: 336049 cord_uid: n3swuykg file: cache/cord-336053-cjq7szcn.json key: cord-336053-cjq7szcn authors: Mottola, Filiberto Fausto; Verde, Nicoletta; Ricciolino, Riccardo; Di Mauro, Marco; Migliaccio, Marco Giuseppe; Carfora, Vincenzo; Spiniello, Giorgio; Coppola, Nicola title: Cardiovascular System in COVID-19: Simply a Viewer or a Leading Actor? date: 2020-08-27 journal: Life (Basel) DOI: 10.3390/life10090165 sha: doc_id: 336053 cord_uid: cjq7szcn file: cache/cord-335955-2bw2sly8.json key: cord-335955-2bw2sly8 authors: Shi, Yuejun; Li, Youwen; Lei, Yingying; Ye, Gang; Shen, Zhou; Sun, Limeng; Luo, Rui; Wang, Dang; Fu, Zhen F.; Xiao, Shaobo; Peng, Guiqing title: A Dimerization-Dependent Mechanism Drives the Endoribonuclease Function of Porcine Reproductive and Respiratory Syndrome Virus nsp11 date: 2016-04-14 journal: J Virol DOI: 10.1128/jvi.03065-15 sha: doc_id: 335955 cord_uid: 2bw2sly8 file: cache/cord-336057-tj9qcuf8.json key: cord-336057-tj9qcuf8 authors: Lv, Yantian; Gu, Binbin; Chen, Ying; Hu, Siming; Ruan, Ting; Xu, Guopeng; Ding, Jian; Xu, Xiao; shen, Xinghua title: No intrauterine vertical transmission in pregnancy with COVID-19: a case report date: 2020-08-05 journal: J Infect Chemother DOI: 10.1016/j.jiac.2020.07.015 sha: doc_id: 336057 cord_uid: tj9qcuf8 file: cache/cord-335802-1kiqfy68.json key: cord-335802-1kiqfy68 authors: Azoulay, Elie; Fartoukh, Muriel; Darmon, Michael; Géri, Guillaume; Voiriot, Guillaume; Dupont, Thibault; Zafrani, Lara; Girodias, Lola; Labbé, Vincent; Dres, Martin; Beurton, Alexandra; Vieillard-Baron, Antoine; Demoule, Alexandre title: Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset date: 2020-08-11 journal: Intensive Care Med DOI: 10.1007/s00134-020-06202-3 sha: doc_id: 335802 cord_uid: 1kiqfy68 file: cache/cord-336488-opjjowcq.json key: cord-336488-opjjowcq authors: Kenanidis, Eustathios; Anagnostis, Panagiotis; Arvaniti, Kostoula; Potoupnis, Michael E; Tsiridis, Eleftherios title: Organizing an Orthopaedic Department During COVID-19 Pandemic to Mitigate In-Hospital Transmission: Experience From Greece date: 2020-06-17 journal: Cureus DOI: 10.7759/cureus.8676 sha: doc_id: 336488 cord_uid: opjjowcq file: cache/cord-336093-ic6q6ke8.json key: cord-336093-ic6q6ke8 authors: Sun, Ying; Wang, Zidao; Tao, Jiali; Wang, Yi; Wu, Andong; Yang, Ziwen; Wang, Kaimei; Shi, Liqiao; Chen, Yu; Guo, Deyin title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.02.002 sha: doc_id: 336093 cord_uid: ic6q6ke8 file: cache/cord-336119-8g37xsys.json key: cord-336119-8g37xsys authors: Nimgampalle, Mallikarjuna; Devanathan, Vasudharani; Saxena, Ambrish title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1782265 sha: doc_id: 336119 cord_uid: 8g37xsys file: cache/cord-336150-l8w7xk0b.json key: cord-336150-l8w7xk0b authors: Rathore, Jitendra Singh; Ghosh, Chaitali title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview date: 2020-08-25 journal: Pathog Dis DOI: 10.1093/femspd/ftaa042 sha: doc_id: 336150 cord_uid: l8w7xk0b file: cache/cord-335916-fh28qrt7.json key: cord-335916-fh28qrt7 authors: Liu, Cuiwei; Zhao, Yanxia; Okwan-Duodu, Derick; Basho, Reva; Cui, Xiaojiang title: COVID-19 in cancer patients: risk, clinical features, and management date: 2020-08-15 journal: Cancer Biol Med DOI: 10.20892/j.issn.2095-3941.2020.0289 sha: doc_id: 335916 cord_uid: fh28qrt7 file: cache/cord-336535-r3a57m57.json key: cord-336535-r3a57m57 authors: Kohmer, Niko; Westhaus, Sandra; Rühl, Cornelia; Ciesek, Sandra; Rabenau, Holger F. title: Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays date: 2020-06-01 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104480 sha: doc_id: 336535 cord_uid: r3a57m57 file: cache/cord-336227-0j0nbm9k.json key: cord-336227-0j0nbm9k authors: Aranda‐Abreu, Gonzalo Emiliano; Aranda‐Martínez, José Dolores; Araújo, Ramiro title: Use of amantadine in a patient with SARS‐CoV‐2 date: 2020-06-24 journal: J Med Virol DOI: 10.1002/jmv.26179 sha: doc_id: 336227 cord_uid: 0j0nbm9k file: cache/cord-336373-xb3jrg75.json key: cord-336373-xb3jrg75 authors: Vivas, Esther X. title: COVID19 and Otology/Neurotology date: 2020-08-22 journal: Otolaryngol Clin North Am DOI: 10.1016/j.otc.2020.08.003 sha: doc_id: 336373 cord_uid: xb3jrg75 file: cache/cord-336142-jmetfa6x.json key: cord-336142-jmetfa6x authors: MacDougall, Heather title: Toronto’s Health Department in Action: Influenza in 1918 and SARS in 2003 date: 2006-10-11 journal: J Hist Med Allied Sci DOI: 10.1093/jhmas/jrl042 sha: doc_id: 336142 cord_uid: jmetfa6x file: cache/cord-336177-p7b7yw28.json key: cord-336177-p7b7yw28 authors: Selvi, Valeria title: Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives date: 2020-09-22 journal: Biomed Res Int DOI: 10.1155/2020/2606058 sha: doc_id: 336177 cord_uid: p7b7yw28 file: cache/cord-336543-ydrmlujj.json key: cord-336543-ydrmlujj authors: Cavalli, Eugenio; Bramanti, Alessia; Ciurleo, Rosella; Tchorbanov, Andrey I.; Giordano, Antonio; Fagone, Paolo; Belizna, Cristina; Bramanti, Placido; Shoenfeld, Yehuda; Nicoletti, Ferdinando title: Entangling COVID-19 associated thrombosis into a secondary antiphospholipid antibody syndrome: Diagnostic and therapeutic perspectives (Review) date: 2020-06-25 journal: Int J Mol Med DOI: 10.3892/ijmm.2020.4659 sha: doc_id: 336543 cord_uid: ydrmlujj file: cache/cord-336364-2ust3qoq.json key: cord-336364-2ust3qoq authors: Artigas, Laura; Coma, Mireia; Matos-Filipe, Pedro; Aguirre-Plans, Joaquim; Farrés, Judith; Valls, Raquel; Fernandez-Fuentes, Narcis; de la Haba-Rodriguez, Juan; Olvera, Alex; Barbera, Jose; Morales, Rafael; Oliva, Baldo; Mas, Jose Manuel title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 journal: PLoS One DOI: 10.1371/journal.pone.0240149 sha: doc_id: 336364 cord_uid: 2ust3qoq file: cache/cord-336517-v7z62tld.json key: cord-336517-v7z62tld authors: Chu, Hsu-Feng; Chen, Chiao-Che; Moses, David C.; Chen, Yau-Hung; Lin, Chao-Hsiung; Tsai, Ying-Chieh; Chou, Chi-Yuan title: Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine date: 2018-08-20 journal: Antiviral Res DOI: 10.1016/j.antiviral.2018.08.011 sha: doc_id: 336517 cord_uid: v7z62tld file: cache/cord-336117-hit4kza8.json key: cord-336117-hit4kza8 authors: Heymann, D.L.; Reinhardt, K. title: Emerging Infections, the International Health Regulations, and Macro-Economy date: 2014-02-27 journal: Encyclopedia of Health Economics DOI: 10.1016/b978-0-12-375678-7.00624-6 sha: doc_id: 336117 cord_uid: hit4kza8 file: cache/cord-336585-19vwpjkt.json key: cord-336585-19vwpjkt authors: Adem, Şevki; Eyupoglu, Volkan; Sarfraz, Iqra; Rasul, Azhar; Zahoor, Ameer Fawad; Ali, Muhammad; Abdalla, Mohnad; Ibrahim, Ibrahim M; Elfiky, Abdo A title: Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19 date: 2020-08-22 journal: Phytomedicine DOI: 10.1016/j.phymed.2020.153310 sha: doc_id: 336585 cord_uid: 19vwpjkt file: cache/cord-336522-y9nzsv95.json key: cord-336522-y9nzsv95 authors: Rosenke, Kyle; Leventhal, Shanna; Moulton, Hong M.; Hatlevig, Susan; Hawman, David; Feldmann, Heinz; Stein, David A. title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date: 2020-09-30 journal: bioRxiv DOI: 10.1101/2020.09.29.319731 sha: doc_id: 336522 cord_uid: y9nzsv95 file: cache/cord-336447-hpnkou41.json key: cord-336447-hpnkou41 authors: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 journal: Rambam Maimonides Med J DOI: 10.5041/rmmj.10418 sha: doc_id: 336447 cord_uid: hpnkou41 file: cache/cord-336561-llwjsds8.json key: cord-336561-llwjsds8 authors: Ghosh, Sanhita; Firdous, Sayeed Mohammad; Nath, Anirban title: siRNA could be a potential therapy for COVID-19 date: 2020-04-22 journal: EXCLI J DOI: 10.17179/excli2020-1328 sha: doc_id: 336561 cord_uid: llwjsds8 file: cache/cord-336366-2y68n8s0.json key: cord-336366-2y68n8s0 authors: Liguori, Claudio; Pierantozzi, Mariangela; Spanetta, Matteo; Sarmati, Loredana; Cesta, Novella; Iannetta, Marco; Ora, Josuel; Mina, Grazia Genga; Puxeddu, Ermanno; Balbi, Ottavia; Pezzuto, Gabriella; Magrini, Andrea; Rogliani, Paola; Andreoni, Massimo; Mercuri, Nicola Biagio title: Depressive and anxiety symptoms in patients with SARS-CoV2 infection date: 2020-09-14 journal: J Affect Disord DOI: 10.1016/j.jad.2020.09.042 sha: doc_id: 336366 cord_uid: 2y68n8s0 file: cache/cord-336628-0evl3wnd.json key: cord-336628-0evl3wnd authors: Neufeldt, Christopher J.; Cerikan, Berati; Cortese, Mirko; Frankish, Jamie; Lee, Ji-Young; Plociennikowska, Agnieszka; Heigwer, Florian; Joecks, Sebastian; Burkart, Sandy S.; Zander, David Y.; Gendarme, Mathieu; El Debs, Bachir; Halama, Niels; Merle, Uta; Boutros, Michael; Binder, Marco; Bartenschlager, Ralf title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 journal: bioRxiv DOI: 10.1101/2020.07.21.212639 sha: doc_id: 336628 cord_uid: 0evl3wnd file: cache/cord-336722-41eqt97y.json key: cord-336722-41eqt97y authors: Sehmi, P.; Cheruiyot, I. title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review date: 2020-06-29 journal: nan DOI: 10.1101/2020.06.27.20105429 sha: doc_id: 336722 cord_uid: 41eqt97y file: cache/cord-336481-vrnxu217.json key: cord-336481-vrnxu217 authors: Bonifácio, Lívia Pimenta; Pereira, Ana Paula Sulino; Araújo, Daniel Cardoso de Almeida e; Balbão, Viviane da Mata Pasti; da Fonseca, Benedito Antônio Lopes; Passos, Afonso Dinis Costa; Bellissimo-Rodrigues, Fernando title: Are SARS-CoV-2 reinfection and Covid-19 recurrence possible? a case report from Brazil date: 2020-09-18 journal: Revista da Sociedade Brasileira de Medicina Tropical DOI: 10.1590/0037-8682-0619-2020 sha: doc_id: 336481 cord_uid: vrnxu217 file: cache/cord-336782-0zkb39v1.json key: cord-336782-0zkb39v1 authors: Fraile Gutiérrez, V.; Ayuela Azcárate, J. M.; Pérez Torres, D.; Zapata, L.; Rodríguez Yakushev, A. L.; Ochagavía Calvo, A. title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine date: 2020-11-02 journal: nan DOI: 10.1016/j.medine.2020.10.002 sha: doc_id: 336782 cord_uid: 0zkb39v1 file: cache/cord-336696-c3rbmysh.json key: cord-336696-c3rbmysh authors: Oberfeld, Blake; Achanta, Aditya; Carpenter, Kendall; Chen, Pamela; Gilette, Nicole M.; Langat, Pinky; Said, Jordan Taylor; Schiff, Abigail E.; Zhou, Allen S.; Barczak, Amy K.; Pillai, Shiv title: SnapShot: COVID-19 date: 2020-04-30 journal: Cell DOI: 10.1016/j.cell.2020.04.013 sha: doc_id: 336696 cord_uid: c3rbmysh file: cache/cord-336560-m5u6ryy9.json key: cord-336560-m5u6ryy9 authors: Boudewijns, Robbert; Thibaut, Hendrik Jan; Kaptein, Suzanne J. F.; Li, Rong; Vergote, Valentijn; Seldeslachts, Laura; De Keyzer, Carolien; Bervoets, Lindsey; Sharma, Sapna; Van Weyenbergh, Johan; Liesenborghs, Laurens; Ma, Ji; Jansen, Sander; Van Looveren, Dominique; Vercruysse, Thomas; Jochmans, Dirk; Wang, Xinyu; Martens, Erik; Roose, Kenny; De Vlieger, Dorien; Schepens, Bert; Van Buyten, Tina; Jacobs, Sofie; Liu, Yanan; Martí-Carreras, Joan; Vanmechelen, Bert; Wawina-Bokalanga, Tony; Delang, Leen; Rocha-Pereira, Joana; Coelmont, Lotte; Chiu, Winston; Leyssen, Pieter; Heylen, Elisabeth; Schols, Dominique; Wang, Lanjiao; Close, Lila; Matthijnssens, Jelle; Van Ranst, Marc; Compernolle, Veerle; Schramm, Georg; Van Laere, Koen; Saelens, Xavier; Callewaert, Nico; Opdenakker, Ghislain; Maes, Piet; Weynand, Birgit; Cawthorne, Christopher; Velde, Greetje Vande; Wang, Zhongde; Neyts, Johan; Dallmeier, Kai title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 journal: bioRxiv DOI: 10.1101/2020.04.23.056838 sha: doc_id: 336560 cord_uid: m5u6ryy9 file: cache/cord-336720-2bf3xzni.json key: cord-336720-2bf3xzni authors: Zhen, Wei; Manji, Ryhana; Smith, Elizabeth; Berry, Gregory J title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-04-22 journal: nan DOI: 10.1101/2020.04.17.20069864 sha: doc_id: 336720 cord_uid: 2bf3xzni file: cache/cord-336394-1xf2sxtv.json key: cord-336394-1xf2sxtv authors: Li, Yu; Zhang, Ziding; Yang, Li; Lian, Xianyi; Xie, Yan; Li, Shen; Xin, Shuyu; Cao, Pengfei; Lu, Jianhong title: The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date: 2020-05-13 journal: iScience DOI: 10.1016/j.isci.2020.101160 sha: doc_id: 336394 cord_uid: 1xf2sxtv file: cache/cord-336752-cpxnof1b.json key: cord-336752-cpxnof1b authors: Zeng, Qi‐Qiang; Zheng, Kenneth I.; Chen, Jun; Jiang, Zheng‐Hao; Tian, Tian; Wang, Xiao‐Bo; Ma, Hong‐Lei; Pan, Ke‐Hua; Yang, Yun‐Jun; Chen, Yong‐Ping; Zheng, Ming‐Hua title: Radiomics‐based model for accurately distinguishing between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) and influenza A infected pneumonia date: 2020-08-13 journal: MedComm (Beijing) DOI: 10.1002/mco2.14 sha: doc_id: 336752 cord_uid: cpxnof1b file: cache/cord-336677-h62angfw.json key: cord-336677-h62angfw authors: Rousseau, Antoine; Fenolland, Jean-Rémi; Labetoulle, Marc title: Sars-Cov-2, Covid-19 Et Œil: Le Point Sur Les Données Publiées date: 2020-05-30 journal: J Fr Ophtalmol DOI: 10.1016/j.jfo.2020.05.003 sha: doc_id: 336677 cord_uid: h62angfw file: cache/cord-336775-d4hi9myk.json key: cord-336775-d4hi9myk authors: Kirtipal, Nikhil; Bharadwaj, Shiv; Kang, Sang Gu title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 journal: Infection, Genetics and Evolution DOI: 10.1016/j.meegid.2020.104502 sha: doc_id: 336775 cord_uid: d4hi9myk file: cache/cord-336605-d4loia11.json key: cord-336605-d4loia11 authors: Zhang, Xue Wu; Yap, Yee Leng title: Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs date: 2004-05-15 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2004.03.035 sha: doc_id: 336605 cord_uid: d4loia11 file: cache/cord-336870-nirg3269.json key: cord-336870-nirg3269 authors: Abebe, Endeshaw Chekol; Dejenie, Tadesse Asmamaw; Shiferaw, Mestet Yibeltal; Malik, Tabarak title: The newly emerged COVID-19 disease: a systemic review date: 2020-07-08 journal: Virol J DOI: 10.1186/s12985-020-01363-5 sha: doc_id: 336870 cord_uid: nirg3269 file: cache/cord-336702-2qa4u8gv.json key: cord-336702-2qa4u8gv authors: Agarwal, Sangya; June, Carl H. title: Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19 date: 2020-04-17 journal: Cancer Discov DOI: 10.1158/2159-8290.cd-20-0473 sha: doc_id: 336702 cord_uid: 2qa4u8gv file: cache/cord-336563-hwemigk7.json key: cord-336563-hwemigk7 authors: Bhimraj, Adarsh; Morgan, Rebecca L; Shumaker, Amy Hirsch; Lavergne, Valery; Baden, Lindsey; Cheng, Vincent Chi-Chung; Edwards, Kathryn M; Gandhi, Rajesh; Muller, William J; O’Horo, John C; Shoham, Shmuel; Murad, M Hassan; Mustafa, Reem A; Sultan, Shahnaz; Falck-Ytter, Yngve title: Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date: 2020-04-27 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa478 sha: doc_id: 336563 cord_uid: hwemigk7 file: cache/cord-336554-n8n5ii5k.json key: cord-336554-n8n5ii5k authors: Singh, Thakur Uttam; Parida, Subhashree; Lingaraju, Madhu Cholenahalli; Kesavan, Manickam; Kumar, Dinesh; Singh, Raj Kumar title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 journal: Pharmacol Rep DOI: 10.1007/s43440-020-00155-6 sha: doc_id: 336554 cord_uid: n8n5ii5k file: cache/cord-337198-4sors3bg.json key: cord-337198-4sors3bg authors: Clementi, Nicola; Criscuolo, Elena; Diotti, Roberta Antonia; Ferrarese, Roberto; Castelli, Matteo; Dagna, Lorenzo; Burioni, Roberto; Clementi, Massimo; Mancini, Nicasio title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01704 sha: doc_id: 337198 cord_uid: 4sors3bg file: cache/cord-336671-vfq5ft08.json key: cord-336671-vfq5ft08 authors: Ai, Jing-Wen; Zhang, Yi; Zhang, Hao-Cheng; Xu, Teng; Zhang, Wen-Hong title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2020.1738905 sha: doc_id: 336671 cord_uid: vfq5ft08 file: cache/cord-337089-ksh62ni0.json key: cord-337089-ksh62ni0 authors: Salajegheh Tazerji, Sina; Magalhães Duarte, Phelipe; Rahimi, Parastoo; Shahabinejad, Fatemeh; Dhakal, Santosh; Singh Malik, Yashpal; Shehata, Awad A.; Lama, Juan; Klein, Jörn; Safdar, Muhammad; Rahman, Md. Tanvir; Filipiak, Krzysztof J.; Rodríguez-Morales, Alfonso J.; Sobur, Md. Abdus; Kabir, Farrokhreza; Vazir, Bita; Mboera, Leonard; Caporale, Marco; Islam, Md. Saiful; Amuasi, John H.; Gharieb, Rasha; Roncada, Paola; Musaad, Sahar; Tilocca, Bruno; Koohi, Mohammad Kazem; Taghipour, Ali; Sait, Ahmet; Subbaram, Kannan; Jahandideh, Alireza; Mortazavi, Pejman; Abedini, Mohammad Amin; Hokey, David A.; Hogan, Unarose; Shaheen, Mohamed N. F.; Elaswad, Ahmed; Elhaig, Mahmoud M.; Fawzy, Mohamed title: Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review date: 2020-09-21 journal: J Transl Med DOI: 10.1186/s12967-020-02534-2 sha: doc_id: 337089 cord_uid: ksh62ni0 file: cache/cord-336711-bnb62wa6.json key: cord-336711-bnb62wa6 authors: Wang, Xiaoyang; Liu, Chenbin; Hong, Liang; Yuan, Cuiyun; Ding, Jiguang; Jia, Qing; Sun, Gangqiang; Peng, Wenxian; Sun, Qingfeng title: CT findings of patients infected with SARS-CoV-2 date: 2020-06-23 journal: BMC Med Imaging DOI: 10.1186/s12880-020-00471-6 sha: doc_id: 336711 cord_uid: bnb62wa6 file: cache/cord-336837-rerp1g1w.json key: cord-336837-rerp1g1w authors: Jones, Nick K; Rivett, Lucy; Sparkes, Dominic; Forrest, Sally; Sridhar, Sushmita; Young, Jamie; Pereira-Dias, Joana; Cormie, Claire; Gill, Harmeet; Reynolds, Nicola; Wantoch, Michelle; Routledge, Matthew; Warne, Ben; Levy, Jack; Córdova Jiménez, William David; Samad, Fathima Nisha Begum; McNicholas, Chris; Ferris, Mark; Gray, Jane; Gill, Michael; Curran, Martin D; Fuller, Stewart; Chaudhry, Afzal; Shaw, Ashley; Bradley, John R; Hannon, Gregory J; Goodfellow, Ian G; Dougan, Gordon; Smith, Kenneth GC; Lehner, Paul J; Wright, Giles; Matheson, Nicholas J; Baker, Stephen; Weekes, Michael P title: Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 date: 2020-06-19 journal: eLife DOI: 10.7554/elife.59391 sha: doc_id: 336837 cord_uid: rerp1g1w file: cache/cord-337220-yv7qdvzi.json key: cord-337220-yv7qdvzi authors: Demeke, Addis; Samaddar, Manalee; Alharbi, Mona G.; Al-Hindi, Rashad R.; Bhunia, Arun K. title: Biosensor and molecular-based methods for the detection of human coronaviruses: A review date: 2020-09-08 journal: Mol Cell Probes DOI: 10.1016/j.mcp.2020.101662 sha: doc_id: 337220 cord_uid: yv7qdvzi file: cache/cord-336742-42ebj3gi.json key: cord-336742-42ebj3gi authors: Demmler, Gail J; Ligon, B.Lee title: Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future date: 2003-07-31 journal: Seminars in Pediatric Infectious Diseases DOI: 10.1016/s1045-1870(03)00056-6 sha: doc_id: 336742 cord_uid: 42ebj3gi file: cache/cord-337093-7pxfzuq0.json key: cord-337093-7pxfzuq0 authors: Hess, David C.; Eldahshan, Wael; Rutkowski, Elizabeth title: COVID-19-Related Stroke date: 2020-05-07 journal: Transl Stroke Res DOI: 10.1007/s12975-020-00818-9 sha: doc_id: 337093 cord_uid: 7pxfzuq0 file: cache/cord-337297-fkw8780t.json key: cord-337297-fkw8780t authors: Fan, Siyuan; Xiao, Meng; Han, Fei; Xia, Peng; Bai, Xiaoyin; Chen, Huan; Zhang, Hongmin; Ding, Xin; Zhao, Hua; Zhao, Jing; Sun, Xuefeng; Jiang, Wei; Wang, Chunyao; Cao, Wei; Guo, Fan; Tian, Ran; Gao, Peng; Wu, Wei; Ma, Jie; Wu, Dong; Liu, Zhengyin; Zhou, Xiang; Wang, Jinglan; Guan, Tianjia; Qin, Yan; Li, Taisheng; Xu, Yingchun; Zhang, Dong; Chen, Yu; Xie, Jing; Li, Yongzhe; Yan, Xiaowei; Zhu, Yicheng; Peng, Bin; Cui, Liying; Zhang, Shuyang; Guan, Hongzhi title: Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study date: 2020-07-10 journal: Front Neurol DOI: 10.3389/fneur.2020.00806 sha: doc_id: 337297 cord_uid: fkw8780t file: cache/cord-336769-5x6xjuew.json key: cord-336769-5x6xjuew authors: Payne, Daniel C.; Smith-Jeffcoat, Sarah E.; Nowak, Gosia; Chukwuma, Uzo; Geibe, Jesse R.; Hawkins, Robert J.; Johnson, Jeffrey A.; Thornburg, Natalie J.; Schiffer, Jarad; Weiner, Zachary; Bankamp, Bettina; Bowen, Michael D.; MacNeil, Adam; Patel, Monita R.; Deussing, Eric; Gillingham, Bruce L.; Tiller, Rebekah; Galloway, Rene; Rogers, Shannon; Whitaker, Brett; Kondas, Ashley; Smith, Peyton; Lee, Christopher; Graziano, James title: SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020 date: 2020-06-12 journal: MMWR Morb Mortal Wkly Rep DOI: 10.15585/mmwr.mm6923e4 sha: doc_id: 336769 cord_uid: 5x6xjuew file: cache/cord-336793-9bbyu1qx.json key: cord-336793-9bbyu1qx authors: Matsuyama, Shutoku; Kawase, Miyuki; Nao, Naganori; Shirato, Kazuya; Ujike, Makoto; Kamitani, Wataru; Shimojima, Masayuki; Fukushi, Shuetsu title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date: 2020-08-24 journal: bioRxiv DOI: 10.1101/2020.08.22.258459 sha: doc_id: 336793 cord_uid: 9bbyu1qx file: cache/cord-336836-54o9vjdl.json key: cord-336836-54o9vjdl authors: Zhen, Wei; Smith, Elizabeth; Manji, Ryhana; Schron, Deborah; Berry, Gregory J. title: Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00783-20 sha: doc_id: 336836 cord_uid: 54o9vjdl file: cache/cord-337026-osgi06o4.json key: cord-337026-osgi06o4 authors: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00360-7 sha: doc_id: 337026 cord_uid: osgi06o4 file: cache/cord-336604-2auhkxce.json key: cord-336604-2auhkxce authors: Kumar, Pramod; Pandey, Rajesh; Sharma, Pooja; Dhar, Mahesh S.; A., Vivekanand; Uppili, Bharathram; Vashisht, Himanshu; Wadhwa, Saruchi; Tyagi, Nishu; Fatihi, Saman; Sharma, Uma; Singh, Priyanka; Lall, Hemlata; Datta, Meena; Gupta, Poonam; Saini, Nidhi; Tewari, Aarti; Nandi, Bibhash; Kumar, Dhirendra; Bag, Satyabrata; Gahlot, Deepanshi; Rathore, Surabhi; Jatana, Nidhi; Jaiswal, Varun; Gogia, Hema; Madan, Preeti; Singh, Simrita; Singh, Prateek; Dash, Debasis; Bala, Manju; Kabra, Sandhya; Singh, Sujeet; Mukerji, Mitali; Thukral, Lipi; Faruq, Mohammed; Agrawal, Anurag; Rakshit, Partha title: Integrated genomic view of SARS-CoV-2 in India date: 2020-08-03 journal: Wellcome Open Res DOI: 10.12688/wellcomeopenres.16119.1 sha: doc_id: 336604 cord_uid: 2auhkxce file: cache/cord-337324-jxtch47t.json key: cord-337324-jxtch47t authors: Qian, Guo-Qing; Yang, Nai-Bin; Ding, Feng; Ma, Ada Hoi Yan; Wang, Zong-Yi; Shen, Yue-Fei; Shi, Chun-Wei; Lian, Xiang; Chu, Jin-Guo; Chen, Lei; Wang, Zhi-Yu; Ren, Da-Wei; Li, Guo-Xiang; Chen, Xue-Qin; Shen, Hua-Jiang; Chen, Xiao-Min title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series date: 2020-02-25 journal: nan DOI: 10.1101/2020.02.23.20026856 sha: doc_id: 337324 cord_uid: jxtch47t file: cache/cord-337105-jlmh79qv.json key: cord-337105-jlmh79qv authors: Jacob, Fadi; Pather, Sarshan R.; Huang, Wei-Kai; Zhang, Feng; Hao Wong, Samuel Zheng; Zhou, Haowen; Cubitt, Beatrice; Fan, Wenqiang; Chen, Catherine Z.; Xu, Miao; Pradhan, Manisha; Zhang, Daniel Y.; Zheng, Wei; Bang, Anne G.; Song, Hongjun; Carlos de la Torre, Juan; Ming, Guo-li title: Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date: 2020-09-21 journal: Cell Stem Cell DOI: 10.1016/j.stem.2020.09.016 sha: doc_id: 337105 cord_uid: jlmh79qv file: cache/cord-337200-2qwty2jp.json key: cord-337200-2qwty2jp authors: Kempfle, J. S.; Löwenheim, H.; Huebner, M. J.; Iro, H.; Mueller, S. K. title: Management von Patienten mit Tracheostoma während der COVID-19-Pandemie: Literaturüberblick und Demonstration date: 2020-06-08 journal: HNO DOI: 10.1007/s00106-020-00892-3 sha: doc_id: 337200 cord_uid: 2qwty2jp file: cache/cord-337339-0vkigjv2.json key: cord-337339-0vkigjv2 authors: Osterrieder, Nikolaus; Bertzbach, Luca D.; Dietert, Kristina; Abdelgawad, Azza; Vladimirova, Daria; Kunec, Dusan; Hoffmann, Donata; Beer, Martin; Gruber, Achim D.; Trimpert, Jakob title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 journal: Viruses DOI: 10.3390/v12070779 sha: doc_id: 337339 cord_uid: 0vkigjv2 file: cache/cord-337032-s4g4g80w.json key: cord-337032-s4g4g80w authors: Gupta, Manoj Kumar; Vemula, Sarojamma; Donde, Ravindra; Gouda, Gayatri; Behera, Lambodar; Vadde, Ramakrishna title: In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date: 2020-04-15 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1751300 sha: doc_id: 337032 cord_uid: s4g4g80w file: cache/cord-337302-fpz2jfuj.json key: cord-337302-fpz2jfuj authors: Abdihamid, Omar; Cai, Changjing; Kapesa, Linda; Zeng, Shan title: The Landscape of COVID-19 in Cancer Patients: Prevalence, Impacts, and Recommendations date: 2020-09-23 journal: Cancer Manag Res DOI: 10.2147/cmar.s272008 sha: doc_id: 337302 cord_uid: fpz2jfuj file: cache/cord-337511-20yaol5r.json key: cord-337511-20yaol5r authors: Ryan, Paul MacDaragh; Caplice, Noel title: COVID-19 and relative angiotensin-converting enzyme 2 deficiency: role in disease severity and therapeutic response date: 2020-06-11 journal: Open Heart DOI: 10.1136/openhrt-2020-001302 sha: doc_id: 337511 cord_uid: 20yaol5r file: cache/cord-337396-g69bb60d.json key: cord-337396-g69bb60d authors: Ogawa, Yoshihiko; Nishida, Koji; Gohma, Iwao; Kasahara, Kei; Yano, Hisakazu title: Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date: 2020-11-07 journal: BMC Res Notes DOI: 10.1186/s13104-020-05365-y sha: doc_id: 337396 cord_uid: g69bb60d file: cache/cord-337599-dyxfsojh.json key: cord-337599-dyxfsojh authors: Ahamad, Shakir; Branch, Scotty; Harrelson, Shea; Hussain, Mohd Kamil; Saquib, Mohammad; Khan, Saeed title: Primed for Global Coronavirus Pandemic: Emerging Research and Clinical Outcome date: 2020-09-19 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2020.112862 sha: doc_id: 337599 cord_uid: dyxfsojh file: cache/cord-337127-pc9hez28.json key: cord-337127-pc9hez28 authors: García-Salido, Alberto; García-Teresa, María Ángeles; Leoz-Gordillo, Inés; Martínez de Azagra-Garde, Amelia; Cabrero-Hernández, Marta; Ramirez-Orellana, Manuel title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a date: 2020-09-30 journal: Med Intensiva DOI: 10.1016/j.medin.2020.09.003 sha: doc_id: 337127 cord_uid: pc9hez28 file: cache/cord-337208-6rs1sgx1.json key: cord-337208-6rs1sgx1 authors: Wang, Jingbo; Wang, Leishi; Li, Luping; Xu, Jiao; Xu, Chun; Li, Xinghai; Liu, Hongyan; Li, Baijun; Yu, Hong; Tian, Xia; Zhang, Zhiyu; Wang, Yan; Zhao, Rui; Liu, Jinyang; Wang, Wei; Liu, Li; Wang, Haitao; Gu, Ye title: Enlightenments of Asymptomatic Cases of SARS-CoV-2 Infection date: 2020-06-30 journal: J Transl Int Med DOI: 10.2478/jtim-2020-0017 sha: doc_id: 337208 cord_uid: 6rs1sgx1 file: cache/cord-337436-3xzgv370.json key: cord-337436-3xzgv370 authors: Khider, Lina; Gendron, Nicolas; Goudot, Guillaume; Chocron, Richard; Hauw‐Berlemont, Caroline; Cheng, Charles; Rivet, Nadia; Pere, Helene; Roffe, Ariel; Clerc, Sébastien; Lebeaux, David; Debuc, Benjamin; Veyer, David; Rance, Bastien; Gaussem, Pascale; Bertil, Sébastien; Badoual, Cécile; Juvin, Philippe; Planquette, Benjamin; Messas, Emmanuel; Sanchez, Olivier; Hulot, Jean‐Sébastien; Diehl, Jean‐Luc; Mirault, Tristan; Smadja, David M. title: Curative anticoagulation prevents endothelial lesion in COVID‐19 patients date: 2020-06-18 journal: J Thromb Haemost DOI: 10.1111/jth.14968 sha: doc_id: 337436 cord_uid: 3xzgv370 file: cache/cord-337444-pqoq8aew.json key: cord-337444-pqoq8aew authors: Doi, Kent; Ikeda, Mahoko; Hayase, Naoki; Moriya, Kyoji; Morimura, Naoto title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series date: 2020-07-03 journal: Crit Care DOI: 10.1186/s13054-020-03078-z sha: doc_id: 337444 cord_uid: pqoq8aew file: cache/cord-337421-4v48kkus.json key: cord-337421-4v48kkus authors: Ribeiro, Servio Pontes; Dattilo, Wesley; Castro e Silva, Alcides; Reis, Alexandre Barbosa; Goes-Neto, Aristoteles; Alcantara, Luiz; Giovanetti, Marta; Coura-vital, Wendel; Fernandes, Geraldo Wilson; Azevedo, Vasco Ariston title: Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil date: 2020-03-27 journal: nan DOI: 10.1101/2020.03.26.20044370 sha: doc_id: 337421 cord_uid: 4v48kkus file: cache/cord-337430-c2vdnml7.json key: cord-337430-c2vdnml7 authors: Timpka, Toomas title: Sports Health During the SARS-Cov-2 Pandemic date: 2020-05-02 journal: Sports Med DOI: 10.1007/s40279-020-01288-7 sha: doc_id: 337430 cord_uid: c2vdnml7 file: cache/cord-337491-ztco6guw.json key: cord-337491-ztco6guw authors: Kucharski, Adam J; 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Lopez Chavarrias, Vicente; Nicoll, Angus; Chamberland, Mary E. title: The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence date: 2011-12-21 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2011.00307.x sha: doc_id: 337372 cord_uid: y43prnko file: cache/cord-337462-9mvk86q6.json key: cord-337462-9mvk86q6 authors: nan title: Humanity tested date: 2020-04-08 journal: Nat Biomed Eng DOI: 10.1038/s41551-020-0553-6 sha: doc_id: 337462 cord_uid: 9mvk86q6 file: cache/cord-337485-nqcnd9py.json key: cord-337485-nqcnd9py authors: Buetti, Niccolò; Wicky, Paul-Henri; Le Hingrat, Quentin; Ruckly, Stéphane; Mazzuchelli, Timothy; Loiodice, Ambre; Trimboli, Pierpaolo; Forni Ogna, Valentina; de Montmollin, Etienne; Bernasconi, Enos; Visseaux, Benoit; Timsit, Jean-François title: SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients date: 2020-10-16 journal: Crit Care DOI: 10.1186/s13054-020-03323-5 sha: doc_id: 337485 cord_uid: nqcnd9py file: cache/cord-337674-mb6ue2hl.json key: cord-337674-mb6ue2hl authors: Voulgaris, Athanasios; 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Has a new era begun? date: 2020-07-17 journal: Sleep Med DOI: 10.1016/j.sleep.2020.07.010 sha: doc_id: 337674 cord_uid: mb6ue2hl file: cache/cord-337700-2n9tswr8.json key: cord-337700-2n9tswr8 authors: Chilimuri, Sridhar; Sun, Haozhe; Alemam, Ahmed; Mantri, Nikhitha; Shehi, Elona; Tejada, Jairo; Yugay, Alla; Nayudu, Suresh K. title: Predictors of Mortality in Adults Admitted with COVID-19: Retrospective Cohort Study from New York City date: 2020-07-08 journal: West J Emerg Med DOI: 10.5811/westjem.2020.6.47919 sha: doc_id: 337700 cord_uid: 2n9tswr8 file: cache/cord-337799-mc1oqhf4.json key: cord-337799-mc1oqhf4 authors: Mak, Gannon CK; Lau, Stephen SY; Wong, Kitty KY; Chow, Nancy LS; Lau, CS; Lam, Edman TK; Chan, Rickjason CW; Tsang, Dominic NC title: Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus date: 2020-10-29 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104684 sha: doc_id: 337799 cord_uid: mc1oqhf4 file: cache/cord-337663-ow1l18li.json key: cord-337663-ow1l18li authors: Qu, Liang G.; Perera, Marlon; Lawrentschuk, Nathan; Umbas, Rainy; Klotz, Laurence title: Scoping review: hotspots for COVID-19 urological research: what is being published and from where? date: 2020-09-09 journal: World J Urol DOI: 10.1007/s00345-020-03434-2 sha: doc_id: 337663 cord_uid: ow1l18li file: cache/cord-337636-3yc0ribg.json key: cord-337636-3yc0ribg authors: Morehouse, Zachary P.; Proctor, Caleb M.; Ryan, Gabriella L.; Nash, Rodney J. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 journal: Virol J DOI: 10.1186/s12985-020-01405-y sha: doc_id: 337636 cord_uid: 3yc0ribg file: cache/cord-337572-kx5hihnr.json key: cord-337572-kx5hihnr authors: Ludwig, Stephan; Zarbock, Alexander title: Coronaviruses and SARS-CoV-2: A Brief Overview date: 2020-04-20 journal: Anesth Analg DOI: 10.1213/ane.0000000000004845 sha: doc_id: 337572 cord_uid: kx5hihnr file: cache/cord-337712-ylqgraos.json key: cord-337712-ylqgraos authors: Heinz, Franz X.; Stiasny, Karin title: Profile of SARS-CoV-2 date: 2020-10-30 journal: Wien Klin Wochenschr DOI: 10.1007/s00508-020-01763-1 sha: doc_id: 337712 cord_uid: ylqgraos file: cache/cord-337753-olc00glo.json key: cord-337753-olc00glo authors: Franco, D.; Gonzalez, C.; Abrego, L. E.; Carrera, J. P.; Diaz, Y.; Caisedo, Y.; Moreno, A.; Chavarria, O.; Gondola, J.; Castillo, M.; Valdespino, E.; Gaitan, M.; Martinez-Mandiche, J.; Hayer, L.; Gonzalez, P.; Lange, C.; Molto, Y.; Mojica, D.; Ramos, R.; Mastelari, M.; Cerezo, L.; Moreno, L.; Donnelly, C. A.; Faria, N. R.; Pascale, J. M.; Lopez-Verges, S.; Martinez, A. A. title: Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. date: 2020-08-04 journal: nan DOI: 10.1101/2020.07.31.20160929 sha: doc_id: 337753 cord_uid: olc00glo file: cache/cord-337854-5ogip9tz.json key: cord-337854-5ogip9tz authors: Huang, Wanqiu; Lin, Dachuan; Wang, Cuini; Bao, Chaohui; Zhang, Zhaoqi; Chen, Xinchun; Zhang, Zheng; Huang, Jian title: The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology date: 2020-07-02 journal: J Infect DOI: 10.1016/j.jinf.2020.06.075 sha: doc_id: 337854 cord_uid: 5ogip9tz file: cache/cord-337595-0p5f5o5v.json key: cord-337595-0p5f5o5v authors: Tagliamento, Marco; Lambertini, Matteo; Genova, Carlo; Barisione, Emanuela; De Maria, Andrea; Grosso, Marco; Poggio, Francesca; Vagge, Stefano; Boccardo, Francesco; Pronzato, Paolo; Del Mastro, Lucia title: Call for ensuring cancer care continuity during COVID-19 pandemic date: 2020-05-07 journal: ESMO Open DOI: 10.1136/esmoopen-2020-000783 sha: doc_id: 337595 cord_uid: 0p5f5o5v file: cache/cord-337692-b89ow1mf.json key: cord-337692-b89ow1mf authors: Petti, S.; Cowling, B. 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M.; Tosoni, Alvise; Kim, YaeJean; Kissoon, Niranjan; Murthy, Srinivas title: Coronavirus Disease 2019 in Critically Ill Children: A Narrative Review of the Literature date: 2020-04-21 journal: Pediatr Crit Care Med DOI: 10.1097/pcc.0000000000002376 sha: doc_id: 338001 cord_uid: jig46hsk file: cache/cord-338023-gb5jgqcg.json key: cord-338023-gb5jgqcg authors: Obara, Shinju title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission date: 2020-08-27 journal: J Anesth DOI: 10.1007/s00540-020-02846-z sha: doc_id: 338023 cord_uid: gb5jgqcg file: cache/cord-337789-pabaoiqs.json key: cord-337789-pabaoiqs authors: Oprinca, George-Călin; Muja, Lilioara-Alexandra title: Postmortem examination of three SARS-CoV-2-positive autopsies including histopathologic and immunohistochemical analysis date: 2020-08-27 journal: Int J Legal Med DOI: 10.1007/s00414-020-02406-w sha: doc_id: 337789 cord_uid: pabaoiqs file: cache/cord-337825-ujq9mxk7.json key: cord-337825-ujq9mxk7 authors: Chen, Bin; Tian, Er-Kang; He, Bin; Tian, Lejin; Han, Ruiying; Wang, Shuangwen; Xiang, Qianrong; Zhang, Shu; El Arnaout, Toufic; Cheng, Wei title: Overview of lethal human coronaviruses date: 2020-06-10 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-0190-2 sha: doc_id: 337825 cord_uid: ujq9mxk7 file: cache/cord-337973-djqzgc1k.json key: cord-337973-djqzgc1k authors: Hao, Siyuan; Ning, Kang; Kuz, Cagla Aksu; Vorhies, Kai; Yan, Ziying; Qiu, Jianming title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.27.271130 sha: doc_id: 337973 cord_uid: djqzgc1k file: cache/cord-338054-n2r4pzan.json key: cord-338054-n2r4pzan authors: Lau, Joseph TF; Kim, Jean H; Tsui, Hi Yi; Griffiths, Sian title: Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date: 2007-03-15 journal: BMC Infect Dis DOI: 10.1186/1471-2334-7-18 sha: doc_id: 338054 cord_uid: n2r4pzan file: cache/cord-337962-9le56say.json key: cord-337962-9le56say authors: Duan, Fuyu; Guo, Liyan; Yang, Liuliu; Han, Yuling; Thakur, Abhimanyu; Nilsson-Payant, Benjamin E.; Wang, Pengfei; Zhang, Zhao; Ma, Chui Yan; Zhou, Xiaoya; Han, Teng; Zhang, Tuo; Wang, Xing; Xu, Dong; Duan, Xiaohua; Xiang, Jenny; Tse, Hung-fat; Liao, Can; Luo, Weiren; Huang, Fang-Ping; Chen, Ya-Wen; Evans, Todd; Schwartz, Robert E.; tenOever, Benjamin; Ho, David D.; Chen, Shuibing; Lian, Qizhou; Chen, Huanhuan Joyce title: Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2 date: 2020-08-20 journal: Res Sq DOI: 10.21203/rs.3.rs-62758/v1 sha: doc_id: 337962 cord_uid: 9le56say file: cache/cord-337867-hqmf6r7t.json key: cord-337867-hqmf6r7t authors: Shim, Byoung-Shik; Park, Sung-Moo; Quan, Ji-Shan; Jere, Dhananjay; Chu, Hyuk; Song, Man Ki; Kim, Dong Wook; Jang, Yong-Suk; Yang, Moon-Sik; Han, Seung Hyun; Park, Yong-Ho; Cho, Chong-Su; Yun, Cheol-Heui title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses date: 2010-12-31 journal: BMC Immunol DOI: 10.1186/1471-2172-11-65 sha: doc_id: 337867 cord_uid: hqmf6r7t file: cache/cord-338152-e8e3lv79.json key: cord-338152-e8e3lv79 authors: Zhang, Peilin; Heyman, Taryn; Salafia, Carolyn; Dygulska, Beata; Lederman, Sanford title: Detection of SARS-CoV-2 in placentas with pathology and vertical transmission date: 2020-08-03 journal: Am J Obstet Gynecol MFM DOI: 10.1016/j.ajogmf.2020.100197 sha: doc_id: 338152 cord_uid: e8e3lv79 file: cache/cord-338203-le5lbw5y.json key: cord-338203-le5lbw5y authors: O’Reilly, GM; Mitchell, RD; Wu, J; Rajiv, P; Bannon‐Murphy, H; Amos, T; Brichko, L; Brennecke, H; Noonan, MP; Mitra, B; Paton, A; Hiller, R; Smit, D; Luckhoff, C; Santamaria, MJ; Cameron, PA title: Epidemiology and clinical features of emergency department patients with suspected COVID‐19: Results from the first month of the COVED Quality Improvement Project (COVED‐2). date: 2020-06-13 journal: Emerg Med Australas DOI: 10.1111/1742-6723.13573 sha: doc_id: 338203 cord_uid: le5lbw5y file: cache/cord-338055-2d6n4cve.json key: cord-338055-2d6n4cve authors: Hassan, Sk. 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date: 2020-06-29 journal: Med DOI: 10.1016/j.medj.2020.06.005 sha: doc_id: 338317 cord_uid: ro041w5l file: cache/cord-338205-sy91rnse.json key: cord-338205-sy91rnse authors: Li, Chenxi; Zhao, Chengxue; Bao, Jingfeng; Tang, Bo; Wang, Yunfeng; Gu, Bing title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.06.045 sha: doc_id: 338205 cord_uid: sy91rnse file: cache/cord-338351-y1t9emu1.json key: cord-338351-y1t9emu1 authors: Ora, Josuel; Puxeddu, Ermanno; Cavalli, Francesco; Giorgino, Federica Maria; Girolami, Andrea; Chiocchi, Marcello; Sergiacomi, Giaunluigi; Federici, Massimo; Rogliani, Paola title: Does bronchoscopy help the diagnosis in Covid-19 infection? date: 2020-06-11 journal: Eur Respir J DOI: 10.1183/13993003.01619-2020 sha: doc_id: 338351 cord_uid: y1t9emu1 file: cache/cord-338498-3238fz73.json key: cord-338498-3238fz73 authors: Kleen, Thomas-Oliver; Galdon, Alicia A.; MacDonald, Andrew S.; Dalgleish, Angus G. title: Mitigating Coronavirus Induced Dysfunctional Immunity for At-Risk Populations in COVID-19: Trained Immunity, BCG and “New Old Friends” date: 2020-09-04 journal: Front Immunol DOI: 10.3389/fimmu.2020.02059 sha: doc_id: 338498 cord_uid: 3238fz73 file: cache/cord-338417-7kw9lws0.json key: cord-338417-7kw9lws0 authors: Singh, Awadhesh Kumar; Gupta, Ritesh; Misra, Anoop title: Comorbidities in COVID-19: Outcomes in hypertensive cohort and controversies with renin angiotensin system blockers date: 2020-04-09 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.03.016 sha: doc_id: 338417 cord_uid: 7kw9lws0 file: cache/cord-338544-eph89g47.json key: cord-338544-eph89g47 authors: Spuntarelli, Valerio; Luciani, M.; Bentivegna, E.; Marini, V.; Falangone, F.; Conforti, G.; Rachele, E. S.; Martelletti, P. title: COVID-19: is it just a lung disease? 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Ataur; Rahman, Md Saidur; Sohag, Abdullah Al Mamun; Dash, Raju; Hossain, Khandkar Shaharina; Farjana, Mithila; Uddin, Md Jamal title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response date: 2020-07-10 journal: Immunol Lett DOI: 10.1016/j.imlet.2020.07.001 sha: doc_id: 338541 cord_uid: 0yiuh017 file: cache/cord-338683-nzgnpi6f.json key: cord-338683-nzgnpi6f authors: Karligkiotis, Apostolos; Arosio, Alberto D.; Battaglia, Paolo; Sileo, Giorgio; Czaczkes, Camilla; Volpi, Luca; Turri‐Zanoni, Mario; Castelnuovo, Paolo title: Changing paradigms in sinus and skull base surgery as the COVID‐19 pandemic evolves: Preliminary experience from a single Italian tertiary care center date: 2020-06-08 journal: Head Neck DOI: 10.1002/hed.26320 sha: doc_id: 338683 cord_uid: nzgnpi6f file: cache/cord-339128-npfoircv.json key: cord-339128-npfoircv authors: Blair, Robert V.; Vaccari, Monica; Doyle-Meyers, Lara A.; Roy, Chad J.; Russell-Lodrigue, Kasi; Fahlberg, Marissa; Monjure, Chris J.; Beddingfield, Brandon; Plante, Kenneth S.; Plante, Jessica A.; Weaver, Scott C.; Qin, Xuebin; Midkiff, Cecily C.; Lehmicke, Gabrielle; Golden, Nadia; Threeton, Breanna; Penney, Toni; Allers, Carolina; Barnes, Mary B.; Pattison, Melissa; Datta, Prasun K.; Maness, Nicholas J.; Birnbaum, Angela; Fischer, Tracy; Bohm, Rudolf P.; Rappaport, Jay title: Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques date: 2020-11-07 journal: Am J Pathol DOI: 10.1016/j.ajpath.2020.10.016 sha: doc_id: 339128 cord_uid: npfoircv file: cache/cord-338734-laeocs3j.json key: cord-338734-laeocs3j authors: Lima, Amorce; Healer, Vicki; Vendrone, Elaine; Silbert, Suzane title: Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date: 2020-06-30 journal: bioRxiv DOI: 10.1101/2020.06.29.179192 sha: doc_id: 338734 cord_uid: laeocs3j file: cache/cord-339241-e2nl766y.json key: cord-339241-e2nl766y authors: Turriziani, Ombretta; Sciandra, Ilaria; Mazzuti, Laura; Di Carlo, Daniele; Bitossi, Camilla; Calabretto, Marianna; Guerrizio, Giuliana; Oliveto, Giuseppe; Riveros Cabral, Rodolfo J.; Viscido, Agnese; Falasca, Francesca; Gentile, Massimo; Pietropaolo, Valeria; Rodio, Donatella M.; Carattoli, Alessandra; Antonelli, Guido title: SARS‐CoV‐2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period date: 2020-08-02 journal: J Med Virol DOI: 10.1002/jmv.26332 sha: doc_id: 339241 cord_uid: e2nl766y file: cache/cord-339303-feiy6xed.json key: cord-339303-feiy6xed authors: Tan, Xiaodong; Li, Shiyue; Wang, Chunhong; Chen, Xiaoqing; Wu, Xiaomin title: Severe Acute Respiratory Syndrome epidemic and change of people's health behavior in China date: 2004-10-17 journal: Health Educ Res DOI: 10.1093/her/cyg074 sha: doc_id: 339303 cord_uid: feiy6xed file: cache/cord-339077-pxf2u68u.json key: cord-339077-pxf2u68u authors: Zerwes, Sebastian; Hernandez Cancino, F.; Liebetrau, D.; Gosslau, Y.; Warm, T.; Märkl, B.; Hyhlik-Dürr, A. title: Erhöhtes Risiko für tiefe Beinvenenthrombosen bei Intensivpatienten mit CoViD-19-Infektion? – Erste Daten date: 2020-06-05 journal: Chirurg DOI: 10.1007/s00104-020-01222-7 sha: doc_id: 339077 cord_uid: pxf2u68u file: cache/cord-339271-t7cxqkp1.json key: cord-339271-t7cxqkp1 authors: Pan, Yanfeng; Yu, Xue; Du, Xinwei; Li, Qingqing; Li, Xianyang; Qin, Tao; Wang, Miaomiao; Jiang, Minlin; Li, Jie; Li, Weiguo; Zhang, Qian; Xu, Zhiwei; Zhang, Lu title: Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date: 2020-04-22 journal: J Infect Dis DOI: 10.1093/infdis/jiaa205 sha: doc_id: 339271 cord_uid: t7cxqkp1 file: cache/cord-338973-73a7uvyz.json key: cord-338973-73a7uvyz authors: Xu, Jiabao; Zhao, Shizhe; Teng, Tieshan; Abdalla, Abualgasim Elgaili; Zhu, Wan; Xie, Longxiang; Wang, Yunlong; Guo, Xiangqian title: Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV date: 2020-02-22 journal: Viruses DOI: 10.3390/v12020244 sha: doc_id: 338973 cord_uid: 73a7uvyz file: cache/cord-338980-pygykil7.json key: cord-338980-pygykil7 authors: Rahaman, Jordon; Siltberg-Liberles, Jessica title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date: 2016-11-09 journal: Genome Biol Evol DOI: 10.1093/gbe/evw246 sha: doc_id: 338980 cord_uid: pygykil7 file: cache/cord-339352-c9uh8vjx.json key: cord-339352-c9uh8vjx authors: Islam, Muhammad Torequl title: Environmental Integrants Affecting the Spreadability of SARS-CoV-12 date: 2020-07-28 journal: Food Environ Virol DOI: 10.1007/s12560-020-09435-z sha: doc_id: 339352 cord_uid: c9uh8vjx file: cache/cord-338744-2kizbzns.json key: cord-338744-2kizbzns authors: González-Castro, A.; Garcia de Lorenzo, A.; Escudero-Acha, P.; Rodriguez-Borregan, J.C. title: Síndrome post-cuidados intensivos después de la pandemia por SARS-CoV-2 date: 2020-04-27 journal: Med Intensiva DOI: 10.1016/j.medin.2020.04.011 sha: doc_id: 338744 cord_uid: 2kizbzns file: cache/cord-339093-mwxkvwaz.json key: cord-339093-mwxkvwaz authors: Li, Wei; Schäfer, Alexandra; Kulkarni, Swarali S.; Liu, Xianglei; Martinez, David R.; Chen, Chuan; Sun, Zehua; Leist, Sarah R.; Drelich, Aleksandra; Zhang, Liyong; Ura, Marcin L.; Berezuk, Alison; Chittori, Sagar; Leopold, Karoline; Mannar, Dhiraj; Srivastava, Shanti S.; Zhu, Xing; Peterson, Eric C.; Tseng, Chien-Te; Mellors, John W.; Falzarano, Darryl; Subramaniam, Sriram; Baric, Ralph S.; Dimitrov, Dimiter S. title: High potency of a bivalent human VH domain in SARS-CoV-2 animal models date: 2020-09-04 journal: Cell DOI: 10.1016/j.cell.2020.09.007 sha: doc_id: 339093 cord_uid: mwxkvwaz file: cache/cord-339172-210dwhgj.json key: cord-339172-210dwhgj authors: Knoops, Kèvin; Kikkert, Marjolein; van den Worm, Sjoerd H. E.; Zevenhoven-Dobbe, Jessika C; van der Meer, Yvonne; Koster, Abraham J; Mommaas, A. Mieke; Snijder, Eric J title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 journal: PLoS Biol DOI: 10.1371/journal.pbio.0060226 sha: doc_id: 339172 cord_uid: 210dwhgj file: cache/cord-339506-pkusvf82.json key: cord-339506-pkusvf82 authors: Zaki, N.; Mohamed, E. A. title: The estimations of the COVID-19 incubation period: a systematic review of the literature date: 2020-05-23 journal: nan DOI: 10.1101/2020.05.20.20108340 sha: doc_id: 339506 cord_uid: pkusvf82 file: cache/cord-339329-8yvre7qc.json key: cord-339329-8yvre7qc authors: Kumar, Prashant; Morawska, Lidia title: Could fighting airborne transmission be the next line of defence against COVID-19 spread? date: 2020-05-23 journal: nan DOI: 10.1016/j.cacint.2020.100033 sha: doc_id: 339329 cord_uid: 8yvre7qc file: cache/cord-339570-vf79fefg.json key: cord-339570-vf79fefg authors: Jain, Vidhi; Kanchan, Tanuj title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists date: 2020-06-22 journal: Eye (Lond) DOI: 10.1038/s41433-020-1051-5 sha: doc_id: 339570 cord_uid: vf79fefg file: cache/cord-339431-kyr5lv15.json key: cord-339431-kyr5lv15 authors: Saçar Demirci, Müşerref Duygu; Adan, Aysun title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 journal: bioRxiv DOI: 10.1101/2020.03.15.992438 sha: doc_id: 339431 cord_uid: kyr5lv15 file: cache/cord-338979-ew046wcr.json key: cord-338979-ew046wcr authors: Jasti, Madhu; Nalleballe, Krishna; Dandu, Vasuki; Onteddu, Sanjeeva title: A review of pathophysiology and neuropsychiatric manifestations of COVID-19 date: 2020-06-03 journal: J Neurol DOI: 10.1007/s00415-020-09950-w sha: doc_id: 338979 cord_uid: ew046wcr file: cache/cord-339459-z22a5yzo.json key: cord-339459-z22a5yzo authors: Mackey, Katherine; King, Valerie J.; Gurley, Susan; Kiefer, Michael; Liederbauer, Erik; Vela, Kathryn; Sonnen, Payten; Kansagara, Devan title: Risks and Impact of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers on SARS-CoV-2 Infection in Adults: A Living Systematic Review date: 2020-05-15 journal: Ann Intern Med DOI: 10.7326/m20-1515 sha: doc_id: 339459 cord_uid: z22a5yzo file: cache/cord-338928-y5l7cf31.json key: cord-338928-y5l7cf31 authors: Leonardi, Matilde; Padovani, Alessandro; McArthur, Justin C. title: Neurological manifestations associated with COVID-19: a review and a call for action date: 2020-05-20 journal: J Neurol DOI: 10.1007/s00415-020-09896-z sha: doc_id: 338928 cord_uid: y5l7cf31 file: cache/cord-338972-uq2ha8xs.json key: cord-338972-uq2ha8xs authors: Olson, Michael T.; Triantafyllou, Tania; Singhal, Saurabh title: Resumption of elective surgery during the COVID-19 pandemic: what lessons can we apply? date: 2020-06-05 journal: Eur Surg DOI: 10.1007/s10353-020-00645-0 sha: doc_id: 338972 cord_uid: uq2ha8xs file: cache/cord-339381-vvh06d2c.json key: cord-339381-vvh06d2c authors: Han, Deheng; Fang, Qiang; Wang, Xingxiang title: SARS‐CoV‐2 was found in the bile juice from a patient with severe COVID‐19 date: 2020-06-12 journal: J Med Virol DOI: 10.1002/jmv.26169 sha: doc_id: 339381 cord_uid: vvh06d2c file: cache/cord-339516-xfwxtjry.json key: cord-339516-xfwxtjry authors: Nakashima, Tsutomu; Suzuki, Hirokazu; Teranishi, Masaaki title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses date: 2020-05-05 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.196 sha: doc_id: 339516 cord_uid: xfwxtjry file: cache/cord-339344-qd73h1ie.json key: cord-339344-qd73h1ie authors: Simon, David; 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Sartorius, Rossella; D’Apice, Luciana; Manco, Roberta; De Berardinis, Piergiuseppe title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 journal: Front Immunol DOI: 10.3389/fimmu.2020.02130 sha: doc_id: 339152 cord_uid: wfakzb6w file: cache/cord-339859-anatn295.json key: cord-339859-anatn295 authors: Paret, Michal; Lighter, Jennifer; Pellett Madan, Rebecca; Raabe, Vanessa N; Shust, Gail F; Ratner, Adam J title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date: 2020-04-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa452 sha: doc_id: 339859 cord_uid: anatn295 file: cache/cord-339521-qfnu319w.json key: cord-339521-qfnu319w authors: Lin, Shiming; Lee, Chih‐Kung; Lee, Shih‐Yuan; Kao, Chuan‐Liang; Lin, Chii‐Wann; Wang, An‐Bang; Hsu, Su‐Ming; Huang, Long‐Sun title: Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy date: 2005-08-08 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2005.00593.x sha: doc_id: 339521 cord_uid: qfnu319w file: cache/cord-339625-ucfjo73c.json key: cord-339625-ucfjo73c authors: Qiu, Xiang; Hong, Chao; Li, Yue; Bao, Wanrong; Gao, Xiao‐Ming title: Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus date: 2012-07-26 journal: Microbiol Immunol DOI: 10.1111/j.1348-0421.2012.00467.x sha: doc_id: 339625 cord_uid: ucfjo73c file: cache/cord-339558-li65qvq9.json key: cord-339558-li65qvq9 authors: Rana, Rashmi; Rathi, Vaishnavi; Ganguly, Nirmal Kumar title: A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date: 2020-11-02 journal: J Proteins Proteom DOI: 10.1007/s42485-020-00052-9 sha: doc_id: 339558 cord_uid: li65qvq9 file: cache/cord-339669-p61j2caf.json key: cord-339669-p61j2caf authors: Monzani, Alice; Genoni, Giulia; Scopinaro, Alice; Pistis, Gianfranco; Kozel, Daniela; Secco, Gioel Gabrio title: QTc evaluation in COVID‐19 patients treated with chloroquine/hydroxychloroquine date: 2020-05-18 journal: Eur J Clin Invest DOI: 10.1111/eci.13258 sha: doc_id: 339669 cord_uid: p61j2caf file: cache/cord-339386-sxyeuiw1.json key: cord-339386-sxyeuiw1 authors: McIntosh, Kenneth; Perlman, Stanley title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 journal: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases DOI: 10.1016/b978-1-4557-4801-3.00157-0 sha: doc_id: 339386 cord_uid: sxyeuiw1 file: cache/cord-339514-0aa58pi6.json key: cord-339514-0aa58pi6 authors: Ho, Yu; Lin, Pi-Hsiu; Liu, Catherine Y.Y; Lee, Su-Ping; Chao, Yu-Chan title: Assembly of human severe acute respiratory syndrome coronavirus-like particles date: 2004-06-11 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2004.04.111 sha: doc_id: 339514 cord_uid: 0aa58pi6 file: cache/cord-339709-49q2xxkw.json key: cord-339709-49q2xxkw authors: sermet, i.; temmam, s.; huon, c.; behillil, s.; gadjos, v.; bigot, t.; lurier, t.; chretien, d.; backovick, m.; Moisan-Delaunay, A.; donati, f.; albert, m.; foucaud, e.; Mesplees, B.; benoist, g.; fayes, a.; duval-arnould, m.; cretolle, c.; charbit, m.; aubart, m.; Auriau, J.; lorrot, m.; Kariyawasam, D.; fertita, l.; Orliaguet, G.; pigneur, b.; Bader-Meunier, B.; briand, c.; toubiana, j.; Guilleminot, T.; van der werf, s.; leruez-ville, m.; eloit, m. title: Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children date: 2020-06-30 journal: nan DOI: 10.1101/2020.06.29.20142596 sha: doc_id: 339709 cord_uid: 49q2xxkw file: cache/cord-339436-0k73tlna.json key: cord-339436-0k73tlna authors: Giagulli, Vito Angelo; Guastamacchia, Edoardo; Magrone, Thea; Jirillo, Emilio; Lisco, Giuseppe; De Pergola, Giovanni; Triggiani, Vincenzo title: Worse progression of COVID‐19 in men: Is Testosterone a key factor? date: 2020-06-11 journal: Andrology DOI: 10.1111/andr.12836 sha: doc_id: 339436 cord_uid: 0k73tlna file: cache/cord-339508-nf6ov39g.json key: cord-339508-nf6ov39g authors: Weil, Ana A.; Newman, Kira L.; Ong, Thuan D.; Davidson, Giana H.; Logue, Jennifer; Brandstetter, Elisabeth; Magedson, Ariana; McDonald, Dylan; McCulloch, Denise J.; Neme, Santiago; Lewis, James; Duchin, Jeff S.; Zhong, Weizhi; Starita, Lea M.; Bedford, Trevor; Roxby, Alison C.; Chu, Helen Y. title: Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle date: 2020-09-01 journal: J Gen Intern Med DOI: 10.1007/s11606-020-06165-7 sha: doc_id: 339508 cord_uid: nf6ov39g file: cache/cord-339568-th2xmhb6.json key: cord-339568-th2xmhb6 authors: Yan, Meitian; Zheng, Yutong; Sun, Yanmei; Wang, Lan; Luan, Liang; Liu, Jing; Tian, Xiao; Wan, Nan title: Analysis of the diagnostic value of serum specific antibody testing for coronavirus disease 2019 date: 2020-06-27 journal: J Med Virol DOI: 10.1002/jmv.26230 sha: doc_id: 339568 cord_uid: th2xmhb6 file: cache/cord-339576-0d6sa9pe.json key: cord-339576-0d6sa9pe authors: Guallar, María Pilar; Meiriño, Rosa; Donat-Vargas, Carolina; Corral, Octavio; Jouvé, Nicolás; Soriano, Vicente title: Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date: 2020-06-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.035 sha: doc_id: 339576 cord_uid: 0d6sa9pe file: cache/cord-339701-j0sr3ifq.json key: cord-339701-j0sr3ifq authors: Mikami, Takahisa; Miyashita, Hirotaka; Yamada, Takayuki; Harrington, Matthew; Steinberg, Daniel; Dunn, Andrew; Siau, Evan title: Risk Factors for Mortality in Patients with COVID-19 in New York City date: 2020-06-30 journal: J Gen Intern Med DOI: 10.1007/s11606-020-05983-z sha: doc_id: 339701 cord_uid: j0sr3ifq file: cache/cord-339772-q814d6l7.json key: cord-339772-q814d6l7 authors: Pach, Szymon; Nguyen, Trung Ngoc; Trimpert, Jakob; Kunec, Dusan; Osterrieder, Nikolaus; Wolber, Gerhard title: ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date: 2020-05-14 journal: bioRxiv DOI: 10.1101/2020.05.14.092767 sha: doc_id: 339772 cord_uid: q814d6l7 file: cache/cord-339524-r0a6a1jw.json key: cord-339524-r0a6a1jw authors: Islam, M. 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A. title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.08.20209692 sha: doc_id: 339524 cord_uid: r0a6a1jw file: cache/cord-339665-nwwutduy.json key: cord-339665-nwwutduy authors: Patel, Ami; Walters, Jewell; Reuschel, Emma L.; Schultheis, Katherine; Parzych, Elizabeth; Gary, Ebony N.; Maricic, Igor; Purwar, Mansi; Eblimit, Zeena; Walker, Susanne N.; Guimet, Diana; Bhojnagarwala, Pratik; Doan, Arthur; Xu, Ziyang; Elwood, Dustin; Reeder, Sophia M.; Pessaint, Laurent; Kim, Kevin Y.; Cook, Anthony; Chokkalingam, Neethu; Finneyfrock, Brad; Tello-Ruiz, Edgar; Dodson, Alan; Choi, Jihae; Generotti, Alison; Harrison, John; Tursi, Nicholas J.; Andrade, Viviane M.; Dia, Yaya; Zaidi, Faraz I.; Andersen, Hanne; Lewis, Mark G.; Muthumani, Kar; Kim, J Joseph; Kulp, Daniel W.; Humeau, Laurent M.; Ramos, Stephanie; Smith, Trevor R.F.; Weiner, David B.; Broderick, Kate E. title: Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date: 2020-07-29 journal: bioRxiv DOI: 10.1101/2020.07.28.225649 sha: doc_id: 339665 cord_uid: nwwutduy file: cache/cord-339762-lh8czr0a.json key: cord-339762-lh8czr0a authors: Ng, Dianna L.; Al Hosani, Farida; Keating, M. Kelly; Gerber, Susan I.; Jones, Tara L.; Metcalfe, Maureen G.; Tong, Suxiang; Tao, Ying; Alami, Negar N.; Haynes, Lia M.; Mutei, Mowafaq Ali; Abdel-Wareth, Laila; Uyeki, Timothy M.; Swerdlow, David L.; Barakat, Maha; Zaki, Sherif R. title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 date: 2016-03-31 journal: The American Journal of Pathology DOI: 10.1016/j.ajpath.2015.10.024 sha: doc_id: 339762 cord_uid: lh8czr0a file: cache/cord-340010-t1m7dxzc.json key: cord-340010-t1m7dxzc authors: Schaefer, Esperance A. K.; Arvind, Ashwini; Bloom, Patricia P.; Chung, Raymond T. title: Interrelationship Between Coronavirus Infection and Liver Disease date: 2020-05-21 journal: Clin Liver Dis (Hoboken) DOI: 10.1002/cld.967 sha: doc_id: 340010 cord_uid: t1m7dxzc file: cache/cord-339752-o6atz33c.json key: cord-339752-o6atz33c authors: Xiao, Li; Sakagami, Hiroshi; Miwa, Nobuhiko title: ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel? date: 2020-04-28 journal: Viruses DOI: 10.3390/v12050491 sha: doc_id: 339752 cord_uid: o6atz33c file: cache/cord-340015-x9frt0jh.json key: cord-340015-x9frt0jh authors: de Carvalho, Werther Brunow; Gibelli, Maria Augusta Bento Cicaroni; Krebs, Vera Lucia Jornada; Calil, Valdenise Martins Laurindo Tuma; Johnston, Cíntia title: Expert recommendations for the care of newborns of mothers with COVID-19 date: 2020-05-11 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e1932 sha: doc_id: 340015 cord_uid: x9frt0jh file: cache/cord-339711-f7xifne8.json key: cord-339711-f7xifne8 authors: Bal, A.; Pozzetto, B.; Trabaud, M.-A.; Escuret, V.; Rabilloud, M.; Langlois-jacques, C.; Paul, A.; Guibert, N.; D'aubarde, C.; Massardier, A.; Boibieux, A.; Morfin, F.; Pitiot, V.; Gueyffier, F.; Lina, B.; Fassier, J. B.; Assant, S. title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.30.20194290 sha: doc_id: 339711 cord_uid: f7xifne8 file: cache/cord-339720-d1stzy8w.json key: cord-339720-d1stzy8w authors: Zhao, Yuan; Wang, Junbin; Kuang, Dexuan; Xu, Jingwen; Yang, Mengli; Ma, Chunxia; Zhao, Siwen; Li, Jingmei; Long, Haiting; Ding, Kaiyun; Gao, Jiahong; Liu, Jiansheng; Wang, Haixuan; Li, Haiyan; Yang, Yun; Yu, Wenhai; Yang, Jing; Zheng, Yinqiu; Wu, Daoju; Lu, Shuaiyao; Liu, Hongqi; Peng, Xiaozhong title: Susceptibility of tree shrew to SARS-CoV-2 infection date: 2020-04-30 journal: bioRxiv DOI: 10.1101/2020.04.30.029736 sha: doc_id: 339720 cord_uid: d1stzy8w file: cache/cord-340103-dc3wye9s.json key: cord-340103-dc3wye9s authors: Pallanti, Stefano title: Importance of SARs-Cov-2 anosmia: From phenomenology to neurobiology date: 2020-05-11 journal: Compr Psychiatry DOI: 10.1016/j.comppsych.2020.152184 sha: doc_id: 340103 cord_uid: dc3wye9s file: cache/cord-339968-s1kmipir.json key: cord-339968-s1kmipir authors: Osier, Faith; Ting, Jenny P. 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S.; Suchard, Melinda title: The global response to the COVID-19 pandemic: how have immunology societies contributed? date: 2020-09-10 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-00428-4 sha: doc_id: 339968 cord_uid: s1kmipir file: cache/cord-339782-rybjc58j.json key: cord-339782-rybjc58j authors: Carmo, Anália; Pereira‐Vaz, João; Mota, Vanda; Mendes, Alexandra; Morais, Célia; da Silva, Andreia Coelho; Camilo, Elisabete; Pinto, Catarina Silva; Cunha, Elizabete; Pereira, Janet; Coucelo, Margarida; Martinho, Patrícia; Correia, Lurdes; Marques, Gilberto; Araújo, Lucília; Rodrigues, Fernando title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 journal: J Med Virol DOI: 10.1002/jmv.26103 sha: doc_id: 339782 cord_uid: rybjc58j file: cache/cord-339934-g6ufz29l.json key: cord-339934-g6ufz29l authors: Yu, Hai-qiong; Sun, Bao-qing; Fang, Zhang-fu; Zhao, Jin-cun; Liu, Xiao-yu; Li, Yi-min; Sun, Xi-zhuo; Liang, Hong-feng; Zhong, Bei; Huang, Zhi-feng; Zheng, Pei-yan; Tian, Li-feng; Qu, Hui-Qi; Liu, De-chen; Wang, Er-yi; Xiao, Xiao-jun; Li, Shi-yue; Ye, Feng; Guan, Li; Hu, Dong-sheng; Hakonarson, Hakon; Liu, Zhi-gang; Zhong, Nan-shan title: Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients date: 2020-05-13 journal: Eur Respir J DOI: 10.1183/13993003.01526-2020 sha: doc_id: 339934 cord_uid: g6ufz29l file: cache/cord-340070-de7sfccy.json key: cord-340070-de7sfccy authors: Pérez-Martinez, Antonio; Guerra-García, Pilar; Melgosa, Marta; Frauca, Esteban; Fernandez-Camblor, Carlota; Remesal, Agustin; Calvo, Cristina title: Clinical outcome of SARS-CoV-2 infection in immunosuppressed children in Spain date: 2020-08-29 journal: Eur J Pediatr DOI: 10.1007/s00431-020-03793-3 sha: doc_id: 340070 cord_uid: de7sfccy file: cache/cord-340114-ycgc6yyc.json key: cord-340114-ycgc6yyc authors: Rajagopal, Kalirajan; Varakumar, Potlapati; Aparna, Baliwada; Byran, Gowramma; Jupudi, Srikanth title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies date: 2020-07-28 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1798285 sha: doc_id: 340114 cord_uid: ycgc6yyc file: cache/cord-339976-tg2jkss7.json key: cord-339976-tg2jkss7 authors: Wang, Haibin; Mao, Yuanli; Ju, Liancai; Zhang, Jing; Liu, Zhiguo; Zhou, Xianzhi; Li, Qinghong; Wang, Yuedong; Kim, Sunghee; Zhang, Lurong title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 journal: Clin Chem DOI: 10.1373/clinchem.2004.031237 sha: doc_id: 339976 cord_uid: tg2jkss7 file: cache/cord-340049-6rqmc89u.json key: cord-340049-6rqmc89u authors: Salvatori, Giovanni; Luberto, Laura; Maffei, Mariano; Aurisicchio, Luigi; Roscilli, Giuseppe; Palombo, Fabio; Marra, Emanuele title: SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines date: 2020-06-03 journal: J Transl Med DOI: 10.1186/s12967-020-02392-y sha: doc_id: 340049 cord_uid: 6rqmc89u file: cache/cord-340028-6oicmeam.json key: cord-340028-6oicmeam authors: Zhavoronkov, Alex title: Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date: 2020-03-31 journal: Aging (Albany NY) DOI: 10.18632/aging.102988 sha: doc_id: 340028 cord_uid: 6oicmeam file: cache/cord-340042-intxyu46.json key: cord-340042-intxyu46 authors: Chaudhry, Sundas Nasir; Hazafa, Abu; Mumtaz, Muhummad; Kalsoom, Ume; Abbas, Saima; Kainaat, Amna; Bilal, Shahid; Zafar, Nauman; Siddique, Aleena; Zafar, Ayesha title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 journal: Life Sci DOI: 10.1016/j.lfs.2020.118421 sha: doc_id: 340042 cord_uid: intxyu46 file: cache/cord-339786-elrzlbsg.json key: cord-339786-elrzlbsg authors: Gurala, Dhineshreddy; Al Moussawi, Hassan; Philipose, Jobin; Abergel, Jeffrey R title: Acute Liver Failure in a COVID-19 Patient Without any Preexisting Liver Disease date: 2020-08-26 journal: Cureus DOI: 10.7759/cureus.10045 sha: doc_id: 339786 cord_uid: elrzlbsg file: cache/cord-340138-u8hxyfml.json key: cord-340138-u8hxyfml authors: Seneviratne, Chaminda Jayampath; Lau, Matthew Wen Jian; Goh, Bee Tin title: The Role of Dentists in COVID-19 Is Beyond Dentistry: Voluntary Medical Engagements and Future Preparedness date: 2020-10-06 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00566 sha: doc_id: 340138 cord_uid: u8hxyfml file: cache/cord-339686-oybnk1j8.json key: cord-339686-oybnk1j8 authors: Suassuna, José Hermógenes Rocco; de Lima, Emerson Quintino; Rocha, Eduardo; Castro, Alan; Burdmann, Emmanuel de Almeida; do Carmo, Lilian Pires de Freitas; Yu, Luis; Ibrahim, Mauricio Younes; Betônico, Gustavo Navarro; Cuvello, Américo Lourenço; Ávila, Maria Olinda Nogueira; Gonçalvez, Anderson R. Roman; Costa, Ciro Bruno Silveira; Bresolin, Nilzete Liberato; de Abreu, Andrea Pio; Lobo, Suzana Margareth Ajeje; do Nascimento, Marcelo Mazza title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine date: 2020-08-26 journal: J Bras Nefrol DOI: 10.1590/2175-8239-jbn-2020-s107 sha: doc_id: 339686 cord_uid: oybnk1j8 file: cache/cord-340063-nmx91h0a.json key: cord-340063-nmx91h0a authors: Müller, Olaf; Neuhann, Florian; Razum, Oliver title: Epidemiologie und Kontrollmaßnahmen bei COVID-19 date: 2020-04-28 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1162-1987 sha: doc_id: 340063 cord_uid: nmx91h0a file: cache/cord-339951-how9cmw8.json key: cord-339951-how9cmw8 authors: Zhou, Yaqing; Han, Tao; Chen, Jiaxin; Hou, Can; Hua, Lei; He, Shu; Guo, Yi; Zhang, Sheng; Wang, Yanjun; Yuan, Jinxia; Zhao, Chenhui; Zhang, Jing; Jia, Qiaowei; Zuo, Xiangrong; Li, Jinhai; Wang, Liansheng; Cao, Quan; Jia, Enzhi title: Clinical and Autoimmune Characteristics of Severe and Critical Cases of COVID‐19 date: 2020-05-14 journal: Clin Transl Sci DOI: 10.1111/cts.12805 sha: doc_id: 339951 cord_uid: how9cmw8 file: cache/cord-339727-q8pjwl3s.json key: cord-339727-q8pjwl3s authors: Sahu, Kamal Kant; Siddiqui, Ahmad Daniyal; Cerny, Jan title: Mesenchymal Stem Cells in COVID-19: A Journey from Bench to Bedside date: 2020-07-30 journal: Lab Med DOI: 10.1093/labmed/lmaa049 sha: doc_id: 339727 cord_uid: q8pjwl3s file: cache/cord-340240-dk48pdqa.json key: cord-340240-dk48pdqa authors: Kuo, Tsun-Yung; Lin, Meei-Yun; Coffman, Robert L; Campbell, John D; Traquina, Paula; Lin, Yi-Jiun; Liu, Luke Tzu-Chi; Cheng, Jinyi; Wu, Yu-Chi; Wu, Chung-Chin; Tang, Wei-Hsuan; Huang, Chung-Guei; Tsao, Kuo-Chien; Shih, Shin-Ru; Chen, Charles title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.08.11.245704 sha: doc_id: 340240 cord_uid: dk48pdqa file: cache/cord-340008-2efzyki4.json key: cord-340008-2efzyki4 authors: Haddadi, Kaveh; Asadian, Leila title: Coronavirus Disease 2019: Latest Data on Neuroinvasive Potential date: 2020-09-17 journal: Iran J Med Sci DOI: 10.30476/ijms.2020.85980.1561 sha: doc_id: 340008 cord_uid: 2efzyki4 file: cache/cord-339726-eg0hajzl.json key: cord-339726-eg0hajzl authors: Jamrozik, Euzebiusz; Heriot, George S.; Selgelid, Michael J. title: Coronavirus Human Infection Challenge Studies: Assessing Potential Benefits and Risks date: 2020-08-25 journal: J Bioeth Inq DOI: 10.1007/s11673-020-10030-x sha: doc_id: 339726 cord_uid: eg0hajzl file: cache/cord-339817-qqitdrz6.json key: cord-339817-qqitdrz6 authors: Sousa Gonçalves, Catarina; Reis Carreira, Nuno; Passos, Dúlio; Barbosa, Ana Luísa; Baltazar, Ana Maria; Wahnon, Alexandra; Abrantes, Ana Mafalda; Garrido, Pedro Miguel; Ferreira, Teresa; Teixeira Silva, Marisa; Alvoeiro, Lourdes title: Erythematous Papular Rash: A Dermatological Feature of COVID-19 date: 2020-06-10 journal: Eur J Case Rep Intern Med DOI: 10.12890/2020_001768 sha: doc_id: 339817 cord_uid: qqitdrz6 file: cache/cord-340260-z13aa1wk.json key: cord-340260-z13aa1wk authors: Farewell, V. T.; Herzberg, A. M.; James, K. W.; Ho, L. M.; Leung, G. 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A.; Shin, Ho-Joon; Vashisht, Kapil; Pandey, Kailash C title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.09.06.284992 sha: doc_id: 340432 cord_uid: vm6m0kb4 file: cache/cord-340535-78bpvtuf.json key: cord-340535-78bpvtuf authors: Elbay, Rümeysa Yeni; Kurtulmuş, Ayşe; Arpacıoğlu, Selim; Karadere, Emrah title: Depression, Anxiety, Stress Levels of Physicians and Associated Factors In Covid-19 Pandemics date: 2020-05-27 journal: Psychiatry Res DOI: 10.1016/j.psychres.2020.113130 sha: doc_id: 340535 cord_uid: 78bpvtuf file: cache/cord-340410-s9haq8y1.json key: cord-340410-s9haq8y1 authors: Fukumoto, Tatsuya; Iwasaki, Sumio; Fujisawa, Shinichi; Hayasaka, Kasumi; Sato, Kaori; Oguri, Satoshi; Taki, Keisuke; Nakakubo, Sho; Kamada, Keisuke; Yamashita, Yu; Konno, Satoshi; Nishida, Mutsumi; Sugita, Junichi; Teshima, Takanori title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-06-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.074 sha: doc_id: 340410 cord_uid: s9haq8y1 file: cache/cord-340252-9gr2iw15.json key: cord-340252-9gr2iw15 authors: Olalla, J.; Correa, A. 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Paz; Diaz, Francisco J. title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 journal: nan DOI: 10.1016/j.remle.2020.05.002 sha: doc_id: 340537 cord_uid: pdvpmydk file: cache/cord-340516-9dfaqsv7.json key: cord-340516-9dfaqsv7 authors: Moore, Anne C.; Dora, Emery G.; Peinovich, Nadine; Tucker, Kiersten P.; Lin, Karen; Cortese, Mario; Tucker, Sean N. title: Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.09.04.283853 sha: doc_id: 340516 cord_uid: 9dfaqsv7 file: cache/cord-340619-3tjquzx8.json key: cord-340619-3tjquzx8 authors: Menghua, Wu; Xin, Zheng; Jianwei, Liu; Yu, Zhang; Qinwei, Yao title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 journal: AIDS Res Ther DOI: 10.1186/s12981-020-00301-3 sha: doc_id: 340619 cord_uid: 3tjquzx8 file: cache/cord-340085-ywg4rhnn.json key: cord-340085-ywg4rhnn authors: Maras, J. 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Piotin, Anays; Godet, Julien; Abessolo-Amougou, Ines; Ederlé, Carole; Enache, Irina; Fraisse, Philippe; Tu Hoang, Thi Cam; Kassegne, Loic; Labani, Aissam; Leyendecker, Pierre; Manien, Louise; Marcot, Christophe; Pamart, Guillaume; Renaud-Picard, Benjamin; Riou, Marianne; Doyen, Virginie; Kessler, Romain; Fafi-Kremer, Samira; Metz-Favre, Carine; Khayath, Naji; de Blay, Frédéric title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation date: 2020-06-27 journal: J Allergy Clin Immunol Pract DOI: 10.1016/j.jaip.2020.06.032 sha: doc_id: 340486 cord_uid: wydlqq2z file: cache/cord-340687-99ad1rwq.json key: cord-340687-99ad1rwq authors: Abourida, Yassamine; Rebahi, Houssam; Oussayeh, Imane; Chichou, Hajar; Fakhir, Bouchra; Soummani, Abderraouf; Jalal, Hicham; Bennaoui, Fatiha; Slitine, Nadia El Idrissi; Maoulainine, Fadl Mrabih Rabou; El Adib, Ahmed Rhassane; Samkaoui, Mohamed Abdenacer title: Management of Severe COVID-19 in Pregnancy date: 2020-07-27 journal: Case Rep Obstet Gynecol DOI: 10.1155/2020/8852816 sha: doc_id: 340687 cord_uid: 99ad1rwq file: cache/cord-340883-zf8jbhdl.json key: cord-340883-zf8jbhdl authors: He, Zhongping; Zhuang, Hui; Zhao, Chunhui; Dong, Qingming; Peng, Guoai; Dwyer, Dominic E title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 journal: Virol J DOI: 10.1186/1743-422x-4-32 sha: doc_id: 340883 cord_uid: zf8jbhdl file: cache/cord-340908-8q7i5ds3.json key: cord-340908-8q7i5ds3 authors: D’Ambrosi, Riccardo; Biazzo, Alessio; Masia, Francesco; Izzo, Vincenzo; Confalonieri, Norberto; Ursino, Nicola; Verde, Francesco title: Guidelines for Resuming Elective Hip and Knee Surgical Activity Following the COVID-19 Pandemic: An Italian Perspective date: 2020-10-13 journal: HSS J DOI: 10.1007/s11420-020-09809-w sha: doc_id: 340908 cord_uid: 8q7i5ds3 file: cache/cord-340563-hsj53inh.json key: cord-340563-hsj53inh authors: Baud, David; Dimopoulou Agri, Varvara; Gibson, Glenn R.; Reid, Gregor; Giannoni, Eric title: Using Probiotics to Flatten the Curve of Coronavirus Disease COVID-2019 Pandemic date: 2020-05-08 journal: Front Public Health DOI: 10.3389/fpubh.2020.00186 sha: doc_id: 340563 cord_uid: hsj53inh file: cache/cord-340629-1fle5fpz.json key: cord-340629-1fle5fpz authors: O’Shea, Helen; Blacklaws, Barbara A.; Collins, Patrick J.; McKillen, John; Fitzgerald, Rose title: Viruses Associated With Foodborne Infections date: 2019-05-21 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.90273-5 sha: doc_id: 340629 cord_uid: 1fle5fpz file: cache/cord-340970-389t032s.json key: cord-340970-389t032s authors: Choy, Wai-Yan; Lin, Shu-Guang; Chan, Paul Kay-Sheung; Tam, John Siu-Lun; Lo, Y M Dennis; Chu, Ida Miu-Ting; Tsai, Sau-Na; Zhong, Ming-Qi; Fung, Kwok-Pui; Waye, Mary Miu-Yee; Tsui, Stephen Kwok-Wing; Ng, Kai-On; Shan, Zhi-Xin; Yang, Min; Wu, Yi-Long; Lin, Zhan-Yi; Ngai, Sai-Ming title: Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development date: 2004-06-01 journal: Clin Chem DOI: 10.1373/clinchem.2003.029801 sha: doc_id: 340970 cord_uid: 389t032s file: cache/cord-341000-9xs8aukq.json key: cord-341000-9xs8aukq authors: Ghiasvand, Fereshteh; Ghadimi, Maryam; Ghadimi, Fatemeh; Safarpour, Samin; Hosseinzadeh, Roghieh; SeyedAlinaghi, SeyedAhmad title: Symmetrical polyneuropathy in Coronavirus Disease 2019 (COVID-19) date: 2020-05-15 journal: IDCases DOI: 10.1016/j.idcr.2020.e00815 sha: doc_id: 341000 cord_uid: 9xs8aukq file: cache/cord-340579-cvze15cj.json key: cord-340579-cvze15cj authors: Dudley, Joseph P; Lee, Nam Taek title: Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date: 2020-03-31 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa354 sha: doc_id: 340579 cord_uid: cvze15cj file: cache/cord-340635-8wki7noy.json key: cord-340635-8wki7noy authors: Yu, Bin; Ikhlas, Shoeb; Ruan, Chunsheng; Zhong, Xingxing; Cai, Dongsheng title: Innate and adaptive immunity of murine neural stem cell-derived piRNA exosomes/microvesicles against pseudotyped SARS-CoV-2 and HIV-based lentivirus date: 2020-11-13 journal: iScience DOI: 10.1016/j.isci.2020.101806 sha: doc_id: 340635 cord_uid: 8wki7noy file: cache/cord-340746-icuzy3vp.json key: cord-340746-icuzy3vp authors: Liang, Yunfei; Wan, Ying; Qiu, Li-wen; Zhou, Jingran; Ni, Bing; Guo, Bo; Zou, Qiang; Zou, Liyun; Zhou, Wei; Jia, Zhengcai; Che, Xiao-yan; Wu, Yuzhang title: Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date: 2005-08-01 journal: Clin Chem DOI: 10.1373/clinchem.2005.051045 sha: doc_id: 340746 cord_uid: icuzy3vp file: cache/cord-340651-g3518bq2.json key: cord-340651-g3518bq2 authors: Hsu, Chung-Hua; Hwang, Kung-Chang; Chao, Chung-Liang; Chang, Steve G. N.; Ho, Mei-Shang; Lin, Jaung-Geng; Chang, Hen-Hong; Kao, Shung-Te; Chen, Yi-Ming; Chou, Pesus title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study date: 2007-05-29 journal: Evid Based Complement Alternat Med DOI: 10.1093/ecam/nem035 sha: doc_id: 340651 cord_uid: g3518bq2 file: cache/cord-341069-kngf6qpe.json key: cord-341069-kngf6qpe authors: Chan, Kwok-Hung; Sridhar, Siddharth; Zhang, Ricky Ruiqi; Chu, Hin; Fung, Agnes Yim-Fong; Chan, Gabriella; Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Hung, Ivan Fan-Ngai; Cheng, Vincent Chi-Chung; Yuen, Kwok-Yung title: Factors affecting stability and infectivity of SARS-CoV-2 date: 2020-07-09 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.07.009 sha: doc_id: 341069 cord_uid: kngf6qpe file: cache/cord-340666-zl9pp2h3.json key: cord-340666-zl9pp2h3 authors: Reifer, Josh; Hayum, Nosson; Heszkel, Benzion; Klagsbald, Ikey; Streva, Vincent A. title: SARS-CoV-2 IgG antibody responses in New York City date: 2020-07-21 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2020.115128 sha: doc_id: 340666 cord_uid: zl9pp2h3 file: cache/cord-341234-2zgfcrwc.json key: cord-341234-2zgfcrwc authors: Hallak, Jorge; Esteves, Sandro C. title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil date: 2020-09-02 journal: Int Braz J Urol DOI: 10.1590/s1677-5538.ibju.2020.06.03 sha: doc_id: 341234 cord_uid: 2zgfcrwc file: cache/cord-340583-kjrxrk50.json key: cord-340583-kjrxrk50 authors: Castro‐Rodriguez, Jose A.; Forno, Erick title: Asthma and COVID‐19 in children – a systematic review and call for data date: 2020-06-18 journal: Pediatr Pulmonol DOI: 10.1002/ppul.24909 sha: doc_id: 340583 cord_uid: kjrxrk50 file: cache/cord-340960-abanr641.json key: cord-340960-abanr641 authors: Brigger, D.; Horn, M.P.; Pennington, L.F.; Powell, A.E.; Siegrist, D.; Weber, B.; Engler, O.; Piezzi, V.; Damonti, L.; Iseli, P.; Hauser, C.; Froehlich, T.K.; Villiger, P.M.; Bachmann, M.F.; Leib, S.L.; Bittel, P.; Fiedler, M.; Largiadèr, C.; Marschall, J.; Stalder, H.; Kim, P.S.; Jardetzky, T.S.; Eggel, A.; Nagler, M. title: Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date: 2020-09-30 journal: Allergy DOI: 10.1111/all.14608 sha: doc_id: 340960 cord_uid: abanr641 file: cache/cord-340799-1awmtj52.json key: cord-340799-1awmtj52 authors: Krajewska, Joanna; Krajewski, Wojciech; Zub, Krzysztof; Zatoński, Tomasz title: Review of practical recommendations for otolaryngologists and head and neck surgeons during the COVID-19 pandemic: Recommendations for otolaryngologists during the COVID-19 pandemic date: 2020-06-06 journal: Auris Nasus Larynx DOI: 10.1016/j.anl.2020.05.022 sha: doc_id: 340799 cord_uid: 1awmtj52 file: cache/cord-340992-88t1c0zs.json key: cord-340992-88t1c0zs authors: Nikolai, Lea A; Meyer, Christian G.; Kremsner, Peter G.; Velavan, Thirumalaisamy P. title: Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date: 2020-09-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.076 sha: doc_id: 340992 cord_uid: 88t1c0zs file: cache/cord-341045-75of9ys6.json key: cord-341045-75of9ys6 authors: Shah, Abdullah; Rashid, Farooq; Aziz, Abdul; Jan, Amin Ullah; Suleman, Muhammad title: Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries date: 2020-09-14 journal: Gene Rep DOI: 10.1016/j.genrep.2020.100886 sha: doc_id: 341045 cord_uid: 75of9ys6 file: cache/cord-341287-i1hyk962.json key: cord-341287-i1hyk962 authors: Smith, Trevor R. F.; Patel, Ami; Ramos, Stephanie; Elwood, Dustin; Zhu, Xizhou; Yan, Jian; Gary, Ebony N.; Walker, Susanne N.; Schultheis, Katherine; Purwar, Mansi; Xu, Ziyang; Walters, Jewell; Bhojnagarwala, Pratik; Yang, Maria; Chokkalingam, Neethu; Pezzoli, Patrick; Parzych, Elizabeth; Reuschel, Emma L.; Doan, Arthur; Tursi, Nicholas; Vasquez, Miguel; Choi, Jihae; Tello-Ruiz, Edgar; Maricic, Igor; Bah, Mamadou A.; Wu, Yuanhan; Amante, Dinah; Park, Daniel H.; Dia, Yaya; Ali, Ali Raza; Zaidi, Faraz I.; Generotti, Alison; Kim, Kevin Y.; Herring, Timothy A.; Reeder, Sophia; Andrade, Viviane M.; Buttigieg, Karen; Zhao, Gan; Wu, Jiun-Ming; Li, Dan; Bao, Linlin; Liu, Jiangning; Deng, Wei; Qin, Chuan; Brown, Ami Shah; Khoshnejad, Makan; Wang, Nianshuang; Chu, Jacqueline; Wrapp, Daniel; McLellan, Jason S.; Muthumani, Kar; Wang, Bin; Carroll, Miles W.; Kim, J. Joseph; Boyer, Jean; Kulp, Daniel W.; Humeau, Laurent M. P. F.; Weiner, David B.; Broderick, Kate E. title: Immunogenicity of a DNA vaccine candidate for COVID-19 date: 2020-05-20 journal: Nat Commun DOI: 10.1038/s41467-020-16505-0 sha: doc_id: 341287 cord_uid: i1hyk962 file: cache/cord-340656-ltd6ueoi.json key: cord-340656-ltd6ueoi authors: Grant, Michael C.; Geoghegan, Luke; Arbyn, Marc; Mohammed, Zakaria; McGuinness, Luke; Clarke, Emily L.; Wade, Ryckie G. title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date: 2020-06-23 journal: PLoS One DOI: 10.1371/journal.pone.0234765 sha: doc_id: 340656 cord_uid: ltd6ueoi file: cache/cord-340821-kelq45dw.json key: cord-340821-kelq45dw authors: Misrahi, James J.; Foster, Joseph A.; Shaw, Frederic E.; Cetron, Martin S. title: HHS/CDC Legal Response to SARS Outbreak date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030721 sha: doc_id: 340821 cord_uid: kelq45dw file: cache/cord-340811-w4x4falm.json key: cord-340811-w4x4falm authors: Frizzelli, Annalisa; Tuttolomondo, Domenico; Aiello, Marina; Majori, Maria; Bertorelli, Giuseppina; Chetta, Alfredo title: What happens to people’s lungs when they get coronavirus disease 2019? date: 2020-05-11 journal: Acta Biomed DOI: 10.23750/abm.v91i2.9574 sha: doc_id: 340811 cord_uid: w4x4falm file: cache/cord-341176-83khavoh.json key: cord-341176-83khavoh authors: Lotfi, Melika; Rezaei, Nima title: CRISPR/Cas13: A potential therapeutic option of COVID-19 date: 2020-09-17 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110738 sha: doc_id: 341176 cord_uid: 83khavoh file: cache/cord-341254-xnj6slby.json key: cord-341254-xnj6slby authors: Li, Hua; Liu, Zhe; He, Yue; Qi, Yingjie; Chen, Jie; Ma, Yuanyuan; Liu, Fujia; Lai, Kaisheng; Zhang, Yong; Jiang, Liu; Wang, Xiangdong; Ge, Junbo title: A new and rapid approach for detecting COVID‐19 based on S1 protein fragments date: 2020-06-05 journal: Clin Transl Med DOI: 10.1002/ctm2.90 sha: doc_id: 341254 cord_uid: xnj6slby file: cache/cord-340857-teq5txm9.json key: cord-340857-teq5txm9 authors: Galloro, Giuseppe; Pisani, Antonio; Zagari, Rocco Maurizio; Lamazza, Antonietta; Cengia, Gianpaolo; Ciliberto, Enrico; Conigliaro, Rita L.; Carrara, Paola Da Massa; Germanà, Bastianello; Pasquale, Luigi title: SAFETY IN DIGESTIVE ENDOSCOPY PROCEDURES IN THE COVID ERA RECOMMENDATIONS IN PROGRES OF THE ITALIAN SOCIETY OF DIGESTIVE ENDOSCOPY date: 2020-05-13 journal: Dig Liver Dis DOI: 10.1016/j.dld.2020.05.002 sha: doc_id: 340857 cord_uid: teq5txm9 file: cache/cord-341246-fz66z2p2.json key: cord-341246-fz66z2p2 authors: Bhattacharyya, Pranab J; Attri, Pawan K; Farooqui, Waseem title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection date: 2020-09-28 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-239104 sha: doc_id: 341246 cord_uid: fz66z2p2 file: cache/cord-341284-jmqdnart.json key: cord-341284-jmqdnart authors: Panagopoulos, Periklis; Petrakis, Vasilis; Panopoulou, Maria; Trypsianis, Grigorios; Penlioglou, Theano; Pnevmatikos, Ioannis; Papazoglou, Dimitrios title: Lopinavir/ritonavir as a third agent in the antiviral regimen for SARS-CoV-2 infection date: 2020-06-12 journal: J Chemother DOI: 10.1080/1120009x.2020.1775424 sha: doc_id: 341284 cord_uid: jmqdnart file: cache/cord-340984-blkhfhe2.json key: cord-340984-blkhfhe2 authors: Gklinos, Panagiotis title: Neurological manifestations of COVID-19: a review of what we know so far date: 2020-05-26 journal: J Neurol DOI: 10.1007/s00415-020-09939-5 sha: doc_id: 340984 cord_uid: blkhfhe2 file: cache/cord-340942-oatf59k0.json key: cord-340942-oatf59k0 authors: Magalhães, Jurandy Júnior Ferraz de; Mendes, Renata Pessoa Germano; Silva, Caroline Targino Alves da; Silva, Severino Jefferson Ribeiro da; Guarines, Klarissa Miranda; Pena, Lindomar title: Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil date: 2020-09-21 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101884 sha: doc_id: 340942 cord_uid: oatf59k0 file: cache/cord-341396-0tn06al2.json key: cord-341396-0tn06al2 authors: Ni, Ling; Ye, Fang; Cheng, Meng-Li; Feng, Yu; Deng, Yong-Qiang; Zhao, Hui; Wei, Peng; Ge, Jiwan; Gou, Mengting; Li, Xiaoli; Sun, Lin; Cao, Tianshu; Wang, Pengzhi; Zhou, Chao; Zhang, Rongrong; Liang, Peng; Guo, Han; Wang, Xinquan; Qin, Cheng-Feng; Chen, Fang; Dong, Chen title: Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals date: 2020-05-03 journal: Immunity DOI: 10.1016/j.immuni.2020.04.023 sha: doc_id: 341396 cord_uid: 0tn06al2 file: cache/cord-341416-6bh08901.json key: cord-341416-6bh08901 authors: Smithgall, Marie C.; Whittier, Susan; Fernandes, Helen title: Laboratory Testing of SARS CoV-2: A New York Institutional Experience date: 2020-07-19 journal: nan DOI: 10.1016/j.yamp.2020.07.002 sha: doc_id: 341416 cord_uid: 6bh08901 file: cache/cord-341543-gcnph9gf.json key: cord-341543-gcnph9gf authors: Kuryntseva, P.; Karamova, K.; Fomin, V.; Selivanovskaya, S.; Galitskaya, P. title: A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia date: 2020-09-23 journal: nan DOI: 10.1101/2020.09.21.20197244 sha: doc_id: 341543 cord_uid: gcnph9gf file: cache/cord-341101-5yvjbr5q.json key: cord-341101-5yvjbr5q authors: Hashem, Anwar M.; Alghamdi, Badrah S.; Algaissi, Abdullah A.; Alshehri, Fahad S.; Bukhari, Abdullah; Alfaleh, Mohamed A.; Memish, Ziad A. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101735 sha: doc_id: 341101 cord_uid: 5yvjbr5q file: cache/cord-341453-9yrvjlpx.json key: cord-341453-9yrvjlpx authors: Clay, Candice C; Donart, Nathan; Fomukong, Ndingsa; Knight, Jennifer B; Overheim, Katie; Tipper, Jennifer; Van Westrienen, Jesse; Hahn, Fletcher; Harrod, Kevin S title: Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses date: 2014-03-19 journal: Immun Ageing DOI: 10.1186/1742-4933-11-4 sha: doc_id: 341453 cord_uid: 9yrvjlpx file: cache/cord-341502-jlzufa28.json key: cord-341502-jlzufa28 authors: Lee, Sungyul; Lee, Young-suk; Choi, Yeon; Son, Ahyeon; Park, Youngran; Lee, Kyung-Min; Kim, Jeesoo; Kim, Jong-Seo; Kim, V. Narry title: The SARS-CoV-2 RNA interactome date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.364497 sha: doc_id: 341502 cord_uid: jlzufa28 file: cache/cord-341524-zvic4xc9.json key: cord-341524-zvic4xc9 authors: KARAKURT, Hamza Umut; PİR, Pınar title: Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks date: 2020-06-21 journal: Turk J Biol DOI: 10.3906/biy-2005-115 sha: doc_id: 341524 cord_uid: zvic4xc9 file: cache/cord-341415-g781zhu6.json key: cord-341415-g781zhu6 authors: Jhaveri, Kenar D.; Meir, Lea R.; Flores Chang, Bessy Suyin; Parikh, Rushang; Wanchoo, Rimda; Barilla-LaBarca, Marie Louise; Bijol, Vanesa; Hajizadeh, Negin title: Thrombotic microangiopathy in a patient with COVID-19 date: 2020-06-07 journal: Kidney Int DOI: 10.1016/j.kint.2020.05.025 sha: doc_id: 341415 cord_uid: g781zhu6 file: cache/cord-341648-z4lflkmo.json key: cord-341648-z4lflkmo authors: Isaacs, David; Britton, Philip; Howard‐Jones, Annaleise; Kesson, Alison; Khatami, Ameneh; Marais, Ben; Nayda, Claire; Outhred, Alexander title: To what extent do children transmit SARS‐CoV‐2 virus? date: 2020-06-16 journal: J Paediatr Child Health DOI: 10.1111/jpc.14937 sha: doc_id: 341648 cord_uid: z4lflkmo file: cache/cord-341474-06113cn0.json key: cord-341474-06113cn0 authors: Huynh, Tien; Wang, Haoran; Luan, Binquan title: In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease date: 2020-05-14 journal: J Phys Chem Lett DOI: 10.1021/acs.jpclett.0c00994 sha: doc_id: 341474 cord_uid: 06113cn0 file: cache/cord-341331-l24oe2pd.json key: cord-341331-l24oe2pd authors: Zheng, Baojia; Wang, Hui; Yu, Cuixiang title: An increasing public health burden arising from children infected with SARS‐CoV2: a systematic review and meta‐analysis date: 2020-08-05 journal: Pediatr Pulmonol DOI: 10.1002/ppul.25008 sha: doc_id: 341331 cord_uid: l24oe2pd file: cache/cord-341670-o1v63zg8.json key: cord-341670-o1v63zg8 authors: Estevez-Ordonez, Dagoberto; Laskay, Nicholas M B; Chagoya, Gustavo; Alam, Yasaman; Atchley, Travis J; Elsayed, Galal A; Farr, George A; Totten, Arthur H; Leal, Sixto M; Fisher, Winfield S title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage date: 2020-05-20 journal: Neurosurgery DOI: 10.1093/neuros/nyaa197 sha: doc_id: 341670 cord_uid: o1v63zg8 file: cache/cord-341804-rnj3wtg4.json key: cord-341804-rnj3wtg4 authors: Jin, Zhe; Liu, Jing-Yi; Feng, Rang; Ji, Lu; Jin, Zi-Li; Li, Hai-Bo title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173326 sha: doc_id: 341804 cord_uid: rnj3wtg4 file: cache/cord-341531-w788qwya.json key: cord-341531-w788qwya authors: Montero Feijoo, A.; Maseda, E.; Adalia Bartolomé, R.; Aguilar, G.; González de Castro, R.; Gómez-Herreras, J. I.; García Palenciano, C.; Pereira, J.; Ramasco Rueda, F.; Samso, E.; Suárez de la Rica, A.; Tamayo Medel, G.; Varela Durán, M. title: Practical recommendations for the perioperative management of patients with suspicion or serious infection by coronavirus SARS-CoV date: 2020-05-04 journal: nan DOI: 10.1016/j.redare.2020.03.002 sha: doc_id: 341531 cord_uid: w788qwya file: cache/cord-341838-lkz8ro90.json key: cord-341838-lkz8ro90 authors: Gervasoni, Cristina; Meraviglia, Paola; Riva, Agostino; Giacomelli, Andrea; Oreni, Letizia; Minisci, Davide; Atzori, Chiara; Ridolfo, Annalisa; Cattaneo, Dario title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa579 sha: doc_id: 341838 cord_uid: lkz8ro90 file: cache/cord-341620-nmrkhx5t.json key: cord-341620-nmrkhx5t authors: Chirico, Francesco; Sacco, Angelo; Bragazzi, Nicola Luigi; Magnavita, Nicola title: Can Air-Conditioning Systems Contribute to the Spread of SARS/MERS/COVID-19 Infection? Insights from a Rapid Review of the Literature date: 2020-08-20 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17176052 sha: doc_id: 341620 cord_uid: nmrkhx5t file: cache/cord-341783-e7xz4utr.json key: cord-341783-e7xz4utr authors: Vistisen, Simon T.; Bodilsen, Jacob; Scheeren, Thomas W.L.; Simonsen, Ulf title: Risk and prognosis of COVID-19 in patients treated with renin–angiotensin–aldosterone inhibitors date: 2020-07-06 journal: Eur J Anaesthesiol DOI: 10.1097/eja.0000000000001277 sha: doc_id: 341783 cord_uid: e7xz4utr file: cache/cord-341819-emjg3dsw.json key: cord-341819-emjg3dsw authors: Kouznetsova, Valentina L.; Zhang, Aidan; Tatineni, Mahidhar; Miller, Mark A.; Tsigelny, Igor F. title: Potential COVID-19 papain-like protease PL(pro) inhibitors: repurposing FDA-approved drugs date: 2020-09-18 journal: PeerJ DOI: 10.7717/peerj.9965 sha: doc_id: 341819 cord_uid: emjg3dsw file: cache/cord-341776-y7kpp10x.json key: cord-341776-y7kpp10x authors: Hamm, C.; Nitschmann, S. title: Zusammenhang zwischen Angiotensinblockade und Influenza-A-Inzidenz date: 2020-06-05 journal: Internist (Berl) DOI: 10.1007/s00108-020-00827-8 sha: doc_id: 341776 cord_uid: y7kpp10x file: cache/cord-341701-zropd3mo.json key: cord-341701-zropd3mo authors: Adhikari, Subash; Nice, Edouard C.; Deutsch, Eric W.; Lane, Lydie; Omenn, Gilbert S.; Pennington, Stephen R.; Paik, Young-Ki; Overall, Christopher M.; Corrales, Fernando J.; Cristea, Ileana M.; Van Eyk, Jennifer E.; Uhlén, Mathias; Lindskog, Cecilia; Chan, Daniel W.; Bairoch, Amos; Waddington, James C.; Justice, Joshua L.; LaBaer, Joshua; Rodriguez, Henry; He, Fuchu; Kostrzewa, Markus; Ping, Peipei; Gundry, Rebekah L.; Stewart, Peter; Srivastava, Sanjeeva; Srivastava, Sudhir; Nogueira, Fabio C. S.; Domont, Gilberto B.; Vandenbrouck, Yves; Lam, Maggie P. Y.; Wennersten, Sara; Vizcaino, Juan Antonio; Wilkins, Marc; Schwenk, Jochen M.; Lundberg, Emma; Bandeira, Nuno; Marko-Varga, Gyorgy; Weintraub, Susan T.; Pineau, Charles; Kusebauch, Ulrike; Moritz, Robert L.; Ahn, Seong Beom; Palmblad, Magnus; Snyder, Michael P.; Aebersold, Ruedi; Baker, Mark S. title: A high-stringency blueprint of the human proteome date: 2020-10-16 journal: Nat Commun DOI: 10.1038/s41467-020-19045-9 sha: doc_id: 341701 cord_uid: zropd3mo file: cache/cord-342013-k54u2q0d.json key: cord-342013-k54u2q0d authors: Martenot, Antoine; Labbassi, Imad; Delfils-Stern, Amélie; Monroy, Oscar; Langlet, Claire; Pichault-Klein, Valérie; Delagreverie, Héloise; De Marcillac, Fanny; Fafi-Kremer, Samira; Deruelle, Philippe; Kuhn, Pierre title: Favorable outcomes among neonates not separated from their symptomatic SARS-CoV-2-infected mothers date: 2020-11-03 journal: Pediatr Res DOI: 10.1038/s41390-020-01226-3 sha: doc_id: 342013 cord_uid: k54u2q0d file: cache/cord-342024-kaku49xd.json key: cord-342024-kaku49xd authors: Espejo, Andrea P; Akgun, Yamac; Al Mana, Abdulaziz F; Tjendra, Youley; Millan, Nicolas C; Gomez-Fernandez, Carmen; Cray, Carolyn title: Review of Current Advances in Serologic Testing for COVID-19 date: 2020-06-25 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa112 sha: doc_id: 342024 cord_uid: kaku49xd file: cache/cord-342091-xus5kxs0.json key: cord-342091-xus5kxs0 authors: YAVARIAN, Jila; SHAFIEI-JANDAGHI, Nazanin-Zahra; SADEGHI, Kaveh; SHATIZADEH MALEKSHAHI, Somayeh; SALIMI, Vahid; NEJATI, Ahmad; AJA-MINEJAD, Fatemeh; GHAVVAMI, Nastaran; SAADATMAND, Fatemeh; MAHFOUZI, Saeedeh; FATEMINASAB, Ghazal; PARHIZGARI, Najmeh; AHMADI, Akramsadat; RAZAVI, Kobra; GHABESHI, Soad; SABERIAN, Mostafa; ZANJANI, Elham; NAMAZI, Fatemeh; SHAHBAZI, Tayebeh; REZAIE, Farshid; ERFANI, Hossein; GOUYA, Mohammad Mehdi; NASR DADRAS, Mohammad; MOKHTARI AZAD, Talat title: First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report date: 2020-08-17 journal: Iran J Public Health DOI: 10.18502/ijph.v49i8.3903 sha: doc_id: 342091 cord_uid: xus5kxs0 file: cache/cord-342139-t2tukk0z.json key: cord-342139-t2tukk0z authors: Livingston, Gill; Rostamipour, Hossein; Gallagher, Paul; Kalafatis, Chris; Shastri, Abhishek; Huzzey, Lauren; Liu, Kathy; Sommerlad, Andrew; Marston, Louise title: Prevalence, management, and outcomes of SARS-CoV-2 infections in older people and those with dementia in mental health wards in London, UK: a retrospective observational study date: 2020-10-05 journal: Lancet Psychiatry DOI: 10.1016/s2215-0366(20)30434-x sha: doc_id: 342139 cord_uid: t2tukk0z file: cache/cord-341970-pho6dksc.json key: cord-341970-pho6dksc authors: Huang, Jun; Ma, Rui; Wu, Chang-you title: Immunization with SARS-CoV S DNA vaccine generates memory CD4(+) and CD8(+) T cell immune responses date: 2006-06-05 journal: Vaccine DOI: 10.1016/j.vaccine.2006.03.058 sha: doc_id: 341970 cord_uid: pho6dksc file: cache/cord-342204-9tgxijvn.json key: cord-342204-9tgxijvn authors: Nuzzo, Domenico; Picone, Pasquale title: Potential neurological effects of severe COVID-19 infection date: 2020-07-03 journal: Neurosci Res DOI: 10.1016/j.neures.2020.06.009 sha: doc_id: 342204 cord_uid: 9tgxijvn file: cache/cord-342254-vdovpfu1.json key: cord-342254-vdovpfu1 authors: Mugheddu, C.; Pizzatti, L.; Sanna, S.; Atzori, L.; Rongioletti, F. title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management date: 2020-06-04 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16625 sha: doc_id: 342254 cord_uid: vdovpfu1 file: cache/cord-341919-8gnthufw.json key: cord-341919-8gnthufw authors: Basi, Saajan; Hamdan, Mohammad; Punekar, Shuja title: Clinical course of a 66-year-old man with an acute ischaemic stroke in the setting of a COVID-19 infection date: 2020-08-23 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-235920 sha: doc_id: 341919 cord_uid: 8gnthufw file: cache/cord-341883-eh0aw3re.json key: cord-341883-eh0aw3re authors: Bellanger, Anne-Pauline; Reboux, Gabriel title: Studying smoking benefit in farmer’s lung to understand Covid-19 date: 2020-08-11 journal: Occup Med (Lond) DOI: 10.1093/occmed/kqaa147 sha: doc_id: 341883 cord_uid: eh0aw3re file: cache/cord-342177-iqt3ghc0.json key: cord-342177-iqt3ghc0 authors: Laine, Roger A title: The case for re-examining glycosylation inhibitors, mimetics, primers and glycosylation decoys as antivirals and anti-inflammatories in COVID19 date: 2020-08-21 journal: Glycobiology DOI: 10.1093/glycob/cwaa083 sha: doc_id: 342177 cord_uid: iqt3ghc0 file: cache/cord-342221-xvrpx9p8.json key: cord-342221-xvrpx9p8 authors: Duan, Qing; Zhu, Hong; Yang, Yi; Li, Weihua; Zhou, Yusen; He, Jun; He, Kun; Zhang, Haojie; Zhou, Tao; Song, Lihua; Gan, Yonghua; Tan, Hua; Jin, Baofeng; Li, Huiyan; Zuo, Tingting; Chen, Dehui; Zhang, Xuemin title: Reovirus, isolated from SARS patients date: 2003 journal: Chin Sci Bull DOI: 10.1007/bf03184165 sha: doc_id: 342221 cord_uid: xvrpx9p8 file: cache/cord-342084-fbtx7rwi.json key: cord-342084-fbtx7rwi authors: Ceccarelli, Giancarlo; Alessandri, Francesco; d'Ettorre, Gabriella; Borrazzo, Cristian; Spagnolello, Ornella; Oliva, Alessandra; Ruberto, Franco; Mastroianni, Claudio M.; Pugliese, Francesco; Venditti, Mario title: IS TEICOPLANIN A COMPLEMENTARY TREATMENT OPTION FOR COVID-19? THE QUESTION REMAINS date: 2020-05-23 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2020.106029 sha: doc_id: 342084 cord_uid: fbtx7rwi file: cache/cord-342144-awtiqxx5.json key: cord-342144-awtiqxx5 authors: Hufert, F.; Spiegel, M. title: Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie date: 2020-04-01 journal: Monatsschr Kinderheilkd DOI: 10.1007/s00112-020-00910-2 sha: doc_id: 342144 cord_uid: awtiqxx5 file: cache/cord-342391-arp07mck.json key: cord-342391-arp07mck authors: Magiorkinis, G.; Magiorkinis, E.; Paraskevis, D.; Vandamme, A.M.; Van Ranst, M.; Moulton, V.; Hatzakis, A. title: Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions date: 2004-09-14 journal: J Med Virol DOI: 10.1002/jmv.20187 sha: doc_id: 342391 cord_uid: arp07mck file: cache/cord-342344-jjnf4yje.json key: cord-342344-jjnf4yje authors: Mello, C. J.; Kamitaki, N.; de Rivera, H.; McCarroll, S. A. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 journal: nan DOI: 10.1101/2020.06.24.20139584 sha: doc_id: 342344 cord_uid: jjnf4yje file: cache/cord-342145-cq6xe5r7.json key: cord-342145-cq6xe5r7 authors: Dao Thi, Viet Loan; Herbst, Konrad; Boerner, Kathleen; Meurer, Matthias; Kremer, Lukas PM; Kirrmaier, Daniel; Freistaedter, Andrew; Papagiannidis, Dimitrios; Galmozzi, Carla; Stanifer, Megan L.; Boulant, Steeve; Klein, Steffen; Chlanda, Petr; Khalid, Dina; Barreto Miranda, Isabel; Schnitzler, Paul; Kräusslich, Hans-Georg; Knop, Michael; Anders, Simon title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 journal: Sci Transl Med DOI: 10.1126/scitranslmed.abc7075 sha: doc_id: 342145 cord_uid: cq6xe5r7 file: cache/cord-342383-ckswlo9o.json key: cord-342383-ckswlo9o authors: Pawlowski, C.; Puranik, A.; Bandi, H.; Venkatakrishnan, A.; Agarwal, V.; Kennedy, R.; O'Horo, J. C.; Gores, G. J.; Williams, A. W.; Halamka, J.; Badley, A. D.; Soundararajan, V. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 journal: nan DOI: 10.1101/2020.07.27.20161976 sha: doc_id: 342383 cord_uid: ckswlo9o file: cache/cord-341976-yts6pzn3.json key: cord-341976-yts6pzn3 authors: Liu, Xintian; Zheng, Xuan; Liu, Bo; Wu, Mingxiang; Zhang, Zhenlu; Zhang, Gangcheng; Su, Xi title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China date: 2020-07-06 journal: Aging (Albany NY) DOI: 10.18632/aging.103417 sha: doc_id: 341976 cord_uid: yts6pzn3 file: cache/cord-342220-lrqt2gcw.json key: cord-342220-lrqt2gcw authors: Dearlove, Bethany; Lewitus, Eric; Bai, Hongjun; Li, Yifan; Reeves, Daniel B.; Joyce, M. Gordon; Scott, Paul T.; Amare, Mihret F.; Vasan, Sandhya; Michael, Nelson L.; Modjarrad, Kayvon; Rolland, Morgane title: A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants date: 2020-09-22 journal: Proc Natl Acad Sci U S A DOI: 10.1073/pnas.2008281117 sha: doc_id: 342220 cord_uid: lrqt2gcw file: cache/cord-342396-n3txsvf7.json key: cord-342396-n3txsvf7 authors: Ciaglia, Elena; Vecchione, Carmine; Puca, Annibale Alessandro title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children date: 2020-04-23 journal: Front Pediatr DOI: 10.3389/fped.2020.00206 sha: doc_id: 342396 cord_uid: n3txsvf7 file: cache/cord-342639-vf9n2vf9.json key: cord-342639-vf9n2vf9 authors: Chang, Chung-ke; Chen, Chia-Min Michael; Chiang, Ming-hui; Hsu, Yen-lan; Huang, Tai-huang title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0065045 sha: doc_id: 342639 cord_uid: vf9n2vf9 file: cache/cord-342340-q6j7vy8u.json key: cord-342340-q6j7vy8u authors: Jefferies, Sarah; French, Nigel; Gilkison, Charlotte; Graham, Giles; Hope, Virginia; Marshall, Jonathan; McElnay, Caroline; McNeill, Andrea; Muellner, Petra; Paine, Shevaun; Prasad, Namrata; Scott, Julia; Sherwood, Jillian; Yang, Liang; Priest, Patricia title: COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study date: 2020-10-14 journal: Lancet Public Health DOI: 10.1016/s2468-2667(20)30225-5 sha: doc_id: 342340 cord_uid: q6j7vy8u file: cache/cord-342362-j7vuoer6.json key: cord-342362-j7vuoer6 authors: Gegúndez-Fernández, José A; Zarranz-Ventura, Javier; Garay-Aramburu, Gonzaga; Muñoz-Negrete, Francisco J; Barrio, Javier Mendicute del; Pablo-Júlvez, Luis; García-Delpech, Salvador; López-Alemany, Antonio; Arnalich-Montiel, Francisco; Cordero-Coma, Miguel; Cárceles, Juan Antonio title: Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19 date: 2020-04-25 journal: Arch Soc Esp Oftalmol DOI: 10.1016/j.oftal.2020.04.002 sha: doc_id: 342362 cord_uid: j7vuoer6 file: cache/cord-342453-1vj9p7vm.json key: cord-342453-1vj9p7vm authors: Ip, A.; Ahn, J.; Zhou, Y.; Goy, A. H.; Hansen, E.; Pecora, A. L.; Sinclaire, B. A.; Bednarz, U.; Marafelias, M.; Mathura, S.; Sawczuk, I. S.; Underwood, J. P.; Walker, D. M.; Prasad, R.; Sweeney, R. L.; Ponce, M. G.; LaCapra, S.; Cunningham, F. J.; Calise, A. G.; Pulver, B. L.; Ruocco, D.; Mojares, G. E.; Eagan, M. P.; Ziontz, K. L.; Mastrokyriakos, P.; Goldberg, S. L. title: Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study date: 2020-08-25 journal: nan DOI: 10.1101/2020.08.20.20178772 sha: doc_id: 342453 cord_uid: 1vj9p7vm file: cache/cord-342189-ya05m58o.json key: cord-342189-ya05m58o authors: Banerjee, Abhik K.; Blanco, Mario R.; Bruce, Emily A.; Honson, Drew D.; Chen, Linlin M.; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A.; Loney, Colin; Thai, Jasmine; Miller, Zachary D.; Lin, Aaron E.; Schmidt, Madaline M.; Stewart, Douglas G.; Goldfarb, Daniel; De Lorenzo, Giuditta; Rihn, Suzannah J.; Voorhees, Rebecca; Botten, Jason W.; Majumdar, Devdoot; Guttman, Mitchell title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 journal: Cell DOI: 10.1016/j.cell.2020.10.004 sha: doc_id: 342189 cord_uid: ya05m58o file: cache/cord-342599-558yn6pu.json key: cord-342599-558yn6pu authors: Rinchai, Darawan; Kabeer, Basirudeen; Toufiq, Mohammed; Calderone, Zohreh; Deola, Sara; Brummaier, Tobias; Garand, Mathieu; Branco, Ricardo; Baldwin, Nicole; Alfaki, Mohamed; Altman, Matthew; Ballestrero, Alberto; Bassetti, Matteo; Zoppoli, Gabriele; De Maria, Andrea; Tang, Benjamin; Bedognetti, Davide; Chaussabel, Damien title: A modular framework for the development of targeted Covid-19 blood transcript profiling panels date: 2020-05-22 journal: bioRxiv DOI: 10.1101/2020.05.20.107243 sha: doc_id: 342599 cord_uid: 558yn6pu file: cache/cord-342681-pqzcy9wu.json key: cord-342681-pqzcy9wu authors: Pongpirul, Wannarat A.; Mott, Joshua A.; Woodring, Joseph V.; Uyeki, Timothy M.; MacArthur, John R.; Vachiraphan, Apichart; Suwanvattana, Pawita; Uttayamakul, Sumonmal; Chunsuttiwat, Supamit; Chotpitayasunondh, Tawee; Pongpirul, Krit; Prasithsirikul, Wisit title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid2607.200598 sha: doc_id: 342681 cord_uid: pqzcy9wu file: cache/cord-342361-eu3rry7p.json key: cord-342361-eu3rry7p authors: Lu, Jiatao; Hu, Shufang; Fan, Rong; Liu, Zhihong; Yin, Xueru; Wang, Qiongya; Lv, Qingquan; Cai, Zhifang; Li, Haijun; Hu, Yuhai; Han, Ying; Hu, Hongping; Gao, Wenyong; Feng, Shibo; Liu, Qiongfang; Li, Hui; Sun, Jian; Peng, Jie; Yi, Xuefeng; Zhou, Zixiao; Guo, Yabing; Hou, Jinlin title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China date: 2020-02-23 journal: nan DOI: 10.1101/2020.02.20.20025510 sha: doc_id: 342361 cord_uid: eu3rry7p file: cache/cord-342294-x18xmrji.json key: cord-342294-x18xmrji authors: Yan, Nao; Wang, Wei; Gao, Yongzhe; Zhou, Junhui; Ye, Jiuhong; Xu, Zhipeng; Cao, Jing; Zhang, Junjian title: Medium Term Follow-Up of 337 Patients With Coronavirus Disease 2019 (COVID-19) in a Fangcang Shelter Hospital in Wuhan, China date: 2020-07-03 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00373 sha: doc_id: 342294 cord_uid: x18xmrji file: cache/cord-342380-lihz7h1k.json key: cord-342380-lihz7h1k authors: Meguid Kassem, Abdel; Talaat, Hala; Shawky, Shereen; Fouad, Rabab; Amer, Khaled; Elnagdy, Tarek; Hassan, Wael A.; Tantawi, Omnia; Abdelmoniem, Reham; Gaber, Yasmine; Badary, Hedy A.; Musa, Sherief title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 journal: Arab J Gastroenterol DOI: 10.1016/j.ajg.2020.07.005 sha: doc_id: 342380 cord_uid: lihz7h1k file: cache/cord-342539-o004ggon.json key: cord-342539-o004ggon authors: Lam, Tommy Tsan-Yuk title: Tracking the genomic footprints of SARS-CoV-2 transmission date: 2020-05-28 journal: Trends Genet DOI: 10.1016/j.tig.2020.05.009 sha: doc_id: 342539 cord_uid: o004ggon file: cache/cord-342456-5gp3cry0.json key: cord-342456-5gp3cry0 authors: Hoagland, Daisy A.; Clarke, Daniel J.B.; Møller, Rasmus; Han, Yuling; Yang, Liuliu; Wojciechowicz, Megan L.; Lachmann, Alexander; Oguntuyo, Kasopefoluwa Y.; Stevens, Christian; Lee, Benhur; Chen, Shuibing; Ma’ayan, Avi; tenOever, Benjamin R title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 journal: bioRxiv DOI: 10.1101/2020.07.12.199687 sha: doc_id: 342456 cord_uid: 5gp3cry0 file: cache/cord-342739-iy9vjpuh.json key: cord-342739-iy9vjpuh authors: Schwartz, David A.; Graham, Ashley L. title: Potential Maternal and Infant Outcomes from Coronavirus 2019-nCoV (SARS-CoV-2) Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections date: 2020-02-10 journal: Viruses DOI: 10.3390/v12020194 sha: doc_id: 342739 cord_uid: iy9vjpuh file: cache/cord-342938-rzhsnkn4.json key: cord-342938-rzhsnkn4 authors: Huang, Bo-Ruei; Lin, Ya-Lan; Wan, Chih-Kang; Wu, Jiin-Torng; Hsu, Chih-Yu; Chiu, Ming-Huang; Huang, Cheng-Hua title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan date: 2020-06-30 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.06.011 sha: doc_id: 342938 cord_uid: rzhsnkn4 file: cache/cord-342942-1s32o9m8.json key: cord-342942-1s32o9m8 authors: Stamatakis, George; Samiotaki, Martina; Mpakali, Anastasia; Panayotou, George; Stratikos, Efstratios title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 journal: bioRxiv DOI: 10.1101/2020.06.22.164681 sha: doc_id: 342942 cord_uid: 1s32o9m8 file: cache/cord-342951-nirue1x4.json key: cord-342951-nirue1x4 authors: Theophanous, Christos; Santoro, Jonathan; Itani, Reem title: Bell’s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-09-04 journal: Brain Dev DOI: 10.1016/j.braindev.2020.08.017 sha: doc_id: 342951 cord_uid: nirue1x4 file: cache/cord-342765-rw8valjp.json key: cord-342765-rw8valjp authors: Wacharapluesadee, Supaporn; Kaewpom, Thongchai; Ampoot, Weenassarin; Ghai, Siriporn; Khamhang, Worrawat; Worachotsueptrakun, Kanthita; Wanthong, Phanni; Nopvichai, Chatchai; Supharatpariyakorn, Thirawat; Putcharoen, Opass; Paitoonpong, Leilani; Suwanpimolkul, Gompol; Jantarabenjakul, Watsamon; Hemachudha, Pasin; Krichphiphat, Artit; Buathong, Rome; Plipat, Tanarak; Hemachudha, Thiravat title: Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19 date: 2020-05-13 journal: J Med Virol DOI: 10.1002/jmv.26005 sha: doc_id: 342765 cord_uid: rw8valjp file: cache/cord-342557-a7q8vp8m.json key: cord-342557-a7q8vp8m authors: Chowdhury, Surid Mohammad; Talukder, Shafi Ahmad; Khan, Akib Mahmud; Afrin, Nadia; Ali, Md Ackas; Islam, Rajib; Parves, Rimon; Al Mamun, Abdulla; Sufian, Md. Abu; Hossain, Md Nayeem; Hossain, Mohammed Akhter; Halim, Mohammad A. title: Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date: 2020-10-23 journal: J Phys Chem B DOI: 10.1021/acs.jpcb.0c05621 sha: doc_id: 342557 cord_uid: a7q8vp8m file: cache/cord-342569-ja96xfns.json key: cord-342569-ja96xfns authors: Azer, Samy A. title: COVID-19: Pathophysiology, diagnosis, complications and Investigational therapeutics date: 2020-08-05 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100738 sha: doc_id: 342569 cord_uid: ja96xfns file: cache/cord-342625-31fe1neb.json key: cord-342625-31fe1neb authors: Baba, Hiroaki; Kanamori, Hajime; Oshima, Kengo; Seike, Issei; Niitsuma-Sugaya, Ikumi; Takei, Kentaro; Sato, Yukio; Tokuda, Koichi; Aoyagi, Tetsuji title: Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide date: 2020-07-01 journal: J Infect Chemother DOI: 10.1016/j.jiac.2020.06.022 sha: doc_id: 342625 cord_uid: 31fe1neb file: cache/cord-342796-f7n8sxbu.json key: cord-342796-f7n8sxbu authors: Stowe, J.; Tessier, E.; Zhao, H.; Guy, R.; Muller-Pebody, B.; Zambon, M.; Andrews, N.; Ramsay, M.; Lopez Bernal, J. title: Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.18.20189647 sha: doc_id: 342796 cord_uid: f7n8sxbu file: cache/cord-342947-dhe31r3a.json key: cord-342947-dhe31r3a authors: Li, Xin; Liu, Minghui; Zhao, Qingchun; Liu, Renwang; Zhang, Hongbing; Dong, Ming; Xu, Song; Liu, Jinghao; Zhao, Honglin; Wei, Sen; Song, Zuoqing; Chen, Gang; Chen, Jun title: Preliminary recommendations for lung surgery during COVID‐19 epidemic period date: 2020-04-14 journal: Thorac Cancer DOI: 10.1111/1759-7714.13423 sha: doc_id: 342947 cord_uid: dhe31r3a file: cache/cord-343029-85ga6r7d.json key: cord-343029-85ga6r7d authors: Haghpanah, Abdolreza; Masjedi, Fatemeh; Alborzi, Saeed; Hosseinpour, Alireza; Dehghani, Anahita; Malekmakan, Leila; Roozbeh, Jamshid title: Potential mechanisms of SARS‐CoV‐2 action on male gonadal function and fertility: Current status and future prospects date: 2020-10-27 journal: Andrologia DOI: 10.1111/and.13883 sha: doc_id: 343029 cord_uid: 85ga6r7d file: cache/cord-342915-r9kv67we.json key: cord-342915-r9kv67we authors: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 journal: Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12173 sha: doc_id: 342915 cord_uid: r9kv67we file: cache/cord-343034-dzvo9v01.json key: cord-343034-dzvo9v01 authors: Chen, Chun-Fan; Chien, Chian-Hsu; Yang, Yi-Ping; Chou, Shih-Jie; Wang, Mong-Lien; Huo, The-Ia; Lin, Chih-Ching title: Role of dipeptidyl peptidase-4 inhibitors in patients with diabetes infected with coronavirus-19 date: 2020-04-29 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000338 sha: doc_id: 343034 cord_uid: dzvo9v01 file: cache/cord-342783-85b4lwh3.json key: cord-342783-85b4lwh3 authors: Prazuck, T.; Colin, M.; Giache, S.; Gubavu, C.; Seve, A.; Rzepecki, V.; Chevereau-Choquet, M.; Kiani, C.; Rodi, V.; Lyonnet, E.; Courtellemont, L.; Guinard, J.; Pialoux, G.; Hocqueloux, L. title: Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date: 2020-05-27 journal: nan DOI: 10.1101/2020.05.27.20112888 sha: doc_id: 342783 cord_uid: 85b4lwh3 file: cache/cord-342902-y1v8wzxq.json key: cord-342902-y1v8wzxq authors: Yuan, Shuofeng; Yin, Xin; Meng, XiangZhi; Chan, Jasper; Ye, Zi-Wei; Riva, Laura; Pache, Lars; Chan, Chris Chun-Yiu; Lai, Pok-Man; Chan, Chris; Poon, Vincent; Matsunaga, Naoko; Pu, Yuan; Yuen, Chun-Kit; Cao, Jianli; Liang, Ronghui; Tang, Kaiming; Sheng, Li; Du, Yushen; Xu, Wan; Sze, Kong-Hung; Zhang, Jinxia; Chu, Hin; Kok, Kin-Hang; To, Kelvin; Jin, Dong-Yan; Sun, Ren; Chanda, Sumit; Yuen, Kwok-Yung title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 journal: Res Sq DOI: 10.21203/rs.3.rs-86169/v1 sha: doc_id: 342902 cord_uid: y1v8wzxq file: cache/cord-343127-n3fs8ph8.json key: cord-343127-n3fs8ph8 authors: Pousa, Pedro A.; de Mendonça, Tamires S.C.; Oliveira, Eduardo A.; e Silva, Ana Cristina Simões title: Extrapulmonary manifestations of COVID-19 in children: a comprehensive review and pathophysiological considerations date: 2020-09-22 journal: J Pediatr (Rio J) DOI: 10.1016/j.jped.2020.08.007 sha: doc_id: 343127 cord_uid: n3fs8ph8 file: cache/cord-342660-xigv4u3f.json key: cord-342660-xigv4u3f authors: Benotmane, I.; Gautier-Vargas, G.; Wendling, M.-J.; Perrin, P.; Velay, A.; Bassand, X.; Bedo, D.; Baldacini, C.; Sagnard, M.; Bozman, D.-F.; Della-Chiesa, M.; Solis, M.; Gallais, F.; Cognard, N.; Olagne, J.; Delagreverie, H.; Gontard, L.; Panaget, B.; Marx, D.; Heibel, F.; Braun-Parvez, L.; Moulin, B.; Caillard, S.; Fafi-Kremer, S. title: In-depth virological assessment of kidney transplant recipients with COVID-19 date: 2020-06-19 journal: nan DOI: 10.1101/2020.06.17.20132076 sha: doc_id: 342660 cord_uid: xigv4u3f file: cache/cord-342983-7o0slu0z.json key: cord-342983-7o0slu0z authors: Killeen, G. F. title: A simple arithmetic rationale for crushing the epidemic curve of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) instead of flattening it date: 2020-05-10 journal: nan DOI: 10.1101/2020.05.06.20093112 sha: doc_id: 342983 cord_uid: 7o0slu0z file: cache/cord-342996-honeavwj.json key: cord-342996-honeavwj authors: Mair-Jenkins, John; Saavedra-Campos, Maria; Baillie, J. Kenneth; Cleary, Paul; Khaw, Fu-Meng; Lim, Wei Shen; Makki, Sophia; Rooney, Kevin D.; Beck, Charles R.; Nguyen-Van-Tam, Jonathan S. title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 journal: J Infect Dis DOI: 10.1093/infdis/jiu396 sha: doc_id: 342996 cord_uid: honeavwj file: cache/cord-343136-kftffes0.json key: cord-343136-kftffes0 authors: Mohon, Abu Naser; Oberding, Lisa; Hundt, Jana; van Marle, Guido; Pabbaraju, Kanti; Berenger, Byron; Lisboa, Luiz; Griener, Thomas; Czub, Markus; Doolan, Cody; Servelitta, Venice; Chiu, Charles; Greninger, Alexander; Jerome, Keith; Pillai, Dylan R. title: Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2 date: 2020-09-15 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113972 sha: doc_id: 343136 cord_uid: kftffes0 file: cache/cord-342857-vj6sw2ne.json key: cord-342857-vj6sw2ne authors: McCullough, Peter A.; Kelly, Ronan J.; Ruocco, Gaetano; Lerma, Edgar; Tumlin, James; Wheelan, Kevin; Katz, Nevin; Lepor, Norman E.; Vijay, Kris; Carter, Harvey; Singh, Bhupinder; McCullough, Sean P.; Bhambi, Brijesh K.; Palazzuoli, Alberto; De Ferrari, Gaetano M; Milligan, Gregory; Safder, Taimur; Tecson, Kristen M.; Wang, Dee Dee; McKinnon; O'Neill, William W.; Zervos, Marcus; Risch, Harvey A. title: Pathophysiological Basis and Rationale for Early Outpatient Treatment of SARS-CoV-2 (COVID-19) Infection date: 2020-08-07 journal: Am J Med DOI: 10.1016/j.amjmed.2020.07.003 sha: doc_id: 342857 cord_uid: vj6sw2ne file: cache/cord-343192-fkc7af9y.json key: cord-343192-fkc7af9y authors: Chen, Siyang; Lu, Hongjia; Liu, Zhewei; Yuan, Weiming title: Comment on “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ‐2 (SARS‐CoV‐2)” date: 2020-05-08 journal: J Med Virol DOI: 10.1002/jmv.25991 sha: doc_id: 343192 cord_uid: fkc7af9y file: cache/cord-342538-5bwsm290.json key: cord-342538-5bwsm290 authors: Izquierdo Lara, R. W.; Elsinga, G.; Heijnen, L.; Oude Munnink, B. B.; Schapendonk, C. M. E.; Nieuwenhuijse, D.; Kon, M.; Lu, L.; Aarestrup, F. M.; Lycett, S.; Medema, G.; Koopmans, M. P. G.; de Graaf, M. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 journal: nan DOI: 10.1101/2020.09.21.20198838 sha: doc_id: 342538 cord_uid: 5bwsm290 file: cache/cord-342756-rgm9ffpk.json key: cord-342756-rgm9ffpk authors: Senger, Mario Roberto; Evangelista, Tereza Cristina Santos; Dantas, Rafael Ferreira; Santana, Marcos Vinicius da Silva; Gonçalves, Luiz Carlos Saramago; de Souza Neto, Lauro Ribeiro; Ferreira, Sabrina Baptista; Silva-Junior, Floriano Paes title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 journal: Mem Inst Oswaldo Cruz DOI: 10.1590/0074-02760200254 sha: doc_id: 342756 cord_uid: rgm9ffpk file: cache/cord-343330-wuzts3mt.json key: cord-343330-wuzts3mt authors: Ramos da Silva, S.; Ju, E.; Meng, W.; Paniz Mondolfi, A. E.; Dacic, S.; Green, A.; Bryce, C.; Grimes, Z.; Fowkes, M. E.; Sordillo, E. M.; Cordon-Cardo, C.; Guo, H.; Gao, S.-J. title: Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19 date: 2020-09-29 journal: nan DOI: 10.1101/2020.09.25.20195818 sha: doc_id: 343330 cord_uid: wuzts3mt file: cache/cord-342776-hkjhqgie.json key: cord-342776-hkjhqgie authors: Jewett, Anahid title: The Potential Effect of Novel Coronavirus SARS-CoV-2 on NK Cells; A Perspective on Potential Therapeutic Interventions date: 2020-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01692 sha: doc_id: 342776 cord_uid: hkjhqgie file: cache/cord-343043-piyt3i0h.json key: cord-343043-piyt3i0h authors: Baker, S. A.; Kowk, S.; Berry, G. J.; Montine, T. 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G.; Svaerke Jorgensen, C.; Iversen, K.; Bayarri-Olmos, R.; Garred, P.; Skjoedt, M.-O. title: SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals date: 2020-07-29 journal: nan DOI: 10.1101/2020.07.27.20162321 sha: doc_id: 343185 cord_uid: lbmbp9ca file: cache/cord-343365-4y9fedcr.json key: cord-343365-4y9fedcr authors: Chang, Christopher title: Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date: 2013-11-30 journal: Clin Rev Allergy Immunol DOI: 10.1007/s12016-013-8399-2 sha: doc_id: 343365 cord_uid: 4y9fedcr file: cache/cord-343148-rp3kmd80.json key: cord-343148-rp3kmd80 authors: Ayatollahi, Parisa; Tarazi, Apameh; Wennberg, Richard title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection date: 2020-09-17 journal: The Canadian journal of neurological sciences. 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H.; Sturek, Michael; Alloosh, Mouhamad; Belsham, Graham J. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.573756 sha: doc_id: 343357 cord_uid: 5nhyumxl file: cache/cord-343618-jjb8da4a.json key: cord-343618-jjb8da4a authors: Nie, Kai; Yang, Yuan-Yuan; Deng, Min-Zi; Wang, Xiao-Yan title: Gastrointestinal insights during the COVID-19 epidemic date: 2020-09-26 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i18.3934 sha: doc_id: 343618 cord_uid: jjb8da4a file: cache/cord-343715-y594iewi.json key: cord-343715-y594iewi authors: Gavriatopoulou, Maria; Korompoki, Eleni; Fotiou, Despina; Ntanasis-Stathopoulos, Ioannis; Psaltopoulou, Theodora; Kastritis, Efstathios; Terpos, Evangelos; Dimopoulos, Meletios A. title: Organ-specific manifestations of COVID-19 infection date: 2020-07-27 journal: Clin Exp Med DOI: 10.1007/s10238-020-00648-x sha: doc_id: 343715 cord_uid: y594iewi file: cache/cord-343766-hlg7t5i5.json key: cord-343766-hlg7t5i5 authors: Vinken, Mathieu title: A putative AOP for pneumonia related to COVID-19 date: 2020-07-20 journal: Arch Toxicol DOI: 10.1007/s00204-020-02860-w sha: doc_id: 343766 cord_uid: hlg7t5i5 file: cache/cord-343566-epvswt7f.json key: cord-343566-epvswt7f authors: Wang, Zhao-Hua; Shu, Chang; Ran, Xiao; Xie, Cui-Hong; Zhang, Lei title: Critically Ill Patients with Coronavirus Disease 2019 in a Designated ICU: Clinical Features and Predictors for Mortality date: 2020-07-20 journal: Risk Manag Healthc Policy DOI: 10.2147/rmhp.s263095 sha: doc_id: 343566 cord_uid: epvswt7f file: cache/cord-343836-daqrym0b.json key: cord-343836-daqrym0b authors: Lange, Clemens; Wolf, Julian; Auw-Haedrich, Claudia; Schlecht, Anja; Boneva, Stefaniya; Lapp, Thabo; Agostini, Hansjürgen; Martin, Gottfried; Reinhard, Thomas; Schlunck, Günther title: Welche Bedeutung hat die Bindehaut als möglicher Übertragungsweg für eine SARS-CoV-2-Infektion? date: 2020-06-22 journal: Ophthalmologe DOI: 10.1007/s00347-020-01150-1 sha: doc_id: 343836 cord_uid: daqrym0b file: cache/cord-344017-qldawc8m.json key: cord-344017-qldawc8m authors: Edouard, S.; Colson, P.; Melenotte, C.; Di Pinto, F.; Thomas, L.; La Scola, B.; Million, M.; Tissot-Dupont, H.; Gautret, P.; Stein, A.; Brouqui, P.; Parola, P.; Lagier, J.-C.; Raoult, D.; Drancourt, Michel title: Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France date: 2020-11-11 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04104-2 sha: doc_id: 344017 cord_uid: qldawc8m file: cache/cord-342786-dl8vjwfn.json key: cord-342786-dl8vjwfn authors: Sattar, Yasar; Ullah, Waqas; Rauf, Hiba; ul Hassan Virk, Hafeez; Yadav, Sunita; Chowdhury, Medhat; Connerney, Michael; Mamtani, Sahil; Pahuja, Mohit; Patel, Raj D.; Mir, Tanveer; Almas, Talal; Moussa Pacha, Homam; Chadi Alraies, M title: COVID-19 Cardiovascular Epidemiology, Cellular Pathogenesis, Clinical Manifestations and Management date: 2020-07-14 journal: Int J Cardiol Heart Vasc DOI: 10.1016/j.ijcha.2020.100589 sha: doc_id: 342786 cord_uid: dl8vjwfn file: cache/cord-343870-g2v7ihud.json key: cord-343870-g2v7ihud authors: Liu, Wei; Zhu, Hai-Liang; Duan, Yongtao title: Virus-, host-, immune-based targets for COVID-19 therapy date: 2020-10-06 journal: Drug Discov Today DOI: 10.1016/j.drudis.2020.10.001 sha: doc_id: 343870 cord_uid: g2v7ihud file: cache/cord-343604-v986m9jd.json key: cord-343604-v986m9jd authors: Vijayakumar, Balaji Gowrivel; Ramesh, Deepthi; Joji, Annu; Jayachandra prakasan, Jayadharini; Kannan, Tharanikkarasu title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173448 sha: doc_id: 343604 cord_uid: v986m9jd file: cache/cord-343691-sjz5og78.json key: cord-343691-sjz5og78 authors: Nakajima, Kei title: Serious Conditions in COVID-19 Accompanied With a Feature of Metabolic Syndrome date: 2020-05-08 journal: J Clin Med Res DOI: 10.14740/jocmr4187 sha: doc_id: 343691 cord_uid: sjz5og78 file: cache/cord-343827-jo61t3m0.json key: cord-343827-jo61t3m0 authors: Qian, Qun; Fan, Lifang; Liu, Weicheng; Li, Jin; Yue, Junqiu; Wang, Mingwei; Ke, Xianliang; Yin, Yan; Chen, Quanjiao; Jiang, Congqing title: Direct evidence of active SARS-CoV-2 replication in the intestine date: 2020-07-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa925 sha: doc_id: 343827 cord_uid: jo61t3m0 file: cache/cord-343845-suoy3ojr.json key: cord-343845-suoy3ojr authors: Martín, Vicente; Fernández-Villa, Tania; de Gomez, María Lamuedra Gil; Mencía, Oscar; Rodríguez, Ana Rivero; Celada, Sofía Reguero; Gomez, Marina Montoro; Guisado, María Teresa Nuevo; Ruiz, Cristina Villa; Flecha, Cristina Díez; Carvajal, Ana; Vázquez, Jose Pedro Fernández title: Prevalencia de la Infección por SARS-CoV-2 en médicos y enfermeras de Atención Primaria y Residencias de Ancianos del Área de Salud de León y Factores asociados date: 2020-06-06 journal: Semergen DOI: 10.1016/j.semerg.2020.05.014 sha: doc_id: 343845 cord_uid: suoy3ojr file: cache/cord-343876-2inr4mcy.json key: cord-343876-2inr4mcy authors: Xie, Qin; Fan, Fang; Fan, Xue-Peng; Wang, Xiao-Jiang; Chen, Ming-Jian; Zhong, Bao-Liang; Chiu, Helen Fung-Kum title: COVID-19 patients managed in psychiatric inpatient settings due to first-episode mental disorders in Wuhan, China: clinical characteristics, treatments, outcomes, and our experiences date: 2020-10-02 journal: Transl Psychiatry DOI: 10.1038/s41398-020-01022-x sha: doc_id: 343876 cord_uid: 2inr4mcy file: cache/cord-343340-zi0rfidc.json key: cord-343340-zi0rfidc authors: Aragón‐Caqueo, Diego; Fernández‐Salinas, Javier; Laroze, David title: Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date: 2020-05-03 journal: J Med Virol DOI: 10.1002/jmv.25929 sha: doc_id: 343340 cord_uid: zi0rfidc file: cache/cord-343476-0chuwvg6.json key: cord-343476-0chuwvg6 authors: MacLean, Oscar A.; Lytras, Spyros; Singer, Joshua B.; Weaver, Steven; Pond, Sergei L. Kosakovsky; Robertson, David L. title: Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date: 2020-05-29 journal: bioRxiv DOI: 10.1101/2020.05.28.122366 sha: doc_id: 343476 cord_uid: 0chuwvg6 file: cache/cord-344006-0iq9s94n.json key: cord-344006-0iq9s94n authors: Atzrodt, Cassandra L.; Maknojia, Insha; McCarthy, Robert D.P.; Oldfield, Tiara M.; Po, Jonathan; Ta, Kenny T.L.; Stepp, Hannah E.; Clements, Thomas P. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 journal: FEBS J DOI: 10.1111/febs.15375 sha: doc_id: 344006 cord_uid: 0iq9s94n file: cache/cord-343850-p4bbb6vm.json key: cord-343850-p4bbb6vm authors: Lin, Meng-Hsuan; Chang, San-Chi; Chiu, Yi-Chih; Jiang, Bo-Chen; Wu, Tsung-Han; Hsu, Chun-Hua title: Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain date: 2020-09-18 journal: ACS Infect Dis DOI: 10.1021/acsinfecdis.0c00441 sha: doc_id: 343850 cord_uid: p4bbb6vm file: cache/cord-343966-bfon094h.json key: cord-343966-bfon094h authors: Djaparidze, L.; Lois, F. A. title: SARS-CoV-2 waves in Europe: A 2-stratum SEIRS model solution date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.09.20210146 sha: doc_id: 343966 cord_uid: bfon094h file: cache/cord-343517-vf32wxkx.json key: cord-343517-vf32wxkx authors: Lokman, Syed Mohammad; Rasheduzzaman, Md.; Salauddin, Asma; Barua, Rocktim; Tanzina, Afsana Yeasmin; Rumi, Meheadi Hasan; Hossain, Md. Imran; Siddiki, Amam Zonaed; Mannan, Adnan; Hasan, Md. Mahbub title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date: 2020-04-11 journal: bioRxiv DOI: 10.1101/2020.04.07.030924 sha: doc_id: 343517 cord_uid: vf32wxkx file: cache/cord-344120-7t5ce2hb.json key: cord-344120-7t5ce2hb authors: Baroutjian, Amanda; Sanchez, Carol; Boneva, Dessy; McKenney, Mark; Elkbuli, Adel title: SARS-CoV-2 pharmacologic therapies and their safety/effectiveness according to level of evidence date: 2020-09-01 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.08.091 sha: doc_id: 344120 cord_uid: 7t5ce2hb file: cache/cord-343757-e4hmo4yc.json key: cord-343757-e4hmo4yc authors: Velavan, Thirumalaisamy P.; Meyer, Christian G. title: The COVID‐19 epidemic date: 2020-02-16 journal: Trop Med Int Health DOI: 10.1111/tmi.13383 sha: doc_id: 343757 cord_uid: e4hmo4yc file: cache/cord-343919-n8884bli.json key: cord-343919-n8884bli authors: Salvio, Gianmaria; Gianfelice, Claudio; Firmani, Francesca; Lunetti, Stefano; Balercia, Giancarlo; Giacchetti, Gilberta title: Bone Metabolism in SARS-CoV-2 Disease: Possible Osteoimmunology and Gender Implications date: 2020-09-01 journal: Clin Rev Bone Miner Metab DOI: 10.1007/s12018-020-09274-3 sha: doc_id: 343919 cord_uid: n8884bli file: cache/cord-344012-npob20n0.json key: cord-344012-npob20n0 authors: Gheblawi, Mahmoud; Wang, Kaiming; Viveiros, Anissa; Nguyen, Quynh; Zhong, Jiu-Chang; Turner, Anthony J.; Raizada, Mohan K.; Grant, Maria B.; Oudit, Gavin Y. title: Angiotensin-Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System: Celebrating the 20th Anniversary of the Discovery of ACE2 date: 2020-05-08 journal: Circ Res DOI: 10.1161/circresaha.120.317015 sha: doc_id: 344012 cord_uid: npob20n0 file: cache/cord-344170-qrupbtem.json key: cord-344170-qrupbtem authors: Biswas, Subrata K; Mudi, Sonchita R title: Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 date: 2020-05-24 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109877 sha: doc_id: 344170 cord_uid: qrupbtem file: cache/cord-344003-oul2hdyq.json key: cord-344003-oul2hdyq authors: Maleki Dana, Parisa; Sadoughi, Fatemeh; Hallajzadeh, Jamal; Asemi, Zatollah; Mansournia, Mohammad Ali; Yousefi, Bahman; Momen-Heravi, Mansooreh title: An Insight into the Sex Differences in COVID-19 Patients: What are the Possible Causes? date: 2020-06-18 journal: Prehospital and disaster medicine DOI: 10.1017/s1049023x20000837 sha: doc_id: 344003 cord_uid: oul2hdyq file: cache/cord-343970-anocx4y1.json key: cord-343970-anocx4y1 authors: Bansal, Rashika; Gubbi, Sriram; Muniyappa, Ranganath title: Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course date: 2020-06-30 journal: Endocrinology DOI: 10.1210/endocr/bqaa112 sha: doc_id: 343970 cord_uid: anocx4y1 file: cache/cord-344356-up53a0k4.json key: cord-344356-up53a0k4 authors: Feaster, Matt; Goh, Ying-Ying title: High Proportion of Asymptomatic SARS-CoV-2 Infections in 9 Long-Term Care Facilities, Pasadena, California, USA, April 2020 date: 2020-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid2610.202694 sha: doc_id: 344356 cord_uid: up53a0k4 file: cache/cord-344213-j3yextjl.json key: cord-344213-j3yextjl authors: Sze, Shirley; Pan, Daniel; Williams, Caroline M L; Barker, Joseph; Minhas, Jatinder S; Miller, Chris; Tang, Julian W; Squire, Iain B; Pareek, Manish title: The need for improved discharge criteria for hospitalised patients with COVID-19—implications for patients in long term care facilities date: 2020-09-19 journal: Age Ageing DOI: 10.1093/ageing/afaa206 sha: doc_id: 344213 cord_uid: j3yextjl file: cache/cord-344236-qp3ianzf.json key: cord-344236-qp3ianzf authors: Ali, Fedaa; Elserafy, Menattallah; Alkordi, Mohamed H.; Amin, Muhamed title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-05-08 journal: bioRxiv DOI: 10.1101/2020.05.08.084384 sha: doc_id: 344236 cord_uid: qp3ianzf file: cache/cord-344270-874i31h8.json key: cord-344270-874i31h8 authors: Radke, Robert M; Frenzel, Tim; Baumgartner, Helmut; Diller, Gerhard-Paul title: Adult congenital heart disease and the COVID-19 pandemic date: 2020-06-10 journal: Heart DOI: 10.1136/heartjnl-2020-317258 sha: doc_id: 344270 cord_uid: 874i31h8 file: cache/cord-344364-vu389d88.json key: cord-344364-vu389d88 authors: Wang, Wei; Zhang, Wei; Zhang, Jingjing; He, Ji; Zhu, Faming title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 journal: HLA DOI: 10.1111/tan.13941 sha: doc_id: 344364 cord_uid: vu389d88 file: cache/cord-344204-qq2vqzc2.json key: cord-344204-qq2vqzc2 authors: Hariharan, Apurva; Hakeem, Abdul Rahman; Radhakrishnan, Subathra; Reddy, Mettu Srinivas; Rela, Mohamed title: The Role and Therapeutic Potential of NF-kappa-B Pathway in Severe COVID-19 Patients date: 2020-11-07 journal: Inflammopharmacology DOI: 10.1007/s10787-020-00773-9 sha: doc_id: 344204 cord_uid: qq2vqzc2 file: cache/cord-343808-uqhiyj56.json key: cord-343808-uqhiyj56 authors: Kuo, Hsiao-I.; Chen, Chi-Chung; Tseng, Wei-Chun; Ju, Lan-Fen; Huang, Bing-Wen title: Assessing impacts of SARS and Avian Flu on international tourism demand to Asia date: 2008-01-07 journal: Tour Manag DOI: 10.1016/j.tourman.2007.10.006 sha: doc_id: 343808 cord_uid: uqhiyj56 file: cache/cord-344180-v8xs5ej8.json key: cord-344180-v8xs5ej8 authors: Vadlamani, Bhaskar S.; Uppal, Timsy; Verma, Subhash C.; Misra, Mano title: Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-10-17 journal: Sensors (Basel) DOI: 10.3390/s20205871 sha: doc_id: 344180 cord_uid: v8xs5ej8 file: cache/cord-344316-mwnnmwnw.json key: cord-344316-mwnnmwnw authors: Herst, C.V.; Burkholz, S.; Sidney, J.; Sette, A.; Harris, P.E.; Massey, S.; Brasel, T.; Cunha-Neto, E.; Rosa, D.S.; Chao, W.C.H.; Carback, R.; Hodge, T.; Wang, L.; Ciotlos, S.; Lloyd, P.; Rubsamen, R. title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design date: 2020-04-28 journal: Vaccine DOI: 10.1016/j.vaccine.2020.04.034 sha: doc_id: 344316 cord_uid: mwnnmwnw file: cache/cord-344038-20n74z3o.json key: cord-344038-20n74z3o authors: Han, Mi Seon; Seong, Moon-Woo; Heo, Eun Young; Park, Ji Hong; Kim, Namhee; Shin, Sue; Cho, Sung Im; Park, Sung Sup; Choi, Eun Hwa title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa447 sha: doc_id: 344038 cord_uid: 20n74z3o file: cache/cord-344419-3wcfpw2z.json key: cord-344419-3wcfpw2z authors: Niedzwiedz, C. L.; O'Donnell, C. A.; Jani, B. D.; Demou, E.; Ho, F. K.; Celis-Morales, C.; Nicholl, B. I.; Mair, F.; Welsh, P.; Sattar, N.; Pell, J.; Katikireddi, S. V. title: Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study date: 2020-04-27 journal: nan DOI: 10.1101/2020.04.22.20075663 sha: doc_id: 344419 cord_uid: 3wcfpw2z file: cache/cord-344064-l3u4l3se.json key: cord-344064-l3u4l3se authors: Ghosh, Rajesh; Chakraborty, Ayon; Biswas, Ashis; Chowdhuri, Snehasis title: Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves date: 2020-11-03 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1841680 sha: doc_id: 344064 cord_uid: l3u4l3se file: cache/cord-344454-hs3tthzi.json key: cord-344454-hs3tthzi authors: nan title: Les animaux contaminés par le SARS-CoV-2 représentent-ils un risque pour l’Homme ? date: 2020-09-15 journal: Bull Acad Natl Med DOI: 10.1016/j.banm.2020.09.010 sha: doc_id: 344454 cord_uid: hs3tthzi file: cache/cord-343864-0258nh92.json key: cord-343864-0258nh92 authors: Straughn, Alex R.; Kakar, Sham S. title: Withaferin A: a potential therapeutic agent against COVID-19 infection date: 2020-07-19 journal: J Ovarian Res DOI: 10.1186/s13048-020-00684-x sha: doc_id: 343864 cord_uid: 0258nh92 file: cache/cord-344266-ug2uew71.json key: cord-344266-ug2uew71 authors: Crema, E. title: The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission date: 2020-08-07 journal: nan DOI: 10.1101/2020.08.06.20169433 sha: doc_id: 344266 cord_uid: ug2uew71 file: cache/cord-344330-zsx7wfyj.json key: cord-344330-zsx7wfyj authors: Su, Shuo; Wong, Gary; Shi, Weifeng; Liu, Jun; Lai, Alexander C.K.; Zhou, Jiyong; Liu, Wenjun; Bi, Yuhai; Gao, George F. title: Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses date: 2016-03-21 journal: Trends Microbiol DOI: 10.1016/j.tim.2016.03.003 sha: doc_id: 344330 cord_uid: zsx7wfyj file: cache/cord-344714-0cam9ipf.json key: cord-344714-0cam9ipf authors: Russo, Maria; Moccia, Stefania; Spagnuolo, Carmela; Tedesco, Idolo; Russo, Gian Luigi title: Roles of flavonoids against coronavirus infection date: 2020-07-28 journal: Chem Biol Interact DOI: 10.1016/j.cbi.2020.109211 sha: doc_id: 344714 cord_uid: 0cam9ipf file: cache/cord-343818-pj1oludh.json key: cord-343818-pj1oludh authors: Liu, Chan; He, Yu; Liu, Lian; Li, Fang; Shi, Yuan title: Children with COVID-19 behaving milder may challenge the public policies: a systematic review and meta-analysis date: 2020-09-01 journal: BMC Pediatr DOI: 10.1186/s12887-020-02316-1 sha: doc_id: 343818 cord_uid: pj1oludh file: cache/cord-344217-kci4uw7u.json key: cord-344217-kci4uw7u authors: Majid, Sabhiya; Farooq, Rabia; Khan, Mosin S.; Rashid, Samia; Bhat, Showkat A.; Wani, Hilal A.; Qureshi, Waseem title: Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses date: 2020-08-25 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00457-z sha: doc_id: 344217 cord_uid: kci4uw7u file: cache/cord-344227-rdlinzrn.json key: cord-344227-rdlinzrn authors: Gralinski, Lisa E.; Sheahan, Timothy P.; Morrison, Thomas E.; Menachery, Vineet D.; Jensen, Kara; Leist, Sarah R.; Whitmore, Alan; Heise, Mark T.; Baric, Ralph S. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 journal: mBio DOI: 10.1128/mbio.01753-18 sha: doc_id: 344227 cord_uid: rdlinzrn file: cache/cord-344614-5zcylf6k.json key: cord-344614-5zcylf6k authors: Moriconi, Diego; Masi, Stefano; Rebelos, Eleni; Virdis, Agostino; Manca, Maria Laura; De Marco, Salvatore; Taddei, Stefano; Nannipieri, Monica title: Obesity prolongs the hospital stay in patients affected by COVID-19, and may impact on SARS-COV-2 shedding date: 2020-06-04 journal: Obes Res Clin Pract DOI: 10.1016/j.orcp.2020.05.009 sha: doc_id: 344614 cord_uid: 5zcylf6k file: cache/cord-344901-mgnaprgt.json key: cord-344901-mgnaprgt authors: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 journal: Ophthalmologe DOI: 10.1007/s00347-020-01097-3 sha: doc_id: 344901 cord_uid: mgnaprgt file: cache/cord-344909-0o55l4iy.json key: cord-344909-0o55l4iy authors: Cross, Robert W.; Prasad, Abhishek N.; Borisevich, Viktoriya; Woolsey, Courtney; Agans, Krystle N.; Deer, Daniel J.; Dobias, Natalie S.; Geisbert, Joan B.; Fenton, Karla A.; Geisbert, Thomas W. title: Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date: 2020-10-14 journal: bioRxiv DOI: 10.1101/2020.10.14.340091 sha: doc_id: 344909 cord_uid: 0o55l4iy file: cache/cord-344070-17oac3bg.json key: cord-344070-17oac3bg authors: Silverman, Justin D; Hupert, Nathaniel; Washburne, Alex D title: Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date: 2020-04-03 journal: nan DOI: 10.1101/2020.04.01.20050542 sha: doc_id: 344070 cord_uid: 17oac3bg file: cache/cord-344778-2p1mm3vg.json key: cord-344778-2p1mm3vg authors: Gasparri, Maria Luisa; Gentilini, Oreste Davide; Lueftner, Diana; Kuehn, Thorsten; Kaidar-Person, Orit; Poortmans, Philip title: Changes in breast cancer management during the Corona Virus Disease 19 pandemic: an international survey of the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) date: 2020-05-29 journal: Breast DOI: 10.1016/j.breast.2020.05.006 sha: doc_id: 344778 cord_uid: 2p1mm3vg file: cache/cord-344829-adlp2rjy.json key: cord-344829-adlp2rjy authors: de Rivero Vaccari, Juan Carlos; Dietrich, W. Dalton; Keane, Robert W.; de Rivero Vaccari, Juan Pablo title: The Inflammasome in Times of COVID-19 date: 2020-10-08 journal: Front Immunol DOI: 10.3389/fimmu.2020.583373 sha: doc_id: 344829 cord_uid: adlp2rjy file: cache/cord-344853-s2p2csrx.json key: cord-344853-s2p2csrx authors: Hendren, Nicholas S.; Drazner, Mark H.; Bozkurt, Biykem; Cooper, Leslie T. title: Description and Proposed Management of the Acute COVID-19 Cardiovascular Syndrome date: 2020-04-16 journal: Circulation DOI: 10.1161/circulationaha.120.047349 sha: doc_id: 344853 cord_uid: s2p2csrx file: cache/cord-344647-jr85915d.json key: cord-344647-jr85915d authors: Joseph, Adrien; Zafrani, Lara; Mabrouki, Asma; Azoulay, Elie; Darmon, Michael title: Acute kidney injury in patients with SARS-CoV-2 infection date: 2020-09-03 journal: Ann Intensive Care DOI: 10.1186/s13613-020-00734-z sha: doc_id: 344647 cord_uid: jr85915d file: cache/cord-344246-sf9cymhc.json key: cord-344246-sf9cymhc authors: Diriba, Kuma; Awulachew, Ephrem; Getu, Eyob title: The effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and the possibility of vertical maternal–fetal transmission: a systematic review and meta-analysis date: 2020-09-04 journal: Eur J Med Res DOI: 10.1186/s40001-020-00439-w sha: doc_id: 344246 cord_uid: sf9cymhc file: cache/cord-344751-i4qnrtjq.json key: cord-344751-i4qnrtjq authors: Van Praet, Jens T.; Coene, Ann-Sofie; Van De Moortele, Kris; Descheemaeker, Patrick; Reynders, Marijke title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 journal: Infection DOI: 10.1007/s15010-020-01523-3 sha: doc_id: 344751 cord_uid: i4qnrtjq file: cache/cord-344949-9zyz4hll.json key: cord-344949-9zyz4hll authors: Luban, Jeremy; Sattler, Rachel; Mühlberger, Elke; Graci, Jason D.; Cao, Liangxian; Weetall, Marla; Trotta, Christopher; Colacino, Joseph M.; Bavari, Sina; Strambio-De-Castillia, Caterina; Suder, Ellen L.; Wang, Yetao; Soloveva, Veronica; Cintron-Lue, Katherine; Naryshkin, Nikolai A.; Pykett, Mark; Welch, Ellen M.; O’Keefe, Kylie; Kong, Ronald; Goodwin, Elizabeth; Jacobson, Allan; Paessler, Slobodan; Peltz, Stuart title: The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date: 2020-08-05 journal: bioRxiv DOI: 10.1101/2020.08.05.238394 sha: doc_id: 344949 cord_uid: 9zyz4hll file: cache/cord-344970-ud1lhkyi.json key: cord-344970-ud1lhkyi authors: Fecchi, Katia; Anticoli, Simona; Peruzzu, Daniela; Iessi, Elisabetta; Gagliardi, Maria Cristina; Matarrese, Paola; Ruggieri, Anna title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01821 sha: doc_id: 344970 cord_uid: ud1lhkyi file: cache/cord-344383-7s4gnxs4.json key: cord-344383-7s4gnxs4 authors: Tee, Augustine K.H.; Oh, Helen M.L.; Hui, K.P.; Lien, Christopher T.C.; Narendran, K.; Heng, B.H.; Ling, A.E. title: Atypical SARS in Geriatric Patient date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030322 sha: doc_id: 344383 cord_uid: 7s4gnxs4 file: cache/cord-344446-5d7yuoz1.json key: cord-344446-5d7yuoz1 authors: Naughton, Sean X.; Raval, Urdhva; Harary, Joyce M.; Pasinetti, Giulio M. title: The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection date: 2020-05-12 journal: J Expo Sci Environ Epidemiol DOI: 10.1038/s41370-020-0232-4 sha: doc_id: 344446 cord_uid: 5d7yuoz1 file: cache/cord-344658-4z2697q6.json key: cord-344658-4z2697q6 authors: Hutasoit, Novana; Kennedy, Byron; Hamilton, Stephanie; Luttick, Angela; Abdul Rahman Rashid, Rizwan; Palanisamy, Suresh title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology date: 2020-08-29 journal: Manuf Lett DOI: 10.1016/j.mfglet.2020.08.007 sha: doc_id: 344658 cord_uid: 4z2697q6 file: cache/cord-344486-iu5flbcl.json key: cord-344486-iu5flbcl authors: Chiotos, Kathleen; Hayes, Molly; Kimberlin, David W; Jones, Sarah B; James, Scott H; Pinninti, Swetha G; Yarbrough, April; Abzug, Mark J; MacBrayne, Christine E; Soma, Vijaya L; Dulek, Daniel E; Vora, Surabhi B; Waghmare, Alpana; Wolf, Joshua; Olivero, Rosemary; Grapentine, Steven; Wattier, Rachel L; Bio, Laura; Cross, Shane J; Dillman, Nicholas O; Downes, Kevin J; Oliveira, Carlos R; Timberlake, Kathryn; Young, Jennifer; Orscheln, Rachel C; Tamma, Pranita D; Schwenk, Hayden T; Zachariah, Philip; Aldrich, Margaret L; Goldman, David L; Groves, Helen E; Rajapakse, Nipunie S; Lamb, Gabriella S; Tribble, Alison C; Hersh, Adam L; Thorell, Emily A; Denison, Mark R; Ratner, Adam J; Newland, Jason G; Nakamura, Mari M title: Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2 date: 2020-09-12 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piaa115 sha: doc_id: 344486 cord_uid: iu5flbcl file: cache/cord-344382-vge4ho2v.json key: cord-344382-vge4ho2v authors: De Flora, Silvio; Balansky, Roumen; La Maestra, Sebastiano title: Rationale for the use of N‐acetylcysteine in both prevention and adjuvant therapy of COVID‐19 date: 2020-08-11 journal: FASEB J DOI: 10.1096/fj.202001807 sha: doc_id: 344382 cord_uid: vge4ho2v file: cache/cord-344884-dcoq9srf.json key: cord-344884-dcoq9srf authors: El Otmani, H.; Moutaouakil, F. title: Neuro-COVID-19: What are we talking about? date: 2020-06-06 journal: Rev Neurol (Paris) DOI: 10.1016/j.neurol.2020.05.004 sha: doc_id: 344884 cord_uid: dcoq9srf file: cache/cord-345033-guisyj11.json key: cord-345033-guisyj11 authors: Massarotti, Claudia; Garolla, Andrea; Maccarini, Elena; Scaruffi, Paola; Stigliani, Sara; Anserini, Paola; Foresta, Carlo title: SARS‐CoV‐2 in the semen: where does it come from? date: 2020-06-13 journal: Andrology DOI: 10.1111/andr.12839 sha: doc_id: 345033 cord_uid: guisyj11 file: cache/cord-345019-i7zm9bt1.json key: cord-345019-i7zm9bt1 authors: Al-Waleedi, Ali Ahmed; Naiene, Jeremias D.; Thabet, Ahmed A. K.; Dandarawe, Adham; Salem, Hanan; Mohammed, Nagat; Al Noban, Maysa; Bin-Azoon, Nasreen Salem; Shawqi, Ammar; Rajamanar, Mohammed; Al-Jariri, Riyadh; Al Hyubaishi, Mansoor; Khanbari, Lina; Thabit, Najib; Obaid, Basel; Baaees, Manal; Assaf, Denise; Senga, Mikiko; Bashir, Ismail Mahat; Mahmoud, Nuha; Cosico, Roy; Smith, Philip; Musani, Altaf title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241260 sha: doc_id: 345019 cord_uid: i7zm9bt1 file: cache/cord-345103-b2wkm03g.json key: cord-345103-b2wkm03g authors: Yao, Hangping; Song, Yutong; Chen, Yong; Wu, Nanping; Xu, Jialu; Sun, Chujie; Zhang, Jiaxing; Weng, Tianhao; Zhang, Zheyuan; Wu, Zhigang; Cheng, Linfang; Shi, Danrong; Lu, Xiangyun; Lei, Jianlin; Crispin, Max; Shi, Yigong; Li, Lanjuan; Li, Sai title: Molecular architecture of the SARS-CoV-2 virus date: 2020-09-06 journal: Cell DOI: 10.1016/j.cell.2020.09.018 sha: doc_id: 345103 cord_uid: b2wkm03g file: cache/cord-345183-80rflm7u.json key: cord-345183-80rflm7u authors: Moore, Nicholas M.; Li, Haiying; Schejbal, Debra; Lindsley, Jennifer; Hayden, Mary K. title: Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2 date: 2020-07-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00938-20 sha: doc_id: 345183 cord_uid: 80rflm7u file: cache/cord-344979-ngujhhp6.json key: cord-344979-ngujhhp6 authors: Lübke, Nadine; Senff, Tina; Scherger, Sara; Hauka, Sandra; Andrée, Marcel; Adams, Ortwin; Timm, Jörg; Walker, Andreas title: Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials date: 2020-08-05 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104579 sha: doc_id: 344979 cord_uid: ngujhhp6 file: cache/cord-344636-go5cw92q.json key: cord-344636-go5cw92q authors: Huang, Wei E.; Lim, Boon; Hsu, Chia‐Chen; Xiong, Dan; Wu, Wei; Yu, Yejiong; Jia, Huidong; Wang, Yun; Zeng, Yida; Ji, Mengmeng; Chang, Hong; Zhang, Xiuming; Wang, Hui; Cui, Zhanfeng title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13586 sha: doc_id: 344636 cord_uid: go5cw92q file: cache/cord-344967-t88pedeb.json key: cord-344967-t88pedeb authors: Tang, Hon Lok; Cheuk, Au; Chu, Kwok Hong; Lee, William; Wong, Sze Ho; Cheng, Yuk Lun; Yu, Alex Wai Yin; Fung, Ka Shun; Tsang, Wai Kay; Chan, Hilda Wai Han; Tong, Kwok Lung title: Severe acute respiratory syndrome in haemodialysis patients: a report of two cases date: 2003-10-17 journal: Nephrol Dial Transplant DOI: 10.1093/ndt/gfg454 sha: doc_id: 344967 cord_uid: t88pedeb file: cache/cord-344934-m0q7rm6z.json key: cord-344934-m0q7rm6z authors: Mahapatra, Sovesh; Nath, Prathul; Chatterjee, Manisha; Das, Neeladrisingha; Kalita, Deepjyoti; Roy, Partha; Satapathi, Soumitra title: Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking date: 2020-04-07 journal: nan DOI: 10.1101/2020.04.05.20054254 sha: doc_id: 344934 cord_uid: m0q7rm6z file: cache/cord-344798-q34j4zxu.json key: cord-344798-q34j4zxu authors: Villalba, María Caridad Montalvo; Ramirez, Odalys Valdés; Jiménez, Mayra Muné; Garcia, Amely Arencibia; Alfonso, Javier Martinez; Baez, Guelsy González; Arrieta, Rosmery Roque; Simón, Dianelvys Rosell; Gainza, Delmis Alvárez; Vazquez, Beatriz Sierra; Aguirre, Sonia Resik; Tirado, Maria Guadalupe Guzmán title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients date: 2020-08-29 journal: Clin Immunol DOI: 10.1016/j.clim.2020.108576 sha: doc_id: 344798 cord_uid: q34j4zxu file: cache/cord-345092-1ztfcpsb.json key: cord-345092-1ztfcpsb authors: Iwasaki, Masae; Saito, Junichi; Zhao, Hailin; Sakamoto, Atsuhiro; Hirota, Kazuyoshi; Ma, Daqing title: Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications date: 2020-10-08 journal: Inflammation DOI: 10.1007/s10753-020-01337-3 sha: doc_id: 345092 cord_uid: 1ztfcpsb file: cache/cord-345275-h0hvaxgx.json key: cord-345275-h0hvaxgx authors: Sun, Mengyao; Xu, Yinghui; He, Hua; Zhang, Li; Wang, Xu; Qiu, Qing; Sun, Chao; Guo, Ye; Qiu, Shi; Ma, Kewei title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.107 sha: doc_id: 345275 cord_uid: h0hvaxgx file: cache/cord-345405-ngpsgn63.json key: cord-345405-ngpsgn63 authors: Tremiliosi, Guilherme C.; Simoes, Luiz Gustavo P.; Minozzi, Daniel T.; Santos, Renato I.; Vilela, Daiane C. B.; Durigon, Edison Luiz; Machado, Rafael Rahal Guaragna; Medina, Douglas Sales; Ribeiro, Lara Kelly; Rosa, Ieda Lucia Viana; Assis, Marcelo; Andrés, Juan; Longo, Elson; Freitas-Junior, Lucio H. title: Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date: 2020-06-26 journal: bioRxiv DOI: 10.1101/2020.06.26.152520 sha: doc_id: 345405 cord_uid: ngpsgn63 file: cache/cord-345296-4z7yfj5s.json key: cord-345296-4z7yfj5s authors: Ho, Mei-Shang; Chen, Wei-Ju; Chen, Hour-Young; Lin, Szu-Fong; Wang, Min-Chin; Di, Jiali; Lu, Yen-Ta; Liu, Ching-Lung; Chang, Shan-Chwen; Chao, Chung-Liang; King, Chwan-Chuen; Chiou, Jeng-Min; Su, Ih-Jen; Yang, Jyh-Yuan title: Neutralizing Antibody Response and SARS Severity date: 2005-11-17 journal: Emerg Infect Dis DOI: 10.3201/eid1111.040659 sha: doc_id: 345296 cord_uid: 4z7yfj5s file: cache/cord-345288-qyz83xx2.json key: cord-345288-qyz83xx2 authors: Pata, Francesco; Bondurri, Andrea; Ferrara, Francesco; Parini, Dario; Rizzo, Gianluca title: Enteral stoma care during COVID‐19 pandemic: practical advice date: 2020-07-21 journal: Colorectal Dis DOI: 10.1111/codi.15279 sha: doc_id: 345288 cord_uid: qyz83xx2 file: cache/cord-344842-9cfbb7p6.json key: cord-344842-9cfbb7p6 authors: Coppola, Maurizio; Mondola, Raffaella title: Potential Unconventional Medicines for the Treatment of SARS-CoV-2 date: 2020-05-19 journal: Drug Res (Stuttg) DOI: 10.1055/a-1170-4624 sha: doc_id: 344842 cord_uid: 9cfbb7p6 file: cache/cord-345139-gyvlikye.json key: cord-345139-gyvlikye authors: Izquierdo-Domínguez, Adriana; Rojas-Lechuga, María Jesús; Mullol, Joaquim; Alobid, Isam title: Pérdida del sentido del olfato durante la pandemia COVID-19 date: 2020-06-12 journal: Med Clin (Barc) DOI: 10.1016/j.medcli.2020.06.006 sha: doc_id: 345139 cord_uid: gyvlikye file: cache/cord-345381-9cckppk2.json key: cord-345381-9cckppk2 authors: Klimek, Ludger; Pfaar, Oliver; Worm, Margitta; Eiwegger, Thomas; Hagemann, Jan; Ollert, Markus; Untersmayr, Eva; Hoffmann-Sommergruber, Karin; Vultaggio, Alessandra; Agache, Ioana; Bavbek, Sevim; Bossios, Apostolos; Casper, Ingrid; Chan, Susan; Chatzipetrou, Alexia; Vogelberg, Christian; Firinu, Davide; Kauppi, Paula; Kolios, Antonios; Kothari, Akash; Matucci, Andrea; Palomares, Oscar; Szépfalusi, Zsolt; Pohl, Wolfgang; Hötzenecker, Wolfram; Rosenkranz, Alexander R.; Bergmann, Karl-Christian; Bieber, Thomas; Buhl, Roland; Buters, Jeroen; Darsow, Ulf; Keil, Thomas; Kleine-Tebbe, Jörg; Lau, Susanne; Maurer, Marcus; Merk, Hans; Mösges, Ralph; Saloga, Joachim; Staubach, Petra; Jappe, Uta; Rabe, Klaus F.; Rabe, Uta; Vogelmeier, Claus; Biedermann, Tilo; Jung, Kirsten; Schlenter, Wolfgang; Ring, Johannes; Chaker, Adam; Wehrmann, Wolfgang; Becker, Sven; Freudelsperger, Laura; Mülleneisen, Norbert; Nemat, Katja; Czech, Wolfgang; Wrede, Holger; Brehler, Randolf; Fuchs, Thomas; Tomazic, Peter-Valentin; Aberer, Werner; Fink-Wagner, Antje-Henriette; Horak, Fritz; Wöhrl, Stefan; Niederberger-Leppin, Verena; Pali-Schöll, Isabella; Pohl, Wolfgang; Roller-Wirnsberger, Regina; Spranger, Otto; Valenta, Rudolf; Akdis, Mübecell; Matricardi, Paolo M.; Spertini, François; Khaltaev, Nicolai; Michel, Jean-Pierre; Nicod, Larent; Schmid-Grendelmeier, Peter; Idzko, Marco; Hamelmann, Eckard; Jakob, Thilo; Werfel, Thomas; Wagenmann, Martin; Taube, Christian; Jensen-Jarolim, Erika; Korn, Stephanie; Hentges, Francois; Schwarze, Jürgen; O´Mahony, Liam; Knol, Edward F.; del Giacco, Stefano; Chivato Pérez, Tomás; Bousquet, Jean; Bedbrook, Anna; Zuberbier, Torsten; Akdis, Cezmi; Jutel, Marek title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-09-07 journal: Allergol Select DOI: 10.5414/alx02166e sha: doc_id: 345381 cord_uid: 9cckppk2 file: cache/cord-345603-mirsz6m8.json key: cord-345603-mirsz6m8 authors: Wehrhahn, Michael C.; Robson, Jennifer; Brown, Suzanne; Bursle, Evan; Byrne, Shane; New, David; Chong, Smathi; Newcombe, James P.; Siversten, Terri; Hadlow, Narelle title: Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic date: 2020-05-04 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104417 sha: doc_id: 345603 cord_uid: mirsz6m8 file: cache/cord-345304-n74m5ucs.json key: cord-345304-n74m5ucs authors: Safadi, Marco Aurelio Palazzi; da Silva, Clovis Artur Almeida title: THE CHALLENGING AND UNPREDICTABLE SPECTRUM OF COVID-19 IN CHILDREN AND ADOLESCENTS date: 2020-09-07 journal: Rev Paul Pediatr DOI: 10.1590/1984-0462/2020/38/2020192 sha: doc_id: 345304 cord_uid: n74m5ucs file: cache/cord-345356-gn1iwis0.json key: cord-345356-gn1iwis0 authors: Glebov, Oleg O. title: Understanding SARS‐CoV‐2 endocytosis for COVID‐19 drug repurposing date: 2020-06-02 journal: FEBS J DOI: 10.1111/febs.15369 sha: doc_id: 345356 cord_uid: gn1iwis0 file: cache/cord-345827-yo3uq03v.json key: cord-345827-yo3uq03v authors: Antiochia, Riccarda title: Developments in biosensors for CoV detection and future trends date: 2020-10-28 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112777 sha: doc_id: 345827 cord_uid: yo3uq03v file: cache/cord-345371-pjbviagq.json key: cord-345371-pjbviagq authors: Lisi, Lucia; Lacal, Pedro Miguel; Barbaccia, Maria Luisa; Graziani, Grazia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 journal: Biochem Pharmacol DOI: 10.1016/j.bcp.2020.114169 sha: doc_id: 345371 cord_uid: pjbviagq file: cache/cord-345841-pq5f82gf.json key: cord-345841-pq5f82gf authors: PATBERG, Elizabeth T.; ADAMS, Tracy; REKAWEK, Patricia; VAHANIAN, Sevan A.; AKERMAN, Meredith; HERNANDEZ, Andrea; RAPKIEWICZ, Amy V.; RAGOLIA, Louis; SICURANZA, Genevieve; CHAVEZ, Martin R.; VINTZILEOS, Anthony M.; KHULLAR, Poonam title: COVID-19 Infection and Placental Histopathology in Women Delivering at Term date: 2020-10-19 journal: Am J Obstet Gynecol DOI: 10.1016/j.ajog.2020.10.020 sha: doc_id: 345841 cord_uid: pq5f82gf file: cache/cord-345101-h0i5o0do.json key: cord-345101-h0i5o0do authors: Koo, Bon-Sang; Oh, Hanseul; Kim, Green; Hwang, Eun-Ha; Jung, Hoyin; Lee, Youngjeon; Kang, Philyong; Park, Jae-Hak; Ryu, Choong-Min; Hong, Jung Joo title: Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date: 2020-08-03 journal: J Infect Dis DOI: 10.1093/infdis/jiaa486 sha: doc_id: 345101 cord_uid: h0i5o0do file: cache/cord-345299-4k7qymqd.json key: cord-345299-4k7qymqd authors: Xiong, Hua-Long; Cao, Jia-Li; Shen, Chen-Guang; Ma, Jian; Qiao, Xiao-Yang; Shi, Tian-Shu; Yang, Yang; Ge, Sheng-Xiang; Zhang, Jun; Zhang, Tian-Ying; Yuan, Quan; Xia, Ning-Shao title: Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date: 2020-06-05 journal: bioRxiv DOI: 10.1101/2020.06.05.135996 sha: doc_id: 345299 cord_uid: 4k7qymqd file: cache/cord-345679-ydwcp75s.json key: cord-345679-ydwcp75s authors: Younas, Amber; Waheed, Samra; Khawaja, Shabnum; Imam, Mehjabeen; Borhany, Munira; Shamsi, Tahir title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN date: 2020-08-24 journal: Transfus Apher Sci DOI: 10.1016/j.transci.2020.102923 sha: doc_id: 345679 cord_uid: ydwcp75s file: cache/cord-345014-qp13h0un.json key: cord-345014-qp13h0un authors: Stein, Richard Albert title: The 2019 coronavirus: Learning curves, lessons, and the weakest link date: 2020-03-13 journal: Int J Clin Pract DOI: 10.1111/ijcp.13488 sha: doc_id: 345014 cord_uid: qp13h0un file: cache/cord-345106-5szz1et3.json key: cord-345106-5szz1et3 authors: Bhattacharya, D. D.; Parai, D. D.; Rout, U. K.; Nanda, R. R.; Kanungo, D. S.; Dash, D. G. C.; Palo, D. S. K.; Giri, D. S.; Choudhary, H. R.; Kshatri, D. J. S.; Turuk, D. J.; Mishra, D. B.; Dash, D. S.; Pati, D. S. title: Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2 date: 2020-09-11 journal: nan DOI: 10.1101/2020.09.11.20192591 sha: doc_id: 345106 cord_uid: 5szz1et3 file: cache/cord-345499-hq5um68k.json key: cord-345499-hq5um68k authors: Xiong, Rui; Zhang, Leike; Li, Shiliang; Sun, Yuan; Ding, Minyi; Wang, Yong; Zhao, Yongliang; Wu, Yan; Shang, Weijuan; Jiang, Xiaming; Shan, Jiwei; Shen, Zihao; Tong, Yi; Xu, Liuxin; Yu, Chen; Liu, Yingle; Zou, Gang; Lavillete, Dimitri; Zhao, Zhenjiang; Wang, Rui; Zhu, Lili; Xiao, Gengfu; Lan, Ke; Li, Honglin; Xu, Ke title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date: 2020-03-12 journal: bioRxiv DOI: 10.1101/2020.03.11.983056 sha: doc_id: 345499 cord_uid: hq5um68k file: cache/cord-345864-87b5qdjx.json key: cord-345864-87b5qdjx authors: Rudolph, James L.; Halladay, Christopher W.; Barber, Malisa; McCongehy, Kevin; Mor, Vince; Nanda, Aman; Gravenstein, Stefan title: Temperature in Nursing Home Residents Systematically Tested for SARS-CoV-2 date: 2020-06-09 journal: J Am Med Dir Assoc DOI: 10.1016/j.jamda.2020.06.009 sha: doc_id: 345864 cord_uid: 87b5qdjx file: cache/cord-345929-z7yfegr5.json key: cord-345929-z7yfegr5 authors: Thakur, Suman S. title: Proteomics and Its Application in Pandemic Diseases date: 2020-11-06 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00824 sha: doc_id: 345929 cord_uid: z7yfegr5 file: cache/cord-345529-f12v6bp0.json key: cord-345529-f12v6bp0 authors: Pan, Q.; Gao, F.; Peng, R.; Li, M. title: Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China date: 2020-06-18 journal: nan DOI: 10.1101/2020.06.16.20133199 sha: doc_id: 345529 cord_uid: f12v6bp0 file: cache/cord-345628-a4c46m2w.json key: cord-345628-a4c46m2w authors: Unudurthi, Sathya D.; Luthra, Priya; Bose, Rajendran J.C.; McCarthy, Jason; Kontaridis, Maria Irene title: Cardiac inflammation in COVID-19: Lessons from heart failure date: 2020-09-21 journal: Life Sci DOI: 10.1016/j.lfs.2020.118482 sha: doc_id: 345628 cord_uid: a4c46m2w file: cache/cord-345854-f0dq94j1.json key: cord-345854-f0dq94j1 authors: Chong, Wai Po; Ip, WK Eddie; Tso, Gloria Hoi Wan; Ng, Man Wai; Wong, Wilfred Hing Sang; Law, Helen Ka Wai; Yung, Raymond WH; Chow, Eudora Y; Au, KL; Chan, Eric YT; Lim, Wilina; Peiris, JS Malik; Lau, Yu Lung title: The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date: 2006-05-04 journal: BMC Infect Dis DOI: 10.1186/1471-2334-6-82 sha: doc_id: 345854 cord_uid: f0dq94j1 file: cache/cord-345225-2s5xd1oc.json key: cord-345225-2s5xd1oc authors: Soares, F.; Villavicencio, A.; Anzanello, M. J.; Fogliatto, F. S.; Idiart, M.; Stevenson, M. title: A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence date: 2020-04-14 journal: nan DOI: 10.1101/2020.04.10.20061036 sha: doc_id: 345225 cord_uid: 2s5xd1oc file: cache/cord-345754-mgixsfcc.json key: cord-345754-mgixsfcc authors: Arena, Patrick J.; Malta, Monica; Rimoin, Anne W.; Strathdee, Steffanie A. title: Race, COVID-19 and deaths of despair date: 2020-07-31 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100485 sha: doc_id: 345754 cord_uid: mgixsfcc file: cache/cord-345992-3ij1vbqp.json key: cord-345992-3ij1vbqp authors: Drosten, Christian; Doerr, Hans Wilhelm; Lim, Wilina; Stöhr, Klaus; Niedrig, Matthias title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 journal: Emerg Infect Dis DOI: 10.3201/eid1012.040416 sha: doc_id: 345992 cord_uid: 3ij1vbqp file: cache/cord-345730-bxwsup70.json key: cord-345730-bxwsup70 authors: Kočar, Eva; Režen, Tadeja; Rozman, Damjana title: Cholesterol, lipoproteins, and COVID-19: basic concepts and clinical applications date: 2020-11-04 journal: Biochim Biophys Acta Mol Cell Biol Lipids DOI: 10.1016/j.bbalip.2020.158849 sha: doc_id: 345730 cord_uid: bxwsup70 file: cache/cord-345887-ymo4mxx7.json key: cord-345887-ymo4mxx7 authors: Pinky; Gupta, Suchi; Krishnakumar, Vishnu; Sharma, Yashvi; Dinda, Amit Kumar; Mohanty, Sujata title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 date: 2020-07-13 journal: Stem Cell Rev Rep DOI: 10.1007/s12015-020-10002-z sha: doc_id: 345887 cord_uid: ymo4mxx7 file: cache/cord-345493-3bb1zuqp.json key: cord-345493-3bb1zuqp authors: Itoyama, Satoru; Keicho, Naoto; Hijikata, Minako; Quy, Tran; Phi, Nguyen Chi; Long, Hoang Thuy; Ha, Le Dang; Ban, Vo Van; Matsushita, Ikumi; Yanai, Hideki; Kirikae, Fumiko; Kirikae, Teruo; Kuratsuji, Tadatoshi; Sasazuki, Takehiko title: Identification of an alternative 5′‐untranslated exon and new polymorphisms of angiotensin‐converting enzyme 2 gene: Lack of association with SARS in the Vietnamese population date: 2005-06-03 journal: Am J Med Genet A DOI: 10.1002/ajmg.a.30779 sha: doc_id: 345493 cord_uid: 3bb1zuqp file: cache/cord-345879-nbfg47x5.json key: cord-345879-nbfg47x5 authors: Bonaz, Bruno; Sinniger, Valérie; Pellissier, Sonia title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? date: 2020-07-29 journal: Bioelectron Med DOI: 10.1186/s42234-020-00051-7 sha: doc_id: 345879 cord_uid: nbfg47x5 file: cache/cord-345999-iiw4cs8p.json key: cord-345999-iiw4cs8p authors: Khare, Prashant; Sahu, Utkarsha; Pandey, Satish Chandra; Samant, Mukesh title: Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date: 2020-09-24 journal: Virus Res DOI: 10.1016/j.virusres.2020.198169 sha: doc_id: 345999 cord_uid: iiw4cs8p file: cache/cord-346032-188gnf8j.json key: cord-346032-188gnf8j authors: Cheung, Ying-Kit; Cheng, Samuel Chak-Sum; Sin, Fion Wan-Yee; Chan, Kin-Tak; Xie, Yong title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 journal: Vaccine DOI: 10.1016/j.vaccine.2007.05.025 sha: doc_id: 346032 cord_uid: 188gnf8j file: cache/cord-346138-ip42zcld.json key: cord-346138-ip42zcld authors: Zhurakivska, Khrystyna; Troiano, Giuseppe; Pannone, Giuseppe; Caponio, Vito Carlo Alberto; Lo Muzio, Lorenzo title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 journal: Front Public Health DOI: 10.3389/fpubh.2020.00487 sha: doc_id: 346138 cord_uid: ip42zcld file: cache/cord-345689-5ns1onkw.json key: cord-345689-5ns1onkw authors: Kusters, Inca C.; Matthews, James; Saluzzo, Jean François title: Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date: 2009-01-30 journal: Vaccines for Biodefense and Emerging and Neglected Diseases DOI: 10.1016/b978-0-12-369408-9.00011-1 sha: doc_id: 345689 cord_uid: 5ns1onkw file: cache/cord-345717-ktajrf7d.json key: cord-345717-ktajrf7d authors: Monagin, Corina; Paccha, Blanca; Liang, Ning; Trufan, Sally; Zhou, Huiqiong; Wu, De; Schneider, Bradley S.; Chmura, Aleksei; Epstein, Jonathan; Daszak, Peter; Ke, Changwen; Rabinowitz, Peter M. title: Serologic and behavioral risk survey of workers with wildlife contact in China date: 2018-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0194647 sha: doc_id: 345717 cord_uid: ktajrf7d file: cache/cord-346222-rzbzlnr4.json key: cord-346222-rzbzlnr4 authors: Kim, Dae-Kyum; Knapp, Jennifer J.; Kuang, Da; Chawla, Aditya; Cassonnet, Patricia; Lee, Hunsang; Sheykhkarimli, Dayag; Samavarchi-Tehrani, Payman; Abdouni, Hala; Rayhan, Ashyad; Li, Roujia; Pogoutse, Oxana; Coyaud, Étienne; van der Werf, Sylvie; Demeret, Caroline; Gingras, Anne-Claude; Taipale, Mikko; Raught, Brian; Jacob, Yves; Roth, Frederick P. title: A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions date: 2020-08-06 journal: G3 (Bethesda) DOI: 10.1534/g3.120.401554 sha: doc_id: 346222 cord_uid: rzbzlnr4 file: cache/cord-346246-2phtdgh4.json key: cord-346246-2phtdgh4 authors: Mattar, Shaikh Abdul Matin; Koh, Samuel Ji Quan; Rama Chandran, Suresh; Cherng, Benjamin Pei Zhi title: Subacute thyroiditis associated with COVID-19 date: 2020-08-25 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-237336 sha: doc_id: 346246 cord_uid: 2phtdgh4 file: cache/cord-346008-6v2gdz4a.json key: cord-346008-6v2gdz4a authors: Jeong, Areum; Sagong, Min title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea date: 2020-06-02 journal: Infect Chemother DOI: 10.3947/ic.2020.52.2.226 sha: doc_id: 346008 cord_uid: 6v2gdz4a file: cache/cord-346092-fo83f99f.json key: cord-346092-fo83f99f authors: Fang, Li‐Qun; De Vlas, Sake J.; Feng, Dan; Liang, Song; Xu, You‐Fu; Zhou, Jie‐Ping; Richardus, Jan Hendrik; Cao, Wu‐Chun title: Geographical spread of SARS in mainland China date: 2009-06-05 journal: Trop Med Int Health DOI: 10.1111/j.1365-3156.2008.02189.x sha: doc_id: 346092 cord_uid: fo83f99f file: cache/cord-346146-yal0ctpq.json key: cord-346146-yal0ctpq authors: Peyronnet, Violaine; Sibiude, Jeanne; Huissoud, Cyril; Lescure, François-Xavier; Lucet, Jean-Christophe; Mandelbrot, Laurent; Nisand, Israel; Belaish-Allart, Joëlle; Vayssière, Christophe; Yazpandanah, Yazdan; Luton, Dominique; Picone, Olivier title: Infection par le SARS-CoV-2 chez les femmes enceintes. Actualisation de l’état des connaissances et de la proposition de prise en charge. CNGOF date: 2020-10-05 journal: Gynecol Obstet Fertil Senol DOI: 10.1016/j.gofs.2020.10.001 sha: doc_id: 346146 cord_uid: yal0ctpq file: cache/cord-346089-u31n0qxa.json key: cord-346089-u31n0qxa authors: McDade, Thomas W.; McNally, Elizabeth M.; Zelikovich, Aaron S.; D’Aquila, Richard; Mustanski, Brian; Miller, Aaron; Vaught, Lauren A.; Reiser, Nina L.; Bogdanovic, Elena; Fallon, Katherine S.; Demonbreun, Alexis R. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-08-14 journal: PLoS One DOI: 10.1371/journal.pone.0237833 sha: doc_id: 346089 cord_uid: u31n0qxa file: cache/cord-346212-mcnr7bcp.json key: cord-346212-mcnr7bcp authors: Bonzano, Chiara; Borroni, Davide; Lancia, Andrea; Bonzano, Elisabetta title: Doxycycline: From Ocular Rosacea to COVID-19 Anosmia. New Insight Into the Coronavirus Outbreak date: 2020-05-08 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00200 sha: doc_id: 346212 cord_uid: mcnr7bcp file: cache/cord-346176-w6uaet7l.json key: cord-346176-w6uaet7l authors: Nayeri, Shadi; Walshe, Margaret; Lee, Sun-Ho; Filice, Melissa; Rho, Stella; Jeyakumar, Ajani; Stempak, Joanne; Smith, Michelle I; Silverberg, Mark S title: Conducting Translational Gastrointestinal Research in the Era of COVID-19 date: 2020-08-26 journal: J Crohns Colitis DOI: 10.1093/ecco-jcc/jjaa171 sha: doc_id: 346176 cord_uid: w6uaet7l file: cache/cord-346015-bzeqs5oh.json key: cord-346015-bzeqs5oh authors: Wang, Yeming; Zhang, Dingyu; Du, Guanhua; Du, Ronghui; Zhao, Jianping; Jin, Yang; Fu, Shouzhi; Gao, Ling; Cheng, Zhenshun; Lu, Qiaofa; Hu, Yi; Luo, Guangwei; Wang, Ke; Lu, Yang; Li, Huadong; Wang, Shuzhen; Ruan, Shunan; Yang, Chengqing; Mei, Chunlin; Wang, Yi; Ding, Dan; Wu, Feng; Tang, Xin; Ye, Xianzhi; Ye, Yingchun; Liu, Bing; Yang, Jie; Yin, Wen; Wang, Aili; Fan, Guohui; Zhou, Fei; Liu, Zhibo; Gu, Xiaoying; Xu, Jiuyang; Shang, Lianhan; Zhang, Yi; Cao, Lianjun; Guo, Tingting; Wan, Yan; Qin, Hong; Jiang, Yushen; Jaki, Thomas; Hayden, Frederick G; Horby, Peter W; Cao, Bin; Wang, Chen title: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial date: 2020-04-29 journal: Lancet DOI: 10.1016/s0140-6736(20)31022-9 sha: doc_id: 346015 cord_uid: bzeqs5oh file: cache/cord-346055-7fa57pmf.json key: cord-346055-7fa57pmf authors: Visani, Giuseppe; Chiarucci, Martina; Guiducci, Barbara; Capalbo, Maria; Isidori, Alessandro title: SARS-CoV-2 impact in a community-based hematological ward in an Italian Red Zone date: 2020-06-13 journal: Ann Hematol DOI: 10.1007/s00277-020-04116-0 sha: doc_id: 346055 cord_uid: 7fa57pmf file: cache/cord-346197-7g5d9x57.json key: cord-346197-7g5d9x57 authors: Capecchi, E.; Di Pietro, G. M.; Luconi, E. title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? date: 2020-07-05 journal: nan DOI: 10.1101/2020.07.02.20142521 sha: doc_id: 346197 cord_uid: 7g5d9x57 file: cache/cord-346263-8znpqcth.json key: cord-346263-8znpqcth authors: Ding, Huiling title: Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu date: 2014-04-13 journal: J Med Humanit DOI: 10.1007/s10912-014-9282-8 sha: doc_id: 346263 cord_uid: 8znpqcth file: cache/cord-346145-hnfeauow.json key: cord-346145-hnfeauow authors: Pillay, Sureshnee; Giandhari, Jennifer; Tegally, Houriiyah; Wilkinson, Eduan; Chimukangara, Benjamin; Lessells, Richard; Moosa, Yunus; Mattison, Stacey; Gazy, Inbal; Fish, Maryam; Singh, Lavanya; Khanyile, Khulekani Sedwell; San, James Emmanuel; Fonseca, Vagner; Giovanetti, Marta; Alcantara, Luiz Carlos; de Oliveira, Tulio title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic date: 2020-08-17 journal: Genes (Basel) DOI: 10.3390/genes11080949 sha: doc_id: 346145 cord_uid: hnfeauow file: cache/cord-346281-sma6e891.json key: cord-346281-sma6e891 authors: Maldonado, Valente; Loza-Mejía; Chávez Alderete, Jaime title: Repositioning of pentoxifylline as an immunomodulator and regulator of the renin-angiotensin system in the treatment of COVID-19 date: 2020-06-09 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109988 sha: doc_id: 346281 cord_uid: sma6e891 file: cache/cord-346291-qqy9ld94.json key: cord-346291-qqy9ld94 authors: Noroozi, Rezvan; Branicki, Wojciech; Pyrc, Krzysztof; Łabaj, Paweł P.; Pośpiech, Ewelina; Taheri, Mohammad; Ghafouri-Fard, Soudeh title: Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions date: 2020-05-21 journal: Cytokine DOI: 10.1016/j.cyto.2020.155143 sha: doc_id: 346291 cord_uid: qqy9ld94 file: cache/cord-346345-jc9bq0zu.json key: cord-346345-jc9bq0zu authors: Smith, Colin M; Komisar, Jonathan R; Mourad, Ahmad; Kincaid, Brian R title: COVID-19-associated brief psychotic disorder date: 2020-08-11 journal: BMJ Case Rep DOI: 10.1136/bcr-2020-236940 sha: doc_id: 346345 cord_uid: jc9bq0zu file: cache/cord-346445-hgqohdct.json key: cord-346445-hgqohdct authors: Toyoshima, Yujiro; Nemoto, Kensaku; Matsumoto, Saki; Nakamura, Yusuke; Kiyotani, Kazuma title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 journal: J Hum Genet DOI: 10.1038/s10038-020-0808-9 sha: doc_id: 346445 cord_uid: hgqohdct file: cache/cord-346325-grt67p73.json key: cord-346325-grt67p73 authors: Reilev, M.; Kristensen, K. 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W. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.24.20111823 sha: doc_id: 346325 cord_uid: grt67p73 file: cache/cord-346331-d0s028wl.json key: cord-346331-d0s028wl authors: Lackey, Kimberly A.; Pace, Ryan M.; Williams, Janet E.; Bode, Lars; Donovan, Sharon M.; Järvinen, Kirsi M.; Seppo, Antti E.; Raiten, Daniel J.; Meehan, Courtney L.; McGuire, Mark A.; McGuire, Michelle K. title: SARS‐CoV‐2 and human milk: What is the evidence? date: 2020-05-30 journal: Matern Child Nutr DOI: 10.1111/mcn.13032 sha: doc_id: 346331 cord_uid: d0s028wl file: cache/cord-346335-el45v0a5.json key: cord-346335-el45v0a5 authors: Tan, H.S. title: Fourier spectral density of the coronavirus genome date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.06.30.180034 sha: doc_id: 346335 cord_uid: el45v0a5 file: cache/cord-346299-2s9j01q7.json key: cord-346299-2s9j01q7 authors: Salim Khan, S Muhammad; Qurieshi, Mariya Amin; Haq, Inaamul; Majid, Sabhiya; Bhat, Arif Akbar; Nabi, Sahila; Ganai, Nisar Ahmad; Zahoor, Nazia; Nisar, Auqfeen; Chowdri, Iqra Nisar; Qazi, Tanzeela Bashir; Kousar, Rafiya; Lone, Abdul Aziz; Sabah, Iram; Nabi, Shahroz; Sumji, Ishtiyaq Ahmad; Kawoosa, Misbah Ferooz; Ayoub, Shifana title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date: 2020-09-04 journal: bioRxiv DOI: 10.1101/2020.09.04.282640 sha: doc_id: 346299 cord_uid: 2s9j01q7 file: cache/cord-346441-b1r6i0wq.json key: cord-346441-b1r6i0wq authors: Polverino, Francesca title: Cigarette Smoking and COVID-19: A Complex Interaction date: 2020-08-01 journal: Am J Respir Crit Care Med DOI: 10.1164/rccm.202005-1646le sha: doc_id: 346441 cord_uid: b1r6i0wq file: cache/cord-346153-9162w7il.json key: cord-346153-9162w7il authors: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 journal: Mucosal Immunol DOI: 10.1038/mi.2008.79 sha: doc_id: 346153 cord_uid: 9162w7il file: cache/cord-346248-6wkyar57.json key: cord-346248-6wkyar57 authors: de Moura, Diogo Turiani Hourneaux; McCarty, Thomas R.; Ribeiro, Igor Braga; Funari, Mateus Pereira; de Oliveira, Pedro Victor Aniz Gomes; de Miranda Neto, Antonio Afonso; do Monte Júnior, Epifânio Silvino; Tustumi, Francisco; Bernardo, Wanderley Marques; de Moura, Eduardo Guimarães Hourneaux; Thompson, Christopher C. title: Diagnostic Characteristics of Serological-Based COVID-19 Testing: A Systematic Review and Meta-Analysis date: 2020-08-06 journal: Clinics (Sao Paulo) DOI: 10.6061/clinics/2020/e2212 sha: doc_id: 346248 cord_uid: 6wkyar57 file: cache/cord-346389-gbmnoo84.json key: cord-346389-gbmnoo84 authors: Callender, Lauren A.; Curran, Michelle; Bates, Stephanie M.; Mairesse, Maelle; Weigandt, Julia; Betts, Catherine J. title: The Impact of Pre-existing Comorbidities and Therapeutic Interventions on COVID-19 date: 2020-08-11 journal: Front Immunol DOI: 10.3389/fimmu.2020.01991 sha: doc_id: 346389 cord_uid: gbmnoo84 file: cache/cord-346403-fuxs1axy.json key: cord-346403-fuxs1axy authors: Davanzo, G. G.; Codo, A. C.; Brunetti, N. S.; Boldrini, V. O.; Knittel, T. L.; Monterio, L. B.; de Moraes, D.; Ferrari, A. J. R.; de Souza, G. F.; Muraro, S. P.; Profeta, G. . S.; Wassano, N. S.; Santos, L. N.; Carregari, V. . C.; Dias, A. . H. S.; Virgilio-da-Silva, J. V.; Castro, I.; Silva-Costa, L. . C.; Palma, A.; Mansour, E.; Ulaf, R. G.; Bernardes, A. F.; Nunes, T. A.; Ribeiro, L. C.; Agrela, M. V.; Moretti, M. L.; Buscaratti, L. I.; Crunfli, F.; Ludwig, R. . G.; Gerhardt, J. A.; Seste-Costa, R.; Forato, J.; Amorin, M. . R.; Texeira, D. A. T.; Parise, P. L.; Martini, M. C.; Bispo-dos-San, title: SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes date: 2020-09-28 journal: nan DOI: 10.1101/2020.09.25.20200329 sha: doc_id: 346403 cord_uid: fuxs1axy file: cache/cord-346512-y5d8q5b9.json key: cord-346512-y5d8q5b9 authors: Pellicciaro, Marco; Granai, Alessandra Vittoria; Marchese, Gloria; Materazzo, Marco; Cotesta, Maria; Santori, Francesca; Giacobbi, Erica; Servadei, Francesca; Grelli, Sandro; Perretta, Tommaso; Meucci, Rosaria; Pistolese, Chiara Adriana; Vanni, Gianluca title: Breast cancer patients with hormone neoadjuvant bridging therapy due to asymptomatic Corona virus infection. Case report, clinical and histopathologic findings date: 2020-10-08 journal: Int J Surg Case Rep DOI: 10.1016/j.ijscr.2020.10.020 sha: doc_id: 346512 cord_uid: y5d8q5b9 file: cache/cord-346544-kk7qyn4w.json key: cord-346544-kk7qyn4w authors: Andersson, M.; Arancibia - Carcamo, C. V.; Auckland, K.; Baillie, J. K.; Barnes, E.; Beneke, T.; Bibi, S.; Carroll, M.; Crook, D.; Dingle, K.; Dold, C.; Downs, L. O.; Dunn, L.; Eyre, D. W.; Gilbert Jaramillo, J.; Harvala Simmonds, H.; Hoosdally, S.; Ijaz, S.; James, T.; James, W.; Jeffery, K.; Justice, A.; Klenerman, P.; Knight, J. C.; Knight, M.; Liu, X.; Lumley, S. F.; Matthews, P. C.; McNaughton, A. L.; Mentzer, A. J.; Mongkolsapaya, J.; Oakley, S.; Oliveira, M. S.; Peto, T.; Ploeg, R. J.; Ratcliff, J.; Roberts, D. J.; Rudkin, J.; Screaton, G.; Semple, M. G.; Skelley, D. T.; Simmonds, P. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.21.20105486 sha: doc_id: 346544 cord_uid: kk7qyn4w file: cache/cord-346413-2njl0fd3.json key: cord-346413-2njl0fd3 authors: Nakazawa, Daigo; Ishizu, Akihiro title: Immunothrombosis in severe COVID-19 date: 2020-08-15 journal: EBioMedicine DOI: 10.1016/j.ebiom.2020.102942 sha: doc_id: 346413 cord_uid: 2njl0fd3 file: cache/cord-346658-ij5sr88p.json key: cord-346658-ij5sr88p authors: Hilgenfeld, Rolf; Pumpor, Ksenia title: Sometimes Intermediates Do the Job! date: 2006-04-07 journal: Chem Biol DOI: 10.1016/j.chembiol.2006.03.002 sha: doc_id: 346658 cord_uid: ij5sr88p file: cache/cord-346530-o65m0whe.json key: cord-346530-o65m0whe authors: Chaumont, H.; San-Galli, A.; Martino, F.; Couratier, C.; Joguet, G.; Carles, M.; Roze, E.; Lannuzel, A. title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection date: 2020-06-12 journal: J Neurol DOI: 10.1007/s00415-020-09986-y sha: doc_id: 346530 cord_uid: o65m0whe file: cache/cord-346532-4xpnd93d.json key: cord-346532-4xpnd93d authors: Strömich, Léonie; Wu, Nan; Barahona, Mauricio; Yaliraki, Sophia N. title: Allosteric Hotspots in the Main Protease of SARS-CoV-2 date: 2020-11-06 journal: bioRxiv DOI: 10.1101/2020.11.06.369439 sha: doc_id: 346532 cord_uid: 4xpnd93d file: cache/cord-346711-2k736hvr.json key: cord-346711-2k736hvr authors: Shetty, Rohit; Murugeswari, Ponnalagu; Chakrabarty, Koushik; Jayadev, Chaitra; Matalia, Himanshu; Ghosh, Arkasubhra; Das, Debashish title: Stem cell therapy in COVID-19 – current evidence and future potential date: 2020-11-09 journal: Cytotherapy DOI: 10.1016/j.jcyt.2020.11.001 sha: doc_id: 346711 cord_uid: 2k736hvr file: cache/cord-346546-yffwd0dc.json key: cord-346546-yffwd0dc authors: Douangamath, Alice; Fearon, Daren; Gehrtz, Paul; Krojer, Tobias; Lukacik, Petra; Owen, C. David; Resnick, Efrat; Strain-Damerell, Claire; Aimon, Anthony; Ábrányi-Balogh, Péter; Brandaõ-Neto, José; Carbery, Anna; Davison, Gemma; Dias, Alexandre; Downes, Thomas D; Dunnett, Louise; Fairhead, Michael; Firth, James D.; Jones, S. Paul; Keely, Aaron; Keserü, György M.; Klein, Hanna F; Martin, Mathew P.; Noble, Martin E. M.; O’Brien, Peter; Powell, Ailsa; Reddi, Rambabu; Skyner, Rachael; Snee, Matthew; Waring, Michael J.; Wild, Conor; London, Nir; von Delft, Frank; Walsh, Martin A. title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date: 2020-05-27 journal: bioRxiv DOI: 10.1101/2020.05.27.118117 sha: doc_id: 346546 cord_uid: yffwd0dc file: cache/cord-346670-34wfy52f.json key: cord-346670-34wfy52f authors: Gobeil, Sophie M-C.; Janowska, Katarzyna; McDowell, Shana; Mansouri, Katayoun; Parks, Robert; Manne, Kartik; Stalls, Victoria; Kopp, Megan; Henderson, Rory; Edwards, Robert J; Haynes, Barton F.; Acharya, Priyamvada title: D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.10.11.335299 sha: doc_id: 346670 cord_uid: 34wfy52f file: cache/cord-346370-jdfsacds.json key: cord-346370-jdfsacds authors: Sergi, Consolato M.; Leung, Alexander K.C. title: The Facemask in Public and Healthcare Workers– A Need not a Belief date: 2020-05-13 journal: Public Health DOI: 10.1016/j.puhe.2020.05.009 sha: doc_id: 346370 cord_uid: jdfsacds file: cache/cord-346555-3hrbea6d.json key: cord-346555-3hrbea6d authors: Hu, Xiumei; An, Taixue; Situ, Bo; Hu, Yuhai; Ou, Zihao; Li, Qiang; He, Xiaojing; Zhang, Ye; Tian, Peifu; Sun, Dehua; Rui, Yongyu; Wang, Qian; Ding, Dan; Zheng, Lei title: Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS‐CoV‐2 date: 2020-06-28 journal: J Clin Lab Anal DOI: 10.1002/jcla.23411 sha: doc_id: 346555 cord_uid: 3hrbea6d file: cache/cord-346763-xdfl659q.json key: cord-346763-xdfl659q authors: Herman, A.; Matthews, M.; Mairlot, M.; Nobile, L.; Fameree, L.; Jacquet, L.‐M.; Baeck, M. title: Drug reaction with eosinophilia and systemic symptoms syndrome in a patient with COVID‐19 date: 2020-08-13 journal: J Eur Acad Dermatol Venereol DOI: 10.1111/jdv.16838 sha: doc_id: 346763 cord_uid: xdfl659q file: cache/cord-346669-7n75m669.json key: cord-346669-7n75m669 authors: Wang, Shixin; Wei, Maoti; Han, Yi; Zhang, Keju; He, Li; Yang, Zhen; Su, Bing; Zhang, Zhilun; Hu, Yilan; Hui, Wuli title: Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date: 2008-02-29 journal: BMC Infect Dis DOI: 10.1186/1471-2334-8-27 sha: doc_id: 346669 cord_uid: 7n75m669 file: cache/cord-346539-kxnrf5g5.json key: cord-346539-kxnrf5g5 authors: Riggioni, Carmen; Comberiati, Pasquale; Giovannini, Mattia; Agache, Ioana; Akdis, Mübeccel; Alves‐Correia, Magna; Antó, Josep M.; Arcolaci, Alessandra; Kursat Azkur, Ahmet; Azkur, Dilek; Beken, Burcin; Boccabella, Cristina; Bousquet, Jean; Breiteneder, Heimo; Carvalho, Daniela; De las Vecillas, Leticia; Diamant, Zuzana; Eguiluz‐Gracia, Ibon; Eiwegger, Thomas; Eyerich, Stefanie; Fokkens, Wytske; Gao, Ya‐dong; Hannachi, Farah; Johnston, Sebastian L.; Jutel, Marek; Karavelia, Aspasia; Klimek, Ludger; Moya, Beatriz; Nadeau, Kari; O'Hehir, Robyn; O'Mahony, Liam; Pfaar, Oliver; Sanak, Marek; Schwarze, Jürgen; Sokolowska, Milena; Torres, María J.; van de Veen, Willem; van Zelm, Menno C.; Wang, De Yun; Zhang, Luo; Jiménez‐Saiz, Rodrigo; Akdis, Cezmi A. title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 journal: Allergy DOI: 10.1111/all.14449 sha: doc_id: 346539 cord_uid: kxnrf5g5 file: cache/cord-346758-pi1hf6xg.json key: cord-346758-pi1hf6xg authors: Egerup, P.; Olsen, L. F.; Christiansen, A.-M. H.; Westergaard, D.; Severinsen, E. R.; Hviid, K. V. R.; Kolte, A. M.; Boje, A. D.; Bertelsen, M.-L. M. F.; Praetorius, L.; Zedeler, A.; Nielsen, J. R.; Bang, D.; Berntsen, S.; Ethelberg-Findsen, J.; Storm, D. M.; Bello-Rodriguez, J.; Ingham, A.; Olle-Lopez, J.; Hoffmann, E.; Wilken-Jensen, C.; Krebs, L.; Joergensen, F. S.; Westh, H. T.; Jorgensen, H. L.; la Cour Freiesleben, N.; Nielsen, H. 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A systematic review of individual participant data date: 2020-11-04 journal: BMC Med DOI: 10.1186/s12916-020-01810-8 sha: doc_id: 346859 cord_uid: r1v6ir8u file: cache/cord-346957-bmajkabp.json key: cord-346957-bmajkabp authors: Lv, Yanbo; Ruan, Zhihua; Wang, Li; Ni, Bing; Wu, Yuzhang title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 journal: BMC Immunol DOI: 10.1186/1471-2172-10-61 sha: doc_id: 346957 cord_uid: bmajkabp file: cache/cord-347079-1zbsbcdd.json key: cord-347079-1zbsbcdd authors: Silverman, Justin D.; Hupert, Nathaniel; Washburne, Alex D. title: Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date: 2020-06-22 journal: Sci Transl Med DOI: 10.1126/scitranslmed.abc1126 sha: doc_id: 347079 cord_uid: 1zbsbcdd file: cache/cord-346816-xys0g8b8.json key: cord-346816-xys0g8b8 authors: Shichijo, S.; Keicho, N.; Long, H.T.; Quy, T.; Phi, N.C.; Ha, L.D.; Ban, V.V.; Itoyama, S.; Hu, C.‐J.; Komatsu, N.; Kirikae, T.; Kirikae, F.; Shirasawa, S.; Kaji, M.; Fukuda, T.; Sata, M.; Kuratsuji, T.; Itoh, K.; Sasazuki, T. title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity date: 2004-10-20 journal: Tissue Antigens DOI: 10.1111/j.1399-0039.2004.00314.x sha: doc_id: 346816 cord_uid: xys0g8b8 file: cache/cord-347104-h168kqjn.json key: cord-347104-h168kqjn authors: Ghosh, Ritwik; De, Kaustav; Roy, Devlina; Mandal, Arpan; Biswas, Subrata; Biswas, Subhrajyoti; Sengupta, Swagatam; Naga, Dinabandhu; Ghosh, Mrinalkanti; Benito-León, Julián title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection date: 2020-11-11 journal: J Neuroimmunol DOI: 10.1016/j.jneuroim.2020.577439 sha: doc_id: 347104 cord_uid: h168kqjn file: cache/cord-346787-uo8k6qic.json key: cord-346787-uo8k6qic authors: Jorgensen, Sarah CJ; Kebriaei, Razieh; Dresser, Linda D title: Remdesivir: Review of pharmacology, pre‐clinical data and emerging clinical experience for COVID‐19 date: 2020-05-23 journal: Pharmacotherapy DOI: 10.1002/phar.2429 sha: doc_id: 346787 cord_uid: uo8k6qic file: cache/cord-346998-01i6zxv8.json key: cord-346998-01i6zxv8 authors: Kulkarni, Spoorthy; Jenner, Bernadette L.; Wilkinson, Ian title: COVID-19 and hypertension date: 2020-05-20 journal: J Renin Angiotensin Aldosterone Syst DOI: 10.1177/1470320320927851 sha: doc_id: 346998 cord_uid: 01i6zxv8 file: cache/cord-346819-11fkgzaa.json key: cord-346819-11fkgzaa authors: Khan, Mohd Imran; Khan, Zainul A.; Baig, Mohammad Hassan; Ahmad, Irfan; Farouk, Abd-ElAziem; Song, Young Goo; Dong, Jae-Jun title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238344 sha: doc_id: 346819 cord_uid: 11fkgzaa file: cache/cord-346960-3empldlo.json key: cord-346960-3empldlo authors: Plebani, M.; Padoan, A.; Sciacovelli, L.; Bonfante, F.; Pagliari, M.; Bozzato, D.; Cosma, C.; Bortolami, A.; Negrini, D.; Zuin, S. title: Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity date: 2020-08-04 journal: nan DOI: 10.1101/2020.08.01.20166546 sha: doc_id: 346960 cord_uid: 3empldlo file: cache/cord-347119-w780f0om.json key: cord-347119-w780f0om authors: Blitz, Matthew J.; Rochelson, Burton; Prasannan, Lakha; Shan, Weiwei; Chervenak, Frank A.; Nimaroff, Michael; Bornstein, Eran title: Race/ethnicity and spatiotemporal trends in SARS-CoV-2 prevalence on obstetrical units in New York date: 2020-08-17 journal: Am J Obstet Gynecol MFM DOI: 10.1016/j.ajogmf.2020.100212 sha: doc_id: 347119 cord_uid: w780f0om file: cache/cord-347121-5drl3xas.json key: cord-347121-5drl3xas authors: Farah, I.; Lalli, G.; Baker, D.; Schumacher, A. title: A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform. date: 2020-09-29 journal: nan DOI: 10.1101/2020.09.28.20203257 sha: doc_id: 347121 cord_uid: 5drl3xas file: cache/cord-347048-qqft4yc9.json key: cord-347048-qqft4yc9 authors: Araten, David J.; Belmont, H. Michael; Schaefer-Cutillo, Julia; Iyengar, Arjun; Mattoo, Aprajita; Reddy, Ramachandra title: Mild Clinical Course of COVID-19 in 3 Patients Receiving Therapeutic Monoclonal Antibodies Targeting C5 Complement for Hematologic Disorders date: 2020-09-12 journal: Am J Case Rep DOI: 10.12659/ajcr.927418 sha: doc_id: 347048 cord_uid: qqft4yc9 file: cache/cord-347030-yx3j6373.json key: cord-347030-yx3j6373 authors: Cao, Xuetao title: COVID-19: immunopathology and its implications for therapy date: 2020-04-09 journal: Nat Rev Immunol DOI: 10.1038/s41577-020-0308-3 sha: doc_id: 347030 cord_uid: yx3j6373 file: cache/cord-347351-emdj66vj.json key: cord-347351-emdj66vj authors: Kampf, Günter; Brüggemann, Yannick; Kaba, Hani E.J.; Steinmann, Joerg; Pfaender, Stephanie; Scheithauer, Simone; Steinmann, Eike title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.09.022 sha: doc_id: 347351 cord_uid: emdj66vj file: cache/cord-347441-8ow952d8.json key: cord-347441-8ow952d8 authors: Parvez, Md Sorwer Alam; Rahman, Mohammad Mahfujur; Morshed, Md Niaz; Rahman, Dolilur; Anwar, Saeed; Hosen, Mohammad Jakir title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date: 2020-06-07 journal: bioRxiv DOI: 10.1101/2020.06.07.138800 sha: doc_id: 347441 cord_uid: 8ow952d8 file: cache/cord-346978-ubkqny8j.json key: cord-346978-ubkqny8j authors: Ranoa, Diana Rose E.; Holland, Robin L.; Alnaji, Fadi G.; Green, Kelsie J.; Wang, Leyi; Brooke, Christopher B.; Burke, Martin D.; Fan, Timothy M.; Hergenrother, Paul J. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 journal: bioRxiv DOI: 10.1101/2020.06.18.159434 sha: doc_id: 346978 cord_uid: ubkqny8j file: cache/cord-347225-gh51ag2x.json key: cord-347225-gh51ag2x authors: Fu, Weihui; Liu, Yan; Xia, Lu; Li, Min; Song, Zhigang; Hu, Huiliang; Yang, Zongguo; Wang, Lin; Cheng, Xiaobo; Wang, Mei; Jiang, Rongrong; Liu, Li; Mao, Xiaoting; Chen, Jun; Ling, Yun; Zhang, Lin; Yan, Jin; Shan, Fei; Steinhart, Corklin; Zhang, Xiaoyan; Zhu, Tongyu; Xu, Jianqing; Lu, Hongzhou title: A clinical pilot study on the safety and efficacy of aerosol inhalation treatment of IFN-κ plus TFF2 in patients with moderate COVID-19 date: 2020-07-29 journal: EClinicalMedicine DOI: 10.1016/j.eclinm.2020.100478 sha: doc_id: 347225 cord_uid: gh51ag2x file: cache/cord-347428-2isuaiyx.json key: cord-347428-2isuaiyx authors: Schulz-Stübner, Sebastian; Kunitz, Oliver title: Hygiene in der Anästhesie in Zeiten der SARS-CoV-2-Pandemie date: 2020-07-31 journal: Anasthesiol Intensivmed Notfallmed Schmerzther DOI: 10.1055/a-1174-7359 sha: doc_id: 347428 cord_uid: 2isuaiyx file: cache/cord-346987-fbqqf00i.json key: cord-346987-fbqqf00i authors: Guo, Yongwen; Jing, Yan; Wang, Yunshi; To, Aileen; Du, Shufang; Wang, Liuzheng; Bai, Ding title: Controls of SARS-CoV-2 transmission in orthodontic practice date: 2020-06-05 journal: Am J Orthod Dentofacial Orthop DOI: 10.1016/j.ajodo.2020.05.006 sha: doc_id: 346987 cord_uid: fbqqf00i file: cache/cord-347128-6lyoz8nn.json key: cord-347128-6lyoz8nn authors: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 journal: Int J Mol Sci DOI: 10.3390/ijms21124549 sha: doc_id: 347128 cord_uid: 6lyoz8nn file: cache/cord-347374-mryazbnq.json key: cord-347374-mryazbnq authors: Okba, Nisreen M.A.; Müller, Marcel A.; Li, Wentao; Wang, Chunyan; GeurtsvanKessel, Corine H.; Corman, Victor M.; Lamers, Mart M.; Sikkema, Reina S.; de Bruin, Erwin; Chandler, Felicity D.; Yazdanpanah, Yazdan; Le Hingrat, Quentin; Descamps, Diane; Houhou-Fidouh, Nadhira; Reusken, Chantal B.E.M.; Bosch, Berend-Jan; Drosten, Christian; Koopmans, Marion P.G.; Haagmans, Bart L. title: Severe Acute Respiratory Syndrome Coronavirus 2−Specific Antibody Responses in Coronavirus Disease Patients date: 2020-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid2607.200841 sha: doc_id: 347374 cord_uid: mryazbnq file: cache/cord-347221-g98q9cga.json key: cord-347221-g98q9cga authors: Piyush, Ravikant; Rajarshi, Keshav; Chatterjee, Aroni; Khan, Rajni; Ray, Shashikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e05007 sha: doc_id: 347221 cord_uid: g98q9cga file: cache/cord-346894-iy35298o.json key: cord-346894-iy35298o authors: Miranda-Schaeubinger, Monica; Blumfield, Einat; Chavhan, Govind B.; Farkas, Amy B.; Joshi, Aparna; Kamps, Shawn E.; Kaplan, Summer L.; Sammer, Marla B. 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Luana; Sze, Raymond W.; Zerr, Danielle M.; Chandra, Tushar; Edwards, Emily A.; Khan, Naeem; Rubio, Eva I.; Vera, Chido D.; Iyer, Ramesh S. title: A primer for pediatric radiologists on infection control in an era of COVID-19 date: 2020-07-07 journal: Pediatr Radiol DOI: 10.1007/s00247-020-04713-1 sha: doc_id: 346894 cord_uid: iy35298o file: cache/cord-347458-za7cot2n.json key: cord-347458-za7cot2n authors: Ruan, Qiurong; Yang, Kun; Wang, Wenxia; Jiang, Lingyu; Song, Jianxin title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China date: 2020-03-03 journal: Intensive Care Med DOI: 10.1007/s00134-020-05991-x sha: doc_id: 347458 cord_uid: za7cot2n file: cache/cord-347460-9vechh4x.json key: cord-347460-9vechh4x authors: Chang, Feng-Yee; Chen, Hsiang-Cheng; Chen, Pei-Jer; Ho, Mei-Shang; Hsieh, Shie-Liang; Lin, Jung-Chung; Liu, Fu-Tong; Sytwu, Huey-Kang title: Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date: 2020-06-04 journal: J Biomed Sci DOI: 10.1186/s12929-020-00663-w sha: doc_id: 347460 cord_uid: 9vechh4x file: cache/cord-347262-q88g1561.json key: cord-347262-q88g1561 authors: Schutzer‐Weissmann, J.; Magee, D.J.; Farquhar‐Smith, P. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 journal: Anaesthesia DOI: 10.1111/anae.15221 sha: doc_id: 347262 cord_uid: q88g1561 file: cache/cord-347462-yz67t10x.json key: cord-347462-yz67t10x authors: Chan, Tak Yeung; Miu, Ka Ying; Tsui, Chung Kan; Yee, Kwok Sang; Chan, Ming Houng title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 journal: J Am Geriatr Soc DOI: 10.1111/j.1532-5415.2004.52362.x sha: doc_id: 347462 cord_uid: yz67t10x file: cache/cord-347484-7vn93t58.json key: cord-347484-7vn93t58 authors: Zamoto, Aya; Taguchi, Fumihiro; Fukushi, Shuetsu; Morikawa, Shigeru; Yamada, Yasuko K. title: Identification of Ferret ACE2 and its Receptor Function for Sars-Coronavirus date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_93 sha: doc_id: 347484 cord_uid: 7vn93t58 file: cache/cord-347208-leo0x10l.json key: cord-347208-leo0x10l authors: Zhou, Y.; He, X.; Zhang, J.; Xue, Y. e.; Liang, M.; Yang, B.; Ma, W.; Zhou, Q.; Chen, L.; Wang, X. title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study date: 2020-06-10 journal: nan DOI: 10.1101/2020.06.09.20076646 sha: doc_id: 347208 cord_uid: leo0x10l file: cache/cord-347263-ci6mv72z.json key: cord-347263-ci6mv72z authors: Berekashvili, k.; Dmytriw, A. A.; Vulkanov, V.; Agarwal, S.; Khaneja, A.; Turkel-Parella, D.; Liff, J.; Farkas, J.; Nandakumar, T.; Zhou, T.; Frontera, J.; Kahn, D. E.; Kim, S.; Humbert, K. A.; Sanger, M. D.; Yaghi, S.; Lord, A.; Arcot, K.; Tiwari, A. title: Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients date: 2020-05-08 journal: nan DOI: 10.1101/2020.05.03.20077206 sha: doc_id: 347263 cord_uid: ci6mv72z file: cache/cord-347289-3yi5tz04.json key: cord-347289-3yi5tz04 authors: Poon, L. . C.; Yang, H.; Dumont, S.; Lee, J. C. S.; Copel, J. A.; Danneels, L.; Wright, A.; Costa, F. Da Silva; Leung, T. Y.; Zhang, Y.; Chen, D.; Prefumo, F. title: ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update date: 2020-06-01 journal: Ultrasound Obstet Gynecol DOI: 10.1002/uog.22061 sha: doc_id: 347289 cord_uid: 3yi5tz04 file: cache/cord-347706-r0rs3ls1.json key: cord-347706-r0rs3ls1 authors: Roberts, Anjeanette; Subbarao, Kanta title: Animal Models for Sars date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_83 sha: doc_id: 347706 cord_uid: r0rs3ls1 file: cache/cord-347516-linjv64o.json key: cord-347516-linjv64o authors: Abdelaziz, Osama S.; Waffa, Zuraiha title: Neuropathogenic human coronaviruses: A review date: 2020-07-20 journal: Rev Med Virol DOI: 10.1002/rmv.2118 sha: doc_id: 347516 cord_uid: linjv64o file: cache/cord-347308-l19snjyf.json key: cord-347308-l19snjyf authors: García-Howard, Marcos; Herranz-Aguirre, Mercedes; Moreno-Galarraga, Laura; Urretavizcaya-Martínez, María; Alegría-Echauri, Josune; Gorría-Redondo, Nerea; Planas-Serra, Laura; Schlüter, Agatha; Gut, Marta; Pujol, Aurora; Aguilera-Albesa, Sergio title: Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 date: 2020-08-06 journal: Front Pediatr DOI: 10.3389/fped.2020.00507 sha: doc_id: 347308 cord_uid: l19snjyf file: cache/cord-347366-0gier0lu.json key: cord-347366-0gier0lu authors: Gurwitz, David title: Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics date: 2020-03-04 journal: Drug Dev Res DOI: 10.1002/ddr.21656 sha: doc_id: 347366 cord_uid: 0gier0lu file: cache/cord-347553-d7q6u7vj.json key: cord-347553-d7q6u7vj authors: Criado, Paulo Ricardo; Pagliari, Carla; Carneiro, Francisca Regina Oliveira; Quaresma, Juarez Antonio Simões title: Lessons from dermatology about inflammatory responses in Covid‐19 date: 2020-07-12 journal: Rev Med Virol DOI: 10.1002/rmv.2130 sha: doc_id: 347553 cord_uid: d7q6u7vj file: cache/cord-347356-uc9dqhyq.json key: cord-347356-uc9dqhyq authors: Cooper, TJ; Woodward, BL; Alom, S; Harky, A title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 journal: HIV Med DOI: 10.1111/hiv.12911 sha: doc_id: 347356 cord_uid: uc9dqhyq file: cache/cord-347714-vxxhglx7.json key: cord-347714-vxxhglx7 authors: Abitogun, Folagbade; Srivastava, R.; Sharma, S.; Komarysta, V.; Akurut, E.; Munir, N.; Macalalad, L.; Olawale, O.; Owolabi, O.; Abayomi, G.; Debnath, S. title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 journal: bioRxiv DOI: 10.1101/2020.10.14.339689 sha: doc_id: 347714 cord_uid: vxxhglx7 file: cache/cord-347613-tjeo62dv.json key: cord-347613-tjeo62dv authors: da Silva, Priscilla Gomes; Mesquita, João Rodrigo; de São José Nascimento, Maria; Ferreira, Vanessa Andreia Martins title: Corrigendum to “Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2”[Sci. Total Environ. 750 (2021) 141483] date: 2020-09-10 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142123 sha: doc_id: 347613 cord_uid: tjeo62dv file: cache/cord-347499-7q47jh14.json key: cord-347499-7q47jh14 authors: Burrel, Sonia; Hausfater, Pierre; Dres, Martin; Pourcher, Valérie; Luyt, Charles-Edouard; Teyssou, Elisa; Soulié, Cathia; Calvez, Vincent; Marcelin, Anne-Geneviève; Boutolleau, David title: Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date: 2020-10-25 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.040 sha: doc_id: 347499 cord_uid: 7q47jh14 file: cache/cord-347731-eqxn6auk.json key: cord-347731-eqxn6auk authors: Garcia‐Cremades, Maria; Solans, Belen P.; Hughes, Emma; Ernest, Jacqueline P.; Wallender, Erika; Aweeka, Francesca; Luetkemeyer, Anne F.; Savic, Radojka M. title: Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date: 2020-05-12 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.1856 sha: doc_id: 347731 cord_uid: eqxn6auk file: cache/cord-347767-aq9niccc.json key: cord-347767-aq9niccc authors: Zhao, Jie; Yang, Xiaodong; Wang, Chenghua; Song, Shuai; Cao, Kun; Wei, Taohua; Ji, Qiaoxue; Zheng, Wanqun; Li, Jiali; Zhou, Xue; Liu, Jie title: Yidu-toxicity blocking lung decoction ameliorates inflammation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome by eliminating IL-6 and TNF-a date: 2020-06-19 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110436 sha: doc_id: 347767 cord_uid: aq9niccc file: cache/cord-347472-n6811ens.json key: cord-347472-n6811ens authors: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 journal: bioRxiv DOI: 10.1101/2020.05.13.094839 sha: doc_id: 347472 cord_uid: n6811ens file: cache/cord-347813-9vfwl7c0.json key: cord-347813-9vfwl7c0 authors: Jackson, M. L. title: Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2 date: 2020-07-02 journal: nan DOI: 10.1101/2020.06.30.20143735 sha: doc_id: 347813 cord_uid: 9vfwl7c0 file: cache/cord-347548-h5fk64p8.json key: cord-347548-h5fk64p8 authors: Zarza, José; Von Horoch, Jorge; Aguayo, Nicolás; Báez, Eugenio title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection date: 2020-08-21 journal: Hematol Transfus Cell Ther DOI: 10.1016/j.htct.2020.08.003 sha: doc_id: 347548 cord_uid: h5fk64p8 file: cache/cord-348192-ibohbjfb.json key: cord-348192-ibohbjfb authors: Odih, Erkison E.; Afolayan, Ayorinde O.; Akintayo, IfeOluwa; Okeke, Iruka N. title: Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks? date: 2020-06-09 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.20-0462 sha: doc_id: 348192 cord_uid: ibohbjfb file: cache/cord-348071-0zlzblwi.json key: cord-348071-0zlzblwi authors: Tseng, Jen-Yu title: Potential implications of SARS-CoV-2 on pregnancy date: 2020-05-13 journal: Taiwan J Obstet Gynecol DOI: 10.1016/j.tjog.2020.03.025 sha: doc_id: 348071 cord_uid: 0zlzblwi file: cache/cord-347734-0z2kin6r.json key: cord-347734-0z2kin6r authors: Armann, J. P.; Unrath, M.; Kirsten, C.; Lueck, C.; Dalpke, A.; Berner, R. title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates date: 2020-07-17 journal: nan DOI: 10.1101/2020.07.16.20155143 sha: doc_id: 347734 cord_uid: 0z2kin6r file: cache/cord-348384-8cvt1fo6.json key: cord-348384-8cvt1fo6 authors: Butsashvili, M.; Gulbiani, L.; Kanchelashvili, G.; Kochlamazashvili, M.; Nioradze, G.; Kamkamidze, G. title: Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population date: 2020-05-19 journal: nan DOI: 10.1101/2020.05.14.20101642 sha: doc_id: 348384 cord_uid: 8cvt1fo6 file: cache/cord-348392-e35cd9sg.json key: cord-348392-e35cd9sg authors: Moraleda, Cinta; Serna-Pascual, Miquel; Soriano-Arandes, Antoni; Simó, Silvia; Epalza, Cristina; Santos, Mar; Grasa, Carlos; Rodríguez, Maria; Soto, Beatriz; Gallego, Nerea; Ruiz, Yolanda; Urretavizcaya-Martínez, María; Pareja, Marta; Sanz-Santaeufemia, Francisco José; Fumadó, Victoria; Lanaspa, Miguel; Jordan, Iolanda; Prieto, Luis; Belda, Sylvia; Toral-Vázquez, Belén; Rincón, Elena; Gil-Villanueva, Nuria; Méndez-Echevarría, Ana; Castillo-Serrano, Ana; Rivière, Jacques G; Soler-Palacín, Pere; Rojo, Pablo; Tagarro, Alfredo title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date: 2020-07-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1042 sha: doc_id: 348392 cord_uid: e35cd9sg file: cache/cord-348283-7xorq5ce.json key: cord-348283-7xorq5ce authors: Naz, Anam; Shahid, Fatima; Butt, Tariq Tahir; Awan, Faryal Mehwish; Ali, Amjad; Malik, Arif title: Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date: 2020-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01663 sha: doc_id: 348283 cord_uid: 7xorq5ce file: cache/cord-348178-6bjimde4.json key: cord-348178-6bjimde4 authors: Li, Ling; Gu, Jiang; Shi, Xicheng; Gong, Encong; Li, Xingwang; Shao, Hongquan; Shi, Xueying; Jiang, Huijun; Gao, Xiaoqiang; Cheng, Daiyun; Guo, Lizhu; Wang, Hao; Shi, Xiaohong; Wang, Peizhi; Zhang, Qianying; Shen, Bing title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 journal: Clin Infect Dis DOI: 10.1086/432720 sha: doc_id: 348178 cord_uid: 6bjimde4 file: cache/cord-347804-kxhasabe.json key: cord-347804-kxhasabe authors: Luo, Ruibang; Wong, Yat-Sing; Lam, Tak-Wah title: Tracking cytosine depletion in SARS-CoV-2 date: 2020-10-26 journal: bioRxiv DOI: 10.1101/2020.10.26.354787 sha: doc_id: 347804 cord_uid: kxhasabe file: cache/cord-348342-iqq8kmn0.json key: cord-348342-iqq8kmn0 authors: Uyoga, S.; Adetifa, I. M. O.; Karanja, H. K.; Nyagwange, J.; Tuju, J.; Wanjiku, P.; Aman, R.; Mwangangi, M.; Amoth, P.; Kasera, K.; Ng'ang'a, W.; Rombo, C.; Yegon, C. K.; Kithi, K.; Odhiambo, E.; Rotich, T.; Orgut, I.; Kihara, S.; Otiende, M.; Bottomley, C.; Mupe, Z. N.; Kagucia, E. W.; Gallagher, K.; Etyang, A.; Voller, S.; Gitonga, J.; Mugo, D.; Agoti, C. N.; Otieno, E.; Ndwiga, L.; Lambe, T.; Wright, D.; Barasa, E.; Tsofa, B.; Bejon, P.; Ochola-Oyier, L. I.; Agweyu, A.; Scott, J. A. G.; Warimwe, G. M. title: Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors date: 2020-07-29 journal: nan DOI: 10.1101/2020.07.27.20162693 sha: doc_id: 348342 cord_uid: iqq8kmn0 file: cache/cord-348360-20eq5meh.json key: cord-348360-20eq5meh authors: Esposito, Dominic; Mehalko, Jennifer; Drew, Matthew; Snead, Kelly; Wall, Vanessa; Taylor, Troy; Frank, Peter; Denson, John-Paul; Hong, Min; Gulten, Gulcin; Sadtler, Kaitlyn; Messing, Simon; Gillette, William title: Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date: 2020-06-04 journal: Protein Expr Purif DOI: 10.1016/j.pep.2020.105686 sha: doc_id: 348360 cord_uid: 20eq5meh file: cache/cord-347965-zluu0i41.json key: cord-347965-zluu0i41 authors: Essahib, Wafaa; Verheyen, Greta; Tournaye, Herman; Van de Velde, Hilde title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts date: 2020-09-21 journal: J Assist Reprod Genet DOI: 10.1007/s10815-020-01952-x sha: doc_id: 347965 cord_uid: zluu0i41 file: cache/cord-348202-6we8e60b.json key: cord-348202-6we8e60b authors: Drake, Daniel H.; De Bonis, Michele; Covella, Michele; Agricola, Eustachio; Zangrillo, Alberto; Zimmerman, Karen G.; Cobey, Frederick C. title: Echo in Pandemic: Front Line Perspective, Expanding Role of Ultrasound and Ethics of Resource Allocation date: 2020-04-10 journal: J Am Soc Echocardiogr DOI: 10.1016/j.echo.2020.04.007 sha: doc_id: 348202 cord_uid: 6we8e60b file: cache/cord-347968-jhnr8k3j.json key: cord-347968-jhnr8k3j authors: Herrera, David; Serrano, Jorge; Roldán, Silvia; Sanz, Mariano title: Is the oral cavity relevant in SARS-CoV-2 pandemic? date: 2020-06-23 journal: Clin Oral Investig DOI: 10.1007/s00784-020-03413-2 sha: doc_id: 347968 cord_uid: jhnr8k3j file: cache/cord-348526-g3asp1ps.json key: cord-348526-g3asp1ps authors: Wang, Wenjun; Wang, Yikai; Zhang, Xin; Li, Yaping; Jia, Xiaoli; Dang, Shuangsuo title: WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019 date: 2020-02-26 journal: nan DOI: 10.1101/2020.02.24.20026682 sha: doc_id: 348526 cord_uid: g3asp1ps file: cache/cord-348010-m3a3utvz.json key: cord-348010-m3a3utvz authors: Wolff, Michael title: On build‐up of epidemiologic models—Development of a SEI(3)RSD model for the spread of SARS‐CoV‐2 date: 2020-10-13 journal: Z Angew Math Mech DOI: 10.1002/zamm.202000230 sha: doc_id: 348010 cord_uid: m3a3utvz file: cache/cord-348301-bk80pps9.json key: cord-348301-bk80pps9 authors: Wahl, Angela; Gralinski, Lisa; Johnson, Claire; Yao, Wenbo; Kovarova, Martina; Dinnon, Kenneth; Liu, Hongwei; Madden, Victoria; Krzystek, Halina; De, Chandrav; White, Kristen; Schäfer, Alexandra; Zaman, Tanzila; Leist, Sarah; Grant, Paul; Gully, Kendra; Askin, Frederic; Browne, Edward; Jones, Corbin; Pickles, Raymond; Baric, Ralph; Garcia, J Victor title: Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801 date: 2020-09-24 journal: Res Sq DOI: 10.21203/rs.3.rs-80404/v1 sha: doc_id: 348301 cord_uid: bk80pps9 file: cache/cord-348748-rxyh58eu.json key: cord-348748-rxyh58eu authors: Gorospe, Luis; Ayala-Carbonero, Ana María; Ureña-Vacas, Almudena; Medina-Díaz, Montserrat; Arrieta, Paola; Mirambeaux-Villalona, Rosa Mariela; Barrios-Barreto, Deisy; Muñoz-Molina, Gemma María; Cabañero-Sánchez, Alberto; Lage-Alfranca, Yolanda; Martín-Martín, Margarita; Benito-Berlinches, Amparo; Alarcón-Rodríguez, Javier title: COVID-19: Thoracic Diagnostic Interventional Procedures in Troubled Times() date: 2020-09-07 journal: Arch Bronconeumol DOI: 10.1016/j.arbr.2020.08.008 sha: doc_id: 348748 cord_uid: rxyh58eu file: cache/cord-348478-ho89o8mj.json key: cord-348478-ho89o8mj authors: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa587 sha: doc_id: 348478 cord_uid: ho89o8mj file: cache/cord-348209-rkkhv4mw.json key: cord-348209-rkkhv4mw authors: Noerz, Dominik; Fischer, Nicole; Schultze, Alexander; Kluge, Stefan; Mayer-Runge, Ulrich; Aepfelbacher, Martin; Pfefferle, Susanne; Luetgehetmann, Marc title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 journal: nan DOI: 10.1101/2020.04.07.20056234 sha: doc_id: 348209 cord_uid: rkkhv4mw file: cache/cord-348723-sf073cmj.json key: cord-348723-sf073cmj authors: Chen, Liang; Li, Xiangjie; Chen, Mingquan; Feng, Yi; Xiong, Chenglong title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 date: 2020-03-30 journal: Cardiovasc Res DOI: 10.1093/cvr/cvaa078 sha: doc_id: 348723 cord_uid: sf073cmj file: cache/cord-347818-93ixqyfp.json key: cord-347818-93ixqyfp authors: Hojyo, Shintaro; Uchida, Mona; Tanaka, Kumiko; Hasebe, Rie; Tanaka, Yuki; Murakami, Masaaki; Hirano, Toshio title: How COVID-19 induces cytokine storm with high mortality date: 2020-10-01 journal: Inflamm Regen DOI: 10.1186/s41232-020-00146-3 sha: doc_id: 347818 cord_uid: 93ixqyfp file: cache/cord-348635-1pb2ag9j.json key: cord-348635-1pb2ag9j authors: Anand, Praveen; Puranik, Arjun; Aravamudan, Murali; Venkatakrishnan, AJ; Soundararajan, Venky title: SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date: 2020-04-30 journal: bioRxiv DOI: 10.1101/2020.04.29.069476 sha: doc_id: 348635 cord_uid: 1pb2ag9j file: cache/cord-348752-bbghqy1a.json key: cord-348752-bbghqy1a authors: Li, Yuguo; Qian, Hua; Hang, Jian; Chen, Xuguang; Hong, Ling; Liang, Peng; Li, Jiansen; Xiao, Shenglan; Wei, Jianjian; Liu, Li; Kang, Min title: Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant date: 2020-04-22 journal: nan DOI: 10.1101/2020.04.16.20067728 sha: doc_id: 348752 cord_uid: bbghqy1a file: cache/cord-348065-0tkx7aas.json key: cord-348065-0tkx7aas authors: Liu, Bing; Han, Junyan; Cheng, Xiaohuan; Yu, Long; Zhang, Li; Wang, Wei; Ni, Lan; Wei, Chaojie; Huang, Yafei; Cheng, Zhenshun title: Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients date: 2020-03-30 journal: nan DOI: 10.1101/2020.03.26.20044768 sha: doc_id: 348065 cord_uid: 0tkx7aas file: cache/cord-348243-e5tdb08v.json key: cord-348243-e5tdb08v authors: Schermer, Bernhard; Fabretti, Francesca; Damagnez, Maximilian; Di Cristanziano, Veronica; Heger, Eva; Arjune, Sita; Tanner, Nathan A.; Imhof, Thomas; Koch, Manuel; Ladha, Alim; Joung, Julia; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Burst, Volker; Zhang, Feng; Klein, Florian; Benzing, Thomas; Müller, Roman-Ulrich title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0238612 sha: doc_id: 348243 cord_uid: e5tdb08v file: cache/cord-348823-u2gm3kyh.json key: cord-348823-u2gm3kyh authors: Baksh, Mizba; Ravat, Virendrasinh; Zaidi, Annam; Patel, Rikinkumar S title: A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic date: 2020-05-18 journal: Cureus DOI: 10.7759/cureus.8188 sha: doc_id: 348823 cord_uid: u2gm3kyh file: cache/cord-348727-o38uplxe.json key: cord-348727-o38uplxe authors: Beaudoin-Bussières, Guillaume; Laumaea, Annemarie; Anand, Sai Priya; Prévost, Jérémie; Gasser, Romain; Goyette, Guillaume; Medjahed, Halima; Perreault, Josée; Tremblay, Tony; Lewin, Antoine; Gokool, Laurie; Morrisseau, Chantal; Bégin, Philippe; Tremblay, Cécile; Martel-Laferrière, Valérie; Kaufmann, Daniel E.; Richard, Jonathan; Bazin, Renée; Finzi, Andrés title: Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date: 2020-07-09 journal: bioRxiv DOI: 10.1101/2020.07.09.194639 sha: doc_id: 348727 cord_uid: o38uplxe file: cache/cord-348455-vcxalkeo.json key: cord-348455-vcxalkeo authors: Graham, N. R.; Whitaker, A. N.; Strother, C. A.; Miles, A. K.; Grier, D.; McElvany, B. D.; Bruce, E. A.; Poynter, M. E.; Pierce, K. K.; Kirkpatrick, B. D.; Stapleton, R. D.; An, G.; Botten, J. W.; Crothers, J. W.; Diehl, S. A. title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.07.15.20154443 sha: doc_id: 348455 cord_uid: vcxalkeo file: cache/cord-348567-rvwxysvc.json key: cord-348567-rvwxysvc authors: Panfili, F. M.; Roversi, M.; D’Argenio, P.; Rossi, P.; Cappa, M.; Fintini, D. title: Possible role of vitamin D in Covid-19 infection in pediatric population date: 2020-06-15 journal: J Endocrinol Invest DOI: 10.1007/s40618-020-01327-0 sha: doc_id: 348567 cord_uid: rvwxysvc file: cache/cord-349070-bqv03u2e.json key: cord-349070-bqv03u2e authors: Jiang, Shih Sheng; Chen, Tsan-Chi; Yang, Jyh-Yuan; Hsiung, Chao A.; Su, Ih-Jen; Liu, Ying-Lan; Chen, Po-Cheng; Juang, Jyh-Lyh title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 journal: Clin Infect Dis DOI: 10.1086/380841 sha: doc_id: 349070 cord_uid: bqv03u2e file: cache/cord-348391-xytmq2f2.json key: cord-348391-xytmq2f2 authors: Wyganowska-Swiatkowska, Marzena; Nohawica, Michal; Grocholewicz, Katarzyna; Nowak, Gerard title: Influence of Herbal Medicines on HMGB1 Release, SARS-CoV-2 Viral Attachment, Acute Respiratory Failure, and Sepsis. A Literature Review date: 2020-06-30 journal: Int J Mol Sci DOI: 10.3390/ijms21134639 sha: doc_id: 348391 cord_uid: xytmq2f2 file: cache/cord-348729-kejlm425.json key: cord-348729-kejlm425 authors: Liu, Xiaoyu; Gao, Fang; Gou, Liming; Chen, Yin; Gu, Yayun; Ao, Lei; Shen, Hongbing; Hu, Zhibin; Guo, Xiling; Gao, Wei title: Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date: 2020-05-04 journal: bioRxiv DOI: 10.1101/2020.05.03.074914 sha: doc_id: 348729 cord_uid: kejlm425 file: cache/cord-348855-lnltoj1n.json key: cord-348855-lnltoj1n authors: Iannaccone, Giulia; Scacciavillani, Roberto; Del Buono, Marco Giuseppe; Camilli, Massimiliano; Ronco, Claudio; Lavie, Carl J.; Abbate, Antonio; Crea, Filippo; Massetti, Massimo; Aspromonte, Nadia title: Weathering the Cytokine Storm in COVID-19: Therapeutic Implications date: 2020-06-29 journal: Cardiorenal Med DOI: 10.1159/000509483 sha: doc_id: 348855 cord_uid: lnltoj1n file: cache/cord-348777-pk9y6vfp.json key: cord-348777-pk9y6vfp authors: Ding, Cheng; Feng, Xuewen; Chen, Yanfei; Yuan, Jing; Yi, Ping; Li, Yongtao; Ni, Qin; Zou, Rongrong; Li, Xiaohe; Sheng, Jifang; Li, Lanjuan; Xu, Kaijin title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 journal: Infect Dis Ther DOI: 10.1007/s40121-020-00337-y sha: doc_id: 348777 cord_uid: pk9y6vfp file: cache/cord-348636-qqcb85uk.json key: cord-348636-qqcb85uk authors: Lekone, Phenyo E. title: Bayesian Analysis of Severe Acute Respiratory Syndrome: The 2003 Hong Kong Epidemic date: 2008-07-09 journal: Biom J DOI: 10.1002/bimj.200710431 sha: doc_id: 348636 cord_uid: qqcb85uk file: cache/cord-348713-tucolje2.json key: cord-348713-tucolje2 authors: Cao, Yanan; Li, Lin; Feng, Zhimin; Wan, Shengqing; Huang, Peide; Sun, Xiaohui; Wen, Fang; Huang, Xuanlin; Ning, Guang; Wang, Weiqing title: Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations date: 2020-02-24 journal: Cell Discov DOI: 10.1038/s41421-020-0147-1 sha: doc_id: 348713 cord_uid: tucolje2 file: cache/cord-349015-5oisrm5s.json key: cord-349015-5oisrm5s authors: Liu, Zhe; Zheng, Huanying; Yuan, Runyu; Li, Mingyue; Lin, Huifang; Peng, Jingju; Xiong, Qianlin; Sun, Jiufeng; Li, Baisheng; Wu, Jie; Hulswit, Ruben J.G.; Bowden, Thomas A.; Rambaut, Andrew; Loman, Nick; Pybus, Oliver G; Ke, Changwen; Lu, Jing title: Identification of a common deletion in the spike protein of SARS-CoV-2 date: 2020-04-02 journal: bioRxiv DOI: 10.1101/2020.03.31.015941 sha: doc_id: 349015 cord_uid: 5oisrm5s file: cache/cord-349031-tbof9yqi.json key: cord-349031-tbof9yqi authors: Chen, Shiu-Jau; Wang, Shao-Cheng; Chen, Yuan-Chuan title: Novel Antiviral Strategies in the Treatment of COVID-19: A Review date: 2020-08-20 journal: Microorganisms DOI: 10.3390/microorganisms8091259 sha: doc_id: 349031 cord_uid: tbof9yqi file: cache/cord-349210-8t4a5qqo.json key: cord-349210-8t4a5qqo authors: Ji, Ping; Chen, Jianmeng; Golding, Amit; Nikolov, Nikolay P.; Saluja, Bhawana; Ren, Yunzhao R.; Sahajwalla, Chandrahas title: Immunomodulatory Therapeutic Proteins in COVID‐19: Current Clinical Development and Clinical Pharmacology Considerations date: 2020-08-10 journal: J Clin Pharmacol DOI: 10.1002/jcph.1729 sha: doc_id: 349210 cord_uid: 8t4a5qqo file: cache/cord-349392-r71g2e9y.json key: cord-349392-r71g2e9y authors: Wang, L. -F.; Eaton, B. T. title: Bats, Civets and the Emergence of SARS date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_13 sha: doc_id: 349392 cord_uid: r71g2e9y file: cache/cord-348773-ulnc9gdv.json key: cord-348773-ulnc9gdv authors: Hammoud, H.; Bendari, A.; Bendari, T.; Bougmiza, I. title: Post mortem pathological findings in COVID-19 cases: A Systematic Review date: 2020-10-14 journal: nan DOI: 10.1101/2020.10.11.20210849 sha: doc_id: 348773 cord_uid: ulnc9gdv file: cache/cord-349029-zyfop43z.json key: cord-349029-zyfop43z authors: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0236976 sha: doc_id: 349029 cord_uid: zyfop43z file: cache/cord-349124-nhnl7zgi.json key: cord-349124-nhnl7zgi authors: de Sandes‐Freitas, Tainá Veras; Canito Brasil, Ivelise Regina; Oliveira Sales, Maria Luiza de Mattos Brito; Studart e Neves Lunguinho, Marina Seixas; Pimentel, Ítalo Rossy Sousa; Josino da Costa, Lucianna Auxi Teixeira; Esmeraldo, Ronaldo de Matos title: Lessons from SARS‐CoV‐2 screening in a Brazilian organ transplant unit date: 2020-07-13 journal: Transpl Infect Dis DOI: 10.1111/tid.13376 sha: doc_id: 349124 cord_uid: nhnl7zgi file: cache/cord-348696-86nbwon2.json key: cord-348696-86nbwon2 authors: Güemes-Villahoz, Noemi; Burgos-Blasco, Barbara; Vidal-Villegas, Beatriz; Garcia-Feijoo, Julián; Arriola-Villalobos, Pedro; Martínez-de-la-Casa, Jose María; Diaz-Valle, David; Konstas, Anastasios G. title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review date: 2020-08-18 journal: Adv Ther DOI: 10.1007/s12325-020-01442-7 sha: doc_id: 348696 cord_uid: 86nbwon2 file: cache/cord-349159-rndtf508.json key: cord-349159-rndtf508 authors: Brosseau, Lisa M; Rosen, Jonathan; Harrison, Robert title: Selecting Controls for Minimizing SARS-CoV-2 Aerosol Transmission in Workplaces and Conserving Respiratory Protective Equipment Supplies date: 2020-08-21 journal: Ann Work Expo Health DOI: 10.1093/annweh/wxaa083 sha: doc_id: 349159 cord_uid: rndtf508 file: cache/cord-349311-yo4up42r.json key: cord-349311-yo4up42r authors: De Maria, Andrea; Varese, Paola; Dentone, Chiara; Barisione, Emanuela; Bassetti, Matteo title: High prevalence of olfactory and taste disorder during SARS‐CoV‐2 infection in outpatients date: 2020-05-17 journal: J Med Virol DOI: 10.1002/jmv.25995 sha: doc_id: 349311 cord_uid: yo4up42r file: cache/cord-349117-xfir3m5p.json key: cord-349117-xfir3m5p authors: Hyseni, Inesa; Molesti, Eleonora; Benincasa, Linda; Piu, Pietro; Casa, Elisa; Temperton, Nigel J; Manenti, Alessandro; Montomoli, Emanuele title: Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays date: 2020-09-10 journal: Viruses DOI: 10.3390/v12091011 sha: doc_id: 349117 cord_uid: xfir3m5p file: cache/cord-349365-2ot1kf2k.json key: cord-349365-2ot1kf2k authors: Shi, Yi; Luo, Haifeng; Jia, Jie; Xiong, Jie; Yang, Dehua; Huang, Bing; Jin, Youxin title: Antisense downregulation of SARS‐CoV gene expression in Vero E6 cells date: 2004-11-15 journal: J Gene Med DOI: 10.1002/jgm.640 sha: doc_id: 349365 cord_uid: 2ot1kf2k file: cache/cord-349226-xzlc1pni.json key: cord-349226-xzlc1pni authors: Khatiwada, Saroj; Subedi, Astha title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 journal: Hum Microb J DOI: 10.1016/j.humic.2020.100073 sha: doc_id: 349226 cord_uid: xzlc1pni file: cache/cord-349541-7g50vg14.json key: cord-349541-7g50vg14 authors: Poulikakos, Dimitrios; Sinha, Smeeta; Kalra, Philip A. title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date: 2020-07-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104545 sha: doc_id: 349541 cord_uid: 7g50vg14 file: cache/cord-349500-603v8lfb.json key: cord-349500-603v8lfb authors: Neurath, Markus F title: Covid-19 and immunomodulation in IBD date: 2020-04-16 journal: Gut DOI: 10.1136/gutjnl-2020-321269 sha: doc_id: 349500 cord_uid: 603v8lfb file: cache/cord-349417-vn7q8wc4.json key: cord-349417-vn7q8wc4 authors: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_1 sha: doc_id: 349417 cord_uid: vn7q8wc4 file: cache/cord-349485-iomk99lv.json key: cord-349485-iomk99lv authors: Eis-Hübinger, Anna M.; Hönemann, Mario; Wenzel, Jürgen J.; Berger, Annemarie; Widera, Marek; Schmidt, Barbara; Aldabbagh, Souhaib; Marx, Benjamin; Streeck, Hendrik; Ciesek, Sandra; Liebert, Uwe G.; Huzly, Daniela; Hengel, Hartmut; Panning, Marcus title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples date: 2020-04-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104381 sha: doc_id: 349485 cord_uid: iomk99lv file: cache/cord-349313-2gupfqnl.json key: cord-349313-2gupfqnl authors: Martinez-Perez, Clara; Alvarez-Peregrina, Cristina; Villa-Collar, Cesar; Sánchez-Tena, Miguel Ángel title: Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19) date: 2020-10-21 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17207690 sha: doc_id: 349313 cord_uid: 2gupfqnl file: cache/cord-349445-yh6ndtgm.json key: cord-349445-yh6ndtgm authors: Mohammed El Tabaa, Manar; Mohammed El Tabaa, Maram title: Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost date: 2020-05-27 journal: Biochem Pharmacol DOI: 10.1016/j.bcp.2020.114057 sha: doc_id: 349445 cord_uid: yh6ndtgm file: cache/cord-349428-i2s41kl7.json key: cord-349428-i2s41kl7 authors: Griffin, Ian; 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Cecilia; Schenkman, Andrew title: The Impact of COVID-19 Infection on Labor and Delivery, Newborn Nursery, and Neonatal Intensive Care Unit: Prospective Observational Data from a Single Hospital System date: 2020-06-13 journal: Am J Perinatol DOI: 10.1055/s-0040-1713416 sha: doc_id: 349428 cord_uid: i2s41kl7 file: cache/cord-349556-k312qkvh.json key: cord-349556-k312qkvh authors: Roldán-Santiago, Ernesto; Benito-Berlinches, Amparo; Martínez-García, Laura; Quereda, Carmen; Rodríguez-Martín, Eulalia; Pérez-Elías, Pilar; López-Pintor, Jose María; Walo-Delgado, P E; Moreno-Zamora, Ana; Fernández-Velasco, Jose Ignacio; García-Abellás, Patricia; Ballester-González, Rubén; Villar, Luisa M; Pérez-Elías, María Jesús title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1422 sha: doc_id: 349556 cord_uid: k312qkvh file: cache/cord-349645-6o8773c5.json key: cord-349645-6o8773c5 authors: Li, He; Xu, Xiao-Long; Dai, Da-Wei; Huang, Zhen-Yu; Ma, Zhuang; Guan, Yan-Jun title: Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date: 2020-06-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.076 sha: doc_id: 349645 cord_uid: 6o8773c5 file: cache/cord-349690-hgdjbeht.json key: cord-349690-hgdjbeht authors: Alonso, Fábio de O. Martinez; Sabino, Bruno Duarte; Guimarães, Maria Angelica Arpon Marandino; Varella, Rafael Brandão title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report date: 2020-08-14 journal: J Med Virol DOI: 10.1002/jmv.26432 sha: doc_id: 349690 cord_uid: hgdjbeht file: cache/cord-349501-p1fttfpr.json key: cord-349501-p1fttfpr authors: Ratia, Kiira; Mesecar, Andrew; O’Brien, Amornrat; Baker, Susan C. title: Chapter 494 Coronavirus Papain-like Peptidases date: 2013-12-31 journal: Handbook of Proteolytic Enzymes DOI: 10.1016/b978-0-12-382219-2.00493-2 sha: doc_id: 349501 cord_uid: p1fttfpr file: cache/cord-349504-oqpjqgv4.json key: cord-349504-oqpjqgv4 authors: Escudero, Dolores; Barrera, Juan A.; Balboa, Salvador; Viñas, Silvia; Martín, Gabriel; Antonio Boga, José title: Análisis de SARS-CoV-2 en el aire de una UCI dedicada a pacientes Covid-19 date: 2020-10-10 journal: Med Intensiva DOI: 10.1016/j.medin.2020.09.004 sha: doc_id: 349504 cord_uid: oqpjqgv4 file: cache/cord-349659-6drnriun.json key: cord-349659-6drnriun authors: Grant, Benjamin D.; Anderson, Caitlin E.; Williford, John R.; Alonzo, Luis F.; Glukhova, Veronika A.; Boyle, David S.; Weigl, Bernhard H.; Nichols, Kevin P. title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents date: 2020-07-01 journal: Anal Chem DOI: 10.1021/acs.analchem.0c01975 sha: doc_id: 349659 cord_uid: 6drnriun file: cache/cord-348899-vynk8q8c.json key: cord-348899-vynk8q8c authors: Jo, Seri; Kim, Suwon; Shin, Dong Hae; Kim, Mi-Sun title: Inhibition of SARS-CoV 3CL protease by flavonoids date: 2019-11-14 journal: J Enzyme Inhib Med Chem DOI: 10.1080/14756366.2019.1690480 sha: doc_id: 348899 cord_uid: vynk8q8c file: cache/cord-349744-8cg5yj20.json key: cord-349744-8cg5yj20 authors: Lassaunière, Ria; Frische, Anders; Harboe, Zitta B; Nielsen, Alex CY; Fomsgaard, Anders; Krogfelt, Karen A; Jørgensen, Charlotte S title: Evaluation of nine commercial SARS-CoV-2 immunoassays date: 2020-04-10 journal: nan DOI: 10.1101/2020.04.09.20056325 sha: doc_id: 349744 cord_uid: 8cg5yj20 file: cache/cord-349794-mhviub6e.json key: cord-349794-mhviub6e authors: Le, Brian L.; Andreoletti, Gaia; Oskotsky, Tomiko; Vallejo-Gracia, Albert; Rosales, Romel; Yu, Katharine; Kosti, Idit; Leon, Kristoffer E.; Bunis, Daniel G.; Li, Christine; Kumar, G. Renuka; White, Kris M.; García-Sastre, Adolfo; Ott, Melanie; Sirota, Marina title: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date: 2020-10-23 journal: bioRxiv DOI: 10.1101/2020.10.23.352666 sha: doc_id: 349794 cord_uid: mhviub6e file: cache/cord-349545-w7c2tu5a.json key: cord-349545-w7c2tu5a authors: Wang, Mengmeng; Chen, Dayang; Wu, Wei; Tang, Huamei; Kan, Lijuan; Zong, Zengyan; Dou, Xiaowen; Ji, Xiang; Xiong, Dan; Zhang, Xiuming title: Analytical performance evaluation of five RT‐PCR kits for severe acute respiratory syndrome coronavirus 2 date: 2020-10-27 journal: J Clin Lab Anal DOI: 10.1002/jcla.23643 sha: doc_id: 349545 cord_uid: w7c2tu5a file: cache/cord-349089-ta07bho2.json key: cord-349089-ta07bho2 authors: Antushevich, Hanna title: Interplays between inflammasomes and viruses, bacteria (pathogenic and probiotic), yeasts and parasites date: 2020-09-22 journal: Immunol Lett DOI: 10.1016/j.imlet.2020.09.004 sha: doc_id: 349089 cord_uid: ta07bho2 file: cache/cord-349682-kpg0vley.json key: cord-349682-kpg0vley authors: Ojha, Probir Kumar; Kar, Supratik; Krishna, Jillella Gopala; Roy, Kunal; Leszczynski, Jerzy title: Therapeutics for COVID-19: from computation to practices—where we are, where we are heading to date: 2020-09-02 journal: Mol Divers DOI: 10.1007/s11030-020-10134-x sha: doc_id: 349682 cord_uid: kpg0vley file: cache/cord-349684-2tioh80m.json key: cord-349684-2tioh80m authors: Pezzotti, Giuseppe; Ohgitani, Eriko; Shin-Ya, Masaharu; Adachi, Tetsuya; Marin, Elia; Boschetto, Francesco; Zhu, Wenliang; Mazda, Osam title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.19.159970 sha: doc_id: 349684 cord_uid: 2tioh80m file: cache/cord-349838-p6vfzbla.json key: cord-349838-p6vfzbla authors: Algwaiz, Ghada; Aljurf, Mahmoud; Koh, Mickey; Horowitz, Mary M.; Ljungman, Per; Weisdorf, Daniel; Saber, Wael; Kodera, Yoshihisa; Szer, Jeff; Jawdat, Dunia; Wood, William A.; Brazauskas, Ruta; Lehmann, Leslie; Pasquini, Marcelo C.; Seber, Adriana; Lu, Pei Hua; Atsuta, Yoshiko; Riches, Marcie; Perales, Miguel-Angel; Worel, Nina; Okamoto, Shinichiro; Srivastava, Alok; Chemaly, Roy F.; Cordonnier, Catherine; Dandoy, Christopher E.; Wingard, John R.; Kharfan-Dabaja, Mohamed A.; Hamadani, Mehdi; Majhail, Navneet S.; Waghmare, Alpana A.; Chao, Nelson; Kröger, Nicolaus; Shaw, Bronwen; Mohty, Mohamad; Niederwieser, Dietger; Greinix, Hildegard; Hashmi, Shahrukh K. title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date: 2020-07-24 journal: Biol Blood Marrow Transplant DOI: 10.1016/j.bbmt.2020.07.021 sha: doc_id: 349838 cord_uid: p6vfzbla file: cache/cord-349774-898tmq14.json key: cord-349774-898tmq14 authors: Zhang, Haiyang; Tu, Jialu; Cao, Chulei; Yang, Ting; Gao, Liangcai title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date: 2020-06-16 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.06.058 sha: doc_id: 349774 cord_uid: 898tmq14 file: cache/cord-349827-0trvostt.json key: cord-349827-0trvostt authors: Tse, Alan C.B.; So, Stella; Sin, Leo title: Crisis management and recovery: how restaurants in Hong Kong responded to SARS date: 2005-01-29 journal: Int J Hosp Manag DOI: 10.1016/j.ijhm.2004.12.001 sha: doc_id: 349827 cord_uid: 0trvostt file: cache/cord-349721-wdjlr4z4.json key: cord-349721-wdjlr4z4 authors: Szpiro, L.; Pizzorno, A.; Durimel, L.; Julien, T.; Traversier, A.; Bouchami, D.; Marie, Y.; Rosa-Calatrava, M.; Terrier, O.; Moules, V. title: Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection date: 2020-08-25 journal: nan DOI: 10.1101/2020.08.22.20180042 sha: doc_id: 349721 cord_uid: wdjlr4z4 file: cache/cord-349912-em1abdrg.json key: cord-349912-em1abdrg authors: Meng, Xiangming; Deng, Yanzhong; Dai, Zhiyong; Meng, Zhisheng title: COVID-19 and anosmia: A review based on up-to-date knowledge date: 2020-06-02 journal: Am J Otolaryngol DOI: 10.1016/j.amjoto.2020.102581 sha: doc_id: 349912 cord_uid: em1abdrg file: cache/cord-350094-nkzbtcfw.json key: cord-350094-nkzbtcfw authors: Barrett, Lisa F.; Lo, Kevin Bryan; Stanek, Steven R.; Walter, James W. title: Self-Limited Gastrointestinal Bleeding in COVID-19 date: 2020-07-15 journal: Clin Res Hepatol Gastroenterol DOI: 10.1016/j.clinre.2020.06.015 sha: doc_id: 350094 cord_uid: nkzbtcfw file: cache/cord-349907-dwhyx97y.json key: cord-349907-dwhyx97y authors: Noh, Ji Yeong; Yoon, Sun-Woo; Kim, Doo-Jin; Lee, Moo-Seung; Kim, Ji-Hyung; Na, Woonsung; Song, Daesub; Jeong, Dae Gwin; Kim, Hye Kwon title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 journal: Arch Virol DOI: 10.1007/s00705-017-3281-9 sha: doc_id: 349907 cord_uid: dwhyx97y file: cache/cord-349821-5ykwwq75.json key: cord-349821-5ykwwq75 authors: Ippolito, G.; Puro, V.; Heptonstall, J. title: Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date: 2006-09-09 journal: Cell Mol Life Sci DOI: 10.1007/s00018-006-6309-y sha: doc_id: 349821 cord_uid: 5ykwwq75 file: cache/cord-349954-bozgrzvf.json key: cord-349954-bozgrzvf authors: Quintaliani, Giuseppe; Reboldi, Gianpaolo; Di Napoli, Anteo; Nordio, Maurizio; Limido, Aurelio; Aucella, Filippo; Messa, Piergiorgio; Brunori, Giuliano title: Exposure to novel coronavirus in patients on renal replacement therapy during the exponential phase of COVID-19 pandemic: survey of the Italian Society of Nephrology date: 2020-07-03 journal: J Nephrol DOI: 10.1007/s40620-020-00794-1 sha: doc_id: 349954 cord_uid: bozgrzvf file: cache/cord-349745-zlhu1jit.json key: cord-349745-zlhu1jit authors: Konrad, Regina; Eberle, Ute; Dangel, Alexandra; Treis, Bianca; Berger, Anja; Bengs, Katja; Fingerle, Volker; Liebl, Bernhard; Ackermann, Nikolaus; Sing, Andreas title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.9.2000173 sha: doc_id: 349745 cord_uid: zlhu1jit file: cache/cord-350045-85jug39x.json key: cord-350045-85jug39x authors: Pruc, Michal; Golik, Dawid; Szarpak, Lukasz; Adam, Ishag; Smereka, Jacek title: Risk of coronavirus infections among medical personnel date: 2020-05-08 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.05.017 sha: doc_id: 350045 cord_uid: 85jug39x file: cache/cord-350015-mg5wiihj.json key: cord-350015-mg5wiihj authors: Chen, Yiyin; Klein, Sabra L.; Garibaldi, Brian T.; Li, Huifen; Wu, Cunjin; Osevala, Nicole M.; Li, Taisheng; Margolick, Joseph B.; Pawelec, Graham; Leng, Sean X. title: Aging in COVID-19: Vulnerability, immunity and intervention date: 2020-10-31 journal: Ageing Res Rev DOI: 10.1016/j.arr.2020.101205 sha: doc_id: 350015 cord_uid: mg5wiihj file: cache/cord-350352-wgppovfx.json key: cord-350352-wgppovfx authors: Temmam, Sarah; Barbarino, Alix; Maso, Djérène; Behillil, Sylvie; Enouf, Vincent; Huon, Christèle; Jaraud, Ambre; Chevallier, Lucie; Backovic, Marija; Pérot, Philippe; Verwaerde, Patrick; Tiret, Laurent; van der Werf, Sylvie; Eloit, Marc title: Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus date: 2020-08-29 journal: One Health DOI: 10.1016/j.onehlt.2020.100164 sha: doc_id: 350352 cord_uid: wgppovfx file: cache/cord-350103-liwvhuzj.json key: cord-350103-liwvhuzj authors: Brooks, Nathan A.; Narayan, Vikram; Hegarty, Paul K.; Zafirakis, Helen; Han, Xiang‐Yang; Kamat, Ashish M. title: The role of the urologist, BCG vaccine administration, and SARS‐CoV‐2: An overview date: 2020-06-22 journal: BJUI Compass DOI: 10.1002/bco2.21 sha: doc_id: 350103 cord_uid: liwvhuzj file: cache/cord-350235-yoy3hj3j.json key: cord-350235-yoy3hj3j authors: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 journal: EMBO Mol Med DOI: 10.15252/emmm.202012463 sha: doc_id: 350235 cord_uid: yoy3hj3j file: cache/cord-350130-c4u0gxp5.json key: cord-350130-c4u0gxp5 authors: Wu, Yi-Chi; Chen, Ching-Sung; Chan, Yu-Jiun title: The outbreak of COVID-19: An overview date: 2020-02-12 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000270 sha: doc_id: 350130 cord_uid: c4u0gxp5 file: cache/cord-349656-baoqgu8v.json key: cord-349656-baoqgu8v authors: Wang, Chen; Zhou, Yi‐Hua; Yang, Hui‐Xia; Poon, Liona C. title: Intrauterine vertical transmission of SARS‐CoV‐2: what we know so far date: 2020-04-07 journal: Ultrasound Obstet Gynecol DOI: 10.1002/uog.22045 sha: doc_id: 349656 cord_uid: baoqgu8v file: cache/cord-350212-448mv4lt.json key: cord-350212-448mv4lt authors: Chiuppesi, Flavia; Salazar, Marcela d’Alincourt; Contreras, Heidi; Nguyen, Vu; Martinez, Joy; Park, Soojin; Nguyen, Jenny; Kha, Mindy; Iniguez, Angelina; Zhou, Qiao; Kaltcheva, Teodora; Levytskyy, Roman; Ebelt, Nancy; Kang, Tae; Wu, Xiwei; Rogers, Tom; Manuel, Edwin; Shostak, Yuriy; Diamond, Don; Wussow, Felix title: Development of a Multi-Antigenic SARS-CoV-2 Vaccine Using a Synthetic Poxvirus Platform date: 2020-07-17 journal: Res Sq DOI: 10.21203/rs.3.rs-40198/v1 sha: doc_id: 350212 cord_uid: 448mv4lt file: cache/cord-350211-vuxs5wtt.json key: cord-350211-vuxs5wtt authors: Johanna, Barón‐Sánchez; Santiago, Cristina; Martín, Gabriela Goizueta‐San; Arca, Roberta; Fernández, Ruth title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 journal: Neurologia DOI: 10.1016/j.nrl.2020.07.006 sha: doc_id: 350211 cord_uid: vuxs5wtt file: cache/cord-350393-j80k2v21.json key: cord-350393-j80k2v21 authors: Chen, Liping; Huang, Shaoping; Yang, Jingmao; Cheng, Xin; Shang, Zhiyin; Lu, Hongzhou; Cheng, Jilin title: Clinical characteristics in patients with SARS‐CoV‐2/HBV co‐infection date: 2020-07-15 journal: J Viral Hepat DOI: 10.1111/jvh.13362 sha: doc_id: 350393 cord_uid: j80k2v21 file: cache/cord-349623-dw5o9i59.json key: cord-349623-dw5o9i59 authors: Miranda, José P.; Osorio, Javiera; Videla, Mauricio; Angel, Gladys; Camponovo, Rossana; Henríquez-Henríquez, Marcela title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.567572 sha: doc_id: 349623 cord_uid: dw5o9i59 file: cache/cord-350286-n7ylgqfu.json key: cord-350286-n7ylgqfu authors: Giri, Rajanish; Bhardwaj, Taniya; Shegane, Meenakshi; Gehi, Bhuvaneshwari R.; Kumar, Prateek; Gadhave, Kundlik; Oldfield, Christopher J.; Uversky, Vladimir N. title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 journal: bioRxiv DOI: 10.1101/2020.03.13.990598 sha: doc_id: 350286 cord_uid: n7ylgqfu file: cache/cord-350104-b99y6n43.json key: cord-350104-b99y6n43 authors: de Zwart, Onno; Veldhuijzen, Irene K.; Elam, Gillian; Aro, Arja R.; Abraham, Thomas; Bishop, George D.; Voeten, Hélène A. C. M.; Richardus, Jan Hendrik; Brug, Johannes title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey date: 2009-01-06 journal: Int J Behav Med DOI: 10.1007/s12529-008-9008-2 sha: doc_id: 350104 cord_uid: b99y6n43 file: cache/cord-350172-w3yoxhsg.json key: cord-350172-w3yoxhsg authors: Mertens, Pascal; De Vos, Nathalie; Martiny, Delphine; Jassoy, Christian; Mirazimi, Ali; Cuypers, Lize; Van den Wijngaert, Sigi; Monteil, Vanessa; Melin, Pierrette; Stoffels, Karolien; Yin, Nicolas; Mileto, Davide; Delaunoy, Sabrina; Magein, Henri; Lagrou, Katrien; Bouzet, Justine; Serrano, Gabriela; Wautier, Magali; Leclipteux, Thierry; Van Ranst, Marc; Vandenberg, Olivier title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00225 sha: doc_id: 350172 cord_uid: w3yoxhsg file: cache/cord-349762-f5no10eq.json key: cord-349762-f5no10eq authors: Nagura-Ikeda, Mayu; Imai, Kazuo; Tabata, Sakiko; Miyoshi, Kazuyasu; Murahara, Nami; Mizuno, Tsukasa; Horiuchi, Midori; Kato, Kento; Imoto, Yoshitaka; Iwata, Maki; Mimura, Satoshi; Ito, Toshimitsu; Tamura, Kaku; Kato, Yasuyuki title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 journal: J Clin Microbiol DOI: 10.1128/jcm.01438-20 sha: doc_id: 349762 cord_uid: f5no10eq file: cache/cord-350182-s10nong7.json key: cord-350182-s10nong7 authors: Milionis, Charalampos; Milioni, Stella Olga title: A brief analysis and hypotheses about the risk of COVID-19 for people with type 1 and type 2 diabetes mellitus date: 2020-07-20 journal: J Diabetes Metab Disord DOI: 10.1007/s40200-020-00592-3 sha: doc_id: 350182 cord_uid: s10nong7 file: cache/cord-349477-3qhpu7v0.json key: cord-349477-3qhpu7v0 authors: Jarynowski, A.; Wojta-Kempa, M.; Krzowski, L. title: An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland date: 2020-10-15 journal: nan DOI: 10.1101/2020.10.14.20090985 sha: doc_id: 349477 cord_uid: 3qhpu7v0 file: cache/cord-350134-gl3qtoug.json key: cord-350134-gl3qtoug authors: Brun, Gilles; Hak, Jean-François; Coze, Stéphanie; Kaphan, Elsa; Carvelli, Julien; Girard, Nadine; Stellmann, Jan-Patrick title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? date: 2020-05-22 journal: Neurol Neuroimmunol Neuroinflamm DOI: 10.1212/nxi.0000000000000777 sha: doc_id: 350134 cord_uid: gl3qtoug file: cache/cord-350189-2su7oqbz.json key: cord-350189-2su7oqbz authors: Elmén, Joacim; Thonberg, Håkan; Ljungberg, Karl; Frieden, Miriam; Westergaard, Majken; Xu, Yunhe; Wahren, Britta; Liang, Zicai; Ørum, Henrik; Koch, Troels; Wahlestedt, Claes title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 journal: Nucleic Acids Res DOI: 10.1093/nar/gki193 sha: doc_id: 350189 cord_uid: 2su7oqbz file: cache/cord-350513-ho32ajsx.json key: cord-350513-ho32ajsx authors: Chen, Paul Chih‐Hsueh; Hsiao, Cheng‐Hsiang title: Re: To KF, Tong JH, Chan PK, et al. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. J Pathol 2004; 202: 157–163 date: 2004-05-07 journal: J Pathol DOI: 10.1002/path.1575 sha: doc_id: 350513 cord_uid: ho32ajsx file: cache/cord-350328-wu1ygt6w.json key: cord-350328-wu1ygt6w authors: Tambyah, P. A. title: SARS: responding to an unknown virus date: 2004-07-14 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-004-1175-8 sha: doc_id: 350328 cord_uid: wu1ygt6w file: cache/cord-350342-j4p8235a.json key: cord-350342-j4p8235a authors: Brocato, Rebecca L.; Principe, Lucia M.; Kim, Robert K.; Zeng, Xiankun; Williams, Janice A.; Liu, Yanan; Li, Rong; Smith, Jeffrey M.; Golden, Joseph W.; Gangemi, Dave; Youssef, Sawsan; Wang, Zhongde; Glanville, Jacob; Hooper, Jay W. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 journal: J Virol DOI: 10.1128/jvi.01683-20 sha: doc_id: 350342 cord_uid: j4p8235a file: cache/cord-350242-4u1iyf0p.json key: cord-350242-4u1iyf0p authors: Yaniv, K.; Shagan, M.; Kramarsky-Winter, E.; Indenbaum, V.; Weil, M.; Elul, M.; Erster, O.; Sela Brown, A.; Mendelson, E.; Mannasse, B.; Shirazi, R.; Lakkakula, S.; Miron, O.; Rinott, E.; Baibich, R. G.; Bigler, I.; Malul, M.; Rishti, R.; Brenner, A.; Lewis, Y. E.; Friedler, E.; Gilboa, Y.; Sabach, S.; Alfiya, Y.; Cheruti, U.; Davidovitch, N.; Bilenko, N.; Moran-Gilad, J.; Berchenko, Y.; Bar-Or, I.; Kushmaro, A. title: City-level SARS-CoV-2 sewage surveillance date: 2020-10-21 journal: nan DOI: 10.1101/2020.10.19.20215244 sha: doc_id: 350242 cord_uid: 4u1iyf0p file: cache/cord-350557-7i7122zi.json key: cord-350557-7i7122zi authors: Rawlings, Stephen A; Ignacio, Caroline; Porrachia, Magali; Du, Pinyi; Smith, Davey M; Chaillon, Antoine title: No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date: 2020-08-07 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofaa325 sha: doc_id: 350557 cord_uid: 7i7122zi file: cache/cord-350095-hsl1hfds.json key: cord-350095-hsl1hfds authors: Shiu, Stephen Y. W.; Reiter, Russel J.; Tan, Dun‐Xian; Pang, Shiu F. title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? date: 2003-06-16 journal: J Pineal Res DOI: 10.1034/j.1600-079x.2003.00068.x sha: doc_id: 350095 cord_uid: hsl1hfds file: cache/cord-350627-4pgish5x.json key: cord-350627-4pgish5x authors: Zhao, Yu; Zhao, Zixian; Wang, Yujia; Zhou, Yueqing; Ma, Yu; Zuo, Wei title: Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date: 2020-01-26 journal: bioRxiv DOI: 10.1101/2020.01.26.919985 sha: doc_id: 350627 cord_uid: 4pgish5x file: cache/cord-350029-1y5ex4d5.json key: cord-350029-1y5ex4d5 authors: McDade, Thomas W.; Sancilio, Amelia title: Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date: 2020-08-09 journal: Am J Hum Biol DOI: 10.1002/ajhb.23483 sha: doc_id: 350029 cord_uid: 1y5ex4d5 file: cache/cord-350437-dq1il88y.json key: cord-350437-dq1il88y authors: Reale, Maria Lucia; Bironzo, Paolo; Bertaglia, Valentina; Palesandro, Erica; Leone, Gianmarco; Tabbò, Fabrizio; Bungaro, Maristella; Audisio, Marco; Mariniello, Annapaola; Rapetti, Simonetta G.; Di Stefano, Rosario F.; Artusio, Elisa; Capelletto, Enrica; Sperone, Paola; Boccuzzi, Adriana; Calandri, Marco; Perboni, Alberto; Malapelle, Umberto; Passiglia, Francesco; Novello, Silvia title: SARS-CoV-2 Infection in Cancer Patients: A Picture of an Italian Onco-Covid Unit date: 2020-08-19 journal: Front Oncol DOI: 10.3389/fonc.2020.01722 sha: doc_id: 350437 cord_uid: dq1il88y file: cache/cord-350401-suefuurq.json key: cord-350401-suefuurq authors: Lima-Setta, Fernanda; Magalhães-Barbosa, Maria Clara de; Rodrigues-Santos, Gustavo; Figueiredo, Elaine Augusta das Neves; Jacques, Melissa de Lorena; Zeitel, Raquel de Seixas; Sapolnik, Roberto; Borges, Cibelle Teixeira da Siva; Lanziotti, Vanessa Soares; Castro, Roberta Esteves Vieira de; Bellinat, Ana Paula Novaes; Silva, Thiago Peres da; Oliveira, Felipe Rezende Caino de; Reis, Bárbara Carvalho Santos dos; Castro, Natália Almeida de Arnaldo Silva Rodriguez; Macedo, João Henrique Garcia Cobas; Scarlato, Ana Carolina Cabral Pinheiro; Riveiro, Paula Marins; Mota, Isabele Coelho Fonseca da; Lorenzo, Vivian Botelho; Lucena, Natalia Martins Lima de; Azevedo, Zina Maria Almeida de; Cunha, Antonio José L.A.; Prata-Barbosa, Arnaldo title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() date: 2020-11-09 journal: J Pediatr (Rio J) DOI: 10.1016/j.jped.2020.10.008 sha: doc_id: 350401 cord_uid: suefuurq file: cache/cord-350451-lf27iuwk.json key: cord-350451-lf27iuwk authors: Benedetti, Francesca; Pachetti, Maria; Marini, Bruna; Ippodrino, Rudy; Ciccozzi, Massimo; Zella, Davide title: SARS‐CoV‐2: March toward adaptation date: 2020-07-11 journal: J Med Virol DOI: 10.1002/jmv.26233 sha: doc_id: 350451 cord_uid: lf27iuwk file: cache/cord-350817-tmszrtju.json key: cord-350817-tmszrtju authors: Hoepel, Willianne; Chen, Hung-Jen; Allahverdiyeva, Sona; Manz, Xue; Aman, Jurjan; Bonta, Peter; Brouwer, Philip; de Taeye, Steven; Caniels, Tom; van der Straten, Karlijn; Golebski, Korneliusz; Griffith, Guillermo; Jonkers, René; Larsen, Mads; Linty, Federica; Neele, Annette; Nouta, Jan; van Baarle, Frank; van Drunen, Cornelis; Vlaar, Alexander; de Bree, Godelieve; Sanders, Rogier; Willemsen, Lisa; Wuhrer, Manfred; Bogaard, Harm Jan; van Gils, Marit; Vidarsson, Gestur; de Winther, Menno; den Dunnen, Jeroen title: Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date: 2020-07-13 journal: bioRxiv DOI: 10.1101/2020.07.13.190140 sha: doc_id: 350817 cord_uid: tmszrtju file: cache/cord-350101-t34myl7l.json key: cord-350101-t34myl7l authors: Henrique Braz‐Silva, Paulo; Pallos, Debora; Giannecchini, Simone; To, Kelvin Kai‐Wang title: SARS‐CoV‐2: What can saliva tell us? date: 2020-05-11 journal: Oral Dis DOI: 10.1111/odi.13365 sha: doc_id: 350101 cord_uid: t34myl7l file: cache/cord-350733-0zghspb8.json key: cord-350733-0zghspb8 authors: Aronson, Jeffrey K.; Auker‐Howlett, Daniel; Ghiara, Virginia; Kelly, Michael P.; Williamson, Jon title: The use of mechanistic reasoning in assessing coronavirus interventions date: 2020-07-15 journal: J Eval Clin Pract DOI: 10.1111/jep.13438 sha: doc_id: 350733 cord_uid: 0zghspb8 file: cache/cord-349923-cja8i0hw.json key: cord-349923-cja8i0hw authors: Habibzadeh, Parham; Stoneman, Emily K title: The Novel Coronavirus: A Bird's Eye View date: 2020-02-05 journal: Int J Occup Environ Med DOI: 10.15171/ijoem.2020.1921 sha: doc_id: 349923 cord_uid: cja8i0hw file: cache/cord-350679-69lv4wbz.json key: cord-350679-69lv4wbz authors: Shinde, Rajesh S.; Naik, Mekhala D.; Shinde, Shital R.; Bhandare, Manish S.; Chaudhari, Vikram A.; Shrikhande, Shailesh V.; Dcruz, Anil K. title: To Do or Not to Do?—A Review of Cancer Surgery Triage Guidelines in COVID-19 Pandemic date: 2020-05-11 journal: Indian J Surg Oncol DOI: 10.1007/s13193-020-01086-7 sha: doc_id: 350679 cord_uid: 69lv4wbz file: cache/cord-350686-q2bu7o4i.json key: cord-350686-q2bu7o4i authors: Bilder, Christopher R; Iwen, Peter C; Abdalhamid, Baha title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa774 sha: doc_id: 350686 cord_uid: q2bu7o4i file: cache/cord-350309-j4oh1z8m.json key: cord-350309-j4oh1z8m authors: Liu, D. X.; Yuan, Q.; Liao, Y. title: Coronavirus envelope protein: A small membrane protein with multiple functions date: 2007-05-29 journal: Cell Mol Life Sci DOI: 10.1007/s00018-007-7103-1 sha: doc_id: 350309 cord_uid: j4oh1z8m file: cache/cord-350737-nrtrhq1f.json key: cord-350737-nrtrhq1f authors: Chen, Xinchun; Zhou, Boping; Li, Meizhong; Liang, Xiaorong; Wang, Huosheng; Yang, Guilin; Wang, Hui; Le, Xiaohua title: Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date: 2004-04-01 journal: J Infect Dis DOI: 10.1086/380397 sha: doc_id: 350737 cord_uid: nrtrhq1f file: cache/cord-350317-a9qd3xdr.json key: cord-350317-a9qd3xdr authors: Xu, Qiannan; Chen, Lihong; Li, Xia; Zheng, Jie title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 date: 2020-11-05 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.10.084 sha: doc_id: 350317 cord_uid: a9qd3xdr file: cache/cord-350505-uh8r2vyz.json key: cord-350505-uh8r2vyz authors: Kalantar-Zadeh, Kourosh; Ward, Stephanie A.; Kalantar-Zadeh, Kamyar; El-Omar, Emad M. title: Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles date: 2020-05-01 journal: ACS Nano DOI: 10.1021/acsnano.0c03402 sha: doc_id: 350505 cord_uid: uh8r2vyz file: cache/cord-350925-1h6pbfwp.json key: cord-350925-1h6pbfwp authors: da Silva, Priscilla Gomes; Nascimento, Maria São José; Soares, Ruben R.G.; Sousa, Sofia I.V.; Mesquita, João R. title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142802 sha: doc_id: 350925 cord_uid: 1h6pbfwp file: cache/cord-350753-qbm145tr.json key: cord-350753-qbm145tr authors: Krüttgen, Alexander; Cornelissen, Christian G.; Dreher, Michael; Hornef, Mathias W.; Imöhl, Matthias; Kleines, Michael title: Determination of SARS-CoV-2 antibodies with assays from Diasorin, Roche and IDvet date: 2020-09-23 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113978 sha: doc_id: 350753 cord_uid: qbm145tr file: cache/cord-350821-0qfoc553.json key: cord-350821-0qfoc553 authors: Jahromi, Reza; Mogharab, Vahid; Jahromi, Hossein; Avazpour, Arezoo title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date: 2020-06-01 journal: bioRxiv DOI: 10.1101/2020.05.29.124107 sha: doc_id: 350821 cord_uid: 0qfoc553 file: cache/cord-350959-bsbz3a1l.json key: cord-350959-bsbz3a1l authors: Dovey, Zachary; Mohamed, Nihal; Gharib, Yasmine; Ratnani, Parita; Hammouda, Nada; Nair, Sujit; Chakravarty, Dimple; Stanislaw, Sobotka; Lantz, Anna; Wiklund, Peter; Kyprianou, Natasha; Tewari, Ash title: Impact of COVID-19 on Prostate Cancer Management: Guidelines for Urologists date: 2020-06-16 journal: nan DOI: 10.1016/j.euros.2020.05.005 sha: doc_id: 350959 cord_uid: bsbz3a1l file: cache/cord-350618-rtilfnzi.json key: cord-350618-rtilfnzi authors: Lambelet, Valentine; Vouga, Manon; Pomar, Léo; Favre, Guillaume; Gerbier, Eva; Panchaud, Alice; Baud, David title: Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date: 2020-05-26 journal: Prenat Diagn DOI: 10.1002/pd.5759 sha: doc_id: 350618 cord_uid: rtilfnzi file: cache/cord-350903-nwagvvc5.json key: cord-350903-nwagvvc5 authors: Softic, Laurent; Brillet, Rozenn; Berry, François; Ahnou, Nazim; Nevers, Quentin; Morin-Dewaele, Margot; Hamadat, Sabah; Bruscella, Patrice; Fourati, Slim; Pawlotsky, Jean-Michel; Ahmed-Belkacem, Abdelhakim title: Inhibition of SARS-CoV-2 Infection by the Cyclophilin Inhibitor Alisporivir (Debio 025) date: 2020-06-23 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.00876-20 sha: doc_id: 350903 cord_uid: nwagvvc5 file: cache/cord-350972-0n4dumgg.json key: cord-350972-0n4dumgg authors: Sing, Chor-Wing; Tan, Kathryn C B; Wong, Ian C K; Cheung, Bernard M Y; Cheung, Ching-Lung title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa992 sha: doc_id: 350972 cord_uid: 0n4dumgg file: cache/cord-351169-y91fdf66.json key: cord-351169-y91fdf66 authors: Phillips, Lia; Pavisic, Jovana; Kaur, Dominder; Dorrello, N. Valerio; Broglie, Larisa; Hijiya, Nobuko title: Successful management of SARS-CoV-2 acute respiratory distress syndrome and newly diagnosed acute lymphoblastic leukemia date: 2020-09-14 journal: Blood Adv DOI: 10.1182/bloodadvances.2020002745 sha: doc_id: 351169 cord_uid: y91fdf66 file: cache/cord-350957-10wcqgaq.json key: cord-350957-10wcqgaq authors: Shen, Zu T.; Sigalov, Alexander B. title: SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice date: 2016-06-28 journal: Sci Rep DOI: 10.1038/srep28672 sha: doc_id: 350957 cord_uid: 10wcqgaq file: cache/cord-350990-tywbe4o2.json key: cord-350990-tywbe4o2 authors: Checchi, Vittorio; Bellini, Pierantonio; Bencivenni, Davide; Consolo, Ugo title: COVID‐19 dentistry‐related aspects: a literature overview date: 2020-07-05 journal: Int Dent J DOI: 10.1111/idj.12601 sha: doc_id: 350990 cord_uid: tywbe4o2 file: cache/cord-350622-8tgxdbyi.json key: cord-350622-8tgxdbyi authors: Palit, Partha; Chattopadhyay, Debprasad; Thomas, Sabu; Kundu, Amit; Kim, Hyung Sik; Rezaei, Nima title: Phytopharmaceuticals mediated Furin and TMPRSS2 receptor blocking: can it be a potential therapeutic option for Covid-19? date: 2020-10-28 journal: Phytomedicine DOI: 10.1016/j.phymed.2020.153396 sha: doc_id: 350622 cord_uid: 8tgxdbyi file: cache/cord-350935-p6euuop3.json key: cord-350935-p6euuop3 authors: Doğan, Tunca; Atas, Heval; Joshi, Vishal; Atakan, Ahmet; Rifaioglu, Ahmet Sureyya; Nalbat, Esra; Nightingale, Andrew; Saidi, Rabie; Volynkin, Vladimir; Zellner, Hermann; Cetin-Atalay, Rengul; Martin, Maria; Atalay, Volkan title: CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date: 2020-09-15 journal: bioRxiv DOI: 10.1101/2020.09.14.296889 sha: doc_id: 350935 cord_uid: p6euuop3 file: cache/cord-351031-e8suoeim.json key: cord-351031-e8suoeim authors: Liang En Ian, Wee; Sim, Xiang Ying Jean; Conceicao, Edwin Philip; Aung, May Kyawt; Tan, Kwee Yuen; Ko, Kwan Ki Karrie; Wong, Hei Man; Wijaya, Limin; Tan, Ban Hock; Venkatachalam, Indumathi; Ling, Moi Lin title: Containing COVID-19 outside the isolation ward: the impact of an infection control bundle on environmental contamination and transmission in a cohorted general ward date: 2020-06-26 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.06.188 sha: doc_id: 351031 cord_uid: e8suoeim file: cache/cord-350992-l6l24pco.json key: cord-350992-l6l24pco authors: Roldan, Eugenia Quiros; Biasiotto, Giorgio; Magro, Paola; Zanella, Isabella title: The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against Sars-Cov-2 infection (COVID-19): A role for iron homeostasis? date: 2020-05-13 journal: Pharmacol Res DOI: 10.1016/j.phrs.2020.104904 sha: doc_id: 350992 cord_uid: l6l24pco file: cache/cord-351002-msjurww1.json key: cord-351002-msjurww1 authors: Ouanes, Y.; Bibi, M.; Baradai, N.; Boukhris, M.; Chaker, K.; Kacem, A.; Hedhli, H.; Mrad Deli, K.; Sellami, A.; Ben Rhouma, S.; Nouira, Y. title: Does BCG protect against SARS-CoV-2 infection ?: elements of proof. date: 2020-05-06 journal: nan DOI: 10.1101/2020.05.01.20087437 sha: doc_id: 351002 cord_uid: msjurww1 file: cache/cord-351100-llyl97ry.json key: cord-351100-llyl97ry authors: Cariani, Lisa; Orena, Beatrice Silvia; Ambrogi, Federico; Gambazza, Simone; Maraschini, Anna; Dodaro, Antonella; Oggioni, Massimo; Orlandi, Annarosa; Pirrone, Alessia; Uceda Renteria, Sara; Bernazzani, Mara; Cantù, Anna Paola; Ceriotti, Ferruccio; Lunghi, Giovanna title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17155313 sha: doc_id: 351100 cord_uid: llyl97ry file: cache/cord-350904-wyg8ikph.json key: cord-350904-wyg8ikph authors: Gubernatorova, E.O.; Gorshkova, E.A.; Polinova, A.I.; Drutskaya, M.D. title: IL-6: relevance for immunopathology of SARS-CoV-2 date: 2020-05-20 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2020.05.009 sha: doc_id: 350904 cord_uid: wyg8ikph file: cache/cord-351028-p5cq2is5.json key: cord-351028-p5cq2is5 authors: Yang, Jia-Wei; Yang, Ling; Luo, Rong-Guang; Xu, Jin-Fu title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond date: 2020-06-27 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.020 sha: doc_id: 351028 cord_uid: p5cq2is5 file: cache/cord-351218-ei8dyxfg.json key: cord-351218-ei8dyxfg authors: Charles Bronson, Stephen title: Letter to the Editor in response to the article “Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? date: 2020-07-03 journal: Diabetes Res Clin Pract DOI: 10.1016/j.diabres.2020.108306 sha: doc_id: 351218 cord_uid: ei8dyxfg file: cache/cord-351038-k2m6woow.json key: cord-351038-k2m6woow authors: Arun Krishnan, R.; Elizabeth Thomas, Rhema; Sukumaran, Ajaikumar; Paul, Jofy K.; Vasudevan, D. M. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 journal: Indian J Clin Biochem DOI: 10.1007/s12291-020-00906-5 sha: doc_id: 351038 cord_uid: k2m6woow file: cache/cord-351115-dy81dtnk.json key: cord-351115-dy81dtnk authors: Wang, Chen; Konecki, Daniel M.; Marciano, David C.; Govindarajan, Harikumar; Williams, Amanda M.; Wastuwidyaningtyas, Brigitta; Bourquard, Thomas; Katsonis, Panagiotis; Lichtarge, Olivier title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 journal: Res Sq DOI: 10.21203/rs.3.rs-95030/v1 sha: doc_id: 351115 cord_uid: dy81dtnk file: cache/cord-351116-jwy6k0ih.json key: cord-351116-jwy6k0ih authors: O'Reilly, GM; Mitchell, RD; Mitra, B; Akhlaghi, H; Tran, V; Furyk, J; Buntine, P; Bannon‐Murphy, H; Amos, T; Udaya Kumar, M; Perkins, E; Prentice, Alexandra; Szwarcberg, Olivia; Loughman, A; Lowry, N; Colwell, S; Noonan, MP; Hiller, R; Paton, A; Smit, D; Cameron, PA title: Epidemiology and clinical features of emergency department patients with suspected and confirmed COVID‐19: A multisite report from the COVED Quality Improvement Project for July 2020 (COVED‐3) date: 2020-09-21 journal: Emerg Med Australas DOI: 10.1111/1742-6723.13651 sha: doc_id: 351116 cord_uid: jwy6k0ih file: cache/cord-351189-56am76lb.json key: cord-351189-56am76lb authors: Rosen, Melissa H; Axelrad, Jordan; Hudesman, David; Rubin, David T; Chang, Shannon title: Management of Acute Severe Ulcerative Colitis in a Pregnant Woman With COVID-19 Infection: A Case Report and Review of the Literature date: 2020-05-12 journal: Inflamm Bowel Dis DOI: 10.1093/ibd/izaa109 sha: doc_id: 351189 cord_uid: 56am76lb file: cache/cord-351278-nm2bq717.json key: cord-351278-nm2bq717 authors: Thompson, Craig; Grayson, Nicholas; Paton, Robert; Lourenço, José; Penman, Bridget; Lee, Lian Ni; Odon, Valerie; Mongkolsapaya, Juthathip; Chinnakannan, Senthil; Dejnirattisai, Wanwisa; Edmans, Matthew; Fyfe, Alexander; Imlach, Carol; Kooblall, Kreepa; Lim, Nicholas; Liu, Chang; Lopez-Camacho, Cesar; McInally, Carol-Anne; Ramamurthy, Narayan; Ratcliff, Jeremy; Supasa, Piyada; Wang, Beibei; Mentzer, Alexander J; Turner, Marc; Semple, Calum; Baillie, John Kenneth; Harvala, Heli; Screaton, Gavin; Temperton, Nigel; Klenerman, Paul; Jarvis, Lisa; Gupta, Sunetra; Simmonds, Peter title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure date: 2020-04-17 journal: nan DOI: 10.1101/2020.04.13.20060467 sha: doc_id: 351278 cord_uid: nm2bq717 file: cache/cord-351092-b01o6f69.json key: cord-351092-b01o6f69 authors: De Francesco, Maria A.; Alberici, Federico; Bossini, Nicola; Scolari, Francesco; Pascucci, Federico; Tomasoni, Gabriele; Caruso, Arnaldo title: Pneumocystis jirevocii and SARS-CoV-2 Co-Infection: A Common Feature in Transplant Recipients? date: 2020-09-18 journal: Vaccines (Basel) DOI: 10.3390/vaccines8030544 sha: doc_id: 351092 cord_uid: b01o6f69 file: cache/cord-351314-atsuh8e2.json key: cord-351314-atsuh8e2 authors: Bryson-Cahn, Chloe; Duchin, Jeffrey; Makarewicz, Vanessa A; Kay, Meagan; Rietberg, Krista; Napolitano, Nathanael; Kamangu, Carole; Dellit, Timothy H; Lynch, John B title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa256 sha: doc_id: 351314 cord_uid: atsuh8e2 file: cache/cord-350949-ystkjdwk.json key: cord-350949-ystkjdwk authors: Gao, Yi-jie; Ye, Lei; Zhang, Jia-shuo; Yin, Yang-xue; Liu, Min; Yu, Hong-biao; Zhou, Rong title: Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date: 2020-08-03 journal: BMC Infect Dis DOI: 10.1186/s12879-020-05274-2 sha: doc_id: 350949 cord_uid: ystkjdwk file: cache/cord-351011-v4zmksio.json key: cord-351011-v4zmksio authors: Golden, Joseph W.; Cline, Curtis R.; Zeng, Xiankun; Garrison, Aura R.; Carey, Brian D.; Mucker, Eric M.; White, Lauren E.; Shamblin, Joshua D.; Brocato, Rebecca L.; Liu, Jun; Babka, April M.; Rauch, Hypaitia B.; Smith, Jeffrey M.; Hollidge, Bradley S.; Fitzpatrick, Collin; Badger, Catherine V.; Hooper, Jay W. title: Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date: 2020-07-09 journal: bioRxiv DOI: 10.1101/2020.07.09.195230 sha: doc_id: 351011 cord_uid: v4zmksio file: cache/cord-350855-gofzhff7.json key: cord-350855-gofzhff7 authors: Hou, Yixuan J.; Okuda, Kenichi; Edwards, Caitlin E.; Martinez, David R.; Asakura, Takanori; Dinnon, Kenneth H.; Kato, Takafumi; Lee, Rhianna E.; Yount, Boyd L.; Mascenik, Teresa M.; Chen, Gang; Olivier, Kenneth N.; Ghio, Andrew; Tse, Longping V.; Leist, Sarah R.; Gralinski, Lisa E.; Schäfer, Alexandra; Dang, Hong; Gilmore, Rodney; Nakano, Satoko; Sun, Ling; Fulcher, M. Leslie; Livraghi-Butrico, Alessandra; Nicely, Nathan I.; Cameron, Mark; Cameron, Cheryl; Kelvin, David J.; de Silva, Aravinda; Margolis, David M.; Markmann, Alena; Bartelt, Luther; Zumwalt, Ross; Martinez, Fernando J.; Salvatore, Steven P.; Borczuk, Alain; Tata, Purushothama R.; Sontake, Vishwaraj; Kimple, Adam; Jaspers, Ilona; O’Neal, Wanda K.; Randell, Scott H.; Boucher, Richard C.; Baric, Ralph S. title: SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract date: 2020-05-27 journal: Cell DOI: 10.1016/j.cell.2020.05.042 sha: doc_id: 350855 cord_uid: gofzhff7 file: cache/cord-351224-jeedo5mc.json key: cord-351224-jeedo5mc authors: GeurtsvanKessel, Corine H.; Okba, Nisreen M. A.; Igloi, Zsofia; Bogers, Susanne; Embregts, Carmen W. E.; Laksono, Brigitta M.; Leijten, Lonneke; Rokx, Casper; Rijnders, Bart; Rahamat-Langendoen, Janette; van den Akker, Johannes P. C.; van Kampen, Jeroen J. A.; van der Eijk, Annemiek A.; van Binnendijk, Rob S.; Haagmans, Bart; Koopmans, Marion title: An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment date: 2020-07-06 journal: Nat Commun DOI: 10.1038/s41467-020-17317-y sha: doc_id: 351224 cord_uid: jeedo5mc file: cache/cord-351283-1y9dfobn.json key: cord-351283-1y9dfobn authors: Tan, Bai‐Hong; Zhang, Yan; Gui, Yue; Wu, Shuang; Li, Yan‐Chao title: The possible impairment of respiratory‐related neural loops may be associated with the silent pneumonia induced by SARS‐CoV‐2 date: 2020-06-11 journal: J Med Virol DOI: 10.1002/jmv.26158 sha: doc_id: 351283 cord_uid: 1y9dfobn file: cache/cord-351107-a5bx74ao.json key: cord-351107-a5bx74ao authors: Phua, Ghee-Chee; Govert, Joseph title: Mechanical Ventilation in an Airborne Epidemic date: 2008-06-30 journal: Clinics in Chest Medicine DOI: 10.1016/j.ccm.2008.01.001 sha: doc_id: 351107 cord_uid: a5bx74ao file: cache/cord-351305-6vtv2xuh.json key: cord-351305-6vtv2xuh authors: Schramm, Markus A.; Venhoff, Nils; Wagner, Dirk; Thiel, Jens; Huzly, Daniela; Craig-Mueller, Nils; Panning, Marcus; Hengel, Hartmut; Kern, Winfried V.; Voll, Reinhard E. title: COVID-19 in a Severely Immunosuppressed Patient With Life-Threatening Eosinophilic Granulomatosis With Polyangiitis date: 2020-08-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.02086 sha: doc_id: 351305 cord_uid: 6vtv2xuh file: cache/cord-351225-dq0xu85c.json key: cord-351225-dq0xu85c authors: Poutanen, Susan M.; McGeer, Allison J. title: Transmission and control of SARS date: 2004 journal: Curr Infect Dis Rep DOI: 10.1007/s11908-004-0012-7 sha: doc_id: 351225 cord_uid: dq0xu85c file: cache/cord-351269-xjy6chia.json key: cord-351269-xjy6chia authors: Wu, Y; Liu, C; Dong, L; Zhang, C; Chen, Y; Liu, J; Zhang, C; Duan, C; Zhang, H; Mol, BW; Dennis, C‐L; Yin, T; Yang, J; Huang, H title: Coronavirus disease 2019 among pregnant Chinese women: case series data on the safety of vaginal birth and breastfeeding date: 2020-05-26 journal: BJOG DOI: 10.1111/1471-0528.16276 sha: doc_id: 351269 cord_uid: xjy6chia file: cache/cord-351321-6d2mn5ok.json key: cord-351321-6d2mn5ok authors: Gouveia, Duarte; Miotello, Guylaine; Gallais, Fabrice; Gaillard, Jean-Charles; Debroas, Stéphanie; Bellanger, Laurent; Lavigne, Jean-Philippe; Sotto, Albert; Grenga, Lucia; Pible, Olivier; Armengaud, Jean title: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date: 2020-06-19 journal: bioRxiv DOI: 10.1101/2020.06.19.161000 sha: doc_id: 351321 cord_uid: 6d2mn5ok file: cache/cord-351430-bpv7p7zo.json key: cord-351430-bpv7p7zo authors: Pequeno, Pedro; Mendel, Bruna; Rosa, Clarissa; Bosholn, Mariane; Souza, Jorge Luiz; Baccaro, Fabricio; Barbosa, Reinaldo; Magnusson, William title: Air transportation, population density and temperature predict the spread of COVID-19 in Brazil date: 2020-06-03 journal: PeerJ DOI: 10.7717/peerj.9322 sha: doc_id: 351430 cord_uid: bpv7p7zo file: cache/cord-351367-ral9sbfy.json key: cord-351367-ral9sbfy authors: Scarlattei, Maura; Baldari, Giorgio; Silva, Mario; Bola, Stefano; Sammartano, Antonino; Migliari, Silvia; Graziani, Tiziano; Cidda, Carla; Sverzellati, Nicola; Ruffini, Livia title: Unknown SARS-CoV-2 pneumonia detected by PET/CT in patients with cancer date: 2020-06-22 journal: Tumori DOI: 10.1177/0300891620935983 sha: doc_id: 351367 cord_uid: ral9sbfy file: cache/cord-351512-h4vigeuy.json key: cord-351512-h4vigeuy authors: Zhang, Lin; Zhao, Wenjing; Sun, Beibei; Huang, Ying; Glänzel, Wolfgang title: How scientific research reacts to international public health emergencies: a global analysis of response patterns date: 2020-06-09 journal: Scientometrics DOI: 10.1007/s11192-020-03531-4 sha: doc_id: 351512 cord_uid: h4vigeuy file: cache/cord-351340-7y19ystp.json key: cord-351340-7y19ystp authors: Rao, Gundu H. R. title: Coronavirus Disease and Acute Vascular Events date: 2020-07-31 journal: Clin Appl Thromb Hemost DOI: 10.1177/1076029620929091 sha: doc_id: 351340 cord_uid: 7y19ystp file: cache/cord-351354-10rusr6j.json key: cord-351354-10rusr6j authors: Chan, Louis Y.; Lee, Nelson; Chan, Paul K.S.; Wu, Alan; Rainer, Timothy H.; Li, Philip K.T.; Fung, Hong; Sung, Joseph JY title: Diagnostic Criteria during SARS Outbreak in Hong Kong date: 2004-06-17 journal: Emerg Infect Dis DOI: 10.3201/eid1006.030618 sha: doc_id: 351354 cord_uid: 10rusr6j file: cache/cord-351489-tzmev77c.json key: cord-351489-tzmev77c authors: Yuan, Shuofeng; Chan, Chris Chun-Yiu; Chik, Kenn Ka-Heng; Tsang, Jessica Oi-Ling; Liang, Ronghui; Cao, Jianli; Tang, Kaiming; Cai, Jian-Piao; Ye, Zi-Wei; Yin, Feifei; To, Kelvin Kai-Wang; Chu, Hin; Jin, Dong-Yan; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung; Chan, Jasper Fuk-Woo title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 journal: Viruses DOI: 10.3390/v12060628 sha: doc_id: 351489 cord_uid: tzmev77c file: cache/cord-351503-2f0sk24j.json key: cord-351503-2f0sk24j authors: Pua, Uei; Wong, Daniel title: What Is Needed to Make Interventional Radiology Ready for COVID-19? Lessons from SARS-CoV Epidemic date: 2020-03-13 journal: Korean J Radiol DOI: 10.3348/kjr.2020.0163 sha: doc_id: 351503 cord_uid: 2f0sk24j file: cache/cord-351532-2yd4wg9v.json key: cord-351532-2yd4wg9v authors: Huang, Yin-Qiu; Tang, Sheng-Quan; Xu, Xiao-Lei; Zeng, Yan-Ming; He, Xiao-Qing; Li, Yao; Harypursat, Vijay; Lu, Yan-Qiu; Wan, Yan; Zhang, Lu; Sun, Qiang-Zhong; Sun, Nan-Nan; Wang, Gui-Xue; Yang, Zhong-Ping; Chen, Yao-Kai title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study date: 2020-07-14 journal: Front Pharmacol DOI: 10.3389/fphar.2020.01071 sha: doc_id: 351532 cord_uid: 2yd4wg9v file: cache/cord-351559-az4pgi9k.json key: cord-351559-az4pgi9k authors: Turjya, Rafeed Rahman; Khan, Md. Abdullah-Al-Kamran; Islam, Abul Bashar Mir Md. Khademul title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 journal: bioRxiv DOI: 10.1101/2020.06.29.177204 sha: doc_id: 351559 cord_uid: az4pgi9k file: cache/cord-351644-pl7xpivx.json key: cord-351644-pl7xpivx authors: Gao, Yelei; Liu, Rui; Zhou, Qi; Wang, Xingmei; Huang, Liping; Shi, Qianling; Wang, Zijun; Lu, Shuya; Li, Weiguo; Ma, Yanfang; Luo, Xufei; Fukuoka, Toshio; Ahn, Hyeong Sik; Lee, Myeong Soo; Luo, Zhengxiu; Liu, Enmei; Chen, Yaolong; Shu, Chang; Tian, Daiyin title: Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis date: 2020-04-17 journal: nan DOI: 10.1101/2020.04.14.20065664 sha: doc_id: 351644 cord_uid: pl7xpivx file: cache/cord-351446-j4ambec5.json key: cord-351446-j4ambec5 authors: Sinonquel, P.; Roelandt, P.; Demedts, I.; van Gerven, L.; Vandenbriele, C.; Wilmer, A.; Van Wijngaerden, E.; Bisschops, R. title: COVID‐19 and gastrointestinal endoscopy: what should be taken into account? date: 2020-04-26 journal: Dig Endosc DOI: 10.1111/den.13706 sha: doc_id: 351446 cord_uid: j4ambec5 file: cache/cord-351662-rmkcb6o3.json key: cord-351662-rmkcb6o3 authors: Huang, Zhifeng; Chen, Hao; Xue, Mingshan; Huang, Huimin; Zheng, Peiyan; Luo, Wenting; Liang, Xueqing; Sun, Baoqing; Zhong, Nanshan title: Characteristics and roles of SARS‐CoV‐2 specific antibodies in patients with different severities of COVID‐19 date: 2020-07-24 journal: Clin Exp Immunol DOI: 10.1111/cei.13500 sha: doc_id: 351662 cord_uid: rmkcb6o3 file: cache/cord-351691-3egwvb59.json key: cord-351691-3egwvb59 authors: Elzupir, Amin O. title: Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 date: 2020-10-23 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1835732 sha: doc_id: 351691 cord_uid: 3egwvb59 file: cache/cord-351482-hzh5tyoo.json key: cord-351482-hzh5tyoo authors: Peng, Xinxia; Gralinski, Lisa; Ferris, Martin T.; Frieman, Matthew B.; Thomas, Matthew J.; Proll, Sean; Korth, Marcus J.; Tisoncik, Jennifer R.; Heise, Mark; Luo, Shujun; Schroth, Gary P.; Tumpey, Terrence M.; Li, Chengjun; Kawaoka, Yoshihiro; Baric, Ralph S.; Katze, Michael G. title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 journal: mBio DOI: 10.1128/mbio.00198-11 sha: doc_id: 351482 cord_uid: hzh5tyoo file: cache/cord-351555-hsgsuor2.json key: cord-351555-hsgsuor2 authors: Constantinou, Constantina; Kolokotroni, Ourania; Mosquera, Maria‐Cecilia; Heraclides, Alexandros; Demetriou, Christiana; Karayiannis, Peter; Quattrocchi, Annalisa; Charalambous, Andreas title: Developing a holistic contingency plan: Challenges and dilemmas for cancer patients during the COVID‐19 date: 2020-07-20 journal: Cancer Med DOI: 10.1002/cam4.3271 sha: doc_id: 351555 cord_uid: hsgsuor2 file: cache/cord-351567-ifoe8x28.json key: cord-351567-ifoe8x28 authors: Rabi, Firas A.; Al Zoubi, Mazhar S.; Kasasbeh, Ghena A.; Salameh, Dunia M.; Al-Nasser, Amjad D. title: SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far date: 2020-03-20 journal: Pathogens DOI: 10.3390/pathogens9030231 sha: doc_id: 351567 cord_uid: ifoe8x28 file: cache/cord-351651-6dbt99h0.json key: cord-351651-6dbt99h0 authors: Sun, Zhong; Thilakavathy, Karuppiah; Kumar, S. Suresh; He, Guozhong; Liu, Shi V. title: Potential Factors Influencing Repeated SARS Outbreaks in China date: 2020-03-03 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17051633 sha: doc_id: 351651 cord_uid: 6dbt99h0 file: cache/cord-351492-8jv7ip67.json key: cord-351492-8jv7ip67 authors: Urwin, S. G.; Lendrem, B. C.; Suklan, J.; Green, K.; Graziadio, S.; Buckle, P.; Dark, P. M.; Gordon, A. L.; Lasserson, D. S.; Nicholson, B.; Price, D. A.; Reynard, C.; Wilcox, M. H.; Prestwich, G.; Tate, V.; Clark, T. W.; Reddy, R. V.; Body, R.; Allen, A. J. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 journal: nan DOI: 10.1101/2020.10.15.20213108 sha: doc_id: 351492 cord_uid: 8jv7ip67 file: cache/cord-351649-87g7g5au.json key: cord-351649-87g7g5au authors: Haagmans, Bart L.; Osterhaus, Albert D.M.E. title: SARS date: 2009-01-30 journal: Vaccines for Biodefense and Emerging and Neglected Diseases DOI: 10.1016/b978-0-12-369408-9.00036-6 sha: doc_id: 351649 cord_uid: 87g7g5au file: cache/cord-351625-1we9wi1g.json key: cord-351625-1we9wi1g authors: Han, Huan; Xu, Zaichao; Cheng, Xiaoming; Zhong, Youquan; Yuan, Li; Wang, Fubing; Li, Yan; Liu, Fang; Jiang, Yingan; Zhu, Chengliang; Xia, Yuchen title: Descriptive, Retrospective Study of the Clinical Characteristics of Asymptomatic COVID-19 Patients date: 2020-10-07 journal: mSphere DOI: 10.1128/msphere.00922-20 sha: doc_id: 351625 cord_uid: 1we9wi1g file: cache/cord-351718-sf5zp5wg.json key: cord-351718-sf5zp5wg authors: Kohli, Utkarsh; Rosebush, Julia C.; Orlov, Nicola M.; Ghavam, Ahmeneh title: COVID-19 pneumonia in an infant with a hemodynamically significant ventricular septal defect date: 2020-10-12 journal: Cardiology in the young DOI: 10.1017/s1047951120003303 sha: doc_id: 351718 cord_uid: sf5zp5wg file: cache/cord-351694-nb7230s1.json key: cord-351694-nb7230s1 authors: Jatt, Lauren P.; Winnett, Alexander; Graber, Christopher J.; Vallone, John; Beenhouwer, David O.; Goetz, Matthew Bidwell title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings date: 2020-06-16 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.301 sha: doc_id: 351694 cord_uid: nb7230s1 file: cache/cord-351845-bli3qm8w.json key: cord-351845-bli3qm8w authors: Prasad, Kartikay; Khatoon, Fatima; Rashid, Summya; Ali, Nemat; AlAsmari, Abdullah F.; Ahmed, Mohammad Z.; Alqahtani, Ali S.; Alqahtani, Mohammed S.; Kumar, Vijay title: Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date: 2020-06-26 journal: Int J Biol Macromol DOI: 10.1016/j.ijbiomac.2020.06.228 sha: doc_id: 351845 cord_uid: bli3qm8w file: cache/cord-351952-lhhjax3s.json key: cord-351952-lhhjax3s authors: Pickering, Suzanne; Betancor, Gilberto; Galão, Rui Pedro; Merrick, Blair; Signell, Adrian W.; Wilson, Harry D.; Kia Ik, Mark Tan; Seow, Jeffrey; Graham, Carl; Acors, Sam; Kouphou, Neophytos; Steel, Kathryn J. A.; Hemmings, Oliver; Patel, Amita; Nebbia, Gaia; Douthwaite, Sam; O’Connell, Lorcan; Luptak, Jakub; McCoy, Laura E.; Brouwer, Philip; van Gils, Marit J.; Sanders, Rogier W.; Martinez Nunez, Rocio; Bisnauthsing, Karen; O’Hara, Geraldine; MacMahon, Eithne; Batra, Rahul; Malim, Michael H.; Neil, Stuart J. D.; Doores, Katie J.; Edgeworth, Jonathan D. title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date: 2020-09-24 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008817 sha: doc_id: 351952 cord_uid: lhhjax3s file: cache/cord-352073-rdhjj72g.json key: cord-352073-rdhjj72g authors: Taniwaki, S.A; Silva, S.O.S; Santana-Clavijo, N.F; Conselheiro, J. A; Barone, G.T; Menezes, A.A.R; Pereira, E.S; Brandão, P.E title: Resource optimization in COVID-19 diagnosis date: 2020-06-26 journal: bioRxiv DOI: 10.1101/2020.06.25.172528 sha: doc_id: 352073 cord_uid: rdhjj72g file: cache/cord-351687-6otr8zl3.json key: cord-351687-6otr8zl3 authors: Yesilkaya, Umit Haluk; Balcioglu, Yasin Hasan title: Neuroimmune correlates of the nervous system involvement of COVID-19: A commentary date: 2020-05-27 journal: J Clin Neurosci DOI: 10.1016/j.jocn.2020.05.056 sha: doc_id: 351687 cord_uid: 6otr8zl3 file: cache/cord-351930-puhm3w42.json key: cord-351930-puhm3w42 authors: Juan, J.; Gil, M. M.; Rong, Z.; Zhang, Y.; Yang, H.; Poon, L. C. Y. title: Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies date: 2020-05-06 journal: nan DOI: 10.1101/2020.05.02.20088484 sha: doc_id: 351930 cord_uid: puhm3w42 file: cache/cord-351837-vasuu70k.json key: cord-351837-vasuu70k authors: Shannon, Ashleigh; Selisko, Barbara; Le, Nhung-Thi-Tuyet; Huchting, Johanna; Touret, Franck; Piorkowski, Géraldine; Fattorini, Véronique; Ferron, François; Decroly, Etienne; Meier, Chris; Coutard, Bruno; Peersen, Olve; Canard, Bruno title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 journal: Nat Commun DOI: 10.1038/s41467-020-18463-z sha: doc_id: 351837 cord_uid: vasuu70k file: cache/cord-351854-5s03f0pp.json key: cord-351854-5s03f0pp authors: Ben-Ami, Roni; Klochendler, Agnes; Seidel, Matan; Sido, Tal; Gurel-Gurevich, Ori; Yassour, Moran; Meshorer, Eran; Benedek, Gil; Fogel, Irit; Oiknine-Djian, Esther; Gertler, Asaf; Rotstein, Zeev; Lavi, Bruno; Dor, Yuval; Wolf, Dana G; Salton, Maayan; Drier, Yotam title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 journal: nan DOI: 10.1101/2020.04.17.20069062 sha: doc_id: 351854 cord_uid: 5s03f0pp file: cache/cord-351835-1s2zsqoq.json key: cord-351835-1s2zsqoq authors: Liu, Zhixin; Xiao, Xiao; Wei, Xiuli; Li, Jian; Yang, Jing; Tan, Huabing; Zhu, Jianyong; Zhang, Qiwei; Wu, Jianguo; Liu, Long title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 date: 2020-03-11 journal: J Med Virol DOI: 10.1002/jmv.25726 sha: doc_id: 351835 cord_uid: 1s2zsqoq file: cache/cord-352030-hnm54k4r.json key: cord-352030-hnm54k4r authors: Liu, Jie; Ouyang, Liu; Guo, Pi; Wu, Hai sheng; Fu, Peng; Chen, Yu liang; Yang, Dan; Han, Xiao yu; Cao, Yu kun; Alwalid, Osamah; Tao, Juan; Peng, Shu yi; Shi, He shui; Yang, Fan; Zheng, Chuan sheng title: Epidemiological, Clinical Characteristics and Outcome of Medical Staff Infected with COVID-19 in Wuhan, China: A Retrospective Case Series Analysis date: 2020-03-13 journal: nan DOI: 10.1101/2020.03.09.20033118 sha: doc_id: 352030 cord_uid: hnm54k4r file: cache/cord-351770-cirq6pfx.json key: cord-351770-cirq6pfx authors: Chen, Wei; Zhang, Jie; Qin, Xijian; Wang, Weixiao; Xu, Miaomiao; Wang, Lin-Fa; Xu, Chuanjun; Tang, Shuangshuang; Liu, Pei; Zhang, Libo; Liu, Xuan; Zhang, Yongchen; Yi, Changhua; Hu, Zhiliang; Yi, Yongxiang title: SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia date: 2020-08-13 journal: Biomedicine & Pharmacotherapy DOI: 10.1016/j.biopha.2020.110629 sha: doc_id: 351770 cord_uid: cirq6pfx file: cache/cord-351864-zozrj7w5.json key: cord-351864-zozrj7w5 authors: Chappleboim, A.; Joseph-Strauss, D.; Rahat, A.; Sharkia, I.; Adam, M.; Kitsberg, D.; Fialkoff, G.; Lotem, M.; Gershon, O.; Schmidtner, A.-K.; Oiknine-Djian, E.; Klochendler, A.; Sadeh, R.; Dor, Y.; Wolf, D.; Habib, N.; Friedman, N. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 journal: nan DOI: 10.1101/2020.08.08.20170746 sha: doc_id: 351864 cord_uid: zozrj7w5 file: cache/cord-352304-tt2q5mgs.json key: cord-352304-tt2q5mgs authors: Sun, Dan; Li, Hui; Lu, Xiao-Xia; Xiao, Han; Ren, Jie; Zhang, Fu-Rong; Liu, Zhi-Sheng title: Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center’s observational study date: 2020-03-19 journal: World J Pediatr DOI: 10.1007/s12519-020-00354-4 sha: doc_id: 352304 cord_uid: tt2q5mgs file: cache/cord-352123-0bflqj1c.json key: cord-352123-0bflqj1c authors: Csiszar, Anna; Jakab, Ferenc; Valencak, Teresa G.; Lanszki, Zsófia; Tóth, Gábor Endre; Kemenesi, Gábor; Tarantini, Stefano; Fazekas-Pongor, Vince; Ungvari, Zoltan title: Companion animals likely do not spread COVID-19 but may get infected themselves date: 2020-08-07 journal: GeroScience DOI: 10.1007/s11357-020-00248-3 sha: doc_id: 352123 cord_uid: 0bflqj1c file: cache/cord-351719-xqmir1ca.json key: cord-351719-xqmir1ca authors: Olaimat, Amin N.; Shahbaz, Hafiz M.; Fatima, Nayab; Munir, Sadia; Holley, Richard A. title: Food Safety During and After the Era of COVID-19 Pandemic date: 2020-08-04 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01854 sha: doc_id: 351719 cord_uid: xqmir1ca file: cache/cord-351896-j6h02ab5.json key: cord-351896-j6h02ab5 authors: Ghannam, Malik; Alshaer, Qasem; Al-Chalabi, Mustafa; Zakarna, Lara; Robertson, Jetter; Manousakis, Georgios title: Neurological involvement of coronavirus disease 2019: a systematic review date: 2020-06-19 journal: J Neurol DOI: 10.1007/s00415-020-09990-2 sha: doc_id: 351896 cord_uid: j6h02ab5 file: cache/cord-351736-4x5u4qsy.json key: cord-351736-4x5u4qsy authors: Fernandez-Garcia, Cristina; Montaner-Ramon, Alicia; Hernandez-Perez, Susana; Camba-Longueira, Fatima; Ribes-Bautista, Carmen; Frick, Marie Antoinette; Castillo-Salinas, Felix title: Severe COVID-19 During Pregnancy and the Subsequent Premature Delivery date: 2020-09-19 journal: Pediatr Neonatol DOI: 10.1016/j.pedneo.2020.09.005 sha: doc_id: 351736 cord_uid: 4x5u4qsy file: cache/cord-352080-3rcqbgl7.json key: cord-352080-3rcqbgl7 authors: Shidham, Vinod B.; Frisch, Nora K.; Layfield, Lester J. title: Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date: 2020-04-10 journal: Cytojournal DOI: 10.25259/cytojournal_24_2020 sha: doc_id: 352080 cord_uid: 3rcqbgl7 file: cache/cord-352059-1bjskqyg.json key: cord-352059-1bjskqyg authors: Gupta, Nivedita; Potdar, Varsha; Praharaj, Ira; Giri, Sidhartha; Sapkal, Gajanan; Yadav, Pragya; Choudhary, Manohar Lal; Dar, Lalit; Sugunan, A.P.; Kaur, Harmanmeet; Munivenkatappa, Ashok; Shastri, Jayanthi; Kaveri, Krishnasamy; Dutta, Shanta; Malhotra, Bharti; Jain, Amita; Nagamani, Kammilli; Shantala, G.B.; Raut, Sharmila; Vegad, M.M.; Sharma, Ajanta; Choudhary, Aashish; Brijwal, Megha; Balakrishnan, Anukumar; Manjunatha, Jayaswamy; Pathak, Manish; Srinivasan, Sivasubramanian; Banu, Hasina; Sharma, Himanshu; Jain, Parul; Sunita, Pakalpati; Ambica, R.; Fageria, Babita; Patel, Disha; Rajbongshi, Gitika; Vijay, Neetu; Narayan, Jitendra; Aggarwal, Neeraj; Nagar, Anu; Gangakhedkar, Raman R.; Abraham, Priya title: Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories date: 2020-04-28 journal: Indian J Med Res DOI: 10.4103/ijmr.ijmr_594_20 sha: doc_id: 352059 cord_uid: 1bjskqyg file: cache/cord-352096-cc3dzycl.json key: cord-352096-cc3dzycl authors: Richman, Douglas D. title: Antiviral Drug Discovery To Address the COVID-19 Pandemic date: 2020-09-25 journal: mBio DOI: 10.1128/mbio.02134-20 sha: doc_id: 352096 cord_uid: cc3dzycl file: cache/cord-351974-1najtyui.json key: cord-351974-1najtyui authors: Smith, E.; Aldus, C. F.; Brainard, J.; Dunham, S.; Hunter, P. R.; Steel, N.; Everden, P. title: Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation date: 2020-08-05 journal: nan DOI: 10.1101/2020.08.04.20165928 sha: doc_id: 351974 cord_uid: 1najtyui file: cache/cord-352296-rpjehijd.json key: cord-352296-rpjehijd authors: Azzi, Lorenzo; Carcano, Giulio; Dalla Gasperina, Daniella; Sessa, Fausto; Maurino, Vittorio; Baj, Andreina title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern date: 2020-05-11 journal: Oral Dis DOI: 10.1111/odi.13368 sha: doc_id: 352296 cord_uid: rpjehijd file: cache/cord-352146-i4ezsclf.json key: cord-352146-i4ezsclf authors: Cimolai, Nevio title: Efficacy of povidone‐iodine to reduce viral load date: 2020-07-31 journal: Oral Dis DOI: 10.1111/odi.13557 sha: doc_id: 352146 cord_uid: i4ezsclf file: cache/cord-352196-rpyoeg9n.json key: cord-352196-rpyoeg9n authors: Alberici, Federico; Delbarba, Elisa; Manenti, Chiara; Econimo, Laura; Valerio, Francesca; Pola, Alessandra; Maffei, Camilla; Possenti, Stefano; Lucca, Bernardo; Cortinovis, Roberta; Terlizzi, Vincenzo; Zappa, Mattia; Saccà, Chiara; Pezzini, Elena; Calcaterra, Eleonora; Piarulli, Paola; Guerini, Alice; Boni, Francesca; Gallico, Agnese; Mucchetti, Alberto; Affatato, Stefania; Bove, Sergio; Bracchi, Martina; Costantino, Ester Maria; Zubani, Roberto; Camerini, Corrado; Gaggia, Paola; Movilli, Ezio; Bossini, Nicola; Gaggiotti, Mario; Scolari, Francesco title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. date: 2020-05-08 journal: Kidney Int DOI: 10.1016/j.kint.2020.04.030 sha: doc_id: 352196 cord_uid: rpyoeg9n file: cache/cord-352228-dzkf7c7l.json key: cord-352228-dzkf7c7l authors: Fontanet, Arnaud; Tondeur, Laura; Madec, Yoann; Grant, Rebecca; Besombes, Camille; Jolly, Nathalie; Fernandes Pellerin, Sandrine; Ungeheuer, Marie-Noelle; Cailleau, Isabelle; Kuhmel, Lucie; Temmam, Sarah; Huon, Christele; Chen, Kuang-Yu; Crescenzo, Bernadette; Munier, Sandie; Demeret, Caroline; Grzelak, Ludivine; Staropoli, Isabelle; Bruel, Timothee; Gallian, Pierre; Cauchemez, Simon; van der Werf, Sylvie; Schwartz, Olivier; Eloit, Marc; Hoen, Bruno title: Cluster of COVID-19 in northern France: A retrospective closed cohort study date: 2020-04-23 journal: nan DOI: 10.1101/2020.04.18.20071134 sha: doc_id: 352228 cord_uid: dzkf7c7l file: cache/cord-352379-q5inrxcm.json key: cord-352379-q5inrxcm authors: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 journal: J Biomed Sci DOI: 10.1007/bf02256318 sha: doc_id: 352379 cord_uid: q5inrxcm file: cache/cord-352509-qrzt4zva.json key: cord-352509-qrzt4zva authors: Chen, Haohui; Xu, Weipan; Paris, Cecile; Reeson, Andrew; Li, Xun title: Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak date: 2020-03-16 journal: nan DOI: 10.1101/2020.03.11.20033688 sha: doc_id: 352509 cord_uid: qrzt4zva file: cache/cord-352230-8mazd3eu.json key: cord-352230-8mazd3eu authors: Beeraka, Narasimha M.; Sadhu, Surya P.; Madhunapantula, SubbaRao V.; Rao Pragada, Rajeswara; Svistunov, Andrey A.; Nikolenko, Vladimir N.; Mikhaleva, Liudmila M.; Aliev, Gjumrakch title: Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date: 2020-09-18 journal: Front Immunol DOI: 10.3389/fimmu.2020.552925 sha: doc_id: 352230 cord_uid: 8mazd3eu file: cache/cord-352341-dhc748pn.json key: cord-352341-dhc748pn authors: Miranda-Zazueta, G.; González-Regueiro, JA; García-Juárez, I.; Moctezuma-Velázquez, C.; López-Díaz, FJ; Pérez-González, B.; Uscanga-Domínguez, LF; Peláez-Luna, M. title: Manejo farmacológico de pacientes con enfermedades hepáticas y pancreáticas que involucran terapias inmunosupresoras. Posicionamiento en el marco de la pandemia de SARS-COV-2 (COVID-19) date: 2020-06-17 journal: Rev Gastroenterol Mex DOI: 10.1016/j.rgmx.2020.06.001 sha: doc_id: 352341 cord_uid: dhc748pn file: cache/cord-352365-b9cmviny.json key: cord-352365-b9cmviny authors: Marchetti, Monia title: COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure date: 2020-06-24 journal: Ann Hematol DOI: 10.1007/s00277-020-04138-8 sha: doc_id: 352365 cord_uid: b9cmviny file: cache/cord-352526-t8odetzw.json key: cord-352526-t8odetzw authors: Pinto, Bruna G G; Oliveira, Antonio E R; Singh, Youvika; Jimenez, Leandro; Gonçalves, Andre N A; Ogava, Rodrigo L T; Creighton, Rachel; Peron, Jean Pierre Schatzmann; Nakaya, Helder I title: ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date: 2020-06-11 journal: J Infect Dis DOI: 10.1093/infdis/jiaa332 sha: doc_id: 352526 cord_uid: t8odetzw file: cache/cord-352281-9huyb4cs.json key: cord-352281-9huyb4cs authors: Ayoub, Houssein H.; Chemaitelly, Hiam; Seedat, Shaheen; Mumtaz, Ghina R.; Makhoul, Monia; Abu-Raddad, Laith J title: Age could be driving variable SARS-CoV-2 epidemic trajectories worldwide date: 2020-04-17 journal: nan DOI: 10.1101/2020.04.13.20059253 sha: doc_id: 352281 cord_uid: 9huyb4cs file: cache/cord-352557-l7sahv5t.json key: cord-352557-l7sahv5t authors: Takla, Michael; Jeevaratnam, Kamalan title: Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety date: 2020-11-13 journal: Saudi Pharm J DOI: 10.1016/j.jsps.2020.11.003 sha: doc_id: 352557 cord_uid: l7sahv5t file: cache/cord-352156-sa8cvyuw.json key: cord-352156-sa8cvyuw authors: Lindeman, Robbert-Jan; Sund, Malin; Löfgren, Jenny; Basso, Trude; Søreide, Kjetil title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries date: 2020-05-06 journal: J Surg Case Rep DOI: 10.1093/jscr/rjaa131 sha: doc_id: 352156 cord_uid: sa8cvyuw file: cache/cord-352562-qfb478sf.json key: cord-352562-qfb478sf authors: Yamamoto, Lidia; dos Santos, Emilly Henrique; Pinto, Lacyane Silva; Rocha, Mussya Cisotto; Kanunfre, Kelly Aparecida; Vallada, Marcelo Genofre; Okay, Thelma Suely title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 journal: Revista do Instituto de Medicina Tropical de Sao Paulo DOI: 10.1590/s1678-9946202062065 sha: doc_id: 352562 cord_uid: qfb478sf file: cache/cord-352433-sts48u9i.json key: cord-352433-sts48u9i authors: Galanti, Marta; Shaman, Jeffrey title: Direct Observation of Repeated Infections With Endemic Coronaviruses date: 2020-07-07 journal: J Infect Dis DOI: 10.1093/infdis/jiaa392 sha: doc_id: 352433 cord_uid: sts48u9i file: cache/cord-352020-9wxwktck.json key: cord-352020-9wxwktck authors: Zhang, Baoshan; Chao, Cara W.; Tsybovsky, Yaroslav; Abiona, Olubukola M.; Hutchinson, Geoffrey B.; Moliva, Juan I.; Olia, Adam S.; Pegu, Amarendra; Phung, Emily; Stewart-Jones, Guillaume B. E.; Verardi, Raffaello; Wang, Lingshu; Wang, Shuishu; Werner, Anne; Yang, Eun Sung; Yap, Christina; Zhou, Tongqing; Mascola, John R.; Sullivan, Nancy J.; Graham, Barney S.; Corbett, Kizzmekia S.; Kwong, Peter D. title: A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone date: 2020-10-23 journal: Sci Rep DOI: 10.1038/s41598-020-74949-2 sha: doc_id: 352020 cord_uid: 9wxwktck file: cache/cord-352256-qxdakdk0.json key: cord-352256-qxdakdk0 authors: Yousefi, Bahman; Valizadeh, Saeid; Ghaffari, Hadi; Vahedi, Azadeh; Karbalaei, Mohsen; Eslami, Majid title: A global treatments for coronaviruses including COVID‐19 date: 2020-05-11 journal: J Cell Physiol DOI: 10.1002/jcp.29785 sha: doc_id: 352256 cord_uid: qxdakdk0 file: cache/cord-352580-l6vkzja0.json key: cord-352580-l6vkzja0 authors: Iltaf, Samar; Fatima, Meraj; Salman, Salma; Salam, Jawwad-us; Abbas, Saira title: Frequency of Neurological Presentations of Coronavirus Disease in Patients Presenting to a Tertiary Care Hospital During the 2019 Coronavirus Disease Pandemic date: 2020-08-18 journal: Cureus DOI: 10.7759/cureus.9846 sha: doc_id: 352580 cord_uid: l6vkzja0 file: cache/cord-352720-z1cvjc2y.json key: cord-352720-z1cvjc2y authors: Díaz-Corvillón, Pilar; Mönckeberg, Max; Barros, Antonia; Illanes, Sebastián E.; Soldati, Arturo; Nien, Jyh-Kae; Schepeler, Manuel; Caradeux, Javier title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 journal: PLoS One DOI: 10.1371/journal.pone.0239887 sha: doc_id: 352720 cord_uid: z1cvjc2y file: cache/cord-352737-3ttrx3lf.json key: cord-352737-3ttrx3lf authors: Cunha, Lucas Leite; Perazzio, Sandro Felix; Azzi, Jamil; Cravedi, Paolo; Riella, Leonardo Vidal title: Remodeling of the Immune Response With Aging: Immunosenescence and Its Potential Impact on COVID-19 Immune Response date: 2020-08-07 journal: Front Immunol DOI: 10.3389/fimmu.2020.01748 sha: doc_id: 352737 cord_uid: 3ttrx3lf file: cache/cord-352065-960xqft4.json key: cord-352065-960xqft4 authors: Rello, Jordi; Belliato, Mirko; Dimopoulos, Meletios-Athanasios; Giamarellos-bourboulis, Evangelos J.; Jaksic, Vladimir; Martin-loeches, Ignacio; Mporas, Iosif; Pelosi, Paolo; Poulakou, Garyphallia; Pournaras, Spyridon; Tamae-kakazu, Maximiliano; Timsit, Jean-François; Waterer, Grant; Tejada, Sofia; Dimopoulos, George title: Update in COVID-19 in the Intensive Care Unit from the 2020 HELLENIC Athens International Symposium date: 2020-10-22 journal: Anaesth Crit Care Pain Med DOI: 10.1016/j.accpm.2020.10.008 sha: doc_id: 352065 cord_uid: 960xqft4 file: cache/cord-352871-0xgjpd80.json key: cord-352871-0xgjpd80 authors: Pérez Bartolomé, Francisco; Quirós, Julia Sánchez- title: Manifestaciones oftalmológicas del SARS-Cov-2: Revisión de la literatura date: 2020-08-08 journal: Arch Soc Esp Oftalmol DOI: 10.1016/j.oftal.2020.07.020 sha: doc_id: 352871 cord_uid: 0xgjpd80 file: cache/cord-352642-u513wnu1.json key: cord-352642-u513wnu1 authors: Patrocínio de Jesus, Rita; Silva, Raquel; Aliyeva, Elzara; Lopes, Luís; Portugalyan, Mihran; Antunes, Liliana; Diaz, Priscila; Costa, Carolina; Araújo, Ana Carolina; Coelho, Sílvia; Mendes, João João; Gomes, Sara; Serra, Isabel; Freitas, Paulo title: Reactivation of SARS-CoV-2 after Asymptomatic Infection while on High-Dose Corticosteroids. Case Report date: 2020-10-02 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00548-x sha: doc_id: 352642 cord_uid: u513wnu1 file: cache/cord-352322-tsjwnvkk.json key: cord-352322-tsjwnvkk authors: Khamassi Khbou, Médiha; Daaloul Jedidi, Monia; Bouaicha Zaafouri, Faten; Benzarti, M’hammed title: Coronaviruses in farm animals: Epidemiology and public health implications date: 2020-09-25 journal: Vet Med Sci DOI: 10.1002/vms3.359 sha: doc_id: 352322 cord_uid: tsjwnvkk file: cache/cord-352943-ztonp62x.json key: cord-352943-ztonp62x authors: Nagpal, Sunil; Srivastava, Divyanshu; Mande, Sharmila S. title: What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date: 2020-08-20 journal: bioRxiv DOI: 10.1101/2020.08.20.258772 sha: doc_id: 352943 cord_uid: ztonp62x file: cache/cord-352668-qjlqsb2k.json key: cord-352668-qjlqsb2k authors: Cabello, Francisco; Sánchez, Froilán; Farré, Josep M.; Montejo, Angel L. title: Consensus on Recommendations for Safe Sexual Activity during the COVID-19 Coronavirus Pandemic date: 2020-07-20 journal: J Clin Med DOI: 10.3390/jcm9072297 sha: doc_id: 352668 cord_uid: qjlqsb2k file: cache/cord-352891-ljmkqdzx.json key: cord-352891-ljmkqdzx authors: Parang, Keykavous; El-Sayed, Naglaa Salem; Kazeminy, Assad J.; Tiwari, Rakesh K. title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 journal: Molecules DOI: 10.3390/molecules25102343 sha: doc_id: 352891 cord_uid: ljmkqdzx file: cache/cord-352909-s11tpfoq.json key: cord-352909-s11tpfoq authors: Sun, Zhiping; 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Tan, Shuoyan; Xu, Tingyang; Liu, Huanxiang; Huang, Junzhou; Yao, Xiaojun title: MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm date: 2020-08-11 journal: Brief Bioinform DOI: 10.1093/bib/bbaa161 sha: doc_id: 352886 cord_uid: 6lzlt6ur file: cache/cord-352741-0pdeehai.json key: cord-352741-0pdeehai authors: Geramizadeh, Bita; Marzban, Mahsa title: Histopathologic Findings of Coronavirus in Lung: A Mini-Review date: 2020-10-12 journal: Clin Pathol DOI: 10.1177/2632010x20951823 sha: doc_id: 352741 cord_uid: 0pdeehai file: cache/cord-352814-fcl2g5wr.json key: cord-352814-fcl2g5wr authors: Balboni, Andrea; Gallina, Laura; Palladini, Alessandra; Prosperi, Santino; Battilani, Mara title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 journal: ScientificWorldJournal DOI: 10.1100/2012/989514 sha: doc_id: 352814 cord_uid: fcl2g5wr file: cache/cord-352863-6cttilm8.json key: cord-352863-6cttilm8 authors: Hennighausen, Lothar; Lee, Hye Kyung title: Activation of the SARS-CoV-2 receptor Ace2 through JAK/STAT-dependent enhancers during pregnancy date: 2020-09-06 journal: Cell Rep DOI: 10.1016/j.celrep.2020.108199 sha: doc_id: 352863 cord_uid: 6cttilm8 file: cache/cord-352905-ge3u32hm.json key: cord-352905-ge3u32hm authors: Galimberti, Sara; Petrini, Mario; Baratè, Claudia; Ricci, Federica; Balducci, Serena; Grassi, Susanna; Guerrini, Francesca; Ciabatti, Elena; Mechelli, Sandra; Di Paolo, Antonello; Baldini, Chiara; Baglietto, Laura; Macera, Lisa; Spezia, Pietro Giorgio; Maggi, Fabrizio title: Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2 date: 2020-09-02 journal: Front Oncol DOI: 10.3389/fonc.2020.01428 sha: doc_id: 352905 cord_uid: ge3u32hm file: cache/cord-352925-abry6oz3.json key: cord-352925-abry6oz3 authors: Lim, Jia Yin; Lie, Sui An; Yian, Ong Yee title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic date: 2020-05-21 journal: J Clin Anesth DOI: 10.1016/j.jclinane.2020.109891 sha: doc_id: 352925 cord_uid: abry6oz3 file: cache/cord-352577-h3652seb.json key: cord-352577-h3652seb authors: Kopić, Jasminka; Paradžik, Maja Tomić title: Expanding the Use of Noninvasive Ventilation During an Epidemic date: 2014-08-27 journal: Disaster Med Public Health Prep DOI: 10.1017/dmp.2014.71 sha: doc_id: 352577 cord_uid: h3652seb file: cache/cord-352849-vd62r8qu.json key: cord-352849-vd62r8qu authors: Artesi, M.; Bontems, S.; Gobbels, P.; Franckh, M.; Boreux, R.; Meex, C.; Melin, P.; Hayette, M.-P.; Bours, V.; Durkin, K. title: Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome date: 2020-05-03 journal: nan DOI: 10.1101/2020.04.28.20083337 sha: doc_id: 352849 cord_uid: vd62r8qu file: cache/cord-353099-38bz0acw.json key: cord-353099-38bz0acw authors: Tang, Mei San; Case, James Brett; Franks, Caroline E.; Chen, Rita E.; Anderson, Neil W.; Henderson, Jeffrey P.; Diamond, Michael S.; Gronowski, Ann M.; Farnsworth, Christopher W. title: Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date: 2020-07-02 journal: bioRxiv DOI: 10.1101/2020.07.01.182220 sha: doc_id: 353099 cord_uid: 38bz0acw file: cache/cord-353200-5csewb1k.json key: cord-353200-5csewb1k authors: Jehi, Lara; Ji, Xinge; Milinovich, Alex; Erzurum, Serpil; Merlino, Amy; Gordon, Steve; Young, James B.; Kattan, Michael W. title: Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date: 2020-08-11 journal: PLoS One DOI: 10.1371/journal.pone.0237419 sha: doc_id: 353200 cord_uid: 5csewb1k file: cache/cord-353103-sdij1d90.json key: cord-353103-sdij1d90 authors: Yao, Xueting; Ye, Fei; Zhang, Miao; Cui, Cheng; Huang, Baoying; Niu, Peihua; Liu, Xu; Zhao, Li; Dong, Erdan; Song, Chunli; Zhan, Siyan; Lu, Roujian; Li, Haiyan; Tan, Wenjie; Liu, Dongyang title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa237 sha: doc_id: 353103 cord_uid: sdij1d90 file: cache/cord-352796-6einbent.json key: cord-352796-6einbent authors: Theodore Coroneo, Minas title: The eye as the discrete but defensible portal of coronavirus infection date: 2020-05-21 journal: Ocul Surf DOI: 10.1016/j.jtos.2020.05.011 sha: doc_id: 352796 cord_uid: 6einbent file: cache/cord-352935-kb0i58z1.json key: cord-352935-kb0i58z1 authors: Aguila, Enrik John T.; Cua, Ian Homer Y. title: Repurposed GI Drugs in the Treatment of COVID-19 date: 2020-06-29 journal: Dig Dis Sci DOI: 10.1007/s10620-020-06430-z sha: doc_id: 352935 cord_uid: kb0i58z1 file: cache/cord-353012-rxhi8wd2.json key: cord-353012-rxhi8wd2 authors: Zhou, Nan; Pan, Ting; Zhang, Junsong; Li, Qianwen; Zhang, Xue; Bai, Chuan; Huang, Feng; Peng, Tao; Zhang, Jianhua; Liu, Chao; Tao, Liang; Zhang, Hui title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 journal: Journal of Biological Chemistry DOI: 10.1074/jbc.m116.716100 sha: doc_id: 353012 cord_uid: rxhi8wd2 file: cache/cord-353274-wozwpvpq.json key: cord-353274-wozwpvpq authors: Borremans, B.; Gamble, A.; Prager, K. C.; Helman, S. K.; McClain, A. M.; Cox, C.; Savage, V.; Lloyd-Smith, J. 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Costa, Carlos Henrique Nery title: Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus date: 2020-08-04 journal: Front Immunol DOI: 10.3389/fimmu.2020.01739 sha: doc_id: 353217 cord_uid: gmc3qrci file: cache/cord-353329-ju3vwlow.json key: cord-353329-ju3vwlow authors: Haroon, Khawaja Hassan; Muhammad, Ahmad; Hussain, Suhail; Patro, Satya Narayana title: COVID-19 Related Cerebrovascular Thromboembolic Complications in Three Young Patients date: 2020-09-28 journal: Case Rep Neurol DOI: 10.1159/000511179 sha: doc_id: 353329 cord_uid: ju3vwlow file: cache/cord-353392-rqeultbq.json key: cord-353392-rqeultbq authors: Kumar, Govindarajan Venkat; Jeyanthi, Venkadapathi; Ramakrishnan, Saminathan title: A short review on antibody therapy for COVID-19 date: 2020-04-20 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100682 sha: doc_id: 353392 cord_uid: rqeultbq file: cache/cord-352934-ypls4zau.json key: cord-352934-ypls4zau authors: Wan, Jinkai; Xing, Shenghui; Ding, Longfei; Wang, Yongheng; Gu, Chenjian; Wu, Yanling; Rong, Bowen; Li, Cheng; Wang, Siqing; Chen, Kun; He, Chenxi; Zhu, Dandan; Yuan, Songhua; Qiu, Chengli; Zhao, Chen; Nie, Lei; Gao, Zhangzhao; Jiao, Jingyu; Zhang, Xiaoyan; Wang, Xiangxi; Ying, Tianlei; Wang, Haibin; Xie, Youhua; Lu, Yanan; Xu, Jianqing; Lan, Fei title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date: 2020-07-03 journal: Cell Rep DOI: 10.1016/j.celrep.2020.107918 sha: doc_id: 352934 cord_uid: ypls4zau file: cache/cord-353209-qkhfp66l.json key: cord-353209-qkhfp66l authors: Steiner, Daniel J.; Cognetti, John S.; Luta, Ethan P.; Klose, Alanna M.; Bucukovski, Joseph; Bryan, Michael R.; Schmuke, Jon J.; Nguyen-Contant, Phuong; Sangster, Mark Y.; Topham, David J.; Miller, Benjamin L. title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.15.153064 sha: doc_id: 353209 cord_uid: qkhfp66l file: cache/cord-352969-rpt7xja6.json key: cord-352969-rpt7xja6 authors: Kataria, Ashish; Yakubu, Idris; Winstead, Ryan; Gowda, Madan; Gupta, Gaurav title: COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice date: 2020-07-15 journal: Transplant Direct DOI: 10.1097/txd.0000000000001031 sha: doc_id: 352969 cord_uid: rpt7xja6 file: cache/cord-353235-jiqhgf56.json key: cord-353235-jiqhgf56 authors: Bigliardi, Guido; Ciolli, Ludovico; Giovannini, Giada; Vandelli, Laura; Dell’Acqua, Maria Luisa; Borzì, Giuseppe Maria; Picchetto, Livio; Rosafio, Francesca; Ricceri, Riccardo; Meletti, Stefano title: Middle cerebral artery ischemic stroke and COVID-19: a case report date: 2020-09-08 journal: J Neurovirol DOI: 10.1007/s13365-020-00898-1 sha: doc_id: 353235 cord_uid: jiqhgf56 file: cache/cord-353365-ujz5nkk3.json key: cord-353365-ujz5nkk3 authors: Pirnay, Jean-Paul; Selhorst, Philippe; Cochez, Christel; Petrillo, Mauro; Claes, Vincent; Van der Beken, Yolien; Verbeken, Gilbert; Degueldre, Julie; T’Sas, France; Van den Eede, Guy; Weuts, Wouter; Smets, Cedric; Mertens, Jan; Geeraerts, Philippe; Ariën, Kevin K.; Neirinckx, Pierre; Soentjens, Patrick title: Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger date: 2020-08-27 journal: Viruses DOI: 10.3390/v12090949 sha: doc_id: 353365 cord_uid: ujz5nkk3 file: cache/cord-353479-kwi8zxo6.json key: cord-353479-kwi8zxo6 authors: Chuang, H.-L.; Leung, W.-S.; Chung, Y.-T.; Chang, Y.-T.; Chen, W.-K. title: Impact of enhanced infection control procedures on clinical outcome following resuscitation attempts date: 2007-11-30 journal: Journal of Hospital Infection DOI: 10.1016/j.jhin.2007.08.015 sha: doc_id: 353479 cord_uid: kwi8zxo6 file: cache/cord-353133-tsqb6pa8.json key: cord-353133-tsqb6pa8 authors: Long, Dustin R.; Sunshine, Jacob E.; Van Cleve, Wil title: Considerations for Assessing Risk of Provider Exposure to SARS-CoV-2 after a Negative Test date: 2020-05-26 journal: Anesthesiology DOI: 10.1097/aln.0000000000003392 sha: doc_id: 353133 cord_uid: tsqb6pa8 file: cache/cord-353293-vjdwh19x.json key: cord-353293-vjdwh19x authors: nan title: Post-COVID-19 global health strategies: the need for an interdisciplinary approach date: 2020-06-11 journal: Aging Clin Exp Res DOI: 10.1007/s40520-020-01616-x sha: doc_id: 353293 cord_uid: vjdwh19x file: cache/cord-353391-o0s2h0y0.json key: cord-353391-o0s2h0y0 authors: Haj Bloukh, Samir; Edis, Zehra; Shaikh, Annis A.; Pathan, Habib M. title: A Look Behind the Scenes at COVID-19: National Strategies of Infection Control and Their Impact on Mortality date: 2020-08-04 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17155616 sha: doc_id: 353391 cord_uid: o0s2h0y0 file: cache/cord-353523-gwud4bb7.json key: cord-353523-gwud4bb7 authors: Abobaker, Anis; Alzwi, Aboubaker title: The Eye: A Possible New Route of Infection in COVID-19 date: 2020-07-27 journal: Disaster medicine and public health preparedness DOI: 10.1017/dmp.2020.270 sha: doc_id: 353523 cord_uid: gwud4bb7 file: cache/cord-353116-7t1prfkr.json key: cord-353116-7t1prfkr authors: Bhargava, Ashish; Fukushima, Elisa Akagi; Levine, Miriam; Zhao, Wei; Tanveer, Farah; Szpunar, Susanna M; Saravolatz, Louis title: Predictors for Severe COVID-19 Infection date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa674 sha: doc_id: 353116 cord_uid: 7t1prfkr file: cache/cord-353484-q7d0ysbo.json key: cord-353484-q7d0ysbo authors: Liu, Xue; Liu, Chao; Liu, Gang; Luo, Wenxin; Xia, Ningshao title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 journal: Theranostics DOI: 10.7150/thno.47987 sha: doc_id: 353484 cord_uid: q7d0ysbo file: cache/cord-353576-f29kmtot.json key: cord-353576-f29kmtot authors: Maricic, T.; Nickel, O.; Aximu-Petri, A.; Essel, E.; Gansauge, M.; Kanis, P.; Macak, D.; Riesenberg, S.; Bokelmann, L.; Zeberg, H.; Meyer, M.; Borte, S.; Paabo, S. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 journal: nan DOI: 10.1101/2020.06.24.20139501 sha: doc_id: 353576 cord_uid: f29kmtot file: cache/cord-353237-rob4ems7.json key: cord-353237-rob4ems7 authors: De Maio, Antonio; Hightower, Lawrence E. title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? date: 2020-05-18 journal: Cell Stress Chaperones DOI: 10.1007/s12192-020-01121-0 sha: doc_id: 353237 cord_uid: rob4ems7 file: cache/cord-353615-9aj5yxkd.json key: cord-353615-9aj5yxkd authors: Colaneri, Marta; Valsecchi, Pietro; Perotti, Luciano; Ludovisi, Serena; Seminari, Elena; Chiara Pieri, Teresa; Sacchi, Paolo; Bruno, Raffaele title: Running out of bullets: the challenging management of acute hepatitis and SARS‐COV‐2 from the SMatteo COvid19 Registry (SMACORE) date: 2020-07-17 journal: Liver Int DOI: 10.1111/liv.14609 sha: doc_id: 353615 cord_uid: 9aj5yxkd file: cache/cord-353599-cw29edwr.json key: cord-353599-cw29edwr authors: Kelleni, Mina T. title: Early use of Non-steroidal anti-inflammatory drugs in COVID-19 might reverse pathogenesis, prevent complications and improve clinical outcomes date: 2020-11-04 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110982 sha: doc_id: 353599 cord_uid: cw29edwr file: cache/cord-353628-f6ew980g.json key: cord-353628-f6ew980g authors: Zayet, Souheil; Ben Abdallah, Yousri; Royer, Pierre‐Yves; Toko‐Tchiundzie, Lynda; Gendrin, Vincent; Klopfenstein, Timothee title: Encephalopathy in patients with COVID‐19: ‘Causality or coincidence?’ date: 2020-05-19 journal: J Med Virol DOI: 10.1002/jmv.26027 sha: doc_id: 353628 cord_uid: f6ew980g file: cache/cord-353475-dtn7h1gj.json key: cord-353475-dtn7h1gj authors: Haddad, Hazem; Walid Al-Zyoud title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 journal: Noncoding RNA Res DOI: 10.1016/j.ncrna.2020.08.002 sha: doc_id: 353475 cord_uid: dtn7h1gj file: cache/cord-353373-zhkqnu0w.json key: cord-353373-zhkqnu0w authors: Seidu, Samuel; Gillies, Clare; Zaccardi, Francesco; Kunutsor, Setor K.; Hartmann‐Boyce, Jamie; Yates, Thomas; Singh, Awadhesh Kumar; Davies, Melanie J.; Khunti, Kamlesh title: The impact of obesity on severe disease and mortality in people with SARS‐CoV‐2: A systematic review and meta‐analysis date: 2020-08-14 journal: Endocrinol Diabetes Metab DOI: 10.1002/edm2.176 sha: doc_id: 353373 cord_uid: zhkqnu0w file: cache/cord-353742-k4gxww2c.json key: cord-353742-k4gxww2c authors: Arévalo, AP; Pagotto, R; Pórfido, J; Daghero, H; Segovia, M; Yamasaki, K; Varela, B; Hill, M; Verdes, JM; Duhalde Vega, M; Bollati-Fogolín, M; Crispo, M title: Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.363242 sha: doc_id: 353742 cord_uid: k4gxww2c file: cache/cord-353551-un4jw7aw.json key: cord-353551-un4jw7aw authors: Margoni, Monica; Gallo, Paolo title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic date: 2020-10-12 journal: Mult Scler J Exp Transl Clin DOI: 10.1177/2055217320966346 sha: doc_id: 353551 cord_uid: un4jw7aw file: cache/cord-353524-3w970ycx.json key: cord-353524-3w970ycx authors: Dömling, Alexander; Gao, Li title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 journal: Chem DOI: 10.1016/j.chempr.2020.04.023 sha: doc_id: 353524 cord_uid: 3w970ycx file: cache/cord-353308-e4s8el0s.json key: cord-353308-e4s8el0s authors: Parashar, Umesh D; Anderson, Larry J title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 journal: Int J Epidemiol DOI: 10.1093/ije/dyh198 sha: doc_id: 353308 cord_uid: e4s8el0s file: cache/cord-353548-kf4om6iu.json key: cord-353548-kf4om6iu authors: Ruiz-Manriquez, J.; León-Lara, X.; Campos-Murguía, A.; Solis-Ortega, A. A.; Pérez-González, B.; Uscanga, L. F.; Peláez-Luna, M. title: Knowledge of Latin American gastroenterologists and endoscopists regarding SARS-CoV-2 infection date: 2020-05-31 journal: Revista de Gastroenterología de México (English Edition) DOI: 10.1016/j.rgmxen.2020.04.002 sha: doc_id: 353548 cord_uid: kf4om6iu file: cache/cord-353342-2n6kqyeo.json key: cord-353342-2n6kqyeo authors: Corman, Victor M.; Albarrak, Ali M.; Omrani, Ali Senosi; Albarrak, Mohammed M.; Farah, Mohamed Elamin; Almasri, Malak; Muth, Doreen; Sieberg, Andrea; Meyer, Benjamin; Assiri, Abdullah M.; Binger, Tabea; Steinhagen, Katja; Lattwein, Erik; Al-Tawfiq, Jaffar; Müller, Marcel A.; Drosten, Christian; Memish, Ziad A. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 journal: Clin Infect Dis DOI: 10.1093/cid/civ951 sha: doc_id: 353342 cord_uid: 2n6kqyeo file: cache/cord-353862-7xe3fvd5.json key: cord-353862-7xe3fvd5 authors: Li, Na; Han, Lefei; Peng, Min; Lv, Yuxia; Ouyang, Yin; Liu, Kui; Yue, Linli; Li, Qiannan; Sun, Guoqiang; Chen, Lin; Yang, Lin title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa352 sha: doc_id: 353862 cord_uid: 7xe3fvd5 file: cache/cord-353509-yfkiaq80.json key: cord-353509-yfkiaq80 authors: Nugraha, Rhea Veda; Ridwansyah, Hastono; Ghozali, Mohammad; Khairani, Astrid Feinisa; Atik, Nur title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 journal: Evid Based Complement Alternat Med DOI: 10.1155/2020/2560645 sha: doc_id: 353509 cord_uid: yfkiaq80 file: cache/cord-353594-z1vxamvp.json key: cord-353594-z1vxamvp authors: Gagiannis, Daniel; Steinestel, Julie; Hackenbroch, Carsten; Schreiner, Benno; Hannemann, Michael; Bloch, Wilhelm; Umathum, Vincent G.; Gebauer, Niklas; Rother, Conn; Stahl, Marcel; Witte, Hanno M.; Steinestel, Konrad title: Clinical, Serological, and Histopathological Similarities Between Severe COVID-19 and Acute Exacerbation of Connective Tissue Disease-Associated Interstitial Lung Disease (CTD-ILD) date: 2020-10-02 journal: Front Immunol DOI: 10.3389/fimmu.2020.587517 sha: doc_id: 353594 cord_uid: z1vxamvp file: cache/cord-353748-y1a52z8e.json key: cord-353748-y1a52z8e authors: Bhattacharya, Rajarshi; Gupta, Aayatti Mallick; Mitra, Suranjita; Mandal, Sukhendu; Biswas, Swadesh R. title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 journal: Virology DOI: 10.1016/j.virol.2020.10.002 sha: doc_id: 353748 cord_uid: y1a52z8e file: cache/cord-353812-4oxbczqe.json key: cord-353812-4oxbczqe authors: Zoghi, Anahita; Ramezani, Mahtab; Roozbeh, Mehrdad; Darzam, Ilad Alavi; Sahraian, Mohammad Ali title: A case of possible atypical demyelinating event of the central nervous system following COVID-19 date: 2020-06-24 journal: Mult Scler Relat Disord DOI: 10.1016/j.msard.2020.102324 sha: doc_id: 353812 cord_uid: 4oxbczqe file: cache/cord-353161-mtq6yh25.json key: cord-353161-mtq6yh25 authors: Rodrigues, João PGLM; Barrera-Vilarmau, Susana; Teixeira, João MC; Seckel, Elizabeth; Kastritis, Panagiotis; Levitt, Michael title: Insights on cross-species transmission of SARS-CoV-2 from structural modeling date: 2020-06-05 journal: bioRxiv DOI: 10.1101/2020.06.05.136861 sha: doc_id: 353161 cord_uid: mtq6yh25 file: cache/cord-353731-7xn7m662.json key: cord-353731-7xn7m662 authors: Heaton, Brook E.; Trimarco, Joseph D.; Hamele, Cait E.; Harding, Alfred T.; Tata, Aleksandra; Zhu, Xinyu; Tata, Purushothama Rao; Smith, Clare M.; Heaton, Nicholas S. title: SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date: 2020-08-18 journal: bioRxiv DOI: 10.1101/2020.08.14.251207 sha: doc_id: 353731 cord_uid: 7xn7m662 file: cache/cord-353963-d3gk3519.json key: cord-353963-d3gk3519 authors: Karampela, Irene; Dalamaga, Maria title: Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19? date: 2020-06-06 journal: Arch Med Res DOI: 10.1016/j.arcmed.2020.06.004 sha: doc_id: 353963 cord_uid: d3gk3519 file: cache/cord-353612-9ux181xg.json key: cord-353612-9ux181xg authors: Josset, Laurence; Menachery, Vineet D.; Gralinski, Lisa E.; Agnihothram, Sudhakar; Sova, Pavel; Carter, Victoria S.; Yount, Boyd L.; Graham, Rachel L.; Baric, Ralph S.; Katze, Michael G. title: Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus date: 2013-04-30 journal: mBio DOI: 10.1128/mbio.00165-13 sha: doc_id: 353612 cord_uid: 9ux181xg file: cache/cord-353826-owoec2ud.json key: cord-353826-owoec2ud authors: Graham, Simon P.; McLean, Rebecca K.; Spencer, Alexandra J.; Belij-Rammerstorfer, Sandra; Wright, Daniel; Ulaszewska, Marta; Edwards, Jane C.; Hayes, Jack W. P.; Martini, Veronica; Thakur, Nazia; Conceicao, Carina; Dietrich, Isabelle; Shelton, Holly; Waters, Ryan; Ludi, Anna; Wilsden, Ginette; Browning, Clare; Bialy, Dagmara; Bhat, Sushant; Stevenson-Leggett, Phoebe; Hollinghurst, Philippa; Gilbride, Ciaran; Pulido, David; Moffat, Katy; Sharpe, Hannah; Allen, Elizabeth; Mioulet, Valerie; Chiu, Chris; Newman, Joseph; Asfor, Amin S.; Burman, Alison; Crossley, Sylvia; Huo, Jiandong; Owens, Raymond J.; Carroll, Miles; Hammond, John A.; Tchilian, Elma; Bailey, Dalan; Charleston, Bryan; Gilbert, Sarah C.; Tuthill, Tobias J.; Lambe, Teresa title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-07-27 journal: NPJ Vaccines DOI: 10.1038/s41541-020-00221-3 sha: doc_id: 353826 cord_uid: owoec2ud file: cache/cord-353923-ou7w3zkv.json key: cord-353923-ou7w3zkv authors: Ren, Shi-Yan; Wang, Wen-Biao; Hao, Ya-Guang; Zhang, Hao-Ran; Wang, Zhi-Chao; Chen, Ye-Lin; Gao, Rong-Ding title: Stability and infectivity of coronaviruses in inanimate environments date: 2020-04-26 journal: World J Clin Cases DOI: 10.12998/wjcc.v8.i8.1391 sha: doc_id: 353923 cord_uid: ou7w3zkv file: cache/cord-353537-skeajydw.json key: cord-353537-skeajydw authors: Zhang, Xian; Chen, Liting; Wei, Jia; Zhou, Jianfeng; Cao, Yang; Wang, Gaoxiang title: Asymptomatic Subclinical Cases of Coronavirus Disease 2019 without Viral Transmission in Three Independent Families date: 2020-09-24 journal: Infect Drug Resist DOI: 10.2147/idr.s261304 sha: doc_id: 353537 cord_uid: skeajydw file: cache/cord-354103-4dldgqzf.json key: cord-354103-4dldgqzf authors: Grubic, Andrew D; Ayazi, Shahin; Zebarjadi, Javad; Tahmasbi, Hamed; Ayazi, Khosro; Jobe, Blair A title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 journal: World J Gastrointest Surg DOI: 10.4240/wjgs.v12.i6.259 sha: doc_id: 354103 cord_uid: 4dldgqzf file: cache/cord-354353-hyz0gmpz.json key: cord-354353-hyz0gmpz authors: Farhangrazi, Z. Shadi; Sancini, Giulio; Hunter, A. Christy; Moghimi, Seyed Moein title: Airborne Particulate Matter and SARS-CoV-2 Partnership: Virus Hitchhiking, Stabilization and Immune Cell Targeting — A Hypothesis date: 2020-09-24 journal: Front Immunol DOI: 10.3389/fimmu.2020.579352 sha: doc_id: 354353 cord_uid: hyz0gmpz file: cache/cord-353659-wtacr6qj.json key: cord-353659-wtacr6qj authors: Almutairi, Nawaf; Schwartz, Robert A. title: Coronavirus Disease‐2019 with Dermatologic Manifestations and Implications: An Unfolding Conundrum date: 2020-05-09 journal: Dermatol Ther DOI: 10.1111/dth.13544 sha: doc_id: 353659 cord_uid: wtacr6qj file: cache/cord-353494-72fvkx7f.json key: cord-353494-72fvkx7f authors: Singh, Rajveer; Gautam, Anupam; Chandel, Shivani; Ghosh, Arijit; Dey, Dhritiman; Roy, Syamal; Ravichandiran, Velayutham; Ghosh, Dipanjan title: Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study date: 2020-10-10 journal: Molecules DOI: 10.3390/molecules25204604 sha: doc_id: 353494 cord_uid: 72fvkx7f file: cache/cord-353887-f4yd7guj.json key: cord-353887-f4yd7guj authors: Tang, Yujun; Liu, Jiajia; Zhang, Dingyi; Xu, Zhenghao; Ji, Jinjun; Wen, Chengping title: Cytokine Storm in COVID-19: The Current Evidence and Treatment Strategies date: 2020-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01708 sha: doc_id: 353887 cord_uid: f4yd7guj file: cache/cord-353716-gxgvhhv1.json key: cord-353716-gxgvhhv1 authors: Kumar, Ashutosh; Narayan, Ravi K.; Kumari, Chiman; Faiq, Muneeb A.; Kulandhasamy, Maheswari; Kant, Kamla; Pareek, Vikas title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients date: 2020-09-30 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110320 sha: doc_id: 353716 cord_uid: gxgvhhv1 file: cache/cord-353777-t8q99tlq.json key: cord-353777-t8q99tlq authors: Jia, Yong; Shen, Gangxu; Zhang, Yujuan; Huang, Keng-Shiang; Ho, Hsing-Ying; Hor, Wei-Shio; Yang, Chih-Hui; Li, Chengdao; Wang, Wei-Lung title: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date: 2020-04-11 journal: bioRxiv DOI: 10.1101/2020.04.09.034942 sha: doc_id: 353777 cord_uid: t8q99tlq file: cache/cord-354051-ro3o27pv.json key: cord-354051-ro3o27pv authors: Peccia, J.; Zulli, A.; Brackney, D. E.; Grubaugh, N. D.; Kaplan, E. H.; Casanovas-Massana, A.; Ko, A. I.; Malik, A. A.; Wang, D.; Wang, M.; Weinberger, D. M.; Omer, S. B. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 journal: nan DOI: 10.1101/2020.05.19.20105999 sha: doc_id: 354051 cord_uid: ro3o27pv file: cache/cord-353704-lfndq85x.json key: cord-353704-lfndq85x authors: Ye, Zi-Wei; Yuan, Shuofeng; Yuen, Kit-San; Fung, Sin-Yee; Chan, Chi-Ping; Jin, Dong-Yan title: Zoonotic origins of human coronaviruses date: 2020-03-15 journal: Int J Biol Sci DOI: 10.7150/ijbs.45472 sha: doc_id: 353704 cord_uid: lfndq85x file: cache/cord-353572-b4mdiont.json key: cord-353572-b4mdiont authors: Zhou, Yadi; Hou, Yuan; Shen, Jiayu; Huang, Yin; Martin, William; Cheng, Feixiong title: Network-based Drug Repurposing for Human Coronavirus date: 2020-02-05 journal: nan DOI: 10.1101/2020.02.03.20020263 sha: doc_id: 353572 cord_uid: b4mdiont file: cache/cord-354315-yfn9vaan.json key: cord-354315-yfn9vaan authors: Meirson, Tomer; Bomze, David; Markel, Gal title: Structural basis of SARS-CoV-2 spike protein induced by ACE2 date: 2020-05-24 journal: bioRxiv DOI: 10.1101/2020.05.24.113175 sha: doc_id: 354315 cord_uid: yfn9vaan file: cache/cord-354261-gdvawnp6.json key: cord-354261-gdvawnp6 authors: Gale, Chris; Knight, Marian; Ladhani, Shamez; Draper, Elizabeth S; Sharkey, Don; Doherty, Cora; Mactier, Helen; Kurinczuk, Jennifer J title: National active surveillance to understand and inform neonatal care in COVID-19 date: 2020-06-14 journal: Arch Dis Child Fetal Neonatal Ed DOI: 10.1136/archdischild-2020-319372 sha: doc_id: 354261 cord_uid: gdvawnp6 file: cache/cord-354458-o2kcd085.json key: cord-354458-o2kcd085 authors: Caffo, Orazio; Zagonel, Vittorina; Baldessari, Cinzia; Berruti, Alfredo; Bortolus, Roberto; Buti, Sebastiano; Ceresoli, Giovanni Luca; Donini, Maddalena; Ermacora, Paola; Fornarini, Giuseppe; Fratino, Lucia; Masini, Cristina; Massari, Francesco; Mosca, Alessandra; Mucciarini, Claudia; Procopio, Giuseppe; Tucci, Marcello; Verri, Elena; Zucali, Paolo; Buttigliero, Consuelo title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 date: 2020-06-18 journal: Ann Oncol DOI: 10.1016/j.annonc.2020.06.005 sha: doc_id: 354458 cord_uid: o2kcd085 file: cache/cord-354510-jlg5je0s.json key: cord-354510-jlg5je0s authors: de Carvalho, A. 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G. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 journal: nan DOI: 10.1101/2020.06.18.20134304 sha: doc_id: 354510 cord_uid: jlg5je0s file: cache/cord-353914-zzla4frm.json key: cord-353914-zzla4frm authors: Hu, Bo; Deng, Qing; Zhou, Qing title: Cardiac involvement of COVID-19: Looking forward to novel discoveries and clinically valuable evidence() date: 2020-09-01 journal: Int J Cardiol DOI: 10.1016/j.ijcard.2020.05.049 sha: doc_id: 353914 cord_uid: zzla4frm file: cache/cord-354101-8a7tohcx.json key: cord-354101-8a7tohcx authors: Silva de Oliveira, Daniela; Medeiros, Nayara I.; Gomes, Juliana A.S. title: Immune response in COVID-19: What do we currently know? date: 2020-09-09 journal: Microb Pathog DOI: 10.1016/j.micpath.2020.104484 sha: doc_id: 354101 cord_uid: 8a7tohcx file: cache/cord-353953-83d0g8ix.json key: cord-353953-83d0g8ix authors: Mendoza, Emelissa J.; Manguiat, Kathy; Wood, Heidi; Drebot, Michael title: Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2 date: 2020-05-31 journal: Curr Protoc Microbiol DOI: 10.1002/cpmc.105 sha: doc_id: 353953 cord_uid: 83d0g8ix file: cache/cord-354080-glcq4qp9.json key: cord-354080-glcq4qp9 authors: Bodro, Marta; Compta, Yaroslau; Llansó, Laura; Esteller, Diana; Doncel-Moriano, Antonio; Mesa, Alex; Rodríguez, Alejandro; Sarto, Jordi; Martínez-Hernandez, Eugenia; Vlagea, Alexandru; Egri, Natalia; Filella, Xavier; Morales-Ruiz, Manuel; Yagüe, Jordi; Soriano, Álex; Graus, Francesc; García, Felipe title: Increased CSF levels of IL-1β, IL-6, and ACE in SARS-CoV-2–associated encephalitis date: 2020-07-01 journal: Neurol Neuroimmunol Neuroinflamm DOI: 10.1212/nxi.0000000000000821 sha: doc_id: 354080 cord_uid: glcq4qp9 file: cache/cord-354030-8tfg881h.json key: cord-354030-8tfg881h authors: Dong, Rong; Chu, Zhugang; Yu, Fuxun; Zha, Yan title: Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date: 2020-07-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.01784 sha: doc_id: 354030 cord_uid: 8tfg881h file: cache/cord-354394-zojhdnlu.json key: cord-354394-zojhdnlu authors: Wang, Wei-Kung; Chen, Shey-Ying; Liu, I-Jung; Chen, Yee-Chun; Chen, Hui-Ling; Yang, Chao-Fu; Chen, Pei-Jer; Yeh, Shiou-Hwei; Kao, Chuan-Liang; Huang, Li-Min; Hsueh, Po-Ren; Wang, Jann-Tay; Sheng, Wang-Hwei; Fang, Chi-Tai; Hung, Chien-Ching; Hsieh, Szu-Min; Su, Chan-Ping; Chiang, Wen-Chu; Yang, Jyh-Yuan; Lin, Jih-Hui; Hsieh, Szu-Chia; Hu, Hsien-Ping; Chiang, Yu-Ping; Wang, Jin-Town; Yang, Pan-Chyr; Chang, Shan-Chwen title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1007.031113 sha: doc_id: 354394 cord_uid: zojhdnlu file: cache/cord-354407-zzxjv666.json key: cord-354407-zzxjv666 authors: Campanacci, Valérie; Egloff, Marie‐Pierre; Longhi, Sonia; Ferron, François; Rancurel, Corinne; Salomoni, Aurelia; Durousseau, Cécile; Tocque, Fabienne; Brémond, Nicolas; Dobbe, Jessika C.; Snijder, Eric J.; Canard, Bruno; Cambillau, Christian title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 journal: Acta Crystallogr D Biol Crystallogr DOI: 10.1107/s0907444903016779 sha: doc_id: 354407 cord_uid: zzxjv666 file: cache/cord-354534-0b7zwzjv.json key: cord-354534-0b7zwzjv authors: Fuccillo, E; Saibene, A M; Canevini, M P; Felisati, G title: Olfactory disorders in coronavirus disease 2019 patients: a systematic literature review date: 2020-09-15 journal: The Journal of laryngology and otology DOI: 10.1017/s0022215120002005 sha: doc_id: 354534 cord_uid: 0b7zwzjv file: cache/cord-354453-uze6ze8o.json key: cord-354453-uze6ze8o authors: McCloskey, Brian; Heymann, David L. title: SARS to novel coronavirus – old lessons and new lessons date: 2020-02-05 journal: Epidemiology and infection DOI: 10.1017/s0950268820000254 sha: doc_id: 354453 cord_uid: uze6ze8o file: cache/cord-353749-2vlc11rx.json key: cord-353749-2vlc11rx authors: Stricker, Raphael B; Fesler, Melissa C title: Flattening the Risk: Pre-Exposure Prophylaxis for COVID-19 date: 2020-10-19 journal: Infect Drug Resist DOI: 10.2147/idr.s264831 sha: doc_id: 353749 cord_uid: 2vlc11rx file: cache/cord-353996-slnyun4l.json key: cord-353996-slnyun4l authors: Baumgartner, M. T.; Lansac-Toha, F. M.; Coelho, M. T. P.; Dobrovolski, R.; Diniz-Filho, J. A. F. title: Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil date: 2020-05-08 journal: nan DOI: 10.1101/2020.05.02.20088013 sha: doc_id: 353996 cord_uid: slnyun4l file: cache/cord-354209-g1zynbul.json key: cord-354209-g1zynbul authors: Person, Bobbie; Sy, Francisco; Holton, Kelly; Govert, Barbara; Liang, Arthur; Garza, Brenda; Gould, Deborah; Hickson, Meredith; McDonald, Marian; Meijer, Cecilia; Smith, Julia; Veto, Liza; Williams, Walter; Zauderer, Laura title: Fear and Stigma: The Epidemic within the SARS Outbreak date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030750 sha: doc_id: 354209 cord_uid: g1zynbul file: cache/cord-354372-vfvnjmv1.json key: cord-354372-vfvnjmv1 authors: Carpenito, L.; D'Ercole, M.; Porta, F.; Di Blasi, E.; Doi, P.; Fagara, G. Redolfi; Rey, R.; Bulfamante, G. title: The autopsy at the time of SARS-CoV-2: Protocol and lessons date: 2020-07-04 journal: Ann Diagn Pathol DOI: 10.1016/j.anndiagpath.2020.151562 sha: doc_id: 354372 cord_uid: vfvnjmv1 file: cache/cord-354349-hbk2p6ej.json key: cord-354349-hbk2p6ej authors: Sardar, Sundus; Sharma, Rohit; Alyamani, Tariq Yousef Mohammad; Aboukamar, Mohamed title: COVID-19 and Plasmodium vivax malaria co-infection date: 2020-06-20 journal: IDCases DOI: 10.1016/j.idcr.2020.e00879 sha: doc_id: 354349 cord_uid: hbk2p6ej file: cache/cord-353873-88ud20oq.json key: cord-353873-88ud20oq authors: Hoyler, Marguerite M.; Abramovitz, Sharon; Aaronson, Jaime; White, Robert S. title: The importance of challenges in COVID-19 screening and testing in the obstetric patient population date: 2020-05-28 journal: J Clin Anesth DOI: 10.1016/j.jclinane.2020.109938 sha: doc_id: 353873 cord_uid: 88ud20oq file: cache/cord-354538-vqi67h6a.json key: cord-354538-vqi67h6a authors: Sydney, Elana R.; Kishore, Preeti; Laniado, Isaac; Rucker, Lisa M.; Bajaj, Komal; Zinaman, Michael J. title: Antibody evidence of SARS-CoV-2 infection in healthcare workers in the Bronx date: 2020-08-26 journal: Infection control and hospital epidemiology DOI: 10.1017/ice.2020.437 sha: doc_id: 354538 cord_uid: vqi67h6a file: cache/cord-354113-j8odxs1h.json key: cord-354113-j8odxs1h authors: Miao, Congliang; Zhuang, Jinqiang; Jin, Mengdi; Xiong, Huanwen; Huang, Peng; Zhao, Qi; Miao, Li; Du, Jiang; Yang, Xinying; Huang, Peijie; Hong, Jiang title: A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19 date: 2020-03-24 journal: nan DOI: 10.1101/2020.03.22.20040782 sha: doc_id: 354113 cord_uid: j8odxs1h file: cache/cord-354134-gb2pf5kb.json key: cord-354134-gb2pf5kb authors: Güemes-Villahoz, Noemi; Burgos-Blasco, Barbara; García-Feijoó, Julián; Sáenz-Francés, Federico; Arriola-Villalobos, Pedro; Martinez-de-la-Casa, Jose María; Benítez-del-Castillo, Jose Manuel; Herrera de la Muela, María title: Conjunctivitis in COVID-19 patients: frequency and clinical presentation date: 2020-08-29 journal: Graefes Arch Clin Exp Ophthalmol DOI: 10.1007/s00417-020-04916-0 sha: doc_id: 354134 cord_uid: gb2pf5kb file: cache/cord-354582-fniymnmf.json key: cord-354582-fniymnmf authors: Ma, Zhiqian; Li, Zhiwei; Dong, Linfang; Yang, Ting; Xiao, Shuqi title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2020.06.003 sha: doc_id: 354582 cord_uid: fniymnmf file: cache/cord-354612-7f91l0n9.json key: cord-354612-7f91l0n9 authors: Villar, Livia Melo; da Costa, Vanessa Duarte; Marques, Bianca Leires; da Silva, Lucas Lima; Santos, Alanna Calheiros; da Fonseca Mendonça, Ana Carolina; Marques, Vanessa Alves; do Nascimento, Giselle Prado; Lewis-Ximenez, Lia Laura; de Paula, Vanessa Salete title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS date: 2020-07-23 journal: J Infect DOI: 10.1016/j.jinf.2020.07.017 sha: doc_id: 354612 cord_uid: 7f91l0n9 file: cache/cord-353911-hp6s6ebh.json key: cord-353911-hp6s6ebh authors: Petráš, Marek; Lesný, Petr; Musil, Jan; Limberková, Radomíra; Pátíková, Alžběta; Jirsa, Milan; Krsek, Daniel; Březovský, Pavel; Koladiya, Abhishek; Vaníková, Šárka; Macková, Barbora; Jírová, Dagmar; Krijt, Matyáš; Králová Lesná, Ivana; Adámková, Věra title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date: 2020-11-03 journal: bioRxiv DOI: 10.1101/2020.11.03.366641 sha: doc_id: 353911 cord_uid: hp6s6ebh file: cache/cord-354148-87tpjvs6.json key: cord-354148-87tpjvs6 authors: Bidra, Avinash S.; Pelletier, Jesse S; Westover, Jonna B; Frank, Samantha; Brown, Seth M; Tessema, Belachew title: Rapid In‐Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Using Povidone‐Iodine Oral Antiseptic Rinse date: 2020-06-16 journal: J Prosthodont DOI: 10.1111/jopr.13209 sha: doc_id: 354148 cord_uid: 87tpjvs6 file: cache/cord-354685-oggtmum4.json key: cord-354685-oggtmum4 authors: Kurup, Drishya; Wirblich, Christoph; Ramage, Holly; Schnell, Matthias J. title: Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2 date: 2020-10-16 journal: NPJ Vaccines DOI: 10.1038/s41541-020-00248-6 sha: doc_id: 354685 cord_uid: oggtmum4 file: cache/cord-354373-lldfoptb.json key: cord-354373-lldfoptb authors: Chi, Jeffrey; Chitty, David; Lee, Meeyoung; Hakim, Nausheen; Lakhani, Shamsah; Rajdev, Lakshmi; Zhu, Xinhua; Saif, Muhammad Wasif title: COVID-19 Clinical Research date: 2020-05-05 journal: J Cell Signal DOI: 10.33696/signaling.1.006 sha: doc_id: 354373 cord_uid: lldfoptb file: cache/cord-354619-pftjhtpo.json key: cord-354619-pftjhtpo authors: Farronato, Marco; Tadakamadla, Santosh K; Ali Quadri, Mir Faeq; Acharya, Shashidhar; Tadakamadla, Jyothi; Love, Robert M.; Jamal, Mohamed; Mulder, Riaan; Maspero, Cinzia; Farronato, Davide; Ivanov, Alexander; Neefs, Dirk; Cagetti, Maria Grazia; de Vito, Danila; Gupta, Rishi J.; Connelly, Stephen Thaddeus; Tartaglia, Gianluca M. title: A Call for Action to Safely Deliver Oral Health Care during and Post COVID-19 Pandemic date: 2020-09-15 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17186704 sha: doc_id: 354619 cord_uid: pftjhtpo file: cache/cord-354608-1me3nopu.json key: cord-354608-1me3nopu authors: Rabinowicz, Shira; Leshem, Eyal; Pessach, Itai M. title: COVID-19 in the Pediatric Population—Review and Current Evidence date: 2020-09-19 journal: Curr Infect Dis Rep DOI: 10.1007/s11908-020-00739-6 sha: doc_id: 354608 cord_uid: 1me3nopu file: cache/cord-354398-f3cg8gi1.json key: cord-354398-f3cg8gi1 authors: Al-Saud, Haya; Al-Romaih, Khaldoun; Bakheet, Razan; Mahmoud, Lina; Al-Harbi, Najla; Alshareef, Ibtihaj; Judia, Sara Bin; Aharbi, Layla; Alzayed, Abdulaziz; Jabaan, Amjad; Alhadrami, Hani; Albarrag, Ahmed; Azhar, Essam I.; Al-Mozaini, Maha Ahmad title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 journal: Ann Saudi Med DOI: 10.5144/0256-4947.2020.373 sha: doc_id: 354398 cord_uid: f3cg8gi1 file: cache/cord-354531-7klivhut.json key: cord-354531-7klivhut authors: Feng, Liqiang; Wang, Qian; Shan, Chao; Yang, Chenchen; Feng, Ying; Wu, Jia; Liu, Xiaolin; Zhou, Yiwu; Jiang, Rendi; Hu, Peiyu; Liu, Xinglong; Zhang, Fan; Li, Pingchao; Niu, Xuefeng; Liu, Yichu; Zheng, Xuehua; Luo, Jia; Sun, Jing; Gu, Yingying; Liu, Bo; Xu, Yongcun; Li, Chufang; Pan, Weiqi; Zhao, Jincun; Ke, Changwen; Chen, Xinwen; Xu, Tao; Zhong, Nanshan; Guan, Suhua; Yuan, Zhiming; Chen, Ling title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques date: 2020-08-21 journal: Nat Commun DOI: 10.1038/s41467-020-18077-5 sha: doc_id: 354531 cord_uid: 7klivhut file: cache/cord-354529-k8p2u7iq.json key: cord-354529-k8p2u7iq authors: Wu, Yongran; Hong, Ke; Ruan, Lianguo; Yang, Xiaobo; Zhang, Jiancheng; Xu, Jiqian; Pan, Shangwen; Ren, Lehao; Chen, Lu; Huang, Chaolin; Shang, You title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 journal: Virol Sin DOI: 10.1007/s12250-020-00281-8 sha: doc_id: 354529 cord_uid: k8p2u7iq file: cache/cord-354773-u86bdmvf.json key: cord-354773-u86bdmvf authors: Suo, Tao; 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Sullivan, Zachary; Diiorio, Daren A.; Low, Sarah A.; Chang, Marvin G.; Bittner, Edward A. title: Multisystem effects of COVID-19: a concise review for practitioners date: 2020-11-04 journal: Postgraduate medicine DOI: 10.1080/00325481.2020.1823094 sha: doc_id: 354720 cord_uid: fu19u2b0 file: cache/cord-354868-pqn59ojj.json key: cord-354868-pqn59ojj authors: Yao, Hebang; Cai, Hongmin; Li, Tingting; Zhou, Bingjie; Qin, Wenming; Lavillette, Dimitri; Li, Dianfan title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date: 2020-09-25 journal: bioRxiv DOI: 10.1101/2020.09.24.312595 sha: doc_id: 354868 cord_uid: pqn59ojj file: cache/cord-354893-tku1dr32.json key: cord-354893-tku1dr32 authors: Shi, Zhengli; Wang, Lin-Fa title: Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology date: 2010-12-24 journal: Genetics and Evolution of Infectious Disease DOI: 10.1016/b978-0-12-384890-1.00027-3 sha: doc_id: 354893 cord_uid: tku1dr32 file: cache/cord-354658-v451z3jq.json key: cord-354658-v451z3jq authors: Rajagopal, Keshava; 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Afsar, Selim title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES date: 2020-06-02 journal: J Reprod Immunol DOI: 10.1016/j.jri.2020.103154 sha: doc_id: 354762 cord_uid: 3a3a3ku9 file: cache/cord-354900-bzv4yhqi.json key: cord-354900-bzv4yhqi authors: Jawhara, Samir title: How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections date: 2020-10-12 journal: Gut Pathog DOI: 10.1186/s13099-020-00385-2 sha: doc_id: 354900 cord_uid: bzv4yhqi file: cache/cord-354943-wxhbwcfr.json key: cord-354943-wxhbwcfr authors: Guo, Li; Ren, Lili; Yang, Siyuan; Xiao, Meng; Chang, De; Yang, Fan; Dela Cruz, Charles S; Wang, Yingying; Wu, Chao; Xiao, Yan; Zhang, Lulu; Han, Lianlian; Dang, Shengyuan; Xu, Yan; Yang, Qi-Wen; Xu, Sheng-Yong; Zhu, Hua-Dong; Xu, Ying-Chun; Jin, Qi; Sharma, Lokesh; Wang, Linghang; Wang, Jianwei title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa310 sha: doc_id: 354943 cord_uid: wxhbwcfr file: cache/cord-354881-7o20cn1x.json key: cord-354881-7o20cn1x authors: Brown, Rebecca C H; Kelly, Dominic; Wilkinson, Dominic; Savulescu, Julian title: The scientific and ethical feasibility of immunity passports date: 2020-10-16 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30766-0 sha: doc_id: 354881 cord_uid: 7o20cn1x file: cache/cord-354597-xubsodnk.json key: cord-354597-xubsodnk authors: Carvalho, Alexandre; Alqusairi, Rana; Adams, Anna; Paul, Michelle; Kothari, Neelay; Peters, Stevany; DeBenedet, Anthony T. title: SARS-CoV-2 Gastrointestinal Infection Causing Hemorrhagic Colitis: Implications for Detection and Transmission of COVID-19 Disease date: 2020-04-17 journal: Am J Gastroenterol DOI: 10.14309/ajg.0000000000000667 sha: doc_id: 354597 cord_uid: xubsodnk file: cache/cord-354950-kmpbdvof.json key: cord-354950-kmpbdvof authors: Demurtas, Olivia C.; Massa, Silvia; Illiano, Elena; De Martinis, Domenico; Chan, Paul K. S.; Di Bonito, Paola; Franconi, Rosella title: Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date: 2016-02-05 journal: Front Plant Sci DOI: 10.3389/fpls.2016.00054 sha: doc_id: 354950 cord_uid: kmpbdvof file: cache/cord-354733-qxivrhj8.json key: cord-354733-qxivrhj8 authors: Gniazdowski, V.; Morris, C. P.; Wohl, S.; Mehoke, T.; Ramakrishnan, S.; Thielen, P.; Powell, H.; Smith, B. D.; Armstrong, D. T.; Herrera, M.; Reifsnyder, C.; Sevdali, M.; Carroll, K. C.; Pekosz, A.; Mostafa, H. H. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 journal: nan DOI: 10.1101/2020.08.05.20168963 sha: doc_id: 354733 cord_uid: qxivrhj8 file: cache/cord-354780-yzyixucr.json key: cord-354780-yzyixucr authors: Lin, Chih-Yen; Wang, Wen-Hung; Urbina, Aspiro Nayim; Tseng, Sung-Pin; Lu, Po-Liang; Chen, Yen-Hsu; Yu, Ming-Lung; Wang, Seng-Fan title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date: 2020-06-13 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.031 sha: doc_id: 354780 cord_uid: yzyixucr file: cache/cord-355283-ny1ju7vc.json key: cord-355283-ny1ju7vc authors: Colombo, L.; Macheda, A.; Gentile, D.; Panizzardi, F.; Pierini, S.; Codazzi, C.; Meloni, L.; Bianchi, F.; Santangelo, G. title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism date: 2020-08-12 journal: Respir Med Case Rep DOI: 10.1016/j.rmcr.2020.101185 sha: doc_id: 355283 cord_uid: ny1ju7vc file: cache/cord-354972-nc496v6s.json key: cord-354972-nc496v6s authors: Margolin, Emmanuel; Burgers, Wendy A.; Sturrock, Edward D.; Mendelson, Marc; Chapman, Rosamund; Douglass, Nicola; Williamson, Anna-Lise; Rybicki, Edward P. title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-00441-3 sha: doc_id: 354972 cord_uid: nc496v6s file: cache/cord-355039-qi4fwqbc.json key: cord-355039-qi4fwqbc authors: Azar, William S.; Njeim, Rachel; Fares, Angie H.; Azar, Nadim S.; Azar, Sami T.; El Sayed, Mazen; Eid, Assaad A. title: COVID-19 and diabetes mellitus: how one pandemic worsens the other date: 2020-08-02 journal: Rev Endocr Metab Disord DOI: 10.1007/s11154-020-09573-6 sha: doc_id: 355039 cord_uid: qi4fwqbc file: cache/cord-355181-affuyn8z.json key: cord-355181-affuyn8z authors: Poggio, Claudio; Colombo, Marco; Arciola, Carla Renata; Greggi, Tiziana; Scribante, Andrea; Dagna, Alberto title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 journal: Materials (Basel) DOI: 10.3390/ma13153244 sha: doc_id: 355181 cord_uid: affuyn8z file: cache/cord-355477-7xd93aqv.json key: cord-355477-7xd93aqv authors: SATIJA, NAMITA; LAL, SUNIL K. title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1408.002 sha: doc_id: 355477 cord_uid: 7xd93aqv file: cache/cord-355306-fj8utkfe.json key: cord-355306-fj8utkfe authors: Xia Chao, Yin; Rötzschke, Olaf; Tan, Eng-King title: The role of IgA in COVID-19 date: 2020-05-23 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.05.057 sha: doc_id: 355306 cord_uid: fj8utkfe file: cache/cord-354824-7fdcu2f0.json key: cord-354824-7fdcu2f0 authors: Wu, Renyi; Wang, Lujing; Kuo, Hsiao-Chen Dina; Shannar, Ahmad; Peter, Rebecca; Chou, Pochung Jordan; Li, Shanyi; Hudlikar, Rasika; Liu, Xia; Liu, Zhigang; Poiani, George J.; Amorosa, Louis; Brunetti, Luigi; Kong, Ah-Ng title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 journal: Curr Pharmacol Rep DOI: 10.1007/s40495-020-00216-7 sha: doc_id: 354824 cord_uid: 7fdcu2f0 file: cache/cord-355422-c4odhdql.json key: cord-355422-c4odhdql authors: Vaira, Luigi Angelo; Salzano, Giovanni; Fois, Alessandro Giuseppe; Piombino, Pasquale; De Riu, Giacomo title: Potential pathogenesis of ageusia and anosmia in COVID‐19 patients date: 2020-04-27 journal: Int Forum Allergy Rhinol DOI: 10.1002/alr.22593 sha: doc_id: 355422 cord_uid: c4odhdql file: cache/cord-355175-uo9fx6jy.json key: cord-355175-uo9fx6jy authors: Ferrazzi, E; Frigerio, L; Savasi, V; Vergani, P; Prefumo, F; Barresi, S; Bianchi, S; Ciriello, E; Facchinetti, F; Gervasi, MT; Iurlaro, E; Kustermann, A; Mangili, G; Mosca, F; Patanè, L; Spazzini, D; Spinillo, A; Trojano, G; Vignali, M; Villa, A; Zuccotti, GV; Parazzini, F; Cetin, I title: Vaginal delivery in SARS‐CoV‐2‐infected pregnant women in Northern Italy: a retrospective analysis date: 2020-05-28 journal: BJOG DOI: 10.1111/1471-0528.16278 sha: doc_id: 355175 cord_uid: uo9fx6jy file: cache/cord-355294-gifsqph6.json key: cord-355294-gifsqph6 authors: García-Suárez, Julio; de la Cruz, Javier; Cedillo, Ángel; Llamas, Pilar; Duarte, Rafael; Jiménez-Yuste, Víctor; Hernández-Rivas, José Ángel; Gil-Manso, Rodrigo; Kwon, Mi; Sánchez-Godoy, Pedro; Martínez-Barranco, Pilar; Colás-Lahuerta, Blanca; Herrera, Pilar; Benito-Parra, Laurentino; Alegre, Adrián; Velasco, Alberto; Matilla, Arturo; Aláez-Usón, María Concepción; Martos-Martínez, Rafael; Martínez-Chamorro, Carmen; Susana-Quiroz, Keina; Del Campo, Juan Francisco; de la Fuente, Adolfo; Herráez, Regina; Pascual, Adriana; Gómez, Elvira; Pérez-Oteyza, Jaime; Ruiz, Elena; Alonso, Arancha; González-Medina, José; Martín-Buitrago, Lucía Núñez; Canales, Miguel; González-Gascón, Isabel; Vicente-Ayuso, María Carmen; Valenciano, Susana; Roa, María García; Monteliu, Pablo Estival; López-Jiménez, Javier; Escobar, Cristián Escolano; Ortiz-Martín, Javier; Diez-Martin, José Luis; Martinez-Lopez, Joaquín title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study date: 2020-10-08 journal: J Hematol Oncol DOI: 10.1186/s13045-020-00970-7 sha: doc_id: 355294 cord_uid: gifsqph6 file: cache/cord-355528-y4a1g6km.json key: cord-355528-y4a1g6km authors: Balla, Mamtha; Merugu, Ganesh Prasad; Patel, Mitra; Koduri, Narayana Murty; Gayam, Vijay; Adapa, Sreedhar; Naramala, Srikanth; Konala, Venu Madhav title: COVID-19, Modern Pandemic: A Systematic Review From Front-Line Health Care Providers’ Perspective date: 2020-03-30 journal: J Clin Med Res DOI: 10.14740/jocmr4142 sha: doc_id: 355528 cord_uid: y4a1g6km file: cache/cord-355122-x3v80bdp.json key: cord-355122-x3v80bdp authors: Desterke, Christophe; Turhan, Ali G.; Bennaceur-Griscelli, Annelise; Griscelli, Frank title: PPARγ cistrome repression during activation of lung monocyte-macrophages in severe COVID-19 date: 2020-09-25 journal: iScience DOI: 10.1016/j.isci.2020.101611 sha: doc_id: 355122 cord_uid: x3v80bdp file: cache/cord-355356-g7lvb8b4.json key: cord-355356-g7lvb8b4 authors: Lamb, Yvette N. title: Remdesivir: First Approval date: 2020-09-01 journal: Drugs DOI: 10.1007/s40265-020-01378-w sha: doc_id: 355356 cord_uid: g7lvb8b4 file: cache/cord-355475-kdubhh73.json key: cord-355475-kdubhh73 authors: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 journal: Oral Surg Oral Med Oral Pathol Oral Radiol DOI: 10.1016/j.oooo.2020.10.022 sha: doc_id: 355475 cord_uid: kdubhh73 file: cache/cord-355439-eqtk51q3.json key: cord-355439-eqtk51q3 authors: Lesko, Catherine R; Bengtson, Angela M title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 journal: Am J Epidemiol DOI: 10.1093/aje/kwaa158 sha: doc_id: 355439 cord_uid: eqtk51q3 file: cache/cord-355567-60sfv60p.json key: cord-355567-60sfv60p authors: Azuma, Kenichi; Yanagi, U; Kagi, Naoki; Kim, Hoon; Ogata, Masayuki; Hayashi, Motoya title: Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control date: 2020-11-03 journal: Environ Health Prev Med DOI: 10.1186/s12199-020-00904-2 sha: doc_id: 355567 cord_uid: 60sfv60p file: cache/cord-355318-qm79gz8w.json key: cord-355318-qm79gz8w authors: Smit, Albertus J.; Fitchett, Jennifer M.; Engelbrecht, Francois A.; Scholes, Robert J.; Dzhivhuho, Godfrey; Sweijd, Neville A. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165634 sha: doc_id: 355318 cord_uid: qm79gz8w file: cache/cord-355560-vsxe97xs.json key: cord-355560-vsxe97xs authors: Alves, Amanda Mandarino; Yvamoto, Erika Yuki; Marzinotto, Maira Andrade Nacimbem; Teixeira, Ana Cristina de Sá; Carrilho, Flair José title: SARS-CoV-2 leading to Acute Pancreatitis: an unusual presentation date: 2020-09-15 journal: Braz J Infect Dis DOI: 10.1016/j.bjid.2020.08.011 sha: doc_id: 355560 cord_uid: vsxe97xs file: cache/cord-355718-7dafsxp9.json key: cord-355718-7dafsxp9 authors: Leong, Hoe‐Nam; Ang, Brenda; Earnest, Arul; Teoh, Cindy; Xu, Wei; Leo, Yee‐Sin title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 date: 2004-08-10 journal: Trop Med Int Health DOI: 10.1111/j.1365-3156.2004.01281.x sha: doc_id: 355718 cord_uid: 7dafsxp9 file: cache/cord-355728-wivk0bm0.json key: cord-355728-wivk0bm0 authors: Schoof, Michael; Faust, Bryan; Saunders, Reuben A.; Sangwan, Smriti; Rezelj, Veronica; Hoppe, Nick; Boone, Morgane; Billesbølle, Christian B.; Puchades, Cristina; Azumaya, Caleigh M.; Kratochvil, Huong T.; Zimanyi, Marcell; Deshpande, Ishan; Liang, Jiahao; Dickinson, Sasha; Nguyen, Henry C.; Chio, Cynthia M.; Merz, Gregory E.; Thompson, Michael C.; Diwanji, Devan; Schaefer, Kaitlin; Anand, Aditya A.; Dobzinski, Niv; Zha, Beth Shoshana; Simoneau, Camille R.; Leon, Kristoffer; White, Kris M.; Chio, Un Seng; Gupta, Meghna; Jin, Mingliang; Li, Fei; Liu, Yanxin; Zhang, Kaihua; Bulkley, David; Sun, Ming; Smith, Amber M.; Rizo, Alexandrea N.; Moss, Frank; Brilot, Axel F.; Pourmal, Sergei; Trenker, Raphael; Pospiech, Thomas; Gupta, Sayan; Barsi-Rhyne, Benjamin; Belyy, Vladislav; Barile-Hill, Andrew W.; Nock, Silke; Liu, Yuwei; Krogan, Nevan J.; Ralston, Corie Y.; Swaney, Danielle L.; García-Sastre, Adolfo; Ott, Melanie; Vignuzzi, Marco; Walter, Peter; Manglik, Aashish title: An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date: 2020-08-17 journal: bioRxiv DOI: 10.1101/2020.08.08.238469 sha: doc_id: 355728 cord_uid: wivk0bm0 file: cache/cord-355514-2qjbc3bd.json key: cord-355514-2qjbc3bd authors: Shibata, Shun; Ishiguro, Takashi; Kobayashi, Yasuhito; Koike, Mayumi; Numano, Tsuyoshi; Shimizu, Yoshihiko; Takayanagi, Noboru title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection date: 2020-07-25 journal: Respir Med Case Rep DOI: 10.1016/j.rmcr.2020.101180 sha: doc_id: 355514 cord_uid: 2qjbc3bd file: cache/cord-355655-l684uy4h.json key: cord-355655-l684uy4h authors: Ning, Ling; Liu, Lei; Li, Wenyuan; Liu, Hongtao; Wang, Jizhou; Yao, Ziqin; Zhang, Shengyu; Zhao, Desheng; Nashan, Björn; Shen, Aizong; Liu, Lianxin; Li, Lei title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report date: 2020-05-08 journal: Am J Transplant DOI: 10.1111/ajt.15897 sha: doc_id: 355655 cord_uid: l684uy4h file: cache/cord-355577-w1yhtbz8.json key: cord-355577-w1yhtbz8 authors: Kowalski, Luiz Paulo; Imamura, Rui; Castro Junior, Gilberto de; Marta, Gustavo Nader; Chaves, Aline Lauda Freitas; Matos, Leandro Luongo; Bento, Ricardo Ferreira title: Effect of the COVID-19 Pandemic on the Activity of Physicians Working in the Areas of Head and Neck Surgery and Otorhinolaryngology date: 2020-05-22 journal: Int Arch Otorhinolaryngol DOI: 10.1055/s-0040-1712169 sha: doc_id: 355577 cord_uid: w1yhtbz8 file: cache/cord-355589-3zdv9zim.json key: cord-355589-3zdv9zim authors: Simons, David; Shahab, Lion; Brown, Jamie; Perski, Olga title: The association of smoking status with SARS‐CoV‐2 infection, hospitalisation and mortality from COVID‐19: A living rapid evidence review with Bayesian meta‐analyses (version 7) date: 2020-10-02 journal: Addiction DOI: 10.1111/add.15276 sha: doc_id: 355589 cord_uid: 3zdv9zim file: cache/cord-355674-mhi85px5.json key: cord-355674-mhi85px5 authors: Siddiqi, Hasan K.; Weber, Brittany; Zhou, Guohai; Regan, James; Fajnzylber, Jesse; Coxen, Kendyll; Corry, Heather; Yu, Xu G.; DiCarli, Marcelo; Li, Jonathan Z.; Bhatt, Deepak L. title: Increased prevalence of myocardial injury in patients with SARS-CoV-2 viremia. date: 2020-11-10 journal: Am J Med DOI: 10.1016/j.amjmed.2020.09.046 sha: doc_id: 355674 cord_uid: mhi85px5 file: cache/cord-355395-rckzi8vz.json key: cord-355395-rckzi8vz authors: Tian, Dandan; Ye, Qing title: Hepatic complications of COVID‐19 and its treatment date: 2020-05-21 journal: J Med Virol DOI: 10.1002/jmv.26036 sha: doc_id: 355395 cord_uid: rckzi8vz file: cache/cord-355734-pz64534w.json key: cord-355734-pz64534w authors: Antonio-Villa, Neftali Eduardo; Bello-Chavolla, Omar Yaxmehen; Vargas-Vázquez, Arsenio; Fermín-Martínez, Carlos A; Márquez-Salinas, Alejandro; Bahena-López, Jessica Paola title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1487 sha: doc_id: 355734 cord_uid: pz64534w file: cache/cord-355672-egjdy7o0.json key: cord-355672-egjdy7o0 authors: Castillo, Edward M.; Coyne, Christopher J.; Brennan, Jesse J.; Tomaszewski, Christian A. title: Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date: 2020-07-02 journal: J Am Coll Emerg Physicians Open DOI: 10.1002/emp2.12172 sha: doc_id: 355672 cord_uid: egjdy7o0 file: cache/cord-355758-tk7eturq.json key: cord-355758-tk7eturq authors: Berrio, Alejandro; Gartner, Valerie; Wray, Gregory A title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.16.300038 sha: doc_id: 355758 cord_uid: tk7eturq file: cache/cord-355811-aq7p1uxo.json key: cord-355811-aq7p1uxo authors: Węglarz-Tomczak, Ewelina; Tomczak, Jakub M.; Giurg, Mirosław; Burda-Grabowska, Małgorzata; Brul, Stanley title: Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date: 2020-05-21 journal: bioRxiv DOI: 10.1101/2020.05.20.107052 sha: doc_id: 355811 cord_uid: aq7p1uxo file: cache/cord-355807-q3bngari.json key: cord-355807-q3bngari authors: Yepes-Pérez, Andres F.; Herrera-Calderon, Oscar; Quintero-Saumeth, Jorge title: Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling date: 2020-10-29 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1837676 sha: doc_id: 355807 cord_uid: q3bngari file: cache/cord-355788-6hteott0.json key: cord-355788-6hteott0 authors: Shirvani, Edris; Samal, Siba K. title: Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2 date: 2020-07-29 journal: Pathogens DOI: 10.3390/pathogens9080619 sha: doc_id: 355788 cord_uid: 6hteott0 file: cache/cord-355841-m6dl8a0w.json key: cord-355841-m6dl8a0w authors: Munz, Maike; Wessendorf, Swen; Koretsis, Georgios; Tewald, Friedemann; Baegi, Reem; Krämer, Stefan; Geissler, Michael; Reinhard, Matthias title: Acute transverse myelitis after COVID-19 pneumonia date: 2020-05-26 journal: J Neurol DOI: 10.1007/s00415-020-09934-w sha: doc_id: 355841 cord_uid: m6dl8a0w file: cache/cord-355760-2a12nsnl.json key: cord-355760-2a12nsnl authors: Shields, A. M.; Faustini, S. E.; Perez-Toledo, M.; Jossi, S.; Aldera, E. L.; Allen, J. D.; Al-Taei, S.; Backhouse, C.; Bosworth, A.; Dunbar, L.; Ebanks, D.; Emmanuel, B.; Grey, J.; Kidd, I. M.; McGinnell, G.; McLoughlin, D.; Morley, G.; O'Neill, J.; Papakonstantinou, D.; Pickles, O.; Poxon, C.; Richter, M.; Walker, E.; Wanigasooriya, K.; Watanabe, Y.; Whalley, C.; Zielinska, A. E.; Crispin, M.; Wraith, D. C.; Beggs, A. D.; Cunningham, A. F.; Drayson, M. T.; Richter, A. G. title: SARS-CoV-2 seroconversion in health care workers date: 2020-05-19 journal: nan DOI: 10.1101/2020.05.18.20105197 sha: doc_id: 355760 cord_uid: 2a12nsnl file: cache/cord-355854-hksq8gy4.json key: cord-355854-hksq8gy4 authors: Pagliaro, Pasquale; Penna, Claudia title: ACE/ACE2 Ratio: A Key Also in 2019 Coronavirus Disease (Covid-19)? date: 2020-06-18 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00335 sha: doc_id: 355854 cord_uid: hksq8gy4 file: cache/cord-355935-psnqrdo2.json key: cord-355935-psnqrdo2 authors: Paez, Antonio; Lopez, Fernando A.; Menezes, Tatiane; Cavalcanti, Renata; Pitta, Maira Galdino da Rocha title: A Spatio‐Temporal Analysis of the Environmental Correlates of COVID‐19 Incidence in Spain date: 2020-06-08 journal: Geogr Anal DOI: 10.1111/gean.12241 sha: doc_id: 355935 cord_uid: psnqrdo2 file: cache/cord-356021-lr3wj8we.json key: cord-356021-lr3wj8we authors: Choudhury, Chinmayee title: Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease date: 2020-06-01 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1771424 sha: doc_id: 356021 cord_uid: lr3wj8we file: cache/cord-356005-zhwtlik6.json key: cord-356005-zhwtlik6 authors: Yazhini, Arangasamy; Sidhanta, Das Swayam Prakash; Srinivasan, Narayanaswamy title: D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.364273 sha: doc_id: 356005 cord_uid: zhwtlik6 file: cache/cord-355924-8sk9al0n.json key: cord-355924-8sk9al0n authors: Allam, Loubna; Ghrifi, Fatima; Mohammed, Hakmi; El Hafidi, Naima; El Jaoudi, Rachid; El Harti, Jaouad; Lmimouni, Badreddine; Belyamani, Lahcen; Ibrahimi, Azeddine title: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date: 2020-10-21 journal: Bioinform Biol Insights DOI: 10.1177/1177932220965505 sha: doc_id: 355924 cord_uid: 8sk9al0n file: cache/cord-355899-wd00f8cw.json key: cord-355899-wd00f8cw authors: Dawson, E. D.; Kuck, L. R.; Blair, R. H.; Taylor, A. W.; Toth, E.; Knight, V.; Rowlen, K. L. title: Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses date: 2020-09-04 journal: nan DOI: 10.1101/2020.09.03.20179598 sha: doc_id: 355899 cord_uid: wd00f8cw file: cache/cord-355943-bezpprrk.json key: cord-355943-bezpprrk authors: Li, Y.; Wang, Y.; Liu, H.; Sun, W.; Ding, B.; Zhao, Y.; Chen, P.; Zhu, L.; Li, Z.; Li, N.; Chang, L.; Wang, H.; Bai, C.; Xu, P. title: Urine Proteome of COVID-19 Patients date: 2020-05-06 journal: nan DOI: 10.1101/2020.05.02.20088666 sha: doc_id: 355943 cord_uid: bezpprrk file: cache/cord-356030-bbj4r81i.json key: cord-356030-bbj4r81i authors: Haehner, Antje; Draf, Julia; Dräger, Sarah; de With, Katja; Hummel, Thomas title: Predictive Value of Sudden Olfactory Loss in the Diagnosis of COVID-19 date: 2020-06-11 journal: ORL J Otorhinolaryngol Relat Spec DOI: 10.1159/000509143 sha: doc_id: 356030 cord_uid: bbj4r81i file: cache/cord-356009-emn2w8if.json key: cord-356009-emn2w8if authors: Roshandel, M. R.; Nateqi, M.; Lak, R.; Aavani, P.; Sari Motlagh, R.; Aghaei Badr, T.; Sfakianos, J.; Kaplan, S. A.; Shariat, S.; Tewari, A. K. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.08.20209544 sha: doc_id: 356009 cord_uid: emn2w8if file: cache/cord-356084-621qzpqd.json key: cord-356084-621qzpqd authors: Qu, Jiuxin; Wu, Chi; Li, Xiaoyong; Zhang, Guobin; Jiang, Zhaofang; Li, Xiaohe; zhu, Qing; Liu, Lei title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa489 sha: doc_id: 356084 cord_uid: 621qzpqd file: cache/cord-356154-ifb3qiz7.json key: cord-356154-ifb3qiz7 authors: Zhang, Rong; Chen, Xiaohua; Huang, Yuqing; Zhang, Qi; Cheng, Yan; Zhang, Nan; Zhang, Haibo; Yang, Bo; Liu, Fang; Liu, Yingle; Lan, Ke title: A Study of Two Cases Co-Infected with SARS-CoV-2 and Human Immunodeficiency Virus date: 2020-09-07 journal: Virol Sin DOI: 10.1007/s12250-020-00280-9 sha: doc_id: 356154 cord_uid: ifb3qiz7 file: cache/cord-355912-ioihqf0r.json key: cord-355912-ioihqf0r authors: Shomuradova, A. S.; Vagida, M. S.; Sheetikov, S. A.; Zornikova, K. V.; Kiryukhin, D.; Titov, A.; Peshkova, I. O.; Khmelevskaya, A.; Dianov, D. V.; Malasheva, M.; Shmelev, A.; Serdyuk, Y.; Bagaev, D. V.; Pivnyuk, A.; Shcherbinin, D. S.; Maleeva, A. V.; Shakirova, N. T.; Pilunov, A.; Malko, D. B.; Khamaganova, E. G.; Biderman, B.; Ivanov, A. V.; Shugay, M.; Efimov, G. A. title: SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors date: 2020-05-25 journal: nan DOI: 10.1101/2020.05.20.20107813 sha: doc_id: 355912 cord_uid: ioihqf0r file: cache/cord-356174-40k6m7l0.json key: cord-356174-40k6m7l0 authors: Ducloyer, Mathilde; Gaborit, Benjamin; Toquet, Claire; Castain, Louise; Bal, Antonin; Arrigoni, Pierre Paul; Lecomte, Raphaël; Clement, Renaud; Sagan, Christine title: Complete post-mortem data in a fatal case of COVID-19: clinical, radiological and pathological correlations date: 2020-08-06 journal: Int J Legal Med DOI: 10.1007/s00414-020-02390-1 sha: doc_id: 356174 cord_uid: 40k6m7l0 file: cache/cord-356150-ivso91ln.json key: cord-356150-ivso91ln authors: Torretta, Sara; Zuccotti, Gianvincenzo; Cristofaro, Valentina; Ettori, Jacopo; Solimeno, Lorenzo; Battilocchi, Ludovica; D’Onghia, Alessandra; Bonsembiante, Anna; Pignataro, Lorenzo; Marchisio, Paola; Capaccio, Pasquale title: Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature date: 2020-08-31 journal: Ear Nose Throat J DOI: 10.1177/0145561320953231 sha: doc_id: 356150 cord_uid: ivso91ln file: cache/cord-356090-oj3d9ail.json key: cord-356090-oj3d9ail authors: Gorgun, D.; Lihan, M.; Kapoor, K.; Tajkhorshid, E. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 journal: bioRxiv DOI: 10.1101/2020.10.27.357350 sha: doc_id: 356090 cord_uid: oj3d9ail file: cache/cord-356166-fpno9zg5.json key: cord-356166-fpno9zg5 authors: Miyakawa, Kei; Jeremiah, Sundararaj Stanleyraj; Ohtake, Norihisa; Matsunaga, Satoko; Yamaoka, Yutaro; Nishi, Mayuko; Morita, Takeshi; Saji, Ryo; Nishii, Mototsugu; Kimura, Hirokazu; Hasegawa, Hideki; Takeuchi, Ichiro; Ryo, Akihide title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles date: 2020-09-15 journal: J Mol Cell Biol DOI: 10.1093/jmcb/mjaa047 sha: doc_id: 356166 cord_uid: fpno9zg5 file: cache/cord-356370-jjl1hbeb.json key: cord-356370-jjl1hbeb authors: Sahajpal, Nikhil Shri; Njau, Allan; Mondal, Ashis K; Ananth, Sudha; Chaubey, Alka; Rojiani, Amyn; Kolhe, Ravindra title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 journal: Future medicinal chemistry DOI: 10.4155/fmc-2020-0129 sha: doc_id: 356370 cord_uid: jjl1hbeb file: cache/cord-356264-q0yqnlyl.json key: cord-356264-q0yqnlyl authors: Armijos-Jaramillo, Vinicio; Yeager, Justin; Muslin, Claire; Perez-Castillo, Yunierkis title: SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-03-23 journal: bioRxiv DOI: 10.1101/2020.03.21.001933 sha: doc_id: 356264 cord_uid: q0yqnlyl file: cache/cord-356195-5pcaxpp9.json key: cord-356195-5pcaxpp9 authors: Jothimani, Dinesh; Venugopal, Radhika; Abedin, Mohammed Forhad; Kaliamoorthy, Ilankumaran; Rela, Mohamed title: COVID-19 and Liver. date: 2020-06-15 journal: J Hepatol DOI: 10.1016/j.jhep.2020.06.006 sha: doc_id: 356195 cord_uid: 5pcaxpp9 file: cache/cord-356364-ipi81ce3.json key: cord-356364-ipi81ce3 authors: Ho, Bo-Lin; Cheng, Shu-Chun; Shi, Lin; Wang, Ting-Yun; Ho, Kuan-I; Chou, Chi-Yuan title: Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date: 2015-12-14 journal: PLoS One DOI: 10.1371/journal.pone.0144865 sha: doc_id: 356364 cord_uid: ipi81ce3 file: cache/cord-356217-igm2t7md.json key: cord-356217-igm2t7md authors: Noda, Sakura; Ma, Jimmy; Romberg, Erin K.; Hernandez, Rafael E.; Ferguson, Mark R. title: Severe COVID-19 initially presenting as mesenteric adenopathy date: 2020-10-10 journal: Pediatr Radiol DOI: 10.1007/s00247-020-04789-9 sha: doc_id: 356217 cord_uid: igm2t7md file: cache/cord-356325-gk5jve0i.json key: cord-356325-gk5jve0i authors: Beaudoin-Bussières, Guillaume; Laumaea, Annemarie; Anand, Sai Priya; Prévost, Jérémie; Gasser, Romain; Goyette, Guillaume; Medjahed, Halima; Perreault, Josée; Tremblay, Tony; Lewin, Antoine; Gokool, Laurie; Morrisseau, Chantal; Bégin, Philippe; Tremblay, Cécile; Martel-Laferrière, Valérie; Kaufmann, Daniel E.; Richard, Jonathan; Bazin, Renée; Finzi, Andrés title: Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals date: 2020-10-16 journal: mBio DOI: 10.1128/mbio.02590-20 sha: doc_id: 356325 cord_uid: gk5jve0i Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-sars-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7522 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7835 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7115 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7071 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6853 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7093 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7244 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7290 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7624 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7669 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7081 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6564 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5975 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5978 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7289 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7798 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7994 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7541 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8038 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8165 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5926 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-015701-0m17unfx author: nan title: Neuartiges Coronavirus (SARS-CoV-2) date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-015701-0m17unfx.txt cache: ./cache/cord-015701-0m17unfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015701-0m17unfx.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-011813-lm105z6n author: Imperiale, Michael J. title: Recurring Themes date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-011813-lm105z6n.txt cache: ./cache/cord-011813-lm105z6n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011813-lm105z6n.txt' === file2bib.sh === id: cord-015181-875gf11z author: Walgate, Robert title: SARS escaped Beijing lab twice date: 2004-04-27 pages: extension: .txt txt: ./txt/cord-015181-875gf11z.txt cache: ./cache/cord-015181-875gf11z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-015181-875gf11z.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-012424-z3mkp9y9 author: Bansal, Poonam title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-012424-z3mkp9y9.txt cache: ./cache/cord-012424-z3mkp9y9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012424-z3mkp9y9.txt' === file2bib.sh === id: cord-007581-nu1shltl author: Wang, Jiun-Ling title: Rhabdomyolysis associated with probable SARS date: 2003-10-01 pages: extension: .txt txt: ./txt/cord-007581-nu1shltl.txt cache: ./cache/cord-007581-nu1shltl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007581-nu1shltl.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-009295-4c0zwhdh author: Bal, A. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 pages: extension: .txt txt: ./txt/cord-009295-4c0zwhdh.txt cache: ./cache/cord-009295-4c0zwhdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009295-4c0zwhdh.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-004634-pkrxiipo author: Brun-Buisson, Christian title: SARS: The challenge of emerging pathogens to the intensivist date: 2003-05-08 pages: extension: .txt txt: ./txt/cord-004634-pkrxiipo.txt cache: ./cache/cord-004634-pkrxiipo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004634-pkrxiipo.txt' === file2bib.sh === id: cord-009573-ghv9uezx author: Karlberg, J title: Do sensational media reports about severe acute respiratory syndrome affect the mindset of healthcare workers? date: 2007-01-02 pages: extension: .txt txt: ./txt/cord-009573-ghv9uezx.txt cache: ./cache/cord-009573-ghv9uezx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-009573-ghv9uezx.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-015183-1eytelxn author: Walgate, Robert title: Latest SARS evidence date: 2003-04-07 pages: extension: .txt txt: ./txt/cord-015183-1eytelxn.txt cache: ./cache/cord-015183-1eytelxn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015183-1eytelxn.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-021055-ebcu3ywq author: Xu, Jianguo title: Inaugural editorial: Towards evidence-based biosafety and biosecurity date: 2019-02-20 pages: extension: .txt txt: ./txt/cord-021055-ebcu3ywq.txt cache: ./cache/cord-021055-ebcu3ywq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-021055-ebcu3ywq.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-015009-3o90pzw7 author: nan title: How and who does SARS kill? date: 2003-06-10 pages: extension: .txt txt: ./txt/cord-015009-3o90pzw7.txt cache: ./cache/cord-015009-3o90pzw7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015009-3o90pzw7.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-016312-u47mb2h0 author: Lu, Pu-Xuan title: Introduction of Emerging Infectious Diseases date: 2015-07-25 pages: extension: .txt txt: ./txt/cord-016312-u47mb2h0.txt cache: ./cache/cord-016312-u47mb2h0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016312-u47mb2h0.txt' === file2bib.sh === id: cord-007049-02p8ug67 author: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 pages: extension: .txt txt: ./txt/cord-007049-02p8ug67.txt cache: ./cache/cord-007049-02p8ug67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007049-02p8ug67.txt' === file2bib.sh === id: cord-004204-cpub9oah author: D’Cunha, Colin title: SARS: Lessons Learned from a Provincial Perspective date: 2004-01-01 pages: extension: .txt txt: ./txt/cord-004204-cpub9oah.txt cache: ./cache/cord-004204-cpub9oah.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004204-cpub9oah.txt' === file2bib.sh === id: cord-014878-n6a9cq47 author: Jun-yi, Ma title: The characteristics and dynamic changes of X-ray chest film in 50 patients with severe acute respiratory syndrome date: 2003 pages: extension: .txt txt: ./txt/cord-014878-n6a9cq47.txt cache: ./cache/cord-014878-n6a9cq47.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-014878-n6a9cq47.txt' === file2bib.sh === id: cord-010050-utbrf4ad author: Fisher, Dale A title: Preventing local transmission of SARS: lessons from Singapore date: 2003-06-02 pages: extension: .txt txt: ./txt/cord-010050-utbrf4ad.txt cache: ./cache/cord-010050-utbrf4ad.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010050-utbrf4ad.txt' === file2bib.sh === id: cord-010384-wyp7hrde author: Iwen, Peter C title: Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-010384-wyp7hrde.txt cache: ./cache/cord-010384-wyp7hrde.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010384-wyp7hrde.txt' === file2bib.sh === id: cord-014938-7evmiuv5 author: Wei-ming, Yan title: Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model date: 2008-01-13 pages: extension: .txt txt: ./txt/cord-014938-7evmiuv5.txt cache: ./cache/cord-014938-7evmiuv5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-014938-7evmiuv5.txt' === file2bib.sh === id: cord-008841-r17qhfsj author: Tomlinson, Brian title: SARS: experience at Prince of Wales Hospital, Hong Kong date: 2003-05-03 pages: extension: .txt txt: ./txt/cord-008841-r17qhfsj.txt cache: ./cache/cord-008841-r17qhfsj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008841-r17qhfsj.txt' === file2bib.sh === id: cord-015516-hx7ktq8j author: nan title: In the Literature date: 2005-10-15 pages: extension: .txt txt: ./txt/cord-015516-hx7ktq8j.txt cache: ./cache/cord-015516-hx7ktq8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015516-hx7ktq8j.txt' === file2bib.sh === id: cord-009697-dq4y89ab author: Yuen, Eddie title: Role of absolute lymphocyte count in the screening of patients with suspected SARS date: 2003-07-25 pages: extension: .txt txt: ./txt/cord-009697-dq4y89ab.txt cache: ./cache/cord-009697-dq4y89ab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009697-dq4y89ab.txt' === file2bib.sh === id: cord-006890-81wv1s33 author: Viret, Jean-Francois title: Development of a SARS vaccine: an industrial perspective on the global race against a global disease date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-006890-81wv1s33.txt cache: ./cache/cord-006890-81wv1s33.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006890-81wv1s33.txt' === file2bib.sh === id: cord-017668-my2l85bn author: Cho, Yeon-Jin title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction date: 2005 pages: extension: .txt txt: ./txt/cord-017668-my2l85bn.txt cache: ./cache/cord-017668-my2l85bn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017668-my2l85bn.txt' === file2bib.sh === id: cord-007713-611sp7uo author: Hughes, J. M. title: Emerging infectious diseases: the public’s view of the problem and what should be expected from the public health community date: 2005 pages: extension: .txt txt: ./txt/cord-007713-611sp7uo.txt cache: ./cache/cord-007713-611sp7uo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007713-611sp7uo.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-014897-rnrlslfh author: Rong-bing, Wang title: Therapeutic effects of integrated traditional Chinese medicine and western medicine in treating severe acute respiratory syndrome date: 2003 pages: extension: .txt txt: ./txt/cord-014897-rnrlslfh.txt cache: ./cache/cord-014897-rnrlslfh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014897-rnrlslfh.txt' === file2bib.sh === id: cord-013269-u1e0kzmm author: Cucinotta, Domenico title: Primum non nocere (first do no harm). The SARS-CoV-2 pandemic course in oldest in Italy date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-013269-u1e0kzmm.txt cache: ./cache/cord-013269-u1e0kzmm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013269-u1e0kzmm.txt' === file2bib.sh === id: cord-017108-vqbl0eov author: Zheng, Xiaolong title: Network-Based Analysis of Beijing SARS Data date: 2008 pages: extension: .txt txt: ./txt/cord-017108-vqbl0eov.txt cache: ./cache/cord-017108-vqbl0eov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017108-vqbl0eov.txt' === file2bib.sh === id: cord-009153-zxx4m1kz author: Heymann, David L title: Dangerous pathogens in the laboratory: from smallpox to today's SARS setbacks and tomorrow's polio-free world date: 2004-05-15 pages: extension: .txt txt: ./txt/cord-009153-zxx4m1kz.txt cache: ./cache/cord-009153-zxx4m1kz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009153-zxx4m1kz.txt' === file2bib.sh === id: cord-007560-nck4f5ny author: Ling, Lowell title: COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-007560-nck4f5ny.txt cache: ./cache/cord-007560-nck4f5ny.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007560-nck4f5ny.txt' === file2bib.sh === id: cord-019048-29wzpwvr author: Franks, Teri J. title: Coronavirus date: 2013-08-26 pages: extension: .txt txt: ./txt/cord-019048-29wzpwvr.txt cache: ./cache/cord-019048-29wzpwvr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-019048-29wzpwvr.txt' === file2bib.sh === id: cord-023140-ytal7wog author: Henderson, Joan C. title: Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore date: 2004-12-09 pages: extension: .txt txt: ./txt/cord-023140-ytal7wog.txt cache: ./cache/cord-023140-ytal7wog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023140-ytal7wog.txt' === file2bib.sh === id: cord-017995-azqjvxtu author: Kwong, Kim-hung title: Spatial Components in Disease Modelling date: 2010 pages: extension: .txt txt: ./txt/cord-017995-azqjvxtu.txt cache: ./cache/cord-017995-azqjvxtu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017995-azqjvxtu.txt' === file2bib.sh === id: cord-015619-msicix98 author: nan title: Virus Structure & Assembly date: 2009-02-24 pages: extension: .txt txt: ./txt/cord-015619-msicix98.txt cache: ./cache/cord-015619-msicix98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015619-msicix98.txt' === file2bib.sh === id: cord-024317-w1ep0wq8 author: Ku, Zhiqiang title: Antibody therapies for the treatment of COVID-19 date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-024317-w1ep0wq8.txt cache: ./cache/cord-024317-w1ep0wq8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-024317-w1ep0wq8.txt' === file2bib.sh === id: cord-016844-lq2bgu7a author: Teksam, Ozlem title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective date: 2013-05-29 pages: extension: .txt txt: ./txt/cord-016844-lq2bgu7a.txt cache: ./cache/cord-016844-lq2bgu7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016844-lq2bgu7a.txt' cp: cannot stat ‘/data-disk/reader-compute/reader-cord/cord/pos/cord-315715-xa6kwguo.pos’: No such file or directory cp: cannot stat ‘/data-disk/reader-compute/reader-cord/cord/wrd/cord-315715-xa6kwguo.wrd’: No such file or directory === file2bib.sh === id: cord-016897-t71f10kv author: Flores, Marco V. title: Preventing Airborne Disease Transmission: Implications for Patients During Mechanical Ventilation date: 2013-05-29 pages: extension: .txt txt: ./txt/cord-016897-t71f10kv.txt cache: ./cache/cord-016897-t71f10kv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016897-t71f10kv.txt' === file2bib.sh === id: cord-017210-5nc8f3a4 author: Pathegama, Mahinda P. title: Interactive Real-time Image Analysis System for Distant Operation date: 2005 pages: extension: .txt txt: ./txt/cord-017210-5nc8f3a4.txt cache: ./cache/cord-017210-5nc8f3a4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017210-5nc8f3a4.txt' === file2bib.sh === id: cord-024100-lk67yfrp author: Plewczynski, Dariusz title: In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening date: 2007-04-24 pages: extension: .txt txt: ./txt/cord-024100-lk67yfrp.txt cache: ./cache/cord-024100-lk67yfrp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-024100-lk67yfrp.txt' === file2bib.sh === id: cord-017942-og0b2l6b author: Chen, Yi-Da title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data date: 2007 pages: extension: .txt txt: ./txt/cord-017942-og0b2l6b.txt cache: ./cache/cord-017942-og0b2l6b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017942-og0b2l6b.txt' === file2bib.sh === id: cord-007567-vst954ef author: Farquharson, Carolyn title: Responding to the severe acute respiratory syndrome (SARS) outbreak: Lessons learned in a Toronto emergency department() date: 2003-06-04 pages: extension: .txt txt: ./txt/cord-007567-vst954ef.txt cache: ./cache/cord-007567-vst954ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007567-vst954ef.txt' === file2bib.sh === id: cord-009891-gqrhbhbn author: Rassool, G. Hussein title: Current issues and forthcoming events date: 2003-09-03 pages: extension: .txt txt: ./txt/cord-009891-gqrhbhbn.txt cache: ./cache/cord-009891-gqrhbhbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-009891-gqrhbhbn.txt' === file2bib.sh === id: cord-017516-qbksb83c author: Si, Yain-Whar title: Hidden Cluster Detection for Infectious Disease Control and Quarantine Management date: 2009-09-30 pages: extension: .txt txt: ./txt/cord-017516-qbksb83c.txt cache: ./cache/cord-017516-qbksb83c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017516-qbksb83c.txt' === file2bib.sh === id: cord-018441-r6wwpfcy author: Taylor, Milton W. title: Emerging Viruses date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-018441-r6wwpfcy.txt cache: ./cache/cord-018441-r6wwpfcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018441-r6wwpfcy.txt' === file2bib.sh === id: cord-023463-vr6uaw3a author: Liu, Wei title: Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date: 2009-06-05 pages: extension: .txt txt: ./txt/cord-023463-vr6uaw3a.txt cache: ./cache/cord-023463-vr6uaw3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023463-vr6uaw3a.txt' === file2bib.sh === id: cord-024613-yump76qu author: Wu, Chunxing title: Recommendations for control and prevention of infections for pediatric orthopedics during the epidemic period of COVID-19 date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-024613-yump76qu.txt cache: ./cache/cord-024613-yump76qu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-024613-yump76qu.txt' === file2bib.sh === id: cord-023867-ti4b03lh author: Zuo, Wei title: SARS Coronavirus and Lung Fibrosis date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-023867-ti4b03lh.txt cache: ./cache/cord-023867-ti4b03lh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023867-ti4b03lh.txt' === file2bib.sh === id: cord-018106-5giapmcf author: Levin, Jacqueline title: Mental Health Care for Survivors and Healthcare Workers in the Aftermath of an Outbreak date: 2019-05-16 pages: extension: .txt txt: ./txt/cord-018106-5giapmcf.txt cache: ./cache/cord-018106-5giapmcf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018106-5giapmcf.txt' === file2bib.sh === id: cord-015503-j99cgsjt author: Tang, Xiaolu title: On the origin and continuing evolution of SARS-CoV-2 date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-015503-j99cgsjt.txt cache: ./cache/cord-015503-j99cgsjt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015503-j99cgsjt.txt' === file2bib.sh === id: cord-022473-l4jniccw author: Wilder-Smith, Annelies title: As Travel Medicine Practitioner during the SARS Outbreak in Singapore date: 2009-11-16 pages: extension: .txt txt: ./txt/cord-022473-l4jniccw.txt cache: ./cache/cord-022473-l4jniccw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-022473-l4jniccw.txt' === file2bib.sh === id: cord-021805-2j07zw6q author: Epstein, Jonathan H. title: Emerging Diseases in Bats date: 2018-09-28 pages: extension: .txt txt: ./txt/cord-021805-2j07zw6q.txt cache: ./cache/cord-021805-2j07zw6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021805-2j07zw6q.txt' === file2bib.sh === id: cord-016921-64mfqks9 author: Schillmeier, Michael title: Risiko-Akteur-Netzwerke date: 2009-08-07 pages: extension: .txt txt: ./txt/cord-016921-64mfqks9.txt cache: ./cache/cord-016921-64mfqks9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016921-64mfqks9.txt' === file2bib.sh === id: cord-023888-w2sbyfy2 author: Beniac, Daniel R. title: Structural Molecular Insights into SARS Coronavirus Cellular Attachment, Entry and Morphogenesis date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-023888-w2sbyfy2.txt cache: ./cache/cord-023888-w2sbyfy2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023888-w2sbyfy2.txt' === file2bib.sh === id: cord-015235-lv8mll28 author: Kim, Hyun title: Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody date: 2014-04-16 pages: extension: .txt txt: ./txt/cord-015235-lv8mll28.txt cache: ./cache/cord-015235-lv8mll28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015235-lv8mll28.txt' === file2bib.sh === id: cord-000333-4prvgmvt author: Darbyshire, Philip title: Nursing heroism in the 21(st )Century' date: 2011-02-16 pages: extension: .txt txt: ./txt/cord-000333-4prvgmvt.txt cache: ./cache/cord-000333-4prvgmvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000333-4prvgmvt.txt' === file2bib.sh === id: cord-017463-repm1vw9 author: Ungchusak, Kumnuan title: Public Health Surveillance: A Vital Alert and Response Function date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-017463-repm1vw9.txt cache: ./cache/cord-017463-repm1vw9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017463-repm1vw9.txt' === file2bib.sh === id: cord-024080-eh3ztsv5 author: Dheda, Keertan title: Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-024080-eh3ztsv5.txt cache: ./cache/cord-024080-eh3ztsv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-024080-eh3ztsv5.txt' cp: cannot stat ‘/data-disk/reader-compute/reader-cord/cord/ent/cord-315715-xa6kwguo.ent’: No such file or directory === file2bib.sh === id: cord-023875-5mu5ra29 author: Keng, Choong-Tat title: Molecular and Biochemical Characterization of the SARS-CoV Accessory Proteins ORF8a, ORF8b and ORF8ab date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-023875-5mu5ra29.txt cache: ./cache/cord-023875-5mu5ra29.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023875-5mu5ra29.txt' === file2bib.sh === id: cord-015613-ls9qus8y author: Macdonald, David W. title: Infectious disease: Inextricable linkages between human and ecosystem health date: 2006-06-06 pages: extension: .txt txt: ./txt/cord-015613-ls9qus8y.txt cache: ./cache/cord-015613-ls9qus8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015613-ls9qus8y.txt' === file2bib.sh === id: cord-023510-gd4phncm author: Chuo, Hsin-You title: Theme Park Visitors’ Responses to the SARS Outbreak in Taiwan date: 2007-05-02 pages: extension: .txt txt: ./txt/cord-023510-gd4phncm.txt cache: ./cache/cord-023510-gd4phncm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023510-gd4phncm.txt' === file2bib.sh === id: cord-017224-naromr0a author: McLeish, Caitriona title: Evolving Biosecurity Frameworks date: 2016-12-06 pages: extension: .txt txt: ./txt/cord-017224-naromr0a.txt cache: ./cache/cord-017224-naromr0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017224-naromr0a.txt' === file2bib.sh === id: cord-018460-wbtaoo0o author: Schomburg, Dietmar title: SARS coronavirus main proteinase 3.4.22.69 date: 2013 pages: extension: .txt txt: ./txt/cord-018460-wbtaoo0o.txt cache: ./cache/cord-018460-wbtaoo0o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018460-wbtaoo0o.txt' === file2bib.sh === id: cord-017489-ftz9190a author: Richards, Guy A. title: Viruses in the Intensive Care Unit (ICU) date: 2005 pages: extension: .txt txt: ./txt/cord-017489-ftz9190a.txt cache: ./cache/cord-017489-ftz9190a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017489-ftz9190a.txt' === file2bib.sh === id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 pages: extension: .txt txt: ./txt/cord-015376-z739ifu5.txt cache: ./cache/cord-015376-z739ifu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015376-z739ifu5.txt' === file2bib.sh === id: cord-016451-k8m2xz0e author: Chertow, Daniel S. title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 pages: extension: .txt txt: ./txt/cord-016451-k8m2xz0e.txt cache: ./cache/cord-016451-k8m2xz0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016451-k8m2xz0e.txt' === file2bib.sh === id: cord-020769-elzkwyz0 author: Day, Brennan title: The new normal: lessons learned from SARS for corporations operating in emerging markets date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-020769-elzkwyz0.txt cache: ./cache/cord-020769-elzkwyz0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-020769-elzkwyz0.txt' === file2bib.sh === id: cord-018057-p1l6xtsq author: Ruan, Li title: SARS Epidemic: SARS Outbreaks in Inner-land of China date: 2008 pages: extension: .txt txt: ./txt/cord-018057-p1l6xtsq.txt cache: ./cache/cord-018057-p1l6xtsq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018057-p1l6xtsq.txt' === file2bib.sh === id: cord-017070-05vlz5dn author: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 pages: extension: .txt txt: ./txt/cord-017070-05vlz5dn.txt cache: ./cache/cord-017070-05vlz5dn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017070-05vlz5dn.txt' === file2bib.sh === id: cord-016120-pz2q62i7 author: Zhang, Jie title: Chai Jing: The Power of Vulnerability date: 2019-02-16 pages: extension: .txt txt: ./txt/cord-016120-pz2q62i7.txt cache: ./cache/cord-016120-pz2q62i7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016120-pz2q62i7.txt' === file2bib.sh === id: cord-025980-85jbwmfv author: Iwasaki, Sumio title: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-025980-85jbwmfv.txt cache: ./cache/cord-025980-85jbwmfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-025980-85jbwmfv.txt' === file2bib.sh === id: cord-028711-zlj48aq7 author: Ridgway, Jessica P. title: Prolonged shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA among patients with coronavirus disease 2019 (COVID-19) date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-028711-zlj48aq7.txt cache: ./cache/cord-028711-zlj48aq7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-028711-zlj48aq7.txt' === file2bib.sh === id: cord-025794-ckrclrwz author: nan title: Mitteilungen der ÖGKJ date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-025794-ckrclrwz.txt cache: ./cache/cord-025794-ckrclrwz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-025794-ckrclrwz.txt' === file2bib.sh === id: cord-026528-1ozgabwk author: Chen, Zhe title: Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-026528-1ozgabwk.txt cache: ./cache/cord-026528-1ozgabwk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-026528-1ozgabwk.txt' === file2bib.sh === id: cord-030420-pgdmz69j author: Brion, Luc P. title: Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-030420-pgdmz69j.txt cache: ./cache/cord-030420-pgdmz69j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-030420-pgdmz69j.txt' === file2bib.sh === id: cord-022776-fz7m177w author: Wong, S.F. title: Severe Acute Respiratory Syndrome and pregnancy date: 2003-12-22 pages: extension: .txt txt: ./txt/cord-022776-fz7m177w.txt cache: ./cache/cord-022776-fz7m177w.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022776-fz7m177w.txt' === file2bib.sh === id: cord-026099-97luq10a author: Kok, J title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-026099-97luq10a.txt cache: ./cache/cord-026099-97luq10a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026099-97luq10a.txt' === file2bib.sh === id: cord-017903-92hnaiyc author: Cieslak, Theodore J. title: Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date: 2018-07-07 pages: extension: .txt txt: ./txt/cord-017903-92hnaiyc.txt cache: ./cache/cord-017903-92hnaiyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017903-92hnaiyc.txt' === file2bib.sh === id: cord-027649-6xn9swsq author: Addetia, Amin title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-027649-6xn9swsq.txt cache: ./cache/cord-027649-6xn9swsq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-027649-6xn9swsq.txt' === file2bib.sh === id: cord-027582-ygforvya author: Mermel, Leonard A. title: Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-027582-ygforvya.txt cache: ./cache/cord-027582-ygforvya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027582-ygforvya.txt' === file2bib.sh === id: cord-027499-mvqoarsh author: Navel, Valentin title: Coronavirus: good or bad news for ocular diseases? date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-027499-mvqoarsh.txt cache: ./cache/cord-027499-mvqoarsh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027499-mvqoarsh.txt' === file2bib.sh === id: cord-022266-nezgzovk author: Henderson, Joan C. title: Tourism and Health Crises date: 2009-11-16 pages: extension: .txt txt: ./txt/cord-022266-nezgzovk.txt cache: ./cache/cord-022266-nezgzovk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022266-nezgzovk.txt' === file2bib.sh === id: cord-015552-pm9kdqdw author: Kreuder-Sonnen, Christian title: China vs the WHO: a behavioural norm conflict in the SARS crisis date: 2019-05-01 pages: extension: .txt txt: ./txt/cord-015552-pm9kdqdw.txt cache: ./cache/cord-015552-pm9kdqdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015552-pm9kdqdw.txt' === file2bib.sh === id: cord-026803-p1o4qc1h author: Maddury, Jyotsna title: Need of the Hour— COVID-19 for Cardiologists date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-026803-p1o4qc1h.txt cache: ./cache/cord-026803-p1o4qc1h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-026803-p1o4qc1h.txt' === file2bib.sh === id: cord-026788-4d3r9rj8 author: Singla, Vikas title: Hepatobiliary and Pancreatic Manifestations of Coronavirus Disease 2019 date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-026788-4d3r9rj8.txt cache: ./cache/cord-026788-4d3r9rj8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026788-4d3r9rj8.txt' === file2bib.sh === id: cord-027309-8siz9rb8 author: Paul, Debjani title: Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-027309-8siz9rb8.txt cache: ./cache/cord-027309-8siz9rb8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027309-8siz9rb8.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-024989-0o6agnrc author: Li, Qihao title: Prediction and analysis of key protein structures of 2019-nCoV date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-024989-0o6agnrc.txt cache: ./cache/cord-024989-0o6agnrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-024989-0o6agnrc.txt' === file2bib.sh === id: cord-026806-pn4lwhr7 author: Zargar, Showkat Ali title: Gastrointestinal Endoscopy during COVID: Do Some, Leave Most date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-026806-pn4lwhr7.txt cache: ./cache/cord-026806-pn4lwhr7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-026806-pn4lwhr7.txt' === file2bib.sh === id: cord-027650-pl6qsojf author: Wang, Yijin title: SARS-CoV-2 infection in liver-Author’s reply date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-027650-pl6qsojf.txt cache: ./cache/cord-027650-pl6qsojf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027650-pl6qsojf.txt' === file2bib.sh === id: cord-033406-xoyt7esk author: Wen, Wen title: Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-033406-xoyt7esk.txt cache: ./cache/cord-033406-xoyt7esk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-033406-xoyt7esk.txt' === file2bib.sh === id: cord-028525-0ckagrt1 author: Yung, Chee Fu title: Household Transmission of SARS-CoV-2 from Adults to Children date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-028525-0ckagrt1.txt cache: ./cache/cord-028525-0ckagrt1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-028525-0ckagrt1.txt' === file2bib.sh === id: cord-025623-1v9614f8 author: Mahapatra, Pallab Sinha title: Surface Treatments to Enhance the Functionality of PPEs date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-025623-1v9614f8.txt cache: ./cache/cord-025623-1v9614f8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-025623-1v9614f8.txt' === file2bib.sh === id: cord-025129-ry85kv9q author: Kashyap, Uddip title: Enhanced Design of PPE Based on Electrostatic Principle to Eliminate Viruses (SARS-CoV-2) date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-025129-ry85kv9q.txt cache: ./cache/cord-025129-ry85kv9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-025129-ry85kv9q.txt' === file2bib.sh === id: cord-028363-7pmro8bu author: Tung-Chen, Yale title: Acute pericarditis due to COVID-19 infection: An underdiagnosed disease? date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-028363-7pmro8bu.txt cache: ./cache/cord-028363-7pmro8bu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-028363-7pmro8bu.txt' === file2bib.sh === id: cord-031289-uxoz0xhk author: Coccolini, Federico title: SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-031289-uxoz0xhk.txt cache: ./cache/cord-031289-uxoz0xhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031289-uxoz0xhk.txt' === file2bib.sh === id: cord-026811-6bdzut3d author: Jha, Ashish K. title: Emerging Treatment and Prevention Strategies against COVID-19: A Brief Update date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-026811-6bdzut3d.txt cache: ./cache/cord-026811-6bdzut3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026811-6bdzut3d.txt' === file2bib.sh === id: cord-027253-wfmm7naa author: Nag, Pooja title: Optical Fiber Sensors for Rapid Screening of COVID-19 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-027253-wfmm7naa.txt cache: ./cache/cord-027253-wfmm7naa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-027253-wfmm7naa.txt' === file2bib.sh === id: cord-033901-itj6v1jl author: Syambani Ulhaq, Z. title: Recurrent positive SARS-CoV-2 RNA tests in recovered and discharged patients() date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-033901-itj6v1jl.txt cache: ./cache/cord-033901-itj6v1jl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-033901-itj6v1jl.txt' === file2bib.sh === id: cord-025119-201ac32t author: Salman, Saad title: Virtual screening of immunomodulatory medicinal compounds as promising anti-SARS-COV-2 inhibitors date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-025119-201ac32t.txt cache: ./cache/cord-025119-201ac32t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-025119-201ac32t.txt' === file2bib.sh === id: cord-026792-jsqa4pmu author: Samanta, Jayanta title: 2019 Novel Coronavirus Infection: Gastrointestinal Manifestations date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-026792-jsqa4pmu.txt cache: ./cache/cord-026792-jsqa4pmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-026792-jsqa4pmu.txt' === file2bib.sh === id: cord-028989-w50thois author: Figueira Gonçalves, Juan Marco title: Clinical challenges in chronic obstructive pulmonary disease in patients who suffered SARS-CoV-2 infection() date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-028989-w50thois.txt cache: ./cache/cord-028989-w50thois.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-028989-w50thois.txt' === file2bib.sh === id: cord-029450-4rnrq78l author: Prattichizzo, Francesco title: Response to: Letter to the Editor on “Bonafè M, Prattichizzo F, Giuliani A, Storci G, Sabbatinelli J, Olivieri F. Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes. Cytokine Growth Factor Rev” by Eugenia Quiros-Roldan, Giorgio Biasiotto and Isabella Zanella date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-029450-4rnrq78l.txt cache: ./cache/cord-029450-4rnrq78l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-029450-4rnrq78l.txt' === file2bib.sh === id: cord-031818-lawd185l author: Rich, Robert Soler title: Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case() date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-031818-lawd185l.txt cache: ./cache/cord-031818-lawd185l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-031818-lawd185l.txt' === file2bib.sh === id: cord-030535-8o7rzb98 author: Zhang, Sheng title: Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-030535-8o7rzb98.txt cache: ./cache/cord-030535-8o7rzb98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-030535-8o7rzb98.txt' === file2bib.sh === id: cord-029167-bq6ogxyq author: Sarada, B. V. title: Fight Against COVID-19: ARCI’s Technologies for Disinfection date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-029167-bq6ogxyq.txt cache: ./cache/cord-029167-bq6ogxyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-029167-bq6ogxyq.txt' === file2bib.sh === id: cord-034021-6h5h3zow author: Thede, Christian title: COVID-19 – Therapiemöglichkeiten mit chinesischen Arzneimitteln in der Akutphase und Rekonvaleszenz date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-034021-6h5h3zow.txt cache: ./cache/cord-034021-6h5h3zow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-034021-6h5h3zow.txt' === file2bib.sh === id: cord-033311-e5axxrm1 author: Abenza Abildúa, M.J. title: Myopathy associated with serious SARS-CoV-2 infection() date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-033311-e5axxrm1.txt cache: ./cache/cord-033311-e5axxrm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033311-e5axxrm1.txt' === file2bib.sh === id: cord-031061-48xwfr9i author: Abdullah, Abdullah title: Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-031061-48xwfr9i.txt cache: ./cache/cord-031061-48xwfr9i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031061-48xwfr9i.txt' === file2bib.sh === id: cord-024786-f33eb1nf author: van Rensburg, V title: Current evidence for directed and supportive investigational therapies against COVID-19 date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-024786-f33eb1nf.txt cache: ./cache/cord-024786-f33eb1nf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-024786-f33eb1nf.txt' === file2bib.sh === id: cord-030923-r0lfot3w author: Liu, Lixin title: Subunit Nanovaccine with Potent Cellular and Mucosal Immunity for COVID-19 date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-030923-r0lfot3w.txt cache: ./cache/cord-030923-r0lfot3w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030923-r0lfot3w.txt' === file2bib.sh === id: cord-033592-j1c2brb4 author: Alvarez Bravo, G. title: Encefalitis anti-NMDA-R secundaria a infección por SARS-CoV-2 Anti–NMDA receptor encephalitis secondary to SARS-CoV-2 infection date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-033592-j1c2brb4.txt cache: ./cache/cord-033592-j1c2brb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-033592-j1c2brb4.txt' === file2bib.sh === id: cord-032811-sdbj26ca author: Hosoki, Koa title: Reply date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-032811-sdbj26ca.txt cache: ./cache/cord-032811-sdbj26ca.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-032811-sdbj26ca.txt' === file2bib.sh === id: cord-029965-bt87kai8 author: Patel, Shailesh Kumar title: The kidney and COVID-19 patients – important considerations date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-029965-bt87kai8.txt cache: ./cache/cord-029965-bt87kai8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-029965-bt87kai8.txt' === file2bib.sh === id: cord-023865-6rafp3x3 author: Surjit, Milan title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-023865-6rafp3x3.txt cache: ./cache/cord-023865-6rafp3x3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023865-6rafp3x3.txt' === file2bib.sh === id: cord-026130-ki7bn67o author: Sharma, Anand Kumar title: Novel Coronavirus Disease (COVID-19) date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-026130-ki7bn67o.txt cache: ./cache/cord-026130-ki7bn67o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026130-ki7bn67o.txt' === file2bib.sh === id: cord-034481-zi9q96lj author: Liu, Yongjian title: Stability of SARS-CoV-2 on environmental surfaces and in human excreta date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-034481-zi9q96lj.txt cache: ./cache/cord-034481-zi9q96lj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-034481-zi9q96lj.txt' === file2bib.sh === id: cord-033551-eojpkxz9 author: Shekh, Shamasoddin title: In silico allicin induced S-thioallylation of SARS-CoV-2 main protease date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-033551-eojpkxz9.txt cache: ./cache/cord-033551-eojpkxz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-033551-eojpkxz9.txt' === file2bib.sh === id: cord-030254-eevqclsy author: Mehta, Chitra title: Management of Coronavirus 2019 date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-030254-eevqclsy.txt cache: ./cache/cord-030254-eevqclsy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-030254-eevqclsy.txt' === file2bib.sh === id: cord-032222-i6gfp4me author: Xue, Ling title: A quick look at the latest developments in the COVID-19 pandemic date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-032222-i6gfp4me.txt cache: ./cache/cord-032222-i6gfp4me.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-032222-i6gfp4me.txt' === file2bib.sh === id: cord-031497-pp0p3en6 author: Rodríguez-Fuster, Alberto title: Tracheal trauma in the context of the current infection by COVID-19. About 2 cases() date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-031497-pp0p3en6.txt cache: ./cache/cord-031497-pp0p3en6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-031497-pp0p3en6.txt' === file2bib.sh === id: cord-033244-u05rw6sk author: Ganesamoorthi, Arimanickam title: Non-availability of anesthesia scavenging system and decontamination of the outflow gas from the anesthesia machine during this COVID-19 pandemic date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-033244-u05rw6sk.txt cache: ./cache/cord-033244-u05rw6sk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-033244-u05rw6sk.txt' === file2bib.sh === id: cord-033333-880jx1bt author: Salman, Saad title: In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-033333-880jx1bt.txt cache: ./cache/cord-033333-880jx1bt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033333-880jx1bt.txt' === file2bib.sh === id: cord-029419-b0w9nomq author: Matthews, Adam title: Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-029419-b0w9nomq.txt cache: ./cache/cord-029419-b0w9nomq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-029419-b0w9nomq.txt' === file2bib.sh === id: cord-030999-27wennun author: Altmann, Daniel M title: Adaptive immunity to SARS-CoV-2 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-030999-27wennun.txt cache: ./cache/cord-030999-27wennun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030999-27wennun.txt' === file2bib.sh === id: cord-025948-6dsx7pey author: Maitra, Arindam title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-025948-6dsx7pey.txt cache: ./cache/cord-025948-6dsx7pey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-025948-6dsx7pey.txt' === file2bib.sh === id: cord-033780-184e64tr author: Smith, Rasheid title: Implications of current and future approaches to coronavirus disease 2019 testing date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-033780-184e64tr.txt cache: ./cache/cord-033780-184e64tr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033780-184e64tr.txt' === file2bib.sh === id: cord-031001-x4iiqq5e author: Hou, Fan Fan title: Personnel protection strategy for healthcare workers in Wuhan during the COVID-19 epidemic date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-031001-x4iiqq5e.txt cache: ./cache/cord-031001-x4iiqq5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031001-x4iiqq5e.txt' === file2bib.sh === id: cord-034354-4xu97je3 author: Wang, Hongye title: SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-034354-4xu97je3.txt cache: ./cache/cord-034354-4xu97je3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-034354-4xu97je3.txt' === file2bib.sh === id: cord-024614-6bu3zo01 author: Tang, Daxing title: Prevention and control strategies for emergency, limited-term, and elective operations in pediatric surgery during the epidemic period of COVID-19 date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-024614-6bu3zo01.txt cache: ./cache/cord-024614-6bu3zo01.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-024614-6bu3zo01.txt' === file2bib.sh === id: cord-102364-t5bt2eb4 author: Yao, Dehui title: Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-102364-t5bt2eb4.txt cache: ./cache/cord-102364-t5bt2eb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102364-t5bt2eb4.txt' === file2bib.sh === id: cord-030654-8yxa1r1c author: Zhang, Changhui title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-030654-8yxa1r1c.txt cache: ./cache/cord-030654-8yxa1r1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030654-8yxa1r1c.txt' === file2bib.sh === id: cord-026340-2nf97zvc author: Singh, Ranjana title: Chloroquine: A Potential Drug in the COVID-19 Scenario date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-026340-2nf97zvc.txt cache: ./cache/cord-026340-2nf97zvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-026340-2nf97zvc.txt' === file2bib.sh === id: cord-029547-9ei1ram3 author: Li, Jingwei title: The epidemiology and therapeutic options for the COVID-19 date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-029547-9ei1ram3.txt cache: ./cache/cord-029547-9ei1ram3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029547-9ei1ram3.txt' === file2bib.sh === id: cord-029813-o2uzcuai author: Rusconi, Stefano title: COVID-19: studying the global pandemic – foreword date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-029813-o2uzcuai.txt cache: ./cache/cord-029813-o2uzcuai.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-029813-o2uzcuai.txt' === file2bib.sh === id: cord-031518-1w14wr0i author: Khodarahmi, Reza title: The ACE2 as a “rescue protein” or “suspect enzyme” in COVID-19: possible application of the “engineered inactive hrsACE2” as a safer therapeutic agent in the treatment of SARS-CoV-2 infection date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-031518-1w14wr0i.txt cache: ./cache/cord-031518-1w14wr0i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031518-1w14wr0i.txt' === file2bib.sh === id: cord-030870-ao5p3ra3 author: Paul, Suman title: Dynamics and risk assessment of SARS-CoV-2 in urban areas: a geographical assessment on Kolkata Municipal Corporation, India date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-030870-ao5p3ra3.txt cache: ./cache/cord-030870-ao5p3ra3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030870-ao5p3ra3.txt' === file2bib.sh === id: cord-031079-9lxhvyyb author: Chen, Li title: The effects of chloroquine and hydroxychloroquine on ACE2 related coronavirus pathology and the cardiovascular system: An evidence based review date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-031079-9lxhvyyb.txt cache: ./cache/cord-031079-9lxhvyyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-031079-9lxhvyyb.txt' === file2bib.sh === id: cord-035274-hu8zshq8 author: Jadali, Zohreh title: Neurologic manifestations of COVID-19: what can we learn from other coronaviruses date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-035274-hu8zshq8.txt cache: ./cache/cord-035274-hu8zshq8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-035274-hu8zshq8.txt' === file2bib.sh === id: cord-032928-m0awip9y author: Sobh, Eman title: Novel coronavirus disease 2019 (COVID-19) non-respiratory involvement date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-032928-m0awip9y.txt cache: ./cache/cord-032928-m0awip9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032928-m0awip9y.txt' === file2bib.sh === id: cord-026111-pb3r74uq author: Thede, Christian title: Mögliche Therapiestrategien bei Covid-19-Erkrankungen mit chinesischen Arzneimitteln date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-026111-pb3r74uq.txt cache: ./cache/cord-026111-pb3r74uq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026111-pb3r74uq.txt' === file2bib.sh === id: cord-102456-6jt4ksha author: Taylor-Cousar, Jennifer L. title: How I Do It: Restarting Respiratory Clinical Research in the Era of the COVID19 Pandemic date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-102456-6jt4ksha.txt cache: ./cache/cord-102456-6jt4ksha.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102456-6jt4ksha.txt' === file2bib.sh === id: cord-103497-1ls2dvzy author: Ganier, C title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-103497-1ls2dvzy.txt cache: ./cache/cord-103497-1ls2dvzy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103497-1ls2dvzy.txt' === file2bib.sh === id: cord-032552-rjuug7er author: Umviligihozo, Gisele title: Sub-Saharan Africa preparedness and response to the COVID-19 pandemic: A perspective of early career African scientists date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-032552-rjuug7er.txt cache: ./cache/cord-032552-rjuug7er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-032552-rjuug7er.txt' === file2bib.sh === id: cord-035292-pan415s7 author: Elmessaoudi-Idrissi, Mohcine title: Structure-guided discovery approach identifies potential lead compounds targeting M(pro) of SARS-CoV-2 date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-035292-pan415s7.txt cache: ./cache/cord-035292-pan415s7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035292-pan415s7.txt' === file2bib.sh === id: cord-032751-pmclolvh author: Head, Katharine J. title: A National Survey Assessing SARS-CoV-2 Vaccination Intentions: Implications for Future Public Health Communication Efforts date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-032751-pmclolvh.txt cache: ./cache/cord-032751-pmclolvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-032751-pmclolvh.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-025251-evnfvc0l author: Nemunaitis, John title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection: let the virus be its own demise date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-025251-evnfvc0l.txt cache: ./cache/cord-025251-evnfvc0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-025251-evnfvc0l.txt' === file2bib.sh === id: cord-103112-m6cg67lz author: Schloer, Sebastian title: Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-103112-m6cg67lz.txt cache: ./cache/cord-103112-m6cg67lz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103112-m6cg67lz.txt' === file2bib.sh === id: cord-035157-97tfcgvq author: Panchin, Alexander Y. title: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-035157-97tfcgvq.txt cache: ./cache/cord-035157-97tfcgvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-035157-97tfcgvq.txt' === file2bib.sh === id: cord-102842-51n5mnjb author: Węglarz-Tomczak, Ewelina title: Ebselen as a highly active inhibitor of PLProCoV2 date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-102842-51n5mnjb.txt cache: ./cache/cord-102842-51n5mnjb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102842-51n5mnjb.txt' === file2bib.sh === id: cord-035026-2qcsfd87 author: Ugwueze, Chidiebere V. title: COVID-19 and Diabetes Mellitus: The Link and Clinical Implications date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-035026-2qcsfd87.txt cache: ./cache/cord-035026-2qcsfd87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-035026-2qcsfd87.txt' === file2bib.sh === id: cord-030934-t7akdu6x author: Bahrami, Afsane title: Genetic and pathogenic characterization of SARS-CoV-2: a review date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-030934-t7akdu6x.txt cache: ./cache/cord-030934-t7akdu6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030934-t7akdu6x.txt' === file2bib.sh === id: cord-035307-r74ovkbd author: Liu, Shuchang title: Attitudes towards Wildlife Consumption inside and outside Hubei Province, China, in Relation to the SARS and COVID-19 Outbreaks date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-035307-r74ovkbd.txt cache: ./cache/cord-035307-r74ovkbd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035307-r74ovkbd.txt' === file2bib.sh === id: cord-033334-p7szd86k author: Mann, Jaclyn Kelly title: The potential of lactoferrin, ovotransferrin and lysozyme as antiviral and immune-modulating agents in COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-033334-p7szd86k.txt cache: ./cache/cord-033334-p7szd86k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-033334-p7szd86k.txt' === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-315715-xa6kwguo' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-315715-xa6kwguo' === file2bib.sh === id: cord-103576-g5de4fwj author: Kriegel, M. title: Predicted Infection Risk via Aerosols date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-103576-g5de4fwj.txt cache: ./cache/cord-103576-g5de4fwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103576-g5de4fwj.txt' === file2bib.sh === id: cord-033010-o5kiadfm author: Durojaye, Olanrewaju Ayodeji title: Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-033010-o5kiadfm.txt cache: ./cache/cord-033010-o5kiadfm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033010-o5kiadfm.txt' === file2bib.sh === id: cord-033951-77tfhm5b author: Ma, Chunlong title: Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-033951-77tfhm5b.txt cache: ./cache/cord-033951-77tfhm5b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033951-77tfhm5b.txt' === file2bib.sh === id: cord-035067-ic843wr9 author: de Almeida, Joana Ferro Machado title: COVID-19 and the gastrointestinal tract: what do we already know? date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-035067-ic843wr9.txt cache: ./cache/cord-035067-ic843wr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-035067-ic843wr9.txt' === file2bib.sh === id: cord-102807-cxtzf5oe author: fiore, j. r. title: FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-102807-cxtzf5oe.txt cache: ./cache/cord-102807-cxtzf5oe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102807-cxtzf5oe.txt' === file2bib.sh === id: cord-104435-y7mxyein author: Alabdulmonem, Waleed title: COVID-19: A global public health disaster date: 2020 pages: extension: .txt txt: ./txt/cord-104435-y7mxyein.txt cache: ./cache/cord-104435-y7mxyein.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-104435-y7mxyein.txt' === file2bib.sh === id: cord-103872-yzqic5vt author: Liu, Zhijin title: Global view on virus infection in non-human primates and implication for public health and wildlife conservation date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-103872-yzqic5vt.txt cache: ./cache/cord-103872-yzqic5vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103872-yzqic5vt.txt' === file2bib.sh === id: cord-034351-5br4faov author: Xu, Shuang-Fei title: Cross-Sectional Seroepidemiologic Study of Coronavirus Disease 2019 (COVID-19) among Close Contacts, Children, and Migrant Workers in Shanghai date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-034351-5br4faov.txt cache: ./cache/cord-034351-5br4faov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-034351-5br4faov.txt' === file2bib.sh === id: cord-035203-dnoc0xcv author: Vaňková, Eva title: Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-035203-dnoc0xcv.txt cache: ./cache/cord-035203-dnoc0xcv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-035203-dnoc0xcv.txt' === file2bib.sh === id: cord-033204-v17d98c9 author: Yen, Wei‐Ting title: Taiwan’s COVID‐19 Management: Developmental State, Digital Governance, and State‐Society Synergy date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-033204-v17d98c9.txt cache: ./cache/cord-033204-v17d98c9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-033204-v17d98c9.txt' === file2bib.sh === id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022084-hap7flng.txt cache: ./cache/cord-022084-hap7flng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022084-hap7flng.txt' === file2bib.sh === id: cord-102411-0mo1198e author: Moreno Borraz, LA title: PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-102411-0mo1198e.txt cache: ./cache/cord-102411-0mo1198e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102411-0mo1198e.txt' === file2bib.sh === id: cord-016160-ugc7ce21 author: Ching, Frank title: Bird Flu, SARS and Beyond date: 2018-03-15 pages: extension: .txt txt: ./txt/cord-016160-ugc7ce21.txt cache: ./cache/cord-016160-ugc7ce21.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016160-ugc7ce21.txt' === file2bib.sh === id: cord-154844-nuqx3tv6 author: Misirli, Goksel title: A comparative analysis for SARS-CoV-2 date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-154844-nuqx3tv6.txt cache: ./cache/cord-154844-nuqx3tv6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-154844-nuqx3tv6.txt' === file2bib.sh === id: cord-035163-tqh5wv12 author: Ijaz, M. Khalid title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-035163-tqh5wv12.txt cache: ./cache/cord-035163-tqh5wv12.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035163-tqh5wv12.txt' === file2bib.sh === id: cord-103709-86hv27vh author: Zhang, Dong Yan title: Prefusion spike protein stabilization through computational mutagenesis date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-103709-86hv27vh.txt cache: ./cache/cord-103709-86hv27vh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103709-86hv27vh.txt' === file2bib.sh === id: cord-127741-h23w89h2 author: Babuji, Yadu title: Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-127741-h23w89h2.txt cache: ./cache/cord-127741-h23w89h2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-127741-h23w89h2.txt' === file2bib.sh === id: cord-153725-jjefjlx2 author: Sahoo, Suban K title: Computational evidence on repurposing the anti-influenza drugs baloxavir acid and baloxavir marboxil against COVID-19 date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-153725-jjefjlx2.txt cache: ./cache/cord-153725-jjefjlx2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-153725-jjefjlx2.txt' === file2bib.sh === id: cord-034371-j3xxmkjd author: Schellack, Natalie title: COVID-19: Guidelines for pharmacists in South Africa date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-034371-j3xxmkjd.txt cache: ./cache/cord-034371-j3xxmkjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-034371-j3xxmkjd.txt' === file2bib.sh === id: cord-103940-a2cqw8kg author: Shi, Yuejun title: Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-103940-a2cqw8kg.txt cache: ./cache/cord-103940-a2cqw8kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103940-a2cqw8kg.txt' === file2bib.sh === id: cord-104081-a3fx8tyd author: Tang, Tiffany title: Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-104081-a3fx8tyd.txt cache: ./cache/cord-104081-a3fx8tyd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-104081-a3fx8tyd.txt' === file2bib.sh === id: cord-102920-z5q3wo7v author: Sang, Eric R. title: Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-102920-z5q3wo7v.txt cache: ./cache/cord-102920-z5q3wo7v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102920-z5q3wo7v.txt' === file2bib.sh === id: cord-138656-8iyynbup author: Furuyama, Taima N. title: Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-138656-8iyynbup.txt cache: ./cache/cord-138656-8iyynbup.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-138656-8iyynbup.txt' === file2bib.sh === id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-104162-fe51v2pt.txt cache: ./cache/cord-104162-fe51v2pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-104162-fe51v2pt.txt' === file2bib.sh === id: cord-146091-kpvxdhcu author: Sanchez-Lorenzo, Arturo title: Anomalous atmospheric circulation favored the spread of COVID-19 in Europe date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-146091-kpvxdhcu.txt cache: ./cache/cord-146091-kpvxdhcu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-146091-kpvxdhcu.txt' === file2bib.sh === id: cord-130351-w9mij6c6 author: Mamidala, Estari title: In silico identification of clinically approved medicines against the main protease of SARS-CoV-2, causative agent of covid-19 date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-130351-w9mij6c6.txt cache: ./cache/cord-130351-w9mij6c6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-130351-w9mij6c6.txt' === file2bib.sh === id: cord-142389-t5swlp04 author: Linden, Matthias title: The foreshadow of a second wave: An analysis of current COVID-19 fatalities in Germany date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-142389-t5swlp04.txt cache: ./cache/cord-142389-t5swlp04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-142389-t5swlp04.txt' === file2bib.sh === id: cord-191741-2vuiafv0 author: Schifanella, L. title: Massive viral replication and cytopathic effects in early COVID-19 pneumonia date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-191741-2vuiafv0.txt cache: ./cache/cord-191741-2vuiafv0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-191741-2vuiafv0.txt' === file2bib.sh === id: cord-048335-5fl0rk90 author: Thompson, Alison K title: Pandemic influenza preparedness: an ethical framework to guide decision-making date: 2006-12-04 pages: extension: .txt txt: ./txt/cord-048335-5fl0rk90.txt cache: ./cache/cord-048335-5fl0rk90.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-048335-5fl0rk90.txt' === file2bib.sh === id: cord-104507-xx7t26rl author: Safari, Saeid title: Extracorporeal Hemoperfusion as a Potential Therapeutic Option for Severe COVID-19 patients; a Narrative Review date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-104507-xx7t26rl.txt cache: ./cache/cord-104507-xx7t26rl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-104507-xx7t26rl.txt' === file2bib.sh === id: cord-103545-2v89ku4o author: Bellos, Ioannis title: Maternal and perinatal outcomes in pregnant women infected by SARS-CoV-2: A meta-analysis date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-103545-2v89ku4o.txt cache: ./cache/cord-103545-2v89ku4o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103545-2v89ku4o.txt' === file2bib.sh === id: cord-154170-7pnz98o6 author: Ponciano, Jos'e Miguel title: Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-154170-7pnz98o6.txt cache: ./cache/cord-154170-7pnz98o6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-154170-7pnz98o6.txt' === file2bib.sh === id: cord-124012-5zxkd2jy author: Schwab, Patrick title: predCOVID-19: A Systematic Study of Clinical Predictive Models for Coronavirus Disease 2019 date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-124012-5zxkd2jy.txt cache: ./cache/cord-124012-5zxkd2jy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-124012-5zxkd2jy.txt' === file2bib.sh === id: cord-146679-g7qioapl author: Jaimes, Javier A. title: Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-146679-g7qioapl.txt cache: ./cache/cord-146679-g7qioapl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-146679-g7qioapl.txt' === file2bib.sh === id: cord-140318-xtx8hl14 author: Martin, Alexandra title: High-sensitivity COVID-19 group testing by digital PCR date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-140318-xtx8hl14.txt cache: ./cache/cord-140318-xtx8hl14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-140318-xtx8hl14.txt' === file2bib.sh === id: cord-189561-jhvwozsn author: Chechetkin, Vladimr R. title: Combining Detection and Reconstruction of Periodic Motifs in Genomic Sequences with Transitional Genome Mapping date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-189561-jhvwozsn.txt cache: ./cache/cord-189561-jhvwozsn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-189561-jhvwozsn.txt' === file2bib.sh === id: cord-138439-wvynetna author: Wei, Xiyi title: Sex Differences in Severity and Mortality Among Patients With COVID-19: Evidence from Pooled Literature Analysis and Insights from Integrated Bioinformatic Analysis date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-138439-wvynetna.txt cache: ./cache/cord-138439-wvynetna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-138439-wvynetna.txt' === file2bib.sh === id: cord-190540-zf5ksac2 author: Rakshit, Kausik title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-190540-zf5ksac2.txt cache: ./cache/cord-190540-zf5ksac2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-190540-zf5ksac2.txt' === file2bib.sh === id: cord-102833-hh4641o0 author: Sarkis-Onofre, Rafael title: Decontamination of N95 respirators against SARS-CoV-2: a scoping review date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-102833-hh4641o0.txt cache: ./cache/cord-102833-hh4641o0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102833-hh4641o0.txt' === file2bib.sh === id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 pages: extension: .txt txt: ./txt/cord-016990-ot1wi3xi.txt cache: ./cache/cord-016990-ot1wi3xi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016990-ot1wi3xi.txt' === file2bib.sh === id: cord-214854-ck61ja2t author: Zhong, Jing title: Rapid and sensitive detection of SARS-CoV-2 with functionalized magnetic nanoparticles date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-214854-ck61ja2t.txt cache: ./cache/cord-214854-ck61ja2t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-214854-ck61ja2t.txt' === file2bib.sh === id: cord-193893-rzurz5bj author: Ma, Zhanshan title: Spatiotemporal fluctuation scaling law and metapopulation modeling of the novel coronavirus (COVID-19) and SARS outbreaks date: 2020-03-08 pages: extension: .txt txt: ./txt/cord-193893-rzurz5bj.txt cache: ./cache/cord-193893-rzurz5bj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-193893-rzurz5bj.txt' === file2bib.sh === id: cord-103662-a4ok5wqc author: Tarek, M. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-103662-a4ok5wqc.txt cache: ./cache/cord-103662-a4ok5wqc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103662-a4ok5wqc.txt' === file2bib.sh === id: cord-103837-iuvigqdx author: Knierman, Michael D. title: The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-103837-iuvigqdx.txt cache: ./cache/cord-103837-iuvigqdx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103837-iuvigqdx.txt' === file2bib.sh === id: cord-196608-k4f79dr4 author: Saha, Sovan title: Computational modeling of Human-nCoV protein-protein interaction network date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-196608-k4f79dr4.txt cache: ./cache/cord-196608-k4f79dr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-196608-k4f79dr4.txt' === file2bib.sh === id: cord-029332-yn603pvb author: nan title: Full Issue PDF date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-029332-yn603pvb.txt cache: ./cache/cord-029332-yn603pvb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029332-yn603pvb.txt' === file2bib.sh === id: cord-104500-m0kfom0x author: Kyriakopoulos, Anthony M. title: The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-104500-m0kfom0x.txt cache: ./cache/cord-104500-m0kfom0x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-104500-m0kfom0x.txt' === file2bib.sh === id: cord-193133-puqcbf8t author: Piplani, Sakshi title: In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-193133-puqcbf8t.txt cache: ./cache/cord-193133-puqcbf8t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-193133-puqcbf8t.txt' === file2bib.sh === id: cord-221611-eeybl35x author: Vijayan, Ramachandran title: Structure-based inhibitor screening of natural products against NSP15 of SARS- CoV-2 revealed Thymopentin and Oleuropein as potent inhibitors date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-221611-eeybl35x.txt cache: ./cache/cord-221611-eeybl35x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-221611-eeybl35x.txt' === file2bib.sh === id: cord-203232-1nnqx1g9 author: Canturk, Semih title: Machine-Learning Driven Drug Repurposing for COVID-19 date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-203232-1nnqx1g9.txt cache: ./cache/cord-203232-1nnqx1g9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-203232-1nnqx1g9.txt' === file2bib.sh === id: cord-158628-71n1tgrw author: Russo, Giulia title: In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-158628-71n1tgrw.txt cache: ./cache/cord-158628-71n1tgrw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-158628-71n1tgrw.txt' === file2bib.sh === id: cord-103659-wpwfqhp2 author: Almqvist, J. title: Neurological manifestations of coronavirus infections: a systematic review date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-103659-wpwfqhp2.txt cache: ./cache/cord-103659-wpwfqhp2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103659-wpwfqhp2.txt' === file2bib.sh === id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 pages: extension: .txt txt: ./txt/cord-103787-qhftb6d7.txt cache: ./cache/cord-103787-qhftb6d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103787-qhftb6d7.txt' === file2bib.sh === id: cord-203191-7ftg6bfx author: Guo, Kai title: Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-203191-7ftg6bfx.txt cache: ./cache/cord-203191-7ftg6bfx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-203191-7ftg6bfx.txt' === file2bib.sh === id: cord-184744-oyc2djxk author: Parvez, Md Sorwer Alam title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-184744-oyc2djxk.txt cache: ./cache/cord-184744-oyc2djxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-184744-oyc2djxk.txt' === file2bib.sh === id: cord-229246-qgp7ksq8 author: Babino, Andres title: Masks and COVID-19: a causal framework for imputing value to public-health interventions date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-229246-qgp7ksq8.txt cache: ./cache/cord-229246-qgp7ksq8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-229246-qgp7ksq8.txt' === file2bib.sh === id: cord-202687-z17knvts author: Angelina, Emilio title: Drug Repurposing to find Inhibitors of SARS-CoV-2 Main Protease date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-202687-z17knvts.txt cache: ./cache/cord-202687-z17knvts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-202687-z17knvts.txt' === file2bib.sh === id: cord-161674-nk0wie0w author: Liu, Zhi title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-161674-nk0wie0w.txt cache: ./cache/cord-161674-nk0wie0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-161674-nk0wie0w.txt' === file2bib.sh === id: cord-103914-ppgx7mci author: Maughan, Elizabeth F. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-103914-ppgx7mci.txt cache: ./cache/cord-103914-ppgx7mci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103914-ppgx7mci.txt' === file2bib.sh === id: cord-151024-qe7c2uks author: Koca, Caglar title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-151024-qe7c2uks.txt cache: ./cache/cord-151024-qe7c2uks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-151024-qe7c2uks.txt' === file2bib.sh === id: cord-206006-8l7hrany author: Wang, Rui title: Mutations on COVID-19 diagnostic targets date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-206006-8l7hrany.txt cache: ./cache/cord-206006-8l7hrany.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-206006-8l7hrany.txt' === file2bib.sh === id: cord-126015-zc7u3g34 author: Krieger, Elizabeth title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-126015-zc7u3g34.txt cache: ./cache/cord-126015-zc7u3g34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-126015-zc7u3g34.txt' === file2bib.sh === id: cord-243806-26n22jbx author: Vandelli, Andrea title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-243806-26n22jbx.txt cache: ./cache/cord-243806-26n22jbx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-243806-26n22jbx.txt' === file2bib.sh === id: cord-190207-en96o8zo author: Jim'enez-Avalos, Gabriel M. title: High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease date: 2020-08-30 pages: extension: .txt txt: ./txt/cord-190207-en96o8zo.txt cache: ./cache/cord-190207-en96o8zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-190207-en96o8zo.txt' === file2bib.sh === id: cord-193136-7g6qr73e author: Bhattacharya, Sujit title: Visible Insights of the Invisible Pandemic: A Scientometric, Altmetric and Topic Trend Analysis date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-193136-7g6qr73e.txt cache: ./cache/cord-193136-7g6qr73e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-193136-7g6qr73e.txt' === file2bib.sh === id: cord-208426-wz3jan5d author: Li, Hongying title: Airborne dispersion of droplets during coughing: a physical model of viral transmission date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-208426-wz3jan5d.txt cache: ./cache/cord-208426-wz3jan5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-208426-wz3jan5d.txt' === file2bib.sh === id: cord-133453-23rfdkuw author: Chen, Jiahui title: Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-133453-23rfdkuw.txt cache: ./cache/cord-133453-23rfdkuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-133453-23rfdkuw.txt' === file2bib.sh === id: cord-217961-2rczhxp2 author: Chitsaz, Mohsen title: A small molecule drug candidate targeting SARS-CoV-2 main protease date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-217961-2rczhxp2.txt cache: ./cache/cord-217961-2rczhxp2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-217961-2rczhxp2.txt' === file2bib.sh === id: cord-122092-gdyt02er author: Fatehi, Farzad title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-122092-gdyt02er.txt cache: ./cache/cord-122092-gdyt02er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-122092-gdyt02er.txt' === file2bib.sh === id: cord-252103-lsaa1nx0 author: Pearks Wilkerson, Alison J title: Coronavirus outbreak in cheetahs: Lessons for SARS date: 2004-03-23 pages: extension: .txt txt: ./txt/cord-252103-lsaa1nx0.txt cache: ./cache/cord-252103-lsaa1nx0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252103-lsaa1nx0.txt' === file2bib.sh === id: cord-199630-2lmwnfda author: Ray, Sumanta title: Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-199630-2lmwnfda.txt cache: ./cache/cord-199630-2lmwnfda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-199630-2lmwnfda.txt' === file2bib.sh === id: cord-103899-6tqm99g1 author: Mirzaei, Rasoul title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-103899-6tqm99g1.txt cache: ./cache/cord-103899-6tqm99g1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103899-6tqm99g1.txt' === file2bib.sh === id: cord-252292-qz9msrl7 author: Wilder-Smith, Annelies title: Experience of Severe Acute Respiratory Syndrome in Singapore: Importation of Cases, and Defense Strategies at the Airport date: 2006-03-08 pages: extension: .txt txt: ./txt/cord-252292-qz9msrl7.txt cache: ./cache/cord-252292-qz9msrl7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252292-qz9msrl7.txt' === file2bib.sh === id: cord-252305-rstxyofq author: Tyan, Kevin title: Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-252305-rstxyofq.txt cache: ./cache/cord-252305-rstxyofq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252305-rstxyofq.txt' === file2bib.sh === id: cord-228152-k4bw8w5g author: Pyzer-Knapp, Edward O. title: Using Bayesian Optimization to Accelerate Virtual Screening for the Discovery of Therapeutics Appropriate for Repurposing for COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-228152-k4bw8w5g.txt cache: ./cache/cord-228152-k4bw8w5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-228152-k4bw8w5g.txt' === file2bib.sh === id: cord-251995-nbqukjzv author: Xiao, Fei title: Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-251995-nbqukjzv.txt cache: ./cache/cord-251995-nbqukjzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-251995-nbqukjzv.txt' === file2bib.sh === id: cord-252761-ro5tj0tx author: Marriott, Deborah title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-252761-ro5tj0tx.txt cache: ./cache/cord-252761-ro5tj0tx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252761-ro5tj0tx.txt' === file2bib.sh === id: cord-196129-3zfeamgs author: Demertzis, Konstantinos title: Flattening the COVID-19 Curve: The"Greek"case in the Global Pandemic date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-196129-3zfeamgs.txt cache: ./cache/cord-196129-3zfeamgs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-196129-3zfeamgs.txt' === file2bib.sh === id: cord-193489-u6ewlh16 author: Wang, Rui title: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-193489-u6ewlh16.txt cache: ./cache/cord-193489-u6ewlh16.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-193489-u6ewlh16.txt' === file2bib.sh === id: cord-252557-f89m6xv5 author: Ong, John title: Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-252557-f89m6xv5.txt cache: ./cache/cord-252557-f89m6xv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252557-f89m6xv5.txt' === file2bib.sh === id: cord-218639-ewkche9r author: Ghavasieh, Arsham title: Multiscale statistical physics of the Human-SARS-CoV-2 interactome date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-218639-ewkche9r.txt cache: ./cache/cord-218639-ewkche9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-218639-ewkche9r.txt' === file2bib.sh === id: cord-252428-w6tsf478 author: Hayashi, Takuma title: Highly conserved binding region of ACE2 as a receptor for SARS-CoV-2 between humans and mammals date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-252428-w6tsf478.txt cache: ./cache/cord-252428-w6tsf478.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252428-w6tsf478.txt' === file2bib.sh === id: cord-252033-43fbfglt author: Plebani, Mario title: Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays? date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-252033-43fbfglt.txt cache: ./cache/cord-252033-43fbfglt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252033-43fbfglt.txt' === file2bib.sh === id: cord-252286-377y9aqx author: Gauss, Tobias title: Preliminary pragmatic lessons from the SARS-CoV-2 pandemic from France date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-252286-377y9aqx.txt cache: ./cache/cord-252286-377y9aqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252286-377y9aqx.txt' === file2bib.sh === id: cord-252015-9oiwcn8q author: Niu, Alex title: COVID-19 in allogeneic stem cell transplant: high false-negative probability and role of CRISPR and convalescent plasma date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-252015-9oiwcn8q.txt cache: ./cache/cord-252015-9oiwcn8q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252015-9oiwcn8q.txt' === file2bib.sh === id: cord-252232-vgq6gjpx author: Hou, Yuxuan title: Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date: 2010-06-22 pages: extension: .txt txt: ./txt/cord-252232-vgq6gjpx.txt cache: ./cache/cord-252232-vgq6gjpx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252232-vgq6gjpx.txt' === file2bib.sh === id: cord-252574-7oh0k139 author: Nicastro, Emanuele title: A Pediatric Emergency Department Protocol to Avoid Intra-Hospital Dispersal of SARS-CoV-2 during the Outbreak in Bergamo, Italy date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-252574-7oh0k139.txt cache: ./cache/cord-252574-7oh0k139.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252574-7oh0k139.txt' === file2bib.sh === id: cord-218886-lqme2j8n author: Asghari, Aref title: Fast Accurate Point of Care COVID-19 Pandemic Diagnosis Enabled Through Advanced Lab-on-a-Chip Optical Biosensors: Opportunities and Challenges date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-218886-lqme2j8n.txt cache: ./cache/cord-218886-lqme2j8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-218886-lqme2j8n.txt' === file2bib.sh === id: cord-103945-q3ry13vp author: de Oliveira, P. M. title: Evolution of spray and aerosol from respiratory releases: theoretical estimates for insight on viral transmission date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-103945-q3ry13vp.txt cache: ./cache/cord-103945-q3ry13vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103945-q3ry13vp.txt' === file2bib.sh === id: cord-197818-asd39zbj author: Wu, Kai title: Magnetic Immunoassays: A Review of Virus and Pathogen Detection Before and Amidst the Coronavirus Disease-19 (COVID-19) date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-197818-asd39zbj.txt cache: ./cache/cord-197818-asd39zbj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-197818-asd39zbj.txt' === file2bib.sh === id: cord-252005-3ld5e7f5 author: Lewis, Nathaniel M title: Household Transmission of SARS-CoV-2 in the United States date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-252005-3ld5e7f5.txt cache: ./cache/cord-252005-3ld5e7f5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252005-3ld5e7f5.txt' === file2bib.sh === id: cord-251961-g0n85kxz author: Li, Guoming title: Safety and efficacy of Artemisinin-Piperaquine for treatment of COVID-19: an open-label, non-randomized, and controlled trial date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-251961-g0n85kxz.txt cache: ./cache/cord-251961-g0n85kxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-251961-g0n85kxz.txt' === file2bib.sh === id: cord-251943-jzaeaxam author: Zhang, Jian‐San title: A serological survey on neutralizing antibody titer of SARS convalescent sera date: 2005-08-24 pages: extension: .txt txt: ./txt/cord-251943-jzaeaxam.txt cache: ./cache/cord-251943-jzaeaxam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-251943-jzaeaxam.txt' === file2bib.sh === id: cord-235691-en6fgilb author: Althouse, Benjamin M. title: Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-235691-en6fgilb.txt cache: ./cache/cord-235691-en6fgilb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-235691-en6fgilb.txt' === file2bib.sh === id: cord-035015-slgywe0c author: Nunn, Alistair V. W. title: SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-035015-slgywe0c.txt cache: ./cache/cord-035015-slgywe0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035015-slgywe0c.txt' === file2bib.sh === id: cord-252234-3txk22yj author: Kaniyala Melanthota, Sindhoora title: Elucidating the microscopic and computational techniques to study the structure and pathology of SARS‐CoVs date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-252234-3txk22yj.txt cache: ./cache/cord-252234-3txk22yj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252234-3txk22yj.txt' === file2bib.sh === id: cord-224516-t5zubl1p author: Daubenschuetz, Tim title: SARS-CoV-2, a Threat to Privacy? date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-224516-t5zubl1p.txt cache: ./cache/cord-224516-t5zubl1p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-224516-t5zubl1p.txt' === file2bib.sh === id: cord-252473-i4pmux28 author: Rogers, Sharon title: Why can't I visit? The ethics of visitation restrictions – lessons learned from SARS date: 2004-08-31 pages: extension: .txt txt: ./txt/cord-252473-i4pmux28.txt cache: ./cache/cord-252473-i4pmux28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252473-i4pmux28.txt' === file2bib.sh === id: cord-104501-e5e0xrou author: Bashash, Davood title: The Prognostic Value of Thrombocytopenia in COVID-19 Patients; a Systematic Review and Meta-Analysis date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-104501-e5e0xrou.txt cache: ./cache/cord-104501-e5e0xrou.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-104501-e5e0xrou.txt' === file2bib.sh === id: cord-220618-segffkbn author: Bonamassa, Ivan title: Geometric characterization of SARS-CoV-2 pandemic events date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-220618-segffkbn.txt cache: ./cache/cord-220618-segffkbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-220618-segffkbn.txt' === file2bib.sh === id: cord-251581-8ubyveyt author: Szymkowiak, Andrzej title: In-store epidemic behavior: scale development and validation date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-251581-8ubyveyt.txt cache: ./cache/cord-251581-8ubyveyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-251581-8ubyveyt.txt' === file2bib.sh === id: cord-252550-yaosufpm author: nan title: Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-252550-yaosufpm.txt cache: ./cache/cord-252550-yaosufpm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252550-yaosufpm.txt' === file2bib.sh === id: cord-179749-qdbmpi7j author: Sacks, Daniel W. title: What can we learn about SARS-CoV-2 prevalence from testing and hospital data? date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-179749-qdbmpi7j.txt cache: ./cache/cord-179749-qdbmpi7j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-179749-qdbmpi7j.txt' === file2bib.sh === id: cord-249166-0w0t631x author: Booss-Bavnbek, Bernhelm title: Dynamics and Control of Covid-19: Comments by Two Mathematicians date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-249166-0w0t631x.txt cache: ./cache/cord-249166-0w0t631x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-249166-0w0t631x.txt' === file2bib.sh === id: cord-252288-klkoerfn author: Zhang, Bicheng title: Immune Phenotyping Based on the Neutrophil-to-Lymphocyte Ratio and IgG Level Predicts Disease Severity and Outcome for Patients With COVID-19 date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-252288-klkoerfn.txt cache: ./cache/cord-252288-klkoerfn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252288-klkoerfn.txt' === file2bib.sh === id: cord-252980-1e28zj1d author: Zhang, Jiahao title: Insights into the cross-species evolution of 2019 novel coronavirus date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-252980-1e28zj1d.txt cache: ./cache/cord-252980-1e28zj1d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252980-1e28zj1d.txt' === file2bib.sh === id: cord-252857-vaq0kwln author: Rejdak, Konrad title: Adamantanes might be protective from COVID-19 in patients with neurological diseases: multiple sclerosis, parkinsonism and cognitive impairment date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-252857-vaq0kwln.txt cache: ./cache/cord-252857-vaq0kwln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252857-vaq0kwln.txt' === file2bib.sh === id: cord-167889-um3djluz author: Chen, Jianguo title: A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19 date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-167889-um3djluz.txt cache: ./cache/cord-167889-um3djluz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-167889-um3djluz.txt' === file2bib.sh === id: cord-252933-bu4oihem author: Xu, Jieqing Jessica title: Renal Infarct in a COVID‐19 Positive Kidney‐Pancreas Transplant Recipient date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-252933-bu4oihem.txt cache: ./cache/cord-252933-bu4oihem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252933-bu4oihem.txt' === file2bib.sh === id: cord-252767-as841xo0 author: Fischer, Bastian title: SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, March to June 2020 date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-252767-as841xo0.txt cache: ./cache/cord-252767-as841xo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252767-as841xo0.txt' === file2bib.sh === id: cord-251986-ajlpb9li author: Li, Yan‐Chao title: The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-251986-ajlpb9li.txt cache: ./cache/cord-251986-ajlpb9li.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-251986-ajlpb9li.txt' === file2bib.sh === id: cord-252873-4tazhf40 author: Kruglikov, Ilja L. title: The role of adipocytes and adipocyte‐like cells in the severity of COVID‐19 infections date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-252873-4tazhf40.txt cache: ./cache/cord-252873-4tazhf40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252873-4tazhf40.txt' === file2bib.sh === id: cord-253006-r2a2ozrc author: Yan, Xiquan title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-253006-r2a2ozrc.txt cache: ./cache/cord-253006-r2a2ozrc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253006-r2a2ozrc.txt' === file2bib.sh === id: cord-252019-tbalg6k5 author: Barra, Gustavo Barcelos title: Analytical Sensitivity and Specificity of Two RT-qPCR Protocols for SARS-CoV-2 Detection Performed in an Automated Workflow date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-252019-tbalg6k5.txt cache: ./cache/cord-252019-tbalg6k5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252019-tbalg6k5.txt' === file2bib.sh === id: cord-253179-pi5uq90z author: Yu, Jing title: SARS-CoV-2 transmission in cancer patients of a tertiary hospital in Wuhan date: 2020-02-25 pages: extension: .txt txt: ./txt/cord-253179-pi5uq90z.txt cache: ./cache/cord-253179-pi5uq90z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-253179-pi5uq90z.txt' === file2bib.sh === id: cord-252818-1gms4zw3 author: Bouayed, Jaouad title: Behavioural manipulation ‐ key to the successful global spread of the new Coronavirus SARS‐Cov‐2? date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-252818-1gms4zw3.txt cache: ./cache/cord-252818-1gms4zw3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252818-1gms4zw3.txt' === file2bib.sh === id: cord-252279-0gozdv43 author: Pal, Amit title: Hydroxychloroquine and Covid-19: A Cellular and Molecular Biology Based Update date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-252279-0gozdv43.txt cache: ./cache/cord-252279-0gozdv43.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252279-0gozdv43.txt' === file2bib.sh === id: cord-253380-oymg1bba author: Karataş, Ayşe title: Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-253380-oymg1bba.txt cache: ./cache/cord-253380-oymg1bba.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253380-oymg1bba.txt' === file2bib.sh === id: cord-253035-tijcxtwx author: Wang, Chen title: A novel coronavirus outbreak of global health concern date: 2020-01-24 pages: extension: .txt txt: ./txt/cord-253035-tijcxtwx.txt cache: ./cache/cord-253035-tijcxtwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253035-tijcxtwx.txt' === file2bib.sh === id: cord-253468-pf0xubii author: Emara, Mohamed H title: Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-253468-pf0xubii.txt cache: ./cache/cord-253468-pf0xubii.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253468-pf0xubii.txt' === file2bib.sh === id: cord-252804-u7tz6xzz author: Ciotti, Marco title: COVID-19 Outbreak: An Overview date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-252804-u7tz6xzz.txt cache: ./cache/cord-252804-u7tz6xzz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252804-u7tz6xzz.txt' === file2bib.sh === id: cord-252456-971d0sir author: Hemida, Maged Gomaa title: The SARS-CoV-2 outbreak from a one health perspective date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-252456-971d0sir.txt cache: ./cache/cord-252456-971d0sir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252456-971d0sir.txt' === file2bib.sh === id: cord-253876-2dc9jq79 author: Pitocco, Dario title: Lack of type 1 diabetes involvement in SARS-COV-2 population: Only a particular coincidence? date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-253876-2dc9jq79.txt cache: ./cache/cord-253876-2dc9jq79.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253876-2dc9jq79.txt' === file2bib.sh === id: cord-252506-8u9oiqoc author: Scarfò, Lydia title: COVID-19 severity and mortality in patients with chronic lymphocytic leukemia: a joint study by ERIC, the European Research Initiative on CLL, and CLL Campus date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-252506-8u9oiqoc.txt cache: ./cache/cord-252506-8u9oiqoc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252506-8u9oiqoc.txt' === file2bib.sh === id: cord-252389-xrdbmosj author: Kumar, Mukesh title: Neurological manifestations and comorbidity associated with COVID-19: an overview date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-252389-xrdbmosj.txt cache: ./cache/cord-252389-xrdbmosj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252389-xrdbmosj.txt' === file2bib.sh === id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-245161-xbw72k4m.txt cache: ./cache/cord-245161-xbw72k4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-245161-xbw72k4m.txt' === file2bib.sh === id: cord-253459-tcn10pho author: Moreau, Gregory Brett title: Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-253459-tcn10pho.txt cache: ./cache/cord-253459-tcn10pho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253459-tcn10pho.txt' === file2bib.sh === id: cord-252919-647zcjgu author: Chen, Yun title: Structure analysis of the receptor binding of 2019-nCoV date: 2020-02-17 pages: extension: .txt txt: ./txt/cord-252919-647zcjgu.txt cache: ./cache/cord-252919-647zcjgu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252919-647zcjgu.txt' === file2bib.sh === id: cord-196265-mvnkkcow author: M'esz'aros, B'alint title: Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-196265-mvnkkcow.txt cache: ./cache/cord-196265-mvnkkcow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-196265-mvnkkcow.txt' === file2bib.sh === id: cord-252910-7qvnj6c8 author: Li, Xin title: The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-252910-7qvnj6c8.txt cache: ./cache/cord-252910-7qvnj6c8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252910-7qvnj6c8.txt' === file2bib.sh === id: cord-253422-m18ngwbt author: Trimarchi, Hernán title: COVID-19 and acute kidney injury in pediatric subjects: is there a place for eculizumab treatment? date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-253422-m18ngwbt.txt cache: ./cache/cord-253422-m18ngwbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253422-m18ngwbt.txt' === file2bib.sh === id: cord-252600-bvh1o64r author: Galasiti Kankanamalage, Anushka C. title: Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date: 2018-04-25 pages: extension: .txt txt: ./txt/cord-252600-bvh1o64r.txt cache: ./cache/cord-252600-bvh1o64r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252600-bvh1o64r.txt' === file2bib.sh === id: cord-252714-idlyl4ga author: Islam, M. Saiful title: Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-252714-idlyl4ga.txt cache: ./cache/cord-252714-idlyl4ga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252714-idlyl4ga.txt' === file2bib.sh === id: cord-253447-4w6caxwu author: Zeng, Xin title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-253447-4w6caxwu.txt cache: ./cache/cord-253447-4w6caxwu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253447-4w6caxwu.txt' === file2bib.sh === id: cord-253851-27nt0op8 author: Koh, David title: SARS: health care work can be hazardous to health date: 2003-06-17 pages: extension: .txt txt: ./txt/cord-253851-27nt0op8.txt cache: ./cache/cord-253851-27nt0op8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253851-27nt0op8.txt' === file2bib.sh === id: cord-253606-o8a0jhx2 author: Mégarbane, Bruno title: Comment on: Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-253606-o8a0jhx2.txt cache: ./cache/cord-253606-o8a0jhx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253606-o8a0jhx2.txt' === file2bib.sh === id: cord-232446-vvb2ffhv author: Mongia, Aanchal title: A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-232446-vvb2ffhv.txt cache: ./cache/cord-232446-vvb2ffhv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-232446-vvb2ffhv.txt' === file2bib.sh === id: cord-253238-ptmxkpae author: Kopel, Jonathan title: Clinical Insights into the Gastrointestinal Manifestations of COVID-19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-253238-ptmxkpae.txt cache: ./cache/cord-253238-ptmxkpae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253238-ptmxkpae.txt' === file2bib.sh === id: cord-254079-pvl44u4d author: Marinella, Mark A. title: COVID-19 pandemic and the stethoscope: don't forget to sanitize date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-254079-pvl44u4d.txt cache: ./cache/cord-254079-pvl44u4d.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254079-pvl44u4d.txt' === file2bib.sh === id: cord-253282-zwl0safn author: Plant, Ewan P. title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date: 2013-01-18 pages: extension: .txt txt: ./txt/cord-253282-zwl0safn.txt cache: ./cache/cord-253282-zwl0safn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253282-zwl0safn.txt' === file2bib.sh === id: cord-253777-h8wy0coq author: Afshar, Hale title: Evolution and resolution of brain involvement associated with SARS- CoV2 infection: A close Clinical – Paraclinical follow up study of a case date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-253777-h8wy0coq.txt cache: ./cache/cord-253777-h8wy0coq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253777-h8wy0coq.txt' === file2bib.sh === id: cord-253201-r6vsa0pw author: Nazari, S. title: Central Nervous System Manifestations in COVID-19 Patients: A Systematic Review and Meta-analysis date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-253201-r6vsa0pw.txt cache: ./cache/cord-253201-r6vsa0pw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253201-r6vsa0pw.txt' === file2bib.sh === id: cord-252049-rgdynmla author: Tomar, Sakshi title: Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CL(pro)): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS date: 2015-06-08 pages: extension: .txt txt: ./txt/cord-252049-rgdynmla.txt cache: ./cache/cord-252049-rgdynmla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252049-rgdynmla.txt' === file2bib.sh === id: cord-253457-gawn4s9g author: Yau, Kevin title: COVID-19 Outbreak in an Urban Hemodialysis Unit date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-253457-gawn4s9g.txt cache: ./cache/cord-253457-gawn4s9g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253457-gawn4s9g.txt' === file2bib.sh === id: cord-171703-n22tr8f2 author: Hanmo, Li title: Robust estimation of SARS-CoV-2 epidemic at US counties date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-171703-n22tr8f2.txt cache: ./cache/cord-171703-n22tr8f2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-171703-n22tr8f2.txt' === file2bib.sh === id: cord-222664-4qyrtzhu author: Coban, Mathew title: Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-222664-4qyrtzhu.txt cache: ./cache/cord-222664-4qyrtzhu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-222664-4qyrtzhu.txt' === file2bib.sh === id: cord-252264-d9i19h8q author: Blackburn, Kyle M. title: Post-infectious neurological disorders date: 2020-08-30 pages: extension: .txt txt: ./txt/cord-252264-d9i19h8q.txt cache: ./cache/cord-252264-d9i19h8q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252264-d9i19h8q.txt' === file2bib.sh === id: cord-252687-7084pfqm author: Szelenberger, Rafal title: Ischemic Stroke among the Symptoms Caused by the COVID-19 Infection date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-252687-7084pfqm.txt cache: ./cache/cord-252687-7084pfqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252687-7084pfqm.txt' === file2bib.sh === id: cord-252991-gvlyn6j7 author: Silva, V. O. title: PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-252991-gvlyn6j7.txt cache: ./cache/cord-252991-gvlyn6j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252991-gvlyn6j7.txt' === file2bib.sh === id: cord-253472-3s142p6u author: Saurabh, Suman title: Author’s reply to correspondence regarding the article ‘Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals’ date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-253472-3s142p6u.txt cache: ./cache/cord-253472-3s142p6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253472-3s142p6u.txt' === file2bib.sh === id: cord-253513-zn87f1lk author: Liu, Jia title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro date: 2020-03-18 pages: extension: .txt txt: ./txt/cord-253513-zn87f1lk.txt cache: ./cache/cord-253513-zn87f1lk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253513-zn87f1lk.txt' === file2bib.sh === id: cord-253933-29tedkf8 author: David, Abel P. title: Tracheostomy guidelines developed at a large academic medical center during the COVID‐19 pandemic date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-253933-29tedkf8.txt cache: ./cache/cord-253933-29tedkf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253933-29tedkf8.txt' === file2bib.sh === id: cord-252671-uf96jgig author: Wang, Yi title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism date: 2016-02-09 pages: extension: .txt txt: ./txt/cord-252671-uf96jgig.txt cache: ./cache/cord-252671-uf96jgig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252671-uf96jgig.txt' === file2bib.sh === id: cord-253124-s3pa4n8a author: Dhamad, Ahmed E. title: COVID-19: molecular and serological detection methods date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-253124-s3pa4n8a.txt cache: ./cache/cord-253124-s3pa4n8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253124-s3pa4n8a.txt' === file2bib.sh === id: cord-253366-03cg831z author: Chakraborty, Hirak title: Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-253366-03cg831z.txt cache: ./cache/cord-253366-03cg831z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253366-03cg831z.txt' === file2bib.sh === id: cord-252922-cdhnlvxv author: West, Erin A. title: Corona Immunitas: study protocol of a nationwide program of SARS-CoV-2 seroprevalence and seroepidemiologic studies in Switzerland date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-252922-cdhnlvxv.txt cache: ./cache/cord-252922-cdhnlvxv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252922-cdhnlvxv.txt' === file2bib.sh === id: cord-253990-m75xwrz9 author: Wang, Zhiguo title: Covid‐19: From structure to therapeutic targeting in studying approved drugs and local DNA vaccination date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-253990-m75xwrz9.txt cache: ./cache/cord-253990-m75xwrz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253990-m75xwrz9.txt' === file2bib.sh === id: cord-253970-sbj869yy author: Agarwal, Amit title: Neurological emergencies associated with COVID-19: stroke and beyond date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-253970-sbj869yy.txt cache: ./cache/cord-253970-sbj869yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253970-sbj869yy.txt' === file2bib.sh === id: cord-253331-z443e8lk author: Stanhope, Michael J. title: Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV date: 2004-03-31 pages: extension: .txt txt: ./txt/cord-253331-z443e8lk.txt cache: ./cache/cord-253331-z443e8lk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253331-z443e8lk.txt' === file2bib.sh === id: cord-253905-zknmfgsh author: Li, Xingguang title: Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-253905-zknmfgsh.txt cache: ./cache/cord-253905-zknmfgsh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253905-zknmfgsh.txt' === file2bib.sh === id: cord-253618-bosb7e63 author: Ramteke, Shobhana title: Novel coronavirus disease 2019 (COVID-19) pandemic: considerations for the biomedical waste sector in India date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-253618-bosb7e63.txt cache: ./cache/cord-253618-bosb7e63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253618-bosb7e63.txt' === file2bib.sh === id: cord-253245-433mg0ke author: Gao, Zhiru title: A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-253245-433mg0ke.txt cache: ./cache/cord-253245-433mg0ke.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253245-433mg0ke.txt' === file2bib.sh === id: cord-254017-4a6fs57r author: Pan, Xiu-wu title: Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-254017-4a6fs57r.txt cache: ./cache/cord-254017-4a6fs57r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254017-4a6fs57r.txt' === file2bib.sh === id: cord-253656-2x4y403o author: Ren, Wenlin title: Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-253656-2x4y403o.txt cache: ./cache/cord-253656-2x4y403o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253656-2x4y403o.txt' === file2bib.sh === id: cord-253869-1ouai07v author: Noorimotlagh, Zahra title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-253869-1ouai07v.txt cache: ./cache/cord-253869-1ouai07v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253869-1ouai07v.txt' === file2bib.sh === id: cord-253456-u9num2o9 author: Zhang, Che title: Clinical and epidemiological characteristics of pediatric SARS-CoV-2 infections in China: A multicenter case series date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-253456-u9num2o9.txt cache: ./cache/cord-253456-u9num2o9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253456-u9num2o9.txt' === file2bib.sh === id: cord-253671-g3ypisig author: Otte, Martin Sylvester title: Riechstörungen bei COVID-19 – aktueller Wissensstand date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-253671-g3ypisig.txt cache: ./cache/cord-253671-g3ypisig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253671-g3ypisig.txt' === file2bib.sh === id: cord-253833-0lajhqn5 author: Misra-Hebert, Anita D title: Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system. date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-253833-0lajhqn5.txt cache: ./cache/cord-253833-0lajhqn5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253833-0lajhqn5.txt' === file2bib.sh === id: cord-254821-px4fe7mn author: Infantino, Maria title: Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-254821-px4fe7mn.txt cache: ./cache/cord-254821-px4fe7mn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254821-px4fe7mn.txt' === file2bib.sh === id: cord-254120-1q8tqeg7 author: Iannone, Primiano title: The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness. date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-254120-1q8tqeg7.txt cache: ./cache/cord-254120-1q8tqeg7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254120-1q8tqeg7.txt' === file2bib.sh === id: cord-253665-1dn3ek34 author: Vishnubalaji, Radhakrishnan title: Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-253665-1dn3ek34.txt cache: ./cache/cord-253665-1dn3ek34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253665-1dn3ek34.txt' === file2bib.sh === id: cord-252725-e3pazjdi author: Khalil, Ayman title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-252725-e3pazjdi.txt cache: ./cache/cord-252725-e3pazjdi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252725-e3pazjdi.txt' === file2bib.sh === id: cord-253704-y0t30xw3 author: Lahiri, Durjoy title: COVID-19 Pandemic: A Neurological Perspective date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-253704-y0t30xw3.txt cache: ./cache/cord-253704-y0t30xw3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253704-y0t30xw3.txt' === file2bib.sh === id: cord-254072-evgw0as5 author: Hsu, Li-Yang title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts date: 2003-06-17 pages: extension: .txt txt: ./txt/cord-254072-evgw0as5.txt cache: ./cache/cord-254072-evgw0as5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254072-evgw0as5.txt' === file2bib.sh === id: cord-254094-ed1epul1 author: Mayoral, Eduardo Pérez-Campos title: Factors related to asymptomatic or severe COVID-19 infection date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-254094-ed1epul1.txt cache: ./cache/cord-254094-ed1epul1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254094-ed1epul1.txt' === file2bib.sh === id: cord-253438-k8iqv1jb author: Li, Yujun title: SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-253438-k8iqv1jb.txt cache: ./cache/cord-253438-k8iqv1jb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253438-k8iqv1jb.txt' === file2bib.sh === id: cord-252528-rgnhfcbx author: Du, Fenghe title: COVID-19: the role of excessive cytokine release and potential ACE2 down-regulation in promoting hypercoagulable state associated with severe illness date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-252528-rgnhfcbx.txt cache: ./cache/cord-252528-rgnhfcbx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252528-rgnhfcbx.txt' === file2bib.sh === id: cord-252965-30pl5tx3 author: Stutt, Richard O. J. H. title: A modelling framework to assess the likely effectiveness of facemasks in combination with ‘lock-down’ in managing the COVID-19 pandemic date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-252965-30pl5tx3.txt cache: ./cache/cord-252965-30pl5tx3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252965-30pl5tx3.txt' === file2bib.sh === id: cord-253431-fjds5cdr author: Erukainure, Ochuko L. title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. (Labiatae) date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-253431-fjds5cdr.txt cache: ./cache/cord-253431-fjds5cdr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253431-fjds5cdr.txt' === file2bib.sh === id: cord-252771-6kwfulqe author: Yue, Jing-Li title: Mental health services for infectious disease outbreaks including COVID-19: a rapid systematic review date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-252771-6kwfulqe.txt cache: ./cache/cord-252771-6kwfulqe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252771-6kwfulqe.txt' === file2bib.sh === id: cord-253615-qylm0koe author: Müller, Marcel A title: Human Coronavirus NL63 Open Reading Frame 3 encodes a virion-incorporated N-glycosylated membrane protein date: 2010-01-15 pages: extension: .txt txt: ./txt/cord-253615-qylm0koe.txt cache: ./cache/cord-253615-qylm0koe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253615-qylm0koe.txt' === file2bib.sh === id: cord-253993-ynrthadj author: Belhassan, Assia title: Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-253993-ynrthadj.txt cache: ./cache/cord-253993-ynrthadj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253993-ynrthadj.txt' === file2bib.sh === id: cord-252597-ea78sjcs author: Ramazzotti, Daniele title: VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-252597-ea78sjcs.txt cache: ./cache/cord-252597-ea78sjcs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252597-ea78sjcs.txt' === file2bib.sh === id: cord-253968-jtr0p930 author: López, Verónica title: Recomendaciones en el manejo de la pandemia por coronavirus SARS-CoV-2 (Covid-19) en pacientes con trasplante renal date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-253968-jtr0p930.txt cache: ./cache/cord-253968-jtr0p930.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253968-jtr0p930.txt' === file2bib.sh === id: cord-254162-tu81j66h author: Bai, Xiyuan title: Hypothesis: alpha-1-antitrypsin is a promising treatment option for COVID-19 date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-254162-tu81j66h.txt cache: ./cache/cord-254162-tu81j66h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254162-tu81j66h.txt' === file2bib.sh === id: cord-253178-c41xejo3 author: Neuman, B.W. title: Supramolecular Architecture of the Coronavirus Particle date: 2016-09-15 pages: extension: .txt txt: ./txt/cord-253178-c41xejo3.txt cache: ./cache/cord-253178-c41xejo3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-253178-c41xejo3.txt' === file2bib.sh === id: cord-254505-mjj8xrer author: Kannan, Saathvik R. title: Infectivity of SARS-CoV-2: there Is Something More than D614G? date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-254505-mjj8xrer.txt cache: ./cache/cord-254505-mjj8xrer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254505-mjj8xrer.txt' === file2bib.sh === id: cord-254318-w8wrn9lx author: Díez, José-María title: Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-254318-w8wrn9lx.txt cache: ./cache/cord-254318-w8wrn9lx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254318-w8wrn9lx.txt' === file2bib.sh === id: cord-253844-y6xdcf20 author: Yesudhas, Dhanusha title: COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-253844-y6xdcf20.txt cache: ./cache/cord-253844-y6xdcf20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253844-y6xdcf20.txt' === file2bib.sh === id: cord-254855-gmy9zyad author: He, Sijia title: PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-254855-gmy9zyad.txt cache: ./cache/cord-254855-gmy9zyad.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254855-gmy9zyad.txt' === file2bib.sh === id: cord-254207-uru7bkr4 author: Singanayagam, Anika title: Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-254207-uru7bkr4.txt cache: ./cache/cord-254207-uru7bkr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254207-uru7bkr4.txt' === file2bib.sh === id: cord-254668-szxhlejx author: Brogna, Barbara title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-254668-szxhlejx.txt cache: ./cache/cord-254668-szxhlejx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254668-szxhlejx.txt' === file2bib.sh === id: cord-254469-7q6xi2xx author: Wang, Fuzhou title: An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-254469-7q6xi2xx.txt cache: ./cache/cord-254469-7q6xi2xx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254469-7q6xi2xx.txt' === file2bib.sh === id: cord-254464-6l7fwylu author: Shingare, Ashay title: COVID‐19 in recent kidney transplant recipients date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-254464-6l7fwylu.txt cache: ./cache/cord-254464-6l7fwylu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254464-6l7fwylu.txt' === file2bib.sh === id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-253502-v2hh3w3r.txt cache: ./cache/cord-253502-v2hh3w3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253502-v2hh3w3r.txt' === file2bib.sh === id: cord-254395-tu4aqczj author: Froggatt, Heather M. title: Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL(pro) Reporter Assay date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-254395-tu4aqczj.txt cache: ./cache/cord-254395-tu4aqczj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254395-tu4aqczj.txt' === file2bib.sh === id: cord-254636-3lr008th author: Shishir, Tushar Ahmed title: In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-254636-3lr008th.txt cache: ./cache/cord-254636-3lr008th.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254636-3lr008th.txt' === file2bib.sh === id: cord-255365-fog62qdu author: Goldstein, Neal D. title: On the importance of early testing even when imperfect in a pandemic such as COVID-19 date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-255365-fog62qdu.txt cache: ./cache/cord-255365-fog62qdu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255365-fog62qdu.txt' === file2bib.sh === id: cord-254884-5rmnwcfd author: Ng, S. M. title: Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) date: 2006-01-21 pages: extension: .txt txt: ./txt/cord-254884-5rmnwcfd.txt cache: ./cache/cord-254884-5rmnwcfd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254884-5rmnwcfd.txt' === file2bib.sh === id: cord-253987-83h861lp author: Tada, Takuya title: A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-253987-83h861lp.txt cache: ./cache/cord-253987-83h861lp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253987-83h861lp.txt' === file2bib.sh === id: cord-254478-scc9wee0 author: To, Kelvin Kai-Wang title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date: 2020-03-23 pages: extension: .txt txt: ./txt/cord-254478-scc9wee0.txt cache: ./cache/cord-254478-scc9wee0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254478-scc9wee0.txt' === file2bib.sh === id: cord-254630-ed5gawoj author: Barron, Sarah P. title: Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy? date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-254630-ed5gawoj.txt cache: ./cache/cord-254630-ed5gawoj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254630-ed5gawoj.txt' === file2bib.sh === id: cord-255264-2kj961en author: Hasan, Syed Shahzad title: Social distancing and the use of PPE by community pharmacy personnel: Does evidence support these measures? date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-255264-2kj961en.txt cache: ./cache/cord-255264-2kj961en.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255264-2kj961en.txt' === file2bib.sh === id: cord-255413-8o884nyp author: Hotez, Peter J. title: The Potential Role of Th17 Immune Responses in Coronavirus Immunopathology and Vaccine-induced Immune Enhancement date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-255413-8o884nyp.txt cache: ./cache/cord-255413-8o884nyp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255413-8o884nyp.txt' === file2bib.sh === id: cord-254452-gqqdx2r5 author: Singh, Awadhesh Kumar title: Remdesivir in COVID-19: A critical review of pharmacology, pre-clinical and clinical studies date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-254452-gqqdx2r5.txt cache: ./cache/cord-254452-gqqdx2r5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254452-gqqdx2r5.txt' === file2bib.sh === id: cord-255458-81ugj38k author: Doll, Michelle E. title: Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-255458-81ugj38k.txt cache: ./cache/cord-255458-81ugj38k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255458-81ugj38k.txt' === file2bib.sh === id: cord-254968-czrgzyr3 author: Zhang, Qiang title: A serological survey of SARS-CoV-2 in cat in Wuhan date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-254968-czrgzyr3.txt cache: ./cache/cord-254968-czrgzyr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254968-czrgzyr3.txt' === file2bib.sh === id: cord-255290-p64apuk1 author: Matheeussen, Veerle title: International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-255290-p64apuk1.txt cache: ./cache/cord-255290-p64apuk1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255290-p64apuk1.txt' === file2bib.sh === id: cord-254825-c5d0wul9 author: Kim, Sei Won title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-254825-c5d0wul9.txt cache: ./cache/cord-254825-c5d0wul9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254825-c5d0wul9.txt' === file2bib.sh === id: cord-255284-ffh1jl40 author: Guery, B title: Syndrome respiratoire aigu sévère date: 2003-06-30 pages: extension: .txt txt: ./txt/cord-255284-ffh1jl40.txt cache: ./cache/cord-255284-ffh1jl40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255284-ffh1jl40.txt' === file2bib.sh === id: cord-255552-k1retwa4 author: Gassen, Nils C. title: Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-255552-k1retwa4.txt cache: ./cache/cord-255552-k1retwa4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255552-k1retwa4.txt' === file2bib.sh === id: cord-255069-9xueqdri author: Leary, Shay title: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-255069-9xueqdri.txt cache: ./cache/cord-255069-9xueqdri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255069-9xueqdri.txt' === file2bib.sh === id: cord-255293-8necodtw author: Phakthanakanok, Krongsakda title: A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-255293-8necodtw.txt cache: ./cache/cord-255293-8necodtw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255293-8necodtw.txt' === file2bib.sh === id: cord-255229-w2xtxo9a author: Edson, Daniel C title: Identification of SARS-CoV-2 in a Proficiency Testing Program date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-255229-w2xtxo9a.txt cache: ./cache/cord-255229-w2xtxo9a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255229-w2xtxo9a.txt' === file2bib.sh === id: cord-254419-qw83atrx author: Bhattacharyya, Rajat title: The Interplay Between Coagulation and Inflammation Pathways in COVID-19-Associated Respiratory Failure: A Narrative Review date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-254419-qw83atrx.txt cache: ./cache/cord-254419-qw83atrx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254419-qw83atrx.txt' === file2bib.sh === id: cord-254446-yxqbe1dj author: Ren, Yunzhao R. title: A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19 date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-254446-yxqbe1dj.txt cache: ./cache/cord-254446-yxqbe1dj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254446-yxqbe1dj.txt' === file2bib.sh === id: cord-255446-wddj6hrv author: McDade, T. W. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-255446-wddj6hrv.txt cache: ./cache/cord-255446-wddj6hrv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255446-wddj6hrv.txt' === file2bib.sh === id: cord-255325-tl5fm2yu author: Goletic, Teufik title: Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-255325-tl5fm2yu.txt cache: ./cache/cord-255325-tl5fm2yu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255325-tl5fm2yu.txt' === file2bib.sh === id: cord-255415-sr81j7my author: Heller, Lindsay K. title: Mustela Vison ACE2 Functions as a Receptor for Sars-Coronavirus date: 2006 pages: extension: .txt txt: ./txt/cord-255415-sr81j7my.txt cache: ./cache/cord-255415-sr81j7my.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255415-sr81j7my.txt' === file2bib.sh === id: cord-255586-wshvvgxg author: He, Shengyang title: Clinical characteristics of “re-positive” discharged COVID-19 pneumonia patients in Wuhan, China date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-255586-wshvvgxg.txt cache: ./cache/cord-255586-wshvvgxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255586-wshvvgxg.txt' === file2bib.sh === id: cord-255752-ofph98ac author: Chegondi, Madhuradhar title: Coronavirus Disease 2019 (COVID-19) Associated With Febrile Status Epilepticus in a Child date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-255752-ofph98ac.txt cache: ./cache/cord-255752-ofph98ac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255752-ofph98ac.txt' === file2bib.sh === id: cord-253252-s8fm5rfa author: Jayaweera, Mahesh title: Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-253252-s8fm5rfa.txt cache: ./cache/cord-253252-s8fm5rfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253252-s8fm5rfa.txt' === file2bib.sh === id: cord-255170-bp3irxlh author: Mark, John title: SARS coronavirus: Unusual lability of the nucleocapsid protein date: 2008-12-12 pages: extension: .txt txt: ./txt/cord-255170-bp3irxlh.txt cache: ./cache/cord-255170-bp3irxlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255170-bp3irxlh.txt' === file2bib.sh === id: cord-255907-t7gpi2vo author: Xu, Yifei title: Unveiling the Origin and Transmission of 2019-nCoV date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-255907-t7gpi2vo.txt cache: ./cache/cord-255907-t7gpi2vo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255907-t7gpi2vo.txt' === file2bib.sh === id: cord-255178-mb784dam author: Velu, P. title: Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-255178-mb784dam.txt cache: ./cache/cord-255178-mb784dam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255178-mb784dam.txt' === file2bib.sh === id: cord-254777-h8hw4m9f author: Tanner, Tamara title: Hyperinflammation and the utility of immunomodulatory medications in children with COVID-19 date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-254777-h8hw4m9f.txt cache: ./cache/cord-254777-h8hw4m9f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254777-h8hw4m9f.txt' === file2bib.sh === id: cord-256075-fudeaq7y author: Audo, Andrea title: Acute Pulmonary Embolism in SARS-CoV-2 Infection Treated with Surgical Embolectomy date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-256075-fudeaq7y.txt cache: ./cache/cord-256075-fudeaq7y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256075-fudeaq7y.txt' === file2bib.sh === id: cord-256217-fnjer0e0 author: Neri, Piergiorgio title: COVID-19 and the eye immunity: lesson learned from the past and possible new therapeutic insights date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-256217-fnjer0e0.txt cache: ./cache/cord-256217-fnjer0e0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256217-fnjer0e0.txt' === file2bib.sh === id: cord-255474-7fq9culd author: Alifano, Marco title: Renin-angiotensin system at the heart of COVID-19 pandemic date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-255474-7fq9culd.txt cache: ./cache/cord-255474-7fq9culd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255474-7fq9culd.txt' === file2bib.sh === id: cord-254886-fl5ar971 author: Arav, Y. title: Understanding the indoor pre-symptomatic transmission mechanism of COVID-19 date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-254886-fl5ar971.txt cache: ./cache/cord-254886-fl5ar971.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254886-fl5ar971.txt' === file2bib.sh === id: cord-255498-npk4zv4i author: Harikrishnan, Pandurangan title: Saliva as a Potential Diagnostic Specimen for COVID-19 Testing date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-255498-npk4zv4i.txt cache: ./cache/cord-255498-npk4zv4i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255498-npk4zv4i.txt' === file2bib.sh === id: cord-255774-ux3c3dzf author: Zhong, H. title: Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-255774-ux3c3dzf.txt cache: ./cache/cord-255774-ux3c3dzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255774-ux3c3dzf.txt' === file2bib.sh === id: cord-255940-chb4iuis author: Walton, David A. title: Facility-Level Approaches for COVID-19 When Caseload Surpasses Surge Capacity date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-255940-chb4iuis.txt cache: ./cache/cord-255940-chb4iuis.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255940-chb4iuis.txt' === file2bib.sh === id: cord-255476-p0gyyl3c author: Hsu, Albert L. title: Placental SARS‐CoV‐2 in a Pregnant Woman with Mild COVID‐19 Disease date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-255476-p0gyyl3c.txt cache: ./cache/cord-255476-p0gyyl3c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255476-p0gyyl3c.txt' === file2bib.sh === id: cord-255913-430lrbyx author: Brufsky, Adam title: DC/L‐SIGNs of Hope in the COVID‐19 Pandemic date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-255913-430lrbyx.txt cache: ./cache/cord-255913-430lrbyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255913-430lrbyx.txt' === file2bib.sh === id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 pages: extension: .txt txt: ./txt/cord-255738-r8zfdsix.txt cache: ./cache/cord-255738-r8zfdsix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255738-r8zfdsix.txt' === file2bib.sh === id: cord-255791-ghrlj6b2 author: Pruijssers, Andrea J. title: Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-255791-ghrlj6b2.txt cache: ./cache/cord-255791-ghrlj6b2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255791-ghrlj6b2.txt' === file2bib.sh === id: cord-254957-jqp1gto6 author: Klann, Kevin title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-254957-jqp1gto6.txt cache: ./cache/cord-254957-jqp1gto6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254957-jqp1gto6.txt' === file2bib.sh === id: cord-256152-8wla6ne4 author: Zeng, Xiang title: Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-256152-8wla6ne4.txt cache: ./cache/cord-256152-8wla6ne4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256152-8wla6ne4.txt' === file2bib.sh === id: cord-256092-bph9ys72 author: Hussain, Aneela N. title: Role of testosterone in COVID-19 patients - a double-edged sword? date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-256092-bph9ys72.txt cache: ./cache/cord-256092-bph9ys72.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256092-bph9ys72.txt' === file2bib.sh === id: cord-255665-srvz2ay0 author: Ferrari, Marco title: COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-255665-srvz2ay0.txt cache: ./cache/cord-255665-srvz2ay0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255665-srvz2ay0.txt' === file2bib.sh === id: cord-256270-7e8zlt3t author: Choy, Ka-Tim title: Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-256270-7e8zlt3t.txt cache: ./cache/cord-256270-7e8zlt3t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256270-7e8zlt3t.txt' === file2bib.sh === id: cord-255252-md0avnqg author: Tang, Julian W. title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date: 2007-07-02 pages: extension: .txt txt: ./txt/cord-255252-md0avnqg.txt cache: ./cache/cord-255252-md0avnqg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255252-md0avnqg.txt' === file2bib.sh === id: cord-256109-dkp0fwe3 author: Mazzulli, Tony title: Severe Acute Respiratory Syndrome–associated Coronavirus in Lung Tissue date: 2004-01-17 pages: extension: .txt txt: ./txt/cord-256109-dkp0fwe3.txt cache: ./cache/cord-256109-dkp0fwe3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256109-dkp0fwe3.txt' === file2bib.sh === id: cord-256375-f4vrcjr1 author: Cabrera Muras, Antonio title: Bilateral Facial Nerve Palsy associated with COVID‐19 and Epstein‐Barr Virus co‐infection date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-256375-f4vrcjr1.txt cache: ./cache/cord-256375-f4vrcjr1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256375-f4vrcjr1.txt' === file2bib.sh === id: cord-255997-oer5lxxr author: Onodi, Fanny title: SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-255997-oer5lxxr.txt cache: ./cache/cord-255997-oer5lxxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255997-oer5lxxr.txt' === file2bib.sh === id: cord-256147-lfwytlj3 author: Gabriella, di Mauro title: SARS-Cov-2 infection: response of human immune system and possible implications for the rapid test and treatment date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-256147-lfwytlj3.txt cache: ./cache/cord-256147-lfwytlj3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256147-lfwytlj3.txt' === file2bib.sh === id: cord-255101-l5ssz750 author: Daval, Mary title: Efficacy of local budesonide therapy in the management of persistent hyposmia in COVID-19 patients without signs of severity: A structured summary of a study protocol for a randomised controlled trial date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-255101-l5ssz750.txt cache: ./cache/cord-255101-l5ssz750.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255101-l5ssz750.txt' === file2bib.sh === id: cord-255602-3pzh5ur9 author: Moscadelli, Andrea title: Fake News and Covid-19 in Italy: Results of a Quantitative Observational Study date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-255602-3pzh5ur9.txt cache: ./cache/cord-255602-3pzh5ur9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255602-3pzh5ur9.txt' === file2bib.sh === id: cord-255755-5jccb3nh author: Saha, Sovan title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-255755-5jccb3nh.txt cache: ./cache/cord-255755-5jccb3nh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255755-5jccb3nh.txt' === file2bib.sh === id: cord-256374-l492w2i2 author: Mackler, Niklas title: Will First-Responders Show Up for Work During a Pandemic? Lessons From a Smallpox Vaccination Survey of Paramedics date: 2007-05-22 pages: extension: .txt txt: ./txt/cord-256374-l492w2i2.txt cache: ./cache/cord-256374-l492w2i2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256374-l492w2i2.txt' === file2bib.sh === id: cord-255631-516epnjw author: Syeda, H. B. title: The Role of Machine Learning Techniques to Tackle COVID-19 Crisis: A Systematic Review. date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-255631-516epnjw.txt cache: ./cache/cord-255631-516epnjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255631-516epnjw.txt' === file2bib.sh === id: cord-256458-3fyul3k2 author: Kolikonda, Murali Krishnan title: Association of Coronavirus Disease 2019 and Stroke: A Rising Concern date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-256458-3fyul3k2.txt cache: ./cache/cord-256458-3fyul3k2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256458-3fyul3k2.txt' === file2bib.sh === id: cord-257008-7q5s1vu1 author: Sharma, Virender K. title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-257008-7q5s1vu1.txt cache: ./cache/cord-257008-7q5s1vu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257008-7q5s1vu1.txt' === file2bib.sh === id: cord-256224-qprj8vlc author: Boixeda, R. title: Is chronic obstructive pulmonary disease a protective factor in SARS-CoV-2 infection? The importance of bronchodilator treatment() date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-256224-qprj8vlc.txt cache: ./cache/cord-256224-qprj8vlc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256224-qprj8vlc.txt' === file2bib.sh === id: cord-255371-o9oxchq6 author: Nguyen, Thanh Thi title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-255371-o9oxchq6.txt cache: ./cache/cord-255371-o9oxchq6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255371-o9oxchq6.txt' === file2bib.sh === id: cord-256303-bpa571ys author: Hotez, Peter J. title: Will COVID-19 become the next neglected tropical disease? date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-256303-bpa571ys.txt cache: ./cache/cord-256303-bpa571ys.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256303-bpa571ys.txt' === file2bib.sh === id: cord-255888-znfgh78m author: Fisher, Dale title: Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-255888-znfgh78m.txt cache: ./cache/cord-255888-znfgh78m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255888-znfgh78m.txt' === file2bib.sh === id: cord-255782-w6nfkdok author: Chikhale, Rupesh V. title: Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-255782-w6nfkdok.txt cache: ./cache/cord-255782-w6nfkdok.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255782-w6nfkdok.txt' === file2bib.sh === id: cord-255895-6at9gelt author: Han, Namshik title: Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-255895-6at9gelt.txt cache: ./cache/cord-255895-6at9gelt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255895-6at9gelt.txt' === file2bib.sh === id: cord-255883-mz6nyisw author: Asif, Muhammad title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-255883-mz6nyisw.txt cache: ./cache/cord-255883-mz6nyisw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255883-mz6nyisw.txt' === file2bib.sh === id: cord-254900-fg5wd0nh author: Havenga, M.J.E. title: Serum‐free transient protein production system based on adenoviral vector and PER.C6 technology: High yield and preserved bioactivity date: 2007-12-13 pages: extension: .txt txt: ./txt/cord-254900-fg5wd0nh.txt cache: ./cache/cord-254900-fg5wd0nh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254900-fg5wd0nh.txt' === file2bib.sh === id: cord-256351-q8lkhklw author: Di Giorgio, Angelo title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-256351-q8lkhklw.txt cache: ./cache/cord-256351-q8lkhklw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256351-q8lkhklw.txt' === file2bib.sh === id: cord-255909-m94j1rh4 author: Shree, Priya title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-255909-m94j1rh4.txt cache: ./cache/cord-255909-m94j1rh4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255909-m94j1rh4.txt' === file2bib.sh === id: cord-255872-e2b7ox6b author: Sallam, M. title: Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-255872-e2b7ox6b.txt cache: ./cache/cord-255872-e2b7ox6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255872-e2b7ox6b.txt' === file2bib.sh === id: cord-255734-038xu4hq author: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 pages: extension: .txt txt: ./txt/cord-255734-038xu4hq.txt cache: ./cache/cord-255734-038xu4hq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255734-038xu4hq.txt' === file2bib.sh === id: cord-255697-trig04hd author: Cheng, Vincent Chi-Chung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 pages: extension: .txt txt: ./txt/cord-255697-trig04hd.txt cache: ./cache/cord-255697-trig04hd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255697-trig04hd.txt' === file2bib.sh === id: cord-256146-d599uera author: Kuiken, Thijs title: Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date: 2003-07-26 pages: extension: .txt txt: ./txt/cord-256146-d599uera.txt cache: ./cache/cord-256146-d599uera.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256146-d599uera.txt' === file2bib.sh === id: cord-256233-k9hdq3z8 author: Lipsky, Martin S. title: Men and COVID-19: A Pathophysiologic Review date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-256233-k9hdq3z8.txt cache: ./cache/cord-256233-k9hdq3z8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256233-k9hdq3z8.txt' === file2bib.sh === id: cord-256023-21b5hanj author: Dowdell, A. K. title: Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-256023-21b5hanj.txt cache: ./cache/cord-256023-21b5hanj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256023-21b5hanj.txt' === file2bib.sh === id: cord-256497-kyer0zjx author: Leyendecker, Pierre title: Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-256497-kyer0zjx.txt cache: ./cache/cord-256497-kyer0zjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256497-kyer0zjx.txt' === file2bib.sh === id: cord-256761-rjss51sq author: Caputo, Leonardo title: Repurposing therapeutic agents and herbal medicines to defeat viral nemesis date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-256761-rjss51sq.txt cache: ./cache/cord-256761-rjss51sq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256761-rjss51sq.txt' === file2bib.sh === id: cord-256500-nlavfnpt author: Zhang, Dan title: COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-256500-nlavfnpt.txt cache: ./cache/cord-256500-nlavfnpt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256500-nlavfnpt.txt' === file2bib.sh === id: cord-256385-g1wcfrfi author: Badraoui, Riadh title: Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-256385-g1wcfrfi.txt cache: ./cache/cord-256385-g1wcfrfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256385-g1wcfrfi.txt' === file2bib.sh === id: cord-257135-xt4w0baw author: Li, Zhengqian title: The brain, another potential target organ, needs early protection from SARS-CoV-2 neuroinvasion date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-257135-xt4w0baw.txt cache: ./cache/cord-257135-xt4w0baw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257135-xt4w0baw.txt' === file2bib.sh === id: cord-253862-jl1zhg13 author: Khalaf, Khalil title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-253862-jl1zhg13.txt cache: ./cache/cord-253862-jl1zhg13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-253862-jl1zhg13.txt' === file2bib.sh === id: cord-255515-7se14455 author: Graudenzi, Alex title: Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-255515-7se14455.txt cache: ./cache/cord-255515-7se14455.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255515-7se14455.txt' === file2bib.sh === id: cord-256556-1zea3wa1 author: Lou, Yan title: Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-256556-1zea3wa1.txt cache: ./cache/cord-256556-1zea3wa1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256556-1zea3wa1.txt' === file2bib.sh === id: cord-256940-yuja99jg author: Wei, Bo title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-256940-yuja99jg.txt cache: ./cache/cord-256940-yuja99jg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256940-yuja99jg.txt' === file2bib.sh === id: cord-257310-wqu7t44n author: Maideniuc, Catalina title: Acute necrotizing myelitis and acute motor axonal neuropathy in a COVID-19 patient date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-257310-wqu7t44n.txt cache: ./cache/cord-257310-wqu7t44n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257310-wqu7t44n.txt' === file2bib.sh === id: cord-257105-vrwuaknf author: Davies, Julie title: Neuropilin-1 as a new potential SARS-CoV-2 infection mediator implicated in the neurologic features and central nervous system involvement of COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-257105-vrwuaknf.txt cache: ./cache/cord-257105-vrwuaknf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257105-vrwuaknf.txt' === file2bib.sh === id: cord-255972-u7v0es5w author: Hashikawa, Andrew title: Child Care in the Time of COVID-19: A Period of Challenge and Opportunity. date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-255972-u7v0es5w.txt cache: ./cache/cord-255972-u7v0es5w.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255972-u7v0es5w.txt' === file2bib.sh === id: cord-257022-6vw88jib author: SHANG, Lei title: Polymorphism of SARS-CoV Genomes date: 2006-04-30 pages: extension: .txt txt: ./txt/cord-257022-6vw88jib.txt cache: ./cache/cord-257022-6vw88jib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257022-6vw88jib.txt' === file2bib.sh === id: cord-256808-lxlerb13 author: Lim, W.S title: Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004 date: 2004-06-02 pages: extension: .txt txt: ./txt/cord-256808-lxlerb13.txt cache: ./cache/cord-256808-lxlerb13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256808-lxlerb13.txt' === file2bib.sh === id: cord-256307-2b1vlda8 author: Bhardwaj, Vijay Kumar title: Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-256307-2b1vlda8.txt cache: ./cache/cord-256307-2b1vlda8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256307-2b1vlda8.txt' === file2bib.sh === id: cord-256702-lwxt4587 author: Song, Lingjie title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-256702-lwxt4587.txt cache: ./cache/cord-256702-lwxt4587.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256702-lwxt4587.txt' === file2bib.sh === id: cord-257191-u5xnmsv8 author: Farshi, Esmaeil title: Investigation of immune cells on elimination of pulmonary‐Infected COVID‐19 and important role of innate immunity, phagocytes date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-257191-u5xnmsv8.txt cache: ./cache/cord-257191-u5xnmsv8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257191-u5xnmsv8.txt' === file2bib.sh === id: cord-255440-ls1l2mlg author: Tindle, Courtney title: Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-255440-ls1l2mlg.txt cache: ./cache/cord-255440-ls1l2mlg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255440-ls1l2mlg.txt' === file2bib.sh === id: cord-257140-ge15qrqg author: Perkmann, T. title: Increasing both specificity and sensitivity of SARS-CoV-2 antibody tests by using an adaptive orthogonal testing approach date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-257140-ge15qrqg.txt cache: ./cache/cord-257140-ge15qrqg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257140-ge15qrqg.txt' === file2bib.sh === id: cord-256904-uq6gy24x author: Bartolini, A. title: Immunochromatographic assays for COVID-19 epidemiological screening: our experience date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-256904-uq6gy24x.txt cache: ./cache/cord-256904-uq6gy24x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256904-uq6gy24x.txt' === file2bib.sh === id: cord-254916-y1rw9q11 author: Ogando, Natacha S. title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-254916-y1rw9q11.txt cache: ./cache/cord-254916-y1rw9q11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-254916-y1rw9q11.txt' === file2bib.sh === id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-255495-xnoppq3y.txt cache: ./cache/cord-255495-xnoppq3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255495-xnoppq3y.txt' === file2bib.sh === id: cord-257398-fmkfo5ju author: Meng, Qing-Bin title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-257398-fmkfo5ju.txt cache: ./cache/cord-257398-fmkfo5ju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257398-fmkfo5ju.txt' === file2bib.sh === id: cord-256633-vls23fu5 author: Dimeglio, Chloé title: The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-256633-vls23fu5.txt cache: ./cache/cord-256633-vls23fu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256633-vls23fu5.txt' === file2bib.sh === id: cord-256888-tdx12ccj author: Bradley, Benjamin T title: Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-256888-tdx12ccj.txt cache: ./cache/cord-256888-tdx12ccj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256888-tdx12ccj.txt' === file2bib.sh === id: cord-256572-sqz8yc7b author: Huo, Jiandong title: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-256572-sqz8yc7b.txt cache: ./cache/cord-256572-sqz8yc7b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256572-sqz8yc7b.txt' === file2bib.sh === id: cord-257399-p6of5fno author: Gentry, Chris A title: Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-257399-p6of5fno.txt cache: ./cache/cord-257399-p6of5fno.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257399-p6of5fno.txt' === file2bib.sh === id: cord-256300-emsvxxs5 author: Tortorici, M. Alejandra title: Structural insights into coronavirus entry date: 2019-08-22 pages: extension: .txt txt: ./txt/cord-256300-emsvxxs5.txt cache: ./cache/cord-256300-emsvxxs5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256300-emsvxxs5.txt' === file2bib.sh === id: cord-257584-v38tjof3 author: Fahmi, Muhamad title: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-257584-v38tjof3.txt cache: ./cache/cord-257584-v38tjof3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257584-v38tjof3.txt' === file2bib.sh === id: cord-257265-lkzytud0 author: Zheng, Fang title: SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-257265-lkzytud0.txt cache: ./cache/cord-257265-lkzytud0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257265-lkzytud0.txt' === file2bib.sh === id: cord-256893-3sh87h2x author: Yang, Li title: COVID-19: immunopathogenesis and Immunotherapeutics date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-256893-3sh87h2x.txt cache: ./cache/cord-256893-3sh87h2x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256893-3sh87h2x.txt' === file2bib.sh === id: cord-257403-jujrazsr author: Yin, Changchuan title: Genotyping coronavirus SARS-CoV-2: Methods and implications date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-257403-jujrazsr.txt cache: ./cache/cord-257403-jujrazsr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257403-jujrazsr.txt' === file2bib.sh === id: cord-257468-woyycghi author: Basso, Trude title: Transmission of infection from non-isolated patients with COVID-19 to health care workers date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-257468-woyycghi.txt cache: ./cache/cord-257468-woyycghi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257468-woyycghi.txt' === file2bib.sh === id: cord-256051-87alqfkd author: Revzin, Margarita V. title: Multisystem Imaging Manifestations of COVID-19, Part 1: Viral Pathogenesis and Pulmonary and Vascular System Complications date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-256051-87alqfkd.txt cache: ./cache/cord-256051-87alqfkd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256051-87alqfkd.txt' === file2bib.sh === id: cord-256537-axbyav1m author: Kimball, Ann Marie title: Emergence of Novel Human Infections: New Insights and New Challenges date: 2016-10-24 pages: extension: .txt txt: ./txt/cord-256537-axbyav1m.txt cache: ./cache/cord-256537-axbyav1m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256537-axbyav1m.txt' === file2bib.sh === id: cord-256020-wrui3i2l author: Fadaka, Adewale Oluwaseun title: Understanding the epidemiology, pathophysiology, diagnosis and management of SARS-CoV-2 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-256020-wrui3i2l.txt cache: ./cache/cord-256020-wrui3i2l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256020-wrui3i2l.txt' === file2bib.sh === id: cord-257258-hu9oxea1 author: Chabner, Bruce A. title: Taking the Longer View of COVID‐19 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-257258-hu9oxea1.txt cache: ./cache/cord-257258-hu9oxea1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257258-hu9oxea1.txt' === file2bib.sh === id: cord-257533-i85dyg8n author: Henn, Wolfram title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-257533-i85dyg8n.txt cache: ./cache/cord-257533-i85dyg8n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-257533-i85dyg8n.txt' === file2bib.sh === id: cord-256156-mywhe6w9 author: Clausen, Thomas Mandel title: SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-256156-mywhe6w9.txt cache: ./cache/cord-256156-mywhe6w9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256156-mywhe6w9.txt' === file2bib.sh === id: cord-256961-935r7w01 author: Lu, S. title: Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-256961-935r7w01.txt cache: ./cache/cord-256961-935r7w01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256961-935r7w01.txt' === file2bib.sh === id: cord-256699-d2tf2g7f author: Brochot, Etienne title: Comparison of different serological assays for SARS-CoV-2 in real life date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-256699-d2tf2g7f.txt cache: ./cache/cord-256699-d2tf2g7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256699-d2tf2g7f.txt' === file2bib.sh === id: cord-257206-av2k44ig author: Chen, Ruey title: Effects of a SARS prevention programme in Taiwan on nursing staff's anxiety, depression and sleep quality: A longitudinal survey date: 2006-02-28 pages: extension: .txt txt: ./txt/cord-257206-av2k44ig.txt cache: ./cache/cord-257206-av2k44ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257206-av2k44ig.txt' === file2bib.sh === id: cord-256982-t6urqus7 author: Wellinghausen, Nele title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-256982-t6urqus7.txt cache: ./cache/cord-256982-t6urqus7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256982-t6urqus7.txt' === file2bib.sh === id: cord-257556-lmws8eed author: Rafiq, Danish title: Three months of COVID‐19: A systematic review and meta‐analysis date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-257556-lmws8eed.txt cache: ./cache/cord-257556-lmws8eed.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257556-lmws8eed.txt' === file2bib.sh === id: cord-257809-bq9ha4d0 author: Mukaino, Masahiko title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-257809-bq9ha4d0.txt cache: ./cache/cord-257809-bq9ha4d0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257809-bq9ha4d0.txt' === file2bib.sh === id: cord-257408-ejhhk1iu author: Goss, Matthew B. title: The Pediatric Solid Organ Transplant Experience with COVID‐19: An Initial Multi‐Center, Multi‐Organ Case Series date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-257408-ejhhk1iu.txt cache: ./cache/cord-257408-ejhhk1iu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257408-ejhhk1iu.txt' === file2bib.sh === id: cord-257719-5s6acr7m author: Poh Ng, Lisa Fong title: The Virus That Changed My World date: 2003-12-22 pages: extension: .txt txt: ./txt/cord-257719-5s6acr7m.txt cache: ./cache/cord-257719-5s6acr7m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257719-5s6acr7m.txt' === file2bib.sh === id: cord-257994-i6hut28h author: Nogee, Daniel title: Covid-19 and the N95 respirator shortage: Closing the gap date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-257994-i6hut28h.txt cache: ./cache/cord-257994-i6hut28h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257994-i6hut28h.txt' === file2bib.sh === id: cord-257142-q79yy6o5 author: Wambier, Carlos Gustavo title: Androgen sensitivity gateway to COVID‐19 disease severity date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-257142-q79yy6o5.txt cache: ./cache/cord-257142-q79yy6o5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257142-q79yy6o5.txt' === file2bib.sh === id: cord-258681-66ct8nod author: Warnock, David G. title: Clinical Trials during the SARS-CoV-2 Pandemic date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-258681-66ct8nod.txt cache: ./cache/cord-258681-66ct8nod.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258681-66ct8nod.txt' === file2bib.sh === id: cord-256508-ce59ovan author: Asselah, Tarik title: COVID-19: discovery, diagnostics and drug development date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-256508-ce59ovan.txt cache: ./cache/cord-256508-ce59ovan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256508-ce59ovan.txt' === file2bib.sh === id: cord-257663-i7wrqh2g author: Principi, Nicola title: Effects of Coronavirus Infections in Children date: 2010-02-17 pages: extension: .txt txt: ./txt/cord-257663-i7wrqh2g.txt cache: ./cache/cord-257663-i7wrqh2g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257663-i7wrqh2g.txt' === file2bib.sh === id: cord-257732-3xuy6tbn author: Azzi, Lorenzo title: Saliva is a reliable tool to detect SARS-CoV-2 date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-257732-3xuy6tbn.txt cache: ./cache/cord-257732-3xuy6tbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257732-3xuy6tbn.txt' === file2bib.sh === id: cord-258255-hzmcrenk author: Jiang, Xuejun title: Asymptomatic SARS‐CoV‐2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-258255-hzmcrenk.txt cache: ./cache/cord-258255-hzmcrenk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258255-hzmcrenk.txt' === file2bib.sh === id: cord-257169-1lk737lw author: Lau, C. S. title: Performance of an automated chemiluminescence SARS-COV-2 IG-G Assay date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-257169-1lk737lw.txt cache: ./cache/cord-257169-1lk737lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257169-1lk737lw.txt' === file2bib.sh === id: cord-256737-ptjng78b author: McBride, Corrin E. title: Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date: 2010-09-01 pages: extension: .txt txt: ./txt/cord-256737-ptjng78b.txt cache: ./cache/cord-256737-ptjng78b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256737-ptjng78b.txt' === file2bib.sh === id: cord-257792-m7nij17v author: Ng, Oi-Wing title: Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection date: 2016-04-12 pages: extension: .txt txt: ./txt/cord-257792-m7nij17v.txt cache: ./cache/cord-257792-m7nij17v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257792-m7nij17v.txt' === file2bib.sh === id: cord-253077-61fmul8c author: Vabret, Nicolas title: Immunology of COVID-19: current state of the science date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-253077-61fmul8c.txt cache: ./cache/cord-253077-61fmul8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253077-61fmul8c.txt' === file2bib.sh === id: cord-257611-z0sng9sx author: Kalantari, Hamidreza title: Determination of COVID-19 prevalence with regards to age range of patients referring to the hospitals located in western Tehran, Iran date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-257611-z0sng9sx.txt cache: ./cache/cord-257611-z0sng9sx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257611-z0sng9sx.txt' === file2bib.sh === id: cord-257613-o0q7hvn3 author: Shafiee, Abbas title: Coronavirus disease 2019: A tissue engineering and regenerative medicine perspective date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-257613-o0q7hvn3.txt cache: ./cache/cord-257613-o0q7hvn3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257613-o0q7hvn3.txt' === file2bib.sh === id: cord-256750-5m7psxri author: Park, Hye Yoon title: Posttraumatic stress disorder and depression of survivors 12 months after the outbreak of Middle East respiratory syndrome in South Korea date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-256750-5m7psxri.txt cache: ./cache/cord-256750-5m7psxri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256750-5m7psxri.txt' === file2bib.sh === id: cord-257698-ed2tqn35 author: Wong, Raymond S.M. title: Index Patient and SARS Outbreak in Hong Kong date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-257698-ed2tqn35.txt cache: ./cache/cord-257698-ed2tqn35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257698-ed2tqn35.txt' === file2bib.sh === id: cord-256872-jekx1czw author: Singh, Manvendra title: A single-cell RNA expression map of human coronavirus entry factors date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-256872-jekx1czw.txt cache: ./cache/cord-256872-jekx1czw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256872-jekx1czw.txt' === file2bib.sh === id: cord-258011-19yfwvki author: Deprest, Jan title: SARS‐CoV2 (COVID‐19) infection: is fetal surgery in times of national disasters reasonable? date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-258011-19yfwvki.txt cache: ./cache/cord-258011-19yfwvki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258011-19yfwvki.txt' === file2bib.sh === id: cord-257058-wf6oxzrk author: Kim, Sinae title: The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-257058-wf6oxzrk.txt cache: ./cache/cord-257058-wf6oxzrk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257058-wf6oxzrk.txt' === file2bib.sh === id: cord-257487-xanqvdhn author: Carbajo-Lozoya, Javier title: Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date: 2012-02-10 pages: extension: .txt txt: ./txt/cord-257487-xanqvdhn.txt cache: ./cache/cord-257487-xanqvdhn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257487-xanqvdhn.txt' === file2bib.sh === id: cord-258113-mnou31j3 author: Wang, Yaping title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-258113-mnou31j3.txt cache: ./cache/cord-258113-mnou31j3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258113-mnou31j3.txt' === file2bib.sh === id: cord-257805-pcp3qgn0 author: Mehta, Harsh title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-257805-pcp3qgn0.txt cache: ./cache/cord-257805-pcp3qgn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257805-pcp3qgn0.txt' === file2bib.sh === id: cord-257729-s0vo7dlk author: Bauer, Melissa title: Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-257729-s0vo7dlk.txt cache: ./cache/cord-257729-s0vo7dlk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257729-s0vo7dlk.txt' === file2bib.sh === id: cord-257876-nzjp1hrz author: Yang, Wenzhong title: Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-257876-nzjp1hrz.txt cache: ./cache/cord-257876-nzjp1hrz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257876-nzjp1hrz.txt' === file2bib.sh === id: cord-258067-par61wwh author: Di Martino, Marcello title: Elective Surgery During the SARS-CoV-2 Pandemic (COVID-19): A Morbimortality Analysis and Recommendations on Patient Prioritisation and Security Measures date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-258067-par61wwh.txt cache: ./cache/cord-258067-par61wwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258067-par61wwh.txt' === file2bib.sh === id: cord-258152-3udtsvga author: Dawood, Ali Adel title: Tunicamycin, an anticancer drug and inhibitor of N- linked glycosylation proteins is reliable to treat COVID-19 date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-258152-3udtsvga.txt cache: ./cache/cord-258152-3udtsvga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-258152-3udtsvga.txt' === file2bib.sh === id: cord-258019-njky7v5x author: Kinaret, Pia A.S. title: Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-258019-njky7v5x.txt cache: ./cache/cord-258019-njky7v5x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258019-njky7v5x.txt' === file2bib.sh === id: cord-258167-jqm3qyfm author: Zhou, Peng title: Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date: 2009-09-18 pages: extension: .txt txt: ./txt/cord-258167-jqm3qyfm.txt cache: ./cache/cord-258167-jqm3qyfm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258167-jqm3qyfm.txt' === file2bib.sh === id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-257456-15bm9psj.txt cache: ./cache/cord-257456-15bm9psj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-257456-15bm9psj.txt' === file2bib.sh === id: cord-258160-v08cs51n author: Wang, Lin-Fa title: Review of Bats and SARS date: 2006-12-17 pages: extension: .txt txt: ./txt/cord-258160-v08cs51n.txt cache: ./cache/cord-258160-v08cs51n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258160-v08cs51n.txt' === file2bib.sh === id: cord-258360-fqrn02lr author: Lee, Jimmy title: No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-258360-fqrn02lr.txt cache: ./cache/cord-258360-fqrn02lr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258360-fqrn02lr.txt' === file2bib.sh === id: cord-257820-4qmajxtb author: Abate, Giulia title: Impact of COVID-19 on Alzheimer’s Disease Risk: Viewpoint for Research Action date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-257820-4qmajxtb.txt cache: ./cache/cord-257820-4qmajxtb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257820-4qmajxtb.txt' === file2bib.sh === id: cord-257789-pdybfft6 author: Diamond, Betty title: SARS-CoV-2 and interferon blockade date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-257789-pdybfft6.txt cache: ./cache/cord-257789-pdybfft6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257789-pdybfft6.txt' === file2bib.sh === id: cord-256688-yy7abob9 author: Chavez, Summer title: Coronavirus Disease (COVID-19): A primer for emergency physicians date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-256688-yy7abob9.txt cache: ./cache/cord-256688-yy7abob9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256688-yy7abob9.txt' === file2bib.sh === id: cord-258576-ywbyflas author: Bösmüller, Hans title: The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-258576-ywbyflas.txt cache: ./cache/cord-258576-ywbyflas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258576-ywbyflas.txt' === file2bib.sh === id: cord-257600-0plhquk9 author: Calles, Antonio title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-257600-0plhquk9.txt cache: ./cache/cord-257600-0plhquk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257600-0plhquk9.txt' === file2bib.sh === id: cord-258701-jyzxu9nk author: Kaushal, Darwin title: Endoscopy in Otorhinolaryngology During Corona Outbreak: A Proposal for Safe Practice date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-258701-jyzxu9nk.txt cache: ./cache/cord-258701-jyzxu9nk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258701-jyzxu9nk.txt' === file2bib.sh === id: cord-258382-ep73us0e author: Braga, Cássia L. title: The renin–angiotensin–aldosterone system: Role in pathogenesis and potential therapeutic target in COVID‐19 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-258382-ep73us0e.txt cache: ./cache/cord-258382-ep73us0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258382-ep73us0e.txt' === file2bib.sh === id: cord-258435-lhn34tc4 author: Tracy, C Shawn title: Public perceptions of quarantine: community-based telephone survey following an infectious disease outbreak date: 2009-12-16 pages: extension: .txt txt: ./txt/cord-258435-lhn34tc4.txt cache: ./cache/cord-258435-lhn34tc4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258435-lhn34tc4.txt' === file2bib.sh === id: cord-258242-xblxjlb5 author: Liu, Tengwen title: Systems Pharmacology and Verification of ShenFuHuang Formula in Zebrafish Model Reveal Multi-Scale Treatment Strategy for Septic Syndrome in COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-258242-xblxjlb5.txt cache: ./cache/cord-258242-xblxjlb5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258242-xblxjlb5.txt' === file2bib.sh === id: cord-258722-1o6zhnnj author: Gbinigie, Kome title: Should azithromycin be used to treat COVID-19? A rapid review date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-258722-1o6zhnnj.txt cache: ./cache/cord-258722-1o6zhnnj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258722-1o6zhnnj.txt' === file2bib.sh === id: cord-258312-3v5t4k8d author: Majachani, Nicole title: A Case of a Newborn Baby Girl Infected with SARS-CoV-2 Due to Transplacental Viral Transmission date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-258312-3v5t4k8d.txt cache: ./cache/cord-258312-3v5t4k8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258312-3v5t4k8d.txt' === file2bib.sh === id: cord-258307-nsdhvc8w author: Maki, Dennis G. title: SARS Revisited: The Challenge of Controlling Emerging Infectious Diseases at the Local, Regional, Federal, and Global Levels date: 2011-10-20 pages: extension: .txt txt: ./txt/cord-258307-nsdhvc8w.txt cache: ./cache/cord-258307-nsdhvc8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258307-nsdhvc8w.txt' === file2bib.sh === id: cord-258084-nkr3lrov author: Juthani, Prerak title: Coronavirus Disease 2019 (COVID-19) Manifestation as Acute Myocardial Infarction in a Young, Healthy Male date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-258084-nkr3lrov.txt cache: ./cache/cord-258084-nkr3lrov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258084-nkr3lrov.txt' === file2bib.sh === id: cord-258281-gxwk8jq9 author: Wenling, Yao title: Pregnancy and COVID-19: management and challenges date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-258281-gxwk8jq9.txt cache: ./cache/cord-258281-gxwk8jq9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258281-gxwk8jq9.txt' === file2bib.sh === id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-258250-zueo1xfa.txt cache: ./cache/cord-258250-zueo1xfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258250-zueo1xfa.txt' === file2bib.sh === id: cord-259084-lwh3rww4 author: Anderson, Cole title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-259084-lwh3rww4.txt cache: ./cache/cord-259084-lwh3rww4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259084-lwh3rww4.txt' === file2bib.sh === id: cord-258859-iaiosjlu author: Wang, Jiao title: Mask use during COVID-19: A risk adjusted strategy() date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-258859-iaiosjlu.txt cache: ./cache/cord-258859-iaiosjlu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258859-iaiosjlu.txt' === file2bib.sh === id: cord-259200-65b267ic author: Harypursat, Vijay title: Six weeks into the 2019 coronavirus disease outbreak: it is time to consider strategies to impede the emergence of new zoonotic infections date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-259200-65b267ic.txt cache: ./cache/cord-259200-65b267ic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259200-65b267ic.txt' === file2bib.sh === id: cord-258533-gds7sdc9 author: Lytras, Theodore title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-258533-gds7sdc9.txt cache: ./cache/cord-258533-gds7sdc9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258533-gds7sdc9.txt' === file2bib.sh === id: cord-257802-vgizgq2y author: Uttamchandani, Mahesh title: Applications of microarrays in pathogen detection and biodefence date: 2008-11-12 pages: extension: .txt txt: ./txt/cord-257802-vgizgq2y.txt cache: ./cache/cord-257802-vgizgq2y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257802-vgizgq2y.txt' === file2bib.sh === id: cord-258268-7ypq0t3d author: Zanin, Luca title: SARS-CoV-2 can induce brain and spine demyelinating lesions date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-258268-7ypq0t3d.txt cache: ./cache/cord-258268-7ypq0t3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258268-7ypq0t3d.txt' === file2bib.sh === id: cord-258905-0hgdtalg author: Bond, Katherine title: Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-258905-0hgdtalg.txt cache: ./cache/cord-258905-0hgdtalg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258905-0hgdtalg.txt' === file2bib.sh === id: cord-257766-z7vcdtcq author: Varadhachary, Atul title: Salivary anti-SARS-CoV-2 IgA as an accessible biomarker of mucosal immunity against COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-257766-z7vcdtcq.txt cache: ./cache/cord-257766-z7vcdtcq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257766-z7vcdtcq.txt' === file2bib.sh === id: cord-259572-8n12n6ym author: Bogensperger, Christina title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-259572-8n12n6ym.txt cache: ./cache/cord-259572-8n12n6ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259572-8n12n6ym.txt' === file2bib.sh === id: cord-258844-b4d79m1f author: Denning, M. title: DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-258844-b4d79m1f.txt cache: ./cache/cord-258844-b4d79m1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258844-b4d79m1f.txt' === file2bib.sh === id: cord-259033-op94wuy4 author: Wendling, Daniel title: Can SARS-CoV-2 trigger reactive arthritis? date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-259033-op94wuy4.txt cache: ./cache/cord-259033-op94wuy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259033-op94wuy4.txt' === file2bib.sh === id: cord-258708-da6x5rxa author: Hafiane, Anouar title: SARS-CoV-2 and the cardiovascular system date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-258708-da6x5rxa.txt cache: ./cache/cord-258708-da6x5rxa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258708-da6x5rxa.txt' === file2bib.sh === id: cord-259185-qg4jwbes author: Vadlamani, B. S. title: Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-259185-qg4jwbes.txt cache: ./cache/cord-259185-qg4jwbes.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259185-qg4jwbes.txt' === file2bib.sh === id: cord-258431-8zgwj2fa author: Strafella, Claudia title: Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-258431-8zgwj2fa.txt cache: ./cache/cord-258431-8zgwj2fa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258431-8zgwj2fa.txt' === file2bib.sh === id: cord-259523-92hz534s author: Pullen, Lara C. title: COVID‐19: transplant works toward adaptation date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-259523-92hz534s.txt cache: ./cache/cord-259523-92hz534s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259523-92hz534s.txt' === file2bib.sh === id: cord-257751-n7w1psr4 author: Halperin, Daniel T. title: Coping With COVID-19: Learning From Past Pandemics to Avoid Pitfalls and Panic date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-257751-n7w1psr4.txt cache: ./cache/cord-257751-n7w1psr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257751-n7w1psr4.txt' === file2bib.sh === id: cord-259471-lsdodl0a author: Pagliano, Pasquale title: Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-259471-lsdodl0a.txt cache: ./cache/cord-259471-lsdodl0a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259471-lsdodl0a.txt' === file2bib.sh === id: cord-259852-skhoro95 author: Oboh, Mary Aigbiremo title: Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-259852-skhoro95.txt cache: ./cache/cord-259852-skhoro95.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259852-skhoro95.txt' === file2bib.sh === id: cord-257958-yehnlabq author: Barh, Debmalya title: Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-257958-yehnlabq.txt cache: ./cache/cord-257958-yehnlabq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257958-yehnlabq.txt' === file2bib.sh === id: cord-259261-fmuozy3w author: Bickler, Stephen W. title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-259261-fmuozy3w.txt cache: ./cache/cord-259261-fmuozy3w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259261-fmuozy3w.txt' === file2bib.sh === id: cord-258548-1u7v1nlr author: Mansueto, Gelsomina title: Can COVID 2019 disease induces a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-258548-1u7v1nlr.txt cache: ./cache/cord-258548-1u7v1nlr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258548-1u7v1nlr.txt' === file2bib.sh === id: cord-258725-z79gel8h author: Wood, R. title: Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-258725-z79gel8h.txt cache: ./cache/cord-258725-z79gel8h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258725-z79gel8h.txt' === file2bib.sh === id: cord-258595-bk35vxlr author: Westhaus, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-258595-bk35vxlr.txt cache: ./cache/cord-258595-bk35vxlr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258595-bk35vxlr.txt' === file2bib.sh === id: cord-259396-vmc2q1bi author: Periyasamy, Petrick title: Aerosolized SARS-CoV-2 transmission risk: Surgical or N95 masks? date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-259396-vmc2q1bi.txt cache: ./cache/cord-259396-vmc2q1bi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259396-vmc2q1bi.txt' === file2bib.sh === id: cord-258223-8dhtwf03 author: Chow, Cristelle title: The Next Pandemic: Supporting COVID-19 Frontline Doctors Through Film Discussion date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-258223-8dhtwf03.txt cache: ./cache/cord-258223-8dhtwf03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258223-8dhtwf03.txt' === file2bib.sh === id: cord-259267-trpo5w11 author: Vilibic-Cavlek, Tatjana title: Severe acute respiratory syndrome coronavirus 2 seroprevalence among personnel in the healthcare facilities of Croatia, 2020 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-259267-trpo5w11.txt cache: ./cache/cord-259267-trpo5w11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259267-trpo5w11.txt' === file2bib.sh === id: cord-259558-remrzrq1 author: LeBlanc, Jason J. title: A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-259558-remrzrq1.txt cache: ./cache/cord-259558-remrzrq1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259558-remrzrq1.txt' === file2bib.sh === id: cord-259238-n2uuaof6 author: Zhang, Bao-Zhong title: SARS-CoV-2 infects human neural progenitor cells and brain organoids date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-259238-n2uuaof6.txt cache: ./cache/cord-259238-n2uuaof6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259238-n2uuaof6.txt' === file2bib.sh === id: cord-259668-nwezszhj author: Ortiz, Alberto title: Complement and protection from tissue injury in COVID-19 date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-259668-nwezszhj.txt cache: ./cache/cord-259668-nwezszhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259668-nwezszhj.txt' === file2bib.sh === id: cord-259340-1ir19s25 author: Das, Rohit Pritam title: Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-259340-1ir19s25.txt cache: ./cache/cord-259340-1ir19s25.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259340-1ir19s25.txt' === file2bib.sh === id: cord-259585-mjtxiu0t author: Occhipinti, Vincenzo title: Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-259585-mjtxiu0t.txt cache: ./cache/cord-259585-mjtxiu0t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259585-mjtxiu0t.txt' === file2bib.sh === id: cord-259660-x9sobzyw author: Mohakud, Nirmal K title: An Assumed Vertical Transmission of SARS-CoV-2 During Pregnancy: A Case Report and Review of Literature date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-259660-x9sobzyw.txt cache: ./cache/cord-259660-x9sobzyw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259660-x9sobzyw.txt' === file2bib.sh === id: cord-259863-ndclxrm7 author: Cooke, William R. title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-259863-ndclxrm7.txt cache: ./cache/cord-259863-ndclxrm7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259863-ndclxrm7.txt' === file2bib.sh === id: cord-259347-3acsko74 author: Cheng, Qi title: Infectivity of human coronavirus in the brain date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-259347-3acsko74.txt cache: ./cache/cord-259347-3acsko74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259347-3acsko74.txt' === file2bib.sh === id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-258724-1qhen1bj.txt cache: ./cache/cord-258724-1qhen1bj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258724-1qhen1bj.txt' === file2bib.sh === id: cord-259593-shrd1s7r author: Qin, Zhao-ling title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 pages: extension: .txt txt: ./txt/cord-259593-shrd1s7r.txt cache: ./cache/cord-259593-shrd1s7r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259593-shrd1s7r.txt' === file2bib.sh === id: cord-259619-sco0d5cc author: Ludvigsson, Johnny title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-259619-sco0d5cc.txt cache: ./cache/cord-259619-sco0d5cc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259619-sco0d5cc.txt' === file2bib.sh === id: cord-259907-yqmi0cqy author: Maxwell, Cynthia title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 date: 2009-10-31 pages: extension: .txt txt: ./txt/cord-259907-yqmi0cqy.txt cache: ./cache/cord-259907-yqmi0cqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-259907-yqmi0cqy.txt' === file2bib.sh === id: cord-258614-7unadw41 author: Ogidigo, Joyce Oloaigbe title: Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-258614-7unadw41.txt cache: ./cache/cord-258614-7unadw41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258614-7unadw41.txt' === file2bib.sh === id: cord-260402-9b1ltcf1 author: Lang, Adam Edward title: More Than Meets the Eye: The Similarities Between COVID-19 and Smoking date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-260402-9b1ltcf1.txt cache: ./cache/cord-260402-9b1ltcf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260402-9b1ltcf1.txt' === file2bib.sh === id: cord-258914-g6pv8zz9 author: Proud, Pamela C. title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-258914-g6pv8zz9.txt cache: ./cache/cord-258914-g6pv8zz9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258914-g6pv8zz9.txt' === file2bib.sh === id: cord-258902-h0wrs01h author: Liu, Xianglei title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-258902-h0wrs01h.txt cache: ./cache/cord-258902-h0wrs01h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258902-h0wrs01h.txt' === file2bib.sh === id: cord-259620-qigfstxt author: Yang, Chen title: Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-259620-qigfstxt.txt cache: ./cache/cord-259620-qigfstxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259620-qigfstxt.txt' === file2bib.sh === id: cord-260034-a1y0enrg author: Karsulovic, Claudio title: mTORC inhibitor Sirolimus deprograms monocytes in “cytokine storm” in SARS-CoV2 secondary hemophagocytic lymphohistiocytosis- like syndrome date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-260034-a1y0enrg.txt cache: ./cache/cord-260034-a1y0enrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260034-a1y0enrg.txt' === file2bib.sh === id: cord-259566-qtlq7a6l author: Guraya, Salman Yousuf title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-259566-qtlq7a6l.txt cache: ./cache/cord-259566-qtlq7a6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259566-qtlq7a6l.txt' === file2bib.sh === id: cord-260310-0gkoanrg author: Kim, Jin Yong title: Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-260310-0gkoanrg.txt cache: ./cache/cord-260310-0gkoanrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260310-0gkoanrg.txt' === file2bib.sh === id: cord-259869-kwzsdhrr author: Baghizadeh Fini, Maryam title: Oral saliva and CVID-19 date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-259869-kwzsdhrr.txt cache: ./cache/cord-259869-kwzsdhrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259869-kwzsdhrr.txt' === file2bib.sh === id: cord-260062-qajk0ov4 author: Mocchegiani, Federico title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-260062-qajk0ov4.txt cache: ./cache/cord-260062-qajk0ov4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-260062-qajk0ov4.txt' === file2bib.sh === id: cord-258624-041cf99j author: Ahmad, Sajjad title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-258624-041cf99j.txt cache: ./cache/cord-258624-041cf99j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258624-041cf99j.txt' === file2bib.sh === id: cord-258873-l9oxmqdp author: Baker, D. title: COVID‐19 vaccine‐readiness for anti‐CD20‐depleting therapy in autoimmune diseases date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-258873-l9oxmqdp.txt cache: ./cache/cord-258873-l9oxmqdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258873-l9oxmqdp.txt' === file2bib.sh === id: cord-258221-pn8gh73b author: Rocha, José Lucas Martins title: Mesenchymal Stromal Cells in Viral Infections: Implications for COVID-19 date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-258221-pn8gh73b.txt cache: ./cache/cord-258221-pn8gh73b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258221-pn8gh73b.txt' === file2bib.sh === id: cord-259935-xyo2pe4g author: Wang, Ching-Ying title: SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date: 2017-05-02 pages: extension: .txt txt: ./txt/cord-259935-xyo2pe4g.txt cache: ./cache/cord-259935-xyo2pe4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259935-xyo2pe4g.txt' === file2bib.sh === id: cord-258128-qtmjgrml author: Mirjalili, Mahtabalsadat title: Coronavirus Disease 2019 (COVID-19) and Transplantation: Pharmacotherapeutic Management of Immunosuppression Regimen date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-258128-qtmjgrml.txt cache: ./cache/cord-258128-qtmjgrml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258128-qtmjgrml.txt' === file2bib.sh === id: cord-260054-iihgc5nr author: Cavallo, Luigi title: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-260054-iihgc5nr.txt cache: ./cache/cord-260054-iihgc5nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260054-iihgc5nr.txt' === file2bib.sh === id: cord-259699-48jg7ci7 author: González-Calatayud, Dra Mariel title: Observational study of the suspected or confirmed cases of sars COV-2 infection needing emergency surgical intervention during the first months of the pandemic in a third level hospital: Case series date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-259699-48jg7ci7.txt cache: ./cache/cord-259699-48jg7ci7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259699-48jg7ci7.txt' === file2bib.sh === id: cord-259968-cr3zf4oa author: Harb, Roa title: Evaluation of Three Commercial Automated Assays for the Detection of anti-SARS-CoV-2 Antibodies date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-259968-cr3zf4oa.txt cache: ./cache/cord-259968-cr3zf4oa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259968-cr3zf4oa.txt' === file2bib.sh === id: cord-260247-akujsk0s author: Hamed, Ehab title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-260247-akujsk0s.txt cache: ./cache/cord-260247-akujsk0s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260247-akujsk0s.txt' === file2bib.sh === id: cord-260550-ld9eieik author: Ng, Man Wai title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date: 2007-06-01 pages: extension: .txt txt: ./txt/cord-260550-ld9eieik.txt cache: ./cache/cord-260550-ld9eieik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260550-ld9eieik.txt' === file2bib.sh === id: cord-260132-lqpk3ig7 author: Quartuccio, Luca title: Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-260132-lqpk3ig7.txt cache: ./cache/cord-260132-lqpk3ig7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260132-lqpk3ig7.txt' === file2bib.sh === id: cord-258630-mvz2l3yj author: Liu, Tiantian title: A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-258630-mvz2l3yj.txt cache: ./cache/cord-258630-mvz2l3yj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258630-mvz2l3yj.txt' === file2bib.sh === id: cord-258792-4lakgpxp author: Yoon, Sung‐Won title: Sovereign Dignity, Nationalism and the Health of a Nation: A Study of China's Response in Combat of Epidemics date: 2008-04-08 pages: extension: .txt txt: ./txt/cord-258792-4lakgpxp.txt cache: ./cache/cord-258792-4lakgpxp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258792-4lakgpxp.txt' === file2bib.sh === id: cord-259993-hlsvu1cg author: Qiu, Wuqi title: The Impacts on Health, Society, and Economy of SARS and H7N9 Outbreaks in China: A Case Comparison Study date: 2018-06-28 pages: extension: .txt txt: ./txt/cord-259993-hlsvu1cg.txt cache: ./cache/cord-259993-hlsvu1cg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259993-hlsvu1cg.txt' === file2bib.sh === id: cord-259747-sl9q63oc author: Remmelink, Myriam title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-259747-sl9q63oc.txt cache: ./cache/cord-259747-sl9q63oc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259747-sl9q63oc.txt' === file2bib.sh === id: cord-260048-yis26g81 author: McNamara, Ryan P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-260048-yis26g81.txt cache: ./cache/cord-260048-yis26g81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260048-yis26g81.txt' === file2bib.sh === id: cord-260191-0u0pu0br author: Haas, W. title: „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date: 2004-05-29 pages: extension: .txt txt: ./txt/cord-260191-0u0pu0br.txt cache: ./cache/cord-260191-0u0pu0br.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260191-0u0pu0br.txt' === file2bib.sh === id: cord-260429-5wsj003j author: Kenyon, Chris title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-260429-5wsj003j.txt cache: ./cache/cord-260429-5wsj003j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260429-5wsj003j.txt' === file2bib.sh === id: cord-260559-n8i52e8q author: Peiris, Malik title: What can we expect from first-generation COVID-19 vaccines? date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-260559-n8i52e8q.txt cache: ./cache/cord-260559-n8i52e8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260559-n8i52e8q.txt' === file2bib.sh === id: cord-260412-yjr83ef6 author: Hotez, Peter J. title: Developing a low-cost and accessible COVID-19 vaccine for global health date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-260412-yjr83ef6.txt cache: ./cache/cord-260412-yjr83ef6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260412-yjr83ef6.txt' === file2bib.sh === id: cord-260365-neili1bd author: Silverstein, Jenna S. title: Acute Respiratory Decompensation Requiring Intubation in Pregnant Women with SARS-CoV-2 (COVID-19) date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-260365-neili1bd.txt cache: ./cache/cord-260365-neili1bd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260365-neili1bd.txt' === file2bib.sh === id: cord-259223-6b07qiw2 author: Feitosa, Eduardo L title: COVID-19: Rational discovery of the therapeutic potential of Melatonin as a SARS-CoV-2 main Protease Inhibitor date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-259223-6b07qiw2.txt cache: ./cache/cord-259223-6b07qiw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259223-6b07qiw2.txt' === file2bib.sh === id: cord-261180-w62mynqb author: Ling, L. title: Infection control in non‐clinical areas during the COVID‐19 pandemic date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-261180-w62mynqb.txt cache: ./cache/cord-261180-w62mynqb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261180-w62mynqb.txt' === file2bib.sh === id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-258172-p54j4zzo.txt cache: ./cache/cord-258172-p54j4zzo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258172-p54j4zzo.txt' === file2bib.sh === id: cord-260925-puuqv6zk author: Wen, Feng title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-260925-puuqv6zk.txt cache: ./cache/cord-260925-puuqv6zk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260925-puuqv6zk.txt' === file2bib.sh === id: cord-260772-n5q2yi7j author: Ji, Dong title: Reply to: ‘No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease’ date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-260772-n5q2yi7j.txt cache: ./cache/cord-260772-n5q2yi7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260772-n5q2yi7j.txt' === file2bib.sh === id: cord-261405-n05wjimk author: Lui, Grace title: Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19 date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-261405-n05wjimk.txt cache: ./cache/cord-261405-n05wjimk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261405-n05wjimk.txt' === file2bib.sh === id: cord-260077-xf4sofyc author: Sawalha, Amr H. title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-260077-xf4sofyc.txt cache: ./cache/cord-260077-xf4sofyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260077-xf4sofyc.txt' === file2bib.sh === id: cord-260315-uau554jj author: Ramirez, Santseharay title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-260315-uau554jj.txt cache: ./cache/cord-260315-uau554jj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260315-uau554jj.txt' === file2bib.sh === id: cord-260886-v1ei9im8 author: Baggett, Travis P. title: COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-260886-v1ei9im8.txt cache: ./cache/cord-260886-v1ei9im8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260886-v1ei9im8.txt' === file2bib.sh === id: cord-260376-29ih5c9v author: Guo, Jian-Ping title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-260376-29ih5c9v.txt cache: ./cache/cord-260376-29ih5c9v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260376-29ih5c9v.txt' === file2bib.sh === id: cord-260180-kojb8efv author: Elsoukkary, Sarah S. title: Autopsy Findings in 32 Patients with COVID-19: A Single-Institution Experience date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-260180-kojb8efv.txt cache: ./cache/cord-260180-kojb8efv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260180-kojb8efv.txt' === file2bib.sh === id: cord-259933-ggx4v0bz author: Dalan, Rinkoo title: The ACE-2 in COVID-19: Foe or Friend? date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-259933-ggx4v0bz.txt cache: ./cache/cord-259933-ggx4v0bz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259933-ggx4v0bz.txt' === file2bib.sh === id: cord-260257-phmd0u6d author: Siegler, Aaron J title: Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-260257-phmd0u6d.txt cache: ./cache/cord-260257-phmd0u6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260257-phmd0u6d.txt' === file2bib.sh === id: cord-260508-z11exbyu author: Wang, Hongru title: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-260508-z11exbyu.txt cache: ./cache/cord-260508-z11exbyu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260508-z11exbyu.txt' === file2bib.sh === id: cord-261059-rcpx4god author: Brenner, Steven Robert title: Erythropoietin Induced Hemoglobin Sub‐Unit Beta may Stimulate Innate Immune RNA Virus Pattern Recognition, Suppress Reactive Oxygen Species, Reduce ACE2 Viral Doorway Opening and Neutrophil Extracellular Traps against Covid‐19 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-261059-rcpx4god.txt cache: ./cache/cord-261059-rcpx4god.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-261059-rcpx4god.txt' === file2bib.sh === id: cord-260854-v7wgb6mr author: Colafrancesco, Serena title: COVID-19 gone bad: A new character in the spectrum of the hyperferritinemic syndrome? date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-260854-v7wgb6mr.txt cache: ./cache/cord-260854-v7wgb6mr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260854-v7wgb6mr.txt' === file2bib.sh === id: cord-260644-5moccf8c author: Hashemi, Seyed Ahmad title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-260644-5moccf8c.txt cache: ./cache/cord-260644-5moccf8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260644-5moccf8c.txt' === file2bib.sh === id: cord-261307-qmh3wtqo author: Evans, Scott E. title: Inducible Epithelial Resistance against Coronavirus Pneumonia in Mice date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-261307-qmh3wtqo.txt cache: ./cache/cord-261307-qmh3wtqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261307-qmh3wtqo.txt' === file2bib.sh === id: cord-259808-82drb14x author: Andrews, Paul L R title: COVID‐19, nausea, and vomiting date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-259808-82drb14x.txt cache: ./cache/cord-259808-82drb14x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259808-82drb14x.txt' === file2bib.sh === id: cord-259925-g28sx9qu author: Saleemi, Mansab Ali title: Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-259925-g28sx9qu.txt cache: ./cache/cord-259925-g28sx9qu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259925-g28sx9qu.txt' === file2bib.sh === id: cord-261297-kbcsa9zj author: Chang, Shan-Chwen title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) date: 2005-03-31 pages: extension: .txt txt: ./txt/cord-261297-kbcsa9zj.txt cache: ./cache/cord-261297-kbcsa9zj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261297-kbcsa9zj.txt' === file2bib.sh === id: cord-260981-647wfa8z author: Torti, Lorenza title: Impact of SARS CoV-2 in Hemoglobinopathies with Immune Disfunction and Epidemiology. A Protective Mechanism from Beta Chain Hemoglobin Defects? date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-260981-647wfa8z.txt cache: ./cache/cord-260981-647wfa8z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260981-647wfa8z.txt' === file2bib.sh === id: cord-260871-dtn5t8ka author: Silva, Marcus Tulius T. title: SARS-CoV-2: Should We Be Concerned about the Nervous System? date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-260871-dtn5t8ka.txt cache: ./cache/cord-260871-dtn5t8ka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-260871-dtn5t8ka.txt' === file2bib.sh === id: cord-260673-gf028lf6 author: Bottemanne, Hugo title: Does the Coronavirus Epidemic Take Advantage of Human Optimism Bias? date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-260673-gf028lf6.txt cache: ./cache/cord-260673-gf028lf6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260673-gf028lf6.txt' === file2bib.sh === id: cord-260238-2p209g2p author: Peiris, J S M title: Severe acute respiratory syndrome date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-260238-2p209g2p.txt cache: ./cache/cord-260238-2p209g2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260238-2p209g2p.txt' === file2bib.sh === id: cord-261110-cnj0e0s9 author: Debarnot, Claire title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date: 2011-02-25 pages: extension: .txt txt: ./txt/cord-261110-cnj0e0s9.txt cache: ./cache/cord-261110-cnj0e0s9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261110-cnj0e0s9.txt' === file2bib.sh === id: cord-260624-rqjeacow author: Gu, Jiang title: Multiple organ infection and the pathogenesis of SARS date: 2005-08-01 pages: extension: .txt txt: ./txt/cord-260624-rqjeacow.txt cache: ./cache/cord-260624-rqjeacow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260624-rqjeacow.txt' === file2bib.sh === id: cord-260407-jf1dnllj author: Tang, Catherine So-kum title: Factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult Chinese in Hong Kong date: 2004-06-11 pages: extension: .txt txt: ./txt/cord-260407-jf1dnllj.txt cache: ./cache/cord-260407-jf1dnllj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260407-jf1dnllj.txt' === file2bib.sh === id: cord-261029-befymalm author: Sultan, Keith title: Review of inflammatory bowel disease and COVID-19 date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-261029-befymalm.txt cache: ./cache/cord-261029-befymalm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261029-befymalm.txt' === file2bib.sh === id: cord-261173-lnjh56ts author: Misra-Hebert, Anita D. title: Impact of the COVID-19 Pandemic on Healthcare Workers’ Risk of Infection and Outcomes in a Large, Integrated Health System date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-261173-lnjh56ts.txt cache: ./cache/cord-261173-lnjh56ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261173-lnjh56ts.txt' === file2bib.sh === id: cord-261921-c97ygxq2 author: Souders, Colby P. title: Considerations for Bedside Urologic Procedures in Patients with Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-261921-c97ygxq2.txt cache: ./cache/cord-261921-c97ygxq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261921-c97ygxq2.txt' === file2bib.sh === id: cord-262180-t4akem15 author: Cheruiyot, Isaac title: Comment on “Encephalopathy in patients with COVID‐19: A review” date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-262180-t4akem15.txt cache: ./cache/cord-262180-t4akem15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262180-t4akem15.txt' === file2bib.sh === id: cord-261025-y49su5uc author: Sampathkumar, Priya title: SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date: 2003-07-31 pages: extension: .txt txt: ./txt/cord-261025-y49su5uc.txt cache: ./cache/cord-261025-y49su5uc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261025-y49su5uc.txt' === file2bib.sh === id: cord-261718-zqoggwnk author: Pietschmann, Jan title: Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-261718-zqoggwnk.txt cache: ./cache/cord-261718-zqoggwnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261718-zqoggwnk.txt' === file2bib.sh === id: cord-260729-b12v3c8c author: de Lang, Anna title: Functional Genomics Highlights Differential Induction of Antiviral Pathways in the Lungs of SARS-CoV–Infected Macaques date: 2007-08-10 pages: extension: .txt txt: ./txt/cord-260729-b12v3c8c.txt cache: ./cache/cord-260729-b12v3c8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260729-b12v3c8c.txt' === file2bib.sh === id: cord-259229-e8m8m4ut author: Samidurai, Arun title: Cardiovascular Complications Associated with COVID-19 and Potential Therapeutic Strategies date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-259229-e8m8m4ut.txt cache: ./cache/cord-259229-e8m8m4ut.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259229-e8m8m4ut.txt' === file2bib.sh === id: cord-260057-2m6jdvtc author: Pandey, Preeti title: Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-260057-2m6jdvtc.txt cache: ./cache/cord-260057-2m6jdvtc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260057-2m6jdvtc.txt' === file2bib.sh === id: cord-260503-yq4dtf8n author: SAMARANAYAKE, LAKSHMAN P. title: Severe acute respiratory syndrome and dentistry A retrospective view date: 2004-09-30 pages: extension: .txt txt: ./txt/cord-260503-yq4dtf8n.txt cache: ./cache/cord-260503-yq4dtf8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260503-yq4dtf8n.txt' === file2bib.sh === id: cord-260866-bzdd4f5h author: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-260866-bzdd4f5h.txt cache: ./cache/cord-260866-bzdd4f5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260866-bzdd4f5h.txt' === file2bib.sh === id: cord-260697-oepk0b1d author: Huang, J. title: COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-260697-oepk0b1d.txt cache: ./cache/cord-260697-oepk0b1d.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260697-oepk0b1d.txt' === file2bib.sh === id: cord-261193-960th627 author: Ohnishi, Kouji title: Evaluation of a non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold as a SARS 3CL protease inhibitor date: 2019-01-15 pages: extension: .txt txt: ./txt/cord-261193-960th627.txt cache: ./cache/cord-261193-960th627.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261193-960th627.txt' === file2bib.sh === id: cord-261253-btwx2vxo author: Yip, Timothy T. C. title: Application of ProteinChip Array Profiling in Serum Biomarker Discovery for Patients Suffering From Severe Acute Respiratory Syndrome date: 2007 pages: extension: .txt txt: ./txt/cord-261253-btwx2vxo.txt cache: ./cache/cord-261253-btwx2vxo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261253-btwx2vxo.txt' === file2bib.sh === id: cord-261111-g1qxo01i author: Kowalewski, Joel title: Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-261111-g1qxo01i.txt cache: ./cache/cord-261111-g1qxo01i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261111-g1qxo01i.txt' === file2bib.sh === id: cord-261414-vqvctafm author: Ian Gallicano, G. title: Molecular targeting of vulnerable RNA sequences in SARS CoV-2: identifying clinical feasibility date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-261414-vqvctafm.txt cache: ./cache/cord-261414-vqvctafm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261414-vqvctafm.txt' === file2bib.sh === id: cord-261075-wqtxhiy8 author: Zhang, Meng title: The nervous system——a new territory being explored of SARS-CoV-2 date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-261075-wqtxhiy8.txt cache: ./cache/cord-261075-wqtxhiy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261075-wqtxhiy8.txt' === file2bib.sh === id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 pages: extension: .txt txt: ./txt/cord-261279-6mef38eo.txt cache: ./cache/cord-261279-6mef38eo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261279-6mef38eo.txt' === file2bib.sh === id: cord-261415-qxl14j2m author: Fu, Yajing title: Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-261415-qxl14j2m.txt cache: ./cache/cord-261415-qxl14j2m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261415-qxl14j2m.txt' === file2bib.sh === id: cord-261834-x5ltmj30 author: Guo, Cheng-Xian title: Epidemiological and clinical features of pediatric COVID-19 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-261834-x5ltmj30.txt cache: ./cache/cord-261834-x5ltmj30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261834-x5ltmj30.txt' === file2bib.sh === id: cord-261634-vfe1lawl author: Riddell, Shane title: The effect of temperature on persistence of SARS-CoV-2 on common surfaces date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-261634-vfe1lawl.txt cache: ./cache/cord-261634-vfe1lawl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261634-vfe1lawl.txt' === file2bib.sh === id: cord-261750-6b1y7yxg author: Kwek, Seow-Khee title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge date: 2006-05-31 pages: extension: .txt txt: ./txt/cord-261750-6b1y7yxg.txt cache: ./cache/cord-261750-6b1y7yxg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261750-6b1y7yxg.txt' === file2bib.sh === id: cord-261662-d0tg9i90 author: Andres, Cristina title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-261662-d0tg9i90.txt cache: ./cache/cord-261662-d0tg9i90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261662-d0tg9i90.txt' === file2bib.sh === id: cord-262000-k32cb9ym author: Li, Xue-Ting title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-262000-k32cb9ym.txt cache: ./cache/cord-262000-k32cb9ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262000-k32cb9ym.txt' === file2bib.sh === id: cord-262068-9ixq8hwb author: Gottardi, Andrea De title: Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-262068-9ixq8hwb.txt cache: ./cache/cord-262068-9ixq8hwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262068-9ixq8hwb.txt' === file2bib.sh === id: cord-261619-31jk1vh6 author: Lindholm, David A title: Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-261619-31jk1vh6.txt cache: ./cache/cord-261619-31jk1vh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261619-31jk1vh6.txt' === file2bib.sh === id: cord-261688-njlxrxv6 author: Yang, Ziwei title: Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-261688-njlxrxv6.txt cache: ./cache/cord-261688-njlxrxv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261688-njlxrxv6.txt' === file2bib.sh === id: cord-262020-ygl8xlhk author: McDermott, Aoibhinn title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-262020-ygl8xlhk.txt cache: ./cache/cord-262020-ygl8xlhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262020-ygl8xlhk.txt' === file2bib.sh === id: cord-262149-qrjprsv5 author: Sarode, Gargi S. title: Clinical status determines the efficacy of salivary and nasopharyngeal samples for detection of SARS-CoV-2 date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-262149-qrjprsv5.txt cache: ./cache/cord-262149-qrjprsv5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262149-qrjprsv5.txt' === file2bib.sh === id: cord-261952-xq6qney7 author: Mazzulli, Tony title: Proteomics and Severe Acute Respiratory Syndrome (SARS): Emerging Technology Meets Emerging Pathogen date: 2005-01-01 pages: extension: .txt txt: ./txt/cord-261952-xq6qney7.txt cache: ./cache/cord-261952-xq6qney7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261952-xq6qney7.txt' === file2bib.sh === id: cord-262159-8y0q45gr author: Ciorba, Andrea title: Don’t forget ototoxicity during the SARS-CoV-2 (Covid-19) pandemic! date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-262159-8y0q45gr.txt cache: ./cache/cord-262159-8y0q45gr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262159-8y0q45gr.txt' === file2bib.sh === id: cord-262107-qso8ewi9 author: Kim, In-Cheol title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-262107-qso8ewi9.txt cache: ./cache/cord-262107-qso8ewi9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262107-qso8ewi9.txt' === file2bib.sh === id: cord-261472-qcu73sdu author: Yao, Yong Xiu title: Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-261472-qcu73sdu.txt cache: ./cache/cord-261472-qcu73sdu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261472-qcu73sdu.txt' === file2bib.sh === id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-260225-bc1hr0fr.txt cache: ./cache/cord-260225-bc1hr0fr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260225-bc1hr0fr.txt' === file2bib.sh === id: cord-262029-zzn74cjr author: Kang, Chang Kyung title: In vitro activity of lopinavir/ritonavir and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2 at concentrations achievable by usual doses date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-262029-zzn74cjr.txt cache: ./cache/cord-262029-zzn74cjr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262029-zzn74cjr.txt' === file2bib.sh === id: cord-262192-w86qc3fq author: Balkhair, Abdullah A. title: COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-262192-w86qc3fq.txt cache: ./cache/cord-262192-w86qc3fq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262192-w86qc3fq.txt' === file2bib.sh === id: cord-261615-p81l6zvz author: Grabbe, Stephan title: Systemische Immunsuppression in Zeiten von COVID‐19: Müssen wir umdenken? date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-261615-p81l6zvz.txt cache: ./cache/cord-261615-p81l6zvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261615-p81l6zvz.txt' === file2bib.sh === id: cord-261470-sqxdwu6j author: Weichmann, Franziska title: Projected supportive effects of Pycnogenol® in patients suffering from multi-dimensional health impairments after a SARS-CoV2 infection date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-261470-sqxdwu6j.txt cache: ./cache/cord-261470-sqxdwu6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261470-sqxdwu6j.txt' === file2bib.sh === id: cord-262145-i29e3fge author: Huang, Kuan-Ying A. title: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-262145-i29e3fge.txt cache: ./cache/cord-262145-i29e3fge.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262145-i29e3fge.txt' === file2bib.sh === id: cord-262268-gm99cadh author: Wang, Jingqiang title: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date: 2003-12-01 pages: extension: .txt txt: ./txt/cord-262268-gm99cadh.txt cache: ./cache/cord-262268-gm99cadh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262268-gm99cadh.txt' === file2bib.sh === id: cord-262266-m0fjt483 author: Peddu, Vikas title: Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-262266-m0fjt483.txt cache: ./cache/cord-262266-m0fjt483.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262266-m0fjt483.txt' === file2bib.sh === id: cord-260565-cdthfl5f author: Burkle, Frederick M. title: Declining Public Health Protections within Autocratic Regimes: Impact on Global Public Health Security, Infectious Disease Outbreaks, Epidemics, and Pandemics date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-260565-cdthfl5f.txt cache: ./cache/cord-260565-cdthfl5f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260565-cdthfl5f.txt' === file2bib.sh === id: cord-262338-ipvzugo8 author: Choi, Jun-Yong title: The pathogenesis and alternative treatment of SARS-CoV2 date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-262338-ipvzugo8.txt cache: ./cache/cord-262338-ipvzugo8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262338-ipvzugo8.txt' === file2bib.sh === id: cord-260618-k0y0fz7k author: Belli, Simone title: Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-260618-k0y0fz7k.txt cache: ./cache/cord-260618-k0y0fz7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260618-k0y0fz7k.txt' === file2bib.sh === id: cord-262420-vw7fnguu author: Moey, Melissa Y.Y. title: Electrocardiographic Changes and Arrhythmias in Hospitalized Patients With COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-262420-vw7fnguu.txt cache: ./cache/cord-262420-vw7fnguu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262420-vw7fnguu.txt' === file2bib.sh === id: cord-262361-3f09z5pf author: Agbelele, Penance title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-262361-3f09z5pf.txt cache: ./cache/cord-262361-3f09z5pf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262361-3f09z5pf.txt' === file2bib.sh === id: cord-262635-fdwd99ah author: Hajra Martínez, Ismael El title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-262635-fdwd99ah.txt cache: ./cache/cord-262635-fdwd99ah.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262635-fdwd99ah.txt' === file2bib.sh === id: cord-261941-xf1k5uj1 author: Stackhouse, Robin A. title: Severe acute respiratory syndrome and tuberculosis date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-261941-xf1k5uj1.txt cache: ./cache/cord-261941-xf1k5uj1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261941-xf1k5uj1.txt' === file2bib.sh === id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-261961-u4d0vvmq.txt cache: ./cache/cord-261961-u4d0vvmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261961-u4d0vvmq.txt' === file2bib.sh === id: cord-262783-uhfnv532 author: Yamamoto, Fumiichiro title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-262783-uhfnv532.txt cache: ./cache/cord-262783-uhfnv532.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262783-uhfnv532.txt' === file2bib.sh === id: cord-262726-lfuxhlki author: Diallo, Aïssatou Bailo title: Daytime variation in SARS-CoV-2 infection and cytokine production date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-262726-lfuxhlki.txt cache: ./cache/cord-262726-lfuxhlki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262726-lfuxhlki.txt' === file2bib.sh === id: cord-262090-nbxzyjvf author: Acharya, Arpan title: SARS-CoV-2 Infection Leads to Neurological Dysfunction date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-262090-nbxzyjvf.txt cache: ./cache/cord-262090-nbxzyjvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262090-nbxzyjvf.txt' === file2bib.sh === id: cord-262328-q7mt0xve author: Wajnberg, Ania title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-262328-q7mt0xve.txt cache: ./cache/cord-262328-q7mt0xve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262328-q7mt0xve.txt' === file2bib.sh === id: cord-262104-oig3qrr7 author: Brüssow, Harald title: COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-262104-oig3qrr7.txt cache: ./cache/cord-262104-oig3qrr7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262104-oig3qrr7.txt' === file2bib.sh === id: cord-262412-bs7quwov author: Kaya, Gürkan title: Clinical and Histopathological Features and Potential Pathological Mechanisms of Skin Lesions in COVID-19: Review of the Literature date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-262412-bs7quwov.txt cache: ./cache/cord-262412-bs7quwov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262412-bs7quwov.txt' === file2bib.sh === id: cord-262276-5nue46dm author: Roussel, Yanis title: SARS-CoV-2: fear versus data date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-262276-5nue46dm.txt cache: ./cache/cord-262276-5nue46dm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262276-5nue46dm.txt' === file2bib.sh === id: cord-261959-pvufajw4 author: Karathanou, Konstantina title: A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-261959-pvufajw4.txt cache: ./cache/cord-261959-pvufajw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261959-pvufajw4.txt' === file2bib.sh === id: cord-262556-gpnp06je author: Behrens, Estuardo title: COVID-19: IFSO LAC Recommendations for the Resumption of Elective Bariatric Surgery date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-262556-gpnp06je.txt cache: ./cache/cord-262556-gpnp06je.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262556-gpnp06je.txt' === file2bib.sh === id: cord-262640-4vr4cm1s author: Nguyen, N. N. title: Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2 date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-262640-4vr4cm1s.txt cache: ./cache/cord-262640-4vr4cm1s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262640-4vr4cm1s.txt' === file2bib.sh === id: cord-262841-nr42rs8f author: Li, Lanjuan title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-262841-nr42rs8f.txt cache: ./cache/cord-262841-nr42rs8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262841-nr42rs8f.txt' === file2bib.sh === id: cord-262043-66qle52a author: Basit, Abdul title: Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-262043-66qle52a.txt cache: ./cache/cord-262043-66qle52a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262043-66qle52a.txt' === file2bib.sh === id: cord-262550-oip5m9br author: Kumar, S. Udhaya title: The Rise and Impact of COVID-19 in India date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-262550-oip5m9br.txt cache: ./cache/cord-262550-oip5m9br.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262550-oip5m9br.txt' === file2bib.sh === id: cord-261435-wcn4bjnw author: Ren, Xianwen title: Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-261435-wcn4bjnw.txt cache: ./cache/cord-261435-wcn4bjnw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261435-wcn4bjnw.txt' === file2bib.sh === id: cord-261876-7rsc803x author: Kaslow, David C. title: Certainty of success: three critical parameters in coronavirus vaccine development date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-261876-7rsc803x.txt cache: ./cache/cord-261876-7rsc803x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261876-7rsc803x.txt' === file2bib.sh === id: cord-262282-9xh51cd1 author: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-262282-9xh51cd1.txt cache: ./cache/cord-262282-9xh51cd1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262282-9xh51cd1.txt' === file2bib.sh === id: cord-262575-06i2nv0t author: Caracciolo, Massimo title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-262575-06i2nv0t.txt cache: ./cache/cord-262575-06i2nv0t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262575-06i2nv0t.txt' === file2bib.sh === id: cord-262428-erlmyzwn author: CABARKAPA, Sonja title: The psychological impact of COVID-19 and other viral epidemics on frontline healthcare workers and ways to address it: A rapid systematic review date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-262428-erlmyzwn.txt cache: ./cache/cord-262428-erlmyzwn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262428-erlmyzwn.txt' === file2bib.sh === id: cord-262415-cj4pjuuc author: Eiros, R. title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-262415-cj4pjuuc.txt cache: ./cache/cord-262415-cj4pjuuc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262415-cj4pjuuc.txt' === file2bib.sh === id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-262485-sx2q5ol4.txt cache: ./cache/cord-262485-sx2q5ol4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262485-sx2q5ol4.txt' === file2bib.sh === id: cord-263031-cco2vh0f author: Vultaggio, Alessandra title: Considerations on Biologicals for Patients with allergic disease in times of the COVID‐19 pandemic: an EAACI Statement date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-263031-cco2vh0f.txt cache: ./cache/cord-263031-cco2vh0f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263031-cco2vh0f.txt' === file2bib.sh === id: cord-262184-uxyb4vih author: Jockusch, Steffen title: A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses that Cause SARS and COVID-19 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-262184-uxyb4vih.txt cache: ./cache/cord-262184-uxyb4vih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262184-uxyb4vih.txt' === file2bib.sh === id: cord-262911-e9z00y3b author: Delpino, M. Victoria title: SARS-CoV-2 Pathogenesis: Imbalance in the Renin-Angiotensin System Favors Lung Fibrosis date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-262911-e9z00y3b.txt cache: ./cache/cord-262911-e9z00y3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262911-e9z00y3b.txt' === file2bib.sh === id: cord-261877-4y37676n author: Xu, Cong title: Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-261877-4y37676n.txt cache: ./cache/cord-261877-4y37676n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261877-4y37676n.txt' === file2bib.sh === id: cord-262766-ndn6iwre author: Easom, Nicholas title: 68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-262766-ndn6iwre.txt cache: ./cache/cord-262766-ndn6iwre.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262766-ndn6iwre.txt' === file2bib.sh === id: cord-262796-syu4wbpi author: Wei, Xiao-Shan title: Diarrhea is associated with prolonged symptoms and viral carriage in COVID-19 date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-262796-syu4wbpi.txt cache: ./cache/cord-262796-syu4wbpi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262796-syu4wbpi.txt' === file2bib.sh === id: cord-262250-o7qhncic author: Habel, J. R. title: Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-262250-o7qhncic.txt cache: ./cache/cord-262250-o7qhncic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262250-o7qhncic.txt' === file2bib.sh === id: cord-261566-fn08b0y2 author: Mudgal, Rajat title: Prospects for mucosal vaccine: shutting the door on SARS-CoV-2 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-261566-fn08b0y2.txt cache: ./cache/cord-261566-fn08b0y2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261566-fn08b0y2.txt' === file2bib.sh === id: cord-262454-bccrvapy author: Szente Fonseca, Silvia Nunes title: Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-262454-bccrvapy.txt cache: ./cache/cord-262454-bccrvapy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262454-bccrvapy.txt' === file2bib.sh === id: cord-262499-68vmdqky author: Bordi, Licia title: Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-262499-68vmdqky.txt cache: ./cache/cord-262499-68vmdqky.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262499-68vmdqky.txt' === file2bib.sh === id: cord-262760-mf1pn587 author: Weber, Stefanie title: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-262760-mf1pn587.txt cache: ./cache/cord-262760-mf1pn587.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262760-mf1pn587.txt' === file2bib.sh === id: cord-262936-yo6jf3ng author: Deng, Jia-gang title: Carry forward advantages of traditional medicines in prevention and control of outbreak of COVID-19 pandemic date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-262936-yo6jf3ng.txt cache: ./cache/cord-262936-yo6jf3ng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262936-yo6jf3ng.txt' === file2bib.sh === id: cord-262441-slh52nxm author: Sakai, Yusuke title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 pages: extension: .txt txt: ./txt/cord-262441-slh52nxm.txt cache: ./cache/cord-262441-slh52nxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262441-slh52nxm.txt' === file2bib.sh === id: cord-262730-1dxeg8ci author: Barón-Sánchez, J. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-262730-1dxeg8ci.txt cache: ./cache/cord-262730-1dxeg8ci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262730-1dxeg8ci.txt' === file2bib.sh === id: cord-260793-bb4h255w author: Brann, David H. title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-260793-bb4h255w.txt cache: ./cache/cord-260793-bb4h255w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260793-bb4h255w.txt' === file2bib.sh === id: cord-262598-zk192s0x author: Tatu, Laurent title: Guillain–Barré syndrome in the COVID-19 era: another occasional cluster? date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-262598-zk192s0x.txt cache: ./cache/cord-262598-zk192s0x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 19 resourceName b'cord-262598-zk192s0x.txt' === file2bib.sh === id: cord-263292-qjfe2t9v author: Sansone, A. title: Addressing male sexual and reproductive health in the wake of COVID-19 outbreak date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-263292-qjfe2t9v.txt cache: ./cache/cord-263292-qjfe2t9v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263292-qjfe2t9v.txt' === file2bib.sh === id: cord-263179-uvq3hzga author: Malik, Zohra R title: A Case of a COVID-19-positive Patient date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-263179-uvq3hzga.txt cache: ./cache/cord-263179-uvq3hzga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263179-uvq3hzga.txt' === file2bib.sh === id: cord-262467-epqqd8n8 author: Chen, Jun title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-262467-epqqd8n8.txt cache: ./cache/cord-262467-epqqd8n8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262467-epqqd8n8.txt' === file2bib.sh === id: cord-263509-wi0um8cm author: Rivera, Victor M title: Actitudes Terapéuticas Hacia La Esclerosis Múltiple En Centroamérica Y El Caribe Frente A La Pandemia De Sars-Cov-2 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-263509-wi0um8cm.txt cache: ./cache/cord-263509-wi0um8cm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263509-wi0um8cm.txt' === file2bib.sh === id: cord-262786-otxpc46a author: Mohammadi, Soheil title: Understanding the Immunologic Characteristics of Neurologic Manifestations of SARS-CoV-2 and Potential Immunological Mechanisms date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-262786-otxpc46a.txt cache: ./cache/cord-262786-otxpc46a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262786-otxpc46a.txt' === file2bib.sh === id: cord-262863-f07v5uk8 author: Bertocchi, Ilaria title: The hidden role of NLRP3 inflammasome in obesity‐related COVID‐19 exacerbations: lessons for drug repurposing date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-262863-f07v5uk8.txt cache: ./cache/cord-262863-f07v5uk8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262863-f07v5uk8.txt' === file2bib.sh === id: cord-263123-5y8cc5eb author: Bian, Jingwei title: Anti-RAS drugs and SARS-CoV-2 infection date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-263123-5y8cc5eb.txt cache: ./cache/cord-263123-5y8cc5eb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263123-5y8cc5eb.txt' === file2bib.sh === id: cord-263583-a1zon98c author: Fabbris, Cristoforo title: Is oro/nasopharyngeal swab for SARS-CoV-2 detection a safe procedure? Complications observed among a case series of 4876 consecutive swabs date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-263583-a1zon98c.txt cache: ./cache/cord-263583-a1zon98c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263583-a1zon98c.txt' === file2bib.sh === id: cord-262735-xj9md751 author: Li, Lian Yong title: Digestive system involvement of novel coronavirus infection: Prevention and control infection from a gastroenterology perspective date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-262735-xj9md751.txt cache: ./cache/cord-262735-xj9md751.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262735-xj9md751.txt' === file2bib.sh === id: cord-262958-tmp6yxlv author: Pinto, Dora title: Structural and functional analysis of a potent sarbecovirus neutralizing antibody date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-262958-tmp6yxlv.txt cache: ./cache/cord-262958-tmp6yxlv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262958-tmp6yxlv.txt' === file2bib.sh === id: cord-263039-uoxaem82 author: Perchetti, Garrett A. title: Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-263039-uoxaem82.txt cache: ./cache/cord-263039-uoxaem82.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263039-uoxaem82.txt' === file2bib.sh === id: cord-263350-i02z0hgx author: Nagata, Noriyo title: Pathological and Virological Analyses of Severe Acute Respiratory Syndrome–Associated Coronavirus Infections in Experimantal Animals date: 2006 pages: extension: .txt txt: ./txt/cord-263350-i02z0hgx.txt cache: ./cache/cord-263350-i02z0hgx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263350-i02z0hgx.txt' === file2bib.sh === id: cord-263279-afdmegq0 author: Uhteg, Katharine title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-263279-afdmegq0.txt cache: ./cache/cord-263279-afdmegq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263279-afdmegq0.txt' === file2bib.sh === id: cord-263471-u3su9loz author: Lam, Meylin Caballeros title: Cardiac magnetic resonance characterization of COVID-19 myocarditis date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-263471-u3su9loz.txt cache: ./cache/cord-263471-u3su9loz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263471-u3su9loz.txt' === file2bib.sh === id: cord-263616-igprqlqr author: Hamid, Hytham K. S. title: Considerations for transanal surgery during COVID‐19 pandemic date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-263616-igprqlqr.txt cache: ./cache/cord-263616-igprqlqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263616-igprqlqr.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10364 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-262844-qeheeqe3 author: Xia, Xuhua title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-262844-qeheeqe3.txt cache: ./cache/cord-262844-qeheeqe3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262844-qeheeqe3.txt' === file2bib.sh === id: cord-263844-ixgejst2 author: Majdic, Gregor title: Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-263844-ixgejst2.txt cache: ./cache/cord-263844-ixgejst2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263844-ixgejst2.txt' === file2bib.sh === id: cord-263002-f3itn0sb author: Wagener, Frank A. D. T. G. title: Targeting the Heme-Heme Oxygenase System to Prevent Severe Complications Following COVID-19 Infections date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-263002-f3itn0sb.txt cache: ./cache/cord-263002-f3itn0sb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263002-f3itn0sb.txt' === file2bib.sh === id: cord-263719-a9mnjr3s author: Lee, A. title: Wuhan novel coronavirus (COVID-19): why global control is challenging? date: 2020-02-29 pages: extension: .txt txt: ./txt/cord-263719-a9mnjr3s.txt cache: ./cache/cord-263719-a9mnjr3s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263719-a9mnjr3s.txt' === file2bib.sh === id: cord-264045-h0vt3r9j author: Pallett, Scott J C title: Serological assays for delayed SARS-CoV-2 case identification – Author's reply date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-264045-h0vt3r9j.txt cache: ./cache/cord-264045-h0vt3r9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264045-h0vt3r9j.txt' === file2bib.sh === id: cord-263452-y2ral8nx author: Watanabe, Yasunori title: Site-specific glycan analysis of the SARS-CoV-2 spike date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-263452-y2ral8nx.txt cache: ./cache/cord-263452-y2ral8nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263452-y2ral8nx.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-263090-29n9tsk9 author: Roy, Susmita title: Dynamical asymmetry exposes 2019-nCoV prefusion spike date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-263090-29n9tsk9.txt cache: ./cache/cord-263090-29n9tsk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263090-29n9tsk9.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 13646 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-264012-q2quyijg author: Lim, Su Bin title: ACE2-expressing endothelial cells in aging mouse brain date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-264012-q2quyijg.txt cache: ./cache/cord-264012-q2quyijg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264012-q2quyijg.txt' === file2bib.sh === id: cord-264461-nzvuugls author: Li, Jing title: Puzzle of highly pathogenic human coronaviruses (2019-nCoV) date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-264461-nzvuugls.txt cache: ./cache/cord-264461-nzvuugls.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264461-nzvuugls.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-264042-4hc2i25r author: Chim, Harvey title: Severe Acute Respiratory Syndrome in a Naval Diver date: 2006-06-17 pages: extension: .txt txt: ./txt/cord-264042-4hc2i25r.txt cache: ./cache/cord-264042-4hc2i25r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264042-4hc2i25r.txt' === file2bib.sh === id: cord-263801-01goni72 author: Sobral, Marcos Felipe Falcão title: Association between climate variables and global transmission oF SARS-CoV-2 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-263801-01goni72.txt cache: ./cache/cord-263801-01goni72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263801-01goni72.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-263481-w5ytp1q7 author: Lokman, Syed Mohammad title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-263481-w5ytp1q7.txt cache: ./cache/cord-263481-w5ytp1q7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263481-w5ytp1q7.txt' === file2bib.sh === id: cord-263308-q0iriid8 author: Piano, Carla title: An Italian Neurology Outpatient Clinic Facing SARS-CoV-2 Pandemic: Data From 2,167 Patients date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-263308-q0iriid8.txt cache: ./cache/cord-263308-q0iriid8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263308-q0iriid8.txt' === file2bib.sh === id: cord-264052-uph136sn author: Wilson, Mitchell P title: Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-264052-uph136sn.txt cache: ./cache/cord-264052-uph136sn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264052-uph136sn.txt' === file2bib.sh === id: cord-263365-ymnbktm5 author: Dube, Geoffrey K. title: COVID‐19 infection in pancreas transplant recipients date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-263365-ymnbktm5.txt cache: ./cache/cord-263365-ymnbktm5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263365-ymnbktm5.txt' === file2bib.sh === id: cord-263456-lqe1yckv author: Craney, Arryn R. title: Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-263456-lqe1yckv.txt cache: ./cache/cord-263456-lqe1yckv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263456-lqe1yckv.txt' === file2bib.sh === id: cord-263874-q0egnzwf author: Khan, Md. Arif title: Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-263874-q0egnzwf.txt cache: ./cache/cord-263874-q0egnzwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263874-q0egnzwf.txt' === file2bib.sh === id: cord-263803-0n41gylj author: Villoutreix, Bruno O. title: Prevention of COVID-19 by drug repurposing: rationale from drugs prescribed for mental disorders date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-263803-0n41gylj.txt cache: ./cache/cord-263803-0n41gylj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263803-0n41gylj.txt' === file2bib.sh === id: cord-262119-s6hc7fxs author: Ostaszewski, Marek title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-262119-s6hc7fxs.txt cache: ./cache/cord-262119-s6hc7fxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262119-s6hc7fxs.txt' === file2bib.sh === id: cord-263167-es806qhz author: Rogers, Thomas F. title: Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-263167-es806qhz.txt cache: ./cache/cord-263167-es806qhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263167-es806qhz.txt' === file2bib.sh === id: cord-264360-eroqjkoh author: Risku, Minna title: Detection of human coronaviruses in children with acute gastroenteritis date: 2010-03-15 pages: extension: .txt txt: ./txt/cord-264360-eroqjkoh.txt cache: ./cache/cord-264360-eroqjkoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264360-eroqjkoh.txt' === file2bib.sh === id: cord-263450-v6vdg8os author: Shegogue, Daniel title: Object-oriented biological system integration: a SARS coronavirus example date: 2005-05-15 pages: extension: .txt txt: ./txt/cord-263450-v6vdg8os.txt cache: ./cache/cord-263450-v6vdg8os.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263450-v6vdg8os.txt' === file2bib.sh === id: cord-263738-8g5ujfaf author: Qian, Jing-Yi title: Acute Kidney Injury in the 2019 Novel Coronavirus Disease date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-263738-8g5ujfaf.txt cache: ./cache/cord-263738-8g5ujfaf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263738-8g5ujfaf.txt' === file2bib.sh === id: cord-263840-1t4ykc01 author: Altay, Ozlem title: Current status of COVID-19 therapies and drug repositioning applications date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-263840-1t4ykc01.txt cache: ./cache/cord-263840-1t4ykc01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263840-1t4ykc01.txt' === file2bib.sh === id: cord-263970-9w6ciglv author: Marquez-Miranda, Valeria title: Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-263970-9w6ciglv.txt cache: ./cache/cord-263970-9w6ciglv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263970-9w6ciglv.txt' === file2bib.sh === id: cord-263224-osf0tkzr author: Maunder, Robert G. title: Long-term Psychological and Occupational Effects of Providing Hospital Healthcare during SARS Outbreak date: 2006-12-17 pages: extension: .txt txt: ./txt/cord-263224-osf0tkzr.txt cache: ./cache/cord-263224-osf0tkzr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263224-osf0tkzr.txt' === file2bib.sh === id: cord-263538-0wozg085 author: Cooch, P. B. title: Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-263538-0wozg085.txt cache: ./cache/cord-263538-0wozg085.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263538-0wozg085.txt' === file2bib.sh === id: cord-263594-jd9ako6c author: Kang, Sisi title: A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-263594-jd9ako6c.txt cache: ./cache/cord-263594-jd9ako6c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263594-jd9ako6c.txt' === file2bib.sh === id: cord-263847-kyak5cy4 author: Shi, Tzu-Hau title: Andrographolide and its fluorescent derivative inhibit the main proteases of 2019-nCoV and SARS-CoV through covalent linkage date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-263847-kyak5cy4.txt cache: ./cache/cord-263847-kyak5cy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263847-kyak5cy4.txt' === file2bib.sh === id: cord-264261-98h1bmb2 author: Caruana, Giorgia title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-264261-98h1bmb2.txt cache: ./cache/cord-264261-98h1bmb2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264261-98h1bmb2.txt' === file2bib.sh === id: cord-263245-2qub96mz author: Singh, D. title: Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-263245-2qub96mz.txt cache: ./cache/cord-263245-2qub96mz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263245-2qub96mz.txt' === file2bib.sh === id: cord-264057-z5arb1k5 author: Goel, S. title: Preparations and limitations for prevention of severe acute respiratory syndrome in a tertiary care centre of India date: 2007-05-18 pages: extension: .txt txt: ./txt/cord-264057-z5arb1k5.txt cache: ./cache/cord-264057-z5arb1k5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264057-z5arb1k5.txt' === file2bib.sh === id: cord-264260-8p6pvjkn author: Peng, Hongbing title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-264260-8p6pvjkn.txt cache: ./cache/cord-264260-8p6pvjkn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264260-8p6pvjkn.txt' === file2bib.sh === id: cord-264646-d7qexyav author: Raza, Syed Shadab title: Mesenchymal Stem Cells: A new front emerge in COVID19 treatment: Mesenchymal Stem Cells therapy for SARS-CoV2 viral infection date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-264646-d7qexyav.txt cache: ./cache/cord-264646-d7qexyav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264646-d7qexyav.txt' === file2bib.sh === id: cord-264013-8jnae6ig author: Tsilingiris, Dimitrios title: Telomere length, epidemiology, and pathogenesis of severe COVID‐19 date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-264013-8jnae6ig.txt cache: ./cache/cord-264013-8jnae6ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264013-8jnae6ig.txt' === file2bib.sh === id: cord-264772-v3a2qmj5 author: Harada, Kouji H. title: Letter to the Editor on “An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)”, Back to Basics date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-264772-v3a2qmj5.txt cache: ./cache/cord-264772-v3a2qmj5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264772-v3a2qmj5.txt' === file2bib.sh === id: cord-263739-xoum5e0k author: Zhang, X.-Y. title: Analysis of the effect of proton pump inhibitors on the course of common COVID-19 date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-263739-xoum5e0k.txt cache: ./cache/cord-263739-xoum5e0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263739-xoum5e0k.txt' === file2bib.sh === id: cord-263945-yli5suxb author: Iancu, Gabriela Mariana title: Viral exanthema as manifestation of SARS-CoV-2 infection: A case report date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-263945-yli5suxb.txt cache: ./cache/cord-263945-yli5suxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263945-yli5suxb.txt' === file2bib.sh === id: cord-262904-0b0ljjq1 author: Lon, Jerome Rumdon title: Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-262904-0b0ljjq1.txt cache: ./cache/cord-262904-0b0ljjq1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262904-0b0ljjq1.txt' === file2bib.sh === id: cord-263965-i8yutik6 author: Relf, Michael V. title: What's Old is New! Similarities Between SARS-CoV-2 and HIV date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-263965-i8yutik6.txt cache: ./cache/cord-263965-i8yutik6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263965-i8yutik6.txt' === file2bib.sh === id: cord-263764-2ewz8ok4 author: Kutter, Jasmin S title: Transmission routes of respiratory viruses among humans date: 2018-01-17 pages: extension: .txt txt: ./txt/cord-263764-2ewz8ok4.txt cache: ./cache/cord-263764-2ewz8ok4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263764-2ewz8ok4.txt' === file2bib.sh === id: cord-264477-2onwu92a author: Brida, Margarita title: The globe on the spotlight: Coronavirus disease 2019 (Covid-19) date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-264477-2onwu92a.txt cache: ./cache/cord-264477-2onwu92a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264477-2onwu92a.txt' === file2bib.sh === id: cord-264497-7xz97awb author: Przedlacki, Jerzy title: Patients’ and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-264497-7xz97awb.txt cache: ./cache/cord-264497-7xz97awb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264497-7xz97awb.txt' === file2bib.sh === id: cord-264915-g5ar0pwb author: Abrams, Rory M.C. title: Severe rapidly progressive Guillain-Barré syndrome in the setting of acute COVID-19 disease date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-264915-g5ar0pwb.txt cache: ./cache/cord-264915-g5ar0pwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264915-g5ar0pwb.txt' === file2bib.sh === id: cord-263508-row2mn17 author: Chan, Jasper Fuk-Woo title: The emerging novel Middle East respiratory syndrome coronavirus: The “knowns” and “unknowns” date: 2013-07-21 pages: extension: .txt txt: ./txt/cord-263508-row2mn17.txt cache: ./cache/cord-263508-row2mn17.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263508-row2mn17.txt' === file2bib.sh === id: cord-264266-6xvj9zey author: Chakrabarti, Sankha Shubhra title: COVID-19 in India: Are Biological and Environmental Factors Helping to Stem the Incidence and Severity? date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-264266-6xvj9zey.txt cache: ./cache/cord-264266-6xvj9zey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264266-6xvj9zey.txt' === file2bib.sh === id: cord-264333-mgeicojq author: Chiotos, Kathleen title: Multisystem Inflammatory Syndrome in Children During the Coronavirus 2019 Pandemic: A Case Series date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-264333-mgeicojq.txt cache: ./cache/cord-264333-mgeicojq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264333-mgeicojq.txt' === file2bib.sh === id: cord-263576-pn2zieek author: Das, Sourav title: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-263576-pn2zieek.txt cache: ./cache/cord-263576-pn2zieek.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263576-pn2zieek.txt' === file2bib.sh === id: cord-264970-232stxxo author: Testa, Sophie title: Switch from oral anticoagulants to parenteral heparin in SARS-CoV-2 hospitalized patients date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-264970-232stxxo.txt cache: ./cache/cord-264970-232stxxo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264970-232stxxo.txt' === file2bib.sh === id: cord-265191-unk6rt7u author: Durrani, Muhammad title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-265191-unk6rt7u.txt cache: ./cache/cord-265191-unk6rt7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265191-unk6rt7u.txt' === file2bib.sh === id: cord-264031-0y7xbgun author: Wierbowski, Shayne D. title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-264031-0y7xbgun.txt cache: ./cache/cord-264031-0y7xbgun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264031-0y7xbgun.txt' === file2bib.sh === id: cord-264709-p835wf4f author: Menezes, A. M. B. title: High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-264709-p835wf4f.txt cache: ./cache/cord-264709-p835wf4f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264709-p835wf4f.txt' === file2bib.sh === id: cord-265111-d44ireu5 author: D’Ardes, Damiano title: Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-265111-d44ireu5.txt cache: ./cache/cord-265111-d44ireu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265111-d44ireu5.txt' === file2bib.sh === id: cord-265170-yv04ijsm author: Ceccarelli, Giancarlo title: Probiotics and COVID-19 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-265170-yv04ijsm.txt cache: ./cache/cord-265170-yv04ijsm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265170-yv04ijsm.txt' === file2bib.sh === id: cord-262673-j2ot35lt author: Ahmed-Hassan, Hanaa title: Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-262673-j2ot35lt.txt cache: ./cache/cord-262673-j2ot35lt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-262673-j2ot35lt.txt' === file2bib.sh === id: cord-263532-q044i7ym author: Goyal, Bhupesh title: Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-263532-q044i7ym.txt cache: ./cache/cord-263532-q044i7ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263532-q044i7ym.txt' === file2bib.sh === id: cord-264614-2x7cdul3 author: Díaz-Guio, Diego Andrés title: COVID-19: Biosafety in the Intensive Care Unit date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-264614-2x7cdul3.txt cache: ./cache/cord-264614-2x7cdul3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264614-2x7cdul3.txt' === file2bib.sh === id: cord-265221-qtkwciym author: Bahadur, Gulam title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-265221-qtkwciym.txt cache: ./cache/cord-265221-qtkwciym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265221-qtkwciym.txt' === file2bib.sh === id: cord-265322-3854ddb9 author: Vavougios, George D. title: A data-driven hypothesis on the epigenetic dysregulation of host metabolism by SARS coronaviral infection: potential implications for the SARS-CoV-2 modus operandi date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-265322-3854ddb9.txt cache: ./cache/cord-265322-3854ddb9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265322-3854ddb9.txt' === file2bib.sh === id: cord-264326-teahway7 author: Eleftheriou, Phaedra title: In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-264326-teahway7.txt cache: ./cache/cord-264326-teahway7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264326-teahway7.txt' === file2bib.sh === id: cord-264421-799n9wqj author: Novelli, Antonio title: Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-264421-799n9wqj.txt cache: ./cache/cord-264421-799n9wqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264421-799n9wqj.txt' === file2bib.sh === id: cord-265128-i0d4lxko author: Gurung, Arun Bahadur title: Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M(pro) enzyme through in silico approach date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-265128-i0d4lxko.txt cache: ./cache/cord-265128-i0d4lxko.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265128-i0d4lxko.txt' === file2bib.sh === id: cord-265350-k9yus2sv author: Han, Guan-Zhu title: Pangolins Harbor SARS-CoV-2-Related Coronaviruses date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-265350-k9yus2sv.txt cache: ./cache/cord-265350-k9yus2sv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265350-k9yus2sv.txt' === file2bib.sh === id: cord-264828-6w13xo2a author: Albini, Adriana title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-264828-6w13xo2a.txt cache: ./cache/cord-264828-6w13xo2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-264828-6w13xo2a.txt' === file2bib.sh === id: cord-264968-ctx39vhi author: Woo, Patrick CY title: Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia date: 2004-03-13 pages: extension: .txt txt: ./txt/cord-264968-ctx39vhi.txt cache: ./cache/cord-264968-ctx39vhi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264968-ctx39vhi.txt' === file2bib.sh === id: cord-259603-bh198xgl author: Snijder, E.J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-259603-bh198xgl.txt cache: ./cache/cord-259603-bh198xgl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259603-bh198xgl.txt' === file2bib.sh === id: cord-265617-e91s6xo8 author: Jouali, Farah title: SARS-CoV-2 Genome Sequence from Morocco, Obtained Using Ion AmpliSeq Technology date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-265617-e91s6xo8.txt cache: ./cache/cord-265617-e91s6xo8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265617-e91s6xo8.txt' === file2bib.sh === id: cord-264924-ds6jv5ek author: Tambyah, Paul A title: Severe acute respiratory syndrome from the trenches, at a Singapore university hospital date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-264924-ds6jv5ek.txt cache: ./cache/cord-264924-ds6jv5ek.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264924-ds6jv5ek.txt' === file2bib.sh === id: cord-265164-ybh5yljw author: Zhao, Bin title: Numerical study of the transport of droplets or particles generated by respiratory system indoors date: 2004-11-24 pages: extension: .txt txt: ./txt/cord-265164-ybh5yljw.txt cache: ./cache/cord-265164-ybh5yljw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265164-ybh5yljw.txt' === file2bib.sh === id: cord-264916-c4n0kyog author: Zimmerman, Keith title: Natural protection of ocular surface from viral infections – a hypothesis date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-264916-c4n0kyog.txt cache: ./cache/cord-264916-c4n0kyog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264916-c4n0kyog.txt' === file2bib.sh === id: cord-264515-nle4axad author: Vlachos, J. title: School closures and SARS-CoV-2. Evidence from Sweden's partial school closure date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-264515-nle4axad.txt cache: ./cache/cord-264515-nle4axad.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264515-nle4axad.txt' === file2bib.sh === id: cord-263457-puf8gjir author: Jayarangaiah, Apoorva title: COVID-19-Associated Coagulopathy: An Exacerbated Immunothrombosis Response date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-263457-puf8gjir.txt cache: ./cache/cord-263457-puf8gjir.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263457-puf8gjir.txt' === file2bib.sh === id: cord-264653-ms6zrrnd author: Bhatnagar, Tarun title: Lopinavir/ritonavir combination therapy amongst symptomatic coronavirus disease 2019 patients in India: Protocol for restricted public health emergency use date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-264653-ms6zrrnd.txt cache: ./cache/cord-264653-ms6zrrnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264653-ms6zrrnd.txt' === file2bib.sh === id: cord-265242-y8t37p0b author: Cui, Wei title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date: 2003-09-15 pages: extension: .txt txt: ./txt/cord-265242-y8t37p0b.txt cache: ./cache/cord-265242-y8t37p0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265242-y8t37p0b.txt' === file2bib.sh === id: cord-265329-bsypo08l author: van Dorp, Lucy title: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-265329-bsypo08l.txt cache: ./cache/cord-265329-bsypo08l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265329-bsypo08l.txt' === file2bib.sh === id: cord-264976-6n9cdex6 author: Corse, Tanner title: Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-264976-6n9cdex6.txt cache: ./cache/cord-264976-6n9cdex6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264976-6n9cdex6.txt' === file2bib.sh === id: cord-265595-55s19mr1 author: Brug, Johannes title: Risk Perceptions and Behaviour: Towards Pandemic Control of Emerging Infectious Diseases: International Research on Risk Perception in the Control of Emerging Infectious Diseases date: 2009-01-06 pages: extension: .txt txt: ./txt/cord-265595-55s19mr1.txt cache: ./cache/cord-265595-55s19mr1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265595-55s19mr1.txt' === file2bib.sh === id: cord-265473-ju81kiyw author: Balmeh, Negar title: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-265473-ju81kiyw.txt cache: ./cache/cord-265473-ju81kiyw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265473-ju81kiyw.txt' === file2bib.sh === id: cord-265599-903w782b author: Woods, R. title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-265599-903w782b.txt cache: ./cache/cord-265599-903w782b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265599-903w782b.txt' === file2bib.sh === id: cord-265353-xwpdq8wo author: Ramzy, Danny title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-265353-xwpdq8wo.txt cache: ./cache/cord-265353-xwpdq8wo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265353-xwpdq8wo.txt' === file2bib.sh === id: cord-265260-n6wm54wz author: Cuong, Hoang Quoc title: Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-265260-n6wm54wz.txt cache: ./cache/cord-265260-n6wm54wz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265260-n6wm54wz.txt' === file2bib.sh === id: cord-262470-nkql7h9x author: Muus, Christoph title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-262470-nkql7h9x.txt cache: ./cache/cord-262470-nkql7h9x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262470-nkql7h9x.txt' === file2bib.sh === id: cord-265682-yac7kzaf author: Eden, John-Sebastian title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-265682-yac7kzaf.txt cache: ./cache/cord-265682-yac7kzaf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265682-yac7kzaf.txt' === file2bib.sh === id: cord-264051-ps0x2es1 author: Li, Wei title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-264051-ps0x2es1.txt cache: ./cache/cord-264051-ps0x2es1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264051-ps0x2es1.txt' === file2bib.sh === id: cord-265277-ymvrserl author: Crooke, Stephen N. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-265277-ymvrserl.txt cache: ./cache/cord-265277-ymvrserl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265277-ymvrserl.txt' === file2bib.sh === id: cord-265155-jbvrcjx8 author: Aroniadis, Olga C. title: Current Knowledge and Research Priorities in the Digestive Manifestations of COVID-19 date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-265155-jbvrcjx8.txt cache: ./cache/cord-265155-jbvrcjx8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265155-jbvrcjx8.txt' === file2bib.sh === id: cord-264974-hspek930 author: Timmis, Kenneth title: The COVID‐19 pandemic: some lessons learned about crisis preparedness and management, and the need for international benchmarking to reduce deficits date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-264974-hspek930.txt cache: ./cache/cord-264974-hspek930.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264974-hspek930.txt' === file2bib.sh === id: cord-265740-wjdeps3h author: Radbel, Jared title: Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-265740-wjdeps3h.txt cache: ./cache/cord-265740-wjdeps3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265740-wjdeps3h.txt' === file2bib.sh === id: cord-265724-fdt00qw1 author: Varadarajan, Saranya title: EMMPRIN/BASIGIN as a biological modulator of oral cancer and COVID-19 interaction: novel propositions date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-265724-fdt00qw1.txt cache: ./cache/cord-265724-fdt00qw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265724-fdt00qw1.txt' === file2bib.sh === id: cord-265598-4h3wx81q author: Hasan, Abdulkarim title: Histopathology Laboratory Paperwork as a Potential Risk of COVID-19 Transmission among the Lab Personnel date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-265598-4h3wx81q.txt cache: ./cache/cord-265598-4h3wx81q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265598-4h3wx81q.txt' === file2bib.sh === id: cord-265366-vmuqbpkk author: Leibowitz, Jill title: Comparison of Clinical and Epidemiologic Characteristics of Young Febrile Infants with and without SARS-CoV-2 Infection date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-265366-vmuqbpkk.txt cache: ./cache/cord-265366-vmuqbpkk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265366-vmuqbpkk.txt' === file2bib.sh === id: cord-265723-6k8196p2 author: Yu, Chengjun title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-265723-6k8196p2.txt cache: ./cache/cord-265723-6k8196p2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265723-6k8196p2.txt' === file2bib.sh === id: cord-266016-555e3ndo author: Hildenwall, Helena title: Paediatric COVID‐19 admissions in a region with open schools during the two first months of the pandemic date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-266016-555e3ndo.txt cache: ./cache/cord-266016-555e3ndo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266016-555e3ndo.txt' === file2bib.sh === id: cord-265529-0n9xxa9h author: John Hann, Angus title: Controversies regarding shielding and susceptibility to COVID‐19 disease in liver transplant recipients in the United Kingdom date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-265529-0n9xxa9h.txt cache: ./cache/cord-265529-0n9xxa9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265529-0n9xxa9h.txt' === file2bib.sh === id: cord-266113-3fp46sov author: Dashti‐Khavidaki, Simin title: Considerations for Statin Therapy in Patients with COVID‐19 date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-266113-3fp46sov.txt cache: ./cache/cord-266113-3fp46sov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266113-3fp46sov.txt' === file2bib.sh === id: cord-265228-afbkp3wm author: Fomsgaard, Anna S. title: An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020 date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-265228-afbkp3wm.txt cache: ./cache/cord-265228-afbkp3wm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265228-afbkp3wm.txt' === file2bib.sh === id: cord-265022-p5cab562 author: Kotfis, Katarzyna title: COVID-19: ICU delirium management during SARS-CoV-2 pandemic date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-265022-p5cab562.txt cache: ./cache/cord-265022-p5cab562.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265022-p5cab562.txt' === file2bib.sh === id: cord-266135-jbc9nml0 author: Princiotta Cariddi, Lucia title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-266135-jbc9nml0.txt cache: ./cache/cord-266135-jbc9nml0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266135-jbc9nml0.txt' === file2bib.sh === id: cord-266168-hxu5u5op author: Grimaud, Emilie title: Delayed acute bronchiolitis in infants hospitalized for COVID‐19 date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-266168-hxu5u5op.txt cache: ./cache/cord-266168-hxu5u5op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266168-hxu5u5op.txt' === file2bib.sh === id: cord-265278-wf5pbvvt author: Fishman, Jay A. title: Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-265278-wf5pbvvt.txt cache: ./cache/cord-265278-wf5pbvvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265278-wf5pbvvt.txt' === file2bib.sh === id: cord-266022-aco5kpaj author: Matusiak, Magdalena title: Expression of SARS-CoV-2 entry receptors in the respiratory tract of healthy individuals, smokers and asthmatics date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-266022-aco5kpaj.txt cache: ./cache/cord-266022-aco5kpaj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266022-aco5kpaj.txt' === file2bib.sh === id: cord-266450-g9vihgbk author: Tran, Michael title: SARS-CoV-2 and pulmonary embolism: who stole the platelets? date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-266450-g9vihgbk.txt cache: ./cache/cord-266450-g9vihgbk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266450-g9vihgbk.txt' === file2bib.sh === id: cord-263438-9ra94uda author: Snowden, Frank M. title: Emerging and reemerging diseases: a historical perspective date: 2008-09-19 pages: extension: .txt txt: ./txt/cord-263438-9ra94uda.txt cache: ./cache/cord-263438-9ra94uda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263438-9ra94uda.txt' === file2bib.sh === id: cord-265262-r01u4jr6 author: Cannarella, Rossella title: Systemic effects of the hormonal treatment of male hypogonadism with preliminary indications for the management of COVID-19 patients date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-265262-r01u4jr6.txt cache: ./cache/cord-265262-r01u4jr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265262-r01u4jr6.txt' === file2bib.sh === id: cord-266324-uvsmbrbf author: Zhang, Hu title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-266324-uvsmbrbf.txt cache: ./cache/cord-266324-uvsmbrbf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266324-uvsmbrbf.txt' === file2bib.sh === id: cord-266512-xh6zed03 author: Scala, Enrico title: Atopic statusprotects from severe complications of COVID‐19 date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-266512-xh6zed03.txt cache: ./cache/cord-266512-xh6zed03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266512-xh6zed03.txt' === file2bib.sh === id: cord-266348-tbr2ynx0 author: Stroemer, A. title: Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-266348-tbr2ynx0.txt cache: ./cache/cord-266348-tbr2ynx0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266348-tbr2ynx0.txt' === file2bib.sh === id: cord-266033-gbx48scp author: Xu, Yu-Huan title: Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 date: 2020-02-25 pages: extension: .txt txt: ./txt/cord-266033-gbx48scp.txt cache: ./cache/cord-266033-gbx48scp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266033-gbx48scp.txt' === file2bib.sh === id: cord-266090-f40v4039 author: Gao, Wei title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-266090-f40v4039.txt cache: ./cache/cord-266090-f40v4039.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266090-f40v4039.txt' === file2bib.sh === id: cord-266350-yybunc6z author: Sinha, Saurabh K. title: An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-266350-yybunc6z.txt cache: ./cache/cord-266350-yybunc6z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266350-yybunc6z.txt' === file2bib.sh === id: cord-265813-2onv9mvl author: Criado, Paulo Ricardo title: Are the cutaneous manifestations during or due to SARS-CoV-2 infection/COVID-19 frequent or not? Revision of possible pathophysiologic mechanisms date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-265813-2onv9mvl.txt cache: ./cache/cord-265813-2onv9mvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265813-2onv9mvl.txt' === file2bib.sh === id: cord-266695-ktbgm0p9 author: Dawson, Liza title: SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-266695-ktbgm0p9.txt cache: ./cache/cord-266695-ktbgm0p9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266695-ktbgm0p9.txt' === file2bib.sh === id: cord-266511-g5h4tazp author: Deslandes, A title: SARS-COV-2 was already spreading in France in late December 2019 date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-266511-g5h4tazp.txt cache: ./cache/cord-266511-g5h4tazp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266511-g5h4tazp.txt' === file2bib.sh === id: cord-266820-exl36jt3 author: Rivera, Frida title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-266820-exl36jt3.txt cache: ./cache/cord-266820-exl36jt3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266820-exl36jt3.txt' === file2bib.sh === id: cord-266564-imj1lcy9 author: Liu, Yangli title: Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-266564-imj1lcy9.txt cache: ./cache/cord-266564-imj1lcy9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266564-imj1lcy9.txt' === file2bib.sh === id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-266150-wox7pnkr.txt cache: ./cache/cord-266150-wox7pnkr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266150-wox7pnkr.txt' === file2bib.sh === id: cord-266480-u8o4eitu author: Colubri, Andrés title: Preventing outbreaks through interactive, experiential real-life simulations date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-266480-u8o4eitu.txt cache: ./cache/cord-266480-u8o4eitu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266480-u8o4eitu.txt' === file2bib.sh === id: cord-266104-xqvwht7c author: Mu, Chenglin title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-266104-xqvwht7c.txt cache: ./cache/cord-266104-xqvwht7c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266104-xqvwht7c.txt' === file2bib.sh === id: cord-265877-dund6unq author: Yang, Q. title: Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-265877-dund6unq.txt cache: ./cache/cord-265877-dund6unq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265877-dund6unq.txt' === file2bib.sh === id: cord-265418-yqe9vdj1 author: Kumar, Nilesh title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-265418-yqe9vdj1.txt cache: ./cache/cord-265418-yqe9vdj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265418-yqe9vdj1.txt' === file2bib.sh === id: cord-266885-a5fdeuvv author: Dlotko, P. title: Covid-19 clinical data analysis using Ball Mapper date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-266885-a5fdeuvv.txt cache: ./cache/cord-266885-a5fdeuvv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266885-a5fdeuvv.txt' === file2bib.sh === id: cord-266034-811lov8f author: Benameur, Karima title: Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-266034-811lov8f.txt cache: ./cache/cord-266034-811lov8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266034-811lov8f.txt' === file2bib.sh === id: cord-266948-n7sltd1b author: Ahamed, Jasimuddin title: Severe aortic stenosis patient risk during the COVID-19 pandemic date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-266948-n7sltd1b.txt cache: ./cache/cord-266948-n7sltd1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266948-n7sltd1b.txt' === file2bib.sh === id: cord-266536-4frv2vb7 author: Martel, Jan title: Could nitric oxide help to prevent or treat COVID-19? date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-266536-4frv2vb7.txt cache: ./cache/cord-266536-4frv2vb7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266536-4frv2vb7.txt' === file2bib.sh === id: cord-266696-w9sb038q author: Zhou, Yi-Hua title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date: 2004-03-15 pages: extension: .txt txt: ./txt/cord-266696-w9sb038q.txt cache: ./cache/cord-266696-w9sb038q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266696-w9sb038q.txt' === file2bib.sh === id: cord-266996-knwpkyg6 author: Kipkorir, Vincent title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-266996-knwpkyg6.txt cache: ./cache/cord-266996-knwpkyg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266996-knwpkyg6.txt' === file2bib.sh === id: cord-266888-ryvk6mte author: Cai, Guoshuai title: Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2 date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-266888-ryvk6mte.txt cache: ./cache/cord-266888-ryvk6mte.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266888-ryvk6mte.txt' === file2bib.sh === id: cord-267013-nbwrl4g3 author: Ruan, R title: Subacute Thyroiditis might be a complication triggered by SARS-CoV-2 date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-267013-nbwrl4g3.txt cache: ./cache/cord-267013-nbwrl4g3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267013-nbwrl4g3.txt' === file2bib.sh === id: cord-266175-4jyltfus author: Brendish, Nathan J title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-266175-4jyltfus.txt cache: ./cache/cord-266175-4jyltfus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266175-4jyltfus.txt' === file2bib.sh === id: cord-265899-skpkuzyu author: Pryzdial, Edward L. G. title: Antiviral anticoagulation date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-265899-skpkuzyu.txt cache: ./cache/cord-265899-skpkuzyu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265899-skpkuzyu.txt' === file2bib.sh === id: cord-266648-962r0vm8 author: Grossberg, Laurie B title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-266648-962r0vm8.txt cache: ./cache/cord-266648-962r0vm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266648-962r0vm8.txt' === file2bib.sh === id: cord-266775-4npowkkz author: Xu, Jun title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 pages: extension: .txt txt: ./txt/cord-266775-4npowkkz.txt cache: ./cache/cord-266775-4npowkkz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266775-4npowkkz.txt' === file2bib.sh === id: cord-266616-boeb1xcp author: Liu, Yu title: Regulatory T cells: A potential weapon to combat COVID‐19? date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-266616-boeb1xcp.txt cache: ./cache/cord-266616-boeb1xcp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266616-boeb1xcp.txt' === file2bib.sh === id: cord-266923-hd1tjj6b author: Padroni, Marina title: Guillain-Barré syndrome following COVID-19: new infection, old complication? date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-266923-hd1tjj6b.txt cache: ./cache/cord-266923-hd1tjj6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-266923-hd1tjj6b.txt' === file2bib.sh === id: cord-266983-hpwebkbi author: Mallhi, Tauqeer Hussain title: Risks of Zoonotic Transmission of COVID-19 During Eid-Ul-Adha in Pakistan date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-266983-hpwebkbi.txt cache: ./cache/cord-266983-hpwebkbi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266983-hpwebkbi.txt' === file2bib.sh === id: cord-266866-z98x80zj author: Sohpal, Vipan Kumar title: Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-266866-z98x80zj.txt cache: ./cache/cord-266866-z98x80zj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266866-z98x80zj.txt' === file2bib.sh === id: cord-266156-xmf4emln author: Miller, Tyler E. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-266156-xmf4emln.txt cache: ./cache/cord-266156-xmf4emln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266156-xmf4emln.txt' === file2bib.sh === id: cord-267308-rgqjolue author: Crovetto, F. title: SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-267308-rgqjolue.txt cache: ./cache/cord-267308-rgqjolue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267308-rgqjolue.txt' === file2bib.sh === id: cord-267579-gkvd0fol author: Yang, Xiaoyu title: Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-267579-gkvd0fol.txt cache: ./cache/cord-267579-gkvd0fol.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267579-gkvd0fol.txt' === file2bib.sh === id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-266036-qhlo99l7.txt cache: ./cache/cord-266036-qhlo99l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266036-qhlo99l7.txt' === file2bib.sh === id: cord-266930-a1mzxmsb author: Rigatti, S. J. title: SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-266930-a1mzxmsb.txt cache: ./cache/cord-266930-a1mzxmsb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266930-a1mzxmsb.txt' === file2bib.sh === id: cord-266755-y2lf7ssp author: Yehualashet, Awgichew Shewasinad title: ACEIs and ARBs and Their Correlation with COVID-19: A Review date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-266755-y2lf7ssp.txt cache: ./cache/cord-266755-y2lf7ssp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266755-y2lf7ssp.txt' === file2bib.sh === id: cord-266988-72uvawth author: Barth, Rolf F. title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-266988-72uvawth.txt cache: ./cache/cord-266988-72uvawth.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266988-72uvawth.txt' === file2bib.sh === id: cord-267388-jz5mm91w author: Cheung, Szeya title: Recurrent Acute Pancreatitis in a Patient with COVID-19 Infection date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-267388-jz5mm91w.txt cache: ./cache/cord-267388-jz5mm91w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267388-jz5mm91w.txt' === file2bib.sh === id: cord-266903-lxtxqdst author: Lee, Jong-Hwan title: A novel rapid detection for SARS-CoV-2 spike 1 antigens using human angiotensin converting enzyme 2 (ACE2) date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-266903-lxtxqdst.txt cache: ./cache/cord-266903-lxtxqdst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266903-lxtxqdst.txt' === file2bib.sh === id: cord-266896-unb9yvjr author: Nihei, Yoshihito title: Continuous extracorporeal treatments in a dialysis patient with COVID-19 date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-266896-unb9yvjr.txt cache: ./cache/cord-266896-unb9yvjr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266896-unb9yvjr.txt' === file2bib.sh === id: cord-266702-6oxtlzqo author: Cristelo, Cecília title: SARS-CoV-2 and Diabetes: New Challenges for the Disease date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-266702-6oxtlzqo.txt cache: ./cache/cord-266702-6oxtlzqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266702-6oxtlzqo.txt' === file2bib.sh === id: cord-265233-v5sq5epy author: Cassorla, Lydia title: Decontamination and Reuse of N95 Filtering Facepiece Respirators: Where Do We Stand? date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-265233-v5sq5epy.txt cache: ./cache/cord-265233-v5sq5epy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265233-v5sq5epy.txt' === file2bib.sh === id: cord-265697-bbvlowyo author: Sang, Eric R. title: Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-265697-bbvlowyo.txt cache: ./cache/cord-265697-bbvlowyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265697-bbvlowyo.txt' === file2bib.sh === id: cord-265855-zf52vl11 author: Mayor-Ibarguren, Ander title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-265855-zf52vl11.txt cache: ./cache/cord-265855-zf52vl11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265855-zf52vl11.txt' === file2bib.sh === id: cord-266869-fs8dn7ir author: Kim, So Young title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-266869-fs8dn7ir.txt cache: ./cache/cord-266869-fs8dn7ir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266869-fs8dn7ir.txt' === file2bib.sh === id: cord-266914-3eatplc2 author: Wang, Yongjin title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date: 2010-06-02 pages: extension: .txt txt: ./txt/cord-266914-3eatplc2.txt cache: ./cache/cord-266914-3eatplc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266914-3eatplc2.txt' === file2bib.sh === id: cord-266052-rcuzi70u author: Liu, Lilong title: Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19 date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-266052-rcuzi70u.txt cache: ./cache/cord-266052-rcuzi70u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266052-rcuzi70u.txt' === file2bib.sh === id: cord-265887-g5zhoyo9 author: Mukherjee, Shruti title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-265887-g5zhoyo9.txt cache: ./cache/cord-265887-g5zhoyo9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265887-g5zhoyo9.txt' === file2bib.sh === id: cord-266558-vd41u2t1 author: Verdecchia, Paolo title: The pivotal link between ACE2 deficiency and SARS-CoV-2 infection date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-266558-vd41u2t1.txt cache: ./cache/cord-266558-vd41u2t1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266558-vd41u2t1.txt' === file2bib.sh === id: cord-267458-uofy7jyx author: Jiang, Xiao-Lin title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-267458-uofy7jyx.txt cache: ./cache/cord-267458-uofy7jyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267458-uofy7jyx.txt' === file2bib.sh === id: cord-267246-hq7g62p5 author: Huang, Su-Hua title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism date: 2015-07-31 pages: extension: .txt txt: ./txt/cord-267246-hq7g62p5.txt cache: ./cache/cord-267246-hq7g62p5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267246-hq7g62p5.txt' === file2bib.sh === id: cord-266444-rw94yls8 author: Dominguez Andres, Ana title: SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-266444-rw94yls8.txt cache: ./cache/cord-266444-rw94yls8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266444-rw94yls8.txt' === file2bib.sh === id: cord-267666-i7uuf3ck author: Sarkar, Bishajit title: Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-267666-i7uuf3ck.txt cache: ./cache/cord-267666-i7uuf3ck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267666-i7uuf3ck.txt' === file2bib.sh === id: cord-267373-nzxbogga author: Antinori, Spinello title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-267373-nzxbogga.txt cache: ./cache/cord-267373-nzxbogga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267373-nzxbogga.txt' === file2bib.sh === id: cord-266308-fjpq1ljp author: Mondal, Priya title: Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-266308-fjpq1ljp.txt cache: ./cache/cord-266308-fjpq1ljp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266308-fjpq1ljp.txt' === file2bib.sh === id: cord-267587-hag6qydb author: Lau, Susanna K.P. title: Engineering Coronaviruses to Evaluate Emergence and Pathogenic Potential date: 2016-04-16 pages: extension: .txt txt: ./txt/cord-267587-hag6qydb.txt cache: ./cache/cord-267587-hag6qydb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267587-hag6qydb.txt' === file2bib.sh === id: cord-266313-b518n9dx author: Cao, Yu-chen title: Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-266313-b518n9dx.txt cache: ./cache/cord-266313-b518n9dx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266313-b518n9dx.txt' === file2bib.sh === id: cord-266987-ikt8r2o1 author: Loeffelholz, Michael J. title: Laboratory diagnosis of emerging human coronavirus infections – the state of the art date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-266987-ikt8r2o1.txt cache: ./cache/cord-266987-ikt8r2o1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266987-ikt8r2o1.txt' === file2bib.sh === id: cord-266710-3wdy16tw author: Fintelman-Rodrigues, Natalia title: Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-266710-3wdy16tw.txt cache: ./cache/cord-266710-3wdy16tw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266710-3wdy16tw.txt' === file2bib.sh === id: cord-267307-kyh0xsrp author: Kasting, Monica L. title: Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-267307-kyh0xsrp.txt cache: ./cache/cord-267307-kyh0xsrp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267307-kyh0xsrp.txt' === file2bib.sh === id: cord-267476-j59tm40d author: Yong, Sarah Ee Fang title: Connecting clusters of COVID-19: an epidemiological and serological investigation date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-267476-j59tm40d.txt cache: ./cache/cord-267476-j59tm40d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267476-j59tm40d.txt' === file2bib.sh === id: cord-267136-1abp6oom author: Lan, Yu-Ching title: Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan date: 2004-12-07 pages: extension: .txt txt: ./txt/cord-267136-1abp6oom.txt cache: ./cache/cord-267136-1abp6oom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267136-1abp6oom.txt' === file2bib.sh === id: cord-267744-asjvf123 author: Lee, Yu-Ching title: Chicken single-chain variable fragments against the SARS-CoV spike protein date: 2007-07-23 pages: extension: .txt txt: ./txt/cord-267744-asjvf123.txt cache: ./cache/cord-267744-asjvf123.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267744-asjvf123.txt' === file2bib.sh === id: cord-267887-ntwvquqz author: Yang, Ren title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-267887-ntwvquqz.txt cache: ./cache/cord-267887-ntwvquqz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267887-ntwvquqz.txt' === file2bib.sh === id: cord-267511-tb69dwg8 author: Talebian, Sepehr title: Why Go NANO on COVID-19 Pandemic? date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-267511-tb69dwg8.txt cache: ./cache/cord-267511-tb69dwg8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267511-tb69dwg8.txt' === file2bib.sh === id: cord-266031-tlrsco40 author: Haghani, Milad title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCoV literature date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-266031-tlrsco40.txt cache: ./cache/cord-266031-tlrsco40.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266031-tlrsco40.txt' === file2bib.sh === id: cord-267134-5gz2dotn author: Sallenave, Jean-Michel title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-267134-5gz2dotn.txt cache: ./cache/cord-267134-5gz2dotn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267134-5gz2dotn.txt' === file2bib.sh === id: cord-267845-18hb5ndr author: Resende, Paola Cristina title: SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-267845-18hb5ndr.txt cache: ./cache/cord-267845-18hb5ndr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267845-18hb5ndr.txt' === file2bib.sh === id: cord-267831-uu883ofc author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-267831-uu883ofc.txt cache: ./cache/cord-267831-uu883ofc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267831-uu883ofc.txt' === file2bib.sh === id: cord-267917-belkwihy author: Peters, Alexandra title: Putting some context to the aerosolization debate around SARS-CoV-2 date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-267917-belkwihy.txt cache: ./cache/cord-267917-belkwihy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267917-belkwihy.txt' === file2bib.sh === id: cord-267588-ruuzr6l1 author: Garnett, Lauren title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-267588-ruuzr6l1.txt cache: ./cache/cord-267588-ruuzr6l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267588-ruuzr6l1.txt' === file2bib.sh === id: cord-267426-3eu9umx5 author: Yao, Hangping title: Patient-derived mutations impact pathogenicity of SARS-CoV-2 date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-267426-3eu9umx5.txt cache: ./cache/cord-267426-3eu9umx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267426-3eu9umx5.txt' === file2bib.sh === id: cord-267115-6jqdi417 author: Giobbe, Giovanni Giuseppe title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-267115-6jqdi417.txt cache: ./cache/cord-267115-6jqdi417.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267115-6jqdi417.txt' === file2bib.sh === id: cord-267770-ik1ib3zb author: Koo, Hyun Jung title: RadioGraphics Update: Radiographic and CT Features of Viral Pneumonia date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-267770-ik1ib3zb.txt cache: ./cache/cord-267770-ik1ib3zb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267770-ik1ib3zb.txt' === file2bib.sh === id: cord-267124-8efdzlc0 author: Wichmann, Dominic title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-267124-8efdzlc0.txt cache: ./cache/cord-267124-8efdzlc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267124-8efdzlc0.txt' === file2bib.sh === id: cord-267762-mzon01fd author: Ferreira, A. title: Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection. date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-267762-mzon01fd.txt cache: ./cache/cord-267762-mzon01fd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267762-mzon01fd.txt' === file2bib.sh === id: cord-267509-w7nfbnbb author: Tian, Yuan title: Review article: gastrointestinal features in COVID‐19 and the possibility of faecal transmission date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-267509-w7nfbnbb.txt cache: ./cache/cord-267509-w7nfbnbb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267509-w7nfbnbb.txt' === file2bib.sh === id: cord-267566-gdjl0qmu author: Kweon, Oh Joo title: Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-267566-gdjl0qmu.txt cache: ./cache/cord-267566-gdjl0qmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267566-gdjl0qmu.txt' === file2bib.sh === id: cord-267610-bzbr9ios author: Anastassopoulou, Cleo title: SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-267610-bzbr9ios.txt cache: ./cache/cord-267610-bzbr9ios.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267610-bzbr9ios.txt' === file2bib.sh === id: cord-267402-kca05rvz author: South, Kieron title: Preceding infection and risk of stroke: An old concept revived by the COVID-19 pandemic date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-267402-kca05rvz.txt cache: ./cache/cord-267402-kca05rvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267402-kca05rvz.txt' === file2bib.sh === id: cord-268034-7id7sfsu author: Auerswald, Heidi title: Assessment of Inactivation Procedures for SARS-CoV-2 date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-268034-7id7sfsu.txt cache: ./cache/cord-268034-7id7sfsu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268034-7id7sfsu.txt' === file2bib.sh === id: cord-267723-loj718vd author: Kloc, Małgorzata title: Macrophages in diabetes mellitus (DM) and COVID-19: do they trigger DM? date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-267723-loj718vd.txt cache: ./cache/cord-267723-loj718vd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267723-loj718vd.txt' === file2bib.sh === id: cord-264814-v4wnmg03 author: Flanagan, Katie L. title: Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-264814-v4wnmg03.txt cache: ./cache/cord-264814-v4wnmg03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264814-v4wnmg03.txt' === file2bib.sh === id: cord-267261-8z4aqfff author: Su, John R. title: Emerging viral infections date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-267261-8z4aqfff.txt cache: ./cache/cord-267261-8z4aqfff.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267261-8z4aqfff.txt' === file2bib.sh === id: cord-267397-b7ogeokm author: Smith, E. R. title: Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-267397-b7ogeokm.txt cache: ./cache/cord-267397-b7ogeokm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267397-b7ogeokm.txt' === file2bib.sh === id: cord-267533-nmgtan4e author: Hu, Zhigang title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-267533-nmgtan4e.txt cache: ./cache/cord-267533-nmgtan4e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267533-nmgtan4e.txt' === file2bib.sh === id: cord-267690-g0kesgjm author: Mueller, Sarina K. title: Considerations for Continuing Semielective and Emergency Otolaryngological Procedures During the COVID-19 Pandemic date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-267690-g0kesgjm.txt cache: ./cache/cord-267690-g0kesgjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267690-g0kesgjm.txt' === file2bib.sh === id: cord-267815-4fw7xgnt author: Peña, Juan A. title: A Survey of Labor and Delivery Practices in New York City during the COVID-19 Pandemic date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-267815-4fw7xgnt.txt cache: ./cache/cord-267815-4fw7xgnt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267815-4fw7xgnt.txt' === file2bib.sh === id: cord-268329-apl6n6jl author: Antunes, Douglas Eulálio title: Will cases of leprosy reaction increase with COVID-19 infection? date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-268329-apl6n6jl.txt cache: ./cache/cord-268329-apl6n6jl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268329-apl6n6jl.txt' === file2bib.sh === id: cord-268340-xwj8ge5t author: Ozaki, Masayuki title: Reducing Aerosol Generation During Ventilator Weaning in a Coronavirus Disease 2019 Patient Using a Supraglottic Airway: A Case Report date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-268340-xwj8ge5t.txt cache: ./cache/cord-268340-xwj8ge5t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268340-xwj8ge5t.txt' === file2bib.sh === id: cord-268335-mfcjldu3 author: Dimeglio, Chloé title: Children are protected against SARS-CoV-2 infection date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-268335-mfcjldu3.txt cache: ./cache/cord-268335-mfcjldu3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268335-mfcjldu3.txt' === file2bib.sh === id: cord-268406-3v309r41 author: Grajewski, Rafael S. title: A missing link between SARS‐CoV‐2 and the eye?: ACE2 expression on the ocular surface date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-268406-3v309r41.txt cache: ./cache/cord-268406-3v309r41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268406-3v309r41.txt' === file2bib.sh === id: cord-267735-y3832u9e author: Sun, Wuping title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-267735-y3832u9e.txt cache: ./cache/cord-267735-y3832u9e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267735-y3832u9e.txt' === file2bib.sh === id: cord-266307-w56rii2p author: Acheampong, Desmond Omane title: Male Predisposition to Severe COVID-19: Review of Evidence and Potential Therapeutic Prospects date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-266307-w56rii2p.txt cache: ./cache/cord-266307-w56rii2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266307-w56rii2p.txt' === file2bib.sh === id: cord-267436-mivxm8oh author: Groneberg, David A title: Treatment and vaccines for severe acute respiratory syndrome date: 2005-03-10 pages: extension: .txt txt: ./txt/cord-267436-mivxm8oh.txt cache: ./cache/cord-267436-mivxm8oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267436-mivxm8oh.txt' === file2bib.sh === id: cord-267971-xgwmda8e author: Tan, Shing Cheng title: Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-267971-xgwmda8e.txt cache: ./cache/cord-267971-xgwmda8e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267971-xgwmda8e.txt' === file2bib.sh === id: cord-268075-kbislbx0 author: Song, Limin title: Cardiovascular Changes in Patients With COVID-19 From Wuhan, China date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-268075-kbislbx0.txt cache: ./cache/cord-268075-kbislbx0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268075-kbislbx0.txt' === file2bib.sh === id: cord-267856-t3ksa18w author: Funk, Colin D. title: A Novel Strategy to Mitigate the Hyperinflammatory Response to COVID-19 by Targeting Leukotrienes date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-267856-t3ksa18w.txt cache: ./cache/cord-267856-t3ksa18w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267856-t3ksa18w.txt' === file2bib.sh === id: cord-268390-npuvodd4 author: Rehman, Aziz ul title: The role of primary and secondary bio-molecules in optical diagnosis of pandemic COVID-19 outbreak date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-268390-npuvodd4.txt cache: ./cache/cord-268390-npuvodd4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268390-npuvodd4.txt' === file2bib.sh === id: cord-268169-xry3nhzt author: Couturier, Aymeric title: Indirect effects of severe acute respiratory syndrome coronavirus 2 on the kidney in coronavirus disease patients date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-268169-xry3nhzt.txt cache: ./cache/cord-268169-xry3nhzt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268169-xry3nhzt.txt' === file2bib.sh === id: cord-268211-egy8rgtl author: Barrasa, Helena title: SARS-Cov-2 in Spanish Intensive Care: Early Experience with 15-day Survival In Vitoria date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-268211-egy8rgtl.txt cache: ./cache/cord-268211-egy8rgtl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268211-egy8rgtl.txt' === file2bib.sh === id: cord-268085-vpzrk8u7 author: Mandal, Amrendra title: Gastrointestinal Manifestations in COVID-19 Infection and Its Practical Applications date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-268085-vpzrk8u7.txt cache: ./cache/cord-268085-vpzrk8u7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268085-vpzrk8u7.txt' === file2bib.sh === id: cord-268468-036i1082 author: Asif, Muhammad title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-268468-036i1082.txt cache: ./cache/cord-268468-036i1082.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268468-036i1082.txt' === file2bib.sh === id: cord-268193-xwptzgvl author: Wang, Tzong-Luen title: Establishing a clinical decision rule of severe acute respiratory syndrome at the emergency department() date: 2003-12-29 pages: extension: .txt txt: ./txt/cord-268193-xwptzgvl.txt cache: ./cache/cord-268193-xwptzgvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268193-xwptzgvl.txt' === file2bib.sh === id: cord-268476-3lxsh1zz author: Skoog, Hunter title: Tracheotomy in the SARS‐CoV‐2 pandemic date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-268476-3lxsh1zz.txt cache: ./cache/cord-268476-3lxsh1zz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268476-3lxsh1zz.txt' === file2bib.sh === id: cord-268484-hf4zflsy author: Davanzo, Riccardo title: Breast feeding at the time of COVID-19: do not forget expressed mother’s milk, please date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-268484-hf4zflsy.txt cache: ./cache/cord-268484-hf4zflsy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268484-hf4zflsy.txt' === file2bib.sh === id: cord-268098-71g1w1mc author: Beckman, M. F. title: Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-268098-71g1w1mc.txt cache: ./cache/cord-268098-71g1w1mc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268098-71g1w1mc.txt' === file2bib.sh === id: cord-267960-r5m7o9dp author: Hourdel, Véronique title: Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-267960-r5m7o9dp.txt cache: ./cache/cord-267960-r5m7o9dp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267960-r5m7o9dp.txt' === file2bib.sh === id: cord-268144-maa8c4a4 author: Zhang, Yuan title: Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization date: 2007-02-17 pages: extension: .txt txt: ./txt/cord-268144-maa8c4a4.txt cache: ./cache/cord-268144-maa8c4a4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268144-maa8c4a4.txt' === file2bib.sh === id: cord-268750-kox3uah2 author: Wong, S. F. title: Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures date: 2004-01-08 pages: extension: .txt txt: ./txt/cord-268750-kox3uah2.txt cache: ./cache/cord-268750-kox3uah2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268750-kox3uah2.txt' === file2bib.sh === id: cord-268065-mxvbbkc4 author: Wei, Maoti title: Epidemiology of Coronavirus Disease 2019 (COVID-19) Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-268065-mxvbbkc4.txt cache: ./cache/cord-268065-mxvbbkc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268065-mxvbbkc4.txt' === file2bib.sh === id: cord-268572-uhak283t author: Woo, Marcel S. title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-268572-uhak283t.txt cache: ./cache/cord-268572-uhak283t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268572-uhak283t.txt' === file2bib.sh === id: cord-268339-jxm69ndw author: Karamitros, Timokratis title: SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date: 2020-03-28 pages: extension: .txt txt: ./txt/cord-268339-jxm69ndw.txt cache: ./cache/cord-268339-jxm69ndw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268339-jxm69ndw.txt' === file2bib.sh === id: cord-267782-4pjfnund author: Lan, Fan-Yun title: Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-267782-4pjfnund.txt cache: ./cache/cord-267782-4pjfnund.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267782-4pjfnund.txt' === file2bib.sh === id: cord-268074-9mact9br author: Bi, Qifang title: Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-268074-9mact9br.txt cache: ./cache/cord-268074-9mact9br.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268074-9mact9br.txt' === file2bib.sh === id: cord-269001-m4mpcoab author: Zullo, Fabrizio title: COVID-19 Antibody Testing in Pregnancy date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-269001-m4mpcoab.txt cache: ./cache/cord-269001-m4mpcoab.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269001-m4mpcoab.txt' === file2bib.sh === id: cord-268049-7xqln70d author: Montrief, Tim title: COVID-19 respiratory support in the emergency department setting date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-268049-7xqln70d.txt cache: ./cache/cord-268049-7xqln70d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268049-7xqln70d.txt' === file2bib.sh === id: cord-268370-kfjujs4z author: Huang, Yu-Tung title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study date: 2009-05-31 pages: extension: .txt txt: ./txt/cord-268370-kfjujs4z.txt cache: ./cache/cord-268370-kfjujs4z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268370-kfjujs4z.txt' === file2bib.sh === id: cord-268755-13xmmin1 author: Meltzer, Martin I. title: Multiple Contact Dates and SARS Incubation Periods date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-268755-13xmmin1.txt cache: ./cache/cord-268755-13xmmin1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-268755-13xmmin1.txt' === file2bib.sh === id: cord-268254-1mg7a17c author: Liu, Li title: High neutralizing antibody titer in intensive care unit patients with COVID-19 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-268254-1mg7a17c.txt cache: ./cache/cord-268254-1mg7a17c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268254-1mg7a17c.txt' === file2bib.sh === id: cord-268140-s5lailkp author: Atal, Shubham title: IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising Therapy? date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-268140-s5lailkp.txt cache: ./cache/cord-268140-s5lailkp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268140-s5lailkp.txt' === file2bib.sh === id: cord-268653-mje0rysp author: Chen, Miaomiao title: Changes in physiology and immune system during pregnancy and coronavirus infection: a review date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-268653-mje0rysp.txt cache: ./cache/cord-268653-mje0rysp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268653-mje0rysp.txt' === file2bib.sh === id: cord-268740-ldz5366v author: Sun, Mei title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-268740-ldz5366v.txt cache: ./cache/cord-268740-ldz5366v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268740-ldz5366v.txt' === file2bib.sh === id: cord-268071-ow2aijmj author: Pachetti, Maria title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-268071-ow2aijmj.txt cache: ./cache/cord-268071-ow2aijmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268071-ow2aijmj.txt' === file2bib.sh === id: cord-268760-31i0mpvn author: Zhang, Qian title: Anosmia and Ageusia as the Only Indicators of Coronavirus Disease 2019 (COVID-19) date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-268760-31i0mpvn.txt cache: ./cache/cord-268760-31i0mpvn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268760-31i0mpvn.txt' === file2bib.sh === id: cord-268492-0rbmqarx author: Alberer, Martin title: Cats and kids: how a feline disease may help us unravel COVID-19 associated paediatric hyperinflammatory syndrome date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-268492-0rbmqarx.txt cache: ./cache/cord-268492-0rbmqarx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268492-0rbmqarx.txt' === file2bib.sh === id: cord-268453-87b298uk author: Ibáñez, Sebastián title: Hydroxychloroquine and chloroquine in COVID-19: should they be used as standard therapy? date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-268453-87b298uk.txt cache: ./cache/cord-268453-87b298uk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268453-87b298uk.txt' === file2bib.sh === id: cord-268283-eja8fkwv author: Iftikhar, Hafsa title: Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-268283-eja8fkwv.txt cache: ./cache/cord-268283-eja8fkwv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268283-eja8fkwv.txt' === file2bib.sh === id: cord-268935-4obwu75u author: Lepak, Alexander J. title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-268935-4obwu75u.txt cache: ./cache/cord-268935-4obwu75u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268935-4obwu75u.txt' === file2bib.sh === id: cord-268330-mo5myrz4 author: Gentile, Pietro title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-268330-mo5myrz4.txt cache: ./cache/cord-268330-mo5myrz4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268330-mo5myrz4.txt' === file2bib.sh === id: cord-268324-86a0n0dc author: Charitos, Ioannis A title: Special features of SARS-CoV-2 in daily practice date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-268324-86a0n0dc.txt cache: ./cache/cord-268324-86a0n0dc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268324-86a0n0dc.txt' === file2bib.sh === id: cord-268425-xg8xnjf9 author: DiNicolantonio, James J. title: Harnessing Adenosine A2A Receptors as a Strategy for Suppressing the Lung Inflammation and Thrombotic Complications of COVID-19: Potential of Pentoxifylline and Dipyridamole date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-268425-xg8xnjf9.txt cache: ./cache/cord-268425-xg8xnjf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268425-xg8xnjf9.txt' === file2bib.sh === id: cord-268206-ino9srb6 author: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-268206-ino9srb6.txt cache: ./cache/cord-268206-ino9srb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268206-ino9srb6.txt' === file2bib.sh === id: cord-268827-qwcbvtna author: Ibanez, Agustin title: COVID-19 in older people with cognitive impairment in Latin America date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-268827-qwcbvtna.txt cache: ./cache/cord-268827-qwcbvtna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268827-qwcbvtna.txt' === file2bib.sh === id: cord-267482-afqfymbq author: Ryu, Seungjin title: Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-267482-afqfymbq.txt cache: ./cache/cord-267482-afqfymbq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-267482-afqfymbq.txt' === file2bib.sh === id: cord-267613-hsc2x36j author: Dittmar, Mark title: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-267613-hsc2x36j.txt cache: ./cache/cord-267613-hsc2x36j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267613-hsc2x36j.txt' === file2bib.sh === id: cord-268224-5tbb8df1 author: Di Gioacchino, Andrea title: The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-268224-5tbb8df1.txt cache: ./cache/cord-268224-5tbb8df1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268224-5tbb8df1.txt' === file2bib.sh === id: cord-268894-amfv3z2y author: Nguyen-Contant, Phuong title: S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-268894-amfv3z2y.txt cache: ./cache/cord-268894-amfv3z2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268894-amfv3z2y.txt' === file2bib.sh === id: cord-268501-z4oztgi0 author: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-268501-z4oztgi0.txt cache: ./cache/cord-268501-z4oztgi0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268501-z4oztgi0.txt' === file2bib.sh === id: cord-269009-0i2bvt77 author: D’Souza, Rohan title: A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID‐19 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-269009-0i2bvt77.txt cache: ./cache/cord-269009-0i2bvt77.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269009-0i2bvt77.txt' === file2bib.sh === id: cord-269071-jbxbknyt author: Giorgianni, Andrea title: Transient acute-onset tetraparesis in a COVID-19 patient date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-269071-jbxbknyt.txt cache: ./cache/cord-269071-jbxbknyt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269071-jbxbknyt.txt' === file2bib.sh === id: cord-268886-mpceglk1 author: Bourne, T. title: ISUOG Consensus Statement on rationalization of gynecological ultrasound services in context of SARS‐CoV‐2 date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-268886-mpceglk1.txt cache: ./cache/cord-268886-mpceglk1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268886-mpceglk1.txt' === file2bib.sh === id: cord-268895-m97zsodx author: Duan, Ping title: Safety considerations during return to work in the context of stable COVID-19 epidemic control: an analysis of health screening results of all returned staff from a hospital date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-268895-m97zsodx.txt cache: ./cache/cord-268895-m97zsodx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268895-m97zsodx.txt' === file2bib.sh === id: cord-268661-a56u5e2o author: Nadeau, S. A. title: The origin and early spread of SARS-CoV-2 in Europe date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-268661-a56u5e2o.txt cache: ./cache/cord-268661-a56u5e2o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268661-a56u5e2o.txt' === file2bib.sh === id: cord-268970-uz7q6z2f author: Ott, Isabel M. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-268970-uz7q6z2f.txt cache: ./cache/cord-268970-uz7q6z2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268970-uz7q6z2f.txt' === file2bib.sh === id: cord-269202-re2djjrc author: Sapino, Anna title: The autopsy debate during the COVID-19 emergency: the Italian experience date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-269202-re2djjrc.txt cache: ./cache/cord-269202-re2djjrc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269202-re2djjrc.txt' === file2bib.sh === id: cord-269283-jm18lj5t author: Uddin, Md Bashir title: Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-269283-jm18lj5t.txt cache: ./cache/cord-269283-jm18lj5t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269283-jm18lj5t.txt' === file2bib.sh === id: cord-269130-zsem29ss author: Lingappan, K. title: Understanding the age divide in COVID-19: why are children overwhelmingly spared? date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-269130-zsem29ss.txt cache: ./cache/cord-269130-zsem29ss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269130-zsem29ss.txt' === file2bib.sh === id: cord-268809-plgip4h6 author: Bielecki, Michel title: Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-268809-plgip4h6.txt cache: ./cache/cord-268809-plgip4h6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268809-plgip4h6.txt' === file2bib.sh === id: cord-269377-ylgyvxtd author: Matos, Ana R. title: COVID-19 Associated Central Nervous System Vasculopathy date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-269377-ylgyvxtd.txt cache: ./cache/cord-269377-ylgyvxtd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269377-ylgyvxtd.txt' === file2bib.sh === id: cord-269114-mdsiv6tr author: Pattabiraman, C. title: Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-269114-mdsiv6tr.txt cache: ./cache/cord-269114-mdsiv6tr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269114-mdsiv6tr.txt' === file2bib.sh === id: cord-269143-8j3m03gc author: Brindisi, Giulia title: Pills to think about in allergic rhinitis children during COVID‐19 era date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-269143-8j3m03gc.txt cache: ./cache/cord-269143-8j3m03gc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269143-8j3m03gc.txt' === file2bib.sh === id: cord-268817-wx96wwpg author: Karp, Donna Grace title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-268817-wx96wwpg.txt cache: ./cache/cord-268817-wx96wwpg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268817-wx96wwpg.txt' === file2bib.sh === id: cord-269021-juh2qkm0 author: Bai, Zhihua title: The Rapid Assessment and Early Warning Models for COVID-19 date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-269021-juh2qkm0.txt cache: ./cache/cord-269021-juh2qkm0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269021-juh2qkm0.txt' === file2bib.sh === id: cord-269568-vwkawh6x author: Ten Hulzen, Richard D. title: Impact of Hearing Loss and Universal Face Masking in the COVID-19 Era. date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-269568-vwkawh6x.txt cache: ./cache/cord-269568-vwkawh6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269568-vwkawh6x.txt' === file2bib.sh === id: cord-269187-lt0uo7q3 author: Saha, Indrajit title: Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-269187-lt0uo7q3.txt cache: ./cache/cord-269187-lt0uo7q3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269187-lt0uo7q3.txt' === file2bib.sh === id: cord-268939-ws74xprt author: Ozoner, Baris title: Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-268939-ws74xprt.txt cache: ./cache/cord-268939-ws74xprt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268939-ws74xprt.txt' === file2bib.sh === id: cord-269555-29t956ik author: Zaconeta, Alberto title: Letter to the editor“SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?” date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-269555-29t956ik.txt cache: ./cache/cord-269555-29t956ik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269555-29t956ik.txt' === file2bib.sh === id: cord-270015-5gtxfkoz author: Mahmood Shah, Sayed Mustafa title: Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-270015-5gtxfkoz.txt cache: ./cache/cord-270015-5gtxfkoz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270015-5gtxfkoz.txt' === file2bib.sh === id: cord-268718-tt07cwrf author: Tan, Heng Wee title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-268718-tt07cwrf.txt cache: ./cache/cord-268718-tt07cwrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268718-tt07cwrf.txt' === file2bib.sh === id: cord-269553-d3hozs14 author: Khan, Suliman title: The spread of novel coronavirus has created an alarming situation worldwide date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-269553-d3hozs14.txt cache: ./cache/cord-269553-d3hozs14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269553-d3hozs14.txt' === file2bib.sh === id: cord-268645-5op2m7pu author: Wu, Zhiqiang title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 pages: extension: .txt txt: ./txt/cord-268645-5op2m7pu.txt cache: ./cache/cord-268645-5op2m7pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268645-5op2m7pu.txt' === file2bib.sh === id: cord-268622-3jireyep author: Babadaei, Mohammad Mahdi Nejadi title: The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-268622-3jireyep.txt cache: ./cache/cord-268622-3jireyep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268622-3jireyep.txt' === file2bib.sh === id: cord-269902-sbp18486 author: Springer, Steffen title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-269902-sbp18486.txt cache: ./cache/cord-269902-sbp18486.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269902-sbp18486.txt' === file2bib.sh === id: cord-269521-vq2m4c8q author: Lucchese, Guglielmo title: Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-269521-vq2m4c8q.txt cache: ./cache/cord-269521-vq2m4c8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269521-vq2m4c8q.txt' === file2bib.sh === id: cord-269488-7fy6exsd author: Zhen, Wei title: Development of a New Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-269488-7fy6exsd.txt cache: ./cache/cord-269488-7fy6exsd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269488-7fy6exsd.txt' === file2bib.sh === id: cord-269718-e1mxmo3a author: Wang, Jingquan title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-269718-e1mxmo3a.txt cache: ./cache/cord-269718-e1mxmo3a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269718-e1mxmo3a.txt' === file2bib.sh === id: cord-269383-1tyorrb0 author: Lai, Christopher K C title: Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-269383-1tyorrb0.txt cache: ./cache/cord-269383-1tyorrb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269383-1tyorrb0.txt' === file2bib.sh === id: cord-269474-94c1mudi author: Nasef, Nehad title: Lessons from SARS: A retrospective study of outpatient care during an infectious disease outbreak date: 2010-07-20 pages: extension: .txt txt: ./txt/cord-269474-94c1mudi.txt cache: ./cache/cord-269474-94c1mudi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269474-94c1mudi.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-269519-8hr8wyrr author: Hirotsu, Yosuke title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-269519-8hr8wyrr.txt cache: ./cache/cord-269519-8hr8wyrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269519-8hr8wyrr.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-269206-160ddfsc author: Ceylan, Rahmiye Figen title: Historical evidence for economic effects of COVID-19 date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-269206-160ddfsc.txt cache: ./cache/cord-269206-160ddfsc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269206-160ddfsc.txt' === file2bib.sh === id: cord-269087-f9hyntvf author: Li, X. title: A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19 date: 2020-04-04 pages: extension: .txt txt: ./txt/cord-269087-f9hyntvf.txt cache: ./cache/cord-269087-f9hyntvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269087-f9hyntvf.txt' === file2bib.sh === id: cord-269454-9gthf2jl author: Kulkarni, Rajesh title: Early-onset symptomatic neonatal COVID-19 infection with high probability of vertical transmission date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-269454-9gthf2jl.txt cache: ./cache/cord-269454-9gthf2jl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269454-9gthf2jl.txt' === file2bib.sh === id: cord-268483-joiajgs4 author: Shah, Vibhuti Kumar title: Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-268483-joiajgs4.txt cache: ./cache/cord-268483-joiajgs4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268483-joiajgs4.txt' === file2bib.sh === id: cord-269025-2j37561h author: Pratelli, Annamaria title: Canine coronavirus inactivation with physical and chemical agents date: 2007-05-21 pages: extension: .txt txt: ./txt/cord-269025-2j37561h.txt cache: ./cache/cord-269025-2j37561h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269025-2j37561h.txt' === file2bib.sh === id: cord-269275-b7xxk48t author: Tang, Xiaojia title: Neurological manifestations in COVID-19 and its possible mechanism date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-269275-b7xxk48t.txt cache: ./cache/cord-269275-b7xxk48t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269275-b7xxk48t.txt' === file2bib.sh === id: cord-268561-vq1uhj5i author: da Silva, Severino Jefferson Ribeiro title: Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19 date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-268561-vq1uhj5i.txt cache: ./cache/cord-268561-vq1uhj5i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268561-vq1uhj5i.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-269470-emzr3dzb author: Menéndez, Cintia A. title: Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-269470-emzr3dzb.txt cache: ./cache/cord-269470-emzr3dzb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269470-emzr3dzb.txt' === file2bib.sh === id: cord-269766-arjoemla author: Dutescu, R. Michael title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-269766-arjoemla.txt cache: ./cache/cord-269766-arjoemla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269766-arjoemla.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-269526-3npk3u5t author: Dehghanbanadaki, Hojat title: Bibliometric analysis of global scientific research on Coronavirus (COVID-19) date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-269526-3npk3u5t.txt cache: ./cache/cord-269526-3npk3u5t.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269526-3npk3u5t.txt' === file2bib.sh === id: cord-269973-sntnmqqd author: To, Kelvin Kai-Wang title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-269973-sntnmqqd.txt cache: ./cache/cord-269973-sntnmqqd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269973-sntnmqqd.txt' === file2bib.sh === id: cord-268795-tjmx6msm author: Sardar, Rahila title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date: 2020-03-21 pages: extension: .txt txt: ./txt/cord-268795-tjmx6msm.txt cache: ./cache/cord-268795-tjmx6msm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268795-tjmx6msm.txt' === file2bib.sh === id: cord-270257-5f95gve3 author: Jeon, Sangeun title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date: 2020-03-28 pages: extension: .txt txt: ./txt/cord-270257-5f95gve3.txt cache: ./cache/cord-270257-5f95gve3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270257-5f95gve3.txt' === file2bib.sh === id: cord-269408-6qncy0nd author: Khonyongwa, Kirstin title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-269408-6qncy0nd.txt cache: ./cache/cord-269408-6qncy0nd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269408-6qncy0nd.txt' === file2bib.sh === id: cord-269946-zb7gcw0m author: Boscolo-Rizzo, Paolo title: New onset of loss of smell or taste in household contacts of home-isolated SARS-CoV-2-positive subjects date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-269946-zb7gcw0m.txt cache: ./cache/cord-269946-zb7gcw0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269946-zb7gcw0m.txt' === file2bib.sh === id: cord-269825-k685efoh author: Hu, Parker title: Early comprehensive testing for COVID-19 is essential to protect trauma centers date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-269825-k685efoh.txt cache: ./cache/cord-269825-k685efoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269825-k685efoh.txt' === file2bib.sh === id: cord-269234-8twdx4g2 author: Koyama, Takahiko title: Variant analysis of SARS-CoV-2 genomes date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-269234-8twdx4g2.txt cache: ./cache/cord-269234-8twdx4g2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269234-8twdx4g2.txt' === file2bib.sh === id: cord-269289-6uog10j4 author: Mabillard, Holly title: Electrolyte Disturbances in SARS-CoV-2 Infection date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-269289-6uog10j4.txt cache: ./cache/cord-269289-6uog10j4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269289-6uog10j4.txt' === file2bib.sh === id: cord-270112-o2exvfy5 author: Ferrarese, Carlo title: An Italian multicenter retrospective-prospective observational study on neurological manifestations of COVID-19 (NEUROCOVID) date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-270112-o2exvfy5.txt cache: ./cache/cord-270112-o2exvfy5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270112-o2exvfy5.txt' === file2bib.sh === id: cord-270635-l8380adr author: Maggi, Enrico title: COVID-19: unanswered questions on immune response and pathogenesis date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-270635-l8380adr.txt cache: ./cache/cord-270635-l8380adr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270635-l8380adr.txt' === file2bib.sh === id: cord-270329-t60t639i author: Schloer, Sebastian title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-270329-t60t639i.txt cache: ./cache/cord-270329-t60t639i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270329-t60t639i.txt' === file2bib.sh === id: cord-269612-pmzdovna author: Pennington, Hugh title: Politics, media and microbiologists date: 2004 pages: extension: .txt txt: ./txt/cord-269612-pmzdovna.txt cache: ./cache/cord-269612-pmzdovna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269612-pmzdovna.txt' === file2bib.sh === id: cord-269496-tnw7sxlh author: Sen Gupta, Parth Sarthi title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-269496-tnw7sxlh.txt cache: ./cache/cord-269496-tnw7sxlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269496-tnw7sxlh.txt' === file2bib.sh === id: cord-269213-tsm6zoe3 author: Slaughter, Laura title: A framework for capturing the interactions between laypersons’ understanding of disease, information gathering behaviors, and actions taken during an epidemic date: 2005-01-30 pages: extension: .txt txt: ./txt/cord-269213-tsm6zoe3.txt cache: ./cache/cord-269213-tsm6zoe3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269213-tsm6zoe3.txt' === file2bib.sh === id: cord-269045-i7vijtol author: Martínez‐Murcia, A. title: Comparative in silico design and validation of GPS™ CoVID‐19 dtec‐RT‐qPCR test date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-269045-i7vijtol.txt cache: ./cache/cord-269045-i7vijtol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269045-i7vijtol.txt' === file2bib.sh === id: cord-270355-5mljrk1h author: Fontanet, Arnaud title: Les enseignements du SRAS date: 2007-02-28 pages: extension: .txt txt: ./txt/cord-270355-5mljrk1h.txt cache: ./cache/cord-270355-5mljrk1h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270355-5mljrk1h.txt' === file2bib.sh === id: cord-269563-2979u47a author: Caetano Silva-Filho, José title: The influence of ABO blood groups on COVID-19 susceptibility and severity: a molecular hypothesis based on carbohydrate-carbohydrate interactions date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-269563-2979u47a.txt cache: ./cache/cord-269563-2979u47a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269563-2979u47a.txt' === file2bib.sh === id: cord-268874-ldja6aa4 author: Park, Sun Hee title: Personal Protective Equipment for Healthcare Workers during the COVID-19 Pandemic date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-268874-ldja6aa4.txt cache: ./cache/cord-268874-ldja6aa4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268874-ldja6aa4.txt' === file2bib.sh === id: cord-270122-xijsj0d8 author: Hogan, Robert Edward title: COVID-19 in Patients With Seizures and Epilepsy: Interpretation of Relevant Knowledge of Presenting Signs and Symptoms date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-270122-xijsj0d8.txt cache: ./cache/cord-270122-xijsj0d8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270122-xijsj0d8.txt' === file2bib.sh === id: cord-269522-38dhwggn author: Hong, Xia title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() date: 2009-08-27 pages: extension: .txt txt: ./txt/cord-269522-38dhwggn.txt cache: ./cache/cord-269522-38dhwggn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269522-38dhwggn.txt' === file2bib.sh === id: cord-270645-tzctvs9q author: Martelletti, Luigi title: Air Pollution and the Novel Covid-19 Disease: a Putative Disease Risk Factor date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-270645-tzctvs9q.txt cache: ./cache/cord-270645-tzctvs9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270645-tzctvs9q.txt' === file2bib.sh === id: cord-270049-54t3w94z author: Campione, Elena title: Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-270049-54t3w94z.txt cache: ./cache/cord-270049-54t3w94z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270049-54t3w94z.txt' === file2bib.sh === id: cord-269537-h3lzl1un author: Banerjee, Aditi title: Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-269537-h3lzl1un.txt cache: ./cache/cord-269537-h3lzl1un.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269537-h3lzl1un.txt' === file2bib.sh === id: cord-270458-7imgvale author: Franchini, Massimo title: The impact of the SARS‐CoV‐2 outbreak on the safety and availability of blood transfusions in Italy date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-270458-7imgvale.txt cache: ./cache/cord-270458-7imgvale.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270458-7imgvale.txt' === file2bib.sh === id: cord-270377-lfcoy8n1 author: Novazzi, Federica title: SARS-CoV-2 positivity in rectal swabs implication for possible transmission date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-270377-lfcoy8n1.txt cache: ./cache/cord-270377-lfcoy8n1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270377-lfcoy8n1.txt' === file2bib.sh === id: cord-270035-1e1wzdri author: Cazzaniga, Marco title: SARS-COV-2 Infection and Kawasaki Disease: Case Report of a Hitherto Unrecognized Association date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-270035-1e1wzdri.txt cache: ./cache/cord-270035-1e1wzdri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270035-1e1wzdri.txt' === file2bib.sh === id: cord-269939-8nvrt5y7 author: Tan, Boon Fei title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-269939-8nvrt5y7.txt cache: ./cache/cord-269939-8nvrt5y7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269939-8nvrt5y7.txt' === file2bib.sh === id: cord-270515-bfjdvfuq author: Deng, Chu-Xia title: The global battle against SARS-CoV-2 and COVID-19 date: 2020-03-15 pages: extension: .txt txt: ./txt/cord-270515-bfjdvfuq.txt cache: ./cache/cord-270515-bfjdvfuq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-270515-bfjdvfuq.txt' === file2bib.sh === id: cord-269871-w41o1krr author: Aggarwal, Shyam title: High Viral Load and Poor Ventilation: Cause of High Mortality From COVID-19 date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-269871-w41o1krr.txt cache: ./cache/cord-269871-w41o1krr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269871-w41o1krr.txt' === file2bib.sh === id: cord-269101-7altkx5u author: Jakhmola Mani, Ruchi title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-269101-7altkx5u.txt cache: ./cache/cord-269101-7altkx5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269101-7altkx5u.txt' === file2bib.sh === id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-269726-z0frgm7s.txt cache: ./cache/cord-269726-z0frgm7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269726-z0frgm7s.txt' === file2bib.sh === id: cord-269707-titu9lm4 author: Hsieh, Ching-Lin title: Structure-based design of prefusion-stabilized SARS-CoV-2 spikes date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-269707-titu9lm4.txt cache: ./cache/cord-269707-titu9lm4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269707-titu9lm4.txt' === file2bib.sh === id: cord-270533-s2d3q4ob author: Lau, Yu-Lung title: SARS: future research and vaccine date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-270533-s2d3q4ob.txt cache: ./cache/cord-270533-s2d3q4ob.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270533-s2d3q4ob.txt' === file2bib.sh === id: cord-270495-2u072mtp author: Lokida, Dewi title: Diagnosis of COVID-19 in a Dengue-Endemic Area date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-270495-2u072mtp.txt cache: ./cache/cord-270495-2u072mtp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270495-2u072mtp.txt' === file2bib.sh === id: cord-270116-r2rnnsfh author: Lippi, Giuseppe title: Current laboratory diagnostics of coronavirus disease 2019 (COVID-19) date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-270116-r2rnnsfh.txt cache: ./cache/cord-270116-r2rnnsfh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270116-r2rnnsfh.txt' === file2bib.sh === id: cord-270064-hidirfkv author: Tort, Fernando L. title: A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date: 2020-04-12 pages: extension: .txt txt: ./txt/cord-270064-hidirfkv.txt cache: ./cache/cord-270064-hidirfkv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270064-hidirfkv.txt' === file2bib.sh === id: cord-270462-d9l3agr0 author: Zeng, Zhi title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-270462-d9l3agr0.txt cache: ./cache/cord-270462-d9l3agr0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270462-d9l3agr0.txt' === file2bib.sh === id: cord-270123-m8utyd1m author: Enmozhi, Sukanth Kumar title: Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-270123-m8utyd1m.txt cache: ./cache/cord-270123-m8utyd1m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270123-m8utyd1m.txt' === file2bib.sh === id: cord-270510-z6qg48nz author: Lauro, A. title: Emergency Endoscopy During the SARS-CoV-2 Pandemic in the North of Italy: Experience from St. Orsola University Hospital—Bologna date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-270510-z6qg48nz.txt cache: ./cache/cord-270510-z6qg48nz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270510-z6qg48nz.txt' === file2bib.sh === id: cord-270665-z4l3lq39 author: Tian, Qing title: Endoscopic mask innovation and protective measures changes during the COVID‐19 pandemic: experience from a Chinese hepato‐biliary‐pancreatic unit date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-270665-z4l3lq39.txt cache: ./cache/cord-270665-z4l3lq39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270665-z4l3lq39.txt' === file2bib.sh === id: cord-270399-yfko8mpc author: Foster, Allison title: It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-270399-yfko8mpc.txt cache: ./cache/cord-270399-yfko8mpc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270399-yfko8mpc.txt' === file2bib.sh === id: cord-270019-er70ehk4 author: Yang, Kunyu title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-270019-er70ehk4.txt cache: ./cache/cord-270019-er70ehk4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270019-er70ehk4.txt' === file2bib.sh === id: cord-270218-578lsck9 author: Gentile, Davide title: Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-270218-578lsck9.txt cache: ./cache/cord-270218-578lsck9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270218-578lsck9.txt' === file2bib.sh === id: cord-270886-m9na7cbm author: Quadeer, Ahmed Abdul title: Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-270886-m9na7cbm.txt cache: ./cache/cord-270886-m9na7cbm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270886-m9na7cbm.txt' === file2bib.sh === id: cord-269465-3fdjqnhb author: Leth-Larsen, Rikke title: The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages date: 2007-05-15 pages: extension: .txt txt: ./txt/cord-269465-3fdjqnhb.txt cache: ./cache/cord-269465-3fdjqnhb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269465-3fdjqnhb.txt' === file2bib.sh === id: cord-270475-mkpn9tz6 author: Requena, Manuel title: COVID-19 and Stroke: incidence and etiological description in a high-volume center. date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-270475-mkpn9tz6.txt cache: ./cache/cord-270475-mkpn9tz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270475-mkpn9tz6.txt' === file2bib.sh === id: cord-269723-gm65p1op author: Tzeng, Nian-Sheng title: What could we learn from SARS when facing the mental health issues related to the COVID-19 outbreak? A nationwide cohort study in Taiwan date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-269723-gm65p1op.txt cache: ./cache/cord-269723-gm65p1op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269723-gm65p1op.txt' === file2bib.sh === id: cord-270613-vnjuubt4 author: Poon, Terence C.W. title: Proteomic analysis reveals platelet factor 4 and beta‐thromboglobulin as prognostic markers in severe acute respiratory syndrome date: 2012-06-28 pages: extension: .txt txt: ./txt/cord-270613-vnjuubt4.txt cache: ./cache/cord-270613-vnjuubt4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270613-vnjuubt4.txt' === file2bib.sh === id: cord-269771-hffxb7bm author: Cheung, Ka Shing title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-269771-hffxb7bm.txt cache: ./cache/cord-269771-hffxb7bm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269771-hffxb7bm.txt' === file2bib.sh === id: cord-270606-r46pbaf0 author: Rashed, Mohamed Z. title: Rapid detection of SARS-CoV-2 antibodies using electrochemical impedance-based detector date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-270606-r46pbaf0.txt cache: ./cache/cord-270606-r46pbaf0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270606-r46pbaf0.txt' === file2bib.sh === id: cord-270622-aofva2ab author: Li, Qizhang title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-270622-aofva2ab.txt cache: ./cache/cord-270622-aofva2ab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270622-aofva2ab.txt' === file2bib.sh === id: cord-270661-e83xe4sp author: Falahi, Shahab title: Transmission routes for SARS-COV-2 infection: Review of Evidence date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-270661-e83xe4sp.txt cache: ./cache/cord-270661-e83xe4sp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270661-e83xe4sp.txt' === file2bib.sh === id: cord-270588-c9rxmo44 author: Algarroba, Gabriela N. title: Visualization of SARS-CoV-2 virus invading the human placenta using electron microscopy date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-270588-c9rxmo44.txt cache: ./cache/cord-270588-c9rxmo44.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270588-c9rxmo44.txt' === file2bib.sh === id: cord-269564-r5mmsnbx author: Hans, Diana title: Rapidly Fatal Infections date: 2008-05-31 pages: extension: .txt txt: ./txt/cord-269564-r5mmsnbx.txt cache: ./cache/cord-269564-r5mmsnbx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269564-r5mmsnbx.txt' === file2bib.sh === id: cord-270278-d61n3v90 author: Choi, S.M.Y. title: Enhancing legal preparedness for the prevention and control of infectious diseases: Experience from severe acute respiratory syndrome in Hong Kong date: 2009-03-31 pages: extension: .txt txt: ./txt/cord-270278-d61n3v90.txt cache: ./cache/cord-270278-d61n3v90.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270278-d61n3v90.txt' === file2bib.sh === id: cord-270474-jaurhjvr author: Xiang, Zhen title: Glucocorticoids improve severe or critical COVID-19 by activating ACE2 and reducing IL-6 levels date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-270474-jaurhjvr.txt cache: ./cache/cord-270474-jaurhjvr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270474-jaurhjvr.txt' === file2bib.sh === id: cord-270743-yyl50z94 author: Haseli, Sara title: Reply to “MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss” date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-270743-yyl50z94.txt cache: ./cache/cord-270743-yyl50z94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270743-yyl50z94.txt' === file2bib.sh === id: cord-269909-1cso5cl4 author: Amatya, Shaili title: Management of newborns exposed to mothers with confirmed or suspected COVID-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-269909-1cso5cl4.txt cache: ./cache/cord-269909-1cso5cl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269909-1cso5cl4.txt' === file2bib.sh === id: cord-270788-w0pewq52 author: Chou, Chih-Fong title: A novel cell-based binding assay system reconstituting interaction between SARS-CoV S protein and its cellular receptor date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-270788-w0pewq52.txt cache: ./cache/cord-270788-w0pewq52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270788-w0pewq52.txt' === file2bib.sh === id: cord-269835-mz7i66qp author: Furfaro, Federica title: SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-269835-mz7i66qp.txt cache: ./cache/cord-269835-mz7i66qp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269835-mz7i66qp.txt' === file2bib.sh === id: cord-270858-ozvdz9ew author: Altmann, Daniel M title: What policy makers need to know about COVID-19 protective immunity date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-270858-ozvdz9ew.txt cache: ./cache/cord-270858-ozvdz9ew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270858-ozvdz9ew.txt' === file2bib.sh === id: cord-270888-8j17ul7k author: Fernández-González, Sara Mª title: ¿Infección Por Sars-Cov-2 Como Desencadenante De Un Síndrome Inflamatorio Sistémico? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-270888-8j17ul7k.txt cache: ./cache/cord-270888-8j17ul7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270888-8j17ul7k.txt' === file2bib.sh === id: cord-270348-5804ffwx author: Angelino, Andrew F. title: Design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 positive patients. date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-270348-5804ffwx.txt cache: ./cache/cord-270348-5804ffwx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270348-5804ffwx.txt' === file2bib.sh === id: cord-270909-wb7mwklo author: Cheng, Vincent C.C. title: Absence of nosocomial transmission of coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in the pre-pandemic phase in Hong Kong date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-270909-wb7mwklo.txt cache: ./cache/cord-270909-wb7mwklo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270909-wb7mwklo.txt' === file2bib.sh === id: cord-269862-krcu3hfa author: Wang, Shui-Mei title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date: 2009-05-25 pages: extension: .txt txt: ./txt/cord-269862-krcu3hfa.txt cache: ./cache/cord-269862-krcu3hfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269862-krcu3hfa.txt' === file2bib.sh === id: cord-271338-v2k9zn87 author: Pujadas, E. title: SARS-CoV-2 Viral Load Predicts COVID-19 Mortality date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-271338-v2k9zn87.txt cache: ./cache/cord-271338-v2k9zn87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271338-v2k9zn87.txt' === file2bib.sh === id: cord-270776-oulnk1b3 author: Chau, Tai-nin title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome date: 2004-08-15 pages: extension: .txt txt: ./txt/cord-270776-oulnk1b3.txt cache: ./cache/cord-270776-oulnk1b3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270776-oulnk1b3.txt' === file2bib.sh === id: cord-270919-0hldozml author: Cortey, Martí title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-270919-0hldozml.txt cache: ./cache/cord-270919-0hldozml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270919-0hldozml.txt' === file2bib.sh === id: cord-270951-6nq3jwgr author: Amerio, Paolo title: COVID‐19 and psoriasis: Should we fear for patients treated with biologics? date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-270951-6nq3jwgr.txt cache: ./cache/cord-270951-6nq3jwgr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270951-6nq3jwgr.txt' === file2bib.sh === id: cord-271404-tu8u1b1d author: Gaunkar, Ridhima B title: COVID-19 in Smokeless Tobacco Habitués: Increased Susceptibility and Transmission date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-271404-tu8u1b1d.txt cache: ./cache/cord-271404-tu8u1b1d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271404-tu8u1b1d.txt' === file2bib.sh === id: cord-270591-0szbkhiz author: Shi, Chen title: Comprehensive Landscape of Heparin Therapy for COVID-19 date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-270591-0szbkhiz.txt cache: ./cache/cord-270591-0szbkhiz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270591-0szbkhiz.txt' === file2bib.sh === id: cord-270935-t9pym9k0 author: Dumyati, Ghinwa title: Does Universal Testing for COVID-19 Work for Everyone? date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-270935-t9pym9k0.txt cache: ./cache/cord-270935-t9pym9k0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270935-t9pym9k0.txt' === file2bib.sh === id: cord-270550-if748w2n author: Bailey, Adam L. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-270550-if748w2n.txt cache: ./cache/cord-270550-if748w2n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270550-if748w2n.txt' === file2bib.sh === id: cord-271174-886xc1n3 author: Lipworth, Brian title: Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-271174-886xc1n3.txt cache: ./cache/cord-271174-886xc1n3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271174-886xc1n3.txt' === file2bib.sh === id: cord-268540-wrjzr3ws author: Park, You Jeong title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-268540-wrjzr3ws.txt cache: ./cache/cord-268540-wrjzr3ws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-268540-wrjzr3ws.txt' === file2bib.sh === id: cord-270698-9w3ap3gz author: Guo, Hua title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-270698-9w3ap3gz.txt cache: ./cache/cord-270698-9w3ap3gz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270698-9w3ap3gz.txt' === file2bib.sh === id: cord-271411-h3k7r2ia author: Pelletier, Jesse S. title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-271411-h3k7r2ia.txt cache: ./cache/cord-271411-h3k7r2ia.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271411-h3k7r2ia.txt' === file2bib.sh === id: cord-270528-3rsv3jlh author: Yazdanpanah, Fereshteh title: The immune system and COVID-19: Friend or foe? date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-270528-3rsv3jlh.txt cache: ./cache/cord-270528-3rsv3jlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270528-3rsv3jlh.txt' === file2bib.sh === id: cord-271495-5906wju4 author: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-271495-5906wju4.txt cache: ./cache/cord-271495-5906wju4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271495-5906wju4.txt' === file2bib.sh === id: cord-270837-xvauo76d author: Hui, David S. title: The 1-Year Impact of Severe Acute Respiratory Syndrome on Pulmonary Function, Exercise Capacity, and Quality of Life in a Cohort of Survivors date: 2005-10-31 pages: extension: .txt txt: ./txt/cord-270837-xvauo76d.txt cache: ./cache/cord-270837-xvauo76d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270837-xvauo76d.txt' === file2bib.sh === id: cord-271014-xzpvupms author: Erikstrup, Christian title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-271014-xzpvupms.txt cache: ./cache/cord-271014-xzpvupms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271014-xzpvupms.txt' === file2bib.sh === id: cord-271419-v6dfel3l author: Adachi, Shun title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-271419-v6dfel3l.txt cache: ./cache/cord-271419-v6dfel3l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271419-v6dfel3l.txt' === file2bib.sh === id: cord-270880-azslipmp author: Cozzupoli, Grazia Maria title: Possible Retinal Impairment Secondary to Ritonavir Use in SARS-CoV-2 Patients: A Narrative Systematic Review date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-270880-azslipmp.txt cache: ./cache/cord-270880-azslipmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270880-azslipmp.txt' === file2bib.sh === id: cord-270964-kxze0470 author: Lau, Kwok-Kwong title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-270964-kxze0470.txt cache: ./cache/cord-270964-kxze0470.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270964-kxze0470.txt' === file2bib.sh === id: cord-271751-46oo9xv5 author: Ingraham, Nicholas E. title: Shining a light on the evidence for hydroxychloroquine in SARS-CoV-2 date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-271751-46oo9xv5.txt cache: ./cache/cord-271751-46oo9xv5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271751-46oo9xv5.txt' === file2bib.sh === id: cord-271090-91lzr4tz author: Edwards, Kathryn M. title: Anticipating SARS-CoV-2 Vaccine Testing, Licensure, and Recommendations for Use date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-271090-91lzr4tz.txt cache: ./cache/cord-271090-91lzr4tz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271090-91lzr4tz.txt' === file2bib.sh === id: cord-270994-1mmqfp7g author: ul Qamar, Muhammad Tahir title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-270994-1mmqfp7g.txt cache: ./cache/cord-270994-1mmqfp7g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270994-1mmqfp7g.txt' === file2bib.sh === id: cord-271211-frkk6w0a author: Han, Yu title: The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID‐19): A Chinese perspective date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-271211-frkk6w0a.txt cache: ./cache/cord-271211-frkk6w0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271211-frkk6w0a.txt' === file2bib.sh === id: cord-272179-wvw5mmy3 author: Calderaro, Adriana title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-272179-wvw5mmy3.txt cache: ./cache/cord-272179-wvw5mmy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272179-wvw5mmy3.txt' === file2bib.sh === id: cord-271371-qs7zge3l author: Gao, Jia title: Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-271371-qs7zge3l.txt cache: ./cache/cord-271371-qs7zge3l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271371-qs7zge3l.txt' === file2bib.sh === id: cord-270683-982eqtog author: Pavel, Shaikh Terkis Islam title: Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-270683-982eqtog.txt cache: ./cache/cord-270683-982eqtog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270683-982eqtog.txt' === file2bib.sh === id: cord-271871-8grkln6o author: Singer, J. S. title: Low Prevalence (0.13%) of COVID-19 Infection in Asymptomatic Pre-operative/Pre-procedure Patients at a Large Academic Medical Center Informs Approaches to Perioperative Care date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-271871-8grkln6o.txt cache: ./cache/cord-271871-8grkln6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271871-8grkln6o.txt' === file2bib.sh === id: cord-270866-olc5r2yx author: Mallet, Jasmina title: Addictions in the COVID-19 era: Current evidence, future perspectives a comprehensive review date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-270866-olc5r2yx.txt cache: ./cache/cord-270866-olc5r2yx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270866-olc5r2yx.txt' === file2bib.sh === id: cord-271469-lozvq3y6 author: Shaikh, Faiq title: Current landscape of Imaging and the potential role for Artificial intelligence in the management of COVID-19 date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-271469-lozvq3y6.txt cache: ./cache/cord-271469-lozvq3y6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271469-lozvq3y6.txt' === file2bib.sh === id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-271188-ewlxy5po.txt cache: ./cache/cord-271188-ewlxy5po.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271188-ewlxy5po.txt' === file2bib.sh === id: cord-271930-9a18h2tr author: Licari, Amelia title: Allergy and asthma in children and adolescents during the COVID outbreak: What we know and how we could prevent allergy and asthma flares date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-271930-9a18h2tr.txt cache: ./cache/cord-271930-9a18h2tr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271930-9a18h2tr.txt' === file2bib.sh === id: cord-272423-o5yinjcz author: Mao, Xiao-Yuan title: iPSCs-Derived Platform: A Feasible Tool for Probing the Neurotropism of SARS-CoV-2 date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-272423-o5yinjcz.txt cache: ./cache/cord-272423-o5yinjcz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272423-o5yinjcz.txt' === file2bib.sh === id: cord-271919-pbs95hy0 author: Desenclos, Jean-Claude title: Introduction of SARS in France, March–April, 2003 date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-271919-pbs95hy0.txt cache: ./cache/cord-271919-pbs95hy0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271919-pbs95hy0.txt' === file2bib.sh === id: cord-272414-oo8kcuf3 author: Chiocchetti, Roberto title: ACE2 Expression in the Cat and the Tiger Gastrointestinal Tracts date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-272414-oo8kcuf3.txt cache: ./cache/cord-272414-oo8kcuf3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272414-oo8kcuf3.txt' === file2bib.sh === id: cord-269756-tid8a464 author: Basso, Luis G. M. title: SARS-CoV fusion peptides induce membrane surface ordering and curvature date: 2016-11-28 pages: extension: .txt txt: ./txt/cord-269756-tid8a464.txt cache: ./cache/cord-269756-tid8a464.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269756-tid8a464.txt' === file2bib.sh === id: cord-271243-8cfyen86 author: Xiao, Y. title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus date: 2008-05-31 pages: extension: .txt txt: ./txt/cord-271243-8cfyen86.txt cache: ./cache/cord-271243-8cfyen86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271243-8cfyen86.txt' === file2bib.sh === id: cord-271505-eot38721 author: Wang, Hongliang title: Molecular pathogenesis of severe acute respiratory syndrome date: 2006-09-28 pages: extension: .txt txt: ./txt/cord-271505-eot38721.txt cache: ./cache/cord-271505-eot38721.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271505-eot38721.txt' === file2bib.sh === id: cord-271027-4omocd8q author: Fronza, R. title: Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-271027-4omocd8q.txt cache: ./cache/cord-271027-4omocd8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271027-4omocd8q.txt' === file2bib.sh === id: cord-272653-01wck9f3 author: Isaacs, David title: Apocalypse perhaps date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-272653-01wck9f3.txt cache: ./cache/cord-272653-01wck9f3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272653-01wck9f3.txt' === file2bib.sh === id: cord-271544-i20105lq author: Poston, Daniel title: Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection date: 2020-10-11 pages: extension: .txt txt: ./txt/cord-271544-i20105lq.txt cache: ./cache/cord-271544-i20105lq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271544-i20105lq.txt' === file2bib.sh === id: cord-271536-pscw933i author: Guo, Zhen-Dong title: Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-271536-pscw933i.txt cache: ./cache/cord-271536-pscw933i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271536-pscw933i.txt' === file2bib.sh === id: cord-271849-wxmr8eki author: Meysman, Pieter title: Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-271849-wxmr8eki.txt cache: ./cache/cord-271849-wxmr8eki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271849-wxmr8eki.txt' === file2bib.sh === id: cord-271998-hdkmwihu author: Rabenau, H. F. title: SARS-coronavirus (SARS-CoV) and the safety of a solvent/detergent (S/D) treated immunoglobulin preparation date: 2005-06-30 pages: extension: .txt txt: ./txt/cord-271998-hdkmwihu.txt cache: ./cache/cord-271998-hdkmwihu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271998-hdkmwihu.txt' === file2bib.sh === id: cord-272019-4uua0zgp author: Sun, Wei title: Changes in coagulation and fibrinolysis of post-SARS osteonecrosis in a Chinese population date: 2006-03-18 pages: extension: .txt txt: ./txt/cord-272019-4uua0zgp.txt cache: ./cache/cord-272019-4uua0zgp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272019-4uua0zgp.txt' === file2bib.sh === id: cord-272450-8a3ir06y author: Iwen, Peter C title: Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-272450-8a3ir06y.txt cache: ./cache/cord-272450-8a3ir06y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-272450-8a3ir06y.txt' === file2bib.sh === id: cord-271339-wt5o9sgm author: Chen, Chao-Ju title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-271339-wt5o9sgm.txt cache: ./cache/cord-271339-wt5o9sgm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271339-wt5o9sgm.txt' === file2bib.sh === id: cord-272734-kawim93f author: Freire-Paspuel, Byron title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-272734-kawim93f.txt cache: ./cache/cord-272734-kawim93f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272734-kawim93f.txt' === file2bib.sh === id: cord-272681-u3p0hsla author: Vargas-Gandica, Jair title: Ageusia and anosmia, a common sign of COVID-19? A case series from four countries date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-272681-u3p0hsla.txt cache: ./cache/cord-272681-u3p0hsla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272681-u3p0hsla.txt' === file2bib.sh === id: cord-271781-cfv0ta10 author: Patel, Kishan P. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-271781-cfv0ta10.txt cache: ./cache/cord-271781-cfv0ta10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271781-cfv0ta10.txt' === file2bib.sh === id: cord-272445-0xauff51 author: Naaber, Paul title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-272445-0xauff51.txt cache: ./cache/cord-272445-0xauff51.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272445-0xauff51.txt' === file2bib.sh === id: cord-270857-8424oq4x author: Hui, David S. title: Exhaled Air Dispersion During Oxygen Delivery Via a Simple Oxygen Mask date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-270857-8424oq4x.txt cache: ./cache/cord-270857-8424oq4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270857-8424oq4x.txt' === file2bib.sh === id: cord-272405-jmwn8pdn author: Parvez, Mohammad K. title: Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date: 2017-08-04 pages: extension: .txt txt: ./txt/cord-272405-jmwn8pdn.txt cache: ./cache/cord-272405-jmwn8pdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272405-jmwn8pdn.txt' === file2bib.sh === id: cord-272633-2vmdf9j6 author: Wong, Gary W.K. title: Out of the East – Emerging infections date: 2006-06-05 pages: extension: .txt txt: ./txt/cord-272633-2vmdf9j6.txt cache: ./cache/cord-272633-2vmdf9j6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272633-2vmdf9j6.txt' === file2bib.sh === id: cord-272501-byfxqsbu author: Motta, Juan Camilo title: Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-272501-byfxqsbu.txt cache: ./cache/cord-272501-byfxqsbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272501-byfxqsbu.txt' === file2bib.sh === id: cord-273451-xnce010o author: Salisbury-Afshar, Elizabeth M. title: Vulnerable Populations: Weathering the Pandemic Storm date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-273451-xnce010o.txt cache: ./cache/cord-273451-xnce010o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273451-xnce010o.txt' === file2bib.sh === id: cord-271915-nvilxnzl author: Adachi, D. title: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date: 2004-12-01 pages: extension: .txt txt: ./txt/cord-271915-nvilxnzl.txt cache: ./cache/cord-271915-nvilxnzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271915-nvilxnzl.txt' === file2bib.sh === id: cord-271701-tx0lqgff author: te Velthuis, Aartjan J.W. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 pages: extension: .txt txt: ./txt/cord-271701-tx0lqgff.txt cache: ./cache/cord-271701-tx0lqgff.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271701-tx0lqgff.txt' === file2bib.sh === id: cord-272292-k0ugjb6f author: Liu, Shih-Jen title: Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates date: 2006-04-12 pages: extension: .txt txt: ./txt/cord-272292-k0ugjb6f.txt cache: ./cache/cord-272292-k0ugjb6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272292-k0ugjb6f.txt' === file2bib.sh === id: cord-271813-nroflfmc author: Deng, Wang title: Positive results for patients with COVID-19 discharged form hospital in Chongqing, China date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-271813-nroflfmc.txt cache: ./cache/cord-271813-nroflfmc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271813-nroflfmc.txt' === file2bib.sh === id: cord-271978-j5enftje author: Zoltán, Köntös title: In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-271978-j5enftje.txt cache: ./cache/cord-271978-j5enftje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271978-j5enftje.txt' === file2bib.sh === id: cord-272009-yxjhfg7m author: Cui, Jie title: Evolutionary Relationships between Bat Coronaviruses and Their Hosts date: 2007-10-17 pages: extension: .txt txt: ./txt/cord-272009-yxjhfg7m.txt cache: ./cache/cord-272009-yxjhfg7m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272009-yxjhfg7m.txt' === file2bib.sh === id: cord-272211-nkv6irr7 author: Hagan, Liesl M. title: Mass Testing for SARS-CoV-2 in 16 Prisons and Jails — Six Jurisdictions, United States, April–May 2020 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-272211-nkv6irr7.txt cache: ./cache/cord-272211-nkv6irr7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272211-nkv6irr7.txt' === file2bib.sh === id: cord-271815-yr1dq258 author: Hulkower, Rachel L. title: Inactivation of surrogate coronaviruses on hard surfaces by health care germicides date: 2011-06-30 pages: extension: .txt txt: ./txt/cord-271815-yr1dq258.txt cache: ./cache/cord-271815-yr1dq258.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271815-yr1dq258.txt' === file2bib.sh === id: cord-272113-j82z4q8x author: Akaji, Kenichi title: Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-272113-j82z4q8x.txt cache: ./cache/cord-272113-j82z4q8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272113-j82z4q8x.txt' === file2bib.sh === id: cord-273074-k8m917i4 author: Fu, Chao-Yang title: Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens date: 2005-12-01 pages: extension: .txt txt: ./txt/cord-273074-k8m917i4.txt cache: ./cache/cord-273074-k8m917i4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273074-k8m917i4.txt' === file2bib.sh === id: cord-272690-r8lv1zzx author: St. John, Ronald K. title: Border Screening for SARS date: 2005-01-17 pages: extension: .txt txt: ./txt/cord-272690-r8lv1zzx.txt cache: ./cache/cord-272690-r8lv1zzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272690-r8lv1zzx.txt' === file2bib.sh === id: cord-272626-bw9lbzvt author: Pizzorno, Andrés title: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-272626-bw9lbzvt.txt cache: ./cache/cord-272626-bw9lbzvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272626-bw9lbzvt.txt' === file2bib.sh === id: cord-273604-0w5shxmf author: Psevdos, George title: Halting a SARS-CoV-2 Outbreak in a U.S. Veterans Affairs Nursing Home date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-273604-0w5shxmf.txt cache: ./cache/cord-273604-0w5shxmf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273604-0w5shxmf.txt' === file2bib.sh === id: cord-272603-nbosceoz author: Lin, Qiuyuan title: Microfluidic Immunoassays for Sensitive and Simultaneous Detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-272603-nbosceoz.txt cache: ./cache/cord-272603-nbosceoz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272603-nbosceoz.txt' === file2bib.sh === id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271920-1dzkgt6w.txt cache: ./cache/cord-271920-1dzkgt6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271920-1dzkgt6w.txt' === file2bib.sh === id: cord-273035-sewfb3q8 author: Kang, Xixiong title: Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome date: 2005-01-01 pages: extension: .txt txt: ./txt/cord-273035-sewfb3q8.txt cache: ./cache/cord-273035-sewfb3q8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273035-sewfb3q8.txt' === file2bib.sh === id: cord-272010-kc0gi3cj author: Anand, Sai Priya title: Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-272010-kc0gi3cj.txt cache: ./cache/cord-272010-kc0gi3cj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272010-kc0gi3cj.txt' === file2bib.sh === id: cord-271723-8qoozmgk author: Gelman, Ram title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-271723-8qoozmgk.txt cache: ./cache/cord-271723-8qoozmgk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271723-8qoozmgk.txt' === file2bib.sh === id: cord-271944-oxtus5vb author: Joseph, Rudman title: Seizure And COVID-19: Association and Review of Potential Mechanism date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-271944-oxtus5vb.txt cache: ./cache/cord-271944-oxtus5vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271944-oxtus5vb.txt' === file2bib.sh === id: cord-273114-eanwxkvt author: Perrone, Serafina title: Report of a series of healthy term newborns from convalescent mothers with COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-273114-eanwxkvt.txt cache: ./cache/cord-273114-eanwxkvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273114-eanwxkvt.txt' === file2bib.sh === id: cord-273685-oxvfxmtr author: Fan, Qihong title: Anal swab findings in an infant with COVID‐19 date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-273685-oxvfxmtr.txt cache: ./cache/cord-273685-oxvfxmtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273685-oxvfxmtr.txt' === file2bib.sh === id: cord-271551-bj2db91j author: Tomczyk, Samuel title: Social Distancing and Stigma: Association Between Compliance With Behavioral Recommendations, Risk Perception, and Stigmatizing Attitudes During the COVID-19 Outbreak date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-271551-bj2db91j.txt cache: ./cache/cord-271551-bj2db91j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271551-bj2db91j.txt' === file2bib.sh === id: cord-272318-8yfg1j0o author: Reddy, Sujan T. title: Cerebrovascular Disease in Patients with COVID-19: A Review of the Literature and Case Series date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-272318-8yfg1j0o.txt cache: ./cache/cord-272318-8yfg1j0o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272318-8yfg1j0o.txt' === file2bib.sh === id: cord-273675-0oiq44gl author: Wu, Di title: To alert coinfection of COVID-19 and dengue virus in developing countries in the dengue-endemic area date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-273675-0oiq44gl.txt cache: ./cache/cord-273675-0oiq44gl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-273675-0oiq44gl.txt' === file2bib.sh === id: cord-272573-wxqly479 author: Maia Chagas, Andre title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-272573-wxqly479.txt cache: ./cache/cord-272573-wxqly479.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272573-wxqly479.txt' === file2bib.sh === id: cord-273314-p1dlzoh1 author: Gadiparthi, Chiranjeevi title: Gastrointestinal Bleeding in Patients with Severe SARS-CoV-2 date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-273314-p1dlzoh1.txt cache: ./cache/cord-273314-p1dlzoh1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273314-p1dlzoh1.txt' === file2bib.sh === id: cord-272602-rywg9mek author: Allison, James R title: Evaluating aerosol and splatter following dental procedures: addressing new challenges for oral healthcare and rehabilitation date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-272602-rywg9mek.txt cache: ./cache/cord-272602-rywg9mek.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272602-rywg9mek.txt' === file2bib.sh === id: cord-273626-zy8qjaai author: Gong, Shu‐ran title: The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models date: 2018-07-28 pages: extension: .txt txt: ./txt/cord-273626-zy8qjaai.txt cache: ./cache/cord-273626-zy8qjaai.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273626-zy8qjaai.txt' === file2bib.sh === id: cord-271648-m2c5bvuj author: Ashour, Hossam M. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-271648-m2c5bvuj.txt cache: ./cache/cord-271648-m2c5bvuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271648-m2c5bvuj.txt' === file2bib.sh === id: cord-272241-2fwz8z8n author: Kumar, Amit title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-272241-2fwz8z8n.txt cache: ./cache/cord-272241-2fwz8z8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272241-2fwz8z8n.txt' === file2bib.sh === id: cord-273351-vq3budip author: Farré, Núria title: Prolonged QT Interval in SARS-CoV-2 Infection: Prevalence and Prognosis date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-273351-vq3budip.txt cache: ./cache/cord-273351-vq3budip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273351-vq3budip.txt' === file2bib.sh === id: cord-273859-tr4s5i7h author: Luis García Garmendia, José title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-273859-tr4s5i7h.txt cache: ./cache/cord-273859-tr4s5i7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273859-tr4s5i7h.txt' === file2bib.sh === id: cord-272654-hh29olk7 author: Bošnjak, Berislav title: Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID-19 convalescent patients revealed by two different detection methods date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-272654-hh29olk7.txt cache: ./cache/cord-272654-hh29olk7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272654-hh29olk7.txt' === file2bib.sh === id: cord-273645-czh3zfb3 author: Lu, Shuaiyao title: Comparison of SARS-CoV-2 infections among 3 species of non-human primates date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-273645-czh3zfb3.txt cache: ./cache/cord-273645-czh3zfb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273645-czh3zfb3.txt' === file2bib.sh === id: cord-273251-k3ltbpnb author: Phipps, Meaghan M. title: Acute Liver Injury in COVID‐19: Prevalence and Association with Clinical Outcomes in a Large US Cohort date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-273251-k3ltbpnb.txt cache: ./cache/cord-273251-k3ltbpnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273251-k3ltbpnb.txt' === file2bib.sh === id: cord-273367-gl266pvt author: Gunawardana, M. title: Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-273367-gl266pvt.txt cache: ./cache/cord-273367-gl266pvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273367-gl266pvt.txt' === file2bib.sh === id: cord-273253-rgqvdzna author: Skowronski, D. M. title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-273253-rgqvdzna.txt cache: ./cache/cord-273253-rgqvdzna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273253-rgqvdzna.txt' === file2bib.sh === id: cord-272986-ebgusf3o author: Cao, Yipeng title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-272986-ebgusf3o.txt cache: ./cache/cord-272986-ebgusf3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272986-ebgusf3o.txt' === file2bib.sh === id: cord-272956-0yumc7em author: Gnavi, Roberto title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-272956-0yumc7em.txt cache: ./cache/cord-272956-0yumc7em.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272956-0yumc7em.txt' === file2bib.sh === id: cord-273083-xrydkiu4 author: Pahmeier, Felix title: A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-273083-xrydkiu4.txt cache: ./cache/cord-273083-xrydkiu4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273083-xrydkiu4.txt' === file2bib.sh === id: cord-273311-dl9u85nh author: Boscolo‐Rizzo, Paolo title: Challenges in interpreting the diagnostic performance of symptoms to predict COVID‐19 status: the case of anosmia date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-273311-dl9u85nh.txt cache: ./cache/cord-273311-dl9u85nh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273311-dl9u85nh.txt' === file2bib.sh === id: cord-273764-itu39mln author: Li, Taisheng title: Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date: 2006-12-20 pages: extension: .txt txt: ./txt/cord-273764-itu39mln.txt cache: ./cache/cord-273764-itu39mln.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273764-itu39mln.txt' === file2bib.sh === id: cord-271259-6kkzh1tp author: Chen, Shuai title: Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode date: 2010-01-01 pages: extension: .txt txt: ./txt/cord-271259-6kkzh1tp.txt cache: ./cache/cord-271259-6kkzh1tp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271259-6kkzh1tp.txt' === file2bib.sh === id: cord-273064-c58nf9vb author: Hallowell, Benjamin D. title: Severe Acute Respiratory Syndrome Coronavirus 2 Prevalence, Seroprevalence, and Exposure among Evacuees from Wuhan, China, 2020 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-273064-c58nf9vb.txt cache: ./cache/cord-273064-c58nf9vb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273064-c58nf9vb.txt' === file2bib.sh === id: cord-273349-penb65x7 author: Zhang, Chao title: Liver injury in COVID-19: management and challenges date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-273349-penb65x7.txt cache: ./cache/cord-273349-penb65x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273349-penb65x7.txt' === file2bib.sh === id: cord-272902-kdkyzfjv author: Naghibzadeh, Mahmoud title: Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-272902-kdkyzfjv.txt cache: ./cache/cord-272902-kdkyzfjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272902-kdkyzfjv.txt' === file2bib.sh === id: cord-273373-5elel6qo author: Wang, Haofeng title: Recent progress in the discovery of inhibitors targeting coronavirus proteases date: 2016-02-19 pages: extension: .txt txt: ./txt/cord-273373-5elel6qo.txt cache: ./cache/cord-273373-5elel6qo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273373-5elel6qo.txt' === file2bib.sh === id: cord-273553-xp4nfnq3 author: Ramatillah, D. L. title: TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-273553-xp4nfnq3.txt cache: ./cache/cord-273553-xp4nfnq3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273553-xp4nfnq3.txt' === file2bib.sh === id: cord-273126-gceffbfp author: Yuan, Kehu title: Suppression of SARS-CoV entry by peptides corresponding to heptad regions on spike glycoprotein date: 2004-07-02 pages: extension: .txt txt: ./txt/cord-273126-gceffbfp.txt cache: ./cache/cord-273126-gceffbfp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273126-gceffbfp.txt' === file2bib.sh === id: cord-272135-a09bf50o author: Brouqui, Philippe title: Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease date: 2009-04-22 pages: extension: .txt txt: ./txt/cord-272135-a09bf50o.txt cache: ./cache/cord-272135-a09bf50o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272135-a09bf50o.txt' === file2bib.sh === id: cord-272419-y3ebt4jm author: Monari, Caterina title: A Focus on the Nowadays Potential Antiviral Strategies in Early Phase of Coronavirus Disease 2019 (Covid-19): A Narrative Review date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-272419-y3ebt4jm.txt cache: ./cache/cord-272419-y3ebt4jm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272419-y3ebt4jm.txt' === file2bib.sh === id: cord-273182-djb0ozrt author: Díez, José María title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-273182-djb0ozrt.txt cache: ./cache/cord-273182-djb0ozrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273182-djb0ozrt.txt' === file2bib.sh === id: cord-272566-rtnhndw3 author: Robertson, M. title: A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-272566-rtnhndw3.txt cache: ./cache/cord-272566-rtnhndw3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272566-rtnhndw3.txt' === file2bib.sh === id: cord-274090-eab7i4f6 author: Gaspari, Valeria title: Can Covid‐19 be a sexually transmitted disease? Posterity will judge date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-274090-eab7i4f6.txt cache: ./cache/cord-274090-eab7i4f6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274090-eab7i4f6.txt' === file2bib.sh === id: cord-273726-24mi50rv author: Aaroe, Ashley title: Potential Neurologic and Oncologic Implications of the Novel Coronavirus date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-273726-24mi50rv.txt cache: ./cache/cord-273726-24mi50rv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273726-24mi50rv.txt' === file2bib.sh === id: cord-273492-i483r91m author: Fulzele, Sadanand title: COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-273492-i483r91m.txt cache: ./cache/cord-273492-i483r91m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273492-i483r91m.txt' === file2bib.sh === id: cord-273613-cpiveo7j author: Cao, Xia title: Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-273613-cpiveo7j.txt cache: ./cache/cord-273613-cpiveo7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273613-cpiveo7j.txt' === file2bib.sh === id: cord-274028-dvsvtsn0 author: Del Brutto, Oscar H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-274028-dvsvtsn0.txt cache: ./cache/cord-274028-dvsvtsn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274028-dvsvtsn0.txt' === file2bib.sh === id: cord-273408-jtpaue0z author: Romeyke, Tobias title: COVID-19 Case Report: An 84-Year-Old Man with Exacerbation of Multiple Comorbidities Due to COVID-19 Managed by a Multidisciplinary Team Using Patient-Reported Outcomes date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-273408-jtpaue0z.txt cache: ./cache/cord-273408-jtpaue0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273408-jtpaue0z.txt' === file2bib.sh === id: cord-272759-dqkjofw2 author: Small, Michael title: Super-spreaders and the rate of transmission of the SARS virus date: 2006-03-15 pages: extension: .txt txt: ./txt/cord-272759-dqkjofw2.txt cache: ./cache/cord-272759-dqkjofw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272759-dqkjofw2.txt' === file2bib.sh === id: cord-273891-7w334xgt author: Kirchdoerfer, Robert N. title: Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date: 2018-03-31 pages: extension: .txt txt: ./txt/cord-273891-7w334xgt.txt cache: ./cache/cord-273891-7w334xgt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273891-7w334xgt.txt' === file2bib.sh === id: cord-272702-7uc4ozjy author: Graham, T. G. W. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-272702-7uc4ozjy.txt cache: ./cache/cord-272702-7uc4ozjy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272702-7uc4ozjy.txt' === file2bib.sh === id: cord-273751-61eeykj1 author: Yang, Zhenwei title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-273751-61eeykj1.txt cache: ./cache/cord-273751-61eeykj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273751-61eeykj1.txt' === file2bib.sh === id: cord-273382-7w8fli6w author: Guderian, Daniela B. title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-273382-7w8fli6w.txt cache: ./cache/cord-273382-7w8fli6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273382-7w8fli6w.txt' === file2bib.sh === id: cord-273426-55vu6b3u author: Iba, Toshiaki title: Coagulopathy of Coronavirus Disease 2019 date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-273426-55vu6b3u.txt cache: ./cache/cord-273426-55vu6b3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273426-55vu6b3u.txt' === file2bib.sh === id: cord-273882-tqdcb3oo author: Pratibha, title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-273882-tqdcb3oo.txt cache: ./cache/cord-273882-tqdcb3oo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273882-tqdcb3oo.txt' === file2bib.sh === id: cord-273961-ja8xggnd author: Nakagawara, Kensuke title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date: 2020-07-26 pages: extension: .txt txt: ./txt/cord-273961-ja8xggnd.txt cache: ./cache/cord-273961-ja8xggnd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273961-ja8xggnd.txt' === file2bib.sh === id: cord-273913-xem3alih author: Marraha, Farah title: A Review of the Dermatological Manifestations of Coronavirus Disease 2019 (COVID-19) date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-273913-xem3alih.txt cache: ./cache/cord-273913-xem3alih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273913-xem3alih.txt' === file2bib.sh === id: cord-273828-557vlq9d author: Brito, Carlos Antunes title: Mechanisms and consequences of COVID-19 associated liver injury: What can we affirm? date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-273828-557vlq9d.txt cache: ./cache/cord-273828-557vlq9d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273828-557vlq9d.txt' === file2bib.sh === id: cord-273898-i7icvsg1 author: Parcell, B. title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-273898-i7icvsg1.txt cache: ./cache/cord-273898-i7icvsg1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273898-i7icvsg1.txt' === file2bib.sh === id: cord-274097-11hvriqy author: Katz, Louis M. title: Is SARS‐CoV‐2 transfusion transmitted? date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-274097-11hvriqy.txt cache: ./cache/cord-274097-11hvriqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274097-11hvriqy.txt' === file2bib.sh === id: cord-274231-2s7ki6g7 author: Ziebuhr, John title: SARS – Unprecedented global response to a newly emerging disease date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-274231-2s7ki6g7.txt cache: ./cache/cord-274231-2s7ki6g7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274231-2s7ki6g7.txt' === file2bib.sh === id: cord-274053-406dfdih author: Srivastava, Kamna title: Association between COVID-19 and cardiovascular disease date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-274053-406dfdih.txt cache: ./cache/cord-274053-406dfdih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274053-406dfdih.txt' === file2bib.sh === id: cord-273723-srfypn7j author: Omar, Sarah title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-273723-srfypn7j.txt cache: ./cache/cord-273723-srfypn7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273723-srfypn7j.txt' === file2bib.sh === id: cord-274439-y9jrdg5n author: Aoyama, Kazuyoshi title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-274439-y9jrdg5n.txt cache: ./cache/cord-274439-y9jrdg5n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274439-y9jrdg5n.txt' === file2bib.sh === id: cord-274343-y9zqbefu author: Petersen, Irene title: Three Quarters of People with SARS-CoV-2 Infection are Asymptomatic: Analysis of English Household Survey Data date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-274343-y9zqbefu.txt cache: ./cache/cord-274343-y9zqbefu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274343-y9zqbefu.txt' === file2bib.sh === id: cord-273893-3nd6ptrg author: Lu, Guangwen title: Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 date: 2013-07-07 pages: extension: .txt txt: ./txt/cord-273893-3nd6ptrg.txt cache: ./cache/cord-273893-3nd6ptrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273893-3nd6ptrg.txt' === file2bib.sh === id: cord-273784-sr6afv60 author: Cazares, Lisa H. title: Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-273784-sr6afv60.txt cache: ./cache/cord-273784-sr6afv60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273784-sr6afv60.txt' === file2bib.sh === id: cord-274508-nigru1o8 author: Lally, Michelle title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-274508-nigru1o8.txt cache: ./cache/cord-274508-nigru1o8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274508-nigru1o8.txt' === file2bib.sh === id: cord-273614-qmp2tqtb author: Tahir, Faryal title: Cardiac Manifestations of Coronavirus Disease 2019 (COVID-19): A Comprehensive Review date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-273614-qmp2tqtb.txt cache: ./cache/cord-273614-qmp2tqtb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273614-qmp2tqtb.txt' === file2bib.sh === id: cord-274007-zndtddty author: Rasmussen, Sonja A. title: Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-274007-zndtddty.txt cache: ./cache/cord-274007-zndtddty.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274007-zndtddty.txt' === file2bib.sh === id: cord-274341-vrwmxwvm author: Frank, Carlos Henrique Michiles title: Guillain–Barré Syndrome Associated with SARS-CoV-2 Infection in a Pediatric Patient date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-274341-vrwmxwvm.txt cache: ./cache/cord-274341-vrwmxwvm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274341-vrwmxwvm.txt' === file2bib.sh === id: cord-274205-e2r38v29 author: Tsunetsugu-Yokota, Yasuko title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen date: 2007-11-28 pages: extension: .txt txt: ./txt/cord-274205-e2r38v29.txt cache: ./cache/cord-274205-e2r38v29.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274205-e2r38v29.txt' === file2bib.sh === id: cord-274122-n9jnu2ah author: Mielech, Anna M. title: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date: 2014-02-01 pages: extension: .txt txt: ./txt/cord-274122-n9jnu2ah.txt cache: ./cache/cord-274122-n9jnu2ah.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274122-n9jnu2ah.txt' === file2bib.sh === id: cord-274680-6pui91uu author: Gao, Chun title: Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-274680-6pui91uu.txt cache: ./cache/cord-274680-6pui91uu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274680-6pui91uu.txt' === file2bib.sh === id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271504-t3y1w9ef.txt cache: ./cache/cord-271504-t3y1w9ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271504-t3y1w9ef.txt' === file2bib.sh === id: cord-274366-t138l6px author: Benetti, Elisa title: ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-274366-t138l6px.txt cache: ./cache/cord-274366-t138l6px.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274366-t138l6px.txt' === file2bib.sh === id: cord-274648-e0daf8w6 author: Madeddu, Paolo title: Cardiovascular complications of COVID-19: evidence, misconceptions, and new opportunities date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-274648-e0daf8w6.txt cache: ./cache/cord-274648-e0daf8w6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274648-e0daf8w6.txt' === file2bib.sh === id: cord-274459-781by93r author: Khalifa, Shaden A. M. title: Comprehensive Overview on Multiple Strategies Fighting COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-274459-781by93r.txt cache: ./cache/cord-274459-781by93r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274459-781by93r.txt' === file2bib.sh === id: cord-274409-4ugdxbmy author: Laskar, Rezwanuzzaman title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-274409-4ugdxbmy.txt cache: ./cache/cord-274409-4ugdxbmy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274409-4ugdxbmy.txt' === file2bib.sh === id: cord-274750-fynxciwg author: Peterson, Danielle title: Calm before the storm: understanding the role of JAK inhibitors in COVID-19 date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-274750-fynxciwg.txt cache: ./cache/cord-274750-fynxciwg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274750-fynxciwg.txt' === file2bib.sh === id: cord-274156-c0c4rjfa author: Chau, J.P.C. title: Infection control practices among hospital health and support workers in Hong Kong date: 2010-08-31 pages: extension: .txt txt: ./txt/cord-274156-c0c4rjfa.txt cache: ./cache/cord-274156-c0c4rjfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274156-c0c4rjfa.txt' === file2bib.sh === id: cord-274513-0biyfhab author: Baumgartner, M. T. title: Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19 date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-274513-0biyfhab.txt cache: ./cache/cord-274513-0biyfhab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274513-0biyfhab.txt' === file2bib.sh === id: cord-273906-s7l0yxc0 author: Ranga, Vipin title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-273906-s7l0yxc0.txt cache: ./cache/cord-273906-s7l0yxc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273906-s7l0yxc0.txt' === file2bib.sh === id: cord-274708-w6gmscv4 author: Mathewson, Alison C. title: Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 date: 2008-11-17 pages: extension: .txt txt: ./txt/cord-274708-w6gmscv4.txt cache: ./cache/cord-274708-w6gmscv4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274708-w6gmscv4.txt' === file2bib.sh === id: cord-275360-uphdzj5l author: Sahajpal, Nikhil Shri title: Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-275360-uphdzj5l.txt cache: ./cache/cord-275360-uphdzj5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275360-uphdzj5l.txt' === file2bib.sh === id: cord-274184-hm516x6p author: Elli, Luca title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-274184-hm516x6p.txt cache: ./cache/cord-274184-hm516x6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274184-hm516x6p.txt' === file2bib.sh === id: cord-274286-07arhrv9 author: Hosier, H. title: First case of placental infection with SARS-CoV-2 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-274286-07arhrv9.txt cache: ./cache/cord-274286-07arhrv9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274286-07arhrv9.txt' === file2bib.sh === id: cord-274852-84m62t4x author: Hogan, Catherine A. title: Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019 date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-274852-84m62t4x.txt cache: ./cache/cord-274852-84m62t4x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274852-84m62t4x.txt' === file2bib.sh === id: cord-274396-l611eisi author: Park, Su-Jin title: Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-274396-l611eisi.txt cache: ./cache/cord-274396-l611eisi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274396-l611eisi.txt' === file2bib.sh === id: cord-274399-cd7cmpoj author: Barzin, Amir title: SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-274399-cd7cmpoj.txt cache: ./cache/cord-274399-cd7cmpoj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274399-cd7cmpoj.txt' === file2bib.sh === id: cord-274313-mrvk9r4w author: Li, Hui title: SARS-CoV-2 and viral sepsis: observations and hypotheses date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-274313-mrvk9r4w.txt cache: ./cache/cord-274313-mrvk9r4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274313-mrvk9r4w.txt' === file2bib.sh === id: cord-274945-6p5de7o2 author: Clevers, Hans title: COVID-19: organoids go viral date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-274945-6p5de7o2.txt cache: ./cache/cord-274945-6p5de7o2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274945-6p5de7o2.txt' === file2bib.sh === id: cord-274008-p3st70u3 author: Mann, E. R. title: Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-274008-p3st70u3.txt cache: ./cache/cord-274008-p3st70u3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274008-p3st70u3.txt' === file2bib.sh === id: cord-273505-pcsw3vmx author: Liu, Xiaosheng title: High-Dose Intravenous Immunoglobulins in the Treatment of Severe Acute Viral Pneumonia: The Known Mechanisms and Clinical Effects date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-273505-pcsw3vmx.txt cache: ./cache/cord-273505-pcsw3vmx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273505-pcsw3vmx.txt' === file2bib.sh === id: cord-274326-msbdrp3e author: Ren, Xiaohan title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-274326-msbdrp3e.txt cache: ./cache/cord-274326-msbdrp3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274326-msbdrp3e.txt' === file2bib.sh === id: cord-274707-mxh38hwd author: Laureano, Ana Flávia Santarine title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 pages: extension: .txt txt: ./txt/cord-274707-mxh38hwd.txt cache: ./cache/cord-274707-mxh38hwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274707-mxh38hwd.txt' === file2bib.sh === id: cord-275108-snqbrxgr author: Daverio, Marco title: Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-275108-snqbrxgr.txt cache: ./cache/cord-275108-snqbrxgr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275108-snqbrxgr.txt' === file2bib.sh === id: cord-274114-fglyfz8p author: Minervina, Anastasia A. title: Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-274114-fglyfz8p.txt cache: ./cache/cord-274114-fglyfz8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274114-fglyfz8p.txt' === file2bib.sh === id: cord-274536-fv7mltj7 author: Tong, Yongqing title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-274536-fv7mltj7.txt cache: ./cache/cord-274536-fv7mltj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274536-fv7mltj7.txt' === file2bib.sh === id: cord-275111-38hgg0jz author: Kumar, Abhishek title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-275111-38hgg0jz.txt cache: ./cache/cord-275111-38hgg0jz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275111-38hgg0jz.txt' === file2bib.sh === id: cord-275404-hv3y4x4g author: Zumla, Alimuddin title: Infection control and MERS-CoV in health-care workers date: 2014-05-20 pages: extension: .txt txt: ./txt/cord-275404-hv3y4x4g.txt cache: ./cache/cord-275404-hv3y4x4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275404-hv3y4x4g.txt' === file2bib.sh === id: cord-275420-zkxyxiv5 author: Crabtree, Scott J. title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-275420-zkxyxiv5.txt cache: ./cache/cord-275420-zkxyxiv5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275420-zkxyxiv5.txt' === file2bib.sh === id: cord-275128-620wf0pb author: White, J. R. title: PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-275128-620wf0pb.txt cache: ./cache/cord-275128-620wf0pb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275128-620wf0pb.txt' === file2bib.sh === id: cord-275250-ilmgy7ce author: Xia, Yong title: Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-275250-ilmgy7ce.txt cache: ./cache/cord-275250-ilmgy7ce.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275250-ilmgy7ce.txt' === file2bib.sh === id: cord-274252-h4occy7h author: de Lima Menezes, Gabriela title: Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-274252-h4occy7h.txt cache: ./cache/cord-274252-h4occy7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274252-h4occy7h.txt' === file2bib.sh === id: cord-274715-dcs1rgd0 author: Mani Mishra, Pushpendra title: Serum albumin-mediated strategy for the effective targeting of SARS-CoV-2 date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-274715-dcs1rgd0.txt cache: ./cache/cord-274715-dcs1rgd0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274715-dcs1rgd0.txt' === file2bib.sh === id: cord-274602-q9i2k304 author: Iqbal, Yousaf title: Psychiatric presentation of patients with acute SARS-CoV-2 infection: a retrospective review of 50 consecutive patients seen by a consultation-liaison psychiatry team date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-274602-q9i2k304.txt cache: ./cache/cord-274602-q9i2k304.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-274602-q9i2k304.txt' === file2bib.sh === id: cord-274279-f99nd3dx author: Fantini, Jacques title: Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-274279-f99nd3dx.txt cache: ./cache/cord-274279-f99nd3dx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274279-f99nd3dx.txt' === file2bib.sh === id: cord-274510-fo7p98np author: Spadera, Lucrezia title: Potential Role of GcMAF in suppressing the severity of COVID-19-induced immune responses: lesson learned from HIV date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-274510-fo7p98np.txt cache: ./cache/cord-274510-fo7p98np.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274510-fo7p98np.txt' === file2bib.sh === id: cord-274416-bmvazgj7 author: Trevisanuto, Daniele title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-274416-bmvazgj7.txt cache: ./cache/cord-274416-bmvazgj7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274416-bmvazgj7.txt' === file2bib.sh === id: cord-274284-mi4n7xty author: Pang, Khang Wen title: Frequency and Clinical Utility of Olfactory Dysfunction in COVID-19: a Systematic Review and Meta-analysis date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-274284-mi4n7xty.txt cache: ./cache/cord-274284-mi4n7xty.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274284-mi4n7xty.txt' === file2bib.sh === id: cord-274761-c2hgkbg6 author: Rosenberg, Eli S. title: Cumulative incidence and diagnosis of SARS-CoV-2 infection in New York date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-274761-c2hgkbg6.txt cache: ./cache/cord-274761-c2hgkbg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274761-c2hgkbg6.txt' === file2bib.sh === id: cord-275452-ymimvoq9 author: Ameen, Fuad title: Covid-19 pandemic outburst in Saudi Arabia: A Glimpse date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-275452-ymimvoq9.txt cache: ./cache/cord-275452-ymimvoq9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275452-ymimvoq9.txt' === file2bib.sh === id: cord-274834-24v2b509 author: Lima, Rosiane title: Establishment of a pediatric COVID-19 biorepository: unique considerations and opportunities for studying the impact of the COVID-19 pandemic on children date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-274834-24v2b509.txt cache: ./cache/cord-274834-24v2b509.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274834-24v2b509.txt' === file2bib.sh === id: cord-274788-oyk8js16 author: Bae, Sanghyuk title: Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-274788-oyk8js16.txt cache: ./cache/cord-274788-oyk8js16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274788-oyk8js16.txt' === file2bib.sh === id: cord-275173-ely3aen3 author: Pickering, Brad S. title: Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-275173-ely3aen3.txt cache: ./cache/cord-275173-ely3aen3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275173-ely3aen3.txt' === file2bib.sh === id: cord-274948-ze6scnae author: Segondy, Michel title: Les Coronavirus humains date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-274948-ze6scnae.txt cache: ./cache/cord-274948-ze6scnae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274948-ze6scnae.txt' === file2bib.sh === id: cord-275023-0z219rcy author: Cerofolini, Linda title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-275023-0z219rcy.txt cache: ./cache/cord-275023-0z219rcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275023-0z219rcy.txt' === file2bib.sh === id: cord-275521-dlp055z8 author: Goldman, Emanuel title: Exaggerated risk of transmission of COVID-19 by fomites date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-275521-dlp055z8.txt cache: ./cache/cord-275521-dlp055z8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275521-dlp055z8.txt' === file2bib.sh === id: cord-274668-lh7c9izt author: Wang, Chaofu title: Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-274668-lh7c9izt.txt cache: ./cache/cord-274668-lh7c9izt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274668-lh7c9izt.txt' === file2bib.sh === id: cord-274521-u8p5lz9o author: Lee, Abby C. title: Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-274521-u8p5lz9o.txt cache: ./cache/cord-274521-u8p5lz9o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274521-u8p5lz9o.txt' === file2bib.sh === id: cord-274591-p34kk4up author: Horby, Peter W, title: Prospects for Emerging Infections in East and Southeast Asia 10 Years after Severe Acute Respiratory Syndrome date: 2013-06-17 pages: extension: .txt txt: ./txt/cord-274591-p34kk4up.txt cache: ./cache/cord-274591-p34kk4up.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274591-p34kk4up.txt' === file2bib.sh === id: cord-275482-ncrhb75f author: Jia, Hong Peng title: Infection of Human Airway Epithelia by Sars Coronavirus is Associated with ACE2 Expression and Localization date: 2006 pages: extension: .txt txt: ./txt/cord-275482-ncrhb75f.txt cache: ./cache/cord-275482-ncrhb75f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275482-ncrhb75f.txt' === file2bib.sh === id: cord-274542-fpzk5k79 author: Patti, Giuseppe title: Questions and Answers on Practical Thrombotic Issues in SARS-CoV-2 Infection: A Guidance Document from the Italian Working Group on Atherosclerosis, Thrombosis and Vascular Biology date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-274542-fpzk5k79.txt cache: ./cache/cord-274542-fpzk5k79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274542-fpzk5k79.txt' === file2bib.sh === id: cord-275604-5u4kikov author: Feehan, Amy K. title: Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 date: 2020-11-17 pages: extension: .txt txt: ./txt/cord-275604-5u4kikov.txt cache: ./cache/cord-275604-5u4kikov.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275604-5u4kikov.txt' === file2bib.sh === id: cord-274280-x5s4l0pp author: Yang, Jinsung title: Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-274280-x5s4l0pp.txt cache: ./cache/cord-274280-x5s4l0pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-274280-x5s4l0pp.txt' === file2bib.sh === id: cord-275552-ijxxeo27 author: Yen, Zui-Shen title: How much would you be willing to pay for preventing a new dangerous infectious disease: A willingness-to-pay study in medical personnel working in the emergency department date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-275552-ijxxeo27.txt cache: ./cache/cord-275552-ijxxeo27.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275552-ijxxeo27.txt' === file2bib.sh === id: cord-274520-c674wkmt author: Moelling, Karin title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-274520-c674wkmt.txt cache: ./cache/cord-274520-c674wkmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274520-c674wkmt.txt' === file2bib.sh === id: cord-274824-kaefedl1 author: Turski, Waldemar A. title: AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-274824-kaefedl1.txt cache: ./cache/cord-274824-kaefedl1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274824-kaefedl1.txt' === file2bib.sh === id: cord-275495-h60x89zi author: Bocksberger, S. title: Temporäre Hyposmie bei COVID-19-Patienten date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-275495-h60x89zi.txt cache: ./cache/cord-275495-h60x89zi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275495-h60x89zi.txt' === file2bib.sh === id: cord-274528-mr81o9cu author: Li, Fei title: Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-274528-mr81o9cu.txt cache: ./cache/cord-274528-mr81o9cu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274528-mr81o9cu.txt' === file2bib.sh === id: cord-275357-yx8lsfdv author: Lu, J. title: Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-275357-yx8lsfdv.txt cache: ./cache/cord-275357-yx8lsfdv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275357-yx8lsfdv.txt' === file2bib.sh === id: cord-275199-y7b12vml author: Suárez-Fariñas, Mayte title: Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-275199-y7b12vml.txt cache: ./cache/cord-275199-y7b12vml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275199-y7b12vml.txt' === file2bib.sh === id: cord-274839-r4jg6wac author: Azam, Faizul title: An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-274839-r4jg6wac.txt cache: ./cache/cord-274839-r4jg6wac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274839-r4jg6wac.txt' === file2bib.sh === id: cord-275439-cdlcv1c9 author: Iwasaki, S. title: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-275439-cdlcv1c9.txt cache: ./cache/cord-275439-cdlcv1c9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275439-cdlcv1c9.txt' === file2bib.sh === id: cord-275004-qzg03dvg author: Veras, Flavio Protasio title: SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-275004-qzg03dvg.txt cache: ./cache/cord-275004-qzg03dvg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275004-qzg03dvg.txt' === file2bib.sh === id: cord-275454-an8xvow3 author: Clark, Andrew E title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-275454-an8xvow3.txt cache: ./cache/cord-275454-an8xvow3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275454-an8xvow3.txt' === file2bib.sh === id: cord-275862-1aqtqaod author: Yang, Xiaodong title: A case of COVID-19 patient with the diarrhea as initial symptom and literature review date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-275862-1aqtqaod.txt cache: ./cache/cord-275862-1aqtqaod.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275862-1aqtqaod.txt' === file2bib.sh === id: cord-275336-lnhkux0m author: Marino Gammazza, Antonella title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-275336-lnhkux0m.txt cache: ./cache/cord-275336-lnhkux0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275336-lnhkux0m.txt' === file2bib.sh === id: cord-275569-i5y23mmz author: de Bernardis, E. title: A putative role for the tobacco mosaic virus in smokers’ resistance to COVID-19 date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-275569-i5y23mmz.txt cache: ./cache/cord-275569-i5y23mmz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275569-i5y23mmz.txt' === file2bib.sh === id: cord-273918-knlc3bxh author: Holmes, Emily A title: Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-273918-knlc3bxh.txt cache: ./cache/cord-273918-knlc3bxh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273918-knlc3bxh.txt' === file2bib.sh === id: cord-275216-dnt88ycw author: Zhang, Xue-Yan title: Biological, clinical and epidemiological features of COVID-19, SARS and MERS and AutoDock simulation of ACE2 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-275216-dnt88ycw.txt cache: ./cache/cord-275216-dnt88ycw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275216-dnt88ycw.txt' === file2bib.sh === id: cord-274141-vujx538o author: Chinsembu, Kazhila C. title: Coronaviruses and Nature’s Pharmacy for the Relief of Coronavirus Disease 2019 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-274141-vujx538o.txt cache: ./cache/cord-274141-vujx538o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274141-vujx538o.txt' === file2bib.sh === id: cord-275784-n6jv72l7 author: Spina, Alfio title: The Management Of Neurosurgical Patients During The Covid-19 Pandemic date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-275784-n6jv72l7.txt cache: ./cache/cord-275784-n6jv72l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275784-n6jv72l7.txt' === file2bib.sh === id: cord-274841-rcdoewwv author: Tay, Matthew Zirui title: The trinity of COVID-19: immunity, inflammation and intervention date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-274841-rcdoewwv.txt cache: ./cache/cord-274841-rcdoewwv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274841-rcdoewwv.txt' === file2bib.sh === id: cord-275191-lgze4zex author: Al-Sadeq, Duaa W. title: The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-275191-lgze4zex.txt cache: ./cache/cord-275191-lgze4zex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275191-lgze4zex.txt' === file2bib.sh === id: cord-275340-q8d7rvnj author: Sun, JingKang title: Advances in the use of chloroquine and hydroxychloroquine for the treatment of COVID-19 date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-275340-q8d7rvnj.txt cache: ./cache/cord-275340-q8d7rvnj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275340-q8d7rvnj.txt' === file2bib.sh === id: cord-275348-jna496x7 author: Kapadia, Sagar U. title: SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date: 2008-06-20 pages: extension: .txt txt: ./txt/cord-275348-jna496x7.txt cache: ./cache/cord-275348-jna496x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275348-jna496x7.txt' === file2bib.sh === id: cord-275438-drywzvx8 author: Satış, Hasan title: Prognostic value of interleukin-18 and its association with other inflammatory markers and disease severity in COVID-19 date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-275438-drywzvx8.txt cache: ./cache/cord-275438-drywzvx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275438-drywzvx8.txt' === file2bib.sh === id: cord-276057-427ji6ze author: Effenberger, Maria title: Faecal calprotectin indicates intestinal inflammation in COVID-19 date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-276057-427ji6ze.txt cache: ./cache/cord-276057-427ji6ze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276057-427ji6ze.txt' === file2bib.sh === id: cord-275960-1m6poddy author: Thieme, C. J. title: The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-275960-1m6poddy.txt cache: ./cache/cord-275960-1m6poddy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275960-1m6poddy.txt' === file2bib.sh === id: cord-276345-xsjh3766 author: Arshad, Yasir title: Detection of SARS-CoV-2 in ophthalmic secretions in Pakistan: A preliminary report date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-276345-xsjh3766.txt cache: ./cache/cord-276345-xsjh3766.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276345-xsjh3766.txt' === file2bib.sh === id: cord-275760-hi9sj0d7 author: Ng, Siew C title: Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-275760-hi9sj0d7.txt cache: ./cache/cord-275760-hi9sj0d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275760-hi9sj0d7.txt' === file2bib.sh === id: cord-275894-puwaty70 author: Wajnberg, A. title: SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-275894-puwaty70.txt cache: ./cache/cord-275894-puwaty70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275894-puwaty70.txt' === file2bib.sh === id: cord-275252-4e3cn50u author: Rad SM, Ali Hosseini title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-275252-4e3cn50u.txt cache: ./cache/cord-275252-4e3cn50u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275252-4e3cn50u.txt' === file2bib.sh === id: cord-276147-30buoweg author: Avancini, Joao title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-276147-30buoweg.txt cache: ./cache/cord-276147-30buoweg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276147-30buoweg.txt' === file2bib.sh === id: cord-275185-9br8lwma author: Zeng, Hao title: The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-275185-9br8lwma.txt cache: ./cache/cord-275185-9br8lwma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275185-9br8lwma.txt' === file2bib.sh === id: cord-275888-6u1o6414 author: Tan, Kian Teo title: N95 acne date: 2004-06-29 pages: extension: .txt txt: ./txt/cord-275888-6u1o6414.txt cache: ./cache/cord-275888-6u1o6414.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275888-6u1o6414.txt' === file2bib.sh === id: cord-275506-3t5gf66c author: Agbuduwe, Charles title: Hematolological Manifestations of COVID‐19: From Cytopenia to Coagulopathy date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-275506-3t5gf66c.txt cache: ./cache/cord-275506-3t5gf66c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275506-3t5gf66c.txt' === file2bib.sh === id: cord-274474-u2fdicgz author: Majumder, Joydeb title: Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-274474-u2fdicgz.txt cache: ./cache/cord-274474-u2fdicgz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274474-u2fdicgz.txt' === file2bib.sh === id: cord-275565-xerr4vki author: Kumar, Manish title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-275565-xerr4vki.txt cache: ./cache/cord-275565-xerr4vki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275565-xerr4vki.txt' === file2bib.sh === id: cord-276350-lcl9jn35 author: Acharya, Dhiraj title: Dysregulation of type I interferon responses in COVID-19 date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-276350-lcl9jn35.txt cache: ./cache/cord-276350-lcl9jn35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276350-lcl9jn35.txt' === file2bib.sh === id: cord-275708-17cz3agx author: Babyn, Paul S. title: Severe acute respiratory syndrome (SARS): chest radiographic features in children date: 2003-11-18 pages: extension: .txt txt: ./txt/cord-275708-17cz3agx.txt cache: ./cache/cord-275708-17cz3agx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275708-17cz3agx.txt' === file2bib.sh === id: cord-275846-7onenxg7 author: Kamikubo, Yasuhiko title: Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2 date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-275846-7onenxg7.txt cache: ./cache/cord-275846-7onenxg7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275846-7onenxg7.txt' === file2bib.sh === id: cord-276980-k8xi2zvh author: Koh, David title: Occupational Health Response to SARS date: 2005-01-17 pages: extension: .txt txt: ./txt/cord-276980-k8xi2zvh.txt cache: ./cache/cord-276980-k8xi2zvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276980-k8xi2zvh.txt' === file2bib.sh === id: cord-276058-1mpp7sbt author: Shlomai, A. title: Global versus focused isolation during the SARS-CoV-2 pandemic-A cost-effectiveness analysis date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-276058-1mpp7sbt.txt cache: ./cache/cord-276058-1mpp7sbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276058-1mpp7sbt.txt' === file2bib.sh === id: cord-276316-7ot9ds34 author: Lei, Chunliang title: Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-276316-7ot9ds34.txt cache: ./cache/cord-276316-7ot9ds34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276316-7ot9ds34.txt' === file2bib.sh === id: cord-276394-s9y11oep author: Liang, W. title: Hindsight: A re-analysis of the severe acute respiratory syndrome outbreak in Beijing date: 2007-10-31 pages: extension: .txt txt: ./txt/cord-276394-s9y11oep.txt cache: ./cache/cord-276394-s9y11oep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276394-s9y11oep.txt' === file2bib.sh === id: cord-276209-5999g9gp author: Poland, Gregory A. title: Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine development date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-276209-5999g9gp.txt cache: ./cache/cord-276209-5999g9gp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276209-5999g9gp.txt' === file2bib.sh === id: cord-275690-83nrzfon author: Stanifer, Megan L. title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-275690-83nrzfon.txt cache: ./cache/cord-275690-83nrzfon.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275690-83nrzfon.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91428 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92756 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-276090-n8c2jpr6 author: Patel, Hiren N. title: Cerebellar Infarction Requiring Surgical Decompression in patient with COVID 19 Pathological Analysis, Brief Review date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-276090-n8c2jpr6.txt cache: ./cache/cord-276090-n8c2jpr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276090-n8c2jpr6.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92797 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-276061-7b8h2sjw author: Zammit, M title: A rise in facial nerve palsies during the coronavirus disease 2019 pandemic date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-276061-7b8h2sjw.txt cache: ./cache/cord-276061-7b8h2sjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276061-7b8h2sjw.txt' === file2bib.sh === id: cord-276995-b003vcdc author: Wiese, Andrew D title: Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-276995-b003vcdc.txt cache: ./cache/cord-276995-b003vcdc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276995-b003vcdc.txt' === file2bib.sh === id: cord-276991-gv1k7u7j author: Zhang, Xu title: Strategies to trace back the origin of COVID-19 date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-276991-gv1k7u7j.txt cache: ./cache/cord-276991-gv1k7u7j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276991-gv1k7u7j.txt' === file2bib.sh === id: cord-275946-ofd2ipvs author: Cheng, Matthew P. title: Serodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-275946-ofd2ipvs.txt cache: ./cache/cord-275946-ofd2ipvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275946-ofd2ipvs.txt' === file2bib.sh === id: cord-276548-bh3w7oas author: Ramkumar, K. title: Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-276548-bh3w7oas.txt cache: ./cache/cord-276548-bh3w7oas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276548-bh3w7oas.txt' === file2bib.sh === id: cord-275858-46jzw94p author: Leung, Janice M. title: COVID-19 and COPD date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-275858-46jzw94p.txt cache: ./cache/cord-275858-46jzw94p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275858-46jzw94p.txt' === file2bib.sh === id: cord-276414-kicu0tv5 author: Bahadur Gurung, Arun title: In silico screening of FDA approved drugs reveals ergotamine and dihydroergotamine as potential coronavirus main protease enzyme inhibitors date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-276414-kicu0tv5.txt cache: ./cache/cord-276414-kicu0tv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276414-kicu0tv5.txt' === file2bib.sh === id: cord-276857-i948aq4b author: Chung, Grace TY title: A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date: 2005-10-18 pages: extension: .txt txt: ./txt/cord-276857-i948aq4b.txt cache: ./cache/cord-276857-i948aq4b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276857-i948aq4b.txt' === file2bib.sh === id: cord-276619-6ndkz1da author: Perrone, Serafina title: Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-276619-6ndkz1da.txt cache: ./cache/cord-276619-6ndkz1da.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276619-6ndkz1da.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-275257-upj8mvzn author: Hwang, E. Shelley title: Surgical Oncologists and the COVID-19 Pandemic: Guiding Cancer Patients Effectively through Turbulence and Change date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-275257-upj8mvzn.txt cache: ./cache/cord-275257-upj8mvzn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275257-upj8mvzn.txt' === file2bib.sh === id: cord-275993-isff6lp2 author: Han, Dong P title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date: 2004-08-15 pages: extension: .txt txt: ./txt/cord-275993-isff6lp2.txt cache: ./cache/cord-275993-isff6lp2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275993-isff6lp2.txt' === file2bib.sh === id: cord-277197-njy99jh4 author: Song, Fang title: COVID‐19: Recommended sampling sites at different stage of the disease date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-277197-njy99jh4.txt cache: ./cache/cord-277197-njy99jh4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277197-njy99jh4.txt' === file2bib.sh === id: cord-275746-3sgbpn13 author: Shimamoto, Yasuhiro title: Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors date: 2015-02-15 pages: extension: .txt txt: ./txt/cord-275746-3sgbpn13.txt cache: ./cache/cord-275746-3sgbpn13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275746-3sgbpn13.txt' === file2bib.sh === id: cord-276013-8dhqa2gj author: Luo, Yung-Hung title: Overview of coronavirus disease 2019: Treatment updates and advances date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-276013-8dhqa2gj.txt cache: ./cache/cord-276013-8dhqa2gj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276013-8dhqa2gj.txt' === file2bib.sh === id: cord-275926-rj23z7po author: Fontanella, Marco M. title: Neurosurgical practice during the SARS-CoV-2 pandemic: a worldwide survey date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-275926-rj23z7po.txt cache: ./cache/cord-275926-rj23z7po.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275926-rj23z7po.txt' === file2bib.sh === id: cord-276361-77cylm1o author: Yamamoto, Norio title: HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus date: 2004-06-04 pages: extension: .txt txt: ./txt/cord-276361-77cylm1o.txt cache: ./cache/cord-276361-77cylm1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276361-77cylm1o.txt' === file2bib.sh === id: cord-276017-2375ipkk author: Chen, Dongsheng title: Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-276017-2375ipkk.txt cache: ./cache/cord-276017-2375ipkk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276017-2375ipkk.txt' === file2bib.sh === id: cord-275979-cx2h5bsw author: Scutelnic, Adrian title: Vascular Events, Vascular Disease and Vascular Risk Factors—Strongly Intertwined with COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-275979-cx2h5bsw.txt cache: ./cache/cord-275979-cx2h5bsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275979-cx2h5bsw.txt' === file2bib.sh === id: cord-276969-mdry8qzv author: Chirumbolo, Salvatore title: Might the many positive COVID19 subjects in Italy have been caused by resident bat‐derived zoonotic β‐coronaviruses instead of the Wuhan (China) outbreak? date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-276969-mdry8qzv.txt cache: ./cache/cord-276969-mdry8qzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276969-mdry8qzv.txt' === file2bib.sh === id: cord-276769-th7iou21 author: Khan, Suliman title: Coronaviruses disease 2019 (COVID-19): causative agent, mental health concerns, and potential management options date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-276769-th7iou21.txt cache: ./cache/cord-276769-th7iou21.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276769-th7iou21.txt' === file2bib.sh === id: cord-276820-l7bd5y8y author: So, Winnie K.W. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-276820-l7bd5y8y.txt cache: ./cache/cord-276820-l7bd5y8y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276820-l7bd5y8y.txt' === file2bib.sh === id: cord-276487-8vkrh70j author: Kang, Sisi title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-276487-8vkrh70j.txt cache: ./cache/cord-276487-8vkrh70j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276487-8vkrh70j.txt' === file2bib.sh === id: cord-277025-gmy51dx4 author: Pfefferle, Susanne title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-277025-gmy51dx4.txt cache: ./cache/cord-277025-gmy51dx4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277025-gmy51dx4.txt' === file2bib.sh === id: cord-275978-pezm1tnw author: Riccardo, Flavia title: Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-275978-pezm1tnw.txt cache: ./cache/cord-275978-pezm1tnw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275978-pezm1tnw.txt' === file2bib.sh === id: cord-276327-wyevh4xv author: Sheng, Calvin C title: Canakinumab to reduce deterioration of cardiac and respiratory function in SARS‐CoV‐2 associated myocardial injury with heightened inflammation (canakinumab in Covid‐19 cardiac injury: The three C study) date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-276327-wyevh4xv.txt cache: ./cache/cord-276327-wyevh4xv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276327-wyevh4xv.txt' === file2bib.sh === id: cord-276139-l13hbucu author: Hashem, A. M. title: Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-276139-l13hbucu.txt cache: ./cache/cord-276139-l13hbucu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276139-l13hbucu.txt' === file2bib.sh === id: cord-276132-tv5y1eqc author: Ray, Upasana title: COVID-19: The Impact in Oncology Care date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-276132-tv5y1eqc.txt cache: ./cache/cord-276132-tv5y1eqc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276132-tv5y1eqc.txt' === file2bib.sh === id: cord-277278-lg38l5gh author: Tang, Olive title: Outcomes of nursing home COVID-19 patients by initial symptoms and comorbidity: Results of universal testing of 1,970 residents date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-277278-lg38l5gh.txt cache: ./cache/cord-277278-lg38l5gh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277278-lg38l5gh.txt' === file2bib.sh === id: cord-277307-wabruzfs author: Gu, Wei title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-277307-wabruzfs.txt cache: ./cache/cord-277307-wabruzfs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277307-wabruzfs.txt' === file2bib.sh === id: cord-276403-yomjm2gg author: Woo, Patrick CY title: Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections date: 2006-10-30 pages: extension: .txt txt: ./txt/cord-276403-yomjm2gg.txt cache: ./cache/cord-276403-yomjm2gg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276403-yomjm2gg.txt' === file2bib.sh === id: cord-276784-8lmg97zc author: Boziki, Marina Kleopatra title: COVID-19 Immunopathology and the Central Nervous System: Implication for Multiple Sclerosis and Other Autoimmune Diseases with Associated Demyelination date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-276784-8lmg97zc.txt cache: ./cache/cord-276784-8lmg97zc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276784-8lmg97zc.txt' === file2bib.sh === id: cord-277342-40d24mvm author: Chen, Yu title: SARS-CoV-2: virus dynamics and host response date: 2020-03-23 pages: extension: .txt txt: ./txt/cord-277342-40d24mvm.txt cache: ./cache/cord-277342-40d24mvm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277342-40d24mvm.txt' === file2bib.sh === id: cord-276234-2nkeq4ud author: Siedlecki, Jakob title: COVID-19: Ophthalmological Aspects of the SARS-CoV 2 Global Pandemic date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-276234-2nkeq4ud.txt cache: ./cache/cord-276234-2nkeq4ud.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276234-2nkeq4ud.txt' === file2bib.sh === id: cord-277014-iz8jo44e author: Hu, Weihua title: Disorders of sodium balance and its clinical implications in COVID-19 patients: a multicenter retrospective study date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-277014-iz8jo44e.txt cache: ./cache/cord-277014-iz8jo44e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277014-iz8jo44e.txt' === file2bib.sh === id: cord-276874-9rjbmsvb author: Ng, M.L. title: Topographic Changes in SARS Coronavirus–infected Cells at Late Stages of Infection date: 2004-11-17 pages: extension: .txt txt: ./txt/cord-276874-9rjbmsvb.txt cache: ./cache/cord-276874-9rjbmsvb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276874-9rjbmsvb.txt' === file2bib.sh === id: cord-277076-yvsyo4l9 author: Berger, A. title: SARS date: 2019-09-12 pages: extension: .txt txt: ./txt/cord-277076-yvsyo4l9.txt cache: ./cache/cord-277076-yvsyo4l9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277076-yvsyo4l9.txt' === file2bib.sh === id: cord-276267-77903fld author: Al‐Ani, Aysha H. title: Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-276267-77903fld.txt cache: ./cache/cord-276267-77903fld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276267-77903fld.txt' === file2bib.sh === id: cord-276335-e1xlwcvc author: Poh, W.P. title: Characterization of cytotoxic T‐lymphocyte epitopes and immune responses to SARS coronavirus spike DNA vaccine expressing the RGD‐integrin‐binding motif date: 2009-05-27 pages: extension: .txt txt: ./txt/cord-276335-e1xlwcvc.txt cache: ./cache/cord-276335-e1xlwcvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276335-e1xlwcvc.txt' === file2bib.sh === id: cord-276481-os1nf3cs author: Ishizaki, Tatsuro title: Estimation of the impact of providing outpatients with information about SARS infection control on their intention of outpatient visit date: 2004-09-30 pages: extension: .txt txt: ./txt/cord-276481-os1nf3cs.txt cache: ./cache/cord-276481-os1nf3cs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276481-os1nf3cs.txt' === file2bib.sh === id: cord-276402-ymxvtyll author: Wei, Jia title: SARS-CoV-2 infection in immunocompromised patients: humoral versus cell-mediated immunity date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-276402-ymxvtyll.txt cache: ./cache/cord-276402-ymxvtyll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276402-ymxvtyll.txt' === file2bib.sh === id: cord-277239-cedoi5jr author: Bray, R. A. title: Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-277239-cedoi5jr.txt cache: ./cache/cord-277239-cedoi5jr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277239-cedoi5jr.txt' === file2bib.sh === id: cord-277039-yo5ojr0s author: Mendenhall, Ian H. title: Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date: 2019-04-17 pages: extension: .txt txt: ./txt/cord-277039-yo5ojr0s.txt cache: ./cache/cord-277039-yo5ojr0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277039-yo5ojr0s.txt' === file2bib.sh === id: cord-275088-wbqznzj7 author: Garrido, Pablo F. title: The Lord of the NanoRings: cyclodextrins and the battle against SARS-CoV-2 date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-275088-wbqznzj7.txt cache: ./cache/cord-275088-wbqznzj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275088-wbqznzj7.txt' === file2bib.sh === id: cord-277440-9nehpbg2 author: Grimm, Christian title: Could an endo-lysosomal ion channel be the Achilles heel of SARS-CoV2? date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-277440-9nehpbg2.txt cache: ./cache/cord-277440-9nehpbg2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277440-9nehpbg2.txt' === file2bib.sh === id: cord-277110-e27lm7rr author: Iria, Neri title: Major cluster of pediatric “ true ” primary chilblains during the COVID‐19 pandemic: a consequence of lifestyle changes due to lockdown date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-277110-e27lm7rr.txt cache: ./cache/cord-277110-e27lm7rr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277110-e27lm7rr.txt' === file2bib.sh === id: cord-276034-a8pixbuc author: Zhi, Yan title: Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein date: 2005-04-25 pages: extension: .txt txt: ./txt/cord-276034-a8pixbuc.txt cache: ./cache/cord-276034-a8pixbuc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276034-a8pixbuc.txt' === file2bib.sh === id: cord-277490-xrgnt6l5 author: Huang, Zhongwei title: Optimal temperature zone for the dispersal of COVID-19 date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-277490-xrgnt6l5.txt cache: ./cache/cord-277490-xrgnt6l5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277490-xrgnt6l5.txt' === file2bib.sh === id: cord-276870-gxtvlji7 author: Bobrowski, Tesia title: Learning from history: do not flatten the curve of antiviral research! date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-276870-gxtvlji7.txt cache: ./cache/cord-276870-gxtvlji7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276870-gxtvlji7.txt' === file2bib.sh === id: cord-277705-6lgt2i7f author: Luan, Junwen title: A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-277705-6lgt2i7f.txt cache: ./cache/cord-277705-6lgt2i7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277705-6lgt2i7f.txt' === file2bib.sh === id: cord-277186-sj8ngpk8 author: He, Qigai title: Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA date: 2005-04-19 pages: extension: .txt txt: ./txt/cord-277186-sj8ngpk8.txt cache: ./cache/cord-277186-sj8ngpk8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277186-sj8ngpk8.txt' === file2bib.sh === id: cord-276358-so390gp4 author: Nieto-Torres, Jose L. title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome date: 2015-11-30 pages: extension: .txt txt: ./txt/cord-276358-so390gp4.txt cache: ./cache/cord-276358-so390gp4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276358-so390gp4.txt' === file2bib.sh === id: cord-276957-pk33dl8q author: Hu, Xuejiao title: Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-276957-pk33dl8q.txt cache: ./cache/cord-276957-pk33dl8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276957-pk33dl8q.txt' === file2bib.sh === id: cord-277137-k3jj5vom author: Anand, Praveen title: SARS-CoV-2 strategically mimics proteolytic activation of human ENaC date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-277137-k3jj5vom.txt cache: ./cache/cord-277137-k3jj5vom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277137-k3jj5vom.txt' === file2bib.sh === id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-277357-lpurk7pe.txt cache: ./cache/cord-277357-lpurk7pe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277357-lpurk7pe.txt' === file2bib.sh === id: cord-276630-qci7khki author: Lima, William Gustavo title: The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-276630-qci7khki.txt cache: ./cache/cord-276630-qci7khki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276630-qci7khki.txt' === file2bib.sh === id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-276908-9jthjf24.txt cache: ./cache/cord-276908-9jthjf24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276908-9jthjf24.txt' === file2bib.sh === id: cord-277763-ihg3te63 author: Moynan, David title: The role of healthcare staff COVID-19 screening in infection prevention & control date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-277763-ihg3te63.txt cache: ./cache/cord-277763-ihg3te63.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-277763-ihg3te63.txt' === file2bib.sh === id: cord-277113-pykf7iw1 author: Wang, Xingyu title: The Clinical Features and Outcomes of Discharged Coronavirus Disease 2019 Patients：A Prospective Cohort Study date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-277113-pykf7iw1.txt cache: ./cache/cord-277113-pykf7iw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277113-pykf7iw1.txt' === file2bib.sh === id: cord-277498-hdhq99k2 author: Chua, Melvin L.K. title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-277498-hdhq99k2.txt cache: ./cache/cord-277498-hdhq99k2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277498-hdhq99k2.txt' === file2bib.sh === id: cord-276895-p85obwp2 author: Carriazo, Sol title: Kidney disease and electrolytes in COVID-19: more than meets the eye date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-276895-p85obwp2.txt cache: ./cache/cord-276895-p85obwp2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276895-p85obwp2.txt' === file2bib.sh === id: cord-277774-kec1o4ys author: Wang, Shangqian title: The need for urogenital tract monitoring in COVID-19 date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-277774-kec1o4ys.txt cache: ./cache/cord-277774-kec1o4ys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277774-kec1o4ys.txt' === file2bib.sh === id: cord-277253-vy0mvzeb author: Liu, Hongbo title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-277253-vy0mvzeb.txt cache: ./cache/cord-277253-vy0mvzeb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277253-vy0mvzeb.txt' === file2bib.sh === id: cord-277760-i4xjk61t author: Castillo, Andrés E. title: Phylogenetic analysis of the first four SARS‐CoV‐2 cases in Chile date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-277760-i4xjk61t.txt cache: ./cache/cord-277760-i4xjk61t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277760-i4xjk61t.txt' === file2bib.sh === id: cord-277188-t33nw4zb author: Fang, Jie title: Efficacy of Early Combination Therapy With Lianhuaqingwen and Arbidol in Moderate and Severe COVID-19 Patients: A Retrospective Cohort Study date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-277188-t33nw4zb.txt cache: ./cache/cord-277188-t33nw4zb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277188-t33nw4zb.txt' === file2bib.sh === id: cord-277486-12uah5qi author: Kopp, Kristen title: Interdisciplinary Model for Scheduling Post-discharge Cardiopulmonary Care of Patients Following Severe and Critical SARS-CoV-2 (Coronavirus) Infection date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-277486-12uah5qi.txt cache: ./cache/cord-277486-12uah5qi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277486-12uah5qi.txt' === file2bib.sh === id: cord-276493-hoaxv5e0 author: Jeong, Gi Uk title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-276493-hoaxv5e0.txt cache: ./cache/cord-276493-hoaxv5e0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276493-hoaxv5e0.txt' === file2bib.sh === id: cord-277731-thazunob author: Smith, Matthew L. title: Biosurfactants: A Covid-19 Perspective date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-277731-thazunob.txt cache: ./cache/cord-277731-thazunob.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277731-thazunob.txt' === file2bib.sh === id: cord-277399-0w8is9xm author: Esteves, Sandro C. title: SARS‐CoV‐2 pandemic and repercussions for male infertility patients: A proposal for the individualized provision of andrological services date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-277399-0w8is9xm.txt cache: ./cache/cord-277399-0w8is9xm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277399-0w8is9xm.txt' === file2bib.sh === id: cord-277210-xaj2623u author: Weinkove, Robert title: Managing haematology and oncology patients during the COVID‐19 pandemic: interim consensus guidance date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-277210-xaj2623u.txt cache: ./cache/cord-277210-xaj2623u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277210-xaj2623u.txt' === file2bib.sh === id: cord-277860-vzyrcmu4 author: Pizzorno, Andrés title: In vitro evaluation of antiviral activity of single and combined repurposable drugs against SARS-CoV-2 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-277860-vzyrcmu4.txt cache: ./cache/cord-277860-vzyrcmu4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277860-vzyrcmu4.txt' === file2bib.sh === id: cord-277683-9cg90zbo author: Panettieri, Reynold A. title: Asthma and COVID: What are the Important Questions? date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-277683-9cg90zbo.txt cache: ./cache/cord-277683-9cg90zbo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277683-9cg90zbo.txt' === file2bib.sh === id: cord-276797-86hc3lbi author: Jamieson, Denise J. title: Emerging infectious disease outbreaks: Old lessons and new challenges for obstetrician-gynecologists date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-276797-86hc3lbi.txt cache: ./cache/cord-276797-86hc3lbi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276797-86hc3lbi.txt' === file2bib.sh === id: cord-277509-khvuiwl1 author: Hashemi, Seyyed Alireza title: Ultra-sensitive viral glycoprotein detection NanoSystem toward accurate tracing SARS-CoV-2 in biological/non-biological media date: 2021-01-01 pages: extension: .txt txt: ./txt/cord-277509-khvuiwl1.txt cache: ./cache/cord-277509-khvuiwl1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277509-khvuiwl1.txt' === file2bib.sh === id: cord-277640-vy7ex5lv author: Calderaro, Adriana title: SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-277640-vy7ex5lv.txt cache: ./cache/cord-277640-vy7ex5lv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277640-vy7ex5lv.txt' === file2bib.sh === id: cord-277911-x916hsg6 author: Wu, Di title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-277911-x916hsg6.txt cache: ./cache/cord-277911-x916hsg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277911-x916hsg6.txt' === file2bib.sh === id: cord-277619-83bve5z0 author: Huang, Victoria W. title: Head and neck survivorship care in the times of the SARS‐CoV‐2 pandemic date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-277619-83bve5z0.txt cache: ./cache/cord-277619-83bve5z0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277619-83bve5z0.txt' === file2bib.sh === id: cord-277735-a9gkath5 author: Leung, Danny Tze Ming title: Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date: 2004-07-15 pages: extension: .txt txt: ./txt/cord-277735-a9gkath5.txt cache: ./cache/cord-277735-a9gkath5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277735-a9gkath5.txt' === file2bib.sh === id: cord-277313-5f5lrn3c author: Hayakawa, Satoshi title: Covid‐19 pandemic and pregnancy date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-277313-5f5lrn3c.txt cache: ./cache/cord-277313-5f5lrn3c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277313-5f5lrn3c.txt' === file2bib.sh === id: cord-277873-4819g00y author: Matson, M. Jeremiah title: Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-277873-4819g00y.txt cache: ./cache/cord-277873-4819g00y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277873-4819g00y.txt' === file2bib.sh === id: cord-277812-4cz2hziz author: Sieni, Elena title: Favourable outcome of coronavirus disease 2019 in a 1‐year‐old girl with acute myeloid leukaemia and severe treatment‐induced immunosuppression date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-277812-4cz2hziz.txt cache: ./cache/cord-277812-4cz2hziz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277812-4cz2hziz.txt' === file2bib.sh === id: cord-277496-9ss09g6h author: Thaweerat, Wajana title: Current evidence on pancreatic involvement in SARS-CoV-2 infection date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-277496-9ss09g6h.txt cache: ./cache/cord-277496-9ss09g6h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277496-9ss09g6h.txt' === file2bib.sh === id: cord-277564-x5qfxag3 author: Kim, Si-Hyun title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-277564-x5qfxag3.txt cache: ./cache/cord-277564-x5qfxag3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277564-x5qfxag3.txt' === file2bib.sh === id: cord-277611-3iynrfzq author: Buetti, Niccolò title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-277611-3iynrfzq.txt cache: ./cache/cord-277611-3iynrfzq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277611-3iynrfzq.txt' === file2bib.sh === id: cord-277260-7se220oz author: Gosain, Rohit title: COVID-19 and Cancer: a Comprehensive Review date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-277260-7se220oz.txt cache: ./cache/cord-277260-7se220oz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277260-7se220oz.txt' === file2bib.sh === id: cord-277345-bbgerem6 author: Pan, A. title: Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-277345-bbgerem6.txt cache: ./cache/cord-277345-bbgerem6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277345-bbgerem6.txt' === file2bib.sh === id: cord-277529-z2r14w2k author: Stella, Alessandro title: Familial Mediterranean Fever and COVID-19: Friends or Foes? date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-277529-z2r14w2k.txt cache: ./cache/cord-277529-z2r14w2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277529-z2r14w2k.txt' === file2bib.sh === id: cord-277549-sg7tzhdm author: Stanley, Kate E. title: Coronavirus disease (COVID-19) and fertility: viral host entry protein expression in male and female reproductive tissues date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-277549-sg7tzhdm.txt cache: ./cache/cord-277549-sg7tzhdm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277549-sg7tzhdm.txt' === file2bib.sh === id: cord-278106-ev1nx60h author: Cancarevic, Ivan title: Coronavirus Disease 2019 (COVID-19) in Cancer Patients date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-278106-ev1nx60h.txt cache: ./cache/cord-278106-ev1nx60h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278106-ev1nx60h.txt' === file2bib.sh === id: cord-278509-k62bsk9b author: Manikandan, Natesan title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-278509-k62bsk9b.txt cache: ./cache/cord-278509-k62bsk9b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278509-k62bsk9b.txt' === file2bib.sh === id: cord-278256-dmrtsxik author: Qiu, Haiyan title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-278256-dmrtsxik.txt cache: ./cache/cord-278256-dmrtsxik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278256-dmrtsxik.txt' === file2bib.sh === id: cord-277679-sc9hugxr author: Khateb, Mohamed title: Coronaviruses and Central Nervous System Manifestations date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-277679-sc9hugxr.txt cache: ./cache/cord-277679-sc9hugxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277679-sc9hugxr.txt' === file2bib.sh === id: cord-277907-x6387i7b author: Tham, Sai Meng title: Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020 date: 2020-11-17 pages: extension: .txt txt: ./txt/cord-277907-x6387i7b.txt cache: ./cache/cord-277907-x6387i7b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277907-x6387i7b.txt' === file2bib.sh === id: cord-277870-o79wph9r author: Han, Yanqiang title: Potential inhibitors for the novel coronavirus (SARS-CoV-2) date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-277870-o79wph9r.txt cache: ./cache/cord-277870-o79wph9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-277870-o79wph9r.txt' === file2bib.sh === id: cord-277410-lt19mijb author: Salvatore, Phillip P title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-277410-lt19mijb.txt cache: ./cache/cord-277410-lt19mijb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277410-lt19mijb.txt' === file2bib.sh === id: cord-278522-e4qa19o6 author: Park, Se Yoon title: Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-278522-e4qa19o6.txt cache: ./cache/cord-278522-e4qa19o6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278522-e4qa19o6.txt' === file2bib.sh === id: cord-277759-zbmzjsvs author: Wang, Luwen title: Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-277759-zbmzjsvs.txt cache: ./cache/cord-277759-zbmzjsvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277759-zbmzjsvs.txt' === file2bib.sh === id: cord-278406-n5e3a09i author: Macauley, Precious title: CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-278406-n5e3a09i.txt cache: ./cache/cord-278406-n5e3a09i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278406-n5e3a09i.txt' === file2bib.sh === id: cord-278225-d0gxb6bx author: Meng, Yifan title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-278225-d0gxb6bx.txt cache: ./cache/cord-278225-d0gxb6bx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278225-d0gxb6bx.txt' === file2bib.sh === id: cord-278050-wl83d6gs author: Morgenstern, Birgit title: Ribavirin and interferon-β synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines date: 2005-01-28 pages: extension: .txt txt: ./txt/cord-278050-wl83d6gs.txt cache: ./cache/cord-278050-wl83d6gs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278050-wl83d6gs.txt' === file2bib.sh === id: cord-278812-5jps95q9 author: Edwards, Sarah J L title: Anthroponotic risk of SARS-CoV-2, precautionary mitigation, and outbreak management date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-278812-5jps95q9.txt cache: ./cache/cord-278812-5jps95q9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278812-5jps95q9.txt' === file2bib.sh === id: cord-278045-hr3r17mz author: Yokota, Isao title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-278045-hr3r17mz.txt cache: ./cache/cord-278045-hr3r17mz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278045-hr3r17mz.txt' === file2bib.sh === id: cord-277491-q18b88lm author: Cao, Ying-Li title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date: 2011-02-11 pages: extension: .txt txt: ./txt/cord-277491-q18b88lm.txt cache: ./cache/cord-277491-q18b88lm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277491-q18b88lm.txt' === file2bib.sh === id: cord-277659-afysef1e author: Hamilton, F. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-277659-afysef1e.txt cache: ./cache/cord-277659-afysef1e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277659-afysef1e.txt' === file2bib.sh === id: cord-277841-7sp8ftbc author: Kumari, Pratibha title: Potential diagnostics and therapeutic approaches in COVID-19 date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-277841-7sp8ftbc.txt cache: ./cache/cord-277841-7sp8ftbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277841-7sp8ftbc.txt' === file2bib.sh === id: cord-277539-xt2nt11e author: Kochhar, Anuraj Singh title: Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date: 2020 pages: extension: .txt txt: ./txt/cord-277539-xt2nt11e.txt cache: ./cache/cord-277539-xt2nt11e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277539-xt2nt11e.txt' === file2bib.sh === id: cord-277585-evw3pu87 author: Malavolta, Marco title: Exploring the Relevance of Senotherapeutics for the Current SARS-CoV-2 Emergency and Similar Future Global Health Threats date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-277585-evw3pu87.txt cache: ./cache/cord-277585-evw3pu87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277585-evw3pu87.txt' === file2bib.sh === id: cord-278370-fuu20ae7 author: Palao, M. title: Multiple Sclerosis following SARS-CoV-2 infection date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-278370-fuu20ae7.txt cache: ./cache/cord-278370-fuu20ae7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278370-fuu20ae7.txt' === file2bib.sh === id: cord-278129-bpuyrsza author: De Haan, Cornelis A. M. title: Hosting the severe acute respiratory syndrome coronavirus: specific cell factors required for infection date: 2006-06-27 pages: extension: .txt txt: ./txt/cord-278129-bpuyrsza.txt cache: ./cache/cord-278129-bpuyrsza.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278129-bpuyrsza.txt' === file2bib.sh === id: cord-278945-q5lzf5o4 author: Hashemi, Seyed Ahmad title: Report of death in children with SARS‐CoV‐2 and Human metapneumovirus (hMPV) co‐infection: is hMPV the trigger? date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-278945-q5lzf5o4.txt cache: ./cache/cord-278945-q5lzf5o4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278945-q5lzf5o4.txt' === file2bib.sh === id: cord-278467-c0jw9dkw author: Tulchinsky, Mark title: The American College of Nuclear Medicine Guidance on Operating Procedures for a Nuclear Medicine Facility During COVID-19 Pandemic date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-278467-c0jw9dkw.txt cache: ./cache/cord-278467-c0jw9dkw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278467-c0jw9dkw.txt' === file2bib.sh === id: cord-278271-rpq62xhl author: Lyu, Jinglu title: Reflection on lower rates of COVID-19 in children: does childhood immunizations offer unexpected protection? date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-278271-rpq62xhl.txt cache: ./cache/cord-278271-rpq62xhl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278271-rpq62xhl.txt' === file2bib.sh === id: cord-277739-eb4z3u66 author: Hu, Ke title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-277739-eb4z3u66.txt cache: ./cache/cord-277739-eb4z3u66.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277739-eb4z3u66.txt' === file2bib.sh === id: cord-278618-7tu5c7m1 author: Romano-Bertrand, Sara title: Sustainability of SARS-CoV-2 in aerosols: Should we worry about airborne transmission? date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-278618-7tu5c7m1.txt cache: ./cache/cord-278618-7tu5c7m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278618-7tu5c7m1.txt' === file2bib.sh === id: cord-278457-yrm5hi3v author: Sung, Heungsup title: Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-278457-yrm5hi3v.txt cache: ./cache/cord-278457-yrm5hi3v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278457-yrm5hi3v.txt' === file2bib.sh === id: cord-278987-3s5p9yw6 author: Hirotsu, Yosuke title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-278987-3s5p9yw6.txt cache: ./cache/cord-278987-3s5p9yw6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278987-3s5p9yw6.txt' === file2bib.sh === id: cord-278123-mq56em3z author: Hasan, Mohammad Rubayet title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-278123-mq56em3z.txt cache: ./cache/cord-278123-mq56em3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278123-mq56em3z.txt' === file2bib.sh === id: cord-278260-3o91v72a author: Halstead, Scott B title: COVID 19 Vaccines: Should we fear ADE? date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-278260-3o91v72a.txt cache: ./cache/cord-278260-3o91v72a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278260-3o91v72a.txt' === file2bib.sh === id: cord-278249-vvhq9vgp author: Blot, Mathieu title: CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDS date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-278249-vvhq9vgp.txt cache: ./cache/cord-278249-vvhq9vgp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278249-vvhq9vgp.txt' === file2bib.sh === id: cord-277816-ncdy9qgb author: Wang, Ji-gan title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-277816-ncdy9qgb.txt cache: ./cache/cord-277816-ncdy9qgb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277816-ncdy9qgb.txt' === file2bib.sh === id: cord-278951-vxrwrzlj author: Huang, Hsien-Hao title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak date: 2006-12-31 pages: extension: .txt txt: ./txt/cord-278951-vxrwrzlj.txt cache: ./cache/cord-278951-vxrwrzlj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278951-vxrwrzlj.txt' === file2bib.sh === id: cord-278491-cnqxsno8 author: Wang, K. title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-278491-cnqxsno8.txt cache: ./cache/cord-278491-cnqxsno8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278491-cnqxsno8.txt' === file2bib.sh === id: cord-279290-wtnnlp4i author: Solorio-Pineda, Saúl title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-279290-wtnnlp4i.txt cache: ./cache/cord-279290-wtnnlp4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279290-wtnnlp4i.txt' === file2bib.sh === id: cord-278678-ivye1qao author: Calvez, R. M. title: Molecular detection of SARS-CoV-2 using a reagent-free approach date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-278678-ivye1qao.txt cache: ./cache/cord-278678-ivye1qao.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278678-ivye1qao.txt' === file2bib.sh === id: cord-278453-ogbmaw3o author: Spiller, Tobias R. title: Development of health care workers' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-278453-ogbmaw3o.txt cache: ./cache/cord-278453-ogbmaw3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278453-ogbmaw3o.txt' === file2bib.sh === id: cord-278440-vti6xp9v author: Paraiso, Ines L title: Potential use of polyphenols in the battle against COVID-19 date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-278440-vti6xp9v.txt cache: ./cache/cord-278440-vti6xp9v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278440-vti6xp9v.txt' === file2bib.sh === id: cord-279476-h7zi82a8 author: Wang, Xueliang title: Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-279476-h7zi82a8.txt cache: ./cache/cord-279476-h7zi82a8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279476-h7zi82a8.txt' === file2bib.sh === id: cord-278093-0twnkv93 author: Perveen, Shagufta title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-278093-0twnkv93.txt cache: ./cache/cord-278093-0twnkv93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278093-0twnkv93.txt' === file2bib.sh === id: cord-278542-vqp6ec6e author: Coyne, Carolyn title: Recommendations for future university pandemic responses: What the first COVID-19 shutdown taught us date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-278542-vqp6ec6e.txt cache: ./cache/cord-278542-vqp6ec6e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278542-vqp6ec6e.txt' === file2bib.sh === id: cord-278182-75u57fw1 author: Goh, Gerard Kian-Meng title: Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-278182-75u57fw1.txt cache: ./cache/cord-278182-75u57fw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278182-75u57fw1.txt' === file2bib.sh === id: cord-278176-o9glkhyv author: Houng, Huo-Shu H title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 pages: extension: .txt txt: ./txt/cord-278176-o9glkhyv.txt cache: ./cache/cord-278176-o9glkhyv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278176-o9glkhyv.txt' === file2bib.sh === id: cord-277443-mv7sk5aa author: Kumaki, Yohichi title: Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol(®) (Poly IC:LC), in a lethal SARS-CoV-infected BALB/c mouse model date: 2016-12-09 pages: extension: .txt txt: ./txt/cord-277443-mv7sk5aa.txt cache: ./cache/cord-277443-mv7sk5aa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277443-mv7sk5aa.txt' === file2bib.sh === id: cord-279260-tdvb0fhv author: Lv, Huibin title: COVID‐19 vaccines: knowing the unknown date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-279260-tdvb0fhv.txt cache: ./cache/cord-279260-tdvb0fhv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279260-tdvb0fhv.txt' === file2bib.sh === id: cord-274802-7ioiwsd8 author: Varghese, Praveen Mathews title: Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-274802-7ioiwsd8.txt cache: ./cache/cord-274802-7ioiwsd8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274802-7ioiwsd8.txt' === file2bib.sh === id: cord-278960-3xw4qjoy author: Evangelista, A. T. title: The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-278960-3xw4qjoy.txt cache: ./cache/cord-278960-3xw4qjoy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278960-3xw4qjoy.txt' === file2bib.sh === id: cord-278649-ge9ike2c author: Makaronidis, Janine title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-278649-ge9ike2c.txt cache: ./cache/cord-278649-ge9ike2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278649-ge9ike2c.txt' === file2bib.sh === id: cord-278169-elhz77ek author: Zhou, Dapeng title: Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-278169-elhz77ek.txt cache: ./cache/cord-278169-elhz77ek.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278169-elhz77ek.txt' === file2bib.sh === id: cord-278055-v2ed3tei author: Sia, Sin Fun title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-278055-v2ed3tei.txt cache: ./cache/cord-278055-v2ed3tei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278055-v2ed3tei.txt' === file2bib.sh === id: cord-279105-e2zjxjox author: Lee, Cheryl Yi-Pin title: Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-279105-e2zjxjox.txt cache: ./cache/cord-279105-e2zjxjox.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279105-e2zjxjox.txt' === file2bib.sh === id: cord-279001-l5ogbl5p author: Wilder-Smith, Annelies title: Can we contain the COVID-19 outbreak with the same measures as for SARS? date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-279001-l5ogbl5p.txt cache: ./cache/cord-279001-l5ogbl5p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279001-l5ogbl5p.txt' === file2bib.sh === id: cord-277830-6fsz9iy7 author: Saikatendu, Kumar Singh title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 pages: extension: .txt txt: ./txt/cord-277830-6fsz9iy7.txt cache: ./cache/cord-277830-6fsz9iy7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277830-6fsz9iy7.txt' === file2bib.sh === id: cord-278238-w1l8h8g8 author: Okba, Nisreen MA title: Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches date: 2017-04-13 pages: extension: .txt txt: ./txt/cord-278238-w1l8h8g8.txt cache: ./cache/cord-278238-w1l8h8g8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278238-w1l8h8g8.txt' === file2bib.sh === id: cord-279132-florvm7z author: K., Branimir title: From apparent to true – from frequency to distributions (II) date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-279132-florvm7z.txt cache: ./cache/cord-279132-florvm7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279132-florvm7z.txt' === file2bib.sh === id: cord-278721-g5zqebju author: Jakhmola, Shweta title: Comorbidity Assessment Is Essential During COVID-19 Treatment date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-278721-g5zqebju.txt cache: ./cache/cord-278721-g5zqebju.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278721-g5zqebju.txt' === file2bib.sh === id: cord-279550-7u2hksxm author: Wang, Kai title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-279550-7u2hksxm.txt cache: ./cache/cord-279550-7u2hksxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279550-7u2hksxm.txt' === file2bib.sh === id: cord-278362-pwi48i20 author: Khan, Abbas title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-278362-pwi48i20.txt cache: ./cache/cord-278362-pwi48i20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278362-pwi48i20.txt' === file2bib.sh === id: cord-279642-0j5828ah author: Stafford, Emma G. title: Pharmacovigilance in Patients with Diabetes: A Data-Driven Analysis Identifying Specific RAS Antagonists with Adverse Pulmonary Safety Profiles That Have Implications for COVID-19 Morbidity and Mortality date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-279642-0j5828ah.txt cache: ./cache/cord-279642-0j5828ah.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279642-0j5828ah.txt' === file2bib.sh === id: cord-278540-gy65bvot author: Chen, I-Yin title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date: 2019-01-29 pages: extension: .txt txt: ./txt/cord-278540-gy65bvot.txt cache: ./cache/cord-278540-gy65bvot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 21 resourceName b'cord-278540-gy65bvot.txt' === file2bib.sh === id: cord-279765-sb1ifyfx author: Isakova-Sivak, Irina title: A promising inactivated whole-virion SARS-CoV-2 vaccine date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-279765-sb1ifyfx.txt cache: ./cache/cord-279765-sb1ifyfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279765-sb1ifyfx.txt' === file2bib.sh === id: cord-278759-pykihnup author: Koh, Yiwen title: Nurses' perceptions of risk from emerging respiratory infectious diseases: A Singapore study date: 2012-03-21 pages: extension: .txt txt: ./txt/cord-278759-pykihnup.txt cache: ./cache/cord-278759-pykihnup.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278759-pykihnup.txt' === file2bib.sh === id: cord-279563-4lu1n0s7 author: Gorzalski, Andrew J. title: High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-279563-4lu1n0s7.txt cache: ./cache/cord-279563-4lu1n0s7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279563-4lu1n0s7.txt' === file2bib.sh === id: cord-277669-uujny2dm author: Lumpuy-Castillo, Jairo title: Cardiovascular Damage in COVID-19: Therapeutic Approaches Targeting the Renin-Angiotensin-Aldosterone System date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-277669-uujny2dm.txt cache: ./cache/cord-277669-uujny2dm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277669-uujny2dm.txt' === file2bib.sh === id: cord-279316-xz7aawem author: MIZUTANI, T. title: Signal Transduction in SARS‐CoV‐Infected Cells date: 2007-04-23 pages: extension: .txt txt: ./txt/cord-279316-xz7aawem.txt cache: ./cache/cord-279316-xz7aawem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279316-xz7aawem.txt' === file2bib.sh === id: cord-279115-eyk8sxk7 author: Cecconi, Maurizio title: Ten things we learned about COVID-19 date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-279115-eyk8sxk7.txt cache: ./cache/cord-279115-eyk8sxk7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279115-eyk8sxk7.txt' === file2bib.sh === id: cord-279439-h4ji0ttm author: Viotti, Manuel title: HUMAN PRE-IMPLANTATION EMBRYOS ARE PERMISSIVE TO SARS-COV-2 ENTRY date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-279439-h4ji0ttm.txt cache: ./cache/cord-279439-h4ji0ttm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279439-h4ji0ttm.txt' === file2bib.sh === id: cord-277874-cr53ycrm author: Neault, N. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-277874-cr53ycrm.txt cache: ./cache/cord-277874-cr53ycrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277874-cr53ycrm.txt' === file2bib.sh === id: cord-278682-s4gfbsqy author: Chan, W-M title: Precautions in ophthalmic practice in a hospital with a major acute SARS outbreak: an experience from Hong Kong date: 2005-04-29 pages: extension: .txt txt: ./txt/cord-278682-s4gfbsqy.txt cache: ./cache/cord-278682-s4gfbsqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278682-s4gfbsqy.txt' === file2bib.sh === id: cord-279616-8gtumtxb author: Wu, Kitty K. title: Posttraumatic Stress after SARS date: 2005-08-17 pages: extension: .txt txt: ./txt/cord-279616-8gtumtxb.txt cache: ./cache/cord-279616-8gtumtxb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279616-8gtumtxb.txt' === file2bib.sh === id: cord-278923-u4gv2e7w author: da Silva, Joyce Kelly R. title: Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-278923-u4gv2e7w.txt cache: ./cache/cord-278923-u4gv2e7w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278923-u4gv2e7w.txt' === file2bib.sh === id: cord-280147-xvzi1i0v author: Consoli, Letizia title: 2019 novel coronavirus (COVID-19) pneumonia complications: the importance of lung ultrasound date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-280147-xvzi1i0v.txt cache: ./cache/cord-280147-xvzi1i0v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280147-xvzi1i0v.txt' === file2bib.sh === id: cord-279158-dsnniuo6 author: Luo, Y. title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-279158-dsnniuo6.txt cache: ./cache/cord-279158-dsnniuo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279158-dsnniuo6.txt' === file2bib.sh === id: cord-279766-s3ms5f56 author: Ye, Zhongde title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis date: 2008-07-28 pages: extension: .txt txt: ./txt/cord-279766-s3ms5f56.txt cache: ./cache/cord-279766-s3ms5f56.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279766-s3ms5f56.txt' === file2bib.sh === id: cord-278325-ykcd7d59 author: Cheung, Carmen Ka Man title: Coronavirus Disease 2019 (COVID-19): A Haematologist's Perspective date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-278325-ykcd7d59.txt cache: ./cache/cord-278325-ykcd7d59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278325-ykcd7d59.txt' === file2bib.sh === id: cord-279584-9x1d1kp1 author: Anderson, E. M. title: Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-279584-9x1d1kp1.txt cache: ./cache/cord-279584-9x1d1kp1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279584-9x1d1kp1.txt' === file2bib.sh === id: cord-279750-if9vphb2 author: Savić, Dragan title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-279750-if9vphb2.txt cache: ./cache/cord-279750-if9vphb2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279750-if9vphb2.txt' === file2bib.sh === id: cord-278839-uu2wlpmp author: Alberca, Ricardo Wesley title: Pregnancy, Viral Infection, and COVID-19 date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-278839-uu2wlpmp.txt cache: ./cache/cord-278839-uu2wlpmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278839-uu2wlpmp.txt' === file2bib.sh === id: cord-279518-z3k7zaw4 author: Xue, Xiaotong title: High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-279518-z3k7zaw4.txt cache: ./cache/cord-279518-z3k7zaw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279518-z3k7zaw4.txt' === file2bib.sh === id: cord-279435-ffgd2ets author: ALBalawi, Hani B title: COVID-19: Precautionary Guidelines for Ophthalmologists date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-279435-ffgd2ets.txt cache: ./cache/cord-279435-ffgd2ets.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279435-ffgd2ets.txt' === file2bib.sh === id: cord-277889-8u685f45 author: Costela-Ruiz, Víctor J. title: SARS-CoV-2 infection: the role of cytokines in COVID-19 disease date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-277889-8u685f45.txt cache: ./cache/cord-277889-8u685f45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277889-8u685f45.txt' === file2bib.sh === id: cord-279223-qvih5qas author: Hascoët, Jean-Michel title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-279223-qvih5qas.txt cache: ./cache/cord-279223-qvih5qas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279223-qvih5qas.txt' === file2bib.sh === id: cord-279172-d2algx16 author: Zheng, Kewen title: Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme date: 2006-11-02 pages: extension: .txt txt: ./txt/cord-279172-d2algx16.txt cache: ./cache/cord-279172-d2algx16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279172-d2algx16.txt' === file2bib.sh === id: cord-279443-2e4gz2bo author: Khan, Suliman title: Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-279443-2e4gz2bo.txt cache: ./cache/cord-279443-2e4gz2bo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279443-2e4gz2bo.txt' === file2bib.sh === id: cord-278648-hkvurb2k author: Menachery, Vineet D. title: Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis date: 2017-11-15 pages: extension: .txt txt: ./txt/cord-278648-hkvurb2k.txt cache: ./cache/cord-278648-hkvurb2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278648-hkvurb2k.txt' === file2bib.sh === id: cord-279474-c5y2lygj author: Bozzo, Caterina Prelli title: IFITM proteins promote SARS-CoV-2 infection of human lung cells date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-279474-c5y2lygj.txt cache: ./cache/cord-279474-c5y2lygj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279474-c5y2lygj.txt' === file2bib.sh === id: cord-279363-4almssg6 author: Crespo, Roland Mojica title: Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-279363-4almssg6.txt cache: ./cache/cord-279363-4almssg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279363-4almssg6.txt' === file2bib.sh === id: cord-279106-3ffa9djf author: Syatila Ab Ghani, Nur title: Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-279106-3ffa9djf.txt cache: ./cache/cord-279106-3ffa9djf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279106-3ffa9djf.txt' === file2bib.sh === id: cord-279754-95zawygq author: Hsu, Yu-Chen title: Risk and Outbreak Communication: Lessons from Taiwan's Experiences in the Post-SARS Era date: 2017-04-01 pages: extension: .txt txt: ./txt/cord-279754-95zawygq.txt cache: ./cache/cord-279754-95zawygq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279754-95zawygq.txt' === file2bib.sh === id: cord-279725-d82sj80v author: Ströher, Ute title: Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date: 2004-04-01 pages: extension: .txt txt: ./txt/cord-279725-d82sj80v.txt cache: ./cache/cord-279725-d82sj80v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279725-d82sj80v.txt' === file2bib.sh === id: cord-279932-bilr71ay author: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-279932-bilr71ay.txt cache: ./cache/cord-279932-bilr71ay.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-279932-bilr71ay.txt' === file2bib.sh === id: cord-280408-0ze1lfnf author: Leon, A. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-280408-0ze1lfnf.txt cache: ./cache/cord-280408-0ze1lfnf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280408-0ze1lfnf.txt' === file2bib.sh === id: cord-279519-4ad8ubrt author: Poochi, Saravana Prabha title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-279519-4ad8ubrt.txt cache: ./cache/cord-279519-4ad8ubrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279519-4ad8ubrt.txt' === file2bib.sh === id: cord-279131-1unb0z79 author: Buijsers, Baranca title: Beneficial non-anticoagulant mechanisms underlying heparin treatment of COVID-19 patients date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-279131-1unb0z79.txt cache: ./cache/cord-279131-1unb0z79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279131-1unb0z79.txt' === file2bib.sh === id: cord-279989-swsxez0a author: Sokolov, Elisaveta title: Non-convulsive status epilepticus: COVID-19 or clozapine induced? date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-279989-swsxez0a.txt cache: ./cache/cord-279989-swsxez0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-279989-swsxez0a.txt' === file2bib.sh === id: cord-279334-j0i9ozsz author: McCreary, Erin K title: Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date: 2020-03-23 pages: extension: .txt txt: ./txt/cord-279334-j0i9ozsz.txt cache: ./cache/cord-279334-j0i9ozsz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279334-j0i9ozsz.txt' === file2bib.sh === id: cord-280043-bm0qkrod author: Esagian, Stepan M. title: Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-280043-bm0qkrod.txt cache: ./cache/cord-280043-bm0qkrod.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280043-bm0qkrod.txt' === file2bib.sh === id: cord-278939-z6kiee09 author: Mani, Janice S. title: Natural product-derived phytochemicals as potential agents against coronaviruses: a review date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-278939-z6kiee09.txt cache: ./cache/cord-278939-z6kiee09.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278939-z6kiee09.txt' === file2bib.sh === id: cord-279861-gk8cow8k author: Glasser, John W. title: Modeling and public health emergency responses: Lessons from SARS date: 2011-01-28 pages: extension: .txt txt: ./txt/cord-279861-gk8cow8k.txt cache: ./cache/cord-279861-gk8cow8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279861-gk8cow8k.txt' === file2bib.sh === id: cord-280001-y7pvj2l1 author: Patel, Robin title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-280001-y7pvj2l1.txt cache: ./cache/cord-280001-y7pvj2l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280001-y7pvj2l1.txt' === file2bib.sh === id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-279576-wt4crton.txt cache: ./cache/cord-279576-wt4crton.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279576-wt4crton.txt' === file2bib.sh === id: cord-280198-bhjw6xc5 author: Olaleye, Omonike A. title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-280198-bhjw6xc5.txt cache: ./cache/cord-280198-bhjw6xc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280198-bhjw6xc5.txt' === file2bib.sh === id: cord-280062-1qrav1d5 author: McClenaghan, Elliot title: The global impact of SARS-CoV-2 in 181 people with cystic fibrosis date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-280062-1qrav1d5.txt cache: ./cache/cord-280062-1qrav1d5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280062-1qrav1d5.txt' === file2bib.sh === id: cord-279940-i2rgjpxf author: Comentale, Giuseppe title: Sars-Cov-2 interference in HEME production: is it the time for an early predictive biomarker? date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-279940-i2rgjpxf.txt cache: ./cache/cord-279940-i2rgjpxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279940-i2rgjpxf.txt' === file2bib.sh === id: cord-280518-2tl0mtb8 author: Xia, Jianhua title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-280518-2tl0mtb8.txt cache: ./cache/cord-280518-2tl0mtb8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280518-2tl0mtb8.txt' === file2bib.sh === id: cord-280392-ij5gtesw author: Gultom, Mitra title: Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-280392-ij5gtesw.txt cache: ./cache/cord-280392-ij5gtesw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280392-ij5gtesw.txt' === file2bib.sh === id: cord-280697-tovty20e author: Rodríguez‐Martínez, Carlos E. title: Efficacy, safety and cost‐effectiveness of hydroxychloroquine in children with COVID‐19: A call for evidence date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-280697-tovty20e.txt cache: ./cache/cord-280697-tovty20e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280697-tovty20e.txt' === file2bib.sh === id: cord-280423-v3r7vo0o author: Desmazes‐Dufeu, Nadine title: Discordant courses of COVID‐19 in a cohabiting couple of lung transplant recipients date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-280423-v3r7vo0o.txt cache: ./cache/cord-280423-v3r7vo0o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280423-v3r7vo0o.txt' === file2bib.sh === id: cord-279629-t1xjy12y author: Nazneen Akhand, Mst Rubaiat title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-279629-t1xjy12y.txt cache: ./cache/cord-279629-t1xjy12y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279629-t1xjy12y.txt' === file2bib.sh === id: cord-280544-1rhu478r author: Korte, Wolfgang title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-280544-1rhu478r.txt cache: ./cache/cord-280544-1rhu478r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-280544-1rhu478r.txt' === file2bib.sh === id: cord-279569-289fu2yb author: Lei, Yu title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-279569-289fu2yb.txt cache: ./cache/cord-279569-289fu2yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279569-289fu2yb.txt' === file2bib.sh === id: cord-280671-0b1qcdwk author: Calderone, Alba title: Selective Estrogen Receptor Modulators in COVID-19: A Possible Therapeutic Option? date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-280671-0b1qcdwk.txt cache: ./cache/cord-280671-0b1qcdwk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280671-0b1qcdwk.txt' === file2bib.sh === id: cord-279976-juz9jnfk author: Xie, Mingxuan title: Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-279976-juz9jnfk.txt cache: ./cache/cord-279976-juz9jnfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279976-juz9jnfk.txt' === file2bib.sh === id: cord-280231-jo3grxd5 author: Hardenberg, Jan‐Hendrik title: Covid‐19, ACE2 and the kidney date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-280231-jo3grxd5.txt cache: ./cache/cord-280231-jo3grxd5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280231-jo3grxd5.txt' === file2bib.sh === id: cord-280774-r2xm164s author: Gallizzi, Romina title: Management of pernio‐like cutaneous manifestations in children during the outbreak of covid‐19. date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-280774-r2xm164s.txt cache: ./cache/cord-280774-r2xm164s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280774-r2xm164s.txt' === file2bib.sh === id: cord-280003-ndpuezpo author: Lou, Bin title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-280003-ndpuezpo.txt cache: ./cache/cord-280003-ndpuezpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280003-ndpuezpo.txt' === file2bib.sh === id: cord-280627-dfnc9g2c author: Wang, Xiong title: Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-280627-dfnc9g2c.txt cache: ./cache/cord-280627-dfnc9g2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280627-dfnc9g2c.txt' === file2bib.sh === id: cord-280914-6k8gpp4y author: Alpaslan Kocamemi, B. title: First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-280914-6k8gpp4y.txt cache: ./cache/cord-280914-6k8gpp4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280914-6k8gpp4y.txt' === file2bib.sh === id: cord-280915-yk872yaz author: Flaherman, Valerie J title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-280915-yk872yaz.txt cache: ./cache/cord-280915-yk872yaz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280915-yk872yaz.txt' === file2bib.sh === id: cord-280050-fktc778q author: Tahir, Shumaila title: Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-280050-fktc778q.txt cache: ./cache/cord-280050-fktc778q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280050-fktc778q.txt' === file2bib.sh === id: cord-279520-zccd1mq5 author: Christian, Michael D. title: Possible SARS Coronavirus Transmission during Cardiopulmonary Resuscitation date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-279520-zccd1mq5.txt cache: ./cache/cord-279520-zccd1mq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279520-zccd1mq5.txt' === file2bib.sh === id: cord-280280-9jr7ekbu author: Bertoncelli, Deborah title: COVID19: potential cardiovascular issues in pediatric patients date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-280280-9jr7ekbu.txt cache: ./cache/cord-280280-9jr7ekbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280280-9jr7ekbu.txt' === file2bib.sh === id: cord-281241-k1adcls8 author: Döhla, M. title: Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-281241-k1adcls8.txt cache: ./cache/cord-281241-k1adcls8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281241-k1adcls8.txt' === file2bib.sh === id: cord-281216-7t647fww author: Goldust, Mohamad title: Performing dermoscopy in the COVID‐19 pandemic date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-281216-7t647fww.txt cache: ./cache/cord-281216-7t647fww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281216-7t647fww.txt' === file2bib.sh === id: cord-280970-gy0kfhy6 author: Peng, Fujun title: Management and Treatment of COVID-19: The Chinese Experience date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-280970-gy0kfhy6.txt cache: ./cache/cord-280970-gy0kfhy6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280970-gy0kfhy6.txt' === file2bib.sh === id: cord-281081-rifr5uub author: Deng, Junhua title: Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-281081-rifr5uub.txt cache: ./cache/cord-281081-rifr5uub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281081-rifr5uub.txt' === file2bib.sh === id: cord-280628-ok62havd author: Groß, Sonja title: SARS-CoV-2 receptor ACE2-dependent implications on the cardiovascular system: From basic science to clinical implications date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-280628-ok62havd.txt cache: ./cache/cord-280628-ok62havd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280628-ok62havd.txt' === file2bib.sh === id: cord-280994-w8dtfjel author: Peng, Qi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-280994-w8dtfjel.txt cache: ./cache/cord-280994-w8dtfjel.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280994-w8dtfjel.txt' === file2bib.sh === id: cord-280350-ay4cnzn5 author: Chan, Jasper F.W. title: Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus date: 2013-10-03 pages: extension: .txt txt: ./txt/cord-280350-ay4cnzn5.txt cache: ./cache/cord-280350-ay4cnzn5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280350-ay4cnzn5.txt' === file2bib.sh === id: cord-281106-vzb5xzza author: Zerwes, S. title: COVID-19-Infektion – Risiko für thrombembolische Komplikationen date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-281106-vzb5xzza.txt cache: ./cache/cord-281106-vzb5xzza.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281106-vzb5xzza.txt' === file2bib.sh === id: cord-281113-t450ccnq author: Mattar, Rejane title: Breath tests for gastrointestinal diseases - will it be safe to conduct breath tests after the COVID-19 pandemic? date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-281113-t450ccnq.txt cache: ./cache/cord-281113-t450ccnq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281113-t450ccnq.txt' === file2bib.sh === id: cord-280961-fka8c69p author: Zhang, Rui title: CT features of SARS-CoV-2 pneumonia according to clinical presentation: a retrospective analysis of 120 consecutive patients from Wuhan city date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-280961-fka8c69p.txt cache: ./cache/cord-280961-fka8c69p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280961-fka8c69p.txt' === file2bib.sh === id: cord-280068-rszu1c48 author: Twomey, Julianne D. title: COVID-19 update: The race to therapeutic development date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-280068-rszu1c48.txt cache: ./cache/cord-280068-rszu1c48.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280068-rszu1c48.txt' === file2bib.sh === id: cord-280029-g1k3zlax author: Gabutti, Giovanni title: Coronavirus: Update Related to the Current Outbreak of COVID-19 date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-280029-g1k3zlax.txt cache: ./cache/cord-280029-g1k3zlax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280029-g1k3zlax.txt' === file2bib.sh === id: cord-280821-kc0ut4oy author: Venturini, Elisabetta title: Treatment of children with COVID-19: position paper of the Italian Society of Pediatric Infectious Disease date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-280821-kc0ut4oy.txt cache: ./cache/cord-280821-kc0ut4oy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280821-kc0ut4oy.txt' === file2bib.sh === id: cord-281248-z2gisufl author: Buonsenso, Danilo title: A Pediatric Strategy for the Next Phase of the SARS–CoV-2 Pandemic date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-281248-z2gisufl.txt cache: ./cache/cord-281248-z2gisufl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281248-z2gisufl.txt' === file2bib.sh === id: cord-279180-xad53zht author: Kumaravel, Santhosh Kumar title: Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-279180-xad53zht.txt cache: ./cache/cord-279180-xad53zht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279180-xad53zht.txt' === file2bib.sh === id: cord-280924-g6062fwk author: Hachim, Mahmood Yaseen title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-280924-g6062fwk.txt cache: ./cache/cord-280924-g6062fwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280924-g6062fwk.txt' === file2bib.sh === id: cord-281005-6gi18vka author: Singh, Praveen Kumar title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-281005-6gi18vka.txt cache: ./cache/cord-281005-6gi18vka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281005-6gi18vka.txt' === file2bib.sh === id: cord-280528-7ivw72l0 author: TUFAN, Abdurrahman title: COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-280528-7ivw72l0.txt cache: ./cache/cord-280528-7ivw72l0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280528-7ivw72l0.txt' === file2bib.sh === id: cord-279346-7del8d2p author: Callendret, Benoît title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 pages: extension: .txt txt: ./txt/cord-279346-7del8d2p.txt cache: ./cache/cord-279346-7del8d2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279346-7del8d2p.txt' === file2bib.sh === id: cord-281294-dnaith3a author: Röhr, Susanne title: Psychosoziale Folgen von Quarantänemaßnahmen bei schwerwiegenden Coronavirus-Ausbrüchen: ein Rapid Review date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-281294-dnaith3a.txt cache: ./cache/cord-281294-dnaith3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281294-dnaith3a.txt' === file2bib.sh === id: cord-281551-0aj2zwx8 author: Schlagenhauf, Patricia title: Repurposing antimalarials and other drugs for COVID-19 date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-281551-0aj2zwx8.txt cache: ./cache/cord-281551-0aj2zwx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281551-0aj2zwx8.txt' === file2bib.sh === id: cord-280662-gakayv6e author: Bian, Jingwei title: Angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 receptor and RAS modulator date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-280662-gakayv6e.txt cache: ./cache/cord-280662-gakayv6e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280662-gakayv6e.txt' === file2bib.sh === id: cord-280172-6o1gqe8v author: Sanami, Samira title: Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-280172-6o1gqe8v.txt cache: ./cache/cord-280172-6o1gqe8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280172-6o1gqe8v.txt' === file2bib.sh === id: cord-280025-4hmecfi0 author: Korber, B title: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-280025-4hmecfi0.txt cache: ./cache/cord-280025-4hmecfi0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280025-4hmecfi0.txt' === file2bib.sh === id: cord-281686-edpyn8fd author: Dalamaga, Maria title: 19 treatment regimens? date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-281686-edpyn8fd.txt cache: ./cache/cord-281686-edpyn8fd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281686-edpyn8fd.txt' === file2bib.sh === id: cord-281393-96j70n2z author: Capai, L. title: Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020. date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-281393-96j70n2z.txt cache: ./cache/cord-281393-96j70n2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281393-96j70n2z.txt' === file2bib.sh === id: cord-280621-tph5n7ak author: Kim, Yunjeong title: Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor date: 2016-03-30 pages: extension: .txt txt: ./txt/cord-280621-tph5n7ak.txt cache: ./cache/cord-280621-tph5n7ak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280621-tph5n7ak.txt' === file2bib.sh === id: cord-281500-5mm1nnwv author: Spadera, Lucrezia title: Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-281500-5mm1nnwv.txt cache: ./cache/cord-281500-5mm1nnwv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281500-5mm1nnwv.txt' === file2bib.sh === id: cord-280958-36ytqapi author: Decker, Summer J title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-280958-36ytqapi.txt cache: ./cache/cord-280958-36ytqapi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280958-36ytqapi.txt' === file2bib.sh === id: cord-280819-z6ucnwk0 author: Achilonu, Ikechukwu title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-280819-z6ucnwk0.txt cache: ./cache/cord-280819-z6ucnwk0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280819-z6ucnwk0.txt' === file2bib.sh === id: cord-281501-ca9oxl7f author: Khan, Shumayila title: Neuropathogenesis of SARS-CoV-2 infection date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-281501-ca9oxl7f.txt cache: ./cache/cord-281501-ca9oxl7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281501-ca9oxl7f.txt' === file2bib.sh === id: cord-281346-bjhdy8mg author: Palacios Cruz, M. title: COVID-19, a worldwide public health emergency() date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-281346-bjhdy8mg.txt cache: ./cache/cord-281346-bjhdy8mg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281346-bjhdy8mg.txt' === file2bib.sh === id: cord-281677-pspmmrq7 author: Schulze-Koops, Hendrik title: Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie e. V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-281677-pspmmrq7.txt cache: ./cache/cord-281677-pspmmrq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281677-pspmmrq7.txt' === file2bib.sh === id: cord-280922-w6a5ec06 author: Sen, Sanjana title: Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-280922-w6a5ec06.txt cache: ./cache/cord-280922-w6a5ec06.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280922-w6a5ec06.txt' === file2bib.sh === id: cord-280979-0vaarrji author: Gauttier, V. title: Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-280979-0vaarrji.txt cache: ./cache/cord-280979-0vaarrji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280979-0vaarrji.txt' === file2bib.sh === id: cord-281254-x7ivjvti author: Chang, Zhijie title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-281254-x7ivjvti.txt cache: ./cache/cord-281254-x7ivjvti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281254-x7ivjvti.txt' === file2bib.sh === id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-280427-smqc23vr.txt cache: ./cache/cord-280427-smqc23vr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280427-smqc23vr.txt' === file2bib.sh === id: cord-281508-zl2url8z author: Pearce, N. title: Is death from Covid-19 a multistep process? date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-281508-zl2url8z.txt cache: ./cache/cord-281508-zl2url8z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281508-zl2url8z.txt' === file2bib.sh === id: cord-281101-gv1sgbk1 author: Shin, Gu-Choul title: Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date: 2006-08-30 pages: extension: .txt txt: ./txt/cord-281101-gv1sgbk1.txt cache: ./cache/cord-281101-gv1sgbk1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281101-gv1sgbk1.txt' === file2bib.sh === id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 pages: extension: .txt txt: ./txt/cord-279691-v5kpmk0b.txt cache: ./cache/cord-279691-v5kpmk0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279691-v5kpmk0b.txt' === file2bib.sh === id: cord-281536-8y7yxcp4 author: Lim, Hocheol title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-281536-8y7yxcp4.txt cache: ./cache/cord-281536-8y7yxcp4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281536-8y7yxcp4.txt' === file2bib.sh === id: cord-282045-pf08iakf author: Chen, Haoyan title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-282045-pf08iakf.txt cache: ./cache/cord-282045-pf08iakf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282045-pf08iakf.txt' === file2bib.sh === id: cord-282043-cs1oyohu author: Giustino, Gennaro title: Coronavirus and Cardiovascular Disease, Myocardial Injury, and Arrhythmia: JACC Focus Seminar date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-282043-cs1oyohu.txt cache: ./cache/cord-282043-cs1oyohu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282043-cs1oyohu.txt' === file2bib.sh === id: cord-282177-8l7zukg4 author: Lin, Yi-Chun title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-282177-8l7zukg4.txt cache: ./cache/cord-282177-8l7zukg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282177-8l7zukg4.txt' === file2bib.sh === id: cord-281699-pxof67pl author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-281699-pxof67pl.txt cache: ./cache/cord-281699-pxof67pl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281699-pxof67pl.txt' === file2bib.sh === id: cord-281679-xmbnpawj author: Meekins, David A. title: Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-281679-xmbnpawj.txt cache: ./cache/cord-281679-xmbnpawj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281679-xmbnpawj.txt' === file2bib.sh === id: cord-281860-zjvrohgg author: Peng, Jing title: Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-281860-zjvrohgg.txt cache: ./cache/cord-281860-zjvrohgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281860-zjvrohgg.txt' === file2bib.sh === id: cord-281793-tj4m01s4 author: Ho, Mitchell title: Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-281793-tj4m01s4.txt cache: ./cache/cord-281793-tj4m01s4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281793-tj4m01s4.txt' === file2bib.sh === id: cord-281528-xy8j5jiv author: Di Paola, Luisa title: The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-281528-xy8j5jiv.txt cache: ./cache/cord-281528-xy8j5jiv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281528-xy8j5jiv.txt' === file2bib.sh === id: cord-282272-wy8do2z6 author: Nelson, Atiba title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-282272-wy8do2z6.txt cache: ./cache/cord-282272-wy8do2z6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282272-wy8do2z6.txt' === file2bib.sh === id: cord-282750-d9sb7o63 author: Benhadou, F. title: Improvement of SARS‐CoV2 symptoms following Guselkumab injection in a psoriatic patient date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-282750-d9sb7o63.txt cache: ./cache/cord-282750-d9sb7o63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282750-d9sb7o63.txt' === file2bib.sh === id: cord-281754-auqh3vtr author: nan title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date: 2017-09-12 pages: extension: .txt txt: ./txt/cord-281754-auqh3vtr.txt cache: ./cache/cord-281754-auqh3vtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281754-auqh3vtr.txt' === file2bib.sh === id: cord-282449-7mxp3sdy author: A, Amouroux title: Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-282449-7mxp3sdy.txt cache: ./cache/cord-282449-7mxp3sdy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282449-7mxp3sdy.txt' === file2bib.sh === id: cord-282576-mcx0xq0w author: Boutin, Catherine-Audrey title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-282576-mcx0xq0w.txt cache: ./cache/cord-282576-mcx0xq0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282576-mcx0xq0w.txt' === file2bib.sh === id: cord-281727-elartlro author: Sun, Jing title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-281727-elartlro.txt cache: ./cache/cord-281727-elartlro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281727-elartlro.txt' === file2bib.sh === id: cord-281512-79g22dk6 author: Aguirre, A. Alonso title: Illicit Wildlife Trade, Wet Markets, and COVID‐19: Preventing Future Pandemics date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-281512-79g22dk6.txt cache: ./cache/cord-281512-79g22dk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281512-79g22dk6.txt' === file2bib.sh === id: cord-281391-0qkku2jd author: Miller-Handley, Hilary title: Treatment Options for COVID-19 in Patients with Reduced or Absent Kidney Function date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-281391-0qkku2jd.txt cache: ./cache/cord-281391-0qkku2jd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281391-0qkku2jd.txt' === file2bib.sh === id: cord-280454-etf32afd author: Moustaqil, Mehdi title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-280454-etf32afd.txt cache: ./cache/cord-280454-etf32afd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280454-etf32afd.txt' === file2bib.sh === id: cord-281571-vob1bu9c author: Tam, Theresa W.S title: The Canadian Pandemic Influenza Plan: an evolution to the approach for national communicable disease emergencies date: 2004-06-30 pages: extension: .txt txt: ./txt/cord-281571-vob1bu9c.txt cache: ./cache/cord-281571-vob1bu9c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281571-vob1bu9c.txt' === file2bib.sh === id: cord-280996-anq680a1 author: Agarwal, Arnav title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-280996-anq680a1.txt cache: ./cache/cord-280996-anq680a1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280996-anq680a1.txt' === file2bib.sh === id: cord-281141-ouno4jpl author: Mahajan, Swapnil title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-281141-ouno4jpl.txt cache: ./cache/cord-281141-ouno4jpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281141-ouno4jpl.txt' === file2bib.sh === id: cord-280939-d478p8u6 author: Abe, Kento T. title: A simple protein-based surrogate neutralization assay for SARS-CoV-2 date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-280939-d478p8u6.txt cache: ./cache/cord-280939-d478p8u6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280939-d478p8u6.txt' === file2bib.sh === id: cord-282318-890mltl8 author: Richard, Mathilde title: Factors determining human-to-human transmissibility of zoonotic pathogens via contact date: 2017-02-28 pages: extension: .txt txt: ./txt/cord-282318-890mltl8.txt cache: ./cache/cord-282318-890mltl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282318-890mltl8.txt' === file2bib.sh === id: cord-282738-aqc9gxlw author: Liu, Anding title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-282738-aqc9gxlw.txt cache: ./cache/cord-282738-aqc9gxlw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282738-aqc9gxlw.txt' === file2bib.sh === id: cord-282338-u01qv3uc author: Cherry, James. D. title: The chronology of the 2002–2003 SARS mini pandemic date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-282338-u01qv3uc.txt cache: ./cache/cord-282338-u01qv3uc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282338-u01qv3uc.txt' === file2bib.sh === id: cord-281161-u896icp9 author: Wang, Jing title: The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-281161-u896icp9.txt cache: ./cache/cord-281161-u896icp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281161-u896icp9.txt' === file2bib.sh === id: cord-281487-x0a9qgjs author: Kim, Min Young title: General Approach to the Clinical Care of Solid Organ Transplant Recipients with COVID-19 Infection: Management for Transplant Recipients date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-281487-x0a9qgjs.txt cache: ./cache/cord-281487-x0a9qgjs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281487-x0a9qgjs.txt' === file2bib.sh === id: cord-281619-fhyamruq author: Burlacu, Alexandru title: Unpuzzling COVID-19 Prothrombotic State: Are Preexisting Thrombophilic Risk Profiles Responsible for Heterogenous Thrombotic Events? date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-281619-fhyamruq.txt cache: ./cache/cord-281619-fhyamruq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281619-fhyamruq.txt' === file2bib.sh === id: cord-281684-m3m4mhye author: Fagre, Anna C. title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-281684-m3m4mhye.txt cache: ./cache/cord-281684-m3m4mhye.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281684-m3m4mhye.txt' === file2bib.sh === id: cord-282965-xguotf4m author: O’Callaghan-Gordo, Cristina title: COVID-19: The Disease of the Anthropocene date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-282965-xguotf4m.txt cache: ./cache/cord-282965-xguotf4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282965-xguotf4m.txt' === file2bib.sh === id: cord-282530-55lhjfm8 author: Carsana, Luca title: Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-282530-55lhjfm8.txt cache: ./cache/cord-282530-55lhjfm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282530-55lhjfm8.txt' === file2bib.sh === id: cord-282821-qvtvpnrr author: Thijsen, Steven title: Elevated nucleoprotein-induced interferon-γ release in COVID-19 patients detected in a SARS-CoV-2 enzyme-linked immunosorbent spot assay date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-282821-qvtvpnrr.txt cache: ./cache/cord-282821-qvtvpnrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282821-qvtvpnrr.txt' === file2bib.sh === id: cord-282795-kje7rn57 author: Zheng, Yue title: Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-282795-kje7rn57.txt cache: ./cache/cord-282795-kje7rn57.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-282795-kje7rn57.txt' === file2bib.sh === id: cord-282371-39qo9afy author: Khulood, Daulat title: Convalescent plasma appears efficacious and safe in COVID-19 date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-282371-39qo9afy.txt cache: ./cache/cord-282371-39qo9afy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282371-39qo9afy.txt' === file2bib.sh === id: cord-281561-r10y2sgb author: Tiwari, Nidhi title: Novel β-Coronavirus (SARS-CoV-2): Current and Future Aspects of Pharmacological Treatments date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-281561-r10y2sgb.txt cache: ./cache/cord-281561-r10y2sgb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281561-r10y2sgb.txt' === file2bib.sh === id: cord-281552-zfjy3m3i author: Alsaadi, Entedar A. J. title: Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-281552-zfjy3m3i.txt cache: ./cache/cord-281552-zfjy3m3i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281552-zfjy3m3i.txt' === file2bib.sh === id: cord-282108-hhnnloxp author: Heister, Paula M. title: Pharmacological hypothesis: TPC2 antagonist tetrandrine as a potential therapeutic agent for COVID‐19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-282108-hhnnloxp.txt cache: ./cache/cord-282108-hhnnloxp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282108-hhnnloxp.txt' === file2bib.sh === id: cord-281937-yztlb0fn author: Sheahan, Timothy P title: The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-281937-yztlb0fn.txt cache: ./cache/cord-281937-yztlb0fn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281937-yztlb0fn.txt' === file2bib.sh === id: cord-282920-s4yixzuy author: Rubin, Elizabeth S. title: Detection of COVID-19 in a Vulvar Lesion date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-282920-s4yixzuy.txt cache: ./cache/cord-282920-s4yixzuy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282920-s4yixzuy.txt' === file2bib.sh === id: cord-282133-5dzzm9s8 author: Watzky, Manon title: Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-282133-5dzzm9s8.txt cache: ./cache/cord-282133-5dzzm9s8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282133-5dzzm9s8.txt' === file2bib.sh === id: cord-281717-kzd9vvci author: Digard, Paul title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-281717-kzd9vvci.txt cache: ./cache/cord-281717-kzd9vvci.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281717-kzd9vvci.txt' === file2bib.sh === id: cord-282732-qym6wji7 author: McLaughlin, Katie-May title: COVID-19-Related Coagulopathy—Is Transferrin a Missing Link? date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-282732-qym6wji7.txt cache: ./cache/cord-282732-qym6wji7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282732-qym6wji7.txt' === file2bib.sh === id: cord-282372-nmii30mc author: Youk, Jeonghwan title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-282372-nmii30mc.txt cache: ./cache/cord-282372-nmii30mc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282372-nmii30mc.txt' === file2bib.sh === id: cord-283193-8qj41kpp author: Chak-Yiu Lee, Andrew title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-283193-8qj41kpp.txt cache: ./cache/cord-283193-8qj41kpp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283193-8qj41kpp.txt' === file2bib.sh === id: cord-282433-p6jl9gxf author: Tu, Xinyi title: Functional polymorphisms of the CCL2 and MBL genes cumulatively increase susceptibility to severe acute respiratory syndrome coronavirus infection date: 2015-03-27 pages: extension: .txt txt: ./txt/cord-282433-p6jl9gxf.txt cache: ./cache/cord-282433-p6jl9gxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282433-p6jl9gxf.txt' === file2bib.sh === id: cord-281726-s1o5l7ns author: Yu, Ignatius T. S. title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date: 2005-05-01 pages: extension: .txt txt: ./txt/cord-281726-s1o5l7ns.txt cache: ./cache/cord-281726-s1o5l7ns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281726-s1o5l7ns.txt' === file2bib.sh === id: cord-282862-kve6fa49 author: Pastick, Katelyn A title: A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-282862-kve6fa49.txt cache: ./cache/cord-282862-kve6fa49.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282862-kve6fa49.txt' === file2bib.sh === id: cord-283413-xapzer5s author: Chan, A. K. M. title: Social media for rapid knowledge dissemination: early experience from the COVID‐19 pandemic date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-283413-xapzer5s.txt cache: ./cache/cord-283413-xapzer5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283413-xapzer5s.txt' === file2bib.sh === id: cord-282895-85if4mnu author: Xiao, Xiaodong title: The SARS-CoV S glycoprotein: expression and functional characterization date: 2003-12-26 pages: extension: .txt txt: ./txt/cord-282895-85if4mnu.txt cache: ./cache/cord-282895-85if4mnu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282895-85if4mnu.txt' === file2bib.sh === id: cord-283197-jjye8t6j author: Ingraham, Nicholas E. title: Fact Versus Science Fiction: Fighting Coronavirus Disease 2019 Requires the Wisdom to Know the Difference date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-283197-jjye8t6j.txt cache: ./cache/cord-283197-jjye8t6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283197-jjye8t6j.txt' === file2bib.sh === id: cord-282106-7k088cqv author: Yang, Zhi-yong title: A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice date: 2004 pages: extension: .txt txt: ./txt/cord-282106-7k088cqv.txt cache: ./cache/cord-282106-7k088cqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282106-7k088cqv.txt' === file2bib.sh === id: cord-283034-ebely0rx author: Brunet, E title: Ileitis as the exclusive manifestation of covid-19. The first reported case date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-283034-ebely0rx.txt cache: ./cache/cord-283034-ebely0rx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283034-ebely0rx.txt' === file2bib.sh === id: cord-282058-it0ojdk3 author: Yu, Yuanqiang title: Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-282058-it0ojdk3.txt cache: ./cache/cord-282058-it0ojdk3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282058-it0ojdk3.txt' === file2bib.sh === id: cord-281887-b511bjdy author: Ribeiro, Reitan title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-281887-b511bjdy.txt cache: ./cache/cord-281887-b511bjdy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281887-b511bjdy.txt' === file2bib.sh === id: cord-282421-yialyuav author: Alcoba-Florez, Julia title: Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-282421-yialyuav.txt cache: ./cache/cord-282421-yialyuav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282421-yialyuav.txt' === file2bib.sh === id: cord-281948-xv7vuypd author: Hoang, Ansel title: COVID-19 in 7780 pediatric patients: A systematic review date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-281948-xv7vuypd.txt cache: ./cache/cord-281948-xv7vuypd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281948-xv7vuypd.txt' === file2bib.sh === id: cord-283116-ib5c3lbi author: Koh, David title: Occupational health responses to COVID‐19: What lessons can we learn from SARS? date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-283116-ib5c3lbi.txt cache: ./cache/cord-283116-ib5c3lbi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283116-ib5c3lbi.txt' === file2bib.sh === id: cord-283196-laerx0n2 author: Bedford, Juliet title: Living with the COVID-19 pandemic: act now with the tools we have date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-283196-laerx0n2.txt cache: ./cache/cord-283196-laerx0n2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283196-laerx0n2.txt' === file2bib.sh === id: cord-282009-a83mun7u author: Pundir, Hemlata title: Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-282009-a83mun7u.txt cache: ./cache/cord-282009-a83mun7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282009-a83mun7u.txt' === file2bib.sh === id: cord-281285-5g1rw202 author: Simonis, Alexander title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-281285-5g1rw202.txt cache: ./cache/cord-281285-5g1rw202.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281285-5g1rw202.txt' === file2bib.sh === id: cord-282560-tofppr3b author: Henderson, Jack A. title: Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-282560-tofppr3b.txt cache: ./cache/cord-282560-tofppr3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282560-tofppr3b.txt' === file2bib.sh === id: cord-282384-qbcqbhk4 author: Savastano, Alfonso title: Peripapillary Retinal Vascular Involvement in Early Post-COVID-19 Patients date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-282384-qbcqbhk4.txt cache: ./cache/cord-282384-qbcqbhk4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282384-qbcqbhk4.txt' === file2bib.sh === id: cord-279406-wwdqh9qs author: Guzman, Norberto A. title: A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-279406-wwdqh9qs.txt cache: ./cache/cord-279406-wwdqh9qs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279406-wwdqh9qs.txt' === file2bib.sh === id: cord-283430-k1ex9fes author: Smithgall, Marie C. title: Third Trimester Placentas of SARS‐CoV‐2‐Positive Women: Histomorphology, including Viral Immunohistochemistry and in Situ Hybridization date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-283430-k1ex9fes.txt cache: ./cache/cord-283430-k1ex9fes.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283430-k1ex9fes.txt' === file2bib.sh === id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-283590-xvnv17zy.txt cache: ./cache/cord-283590-xvnv17zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283590-xvnv17zy.txt' === file2bib.sh === id: cord-282964-dmc8mlxu author: Wathore, Roshan title: Understanding air and water borne transmission and survival of coronavirus: Insights and way forward for SARS-CoV-2 date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-282964-dmc8mlxu.txt cache: ./cache/cord-282964-dmc8mlxu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282964-dmc8mlxu.txt' === file2bib.sh === id: cord-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-283411-40ojqv1y.txt cache: ./cache/cord-283411-40ojqv1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283411-40ojqv1y.txt' === file2bib.sh === id: cord-282539-skzosh6u author: Casadevall, Arturo title: Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-282539-skzosh6u.txt cache: ./cache/cord-282539-skzosh6u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282539-skzosh6u.txt' === file2bib.sh === id: cord-282899-kp114q7n author: Biswas, Saurav title: Blood clots in COVID-19 patients: Simplifying the curious mystery date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-282899-kp114q7n.txt cache: ./cache/cord-282899-kp114q7n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282899-kp114q7n.txt' === file2bib.sh === id: cord-283109-ka3n9pft author: Arumugam, Arunkumar title: The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-283109-ka3n9pft.txt cache: ./cache/cord-283109-ka3n9pft.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283109-ka3n9pft.txt' === file2bib.sh === id: cord-283152-wav0d0ws author: Patel, Sanjay K. S. title: Deploying Biomolecules as Anti-COVID-19 Agents date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-283152-wav0d0ws.txt cache: ./cache/cord-283152-wav0d0ws.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283152-wav0d0ws.txt' === file2bib.sh === id: cord-283127-jetmocvk author: Wang, Denong title: Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date: 2015-03-12 pages: extension: .txt txt: ./txt/cord-283127-jetmocvk.txt cache: ./cache/cord-283127-jetmocvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283127-jetmocvk.txt' === file2bib.sh === id: cord-283823-8n1cy0hj author: Parikh, Bijal A. title: The Brief Case: “Not Positive” or “Not Sure”—COVID-19-Negative Results in a Symptomatic Patient date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-283823-8n1cy0hj.txt cache: ./cache/cord-283823-8n1cy0hj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283823-8n1cy0hj.txt' === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-266738-8xx1xm2d' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-266738-8xx1xm2d' === file2bib.sh === id: cord-283138-18q23z8l author: Balasubramanian, S. title: Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-283138-18q23z8l.txt cache: ./cache/cord-283138-18q23z8l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283138-18q23z8l.txt' === file2bib.sh === id: cord-283512-qly8iclf author: Na, Ki Ryang title: Acute Kidney Injury and Kidney Damage in COVID-19 Patients date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-283512-qly8iclf.txt cache: ./cache/cord-283512-qly8iclf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283512-qly8iclf.txt' === file2bib.sh === id: cord-282317-k9mtf6yl author: Srivastava, Vivek title: Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2 date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-282317-k9mtf6yl.txt cache: ./cache/cord-282317-k9mtf6yl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282317-k9mtf6yl.txt' === file2bib.sh === id: cord-282858-zikoui4h author: Graudenz, Gustavo Silveira title: SARS-CoV-2. Long Distance Airborne Transmission and its Public Health Implications date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-282858-zikoui4h.txt cache: ./cache/cord-282858-zikoui4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282858-zikoui4h.txt' === file2bib.sh === id: cord-283372-c20i99qa author: Sanchis-Gomar, Fabian title: Amiodarone in the COVID-19 Era: Treatment for Symptomatic Patients Only, or Drug to Prevent Infection? date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-283372-c20i99qa.txt cache: ./cache/cord-283372-c20i99qa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283372-c20i99qa.txt' === file2bib.sh === id: cord-282817-vtzpf2wr author: Byrne, Hannah title: A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications date: 2013-10-02 pages: extension: .txt txt: ./txt/cord-282817-vtzpf2wr.txt cache: ./cache/cord-282817-vtzpf2wr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282817-vtzpf2wr.txt' === file2bib.sh === id: cord-282990-qb4wk4yb author: Chen, Zhuo title: Safety considerations in the bioanalytical laboratories handling specimens from coronavirus disease 2019 patients date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-282990-qb4wk4yb.txt cache: ./cache/cord-282990-qb4wk4yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282990-qb4wk4yb.txt' === file2bib.sh === id: cord-283818-4m9p717r author: Yan, Chao title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-283818-4m9p717r.txt cache: ./cache/cord-283818-4m9p717r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283818-4m9p717r.txt' === file2bib.sh === id: cord-282635-ffq8kpij author: Tierraseca, Melody Sánchez title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-282635-ffq8kpij.txt cache: ./cache/cord-282635-ffq8kpij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282635-ffq8kpij.txt' === file2bib.sh === id: cord-282853-l0c69uul author: Massad, Eduardo title: Forecasting versus projection models in epidemiology: The case of the SARS epidemics date: 2005-03-30 pages: extension: .txt txt: ./txt/cord-282853-l0c69uul.txt cache: ./cache/cord-282853-l0c69uul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282853-l0c69uul.txt' === file2bib.sh === id: cord-283699-c4jjdj5o author: Eslami, Gholamali title: The impact of sofosbuvir/daclatasvir or ribavirin in patients with severe COVID-19 date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-283699-c4jjdj5o.txt cache: ./cache/cord-283699-c4jjdj5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283699-c4jjdj5o.txt' === file2bib.sh === id: cord-283716-tleh9323 author: Amatore, F. title: SARS‐CoV‐2 infection presenting as a febrile rash date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-283716-tleh9323.txt cache: ./cache/cord-283716-tleh9323.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283716-tleh9323.txt' === file2bib.sh === id: cord-282724-zzkqb0u2 author: Moore, Jason H. title: Ideas for how informaticians can get involved with COVID-19 research date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-282724-zzkqb0u2.txt cache: ./cache/cord-282724-zzkqb0u2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282724-zzkqb0u2.txt' === file2bib.sh === id: cord-283705-ia65pade author: de Gabory, Ludovic title: Le virus influenza, le SARS-CoV2 et les voies aériennes : mise au point pour l’Otorhinolaryngologiste date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-283705-ia65pade.txt cache: ./cache/cord-283705-ia65pade.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283705-ia65pade.txt' === file2bib.sh === id: cord-282604-xp71rkxc author: Nikolaev, EN title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-282604-xp71rkxc.txt cache: ./cache/cord-282604-xp71rkxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282604-xp71rkxc.txt' === file2bib.sh === id: cord-283984-jch0ja1o author: Loizzo, Monica R. title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species date: 2008-03-20 pages: extension: .txt txt: ./txt/cord-283984-jch0ja1o.txt cache: ./cache/cord-283984-jch0ja1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283984-jch0ja1o.txt' === file2bib.sh === id: cord-283310-5wam14aa author: Bevova, M. R. title: The New Coronavirus COVID-19 Infection date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-283310-5wam14aa.txt cache: ./cache/cord-283310-5wam14aa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283310-5wam14aa.txt' === file2bib.sh === id: cord-282142-76jr4p7n author: Wang, Yun title: Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-282142-76jr4p7n.txt cache: ./cache/cord-282142-76jr4p7n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282142-76jr4p7n.txt' === file2bib.sh === id: cord-284464-avriske3 author: Liu, Tao title: Recurrent positive SARS‐CoV‐2: Immune certificate may not be valid date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-284464-avriske3.txt cache: ./cache/cord-284464-avriske3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284464-avriske3.txt' === file2bib.sh === id: cord-282771-iwpx02v3 author: Dietzel, Steffen title: A joint action in times of pandemic: the German BioImaging recommendations for operating imaging core facilities during the SARS‐Cov‐2 emergency date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-282771-iwpx02v3.txt cache: ./cache/cord-282771-iwpx02v3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282771-iwpx02v3.txt' === file2bib.sh === id: cord-283376-6wolrfvk author: Yin, M. title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-283376-6wolrfvk.txt cache: ./cache/cord-283376-6wolrfvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283376-6wolrfvk.txt' === file2bib.sh === id: cord-284028-l0r7f9sr author: Lee, Chi-Wei title: A loophole in international quarantine procedures disclosed during the SARS crisis date: 2004-12-30 pages: extension: .txt txt: ./txt/cord-284028-l0r7f9sr.txt cache: ./cache/cord-284028-l0r7f9sr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284028-l0r7f9sr.txt' === file2bib.sh === id: cord-283253-qdq4mfz3 author: Davlantes, Elizabeth title: Notes from the Field: COVID-19 Prevention Practices in State Prisons — Puerto Rico, 2020 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-283253-qdq4mfz3.txt cache: ./cache/cord-283253-qdq4mfz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283253-qdq4mfz3.txt' === file2bib.sh === id: cord-283948-rb9rrkxb author: Gavriilidis, Paschalis title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-283948-rb9rrkxb.txt cache: ./cache/cord-283948-rb9rrkxb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283948-rb9rrkxb.txt' === file2bib.sh === id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-281281-knelqmzx.txt cache: ./cache/cord-281281-knelqmzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281281-knelqmzx.txt' === file2bib.sh === id: cord-284444-mgxxbm0u author: Reychler, G. title: Nebulization: A potential source of SARS-CoV-2 transmission date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-284444-mgxxbm0u.txt cache: ./cache/cord-284444-mgxxbm0u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284444-mgxxbm0u.txt' === file2bib.sh === id: cord-283439-hqdq2qrh author: Rahman, Mohammad Tariqur title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-283439-hqdq2qrh.txt cache: ./cache/cord-283439-hqdq2qrh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283439-hqdq2qrh.txt' === file2bib.sh === id: cord-282571-ilf73g71 author: Ni, Wentao title: Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-282571-ilf73g71.txt cache: ./cache/cord-282571-ilf73g71.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282571-ilf73g71.txt' === file2bib.sh === id: cord-283895-1p5uog38 author: Trottier, J. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-283895-1p5uog38.txt cache: ./cache/cord-283895-1p5uog38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283895-1p5uog38.txt' === file2bib.sh === id: cord-284302-odvv2yn3 author: Minagorre, Pedro J. Alcalá title: CAMBIOS A PARTIR DE LA COVID-19. UNA PERSPECTIVA DESDE LA PEDIATRÍA INTERNA HOSPITALARIA date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-284302-odvv2yn3.txt cache: ./cache/cord-284302-odvv2yn3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284302-odvv2yn3.txt' === file2bib.sh === id: cord-282867-kbyxdegu author: Shah, Sayed Zulfiqar Ali title: Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-282867-kbyxdegu.txt cache: ./cache/cord-282867-kbyxdegu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282867-kbyxdegu.txt' === file2bib.sh === id: cord-283120-hyzk59qv author: Sharma, Ashish title: Liver disease and outcomes among COVID-19 hospitalized patients- a systematic review and meta-analysis date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-283120-hyzk59qv.txt cache: ./cache/cord-283120-hyzk59qv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283120-hyzk59qv.txt' === file2bib.sh === id: cord-283491-y6t64pux author: Brzezinski, Dariusz title: Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-283491-y6t64pux.txt cache: ./cache/cord-283491-y6t64pux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283491-y6t64pux.txt' === file2bib.sh === id: cord-284091-1dj4yxkz author: Duart, Gerard title: SARS-CoV-2 envelope protein topology in eukaryotic membranes date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-284091-1dj4yxkz.txt cache: ./cache/cord-284091-1dj4yxkz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284091-1dj4yxkz.txt' === file2bib.sh === id: cord-284008-vlwdtjbe author: Li, Na title: The Application of Corticosteroids in COVID-19: A Two-edged Sword date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-284008-vlwdtjbe.txt cache: ./cache/cord-284008-vlwdtjbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284008-vlwdtjbe.txt' === file2bib.sh === id: cord-284163-3jmqzemf author: Seffer, Malin-Theres title: Heparin 2.0: A New Approach to the Infection Crisis date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-284163-3jmqzemf.txt cache: ./cache/cord-284163-3jmqzemf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284163-3jmqzemf.txt' === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-324559-p92y5er2' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-324559-p92y5er2' === file2bib.sh === id: cord-283486-ji0e8yoo author: Radulesco, Thomas title: Safety and Impact of Nasal Lavages During Viral Infections Such as SARS-CoV-2 date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-283486-ji0e8yoo.txt cache: ./cache/cord-283486-ji0e8yoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283486-ji0e8yoo.txt' === file2bib.sh === id: cord-284559-g9szoh3g author: Bartoloni, Elena title: Hypertension and SARS-Cov-2 infection: is inflammation the missing link? date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-284559-g9szoh3g.txt cache: ./cache/cord-284559-g9szoh3g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284559-g9szoh3g.txt' === file2bib.sh === id: cord-283380-l60yyr6l author: Grabbe, Stephan title: Systemic immunosuppression in times of COVID‐19: Do we need to rethink our standards? date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-283380-l60yyr6l.txt cache: ./cache/cord-283380-l60yyr6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283380-l60yyr6l.txt' === file2bib.sh === id: cord-283786-d65njv7b author: Toptan, Tuna title: Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-283786-d65njv7b.txt cache: ./cache/cord-283786-d65njv7b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283786-d65njv7b.txt' === file2bib.sh === id: cord-283579-aejbfk3l author: Hilda, Awoyelu Elukunbi title: Phyloevolutionary analysis of SARS-CoV-2 in Nigeria date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-283579-aejbfk3l.txt cache: ./cache/cord-283579-aejbfk3l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283579-aejbfk3l.txt' === file2bib.sh === id: cord-284625-to6w5hm2 author: Duan, Xiaopei title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-284625-to6w5hm2.txt cache: ./cache/cord-284625-to6w5hm2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284625-to6w5hm2.txt' === file2bib.sh === id: cord-283749-j4600733 author: Itoyama, Satoru title: ACE1 polymorphism and progression of SARS date: 2004-10-22 pages: extension: .txt txt: ./txt/cord-283749-j4600733.txt cache: ./cache/cord-283749-j4600733.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283749-j4600733.txt' === file2bib.sh === id: cord-284102-rovyvv45 author: Wagner, Teresa R. title: NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-284102-rovyvv45.txt cache: ./cache/cord-284102-rovyvv45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284102-rovyvv45.txt' === file2bib.sh === id: cord-279255-v861kk0i author: Dhama, Kuldeep title: Coronavirus Disease 2019–COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-279255-v861kk0i.txt cache: ./cache/cord-279255-v861kk0i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-279255-v861kk0i.txt' === file2bib.sh === id: cord-284702-reu77suz author: Lau, Suet-Ting title: Tachycardia amongst subjects recovering from severe acute respiratory syndrome (SARS) date: 2005-04-08 pages: extension: .txt txt: ./txt/cord-284702-reu77suz.txt cache: ./cache/cord-284702-reu77suz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284702-reu77suz.txt' === file2bib.sh === id: cord-283367-azzy2t1a author: Rahman, Asma title: Neurological manifestations in COVID-19: A narrative review date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-283367-azzy2t1a.txt cache: ./cache/cord-283367-azzy2t1a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283367-azzy2t1a.txt' === file2bib.sh === id: cord-284045-scd3f8vk author: Pape, Constantin title: Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-284045-scd3f8vk.txt cache: ./cache/cord-284045-scd3f8vk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284045-scd3f8vk.txt' === file2bib.sh === id: cord-283249-pk5sc2ca author: Yoshida, Wataru title: Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers date: 2006-09-15 pages: extension: .txt txt: ./txt/cord-283249-pk5sc2ca.txt cache: ./cache/cord-283249-pk5sc2ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283249-pk5sc2ca.txt' === file2bib.sh === id: cord-284862-nhihxog0 author: Kroemer, Marie title: COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-284862-nhihxog0.txt cache: ./cache/cord-284862-nhihxog0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284862-nhihxog0.txt' === file2bib.sh === id: cord-284449-z7r4n0w7 author: Ma, L. title: Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-284449-z7r4n0w7.txt cache: ./cache/cord-284449-z7r4n0w7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284449-z7r4n0w7.txt' === file2bib.sh === id: cord-285362-7dc2gox0 author: Jacot, Damien title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-285362-7dc2gox0.txt cache: ./cache/cord-285362-7dc2gox0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285362-7dc2gox0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45469 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47054 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47477 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-282839-3ii79g6j author: Moreno-Fernández Ayala, Daniel J. title: Age-related mitochondrial dysfunction as a key factor in COVID-19 disease date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-282839-3ii79g6j.txt cache: ./cache/cord-282839-3ii79g6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282839-3ii79g6j.txt' === file2bib.sh === id: cord-285053-ah9z9luw author: Freedman, David O title: In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-285053-ah9z9luw.txt cache: ./cache/cord-285053-ah9z9luw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285053-ah9z9luw.txt' === file2bib.sh === id: cord-284841-flhfagp3 author: Nicol, Thomas title: Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech) date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-284841-flhfagp3.txt cache: ./cache/cord-284841-flhfagp3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284841-flhfagp3.txt' === file2bib.sh === id: cord-283912-ha2xwjzy author: Zheng, Meijuan title: Serum inflammatory factors are positively correlated with the production of specific antibodies in coronavirus disease 2019 patients date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-283912-ha2xwjzy.txt cache: ./cache/cord-283912-ha2xwjzy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283912-ha2xwjzy.txt' === file2bib.sh === id: cord-285168-qkadqohe author: Delatorre, Edson title: Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-285168-qkadqohe.txt cache: ./cache/cord-285168-qkadqohe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285168-qkadqohe.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-283432-od5nnxvg author: Morawska, Lidia title: How can airborne transmission of COVID-19 indoors be minimised? date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-283432-od5nnxvg.txt cache: ./cache/cord-283432-od5nnxvg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283432-od5nnxvg.txt' === file2bib.sh === id: cord-284398-rhfwbyav author: Aboubakr, Hamada A. title: Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-284398-rhfwbyav.txt cache: ./cache/cord-284398-rhfwbyav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284398-rhfwbyav.txt' === file2bib.sh === id: cord-284879-sjkni2uc author: Song, Suk-Kyoon title: IgG Seroprevalence of COVID-19 among Individuals without a History of the Coronavirus Disease Infection in Daegu, Korea date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-284879-sjkni2uc.txt cache: ./cache/cord-284879-sjkni2uc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284879-sjkni2uc.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-283352-0l1ggmhx author: Javelot, H title: Panic and pandemic: narrative review of the literature on the links and risks of panic disorder as a consequence of the SARS-CoV-2 pandemic date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-283352-0l1ggmhx.txt cache: ./cache/cord-283352-0l1ggmhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283352-0l1ggmhx.txt' === file2bib.sh === id: cord-284829-dge21g0g author: Dinakaran, Damodharan title: Neuropsychiatric aspects of COVID-19 Pandemic: A Selective Review date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-284829-dge21g0g.txt cache: ./cache/cord-284829-dge21g0g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284829-dge21g0g.txt' === file2bib.sh === id: cord-284791-bgodmbru author: Whitworth, Carrie title: Persistence of Bacteriophage Phi 6 on Porous and Nonporous Surfaces and the Potential for Its Use as an Ebola Virus or Coronavirus Surrogate date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-284791-bgodmbru.txt cache: ./cache/cord-284791-bgodmbru.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284791-bgodmbru.txt' === file2bib.sh === id: cord-284589-j1609xlu author: Sedova, Mayya title: Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-284589-j1609xlu.txt cache: ./cache/cord-284589-j1609xlu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284589-j1609xlu.txt' === file2bib.sh === id: cord-283779-mudwcypl author: Lauretani, Fulvio title: Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-283779-mudwcypl.txt cache: ./cache/cord-283779-mudwcypl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283779-mudwcypl.txt' === file2bib.sh === id: cord-282878-8qgsq2km author: Fignani, Daniela title: SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-282878-8qgsq2km.txt cache: ./cache/cord-282878-8qgsq2km.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282878-8qgsq2km.txt' === file2bib.sh === id: cord-285430-o086q2qa author: Gribble, Karleen title: Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-285430-o086q2qa.txt cache: ./cache/cord-285430-o086q2qa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285430-o086q2qa.txt' === file2bib.sh === id: cord-284873-m1ehdydr author: Cadegiani, Flavio A. title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-284873-m1ehdydr.txt cache: ./cache/cord-284873-m1ehdydr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284873-m1ehdydr.txt' === file2bib.sh === id: cord-284068-sbon3aes author: Mok, Chee Keng title: Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-284068-sbon3aes.txt cache: ./cache/cord-284068-sbon3aes.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284068-sbon3aes.txt' === file2bib.sh === id: cord-284387-cjziykrz author: Garcia-Castrillo, Luis title: European Society For Emergency Medicine position paper on emergency medical systems’ response to COVID-19 date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-284387-cjziykrz.txt cache: ./cache/cord-284387-cjziykrz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284387-cjziykrz.txt' === file2bib.sh === id: cord-284498-54j6ys8s author: Ihsanullah, Ihsanullah title: Coronavirus 2 (SARS-CoV-2) in water environments: Current status, challenges and research opportunities date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-284498-54j6ys8s.txt cache: ./cache/cord-284498-54j6ys8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284498-54j6ys8s.txt' === file2bib.sh === id: cord-285018-l26px1bc author: Ong, David S.Y. title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-285018-l26px1bc.txt cache: ./cache/cord-285018-l26px1bc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285018-l26px1bc.txt' === file2bib.sh === id: cord-284734-qioy7eso author: Pourahmad, Ramtin title: Efficacy of Plasmapheresis and Immunoglobulin Replacement Therapy (IVIG) on Patients with COVID-19 date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-284734-qioy7eso.txt cache: ./cache/cord-284734-qioy7eso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284734-qioy7eso.txt' === file2bib.sh === id: cord-282947-3hgku2e4 author: Wong, Hui Hui title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date: 2017-12-30 pages: extension: .txt txt: ./txt/cord-282947-3hgku2e4.txt cache: ./cache/cord-282947-3hgku2e4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282947-3hgku2e4.txt' === file2bib.sh === id: cord-284042-awl5bb0j author: Carrascosa, J.M. title: Cutaneous Manifestations in the Context of SARS-CoV-2 Infection (COVID-19)() date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-284042-awl5bb0j.txt cache: ./cache/cord-284042-awl5bb0j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284042-awl5bb0j.txt' === file2bib.sh === id: cord-285179-26ey3fm8 author: Chan, Kwok-Hung title: Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests date: 2013-04-10 pages: extension: .txt txt: ./txt/cord-285179-26ey3fm8.txt cache: ./cache/cord-285179-26ey3fm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285179-26ey3fm8.txt' === file2bib.sh === id: cord-285527-1mceq6v0 author: Kinloch, Natalie N title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-285527-1mceq6v0.txt cache: ./cache/cord-285527-1mceq6v0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285527-1mceq6v0.txt' === file2bib.sh === id: cord-284366-snajbvr9 author: Han, Zhiyong title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-284366-snajbvr9.txt cache: ./cache/cord-284366-snajbvr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284366-snajbvr9.txt' === file2bib.sh === id: cord-283956-zgrtux7i author: Amin, Sk. Abdul title: Fight against novel coronavirus: A perspective of medicinal chemists date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-283956-zgrtux7i.txt cache: ./cache/cord-283956-zgrtux7i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-283956-zgrtux7i.txt' === file2bib.sh === id: cord-285315-7r44j3q9 author: Bein, Berthold title: SARS-CoV-2/COVID-19: Empfehlungen zu Diagnostik und Therapie date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-285315-7r44j3q9.txt cache: ./cache/cord-285315-7r44j3q9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285315-7r44j3q9.txt' === file2bib.sh === id: cord-283440-8du0s33p author: Ciuca, Ioana M title: COVID-19 in Children: An Ample Review date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-283440-8du0s33p.txt cache: ./cache/cord-283440-8du0s33p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283440-8du0s33p.txt' === file2bib.sh === id: cord-283861-kcv1bmyx author: Zou, J. title: Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-283861-kcv1bmyx.txt cache: ./cache/cord-283861-kcv1bmyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283861-kcv1bmyx.txt' === file2bib.sh === id: cord-285787-xvi5miqw author: Bell, Jennifer AH title: SARS and hospital priority setting: a qualitative case study and evaluation date: 2004-12-19 pages: extension: .txt txt: ./txt/cord-285787-xvi5miqw.txt cache: ./cache/cord-285787-xvi5miqw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285787-xvi5miqw.txt' === file2bib.sh === id: cord-284526-a5kgo4ct author: Gavriilaki, Eleni title: Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-284526-a5kgo4ct.txt cache: ./cache/cord-284526-a5kgo4ct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284526-a5kgo4ct.txt' === file2bib.sh === id: cord-284867-p4jgyusp author: Schöler, Lara title: A Novel In-Cell ELISA Assay Allows Rapid and Automated Quantification of SARS-CoV-2 to Analyze Neutralizing Antibodies and Antiviral Compounds date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-284867-p4jgyusp.txt cache: ./cache/cord-284867-p4jgyusp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284867-p4jgyusp.txt' === file2bib.sh === id: cord-285569-ei9w19i7 author: Shah, Aditya title: Guide to Understanding the 2019 Novel Coronavirus date: 2020-02-28 pages: extension: .txt txt: ./txt/cord-285569-ei9w19i7.txt cache: ./cache/cord-285569-ei9w19i7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285569-ei9w19i7.txt' === file2bib.sh === id: cord-284978-vh1x6pg9 author: Jang, Hongje title: Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date: 2013-02-18 pages: extension: .txt txt: ./txt/cord-284978-vh1x6pg9.txt cache: ./cache/cord-284978-vh1x6pg9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284978-vh1x6pg9.txt' === file2bib.sh === id: cord-284925-vy2li9lz author: Lam, Dennis Shun Chiu title: COVID-19: Special Precautions in Ophthalmic Practice and FAQs on Personal Protection and Mask Selection date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-284925-vy2li9lz.txt cache: ./cache/cord-284925-vy2li9lz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284925-vy2li9lz.txt' === file2bib.sh === id: cord-284627-qvz63m93 author: Banerjee, Shuvam title: Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-284627-qvz63m93.txt cache: ./cache/cord-284627-qvz63m93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284627-qvz63m93.txt' === file2bib.sh === id: cord-285557-my16g91c author: Berger, A. title: Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date: 2004-01-31 pages: extension: .txt txt: ./txt/cord-285557-my16g91c.txt cache: ./cache/cord-285557-my16g91c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285557-my16g91c.txt' === file2bib.sh === id: cord-284234-9cd2v6bt author: Sebastian, S title: Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-284234-9cd2v6bt.txt cache: ./cache/cord-284234-9cd2v6bt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284234-9cd2v6bt.txt' === file2bib.sh === id: cord-285254-8a1cia8s author: Parry, Nicola M.A. title: COVID-19 and pets: When pandemic meets panic date: 2020-12-31 pages: extension: .txt txt: ./txt/cord-285254-8a1cia8s.txt cache: ./cache/cord-285254-8a1cia8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285254-8a1cia8s.txt' === file2bib.sh === id: cord-284954-uuqchon4 author: Plebani, Mario title: SARS-CoV-2 antibody-based SURVEILLANCE: New light in the SHADOW date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-284954-uuqchon4.txt cache: ./cache/cord-284954-uuqchon4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284954-uuqchon4.txt' === file2bib.sh === id: cord-285111-qjclp51i author: Davanzo, Riccardo title: Breastfeeding and coronavirus disease‐2019: Ad interim indications of the Italian Society of Neonatology endorsed by the Union of European Neonatal & Perinatal Societies date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-285111-qjclp51i.txt cache: ./cache/cord-285111-qjclp51i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285111-qjclp51i.txt' === file2bib.sh === id: cord-284191-05djnz4p author: Bert, Nina Le title: Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-284191-05djnz4p.txt cache: ./cache/cord-284191-05djnz4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284191-05djnz4p.txt' === file2bib.sh === id: cord-285755-zblitbo0 author: Zhang, F. title: Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-285755-zblitbo0.txt cache: ./cache/cord-285755-zblitbo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285755-zblitbo0.txt' === file2bib.sh === id: cord-285711-2utcn0hw author: Elliott, Robert title: COVID-19 Related Mortality During Management of a Hepatic Abscess date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-285711-2utcn0hw.txt cache: ./cache/cord-285711-2utcn0hw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285711-2utcn0hw.txt' === file2bib.sh === id: cord-283850-kt8n6pg2 author: Steardo, Luca title: Psychiatric face of COVID-19 date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-283850-kt8n6pg2.txt cache: ./cache/cord-283850-kt8n6pg2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283850-kt8n6pg2.txt' === file2bib.sh === id: cord-285852-ocu69od2 author: Luqman, Zubair title: Disinfection of corona virus in histopathology laboratories date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-285852-ocu69od2.txt cache: ./cache/cord-285852-ocu69od2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285852-ocu69od2.txt' === file2bib.sh === id: cord-285426-iyl12ber author: Ghavami, Shaghayegh Baradaran title: IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-285426-iyl12ber.txt cache: ./cache/cord-285426-iyl12ber.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285426-iyl12ber.txt' === file2bib.sh === id: cord-285162-srkd3wh0 author: Jung, F. title: How we should respond to the Coronavirus SARS-CoV-2 outbreak: A German perspective date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-285162-srkd3wh0.txt cache: ./cache/cord-285162-srkd3wh0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285162-srkd3wh0.txt' === file2bib.sh === id: cord-284429-d7qxfo6d author: Trezza, Alfonso title: An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-284429-d7qxfo6d.txt cache: ./cache/cord-284429-d7qxfo6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284429-d7qxfo6d.txt' === file2bib.sh === id: cord-284478-c1uj3jra author: Schub, David title: High levels of SARS-CoV-2–specific T cells with restricted functionality in severe courses of COVID-19 date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-284478-c1uj3jra.txt cache: ./cache/cord-284478-c1uj3jra.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284478-c1uj3jra.txt' === file2bib.sh === id: cord-284950-qqje5s04 author: Venkataraman, Thiagarajan title: The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis date: 2017-07-31 pages: extension: .txt txt: ./txt/cord-284950-qqje5s04.txt cache: ./cache/cord-284950-qqje5s04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284950-qqje5s04.txt' === file2bib.sh === id: cord-285440-srtkqr13 author: Zhang, Jianguo title: Web-based electronic patient records for collaborative medical applications date: 2004-12-20 pages: extension: .txt txt: ./txt/cord-285440-srtkqr13.txt cache: ./cache/cord-285440-srtkqr13.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285440-srtkqr13.txt' === file2bib.sh === id: cord-286001-pu1fetq7 author: Zang, Ruochen title: TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-286001-pu1fetq7.txt cache: ./cache/cord-286001-pu1fetq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286001-pu1fetq7.txt' === file2bib.sh === id: cord-286038-a62k3lma author: Klimke, A. title: Hydroxychloroquine as an aerosol might markedly reduce and even prevent severe clinical symptoms after SARS-CoV-2 infection date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-286038-a62k3lma.txt cache: ./cache/cord-286038-a62k3lma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286038-a62k3lma.txt' === file2bib.sh === id: cord-285449-frft2h85 author: Guillon, Patrice title: Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies date: 2008-09-25 pages: extension: .txt txt: ./txt/cord-285449-frft2h85.txt cache: ./cache/cord-285449-frft2h85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285449-frft2h85.txt' === file2bib.sh === id: cord-285159-gytebbua author: Eydoux, Cecilia title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-285159-gytebbua.txt cache: ./cache/cord-285159-gytebbua.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285159-gytebbua.txt' === file2bib.sh === id: cord-285486-99trkti1 author: Abd-Elsalam, Sherief title: Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-285486-99trkti1.txt cache: ./cache/cord-285486-99trkti1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285486-99trkti1.txt' === file2bib.sh === id: cord-285896-lb8toc1m author: Beurton, Alexandra title: Limiting positive end-expiratory pressure to protect renal function in SARS-CoV-2 critically ill patients date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-285896-lb8toc1m.txt cache: ./cache/cord-285896-lb8toc1m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285896-lb8toc1m.txt' === file2bib.sh === id: cord-285203-ilxd0ih9 author: Paradiso, Angelo Virgilio title: Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-285203-ilxd0ih9.txt cache: ./cache/cord-285203-ilxd0ih9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285203-ilxd0ih9.txt' === file2bib.sh === id: cord-285758-c18arb6s author: Jiang, Shibo title: SARS Vaccine Development date: 2005-07-17 pages: extension: .txt txt: ./txt/cord-285758-c18arb6s.txt cache: ./cache/cord-285758-c18arb6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285758-c18arb6s.txt' === file2bib.sh === id: cord-285848-37dmv4ep author: Fu, Xiao-Wei title: Review of possible psychological impacts of COVID-19 on frontline medical staff and reduction strategies date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-285848-37dmv4ep.txt cache: ./cache/cord-285848-37dmv4ep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285848-37dmv4ep.txt' === file2bib.sh === id: cord-285739-0enn5bzn author: Gutiérrez Rodríguez, José title: Variables asociadas a mortalidad en una población de pacientes mayores de 80 años y con algún grado de dependencia funcional hospitalizados por COVID-19 en un Servicio de Geriatría date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-285739-0enn5bzn.txt cache: ./cache/cord-285739-0enn5bzn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285739-0enn5bzn.txt' === file2bib.sh === id: cord-285944-8lapwnuw author: Suwanwongse, Kulachanya title: Hyperpyrexia in COVID‐19 patients date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-285944-8lapwnuw.txt cache: ./cache/cord-285944-8lapwnuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285944-8lapwnuw.txt' === file2bib.sh === id: cord-285467-uxfk6k3c author: Ragni, Enrico title: Management of osteoarthritis during COVID‐19 pandemic date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-285467-uxfk6k3c.txt cache: ./cache/cord-285467-uxfk6k3c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285467-uxfk6k3c.txt' === file2bib.sh === id: cord-284573-w0sk622m author: Caduff, Carlo title: What Went Wrong: Corona and the World after the Full Stop date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-284573-w0sk622m.txt cache: ./cache/cord-284573-w0sk622m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284573-w0sk622m.txt' === file2bib.sh === id: cord-283485-xit6najq author: Van Damme, Wim title: The COVID-19 pandemic: diverse contexts; different epidemics—how and why? date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-283485-xit6najq.txt cache: ./cache/cord-283485-xit6najq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283485-xit6najq.txt' === file2bib.sh === id: cord-285603-f4572w5m author: Ortega, Joseph T. title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-285603-f4572w5m.txt cache: ./cache/cord-285603-f4572w5m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-285603-f4572w5m.txt' === file2bib.sh === id: cord-285490-tpsf05ca author: Solís, José Gabriel title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-285490-tpsf05ca.txt cache: ./cache/cord-285490-tpsf05ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285490-tpsf05ca.txt' === file2bib.sh === id: cord-284037-nj5jo1ev author: Kwee, Thomas C. title: Chest CT in COVID-19: What the Radiologist Needs to Know date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-284037-nj5jo1ev.txt cache: ./cache/cord-284037-nj5jo1ev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284037-nj5jo1ev.txt' === file2bib.sh === id: cord-285580-gq7400tq author: Pieretti, Joana C. title: Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-285580-gq7400tq.txt cache: ./cache/cord-285580-gq7400tq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285580-gq7400tq.txt' === file2bib.sh === id: cord-284038-93s3ffoy author: Keyhanian, Kiandokht title: SARS-CoV-2 and nervous system: From pathogenesis to clinical manifestation date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-284038-93s3ffoy.txt cache: ./cache/cord-284038-93s3ffoy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284038-93s3ffoy.txt' === file2bib.sh === id: cord-285965-mar8zt2t author: Su, Liang title: The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19 date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-285965-mar8zt2t.txt cache: ./cache/cord-285965-mar8zt2t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285965-mar8zt2t.txt' === file2bib.sh === id: cord-285469-b61y9ezi author: Hernández-Fernández, Francisco title: Cerebrovascular disease in patients with COVID-19: neuroimaging, histological and clinical description date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-285469-b61y9ezi.txt cache: ./cache/cord-285469-b61y9ezi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285469-b61y9ezi.txt' === file2bib.sh === id: cord-285806-363ivs67 author: Magro, Giuseppe title: SARS-CoV-2 and COVID-19: is interleukin-6 (IL-6) the 'culprit lesion' of ARDS onset? What is there besides Tocilizumab? SGP130Fc date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-285806-363ivs67.txt cache: ./cache/cord-285806-363ivs67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285806-363ivs67.txt' === file2bib.sh === id: cord-283824-c7y9zf7o author: Opitz, Sven title: Regulating epidemic space: the nomos of global circulation date: 2015-02-20 pages: extension: .txt txt: ./txt/cord-283824-c7y9zf7o.txt cache: ./cache/cord-283824-c7y9zf7o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283824-c7y9zf7o.txt' === file2bib.sh === id: cord-286390-ytgw3j4s author: Case, James Brett title: Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-286390-ytgw3j4s.txt cache: ./cache/cord-286390-ytgw3j4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286390-ytgw3j4s.txt' === file2bib.sh === id: cord-285960-1zuhilmu author: Conly, John title: Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-285960-1zuhilmu.txt cache: ./cache/cord-285960-1zuhilmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285960-1zuhilmu.txt' === file2bib.sh === id: cord-285636-cs26uuwx author: Singh, N. K. title: Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-285636-cs26uuwx.txt cache: ./cache/cord-285636-cs26uuwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285636-cs26uuwx.txt' === file2bib.sh === id: cord-286084-2275xvxb author: Dixit, Alok title: Ivermectin: Potential Role as Repurposed Drug for COVID-19 date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-286084-2275xvxb.txt cache: ./cache/cord-286084-2275xvxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286084-2275xvxb.txt' === file2bib.sh === id: cord-286919-fny060vk author: Lahfaoui, M title: Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-286919-fny060vk.txt cache: ./cache/cord-286919-fny060vk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286919-fny060vk.txt' === file2bib.sh === id: cord-286015-oonfpa0c author: Verbeure, Birgit title: Patent pools and diagnostic testing date: 2006-01-27 pages: extension: .txt txt: ./txt/cord-286015-oonfpa0c.txt cache: ./cache/cord-286015-oonfpa0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286015-oonfpa0c.txt' === file2bib.sh === id: cord-286365-fy0a8mb4 author: ElHawary, Hassan title: Bibliometric Analysis of Early COVID-19 Research: The Top 50 Cited Papers date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-286365-fy0a8mb4.txt cache: ./cache/cord-286365-fy0a8mb4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286365-fy0a8mb4.txt' === file2bib.sh === id: cord-286341-16tghl48 author: CONCHA-MEJIA, A. title: CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-286341-16tghl48.txt cache: ./cache/cord-286341-16tghl48.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286341-16tghl48.txt' === file2bib.sh === id: cord-285865-1gsy43a0 author: Wu, Guang title: Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species date: 2004-12-09 pages: extension: .txt txt: ./txt/cord-285865-1gsy43a0.txt cache: ./cache/cord-285865-1gsy43a0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285865-1gsy43a0.txt' === file2bib.sh === id: cord-285748-us5do6c2 author: Cheng, Yongqian title: SARS-CoV-2-Related Kidney Injury: Current Concern and Challenges date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-285748-us5do6c2.txt cache: ./cache/cord-285748-us5do6c2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285748-us5do6c2.txt' === file2bib.sh === id: cord-286029-rafcdzhm author: Bogaards, Johannes Antonie title: The potential of targeted antibody prophylaxis in SARS outbreak control: A mathematic analysis() date: 2006-05-05 pages: extension: .txt txt: ./txt/cord-286029-rafcdzhm.txt cache: ./cache/cord-286029-rafcdzhm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286029-rafcdzhm.txt' === file2bib.sh === id: cord-286429-voem879q author: Shao, Yi‐Ming title: Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors date: 2007-08-23 pages: extension: .txt txt: ./txt/cord-286429-voem879q.txt cache: ./cache/cord-286429-voem879q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286429-voem879q.txt' === file2bib.sh === id: cord-286014-cc99e24x author: Jang, T.-N title: Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases date: 2003-11-05 pages: extension: .txt txt: ./txt/cord-286014-cc99e24x.txt cache: ./cache/cord-286014-cc99e24x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286014-cc99e24x.txt' === file2bib.sh === id: cord-286269-vrjyj2y1 author: Sagheb, Setareh title: Two seriously ill neonates born to mothers with COVID-19 pneumonia- a case report date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-286269-vrjyj2y1.txt cache: ./cache/cord-286269-vrjyj2y1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286269-vrjyj2y1.txt' === file2bib.sh === id: cord-286130-4f7otdx1 author: Xavier, Joilson title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-286130-4f7otdx1.txt cache: ./cache/cord-286130-4f7otdx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286130-4f7otdx1.txt' === file2bib.sh === id: cord-285907-xoiju5ub author: Chang, Shang-Miao title: Comparative study of patients with and without SARS WHO fulfilled the WHO SARS case definition date: 2005-05-31 pages: extension: .txt txt: ./txt/cord-285907-xoiju5ub.txt cache: ./cache/cord-285907-xoiju5ub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285907-xoiju5ub.txt' === file2bib.sh === id: cord-286466-scokdxp2 author: Tani, Hideki title: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-286466-scokdxp2.txt cache: ./cache/cord-286466-scokdxp2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286466-scokdxp2.txt' === file2bib.sh === id: cord-286168-019rcbpg author: Vindegaard, Nina title: COVID-19 pandemic and mental health consequences: systematic review of the current evidence date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-286168-019rcbpg.txt cache: ./cache/cord-286168-019rcbpg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286168-019rcbpg.txt' === file2bib.sh === id: cord-287100-xkp8a9b9 author: López-Díaz, Álvaro title: COVID-19 Infection During Pregnancy and Risk of Neurodevelopmental Disorders in Offspring: Time for Collaborative Research date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-287100-xkp8a9b9.txt cache: ./cache/cord-287100-xkp8a9b9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287100-xkp8a9b9.txt' === file2bib.sh === id: cord-285647-9tegcrc3 author: Estrada, Ernesto title: Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-285647-9tegcrc3.txt cache: ./cache/cord-285647-9tegcrc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285647-9tegcrc3.txt' === file2bib.sh === id: cord-286895-i3g4ad4z author: Panciani, Pier Paolo title: SARS-CoV-2: “Three-steps” infection model and CSF diagnostic implication date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-286895-i3g4ad4z.txt cache: ./cache/cord-286895-i3g4ad4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286895-i3g4ad4z.txt' === file2bib.sh === id: cord-286290-85l99l13 author: Goddard, N.L. title: Lessons learned from SARS: The experience of the Health Protection Agency, England date: 2005-11-16 pages: extension: .txt txt: ./txt/cord-286290-85l99l13.txt cache: ./cache/cord-286290-85l99l13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286290-85l99l13.txt' === file2bib.sh === id: cord-286713-14i38xtt author: Guarner, Jeannette title: Three Emerging Coronaviruses in Two Decades: The Story of SARS, MERS, and Now COVID-19 date: 2020-02-13 pages: extension: .txt txt: ./txt/cord-286713-14i38xtt.txt cache: ./cache/cord-286713-14i38xtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286713-14i38xtt.txt' === file2bib.sh === id: cord-286555-rz88g3ze author: Petrovan, Vlad title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-286555-rz88g3ze.txt cache: ./cache/cord-286555-rz88g3ze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286555-rz88g3ze.txt' === file2bib.sh === id: cord-285979-ha5nszxi author: Rojas, Manuel title: Convalescent plasma in Covid-19: Possible mechanisms of action date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-285979-ha5nszxi.txt cache: ./cache/cord-285979-ha5nszxi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285979-ha5nszxi.txt' === file2bib.sh === id: cord-284376-plwyjhl8 author: Fu, Xinmiao title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-284376-plwyjhl8.txt cache: ./cache/cord-284376-plwyjhl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284376-plwyjhl8.txt' === file2bib.sh === id: cord-286631-3fmg3scx author: Pormohammad, Ali title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-286631-3fmg3scx.txt cache: ./cache/cord-286631-3fmg3scx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286631-3fmg3scx.txt' === file2bib.sh === id: cord-286573-k4khwvt7 author: Peng, Michael title: The Role of the Ocular Tissue in SARS-CoV-2 Transmission date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-286573-k4khwvt7.txt cache: ./cache/cord-286573-k4khwvt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286573-k4khwvt7.txt' === file2bib.sh === id: cord-285822-b5itedu3 author: Carlos Marín-Gabriel, José title: Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-285822-b5itedu3.txt cache: ./cache/cord-285822-b5itedu3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285822-b5itedu3.txt' === file2bib.sh === id: cord-286301-7sjw5ci7 author: Sadasivan, Jibin title: Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date: 2017-04-18 pages: extension: .txt txt: ./txt/cord-286301-7sjw5ci7.txt cache: ./cache/cord-286301-7sjw5ci7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286301-7sjw5ci7.txt' === file2bib.sh === id: cord-286703-ipoj13va author: de Wilde, Adriaan H. title: Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date: 2017-01-15 pages: extension: .txt txt: ./txt/cord-286703-ipoj13va.txt cache: ./cache/cord-286703-ipoj13va.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286703-ipoj13va.txt' === file2bib.sh === id: cord-286006-t5gj0k54 author: Nicholas, David B. title: Pediatric epidemic crisis: Lessons for policy and practice development date: 2008-12-31 pages: extension: .txt txt: ./txt/cord-286006-t5gj0k54.txt cache: ./cache/cord-286006-t5gj0k54.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286006-t5gj0k54.txt' === file2bib.sh === id: cord-286121-ltaxmp3u author: Xu, Ke title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date: 2009-06-05 pages: extension: .txt txt: ./txt/cord-286121-ltaxmp3u.txt cache: ./cache/cord-286121-ltaxmp3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286121-ltaxmp3u.txt' === file2bib.sh === id: cord-287256-hgqz1bcs author: Magurano, Fabio title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-287256-hgqz1bcs.txt cache: ./cache/cord-287256-hgqz1bcs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287256-hgqz1bcs.txt' === file2bib.sh === id: cord-287043-53oy5w34 author: Reyes‐Bueno, José Antonio title: Miller‐Fisher syndrome after SARS‐CoV‐2 infection date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-287043-53oy5w34.txt cache: ./cache/cord-287043-53oy5w34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287043-53oy5w34.txt' === file2bib.sh === id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-286343-s8n1ldol.txt cache: ./cache/cord-286343-s8n1ldol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286343-s8n1ldol.txt' === file2bib.sh === id: cord-287499-zcizdc7s author: Thompson, Hayley A title: SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-287499-zcizdc7s.txt cache: ./cache/cord-287499-zcizdc7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287499-zcizdc7s.txt' === file2bib.sh === id: cord-286217-3uklf2u2 author: Jiang, He-wei title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-286217-3uklf2u2.txt cache: ./cache/cord-286217-3uklf2u2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286217-3uklf2u2.txt' === file2bib.sh === id: cord-287289-zgehbwve author: Schmidt, M. title: FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-287289-zgehbwve.txt cache: ./cache/cord-287289-zgehbwve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287289-zgehbwve.txt' === file2bib.sh === id: cord-285700-9q6vwoct author: Grzelak, Ludivine title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-285700-9q6vwoct.txt cache: ./cache/cord-285700-9q6vwoct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285700-9q6vwoct.txt' === file2bib.sh === id: cord-286072-kgpvdb42 author: Sa Ribero, Margarida title: Interplay between SARS-CoV-2 and the type I interferon response date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-286072-kgpvdb42.txt cache: ./cache/cord-286072-kgpvdb42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286072-kgpvdb42.txt' === file2bib.sh === id: cord-287101-k3zq75zc author: Micheli, V. title: Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-287101-k3zq75zc.txt cache: ./cache/cord-287101-k3zq75zc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287101-k3zq75zc.txt' === file2bib.sh === id: cord-287349-1zcq7kzx author: Chen, James title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-287349-1zcq7kzx.txt cache: ./cache/cord-287349-1zcq7kzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-287349-1zcq7kzx.txt' === file2bib.sh === id: cord-287682-97fquq16 author: Daubin, Cédric title: Is a COPD patient protected against SARS-CoV-2 virus? date: 2020-10-03 pages: extension: .txt txt: ./txt/cord-287682-97fquq16.txt cache: ./cache/cord-287682-97fquq16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287682-97fquq16.txt' === file2bib.sh === id: cord-287338-pws42iay author: Gendelman, Omer title: Continuous hydroxychloroquine or colchicine therapy does not prevent infection with SARS-CoV-2: Insights from a large healthcare database analysis date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-287338-pws42iay.txt cache: ./cache/cord-287338-pws42iay.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287338-pws42iay.txt' === file2bib.sh === id: cord-286441-nl3kuqw3 author: Murray, D. D. title: Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-286441-nl3kuqw3.txt cache: ./cache/cord-286441-nl3kuqw3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286441-nl3kuqw3.txt' === file2bib.sh === id: cord-287220-mpnuhqwg author: Giuliani, C. title: Breastfeeding during the COVID-19 pandemic: suggestions on behalf of Woman Study Group of AMD date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-287220-mpnuhqwg.txt cache: ./cache/cord-287220-mpnuhqwg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287220-mpnuhqwg.txt' === file2bib.sh === id: cord-286638-bqxyb61p author: Singh, Awadhesh Kumar title: Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-286638-bqxyb61p.txt cache: ./cache/cord-286638-bqxyb61p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286638-bqxyb61p.txt' === file2bib.sh === id: cord-287447-5lzzobl3 author: Keyaerts, Els title: In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date: 2004-10-08 pages: extension: .txt txt: ./txt/cord-287447-5lzzobl3.txt cache: ./cache/cord-287447-5lzzobl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287447-5lzzobl3.txt' === file2bib.sh === id: cord-287210-sars5dmi author: Woo, Patrick C. Y. title: Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia date: 2005-12-01 pages: extension: .txt txt: ./txt/cord-287210-sars5dmi.txt cache: ./cache/cord-287210-sars5dmi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287210-sars5dmi.txt' === file2bib.sh === id: cord-286472-pqtem19t author: McFee, R.B. title: MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-286472-pqtem19t.txt cache: ./cache/cord-286472-pqtem19t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286472-pqtem19t.txt' === file2bib.sh === id: cord-288010-i9zrojoo author: Jia, Yuanyuan title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-288010-i9zrojoo.txt cache: ./cache/cord-288010-i9zrojoo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288010-i9zrojoo.txt' === file2bib.sh === id: cord-287448-hwsr1804 author: Bigaut, Kévin title: Guillain-Barré syndrome related to SARS-CoV-2 infection date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-287448-hwsr1804.txt cache: ./cache/cord-287448-hwsr1804.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287448-hwsr1804.txt' === file2bib.sh === id: cord-287497-93oiiqqi author: Tagliamento, Marco title: Italian survey on managing immune checkpoint inhibitors in oncology during COVID‐19 outbreak date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-287497-93oiiqqi.txt cache: ./cache/cord-287497-93oiiqqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287497-93oiiqqi.txt' === file2bib.sh === id: cord-286854-0s7oq0uv author: Jin, Xi title: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-286854-0s7oq0uv.txt cache: ./cache/cord-286854-0s7oq0uv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286854-0s7oq0uv.txt' === file2bib.sh === id: cord-288484-qy619tfg author: Bernard‐Valnet, R. title: Two patients with acute meningoencephalitis concomitant with SARS‐CoV‐2 infection date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-288484-qy619tfg.txt cache: ./cache/cord-288484-qy619tfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288484-qy619tfg.txt' === file2bib.sh === id: cord-286901-whvq8y1p author: Vidali, Sofia title: D-dimer as an indicator of prognosis in SARS-CoV-2 infection: a systematic review date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-286901-whvq8y1p.txt cache: ./cache/cord-286901-whvq8y1p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286901-whvq8y1p.txt' === file2bib.sh === id: cord-288070-qwax5tg9 author: Robilotti, E. V. title: Determinants of Severity in Cancer Patients with COVID-19 Illness date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-288070-qwax5tg9.txt cache: ./cache/cord-288070-qwax5tg9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288070-qwax5tg9.txt' === file2bib.sh === id: cord-287321-1ro10ujr author: Alpaydin, Aylin Ozgen title: Clinical and Radiological Diagnosis of Non‐SARS‐CoV‐2 Viruses in the Era of Covid‐19 Pandemic date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-287321-1ro10ujr.txt cache: ./cache/cord-287321-1ro10ujr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287321-1ro10ujr.txt' === file2bib.sh === id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-287228-0qm939ve.txt cache: ./cache/cord-287228-0qm939ve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287228-0qm939ve.txt' === file2bib.sh === id: cord-286923-o4fj8kx0 author: Berhan, Yifru title: What immunological and hormonal protective factors lower the risk of COVID-19 related deaths in pregnant women? date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-286923-o4fj8kx0.txt cache: ./cache/cord-286923-o4fj8kx0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286923-o4fj8kx0.txt' === file2bib.sh === id: cord-287372-ya5uvoki author: Böszörményi, Kinga P. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-287372-ya5uvoki.txt cache: ./cache/cord-287372-ya5uvoki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287372-ya5uvoki.txt' === file2bib.sh === id: cord-287205-k64svq6n author: Pollet, Jeroen title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-287205-k64svq6n.txt cache: ./cache/cord-287205-k64svq6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287205-k64svq6n.txt' === file2bib.sh === id: cord-286537-7ri2p5b8 author: Lee, Ting-Wai title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide date: 2005-11-11 pages: extension: .txt txt: ./txt/cord-286537-7ri2p5b8.txt cache: ./cache/cord-286537-7ri2p5b8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286537-7ri2p5b8.txt' === file2bib.sh === id: cord-286870-92eckkhk author: Gul, Seref title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-286870-92eckkhk.txt cache: ./cache/cord-286870-92eckkhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286870-92eckkhk.txt' === file2bib.sh === id: cord-287628-lzqsh3jf author: Gomersall, Charles D. title: Transmission of SARS to healthcare workers. The experience of a Hong Kong ICU date: 2006-02-25 pages: extension: .txt txt: ./txt/cord-287628-lzqsh3jf.txt cache: ./cache/cord-287628-lzqsh3jf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287628-lzqsh3jf.txt' === file2bib.sh === id: cord-288584-wql253d8 author: Rivera-Oyola, Ryan title: Dermatologic findings in two patients with COVID-19 date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-288584-wql253d8.txt cache: ./cache/cord-288584-wql253d8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288584-wql253d8.txt' === file2bib.sh === id: cord-287658-c2lljdi7 author: Lopez-Rincon, Alejandro title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-287658-c2lljdi7.txt cache: ./cache/cord-287658-c2lljdi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287658-c2lljdi7.txt' === file2bib.sh === id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-286298-pn9nwl64.txt cache: ./cache/cord-286298-pn9nwl64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286298-pn9nwl64.txt' === file2bib.sh === id: cord-287091-a3nieh5p author: Kumar, Anuj title: Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-287091-a3nieh5p.txt cache: ./cache/cord-287091-a3nieh5p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287091-a3nieh5p.txt' === file2bib.sh === id: cord-287847-rmhvc5n5 author: Miles, Brett A. title: Tracheostomy during SARS‐CoV‐2 pandemic: Recommendations from the New York Head and Neck Society date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-287847-rmhvc5n5.txt cache: ./cache/cord-287847-rmhvc5n5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287847-rmhvc5n5.txt' === file2bib.sh === id: cord-287604-w0ktwl8q author: Patel, Chirag N. title: Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-287604-w0ktwl8q.txt cache: ./cache/cord-287604-w0ktwl8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287604-w0ktwl8q.txt' === file2bib.sh === id: cord-287222-wojyisu0 author: Zhou, Min title: Coronavirus disease 2019 (COVID-19): a clinical update date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-287222-wojyisu0.txt cache: ./cache/cord-287222-wojyisu0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287222-wojyisu0.txt' === file2bib.sh === id: cord-287247-vv0zc0gd author: Gutman, Julie R. title: Malaria and Parasitic Neglected Tropical Diseases: Potential Syndemics with COVID-19? date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-287247-vv0zc0gd.txt cache: ./cache/cord-287247-vv0zc0gd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287247-vv0zc0gd.txt' === file2bib.sh === id: cord-287644-ay0vv27m author: Blackall, Douglas title: Rapid Establishment of a COVID‐19 Convalescent Plasma Program in a Regional Healthcare Delivery Network date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-287644-ay0vv27m.txt cache: ./cache/cord-287644-ay0vv27m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287644-ay0vv27m.txt' === file2bib.sh === id: cord-288051-wp8v2mc5 author: Sánchez-González, Álvaro title: What Should Be Known by a Urologist About the Medical Management of COVID-19’s Patients? date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-288051-wp8v2mc5.txt cache: ./cache/cord-288051-wp8v2mc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288051-wp8v2mc5.txt' === file2bib.sh === id: cord-288553-fez60jyn author: Colaneri, Marta title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-288553-fez60jyn.txt cache: ./cache/cord-288553-fez60jyn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288553-fez60jyn.txt' === file2bib.sh === id: cord-287172-h8zoplkm author: Ghobrial, Moheb title: The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-287172-h8zoplkm.txt cache: ./cache/cord-287172-h8zoplkm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287172-h8zoplkm.txt' === file2bib.sh === id: cord-287054-zmxpuynv author: Li, Ning title: Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-287054-zmxpuynv.txt cache: ./cache/cord-287054-zmxpuynv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287054-zmxpuynv.txt' === file2bib.sh === id: cord-288146-xqxznv1r author: Kohyama, Shunsuke title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date: 2009-09-11 pages: extension: .txt txt: ./txt/cord-288146-xqxznv1r.txt cache: ./cache/cord-288146-xqxznv1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288146-xqxznv1r.txt' === file2bib.sh === id: cord-287488-h102xn29 author: Araujo, Danielle Bastos title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-287488-h102xn29.txt cache: ./cache/cord-287488-h102xn29.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287488-h102xn29.txt' === file2bib.sh === id: cord-287653-69nfi379 author: Lacy, J. Matthew title: COVID-19: POSTMORTEM DIAGNOSTIC AND BIOSAFETY CONSIDERATIONS date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-287653-69nfi379.txt cache: ./cache/cord-287653-69nfi379.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287653-69nfi379.txt' === file2bib.sh === id: cord-287459-k9x3z2h1 author: Abu-Farha, Mohamed title: The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-287459-k9x3z2h1.txt cache: ./cache/cord-287459-k9x3z2h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287459-k9x3z2h1.txt' === file2bib.sh === id: cord-288660-z0k2ui3y author: Edler, Alice A. title: Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology date: 2006-02-28 pages: extension: .txt txt: ./txt/cord-288660-z0k2ui3y.txt cache: ./cache/cord-288660-z0k2ui3y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288660-z0k2ui3y.txt' === file2bib.sh === id: cord-287410-boxxlopy author: Devi, Arpita title: In silico designing of multi-epitope vaccine construct against human coronavirus infections date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-287410-boxxlopy.txt cache: ./cache/cord-287410-boxxlopy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-287410-boxxlopy.txt' === file2bib.sh === id: cord-288398-vnra553x author: Yogeswaran, Athiththan title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-288398-vnra553x.txt cache: ./cache/cord-288398-vnra553x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288398-vnra553x.txt' === file2bib.sh === id: cord-288357-3mqoexcr author: Liu, Pei title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-288357-3mqoexcr.txt cache: ./cache/cord-288357-3mqoexcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288357-3mqoexcr.txt' === file2bib.sh === id: cord-287477-aios0h8s author: Sicari, Daria title: Role of the early secretory pathway in SARS-CoV-2 infection date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-287477-aios0h8s.txt cache: ./cache/cord-287477-aios0h8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287477-aios0h8s.txt' === file2bib.sh === id: cord-288066-sh6n2c3n author: Mohamed, Mohamed S. title: Sex differences in COVID-19: the role of androgens in disease severity and progression date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-288066-sh6n2c3n.txt cache: ./cache/cord-288066-sh6n2c3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288066-sh6n2c3n.txt' === file2bib.sh === id: cord-287156-3plpi6i9 author: Lassandro, Giuseppe title: Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-287156-3plpi6i9.txt cache: ./cache/cord-287156-3plpi6i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287156-3plpi6i9.txt' === file2bib.sh === id: cord-288651-bgo8istm author: SHI, Yi title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date: 2005-03-17 pages: extension: .txt txt: ./txt/cord-288651-bgo8istm.txt cache: ./cache/cord-288651-bgo8istm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288651-bgo8istm.txt' === file2bib.sh === id: cord-288692-v471648u author: Yip, Shea Ping title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 pages: extension: .txt txt: ./txt/cord-288692-v471648u.txt cache: ./cache/cord-288692-v471648u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288692-v471648u.txt' === file2bib.sh === id: cord-288231-vg8bwed9 author: Haagmans, Bart L. title: The Application of Genomics to Emerging Zoonotic Viral Diseases date: 2009-10-26 pages: extension: .txt txt: ./txt/cord-288231-vg8bwed9.txt cache: ./cache/cord-288231-vg8bwed9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288231-vg8bwed9.txt' === file2bib.sh === id: cord-289079-m417oxpc author: Waggershauser, Constanze H. title: Letter: immunotherapy in IBD patients in a SARS‐CoV‐2 endemic area date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-289079-m417oxpc.txt cache: ./cache/cord-289079-m417oxpc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289079-m417oxpc.txt' === file2bib.sh === id: cord-289255-qwzg7prx author: Seligman, Stephen J. title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date: 2007-02-15 pages: extension: .txt txt: ./txt/cord-289255-qwzg7prx.txt cache: ./cache/cord-289255-qwzg7prx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289255-qwzg7prx.txt' === file2bib.sh === id: cord-288271-p074ffpt author: Mathies, D. title: A Case of SARS‐CoV‐2‐pneumonia with successful antiviral therapy in a 77‐year‐old male with heart transplant date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-288271-p074ffpt.txt cache: ./cache/cord-288271-p074ffpt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288271-p074ffpt.txt' === file2bib.sh === id: cord-288025-skkpkqw6 author: Eslami, Hadi title: The role of environmental factors to transmission of SARS-CoV-2 (COVID-19) date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-288025-skkpkqw6.txt cache: ./cache/cord-288025-skkpkqw6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288025-skkpkqw6.txt' === file2bib.sh === id: cord-288017-f9b3t0ts author: Kabeerdoss, Jayakanthan title: Understanding immunopathological fallout of human coronavirus infections including COVID‐19: Will they cross the path of rheumatologists? date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-288017-f9b3t0ts.txt cache: ./cache/cord-288017-f9b3t0ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288017-f9b3t0ts.txt' === file2bib.sh === id: cord-288153-2qsh2dlk author: Hays, Priya title: Clinical sequelae of the novel coronavirus: does COVID-19 infection predispose patients to cancer? date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-288153-2qsh2dlk.txt cache: ./cache/cord-288153-2qsh2dlk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288153-2qsh2dlk.txt' === file2bib.sh === id: cord-288197-drto66xt author: Chen, Huijun title: Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records date: 2020-02-12 pages: extension: .txt txt: ./txt/cord-288197-drto66xt.txt cache: ./cache/cord-288197-drto66xt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288197-drto66xt.txt' === file2bib.sh === id: cord-286655-5vorrnq3 author: Vivek-Ananth, R.P. title: In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-286655-5vorrnq3.txt cache: ./cache/cord-286655-5vorrnq3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286655-5vorrnq3.txt' === file2bib.sh === id: cord-288255-p8uzrsbd author: Goossens, Gijs H. title: Obesity and COVID-19: A Perspective from the European Association for the Study of Obesity on Immunological Perturbations, Therapeutic Challenges, and Opportunities in Obesity date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-288255-p8uzrsbd.txt cache: ./cache/cord-288255-p8uzrsbd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288255-p8uzrsbd.txt' === file2bib.sh === id: cord-287991-10jz1dz2 author: Goshen-Lago, Tal title: The Potential Role of Immune Alteration in the Cancer–COVID19 Equation—A Prospective Longitudinal Study date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-287991-10jz1dz2.txt cache: ./cache/cord-287991-10jz1dz2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287991-10jz1dz2.txt' === file2bib.sh === id: cord-288558-rthnj6wd author: Cheng, V. C. C. title: Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date: 2004-02-15 pages: extension: .txt txt: ./txt/cord-288558-rthnj6wd.txt cache: ./cache/cord-288558-rthnj6wd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288558-rthnj6wd.txt' === file2bib.sh === id: cord-288758-onis9xmo author: Peng, Z. title: Exhaled CO2 as COVID-19 infection risk proxy for different indoor environments and activities date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-288758-onis9xmo.txt cache: ./cache/cord-288758-onis9xmo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288758-onis9xmo.txt' === file2bib.sh === id: cord-288284-fghu8ouc author: Hawryluck, Laura title: Clinical review: SARS – lessons in disaster management date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-288284-fghu8ouc.txt cache: ./cache/cord-288284-fghu8ouc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288284-fghu8ouc.txt' === file2bib.sh === id: cord-288500-ko4eda9w author: Zheng, Ruijun title: Prevalence and associated factors of depression and anxiety among nurses during the outbreak of COVID-19 in China: A cross-sectional study date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-288500-ko4eda9w.txt cache: ./cache/cord-288500-ko4eda9w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288500-ko4eda9w.txt' === file2bib.sh === id: cord-288632-2aliqy8p author: Phillips, Nicole title: The Perfect Storm: COVID-19 Health Disparities in US Blacks date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-288632-2aliqy8p.txt cache: ./cache/cord-288632-2aliqy8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288632-2aliqy8p.txt' === file2bib.sh === id: cord-288920-xkfcc2dx author: Broxmeyer, L title: SARS: Just another viral acronym? date: 2003-08-31 pages: extension: .txt txt: ./txt/cord-288920-xkfcc2dx.txt cache: ./cache/cord-288920-xkfcc2dx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288920-xkfcc2dx.txt' === file2bib.sh === id: cord-287501-7it4kh0e author: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 pages: extension: .txt txt: ./txt/cord-287501-7it4kh0e.txt cache: ./cache/cord-287501-7it4kh0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287501-7it4kh0e.txt' === file2bib.sh === id: cord-289134-ne3tjt5g author: Xing, Yue title: Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-289134-ne3tjt5g.txt cache: ./cache/cord-289134-ne3tjt5g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289134-ne3tjt5g.txt' === file2bib.sh === id: cord-288756-r96izsyq author: Wu, Zhiqiang title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-288756-r96izsyq.txt cache: ./cache/cord-288756-r96izsyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288756-r96izsyq.txt' === file2bib.sh === id: cord-288639-wy07nao0 author: Earnest, Arul title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore date: 2005-05-11 pages: extension: .txt txt: ./txt/cord-288639-wy07nao0.txt cache: ./cache/cord-288639-wy07nao0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288639-wy07nao0.txt' === file2bib.sh === id: cord-288998-0by0bkgs author: Colarusso, Chiara title: A lesson from a saboteur: high molecular weight kininogen (HMWK) impact in COVID‐19 date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-288998-0by0bkgs.txt cache: ./cache/cord-288998-0by0bkgs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288998-0by0bkgs.txt' === file2bib.sh === id: cord-288670-1vlowf2n author: Yang, Naidi title: Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19 date: 2020-03-15 pages: extension: .txt txt: ./txt/cord-288670-1vlowf2n.txt cache: ./cache/cord-288670-1vlowf2n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288670-1vlowf2n.txt' === file2bib.sh === id: cord-288731-x2cwyvb7 author: Puenpa, Jiratchaya title: Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-288731-x2cwyvb7.txt cache: ./cache/cord-288731-x2cwyvb7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288731-x2cwyvb7.txt' === file2bib.sh === id: cord-289349-imkgpwn0 author: Qiu, Li title: Strong immunity in the early two years of age links to frequent immunization of routine vaccines date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-289349-imkgpwn0.txt cache: ./cache/cord-289349-imkgpwn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289349-imkgpwn0.txt' === file2bib.sh === id: cord-287742-y1j9x5ne author: Lee, Kai Wei title: Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-287742-y1j9x5ne.txt cache: ./cache/cord-287742-y1j9x5ne.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287742-y1j9x5ne.txt' === file2bib.sh === id: cord-289332-hvakv08t author: Chen, Guoqian title: Pathogenic role of HMGB1 in SARS? date: 2004-04-30 pages: extension: .txt txt: ./txt/cord-289332-hvakv08t.txt cache: ./cache/cord-289332-hvakv08t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289332-hvakv08t.txt' === file2bib.sh === id: cord-289490-u0f0zyad author: Lumba, Rishi title: Neonate Born to a Mother with a Diagnosis of Suspected Intra-Amniotic Infection versus COVID-19 or Both date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-289490-u0f0zyad.txt cache: ./cache/cord-289490-u0f0zyad.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289490-u0f0zyad.txt' === file2bib.sh === id: cord-288733-c51lfwd6 author: Kavanagh, Oisín title: Inhaled Hydroxychloroquine to Improve Efficacy and Reduce Harm in the Treatment of COVID-19 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-288733-c51lfwd6.txt cache: ./cache/cord-288733-c51lfwd6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288733-c51lfwd6.txt' === file2bib.sh === id: cord-287304-h6wj7m8u author: Keil, Roger title: Governing the Sick City: Urban Governance in the Age of Emerging Infectious Disease date: 2007-12-07 pages: extension: .txt txt: ./txt/cord-287304-h6wj7m8u.txt cache: ./cache/cord-287304-h6wj7m8u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287304-h6wj7m8u.txt' === file2bib.sh === id: cord-289282-4oz6r7op author: Hon, Kam Lun title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-289282-4oz6r7op.txt cache: ./cache/cord-289282-4oz6r7op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289282-4oz6r7op.txt' === file2bib.sh === id: cord-288403-m6qe57he author: Abbas, K. M. title: Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-288403-m6qe57he.txt cache: ./cache/cord-288403-m6qe57he.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288403-m6qe57he.txt' === file2bib.sh === id: cord-289038-15yp9uqy author: Chow, Jonathan Tak-Sum title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-289038-15yp9uqy.txt cache: ./cache/cord-289038-15yp9uqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289038-15yp9uqy.txt' === file2bib.sh === id: cord-289364-p31gt533 author: AlFehaidi, Alanoud title: A case of SARS-CoV-2 re-infection date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-289364-p31gt533.txt cache: ./cache/cord-289364-p31gt533.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-289364-p31gt533.txt' === file2bib.sh === id: cord-286683-mettlmhz author: Ortiz-Prado, Esteban title: Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-286683-mettlmhz.txt cache: ./cache/cord-286683-mettlmhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286683-mettlmhz.txt' === file2bib.sh === id: cord-290378-h4cof32m author: Guy, Tiphaine title: High-flow nasal oxygen: a safe, efficient treatment for COVID-19 patients not in an ICU date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-290378-h4cof32m.txt cache: ./cache/cord-290378-h4cof32m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290378-h4cof32m.txt' === file2bib.sh === id: cord-288644-ywaefpe8 author: Rodon, Jordi title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-288644-ywaefpe8.txt cache: ./cache/cord-288644-ywaefpe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288644-ywaefpe8.txt' === file2bib.sh === id: cord-289216-g4kqi560 author: Malecki, M. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-289216-g4kqi560.txt cache: ./cache/cord-289216-g4kqi560.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289216-g4kqi560.txt' === file2bib.sh === id: cord-289599-7vsynfgn author: Kostoff, Ronald N. title: COVID-19 vaccine safety date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-289599-7vsynfgn.txt cache: ./cache/cord-289599-7vsynfgn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-289599-7vsynfgn.txt' === file2bib.sh === id: cord-290056-x74cq2k5 author: Delgado-Roche, Livan title: Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-290056-x74cq2k5.txt cache: ./cache/cord-290056-x74cq2k5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290056-x74cq2k5.txt' === file2bib.sh === id: cord-288824-sygnmiun author: Lam, SD title: SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-288824-sygnmiun.txt cache: ./cache/cord-288824-sygnmiun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288824-sygnmiun.txt' === file2bib.sh === id: cord-287819-qzg4bhoy author: Priftis, Konstantinos title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-287819-qzg4bhoy.txt cache: ./cache/cord-287819-qzg4bhoy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287819-qzg4bhoy.txt' === file2bib.sh === id: cord-289522-7u3d6nfc author: Ebrahimi, Mina title: COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-289522-7u3d6nfc.txt cache: ./cache/cord-289522-7u3d6nfc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289522-7u3d6nfc.txt' === file2bib.sh === id: cord-289101-ko1knslk author: Fu, Weihui title: An open-label, randomized trial of the combination of IFN-κ plus TFF2 with standard care in the treatment of patients with moderate COVID-19 date: 2020-09-20 pages: extension: .txt txt: ./txt/cord-289101-ko1knslk.txt cache: ./cache/cord-289101-ko1knslk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289101-ko1knslk.txt' === file2bib.sh === id: cord-289144-d6fgs8qg author: Sieńko, Jerzy title: COVID-19: The Influence of ACE Genotype and ACE-I and ARBs on the Course of SARS-CoV-2 Infection in Elderly Patients date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-289144-d6fgs8qg.txt cache: ./cache/cord-289144-d6fgs8qg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289144-d6fgs8qg.txt' === file2bib.sh === id: cord-289740-nsiycudn author: Smithgall, Marie C. title: Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2 date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-289740-nsiycudn.txt cache: ./cache/cord-289740-nsiycudn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289740-nsiycudn.txt' === file2bib.sh === id: cord-289813-kq3ayyip author: Arnaez, Juan title: The Impact of the Current SARS-CoV-2 Pandemic on Neonatal Care date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-289813-kq3ayyip.txt cache: ./cache/cord-289813-kq3ayyip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289813-kq3ayyip.txt' === file2bib.sh === id: cord-290170-s6wjitfo author: Kuhrt, Katy title: Placental abruption in a twin pregnancy at 32 weeks’ gestation complicated by COVID-19, without vertical transmission to the babies. date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-290170-s6wjitfo.txt cache: ./cache/cord-290170-s6wjitfo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290170-s6wjitfo.txt' === file2bib.sh === id: cord-289076-8iymevqm author: Marjanovic, Zdravko title: The relevance of psychosocial variables and working conditions in predicting nurses’ coping strategies during the SARS crisis: An online questionnaire survey date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-289076-8iymevqm.txt cache: ./cache/cord-289076-8iymevqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289076-8iymevqm.txt' === file2bib.sh === id: cord-289574-engwi8h3 author: An, Peng-jiao title: Biochemical indicators of coronavirus disease 2019 exacerbation and the clinical implications date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-289574-engwi8h3.txt cache: ./cache/cord-289574-engwi8h3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289574-engwi8h3.txt' === file2bib.sh === id: cord-288862-upcsvjuo author: Wang, Junmei title: Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-288862-upcsvjuo.txt cache: ./cache/cord-288862-upcsvjuo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288862-upcsvjuo.txt' === file2bib.sh === id: cord-289064-435bp4rt author: Muniangi-Muhitu, Hermine title: Covid-19 and Diabetes: A Complex Bidirectional Relationship date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-289064-435bp4rt.txt cache: ./cache/cord-289064-435bp4rt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289064-435bp4rt.txt' === file2bib.sh === id: cord-290758-kz0qfy3r author: Hui, David S. title: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China date: 2020-02-29 pages: extension: .txt txt: ./txt/cord-290758-kz0qfy3r.txt cache: ./cache/cord-290758-kz0qfy3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290758-kz0qfy3r.txt' === file2bib.sh === id: cord-290429-0d34abdo author: Elengoe, Asita title: COVID-19 Outbreak in Malaysia date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-290429-0d34abdo.txt cache: ./cache/cord-290429-0d34abdo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290429-0d34abdo.txt' === file2bib.sh === id: cord-290068-s1gdbsfx author: Hon, KLE title: Clinical presentations and outcome of severe acute respiratory syndrome in children date: 2003-05-17 pages: extension: .txt txt: ./txt/cord-290068-s1gdbsfx.txt cache: ./cache/cord-290068-s1gdbsfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290068-s1gdbsfx.txt' === file2bib.sh === id: cord-289890-sf2uxubd author: Rushworth, S. A. title: Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-289890-sf2uxubd.txt cache: ./cache/cord-289890-sf2uxubd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289890-sf2uxubd.txt' === file2bib.sh === id: cord-289947-z2dw2eaz author: Wong, River Chun-Wai title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-289947-z2dw2eaz.txt cache: ./cache/cord-289947-z2dw2eaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289947-z2dw2eaz.txt' === file2bib.sh === id: cord-289598-t8upoq9a author: Yoon, Jane C title: COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-289598-t8upoq9a.txt cache: ./cache/cord-289598-t8upoq9a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289598-t8upoq9a.txt' === file2bib.sh === id: cord-289476-8wh3hn0n author: Leiker, Brenna title: COVID - 19 BRIEF INTRODUCTION IN MENTAL HEALTH CONSIDERATIONS FOR HEALTH CARE WORKERS AND PATIENTS date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-289476-8wh3hn0n.txt cache: ./cache/cord-289476-8wh3hn0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289476-8wh3hn0n.txt' === file2bib.sh === id: cord-288818-6uvb4qsk author: Tanveer, Faouzia title: Ethics, pandemic and environment; looking at the future of low middle income countries date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-288818-6uvb4qsk.txt cache: ./cache/cord-288818-6uvb4qsk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288818-6uvb4qsk.txt' === file2bib.sh === id: cord-290123-scd9u8ix author: Mustafa, Mujahed I. title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-290123-scd9u8ix.txt cache: ./cache/cord-290123-scd9u8ix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290123-scd9u8ix.txt' === file2bib.sh === id: cord-290066-umthoftd author: Jia, Xingwang title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-290066-umthoftd.txt cache: ./cache/cord-290066-umthoftd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290066-umthoftd.txt' === file2bib.sh === id: cord-289716-nleql08z author: Tsitsilonis, Ourania E. title: Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-289716-nleql08z.txt cache: ./cache/cord-289716-nleql08z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289716-nleql08z.txt' === file2bib.sh === id: cord-289003-vov6o1jx author: Burdet, C. title: Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-289003-vov6o1jx.txt cache: ./cache/cord-289003-vov6o1jx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289003-vov6o1jx.txt' === file2bib.sh === id: cord-289520-i6pv90s9 author: Harris, Carlyn title: An evidence-based framework for priority clinical research questions for COVID-19 date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-289520-i6pv90s9.txt cache: ./cache/cord-289520-i6pv90s9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289520-i6pv90s9.txt' === file2bib.sh === id: cord-290414-8i8g0xdc author: Chuan, Ong Sze title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-290414-8i8g0xdc.txt cache: ./cache/cord-290414-8i8g0xdc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290414-8i8g0xdc.txt' === file2bib.sh === id: cord-290001-603qy8ml author: Pimentel, Lígia L. title: Cholesterol, inflammation, and phospholipids: COVID-19 share traits with cardiovascular disease date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-290001-603qy8ml.txt cache: ./cache/cord-290001-603qy8ml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290001-603qy8ml.txt' === file2bib.sh === id: cord-289719-64ugdvfe author: Tenforde, Mark W. title: Characteristics of Adult Outpatients and Inpatients with COVID-19 — 11 Academic Medical Centers, United States, March–May 2020 date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-289719-64ugdvfe.txt cache: ./cache/cord-289719-64ugdvfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-289719-64ugdvfe.txt' === file2bib.sh === id: cord-289377-2vqqabum author: Yubero, P. title: Evidence for immunity to SARS-CoV-2 from epidemiological data series date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-289377-2vqqabum.txt cache: ./cache/cord-289377-2vqqabum.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289377-2vqqabum.txt' === file2bib.sh === id: cord-289588-n61gz7pi author: Samudrala, Pavan Kumar title: Virology, pathogenesis, diagnosis and in-line treatment of COVID-19 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-289588-n61gz7pi.txt cache: ./cache/cord-289588-n61gz7pi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289588-n61gz7pi.txt' === file2bib.sh === id: cord-290796-x9xqqcj6 author: Stefanelli, P. title: Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-290796-x9xqqcj6.txt cache: ./cache/cord-290796-x9xqqcj6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290796-x9xqqcj6.txt' === file2bib.sh === id: cord-290776-l6ajq6vp author: Frithiof, Robert title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-290776-l6ajq6vp.txt cache: ./cache/cord-290776-l6ajq6vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290776-l6ajq6vp.txt' === file2bib.sh === id: cord-290218-dvyeg5fk author: Jiang, Yi title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-290218-dvyeg5fk.txt cache: ./cache/cord-290218-dvyeg5fk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290218-dvyeg5fk.txt' === file2bib.sh === id: cord-289711-4ab3d00h author: Yarmarkovich, Mark title: Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-289711-4ab3d00h.txt cache: ./cache/cord-289711-4ab3d00h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289711-4ab3d00h.txt' === file2bib.sh === id: cord-290445-vb53bih9 author: Ahmed, Shiek SSJ title: Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-290445-vb53bih9.txt cache: ./cache/cord-290445-vb53bih9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290445-vb53bih9.txt' === file2bib.sh === id: cord-290333-996tmrgo author: Chiu, Cheng-Hsun title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-290333-996tmrgo.txt cache: ./cache/cord-290333-996tmrgo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290333-996tmrgo.txt' === file2bib.sh === id: cord-290851-1e5e033r author: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 pages: extension: .txt txt: ./txt/cord-290851-1e5e033r.txt cache: ./cache/cord-290851-1e5e033r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290851-1e5e033r.txt' === file2bib.sh === id: cord-290148-6cxndab8 author: Rossi, Gian Paolo title: Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-290148-6cxndab8.txt cache: ./cache/cord-290148-6cxndab8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290148-6cxndab8.txt' === file2bib.sh === id: cord-290690-53t7df81 author: Roberts, David J. title: Life in Times of COVID‐19 date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-290690-53t7df81.txt cache: ./cache/cord-290690-53t7df81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290690-53t7df81.txt' === file2bib.sh === id: cord-290209-gkx57lyq author: Losurdo, Pasquale title: Impact of lockdown for SARS-CoV-2 (COVID-19) on surgical site infection rates: a monocentric observational cohort study date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-290209-gkx57lyq.txt cache: ./cache/cord-290209-gkx57lyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290209-gkx57lyq.txt' === file2bib.sh === id: cord-289407-8fje16z1 author: Moore, G. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-289407-8fje16z1.txt cache: ./cache/cord-289407-8fje16z1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289407-8fje16z1.txt' === file2bib.sh === id: cord-290277-ndfoppoq author: Bahl, Prateek title: Airborne or droplet precautions for health workers treating COVID-19? date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-290277-ndfoppoq.txt cache: ./cache/cord-290277-ndfoppoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290277-ndfoppoq.txt' === file2bib.sh === id: cord-289114-ifnk41oq author: Singh, Angaraj title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-289114-ifnk41oq.txt cache: ./cache/cord-289114-ifnk41oq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289114-ifnk41oq.txt' === file2bib.sh === id: cord-289905-dvl2pud2 author: Gan, Rosemary title: COVID-19 as a Viral Functional ACE2 Deficiency Disorder with ACE2 Related Multi-organ Disease date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-289905-dvl2pud2.txt cache: ./cache/cord-289905-dvl2pud2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289905-dvl2pud2.txt' === file2bib.sh === id: cord-290671-6p23qxb8 author: Jiang, Shibo title: An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies date: 2020-01-31 pages: extension: .txt txt: ./txt/cord-290671-6p23qxb8.txt cache: ./cache/cord-290671-6p23qxb8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290671-6p23qxb8.txt' === file2bib.sh === id: cord-290802-761wqgbe author: Zhao, Zheng title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-290802-761wqgbe.txt cache: ./cache/cord-290802-761wqgbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290802-761wqgbe.txt' === file2bib.sh === id: cord-290257-2u228xe9 author: Hsu, Chih-Cheng title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan date: 2006-05-05 pages: extension: .txt txt: ./txt/cord-290257-2u228xe9.txt cache: ./cache/cord-290257-2u228xe9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290257-2u228xe9.txt' === file2bib.sh === id: cord-290845-bf1q4k6t author: Bouchghoul, Hanane title: Do pregnant women have protective immunity against COVID‐19? date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-290845-bf1q4k6t.txt cache: ./cache/cord-290845-bf1q4k6t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290845-bf1q4k6t.txt' === file2bib.sh === id: cord-290254-m9l8ntur author: Rodriguez-Manzano, J. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-290254-m9l8ntur.txt cache: ./cache/cord-290254-m9l8ntur.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290254-m9l8ntur.txt' === file2bib.sh === id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-289612-4x5t4c5u.txt cache: ./cache/cord-289612-4x5t4c5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289612-4x5t4c5u.txt' === file2bib.sh === id: cord-290598-wquwtovs author: li, s. title: Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-290598-wquwtovs.txt cache: ./cache/cord-290598-wquwtovs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290598-wquwtovs.txt' === file2bib.sh === id: cord-290813-6ylwj5je author: Ng, Enders K. O. title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 pages: extension: .txt txt: ./txt/cord-290813-6ylwj5je.txt cache: ./cache/cord-290813-6ylwj5je.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290813-6ylwj5je.txt' === file2bib.sh === id: cord-290792-ggcz1zfw author: Qutob, N. title: Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-290792-ggcz1zfw.txt cache: ./cache/cord-290792-ggcz1zfw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290792-ggcz1zfw.txt' === file2bib.sh === id: cord-289892-yh1lioyz author: Bai, Bingke title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 pages: extension: .txt txt: ./txt/cord-289892-yh1lioyz.txt cache: ./cache/cord-289892-yh1lioyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289892-yh1lioyz.txt' === file2bib.sh === id: cord-289852-4uxb70rh author: Kassem, Dina H. title: Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-289852-4uxb70rh.txt cache: ./cache/cord-289852-4uxb70rh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289852-4uxb70rh.txt' === file2bib.sh === id: cord-290895-tb0xald0 author: Indu, Purushothaman title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-290895-tb0xald0.txt cache: ./cache/cord-290895-tb0xald0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290895-tb0xald0.txt' === file2bib.sh === id: cord-290443-naulq6q7 author: Battistoni, Allegra title: Might renin–angiotensin system blockers play a role in the COVID-19 pandemic? date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-290443-naulq6q7.txt cache: ./cache/cord-290443-naulq6q7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290443-naulq6q7.txt' === file2bib.sh === id: cord-290950-v28kilvn author: Peyrony, Olivier title: Surfaces and equipment contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Emergency Department at a university hospital date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-290950-v28kilvn.txt cache: ./cache/cord-290950-v28kilvn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290950-v28kilvn.txt' === file2bib.sh === id: cord-290290-wyx9ib7s author: Sinegubova, Maria V. title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-290290-wyx9ib7s.txt cache: ./cache/cord-290290-wyx9ib7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290290-wyx9ib7s.txt' === file2bib.sh === id: cord-290863-f0wpsaip author: Tenforde, Mark W. title: Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-290863-f0wpsaip.txt cache: ./cache/cord-290863-f0wpsaip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290863-f0wpsaip.txt' === file2bib.sh === id: cord-291052-nstfe15a author: Cag, Yasemin title: A novel approach to managing COVID-19 patients; results of lopinavir plus doxycycline cohort date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-291052-nstfe15a.txt cache: ./cache/cord-291052-nstfe15a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291052-nstfe15a.txt' === file2bib.sh === id: cord-291194-cl3nu5cm author: DURDAĞI, Serdar title: Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-291194-cl3nu5cm.txt cache: ./cache/cord-291194-cl3nu5cm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291194-cl3nu5cm.txt' === file2bib.sh === id: cord-290195-8uaai9nv author: Stebbing, Justin title: Mechanism of baricitinib supports artificial intelligence‐predicted testing in COVID‐19 patients date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-290195-8uaai9nv.txt cache: ./cache/cord-290195-8uaai9nv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290195-8uaai9nv.txt' === file2bib.sh === id: cord-291047-mpahl77t author: Alm, Erik title: Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-291047-mpahl77t.txt cache: ./cache/cord-291047-mpahl77t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291047-mpahl77t.txt' === file2bib.sh === id: cord-290993-bsnja161 author: McAuliffe, Josephine title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 pages: extension: .txt txt: ./txt/cord-290993-bsnja161.txt cache: ./cache/cord-290993-bsnja161.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290993-bsnja161.txt' === file2bib.sh === id: cord-291012-y0ufzx93 author: Ye, Qing title: SARS-CoV-2 infection causes transient olfactory dysfunction in mice date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-291012-y0ufzx93.txt cache: ./cache/cord-291012-y0ufzx93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291012-y0ufzx93.txt' === file2bib.sh === id: cord-290687-kc7t1y5o author: Ray, Soumi title: Susceptibility and Sustainability of India against CoVid19: a multivariate approach date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-290687-kc7t1y5o.txt cache: ./cache/cord-290687-kc7t1y5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290687-kc7t1y5o.txt' === file2bib.sh === id: cord-290428-zrlqzbss author: de Faria Coelho-Ravagnani, Christianne title: Dietary recommendations during the COVID-19 pandemic date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-290428-zrlqzbss.txt cache: ./cache/cord-290428-zrlqzbss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290428-zrlqzbss.txt' === file2bib.sh === id: cord-291024-9g4om4sf author: Isakbaeva, Elmira T. title: SARS-associated Coronavirus Transmission, United States date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-291024-9g4om4sf.txt cache: ./cache/cord-291024-9g4om4sf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291024-9g4om4sf.txt' === file2bib.sh === id: cord-291374-1bpcj9dw author: Pernazza, Angelina title: Early histologic findings of pulmonary SARS-CoV-2 infection detected in a surgical specimen date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-291374-1bpcj9dw.txt cache: ./cache/cord-291374-1bpcj9dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291374-1bpcj9dw.txt' === file2bib.sh === id: cord-287758-da11ypiy author: Mônica Vitalino de Almeida, Sinara title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-287758-da11ypiy.txt cache: ./cache/cord-287758-da11ypiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-287758-da11ypiy.txt' === file2bib.sh === id: cord-291467-vv2lrx2p author: Qing, Huiling title: The possibility of COVID‐19 transmission from eye to nose date: 2020-03-18 pages: extension: .txt txt: ./txt/cord-291467-vv2lrx2p.txt cache: ./cache/cord-291467-vv2lrx2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291467-vv2lrx2p.txt' === file2bib.sh === id: cord-290904-ngvhk0qy author: Zheng, Zhiqiang title: Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-290904-ngvhk0qy.txt cache: ./cache/cord-290904-ngvhk0qy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290904-ngvhk0qy.txt' === file2bib.sh === id: cord-291028-ejidqmpm author: Montero Feijoo, A. title: Recomendaciones prácticas para el manejo perioperatorio del paciente con sospecha o infección grave por coronavirus SARS-CoV-2 date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-291028-ejidqmpm.txt cache: ./cache/cord-291028-ejidqmpm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291028-ejidqmpm.txt' === file2bib.sh === id: cord-291361-2vn1o7ag author: Li, Jing title: Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-291361-2vn1o7ag.txt cache: ./cache/cord-291361-2vn1o7ag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291361-2vn1o7ag.txt' === file2bib.sh === id: cord-291222-n8kgsz2e author: Park, Benjamin J. title: Lack of SARS Transmission among Healthcare Workers, United States date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-291222-n8kgsz2e.txt cache: ./cache/cord-291222-n8kgsz2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291222-n8kgsz2e.txt' === file2bib.sh === id: cord-291436-cu5o8ipw author: Martínez-Hernández, Fernando title: Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-291436-cu5o8ipw.txt cache: ./cache/cord-291436-cu5o8ipw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291436-cu5o8ipw.txt' === file2bib.sh === id: cord-291281-ygrh8ces author: Durner, J. title: Critical Questions when Interpreting Coronavirus PCR Diagnostics date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-291281-ygrh8ces.txt cache: ./cache/cord-291281-ygrh8ces.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291281-ygrh8ces.txt' === file2bib.sh === id: cord-291420-40xsypzt author: Nelson-Sathi, Shijulal title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-291420-40xsypzt.txt cache: ./cache/cord-291420-40xsypzt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291420-40xsypzt.txt' === file2bib.sh === id: cord-291014-cfnoxhtd author: Zheng, Jian title: Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-291014-cfnoxhtd.txt cache: ./cache/cord-291014-cfnoxhtd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291014-cfnoxhtd.txt' === file2bib.sh === id: cord-290677-3gdcyrrz author: De Virgiliis, Francesco title: Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19 date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-290677-3gdcyrrz.txt cache: ./cache/cord-290677-3gdcyrrz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290677-3gdcyrrz.txt' === file2bib.sh === id: cord-291517-ifei60ly author: Dixon, Luke title: COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-291517-ifei60ly.txt cache: ./cache/cord-291517-ifei60ly.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291517-ifei60ly.txt' === file2bib.sh === id: cord-290472-w77cmljm author: Sharon, Donald title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 pages: extension: .txt txt: ./txt/cord-290472-w77cmljm.txt cache: ./cache/cord-290472-w77cmljm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290472-w77cmljm.txt' === file2bib.sh === id: cord-291393-iht5zndl author: De Angelis, Giulia title: Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-291393-iht5zndl.txt cache: ./cache/cord-291393-iht5zndl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291393-iht5zndl.txt' === file2bib.sh === id: cord-291356-df5n5v09 author: Verma, Saguna title: ACE2 receptor expression in testes: implications in coronavirus disease 2019 pathogenesis date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-291356-df5n5v09.txt cache: ./cache/cord-291356-df5n5v09.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291356-df5n5v09.txt' === file2bib.sh === id: cord-291190-f6km3c7z author: Nasi, Aikaterini title: Reactive oxygen species as an initiator of toxic innate immune responses in retort to SARS-CoV-2 in an ageing population, consider N-acetylcysteine as early therapeutic intervention date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-291190-f6km3c7z.txt cache: ./cache/cord-291190-f6km3c7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291190-f6km3c7z.txt' === file2bib.sh === id: cord-291264-akuvt5ig author: Schnichels, Sven title: Kann SARS-CoV-2 das Auge infizieren? – Ein Überblick über den Rezeptorstatus in okularem Gewebe date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-291264-akuvt5ig.txt cache: ./cache/cord-291264-akuvt5ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291264-akuvt5ig.txt' === file2bib.sh === id: cord-290978-e7imc11r author: Shevachman, M. title: A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-290978-e7imc11r.txt cache: ./cache/cord-290978-e7imc11r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290978-e7imc11r.txt' === file2bib.sh === id: cord-291149-j70b7kyi author: Leuzinger, K. title: Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-291149-j70b7kyi.txt cache: ./cache/cord-291149-j70b7kyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291149-j70b7kyi.txt' === file2bib.sh === id: cord-291323-kbjyd5g3 author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-291323-kbjyd5g3.txt cache: ./cache/cord-291323-kbjyd5g3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291323-kbjyd5g3.txt' === file2bib.sh === id: cord-291459-m56dy8us author: Hraiech, Sami title: Lack of viral clearance by the combination of hydroxychloroquine and azithromycin or lopinavir and ritonavir in SARS-CoV-2-related acute respiratory distress syndrome date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-291459-m56dy8us.txt cache: ./cache/cord-291459-m56dy8us.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291459-m56dy8us.txt' === file2bib.sh === id: cord-291613-pfgy9ztl author: Farshidpour, Maham title: A brief review of liver injury in patients with Corona Virus Disease-19 during the pandemic date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-291613-pfgy9ztl.txt cache: ./cache/cord-291613-pfgy9ztl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291613-pfgy9ztl.txt' === file2bib.sh === id: cord-291505-vt5vpp60 author: Rusconi, Chiara title: SARS-CoV-2 Interstitial Pneumonia Treated With Tocilizumab in a Patient Affected by Classical Hodgkin Lymphoma date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-291505-vt5vpp60.txt cache: ./cache/cord-291505-vt5vpp60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291505-vt5vpp60.txt' === file2bib.sh === id: cord-291738-nak5357h author: Padoan, Andrea title: Clinical performances of an ELISA for SARS-CoV-2 antibody assay and correlation with neutralization activity date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-291738-nak5357h.txt cache: ./cache/cord-291738-nak5357h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291738-nak5357h.txt' === file2bib.sh === id: cord-291363-re45w37d author: Sanville, Bradley title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-291363-re45w37d.txt cache: ./cache/cord-291363-re45w37d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291363-re45w37d.txt' === file2bib.sh === id: cord-291176-evb6yt0r author: Giorgi Rossi, Paolo title: Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-291176-evb6yt0r.txt cache: ./cache/cord-291176-evb6yt0r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291176-evb6yt0r.txt' === file2bib.sh === id: cord-291388-tt9eq7e0 author: Wang, Jann-Tay title: Clinical Manifestations, Laboratory Findings, and Treatment Outcomes of SARS Patients date: 2004-05-17 pages: extension: .txt txt: ./txt/cord-291388-tt9eq7e0.txt cache: ./cache/cord-291388-tt9eq7e0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291388-tt9eq7e0.txt' === file2bib.sh === id: cord-291248-0kuc9jv9 author: Al-Sehemi, Abdullah G. title: Potential of NO donor furoxan as SARS-CoV-2 main protease (M(pro)) inhibitors: in silico analysis date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-291248-0kuc9jv9.txt cache: ./cache/cord-291248-0kuc9jv9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291248-0kuc9jv9.txt' === file2bib.sh === id: cord-291156-zxg3dsm3 author: Bernasconi, Anna title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-291156-zxg3dsm3.txt cache: ./cache/cord-291156-zxg3dsm3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291156-zxg3dsm3.txt' === file2bib.sh === id: cord-291577-nf80kih2 author: Baluku, Joseph Baruch title: HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-291577-nf80kih2.txt cache: ./cache/cord-291577-nf80kih2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291577-nf80kih2.txt' === file2bib.sh === id: cord-291642-xfkdxnfb author: Howley, Fergal title: Late presentation of ‘Lemierre’s syndrome’: how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-291642-xfkdxnfb.txt cache: ./cache/cord-291642-xfkdxnfb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291642-xfkdxnfb.txt' === file2bib.sh === id: cord-291513-vpehn6nx author: Minich, Jeremiah title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-291513-vpehn6nx.txt cache: ./cache/cord-291513-vpehn6nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291513-vpehn6nx.txt' === file2bib.sh === id: cord-292025-dr611nse author: Kam, Kai-qian title: Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-292025-dr611nse.txt cache: ./cache/cord-292025-dr611nse.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292025-dr611nse.txt' === file2bib.sh === id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-291360-z19ri377.txt cache: ./cache/cord-291360-z19ri377.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291360-z19ri377.txt' === file2bib.sh === id: cord-291552-qv6koo6g author: KWAN, AMBROSE CHI‐PONG title: Severe acute respiratory syndrome‐related diarrhea date: 2005-02-23 pages: extension: .txt txt: ./txt/cord-291552-qv6koo6g.txt cache: ./cache/cord-291552-qv6koo6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291552-qv6koo6g.txt' === file2bib.sh === id: cord-291710-ixun0c8g author: Su, Haixia title: Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-291710-ixun0c8g.txt cache: ./cache/cord-291710-ixun0c8g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291710-ixun0c8g.txt' === file2bib.sh === id: cord-276758-k2imddzr author: Siegel, Jane D. title: 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date: 2007-12-07 pages: extension: .txt txt: ./txt/cord-276758-k2imddzr.txt cache: ./cache/cord-276758-k2imddzr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-276758-k2imddzr.txt' === file2bib.sh === id: cord-290948-cuu78cvl author: Imbert, Isabelle title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date: 2008-02-05 pages: extension: .txt txt: ./txt/cord-290948-cuu78cvl.txt cache: ./cache/cord-290948-cuu78cvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290948-cuu78cvl.txt' === file2bib.sh === id: cord-290744-m0vpizuh author: Kindler, E. title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-290744-m0vpizuh.txt cache: ./cache/cord-290744-m0vpizuh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290744-m0vpizuh.txt' === file2bib.sh === id: cord-291315-y40s45iv author: Logunov, Denis Y title: Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-291315-y40s45iv.txt cache: ./cache/cord-291315-y40s45iv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291315-y40s45iv.txt' === file2bib.sh === id: cord-291991-on70zzn0 author: Jaimes, Javier A. title: Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-291991-on70zzn0.txt cache: ./cache/cord-291991-on70zzn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291991-on70zzn0.txt' === file2bib.sh === id: cord-291920-gtzc69lc author: Meyers, Kristin J. title: A cross‐sectional community‐based observational study of asymptomatic SARS‐CoV‐2 prevalence in the greater Indianapolis area date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-291920-gtzc69lc.txt cache: ./cache/cord-291920-gtzc69lc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291920-gtzc69lc.txt' === file2bib.sh === id: cord-291523-4dtk1kyh author: Nguyen, Thanh Thi title: Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-291523-4dtk1kyh.txt cache: ./cache/cord-291523-4dtk1kyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291523-4dtk1kyh.txt' === file2bib.sh === id: cord-291588-tp89j1kk author: Dorche, Maryam Sharifian title: Neurological complications of coronavirus infection; a comparative review and lessons learned during the COVID-19 pandemic date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-291588-tp89j1kk.txt cache: ./cache/cord-291588-tp89j1kk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291588-tp89j1kk.txt' === file2bib.sh === id: cord-291113-iizj932l author: Cumbo, Enzo title: Alternative Methods of Sterilization in Dental Practices Against COVID-19 date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-291113-iizj932l.txt cache: ./cache/cord-291113-iizj932l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291113-iizj932l.txt' === file2bib.sh === id: cord-291729-4l4v9jxd author: de Salazar, Adolfo title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-291729-4l4v9jxd.txt cache: ./cache/cord-291729-4l4v9jxd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291729-4l4v9jxd.txt' === file2bib.sh === id: cord-291747-3du4jluy author: Habashy, Noha H. title: The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-291747-3du4jluy.txt cache: ./cache/cord-291747-3du4jluy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291747-3du4jluy.txt' === file2bib.sh === id: cord-291809-b7sosrc7 author: Iacovoni, Attilio title: A case series of Novel-Coronavirus infection in heart transplantation from two centers in the pandemic area in the North of Italy date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-291809-b7sosrc7.txt cache: ./cache/cord-291809-b7sosrc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291809-b7sosrc7.txt' === file2bib.sh === id: cord-291076-p350i54m author: Wang, Renxi title: The role of C5a in acute lung injury induced by highly pathogenic viral infections date: 2015-05-06 pages: extension: .txt txt: ./txt/cord-291076-p350i54m.txt cache: ./cache/cord-291076-p350i54m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291076-p350i54m.txt' === file2bib.sh === id: cord-291726-8670s4st author: Che, Xiao-yan title: A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date: 2006-07-01 pages: extension: .txt txt: ./txt/cord-291726-8670s4st.txt cache: ./cache/cord-291726-8670s4st.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291726-8670s4st.txt' === file2bib.sh === id: cord-291847-x3b6j5d0 author: Chan, K. H. title: The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus date: 2011-10-01 pages: extension: .txt txt: ./txt/cord-291847-x3b6j5d0.txt cache: ./cache/cord-291847-x3b6j5d0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291847-x3b6j5d0.txt' === file2bib.sh === id: cord-289535-srrfr1es author: Tregoning, J. S. title: Vaccines for COVID‐19 date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-289535-srrfr1es.txt cache: ./cache/cord-289535-srrfr1es.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289535-srrfr1es.txt' === file2bib.sh === id: cord-292152-gmru83ac author: Makrinioti, Heidi title: Intussusception in two children with SARS-CoV-2 infection in children date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-292152-gmru83ac.txt cache: ./cache/cord-292152-gmru83ac.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292152-gmru83ac.txt' === file2bib.sh === id: cord-292250-jjhpwgfa author: Heinz, Nicole title: A case of an Infant with SARS‐CoV‐2 hepatitis early after liver transplantation date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-292250-jjhpwgfa.txt cache: ./cache/cord-292250-jjhpwgfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292250-jjhpwgfa.txt' === file2bib.sh === id: cord-291677-zcbyhsf1 author: Wilamowski, M. title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-291677-zcbyhsf1.txt cache: ./cache/cord-291677-zcbyhsf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291677-zcbyhsf1.txt' === file2bib.sh === id: cord-291687-kwu0otpi author: Judson, Gregory L. title: Cardiovascular Implications and Therapeutic Considerations in COVID-19 Infection date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-291687-kwu0otpi.txt cache: ./cache/cord-291687-kwu0otpi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291687-kwu0otpi.txt' === file2bib.sh === id: cord-291987-zpkzzldu author: To, Kelvin KW title: False-positive SARS-CoV-2 serology in three children with Kawasaki disease date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-291987-zpkzzldu.txt cache: ./cache/cord-291987-zpkzzldu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291987-zpkzzldu.txt' === file2bib.sh === id: cord-292002-g0v0xc21 author: Yang, Wenjing title: The role of imaging in 2019 novel coronavirus pneumonia (COVID-19) date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-292002-g0v0xc21.txt cache: ./cache/cord-292002-g0v0xc21.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292002-g0v0xc21.txt' === file2bib.sh === id: cord-291655-l7mg5a0z author: Ku, C. W. title: Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-291655-l7mg5a0z.txt cache: ./cache/cord-291655-l7mg5a0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291655-l7mg5a0z.txt' === file2bib.sh === id: cord-291965-9r9ll83m author: Pfefferle, Susanne title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date: 2009-09-17 pages: extension: .txt txt: ./txt/cord-291965-9r9ll83m.txt cache: ./cache/cord-291965-9r9ll83m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291965-9r9ll83m.txt' === file2bib.sh === id: cord-291590-24psoaer author: Ogando, Natacha S. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-291590-24psoaer.txt cache: ./cache/cord-291590-24psoaer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291590-24psoaer.txt' === file2bib.sh === id: cord-292236-eudcs9t2 author: Wang, Yishan title: Asymptomatic cases with SARS‐CoV‐2 infection date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-292236-eudcs9t2.txt cache: ./cache/cord-292236-eudcs9t2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292236-eudcs9t2.txt' === file2bib.sh === id: cord-292578-co5essuw author: Johnson, Marina title: Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-292578-co5essuw.txt cache: ./cache/cord-292578-co5essuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292578-co5essuw.txt' === file2bib.sh === id: cord-292015-pfvgpf7v author: Brouwer, A. F. title: SARS-CoV-2 surveillance in decedents in a large, urban medical examiner's office date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-292015-pfvgpf7v.txt cache: ./cache/cord-292015-pfvgpf7v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292015-pfvgpf7v.txt' === file2bib.sh === id: cord-292650-i95upz10 author: Marafini, Irene title: LOW FREQUENCY OF COVID-19 IN INFLAMMATORY BOWEL DISEASES date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-292650-i95upz10.txt cache: ./cache/cord-292650-i95upz10.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292650-i95upz10.txt' === file2bib.sh === id: cord-291397-look6ddt author: Roberto, Palumbo title: Current treatment of COVID-19 in renal patients: hope or hype? date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-291397-look6ddt.txt cache: ./cache/cord-291397-look6ddt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291397-look6ddt.txt' === file2bib.sh === id: cord-291790-z5rwznmv author: Li, Qianqian title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-291790-z5rwznmv.txt cache: ./cache/cord-291790-z5rwznmv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291790-z5rwznmv.txt' === file2bib.sh === id: cord-291595-8241pjpe author: Mahmudpour, Mehdi title: COVID-19 cytokine storm: The anger of inflammation date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-291595-8241pjpe.txt cache: ./cache/cord-291595-8241pjpe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291595-8241pjpe.txt' === file2bib.sh === id: cord-291627-5dqwyd9r author: Yadav, Rakhee title: SARS-CoV-2-host dynamics: Increased risk of adverse outcomes of COVID-19 in obesity date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-291627-5dqwyd9r.txt cache: ./cache/cord-291627-5dqwyd9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291627-5dqwyd9r.txt' === file2bib.sh === id: cord-291923-jvbehgb7 author: Rajoli, R. K. title: Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-291923-jvbehgb7.txt cache: ./cache/cord-291923-jvbehgb7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291923-jvbehgb7.txt' === file2bib.sh === id: cord-292580-caxb9ob9 author: Chang, Z title: RNAi therapeutics: Can siRNAs conquer SARS? date: 2005-11-10 pages: extension: .txt txt: ./txt/cord-292580-caxb9ob9.txt cache: ./cache/cord-292580-caxb9ob9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292580-caxb9ob9.txt' === file2bib.sh === id: cord-292337-74c69z28 author: Tsai, Shin-Han title: Transporting Patient with Suspected SARS date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-292337-74c69z28.txt cache: ./cache/cord-292337-74c69z28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292337-74c69z28.txt' === file2bib.sh === id: cord-292423-jupcit75 author: Narkhede, Rohan R. title: Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-292423-jupcit75.txt cache: ./cache/cord-292423-jupcit75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292423-jupcit75.txt' === file2bib.sh === id: cord-291954-wormplcu author: Sakulkonkij, Parichart title: A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-291954-wormplcu.txt cache: ./cache/cord-291954-wormplcu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291954-wormplcu.txt' === file2bib.sh === id: cord-292045-pnid9dmq author: Kumar, Manish title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-292045-pnid9dmq.txt cache: ./cache/cord-292045-pnid9dmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292045-pnid9dmq.txt' === file2bib.sh === id: cord-291624-fod0eyuj author: Malone, Robert W. title: COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-291624-fod0eyuj.txt cache: ./cache/cord-291624-fod0eyuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291624-fod0eyuj.txt' === file2bib.sh === id: cord-292256-jp80u828 author: Moriguchi, Takeshi title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-292256-jp80u828.txt cache: ./cache/cord-292256-jp80u828.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292256-jp80u828.txt' === file2bib.sh === id: cord-291719-1ku6cmwj author: Hajjo, Rima title: A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-291719-1ku6cmwj.txt cache: ./cache/cord-291719-1ku6cmwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291719-1ku6cmwj.txt' === file2bib.sh === id: cord-292462-zbjig3pt author: Backhaus, Andreas title: Common Pitfalls in the Interpretation of COVID-19 Data and Statistics date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-292462-zbjig3pt.txt cache: ./cache/cord-292462-zbjig3pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292462-zbjig3pt.txt' === file2bib.sh === id: cord-292972-p7ifetgw author: Jiang, Xuan title: Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS? date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-292972-p7ifetgw.txt cache: ./cache/cord-292972-p7ifetgw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292972-p7ifetgw.txt' === file2bib.sh === id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-292347-d7xq7x5g.txt cache: ./cache/cord-292347-d7xq7x5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292347-d7xq7x5g.txt' === file2bib.sh === id: cord-292050-x3isowrt author: Ackerman, Emily E. title: Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-292050-x3isowrt.txt cache: ./cache/cord-292050-x3isowrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292050-x3isowrt.txt' === file2bib.sh === id: cord-292274-upwn9o2m author: Ghaffari, Abdi title: COVID-19 Serological Tests: How Well Do They Actually Perform? date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-292274-upwn9o2m.txt cache: ./cache/cord-292274-upwn9o2m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292274-upwn9o2m.txt' === file2bib.sh === id: cord-292367-ocbsmmt6 author: El-Masri, Maher M. title: Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date: 2012-02-29 pages: extension: .txt txt: ./txt/cord-292367-ocbsmmt6.txt cache: ./cache/cord-292367-ocbsmmt6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292367-ocbsmmt6.txt' === file2bib.sh === id: cord-291644-5y0ioety author: Akiyama, Tomohiro title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-291644-5y0ioety.txt cache: ./cache/cord-291644-5y0ioety.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291644-5y0ioety.txt' === file2bib.sh === id: cord-292350-cmrtg91a author: Mondal, Samhati title: Thromboembolic disease in COVID-19 patients: A brief narrative review date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-292350-cmrtg91a.txt cache: ./cache/cord-292350-cmrtg91a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292350-cmrtg91a.txt' === file2bib.sh === id: cord-292173-95t89yee author: Villani, Federico Alcide title: COVID-19 and Dentistry: Prevention in Dental Practice, a Literature Review date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-292173-95t89yee.txt cache: ./cache/cord-292173-95t89yee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292173-95t89yee.txt' === file2bib.sh === id: cord-292030-cjz4nuag author: Qiu, Guangyu title: Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-292030-cjz4nuag.txt cache: ./cache/cord-292030-cjz4nuag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292030-cjz4nuag.txt' === file2bib.sh === id: cord-293059-2iwzieqm author: Tao, Huaqiang title: Dysimmunity and inflammatory storm: Watch out for bone lesions in COVID-19 infection date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-293059-2iwzieqm.txt cache: ./cache/cord-293059-2iwzieqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293059-2iwzieqm.txt' === file2bib.sh === id: cord-292209-d1ty9etr author: Horta, Bernardo L title: Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-292209-d1ty9etr.txt cache: ./cache/cord-292209-d1ty9etr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292209-d1ty9etr.txt' === file2bib.sh === id: cord-292874-6zjqflhz author: SØRENSEN, MORTEN DRÆBY title: Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date: 2006-05-10 pages: extension: .txt txt: ./txt/cord-292874-6zjqflhz.txt cache: ./cache/cord-292874-6zjqflhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292874-6zjqflhz.txt' === file2bib.sh === id: cord-292733-dya40tln author: Lancman, Guido title: Severe COVID-19 virus reactivation following treatment for B cell acute lymphoblastic leukemia date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-292733-dya40tln.txt cache: ./cache/cord-292733-dya40tln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292733-dya40tln.txt' === file2bib.sh === id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-292416-3hhi4wps.txt cache: ./cache/cord-292416-3hhi4wps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292416-3hhi4wps.txt' === file2bib.sh === id: cord-292600-mgvrbfzd author: Ly, T. D. A. title: Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020. date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-292600-mgvrbfzd.txt cache: ./cache/cord-292600-mgvrbfzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292600-mgvrbfzd.txt' === file2bib.sh === id: cord-291561-sxvgue36 author: Haixu, Liang title: Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date: 2019-11-25 pages: extension: .txt txt: ./txt/cord-291561-sxvgue36.txt cache: ./cache/cord-291561-sxvgue36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291561-sxvgue36.txt' === file2bib.sh === id: cord-292673-00s3wgem author: Buonaguro, Luigi title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-292673-00s3wgem.txt cache: ./cache/cord-292673-00s3wgem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292673-00s3wgem.txt' === file2bib.sh === id: cord-293517-8derad2p author: Fischer, Johannes C. title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-293517-8derad2p.txt cache: ./cache/cord-293517-8derad2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293517-8derad2p.txt' === file2bib.sh === id: cord-292544-m7jyydf1 author: Grau-Pujol, Berta title: Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-292544-m7jyydf1.txt cache: ./cache/cord-292544-m7jyydf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292544-m7jyydf1.txt' === file2bib.sh === id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-292751-tk1oggi9.txt cache: ./cache/cord-292751-tk1oggi9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292751-tk1oggi9.txt' === file2bib.sh === id: cord-292386-hfbgigj6 author: Borges, Lysandro Pinto title: Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-292386-hfbgigj6.txt cache: ./cache/cord-292386-hfbgigj6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292386-hfbgigj6.txt' === file2bib.sh === id: cord-292004-9rpoll7y author: Mitchell, Hugh D. title: The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections date: 2019-09-20 pages: extension: .txt txt: ./txt/cord-292004-9rpoll7y.txt cache: ./cache/cord-292004-9rpoll7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292004-9rpoll7y.txt' === file2bib.sh === id: cord-292561-iy06b9h9 author: Miesbach, Wolfgang title: COVID-19: Coagulopathy, Risk of Thrombosis, and the Rationale for Anticoagulation date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-292561-iy06b9h9.txt cache: ./cache/cord-292561-iy06b9h9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292561-iy06b9h9.txt' === file2bib.sh === id: cord-292387-2xv3wgaq author: D′Agostino, Armando title: Brief Psychotic Disorder During the National Lockdown in Italy: An Emerging Clinical Phenomenon of the COVID-19 Pandemic date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-292387-2xv3wgaq.txt cache: ./cache/cord-292387-2xv3wgaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292387-2xv3wgaq.txt' === file2bib.sh === id: cord-293315-kx4x2g24 author: Colmenero, I. title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-293315-kx4x2g24.txt cache: ./cache/cord-293315-kx4x2g24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293315-kx4x2g24.txt' === file2bib.sh === id: cord-293080-b4pxjrcj author: Zhang, Chunyan title: Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-293080-b4pxjrcj.txt cache: ./cache/cord-293080-b4pxjrcj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293080-b4pxjrcj.txt' === file2bib.sh === id: cord-292657-gq3965se author: Das, Piyanki title: Decoding the global outbreak of COVID-19: the nature is behind the scene date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-292657-gq3965se.txt cache: ./cache/cord-292657-gq3965se.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292657-gq3965se.txt' === file2bib.sh === id: cord-293169-rd12xwvl author: Black, Margaret A. title: Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-293169-rd12xwvl.txt cache: ./cache/cord-293169-rd12xwvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293169-rd12xwvl.txt' === file2bib.sh === id: cord-293544-nemw29r7 author: Valdivia, Arantxa title: Qualitative assessment of SARS‐CoV‐2‐specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-293544-nemw29r7.txt cache: ./cache/cord-293544-nemw29r7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293544-nemw29r7.txt' === file2bib.sh === id: cord-292675-tkyngspy author: Qi, Furong title: Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-292675-tkyngspy.txt cache: ./cache/cord-292675-tkyngspy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292675-tkyngspy.txt' === file2bib.sh === id: cord-293265-qqxlwpju author: Zeng, Yong title: Clinical characteristics of 9 cancer patients with SARS-CoV-2 infection date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-293265-qqxlwpju.txt cache: ./cache/cord-293265-qqxlwpju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293265-qqxlwpju.txt' === file2bib.sh === id: cord-293557-jcgc93it author: Recalde, Borja title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-293557-jcgc93it.txt cache: ./cache/cord-293557-jcgc93it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293557-jcgc93it.txt' === file2bib.sh === id: cord-293615-f1e6hs11 author: Dockery, Dominique M. title: The Ocular Manifestations and Transmission of COVID-19; Recommendations for Prevention date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-293615-f1e6hs11.txt cache: ./cache/cord-293615-f1e6hs11.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293615-f1e6hs11.txt' === file2bib.sh === id: cord-292041-a65kfw80 author: Orienti, Isabella title: Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19 date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-292041-a65kfw80.txt cache: ./cache/cord-292041-a65kfw80.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292041-a65kfw80.txt' === file2bib.sh === id: cord-292880-zegtr19k author: Hu, Fuying title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-292880-zegtr19k.txt cache: ./cache/cord-292880-zegtr19k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292880-zegtr19k.txt' === file2bib.sh === id: cord-293082-fw7deem8 author: Zhang, Guangzhi title: Animal coronaviruses and SARS‐CoV‐2 date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-293082-fw7deem8.txt cache: ./cache/cord-293082-fw7deem8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293082-fw7deem8.txt' === file2bib.sh === id: cord-293579-w5sub348 author: Che, Xiao-yan title: Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date: 2005-06-15 pages: extension: .txt txt: ./txt/cord-293579-w5sub348.txt cache: ./cache/cord-293579-w5sub348.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293579-w5sub348.txt' === file2bib.sh === id: cord-292988-q1yz9y8k author: Zumla, Alimuddin title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-292988-q1yz9y8k.txt cache: ./cache/cord-292988-q1yz9y8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292988-q1yz9y8k.txt' === file2bib.sh === id: cord-293710-f1tzt6jb author: Karolyi, M. title: Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-293710-f1tzt6jb.txt cache: ./cache/cord-293710-f1tzt6jb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293710-f1tzt6jb.txt' === file2bib.sh === id: cord-293389-3h9vsc1a author: Risitano, Antonio M. title: Complement as a target in COVID-19? date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-293389-3h9vsc1a.txt cache: ./cache/cord-293389-3h9vsc1a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293389-3h9vsc1a.txt' === file2bib.sh === id: cord-293564-6xtg8uqt author: Hara, Tasuku title: Infection risk in a gastroenterological ward during a nosocomial COVID‐19 infection event date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-293564-6xtg8uqt.txt cache: ./cache/cord-293564-6xtg8uqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293564-6xtg8uqt.txt' === file2bib.sh === id: cord-293180-f1ulk9ce author: Li, R W K title: Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs date: 2004-08-14 pages: extension: .txt txt: ./txt/cord-293180-f1ulk9ce.txt cache: ./cache/cord-293180-f1ulk9ce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293180-f1ulk9ce.txt' === file2bib.sh === id: cord-293826-2p7dqacd author: Lee, Cheryl Yi-Pin title: Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-293826-2p7dqacd.txt cache: ./cache/cord-293826-2p7dqacd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293826-2p7dqacd.txt' === file2bib.sh === id: cord-292985-w62xaa4f author: Römer, Rudolf A. title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-292985-w62xaa4f.txt cache: ./cache/cord-292985-w62xaa4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292985-w62xaa4f.txt' === file2bib.sh === id: cord-293890-thfros7x author: Carbo, Ellen C. title: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-293890-thfros7x.txt cache: ./cache/cord-293890-thfros7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293890-thfros7x.txt' === file2bib.sh === id: cord-293127-c27qh5y7 author: Monteleone, Pedro AA title: A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments date: 2020 pages: extension: .txt txt: ./txt/cord-293127-c27qh5y7.txt cache: ./cache/cord-293127-c27qh5y7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293127-c27qh5y7.txt' === file2bib.sh === id: cord-293688-g6kag5ij author: Nora, Holtmann title: Assessment of SARS-CoV-2 in human semen - a cohort study date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-293688-g6kag5ij.txt cache: ./cache/cord-293688-g6kag5ij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293688-g6kag5ij.txt' === file2bib.sh === id: cord-293056-kz3w0nfh author: Indes, Jeffrey E. title: Early Experience with Arterial Thromboembolic Complications in Patents with COVID-19 date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-293056-kz3w0nfh.txt cache: ./cache/cord-293056-kz3w0nfh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293056-kz3w0nfh.txt' === file2bib.sh === id: cord-293543-87ulnpdm author: Shalhoub, Sarah title: Interferon beta-1b for COVID-19 date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-293543-87ulnpdm.txt cache: ./cache/cord-293543-87ulnpdm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293543-87ulnpdm.txt' === file2bib.sh === id: cord-293692-t5rfvyvj author: Kazi, Sajida title: The delights and perils of publishing, knowledge-sharing and critique during a pandemic: Observations from COVID-19 coagulopathies date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-293692-t5rfvyvj.txt cache: ./cache/cord-293692-t5rfvyvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293692-t5rfvyvj.txt' === file2bib.sh === id: cord-292836-1o2ynvy3 author: Ogimi, Chikara title: What’s New With the Old Coronaviruses? date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-292836-1o2ynvy3.txt cache: ./cache/cord-292836-1o2ynvy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292836-1o2ynvy3.txt' === file2bib.sh === id: cord-293382-uyat0w58 author: Walker, Susanne N. title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-293382-uyat0w58.txt cache: ./cache/cord-293382-uyat0w58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293382-uyat0w58.txt' === file2bib.sh === id: cord-293136-lfwqzf8m author: Escosa‐García, Luis title: Ten key points about COVID‐19 in children: the shadows on the wall date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-293136-lfwqzf8m.txt cache: ./cache/cord-293136-lfwqzf8m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293136-lfwqzf8m.txt' === file2bib.sh === id: cord-293503-e7be12qb author: Xiang, Chao title: CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-293503-e7be12qb.txt cache: ./cache/cord-293503-e7be12qb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293503-e7be12qb.txt' === file2bib.sh === id: cord-293415-u9onutny author: Amendola, A. title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-293415-u9onutny.txt cache: ./cache/cord-293415-u9onutny.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293415-u9onutny.txt' === file2bib.sh === id: cord-293167-3bd3adip author: Nepal, Gaurav title: Neurological manifestations of COVID-19: a systematic review date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-293167-3bd3adip.txt cache: ./cache/cord-293167-3bd3adip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293167-3bd3adip.txt' === file2bib.sh === id: cord-294028-pcc6mucj author: Caussy, Cyrielle title: Obesity is Associated with Severe Forms of COVID‐19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-294028-pcc6mucj.txt cache: ./cache/cord-294028-pcc6mucj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294028-pcc6mucj.txt' === file2bib.sh === id: cord-293301-7bmj8qsv author: Buonanno, Giorgio title: Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-293301-7bmj8qsv.txt cache: ./cache/cord-293301-7bmj8qsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293301-7bmj8qsv.txt' === file2bib.sh === id: cord-292883-7hvq9qaj author: Nguyen-Contant, Phuong title: S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-292883-7hvq9qaj.txt cache: ./cache/cord-292883-7hvq9qaj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292883-7hvq9qaj.txt' === file2bib.sh === id: cord-293367-0fe62h2f author: Henderson, Lauren A. title: American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS‐C) Associated with SARS‐CoV‐2 and Hyperinflammation in COVID‐19. Version 1 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-293367-0fe62h2f.txt cache: ./cache/cord-293367-0fe62h2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293367-0fe62h2f.txt' === file2bib.sh === id: cord-294120-8fxrqorg author: Guebre-Xabier, Mimi title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-294120-8fxrqorg.txt cache: ./cache/cord-294120-8fxrqorg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294120-8fxrqorg.txt' === file2bib.sh === id: cord-294410-iy57tjx5 author: Zhang, Shengnan title: (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain date: 2010-12-23 pages: extension: .txt txt: ./txt/cord-294410-iy57tjx5.txt cache: ./cache/cord-294410-iy57tjx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294410-iy57tjx5.txt' === file2bib.sh === id: cord-294199-o8w35pdy author: Zhang, Qiangzhe title: Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-294199-o8w35pdy.txt cache: ./cache/cord-294199-o8w35pdy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294199-o8w35pdy.txt' === file2bib.sh === id: cord-294385-6dlgv3tb author: Tong, Xin title: Surveillance of SARS‐CoV‐2 infection among frontline health care workers in Wuhan during COVID‐19 outbreak date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-294385-6dlgv3tb.txt cache: ./cache/cord-294385-6dlgv3tb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294385-6dlgv3tb.txt' === file2bib.sh === id: cord-293578-yu2i0u2h author: Kusadasi, Nuray title: A Pathophysiological Perspective on the SARS-CoV-2 Coagulopathy date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-293578-yu2i0u2h.txt cache: ./cache/cord-293578-yu2i0u2h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293578-yu2i0u2h.txt' === file2bib.sh === id: cord-294392-a8s66g96 author: Zhang, Shuai title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-294392-a8s66g96.txt cache: ./cache/cord-294392-a8s66g96.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294392-a8s66g96.txt' === file2bib.sh === id: cord-294262-yvbufnf4 author: Fernandez-Nieto, D. title: Comment on: “To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out. Characterization of herpetic lesions in hospitalized COVID-19 patients.” date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-294262-yvbufnf4.txt cache: ./cache/cord-294262-yvbufnf4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294262-yvbufnf4.txt' === file2bib.sh === id: cord-293274-ysr1l557 author: Perisé-Barrios, Ana Judith title: Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-293274-ysr1l557.txt cache: ./cache/cord-293274-ysr1l557.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293274-ysr1l557.txt' === file2bib.sh === id: cord-293860-6kz0iws6 author: Qutayba Almerie, Muhammad title: The Association between Obesity and Poor Outcome after COVID-19 Indicates a Potential Therapeutic Role for Montelukast date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-293860-6kz0iws6.txt cache: ./cache/cord-293860-6kz0iws6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293860-6kz0iws6.txt' === file2bib.sh === id: cord-292742-mio4przi author: McAloose, Denise title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-292742-mio4przi.txt cache: ./cache/cord-292742-mio4przi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292742-mio4przi.txt' === file2bib.sh === id: cord-293304-kakxmc14 author: Achutha, A. S. title: Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-293304-kakxmc14.txt cache: ./cache/cord-293304-kakxmc14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293304-kakxmc14.txt' === file2bib.sh === id: cord-294122-ou3wj4rz author: Hwang, Stephen W title: Population mortality during the outbreak of Severe Acute Respiratory Syndrome in Toronto date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-294122-ou3wj4rz.txt cache: ./cache/cord-294122-ou3wj4rz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294122-ou3wj4rz.txt' === file2bib.sh === id: cord-293732-rxd1lyi7 author: Manoj, M.G. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-293732-rxd1lyi7.txt cache: ./cache/cord-293732-rxd1lyi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293732-rxd1lyi7.txt' === file2bib.sh === id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-294335-qnu19ru5.txt cache: ./cache/cord-294335-qnu19ru5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294335-qnu19ru5.txt' === file2bib.sh === id: cord-294498-fv545rfa author: Spiegel, Martin title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein date: 2004-07-31 pages: extension: .txt txt: ./txt/cord-294498-fv545rfa.txt cache: ./cache/cord-294498-fv545rfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294498-fv545rfa.txt' === file2bib.sh === id: cord-294069-7zr77r71 author: Hu, Xiaowen title: The distribution of SARS-CoV-2 contamination on the environmental surfaces during incubation period of COVID-19 patients date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-294069-7zr77r71.txt cache: ./cache/cord-294069-7zr77r71.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294069-7zr77r71.txt' === file2bib.sh === id: cord-294295-sd5893ii author: Badua, Christian Luke D.C. title: Genomic and Proteomic Mutation Landscapes of SARS‐CoV‐2 date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-294295-sd5893ii.txt cache: ./cache/cord-294295-sd5893ii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294295-sd5893ii.txt' === file2bib.sh === id: cord-294073-65h2mkdy author: Ke, Jia title: Strategies and recommendations for the management of gastrointestinal surgery during the COVID-19 pandemic: experience shared by Chinese surgeons date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-294073-65h2mkdy.txt cache: ./cache/cord-294073-65h2mkdy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294073-65h2mkdy.txt' === file2bib.sh === id: cord-294644-xuafsnxm author: Herrmann, Burkhard L. title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-294644-xuafsnxm.txt cache: ./cache/cord-294644-xuafsnxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294644-xuafsnxm.txt' === file2bib.sh === id: cord-293655-2ab7wdsk author: Mandic-Rajcevic, S. title: Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy) date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-293655-2ab7wdsk.txt cache: ./cache/cord-293655-2ab7wdsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293655-2ab7wdsk.txt' === file2bib.sh === id: cord-293858-dk4snw9r author: Yang, Lin title: Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date: 2019-02-14 pages: extension: .txt txt: ./txt/cord-293858-dk4snw9r.txt cache: ./cache/cord-293858-dk4snw9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293858-dk4snw9r.txt' === file2bib.sh === id: cord-293988-f5gvwjyh author: Musso, Nicolò title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-293988-f5gvwjyh.txt cache: ./cache/cord-293988-f5gvwjyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293988-f5gvwjyh.txt' === file2bib.sh === id: cord-293259-o51fnvuw author: Sinaei, Reza title: Why COVID-19 is less frequent and severe in children: a narrative review date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-293259-o51fnvuw.txt cache: ./cache/cord-293259-o51fnvuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293259-o51fnvuw.txt' === file2bib.sh === id: cord-293765-xpc4yizb author: Huang, Jia-Ling title: Th2 predominance and CD8+ memory T cell depletion in patients with severe acute respiratory syndrome() date: 2005-02-24 pages: extension: .txt txt: ./txt/cord-293765-xpc4yizb.txt cache: ./cache/cord-293765-xpc4yizb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293765-xpc4yizb.txt' === file2bib.sh === id: cord-294212-nlekz39f author: Wang, Dongliang title: Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-294212-nlekz39f.txt cache: ./cache/cord-294212-nlekz39f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294212-nlekz39f.txt' === file2bib.sh === id: cord-294134-o9bx1gn7 author: Brecher, Stephen M. title: Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-294134-o9bx1gn7.txt cache: ./cache/cord-294134-o9bx1gn7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294134-o9bx1gn7.txt' === file2bib.sh === id: cord-294372-pec1886j author: Greene, Dina N. title: Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-294372-pec1886j.txt cache: ./cache/cord-294372-pec1886j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294372-pec1886j.txt' === file2bib.sh === id: cord-293736-nyvwv31m author: Méry, Geoffroy title: COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-293736-nyvwv31m.txt cache: ./cache/cord-293736-nyvwv31m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293736-nyvwv31m.txt' === file2bib.sh === id: cord-293831-28ddm9um author: Qian, Mengcen title: Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-293831-28ddm9um.txt cache: ./cache/cord-293831-28ddm9um.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293831-28ddm9um.txt' === file2bib.sh === id: cord-294692-qfz6a1kc author: Ortega, Karem L. title: SARS-CoV-2 and dentistry date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-294692-qfz6a1kc.txt cache: ./cache/cord-294692-qfz6a1kc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294692-qfz6a1kc.txt' === file2bib.sh === id: cord-293715-lipme817 author: Hutchison, Lisa title: Neuropsychiatric Symptoms in an Adolescent Boy with Multisystem Inflammatory Syndrome in Children (MIS-C) date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-293715-lipme817.txt cache: ./cache/cord-293715-lipme817.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293715-lipme817.txt' === file2bib.sh === id: cord-293946-4bquxdqa author: Huong, Nguyen Quynh title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-293946-4bquxdqa.txt cache: ./cache/cord-293946-4bquxdqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293946-4bquxdqa.txt' === file2bib.sh === id: cord-293991-x5zdo8t2 author: Wheatley, A. K. title: Evolution of immunity to SARS-CoV-2 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-293991-x5zdo8t2.txt cache: ./cache/cord-293991-x5zdo8t2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293991-x5zdo8t2.txt' === file2bib.sh === id: cord-294558-cqa58db8 author: Wang, Yubo title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-294558-cqa58db8.txt cache: ./cache/cord-294558-cqa58db8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294558-cqa58db8.txt' === file2bib.sh === id: cord-294237-6hovffso author: Cherry, James D title: SARS: The First Pandemic of the 21(st) Century date: 2004 pages: extension: .txt txt: ./txt/cord-294237-6hovffso.txt cache: ./cache/cord-294237-6hovffso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294237-6hovffso.txt' === file2bib.sh === id: cord-294677-l1b4mw9d author: Prashantha, C.N. title: Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-294677-l1b4mw9d.txt cache: ./cache/cord-294677-l1b4mw9d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294677-l1b4mw9d.txt' === file2bib.sh === id: cord-294537-wpq1492g author: Ritschl, Paul V. title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-294537-wpq1492g.txt cache: ./cache/cord-294537-wpq1492g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294537-wpq1492g.txt' === file2bib.sh === id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-291916-5yqc3zcx.txt cache: ./cache/cord-291916-5yqc3zcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291916-5yqc3zcx.txt' === file2bib.sh === id: cord-294704-prizmksg author: Lateef, Fatimah title: New paradigm for protection:: The emergency ambulance services in the time of severe acute respiratory syndrome date: 2004-06-16 pages: extension: .txt txt: ./txt/cord-294704-prizmksg.txt cache: ./cache/cord-294704-prizmksg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294704-prizmksg.txt' === file2bib.sh === id: cord-294275-pp0vlaye author: Li, Jingjing title: Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-294275-pp0vlaye.txt cache: ./cache/cord-294275-pp0vlaye.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294275-pp0vlaye.txt' === file2bib.sh === id: cord-294666-xlyuhzo9 author: Arguin, Paul M. title: Health Communication during SARS date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-294666-xlyuhzo9.txt cache: ./cache/cord-294666-xlyuhzo9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294666-xlyuhzo9.txt' === file2bib.sh === id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-294718-n3gx862b.txt cache: ./cache/cord-294718-n3gx862b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294718-n3gx862b.txt' === file2bib.sh === id: cord-294592-zwvr57a0 author: Mukherjee, Moumita title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-294592-zwvr57a0.txt cache: ./cache/cord-294592-zwvr57a0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294592-zwvr57a0.txt' === file2bib.sh === id: cord-294440-zd0arwmr author: Sacco, Guillaume title: COVID-19 in seniors: Findings and lessons from mass screening in a nursing home date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-294440-zd0arwmr.txt cache: ./cache/cord-294440-zd0arwmr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294440-zd0arwmr.txt' === file2bib.sh === id: cord-293559-c78wcr8m author: Rego, Gabriel N. A. title: Current Clinical Trials Protocols and the Global Effort for Immunization against SARS-CoV-2 date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-293559-c78wcr8m.txt cache: ./cache/cord-293559-c78wcr8m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293559-c78wcr8m.txt' === file2bib.sh === id: cord-295029-zki5ac2g author: Pena, Robert C.F. title: In Reply to the Letter to the Editor Regarding “Coronavirus Neurosurgical/Head and Neck Drape to Prevent Aerosolization of Coronavirus Disease 2019 (COVID-19): The Lenox Hill Hospital/Northwell Health Solution” date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-295029-zki5ac2g.txt cache: ./cache/cord-295029-zki5ac2g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295029-zki5ac2g.txt' === file2bib.sh === id: cord-293938-40zyv1h8 author: Jonsdottir, Hulda R. title: Coronaviruses and the human airway: a universal system for virus-host interaction studies date: 2016-02-06 pages: extension: .txt txt: ./txt/cord-293938-40zyv1h8.txt cache: ./cache/cord-293938-40zyv1h8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293938-40zyv1h8.txt' === file2bib.sh === id: cord-295742-d11ty5ed author: van Dam, Peter A. title: High mortality of cancer patients in times of SARS-Cov-2: do not generalize! date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-295742-d11ty5ed.txt cache: ./cache/cord-295742-d11ty5ed.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295742-d11ty5ed.txt' === file2bib.sh === id: cord-294696-pm6pfeeb author: Kunz, Y. title: Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-294696-pm6pfeeb.txt cache: ./cache/cord-294696-pm6pfeeb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294696-pm6pfeeb.txt' === file2bib.sh === id: cord-294861-inlaz4od author: Liu, Chen title: Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-294861-inlaz4od.txt cache: ./cache/cord-294861-inlaz4od.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294861-inlaz4od.txt' === file2bib.sh === id: cord-293547-29i3u83s author: Pfaar, O title: COVID‐19 pandemic: Practical considerations on the organization of an allergy clinic – an EAACI/ARIA Position Paper date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-293547-29i3u83s.txt cache: ./cache/cord-293547-29i3u83s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293547-29i3u83s.txt' === file2bib.sh === id: cord-294854-rvrgcugn author: Hu, Biying title: The cytokine storm and COVID‐19 date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-294854-rvrgcugn.txt cache: ./cache/cord-294854-rvrgcugn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294854-rvrgcugn.txt' === file2bib.sh === id: cord-294551-s3nsiano author: Muller, M. P. title: Early diagnosis of SARS: lessons from the Toronto SARS outbreak date: 2006-04-04 pages: extension: .txt txt: ./txt/cord-294551-s3nsiano.txt cache: ./cache/cord-294551-s3nsiano.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294551-s3nsiano.txt' === file2bib.sh === id: cord-294304-9w6zt778 author: Doanvo, Anhvinh title: Machine Learning Maps Research Needs in COVID-19 Literature date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-294304-9w6zt778.txt cache: ./cache/cord-294304-9w6zt778.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294304-9w6zt778.txt' === file2bib.sh === id: cord-295302-vwrxentv author: Shivarov, Velizar title: Potential SARS-CoV-2 Preimmune IgM Epitopes date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-295302-vwrxentv.txt cache: ./cache/cord-295302-vwrxentv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295302-vwrxentv.txt' === file2bib.sh === id: cord-294571-qd0qjo3y author: Rothan, Hussin A. title: Molecular Aspects of COVID-19 Differential Pathogenesis date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-294571-qd0qjo3y.txt cache: ./cache/cord-294571-qd0qjo3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294571-qd0qjo3y.txt' === file2bib.sh === id: cord-293481-bmfj50fb author: Malin, Jakob J. title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-293481-bmfj50fb.txt cache: ./cache/cord-293481-bmfj50fb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293481-bmfj50fb.txt' === file2bib.sh === id: cord-295061-58tj4csz author: Wilder‐Smith, Annelies title: Short communication: Low risk of transmission of severe acute respiratory syndrome on airplanes: the Singapore experience date: 2003-10-22 pages: extension: .txt txt: ./txt/cord-295061-58tj4csz.txt cache: ./cache/cord-295061-58tj4csz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295061-58tj4csz.txt' === file2bib.sh === id: cord-294698-mtfrbn87 author: Kim, H. K. title: Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date: 2016-05-23 pages: extension: .txt txt: ./txt/cord-294698-mtfrbn87.txt cache: ./cache/cord-294698-mtfrbn87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294698-mtfrbn87.txt' === file2bib.sh === id: cord-294590-1niaplc2 author: Schrag, Stephanie J. title: SARS Surveillance during Emergency Public Health Response, United States, March–July 2003 date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-294590-1niaplc2.txt cache: ./cache/cord-294590-1niaplc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294590-1niaplc2.txt' === file2bib.sh === id: cord-293701-u4ntxo0y author: Su, Shan title: Learning from the past: development of safe and effective COVID-19 vaccines date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-293701-u4ntxo0y.txt cache: ./cache/cord-293701-u4ntxo0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293701-u4ntxo0y.txt' === file2bib.sh === id: cord-293852-r72c6584 author: Greco, S. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-293852-r72c6584.txt cache: ./cache/cord-293852-r72c6584.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293852-r72c6584.txt' === file2bib.sh === id: cord-294501-1nf98mpb author: Bonafè, Massimiliano title: Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-294501-1nf98mpb.txt cache: ./cache/cord-294501-1nf98mpb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294501-1nf98mpb.txt' === file2bib.sh === id: cord-295034-em6z8mlu author: Daverey, Achlesh title: COVID-19: Eco-friendly hand hygiene for human and environmental safety date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-295034-em6z8mlu.txt cache: ./cache/cord-295034-em6z8mlu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295034-em6z8mlu.txt' === file2bib.sh === id: cord-294921-h44tct43 author: Greninger, Alexander L. title: The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-294921-h44tct43.txt cache: ./cache/cord-294921-h44tct43.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294921-h44tct43.txt' === file2bib.sh === id: cord-294999-a5x8bmfr author: Plotkin, Stanley A title: The New Coronavirus, the Current King of China date: 2020-02-21 pages: extension: .txt txt: ./txt/cord-294999-a5x8bmfr.txt cache: ./cache/cord-294999-a5x8bmfr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294999-a5x8bmfr.txt' === file2bib.sh === id: cord-294427-6eiligyy author: Salimi, Ali title: The North American Layman's Understanding of COVID-19: Are We Doing Enough? date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-294427-6eiligyy.txt cache: ./cache/cord-294427-6eiligyy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294427-6eiligyy.txt' === file2bib.sh === id: cord-294115-7t7kubf6 author: Miralles, Oriol title: Unmet needs, health policies, and actions during the COVID-19 pandemic: a report from six European countries date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-294115-7t7kubf6.txt cache: ./cache/cord-294115-7t7kubf6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294115-7t7kubf6.txt' === file2bib.sh === id: cord-294582-flkjekyo author: Hijikata, Atsushi title: Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-294582-flkjekyo.txt cache: ./cache/cord-294582-flkjekyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294582-flkjekyo.txt' === file2bib.sh === id: cord-294788-9usyb1nn author: Baek, Woong Kee title: A Comprehensive Review of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-294788-9usyb1nn.txt cache: ./cache/cord-294788-9usyb1nn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294788-9usyb1nn.txt' === file2bib.sh === id: cord-294912-xl0wzi16 author: Alteri, Claudia title: Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-294912-xl0wzi16.txt cache: ./cache/cord-294912-xl0wzi16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294912-xl0wzi16.txt' === file2bib.sh === id: cord-294136-e69ao8j0 author: Han, Dongsheng title: COVID-19: Insight into the asymptomatic SARS-COV-2 infection and transmission date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-294136-e69ao8j0.txt cache: ./cache/cord-294136-e69ao8j0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294136-e69ao8j0.txt' === file2bib.sh === id: cord-295545-ruxz77i8 author: Hennighausen, Lothar title: Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-295545-ruxz77i8.txt cache: ./cache/cord-295545-ruxz77i8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295545-ruxz77i8.txt' === file2bib.sh === id: cord-295142-5sqkdpi8 author: Han, Y. title: The active lung microbiota landscape of COVID-19 patients date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-295142-5sqkdpi8.txt cache: ./cache/cord-295142-5sqkdpi8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295142-5sqkdpi8.txt' === file2bib.sh === id: cord-294789-07hto8qn author: Schoch-Spana, Monica title: The public’s role in COVID-19 vaccination: human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-294789-07hto8qn.txt cache: ./cache/cord-294789-07hto8qn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294789-07hto8qn.txt' === file2bib.sh === id: cord-295548-o877eog6 author: Antonio, G.E title: Imaging in Severe Acute Respiratory Syndrome (SARS) date: 2003-10-21 pages: extension: .txt txt: ./txt/cord-295548-o877eog6.txt cache: ./cache/cord-295548-o877eog6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295548-o877eog6.txt' === file2bib.sh === id: cord-294931-a77g9rjo author: Zhang, Linqi title: Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals date: 2005-11-18 pages: extension: .txt txt: ./txt/cord-294931-a77g9rjo.txt cache: ./cache/cord-294931-a77g9rjo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294931-a77g9rjo.txt' === file2bib.sh === id: cord-295075-cqbayzat author: Rajnarayanan, Rajendram V. title: “Teaching old drugs to kill new bugs”: structure-based discovery of anti-SARS drugs date: 2004-08-20 pages: extension: .txt txt: ./txt/cord-295075-cqbayzat.txt cache: ./cache/cord-295075-cqbayzat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295075-cqbayzat.txt' === file2bib.sh === id: cord-294910-gnc04ax1 author: Nogueira, Paulo Jorge title: The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-294910-gnc04ax1.txt cache: ./cache/cord-294910-gnc04ax1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294910-gnc04ax1.txt' === file2bib.sh === id: cord-294349-ps3qlho2 author: Al-Sharif, Eman title: Ocular tropism of coronavirus (CoVs): a comparison of the interaction between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-294349-ps3qlho2.txt cache: ./cache/cord-294349-ps3qlho2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294349-ps3qlho2.txt' === file2bib.sh === id: cord-295130-e7j7kac0 author: Moreno-Contreras, Joaquín title: Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-295130-e7j7kac0.txt cache: ./cache/cord-295130-e7j7kac0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295130-e7j7kac0.txt' === file2bib.sh === id: cord-295800-w0dup04b author: So, Loletta K-Y title: Development of a standard treatment protocol for severe acute respiratory syndrome date: 2003-05-10 pages: extension: .txt txt: ./txt/cord-295800-w0dup04b.txt cache: ./cache/cord-295800-w0dup04b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295800-w0dup04b.txt' === file2bib.sh === id: cord-295864-kwdvais7 author: Flahault, Antoine title: Has China faced only a herald wave of SARS-CoV-2? date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-295864-kwdvais7.txt cache: ./cache/cord-295864-kwdvais7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295864-kwdvais7.txt' === file2bib.sh === id: cord-295121-4xemmaqt author: Ferreira, Eliane de Oliveira title: Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-295121-4xemmaqt.txt cache: ./cache/cord-295121-4xemmaqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295121-4xemmaqt.txt' === file2bib.sh === id: cord-295257-iguhy1z8 author: Calcagnile, Matteo title: ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-295257-iguhy1z8.txt cache: ./cache/cord-295257-iguhy1z8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295257-iguhy1z8.txt' === file2bib.sh === id: cord-295051-upyar7en author: Ahmadian, Elham title: Covid‐19 and kidney injury: Pathophysiology and molecular mechanisms date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-295051-upyar7en.txt cache: ./cache/cord-295051-upyar7en.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295051-upyar7en.txt' === file2bib.sh === id: cord-294856-eeh2a0t8 author: Lambert, Paul-Henri title: Consensus Summary Report for CEPI/BC March 12-13, 2020 Meeting: Assessment of Risk of Disease Enhancement with COVID-19 Vaccines date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-294856-eeh2a0t8.txt cache: ./cache/cord-294856-eeh2a0t8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294856-eeh2a0t8.txt' === file2bib.sh === id: cord-294933-oc2glu4a author: Cinesi Gómez, César title: Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-294933-oc2glu4a.txt cache: ./cache/cord-294933-oc2glu4a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294933-oc2glu4a.txt' === file2bib.sh === id: cord-294363-bv6xa8v8 author: Zhou, Hong title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-294363-bv6xa8v8.txt cache: ./cache/cord-294363-bv6xa8v8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294363-bv6xa8v8.txt' === file2bib.sh === id: cord-295375-nakxfhxk author: Yu, Yang title: Assessment of the quality of systematic reviews on COVID‐19: A comparative study of previous coronavirus outbreaks date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-295375-nakxfhxk.txt cache: ./cache/cord-295375-nakxfhxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295375-nakxfhxk.txt' === file2bib.sh === id: cord-295733-f3rt1fyk author: Ge, Tianxiang title: Evaluation of disinfection procedures in a designated hospital for COVID-19 date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-295733-f3rt1fyk.txt cache: ./cache/cord-295733-f3rt1fyk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295733-f3rt1fyk.txt' === file2bib.sh === id: cord-295973-41jqgsv0 author: Singh, Awadhesh Kumar title: Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-295973-41jqgsv0.txt cache: ./cache/cord-295973-41jqgsv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295973-41jqgsv0.txt' === file2bib.sh === id: cord-294527-fct2y5vn author: Guadarrama-Ortiz, Parménides title: Neurological Aspects of SARS-CoV-2 Infection: Mechanisms and Manifestations date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-294527-fct2y5vn.txt cache: ./cache/cord-294527-fct2y5vn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294527-fct2y5vn.txt' === file2bib.sh === id: cord-295525-emrwcx0m author: To, Kelvin Kai-Wang title: Consistent Detection of 2019 Novel Coronavirus in Saliva date: 2020-02-12 pages: extension: .txt txt: ./txt/cord-295525-emrwcx0m.txt cache: ./cache/cord-295525-emrwcx0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295525-emrwcx0m.txt' === file2bib.sh === id: cord-294441-nehorqhi author: O’Brien, Stephen J. title: Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS date: 2006-08-31 pages: extension: .txt txt: ./txt/cord-294441-nehorqhi.txt cache: ./cache/cord-294441-nehorqhi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294441-nehorqhi.txt' === file2bib.sh === id: cord-295274-gzkfy70s author: Mecham, Jeffrey C. title: Utility of Tracheostomy in Patients With COVID‐19 and Other Special Considerations date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-295274-gzkfy70s.txt cache: ./cache/cord-295274-gzkfy70s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295274-gzkfy70s.txt' === file2bib.sh === id: cord-294831-pem059zk author: Zhang, Ling-Pu title: Focus on a 2019-novel coronavirus (SARS-CoV-2) date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-294831-pem059zk.txt cache: ./cache/cord-294831-pem059zk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294831-pem059zk.txt' === file2bib.sh === id: cord-296020-kje1wiah author: Patoulias, Dimitrios title: Diabetes mellitus and SARS-CoV-2-related mortality: the impact of acute hyperglycemic crises and some further considerations date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-296020-kje1wiah.txt cache: ./cache/cord-296020-kje1wiah.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296020-kje1wiah.txt' === file2bib.sh === id: cord-295041-5vpawtef author: Jakhmola, Shweta title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-295041-5vpawtef.txt cache: ./cache/cord-295041-5vpawtef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295041-5vpawtef.txt' === file2bib.sh === id: cord-296128-kjoi54ea author: Balestri, Riccardo title: Do we have serological evidences that chilblain‐like lesions are related to SARS‐CoV‐2? A review of the literature date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-296128-kjoi54ea.txt cache: ./cache/cord-296128-kjoi54ea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296128-kjoi54ea.txt' === file2bib.sh === id: cord-294429-isivkz8b author: Grifoni, Alba title: Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-294429-isivkz8b.txt cache: ./cache/cord-294429-isivkz8b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294429-isivkz8b.txt' === file2bib.sh === id: cord-295957-s17z2ccf author: Bordi, Licia title: Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-295957-s17z2ccf.txt cache: ./cache/cord-295957-s17z2ccf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295957-s17z2ccf.txt' === file2bib.sh === id: cord-295846-quhnesbr author: Li, Huan title: Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-295846-quhnesbr.txt cache: ./cache/cord-295846-quhnesbr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295846-quhnesbr.txt' === file2bib.sh === id: cord-296007-1gsgd22t author: Mohseni, Amir Hossein title: Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-296007-1gsgd22t.txt cache: ./cache/cord-296007-1gsgd22t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296007-1gsgd22t.txt' === file2bib.sh === id: cord-295508-yhdj5m0e author: Yang, Li-Tao title: Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients date: 2006-06-16 pages: extension: .txt txt: ./txt/cord-295508-yhdj5m0e.txt cache: ./cache/cord-295508-yhdj5m0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295508-yhdj5m0e.txt' === file2bib.sh === id: cord-295559-yc8q62z8 author: Qian, Zhaohui title: Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date: 2013-10-03 pages: extension: .txt txt: ./txt/cord-295559-yc8q62z8.txt cache: ./cache/cord-295559-yc8q62z8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295559-yc8q62z8.txt' === file2bib.sh === id: cord-295765-c7o2ukm6 author: Silvas, Jesus A. title: Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-295765-c7o2ukm6.txt cache: ./cache/cord-295765-c7o2ukm6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295765-c7o2ukm6.txt' === file2bib.sh === id: cord-294812-nnlzwaf1 author: Desforges, Marc title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 pages: extension: .txt txt: ./txt/cord-294812-nnlzwaf1.txt cache: ./cache/cord-294812-nnlzwaf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294812-nnlzwaf1.txt' === file2bib.sh === id: cord-296148-za3j19k5 author: Rosenzweig, Ivana title: Does damage to hypothalamic paraventricular nucleus underlie symptoms of ultradian rhythm disorder and an increased anxiety in coronavirus disease 2019? date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-296148-za3j19k5.txt cache: ./cache/cord-296148-za3j19k5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296148-za3j19k5.txt' === file2bib.sh === id: cord-295455-km0qcmlh author: Fehr, Anthony R. title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-295455-km0qcmlh.txt cache: ./cache/cord-295455-km0qcmlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295455-km0qcmlh.txt' === file2bib.sh === id: cord-295850-nb6miso7 author: Zhang, Chuan-hai title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain date: 2005-05-02 pages: extension: .txt txt: ./txt/cord-295850-nb6miso7.txt cache: ./cache/cord-295850-nb6miso7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295850-nb6miso7.txt' === file2bib.sh === id: cord-296054-s8pibdeg author: Hanson, K. E. title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-296054-s8pibdeg.txt cache: ./cache/cord-296054-s8pibdeg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296054-s8pibdeg.txt' === file2bib.sh === id: cord-296195-m2wwlvgx author: Chen, Chung-Jen title: Toona sinensis Roem tender leaf extract inhibits SARS coronavirus replication date: 2008-10-30 pages: extension: .txt txt: ./txt/cord-296195-m2wwlvgx.txt cache: ./cache/cord-296195-m2wwlvgx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296195-m2wwlvgx.txt' === file2bib.sh === id: cord-296214-xeezt6f7 author: Sabatino, Jolanda title: Women's perspective on the COVID-19 pandemic: Walking into a post-peak phase date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-296214-xeezt6f7.txt cache: ./cache/cord-296214-xeezt6f7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296214-xeezt6f7.txt' === file2bib.sh === id: cord-295603-mk9oartb author: Yu, Xiaoqi title: Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-295603-mk9oartb.txt cache: ./cache/cord-295603-mk9oartb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295603-mk9oartb.txt' === file2bib.sh === id: cord-296043-jc74soom author: Butterfield, T. R. title: Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-296043-jc74soom.txt cache: ./cache/cord-296043-jc74soom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296043-jc74soom.txt' === file2bib.sh === id: cord-296147-yfcp0xf2 author: Mairesse, Antoine title: High clinical performance and quantitative assessment of antibody kinetics using a dual recognition assay for the detection of SARS-CoV-2 IgM and IgG antibodies date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-296147-yfcp0xf2.txt cache: ./cache/cord-296147-yfcp0xf2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296147-yfcp0xf2.txt' === file2bib.sh === id: cord-296259-4kdblf4z author: Oudit, Gavin Y title: Plasma angiotensin-converting enzyme 2: novel biomarker in heart failure with implications for COVID-19 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-296259-4kdblf4z.txt cache: ./cache/cord-296259-4kdblf4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296259-4kdblf4z.txt' === file2bib.sh === id: cord-296109-kco85lqn author: Vanuytsel, Kim title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-296109-kco85lqn.txt cache: ./cache/cord-296109-kco85lqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296109-kco85lqn.txt' === file2bib.sh === id: cord-295792-hajvtzj9 author: Álvez, Fernando title: SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-295792-hajvtzj9.txt cache: ./cache/cord-295792-hajvtzj9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295792-hajvtzj9.txt' === file2bib.sh === id: cord-296031-r6iqiy1n author: Tattan-Birch, H. title: COVID-19, smoking, vaping and quitting: A representative population survey in England date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-296031-r6iqiy1n.txt cache: ./cache/cord-296031-r6iqiy1n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296031-r6iqiy1n.txt' === file2bib.sh === id: cord-295433-olmein3q author: Banerjee, Arinjay title: Bats and Coronaviruses date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-295433-olmein3q.txt cache: ./cache/cord-295433-olmein3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295433-olmein3q.txt' === file2bib.sh === id: cord-296187-nnv2e7gr author: Mulgaonkar, Nirmitee title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-296187-nnv2e7gr.txt cache: ./cache/cord-296187-nnv2e7gr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296187-nnv2e7gr.txt' === file2bib.sh === id: cord-296556-fr8x8j3i author: Chaccour, Carlos title: Ivermectin and COVID-19: Keeping Rigor in Times of Urgency date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-296556-fr8x8j3i.txt cache: ./cache/cord-296556-fr8x8j3i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296556-fr8x8j3i.txt' === file2bib.sh === id: cord-295514-vhymj0rw author: Lim, Peter A title: Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: Severe acute respiratory syndrome date: 2004-08-01 pages: extension: .txt txt: ./txt/cord-295514-vhymj0rw.txt cache: ./cache/cord-295514-vhymj0rw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295514-vhymj0rw.txt' === file2bib.sh === id: cord-296095-onereai5 author: Vardhan, Seshu title: In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-296095-onereai5.txt cache: ./cache/cord-296095-onereai5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296095-onereai5.txt' === file2bib.sh === id: cord-295946-p9enjxiq author: Hattori, Shin-ichiro title: GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-295946-p9enjxiq.txt cache: ./cache/cord-295946-p9enjxiq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295946-p9enjxiq.txt' === file2bib.sh === id: cord-296271-85io9yvy author: Chong, Woon H. title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-296271-85io9yvy.txt cache: ./cache/cord-296271-85io9yvy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296271-85io9yvy.txt' === file2bib.sh === id: cord-296356-qkvafy69 author: Garman, Elspeth title: SARS Proteomics Reveals Viral Secrets date: 2005-11-30 pages: extension: .txt txt: ./txt/cord-296356-qkvafy69.txt cache: ./cache/cord-296356-qkvafy69.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296356-qkvafy69.txt' === file2bib.sh === id: cord-296339-23yi8so0 author: Mok, Wendy title: Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens date: 2007-09-26 pages: extension: .txt txt: ./txt/cord-296339-23yi8so0.txt cache: ./cache/cord-296339-23yi8so0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296339-23yi8so0.txt' === file2bib.sh === id: cord-296619-uhhndp0a author: Kondo, Yuki title: Coinfection with SARS-CoV-2 and influenza A virus date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-296619-uhhndp0a.txt cache: ./cache/cord-296619-uhhndp0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296619-uhhndp0a.txt' === file2bib.sh === id: cord-295830-1sbnewog author: Kim, Sung-Jae title: A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-295830-1sbnewog.txt cache: ./cache/cord-295830-1sbnewog.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295830-1sbnewog.txt' === file2bib.sh === id: cord-296483-x95lwwnm author: Kranke, Peter title: Geburtshilfliche Anästhesie während der SARS-CoV-2-Pandemie: Übersicht der Handlungsempfehlungen date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-296483-x95lwwnm.txt cache: ./cache/cord-296483-x95lwwnm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296483-x95lwwnm.txt' === file2bib.sh === id: cord-296268-kb7fgfaq author: Mendonça, Luiza title: SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-296268-kb7fgfaq.txt cache: ./cache/cord-296268-kb7fgfaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296268-kb7fgfaq.txt' === file2bib.sh === id: cord-296551-efqt3tw2 author: Fukushi, Shuetsu title: Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry Mediated by SARS Coronavirus Spike Proteins date: 2007-11-28 pages: extension: .txt txt: ./txt/cord-296551-efqt3tw2.txt cache: ./cache/cord-296551-efqt3tw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296551-efqt3tw2.txt' === file2bib.sh === id: cord-296917-yk574m99 author: Kumar, Sathish title: Aerosol‐mediated transmission of SARS‐Cov‐2 or COVID‐19 in the cardiac surgical operating room date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-296917-yk574m99.txt cache: ./cache/cord-296917-yk574m99.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296917-yk574m99.txt' === file2bib.sh === id: cord-296390-jv86w4j9 author: Shao, Chen title: Evolution of SARS-Co-2 RNA test results in a fatal Covid-19 patient: a case report date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-296390-jv86w4j9.txt cache: ./cache/cord-296390-jv86w4j9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296390-jv86w4j9.txt' === file2bib.sh === id: cord-296362-9vi8xwu7 author: Wang, Jian-Min title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function date: 2008-09-12 pages: extension: .txt txt: ./txt/cord-296362-9vi8xwu7.txt cache: ./cache/cord-296362-9vi8xwu7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296362-9vi8xwu7.txt' === file2bib.sh === id: cord-296517-414grqif author: Wong, Gary title: MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease date: 2015-10-14 pages: extension: .txt txt: ./txt/cord-296517-414grqif.txt cache: ./cache/cord-296517-414grqif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296517-414grqif.txt' === file2bib.sh === id: cord-296375-gf0mgz5x author: Zhang, Xi title: Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-296375-gf0mgz5x.txt cache: ./cache/cord-296375-gf0mgz5x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296375-gf0mgz5x.txt' === file2bib.sh === id: cord-296762-sc6crkkw author: Ali, Fedaa title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-296762-sc6crkkw.txt cache: ./cache/cord-296762-sc6crkkw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296762-sc6crkkw.txt' === file2bib.sh === id: cord-296492-knofua00 author: Qiu, L. title: Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-296492-knofua00.txt cache: ./cache/cord-296492-knofua00.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296492-knofua00.txt' === file2bib.sh === id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-294108-uvnh0s9r.txt cache: ./cache/cord-294108-uvnh0s9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294108-uvnh0s9r.txt' === file2bib.sh === id: cord-296579-oa67njov author: d’Ettorre, Gabriella title: Analysis of type I IFN response and T cell activation in severe COVID-19/HIV-1 coinfection: A case report date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-296579-oa67njov.txt cache: ./cache/cord-296579-oa67njov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296579-oa67njov.txt' === file2bib.sh === id: cord-295794-glcg36si author: Seghers, Victor J. title: After the initial COVID-19 surge: a phased radiology departmental re-opening plan date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-295794-glcg36si.txt cache: ./cache/cord-295794-glcg36si.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295794-glcg36si.txt' === file2bib.sh === id: cord-296331-i4hyzqcv author: Adapa, Sreedhar title: COVID-19 Pandemic Causing Acute Kidney Injury and Impact on Patients With Chronic Kidney Disease and Renal Transplantation date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-296331-i4hyzqcv.txt cache: ./cache/cord-296331-i4hyzqcv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296331-i4hyzqcv.txt' === file2bib.sh === id: cord-296392-2u9mz6d3 author: Sarıgül, Figen title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-296392-2u9mz6d3.txt cache: ./cache/cord-296392-2u9mz6d3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296392-2u9mz6d3.txt' === file2bib.sh === id: cord-295523-5pv7kw6i author: Picchianti Diamanti, Andrea title: Cytokine Release Syndrome in COVID-19 Patients, A New Scenario for an Old Concern: The Fragile Balance between Infections and Autoimmunity date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-295523-5pv7kw6i.txt cache: ./cache/cord-295523-5pv7kw6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295523-5pv7kw6i.txt' === file2bib.sh === id: cord-296767-mgr32ftl author: Große, Karsten title: SARS‐CoV‐2 as an extrahepatic precipitator of acute‐on‐chronic liver failure date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-296767-mgr32ftl.txt cache: ./cache/cord-296767-mgr32ftl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296767-mgr32ftl.txt' === file2bib.sh === id: cord-297202-oup8ptya author: Beer, Martin title: SARS‐CoV‐2 vaccination—A plea for fast and coordinated action date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-297202-oup8ptya.txt cache: ./cache/cord-297202-oup8ptya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297202-oup8ptya.txt' === file2bib.sh === id: cord-296227-dm1wkpnv author: Liao, L. title: Can N95 respirators be reused after disinfection? And for how many times? date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-296227-dm1wkpnv.txt cache: ./cache/cord-296227-dm1wkpnv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296227-dm1wkpnv.txt' === file2bib.sh === id: cord-296237-i9cti2ok author: Díez, José-María title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-296237-i9cti2ok.txt cache: ./cache/cord-296237-i9cti2ok.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296237-i9cti2ok.txt' === file2bib.sh === id: cord-296950-9dldbs6o author: El-Zein, Rayan S title: COVID-19-associated meningoencephalitis treated with intravenous immunoglobulin date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-296950-9dldbs6o.txt cache: ./cache/cord-296950-9dldbs6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296950-9dldbs6o.txt' === file2bib.sh === id: cord-297023-0qlo0mun author: Park, Sung‐Soo title: Mass screening of healthcare personnel for SARS-CoV-2 in the northern emirates date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-297023-0qlo0mun.txt cache: ./cache/cord-297023-0qlo0mun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297023-0qlo0mun.txt' === file2bib.sh === id: cord-296388-ayfdsn07 author: Maziarz, Mariusz title: Agent‐based modelling for SARS‐CoV‐2 epidemic prediction and intervention assessment: A methodological appraisal date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-296388-ayfdsn07.txt cache: ./cache/cord-296388-ayfdsn07.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296388-ayfdsn07.txt' === file2bib.sh === id: cord-296219-zzg9hds0 author: Battaglini, Denise title: Neurological Manifestations of Severe SARS-CoV-2 Infection: Potential Mechanisms and Implications of Individualized Mechanical Ventilation Settings date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-296219-zzg9hds0.txt cache: ./cache/cord-296219-zzg9hds0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296219-zzg9hds0.txt' === file2bib.sh === id: cord-296426-upwsdgso author: Virmani, Sarthak title: Identifying a Kidney Transplant Recipient COVID Phenotype to Aid Test Utilization in the Setting of Limited Testing Availability - Does One Exist? date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-296426-upwsdgso.txt cache: ./cache/cord-296426-upwsdgso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296426-upwsdgso.txt' === file2bib.sh === id: cord-297217-pe6mehjv author: Simpson, A. Hamish R. W. title: COVID-19: potential transmission through aerosols in surgical procedures and blood products date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-297217-pe6mehjv.txt cache: ./cache/cord-297217-pe6mehjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297217-pe6mehjv.txt' === file2bib.sh === id: cord-296657-mymndjvd author: Higuchi, Yusuke title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-296657-mymndjvd.txt cache: ./cache/cord-296657-mymndjvd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296657-mymndjvd.txt' === file2bib.sh === id: cord-296250-7ln7p715 author: Wang, Sheng-Fan title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-296250-7ln7p715.txt cache: ./cache/cord-296250-7ln7p715.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296250-7ln7p715.txt' === file2bib.sh === id: cord-297197-klr208kp author: Weizman, Yehuda title: Use of Wearable Technology to Enhance Response to the COVID-19 Pandemic date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-297197-klr208kp.txt cache: ./cache/cord-297197-klr208kp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297197-klr208kp.txt' === file2bib.sh === id: cord-296306-xcomjvaa author: Rivett, Lucy title: Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-296306-xcomjvaa.txt cache: ./cache/cord-296306-xcomjvaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296306-xcomjvaa.txt' === file2bib.sh === id: cord-297208-f4ob3ox6 author: Pisano, Antonio title: Cardiothoracic surgery at the time of COVID-19 pandemic: lessons from the East (and from a previous epidemic) for western battlefields date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-297208-f4ob3ox6.txt cache: ./cache/cord-297208-f4ob3ox6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297208-f4ob3ox6.txt' === file2bib.sh === id: cord-295431-p9iy7uaf author: Atangana, Ernestine title: Facemasks simple but powerful weapons to protect against COVID-19 spread: Can they have sides effects? date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-295431-p9iy7uaf.txt cache: ./cache/cord-295431-p9iy7uaf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295431-p9iy7uaf.txt' === file2bib.sh === id: cord-296440-18vpg419 author: Beurnier, Antoine title: Characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who require hospitalisation date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-296440-18vpg419.txt cache: ./cache/cord-296440-18vpg419.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296440-18vpg419.txt' === file2bib.sh === id: cord-296605-p67twx7a author: LAU, Arthur Chun-Wing title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date: 2004-03-10 pages: extension: .txt txt: ./txt/cord-296605-p67twx7a.txt cache: ./cache/cord-296605-p67twx7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296605-p67twx7a.txt' === file2bib.sh === id: cord-296649-h6oyjz56 author: Scherf-Clavel, Oliver title: Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-296649-h6oyjz56.txt cache: ./cache/cord-296649-h6oyjz56.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296649-h6oyjz56.txt' === file2bib.sh === id: cord-296319-fwn97wds author: Juno, J. A. title: Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-296319-fwn97wds.txt cache: ./cache/cord-296319-fwn97wds.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296319-fwn97wds.txt' === file2bib.sh === id: cord-296676-2anl2agl author: Goldberg, Michael F. title: Neuroradiologic manifestations of COVID-19: what the emergency radiologist needs to know date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-296676-2anl2agl.txt cache: ./cache/cord-296676-2anl2agl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296676-2anl2agl.txt' === file2bib.sh === id: cord-296602-19noki6p author: Law, Helen KW title: Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells date: 2009-06-08 pages: extension: .txt txt: ./txt/cord-296602-19noki6p.txt cache: ./cache/cord-296602-19noki6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296602-19noki6p.txt' === file2bib.sh === id: cord-297256-i9468t8v author: Cesari, Matteo title: Geriatric Medicine in Italy in the Time of Covid-19 date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-297256-i9468t8v.txt cache: ./cache/cord-297256-i9468t8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297256-i9468t8v.txt' === file2bib.sh === id: cord-294700-pb5k21da author: Dulek, Daniel E title: Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute COVID-19 in Pediatric Patients date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-294700-pb5k21da.txt cache: ./cache/cord-294700-pb5k21da.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294700-pb5k21da.txt' === file2bib.sh === id: cord-295144-tyyc81uc author: Stradner, Martin H. title: Rheumatic Musculoskeletal Diseases and COVID-19 A Review of the First 6 Months of the Pandemic date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-295144-tyyc81uc.txt cache: ./cache/cord-295144-tyyc81uc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295144-tyyc81uc.txt' === file2bib.sh === id: cord-297630-eabtzfd0 author: Manganaro, Marco title: First considerations on the SARS-CoV-2 epidemic in the Dialysis Units of Piedmont and Aosta Valley, Northern Italy date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-297630-eabtzfd0.txt cache: ./cache/cord-297630-eabtzfd0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297630-eabtzfd0.txt' === file2bib.sh === id: cord-296494-6kn4mr04 author: Saban-Ruiz, J. title: COVID-19: A Personalized Cardiometabolic Approach for Reducing Complications and Costs. The Role of Aging Beyond Topics date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-296494-6kn4mr04.txt cache: ./cache/cord-296494-6kn4mr04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296494-6kn4mr04.txt' === file2bib.sh === id: cord-296981-tded20ih author: Gilmore, Kerry title: In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-296981-tded20ih.txt cache: ./cache/cord-296981-tded20ih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296981-tded20ih.txt' === file2bib.sh === id: cord-297381-1upz6dsy author: Sánchez‐Duque, Jorge A. title: Are we now observing an increasing number of coinfections between SARS‐CoV‐2 and other respiratory pathogens? date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-297381-1upz6dsy.txt cache: ./cache/cord-297381-1upz6dsy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297381-1upz6dsy.txt' === file2bib.sh === id: cord-297439-xg0pkjrh author: Gao, Jing title: The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-297439-xg0pkjrh.txt cache: ./cache/cord-297439-xg0pkjrh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297439-xg0pkjrh.txt' === file2bib.sh === id: cord-297432-2edncbgn author: Helleberg, Marie title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-297432-2edncbgn.txt cache: ./cache/cord-297432-2edncbgn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297432-2edncbgn.txt' === file2bib.sh === id: cord-296986-8fuj072z author: Kumar, Manish title: A chronicle of SARS-CoV-2: Part-I - Epidemiology, diagnosis, prognosis, transmission and treatment date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-296986-8fuj072z.txt cache: ./cache/cord-296986-8fuj072z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296986-8fuj072z.txt' === file2bib.sh === id: cord-296692-t5p09le8 author: Elgin, T.G. title: The changing landscape of SARS-CoV-2: Implications for the maternal-infant dyad date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-296692-t5p09le8.txt cache: ./cache/cord-296692-t5p09le8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296692-t5p09le8.txt' === file2bib.sh === id: cord-294800-akr4f5p8 author: Kabir, Md. Tanvir title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-294800-akr4f5p8.txt cache: ./cache/cord-294800-akr4f5p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294800-akr4f5p8.txt' === file2bib.sh === id: cord-297365-11es4w0u author: Peng, Hui title: Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-297365-11es4w0u.txt cache: ./cache/cord-297365-11es4w0u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297365-11es4w0u.txt' === file2bib.sh === id: cord-296977-yzhsdz9c author: Soares, R. R. G. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-296977-yzhsdz9c.txt cache: ./cache/cord-296977-yzhsdz9c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296977-yzhsdz9c.txt' === file2bib.sh === id: cord-297423-iefq0fh0 author: Bushman, Dena title: Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-297423-iefq0fh0.txt cache: ./cache/cord-297423-iefq0fh0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297423-iefq0fh0.txt' === file2bib.sh === id: cord-297463-mmmwi8de author: Hsu, You-Ren title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors date: 2013-03-15 pages: extension: .txt txt: ./txt/cord-297463-mmmwi8de.txt cache: ./cache/cord-297463-mmmwi8de.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297463-mmmwi8de.txt' === file2bib.sh === id: cord-297127-nhgm09db author: Hasseli, Rebecca title: National registry for patients with inflammatory rheumatic diseases (IRD) infected with SARS-CoV-2 in Germany (ReCoVery): a valuable mean to gain rapid and reliable knowledge of the clinical course of SARS-CoV-2 infections in patients with IRD date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-297127-nhgm09db.txt cache: ./cache/cord-297127-nhgm09db.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297127-nhgm09db.txt' === file2bib.sh === id: cord-296672-i267t23m author: Wang, Shui-Mei title: Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain date: 2008-07-01 pages: extension: .txt txt: ./txt/cord-296672-i267t23m.txt cache: ./cache/cord-296672-i267t23m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296672-i267t23m.txt' === file2bib.sh === id: cord-296232-6zj99nuw author: Talukdar, Jayanta title: Potential of natural astaxanthin in alleviating the risk of cytokine storm in COVID-19 date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-296232-6zj99nuw.txt cache: ./cache/cord-296232-6zj99nuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296232-6zj99nuw.txt' === file2bib.sh === id: cord-297178-moxhk2e0 author: Novaes Rocha, Vinicius title: Viral replication of SARS-CoV-2 could be self-limitative - the role of the renin-angiotensin system on COVID-19 pathophysiology date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-297178-moxhk2e0.txt cache: ./cache/cord-297178-moxhk2e0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297178-moxhk2e0.txt' === file2bib.sh === id: cord-297168-t6zf5k99 author: Brüssow, Harald title: The Novel Coronavirus – A Snapshot of Current Knowledge date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-297168-t6zf5k99.txt cache: ./cache/cord-297168-t6zf5k99.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297168-t6zf5k99.txt' === file2bib.sh === id: cord-296881-2g81sjnl author: Nabil, Ahmed title: Current coronavirus (SARS-CoV-2) epidemiological, diagnostic and therapeutic approaches: An updated review until June 2020 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-296881-2g81sjnl.txt cache: ./cache/cord-296881-2g81sjnl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296881-2g81sjnl.txt' === file2bib.sh === id: cord-297072-f5lmstyn author: Struck, Anna-Winona title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 date: 2012-01-16 pages: extension: .txt txt: ./txt/cord-297072-f5lmstyn.txt cache: ./cache/cord-297072-f5lmstyn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297072-f5lmstyn.txt' === file2bib.sh === id: cord-297826-2nruf2g7 author: Tian, Jing-Hui title: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-297826-2nruf2g7.txt cache: ./cache/cord-297826-2nruf2g7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-297826-2nruf2g7.txt' === file2bib.sh === id: cord-297326-n0fpu8s3 author: ÁLVAREZ, E. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 pages: extension: .txt txt: ./txt/cord-297326-n0fpu8s3.txt cache: ./cache/cord-297326-n0fpu8s3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297326-n0fpu8s3.txt' === file2bib.sh === id: cord-297451-p5rlquym author: Luz María Trujillo, G title: Relación Entre Covid-19 Y Síndrome De Guillain-Barre En Adultos.Revisión Sistemática date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-297451-p5rlquym.txt cache: ./cache/cord-297451-p5rlquym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297451-p5rlquym.txt' === file2bib.sh === id: cord-297652-ut6e1ysz author: Vanden Eynde, Jean Jacques title: COVID-19: A Brief Overview of the Discovery Clinical Trial date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-297652-ut6e1ysz.txt cache: ./cache/cord-297652-ut6e1ysz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297652-ut6e1ysz.txt' === file2bib.sh === id: cord-297418-36j840wm author: Carneiro Leão, Jair title: Coronaviridae ‐ old friends, new enemy! date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-297418-36j840wm.txt cache: ./cache/cord-297418-36j840wm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297418-36j840wm.txt' === file2bib.sh === id: cord-297324-me5ff1pb author: Zeng, Rong title: Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date: 2004-07-30 pages: extension: .txt txt: ./txt/cord-297324-me5ff1pb.txt cache: ./cache/cord-297324-me5ff1pb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297324-me5ff1pb.txt' === file2bib.sh === id: cord-297832-picpuzvo author: Salazar, Rafael title: Decreased Mortality in Patients With Severe Bronchospasm Associated With SARS-CoV-2: An Alternative to Invasive Mechanical Ventilation date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-297832-picpuzvo.txt cache: ./cache/cord-297832-picpuzvo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297832-picpuzvo.txt' === file2bib.sh === id: cord-297641-bgmib6xb author: Meng, Xiujuan title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-297641-bgmib6xb.txt cache: ./cache/cord-297641-bgmib6xb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297641-bgmib6xb.txt' === file2bib.sh === id: cord-297918-840thddt author: Yilmaz, Umut title: COVID-19: neurologische Manifestationen: Was wir bisher wissen date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-297918-840thddt.txt cache: ./cache/cord-297918-840thddt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297918-840thddt.txt' === file2bib.sh === id: cord-296997-ba7f2mf3 author: Sikora, Mateusz title: Map of SARS-CoV-2 spike epitopes not shielded by glycans date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-296997-ba7f2mf3.txt cache: ./cache/cord-296997-ba7f2mf3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-296997-ba7f2mf3.txt' === file2bib.sh === id: cord-297470-lx3xwg92 author: Pan, Yunbao title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-297470-lx3xwg92.txt cache: ./cache/cord-297470-lx3xwg92.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297470-lx3xwg92.txt' === file2bib.sh === id: cord-297323-l3f12hg4 author: Amor, Sandra title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-297323-l3f12hg4.txt cache: ./cache/cord-297323-l3f12hg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297323-l3f12hg4.txt' === file2bib.sh === id: cord-297708-uocs65sl author: Alders, N. title: COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-297708-uocs65sl.txt cache: ./cache/cord-297708-uocs65sl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297708-uocs65sl.txt' === file2bib.sh === id: cord-297786-jz1d1m2e author: Hasan, Md. Mahbub title: Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-297786-jz1d1m2e.txt cache: ./cache/cord-297786-jz1d1m2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297786-jz1d1m2e.txt' === file2bib.sh === id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-296588-q2716lda.txt cache: ./cache/cord-296588-q2716lda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296588-q2716lda.txt' === file2bib.sh === id: cord-297671-3d3gcn6k author: Venn, April M.R. title: A case series of pediatric croup with COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-297671-3d3gcn6k.txt cache: ./cache/cord-297671-3d3gcn6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297671-3d3gcn6k.txt' === file2bib.sh === id: cord-297878-c4cq92x8 author: Ali, Mohammed title: ST-Elevation Myocardial Infarction in a 27-Year-Old Male With COVID-19 date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-297878-c4cq92x8.txt cache: ./cache/cord-297878-c4cq92x8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297878-c4cq92x8.txt' === file2bib.sh === id: cord-297132-lhfa9fl5 author: Aghagoli, Ghazal title: Neurological Involvement in COVID-19 and Potential Mechanisms: A Review date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-297132-lhfa9fl5.txt cache: ./cache/cord-297132-lhfa9fl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297132-lhfa9fl5.txt' === file2bib.sh === id: cord-297684-9q3oopaz author: Dobaño, Carlota title: Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-297684-9q3oopaz.txt cache: ./cache/cord-297684-9q3oopaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297684-9q3oopaz.txt' === file2bib.sh === id: cord-296661-6ndn2qxc author: Lu, Dingnan title: Primary concentration – The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-296661-6ndn2qxc.txt cache: ./cache/cord-296661-6ndn2qxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296661-6ndn2qxc.txt' === file2bib.sh === id: cord-297327-19dfgfz6 author: Drożdżal, Sylwester title: COVID-19: Pain Management in Patients with SARS-CoV-2 Infection—Molecular Mechanisms, Challenges, and Perspectives date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-297327-19dfgfz6.txt cache: ./cache/cord-297327-19dfgfz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297327-19dfgfz6.txt' === file2bib.sh === id: cord-297842-hkr1wm3k author: Tilley, Kimberly title: A Cross-Sectional Study Examining the Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in a University Student Population date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-297842-hkr1wm3k.txt cache: ./cache/cord-297842-hkr1wm3k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297842-hkr1wm3k.txt' === file2bib.sh === id: cord-297942-6wdwrttn author: Li, Taisheng title: Diagnosis and clinical management of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection: an operational recommendation of Peking Union Medical College Hospital (V2.0): Working Group of 2019 Novel Coronavirus, Peking Union Medical College Hospital date: 2020-03-14 pages: extension: .txt txt: ./txt/cord-297942-6wdwrttn.txt cache: ./cache/cord-297942-6wdwrttn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297942-6wdwrttn.txt' === file2bib.sh === id: cord-297693-lqyc49t6 author: Samec, Matthew J title: 80-year-old man with dyspnoea and bilateral groundglass infiltrates: an elusive case of COVID-19 date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-297693-lqyc49t6.txt cache: ./cache/cord-297693-lqyc49t6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297693-lqyc49t6.txt' === file2bib.sh === id: cord-296378-ki93iltt author: Smith, Joan C. title: Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-296378-ki93iltt.txt cache: ./cache/cord-296378-ki93iltt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296378-ki93iltt.txt' === file2bib.sh === id: cord-298056-svwtfshi author: Fabio, Ciceri title: Early predictors of clinical outcomes of COVID-19 outbreak in Milan, Italy date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-298056-svwtfshi.txt cache: ./cache/cord-298056-svwtfshi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298056-svwtfshi.txt' === file2bib.sh === id: cord-297702-vxcj25sn author: Chen, Yuxin title: A comprehensive, longitudinal analysis of humoral responses specific to four recombinant antigens of SARS-CoV-2 in severe and non-severe COVID-19 patients date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-297702-vxcj25sn.txt cache: ./cache/cord-297702-vxcj25sn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297702-vxcj25sn.txt' === file2bib.sh === id: cord-297209-84gs67bn author: Livanos, A. E. title: Gastrointestinal involvement attenuates COVID-19 severity and mortality date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-297209-84gs67bn.txt cache: ./cache/cord-297209-84gs67bn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297209-84gs67bn.txt' === file2bib.sh === id: cord-297787-t9neub6d author: Fu, Ziyang title: Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-297787-t9neub6d.txt cache: ./cache/cord-297787-t9neub6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297787-t9neub6d.txt' === file2bib.sh === id: cord-297691-w4cdfwv0 author: Nikaeen, Ghazal title: Application of nanomaterials in treatment, anti-infection and detection of coronaviruses date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-297691-w4cdfwv0.txt cache: ./cache/cord-297691-w4cdfwv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297691-w4cdfwv0.txt' === file2bib.sh === id: cord-298216-iq7fenxm author: Jiang, Chao title: Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-298216-iq7fenxm.txt cache: ./cache/cord-298216-iq7fenxm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298216-iq7fenxm.txt' === file2bib.sh === id: cord-297599-y4lu8m4k author: Luo, Hua title: Anti-COVID-19 drug screening: Frontier concepts and core technologies date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-297599-y4lu8m4k.txt cache: ./cache/cord-297599-y4lu8m4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297599-y4lu8m4k.txt' === file2bib.sh === id: cord-298321-8871aifz author: Laamarti, Meriem title: Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-298321-8871aifz.txt cache: ./cache/cord-298321-8871aifz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298321-8871aifz.txt' === file2bib.sh === id: cord-297775-ug4ovsws author: Hosie, Margaret J title: Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-297775-ug4ovsws.txt cache: ./cache/cord-297775-ug4ovsws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297775-ug4ovsws.txt' === file2bib.sh === id: cord-297989-4grwa4ab author: Li, Yunjin title: Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2 date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-297989-4grwa4ab.txt cache: ./cache/cord-297989-4grwa4ab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297989-4grwa4ab.txt' === file2bib.sh === id: cord-297681-m0cckidw author: Na, Joo-Young title: [Secondary Publication] Standard Operating Procedure for Post-mortem Inspection in a Focus on Coronavirus Disease-19: the Korean Society for Legal Medicine date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-297681-m0cckidw.txt cache: ./cache/cord-297681-m0cckidw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297681-m0cckidw.txt' === file2bib.sh === id: cord-297747-kifqgskc author: Lupala, Cecylia S. title: Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-297747-kifqgskc.txt cache: ./cache/cord-297747-kifqgskc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297747-kifqgskc.txt' === file2bib.sh === id: cord-298079-hgdyxk98 author: Hsu, Jeffrey J. title: Heart Transplantation in the Early Phase of the COVID‐19 Pandemic: A Single‐Center Case Series date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-298079-hgdyxk98.txt cache: ./cache/cord-298079-hgdyxk98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298079-hgdyxk98.txt' === file2bib.sh === id: cord-298075-lzuxlzb0 author: Mao, Kang title: Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology? date: 2020-03-23 pages: extension: .txt txt: ./txt/cord-298075-lzuxlzb0.txt cache: ./cache/cord-298075-lzuxlzb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298075-lzuxlzb0.txt' === file2bib.sh === id: cord-297859-p57pl45i author: Mahlke, Lutz title: Chirurgie in der SARS-CoV-2-Pandemie: Empfehlungen zum operativen Vorgehen date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-297859-p57pl45i.txt cache: ./cache/cord-297859-p57pl45i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297859-p57pl45i.txt' === file2bib.sh === id: cord-297974-sduz0j35 author: Bokelmann, L. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-297974-sduz0j35.txt cache: ./cache/cord-297974-sduz0j35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297974-sduz0j35.txt' === file2bib.sh === id: cord-297884-a6yrtuwf author: Burke, R. M. title: Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-297884-a6yrtuwf.txt cache: ./cache/cord-297884-a6yrtuwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297884-a6yrtuwf.txt' === file2bib.sh === id: cord-298693-x25r0gtt author: Advani, Sonali D. title: Are we forgetting the “universal” in universal masking? Current challenges and future solutions date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-298693-x25r0gtt.txt cache: ./cache/cord-298693-x25r0gtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298693-x25r0gtt.txt' === file2bib.sh === id: cord-298327-j04nyg5y author: Lv, Zhihua title: Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-298327-j04nyg5y.txt cache: ./cache/cord-298327-j04nyg5y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298327-j04nyg5y.txt' === file2bib.sh === id: cord-298725-da71febn author: Okuhama, Ayako title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan date: 2020-11-17 pages: extension: .txt txt: ./txt/cord-298725-da71febn.txt cache: ./cache/cord-298725-da71febn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298725-da71febn.txt' === file2bib.sh === id: cord-297941-7yut9vt4 author: Haq, M. title: Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-297941-7yut9vt4.txt cache: ./cache/cord-297941-7yut9vt4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297941-7yut9vt4.txt' === file2bib.sh === id: cord-298343-nvuc1j7t author: Ma, J. title: Exhaled breath is a significant source of SARS-CoV-2 emission date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-298343-nvuc1j7t.txt cache: ./cache/cord-298343-nvuc1j7t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298343-nvuc1j7t.txt' === file2bib.sh === id: cord-298242-iuskpoug author: Yu, Alvin title: A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-298242-iuskpoug.txt cache: ./cache/cord-298242-iuskpoug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-298242-iuskpoug.txt' === file2bib.sh === id: cord-298722-rmibv5z7 author: Abdel-latif, Rania G title: Statin therapy and SAR-COV-2: an available and potential therapy? date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-298722-rmibv5z7.txt cache: ./cache/cord-298722-rmibv5z7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298722-rmibv5z7.txt' === file2bib.sh === id: cord-298406-7wfdwou8 author: Sun, Haifang title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-298406-7wfdwou8.txt cache: ./cache/cord-298406-7wfdwou8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298406-7wfdwou8.txt' === file2bib.sh === id: cord-297236-wnuvofwr author: Zhang, Si title: SARS-CoV-2 binds platelet ACE2 to enhance thrombosis in COVID-19 date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-297236-wnuvofwr.txt cache: ./cache/cord-297236-wnuvofwr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297236-wnuvofwr.txt' === file2bib.sh === id: cord-298639-v9yg80jw author: Chen, Yuxin title: High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-298639-v9yg80jw.txt cache: ./cache/cord-298639-v9yg80jw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298639-v9yg80jw.txt' === file2bib.sh === id: cord-298850-tgxfki7n author: Figuero-Pérez, Luis title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-298850-tgxfki7n.txt cache: ./cache/cord-298850-tgxfki7n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298850-tgxfki7n.txt' === file2bib.sh === id: cord-298482-r7lallv0 author: De Maio, Flavio title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-298482-r7lallv0.txt cache: ./cache/cord-298482-r7lallv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298482-r7lallv0.txt' === file2bib.sh === id: cord-298679-w0yp4u19 author: Iftimie, Simona title: Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-298679-w0yp4u19.txt cache: ./cache/cord-298679-w0yp4u19.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298679-w0yp4u19.txt' === file2bib.sh === id: cord-298083-4h3tg6hg author: Ho, Tin-Yun title: Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein date: 2004-01-23 pages: extension: .txt txt: ./txt/cord-298083-4h3tg6hg.txt cache: ./cache/cord-298083-4h3tg6hg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298083-4h3tg6hg.txt' === file2bib.sh === id: cord-298440-0pb8ssj2 author: Rascón-Ramírez, Fernando J title: Supra and infratentorial massive strokes in previously healthy young patients with SARS-CoV-2. The role of neurosurgery date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-298440-0pb8ssj2.txt cache: ./cache/cord-298440-0pb8ssj2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298440-0pb8ssj2.txt' === file2bib.sh === id: cord-297800-hnx213kp author: Bi, Qifang title: Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-297800-hnx213kp.txt cache: ./cache/cord-297800-hnx213kp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297800-hnx213kp.txt' === file2bib.sh === id: cord-299354-rmjohbse author: Chen, Fu-Lun title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-299354-rmjohbse.txt cache: ./cache/cord-299354-rmjohbse.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-299354-rmjohbse.txt' === file2bib.sh === id: cord-298696-rsifxvtj author: Lim, Meng-Kin title: Global response to pandemic flu: more research needed on a critical front date: 2006-10-13 pages: extension: .txt txt: ./txt/cord-298696-rsifxvtj.txt cache: ./cache/cord-298696-rsifxvtj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298696-rsifxvtj.txt' === file2bib.sh === id: cord-298902-afek8kgr author: Li, Xingguang title: Transmission dynamics and evolutionary history of 2019‐nCoV date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-298902-afek8kgr.txt cache: ./cache/cord-298902-afek8kgr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298902-afek8kgr.txt' === file2bib.sh === id: cord-298172-iyxyennq author: Guo, Youjia title: Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-298172-iyxyennq.txt cache: ./cache/cord-298172-iyxyennq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298172-iyxyennq.txt' === file2bib.sh === id: cord-298281-wkje5jyt author: Chan, Vinson Wai-Shun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-298281-wkje5jyt.txt cache: ./cache/cord-298281-wkje5jyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298281-wkje5jyt.txt' === file2bib.sh === id: cord-298866-dzatps7b author: Licskai, Christopher title: Key highlights from the Canadian Thoracic Society’s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-298866-dzatps7b.txt cache: ./cache/cord-298866-dzatps7b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298866-dzatps7b.txt' === file2bib.sh === id: cord-297879-6xb25uhx author: Moncunill, G. title: SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-297879-6xb25uhx.txt cache: ./cache/cord-297879-6xb25uhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297879-6xb25uhx.txt' === file2bib.sh === id: cord-298886-xidaim04 author: Leszczyński, Piotr title: COVID-19: a short message to rheumatologists date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-298886-xidaim04.txt cache: ./cache/cord-298886-xidaim04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298886-xidaim04.txt' === file2bib.sh === id: cord-298098-4dfqlebp author: Xu, Ruodan title: Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-298098-4dfqlebp.txt cache: ./cache/cord-298098-4dfqlebp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298098-4dfqlebp.txt' === file2bib.sh === id: cord-299024-jkqdzt87 author: Mangner, Norman title: Paraneoplastic syndrome and SARS-CoV-2 – incremental effect of two thrombogenic conditions? date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-299024-jkqdzt87.txt cache: ./cache/cord-299024-jkqdzt87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299024-jkqdzt87.txt' === file2bib.sh === id: cord-297870-m7n43k4p author: Azevedo, Rafael Bellotti title: Covid-19 and the cardiovascular system: a comprehensive review date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-297870-m7n43k4p.txt cache: ./cache/cord-297870-m7n43k4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297870-m7n43k4p.txt' === file2bib.sh === id: cord-299432-lbv69du4 author: Franklin, Alan B. title: Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-299432-lbv69du4.txt cache: ./cache/cord-299432-lbv69du4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299432-lbv69du4.txt' === file2bib.sh === id: cord-298067-awo3smgp author: Li, Huanjie title: Transmission Routes Analysis of SARS-CoV-2: A Systematic Review and Case Report date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-298067-awo3smgp.txt cache: ./cache/cord-298067-awo3smgp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298067-awo3smgp.txt' === file2bib.sh === id: cord-298669-g2up0cfi author: Pollock, David D title: Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-298669-g2up0cfi.txt cache: ./cache/cord-298669-g2up0cfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298669-g2up0cfi.txt' === file2bib.sh === id: cord-297332-rzf0cw1x author: Wang, Qidi title: Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates date: 2016-04-11 pages: extension: .txt txt: ./txt/cord-297332-rzf0cw1x.txt cache: ./cache/cord-297332-rzf0cw1x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297332-rzf0cw1x.txt' === file2bib.sh === id: cord-298773-vnmc6nqd author: Pfeiffer, Julie K. title: Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? date: 2015-01-20 pages: extension: .txt txt: ./txt/cord-298773-vnmc6nqd.txt cache: ./cache/cord-298773-vnmc6nqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298773-vnmc6nqd.txt' === file2bib.sh === id: cord-299443-nggl87u6 author: Stockman, Lauren J. title: Coronavirus Antibodies in Bat Biologists date: 2008-06-17 pages: extension: .txt txt: ./txt/cord-299443-nggl87u6.txt cache: ./cache/cord-299443-nggl87u6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299443-nggl87u6.txt' === file2bib.sh === id: cord-298989-qk0k2lmz author: , Umesh title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-298989-qk0k2lmz.txt cache: ./cache/cord-298989-qk0k2lmz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298989-qk0k2lmz.txt' === file2bib.sh === id: cord-298967-vjyh1xvh author: Bertossi, Dario title: Safety guidelines for non‐surgical facial procedures during covid‐19 outbreak date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-298967-vjyh1xvh.txt cache: ./cache/cord-298967-vjyh1xvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298967-vjyh1xvh.txt' === file2bib.sh === id: cord-298991-5qae0ege author: Aiello, Francesco title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-298991-5qae0ege.txt cache: ./cache/cord-298991-5qae0ege.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298991-5qae0ege.txt' === file2bib.sh === id: cord-298777-hit7rs6q author: Zhang, Linjie title: What we know so far about Coronavirus Disease 2019 in children: A meta‐analysis of 551 laboratory‐confirmed cases date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-298777-hit7rs6q.txt cache: ./cache/cord-298777-hit7rs6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298777-hit7rs6q.txt' === file2bib.sh === id: cord-298505-r7ihqb96 author: Górski, Andrzej title: Sepsis, Phages, and COVID-19 date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-298505-r7ihqb96.txt cache: ./cache/cord-298505-r7ihqb96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298505-r7ihqb96.txt' === file2bib.sh === id: cord-299133-09mbiqrr author: Smither, Sophie J. title: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-299133-09mbiqrr.txt cache: ./cache/cord-299133-09mbiqrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299133-09mbiqrr.txt' === file2bib.sh === id: cord-298490-p1msabl5 author: Obukhov, Alexander G. title: SARS-CoV-2 Infections and ACE2: Clinical Outcomes Linked With Increased Morbidity and Mortality in Individuals With Diabetes date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-298490-p1msabl5.txt cache: ./cache/cord-298490-p1msabl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298490-p1msabl5.txt' === file2bib.sh === id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-298036-2zurc60t.txt cache: ./cache/cord-298036-2zurc60t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298036-2zurc60t.txt' === file2bib.sh === id: cord-299422-s5evsj96 author: Abdollahi, Alireza title: The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-299422-s5evsj96.txt cache: ./cache/cord-299422-s5evsj96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299422-s5evsj96.txt' === file2bib.sh === id: cord-298716-pubhq564 author: Bryche, Bertrand title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-298716-pubhq564.txt cache: ./cache/cord-298716-pubhq564.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298716-pubhq564.txt' === file2bib.sh === id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-298441-77w86l8q.txt cache: ./cache/cord-298441-77w86l8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298441-77w86l8q.txt' === file2bib.sh === id: cord-298372-4pw1y404 author: Koch, Lionel title: Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-298372-4pw1y404.txt cache: ./cache/cord-298372-4pw1y404.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298372-4pw1y404.txt' === file2bib.sh === id: cord-299156-1dwsm3ie author: Shemer, Asaf title: Ocular involvement in coronavirus disease 2019 (COVID-19): a clinical and molecular analysis date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-299156-1dwsm3ie.txt cache: ./cache/cord-299156-1dwsm3ie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299156-1dwsm3ie.txt' === file2bib.sh === id: cord-298426-hhly45md author: Zhang, Shan-Yan title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-298426-hhly45md.txt cache: ./cache/cord-298426-hhly45md.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298426-hhly45md.txt' === file2bib.sh === id: cord-298894-t5hyfum3 author: Rifino, Nicola title: Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital, Bergamo, Italy date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-298894-t5hyfum3.txt cache: ./cache/cord-298894-t5hyfum3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298894-t5hyfum3.txt' === file2bib.sh === id: cord-298301-p1zj6jg9 author: Dey, Lopamudra title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-298301-p1zj6jg9.txt cache: ./cache/cord-298301-p1zj6jg9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298301-p1zj6jg9.txt' === file2bib.sh === id: cord-299308-gza1pwx6 author: Laxminarayan, Ramanan title: Is Gradual and Controlled Approach to Herd Protection a Valid Strategy to Curb the COVID-19 Pandemic? date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-299308-gza1pwx6.txt cache: ./cache/cord-299308-gza1pwx6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299308-gza1pwx6.txt' === file2bib.sh === id: cord-299148-uge5uodk author: Wang, Qiang title: A Method To Prevent SARS-CoV-2 IgM False Positives in Gold Immunochromatography and Enzyme-Linked Immunosorbent Assays date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-299148-uge5uodk.txt cache: ./cache/cord-299148-uge5uodk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299148-uge5uodk.txt' === file2bib.sh === id: cord-298227-av1ev8ta author: Kähler, Christian J. title: Fundamental protective mechanisms of face masks against droplet infections date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-298227-av1ev8ta.txt cache: ./cache/cord-298227-av1ev8ta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298227-av1ev8ta.txt' === file2bib.sh === id: cord-299105-3ivzmiqn author: Cheng, Yi‐Qiang title: Deciphering the Biosynthetic Codes for the Potent Anti‐SARS‐CoV Cyclodepsipeptide Valinomycin in Streptomyces tsusimaensis ATCC 15141 date: 2006-03-01 pages: extension: .txt txt: ./txt/cord-299105-3ivzmiqn.txt cache: ./cache/cord-299105-3ivzmiqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299105-3ivzmiqn.txt' === file2bib.sh === id: cord-299520-2khjhows author: Dalla Volta, Alberto title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-299520-2khjhows.txt cache: ./cache/cord-299520-2khjhows.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299520-2khjhows.txt' === file2bib.sh === id: cord-299082-s8bm40vy author: Wang, Yueying title: Cardiac arrhythmias in patients with COVID‐19 date: 2020-07-26 pages: extension: .txt txt: ./txt/cord-299082-s8bm40vy.txt cache: ./cache/cord-299082-s8bm40vy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299082-s8bm40vy.txt' === file2bib.sh === id: cord-299552-rgrm8dil author: Bianchi, Martina title: Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-299552-rgrm8dil.txt cache: ./cache/cord-299552-rgrm8dil.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299552-rgrm8dil.txt' === file2bib.sh === id: cord-299449-226dd23u author: Bernhardt, Denise title: Neuro-oncology Management During the COVID-19 Pandemic With a Focus on WHO Grade III and IV Gliomas date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-299449-226dd23u.txt cache: ./cache/cord-299449-226dd23u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299449-226dd23u.txt' === file2bib.sh === id: cord-298350-pq1dcz3a author: Ryan, Jeffrey R. title: Category C Diseases and Agents date: 2016-03-25 pages: extension: .txt txt: ./txt/cord-298350-pq1dcz3a.txt cache: ./cache/cord-298350-pq1dcz3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298350-pq1dcz3a.txt' === file2bib.sh === id: cord-298461-tyhtdawb author: Zhao, L. title: COVID-19: Effects of weather conditions on the propagation of respiratory droplets date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-298461-tyhtdawb.txt cache: ./cache/cord-298461-tyhtdawb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298461-tyhtdawb.txt' === file2bib.sh === id: cord-299853-pvugij9l author: Patil, Uday P. title: Newborns of COVID-19 mothers: short-term outcomes of colocating and breastfeeding from the pandemic’s epicenter date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-299853-pvugij9l.txt cache: ./cache/cord-299853-pvugij9l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299853-pvugij9l.txt' === file2bib.sh === id: cord-299472-pmqqemku author: Yang, Naibin title: In-flight Transmission Cluster of COVID-19: A Retrospective Case Series date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-299472-pmqqemku.txt cache: ./cache/cord-299472-pmqqemku.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299472-pmqqemku.txt' === file2bib.sh === id: cord-299810-e57pwgnx author: Martelloni, Gabriele title: Modelling the downhill of the Sars-Cov-2 in Italy and a universal forecast of the epidemic in the world date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-299810-e57pwgnx.txt cache: ./cache/cord-299810-e57pwgnx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299810-e57pwgnx.txt' === file2bib.sh === id: cord-299544-r3cqvf0c author: de Souza, T. H. title: Clinical Manifestations of Children with COVID-19: a Systematic Review date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-299544-r3cqvf0c.txt cache: ./cache/cord-299544-r3cqvf0c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299544-r3cqvf0c.txt' === file2bib.sh === id: cord-300024-169g2ih5 author: Flemming, S. title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-300024-169g2ih5.txt cache: ./cache/cord-300024-169g2ih5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300024-169g2ih5.txt' === file2bib.sh === id: cord-299122-djfj4262 author: Yu, Hua title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date: 2007-03-15 pages: extension: .txt txt: ./txt/cord-299122-djfj4262.txt cache: ./cache/cord-299122-djfj4262.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299122-djfj4262.txt' === file2bib.sh === id: cord-298899-lkrmg5qr author: Xie, Yewei title: Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-298899-lkrmg5qr.txt cache: ./cache/cord-298899-lkrmg5qr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298899-lkrmg5qr.txt' === file2bib.sh === id: cord-300018-3uzau7if author: Mak, Gannon C.K. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-300018-3uzau7if.txt cache: ./cache/cord-300018-3uzau7if.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300018-3uzau7if.txt' === file2bib.sh === id: cord-299333-qu0bmov5 author: Reddy, Gireesh B. title: Clinical Characteristics and Multisystem Imaging Findings of COVID-19: An Overview for Orthopedic Surgeons date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-299333-qu0bmov5.txt cache: ./cache/cord-299333-qu0bmov5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299333-qu0bmov5.txt' === file2bib.sh === id: cord-299711-m5gb03is author: Udrea, Ana-Maria title: Laser irradiated phenothiazines: New potential treatment for COVID-19 explored by molecular docking date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-299711-m5gb03is.txt cache: ./cache/cord-299711-m5gb03is.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299711-m5gb03is.txt' === file2bib.sh === id: cord-299940-nvlcwcz8 author: Rastrelli, Giulia title: Low testosterone levels predict clinical adverse outcomes in SARS‐CoV‐2 pneumonia patients date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-299940-nvlcwcz8.txt cache: ./cache/cord-299940-nvlcwcz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299940-nvlcwcz8.txt' === file2bib.sh === id: cord-299781-9d5g5xaw author: Hrusak, Ondrej title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-299781-9d5g5xaw.txt cache: ./cache/cord-299781-9d5g5xaw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299781-9d5g5xaw.txt' === file2bib.sh === id: cord-299679-6z9e5gi6 author: Rello, Jordi title: Clinical phenotypes of SARS-CoV-2: implications for clinicians and researchers date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-299679-6z9e5gi6.txt cache: ./cache/cord-299679-6z9e5gi6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299679-6z9e5gi6.txt' === file2bib.sh === id: cord-299470-sqqer16k author: Chappell, J. G. title: Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-299470-sqqer16k.txt cache: ./cache/cord-299470-sqqer16k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299470-sqqer16k.txt' === file2bib.sh === id: cord-299999-jra1yu6a author: Tattar, R. title: COVID PDPs date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-299999-jra1yu6a.txt cache: ./cache/cord-299999-jra1yu6a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299999-jra1yu6a.txt' === file2bib.sh === id: cord-298920-1lc2xf7u author: Bello-Perez, Melissa title: Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-298920-1lc2xf7u.txt cache: ./cache/cord-298920-1lc2xf7u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298920-1lc2xf7u.txt' === file2bib.sh === id: cord-300041-1d9xu4ts author: Chen, Sharon C-A title: Focus on SARS-CoV-2 and COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-300041-1d9xu4ts.txt cache: ./cache/cord-300041-1d9xu4ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300041-1d9xu4ts.txt' === file2bib.sh === id: cord-299491-8rfm0jxh author: Xiao, Shenglan title: Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date: 2017-07-20 pages: extension: .txt txt: ./txt/cord-299491-8rfm0jxh.txt cache: ./cache/cord-299491-8rfm0jxh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299491-8rfm0jxh.txt' === file2bib.sh === id: cord-299480-mehwd0dk author: Liu, Zheng-Xue title: Identification of single-chain antibody fragments specific against SARS-associated coronavirus from phage-displayed antibody library date: 2005-04-08 pages: extension: .txt txt: ./txt/cord-299480-mehwd0dk.txt cache: ./cache/cord-299480-mehwd0dk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299480-mehwd0dk.txt' === file2bib.sh === id: cord-298734-h286m32c author: Xia, Siyu title: Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-298734-h286m32c.txt cache: ./cache/cord-298734-h286m32c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298734-h286m32c.txt' === file2bib.sh === id: cord-299989-p59u6qa0 author: Zhang, Lei title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-299989-p59u6qa0.txt cache: ./cache/cord-299989-p59u6qa0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299989-p59u6qa0.txt' === file2bib.sh === id: cord-299560-np6nfvf2 author: Hendaus, Mohamed A. title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-299560-np6nfvf2.txt cache: ./cache/cord-299560-np6nfvf2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299560-np6nfvf2.txt' === file2bib.sh === id: cord-299093-zp07aqpm author: Harrison, Andrew G. title: Mechanisms of SARS-CoV-2 transmission and pathogenesis date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-299093-zp07aqpm.txt cache: ./cache/cord-299093-zp07aqpm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299093-zp07aqpm.txt' === file2bib.sh === id: cord-300046-orlga9qf author: Gomes da Silva, J. title: Health literacy of inland population in the mitigation phase 3.2. of COVID-19's pandemic in Portugal - a descriptive cohort study date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-300046-orlga9qf.txt cache: ./cache/cord-300046-orlga9qf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300046-orlga9qf.txt' === file2bib.sh === id: cord-299346-f13xly6q author: Awad, Mohamed E. title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-299346-f13xly6q.txt cache: ./cache/cord-299346-f13xly6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299346-f13xly6q.txt' === file2bib.sh === id: cord-300174-5pt9jmyz author: Deng, Wei title: Therapeutic efficacy of Pudilan Xiaoyan Oral Liquid (PDL) for COVID-19 in vitro and in vivo date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-300174-5pt9jmyz.txt cache: ./cache/cord-300174-5pt9jmyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-300174-5pt9jmyz.txt' === file2bib.sh === id: cord-300138-1s87msv2 author: Jang, Youngeun title: Olfactory and taste disorder: The first and only sign in a patient with SARS-CoV-2 pneumonia date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-300138-1s87msv2.txt cache: ./cache/cord-300138-1s87msv2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300138-1s87msv2.txt' === file2bib.sh === id: cord-298156-d0pb1kik author: Cheval, Sorin title: Observed and Potential Impacts of the COVID-19 Pandemic on the Environment date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-298156-d0pb1kik.txt cache: ./cache/cord-298156-d0pb1kik.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298156-d0pb1kik.txt' === file2bib.sh === id: cord-300300-jqi4ylrx author: Lin, Ray Junhao title: From SARS to COVID‐19: the Singapore journey date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-300300-jqi4ylrx.txt cache: ./cache/cord-300300-jqi4ylrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300300-jqi4ylrx.txt' === file2bib.sh === id: cord-300156-ags07bc5 author: Zhou, Yunyun title: Ocular Findings and Proportion with Conjunctival SARS-COV-2 in COVID-19 Patients date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-300156-ags07bc5.txt cache: ./cache/cord-300156-ags07bc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300156-ags07bc5.txt' === file2bib.sh === id: cord-300191-vpc7p0d6 author: Bektaş, Osman title: The relationship between severe acute respiratory syndrome coronavirus 2 (SARS - COV - 2) pandemic and fragmented QRS date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-300191-vpc7p0d6.txt cache: ./cache/cord-300191-vpc7p0d6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300191-vpc7p0d6.txt' === file2bib.sh === id: cord-299565-shlhreve author: Sweileh, Waleed M. title: Global research trends of World Health Organization’s top eight emerging pathogens date: 2017-02-08 pages: extension: .txt txt: ./txt/cord-299565-shlhreve.txt cache: ./cache/cord-299565-shlhreve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299565-shlhreve.txt' === file2bib.sh === id: cord-299783-8ti6r0eh author: Bruni, M. title: Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-299783-8ti6r0eh.txt cache: ./cache/cord-299783-8ti6r0eh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299783-8ti6r0eh.txt' === file2bib.sh === id: cord-300322-koqm5yxq author: Li, Fang title: Interactions Between Sars Coronavirus and its Receptor date: 2006 pages: extension: .txt txt: ./txt/cord-300322-koqm5yxq.txt cache: ./cache/cord-300322-koqm5yxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300322-koqm5yxq.txt' === file2bib.sh === id: cord-299899-is815pol author: He, Jingjing title: Proportion of asymptomatic coronavirus disease 2019 (COVID‐19): a systematic review and meta‐analysis date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-299899-is815pol.txt cache: ./cache/cord-299899-is815pol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299899-is815pol.txt' === file2bib.sh === id: cord-300604-xx2d1s41 author: Li, Juyi title: Association between ABO blood groups and risk of SARS‐CoV‐2 pneumonia date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-300604-xx2d1s41.txt cache: ./cache/cord-300604-xx2d1s41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300604-xx2d1s41.txt' === file2bib.sh === id: cord-300149-djclli8n author: Ruan, Yijun title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection date: 2003-05-24 pages: extension: .txt txt: ./txt/cord-300149-djclli8n.txt cache: ./cache/cord-300149-djclli8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300149-djclli8n.txt' === file2bib.sh === id: cord-299835-92karhpl author: Ho, Khek Y. title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-299835-92karhpl.txt cache: ./cache/cord-299835-92karhpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299835-92karhpl.txt' === file2bib.sh === id: cord-299116-1agfnjvq author: Bunders, Madeleine title: Implications of sex differences in immunity for SARS-CoV-2 pathogenesis and design of therapeutic interventions date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-299116-1agfnjvq.txt cache: ./cache/cord-299116-1agfnjvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299116-1agfnjvq.txt' === file2bib.sh === id: cord-300395-87bl6e38 author: Behrmann, Ole title: Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-300395-87bl6e38.txt cache: ./cache/cord-300395-87bl6e38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300395-87bl6e38.txt' === file2bib.sh === id: cord-300423-q2i328sz author: Bai, Lei title: Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-300423-q2i328sz.txt cache: ./cache/cord-300423-q2i328sz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300423-q2i328sz.txt' === file2bib.sh === id: cord-300458-jeuwaj50 author: Maisch, Bernhard title: COVID-19—What we know and what we need to know: There are more questions than answers date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-300458-jeuwaj50.txt cache: ./cache/cord-300458-jeuwaj50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300458-jeuwaj50.txt' === file2bib.sh === id: cord-300117-rlpzejjt author: Coutard, B. title: The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade date: 2020-02-10 pages: extension: .txt txt: ./txt/cord-300117-rlpzejjt.txt cache: ./cache/cord-300117-rlpzejjt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300117-rlpzejjt.txt' === file2bib.sh === id: cord-299927-ixuvy2g4 author: Frontera, Jennifer title: Global Consortium Study of Neurological Dysfunction in COVID-19 (GCS-NeuroCOVID): Study Design and Rationale date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-299927-ixuvy2g4.txt cache: ./cache/cord-299927-ixuvy2g4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299927-ixuvy2g4.txt' === file2bib.sh === id: cord-299499-66qh3r75 author: Guilamo-Ramos, Vincent title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-299499-66qh3r75.txt cache: ./cache/cord-299499-66qh3r75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299499-66qh3r75.txt' === file2bib.sh === id: cord-299635-bxdf27sv author: Squire, M. M. title: Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-299635-bxdf27sv.txt cache: ./cache/cord-299635-bxdf27sv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299635-bxdf27sv.txt' === file2bib.sh === id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 pages: extension: .txt txt: ./txt/cord-300685-bcjnujlj.txt cache: ./cache/cord-300685-bcjnujlj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300685-bcjnujlj.txt' === file2bib.sh === id: cord-300697-p96i25uc author: Chen, Taojiang title: A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-300697-p96i25uc.txt cache: ./cache/cord-300697-p96i25uc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300697-p96i25uc.txt' === file2bib.sh === id: cord-299911-v95pf3eg author: El-Ghiaty, Mahmoud A. title: Cytochrome P450-mediated drug interactions in COVID-19 patients: current findings and possible mechanisms date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-299911-v95pf3eg.txt cache: ./cache/cord-299911-v95pf3eg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299911-v95pf3eg.txt' === file2bib.sh === id: cord-300324-95fty9yi author: Ni Lochlainn, M. title: Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-300324-95fty9yi.txt cache: ./cache/cord-300324-95fty9yi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300324-95fty9yi.txt' === file2bib.sh === id: cord-300466-sk9iilum author: Kong, Wen-Hua title: Serologic Response to SARS-CoV-2 in COVID-19 Patients with Different Severity date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-300466-sk9iilum.txt cache: ./cache/cord-300466-sk9iilum.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300466-sk9iilum.txt' === file2bib.sh === id: cord-300923-5cyxr98s author: Younger, David S title: Postmortem Neuropathology in Covid‐19 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-300923-5cyxr98s.txt cache: ./cache/cord-300923-5cyxr98s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300923-5cyxr98s.txt' === file2bib.sh === id: cord-301183-k39e12cq author: Pham, Tho D. title: SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-301183-k39e12cq.txt cache: ./cache/cord-301183-k39e12cq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301183-k39e12cq.txt' === file2bib.sh === id: cord-300194-nsp53lv6 author: Rath, Soumya Lipsa title: Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-300194-nsp53lv6.txt cache: ./cache/cord-300194-nsp53lv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300194-nsp53lv6.txt' === file2bib.sh === id: cord-300848-0igfcixy author: Meijers, Björn title: The clinical characteristics of coronavirus-associated nephropathy date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-300848-0igfcixy.txt cache: ./cache/cord-300848-0igfcixy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300848-0igfcixy.txt' === file2bib.sh === id: cord-300950-ag0sql4i author: Lin, John title: Potential therapeutic options for coronavirus disease 2019: using knowledge of past outbreaks to guide future treatment date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-300950-ag0sql4i.txt cache: ./cache/cord-300950-ag0sql4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300950-ag0sql4i.txt' === file2bib.sh === id: cord-300707-k9uk14b3 author: Bouwman, Kim M. title: Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-300707-k9uk14b3.txt cache: ./cache/cord-300707-k9uk14b3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300707-k9uk14b3.txt' === file2bib.sh === id: cord-300783-pvn2qq0f author: Sadykov, Mukhtar title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-300783-pvn2qq0f.txt cache: ./cache/cord-300783-pvn2qq0f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300783-pvn2qq0f.txt' === file2bib.sh === id: cord-300040-rvrp5zvv author: Dutta, Noton Kumar title: Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine date: 2008-06-15 pages: extension: .txt txt: ./txt/cord-300040-rvrp5zvv.txt cache: ./cache/cord-300040-rvrp5zvv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300040-rvrp5zvv.txt' === file2bib.sh === id: cord-300319-9k8zseao author: Cinatl Jr., J. title: Infection of cultured intestinal epithelial cells with severe acute respiratory syndrome coronavirus date: 2004 pages: extension: .txt txt: ./txt/cord-300319-9k8zseao.txt cache: ./cache/cord-300319-9k8zseao.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300319-9k8zseao.txt' === file2bib.sh === id: cord-301106-qskwujpa author: Gambato, Martina title: Clinical implications of COVID-19 in patients with chronic liver disease and liver tumor date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-301106-qskwujpa.txt cache: ./cache/cord-301106-qskwujpa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301106-qskwujpa.txt' === file2bib.sh === id: cord-300850-59j1m2tm author: Peron, Jean Pierre Schatzmann title: Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE) date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-300850-59j1m2tm.txt cache: ./cache/cord-300850-59j1m2tm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300850-59j1m2tm.txt' === file2bib.sh === id: cord-298535-wmxlu3l1 author: Agnihothram, Sudhakar title: Evaluation of Serologic and Antigenic Relationships Between Middle Eastern Respiratory Syndrome Coronavirus and Other Coronaviruses to Develop Vaccine Platforms for the Rapid Response to Emerging Coronaviruses date: 2013-11-18 pages: extension: .txt txt: ./txt/cord-298535-wmxlu3l1.txt cache: ./cache/cord-298535-wmxlu3l1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298535-wmxlu3l1.txt' === file2bib.sh === id: cord-300063-5jemq8nm author: Rane, Jitendra Subhash title: Targeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-300063-5jemq8nm.txt cache: ./cache/cord-300063-5jemq8nm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300063-5jemq8nm.txt' === file2bib.sh === id: cord-301151-f6vya3qh author: Zhu, Xiaojuan title: Co-infection with respiratory pathogens among COVID-2019 cases date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-301151-f6vya3qh.txt cache: ./cache/cord-301151-f6vya3qh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301151-f6vya3qh.txt' === file2bib.sh === id: cord-300272-95o8yd7h author: Thépaut, Michel title: DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-300272-95o8yd7h.txt cache: ./cache/cord-300272-95o8yd7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300272-95o8yd7h.txt' === file2bib.sh === id: cord-300078-svu06v9c author: Haghani, Milad title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-300078-svu06v9c.txt cache: ./cache/cord-300078-svu06v9c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300078-svu06v9c.txt' === file2bib.sh === id: cord-300532-4d6fnjt8 author: Wang, Jiao title: Disinfection technology of hospital wastes and wastewater: Suggestions for disinfection strategy during coronavirus Disease 2019 (COVID-19) pandemic in China date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-300532-4d6fnjt8.txt cache: ./cache/cord-300532-4d6fnjt8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300532-4d6fnjt8.txt' === file2bib.sh === id: cord-301079-n1nytr6k author: Tan, Li title: Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-301079-n1nytr6k.txt cache: ./cache/cord-301079-n1nytr6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301079-n1nytr6k.txt' === file2bib.sh === id: cord-301080-xr7kl573 author: Sakanashi, Daisuke title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-301080-xr7kl573.txt cache: ./cache/cord-301080-xr7kl573.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301080-xr7kl573.txt' === file2bib.sh === id: cord-300696-alpztpzw author: Dilek, Tugce Damla title: THE IMPACT OF SARS-COV 2 ON THE ANXIETY LEVELS OF SUBJECTS AND ON THE ANXIETY AND DEPRESSION LEVELS OF THEIR PARENTS date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-300696-alpztpzw.txt cache: ./cache/cord-300696-alpztpzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300696-alpztpzw.txt' === file2bib.sh === id: cord-300784-4jeaqqn9 author: Ma, Huan title: COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-300784-4jeaqqn9.txt cache: ./cache/cord-300784-4jeaqqn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300784-4jeaqqn9.txt' === file2bib.sh === id: cord-300627-7x4me5lx author: Ng, W. F. title: The placentas of patients with severe acute respiratory syndrome: a pathophysiological evaluation date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-300627-7x4me5lx.txt cache: ./cache/cord-300627-7x4me5lx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300627-7x4me5lx.txt' === file2bib.sh === id: cord-301324-2tyl1r2l author: Zhan, Jing title: Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-301324-2tyl1r2l.txt cache: ./cache/cord-301324-2tyl1r2l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301324-2tyl1r2l.txt' === file2bib.sh === id: cord-301167-101lnq4f author: Liu, Quanjun title: Microarray-in-a-Tube for Detection of Multiple Viruses date: 2007-02-01 pages: extension: .txt txt: ./txt/cord-301167-101lnq4f.txt cache: ./cache/cord-301167-101lnq4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301167-101lnq4f.txt' === file2bib.sh === id: cord-300608-eju7wnb9 author: Sheervalilou, Roghayeh title: COVID‐19 under spotlight: A close look at the origin, transmission, diagnosis, and treatment of the 2019‐nCoV disease date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-300608-eju7wnb9.txt cache: ./cache/cord-300608-eju7wnb9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300608-eju7wnb9.txt' === file2bib.sh === id: cord-300320-07tdrd4w author: Siordia, Juan A. title: Systematic and Statistical Review of Coronavirus Disease 19 Treatment Trials date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-300320-07tdrd4w.txt cache: ./cache/cord-300320-07tdrd4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300320-07tdrd4w.txt' === file2bib.sh === id: cord-300774-5mrkmctl author: Hernández-Mora, Miguel Górgolas title: Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-300774-5mrkmctl.txt cache: ./cache/cord-300774-5mrkmctl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300774-5mrkmctl.txt' === file2bib.sh === id: cord-301216-a0rkpez7 author: Perez, Adriana title: Presentation of SARS-CoV-2 Infection As Cholestatic Jaundice in Two Healthy Adolescents date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-301216-a0rkpez7.txt cache: ./cache/cord-301216-a0rkpez7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301216-a0rkpez7.txt' === file2bib.sh === id: cord-300640-9pvhaz8q author: Parackova, Zuzana title: Disharmonic Inflammatory Signatures in COVID-19: Augmented Neutrophils’ but Impaired Monocytes’ and Dendritic Cells’ Responsiveness date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-300640-9pvhaz8q.txt cache: ./cache/cord-300640-9pvhaz8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300640-9pvhaz8q.txt' === file2bib.sh === id: cord-300978-busx8w6s author: Apetrii, Mugurel title: A brand-new cardiorenal syndrome in the Coronavirus Disease- 2019 (COVID-19) setting date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-300978-busx8w6s.txt cache: ./cache/cord-300978-busx8w6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300978-busx8w6s.txt' === file2bib.sh === id: cord-300866-cso6l6ze author: Bao, Yi title: Clinical Features of COVID-19 in a Young Man with Massive Cerebral Hemorrhage—Case Report date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-300866-cso6l6ze.txt cache: ./cache/cord-300866-cso6l6ze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300866-cso6l6ze.txt' === file2bib.sh === id: cord-301025-cf2jcw6x author: Musca, Serban C. title: A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine's Prophylactic Effect Against Infection With SARS-CoV-2 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-301025-cf2jcw6x.txt cache: ./cache/cord-301025-cf2jcw6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301025-cf2jcw6x.txt' === file2bib.sh === id: cord-300445-qzu4gz2d author: Zhang, Xiao-lei title: Pharmacological and cardiovascular perspectives on the treatment of COVID-19 with chloroquine derivatives date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-300445-qzu4gz2d.txt cache: ./cache/cord-300445-qzu4gz2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300445-qzu4gz2d.txt' === file2bib.sh === id: cord-301026-spgidqh3 author: Das, Shaoli title: In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-301026-spgidqh3.txt cache: ./cache/cord-301026-spgidqh3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301026-spgidqh3.txt' === file2bib.sh === id: cord-300847-ycuiso0g author: Li, Wei title: Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-300847-ycuiso0g.txt cache: ./cache/cord-300847-ycuiso0g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300847-ycuiso0g.txt' === file2bib.sh === id: cord-301484-y9l2hmqf author: MASSAROTTI, Claudia title: Asymptomatic SARS‐CoV‐2 infections in pregnant patients in an Italian city during complete lockdown date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-301484-y9l2hmqf.txt cache: ./cache/cord-301484-y9l2hmqf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301484-y9l2hmqf.txt' === file2bib.sh === id: cord-300964-knc0ruou author: Hoffman, Tove title: Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-300964-knc0ruou.txt cache: ./cache/cord-300964-knc0ruou.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300964-knc0ruou.txt' === file2bib.sh === id: cord-300625-fvirvpyl author: Srinivasan, Suhas title: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-300625-fvirvpyl.txt cache: ./cache/cord-300625-fvirvpyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300625-fvirvpyl.txt' === file2bib.sh === id: cord-301303-44sk478e author: Wu, Vin-Cent title: Renal hypouricemia is an ominous sign in patients with severe acute respiratory syndrome date: 2008-02-21 pages: extension: .txt txt: ./txt/cord-301303-44sk478e.txt cache: ./cache/cord-301303-44sk478e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301303-44sk478e.txt' === file2bib.sh === id: cord-301251-6f2nzvhz author: Cheemarla, N. R. title: Host response-based screening to identify undiagnosed cases of COVID-19and expand testing capacity date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-301251-6f2nzvhz.txt cache: ./cache/cord-301251-6f2nzvhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301251-6f2nzvhz.txt' === file2bib.sh === id: cord-300793-tuq8z6gm author: Weiss, Robin A title: Social and environmental risk factors in the emergence of infectious diseases date: 2004 pages: extension: .txt txt: ./txt/cord-300793-tuq8z6gm.txt cache: ./cache/cord-300793-tuq8z6gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300793-tuq8z6gm.txt' === file2bib.sh === id: cord-301226-hmc2wmst author: Randazzo, Walter title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-301226-hmc2wmst.txt cache: ./cache/cord-301226-hmc2wmst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301226-hmc2wmst.txt' === file2bib.sh === id: cord-300968-dtaasxk1 author: Kliger, Yossef title: From genome to antivirals: SARS as a test tube date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-300968-dtaasxk1.txt cache: ./cache/cord-300968-dtaasxk1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300968-dtaasxk1.txt' === file2bib.sh === id: cord-301454-ayf42grs author: Phyu Khin, Phyu title: A potential therapeutic combination for treatment of COVID-19: synergistic effect of DPP4 and RAAS suppression date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-301454-ayf42grs.txt cache: ./cache/cord-301454-ayf42grs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301454-ayf42grs.txt' === file2bib.sh === id: cord-300899-yi2mx91a author: Kaur, Satinder title: Understanding COVID-19 transmission, health impacts and mitigation: timely social distancing is the key date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-300899-yi2mx91a.txt cache: ./cache/cord-300899-yi2mx91a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300899-yi2mx91a.txt' === file2bib.sh === id: cord-301638-2f8r37ns author: Bonney, Glenn Kunnath title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-301638-2f8r37ns.txt cache: ./cache/cord-301638-2f8r37ns.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301638-2f8r37ns.txt' === file2bib.sh === id: cord-301292-yaii6e16 author: Kuk, Anthony Y. C. title: The estimation of SARS incubation distribution from serial interval data using a convolution likelihood date: 2005-07-12 pages: extension: .txt txt: ./txt/cord-301292-yaii6e16.txt cache: ./cache/cord-301292-yaii6e16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301292-yaii6e16.txt' === file2bib.sh === id: cord-300791-417tzufc author: Austin, Zubin title: Pharmacy practice in times of civil crisis: The experience of SARS and “the blackout” in Ontario, Canada date: 2007-10-16 pages: extension: .txt txt: ./txt/cord-300791-417tzufc.txt cache: ./cache/cord-300791-417tzufc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300791-417tzufc.txt' === file2bib.sh === id: cord-301313-9595vm0k author: OKBA, NISREEN M.A. title: SARS-CoV-2 specific antibody responses in COVID-19 patients date: 2020-03-20 pages: extension: .txt txt: ./txt/cord-301313-9595vm0k.txt cache: ./cache/cord-301313-9595vm0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301313-9595vm0k.txt' === file2bib.sh === id: cord-300763-3ateeei3 author: Vannabouathong, Christopher title: Novel Coronavirus COVID-19: Current Evidence and Evolving Strategies date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-300763-3ateeei3.txt cache: ./cache/cord-300763-3ateeei3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300763-3ateeei3.txt' === file2bib.sh === id: cord-302015-z2k6wuhm author: Bonardel, Claire title: Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-302015-z2k6wuhm.txt cache: ./cache/cord-302015-z2k6wuhm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302015-z2k6wuhm.txt' === file2bib.sh === id: cord-301233-nenw0f81 author: Naydenova, Katerina title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-301233-nenw0f81.txt cache: ./cache/cord-301233-nenw0f81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301233-nenw0f81.txt' === file2bib.sh === id: cord-301942-ppa7gb95 author: Neuman, Benjamin W. title: Ultrastructure of SARS-CoV, FIPV, and MHV Revealed by Electron Cryomicroscopy date: 2006 pages: extension: .txt txt: ./txt/cord-301942-ppa7gb95.txt cache: ./cache/cord-301942-ppa7gb95.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301942-ppa7gb95.txt' === file2bib.sh === id: cord-301603-gdxvbspx author: Sokouti, Massoud title: Comparative Global Epidemiological Investigation of SARS-CoV-2 and SARS-CoV Diseases Using Meta-MUMS Tool Through Incidence, Mortality, and Recovery Rates date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-301603-gdxvbspx.txt cache: ./cache/cord-301603-gdxvbspx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301603-gdxvbspx.txt' === file2bib.sh === id: cord-301590-70qmpccs author: Campos, António title: The Paradigm Shift of Ophthalmology in the COVID-19 Era date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-301590-70qmpccs.txt cache: ./cache/cord-301590-70qmpccs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301590-70qmpccs.txt' === file2bib.sh === id: cord-301978-9uu318tp author: Yin, Xiaoping title: A mild type of childhood Covid-19 - A case report date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-301978-9uu318tp.txt cache: ./cache/cord-301978-9uu318tp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301978-9uu318tp.txt' === file2bib.sh === id: cord-300963-1n1f8mf2 author: Gajendran, Mahesh title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-300963-1n1f8mf2.txt cache: ./cache/cord-300963-1n1f8mf2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300963-1n1f8mf2.txt' === file2bib.sh === id: cord-300991-ipy24zxp author: Khan, Amira Sayed title: Obesity and COVID-19: Oro-Naso-Sensory Perception date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-300991-ipy24zxp.txt cache: ./cache/cord-300991-ipy24zxp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300991-ipy24zxp.txt' === file2bib.sh === id: cord-301693-3hsu2u1k author: He, Yuwen title: Value of Viral Nucleic Acid in Sputum and Feces and Specific IgM/IgG in Serum for the Diagnosis of Coronavirus Disease 2019 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-301693-3hsu2u1k.txt cache: ./cache/cord-301693-3hsu2u1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301693-3hsu2u1k.txt' === file2bib.sh === id: cord-301388-p3juk2vv author: Yen, Muh-Yong title: Recommendations for protecting against and mitigating the COVID-19 pandemic in long-term care facilities date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-301388-p3juk2vv.txt cache: ./cache/cord-301388-p3juk2vv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301388-p3juk2vv.txt' === file2bib.sh === id: cord-302125-96w0nh9q author: Péré, Hélène title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-302125-96w0nh9q.txt cache: ./cache/cord-302125-96w0nh9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302125-96w0nh9q.txt' === file2bib.sh === id: cord-301744-rx7ywew5 author: Kelleni, Mina T. title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-301744-rx7ywew5.txt cache: ./cache/cord-301744-rx7ywew5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301744-rx7ywew5.txt' === file2bib.sh === id: cord-301641-epr1sct6 author: Kumar, Durgesh title: Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-301641-epr1sct6.txt cache: ./cache/cord-301641-epr1sct6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301641-epr1sct6.txt' === file2bib.sh === id: cord-301227-ica5x0r1 author: Sun, Yi-Sheng title: A SARS-CoV-2 variant with the 12-bp deletion at E gene date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-301227-ica5x0r1.txt cache: ./cache/cord-301227-ica5x0r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301227-ica5x0r1.txt' === file2bib.sh === id: cord-301633-t8s4s0wo author: Gralinski, Lisa E. title: Return of the Coronavirus: 2019-nCoV date: 2020-01-24 pages: extension: .txt txt: ./txt/cord-301633-t8s4s0wo.txt cache: ./cache/cord-301633-t8s4s0wo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301633-t8s4s0wo.txt' === file2bib.sh === id: cord-302075-ctd9sutv author: Tetro, Jason A. title: Is COVID-19 receiving ADE from other coronaviruses? date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-302075-ctd9sutv.txt cache: ./cache/cord-302075-ctd9sutv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302075-ctd9sutv.txt' === file2bib.sh === id: cord-301115-sedfbjlw author: Han, Mingfeng title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-301115-sedfbjlw.txt cache: ./cache/cord-301115-sedfbjlw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301115-sedfbjlw.txt' === file2bib.sh === id: cord-302147-6r67g5zk author: Kayaaslan, Bircan title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-302147-6r67g5zk.txt cache: ./cache/cord-302147-6r67g5zk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-302147-6r67g5zk.txt' === file2bib.sh === id: cord-301828-qux5hvcw author: Khalifa, Ibrahim title: Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-301828-qux5hvcw.txt cache: ./cache/cord-301828-qux5hvcw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301828-qux5hvcw.txt' === file2bib.sh === id: cord-300716-urmogf97 author: Briguglio, Matteo title: Disentangling the Hypothesis of Host Dysosmia and SARS-CoV-2: The Bait Symptom That Hides Neglected Neurophysiological Routes date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-300716-urmogf97.txt cache: ./cache/cord-300716-urmogf97.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300716-urmogf97.txt' === file2bib.sh === id: cord-301547-d4wt9dqp author: Seng, J. J. B. title: Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-301547-d4wt9dqp.txt cache: ./cache/cord-301547-d4wt9dqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301547-d4wt9dqp.txt' === file2bib.sh === id: cord-302160-4yfvspaq author: Ruetalo, Natalia title: Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-302160-4yfvspaq.txt cache: ./cache/cord-302160-4yfvspaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302160-4yfvspaq.txt' === file2bib.sh === id: cord-301556-f3m9gwvo author: Huang, Jessie title: SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-301556-f3m9gwvo.txt cache: ./cache/cord-301556-f3m9gwvo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301556-f3m9gwvo.txt' === file2bib.sh === id: cord-301535-eui41zyg author: Chandler-Brown, Devon title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-301535-eui41zyg.txt cache: ./cache/cord-301535-eui41zyg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301535-eui41zyg.txt' === file2bib.sh === id: cord-301779-y07xjnpe author: Fox, Sharon E title: Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-301779-y07xjnpe.txt cache: ./cache/cord-301779-y07xjnpe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301779-y07xjnpe.txt' === file2bib.sh === id: cord-301921-i1o18nmw author: Sernicola, Alvise title: How to Deal With Post-viral Cutaneous Eruptions in the Era of Coronavirus Infection date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-301921-i1o18nmw.txt cache: ./cache/cord-301921-i1o18nmw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301921-i1o18nmw.txt' === file2bib.sh === id: cord-301947-b6nwaost author: Millán-Oñate, José title: Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-301947-b6nwaost.txt cache: ./cache/cord-301947-b6nwaost.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301947-b6nwaost.txt' === file2bib.sh === id: cord-302146-51hof7it author: Cross, Thomas J. title: Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-302146-51hof7it.txt cache: ./cache/cord-302146-51hof7it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302146-51hof7it.txt' === file2bib.sh === id: cord-301811-ykpiorgo author: Tanaka, Takuma title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-301811-ykpiorgo.txt cache: ./cache/cord-301811-ykpiorgo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301811-ykpiorgo.txt' === file2bib.sh === id: cord-302485-hhsa76k8 author: Wu, Yuntao title: SARS-CoV-2 is an appropriate name for the new coronavirus date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-302485-hhsa76k8.txt cache: ./cache/cord-302485-hhsa76k8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302485-hhsa76k8.txt' === file2bib.sh === id: cord-302238-l8j1vy0y author: Shah, Prakesh S. title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-302238-l8j1vy0y.txt cache: ./cache/cord-302238-l8j1vy0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302238-l8j1vy0y.txt' === file2bib.sh === id: cord-301622-mn59vszt author: Jomah, Shahamah title: Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-301622-mn59vszt.txt cache: ./cache/cord-301622-mn59vszt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301622-mn59vszt.txt' === file2bib.sh === id: cord-302358-vou46eie author: Fomsgaard, Anna S title: An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-302358-vou46eie.txt cache: ./cache/cord-302358-vou46eie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302358-vou46eie.txt' === file2bib.sh === id: cord-301626-7ow1jja4 author: Li, Shih-Wen title: SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6 date: 2016-05-05 pages: extension: .txt txt: ./txt/cord-301626-7ow1jja4.txt cache: ./cache/cord-301626-7ow1jja4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301626-7ow1jja4.txt' === file2bib.sh === id: cord-301771-43fl2gwp author: Ouassou, Hayat title: The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-301771-43fl2gwp.txt cache: ./cache/cord-301771-43fl2gwp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301771-43fl2gwp.txt' === file2bib.sh === id: cord-302166-tah3jdw0 author: Zhang, Shen-Ying title: Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity? date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-302166-tah3jdw0.txt cache: ./cache/cord-302166-tah3jdw0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302166-tah3jdw0.txt' === file2bib.sh === id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-301823-fbeb1nw1.txt cache: ./cache/cord-301823-fbeb1nw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301823-fbeb1nw1.txt' === file2bib.sh === id: cord-302228-n5o6jfs2 author: Lodise, Thomas P. title: COVID‐19: Important Therapy Considerations and Approaches in this Hour of Need date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-302228-n5o6jfs2.txt cache: ./cache/cord-302228-n5o6jfs2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302228-n5o6jfs2.txt' === file2bib.sh === id: cord-302527-n53d5en0 author: Dadlani, Shashi title: SARS-CoV-2 Transmission in a Dental Practice in Spain: After the Outbreak date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-302527-n53d5en0.txt cache: ./cache/cord-302527-n53d5en0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302527-n53d5en0.txt' === file2bib.sh === id: cord-303173-q88zdf03 author: Panchaud, Alice title: An international registry for emergent pathogens and pregnancy date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-303173-q88zdf03.txt cache: ./cache/cord-303173-q88zdf03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-303173-q88zdf03.txt' === file2bib.sh === id: cord-301876-d2j9wpqk author: Kalita, Parismita title: Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2 date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-301876-d2j9wpqk.txt cache: ./cache/cord-301876-d2j9wpqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301876-d2j9wpqk.txt' === file2bib.sh === id: cord-302541-0upiu6iq author: Gupta, Abhishek title: Lockdown—the only solution to defeat COVID-19 date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-302541-0upiu6iq.txt cache: ./cache/cord-302541-0upiu6iq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302541-0upiu6iq.txt' === file2bib.sh === id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-302409-40ktyt5q.txt cache: ./cache/cord-302409-40ktyt5q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302409-40ktyt5q.txt' === file2bib.sh === id: cord-302111-kg0dmgq0 author: Darden, Dijoia B. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-302111-kg0dmgq0.txt cache: ./cache/cord-302111-kg0dmgq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302111-kg0dmgq0.txt' === file2bib.sh === id: cord-302115-r39ser2c author: Matricardi, Paolo Maria title: The first, holistic immunological model of COVID‐19: implications for prevention, diagnosis, and public health measures date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-302115-r39ser2c.txt cache: ./cache/cord-302115-r39ser2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302115-r39ser2c.txt' === file2bib.sh === id: cord-302735-zal2gr28 author: Priyanka title: Aerosol transmission of SARS-CoV-2: The unresolved paradox date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-302735-zal2gr28.txt cache: ./cache/cord-302735-zal2gr28.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302735-zal2gr28.txt' === file2bib.sh === id: cord-301157-tu3iig9o author: Felsenstein, Susanna title: Presentation, Treatment Response and Short-Term Outcomes in Paediatric Multisystem Inflammatory Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS) date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-301157-tu3iig9o.txt cache: ./cache/cord-301157-tu3iig9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301157-tu3iig9o.txt' === file2bib.sh === id: cord-303022-9hqoq7tf author: Madapusi Balaji, Thodur title: Oral cancer and periodontal disease increase the risk of COVID 19? A mechanism mediated through furin and cathepsin overexpression date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-303022-9hqoq7tf.txt cache: ./cache/cord-303022-9hqoq7tf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303022-9hqoq7tf.txt' === file2bib.sh === id: cord-302584-fwdpzv85 author: Zhu, Ying title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date: 2005-01-01 pages: extension: .txt txt: ./txt/cord-302584-fwdpzv85.txt cache: ./cache/cord-302584-fwdpzv85.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302584-fwdpzv85.txt' === file2bib.sh === id: cord-301730-flv5lnv8 author: Pandey, Anamika title: Natural Plant Products: A Less Focused Aspect for the COVID-19 Viral Outbreak date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-301730-flv5lnv8.txt cache: ./cache/cord-301730-flv5lnv8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301730-flv5lnv8.txt' === file2bib.sh === id: cord-301943-qdtfjdxr author: Javelot, H title: Panique et pandémie: revue de la littérature sur les liens entre le trouble panique et l'épidémie à SARS-CoV-2 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-301943-qdtfjdxr.txt cache: ./cache/cord-301943-qdtfjdxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301943-qdtfjdxr.txt' === file2bib.sh === id: cord-302920-jkr438p9 author: Gasser, Romain title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-302920-jkr438p9.txt cache: ./cache/cord-302920-jkr438p9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302920-jkr438p9.txt' === file2bib.sh === id: cord-301946-erzh30mt author: Kwak-Kim, Joanne title: COVID-19 and immunomodulation treatment for women with reproductive failures date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-301946-erzh30mt.txt cache: ./cache/cord-301946-erzh30mt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301946-erzh30mt.txt' === file2bib.sh === id: cord-302381-oujsmf8d author: Rankin, John title: Godzilla in the corridor: The Ontario SARS crisis in historical perspective date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-302381-oujsmf8d.txt cache: ./cache/cord-302381-oujsmf8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302381-oujsmf8d.txt' === file2bib.sh === id: cord-302442-jhio7mrl author: Chrzanowski, Wojciech title: Can Stem Cells Beat COVID-19: Advancing Stem Cells and Extracellular Vesicles Toward Mainstream Medicine for Lung Injuries Associated With SARS-CoV-2 Infections date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-302442-jhio7mrl.txt cache: ./cache/cord-302442-jhio7mrl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302442-jhio7mrl.txt' === file2bib.sh === id: cord-302786-ibt7mupq author: Suwanwongse, Kulachanya title: Fatal Outcome in a Kidney-Pancreas Transplant Recipient With COVID-19 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-302786-ibt7mupq.txt cache: ./cache/cord-302786-ibt7mupq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302786-ibt7mupq.txt' === file2bib.sh === id: cord-302608-fw4pmaoc author: Huang, Jiao-Mei title: Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-302608-fw4pmaoc.txt cache: ./cache/cord-302608-fw4pmaoc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302608-fw4pmaoc.txt' === file2bib.sh === id: cord-302020-ypsh3rjv author: Kim, Dongwan title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-302020-ypsh3rjv.txt cache: ./cache/cord-302020-ypsh3rjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302020-ypsh3rjv.txt' === file2bib.sh === id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-300399-21xozruq.txt cache: ./cache/cord-300399-21xozruq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300399-21xozruq.txt' === file2bib.sh === id: cord-303056-bdse9o26 author: Okada, Masaji title: Development of vaccines and passive immunotherapy against SARS corona virus using SCID-PBL/hu mouse models date: 2007-04-20 pages: extension: .txt txt: ./txt/cord-303056-bdse9o26.txt cache: ./cache/cord-303056-bdse9o26.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303056-bdse9o26.txt' === file2bib.sh === id: cord-303384-bgvagdft author: Bilinska, Katarzyna title: Anosmia in COVID-19: A Bumpy Road to Establishing a Cellular Mechanism date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-303384-bgvagdft.txt cache: ./cache/cord-303384-bgvagdft.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303384-bgvagdft.txt' === file2bib.sh === id: cord-302163-0jav84zw author: Anastassopoulou, Cleo title: Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-302163-0jav84zw.txt cache: ./cache/cord-302163-0jav84zw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302163-0jav84zw.txt' === file2bib.sh === id: cord-302393-hrz3bypr author: Omrani, Ali S. title: The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-302393-hrz3bypr.txt cache: ./cache/cord-302393-hrz3bypr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302393-hrz3bypr.txt' === file2bib.sh === id: cord-303061-vvzkpetn author: Olyaee, Mohammad Hossein title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-303061-vvzkpetn.txt cache: ./cache/cord-303061-vvzkpetn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303061-vvzkpetn.txt' === file2bib.sh === id: cord-302616-1uwrcvjx author: Steenblock, Charlotte title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-302616-1uwrcvjx.txt cache: ./cache/cord-302616-1uwrcvjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302616-1uwrcvjx.txt' === file2bib.sh === id: cord-303135-rx21ajiw author: Jian, Li title: Perspective: COVID-19, implications of nasal diseases and consequences for their management date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-303135-rx21ajiw.txt cache: ./cache/cord-303135-rx21ajiw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303135-rx21ajiw.txt' === file2bib.sh === id: cord-302813-963ypqow author: Tegally, H. title: Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-302813-963ypqow.txt cache: ./cache/cord-302813-963ypqow.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302813-963ypqow.txt' === file2bib.sh === id: cord-302939-z0071rwa author: Erdeve, Ömer title: The Turkish Neonatal Society proposal for the management of COVID-19 in the neonatal intensive care unit date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-302939-z0071rwa.txt cache: ./cache/cord-302939-z0071rwa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302939-z0071rwa.txt' === file2bib.sh === id: cord-302902-34vftqt9 author: Law, Brenda Hiu Yan title: Effect of COVID-19 Precautions on Neonatal Resuscitation Practice: A Balance Between Healthcare Provider Safety, Infection Control, and Effective Neonatal Care date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-302902-34vftqt9.txt cache: ./cache/cord-302902-34vftqt9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302902-34vftqt9.txt' === file2bib.sh === id: cord-302733-rfuyd041 author: Dellicour, Simon title: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-302733-rfuyd041.txt cache: ./cache/cord-302733-rfuyd041.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302733-rfuyd041.txt' === file2bib.sh === id: cord-303363-uu9hb1c9 author: Karimi, Mehran title: Implications of SARSr-CoV 2 infection in thalassemias: Do patients fall into the “high clinical risk” category? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-303363-uu9hb1c9.txt cache: ./cache/cord-303363-uu9hb1c9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303363-uu9hb1c9.txt' === file2bib.sh === id: cord-303018-3ka72y3p author: Ng, Siew C title: COVID-19 and the gastrointestinal tract: more than meets the eye date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-303018-3ka72y3p.txt cache: ./cache/cord-303018-3ka72y3p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303018-3ka72y3p.txt' === file2bib.sh === id: cord-301677-b6mnn27h author: Soleimanian, Saeede title: Harnessing Memory NK Cell to Protect Against COVID-19 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-301677-b6mnn27h.txt cache: ./cache/cord-301677-b6mnn27h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301677-b6mnn27h.txt' === file2bib.sh === id: cord-301974-4wn40ivq author: Berry, Jody D title: Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus date: 2004-09-01 pages: extension: .txt txt: ./txt/cord-301974-4wn40ivq.txt cache: ./cache/cord-301974-4wn40ivq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301974-4wn40ivq.txt' === file2bib.sh === id: cord-303017-4zx94rm6 author: Barbieri, Antonio title: Can Beta-2-Adrenergic Pathway Be a New Target to Combat SARS-CoV-2 Hyperinflammatory Syndrome?—Lessons Learned From Cancer date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-303017-4zx94rm6.txt cache: ./cache/cord-303017-4zx94rm6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303017-4zx94rm6.txt' === file2bib.sh === id: cord-302316-raf5rlkq author: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-302316-raf5rlkq.txt cache: ./cache/cord-302316-raf5rlkq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302316-raf5rlkq.txt' === file2bib.sh === id: cord-303027-r2jgu2be author: Lu, Yen-Ta title: Viral load and outcome in SARS infection: The role of personal protective equipment in the emergency department date: 2006-01-24 pages: extension: .txt txt: ./txt/cord-303027-r2jgu2be.txt cache: ./cache/cord-303027-r2jgu2be.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303027-r2jgu2be.txt' === file2bib.sh === id: cord-303539-gimz41yb author: Goudouris, Ekaterini S. title: Laboratory diagnosis of COVID-19() date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-303539-gimz41yb.txt cache: ./cache/cord-303539-gimz41yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-303539-gimz41yb.txt' === file2bib.sh === id: cord-302576-fv2ib5vc author: Barisione, Emanuela title: Fibrotic progression and radiologic correlation in matched lung samples from COVID-19 post-mortems date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-302576-fv2ib5vc.txt cache: ./cache/cord-302576-fv2ib5vc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-302576-fv2ib5vc.txt' === file2bib.sh === id: cord-302414-g5onwhg1 author: Tahir ul Qamar, Muhammad title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-302414-g5onwhg1.txt cache: ./cache/cord-302414-g5onwhg1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302414-g5onwhg1.txt' === file2bib.sh === id: cord-303171-u5jrbsii author: Yang, Gee-Gwo title: SARS-associated Coronavirus Infection in Teenagers date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-303171-u5jrbsii.txt cache: ./cache/cord-303171-u5jrbsii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303171-u5jrbsii.txt' === file2bib.sh === id: cord-302707-cap2rgf7 author: Ng, Dianna L. title: SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-302707-cap2rgf7.txt cache: ./cache/cord-302707-cap2rgf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302707-cap2rgf7.txt' === file2bib.sh === id: cord-303069-ss6g3jkg author: Jakhar, Renu title: An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-303069-ss6g3jkg.txt cache: ./cache/cord-303069-ss6g3jkg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303069-ss6g3jkg.txt' === file2bib.sh === id: cord-303330-zh8wzza5 author: Magleby, Reed title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-303330-zh8wzza5.txt cache: ./cache/cord-303330-zh8wzza5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303330-zh8wzza5.txt' === file2bib.sh === id: cord-302806-1e99cygs author: Bozkurt, Banu title: The COVID-19 Pandemic: Clinical Information for Ophthalmologists date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-302806-1e99cygs.txt cache: ./cache/cord-302806-1e99cygs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302806-1e99cygs.txt' === file2bib.sh === id: cord-303959-e1654g5j author: Vitiello, Antonio title: COVID-19 Patients with Pulmonary Fibrotic Tissue: Clinical Pharmacological Rational of Antifibrotic Therapy date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-303959-e1654g5j.txt cache: ./cache/cord-303959-e1654g5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303959-e1654g5j.txt' === file2bib.sh === id: cord-302195-25gjbyi1 author: Al Huraimel, Khalid title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-302195-25gjbyi1.txt cache: ./cache/cord-302195-25gjbyi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302195-25gjbyi1.txt' === file2bib.sh === id: cord-302821-b9ikg0xy author: Gawałko, Monika title: COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-302821-b9ikg0xy.txt cache: ./cache/cord-302821-b9ikg0xy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302821-b9ikg0xy.txt' === file2bib.sh === id: cord-303143-4sksz6xz author: Wu, Y. P. title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients date: 2009-03-19 pages: extension: .txt txt: ./txt/cord-303143-4sksz6xz.txt cache: ./cache/cord-303143-4sksz6xz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303143-4sksz6xz.txt' === file2bib.sh === id: cord-303216-1pbuywz6 author: Das, Gaurav title: Neurological Insights of COVID-19 Pandemic date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-303216-1pbuywz6.txt cache: ./cache/cord-303216-1pbuywz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303216-1pbuywz6.txt' === file2bib.sh === id: cord-303377-lkewcf8a author: Dimke, H. title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-303377-lkewcf8a.txt cache: ./cache/cord-303377-lkewcf8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303377-lkewcf8a.txt' === file2bib.sh === id: cord-303407-n7j56sci author: Popofsky, Stephanie title: Impact of Maternal SARS-CoV-2 Detection on Breastfeeding Due to Infant Separation at Birth date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-303407-n7j56sci.txt cache: ./cache/cord-303407-n7j56sci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303407-n7j56sci.txt' === file2bib.sh === id: cord-302912-aqutzlx4 author: Liu, Ziteng title: The Inhibitory Effect of Curcumin on Virus-Induced Cytokine Storm and Its Potential Use in the Associated Severe Pneumonia date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-302912-aqutzlx4.txt cache: ./cache/cord-302912-aqutzlx4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302912-aqutzlx4.txt' === file2bib.sh === id: cord-303659-mzez7v4d author: Elsayed, Sarah M title: The Possibility and Cause of Relapse After Previously Recovering From COVID-19: A Systematic Review date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-303659-mzez7v4d.txt cache: ./cache/cord-303659-mzez7v4d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303659-mzez7v4d.txt' === file2bib.sh === id: cord-303506-rqerh2u3 author: Patel, V. title: A call for governments to pause Twitter censorship: a cross-sectional study using Twitter data as social-spatial sensors of COVID-19/SARS-CoV-2 research diffusion date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-303506-rqerh2u3.txt cache: ./cache/cord-303506-rqerh2u3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303506-rqerh2u3.txt' === file2bib.sh === id: cord-303960-86mukxg1 author: Rahimi, Farid title: Tackling the COVID-19 Pandemic date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-303960-86mukxg1.txt cache: ./cache/cord-303960-86mukxg1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303960-86mukxg1.txt' === file2bib.sh === id: cord-302983-3v5bc80z author: Matterne, Uwe title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-302983-3v5bc80z.txt cache: ./cache/cord-302983-3v5bc80z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302983-3v5bc80z.txt' === file2bib.sh === id: cord-303832-1kcqhgjw author: Dai, Manman title: Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-303832-1kcqhgjw.txt cache: ./cache/cord-303832-1kcqhgjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303832-1kcqhgjw.txt' === file2bib.sh === id: cord-303297-fiievwy7 author: Oberemok, Volodymyr V. title: SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-303297-fiievwy7.txt cache: ./cache/cord-303297-fiievwy7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303297-fiievwy7.txt' === file2bib.sh === id: cord-303111-iv4lzpev author: Almazán, Fernando title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 pages: extension: .txt txt: ./txt/cord-303111-iv4lzpev.txt cache: ./cache/cord-303111-iv4lzpev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303111-iv4lzpev.txt' === file2bib.sh === id: cord-303787-dx1n8jap author: Vonck, Kristl title: Neurological manifestations and neuro‐invasive mechanisms of the severe acute respiratory syndrome coronavirus type 2 date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-303787-dx1n8jap.txt cache: ./cache/cord-303787-dx1n8jap.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303787-dx1n8jap.txt' === file2bib.sh === id: cord-304139-ya3d7u9b author: Bosmann, Markus title: Complement Activation during Critical Illness: Current Findings and an Outlook in the Era of COVID-19 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-304139-ya3d7u9b.txt cache: ./cache/cord-304139-ya3d7u9b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304139-ya3d7u9b.txt' === file2bib.sh === id: cord-303609-9217t0ui author: Baselga, María Trinidad title: Trombosis y COVID-19: revisión de alcance date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-303609-9217t0ui.txt cache: ./cache/cord-303609-9217t0ui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303609-9217t0ui.txt' === file2bib.sh === id: cord-304115-xs54f295 author: Zamaniyan, Marzieh title: Preterm delivery in pregnant woman with critical COVID‐19 pneumonia and vertical transmission date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-304115-xs54f295.txt cache: ./cache/cord-304115-xs54f295.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304115-xs54f295.txt' === file2bib.sh === id: cord-303868-aes92l6s author: Steffen, Tara L. title: The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-303868-aes92l6s.txt cache: ./cache/cord-303868-aes92l6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303868-aes92l6s.txt' === file2bib.sh === id: cord-304176-yloqrblw author: Tunesi, S. title: Prescribing COVID-19 treatments: what we should never forget date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-304176-yloqrblw.txt cache: ./cache/cord-304176-yloqrblw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304176-yloqrblw.txt' === file2bib.sh === id: cord-303745-wx3udkee author: Martinez-Fleta, P. title: SARS-Cov-2 cysteine-like protease (Mpro) is immunogenic and can be detected in serum and saliva of COVID-19-seropositive individuals date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-303745-wx3udkee.txt cache: ./cache/cord-303745-wx3udkee.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303745-wx3udkee.txt' === file2bib.sh === id: cord-304031-poh3te9j author: Leder, K. title: Respiratory infections during air travel date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-304031-poh3te9j.txt cache: ./cache/cord-304031-poh3te9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304031-poh3te9j.txt' === file2bib.sh === id: cord-304101-b9na3yf6 author: Yong, Suh Kuan title: Molecular Targets for the Testing of COVID‐19 date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-304101-b9na3yf6.txt cache: ./cache/cord-304101-b9na3yf6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304101-b9na3yf6.txt' === file2bib.sh === id: cord-304232-c0cpx2q3 author: Opriessnig, Tanja title: Update on possible animal sources for COVID‐19 in humans date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-304232-c0cpx2q3.txt cache: ./cache/cord-304232-c0cpx2q3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304232-c0cpx2q3.txt' === file2bib.sh === id: cord-304088-xkg0ylz8 author: Zhu, Han title: Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-304088-xkg0ylz8.txt cache: ./cache/cord-304088-xkg0ylz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304088-xkg0ylz8.txt' === file2bib.sh === id: cord-304487-ycvu5l5f author: Wertheim, Joel O title: A glimpse into the origins of genetic diversity in SARS-CoV-2 date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-304487-ycvu5l5f.txt cache: ./cache/cord-304487-ycvu5l5f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304487-ycvu5l5f.txt' === file2bib.sh === id: cord-304574-03s404s5 author: Luciani, Lorenzo G. title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. Urinary Frequency as a Possible Overlooked Symptom in COVID-19 Patients: Does SARS-CoV-2 Cause Viral Cystitis? Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-304574-03s404s5.txt cache: ./cache/cord-304574-03s404s5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-304574-03s404s5.txt' === file2bib.sh === id: cord-303941-3lg1bzsi author: Han, Hui-Ju title: Bats as reservoirs of severe emerging infectious diseases date: 2015-07-02 pages: extension: .txt txt: ./txt/cord-303941-3lg1bzsi.txt cache: ./cache/cord-303941-3lg1bzsi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303941-3lg1bzsi.txt' === file2bib.sh === id: cord-303934-8gh3q7p3 author: Sungnak, Waradon title: SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-303934-8gh3q7p3.txt cache: ./cache/cord-303934-8gh3q7p3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303934-8gh3q7p3.txt' === file2bib.sh === id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-303665-l57e54hu.txt cache: ./cache/cord-303665-l57e54hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303665-l57e54hu.txt' === file2bib.sh === id: cord-304372-6eqnr52t author: Stolle, Claudia title: Bedarfe der Langzeitpflege in der COVID-19-Pandemie date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-304372-6eqnr52t.txt cache: ./cache/cord-304372-6eqnr52t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304372-6eqnr52t.txt' === file2bib.sh === id: cord-304379-4mfyxp6h author: Wang, Jin title: Mathematical models for COVID-19: applications, limitations, and potentials date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-304379-4mfyxp6h.txt cache: ./cache/cord-304379-4mfyxp6h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304379-4mfyxp6h.txt' === file2bib.sh === id: cord-303661-etb19d6y author: Shin, Hyoung-Shik title: Empirical Treatment and Prevention of COVID-19 date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-303661-etb19d6y.txt cache: ./cache/cord-303661-etb19d6y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303661-etb19d6y.txt' === file2bib.sh === id: cord-303692-py908dt8 author: Langley, Caroline title: Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement date: 2019-01-01 pages: extension: .txt txt: ./txt/cord-303692-py908dt8.txt cache: ./cache/cord-303692-py908dt8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303692-py908dt8.txt' === file2bib.sh === id: cord-303880-zv4nbz9p author: Tsikala Vafea, Maria title: Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-303880-zv4nbz9p.txt cache: ./cache/cord-303880-zv4nbz9p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303880-zv4nbz9p.txt' === file2bib.sh === id: cord-304201-fziv9a9k author: Chiang, Chi-Huei title: Eight-Month Prospective Study of 14 Patients With Hospital-Acquired Severe Acute Respiratory Syndrome date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-304201-fziv9a9k.txt cache: ./cache/cord-304201-fziv9a9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304201-fziv9a9k.txt' === file2bib.sh === id: cord-304073-f3iwclkm author: Mullick, Jhinuk Basu title: Animal Models to Study Emerging Technologies Against SARS-CoV-2 date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-304073-f3iwclkm.txt cache: ./cache/cord-304073-f3iwclkm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304073-f3iwclkm.txt' === file2bib.sh === id: cord-304282-om2xc4bs author: Berhan, Yifru title: Will Africa be Devastated by Covid-19 as Many Predicted? Perspective and Prospective date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-304282-om2xc4bs.txt cache: ./cache/cord-304282-om2xc4bs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304282-om2xc4bs.txt' === file2bib.sh === id: cord-304263-5kddk5fa author: C., Selvaa Kumar title: Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-304263-5kddk5fa.txt cache: ./cache/cord-304263-5kddk5fa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304263-5kddk5fa.txt' === file2bib.sh === id: cord-304295-3mpymd8a author: Khan, Muhammad Muzamil title: Emergence of novel coronavirus and progress toward treatment and vaccine date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-304295-3mpymd8a.txt cache: ./cache/cord-304295-3mpymd8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304295-3mpymd8a.txt' === file2bib.sh === id: cord-304839-lesa5u2n author: Jiang, Fang title: Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19) date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-304839-lesa5u2n.txt cache: ./cache/cord-304839-lesa5u2n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304839-lesa5u2n.txt' === file2bib.sh === id: cord-303054-s1clwunc author: Velly, Lionel title: Guidelines: Anaesthesia in the context of COVID-19 pandemic date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-303054-s1clwunc.txt cache: ./cache/cord-303054-s1clwunc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303054-s1clwunc.txt' === file2bib.sh === id: cord-304340-9mrtic2k author: Karacan, Ilker title: The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-304340-9mrtic2k.txt cache: ./cache/cord-304340-9mrtic2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304340-9mrtic2k.txt' === file2bib.sh === id: cord-304584-jxha3rz8 author: Giacomo, Di title: SARS-COV-2 infection in cancer patients undergoing checkpoint blockade: clinical course and outcome date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-304584-jxha3rz8.txt cache: ./cache/cord-304584-jxha3rz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304584-jxha3rz8.txt' === file2bib.sh === id: cord-304271-vyayyk50 author: Qin, Yuan-Yuan title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-304271-vyayyk50.txt cache: ./cache/cord-304271-vyayyk50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304271-vyayyk50.txt' === file2bib.sh === id: cord-304787-fohgekp4 author: Prazuck, Thierry title: Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-304787-fohgekp4.txt cache: ./cache/cord-304787-fohgekp4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304787-fohgekp4.txt' === file2bib.sh === id: cord-304321-y177sqee author: Cho, Ryan H. W. title: Pearls of experience for safe and efficient hospital practices in otorhinolaryngology—head and neck surgery in Hong Kong during the 2019 novel coronavirus disease (COVID-19) pandemic date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-304321-y177sqee.txt cache: ./cache/cord-304321-y177sqee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304321-y177sqee.txt' === file2bib.sh === id: cord-304742-ytf2ilw4 author: Albini, Adriana title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based antihypertensive therapies—reply date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-304742-ytf2ilw4.txt cache: ./cache/cord-304742-ytf2ilw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304742-ytf2ilw4.txt' === file2bib.sh === id: cord-304480-azosg1tt author: Hu, Donghua title: Studies on the interactions of Ti-containing polyoxometalates (POMs) with SARS-CoV 3CL(pro) by molecular modeling date: 2006-09-05 pages: extension: .txt txt: ./txt/cord-304480-azosg1tt.txt cache: ./cache/cord-304480-azosg1tt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304480-azosg1tt.txt' === file2bib.sh === id: cord-303741-1ou0cy5k author: Stafstrom, Carl E. title: COVID-19: Neurological Considerations in Neonates and Children date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-303741-1ou0cy5k.txt cache: ./cache/cord-303741-1ou0cy5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303741-1ou0cy5k.txt' === file2bib.sh === id: cord-304355-y3fagw3t author: Pan, Boyu title: Chinese herbal compounds against SARS-CoV-2: puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-304355-y3fagw3t.txt cache: ./cache/cord-304355-y3fagw3t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304355-y3fagw3t.txt' === file2bib.sh === id: cord-304388-pth2d40p author: Lai, Chih-Cheng title: Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-304388-pth2d40p.txt cache: ./cache/cord-304388-pth2d40p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304388-pth2d40p.txt' === file2bib.sh === id: cord-304550-6j1pb1pu author: Yongchen, Zhang title: Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-304550-6j1pb1pu.txt cache: ./cache/cord-304550-6j1pb1pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304550-6j1pb1pu.txt' === file2bib.sh === id: cord-303917-2tu707ng author: Zhang, Lei title: Potential interventions for novel coronavirus in China: A systematic review date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-303917-2tu707ng.txt cache: ./cache/cord-303917-2tu707ng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303917-2tu707ng.txt' === file2bib.sh === id: cord-304016-4o2bpedp author: Hanage, William P. title: COVID-19: US federal accountability for entry, spread, and inequities—lessons for the future date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-304016-4o2bpedp.txt cache: ./cache/cord-304016-4o2bpedp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304016-4o2bpedp.txt' === file2bib.sh === id: cord-304280-2a84u4tm author: Masic, Izet title: Public Health Aspects of COVID-19 Infection with Focus on Cardiovascular Diseases date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-304280-2a84u4tm.txt cache: ./cache/cord-304280-2a84u4tm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304280-2a84u4tm.txt' === file2bib.sh === id: cord-304724-luql6159 author: Paderno, Alberto title: Smell and taste alterations in Covid‐19: a cross‐sectional analysis of different cohorts date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-304724-luql6159.txt cache: ./cache/cord-304724-luql6159.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304724-luql6159.txt' === file2bib.sh === id: cord-304815-3datxv8j author: Gronvall, Gigi Kwik title: The Scientific Response to a Pandemic date: 2006-02-24 pages: extension: .txt txt: ./txt/cord-304815-3datxv8j.txt cache: ./cache/cord-304815-3datxv8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304815-3datxv8j.txt' === file2bib.sh === id: cord-304792-8sdxqmkb author: Khan, Md. Abdullah-Al-Kamran title: SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-304792-8sdxqmkb.txt cache: ./cache/cord-304792-8sdxqmkb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304792-8sdxqmkb.txt' === file2bib.sh === id: cord-304718-w469n0o8 author: Wang, Yan title: Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection date: 2009-05-01 pages: extension: .txt txt: ./txt/cord-304718-w469n0o8.txt cache: ./cache/cord-304718-w469n0o8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304718-w469n0o8.txt' === file2bib.sh === id: cord-303517-8971aq02 author: Cajamarca-Baron, Jairo title: SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-303517-8971aq02.txt cache: ./cache/cord-303517-8971aq02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303517-8971aq02.txt' === file2bib.sh === id: cord-304791-wv4qu9xm author: Carfora, Vincenzo title: Anticoagulant treatment in COVID-19: a narrative review date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-304791-wv4qu9xm.txt cache: ./cache/cord-304791-wv4qu9xm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304791-wv4qu9xm.txt' === file2bib.sh === id: cord-304544-tqtdjh2m author: Enes, Ak title: Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-304544-tqtdjh2m.txt cache: ./cache/cord-304544-tqtdjh2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304544-tqtdjh2m.txt' === file2bib.sh === id: cord-304356-jyp9gjh9 author: Grant, Rogan A. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-304356-jyp9gjh9.txt cache: ./cache/cord-304356-jyp9gjh9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304356-jyp9gjh9.txt' === file2bib.sh === id: cord-304898-he57l0y7 author: Belghmaidi, Sarah title: Third Cranial Nerve Palsy Presenting with Unilateral Diplopia and Strabismus in a 24-Year-Old Woman with COVID-19 date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-304898-he57l0y7.txt cache: ./cache/cord-304898-he57l0y7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304898-he57l0y7.txt' === file2bib.sh === id: cord-304734-r0k1rfmt author: Moreno-Casbas, María Teresa title: Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-304734-r0k1rfmt.txt cache: ./cache/cord-304734-r0k1rfmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304734-r0k1rfmt.txt' === file2bib.sh === id: cord-305054-4d84b2g6 author: Liu, Yuan title: The selection of reference genome and the search for the origin of SARS-CoV-2 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-305054-4d84b2g6.txt cache: ./cache/cord-305054-4d84b2g6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305054-4d84b2g6.txt' === file2bib.sh === id: cord-304871-gva617yp author: Zheng, Ting title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-304871-gva617yp.txt cache: ./cache/cord-304871-gva617yp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304871-gva617yp.txt' === file2bib.sh === id: cord-304418-k9owyolj author: Le Maréchal, M. title: COVID-19 in clinical practice: a narrative synthesis date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-304418-k9owyolj.txt cache: ./cache/cord-304418-k9owyolj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304418-k9owyolj.txt' === file2bib.sh === id: cord-304254-67brxejx author: Wei, Ping title: The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase date: 2006-01-20 pages: extension: .txt txt: ./txt/cord-304254-67brxejx.txt cache: ./cache/cord-304254-67brxejx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304254-67brxejx.txt' === file2bib.sh === id: cord-304457-8g36h1bz author: Idelsis, E.-M. title: Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-304457-8g36h1bz.txt cache: ./cache/cord-304457-8g36h1bz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304457-8g36h1bz.txt' === file2bib.sh === id: cord-304660-w7rs2dvt author: Bharadwaj, Shiv title: SARS-CoV-2 M(pro) inhibitors: identification of anti-SARS-CoV-2 M(pro) compounds from FDA approved drugs date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-304660-w7rs2dvt.txt cache: ./cache/cord-304660-w7rs2dvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304660-w7rs2dvt.txt' === file2bib.sh === id: cord-305104-jk6ai1od author: Escribese, María M title: Cross‐sectional pilot study exploring the feasibility of a rapid SARS‐CoV‐2 immunization test in health and non‐healthcare workers date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-305104-jk6ai1od.txt cache: ./cache/cord-305104-jk6ai1od.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305104-jk6ai1od.txt' === file2bib.sh === id: cord-305139-851v2qr3 author: Peys, Elise title: Haemoptysis as the first presentation of COVID-19: a case report date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-305139-851v2qr3.txt cache: ./cache/cord-305139-851v2qr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305139-851v2qr3.txt' === file2bib.sh === id: cord-305234-nclk7bbo author: Do, Mytrang H. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-305234-nclk7bbo.txt cache: ./cache/cord-305234-nclk7bbo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305234-nclk7bbo.txt' === file2bib.sh === id: cord-305091-tfn2pyc6 author: Tripathi, Praveen Kumar title: Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2 date: 2020-12-01 pages: extension: .txt txt: ./txt/cord-305091-tfn2pyc6.txt cache: ./cache/cord-305091-tfn2pyc6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305091-tfn2pyc6.txt' === file2bib.sh === id: cord-305931-0pgu2gvh author: Janus, Scott E title: COVID19: a case report of thrombus in transit date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-305931-0pgu2gvh.txt cache: ./cache/cord-305931-0pgu2gvh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305931-0pgu2gvh.txt' === file2bib.sh === id: cord-302382-eifh95zm author: Owji, Hajar title: Immunotherapeutic approaches to curtail COVID-19 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-302382-eifh95zm.txt cache: ./cache/cord-302382-eifh95zm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-302382-eifh95zm.txt' === file2bib.sh === id: cord-305788-z75yv88e author: Agergaard, Charlotte Nielsen title: Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305788-z75yv88e.txt cache: ./cache/cord-305788-z75yv88e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305788-z75yv88e.txt' === file2bib.sh === id: cord-304617-5ozf18lg author: Al-Khafaji, Khattab title: Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-304617-5ozf18lg.txt cache: ./cache/cord-304617-5ozf18lg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304617-5ozf18lg.txt' === file2bib.sh === id: cord-305130-vz72ldbo author: Keil, Shawn D. title: Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-305130-vz72ldbo.txt cache: ./cache/cord-305130-vz72ldbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305130-vz72ldbo.txt' === file2bib.sh === id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 pages: extension: .txt txt: ./txt/cord-304058-i8cywew0.txt cache: ./cache/cord-304058-i8cywew0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304058-i8cywew0.txt' === file2bib.sh === id: cord-305093-og4k3fc7 author: Konno, Yoriyuki title: SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-305093-og4k3fc7.txt cache: ./cache/cord-305093-og4k3fc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305093-og4k3fc7.txt' === file2bib.sh === id: cord-305223-go75cs6r author: Wang, Yafei title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-305223-go75cs6r.txt cache: ./cache/cord-305223-go75cs6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305223-go75cs6r.txt' === file2bib.sh === id: cord-305025-pqye1ebh author: Sharifi, Majid title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305025-pqye1ebh.txt cache: ./cache/cord-305025-pqye1ebh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305025-pqye1ebh.txt' === file2bib.sh === id: cord-305341-nokybn2a author: Zeng, Fanya title: Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments date: 2004-03-19 pages: extension: .txt txt: ./txt/cord-305341-nokybn2a.txt cache: ./cache/cord-305341-nokybn2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305341-nokybn2a.txt' === file2bib.sh === id: cord-305266-fuaq4ujb author: Gong, Yue title: Early Research on COVID-19: A Bibliometric Analysis date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-305266-fuaq4ujb.txt cache: ./cache/cord-305266-fuaq4ujb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305266-fuaq4ujb.txt' === file2bib.sh === id: cord-305511-gdpxvqkk author: Dave, Gaurav S. title: High affinity interaction of Solanum tuberosum and Brassica juncea residue smoke water compounds with proteins involved in coronavirus infection date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-305511-gdpxvqkk.txt cache: ./cache/cord-305511-gdpxvqkk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305511-gdpxvqkk.txt' === file2bib.sh === id: cord-305581-0bqxwh1o author: Hassan, Sk. Sarif title: Molecular phylogeny and missense mutations of envelope proteins across coronaviruses date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-305581-0bqxwh1o.txt cache: ./cache/cord-305581-0bqxwh1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305581-0bqxwh1o.txt' === file2bib.sh === id: cord-305270-vos341i1 author: Conte, Luana title: Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-305270-vos341i1.txt cache: ./cache/cord-305270-vos341i1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305270-vos341i1.txt' === file2bib.sh === id: cord-305521-lkou3ycu author: Michel, W. title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-305521-lkou3ycu.txt cache: ./cache/cord-305521-lkou3ycu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305521-lkou3ycu.txt' === file2bib.sh === id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 pages: extension: .txt txt: ./txt/cord-304498-ty41xob0.txt cache: ./cache/cord-304498-ty41xob0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304498-ty41xob0.txt' === file2bib.sh === id: cord-305616-2obemy16 author: Montes, Maria Teresa title: Neonatal nursing in the COVID-19 pandemic: can we improve the future? date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-305616-2obemy16.txt cache: ./cache/cord-305616-2obemy16.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305616-2obemy16.txt' === file2bib.sh === id: cord-305059-8z54lw2d author: Qu, Jie-Ming title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 pages: extension: .txt txt: ./txt/cord-305059-8z54lw2d.txt cache: ./cache/cord-305059-8z54lw2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305059-8z54lw2d.txt' === file2bib.sh === id: cord-305330-mklkugj5 author: Moiseev, Sergey title: Cancer in intensive care unit patients with COVID-19 date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-305330-mklkugj5.txt cache: ./cache/cord-305330-mklkugj5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305330-mklkugj5.txt' === file2bib.sh === id: cord-304943-thg4fqi2 author: Noor, Aziz Ullah title: Epidemiology of CoViD-19 Pandemic: Recovery and mortality ratio around the globe date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-304943-thg4fqi2.txt cache: ./cache/cord-304943-thg4fqi2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304943-thg4fqi2.txt' === file2bib.sh === id: cord-304899-vruq4r7z author: Guihot, Amélie title: Syndrome respiratoire aigu sévère : une épidémie singulière de pneumonie virale date: 2004-03-31 pages: extension: .txt txt: ./txt/cord-304899-vruq4r7z.txt cache: ./cache/cord-304899-vruq4r7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304899-vruq4r7z.txt' === file2bib.sh === id: cord-304479-uxp1kg86 author: Goodarzi, Pedram title: Coronavirus disease 2019 (COVID-19): Immunological approaches and emerging pharmacologic treatments date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-304479-uxp1kg86.txt cache: ./cache/cord-304479-uxp1kg86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304479-uxp1kg86.txt' === file2bib.sh === id: cord-303585-8py6joh6 author: Verma, Surjeet title: Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19) date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-303585-8py6joh6.txt cache: ./cache/cord-303585-8py6joh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303585-8py6joh6.txt' === file2bib.sh === id: cord-305798-7b8rua4z author: Rivas-García, S title: Rhabdomyolysis as the main manifestation of coronavirus disease 2019 date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-305798-7b8rua4z.txt cache: ./cache/cord-305798-7b8rua4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305798-7b8rua4z.txt' === file2bib.sh === id: cord-305742-wf6qxplf author: Gomez, Santiago A. title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305742-wf6qxplf.txt cache: ./cache/cord-305742-wf6qxplf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305742-wf6qxplf.txt' === file2bib.sh === id: cord-304306-rxjahqwh author: Vlachakis, Dimitrios title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-304306-rxjahqwh.txt cache: ./cache/cord-304306-rxjahqwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304306-rxjahqwh.txt' === file2bib.sh === id: cord-303651-fkdep6cp author: Thompson, Robin N. title: Key questions for modelling COVID-19 exit strategies date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-303651-fkdep6cp.txt cache: ./cache/cord-303651-fkdep6cp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303651-fkdep6cp.txt' === file2bib.sh === id: cord-305587-xtqvtleb author: Ma, Cuiqing title: From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-305587-xtqvtleb.txt cache: ./cache/cord-305587-xtqvtleb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305587-xtqvtleb.txt' === file2bib.sh === id: cord-306390-pzzev8hd author: Reisinger, Emil C. title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-306390-pzzev8hd.txt cache: ./cache/cord-306390-pzzev8hd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306390-pzzev8hd.txt' === file2bib.sh === id: cord-305610-v1hn934x author: Kerslake, Rachel title: Co-expression of peripheral olfactory receptors with SARS-CoV-2 infection mediators: Potential implications beyond loss of smell as a COVID-19 symptom date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-305610-v1hn934x.txt cache: ./cache/cord-305610-v1hn934x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305610-v1hn934x.txt' === file2bib.sh === id: cord-305632-xbji6g5x author: Uccelli, Matteo title: COVID-19 and Obesity: Is Bariatric Surgery Protective? Retrospective Analysis on 2145 Patients Undergone Bariatric-Metabolic Surgery from High Volume Center in Italy (Lombardy) date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-305632-xbji6g5x.txt cache: ./cache/cord-305632-xbji6g5x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305632-xbji6g5x.txt' === file2bib.sh === id: cord-305589-ofpna4k1 author: Schubert, Katharina title: SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-305589-ofpna4k1.txt cache: ./cache/cord-305589-ofpna4k1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305589-ofpna4k1.txt' === file2bib.sh === id: cord-305704-grzrkff9 author: Almutairi, Abdulelah title: Dermatological Manifestations in Patients With SARS-CoV-2: A Systematic Review date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-305704-grzrkff9.txt cache: ./cache/cord-305704-grzrkff9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305704-grzrkff9.txt' === file2bib.sh === id: cord-305134-s7h6bpof author: Mackman, Nigel title: Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-305134-s7h6bpof.txt cache: ./cache/cord-305134-s7h6bpof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305134-s7h6bpof.txt' === file2bib.sh === id: cord-305263-fgwf6wy3 author: Wang, Ben X. title: The yin and yang of viruses and interferons date: 2012-02-07 pages: extension: .txt txt: ./txt/cord-305263-fgwf6wy3.txt cache: ./cache/cord-305263-fgwf6wy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305263-fgwf6wy3.txt' === file2bib.sh === id: cord-304013-nzigx0k0 author: Lipinski, Tom title: Review of ventilation strategies to reduce the risk of disease transmission in high occupancy buildings date: 2020-09-13 pages: extension: .txt txt: ./txt/cord-304013-nzigx0k0.txt cache: ./cache/cord-304013-nzigx0k0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304013-nzigx0k0.txt' === file2bib.sh === id: cord-305703-ypeibwje author: Veronese, Nicola title: Use of Corticosteroids in Coronavirus Disease 2019 Pneumonia: A Systematic Review of the Literature date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-305703-ypeibwje.txt cache: ./cache/cord-305703-ypeibwje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305703-ypeibwje.txt' === file2bib.sh === id: cord-305591-ir3wz6nr author: Ji, Danyang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-305591-ir3wz6nr.txt cache: ./cache/cord-305591-ir3wz6nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305591-ir3wz6nr.txt' === file2bib.sh === id: cord-306085-gnrnsxej author: Hassan, Sk. Sarif title: SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-306085-gnrnsxej.txt cache: ./cache/cord-306085-gnrnsxej.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306085-gnrnsxej.txt' === file2bib.sh === id: cord-306486-y6a4u0vh author: Wang, Bin title: Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-306486-y6a4u0vh.txt cache: ./cache/cord-306486-y6a4u0vh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306486-y6a4u0vh.txt' === file2bib.sh === id: cord-305274-mcsdem7y author: Beniac, Daniel R. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 pages: extension: .txt txt: ./txt/cord-305274-mcsdem7y.txt cache: ./cache/cord-305274-mcsdem7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305274-mcsdem7y.txt' === file2bib.sh === id: cord-305640-tgowzrqo author: Li, Yong-Hua title: Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: Comparison with results of other viral markers date: 2005-07-15 pages: extension: .txt txt: ./txt/cord-305640-tgowzrqo.txt cache: ./cache/cord-305640-tgowzrqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305640-tgowzrqo.txt' === file2bib.sh === id: cord-306308-zjq6cscm author: de Moura, Ronald Rodrigues title: Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-306308-zjq6cscm.txt cache: ./cache/cord-306308-zjq6cscm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306308-zjq6cscm.txt' === file2bib.sh === id: cord-305534-936peb1n author: Johnson, Kemmian D. title: Pulmonary and Extra-Pulmonary Clinical Manifestations of COVID-19 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-305534-936peb1n.txt cache: ./cache/cord-305534-936peb1n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305534-936peb1n.txt' === file2bib.sh === id: cord-306373-61snvddh author: Xu, Xiao-Wei title: Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series date: 2020-02-19 pages: extension: .txt txt: ./txt/cord-306373-61snvddh.txt cache: ./cache/cord-306373-61snvddh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306373-61snvddh.txt' === file2bib.sh === id: cord-306108-ja0wyr5w author: B K, Anupama title: A Review of Acute Myocardial Injury in Coronavirus Disease 2019 date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-306108-ja0wyr5w.txt cache: ./cache/cord-306108-ja0wyr5w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306108-ja0wyr5w.txt' === file2bib.sh === id: cord-306675-kwrm8whn author: Crespo Sabarís, R title: “SARS-CoV-2: una presentación peculiar” date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-306675-kwrm8whn.txt cache: ./cache/cord-306675-kwrm8whn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306675-kwrm8whn.txt' === file2bib.sh === id: cord-305956-l02xdq87 author: Alqahtani, Saleh A title: Liver injury in COVID-19: The current evidence date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-305956-l02xdq87.txt cache: ./cache/cord-305956-l02xdq87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305956-l02xdq87.txt' === file2bib.sh === id: cord-305582-3hmsknon author: Li, Lei title: Therapeutic strategies for critically ill patients with COVID-19 date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-305582-3hmsknon.txt cache: ./cache/cord-305582-3hmsknon.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305582-3hmsknon.txt' === file2bib.sh === id: cord-305496-t8ykkekl author: Stone, E. Taylor title: Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-305496-t8ykkekl.txt cache: ./cache/cord-305496-t8ykkekl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305496-t8ykkekl.txt' === file2bib.sh === id: cord-306017-4wf4yhyz author: d'Aloja, Ernesto title: COVID-19 and medical liability: Italy denies the shield to its heroes date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-306017-4wf4yhyz.txt cache: ./cache/cord-306017-4wf4yhyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306017-4wf4yhyz.txt' === file2bib.sh === id: cord-306465-7kevsl1z author: Agarwal, Krishna Mohan title: Study and Overview of the Novel Corona Virus Disease (COVID-19) date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-306465-7kevsl1z.txt cache: ./cache/cord-306465-7kevsl1z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306465-7kevsl1z.txt' === file2bib.sh === id: cord-306581-g3d0lqxp author: Khattab, Mohamed H. title: Early detection of SARS-CoV-2 from staging PET-CT date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-306581-g3d0lqxp.txt cache: ./cache/cord-306581-g3d0lqxp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306581-g3d0lqxp.txt' === file2bib.sh === id: cord-305763-160heazx author: Lai, Chih-Cheng title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-305763-160heazx.txt cache: ./cache/cord-305763-160heazx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305763-160heazx.txt' === file2bib.sh === id: cord-306598-xe0pq0ik author: Zhou, Mi title: Re-emergence of SARS-CoV2 in a discharged COVID-19 case date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-306598-xe0pq0ik.txt cache: ./cache/cord-306598-xe0pq0ik.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306598-xe0pq0ik.txt' === file2bib.sh === id: cord-306332-ug6pare2 author: Chen, Ze-Liang title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-306332-ug6pare2.txt cache: ./cache/cord-306332-ug6pare2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-306332-ug6pare2.txt' === file2bib.sh === id: cord-306508-xpwluph5 author: Nkengasong, John title: China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response date: 2020-01-27 pages: extension: .txt txt: ./txt/cord-306508-xpwluph5.txt cache: ./cache/cord-306508-xpwluph5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306508-xpwluph5.txt' === file2bib.sh === id: cord-305816-06lddk87 author: Musarrat, Farhana title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-305816-06lddk87.txt cache: ./cache/cord-305816-06lddk87.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305816-06lddk87.txt' === file2bib.sh === id: cord-305770-xygg4lxu author: Busetto, Gian Maria title: SARS-CoV-2 Infection and High-Risk Non-Muscle-Invasive Bladder Cancer: Are There Any Common Features? date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-305770-xygg4lxu.txt cache: ./cache/cord-305770-xygg4lxu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305770-xygg4lxu.txt' === file2bib.sh === id: cord-307113-mu3ow7m4 author: Colmenero, I. title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-307113-mu3ow7m4.txt cache: ./cache/cord-307113-mu3ow7m4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307113-mu3ow7m4.txt' === file2bib.sh === id: cord-305755-6jup93v4 author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-305755-6jup93v4.txt cache: ./cache/cord-305755-6jup93v4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305755-6jup93v4.txt' === file2bib.sh === id: cord-306034-1u29o2id author: Cazzolla, Angela P. title: Taste and Smell Disorders in COVID-19 Patients: Role of Interleukin-6 date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-306034-1u29o2id.txt cache: ./cache/cord-306034-1u29o2id.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306034-1u29o2id.txt' === file2bib.sh === id: cord-306351-ka6asw3m author: Alsuliman, Tamim title: A review of potential treatments to date in COVID-19 patients according to the stage of the disease date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-306351-ka6asw3m.txt cache: ./cache/cord-306351-ka6asw3m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306351-ka6asw3m.txt' === file2bib.sh === id: cord-306826-vbfdxoc2 author: Solerte, Sebastiano Bruno title: Dipeptidyl peptidase-4 (DPP4) inhibition in COVID-19 date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-306826-vbfdxoc2.txt cache: ./cache/cord-306826-vbfdxoc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306826-vbfdxoc2.txt' === file2bib.sh === id: cord-305262-23qylbmg author: Rowan, Neil J. title: Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic – Implications for efficacy, re-use and sustainable waste management date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-305262-23qylbmg.txt cache: ./cache/cord-305262-23qylbmg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305262-23qylbmg.txt' === file2bib.sh === id: cord-305856-xt3zxajf author: Shanmugam, Chandrakumar title: COVID-2019 – A comprehensive pathology insight date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-305856-xt3zxajf.txt cache: ./cache/cord-305856-xt3zxajf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305856-xt3zxajf.txt' === file2bib.sh === id: cord-306749-qetf3uur author: Caves, N.D. title: Attitudes to basic life support among medical students following the 2003 SARS outbreak in Hong Kong() date: 2005-10-10 pages: extension: .txt txt: ./txt/cord-306749-qetf3uur.txt cache: ./cache/cord-306749-qetf3uur.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306749-qetf3uur.txt' === file2bib.sh === id: cord-306365-7cydmgn2 author: Ami, Yasushi title: Co‐infection of respiratory bacterium with severe acute respiratory syndrome coronavirus induces an exacerbated pneumonia in mice date: 2008-04-01 pages: extension: .txt txt: ./txt/cord-306365-7cydmgn2.txt cache: ./cache/cord-306365-7cydmgn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306365-7cydmgn2.txt' === file2bib.sh === id: cord-305858-gp1u4kh7 author: Song, Xiang title: High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-305858-gp1u4kh7.txt cache: ./cache/cord-305858-gp1u4kh7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305858-gp1u4kh7.txt' === file2bib.sh === id: cord-305564-dj3vj4tk author: DeDiego, Marta L. title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date: 2008-07-01 pages: extension: .txt txt: ./txt/cord-305564-dj3vj4tk.txt cache: ./cache/cord-305564-dj3vj4tk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305564-dj3vj4tk.txt' === file2bib.sh === id: cord-306718-7wp5jmxe author: Remaeus, Katarina title: Characteristics and short‐term obstetric outcomes in a case series of 67 women tested positive for SARS‐CoV‐2 in Stockholm, Sweden date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-306718-7wp5jmxe.txt cache: ./cache/cord-306718-7wp5jmxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306718-7wp5jmxe.txt' === file2bib.sh === id: cord-306177-5wefp31y author: Iheagwam, Franklyn Nonso title: Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-306177-5wefp31y.txt cache: ./cache/cord-306177-5wefp31y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306177-5wefp31y.txt' === file2bib.sh === id: cord-307536-qeo5dfxg author: Feng, Ye title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-307536-qeo5dfxg.txt cache: ./cache/cord-307536-qeo5dfxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307536-qeo5dfxg.txt' === file2bib.sh === id: cord-307213-i8yijbiu author: Ip, Jonathan Daniel title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-307213-i8yijbiu.txt cache: ./cache/cord-307213-i8yijbiu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307213-i8yijbiu.txt' === file2bib.sh === id: cord-306819-otabtxin author: Asensio-Samper, JM title: Recomendaciones Prácticas Para El Manejo Del Paciente Con Dolor Crónico Durante La Pandemia De COVID-19 date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-306819-otabtxin.txt cache: ./cache/cord-306819-otabtxin.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306819-otabtxin.txt' === file2bib.sh === id: cord-307070-tqxvu3pu author: Iqbal, Phool title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date: 2020-09-20 pages: extension: .txt txt: ./txt/cord-307070-tqxvu3pu.txt cache: ./cache/cord-307070-tqxvu3pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307070-tqxvu3pu.txt' === file2bib.sh === id: cord-304626-ffao7vka author: Mellors, Jack title: Viral Evasion of the Complement System and Its Importance for Vaccines and Therapeutics date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-304626-ffao7vka.txt cache: ./cache/cord-304626-ffao7vka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304626-ffao7vka.txt' === file2bib.sh === id: cord-306748-i9ndb71n author: Kobia, Francis title: COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness? date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-306748-i9ndb71n.txt cache: ./cache/cord-306748-i9ndb71n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306748-i9ndb71n.txt' === file2bib.sh === id: cord-306832-w8s282nq author: Tarragón, Blanca title: FRACASO RENAL AGUDO EN PACIENTES HOSPITALIZADOS POR COVID-19 date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-306832-w8s282nq.txt cache: ./cache/cord-306832-w8s282nq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306832-w8s282nq.txt' === file2bib.sh === id: cord-307489-2liu4anc author: Elavia, Nasha title: An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-307489-2liu4anc.txt cache: ./cache/cord-307489-2liu4anc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307489-2liu4anc.txt' === file2bib.sh === id: cord-307208-tw6mwa5v author: Cabrera Villegas, Antonio title: [(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2 date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-307208-tw6mwa5v.txt cache: ./cache/cord-307208-tw6mwa5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307208-tw6mwa5v.txt' === file2bib.sh === id: cord-307853-m1q1sjr4 author: Majumder, Satyabrata title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-307853-m1q1sjr4.txt cache: ./cache/cord-307853-m1q1sjr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307853-m1q1sjr4.txt' === file2bib.sh === id: cord-307248-8e34ndn4 author: Klimek, Ludger title: Handling of allergen immunotherapy in the COVID‐19 pandemic: An ARIA‐EAACI statement date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-307248-8e34ndn4.txt cache: ./cache/cord-307248-8e34ndn4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307248-8e34ndn4.txt' === file2bib.sh === id: cord-305422-t8azymo7 author: Yi, Ye title: COVID-19: what has been learned and to be learned about the novel coronavirus disease date: 2020-03-15 pages: extension: .txt txt: ./txt/cord-305422-t8azymo7.txt cache: ./cache/cord-305422-t8azymo7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305422-t8azymo7.txt' === file2bib.sh === id: cord-307109-nz8qvuw6 author: Martinez, Miguel Angel title: Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-307109-nz8qvuw6.txt cache: ./cache/cord-307109-nz8qvuw6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307109-nz8qvuw6.txt' === file2bib.sh === id: cord-307460-v6xgkg1p author: Hsu, Yu-Lung title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-307460-v6xgkg1p.txt cache: ./cache/cord-307460-v6xgkg1p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307460-v6xgkg1p.txt' === file2bib.sh === id: cord-307504-cogk5kig author: Zhu, Yuanmei title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date: 2020-03-28 pages: extension: .txt txt: ./txt/cord-307504-cogk5kig.txt cache: ./cache/cord-307504-cogk5kig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307504-cogk5kig.txt' === file2bib.sh === id: cord-307596-0bbxyyea author: Parhar, Harman S. title: Topical preparations to reduce SARS‐CoV‐2 aerosolization in head and neck mucosal surgery date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-307596-0bbxyyea.txt cache: ./cache/cord-307596-0bbxyyea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307596-0bbxyyea.txt' === file2bib.sh === id: cord-307044-4czeehkq author: Liu, Jiaye title: Longitudinal Changes of Liver Function and Hepatitis B Reactivation in COVID‐19 Patients with Pre‐existing Chronic HBV Infection date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-307044-4czeehkq.txt cache: ./cache/cord-307044-4czeehkq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307044-4czeehkq.txt' === file2bib.sh === id: cord-306760-05my504t author: Turner, Dan title: Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-306760-05my504t.txt cache: ./cache/cord-306760-05my504t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306760-05my504t.txt' === file2bib.sh === id: cord-307842-7q2jd0mf author: Fox, Alisa title: Robust and specific secretory IgA against SARS-CoV-2 detected in human milk date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-307842-7q2jd0mf.txt cache: ./cache/cord-307842-7q2jd0mf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307842-7q2jd0mf.txt' === file2bib.sh === id: cord-306438-db2rqz4d author: Kalathiya, Umesh title: Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-306438-db2rqz4d.txt cache: ./cache/cord-306438-db2rqz4d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306438-db2rqz4d.txt' === file2bib.sh === id: cord-305959-x061q8t7 author: Davoudi-Monfared, Effat title: A Randomized Clinical Trial of the Efficacy and Safety of Interferon β-1a in Treatment of Severe COVID-19 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-305959-x061q8t7.txt cache: ./cache/cord-305959-x061q8t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305959-x061q8t7.txt' === file2bib.sh === id: cord-307436-qcdlcxyb author: Bui, L. V. title: Estimation of the incubation period of SARS-CoV-2 in Vietnam date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-307436-qcdlcxyb.txt cache: ./cache/cord-307436-qcdlcxyb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307436-qcdlcxyb.txt' === file2bib.sh === id: cord-307815-reg04lpt author: Brancatella, Alessandro title: Is subacute thyroiditis an underestimated manifestation of SARS-CoV-2 infection? Insights from a case series date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-307815-reg04lpt.txt cache: ./cache/cord-307815-reg04lpt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307815-reg04lpt.txt' === file2bib.sh === id: cord-307702-n74wvika author: Durant, Thomas J S title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-307702-n74wvika.txt cache: ./cache/cord-307702-n74wvika.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307702-n74wvika.txt' === file2bib.sh === id: cord-307701-fujejfwb author: Gaurav, Shubham title: Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-307701-fujejfwb.txt cache: ./cache/cord-307701-fujejfwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307701-fujejfwb.txt' === file2bib.sh === id: cord-307463-bheq9p5w author: Rödel, Franz title: Low-dose radiation therapy for COVID-19 pneumopathy: what is the evidence? date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-307463-bheq9p5w.txt cache: ./cache/cord-307463-bheq9p5w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307463-bheq9p5w.txt' === file2bib.sh === id: cord-307227-x6xketcn author: Martin, William R. title: Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-307227-x6xketcn.txt cache: ./cache/cord-307227-x6xketcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307227-x6xketcn.txt' === file2bib.sh === id: cord-307671-f9l2l8fi author: Said, Mohammed title: The Forgotten Element in the Resumption of Elective Bariatric Surgery During the COVID-19 Pandemic: the Patient Consent! date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-307671-f9l2l8fi.txt cache: ./cache/cord-307671-f9l2l8fi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307671-f9l2l8fi.txt' === file2bib.sh === id: cord-307885-butuv3n1 author: Galvani, Alison P. title: Emerging Infections: What Have We Learned from SARS? date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-307885-butuv3n1.txt cache: ./cache/cord-307885-butuv3n1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-307885-butuv3n1.txt' === file2bib.sh === id: cord-306431-r83n27la author: Chan, Chak-Ming title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function date: 2009-05-04 pages: extension: .txt txt: ./txt/cord-306431-r83n27la.txt cache: ./cache/cord-306431-r83n27la.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306431-r83n27la.txt' === file2bib.sh === id: cord-308021-cnf4xljc author: Kohns Vasconcelos, Malte title: SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-308021-cnf4xljc.txt cache: ./cache/cord-308021-cnf4xljc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308021-cnf4xljc.txt' === file2bib.sh === id: cord-306414-2dv3qced author: Gutierrez, Lucas title: Deciphering the TCR Repertoire to Solve the COVID-19 Mystery date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-306414-2dv3qced.txt cache: ./cache/cord-306414-2dv3qced.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306414-2dv3qced.txt' === file2bib.sh === id: cord-307502-vuju89lc author: Leipe, J. title: SARS-CoV-2 & Rheuma: Konsequenzen der SARS-CoV-2-Pandemie für Patienten mit entzündlich rheumatischen Erkrankungen. Ein Vergleich der Handlungsempfehlungen rheumatologischer Fachgesellschaften und Risikobewertung verschiedener antirheumatischer Therapien date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-307502-vuju89lc.txt cache: ./cache/cord-307502-vuju89lc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307502-vuju89lc.txt' === file2bib.sh === id: cord-306901-uuwgpuhw author: Roy, Sylvie title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-306901-uuwgpuhw.txt cache: ./cache/cord-306901-uuwgpuhw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306901-uuwgpuhw.txt' === file2bib.sh === id: cord-306881-wrd2rhjz author: Gehrie, Eric title: Transfusion Service Response to the COVID-19 Pandemic date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-306881-wrd2rhjz.txt cache: ./cache/cord-306881-wrd2rhjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306881-wrd2rhjz.txt' === file2bib.sh === id: cord-307556-k2lavvca author: Jang, Hongje title: Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date: 2013-02-18 pages: extension: .txt txt: ./txt/cord-307556-k2lavvca.txt cache: ./cache/cord-307556-k2lavvca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307556-k2lavvca.txt' === file2bib.sh === id: cord-308071-1bk3xuwf author: Lang, Christian title: Lung transplantation for COVID-19-associated acute respiratory distress syndrome in a PCR-positive patient date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-308071-1bk3xuwf.txt cache: ./cache/cord-308071-1bk3xuwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308071-1bk3xuwf.txt' === file2bib.sh === id: cord-307653-nyr6mtj1 author: Palmeira, Patricia title: Why is SARS-CoV-2 infection milder among children? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-307653-nyr6mtj1.txt cache: ./cache/cord-307653-nyr6mtj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307653-nyr6mtj1.txt' === file2bib.sh === id: cord-308080-1heu9vuv author: Simulundu, Edgar title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-308080-1heu9vuv.txt cache: ./cache/cord-308080-1heu9vuv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308080-1heu9vuv.txt' === file2bib.sh === id: cord-307303-9mzs5dl4 author: Barnett, Daniel J. title: The Application of the Haddon Matrix to Public Health Readiness and Response Planning date: 2005-02-02 pages: extension: .txt txt: ./txt/cord-307303-9mzs5dl4.txt cache: ./cache/cord-307303-9mzs5dl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307303-9mzs5dl4.txt' === file2bib.sh === id: cord-307490-b4un4703 author: Chan, Sophia S.C. title: Improving older adults’ knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study date: 2007-09-30 pages: extension: .txt txt: ./txt/cord-307490-b4un4703.txt cache: ./cache/cord-307490-b4un4703.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307490-b4un4703.txt' === file2bib.sh === id: cord-306835-juitltpi author: Babaei, Fatemeh title: Curcumin (a constituent of turmeric): New treatment option against COVID‐19 date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-306835-juitltpi.txt cache: ./cache/cord-306835-juitltpi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306835-juitltpi.txt' === file2bib.sh === id: cord-308356-ojx3tasi author: Schwarz, Silke title: Corona bei Kindern: Die Co-Ki Studie: Relevanz von SARS-CoV-2 in der ambulanten pädiatrischen Versorgung in Deutschland date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-308356-ojx3tasi.txt cache: ./cache/cord-308356-ojx3tasi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308356-ojx3tasi.txt' === file2bib.sh === id: cord-307160-1vz0gw1w author: Morais-Almeida, Mário title: COVID-19, asthma, and biologic therapies: What we need to know date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-307160-1vz0gw1w.txt cache: ./cache/cord-307160-1vz0gw1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307160-1vz0gw1w.txt' === file2bib.sh === id: cord-308288-3ewdy5l3 author: Domingues, Renan Barros title: First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-308288-3ewdy5l3.txt cache: ./cache/cord-308288-3ewdy5l3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308288-3ewdy5l3.txt' === file2bib.sh === id: cord-307942-t8165mdx author: Zwald, Marissa L. title: Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-307942-t8165mdx.txt cache: ./cache/cord-307942-t8165mdx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307942-t8165mdx.txt' === file2bib.sh === id: cord-305745-9lngdjow author: Solnier, Julia title: Flavonoids: A complementary approach to conventional therapy of COVID-19? date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-305745-9lngdjow.txt cache: ./cache/cord-305745-9lngdjow.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305745-9lngdjow.txt' === file2bib.sh === id: cord-307242-e20gtx0z author: Jegouic, Sophie M. title: Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-307242-e20gtx0z.txt cache: ./cache/cord-307242-e20gtx0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307242-e20gtx0z.txt' === file2bib.sh === id: cord-307285-bxy0zsc7 author: Dar Odeh, Najla title: COVID-19: Present and Future Challenges for Dental Practice date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-307285-bxy0zsc7.txt cache: ./cache/cord-307285-bxy0zsc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307285-bxy0zsc7.txt' === file2bib.sh === id: cord-307605-8zgyar7e author: Klimek, Ludger title: Management von Anaphylaxie-gefährdeten Patienten während der Covid-19-Pandemie: Ein Positionspapier des Ärzteverbandes Deutscher Allergologen (AeDA)A, der Deutschen Gesellschaft für Allergologie und klinische Immunologie (DGAKI)B, der Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)C und des Deutschen Allergie- und Asthmabundes (DAAB)D date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-307605-8zgyar7e.txt cache: ./cache/cord-307605-8zgyar7e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307605-8zgyar7e.txt' === file2bib.sh === id: cord-308279-gsk4qel5 author: Suzuki, Yuichiro J. title: The viral protein fragment theory of COVID-19 pathogenesis date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-308279-gsk4qel5.txt cache: ./cache/cord-308279-gsk4qel5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308279-gsk4qel5.txt' === file2bib.sh === id: cord-306770-hjzlj8k3 author: Mick, Paul title: Aerosol-generating otolaryngology procedures and the need for enhanced PPE during the COVID-19 pandemic: a literature review date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-306770-hjzlj8k3.txt cache: ./cache/cord-306770-hjzlj8k3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306770-hjzlj8k3.txt' === file2bib.sh === id: cord-307263-znuqdzdp author: Sun, Niuniu title: A Qualitative Study on the Psychological Experience of Caregivers of COVID-19 Patients date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-307263-znuqdzdp.txt cache: ./cache/cord-307263-znuqdzdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307263-znuqdzdp.txt' === file2bib.sh === id: cord-308077-hbxpn5a1 author: Siepmann, Timo title: Variability of symptoms in neuralgic amyotrophy following infection with SARS‐CoV‐2 date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-308077-hbxpn5a1.txt cache: ./cache/cord-308077-hbxpn5a1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308077-hbxpn5a1.txt' === file2bib.sh === id: cord-307858-274a699i author: Hotez, Peter J. title: COVID-19 vaccines: neutralizing antibodies and the alum advantage date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-307858-274a699i.txt cache: ./cache/cord-307858-274a699i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307858-274a699i.txt' === file2bib.sh === id: cord-307770-1igydu3y author: Rawson, Timothy M title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-307770-1igydu3y.txt cache: ./cache/cord-307770-1igydu3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307770-1igydu3y.txt' === file2bib.sh === id: cord-308224-cqi1x92w author: Wu, Lianhua title: Clinical study on the related markers of blood coagulation in the patients with ANFH after SARS date: 2007-10-01 pages: extension: .txt txt: ./txt/cord-308224-cqi1x92w.txt cache: ./cache/cord-308224-cqi1x92w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308224-cqi1x92w.txt' === file2bib.sh === id: cord-308142-3x3n6cpt author: Lee, Nelson title: Chikungunya Fever, Hong Kong date: 2006-11-17 pages: extension: .txt txt: ./txt/cord-308142-3x3n6cpt.txt cache: ./cache/cord-308142-3x3n6cpt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308142-3x3n6cpt.txt' === file2bib.sh === id: cord-308358-2bap7iih author: Friedland, Robert P title: The role for the metagenome in the pathogenesis of COVID-19 date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-308358-2bap7iih.txt cache: ./cache/cord-308358-2bap7iih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308358-2bap7iih.txt' === file2bib.sh === id: cord-308093-m40czdsr author: Matthews, M. M. title: COVID-19 serological survey using micro blood sampling date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-308093-m40czdsr.txt cache: ./cache/cord-308093-m40czdsr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308093-m40czdsr.txt' === file2bib.sh === id: cord-307932-7t41wvw3 author: Guo, Xiaoqin title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-307932-7t41wvw3.txt cache: ./cache/cord-307932-7t41wvw3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307932-7t41wvw3.txt' === file2bib.sh === id: cord-307287-zpq6byml author: Poulsen, Nadia Nicholine title: Cyclosporine and COVID‐19: Risk or Favorable? date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-307287-zpq6byml.txt cache: ./cache/cord-307287-zpq6byml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307287-zpq6byml.txt' === file2bib.sh === id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 pages: extension: .txt txt: ./txt/cord-306424-gf0bglm0.txt cache: ./cache/cord-306424-gf0bglm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306424-gf0bglm0.txt' === file2bib.sh === id: cord-308576-iw8oobbe author: Wuxing, Dai title: Expression and purification of SARS coronavirus membrane protein date: 2004 pages: extension: .txt txt: ./txt/cord-308576-iw8oobbe.txt cache: ./cache/cord-308576-iw8oobbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308576-iw8oobbe.txt' === file2bib.sh === id: cord-308075-1ftswsm8 author: Segura, Patricia Sanz title: Involvement of the digestive system in COVID-19. A review date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-308075-1ftswsm8.txt cache: ./cache/cord-308075-1ftswsm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308075-1ftswsm8.txt' === file2bib.sh === id: cord-307406-59yh48tt author: de Loyola, Mariana Braccialli title: Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-307406-59yh48tt.txt cache: ./cache/cord-307406-59yh48tt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307406-59yh48tt.txt' === file2bib.sh === id: cord-308123-eu0azqfu author: Lee, Yun Young title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-308123-eu0azqfu.txt cache: ./cache/cord-308123-eu0azqfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308123-eu0azqfu.txt' === file2bib.sh === id: cord-308499-xqmguqyi author: Ahmed, Sakir title: Reply to Rheumatologists’ perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-308499-xqmguqyi.txt cache: ./cache/cord-308499-xqmguqyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308499-xqmguqyi.txt' === file2bib.sh === id: cord-307229-wjx90xki author: da Silveira, Matheus Pelinski title: Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-307229-wjx90xki.txt cache: ./cache/cord-307229-wjx90xki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307229-wjx90xki.txt' === file2bib.sh === id: cord-308302-5yns1hg9 author: Wu, Gang title: A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-308302-5yns1hg9.txt cache: ./cache/cord-308302-5yns1hg9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308302-5yns1hg9.txt' === file2bib.sh === id: cord-308501-z3eiac25 author: Zhu, Chengliang title: nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-308501-z3eiac25.txt cache: ./cache/cord-308501-z3eiac25.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308501-z3eiac25.txt' === file2bib.sh === id: cord-308234-4obggisp author: Ford, Nathan title: Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID‐19: initial assessment date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-308234-4obggisp.txt cache: ./cache/cord-308234-4obggisp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308234-4obggisp.txt' === file2bib.sh === id: cord-308408-aciaj30k author: Paneesha, S. title: Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-308408-aciaj30k.txt cache: ./cache/cord-308408-aciaj30k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308408-aciaj30k.txt' === file2bib.sh === id: cord-307036-n44yml79 author: Ng, Oi-Wing title: Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date: 2014-07-14 pages: extension: .txt txt: ./txt/cord-307036-n44yml79.txt cache: ./cache/cord-307036-n44yml79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307036-n44yml79.txt' === file2bib.sh === id: cord-306733-df36w6l7 author: Rosales-Mendoza, Sergio title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-306733-df36w6l7.txt cache: ./cache/cord-306733-df36w6l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-306733-df36w6l7.txt' === file2bib.sh === id: cord-308800-b8gtwdxc author: Goldhaber-Fiebert, Sara N. title: Low-flow Nasal Cannula and Potential Nosocomial Spread of COVID-19 date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-308800-b8gtwdxc.txt cache: ./cache/cord-308800-b8gtwdxc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308800-b8gtwdxc.txt' === file2bib.sh === id: cord-308786-e6rv5csl author: Alamri, Mubarak A. title: Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-308786-e6rv5csl.txt cache: ./cache/cord-308786-e6rv5csl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308786-e6rv5csl.txt' === file2bib.sh === id: cord-308100-tvk47fd7 author: Soetikno, Roy title: Considerations in performing endoscopy during the COVID-19 pandemic date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-308100-tvk47fd7.txt cache: ./cache/cord-308100-tvk47fd7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308100-tvk47fd7.txt' === file2bib.sh === id: cord-308715-uo6h1h2e author: Chandra, Aman title: Personal protective equipment (PPE) for vitreoretinal surgery during COVID-19 date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-308715-uo6h1h2e.txt cache: ./cache/cord-308715-uo6h1h2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308715-uo6h1h2e.txt' === file2bib.sh === id: cord-308231-1t70vkxm author: Childs, S. J. title: Could Deficiencies in South African Data Be the Explanation for Its Early SARS-CoV-2 Peak? date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-308231-1t70vkxm.txt cache: ./cache/cord-308231-1t70vkxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308231-1t70vkxm.txt' === file2bib.sh === id: cord-308310-wtmjt3hf author: Zha, Lisha title: Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-308310-wtmjt3hf.txt cache: ./cache/cord-308310-wtmjt3hf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308310-wtmjt3hf.txt' === file2bib.sh === id: cord-308256-jy20xtwx author: Wells, P. M. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-308256-jy20xtwx.txt cache: ./cache/cord-308256-jy20xtwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308256-jy20xtwx.txt' === file2bib.sh === id: cord-308110-cco3aq4n author: Okamoto, Mika title: The chemokine receptor antagonist cenicriviroc inhibits the replication of SARS-CoV-2 in vitro date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-308110-cco3aq4n.txt cache: ./cache/cord-308110-cco3aq4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308110-cco3aq4n.txt' === file2bib.sh === id: cord-308752-uylvtqlu author: Miao, Y. title: First case of acute pancreatitis related to SARS‐CoV‐2 infection date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-308752-uylvtqlu.txt cache: ./cache/cord-308752-uylvtqlu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308752-uylvtqlu.txt' === file2bib.sh === id: cord-307811-6e3j0pn7 author: Hao, Wei title: Binding of the SARS-CoV-2 Spike Protein to Glycans date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-307811-6e3j0pn7.txt cache: ./cache/cord-307811-6e3j0pn7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307811-6e3j0pn7.txt' === file2bib.sh === id: cord-308760-xonuu04p author: Clerici, Bianca title: A case of newly diagnosed immune thrombocytopenia in the COVID-19 era date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-308760-xonuu04p.txt cache: ./cache/cord-308760-xonuu04p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308760-xonuu04p.txt' === file2bib.sh === id: cord-308740-06jr58kz author: Lazaridis, Charalampos title: Involvement of Cardiovascular System As The Critical Point in Coronavirus Disease 2019 (COVID-19) Prognosis and Recovery date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-308740-06jr58kz.txt cache: ./cache/cord-308740-06jr58kz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308740-06jr58kz.txt' === file2bib.sh === id: cord-308831-u5bj1sod author: Chaung, Jenna title: Coinfection with COVID‐19 and Coronavirus HKU1 – the critical need for repeat testing if clinically indicated date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-308831-u5bj1sod.txt cache: ./cache/cord-308831-u5bj1sod.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308831-u5bj1sod.txt' === file2bib.sh === id: cord-308424-crvnzr44 author: Mascarenhas, Victor Hugo Alves title: Care recommendations for parturient and postpartum women and newborns during the COVID-19 pandemic: a scoping review date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-308424-crvnzr44.txt cache: ./cache/cord-308424-crvnzr44.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308424-crvnzr44.txt' === file2bib.sh === id: cord-309304-glcxrh7t author: Flemming, Sven title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-309304-glcxrh7t.txt cache: ./cache/cord-309304-glcxrh7t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309304-glcxrh7t.txt' === file2bib.sh === id: cord-308342-ycdok8fc author: Shutler, J. title: Risk of SARS-CoV-2 infection from contaminated water systems date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-308342-ycdok8fc.txt cache: ./cache/cord-308342-ycdok8fc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308342-ycdok8fc.txt' === file2bib.sh === id: cord-308667-6jr3z9wx author: Papachristodoulou, Eleni title: Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-308667-6jr3z9wx.txt cache: ./cache/cord-308667-6jr3z9wx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308667-6jr3z9wx.txt' === file2bib.sh === id: cord-308597-ieju8gd8 author: de Carvalho, Renata Cristina title: The interference of COVID-19 in the male reproductive system: Important questions and the future of assisted reproduction techniques date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-308597-ieju8gd8.txt cache: ./cache/cord-308597-ieju8gd8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308597-ieju8gd8.txt' === file2bib.sh === id: cord-308400-8wihm63b author: Kanellopoulou, A. title: Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-308400-8wihm63b.txt cache: ./cache/cord-308400-8wihm63b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308400-8wihm63b.txt' === file2bib.sh === id: cord-309394-vroscj3m author: Belingheri, Michael title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-309394-vroscj3m.txt cache: ./cache/cord-309394-vroscj3m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309394-vroscj3m.txt' === file2bib.sh === id: cord-309091-te15ahvw author: Larson, Derek title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-309091-te15ahvw.txt cache: ./cache/cord-309091-te15ahvw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309091-te15ahvw.txt' === file2bib.sh === id: cord-308252-qwoo7b1l author: Cardinale, Vincenzo title: Intestinal permeability changes with bacterial translocation as key events modulating systemic host immune response to SARS-CoV-2: A working hypothesis date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-308252-qwoo7b1l.txt cache: ./cache/cord-308252-qwoo7b1l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308252-qwoo7b1l.txt' === file2bib.sh === id: cord-308507-hp6m6qrn author: Gan, Yi-Ru title: Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase date: 2005-10-19 pages: extension: .txt txt: ./txt/cord-308507-hp6m6qrn.txt cache: ./cache/cord-308507-hp6m6qrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308507-hp6m6qrn.txt' === file2bib.sh === id: cord-309370-g8d3w7it author: Insausti-García, Alfredo title: Papillophlebitis in a COVID-19 patient: Inflammation and hypercoagulable state date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-309370-g8d3w7it.txt cache: ./cache/cord-309370-g8d3w7it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309370-g8d3w7it.txt' === file2bib.sh === id: cord-308994-4nljzm8a author: Tang, Zhongmin title: Insights from nanotechnology in COVID-19 treatment date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-308994-4nljzm8a.txt cache: ./cache/cord-308994-4nljzm8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308994-4nljzm8a.txt' === file2bib.sh === id: cord-308736-kpz0o1ag author: Heßling, Martin title: Ultraviolet irradiation doses for coronavirus inactivation – review and analysis of coronavirus photoinactivation studies date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-308736-kpz0o1ag.txt cache: ./cache/cord-308736-kpz0o1ag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308736-kpz0o1ag.txt' === file2bib.sh === id: cord-309206-kq77whdx author: Yan, Victoria C. title: Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-309206-kq77whdx.txt cache: ./cache/cord-309206-kq77whdx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309206-kq77whdx.txt' === file2bib.sh === id: cord-308615-4fobikeh author: AKTAS, Busra title: Gut-lung axis and dysbiosis in COVID-19 date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-308615-4fobikeh.txt cache: ./cache/cord-308615-4fobikeh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308615-4fobikeh.txt' === file2bib.sh === id: cord-309513-dleo9rpl author: Zhang, Huilan title: Histopathologic Changes and SARS–CoV-2 Immunostaining in the Lung of a Patient With COVID-19 date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-309513-dleo9rpl.txt cache: ./cache/cord-309513-dleo9rpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309513-dleo9rpl.txt' === file2bib.sh === id: cord-309577-438fotfd author: Xing, Yuhan title: Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-309577-438fotfd.txt cache: ./cache/cord-309577-438fotfd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309577-438fotfd.txt' === file2bib.sh === id: cord-309317-cgs0sui7 author: Galeotti, Caroline title: Autoimmune and inflammatory diseases following COVID-19 date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-309317-cgs0sui7.txt cache: ./cache/cord-309317-cgs0sui7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309317-cgs0sui7.txt' === file2bib.sh === id: cord-308833-ei1faruy author: Zheng, Xiaohong title: Experimental investigation of integrated air purifying technology for bioaerosol removal and inactivation in central air-conditioning system date: 2004 pages: extension: .txt txt: ./txt/cord-308833-ei1faruy.txt cache: ./cache/cord-308833-ei1faruy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308833-ei1faruy.txt' === file2bib.sh === id: cord-309650-6xz9gjq0 author: Chou, Roger title: Update Alert 4: Epidemiology of and Risk Factors for Coronavirus Infection in Health Care Workers date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-309650-6xz9gjq0.txt cache: ./cache/cord-309650-6xz9gjq0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309650-6xz9gjq0.txt' === file2bib.sh === id: cord-308583-vtmwv8zl author: Du, Qishi title: Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase date: 2005-02-15 pages: extension: .txt txt: ./txt/cord-308583-vtmwv8zl.txt cache: ./cache/cord-308583-vtmwv8zl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308583-vtmwv8zl.txt' === file2bib.sh === id: cord-309869-gk0svt2f author: Wiwanitkit, Viroj title: SARS-CoV-2 in Semen date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-309869-gk0svt2f.txt cache: ./cache/cord-309869-gk0svt2f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309869-gk0svt2f.txt' === file2bib.sh === id: cord-309074-pys4aa60 author: Huang, Victoria W. title: Telehealth in the times of SARS-CoV-2 infection for the Otolaryngologist date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-309074-pys4aa60.txt cache: ./cache/cord-309074-pys4aa60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309074-pys4aa60.txt' === file2bib.sh === id: cord-308945-i2agpvhk author: Phipps, William S title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-308945-i2agpvhk.txt cache: ./cache/cord-308945-i2agpvhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308945-i2agpvhk.txt' === file2bib.sh === id: cord-309193-v8lphej4 author: Lemriss, Sanaâ title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-309193-v8lphej4.txt cache: ./cache/cord-309193-v8lphej4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309193-v8lphej4.txt' === file2bib.sh === id: cord-309360-cpis1l4u author: Barrios-López, J. M. title: Ischaemic stroke and SARS-CoV-2 infection: A causal or incidental association? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-309360-cpis1l4u.txt cache: ./cache/cord-309360-cpis1l4u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309360-cpis1l4u.txt' === file2bib.sh === id: cord-308996-tf0v2ojk author: Maas, Angela HEM title: The Coronavirus Disease 2019 Outbreak Highlights the Importance of Sex-sensitive Medicine date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-308996-tf0v2ojk.txt cache: ./cache/cord-308996-tf0v2ojk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308996-tf0v2ojk.txt' === file2bib.sh === id: cord-309289-vm0k7hfx author: Rothan, Hussin A. title: The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-309289-vm0k7hfx.txt cache: ./cache/cord-309289-vm0k7hfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309289-vm0k7hfx.txt' === file2bib.sh === id: cord-308912-2pd801t1 author: Bensimon, Cécile M. title: A qualitative study of the duty to care in communicable disease outbreaks date: 2007-12-31 pages: extension: .txt txt: ./txt/cord-308912-2pd801t1.txt cache: ./cache/cord-308912-2pd801t1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308912-2pd801t1.txt' === file2bib.sh === id: cord-309120-05bg7rfa author: Niazi, Sadegh title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-309120-05bg7rfa.txt cache: ./cache/cord-309120-05bg7rfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309120-05bg7rfa.txt' === file2bib.sh === id: cord-309737-u960ftdm author: Lolachi, Sanaz title: Macrophage activation syndrome as an unusual presentation of paucisymptomatic severe acute respiratory syndrome coronavirus 2 infection: A case report date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-309737-u960ftdm.txt cache: ./cache/cord-309737-u960ftdm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309737-u960ftdm.txt' === file2bib.sh === id: cord-309517-yh4d414y author: Yu, Chao title: Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-309517-yh4d414y.txt cache: ./cache/cord-309517-yh4d414y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309517-yh4d414y.txt' === file2bib.sh === id: cord-309794-scqkyr5g author: Sharif‐Askari, Fatemeh Saheb title: Are patients with chronic rhinosinusitis with nasal polyps at a decreased risk of COVID‐19 infection? date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-309794-scqkyr5g.txt cache: ./cache/cord-309794-scqkyr5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309794-scqkyr5g.txt' === file2bib.sh === id: cord-309200-t2xugb8l author: Asadi, Sima title: The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-309200-t2xugb8l.txt cache: ./cache/cord-309200-t2xugb8l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309200-t2xugb8l.txt' === file2bib.sh === id: cord-309856-flkjl1dm author: Westblade, Lars F. title: SARS-CoV-2 Viral Load Predicts Mortality in Patients with and Without Cancer Who Are Hospitalized with COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-309856-flkjl1dm.txt cache: ./cache/cord-309856-flkjl1dm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309856-flkjl1dm.txt' === file2bib.sh === id: cord-309418-dx6e0lri author: Segalés, Joaquim title: Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-309418-dx6e0lri.txt cache: ./cache/cord-309418-dx6e0lri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309418-dx6e0lri.txt' === file2bib.sh === id: cord-309914-1lpl26eo author: Peterson, Danielle title: The use of Janus kinase inhibitors in the time of SARS-CoV-2 date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-309914-1lpl26eo.txt cache: ./cache/cord-309914-1lpl26eo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309914-1lpl26eo.txt' === file2bib.sh === id: cord-308451-pmwmfl3w author: Chiang, Shu-Fen title: SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells date: 2010-07-27 pages: extension: .txt txt: ./txt/cord-308451-pmwmfl3w.txt cache: ./cache/cord-308451-pmwmfl3w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308451-pmwmfl3w.txt' === file2bib.sh === id: cord-309629-7jtnhn65 author: Thomas, Viju title: International society for gynecologic endoscopy (ISGE) guidelines and recommendations on gynecological endoscopy during the evolutionary phases of the SARS-CoV-2 pandemic date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-309629-7jtnhn65.txt cache: ./cache/cord-309629-7jtnhn65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309629-7jtnhn65.txt' === file2bib.sh === id: cord-309541-2vqk7fx1 author: Sekizuka, Tsuyoshi title: Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-309541-2vqk7fx1.txt cache: ./cache/cord-309541-2vqk7fx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309541-2vqk7fx1.txt' === file2bib.sh === id: cord-309633-1cd74xdl author: Rogers, Julia H. title: Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-309633-1cd74xdl.txt cache: ./cache/cord-309633-1cd74xdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309633-1cd74xdl.txt' === file2bib.sh === id: cord-309319-si5c14e8 author: Cao, Chunxiang title: Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China date: 2016-08-15 pages: extension: .txt txt: ./txt/cord-309319-si5c14e8.txt cache: ./cache/cord-309319-si5c14e8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309319-si5c14e8.txt' === file2bib.sh === id: cord-307860-iqk1yiw4 author: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-307860-iqk1yiw4.txt cache: ./cache/cord-307860-iqk1yiw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307860-iqk1yiw4.txt' === file2bib.sh === id: cord-309582-ihrj84hr author: AlNaamani, Khalid title: Medical research during the COVID-19 pandemic date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-309582-ihrj84hr.txt cache: ./cache/cord-309582-ihrj84hr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309582-ihrj84hr.txt' === file2bib.sh === id: cord-309986-p7pqla6l author: Harkin, Timothy J title: Delayed diagnosis of COVID-19 in a 34-year-old man with atypical presentation date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-309986-p7pqla6l.txt cache: ./cache/cord-309986-p7pqla6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309986-p7pqla6l.txt' === file2bib.sh === id: cord-308370-9av7qw10 author: Islam, Rajib title: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-308370-9av7qw10.txt cache: ./cache/cord-308370-9av7qw10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308370-9av7qw10.txt' === file2bib.sh === id: cord-309540-4pk5tq5w author: Brandsma, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-309540-4pk5tq5w.txt cache: ./cache/cord-309540-4pk5tq5w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309540-4pk5tq5w.txt' === file2bib.sh === id: cord-309182-t9ywnshj author: Premkumar, Lakshmanane title: The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-309182-t9ywnshj.txt cache: ./cache/cord-309182-t9ywnshj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309182-t9ywnshj.txt' === file2bib.sh === id: cord-310051-bl8l4bgo author: Leitner, Thomas title: Where did SARS-CoV-2 come from? date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-310051-bl8l4bgo.txt cache: ./cache/cord-310051-bl8l4bgo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310051-bl8l4bgo.txt' === file2bib.sh === id: cord-309554-ctc84tfy author: Pang, Ronald TK title: Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome date: 2006-03-01 pages: extension: .txt txt: ./txt/cord-309554-ctc84tfy.txt cache: ./cache/cord-309554-ctc84tfy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309554-ctc84tfy.txt' === file2bib.sh === id: cord-310299-isdsestc author: Hosseini, Akram A. title: Delirium as a presenting feature in COVID-19: neuroinvasive infection or autoimmune encephalopathy? date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-310299-isdsestc.txt cache: ./cache/cord-310299-isdsestc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310299-isdsestc.txt' === file2bib.sh === id: cord-310160-55yltan1 author: Pham, Jimmykim title: Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-310160-55yltan1.txt cache: ./cache/cord-310160-55yltan1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310160-55yltan1.txt' === file2bib.sh === id: cord-310291-z79x349o author: Holland, LaRinda A. title: An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-310291-z79x349o.txt cache: ./cache/cord-310291-z79x349o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310291-z79x349o.txt' === file2bib.sh === id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 pages: extension: .txt txt: ./txt/cord-309043-dlmx12vt.txt cache: ./cache/cord-309043-dlmx12vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309043-dlmx12vt.txt' === file2bib.sh === id: cord-309411-2dfiwo65 author: Paris, Kristina A. title: Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-309411-2dfiwo65.txt cache: ./cache/cord-309411-2dfiwo65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309411-2dfiwo65.txt' === file2bib.sh === id: cord-309934-kcyao9i9 author: Tan, Emily L.C. title: Inhibition of SARS Coronavirus Infection In Vitro with Clinically Approved Antiviral Drugs date: 2004-04-17 pages: extension: .txt txt: ./txt/cord-309934-kcyao9i9.txt cache: ./cache/cord-309934-kcyao9i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309934-kcyao9i9.txt' === file2bib.sh === id: cord-309147-c3ikb81g author: Nadeem, Muhammad Shahid title: Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19) date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-309147-c3ikb81g.txt cache: ./cache/cord-309147-c3ikb81g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309147-c3ikb81g.txt' === file2bib.sh === id: cord-309876-l0xginsa author: Vena, Antonio title: Prevalence of Antibodies to SARS-CoV-2 in Italian Adults and Associated Risk Factors date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-309876-l0xginsa.txt cache: ./cache/cord-309876-l0xginsa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309876-l0xginsa.txt' === file2bib.sh === id: cord-310008-hwpn7ti1 author: Lyons-Weiler, James title: Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-310008-hwpn7ti1.txt cache: ./cache/cord-310008-hwpn7ti1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310008-hwpn7ti1.txt' === file2bib.sh === id: cord-309302-n6cd2fc3 author: Wang, Li title: Clinical management of lung cancer patients during the outbreak of COVID-19 epidemic date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-309302-n6cd2fc3.txt cache: ./cache/cord-309302-n6cd2fc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309302-n6cd2fc3.txt' === file2bib.sh === id: cord-309728-7vfotgrr author: Johnson, Kristen M. title: Managing COVID‐19 in Renal Transplant Recipients: A Review of Recent Literature and Case Supporting Corticosteroid‐sparing Immunosuppression date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-309728-7vfotgrr.txt cache: ./cache/cord-309728-7vfotgrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309728-7vfotgrr.txt' === file2bib.sh === id: cord-309970-jkmjiika author: Liu, Qin title: From SARS to COVID-19: What lessons have we learned? date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-309970-jkmjiika.txt cache: ./cache/cord-309970-jkmjiika.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309970-jkmjiika.txt' === file2bib.sh === id: cord-309138-44qpk2vf author: Khanna, Kanika title: Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date: 2020-10-03 pages: extension: .txt txt: ./txt/cord-309138-44qpk2vf.txt cache: ./cache/cord-309138-44qpk2vf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309138-44qpk2vf.txt' === file2bib.sh === id: cord-309089-ex9nh1yi author: Coperchini, Francesca title: The Cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-309089-ex9nh1yi.txt cache: ./cache/cord-309089-ex9nh1yi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309089-ex9nh1yi.txt' === file2bib.sh === id: cord-309915-isw1arrp author: Perez-Jurado, L. A. title: Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men? date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-309915-isw1arrp.txt cache: ./cache/cord-309915-isw1arrp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309915-isw1arrp.txt' === file2bib.sh === id: cord-310096-a242g5kg author: Yokota, I. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-310096-a242g5kg.txt cache: ./cache/cord-310096-a242g5kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310096-a242g5kg.txt' === file2bib.sh === id: cord-310027-846vp7ii author: Ma, Lin-Lu title: Coronavirus Disease 2019 Related Clinical Studies: A Cross-Sectional Analysis date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-310027-846vp7ii.txt cache: ./cache/cord-310027-846vp7ii.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310027-846vp7ii.txt' === file2bib.sh === id: cord-309588-kw4d32dt author: Chan, Michael H.M. title: Steroid-induced osteonecrosis in severe acute respiratory syndrome: a retrospective analysis of biochemical markers of bone metabolism and corticosteroid therapy date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-309588-kw4d32dt.txt cache: ./cache/cord-309588-kw4d32dt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309588-kw4d32dt.txt' === file2bib.sh === id: cord-309999-izdl0f2i author: Qin, Ede title: Immunogenicity and protective efficacy in monkeys of purified inactivated Vero-cell SARS vaccine date: 2006-02-13 pages: extension: .txt txt: ./txt/cord-309999-izdl0f2i.txt cache: ./cache/cord-309999-izdl0f2i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309999-izdl0f2i.txt' === file2bib.sh === id: cord-308428-zw26usmh author: Walter, Justin D. title: Highly potent bispecific sybodies neutralize SARS-CoV-2 date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-308428-zw26usmh.txt cache: ./cache/cord-308428-zw26usmh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308428-zw26usmh.txt' === file2bib.sh === id: cord-309829-3dlfcy31 author: Parupudi, Tejasvi title: Evidence-based point-of-care technology development during the COVID-19 pandemic date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-309829-3dlfcy31.txt cache: ./cache/cord-309829-3dlfcy31.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309829-3dlfcy31.txt' === file2bib.sh === id: cord-309729-nd48uh8e author: Antunes, Adriane E.C. title: Potential contribution of beneficial microbes to face the COVID- 19 pandemic date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-309729-nd48uh8e.txt cache: ./cache/cord-309729-nd48uh8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309729-nd48uh8e.txt' === file2bib.sh === id: cord-309898-sju15hev author: Hu, Yiwen title: Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-309898-sju15hev.txt cache: ./cache/cord-309898-sju15hev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309898-sju15hev.txt' === file2bib.sh === id: cord-310687-qw164eyl author: Chan, Ming-Chin title: Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-310687-qw164eyl.txt cache: ./cache/cord-310687-qw164eyl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310687-qw164eyl.txt' === file2bib.sh === id: cord-310091-x31g02xw author: Zhang, Zhilan title: Pan-cancer analysis reveals that ACE2 is positively associated with immunotherapy response and is a potential protective factor for cancer progression date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-310091-x31g02xw.txt cache: ./cache/cord-310091-x31g02xw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310091-x31g02xw.txt' === file2bib.sh === id: cord-309930-zlzuoeh2 author: Zhou, Zhiming title: Coronavirus disease 2019: initial chest CT findings date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-309930-zlzuoeh2.txt cache: ./cache/cord-309930-zlzuoeh2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309930-zlzuoeh2.txt' === file2bib.sh === id: cord-310230-9wfb43gt author: Ghorbani, Mahdi title: Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-310230-9wfb43gt.txt cache: ./cache/cord-310230-9wfb43gt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310230-9wfb43gt.txt' === file2bib.sh === id: cord-310464-lkdkdque author: Rayko, Mikhail title: Quality control of low-frequency variants in SARS-CoV-2 genomes date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-310464-lkdkdque.txt cache: ./cache/cord-310464-lkdkdque.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310464-lkdkdque.txt' === file2bib.sh === id: cord-309931-cpzp33b3 author: Zawawi, Ayat title: The impact of COVID-19 pandemic on malaria elimination date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-309931-cpzp33b3.txt cache: ./cache/cord-309931-cpzp33b3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309931-cpzp33b3.txt' === file2bib.sh === id: cord-310419-s3qkscw7 author: Lephart, Paul R. title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-310419-s3qkscw7.txt cache: ./cache/cord-310419-s3qkscw7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310419-s3qkscw7.txt' === file2bib.sh === id: cord-309323-yflng8m3 author: Thomas, T. title: COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-309323-yflng8m3.txt cache: ./cache/cord-309323-yflng8m3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309323-yflng8m3.txt' === file2bib.sh === id: cord-310184-qth1y88o author: Alunno, Alessia title: Storm, typhoon, cyclone or hurricane in patients with COVID-19? Beware of the same storm that has a different origin date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-310184-qth1y88o.txt cache: ./cache/cord-310184-qth1y88o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310184-qth1y88o.txt' === file2bib.sh === id: cord-309556-xv3413k1 author: Chow, Ryan D. title: The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-309556-xv3413k1.txt cache: ./cache/cord-309556-xv3413k1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309556-xv3413k1.txt' === file2bib.sh === id: cord-310879-b8tdug93 author: Beddingfield, Brandon J. title: In the Age of CoVID: Genomic Changes Over the Lifespan Help Explain Severe SARS-CoV-2 Disease date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-310879-b8tdug93.txt cache: ./cache/cord-310879-b8tdug93.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310879-b8tdug93.txt' === file2bib.sh === id: cord-310042-9z8rkzq8 author: Aysha, Al‐Ani title: Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-310042-9z8rkzq8.txt cache: ./cache/cord-310042-9z8rkzq8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310042-9z8rkzq8.txt' === file2bib.sh === id: cord-310333-70ldbw3r author: de Souza, Wanderley title: COVID-19 and parasitology date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-310333-70ldbw3r.txt cache: ./cache/cord-310333-70ldbw3r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-310333-70ldbw3r.txt' === file2bib.sh === id: cord-308857-otsrexqu author: Goel, Saurav title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-308857-otsrexqu.txt cache: ./cache/cord-308857-otsrexqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308857-otsrexqu.txt' === file2bib.sh === id: cord-310221-car394ou author: Chandrashekar, Abishek title: SARS-CoV-2 infection protects against rechallenge in rhesus macaques date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-310221-car394ou.txt cache: ./cache/cord-310221-car394ou.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310221-car394ou.txt' === file2bib.sh === id: cord-310061-nro623aa author: Valitutto, Marc T. title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-310061-nro623aa.txt cache: ./cache/cord-310061-nro623aa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310061-nro623aa.txt' === file2bib.sh === id: cord-310195-am3u7z76 author: Waller, J. title: Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-310195-am3u7z76.txt cache: ./cache/cord-310195-am3u7z76.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310195-am3u7z76.txt' === file2bib.sh === id: cord-310392-fmobf1f1 author: Sekizuka, Tsuyoshi title: SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-310392-fmobf1f1.txt cache: ./cache/cord-310392-fmobf1f1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310392-fmobf1f1.txt' === file2bib.sh === id: cord-308066-lrbi5198 author: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 pages: extension: .txt txt: ./txt/cord-308066-lrbi5198.txt cache: ./cache/cord-308066-lrbi5198.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308066-lrbi5198.txt' === file2bib.sh === id: cord-310692-8fuj9td2 author: Coste, A. T. title: Indication for SARS-CoV-2 serology: first month follow-up date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-310692-8fuj9td2.txt cache: ./cache/cord-310692-8fuj9td2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310692-8fuj9td2.txt' === file2bib.sh === id: cord-310594-i0586vfw author: Weemaes, Matthias title: Laboratory information system requirements to manage the COVID-19 pandemic: a report from the Belgian national reference testing center date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-310594-i0586vfw.txt cache: ./cache/cord-310594-i0586vfw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310594-i0586vfw.txt' === file2bib.sh === id: cord-310064-p8u424ch author: Katz, Andrew P. title: False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-310064-p8u424ch.txt cache: ./cache/cord-310064-p8u424ch.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310064-p8u424ch.txt' === file2bib.sh === id: cord-310017-c8rd714a author: Popa, Alexandra title: Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-310017-c8rd714a.txt cache: ./cache/cord-310017-c8rd714a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310017-c8rd714a.txt' === file2bib.sh === id: cord-310631-ru5f69qg author: Joachim, Denner title: SARS-CoV-2 and enhancing antibodies date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-310631-ru5f69qg.txt cache: ./cache/cord-310631-ru5f69qg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310631-ru5f69qg.txt' === file2bib.sh === id: cord-310063-8nbmrjrw author: Selva, K. J. title: Distinct systems serology features in children, elderly and COVID patients date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-310063-8nbmrjrw.txt cache: ./cache/cord-310063-8nbmrjrw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310063-8nbmrjrw.txt' === file2bib.sh === id: cord-310201-70fj4fhr author: Wei, D.-Q. title: Anti-SARS drug screening by molecular docking date: 2006-05-22 pages: extension: .txt txt: ./txt/cord-310201-70fj4fhr.txt cache: ./cache/cord-310201-70fj4fhr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310201-70fj4fhr.txt' === file2bib.sh === id: cord-310062-mmlh9i1o author: Luo, Haibin title: In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS date: 2004-12-01 pages: extension: .txt txt: ./txt/cord-310062-mmlh9i1o.txt cache: ./cache/cord-310062-mmlh9i1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310062-mmlh9i1o.txt' === file2bib.sh === id: cord-310477-vniokol0 author: Pontes, Camila title: Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-310477-vniokol0.txt cache: ./cache/cord-310477-vniokol0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310477-vniokol0.txt' === file2bib.sh === id: cord-310411-l0slp1wa author: Rusanen, J. title: Rapid homogeneous assay for detecting antibodies against SARS-CoV-2 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-310411-l0slp1wa.txt cache: ./cache/cord-310411-l0slp1wa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310411-l0slp1wa.txt' === file2bib.sh === id: cord-310623-zbjgr9jk author: Ellington, Sascha title: Characteristics of Women of Reproductive Age with Laboratory-Confirmed SARS-CoV-2 Infection by Pregnancy Status — United States, January 22–June 7, 2020 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-310623-zbjgr9jk.txt cache: ./cache/cord-310623-zbjgr9jk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310623-zbjgr9jk.txt' === file2bib.sh === id: cord-310124-3bc8zeww author: Ratajczak, Mariusz Z. title: SARS-CoV-2 Entry Receptor ACE2 Is Expressed on Very Small CD45(−) Precursors of Hematopoietic and Endothelial Cells and in Response to Virus Spike Protein Activates the Nlrp3 Inflammasome date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-310124-3bc8zeww.txt cache: ./cache/cord-310124-3bc8zeww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310124-3bc8zeww.txt' === file2bib.sh === id: cord-310753-sv88b0dt author: Marks, M. title: Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-310753-sv88b0dt.txt cache: ./cache/cord-310753-sv88b0dt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310753-sv88b0dt.txt' === file2bib.sh === id: cord-309619-glb2y82u author: Domingo, Pere title: The four horsemen of a viral Apocalypse: The pathogenesis of SARS-CoV-2 infection (COVID-19) date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-309619-glb2y82u.txt cache: ./cache/cord-309619-glb2y82u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309619-glb2y82u.txt' === file2bib.sh === id: cord-310946-rjwyirld author: Wiseman, Jessica title: False negative SARS-CoV-2 PCR - A case report and literature review date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-310946-rjwyirld.txt cache: ./cache/cord-310946-rjwyirld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310946-rjwyirld.txt' === file2bib.sh === id: cord-310239-mmvuij3k author: Arentz, Susan title: Clinical significance summary: Preliminary results of a rapid review of zinc for the prevention and treatment of SARS-CoV-2 and other acute viral respiratory infections date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-310239-mmvuij3k.txt cache: ./cache/cord-310239-mmvuij3k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310239-mmvuij3k.txt' === file2bib.sh === id: cord-310651-pxfwe67t author: Leung, Gabriel M. title: SARS-CoV Antibody Prevalence in All Hong Kong Patient Contacts date: 2004-09-17 pages: extension: .txt txt: ./txt/cord-310651-pxfwe67t.txt cache: ./cache/cord-310651-pxfwe67t.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310651-pxfwe67t.txt' === file2bib.sh === id: cord-310331-29srzbuk author: Xu, Jiuyang title: 2019 novel Coronavirus outbreak: a quiz or final exam? date: 2020-03-20 pages: extension: .txt txt: ./txt/cord-310331-29srzbuk.txt cache: ./cache/cord-310331-29srzbuk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310331-29srzbuk.txt' === file2bib.sh === id: cord-310438-744r7gc3 author: Chan, Ta-Chien title: The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date: 2010-06-25 pages: extension: .txt txt: ./txt/cord-310438-744r7gc3.txt cache: ./cache/cord-310438-744r7gc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310438-744r7gc3.txt' === file2bib.sh === id: cord-311207-qkkn0297 author: Pegoraro, Manuela title: Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-311207-qkkn0297.txt cache: ./cache/cord-311207-qkkn0297.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311207-qkkn0297.txt' === file2bib.sh === id: cord-310396-jitao9k0 author: Lei, Yu title: MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date: 2009-03-07 pages: extension: .txt txt: ./txt/cord-310396-jitao9k0.txt cache: ./cache/cord-310396-jitao9k0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310396-jitao9k0.txt' === file2bib.sh === id: cord-310507-5h6egve4 author: van Doorn, Amarylle S. title: Systematic review with meta‐analysis: SARS‐CoV‐2 stool testing and the potential for faecal‐oral transmission date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-310507-5h6egve4.txt cache: ./cache/cord-310507-5h6egve4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310507-5h6egve4.txt' === file2bib.sh === id: cord-310774-rpc8hrrx author: Yang, Chongtu title: Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-310774-rpc8hrrx.txt cache: ./cache/cord-310774-rpc8hrrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310774-rpc8hrrx.txt' === file2bib.sh === id: cord-311333-shvtfxog author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-311333-shvtfxog.txt cache: ./cache/cord-311333-shvtfxog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311333-shvtfxog.txt' === file2bib.sh === id: cord-311105-8edwb59c author: Karamese, M. title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-311105-8edwb59c.txt cache: ./cache/cord-311105-8edwb59c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311105-8edwb59c.txt' === file2bib.sh === id: cord-310803-iig414jg author: Khazeei Tabari, Mohammad Amin title: Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-310803-iig414jg.txt cache: ./cache/cord-310803-iig414jg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310803-iig414jg.txt' === file2bib.sh === id: cord-310624-3kojrkz7 author: Flores-Alanis, Alejandro title: The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789 date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-310624-3kojrkz7.txt cache: ./cache/cord-310624-3kojrkz7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310624-3kojrkz7.txt' === file2bib.sh === id: cord-310605-r63sg73c author: Dorward, D. A. title: Tissue-specific tolerance in fatal Covid-19 date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-310605-r63sg73c.txt cache: ./cache/cord-310605-r63sg73c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310605-r63sg73c.txt' === file2bib.sh === id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-310920-itqwhi6a.txt cache: ./cache/cord-310920-itqwhi6a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310920-itqwhi6a.txt' === file2bib.sh === id: cord-310606-msmh7d8m author: Westerhuis, B. M. title: Severe COVID-19 patients display a back boost of seasonal coronavirus-specific antibodies date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-310606-msmh7d8m.txt cache: ./cache/cord-310606-msmh7d8m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310606-msmh7d8m.txt' === file2bib.sh === id: cord-310691-6danlh8h author: Ma, Simin title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-310691-6danlh8h.txt cache: ./cache/cord-310691-6danlh8h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310691-6danlh8h.txt' === file2bib.sh === id: cord-311358-nrj4aysh author: Peng, Yuzhu title: Is novel coronavirus disease (COVID‐19) transmitted through conjunctiva? date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-311358-nrj4aysh.txt cache: ./cache/cord-311358-nrj4aysh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311358-nrj4aysh.txt' === file2bib.sh === id: cord-310909-nc82a70n author: Qiu, Maofeng title: Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date: 2005-04-13 pages: extension: .txt txt: ./txt/cord-310909-nc82a70n.txt cache: ./cache/cord-310909-nc82a70n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310909-nc82a70n.txt' === file2bib.sh === id: cord-311123-swiewewq author: Zhuang, Shu-Fan title: Low-grade fever during COVID-19 convalescence: A report of 3 cases date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-311123-swiewewq.txt cache: ./cache/cord-311123-swiewewq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311123-swiewewq.txt' === file2bib.sh === id: cord-310857-i9v9antx author: Blaisdell, Laura L. title: Preventing and Mitigating SARS-CoV-2 Transmission — Four Overnight Camps, Maine, June–August 2020 date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-310857-i9v9antx.txt cache: ./cache/cord-310857-i9v9antx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310857-i9v9antx.txt' === file2bib.sh === id: cord-311216-mfqlv3nh author: Buckley, Leo F. title: Cardiovascular Pharmacology in the Time of COVID-19: A Focus on Angiotensin-Converting Enzyme 2 date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-311216-mfqlv3nh.txt cache: ./cache/cord-311216-mfqlv3nh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311216-mfqlv3nh.txt' === file2bib.sh === id: cord-310680-klywz85w author: Li, Qihan title: The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date: 2005-04-06 pages: extension: .txt txt: ./txt/cord-310680-klywz85w.txt cache: ./cache/cord-310680-klywz85w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310680-klywz85w.txt' === file2bib.sh === id: cord-310928-g553afo9 author: Murch, Simon H title: Common determinants of severe Covid-19 infection are explicable by SARS-CoV-2 secreted glycoprotein interaction with the CD33-related Siglecs, Siglec-3 and Siglec-5/14 date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-310928-g553afo9.txt cache: ./cache/cord-310928-g553afo9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310928-g553afo9.txt' === file2bib.sh === id: cord-307148-k1uo3fxm author: Bradshaw, Patrick C. title: COVID-19: Proposing a Ketone-Based Metabolic Therapy as a Treatment to Blunt the Cytokine Storm date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-307148-k1uo3fxm.txt cache: ./cache/cord-307148-k1uo3fxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-307148-k1uo3fxm.txt' === file2bib.sh === id: cord-310657-04pp0o74 author: Lu, Renfei title: A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-310657-04pp0o74.txt cache: ./cache/cord-310657-04pp0o74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310657-04pp0o74.txt' === file2bib.sh === id: cord-311066-62edsbfc author: Cox, Brian J. title: Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-311066-62edsbfc.txt cache: ./cache/cord-311066-62edsbfc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311066-62edsbfc.txt' === file2bib.sh === id: cord-310790-3ikgmiof author: Cherrak, Sabri Ahmed title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-310790-3ikgmiof.txt cache: ./cache/cord-310790-3ikgmiof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310790-3ikgmiof.txt' === file2bib.sh === id: cord-311035-s3tkbh9r author: Procko, Erik title: Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-311035-s3tkbh9r.txt cache: ./cache/cord-311035-s3tkbh9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311035-s3tkbh9r.txt' === file2bib.sh === id: cord-311604-qsc3nks6 author: Wong, River Chun‐Wai title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-311604-qsc3nks6.txt cache: ./cache/cord-311604-qsc3nks6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311604-qsc3nks6.txt' === file2bib.sh === id: cord-311429-adcmgd1i author: Salzberger, B. title: Epidemiologie von SARS-CoV-2/COVID 19: Aktueller Stand date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-311429-adcmgd1i.txt cache: ./cache/cord-311429-adcmgd1i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311429-adcmgd1i.txt' === file2bib.sh === id: cord-311144-tumtzad8 author: Franco-Muñoz, Carlos title: Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-311144-tumtzad8.txt cache: ./cache/cord-311144-tumtzad8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311144-tumtzad8.txt' === file2bib.sh === id: cord-310947-aqau2n7q author: Pan, Ji'An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 pages: extension: .txt txt: ./txt/cord-310947-aqau2n7q.txt cache: ./cache/cord-310947-aqau2n7q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310947-aqau2n7q.txt' === file2bib.sh === id: cord-311240-o0zyt2vb author: Motayo, Babatunde Olarenwaju title: Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-311240-o0zyt2vb.txt cache: ./cache/cord-311240-o0zyt2vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311240-o0zyt2vb.txt' === file2bib.sh === id: cord-311026-mpr3xb2a author: Petersen, Eskild title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-311026-mpr3xb2a.txt cache: ./cache/cord-311026-mpr3xb2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311026-mpr3xb2a.txt' === file2bib.sh === id: cord-311696-ccbc1k1m author: Pelisser, Michel title: Sports balls as potential SARS-CoV-2 transmission vectors date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-311696-ccbc1k1m.txt cache: ./cache/cord-311696-ccbc1k1m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311696-ccbc1k1m.txt' === file2bib.sh === id: cord-311214-eqwxkwqa author: Kumar, Roshan title: Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-311214-eqwxkwqa.txt cache: ./cache/cord-311214-eqwxkwqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311214-eqwxkwqa.txt' === file2bib.sh === id: cord-311114-ggcpsjk8 author: Radhakrishnan, Chandni title: Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-311114-ggcpsjk8.txt cache: ./cache/cord-311114-ggcpsjk8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311114-ggcpsjk8.txt' === file2bib.sh === id: cord-311012-wyglrpqh author: Meyers, Craig title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-311012-wyglrpqh.txt cache: ./cache/cord-311012-wyglrpqh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311012-wyglrpqh.txt' === file2bib.sh === id: cord-311633-i9ret7bw author: Péré, Hélène title: Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-311633-i9ret7bw.txt cache: ./cache/cord-311633-i9ret7bw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311633-i9ret7bw.txt' === file2bib.sh === id: cord-311044-kjx0z1hc author: Rubio-Pérez, Inés title: COVID-19: key concepts for the surgeon date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-311044-kjx0z1hc.txt cache: ./cache/cord-311044-kjx0z1hc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311044-kjx0z1hc.txt' === file2bib.sh === id: cord-311445-b6bc6vwd author: Bansal, Kanika title: Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-311445-b6bc6vwd.txt cache: ./cache/cord-311445-b6bc6vwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311445-b6bc6vwd.txt' === file2bib.sh === id: cord-311264-zn7ydrvh author: Deurenberg-Yap, M. title: The Singaporean response to the SARS outbreak: knowledge sufficiency versus public trust date: 2005-06-17 pages: extension: .txt txt: ./txt/cord-311264-zn7ydrvh.txt cache: ./cache/cord-311264-zn7ydrvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311264-zn7ydrvh.txt' === file2bib.sh === id: cord-311766-m9yv4qkm author: Demey, Baptiste title: Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-311766-m9yv4qkm.txt cache: ./cache/cord-311766-m9yv4qkm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311766-m9yv4qkm.txt' === file2bib.sh === id: cord-311905-4yu29b49 author: Kakoulidis, Ioannis title: SARS-CoV-2 infection and glucose homeostasis in pregnancy. What about antenatal corticosteroids? date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-311905-4yu29b49.txt cache: ./cache/cord-311905-4yu29b49.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311905-4yu29b49.txt' === file2bib.sh === id: cord-312036-5867bc6i author: Decker, Annegrit title: Prolonged SARS‐CoV‐2 shedding and mild course of COVID‐19 in a patient after recent heart transplantation date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-312036-5867bc6i.txt cache: ./cache/cord-312036-5867bc6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312036-5867bc6i.txt' === file2bib.sh === id: cord-311762-f6muhf3d author: Chen, Yu Wai title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates date: 2020-02-21 pages: extension: .txt txt: ./txt/cord-311762-f6muhf3d.txt cache: ./cache/cord-311762-f6muhf3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311762-f6muhf3d.txt' === file2bib.sh === id: cord-311635-hf6vrbyx author: Reuken, Philipp Alexander title: Between Fear and Courage: Attitudes, Beliefs, and Behavior of Liver Transplantation Recipients and Waiting List Candidates during the COVID‐19 Pandemic date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-311635-hf6vrbyx.txt cache: ./cache/cord-311635-hf6vrbyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311635-hf6vrbyx.txt' === file2bib.sh === id: cord-312476-20ifwznd author: Kline, Jeffrey A. title: Crash Course in Decision Making date: 2008-01-08 pages: extension: .txt txt: ./txt/cord-312476-20ifwznd.txt cache: ./cache/cord-312476-20ifwznd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312476-20ifwznd.txt' === file2bib.sh === id: cord-311377-ffkwis40 author: Forns, Xavier title: Inmunosupresión en el trasplante hepático en la era Covid-19 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-311377-ffkwis40.txt cache: ./cache/cord-311377-ffkwis40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311377-ffkwis40.txt' === file2bib.sh === id: cord-311446-afhw0450 author: Suhandynata, Raymond T title: Multi-platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19 date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-311446-afhw0450.txt cache: ./cache/cord-311446-afhw0450.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311446-afhw0450.txt' === file2bib.sh === id: cord-311585-h4holhit author: Ling, R. title: Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-311585-h4holhit.txt cache: ./cache/cord-311585-h4holhit.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311585-h4holhit.txt' === file2bib.sh === id: cord-312170-p2yrbosz author: Chiu, Man-Chun title: Suggested management of immunocompromized kidney patients suffering from SARS date: 2003-10-24 pages: extension: .txt txt: ./txt/cord-312170-p2yrbosz.txt cache: ./cache/cord-312170-p2yrbosz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312170-p2yrbosz.txt' === file2bib.sh === id: cord-311545-3rll9mca author: Bentley, Gillian R title: Don't blame the BAME: Ethnic and structural inequalities in susceptibilities to COVID‐19 date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-311545-3rll9mca.txt cache: ./cache/cord-311545-3rll9mca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311545-3rll9mca.txt' === file2bib.sh === id: cord-311782-d2t8bzio author: Fiore, Josè Ramòn title: Results from a survey in healthy blood donors in South Eastern Italy indicate that we are far away from herd immunity to SARS‐CoV‐2 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-311782-d2t8bzio.txt cache: ./cache/cord-311782-d2t8bzio.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311782-d2t8bzio.txt' === file2bib.sh === id: cord-312005-9so3orib author: Klussmeier, Anja title: Etablierung der PCR-basierten SARS-CoV-2-Testung im Hochdurchsatz date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-312005-9so3orib.txt cache: ./cache/cord-312005-9so3orib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312005-9so3orib.txt' === file2bib.sh === id: cord-311523-erntrh3p author: Gisondi, P title: Dermatologists and SARS‐CoV‐2: The impact of the pandemic on daily practice date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-311523-erntrh3p.txt cache: ./cache/cord-311523-erntrh3p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311523-erntrh3p.txt' === file2bib.sh === id: cord-311926-n7co0jtu author: Donà, Daniele title: COVID-19 Pandemic: Perspective of an Italian Tertiary Care Pediatric Center date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-311926-n7co0jtu.txt cache: ./cache/cord-311926-n7co0jtu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311926-n7co0jtu.txt' === file2bib.sh === id: cord-311610-uniz8tuc author: Wang, Shi-Yi title: The impact on neonatal mortality of shifting childbirth services among levels of hospitals: Taiwan's experience date: 2009-06-08 pages: extension: .txt txt: ./txt/cord-311610-uniz8tuc.txt cache: ./cache/cord-311610-uniz8tuc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311610-uniz8tuc.txt' === file2bib.sh === id: cord-311535-ppkwd1kp author: Korakas, Emmanouil title: Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-311535-ppkwd1kp.txt cache: ./cache/cord-311535-ppkwd1kp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311535-ppkwd1kp.txt' === file2bib.sh === id: cord-312473-7i7efdp2 author: Sidhom, John-William title: Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-312473-7i7efdp2.txt cache: ./cache/cord-312473-7i7efdp2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312473-7i7efdp2.txt' === file2bib.sh === id: cord-310304-f28tjmi8 author: Alcendor, Donald J. title: Racial Disparities-Associated COVID-19 Mortality among Minority Populations in the US date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-310304-f28tjmi8.txt cache: ./cache/cord-310304-f28tjmi8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310304-f28tjmi8.txt' === file2bib.sh === id: cord-311758-wof4yi39 author: Clauw, Daniel J. title: Considering the potential for an increase in chronic pain after the COVID-19 pandemic date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-311758-wof4yi39.txt cache: ./cache/cord-311758-wof4yi39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311758-wof4yi39.txt' === file2bib.sh === id: cord-311673-z4hkw17g author: Uzzan, Mathieu title: Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-311673-z4hkw17g.txt cache: ./cache/cord-311673-z4hkw17g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311673-z4hkw17g.txt' === file2bib.sh === id: cord-312340-hpuoren5 author: Holstein, Sarah A. title: Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-312340-hpuoren5.txt cache: ./cache/cord-312340-hpuoren5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312340-hpuoren5.txt' === file2bib.sh === id: cord-311843-un6urdb1 author: Baray, Juwel Chandra title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-311843-un6urdb1.txt cache: ./cache/cord-311843-un6urdb1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311843-un6urdb1.txt' === file2bib.sh === id: cord-312401-y1tat1bf author: Sakurai, Aki title: Natural History of Asymptomatic SARS-CoV-2 Infection date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-312401-y1tat1bf.txt cache: ./cache/cord-312401-y1tat1bf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312401-y1tat1bf.txt' === file2bib.sh === id: cord-311730-189vax2m author: Becker, Richard C. title: Covid-19 treatment update: follow the scientific evidence date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-311730-189vax2m.txt cache: ./cache/cord-311730-189vax2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311730-189vax2m.txt' === file2bib.sh === id: cord-312065-nqy7m38f author: Peng, Philip W. H. title: Infection control and anesthesia: Lessons learned from the Toronto SARS outbreak date: 2003 pages: extension: .txt txt: ./txt/cord-312065-nqy7m38f.txt cache: ./cache/cord-312065-nqy7m38f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312065-nqy7m38f.txt' === file2bib.sh === id: cord-311029-x0lk4110 author: Palermo, Sara title: Covid-19 Pandemic: Maximizing Future Vaccination Treatments Considering Aging and Frailty date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-311029-x0lk4110.txt cache: ./cache/cord-311029-x0lk4110.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311029-x0lk4110.txt' === file2bib.sh === id: cord-311835-dmqfij6j author: Siu, Kam-Leung title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 date: 2014-01-13 pages: extension: .txt txt: ./txt/cord-311835-dmqfij6j.txt cache: ./cache/cord-311835-dmqfij6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311835-dmqfij6j.txt' === file2bib.sh === id: cord-312646-hfv7ce3f author: Pfützner, Andreas title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV- 2 in a community screening setting shows low sensitivity date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-312646-hfv7ce3f.txt cache: ./cache/cord-312646-hfv7ce3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312646-hfv7ce3f.txt' === file2bib.sh === id: cord-312524-ee5xw1r8 author: Moustafa, Ahmed M. title: Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-312524-ee5xw1r8.txt cache: ./cache/cord-312524-ee5xw1r8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312524-ee5xw1r8.txt' === file2bib.sh === id: cord-312275-plqturzi author: Nielsen, Sandra C.A. title: Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-312275-plqturzi.txt cache: ./cache/cord-312275-plqturzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312275-plqturzi.txt' === file2bib.sh === id: cord-311415-wwwqqvca author: Alamri, Mubarak A. title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-311415-wwwqqvca.txt cache: ./cache/cord-311415-wwwqqvca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311415-wwwqqvca.txt' === file2bib.sh === id: cord-311918-gifwg2ho author: BENDER, Whitney R. title: Universal Testing for SARS-CoV-2 in Two Philadelphia Hospitals: Carrier Prevalence and Symptom Development Over Two Weeks date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-311918-gifwg2ho.txt cache: ./cache/cord-311918-gifwg2ho.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311918-gifwg2ho.txt' === file2bib.sh === id: cord-312278-rin733w4 author: Wang, Yung‐Chih title: Current diagnostic tools for coronaviruses–From laboratory diagnosis to POC diagnosis for COVID‐19 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-312278-rin733w4.txt cache: ./cache/cord-312278-rin733w4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312278-rin733w4.txt' === file2bib.sh === id: cord-312160-2820aftb author: Ibrahim, Mahmoud A.A. title: In silico Drug Discovery of Major Metabolites from Spices as SARS-CoV-2 Main Protease Inhibitors date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-312160-2820aftb.txt cache: ./cache/cord-312160-2820aftb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312160-2820aftb.txt' === file2bib.sh === id: cord-311477-gm0vg53l author: Doboszewska, Urszula title: Targeting zinc metalloenzymes in COVID‐19 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-311477-gm0vg53l.txt cache: ./cache/cord-311477-gm0vg53l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311477-gm0vg53l.txt' === file2bib.sh === id: cord-312027-5tntdjp9 author: Charlton, Carmen L. title: Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-312027-5tntdjp9.txt cache: ./cache/cord-312027-5tntdjp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312027-5tntdjp9.txt' === file2bib.sh === id: cord-312559-ygh507x2 author: Fiesco-Sepulveda, K. Y. title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-312559-ygh507x2.txt cache: ./cache/cord-312559-ygh507x2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312559-ygh507x2.txt' === file2bib.sh === id: cord-312444-c1dz5o85 author: Faure‐Bardon, V title: How should we treat pregnant women infected with SARS‐CoV‐2? date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-312444-c1dz5o85.txt cache: ./cache/cord-312444-c1dz5o85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312444-c1dz5o85.txt' === file2bib.sh === id: cord-311599-m400cal3 author: Lehmann, Christian title: A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses date: 2008-05-31 pages: extension: .txt txt: ./txt/cord-311599-m400cal3.txt cache: ./cache/cord-311599-m400cal3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311599-m400cal3.txt' === file2bib.sh === id: cord-310636-y7n22ykt author: Garcia-Beltran, W. F. title: COVID-19 neutralizing antibodies predict disease severity and survival date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-310636-y7n22ykt.txt cache: ./cache/cord-310636-y7n22ykt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310636-y7n22ykt.txt' === file2bib.sh === id: cord-311948-3v311fnd author: Ishiguro, Takashi title: Clinical Course and Findings of 14 Patients with COVID-19 Compared with 5 Patients with Conventional Human Coronavirus Pneumonia date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-311948-3v311fnd.txt cache: ./cache/cord-311948-3v311fnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311948-3v311fnd.txt' === file2bib.sh === id: cord-311383-1aqt65cc author: Tan, Jinzhi title: The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-311383-1aqt65cc.txt cache: ./cache/cord-311383-1aqt65cc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311383-1aqt65cc.txt' === file2bib.sh === id: cord-312350-klxw65qa author: Khan, Zafran title: Diagnostic approaches and potential therapeutic options for coronavirus disease (COVID-19) date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-312350-klxw65qa.txt cache: ./cache/cord-312350-klxw65qa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312350-klxw65qa.txt' === file2bib.sh === id: cord-312663-hhd5f823 author: Fiorino, Gionata title: Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-312663-hhd5f823.txt cache: ./cache/cord-312663-hhd5f823.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312663-hhd5f823.txt' === file2bib.sh === id: cord-311965-3x3tjzhi author: Alexander, Jan title: Early Nutritional Interventions with Zinc, Selenium and Vitamin D for Raising Anti-Viral Resistance Against Progressive COVID-19 date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-311965-3x3tjzhi.txt cache: ./cache/cord-311965-3x3tjzhi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311965-3x3tjzhi.txt' === file2bib.sh === id: cord-312509-m3p9fuq0 author: Tohidinia, Maryam title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-312509-m3p9fuq0.txt cache: ./cache/cord-312509-m3p9fuq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312509-m3p9fuq0.txt' === file2bib.sh === id: cord-312561-9o2fhi6e author: Hung, I.F.N. title: Viral Loads in Clinical Specimens and SARS Manifestations date: 2004-09-17 pages: extension: .txt txt: ./txt/cord-312561-9o2fhi6e.txt cache: ./cache/cord-312561-9o2fhi6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312561-9o2fhi6e.txt' === file2bib.sh === id: cord-312849-vgzvpwz9 author: Eckbo, Eric J. title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-312849-vgzvpwz9.txt cache: ./cache/cord-312849-vgzvpwz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312849-vgzvpwz9.txt' === file2bib.sh === id: cord-312367-24huwt3y author: Coelho, Camila title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-312367-24huwt3y.txt cache: ./cache/cord-312367-24huwt3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312367-24huwt3y.txt' === file2bib.sh === id: cord-311332-n8tvglif author: Kostoff, Ronald N. title: Literature-related discovery: Potential treatments and preventatives for SARS() date: 2011-04-20 pages: extension: .txt txt: ./txt/cord-311332-n8tvglif.txt cache: ./cache/cord-311332-n8tvglif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311332-n8tvglif.txt' === file2bib.sh === id: cord-311566-x8n1bbwn author: Aouidate, Adnane title: Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-311566-x8n1bbwn.txt cache: ./cache/cord-311566-x8n1bbwn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311566-x8n1bbwn.txt' === file2bib.sh === id: cord-311125-v9ddes3c author: Cooper, Keiland W. title: COVID-19 and the chemical senses: supporting players take center stage date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-311125-v9ddes3c.txt cache: ./cache/cord-311125-v9ddes3c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311125-v9ddes3c.txt' === file2bib.sh === id: cord-312178-tojgojjf author: Segars, James title: Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known? date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-312178-tojgojjf.txt cache: ./cache/cord-312178-tojgojjf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312178-tojgojjf.txt' === file2bib.sh === id: cord-312997-wcqdksfg author: Favresse, Julien title: Clinical performance of the Elecsys electrochemiluminescent immunoassay for the detection of SARS-CoV-2 total antibodies date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-312997-wcqdksfg.txt cache: ./cache/cord-312997-wcqdksfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312997-wcqdksfg.txt' === file2bib.sh === id: cord-312702-fruzsn26 author: Finch, Courtney L. title: Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-312702-fruzsn26.txt cache: ./cache/cord-312702-fruzsn26.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312702-fruzsn26.txt' === file2bib.sh === id: cord-312533-4u3bmb0e author: Shen, Li Wen title: TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections date: 2017-08-01 pages: extension: .txt txt: ./txt/cord-312533-4u3bmb0e.txt cache: ./cache/cord-312533-4u3bmb0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312533-4u3bmb0e.txt' === file2bib.sh === id: cord-312488-uzhj4i1q author: Petrosillo, Nicola title: SARS-CoV-2, “common cold” coronaviruses’ cross-reactivity and “herd immunity”: The razor of Ockham (1285-1347)? date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-312488-uzhj4i1q.txt cache: ./cache/cord-312488-uzhj4i1q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312488-uzhj4i1q.txt' === file2bib.sh === id: cord-312697-ffxcze6c author: Dübel, Stefan title: Rekombinante, vollständig humane Antikörper zur Behandlung akuter COVID-19 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-312697-ffxcze6c.txt cache: ./cache/cord-312697-ffxcze6c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-312697-ffxcze6c.txt' === file2bib.sh === id: cord-312664-tgpaidhp author: Liang, Julia title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-312664-tgpaidhp.txt cache: ./cache/cord-312664-tgpaidhp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312664-tgpaidhp.txt' === file2bib.sh === id: cord-312305-ll29frwc author: Sun, Shihui title: Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-312305-ll29frwc.txt cache: ./cache/cord-312305-ll29frwc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312305-ll29frwc.txt' === file2bib.sh === id: cord-312632-g4250q6l author: Cai, Xiaofang title: Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-312632-g4250q6l.txt cache: ./cache/cord-312632-g4250q6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312632-g4250q6l.txt' === file2bib.sh === id: cord-312414-g5px0b65 author: Takagi, Akira title: An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-312414-g5px0b65.txt cache: ./cache/cord-312414-g5px0b65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312414-g5px0b65.txt' === file2bib.sh === id: cord-312670-hi3fjne4 author: Corman, V. M. title: Coronaviren als Ursache respiratorischer Infektionen date: 2019-08-27 pages: extension: .txt txt: ./txt/cord-312670-hi3fjne4.txt cache: ./cache/cord-312670-hi3fjne4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312670-hi3fjne4.txt' === file2bib.sh === id: cord-312652-zhccmfgw author: Hu, Xiumei title: Impact of Heat-Inactivation on the detection of SARS-CoV-2 IgM and IgG Antibody by ELISA date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-312652-zhccmfgw.txt cache: ./cache/cord-312652-zhccmfgw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312652-zhccmfgw.txt' === file2bib.sh === id: cord-312633-cks6aij2 author: Cotten, Matthew title: Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus date: 2013-05-17 pages: extension: .txt txt: ./txt/cord-312633-cks6aij2.txt cache: ./cache/cord-312633-cks6aij2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312633-cks6aij2.txt' === file2bib.sh === id: cord-312736-bm6t2bxz author: Bach, Paxton title: Innovative strategies to support physical distancing among individuals with active addiction date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-312736-bm6t2bxz.txt cache: ./cache/cord-312736-bm6t2bxz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312736-bm6t2bxz.txt' === file2bib.sh === id: cord-313099-rpdlk1b6 author: Han, Xiaoyu title: Severe Acute Respiratory Syndrome Coronavirus 2 among Asymptomatic Workers Screened for Work Resumption, China date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-313099-rpdlk1b6.txt cache: ./cache/cord-313099-rpdlk1b6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313099-rpdlk1b6.txt' === file2bib.sh === id: cord-312684-3i2r2ahr author: Iba, Toshiaki title: Coagulopathy in COVID‐19 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-312684-3i2r2ahr.txt cache: ./cache/cord-312684-3i2r2ahr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312684-3i2r2ahr.txt' === file2bib.sh === id: cord-313058-nrrl4kjc author: Rivas, Magali Noval title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-313058-nrrl4kjc.txt cache: ./cache/cord-313058-nrrl4kjc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313058-nrrl4kjc.txt' === file2bib.sh === id: cord-312950-ggywr91e author: Fuller, Julie title: Surveillance for Febrile Respiratory Infections during Cobra Gold 2003 date: 2006-05-17 pages: extension: .txt txt: ./txt/cord-312950-ggywr91e.txt cache: ./cache/cord-312950-ggywr91e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312950-ggywr91e.txt' === file2bib.sh === id: cord-312115-foy3dsq4 author: Sekine, Takuya title: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-312115-foy3dsq4.txt cache: ./cache/cord-312115-foy3dsq4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312115-foy3dsq4.txt' === file2bib.sh === id: cord-313246-2gtiqrnj author: Hazra, Aniruddha title: Coinfections with SARS-CoV-2 and other respiratory pathogens date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-313246-2gtiqrnj.txt cache: ./cache/cord-313246-2gtiqrnj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-313246-2gtiqrnj.txt' === file2bib.sh === id: cord-311848-8n9ee57a author: Giesen, Nicola title: Evidence-based Management of COVID-19 in Cancer Patients – Guideline by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-311848-8n9ee57a.txt cache: ./cache/cord-311848-8n9ee57a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311848-8n9ee57a.txt' === file2bib.sh === id: cord-312722-talu4geh author: Ahmed, Nausheen title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-312722-talu4geh.txt cache: ./cache/cord-312722-talu4geh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312722-talu4geh.txt' === file2bib.sh === id: cord-312560-onfabcfv author: Klingler, J. title: Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-312560-onfabcfv.txt cache: ./cache/cord-312560-onfabcfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312560-onfabcfv.txt' === file2bib.sh === id: cord-312971-r9sggqh8 author: Mancino, Enrica title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-312971-r9sggqh8.txt cache: ./cache/cord-312971-r9sggqh8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312971-r9sggqh8.txt' === file2bib.sh === id: cord-313345-zwe3tmq0 author: Chou, Roger title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-313345-zwe3tmq0.txt cache: ./cache/cord-313345-zwe3tmq0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313345-zwe3tmq0.txt' === file2bib.sh === id: cord-313084-l7odplqg author: Sampson, Victoria title: Could there be a link between oral hygiene and the severity of SARS-CoV-2 infections? date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-313084-l7odplqg.txt cache: ./cache/cord-313084-l7odplqg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313084-l7odplqg.txt' === file2bib.sh === id: cord-313215-diqfmitr author: Luo, Lei title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-313215-diqfmitr.txt cache: ./cache/cord-313215-diqfmitr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313215-diqfmitr.txt' === file2bib.sh === id: cord-312708-9ywu6r2t author: Sharma, Dhruv title: Cadaveric Simulation of Otologic Procedures: An Analysis of Droplet Splatter Patterns During the COVID-19 Pandemic date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-312708-9ywu6r2t.txt cache: ./cache/cord-312708-9ywu6r2t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312708-9ywu6r2t.txt' === file2bib.sh === id: cord-311847-2czqs84q author: Pennisi, Manuela title: SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-311847-2czqs84q.txt cache: ./cache/cord-311847-2czqs84q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311847-2czqs84q.txt' === file2bib.sh === id: cord-313316-l147b7jk author: Freudenthal, Bernard title: Misuse of SARS-CoV-2 testing in symptomatic health-care staff in the UK date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-313316-l147b7jk.txt cache: ./cache/cord-313316-l147b7jk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-313316-l147b7jk.txt' === file2bib.sh === id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-312477-2y88gzji.txt cache: ./cache/cord-312477-2y88gzji.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312477-2y88gzji.txt' === file2bib.sh === id: cord-312743-9e4yufo5 author: Breiman, Adrien title: Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-312743-9e4yufo5.txt cache: ./cache/cord-312743-9e4yufo5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312743-9e4yufo5.txt' === file2bib.sh === id: cord-312434-yx24golq author: Deng, Ziqin title: Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-312434-yx24golq.txt cache: ./cache/cord-312434-yx24golq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312434-yx24golq.txt' === file2bib.sh === id: cord-312619-7jpf81yz author: Ilyas, Sadia title: Disinfection technology and strategies for COVID-19 hospital and bio-medical waste management date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-312619-7jpf81yz.txt cache: ./cache/cord-312619-7jpf81yz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312619-7jpf81yz.txt' === file2bib.sh === id: cord-312899-ot5pvtbl author: Chen, F title: In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds date: 2004-09-30 pages: extension: .txt txt: ./txt/cord-312899-ot5pvtbl.txt cache: ./cache/cord-312899-ot5pvtbl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312899-ot5pvtbl.txt' === file2bib.sh === id: cord-312740-2ro2p77q author: Babadaei, Mohammad Mahdi Nejadi title: Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-312740-2ro2p77q.txt cache: ./cache/cord-312740-2ro2p77q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312740-2ro2p77q.txt' === file2bib.sh === id: cord-312984-rzryn3on author: Pan, Daniel title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-312984-rzryn3on.txt cache: ./cache/cord-312984-rzryn3on.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312984-rzryn3on.txt' === file2bib.sh === id: cord-313265-lff5cajm author: Conway, Michael J. title: Identification of coronavirus sequences in carp cDNA from Wuhan, China date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-313265-lff5cajm.txt cache: ./cache/cord-313265-lff5cajm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313265-lff5cajm.txt' === file2bib.sh === id: cord-313349-ikjivfce author: Finsterer, Josef title: Causes of hypogeusia/hyposmia in SARS‐CoV2 infected patients date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-313349-ikjivfce.txt cache: ./cache/cord-313349-ikjivfce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313349-ikjivfce.txt' === file2bib.sh === id: cord-313076-531wksez author: Rauch, J. N. title: CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-313076-531wksez.txt cache: ./cache/cord-313076-531wksez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313076-531wksez.txt' === file2bib.sh === id: cord-312730-4ejjmab4 author: Wong, Rebecca S. Y. title: The SARS-CoV-2 Outbreak: an Epidemiological and Clinical Perspective date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-312730-4ejjmab4.txt cache: ./cache/cord-312730-4ejjmab4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312730-4ejjmab4.txt' === file2bib.sh === id: cord-313082-n3bo9jw1 author: Tenenbein, Paul title: The case for routine screening for SARS-CoV-2 before surgery date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-313082-n3bo9jw1.txt cache: ./cache/cord-313082-n3bo9jw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313082-n3bo9jw1.txt' === file2bib.sh === id: cord-313603-y8p9bmph author: Akter, Shahina title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-313603-y8p9bmph.txt cache: ./cache/cord-313603-y8p9bmph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313603-y8p9bmph.txt' === file2bib.sh === id: cord-313756-2pqpk3v7 author: De Vriese, An S. title: In Reply to ‘Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?’ date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-313756-2pqpk3v7.txt cache: ./cache/cord-313756-2pqpk3v7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313756-2pqpk3v7.txt' === file2bib.sh === id: cord-313571-umcbulcw author: Martínez-Murcia, Antonio title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-313571-umcbulcw.txt cache: ./cache/cord-313571-umcbulcw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313571-umcbulcw.txt' === file2bib.sh === id: cord-313247-55loucvc author: Pipes, Lenore title: Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-313247-55loucvc.txt cache: ./cache/cord-313247-55loucvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313247-55loucvc.txt' === file2bib.sh === id: cord-313371-fdyfg0kf author: Brancatella, Alessandro title: Subacute Thyroiditis After Sars-COV-2 Infection date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-313371-fdyfg0kf.txt cache: ./cache/cord-313371-fdyfg0kf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313371-fdyfg0kf.txt' === file2bib.sh === id: cord-313305-tih33rys author: Castro, Rodolfo title: COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-313305-tih33rys.txt cache: ./cache/cord-313305-tih33rys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313305-tih33rys.txt' === file2bib.sh === id: cord-312991-ypgrw78s author: Wang, Zhi-Gang title: Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV date: 2005-09-12 pages: extension: .txt txt: ./txt/cord-312991-ypgrw78s.txt cache: ./cache/cord-312991-ypgrw78s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312991-ypgrw78s.txt' === file2bib.sh === id: cord-313193-q5zeoqlb author: Carrat, F. title: Seroprevalence of SARS-CoV-2 among adults in three regions of France following the lockdown and associated risk factors: a multicohort study. date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-313193-q5zeoqlb.txt cache: ./cache/cord-313193-q5zeoqlb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313193-q5zeoqlb.txt' === file2bib.sh === id: cord-313505-2lr4xara author: Resende, Paola Cristina title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-313505-2lr4xara.txt cache: ./cache/cord-313505-2lr4xara.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313505-2lr4xara.txt' === file2bib.sh === id: cord-313627-g1iqhsdk author: Zou, Xiaojing title: Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-313627-g1iqhsdk.txt cache: ./cache/cord-313627-g1iqhsdk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313627-g1iqhsdk.txt' === file2bib.sh === id: cord-313117-0qur0isb author: Gardinassi, Luiz G. title: Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-313117-0qur0isb.txt cache: ./cache/cord-313117-0qur0isb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313117-0qur0isb.txt' === file2bib.sh === id: cord-313379-6sa6oc6u author: Bahar, B. title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-313379-6sa6oc6u.txt cache: ./cache/cord-313379-6sa6oc6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313379-6sa6oc6u.txt' === file2bib.sh === id: cord-312999-3erodkv9 author: Hassan, Sk. Sarif title: Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-312999-3erodkv9.txt cache: ./cache/cord-312999-3erodkv9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312999-3erodkv9.txt' === file2bib.sh === id: cord-313458-ka02rsla author: Zhou, Yitian title: Single-cell transcriptional profile of ACE2 in healthy and failing human hearts date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-313458-ka02rsla.txt cache: ./cache/cord-313458-ka02rsla.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313458-ka02rsla.txt' === file2bib.sh === id: cord-313275-znrvkmee author: Bwire, G. M. title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-313275-znrvkmee.txt cache: ./cache/cord-313275-znrvkmee.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313275-znrvkmee.txt' === file2bib.sh === id: cord-312677-rwznqiib author: Razmi, Mahdieh title: Immunomodulatory-Based Therapy as a Potential Promising Treatment Strategy against Severe COVID-19 Patients: A Systematic Review date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-312677-rwznqiib.txt cache: ./cache/cord-312677-rwznqiib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312677-rwznqiib.txt' === file2bib.sh === id: cord-313460-oao2zppd author: D’Ardes, Damiano title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-313460-oao2zppd.txt cache: ./cache/cord-313460-oao2zppd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313460-oao2zppd.txt' === file2bib.sh === id: cord-313174-ig0h2s6l author: Hecht, Jonathon L. title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-313174-ig0h2s6l.txt cache: ./cache/cord-313174-ig0h2s6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313174-ig0h2s6l.txt' === file2bib.sh === id: cord-313415-5qrpucr4 author: Lai, Rongtao title: Sentinel surveillance strategies for early detection of coronavirus disease in fever clinics: experience from China date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-313415-5qrpucr4.txt cache: ./cache/cord-313415-5qrpucr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313415-5qrpucr4.txt' === file2bib.sh === id: cord-313537-920tgv1j author: Carbonell, Ana Piera title: Covid-19 y tromboprofilaxis: recomendaciones para nuestra práctica clínica en atención primaria date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-313537-920tgv1j.txt cache: ./cache/cord-313537-920tgv1j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313537-920tgv1j.txt' === file2bib.sh === id: cord-313984-7wvfnag1 author: Remy, Kenneth E title: Immunotherapies for COVID-19: lessons learned from sepsis date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-313984-7wvfnag1.txt cache: ./cache/cord-313984-7wvfnag1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313984-7wvfnag1.txt' === file2bib.sh === id: cord-313282-z5cues67 author: Schaefer, Inga-Marie title: In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-313282-z5cues67.txt cache: ./cache/cord-313282-z5cues67.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313282-z5cues67.txt' === file2bib.sh === id: cord-313795-jr3n3uo9 author: McAuley, Julie L. title: Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-313795-jr3n3uo9.txt cache: ./cache/cord-313795-jr3n3uo9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313795-jr3n3uo9.txt' === file2bib.sh === id: cord-313356-ninzeazy author: Fiorillo, Luca title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-313356-ninzeazy.txt cache: ./cache/cord-313356-ninzeazy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313356-ninzeazy.txt' === file2bib.sh === id: cord-312918-iof45k1r author: Ortolani, Claudio title: Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-312918-iof45k1r.txt cache: ./cache/cord-312918-iof45k1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312918-iof45k1r.txt' === file2bib.sh === id: cord-313541-fpqwzf9k author: Ulloa, S. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-313541-fpqwzf9k.txt cache: ./cache/cord-313541-fpqwzf9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313541-fpqwzf9k.txt' === file2bib.sh === id: cord-314124-yk4y0kea author: Tsou, Ian Y. title: Severe acute respiratory syndrome (SARS) in a paediatric cluster in Singapore date: 2003-08-20 pages: extension: .txt txt: ./txt/cord-314124-yk4y0kea.txt cache: ./cache/cord-314124-yk4y0kea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314124-yk4y0kea.txt' === file2bib.sh === id: cord-313227-6zwkfzab author: Scala, Stefania title: Fighting the Host Reaction to SARS-COv-2 in Critically Ill Patients: The Possible Contribution of Off-Label Drugs date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-313227-6zwkfzab.txt cache: ./cache/cord-313227-6zwkfzab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313227-6zwkfzab.txt' === file2bib.sh === id: cord-313427-6y4zvrmn author: Mani, Nandita S title: Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-313427-6y4zvrmn.txt cache: ./cache/cord-313427-6y4zvrmn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313427-6y4zvrmn.txt' === file2bib.sh === id: cord-312038-g76cpjp7 author: Brunaugh, Ashlee D. title: Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-312038-g76cpjp7.txt cache: ./cache/cord-312038-g76cpjp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312038-g76cpjp7.txt' === file2bib.sh === id: cord-312884-anlp8lab author: Iyer, Gayatri R. title: Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-312884-anlp8lab.txt cache: ./cache/cord-312884-anlp8lab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312884-anlp8lab.txt' === file2bib.sh === id: cord-314229-9k2dd95b author: Spaccaferri, G. title: Cas groupés d’infections au nouveau coronavirus (SARS-CoV-2) aux Contamines-Montjoie, Haute-Savoie, janvier–février 2020 date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-314229-9k2dd95b.txt cache: ./cache/cord-314229-9k2dd95b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314229-9k2dd95b.txt' === file2bib.sh === id: cord-313489-i969aqn9 author: Galbadage, Thushara title: Does COVID-19 Spread Through Droplets Alone? date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-313489-i969aqn9.txt cache: ./cache/cord-313489-i969aqn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313489-i969aqn9.txt' === file2bib.sh === id: cord-314111-bqmfmcfm author: Yazdanpanah, Yazdan title: Les antirétroviraux ont-ils une place dans le traitement du syndrome respiratoire aigu sévère ? date: 2006-01-31 pages: extension: .txt txt: ./txt/cord-314111-bqmfmcfm.txt cache: ./cache/cord-314111-bqmfmcfm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314111-bqmfmcfm.txt' === file2bib.sh === id: cord-314025-h9gj814e author: Lai, Mary Y. Y. title: Survival of Severe Acute Respiratory Syndrome Coronavirus date: 2005-10-01 pages: extension: .txt txt: ./txt/cord-314025-h9gj814e.txt cache: ./cache/cord-314025-h9gj814e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314025-h9gj814e.txt' === file2bib.sh === id: cord-313268-j51zyodw author: Zeng, Xiangxiang title: Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-313268-j51zyodw.txt cache: ./cache/cord-313268-j51zyodw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313268-j51zyodw.txt' === file2bib.sh === id: cord-313028-0nhgxoim author: Huang, Chaolin title: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China date: 2020-01-24 pages: extension: .txt txt: ./txt/cord-313028-0nhgxoim.txt cache: ./cache/cord-313028-0nhgxoim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313028-0nhgxoim.txt' === file2bib.sh === id: cord-314072-av3r7it7 author: Liu, Zhuoming title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date: 2020-11-08 pages: extension: .txt txt: ./txt/cord-314072-av3r7it7.txt cache: ./cache/cord-314072-av3r7it7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314072-av3r7it7.txt' === file2bib.sh === id: cord-313639-qpt47sx2 author: Zheng, Yi title: Clinical characteristics of 34 COVID-19 patients admitted to intensive care unit in Hangzhou, China date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-313639-qpt47sx2.txt cache: ./cache/cord-313639-qpt47sx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313639-qpt47sx2.txt' === file2bib.sh === id: cord-314013-g091lv0s author: Belladonna, Maria Laura title: Potential Benefits of Tryptophan Metabolism to the Efficacy of Tocilizumab in COVID-19 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-314013-g091lv0s.txt cache: ./cache/cord-314013-g091lv0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314013-g091lv0s.txt' === file2bib.sh === id: cord-314679-lmfalzni author: Sangith, Nikhil title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-314679-lmfalzni.txt cache: ./cache/cord-314679-lmfalzni.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314679-lmfalzni.txt' === file2bib.sh === id: cord-312486-rumqopg0 author: Jacob, Chaim Oscar title: On the genetics and immunopathogenesis of COVID-19 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-312486-rumqopg0.txt cache: ./cache/cord-312486-rumqopg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312486-rumqopg0.txt' === file2bib.sh === id: cord-314663-8cf0jci9 author: Ampuero, M. title: SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results. date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-314663-8cf0jci9.txt cache: ./cache/cord-314663-8cf0jci9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314663-8cf0jci9.txt' === file2bib.sh === id: cord-312955-gs65c3fy author: Schreiber, Gideon title: The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-312955-gs65c3fy.txt cache: ./cache/cord-312955-gs65c3fy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312955-gs65c3fy.txt' === file2bib.sh === id: cord-314107-x6e1jhcd author: Walker, M. title: SARS-CoV-2 Infection and Stroke: Coincident or Causal? date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-314107-x6e1jhcd.txt cache: ./cache/cord-314107-x6e1jhcd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314107-x6e1jhcd.txt' === file2bib.sh === id: cord-314445-4cb4a9r5 author: McNamara, Ryan P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-314445-4cb4a9r5.txt cache: ./cache/cord-314445-4cb4a9r5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314445-4cb4a9r5.txt' === file2bib.sh === id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-312996-qzu8pkyt.txt cache: ./cache/cord-312996-qzu8pkyt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312996-qzu8pkyt.txt' === file2bib.sh === id: cord-313805-6mnclfeg author: Suzuki, Yuichiro J. title: SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-313805-6mnclfeg.txt cache: ./cache/cord-313805-6mnclfeg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313805-6mnclfeg.txt' === file2bib.sh === id: cord-314381-ltil9hwl author: Cheng, Cecilia title: The psychology behind the masks: Psychological responses to the severe acute respiratory syndrome outbreak in different regions date: 2004-03-11 pages: extension: .txt txt: ./txt/cord-314381-ltil9hwl.txt cache: ./cache/cord-314381-ltil9hwl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314381-ltil9hwl.txt' === file2bib.sh === id: cord-314051-dr27bsvt author: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-314051-dr27bsvt.txt cache: ./cache/cord-314051-dr27bsvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314051-dr27bsvt.txt' === file2bib.sh === id: cord-314386-cxq9v218 author: Nitsche, Andreas title: SARS Coronavirus Detection date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-314386-cxq9v218.txt cache: ./cache/cord-314386-cxq9v218.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314386-cxq9v218.txt' === file2bib.sh === id: cord-314109-wb45naw2 author: Maiese, Kenneth title: The Mechanistic Target of Rapamycin (mTOR): Novel Considerations as an Antiviral Treatment date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-314109-wb45naw2.txt cache: ./cache/cord-314109-wb45naw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314109-wb45naw2.txt' === file2bib.sh === id: cord-314024-n6l2804j author: Gonçalves, Antonio title: Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-314024-n6l2804j.txt cache: ./cache/cord-314024-n6l2804j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314024-n6l2804j.txt' === file2bib.sh === id: cord-313755-y7regza1 author: Mitra, Kartik title: Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-313755-y7regza1.txt cache: ./cache/cord-313755-y7regza1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313755-y7regza1.txt' === file2bib.sh === id: cord-314714-ehxxvenb author: Pang, Xiaocong title: Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-314714-ehxxvenb.txt cache: ./cache/cord-314714-ehxxvenb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314714-ehxxvenb.txt' === file2bib.sh === id: cord-313728-08kwkbmd author: Binda, Barbara title: Follow-up and Management of Kidney Transplant Recipients During the COVID-19 Lockdown: the experience of an Italian Transplant Center, Including Two Cases of COVID-19 Pneumonia date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-313728-08kwkbmd.txt cache: ./cache/cord-313728-08kwkbmd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313728-08kwkbmd.txt' === file2bib.sh === id: cord-314489-e5r5s5ee author: Katsidzira, Leolin title: The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-314489-e5r5s5ee.txt cache: ./cache/cord-314489-e5r5s5ee.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314489-e5r5s5ee.txt' === file2bib.sh === id: cord-314574-3e6u4aza author: Tian, Xiaolong title: Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody date: 2020-02-17 pages: extension: .txt txt: ./txt/cord-314574-3e6u4aza.txt cache: ./cache/cord-314574-3e6u4aza.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314574-3e6u4aza.txt' === file2bib.sh === id: cord-314070-8qz23nn4 author: Gubbi, Sriram title: Catecholamine physiology and its implications in patients with COVID-19 date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-314070-8qz23nn4.txt cache: ./cache/cord-314070-8qz23nn4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314070-8qz23nn4.txt' === file2bib.sh === id: cord-313829-pjscmen8 author: Caballero, A.E. title: COVID-19 in people living with diabetes: An international consensus date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-313829-pjscmen8.txt cache: ./cache/cord-313829-pjscmen8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313829-pjscmen8.txt' === file2bib.sh === id: cord-314798-n6oofe3i author: Stall, N. M. title: Sex-specific differences in COVID-19 testing, cases and outcomes: a population-wide study in Ontario, Canada date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-314798-n6oofe3i.txt cache: ./cache/cord-314798-n6oofe3i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314798-n6oofe3i.txt' === file2bib.sh === id: cord-313344-rqvi2ksc author: Farcas, Gabriella A. title: Fatal Severe Acute Respiratory Syndrome Is Associated with Multiorgan Involvement by Coronavirus date: 2005-01-15 pages: extension: .txt txt: ./txt/cord-313344-rqvi2ksc.txt cache: ./cache/cord-313344-rqvi2ksc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313344-rqvi2ksc.txt' === file2bib.sh === id: cord-313754-f4sq45gy author: Wong, Chi-Yan title: Practice of habitual and volitional health behaviors to prevent severe acute respiratory syndrome among Chinese adolescents in Hong Kong date: 2005-03-31 pages: extension: .txt txt: ./txt/cord-313754-f4sq45gy.txt cache: ./cache/cord-313754-f4sq45gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313754-f4sq45gy.txt' === file2bib.sh === id: cord-314669-lvibjx97 author: Shang, Guifang title: Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 date: 2007-11-26 pages: extension: .txt txt: ./txt/cord-314669-lvibjx97.txt cache: ./cache/cord-314669-lvibjx97.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314669-lvibjx97.txt' === file2bib.sh === id: cord-314515-p40x3cxr author: NGAI, Jenny C. title: The long‐term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status date: 2010-03-19 pages: extension: .txt txt: ./txt/cord-314515-p40x3cxr.txt cache: ./cache/cord-314515-p40x3cxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314515-p40x3cxr.txt' === file2bib.sh === id: cord-314926-4bltio08 author: Ha, Le Dang title: Lack of SARS Transmission among Public Hospital Workers, Vietnam date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-314926-4bltio08.txt cache: ./cache/cord-314926-4bltio08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314926-4bltio08.txt' === file2bib.sh === id: cord-314880-0cfq52hn author: Meireles, Pedro Antunes title: Acalculous Acute Pancreatitis in a COVID-19 Patient date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-314880-0cfq52hn.txt cache: ./cache/cord-314880-0cfq52hn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314880-0cfq52hn.txt' === file2bib.sh === id: cord-314369-o4nis91y author: Lopez-Lopes, G. I. S. title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-314369-o4nis91y.txt cache: ./cache/cord-314369-o4nis91y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314369-o4nis91y.txt' === file2bib.sh === id: cord-314793-kb319t4c author: Borroni, Barbara title: Diaphragmatic myoclonus due to SARS-CoV-2 infection date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-314793-kb319t4c.txt cache: ./cache/cord-314793-kb319t4c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314793-kb319t4c.txt' === file2bib.sh === id: cord-314796-bek92zs9 author: Hartung, Hans-Peter title: COVID-19 and management of neuroimmunological disorders date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-314796-bek92zs9.txt cache: ./cache/cord-314796-bek92zs9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314796-bek92zs9.txt' === file2bib.sh === id: cord-314321-klb8oe9q author: Chen, Serena H. title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-314321-klb8oe9q.txt cache: ./cache/cord-314321-klb8oe9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314321-klb8oe9q.txt' === file2bib.sh === id: cord-315337-vgi91uzg author: Mizutani, Tetsuya title: Characterization of Persistent SARS-CoV Infection in Vero E6 Cells date: 2006 pages: extension: .txt txt: ./txt/cord-315337-vgi91uzg.txt cache: ./cache/cord-315337-vgi91uzg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315337-vgi91uzg.txt' === file2bib.sh === id: cord-314933-wq1xo0z0 author: Zores, Florian title: COVID and the Renin-Angiotensin System: Are Hypertension or Its Treatments Deleterious? date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-314933-wq1xo0z0.txt cache: ./cache/cord-314933-wq1xo0z0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314933-wq1xo0z0.txt' === file2bib.sh === id: cord-314687-kyj6etnc author: Gunalan, Vithiagaran title: A putative diacidic motif in the SARS-CoV ORF6 protein influences its subcellular localization and suppression of expression of co-transfected expression constructs date: 2011-10-25 pages: extension: .txt txt: ./txt/cord-314687-kyj6etnc.txt cache: ./cache/cord-314687-kyj6etnc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314687-kyj6etnc.txt' === file2bib.sh === id: cord-314135-udce22id author: Geisslinger, Franz title: Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-314135-udce22id.txt cache: ./cache/cord-314135-udce22id.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314135-udce22id.txt' === file2bib.sh === id: cord-313910-bwe2f7xf author: Bojadzic, Damir title: Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-313910-bwe2f7xf.txt cache: ./cache/cord-313910-bwe2f7xf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313910-bwe2f7xf.txt' === file2bib.sh === id: cord-314546-fbddxbhd author: Ko, Meehyun title: Comparative analysis of antiviral efficacy of FDA‐approved drugs against SARS‐CoV‐2 in human lung cells date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-314546-fbddxbhd.txt cache: ./cache/cord-314546-fbddxbhd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314546-fbddxbhd.txt' === file2bib.sh === id: cord-314694-g0pes5o3 author: Cortiula, F. title: Managing COVID-19 in the oncology clinic and avoiding the distraction effect date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-314694-g0pes5o3.txt cache: ./cache/cord-314694-g0pes5o3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314694-g0pes5o3.txt' === file2bib.sh === id: cord-315288-fcx4q6mp author: Hussain, Mohammed Hassan title: Tracheal swab from front of neck airway for SARS-CoV-2; a bronchial foreign body date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-315288-fcx4q6mp.txt cache: ./cache/cord-315288-fcx4q6mp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315288-fcx4q6mp.txt' === file2bib.sh === id: cord-315198-v4ay9kwg author: Siddiqui, Ruqaiyyah title: SARS-CoV-2: The Increasing Importance of Water Filtration against Highly Pathogenic Microbes date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-315198-v4ay9kwg.txt cache: ./cache/cord-315198-v4ay9kwg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315198-v4ay9kwg.txt' === file2bib.sh === id: cord-314822-lmoc0xwi author: Flegel, Willy A. title: CoVID‐19 insights from transfusion medicine date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-314822-lmoc0xwi.txt cache: ./cache/cord-314822-lmoc0xwi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314822-lmoc0xwi.txt' === file2bib.sh === id: cord-314947-fy1lqk00 author: WU, Xiao Dong title: The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells date: 2004-10-17 pages: extension: .txt txt: ./txt/cord-314947-fy1lqk00.txt cache: ./cache/cord-314947-fy1lqk00.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314947-fy1lqk00.txt' === file2bib.sh === id: cord-314662-nem6dw34 author: Nakra, Natasha A. title: Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-314662-nem6dw34.txt cache: ./cache/cord-314662-nem6dw34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314662-nem6dw34.txt' === file2bib.sh === id: cord-315283-xwan2t1u author: Ooi, Setthasorn Zhi Yang title: Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-315283-xwan2t1u.txt cache: ./cache/cord-315283-xwan2t1u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315283-xwan2t1u.txt' === file2bib.sh === id: cord-314311-xbpb9nfi author: Ge, Huipeng title: The epidemiology and clinical information about COVID-19 date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-314311-xbpb9nfi.txt cache: ./cache/cord-314311-xbpb9nfi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314311-xbpb9nfi.txt' === file2bib.sh === id: cord-314901-b18vy7dc author: Ali, Elrazi title: A Case of Fulminant Liver Failure in a 24-Year-Old Man with Coinfection with Hepatitis B Virus and SARS-CoV-2 date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-314901-b18vy7dc.txt cache: ./cache/cord-314901-b18vy7dc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314901-b18vy7dc.txt' === file2bib.sh === id: cord-315129-p31vm79o author: Bock, Jens-Ole title: Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-315129-p31vm79o.txt cache: ./cache/cord-315129-p31vm79o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315129-p31vm79o.txt' === file2bib.sh === id: cord-315046-ltmuw6f8 author: Li, Keying title: SARS‐CoV‐2 infection‐induced immune responses: friends or foes? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-315046-ltmuw6f8.txt cache: ./cache/cord-315046-ltmuw6f8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-315046-ltmuw6f8.txt' === file2bib.sh === id: cord-314932-edf9xjwr author: Yan, Junqiang title: Research Progress of Drug Treatment in Novel Coronavirus Pneumonia date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-314932-edf9xjwr.txt cache: ./cache/cord-314932-edf9xjwr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314932-edf9xjwr.txt' === file2bib.sh === id: cord-314102-8jf3fnqe author: Wu, Jie title: Advances in research on ACE2 as a receptor for 2019-nCoV date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-314102-8jf3fnqe.txt cache: ./cache/cord-314102-8jf3fnqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314102-8jf3fnqe.txt' === file2bib.sh === id: cord-315152-v3l33up6 author: Figlerowicz, Magdalena title: First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-315152-v3l33up6.txt cache: ./cache/cord-315152-v3l33up6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315152-v3l33up6.txt' === file2bib.sh === id: cord-314948-7tnrfk24 author: Borrás, A title: Pandemia del SARS-CoV-2 y reproducción asistida date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-314948-7tnrfk24.txt cache: ./cache/cord-314948-7tnrfk24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314948-7tnrfk24.txt' === file2bib.sh === id: cord-314734-ai0hz4uq author: Hung, Ivan Fan-Ngai title: SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: a case series date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-314734-ai0hz4uq.txt cache: ./cache/cord-314734-ai0hz4uq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314734-ai0hz4uq.txt' === file2bib.sh === id: cord-314171-431buxxr author: Dariya, Begum title: Understanding novel COVID-19: its impact on organ failure and risk assessment for diabetic and cancer patients date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-314171-431buxxr.txt cache: ./cache/cord-314171-431buxxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314171-431buxxr.txt' === file2bib.sh === id: cord-314333-hkyiy1gm author: Nagata, Noriyo title: Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice date: 2008-06-30 pages: extension: .txt txt: ./txt/cord-314333-hkyiy1gm.txt cache: ./cache/cord-314333-hkyiy1gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314333-hkyiy1gm.txt' === file2bib.sh === id: cord-315056-ohyb6oa0 author: Xu, Juanjuan title: Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-315056-ohyb6oa0.txt cache: ./cache/cord-315056-ohyb6oa0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315056-ohyb6oa0.txt' === file2bib.sh === id: cord-314746-1o0rf0ii author: Bergasa-Caceres, Fernando title: Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-314746-1o0rf0ii.txt cache: ./cache/cord-314746-1o0rf0ii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314746-1o0rf0ii.txt' === file2bib.sh === id: cord-315289-4x229n8n author: Foresta, C. title: Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-315289-4x229n8n.txt cache: ./cache/cord-315289-4x229n8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315289-4x229n8n.txt' === file2bib.sh === id: cord-315424-i3nnennw author: Willer, Brittany L. title: The otolaryngologist’s and anesthesiologist’s collaborative role in a pandemic: a large quaternary pediatric center’s experience with COVID-19 preparation and simulation date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-315424-i3nnennw.txt cache: ./cache/cord-315424-i3nnennw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315424-i3nnennw.txt' === file2bib.sh === id: cord-315328-8g40ukml author: Clementi, Nicola title: Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-315328-8g40ukml.txt cache: ./cache/cord-315328-8g40ukml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315328-8g40ukml.txt' === file2bib.sh === id: cord-314676-ndke9agh author: Gollapalli, Pavan title: Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-314676-ndke9agh.txt cache: ./cache/cord-314676-ndke9agh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314676-ndke9agh.txt' === file2bib.sh === id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-312741-0au4nctt.txt cache: ./cache/cord-312741-0au4nctt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312741-0au4nctt.txt' === file2bib.sh === id: cord-315465-u3zq9k5j author: de Jesus, Myrela Conceição Santos title: Family COVID-19 cluster analysis of an infant without respiratory symptoms date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-315465-u3zq9k5j.txt cache: ./cache/cord-315465-u3zq9k5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315465-u3zq9k5j.txt' === file2bib.sh === id: cord-315388-8sv00zqz author: Ghosh, Ritwik title: Famotidine against SARS-CoV2: A hope or hype? date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-315388-8sv00zqz.txt cache: ./cache/cord-315388-8sv00zqz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-315388-8sv00zqz.txt' === file2bib.sh === id: cord-314572-1pou702r author: Lin, Ya-Hui title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date: 2016-10-14 pages: extension: .txt txt: ./txt/cord-314572-1pou702r.txt cache: ./cache/cord-314572-1pou702r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314572-1pou702r.txt' === file2bib.sh === id: cord-315453-mbv8vb2r author: Jean, Shio-Shin title: Old and re-purposed drugs for the treatment of COVID-19 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-315453-mbv8vb2r.txt cache: ./cache/cord-315453-mbv8vb2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315453-mbv8vb2r.txt' === file2bib.sh === id: cord-313684-61hkogdh author: Samaddar, Arghadip title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-313684-61hkogdh.txt cache: ./cache/cord-313684-61hkogdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313684-61hkogdh.txt' === file2bib.sh === id: cord-315556-84rgd2s9 author: Pilotto, A. title: Steroid-responsive severe encephalopathy in SARS-CoV-2 infection date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-315556-84rgd2s9.txt cache: ./cache/cord-315556-84rgd2s9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315556-84rgd2s9.txt' === file2bib.sh === id: cord-315278-iv2zj67t author: Moazzam, Zorays title: Intussusception in an infant as a manifestation of COVID-19 date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-315278-iv2zj67t.txt cache: ./cache/cord-315278-iv2zj67t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315278-iv2zj67t.txt' === file2bib.sh === id: cord-315760-9g8901v6 author: Teng, Xufei title: Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date: 2020-08-30 pages: extension: .txt txt: ./txt/cord-315760-9g8901v6.txt cache: ./cache/cord-315760-9g8901v6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315760-9g8901v6.txt' === file2bib.sh === id: cord-315064-2mgv9j6n author: Escher, Felicitas title: Detection of viral SARS‐CoV‐2 genomes and histopathological changes in endomyocardial biopsies date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-315064-2mgv9j6n.txt cache: ./cache/cord-315064-2mgv9j6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315064-2mgv9j6n.txt' === file2bib.sh === id: cord-313957-hviv5zar author: Masucci, Maria Grazia title: Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-313957-hviv5zar.txt cache: ./cache/cord-313957-hviv5zar.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313957-hviv5zar.txt' === file2bib.sh === id: cord-315604-a6fvsd45 author: Maurya, Santosh K. title: Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-315604-a6fvsd45.txt cache: ./cache/cord-315604-a6fvsd45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315604-a6fvsd45.txt' === file2bib.sh === id: cord-315632-29x6l5yh author: Rali, Aniket S title: High-flow Nasal Cannula Oxygenation Revisited in COVID-19 date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-315632-29x6l5yh.txt cache: ./cache/cord-315632-29x6l5yh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315632-29x6l5yh.txt' === file2bib.sh === id: cord-315585-bjij8ds7 author: Wee, Liang En title: Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-315585-bjij8ds7.txt cache: ./cache/cord-315585-bjij8ds7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315585-bjij8ds7.txt' === file2bib.sh === id: cord-315411-11mq8wll author: Rahman, Mohammad Azizur title: Neurobiochemical Cross-talk Between COVID-19 and Alzheimer’s Disease date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-315411-11mq8wll.txt cache: ./cache/cord-315411-11mq8wll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315411-11mq8wll.txt' === file2bib.sh === id: cord-314451-mqnqjn0c author: Roberts, Anjeanette title: A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice date: 2007-01-12 pages: extension: .txt txt: ./txt/cord-314451-mqnqjn0c.txt cache: ./cache/cord-314451-mqnqjn0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314451-mqnqjn0c.txt' === file2bib.sh === id: cord-315866-6vcts4w3 author: Chan, KC Allen title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study date: 2005-04-09 pages: extension: .txt txt: ./txt/cord-315866-6vcts4w3.txt cache: ./cache/cord-315866-6vcts4w3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315866-6vcts4w3.txt' === file2bib.sh === id: cord-315666-ngozukzj author: Altundag, Aytug title: Olfactory Cleft Measurements and COVID-19–Related Anosmia date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-315666-ngozukzj.txt cache: ./cache/cord-315666-ngozukzj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315666-ngozukzj.txt' === file2bib.sh === id: cord-315617-mhm9wh9q author: Gottschalk, René title: Bioterrorism: is it a real threat? date: 2004-09-02 pages: extension: .txt txt: ./txt/cord-315617-mhm9wh9q.txt cache: ./cache/cord-315617-mhm9wh9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315617-mhm9wh9q.txt' === file2bib.sh === id: cord-315637-7td617dm author: Rothe, M. title: A systematic review of mask disinfection and reuse for SARS-CoV-2 date: 2020-11-12 pages: extension: .txt txt: ./txt/cord-315637-7td617dm.txt cache: ./cache/cord-315637-7td617dm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315637-7td617dm.txt' === file2bib.sh === id: cord-315440-he7sm7nj author: Wassie, Gizachew Tadesse title: Incubation period of SARS-CoV-2: A systematic review and meta-analysis date: 2020-10-11 pages: extension: .txt txt: ./txt/cord-315440-he7sm7nj.txt cache: ./cache/cord-315440-he7sm7nj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315440-he7sm7nj.txt' === file2bib.sh === id: cord-315972-5g2hnk1x author: Tong, Suxiang title: Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya date: 2009-03-17 pages: extension: .txt txt: ./txt/cord-315972-5g2hnk1x.txt cache: ./cache/cord-315972-5g2hnk1x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315972-5g2hnk1x.txt' === file2bib.sh === id: cord-316180-g3lfecp0 author: Zhang, Jingshu title: Membrane heist: Coronavirus host membrane remodeling during replication date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-316180-g3lfecp0.txt cache: ./cache/cord-316180-g3lfecp0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316180-g3lfecp0.txt' === file2bib.sh === id: cord-315085-rucfowvv author: Sekulic, Miroslav title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-315085-rucfowvv.txt cache: ./cache/cord-315085-rucfowvv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315085-rucfowvv.txt' === file2bib.sh === id: cord-315448-bosazmlm author: Crawford, Katharine H D title: Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-315448-bosazmlm.txt cache: ./cache/cord-315448-bosazmlm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315448-bosazmlm.txt' === file2bib.sh === id: cord-315849-e16lln3f author: Takayama, Kazuo title: In vitro and Animal Models for SARS-CoV-2 research date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-315849-e16lln3f.txt cache: ./cache/cord-315849-e16lln3f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315849-e16lln3f.txt' === file2bib.sh === id: cord-314960-f4hj35dr author: Kissler, Stephen M title: Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-314960-f4hj35dr.txt cache: ./cache/cord-314960-f4hj35dr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314960-f4hj35dr.txt' === file2bib.sh === id: cord-314833-6fue84x6 author: Chang, Chung-ke title: The SARS coronavirus nucleocapsid protein – Forms and functions date: 2014-01-11 pages: extension: .txt txt: ./txt/cord-314833-6fue84x6.txt cache: ./cache/cord-314833-6fue84x6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314833-6fue84x6.txt' === file2bib.sh === id: cord-315498-gpzee1f2 author: Parkinson, N. title: Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-315498-gpzee1f2.txt cache: ./cache/cord-315498-gpzee1f2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315498-gpzee1f2.txt' === file2bib.sh === id: cord-315181-emf4i6ir author: Ryoo, Nayoung title: Coping with Dementia in the Middle of the COVID-19 Pandemic date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-315181-emf4i6ir.txt cache: ./cache/cord-315181-emf4i6ir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315181-emf4i6ir.txt' === file2bib.sh === id: cord-314439-ufeiv47z author: Barkan, Elad title: Comparison of SARS-CoV-2 Exit Strategies Building Blocks date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-314439-ufeiv47z.txt cache: ./cache/cord-314439-ufeiv47z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314439-ufeiv47z.txt' === file2bib.sh === id: cord-315968-q2rxj90s author: Douglas, Jennifer E. title: Management of a Unique Sinonasal Undifferentiated Carcinoma Subtype in the Era of SARS-CoV-2 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-315968-q2rxj90s.txt cache: ./cache/cord-315968-q2rxj90s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315968-q2rxj90s.txt' === file2bib.sh === id: cord-316083-f1h2j6jx author: Alamri, Ahmad title: nan date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-316083-f1h2j6jx.txt cache: ./cache/cord-316083-f1h2j6jx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316083-f1h2j6jx.txt' === file2bib.sh === id: cord-315641-bzfrd7xj author: Abenavoli, Fabio Massimo title: Plastic Surgery in the Age of Coronavirus date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-315641-bzfrd7xj.txt cache: ./cache/cord-315641-bzfrd7xj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315641-bzfrd7xj.txt' === file2bib.sh === id: cord-315576-bgcqkz0p author: Yamamoto, Naoki title: Apparent difference in fatalities between Central Europe and East Asia due to SARS-COV-2 and COVID-19: Four hypotheses for possible explanation date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-315576-bgcqkz0p.txt cache: ./cache/cord-315576-bgcqkz0p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315576-bgcqkz0p.txt' === file2bib.sh === id: cord-314942-eym2rh8v author: El Tabaa, Manar Mohammed title: New putative insights into neprilysin (NEP)-dependent pharmacotherapeutic role of roflumilast in treating COVID-19 date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-314942-eym2rh8v.txt cache: ./cache/cord-314942-eym2rh8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314942-eym2rh8v.txt' === file2bib.sh === id: cord-315058-t7bq4yqw author: Brand, Samuel P C title: Forecasting the scale of the COVID-19 epidemic in Kenya date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-315058-t7bq4yqw.txt cache: ./cache/cord-315058-t7bq4yqw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315058-t7bq4yqw.txt' === file2bib.sh === id: cord-314937-jrxu65bl author: Kuwelker, K. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-314937-jrxu65bl.txt cache: ./cache/cord-314937-jrxu65bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314937-jrxu65bl.txt' === file2bib.sh === id: cord-315931-kc8gnj6z author: Klempt, Petr title: Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-315931-kc8gnj6z.txt cache: ./cache/cord-315931-kc8gnj6z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315931-kc8gnj6z.txt' === file2bib.sh === id: cord-316498-f43apjul author: Karlsson, Jan Olof G title: May Mangafodipir or Other SOD Mimetics Contribute to Better Care in COVID-19 Patients? date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-316498-f43apjul.txt cache: ./cache/cord-316498-f43apjul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316498-f43apjul.txt' === file2bib.sh === id: cord-316080-y6ypbdtu author: Fajnzylber, J. M. title: SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-316080-y6ypbdtu.txt cache: ./cache/cord-316080-y6ypbdtu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316080-y6ypbdtu.txt' === file2bib.sh === id: cord-315415-3aotsb2g author: Dong, Jianbo title: Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2 date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-315415-3aotsb2g.txt cache: ./cache/cord-315415-3aotsb2g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315415-3aotsb2g.txt' === file2bib.sh === id: cord-316018-zrui9i5z author: Bristow, Michael R. title: Dynamic Regulation of SARS-CoV-2 Binding and Cell Entry Mechanisms in Remodeled Human Ventricular Myocardium date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-316018-zrui9i5z.txt cache: ./cache/cord-316018-zrui9i5z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316018-zrui9i5z.txt' === file2bib.sh === id: cord-315756-g6g34uvh author: Danchin, A. title: Immunity after COVID-19: protection or sensitization ? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-315756-g6g34uvh.txt cache: ./cache/cord-315756-g6g34uvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315756-g6g34uvh.txt' === file2bib.sh === id: cord-315193-z6v6s46n author: Adhikari, Nilanjan title: Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date: 2017-07-14 pages: extension: .txt txt: ./txt/cord-315193-z6v6s46n.txt cache: ./cache/cord-315193-z6v6s46n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315193-z6v6s46n.txt' === file2bib.sh === id: cord-315652-hct9yh3n author: Wehbe, Zena title: Molecular Insights Into SARS COV-2 Interaction With Cardiovascular Disease: Role of RAAS and MAPK Signaling date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-315652-hct9yh3n.txt cache: ./cache/cord-315652-hct9yh3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315652-hct9yh3n.txt' === file2bib.sh === id: cord-316003-xt59voyt author: Say, Daphne S. title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-316003-xt59voyt.txt cache: ./cache/cord-316003-xt59voyt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316003-xt59voyt.txt' === file2bib.sh === id: cord-315982-iuez41zj author: Achdout, Hagit title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-315982-iuez41zj.txt cache: ./cache/cord-315982-iuez41zj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315982-iuez41zj.txt' === file2bib.sh === id: cord-315951-5gsbtfag author: Kiemer, Lars title: Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date: 2004-06-06 pages: extension: .txt txt: ./txt/cord-315951-5gsbtfag.txt cache: ./cache/cord-315951-5gsbtfag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315951-5gsbtfag.txt' === file2bib.sh === id: cord-315754-dq2empne author: Hasan, Anwarul title: A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-315754-dq2empne.txt cache: ./cache/cord-315754-dq2empne.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315754-dq2empne.txt' === file2bib.sh === id: cord-315611-xbj41ekc author: Ahmad, Mohammed title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-315611-xbj41ekc.txt cache: ./cache/cord-315611-xbj41ekc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315611-xbj41ekc.txt' === file2bib.sh === id: cord-316425-fnlgeubu author: Rahimi, Farid title: Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-316425-fnlgeubu.txt cache: ./cache/cord-316425-fnlgeubu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316425-fnlgeubu.txt' === file2bib.sh === id: cord-315685-ute3dxwu author: Ehaideb, Salleh N. title: Evidence of a wide gap between COVID-19 in humans and animal models: a systematic review date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-315685-ute3dxwu.txt cache: ./cache/cord-315685-ute3dxwu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315685-ute3dxwu.txt' === file2bib.sh === id: cord-316345-a1cirnya author: Comas, Carmina title: COVID‐19 and pregnancy: An opportunity to correct an historic gender bias date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-316345-a1cirnya.txt cache: ./cache/cord-316345-a1cirnya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316345-a1cirnya.txt' === file2bib.sh === id: cord-316117-o29773cz author: Menzella, Francesco title: Pharmacologicaltreatment of COVID-19: lights and shadows date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-316117-o29773cz.txt cache: ./cache/cord-316117-o29773cz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316117-o29773cz.txt' === file2bib.sh === id: cord-316646-rd3zl9qz author: Lebedin, Y. S. title: Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-316646-rd3zl9qz.txt cache: ./cache/cord-316646-rd3zl9qz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316646-rd3zl9qz.txt' === file2bib.sh === id: cord-316186-254z62e4 author: Kario, Kazuomi title: COVID‐19 and hypertension—evidence and practical management: Guidance from the HOPE Asia Network date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-316186-254z62e4.txt cache: ./cache/cord-316186-254z62e4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316186-254z62e4.txt' === file2bib.sh === id: cord-316096-3fnwosst author: Jin, Huali title: Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice date: 2005-03-25 pages: extension: .txt txt: ./txt/cord-316096-3fnwosst.txt cache: ./cache/cord-316096-3fnwosst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316096-3fnwosst.txt' === file2bib.sh === id: cord-316374-mzomj1ab author: Brufsky, Adam title: Boning up: amino-bisphophonates as immunostimulants and endosomal disruptors of dendritic cell in SARS-CoV-2 infection date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-316374-mzomj1ab.txt cache: ./cache/cord-316374-mzomj1ab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316374-mzomj1ab.txt' === file2bib.sh === id: cord-316667-b1xabkzk author: Konopka, Kristine E. title: Diffuse Alveolar Damage (DAD) from Coronavirus Disease 2019 Infection is Morphologically Indistinguishable from Other Causes of DAD date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-316667-b1xabkzk.txt cache: ./cache/cord-316667-b1xabkzk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316667-b1xabkzk.txt' === file2bib.sh === id: cord-315656-asvf4roo author: Wu, Junjiao title: Revisiting the Immune Balance Theory: A Neurological Insight Into the Epidemic of COVID-19 and Its Alike date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-315656-asvf4roo.txt cache: ./cache/cord-315656-asvf4roo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315656-asvf4roo.txt' === file2bib.sh === id: cord-316330-55nd3pwe author: Ramos-Lopez, Omar title: Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-316330-55nd3pwe.txt cache: ./cache/cord-316330-55nd3pwe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316330-55nd3pwe.txt' === file2bib.sh === id: cord-316129-mjg3un0l author: Khamar, Pooja title: Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-316129-mjg3un0l.txt cache: ./cache/cord-316129-mjg3un0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316129-mjg3un0l.txt' === file2bib.sh === id: cord-316946-bxfdq8e1 author: Danion, François title: The Good, the Bad, and the Hoax: When Publication Instantaneously Impacts Treatment Strategies for COVID-19 date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-316946-bxfdq8e1.txt cache: ./cache/cord-316946-bxfdq8e1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316946-bxfdq8e1.txt' === file2bib.sh === id: cord-316066-pge0vx04 author: Zhang, Zheng title: Longitudinal alteration of circulating dendritic cell subsets and its correlation with steroid treatment in patients with severe acute respiratory syndrome date: 2005-06-16 pages: extension: .txt txt: ./txt/cord-316066-pge0vx04.txt cache: ./cache/cord-316066-pge0vx04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316066-pge0vx04.txt' === file2bib.sh === id: cord-315462-u2dj79yw author: Hewitt, Judith A. title: ACTIVating Resources for the COVID-19 Pandemic: In vivo Models for Vaccines and Therapeutics date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-315462-u2dj79yw.txt cache: ./cache/cord-315462-u2dj79yw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315462-u2dj79yw.txt' === file2bib.sh === id: cord-316215-4mj7n0ax author: Haveri, Anu title: Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020 date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-316215-4mj7n0ax.txt cache: ./cache/cord-316215-4mj7n0ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316215-4mj7n0ax.txt' === file2bib.sh === id: cord-316880-hbw6jbz5 author: Sutton, Melissa title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-316880-hbw6jbz5.txt cache: ./cache/cord-316880-hbw6jbz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-316880-hbw6jbz5.txt' === file2bib.sh === id: cord-316616-j82q99in author: Su, Yen-Bo title: Cardiovascular manifestation and treatment in COVID-19 date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-316616-j82q99in.txt cache: ./cache/cord-316616-j82q99in.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316616-j82q99in.txt' === file2bib.sh === id: cord-316617-8cqxz3wi author: Ward, Michael P. title: SARS‐CoV‐2, where to now? date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-316617-8cqxz3wi.txt cache: ./cache/cord-316617-8cqxz3wi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316617-8cqxz3wi.txt' === file2bib.sh === id: cord-315696-43wmazxa author: Marinaki, Smaragdi title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients’ Lives and Allografts date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-315696-43wmazxa.txt cache: ./cache/cord-315696-43wmazxa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315696-43wmazxa.txt' === file2bib.sh === id: cord-315970-m5o962yw author: Di Ciaula, Agostino title: COVID‐19, internists and resilience: the north‐south Italy outbreak. date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-315970-m5o962yw.txt cache: ./cache/cord-315970-m5o962yw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315970-m5o962yw.txt' === file2bib.sh === id: cord-316930-0s7k9guq author: Caldas, Lucio Ayres title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-316930-0s7k9guq.txt cache: ./cache/cord-316930-0s7k9guq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316930-0s7k9guq.txt' === file2bib.sh === id: cord-316979-uadlclsv author: Pierri, Ciro Leonardo title: SARS-CoV-2 spike protein: flexibility as a new target for fighting infection date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-316979-uadlclsv.txt cache: ./cache/cord-316979-uadlclsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316979-uadlclsv.txt' === file2bib.sh === id: cord-316705-3wzurnfp author: Lalmuanawma, Samuel title: Applications of Machine Learning and Artificial Intelligence for Covid-19 (SARS-CoV-2) pandemic: A review date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-316705-3wzurnfp.txt cache: ./cache/cord-316705-3wzurnfp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316705-3wzurnfp.txt' === file2bib.sh === id: cord-316179-kmdxltie author: Fozouni, P. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-316179-kmdxltie.txt cache: ./cache/cord-316179-kmdxltie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316179-kmdxltie.txt' === file2bib.sh === id: cord-316712-1ngcwdln author: Laxminarayan, Ramanan title: India’s Battle against COVID-19: Progress and Challenges date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-316712-1ngcwdln.txt cache: ./cache/cord-316712-1ngcwdln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316712-1ngcwdln.txt' === file2bib.sh === id: cord-316970-n2dly3oa author: Kerbaj, Jad title: COVID-19: The New Caledonia experience date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-316970-n2dly3oa.txt cache: ./cache/cord-316970-n2dly3oa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316970-n2dly3oa.txt' === file2bib.sh === id: cord-317067-u90zkjk9 author: Trottein, François title: Potential causes and consequences of gastrointestinal disorders during a SARS-CoV-2 infection date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-317067-u90zkjk9.txt cache: ./cache/cord-317067-u90zkjk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317067-u90zkjk9.txt' === file2bib.sh === id: cord-316670-x9x54fxw author: Flinck, Heini title: Comparison of two fully automated tests detecting antibodies against nucleocapsid N and spike S1/S2 proteins in COVID-19 date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-316670-x9x54fxw.txt cache: ./cache/cord-316670-x9x54fxw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316670-x9x54fxw.txt' === file2bib.sh === id: cord-316493-wszoi6p2 author: Zhou, Weimin title: First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood date: 2013-09-16 pages: extension: .txt txt: ./txt/cord-316493-wszoi6p2.txt cache: ./cache/cord-316493-wszoi6p2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316493-wszoi6p2.txt' === file2bib.sh === id: cord-316702-dj2fo8sn author: Vignesh, Ramachandran title: Is Herd Immunity Against SARS-CoV-2 a Silver Lining? date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-316702-dj2fo8sn.txt cache: ./cache/cord-316702-dj2fo8sn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316702-dj2fo8sn.txt' === file2bib.sh === id: cord-316859-h8lfmr3e author: Mu, Jingfang title: SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-316859-h8lfmr3e.txt cache: ./cache/cord-316859-h8lfmr3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316859-h8lfmr3e.txt' === file2bib.sh === id: cord-316255-93srx4s7 author: Cacho, Pedro Muñoz title: Can climatic factors explain the differences in COVID-19 incidence and severity across the Spanish regions?: An ecological study date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-316255-93srx4s7.txt cache: ./cache/cord-316255-93srx4s7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316255-93srx4s7.txt' === file2bib.sh === id: cord-317000-bfc51e0m author: Visci, G. title: Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-317000-bfc51e0m.txt cache: ./cache/cord-317000-bfc51e0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317000-bfc51e0m.txt' === file2bib.sh === id: cord-316632-rr9f88oi author: Kimura, Yurika title: Society of swallowing and dysphagia of Japan: Position statement on dysphagia management during the COVID-19 outbreak date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-316632-rr9f88oi.txt cache: ./cache/cord-316632-rr9f88oi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316632-rr9f88oi.txt' === file2bib.sh === id: cord-317355-z5tk3v3b author: Dunker, Susanne title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-317355-z5tk3v3b.txt cache: ./cache/cord-317355-z5tk3v3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317355-z5tk3v3b.txt' === file2bib.sh === id: cord-316814-9fv9xrln author: Li, Hong-Ye title: Use of GFP to Investigate Expression of Plant-Derived Vaccines date: 2009 pages: extension: .txt txt: ./txt/cord-316814-9fv9xrln.txt cache: ./cache/cord-316814-9fv9xrln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316814-9fv9xrln.txt' === file2bib.sh === id: cord-316095-jzyb4jn5 author: Falahchai, Mehran title: Dental care management during the COVID‐19 outbreak date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-316095-jzyb4jn5.txt cache: ./cache/cord-316095-jzyb4jn5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316095-jzyb4jn5.txt' === file2bib.sh === id: cord-317129-wa1j2f6b author: Zhang, Jia title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 pages: extension: .txt txt: ./txt/cord-317129-wa1j2f6b.txt cache: ./cache/cord-317129-wa1j2f6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317129-wa1j2f6b.txt' === file2bib.sh === id: cord-316432-xemz7zn9 author: Talaie, Haleh title: Is there any potential management against COVID-19? A systematic review and meta-analysis date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-316432-xemz7zn9.txt cache: ./cache/cord-316432-xemz7zn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316432-xemz7zn9.txt' === file2bib.sh === id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 pages: extension: .txt txt: ./txt/cord-316525-uadfehr6.txt cache: ./cache/cord-316525-uadfehr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316525-uadfehr6.txt' === file2bib.sh === id: cord-316723-srenbxa7 author: Zhao, Jincun title: Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus date: 2004-11-23 pages: extension: .txt txt: ./txt/cord-316723-srenbxa7.txt cache: ./cache/cord-316723-srenbxa7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316723-srenbxa7.txt' === file2bib.sh === id: cord-317042-dll3qt4g author: Lv, Jun title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-317042-dll3qt4g.txt cache: ./cache/cord-317042-dll3qt4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317042-dll3qt4g.txt' === file2bib.sh === id: cord-316232-7w1vrx96 author: Radon, K. title: Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19) date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-316232-7w1vrx96.txt cache: ./cache/cord-316232-7w1vrx96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316232-7w1vrx96.txt' === file2bib.sh === id: cord-317429-pp6hb4q5 author: Aslam, Saima title: COVID-19: Yet another coronavirus challenge in transplantation date: 2020-03-14 pages: extension: .txt txt: ./txt/cord-317429-pp6hb4q5.txt cache: ./cache/cord-317429-pp6hb4q5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317429-pp6hb4q5.txt' === file2bib.sh === id: cord-316658-zwxtbena author: Butler, S. E. title: Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-316658-zwxtbena.txt cache: ./cache/cord-316658-zwxtbena.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316658-zwxtbena.txt' === file2bib.sh === id: cord-316536-jpbfgwhl author: Raj, V. Stalin title: Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC date: 2013-03-13 pages: extension: .txt txt: ./txt/cord-316536-jpbfgwhl.txt cache: ./cache/cord-316536-jpbfgwhl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316536-jpbfgwhl.txt' === file2bib.sh === id: cord-317057-c2bwky6e author: Pickering, S. title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-317057-c2bwky6e.txt cache: ./cache/cord-317057-c2bwky6e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317057-c2bwky6e.txt' === file2bib.sh === id: cord-316623-tv5yyfak author: Zhang, Jianmin title: Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase date: 2008-03-04 pages: extension: .txt txt: ./txt/cord-316623-tv5yyfak.txt cache: ./cache/cord-316623-tv5yyfak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316623-tv5yyfak.txt' === file2bib.sh === id: cord-317523-idji1l0a author: Xu, Huanzhou title: SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-317523-idji1l0a.txt cache: ./cache/cord-317523-idji1l0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317523-idji1l0a.txt' === file2bib.sh === id: cord-316894-zhmuzv7z author: Stetzenbach, L.D. title: Airborne Infectious Microorganisms date: 2009-02-17 pages: extension: .txt txt: ./txt/cord-316894-zhmuzv7z.txt cache: ./cache/cord-316894-zhmuzv7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316894-zhmuzv7z.txt' === file2bib.sh === id: cord-317246-8c7d5ynz author: Cagetti, Maria Grazia title: Could SARS‐CoV‐2 burst the use of Non‐Invasive and Minimally Invasive treatments in paediatric dentistry? date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-317246-8c7d5ynz.txt cache: ./cache/cord-317246-8c7d5ynz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317246-8c7d5ynz.txt' === file2bib.sh === id: cord-317085-qc8bfb9g author: Zhang, Nan title: Risk Factors for Poor Outcomes of Diabetes Patients With COVID-19: A Single-Center, Retrospective Study in Early Outbreak in China date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-317085-qc8bfb9g.txt cache: ./cache/cord-317085-qc8bfb9g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317085-qc8bfb9g.txt' === file2bib.sh === id: cord-316788-4x5l2h4d author: Ryu, Young Bae title: Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition date: 2010-11-15 pages: extension: .txt txt: ./txt/cord-316788-4x5l2h4d.txt cache: ./cache/cord-316788-4x5l2h4d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316788-4x5l2h4d.txt' === file2bib.sh === id: cord-317227-zb434ve3 author: Beck, Bo Ram title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-317227-zb434ve3.txt cache: ./cache/cord-317227-zb434ve3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317227-zb434ve3.txt' === file2bib.sh === id: cord-316845-k9zvsfvj author: Robertson, Mary M. title: Gilles de la Tourette Syndrome: advice in the times of COVID-19 date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-316845-k9zvsfvj.txt cache: ./cache/cord-316845-k9zvsfvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316845-k9zvsfvj.txt' === file2bib.sh === id: cord-317240-d7ioosi6 author: Shah, Niyati title: Review: An insight into coronaviruses: Challenges, security and scope date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-317240-d7ioosi6.txt cache: ./cache/cord-317240-d7ioosi6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317240-d7ioosi6.txt' === file2bib.sh === id: cord-317608-otd81rvy author: Corman, Victor M. title: SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-317608-otd81rvy.txt cache: ./cache/cord-317608-otd81rvy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317608-otd81rvy.txt' === file2bib.sh === id: cord-317563-mu47vvma author: Yuan, Chunhui title: Viral loads in throat and anal swabs in children infected with SARS-CoV-2 date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-317563-mu47vvma.txt cache: ./cache/cord-317563-mu47vvma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317563-mu47vvma.txt' === file2bib.sh === id: cord-317647-vcktnsv8 author: Wang, Yinhua title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-317647-vcktnsv8.txt cache: ./cache/cord-317647-vcktnsv8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317647-vcktnsv8.txt' === file2bib.sh === id: cord-315730-fzgxuak7 author: Penman, Sophie L. title: Safety perspectives on presently considered drugs for the treatment of COVID‐19 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-315730-fzgxuak7.txt cache: ./cache/cord-315730-fzgxuak7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-315730-fzgxuak7.txt' === file2bib.sh === id: cord-317151-cxx5pcln author: Papa, Alfredo title: Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-317151-cxx5pcln.txt cache: ./cache/cord-317151-cxx5pcln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317151-cxx5pcln.txt' === file2bib.sh === id: cord-316260-1t3ifsfi author: Nogueira-de-Almeida, Carlos Alberto title: COVID-19 and obesity in childhood and adolescence: A clinical review()() date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-316260-1t3ifsfi.txt cache: ./cache/cord-316260-1t3ifsfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-316260-1t3ifsfi.txt' === file2bib.sh === id: cord-317359-7yuygcew author: Straccia, Patrizia title: Description of a new biosafe procedure for cytological specimens from patients with COVID‐19 processed by liquid‐based preparations date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-317359-7yuygcew.txt cache: ./cache/cord-317359-7yuygcew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317359-7yuygcew.txt' === file2bib.sh === id: cord-317761-tkqmu1va author: Shukla, Ashutosh M title: Chloroquine and hydroxychloroquine in the context of COVID-19 date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-317761-tkqmu1va.txt cache: ./cache/cord-317761-tkqmu1va.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317761-tkqmu1va.txt' === file2bib.sh === id: cord-318205-qxkel0ww author: Parkulo, Mark A. title: Risk of SARS-CoV-2 Transmission Among Coworkers in a Surgical Environment date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-318205-qxkel0ww.txt cache: ./cache/cord-318205-qxkel0ww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318205-qxkel0ww.txt' === file2bib.sh === id: cord-317123-0tdfvlqd author: Tan, Xiaotian title: Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-317123-0tdfvlqd.txt cache: ./cache/cord-317123-0tdfvlqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317123-0tdfvlqd.txt' === file2bib.sh === id: cord-317591-qa6oxy4j author: Fukushima, Akiko title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 pages: extension: .txt txt: ./txt/cord-317591-qa6oxy4j.txt cache: ./cache/cord-317591-qa6oxy4j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317591-qa6oxy4j.txt' === file2bib.sh === id: cord-317092-5qba9jiq author: Singh, Tulika title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-317092-5qba9jiq.txt cache: ./cache/cord-317092-5qba9jiq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317092-5qba9jiq.txt' === file2bib.sh === id: cord-317928-doj39520 author: Thum, Thomas title: SARS-CoV-2 receptor ACE2 expression in the human heart: cause of a post-pandemic wave of heart failure? date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-317928-doj39520.txt cache: ./cache/cord-317928-doj39520.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317928-doj39520.txt' === file2bib.sh === id: cord-317423-3nkzp1z2 author: Turk, Can title: In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-317423-3nkzp1z2.txt cache: ./cache/cord-317423-3nkzp1z2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317423-3nkzp1z2.txt' === file2bib.sh === id: cord-318253-vp22xd8p author: Parisi, Ortensia Ilaria title: “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-318253-vp22xd8p.txt cache: ./cache/cord-318253-vp22xd8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318253-vp22xd8p.txt' === file2bib.sh === id: cord-317379-ljdaj80d author: Faure‐Bardon, V. title: Anatomical and timely assessment of protein expression of angiotensin‐converting enzyme 2, SARS‐CoV‐2 specific receptor, in fetal and placental tissues: new insight for perinatal counseling date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-317379-ljdaj80d.txt cache: ./cache/cord-317379-ljdaj80d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317379-ljdaj80d.txt' === file2bib.sh === id: cord-317906-u5z5cpfk author: Gupta, Ishita title: Atypical Neurological Manifestations of COVID-19 date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-317906-u5z5cpfk.txt cache: ./cache/cord-317906-u5z5cpfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317906-u5z5cpfk.txt' === file2bib.sh === id: cord-317971-kuwargnp author: Opatz, Till title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-317971-kuwargnp.txt cache: ./cache/cord-317971-kuwargnp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317971-kuwargnp.txt' === file2bib.sh === id: cord-317573-wp2wr3b5 author: Peng, Hui title: Human memory T cell responses to SARS-CoV E protein date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-317573-wp2wr3b5.txt cache: ./cache/cord-317573-wp2wr3b5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317573-wp2wr3b5.txt' === file2bib.sh === id: cord-317233-k3wuqwyu author: Lorenzo-Redondo, Ramon title: A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-317233-k3wuqwyu.txt cache: ./cache/cord-317233-k3wuqwyu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317233-k3wuqwyu.txt' === file2bib.sh === id: cord-317413-w2xfdwea author: Maurya, Vimal K. title: Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-317413-w2xfdwea.txt cache: ./cache/cord-317413-w2xfdwea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317413-w2xfdwea.txt' === file2bib.sh === id: cord-318036-t05ummop author: Peng, Liang title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples date: 2020-02-25 pages: extension: .txt txt: ./txt/cord-318036-t05ummop.txt cache: ./cache/cord-318036-t05ummop.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318036-t05ummop.txt' === file2bib.sh === id: cord-318239-2sraqm6e author: Phan, Lan T. title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-318239-2sraqm6e.txt cache: ./cache/cord-318239-2sraqm6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318239-2sraqm6e.txt' === file2bib.sh === id: cord-318204-t024w7h6 author: Fang, Ferric C title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-318204-t024w7h6.txt cache: ./cache/cord-318204-t024w7h6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318204-t024w7h6.txt' === file2bib.sh === id: cord-317593-tajy3p9e author: Xi, AIqi title: Epidemiological and clinical characteristics of discharged patients infected with SARS-CoV-2 on the Qinghai plateau date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-317593-tajy3p9e.txt cache: ./cache/cord-317593-tajy3p9e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317593-tajy3p9e.txt' === file2bib.sh === id: cord-317468-pnxni1x5 author: Louie, Philip K. title: Early Peri-operative Outcomes Were Unchanged in Patients Undergoing Spine Surgery During the COVID-19 Pandemic in New York City date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-317468-pnxni1x5.txt cache: ./cache/cord-317468-pnxni1x5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317468-pnxni1x5.txt' === file2bib.sh === id: cord-318426-kv7aa0og author: Kritsotakis, Evangelos I. title: On the importance of population-based serological surveys of SARS-CoV-2 without overlooking their inherent uncertainties date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-318426-kv7aa0og.txt cache: ./cache/cord-318426-kv7aa0og.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318426-kv7aa0og.txt' === file2bib.sh === id: cord-317820-od9l7p1r author: Goker Bagca, Bakiye title: Overview of the COVID-19 and JAK/STAT Pathway Inhibition: Ruxolitinib Perspective date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-317820-od9l7p1r.txt cache: ./cache/cord-317820-od9l7p1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317820-od9l7p1r.txt' === file2bib.sh === id: cord-317693-l08q2lhp author: Jacob, Michelle Cristine Medeiros title: Animal-based food systems are unsafe: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fosters the debate on meat consumption date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-317693-l08q2lhp.txt cache: ./cache/cord-317693-l08q2lhp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317693-l08q2lhp.txt' === file2bib.sh === id: cord-318126-gg68o52z author: Zhou, Juan title: Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-318126-gg68o52z.txt cache: ./cache/cord-318126-gg68o52z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318126-gg68o52z.txt' === file2bib.sh === id: cord-317707-r0q7ipa6 author: Saracco, Margherita title: Carrying on with Liver Transplantation during the COVID-19 emergency: Report from Piedmont Region date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-317707-r0q7ipa6.txt cache: ./cache/cord-317707-r0q7ipa6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317707-r0q7ipa6.txt' === file2bib.sh === id: cord-318018-ybdkp398 author: Bruni, Margherita title: Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-318018-ybdkp398.txt cache: ./cache/cord-318018-ybdkp398.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318018-ybdkp398.txt' === file2bib.sh === id: cord-317622-o10ntfi8 author: Evans, Ronald M. title: Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-317622-o10ntfi8.txt cache: ./cache/cord-317622-o10ntfi8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317622-o10ntfi8.txt' === file2bib.sh === id: cord-318006-9op556q2 author: Luo, Y. R. title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-318006-9op556q2.txt cache: ./cache/cord-318006-9op556q2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318006-9op556q2.txt' === file2bib.sh === id: cord-318164-6rqi17oz author: Paoli, D. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-318164-6rqi17oz.txt cache: ./cache/cord-318164-6rqi17oz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318164-6rqi17oz.txt' === file2bib.sh === id: cord-317333-unrd76bo author: Danesh, Ali title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date: 2011-01-05 pages: extension: .txt txt: ./txt/cord-317333-unrd76bo.txt cache: ./cache/cord-317333-unrd76bo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317333-unrd76bo.txt' === file2bib.sh === id: cord-318499-uihof6k6 author: Beddingfield, Brandon title: The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-318499-uihof6k6.txt cache: ./cache/cord-318499-uihof6k6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318499-uihof6k6.txt' === file2bib.sh === id: cord-318048-6nvi63rq author: Arshad, Usman title: Prioritisation of Anti‐SARS‐Cov‐2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-318048-6nvi63rq.txt cache: ./cache/cord-318048-6nvi63rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318048-6nvi63rq.txt' === file2bib.sh === id: cord-316126-j51dik7f author: Zhang, X. Sophie title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-316126-j51dik7f.txt cache: ./cache/cord-316126-j51dik7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316126-j51dik7f.txt' === file2bib.sh === id: cord-318342-eipscagh author: Chen, Juan title: The Impact of COVID-19 on Blood Glucose: A Systematic Review and Meta-Analysis date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-318342-eipscagh.txt cache: ./cache/cord-318342-eipscagh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318342-eipscagh.txt' === file2bib.sh === id: cord-318235-2e5er0x0 author: Yanai, Hidekatsu title: Adiposity is the Crucial Enhancer of COVID-19 date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-318235-2e5er0x0.txt cache: ./cache/cord-318235-2e5er0x0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318235-2e5er0x0.txt' === file2bib.sh === id: cord-318715-p6agoqu8 author: Belser, Jessica A title: Assessment of SARS-CoV-2 replication in the context of other respiratory viruses date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-318715-p6agoqu8.txt cache: ./cache/cord-318715-p6agoqu8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318715-p6agoqu8.txt' === file2bib.sh === id: cord-318069-logh6rnu author: Ordás, Carlos M. title: Concurrent tonic pupil and trochlear nerve palsy in COVID-19 date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-318069-logh6rnu.txt cache: ./cache/cord-318069-logh6rnu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-318069-logh6rnu.txt' === file2bib.sh === id: cord-318920-njurbf3d author: Romana Ponziani, Francesca title: Liver involvement is not associated with mortality: results from a large cohort of SARS‐CoV‐2 positive patients date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-318920-njurbf3d.txt cache: ./cache/cord-318920-njurbf3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318920-njurbf3d.txt' === file2bib.sh === id: cord-317863-xf0bn3cv author: Pata, Ramakanth title: Probability of COVID-19 Being the Culprit in Neurocognitive Deception: A Case Series of Incidental Strokes in ICU Patients With COVID-19 date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-317863-xf0bn3cv.txt cache: ./cache/cord-317863-xf0bn3cv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317863-xf0bn3cv.txt' === file2bib.sh === id: cord-318483-il5aq8py author: Perez Gaxiola, G. title: Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-318483-il5aq8py.txt cache: ./cache/cord-318483-il5aq8py.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318483-il5aq8py.txt' === file2bib.sh === id: cord-318738-7dgbc4um author: Schmidt, Marco Florian title: Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening date: 2008-03-17 pages: extension: .txt txt: ./txt/cord-318738-7dgbc4um.txt cache: ./cache/cord-318738-7dgbc4um.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318738-7dgbc4um.txt' === file2bib.sh === id: cord-318766-vx0dnnxh author: Wendt, Ralph title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-318766-vx0dnnxh.txt cache: ./cache/cord-318766-vx0dnnxh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318766-vx0dnnxh.txt' === file2bib.sh === id: cord-318934-dxipu00r author: Matsuyama, Shutoku title: Enhancement of SARS-CoV Infection by Proteases date: 2006 pages: extension: .txt txt: ./txt/cord-318934-dxipu00r.txt cache: ./cache/cord-318934-dxipu00r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318934-dxipu00r.txt' === file2bib.sh === id: cord-318316-9unfl966 author: Ortega, Joseph T. title: Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-318316-9unfl966.txt cache: ./cache/cord-318316-9unfl966.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318316-9unfl966.txt' === file2bib.sh === id: cord-318492-uu1p1rgi author: Mansueto, Gelsomina title: COVID-19: Brief Check Point Through The Pathologist's Eye (autopsy archive) date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-318492-uu1p1rgi.txt cache: ./cache/cord-318492-uu1p1rgi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318492-uu1p1rgi.txt' === file2bib.sh === id: cord-318029-xd7nuahh author: Ke, Chunjin title: 2019 novel coronavirus disease (COVID-19) in hemodialysis patients: a report of two cases date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-318029-xd7nuahh.txt cache: ./cache/cord-318029-xd7nuahh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318029-xd7nuahh.txt' === file2bib.sh === id: cord-318387-s4d442kx author: Wang, Ming title: Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-318387-s4d442kx.txt cache: ./cache/cord-318387-s4d442kx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318387-s4d442kx.txt' === file2bib.sh === id: cord-317786-iv1br2oj author: Waterfield, T. title: Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study. date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-317786-iv1br2oj.txt cache: ./cache/cord-317786-iv1br2oj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317786-iv1br2oj.txt' === file2bib.sh === id: cord-318339-j35w1vsw author: Stockman, Lauren J title: SARS: Systematic Review of Treatment Effects date: 2006-09-12 pages: extension: .txt txt: ./txt/cord-318339-j35w1vsw.txt cache: ./cache/cord-318339-j35w1vsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318339-j35w1vsw.txt' === file2bib.sh === id: cord-319236-gxcs77pl author: Chen, Qingyan title: Can we migrate COVID-19 spreading risk? date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-319236-gxcs77pl.txt cache: ./cache/cord-319236-gxcs77pl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319236-gxcs77pl.txt' === file2bib.sh === id: cord-319022-1twsxzcd author: Desai, Antonio title: The role of anti-hypertensive treatment, comorbidities and early introduction of LMWH in the setting of COVID-19: A retrospective, observational study in Northern Italy() date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-319022-1twsxzcd.txt cache: ./cache/cord-319022-1twsxzcd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319022-1twsxzcd.txt' === file2bib.sh === id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-317037-1qydcc5e.txt cache: ./cache/cord-317037-1qydcc5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317037-1qydcc5e.txt' === file2bib.sh === id: cord-317435-4yuw7jo3 author: Zhou, Yadi title: Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-317435-4yuw7jo3.txt cache: ./cache/cord-317435-4yuw7jo3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317435-4yuw7jo3.txt' === file2bib.sh === id: cord-318957-gp5drg71 author: Freedman, Matthew title: Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography date: 2004-06-30 pages: extension: .txt txt: ./txt/cord-318957-gp5drg71.txt cache: ./cache/cord-318957-gp5drg71.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318957-gp5drg71.txt' === file2bib.sh === id: cord-318262-w8oixzdg author: Chevance, A title: Ensuring mental health care during the SARS-CoV-2 epidemic in France: a narrative review date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-318262-w8oixzdg.txt cache: ./cache/cord-318262-w8oixzdg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318262-w8oixzdg.txt' === file2bib.sh === id: cord-318184-atlslk0e author: Germain, N. title: Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-318184-atlslk0e.txt cache: ./cache/cord-318184-atlslk0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318184-atlslk0e.txt' === file2bib.sh === id: cord-319184-voc0eqb9 author: Abduljalil, Jameel M. title: Laboratory diagnosis of SARS-CoV-2: available approaches and limitations date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-319184-voc0eqb9.txt cache: ./cache/cord-319184-voc0eqb9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319184-voc0eqb9.txt' === file2bib.sh === id: cord-319023-ucm8frol author: Nuzzo, Andrea title: Universal Shelter-in-Place vs. Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-319023-ucm8frol.txt cache: ./cache/cord-319023-ucm8frol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319023-ucm8frol.txt' === file2bib.sh === id: cord-318789-ylxh8vi2 author: Byrne, R. L. title: Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis. date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-318789-ylxh8vi2.txt cache: ./cache/cord-318789-ylxh8vi2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318789-ylxh8vi2.txt' === file2bib.sh === id: cord-319158-n8e2n30b author: Mackenzie, John S title: COVID-19: a novel zoonotic disease caused by a coronavirus from China: what we know and what we don’t date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-319158-n8e2n30b.txt cache: ./cache/cord-319158-n8e2n30b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319158-n8e2n30b.txt' === file2bib.sh === id: cord-317628-1inxq7t5 author: Cuccarese, Michael F. title: Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-317628-1inxq7t5.txt cache: ./cache/cord-317628-1inxq7t5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317628-1inxq7t5.txt' === file2bib.sh === id: cord-319540-kivk3h1k author: Uhe, Tobias title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-319540-kivk3h1k.txt cache: ./cache/cord-319540-kivk3h1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319540-kivk3h1k.txt' === file2bib.sh === id: cord-319100-3gdawhfn author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-319100-3gdawhfn.txt cache: ./cache/cord-319100-3gdawhfn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319100-3gdawhfn.txt' === file2bib.sh === id: cord-318364-5bmdzgla author: Sun, Xinjuan title: Cytokine storm intervention in the early stages of COVID-19 pneumonia date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-318364-5bmdzgla.txt cache: ./cache/cord-318364-5bmdzgla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318364-5bmdzgla.txt' === file2bib.sh === id: cord-317795-689at1qx author: Bielicki, Julia A title: Monitoring approaches for health-care workers during the COVID-19 pandemic date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-317795-689at1qx.txt cache: ./cache/cord-317795-689at1qx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317795-689at1qx.txt' === file2bib.sh === id: cord-318625-hf7fgtnp author: Vashi, Yoya title: Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-318625-hf7fgtnp.txt cache: ./cache/cord-318625-hf7fgtnp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318625-hf7fgtnp.txt' === file2bib.sh === id: cord-319164-wbrnhpgs author: Luellen, E. title: A Machine Learning Explanation of Incidence Inequalities of SARS-CoV-2 Across 88 Days in 157 Countries date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-319164-wbrnhpgs.txt cache: ./cache/cord-319164-wbrnhpgs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319164-wbrnhpgs.txt' === file2bib.sh === id: cord-319337-w9zyshzb author: Yu, Jingyou title: DNA vaccine protection against SARS-CoV-2 in rhesus macaques date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-319337-w9zyshzb.txt cache: ./cache/cord-319337-w9zyshzb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319337-w9zyshzb.txt' === file2bib.sh === id: cord-319590-f9qcabcx author: Han, Yanxiao title: Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-319590-f9qcabcx.txt cache: ./cache/cord-319590-f9qcabcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319590-f9qcabcx.txt' === file2bib.sh === id: cord-319089-hxpoy4gd author: Du, Li title: Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-319089-hxpoy4gd.txt cache: ./cache/cord-319089-hxpoy4gd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319089-hxpoy4gd.txt' === file2bib.sh === id: cord-319273-ok2p1h9f author: Lai, Yu-Ju title: Severe acute respiratory syndrome coronavirus-2 and the deduction effect of angiotensin-converting enzyme 2 in pregnancy date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-319273-ok2p1h9f.txt cache: ./cache/cord-319273-ok2p1h9f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319273-ok2p1h9f.txt' === file2bib.sh === id: cord-318444-sgm24q1i author: Walter, Justin D. title: Sybodies targeting the SARS-CoV-2 receptor-binding domain date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-318444-sgm24q1i.txt cache: ./cache/cord-318444-sgm24q1i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318444-sgm24q1i.txt' === file2bib.sh === id: cord-319194-ukuia48s author: Liò, Pietro title: Phylogenomics and bioinformatics of SARS-CoV date: 2004-02-04 pages: extension: .txt txt: ./txt/cord-319194-ukuia48s.txt cache: ./cache/cord-319194-ukuia48s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319194-ukuia48s.txt' === file2bib.sh === id: cord-319580-awtp0mpg author: McCartney, Stephen A. title: Obesity as a contributor to immunopathology in pregnant and non‐pregnant adults with COVID‐19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-319580-awtp0mpg.txt cache: ./cache/cord-319580-awtp0mpg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319580-awtp0mpg.txt' === file2bib.sh === id: cord-316647-jj8anf5g author: Shang, You title: Management of critically ill patients with COVID-19 in ICU: statement from front-line intensive care experts in Wuhan, China date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-316647-jj8anf5g.txt cache: ./cache/cord-316647-jj8anf5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316647-jj8anf5g.txt' === file2bib.sh === id: cord-319241-div9rzax author: Singh, Bhuchitra title: Severe Acute Respiratory Syndrome‐Corona Virus‐2 (SARS‐CoV‐2) and its Effect on Gametogenesis and Early Pregnancy date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-319241-div9rzax.txt cache: ./cache/cord-319241-div9rzax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319241-div9rzax.txt' === file2bib.sh === id: cord-318909-h5b7mncf author: Liguori, Claudio title: Subjective neurological symptoms frequently occur in patients with SARS-CoV2 infection date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-318909-h5b7mncf.txt cache: ./cache/cord-318909-h5b7mncf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318909-h5b7mncf.txt' === file2bib.sh === id: cord-319749-je0l22l5 author: Lippi, Alice title: SARS‐CoV‐2: At the Crossroad Between Aging and Neurodegeneration date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-319749-je0l22l5.txt cache: ./cache/cord-319749-je0l22l5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319749-je0l22l5.txt' === file2bib.sh === id: cord-319351-hcxbkvgd author: Benrahma, H. title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-319351-hcxbkvgd.txt cache: ./cache/cord-319351-hcxbkvgd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319351-hcxbkvgd.txt' === file2bib.sh === id: cord-319469-fkuqs3ie author: Ray, A. title: Seroprevalence of anti-SARS-CoV-2 IgG antibody in hospitalized patients in a tertiary referral center in North India date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-319469-fkuqs3ie.txt cache: ./cache/cord-319469-fkuqs3ie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319469-fkuqs3ie.txt' === file2bib.sh === id: cord-319718-blqzi69t author: Zhang, L. title: Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-319718-blqzi69t.txt cache: ./cache/cord-319718-blqzi69t.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319718-blqzi69t.txt' === file2bib.sh === id: cord-319447-xanewi59 author: Sun, Jiya title: Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-319447-xanewi59.txt cache: ./cache/cord-319447-xanewi59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319447-xanewi59.txt' === file2bib.sh === id: cord-318478-fn0gcxbb author: Ziv, Omer title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-318478-fn0gcxbb.txt cache: ./cache/cord-318478-fn0gcxbb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318478-fn0gcxbb.txt' === file2bib.sh === id: cord-319333-jwbgytwd author: Radmard, Sara title: Inpatient Neurology Consultations During the Onset of the SARS-CoV-2 New York City Pandemic: A Single Center Case Series date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-319333-jwbgytwd.txt cache: ./cache/cord-319333-jwbgytwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319333-jwbgytwd.txt' === file2bib.sh === id: cord-319797-455ldhiy author: Kumar, Deepali title: COVID‐19: A global transplant perspective on successfully navigating a pandemic date: 2020-04-12 pages: extension: .txt txt: ./txt/cord-319797-455ldhiy.txt cache: ./cache/cord-319797-455ldhiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319797-455ldhiy.txt' === file2bib.sh === id: cord-318938-7d731q65 author: Wallentin, Lars title: Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-318938-7d731q65.txt cache: ./cache/cord-318938-7d731q65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318938-7d731q65.txt' === file2bib.sh === id: cord-320085-n9i54wzh author: Pfefferle, Susanne title: Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-320085-n9i54wzh.txt cache: ./cache/cord-320085-n9i54wzh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320085-n9i54wzh.txt' === file2bib.sh === id: cord-319831-e07vt846 author: Popescu, Saskia title: Roadblocks to Infection Prevention Efforts in Health Care: SARS-CoV-2/COVID-19 Response date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-319831-e07vt846.txt cache: ./cache/cord-319831-e07vt846.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319831-e07vt846.txt' === file2bib.sh === id: cord-319728-d0kf9gme author: Lucchini, Matteo title: Is serological response to SARS-CoV-2 preserved in MS patients on ocrelizumab treatment? A case report date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-319728-d0kf9gme.txt cache: ./cache/cord-319728-d0kf9gme.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319728-d0kf9gme.txt' === file2bib.sh === id: cord-319955-spnykv96 author: Arafah, Azher title: S1 Subunit and Host Proteases as Potential Therapeutic Avenues for the Treatment of COVID-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-319955-spnykv96.txt cache: ./cache/cord-319955-spnykv96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319955-spnykv96.txt' === file2bib.sh === id: cord-319664-gyktrd36 author: Mancini, Fabiola title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-319664-gyktrd36.txt cache: ./cache/cord-319664-gyktrd36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-319664-gyktrd36.txt' === file2bib.sh === id: cord-320087-iu4ulxtu author: Lampe, Anne title: Guillain-Barré syndrome and SARS-CoV-2 date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-320087-iu4ulxtu.txt cache: ./cache/cord-320087-iu4ulxtu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320087-iu4ulxtu.txt' === file2bib.sh === id: cord-317952-4oa9hfb4 author: Bourgonje, Arno R. title: Angiotensin‐converting enzyme‐2 (ACE2), SARS‐CoV‐2 and pathophysiology of coronavirus disease 2019 (COVID‐19) date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-317952-4oa9hfb4.txt cache: ./cache/cord-317952-4oa9hfb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317952-4oa9hfb4.txt' === file2bib.sh === id: cord-319900-16osnnga author: Arcadepani, Felipe B. title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-319900-16osnnga.txt cache: ./cache/cord-319900-16osnnga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319900-16osnnga.txt' === file2bib.sh === id: cord-319571-fspmgg4s author: Sehailia, Moussa title: Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-319571-fspmgg4s.txt cache: ./cache/cord-319571-fspmgg4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319571-fspmgg4s.txt' === file2bib.sh === id: cord-319935-ni6a8vje author: Somsen, G. A. title: Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-319935-ni6a8vje.txt cache: ./cache/cord-319935-ni6a8vje.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319935-ni6a8vje.txt' === file2bib.sh === id: cord-319013-oytqcifa author: Focosi, Daniele title: Convalescent Plasma Therapy for COVID-19: State of the Art date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-319013-oytqcifa.txt cache: ./cache/cord-319013-oytqcifa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319013-oytqcifa.txt' === file2bib.sh === id: cord-319707-j8y9gt2o author: Kato, Verstrepen title: Neurological manifestations of COVID-19, SARS and MERS date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-319707-j8y9gt2o.txt cache: ./cache/cord-319707-j8y9gt2o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319707-j8y9gt2o.txt' === file2bib.sh === id: cord-319864-t6ql9hz2 author: Lima, Amorce title: Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-319864-t6ql9hz2.txt cache: ./cache/cord-319864-t6ql9hz2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319864-t6ql9hz2.txt' === file2bib.sh === id: cord-320428-sg3srt8r author: Ling, Zhoukun title: Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-320428-sg3srt8r.txt cache: ./cache/cord-320428-sg3srt8r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320428-sg3srt8r.txt' === file2bib.sh === id: cord-319706-2e9jrv0s author: Ebinger, Joseph E. title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-319706-2e9jrv0s.txt cache: ./cache/cord-319706-2e9jrv0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319706-2e9jrv0s.txt' === file2bib.sh === id: cord-319876-psilbis0 author: Zhu, Jian title: COVID-19 Epidemic: Clinical Characteristics of Patients in Pediatric Isolation Ward date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-319876-psilbis0.txt cache: ./cache/cord-319876-psilbis0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319876-psilbis0.txt' === file2bib.sh === id: cord-319920-vn5si7xm author: Sampogna, Gianluca title: Spinal cord dysfunction after COVID-19 infection date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-319920-vn5si7xm.txt cache: ./cache/cord-319920-vn5si7xm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319920-vn5si7xm.txt' === file2bib.sh === id: cord-319930-ymqnb54a author: Kremer, Stéphane title: Brain MRI Findings in Severe COVID-19: A Retrospective Observational Study date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-319930-ymqnb54a.txt cache: ./cache/cord-319930-ymqnb54a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319930-ymqnb54a.txt' === file2bib.sh === id: cord-318786-qd0k8174 author: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-318786-qd0k8174.txt cache: ./cache/cord-318786-qd0k8174.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318786-qd0k8174.txt' === file2bib.sh === id: cord-319408-841c0g1c author: Salvatore, Christine M title: Neonatal management and outcomes during the COVID-19 pandemic: an observation cohort study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-319408-841c0g1c.txt cache: ./cache/cord-319408-841c0g1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319408-841c0g1c.txt' === file2bib.sh === id: cord-319555-pccqo36g author: Beggs, Clive B. title: Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-319555-pccqo36g.txt cache: ./cache/cord-319555-pccqo36g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319555-pccqo36g.txt' === file2bib.sh === id: cord-320063-n9qzbnup author: Calender, Alain title: Modeling Potential Autophagy Pathways in COVID-19 and Sarcoidosis date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-320063-n9qzbnup.txt cache: ./cache/cord-320063-n9qzbnup.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320063-n9qzbnup.txt' === file2bib.sh === id: cord-320350-zeeozmm9 author: Nisoli, Enzo title: COVID-19 and Hartnup disease: an affair of intestinal amino acid malabsorption date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-320350-zeeozmm9.txt cache: ./cache/cord-320350-zeeozmm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320350-zeeozmm9.txt' === file2bib.sh === id: cord-320169-dtv7to3l author: Liu, Yen-Chin title: COVID-19: the First Documented Coronavirus Pandemic in History date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-320169-dtv7to3l.txt cache: ./cache/cord-320169-dtv7to3l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320169-dtv7to3l.txt' === file2bib.sh === id: cord-319855-78xmxymu author: BR, Bharath title: In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19 date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-319855-78xmxymu.txt cache: ./cache/cord-319855-78xmxymu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319855-78xmxymu.txt' === file2bib.sh === id: cord-320535-fo4lzcav author: Geyer, Howard L. title: Movement Disorders in COVID-19: Whither Art Thou? date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-320535-fo4lzcav.txt cache: ./cache/cord-320535-fo4lzcav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320535-fo4lzcav.txt' === file2bib.sh === id: cord-319964-ju9japd8 author: Lu, Jing title: Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China date: 2020-04-04 pages: extension: .txt txt: ./txt/cord-319964-ju9japd8.txt cache: ./cache/cord-319964-ju9japd8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319964-ju9japd8.txt' === file2bib.sh === id: cord-320149-3q4q98a6 author: Di Carlo, Davide Tiziano title: Exploring the clinical association between neurological symptoms and COVID-19 pandemic outbreak: a systematic review of current literature date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-320149-3q4q98a6.txt cache: ./cache/cord-320149-3q4q98a6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320149-3q4q98a6.txt' === file2bib.sh === id: cord-320266-7gzx6ljt author: Vigneshwar, Navin G. title: Positive tracheal SARS-CoV-2 RNA test after three negative SARS-CoV-2 RNA tests in a patient with COVID-19 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-320266-7gzx6ljt.txt cache: ./cache/cord-320266-7gzx6ljt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320266-7gzx6ljt.txt' === file2bib.sh === id: cord-319519-mb9ofh12 author: Ding, J. title: A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-319519-mb9ofh12.txt cache: ./cache/cord-319519-mb9ofh12.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319519-mb9ofh12.txt' === file2bib.sh === id: cord-320054-wqpr8v3p author: Yuan, Xianlin title: The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-320054-wqpr8v3p.txt cache: ./cache/cord-320054-wqpr8v3p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320054-wqpr8v3p.txt' === file2bib.sh === id: cord-320127-55h4hhm3 author: Mazingi, Dennis title: Mitigating the impact of COVID-19 on children's surgery in Africa date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-320127-55h4hhm3.txt cache: ./cache/cord-320127-55h4hhm3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320127-55h4hhm3.txt' === file2bib.sh === id: cord-320567-7je1i8qd author: Muenchhoff, Maximilian title: Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-320567-7je1i8qd.txt cache: ./cache/cord-320567-7je1i8qd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320567-7je1i8qd.txt' === file2bib.sh === id: cord-320717-wk4zxmz9 author: Li, Yang title: Lack of Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2, China date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-320717-wk4zxmz9.txt cache: ./cache/cord-320717-wk4zxmz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320717-wk4zxmz9.txt' === file2bib.sh === id: cord-320455-doup2bqq author: Werion, Alexis title: SARS-CoV-2 Causes a Specific Dysfunction of the Kidney Proximal Tubule date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-320455-doup2bqq.txt cache: ./cache/cord-320455-doup2bqq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320455-doup2bqq.txt' === file2bib.sh === id: cord-320207-cwt7dswz author: Zeng, Yingchun title: The nucleocapsid protein of SARS-associated coronavirus inhibits B23 phosphorylation date: 2008-05-02 pages: extension: .txt txt: ./txt/cord-320207-cwt7dswz.txt cache: ./cache/cord-320207-cwt7dswz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320207-cwt7dswz.txt' === file2bib.sh === id: cord-319501-a2x1hvkk author: Wong, Lok-Yin Roy title: A molecular arms race between host innate antiviral response and emerging human coronaviruses date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-319501-a2x1hvkk.txt cache: ./cache/cord-319501-a2x1hvkk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319501-a2x1hvkk.txt' === file2bib.sh === id: cord-319833-u9uuuu38 author: Rodriguez-Martinez, Carlos E. title: Decontamination and reuse of N95 filtering facemask respirators: a systematic review of the literature date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-319833-u9uuuu38.txt cache: ./cache/cord-319833-u9uuuu38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319833-u9uuuu38.txt' === file2bib.sh === id: cord-320308-pzex799x author: Erol, Adnan title: Role of oxidized LDL-induced “trained macrophages” in the pathogenesis of COVID-19 and benefits of pioglitazone: A hypothesis date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-320308-pzex799x.txt cache: ./cache/cord-320308-pzex799x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320308-pzex799x.txt' === file2bib.sh === id: cord-320646-xk77u4g0 author: Zumla, Alimuddin title: The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-320646-xk77u4g0.txt cache: ./cache/cord-320646-xk77u4g0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320646-xk77u4g0.txt' === file2bib.sh === id: cord-318944-13zk6cco author: Bizzoca, Maria Eleonora title: Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-318944-13zk6cco.txt cache: ./cache/cord-318944-13zk6cco.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318944-13zk6cco.txt' === file2bib.sh === id: cord-319983-e4f2sfl4 author: Tripathi, Shweta title: The COVID-19: Current understanding date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-319983-e4f2sfl4.txt cache: ./cache/cord-319983-e4f2sfl4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319983-e4f2sfl4.txt' === file2bib.sh === id: cord-320627-7vi6skvh author: Horejsh, Douglas title: A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry date: 2005-01-19 pages: extension: .txt txt: ./txt/cord-320627-7vi6skvh.txt cache: ./cache/cord-320627-7vi6skvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320627-7vi6skvh.txt' === file2bib.sh === id: cord-320158-6dh9e5rg author: Hansen, Richard title: Adaptations to the current ECCO/ESPGHAN guidelines on the management of paediatric acute severe colitis in the context of the COVID-19 pandemic: a RAND appropriateness panel date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-320158-6dh9e5rg.txt cache: ./cache/cord-320158-6dh9e5rg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320158-6dh9e5rg.txt' === file2bib.sh === id: cord-320826-o6ih2f23 author: Blairon, Laurent title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-320826-o6ih2f23.txt cache: ./cache/cord-320826-o6ih2f23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320826-o6ih2f23.txt' === file2bib.sh === id: cord-320612-vam0bli3 author: Höring, Steffen title: Management of a Hospital-Wide COVID-19 Outbreak Affecting Patients and Healthcare Workers date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-320612-vam0bli3.txt cache: ./cache/cord-320612-vam0bli3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320612-vam0bli3.txt' === file2bib.sh === id: cord-319704-xzhoa03d author: Zuercher, S. J. title: Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-319704-xzhoa03d.txt cache: ./cache/cord-319704-xzhoa03d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319704-xzhoa03d.txt' === file2bib.sh === id: cord-320729-imyfo83x author: Spiga, Ottavia title: Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein date: 2003-10-10 pages: extension: .txt txt: ./txt/cord-320729-imyfo83x.txt cache: ./cache/cord-320729-imyfo83x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320729-imyfo83x.txt' === file2bib.sh === id: cord-320619-r466dc5t author: Chand Dakal, Tikam title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-320619-r466dc5t.txt cache: ./cache/cord-320619-r466dc5t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320619-r466dc5t.txt' === file2bib.sh === id: cord-320466-l7017jis author: Akgun, Emel title: Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-320466-l7017jis.txt cache: ./cache/cord-320466-l7017jis.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320466-l7017jis.txt' === file2bib.sh === id: cord-319781-6thdg2up author: Payne, Kelly title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-319781-6thdg2up.txt cache: ./cache/cord-319781-6thdg2up.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319781-6thdg2up.txt' === file2bib.sh === id: cord-320401-itltvh3f author: Clementi, Nicola title: NARINGENIN IS A POWERFUL INHIBITOR OF SARS-CoV-2 INFECTION IN VITRO date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-320401-itltvh3f.txt cache: ./cache/cord-320401-itltvh3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320401-itltvh3f.txt' === file2bib.sh === id: cord-320333-audnwp8t author: Chen, Qi-Lin title: Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-320333-audnwp8t.txt cache: ./cache/cord-320333-audnwp8t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320333-audnwp8t.txt' === file2bib.sh === id: cord-320740-npoje09j author: Musa, Arif title: Remdesivir for the Treatment of COVID-19: A Systematic Review of the Literature date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-320740-npoje09j.txt cache: ./cache/cord-320740-npoje09j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320740-npoje09j.txt' === file2bib.sh === id: cord-319248-ynoxec7k author: Matsuyama, Toshifumi title: An aberrant STAT pathway is central to COVID-19 date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-319248-ynoxec7k.txt cache: ./cache/cord-319248-ynoxec7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319248-ynoxec7k.txt' === file2bib.sh === id: cord-320270-lduhhdld author: Obek, Can title: Management of prostate cancer patients during COVID-19 pandemic date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-320270-lduhhdld.txt cache: ./cache/cord-320270-lduhhdld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320270-lduhhdld.txt' === file2bib.sh === id: cord-320417-01l27d99 author: Wang, Hai-Long title: The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-320417-01l27d99.txt cache: ./cache/cord-320417-01l27d99.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320417-01l27d99.txt' === file2bib.sh === id: cord-320902-1hfxju5f author: Filocamo, Giovanni title: Use of anakinra in severe COVID-19: a case report date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-320902-1hfxju5f.txt cache: ./cache/cord-320902-1hfxju5f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320902-1hfxju5f.txt' === file2bib.sh === id: cord-320882-cr0ccsnp author: Li Volti, Giovanni title: Smoking and SARS-CoV-2 Disease (COVID-19): Dangerous Liaisons or Confusing Relationships? date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-320882-cr0ccsnp.txt cache: ./cache/cord-320882-cr0ccsnp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320882-cr0ccsnp.txt' === file2bib.sh === id: cord-319799-h9kot3og author: Schäfer, Alexandra title: Epigenetic Landscape during Coronavirus Infection date: 2017-02-15 pages: extension: .txt txt: ./txt/cord-319799-h9kot3og.txt cache: ./cache/cord-319799-h9kot3og.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319799-h9kot3og.txt' === file2bib.sh === id: cord-321049-9ozn6il7 author: de Almeida, Paula Rodrigues title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-321049-9ozn6il7.txt cache: ./cache/cord-321049-9ozn6il7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321049-9ozn6il7.txt' === file2bib.sh === id: cord-321208-zemex8bf author: Reina, Jordi title: Evaluación de diferentes genes en la detección por RT-PCR del SARS-CoV-2 en muestras respiratorias y su evolución en la infección date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-321208-zemex8bf.txt cache: ./cache/cord-321208-zemex8bf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321208-zemex8bf.txt' === file2bib.sh === id: cord-320560-yn3bbkdh author: Kohanski, Michael A. title: Review of indoor aerosol generation, transport, and control in the context of COVID‐19 date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-320560-yn3bbkdh.txt cache: ./cache/cord-320560-yn3bbkdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320560-yn3bbkdh.txt' === file2bib.sh === id: cord-320511-qnxj7d9l author: Hueston, Linda title: The antibody response to SARS-CoV-2 infection date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-320511-qnxj7d9l.txt cache: ./cache/cord-320511-qnxj7d9l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320511-qnxj7d9l.txt' === file2bib.sh === id: cord-320704-rrq6x25k author: Sharma, Shruti title: COVID-19: A Concern for Cardiovascular Disease Patients date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-320704-rrq6x25k.txt cache: ./cache/cord-320704-rrq6x25k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320704-rrq6x25k.txt' === file2bib.sh === id: cord-321146-dd8z5c6d author: Mishra, Rakesh title: SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-321146-dd8z5c6d.txt cache: ./cache/cord-321146-dd8z5c6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321146-dd8z5c6d.txt' === file2bib.sh === id: cord-321308-rwxhdg8r author: Grubaugh, Nathan D. title: Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-321308-rwxhdg8r.txt cache: ./cache/cord-321308-rwxhdg8r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321308-rwxhdg8r.txt' === file2bib.sh === id: cord-320848-bz9pf2p6 author: Sepehrinezhad, Ali title: COVID-19 virus may have neuroinvasive potential and cause neurological complications: a perspective review date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-320848-bz9pf2p6.txt cache: ./cache/cord-320848-bz9pf2p6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320848-bz9pf2p6.txt' === file2bib.sh === id: cord-320673-4guarm0k author: Lopera, E. title: Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-320673-4guarm0k.txt cache: ./cache/cord-320673-4guarm0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320673-4guarm0k.txt' === file2bib.sh === id: cord-320829-uepneyug author: He, Zhongping title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 pages: extension: .txt txt: ./txt/cord-320829-uepneyug.txt cache: ./cache/cord-320829-uepneyug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320829-uepneyug.txt' === file2bib.sh === id: cord-320175-w00rcvd8 author: Shi, Jiahai title: The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain date: 2006-02-08 pages: extension: .txt txt: ./txt/cord-320175-w00rcvd8.txt cache: ./cache/cord-320175-w00rcvd8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320175-w00rcvd8.txt' === file2bib.sh === id: cord-320864-k9zksbyt author: Remes-Troche, J. M. title: Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-320864-k9zksbyt.txt cache: ./cache/cord-320864-k9zksbyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320864-k9zksbyt.txt' === file2bib.sh === id: cord-320681-b3ui95vx author: Zhang, Rui title: COVID-19: Melatonin as a potential adjuvant treatment date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-320681-b3ui95vx.txt cache: ./cache/cord-320681-b3ui95vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320681-b3ui95vx.txt' === file2bib.sh === id: cord-321027-64y43o0y author: Andreano, Emanuele title: Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-321027-64y43o0y.txt cache: ./cache/cord-321027-64y43o0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321027-64y43o0y.txt' === file2bib.sh === id: cord-320165-1b6sycgv author: Guo, Qirui title: Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-320165-1b6sycgv.txt cache: ./cache/cord-320165-1b6sycgv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320165-1b6sycgv.txt' === file2bib.sh === id: cord-321315-bzmokdzk author: Tanacan, Atakan title: The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-321315-bzmokdzk.txt cache: ./cache/cord-321315-bzmokdzk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321315-bzmokdzk.txt' === file2bib.sh === id: cord-319877-izn315hb author: de Wit, Emmie title: SARS and MERS: recent insights into emerging coronaviruses date: 2016-06-27 pages: extension: .txt txt: ./txt/cord-319877-izn315hb.txt cache: ./cache/cord-319877-izn315hb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319877-izn315hb.txt' === file2bib.sh === id: cord-320970-ru2iw0py author: Peeling, Rosanna W title: Serology testing in the COVID-19 pandemic response date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-320970-ru2iw0py.txt cache: ./cache/cord-320970-ru2iw0py.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320970-ru2iw0py.txt' === file2bib.sh === id: cord-320845-imxby1b1 author: Morley, G. L. title: Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-320845-imxby1b1.txt cache: ./cache/cord-320845-imxby1b1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320845-imxby1b1.txt' === file2bib.sh === id: cord-320788-ln8ddyuj author: Wang, Chun-Hua title: Persistence of lung inflammation and lung cytokines with high-resolution CT abnormalities during recovery from SARS date: 2005-05-11 pages: extension: .txt txt: ./txt/cord-320788-ln8ddyuj.txt cache: ./cache/cord-320788-ln8ddyuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320788-ln8ddyuj.txt' === file2bib.sh === id: cord-320587-936cavob author: Ruscio, M. title: Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-320587-936cavob.txt cache: ./cache/cord-320587-936cavob.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320587-936cavob.txt' === file2bib.sh === id: cord-320860-qt84oicg author: Zhang, Aining title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-320860-qt84oicg.txt cache: ./cache/cord-320860-qt84oicg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320860-qt84oicg.txt' === file2bib.sh === id: cord-320092-0qnvydux author: Ehsani, Sepehr title: COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-320092-0qnvydux.txt cache: ./cache/cord-320092-0qnvydux.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320092-0qnvydux.txt' === file2bib.sh === id: cord-321380-e5zq15hz author: del Campo, P. Lázaro title: No transmission of SARS-CoV-2 in a patient undergoing allogeneic Hematopoietic Cell Transplantation from a matched-related donor with unknown COVID-19 date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-321380-e5zq15hz.txt cache: ./cache/cord-321380-e5zq15hz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321380-e5zq15hz.txt' === file2bib.sh === id: cord-320787-dwyyjq6o author: La Rosa, Giuseppina title: First detection of SARS-CoV-2 in untreated wastewaters in Italy date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-320787-dwyyjq6o.txt cache: ./cache/cord-320787-dwyyjq6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320787-dwyyjq6o.txt' === file2bib.sh === id: cord-321455-ooouqna7 author: Li, Tao title: Characteristics of laboratory indexes in COVID-19 patients with non-severe symptoms in Hefei City, China: diagnostic value in organ injuries date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-321455-ooouqna7.txt cache: ./cache/cord-321455-ooouqna7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321455-ooouqna7.txt' === file2bib.sh === id: cord-321155-dty18esg author: Zhang, Rongxin title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-321155-dty18esg.txt cache: ./cache/cord-321155-dty18esg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321155-dty18esg.txt' === file2bib.sh === id: cord-320490-3jmo35jc author: Ismail, Saba title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 pages: extension: .txt txt: ./txt/cord-320490-3jmo35jc.txt cache: ./cache/cord-320490-3jmo35jc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320490-3jmo35jc.txt' === file2bib.sh === id: cord-320964-1gg33gdn author: Sampieri, Clara Luz title: Revisión de nuevas evidencias acerca de la posible transmisión vertical de la COVID-19 date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-320964-1gg33gdn.txt cache: ./cache/cord-320964-1gg33gdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320964-1gg33gdn.txt' === file2bib.sh === id: cord-320909-p93gxjm2 author: Natoli, S. title: Does SARS‐Cov‐2 invade the brain? Translational lessons from animal models date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-320909-p93gxjm2.txt cache: ./cache/cord-320909-p93gxjm2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320909-p93gxjm2.txt' === file2bib.sh === id: cord-321670-f2d4bykp author: Longardt, Ann Carolin title: Perinatale Aspekte der SARS-CoV-2 Infektion date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-321670-f2d4bykp.txt cache: ./cache/cord-321670-f2d4bykp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321670-f2d4bykp.txt' === file2bib.sh === id: cord-321603-lbbsnriv author: Rao, Mohan title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-321603-lbbsnriv.txt cache: ./cache/cord-321603-lbbsnriv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321603-lbbsnriv.txt' === file2bib.sh === id: cord-321235-h3w8827o author: Cabrera Alvargonzalez, Jorge Julio title: Pooling for SARS-CoV-2 control in care institutions date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-321235-h3w8827o.txt cache: ./cache/cord-321235-h3w8827o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321235-h3w8827o.txt' === file2bib.sh === id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-319754-5isw53wl.txt cache: ./cache/cord-319754-5isw53wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319754-5isw53wl.txt' === file2bib.sh === id: cord-320815-p9oh54nt author: Gentile, Pietro title: Research progress on Mesenchymal Stem Cells (MSCs), Adipose-Derived Mesenchymal Stem Cells (AD-MSCs), Drugs, and Vaccines in Inhibiting COVID-19 Disease date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-320815-p9oh54nt.txt cache: ./cache/cord-320815-p9oh54nt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320815-p9oh54nt.txt' === file2bib.sh === id: cord-321369-xzu2faol author: Andreano, Emanuele title: Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-321369-xzu2faol.txt cache: ./cache/cord-321369-xzu2faol.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321369-xzu2faol.txt' === file2bib.sh === id: cord-320331-wtxja5i9 author: Cabbab, Iris Louise N. title: Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-320331-wtxja5i9.txt cache: ./cache/cord-320331-wtxja5i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320331-wtxja5i9.txt' === file2bib.sh === id: cord-321564-6950p8i9 author: Wang, Shiu‐Mei title: Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date: 2019-07-10 pages: extension: .txt txt: ./txt/cord-321564-6950p8i9.txt cache: ./cache/cord-321564-6950p8i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321564-6950p8i9.txt' === file2bib.sh === id: cord-321664-3qlfsei6 author: Somsen, G Aernout title: Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-321664-3qlfsei6.txt cache: ./cache/cord-321664-3qlfsei6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321664-3qlfsei6.txt' === file2bib.sh === id: cord-321580-3ru92tra author: Hadler, James L title: Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-321580-3ru92tra.txt cache: ./cache/cord-321580-3ru92tra.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321580-3ru92tra.txt' === file2bib.sh === id: cord-321468-nkl2mls8 author: Yang, Mo title: Thrombopoietin levels increased in patients with severe acute respiratory syndrome date: 2008-03-07 pages: extension: .txt txt: ./txt/cord-321468-nkl2mls8.txt cache: ./cache/cord-321468-nkl2mls8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-321468-nkl2mls8.txt' === file2bib.sh === id: cord-321624-z2mntwef author: Kowitdamrong, Ekasit title: Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-321624-z2mntwef.txt cache: ./cache/cord-321624-z2mntwef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321624-z2mntwef.txt' === file2bib.sh === id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-320935-3n157yl4.txt cache: ./cache/cord-320935-3n157yl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320935-3n157yl4.txt' === file2bib.sh === id: cord-321131-f8qeytxc author: Zhou, Yanchen title: Protease inhibitors targeting coronavirus and filovirus entry date: 2015-04-30 pages: extension: .txt txt: ./txt/cord-321131-f8qeytxc.txt cache: ./cache/cord-321131-f8qeytxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321131-f8qeytxc.txt' === file2bib.sh === id: cord-321259-wio2b49i author: Carmona-Gutierrez, Didac title: Digesting the crisis: autophagy and coronaviruses date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-321259-wio2b49i.txt cache: ./cache/cord-321259-wio2b49i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321259-wio2b49i.txt' === file2bib.sh === id: cord-321598-ae241pmd author: de Vries, A.P.J. title: Immediate impact of COVID-19 on transplant activity in the Netherlands date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-321598-ae241pmd.txt cache: ./cache/cord-321598-ae241pmd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321598-ae241pmd.txt' === file2bib.sh === id: cord-321552-lsz1onrj author: Membrilla, Javier A. title: Headache as a Cardinal Symptom of Coronavirus Disease 2019: A Cross‐Sectional Study date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-321552-lsz1onrj.txt cache: ./cache/cord-321552-lsz1onrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321552-lsz1onrj.txt' === file2bib.sh === id: cord-321933-cq0fa3hs author: Koff, Alan G. title: Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-321933-cq0fa3hs.txt cache: ./cache/cord-321933-cq0fa3hs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321933-cq0fa3hs.txt' === file2bib.sh === id: cord-321549-r7bmtloy author: Jendrny, Paula title: Scent dog identification of samples from COVID-19 patients – a pilot study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-321549-r7bmtloy.txt cache: ./cache/cord-321549-r7bmtloy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321549-r7bmtloy.txt' === file2bib.sh === id: cord-322044-4eejzpmn author: Frediansyah, Andri title: Remdesivir and its antiviral activity against COVID-19: A systematic review date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-322044-4eejzpmn.txt cache: ./cache/cord-322044-4eejzpmn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322044-4eejzpmn.txt' === file2bib.sh === id: cord-322204-kc7dy2za author: Khalil, Asma title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-322204-kc7dy2za.txt cache: ./cache/cord-322204-kc7dy2za.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-322204-kc7dy2za.txt' === file2bib.sh === id: cord-321784-nubu5fuz author: Salazar, E. title: Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-321784-nubu5fuz.txt cache: ./cache/cord-321784-nubu5fuz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321784-nubu5fuz.txt' === file2bib.sh === id: cord-320831-owfnttqr author: Klimek, Ludger title: Allergen immunotherapy in the current COVID-19 pandemic: A position paper of AeDA, ARIA, EAACI, DGAKI and GPA: Position paper of the German ARIA Group(A) in cooperation with the Austrian ARIA Group(B), the Swiss ARIA Group(C), German Society for Applied Allergology (AEDA)(D), German Society for Allergology and Clinical Immunology (DGAKI)(E), Society for Pediatric Allergology (GPA)(F) in cooperation with AG Clinical Immunology, Allergology and Environmental Medicine of the DGHNO-KHC(G) and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-320831-owfnttqr.txt cache: ./cache/cord-320831-owfnttqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320831-owfnttqr.txt' === file2bib.sh === id: cord-321770-g5xcfhnh author: de Farias, Emmerson Carlos Franco title: MULTISYSTEM INFLAMMATORY SYNDROME IN A CHILD ASSOCIATED WITH CORONAVIRUS DISEASE 19 IN THE BRAZILIAN AMAZON: FATAL OUTCOME IN AN INFANT date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-321770-g5xcfhnh.txt cache: ./cache/cord-321770-g5xcfhnh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321770-g5xcfhnh.txt' === file2bib.sh === id: cord-321267-ihd30qi0 author: Daughton, Christian G. title: Natural experiment concept to accelerate the Re-purposing of existing therapeutics for Covid-19 date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-321267-ihd30qi0.txt cache: ./cache/cord-321267-ihd30qi0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321267-ihd30qi0.txt' === file2bib.sh === id: cord-321358-plxz5mkg author: Zheng, Jun title: SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat date: 2020-03-15 pages: extension: .txt txt: ./txt/cord-321358-plxz5mkg.txt cache: ./cache/cord-321358-plxz5mkg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321358-plxz5mkg.txt' === file2bib.sh === id: cord-321231-zlpa3x2x author: Anand, Pratima title: Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-321231-zlpa3x2x.txt cache: ./cache/cord-321231-zlpa3x2x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321231-zlpa3x2x.txt' === file2bib.sh === id: cord-321691-46la29tm author: Hsueh, Po-Ren title: SARS Antibody Test for Serosurveillance date: 2004-09-17 pages: extension: .txt txt: ./txt/cord-321691-46la29tm.txt cache: ./cache/cord-321691-46la29tm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321691-46la29tm.txt' === file2bib.sh === id: cord-322141-4a81mapc author: Rizzo, Emanuele title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-322141-4a81mapc.txt cache: ./cache/cord-322141-4a81mapc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322141-4a81mapc.txt' === file2bib.sh === id: cord-322005-70snojec author: Yao, Pingping title: Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-322005-70snojec.txt cache: ./cache/cord-322005-70snojec.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322005-70snojec.txt' === file2bib.sh === id: cord-321714-yhruzu7f author: Ryu, Young Bae title: SARS-CoV 3CL(pro) inhibitory effects of quinone-methide triterpenes from Tripterygium regelii date: 2010-03-15 pages: extension: .txt txt: ./txt/cord-321714-yhruzu7f.txt cache: ./cache/cord-321714-yhruzu7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321714-yhruzu7f.txt' === file2bib.sh === id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-315339-dcui85lw.txt cache: ./cache/cord-315339-dcui85lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-315339-dcui85lw.txt' === file2bib.sh === id: cord-320632-369kax2m author: Song, Yang title: COVID-19 Treatment: Close to a Cure? – A Rapid Review of Pharmacotherapies for the Novel Coronavirus date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-320632-369kax2m.txt cache: ./cache/cord-320632-369kax2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320632-369kax2m.txt' === file2bib.sh === id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-321855-7b1c2xdh.txt cache: ./cache/cord-321855-7b1c2xdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321855-7b1c2xdh.txt' === file2bib.sh === id: cord-321867-7n88rl6p author: Jee, J. title: Oncologic Immunomodulatory Agents in Patients with Cancer and COVID-19 date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-321867-7n88rl6p.txt cache: ./cache/cord-321867-7n88rl6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321867-7n88rl6p.txt' === file2bib.sh === id: cord-321568-okvt1fg3 author: Alberca, Ricardo Wesley title: Perspective: The Potential Effects of Naringenin in COVID-19 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-321568-okvt1fg3.txt cache: ./cache/cord-321568-okvt1fg3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321568-okvt1fg3.txt' === file2bib.sh === id: cord-321797-2xhusfth author: Lee‐Baggley, Dayna title: Coping with the threat of severe acute respiratory syndrome: Role of threat appraisals and coping responses in health behaviors date: 2004-03-11 pages: extension: .txt txt: ./txt/cord-321797-2xhusfth.txt cache: ./cache/cord-321797-2xhusfth.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321797-2xhusfth.txt' === file2bib.sh === id: cord-321819-lqyo9px1 author: Chaw, Liling title: Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei date: 2020-11-17 pages: extension: .txt txt: ./txt/cord-321819-lqyo9px1.txt cache: ./cache/cord-321819-lqyo9px1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321819-lqyo9px1.txt' === file2bib.sh === id: cord-322148-sfr9twfa author: Verbeek, P. Richard title: Loss of Paramedic Availability in an Urban Emergency Medical Services System during a Severe Acute Respiratory Syndrome Outbreak date: 2008-06-28 pages: extension: .txt txt: ./txt/cord-322148-sfr9twfa.txt cache: ./cache/cord-322148-sfr9twfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322148-sfr9twfa.txt' === file2bib.sh === id: cord-322212-8xrehbd1 author: Wang, Hanyin title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-322212-8xrehbd1.txt cache: ./cache/cord-322212-8xrehbd1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322212-8xrehbd1.txt' === file2bib.sh === id: cord-320912-jfeu4tho author: Fukui, M. title: Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-320912-jfeu4tho.txt cache: ./cache/cord-320912-jfeu4tho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320912-jfeu4tho.txt' === file2bib.sh === id: cord-322311-cg5xwx5a author: Broder, Kari title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-322311-cg5xwx5a.txt cache: ./cache/cord-322311-cg5xwx5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322311-cg5xwx5a.txt' === file2bib.sh === id: cord-322417-9e95m4kz author: Segovia-Juarez, Jose title: High altitude reduces infection rate of COVID-19 but not case-fatality rate date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-322417-9e95m4kz.txt cache: ./cache/cord-322417-9e95m4kz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322417-9e95m4kz.txt' === file2bib.sh === id: cord-321854-cy8vyb6j author: Ripperger, Tyler J. title: Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-321854-cy8vyb6j.txt cache: ./cache/cord-321854-cy8vyb6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321854-cy8vyb6j.txt' === file2bib.sh === id: cord-322473-fmob6k0q author: Charpiat, Bruno title: Proton Pump Inhibitors are Risk Factors for Viral Infections: Even for COVID-19? date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-322473-fmob6k0q.txt cache: ./cache/cord-322473-fmob6k0q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322473-fmob6k0q.txt' === file2bib.sh === id: cord-322585-5gio6ruj author: Lanari, Marcello title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-322585-5gio6ruj.txt cache: ./cache/cord-322585-5gio6ruj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322585-5gio6ruj.txt' === file2bib.sh === id: cord-322007-xy66t0ls author: Humbert, S title: COVID-19 as a cause of immune thrombocytopenia date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-322007-xy66t0ls.txt cache: ./cache/cord-322007-xy66t0ls.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322007-xy66t0ls.txt' === file2bib.sh === id: cord-322388-c2nymio9 author: Manopo, Ivanus title: Evaluation of a safe and sensitive Spike protein-based immunofluorescence assay for the detection of antibody responses to SARS-CoV date: 2005-01-31 pages: extension: .txt txt: ./txt/cord-322388-c2nymio9.txt cache: ./cache/cord-322388-c2nymio9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322388-c2nymio9.txt' === file2bib.sh === id: cord-322456-5at1euqm author: Rokohl, Alexander C. title: Die Rolle der Augenheilkunde in der COVID-19-Pandemie date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-322456-5at1euqm.txt cache: ./cache/cord-322456-5at1euqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322456-5at1euqm.txt' === file2bib.sh === id: cord-321858-c5m4dj9m author: Yoshizawa, Shin-ichiro title: Evaluation of an octahydroisochromene scaffold used as a novel SARS 3CL protease inhibitor date: 2020-02-15 pages: extension: .txt txt: ./txt/cord-321858-c5m4dj9m.txt cache: ./cache/cord-321858-c5m4dj9m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321858-c5m4dj9m.txt' === file2bib.sh === id: cord-322603-8ajckhzc author: Wongsawat, Jurai title: Risk of novel coronavirus 2019 transmission from children to caregivers: A case series date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-322603-8ajckhzc.txt cache: ./cache/cord-322603-8ajckhzc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322603-8ajckhzc.txt' === file2bib.sh === id: cord-321013-8pkrg0mx author: McBride, Ruth title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 pages: extension: .txt txt: ./txt/cord-321013-8pkrg0mx.txt cache: ./cache/cord-321013-8pkrg0mx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321013-8pkrg0mx.txt' === file2bib.sh === id: cord-321938-pda4a5n7 author: Weisshoff, Hardy title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-321938-pda4a5n7.txt cache: ./cache/cord-321938-pda4a5n7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321938-pda4a5n7.txt' === file2bib.sh === id: cord-321166-nvphu1fm author: Thomson, Emma C. title: The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-321166-nvphu1fm.txt cache: ./cache/cord-321166-nvphu1fm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321166-nvphu1fm.txt' === file2bib.sh === id: cord-322051-89wgv100 author: Tanasa, Ingrid Andrada title: Anosmia and ageusia associated with coronavirus infection (COVID-19) - what is known? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-322051-89wgv100.txt cache: ./cache/cord-322051-89wgv100.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322051-89wgv100.txt' === file2bib.sh === id: cord-322724-7l1668bf author: Challener, Douglas title: In Reply - Repeated testing in SARS-CoV-2 infection date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-322724-7l1668bf.txt cache: ./cache/cord-322724-7l1668bf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322724-7l1668bf.txt' === file2bib.sh === id: cord-322650-q8inhgtr author: Fung, Yin-Wan Wendy title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date: 2004-08-15 pages: extension: .txt txt: ./txt/cord-322650-q8inhgtr.txt cache: ./cache/cord-322650-q8inhgtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322650-q8inhgtr.txt' === file2bib.sh === id: cord-322184-kgv9f58a author: Sohn, Yujin title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-322184-kgv9f58a.txt cache: ./cache/cord-322184-kgv9f58a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322184-kgv9f58a.txt' === file2bib.sh === id: cord-322789-9elfpx0e author: Abbaspour Kasgari, Hamideh title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-322789-9elfpx0e.txt cache: ./cache/cord-322789-9elfpx0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322789-9elfpx0e.txt' === file2bib.sh === id: cord-322503-fynprt6f author: Thakur, Aarzoo title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-322503-fynprt6f.txt cache: ./cache/cord-322503-fynprt6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322503-fynprt6f.txt' === file2bib.sh === id: cord-319780-rfj9t99r author: Alexander, S.P.H. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-319780-rfj9t99r.txt cache: ./cache/cord-319780-rfj9t99r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319780-rfj9t99r.txt' === file2bib.sh === id: cord-322807-b24ujorz author: Koyama, Takahiko title: Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-322807-b24ujorz.txt cache: ./cache/cord-322807-b24ujorz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322807-b24ujorz.txt' === file2bib.sh === id: cord-321742-cstub5zz author: Tovar, Isabel title: Rationale for the Use of Radiation-Activated Mesenchymal Stromal/Stem Cells in Acute Respiratory Distress Syndrome date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-321742-cstub5zz.txt cache: ./cache/cord-321742-cstub5zz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321742-cstub5zz.txt' === file2bib.sh === id: cord-322329-zqjiiy4l author: Liu, Chunyu title: Establishment of a reference panel for the detection of anti-SARS-CoV antibodies date: 2007-06-30 pages: extension: .txt txt: ./txt/cord-322329-zqjiiy4l.txt cache: ./cache/cord-322329-zqjiiy4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322329-zqjiiy4l.txt' === file2bib.sh === id: cord-322087-gj5mfzxz author: de Sanctis, Vincenzo title: Coronavirus Disease 2019 (COVID-19) in adolescents: An update on current clinical and diagnostic characteristics date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-322087-gj5mfzxz.txt cache: ./cache/cord-322087-gj5mfzxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322087-gj5mfzxz.txt' === file2bib.sh === id: cord-321800-0h28pg3b author: Klingelhöfer, Doris title: Coronavirus: An insight into global research until outbreak of COVID-19 and its implications for the future date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-321800-0h28pg3b.txt cache: ./cache/cord-321800-0h28pg3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321800-0h28pg3b.txt' === file2bib.sh === id: cord-322672-gjph61cq author: Ashok, Vishnu title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-322672-gjph61cq.txt cache: ./cache/cord-322672-gjph61cq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322672-gjph61cq.txt' === file2bib.sh === id: cord-322596-vfmzk2el author: Ming, Yi title: Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-322596-vfmzk2el.txt cache: ./cache/cord-322596-vfmzk2el.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322596-vfmzk2el.txt' === file2bib.sh === id: cord-322451-cwpz4akv author: Hsin, Dena Hsin-Chen title: Heroes of SARS: professional roles and ethics of health care workers date: 2004-07-27 pages: extension: .txt txt: ./txt/cord-322451-cwpz4akv.txt cache: ./cache/cord-322451-cwpz4akv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322451-cwpz4akv.txt' === file2bib.sh === id: cord-322345-rq5gh710 author: Zheng, Fang title: A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-322345-rq5gh710.txt cache: ./cache/cord-322345-rq5gh710.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322345-rq5gh710.txt' === file2bib.sh === id: cord-322009-0cwljo0c author: Ma, Ling title: Coinfection of SARS-CoV-2 and Other Respiratory Pathogens date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-322009-0cwljo0c.txt cache: ./cache/cord-322009-0cwljo0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322009-0cwljo0c.txt' === file2bib.sh === id: cord-322129-uyswj4ow author: Melin, Amanda D. title: Comparative ACE2 variation and primate COVID-19 risk date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-322129-uyswj4ow.txt cache: ./cache/cord-322129-uyswj4ow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322129-uyswj4ow.txt' === file2bib.sh === id: cord-322812-9u3ptqjs author: Wells, Philippa M. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-322812-9u3ptqjs.txt cache: ./cache/cord-322812-9u3ptqjs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322812-9u3ptqjs.txt' === file2bib.sh === id: cord-321901-zpi7uis1 author: Roberts, Anjeanette title: Animal models and antibody assays for evaluating candidate SARS vaccines: Summary of a technical meeting 25–26 August 2005, London, UK date: 2006-11-30 pages: extension: .txt txt: ./txt/cord-321901-zpi7uis1.txt cache: ./cache/cord-321901-zpi7uis1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321901-zpi7uis1.txt' === file2bib.sh === id: cord-323241-1twnqr4k author: Patrì, Angela title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-323241-1twnqr4k.txt cache: ./cache/cord-323241-1twnqr4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323241-1twnqr4k.txt' === file2bib.sh === id: cord-322641-mz0b91xr author: Farnsworth, Christopher W title: SARS-CoV-2 Serology: Much Hype, Little Data date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-322641-mz0b91xr.txt cache: ./cache/cord-322641-mz0b91xr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322641-mz0b91xr.txt' === file2bib.sh === id: cord-323148-rsjocuh3 author: Assaad, Souad title: Risk of death of cancer patients presenting with severe symptoms of infection, with or without documented COVID-19 date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-323148-rsjocuh3.txt cache: ./cache/cord-323148-rsjocuh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323148-rsjocuh3.txt' === file2bib.sh === id: cord-321673-v5o49ees author: Nieto-Torres, Jose L. title: Relevance of Viroporin Ion Channel Activity on Viral Replication and Pathogenesis date: 2015-07-03 pages: extension: .txt txt: ./txt/cord-321673-v5o49ees.txt cache: ./cache/cord-321673-v5o49ees.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321673-v5o49ees.txt' === file2bib.sh === id: cord-323131-l726qv1g author: Atogebania, Julius Wedam title: An Invited Commentary on ‘ Evidence Based Management Guideline for the COVID-19 Pandemic- Review article’ date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-323131-l726qv1g.txt cache: ./cache/cord-323131-l726qv1g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323131-l726qv1g.txt' === file2bib.sh === id: cord-322102-4fi0y96f author: Zimmermann, Matthias title: Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic date: 2020-04-04 pages: extension: .txt txt: ./txt/cord-322102-4fi0y96f.txt cache: ./cache/cord-322102-4fi0y96f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322102-4fi0y96f.txt' === file2bib.sh === id: cord-322385-sc2vxxnn author: Ebinger, J. title: SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-322385-sc2vxxnn.txt cache: ./cache/cord-322385-sc2vxxnn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322385-sc2vxxnn.txt' === file2bib.sh === id: cord-322837-tqgwgvo0 author: Gable, Lance title: Legal and Ethical Implications of Wastewater SARS-CoV-2 Monitoring for COVID-19 Surveillance date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-322837-tqgwgvo0.txt cache: ./cache/cord-322837-tqgwgvo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322837-tqgwgvo0.txt' === file2bib.sh === id: cord-323449-r1gyjxei author: Kim, Uh Jin title: Air and Environmental Contamination Caused by COVID-19 Patients: a Multi-Center Study date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-323449-r1gyjxei.txt cache: ./cache/cord-323449-r1gyjxei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323449-r1gyjxei.txt' === file2bib.sh === id: cord-323216-rgj8vs9z author: Plotkin, Stanley A title: Vaccination Against Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-323216-rgj8vs9z.txt cache: ./cache/cord-323216-rgj8vs9z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323216-rgj8vs9z.txt' === file2bib.sh === id: cord-322877-jy1uvwre author: Yuen, Kenneth S.C. title: Ocular screening in severe acute respiratory syndrome date: 2004-03-30 pages: extension: .txt txt: ./txt/cord-322877-jy1uvwre.txt cache: ./cache/cord-322877-jy1uvwre.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322877-jy1uvwre.txt' === file2bib.sh === id: cord-323394-osx7llte author: Lanser, Lukas title: Evaluating the clinical utility and sensitivity of SARS-CoV-2 antigen testing in relation to RT-PCR Ct values date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-323394-osx7llte.txt cache: ./cache/cord-323394-osx7llte.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323394-osx7llte.txt' === file2bib.sh === id: cord-323440-u3iz79kk author: de Niet, Annikki title: The role of children in the transmission of mild SARS‐CoV‐2 infection date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-323440-u3iz79kk.txt cache: ./cache/cord-323440-u3iz79kk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323440-u3iz79kk.txt' === file2bib.sh === id: cord-322834-rl6yum7n author: Wallinga, Jacco title: Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures date: 2004-09-15 pages: extension: .txt txt: ./txt/cord-322834-rl6yum7n.txt cache: ./cache/cord-322834-rl6yum7n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322834-rl6yum7n.txt' === file2bib.sh === id: cord-323072-4rsgeag7 author: Han, Xueqing title: The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date: 2004-12-01 pages: extension: .txt txt: ./txt/cord-323072-4rsgeag7.txt cache: ./cache/cord-323072-4rsgeag7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323072-4rsgeag7.txt' === file2bib.sh === id: cord-323095-q8tj826i author: Sokolowska, Milena title: Outsmarting SARS-CoV-2 by empowering a decoy ACE2 date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-323095-q8tj826i.txt cache: ./cache/cord-323095-q8tj826i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323095-q8tj826i.txt' === file2bib.sh === id: cord-322562-3gvsn9vf author: Hatada, Ryo title: Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-322562-3gvsn9vf.txt cache: ./cache/cord-322562-3gvsn9vf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322562-3gvsn9vf.txt' === file2bib.sh === id: cord-322348-8opy5z9h author: Morelli, Mara title: Parents and Children During the COVID-19 Lockdown: The Influence of Parenting Distress and Parenting Self-Efficacy on Children’s Emotional Well-Being date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-322348-8opy5z9h.txt cache: ./cache/cord-322348-8opy5z9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322348-8opy5z9h.txt' === file2bib.sh === id: cord-323383-dmzhywb9 author: Lundon, DJ title: Early Mortality Risk Stratification after SARS-CoV-2 Infection date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-323383-dmzhywb9.txt cache: ./cache/cord-323383-dmzhywb9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323383-dmzhywb9.txt' === file2bib.sh === id: cord-323603-99d0wv1h author: Nunez Garcia, B. title: Real-world data: Cancer and SARS-CoV-2 infection date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-323603-99d0wv1h.txt cache: ./cache/cord-323603-99d0wv1h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323603-99d0wv1h.txt' === file2bib.sh === id: cord-323061-0i5w7vm9 author: Kharel Sitaula, Ranju title: Unfolding COVID-19: Lessons-in-Learning in Ophthalmology date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-323061-0i5w7vm9.txt cache: ./cache/cord-323061-0i5w7vm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323061-0i5w7vm9.txt' === file2bib.sh === id: cord-322980-rembksdr author: Talwar, Shivangi title: Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020 date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-322980-rembksdr.txt cache: ./cache/cord-322980-rembksdr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322980-rembksdr.txt' === file2bib.sh === id: cord-323038-hmi061vn author: Lai, Christopher K C title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-323038-hmi061vn.txt cache: ./cache/cord-323038-hmi061vn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323038-hmi061vn.txt' === file2bib.sh === id: cord-323389-8vp57c1o author: Wei, S. title: Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2. date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-323389-8vp57c1o.txt cache: ./cache/cord-323389-8vp57c1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323389-8vp57c1o.txt' === file2bib.sh === id: cord-322811-6lebh7ca author: Baig, Mirza S. title: Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-322811-6lebh7ca.txt cache: ./cache/cord-322811-6lebh7ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322811-6lebh7ca.txt' === file2bib.sh === id: cord-323327-08p122lw author: van de Veerdonk, Frank L. title: Blocking IL-1 to prevent respiratory failure in COVID-19 date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-323327-08p122lw.txt cache: ./cache/cord-323327-08p122lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323327-08p122lw.txt' === file2bib.sh === id: cord-323908-8dgngwmw author: He, Zhesheng title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-323908-8dgngwmw.txt cache: ./cache/cord-323908-8dgngwmw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323908-8dgngwmw.txt' === file2bib.sh === id: cord-323024-blc3mnbj author: Bernard-Valnet, R. title: CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-323024-blc3mnbj.txt cache: ./cache/cord-323024-blc3mnbj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323024-blc3mnbj.txt' === file2bib.sh === id: cord-322908-e3gok0ot author: Huang, Fangfang title: A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19) date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-322908-e3gok0ot.txt cache: ./cache/cord-322908-e3gok0ot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322908-e3gok0ot.txt' === file2bib.sh === id: cord-322942-y4zd2oui author: Olagnier, David title: Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-322942-y4zd2oui.txt cache: ./cache/cord-322942-y4zd2oui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322942-y4zd2oui.txt' === file2bib.sh === id: cord-323094-zugrtvyo author: Rose, R. title: Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-323094-zugrtvyo.txt cache: ./cache/cord-323094-zugrtvyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323094-zugrtvyo.txt' === file2bib.sh === id: cord-322957-clf8f90t author: Crespo, Javier title: Resumption of activity in gastroenterology departments. Recommendations by SEPD, AEEH, GETECCU and AEG date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-322957-clf8f90t.txt cache: ./cache/cord-322957-clf8f90t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322957-clf8f90t.txt' === file2bib.sh === id: cord-323092-j2u0ny2u author: Crosby, James C. title: COVID‐19: A review of therapeutics under investigation date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-323092-j2u0ny2u.txt cache: ./cache/cord-323092-j2u0ny2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323092-j2u0ny2u.txt' === file2bib.sh === id: cord-323514-jaom3p6s author: He, Yuxian title: A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date: 2006-05-26 pages: extension: .txt txt: ./txt/cord-323514-jaom3p6s.txt cache: ./cache/cord-323514-jaom3p6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323514-jaom3p6s.txt' === file2bib.sh === id: cord-323185-n0rubc72 author: Varshney, Bhavna title: SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date: 2012-01-12 pages: extension: .txt txt: ./txt/cord-323185-n0rubc72.txt cache: ./cache/cord-323185-n0rubc72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323185-n0rubc72.txt' === file2bib.sh === id: cord-321918-9jwma2y6 author: Xiu, Siyu title: Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-321918-9jwma2y6.txt cache: ./cache/cord-321918-9jwma2y6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321918-9jwma2y6.txt' === file2bib.sh === id: cord-323324-h2a25xym author: Armijos‐Jaramillo, Vinicio title: SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-323324-h2a25xym.txt cache: ./cache/cord-323324-h2a25xym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323324-h2a25xym.txt' === file2bib.sh === id: cord-321768-oevswvvd author: Duan, Ya-qi title: Deficiency of Tfh Cells and Germinal Center in Deceased COVID-19 Patients date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-321768-oevswvvd.txt cache: ./cache/cord-321768-oevswvvd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321768-oevswvvd.txt' === file2bib.sh === id: cord-323622-229kub7c author: Ou, Xueting title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-323622-229kub7c.txt cache: ./cache/cord-323622-229kub7c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323622-229kub7c.txt' === file2bib.sh === id: cord-320663-xypg6evo author: Market, Marisa title: Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-320663-xypg6evo.txt cache: ./cache/cord-320663-xypg6evo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320663-xypg6evo.txt' === file2bib.sh === id: cord-322955-7dw32xby author: Kathwate, Gunderao H title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-322955-7dw32xby.txt cache: ./cache/cord-322955-7dw32xby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322955-7dw32xby.txt' === file2bib.sh === id: cord-323397-5yop6clu author: Albalate, M. title: Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-323397-5yop6clu.txt cache: ./cache/cord-323397-5yop6clu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323397-5yop6clu.txt' === file2bib.sh === id: cord-323839-a4oejky0 author: Sasaki, Michihito title: SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-323839-a4oejky0.txt cache: ./cache/cord-323839-a4oejky0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323839-a4oejky0.txt' === file2bib.sh === id: cord-323831-1qadv7r1 author: Coleman, H title: Severe acute respiratory syndrome coronavirus-2 in post-laryngectomy patients: case series of four patients date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-323831-1qadv7r1.txt cache: ./cache/cord-323831-1qadv7r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323831-1qadv7r1.txt' === file2bib.sh === id: cord-323105-gqqzekfk author: Lin, Chen-Si title: Enhancement of anti-murine colon cancer immunity by fusion of a SARS fragment to a low-immunogenic carcinoembryonic antigen date: 2012-02-03 pages: extension: .txt txt: ./txt/cord-323105-gqqzekfk.txt cache: ./cache/cord-323105-gqqzekfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323105-gqqzekfk.txt' === file2bib.sh === id: cord-323424-86wh4u6l author: Santos, M. M. title: Survival and predictors of deaths of patients hospitalised due to COVID-19 from a retrospective and multicentre cohort study in Brazil date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-323424-86wh4u6l.txt cache: ./cache/cord-323424-86wh4u6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323424-86wh4u6l.txt' === file2bib.sh === id: cord-323596-dh7oh54z author: Advani, Sonali D. title: Assessing severe acute respiratory coronavirus virus 2 (SARS-CoV-2) preparedness in US community hospitals: A forgotten entity date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-323596-dh7oh54z.txt cache: ./cache/cord-323596-dh7oh54z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323596-dh7oh54z.txt' === file2bib.sh === id: cord-322446-ddv86eoy author: Sharma, Kulbhushan title: SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date: 2011-05-27 pages: extension: .txt txt: ./txt/cord-322446-ddv86eoy.txt cache: ./cache/cord-322446-ddv86eoy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322446-ddv86eoy.txt' === file2bib.sh === id: cord-323695-jkik03lb author: Paolo, Gisondi title: Incidence rates of hospitalization and death from COVID-19 in patients with psoriasis receiving biological treatment: a Northern Italy experience date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-323695-jkik03lb.txt cache: ./cache/cord-323695-jkik03lb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323695-jkik03lb.txt' === file2bib.sh === id: cord-323468-xn7anxj6 author: Olloquequi, Jordi title: COVID‐19 Susceptibility in chronic obstructive pulmonary disease date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-323468-xn7anxj6.txt cache: ./cache/cord-323468-xn7anxj6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323468-xn7anxj6.txt' === file2bib.sh === id: cord-323930-pl3qlcpo author: Sohail, Ayesha title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-323930-pl3qlcpo.txt cache: ./cache/cord-323930-pl3qlcpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323930-pl3qlcpo.txt' === file2bib.sh === id: cord-324128-css42bsb author: Boukli, Narjis title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-324128-css42bsb.txt cache: ./cache/cord-324128-css42bsb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324128-css42bsb.txt' === file2bib.sh === id: cord-323481-uz6usokd author: Wang, Yixuan title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures date: 2020-03-29 pages: extension: .txt txt: ./txt/cord-323481-uz6usokd.txt cache: ./cache/cord-323481-uz6usokd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323481-uz6usokd.txt' === file2bib.sh === id: cord-323093-u3ozc9ry author: Rathnayake, Athri D. title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-323093-u3ozc9ry.txt cache: ./cache/cord-323093-u3ozc9ry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323093-u3ozc9ry.txt' === file2bib.sh === id: cord-323828-ug2duzw1 author: Ni, Dongchun title: Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-323828-ug2duzw1.txt cache: ./cache/cord-323828-ug2duzw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323828-ug2duzw1.txt' === file2bib.sh === id: cord-323489-ro7kbnu3 author: Arenas, María Dolores title: Protection of nephrology health professionals during the COVID-19 pandemic date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-323489-ro7kbnu3.txt cache: ./cache/cord-323489-ro7kbnu3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323489-ro7kbnu3.txt' === file2bib.sh === id: cord-323871-2hx4fuk2 author: Ho, Sheau Ling title: Structural bioinformatics analysis of free cysteines in protein environments date: 2009-03-14 pages: extension: .txt txt: ./txt/cord-323871-2hx4fuk2.txt cache: ./cache/cord-323871-2hx4fuk2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323871-2hx4fuk2.txt' === file2bib.sh === id: cord-324255-ize21we2 author: Fouchier, Ron A. M. title: Koch's postulates fulfilled for SARS virus date: 2003 pages: extension: .txt txt: ./txt/cord-324255-ize21we2.txt cache: ./cache/cord-324255-ize21we2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324255-ize21we2.txt' === file2bib.sh === id: cord-322885-ob5euspo author: Durdagi, Serdar title: Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-322885-ob5euspo.txt cache: ./cache/cord-322885-ob5euspo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322885-ob5euspo.txt' === file2bib.sh === id: cord-322913-sq9mq6f1 author: Ciabattini, Annalisa title: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-322913-sq9mq6f1.txt cache: ./cache/cord-322913-sq9mq6f1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322913-sq9mq6f1.txt' === file2bib.sh === id: cord-324102-75v4ebag author: Garcia Rodriguez, Alejandro title: SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? Case report date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-324102-75v4ebag.txt cache: ./cache/cord-324102-75v4ebag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324102-75v4ebag.txt' === file2bib.sh === id: cord-323807-e220ut9u author: Bassetti, Matteo title: The novel Chinese coronavirus (2019‐nCoV) infections: Challenges for fighting the storm date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-323807-e220ut9u.txt cache: ./cache/cord-323807-e220ut9u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323807-e220ut9u.txt' === file2bib.sh === id: cord-324246-liyk6mna author: Shakoor, Hira title: Be well: A potential role for vitamin B in COVID-19 date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-324246-liyk6mna.txt cache: ./cache/cord-324246-liyk6mna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324246-liyk6mna.txt' === file2bib.sh === id: cord-323618-d09b65gd author: Vabret, A. title: Coronavirus humains (HCoV) date: 2008-05-05 pages: extension: .txt txt: ./txt/cord-323618-d09b65gd.txt cache: ./cache/cord-323618-d09b65gd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323618-d09b65gd.txt' === file2bib.sh === id: cord-323967-2mo915u1 author: Miersch, Shane title: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-323967-2mo915u1.txt cache: ./cache/cord-323967-2mo915u1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323967-2mo915u1.txt' === file2bib.sh === id: cord-324270-8rgkop42 author: Renaud-Picard, Benjamin title: Delayed pulmonary abscess following COVID-19 pneumonia: a case report date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-324270-8rgkop42.txt cache: ./cache/cord-324270-8rgkop42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324270-8rgkop42.txt' === file2bib.sh === id: cord-324357-ys4tqy5x author: nan title: Hygiene at home: A bulwark against COVID-19 to be protect from SARS-CoV-2 date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-324357-ys4tqy5x.txt cache: ./cache/cord-324357-ys4tqy5x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324357-ys4tqy5x.txt' === file2bib.sh === id: cord-324251-wgtatr8v author: Joshi, Madhvi title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-324251-wgtatr8v.txt cache: ./cache/cord-324251-wgtatr8v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324251-wgtatr8v.txt' === file2bib.sh === id: cord-324480-7u5lh4jx author: Sharma, A. title: Structural stability of SARS-CoV-2 degrades with temperature date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-324480-7u5lh4jx.txt cache: ./cache/cord-324480-7u5lh4jx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324480-7u5lh4jx.txt' === file2bib.sh === id: cord-323832-w19ump0o author: Mishra, Vijaya Nath title: Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-323832-w19ump0o.txt cache: ./cache/cord-323832-w19ump0o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323832-w19ump0o.txt' === file2bib.sh === id: cord-323905-ayufx3wv author: Kort, N. P. title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-323905-ayufx3wv.txt cache: ./cache/cord-323905-ayufx3wv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323905-ayufx3wv.txt' === file2bib.sh === id: cord-324518-a346cjx4 author: Zhang, Zhibin title: The outbreak pattern of the SARS cases in Asia date: 2004 pages: extension: .txt txt: ./txt/cord-324518-a346cjx4.txt cache: ./cache/cord-324518-a346cjx4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324518-a346cjx4.txt' === file2bib.sh === id: cord-324644-sz5n7a5z author: Rehman, Mahin title: Atypical Manifestation of COVID-19-Induced Myocarditis date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-324644-sz5n7a5z.txt cache: ./cache/cord-324644-sz5n7a5z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324644-sz5n7a5z.txt' === file2bib.sh === id: cord-323643-lu3ngt6r author: Chow, C.B. title: Post-SARS infection control in the hospital and clinic date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-323643-lu3ngt6r.txt cache: ./cache/cord-323643-lu3ngt6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323643-lu3ngt6r.txt' === file2bib.sh === id: cord-324800-l8xl4g2a author: Eisenberg, Michael L. title: Coronavirus Disease 2019 (COVID-19) and men’s reproductive health date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-324800-l8xl4g2a.txt cache: ./cache/cord-324800-l8xl4g2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324800-l8xl4g2a.txt' === file2bib.sh === id: cord-324307-2zbm4iwn author: Kam, Kai-qian title: A Well Infant With Coronavirus Disease 2019 With High Viral Load date: 2020-02-28 pages: extension: .txt txt: ./txt/cord-324307-2zbm4iwn.txt cache: ./cache/cord-324307-2zbm4iwn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324307-2zbm4iwn.txt' === file2bib.sh === id: cord-324344-dxuabscn author: Zhao, Xuesen title: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date: 2020-04-05 pages: extension: .txt txt: ./txt/cord-324344-dxuabscn.txt cache: ./cache/cord-324344-dxuabscn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324344-dxuabscn.txt' === file2bib.sh === id: cord-324325-rmlrhyf2 author: Chan, Wai S title: Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date: 2005-05-13 pages: extension: .txt txt: ./txt/cord-324325-rmlrhyf2.txt cache: ./cache/cord-324325-rmlrhyf2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324325-rmlrhyf2.txt' === file2bib.sh === id: cord-322660-bis2arbu author: Alexander, Regi title: Guidance for the Treatment and Management of COVID‐19 Among People with Intellectual Disabilities date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-322660-bis2arbu.txt cache: ./cache/cord-322660-bis2arbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322660-bis2arbu.txt' === file2bib.sh === id: cord-323943-9916y6x0 author: Platt, Daniel E title: Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-323943-9916y6x0.txt cache: ./cache/cord-323943-9916y6x0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323943-9916y6x0.txt' === file2bib.sh === id: cord-323666-t7cshj05 author: Cegolon, L. title: Nasal Disinfection for the Prevention and Control of COVID-19: A Scoping Review on Potential Chemo-preventive Agents. date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-323666-t7cshj05.txt cache: ./cache/cord-323666-t7cshj05.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323666-t7cshj05.txt' === file2bib.sh === id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-324295-9c1zxjng.txt cache: ./cache/cord-324295-9c1zxjng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324295-9c1zxjng.txt' === file2bib.sh === id: cord-324651-8teb5jrn author: Filippini, Antonio title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-324651-8teb5jrn.txt cache: ./cache/cord-324651-8teb5jrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324651-8teb5jrn.txt' === file2bib.sh === id: cord-323882-127c5bve author: Yu, Wen-Bin title: Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-323882-127c5bve.txt cache: ./cache/cord-323882-127c5bve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323882-127c5bve.txt' === file2bib.sh === id: cord-324902-18h0maxi author: Liu, Xuemei title: Patterns of IgG and IgM antibody response in COVID-19 patients date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-324902-18h0maxi.txt cache: ./cache/cord-324902-18h0maxi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324902-18h0maxi.txt' === file2bib.sh === id: cord-324345-j43rpvwk author: Leong, Hoe Nam title: SARS – My personal battle date: 2010-11-19 pages: extension: .txt txt: ./txt/cord-324345-j43rpvwk.txt cache: ./cache/cord-324345-j43rpvwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324345-j43rpvwk.txt' === file2bib.sh === id: cord-325045-ak7rouhb author: Sotgiu, Giovanni title: Advanced forecasting of SARS‐CoV‐2‐related deaths in Italy, Germany, Spain, and New York State date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-325045-ak7rouhb.txt cache: ./cache/cord-325045-ak7rouhb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325045-ak7rouhb.txt' === file2bib.sh === id: cord-324288-qgxswltx author: Padhi, Sunali title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-324288-qgxswltx.txt cache: ./cache/cord-324288-qgxswltx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324288-qgxswltx.txt' === file2bib.sh === id: cord-324727-bj8oei0v author: Zhang, Xiaomei title: Management of Digestive Disorders and Procedures Associated With COVID-19 date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-324727-bj8oei0v.txt cache: ./cache/cord-324727-bj8oei0v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324727-bj8oei0v.txt' === file2bib.sh === id: cord-323822-jtbfpx88 author: Barnett, Brad P. title: Potential of Ocular Transmission of SARS-CoV-2: A Review date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-323822-jtbfpx88.txt cache: ./cache/cord-323822-jtbfpx88.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323822-jtbfpx88.txt' === file2bib.sh === id: cord-323737-6ajqy0ch author: Jiang, Yuanyuan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-323737-6ajqy0ch.txt cache: ./cache/cord-323737-6ajqy0ch.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323737-6ajqy0ch.txt' === file2bib.sh === id: cord-323824-74xvvwrw author: de Oliveira, Osmair Vital title: Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-323824-74xvvwrw.txt cache: ./cache/cord-323824-74xvvwrw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323824-74xvvwrw.txt' === file2bib.sh === id: cord-324938-2lu9z5b2 author: Wu, Li-Ping title: Duration of Antibody Responses after Severe Acute Respiratory Syndrome date: 2007-10-17 pages: extension: .txt txt: ./txt/cord-324938-2lu9z5b2.txt cache: ./cache/cord-324938-2lu9z5b2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324938-2lu9z5b2.txt' === file2bib.sh === id: cord-324531-lpoelp91 author: Artesi, Maria title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-324531-lpoelp91.txt cache: ./cache/cord-324531-lpoelp91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324531-lpoelp91.txt' === file2bib.sh === id: cord-324638-gwd8qin6 author: Chiu, Rossa WK title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 pages: extension: .txt txt: ./txt/cord-324638-gwd8qin6.txt cache: ./cache/cord-324638-gwd8qin6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324638-gwd8qin6.txt' === file2bib.sh === id: cord-324557-4u8dja0n author: Leblanc, Jean‐François title: Risk of Transmission of Severe Acute Respiratory Syndrome Coronavirus‐2 by Transfusion: A Literature Review date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-324557-4u8dja0n.txt cache: ./cache/cord-324557-4u8dja0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324557-4u8dja0n.txt' === file2bib.sh === id: cord-324328-olnwynfu author: Nakamichi, K. title: Outcomes associated with SARS-CoV-2 viral clades in COVID-19 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-324328-olnwynfu.txt cache: ./cache/cord-324328-olnwynfu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324328-olnwynfu.txt' === file2bib.sh === id: cord-324165-afdmsbw2 author: Joo, Heesoo title: The effects of past SARS experience and proximity on declines in numbers of travelers to the Republic of Korea during the 2015 MERS outbreak: A retrospective study date: 2019-08-31 pages: extension: .txt txt: ./txt/cord-324165-afdmsbw2.txt cache: ./cache/cord-324165-afdmsbw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324165-afdmsbw2.txt' === file2bib.sh === id: cord-324892-mg2dziuw author: Carneiro, João title: CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-324892-mg2dziuw.txt cache: ./cache/cord-324892-mg2dziuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324892-mg2dziuw.txt' === file2bib.sh === id: cord-323980-rcyjthze author: Willems, Laurent M. title: SARS-CoV-2-related rapid reorganization of an epilepsy outpatient clinic from personal appointments to telemedicine services: A German single-center experience date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-323980-rcyjthze.txt cache: ./cache/cord-323980-rcyjthze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323980-rcyjthze.txt' === file2bib.sh === id: cord-324963-zg3ghl2m author: Salzberger, B. title: COVID-19 – eine neue und vielseitige Herausforderung date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-324963-zg3ghl2m.txt cache: ./cache/cord-324963-zg3ghl2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324963-zg3ghl2m.txt' === file2bib.sh === id: cord-323685-gjocoa60 author: Tsai, Shang-Jui title: Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-323685-gjocoa60.txt cache: ./cache/cord-323685-gjocoa60.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323685-gjocoa60.txt' === file2bib.sh === id: cord-324888-oak27okj author: Leng, Ling title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-324888-oak27okj.txt cache: ./cache/cord-324888-oak27okj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324888-oak27okj.txt' === file2bib.sh === id: cord-324752-t50bg7pq author: Lavery, Michael Joseph title: Cutaneous manifestations of COVID-19 in children (and adults): A virus that does not discriminate date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-324752-t50bg7pq.txt cache: ./cache/cord-324752-t50bg7pq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324752-t50bg7pq.txt' === file2bib.sh === id: cord-324623-x6eom6kh author: Zhang, Jingyi title: Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-324623-x6eom6kh.txt cache: ./cache/cord-324623-x6eom6kh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324623-x6eom6kh.txt' === file2bib.sh === id: cord-324707-9ld73wv1 author: Mitjà, Oriol title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-324707-9ld73wv1.txt cache: ./cache/cord-324707-9ld73wv1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324707-9ld73wv1.txt' === file2bib.sh === id: cord-325134-z9n17z72 author: Nolan, Brodie title: Recommendations for emergency departments receiving patients with vital signs absent from paramedics during COVID-19 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-325134-z9n17z72.txt cache: ./cache/cord-325134-z9n17z72.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325134-z9n17z72.txt' === file2bib.sh === id: cord-324265-j3v3i8vm author: Marietta, Marco title: COVID-19, coagulopathy and venous thromboembolism: more questions than answers date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-324265-j3v3i8vm.txt cache: ./cache/cord-324265-j3v3i8vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324265-j3v3i8vm.txt' === file2bib.sh === id: cord-324856-hf969tav author: Abir, Tanvir title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-324856-hf969tav.txt cache: ./cache/cord-324856-hf969tav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324856-hf969tav.txt' === file2bib.sh === id: cord-325070-583innd7 author: Lee, Lennard Y.W. title: Utility of COVID-19 Screening in Cancer Patients date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-325070-583innd7.txt cache: ./cache/cord-325070-583innd7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325070-583innd7.txt' === file2bib.sh === id: cord-324166-6ydn2bvy author: Kumar, Neeraj title: Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-324166-6ydn2bvy.txt cache: ./cache/cord-324166-6ydn2bvy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324166-6ydn2bvy.txt' === file2bib.sh === id: cord-325320-v9e2axf4 author: Vigil‐De Gracia, P. title: Pregnancies recovered from SARS‐CoV‐2 infection in the second and third trimesters: obstetric evolution date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-325320-v9e2axf4.txt cache: ./cache/cord-325320-v9e2axf4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325320-v9e2axf4.txt' === file2bib.sh === id: cord-324405-6uanhe2p author: Burke, Rachel M. title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-324405-6uanhe2p.txt cache: ./cache/cord-324405-6uanhe2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324405-6uanhe2p.txt' === file2bib.sh === id: cord-323940-ubazgvov author: Cafiero, Concetta title: Pharmacogenomics and Pharmacogenetics: In Silico Prediction of Drug Effects in Treatments for Novel Coronavirus SARS-CoV2 Disease date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-323940-ubazgvov.txt cache: ./cache/cord-323940-ubazgvov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323940-ubazgvov.txt' === file2bib.sh === id: cord-325377-g68onkjt author: Dey, Anusree title: COVID-19: Scientific Overview of the global Pandemic date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-325377-g68onkjt.txt cache: ./cache/cord-325377-g68onkjt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325377-g68onkjt.txt' === file2bib.sh === id: cord-324619-y7gilopu author: Alam, S.B. title: Severe acute respiratory syndrome coronavirus‐2 may be an underappreciated pathogen of the central nervous system date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-324619-y7gilopu.txt cache: ./cache/cord-324619-y7gilopu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324619-y7gilopu.txt' === file2bib.sh === id: cord-325420-e9fjo7tl author: Xiao, Xia title: Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-325420-e9fjo7tl.txt cache: ./cache/cord-325420-e9fjo7tl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325420-e9fjo7tl.txt' === file2bib.sh === id: cord-325055-todb1d4x author: Rychter, Anna Maria title: Should patients with obesity be more afraid of COVID‐19? date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-325055-todb1d4x.txt cache: ./cache/cord-325055-todb1d4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325055-todb1d4x.txt' === file2bib.sh === id: cord-325452-2sywbgje author: Sun, Pengfei title: Understanding of COVID‐19 based on current evidence date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-325452-2sywbgje.txt cache: ./cache/cord-325452-2sywbgje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325452-2sywbgje.txt' === file2bib.sh === id: cord-324949-sqy03dks author: Poe, Francis L. title: N-Acetylcysteine: a potential therapeutic agent for SARS-CoV-2 date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-324949-sqy03dks.txt cache: ./cache/cord-324949-sqy03dks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324949-sqy03dks.txt' === file2bib.sh === id: cord-325019-hznnoxw6 author: Benavides-Cordoba, Vicente title: Drug Repositioning for COVID-19 date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-325019-hznnoxw6.txt cache: ./cache/cord-325019-hznnoxw6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325019-hznnoxw6.txt' === file2bib.sh === id: cord-325293-nwxtyrpl author: Akhtar, Hubba title: COVID-19 (SARS-CoV-2) Infection in Pregnancy: A Systematic Review date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-325293-nwxtyrpl.txt cache: ./cache/cord-325293-nwxtyrpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325293-nwxtyrpl.txt' === file2bib.sh === id: cord-325014-n7mnhk2v author: Gujski, Mariusz title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 pages: extension: .txt txt: ./txt/cord-325014-n7mnhk2v.txt cache: ./cache/cord-325014-n7mnhk2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325014-n7mnhk2v.txt' === file2bib.sh === id: cord-325038-q7gxw1go author: Joyce, Andrew A title: Changes in Interventional Pain Physician Decision-Making, Practice Patterns, and Mental Health During the Early Phase of the SARS-CoV-2 Global Pandemic date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-325038-q7gxw1go.txt cache: ./cache/cord-325038-q7gxw1go.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325038-q7gxw1go.txt' === file2bib.sh === id: cord-325473-hrdanbn1 author: Ghahremanpour, Mohammad M. title: Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-325473-hrdanbn1.txt cache: ./cache/cord-325473-hrdanbn1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325473-hrdanbn1.txt' === file2bib.sh === id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-325113-sou8xyld.txt cache: ./cache/cord-325113-sou8xyld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325113-sou8xyld.txt' === file2bib.sh === id: cord-325348-yi6yu5l1 author: Zhang, G. title: Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-325348-yi6yu5l1.txt cache: ./cache/cord-325348-yi6yu5l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325348-yi6yu5l1.txt' === file2bib.sh === id: cord-325657-s2vdazq0 author: Huang, Yan-Jang S. title: SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-325657-s2vdazq0.txt cache: ./cache/cord-325657-s2vdazq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325657-s2vdazq0.txt' === file2bib.sh === id: cord-325421-1ysn0kyr author: Christensen, Johanna title: Covid-19 Viremia, Serologies and Clinical Course in a Case Series of Transplant Recipients date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-325421-1ysn0kyr.txt cache: ./cache/cord-325421-1ysn0kyr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325421-1ysn0kyr.txt' === file2bib.sh === id: cord-325498-4yciuh1n author: Del Brutto, Oscar H. title: Incident SARS-CoV-2 Infection and a Shared Latrine date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-325498-4yciuh1n.txt cache: ./cache/cord-325498-4yciuh1n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325498-4yciuh1n.txt' === file2bib.sh === id: cord-324919-ciamusjs author: Scialo, Filippo title: ACE2: The Major Cell Entry Receptor for SARS-CoV-2 date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-324919-ciamusjs.txt cache: ./cache/cord-324919-ciamusjs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324919-ciamusjs.txt' === file2bib.sh === id: cord-325213-e6i6buow author: Mak, Ivan Wing Chit title: Risk factors for chronic post-traumatic stress disorder (PTSD) in SARS survivors date: 2010-09-15 pages: extension: .txt txt: ./txt/cord-325213-e6i6buow.txt cache: ./cache/cord-325213-e6i6buow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325213-e6i6buow.txt' === file2bib.sh === id: cord-325136-oyizfh2z author: Pham, Quang Thai title: The first 100 days of SARS-CoV-2 control in Vietnam date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-325136-oyizfh2z.txt cache: ./cache/cord-325136-oyizfh2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325136-oyizfh2z.txt' === file2bib.sh === id: cord-325197-j1uo8qmf author: Crimi, Ettore title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-325197-j1uo8qmf.txt cache: ./cache/cord-325197-j1uo8qmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325197-j1uo8qmf.txt' === file2bib.sh === id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-325529-pid58g2r.txt cache: ./cache/cord-325529-pid58g2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325529-pid58g2r.txt' === file2bib.sh === id: cord-325172-a8ntxnmm author: Yip, Ming Shum title: Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-325172-a8ntxnmm.txt cache: ./cache/cord-325172-a8ntxnmm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325172-a8ntxnmm.txt' === file2bib.sh === id: cord-325449-fl6ob5ja author: Wang, Jing title: COVID-19 and diabetes: the contributions of hyperglycemia date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-325449-fl6ob5ja.txt cache: ./cache/cord-325449-fl6ob5ja.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325449-fl6ob5ja.txt' === file2bib.sh === id: cord-325419-15vm22d8 author: Dai, C. L. title: Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-325419-15vm22d8.txt cache: ./cache/cord-325419-15vm22d8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325419-15vm22d8.txt' === file2bib.sh === id: cord-325593-ww2vq3n4 author: Hendren, Nicholas S. title: Unique Patterns of Cardiovascular Involvement in COVID-19 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-325593-ww2vq3n4.txt cache: ./cache/cord-325593-ww2vq3n4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325593-ww2vq3n4.txt' === file2bib.sh === id: cord-325595-y9ae6zbr author: Montopoli, M. title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-325595-y9ae6zbr.txt cache: ./cache/cord-325595-y9ae6zbr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325595-y9ae6zbr.txt' === file2bib.sh === id: cord-325460-4fhegc0z author: Jacobs, Werner title: Fatal lymphocytic cardiac damage in coronavirus disease 2019 (COVID‐19): autopsy reveals a ferroptosis signature date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-325460-4fhegc0z.txt cache: ./cache/cord-325460-4fhegc0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325460-4fhegc0z.txt' === file2bib.sh === id: cord-325863-3t73v4ng author: Foss, Francine M. title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-325863-3t73v4ng.txt cache: ./cache/cord-325863-3t73v4ng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325863-3t73v4ng.txt' === file2bib.sh === id: cord-325598-gy809ee0 author: Lyne, Cloutier title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-325598-gy809ee0.txt cache: ./cache/cord-325598-gy809ee0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325598-gy809ee0.txt' === file2bib.sh === id: cord-325324-kh2aal5n author: Teng, Shaolei title: ACE2 Enhance Viral Infection or Viral Infection Aggravate the Underlying Diseases date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-325324-kh2aal5n.txt cache: ./cache/cord-325324-kh2aal5n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325324-kh2aal5n.txt' === file2bib.sh === id: cord-324970-yty7aajj author: Ma, Di title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-324970-yty7aajj.txt cache: ./cache/cord-324970-yty7aajj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324970-yty7aajj.txt' === file2bib.sh === id: cord-325261-bdumhy5b author: Clemente, Valentino title: Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19 date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-325261-bdumhy5b.txt cache: ./cache/cord-325261-bdumhy5b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325261-bdumhy5b.txt' === file2bib.sh === id: cord-325991-dktffiaa author: Gross, Oliver title: COVID-19-associated nephritis: early warning for disease severity and complications? date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-325991-dktffiaa.txt cache: ./cache/cord-325991-dktffiaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325991-dktffiaa.txt' === file2bib.sh === id: cord-325959-uqg2xkie author: Bundschuh, Christian title: Evaluation of the EDI enzyme linked immunosorbent assays for the detection of SARS-CoV-2 IgM and IgG antibodies in human plasma date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-325959-uqg2xkie.txt cache: ./cache/cord-325959-uqg2xkie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325959-uqg2xkie.txt' === file2bib.sh === id: cord-325744-i3r3ff3t author: Chan, Angelina O. M. title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore date: 2004-05-17 pages: extension: .txt txt: ./txt/cord-325744-i3r3ff3t.txt cache: ./cache/cord-325744-i3r3ff3t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325744-i3r3ff3t.txt' === file2bib.sh === id: cord-326375-8m4110k3 author: Seitzman, Gerami D. title: No Time for Tears date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-326375-8m4110k3.txt cache: ./cache/cord-326375-8m4110k3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326375-8m4110k3.txt' === file2bib.sh === id: cord-325783-pqonn0as author: Nicholls, John M title: Lung pathology of fatal severe acute respiratory syndrome date: 2003-05-24 pages: extension: .txt txt: ./txt/cord-325783-pqonn0as.txt cache: ./cache/cord-325783-pqonn0as.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325783-pqonn0as.txt' === file2bib.sh === id: cord-326198-6okk3u49 author: Walker, A. title: Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-326198-6okk3u49.txt cache: ./cache/cord-326198-6okk3u49.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326198-6okk3u49.txt' === file2bib.sh === id: cord-325124-0hxan9rw author: Li, Chenyu title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-325124-0hxan9rw.txt cache: ./cache/cord-325124-0hxan9rw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325124-0hxan9rw.txt' === file2bib.sh === id: cord-326503-ljle4vq3 author: Morioka, Shinichiro title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-326503-ljle4vq3.txt cache: ./cache/cord-326503-ljle4vq3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326503-ljle4vq3.txt' === file2bib.sh === id: cord-325234-skshcrh1 author: Jin, Tingxu title: SARS-CoV-2 presented in the air of an intensive care unit (ICU) date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-325234-skshcrh1.txt cache: ./cache/cord-325234-skshcrh1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325234-skshcrh1.txt' === file2bib.sh === id: cord-326305-mjd5agvf author: Ashraf, Mohammad Ali title: The application of direct viral cytopathic hypothesis to design drug trials in the battle against COVID-19 date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-326305-mjd5agvf.txt cache: ./cache/cord-326305-mjd5agvf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326305-mjd5agvf.txt' === file2bib.sh === id: cord-325609-n6dpac6i author: Dawson, Kathryn L. title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 - single center experience. date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-325609-n6dpac6i.txt cache: ./cache/cord-325609-n6dpac6i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325609-n6dpac6i.txt' === file2bib.sh === id: cord-325936-rwxg187r author: Eyal, Nir title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-325936-rwxg187r.txt cache: ./cache/cord-325936-rwxg187r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325936-rwxg187r.txt' === file2bib.sh === id: cord-326254-8dlxsf57 author: Glasbey, T. title: Flawed disinfectant recommendations during a pandemic date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-326254-8dlxsf57.txt cache: ./cache/cord-326254-8dlxsf57.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326254-8dlxsf57.txt' === file2bib.sh === id: cord-325614-e9hnhzfg author: Todorov, German title: A Possible Path towards Rapid Development of Live-Attenuated SARS-CoV-2 Vaccines: Plunging into the Natural Pool date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-325614-e9hnhzfg.txt cache: ./cache/cord-325614-e9hnhzfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325614-e9hnhzfg.txt' === file2bib.sh === id: cord-326514-7plamtl8 author: Veerus, Piret title: Seroprevalence of SARS‐CoV‐2 antibodies among pregnant women in Estonia: a call for epidemiological studies date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-326514-7plamtl8.txt cache: ./cache/cord-326514-7plamtl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326514-7plamtl8.txt' === file2bib.sh === id: cord-325479-2r4oomdp author: Torii, Shotaro title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-325479-2r4oomdp.txt cache: ./cache/cord-325479-2r4oomdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325479-2r4oomdp.txt' === file2bib.sh === id: cord-326341-egtnqlov author: Liotti, Flora Marzia title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-326341-egtnqlov.txt cache: ./cache/cord-326341-egtnqlov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326341-egtnqlov.txt' === file2bib.sh === id: cord-325282-20l9xcmg author: Helal, Mohamed A. title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-325282-20l9xcmg.txt cache: ./cache/cord-325282-20l9xcmg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325282-20l9xcmg.txt' === file2bib.sh === id: cord-326150-cf4rlqe5 author: Carrascosa, J M title: Manifestaciones cutáneas en el contexto de la infección por SARS-CoV-2 (COVID-19) date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-326150-cf4rlqe5.txt cache: ./cache/cord-326150-cf4rlqe5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326150-cf4rlqe5.txt' === file2bib.sh === id: cord-326045-x8xntne7 author: Chng, Shu-Sin title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate date: 2004-12-20 pages: extension: .txt txt: ./txt/cord-326045-x8xntne7.txt cache: ./cache/cord-326045-x8xntne7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326045-x8xntne7.txt' === file2bib.sh === id: cord-326169-delehk6x author: CJ Jorgensen, Sarah title: Baricitinib: A review of pharmacology, safety and emerging clinical experience in COVID‐19 date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-326169-delehk6x.txt cache: ./cache/cord-326169-delehk6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326169-delehk6x.txt' === file2bib.sh === id: cord-326273-6rp12py3 author: Chow, Kuan-Chih title: Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date: 2004-04-01 pages: extension: .txt txt: ./txt/cord-326273-6rp12py3.txt cache: ./cache/cord-326273-6rp12py3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326273-6rp12py3.txt' === file2bib.sh === id: cord-325910-qiay8n43 author: Green, D. A. title: Clinical Performance of SARS-CoV-2 Molecular Testing date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-325910-qiay8n43.txt cache: ./cache/cord-325910-qiay8n43.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325910-qiay8n43.txt' === file2bib.sh === id: cord-326736-jd6fvaop author: Bosco-Lauth, Angela M. title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-326736-jd6fvaop.txt cache: ./cache/cord-326736-jd6fvaop.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326736-jd6fvaop.txt' === file2bib.sh === id: cord-325958-1v1pg2z0 author: Lange, Clemens title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-325958-1v1pg2z0.txt cache: ./cache/cord-325958-1v1pg2z0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325958-1v1pg2z0.txt' === file2bib.sh === id: cord-326718-jboiufoq author: Deming, Meagan E. title: COVID-19 and Lessons to Be Learned from Prior Coronavirus Outbreaks date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-326718-jboiufoq.txt cache: ./cache/cord-326718-jboiufoq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326718-jboiufoq.txt' === file2bib.sh === id: cord-326581-31trqhi1 author: Ihling, Christian title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-326581-31trqhi1.txt cache: ./cache/cord-326581-31trqhi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326581-31trqhi1.txt' === file2bib.sh === id: cord-325669-6kjlcakt author: Fogacci, Silvia title: Management of pregnancy-related hypertensive disorders in patients infected with SARS CoV-2: pharmacological and clinical issues date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-325669-6kjlcakt.txt cache: ./cache/cord-325669-6kjlcakt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325669-6kjlcakt.txt' === file2bib.sh === id: cord-325559-di8lljoi author: Cappello, Francesco title: Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-325559-di8lljoi.txt cache: ./cache/cord-325559-di8lljoi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325559-di8lljoi.txt' === file2bib.sh === id: cord-326282-uxn64olw author: Lu, Maolin title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 pages: extension: .txt txt: ./txt/cord-326282-uxn64olw.txt cache: ./cache/cord-326282-uxn64olw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326282-uxn64olw.txt' === file2bib.sh === id: cord-326148-9wpxm5of author: Van Walle, I. title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-326148-9wpxm5of.txt cache: ./cache/cord-326148-9wpxm5of.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326148-9wpxm5of.txt' === file2bib.sh === id: cord-325830-mrtpihc7 author: Nelson, Philipp P. title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-325830-mrtpihc7.txt cache: ./cache/cord-325830-mrtpihc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325830-mrtpihc7.txt' === file2bib.sh === id: cord-324953-3sacf4wu author: Childs, James E. title: Introduction: Conceptualizing and Partitioning the Emergence Process of Zoonotic Viruses from Wildlife to Humans date: 2007 pages: extension: .txt txt: ./txt/cord-324953-3sacf4wu.txt cache: ./cache/cord-324953-3sacf4wu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324953-3sacf4wu.txt' === file2bib.sh === id: cord-326888-0p8nctpy author: Gercina, Anne Caroline title: What is the best mouthrinse against Coronaviruses? date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-326888-0p8nctpy.txt cache: ./cache/cord-326888-0p8nctpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-326888-0p8nctpy.txt' === file2bib.sh === id: cord-326406-n0qi6gs8 author: Creed, Marina title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-326406-n0qi6gs8.txt cache: ./cache/cord-326406-n0qi6gs8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326406-n0qi6gs8.txt' === file2bib.sh === id: cord-326427-06djb0sd author: Cao, Dongmei title: Vaginal delivery in women with COVID-19: report of two cases date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-326427-06djb0sd.txt cache: ./cache/cord-326427-06djb0sd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326427-06djb0sd.txt' === file2bib.sh === id: cord-326965-xrnhkcsv author: Lacout, Carole title: A new diagnosis of systemic capillary leak syndrome in a patient with COVID-19 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-326965-xrnhkcsv.txt cache: ./cache/cord-326965-xrnhkcsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326965-xrnhkcsv.txt' === file2bib.sh === id: cord-326730-aprb819p author: Perkmann, T. title: Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-326730-aprb819p.txt cache: ./cache/cord-326730-aprb819p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326730-aprb819p.txt' === file2bib.sh === id: cord-327169-sz4ildnd author: Mondoni, Michele title: Utility and safety of bronchoscopy during SARS-CoV-2 outbreak in Italy: a retrospective, multicenter study date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-327169-sz4ildnd.txt cache: ./cache/cord-327169-sz4ildnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327169-sz4ildnd.txt' === file2bib.sh === id: cord-326257-rcv8sh22 author: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-326257-rcv8sh22.txt cache: ./cache/cord-326257-rcv8sh22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326257-rcv8sh22.txt' === file2bib.sh === id: cord-326013-5i35zdmv author: Carpinteiro, Alexander title: Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-326013-5i35zdmv.txt cache: ./cache/cord-326013-5i35zdmv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326013-5i35zdmv.txt' === file2bib.sh === id: cord-324926-3c5ab73l author: Xia, Shuai title: A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike date: 2019-04-10 pages: extension: .txt txt: ./txt/cord-324926-3c5ab73l.txt cache: ./cache/cord-324926-3c5ab73l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324926-3c5ab73l.txt' === file2bib.sh === id: cord-325481-uzch2hwd author: Simmons, Graham title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date: 2011-05-01 pages: extension: .txt txt: ./txt/cord-325481-uzch2hwd.txt cache: ./cache/cord-325481-uzch2hwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325481-uzch2hwd.txt' === file2bib.sh === id: cord-327028-dbvucvy3 author: Zhang, Cantong title: Controversial treatments: An updated understanding of the coronavirus disease 2019 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-327028-dbvucvy3.txt cache: ./cache/cord-327028-dbvucvy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327028-dbvucvy3.txt' === file2bib.sh === id: cord-326721-2v5wkjrq author: Xiao, Wenlei title: A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-326721-2v5wkjrq.txt cache: ./cache/cord-326721-2v5wkjrq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326721-2v5wkjrq.txt' === file2bib.sh === id: cord-326393-gxy1w0qk author: Martino, Marcello Di title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-326393-gxy1w0qk.txt cache: ./cache/cord-326393-gxy1w0qk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326393-gxy1w0qk.txt' === file2bib.sh === id: cord-319933-yp9ofhi8 author: Ruiz, Sara I. title: Chapter 38 Animal Models of Human Viral Diseases date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-319933-yp9ofhi8.txt cache: ./cache/cord-319933-yp9ofhi8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319933-yp9ofhi8.txt' === file2bib.sh === id: cord-326706-75mjs6vm author: Waterfield, Thomas title: Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-326706-75mjs6vm.txt cache: ./cache/cord-326706-75mjs6vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326706-75mjs6vm.txt' === file2bib.sh === id: cord-326882-bbn1tfq5 author: Li, Quan title: Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-326882-bbn1tfq5.txt cache: ./cache/cord-326882-bbn1tfq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326882-bbn1tfq5.txt' === file2bib.sh === id: cord-326643-obfvi3ms author: Lo Giudice, Roberto title: The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in Dentistry. Management of Biological Risk in Dental Practice date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-326643-obfvi3ms.txt cache: ./cache/cord-326643-obfvi3ms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326643-obfvi3ms.txt' === file2bib.sh === id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-324324-8ybfiz8f.txt cache: ./cache/cord-324324-8ybfiz8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324324-8ybfiz8f.txt' === file2bib.sh === id: cord-326337-s0fp5z1q author: Chan, Kui K. title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-326337-s0fp5z1q.txt cache: ./cache/cord-326337-s0fp5z1q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326337-s0fp5z1q.txt' === file2bib.sh === id: cord-326568-twv2i3fb author: Bruminhent, Jackrapong title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-326568-twv2i3fb.txt cache: ./cache/cord-326568-twv2i3fb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326568-twv2i3fb.txt' === file2bib.sh === id: cord-326320-flfrdrbi author: Choudhary, Shalki title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-326320-flfrdrbi.txt cache: ./cache/cord-326320-flfrdrbi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326320-flfrdrbi.txt' === file2bib.sh === id: cord-326911-va3x6au2 author: Ramos-Mandujano, G. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-326911-va3x6au2.txt cache: ./cache/cord-326911-va3x6au2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326911-va3x6au2.txt' === file2bib.sh === id: cord-326666-melz5fq4 author: Sun, Weitao title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-326666-melz5fq4.txt cache: ./cache/cord-326666-melz5fq4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326666-melz5fq4.txt' === file2bib.sh === id: cord-326833-boxgt4kb author: Marimuthu, Janakiram title: HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-326833-boxgt4kb.txt cache: ./cache/cord-326833-boxgt4kb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326833-boxgt4kb.txt' === file2bib.sh === id: cord-326532-2ehuuvnx author: Götzinger, Florian title: COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-326532-2ehuuvnx.txt cache: ./cache/cord-326532-2ehuuvnx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326532-2ehuuvnx.txt' === file2bib.sh === id: cord-327273-7ntp7x8d author: Street, Renée title: COVID-19 wastewater surveillance: An African perspective date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-327273-7ntp7x8d.txt cache: ./cache/cord-327273-7ntp7x8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327273-7ntp7x8d.txt' === file2bib.sh === id: cord-327272-fspxett8 author: Buonaguro, Luigi title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-327272-fspxett8.txt cache: ./cache/cord-327272-fspxett8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327272-fspxett8.txt' === file2bib.sh === id: cord-326929-ytix4l1o author: Samillan, V. J. title: Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-326929-ytix4l1o.txt cache: ./cache/cord-326929-ytix4l1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326929-ytix4l1o.txt' === file2bib.sh === id: cord-325112-7ie23c7f author: Heimer, Carol A. title: The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date: 2018-10-04 pages: extension: .txt txt: ./txt/cord-325112-7ie23c7f.txt cache: ./cache/cord-325112-7ie23c7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325112-7ie23c7f.txt' === file2bib.sh === id: cord-325966-0g7a9s5z author: Shih, Hsin-I. title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-325966-0g7a9s5z.txt cache: ./cache/cord-325966-0g7a9s5z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325966-0g7a9s5z.txt' === file2bib.sh === id: cord-327214-kcbxyhhh author: Eketunde, Adenike O title: A Review of Postmortem Findings in Patients With COVID-19 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-327214-kcbxyhhh.txt cache: ./cache/cord-327214-kcbxyhhh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327214-kcbxyhhh.txt' === file2bib.sh === id: cord-327095-y2zsm8sc author: Boretti, Alberto title: Favipiravir use for SARS CoV-2 infection date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-327095-y2zsm8sc.txt cache: ./cache/cord-327095-y2zsm8sc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327095-y2zsm8sc.txt' === file2bib.sh === id: cord-326864-i1r3bv4p author: Hon, Kam Lun title: Coronavirus disease 2019 (COVID-19): latest developments in potential treatments date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-326864-i1r3bv4p.txt cache: ./cache/cord-326864-i1r3bv4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326864-i1r3bv4p.txt' === file2bib.sh === id: cord-326916-bakwk4tm author: Fauver, Joseph R. title: Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-326916-bakwk4tm.txt cache: ./cache/cord-326916-bakwk4tm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326916-bakwk4tm.txt' === file2bib.sh === id: cord-327240-nohxk3y6 author: Muller, Matthew P. title: Adverse Events Associated with High‐Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome date: 2012-01-06 pages: extension: .txt txt: ./txt/cord-327240-nohxk3y6.txt cache: ./cache/cord-327240-nohxk3y6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327240-nohxk3y6.txt' === file2bib.sh === id: cord-327005-7zgolyqf author: Zhang, Lan title: Clinical Features of 33 Cases in Children Infected With SARS-CoV-2 in Anhui Province, China–A Multi-Center Retrospective Cohort Study date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-327005-7zgolyqf.txt cache: ./cache/cord-327005-7zgolyqf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327005-7zgolyqf.txt' === file2bib.sh === id: cord-326883-j7pbe50g author: Stöbe, Stephan title: Echocardiographic characteristics of patients with SARS-CoV-2 infection date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-326883-j7pbe50g.txt cache: ./cache/cord-326883-j7pbe50g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326883-j7pbe50g.txt' === file2bib.sh === id: cord-326710-vc9wkcro author: Stevens, Bryan title: Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-326710-vc9wkcro.txt cache: ./cache/cord-326710-vc9wkcro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326710-vc9wkcro.txt' === file2bib.sh === id: cord-327086-u3l8nr73 author: Mauvais-Jarvis, Franck title: Estradiol, Progesterone, Immunomodulation, and COVID-19 Outcomes date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-327086-u3l8nr73.txt cache: ./cache/cord-327086-u3l8nr73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327086-u3l8nr73.txt' === file2bib.sh === id: cord-327138-l2m2g0v8 author: Ren, Chao title: Comparison of clinical laboratory tests between bacterial sepsis and SARS-CoV-2-associated viral sepsis date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-327138-l2m2g0v8.txt cache: ./cache/cord-327138-l2m2g0v8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327138-l2m2g0v8.txt' === file2bib.sh === id: cord-327459-tyhy784d author: Gómez-Rial, J. title: A strategy targeting monocyte-macrophage differentiation to avoid pulmonary complications in SARS-Cov2 infection date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-327459-tyhy784d.txt cache: ./cache/cord-327459-tyhy784d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327459-tyhy784d.txt' === file2bib.sh === id: cord-327431-dnppshnv author: Hognon, Cécilia title: Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-327431-dnppshnv.txt cache: ./cache/cord-327431-dnppshnv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327431-dnppshnv.txt' === file2bib.sh === id: cord-327124-kzavc4ez author: Wang, Ming title: SARS-CoV Infection in a Restaurant from Palm Civet date: 2005-12-17 pages: extension: .txt txt: ./txt/cord-327124-kzavc4ez.txt cache: ./cache/cord-327124-kzavc4ez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327124-kzavc4ez.txt' === file2bib.sh === id: cord-326983-h6gdck2u author: Ferretti, Andrew P. title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-326983-h6gdck2u.txt cache: ./cache/cord-326983-h6gdck2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326983-h6gdck2u.txt' === file2bib.sh === id: cord-327601-4uqgwlnx author: Bangash, Mansoor N. title: SARS-CoV-2: is the liver merely a bystander to severe disease? date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-327601-4uqgwlnx.txt cache: ./cache/cord-327601-4uqgwlnx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327601-4uqgwlnx.txt' === file2bib.sh === id: cord-327247-dbcacphq author: Grace, Sherry L. title: The Occupational and Psychosocial Impact of SARS on Academic Physicians in Three Affected Hospitals date: 2011-04-12 pages: extension: .txt txt: ./txt/cord-327247-dbcacphq.txt cache: ./cache/cord-327247-dbcacphq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327247-dbcacphq.txt' === file2bib.sh === id: cord-327499-4aps0kvp author: Zhang, Wei title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes date: 2020-02-17 pages: extension: .txt txt: ./txt/cord-327499-4aps0kvp.txt cache: ./cache/cord-327499-4aps0kvp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327499-4aps0kvp.txt' === file2bib.sh === id: cord-327084-r12copka author: Zhang, Chenxi title: Survey of Insomnia and Related Social Psychological Factors Among Medical Staff Involved in the 2019 Novel Coronavirus Disease Outbreak date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-327084-r12copka.txt cache: ./cache/cord-327084-r12copka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327084-r12copka.txt' === file2bib.sh === id: cord-326984-o27rp468 author: CHIEN, Jung‐Yien title: Temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome date: 2006-10-16 pages: extension: .txt txt: ./txt/cord-326984-o27rp468.txt cache: ./cache/cord-326984-o27rp468.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326984-o27rp468.txt' === file2bib.sh === id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-327259-7o7fs4yb.txt cache: ./cache/cord-327259-7o7fs4yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327259-7o7fs4yb.txt' === file2bib.sh === id: cord-327501-8s6dvanf author: Schwaiger, Julia title: No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-327501-8s6dvanf.txt cache: ./cache/cord-327501-8s6dvanf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327501-8s6dvanf.txt' === file2bib.sh === id: cord-327520-qj7coqfr author: Wei, Yulong title: Coronavirus genomes carry the signatures of their habitats date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-327520-qj7coqfr.txt cache: ./cache/cord-327520-qj7coqfr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327520-qj7coqfr.txt' === file2bib.sh === id: cord-327454-o1mrpgvj author: Hemmati-Dinarvand, Farshad title: Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-327454-o1mrpgvj.txt cache: ./cache/cord-327454-o1mrpgvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327454-o1mrpgvj.txt' === file2bib.sh === id: cord-327318-qhrsli0b author: Shen, Qian title: Consensus recommendations for the care of children receiving chronic dialysis in association with the COVID-19 epidemic date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-327318-qhrsli0b.txt cache: ./cache/cord-327318-qhrsli0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327318-qhrsli0b.txt' === file2bib.sh === id: cord-327653-2gn9h4i2 author: Vallinoto, Antonio Carlos Rosário title: The challenges of COVID-19 in the Brazilian Amazonian communities and the importance of seroepidemiological surveillance studies date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-327653-2gn9h4i2.txt cache: ./cache/cord-327653-2gn9h4i2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327653-2gn9h4i2.txt' === file2bib.sh === id: cord-327862-zcg3baym author: Luo, Yiqi Ruben title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-327862-zcg3baym.txt cache: ./cache/cord-327862-zcg3baym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327862-zcg3baym.txt' === file2bib.sh === id: cord-327912-wfjdxgxh author: Swann, Heather title: Minimal system for assembly of SARS-CoV-2 virus like particles date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-327912-wfjdxgxh.txt cache: ./cache/cord-327912-wfjdxgxh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327912-wfjdxgxh.txt' === file2bib.sh === id: cord-327263-d5mmeu96 author: Christoff, A. P. title: Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-327263-d5mmeu96.txt cache: ./cache/cord-327263-d5mmeu96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327263-d5mmeu96.txt' === file2bib.sh === id: cord-326498-8oa5gkrp author: Gemmati, Donato title: COVID-19 and Individual Genetic Susceptibility/Receptivity: Role of ACE1/ACE2 Genes, Immunity, Inflammation and Coagulation. Might the Double X-Chromosome in Females Be Protective against SARS-CoV-2 Compared to the Single X-Chromosome in Males? date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-326498-8oa5gkrp.txt cache: ./cache/cord-326498-8oa5gkrp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326498-8oa5gkrp.txt' === file2bib.sh === id: cord-325971-volbaipv author: Neupane, Karun title: Potential Treatment Options for COVID-19: A Comprehensive Review of Global Pharmacological Development Efforts date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-325971-volbaipv.txt cache: ./cache/cord-325971-volbaipv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325971-volbaipv.txt' === file2bib.sh === id: cord-327349-rxb6zfoc author: Au, Lewis title: Cancer, COVID-19, and antiviral immunity: the CAPTURE study date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-327349-rxb6zfoc.txt cache: ./cache/cord-327349-rxb6zfoc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327349-rxb6zfoc.txt' === file2bib.sh === id: cord-327392-9psblokc author: Srivastava, A.K. title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-327392-9psblokc.txt cache: ./cache/cord-327392-9psblokc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-327392-9psblokc.txt' === file2bib.sh === id: cord-328122-nfvbog77 author: Tresoldi, Ilaria title: SARS‐COV‐2 and infectivity: Possible increase in infectivity associated to integrin motif expression date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-328122-nfvbog77.txt cache: ./cache/cord-328122-nfvbog77.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328122-nfvbog77.txt' === file2bib.sh === id: cord-327134-egp4t82x author: Mukherjee, Prasenjit title: Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits date: 2008-04-01 pages: extension: .txt txt: ./txt/cord-327134-egp4t82x.txt cache: ./cache/cord-327134-egp4t82x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327134-egp4t82x.txt' === file2bib.sh === id: cord-327799-ngzvdd8c author: Chaumont, Claire title: The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-327799-ngzvdd8c.txt cache: ./cache/cord-327799-ngzvdd8c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-327799-ngzvdd8c.txt' === file2bib.sh === id: cord-326956-oz047qmf author: Lu, Yiping title: Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-326956-oz047qmf.txt cache: ./cache/cord-326956-oz047qmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326956-oz047qmf.txt' === file2bib.sh === id: cord-327511-e3idvknz author: Trifan, G. title: Characteristics of a Diverse Cohort of Stroke Patients with SARS-CoV-2 and Outcome by Sex date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-327511-e3idvknz.txt cache: ./cache/cord-327511-e3idvknz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327511-e3idvknz.txt' === file2bib.sh === id: cord-327933-u0fcs3yg author: Doná, Daniele title: Pediatric transplantation in Europe during the COVID‐19 pandemic: early impact on activity and healthcare date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-327933-u0fcs3yg.txt cache: ./cache/cord-327933-u0fcs3yg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327933-u0fcs3yg.txt' === file2bib.sh === id: cord-328011-6lf3no6u author: Zayed, Hatem title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-328011-6lf3no6u.txt cache: ./cache/cord-328011-6lf3no6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328011-6lf3no6u.txt' === file2bib.sh === id: cord-328074-pcvdr052 author: Fuereder, Thorsten title: Circumnavigating the challenges of COVID-19 in oncology date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-328074-pcvdr052.txt cache: ./cache/cord-328074-pcvdr052.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328074-pcvdr052.txt' === file2bib.sh === id: cord-327681-c2kmog0g author: Feng, Zhilan title: Timely identification of optimal control strategies for emerging infectious diseases() date: 2009-07-07 pages: extension: .txt txt: ./txt/cord-327681-c2kmog0g.txt cache: ./cache/cord-327681-c2kmog0g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327681-c2kmog0g.txt' === file2bib.sh === id: cord-327920-51s4figy author: Kohler, Philipp P. title: Prevalence of SARS-CoV-2 antibodies among Swiss hospital workers: Results of a prospective cohort study date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-327920-51s4figy.txt cache: ./cache/cord-327920-51s4figy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327920-51s4figy.txt' === file2bib.sh === id: cord-328073-bqeffvzl author: Limonta, Daniel title: Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-328073-bqeffvzl.txt cache: ./cache/cord-328073-bqeffvzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328073-bqeffvzl.txt' === file2bib.sh === id: cord-328242-afof417h author: Nuñez, M. A. title: Invasion Science and the Global Spread of SARS-CoV-2 date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-328242-afof417h.txt cache: ./cache/cord-328242-afof417h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328242-afof417h.txt' === file2bib.sh === id: cord-328209-uc37poce author: Javid, Babak title: Impact of population mask wearing on Covid-19 post lockdown date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-328209-uc37poce.txt cache: ./cache/cord-328209-uc37poce.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328209-uc37poce.txt' === file2bib.sh === id: cord-327808-k3jec87p author: Zhu, Yunkai title: The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-327808-k3jec87p.txt cache: ./cache/cord-327808-k3jec87p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327808-k3jec87p.txt' === file2bib.sh === id: cord-327405-xgtqfwyn author: Liu, Bing title: Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-327405-xgtqfwyn.txt cache: ./cache/cord-327405-xgtqfwyn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327405-xgtqfwyn.txt' === file2bib.sh === id: cord-328499-d6cvaxm9 author: Matzkies, Lucie-Marie title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-328499-d6cvaxm9.txt cache: ./cache/cord-328499-d6cvaxm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328499-d6cvaxm9.txt' === file2bib.sh === id: cord-327661-osx42wdh author: Schaefer, E. J. title: Coronavirus Disease-2019 Case, Death, and Testing Rates in the United States and Worldwide: Primary Data and Review date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-327661-osx42wdh.txt cache: ./cache/cord-327661-osx42wdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327661-osx42wdh.txt' === file2bib.sh === id: cord-328069-a9fi9ssg author: Pathan, Refat Khan title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-328069-a9fi9ssg.txt cache: ./cache/cord-328069-a9fi9ssg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328069-a9fi9ssg.txt' === file2bib.sh === id: cord-327690-di7hfghi author: Yang, Xiaobo title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-327690-di7hfghi.txt cache: ./cache/cord-327690-di7hfghi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327690-di7hfghi.txt' === file2bib.sh === id: cord-328505-5fkpnbdb author: Thornton, Jeanine Rempe title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-328505-5fkpnbdb.txt cache: ./cache/cord-328505-5fkpnbdb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328505-5fkpnbdb.txt' === file2bib.sh === id: cord-328040-5qd05e4r author: Zhao, Xin-Ying title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-328040-5qd05e4r.txt cache: ./cache/cord-328040-5qd05e4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328040-5qd05e4r.txt' === file2bib.sh === id: cord-327575-5pcnuqgy author: Morrisette, Taylor title: The Pharmacokinetic and Pharmacodynamic Properties of Hydroxychloroquine and Dose Selection for COVID-19: Putting the Cart Before the Horse date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-327575-5pcnuqgy.txt cache: ./cache/cord-327575-5pcnuqgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327575-5pcnuqgy.txt' === file2bib.sh === id: cord-327654-9g8zcxaa author: Chi, Xiaojing title: Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-327654-9g8zcxaa.txt cache: ./cache/cord-327654-9g8zcxaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327654-9g8zcxaa.txt' === file2bib.sh === id: cord-328680-zdwep5b2 author: Burr, Tyler title: NMDA-receptor encephalitis associated with COVID-19 infection in a toddler date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-328680-zdwep5b2.txt cache: ./cache/cord-328680-zdwep5b2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328680-zdwep5b2.txt' === file2bib.sh === id: cord-328704-m2seavg6 author: Malfertheiner, Peter title: COVID-19: Don't Neglect the Gastrointestinal Tract! date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-328704-m2seavg6.txt cache: ./cache/cord-328704-m2seavg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328704-m2seavg6.txt' === file2bib.sh === id: cord-327711-welf0eb1 author: Zhou, Daming title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-327711-welf0eb1.txt cache: ./cache/cord-327711-welf0eb1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327711-welf0eb1.txt' === file2bib.sh === id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-326017-qw4qynqv.txt cache: ./cache/cord-326017-qw4qynqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326017-qw4qynqv.txt' === file2bib.sh === id: cord-327685-fymfqvp3 author: Channappanavar, Rudragouda title: Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date: 2017-05-02 pages: extension: .txt txt: ./txt/cord-327685-fymfqvp3.txt cache: ./cache/cord-327685-fymfqvp3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327685-fymfqvp3.txt' === file2bib.sh === id: cord-328712-7q9mg2tu author: Moore, Nicholas title: Chloroquine for COVID-19 Infection date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-328712-7q9mg2tu.txt cache: ./cache/cord-328712-7q9mg2tu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328712-7q9mg2tu.txt' === file2bib.sh === id: cord-328381-bfvdhai8 author: Hattermann, K. title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-328381-bfvdhai8.txt cache: ./cache/cord-328381-bfvdhai8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328381-bfvdhai8.txt' === file2bib.sh === id: cord-327721-y39751g4 author: Zhang, Yan title: Emotional “inflection point” in public health emergencies with the 2019 New Coronavirus Pneumonia (NCP) in China date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-327721-y39751g4.txt cache: ./cache/cord-327721-y39751g4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327721-y39751g4.txt' === file2bib.sh === id: cord-328187-9zd79gai author: Zhang, Yali title: Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-328187-9zd79gai.txt cache: ./cache/cord-328187-9zd79gai.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328187-9zd79gai.txt' === file2bib.sh === id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-327000-oyg3oyx1.txt cache: ./cache/cord-327000-oyg3oyx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327000-oyg3oyx1.txt' === file2bib.sh === id: cord-328262-hw8swbt5 author: O’Neill, Luke A. J. title: BCG-induced trained immunity: can it offer protection against COVID-19? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-328262-hw8swbt5.txt cache: ./cache/cord-328262-hw8swbt5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328262-hw8swbt5.txt' === file2bib.sh === id: cord-328686-5ik5em5a author: Zhao, L. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-328686-5ik5em5a.txt cache: ./cache/cord-328686-5ik5em5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328686-5ik5em5a.txt' === file2bib.sh === id: cord-327894-b0bsseui author: Pecellín, Lidia Gestoso title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-327894-b0bsseui.txt cache: ./cache/cord-327894-b0bsseui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327894-b0bsseui.txt' === file2bib.sh === id: cord-328373-cubp1cc1 author: Jiang, Yanfang title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-328373-cubp1cc1.txt cache: ./cache/cord-328373-cubp1cc1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328373-cubp1cc1.txt' === file2bib.sh === id: cord-328585-1rkrrx8a author: Lu, Shuai title: The immunodominant and neutralization linear epitopes for SARS-CoV-2 date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-328585-1rkrrx8a.txt cache: ./cache/cord-328585-1rkrrx8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328585-1rkrrx8a.txt' === file2bib.sh === id: cord-328587-vctvcyim author: Jun, Sun title: The hypothesis that SARS-CoV-2 affects male reproductive ability by regulating autophagy date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-328587-vctvcyim.txt cache: ./cache/cord-328587-vctvcyim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328587-vctvcyim.txt' === file2bib.sh === id: cord-327616-uu9uygic author: Wazny, Vanessa title: Vascular underpinning of COVID-19 date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-327616-uu9uygic.txt cache: ./cache/cord-327616-uu9uygic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327616-uu9uygic.txt' === file2bib.sh === id: cord-328325-yonbkrwe author: Nielsen, Sandra C. A. title: B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-328325-yonbkrwe.txt cache: ./cache/cord-328325-yonbkrwe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328325-yonbkrwe.txt' === file2bib.sh === id: cord-327063-ea7a1xfl author: Dhama, Kuldeep title: SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-327063-ea7a1xfl.txt cache: ./cache/cord-327063-ea7a1xfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327063-ea7a1xfl.txt' === file2bib.sh === id: cord-327890-ocisq7e4 author: Pallett, Scott J C title: Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-327890-ocisq7e4.txt cache: ./cache/cord-327890-ocisq7e4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327890-ocisq7e4.txt' === file2bib.sh === id: cord-327622-ezgufe24 author: Kaur, Ramandeep title: Practical strategies to reduce nosocomial transmission to healthcare professionals providing respiratory care to patients with COVID-19 date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-327622-ezgufe24.txt cache: ./cache/cord-327622-ezgufe24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327622-ezgufe24.txt' === file2bib.sh === id: cord-328479-1tzysg7u author: Chen, Jianjun title: Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-328479-1tzysg7u.txt cache: ./cache/cord-328479-1tzysg7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328479-1tzysg7u.txt' === file2bib.sh === id: cord-328042-e1is656g author: Klein, Steffen title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-328042-e1is656g.txt cache: ./cache/cord-328042-e1is656g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328042-e1is656g.txt' === file2bib.sh === id: cord-329069-ejdunj41 author: Yang, He S title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-329069-ejdunj41.txt cache: ./cache/cord-329069-ejdunj41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329069-ejdunj41.txt' === file2bib.sh === id: cord-328064-7owd28rr author: Callahan, Cody J. title: Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-328064-7owd28rr.txt cache: ./cache/cord-328064-7owd28rr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328064-7owd28rr.txt' === file2bib.sh === id: cord-328856-1l7x72j7 author: Ucciferri, Claudio title: Pidotimod in Paucisymptomatic SARS-CoV2 Infected Patients date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-328856-1l7x72j7.txt cache: ./cache/cord-328856-1l7x72j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328856-1l7x72j7.txt' === file2bib.sh === id: cord-328762-2b1pl8jr author: Fuest, Matthias title: Postmortem conjunctival and nasopharyngeal swabs in SARS‐CoV‐2 infected and uninfected patients date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-328762-2b1pl8jr.txt cache: ./cache/cord-328762-2b1pl8jr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328762-2b1pl8jr.txt' === file2bib.sh === id: cord-328113-eczjjc2v author: D’Alessandro, Angelo title: Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-328113-eczjjc2v.txt cache: ./cache/cord-328113-eczjjc2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328113-eczjjc2v.txt' === file2bib.sh === id: cord-328471-oz99upzz author: Ahmad, Jamshaid title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-328471-oz99upzz.txt cache: ./cache/cord-328471-oz99upzz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328471-oz99upzz.txt' === file2bib.sh === id: cord-328396-p2gvpe8i author: Kaur, Savneet title: The Enigma of Endothelium in COVID-19 date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-328396-p2gvpe8i.txt cache: ./cache/cord-328396-p2gvpe8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328396-p2gvpe8i.txt' === file2bib.sh === id: cord-328687-clr1e9p6 author: Zhou, Fuling title: Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-328687-clr1e9p6.txt cache: ./cache/cord-328687-clr1e9p6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328687-clr1e9p6.txt' === file2bib.sh === id: cord-328705-024y5k72 author: Rahman, Md. Mahbubur title: Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-328705-024y5k72.txt cache: ./cache/cord-328705-024y5k72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328705-024y5k72.txt' === file2bib.sh === id: cord-329363-kaw3h5xm author: Vardeny, Orly title: Applying the Lessons of Influenza to COVID-19 During a Time of Uncertainty date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-329363-kaw3h5xm.txt cache: ./cache/cord-329363-kaw3h5xm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329363-kaw3h5xm.txt' === file2bib.sh === id: cord-328778-mjzsz7rz author: Steinchen, N. title: Biologikatherapie nach COVID-19-Infektion: Keine Reaktivierung einer COVID-19-Infektion bei positivem Antikörperstatus SARS-CoV-2 unter Biologikatherapie date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-328778-mjzsz7rz.txt cache: ./cache/cord-328778-mjzsz7rz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328778-mjzsz7rz.txt' === file2bib.sh === id: cord-328853-0iqdqcp6 author: Neidleman, Jason title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-328853-0iqdqcp6.txt cache: ./cache/cord-328853-0iqdqcp6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328853-0iqdqcp6.txt' === file2bib.sh === id: cord-328409-px92ff89 author: Hornuss, Daniel title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-328409-px92ff89.txt cache: ./cache/cord-328409-px92ff89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328409-px92ff89.txt' === file2bib.sh === id: cord-329290-vqvujry3 author: Kempker, Russell R title: Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-329290-vqvujry3.txt cache: ./cache/cord-329290-vqvujry3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329290-vqvujry3.txt' === file2bib.sh === id: cord-328659-miujzgtd author: Mishra, Akhilesh title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-328659-miujzgtd.txt cache: ./cache/cord-328659-miujzgtd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328659-miujzgtd.txt' === file2bib.sh === id: cord-329186-0eoz4npg author: Xia, Shuai title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-329186-0eoz4npg.txt cache: ./cache/cord-329186-0eoz4npg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329186-0eoz4npg.txt' === file2bib.sh === id: cord-328695-nptfd6c2 author: Tengs, Torstein title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-328695-nptfd6c2.txt cache: ./cache/cord-328695-nptfd6c2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328695-nptfd6c2.txt' === file2bib.sh === id: cord-328289-3h3kmjlz author: Iadecola, Costantino title: Effects of COVID-19 on the nervous system date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-328289-3h3kmjlz.txt cache: ./cache/cord-328289-3h3kmjlz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328289-3h3kmjlz.txt' === file2bib.sh === id: cord-329221-miztel9l author: rudolf, f. title: Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-329221-miztel9l.txt cache: ./cache/cord-329221-miztel9l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329221-miztel9l.txt' === file2bib.sh === id: cord-327997-noqbcxua author: Wu, Kevin E. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-327997-noqbcxua.txt cache: ./cache/cord-327997-noqbcxua.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327997-noqbcxua.txt' === file2bib.sh === id: cord-328484-4iptwc3n author: Li, Tao title: Clinical Characteristics of 312 Hospitalized Older Patients with COVID-19 in Wuhan, China date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-328484-4iptwc3n.txt cache: ./cache/cord-328484-4iptwc3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328484-4iptwc3n.txt' === file2bib.sh === id: cord-328003-yovp8squ author: Duan, Liangwei title: The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-328003-yovp8squ.txt cache: ./cache/cord-328003-yovp8squ.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328003-yovp8squ.txt' === file2bib.sh === id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-329311-p68kr4ga.txt cache: ./cache/cord-329311-p68kr4ga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329311-p68kr4ga.txt' === file2bib.sh === id: cord-328683-zvabpty9 author: Fontanet, A. title: SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-328683-zvabpty9.txt cache: ./cache/cord-328683-zvabpty9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328683-zvabpty9.txt' === file2bib.sh === id: cord-328395-2cakgmsj author: Oxford, Alexandra E. title: Endothelial Cell Contributions to COVID-19 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-328395-2cakgmsj.txt cache: ./cache/cord-328395-2cakgmsj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328395-2cakgmsj.txt' === file2bib.sh === id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-329395-4k8js9v2.txt cache: ./cache/cord-329395-4k8js9v2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329395-4k8js9v2.txt' === file2bib.sh === id: cord-329710-vqorb6j7 author: Kumar, Krishna title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-329710-vqorb6j7.txt cache: ./cache/cord-329710-vqorb6j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329710-vqorb6j7.txt' === file2bib.sh === id: cord-329454-69z28yli author: Humar, Atul title: Severe acute respiratory syndrome and the liver date: 2004-01-30 pages: extension: .txt txt: ./txt/cord-329454-69z28yli.txt cache: ./cache/cord-329454-69z28yli.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329454-69z28yli.txt' === file2bib.sh === id: cord-329129-t84pu00z author: Zuo, J title: Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-329129-t84pu00z.txt cache: ./cache/cord-329129-t84pu00z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329129-t84pu00z.txt' === file2bib.sh === id: cord-328644-odtue60a author: Comandatore, Francesco title: Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-328644-odtue60a.txt cache: ./cache/cord-328644-odtue60a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328644-odtue60a.txt' === file2bib.sh === id: cord-329328-c6svx4qa author: Reydon, Thomas A. C. title: How can science be well-ordered in times of crisis? Learning from the SARS-CoV-2 pandemic date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-329328-c6svx4qa.txt cache: ./cache/cord-329328-c6svx4qa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329328-c6svx4qa.txt' === file2bib.sh === id: cord-328962-1c4vqaqr author: Benítez-Cardoza, Claudia Guadalupe title: Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-328962-1c4vqaqr.txt cache: ./cache/cord-328962-1c4vqaqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328962-1c4vqaqr.txt' === file2bib.sh === id: cord-329473-dtlwjndn author: Guo, Ao-Xiang title: The clinical characteristics and mortal causes analysis of COVID-19 death patients date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-329473-dtlwjndn.txt cache: ./cache/cord-329473-dtlwjndn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329473-dtlwjndn.txt' === file2bib.sh === id: cord-329840-f3dsu36p author: Hati, Sanchita title: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-329840-f3dsu36p.txt cache: ./cache/cord-329840-f3dsu36p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329840-f3dsu36p.txt' === file2bib.sh === id: cord-328246-boxsf2sz author: Hadi-Alijanvand, Hamid title: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-328246-boxsf2sz.txt cache: ./cache/cord-328246-boxsf2sz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328246-boxsf2sz.txt' === file2bib.sh === id: cord-329193-xuxbqbsf author: Park, Soo-kyung title: Detection of SARS-CoV-2 in Fecal Samples from Patients with Asymptomatic and Mild COVID-19 in Korea date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-329193-xuxbqbsf.txt cache: ./cache/cord-329193-xuxbqbsf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329193-xuxbqbsf.txt' === file2bib.sh === id: cord-330074-5iqqgy65 author: Patel, Smit D. title: Malignant Cerebral Ischemia in A COVID-19 Infected Patient: Case Review and Histopathological Findings date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-330074-5iqqgy65.txt cache: ./cache/cord-330074-5iqqgy65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330074-5iqqgy65.txt' === file2bib.sh === id: cord-328960-46zui1sl author: Hillen, Hauke S. title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-328960-46zui1sl.txt cache: ./cache/cord-328960-46zui1sl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328960-46zui1sl.txt' === file2bib.sh === id: cord-328865-ekgqdjlk author: Anand, Shuchi title: Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-328865-ekgqdjlk.txt cache: ./cache/cord-328865-ekgqdjlk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328865-ekgqdjlk.txt' === file2bib.sh === id: cord-329200-o5hxpl8f author: Houlihan, Catherine F title: The complexities of SARS-CoV-2 serology date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-329200-o5hxpl8f.txt cache: ./cache/cord-329200-o5hxpl8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329200-o5hxpl8f.txt' === file2bib.sh === id: cord-329308-ipui7lo6 author: Lim, Soo title: Proper Management of People with Obesity during the COVID-19 Pandemic date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-329308-ipui7lo6.txt cache: ./cache/cord-329308-ipui7lo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329308-ipui7lo6.txt' === file2bib.sh === id: cord-329262-ybr1auo2 author: Moriel‐Carretero, María title: The hypothetical role of Phosphatidic Acid in subverting ER membranes during SARS‐CoV infection date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-329262-ybr1auo2.txt cache: ./cache/cord-329262-ybr1auo2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329262-ybr1auo2.txt' === file2bib.sh === id: cord-329010-n0mz098o author: McKee, Dwight L. title: Candidate drugs against SARS-CoV-2 and COVID-19 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-329010-n0mz098o.txt cache: ./cache/cord-329010-n0mz098o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329010-n0mz098o.txt' === file2bib.sh === id: cord-329877-vish6v8e author: Lapinsky, Stephen E. title: ICU management of severe acute respiratory syndrome date: 2003-05-09 pages: extension: .txt txt: ./txt/cord-329877-vish6v8e.txt cache: ./cache/cord-329877-vish6v8e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329877-vish6v8e.txt' === file2bib.sh === id: cord-329643-hhk900c1 author: Skalina, K. A. title: Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-329643-hhk900c1.txt cache: ./cache/cord-329643-hhk900c1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329643-hhk900c1.txt' === file2bib.sh === id: cord-328000-i9tzr13z author: Cockrell, Adam S. title: Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date: 2018-07-24 pages: extension: .txt txt: ./txt/cord-328000-i9tzr13z.txt cache: ./cache/cord-328000-i9tzr13z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328000-i9tzr13z.txt' === file2bib.sh === id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 pages: extension: .txt txt: ./txt/cord-329794-msxrdhb3.txt cache: ./cache/cord-329794-msxrdhb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329794-msxrdhb3.txt' === file2bib.sh === id: cord-329853-kf3kh26y author: Trimarchi, Hernán title: Eculizumab, SARS-CoV-2 and atypical hemolytic uremic syndrome date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-329853-kf3kh26y.txt cache: ./cache/cord-329853-kf3kh26y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329853-kf3kh26y.txt' === file2bib.sh === id: cord-328287-3qgzulgj author: Moni, Mohammad Ali title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 pages: extension: .txt txt: ./txt/cord-328287-3qgzulgj.txt cache: ./cache/cord-328287-3qgzulgj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328287-3qgzulgj.txt' === file2bib.sh === id: cord-329904-e05ywn5e author: Jose, Merin title: Fatal Superimposed Bacterial Sepsis in a Healthy Coronavirus (COVID-19) Patient date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-329904-e05ywn5e.txt cache: ./cache/cord-329904-e05ywn5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329904-e05ywn5e.txt' === file2bib.sh === id: cord-330045-4gj9d181 author: Sun, Jiufeng title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-330045-4gj9d181.txt cache: ./cache/cord-330045-4gj9d181.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330045-4gj9d181.txt' === file2bib.sh === id: cord-330031-c1n994j6 author: Kratzel, Annika title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-330031-c1n994j6.txt cache: ./cache/cord-330031-c1n994j6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330031-c1n994j6.txt' === file2bib.sh === id: cord-329944-ywusapij author: Harbourt, D. title: Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-329944-ywusapij.txt cache: ./cache/cord-329944-ywusapij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329944-ywusapij.txt' === file2bib.sh === id: cord-329011-spiuqngp author: Huang, Yuan title: Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-329011-spiuqngp.txt cache: ./cache/cord-329011-spiuqngp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329011-spiuqngp.txt' === file2bib.sh === id: cord-329041-coryaz2s author: Brown, Ariane J. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-329041-coryaz2s.txt cache: ./cache/cord-329041-coryaz2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329041-coryaz2s.txt' === file2bib.sh === id: cord-329392-fufattj8 author: den Hartog, Gerco title: SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-329392-fufattj8.txt cache: ./cache/cord-329392-fufattj8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329392-fufattj8.txt' === file2bib.sh === id: cord-330067-ujhgb3b0 author: Huang, Yi title: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes date: 2007-10-02 pages: extension: .txt txt: ./txt/cord-330067-ujhgb3b0.txt cache: ./cache/cord-330067-ujhgb3b0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330067-ujhgb3b0.txt' === file2bib.sh === id: cord-329707-89zyu8bl author: Zhang, Xue title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date: 2006-11-30 pages: extension: .txt txt: ./txt/cord-329707-89zyu8bl.txt cache: ./cache/cord-329707-89zyu8bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329707-89zyu8bl.txt' === file2bib.sh === id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-329504-91te3nu8.txt cache: ./cache/cord-329504-91te3nu8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329504-91te3nu8.txt' === file2bib.sh === id: cord-329318-eo8auo1f author: Gusarov, Sergey title: COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2 date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-329318-eo8auo1f.txt cache: ./cache/cord-329318-eo8auo1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329318-eo8auo1f.txt' === file2bib.sh === id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 pages: extension: .txt txt: ./txt/cord-329493-ueqlhgn0.txt cache: ./cache/cord-329493-ueqlhgn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329493-ueqlhgn0.txt' === file2bib.sh === id: cord-329914-3b233vxl author: Plantier, L. title: Pratique des explorations fonctionnelles respiratoires pendant l’épidémie COVID-19 date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-329914-3b233vxl.txt cache: ./cache/cord-329914-3b233vxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329914-3b233vxl.txt' === file2bib.sh === id: cord-329971-09ubsq2k author: Tranoulis, Anastasios title: Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-329971-09ubsq2k.txt cache: ./cache/cord-329971-09ubsq2k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-329971-09ubsq2k.txt' === file2bib.sh === id: cord-330473-f03ka7bd author: Yuan, Meng title: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date: 2020-03-14 pages: extension: .txt txt: ./txt/cord-330473-f03ka7bd.txt cache: ./cache/cord-330473-f03ka7bd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330473-f03ka7bd.txt' === file2bib.sh === id: cord-329825-e9mepqvn author: Giamarellos-Bourboulis, Evangelos J. title: Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-329825-e9mepqvn.txt cache: ./cache/cord-329825-e9mepqvn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329825-e9mepqvn.txt' === file2bib.sh === id: cord-330692-rqwkkfp0 author: He, Daihai title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-330692-rqwkkfp0.txt cache: ./cache/cord-330692-rqwkkfp0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-330692-rqwkkfp0.txt' === file2bib.sh === id: cord-329240-atisrhas author: Fedorenko, Aliza title: Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-329240-atisrhas.txt cache: ./cache/cord-329240-atisrhas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329240-atisrhas.txt' === file2bib.sh === id: cord-328557-f6o1aynz author: Samad, Abdus title: Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-328557-f6o1aynz.txt cache: ./cache/cord-328557-f6o1aynz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328557-f6o1aynz.txt' === file2bib.sh === id: cord-330061-q4xi260z author: Ferreira, João Guimarães title: Pneumothorax as a late complication of COVID-19 date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-330061-q4xi260z.txt cache: ./cache/cord-330061-q4xi260z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330061-q4xi260z.txt' === file2bib.sh === id: cord-329959-4yecwdlo author: Lin, Min-Han title: Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes date: 2017-12-28 pages: extension: .txt txt: ./txt/cord-329959-4yecwdlo.txt cache: ./cache/cord-329959-4yecwdlo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329959-4yecwdlo.txt' === file2bib.sh === id: cord-330093-asba80bi author: Leung, Janice M. title: Smoking, ACE-2 and COVID-19: ongoing controversies date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-330093-asba80bi.txt cache: ./cache/cord-330093-asba80bi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330093-asba80bi.txt' === file2bib.sh === id: cord-330478-g9n2mfni author: Hattenbach, Lars-Olof title: Krisenstrategien der Kliniken während der Pandemie date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-330478-g9n2mfni.txt cache: ./cache/cord-330478-g9n2mfni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330478-g9n2mfni.txt' === file2bib.sh === id: cord-330121-eadu2ba3 author: Gudmundsdottir, Ágústa title: Inactivation of SARS‐CoV‐2 and HCoV‐229E in vitro by ColdZyme® a medical device mouth spray against common cold date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-330121-eadu2ba3.txt cache: ./cache/cord-330121-eadu2ba3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330121-eadu2ba3.txt' === file2bib.sh === id: cord-330129-izr62c68 author: Omer, Sumaira title: Preventive measures and management of COVID-19 in pregnancy date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-330129-izr62c68.txt cache: ./cache/cord-330129-izr62c68.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330129-izr62c68.txt' === file2bib.sh === id: cord-330387-7lci44w5 author: Bird, Paul title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-330387-7lci44w5.txt cache: ./cache/cord-330387-7lci44w5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330387-7lci44w5.txt' === file2bib.sh === id: cord-329190-kv9n2qj3 author: Rabaan, Ali A. title: A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective date: 2017-09-01 pages: extension: .txt txt: ./txt/cord-329190-kv9n2qj3.txt cache: ./cache/cord-329190-kv9n2qj3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329190-kv9n2qj3.txt' === file2bib.sh === id: cord-330433-y5dvlcda author: Olivieri, Emily R. title: Analysis of SARS-CoV Receptor Activity of ACE2 Orthologs date: 2006 pages: extension: .txt txt: ./txt/cord-330433-y5dvlcda.txt cache: ./cache/cord-330433-y5dvlcda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330433-y5dvlcda.txt' === file2bib.sh === id: cord-330022-n3d130t8 author: Pan, Daniel title: The impact of ethnicity on clinical outcomes in COVID-19: A systematic review date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-330022-n3d130t8.txt cache: ./cache/cord-330022-n3d130t8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330022-n3d130t8.txt' === file2bib.sh === id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-330131-yfhrmbvx.txt cache: ./cache/cord-330131-yfhrmbvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330131-yfhrmbvx.txt' === file2bib.sh === id: cord-330338-i6ozygkp author: Babacic, H. title: Global between-countries variance in SARS-CoV-2 mortality is driven by reported prevalence, age distribution, and case detection rate date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-330338-i6ozygkp.txt cache: ./cache/cord-330338-i6ozygkp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330338-i6ozygkp.txt' === file2bib.sh === id: cord-330536-q8zr0mkl author: Lopinto, Julien title: Severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-330536-q8zr0mkl.txt cache: ./cache/cord-330536-q8zr0mkl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330536-q8zr0mkl.txt' === file2bib.sh === id: cord-330213-reb9vo7x author: Miladi, Milad title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-330213-reb9vo7x.txt cache: ./cache/cord-330213-reb9vo7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330213-reb9vo7x.txt' === file2bib.sh === id: cord-330369-75cotmn2 author: López, Verónica title: Recommendations on management of the SARS-CoV-2 coronavirus pandemic (Covid-19) in kidney transplant patients date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-330369-75cotmn2.txt cache: ./cache/cord-330369-75cotmn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330369-75cotmn2.txt' === file2bib.sh === id: cord-330717-uzrxtgrg author: Gupta, Madhu title: The need for COVID-19 research in low- and middle-income countries date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-330717-uzrxtgrg.txt cache: ./cache/cord-330717-uzrxtgrg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330717-uzrxtgrg.txt' === file2bib.sh === id: cord-330807-abi8pra7 author: Garcia-Pachon, Eduardo title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-330807-abi8pra7.txt cache: ./cache/cord-330807-abi8pra7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330807-abi8pra7.txt' === file2bib.sh === id: cord-330198-pwkxgbxk author: Cai, Xiaofang title: Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19 date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-330198-pwkxgbxk.txt cache: ./cache/cord-330198-pwkxgbxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330198-pwkxgbxk.txt' === file2bib.sh === id: cord-330200-l6bnxi40 author: Huang, Jianping title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-330200-l6bnxi40.txt cache: ./cache/cord-330200-l6bnxi40.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330200-l6bnxi40.txt' === file2bib.sh === id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-329102-2y49kcwu.txt cache: ./cache/cord-329102-2y49kcwu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329102-2y49kcwu.txt' === file2bib.sh === id: cord-329876-4cgrjnjo author: Lei, Jian title: Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin date: 2016-05-30 pages: extension: .txt txt: ./txt/cord-329876-4cgrjnjo.txt cache: ./cache/cord-329876-4cgrjnjo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329876-4cgrjnjo.txt' === file2bib.sh === id: cord-330384-yujbcwg5 author: Al-Mulla, Fahd title: A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-330384-yujbcwg5.txt cache: ./cache/cord-330384-yujbcwg5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330384-yujbcwg5.txt' === file2bib.sh === id: cord-330266-uypjqif7 author: Firpo, Mason R. title: Targeting Polyamines Inhibits Coronavirus Infection by Reducing Cellular Attachment and Entry date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-330266-uypjqif7.txt cache: ./cache/cord-330266-uypjqif7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330266-uypjqif7.txt' === file2bib.sh === id: cord-330887-q5i8lpan author: Li, K. title: The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-330887-q5i8lpan.txt cache: ./cache/cord-330887-q5i8lpan.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330887-q5i8lpan.txt' === file2bib.sh === id: cord-330597-nftwj0d5 author: Hopfer, Helmut title: Hunting coronavirus by transmission electron microscopy – a guide to SARS‐CoV‐2‐associated ultrastructural pathology in COVID‐19 tissues date: 2020-09-27 pages: extension: .txt txt: ./txt/cord-330597-nftwj0d5.txt cache: ./cache/cord-330597-nftwj0d5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330597-nftwj0d5.txt' === file2bib.sh === id: cord-329890-wg23sa1u author: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 pages: extension: .txt txt: ./txt/cord-329890-wg23sa1u.txt cache: ./cache/cord-329890-wg23sa1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329890-wg23sa1u.txt' === file2bib.sh === id: cord-330607-zn4urrxc author: Chi, Qiong title: Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-330607-zn4urrxc.txt cache: ./cache/cord-330607-zn4urrxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330607-zn4urrxc.txt' === file2bib.sh === id: cord-330626-0aidit63 author: Sepulveda, Jorge title: Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-330626-0aidit63.txt cache: ./cache/cord-330626-0aidit63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330626-0aidit63.txt' === file2bib.sh === id: cord-330873-hwbdreul author: Yang, Wan title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-330873-hwbdreul.txt cache: ./cache/cord-330873-hwbdreul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330873-hwbdreul.txt' === file2bib.sh === id: cord-331283-bfyoavon author: Meca-Lallana, Dra. Virginia title: COVID-19 IN 7 MULTIPLE SCLEROSIS PATIENTS IN TREATMENT WITH ANTI-CD20 THERAPIES date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-331283-bfyoavon.txt cache: ./cache/cord-331283-bfyoavon.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331283-bfyoavon.txt' === file2bib.sh === id: cord-331002-7uojryqz author: Valent, Francesca title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-331002-7uojryqz.txt cache: ./cache/cord-331002-7uojryqz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331002-7uojryqz.txt' === file2bib.sh === id: cord-330779-mso2zfom author: Sunkari, Emmanuel Daanoba title: Sources and routes of SARS-CoV-2 transmission in water systems in Africa: Are there any sustainable remedies? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-330779-mso2zfom.txt cache: ./cache/cord-330779-mso2zfom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330779-mso2zfom.txt' === file2bib.sh === id: cord-330287-bkqjkhwu author: Miller, Danielle title: Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-330287-bkqjkhwu.txt cache: ./cache/cord-330287-bkqjkhwu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330287-bkqjkhwu.txt' === file2bib.sh === id: cord-330868-7ocseuz3 author: Donnelly, Christl A title: Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong date: 2003-05-24 pages: extension: .txt txt: ./txt/cord-330868-7ocseuz3.txt cache: ./cache/cord-330868-7ocseuz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330868-7ocseuz3.txt' === file2bib.sh === id: cord-330337-d41imvo7 author: Basu, Souradip title: Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-330337-d41imvo7.txt cache: ./cache/cord-330337-d41imvo7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330337-d41imvo7.txt' === file2bib.sh === id: cord-330701-k68b0wqe author: Gerc, Vjekoslav title: Cardiovascular Diseases (CVDs) in COVID-19 Pandemic Era date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-330701-k68b0wqe.txt cache: ./cache/cord-330701-k68b0wqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330701-k68b0wqe.txt' === file2bib.sh === id: cord-330908-402eb8wg author: Tsuji, Motonori title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-330908-402eb8wg.txt cache: ./cache/cord-330908-402eb8wg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330908-402eb8wg.txt' === file2bib.sh === id: cord-331300-u5fltc10 author: Patel, Jay title: Viability of SARS‐CoV‐2 in faecal bio‐aerosols date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-331300-u5fltc10.txt cache: ./cache/cord-331300-u5fltc10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331300-u5fltc10.txt' === file2bib.sh === id: cord-331140-5b0y1xzb author: Cardona Maya, Walter D. title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-331140-5b0y1xzb.txt cache: ./cache/cord-331140-5b0y1xzb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-331140-5b0y1xzb.txt' === file2bib.sh === id: cord-331428-6pvr2vew author: Heffernan, Kevin S. title: Exercise as medicine for COVID-19: on PPAR with emerging pharmacotherapy date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-331428-6pvr2vew.txt cache: ./cache/cord-331428-6pvr2vew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331428-6pvr2vew.txt' === file2bib.sh === id: cord-331010-4phhz79k author: Knight, M. title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-331010-4phhz79k.txt cache: ./cache/cord-331010-4phhz79k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331010-4phhz79k.txt' === file2bib.sh === id: cord-330814-7incf20e author: Parikh, Priyanka A title: COVID-19 Pandemic: Knowledge and Perceptions of the Public and Healthcare Professionals date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-330814-7incf20e.txt cache: ./cache/cord-330814-7incf20e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330814-7incf20e.txt' === file2bib.sh === id: cord-331060-b3z1zb4t author: Cruickshank, Marilyn title: COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-331060-b3z1zb4t.txt cache: ./cache/cord-331060-b3z1zb4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331060-b3z1zb4t.txt' === file2bib.sh === id: cord-330690-cupy89gl author: Vierucci, Francesco title: How COVID-19 Pandemic Changed Children and Adolescents Use of the Emergency Department: the Experience of a Secondary Care Pediatric Unit in Central Italy date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-330690-cupy89gl.txt cache: ./cache/cord-330690-cupy89gl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330690-cupy89gl.txt' === file2bib.sh === id: cord-331076-ak481qew author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-331076-ak481qew.txt cache: ./cache/cord-331076-ak481qew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331076-ak481qew.txt' === file2bib.sh === id: cord-330743-o11d0aa1 author: Yu, Xi title: Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-330743-o11d0aa1.txt cache: ./cache/cord-330743-o11d0aa1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330743-o11d0aa1.txt' === file2bib.sh === id: cord-330315-upcf15q5 author: Oudshoorn, Diede title: Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication date: 2017-11-21 pages: extension: .txt txt: ./txt/cord-330315-upcf15q5.txt cache: ./cache/cord-330315-upcf15q5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330315-upcf15q5.txt' === file2bib.sh === id: cord-330827-gu2mt6zp author: Shanmugaraj, Balamurugan title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-330827-gu2mt6zp.txt cache: ./cache/cord-330827-gu2mt6zp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330827-gu2mt6zp.txt' === file2bib.sh === id: cord-330324-4hqhty5o author: Yu, Meng title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date: 2008-02-29 pages: extension: .txt txt: ./txt/cord-330324-4hqhty5o.txt cache: ./cache/cord-330324-4hqhty5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330324-4hqhty5o.txt' === file2bib.sh === id: cord-331109-a8e7r80d author: Ibrahim, Yassmin S. title: Case Report: Paralytic Ileus: A Potential Extrapulmonary Manifestation of Severe COVID-19 date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-331109-a8e7r80d.txt cache: ./cache/cord-331109-a8e7r80d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331109-a8e7r80d.txt' === file2bib.sh === id: cord-331423-5wpx0bd0 author: Pelea, Teodor title: SARS-CoV-2 associated Guillain–Barré syndrome date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-331423-5wpx0bd0.txt cache: ./cache/cord-331423-5wpx0bd0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331423-5wpx0bd0.txt' === file2bib.sh === id: cord-330944-54xmnum8 author: Hsu, You-Ren title: Investigation of C-terminal domain of SARS nucleocapsid protein–Duplex DNA interaction using transistors and binding-site models date: 2014-03-31 pages: extension: .txt txt: ./txt/cord-330944-54xmnum8.txt cache: ./cache/cord-330944-54xmnum8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330944-54xmnum8.txt' === file2bib.sh === id: cord-331571-v01kstbr author: Rossoff, Jenna title: Benign course of SARS‐CoV‐2 infection in a series of pediatric oncology patients date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-331571-v01kstbr.txt cache: ./cache/cord-331571-v01kstbr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331571-v01kstbr.txt' === file2bib.sh === id: cord-331465-humpwwk2 author: Canaday, David H title: On setting expectations for a SARS-CoV-2 Vaccine date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-331465-humpwwk2.txt cache: ./cache/cord-331465-humpwwk2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331465-humpwwk2.txt' === file2bib.sh === id: cord-331055-5ni0jxij author: Bouche, Pierre-Alban title: Were protective procedures against SARS-CoV-2 effective in an orthopaedic and trauma centre during the lockdown period? A retrospective study date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-331055-5ni0jxij.txt cache: ./cache/cord-331055-5ni0jxij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331055-5ni0jxij.txt' === file2bib.sh === id: cord-330465-16j5vm7h author: Marciniec, Krzysztof title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-330465-16j5vm7h.txt cache: ./cache/cord-330465-16j5vm7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330465-16j5vm7h.txt' === file2bib.sh === id: cord-330715-olypwdoq author: Sun, Zeyu title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date: 2020-08-30 pages: extension: .txt txt: ./txt/cord-330715-olypwdoq.txt cache: ./cache/cord-330715-olypwdoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330715-olypwdoq.txt' === file2bib.sh === id: cord-331701-izkz1hz4 author: Eden, John-Sebastian title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-331701-izkz1hz4.txt cache: ./cache/cord-331701-izkz1hz4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331701-izkz1hz4.txt' === file2bib.sh === id: cord-331147-numz9onx author: Al‐Kofahi, Mahmoud title: Finding the Dose for Hydroxychloroquine Prophylaxis for COVID‐19: The Desperate Search for Effectiveness date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-331147-numz9onx.txt cache: ./cache/cord-331147-numz9onx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331147-numz9onx.txt' === file2bib.sh === id: cord-331429-mh2hd5fe author: Srikantiah, Padmini title: SARS Clinical Features, United States, 2003 date: 2005-01-17 pages: extension: .txt txt: ./txt/cord-331429-mh2hd5fe.txt cache: ./cache/cord-331429-mh2hd5fe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331429-mh2hd5fe.txt' === file2bib.sh === id: cord-330849-yt44k88m author: Han, Rachel H. title: Planning for Mental Health Needs During COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-330849-yt44k88m.txt cache: ./cache/cord-330849-yt44k88m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330849-yt44k88m.txt' === file2bib.sh === id: cord-331243-0u65qguq author: Ucciferri, Claudio title: Role of monoclonal antibody drugs in the treatment of COVID-19 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-331243-0u65qguq.txt cache: ./cache/cord-331243-0u65qguq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331243-0u65qguq.txt' === file2bib.sh === id: cord-330583-ltkpt80u author: Lee, Kyu-Myoung title: Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date: 2019-04-22 pages: extension: .txt txt: ./txt/cord-330583-ltkpt80u.txt cache: ./cache/cord-330583-ltkpt80u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330583-ltkpt80u.txt' === file2bib.sh === id: cord-331066-ediowz4s author: Chechetkin, Vladimir R. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-331066-ediowz4s.txt cache: ./cache/cord-331066-ediowz4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331066-ediowz4s.txt' === file2bib.sh === id: cord-331087-kpze9xux author: Siddiqui, S. title: SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-331087-kpze9xux.txt cache: ./cache/cord-331087-kpze9xux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331087-kpze9xux.txt' === file2bib.sh === id: cord-331930-w2055c42 author: Tso, Eugene Y. K. title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date: 2004-05-01 pages: extension: .txt txt: ./txt/cord-331930-w2055c42.txt cache: ./cache/cord-331930-w2055c42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-331930-w2055c42.txt' === file2bib.sh === id: cord-330994-6nu7utu1 author: Abdelrheem, Doaa A. title: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-330994-6nu7utu1.txt cache: ./cache/cord-330994-6nu7utu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330994-6nu7utu1.txt' === file2bib.sh === id: cord-331520-o9e4qqn4 author: Kistler, Christine E. title: The Winter Respiratory Viral Season During the COVID-19 Pandemic date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-331520-o9e4qqn4.txt cache: ./cache/cord-331520-o9e4qqn4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331520-o9e4qqn4.txt' === file2bib.sh === id: cord-331831-gw42e6ce author: Moore, Luke S P title: Near-patient SARS-CoV-2 molecular platforms: new-old tools for new-old problems date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-331831-gw42e6ce.txt cache: ./cache/cord-331831-gw42e6ce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331831-gw42e6ce.txt' === file2bib.sh === id: cord-331856-j0gedx43 author: Basile, K. title: Accuracy amidst ambiguity: false positive SARS-CoV-2 nucleic acid tests when COVID-19 prevalence is low date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-331856-j0gedx43.txt cache: ./cache/cord-331856-j0gedx43.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331856-j0gedx43.txt' === file2bib.sh === id: cord-331193-33cyvidx author: Mawhinney, Jamie A title: Neurotropism of SARS-CoV-2: COVID-19 presenting with an acute manic episode date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-331193-33cyvidx.txt cache: ./cache/cord-331193-33cyvidx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331193-33cyvidx.txt' === file2bib.sh === id: cord-331825-dwi350c0 author: Teherani, Mehgan F title: Burden of illness in households with SARS-CoV-2 infected children date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-331825-dwi350c0.txt cache: ./cache/cord-331825-dwi350c0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331825-dwi350c0.txt' === file2bib.sh === id: cord-331472-kd4uxcve author: Shahid, Zainab title: COVID‐19 and Older Adults: What We Know date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-331472-kd4uxcve.txt cache: ./cache/cord-331472-kd4uxcve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331472-kd4uxcve.txt' === file2bib.sh === id: cord-331517-o5ejfq86 author: Hirayama, Takehisa title: Guillain-Barré syndrome after COVID-19 in Japan date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-331517-o5ejfq86.txt cache: ./cache/cord-331517-o5ejfq86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331517-o5ejfq86.txt' === file2bib.sh === id: cord-331277-fjsuo3yy author: Hoste, Alexis C.R. title: Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: A screening tool and a point-of-care test date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-331277-fjsuo3yy.txt cache: ./cache/cord-331277-fjsuo3yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331277-fjsuo3yy.txt' === file2bib.sh === id: cord-331039-qgom2e3n author: Kavitha, Kuppuswamy title: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-331039-qgom2e3n.txt cache: ./cache/cord-331039-qgom2e3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331039-qgom2e3n.txt' === file2bib.sh === id: cord-331807-ooym5eh3 author: Wu, Tao title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-331807-ooym5eh3.txt cache: ./cache/cord-331807-ooym5eh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331807-ooym5eh3.txt' === file2bib.sh === id: cord-331611-pwj226j0 author: Shrimp, Jonathan H. title: An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-331611-pwj226j0.txt cache: ./cache/cord-331611-pwj226j0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331611-pwj226j0.txt' === file2bib.sh === id: cord-331790-0w0pjjg1 author: Abu Jawdeh, Bassam G. title: COVID-19 in Kidney Transplantation: Outcomes, Immunosuppression Management and Operational Challenges date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-331790-0w0pjjg1.txt cache: ./cache/cord-331790-0w0pjjg1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-331790-0w0pjjg1.txt' === file2bib.sh === id: cord-331155-jkm4fuw4 author: Nakashima, Akiko title: Virus database annotations assist in tracing information on patients infected with emerging pathogens date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-331155-jkm4fuw4.txt cache: ./cache/cord-331155-jkm4fuw4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331155-jkm4fuw4.txt' === file2bib.sh === id: cord-331666-iwkuwnun author: Schweitzer, Wolf title: Implications for forensic death investigations from first Swiss post-mortem CT in a case of non-hospital treatment with COVID-19 date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-331666-iwkuwnun.txt cache: ./cache/cord-331666-iwkuwnun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331666-iwkuwnun.txt' === file2bib.sh === id: cord-331617-1ytcd0ax author: Horvath, Karl title: Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-331617-1ytcd0ax.txt cache: ./cache/cord-331617-1ytcd0ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331617-1ytcd0ax.txt' === file2bib.sh === id: cord-332080-923jpec0 author: Lai, Chih-Cheng title: In vitro diagnostics of coronavirus disease 2019: technologies and application date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-332080-923jpec0.txt cache: ./cache/cord-332080-923jpec0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332080-923jpec0.txt' === file2bib.sh === id: cord-331496-5xak7z6b author: Garnett, Emily title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-331496-5xak7z6b.txt cache: ./cache/cord-331496-5xak7z6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331496-5xak7z6b.txt' === file2bib.sh === id: cord-331547-uqmjhhna author: Bonalumi, Giorgia title: A call to action becomes practice: cardiac and vascular surgery during the COVID-19 pandemic based on the Lombardy emergency guidelines date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-331547-uqmjhhna.txt cache: ./cache/cord-331547-uqmjhhna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331547-uqmjhhna.txt' === file2bib.sh === id: cord-331558-6rqd3fmj author: Sun, Chuan-bin title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-331558-6rqd3fmj.txt cache: ./cache/cord-331558-6rqd3fmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331558-6rqd3fmj.txt' === file2bib.sh === id: cord-331871-colmj7uk author: Feehan, A. K. title: Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-331871-colmj7uk.txt cache: ./cache/cord-331871-colmj7uk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331871-colmj7uk.txt' === file2bib.sh === id: cord-331835-nuhrd92z author: Hung, Kevin K. C. title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-331835-nuhrd92z.txt cache: ./cache/cord-331835-nuhrd92z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-331835-nuhrd92z.txt' === file2bib.sh === id: cord-332134-88wfcc3y author: Li, Tingting title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-332134-88wfcc3y.txt cache: ./cache/cord-332134-88wfcc3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332134-88wfcc3y.txt' === file2bib.sh === id: cord-331927-b7pfm3i0 author: Winn, Soe P title: Diabetic Ketoacidosis in Coronavirus Disease Patients With Type 2 Diabetes Mellitus date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-331927-b7pfm3i0.txt cache: ./cache/cord-331927-b7pfm3i0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331927-b7pfm3i0.txt' === file2bib.sh === id: cord-331541-u0xm9a89 author: Lankes, Heather A title: Biospecimen Collection During the COVID-19 Pandemic: Considerations for Biobanking date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-331541-u0xm9a89.txt cache: ./cache/cord-331541-u0xm9a89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331541-u0xm9a89.txt' === file2bib.sh === id: cord-332292-n7k4va9k author: Yen, Yung-Feng title: Olfactory disorder in patients infected with SARS-CoV-2 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-332292-n7k4va9k.txt cache: ./cache/cord-332292-n7k4va9k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332292-n7k4va9k.txt' === file2bib.sh === id: cord-331022-tek4u751 author: Sinderewicz, Emilia title: Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-331022-tek4u751.txt cache: ./cache/cord-331022-tek4u751.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331022-tek4u751.txt' === file2bib.sh === id: cord-332076-b0qtzzac author: Zhen, Wei title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-332076-b0qtzzac.txt cache: ./cache/cord-332076-b0qtzzac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332076-b0qtzzac.txt' === file2bib.sh === id: cord-332178-0xyrmk5a author: Chadchan, Sangappa B. title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-332178-0xyrmk5a.txt cache: ./cache/cord-332178-0xyrmk5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332178-0xyrmk5a.txt' === file2bib.sh === id: cord-332196-03cklmm3 author: Kennedy, Amy J. title: Retesting for severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Patterns of testing from a large US healthcare system date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-332196-03cklmm3.txt cache: ./cache/cord-332196-03cklmm3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332196-03cklmm3.txt' === file2bib.sh === id: cord-332268-x30svp5y author: Bearden, Donna M. title: COVID-19: a primer for healthcare providers date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-332268-x30svp5y.txt cache: ./cache/cord-332268-x30svp5y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332268-x30svp5y.txt' === file2bib.sh === id: cord-331680-qlzhtxs0 author: Goryachev, A.N. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-331680-qlzhtxs0.txt cache: ./cache/cord-331680-qlzhtxs0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331680-qlzhtxs0.txt' === file2bib.sh === id: cord-331878-ww9fu8ey author: Gao, Xiaopan title: Crystal structure of SARS-CoV-2 papain-like protease date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-331878-ww9fu8ey.txt cache: ./cache/cord-331878-ww9fu8ey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331878-ww9fu8ey.txt' === file2bib.sh === id: cord-332271-slouuryl author: Baker, Jeremy D. title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-332271-slouuryl.txt cache: ./cache/cord-332271-slouuryl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332271-slouuryl.txt' === file2bib.sh === id: cord-331563-4yvfdqbq author: Chughtai, Abrar Ahmad title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis date: 2013-05-31 pages: extension: .txt txt: ./txt/cord-331563-4yvfdqbq.txt cache: ./cache/cord-331563-4yvfdqbq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331563-4yvfdqbq.txt' === file2bib.sh === id: cord-331786-wgt7kg6f author: Diego-Martin, Borja title: Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-331786-wgt7kg6f.txt cache: ./cache/cord-331786-wgt7kg6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331786-wgt7kg6f.txt' === file2bib.sh === id: cord-332013-bl5d4xkc author: Sánchez-Álvarez, J. Emilio title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-332013-bl5d4xkc.txt cache: ./cache/cord-332013-bl5d4xkc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332013-bl5d4xkc.txt' === file2bib.sh === id: cord-331094-22366b81 author: Ianevski, Aleksandr title: Potential Antiviral Options against SARS-CoV-2 Infection date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-331094-22366b81.txt cache: ./cache/cord-331094-22366b81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331094-22366b81.txt' === file2bib.sh === id: cord-332245-yfj1kkj7 author: nan title: SARS-CoV-2 Infektion bei Kindern und Jugendlichen: Ein Literaturüberblick der AG Infektiologie der ÖGKJ1 date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-332245-yfj1kkj7.txt cache: ./cache/cord-332245-yfj1kkj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332245-yfj1kkj7.txt' === file2bib.sh === id: cord-332185-a96r1k7a author: Zhang, Shuyuan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-332185-a96r1k7a.txt cache: ./cache/cord-332185-a96r1k7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332185-a96r1k7a.txt' === file2bib.sh === id: cord-332065-afq26621 author: Ghanchi, Hammad title: Racial Disparity Amongst Stroke Patients During the Coronavirus Disease 2019 Pandemic date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-332065-afq26621.txt cache: ./cache/cord-332065-afq26621.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332065-afq26621.txt' === file2bib.sh === id: cord-332469-zegawla5 author: Li, Wei title: The characteristics of household transmission of COVID-19 date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-332469-zegawla5.txt cache: ./cache/cord-332469-zegawla5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332469-zegawla5.txt' === file2bib.sh === id: cord-332312-od3vjuw5 author: Pagani, G. title: Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA). date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-332312-od3vjuw5.txt cache: ./cache/cord-332312-od3vjuw5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332312-od3vjuw5.txt' === file2bib.sh === id: cord-329844-w969lczb author: Robson, B. title: Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-329844-w969lczb.txt cache: ./cache/cord-329844-w969lczb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329844-w969lczb.txt' === file2bib.sh === id: cord-332300-5osg046o author: Yu, Luo title: Catching and killing of airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-332300-5osg046o.txt cache: ./cache/cord-332300-5osg046o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332300-5osg046o.txt' === file2bib.sh === id: cord-332207-dmxbk7ad author: Sastry, Sangeeta R. title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-332207-dmxbk7ad.txt cache: ./cache/cord-332207-dmxbk7ad.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332207-dmxbk7ad.txt' === file2bib.sh === id: cord-332458-2kwfcgz9 author: Ji, Henry title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-332458-2kwfcgz9.txt cache: ./cache/cord-332458-2kwfcgz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332458-2kwfcgz9.txt' === file2bib.sh === id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-330800-s91zfzfi.txt cache: ./cache/cord-330800-s91zfzfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330800-s91zfzfi.txt' === file2bib.sh === id: cord-332150-j76726no author: De Stefano, Ludovico title: A “Window of Therapeutic Opportunity” for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-332150-j76726no.txt cache: ./cache/cord-332150-j76726no.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332150-j76726no.txt' === file2bib.sh === id: cord-332374-cbiw6yvb author: Israeli, Ofir title: Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-332374-cbiw6yvb.txt cache: ./cache/cord-332374-cbiw6yvb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332374-cbiw6yvb.txt' === file2bib.sh === id: cord-331375-tbuijeje author: Villalobos, Carlos title: SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-331375-tbuijeje.txt cache: ./cache/cord-331375-tbuijeje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331375-tbuijeje.txt' === file2bib.sh === id: cord-332278-2p64ab2z author: Vivas, David title: Recomendaciones sobre el tratamiento antitrombótico durante la pandemia COVID-19. Posicionamiento del Grupo de Trabajo de Trombosis Cardiovascular de la Sociedad Española de Cardiología date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-332278-2p64ab2z.txt cache: ./cache/cord-332278-2p64ab2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332278-2p64ab2z.txt' === file2bib.sh === id: cord-332510-x3znuwc0 author: Freire-Álvarez, Eric title: COVID-19-associated encephalitis successfully treated with combination therapy date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-332510-x3znuwc0.txt cache: ./cache/cord-332510-x3znuwc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332510-x3znuwc0.txt' === file2bib.sh === id: cord-332537-rtdu4jae author: Tong, Tommy R. title: Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date: 2005-05-01 pages: extension: .txt txt: ./txt/cord-332537-rtdu4jae.txt cache: ./cache/cord-332537-rtdu4jae.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332537-rtdu4jae.txt' === file2bib.sh === id: cord-332555-jfqlkd72 author: Du, Hengzhi title: The potential effects of DPP‐4 inhibitors on cardiovascular system in COVID‐19 patients date: 2020-07-26 pages: extension: .txt txt: ./txt/cord-332555-jfqlkd72.txt cache: ./cache/cord-332555-jfqlkd72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332555-jfqlkd72.txt' === file2bib.sh === id: cord-332448-5fz8ef4f author: Mutnal, M. B. title: Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-332448-5fz8ef4f.txt cache: ./cache/cord-332448-5fz8ef4f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332448-5fz8ef4f.txt' === file2bib.sh === id: cord-332723-rz1iilsv author: Creager, Hannah M. title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-332723-rz1iilsv.txt cache: ./cache/cord-332723-rz1iilsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332723-rz1iilsv.txt' === file2bib.sh === id: cord-332348-yi85sfks author: Liang, Yujie title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-332348-yi85sfks.txt cache: ./cache/cord-332348-yi85sfks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332348-yi85sfks.txt' === file2bib.sh === id: cord-332457-gan10za0 author: de Ángel Solá, David E. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-332457-gan10za0.txt cache: ./cache/cord-332457-gan10za0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332457-gan10za0.txt' === file2bib.sh === id: cord-333092-78vo7i6v author: Taksande, Amar title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-333092-78vo7i6v.txt cache: ./cache/cord-333092-78vo7i6v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333092-78vo7i6v.txt' === file2bib.sh === id: cord-333140-cdikbi1l author: Zhao, Helong title: Imatinib is not a potent anti-SARS-CoV-2 drug date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-333140-cdikbi1l.txt cache: ./cache/cord-333140-cdikbi1l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333140-cdikbi1l.txt' === file2bib.sh === id: cord-332592-bfqsyiyf author: Goette, Andreas title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-332592-bfqsyiyf.txt cache: ./cache/cord-332592-bfqsyiyf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332592-bfqsyiyf.txt' === file2bib.sh === id: cord-332303-0bbw64p5 author: Schuit, Michael title: Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-332303-0bbw64p5.txt cache: ./cache/cord-332303-0bbw64p5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332303-0bbw64p5.txt' === file2bib.sh === id: cord-332179-du1zjupf author: Sayed, Shomoita title: COVID-19 and Diabetes; possible role of polymorphism and rise of telemedicine date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-332179-du1zjupf.txt cache: ./cache/cord-332179-du1zjupf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332179-du1zjupf.txt' === file2bib.sh === id: cord-333018-2h8y118z author: Sun, Xingxing title: Safety Considerations for Neuraxial Anaesthesia in Parturients with COVID-19 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-333018-2h8y118z.txt cache: ./cache/cord-333018-2h8y118z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333018-2h8y118z.txt' === file2bib.sh === id: cord-332557-qm3qfvry author: Lau, Susanna K.P. title: SARS Coronavirus Detection Methods date: 2005-07-17 pages: extension: .txt txt: ./txt/cord-332557-qm3qfvry.txt cache: ./cache/cord-332557-qm3qfvry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332557-qm3qfvry.txt' === file2bib.sh === id: cord-332522-adul9nzf author: Wu, Qingfa title: Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date: 2004-04-02 pages: extension: .txt txt: ./txt/cord-332522-adul9nzf.txt cache: ./cache/cord-332522-adul9nzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332522-adul9nzf.txt' === file2bib.sh === id: cord-333176-6v7ficfk author: Snell, Jonathan title: SARS-CoV-2 infection and its association with thrombosis and ischemic stroke: A review COVID-19, thrombosis, and ischemic stroke date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-333176-6v7ficfk.txt cache: ./cache/cord-333176-6v7ficfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333176-6v7ficfk.txt' === file2bib.sh === id: cord-332595-874tpi09 author: Salehi, Najmeh title: Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-332595-874tpi09.txt cache: ./cache/cord-332595-874tpi09.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332595-874tpi09.txt' === file2bib.sh === id: cord-331910-s474ecvk author: Thota, Sai Manohar title: Natural products as home‐based prophylactic and symptom management agents in the setting of COVID‐19 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-331910-s474ecvk.txt cache: ./cache/cord-331910-s474ecvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331910-s474ecvk.txt' === file2bib.sh === id: cord-332672-fbwz8oxp author: Wang, Manli title: Bats as animal reservoirs for the SARS coronavirus: Hypothesis proved after 10 years of virus hunting date: 2013-10-30 pages: extension: .txt txt: ./txt/cord-332672-fbwz8oxp.txt cache: ./cache/cord-332672-fbwz8oxp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332672-fbwz8oxp.txt' === file2bib.sh === id: cord-332071-bqvn3ceq author: Lee, Jeong Seok title: Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-332071-bqvn3ceq.txt cache: ./cache/cord-332071-bqvn3ceq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332071-bqvn3ceq.txt' === file2bib.sh === id: cord-333121-kt6t41ff author: Kwenandar, Felix title: Coronavirus Disease 2019 and Cardiovascular System: A Narrative Review date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-333121-kt6t41ff.txt cache: ./cache/cord-333121-kt6t41ff.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333121-kt6t41ff.txt' === file2bib.sh === id: cord-332970-atwz3rgf author: Gentile, Pietro title: Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-332970-atwz3rgf.txt cache: ./cache/cord-332970-atwz3rgf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332970-atwz3rgf.txt' === file2bib.sh === id: cord-332480-3uodkrkp author: Bonam, Srinivasa Reddy title: Adjunct immunotherapies for the management of severely ill COVID-19 patients date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-332480-3uodkrkp.txt cache: ./cache/cord-332480-3uodkrkp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332480-3uodkrkp.txt' === file2bib.sh === id: cord-333200-yka7wfbi author: Dhampalwar, Swapnil title: Treatment armamentarium of COVID-19: Evolving strategies & evidence so far date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-333200-yka7wfbi.txt cache: ./cache/cord-333200-yka7wfbi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333200-yka7wfbi.txt' === file2bib.sh === id: cord-332276-gs80celr author: Tan, Yee‐Joo title: Regulation of cell death during infection by the severe acute respiratory syndrome coronavirus and other coronaviruses date: 2007-08-20 pages: extension: .txt txt: ./txt/cord-332276-gs80celr.txt cache: ./cache/cord-332276-gs80celr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332276-gs80celr.txt' === file2bib.sh === id: cord-332962-8y3t0r2d author: Xu, Xi title: Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 date: 2020-02-28 pages: extension: .txt txt: ./txt/cord-332962-8y3t0r2d.txt cache: ./cache/cord-332962-8y3t0r2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332962-8y3t0r2d.txt' === file2bib.sh === id: cord-332716-1d89j7jh author: Choi, Marcelo title: El SRAA y el SARS-CoV-2: el acertijo a resolver date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-332716-1d89j7jh.txt cache: ./cache/cord-332716-1d89j7jh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332716-1d89j7jh.txt' === file2bib.sh === id: cord-333239-nj5dma98 author: Ducrest, P. J. title: Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2 date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-333239-nj5dma98.txt cache: ./cache/cord-333239-nj5dma98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333239-nj5dma98.txt' === file2bib.sh === id: cord-333195-m4gvpsf8 author: Lu, Renfei title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-333195-m4gvpsf8.txt cache: ./cache/cord-333195-m4gvpsf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333195-m4gvpsf8.txt' === file2bib.sh === id: cord-332153-fczf3lzc author: Azkur, Ahmet Kursat title: Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19 date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-332153-fczf3lzc.txt cache: ./cache/cord-332153-fczf3lzc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332153-fczf3lzc.txt' === file2bib.sh === id: cord-333453-v3gap8kj author: Dima, Mirabela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-333453-v3gap8kj.txt cache: ./cache/cord-333453-v3gap8kj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333453-v3gap8kj.txt' === file2bib.sh === id: cord-332820-6qx6svs5 author: Buck, M. D. title: Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-332820-6qx6svs5.txt cache: ./cache/cord-332820-6qx6svs5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332820-6qx6svs5.txt' === file2bib.sh === id: cord-333234-yvixy77x author: Triposkiadis, Filippos title: Renin-angiotensin-system inhibition in the context of corona virus disease-19: experimental evidence, observational studies, and clinical implications date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-333234-yvixy77x.txt cache: ./cache/cord-333234-yvixy77x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333234-yvixy77x.txt' === file2bib.sh === id: cord-332827-gll4nqdd author: Peixe, Paula title: Hepatology in the COVID Era: Another C Virus, again Challenging the Liver date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-332827-gll4nqdd.txt cache: ./cache/cord-332827-gll4nqdd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332827-gll4nqdd.txt' === file2bib.sh === id: cord-333042-icgsbelo author: Fisher, Kiva A. title: Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities — United States, July 2020 date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-333042-icgsbelo.txt cache: ./cache/cord-333042-icgsbelo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333042-icgsbelo.txt' === file2bib.sh === id: cord-331897-4wnoa4l7 author: Cai, Yi title: Temporal event searches based on event maps and relationships() date: 2019-09-25 pages: extension: .txt txt: ./txt/cord-331897-4wnoa4l7.txt cache: ./cache/cord-331897-4wnoa4l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331897-4wnoa4l7.txt' === file2bib.sh === id: cord-332654-nav15g8k author: Paniri, Alireza title: Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-332654-nav15g8k.txt cache: ./cache/cord-332654-nav15g8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332654-nav15g8k.txt' === file2bib.sh === id: cord-333080-qytwbsne author: Alahari, Suresh K. title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-333080-qytwbsne.txt cache: ./cache/cord-333080-qytwbsne.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333080-qytwbsne.txt' === file2bib.sh === id: cord-332404-va3rxy5p author: Landeros, A. title: An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-332404-va3rxy5p.txt cache: ./cache/cord-332404-va3rxy5p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332404-va3rxy5p.txt' === file2bib.sh === id: cord-333041-69n2wwn3 author: Pal, Anandita title: Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-333041-69n2wwn3.txt cache: ./cache/cord-333041-69n2wwn3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333041-69n2wwn3.txt' === file2bib.sh === id: cord-332948-h297ukuu author: Olotu, Fisayo A. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-332948-h297ukuu.txt cache: ./cache/cord-332948-h297ukuu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332948-h297ukuu.txt' === file2bib.sh === id: cord-333420-qqyg9um9 author: Zhu, Xun title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-333420-qqyg9um9.txt cache: ./cache/cord-333420-qqyg9um9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333420-qqyg9um9.txt' === file2bib.sh === id: cord-333606-5z3kumu9 author: Lee, SangJoon title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-333606-5z3kumu9.txt cache: ./cache/cord-333606-5z3kumu9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333606-5z3kumu9.txt' === file2bib.sh === id: cord-333465-cha7ndv5 author: Horspool, A. M. title: Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-333465-cha7ndv5.txt cache: ./cache/cord-333465-cha7ndv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333465-cha7ndv5.txt' === file2bib.sh === id: cord-332539-v1bfm57x author: Gohl, Daryl M. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-332539-v1bfm57x.txt cache: ./cache/cord-332539-v1bfm57x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332539-v1bfm57x.txt' === file2bib.sh === id: cord-333429-bq7kfpby author: Shi, Ding title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-333429-bq7kfpby.txt cache: ./cache/cord-333429-bq7kfpby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333429-bq7kfpby.txt' === file2bib.sh === id: cord-333532-vrfduv5a author: Patel, Kishan Pravin title: COVID-19 Patients: Are Current Isolation Guidelines Effective Enough? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-333532-vrfduv5a.txt cache: ./cache/cord-333532-vrfduv5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333532-vrfduv5a.txt' === file2bib.sh === id: cord-332680-zfn81hew author: Chan, Chieh-Kai title: Renin-Angiotensin-Aldosterone System Inhibitors and Risks of Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Systematic Review and Meta-Analysis date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-332680-zfn81hew.txt cache: ./cache/cord-332680-zfn81hew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332680-zfn81hew.txt' === file2bib.sh === id: cord-333381-wz70o9tt author: Liu, Shao title: Providing pharmacy services during the coronavirus pandemic date: 2020-03-28 pages: extension: .txt txt: ./txt/cord-333381-wz70o9tt.txt cache: ./cache/cord-333381-wz70o9tt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333381-wz70o9tt.txt' === file2bib.sh === id: cord-332778-rf47ptj6 author: Vivarelli, Silvia title: Cancer Management during COVID-19 Pandemic: Is Immune Checkpoint Inhibitors-Based Immunotherapy Harmful or Beneficial? date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-332778-rf47ptj6.txt cache: ./cache/cord-332778-rf47ptj6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332778-rf47ptj6.txt' === file2bib.sh === id: cord-333713-nz36i2oa author: Andonegui-Elguera, Sergio title: Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-333713-nz36i2oa.txt cache: ./cache/cord-333713-nz36i2oa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333713-nz36i2oa.txt' === file2bib.sh === id: cord-333326-n9ifhw5s author: Wardell, Hanna title: Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Febrile Neonates date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-333326-n9ifhw5s.txt cache: ./cache/cord-333326-n9ifhw5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333326-n9ifhw5s.txt' === file2bib.sh === id: cord-333487-zem2d4y6 author: Thomaz Ugliara Barone, Mark title: The Impact of COVID-19 on People with Diabetes in Brazil date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-333487-zem2d4y6.txt cache: ./cache/cord-333487-zem2d4y6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333487-zem2d4y6.txt' === file2bib.sh === id: cord-332610-t99l3zii author: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 pages: extension: .txt txt: ./txt/cord-332610-t99l3zii.txt cache: ./cache/cord-332610-t99l3zii.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332610-t99l3zii.txt' === file2bib.sh === id: cord-333099-hy4nmy7l author: Thoms, Matthias title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-333099-hy4nmy7l.txt cache: ./cache/cord-333099-hy4nmy7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333099-hy4nmy7l.txt' === file2bib.sh === id: cord-333929-oprpgcyr author: Lee, Justin title: Impact of Severe Acute Respiratory Syndrome on Patient Access to Palliative Radiation Therapy date: 2005-01-31 pages: extension: .txt txt: ./txt/cord-333929-oprpgcyr.txt cache: ./cache/cord-333929-oprpgcyr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333929-oprpgcyr.txt' === file2bib.sh === id: cord-332109-ont0tqpn author: Wei, Yufeng title: Substance Use Disorder in the COVID-19 Pandemic: A Systematic Review of Vulnerabilities and Complications date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-332109-ont0tqpn.txt cache: ./cache/cord-332109-ont0tqpn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332109-ont0tqpn.txt' === file2bib.sh === id: cord-333174-g10kvc0c author: Ahmed, Sinthyia title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-333174-g10kvc0c.txt cache: ./cache/cord-333174-g10kvc0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333174-g10kvc0c.txt' === file2bib.sh === id: cord-332832-kjppd6uz author: Ward, B. J. title: Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-332832-kjppd6uz.txt cache: ./cache/cord-332832-kjppd6uz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332832-kjppd6uz.txt' === file2bib.sh === id: cord-333515-llqpfhwg author: Zhao, Juanjuan title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-333515-llqpfhwg.txt cache: ./cache/cord-333515-llqpfhwg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333515-llqpfhwg.txt' === file2bib.sh === id: cord-333682-ktbnrkwh author: Dong, Yunzhu title: Antibodies in the breast milk of a maternal woman with COVID-19 date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-333682-ktbnrkwh.txt cache: ./cache/cord-333682-ktbnrkwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333682-ktbnrkwh.txt' === file2bib.sh === id: cord-333144-gyuh2fvl author: Siddiqui, Arif Jamal title: Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-333144-gyuh2fvl.txt cache: ./cache/cord-333144-gyuh2fvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333144-gyuh2fvl.txt' === file2bib.sh === id: cord-333264-jdvb8px4 author: Hanke, Leo title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-333264-jdvb8px4.txt cache: ./cache/cord-333264-jdvb8px4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333264-jdvb8px4.txt' === file2bib.sh === id: cord-333670-qv1orlv5 author: Mutti, Luciano title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-333670-qv1orlv5.txt cache: ./cache/cord-333670-qv1orlv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333670-qv1orlv5.txt' === file2bib.sh === id: cord-333089-ufyzqgqk author: Aguilar-Pineda, Jorge Alberto title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-333089-ufyzqgqk.txt cache: ./cache/cord-333089-ufyzqgqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333089-ufyzqgqk.txt' === file2bib.sh === id: cord-333688-bykbyojs author: Wang, Junxue title: Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-333688-bykbyojs.txt cache: ./cache/cord-333688-bykbyojs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333688-bykbyojs.txt' === file2bib.sh === id: cord-333320-ndmmbckb author: Samore, M. title: SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-333320-ndmmbckb.txt cache: ./cache/cord-333320-ndmmbckb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333320-ndmmbckb.txt' === file2bib.sh === id: cord-333738-3xtb8gye author: Rabets, A. title: Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-333738-3xtb8gye.txt cache: ./cache/cord-333738-3xtb8gye.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333738-3xtb8gye.txt' === file2bib.sh === id: cord-333632-i2bjap7m author: Senthil Kumar, K. J. title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-333632-i2bjap7m.txt cache: ./cache/cord-333632-i2bjap7m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333632-i2bjap7m.txt' === file2bib.sh === id: cord-333654-8rg99di5 author: Pillai, Presaad title: COVID-19 AND MAJOR ORGAN THROMBOEMBOLISM: MANIFESTATIONS IN NEUROVASCULAR AND CARDIOVASCULAR SYSTEMS. date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-333654-8rg99di5.txt cache: ./cache/cord-333654-8rg99di5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333654-8rg99di5.txt' === file2bib.sh === id: cord-334194-28ygsbo1 author: Qiu, Tianyi title: Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-334194-28ygsbo1.txt cache: ./cache/cord-334194-28ygsbo1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334194-28ygsbo1.txt' === file2bib.sh === id: cord-333368-kjrk8nn9 author: Huizinga, Gabrielle P title: The Collision of Meta-Inflammation and SARS-CoV-2 Pandemic Infection date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-333368-kjrk8nn9.txt cache: ./cache/cord-333368-kjrk8nn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333368-kjrk8nn9.txt' === file2bib.sh === id: cord-334012-b2akycst author: Liguori, Claudio title: Sleep and wake impairment in patients with SARS-CoV2 infection date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-334012-b2akycst.txt cache: ./cache/cord-334012-b2akycst.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334012-b2akycst.txt' === file2bib.sh === id: cord-334162-j8m2zqbr author: Hoechter, D. J. title: Besonderheiten der kardiopulmonalen Reanimation zu Zeiten von SARS-CoV-2 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-334162-j8m2zqbr.txt cache: ./cache/cord-334162-j8m2zqbr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334162-j8m2zqbr.txt' === file2bib.sh === id: cord-334099-rtv6xm90 author: Farrow, Robert title: Early Multi-organ Point-of-Care Ultrasound Evaluation of Respiratory Distress During SARS-CoV-2 Outbreak: Case Report date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-334099-rtv6xm90.txt cache: ./cache/cord-334099-rtv6xm90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334099-rtv6xm90.txt' === file2bib.sh === id: cord-334299-0zn1z7rc author: Ahmed, Warish title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-334299-0zn1z7rc.txt cache: ./cache/cord-334299-0zn1z7rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334299-0zn1z7rc.txt' === file2bib.sh === id: cord-333696-3ci9re9a author: Alomari, Safwan O. title: COVID-19 and the Central Nervous System date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-333696-3ci9re9a.txt cache: ./cache/cord-333696-3ci9re9a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333696-3ci9re9a.txt' === file2bib.sh === id: cord-333909-uco4c946 author: Murray, Meghan T. title: Mitigating a COVID-19 Outbreak Among Major League Baseball Players — United States, 2020 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-333909-uco4c946.txt cache: ./cache/cord-333909-uco4c946.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333909-uco4c946.txt' === file2bib.sh === id: cord-334278-ajdjfzd2 author: Gilis, M. title: Caractéristiques de la COVID-19 chez les patients âgés de 75 ans et plus, hospitalisés date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-334278-ajdjfzd2.txt cache: ./cache/cord-334278-ajdjfzd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334278-ajdjfzd2.txt' === file2bib.sh === id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-331673-xv1tcugl.txt cache: ./cache/cord-331673-xv1tcugl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331673-xv1tcugl.txt' === file2bib.sh === id: cord-334300-hnrmaytm author: Ventura Fernandes, Bianca H title: Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-334300-hnrmaytm.txt cache: ./cache/cord-334300-hnrmaytm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334300-hnrmaytm.txt' === file2bib.sh === id: cord-333712-sdtxi8xw author: Yu, Ping title: Geographical structure of bat SARS-related coronaviruses date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-333712-sdtxi8xw.txt cache: ./cache/cord-333712-sdtxi8xw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333712-sdtxi8xw.txt' === file2bib.sh === id: cord-333498-d25qfq0f author: Chitranshi, Nitin title: Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL(pro) targeting repurposed drug candidates date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-333498-d25qfq0f.txt cache: ./cache/cord-333498-d25qfq0f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333498-d25qfq0f.txt' === file2bib.sh === id: cord-333999-k92fmnq7 author: Yang, Chih-Jen title: Remdesivir Use in the Coronavirus Disease 2019 Pandemic: A Mini-Review date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-333999-k92fmnq7.txt cache: ./cache/cord-333999-k92fmnq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333999-k92fmnq7.txt' === file2bib.sh === id: cord-333391-6l0cpvgr author: Bortolotti, Daria title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-333391-6l0cpvgr.txt cache: ./cache/cord-333391-6l0cpvgr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333391-6l0cpvgr.txt' === file2bib.sh === id: cord-333805-xmqs2ax7 author: Romoli, Michele title: A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-333805-xmqs2ax7.txt cache: ./cache/cord-333805-xmqs2ax7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333805-xmqs2ax7.txt' === file2bib.sh === id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-333730-qsx0m68e.txt cache: ./cache/cord-333730-qsx0m68e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333730-qsx0m68e.txt' === file2bib.sh === id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-315598-qwh72inx.txt cache: ./cache/cord-315598-qwh72inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-315598-qwh72inx.txt' === file2bib.sh === id: cord-333547-88dkh6xd author: Hasan, Shadi W. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-333547-88dkh6xd.txt cache: ./cache/cord-333547-88dkh6xd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333547-88dkh6xd.txt' === file2bib.sh === id: cord-333863-mtljy3s6 author: Hong, Nan title: Evaluation of ocular symptoms and tropism of SARS‐CoV‐2 in patients confirmed with COVID‐19 date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-333863-mtljy3s6.txt cache: ./cache/cord-333863-mtljy3s6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333863-mtljy3s6.txt' === file2bib.sh === id: cord-334321-3c10ecgd author: Arora, S. title: Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-334321-3c10ecgd.txt cache: ./cache/cord-334321-3c10ecgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334321-3c10ecgd.txt' === file2bib.sh === id: cord-334378-dqtnj3y3 author: Zhang, Yi title: Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2 date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-334378-dqtnj3y3.txt cache: ./cache/cord-334378-dqtnj3y3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334378-dqtnj3y3.txt' === file2bib.sh === id: cord-334430-1udn20wo author: Qin, Li title: The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice date: 2007 pages: extension: .txt txt: ./txt/cord-334430-1udn20wo.txt cache: ./cache/cord-334430-1udn20wo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334430-1udn20wo.txt' === file2bib.sh === id: cord-334425-6zrmavps author: SanJuan-Reyes, Sindy title: COVID-19 in the environment date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-334425-6zrmavps.txt cache: ./cache/cord-334425-6zrmavps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334425-6zrmavps.txt' === file2bib.sh === id: cord-334049-r3rlykli author: Lobo-Galo, Naún title: FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-334049-r3rlykli.txt cache: ./cache/cord-334049-r3rlykli.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334049-r3rlykli.txt' === file2bib.sh === id: cord-333754-copxoyqu author: Ma, Hsin-Chieh title: Expression and membrane integration of SARS-CoV M protein date: 2008-04-09 pages: extension: .txt txt: ./txt/cord-333754-copxoyqu.txt cache: ./cache/cord-333754-copxoyqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333754-copxoyqu.txt' === file2bib.sh === id: cord-334443-3pyu8ucs author: He, Yu title: Public health might be endangered by possible prolonged discharge of SARS-CoV-2 in stool date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-334443-3pyu8ucs.txt cache: ./cache/cord-334443-3pyu8ucs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334443-3pyu8ucs.txt' === file2bib.sh === id: cord-333897-isodrtly author: Shenoy, Niraj title: Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting? date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-333897-isodrtly.txt cache: ./cache/cord-333897-isodrtly.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333897-isodrtly.txt' === file2bib.sh === id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-332992-8rmqg4rf.txt cache: ./cache/cord-332992-8rmqg4rf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332992-8rmqg4rf.txt' === file2bib.sh === id: cord-334309-rddznfax author: Craver, Randall title: Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-334309-rddznfax.txt cache: ./cache/cord-334309-rddznfax.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334309-rddznfax.txt' === file2bib.sh === id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-333524-a6p6ma8r.txt cache: ./cache/cord-333524-a6p6ma8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333524-a6p6ma8r.txt' === file2bib.sh === id: cord-334220-sqvfr31q author: Messina, Francesco title: Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-334220-sqvfr31q.txt cache: ./cache/cord-334220-sqvfr31q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334220-sqvfr31q.txt' === file2bib.sh === id: cord-334188-bggt1i2e author: Solari, Domenico title: The nose lid for the endoscopic endonasal procedures during COVID-19 era: technical note date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-334188-bggt1i2e.txt cache: ./cache/cord-334188-bggt1i2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334188-bggt1i2e.txt' === file2bib.sh === id: cord-334540-ggnkdnky author: Singh, Pankaj title: Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-334540-ggnkdnky.txt cache: ./cache/cord-334540-ggnkdnky.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334540-ggnkdnky.txt' === file2bib.sh === id: cord-334210-lhadzo7o author: Lepak, Alexander J title: Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-334210-lhadzo7o.txt cache: ./cache/cord-334210-lhadzo7o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334210-lhadzo7o.txt' === file2bib.sh === id: cord-334175-x10bbv7y author: Okur, Hacer Kuzu title: Preliminary report of In vitro and In vivo Effectiveness of Dornase alfa on SARS-CoV-2 infection date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-334175-x10bbv7y.txt cache: ./cache/cord-334175-x10bbv7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334175-x10bbv7y.txt' === file2bib.sh === id: cord-334735-up81jotp author: Gillissen, Adrian title: Das schwere akute Atemwegssyndrom (SARS) date: 2003 pages: extension: .txt txt: ./txt/cord-334735-up81jotp.txt cache: ./cache/cord-334735-up81jotp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334735-up81jotp.txt' === file2bib.sh === id: cord-334313-v2syspu6 author: Long, S. Wesley title: Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-334313-v2syspu6.txt cache: ./cache/cord-334313-v2syspu6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334313-v2syspu6.txt' === file2bib.sh === id: cord-334945-lxowaacg author: Luo, Yi title: Asymptomatic SARS-CoV-2 Infection in Household Contacts of a Healthcare Provider, Wuhan, China date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-334945-lxowaacg.txt cache: ./cache/cord-334945-lxowaacg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334945-lxowaacg.txt' === file2bib.sh === id: cord-334518-mjr6u7ak author: Hu, X. title: Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-334518-mjr6u7ak.txt cache: ./cache/cord-334518-mjr6u7ak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334518-mjr6u7ak.txt' === file2bib.sh === id: cord-334584-xh41koro author: Dilucca, Maddalena title: Temporal evolution and adaptation of SARS-COV 2 codon usage date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-334584-xh41koro.txt cache: ./cache/cord-334584-xh41koro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334584-xh41koro.txt' === file2bib.sh === id: cord-334858-wxexl0qy author: Lozada-Nur, Francina title: Dysgeusia in COVID-19: possible mechanisms and implications date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-334858-wxexl0qy.txt cache: ./cache/cord-334858-wxexl0qy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334858-wxexl0qy.txt' === file2bib.sh === id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-334603-yt2pmxi3.txt cache: ./cache/cord-334603-yt2pmxi3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334603-yt2pmxi3.txt' === file2bib.sh === id: cord-334582-ccg27nmf author: Bonora, Benedetta Maria title: Glycaemic Control Among People with Type 1 Diabetes During Lockdown for the SARS-CoV-2 Outbreak in Italy date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-334582-ccg27nmf.txt cache: ./cache/cord-334582-ccg27nmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334582-ccg27nmf.txt' === file2bib.sh === id: cord-334833-7gv1c7we author: Ding, Yanqing title: The clinical pathology of severe acute respiratory syndrome (SARS): a report from China date: 2003-07-01 pages: extension: .txt txt: ./txt/cord-334833-7gv1c7we.txt cache: ./cache/cord-334833-7gv1c7we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334833-7gv1c7we.txt' === file2bib.sh === id: cord-334228-n69iewmx author: Li, Chunmei title: Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity date: 2016-02-16 pages: extension: .txt txt: ./txt/cord-334228-n69iewmx.txt cache: ./cache/cord-334228-n69iewmx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334228-n69iewmx.txt' === file2bib.sh === id: cord-335156-l4jie8g6 author: Andreozzi, Fabio title: Eosinopenia and COVID-19 patients: So specific ? date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-335156-l4jie8g6.txt cache: ./cache/cord-335156-l4jie8g6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335156-l4jie8g6.txt' === file2bib.sh === id: cord-334628-axon4jdc author: Lee, Saemi title: Genetic Characteristics of Coronaviruses from Korean Bats in 2016 date: 2017-07-19 pages: extension: .txt txt: ./txt/cord-334628-axon4jdc.txt cache: ./cache/cord-334628-axon4jdc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334628-axon4jdc.txt' === file2bib.sh === id: cord-334268-n2hon61o author: Ren, Yanfang title: Risk for dental healthcare professionals during the COVID-19 global pandemic: an evidence-based assessment date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-334268-n2hon61o.txt cache: ./cache/cord-334268-n2hon61o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334268-n2hon61o.txt' === file2bib.sh === id: cord-334688-0i1pu8wc author: Martos Pérez, F. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-334688-0i1pu8wc.txt cache: ./cache/cord-334688-0i1pu8wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334688-0i1pu8wc.txt' === file2bib.sh === id: cord-333868-qrnsmhws author: Rothman, Richard E. title: Respiratory Hygiene in the Emergency Department date: 2006-08-23 pages: extension: .txt txt: ./txt/cord-333868-qrnsmhws.txt cache: ./cache/cord-333868-qrnsmhws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333868-qrnsmhws.txt' === file2bib.sh === id: cord-333703-1ku3jc9s author: Kraus, Aurora title: A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date: 2020-11-08 pages: extension: .txt txt: ./txt/cord-333703-1ku3jc9s.txt cache: ./cache/cord-333703-1ku3jc9s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333703-1ku3jc9s.txt' === file2bib.sh === id: cord-335172-5ig907on author: Busse, Laurence W. title: COVID-19 and the RAAS—a potential role for angiotensin II? date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-335172-5ig907on.txt cache: ./cache/cord-335172-5ig907on.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335172-5ig907on.txt' === file2bib.sh === id: cord-334277-g3go3u02 author: Kovac, Marc title: EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA) date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-334277-g3go3u02.txt cache: ./cache/cord-334277-g3go3u02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334277-g3go3u02.txt' === file2bib.sh === id: cord-334988-brumg6jh author: Traugott, Marianna title: Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in Different Stages of Infection: Comparison of Commercial Enzyme-Linked Immunosorbent Assays and Rapid Tests date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-334988-brumg6jh.txt cache: ./cache/cord-334988-brumg6jh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334988-brumg6jh.txt' === file2bib.sh === id: cord-334715-902pfxyz author: Sirico, Domenico title: Cardiac imaging in congenital heart disease during the coronavirus disease-2019 pandemic: recommendations from the Working Group on Congenital Heart Disease of the Italian Society of Cardiology date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-334715-902pfxyz.txt cache: ./cache/cord-334715-902pfxyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334715-902pfxyz.txt' === file2bib.sh === id: cord-333122-xw8o189s author: Blasiak, A. title: IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-333122-xw8o189s.txt cache: ./cache/cord-333122-xw8o189s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333122-xw8o189s.txt' === file2bib.sh === id: cord-334612-lxqcvqca author: Rao, Nirmala title: Sars, preschool routines and children’s behaviour: Observations from preschools in Hong Kong date: 2006 pages: extension: .txt txt: ./txt/cord-334612-lxqcvqca.txt cache: ./cache/cord-334612-lxqcvqca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334612-lxqcvqca.txt' === file2bib.sh === id: cord-335155-x9az3twa author: Qi, Zhen title: Phylogeny of SARS-CoV as inferred from complete genome comparison date: 2003 pages: extension: .txt txt: ./txt/cord-335155-x9az3twa.txt cache: ./cache/cord-335155-x9az3twa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335155-x9az3twa.txt' === file2bib.sh === id: cord-333520-v2sb90rc author: Gardin, Chiara title: Could Mesenchymal Stem Cell-Derived Exosomes Be a Therapeutic Option for Critically Ill COVID-19 Patients? date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-333520-v2sb90rc.txt cache: ./cache/cord-333520-v2sb90rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333520-v2sb90rc.txt' === file2bib.sh === id: cord-333763-45dzsn2j author: Bestle, Dorothea title: TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-333763-45dzsn2j.txt cache: ./cache/cord-333763-45dzsn2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333763-45dzsn2j.txt' === file2bib.sh === id: cord-334790-lav794w0 author: Jin, Huijuan title: Consensus for prevention and management of coronavirus disease 2019 (COVID-19) for neurologists date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-334790-lav794w0.txt cache: ./cache/cord-334790-lav794w0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334790-lav794w0.txt' === file2bib.sh === id: cord-334891-4jgtxg07 author: Choudhury, Abhigyan title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-334891-4jgtxg07.txt cache: ./cache/cord-334891-4jgtxg07.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334891-4jgtxg07.txt' === file2bib.sh === id: cord-335270-edga753o author: Lopez-Alvarez, Diana title: Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-335270-edga753o.txt cache: ./cache/cord-335270-edga753o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335270-edga753o.txt' === file2bib.sh === id: cord-334960-l5q5wc06 author: Park, Su Eun title: Epidemiology, virology, and clinical features of severe acute respiratory syndrome -coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19) date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-334960-l5q5wc06.txt cache: ./cache/cord-334960-l5q5wc06.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334960-l5q5wc06.txt' === file2bib.sh === id: cord-334976-53cd16w5 author: Jo, Seri title: Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-334976-53cd16w5.txt cache: ./cache/cord-334976-53cd16w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334976-53cd16w5.txt' === file2bib.sh === id: cord-335077-ievtvhge author: Hogan, Catherine A. title: Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-335077-ievtvhge.txt cache: ./cache/cord-335077-ievtvhge.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335077-ievtvhge.txt' === file2bib.sh === id: cord-334550-xb0alubj author: Samaddar, Arghadip title: The Enigma of Low COVID-19 Fatality Rate in India date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-334550-xb0alubj.txt cache: ./cache/cord-334550-xb0alubj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334550-xb0alubj.txt' === file2bib.sh === id: cord-334495-7y1la856 author: Agricola, Eustachio title: Heart and Lung Multimodality Imaging in COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-334495-7y1la856.txt cache: ./cache/cord-334495-7y1la856.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334495-7y1la856.txt' === file2bib.sh === id: cord-334695-cjxlw1tu author: Kam, Yiu-Wing title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date: 2009-11-17 pages: extension: .txt txt: ./txt/cord-334695-cjxlw1tu.txt cache: ./cache/cord-334695-cjxlw1tu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-334695-cjxlw1tu.txt' === file2bib.sh === id: cord-335599-98ovzui5 author: Raony, Ícaro title: Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-335599-98ovzui5.txt cache: ./cache/cord-335599-98ovzui5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335599-98ovzui5.txt' === file2bib.sh === id: cord-335844-dybozins author: Berkowitz, Kathleen M. title: IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-335844-dybozins.txt cache: ./cache/cord-335844-dybozins.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335844-dybozins.txt' === file2bib.sh === id: cord-334973-jemeyudi author: Wu, Dingye title: Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-334973-jemeyudi.txt cache: ./cache/cord-334973-jemeyudi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334973-jemeyudi.txt' === file2bib.sh === id: cord-335118-oa9jfots author: Taka, E. title: Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-335118-oa9jfots.txt cache: ./cache/cord-335118-oa9jfots.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335118-oa9jfots.txt' === file2bib.sh === id: cord-335347-vxl2flbn author: Diercks, Gillian R. title: Asymptomatic COVID-19 Infection in a Child with Nasal Foreign Body date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-335347-vxl2flbn.txt cache: ./cache/cord-335347-vxl2flbn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335347-vxl2flbn.txt' === file2bib.sh === id: cord-335302-6wsx0jby author: Mahy, Brian W.J. title: The diversity of viruses infecting humans date: 2011-12-12 pages: extension: .txt txt: ./txt/cord-335302-6wsx0jby.txt cache: ./cache/cord-335302-6wsx0jby.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335302-6wsx0jby.txt' === file2bib.sh === id: cord-335338-wzxjn5ip author: Wei, Lan title: Pathology of the thyroid in severe acute respiratory syndrome() date: 2006-09-25 pages: extension: .txt txt: ./txt/cord-335338-wzxjn5ip.txt cache: ./cache/cord-335338-wzxjn5ip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335338-wzxjn5ip.txt' === file2bib.sh === id: cord-335932-0phqok4g author: Vanhems, Philippe title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-335932-0phqok4g.txt cache: ./cache/cord-335932-0phqok4g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335932-0phqok4g.txt' === file2bib.sh === id: cord-334717-zg9f19p8 author: Chung, Mina K. title: SARS-CoV-2 and ACE2: The biology and clinical data settling the ARB and ACEI controversy date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-334717-zg9f19p8.txt cache: ./cache/cord-334717-zg9f19p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334717-zg9f19p8.txt' === file2bib.sh === id: cord-335652-v98gv5uf author: Salazar, Cecilia title: Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-335652-v98gv5uf.txt cache: ./cache/cord-335652-v98gv5uf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335652-v98gv5uf.txt' === file2bib.sh === id: cord-334624-chnibsa1 author: Hayn, Manuel title: Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-334624-chnibsa1.txt cache: ./cache/cord-334624-chnibsa1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334624-chnibsa1.txt' === file2bib.sh === id: cord-335375-n6q70o35 author: Chan, Paul K. S. title: Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date: 2005-07-01 pages: extension: .txt txt: ./txt/cord-335375-n6q70o35.txt cache: ./cache/cord-335375-n6q70o35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335375-n6q70o35.txt' === file2bib.sh === id: cord-334884-ig6n9cet author: Jiménez-Alberto, Alicia title: Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-334884-ig6n9cet.txt cache: ./cache/cord-334884-ig6n9cet.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334884-ig6n9cet.txt' === file2bib.sh === id: cord-336026-x02f7byo author: Lommatzsch, Marek title: COVID‐19 in a patient with severe asthma treated with Omalizumab date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-336026-x02f7byo.txt cache: ./cache/cord-336026-x02f7byo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-336026-x02f7byo.txt' === file2bib.sh === id: cord-336094-ssr5y4u3 author: Blumberg, Dean A. title: Vertical Transmission of SARS-CoV-2: What is the Optimal Definition? date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-336094-ssr5y4u3.txt cache: ./cache/cord-336094-ssr5y4u3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336094-ssr5y4u3.txt' === file2bib.sh === id: cord-335292-x2vjzp18 author: Nagashima, S. title: The Endothelial Dysfunction and Pyroptosis Driving the SARS-CoV-2 Immune-Thrombosis date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-335292-x2vjzp18.txt cache: ./cache/cord-335292-x2vjzp18.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335292-x2vjzp18.txt' === file2bib.sh === id: cord-336103-ufvq0ngl author: Sharma, R. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-336103-ufvq0ngl.txt cache: ./cache/cord-336103-ufvq0ngl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336103-ufvq0ngl.txt' === file2bib.sh === id: cord-335446-8l1vfsbc author: Liao, M. title: The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing date: 2020-02-26 pages: extension: .txt txt: ./txt/cord-335446-8l1vfsbc.txt cache: ./cache/cord-335446-8l1vfsbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335446-8l1vfsbc.txt' === file2bib.sh === id: cord-336057-tj9qcuf8 author: Lv, Yantian title: No intrauterine vertical transmission in pregnancy with COVID-19: a case report date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-336057-tj9qcuf8.txt cache: ./cache/cord-336057-tj9qcuf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336057-tj9qcuf8.txt' === file2bib.sh === id: cord-334773-yw2qgv13 author: Lisco, Giuseppe title: Hypothesized mechanisms explaining poor prognosis in type 2 diabetes patients with COVID-19: a review date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-334773-yw2qgv13.txt cache: ./cache/cord-334773-yw2qgv13.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334773-yw2qgv13.txt' === file2bib.sh === id: cord-335075-6wo2o5pp author: Bangaru, Sandhya title: Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-335075-6wo2o5pp.txt cache: ./cache/cord-335075-6wo2o5pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335075-6wo2o5pp.txt' === file2bib.sh === id: cord-335364-qwjuzebd author: Fernandez-Rivas, G. title: Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-335364-qwjuzebd.txt cache: ./cache/cord-335364-qwjuzebd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335364-qwjuzebd.txt' === file2bib.sh === id: cord-335784-v7nbck0n author: Barak, N. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-335784-v7nbck0n.txt cache: ./cache/cord-335784-v7nbck0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335784-v7nbck0n.txt' === file2bib.sh === id: cord-335591-r0x8yaqj author: Ohnishi, Kazuo title: Establishment and Characterization of Monoclonal Antibodies Against SARS Coronavirus date: 2007-11-28 pages: extension: .txt txt: ./txt/cord-335591-r0x8yaqj.txt cache: ./cache/cord-335591-r0x8yaqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335591-r0x8yaqj.txt' === file2bib.sh === id: cord-334849-8rblgq9b author: LoPresti, Marissa title: The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-334849-8rblgq9b.txt cache: ./cache/cord-334849-8rblgq9b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334849-8rblgq9b.txt' === file2bib.sh === id: cord-335467-0b0m8v5r author: Saha, Asit title: Novel coronavirus SARS‐CoV‐2 (Covid‐19) dynamics inside the human body date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-335467-0b0m8v5r.txt cache: ./cache/cord-335467-0b0m8v5r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335467-0b0m8v5r.txt' === file2bib.sh === id: cord-335619-t3yv5y7h author: Wang, Song-mi title: Screening of SARS-CoV-2 in 299 Hospitalized Children with Hemato-oncological Diseases: A Multicenter Survey in Hubei, China date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-335619-t3yv5y7h.txt cache: ./cache/cord-335619-t3yv5y7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335619-t3yv5y7h.txt' === file2bib.sh === id: cord-336012-8klkojpo author: Harilal, Divinlal title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-336012-8klkojpo.txt cache: ./cache/cord-336012-8klkojpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336012-8klkojpo.txt' === file2bib.sh === id: cord-335859-k37jivp6 author: Wu, Daphne C. title: Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-335859-k37jivp6.txt cache: ./cache/cord-335859-k37jivp6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335859-k37jivp6.txt' === file2bib.sh === id: cord-335648-lbmhprjn author: Estrich, Cameron G. title: Estimating COVID-19 prevalence and infection control practices among US dentists date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-335648-lbmhprjn.txt cache: ./cache/cord-335648-lbmhprjn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335648-lbmhprjn.txt' === file2bib.sh === id: cord-335768-ry5boej6 author: Chauhan, Shaylika title: Comprehensive review of coronavirus disease 2019 (COVID-19) date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-335768-ry5boej6.txt cache: ./cache/cord-335768-ry5boej6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335768-ry5boej6.txt' === file2bib.sh === id: cord-335386-eflyypev author: Steinman, Jonathan Baruch title: Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-335386-eflyypev.txt cache: ./cache/cord-335386-eflyypev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335386-eflyypev.txt' === file2bib.sh === id: cord-335122-8s3bcyo8 author: Marshall, Steve title: COVID-19: What do we know? date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-335122-8s3bcyo8.txt cache: ./cache/cord-335122-8s3bcyo8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335122-8s3bcyo8.txt' === file2bib.sh === id: cord-335610-3v8140b6 author: Prasanth, D. S. N. B. K. title: In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2 date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-335610-3v8140b6.txt cache: ./cache/cord-335610-3v8140b6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335610-3v8140b6.txt' === file2bib.sh === id: cord-335492-od3c25qg author: UGUREL, Osman Mutluhan title: An updated analysis of variations in SARS-CoV-2 genome date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-335492-od3c25qg.txt cache: ./cache/cord-335492-od3c25qg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335492-od3c25qg.txt' === file2bib.sh === id: cord-335538-thd5oaef author: Ji, Xiaoyang title: TWIRLS, a knowledge‐mining technology, suggests a possible mechanism for the pathological changes in the human host after coronavirus infection via ACE2 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-335538-thd5oaef.txt cache: ./cache/cord-335538-thd5oaef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335538-thd5oaef.txt' === file2bib.sh === id: cord-336227-0j0nbm9k author: Aranda‐Abreu, Gonzalo Emiliano title: Use of amantadine in a patient with SARS‐CoV‐2 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-336227-0j0nbm9k.txt cache: ./cache/cord-336227-0j0nbm9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336227-0j0nbm9k.txt' === file2bib.sh === id: cord-334564-bqh9jkds author: Raony, Ícaro title: Psycho-Neuroendocrine-Immune Interactions in COVID-19: Potential Impacts on Mental Health date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-334564-bqh9jkds.txt cache: ./cache/cord-334564-bqh9jkds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334564-bqh9jkds.txt' === file2bib.sh === id: cord-335443-iv2gs3kg author: Kim, Youngchang title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-335443-iv2gs3kg.txt cache: ./cache/cord-335443-iv2gs3kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335443-iv2gs3kg.txt' === file2bib.sh === id: cord-336488-opjjowcq author: Kenanidis, Eustathios title: Organizing an Orthopaedic Department During COVID-19 Pandemic to Mitigate In-Hospital Transmission: Experience From Greece date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-336488-opjjowcq.txt cache: ./cache/cord-336488-opjjowcq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336488-opjjowcq.txt' === file2bib.sh === id: cord-335293-pac6wbgz author: Nijman, Ruud G. title: Pediatric Inflammatory Multisystem Syndrome: Statement by the Pediatric Section of the European Society for Emergency Medicine and European Academy of Pediatrics date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-335293-pac6wbgz.txt cache: ./cache/cord-335293-pac6wbgz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335293-pac6wbgz.txt' === file2bib.sh === id: cord-336561-llwjsds8 author: Ghosh, Sanhita title: siRNA could be a potential therapy for COVID-19 date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-336561-llwjsds8.txt cache: ./cache/cord-336561-llwjsds8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336561-llwjsds8.txt' === file2bib.sh === id: cord-336535-r3a57m57 author: Kohmer, Niko title: Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-336535-r3a57m57.txt cache: ./cache/cord-336535-r3a57m57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336535-r3a57m57.txt' === file2bib.sh === id: cord-335802-1kiqfy68 author: Azoulay, Elie title: Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-335802-1kiqfy68.txt cache: ./cache/cord-335802-1kiqfy68.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335802-1kiqfy68.txt' === file2bib.sh === id: cord-336373-xb3jrg75 author: Vivas, Esther X. title: COVID19 and Otology/Neurotology date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-336373-xb3jrg75.txt cache: ./cache/cord-336373-xb3jrg75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336373-xb3jrg75.txt' === file2bib.sh === id: cord-336022-b2fwktld author: Addetia, Amin title: Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-336022-b2fwktld.txt cache: ./cache/cord-336022-b2fwktld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336022-b2fwktld.txt' === file2bib.sh === id: cord-336366-2y68n8s0 author: Liguori, Claudio title: Depressive and anxiety symptoms in patients with SARS-CoV2 infection date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-336366-2y68n8s0.txt cache: ./cache/cord-336366-2y68n8s0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336366-2y68n8s0.txt' === file2bib.sh === id: cord-335958-dtvlo0kz author: Satyam, Rohit title: Deciphering the SSR incidences across viral members of Coronaviridae family date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-335958-dtvlo0kz.txt cache: ./cache/cord-335958-dtvlo0kz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335958-dtvlo0kz.txt' === file2bib.sh === id: cord-336066-n9yq8enz author: Lai, Chien‐Chen title: Proteomic analysis of up‐regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C‐like protease date: 2007-04-04 pages: extension: .txt txt: ./txt/cord-336066-n9yq8enz.txt cache: ./cache/cord-336066-n9yq8enz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336066-n9yq8enz.txt' === file2bib.sh === id: cord-336522-y9nzsv95 author: Rosenke, Kyle title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-336522-y9nzsv95.txt cache: ./cache/cord-336522-y9nzsv95.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336522-y9nzsv95.txt' === file2bib.sh === id: cord-336722-41eqt97y author: Sehmi, P. title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-336722-41eqt97y.txt cache: ./cache/cord-336722-41eqt97y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336722-41eqt97y.txt' === file2bib.sh === id: cord-336481-vrnxu217 author: Bonifácio, Lívia Pimenta title: Are SARS-CoV-2 reinfection and Covid-19 recurrence possible? a case report from Brazil date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-336481-vrnxu217.txt cache: ./cache/cord-336481-vrnxu217.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336481-vrnxu217.txt' === file2bib.sh === id: cord-335137-5qt286kc author: Chatterjee, Swapan K. title: Molecular Pathogenesis, Immunopathogenesis and Novel Therapeutic Strategy Against COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-335137-5qt286kc.txt cache: ./cache/cord-335137-5qt286kc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335137-5qt286kc.txt' === file2bib.sh === id: cord-336394-1xf2sxtv author: Li, Yu title: The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-336394-1xf2sxtv.txt cache: ./cache/cord-336394-1xf2sxtv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336394-1xf2sxtv.txt' === file2bib.sh === id: cord-335040-1qa6pe4v author: Rogstam, Annika title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-335040-1qa6pe4v.txt cache: ./cache/cord-335040-1qa6pe4v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335040-1qa6pe4v.txt' === file2bib.sh === id: cord-336053-cjq7szcn author: Mottola, Filiberto Fausto title: Cardiovascular System in COVID-19: Simply a Viewer or a Leading Actor? date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-336053-cjq7szcn.txt cache: ./cache/cord-336053-cjq7szcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336053-cjq7szcn.txt' === file2bib.sh === id: cord-335916-fh28qrt7 author: Liu, Cuiwei title: COVID-19 in cancer patients: risk, clinical features, and management date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-335916-fh28qrt7.txt cache: ./cache/cord-335916-fh28qrt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335916-fh28qrt7.txt' === file2bib.sh === id: cord-336696-c3rbmysh author: Oberfeld, Blake title: SnapShot: COVID-19 date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-336696-c3rbmysh.txt cache: ./cache/cord-336696-c3rbmysh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336696-c3rbmysh.txt' === file2bib.sh === id: cord-336117-hit4kza8 author: Heymann, D.L. title: Emerging Infections, the International Health Regulations, and Macro-Economy date: 2014-02-27 pages: extension: .txt txt: ./txt/cord-336117-hit4kza8.txt cache: ./cache/cord-336117-hit4kza8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336117-hit4kza8.txt' === file2bib.sh === id: cord-336605-d4loia11 author: Zhang, Xue Wu title: Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs date: 2004-05-15 pages: extension: .txt txt: ./txt/cord-336605-d4loia11.txt cache: ./cache/cord-336605-d4loia11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336605-d4loia11.txt' === file2bib.sh === id: cord-336720-2bf3xzni author: Zhen, Wei title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-336720-2bf3xzni.txt cache: ./cache/cord-336720-2bf3xzni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336720-2bf3xzni.txt' === file2bib.sh === id: cord-336119-8g37xsys author: Nimgampalle, Mallikarjuna title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-336119-8g37xsys.txt cache: ./cache/cord-336119-8g37xsys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336119-8g37xsys.txt' === file2bib.sh === id: cord-336049-n3swuykg author: Ahmed, Mubbasheer title: Multisystem inflammatory syndrome in children: A systematic review date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-336049-n3swuykg.txt cache: ./cache/cord-336049-n3swuykg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336049-n3swuykg.txt' === file2bib.sh === id: cord-336585-19vwpjkt author: Adem, Şevki title: Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19 date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-336585-19vwpjkt.txt cache: ./cache/cord-336585-19vwpjkt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336585-19vwpjkt.txt' === file2bib.sh === id: cord-335377-zrbn637z author: Ishimaru, Daniella title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date: 2012-12-26 pages: extension: .txt txt: ./txt/cord-335377-zrbn637z.txt cache: ./cache/cord-335377-zrbn637z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335377-zrbn637z.txt' === file2bib.sh === id: cord-336752-cpxnof1b author: Zeng, Qi‐Qiang title: Radiomics‐based model for accurately distinguishing between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) and influenza A infected pneumonia date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-336752-cpxnof1b.txt cache: ./cache/cord-336752-cpxnof1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336752-cpxnof1b.txt' === file2bib.sh === id: cord-336677-h62angfw author: Rousseau, Antoine title: Sars-Cov-2, Covid-19 Et Œil: Le Point Sur Les Données Publiées date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-336677-h62angfw.txt cache: ./cache/cord-336677-h62angfw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336677-h62angfw.txt' === file2bib.sh === id: cord-336517-v7z62tld author: Chu, Hsu-Feng title: Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine date: 2018-08-20 pages: extension: .txt txt: ./txt/cord-336517-v7z62tld.txt cache: ./cache/cord-336517-v7z62tld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336517-v7z62tld.txt' === file2bib.sh === id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-335567-ssnvr6nj.txt cache: ./cache/cord-335567-ssnvr6nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335567-ssnvr6nj.txt' === file2bib.sh === id: cord-335938-hscgmis5 author: Gralinski, Lisa E. title: Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury date: 2013-08-06 pages: extension: .txt txt: ./txt/cord-335938-hscgmis5.txt cache: ./cache/cord-335938-hscgmis5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-335938-hscgmis5.txt' === file2bib.sh === id: cord-336702-2qa4u8gv author: Agarwal, Sangya title: Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19 date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-336702-2qa4u8gv.txt cache: ./cache/cord-336702-2qa4u8gv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336702-2qa4u8gv.txt' === file2bib.sh === id: cord-336093-ic6q6ke8 author: Sun, Ying title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 pages: extension: .txt txt: ./txt/cord-336093-ic6q6ke8.txt cache: ./cache/cord-336093-ic6q6ke8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336093-ic6q6ke8.txt' === file2bib.sh === id: cord-336543-ydrmlujj author: Cavalli, Eugenio title: Entangling COVID-19 associated thrombosis into a secondary antiphospholipid antibody syndrome: Diagnostic and therapeutic perspectives (Review) date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-336543-ydrmlujj.txt cache: ./cache/cord-336543-ydrmlujj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336543-ydrmlujj.txt' === file2bib.sh === id: cord-333262-xvfl7ycj author: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-333262-xvfl7ycj.txt cache: ./cache/cord-333262-xvfl7ycj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333262-xvfl7ycj.txt' === file2bib.sh === id: cord-336793-9bbyu1qx author: Matsuyama, Shutoku title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-336793-9bbyu1qx.txt cache: ./cache/cord-336793-9bbyu1qx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336793-9bbyu1qx.txt' === file2bib.sh === id: cord-335955-2bw2sly8 author: Shi, Yuejun title: A Dimerization-Dependent Mechanism Drives the Endoribonuclease Function of Porcine Reproductive and Respiratory Syndrome Virus nsp11 date: 2016-04-14 pages: extension: .txt txt: ./txt/cord-335955-2bw2sly8.txt cache: ./cache/cord-335955-2bw2sly8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335955-2bw2sly8.txt' === file2bib.sh === id: cord-336177-p7b7yw28 author: Selvi, Valeria title: Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-336177-p7b7yw28.txt cache: ./cache/cord-336177-p7b7yw28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336177-p7b7yw28.txt' === file2bib.sh === id: cord-336870-nirg3269 author: Abebe, Endeshaw Chekol title: The newly emerged COVID-19 disease: a systemic review date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-336870-nirg3269.txt cache: ./cache/cord-336870-nirg3269.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336870-nirg3269.txt' === file2bib.sh === id: cord-336364-2ust3qoq author: Artigas, Laura title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-336364-2ust3qoq.txt cache: ./cache/cord-336364-2ust3qoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336364-2ust3qoq.txt' === file2bib.sh === id: cord-337093-7pxfzuq0 author: Hess, David C. title: COVID-19-Related Stroke date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-337093-7pxfzuq0.txt cache: ./cache/cord-337093-7pxfzuq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337093-7pxfzuq0.txt' === file2bib.sh === id: cord-337220-yv7qdvzi author: Demeke, Addis title: Biosensor and molecular-based methods for the detection of human coronaviruses: A review date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-337220-yv7qdvzi.txt cache: ./cache/cord-337220-yv7qdvzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337220-yv7qdvzi.txt' === file2bib.sh === id: cord-336671-vfq5ft08 author: Ai, Jing-Wen title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-336671-vfq5ft08.txt cache: ./cache/cord-336671-vfq5ft08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336671-vfq5ft08.txt' === file2bib.sh === id: cord-336150-l8w7xk0b author: Rathore, Jitendra Singh title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-336150-l8w7xk0b.txt cache: ./cache/cord-336150-l8w7xk0b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336150-l8w7xk0b.txt' === file2bib.sh === id: cord-336560-m5u6ryy9 author: Boudewijns, Robbert title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-336560-m5u6ryy9.txt cache: ./cache/cord-336560-m5u6ryy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336560-m5u6ryy9.txt' === file2bib.sh === id: cord-336711-bnb62wa6 author: Wang, Xiaoyang title: CT findings of patients infected with SARS-CoV-2 date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-336711-bnb62wa6.txt cache: ./cache/cord-336711-bnb62wa6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336711-bnb62wa6.txt' === file2bib.sh === id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-336447-hpnkou41.txt cache: ./cache/cord-336447-hpnkou41.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336447-hpnkou41.txt' === file2bib.sh === id: cord-336628-0evl3wnd author: Neufeldt, Christopher J. title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-336628-0evl3wnd.txt cache: ./cache/cord-336628-0evl3wnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336628-0evl3wnd.txt' === file2bib.sh === id: cord-335308-5kh7wgvx author: Ponnusamy, Rajesh title: Variable Oligomerization Modes in Coronavirus Non-structural Protein 9 date: 2008-11-28 pages: extension: .txt txt: ./txt/cord-335308-5kh7wgvx.txt cache: ./cache/cord-335308-5kh7wgvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335308-5kh7wgvx.txt' === file2bib.sh === id: cord-336769-5x6xjuew author: Payne, Daniel C. title: SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-336769-5x6xjuew.txt cache: ./cache/cord-336769-5x6xjuew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336769-5x6xjuew.txt' === file2bib.sh === id: cord-336742-42ebj3gi author: Demmler, Gail J title: Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future date: 2003-07-31 pages: extension: .txt txt: ./txt/cord-336742-42ebj3gi.txt cache: ./cache/cord-336742-42ebj3gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336742-42ebj3gi.txt' === file2bib.sh === id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-337198-4sors3bg.txt cache: ./cache/cord-337198-4sors3bg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337198-4sors3bg.txt' === file2bib.sh === id: cord-337026-osgi06o4 author: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-337026-osgi06o4.txt cache: ./cache/cord-337026-osgi06o4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337026-osgi06o4.txt' === file2bib.sh === id: cord-336837-rerp1g1w author: Jones, Nick K title: Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-336837-rerp1g1w.txt cache: ./cache/cord-336837-rerp1g1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336837-rerp1g1w.txt' === file2bib.sh === id: cord-336836-54o9vjdl author: Zhen, Wei title: Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-336836-54o9vjdl.txt cache: ./cache/cord-336836-54o9vjdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336836-54o9vjdl.txt' === file2bib.sh === id: cord-337200-2qwty2jp author: Kempfle, J. S. title: Management von Patienten mit Tracheostoma während der COVID-19-Pandemie: Literaturüberblick und Demonstration date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-337200-2qwty2jp.txt cache: ./cache/cord-337200-2qwty2jp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337200-2qwty2jp.txt' === file2bib.sh === id: cord-336782-0zkb39v1 author: Fraile Gutiérrez, V. title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-336782-0zkb39v1.txt cache: ./cache/cord-336782-0zkb39v1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336782-0zkb39v1.txt' === file2bib.sh === id: cord-337599-dyxfsojh author: Ahamad, Shakir title: Primed for Global Coronavirus Pandemic: Emerging Research and Clinical Outcome date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-337599-dyxfsojh.txt cache: ./cache/cord-337599-dyxfsojh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337599-dyxfsojh.txt' === file2bib.sh === id: cord-337208-6rs1sgx1 author: Wang, Jingbo title: Enlightenments of Asymptomatic Cases of SARS-CoV-2 Infection date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-337208-6rs1sgx1.txt cache: ./cache/cord-337208-6rs1sgx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337208-6rs1sgx1.txt' === file2bib.sh === id: cord-337127-pc9hez28 author: García-Salido, Alberto title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-337127-pc9hez28.txt cache: ./cache/cord-337127-pc9hez28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337127-pc9hez28.txt' === file2bib.sh === id: cord-337602-5evfkk70 author: Focosi, Daniele title: Anti‐A Isohemagglutinin titers and SARS‐CoV2 neutralization: implications for children and convalescent plasma selection date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-337602-5evfkk70.txt cache: ./cache/cord-337602-5evfkk70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337602-5evfkk70.txt' === file2bib.sh === id: cord-337396-g69bb60d author: Ogawa, Yoshihiko title: Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-337396-g69bb60d.txt cache: ./cache/cord-337396-g69bb60d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337396-g69bb60d.txt' === file2bib.sh === id: cord-337491-ztco6guw author: Kucharski, Adam J title: Using serological data to understand unobserved SARS-CoV-2 risk in health-care settings date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-337491-ztco6guw.txt cache: ./cache/cord-337491-ztco6guw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337491-ztco6guw.txt' === file2bib.sh === id: cord-337436-3xzgv370 author: Khider, Lina title: Curative anticoagulation prevents endothelial lesion in COVID‐19 patients date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-337436-3xzgv370.txt cache: ./cache/cord-337436-3xzgv370.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337436-3xzgv370.txt' === file2bib.sh === id: cord-337444-pqoq8aew author: Doi, Kent title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-337444-pqoq8aew.txt cache: ./cache/cord-337444-pqoq8aew.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337444-pqoq8aew.txt' === file2bib.sh === id: cord-337324-jxtch47t author: Qian, Guo-Qing title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series date: 2020-02-25 pages: extension: .txt txt: ./txt/cord-337324-jxtch47t.txt cache: ./cache/cord-337324-jxtch47t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337324-jxtch47t.txt' === file2bib.sh === id: cord-337854-5ogip9tz author: Huang, Wanqiu title: The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-337854-5ogip9tz.txt cache: ./cache/cord-337854-5ogip9tz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337854-5ogip9tz.txt' === file2bib.sh === id: cord-337557-ct43uoir author: Guetl, Katharina title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-337557-ct43uoir.txt cache: ./cache/cord-337557-ct43uoir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337557-ct43uoir.txt' === file2bib.sh === id: cord-337339-0vkigjv2 author: Osterrieder, Nikolaus title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-337339-0vkigjv2.txt cache: ./cache/cord-337339-0vkigjv2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337339-0vkigjv2.txt' === file2bib.sh === id: cord-337089-ksh62ni0 author: Salajegheh Tazerji, Sina title: Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-337089-ksh62ni0.txt cache: ./cache/cord-337089-ksh62ni0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337089-ksh62ni0.txt' === file2bib.sh === id: cord-337462-9mvk86q6 author: nan title: Humanity tested date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-337462-9mvk86q6.txt cache: ./cache/cord-337462-9mvk86q6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337462-9mvk86q6.txt' === file2bib.sh === id: cord-337430-c2vdnml7 author: Timpka, Toomas title: Sports Health During the SARS-Cov-2 Pandemic date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-337430-c2vdnml7.txt cache: ./cache/cord-337430-c2vdnml7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337430-c2vdnml7.txt' === file2bib.sh === id: cord-337304-2ad2m317 author: Chang, Le title: Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-337304-2ad2m317.txt cache: ./cache/cord-337304-2ad2m317.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337304-2ad2m317.txt' === file2bib.sh === id: cord-337297-fkw8780t author: Fan, Siyuan title: Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-337297-fkw8780t.txt cache: ./cache/cord-337297-fkw8780t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337297-fkw8780t.txt' === file2bib.sh === id: cord-337032-s4g4g80w author: Gupta, Manoj Kumar title: In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-337032-s4g4g80w.txt cache: ./cache/cord-337032-s4g4g80w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337032-s4g4g80w.txt' === file2bib.sh === id: cord-337179-qytruuif author: Guazzi, Marco title: The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-337179-qytruuif.txt cache: ./cache/cord-337179-qytruuif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337179-qytruuif.txt' === file2bib.sh === id: cord-336938-03366q9t author: Thacker, Vivek V title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-336938-03366q9t.txt cache: ./cache/cord-336938-03366q9t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336938-03366q9t.txt' === file2bib.sh === id: cord-337511-20yaol5r author: Ryan, Paul MacDaragh title: COVID-19 and relative angiotensin-converting enzyme 2 deficiency: role in disease severity and therapeutic response date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-337511-20yaol5r.txt cache: ./cache/cord-337511-20yaol5r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337511-20yaol5r.txt' === file2bib.sh === id: cord-336142-jmetfa6x author: MacDougall, Heather title: Toronto’s Health Department in Action: Influenza in 1918 and SARS in 2003 date: 2006-10-11 pages: extension: .txt txt: ./txt/cord-336142-jmetfa6x.txt cache: ./cache/cord-336142-jmetfa6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336142-jmetfa6x.txt' === file2bib.sh === id: cord-337646-gkcm6ds0 author: nan title: The Federation’s Pages: WFPHA: World Federation of Public Health Associations www.wfpha.org Bettina Borisch and Marta Lomazzi, Federation’s Pages Editors date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-337646-gkcm6ds0.txt cache: ./cache/cord-337646-gkcm6ds0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337646-gkcm6ds0.txt' === file2bib.sh === id: cord-337700-2n9tswr8 author: Chilimuri, Sridhar title: Predictors of Mortality in Adults Admitted with COVID-19: Retrospective Cohort Study from New York City date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-337700-2n9tswr8.txt cache: ./cache/cord-337700-2n9tswr8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337700-2n9tswr8.txt' === file2bib.sh === id: cord-337595-0p5f5o5v author: Tagliamento, Marco title: Call for ensuring cancer care continuity during COVID-19 pandemic date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-337595-0p5f5o5v.txt cache: ./cache/cord-337595-0p5f5o5v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-337595-0p5f5o5v.txt' === file2bib.sh === id: cord-335597-anrzcsrt author: nan title: 44. Jahrestagung der Österreichischen Gesellschaft für Pneumologie date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-335597-anrzcsrt.txt cache: ./cache/cord-335597-anrzcsrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335597-anrzcsrt.txt' === file2bib.sh === id: cord-336909-nnxa5ant author: Guedez-López, Gladys Virginia title: Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-336909-nnxa5ant.txt cache: ./cache/cord-336909-nnxa5ant.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336909-nnxa5ant.txt' === file2bib.sh === id: cord-336563-hwemigk7 author: Bhimraj, Adarsh title: Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-336563-hwemigk7.txt cache: ./cache/cord-336563-hwemigk7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336563-hwemigk7.txt' === file2bib.sh === id: cord-336775-d4hi9myk author: Kirtipal, Nikhil title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-336775-d4hi9myk.txt cache: ./cache/cord-336775-d4hi9myk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336775-d4hi9myk.txt' === file2bib.sh === id: cord-337799-mc1oqhf4 author: Mak, Gannon CK title: Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-337799-mc1oqhf4.txt cache: ./cache/cord-337799-mc1oqhf4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337799-mc1oqhf4.txt' === file2bib.sh === id: cord-336604-2auhkxce author: Kumar, Pramod title: Integrated genomic view of SARS-CoV-2 in India date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-336604-2auhkxce.txt cache: ./cache/cord-336604-2auhkxce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336604-2auhkxce.txt' === file2bib.sh === id: cord-337421-4v48kkus author: Ribeiro, Servio Pontes title: Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-337421-4v48kkus.txt cache: ./cache/cord-337421-4v48kkus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337421-4v48kkus.txt' === file2bib.sh === id: cord-337485-nqcnd9py author: Buetti, Niccolò title: SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-337485-nqcnd9py.txt cache: ./cache/cord-337485-nqcnd9py.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337485-nqcnd9py.txt' === file2bib.sh === id: cord-337753-olc00glo author: Franco, D. title: Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-337753-olc00glo.txt cache: ./cache/cord-337753-olc00glo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337753-olc00glo.txt' === file2bib.sh === id: cord-337809-bxvgr6qg author: Xiong, Yong title: Family cluster of three recovered cases of pneumonia due to severe acute respiratory syndrome coronavirus 2 infection date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-337809-bxvgr6qg.txt cache: ./cache/cord-337809-bxvgr6qg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337809-bxvgr6qg.txt' === file2bib.sh === id: cord-336810-77wq9laa author: Klocperk, Adam title: Complex Immunometabolic Profiling Reveals the Activation of Cellular Immunity and Biliary Lesions in Patients with Severe COVID-19 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-336810-77wq9laa.txt cache: ./cache/cord-336810-77wq9laa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336810-77wq9laa.txt' === file2bib.sh === id: cord-337572-kx5hihnr author: Ludwig, Stephan title: Coronaviruses and SARS-CoV-2: A Brief Overview date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-337572-kx5hihnr.txt cache: ./cache/cord-337572-kx5hihnr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337572-kx5hihnr.txt' === file2bib.sh === id: cord-337302-fpz2jfuj author: Abdihamid, Omar title: The Landscape of COVID-19 in Cancer Patients: Prevalence, Impacts, and Recommendations date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-337302-fpz2jfuj.txt cache: ./cache/cord-337302-fpz2jfuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337302-fpz2jfuj.txt' === file2bib.sh === id: cord-337674-mb6ue2hl author: Voulgaris, Athanasios title: Sleep medicine and COVID-19. Has a new era begun? date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-337674-mb6ue2hl.txt cache: ./cache/cord-337674-mb6ue2hl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337674-mb6ue2hl.txt' === file2bib.sh === id: cord-338152-e8e3lv79 author: Zhang, Peilin title: Detection of SARS-CoV-2 in placentas with pathology and vertical transmission date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-338152-e8e3lv79.txt cache: ./cache/cord-338152-e8e3lv79.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338152-e8e3lv79.txt' === file2bib.sh === id: cord-337973-djqzgc1k author: Hao, Siyuan title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-337973-djqzgc1k.txt cache: ./cache/cord-337973-djqzgc1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337973-djqzgc1k.txt' === file2bib.sh === id: cord-338225-8dlxnpcn author: De Meyer, Sandra title: Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-338225-8dlxnpcn.txt cache: ./cache/cord-338225-8dlxnpcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338225-8dlxnpcn.txt' === file2bib.sh === id: cord-337636-3yc0ribg author: Morehouse, Zachary P. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-337636-3yc0ribg.txt cache: ./cache/cord-337636-3yc0ribg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337636-3yc0ribg.txt' === file2bib.sh === id: cord-337372-y43prnko author: bin‐Reza, Faisal title: The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence date: 2011-12-21 pages: extension: .txt txt: ./txt/cord-337372-y43prnko.txt cache: ./cache/cord-337372-y43prnko.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337372-y43prnko.txt' === file2bib.sh === id: cord-338023-gb5jgqcg author: Obara, Shinju title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-338023-gb5jgqcg.txt cache: ./cache/cord-338023-gb5jgqcg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338023-gb5jgqcg.txt' === file2bib.sh === id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 pages: extension: .txt txt: ./txt/cord-337673-1nau263l.txt cache: ./cache/cord-337673-1nau263l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337673-1nau263l.txt' === file2bib.sh === id: cord-338123-4pshh5ov author: nan title: SARS Alert Applicability date: 2004-08-17 pages: extension: .txt txt: ./txt/cord-338123-4pshh5ov.txt cache: ./cache/cord-338123-4pshh5ov.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338123-4pshh5ov.txt' === file2bib.sh === id: cord-337137-0ey40gzw author: Lo, Anthony WI title: How the SARS coronavirus causes disease: host or organism? date: 2005-12-17 pages: extension: .txt txt: ./txt/cord-337137-0ey40gzw.txt cache: ./cache/cord-337137-0ey40gzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337137-0ey40gzw.txt' === file2bib.sh === id: cord-338097-kdrq81w5 author: Brescia, Marilia D'Elboux Guimarães title: “Green July” 2020 and Another Good Reason to Quit Smoking: Help to Stop Spreading SARS-COV-2 and Save Lives! date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-338097-kdrq81w5.txt cache: ./cache/cord-338097-kdrq81w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338097-kdrq81w5.txt' === file2bib.sh === id: cord-338333-yvm3d6xy author: Tu, Danna title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-338333-yvm3d6xy.txt cache: ./cache/cord-338333-yvm3d6xy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338333-yvm3d6xy.txt' === file2bib.sh === id: cord-338001-jig46hsk author: Ong, Jacqueline S. M. title: Coronavirus Disease 2019 in Critically Ill Children: A Narrative Review of the Literature date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-338001-jig46hsk.txt cache: ./cache/cord-338001-jig46hsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338001-jig46hsk.txt' === file2bib.sh === id: cord-338054-n2r4pzan author: Lau, Joseph TF title: Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date: 2007-03-15 pages: extension: .txt txt: ./txt/cord-338054-n2r4pzan.txt cache: ./cache/cord-338054-n2r4pzan.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338054-n2r4pzan.txt' === file2bib.sh === id: cord-337663-ow1l18li author: Qu, Liang G. title: Scoping review: hotspots for COVID-19 urological research: what is being published and from where? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-337663-ow1l18li.txt cache: ./cache/cord-337663-ow1l18li.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337663-ow1l18li.txt' === file2bib.sh === id: cord-338359-pd4bfjet author: Yu, J. title: Risk assessment of admission procedures for cancer patients during the convalescence of COVID-19 date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-338359-pd4bfjet.txt cache: ./cache/cord-338359-pd4bfjet.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338359-pd4bfjet.txt' === file2bib.sh === id: cord-337681-579cz2tc author: Sk, Md Fulbabu title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-337681-579cz2tc.txt cache: ./cache/cord-337681-579cz2tc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337681-579cz2tc.txt' === file2bib.sh === id: cord-337896-mct29erg author: Kornbluth, Asher title: Management of Inflammatory Bowel Disease and COVID-19 in New York City 2020: The Epicenter of IBD in the First Epicenter of the Global Pandemic date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-337896-mct29erg.txt cache: ./cache/cord-337896-mct29erg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337896-mct29erg.txt' === file2bib.sh === id: cord-338203-le5lbw5y author: O’Reilly, GM title: Epidemiology and clinical features of emergency department patients with suspected COVID‐19: Results from the first month of the COVED Quality Improvement Project (COVED‐2). date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-338203-le5lbw5y.txt cache: ./cache/cord-338203-le5lbw5y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338203-le5lbw5y.txt' === file2bib.sh === id: cord-338543-q6cl5kjp author: Salguero, Francisco J. title: Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-338543-q6cl5kjp.txt cache: ./cache/cord-338543-q6cl5kjp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338543-q6cl5kjp.txt' === file2bib.sh === id: cord-337692-b89ow1mf author: Petti, S. title: Ecologic association between influenza and COVID-19 mortality rates in European countries date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-337692-b89ow1mf.txt cache: ./cache/cord-337692-b89ow1mf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337692-b89ow1mf.txt' === file2bib.sh === id: cord-337789-pabaoiqs author: Oprinca, George-Călin title: Postmortem examination of three SARS-CoV-2-positive autopsies including histopathologic and immunohistochemical analysis date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-337789-pabaoiqs.txt cache: ./cache/cord-337789-pabaoiqs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337789-pabaoiqs.txt' === file2bib.sh === id: cord-338351-y1t9emu1 author: Ora, Josuel title: Does bronchoscopy help the diagnosis in Covid-19 infection? date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-338351-y1t9emu1.txt cache: ./cache/cord-338351-y1t9emu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338351-y1t9emu1.txt' === file2bib.sh === id: cord-338544-eph89g47 author: Spuntarelli, Valerio title: COVID-19: is it just a lung disease? A case-based review date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-338544-eph89g47.txt cache: ./cache/cord-338544-eph89g47.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338544-eph89g47.txt' === file2bib.sh === id: cord-338723-3vm23fgy author: Lee, In-Hee title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-338723-3vm23fgy.txt cache: ./cache/cord-338723-3vm23fgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338723-3vm23fgy.txt' === file2bib.sh === id: cord-337105-jlmh79qv author: Jacob, Fadi title: Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-337105-jlmh79qv.txt cache: ./cache/cord-337105-jlmh79qv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337105-jlmh79qv.txt' === file2bib.sh === id: cord-338243-njkhwkwk author: Zhang, Dayi title: Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-338243-njkhwkwk.txt cache: ./cache/cord-338243-njkhwkwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338243-njkhwkwk.txt' === file2bib.sh === id: cord-337867-hqmf6r7t author: Shim, Byoung-Shik title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses date: 2010-12-31 pages: extension: .txt txt: ./txt/cord-337867-hqmf6r7t.txt cache: ./cache/cord-337867-hqmf6r7t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337867-hqmf6r7t.txt' === file2bib.sh === id: cord-337962-9le56say author: Duan, Fuyu title: Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-337962-9le56say.txt cache: ./cache/cord-337962-9le56say.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337962-9le56say.txt' === file2bib.sh === id: cord-337712-ylqgraos author: Heinz, Franz X. title: Profile of SARS-CoV-2 date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-337712-ylqgraos.txt cache: ./cache/cord-337712-ylqgraos.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337712-ylqgraos.txt' === file2bib.sh === id: cord-338798-xsun927w author: Ciorba, Andrea title: Ototoxicity prevention during the SARS-CoV-2 (Covid-19) emergency date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-338798-xsun927w.txt cache: ./cache/cord-338798-xsun927w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338798-xsun927w.txt' === file2bib.sh === id: cord-338140-p88fgojk author: Cervantes-Pérez, Enrique title: Medical Nutrition Therapy in Hospitalized Patients With SARS-CoV-2 (COVID-19) Infection in a Non-critical Care Setting: Knowledge in Progress date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-338140-p88fgojk.txt cache: ./cache/cord-338140-p88fgojk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338140-p88fgojk.txt' === file2bib.sh === id: cord-338647-dtuohsf5 author: Başcı, Semih title: Outcome of COVID-19 in patients with chronic myeloid leukemia receiving tyrosine kinase inhibitors date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-338647-dtuohsf5.txt cache: ./cache/cord-338647-dtuohsf5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338647-dtuohsf5.txt' === file2bib.sh === id: cord-338790-rvdoq616 author: Wang, Xiaowen title: Be aware of acute kidney injury in critically ill children with COVID-19 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-338790-rvdoq616.txt cache: ./cache/cord-338790-rvdoq616.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338790-rvdoq616.txt' === file2bib.sh === id: cord-338417-7kw9lws0 author: Singh, Awadhesh Kumar title: Comorbidities in COVID-19: Outcomes in hypertensive cohort and controversies with renin angiotensin system blockers date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-338417-7kw9lws0.txt cache: ./cache/cord-338417-7kw9lws0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338417-7kw9lws0.txt' === file2bib.sh === id: cord-337812-arivkkj0 author: Chu, Ling-Hon Matthew title: Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry date: 2006-03-07 pages: extension: .txt txt: ./txt/cord-337812-arivkkj0.txt cache: ./cache/cord-337812-arivkkj0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337812-arivkkj0.txt' === file2bib.sh === id: cord-338041-gl65i3s0 author: Tang, Qin title: Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date: 2015-11-26 pages: extension: .txt txt: ./txt/cord-338041-gl65i3s0.txt cache: ./cache/cord-338041-gl65i3s0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338041-gl65i3s0.txt' === file2bib.sh === id: cord-338320-jc00ulx5 author: Siu, Kam-Leung title: Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain date: 2014-02-10 pages: extension: .txt txt: ./txt/cord-338320-jc00ulx5.txt cache: ./cache/cord-338320-jc00ulx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338320-jc00ulx5.txt' === file2bib.sh === id: cord-338755-f5g2r4n9 author: Alam, Nawsad title: A spike with which to beat COVID-19? date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-338755-f5g2r4n9.txt cache: ./cache/cord-338755-f5g2r4n9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338755-f5g2r4n9.txt' === file2bib.sh === id: cord-338317-ro041w5l author: Lockhart, Sam M. title: When two pandemics meet: Why is obesity associated with increased COVID-19 mortality? date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-338317-ro041w5l.txt cache: ./cache/cord-338317-ro041w5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338317-ro041w5l.txt' === file2bib.sh === id: cord-338403-mfde6juv author: Li, Bo title: Prevalence and impact of cardiovascular metabolic diseases on COVID-19 in China date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-338403-mfde6juv.txt cache: ./cache/cord-338403-mfde6juv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338403-mfde6juv.txt' === file2bib.sh === id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-336554-n8n5ii5k.txt cache: ./cache/cord-336554-n8n5ii5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336554-n8n5ii5k.txt' === file2bib.sh === id: cord-339570-vf79fefg author: Jain, Vidhi title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-339570-vf79fefg.txt cache: ./cache/cord-339570-vf79fefg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339570-vf79fefg.txt' === file2bib.sh === id: cord-338578-e0aiknb6 author: Patel, Kajal title: Applying the WHO ICF Framework to the Outcome Measures Used in the Evaluation of Long-Term Clinical Outcomes in Coronavirus Outbreaks date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-338578-e0aiknb6.txt cache: ./cache/cord-338578-e0aiknb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338578-e0aiknb6.txt' === file2bib.sh === id: cord-338055-2d6n4cve author: Hassan, Sk. Sarif title: A unique view of SARS-CoV-2 through the lens of ORF8 protein date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-338055-2d6n4cve.txt cache: ./cache/cord-338055-2d6n4cve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338055-2d6n4cve.txt' === file2bib.sh === id: cord-338689-4u1ezk64 author: Ata, Fateen title: COVID-19 presenting with diarrhoea and hyponatraemia date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-338689-4u1ezk64.txt cache: ./cache/cord-338689-4u1ezk64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338689-4u1ezk64.txt' === file2bib.sh === id: cord-338751-2eo7ityc author: Anzalone, Nicoletta title: Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-338751-2eo7ityc.txt cache: ./cache/cord-338751-2eo7ityc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338751-2eo7ityc.txt' === file2bib.sh === id: cord-338468-c0jv3i1t author: Kanduc, Darja title: From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-338468-c0jv3i1t.txt cache: ./cache/cord-338468-c0jv3i1t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338468-c0jv3i1t.txt' === file2bib.sh === id: cord-339352-c9uh8vjx author: Islam, Muhammad Torequl title: Environmental Integrants Affecting the Spreadability of SARS-CoV-12 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-339352-c9uh8vjx.txt cache: ./cache/cord-339352-c9uh8vjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339352-c9uh8vjx.txt' === file2bib.sh === id: cord-339077-pxf2u68u author: Zerwes, Sebastian title: Erhöhtes Risiko für tiefe Beinvenenthrombosen bei Intensivpatienten mit CoViD-19-Infektion? – Erste Daten date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-339077-pxf2u68u.txt cache: ./cache/cord-339077-pxf2u68u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339077-pxf2u68u.txt' === file2bib.sh === id: cord-338923-hc7gagnq author: Jääskeläinen, AJ title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-338923-hc7gagnq.txt cache: ./cache/cord-338923-hc7gagnq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338923-hc7gagnq.txt' === file2bib.sh === id: cord-338648-5evr2v3r author: Shental, Noam title: Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-338648-5evr2v3r.txt cache: ./cache/cord-338648-5evr2v3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338648-5evr2v3r.txt' === file2bib.sh === id: cord-338744-2kizbzns author: González-Castro, A. title: Síndrome post-cuidados intensivos después de la pandemia por SARS-CoV-2 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-338744-2kizbzns.txt cache: ./cache/cord-338744-2kizbzns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338744-2kizbzns.txt' === file2bib.sh === id: cord-339241-e2nl766y author: Turriziani, Ombretta title: SARS‐CoV‐2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-339241-e2nl766y.txt cache: ./cache/cord-339241-e2nl766y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339241-e2nl766y.txt' === file2bib.sh === id: cord-339303-feiy6xed author: Tan, Xiaodong title: Severe Acute Respiratory Syndrome epidemic and change of people's health behavior in China date: 2004-10-17 pages: extension: .txt txt: ./txt/cord-339303-feiy6xed.txt cache: ./cache/cord-339303-feiy6xed.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339303-feiy6xed.txt' === file2bib.sh === id: cord-338684-po3hfibp author: Cheong, Kai Xiong title: Systematic Review of Ocular Involvement of SARS-CoV-2 in Coronavirus Disease 2019 date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-338684-po3hfibp.txt cache: ./cache/cord-338684-po3hfibp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338684-po3hfibp.txt' === file2bib.sh === id: cord-339128-npfoircv author: Blair, Robert V. title: Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-339128-npfoircv.txt cache: ./cache/cord-339128-npfoircv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339128-npfoircv.txt' === file2bib.sh === id: cord-339329-8yvre7qc author: Kumar, Prashant title: Could fighting airborne transmission be the next line of defence against COVID-19 spread? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-339329-8yvre7qc.txt cache: ./cache/cord-339329-8yvre7qc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339329-8yvre7qc.txt' === file2bib.sh === id: cord-338775-gh3a0wuf author: Gulersen, Moti title: Histopathological evaluation of placentas after diagnosis of maternal SARS-CoV-2 infection date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-338775-gh3a0wuf.txt cache: ./cache/cord-338775-gh3a0wuf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338775-gh3a0wuf.txt' === file2bib.sh === id: cord-339381-vvh06d2c author: Han, Deheng title: SARS‐CoV‐2 was found in the bile juice from a patient with severe COVID‐19 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-339381-vvh06d2c.txt cache: ./cache/cord-339381-vvh06d2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339381-vvh06d2c.txt' === file2bib.sh === id: cord-338734-laeocs3j author: Lima, Amorce title: Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-338734-laeocs3j.txt cache: ./cache/cord-338734-laeocs3j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338734-laeocs3j.txt' === file2bib.sh === id: cord-339271-t7cxqkp1 author: Pan, Yanfeng title: Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-339271-t7cxqkp1.txt cache: ./cache/cord-339271-t7cxqkp1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339271-t7cxqkp1.txt' === file2bib.sh === id: cord-339516-xfwxtjry author: Nakashima, Tsutomu title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-339516-xfwxtjry.txt cache: ./cache/cord-339516-xfwxtjry.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339516-xfwxtjry.txt' === file2bib.sh === id: cord-338741-gy3ovkrt author: Sethi, Atin title: Evaluation of Current Therapies for COVID-19 Treatment date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-338741-gy3ovkrt.txt cache: ./cache/cord-338741-gy3ovkrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338741-gy3ovkrt.txt' === file2bib.sh === id: cord-339859-anatn295 author: Paret, Michal title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-339859-anatn295.txt cache: ./cache/cord-339859-anatn295.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339859-anatn295.txt' === file2bib.sh === id: cord-338972-uq2ha8xs author: Olson, Michael T. title: Resumption of elective surgery during the COVID-19 pandemic: what lessons can we apply? date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-338972-uq2ha8xs.txt cache: ./cache/cord-338972-uq2ha8xs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338972-uq2ha8xs.txt' === file2bib.sh === id: cord-338928-y5l7cf31 author: Leonardi, Matilde title: Neurological manifestations associated with COVID-19: a review and a call for action date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-338928-y5l7cf31.txt cache: ./cache/cord-338928-y5l7cf31.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338928-y5l7cf31.txt' === file2bib.sh === id: cord-338683-nzgnpi6f author: Karligkiotis, Apostolos title: Changing paradigms in sinus and skull base surgery as the COVID‐19 pandemic evolves: Preliminary experience from a single Italian tertiary care center date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-338683-nzgnpi6f.txt cache: ./cache/cord-338683-nzgnpi6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338683-nzgnpi6f.txt' === file2bib.sh === id: cord-338365-9sd62a2w author: Patrício Silva, Ana L. title: Increased plastic pollution due to Covid-19 pandemic: challenges and recommendations date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-338365-9sd62a2w.txt cache: ./cache/cord-338365-9sd62a2w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338365-9sd62a2w.txt' === file2bib.sh === id: cord-338680-wwlttymp author: Khonyongwa, K. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-338680-wwlttymp.txt cache: ./cache/cord-338680-wwlttymp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338680-wwlttymp.txt' === file2bib.sh === id: cord-338517-1mxcssjj author: Ishay, Yuval title: Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-338517-1mxcssjj.txt cache: ./cache/cord-338517-1mxcssjj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-338517-1mxcssjj.txt' === file2bib.sh === id: cord-336000-v88bq4bx author: Barco, Stefano title: Enoxaparin for primary thromboprophylaxis in ambulatory patients with coronavirus disease-2019 (the OVID study): a structured summary of a study protocol for a randomized controlled trial date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-336000-v88bq4bx.txt cache: ./cache/cord-336000-v88bq4bx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336000-v88bq4bx.txt' === file2bib.sh === id: cord-340010-t1m7dxzc author: Schaefer, Esperance A. K. title: Interrelationship Between Coronavirus Infection and Liver Disease date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-340010-t1m7dxzc.txt cache: ./cache/cord-340010-t1m7dxzc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340010-t1m7dxzc.txt' === file2bib.sh === id: cord-339669-p61j2caf author: Monzani, Alice title: QTc evaluation in COVID‐19 patients treated with chloroquine/hydroxychloroquine date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-339669-p61j2caf.txt cache: ./cache/cord-339669-p61j2caf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339669-p61j2caf.txt' === file2bib.sh === id: cord-338205-sy91rnse author: Li, Chenxi title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-338205-sy91rnse.txt cache: ./cache/cord-338205-sy91rnse.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338205-sy91rnse.txt' === file2bib.sh === id: cord-339009-wcoch07b author: File, Thomas M. title: Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date: 2012-08-23 pages: extension: .txt txt: ./txt/cord-339009-wcoch07b.txt cache: ./cache/cord-339009-wcoch07b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339009-wcoch07b.txt' === file2bib.sh === id: cord-339670-lq46nj8j author: Takahashi, Nozomi title: Clinical course of a critically ill patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-339670-lq46nj8j.txt cache: ./cache/cord-339670-lq46nj8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339670-lq46nj8j.txt' === file2bib.sh === id: cord-339576-0d6sa9pe author: Guallar, María Pilar title: Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-339576-0d6sa9pe.txt cache: ./cache/cord-339576-0d6sa9pe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339576-0d6sa9pe.txt' === file2bib.sh === id: cord-339568-th2xmhb6 author: Yan, Meitian title: Analysis of the diagnostic value of serum specific antibody testing for coronavirus disease 2019 date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-339568-th2xmhb6.txt cache: ./cache/cord-339568-th2xmhb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339568-th2xmhb6.txt' === file2bib.sh === id: cord-338901-1kzy7rts author: Li, Heng title: Overview of therapeutic drug research for COVID-19 in China date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-338901-1kzy7rts.txt cache: ./cache/cord-338901-1kzy7rts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338901-1kzy7rts.txt' === file2bib.sh === id: cord-338979-ew046wcr author: Jasti, Madhu title: A review of pathophysiology and neuropsychiatric manifestations of COVID-19 date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-338979-ew046wcr.txt cache: ./cache/cord-338979-ew046wcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338979-ew046wcr.txt' === file2bib.sh === id: cord-339431-kyr5lv15 author: Saçar Demirci, Müşerref Duygu title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-339431-kyr5lv15.txt cache: ./cache/cord-339431-kyr5lv15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339431-kyr5lv15.txt' === file2bib.sh === id: cord-339514-0aa58pi6 author: Ho, Yu title: Assembly of human severe acute respiratory syndrome coronavirus-like particles date: 2004-06-11 pages: extension: .txt txt: ./txt/cord-339514-0aa58pi6.txt cache: ./cache/cord-339514-0aa58pi6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339514-0aa58pi6.txt' === file2bib.sh === id: cord-339459-z22a5yzo author: Mackey, Katherine title: Risks and Impact of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers on SARS-CoV-2 Infection in Adults: A Living Systematic Review date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-339459-z22a5yzo.txt cache: ./cache/cord-339459-z22a5yzo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339459-z22a5yzo.txt' === file2bib.sh === id: cord-338541-0yiuh017 author: Hannan, Md. Abdul title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-338541-0yiuh017.txt cache: ./cache/cord-338541-0yiuh017.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338541-0yiuh017.txt' === file2bib.sh === id: cord-339625-ucfjo73c author: Qiu, Xiang title: Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus date: 2012-07-26 pages: extension: .txt txt: ./txt/cord-339625-ucfjo73c.txt cache: ./cache/cord-339625-ucfjo73c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339625-ucfjo73c.txt' === file2bib.sh === id: cord-339524-r0a6a1jw author: Islam, M. T. title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-339524-r0a6a1jw.txt cache: ./cache/cord-339524-r0a6a1jw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339524-r0a6a1jw.txt' === file2bib.sh === id: cord-338436-0z828org author: Tzou, Philip L. title: Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-338436-0z828org.txt cache: ./cache/cord-338436-0z828org.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338436-0z828org.txt' === file2bib.sh === id: cord-339772-q814d6l7 author: Pach, Szymon title: ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-339772-q814d6l7.txt cache: ./cache/cord-339772-q814d6l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339772-q814d6l7.txt' === file2bib.sh === id: cord-339521-qfnu319w author: Lin, Shiming title: Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy date: 2005-08-08 pages: extension: .txt txt: ./txt/cord-339521-qfnu319w.txt cache: ./cache/cord-339521-qfnu319w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339521-qfnu319w.txt' === file2bib.sh === id: cord-339762-lh8czr0a author: Ng, Dianna L. title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 date: 2016-03-31 pages: extension: .txt txt: ./txt/cord-339762-lh8czr0a.txt cache: ./cache/cord-339762-lh8czr0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339762-lh8czr0a.txt' === file2bib.sh === id: cord-338980-pygykil7 author: Rahaman, Jordon title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date: 2016-11-09 pages: extension: .txt txt: ./txt/cord-338980-pygykil7.txt cache: ./cache/cord-338980-pygykil7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338980-pygykil7.txt' === file2bib.sh === id: cord-339012-4juhmjaj author: Hou, Wei title: Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-339012-4juhmjaj.txt cache: ./cache/cord-339012-4juhmjaj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339012-4juhmjaj.txt' === file2bib.sh === id: cord-339019-vgnxhksv author: Lee, Ting-Wai title: Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase date: 2007-02-23 pages: extension: .txt txt: ./txt/cord-339019-vgnxhksv.txt cache: ./cache/cord-339019-vgnxhksv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339019-vgnxhksv.txt' === file2bib.sh === id: cord-339701-j0sr3ifq author: Mikami, Takahisa title: Risk Factors for Mortality in Patients with COVID-19 in New York City date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-339701-j0sr3ifq.txt cache: ./cache/cord-339701-j0sr3ifq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339701-j0sr3ifq.txt' === file2bib.sh === id: cord-339506-pkusvf82 author: Zaki, N. title: The estimations of the COVID-19 incubation period: a systematic review of the literature date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-339506-pkusvf82.txt cache: ./cache/cord-339506-pkusvf82.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339506-pkusvf82.txt' === file2bib.sh === id: cord-339782-rybjc58j author: Carmo, Anália title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-339782-rybjc58j.txt cache: ./cache/cord-339782-rybjc58j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339782-rybjc58j.txt' === file2bib.sh === id: cord-339709-49q2xxkw author: sermet, i. title: Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-339709-49q2xxkw.txt cache: ./cache/cord-339709-49q2xxkw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339709-49q2xxkw.txt' === file2bib.sh === id: cord-339934-g6ufz29l author: Yu, Hai-qiong title: Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-339934-g6ufz29l.txt cache: ./cache/cord-339934-g6ufz29l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339934-g6ufz29l.txt' === file2bib.sh === id: cord-339508-nf6ov39g author: Weil, Ana A. title: Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-339508-nf6ov39g.txt cache: ./cache/cord-339508-nf6ov39g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339508-nf6ov39g.txt' === file2bib.sh === id: cord-339344-qd73h1ie author: Simon, David title: Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-339344-qd73h1ie.txt cache: ./cache/cord-339344-qd73h1ie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339344-qd73h1ie.txt' === file2bib.sh === id: cord-337825-ujq9mxk7 author: Chen, Bin title: Overview of lethal human coronaviruses date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-337825-ujq9mxk7.txt cache: ./cache/cord-337825-ujq9mxk7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337825-ujq9mxk7.txt' === file2bib.sh === id: cord-340015-x9frt0jh author: de Carvalho, Werther Brunow title: Expert recommendations for the care of newborns of mothers with COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-340015-x9frt0jh.txt cache: ./cache/cord-340015-x9frt0jh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340015-x9frt0jh.txt' === file2bib.sh === id: cord-340103-dc3wye9s author: Pallanti, Stefano title: Importance of SARs-Cov-2 anosmia: From phenomenology to neurobiology date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-340103-dc3wye9s.txt cache: ./cache/cord-340103-dc3wye9s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340103-dc3wye9s.txt' === file2bib.sh === id: cord-339711-f7xifne8 author: Bal, A. title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-339711-f7xifne8.txt cache: ./cache/cord-339711-f7xifne8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339711-f7xifne8.txt' === file2bib.sh === id: cord-340070-de7sfccy author: Pérez-Martinez, Antonio title: Clinical outcome of SARS-CoV-2 infection in immunosuppressed children in Spain date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-340070-de7sfccy.txt cache: ./cache/cord-340070-de7sfccy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340070-de7sfccy.txt' === file2bib.sh === id: cord-339752-o6atz33c author: Xiao, Li title: ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel? date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-339752-o6atz33c.txt cache: ./cache/cord-339752-o6atz33c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339752-o6atz33c.txt' === file2bib.sh === id: cord-340049-6rqmc89u author: Salvatori, Giovanni title: SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-340049-6rqmc89u.txt cache: ./cache/cord-340049-6rqmc89u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340049-6rqmc89u.txt' === file2bib.sh === id: cord-339720-d1stzy8w author: Zhao, Yuan title: Susceptibility of tree shrew to SARS-CoV-2 infection date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-339720-d1stzy8w.txt cache: ./cache/cord-339720-d1stzy8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339720-d1stzy8w.txt' === file2bib.sh === id: cord-339558-li65qvq9 author: Rana, Rashmi title: A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-339558-li65qvq9.txt cache: ./cache/cord-339558-li65qvq9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339558-li65qvq9.txt' === file2bib.sh === id: cord-338973-73a7uvyz author: Xu, Jiabao title: Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-338973-73a7uvyz.txt cache: ./cache/cord-338973-73a7uvyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338973-73a7uvyz.txt' === file2bib.sh === id: cord-340240-dk48pdqa author: Kuo, Tsun-Yung title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-340240-dk48pdqa.txt cache: ./cache/cord-340240-dk48pdqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340240-dk48pdqa.txt' === file2bib.sh === id: cord-340336-u59l0taa author: Perchetti, Garrett A. title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-340336-u59l0taa.txt cache: ./cache/cord-340336-u59l0taa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340336-u59l0taa.txt' === file2bib.sh === id: cord-339817-qqitdrz6 author: Sousa Gonçalves, Catarina title: Erythematous Papular Rash: A Dermatological Feature of COVID-19 date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-339817-qqitdrz6.txt cache: ./cache/cord-339817-qqitdrz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339817-qqitdrz6.txt' === file2bib.sh === id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-339976-tg2jkss7.txt cache: ./cache/cord-339976-tg2jkss7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339976-tg2jkss7.txt' === file2bib.sh === id: cord-338498-3238fz73 author: Kleen, Thomas-Oliver title: Mitigating Coronavirus Induced Dysfunctional Immunity for At-Risk Populations in COVID-19: Trained Immunity, BCG and “New Old Friends” date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-338498-3238fz73.txt cache: ./cache/cord-338498-3238fz73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338498-3238fz73.txt' === file2bib.sh === id: cord-339786-elrzlbsg author: Gurala, Dhineshreddy title: Acute Liver Failure in a COVID-19 Patient Without any Preexisting Liver Disease date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-339786-elrzlbsg.txt cache: ./cache/cord-339786-elrzlbsg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339786-elrzlbsg.txt' === file2bib.sh === id: cord-339665-nwwutduy author: Patel, Ami title: Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-339665-nwwutduy.txt cache: ./cache/cord-339665-nwwutduy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339665-nwwutduy.txt' === file2bib.sh === id: cord-340114-ycgc6yyc author: Rajagopal, Kalirajan title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-340114-ycgc6yyc.txt cache: ./cache/cord-340114-ycgc6yyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340114-ycgc6yyc.txt' === file2bib.sh === id: cord-339951-how9cmw8 author: Zhou, Yaqing title: Clinical and Autoimmune Characteristics of Severe and Critical Cases of COVID‐19 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-339951-how9cmw8.txt cache: ./cache/cord-339951-how9cmw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339951-how9cmw8.txt' === file2bib.sh === id: cord-340205-cwn0gx7h author: Chen, Yih-Ting title: Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-340205-cwn0gx7h.txt cache: ./cache/cord-340205-cwn0gx7h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340205-cwn0gx7h.txt' === file2bib.sh === id: cord-340201-ai4apr4w author: List, Wolfgang title: Occurrence of SARS-CoV-2 in the intraocular milieu date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-340201-ai4apr4w.txt cache: ./cache/cord-340201-ai4apr4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340201-ai4apr4w.txt' === file2bib.sh === id: cord-340291-bah2ege0 author: Kohmer, Niko title: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-340291-bah2ege0.txt cache: ./cache/cord-340291-bah2ege0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340291-bah2ege0.txt' === file2bib.sh === id: cord-340138-u8hxyfml author: Seneviratne, Chaminda Jayampath title: The Role of Dentists in COVID-19 Is Beyond Dentistry: Voluntary Medical Engagements and Future Preparedness date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-340138-u8hxyfml.txt cache: ./cache/cord-340138-u8hxyfml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340138-u8hxyfml.txt' === file2bib.sh === id: cord-340351-ee8wjp5u author: Jiang, Fa-Chun title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-340351-ee8wjp5u.txt cache: ./cache/cord-340351-ee8wjp5u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340351-ee8wjp5u.txt' === file2bib.sh === id: cord-340063-nmx91h0a author: Müller, Olaf title: Epidemiologie und Kontrollmaßnahmen bei COVID-19 date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-340063-nmx91h0a.txt cache: ./cache/cord-340063-nmx91h0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340063-nmx91h0a.txt' === file2bib.sh === id: cord-340323-xz6v95yy author: Urbach, Horst title: Notfällige Neurointerventionen, Covid-19 und Thorax-CT: SOP und Literaturübersicht date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-340323-xz6v95yy.txt cache: ./cache/cord-340323-xz6v95yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-340323-xz6v95yy.txt' === file2bib.sh === id: cord-340008-2efzyki4 author: Haddadi, Kaveh title: Coronavirus Disease 2019: Latest Data on Neuroinvasive Potential date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-340008-2efzyki4.txt cache: ./cache/cord-340008-2efzyki4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340008-2efzyki4.txt' === file2bib.sh === id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 pages: extension: .txt txt: ./txt/cord-339172-210dwhgj.txt cache: ./cache/cord-339172-210dwhgj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339172-210dwhgj.txt' === file2bib.sh === id: cord-340279-bq5owwot author: Espíndola, Otávio de Melo title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-340279-bq5owwot.txt cache: ./cache/cord-340279-bq5owwot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-340279-bq5owwot.txt' === file2bib.sh === id: cord-340410-s9haq8y1 author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-340410-s9haq8y1.txt cache: ./cache/cord-340410-s9haq8y1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340410-s9haq8y1.txt' === file2bib.sh === id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-339386-sxyeuiw1.txt cache: ./cache/cord-339386-sxyeuiw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339386-sxyeuiw1.txt' === file2bib.sh === id: cord-339436-0k73tlna author: Giagulli, Vito Angelo title: Worse progression of COVID‐19 in men: Is Testosterone a key factor? date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-339436-0k73tlna.txt cache: ./cache/cord-339436-0k73tlna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339436-0k73tlna.txt' === file2bib.sh === id: cord-340260-z13aa1wk author: Farewell, V. T. title: SARS incubation and quarantine times: when is an exposed individual known to be disease free? date: 2005-10-19 pages: extension: .txt txt: ./txt/cord-340260-z13aa1wk.txt cache: ./cache/cord-340260-z13aa1wk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340260-z13aa1wk.txt' === file2bib.sh === id: cord-340523-wujzihbn author: Ravelli, Angelo title: Kawasaki disease or Kawasaki syndrome? date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-340523-wujzihbn.txt cache: ./cache/cord-340523-wujzihbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340523-wujzihbn.txt' === file2bib.sh === id: cord-340252-9gr2iw15 author: Olalla, J. title: Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-340252-9gr2iw15.txt cache: ./cache/cord-340252-9gr2iw15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340252-9gr2iw15.txt' === file2bib.sh === id: cord-339727-q8pjwl3s author: Sahu, Kamal Kant title: Mesenchymal Stem Cells in COVID-19: A Journey from Bench to Bedside date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-339727-q8pjwl3s.txt cache: ./cache/cord-339727-q8pjwl3s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339727-q8pjwl3s.txt' === file2bib.sh === id: cord-341069-kngf6qpe author: Chan, Kwok-Hung title: Factors affecting stability and infectivity of SARS-CoV-2 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-341069-kngf6qpe.txt cache: ./cache/cord-341069-kngf6qpe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-341069-kngf6qpe.txt' === file2bib.sh === id: cord-340535-78bpvtuf author: Elbay, Rümeysa Yeni title: Depression, Anxiety, Stress Levels of Physicians and Associated Factors In Covid-19 Pandemics date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-340535-78bpvtuf.txt cache: ./cache/cord-340535-78bpvtuf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340535-78bpvtuf.txt' === file2bib.sh === id: cord-339726-eg0hajzl author: Jamrozik, Euzebiusz title: Coronavirus Human Infection Challenge Studies: Assessing Potential Benefits and Risks date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-339726-eg0hajzl.txt cache: ./cache/cord-339726-eg0hajzl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339726-eg0hajzl.txt' === file2bib.sh === id: cord-340590-7jql1ftj author: Massullo, Domenico title: Mountain Rescue During the COVID-19 Outbreak: Considerations and Practical Implications date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-340590-7jql1ftj.txt cache: ./cache/cord-340590-7jql1ftj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340590-7jql1ftj.txt' === file2bib.sh === id: cord-339968-s1kmipir author: Osier, Faith title: The global response to the COVID-19 pandemic: how have immunology societies contributed? date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-339968-s1kmipir.txt cache: ./cache/cord-339968-s1kmipir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339968-s1kmipir.txt' === file2bib.sh === id: cord-338589-1ent68fx author: Stoddard, Shana V. title: Optimization Rules for SARS-CoV-2 M(pro) Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-338589-1ent68fx.txt cache: ./cache/cord-338589-1ent68fx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338589-1ent68fx.txt' === file2bib.sh === id: cord-340432-vm6m0kb4 author: Srivastava, Sukrit title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-340432-vm6m0kb4.txt cache: ./cache/cord-340432-vm6m0kb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340432-vm6m0kb4.txt' === file2bib.sh === id: cord-340042-intxyu46 author: Chaudhry, Sundas Nasir title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-340042-intxyu46.txt cache: ./cache/cord-340042-intxyu46.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340042-intxyu46.txt' === file2bib.sh === id: cord-340619-3tjquzx8 author: Menghua, Wu title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-340619-3tjquzx8.txt cache: ./cache/cord-340619-3tjquzx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340619-3tjquzx8.txt' === file2bib.sh === id: cord-340305-jtvn9tlm author: Cimolai, Nevio title: A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-340305-jtvn9tlm.txt cache: ./cache/cord-340305-jtvn9tlm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340305-jtvn9tlm.txt' === file2bib.sh === id: cord-338889-7hd3iibk author: Solbakk, Jan Helge title: Back to WHAT? The role of research ethics in pandemic times date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-338889-7hd3iibk.txt cache: ./cache/cord-338889-7hd3iibk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338889-7hd3iibk.txt' === file2bib.sh === id: cord-339686-oybnk1j8 author: Suassuna, José Hermógenes Rocco title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-339686-oybnk1j8.txt cache: ./cache/cord-339686-oybnk1j8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339686-oybnk1j8.txt' === file2bib.sh === id: cord-340415-6fte7krp author: Thevarajan, Irani title: Clinical presentation and management of COVID‐19 date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-340415-6fte7krp.txt cache: ./cache/cord-340415-6fte7krp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340415-6fte7krp.txt' === file2bib.sh === id: cord-340666-zl9pp2h3 author: Reifer, Josh title: SARS-CoV-2 IgG antibody responses in New York City date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-340666-zl9pp2h3.txt cache: ./cache/cord-340666-zl9pp2h3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340666-zl9pp2h3.txt' === file2bib.sh === id: cord-340486-wydlqq2z author: Grandbastien, Manon title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-340486-wydlqq2z.txt cache: ./cache/cord-340486-wydlqq2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340486-wydlqq2z.txt' === file2bib.sh === id: cord-341000-9xs8aukq author: Ghiasvand, Fereshteh title: Symmetrical polyneuropathy in Coronavirus Disease 2019 (COVID-19) date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-341000-9xs8aukq.txt cache: ./cache/cord-341000-9xs8aukq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341000-9xs8aukq.txt' === file2bib.sh === id: cord-340579-cvze15cj author: Dudley, Joseph P title: Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-340579-cvze15cj.txt cache: ./cache/cord-340579-cvze15cj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340579-cvze15cj.txt' === file2bib.sh === id: cord-340357-gyvvcnuf author: Fallahi, Hamid Reza title: Being a front-line dentist during the Covid-19 pandemic: a literature review date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-340357-gyvvcnuf.txt cache: ./cache/cord-340357-gyvvcnuf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340357-gyvvcnuf.txt' === file2bib.sh === id: cord-340687-99ad1rwq author: Abourida, Yassamine title: Management of Severe COVID-19 in Pregnancy date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-340687-99ad1rwq.txt cache: ./cache/cord-340687-99ad1rwq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340687-99ad1rwq.txt' === file2bib.sh === id: cord-341045-75of9ys6 author: Shah, Abdullah title: Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-341045-75of9ys6.txt cache: ./cache/cord-341045-75of9ys6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341045-75of9ys6.txt' === file2bib.sh === id: cord-340537-pdvpmydk author: Bañon-Gonzalez, Rafael title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-340537-pdvpmydk.txt cache: ./cache/cord-340537-pdvpmydk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340537-pdvpmydk.txt' === file2bib.sh === id: cord-339093-mwxkvwaz author: Li, Wei title: High potency of a bivalent human VH domain in SARS-CoV-2 animal models date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-339093-mwxkvwaz.txt cache: ./cache/cord-339093-mwxkvwaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339093-mwxkvwaz.txt' === file2bib.sh === id: cord-340028-6oicmeam author: Zhavoronkov, Alex title: Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-340028-6oicmeam.txt cache: ./cache/cord-340028-6oicmeam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340028-6oicmeam.txt' === file2bib.sh === id: cord-340908-8q7i5ds3 author: D’Ambrosi, Riccardo title: Guidelines for Resuming Elective Hip and Knee Surgical Activity Following the COVID-19 Pandemic: An Italian Perspective date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-340908-8q7i5ds3.txt cache: ./cache/cord-340908-8q7i5ds3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340908-8q7i5ds3.txt' === file2bib.sh === id: cord-340563-hsj53inh author: Baud, David title: Using Probiotics to Flatten the Curve of Coronavirus Disease COVID-2019 Pandemic date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-340563-hsj53inh.txt cache: ./cache/cord-340563-hsj53inh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340563-hsj53inh.txt' === file2bib.sh === id: cord-339152-wfakzb6w author: Trovato, Maria title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-339152-wfakzb6w.txt cache: ./cache/cord-339152-wfakzb6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339152-wfakzb6w.txt' === file2bib.sh === id: cord-340581-ngwgb3y0 author: Abassi, Zaid title: ACE2, COVID-19 Infection, Inflammation, and Coagulopathy: Missing Pieces in the Puzzle date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-340581-ngwgb3y0.txt cache: ./cache/cord-340581-ngwgb3y0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340581-ngwgb3y0.txt' === file2bib.sh === id: cord-341246-fz66z2p2 author: Bhattacharyya, Pranab J title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-341246-fz66z2p2.txt cache: ./cache/cord-341246-fz66z2p2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341246-fz66z2p2.txt' === file2bib.sh === id: cord-340883-zf8jbhdl author: He, Zhongping title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 pages: extension: .txt txt: ./txt/cord-340883-zf8jbhdl.txt cache: ./cache/cord-340883-zf8jbhdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340883-zf8jbhdl.txt' === file2bib.sh === id: cord-341284-jmqdnart author: Panagopoulos, Periklis title: Lopinavir/ritonavir as a third agent in the antiviral regimen for SARS-CoV-2 infection date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-341284-jmqdnart.txt cache: ./cache/cord-341284-jmqdnart.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341284-jmqdnart.txt' === file2bib.sh === id: cord-340992-88t1c0zs author: Nikolai, Lea A title: Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-340992-88t1c0zs.txt cache: ./cache/cord-340992-88t1c0zs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340992-88t1c0zs.txt' === file2bib.sh === id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-340627-xyvzgkxl.txt cache: ./cache/cord-340627-xyvzgkxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340627-xyvzgkxl.txt' === file2bib.sh === id: cord-341254-xnj6slby author: Li, Hua title: A new and rapid approach for detecting COVID‐19 based on S1 protein fragments date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-341254-xnj6slby.txt cache: ./cache/cord-341254-xnj6slby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341254-xnj6slby.txt' === file2bib.sh === id: cord-340651-g3518bq2 author: Hsu, Chung-Hua title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-340651-g3518bq2.txt cache: ./cache/cord-340651-g3518bq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340651-g3518bq2.txt' === file2bib.sh === id: cord-340811-w4x4falm author: Frizzelli, Annalisa title: What happens to people’s lungs when they get coronavirus disease 2019? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-340811-w4x4falm.txt cache: ./cache/cord-340811-w4x4falm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340811-w4x4falm.txt' === file2bib.sh === id: cord-340970-389t032s author: Choy, Wai-Yan title: Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development date: 2004-06-01 pages: extension: .txt txt: ./txt/cord-340970-389t032s.txt cache: ./cache/cord-340970-389t032s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340970-389t032s.txt' === file2bib.sh === id: cord-341648-z4lflkmo author: Isaacs, David title: To what extent do children transmit SARS‐CoV‐2 virus? date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-341648-z4lflkmo.txt cache: ./cache/cord-341648-z4lflkmo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341648-z4lflkmo.txt' === file2bib.sh === id: cord-340821-kelq45dw author: Misrahi, James J. title: HHS/CDC Legal Response to SARS Outbreak date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-340821-kelq45dw.txt cache: ./cache/cord-340821-kelq45dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340821-kelq45dw.txt' === file2bib.sh === id: cord-341543-gcnph9gf author: Kuryntseva, P. title: A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-341543-gcnph9gf.txt cache: ./cache/cord-341543-gcnph9gf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341543-gcnph9gf.txt' === file2bib.sh === id: cord-341415-g781zhu6 author: Jhaveri, Kenar D. title: Thrombotic microangiopathy in a patient with COVID-19 date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-341415-g781zhu6.txt cache: ./cache/cord-341415-g781zhu6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341415-g781zhu6.txt' === file2bib.sh === id: cord-341234-2zgfcrwc author: Hallak, Jorge title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-341234-2zgfcrwc.txt cache: ./cache/cord-341234-2zgfcrwc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341234-2zgfcrwc.txt' === file2bib.sh === id: cord-340472-9ijlj4so author: Li, Wenhui title: Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 date: 2005-03-24 pages: extension: .txt txt: ./txt/cord-340472-9ijlj4so.txt cache: ./cache/cord-340472-9ijlj4so.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340472-9ijlj4so.txt' === file2bib.sh === id: cord-341776-y7kpp10x author: Hamm, C. title: Zusammenhang zwischen Angiotensinblockade und Influenza-A-Inzidenz date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-341776-y7kpp10x.txt cache: ./cache/cord-341776-y7kpp10x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-341776-y7kpp10x.txt' === file2bib.sh === id: cord-341670-o1v63zg8 author: Estevez-Ordonez, Dagoberto title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-341670-o1v63zg8.txt cache: ./cache/cord-341670-o1v63zg8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341670-o1v63zg8.txt' === file2bib.sh === id: cord-340857-teq5txm9 author: Galloro, Giuseppe title: SAFETY IN DIGESTIVE ENDOSCOPY PROCEDURES IN THE COVID ERA RECOMMENDATIONS IN PROGRES OF THE ITALIAN SOCIETY OF DIGESTIVE ENDOSCOPY date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-340857-teq5txm9.txt cache: ./cache/cord-340857-teq5txm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340857-teq5txm9.txt' === file2bib.sh === id: cord-340984-blkhfhe2 author: Gklinos, Panagiotis title: Neurological manifestations of COVID-19: a review of what we know so far date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-340984-blkhfhe2.txt cache: ./cache/cord-340984-blkhfhe2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340984-blkhfhe2.txt' === file2bib.sh === id: cord-340583-kjrxrk50 author: Castro‐Rodriguez, Jose A. title: Asthma and COVID‐19 in children – a systematic review and call for data date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-340583-kjrxrk50.txt cache: ./cache/cord-340583-kjrxrk50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340583-kjrxrk50.txt' === file2bib.sh === id: cord-341396-0tn06al2 author: Ni, Ling title: Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-341396-0tn06al2.txt cache: ./cache/cord-341396-0tn06al2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341396-0tn06al2.txt' === file2bib.sh === id: cord-341783-e7xz4utr author: Vistisen, Simon T. title: Risk and prognosis of COVID-19 in patients treated with renin–angiotensin–aldosterone inhibitors date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-341783-e7xz4utr.txt cache: ./cache/cord-341783-e7xz4utr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341783-e7xz4utr.txt' === file2bib.sh === id: cord-340656-ltd6ueoi author: Grant, Michael C. title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-340656-ltd6ueoi.txt cache: ./cache/cord-340656-ltd6ueoi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340656-ltd6ueoi.txt' === file2bib.sh === id: cord-341804-rnj3wtg4 author: Jin, Zhe title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-341804-rnj3wtg4.txt cache: ./cache/cord-341804-rnj3wtg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341804-rnj3wtg4.txt' === file2bib.sh === id: cord-340189-jo38hjqa author: Bar-On, Yinon M title: SARS-CoV-2 (COVID-19) by the numbers date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-340189-jo38hjqa.txt cache: ./cache/cord-340189-jo38hjqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340189-jo38hjqa.txt' === file2bib.sh === id: cord-341416-6bh08901 author: Smithgall, Marie C. title: Laboratory Testing of SARS CoV-2: A New York Institutional Experience date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-341416-6bh08901.txt cache: ./cache/cord-341416-6bh08901.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341416-6bh08901.txt' === file2bib.sh === id: cord-342254-vdovpfu1 author: Mugheddu, C. title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-342254-vdovpfu1.txt cache: ./cache/cord-342254-vdovpfu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342254-vdovpfu1.txt' === file2bib.sh === id: cord-341883-eh0aw3re author: Bellanger, Anne-Pauline title: Studying smoking benefit in farmer’s lung to understand Covid-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-341883-eh0aw3re.txt cache: ./cache/cord-341883-eh0aw3re.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341883-eh0aw3re.txt' === file2bib.sh === id: cord-340085-ywg4rhnn author: Maras, J. S. title: Multi-Omics integration analysis of respiratory specimen characterizes baseline molecular determinants associated with COVID-19 diagnosis. date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-340085-ywg4rhnn.txt cache: ./cache/cord-340085-ywg4rhnn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340085-ywg4rhnn.txt' === file2bib.sh === id: cord-340516-9dfaqsv7 author: Moore, Anne C. title: Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-340516-9dfaqsv7.txt cache: ./cache/cord-340516-9dfaqsv7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340516-9dfaqsv7.txt' === file2bib.sh === id: cord-340635-8wki7noy author: Yu, Bin title: Innate and adaptive immunity of murine neural stem cell-derived piRNA exosomes/microvesicles against pseudotyped SARS-CoV-2 and HIV-based lentivirus date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-340635-8wki7noy.txt cache: ./cache/cord-340635-8wki7noy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340635-8wki7noy.txt' === file2bib.sh === id: cord-340960-abanr641 author: Brigger, D. title: Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-340960-abanr641.txt cache: ./cache/cord-340960-abanr641.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340960-abanr641.txt' === file2bib.sh === id: cord-340942-oatf59k0 author: Magalhães, Jurandy Júnior Ferraz de title: Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-340942-oatf59k0.txt cache: ./cache/cord-340942-oatf59k0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340942-oatf59k0.txt' === file2bib.sh === id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-341838-lkz8ro90.txt cache: ./cache/cord-341838-lkz8ro90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341838-lkz8ro90.txt' === file2bib.sh === id: cord-341524-zvic4xc9 author: KARAKURT, Hamza Umut title: Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-341524-zvic4xc9.txt cache: ./cache/cord-341524-zvic4xc9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341524-zvic4xc9.txt' === file2bib.sh === id: cord-340163-ex03l0pc author: Hu, Tingting title: A comparison of COVID-19, SARS and MERS date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-340163-ex03l0pc.txt cache: ./cache/cord-340163-ex03l0pc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340163-ex03l0pc.txt' === file2bib.sh === id: cord-341819-emjg3dsw author: Kouznetsova, Valentina L. title: Potential COVID-19 papain-like protease PL(pro) inhibitors: repurposing FDA-approved drugs date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-341819-emjg3dsw.txt cache: ./cache/cord-341819-emjg3dsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341819-emjg3dsw.txt' === file2bib.sh === id: cord-342084-fbtx7rwi author: Ceccarelli, Giancarlo title: IS TEICOPLANIN A COMPLEMENTARY TREATMENT OPTION FOR COVID-19? THE QUESTION REMAINS date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-342084-fbtx7rwi.txt cache: ./cache/cord-342084-fbtx7rwi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342084-fbtx7rwi.txt' === file2bib.sh === id: cord-342091-xus5kxs0 author: YAVARIAN, Jila title: First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-342091-xus5kxs0.txt cache: ./cache/cord-342091-xus5kxs0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342091-xus5kxs0.txt' === file2bib.sh === id: cord-341331-l24oe2pd author: Zheng, Baojia title: An increasing public health burden arising from children infected with SARS‐CoV2: a systematic review and meta‐analysis date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-341331-l24oe2pd.txt cache: ./cache/cord-341331-l24oe2pd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341331-l24oe2pd.txt' === file2bib.sh === id: cord-341176-83khavoh author: Lotfi, Melika title: CRISPR/Cas13: A potential therapeutic option of COVID-19 date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-341176-83khavoh.txt cache: ./cache/cord-341176-83khavoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341176-83khavoh.txt' === file2bib.sh === id: cord-341502-jlzufa28 author: Lee, Sungyul title: The SARS-CoV-2 RNA interactome date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-341502-jlzufa28.txt cache: ./cache/cord-341502-jlzufa28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341502-jlzufa28.txt' === file2bib.sh === id: cord-342013-k54u2q0d author: Martenot, Antoine title: Favorable outcomes among neonates not separated from their symptomatic SARS-CoV-2-infected mothers date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-342013-k54u2q0d.txt cache: ./cache/cord-342013-k54u2q0d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342013-k54u2q0d.txt' === file2bib.sh === id: cord-341531-w788qwya author: Montero Feijoo, A. title: Practical recommendations for the perioperative management of patients with suspicion or serious infection by coronavirus SARS-CoV date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-341531-w788qwya.txt cache: ./cache/cord-341531-w788qwya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341531-w788qwya.txt' === file2bib.sh === id: cord-342391-arp07mck author: Magiorkinis, G. title: Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions date: 2004-09-14 pages: extension: .txt txt: ./txt/cord-342391-arp07mck.txt cache: ./cache/cord-342391-arp07mck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342391-arp07mck.txt' === file2bib.sh === id: cord-341101-5yvjbr5q author: Hashem, Anwar M. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-341101-5yvjbr5q.txt cache: ./cache/cord-341101-5yvjbr5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341101-5yvjbr5q.txt' === file2bib.sh === id: cord-342177-iqt3ghc0 author: Laine, Roger A title: The case for re-examining glycosylation inhibitors, mimetics, primers and glycosylation decoys as antivirals and anti-inflammatories in COVID19 date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-342177-iqt3ghc0.txt cache: ./cache/cord-342177-iqt3ghc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342177-iqt3ghc0.txt' === file2bib.sh === id: cord-340746-icuzy3vp author: Liang, Yunfei title: Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date: 2005-08-01 pages: extension: .txt txt: ./txt/cord-340746-icuzy3vp.txt cache: ./cache/cord-340746-icuzy3vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340746-icuzy3vp.txt' === file2bib.sh === id: cord-342204-9tgxijvn author: Nuzzo, Domenico title: Potential neurological effects of severe COVID-19 infection date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-342204-9tgxijvn.txt cache: ./cache/cord-342204-9tgxijvn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342204-9tgxijvn.txt' === file2bib.sh === id: cord-341970-pho6dksc author: Huang, Jun title: Immunization with SARS-CoV S DNA vaccine generates memory CD4(+) and CD8(+) T cell immune responses date: 2006-06-05 pages: extension: .txt txt: ./txt/cord-341970-pho6dksc.txt cache: ./cache/cord-341970-pho6dksc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341970-pho6dksc.txt' === file2bib.sh === id: cord-342539-o004ggon author: Lam, Tommy Tsan-Yuk title: Tracking the genomic footprints of SARS-CoV-2 transmission date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-342539-o004ggon.txt cache: ./cache/cord-342539-o004ggon.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342539-o004ggon.txt' === file2bib.sh === id: cord-340799-1awmtj52 author: Krajewska, Joanna title: Review of practical recommendations for otolaryngologists and head and neck surgeons during the COVID-19 pandemic: Recommendations for otolaryngologists during the COVID-19 pandemic date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-340799-1awmtj52.txt cache: ./cache/cord-340799-1awmtj52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340799-1awmtj52.txt' === file2bib.sh === id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 pages: extension: .txt txt: ./txt/cord-340629-1fle5fpz.txt cache: ./cache/cord-340629-1fle5fpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340629-1fle5fpz.txt' === file2bib.sh === id: cord-342396-n3txsvf7 author: Ciaglia, Elena title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-342396-n3txsvf7.txt cache: ./cache/cord-342396-n3txsvf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342396-n3txsvf7.txt' === file2bib.sh === id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-342344-jjnf4yje.txt cache: ./cache/cord-342344-jjnf4yje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342344-jjnf4yje.txt' === file2bib.sh === id: cord-342144-awtiqxx5 author: Hufert, F. title: Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-342144-awtiqxx5.txt cache: ./cache/cord-342144-awtiqxx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342144-awtiqxx5.txt' === file2bib.sh === id: cord-342221-xvrpx9p8 author: Duan, Qing title: Reovirus, isolated from SARS patients date: 2003 pages: extension: .txt txt: ./txt/cord-342221-xvrpx9p8.txt cache: ./cache/cord-342221-xvrpx9p8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-342221-xvrpx9p8.txt' === file2bib.sh === id: cord-341474-06113cn0 author: Huynh, Tien title: In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-341474-06113cn0.txt cache: ./cache/cord-341474-06113cn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341474-06113cn0.txt' === file2bib.sh === id: cord-341919-8gnthufw author: Basi, Saajan title: Clinical course of a 66-year-old man with an acute ischaemic stroke in the setting of a COVID-19 infection date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-341919-8gnthufw.txt cache: ./cache/cord-341919-8gnthufw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341919-8gnthufw.txt' === file2bib.sh === id: cord-342951-nirue1x4 author: Theophanous, Christos title: Bell’s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-342951-nirue1x4.txt cache: ./cache/cord-342951-nirue1x4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342951-nirue1x4.txt' === file2bib.sh === id: cord-341287-i1hyk962 author: Smith, Trevor R. F. title: Immunogenicity of a DNA vaccine candidate for COVID-19 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-341287-i1hyk962.txt cache: ./cache/cord-341287-i1hyk962.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341287-i1hyk962.txt' === file2bib.sh === id: cord-342681-pqzcy9wu author: Pongpirul, Wannarat A. title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-342681-pqzcy9wu.txt cache: ./cache/cord-342681-pqzcy9wu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342681-pqzcy9wu.txt' === file2bib.sh === id: cord-342938-rzhsnkn4 author: Huang, Bo-Ruei title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-342938-rzhsnkn4.txt cache: ./cache/cord-342938-rzhsnkn4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342938-rzhsnkn4.txt' === file2bib.sh === id: cord-342361-eu3rry7p author: Lu, Jiatao title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China date: 2020-02-23 pages: extension: .txt txt: ./txt/cord-342361-eu3rry7p.txt cache: ./cache/cord-342361-eu3rry7p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342361-eu3rry7p.txt' === file2bib.sh === id: cord-341620-nmrkhx5t author: Chirico, Francesco title: Can Air-Conditioning Systems Contribute to the Spread of SARS/MERS/COVID-19 Infection? Insights from a Rapid Review of the Literature date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-341620-nmrkhx5t.txt cache: ./cache/cord-341620-nmrkhx5t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341620-nmrkhx5t.txt' === file2bib.sh === id: cord-342765-rw8valjp author: Wacharapluesadee, Supaporn title: Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19 date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-342765-rw8valjp.txt cache: ./cache/cord-342765-rw8valjp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342765-rw8valjp.txt' === file2bib.sh === id: cord-341976-yts6pzn3 author: Liu, Xintian title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-341976-yts6pzn3.txt cache: ./cache/cord-341976-yts6pzn3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341976-yts6pzn3.txt' === file2bib.sh === id: cord-342294-x18xmrji author: Yan, Nao title: Medium Term Follow-Up of 337 Patients With Coronavirus Disease 2019 (COVID-19) in a Fangcang Shelter Hospital in Wuhan, China date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-342294-x18xmrji.txt cache: ./cache/cord-342294-x18xmrji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342294-x18xmrji.txt' === file2bib.sh === id: cord-342625-31fe1neb author: Baba, Hiroaki title: Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-342625-31fe1neb.txt cache: ./cache/cord-342625-31fe1neb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342625-31fe1neb.txt' === file2bib.sh === id: cord-342362-j7vuoer6 author: Gegúndez-Fernández, José A title: Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19 date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-342362-j7vuoer6.txt cache: ./cache/cord-342362-j7vuoer6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342362-j7vuoer6.txt' === file2bib.sh === id: cord-342024-kaku49xd author: Espejo, Andrea P title: Review of Current Advances in Serologic Testing for COVID-19 date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-342024-kaku49xd.txt cache: ./cache/cord-342024-kaku49xd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342024-kaku49xd.txt' === file2bib.sh === id: cord-342453-1vj9p7vm author: Ip, A. title: Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-342453-1vj9p7vm.txt cache: ./cache/cord-342453-1vj9p7vm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342453-1vj9p7vm.txt' === file2bib.sh === id: cord-342947-dhe31r3a author: Li, Xin title: Preliminary recommendations for lung surgery during COVID‐19 epidemic period date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-342947-dhe31r3a.txt cache: ./cache/cord-342947-dhe31r3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342947-dhe31r3a.txt' === file2bib.sh === id: cord-343034-dzvo9v01 author: Chen, Chun-Fan title: Role of dipeptidyl peptidase-4 inhibitors in patients with diabetes infected with coronavirus-19 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-343034-dzvo9v01.txt cache: ./cache/cord-343034-dzvo9v01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343034-dzvo9v01.txt' === file2bib.sh === id: cord-342380-lihz7h1k author: Meguid Kassem, Abdel title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-342380-lihz7h1k.txt cache: ./cache/cord-342380-lihz7h1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342380-lihz7h1k.txt' === file2bib.sh === id: cord-342139-t2tukk0z author: Livingston, Gill title: Prevalence, management, and outcomes of SARS-CoV-2 infections in older people and those with dementia in mental health wards in London, UK: a retrospective observational study date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-342139-t2tukk0z.txt cache: ./cache/cord-342139-t2tukk0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342139-t2tukk0z.txt' === file2bib.sh === id: cord-342983-7o0slu0z author: Killeen, G. F. title: A simple arithmetic rationale for crushing the epidemic curve of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) instead of flattening it date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-342983-7o0slu0z.txt cache: ./cache/cord-342983-7o0slu0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342983-7o0slu0z.txt' === file2bib.sh === id: cord-342599-558yn6pu author: Rinchai, Darawan title: A modular framework for the development of targeted Covid-19 blood transcript profiling panels date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-342599-558yn6pu.txt cache: ./cache/cord-342599-558yn6pu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342599-558yn6pu.txt' === file2bib.sh === id: cord-341453-9yrvjlpx author: Clay, Candice C title: Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses date: 2014-03-19 pages: extension: .txt txt: ./txt/cord-341453-9yrvjlpx.txt cache: ./cache/cord-341453-9yrvjlpx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341453-9yrvjlpx.txt' === file2bib.sh === id: cord-342569-ja96xfns author: Azer, Samy A. title: COVID-19: Pathophysiology, diagnosis, complications and Investigational therapeutics date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-342569-ja96xfns.txt cache: ./cache/cord-342569-ja96xfns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342569-ja96xfns.txt' === file2bib.sh === id: cord-342639-vf9n2vf9 author: Chang, Chung-ke title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 pages: extension: .txt txt: ./txt/cord-342639-vf9n2vf9.txt cache: ./cache/cord-342639-vf9n2vf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342639-vf9n2vf9.txt' === file2bib.sh === id: cord-342731-rilr45yb author: Donia, Ahmed title: RNA interference as a promising treatment against SARS-CoV-2 date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-342731-rilr45yb.txt cache: ./cache/cord-342731-rilr45yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342731-rilr45yb.txt' === file2bib.sh === id: cord-343192-fkc7af9y author: Chen, Siyang title: Comment on “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ‐2 (SARS‐CoV‐2)” date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-343192-fkc7af9y.txt cache: ./cache/cord-343192-fkc7af9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343192-fkc7af9y.txt' === file2bib.sh === id: cord-342660-xigv4u3f author: Benotmane, I. title: In-depth virological assessment of kidney transplant recipients with COVID-19 date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-342660-xigv4u3f.txt cache: ./cache/cord-342660-xigv4u3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342660-xigv4u3f.txt' === file2bib.sh === id: cord-342383-ckswlo9o author: Pawlowski, C. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-342383-ckswlo9o.txt cache: ./cache/cord-342383-ckswlo9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342383-ckswlo9o.txt' === file2bib.sh === id: cord-342783-85b4lwh3 author: Prazuck, T. title: Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-342783-85b4lwh3.txt cache: ./cache/cord-342783-85b4lwh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342783-85b4lwh3.txt' === file2bib.sh === id: cord-342857-vj6sw2ne author: McCullough, Peter A. title: Pathophysiological Basis and Rationale for Early Outpatient Treatment of SARS-CoV-2 (COVID-19) Infection date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-342857-vj6sw2ne.txt cache: ./cache/cord-342857-vj6sw2ne.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342857-vj6sw2ne.txt' === file2bib.sh === id: cord-342557-a7q8vp8m author: Chowdhury, Surid Mohammad title: Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-342557-a7q8vp8m.txt cache: ./cache/cord-342557-a7q8vp8m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342557-a7q8vp8m.txt' === file2bib.sh === id: cord-342340-q6j7vy8u author: Jefferies, Sarah title: COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-342340-q6j7vy8u.txt cache: ./cache/cord-342340-q6j7vy8u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342340-q6j7vy8u.txt' === file2bib.sh === id: cord-343273-zaaraiy7 author: Hensley, Lisa E. title: Interferon-β 1a and SARS Coronavirus Replication date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-343273-zaaraiy7.txt cache: ./cache/cord-343273-zaaraiy7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343273-zaaraiy7.txt' === file2bib.sh === id: cord-342942-1s32o9m8 author: Stamatakis, George title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-342942-1s32o9m8.txt cache: ./cache/cord-342942-1s32o9m8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342942-1s32o9m8.txt' === file2bib.sh === id: cord-343136-kftffes0 author: Mohon, Abu Naser title: Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-343136-kftffes0.txt cache: ./cache/cord-343136-kftffes0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343136-kftffes0.txt' === file2bib.sh === id: cord-342796-f7n8sxbu author: Stowe, J. title: Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-342796-f7n8sxbu.txt cache: ./cache/cord-342796-f7n8sxbu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342796-f7n8sxbu.txt' === file2bib.sh === id: cord-342456-5gp3cry0 author: Hoagland, Daisy A. title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-342456-5gp3cry0.txt cache: ./cache/cord-342456-5gp3cry0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342456-5gp3cry0.txt' === file2bib.sh === id: cord-343712-gn7fw891 author: Taglauer, Elizabeth title: Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-343712-gn7fw891.txt cache: ./cache/cord-343712-gn7fw891.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343712-gn7fw891.txt' === file2bib.sh === id: cord-343800-nbydaoac author: Cerutti, Francesco title: Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2 date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-343800-nbydaoac.txt cache: ./cache/cord-343800-nbydaoac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343800-nbydaoac.txt' === file2bib.sh === id: cord-343415-lj2trn85 author: Del Barba, Paolo title: COVID‐19 cardiac involvement in a 38‐day old infant date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-343415-lj2trn85.txt cache: ./cache/cord-343415-lj2trn85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343415-lj2trn85.txt' === file2bib.sh === id: cord-343148-rp3kmd80 author: Ayatollahi, Parisa title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-343148-rp3kmd80.txt cache: ./cache/cord-343148-rp3kmd80.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343148-rp3kmd80.txt' === file2bib.sh === id: cord-343586-28ezisog author: Rocca, María Florencia title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-343586-28ezisog.txt cache: ./cache/cord-343586-28ezisog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-343586-28ezisog.txt' === file2bib.sh === id: cord-343029-85ga6r7d author: Haghpanah, Abdolreza title: Potential mechanisms of SARS‐CoV‐2 action on male gonadal function and fertility: Current status and future prospects date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-343029-85ga6r7d.txt cache: ./cache/cord-343029-85ga6r7d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343029-85ga6r7d.txt' === file2bib.sh === id: cord-343330-wuzts3mt author: Ramos da Silva, S. title: Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19 date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-343330-wuzts3mt.txt cache: ./cache/cord-343330-wuzts3mt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343330-wuzts3mt.txt' === file2bib.sh === id: cord-343523-xb4ee5r5 author: Azouz, Haya title: COVID-19 in an Infant with Congenital Adrenal Hyperplasia: A Case Report date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-343523-xb4ee5r5.txt cache: ./cache/cord-343523-xb4ee5r5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343523-xb4ee5r5.txt' === file2bib.sh === id: cord-343090-dsjq98ks author: Fragkou, Paraskevi C. title: Review of trials currently testing treatment and prevention of COVID-19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-343090-dsjq98ks.txt cache: ./cache/cord-343090-dsjq98ks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343090-dsjq98ks.txt' === file2bib.sh === id: cord-342220-lrqt2gcw author: Dearlove, Bethany title: A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-342220-lrqt2gcw.txt cache: ./cache/cord-342220-lrqt2gcw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342220-lrqt2gcw.txt' === file2bib.sh === id: cord-342776-hkjhqgie author: Jewett, Anahid title: The Potential Effect of Novel Coronavirus SARS-CoV-2 on NK Cells; A Perspective on Potential Therapeutic Interventions date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-342776-hkjhqgie.txt cache: ./cache/cord-342776-hkjhqgie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342776-hkjhqgie.txt' === file2bib.sh === id: cord-343317-97n1j0jj author: Duan, Xiaohua title: Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-343317-97n1j0jj.txt cache: ./cache/cord-343317-97n1j0jj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343317-97n1j0jj.txt' === file2bib.sh === id: cord-343128-sh77c0af author: Bwire, G. M. title: Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-343128-sh77c0af.txt cache: ./cache/cord-343128-sh77c0af.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343128-sh77c0af.txt' === file2bib.sh === id: cord-343515-fad1yyqx author: Felgenhauer, Ulrike title: Inhibition of SARS–CoV-2 by type I and type III interferons date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-343515-fad1yyqx.txt cache: ./cache/cord-343515-fad1yyqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343515-fad1yyqx.txt' === file2bib.sh === id: cord-343333-4krrmjio author: Salazar, Martín title: COVID-19, Hipertensión y Enfermedad cardiovascular date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-343333-4krrmjio.txt cache: ./cache/cord-343333-4krrmjio.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343333-4krrmjio.txt' === file2bib.sh === id: cord-343766-hlg7t5i5 author: Vinken, Mathieu title: A putative AOP for pneumonia related to COVID-19 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-343766-hlg7t5i5.txt cache: ./cache/cord-343766-hlg7t5i5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-343766-hlg7t5i5.txt' === file2bib.sh === id: cord-343836-daqrym0b author: Lange, Clemens title: Welche Bedeutung hat die Bindehaut als möglicher Übertragungsweg für eine SARS-CoV-2-Infektion? date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-343836-daqrym0b.txt cache: ./cache/cord-343836-daqrym0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343836-daqrym0b.txt' === file2bib.sh === id: cord-342739-iy9vjpuh author: Schwartz, David A. title: Potential Maternal and Infant Outcomes from Coronavirus 2019-nCoV (SARS-CoV-2) Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections date: 2020-02-10 pages: extension: .txt txt: ./txt/cord-342739-iy9vjpuh.txt cache: ./cache/cord-342739-iy9vjpuh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342739-iy9vjpuh.txt' === file2bib.sh === id: cord-343043-piyt3i0h author: Baker, S. A. title: Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation. date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-343043-piyt3i0h.txt cache: ./cache/cord-343043-piyt3i0h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343043-piyt3i0h.txt' === file2bib.sh === id: cord-342538-5bwsm290 author: Izquierdo Lara, R. W. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-342538-5bwsm290.txt cache: ./cache/cord-342538-5bwsm290.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342538-5bwsm290.txt' === file2bib.sh === id: cord-342145-cq6xe5r7 author: Dao Thi, Viet Loan title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-342145-cq6xe5r7.txt cache: ./cache/cord-342145-cq6xe5r7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342145-cq6xe5r7.txt' === file2bib.sh === id: cord-342902-y1v8wzxq author: Yuan, Shuofeng title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-342902-y1v8wzxq.txt cache: ./cache/cord-342902-y1v8wzxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342902-y1v8wzxq.txt' === file2bib.sh === id: cord-342996-honeavwj author: Mair-Jenkins, John title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 pages: extension: .txt txt: ./txt/cord-342996-honeavwj.txt cache: ./cache/cord-342996-honeavwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342996-honeavwj.txt' === file2bib.sh === id: cord-343618-jjb8da4a author: Nie, Kai title: Gastrointestinal insights during the COVID-19 epidemic date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-343618-jjb8da4a.txt cache: ./cache/cord-343618-jjb8da4a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343618-jjb8da4a.txt' === file2bib.sh === id: cord-341701-zropd3mo author: Adhikari, Subash title: A high-stringency blueprint of the human proteome date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-341701-zropd3mo.txt cache: ./cache/cord-341701-zropd3mo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341701-zropd3mo.txt' === file2bib.sh === id: cord-342915-r9kv67we author: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 pages: extension: .txt txt: ./txt/cord-342915-r9kv67we.txt cache: ./cache/cord-342915-r9kv67we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342915-r9kv67we.txt' === file2bib.sh === id: cord-343604-v986m9jd author: Vijayakumar, Balaji Gowrivel title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-343604-v986m9jd.txt cache: ./cache/cord-343604-v986m9jd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343604-v986m9jd.txt' === file2bib.sh === id: cord-343870-g2v7ihud author: Liu, Wei title: Virus-, host-, immune-based targets for COVID-19 therapy date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-343870-g2v7ihud.txt cache: ./cache/cord-343870-g2v7ihud.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343870-g2v7ihud.txt' === file2bib.sh === id: cord-343127-n3fs8ph8 author: Pousa, Pedro A. title: Extrapulmonary manifestations of COVID-19 in children: a comprehensive review and pathophysiological considerations date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-343127-n3fs8ph8.txt cache: ./cache/cord-343127-n3fs8ph8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343127-n3fs8ph8.txt' === file2bib.sh === id: cord-343502-1n0o4akm author: Chen, Zhang-Ren title: Pharmacotherapics Advice in Guidelines for COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-343502-1n0o4akm.txt cache: ./cache/cord-343502-1n0o4akm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343502-1n0o4akm.txt' === file2bib.sh === id: cord-344170-qrupbtem author: Biswas, Subrata K title: Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-344170-qrupbtem.txt cache: ./cache/cord-344170-qrupbtem.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344170-qrupbtem.txt' === file2bib.sh === id: cord-343827-jo61t3m0 author: Qian, Qun title: Direct evidence of active SARS-CoV-2 replication in the intestine date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-343827-jo61t3m0.txt cache: ./cache/cord-343827-jo61t3m0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343827-jo61t3m0.txt' === file2bib.sh === id: cord-343569-9th5bcv0 author: Fu, Yu-Zhi title: SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-343569-9th5bcv0.txt cache: ./cache/cord-343569-9th5bcv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343569-9th5bcv0.txt' === file2bib.sh === id: cord-343455-v1648kng author: Zhu, Na title: Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-343455-v1648kng.txt cache: ./cache/cord-343455-v1648kng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343455-v1648kng.txt' === file2bib.sh === id: cord-343185-lbmbp9ca author: Hansen, C. B. title: SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-343185-lbmbp9ca.txt cache: ./cache/cord-343185-lbmbp9ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343185-lbmbp9ca.txt' === file2bib.sh === id: cord-343357-5nhyumxl author: Heegaard, Peter M. H. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-343357-5nhyumxl.txt cache: ./cache/cord-343357-5nhyumxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343357-5nhyumxl.txt' === file2bib.sh === id: cord-343362-4u2re1cu author: Liu, Jianjun title: SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis date: 2005-02-22 pages: extension: .txt txt: ./txt/cord-343362-4u2re1cu.txt cache: ./cache/cord-343362-4u2re1cu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343362-4u2re1cu.txt' === file2bib.sh === id: cord-343691-sjz5og78 author: Nakajima, Kei title: Serious Conditions in COVID-19 Accompanied With a Feature of Metabolic Syndrome date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-343691-sjz5og78.txt cache: ./cache/cord-343691-sjz5og78.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343691-sjz5og78.txt' === file2bib.sh === id: cord-343566-epvswt7f author: Wang, Zhao-Hua title: Critically Ill Patients with Coronavirus Disease 2019 in a Designated ICU: Clinical Features and Predictors for Mortality date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-343566-epvswt7f.txt cache: ./cache/cord-343566-epvswt7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343566-epvswt7f.txt' === file2bib.sh === id: cord-343757-e4hmo4yc author: Velavan, Thirumalaisamy P. title: The COVID‐19 epidemic date: 2020-02-16 pages: extension: .txt txt: ./txt/cord-343757-e4hmo4yc.txt cache: ./cache/cord-343757-e4hmo4yc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343757-e4hmo4yc.txt' === file2bib.sh === id: cord-344017-qldawc8m author: Edouard, S. title: Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-344017-qldawc8m.txt cache: ./cache/cord-344017-qldawc8m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344017-qldawc8m.txt' === file2bib.sh === id: cord-343476-0chuwvg6 author: MacLean, Oscar A. title: Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-343476-0chuwvg6.txt cache: ./cache/cord-343476-0chuwvg6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343476-0chuwvg6.txt' === file2bib.sh === id: cord-343143-tzuhig3f author: Chen, Rong-chang title: Treatment of Severe Acute Respiratory Syndrome With Glucosteroids The Guangzhou Experience date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-343143-tzuhig3f.txt cache: ./cache/cord-343143-tzuhig3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343143-tzuhig3f.txt' === file2bib.sh === id: cord-343082-46lo7xtx author: Awasthi, Ankit title: OUTBREAK of novel corona virus disease (COVID-19): Antecedence and aftermath date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-343082-46lo7xtx.txt cache: ./cache/cord-343082-46lo7xtx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343082-46lo7xtx.txt' === file2bib.sh === id: cord-343517-vf32wxkx author: Lokman, Syed Mohammad title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-343517-vf32wxkx.txt cache: ./cache/cord-343517-vf32wxkx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343517-vf32wxkx.txt' === file2bib.sh === id: cord-344213-j3yextjl author: Sze, Shirley title: The need for improved discharge criteria for hospitalised patients with COVID-19—implications for patients in long term care facilities date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-344213-j3yextjl.txt cache: ./cache/cord-344213-j3yextjl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344213-j3yextjl.txt' === file2bib.sh === id: cord-341987-lsvifqyo author: Kalyanasundaram, Sridhar title: Novel Corona Virus Pandemic and Neonatal Care: It’s Too Early to Speculate on Impact! date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-341987-lsvifqyo.txt cache: ./cache/cord-341987-lsvifqyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341987-lsvifqyo.txt' === file2bib.sh === id: cord-342189-ya05m58o author: Banerjee, Abhik K. title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-342189-ya05m58o.txt cache: ./cache/cord-342189-ya05m58o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342189-ya05m58o.txt' === file2bib.sh === id: cord-344356-up53a0k4 author: Feaster, Matt title: High Proportion of Asymptomatic SARS-CoV-2 Infections in 9 Long-Term Care Facilities, Pasadena, California, USA, April 2020 date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-344356-up53a0k4.txt cache: ./cache/cord-344356-up53a0k4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344356-up53a0k4.txt' === file2bib.sh === id: cord-344038-20n74z3o author: Han, Mi Seon title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-344038-20n74z3o.txt cache: ./cache/cord-344038-20n74z3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344038-20n74z3o.txt' === file2bib.sh === id: cord-343845-suoy3ojr author: Martín, Vicente title: Prevalencia de la Infección por SARS-CoV-2 en médicos y enfermeras de Atención Primaria y Residencias de Ancianos del Área de Salud de León y Factores asociados date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-343845-suoy3ojr.txt cache: ./cache/cord-343845-suoy3ojr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343845-suoy3ojr.txt' === file2bib.sh === id: cord-344901-mgnaprgt author: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-344901-mgnaprgt.txt cache: ./cache/cord-344901-mgnaprgt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344901-mgnaprgt.txt' === file2bib.sh === id: cord-344454-hs3tthzi author: nan title: Les animaux contaminés par le SARS-CoV-2 représentent-ils un risque pour l’Homme ? date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-344454-hs3tthzi.txt cache: ./cache/cord-344454-hs3tthzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344454-hs3tthzi.txt' === file2bib.sh === id: cord-344003-oul2hdyq author: Maleki Dana, Parisa title: An Insight into the Sex Differences in COVID-19 Patients: What are the Possible Causes? date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-344003-oul2hdyq.txt cache: ./cache/cord-344003-oul2hdyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344003-oul2hdyq.txt' === file2bib.sh === id: cord-344364-vu389d88 author: Wang, Wei title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-344364-vu389d88.txt cache: ./cache/cord-344364-vu389d88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344364-vu389d88.txt' === file2bib.sh === id: cord-343340-zi0rfidc author: Aragón‐Caqueo, Diego title: Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-343340-zi0rfidc.txt cache: ./cache/cord-343340-zi0rfidc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343340-zi0rfidc.txt' === file2bib.sh === id: cord-344236-qp3ianzf author: Ali, Fedaa title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-344236-qp3ianzf.txt cache: ./cache/cord-344236-qp3ianzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344236-qp3ianzf.txt' === file2bib.sh === id: cord-343365-4y9fedcr author: Chang, Christopher title: Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date: 2013-11-30 pages: extension: .txt txt: ./txt/cord-343365-4y9fedcr.txt cache: ./cache/cord-343365-4y9fedcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343365-4y9fedcr.txt' === file2bib.sh === id: cord-343919-n8884bli author: Salvio, Gianmaria title: Bone Metabolism in SARS-CoV-2 Disease: Possible Osteoimmunology and Gender Implications date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-343919-n8884bli.txt cache: ./cache/cord-343919-n8884bli.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343919-n8884bli.txt' === file2bib.sh === id: cord-343876-2inr4mcy author: Xie, Qin title: COVID-19 patients managed in psychiatric inpatient settings due to first-episode mental disorders in Wuhan, China: clinical characteristics, treatments, outcomes, and our experiences date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-343876-2inr4mcy.txt cache: ./cache/cord-343876-2inr4mcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343876-2inr4mcy.txt' === file2bib.sh === id: cord-344120-7t5ce2hb author: Baroutjian, Amanda title: SARS-CoV-2 pharmacologic therapies and their safety/effectiveness according to level of evidence date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-344120-7t5ce2hb.txt cache: ./cache/cord-344120-7t5ce2hb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344120-7t5ce2hb.txt' === file2bib.sh === id: cord-344316-mwnnmwnw author: Herst, C.V. title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-344316-mwnnmwnw.txt cache: ./cache/cord-344316-mwnnmwnw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344316-mwnnmwnw.txt' === file2bib.sh === id: cord-342786-dl8vjwfn author: Sattar, Yasar title: COVID-19 Cardiovascular Epidemiology, Cellular Pathogenesis, Clinical Manifestations and Management date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-342786-dl8vjwfn.txt cache: ./cache/cord-342786-dl8vjwfn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342786-dl8vjwfn.txt' === file2bib.sh === id: cord-344270-874i31h8 author: Radke, Robert M title: Adult congenital heart disease and the COVID-19 pandemic date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-344270-874i31h8.txt cache: ./cache/cord-344270-874i31h8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344270-874i31h8.txt' === file2bib.sh === id: cord-343864-0258nh92 author: Straughn, Alex R. title: Withaferin A: a potential therapeutic agent against COVID-19 infection date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-343864-0258nh92.txt cache: ./cache/cord-343864-0258nh92.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343864-0258nh92.txt' === file2bib.sh === id: cord-344446-5d7yuoz1 author: Naughton, Sean X. title: The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-344446-5d7yuoz1.txt cache: ./cache/cord-344446-5d7yuoz1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344446-5d7yuoz1.txt' === file2bib.sh === id: cord-343850-p4bbb6vm author: Lin, Meng-Hsuan title: Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-343850-p4bbb6vm.txt cache: ./cache/cord-343850-p4bbb6vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343850-p4bbb6vm.txt' === file2bib.sh === id: cord-344383-7s4gnxs4 author: Tee, Augustine K.H. title: Atypical SARS in Geriatric Patient date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-344383-7s4gnxs4.txt cache: ./cache/cord-344383-7s4gnxs4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344383-7s4gnxs4.txt' === file2bib.sh === id: cord-344751-i4qnrtjq author: Van Praet, Jens T. title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-344751-i4qnrtjq.txt cache: ./cache/cord-344751-i4qnrtjq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344751-i4qnrtjq.txt' === file2bib.sh === id: cord-344884-dcoq9srf author: El Otmani, H. title: Neuro-COVID-19: What are we talking about? date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-344884-dcoq9srf.txt cache: ./cache/cord-344884-dcoq9srf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344884-dcoq9srf.txt' === file2bib.sh === id: cord-345033-guisyj11 author: Massarotti, Claudia title: SARS‐CoV‐2 in the semen: where does it come from? date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-345033-guisyj11.txt cache: ./cache/cord-345033-guisyj11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345033-guisyj11.txt' === file2bib.sh === id: cord-344614-5zcylf6k author: Moriconi, Diego title: Obesity prolongs the hospital stay in patients affected by COVID-19, and may impact on SARS-COV-2 shedding date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-344614-5zcylf6k.txt cache: ./cache/cord-344614-5zcylf6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344614-5zcylf6k.txt' === file2bib.sh === id: cord-344658-4z2697q6 author: Hutasoit, Novana title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-344658-4z2697q6.txt cache: ./cache/cord-344658-4z2697q6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344658-4z2697q6.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45813 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46140 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45725 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-344180-v8xs5ej8 author: Vadlamani, Bhaskar S. title: Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-344180-v8xs5ej8.txt cache: ./cache/cord-344180-v8xs5ej8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344180-v8xs5ej8.txt' === file2bib.sh === id: cord-344266-ug2uew71 author: Crema, E. title: The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-344266-ug2uew71.txt cache: ./cache/cord-344266-ug2uew71.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344266-ug2uew71.txt' === file2bib.sh === id: cord-344967-t88pedeb author: Tang, Hon Lok title: Severe acute respiratory syndrome in haemodialysis patients: a report of two cases date: 2003-10-17 pages: extension: .txt txt: ./txt/cord-344967-t88pedeb.txt cache: ./cache/cord-344967-t88pedeb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344967-t88pedeb.txt' === file2bib.sh === id: cord-343970-anocx4y1 author: Bansal, Rashika title: Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-343970-anocx4y1.txt cache: ./cache/cord-343970-anocx4y1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343970-anocx4y1.txt' === file2bib.sh === id: cord-344419-3wcfpw2z author: Niedzwiedz, C. L. title: Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-344419-3wcfpw2z.txt cache: ./cache/cord-344419-3wcfpw2z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344419-3wcfpw2z.txt' === file2bib.sh === id: cord-343715-y594iewi author: Gavriatopoulou, Maria title: Organ-specific manifestations of COVID-19 infection date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-343715-y594iewi.txt cache: ./cache/cord-343715-y594iewi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343715-y594iewi.txt' === file2bib.sh === id: cord-344842-9cfbb7p6 author: Coppola, Maurizio title: Potential Unconventional Medicines for the Treatment of SARS-CoV-2 date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-344842-9cfbb7p6.txt cache: ./cache/cord-344842-9cfbb7p6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-344842-9cfbb7p6.txt' === file2bib.sh === id: cord-344647-jr85915d author: Joseph, Adrien title: Acute kidney injury in patients with SARS-CoV-2 infection date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-344647-jr85915d.txt cache: ./cache/cord-344647-jr85915d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344647-jr85915d.txt' === file2bib.sh === id: cord-344204-qq2vqzc2 author: Hariharan, Apurva title: The Role and Therapeutic Potential of NF-kappa-B Pathway in Severe COVID-19 Patients date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-344204-qq2vqzc2.txt cache: ./cache/cord-344204-qq2vqzc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344204-qq2vqzc2.txt' === file2bib.sh === id: cord-344778-2p1mm3vg author: Gasparri, Maria Luisa title: Changes in breast cancer management during the Corona Virus Disease 19 pandemic: an international survey of the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-344778-2p1mm3vg.txt cache: ./cache/cord-344778-2p1mm3vg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344778-2p1mm3vg.txt' === file2bib.sh === id: cord-343818-pj1oludh author: Liu, Chan title: Children with COVID-19 behaving milder may challenge the public policies: a systematic review and meta-analysis date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-343818-pj1oludh.txt cache: ./cache/cord-343818-pj1oludh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343818-pj1oludh.txt' === file2bib.sh === id: cord-344070-17oac3bg author: Silverman, Justin D title: Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-344070-17oac3bg.txt cache: ./cache/cord-344070-17oac3bg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344070-17oac3bg.txt' === file2bib.sh === id: cord-345299-4k7qymqd author: Xiong, Hua-Long title: Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-345299-4k7qymqd.txt cache: ./cache/cord-345299-4k7qymqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345299-4k7qymqd.txt' === file2bib.sh === id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-344006-0iq9s94n.txt cache: ./cache/cord-344006-0iq9s94n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344006-0iq9s94n.txt' === file2bib.sh === id: cord-344330-zsx7wfyj author: Su, Shuo title: Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses date: 2016-03-21 pages: extension: .txt txt: ./txt/cord-344330-zsx7wfyj.txt cache: ./cache/cord-344330-zsx7wfyj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344330-zsx7wfyj.txt' === file2bib.sh === id: cord-344979-ngujhhp6 author: Lübke, Nadine title: Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-344979-ngujhhp6.txt cache: ./cache/cord-344979-ngujhhp6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344979-ngujhhp6.txt' === file2bib.sh === id: cord-345304-n74m5ucs author: Safadi, Marco Aurelio Palazzi title: THE CHALLENGING AND UNPREDICTABLE SPECTRUM OF COVID-19 IN CHILDREN AND ADOLESCENTS date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-345304-n74m5ucs.txt cache: ./cache/cord-345304-n74m5ucs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345304-n74m5ucs.txt' === file2bib.sh === id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-344970-ud1lhkyi.txt cache: ./cache/cord-344970-ud1lhkyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344970-ud1lhkyi.txt' === file2bib.sh === id: cord-344382-vge4ho2v author: De Flora, Silvio title: Rationale for the use of N‐acetylcysteine in both prevention and adjuvant therapy of COVID‐19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-344382-vge4ho2v.txt cache: ./cache/cord-344382-vge4ho2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344382-vge4ho2v.txt' === file2bib.sh === id: cord-345854-f0dq94j1 author: Chong, Wai Po title: The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date: 2006-05-04 pages: extension: .txt txt: ./txt/cord-345854-f0dq94j1.txt cache: ./cache/cord-345854-f0dq94j1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345854-f0dq94j1.txt' === file2bib.sh === id: cord-345754-mgixsfcc author: Arena, Patrick J. title: Race, COVID-19 and deaths of despair date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-345754-mgixsfcc.txt cache: ./cache/cord-345754-mgixsfcc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345754-mgixsfcc.txt' === file2bib.sh === id: cord-345288-qyz83xx2 author: Pata, Francesco title: Enteral stoma care during COVID‐19 pandemic: practical advice date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-345288-qyz83xx2.txt cache: ./cache/cord-345288-qyz83xx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345288-qyz83xx2.txt' === file2bib.sh === id: cord-344246-sf9cymhc author: Diriba, Kuma title: The effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and the possibility of vertical maternal–fetal transmission: a systematic review and meta-analysis date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-344246-sf9cymhc.txt cache: ./cache/cord-344246-sf9cymhc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344246-sf9cymhc.txt' === file2bib.sh === id: cord-343966-bfon094h author: Djaparidze, L. title: SARS-CoV-2 waves in Europe: A 2-stratum SEIRS model solution date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-343966-bfon094h.txt cache: ./cache/cord-343966-bfon094h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343966-bfon094h.txt' === file2bib.sh === id: cord-345101-h0i5o0do author: Koo, Bon-Sang title: Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-345101-h0i5o0do.txt cache: ./cache/cord-345101-h0i5o0do.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345101-h0i5o0do.txt' === file2bib.sh === id: cord-345014-qp13h0un author: Stein, Richard Albert title: The 2019 coronavirus: Learning curves, lessons, and the weakest link date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-345014-qp13h0un.txt cache: ./cache/cord-345014-qp13h0un.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345014-qp13h0un.txt' === file2bib.sh === id: cord-345019-i7zm9bt1 author: Al-Waleedi, Ali Ahmed title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-345019-i7zm9bt1.txt cache: ./cache/cord-345019-i7zm9bt1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345019-i7zm9bt1.txt' === file2bib.sh === id: cord-345603-mirsz6m8 author: Wehrhahn, Michael C. title: Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-345603-mirsz6m8.txt cache: ./cache/cord-345603-mirsz6m8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345603-mirsz6m8.txt' === file2bib.sh === id: cord-345864-87b5qdjx author: Rudolph, James L. title: Temperature in Nursing Home Residents Systematically Tested for SARS-CoV-2 date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-345864-87b5qdjx.txt cache: ./cache/cord-345864-87b5qdjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345864-87b5qdjx.txt' === file2bib.sh === id: cord-345183-80rflm7u author: Moore, Nicholas M. title: Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-345183-80rflm7u.txt cache: ./cache/cord-345183-80rflm7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345183-80rflm7u.txt' === file2bib.sh === id: cord-343808-uqhiyj56 author: Kuo, Hsiao-I. title: Assessing impacts of SARS and Avian Flu on international tourism demand to Asia date: 2008-01-07 pages: extension: .txt txt: ./txt/cord-343808-uqhiyj56.txt cache: ./cache/cord-343808-uqhiyj56.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343808-uqhiyj56.txt' === file2bib.sh === id: cord-344217-kci4uw7u author: Majid, Sabhiya title: Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-344217-kci4uw7u.txt cache: ./cache/cord-344217-kci4uw7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344217-kci4uw7u.txt' === file2bib.sh === id: cord-344227-rdlinzrn author: Gralinski, Lisa E. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 pages: extension: .txt txt: ./txt/cord-344227-rdlinzrn.txt cache: ./cache/cord-344227-rdlinzrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344227-rdlinzrn.txt' === file2bib.sh === id: cord-344934-m0q7rm6z author: Mahapatra, Sovesh title: Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-344934-m0q7rm6z.txt cache: ./cache/cord-344934-m0q7rm6z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344934-m0q7rm6z.txt' === file2bib.sh === id: cord-345275-h0hvaxgx author: Sun, Mengyao title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-345275-h0hvaxgx.txt cache: ./cache/cord-345275-h0hvaxgx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345275-h0hvaxgx.txt' === file2bib.sh === id: cord-345139-gyvlikye author: Izquierdo-Domínguez, Adriana title: Pérdida del sentido del olfato durante la pandemia COVID-19 date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-345139-gyvlikye.txt cache: ./cache/cord-345139-gyvlikye.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345139-gyvlikye.txt' === file2bib.sh === id: cord-345356-gn1iwis0 author: Glebov, Oleg O. title: Understanding SARS‐CoV‐2 endocytosis for COVID‐19 drug repurposing date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-345356-gn1iwis0.txt cache: ./cache/cord-345356-gn1iwis0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345356-gn1iwis0.txt' === file2bib.sh === id: cord-344909-0o55l4iy author: Cross, Robert W. title: Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-344909-0o55l4iy.txt cache: ./cache/cord-344909-0o55l4iy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344909-0o55l4iy.txt' === file2bib.sh === id: cord-345679-ydwcp75s author: Younas, Amber title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-345679-ydwcp75s.txt cache: ./cache/cord-345679-ydwcp75s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345679-ydwcp75s.txt' === file2bib.sh === id: cord-345529-f12v6bp0 author: Pan, Q. title: Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-345529-f12v6bp0.txt cache: ./cache/cord-345529-f12v6bp0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345529-f12v6bp0.txt' === file2bib.sh === id: cord-345929-z7yfegr5 author: Thakur, Suman S. title: Proteomics and Its Application in Pandemic Diseases date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-345929-z7yfegr5.txt cache: ./cache/cord-345929-z7yfegr5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345929-z7yfegr5.txt' === file2bib.sh === id: cord-344853-s2p2csrx author: Hendren, Nicholas S. title: Description and Proposed Management of the Acute COVID-19 Cardiovascular Syndrome date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-344853-s2p2csrx.txt cache: ./cache/cord-344853-s2p2csrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344853-s2p2csrx.txt' === file2bib.sh === id: cord-344636-go5cw92q author: Huang, Wei E. title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-344636-go5cw92q.txt cache: ./cache/cord-344636-go5cw92q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344636-go5cw92q.txt' === file2bib.sh === id: cord-344798-q34j4zxu author: Villalba, María Caridad Montalvo title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-344798-q34j4zxu.txt cache: ./cache/cord-344798-q34j4zxu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344798-q34j4zxu.txt' === file2bib.sh === id: cord-345106-5szz1et3 author: Bhattacharya, D. D. title: Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2 date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-345106-5szz1et3.txt cache: ./cache/cord-345106-5szz1et3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345106-5szz1et3.txt' === file2bib.sh === id: cord-345992-3ij1vbqp author: Drosten, Christian title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 pages: extension: .txt txt: ./txt/cord-345992-3ij1vbqp.txt cache: ./cache/cord-345992-3ij1vbqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345992-3ij1vbqp.txt' === file2bib.sh === id: cord-346222-rzbzlnr4 author: Kim, Dae-Kyum title: A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-346222-rzbzlnr4.txt cache: ./cache/cord-346222-rzbzlnr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346222-rzbzlnr4.txt' === file2bib.sh === id: cord-345296-4z7yfj5s author: Ho, Mei-Shang title: Neutralizing Antibody Response and SARS Severity date: 2005-11-17 pages: extension: .txt txt: ./txt/cord-345296-4z7yfj5s.txt cache: ./cache/cord-345296-4z7yfj5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345296-4z7yfj5s.txt' === file2bib.sh === id: cord-344012-npob20n0 author: Gheblawi, Mahmoud title: Angiotensin-Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System: Celebrating the 20th Anniversary of the Discovery of ACE2 date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-344012-npob20n0.txt cache: ./cache/cord-344012-npob20n0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344012-npob20n0.txt' === file2bib.sh === id: cord-344949-9zyz4hll author: Luban, Jeremy title: The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-344949-9zyz4hll.txt cache: ./cache/cord-344949-9zyz4hll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344949-9zyz4hll.txt' === file2bib.sh === id: cord-346008-6v2gdz4a author: Jeong, Areum title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-346008-6v2gdz4a.txt cache: ./cache/cord-346008-6v2gdz4a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346008-6v2gdz4a.txt' === file2bib.sh === id: cord-345103-b2wkm03g author: Yao, Hangping title: Molecular architecture of the SARS-CoV-2 virus date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-345103-b2wkm03g.txt cache: ./cache/cord-345103-b2wkm03g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345103-b2wkm03g.txt' === file2bib.sh === id: cord-344714-0cam9ipf author: Russo, Maria title: Roles of flavonoids against coronavirus infection date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-344714-0cam9ipf.txt cache: ./cache/cord-344714-0cam9ipf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344714-0cam9ipf.txt' === file2bib.sh === id: cord-342756-rgm9ffpk author: Senger, Mario Roberto title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-342756-rgm9ffpk.txt cache: ./cache/cord-342756-rgm9ffpk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342756-rgm9ffpk.txt' === file2bib.sh === id: cord-345225-2s5xd1oc author: Soares, F. title: A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-345225-2s5xd1oc.txt cache: ./cache/cord-345225-2s5xd1oc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345225-2s5xd1oc.txt' === file2bib.sh === id: cord-344829-adlp2rjy author: de Rivero Vaccari, Juan Carlos title: The Inflammasome in Times of COVID-19 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-344829-adlp2rjy.txt cache: ./cache/cord-344829-adlp2rjy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344829-adlp2rjy.txt' === file2bib.sh === id: cord-345827-yo3uq03v author: Antiochia, Riccarda title: Developments in biosensors for CoV detection and future trends date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-345827-yo3uq03v.txt cache: ./cache/cord-345827-yo3uq03v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345827-yo3uq03v.txt' === file2bib.sh === id: cord-345405-ngpsgn63 author: Tremiliosi, Guilherme C. title: Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-345405-ngpsgn63.txt cache: ./cache/cord-345405-ngpsgn63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345405-ngpsgn63.txt' === file2bib.sh === id: cord-346055-7fa57pmf author: Visani, Giuseppe title: SARS-CoV-2 impact in a community-based hematological ward in an Italian Red Zone date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-346055-7fa57pmf.txt cache: ./cache/cord-346055-7fa57pmf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346055-7fa57pmf.txt' === file2bib.sh === id: cord-346092-fo83f99f author: Fang, Li‐Qun title: Geographical spread of SARS in mainland China date: 2009-06-05 pages: extension: .txt txt: ./txt/cord-346092-fo83f99f.txt cache: ./cache/cord-346092-fo83f99f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346092-fo83f99f.txt' === file2bib.sh === id: cord-346197-7g5d9x57 author: Capecchi, E. title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-346197-7g5d9x57.txt cache: ./cache/cord-346197-7g5d9x57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346197-7g5d9x57.txt' === file2bib.sh === id: cord-345841-pq5f82gf author: PATBERG, Elizabeth T. title: COVID-19 Infection and Placental Histopathology in Women Delivering at Term date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-345841-pq5f82gf.txt cache: ./cache/cord-345841-pq5f82gf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345841-pq5f82gf.txt' === file2bib.sh === id: cord-345381-9cckppk2 author: Klimek, Ludger title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-345381-9cckppk2.txt cache: ./cache/cord-345381-9cckppk2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345381-9cckppk2.txt' === file2bib.sh === id: cord-346089-u31n0qxa author: McDade, Thomas W. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-346089-u31n0qxa.txt cache: ./cache/cord-346089-u31n0qxa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346089-u31n0qxa.txt' === file2bib.sh === id: cord-344486-iu5flbcl author: Chiotos, Kathleen title: Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2 date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-344486-iu5flbcl.txt cache: ./cache/cord-344486-iu5flbcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344486-iu5flbcl.txt' === file2bib.sh === id: cord-346032-188gnf8j author: Cheung, Ying-Kit title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 pages: extension: .txt txt: ./txt/cord-346032-188gnf8j.txt cache: ./cache/cord-346032-188gnf8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346032-188gnf8j.txt' === file2bib.sh === id: cord-345493-3bb1zuqp author: Itoyama, Satoru title: Identification of an alternative 5′‐untranslated exon and new polymorphisms of angiotensin‐converting enzyme 2 gene: Lack of association with SARS in the Vietnamese population date: 2005-06-03 pages: extension: .txt txt: ./txt/cord-345493-3bb1zuqp.txt cache: ./cache/cord-345493-3bb1zuqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345493-3bb1zuqp.txt' === file2bib.sh === id: cord-345999-iiw4cs8p author: Khare, Prashant title: Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-345999-iiw4cs8p.txt cache: ./cache/cord-345999-iiw4cs8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345999-iiw4cs8p.txt' === file2bib.sh === id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-346138-ip42zcld.txt cache: ./cache/cord-346138-ip42zcld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346138-ip42zcld.txt' === file2bib.sh === id: cord-345730-bxwsup70 author: Kočar, Eva title: Cholesterol, lipoproteins, and COVID-19: basic concepts and clinical applications date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-345730-bxwsup70.txt cache: ./cache/cord-345730-bxwsup70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345730-bxwsup70.txt' === file2bib.sh === id: cord-344064-l3u4l3se author: Ghosh, Rajesh title: Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-344064-l3u4l3se.txt cache: ./cache/cord-344064-l3u4l3se.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344064-l3u4l3se.txt' === file2bib.sh === id: cord-345879-nbfg47x5 author: Bonaz, Bruno title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-345879-nbfg47x5.txt cache: ./cache/cord-345879-nbfg47x5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345879-nbfg47x5.txt' === file2bib.sh === id: cord-345499-hq5um68k author: Xiong, Rui title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-345499-hq5um68k.txt cache: ./cache/cord-345499-hq5um68k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345499-hq5um68k.txt' === file2bib.sh === id: cord-346176-w6uaet7l author: Nayeri, Shadi title: Conducting Translational Gastrointestinal Research in the Era of COVID-19 date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-346176-w6uaet7l.txt cache: ./cache/cord-346176-w6uaet7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346176-w6uaet7l.txt' === file2bib.sh === id: cord-346441-b1r6i0wq author: Polverino, Francesca title: Cigarette Smoking and COVID-19: A Complex Interaction date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-346441-b1r6i0wq.txt cache: ./cache/cord-346441-b1r6i0wq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346441-b1r6i0wq.txt' === file2bib.sh === id: cord-346291-qqy9ld94 author: Noroozi, Rezvan title: Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-346291-qqy9ld94.txt cache: ./cache/cord-346291-qqy9ld94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346291-qqy9ld94.txt' === file2bib.sh === id: cord-345887-ymo4mxx7 author: Pinky title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-345887-ymo4mxx7.txt cache: ./cache/cord-345887-ymo4mxx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345887-ymo4mxx7.txt' === file2bib.sh === id: cord-345717-ktajrf7d author: Monagin, Corina title: Serologic and behavioral risk survey of workers with wildlife contact in China date: 2018-04-03 pages: extension: .txt txt: ./txt/cord-345717-ktajrf7d.txt cache: ./cache/cord-345717-ktajrf7d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345717-ktajrf7d.txt' === file2bib.sh === id: cord-346345-jc9bq0zu author: Smith, Colin M title: COVID-19-associated brief psychotic disorder date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-346345-jc9bq0zu.txt cache: ./cache/cord-346345-jc9bq0zu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346345-jc9bq0zu.txt' === file2bib.sh === id: cord-346413-2njl0fd3 author: Nakazawa, Daigo title: Immunothrombosis in severe COVID-19 date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-346413-2njl0fd3.txt cache: ./cache/cord-346413-2njl0fd3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346413-2njl0fd3.txt' === file2bib.sh === id: cord-346530-o65m0whe author: Chaumont, H. title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-346530-o65m0whe.txt cache: ./cache/cord-346530-o65m0whe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346530-o65m0whe.txt' === file2bib.sh === id: cord-346153-9162w7il author: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 pages: extension: .txt txt: ./txt/cord-346153-9162w7il.txt cache: ./cache/cord-346153-9162w7il.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346153-9162w7il.txt' === file2bib.sh === id: cord-345628-a4c46m2w author: Unudurthi, Sathya D. title: Cardiac inflammation in COVID-19: Lessons from heart failure date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-345628-a4c46m2w.txt cache: ./cache/cord-345628-a4c46m2w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-345628-a4c46m2w.txt' === file2bib.sh === id: cord-346763-xdfl659q author: Herman, A. title: Drug reaction with eosinophilia and systemic symptoms syndrome in a patient with COVID‐19 date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-346763-xdfl659q.txt cache: ./cache/cord-346763-xdfl659q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346763-xdfl659q.txt' === file2bib.sh === id: cord-346015-bzeqs5oh author: Wang, Yeming title: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-346015-bzeqs5oh.txt cache: ./cache/cord-346015-bzeqs5oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346015-bzeqs5oh.txt' === file2bib.sh === id: cord-346512-y5d8q5b9 author: Pellicciaro, Marco title: Breast cancer patients with hormone neoadjuvant bridging therapy due to asymptomatic Corona virus infection. Case report, clinical and histopathologic findings date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-346512-y5d8q5b9.txt cache: ./cache/cord-346512-y5d8q5b9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346512-y5d8q5b9.txt' === file2bib.sh === id: cord-346532-4xpnd93d author: Strömich, Léonie title: Allosteric Hotspots in the Main Protease of SARS-CoV-2 date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-346532-4xpnd93d.txt cache: ./cache/cord-346532-4xpnd93d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346532-4xpnd93d.txt' === file2bib.sh === id: cord-346445-hgqohdct author: Toyoshima, Yujiro title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-346445-hgqohdct.txt cache: ./cache/cord-346445-hgqohdct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346445-hgqohdct.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-346299-2s9j01q7 author: Salim Khan, S Muhammad title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-346299-2s9j01q7.txt cache: ./cache/cord-346299-2s9j01q7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346299-2s9j01q7.txt' === file2bib.sh === id: cord-346658-ij5sr88p author: Hilgenfeld, Rolf title: Sometimes Intermediates Do the Job! date: 2006-04-07 pages: extension: .txt txt: ./txt/cord-346658-ij5sr88p.txt cache: ./cache/cord-346658-ij5sr88p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346658-ij5sr88p.txt' === file2bib.sh === id: cord-346370-jdfsacds author: Sergi, Consolato M. title: The Facemask in Public and Healthcare Workers– A Need not a Belief date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-346370-jdfsacds.txt cache: ./cache/cord-346370-jdfsacds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346370-jdfsacds.txt' === file2bib.sh === id: cord-346555-3hrbea6d author: Hu, Xiumei title: Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS‐CoV‐2 date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-346555-3hrbea6d.txt cache: ./cache/cord-346555-3hrbea6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346555-3hrbea6d.txt' === file2bib.sh === id: cord-346325-grt67p73 author: Reilev, M. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-346325-grt67p73.txt cache: ./cache/cord-346325-grt67p73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346325-grt67p73.txt' === file2bib.sh === id: cord-347090-sqw7n1v2 author: Rodriguez-Gonzalez, Moises title: New onset severe right ventricular failure associated with COVID-19 in a young infant without previous heart disease date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-347090-sqw7n1v2.txt cache: ./cache/cord-347090-sqw7n1v2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347090-sqw7n1v2.txt' === file2bib.sh === id: cord-346248-6wkyar57 author: de Moura, Diogo Turiani Hourneaux title: Diagnostic Characteristics of Serological-Based COVID-19 Testing: A Systematic Review and Meta-Analysis date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-346248-6wkyar57.txt cache: ./cache/cord-346248-6wkyar57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346248-6wkyar57.txt' === file2bib.sh === id: cord-346403-fuxs1axy author: Davanzo, G. G. title: SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-346403-fuxs1axy.txt cache: ./cache/cord-346403-fuxs1axy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346403-fuxs1axy.txt' === file2bib.sh === id: cord-346816-xys0g8b8 author: Shichijo, S. title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity date: 2004-10-20 pages: extension: .txt txt: ./txt/cord-346816-xys0g8b8.txt cache: ./cache/cord-346816-xys0g8b8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346816-xys0g8b8.txt' === file2bib.sh === id: cord-346711-2k736hvr author: Shetty, Rohit title: Stem cell therapy in COVID-19 – current evidence and future potential date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-346711-2k736hvr.txt cache: ./cache/cord-346711-2k736hvr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346711-2k736hvr.txt' === file2bib.sh === id: cord-347030-yx3j6373 author: Cao, Xuetao title: COVID-19: immunopathology and its implications for therapy date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-347030-yx3j6373.txt cache: ./cache/cord-347030-yx3j6373.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347030-yx3j6373.txt' === file2bib.sh === id: cord-347119-w780f0om author: Blitz, Matthew J. title: Race/ethnicity and spatiotemporal trends in SARS-CoV-2 prevalence on obstetrical units in New York date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-347119-w780f0om.txt cache: ./cache/cord-347119-w780f0om.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347119-w780f0om.txt' === file2bib.sh === id: cord-345092-1ztfcpsb author: Iwasaki, Masae title: Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-345092-1ztfcpsb.txt cache: ./cache/cord-345092-1ztfcpsb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345092-1ztfcpsb.txt' === file2bib.sh === id: cord-347428-2isuaiyx author: Schulz-Stübner, Sebastian title: Hygiene in der Anästhesie in Zeiten der SARS-CoV-2-Pandemie date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-347428-2isuaiyx.txt cache: ./cache/cord-347428-2isuaiyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347428-2isuaiyx.txt' === file2bib.sh === id: cord-347441-8ow952d8 author: Parvez, Md Sorwer Alam title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-347441-8ow952d8.txt cache: ./cache/cord-347441-8ow952d8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347441-8ow952d8.txt' === file2bib.sh === id: cord-346335-el45v0a5 author: Tan, H.S. title: Fourier spectral density of the coronavirus genome date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-346335-el45v0a5.txt cache: ./cache/cord-346335-el45v0a5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346335-el45v0a5.txt' === file2bib.sh === id: cord-346677-20ky3t6y author: Sun, Pengfei title: Clinical characteristics of hospitalized patients with SARS‐CoV‐2 infection: A single arm meta‐analysis date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-346677-20ky3t6y.txt cache: ./cache/cord-346677-20ky3t6y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346677-20ky3t6y.txt' === file2bib.sh === id: cord-347458-za7cot2n author: Ruan, Qiurong title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-347458-za7cot2n.txt cache: ./cache/cord-347458-za7cot2n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347458-za7cot2n.txt' === file2bib.sh === id: cord-346960-3empldlo author: Plebani, M. title: Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-346960-3empldlo.txt cache: ./cache/cord-346960-3empldlo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346960-3empldlo.txt' === file2bib.sh === id: cord-345371-pjbviagq author: Lisi, Lucia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-345371-pjbviagq.txt cache: ./cache/cord-345371-pjbviagq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345371-pjbviagq.txt' === file2bib.sh === id: cord-347484-7vn93t58 author: Zamoto, Aya title: Identification of Ferret ACE2 and its Receptor Function for Sars-Coronavirus date: 2006 pages: extension: .txt txt: ./txt/cord-347484-7vn93t58.txt cache: ./cache/cord-347484-7vn93t58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347484-7vn93t58.txt' === file2bib.sh === id: cord-346331-d0s028wl author: Lackey, Kimberly A. title: SARS‐CoV‐2 and human milk: What is the evidence? date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-346331-d0s028wl.txt cache: ./cache/cord-346331-d0s028wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346331-d0s028wl.txt' === file2bib.sh === id: cord-346758-pi1hf6xg author: Egerup, P. title: Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-346758-pi1hf6xg.txt cache: ./cache/cord-346758-pi1hf6xg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346758-pi1hf6xg.txt' === file2bib.sh === id: cord-347048-qqft4yc9 author: Araten, David J. title: Mild Clinical Course of COVID-19 in 3 Patients Receiving Therapeutic Monoclonal Antibodies Targeting C5 Complement for Hematologic Disorders date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-347048-qqft4yc9.txt cache: ./cache/cord-347048-qqft4yc9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347048-qqft4yc9.txt' === file2bib.sh === id: cord-347104-h168kqjn author: Ghosh, Ritwik title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-347104-h168kqjn.txt cache: ./cache/cord-347104-h168kqjn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347104-h168kqjn.txt' === file2bib.sh === id: cord-346546-yffwd0dc author: Douangamath, Alice title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-346546-yffwd0dc.txt cache: ./cache/cord-346546-yffwd0dc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346546-yffwd0dc.txt' === file2bib.sh === id: cord-346281-sma6e891 author: Maldonado, Valente title: Repositioning of pentoxifylline as an immunomodulator and regulator of the renin-angiotensin system in the treatment of COVID-19 date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-346281-sma6e891.txt cache: ./cache/cord-346281-sma6e891.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346281-sma6e891.txt' === file2bib.sh === id: cord-346145-hnfeauow author: Pillay, Sureshnee title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-346145-hnfeauow.txt cache: ./cache/cord-346145-hnfeauow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346145-hnfeauow.txt' === file2bib.sh === id: cord-346669-7n75m669 author: Wang, Shixin title: Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date: 2008-02-29 pages: extension: .txt txt: ./txt/cord-346669-7n75m669.txt cache: ./cache/cord-346669-7n75m669.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346669-7n75m669.txt' === file2bib.sh === id: cord-346544-kk7qyn4w author: Andersson, M. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-346544-kk7qyn4w.txt cache: ./cache/cord-346544-kk7qyn4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346544-kk7qyn4w.txt' === file2bib.sh === id: cord-346998-01i6zxv8 author: Kulkarni, Spoorthy title: COVID-19 and hypertension date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-346998-01i6zxv8.txt cache: ./cache/cord-346998-01i6zxv8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346998-01i6zxv8.txt' === file2bib.sh === id: cord-347613-tjeo62dv author: da Silva, Priscilla Gomes title: Corrigendum to “Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2”[Sci. Total Environ. 750 (2021) 141483] date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-347613-tjeo62dv.txt cache: ./cache/cord-347613-tjeo62dv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347613-tjeo62dv.txt' === file2bib.sh === id: cord-347374-mryazbnq author: Okba, Nisreen M.A. title: Severe Acute Respiratory Syndrome Coronavirus 2−Specific Antibody Responses in Coronavirus Disease Patients date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-347374-mryazbnq.txt cache: ./cache/cord-347374-mryazbnq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347374-mryazbnq.txt' === file2bib.sh === id: cord-346146-yal0ctpq author: Peyronnet, Violaine title: Infection par le SARS-CoV-2 chez les femmes enceintes. Actualisation de l’état des connaissances et de la proposition de prise en charge. CNGOF date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-346146-yal0ctpq.txt cache: ./cache/cord-346146-yal0ctpq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346146-yal0ctpq.txt' === file2bib.sh === id: cord-346930-gl573ip9 author: Hussain, Azhar title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-346930-gl573ip9.txt cache: ./cache/cord-346930-gl573ip9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346930-gl573ip9.txt' === file2bib.sh === id: cord-347706-r0rs3ls1 author: Roberts, Anjeanette title: Animal Models for Sars date: 2006 pages: extension: .txt txt: ./txt/cord-347706-r0rs3ls1.txt cache: ./cache/cord-347706-r0rs3ls1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347706-r0rs3ls1.txt' === file2bib.sh === id: cord-346819-11fkgzaa author: Khan, Mohd Imran title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-346819-11fkgzaa.txt cache: ./cache/cord-346819-11fkgzaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346819-11fkgzaa.txt' === file2bib.sh === id: cord-346957-bmajkabp author: Lv, Yanbo title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 pages: extension: .txt txt: ./txt/cord-346957-bmajkabp.txt cache: ./cache/cord-346957-bmajkabp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346957-bmajkabp.txt' === file2bib.sh === id: cord-348071-0zlzblwi author: Tseng, Jen-Yu title: Potential implications of SARS-CoV-2 on pregnancy date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-348071-0zlzblwi.txt cache: ./cache/cord-348071-0zlzblwi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-348071-0zlzblwi.txt' === file2bib.sh === id: cord-347208-leo0x10l author: Zhou, Y. title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-347208-leo0x10l.txt cache: ./cache/cord-347208-leo0x10l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347208-leo0x10l.txt' === file2bib.sh === id: cord-347804-kxhasabe author: Luo, Ruibang title: Tracking cytosine depletion in SARS-CoV-2 date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-347804-kxhasabe.txt cache: ./cache/cord-347804-kxhasabe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347804-kxhasabe.txt' === file2bib.sh === id: cord-347548-h5fk64p8 author: Zarza, José title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-347548-h5fk64p8.txt cache: ./cache/cord-347548-h5fk64p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347548-h5fk64p8.txt' === file2bib.sh === id: cord-346859-r1v6ir8u author: Mallett, Sue title: At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-346859-r1v6ir8u.txt cache: ./cache/cord-346859-r1v6ir8u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-346859-r1v6ir8u.txt' === file2bib.sh === id: cord-347263-ci6mv72z author: Berekashvili, k. title: Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-347263-ci6mv72z.txt cache: ./cache/cord-347263-ci6mv72z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347263-ci6mv72z.txt' === file2bib.sh === id: cord-346263-8znpqcth author: Ding, Huiling title: Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu date: 2014-04-13 pages: extension: .txt txt: ./txt/cord-346263-8znpqcth.txt cache: ./cache/cord-346263-8znpqcth.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346263-8znpqcth.txt' === file2bib.sh === id: cord-347499-7q47jh14 author: Burrel, Sonia title: Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-347499-7q47jh14.txt cache: ./cache/cord-347499-7q47jh14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347499-7q47jh14.txt' === file2bib.sh === id: cord-347308-l19snjyf author: García-Howard, Marcos title: Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-347308-l19snjyf.txt cache: ./cache/cord-347308-l19snjyf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347308-l19snjyf.txt' === file2bib.sh === id: cord-347516-linjv64o author: Abdelaziz, Osama S. title: Neuropathogenic human coronaviruses: A review date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-347516-linjv64o.txt cache: ./cache/cord-347516-linjv64o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347516-linjv64o.txt' === file2bib.sh === id: cord-346787-uo8k6qic author: Jorgensen, Sarah CJ title: Remdesivir: Review of pharmacology, pre‐clinical data and emerging clinical experience for COVID‐19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-346787-uo8k6qic.txt cache: ./cache/cord-346787-uo8k6qic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346787-uo8k6qic.txt' === file2bib.sh === id: cord-346670-34wfy52f author: Gobeil, Sophie M-C. title: D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-346670-34wfy52f.txt cache: ./cache/cord-346670-34wfy52f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346670-34wfy52f.txt' === file2bib.sh === id: cord-348392-e35cd9sg author: Moraleda, Cinta title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-348392-e35cd9sg.txt cache: ./cache/cord-348392-e35cd9sg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348392-e35cd9sg.txt' === file2bib.sh === id: cord-347366-0gier0lu author: Gurwitz, David title: Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-347366-0gier0lu.txt cache: ./cache/cord-347366-0gier0lu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347366-0gier0lu.txt' === file2bib.sh === id: cord-348384-8cvt1fo6 author: Butsashvili, M. title: Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-348384-8cvt1fo6.txt cache: ./cache/cord-348384-8cvt1fo6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348384-8cvt1fo6.txt' === file2bib.sh === id: cord-347734-0z2kin6r author: Armann, J. P. title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-347734-0z2kin6r.txt cache: ./cache/cord-347734-0z2kin6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347734-0z2kin6r.txt' === file2bib.sh === id: cord-347462-yz67t10x author: Chan, Tak Yeung title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 pages: extension: .txt txt: ./txt/cord-347462-yz67t10x.txt cache: ./cache/cord-347462-yz67t10x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347462-yz67t10x.txt' === file2bib.sh === id: cord-347767-aq9niccc author: Zhao, Jie title: Yidu-toxicity blocking lung decoction ameliorates inflammation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome by eliminating IL-6 and TNF-a date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-347767-aq9niccc.txt cache: ./cache/cord-347767-aq9niccc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347767-aq9niccc.txt' === file2bib.sh === id: cord-347262-q88g1561 author: Schutzer‐Weissmann, J. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-347262-q88g1561.txt cache: ./cache/cord-347262-q88g1561.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347262-q88g1561.txt' === file2bib.sh === id: cord-347221-g98q9cga author: Piyush, Ravikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-347221-g98q9cga.txt cache: ./cache/cord-347221-g98q9cga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347221-g98q9cga.txt' === file2bib.sh === id: cord-348192-ibohbjfb author: Odih, Erkison E. title: Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks? date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-348192-ibohbjfb.txt cache: ./cache/cord-348192-ibohbjfb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348192-ibohbjfb.txt' === file2bib.sh === id: cord-346978-ubkqny8j author: Ranoa, Diana Rose E. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-346978-ubkqny8j.txt cache: ./cache/cord-346978-ubkqny8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346978-ubkqny8j.txt' === file2bib.sh === id: cord-347965-zluu0i41 author: Essahib, Wafaa title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-347965-zluu0i41.txt cache: ./cache/cord-347965-zluu0i41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347965-zluu0i41.txt' === file2bib.sh === id: cord-347813-9vfwl7c0 author: Jackson, M. L. title: Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2 date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-347813-9vfwl7c0.txt cache: ./cache/cord-347813-9vfwl7c0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347813-9vfwl7c0.txt' === file2bib.sh === id: cord-348360-20eq5meh author: Esposito, Dominic title: Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-348360-20eq5meh.txt cache: ./cache/cord-348360-20eq5meh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348360-20eq5meh.txt' === file2bib.sh === id: cord-346987-fbqqf00i author: Guo, Yongwen title: Controls of SARS-CoV-2 transmission in orthodontic practice date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-346987-fbqqf00i.txt cache: ./cache/cord-346987-fbqqf00i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346987-fbqqf00i.txt' === file2bib.sh === id: cord-347356-uc9dqhyq author: Cooper, TJ title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-347356-uc9dqhyq.txt cache: ./cache/cord-347356-uc9dqhyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347356-uc9dqhyq.txt' === file2bib.sh === id: cord-348727-o38uplxe author: Beaudoin-Bussières, Guillaume title: Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-348727-o38uplxe.txt cache: ./cache/cord-348727-o38uplxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348727-o38uplxe.txt' === file2bib.sh === id: cord-348178-6bjimde4 author: Li, Ling title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 pages: extension: .txt txt: ./txt/cord-348178-6bjimde4.txt cache: ./cache/cord-348178-6bjimde4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348178-6bjimde4.txt' === file2bib.sh === id: cord-347225-gh51ag2x author: Fu, Weihui title: A clinical pilot study on the safety and efficacy of aerosol inhalation treatment of IFN-κ plus TFF2 in patients with moderate COVID-19 date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-347225-gh51ag2x.txt cache: ./cache/cord-347225-gh51ag2x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347225-gh51ag2x.txt' === file2bib.sh === id: cord-348748-rxyh58eu author: Gorospe, Luis title: COVID-19: Thoracic Diagnostic Interventional Procedures in Troubled Times() date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-348748-rxyh58eu.txt cache: ./cache/cord-348748-rxyh58eu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348748-rxyh58eu.txt' === file2bib.sh === id: cord-347079-1zbsbcdd author: Silverman, Justin D. title: Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-347079-1zbsbcdd.txt cache: ./cache/cord-347079-1zbsbcdd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347079-1zbsbcdd.txt' === file2bib.sh === id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-347714-vxxhglx7.txt cache: ./cache/cord-347714-vxxhglx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347714-vxxhglx7.txt' === file2bib.sh === id: cord-348342-iqq8kmn0 author: Uyoga, S. title: Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-348342-iqq8kmn0.txt cache: ./cache/cord-348342-iqq8kmn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348342-iqq8kmn0.txt' === file2bib.sh === id: cord-346389-gbmnoo84 author: Callender, Lauren A. title: The Impact of Pre-existing Comorbidities and Therapeutic Interventions on COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-346389-gbmnoo84.txt cache: ./cache/cord-346389-gbmnoo84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346389-gbmnoo84.txt' === file2bib.sh === id: cord-347553-d7q6u7vj author: Criado, Paulo Ricardo title: Lessons from dermatology about inflammatory responses in Covid‐19 date: 2020-07-12 pages: extension: .txt txt: ./txt/cord-347553-d7q6u7vj.txt cache: ./cache/cord-347553-d7q6u7vj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347553-d7q6u7vj.txt' === file2bib.sh === id: cord-348209-rkkhv4mw author: Noerz, Dominik title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-348209-rkkhv4mw.txt cache: ./cache/cord-348209-rkkhv4mw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348209-rkkhv4mw.txt' === file2bib.sh === id: cord-347731-eqxn6auk author: Garcia‐Cremades, Maria title: Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-347731-eqxn6auk.txt cache: ./cache/cord-347731-eqxn6auk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347731-eqxn6auk.txt' === file2bib.sh === id: cord-348478-ho89o8mj author: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-348478-ho89o8mj.txt cache: ./cache/cord-348478-ho89o8mj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348478-ho89o8mj.txt' === file2bib.sh === id: cord-348723-sf073cmj author: Chen, Liang title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-348723-sf073cmj.txt cache: ./cache/cord-348723-sf073cmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348723-sf073cmj.txt' === file2bib.sh === id: cord-348526-g3asp1ps author: Wang, Wenjun title: WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019 date: 2020-02-26 pages: extension: .txt txt: ./txt/cord-348526-g3asp1ps.txt cache: ./cache/cord-348526-g3asp1ps.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348526-g3asp1ps.txt' === file2bib.sh === id: cord-346894-iy35298o author: Miranda-Schaeubinger, Monica title: A primer for pediatric radiologists on infection control in an era of COVID-19 date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-346894-iy35298o.txt cache: ./cache/cord-346894-iy35298o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346894-iy35298o.txt' === file2bib.sh === id: cord-348823-u2gm3kyh author: Baksh, Mizba title: A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-348823-u2gm3kyh.txt cache: ./cache/cord-348823-u2gm3kyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348823-u2gm3kyh.txt' === file2bib.sh === id: cord-347968-jhnr8k3j author: Herrera, David title: Is the oral cavity relevant in SARS-CoV-2 pandemic? date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-347968-jhnr8k3j.txt cache: ./cache/cord-347968-jhnr8k3j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347968-jhnr8k3j.txt' === file2bib.sh === id: cord-348635-1pb2ag9j author: Anand, Praveen title: SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-348635-1pb2ag9j.txt cache: ./cache/cord-348635-1pb2ag9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348635-1pb2ag9j.txt' === file2bib.sh === id: cord-347472-n6811ens author: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-347472-n6811ens.txt cache: ./cache/cord-347472-n6811ens.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347472-n6811ens.txt' === file2bib.sh === id: cord-348202-6we8e60b author: Drake, Daniel H. title: Echo in Pandemic: Front Line Perspective, Expanding Role of Ultrasound and Ethics of Resource Allocation date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-348202-6we8e60b.txt cache: ./cache/cord-348202-6we8e60b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348202-6we8e60b.txt' === file2bib.sh === id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 pages: extension: .txt txt: ./txt/cord-349070-bqv03u2e.txt cache: ./cache/cord-349070-bqv03u2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349070-bqv03u2e.txt' === file2bib.sh === id: cord-348752-bbghqy1a author: Li, Yuguo title: Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-348752-bbghqy1a.txt cache: ./cache/cord-348752-bbghqy1a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348752-bbghqy1a.txt' === file2bib.sh === id: cord-348065-0tkx7aas author: Liu, Bing title: Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-348065-0tkx7aas.txt cache: ./cache/cord-348065-0tkx7aas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348065-0tkx7aas.txt' === file2bib.sh === id: cord-347351-emdj66vj author: Kampf, Günter title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-347351-emdj66vj.txt cache: ./cache/cord-347351-emdj66vj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347351-emdj66vj.txt' === file2bib.sh === id: cord-348301-bk80pps9 author: Wahl, Angela title: Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801 date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-348301-bk80pps9.txt cache: ./cache/cord-348301-bk80pps9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348301-bk80pps9.txt' === file2bib.sh === id: cord-347460-9vechh4x author: Chang, Feng-Yee title: Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-347460-9vechh4x.txt cache: ./cache/cord-347460-9vechh4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347460-9vechh4x.txt' === file2bib.sh === id: cord-347289-3yi5tz04 author: Poon, L. . C. title: ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-347289-3yi5tz04.txt cache: ./cache/cord-347289-3yi5tz04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347289-3yi5tz04.txt' === file2bib.sh === id: cord-348713-tucolje2 author: Cao, Yanan title: Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations date: 2020-02-24 pages: extension: .txt txt: ./txt/cord-348713-tucolje2.txt cache: ./cache/cord-348713-tucolje2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348713-tucolje2.txt' === file2bib.sh === id: cord-348243-e5tdb08v author: Schermer, Bernhard title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-348243-e5tdb08v.txt cache: ./cache/cord-348243-e5tdb08v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348243-e5tdb08v.txt' === file2bib.sh === id: cord-349015-5oisrm5s author: Liu, Zhe title: Identification of a common deletion in the spike protein of SARS-CoV-2 date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-349015-5oisrm5s.txt cache: ./cache/cord-349015-5oisrm5s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349015-5oisrm5s.txt' === file2bib.sh === id: cord-349124-nhnl7zgi author: de Sandes‐Freitas, Tainá Veras title: Lessons from SARS‐CoV‐2 screening in a Brazilian organ transplant unit date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-349124-nhnl7zgi.txt cache: ./cache/cord-349124-nhnl7zgi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349124-nhnl7zgi.txt' === file2bib.sh === id: cord-349311-yo4up42r author: De Maria, Andrea title: High prevalence of olfactory and taste disorder during SARS‐CoV‐2 infection in outpatients date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-349311-yo4up42r.txt cache: ./cache/cord-349311-yo4up42r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349311-yo4up42r.txt' === file2bib.sh === id: cord-349541-7g50vg14 author: Poulikakos, Dimitrios title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-349541-7g50vg14.txt cache: ./cache/cord-349541-7g50vg14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349541-7g50vg14.txt' === file2bib.sh === id: cord-348729-kejlm425 author: Liu, Xiaoyu title: Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-348729-kejlm425.txt cache: ./cache/cord-348729-kejlm425.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348729-kejlm425.txt' === file2bib.sh === id: cord-348777-pk9y6vfp author: Ding, Cheng title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-348777-pk9y6vfp.txt cache: ./cache/cord-348777-pk9y6vfp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348777-pk9y6vfp.txt' === file2bib.sh === id: cord-349485-iomk99lv author: Eis-Hübinger, Anna M. title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-349485-iomk99lv.txt cache: ./cache/cord-349485-iomk99lv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349485-iomk99lv.txt' === file2bib.sh === id: cord-347818-93ixqyfp author: Hojyo, Shintaro title: How COVID-19 induces cytokine storm with high mortality date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-347818-93ixqyfp.txt cache: ./cache/cord-347818-93ixqyfp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347818-93ixqyfp.txt' === file2bib.sh === id: cord-349501-p1fttfpr author: Ratia, Kiira title: Chapter 494 Coronavirus Papain-like Peptidases date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-349501-p1fttfpr.txt cache: ./cache/cord-349501-p1fttfpr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349501-p1fttfpr.txt' === file2bib.sh === id: cord-348455-vcxalkeo author: Graham, N. R. title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-348455-vcxalkeo.txt cache: ./cache/cord-348455-vcxalkeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348455-vcxalkeo.txt' === file2bib.sh === id: cord-348696-86nbwon2 author: Güemes-Villahoz, Noemi title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-348696-86nbwon2.txt cache: ./cache/cord-348696-86nbwon2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348696-86nbwon2.txt' === file2bib.sh === id: cord-348567-rvwxysvc author: Panfili, F. M. title: Possible role of vitamin D in Covid-19 infection in pediatric population date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-348567-rvwxysvc.txt cache: ./cache/cord-348567-rvwxysvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348567-rvwxysvc.txt' === file2bib.sh === id: cord-348283-7xorq5ce author: Naz, Anam title: Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-348283-7xorq5ce.txt cache: ./cache/cord-348283-7xorq5ce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348283-7xorq5ce.txt' === file2bib.sh === id: cord-349690-hgdjbeht author: Alonso, Fábio de O. Martinez title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-349690-hgdjbeht.txt cache: ./cache/cord-349690-hgdjbeht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349690-hgdjbeht.txt' === file2bib.sh === id: cord-349545-w7c2tu5a author: Wang, Mengmeng title: Analytical performance evaluation of five RT‐PCR kits for severe acute respiratory syndrome coronavirus 2 date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-349545-w7c2tu5a.txt cache: ./cache/cord-349545-w7c2tu5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349545-w7c2tu5a.txt' === file2bib.sh === id: cord-349556-k312qkvh author: Roldán-Santiago, Ernesto title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-349556-k312qkvh.txt cache: ./cache/cord-349556-k312qkvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349556-k312qkvh.txt' === file2bib.sh === id: cord-350094-nkzbtcfw author: Barrett, Lisa F. title: Self-Limited Gastrointestinal Bleeding in COVID-19 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-350094-nkzbtcfw.txt cache: ./cache/cord-350094-nkzbtcfw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350094-nkzbtcfw.txt' === file2bib.sh === id: cord-349504-oqpjqgv4 author: Escudero, Dolores title: Análisis de SARS-CoV-2 en el aire de una UCI dedicada a pacientes Covid-19 date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-349504-oqpjqgv4.txt cache: ./cache/cord-349504-oqpjqgv4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349504-oqpjqgv4.txt' === file2bib.sh === id: cord-349031-tbof9yqi author: Chen, Shiu-Jau title: Novel Antiviral Strategies in the Treatment of COVID-19: A Review date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-349031-tbof9yqi.txt cache: ./cache/cord-349031-tbof9yqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349031-tbof9yqi.txt' === file2bib.sh === id: cord-349912-em1abdrg author: Meng, Xiangming title: COVID-19 and anosmia: A review based on up-to-date knowledge date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-349912-em1abdrg.txt cache: ./cache/cord-349912-em1abdrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349912-em1abdrg.txt' === file2bib.sh === id: cord-348855-lnltoj1n author: Iannaccone, Giulia title: Weathering the Cytokine Storm in COVID-19: Therapeutic Implications date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-348855-lnltoj1n.txt cache: ./cache/cord-348855-lnltoj1n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348855-lnltoj1n.txt' === file2bib.sh === id: cord-349417-vn7q8wc4 author: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 pages: extension: .txt txt: ./txt/cord-349417-vn7q8wc4.txt cache: ./cache/cord-349417-vn7q8wc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349417-vn7q8wc4.txt' === file2bib.sh === id: cord-348636-qqcb85uk author: Lekone, Phenyo E. title: Bayesian Analysis of Severe Acute Respiratory Syndrome: The 2003 Hong Kong Epidemic date: 2008-07-09 pages: extension: .txt txt: ./txt/cord-348636-qqcb85uk.txt cache: ./cache/cord-348636-qqcb85uk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348636-qqcb85uk.txt' === file2bib.sh === id: cord-349365-2ot1kf2k author: Shi, Yi title: Antisense downregulation of SARS‐CoV gene expression in Vero E6 cells date: 2004-11-15 pages: extension: .txt txt: ./txt/cord-349365-2ot1kf2k.txt cache: ./cache/cord-349365-2ot1kf2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349365-2ot1kf2k.txt' === file2bib.sh === id: cord-350045-85jug39x author: Pruc, Michal title: Risk of coronavirus infections among medical personnel date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-350045-85jug39x.txt cache: ./cache/cord-350045-85jug39x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350045-85jug39x.txt' === file2bib.sh === id: cord-349659-6drnriun author: Grant, Benjamin D. title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-349659-6drnriun.txt cache: ./cache/cord-349659-6drnriun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349659-6drnriun.txt' === file2bib.sh === id: cord-349744-8cg5yj20 author: Lassaunière, Ria title: Evaluation of nine commercial SARS-CoV-2 immunoassays date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-349744-8cg5yj20.txt cache: ./cache/cord-349744-8cg5yj20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349744-8cg5yj20.txt' === file2bib.sh === id: cord-349645-6o8773c5 author: Li, He title: Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-349645-6o8773c5.txt cache: ./cache/cord-349645-6o8773c5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349645-6o8773c5.txt' === file2bib.sh === id: cord-349029-zyfop43z author: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-349029-zyfop43z.txt cache: ./cache/cord-349029-zyfop43z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349029-zyfop43z.txt' === file2bib.sh === id: cord-349428-i2s41kl7 author: Griffin, Ian title: The Impact of COVID-19 Infection on Labor and Delivery, Newborn Nursery, and Neonatal Intensive Care Unit: Prospective Observational Data from a Single Hospital System date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-349428-i2s41kl7.txt cache: ./cache/cord-349428-i2s41kl7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349428-i2s41kl7.txt' === file2bib.sh === id: cord-349656-baoqgu8v author: Wang, Chen title: Intrauterine vertical transmission of SARS‐CoV‐2: what we know so far date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-349656-baoqgu8v.txt cache: ./cache/cord-349656-baoqgu8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349656-baoqgu8v.txt' === file2bib.sh === id: cord-348773-ulnc9gdv author: Hammoud, H. title: Post mortem pathological findings in COVID-19 cases: A Systematic Review date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-348773-ulnc9gdv.txt cache: ./cache/cord-348773-ulnc9gdv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348773-ulnc9gdv.txt' === file2bib.sh === id: cord-349745-zlhu1jit author: Konrad, Regina title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-349745-zlhu1jit.txt cache: ./cache/cord-349745-zlhu1jit.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349745-zlhu1jit.txt' === file2bib.sh === id: cord-350352-wgppovfx author: Temmam, Sarah title: Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-350352-wgppovfx.txt cache: ./cache/cord-350352-wgppovfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350352-wgppovfx.txt' === file2bib.sh === id: cord-349226-xzlc1pni author: Khatiwada, Saroj title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-349226-xzlc1pni.txt cache: ./cache/cord-349226-xzlc1pni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349226-xzlc1pni.txt' === file2bib.sh === id: cord-350513-ho32ajsx author: Chen, Paul Chih‐Hsueh title: Re: To KF, Tong JH, Chan PK, et al. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. J Pathol 2004; 202: 157–163 date: 2004-05-07 pages: extension: .txt txt: ./txt/cord-350513-ho32ajsx.txt cache: ./cache/cord-350513-ho32ajsx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350513-ho32ajsx.txt' === file2bib.sh === id: cord-349159-rndtf508 author: Brosseau, Lisa M title: Selecting Controls for Minimizing SARS-CoV-2 Aerosol Transmission in Workplaces and Conserving Respiratory Protective Equipment Supplies date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-349159-rndtf508.txt cache: ./cache/cord-349159-rndtf508.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-349159-rndtf508.txt' === file2bib.sh === id: cord-349794-mhviub6e author: Le, Brian L. title: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-349794-mhviub6e.txt cache: ./cache/cord-349794-mhviub6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349794-mhviub6e.txt' === file2bib.sh === id: cord-350393-j80k2v21 author: Chen, Liping title: Clinical characteristics in patients with SARS‐CoV‐2/HBV co‐infection date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-350393-j80k2v21.txt cache: ./cache/cord-350393-j80k2v21.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350393-j80k2v21.txt' === file2bib.sh === id: cord-349721-wdjlr4z4 author: Szpiro, L. title: Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-349721-wdjlr4z4.txt cache: ./cache/cord-349721-wdjlr4z4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349721-wdjlr4z4.txt' === file2bib.sh === id: cord-349827-0trvostt author: Tse, Alan C.B. title: Crisis management and recovery: how restaurants in Hong Kong responded to SARS date: 2005-01-29 pages: extension: .txt txt: ./txt/cord-349827-0trvostt.txt cache: ./cache/cord-349827-0trvostt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349827-0trvostt.txt' === file2bib.sh === id: cord-348899-vynk8q8c author: Jo, Seri title: Inhibition of SARS-CoV 3CL protease by flavonoids date: 2019-11-14 pages: extension: .txt txt: ./txt/cord-348899-vynk8q8c.txt cache: ./cache/cord-348899-vynk8q8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348899-vynk8q8c.txt' === file2bib.sh === id: cord-349774-898tmq14 author: Zhang, Haiyang title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-349774-898tmq14.txt cache: ./cache/cord-349774-898tmq14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349774-898tmq14.txt' === file2bib.sh === id: cord-350134-gl3qtoug author: Brun, Gilles title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-350134-gl3qtoug.txt cache: ./cache/cord-350134-gl3qtoug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350134-gl3qtoug.txt' === file2bib.sh === id: cord-349392-r71g2e9y author: Wang, L. -F. title: Bats, Civets and the Emergence of SARS date: 2007 pages: extension: .txt txt: ./txt/cord-349392-r71g2e9y.txt cache: ./cache/cord-349392-r71g2e9y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349392-r71g2e9y.txt' === file2bib.sh === id: cord-350235-yoy3hj3j author: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-350235-yoy3hj3j.txt cache: ./cache/cord-350235-yoy3hj3j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350235-yoy3hj3j.txt' === file2bib.sh === id: cord-349838-p6vfzbla author: Algwaiz, Ghada title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-349838-p6vfzbla.txt cache: ./cache/cord-349838-p6vfzbla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349838-p6vfzbla.txt' === file2bib.sh === id: cord-350103-liwvhuzj author: Brooks, Nathan A. title: The role of the urologist, BCG vaccine administration, and SARS‐CoV‐2: An overview date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-350103-liwvhuzj.txt cache: ./cache/cord-350103-liwvhuzj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350103-liwvhuzj.txt' === file2bib.sh === id: cord-349954-bozgrzvf author: Quintaliani, Giuseppe title: Exposure to novel coronavirus in patients on renal replacement therapy during the exponential phase of COVID-19 pandemic: survey of the Italian Society of Nephrology date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-349954-bozgrzvf.txt cache: ./cache/cord-349954-bozgrzvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349954-bozgrzvf.txt' === file2bib.sh === id: cord-348391-xytmq2f2 author: Wyganowska-Swiatkowska, Marzena title: Influence of Herbal Medicines on HMGB1 Release, SARS-CoV-2 Viral Attachment, Acute Respiratory Failure, and Sepsis. A Literature Review date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-348391-xytmq2f2.txt cache: ./cache/cord-348391-xytmq2f2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348391-xytmq2f2.txt' === file2bib.sh === id: cord-349907-dwhyx97y author: Noh, Ji Yeong title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 pages: extension: .txt txt: ./txt/cord-349907-dwhyx97y.txt cache: ./cache/cord-349907-dwhyx97y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349907-dwhyx97y.txt' === file2bib.sh === id: cord-349313-2gupfqnl author: Martinez-Perez, Clara title: Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19) date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-349313-2gupfqnl.txt cache: ./cache/cord-349313-2gupfqnl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349313-2gupfqnl.txt' === file2bib.sh === id: cord-350451-lf27iuwk author: Benedetti, Francesca title: SARS‐CoV‐2: March toward adaptation date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-350451-lf27iuwk.txt cache: ./cache/cord-350451-lf27iuwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350451-lf27iuwk.txt' === file2bib.sh === id: cord-350095-hsl1hfds author: Shiu, Stephen Y. W. title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? date: 2003-06-16 pages: extension: .txt txt: ./txt/cord-350095-hsl1hfds.txt cache: ./cache/cord-350095-hsl1hfds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350095-hsl1hfds.txt' === file2bib.sh === id: cord-350101-t34myl7l author: Henrique Braz‐Silva, Paulo title: SARS‐CoV‐2: What can saliva tell us? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-350101-t34myl7l.txt cache: ./cache/cord-350101-t34myl7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350101-t34myl7l.txt' === file2bib.sh === id: cord-349210-8t4a5qqo author: Ji, Ping title: Immunomodulatory Therapeutic Proteins in COVID‐19: Current Clinical Development and Clinical Pharmacology Considerations date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-349210-8t4a5qqo.txt cache: ./cache/cord-349210-8t4a5qqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349210-8t4a5qqo.txt' === file2bib.sh === id: cord-350130-c4u0gxp5 author: Wu, Yi-Chi title: The outbreak of COVID-19: An overview date: 2020-02-12 pages: extension: .txt txt: ./txt/cord-350130-c4u0gxp5.txt cache: ./cache/cord-350130-c4u0gxp5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350130-c4u0gxp5.txt' === file2bib.sh === id: cord-350182-s10nong7 author: Milionis, Charalampos title: A brief analysis and hypotheses about the risk of COVID-19 for people with type 1 and type 2 diabetes mellitus date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-350182-s10nong7.txt cache: ./cache/cord-350182-s10nong7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350182-s10nong7.txt' === file2bib.sh === id: cord-350242-4u1iyf0p author: Yaniv, K. title: City-level SARS-CoV-2 sewage surveillance date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-350242-4u1iyf0p.txt cache: ./cache/cord-350242-4u1iyf0p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350242-4u1iyf0p.txt' === file2bib.sh === id: cord-350627-4pgish5x author: Zhao, Yu title: Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date: 2020-01-26 pages: extension: .txt txt: ./txt/cord-350627-4pgish5x.txt cache: ./cache/cord-350627-4pgish5x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350627-4pgish5x.txt' === file2bib.sh === id: cord-349623-dw5o9i59 author: Miranda, José P. title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-349623-dw5o9i59.txt cache: ./cache/cord-349623-dw5o9i59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349623-dw5o9i59.txt' === file2bib.sh === id: cord-349500-603v8lfb author: Neurath, Markus F title: Covid-19 and immunomodulation in IBD date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-349500-603v8lfb.txt cache: ./cache/cord-349500-603v8lfb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349500-603v8lfb.txt' === file2bib.sh === id: cord-350686-q2bu7o4i author: Bilder, Christopher R title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-350686-q2bu7o4i.txt cache: ./cache/cord-350686-q2bu7o4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350686-q2bu7o4i.txt' === file2bib.sh === id: cord-347121-5drl3xas author: Farah, I. title: A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform. date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-347121-5drl3xas.txt cache: ./cache/cord-347121-5drl3xas.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347121-5drl3xas.txt' === file2bib.sh === id: cord-350029-1y5ex4d5 author: McDade, Thomas W. title: Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-350029-1y5ex4d5.txt cache: ./cache/cord-350029-1y5ex4d5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350029-1y5ex4d5.txt' === file2bib.sh === id: cord-350557-7i7122zi author: Rawlings, Stephen A title: No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-350557-7i7122zi.txt cache: ./cache/cord-350557-7i7122zi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350557-7i7122zi.txt' === file2bib.sh === id: cord-349684-2tioh80m author: Pezzotti, Giuseppe title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-349684-2tioh80m.txt cache: ./cache/cord-349684-2tioh80m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349684-2tioh80m.txt' === file2bib.sh === id: cord-349821-5ykwwq75 author: Ippolito, G. title: Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date: 2006-09-09 pages: extension: .txt txt: ./txt/cord-349821-5ykwwq75.txt cache: ./cache/cord-349821-5ykwwq75.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349821-5ykwwq75.txt' === file2bib.sh === id: cord-348010-m3a3utvz author: Wolff, Michael title: On build‐up of epidemiologic models—Development of a SEI(3)RSD model for the spread of SARS‐CoV‐2 date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-348010-m3a3utvz.txt cache: ./cache/cord-348010-m3a3utvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348010-m3a3utvz.txt' === file2bib.sh === id: cord-349117-xfir3m5p author: Hyseni, Inesa title: Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-349117-xfir3m5p.txt cache: ./cache/cord-349117-xfir3m5p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349117-xfir3m5p.txt' === file2bib.sh === id: cord-350317-a9qd3xdr author: Xu, Qiannan title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-350317-a9qd3xdr.txt cache: ./cache/cord-350317-a9qd3xdr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350317-a9qd3xdr.txt' === file2bib.sh === id: cord-350211-vuxs5wtt author: Johanna, Barón‐Sánchez title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-350211-vuxs5wtt.txt cache: ./cache/cord-350211-vuxs5wtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350211-vuxs5wtt.txt' === file2bib.sh === id: cord-349923-cja8i0hw author: Habibzadeh, Parham title: The Novel Coronavirus: A Bird's Eye View date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-349923-cja8i0hw.txt cache: ./cache/cord-349923-cja8i0hw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349923-cja8i0hw.txt' === file2bib.sh === id: cord-350328-wu1ygt6w author: Tambyah, P. A. title: SARS: responding to an unknown virus date: 2004-07-14 pages: extension: .txt txt: ./txt/cord-350328-wu1ygt6w.txt cache: ./cache/cord-350328-wu1ygt6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350328-wu1ygt6w.txt' === file2bib.sh === id: cord-350737-nrtrhq1f author: Chen, Xinchun title: Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date: 2004-04-01 pages: extension: .txt txt: ./txt/cord-350737-nrtrhq1f.txt cache: ./cache/cord-350737-nrtrhq1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350737-nrtrhq1f.txt' === file2bib.sh === id: cord-346539-kxnrf5g5 author: Riggioni, Carmen title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-346539-kxnrf5g5.txt cache: ./cache/cord-346539-kxnrf5g5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346539-kxnrf5g5.txt' === file2bib.sh === id: cord-349682-kpg0vley author: Ojha, Probir Kumar title: Therapeutics for COVID-19: from computation to practices—where we are, where we are heading to date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-349682-kpg0vley.txt cache: ./cache/cord-349682-kpg0vley.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349682-kpg0vley.txt' === file2bib.sh === id: cord-349762-f5no10eq author: Nagura-Ikeda, Mayu title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-349762-f5no10eq.txt cache: ./cache/cord-349762-f5no10eq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349762-f5no10eq.txt' === file2bib.sh === id: cord-350679-69lv4wbz author: Shinde, Rajesh S. title: To Do or Not to Do?—A Review of Cancer Surgery Triage Guidelines in COVID-19 Pandemic date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-350679-69lv4wbz.txt cache: ./cache/cord-350679-69lv4wbz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350679-69lv4wbz.txt' === file2bib.sh === id: cord-350401-suefuurq author: Lima-Setta, Fernanda title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-350401-suefuurq.txt cache: ./cache/cord-350401-suefuurq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350401-suefuurq.txt' === file2bib.sh === id: cord-350903-nwagvvc5 author: Softic, Laurent title: Inhibition of SARS-CoV-2 Infection by the Cyclophilin Inhibitor Alisporivir (Debio 025) date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-350903-nwagvvc5.txt cache: ./cache/cord-350903-nwagvvc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350903-nwagvvc5.txt' === file2bib.sh === id: cord-350733-0zghspb8 author: Aronson, Jeffrey K. title: The use of mechanistic reasoning in assessing coronavirus interventions date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-350733-0zghspb8.txt cache: ./cache/cord-350733-0zghspb8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350733-0zghspb8.txt' === file2bib.sh === id: cord-350505-uh8r2vyz author: Kalantar-Zadeh, Kourosh title: Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-350505-uh8r2vyz.txt cache: ./cache/cord-350505-uh8r2vyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350505-uh8r2vyz.txt' === file2bib.sh === id: cord-350972-0n4dumgg author: Sing, Chor-Wing title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-350972-0n4dumgg.txt cache: ./cache/cord-350972-0n4dumgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350972-0n4dumgg.txt' === file2bib.sh === id: cord-350821-0qfoc553 author: Jahromi, Reza title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-350821-0qfoc553.txt cache: ./cache/cord-350821-0qfoc553.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350821-0qfoc553.txt' === file2bib.sh === id: cord-350753-qbm145tr author: Krüttgen, Alexander title: Determination of SARS-CoV-2 antibodies with assays from Diasorin, Roche and IDvet date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-350753-qbm145tr.txt cache: ./cache/cord-350753-qbm145tr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350753-qbm145tr.txt' === file2bib.sh === id: cord-350104-b99y6n43 author: de Zwart, Onno title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey date: 2009-01-06 pages: extension: .txt txt: ./txt/cord-350104-b99y6n43.txt cache: ./cache/cord-350104-b99y6n43.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350104-b99y6n43.txt' === file2bib.sh === id: cord-347128-6lyoz8nn author: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-347128-6lyoz8nn.txt cache: ./cache/cord-347128-6lyoz8nn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347128-6lyoz8nn.txt' === file2bib.sh === id: cord-350342-j4p8235a author: Brocato, Rebecca L. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-350342-j4p8235a.txt cache: ./cache/cord-350342-j4p8235a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350342-j4p8235a.txt' === file2bib.sh === id: cord-350189-2su7oqbz author: Elmén, Joacim title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 pages: extension: .txt txt: ./txt/cord-350189-2su7oqbz.txt cache: ./cache/cord-350189-2su7oqbz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350189-2su7oqbz.txt' === file2bib.sh === id: cord-350309-j4oh1z8m author: Liu, D. X. title: Coronavirus envelope protein: A small membrane protein with multiple functions date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-350309-j4oh1z8m.txt cache: ./cache/cord-350309-j4oh1z8m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350309-j4oh1z8m.txt' === file2bib.sh === id: cord-351169-y91fdf66 author: Phillips, Lia title: Successful management of SARS-CoV-2 acute respiratory distress syndrome and newly diagnosed acute lymphoblastic leukemia date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-351169-y91fdf66.txt cache: ./cache/cord-351169-y91fdf66.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351169-y91fdf66.txt' === file2bib.sh === id: cord-349089-ta07bho2 author: Antushevich, Hanna title: Interplays between inflammasomes and viruses, bacteria (pathogenic and probiotic), yeasts and parasites date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-349089-ta07bho2.txt cache: ./cache/cord-349089-ta07bho2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-349089-ta07bho2.txt' === file2bib.sh === id: cord-350015-mg5wiihj author: Chen, Yiyin title: Aging in COVID-19: Vulnerability, immunity and intervention date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-350015-mg5wiihj.txt cache: ./cache/cord-350015-mg5wiihj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350015-mg5wiihj.txt' === file2bib.sh === id: cord-351218-ei8dyxfg author: Charles Bronson, Stephen title: Letter to the Editor in response to the article “Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-351218-ei8dyxfg.txt cache: ./cache/cord-351218-ei8dyxfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351218-ei8dyxfg.txt' === file2bib.sh === id: cord-350212-448mv4lt author: Chiuppesi, Flavia title: Development of a Multi-Antigenic SARS-CoV-2 Vaccine Using a Synthetic Poxvirus Platform date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-350212-448mv4lt.txt cache: ./cache/cord-350212-448mv4lt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350212-448mv4lt.txt' === file2bib.sh === id: cord-350437-dq1il88y author: Reale, Maria Lucia title: SARS-CoV-2 Infection in Cancer Patients: A Picture of an Italian Onco-Covid Unit date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-350437-dq1il88y.txt cache: ./cache/cord-350437-dq1il88y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350437-dq1il88y.txt' === file2bib.sh === id: cord-350817-tmszrtju author: Hoepel, Willianne title: Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-350817-tmszrtju.txt cache: ./cache/cord-350817-tmszrtju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350817-tmszrtju.txt' === file2bib.sh === id: cord-351314-atsuh8e2 author: Bryson-Cahn, Chloe title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-351314-atsuh8e2.txt cache: ./cache/cord-351314-atsuh8e2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351314-atsuh8e2.txt' === file2bib.sh === id: cord-349445-yh6ndtgm author: Mohammed El Tabaa, Manar title: Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-349445-yh6ndtgm.txt cache: ./cache/cord-349445-yh6ndtgm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349445-yh6ndtgm.txt' === file2bib.sh === id: cord-351028-p5cq2is5 author: Yang, Jia-Wei title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-351028-p5cq2is5.txt cache: ./cache/cord-351028-p5cq2is5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351028-p5cq2is5.txt' === file2bib.sh === id: cord-350172-w3yoxhsg author: Mertens, Pascal title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-350172-w3yoxhsg.txt cache: ./cache/cord-350172-w3yoxhsg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350172-w3yoxhsg.txt' === file2bib.sh === id: cord-351283-1y9dfobn author: Tan, Bai‐Hong title: The possible impairment of respiratory‐related neural loops may be associated with the silent pneumonia induced by SARS‐CoV‐2 date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-351283-1y9dfobn.txt cache: ./cache/cord-351283-1y9dfobn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351283-1y9dfobn.txt' === file2bib.sh === id: cord-351002-msjurww1 author: Ouanes, Y. title: Does BCG protect against SARS-CoV-2 infection ?: elements of proof. date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-351002-msjurww1.txt cache: ./cache/cord-351002-msjurww1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351002-msjurww1.txt' === file2bib.sh === id: cord-350925-1h6pbfwp author: da Silva, Priscilla Gomes title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-350925-1h6pbfwp.txt cache: ./cache/cord-350925-1h6pbfwp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350925-1h6pbfwp.txt' === file2bib.sh === id: cord-351116-jwy6k0ih author: O'Reilly, GM title: Epidemiology and clinical features of emergency department patients with suspected and confirmed COVID‐19: A multisite report from the COVED Quality Improvement Project for July 2020 (COVED‐3) date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-351116-jwy6k0ih.txt cache: ./cache/cord-351116-jwy6k0ih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351116-jwy6k0ih.txt' === file2bib.sh === id: cord-350990-tywbe4o2 author: Checchi, Vittorio title: COVID‐19 dentistry‐related aspects: a literature overview date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-350990-tywbe4o2.txt cache: ./cache/cord-350990-tywbe4o2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350990-tywbe4o2.txt' === file2bib.sh === id: cord-351092-b01o6f69 author: De Francesco, Maria A. title: Pneumocystis jirevocii and SARS-CoV-2 Co-Infection: A Common Feature in Transplant Recipients? date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-351092-b01o6f69.txt cache: ./cache/cord-351092-b01o6f69.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351092-b01o6f69.txt' === file2bib.sh === id: cord-351189-56am76lb author: Rosen, Melissa H title: Management of Acute Severe Ulcerative Colitis in a Pregnant Woman With COVID-19 Infection: A Case Report and Review of the Literature date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-351189-56am76lb.txt cache: ./cache/cord-351189-56am76lb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351189-56am76lb.txt' === file2bib.sh === id: cord-349477-3qhpu7v0 author: Jarynowski, A. title: An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-349477-3qhpu7v0.txt cache: ./cache/cord-349477-3qhpu7v0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349477-3qhpu7v0.txt' === file2bib.sh === id: cord-351100-llyl97ry author: Cariani, Lisa title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-351100-llyl97ry.txt cache: ./cache/cord-351100-llyl97ry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-351100-llyl97ry.txt' === file2bib.sh === id: cord-351031-e8suoeim author: Liang En Ian, Wee title: Containing COVID-19 outside the isolation ward: the impact of an infection control bundle on environmental contamination and transmission in a cohorted general ward date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-351031-e8suoeim.txt cache: ./cache/cord-351031-e8suoeim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351031-e8suoeim.txt' === file2bib.sh === id: cord-351278-nm2bq717 author: Thompson, Craig title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-351278-nm2bq717.txt cache: ./cache/cord-351278-nm2bq717.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351278-nm2bq717.txt' === file2bib.sh === id: cord-350959-bsbz3a1l author: Dovey, Zachary title: Impact of COVID-19 on Prostate Cancer Management: Guidelines for Urologists date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-350959-bsbz3a1l.txt cache: ./cache/cord-350959-bsbz3a1l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350959-bsbz3a1l.txt' === file2bib.sh === id: cord-350622-8tgxdbyi author: Palit, Partha title: Phytopharmaceuticals mediated Furin and TMPRSS2 receptor blocking: can it be a potential therapeutic option for Covid-19? date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-350622-8tgxdbyi.txt cache: ./cache/cord-350622-8tgxdbyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350622-8tgxdbyi.txt' === file2bib.sh === id: cord-351305-6vtv2xuh author: Schramm, Markus A. title: COVID-19 in a Severely Immunosuppressed Patient With Life-Threatening Eosinophilic Granulomatosis With Polyangiitis date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-351305-6vtv2xuh.txt cache: ./cache/cord-351305-6vtv2xuh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351305-6vtv2xuh.txt' === file2bib.sh === id: cord-351503-2f0sk24j author: Pua, Uei title: What Is Needed to Make Interventional Radiology Ready for COVID-19? Lessons from SARS-CoV Epidemic date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-351503-2f0sk24j.txt cache: ./cache/cord-351503-2f0sk24j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-351503-2f0sk24j.txt' === file2bib.sh === id: cord-350855-gofzhff7 author: Hou, Yixuan J. title: SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-350855-gofzhff7.txt cache: ./cache/cord-350855-gofzhff7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350855-gofzhff7.txt' === file2bib.sh === id: cord-350957-10wcqgaq author: Shen, Zu T. title: SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice date: 2016-06-28 pages: extension: .txt txt: ./txt/cord-350957-10wcqgaq.txt cache: ./cache/cord-350957-10wcqgaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350957-10wcqgaq.txt' === file2bib.sh === id: cord-351038-k2m6woow author: Arun Krishnan, R. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-351038-k2m6woow.txt cache: ./cache/cord-351038-k2m6woow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351038-k2m6woow.txt' === file2bib.sh === id: cord-350949-ystkjdwk author: Gao, Yi-jie title: Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-350949-ystkjdwk.txt cache: ./cache/cord-350949-ystkjdwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350949-ystkjdwk.txt' === file2bib.sh === id: cord-351224-jeedo5mc author: GeurtsvanKessel, Corine H. title: An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-351224-jeedo5mc.txt cache: ./cache/cord-351224-jeedo5mc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351224-jeedo5mc.txt' === file2bib.sh === id: cord-351354-10rusr6j author: Chan, Louis Y. title: Diagnostic Criteria during SARS Outbreak in Hong Kong date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-351354-10rusr6j.txt cache: ./cache/cord-351354-10rusr6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351354-10rusr6j.txt' === file2bib.sh === id: cord-351107-a5bx74ao author: Phua, Ghee-Chee title: Mechanical Ventilation in an Airborne Epidemic date: 2008-06-30 pages: extension: .txt txt: ./txt/cord-351107-a5bx74ao.txt cache: ./cache/cord-351107-a5bx74ao.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351107-a5bx74ao.txt' === file2bib.sh === id: cord-351718-sf5zp5wg author: Kohli, Utkarsh title: COVID-19 pneumonia in an infant with a hemodynamically significant ventricular septal defect date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-351718-sf5zp5wg.txt cache: ./cache/cord-351718-sf5zp5wg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351718-sf5zp5wg.txt' === file2bib.sh === id: cord-351694-nb7230s1 author: Jatt, Lauren P. title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-351694-nb7230s1.txt cache: ./cache/cord-351694-nb7230s1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351694-nb7230s1.txt' === file2bib.sh === id: cord-351269-xjy6chia author: Wu, Y title: Coronavirus disease 2019 among pregnant Chinese women: case series data on the safety of vaginal birth and breastfeeding date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-351269-xjy6chia.txt cache: ./cache/cord-351269-xjy6chia.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351269-xjy6chia.txt' === file2bib.sh === id: cord-351446-j4ambec5 author: Sinonquel, P. title: COVID‐19 and gastrointestinal endoscopy: what should be taken into account? date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-351446-j4ambec5.txt cache: ./cache/cord-351446-j4ambec5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351446-j4ambec5.txt' === file2bib.sh === id: cord-351340-7y19ystp author: Rao, Gundu H. R. title: Coronavirus Disease and Acute Vascular Events date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-351340-7y19ystp.txt cache: ./cache/cord-351340-7y19ystp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351340-7y19ystp.txt' === file2bib.sh === id: cord-351367-ral9sbfy author: Scarlattei, Maura title: Unknown SARS-CoV-2 pneumonia detected by PET/CT in patients with cancer date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-351367-ral9sbfy.txt cache: ./cache/cord-351367-ral9sbfy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351367-ral9sbfy.txt' === file2bib.sh === id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-351559-az4pgi9k.txt cache: ./cache/cord-351559-az4pgi9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351559-az4pgi9k.txt' === file2bib.sh === id: cord-351115-dy81dtnk author: Wang, Chen title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-351115-dy81dtnk.txt cache: ./cache/cord-351115-dy81dtnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351115-dy81dtnk.txt' === file2bib.sh === id: cord-351835-1s2zsqoq author: Liu, Zhixin title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-351835-1s2zsqoq.txt cache: ./cache/cord-351835-1s2zsqoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351835-1s2zsqoq.txt' === file2bib.sh === id: cord-351691-3egwvb59 author: Elzupir, Amin O. title: Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-351691-3egwvb59.txt cache: ./cache/cord-351691-3egwvb59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351691-3egwvb59.txt' === file2bib.sh === id: cord-351687-6otr8zl3 author: Yesilkaya, Umit Haluk title: Neuroimmune correlates of the nervous system involvement of COVID-19: A commentary date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-351687-6otr8zl3.txt cache: ./cache/cord-351687-6otr8zl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-351687-6otr8zl3.txt' === file2bib.sh === id: cord-351662-rmkcb6o3 author: Huang, Zhifeng title: Characteristics and roles of SARS‐CoV‐2 specific antibodies in patients with different severities of COVID‐19 date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-351662-rmkcb6o3.txt cache: ./cache/cord-351662-rmkcb6o3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351662-rmkcb6o3.txt' === file2bib.sh === id: cord-350618-rtilfnzi author: Lambelet, Valentine title: Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-350618-rtilfnzi.txt cache: ./cache/cord-350618-rtilfnzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350618-rtilfnzi.txt' === file2bib.sh === id: cord-351011-v4zmksio author: Golden, Joseph W. title: Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-351011-v4zmksio.txt cache: ./cache/cord-351011-v4zmksio.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351011-v4zmksio.txt' === file2bib.sh === id: cord-352073-rdhjj72g author: Taniwaki, S.A title: Resource optimization in COVID-19 diagnosis date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-352073-rdhjj72g.txt cache: ./cache/cord-352073-rdhjj72g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352073-rdhjj72g.txt' === file2bib.sh === id: cord-352146-i4ezsclf author: Cimolai, Nevio title: Efficacy of povidone‐iodine to reduce viral load date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-352146-i4ezsclf.txt cache: ./cache/cord-352146-i4ezsclf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-352146-i4ezsclf.txt' === file2bib.sh === id: cord-351430-bpv7p7zo author: Pequeno, Pedro title: Air transportation, population density and temperature predict the spread of COVID-19 in Brazil date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-351430-bpv7p7zo.txt cache: ./cache/cord-351430-bpv7p7zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351430-bpv7p7zo.txt' === file2bib.sh === id: cord-350935-p6euuop3 author: Doğan, Tunca title: CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-350935-p6euuop3.txt cache: ./cache/cord-350935-p6euuop3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350935-p6euuop3.txt' === file2bib.sh === id: cord-351225-dq0xu85c author: Poutanen, Susan M. title: Transmission and control of SARS date: 2004 pages: extension: .txt txt: ./txt/cord-351225-dq0xu85c.txt cache: ./cache/cord-351225-dq0xu85c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351225-dq0xu85c.txt' === file2bib.sh === id: cord-351625-1we9wi1g author: Han, Huan title: Descriptive, Retrospective Study of the Clinical Characteristics of Asymptomatic COVID-19 Patients date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-351625-1we9wi1g.txt cache: ./cache/cord-351625-1we9wi1g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351625-1we9wi1g.txt' === file2bib.sh === id: cord-352296-rpjehijd author: Azzi, Lorenzo title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-352296-rpjehijd.txt cache: ./cache/cord-352296-rpjehijd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352296-rpjehijd.txt' === file2bib.sh === id: cord-350904-wyg8ikph author: Gubernatorova, E.O. title: IL-6: relevance for immunopathology of SARS-CoV-2 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-350904-wyg8ikph.txt cache: ./cache/cord-350904-wyg8ikph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350904-wyg8ikph.txt' === file2bib.sh === id: cord-351489-tzmev77c author: Yuan, Shuofeng title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-351489-tzmev77c.txt cache: ./cache/cord-351489-tzmev77c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351489-tzmev77c.txt' === file2bib.sh === id: cord-351644-pl7xpivx author: Gao, Yelei title: Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-351644-pl7xpivx.txt cache: ./cache/cord-351644-pl7xpivx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351644-pl7xpivx.txt' === file2bib.sh === id: cord-351930-puhm3w42 author: Juan, J. title: Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-351930-puhm3w42.txt cache: ./cache/cord-351930-puhm3w42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351930-puhm3w42.txt' === file2bib.sh === id: cord-351736-4x5u4qsy author: Fernandez-Garcia, Cristina title: Severe COVID-19 During Pregnancy and the Subsequent Premature Delivery date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-351736-4x5u4qsy.txt cache: ./cache/cord-351736-4x5u4qsy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351736-4x5u4qsy.txt' === file2bib.sh === id: cord-352096-cc3dzycl author: Richman, Douglas D. title: Antiviral Drug Discovery To Address the COVID-19 Pandemic date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-352096-cc3dzycl.txt cache: ./cache/cord-352096-cc3dzycl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352096-cc3dzycl.txt' === file2bib.sh === id: cord-350992-l6l24pco author: Roldan, Eugenia Quiros title: The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against Sars-Cov-2 infection (COVID-19): A role for iron homeostasis? date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-350992-l6l24pco.txt cache: ./cache/cord-350992-l6l24pco.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350992-l6l24pco.txt' === file2bib.sh === id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-351854-5s03f0pp.txt cache: ./cache/cord-351854-5s03f0pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351854-5s03f0pp.txt' === file2bib.sh === id: cord-351321-6d2mn5ok author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-351321-6d2mn5ok.txt cache: ./cache/cord-351321-6d2mn5ok.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351321-6d2mn5ok.txt' === file2bib.sh === id: cord-351567-ifoe8x28 author: Rabi, Firas A. title: SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far date: 2020-03-20 pages: extension: .txt txt: ./txt/cord-351567-ifoe8x28.txt cache: ./cache/cord-351567-ifoe8x28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351567-ifoe8x28.txt' === file2bib.sh === id: cord-351532-2yd4wg9v author: Huang, Yin-Qiu title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-351532-2yd4wg9v.txt cache: ./cache/cord-351532-2yd4wg9v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351532-2yd4wg9v.txt' === file2bib.sh === id: cord-351651-6dbt99h0 author: Sun, Zhong title: Potential Factors Influencing Repeated SARS Outbreaks in China date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-351651-6dbt99h0.txt cache: ./cache/cord-351651-6dbt99h0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351651-6dbt99h0.txt' === file2bib.sh === id: cord-351845-bli3qm8w author: Prasad, Kartikay title: Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-351845-bli3qm8w.txt cache: ./cache/cord-351845-bli3qm8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351845-bli3qm8w.txt' === file2bib.sh === id: cord-352304-tt2q5mgs author: Sun, Dan title: Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center’s observational study date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-352304-tt2q5mgs.txt cache: ./cache/cord-352304-tt2q5mgs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352304-tt2q5mgs.txt' === file2bib.sh === id: cord-351770-cirq6pfx author: Chen, Wei title: SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-351770-cirq6pfx.txt cache: ./cache/cord-351770-cirq6pfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351770-cirq6pfx.txt' === file2bib.sh === id: cord-351512-h4vigeuy author: Zhang, Lin title: How scientific research reacts to international public health emergencies: a global analysis of response patterns date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-351512-h4vigeuy.txt cache: ./cache/cord-351512-h4vigeuy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351512-h4vigeuy.txt' === file2bib.sh === id: cord-351974-1najtyui author: Smith, E. title: Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-351974-1najtyui.txt cache: ./cache/cord-351974-1najtyui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351974-1najtyui.txt' === file2bib.sh === id: cord-351952-lhhjax3s author: Pickering, Suzanne title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-351952-lhhjax3s.txt cache: ./cache/cord-351952-lhhjax3s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351952-lhhjax3s.txt' === file2bib.sh === id: cord-351492-8jv7ip67 author: Urwin, S. G. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-351492-8jv7ip67.txt cache: ./cache/cord-351492-8jv7ip67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351492-8jv7ip67.txt' === file2bib.sh === id: cord-352341-dhc748pn author: Miranda-Zazueta, G. title: Manejo farmacológico de pacientes con enfermedades hepáticas y pancreáticas que involucran terapias inmunosupresoras. Posicionamiento en el marco de la pandemia de SARS-COV-2 (COVID-19) date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-352341-dhc748pn.txt cache: ./cache/cord-352341-dhc748pn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352341-dhc748pn.txt' === file2bib.sh === id: cord-352196-rpyoeg9n author: Alberici, Federico title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-352196-rpyoeg9n.txt cache: ./cache/cord-352196-rpyoeg9n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352196-rpyoeg9n.txt' === file2bib.sh === id: cord-351719-xqmir1ca author: Olaimat, Amin N. title: Food Safety During and After the Era of COVID-19 Pandemic date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-351719-xqmir1ca.txt cache: ./cache/cord-351719-xqmir1ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351719-xqmir1ca.txt' === file2bib.sh === id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-351864-zozrj7w5.txt cache: ./cache/cord-351864-zozrj7w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351864-zozrj7w5.txt' === file2bib.sh === id: cord-352030-hnm54k4r author: Liu, Jie title: Epidemiological, Clinical Characteristics and Outcome of Medical Staff Infected with COVID-19 in Wuhan, China: A Retrospective Case Series Analysis date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-352030-hnm54k4r.txt cache: ./cache/cord-352030-hnm54k4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352030-hnm54k4r.txt' === file2bib.sh === id: cord-352526-t8odetzw author: Pinto, Bruna G G title: ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-352526-t8odetzw.txt cache: ./cache/cord-352526-t8odetzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352526-t8odetzw.txt' === file2bib.sh === id: cord-352156-sa8cvyuw author: Lindeman, Robbert-Jan title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-352156-sa8cvyuw.txt cache: ./cache/cord-352156-sa8cvyuw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352156-sa8cvyuw.txt' === file2bib.sh === id: cord-352580-l6vkzja0 author: Iltaf, Samar title: Frequency of Neurological Presentations of Coronavirus Disease in Patients Presenting to a Tertiary Care Hospital During the 2019 Coronavirus Disease Pandemic date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-352580-l6vkzja0.txt cache: ./cache/cord-352580-l6vkzja0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352580-l6vkzja0.txt' === file2bib.sh === id: cord-352123-0bflqj1c author: Csiszar, Anna title: Companion animals likely do not spread COVID-19 but may get infected themselves date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-352123-0bflqj1c.txt cache: ./cache/cord-352123-0bflqj1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352123-0bflqj1c.txt' === file2bib.sh === id: cord-352925-abry6oz3 author: Lim, Jia Yin title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-352925-abry6oz3.txt cache: ./cache/cord-352925-abry6oz3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-352925-abry6oz3.txt' === file2bib.sh === id: cord-352080-3rcqbgl7 author: Shidham, Vinod B. title: Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-352080-3rcqbgl7.txt cache: ./cache/cord-352080-3rcqbgl7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352080-3rcqbgl7.txt' === file2bib.sh === id: cord-351649-87g7g5au author: Haagmans, Bart L. title: SARS date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-351649-87g7g5au.txt cache: ./cache/cord-351649-87g7g5au.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351649-87g7g5au.txt' === file2bib.sh === id: cord-352509-qrzt4zva author: Chen, Haohui title: Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-352509-qrzt4zva.txt cache: ./cache/cord-352509-qrzt4zva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352509-qrzt4zva.txt' === file2bib.sh === id: cord-352642-u513wnu1 author: Patrocínio de Jesus, Rita title: Reactivation of SARS-CoV-2 after Asymptomatic Infection while on High-Dose Corticosteroids. Case Report date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-352642-u513wnu1.txt cache: ./cache/cord-352642-u513wnu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352642-u513wnu1.txt' === file2bib.sh === id: cord-351896-j6h02ab5 author: Ghannam, Malik title: Neurological involvement of coronavirus disease 2019: a systematic review date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-351896-j6h02ab5.txt cache: ./cache/cord-351896-j6h02ab5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351896-j6h02ab5.txt' === file2bib.sh === id: cord-352365-b9cmviny author: Marchetti, Monia title: COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-352365-b9cmviny.txt cache: ./cache/cord-352365-b9cmviny.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352365-b9cmviny.txt' === file2bib.sh === id: cord-351555-hsgsuor2 author: Constantinou, Constantina title: Developing a holistic contingency plan: Challenges and dilemmas for cancer patients during the COVID‐19 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-351555-hsgsuor2.txt cache: ./cache/cord-351555-hsgsuor2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351555-hsgsuor2.txt' === file2bib.sh === id: cord-352228-dzkf7c7l author: Fontanet, Arnaud title: Cluster of COVID-19 in northern France: A retrospective closed cohort study date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-352228-dzkf7c7l.txt cache: ./cache/cord-352228-dzkf7c7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352228-dzkf7c7l.txt' === file2bib.sh === id: cord-352433-sts48u9i author: Galanti, Marta title: Direct Observation of Repeated Infections With Endemic Coronaviruses date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-352433-sts48u9i.txt cache: ./cache/cord-352433-sts48u9i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352433-sts48u9i.txt' === file2bib.sh === id: cord-351837-vasuu70k author: Shannon, Ashleigh title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-351837-vasuu70k.txt cache: ./cache/cord-351837-vasuu70k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351837-vasuu70k.txt' === file2bib.sh === id: cord-352799-qmzh976f author: Paquin, Leo J. title: Was WHO SARS-related Travel Advisory for Toronto Ethical? date: 2007-05-01 pages: extension: .txt txt: ./txt/cord-352799-qmzh976f.txt cache: ./cache/cord-352799-qmzh976f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352799-qmzh976f.txt' === file2bib.sh === id: cord-352059-1bjskqyg author: Gupta, Nivedita title: Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-352059-1bjskqyg.txt cache: ./cache/cord-352059-1bjskqyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352059-1bjskqyg.txt' === file2bib.sh === id: cord-352909-s11tpfoq author: Sun, Zhiping title: Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-352909-s11tpfoq.txt cache: ./cache/cord-352909-s11tpfoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352909-s11tpfoq.txt' === file2bib.sh === id: cord-352779-zdtpnip0 author: Patti, Ravi Karan title: Subacute Aspergillosis “Fungal Balls” Complicating COVID-19 date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-352779-zdtpnip0.txt cache: ./cache/cord-352779-zdtpnip0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352779-zdtpnip0.txt' === file2bib.sh === id: cord-352256-qxdakdk0 author: Yousefi, Bahman title: A global treatments for coronaviruses including COVID‐19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-352256-qxdakdk0.txt cache: ./cache/cord-352256-qxdakdk0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352256-qxdakdk0.txt' === file2bib.sh === id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 pages: extension: .txt txt: ./txt/cord-351482-hzh5tyoo.txt cache: ./cache/cord-351482-hzh5tyoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351482-hzh5tyoo.txt' === file2bib.sh === id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-350286-n7ylgqfu.txt cache: ./cache/cord-350286-n7ylgqfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350286-n7ylgqfu.txt' === file2bib.sh === id: cord-352281-9huyb4cs author: Ayoub, Houssein H. title: Age could be driving variable SARS-CoV-2 epidemic trajectories worldwide date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-352281-9huyb4cs.txt cache: ./cache/cord-352281-9huyb4cs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352281-9huyb4cs.txt' === file2bib.sh === id: cord-353099-38bz0acw author: Tang, Mei San title: Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-353099-38bz0acw.txt cache: ./cache/cord-353099-38bz0acw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353099-38bz0acw.txt' === file2bib.sh === id: cord-352741-0pdeehai author: Geramizadeh, Bita title: Histopathologic Findings of Coronavirus in Lung: A Mini-Review date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-352741-0pdeehai.txt cache: ./cache/cord-352741-0pdeehai.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352741-0pdeehai.txt' === file2bib.sh === id: cord-352935-kb0i58z1 author: Aguila, Enrik John T. title: Repurposed GI Drugs in the Treatment of COVID-19 date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-352935-kb0i58z1.txt cache: ./cache/cord-352935-kb0i58z1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352935-kb0i58z1.txt' === file2bib.sh === id: cord-352871-0xgjpd80 author: Pérez Bartolomé, Francisco title: Manifestaciones oftalmológicas del SARS-Cov-2: Revisión de la literatura date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-352871-0xgjpd80.txt cache: ./cache/cord-352871-0xgjpd80.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352871-0xgjpd80.txt' === file2bib.sh === id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-352720-z1cvjc2y.txt cache: ./cache/cord-352720-z1cvjc2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352720-z1cvjc2y.txt' === file2bib.sh === id: cord-352943-ztonp62x author: Nagpal, Sunil title: What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-352943-ztonp62x.txt cache: ./cache/cord-352943-ztonp62x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352943-ztonp62x.txt' === file2bib.sh === id: cord-352891-ljmkqdzx author: Parang, Keykavous title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-352891-ljmkqdzx.txt cache: ./cache/cord-352891-ljmkqdzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352891-ljmkqdzx.txt' === file2bib.sh === id: cord-352065-960xqft4 author: Rello, Jordi title: Update in COVID-19 in the Intensive Care Unit from the 2020 HELLENIC Athens International Symposium date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-352065-960xqft4.txt cache: ./cache/cord-352065-960xqft4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352065-960xqft4.txt' === file2bib.sh === id: cord-352020-9wxwktck author: Zhang, Baoshan title: A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-352020-9wxwktck.txt cache: ./cache/cord-352020-9wxwktck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352020-9wxwktck.txt' === file2bib.sh === id: cord-353217-gmc3qrci author: de Miranda Santos, Isabel Kinney Ferreira title: Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-353217-gmc3qrci.txt cache: ./cache/cord-353217-gmc3qrci.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353217-gmc3qrci.txt' === file2bib.sh === id: cord-352849-vd62r8qu author: Artesi, M. title: Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-352849-vd62r8qu.txt cache: ./cache/cord-352849-vd62r8qu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352849-vd62r8qu.txt' === file2bib.sh === id: cord-352768-16vgnq14 author: Tang, Qingquan title: Application of siRNA Against SARS in the Rhesus Macaque Model date: 2008 pages: extension: .txt txt: ./txt/cord-352768-16vgnq14.txt cache: ./cache/cord-352768-16vgnq14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352768-16vgnq14.txt' === file2bib.sh === id: cord-352668-qjlqsb2k author: Cabello, Francisco title: Consensus on Recommendations for Safe Sexual Activity during the COVID-19 Coronavirus Pandemic date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-352668-qjlqsb2k.txt cache: ./cache/cord-352668-qjlqsb2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352668-qjlqsb2k.txt' === file2bib.sh === id: cord-353103-sdij1d90 author: Yao, Xueting title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 pages: extension: .txt txt: ./txt/cord-353103-sdij1d90.txt cache: ./cache/cord-353103-sdij1d90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353103-sdij1d90.txt' === file2bib.sh === id: cord-352863-6cttilm8 author: Hennighausen, Lothar title: Activation of the SARS-CoV-2 receptor Ace2 through JAK/STAT-dependent enhancers during pregnancy date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-352863-6cttilm8.txt cache: ./cache/cord-352863-6cttilm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352863-6cttilm8.txt' === file2bib.sh === id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 pages: extension: .txt txt: ./txt/cord-352379-q5inrxcm.txt cache: ./cache/cord-352379-q5inrxcm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352379-q5inrxcm.txt' === file2bib.sh === id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 pages: extension: .txt txt: ./txt/cord-352814-fcl2g5wr.txt cache: ./cache/cord-352814-fcl2g5wr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352814-fcl2g5wr.txt' === file2bib.sh === id: cord-352557-l7sahv5t author: Takla, Michael title: Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-352557-l7sahv5t.txt cache: ./cache/cord-352557-l7sahv5t.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352557-l7sahv5t.txt' === file2bib.sh === id: cord-352577-h3652seb author: Kopić, Jasminka title: Expanding the Use of Noninvasive Ventilation During an Epidemic date: 2014-08-27 pages: extension: .txt txt: ./txt/cord-352577-h3652seb.txt cache: ./cache/cord-352577-h3652seb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352577-h3652seb.txt' === file2bib.sh === id: cord-352911-9wbq9qo2 author: de Oliveira, Pedro Gonçalves title: Diacerein: a potential multi-target therapeutic drug for COVID-19 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-352911-9wbq9qo2.txt cache: ./cache/cord-352911-9wbq9qo2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352911-9wbq9qo2.txt' === file2bib.sh === id: cord-353133-tsqb6pa8 author: Long, Dustin R. title: Considerations for Assessing Risk of Provider Exposure to SARS-CoV-2 after a Negative Test date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-353133-tsqb6pa8.txt cache: ./cache/cord-353133-tsqb6pa8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353133-tsqb6pa8.txt' === file2bib.sh === id: cord-353479-kwi8zxo6 author: Chuang, H.-L. title: Impact of enhanced infection control procedures on clinical outcome following resuscitation attempts date: 2007-11-30 pages: extension: .txt txt: ./txt/cord-353479-kwi8zxo6.txt cache: ./cache/cord-353479-kwi8zxo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353479-kwi8zxo6.txt' === file2bib.sh === id: cord-353072-n92atcrx author: Kadkhoda, Kamran title: COVID-19: an Immunopathological View date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-353072-n92atcrx.txt cache: ./cache/cord-353072-n92atcrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353072-n92atcrx.txt' === file2bib.sh === id: cord-353329-ju3vwlow author: Haroon, Khawaja Hassan title: COVID-19 Related Cerebrovascular Thromboembolic Complications in Three Young Patients date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-353329-ju3vwlow.txt cache: ./cache/cord-353329-ju3vwlow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353329-ju3vwlow.txt' === file2bib.sh === id: cord-353392-rqeultbq author: Kumar, Govindarajan Venkat title: A short review on antibody therapy for COVID-19 date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-353392-rqeultbq.txt cache: ./cache/cord-353392-rqeultbq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353392-rqeultbq.txt' === file2bib.sh === id: cord-353523-gwud4bb7 author: Abobaker, Anis title: The Eye: A Possible New Route of Infection in COVID-19 date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-353523-gwud4bb7.txt cache: ./cache/cord-353523-gwud4bb7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353523-gwud4bb7.txt' === file2bib.sh === id: cord-352737-3ttrx3lf author: Cunha, Lucas Leite title: Remodeling of the Immune Response With Aging: Immunosenescence and Its Potential Impact on COVID-19 Immune Response date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-352737-3ttrx3lf.txt cache: ./cache/cord-352737-3ttrx3lf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352737-3ttrx3lf.txt' === file2bib.sh === id: cord-353742-k4gxww2c author: Arévalo, AP title: Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-353742-k4gxww2c.txt cache: ./cache/cord-353742-k4gxww2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353742-k4gxww2c.txt' === file2bib.sh === id: cord-352934-ypls4zau author: Wan, Jinkai title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-352934-ypls4zau.txt cache: ./cache/cord-352934-ypls4zau.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352934-ypls4zau.txt' === file2bib.sh === id: cord-352905-ge3u32hm author: Galimberti, Sara title: Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2 date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-352905-ge3u32hm.txt cache: ./cache/cord-352905-ge3u32hm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352905-ge3u32hm.txt' === file2bib.sh === id: cord-353209-qkhfp66l author: Steiner, Daniel J. title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-353209-qkhfp66l.txt cache: ./cache/cord-353209-qkhfp66l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353209-qkhfp66l.txt' === file2bib.sh === id: cord-353235-jiqhgf56 author: Bigliardi, Guido title: Middle cerebral artery ischemic stroke and COVID-19: a case report date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-353235-jiqhgf56.txt cache: ./cache/cord-353235-jiqhgf56.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353235-jiqhgf56.txt' === file2bib.sh === id: cord-352678-8f2ygul2 author: Prasad, Ashish title: Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading? date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-352678-8f2ygul2.txt cache: ./cache/cord-352678-8f2ygul2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352678-8f2ygul2.txt' === file2bib.sh === id: cord-353200-5csewb1k author: Jehi, Lara title: Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-353200-5csewb1k.txt cache: ./cache/cord-353200-5csewb1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353200-5csewb1k.txt' === file2bib.sh === id: cord-352562-qfb478sf author: Yamamoto, Lidia title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-352562-qfb478sf.txt cache: ./cache/cord-352562-qfb478sf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352562-qfb478sf.txt' === file2bib.sh === id: cord-352886-6lzlt6ur author: Bai, Qifeng title: MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-352886-6lzlt6ur.txt cache: ./cache/cord-352886-6lzlt6ur.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352886-6lzlt6ur.txt' === file2bib.sh === id: cord-353092-4hz2yyl5 author: Sama, Iziah E title: Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin–angiotensin–aldosterone inhibitors date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-353092-4hz2yyl5.txt cache: ./cache/cord-353092-4hz2yyl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353092-4hz2yyl5.txt' === file2bib.sh === id: cord-353615-9aj5yxkd author: Colaneri, Marta title: Running out of bullets: the challenging management of acute hepatitis and SARS‐COV‐2 from the SMatteo COvid19 Registry (SMACORE) date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-353615-9aj5yxkd.txt cache: ./cache/cord-353615-9aj5yxkd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353615-9aj5yxkd.txt' === file2bib.sh === id: cord-353475-dtn7h1gj author: Haddad, Hazem title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-353475-dtn7h1gj.txt cache: ./cache/cord-353475-dtn7h1gj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353475-dtn7h1gj.txt' === file2bib.sh === id: cord-352230-8mazd3eu author: Beeraka, Narasimha M. title: Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-352230-8mazd3eu.txt cache: ./cache/cord-352230-8mazd3eu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352230-8mazd3eu.txt' === file2bib.sh === id: cord-353551-un4jw7aw author: Margoni, Monica title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-353551-un4jw7aw.txt cache: ./cache/cord-353551-un4jw7aw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353551-un4jw7aw.txt' === file2bib.sh === id: cord-353963-d3gk3519 author: Karampela, Irene title: Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19? date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-353963-d3gk3519.txt cache: ./cache/cord-353963-d3gk3519.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353963-d3gk3519.txt' === file2bib.sh === id: cord-353116-7t1prfkr author: Bhargava, Ashish title: Predictors for Severe COVID-19 Infection date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-353116-7t1prfkr.txt cache: ./cache/cord-353116-7t1prfkr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353116-7t1prfkr.txt' === file2bib.sh === id: cord-353229-k3zerr83 author: Akca, Ummusen Kaya title: Kawasaki-like disease in children with COVID-19 date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-353229-k3zerr83.txt cache: ./cache/cord-353229-k3zerr83.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353229-k3zerr83.txt' === file2bib.sh === id: cord-353237-rob4ems7 author: De Maio, Antonio title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-353237-rob4ems7.txt cache: ./cache/cord-353237-rob4ems7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353237-rob4ems7.txt' === file2bib.sh === id: cord-353599-cw29edwr author: Kelleni, Mina T. title: Early use of Non-steroidal anti-inflammatory drugs in COVID-19 might reverse pathogenesis, prevent complications and improve clinical outcomes date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-353599-cw29edwr.txt cache: ./cache/cord-353599-cw29edwr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353599-cw29edwr.txt' === file2bib.sh === id: cord-353628-f6ew980g author: Zayet, Souheil title: Encephalopathy in patients with COVID‐19: ‘Causality or coincidence?’ date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-353628-f6ew980g.txt cache: ./cache/cord-353628-f6ew980g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353628-f6ew980g.txt' === file2bib.sh === id: cord-354458-o2kcd085 author: Caffo, Orazio title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-354458-o2kcd085.txt cache: ./cache/cord-354458-o2kcd085.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354458-o2kcd085.txt' === file2bib.sh === id: cord-353812-4oxbczqe author: Zoghi, Anahita title: A case of possible atypical demyelinating event of the central nervous system following COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-353812-4oxbczqe.txt cache: ./cache/cord-353812-4oxbczqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353812-4oxbczqe.txt' === file2bib.sh === id: cord-353373-zhkqnu0w author: Seidu, Samuel title: The impact of obesity on severe disease and mortality in people with SARS‐CoV‐2: A systematic review and meta‐analysis date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-353373-zhkqnu0w.txt cache: ./cache/cord-353373-zhkqnu0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353373-zhkqnu0w.txt' === file2bib.sh === id: cord-353659-wtacr6qj author: Almutairi, Nawaf title: Coronavirus Disease‐2019 with Dermatologic Manifestations and Implications: An Unfolding Conundrum date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-353659-wtacr6qj.txt cache: ./cache/cord-353659-wtacr6qj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353659-wtacr6qj.txt' === file2bib.sh === id: cord-353274-wozwpvpq author: Borremans, B. title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-353274-wozwpvpq.txt cache: ./cache/cord-353274-wozwpvpq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353274-wozwpvpq.txt' === file2bib.sh === id: cord-353576-f29kmtot author: Maricic, T. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-353576-f29kmtot.txt cache: ./cache/cord-353576-f29kmtot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353576-f29kmtot.txt' === file2bib.sh === id: cord-353012-rxhi8wd2 author: Zhou, Nan title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 pages: extension: .txt txt: ./txt/cord-353012-rxhi8wd2.txt cache: ./cache/cord-353012-rxhi8wd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353012-rxhi8wd2.txt' === file2bib.sh === id: cord-352796-6einbent author: Theodore Coroneo, Minas title: The eye as the discrete but defensible portal of coronavirus infection date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-352796-6einbent.txt cache: ./cache/cord-352796-6einbent.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352796-6einbent.txt' === file2bib.sh === id: cord-352322-tsjwnvkk author: Khamassi Khbou, Médiha title: Coronaviruses in farm animals: Epidemiology and public health implications date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-352322-tsjwnvkk.txt cache: ./cache/cord-352322-tsjwnvkk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352322-tsjwnvkk.txt' === file2bib.sh === id: cord-353293-vjdwh19x author: nan title: Post-COVID-19 global health strategies: the need for an interdisciplinary approach date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-353293-vjdwh19x.txt cache: ./cache/cord-353293-vjdwh19x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353293-vjdwh19x.txt' === file2bib.sh === id: cord-354101-8a7tohcx author: Silva de Oliveira, Daniela title: Immune response in COVID-19: What do we currently know? date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-354101-8a7tohcx.txt cache: ./cache/cord-354101-8a7tohcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354101-8a7tohcx.txt' === file2bib.sh === id: cord-353548-kf4om6iu author: Ruiz-Manriquez, J. title: Knowledge of Latin American gastroenterologists and endoscopists regarding SARS-CoV-2 infection date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-353548-kf4om6iu.txt cache: ./cache/cord-353548-kf4om6iu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353548-kf4om6iu.txt' === file2bib.sh === id: cord-353365-ujz5nkk3 author: Pirnay, Jean-Paul title: Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-353365-ujz5nkk3.txt cache: ./cache/cord-353365-ujz5nkk3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353365-ujz5nkk3.txt' === file2bib.sh === id: cord-354261-gdvawnp6 author: Gale, Chris title: National active surveillance to understand and inform neonatal care in COVID-19 date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-354261-gdvawnp6.txt cache: ./cache/cord-354261-gdvawnp6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354261-gdvawnp6.txt' === file2bib.sh === id: cord-353914-zzla4frm author: Hu, Bo title: Cardiac involvement of COVID-19: Looking forward to novel discoveries and clinically valuable evidence() date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-353914-zzla4frm.txt cache: ./cache/cord-353914-zzla4frm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-353914-zzla4frm.txt' === file2bib.sh === id: cord-353524-3w970ycx author: Dömling, Alexander title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-353524-3w970ycx.txt cache: ./cache/cord-353524-3w970ycx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353524-3w970ycx.txt' === file2bib.sh === id: cord-354080-glcq4qp9 author: Bodro, Marta title: Increased CSF levels of IL-1β, IL-6, and ACE in SARS-CoV-2–associated encephalitis date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-354080-glcq4qp9.txt cache: ./cache/cord-354080-glcq4qp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354080-glcq4qp9.txt' === file2bib.sh === id: cord-353537-skeajydw author: Zhang, Xian title: Asymptomatic Subclinical Cases of Coronavirus Disease 2019 without Viral Transmission in Three Independent Families date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-353537-skeajydw.txt cache: ./cache/cord-353537-skeajydw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353537-skeajydw.txt' === file2bib.sh === id: cord-353731-7xn7m662 author: Heaton, Brook E. title: SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-353731-7xn7m662.txt cache: ./cache/cord-353731-7xn7m662.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353731-7xn7m662.txt' === file2bib.sh === id: cord-354051-ro3o27pv author: Peccia, J. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-354051-ro3o27pv.txt cache: ./cache/cord-354051-ro3o27pv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354051-ro3o27pv.txt' === file2bib.sh === id: cord-353716-gxgvhhv1 author: Kumar, Ashutosh title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-353716-gxgvhhv1.txt cache: ./cache/cord-353716-gxgvhhv1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353716-gxgvhhv1.txt' === file2bib.sh === id: cord-353862-7xe3fvd5 author: Li, Na title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-353862-7xe3fvd5.txt cache: ./cache/cord-353862-7xe3fvd5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353862-7xe3fvd5.txt' === file2bib.sh === id: cord-352969-rpt7xja6 author: Kataria, Ashish title: COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-352969-rpt7xja6.txt cache: ./cache/cord-352969-rpt7xja6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352969-rpt7xja6.txt' === file2bib.sh === id: cord-354353-hyz0gmpz author: Farhangrazi, Z. Shadi title: Airborne Particulate Matter and SARS-CoV-2 Partnership: Virus Hitchhiking, Stabilization and Immune Cell Targeting — A Hypothesis date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-354353-hyz0gmpz.txt cache: ./cache/cord-354353-hyz0gmpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354353-hyz0gmpz.txt' === file2bib.sh === id: cord-353748-y1a52z8e author: Bhattacharya, Rajarshi title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 pages: extension: .txt txt: ./txt/cord-353748-y1a52z8e.txt cache: ./cache/cord-353748-y1a52z8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353748-y1a52z8e.txt' === file2bib.sh === id: cord-354538-vqi67h6a author: Sydney, Elana R. title: Antibody evidence of SARS-CoV-2 infection in healthcare workers in the Bronx date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-354538-vqi67h6a.txt cache: ./cache/cord-354538-vqi67h6a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354538-vqi67h6a.txt' === file2bib.sh === id: cord-354407-zzxjv666 author: Campanacci, Valérie title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 pages: extension: .txt txt: ./txt/cord-354407-zzxjv666.txt cache: ./cache/cord-354407-zzxjv666.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354407-zzxjv666.txt' === file2bib.sh === id: cord-353777-t8q99tlq author: Jia, Yong title: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-353777-t8q99tlq.txt cache: ./cache/cord-353777-t8q99tlq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353777-t8q99tlq.txt' === file2bib.sh === id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-353342-2n6kqyeo.txt cache: ./cache/cord-353342-2n6kqyeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353342-2n6kqyeo.txt' === file2bib.sh === id: cord-353873-88ud20oq author: Hoyler, Marguerite M. title: The importance of challenges in COVID-19 screening and testing in the obstetric patient population date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-353873-88ud20oq.txt cache: ./cache/cord-353873-88ud20oq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353873-88ud20oq.txt' === file2bib.sh === id: cord-353308-e4s8el0s author: Parashar, Umesh D title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 pages: extension: .txt txt: ./txt/cord-353308-e4s8el0s.txt cache: ./cache/cord-353308-e4s8el0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353308-e4s8el0s.txt' === file2bib.sh === id: cord-353494-72fvkx7f author: Singh, Rajveer title: Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-353494-72fvkx7f.txt cache: ./cache/cord-353494-72fvkx7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353494-72fvkx7f.txt' === file2bib.sh === id: cord-354612-7f91l0n9 author: Villar, Livia Melo title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-354612-7f91l0n9.txt cache: ./cache/cord-354612-7f91l0n9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354612-7f91l0n9.txt' === file2bib.sh === id: cord-354534-0b7zwzjv author: Fuccillo, E title: Olfactory disorders in coronavirus disease 2019 patients: a systematic literature review date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-354534-0b7zwzjv.txt cache: ./cache/cord-354534-0b7zwzjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354534-0b7zwzjv.txt' === file2bib.sh === id: cord-354510-jlg5je0s author: de Carvalho, A. F. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-354510-jlg5je0s.txt cache: ./cache/cord-354510-jlg5je0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354510-jlg5je0s.txt' === file2bib.sh === id: cord-354349-hbk2p6ej author: Sardar, Sundus title: COVID-19 and Plasmodium vivax malaria co-infection date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-354349-hbk2p6ej.txt cache: ./cache/cord-354349-hbk2p6ej.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354349-hbk2p6ej.txt' === file2bib.sh === id: cord-353826-owoec2ud author: Graham, Simon P. title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-353826-owoec2ud.txt cache: ./cache/cord-353826-owoec2ud.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353826-owoec2ud.txt' === file2bib.sh === id: cord-353953-83d0g8ix author: Mendoza, Emelissa J. title: Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2 date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-353953-83d0g8ix.txt cache: ./cache/cord-353953-83d0g8ix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353953-83d0g8ix.txt' === file2bib.sh === id: cord-353911-hp6s6ebh author: Petráš, Marek title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-353911-hp6s6ebh.txt cache: ./cache/cord-353911-hp6s6ebh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353911-hp6s6ebh.txt' === file2bib.sh === id: cord-354103-4dldgqzf author: Grubic, Andrew D title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-354103-4dldgqzf.txt cache: ./cache/cord-354103-4dldgqzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354103-4dldgqzf.txt' === file2bib.sh === id: cord-354453-uze6ze8o author: McCloskey, Brian title: SARS to novel coronavirus – old lessons and new lessons date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-354453-uze6ze8o.txt cache: ./cache/cord-354453-uze6ze8o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354453-uze6ze8o.txt' === file2bib.sh === id: cord-353923-ou7w3zkv author: Ren, Shi-Yan title: Stability and infectivity of coronaviruses in inanimate environments date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-353923-ou7w3zkv.txt cache: ./cache/cord-353923-ou7w3zkv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-353923-ou7w3zkv.txt' === file2bib.sh === id: cord-354394-zojhdnlu author: Wang, Wei-Kung title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-354394-zojhdnlu.txt cache: ./cache/cord-354394-zojhdnlu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354394-zojhdnlu.txt' === file2bib.sh === id: cord-353594-z1vxamvp author: Gagiannis, Daniel title: Clinical, Serological, and Histopathological Similarities Between Severe COVID-19 and Acute Exacerbation of Connective Tissue Disease-Associated Interstitial Lung Disease (CTD-ILD) date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-353594-z1vxamvp.txt cache: ./cache/cord-353594-z1vxamvp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353594-z1vxamvp.txt' === file2bib.sh === id: cord-353749-2vlc11rx author: Stricker, Raphael B title: Flattening the Risk: Pre-Exposure Prophylaxis for COVID-19 date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-353749-2vlc11rx.txt cache: ./cache/cord-353749-2vlc11rx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353749-2vlc11rx.txt' === file2bib.sh === id: cord-354209-g1zynbul author: Person, Bobbie title: Fear and Stigma: The Epidemic within the SARS Outbreak date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-354209-g1zynbul.txt cache: ./cache/cord-354209-g1zynbul.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354209-g1zynbul.txt' === file2bib.sh === id: cord-354373-lldfoptb author: Chi, Jeffrey title: COVID-19 Clinical Research date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-354373-lldfoptb.txt cache: ./cache/cord-354373-lldfoptb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354373-lldfoptb.txt' === file2bib.sh === id: cord-353612-9ux181xg author: Josset, Laurence title: Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus date: 2013-04-30 pages: extension: .txt txt: ./txt/cord-353612-9ux181xg.txt cache: ./cache/cord-353612-9ux181xg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353612-9ux181xg.txt' === file2bib.sh === id: cord-354113-j8odxs1h author: Miao, Congliang title: A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19 date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-354113-j8odxs1h.txt cache: ./cache/cord-354113-j8odxs1h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354113-j8odxs1h.txt' === file2bib.sh === id: cord-353161-mtq6yh25 author: Rodrigues, João PGLM title: Insights on cross-species transmission of SARS-CoV-2 from structural modeling date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-353161-mtq6yh25.txt cache: ./cache/cord-353161-mtq6yh25.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353161-mtq6yh25.txt' === file2bib.sh === id: cord-354315-yfn9vaan author: Meirson, Tomer title: Structural basis of SARS-CoV-2 spike protein induced by ACE2 date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-354315-yfn9vaan.txt cache: ./cache/cord-354315-yfn9vaan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354315-yfn9vaan.txt' === file2bib.sh === id: cord-354762-3a3a3ku9 author: Afsar, Cigdem Usul title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-354762-3a3a3ku9.txt cache: ./cache/cord-354762-3a3a3ku9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354762-3a3a3ku9.txt' === file2bib.sh === id: cord-353391-o0s2h0y0 author: Haj Bloukh, Samir title: A Look Behind the Scenes at COVID-19: National Strategies of Infection Control and Their Impact on Mortality date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-353391-o0s2h0y0.txt cache: ./cache/cord-353391-o0s2h0y0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353391-o0s2h0y0.txt' === file2bib.sh === id: cord-353509-yfkiaq80 author: Nugraha, Rhea Veda title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-353509-yfkiaq80.txt cache: ./cache/cord-353509-yfkiaq80.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353509-yfkiaq80.txt' === file2bib.sh === id: cord-354134-gb2pf5kb author: Güemes-Villahoz, Noemi title: Conjunctivitis in COVID-19 patients: frequency and clinical presentation date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-354134-gb2pf5kb.txt cache: ./cache/cord-354134-gb2pf5kb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354134-gb2pf5kb.txt' === file2bib.sh === id: cord-353572-b4mdiont author: Zhou, Yadi title: Network-based Drug Repurposing for Human Coronavirus date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-353572-b4mdiont.txt cache: ./cache/cord-353572-b4mdiont.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353572-b4mdiont.txt' === file2bib.sh === id: cord-354148-87tpjvs6 author: Bidra, Avinash S. title: Rapid In‐Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Using Povidone‐Iodine Oral Antiseptic Rinse date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-354148-87tpjvs6.txt cache: ./cache/cord-354148-87tpjvs6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354148-87tpjvs6.txt' === file2bib.sh === id: cord-354948-q5eouyi2 author: Tsao, Kuo‐Chien title: False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome date: 2005-09-19 pages: extension: .txt txt: ./txt/cord-354948-q5eouyi2.txt cache: ./cache/cord-354948-q5eouyi2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354948-q5eouyi2.txt' === file2bib.sh === id: cord-354780-yzyixucr author: Lin, Chih-Yen title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-354780-yzyixucr.txt cache: ./cache/cord-354780-yzyixucr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354780-yzyixucr.txt' === file2bib.sh === id: cord-354372-vfvnjmv1 author: Carpenito, L. title: The autopsy at the time of SARS-CoV-2: Protocol and lessons date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-354372-vfvnjmv1.txt cache: ./cache/cord-354372-vfvnjmv1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354372-vfvnjmv1.txt' === file2bib.sh === id: cord-353484-q7d0ysbo author: Liu, Xue title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-353484-q7d0ysbo.txt cache: ./cache/cord-353484-q7d0ysbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353484-q7d0ysbo.txt' === file2bib.sh === id: cord-353704-lfndq85x author: Ye, Zi-Wei title: Zoonotic origins of human coronaviruses date: 2020-03-15 pages: extension: .txt txt: ./txt/cord-353704-lfndq85x.txt cache: ./cache/cord-353704-lfndq85x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353704-lfndq85x.txt' === file2bib.sh === id: cord-354720-fu19u2b0 author: White-Dzuro, Gabrielle title: Multisystem effects of COVID-19: a concise review for practitioners date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-354720-fu19u2b0.txt cache: ./cache/cord-354720-fu19u2b0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354720-fu19u2b0.txt' === file2bib.sh === id: cord-355283-ny1ju7vc author: Colombo, L. title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-355283-ny1ju7vc.txt cache: ./cache/cord-355283-ny1ju7vc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355283-ny1ju7vc.txt' === file2bib.sh === id: cord-353996-slnyun4l author: Baumgartner, M. T. title: Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-353996-slnyun4l.txt cache: ./cache/cord-353996-slnyun4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353996-slnyun4l.txt' === file2bib.sh === id: cord-354597-xubsodnk author: Carvalho, Alexandre title: SARS-CoV-2 Gastrointestinal Infection Causing Hemorrhagic Colitis: Implications for Detection and Transmission of COVID-19 Disease date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-354597-xubsodnk.txt cache: ./cache/cord-354597-xubsodnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354597-xubsodnk.txt' === file2bib.sh === id: cord-354529-k8p2u7iq author: Wu, Yongran title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-354529-k8p2u7iq.txt cache: ./cache/cord-354529-k8p2u7iq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354529-k8p2u7iq.txt' === file2bib.sh === id: cord-355422-c4odhdql author: Vaira, Luigi Angelo title: Potential pathogenesis of ageusia and anosmia in COVID‐19 patients date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-355422-c4odhdql.txt cache: ./cache/cord-355422-c4odhdql.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355422-c4odhdql.txt' === file2bib.sh === id: cord-354619-pftjhtpo author: Farronato, Marco title: A Call for Action to Safely Deliver Oral Health Care during and Post COVID-19 Pandemic date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-354619-pftjhtpo.txt cache: ./cache/cord-354619-pftjhtpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354619-pftjhtpo.txt' === file2bib.sh === id: cord-355306-fj8utkfe author: Xia Chao, Yin title: The role of IgA in COVID-19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-355306-fj8utkfe.txt cache: ./cache/cord-355306-fj8utkfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355306-fj8utkfe.txt' === file2bib.sh === id: cord-354773-u86bdmvf author: Suo, Tao title: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-354773-u86bdmvf.txt cache: ./cache/cord-354773-u86bdmvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354773-u86bdmvf.txt' === file2bib.sh === id: cord-354900-bzv4yhqi author: Jawhara, Samir title: How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-354900-bzv4yhqi.txt cache: ./cache/cord-354900-bzv4yhqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354900-bzv4yhqi.txt' === file2bib.sh === id: cord-354868-pqn59ojj author: Yao, Hebang title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-354868-pqn59ojj.txt cache: ./cache/cord-354868-pqn59ojj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354868-pqn59ojj.txt' === file2bib.sh === id: cord-354398-f3cg8gi1 author: Al-Saud, Haya title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 pages: extension: .txt txt: ./txt/cord-354398-f3cg8gi1.txt cache: ./cache/cord-354398-f3cg8gi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354398-f3cg8gi1.txt' === file2bib.sh === id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-354733-qxivrhj8.txt cache: ./cache/cord-354733-qxivrhj8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354733-qxivrhj8.txt' === file2bib.sh === id: cord-354685-oggtmum4 author: Kurup, Drishya title: Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2 date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-354685-oggtmum4.txt cache: ./cache/cord-354685-oggtmum4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354685-oggtmum4.txt' === file2bib.sh === id: cord-354608-1me3nopu author: Rabinowicz, Shira title: COVID-19 in the Pediatric Population—Review and Current Evidence date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-354608-1me3nopu.txt cache: ./cache/cord-354608-1me3nopu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354608-1me3nopu.txt' === file2bib.sh === id: cord-354881-7o20cn1x author: Brown, Rebecca C H title: The scientific and ethical feasibility of immunity passports date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-354881-7o20cn1x.txt cache: ./cache/cord-354881-7o20cn1x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354881-7o20cn1x.txt' === file2bib.sh === id: cord-355841-m6dl8a0w author: Munz, Maike title: Acute transverse myelitis after COVID-19 pneumonia date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-355841-m6dl8a0w.txt cache: ./cache/cord-355841-m6dl8a0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355841-m6dl8a0w.txt' === file2bib.sh === id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 pages: extension: .txt txt: ./txt/cord-354943-wxhbwcfr.txt cache: ./cache/cord-354943-wxhbwcfr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354943-wxhbwcfr.txt' === file2bib.sh === id: cord-354030-8tfg881h author: Dong, Rong title: Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-354030-8tfg881h.txt cache: ./cache/cord-354030-8tfg881h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354030-8tfg881h.txt' === file2bib.sh === id: cord-355560-vsxe97xs author: Alves, Amanda Mandarino title: SARS-CoV-2 leading to Acute Pancreatitis: an unusual presentation date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-355560-vsxe97xs.txt cache: ./cache/cord-355560-vsxe97xs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355560-vsxe97xs.txt' === file2bib.sh === id: cord-355674-mhi85px5 author: Siddiqi, Hasan K. title: Increased prevalence of myocardial injury in patients with SARS-CoV-2 viremia. date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-355674-mhi85px5.txt cache: ./cache/cord-355674-mhi85px5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355674-mhi85px5.txt' === file2bib.sh === id: cord-355672-egjdy7o0 author: Castillo, Edward M. title: Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-355672-egjdy7o0.txt cache: ./cache/cord-355672-egjdy7o0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355672-egjdy7o0.txt' === file2bib.sh === id: cord-353887-f4yd7guj author: Tang, Yujun title: Cytokine Storm in COVID-19: The Current Evidence and Treatment Strategies date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-353887-f4yd7guj.txt cache: ./cache/cord-353887-f4yd7guj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353887-f4yd7guj.txt' === file2bib.sh === id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-354536-c9v9kbw8.txt cache: ./cache/cord-354536-c9v9kbw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354536-c9v9kbw8.txt' === file2bib.sh === id: cord-354893-tku1dr32 author: Shi, Zhengli title: Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology date: 2010-12-24 pages: extension: .txt txt: ./txt/cord-354893-tku1dr32.txt cache: ./cache/cord-354893-tku1dr32.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354893-tku1dr32.txt' === file2bib.sh === id: cord-355475-kdubhh73 author: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-355475-kdubhh73.txt cache: ./cache/cord-355475-kdubhh73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355475-kdubhh73.txt' === file2bib.sh === id: cord-355175-uo9fx6jy author: Ferrazzi, E title: Vaginal delivery in SARS‐CoV‐2‐infected pregnant women in Northern Italy: a retrospective analysis date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-355175-uo9fx6jy.txt cache: ./cache/cord-355175-uo9fx6jy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355175-uo9fx6jy.txt' === file2bib.sh === id: cord-355718-7dafsxp9 author: Leong, Hoe‐Nam title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 date: 2004-08-10 pages: extension: .txt txt: ./txt/cord-355718-7dafsxp9.txt cache: ./cache/cord-355718-7dafsxp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355718-7dafsxp9.txt' === file2bib.sh === id: cord-355655-l684uy4h author: Ning, Ling title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-355655-l684uy4h.txt cache: ./cache/cord-355655-l684uy4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355655-l684uy4h.txt' === file2bib.sh === id: cord-355477-7xd93aqv author: SATIJA, NAMITA title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 pages: extension: .txt txt: ./txt/cord-355477-7xd93aqv.txt cache: ./cache/cord-355477-7xd93aqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355477-7xd93aqv.txt' === file2bib.sh === id: cord-355811-aq7p1uxo author: Węglarz-Tomczak, Ewelina title: Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-355811-aq7p1uxo.txt cache: ./cache/cord-355811-aq7p1uxo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355811-aq7p1uxo.txt' === file2bib.sh === id: cord-355514-2qjbc3bd author: Shibata, Shun title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-355514-2qjbc3bd.txt cache: ./cache/cord-355514-2qjbc3bd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355514-2qjbc3bd.txt' === file2bib.sh === id: cord-355439-eqtk51q3 author: Lesko, Catherine R title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-355439-eqtk51q3.txt cache: ./cache/cord-355439-eqtk51q3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355439-eqtk51q3.txt' === file2bib.sh === id: cord-354763-odzrco6q author: Drake, John M. title: Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date: 2006-12-20 pages: extension: .txt txt: ./txt/cord-354763-odzrco6q.txt cache: ./cache/cord-354763-odzrco6q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354763-odzrco6q.txt' === file2bib.sh === id: cord-355758-tk7eturq author: Berrio, Alejandro title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-355758-tk7eturq.txt cache: ./cache/cord-355758-tk7eturq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355758-tk7eturq.txt' === file2bib.sh === id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-354582-fniymnmf.txt cache: ./cache/cord-354582-fniymnmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354582-fniymnmf.txt' === file2bib.sh === id: cord-355395-rckzi8vz author: Tian, Dandan title: Hepatic complications of COVID‐19 and its treatment date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-355395-rckzi8vz.txt cache: ./cache/cord-355395-rckzi8vz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355395-rckzi8vz.txt' === file2bib.sh === id: cord-356030-bbj4r81i author: Haehner, Antje title: Predictive Value of Sudden Olfactory Loss in the Diagnosis of COVID-19 date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-356030-bbj4r81i.txt cache: ./cache/cord-356030-bbj4r81i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356030-bbj4r81i.txt' === file2bib.sh === id: cord-355294-gifsqph6 author: García-Suárez, Julio title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-355294-gifsqph6.txt cache: ./cache/cord-355294-gifsqph6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355294-gifsqph6.txt' === file2bib.sh === id: cord-355760-2a12nsnl author: Shields, A. M. title: SARS-CoV-2 seroconversion in health care workers date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-355760-2a12nsnl.txt cache: ./cache/cord-355760-2a12nsnl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355760-2a12nsnl.txt' === file2bib.sh === id: cord-356154-ifb3qiz7 author: Zhang, Rong title: A Study of Two Cases Co-Infected with SARS-CoV-2 and Human Immunodeficiency Virus date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-356154-ifb3qiz7.txt cache: ./cache/cord-356154-ifb3qiz7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356154-ifb3qiz7.txt' === file2bib.sh === id: cord-355728-wivk0bm0 author: Schoof, Michael title: An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-355728-wivk0bm0.txt cache: ./cache/cord-355728-wivk0bm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355728-wivk0bm0.txt' === file2bib.sh === id: cord-355854-hksq8gy4 author: Pagliaro, Pasquale title: ACE/ACE2 Ratio: A Key Also in 2019 Coronavirus Disease (Covid-19)? date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-355854-hksq8gy4.txt cache: ./cache/cord-355854-hksq8gy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355854-hksq8gy4.txt' === file2bib.sh === id: cord-355734-pz64534w author: Antonio-Villa, Neftali Eduardo title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-355734-pz64534w.txt cache: ./cache/cord-355734-pz64534w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355734-pz64534w.txt' === file2bib.sh === id: cord-356084-621qzpqd author: Qu, Jiuxin title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-356084-621qzpqd.txt cache: ./cache/cord-356084-621qzpqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356084-621qzpqd.txt' === file2bib.sh === id: cord-356166-fpno9zg5 author: Miyakawa, Kei title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-356166-fpno9zg5.txt cache: ./cache/cord-356166-fpno9zg5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356166-fpno9zg5.txt' === file2bib.sh === id: cord-355181-affuyn8z author: Poggio, Claudio title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-355181-affuyn8z.txt cache: ./cache/cord-355181-affuyn8z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355181-affuyn8z.txt' === file2bib.sh === id: cord-356005-zhwtlik6 author: Yazhini, Arangasamy title: D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-356005-zhwtlik6.txt cache: ./cache/cord-356005-zhwtlik6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356005-zhwtlik6.txt' === file2bib.sh === id: cord-355356-g7lvb8b4 author: Lamb, Yvette N. title: Remdesivir: First Approval date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-355356-g7lvb8b4.txt cache: ./cache/cord-355356-g7lvb8b4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355356-g7lvb8b4.txt' === file2bib.sh === id: cord-355577-w1yhtbz8 author: Kowalski, Luiz Paulo title: Effect of the COVID-19 Pandemic on the Activity of Physicians Working in the Areas of Head and Neck Surgery and Otorhinolaryngology date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-355577-w1yhtbz8.txt cache: ./cache/cord-355577-w1yhtbz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355577-w1yhtbz8.txt' === file2bib.sh === id: cord-356370-jjl1hbeb author: Sahajpal, Nikhil Shri title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-356370-jjl1hbeb.txt cache: ./cache/cord-356370-jjl1hbeb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356370-jjl1hbeb.txt' === file2bib.sh === id: cord-356325-gk5jve0i author: Beaudoin-Bussières, Guillaume title: Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-356325-gk5jve0i.txt cache: ./cache/cord-356325-gk5jve0i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356325-gk5jve0i.txt' === file2bib.sh === id: cord-354531-7klivhut author: Feng, Liqiang title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-354531-7klivhut.txt cache: ./cache/cord-354531-7klivhut.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354531-7klivhut.txt' === file2bib.sh === id: cord-356150-ivso91ln author: Torretta, Sara title: Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-356150-ivso91ln.txt cache: ./cache/cord-356150-ivso91ln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356150-ivso91ln.txt' === file2bib.sh === id: cord-355788-6hteott0 author: Shirvani, Edris title: Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2 date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-355788-6hteott0.txt cache: ./cache/cord-355788-6hteott0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355788-6hteott0.txt' === file2bib.sh === id: cord-354658-v451z3jq author: Rajagopal, Keshava title: Advanced Pulmonary and Cardiac Support of COVID-19 Patients: Emerging Recommendations From ASAIO—A “Living Working Document” date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-354658-v451z3jq.txt cache: ./cache/cord-354658-v451z3jq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354658-v451z3jq.txt' === file2bib.sh === id: cord-355589-3zdv9zim author: Simons, David title: The association of smoking status with SARS‐CoV‐2 infection, hospitalisation and mortality from COVID‐19: A living rapid evidence review with Bayesian meta‐analyses (version 7) date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-355589-3zdv9zim.txt cache: ./cache/cord-355589-3zdv9zim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355589-3zdv9zim.txt' === file2bib.sh === id: cord-356174-40k6m7l0 author: Ducloyer, Mathilde title: Complete post-mortem data in a fatal case of COVID-19: clinical, radiological and pathological correlations date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-356174-40k6m7l0.txt cache: ./cache/cord-356174-40k6m7l0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356174-40k6m7l0.txt' === file2bib.sh === id: cord-356217-igm2t7md author: Noda, Sakura title: Severe COVID-19 initially presenting as mesenteric adenopathy date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-356217-igm2t7md.txt cache: ./cache/cord-356217-igm2t7md.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356217-igm2t7md.txt' === file2bib.sh === id: cord-355039-qi4fwqbc author: Azar, William S. title: COVID-19 and diabetes mellitus: how one pandemic worsens the other date: 2020-08-02 pages: extension: .txt txt: ./txt/cord-355039-qi4fwqbc.txt cache: ./cache/cord-355039-qi4fwqbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355039-qi4fwqbc.txt' === file2bib.sh === id: cord-355943-bezpprrk author: Li, Y. title: Urine Proteome of COVID-19 Patients date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-355943-bezpprrk.txt cache: ./cache/cord-355943-bezpprrk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355943-bezpprrk.txt' === file2bib.sh === id: cord-355528-y4a1g6km author: Balla, Mamtha title: COVID-19, Modern Pandemic: A Systematic Review From Front-Line Health Care Providers’ Perspective date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-355528-y4a1g6km.txt cache: ./cache/cord-355528-y4a1g6km.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355528-y4a1g6km.txt' === file2bib.sh === id: cord-355924-8sk9al0n author: Allam, Loubna title: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-355924-8sk9al0n.txt cache: ./cache/cord-355924-8sk9al0n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355924-8sk9al0n.txt' === file2bib.sh === id: cord-354824-7fdcu2f0 author: Wu, Renyi title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-354824-7fdcu2f0.txt cache: ./cache/cord-354824-7fdcu2f0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354824-7fdcu2f0.txt' === file2bib.sh === id: cord-356195-5pcaxpp9 author: Jothimani, Dinesh title: COVID-19 and Liver. date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-356195-5pcaxpp9.txt cache: ./cache/cord-356195-5pcaxpp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356195-5pcaxpp9.txt' === file2bib.sh === id: cord-354950-kmpbdvof author: Demurtas, Olivia C. title: Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date: 2016-02-05 pages: extension: .txt txt: ./txt/cord-354950-kmpbdvof.txt cache: ./cache/cord-354950-kmpbdvof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354950-kmpbdvof.txt' === file2bib.sh === id: cord-356009-emn2w8if author: Roshandel, M. R. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-356009-emn2w8if.txt cache: ./cache/cord-356009-emn2w8if.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356009-emn2w8if.txt' === file2bib.sh === id: cord-355899-wd00f8cw author: Dawson, E. D. title: Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-355899-wd00f8cw.txt cache: ./cache/cord-355899-wd00f8cw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355899-wd00f8cw.txt' === file2bib.sh === id: cord-355122-x3v80bdp author: Desterke, Christophe title: PPARγ cistrome repression during activation of lung monocyte-macrophages in severe COVID-19 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-355122-x3v80bdp.txt cache: ./cache/cord-355122-x3v80bdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355122-x3v80bdp.txt' === file2bib.sh === id: cord-355567-60sfv60p author: Azuma, Kenichi title: Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-355567-60sfv60p.txt cache: ./cache/cord-355567-60sfv60p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355567-60sfv60p.txt' === file2bib.sh === id: cord-356264-q0yqnlyl author: Armijos-Jaramillo, Vinicio title: SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-03-23 pages: extension: .txt txt: ./txt/cord-356264-q0yqnlyl.txt cache: ./cache/cord-356264-q0yqnlyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356264-q0yqnlyl.txt' === file2bib.sh === id: cord-355935-psnqrdo2 author: Paez, Antonio title: A Spatio‐Temporal Analysis of the Environmental Correlates of COVID‐19 Incidence in Spain date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-355935-psnqrdo2.txt cache: ./cache/cord-355935-psnqrdo2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355935-psnqrdo2.txt' === file2bib.sh === id: cord-356364-ipi81ce3 author: Ho, Bo-Lin title: Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date: 2015-12-14 pages: extension: .txt txt: ./txt/cord-356364-ipi81ce3.txt cache: ./cache/cord-356364-ipi81ce3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-356364-ipi81ce3.txt' === file2bib.sh === id: cord-354972-nc496v6s author: Margolin, Emmanuel title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-354972-nc496v6s.txt cache: ./cache/cord-354972-nc496v6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354972-nc496v6s.txt' === file2bib.sh === id: cord-356021-lr3wj8we author: Choudhury, Chinmayee title: Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-356021-lr3wj8we.txt cache: ./cache/cord-356021-lr3wj8we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-356021-lr3wj8we.txt' === file2bib.sh === id: cord-356090-oj3d9ail author: Gorgun, D. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-356090-oj3d9ail.txt cache: ./cache/cord-356090-oj3d9ail.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356090-oj3d9ail.txt' === file2bib.sh === id: cord-355807-q3bngari author: Yepes-Pérez, Andres F. title: Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-355807-q3bngari.txt cache: ./cache/cord-355807-q3bngari.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355807-q3bngari.txt' === file2bib.sh === id: cord-355912-ioihqf0r author: Shomuradova, A. S. title: SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-355912-ioihqf0r.txt cache: ./cache/cord-355912-ioihqf0r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355912-ioihqf0r.txt' === file2bib.sh === id: cord-355318-qm79gz8w author: Smit, Albertus J. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-355318-qm79gz8w.txt cache: ./cache/cord-355318-qm79gz8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-355318-qm79gz8w.txt' Que is empty; done keyword-sars-cord === reduce.pl bib === id = cord-015009-3o90pzw7 author = nan title = How and who does SARS kill? date = 2003-06-10 pages = extension = .txt mime = text/plain words = 911 sentences = 46 flesch = 60 summary = Analysis of the complete genome sequence of the SARS virus, published in May 11 , suggests that it is not closely related to any of the three previously identified coronavirus subfamilies, nor does it seem to have arisen through a chance genetic recombination between known coronaviruses12. "Its unique sequence suggests that it has evolved independently from the other members of the family, in some animal host, for a long time," says Malik Peiris, a virologist at the University of Hong Kong. Recent investigations by researchers at the China Agricultural University in Beijing, for instance, have failed to find SARS-like coronaviruses in 732 animals from 54 wild and 11 domestic species in southern China, including palm civets. "The animals walk in and out of their houses," says Kenneth Shortridge, who led the University of Hong Kong's efforts to monitor avian viruses in southern China until his retirement last year. cache = ./cache/cord-015009-3o90pzw7.txt txt = ./txt/cord-015009-3o90pzw7.txt === reduce.pl bib === id = cord-007581-nu1shltl author = Wang, Jiun-Ling title = Rhabdomyolysis associated with probable SARS date = 2003-10-01 pages = extension = .txt mime = text/plain words = 1197 sentences = 87 flesch = 59 summary = Four type II patients were treated with angiotensin-converting enzyme (ACE) inhibitors when they had the first angioedema attack, as compared with none with type I disease. Previous studies have pointed out that patients with probable SARS may have abnormal laboratory examination results, including elevated creatine kinase levels (2-4). We report 3 patients with probable SARS who developed rhabdomyolysis. The first patient was a 38-year-old woman who suffered from probable SARS during a nosocomial outbreak in Taiwan (5) . Serum creatine kinase level increased from 378 to 7659 U/L from April 24 to 30, and renal failure developed. Elevated serum creatine kinase levels of up to 3000 U/L have been noted in previous patients with SARS. We conclude that rhabdomyolysis-associated renal failure may be another unusual but severe presentation of SARS. Patients with SARS should have their creatine kinase levels monitored carefully, even if initial levels are only slightly elevated. cache = ./cache/cord-007581-nu1shltl.txt txt = ./txt/cord-007581-nu1shltl.txt === reduce.pl bib === id = cord-004634-pkrxiipo author = Brun-Buisson, Christian title = SARS: The challenge of emerging pathogens to the intensivist date = 2003-05-08 pages = extension = .txt mime = text/plain words = 1206 sentences = 58 flesch = 53 summary = In late February 2003, the WHO issued a worldwide public health alert on the emergence of a new epidemic of acute respiratory disease first identified in Asian countries since November 2002. In a few weeks, the new agent causing this "severe acute respiratory syndrome" (SARS), a coronavirus, has been identified, sequenced, and tests have been developed for diagnosis [1] . As of the end of April 2003, about 5,000 suspected or probable cases have been reported to the WHO from 27 countries [2] , with a vast majority from inland China (57% of reported cases), which appears to be at the origin of the epidemic, and Hong Kong (32%). In North America, however, an outbreak soon occurred in Toronto, Canada, following an household epidemic which appeared secondary to contamination of a Canadian resident of Asian origin who visited relatives in Hong Kong in February 2003 [3] . Affected areas-severe acute respiratory syndrome (SARS) A Major Outbreak of Severe Acute Respiratory Syndrome in Hong Kong cache = ./cache/cord-004634-pkrxiipo.txt txt = ./txt/cord-004634-pkrxiipo.txt === reduce.pl bib === id = cord-006890-81wv1s33 author = Viret, Jean-Francois title = Development of a SARS vaccine: an industrial perspective on the global race against a global disease date = 2014-01-09 pages = extension = .txt mime = text/plain words = 2069 sentences = 78 flesch = 38 summary = The high profile of SARS in the international news media contributed to early public disease awareness but also caused fear in both affected and unaffected populations, placing additional political and economic pressure on authorities to act on the threat despite of an insufficient basis for informed decisions. Once the global scale of the outbreak became fully apparent, the scientific community, supported by the WHO, committed to '...the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models and correlates of protection in humans.' an unparalleled collaborative effort. More specifically, in spite of the fortunate capability to propagate the SARS-CoV on a well-accepted cell substrate (VERO), the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models of persistent infection and correlates of protection in humans. cache = ./cache/cord-006890-81wv1s33.txt txt = ./txt/cord-006890-81wv1s33.txt === reduce.pl bib === id = cord-000333-4prvgmvt author = Darbyshire, Philip title = Nursing heroism in the 21(st )Century' date = 2011-02-16 pages = extension = .txt mime = text/plain words = 5166 sentences = 275 flesch = 63 summary = Gary Carr, who was a Nurse Practitioner at the AIDS Clinic at San Francisco General Hospital, described the perverse ambivalence of a wider community that lauds and praises nurses for their 'heroic efforts' in the face of such public health crises. When, two decades later, SARS emerged as a potentially lethal viral infection, nurses and health care staff again faced considerable dangers as they strove to treat patients and protect their communities. In addition, Hall and colleagues in the US reported that: "Nursing assistants working in long-term care facilities have the highest incidence of workplace violence of any American worker". Perhaps if we return to the definition of heroism as 'providing service in the face of extreme personal danger', then our Emergency Department nurses should allow themselves to feel, at least somewhat heroic. So too, the health, wellbeing, safety and experiences of patients, clients and families are dependent upon the often invisible and overlooked caring practices of nurses. cache = ./cache/cord-000333-4prvgmvt.txt txt = ./txt/cord-000333-4prvgmvt.txt === reduce.pl bib === id = cord-007567-vst954ef author = Farquharson, Carolyn title = Responding to the severe acute respiratory syndrome (SARS) outbreak: Lessons learned in a Toronto emergency department() date = 2003-06-04 pages = extension = .txt mime = text/plain words = 4228 sentences = 234 flesch = 57 summary = 3 Epidemiologic evidence indicates that transmission of the illness occurs with close person-toperson contact (to household members, health care workers, or nearby patients who were not protected by contact or respiratory isolation precautions) and through droplet secretions. In an effort to deal with the transmission and onset of illness within health care and community settings, the province of Ontario designated a Provincial Operations Centre (POC), which was responsible for issuing directives to hospitals about patient care and infection control practices. Some had normal chest radiography with no infiltrates demonstrated (yet) but had symptoms of fever, headache, myalgia, and malaise, and 1 of 3 distinct exposures: they had either traveled to Vietnam, China, Hong Kong, Singapore, or Taiwan; they had been exposed to a person with SARS; or they had been a health care worker, patient, or visitor in a hospital in the GTA where there had been recorded cases of SARS transmission. cache = ./cache/cord-007567-vst954ef.txt txt = ./txt/cord-007567-vst954ef.txt === reduce.pl bib === id = cord-007049-02p8ug67 author = McGeer, Allison title = Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date = 2004-07-15 pages = extension = .txt mime = text/plain words = 1613 sentences = 92 flesch = 48 summary = In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants cache = ./cache/cord-007049-02p8ug67.txt txt = ./txt/cord-007049-02p8ug67.txt === reduce.pl bib === id = cord-008841-r17qhfsj author = Tomlinson, Brian title = SARS: experience at Prince of Wales Hospital, Hong Kong date = 2003-05-03 pages = extension = .txt mime = text/plain words = 1754 sentences = 108 flesch = 58 summary = THE LANCET • Vol 361 • May 3, 2003 • www.thelancet.com COMMENTARY The Prince of Wales Hospital (PWH) has been at the forefront of the outbreak of severe acute respiratory syndrome (SARS) in Hong Kong. Three major reasons for spread of infection to health-care workers have been: failure to apply isolation precautions to cases not yet identified as SARS, breaches of procedure, and inadequate precautions. "Super-spreaders" may be prone to carry a high viral load because of defects in their COMMENTARY SARS: experience at Prince of Wales Hospital, Hong Kong immune system, as could be the case in the patient with end-stage renal failure implicated in the Amoy Gardens outbreak and another with renal failure at the centre of an outbreak in Singapore. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong cache = ./cache/cord-008841-r17qhfsj.txt txt = ./txt/cord-008841-r17qhfsj.txt === reduce.pl bib === id = cord-009153-zxx4m1kz author = Heymann, David L title = Dangerous pathogens in the laboratory: from smallpox to today's SARS setbacks and tomorrow's polio-free world date = 2004-05-15 pages = extension = .txt mime = text/plain words = 2790 sentences = 147 flesch = 48 summary = THE LANCET • Vol 363 • May 15, 2004 • www.thelancet.com COMMENTARY Less than a year after an unprecedented international public-health effort interrupted human-to-human transmission of the coronavirus that causes severe acute respiratory syndrome (SARS-CoV), some human beings are again infected. 2 Auspiciously, the new SARS cases are occurring as WHO's Biosafety Advisory Group prepares to examine the long-term containment of poliovirus stocks, the risks of which will rapidly increase after interruption of transmission and the ending of immunisation with oral poliovirus vaccine. 3 The recent outbreak of nine cases of SARS in China, with one death, underlines again the challenges of maintaining appropriate biosafety conditions in laboratories working with dangerous pathogens. During the SARS outbreak last year, many specimens were obtained from human cases of SARS COMMENTARY Dangerous pathogens in the laboratory: from smallpox to today's SARS setbacks and tomorrow's polio-free world and sent to many different national and international laboratories for various studies. cache = ./cache/cord-009153-zxx4m1kz.txt txt = ./txt/cord-009153-zxx4m1kz.txt === reduce.pl bib === id = cord-010384-wyp7hrde author = Iwen, Peter C title = Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1633 sentences = 64 flesch = 40 summary = The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. cache = ./cache/cord-010384-wyp7hrde.txt txt = ./txt/cord-010384-wyp7hrde.txt === reduce.pl bib === id = cord-016120-pz2q62i7 author = Zhang, Jie title = Chai Jing: The Power of Vulnerability date = 2019-02-16 pages = extension = .txt mime = text/plain words = 7940 sentences = 335 flesch = 52 summary = This uneasiness with emotion, which is perceived to be opposite to journalistic objectivity, as well as the questioning of Chai's sincerity, which is an innate paradox of the new documentary movement itself (some questioned whether the filmmakers are using the stories of the marginalized people for their own identity politics), provides a lens into the media consumption habits of the Chinese public in the first two decades of the twenty-first century. Chai left the CCTV in 2014 and returned to the public sphere in 2015 with her documentary Under the Dome, which uses a TED talk format to combine personal testimonials, graphs and data, animation, and interviews to investigate the causes of China's air pollution. Chai's embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. cache = ./cache/cord-016120-pz2q62i7.txt txt = ./txt/cord-016120-pz2q62i7.txt === reduce.pl bib === id = cord-015516-hx7ktq8j author = nan title = In the Literature date = 2005-10-15 pages = extension = .txt mime = text/plain words = 1499 sentences = 80 flesch = 46 summary = Experimental pulmonary infection with SARS coronavirus infection in mice reduced the expression of ACE2 in the lungs and, as also occurs in humans, caused diffuse lung injury. On the basis of these findings, the investigators proposed that the severe pulmonary alveolar injury seen in patients with SARS is the consequence of SARS coronavirus spike surface protein-associated down-regulation of ACE2. The authors suggest that recombinant ACE2 protein could be a potential therapeutic agent in this and related pulmonary infections and diffuse alveolar injuries. In patients with chronic infections involving the exit site or tunnel portion of peritoneal dialysis catheters, treatment with antibiotics and local care is often unsuccessful. This procedure was used by Crabtree and Burchette in 13 consecutive patients with chronic peritoneal dialysis catheter infections that had been present for a mean duration of 3.2 months, with successful results for all 13. Three patients subsequently had their catheters removed because of peritonitis without exit-site or tunnel infection at months 8-11. cache = ./cache/cord-015516-hx7ktq8j.txt txt = ./txt/cord-015516-hx7ktq8j.txt === reduce.pl bib === id = cord-014897-rnrlslfh author = Rong-bing, Wang title = Therapeutic effects of integrated traditional Chinese medicine and western medicine in treating severe acute respiratory syndrome date = 2003 pages = extension = .txt mime = text/plain words = 2324 sentences = 103 flesch = 52 summary = The comprehensive effect on relieving fever, cell-mediated immunity, pulmonary inflammation and secondary infection was compared between the two groups.Results: The therapeutic effect in the ICWM group was better than that in the control group in such aspects as steadily lowering body temperature, alleviating general symptoms, accelerating the absorption of pulmonary infiltration and easing cellular immunity suppression.Conclusion: The therapeutic effect of ICWM is better in treating SARS than that of western medicine alone. In order to elevate the therapeutic effects, lighten patients" symptoms, improve the pulmonary inflammation and cellular immune inhibition that occurred in the course of the illness, a clinical study of the treatment of 68 SARS patients with integrated traditional Chinese and western medicine (ICWM), which was controlled with 67 patients treated with western medicine alone, was carried out. cache = ./cache/cord-014897-rnrlslfh.txt txt = ./txt/cord-014897-rnrlslfh.txt === reduce.pl bib === id = cord-016451-k8m2xz0e author = Chertow, Daniel S. title = Influenza, Measles, SARS, MERS, and Smallpox date = 2020-01-03 pages = extension = .txt mime = text/plain words = 6141 sentences = 365 flesch = 41 summary = Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection cache = ./cache/cord-016451-k8m2xz0e.txt txt = ./txt/cord-016451-k8m2xz0e.txt === reduce.pl bib === id = cord-016844-lq2bgu7a author = Teksam, Ozlem title = Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective date = 2013-05-29 pages = extension = .txt mime = text/plain words = 3932 sentences = 206 flesch = 45 summary = title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective Invasive mechanical ventilation (IMV) is a critical intervention in many cases of acute respiratory failure (ARF), but there are absolute risks associated with endotracheal intubation (ETI). Additionally, the World Health Organization's interim guidelines on the prevention and control of acute respiratory diseases associated with health care have included NIV among the aerosol-generating procedures in which there is possibly an increased risk of respiratory pathogen transmission [ 11 ] . Nonetheless, after the most important two viral pandemics during the last decade, especially the last one with infl uenza A(H1N1), most of the societies including above-mentioned and the European Respiratory Society, European Society of Intensive Care Medicine, and The American Association for Respiratory Care have recommended that NIV not be used to treat ARF due to H1N1, particularly in severely ill patients. cache = ./cache/cord-016844-lq2bgu7a.txt txt = ./txt/cord-016844-lq2bgu7a.txt === reduce.pl bib === id = cord-017668-my2l85bn author = Cho, Yeon-Jin title = Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction date = 2005 pages = extension = .txt mime = text/plain words = 2084 sentences = 140 flesch = 60 summary = title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction We present a new method that generates prediction rules for SARS-CoV protease cleavage sites. Experimental results show that the method could generate new rules for cleavage site prediction, which are more general and accurate than consensus patterns. In this paper, we present new approaches to rule generation for the cleavage site prediction, and the rule is represented in an explicit form such as "if L@p2 and R@p3, then cleavage". We used the methods of rule extraction from neural networks and knowledge-based genetic algorithms in this paper. used feed-forward neural networks for SARS-CoV cleavage site analysis [11] . Domain knowledge was obtained by extracting rules from consensus patterns, decision tree and neural networks. Finally, we compare the rule performances between decision tree, neural network and knowledge-based genetic algorithm (KBGA). We presented a new method that generates rules and improves quality of the rules with the subject of SARS-CoV protease cleav-age site prediction. cache = ./cache/cord-017668-my2l85bn.txt txt = ./txt/cord-017668-my2l85bn.txt === reduce.pl bib === id = cord-007560-nck4f5ny author = Ling, Lowell title = COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics date = 2020-02-20 pages = extension = .txt mime = text/plain words = 2803 sentences = 135 flesch = 40 summary = Infection control Outbreak SARS-CoV-2 strategies during mechanical ventilation and prevention of hospital acquired infections is likely to contribute to improved outcomes in critically ill patients. If full airborne precautions are not possible due to limited facilities or overwhelming numbers of cases, other measures that may decrease risk of nosocomial transmission include cohorting of patients in dedicated wards, or physical separation, supported by disciplined use of PPE, universal contact and droplet precautions and adequate ward ventilation [15, [19] [20] [21] . Within the ICU, and with HCW protected by high-level PPE (including an N95 mask), non-invasive ventilation (NIV) and HFNO use during SARS-CoV and 2009 influenza epidemic was not clearly associated with an increased risk in HCW [24, 25] . Anyone who develops symptoms that could suggest a coronavirus infection are encouraged to call a single emergency number and if COVID-19 is suspected, they are managed at their location by a specialised medical team equipped with PPE to prevent viral contamination, and when necessary, hospitalised in an intensive care unit. cache = ./cache/cord-007560-nck4f5ny.txt txt = ./txt/cord-007560-nck4f5ny.txt === reduce.pl bib === id = cord-016897-t71f10kv author = Flores, Marco V. title = Preventing Airborne Disease Transmission: Implications for Patients During Mechanical Ventilation date = 2013-05-29 pages = extension = .txt mime = text/plain words = 3661 sentences = 196 flesch = 46 summary = We discuss the risk of transmitting these procedures and the strategies for mechanical ventilation in future airborne epidemics with special consideration given to the issue of protecting health care workers (HCWs). In contrast to the situation regarding severe acute respiratory syndrome (SARS) or tuberculosis prevention in HCWs, little attention has been given to the importance of HCWs personal protective equipment (PPE) (gowns, gloves, masks) for prevention and management of infl uenza. There is also potential for NIV to reduce the need for intubation in patients with infl uenza pneumonia or chronic respiratory disease, facilitate extubation, and widen the provision of ventilator support outside the intensive care unit (ICU). Evaluation of droplet dispersion during non-invasive ventilation, oxygen therapy, nebulizer treatment and chest physiotherapy in clinical practice: implications for management of pandemic infl uenza and other airbone infections Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review cache = ./cache/cord-016897-t71f10kv.txt txt = ./txt/cord-016897-t71f10kv.txt === reduce.pl bib === id = cord-015183-1eytelxn author = Walgate, Robert title = Latest SARS evidence date = 2003-04-07 pages = extension = .txt mime = text/plain words = 1055 sentences = 68 flesch = 71 summary = The outbreak of SARS (Severe Acute Respiratory Syndrome) that originated in China is, with "95-97% certainty," caused by a completely new type of coronavirus, according to Julie Hall, who is responsible for the World Health Organization's Global Alert, Response and Operations Network. In patients, we'd also like to see the curves of IgM [specific to this virus], to show people have an acute response, and then IgG, which takes two to three weeks to level up, and stays with you, to show that it wasn't just a passing extraneous infection." Moreover "We have lots of blood samples to test this in now," Hall said, so the results should not be long coming. Günther said he and Drosten had isolated three short DNA sequences from the coronavirus in a tissue sample from the "index case" (first case) of SARS in Germany, by a random amplification, lowstringency PCR approach. cache = ./cache/cord-015183-1eytelxn.txt txt = ./txt/cord-015183-1eytelxn.txt === reduce.pl bib === id = cord-012424-z3mkp9y9 author = Bansal, Poonam title = Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) date = 2020-08-13 pages = extension = .txt mime = text/plain words = 498 sentences = 45 flesch = 46 summary = title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) We write in reference to a previously reported case of acute necrotizing encephalopathy (ANE) associated with acute SARS-COV-2 infection (1) . Repeat MRI brain without contrast showed residual T2 hyperintensities and hemosiderin deposition in the medial thalami; the former were significantly improved from previous. Several cases of COVID-19 associated ANE have now been reported (Table) . Immunotherapy has some role in the treatment of COVID-19 associated ANE, as described in the literature (1, 4, 5 COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia Acute necrotizing encephalopathy and myocarditis in a young patient with COVID-19 Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid COVID-19-associated acute necrotising encephalopathy successfully treated with steroids and polyvalent immunoglobulin with unusual IgG targeting the cerebral fibre network Does SARS-Cov-2 invade the brain? cache = ./cache/cord-012424-z3mkp9y9.txt txt = ./txt/cord-012424-z3mkp9y9.txt === reduce.pl bib === id = cord-017942-og0b2l6b author = Chen, Yi-Da title = Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data date = 2007 pages = extension = .txt mime = text/plain words = 3673 sentences = 201 flesch = 48 summary = title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data In this research, we use Taiwan SARS data to investigate the differences in connectivity between personal and geographical contacts in the construction of social networks for these diseases. In 1985, Klovdahl [6] used AIDS as an example to illustrate the usefulness of Social Network Analysis (SNA) in studying the transmission of an infectious disease. However, from these two studies, we can see that incorporating geographical contacts into SNA provides us a good way to find potential connections among patients and to see the role that those geographical locations play in disease outbreaks. The studies of SNA in epidemiology primarily use personal contacts to construct social networks and model the transmission of diseases. In this research, by using Taiwan SARS data as the test dataset, we further investigate the differences in connectivity between personal and geographical contacts in the network construction for these diseases. cache = ./cache/cord-017942-og0b2l6b.txt txt = ./txt/cord-017942-og0b2l6b.txt === reduce.pl bib === id = cord-011813-lm105z6n author = Imperiale, Michael J. title = Recurring Themes date = 2020-07-08 pages = extension = .txt mime = text/plain words = 309 sentences = 28 flesch = 68 summary = to ask whether mSphere would be interested in publishing a summary of a conference being held at that time in Singapore to commemorate the 20th anniversary of the first Nipah virus outbreak. Having attended a similar conference on Ebola and other emerging infectious diseases a couple of years earlier, I knew that the topics of discussion and the information presented at such a meeting are of interest and importance to the microbial sciences community. I therefore told Benhur that we were absolutely interested: the report from the Nipah@20 conference is published with this editorial (1). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was beginning its journey from Wuhan, China to the rest of the world, and as of the time I am writing this, well over 10 million cases and half a million deaths have been reported. As the authors of the Nipah@20 conference summary note, the similarities in terms of what the world needs to respond to such emerging diseases are many. cache = ./cache/cord-011813-lm105z6n.txt txt = ./txt/cord-011813-lm105z6n.txt === reduce.pl bib === id = cord-010050-utbrf4ad author = Fisher, Dale A title = Preventing local transmission of SARS: lessons from Singapore date = 2003-06-02 pages = extension = .txt mime = text/plain words = 2363 sentences = 134 flesch = 54 summary = 4 Instituting this Preventing local transmission of SARS: lessons from Singapore Clinical record At 11:30 on 8 April 2003, a 64-year-old man presented to the National University Hospital emergency department (ED) complaining of light headedness for 3 days, and dry cough and body aches for 2 days. Australia must ensure rapid identification of a potential index case at points of initial contact in hospitals, community clinics and general practices across the country. 1, 2 In countries with the resources to implement full and effective contact and respiratory isolation for all suspect patients, local transmission of the virus has been almost non-existent. Provided there is consistent early identification of imported suspect cases, then Australia's healthcare system can manage these patients with appropriate isolation to prevent secondary transmission. Each health jurisdiction in Australia must have a plan for managing a local SARS outbreak, which should include prompt hospital and community responses, and an ability to meet potential needs at short notice. cache = ./cache/cord-010050-utbrf4ad.txt txt = ./txt/cord-010050-utbrf4ad.txt === reduce.pl bib === id = cord-015181-875gf11z author = Walgate, Robert title = SARS escaped Beijing lab twice date = 2004-04-27 pages = extension = .txt mime = text/plain words = 614 sentences = 42 flesch = 71 summary = Email: Walgate@scienceanalysed.com The latest outbreak of severe acute respiratory syndrome (SARS) in China, with eight confirmed or suspected cases so far and hundreds quarantined, involves two researchers who were working with the virus in a Beijing research lab, the World Health Organization (WHO) said on Monday (April 26). "We suspect two people, a 26-year-old female postgraduate student and a 31-year-old male postdoc, were both infected, apparently in two separate incidents," Bob Dietz, WHO spokesman in Beijing, told us. China has level three research guidelines and rules in place for handling the SARS virus, which are "of acceptable quality" to WHO, Dietz told us. They are going to go into the labs with Ministry of Health people and find out what happened here," Dietz said. " We've been told we'll have full access, be able to test all the surfaces, interview people who worked there, and look at documentation to find out what was being done," Dietz said. cache = ./cache/cord-015181-875gf11z.txt txt = ./txt/cord-015181-875gf11z.txt === reduce.pl bib === id = cord-009573-ghv9uezx author = Karlberg, J title = Do sensational media reports about severe acute respiratory syndrome affect the mindset of healthcare workers? date = 2007-01-02 pages = extension = .txt mime = text/plain words = 1047 sentences = 66 flesch = 68 summary = The doctor at Huddinge Hospital called the Karolinska Hospital, and told the mother that an isolation room would be available for them at the hospital. That afternoon, the mother and son arrived at the Astrid Lindgren's Children's Hospital of the Karolinska Hospital, and a doctor and nurse met them. Because the doctors and other hospital staff now regarded her son as a suspected SARS case, the mother was concerned about returning home to her daughter and mother. A few days later the mother called the hospital and was told that the laboratory results were negative for SARS. We are concerned because, at the time of writing, there has not been any report of this suspected SARS case to the Swedish Institute for Infectious Disease Control or to WHO. We believe that heightened anxiety about SARS, brought about by the popular media's exaggerated reporting of the outbreak in Hong Kong, affected the way Swedish healthcare professionals reacted. cache = ./cache/cord-009573-ghv9uezx.txt txt = ./txt/cord-009573-ghv9uezx.txt === reduce.pl bib === id = cord-015503-j99cgsjt author = Tang, Xiaolu title = On the origin and continuing evolution of SARS-CoV-2 date = 2020-03-03 pages = extension = .txt mime = text/plain words = 5243 sentences = 292 flesch = 59 summary = Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Further, the genomic sequences of SARS-CoV-2 viruses isolated from a number of patients share sequence identity higher than 99.9%, suggesting a very recent host shift into humans [1] [2] [3] . cache = ./cache/cord-015503-j99cgsjt.txt txt = ./txt/cord-015503-j99cgsjt.txt === reduce.pl bib === id = cord-017108-vqbl0eov author = Zheng, Xiaolong title = Network-Based Analysis of Beijing SARS Data date = 2008 pages = extension = .txt mime = text/plain words = 2427 sentences = 158 flesch = 56 summary = Instead, a strategy that focuses on nodes (e.g., patients, locations, or occupations) with high degree and strength may lead to more effective outbreak control and management. A public health implication of this finding is that the traditional disease control approach based on random immunization (which has been shown to be effective in many epidemic outbreaks [8] ) may not be effective (unless, of course, the entire population can be treated), because untreated hubs, albeit small in number, can still lead to rapid and large-scale infections [8] . In this section, we analyze the SARS transmission patterns based on the weighted occupation network (WON) as shown in Fig. 7 . To better understand the SARS epidemic transmission patterns and evolution, we have studied three networks derived from the patient survey data, including a patient contact network, a weighted district network, and a weighted occupation network. cache = ./cache/cord-017108-vqbl0eov.txt txt = ./txt/cord-017108-vqbl0eov.txt === reduce.pl bib === id = cord-018106-5giapmcf author = Levin, Jacqueline title = Mental Health Care for Survivors and Healthcare Workers in the Aftermath of an Outbreak date = 2019-05-16 pages = extension = .txt mime = text/plain words = 4253 sentences = 182 flesch = 36 summary = Similar findings have been reported in multiple studies indicating acute and persistently elevated stress levels as well as other emotional sequelae of healthcare workers during and after pandemic disease outbreaks [10] [11] [12] . A study of the psychological impact of the 2003 SARS outbreak on healthcare workers in Singapore found that support from supervisors and colleagues was a significant negative predictor for psychiatric symptoms and PTSD, in addition to clear communication of directives and precautionary measures which also helped reduce psychiatric symptoms [15] . Providing psychiatric care to survivors and healthcare workers in the aftermath of a pandemic outbreak is a complicated, but crucial, imperative in the service of reducing the burden of human suffering. cache = ./cache/cord-018106-5giapmcf.txt txt = ./txt/cord-018106-5giapmcf.txt === reduce.pl bib === id = cord-015552-pm9kdqdw author = Kreuder-Sonnen, Christian title = China vs the WHO: a behavioural norm conflict in the SARS crisis date = 2019-05-01 pages = extension = .txt mime = text/plain words = 8263 sentences = 390 flesch = 46 summary = On the one hand, the established norm of sovereignty, particularly the principle of non-interference, had structured a regime for dealing with infectious disease outbreaks that provided ground rules of conduct but ascribed decision-making authority to member states alone. 33 This sediment of the unfinished IHR revision process reveals the limited degree to which the emerging norm of global health security had been accepted prior to the SARS outbreak: the powers conferred upon the WHO to deal with infectious disease outbreaks remained extremely limited and-apart from the outbreak information issue-mostly subject to member-state agreement. 35 This section of the article analyses the actions of China and the WHO during the SARS crisis as representing a behavioural norm conflict over the relative priority of sovereignty and global health security. cache = ./cache/cord-015552-pm9kdqdw.txt txt = ./txt/cord-015552-pm9kdqdw.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-009295-4c0zwhdh author = Bal, A. title = Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date = 2020-03-28 pages = extension = .txt mime = text/plain words = 1253 sentences = 73 flesch = 56 summary = title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) The phylogenetic analysis using the 571 WGS of SARS-CoV-2 publicly available (as of March 17th 2020) found that this sequence clustered with a sequence (EPI_-ISL_408488) collected in Jiangsu, China, on January 19th, suggesting a separate introduction from Asia (Fig. 1) . Compared to the reference SARS-CoV-2 sequence, a three-nucleotide deletion in open reading frame 1a (ORF1a) at positions 1607e1609 was identified. Letter to the Editor / Clinical Microbiology and Infection xxx (xxxx) xxx SARS-CoV-2 sequences were not further compared between the two patients due to largely incomplete coverage of the SARS-CoV-2 genome in sample #1. Despite low viral loads, the mNGS workflow used herein allowed us to characterize the wholegenome sequences of SARS-CoV-2 isolated from an asymptomatic patient in two clinical samples collected 1 day apart. cache = ./cache/cord-009295-4c0zwhdh.txt txt = ./txt/cord-009295-4c0zwhdh.txt === reduce.pl bib === id = cord-007713-611sp7uo author = Hughes, J. M. title = Emerging infectious diseases: the public’s view of the problem and what should be expected from the public health community date = 2005 pages = extension = .txt mime = text/plain words = 2683 sentences = 135 flesch = 43 summary = In 2003 alone, a newly recognized coronavirus spread across five continents sickening more than 8,000 people and causing 774 deaths from a new disease designated severe acute respiratory syndrome (SARS) [4] , the exotic animal trade resulted in the first cases of human monkeypox in the Western hemisphere [5] , and highly pathogenic strains of avian influenza virus killed humans and devastated the poultry industry in parts of Asia [6] -further heightening fears of pandemic influenza. Improving preparedness and response: lessons learned from recent outbreaks -Strengthening existing and developing new national and international partnerships -Training and educating a multidisciplinary workforce -Ensuring "full use" of investments -Encouraging transparency and political will -Fostering a global commitment to address inequities -Developing and implementing preparedness plans and research agendas -Proactively communicating with health professionals, the media, and the public While the first line of defense in controlling an outbreak remains strong national surveillance systems that can readily detect outbreaks, the SARS experience highlighted the importance of global disease detection efforts [13] . cache = ./cache/cord-007713-611sp7uo.txt txt = ./txt/cord-007713-611sp7uo.txt === reduce.pl bib === id = cord-019048-29wzpwvr author = Franks, Teri J. title = Coronavirus date = 2013-08-26 pages = extension = .txt mime = text/plain words = 2805 sentences = 135 flesch = 47 summary = From discovery to mid-September 2013, HCoV-EMC, renamed MERS-CoV, (de Groot 2013 ) caused 132 laboratory-confi rmed cases of severe acute pneumonia including 58 deaths. Certain structural proteins are common to all coronaviruses: the spike glycoprotein S, an envelope glycoprotein that mediates receptor-binding and membrane fusion; the envelope spanning glycoprotein M, which contributes to the thickness of the envelop; the envelope protein E, which has been identifi ed as a virulence factor SARS-CoV ; and the nucleocapsid protein N, with its function in genome encapsidation, RNA synthesis and translation, and as a type I interferon antagonist ( Fig. 13 .2 ). Initial signs and symptoms of SARS are nonspecifi c and common, which generates a wide differential diagnosis of respiratory pathogens including infl uenza virus, parainfl uenza Fig. 13.4 Acute-phase DAD in SARS patient. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection cache = ./cache/cord-019048-29wzpwvr.txt txt = ./txt/cord-019048-29wzpwvr.txt === reduce.pl bib === id = cord-015701-0m17unfx author = nan title = Neuartiges Coronavirus (SARS-CoV-2) date = 2020-02-24 pages = extension = .txt mime = text/plain words = 80 sentences = 15 flesch = 80 summary = key: cord-015701-0m17unfx authors: nan title: Neuartiges Coronavirus (SARS-CoV-2) date: 2020-02-24 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1113-3096 sha: doc_id: 15701 cord_uid: 0m17unfx nan . Von der Gabe von Kortikosteroiden wird eher abgeraten. An einem Impfstoff gegen SARS-CoV-2 wird fieberhaft gearbeitet. Auch im Idealfall dürften entsprechende Zulassungsstudien aber nicht vor Ende 2020 zu erwarten sein. china World Health Organization. Novel Coronavirus (SARS-CoV-2) situation reports First Case of 2019 Novel Coronavirus in the United States cache = ./cache/cord-015701-0m17unfx.txt txt = ./txt/cord-015701-0m17unfx.txt === reduce.pl bib === id = cord-009697-dq4y89ab author = Yuen, Eddie title = Role of absolute lymphocyte count in the screening of patients with suspected SARS date = 2003-07-25 pages = extension = .txt mime = text/plain words = 1510 sentences = 92 flesch = 59 summary = 3 This multicentre, placebo-controlled, randomized, double-blind trial in 6213 patients with acute ST-elevation myocardial infarct (STEMI) found that magnesium sulphate, (2 g intravenous bolus over 15 min followed by a 17 g infusion over 24 h), administered within 6 hours of onset of symptoms did not have any effect on the primary end-point of 30 day all-cause mortality when compared with placebo (15.3% 30 day mortality in the magnesium group vs 15.2% in the placebo group; odds ratio 1.0; 95% CI 0.9-1.2; P = 0.96). As the investigators point out in the discussion of their paper, this means that 68 684 patients have been studied over the past 22 years in 14 randomized trials of magnesium in myocardial infarction. Second, a multicentre, placebo-controlled, randomized, double-blind trial of intravenous magnesium sulphate in 248 patients with acute severe asthma was recently reported. cache = ./cache/cord-009697-dq4y89ab.txt txt = ./txt/cord-009697-dq4y89ab.txt === reduce.pl bib === id = cord-009891-gqrhbhbn author = Rassool, G. Hussein title = Current issues and forthcoming events date = 2003-09-03 pages = extension = .txt mime = text/plain words = 3466 sentences = 168 flesch = 49 summary = The Centers for Disease Control and Prevention (CDC), USA, reports that 'transmission to health care workers appears to have occurred after close contact with symptomatic individuals (e.g. persons with fever or respiratory symptoms) before recommended infection control precautions for SARS were implemented (i.e. unprotected exposures).' There is also a possibility that the causative agent can remain viable for extended periods of time after drying on environmental surfaces. Preliminary results of a large-scale trial of a candidate AIDS vaccine announced by the US-based biotechnology company VaxGen suggest that it is possible to protect some individuals from HIV infection. The result is that poor diagnosis of pain in cancer patients remains a significant problem, with many physicians finding it difficult to differentiate between the various pain types; and, many underestimating its severity. Poor diagnosis, poor assessment, the choice of less appropriate treatments, plus patients and physicians fears about controlled drugs such as morphine all contribute to under treatment of cancer pain. cache = ./cache/cord-009891-gqrhbhbn.txt txt = ./txt/cord-009891-gqrhbhbn.txt === reduce.pl bib === id = cord-018441-r6wwpfcy author = Taylor, Milton W. title = Emerging Viruses date = 2014-07-22 pages = extension = .txt mime = text/plain words = 3674 sentences = 210 flesch = 63 summary = Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). cache = ./cache/cord-018441-r6wwpfcy.txt txt = ./txt/cord-018441-r6wwpfcy.txt === reduce.pl bib === id = cord-017210-5nc8f3a4 author = Pathegama, Mahinda P. title = Interactive Real-time Image Analysis System for Distant Operation date = 2005 pages = extension = .txt mime = text/plain words = 2415 sentences = 129 flesch = 43 summary = This paper reports on the development and implementation of an integrated and interactive system for cell analysis featuring remote operation and real-time analysis for generating analytical data from microscopic images. Advancement of image processing techniques is a welcome adjunct in electronmicroscopic cell analysis and is the object of increasing interest in research for the enhancement of accuracy in disease diagnosis. The emergence and rapid spread of SARS (Severe Acute Respiratory Syndrome) has dramatically emphasised the need for both collaborative international networks [4] and linking of personnel from distant locations with laboratories monitoring and analysing test samples of the causative agent by electron microscopy. Remote users would derive considerable benefit from a system endowed with facilities enabling image acquisition, camera control, real-time monitoring, automated pattern recognition for cell feature extraction and quantitative result generation. The techniques used aid in image enhancement and provide feature highlighting needed for quantitative report generation on each cell object detected in the microscopic image. cache = ./cache/cord-017210-5nc8f3a4.txt txt = ./txt/cord-017210-5nc8f3a4.txt === reduce.pl bib === id = cord-017516-qbksb83c author = Si, Yain-Whar title = Hidden Cluster Detection for Infectious Disease Control and Quarantine Management date = 2009-09-30 pages = extension = .txt mime = text/plain words = 3358 sentences = 158 flesch = 46 summary = Our prototype Infectious Disease Detection and Quarantine Management System (IDDQMS), which can identify and trace clusters of infection by mining patients' history, is introduced in this paper. The SARS (Severe Acute Respiratory Syndrome) outbreak in 2003 and recent world-wide avian flu infections have contributed to the urgent need to search for efficient methods for prevention and control of highly infectious diseases. Given this background, this research aims to develop a decision support system which can be used to locate the source of an outbreak by mining clusters and communities from the patients' past activities (testimonies) using techniques from infectious disease control, information visualization, and database management systems. IDDQMS (see Figure 1 ) consists of four modules; information extraction, data analysis, hidden cluster detection, and quarantine management. In this paper, we have described our novel prototype system on Infectious Disease Detection and Quarantine Management, which can be used to identify and trace clusters of infection by mining patients' history. cache = ./cache/cord-017516-qbksb83c.txt txt = ./txt/cord-017516-qbksb83c.txt === reduce.pl bib === id = cord-016312-u47mb2h0 author = Lu, Pu-Xuan title = Introduction of Emerging Infectious Diseases date = 2015-07-25 pages = extension = .txt mime = text/plain words = 1780 sentences = 115 flesch = 51 summary = Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specific preventive or control measures. Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specifi c preventive or control measures. Cases in point are the epidemics of SARS in 2003 and H7N9 avian infl uenza around 2006, which have eloquently demonstrated their great threats to human health, society, and economy. Such contagious diseases did not exist in the past and newly emerge due to new pathogens such as AIDS, severe acute respiratory syndrome (SARS), human infection with highly pathogenic avian infl uenza H5N1, infl uenza A (HlN1), and human infection with avian infl uenza H7N9. revealed that 60.3 % EIDs were zoonotic, with 71.8 % caused by wild animals, such as human avian infl uenza and Ebola virus. cache = ./cache/cord-016312-u47mb2h0.txt txt = ./txt/cord-016312-u47mb2h0.txt === reduce.pl bib === id = cord-017463-repm1vw9 author = Ungchusak, Kumnuan title = Public Health Surveillance: A Vital Alert and Response Function date = 2018-07-27 pages = extension = .txt mime = text/plain words = 5671 sentences = 273 flesch = 40 summary = We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. cache = ./cache/cord-017463-repm1vw9.txt txt = ./txt/cord-017463-repm1vw9.txt === reduce.pl bib === id = cord-017995-azqjvxtu author = Kwong, Kim-hung title = Spatial Components in Disease Modelling date = 2010 pages = extension = .txt mime = text/plain words = 3117 sentences = 174 flesch = 47 summary = Modelling of infectious diseases could help gain further understanding of their diffusion processes that provide knowledge on the detection of epidemics and decision making for future infection control measures. This research made an attempt to map different phases of the spatial diffusion of SARS in Hong Kong to identify the underlying spatial factors attributing to its transmission patterns. Socio-economic factors found statistically significant against SARS incidence included the following: c) percentage of population aged over 65, g) average number of rooms per household, and h) net residential density ( Table 1 ). Certain socio-economic factors (i.e., average number of rooms per household, percentage of elderly population, and net residential density) were found to correlate positively with the occurrence of SARS in Hong Kong, indicating their potential influence in the disease transmission. This research mapped different development phases of the SARS epidemic in Hong Kong and employed the Pearson's correlation to isolate environmental factors and socio-economic factors of significant pertinence to the disease. cache = ./cache/cord-017995-azqjvxtu.txt txt = ./txt/cord-017995-azqjvxtu.txt === reduce.pl bib === id = cord-004204-cpub9oah author = D’Cunha, Colin title = SARS: Lessons Learned from a Provincial Perspective date = 2004-01-01 pages = extension = .txt mime = text/plain words = 1538 sentences = 93 flesch = 55 summary = T o say that SARS was a unique threat, and one that challenged public health and the entire health system in Ontario could be viewed as somewhat of an understatement. Never had the modern public health or the health care system been put to such a test or been put under such pressure to respond as during the two phases of SARS outbreaks earlier this year. The very uniqueness and stress that the SARS outbreaks placed on our system inevitably revealed the weaknesses and the areas where change or fortification in our public health defenses was needed in order for us to meet successfully future challenges. Funding for public health services in Ontario is based on a mixed model with municipal and provincial partners contributing to the funding. Other public health professionals should be cross-trained in communicable disease management to create additional surge capacity. A Report of the National Advisory Committee on SARS and Public Health cache = ./cache/cord-004204-cpub9oah.txt txt = ./txt/cord-004204-cpub9oah.txt === reduce.pl bib === id = cord-014878-n6a9cq47 author = Jun-yi, Ma title = The characteristics and dynamic changes of X-ray chest film in 50 patients with severe acute respiratory syndrome date = 2003 pages = extension = .txt mime = text/plain words = 1386 sentences = 68 flesch = 61 summary = The characteristics and dynamic changes of chest film in 50 SARS patients in Hebei Province were analysed by the authors and reported as follows. X-ray chest films of all the patients taken every 2--3 days in the hospitalized period were collected and those with significant changes were analysed. Because there lacks definite epidemiological contacting history in part of the patients, the disease shows no specificity in clinical manifestation and blood cell examination, and the therapeutic effect could give no help to diagnosis, it is of vital importance in clinical practice to decide whether there is lesion occurring in the lung through X-ray chest film examination for early diagnosis of SARS. The figure of chest film of SARS patients is characterized as follows: ( 1 ) Lesions often oc-curred at the lower field and outer zone of the lung; (2) Lesions are mostly multiply presented; Characteristics of X-ray chest film figure in patients with SARS cache = ./cache/cord-014878-n6a9cq47.txt txt = ./txt/cord-014878-n6a9cq47.txt === reduce.pl bib === id = cord-015376-z739ifu5 author = Savarino, Andrea title = Potential therapies for coronaviruses date = 2006-08-31 pages = extension = .txt mime = text/plain words = 6361 sentences = 313 flesch = 48 summary = These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. cache = ./cache/cord-015376-z739ifu5.txt txt = ./txt/cord-015376-z739ifu5.txt === reduce.pl bib === id = cord-015619-msicix98 author = nan title = Virus Structure & Assembly date = 2009-02-24 pages = extension = .txt mime = text/plain words = 3302 sentences = 164 flesch = 45 summary = The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature's best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. cache = ./cache/cord-015619-msicix98.txt txt = ./txt/cord-015619-msicix98.txt === reduce.pl bib === id = cord-015613-ls9qus8y author = Macdonald, David W. title = Infectious disease: Inextricable linkages between human and ecosystem health date = 2006-06-06 pages = extension = .txt mime = text/plain words = 6157 sentences = 300 flesch = 47 summary = Several papers, including those on rabies in Ethiopian wolves, Canis simensis (Randall et al., 2006) , and African wild dogs, Lycaon pictus (Vial et al., 2006) , disease in Island foxes, Urocyon littoralis (Clifford et al., 2006) , squirrel parapox virus (SQPV) in red squirrels, Sciurus vulgaris (Gurnell et al., 2006) , and devil facial tumour disease (DFTD) in Tasmanian devils, Sarcophilus harrisii (Hawkins et al., 2006) examine this theme. The importance of reservoir identification is classically illustrated by a range of papers in this Special Issue, for example the ongoing dilemma facing bovine tuberculosis control , the diseases emerging from bats (Breed et al., 2006) , phocine distemper virus (PDV) in northern seal population (Hall et al., 2006) and the canid pathogens threatening Island foxes (Clifford et al., 2006) . cache = ./cache/cord-015613-ls9qus8y.txt txt = ./txt/cord-015613-ls9qus8y.txt === reduce.pl bib === id = cord-023140-ytal7wog author = Henderson, Joan C. title = Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore date = 2004-12-09 pages = extension = .txt mime = text/plain words = 3949 sentences = 163 flesch = 48 summary = title: Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore The sudden outbreak of severe acute respiratory syndrome (SARS) in Singapore in 2003 was a grave crisis for the tourism industry as a whole and highlights the importance of effectively managing and planning for such occurrences. It focuses on how the epidemic impacted on Singapore's hotel sector and management reactions to it, affording insights into the problems caused by outbreaks of infectious disease at destinations and possible responses. The epidemic of SARS in 2003 was an exceptional crisis for Singapore's hotels and an exacting test for its managers, in which advances to near normality were dictated by outside developments and agencies as much as their own efforts. Managing a health-related crisis: severe acute respiratory syndrome (SARS) in Singapore Chaos, crises and disasters: a strategic approach to crisis management in the tourism industry cache = ./cache/cord-023140-ytal7wog.txt txt = ./txt/cord-023140-ytal7wog.txt === reduce.pl bib === id = cord-013269-u1e0kzmm author = Cucinotta, Domenico title = Primum non nocere (first do no harm). The SARS-CoV-2 pandemic course in oldest in Italy date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1602 sentences = 94 flesch = 54 summary = Maybe a bad strategy and lack of timely intervention togheter with concurrent social events, comorbidities of oldest persons, bed rest, inadequate nutritional support and drugs' side effects and infection of health professionals proved fatal for many. Different opinions among scientists, as occurred recently in COVID-19 pandemia in Italy, combined with the difficulties due to comorbidities and dependency of oldest persons have resulted in strategic errors, a significant part of which proved fatal for the patient and catastrofic for the society. On January 18 the Medical Literature Guide Amedeo (1) drowes the attention to a study of the Imperial College of London on the real high number of cases in Wuhan and on 23 the Chinese government put millions of people in quarantine, with severe travel restriction starting from 25. bas a consequence of the lack of a timely intervention with no appropriate prevention methodologies, virus entered into hospitals, nursing homes, day centers and doctor's offices. et al Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China cache = ./cache/cord-013269-u1e0kzmm.txt txt = ./txt/cord-013269-u1e0kzmm.txt === reduce.pl bib === id = cord-016921-64mfqks9 author = Schillmeier, Michael title = Risiko-Akteur-Netzwerke date = 2009-08-07 pages = extension = .txt mime = text/plain words = 3555 sentences = 398 flesch = 55 summary = Should SARS continue to spread, the global economic consequences -already estimated at around US $ 30 billion -could be great in a closely interconnected and interdependent world." (WHO 2003: 5) Die Welt bekam es mit einem Akteur zu tun, der in der Lage war, gesellschaftliches und individuelles Leben zu tangieren, zu bedrohen oder gar zu vernichten. Gerade die Möglichkeit, dass wir Menschen mit Hilfe von Flugzeugen weltweit schnell von einem Ort zum anderen reisen können, machte die Gefährlichkeit des SARS-Virus aus, da dieser das Risiko darstellte, als eine Art blinder Passagier mitzureisen und sich so ebenso global entlang dieser Flugrouten und darüber hinaus auszubreiten. SARS markiert ein "kosmo-politisches Ereignis" (Schillmeier & Pohler 2006) : Es stellt einen grenzüberschreitenden, öffentlichen Akteur dar, der nicht nur gesellschaftliche Ordnungsmuster, sondern auch die etablierten Routinen seiner Beschreibung kontingent erscheinen lässt und reformuliert. Bereits an dieser Stelle lässt sich erkennen, dass mit dem Risiko-Akteur SARS eine prozessuale, man könnte auch sagen, eine propagationale Perspektive von Handlung erforderlich ist, die sich der klassischen Konzeptionen und Begrifflichkeiten sozialwissenschaftlicher Methode entziehen. cache = ./cache/cord-016921-64mfqks9.txt txt = ./txt/cord-016921-64mfqks9.txt === reduce.pl bib === === reduce.pl bib === id = cord-015235-lv8mll28 author = Kim, Hyun title = Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody date = 2014-04-16 pages = extension = .txt mime = text/plain words = 5855 sentences = 323 flesch = 60 summary = The receptor-binding domain (RBD) positioned in S1 can specifically bind to angiotensin-converting enzyme 2 (ACE2) on target cells, and ACE2 regulates the balance between vasoconstrictors and vasodilators within the heart and kidneys. Infection of SARS-CoV is initiated by binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) functional receptor expressed on target cells (Li et al. Our cellular enzyme-linked immunosorbent assay (ELISA) and competitive binding assay using a polyclonal ACE2 antibody indicated that our prepared recombinant RBD fusion protein binds to various tissues as well as NIH3T3 and HEK293 cells through ACE2. After washing with PBS, the RBD fusion protein was incubated for 1 h at room temperature to bind with the ACE2 molecules on the cell membranes. Next, we examined whether RBD binding was blocked by the ACE2 antibody in a Western blot using mouse tissue cell lysates with a pair of membranes. cache = ./cache/cord-015235-lv8mll28.txt txt = ./txt/cord-015235-lv8mll28.txt === reduce.pl bib === id = cord-018460-wbtaoo0o author = Schomburg, Dietmar title = SARS coronavirus main proteinase 3.4.22.69 date = 2013 pages = extension = .txt mime = text/plain words = 6007 sentences = 743 flesch = 70 summary = cache = ./cache/cord-018460-wbtaoo0o.txt txt = ./txt/cord-018460-wbtaoo0o.txt === reduce.pl bib === id = cord-021055-ebcu3ywq author = Xu, Jianguo title = Inaugural editorial: Towards evidence-based biosafety and biosecurity date = 2019-02-20 pages = extension = .txt mime = text/plain words = 826 sentences = 61 flesch = 42 summary = China has experienced significant biosecurity and biosafety challenges and is the only nation that has been subjected to a bioweapon assault. 2 The SARS epidemic served as a timeous practical reminder to both China and the world that emerging infectious diseases could significantly threaten national and global safety and security. [3] [4] [5] [6] [7] The 2004 SARS outbreak in North China resulted from a series of flaws in the biosafety protocol at a national institute in Beijing, 5 resulting in infection of four laboratory workers. We propose that the scope of biosecurity and biosafety should include all relevant areas with the potential to cause death, social disruption and panic, economic breakdown, and/or national crisis (e.g. emerging infectious diseases, bioweapons, bioterror, laboratory biosafety, antibiotic-resistant bacterial super-strains, harmful invasive plant or animal species, misuse of synthetic biological technology, misuse of human genetic information, etc.). cache = ./cache/cord-021055-ebcu3ywq.txt txt = ./txt/cord-021055-ebcu3ywq.txt === reduce.pl bib === id = cord-020769-elzkwyz0 author = Day, Brennan title = The new normal: lessons learned from SARS for corporations operating in emerging markets date = 2004-07-01 pages = extension = .txt mime = text/plain words = 6422 sentences = 312 flesch = 55 summary = This paper uses the recent SARS epidemic as a background to highlight the importance of crisis planning, particularly in emerging economies, and suggests how organizations can address these concerns. This paper will start by presenting background information on the SARS epidemic and the impact on organizations, especially those operating in emerging markets. Since emerging markets are increasingly important to the world economy and are at the same time susceptible to outbreaks of infectious diseases, we need to understand how we are linked together on an interdependent global level. If just three of the Asian emerging economies -China, India, and Indonesia -are able to maintain this growth rate of 6 percent per year, the Organisation for Economic Co-operation and Development (OECD) has estimated that by 2010 approximately 700 million people in those countries will have an average income equivalent to that of Spain today. cache = ./cache/cord-020769-elzkwyz0.txt txt = ./txt/cord-020769-elzkwyz0.txt === reduce.pl bib === id = cord-016160-ugc7ce21 author = Ching, Frank title = Bird Flu, SARS and Beyond date = 2018-03-15 pages = extension = .txt mime = text/plain words = 19410 sentences = 1034 flesch = 62 summary = At the end of 2002, unknown to anyone in Hong Kong, another deadly virus was circulating in neighboring Guangdong Province, propagating a disease that had no name but which was preliminarily dubbed atypical pneumonia in China and later renamed Severe Acute Respiratory Syndrome, or SARS, by the World Health Organization. And now it's been identified by all the other laboratories." 76 Also, just as Hong Kong University publicized its breakthrough before the CDC's announcement, so the university was able to get its scientific discovery into print first, with the publication of a paper in the online Lancet on April 8, 2003, "Coronavirus as a possible cause of severe acute respiratory syndrome." The success was very much the result of a group effort, as the list of authors shows, with Malik Peiris as the lead writer, K.Y. Yuen as the last writer and others, including Guan Yi, Leo Poon, John Nicholls and K.H. Chan, in between. cache = ./cache/cord-016160-ugc7ce21.txt txt = ./txt/cord-016160-ugc7ce21.txt === reduce.pl bib === id = cord-023867-ti4b03lh author = Zuo, Wei title = SARS Coronavirus and Lung Fibrosis date = 2009-07-22 pages = extension = .txt mime = text/plain words = 4277 sentences = 244 flesch = 51 summary = The mechanisms by which SARS-CoV infection causes lung fibrosis are not fully understood, but transforming growth factor-β (TGF-β) and angiotensin-converting enzyme 2 (ACE2)-mediated lung fibrosis are among the most documented ones. Therefore, SARS-CoV infection may lead to lung fibrosis through multiple signaling pathways and TGF-β activation is one of the major contributors. ACE2 proteins are expressed by alveolar epithelial cells, the primary targets of SARS-CoV in lung. Altogether, infection with SARS-CoV results in ACE2 downregulation through the binding of SARS-CoV spike protein to ACE2, and this spike protein-mediated ACE2 downregulation is responsible for the pathogenesis of lung fibrosis by upregulating ANG-II and activating TGF-b signaling. Both the TGF-b/Smad and the ACE2/ANG-II/CTGF pathways contribute to myofibroblast activation and ECM accumulation, collectively leading to the final lung fibrosis Role of extracellular signal-regulated kinase, p38 kinase, and activator protein-1 in transforming growth factor-beta 1-induced alpha smooth muscle actin expression in human fetal lung fibroblasts in vitro Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling cache = ./cache/cord-023867-ti4b03lh.txt txt = ./txt/cord-023867-ti4b03lh.txt === reduce.pl bib === id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 pages = extension = .txt mime = text/plain words = 19585 sentences = 1132 flesch = 36 summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. cache = ./cache/cord-016990-ot1wi3xi.txt txt = ./txt/cord-016990-ot1wi3xi.txt === reduce.pl bib === id = cord-023463-vr6uaw3a author = Liu, Wei title = Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date = 2009-06-05 pages = extension = .txt mime = text/plain words = 3859 sentences = 180 flesch = 47 summary = Objective To evaluate possible severe acute respiratory syndrome (SARS) infection associated risk factors in a SARS affected hospital in Beijing by means of a case control study. Results Multivariate analysis confirmed the strong role of performing chest compression (or intubation, which is highly correlated), contact with respiratory secretion, and emergency care experience as risk factors to acquire SARS infection. Measures to prevent nosocomial infection included establishing isolation wards for triage SARS patients; training and monitoring hospital staff in infection-control procedures; active and passive screening of HCWs; enforcement of droplet and contact precautions; and compliance with the use of PPE. In summary, this study identified exposure to high-risk procedures (such as chest compression), and contact with respiratory secretions to be significant risk factors for SARS infection among HCWs in a hospital in Beijing. cache = ./cache/cord-023463-vr6uaw3a.txt txt = ./txt/cord-023463-vr6uaw3a.txt === reduce.pl bib === === reduce.pl bib === id = cord-014938-7evmiuv5 author = Wei-ming, Yan title = Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model date = 2008-01-13 pages = extension = .txt mime = text/plain words = 1092 sentences = 64 flesch = 43 summary = title: Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model To evaluate the role of murine fibrinogen like protein 2 (mfgl2) /fibroleukin in lung impairment in Severe acute respiratory syndrome (SARS), a murine SARS model induced by Murine hepatitis virus strain 3 (MHV-3) through trachea was established. In a separate experiment, tissues including lungs, spleen, liver, kidneys, intestine, heart, brain were collected at a series of time points from Balb/cJ mice infected with MHV-3 through trachea. Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung The clinical pathology of severe acute respiratory syndrome (SARS): a report from China Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR A novel coronavirus associated with severe acute respiratory syndrome cache = ./cache/cord-014938-7evmiuv5.txt txt = ./txt/cord-014938-7evmiuv5.txt === reduce.pl bib === id = cord-018057-p1l6xtsq author = Ruan, Li title = SARS Epidemic: SARS Outbreaks in Inner-land of China date = 2008 pages = extension = .txt mime = text/plain words = 7509 sentences = 359 flesch = 49 summary = Since 2002, SARS has broken out three times: the first epidemic spread worldwide from November 2002 to July 2003 (WHO, 2004) ; the second spread locally in Guangdong province between December 2003 and February 2004 (Liang et al., 2004) ; and the third developed on a small scale from laboratory infection in the inner-land of China from March to April 2004 (Ministry of Health, People's Republic of China, 2004) . A study in Guangdong found SARS cases among people, such as restaurant cooks and meat animal's vendors or purchasers, who had no history of contact with SARS patients but had been in contact with wild animals Peng et al., 2003; Yang et al., 2003 ; Leadership Group of SARS Prevention and Control in Beijing, Epidemiological features of severe acute respiratory syndrome in Beijing, 2003; Chinese Center for Disease Control and Prevention, 2003) . cache = ./cache/cord-018057-p1l6xtsq.txt txt = ./txt/cord-018057-p1l6xtsq.txt === reduce.pl bib === id = cord-022266-nezgzovk author = Henderson, Joan C. title = Tourism and Health Crises date = 2009-11-16 pages = extension = .txt mime = text/plain words = 7964 sentences = 394 flesch = 52 summary = Such situations and approaches to their resolution represent the subject of this chapter in which health risks when traveling and on arrival at destinations are considered, with a section devoted to infectious diseases affecting humans and animals and birds. Health is a major public and private concern in general and a key element in destination choice and visitor satisfaction, with individuals and the tourism industry likely to shun environments where there might be a risk to tourist well-being. Some studies have concluded that the health of as many as 50% of participants is impaired by the experience of international tourism (Dawood, 1989) and the rise in foreign travel has been accompanied by an increased incidence of disease, especially that of a tropical nature (Connor, 2005) . Some initiatives to minimize unnecessary dangers and avoid serious injuries in the fi eld of adventure tourism are operator accreditation schemes, strict health and safety rules, codes of conduct, staff training and the education and prior assessment of participants (Bentley and Page, 2001) . cache = ./cache/cord-022266-nezgzovk.txt txt = ./txt/cord-022266-nezgzovk.txt === reduce.pl bib === id = cord-017224-naromr0a author = McLeish, Caitriona title = Evolving Biosecurity Frameworks date = 2016-12-06 pages = extension = .txt mime = text/plain words = 6005 sentences = 257 flesch = 44 summary = The relationship between infectious disease and security concerns has undergone an evolution since the end of the Cold War. What was previously seen as two separate domains – public health and national security – have, through various events and disease outbreaks in the last 15 years, become intertwined and as a result biosecurity policies now need to address a spectrum of disease threats that encompass natural outbreaks, accidental releases and the deliberate use of disease as weapons. Calling it niche is not to say that bioterrorism had not been considered a security threat prior to 2001many commentators had noted the potential (see for example Stern, 1993; Tucker, 1996 Tucker, , 2000 Moodie and Roberts, 1997; Smithson and Levy, 2000) ; table top exercises had been conducted, domestic preparedness programmes initiated (Guillemin, 2011, p7) , and in countries such as the US, policy directives had been crafted that gave the highest priority to "developing effective capabilities to detect, prevent, defeat and manage the consequences of nuclear, biological or chemical materials or weapons use by terrorists" (United States, 1995) . cache = ./cache/cord-017224-naromr0a.txt txt = ./txt/cord-017224-naromr0a.txt === reduce.pl bib === id = cord-017903-92hnaiyc author = Cieslak, Theodore J. title = Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date = 2018-07-07 pages = extension = .txt mime = text/plain words = 7492 sentences = 335 flesch = 46 summary = These two facilities cared for seven Ebola virus disease (EVD) patients during the 2014-2016 outbreak, while another two were cared for at the National Institutes of Health's Special Clinical Studies Unit, which had also developed HLCC capability. First, patients harboring diseases caused by pathogens that require handling under BSL-4 conditions in the laboratory would seem to be obvious candidates for clinical management under HLCC conditions. Lujo virus, an Old World arenavirus closely related to Lassa, was first described in 2008 as the cause of a single outbreak of viral hemorrhagic fever involving five patients in Lusaka, Zambia, and Johannesburg, South Africa (the name, Lujo, derives from the two cities) [20] . It would seem prudent to manage patients potentially harboring such diseases under HLCC conditions when feasible and to handle their causative viruses in a BSL-4 laboratory. cache = ./cache/cord-017903-92hnaiyc.txt txt = ./txt/cord-017903-92hnaiyc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017070-05vlz5dn author = Dimitrov, Dimiter S. title = Human Monoclonal Antibodies Against HIV and Emerging Viruses date = 2008 pages = extension = .txt mime = text/plain words = 6662 sentences = 299 flesch = 38 summary = These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association cache = ./cache/cord-017070-05vlz5dn.txt txt = ./txt/cord-017070-05vlz5dn.txt === reduce.pl bib === === reduce.pl bib === id = cord-023888-w2sbyfy2 author = Beniac, Daniel R. title = Structural Molecular Insights into SARS Coronavirus Cellular Attachment, Entry and Morphogenesis date = 2009-07-22 pages = extension = .txt mime = text/plain words = 4349 sentences = 238 flesch = 57 summary = Receptor binding results in structural changes that have been observed in the spike molecule, and these appear to be the initial step in viral membrane fusion. However, despite the size differences, the SARS-CoV spike performs the same fundamental task in viral entry to the host cell as other smaller type 1 viral fusion proteins, such as the influenza hemagglutinin (HA) (~220 kD per trimer). This structural data has been modeled into a scheme to propose a mechanism for SARS-CoV spike-mediated membrane fusion (Figs. Our cryo-EM results show that it is possible for the spike to attach to three ACE2 receptors at once; this may serve to hold on to the host membrane like a tripod so as to accurately orientate the fusion core ( Fig. 3.7) . cache = ./cache/cord-023888-w2sbyfy2.txt txt = ./txt/cord-023888-w2sbyfy2.txt === reduce.pl bib === id = cord-021805-2j07zw6q author = Epstein, Jonathan H. title = Emerging Diseases in Bats date = 2018-09-28 pages = extension = .txt mime = text/plain words = 4160 sentences = 214 flesch = 50 summary = 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. cache = ./cache/cord-021805-2j07zw6q.txt txt = ./txt/cord-021805-2j07zw6q.txt === reduce.pl bib === id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 pages = extension = .txt mime = text/plain words = 19181 sentences = 1041 flesch = 43 summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. cache = ./cache/cord-022084-hap7flng.txt txt = ./txt/cord-022084-hap7flng.txt === reduce.pl bib === id = cord-017489-ftz9190a author = Richards, Guy A. title = Viruses in the Intensive Care Unit (ICU) date = 2005 pages = extension = .txt mime = text/plain words = 5792 sentences = 330 flesch = 44 summary = Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. cache = ./cache/cord-017489-ftz9190a.txt txt = ./txt/cord-017489-ftz9190a.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-024613-yump76qu author = Wu, Chunxing title = Recommendations for control and prevention of infections for pediatric orthopedics during the epidemic period of COVID-19 date = 2020-04-23 pages = extension = .txt mime = text/plain words = 3818 sentences = 273 flesch = 43 summary = Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares, for clinical practices of pediatric orthopedics according to the physicochemical properties of SARS-CoV-2. Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares for pediatric orthopedics, pediatric surgery and others. reCommendAtion formAtion proCeSS Given the high demand of patients for medical treatment and the need to protect medical staff from infectious diseases, a recommendation working group "Recommendation Formulating Team for Pediatric Orthopedic Infection controls during the Epidemic's Period of COVID-19" (including all authors) was formed to focus on relevant issues for protection of medical staff in pediatric surgery, pediatric orthopedics, infectious diseases department, anesthesiology department, and nursing department to hospital administrators. cache = ./cache/cord-024613-yump76qu.txt txt = ./txt/cord-024613-yump76qu.txt === reduce.pl bib === id = cord-024100-lk67yfrp author = Plewczynski, Dariusz title = In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening date = 2007-04-24 pages = extension = .txt mime = text/plain words = 2398 sentences = 135 flesch = 47 summary = Selected molecules having close structural relationship to a 2‐methyl‐2,4‐pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors. In this study, we exploited structural homologs of SARS-CoV protease co-crystallized with small molecules to explore opportunities for drug design of potential inhibitors for this therapeutic target enzyme. We have explored the use of structural information contained in PDB database for an in silico virtual drug discovery campaign using, as a case study, the main protease of SARS-CoV. Using this method, plausible inhibitors were generated as based only on the set of ligands from crystallized complexes of a protein Figure 1 : Two dimensional chemical structures presented in Table II: Plewczynski et al. The docking was performed on small molecules and short peptides extracted from protein-ligand complexes of the viral cysteine proteases of trypsin-fold. Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease cache = ./cache/cord-024100-lk67yfrp.txt txt = ./txt/cord-024100-lk67yfrp.txt === reduce.pl bib === id = cord-024317-w1ep0wq8 author = Ku, Zhiqiang title = Antibody therapies for the treatment of COVID-19 date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2215 sentences = 152 flesch = 47 summary = Here, we discuss some of the most active areas of developing strategies to treat COVID-19, focusing on approaches to generate neutralizing antibodies against SARS-CoV-2 for prophylactic and therapeutic treatment of COVID-19. SIGNIFICANCE: Development of SARS-CoV-2 neutralizing antibodies with the desired efficacy and safety profile is a critical part of the toolbox of therapies for the treatment of COVID-19. The spike protein of SARS-CoV-2 plays an essential role in virus entry into host cells and is a primary target of neutralizing antibodies 5, 9 (Figures 1C,D) . Two MERS-CoV neutralizing mAbs, G2 and 7D10, target the S1-NTD region and function by blocking spike protein interaction with the host receptor DPP4 47, 48 . In the monkey study, researchers found that rhesus macaques infected with SARS-CoV-2 through the intratracheal route had mild illness, and their lungs showed signs of pneumonia similar to those in humans with COVID-19 58 . cache = ./cache/cord-024317-w1ep0wq8.txt txt = ./txt/cord-024317-w1ep0wq8.txt === reduce.pl bib === id = cord-023510-gd4phncm author = Chuo, Hsin-You title = Theme Park Visitors’ Responses to the SARS Outbreak in Taiwan date = 2007-05-02 pages = extension = .txt mime = text/plain words = 5264 sentences = 230 flesch = 48 summary = 1. Can a significant discriminant function be developed to interpret the differences between respondents who did and did not visit theme parks during the SARS outbreak period in Taiwan on the basis of their personal characteristics? In addition to the information of respondents' general demographics, their patronage frequency in the last year and whether they visited theme parks in the period of the SARS outbreak, the question content also consisted of scale items to measure ''benefit sought,'' ''product involvement,'' and ''risk perception.'' Ten individual benefit scale items were derived from Pearce's (1993) Leisure Ladder Model for theme park visitors. Thus, on the one hand, whether or not the respondents visited theme parks during the SARS outbreak was adopted to be the dependant (criterion) variable; on the other, respondents' age, their patronage frequency in the last year, and the factors condensed from scale items of respondents' risk perception, benefit sought, and product involvement were adopted to be the independent variables (predictors) in the developing discriminant function. cache = ./cache/cord-023510-gd4phncm.txt txt = ./txt/cord-023510-gd4phncm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023875-5mu5ra29 author = Keng, Choong-Tat title = Molecular and Biochemical Characterization of the SARS-CoV Accessory Proteins ORF8a, ORF8b and ORF8ab date = 2009-07-22 pages = extension = .txt mime = text/plain words = 5219 sentences = 242 flesch = 49 summary = Epidemiological studies have revealed that the part of the viral genome that encodes for ORF8a and ORF8b showed major variations and the animal isolates contain an additional 29-nucleotide sequence which is absent in most of the human isolates. Although the mutations in the ORF8 region do not appear to have any adverse effect on the survival of the virus, it is conceivable that the ORF8a, ORF8b and ORF8ab proteins have different stabilities and/or functions, and hence would contribute differently to viral replication and/or pathogenesis in vivo. Since SARS-CoV grows well in cell culture, different groups also generated ORF8a and ORF8b specific antibodies in order to determine their expression during infection in vitro. As described above, the accessory proteins ORF8a and ORF8b are expressed during infection in vitro, but replacing them with ORF8ab does not affect SARS-CoV replication in cell culture or small animal models. cache = ./cache/cord-023875-5mu5ra29.txt txt = ./txt/cord-023875-5mu5ra29.txt === reduce.pl bib === === reduce.pl bib === id = cord-024080-eh3ztsv5 author = Dheda, Keertan title = Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date = 2020-04-17 pages = extension = .txt mime = text/plain words = 3953 sentences = 214 flesch = 44 summary = Recent data from infections in special contexts such as cruise liners (9) and in close contacts of COVID-19 patients (10) have demonstrated that SARS-CoV-2-specific RT-PCR may be positive in the early phase of the disease, and that viral shedding in the asymptomatic phase and in the early prodromal phase can be considerable. (19) This false negativity phenomenon may be due to several factors, including a low viral load below the detection limit of the assay, low sample volume or cellular mass during acquisition, sampling location (upper versus lower respiratory tract), sample degradation during transport or storage, sample processing methodology and the timing of sampling in relation to the stage of the disease (RT-PCR positivity may progressively increase during the course of the disease). In patients with more severe diseases, including those with lower respiratory tract infection, but also in individuals with mild disease, high viral loads can be detected often for several days after the resolution of symptoms. cache = ./cache/cord-024080-eh3ztsv5.txt txt = ./txt/cord-024080-eh3ztsv5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-022473-l4jniccw author = Wilder-Smith, Annelies title = As Travel Medicine Practitioner during the SARS Outbreak in Singapore date = 2009-11-16 pages = extension = .txt mime = text/plain words = 2887 sentences = 184 flesch = 71 summary = In the first week after our first cases, the WHO named the disease "SARS", and they sent out global alerts. In Singapore, the outbreak was initially only hospital based, but in April the news was out that SARS had affected a large vegetable market. The news of the death of Carlo Urbani, the Italian WHO doctor who was instrumental in the control of SARS in Vietnam, sent our hospital staff into depression. In total, we lost a total of five healthcare workers to SARS in Singapore: 2 doctors, 1 nursing officer, 1 nursing aide and 1 hospital attendant. Two to three weeks into the epidemic it became clear, that infection control measures were effective; no more new cases occurred amongst the staff of our hospital. The SARS outbreak in Singapore can be traced to the first imported case. New imported SARS cases therefore need not lead to major outbreaks if systems are in place to identify and isolate them early. cache = ./cache/cord-022473-l4jniccw.txt txt = ./txt/cord-022473-l4jniccw.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023865-6rafp3x3 author = Surjit, Milan title = The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date = 2009-07-22 pages = extension = .txt mime = text/plain words = 9210 sentences = 448 flesch = 45 summary = Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese's laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells cache = ./cache/cord-023865-6rafp3x3.txt txt = ./txt/cord-023865-6rafp3x3.txt === reduce.pl bib === === reduce.pl bib === id = cord-022776-fz7m177w author = Wong, S.F. title = Severe Acute Respiratory Syndrome and pregnancy date = 2003-12-22 pages = extension = .txt mime = text/plain words = 1463 sentences = 92 flesch = 56 summary = Severe Acute Respiratory Syndrome (SARS) has already had an enormous impact on society and medical practice but presents special problems in pregnancy. The following comments are based on the experience of those in Hong Kong caring for patients with SARS in pregnancy of which there have been 10 at the time of writing in May 2003. The risk of cross infection is particularly high at the time of vaginal or operative deliveries, especially when there is maternal viraemia. There have not been any fetal problems reported in the very few women given ribavarin in the second half of pregnancy 2,3 . Our own experience with SARS in Hong Kong is in keeping with the extra risk of pregnancy in viral illness. Therefore, it is tempting to recommend early delivery or termination of pregnancy in pregnant women who are seriously ill with SARS. cache = ./cache/cord-022776-fz7m177w.txt txt = ./txt/cord-022776-fz7m177w.txt === reduce.pl bib === id = cord-025794-ckrclrwz author = nan title = Mitteilungen der ÖGKJ date = 2020-06-02 pages = extension = .txt mime = text/plain words = 911 sentences = 133 flesch = 58 summary = Vom Roten Kreuz werden zusätzlich auch Kontaktpersonen von gesicherten SARS-CoV2 Fällen getestet, sodass diese gezielte Testung von Kindern als Kontaktpersonen die wahrscheinlichste Erklärung für die höheren Positivitätsraten in den behördlichen Angaben -verglichen mit den Daten allein aus den Kinderabteilungen -ist. Wenn eine Infektion ausgeschlossen werden kann, bedeutet dies für Mutter, Kind und auch das betreuende Personal eine enorme Erleichterung der Situation. Wenn die Mutter so krank ist, dass sie sich nicht selbst um das Kind kümmern kann, sollte das Neugeborene, nach Abwägung der individuellen Situation und den vorhandenen Optionen vor Ort, temporär von ihr getrennt und als Kontaktperson eines COVID-19-Falls eingestuft werden. Wenn eine Mutter (unabhängig von einem möglichen Verdacht auf SARS-CoV2-Infektion) sich entschieden hat, nicht zu stillen, ist es immer wünschenswert, dass das Neugeborene auf alle Fälle Kolostrum erhalten sollte. bei Einstufung als Verdachtsfall werden Mutter und Kind gemeinsam isoliert und wie jeder Isolationsfall den Richtlinien der Klinik entsprechend durch die Pflege betreut. cache = ./cache/cord-025794-ckrclrwz.txt txt = ./txt/cord-025794-ckrclrwz.txt === reduce.pl bib === id = cord-025119-201ac32t author = Salman, Saad title = Virtual screening of immunomodulatory medicinal compounds as promising anti-SARS-COV-2 inhibitors date = 2020-05-21 pages = extension = .txt mime = text/plain words = 3144 sentences = 162 flesch = 37 summary = Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Here, we analyzed different medicinal compounds using a virtual screening method to obtain promising inhibitors for these viral proteins that could be further utilized for SARS-COV-2 treatment. More than 300 medicinal compounds with immunomodulatory and antiviral activity were added to the Raccoon2 plugin of Autodock vina to perform virtual screening to obtain promising inhibitors for SARS-COV-2 proteins. This study aimed to obtain novel drug candidates that have the capability to interact with the active site of all of these viral proteins and should possess efficient pharmacokinetic profile with low toxicity to ensure safety during administration. • Docking interaction of immunomodulatory medicinal compounds library filtered six promising medicinal compounds against severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) viral proteins. cache = ./cache/cord-025119-201ac32t.txt txt = ./txt/cord-025119-201ac32t.txt === reduce.pl bib === id = cord-025129-ry85kv9q author = Kashyap, Uddip title = Enhanced Design of PPE Based on Electrostatic Principle to Eliminate Viruses (SARS-CoV-2) date = 2020-05-23 pages = extension = .txt mime = text/plain words = 3094 sentences = 178 flesch = 61 summary = In this work, we propose a sanitization procedure of the personal protective equipment (PPE), such as gloves and masks, before and after the use, by employing high voltage charge generator (30 kV) from a very low DC source of 5 V to eliminate the virus from the surface of PPE. The high electric field alters the induced dipole of the protein of the virus, causing permanent damage in terms of electroporation. The negative terminal of the high voltage output can be grounded, and the positive terminal is connected to a metallic layer with a coating of CNT or ablate nano-grooves with Lithography. However, in the current work, the step-up negative high voltage charge is grounded, and the positive charges are allowed to accumulate over the metallic surface. The high electric field alters the induced dipole of the protein of the virus (Sharp and Honig 1990) , causing permanent damage in terms of electroporation (Liu et al. cache = ./cache/cord-025129-ry85kv9q.txt txt = ./txt/cord-025129-ry85kv9q.txt === reduce.pl bib === id = cord-026340-2nf97zvc author = Singh, Ranjana title = Chloroquine: A Potential Drug in the COVID-19 Scenario date = 2020-06-07 pages = extension = .txt mime = text/plain words = 7542 sentences = 412 flesch = 55 summary = In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell's receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. cache = ./cache/cord-026340-2nf97zvc.txt txt = ./txt/cord-026340-2nf97zvc.txt === reduce.pl bib === id = cord-024614-6bu3zo01 author = Tang, Daxing title = Prevention and control strategies for emergency, limited-term, and elective operations in pediatric surgery during the epidemic period of COVID-19 date = 2020-03-26 pages = extension = .txt mime = text/plain words = 5846 sentences = 300 flesch = 43 summary = Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the "Technical Guidelines for the Prevention and Control of New Coronavirus Infection in Medical Institutions (First Edition)," 17 "Diagnosis and Treatment Plan on the New Coronavirus inflicted pneumonia (Sixth trial edition, revised)" 2 (both released by the National Health Commission of China), "Recommendations for the Prevention and Control of General Surgery in the Background of New Coronavirus Outbreak," 6 and other relevant latest reports, we propose the following control measures and practical strategies for pediatric surgery practice during the COVID-19 epidemic. cache = ./cache/cord-024614-6bu3zo01.txt txt = ./txt/cord-024614-6bu3zo01.txt === reduce.pl bib === id = cord-025980-85jbwmfv author = Iwasaki, Sumio title = Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date = 2020-06-04 pages = extension = .txt mime = text/plain words = 626 sentences = 42 flesch = 61 summary = We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in 76 patients including ten coronavirus disease 2019 (COVID-19) patients. Figure 1C shows To our knowledge, a few studies compared viral load between nasopharyngeal and saliva samples. The viral loads were 5-times higher in saliva than in nasopharyngeal samples in one study (5) , whereas they were lower in saliva in two studies (6, 8) . Our results showed that the viral load was equivalent at earlier time points but lower in saliva than in nasopharyngeal samples at convalescent phase. Saliva is more sensitive for SARS-CoV-2 detectionin COVID-19 patients than nasopharyngeal swabs. Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-025980-85jbwmfv.txt txt = ./txt/cord-025980-85jbwmfv.txt === reduce.pl bib === id = cord-026811-6bdzut3d author = Jha, Ashish K. title = Emerging Treatment and Prevention Strategies against COVID-19: A Brief Update date = 2020-05-16 pages = extension = .txt mime = text/plain words = 2684 sentences = 148 flesch = 45 summary = We have highlighted here the potential therapeutic role of remdesivir, chloroquine/ hydroxychloroquine (HCQ), lopinavir/ritonavir, and convalescent plasma in patients with SARS-CoV-2 infection. However, interpretation of the result of this study is limited by the lack of a randomized control group, small sample size, exclusion of serious cases (creatinine clearance <30 mL/min and >five-time elevation of serum aminotransferase), variable duration of remdesivir administration, noncollection of viral load data, adverse effects, and short-term follow-up. Early results obtained from more than 100 patients enrolled in studies conducted in the China showed the superiority of chloroquine compared with the controls in terms of reduction of exacerbation of pneumonia, duration of symptoms, and delay of viral clearance, all in the absence of severe side effects. A systematic review and exploratory meta-analysis from 32 studies of SARS coronavirus infection and severe influenza showed a statistically significant reduction in the pooled odds of mortality following treatment with convalescent plasma compared with placebo (odds ratio = 0.25; 95% confidence interval [CI]:0.14-0.45; I[2] = 0%). cache = ./cache/cord-026811-6bdzut3d.txt txt = ./txt/cord-026811-6bdzut3d.txt === reduce.pl bib === id = cord-024786-f33eb1nf author = van Rensburg, V title = Current evidence for directed and supportive investigational therapies against COVID-19 date = 2020-04-24 pages = extension = .txt mime = text/plain words = 4411 sentences = 279 flesch = 49 summary = Multiple trials across the globe are currently underway to assess the efficacy of CQ for the treatment and prevention of COVID-19, but no published, peer-reviewed results are available at the time of writing. [33] The rationale for the use of lopinavir/ritonavir (LPV/r) in COVID-19 stems from its in vitro activity against SARS-CoV-1, [34] as well as from a retrospective, multicentre cohort study evaluating LPV/r as early treatment in SARS-CoV-1, which demonstrated decreased mortality and intubation rates. [50] At the time of writing, there were no published peer-reviewed trials or case studies evaluating favipiravir in COVID-19, and its use is not currently recommended outside of clinical trials. A systematic review of treatment options in SARS-CoV-1 infection included corticosteroids' effects on mortality, in vitro inhibition of SARS viral replication and acute respiratory distress syndrome. Drugs that purportedly inhibit SARS-CoV-2 replication (such as the investigational antivirals) or viral entry and replication (CQ and HCQ) may therefore be more effective when given earlier in the COVID-19 disease course. cache = ./cache/cord-024786-f33eb1nf.txt txt = ./txt/cord-024786-f33eb1nf.txt === reduce.pl bib === id = cord-027499-mvqoarsh author = Navel, Valentin title = Coronavirus: good or bad news for ocular diseases? date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1395 sentences = 81 flesch = 44 summary = Even if SARS-CoV-2 involves conjunctivitis and external ocular infections, 12 there are not yet published data describing the effects of a reduction of air pollutants on the ocular surface during the quarantine period, and a putative decrease in some ocular complaints-individuals being at home and less exposed to pollens and atmospheric pollutants. 16 17 SARS-CoV-2 patients without any ocular symptoms could Open access Figure 1 The decrease of global air pollution following the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic (satellite images from NASA and European Space Agency). 22 In conclusion, even if individuals are less exposed to air pollutants and environmental allergens during quarantine weeks, SARS-CoV-2 seems to be a foe both for ophthalmologists-with a risk of infection through contact with eye secretions of patients-and for patients-with a delay in their medical management. SARS-CoV-2 in the ocular surface of COVID-19 patients cache = ./cache/cord-027499-mvqoarsh.txt txt = ./txt/cord-027499-mvqoarsh.txt === reduce.pl bib === id = cord-026111-pb3r74uq author = Thede, Christian title = Mögliche Therapiestrategien bei Covid-19-Erkrankungen mit chinesischen Arzneimitteln date = 2020-06-05 pages = extension = .txt mime = text/plain words = 7593 sentences = 1140 flesch = 61 summary = Abschließend werden vorläufige Behandlungsvorschläge mit chinesischen Arzneimitteln für das offenbar zentrale Dysharmoniemuster -eine Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) und der Transformation von Flüssigkeiten im Rahmen einer Akkumulation von humor ("Feuchtigkeit", shi) mit Toxischem − für die sich bei schweren Verläufen entwickelnde Pneumonie vorgestellt. Wie in den meisten anderen Rezepturen aus diesem Therapieprotokoll findet sich auch hier Ephedrae herba (Mahuang) in Kombination mit aromatischen Arzneien sowohl zur Elimination der Akkumulation von humor ("Feuchtigkeit", shi) als auch der Entfaltung des qi pulmonale (Qi des Fk "Lunge", feiqi). Obwohl das Krankheitsmuster "yidu" (Epidemisch-Toxisches) genannt wird, wird auch hier primär die Kombination von "Dekokt mit Ephedra, Prunus armeniaca, Gypsum und Glycyrrhiza" (Maxing shigan tang) mit aromatischen und diuretischen Arzneien zur Lösung der humor-Akkumulation ("Feuchtigkeit", shi) und somit der Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) eingesetzt. cache = ./cache/cord-026111-pb3r74uq.txt txt = ./txt/cord-026111-pb3r74uq.txt === reduce.pl bib === id = cord-026099-97luq10a author = Kok, J title = Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus date = 2020-06-05 pages = extension = .txt mime = text/plain words = 761 sentences = 42 flesch = 54 summary = title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus We reported that the sensitivity, specificity, positive predictive value (PPV) and negative predictive value of the AusDiagnostics RUO assay was 100%, 92.16%, 55.56% and 100%, respectively when compared to our RT-PCR assay. Even if the specificity of the AusDiagnostics RUO assay was 99% (i.e. a 1% false positive rate), given the current prevalence of COVID-19 infection in NSW of 0.84%, the calculated PPV of the assay would be 54.15%, which is concordant with our findings. Cohen et al also estimated false positive rates of up to 7% in commercial diagnostics assays detecting SARS-CoV-2 [Cohen] . Furthermore, false positive RT-PCR results have also been reported from commercial kits that have been contaminated with SARS-CoV-2 sequences [Bustin] . Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus cache = ./cache/cord-026099-97luq10a.txt txt = ./txt/cord-026099-97luq10a.txt === reduce.pl bib === id = cord-026806-pn4lwhr7 author = Zargar, Showkat Ali title = Gastrointestinal Endoscopy during COVID: Do Some, Leave Most date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1498 sentences = 91 flesch = 54 summary = Therefore, these guidelines cannot be applied uniformly all over India and more or less usual business can start with caveat of complete adherence to standard operating procedure of infectious control protocols in combination with adherence to social distancing, frequent hand washing, use of protective gears, and organization of endoscopy teams and space in green zones. Chinese data are testimony to the fact that in Wuhan, China-epicenter of COVID-19-that in the initial weeks HCWs accounted for large number of total cases which was significantly reduced following adherence to infectious control practices. The informed consent requires "detailed and transparent" discussion on issues as follows: (1) acquisition of infection by HCWs from asymptomatic COVID-19 patient and also patient may develop full-fledged infection in postprocedure period blaming the endoscopist; (2) chances of acquisition of infection despite of adherence to infectious control protocols; and (3) risks involved in postponing otherwise medically indicated, time-sensitive procedure and reasons for delaying it. cache = ./cache/cord-026806-pn4lwhr7.txt txt = ./txt/cord-026806-pn4lwhr7.txt === reduce.pl bib === id = cord-024989-0o6agnrc author = Li, Qihao title = Prediction and analysis of key protein structures of 2019-nCoV date = 2020-05-12 pages = extension = .txt mime = text/plain words = 3244 sentences = 172 flesch = 58 summary = Aim: The purpose of this study was to predict and analyze the structure and function of 2019-novel Coronavirus (nCoV) key proteins. Differential key protein structure analysis of 2019-nCoV Although some amino acids were inserted in two positions of nsp3 in orf1ab [23] , the insertion sites were in the nsp3b and nsp3c regions, which are mainly related to the binding reaction of nucleic acids. Back-mutating mutant amino acids to study the functional change of RBD of S protein In order to study the effect of interactional amino acid changes in 2019-nCoV-ACE2 binding region RBD, we mutated the changed three amino acid residues (Glu 470 , Gln 484 and Asn 487 ) within the RBD structure back to the original amino acids. • We elaborated the sequence and structure differences in each key protein of 2019-nCoV and other bat SARS coronaviruses (CoVs). cache = ./cache/cord-024989-0o6agnrc.txt txt = ./txt/cord-024989-0o6agnrc.txt === reduce.pl bib === id = cord-025251-evnfvc0l author = Nemunaitis, John title = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection: let the virus be its own demise date = 2020-05-26 pages = extension = .txt mime = text/plain words = 7308 sentences = 397 flesch = 38 summary = Herein we describe the rationale and potential of repurposing a dual plasmid, Vigil (pbi-shRNA(furin)-GM-CSF), now in Phase III cancer trials, for the treatment of and, in certain circumstances, enhancement of the immune response to SARS-CoV-2. A recent publication from Nankai University (Tianjin, China) on SARS-CoV-2 reported that genome sequence analysis revealed a section of genes that was not present in SARS-CoV that had a cleavage site similar to HIV and Ebola which carry viral proteins necessary for fusogenic activity of viral species to the human cell membrane. Another immunotherapeutic intervention would be to increase the pulmonary expression of GM-CSF, which, in vivo, redirects macrophages from an M1 state of activation to an M2 activation state and enhances expression of anti-inflammatory mediators and perhaps allow more time for patients to mount an effective immune response against SARS-CoV-2 [25] . Similar to SARS-CoV-2, alveolar epithelial cells are the primary target of influenza virus (IV) and are the first site of entry and support for viral propagation and replication. cache = ./cache/cord-025251-evnfvc0l.txt txt = ./txt/cord-025251-evnfvc0l.txt === reduce.pl bib === id = cord-027582-ygforvya author = Mermel, Leonard A. title = Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1420 sentences = 92 flesch = 47 summary = title: Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) Patients with coronavirus disease 2019 (COVID-19) infection may respiratory tract specimens positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) for several days while in isolation precautions or for several weeks after removal from isolation precautions. Thus, decisions regarding discontinuing isolation precautions for severely immunocompromised patients, or possibly those who are otherwise critically ill with COVID-19 infection, should be based on a high SARS-CoV-2 PCR cycle threshold. Are patients infectious if they previously had a COVID-19 infection, met criteria for removal from isolation precautions, and they have SARS-CoV-2 PCR-positive respiratory tract specimens over the next several weeks? cache = ./cache/cord-027582-ygforvya.txt txt = ./txt/cord-027582-ygforvya.txt === reduce.pl bib === id = cord-027309-8siz9rb8 author = Paul, Debjani title = Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2269 sentences = 136 flesch = 51 summary = The recent pandemic of COVID-19 caused by the novel coronavirus (SARS-CoV-2) has drawn attention to the need for developing rapid and accurate diagnostic tests. The widespread use of these immunodiagnostic tests in clinical settings, in spite of their shortcomings, emphasizes the need for developing rapid and point-of-care (POC) tests that are based on molecular diagnostics (i.e., tests that detect the viral RNA directly in a manner similar to RT-PCR). We believe we can build on our past experience with isothermal DNA amplification techniques and paperfluidic devices to develop an isothermal amplification-based molecular diagnostic test for COVID-19 that can be deployed more easily. The ID NOW COVID-19 assay from Abbott, which recently got an emergency use authorization (EUA) from the US government for clinical use, detects SARS-CoV-2 RNA using an isothermal amplification test and can enable a clinical decision in as early as 13 min (ID NOWTM Covid-19 2020). cache = ./cache/cord-027309-8siz9rb8.txt txt = ./txt/cord-027309-8siz9rb8.txt === reduce.pl bib === id = cord-026130-ki7bn67o author = Sharma, Anand Kumar title = Novel Coronavirus Disease (COVID-19) date = 2020-06-05 pages = extension = .txt mime = text/plain words = 5073 sentences = 330 flesch = 57 summary = In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. cache = ./cache/cord-026130-ki7bn67o.txt txt = ./txt/cord-026130-ki7bn67o.txt === reduce.pl bib === id = cord-027253-wfmm7naa author = Nag, Pooja title = Optical Fiber Sensors for Rapid Screening of COVID-19 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1710 sentences = 94 flesch = 45 summary = The article provides an overview of evanescent wave absorbance and localized surface plasmon resonance-based optic fiber platform for potential screening of COVID-19. Two alternative approaches for viral infection diagnostics are possible and practiced: the first involves serological investigations for measurement of elevated biomarker levels, for example, measurement of immunoglobin M (IgM) and immunoglobin G (IgG), while the second involves direct determination of the virus itself, utilizing its unique cellular proteins. This report explores the possible approaches of development of a point of care, low-cost evanescent wave absorbance (EWA)-based optical fiber sensor for quick and specific diagnosis of SARS-CoV-2. The wave is very sensitive to changes in refractive index at the interface and this property is utilized to develop EWA-based fiber optic sensors. While Fig. 3b has specific surface proteins (of the virus) immobilized on the optical fiber for detection of IgG and/or IgM (produced as an immune response). cache = ./cache/cord-027253-wfmm7naa.txt txt = ./txt/cord-027253-wfmm7naa.txt === reduce.pl bib === id = cord-026792-jsqa4pmu author = Samanta, Jayanta title = 2019 Novel Coronavirus Infection: Gastrointestinal Manifestations date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3792 sentences = 218 flesch = 51 summary = The modern world is facing a major public health crisis due to novel corona virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) which has caused a pandemic involving at least 210 countries. The extrapulmonary effects and modes of transmission gained attention when the first confirmed case of SARS-CoV-2 reported from the United States had gastrointestinal (GI) complaints of nausea and vomiting followed later by diarrhea and patient's fecal specimen tested positive on day 7 of illness. This review aims to comprehensively outline the GI manifestations of this virus, its potential to spread via the feco-oral route and its implications and an overview of management strategies for other GI diseases, such as inflammatory bowel disease (IBD) coexisting with coronavirus-19 disease (COVID-19) infection. cache = ./cache/cord-026792-jsqa4pmu.txt txt = ./txt/cord-026792-jsqa4pmu.txt === reduce.pl bib === id = cord-028711-zlj48aq7 author = Ridgway, Jessica P. title = Prolonged shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA among patients with coronavirus disease 2019 (COVID-19) date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1005 sentences = 88 flesch = 61 summary = Early reports from China indicate that severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA may persist in the respiratory tracts of patients with coronavirus disease 2019 (COVID-19) for several weeks after symptom onset. To estimate the duration of SARS-CoV-2 RNA shedding, we conducted a multisite study among patients who had nasopharyngeal specimens tested for SARS-CoV-2 RNA via real-time polymerase chain reaction (PCR) assay at Providence St Joseph Health (a 51-hospital healthcare organization based in Renton, Washington), University of Chicago Medicine in Chicago, Illinois, and NorthShore University HealthSystem (a 5-hospital healthcare system based in Evanston, Illinois). 4 Our findings that SARS-CoV-2 PCR tests remain positive for >3 weeks in most patients suggest that patients following the test-based strategy may remain on precautions for prolonged periods. It was a retrospective cohort study among patients with COVID-19 who underwent SARS-CoV-2 PCR testing at the discretion of their medical providers. Duration of SARS-CoV-2 RNA Detection No. of Days After 1 st Positive SARS-CoV-2 PCR Test cache = ./cache/cord-028711-zlj48aq7.txt txt = ./txt/cord-028711-zlj48aq7.txt === reduce.pl bib === id = cord-030870-ao5p3ra3 author = Paul, Suman title = Dynamics and risk assessment of SARS-CoV-2 in urban areas: a geographical assessment on Kolkata Municipal Corporation, India date = 2020-08-25 pages = extension = .txt mime = text/plain words = 6496 sentences = 323 flesch = 60 summary = Nearly 85% cases are reported from major cities of India and most interestingly, Mumbai, Delhi, Ahmedabad, Chennai, Thane, Pune, Kolkata become the most contributing urban centres to SARS-CoV-2 cases (as on 19 May, 2020). Further an attempt has also been made to quantify and assess the hotspot zones along with risks of the concentrated areas of Kolkata (one of the Metro city) for proper understanding of transmission of diseases in the congested and unhealthy places as a case study [9, 15, 16] . Based on socio-economic data of slum of Kolkata Municipal Corporation and containment zone data and containment zone data from different web sources we have selected the following indicators for quantity exposure, sensitivity and resilience for assessing the risk [22] infector disease like SARS-CoV-2 (see Table 1 ). As Kolkata has experienced 1st case of SARS-CoV-2, here we have taken ward wise containment zone to find out the nature of hot spots located in the Municipal area. cache = ./cache/cord-030870-ao5p3ra3.txt txt = ./txt/cord-030870-ao5p3ra3.txt === reduce.pl bib === id = cord-030654-8yxa1r1c author = Zhang, Changhui title = Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4281 sentences = 289 flesch = 62 summary = This structure was revealed to be a horseshoe-like tetramer, which may play an essential role in nsp9 oligomerization and in the regulation of viral nucleic acid binding during the replication of the virus. The initial structure solved by molecular replacement showed that six SARS-CoV-2 nsp9 protomers form an OB-fold cluster in an asymmetric unit ( Supplementary Fig. 1a ). To obtain more information about the protein interfaces and the likely biological assemblies of the OB-fold cluster, we calculated the structure of SARS-CoV-2 nsp9 using PDBe-PISA [27] . These three contact surfaces in interface I b/c contribute a hydrophobic base with eight hydrogen bonds and one salt bridge, making the SARS-CoV-2 nsp9 tetramer extremely stable in the crystal structure. In this present study, we observed the nucleic acid-binding ability of SARS-CoV-2 nsp9, using the electrophoretic mobility The molecules in these two interfaces are shown as cartoons and colored and labeled as in Fig. 2a . cache = ./cache/cord-030654-8yxa1r1c.txt txt = ./txt/cord-030654-8yxa1r1c.txt === reduce.pl bib === id = cord-026788-4d3r9rj8 author = Singla, Vikas title = Hepatobiliary and Pancreatic Manifestations of Coronavirus Disease 2019 date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1952 sentences = 133 flesch = 50 summary = The disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the Coronaviridae family. Drugs used to treat severe COVID-19 may cause liver injury and may have an effect on the underlying disease activity. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has spread throughout the globe in a very short span of time, which is beyond the imagination of most of us. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in November 2002 and resulted in more than 800 deaths. Patients with decompensated liver disease may be more prone to infection by SARS-CoV-2 because of underlying immunocompromised state, and the disease may be severe in these patients. In conclusion, SARS-CoV2 can cause hepatic and pancreatic injury, which is more common in patients with severe disease. cache = ./cache/cord-026788-4d3r9rj8.txt txt = ./txt/cord-026788-4d3r9rj8.txt === reduce.pl bib === id = cord-028363-7pmro8bu author = Tung-Chen, Yale title = Acute pericarditis due to COVID-19 infection: An underdiagnosed disease? date = 2020-07-10 pages = extension = .txt mime = text/plain words = 1427 sentences = 83 flesch = 51 summary = 4 Gradually a therapeutic scheme is being established that would include hydroxychloroquine and azithromycin 5 (or in other cases lopinavir/ritonavir) in the early stages of moderate disease that does not require treatment in ICU (Intensive Care Unit) but given the analytical indication (elevation of ddimer) and imaging (thrombosis in CTPA) in many cases, should be evaluated the early inclusion of low molecular weight heparin (LMWH) at doses of at least high-risk prophylaxis in all these patients without thrombopenia <20,000 platelets or acute bleeding and manifesting high d-dimer. 5 In another study, 83 patients with severe and critical COVID-19 infection underwent a CT scan, 6 chest pain was reported in 6% of the patients and pericardial effusion was found in 4.8%, which suggests that acute pericarditis could be an under diagnosed pathology, and therefore, not correctly managed and treated. This is the first case report to describe an acute pericarditis episode due to SARS-CoV-2, which might be an under diagnosed condition in this pandemic, and therefore not correctly managed. cache = ./cache/cord-028363-7pmro8bu.txt txt = ./txt/cord-028363-7pmro8bu.txt === reduce.pl bib === id = cord-025623-1v9614f8 author = Mahapatra, Pallab Sinha title = Surface Treatments to Enhance the Functionality of PPEs date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2039 sentences = 131 flesch = 48 summary = This paper focuses on improving PPE functionality in a scalable manner by surface treatment and coating with appropriate materials and other functional enhancements, such as exposure to UV rays or other sterilizing agents (e.g., hydrogen peroxide). Surface treatments to enhance resistance against diseasecausing microbes, i.e., antimicrobial coatings, have the potential to improve PPE functionalities dramatically. Hydrophobic coatings make it difficult for droplets/particles to adhere on surfaces and are known to provide antimicrobial characteristics, which are retained after multiple washes; antibacterial and antifungal properties were demonstrated by Mukherjee et al. Klibanov's group at MIT has shown extended functionality of hydrophobic coating characteristics against influenza viruses, which get transmitted through respiratory droplets, like SARS-CoV-2; Halder et al. Scalable surface treatment strategies that combine antiviral action with liquid-repelling properties are one of many possible approaches to enhance the functionality of PPEs, thereby serving to satisfy their high demand in the healthcare industry and other fronts where the COVID-19 pandemic is being fought. cache = ./cache/cord-025623-1v9614f8.txt txt = ./txt/cord-025623-1v9614f8.txt === reduce.pl bib === id = cord-029547-9ei1ram3 author = Li, Jingwei title = The epidemiology and therapeutic options for the COVID-19 date = 2020-05-28 pages = extension = .txt mime = text/plain words = 7841 sentences = 499 flesch = 48 summary = According to the Diagnosis and Treatment Program of Novel Coronavirus Pneumonia, only a suspected case has one of the pieces of evidence of etiology or serology, such as positive nucleic acid, confirmation of gene sequencing, and virus specific antibody, to be confirmed to be COVID-19 patient, 55 and the suspected cases were identified by a comprehensive analysis of epidemiological history and clinical manifestations. 64 There have been tens of clinical trials to confirm the safety and efficiency of chloroquine in treating COVID-19 patients, and its mechanism can be described as interfering with the glycosylation of ACE2 or alkalizing the phagolysosome to inhibit viral replication, 65, 66 which prevents the SARS-Cov-2 entering the host cells. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial cache = ./cache/cord-029547-9ei1ram3.txt txt = ./txt/cord-029547-9ei1ram3.txt === reduce.pl bib === id = cord-027649-6xn9swsq author = Addetia, Amin title = Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates date = 2020-06-23 pages = extension = .txt mime = text/plain words = 449 sentences = 47 flesch = 52 summary = title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates Sequence reads were trimmed using Trimommatic v0.38 (5) , aligned to the SARS-CoV-2 reference genome (NC_045512.2) using BBMap (https://sourceforge.net/projects/bbmap/), trimmed of synthetic PCR primers using Primerclip (https://github.com/swiftbiosciences/primerclip) if appropriate, and visualized in Geneious v11.1.4 (6) . Interestingly, ORF6 of SARS-CoV-2 interacts with the mRNA export proteins NUP98 and RAE1, and may inhibit cellular translation (10) . We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization An 81 nucleotide deletion in SARS-CoV Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein A SARS-CoV-2 protein interaction map reveals targets for drug repurposing A 227-nucleotide deletion beginning at nt 27,524 was identified in b) WA-UW-5812 and resulted in the fusion of ORF7a and ORF7b. cache = ./cache/cord-027649-6xn9swsq.txt txt = ./txt/cord-027649-6xn9swsq.txt === reduce.pl bib === id = cord-026803-p1o4qc1h author = Maddury, Jyotsna title = Need of the Hour— COVID-19 for Cardiologists date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1671 sentences = 111 flesch = 46 summary = The most distressing pandemic at present is coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial studies showed low association of chronic cardiac diseases (10%) in COVID-19 patients along with the acute cardiac injury accounting to 23%. These reports with new information urge cardiologists to warn patients about the potential risk and encourage them to practice "additional, reasonable precautions" for those with underlying heart disease. As SARS-CoV-2 and MERS-CoV have similar pathogenicity, myocardial injury caused due to SARS-CoV-2 infection may be immune mediated through the ACE2 receptor or cytokine storm and/or hypoxia due to acute respiratory distress syndrome (ARDS). As there is an increased risk of secondary infections with COVID-19, patients are advised to remain current with vaccinations, including the pneumococcal vaccine and influenza vaccine in accordance with current ACC/American Heart Association (AHA) guidelines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges cache = ./cache/cord-026803-p1o4qc1h.txt txt = ./txt/cord-026803-p1o4qc1h.txt === reduce.pl bib === id = cord-028525-0ckagrt1 author = Yung, Chee Fu title = Household Transmission of SARS-CoV-2 from Adults to Children date = 2020-07-04 pages = extension = .txt mime = text/plain words = 1706 sentences = 89 flesch = 56 summary = Beginning on March 5, because of concern that infected children might not display symptoms, the Ministry of Health Singapore implemented screening for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction from nasopharyngeal swabs for all pediatric household contacts (regardless of symptoms) of persons with laboratory-confirmed COVID-19. During March and April, among 137 households with a total of 223 adults (index patients) with laboratory-confirmed COVID-19, 213 children aged ≤16 years were tested for SARS-6 CoV-2; 13 cases were detected in seven households, for an attack rate of 6.1% among children and 5.2% of households with confirmed exposure to COVID-19 (Table) . Based on systematic surveillance and screening of children who were household contacts of persons with confirmed COVID-19, the attack rate of SARS-CoV-2 infection in children was 6.1%. The low attack rate suggests that strict compliance with infection control may be able to eliminate or reduce the risk of transmission from adults to children in household settings. cache = ./cache/cord-028525-0ckagrt1.txt txt = ./txt/cord-028525-0ckagrt1.txt === reduce.pl bib === id = cord-027650-pl6qsojf author = Wang, Yijin title = SARS-CoV-2 infection in liver-Author’s reply date = 2020-06-23 pages = extension = .txt mime = text/plain words = 1065 sentences = 64 flesch = 40 summary = In light of the low percentage of hepatocytes expressing ACE2, but not absolute absence, it is not surprisingly that SARS-CoV-2 is capable of causing liver injury directly. It is therefore assumed that viral direct effect in liver might not operate absolutely through ACE2 expression, and other receptors could not be excluded. Alternatively, the finding of up-regulated ACE2 expression in hepatocytes in cirrhotic liver inspired us to speculate that SARS-CoV-2 infection might induce compensatory hyperplasia of hepatocytes, which are possibly derived from highly expressed ACE2 cholangiocytes [16] . All in all, our data fully support a direct role of SARS-CoV-2 in COVID-19 related hepatic impairment. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway cache = ./cache/cord-027650-pl6qsojf.txt txt = ./txt/cord-027650-pl6qsojf.txt === reduce.pl bib === id = cord-030420-pgdmz69j author = Brion, Luc P. title = Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date = 2020-08-13 pages = extension = .txt mime = text/plain words = 193 sentences = 21 flesch = 63 summary = key: cord-030420-pgdmz69j title: Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) cord_uid: pgdmz69j As consistent with Lamouroux's statement that ACE2 is low in the first trimester, ACE2 37 RNA expression is developmentally regulated with extremely low expression at 6-14 weeks, 38 although there is high expression at 24 weeks of gestation. 3 ACE2 RNA is highly expressed in 39 human villous, extravillous and syncytiotrophoblast as well as in several fetal organ cells (heart, 40 liver, and lung but not kidney) at 24 weeks of gestation. Evidence for and 65 against vertical transmission for SARS-CoV-2 (COVID-19) Clinical features of patients infected 69 with 2019 novel coronavirus in Wuhan The SARS-CoV-2 receptor ACE2 expression of 71 maternal-fetal interface and fetal organs by single-cell transcriptome study The expression and localization of 74 the human placental prorenin/renin-angiotensin system throughout pregnancy: roles in 75 trophoblast invasion and angiogenesis? Miscarriage in a Pregnant Woman With SARS-CoV-2 Infection cache = ./cache/cord-030420-pgdmz69j.txt txt = ./txt/cord-030420-pgdmz69j.txt === reduce.pl bib === id = cord-026528-1ozgabwk author = Chen, Zhe title = Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination date = 2020-06-09 pages = extension = .txt mime = text/plain words = 225 sentences = 26 flesch = 70 summary = key: cord-026528-1ozgabwk title: Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination cord_uid: 1ozgabwk We appreciate that Dr. Carosso brought up several important points about our paper, 16 which are worth discussing and clarifying. 17 We stated that we did not find SARS-CoV-2 in lower female genital tract and our 18 results may provide evidence to guide the choice of delivery method for COVID-19 19 pregnant women. However, a high incidence of cesarean sections was mentioned 22 by Dr. Carosso. It might result from concerns that SARS-CoV-2 exists in vagina. It 23 was a reasonable suspicion since SARS-CoV-2 had been identified in anal swabs, 24 urine, and tears in an early time. Review of the 2019 novel coronavirus 53 (SARS-CoV-2) based on current evidence Severe 58 COVID-19 during Pregnancy and Possible Vertical Transmission Severe Acute Respiratory Syndrome Coronavirus 2 63 (SARS-CoV-2) Vertical Transmission in Neonates Born to Mothers With 64 cache = ./cache/cord-026528-1ozgabwk.txt txt = ./txt/cord-026528-1ozgabwk.txt === reduce.pl bib === id = cord-030923-r0lfot3w author = Liu, Lixin title = Subunit Nanovaccine with Potent Cellular and Mucosal Immunity for COVID-19 date = 2020-08-18 pages = extension = .txt mime = text/plain words = 3704 sentences = 221 flesch = 57 summary = [Image: see text] To combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we formulated the S1 subunit of the virus with two adjuvants, amphiphilic adjuvant monophosphoryl lipid A for Toll-like receptor 4 and CpG oligodeoxynucleotide for Toll-like receptor 9, into cationic liposomes to produce a potent, safer, and translatable nanovaccine. NANOVACCINE MPLA/CpG-loaded liposome particle, p(M+C), was produced via a thin-film hydration approach by using cationic 1,2dioleoyl-3-trimethylammonium-propane (DOTAP), helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and cholesterol as carrier materials. Previous research on vaccines using the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) as the subunit showed that the antibodies could effectively prevent the coronavirus from binding to the cell and undergoing membrane fusion, neutralizing the virus during infection. Moreover, MPLA/CpG-loaded liposomes alone can be used as nanoparticulate adjuvants of a coronavirus vaccine with different antigens to enhance an innate immunity and thus a cellular immune response. cache = ./cache/cord-030923-r0lfot3w.txt txt = ./txt/cord-030923-r0lfot3w.txt === reduce.pl bib === id = cord-030535-8o7rzb98 author = Zhang, Sheng title = Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists date = 2020-08-12 pages = extension = .txt mime = text/plain words = 2718 sentences = 178 flesch = 59 summary = The tutorial begins with the X-ray crystallographic structure of the main protease (Mpro) of the SARS coronavirus (SARS-CoV) bound to a peptide substrate and then uses the UCSF Chimera software to modify the substrate to create a cyclic peptide inhibitor within the Mpro active site. In this tutorial, we will use the X-ray crystallographic structure of the homologous SARS-CoV M pro bound to a protein substrate to recapitulate the design of a cyclic peptide inhibitor of the SARS-CoV-2 M pro . 8 We will first use the molecular modeling software UCSF Chimera to visualize the X-ray crystallographic structure of the SARS-CoV M pro bound to the protein substrate. In structure-based drug design, we would typically now synthesize the cyclic peptide inhibitor and evaluate its activity experimentally through studying its ability to block the cleavage of a fluorogenic peptide substrate by SARS-CoV-2 M pro . cache = ./cache/cord-030535-8o7rzb98.txt txt = ./txt/cord-030535-8o7rzb98.txt === reduce.pl bib === id = cord-029419-b0w9nomq author = Matthews, Adam title = Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 3955 sentences = 186 flesch = 54 summary = Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to 'fix' ourselves and the planet, including new viral outbreaks. cache = ./cache/cord-029419-b0w9nomq.txt txt = ./txt/cord-029419-b0w9nomq.txt === reduce.pl bib === id = cord-028989-w50thois author = Figueira Gonçalves, Juan Marco title = Clinical challenges in chronic obstructive pulmonary disease in patients who suffered SARS-CoV-2 infection() date = 2020-07-10 pages = extension = .txt mime = text/plain words = 2005 sentences = 100 flesch = 44 summary = Reported complications of SARS-CoV-2 infection, such as extensive pneumonia/acute lung damage or adult acute respiratory distress syndrome, the occurrence of myocarditis/cardiac arrhythmias or the development of thromboembolic 2/7 episodes are events that may worsen the baseline condition of the COPD patient surviving the process, having to take into account their existence when planning their outpatient follow-up. Despite the lack of sufficient evidence at the moment, the results reported to date and the pathogenic mechanisms plausibly involved, make it advisable to consider this aspect in those patients with COPD who, after hospital discharge, develop in the medium to long term an increase in dyspnoea not justified by spirometric parameters. In the SARS-CoV-1 epidemic, some of the survivors developed avascular necrosis, pulmonary fibrosis, and dyslipidaemia after viral infection 15, 16 , which may have a relevant impact on those patients who already had some underlying respiratory or cardiovascular condition. cache = ./cache/cord-028989-w50thois.txt txt = ./txt/cord-028989-w50thois.txt === reduce.pl bib === id = cord-030254-eevqclsy author = Mehta, Chitra title = Management of Coronavirus 2019 date = 2020-04-24 pages = extension = .txt mime = text/plain words = 4032 sentences = 287 flesch = 56 summary = A suspected case has been defined as a patient with acute onset respiratory infection with fever, cough, sore throat, and an epidemiological link in the form of a history of travel 14 days prior to the onset of symptoms to countries afflicted with COVID-19, or a close contact with a confirmed or probable case of COVID-19 14 days prior to symptom onset, or some acute respiratory infection requiring hospitalization with no other etiology fully explaining the clinical presentation, as per WHO guidelines. • In patients with severe COVID-19 infection requiring supplemental oxygen, lopinavir/ritonavir combination plus hydroxychloroquine plus favipiravir 1,600 mg (eight tablets) twice daily as a loading dose followed by 600 mg (three tablets) every 8 hours for 14 days is being used. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical management of severe acute respiratory infection when COVID-19 disease is suspected. cache = ./cache/cord-030254-eevqclsy.txt txt = ./txt/cord-030254-eevqclsy.txt === reduce.pl bib === id = cord-029450-4rnrq78l author = Prattichizzo, Francesco title = Response to: Letter to the Editor on “Bonafè M, Prattichizzo F, Giuliani A, Storci G, Sabbatinelli J, Olivieri F. Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes. Cytokine Growth Factor Rev” by Eugenia Quiros-Roldan, Giorgio Biasiotto and Isabella Zanella date = 2020-07-18 pages = extension = .txt mime = text/plain words = 1570 sentences = 73 flesch = 45 summary = Preliminary data on an Italian cohort suggest that only a minor portion of HIV-positive patients with probable SARS-CoV-2 infection died, which yields a low case-fatality rate if compared to other highrisk populations [3] . Of note, the mean age of all the four HIV-positive cohorts was lower compared to other reports showing data of SARS-CoV-2 infection in the general population [7] . On the basis of the literature above, we posit that testing for T-cell senescence markers (e.g. PD-1, Tim-3, CTLA-4, and TIGIT) [9] and measuring major inflammatory markers in HIV-SARS-CoV-2 co-infected patients is mandatory to disentangle the relevance of immune senescence and inflamm-aging in the COVID-19 outcome in this specific population. A randomized controlled trial evaluating the efficacy of a triple antiviral therapy with combined interferon beta-1b, ribavirin, and lopinavir-ritonavir on COVID-19 patients proved the superiority of the triple antiviral therapy compared to lopinavirritonavir alone in terms of improved clinical recovery and faster rate of viral clearance, with a striking suppression of IL-6 levels in the interferon arm of the study after 48 hours of treatment [17] . cache = ./cache/cord-029450-4rnrq78l.txt txt = ./txt/cord-029450-4rnrq78l.txt === reduce.pl bib === id = cord-025948-6dsx7pey author = Maitra, Arindam title = Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date = 2020-06-04 pages = extension = .txt mime = text/plain words = 7218 sentences = 382 flesch = 56 summary = Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. We have initiated a study on sequencing of SARS-CoV-2 genome from swab samples obtained from infected individuals from different regions of West Bengal in Eastern India and report here the first nine sequences and the results of analysis of the sequence data with respect to other sequences reported from the country until date. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. We have also detected emergence of mutations in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. cache = ./cache/cord-025948-6dsx7pey.txt txt = ./txt/cord-025948-6dsx7pey.txt === reduce.pl bib === id = cord-029167-bq6ogxyq author = Sarada, B. V. title = Fight Against COVID-19: ARCI’s Technologies for Disinfection date = 2020-07-14 pages = extension = .txt mime = text/plain words = 2831 sentences = 137 flesch = 47 summary = In this context, ARCI has quickly made efforts to develop disinfection systems including a UVC-based disinfection trolley, honeycomb air heater and a fogging chamber using UVC germicidal lamps, dry heat sterilization and HOCl-based chemical disinfectant to provide rapid and effective inactivation of microorganisms causing the pandemic. Though the virus survives as aerosols and on environmental surfaces for various durations of time, it can easily be inactivated by several types of physical and chemical disinfection methods (Mackenzie 2020) including UVC disinfection (Malayeri et al. Physical, dry heat and chemical disinfection methods have been developed by using UVC lamps, honeycomb air heater and HOCl fogging system, respectively. (MIL), has co-developed a UVC disinfection trolley to fight against COVID-19 by a simple physical process where rapid cleaning is possible within few minutes especially in hospital settings avoiding the use of harsh chemicals. cache = ./cache/cord-029167-bq6ogxyq.txt txt = ./txt/cord-029167-bq6ogxyq.txt === reduce.pl bib === id = cord-033406-xoyt7esk author = Wen, Wen title = Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient date = 2020-09-11 pages = extension = .txt mime = text/plain words = 358 sentences = 30 flesch = 58 summary = title: Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient The patient presented to Anqing Municipal Hospital (Anhui province) with a positive result on nasopharyngeal swabs for SARS-CoV-2 and discharged in good clinical condition after consecutive negative results On February 9, 2020. 3 In our report, the patient recovered from COVID-19 and developed a lung infection with GGO 82 days later after being discharged from hospital. This study is part of the project of "Construction of a bio-information platform for novel coronavirus pneumonia Chest computed tomography show completely absorbed lesion when he was discharged on May 28, 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing cache = ./cache/cord-033406-xoyt7esk.txt txt = ./txt/cord-033406-xoyt7esk.txt === reduce.pl bib === id = cord-031061-48xwfr9i author = Abdullah, Abdullah title = Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 date = 2020-08-16 pages = extension = .txt mime = text/plain words = 2530 sentences = 153 flesch = 43 summary = title: Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 The convalescent sera of the recovered COVID-19 patients are containing antiviral neutralizing antibodies and is used therapeutically for infected individuals by SARS-CoV-2 and for the purpose of prophylaxis in exposed individuals. Three SARS-CoV-1 infected patients were treated with 500ml of convalescent sera, the reduction in viral titer and mortality were recorded (39) . Three MERS infected patients were also treated with Convalescent or Passive antibody therapy, two of them produce nAbs and remaining one not (40) , this study highlights the limitation in using of convalescent sera it means that the recovered individual may not have enough titer of nAbs (41) . The available information on the use of convalescent sera or passive immunization for the treatment of SARS-CoV-2 suggests that early administration of convalescent serum reduces viral abundance and was found safe. cache = ./cache/cord-031061-48xwfr9i.txt txt = ./txt/cord-031061-48xwfr9i.txt === reduce.pl bib === id = cord-030999-27wennun author = Altmann, Daniel M title = Adaptive immunity to SARS-CoV-2 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 4374 sentences = 191 flesch = 42 summary = The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. Since many key questions about durability of the antibody response and about correlates of protection have been hard to address in this short timeframe, there has been value in recourse to the coronavirus immunology literature, especially in relation to SARS and MERS [16] [17] [18] [19] . Experience to date with SARS-CoV-2 suggests that this may not prove to be an infection that throws up insurmountable confounders to vaccine design-approaches that can safely and durably elicit neutralizing antibody look likely to work. Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals cache = ./cache/cord-030999-27wennun.txt txt = ./txt/cord-030999-27wennun.txt === reduce.pl bib === id = cord-032222-i6gfp4me author = Xue, Ling title = A quick look at the latest developments in the COVID-19 pandemic date = 2020-09-10 pages = extension = .txt mime = text/plain words = 2867 sentences = 206 flesch = 49 summary = Later, the Coronavirus Study Group of the International Committee on Taxonomy of Viruses formally named this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is a novel coronavirus, and an effective vaccine has yet to be developed. 51 A recombinant adenovirus type 5 vector vaccine, developed by Chen Wei's team, showed good safety and immunogenicity in a phase I clinical trial, rapidly inducing both humoral and T-cell responses against SARS-CoV-2 in most participants. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia cache = ./cache/cord-032222-i6gfp4me.txt txt = ./txt/cord-032222-i6gfp4me.txt === reduce.pl bib === id = cord-031289-uxoz0xhk author = Coccolini, Federico title = SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients date = 2020-05-18 pages = extension = .txt mime = text/plain words = 1326 sentences = 98 flesch = 51 summary = title: SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients The present article represents the very first positive result describing the presence of the virus in peritoneal fluid during an emergency surgical procedure in a COVID-19 sick patient. Interestingly, the nasal swab contained less SARS-CoV-2 RNA virus compared to the viral fluid that scored positive in 2 targets out of 3. This indicates that the viral load in the peritoneal fluid was higher compared to the upper respiratory material and suggests that the surgical operation was indeed a procedure at risk of infection. As no information exist about the virus passage to peritoneal cavity and fluids, present data may suggest that potentially all people even those with mild to moderate respiratory symptoms by SARS-CoV-2 could present viral load in peritoneal fluid, thus increasing the exposure and contagion risks for the entire surgical staff.Peritoneal fluid contamination with blood of feces may interfere with the virus detection. cache = ./cache/cord-031289-uxoz0xhk.txt txt = ./txt/cord-031289-uxoz0xhk.txt === reduce.pl bib === id = cord-031079-9lxhvyyb author = Chen, Li title = The effects of chloroquine and hydroxychloroquine on ACE2 related coronavirus pathology and the cardiovascular system: An evidence based review date = 2020-07-27 pages = extension = .txt mime = text/plain words = 5660 sentences = 354 flesch = 47 summary = CQ and HCQ may be potential inhibitors of SARS-CoV-2 entry into host cells, which is mediated via the angiotensin-converting enzyme 2 (ACE2), and may also inhibit subsequent intracellular processes which lead to COVID-19, including damage to the cardiovascular system. CQ and HCQ could potentially be useful drugs in the treatment of COVID-19 and other ACE2 involved virus infections, but the antiviral effects of CQ and HCQ need to be tested in more well-designed clinical randomized studies and their actions on the cardiovascular system need to be further elucidated. CQ and its more soluble and less toxic metabolite HCQ are primarily used for prophylaxis and treatment of malaria, but they have also been reported to effectively inhibit the effects of certain viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza A H5N. 40, 41 Several studies have reported that 3% to 29% of COVID-19 patients develop acute respiratory distress syndrome (ARDS) which is a common complication and cause of death as a result of SARS-CoV-2 infection. cache = ./cache/cord-031079-9lxhvyyb.txt txt = ./txt/cord-031079-9lxhvyyb.txt === reduce.pl bib === id = cord-032552-rjuug7er author = Umviligihozo, Gisele title = Sub-Saharan Africa preparedness and response to the COVID-19 pandemic: A perspective of early career African scientists date = 2020-07-08 pages = extension = .txt mime = text/plain words = 5927 sentences = 290 flesch = 46 summary = As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. cache = ./cache/cord-032552-rjuug7er.txt txt = ./txt/cord-032552-rjuug7er.txt === reduce.pl bib === id = cord-031818-lawd185l author = Rich, Robert Soler title = Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case() date = 2020-09-12 pages = extension = .txt mime = text/plain words = 973 sentences = 58 flesch = 48 summary = title: Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Letter to the Editor Expanded Mesenchymal Stem Cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case in Spain To the Editor: When the natural immune response does not control the replication of the SARS-CoV-2 coronavirus, it induces the production of macrophages and granulocytes with the consequent massive release of CD4 + T cells that produce IL-6 and other proinflammatory cytokines, resulting in lung tissue damage 1,2 . This challenge was faced by researchers from the University of Shanghai, intravenously infusing a suspension of mesenchymal cells (MSC), reporting rapid clinical, radiological and laboratory improvements, comparing them with those of the untreated control group 5 ; effects attributable to the massive release of anti-inflammatory and pro-regenerative cytokines from these cells that are trapped in the pulmonary capillaries. cache = ./cache/cord-031818-lawd185l.txt txt = ./txt/cord-031818-lawd185l.txt === reduce.pl bib === id = cord-033333-880jx1bt author = Salman, Saad title = In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3431 sentences = 226 flesch = 53 summary = The molecular docking was performed for these inhalers including human neutralizing S230 light chain-antibody (monoclonal antibodies [mAbs]), alpha-1-antitrypsin (AAT), short-palate-lung and nasal-epithelial clone-1-derived peptides (SPLUNC1) and dornase-alfa (DA) against spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to assess their inhibitory activity. Protein-protein interaction (PPI) of COVID-19 spike glycoprotein with alpha-1-antitrypsin (1atu), dornase-alfa (4AWN), angiotensin-converting enzyme-2 (ACE-2) (PDB ID:1R4L), human palate, lung and nasal epithelium clone protein (SPLUNC1) (4n4x) and human neutralizing the S230 light chain antibody was evaluated through HawkDock. We attempted to address this issue by analyzing a variety of protein/peptide-based inhalers/antimucolytic agents and previously utilized mAb (used in asthma) to observe their possible interaction with the SARS-CoV-2 spike protein. • Molecular docking analysis of protein/peptide-based inhalers revealed that the S230 light chain antibody and dornase-alfa demonstrated a strong affinity for SARS-CoV-2 spike protein. cache = ./cache/cord-033333-880jx1bt.txt txt = ./txt/cord-033333-880jx1bt.txt === reduce.pl bib === id = cord-029965-bt87kai8 author = Patel, Shailesh Kumar title = The kidney and COVID-19 patients – important considerations date = 2020-08-01 pages = extension = .txt mime = text/plain words = 1049 sentences = 78 flesch = 48 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily affects the lungs, however, this virus can also affect other organs such as intestine, kidney, heart, and brain [1] [2] [3] . Studies reporting albuminuria and haematuria in the COVID-19 patients along with the detection of viral RNA from the urine samples further support the potential tropism of the SARS-CoV-2 for the renal tissues [4, 12] . Therefore, along with clinical management for pneumonia, potential intervention to protect the kidneys from the virus tropism and cytokine storm must be considered to minimize the mortalities associated with acute renal failure (Figure 1 ). Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China cache = ./cache/cord-029965-bt87kai8.txt txt = ./txt/cord-029965-bt87kai8.txt === reduce.pl bib === id = cord-033901-itj6v1jl author = Syambani Ulhaq, Z. title = Recurrent positive SARS-CoV-2 RNA tests in recovered and discharged patients() date = 2020-10-17 pages = extension = .txt mime = text/plain words = 819 sentences = 66 flesch = 55 summary = The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic remains a global concern that requires a comprehensive approach to reduce rapid transmission, starting from case detection, inpatient care, as well as post-hospital management. However, concerns have risen over recent reports of increasing re-detectable positive (RP) SARS-CoV-2 RNA tests observed among recovered and discharged patients 1-2 . Aiming to summarize the current evidence, a meta-analysis was performed to estimate the prevalence of RP SARS-CoV-2 RNA tests among recovered patients, in addition to the days of RNA-positive conversion since last negative/discharge. A comprehensive literature search was conducted through an electronic database dated up to May 2020, with search terms such as "recovered/discharged patients", "coronavirus 2019/COVID-19", "SARS-CoV-2", "positive PCR" used in combination without language restriction. 1. Observational studies or case reports that described some RP SARS-CoV-2 RNA tests among recovered/discharged patients. Positive SARS-Cov-2 test in a woman with COVID-19 at 22 days after hospital discharge: A case report cache = ./cache/cord-033901-itj6v1jl.txt txt = ./txt/cord-033901-itj6v1jl.txt === reduce.pl bib === id = cord-034021-6h5h3zow author = Thede, Christian title = COVID-19 – Therapiemöglichkeiten mit chinesischen Arzneimitteln in der Akutphase und Rekonvaleszenz date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1599 sentences = 204 flesch = 46 summary = Wenngleich diese Berichte noch mit einer gewissen Vorsicht zu betrachten sind und die Ergebnisse erster kontrollierter randomisierter Studien zum Einsatz von CAM bei COVID-19 noch ausstehen, kann der Einsatz chinesischer Medizin eine Bereicherung des zur Zeit noch sehr kargen Spektrums an Therapiemöglichkeiten bei SARS-CoV-2-Infektionen darstellen. In der vorliegenden Arbeit sollen, basierend auf dem in China entwickelten Konsens zum dominierenden Krankheitsmechanismus und der daraufhin unter der Ägide der staatlichen Gesundheitsbehörden entwickelten Therapieprotokolle [5] , Therapieoptionen für ausgewählte Krankheitsphasen einer COVID-19-Erkrankung vorgestellt werden: zum einen für die Phase der beginnenden Pneumonie, also für spätambulante bis frühstationäre Stadien, und zum anderen für mögliche Entwicklungen nach überstandener Akuterkrankung, also poststationäre Stadien mit klinischen Problemen. Dazu gehören persistierende restriktive Ventilationsstörungen oder eine Fatigue-Symptomatik, die angesichts der zunehmenden Zahl von Personen, die eine COVID-19-Erkrankung durchgemacht haben, wachsende Bedeutung erlangen und für welche die etablierte Medizin bisher keine Lösungen gefunden hat. Während coronavirusassoziierte Fatigue-Symptomatik bisAngesichts der persistierenden SARS-CoV-2-Pandemie und noch immer mangelnder Therapieoptionen werden in der vorliegenden Arbeit Therapiemöglichkeiten mit chinesischen Arzneimitteln erörtert, die sich in ersten Beobachtungsstudien als Erfolg versprechend erwiesen haben. cache = ./cache/cord-034021-6h5h3zow.txt txt = ./txt/cord-034021-6h5h3zow.txt === reduce.pl bib === id = cord-032751-pmclolvh author = Head, Katharine J. title = A National Survey Assessing SARS-CoV-2 Vaccination Intentions: Implications for Future Public Health Communication Efforts date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5086 sentences = 305 flesch = 48 summary = Research Question 2: What are the SARS-CoV-2 vaccine behavioral intentions of adults in the U.S. when a health care provider recommends the vaccine? Importantly, because vaccine intent and/or need may be different for people who were previously infected with SARS-CoV-2 and perceived threat variables (discussed below) are usually only measured for future threats, only participants who answered "no" to the question "do you believe that you've had COVID-19" are included in the current study (n = 3,159). Step 3 of the hierarchical regression model, with all variables included, less education was associated with lower intent to receive a SARS-CoV-2 vaccine. The health belief variables that were significant in the full regression model were all positively associated with intent to receive a SARS-CoV-2 vaccine. cache = ./cache/cord-032751-pmclolvh.txt txt = ./txt/cord-032751-pmclolvh.txt === reduce.pl bib === id = cord-029813-o2uzcuai author = Rusconi, Stefano title = COVID-19: studying the global pandemic – foreword date = 2020-07-27 pages = extension = .txt mime = text/plain words = 2723 sentences = 131 flesch = 43 summary = This special issue of Future Virology contains nine articles on diverse aspects of the COVID-19 pandemic and its causative agent, SARS-CoV-2. The topics range from basic virology on coronavirus evolution and replication to identification of repurposed therapeutics for clinical testing to public health issues including the conundrums of asymptomatic viral transmission and risks to homeless populations. The Commentary by Parvez [1] briefly reviews the detection of SARS-CoV-2 RNA in fecal samples, including its persistence, and the finding of gastrointestinal complaints in a minority of hospitalized patients. While it is clear that this phytochemical has multiple pharmacological activities, as reviewed previously [10] , this in silico report does not provide biologic data on rutin's possible effects in SARS-CoV-2 infection. Detection of relatively high SARS-CoV-2 RNA loads in upper respiratory tract samples has been reported in both presymptomatic (late incubation period) and truly asymptomatic infected persons. Transmission and clinical characteristics of asymptomatic patients with SARS-CoV-2 infection cache = ./cache/cord-029813-o2uzcuai.txt txt = ./txt/cord-029813-o2uzcuai.txt === reduce.pl bib === id = cord-033311-e5axxrm1 author = Abenza Abildúa, M.J. title = Myopathy associated with serious SARS-CoV-2 infection() date = 2020-10-07 pages = extension = .txt mime = text/plain words = 831 sentences = 63 flesch = 49 summary = 1,2 Reports of neurological symptoms associated with the infection are increasingly frequent, and include cases of Guillain-Barré syndrome, stroke, intraparenchymal haemorrhage, and cerebral thrombosis. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] We present the case of a 45-year-old woman with no relevant history who was admitted to the ICU due to severe respiratory insufficiency secondary to bilateral pneumonia, with positive nasal swab PCR results for SARS-CoV-2; therefore, the patient met the World Health Organization criteria for COVID-19. The muscle study showed positive sharp waves at rest, reduced motor unit potential amplitude and duration, and no polyphasia, especially in the abductor digiti minimi and the tibialis anterior (Fig. 2) . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS-CoV2 infection: causality or coincidence? Guillain-Barré syndrome associated with SARS-CoV2 Patients with COVID-19 and neurological manifestations show indetectable SARS-CoV2 cache = ./cache/cord-033311-e5axxrm1.txt txt = ./txt/cord-033311-e5axxrm1.txt === reduce.pl bib === id = cord-033010-o5kiadfm author = Durojaye, Olanrewaju Ayodeji title = Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date = 2020-10-02 pages = extension = .txt mime = text/plain words = 8125 sentences = 375 flesch = 53 summary = RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Our current study took advantage of the availability of the SARS CoV main proteinase amino acid sequence to map out the nucleotide coding region for the same protein in the 2019-nCoV. The predicted secondary structure composition shows a high degree of alpha helix and beta sheets, respectively, occupying 45 and 47% of the total residues with the percentage loop occupancy at 8% regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology. cache = ./cache/cord-033010-o5kiadfm.txt txt = ./txt/cord-033010-o5kiadfm.txt === reduce.pl bib === id = cord-033592-j1c2brb4 author = Alvarez Bravo, G. title = Encefalitis anti-NMDA-R secundaria a infección por SARS-CoV-2 Anti–NMDA receptor encephalitis secondary to SARS-CoV-2 infection date = 2020-10-09 pages = extension = .txt mime = text/plain words = 1073 sentences = 73 flesch = 42 summary = Coronavirus disease 2019 (COVID-19), which is caused by infection with the SARS-CoV-2 coronavirus and has caused a global pandemic, presents a wide spectrum of manifestations ranging from asymptomaticity to severe infection causing systemic failure and death. We present the case of a patient with anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis secondary to SARS-CoV-2 infection. 3 In this case, we suspect that SARS-CoV-2 infection acted as a trigger for the onset of anti-NMDAR encephalitis. 4, 5 Identifying autoimmune phenomena in patients with COVID-19 has enabled us to detect some immune-mediated neurological conditions, such as Guillain-Barré syndrome, acute necrotising encephalitis, myelitis, limbic encephalitis, and multiple cranial neuropathy associated with SARS-CoV-2 infection. [6] [7] [8] This case illustrates the slow clinical progression of a patient with anti-NMDAR encephalitis and COVID-19. To our knowledge, this is the first case of anti-NMDAR encephalitis associated with COVID-19. cache = ./cache/cord-033592-j1c2brb4.txt txt = ./txt/cord-033592-j1c2brb4.txt === reduce.pl bib === id = cord-032928-m0awip9y author = Sobh, Eman title = Novel coronavirus disease 2019 (COVID-19) non-respiratory involvement date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4021 sentences = 242 flesch = 43 summary = Coronavirus disease 2019 (COVID-19) is caused by a novel single-strand ribonucleic acid (RNA) coronavirus known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 primary attacks the lower respiratory system causing viral pneumonia, but it may also affect the heart, gastrointestinal system, liver, kidney, and central nervous system leading to multiple organ failure [3] . Other researchers found elevated serum troponin levels in many patients infected with COVID-19, and it was associated with more severe disease and poor prognosis [21] . The mechanism behind acute myocardial injury caused by SARS-CoV-2 infection might be related to human angiotensin-converting enzyme 2 receptor (ACE2) [20] which are highly expressed in the heart [11] . The results of previous reports indicate that cardiac injury, arrhythmia, and venous thromboembolism should be considered in any suspected or confirmed COVID-19 case and the patient should undergo a prompt clinical evaluation. cache = ./cache/cord-032928-m0awip9y.txt txt = ./txt/cord-032928-m0awip9y.txt === reduce.pl bib === id = cord-031518-1w14wr0i author = Khodarahmi, Reza title = The ACE2 as a “rescue protein” or “suspect enzyme” in COVID-19: possible application of the “engineered inactive hrsACE2” as a safer therapeutic agent in the treatment of SARS-CoV-2 infection date = 2020-09-07 pages = extension = .txt mime = text/plain words = 4651 sentences = 190 flesch = 42 summary = The authors expressed that hrsACE2 can block early entry of SARS-CoV-2 infections in various host cells, especially alveolar epithelial type II cells, as a viral reservoir and stated that they cannot make any predictions with respect to the effect of the recombinant protein on the later stages of COVID-19 and, also, honestly mentioned the study limitations. Moreover, since ACE2 is expressed in various tissues including the heart, kidney tubules, the luminal surface of the small intestine and blood vessels [2] and references therein), SARS-CoV-2could also infect these tissues, so that clinically, SARS-CoV-2 has been found in the urine, and cardiovascular and renal dysfunctions have been reported for many patients with COVID-19. As mentioned above, patients with COVID-19 have significantly elevated levels of plasma angiotensin II compared to that of healthy individual and membrane-bound ACE2 (in addition to protecting from lung injury, based on its catalytic domain) is the critical in vivo SARS-CoV spike glycoprotein receptor. cache = ./cache/cord-031518-1w14wr0i.txt txt = ./txt/cord-031518-1w14wr0i.txt === reduce.pl bib === id = cord-033551-eojpkxz9 author = Shekh, Shamasoddin title = In silico allicin induced S-thioallylation of SARS-CoV-2 main protease date = 2020-09-16 pages = extension = .txt mime = text/plain words = 3910 sentences = 248 flesch = 54 summary = In the current report, using virtual screening methods, reactive sulfur species allicin is subjecting for covalent docking at the active site of SARS-CoV-2 M(pro) using PX-12 as a benchmark reference compound. Figure 1a shows the structure of SARS-CoV-2 M pro with free cysteine thiols and active site dyad residues. Figure 2b shows the formation of cysteine allyl disulfide at the Cys-145 residue of SARS-CoV-2 M pro after covalent docking with allicin. Figure 4b and c show the formation of cysteine allyl disulfide at Cys-85 and Cys-156 residue of SARS-CoV-2 M pro after covalent docking with allyl sulfenic acid. Table-S2 provides a summary of covalent docking of allicin/PX-12/allyl sulfenic acid at cysteine thiols of four different co-crystal structures of SARS-CoV-2 M pro . Figure 5b shows the sulfur mediated hydrogen bonding by the sulfur of allyl disulfide formed after covalent docking of allicin at the active site of SARS-CoV-2 M pro . cache = ./cache/cord-033551-eojpkxz9.txt txt = ./txt/cord-033551-eojpkxz9.txt === reduce.pl bib === id = cord-033780-184e64tr author = Smith, Rasheid title = Implications of current and future approaches to coronavirus disease 2019 testing date = 2020-10-13 pages = extension = .txt mime = text/plain words = 3266 sentences = 154 flesch = 44 summary = The current reality is that SARS-CoV-2 is a highly transmissible airborne disease with a broad presentation of symptoms and leaves lasting damage in severe cases, and for which there is a scarcity of effective medications to treat it. Using the cycle threshold value in this manner only informs as to the presence of the virus and may not reveal disease progression, severity and viral load in the sample; and as such the results are largely qualitative despite the inherent quantitative nature of real-time RT-PCR [27] . Nevertheless, initial studies have demonstrated that chest CT imaging is more accurate than RT-PCR at detecting SARS-CoV-2 patients [32] with 97.2% versus 83% in the early stages of infection [33] . Immunoassays (antibody serum tests), such as enzyme-linked immunosorbent assays (ELISAs), are used to detect the presence of serum antibodies (either IgA, IgG or IgM) to viral proteins and can indicate when a person has developed an immune response to SARS-CoV-2. Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor cache = ./cache/cord-033780-184e64tr.txt txt = ./txt/cord-033780-184e64tr.txt === reduce.pl bib === id = cord-034354-4xu97je3 author = Wang, Hongye title = SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution date = 2020-10-21 pages = extension = .txt mime = text/plain words = 3678 sentences = 245 flesch = 53 summary = The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. Using the SARS-CoV-2 proteome microarray, we screened IgM and IgG antibodies in the serum of 10 COVID-19 patients who were in the early stage of infection (days of symptoms onset, 3.0 ± 5.92) (Supporting Information, Table S2 ) to construct a landscape of humoral responses to the SARS-CoV-2 proteome (Figure 2 ). Sixty-one (61) IgG and IgM antibody epitopes were identified in seven SARS-CoV-2 proteins (M, N, S, Orf1ab, Orf3a, Orf7a, and Orf8) with a Z-score higher than 3 in at least one COVID-19 patient (Table 1) . Furthermore, we constructed the first landscape of B-cell epitopes of serum IgM and IgG antibodies, representing the comprehensive antibody response of COVID-19 patients to SARS-CoV-2 infection (Figures 2−4) . cache = ./cache/cord-034354-4xu97je3.txt txt = ./txt/cord-034354-4xu97je3.txt === reduce.pl bib === id = cord-033244-u05rw6sk author = Ganesamoorthi, Arimanickam title = Non-availability of anesthesia scavenging system and decontamination of the outflow gas from the anesthesia machine during this COVID-19 pandemic date = 2020-10-06 pages = extension = .txt mime = text/plain words = 984 sentences = 57 flesch = 45 summary = The HMEF/HEPA filter can be connected to the AGS, even if the anesthesia machine ventilator is used for prolonged ventilation of critically ill patients, like an ICU ventilator when a shortage arises in this COVID-19 pandemic (COVID-19: Usage of Dräger anaesthesia devices for long-term ventilation dated 19 may 2020, 2020). Authors' contributions AG conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable and contributed to the writing and editing of the final version of the manuscript. ViVi conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable, and contributed to the review of literature, and writing and editing of the final version of the manuscript. cache = ./cache/cord-033244-u05rw6sk.txt txt = ./txt/cord-033244-u05rw6sk.txt === reduce.pl bib === id = cord-030934-t7akdu6x author = Bahrami, Afsane title = Genetic and pathogenic characterization of SARS-CoV-2: a review date = 2020-08-26 pages = extension = .txt mime = text/plain words = 6472 sentences = 356 flesch = 45 summary = The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. Bioinformatics analysis of the viral genome from one COVID-19 patient shared 89 and 82% sequence similarity with bat SARS-like-CoVZXC21 and human SARS-CoV, respectively [41] . In a recent report it was shown that SARS-CoV-2's S-protein entry into 293/human ACE2 receptor cells is primarily mediated via endocytosis, and that PIKfyve, a TPC2 and cathepsin L are crucial for virus entry. Findings of an open-label nonrandomized clinical trial among 22 infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in COVID-19 cases and its effectiveness is promoted by azithromycin [99] . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response cache = ./cache/cord-030934-t7akdu6x.txt txt = ./txt/cord-030934-t7akdu6x.txt === reduce.pl bib === id = cord-032811-sdbj26ca author = Hosoki, Koa title = Reply date = 2020-09-29 pages = extension = .txt mime = text/plain words = 666 sentences = 50 flesch = 52 summary = They suggest that suppression of angiotensin-converting enzyme-2 (ACE-2) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could impair the hydrolysis of des-Arg 9 -bradykinin and stimulate the bradykinin receptor type 1 (BKB1) pathway to induce leakage of fluid into the lungs. 4 However, other studies suggest that SARS-CoV-2 may upregulate the expression of ACE-2 in patients with coronavirus disease 2019 (COVID-19) or influenza pneumonia in alveolar epithelial cells, endothelial cells, and lymphocytes in perivascular tissue than in uninfected control autopsy lung. 7 We favor a third hypothesis, where excessive and prolonged secretion of type I and type III IFNs in the airways contributes to loss of lung epithelial barrier function during COVID-19 and other RNA virus infections (Fig 1, A) . Because IFN-l contributes to loss of lung epithelial barrier function, 8 we hypothesize that entry of SARS-CoV-2 via ACE-2 can stimulate secretion of IFN-l and induce leakage of fluid into the lungs (Fig 1, A) . cache = ./cache/cord-032811-sdbj26ca.txt txt = ./txt/cord-032811-sdbj26ca.txt === reduce.pl bib === id = cord-031001-x4iiqq5e author = Hou, Fan Fan title = Personnel protection strategy for healthcare workers in Wuhan during the COVID-19 epidemic date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2512 sentences = 127 flesch = 51 summary = DESIGN: During the COVID-19 pandemic, 943 healthcare staff sent from Guangzhou to Wuhan to care for patients with suspected/confirmed COVID-19 received infection precaution training before their mission and were equipped with Level 2/3 personal protective equipment (PPE), in accordance with guidelines from the National Health Commission of China. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53 out of 1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126 out of 2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53/1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126/2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively (Table 3) . cache = ./cache/cord-031001-x4iiqq5e.txt txt = ./txt/cord-031001-x4iiqq5e.txt === reduce.pl bib === id = cord-031497-pp0p3en6 author = Rodríguez-Fuster, Alberto title = Tracheal trauma in the context of the current infection by COVID-19. About 2 cases() date = 2020-09-06 pages = extension = .txt mime = text/plain words = 1153 sentences = 79 flesch = 53 summary = Various authors and scientific societies have recommended limiting the number of airway procedures and manipulations and introducing stringent protection measures for health personnel in order to minimize the risk of infection. [2] [3] [4] We report 2 cases of patients diagnosed with SARS-CoV-2 infection and tracheal iatrogenic rupture following airway manipulation. She required OTI + MV for respiratory failure, and during the procedure she incurred a tracheal lesion confirmed by computed tomography and fiberoptic bronchoscopy to be a rupture of the pars membranacea measuring approximately 2 cm. To minimize the risk of aerosols, the patient was maintained in complete muscle relaxation throughout the procedure; preoxygenation and ventilatory pauses-apneas-were performed (as far as possible) in accordance with the recommendations described for tracheotomy. Emergency tracheal intubation in 202 patients with COVID-19 in Wuhan, China: lessons learnt and international expert recommendations Tracheal trauma after difficult airway management in morbidly obese patients with COVID-19 cache = ./cache/cord-031497-pp0p3en6.txt txt = ./txt/cord-031497-pp0p3en6.txt === reduce.pl bib === id = cord-034481-zi9q96lj author = Liu, Yongjian title = Stability of SARS-CoV-2 on environmental surfaces and in human excreta date = 2020-11-01 pages = extension = .txt mime = text/plain words = 762 sentences = 54 flesch = 66 summary = Although close exposure to respiratory droplets from an infected patient is the main transmission route of SARS-CoV-2, touching contaminated surfaces and objects might also contribute to transmission of this virus. Here, we provide a report of our study of the stability of SARS-CoV-2 on various environmental surfaces and in human excreta (feces and urine). SARS-CoV-2 was more stable in urine than in feces, and infectious virus was detected up to 3 days in two adult urine and 4 days in one child urine. Prior to our study, two research teams had just reported the stability of SARS-CoV-2 on different material surfaces [4, 5] . In comparison with the above two studies, our data displayed a prolonged survival time of this virus on environmental surfaces. In Chin's study, a five microliters of virus stock with the infectious titer of 10 6.8 TCID 50 /ml was deposited on the surface. cache = ./cache/cord-034481-zi9q96lj.txt txt = ./txt/cord-034481-zi9q96lj.txt === reduce.pl bib === id = cord-033334-p7szd86k author = Mann, Jaclyn Kelly title = The potential of lactoferrin, ovotransferrin and lysozyme as antiviral and immune-modulating agents in COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 7284 sentences = 366 flesch = 33 summary = Enhanced phagocytic activity as well as cytokine production of macrophages Enhanced intestinal immune responses: dendritic cell maturation, Th1/Th2 balance restored and humoral immunity promoted [77, 78] Peptides Anti-inflammatory Downregulates IL-6 and TNF-␣ and myeloperoxidase activity in peritonitis Binds to angiotensin II receptor type 1 to inhibit angiotensin II pro-inflammatory activity ACE inhibitory activity (antihypertensive) [79] [80] [81] [82] Intact Iron-binding activity* Sequestering free iron [83] Intact and peptides Antioxidant* Sequestering free iron Free radical scavenging [79, 84] Lysozyme Intact and peptides Antiviral Inhibits viral entry by binding to cell receptors or virus -cationic and hydrophobic nature is required rather than enzymatic activity Binds nucleic acids Inhibits virus-induced cell fusion Affects cell signaling, including NF-B pathway, to influence susceptibility to infection [85] [86] [87] [88] Intact and/or peptides Antibacterial Hydrolyzes cell wall of gram-positive bacteria (enzyme activity) Insert into and form pores in negatively charged bacterial membranes [40] † Specific anticoronavirus activity has been demonstrated: inhibits SARS-CoV cell entry by binding to HSPGs; inhibits entry and postentry steps of SARS-CoV-2 replication and elevates interferon-stimulated genes in SARS-CoV-2-infected cells. cache = ./cache/cord-033334-p7szd86k.txt txt = ./txt/cord-033334-p7szd86k.txt === reduce.pl bib === id = cord-035026-2qcsfd87 author = Ugwueze, Chidiebere V. title = COVID-19 and Diabetes Mellitus: The Link and Clinical Implications date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5413 sentences = 329 flesch = 44 summary = The effect of glucocorticoids and catecholamines, invasion of the pancreatic islet cells, drugs used in the treatment of COVID-19, and the lockdown policy may impact negatively on glycemic control of diabetic patients. [40] showed that the clinical outcomes in COVID-19-positive patients with coexisting diabetes and hypertension who use ACE inhibitor or angiotensin II receptor blocker were comparable to those not using the drugs. A clinical trial (NCT04318418) was designed to determine the effect of ACE inhibitors and angiotensin II type 1 receptor blockers on the severity of COVID-19 infection [41] . Some authors have considered the rapidity of worsening glycemic control in stable diabetic patients with CO-VID-19 requiring the use of high insulin dose and suggested the possibility of pancreatic invasion by the SARS-CoV-2 [57, 58] . Once the entry of the virus is established, there is a downregulation of ACE2 receptor and a corresponding Ugwueze/Ezeokpo/Nnolim/Agim/ Anikpo/Onyekachi Dubai Diabetes Endocrinol J 6 DOI: 10.1159/000511354 activation of renin-angiotensin-aldosterone system, which is responsible for the cardiac and pulmonary complications of COVID-19 infection [75] . cache = ./cache/cord-035026-2qcsfd87.txt txt = ./txt/cord-035026-2qcsfd87.txt === reduce.pl bib === id = cord-035203-dnoc0xcv author = Vaňková, Eva title = Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5754 sentences = 290 flesch = 43 summary = Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. In the present study, we have investigated FDM 3D-printed PLA structure and porosity after exposure to common chemical disinfectants including ethanol, isopropanol and a commercial disinfectant containing sodium hypochlorite, which are easily accessible. In addition, we examined the efficiency of PLA disinfection after artificial contamination with bacteria (Staphylococcus epidermidis, Escherichia coli), a yeast fungus (Candida albicans), viruses (SARS-CoV-2 and human adenovirus -HAdV) or natural contamination by wearing the masks. The effect of immersing in three chemical disinfectants (96% ethanol, 70% isopropanol and the commercial disinfectant and bleach SAVO Original, Unilever ČR s.r.o., Czech Republic containing 0.85% sodium hypochlorite diluted with water (2:9)) was tested by repeated (5 × 15 min) cycles and long-term (24 h) exposure. Effect of ethanol, isopropanol and sodium hypochlorite on disinfection of PLA material contaminated with bacteria, yeast fungus or viruses cache = ./cache/cord-035203-dnoc0xcv.txt txt = ./txt/cord-035203-dnoc0xcv.txt === reduce.pl bib === id = cord-035163-tqh5wv12 author = Ijaz, M. Khalid title = Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date = 2020-09-08 pages = extension = .txt mime = text/plain words = 6841 sentences = 345 flesch = 46 summary = In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . cache = ./cache/cord-035163-tqh5wv12.txt txt = ./txt/cord-035163-tqh5wv12.txt === reduce.pl bib === id = cord-102364-t5bt2eb4 author = Yao, Dehui title = Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1852 sentences = 104 flesch = 54 summary = In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor. Antibodies targeting the spike glycoprotein of SARS-CoV and MERS-CoV, especially its receptor-binding domain (RBD), was found to efficiently neutralize virus infection [1, 2] . In this work, we engineered a human ferritin heavy chain (HFtn) by fusing and presenting the RBM of its spike glycoprotein as potential vaccine of SARS-CoV-2. cache = ./cache/cord-102364-t5bt2eb4.txt txt = ./txt/cord-102364-t5bt2eb4.txt === reduce.pl bib === id = cord-033951-77tfhm5b author = Ma, Chunlong title = Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors date = 2020-10-09 pages = extension = .txt mime = text/plain words = 6998 sentences = 428 flesch = 60 summary = In this study, we investigated the mechanism of action of six previously reported M(pro) inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. 31 Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin were recently reported as SARS-CoV-2 M pro inhibitors with IC 50 values ranging from 0.67 to 21.39 μM in the FRET-based enzymatic assay. Collectively, our results showed that in the absence of DTT, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 nonspecifically inhibit all six viral cysteine proteases including SARS-CoV-2 M pro . Collectively, the enzymatic assay results suggest that ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are promiscuous cysteine protease inhibitors that inhibit not only M pro but also five other related and unrelated viral cysteine proteases including SARS-CoV-2 PL pro and EV-A71 and EV-D68 2A pro and 3C pro in the absence of DTT, and the cache = ./cache/cord-033951-77tfhm5b.txt txt = ./txt/cord-033951-77tfhm5b.txt === reduce.pl bib === id = cord-029332-yn603pvb author = nan title = Full Issue PDF date = 2020-07-15 pages = extension = .txt mime = text/plain words = 11306 sentences = 633 flesch = 41 summary = Included are cases of Brugada type I pattern positivization (1) in the context of fever, one of the most common presenting symptoms of the disease (2); electrical ventricular storm (3); transient atrioventricular block in the absence of myocarditis (4); sinus node dysfunction requiring pacemaker implantation (5) ; and finally a provocative report on the use of amiodarone as a possible treatment for COVID-19 (6) . In addition to cases of direct myocardial injury, some with pathological evidence, we also present 2 cases of takotsubo cardiomyopathy (16, 17) Two cases highlight the special circumstances faced by patients with left ventricular assist devices (18, 19) , which include the inability to tolerate prone positioning to augment respiratory support because of the mechanical equipment and the hypothesis that mechanical circulatory support may provide a type of protection against the most serious hemodynamic consequences of severe acute respiratory syndrome coronavirus-2 infection. cache = ./cache/cord-029332-yn603pvb.txt txt = ./txt/cord-029332-yn603pvb.txt === reduce.pl bib === id = cord-035067-ic843wr9 author = de Almeida, Joana Ferro Machado title = COVID-19 and the gastrointestinal tract: what do we already know? date = 2020-11-05 pages = extension = .txt mime = text/plain words = 5453 sentences = 336 flesch = 56 summary = Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. Information on country of origin, mean age, different comorbidities, typical symptoms (fever, cough, and dyspnea, among others), gastrointestinal symptoms (diarrhea, nausea, vomiting, and abdominal pain), and the presence of viral RNA in feces, when cited, were included in this study for analysis. (19) According to the descriptive, cross-sectional, multicenter study (three hospitals in Hubei, China) by Pan et al., with 204 patients, in which 107 were male, mean age of 52.91±15.98 years, 103 (50.5%) reported some gastrointestinal symptom, such as lack of appetite (81; 78.6%), diarrhea (35; 34.0%), vomiting (4; 3.9%), and abdominal pain (2; 1.9%). (26) Cipriano et al., conducted a systematic review with six studies of patients from China, which points to the possibility of SARS-CoV-2 infection in the gastrointestinal tract and fecal-oral transmission. cache = ./cache/cord-035067-ic843wr9.txt txt = ./txt/cord-035067-ic843wr9.txt === reduce.pl bib === id = cord-102456-6jt4ksha author = Taylor-Cousar, Jennifer L. title = How I Do It: Restarting Respiratory Clinical Research in the Era of the COVID19 Pandemic date = 2020-11-13 pages = extension = .txt mime = text/plain words = 4068 sentences = 168 flesch = 35 summary = However, now that we have navigated the initial surge of SARS-CoV-2 cases, many are considering how to reintroduce non-COVID-19 clinical research conduct while protecting participants, staff and ensuring data integrity. Here we review key considerations and suggest a step-wise approach for resuming clinical research including observational research, registry trials, and interventional trials, as well as potential data confounding related to COVID-19 infections that are important to consider as research studies restart and data are analyzed. In the spirit of "Do No Harm", it is critical that institutional policies and processes are in place to ensure that there is no significant additional risk of contracting viral respiratory or other infections in the normal course of participation in research studies; now during the COVID-19 pandemic, these principles are even more critical. Throughout the subject's participation in clinical research during the pandemic, she expressed her appreciation for the opportunity to continue in the study from which she believed she was benefiting, with minimal risk of exposure to infection from SARS-CoV-2. cache = ./cache/cord-102456-6jt4ksha.txt txt = ./txt/cord-102456-6jt4ksha.txt === reduce.pl bib === id = cord-033204-v17d98c9 author = Yen, Wei‐Ting title = Taiwan’s COVID‐19 Management: Developmental State, Digital Governance, and State‐Society Synergy date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6583 sentences = 387 flesch = 53 summary = The country's success mainly lies in three factors: (1) reliance on the mask policy as the main disease prevention measure and the ability to quickly expand mask production capacity; (2) use of big data and technology to enhance effective implementation of disease prevention and detection measures; and (3) strong state‐society relations favoring transparency, communication, and collaboration. I then turn to the crisis management framework, discussing how the developmental state foundations and the democratic regime lead to Taiwan's success on mask policy, digital governance, and strong state-society collaboration and communication. Moreover, the capacity of a government to define and communicate the uncertainty the crisis brings is also an essential element in an effective response because collective sense-making can help increase citizens' voluntary compliance. Specifically, during COVID-19, digital governance helped improve disease detection through integrated databases of people's health records and travel history, through more accurate contact tracing, and through active surveillance tracking for people under quarantine. cache = ./cache/cord-033204-v17d98c9.txt txt = ./txt/cord-033204-v17d98c9.txt === reduce.pl bib === id = cord-035292-pan415s7 author = Elmessaoudi-Idrissi, Mohcine title = Structure-guided discovery approach identifies potential lead compounds targeting M(pro) of SARS-CoV-2 date = 2020-11-11 pages = extension = .txt mime = text/plain words = 1758 sentences = 125 flesch = 53 summary = Targeting the SARS-CoV-2 M(pro) crystal structure (PDB ID: 6LU7) a combination of in silico screening, molecular docking, and dynamic approaches, a set of 5000 compounds of the ZINC database were screened. As a result, we identified and ranked the top 20 compounds based on the scores of ligand-interaction, their drug-likeness properties, and their predicted antiviral efficacies. Taking the advantage of the main protease (M pro ) structure that became available recently [14] , we carried out a virtual in silico screening of nearly 5000 ZINC compound database to identify new inhibitors targeting the SARS-CoV-2. The docking simulations showed, by a ranking of binding energies score, that compound 2-[2-(2Fig. 1 Structure of SARS-CoV-2 main protease M pro . Based on our computational strategy, the pharmacokinetic properties and drug-likeness of the top 20 ranked scoring molecules that show the potential of M pro inhibitors of the SARS-CoV-2 are shown in supplementary table 1. cache = ./cache/cord-035292-pan415s7.txt txt = ./txt/cord-035292-pan415s7.txt === reduce.pl bib === id = cord-035157-97tfcgvq author = Panchin, Alexander Y. title = Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2803 sentences = 196 flesch = 57 summary = RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). SARS-CoV-2 is closely related to the bat coronavirus RaTG13 with around 96% whole genome nucleotide sequence identity . We compared the relative frequencies of single nucleotide variations (which we will refer to as mutations) in SARS-CoV-2 with the relative frequencies of substitutions that it acquired since the divergence with its last common ancestor with a closely related coronavirus from bats RaTG13. On the other hand, the substitution profile of SARS-CoV-2 turned out to be quite similar to that of the other coronaviruses, lending further support to existing scenarios of its natural origin (Andersen et al., 2020) and suggesting that the changes in SARS-CoV-2 mutation frequencies have accompanied its transition to human hosts. cache = ./cache/cord-035157-97tfcgvq.txt txt = ./txt/cord-035157-97tfcgvq.txt === reduce.pl bib === id = cord-102842-51n5mnjb author = Węglarz-Tomczak, Ewelina title = Ebselen as a highly active inhibitor of PLProCoV2 date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3320 sentences = 196 flesch = 56 summary = In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range. Here, we demonstrate that ebselen inhibits activity of the essential viral enzyme, namely, papain-like protease (PL pro ) from SARS-CoV-2 (PL pro CoV2) in low micromolar range. We applied ebselen as a possible inhibitor and, indeed, it suppresses PL Pro activity from CoV2 with inhibition constants approximately equal 2 μM (Table 1 and Figure 3 ). Our results were further illustrated by the use of molecular modeling to study the binding mode of ebselen with PL Pro SARS ( Figure 4 ) and PL Pro CoV2 (Figure 4 and 5) . This study confirmed our primary assumption that ebselen binds to the PL Pro CoV2 active site covalently and, thus, convinced us of our hypothesis about an irreversible mechanism of inhibition. cache = ./cache/cord-102842-51n5mnjb.txt txt = ./txt/cord-102842-51n5mnjb.txt === reduce.pl bib === id = cord-035274-hu8zshq8 author = Jadali, Zohreh title = Neurologic manifestations of COVID-19: what can we learn from other coronaviruses date = 2020-11-11 pages = extension = .txt mime = text/plain words = 703 sentences = 57 flesch = 43 summary = Like other coronaviruses, SARS-CoV-2 is neurotropic and may spread to the nervous system via similar mechanisms. Neurotropic and neuroinvasive properties of SARS-CoV-2 are supported by several observations including the presence of virus particles in the cerebrospinal fluid of patients with significant nervous system symptoms [3] . Currently, it is difficult to distinguish whether neurological complications of COVID-19 are a consequence of direct or indirect effects of viral infection. Another mechanism relies on blood circulation and angiotensin-converting enzyme 2 (ACE2) receptors that are expressed on glial cells, neurons, and capillary endothelium and are involved in virus entry [4] . Molecular mimicry that could be associated with the development of autoimmunity is another mechanism by which SARS-CoV-2 may trigger an immune response against nervous system-specific proteins [5] . Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ACE2: Angiotensin-converting enzyme 2 COVID-19 and SARS-Cov-2 infection: pathophysiology and clinical effects on the nervous system The author(s) read and approved the final manuscript. cache = ./cache/cord-035274-hu8zshq8.txt txt = ./txt/cord-035274-hu8zshq8.txt === reduce.pl bib === id = cord-103576-g5de4fwj author = Kriegel, M. title = Predicted Infection Risk via Aerosols date = 2020-10-12 pages = extension = .txt mime = text/plain words = 4012 sentences = 284 flesch = 62 summary = 34 In order to perform an infection risk assessment for the airborne transmission in the far field 35 and to introduce appropriate preventive measures, it would be necessary to know the amount The so-called aerosols (liquid or solid particles in a dispersed phase with a fluid) as well as 50 droplets differ by size. In equation (3), the number of infectious persons (I), the quanta emission rate depending on 74 the activity (q), the pulmonary ventilation rate of exposed susceptible persons (Qb), the 75 duration of stay (t) and the volume flow of pathogen free air (Q) was used. To calculate the predicted 156 infection risk via aerosols (PIRA) in the far field of a room the concentration of quanta (c(t)) 157 and the respiratory rate (Qb) has to be known. To reduce the risk of infection via aerosols the necessary volume flow of virus-free air 327 depending on the exposure time can be seen in Figure 5 . cache = ./cache/cord-103576-g5de4fwj.txt txt = ./txt/cord-103576-g5de4fwj.txt === reduce.pl bib === id = cord-035015-slgywe0c author = Nunn, Alistair V. W. title = SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date = 2020-11-09 pages = extension = .txt mime = text/plain words = 14660 sentences = 715 flesch = 36 summary = Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. cache = ./cache/cord-035015-slgywe0c.txt txt = ./txt/cord-035015-slgywe0c.txt === reduce.pl bib === id = cord-035307-r74ovkbd author = Liu, Shuchang title = Attitudes towards Wildlife Consumption inside and outside Hubei Province, China, in Relation to the SARS and COVID-19 Outbreaks date = 2020-11-11 pages = extension = .txt mime = text/plain words = 4133 sentences = 200 flesch = 54 summary = Our study results indicate over the period between the SARS epidemic to the outbreak of the COVID-19 pandemic, attitudes towards the consumption of wildlife in China have changed significantly. Therefore, our aim in this study was to determine changes in attitudes towards wildlife consumption in Chinese adults in relation to the SARS and COVID-19 outbreaks with a particular focus on Hubei Province. cache = ./cache/cord-035307-r74ovkbd.txt txt = ./txt/cord-035307-r74ovkbd.txt === reduce.pl bib === id = cord-048335-5fl0rk90 author = Thompson, Alison K title = Pandemic influenza preparedness: an ethical framework to guide decision-making date = 2006-12-04 pages = extension = .txt mime = text/plain words = 7950 sentences = 380 flesch = 45 summary = The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The significance of this ethical framework is a) in the unique collaborative approach taken to its development that involved ethicists with different areas of expertise and a variety of health care stakeholders, and b) that it fills an important need in pandemic planning for an ethical framework to guide decision-making that has been unmet in most pandemic planning processes world wide. The second part of the framework identifies ten key ethical values that should inform the pandemic influenza planning process and decision-making during an outbreak. cache = ./cache/cord-048335-5fl0rk90.txt txt = ./txt/cord-048335-5fl0rk90.txt === reduce.pl bib === id = cord-103112-m6cg67lz author = Schloer, Sebastian title = Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date = 2020-08-16 pages = extension = .txt mime = text/plain words = 1554 sentences = 91 flesch = 51 summary = As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. cache = ./cache/cord-103112-m6cg67lz.txt txt = ./txt/cord-103112-m6cg67lz.txt === reduce.pl bib === id = cord-034351-5br4faov author = Xu, Shuang-Fei title = Cross-Sectional Seroepidemiologic Study of Coronavirus Disease 2019 (COVID-19) among Close Contacts, Children, and Migrant Workers in Shanghai date = 2020-10-02 pages = extension = .txt mime = text/plain words = 3445 sentences = 187 flesch = 51 summary = (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. Since the first known case of pneumonia infected with the novel coronavirus was reported in the city of Wuhan in late December of 2019, Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and announced by the World Health Organization on 11 February 2020, unexpectedly and quickly spread in China and many other countries with rapid geographical expansion and a sudden increase in the number of cases [1, 2] . cache = ./cache/cord-034351-5br4faov.txt txt = ./txt/cord-034351-5br4faov.txt === reduce.pl bib === id = cord-103497-1ls2dvzy author = Ganier, C title = CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date = 2020-05-29 pages = extension = .txt mime = text/plain words = 1427 sentences = 90 flesch = 53 summary = title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). The ACE2 receptor has been shown to mediate uptake of the virus responsible for COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in human cells (Hoffmann, Kleine-Weber, Schroeder, et al. In order to define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). cache = ./cache/cord-103497-1ls2dvzy.txt txt = ./txt/cord-103497-1ls2dvzy.txt === reduce.pl bib === id = cord-102411-0mo1198e author = Moreno Borraz, LA title = PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date = 2020-11-13 pages = extension = .txt mime = text/plain words = 3432 sentences = 268 flesch = 55 summary = Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. El objetivo principal del estudio fue conocer la prevalencia de infección por Coronavirus SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia de Zaragoza en el pico de la pandemia en España, entre el 20 de marzo y el 21 de abril de 2020. cache = ./cache/cord-102411-0mo1198e.txt txt = ./txt/cord-102411-0mo1198e.txt === reduce.pl bib === id = cord-102920-z5q3wo7v author = Sang, Eric R. title = Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date = 2020-06-28 pages = extension = .txt mime = text/plain words = 6437 sentences = 316 flesch = 44 summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Along with showing a broad susceptibility potential across mammalian species based on structural analysis [26] [27] [28] , our results further reveal that domestic animals including dogs, pigs, cattle and goats may evolve previously unexamined immunogenetic diversity to restrict SARS-CoV2 infections. In addition to structural analysis of simulated S-RBD-ACE2 interaction, we propose that several immunogenetic factors, including the evolution of S-binding-void ACE2 isoforms in some domestic animals, the species-specific IFN system, and epigenetic regulation of IFN-stimulated property of host ACE2 genes, contribute to the viral susceptibility and the development of COVID-19-like symptoms in certain animal species [15, 38, 39, 49] . cache = ./cache/cord-102920-z5q3wo7v.txt txt = ./txt/cord-102920-z5q3wo7v.txt === reduce.pl bib === id = cord-103709-86hv27vh author = Zhang, Dong Yan title = Prefusion spike protein stabilization through computational mutagenesis date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3243 sentences = 184 flesch = 53 summary = The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We subject the selected residues to computational redesign using Eris to find the stabilizing mutations by calculating the change in free energy ∆∆ = ∆ − ∆ , where ∆ and ∆ are the free energies of the mutant protein and wild type proteins correspondingly. After the designation of the mutation sites, the pipeline utilizes Eris to determine the changes in free energies of the mutants. We analyze the conservation score, RMSF, and SASA of residues in the spike protein through the pipeline. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes cache = ./cache/cord-103709-86hv27vh.txt txt = ./txt/cord-103709-86hv27vh.txt === reduce.pl bib === id = cord-103662-a4ok5wqc author = Tarek, M. title = Custommune: a web tool to design personalized and population-targeted vaccine epitopes date = 2020-04-29 pages = extension = .txt mime = text/plain words = 8116 sentences = 454 flesch = 45 summary = When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. cache = ./cache/cord-103662-a4ok5wqc.txt txt = ./txt/cord-103662-a4ok5wqc.txt === reduce.pl bib === id = cord-103787-qhftb6d7 author = Garcia, Elizabeth P. title = Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date = 2005-10-31 pages = extension = .txt mime = text/plain words = 7354 sentences = 355 flesch = 47 summary = Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. cache = ./cache/cord-103787-qhftb6d7.txt txt = ./txt/cord-103787-qhftb6d7.txt === reduce.pl bib === id = cord-102807-cxtzf5oe author = fiore, j. r. title = FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1686 sentences = 135 flesch = 67 summary = title: FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint ABSTRACT 27 28 Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors 29 from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint Studies on blood donor cohorts are useful to evaluate the prevalence, incidence and natural course 63 of infectious diseases in the general population and may thus help to assess both the viral 64 circulation and the evolution of the COVID-19 outbreak. We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM 66 and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general 67 population three months after the local start of the epidemic. cache = ./cache/cord-102807-cxtzf5oe.txt txt = ./txt/cord-102807-cxtzf5oe.txt === reduce.pl bib === id = cord-034371-j3xxmkjd author = Schellack, Natalie title = COVID-19: Guidelines for pharmacists in South Africa date = 2020-06-10 pages = extension = .txt mime = text/plain words = 5039 sentences = 344 flesch = 54 summary = This evidence-based review is aimed at providing guidance for pharmacists in community, hospital and other settings in South Africa, on the management of patients with suspected or confirmed coronavirus disease 2019, or COVID-19. • Epidemiology • The virus, its modes of transmission and incubation period • Symptom identification, including the differentiation between influenza, allergic rhinitis, sinusitis and COVID-19 • Social media myths and misinformation • Treatment guidelines and medicines that may need to be kept in stock • Treatment and prevention options, including an update on vaccine development • The case for and against the use of NSAIDs, ACE-inhibitors and angiotensin receptor blockers (ARBs) in patients with COVID-19 • Interventions and patient counselling by the pharmacist. The current NDoH/NICD guidelines do not recommend the use of chloroquine (CQ)/ hydroxychloroquine (HCQ), due to insufficient evidence, in the treatment of patients with suspected or confirmed COVID-19. cache = ./cache/cord-034371-j3xxmkjd.txt txt = ./txt/cord-034371-j3xxmkjd.txt === reduce.pl bib === id = cord-102833-hh4641o0 author = Sarkis-Onofre, Rafael title = Decontamination of N95 respirators against SARS-CoV-2: a scoping review date = 2020-11-13 pages = extension = .txt mime = text/plain words = 5948 sentences = 343 flesch = 38 summary = These masks are intended for single use and, based on the manufacturer's instructions, they are heat sensitive and not designed to be sterilized; however, due to their high costs and limited availability [6, 13] , different methods to decontaminate N95 [5, 13, [15] [16] [17] [18] [19] respirators have been discussed to allow multiple usages. (2020) performed an in vitro study and compared the use of a high-level decontamination cabinet that generates aerosolized peracetic acid and hydrogen peroxide with ultraviolet C light and dry heat at 70 °C for 30 minutes. Decontamination and Reuse of N95 Respirators with Hydrogen Peroxide Vapor to Address Worldwide Personal Protective Equipment Shortages During the SARS-CoV-2 (COVID-19) Pandemic Decontamination and reuse of surgical masks and N95 filtering facepiece respirators during COVID-19 pandemic: a systematic review Decontamination of face masks and filtering facepiece respirators via ultraviolet germicidal irradiation, hydrogen peroxide vaporisation, and use of dry heat inactivates an infectious SARS-CoV-2 surrogate virus cache = ./cache/cord-102833-hh4641o0.txt txt = ./txt/cord-102833-hh4641o0.txt === reduce.pl bib === id = cord-103659-wpwfqhp2 author = Almqvist, J. title = Neurological manifestations of coronavirus infections: a systematic review date = 2020-09-01 pages = extension = .txt mime = text/plain words = 6075 sentences = 463 flesch = 46 summary = In order to optimize diagnostic workup of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we systematically reviewed neurological and neuroradiological manifestations of SARS-CoV-2 and all other known human coronavirus species (HCoV). . https://doi.org/10.1101/2020.08.26.20182196 doi: medRxiv preprint symptoms/complications, neuropathological findings and/or neuroimaging findings associated to acute or prior coronavirus infection. Several case reports, comprising a total of 11 patients, described neurological complications in SARS-CoV-1, among them critical illness neuro-/myopathy, seizures, persistent sleeping difficulties, persistent anosmia, delirium and generalized pain (Table e-6). Several common neurological symptoms among SARS-CoV-2 patients have been described in these studies, such as fatigue (44 -64% of patients), 42 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Retrospective Observational Study of Brain Magnetic Resonance Imaging Findings in Patients with Acute SARS-CoV-2 Infection and Neurological Manifestations cache = ./cache/cord-103659-wpwfqhp2.txt txt = ./txt/cord-103659-wpwfqhp2.txt === reduce.pl bib === id = cord-104081-a3fx8tyd author = Tang, Tiffany title = Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date = 2020-10-05 pages = extension = .txt mime = text/plain words = 4004 sentences = 206 flesch = 57 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Our results demonstrate that S1/S2 pre-cleavage is essential for plasma membrane entry into Calu-3 cells, a model lung epithelial cell line, but not for endosomal entry Vero E6 cells, a model cell culture line, and that other proteases in addition to furin are responsible for processing SARS-CoV-2 S1/S2. dec-RVKR-CMK treatment had no significant impact on SARS-CoV S mediated infection of Vero E6 and Calu-3 cells (Figure 6A and 6B) , suggesting that dec-RVKR-CMK impacts on SARS-CoV-2 S is due to inhibiting the S1/S2 pre-cleavage and not due to some general effect on protein expression. Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2 Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells cache = ./cache/cord-104081-a3fx8tyd.txt txt = ./txt/cord-104081-a3fx8tyd.txt === reduce.pl bib === id = cord-103837-iuvigqdx author = Knierman, Michael D. title = The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date = 2020-11-13 pages = extension = .txt mime = text/plain words = 8578 sentences = 439 flesch = 54 summary = Mass spectrometry is used to identify 526 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The ability to automate and miniaturize the MAPPs assay enables facile identification of 1000's of naturally processed and displayed HLA-II peptides from human DCs. Using this approach, we were able J o u r n a l P r e -p r o o f to determine the precise regions and sequences of peptides from SARS-CoV-2 spike glycoprotein ECD derived from a panel of healthy subjects presented for immune surveillance by T-cells. We observed a total of 526 unique peptide sequences contained within 73 clusters distributed across each segment of the SARS-CoV-2 spike glycoprotein ECD presented by human DCs (Figure 2 and Supplemental Table S2 ). cache = ./cache/cord-103837-iuvigqdx.txt txt = ./txt/cord-103837-iuvigqdx.txt === reduce.pl bib === id = cord-103545-2v89ku4o author = Bellos, Ioannis title = Maternal and perinatal outcomes in pregnant women infected by SARS-CoV-2: A meta-analysis date = 2020-11-13 pages = extension = .txt mime = text/plain words = 5197 sentences = 333 flesch = 48 summary = The following data were planned to be extracted from each of the included studies: name of first author, country, maternal age, medical history (diabetes mellitus, hypothyroidism or polycystic ovary syndrome), symptoms (fever, cough, shortness of breath, diarrhea, nausea/vomiting, myalgia, fatigue, headache, sore throat, nasal congestion, abdominal pain, chest pain), radiological signs, presence of co-infection (bacterial or influenza), laboratory tests (lymphopenia, thrombocytopenia, increased Creactive protein, procalcitonin, ferritin, liver function tests and D-dimers), type of treatment, pregnancy outcomes (fetal distress, premature rupture of membranes-PROM, placenta previa, preeclampsia, preterm birth, cesarean section, stillbirth), maternal outcomes (admission to intensive care unit-ICU or death), neonatal outcomes (gender, gestational age, birthweight, 1-minute/5-minute Apgar score, horizontal/vertical transmission, admission to ICU, mechanical ventilation, sepsis and death). As a result, the present meta-analysis was based on 16 observational studies [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] and 44 case reports/series , including a total of 920 neonates born to women with SARS-CoV-2 infection. cache = ./cache/cord-103545-2v89ku4o.txt txt = ./txt/cord-103545-2v89ku4o.txt === reduce.pl bib === id = cord-122092-gdyt02er author = Fatehi, Farzad title = Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date = 2020-10-18 pages = extension = .txt mime = text/plain words = 10080 sentences = 511 flesch = 55 summary = Comparison of different scenarios is based on tissue damage and viral load, highlighting the impact(s) of antibodies and adaptive cell-mediated immune response on infection dynamics. Surprisingly, our model also suggests that early treatment by either therapy alone can actually increase the duration of infection compared with a later therapy start, likely because suppressing virus production results in a reduced immune response. The model also includes non-structural proteins that are important for the viral life cycle, such as the replicase-transcriptase complex (RTC), and keeps track of the numbers of gRNAs (and subgenomic sgRNAs) at different stages of the replication process. We have included additional reactions into the model that describe remdesivir binding to the RTC complexes on the gRNAs and sgRNAs to capture this (see SI for details), and track the effect of a given, fixed number of remdesivir molecules per cell on the release of viral particles from an infected host cell. cache = ./cache/cord-122092-gdyt02er.txt txt = ./txt/cord-122092-gdyt02er.txt === reduce.pl bib === id = cord-103940-a2cqw8kg author = Shi, Yuejun title = Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date = 2020-06-09 pages = extension = .txt mime = text/plain words = 3207 sentences = 216 flesch = 63 summary = Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. In this study, 130 we selected SARS-CoV, SARS-CoV-2, and HCoV-229E as models, which adopt the 131 two RBD states, and evaluated and compared immune responses to the S trimers and 132 7 RBDs of these coronaviruses through immunological and bioinformatics approaches. 133 We also investigated the mechanism through which the HCoV-229E S trimer 134 produced effective nAbs. Finally, we provide possible vaccine strategies for alphaTo address this issue, we performed B-cell epitope predictions for the S trimers 152 and RBDs of alpha-CoV (HCoV-229E) and beta-CoVs (SARS-CoV and 153 SARS-CoV-2). Taken together, these results showed that the intact and stable S1 subunit of 240 HCoV-229E is a prerequisite for the production of effective nAbs. Furthermore, our experimental results show that RBD has a higher ability to bind 242 12 to the receptor hAPN (Fig. 4B) , which indicates that the characteristics of RBD itself 243 may lead to the generation of less neutralizing antibodies. cache = ./cache/cord-103940-a2cqw8kg.txt txt = ./txt/cord-103940-a2cqw8kg.txt === reduce.pl bib === id = cord-103914-ppgx7mci author = Maughan, Elizabeth F. title = Cell-intrinsic differences between human airway epithelial cells from children and adults date = 2020-04-20 pages = extension = .txt mime = text/plain words = 8186 sentences = 419 flesch = 47 summary = Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). cache = ./cache/cord-103914-ppgx7mci.txt txt = ./txt/cord-103914-ppgx7mci.txt === reduce.pl bib === id = cord-103872-yzqic5vt author = Liu, Zhijin title = Global view on virus infection in non-human primates and implication for public health and wildlife conservation date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1310 sentences = 81 flesch = 51 summary = Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans and vice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission. First, we generated a summary statistics of worldwide reported VI-NHPs. We then 61 identified and predicted NHP species with a high risk of virus transmission from humans and 62 predicted geographic locations where disease outbreaks are likely to occur. Since centrality in primate-virus networks could assess the potential for the 72 circulation of viruses among NHPs and humans, we estimated the centrality using four metrics: 73 strength degree centrality, eigenvector centrality, betweenness centrality, and closeness centrality 74 implemented in the R package "igraph" and UCINET 6. Centrality in primate-parasite networks 225 reveals the potential for the transmission of emerging infectious diseases to humans cache = ./cache/cord-103872-yzqic5vt.txt txt = ./txt/cord-103872-yzqic5vt.txt === reduce.pl bib === id = cord-127741-h23w89h2 author = Babuji, Yadu title = Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release date = 2020-05-28 pages = extension = .txt mime = text/plain words = 2439 sentences = 149 flesch = 49 summary = In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. For example, these data now include the 2D and 3D molecular descriptors, computed molecular fingerprints, 2D images representing the molecule, and canonical simplified molecular-input line-entry system (SMILES) [6] structural representations to speed development of machine learning models. We expect forthcoming data releases to extend to molecular conformers; incorporate the results of natural language processing extractions of drugs from COVID-related literature; provide the results of molecular docking simulations against SARS-CoV-2 viral and host proteins; and include the trained machine learning models that the team is building to identify top candidates for running various, more expensive calculations. cache = ./cache/cord-127741-h23w89h2.txt txt = ./txt/cord-127741-h23w89h2.txt === reduce.pl bib === id = cord-104435-y7mxyein author = Alabdulmonem, Waleed title = COVID-19: A global public health disaster date = 2020 pages = extension = .txt mime = text/plain words = 596 sentences = 40 flesch = 58 summary = [4] As compared to the previous CoVs, the infectivity rate of SARS-CoV-2 is comparatively much higher, and the mode of transmission of this deadly virus is primarily by respiratory droplets from an infected individual to others through coughing, sneezing within a distance up to 6 feet, or touching of infected surfaces, where the viral particles are present. [9] The transmission of virus can be decreased to a large extent by adopting strict infection control policies, which are basically a team base efforts and everyone has to play their roles. [8, 9] Being an enveloped virus, SARs-CoV-2 is comparatively easy to disinfect; therefore, hands hygiene plays a vital preventive tool from getting infected, washing hands frequently with soap and water or using alcohol-based hand sanitizers to disinfect hands have strongly been recommended by the WHO. Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica) cache = ./cache/cord-104435-y7mxyein.txt txt = ./txt/cord-104435-y7mxyein.txt === reduce.pl bib === id = cord-104500-m0kfom0x author = Kyriakopoulos, Anthony M. title = The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review date = 2020-09-21 pages = extension = .txt mime = text/plain words = 6842 sentences = 357 flesch = 40 summary = A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20(th) of August 2020. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. Following this initial selection stage, further screening was performed by all reviewers, using the previously described search items to identify parameters determining the global impact of COVID-19 due to SSEs. Identified parameters included the global impact of immunity and vaccination, the holy cup and religion transmission, and the austerity caused by COVID-19 and other coronavirus epidemics due to restrictions applied. cache = ./cache/cord-104500-m0kfom0x.txt txt = ./txt/cord-104500-m0kfom0x.txt === reduce.pl bib === id = cord-103945-q3ry13vp author = de Oliveira, P. M. title = Evolution of spray and aerosol from respiratory releases: theoretical estimates for insight on viral transmission date = 2020-07-24 pages = extension = .txt mime = text/plain words = 9274 sentences = 485 flesch = 59 summary = By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. The Lagrangian framework, given in Sec. 2(a), is considered in one (vertical) dimension and droplet clouds for two exhalation modes, speaking and coughing, are released at the height of the emitter's mouth (1.5 m) and then let settle by gravity while evaporating in ambient air. cache = ./cache/cord-103945-q3ry13vp.txt txt = ./txt/cord-103945-q3ry13vp.txt === reduce.pl bib === id = cord-104162-fe51v2pt author = Zhang, Chiyu title = Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3745 sentences = 208 flesch = 49 summary = Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). cache = ./cache/cord-104162-fe51v2pt.txt txt = ./txt/cord-104162-fe51v2pt.txt === reduce.pl bib === id = cord-104507-xx7t26rl author = Safari, Saeid title = Extracorporeal Hemoperfusion as a Potential Therapeutic Option for Severe COVID-19 patients; a Narrative Review date = 2020-08-22 pages = extension = .txt mime = text/plain words = 3425 sentences = 173 flesch = 31 summary = Based on previous experience of blood purification to treat cytokine storm syndrome (CSS) in severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), here we aimed to review the current literature on extracorporeal hemoperfusion as a potential therapeutic option for CSS-associated conditions, with a focus on severe COVID-19. To date, various centers in different countries including Italy, China, USA, Germany, and Iran have reported or are investigating the beneficial effects of different hemoperfusion systems, including HA380/HA330 cartridges, CytoSorb, and polymyxin B immobilized fiber column in treatment of critically-ill COVID-19 patients. To date, a large number of experimental and clinical data, mostly from case reports and case series, have introduced CytoSorb as an effective rescue therapy for removal of inflammatory cytokines and achievement of hemodynamic stabilization in critically ill patients with septic shock and kidney failure (47) (48) (49) . cache = ./cache/cord-104507-xx7t26rl.txt txt = ./txt/cord-104507-xx7t26rl.txt === reduce.pl bib === id = cord-146091-kpvxdhcu author = Sanchez-Lorenzo, Arturo title = Anomalous atmospheric circulation favored the spread of COVID-19 in Europe date = 2020-04-26 pages = extension = .txt mime = text/plain words = 3235 sentences = 166 flesch = 52 summary = In this study we show that an unusual persistent anticyclonic situation prevailing in southwestern Europe during February 2020 (i.e. anomalously strong positive phase of the North Atlantic and Arctic Oscillations) could have resulted in favorable conditions, in terms of air temperature and humidity, in Italy and Spain for a quicker spread of the virus compared with the rest of the European countries. These results evidence that it seems plausible that the positive phase of the NAO, and the atmospheric conditions associated with it, provided optimal conditions for the spread of the COVID-19 in southern countries like Spain and Italy, where both the start and the most severe impacts of the outbreak in Europe were located. Taking into account these results, we claim that the major initial outbreaks of COVID-19 in Europe (i.e., Italy and Spain) may be favored by an anomalous atmospheric circulation pattern in February, characterized by a positive phase of the NAO and AO. cache = ./cache/cord-146091-kpvxdhcu.txt txt = ./txt/cord-146091-kpvxdhcu.txt === reduce.pl bib === id = cord-130351-w9mij6c6 author = Mamidala, Estari title = In silico identification of clinically approved medicines against the main protease of SARS-CoV-2, causative agent of covid-19 date = 2020-04-25 pages = extension = .txt mime = text/plain words = 2676 sentences = 155 flesch = 50 summary = In the present study, we report the potential inhibitory activity of some FDA approved drugs against SARS-CoV-2 main protease by molecular docking study to investigate their binding affinity in protease active site. Docking studies revealed that drug Oseltamivir (anti-H1N1 drug), Rifampin (anti-TB drug), Maraviroc, Etravirine, Indinavir, Rilpivirine (anti-HIV drugs) and Atovaquone, Quinidine, Halofantrine, Amodiaquine, Tetracylcine, Azithromycin, hydroxycholoroquine (anti-malarial drugs) among others binds in the active site of the protease with similar or higher affinity. 11 The free energy (DG) binding of SARS-CoV-2 viral protease with the selected FDA approved drugs was created by means of this molecular docking package. Oseltamivir and Zanamivir, two FDA approved drugs docked with SARS-CoV-2 main protease and obtained binding energy is −7.39 kcal/mol and -3.88 kcal/mol respectively (Table-2 Figure 2 ). cache = ./cache/cord-130351-w9mij6c6.txt txt = ./txt/cord-130351-w9mij6c6.txt === reduce.pl bib === id = cord-103899-6tqm99g1 author = Mirzaei, Rasoul title = The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date = 2020-11-13 pages = extension = .txt mime = text/plain words = 9756 sentences = 554 flesch = 47 summary = Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. This review will summarize the recent discoveries associated with miRNAs in various respiratory infections caused by viruses, especially coronavirus, and address all feasible therapeutic options to mitigate the burden of VRIs. The humoral immunity is immunologically categorized as an acquired immune response in which T helper cells collaborate with B cells to differentiate these types of cells to plasma cells [17] [18] [19] . The immune responses against VRIs, such as IV, hRV, human coronavirus (HcoV), hMPV, and RSV, are correlated with the aberrant expression of several miRNAs in epithelial cells and participate in the pathogenesis of chronic and acute forms of respiratory disorders (Table 1 ) [16] . cache = ./cache/cord-103899-6tqm99g1.txt txt = ./txt/cord-103899-6tqm99g1.txt === reduce.pl bib === id = cord-142389-t5swlp04 author = Linden, Matthias title = The foreshadow of a second wave: An analysis of current COVID-19 fatalities in Germany date = 2020-10-12 pages = extension = .txt mime = text/plain words = 3725 sentences = 272 flesch = 65 summary = We investigated this apparent discrepancy using age-stratified case and death reports [3] , and an age-dependent infection fatality rate (IFR). From this age-dependent IFR we predict the temporal evolution of the COVID-19associated deaths by delaying each age group's observed weekly cases by two weeks and multiplying by the IFR (see supplementary material). The observed number deaths (black) in each age group matches well the predicted deaths calculated from the case numbers (color) using an age-dependent infection-fatality rate from a metaanalysis [4] . b. IFR calculation The overall goal is to estimate death numbers from past reported cases per age group and compare them to the observed number of deaths. c. Estimating the number of deaths from the reported SARS-CoV-2 cases The number of deaths is estimated by multiplying the published weekly number of reported cases in 5-years-wide age groups by the associated IFR (equation (2)). cache = ./cache/cord-142389-t5swlp04.txt txt = ./txt/cord-142389-t5swlp04.txt === reduce.pl bib === id = cord-138439-wvynetna author = Wei, Xiyi title = Sex Differences in Severity and Mortality Among Patients With COVID-19: Evidence from Pooled Literature Analysis and Insights from Integrated Bioinformatic Analysis date = 2020-03-30 pages = extension = .txt mime = text/plain words = 4720 sentences = 290 flesch = 50 summary = Objective: To conduct a meta-analysis of current studies that examined sex differences in severity and mortality in patients with COVID-19, and identify potential mechanisms underpinning these differences. Methods: We performed a systematic review to collate data from observational studies examining associations of sex differences with clinical outcomes of COVID-19. Conclusions: This meta-analysis detected an increased severity and mortality rate in the male populations with COVID-19, which might be attributable to the sex-based differences in cellular compositions and immunological microenvironments of the lung. However, whether the sex difference is related to the risk factors for infection, severity, and mortality of COVID-19 is still lacking a comprehensive analysis based on the integration of new studies. ACE2 as a receptor of SARS-CoV and spike protein can be primed by TMPRSS2 are exploited to entry into target cells, which play an vital role in coronavirus pneumonia infection. cache = ./cache/cord-138439-wvynetna.txt txt = ./txt/cord-138439-wvynetna.txt === reduce.pl bib === id = cord-126015-zc7u3g34 author = Krieger, Elizabeth title = Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date = 2020-05-13 pages = extension = .txt mime = text/plain words = 6421 sentences = 348 flesch = 42 summary = To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. The HLA genes exhibit extreme allelic polymorphisms and present viral peptides on host HLA molecules to T cells to trigger an adaptive immune response. A quantitative approach relating differences in cytokine levels and polymorphisms in the immune response pathways may help identify patients at risk of severe disease. cache = ./cache/cord-126015-zc7u3g34.txt txt = ./txt/cord-126015-zc7u3g34.txt === reduce.pl bib === id = cord-154844-nuqx3tv6 author = Misirli, Goksel title = A comparative analysis for SARS-CoV-2 date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1660 sentences = 112 flesch = 58 summary = Comparative analyses particularly can play a key role to reveal structural changes in proteins due to mutations, which can lead to behavioural changes, such as the increased binding of the SARS-CoV-2 surface glycoprotein to human ACE2 receptors. Starting with a SARS-CoV-2 genome sequence, the report shows visualising DNA sequence features, deriving amino acid sequences, and aligning different genomes to analyse mutations and differences. The report provides further insights into how the SARS-CoV-2 surface glycoprotein mutated for higher binding affinity to human ACE2 receptors, compared to the SARS-CoV protein, by integrating existing 3D protein models. Here, we integrated secondary structure predictions and realigned the sequences in order to show how these five mutations may affect the binding of the SARS-CoV-2 protein ( Figure 6 ). Compared to the SARS-CoV secondary structures, both the CLC Genomics Workbench predictions and the SARS-CoV-2 '6W41' model reveal additional beta strands in the mutated region (shown using the dashed box in Figure 6 ) of the surface glycoprotein. cache = ./cache/cord-154844-nuqx3tv6.txt txt = ./txt/cord-154844-nuqx3tv6.txt === reduce.pl bib === id = cord-140318-xtx8hl14 author = Martin, Alexandra title = High-sensitivity COVID-19 group testing by digital PCR date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4252 sentences = 213 flesch = 58 summary = Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. The results for SARS-CoV-2 detection by RT-dPCR in groups of 8 samples, detailed in Tables 1 and 2 , are in concordance with the reference individual RT-PCR testing for 52 groups (corresponding for 416 samples), out of which 32 were RT-PCR negative groups and 20 groups contained at least one RT-PCR+ sample. In this work, we assessed the sensitivity and specificity of group testing combined with digital PCR for SARS-CoV-2 detection. cache = ./cache/cord-140318-xtx8hl14.txt txt = ./txt/cord-140318-xtx8hl14.txt === reduce.pl bib === id = cord-133453-23rfdkuw author = Chen, Jiahui title = Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies date = 2020-10-13 pages = extension = .txt mime = text/plain words = 8184 sentences = 485 flesch = 54 summary = By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. The vaccination mechanism is to stimulate the primary immune response of the human body, which will activate T cells and B cells to generate the antibodies and long-lived memory cells that prevent infectious diseases, which is one of the most effective and economical means for combating with COVID-19 at this stage. Notably, understanding how mutations have changed the SARS-CoV-2 structure, function, infectivity, activity, and virulence is of great importance for coming up with life-saving strategies in virus control, containment, prevention, and medication, especially in the antibodies and vaccines development. Next, we study the BFE changes ∆∆G induced by 39 mutations on the SARS-CoV-2 S protein RBD for the antibody Fab 2-4 (PDB: 6XEY) in Figure 6 . cache = ./cache/cord-133453-23rfdkuw.txt txt = ./txt/cord-133453-23rfdkuw.txt === reduce.pl bib === id = cord-124012-5zxkd2jy author = Schwab, Patrick title = predCOVID-19: A Systematic Study of Clinical Predictive Models for Coronavirus Disease 2019 date = 2020-05-17 pages = extension = .txt mime = text/plain words = 5098 sentences = 247 flesch = 38 summary = Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. In addition, [48] performed a cohort study for clinical and laboratory predictors of COVID-19 related inhospital mortality that identified baseline neutrophil count, age Fig. 2 : The presented multistage machine-learning pipeline consists of preprocessing (light purple) the input data x, developing multiple candidate models using the given dataset (orange), selecting the best candidate model for evaluation (blue), and evaluating the selected best model's outputsŷ. Owing to the recent emergence of SARS-CoV-2, there currently exists, to the best of our knowledge, no prior systematic study on clinical predictive models that predict likelihood of a positive SARS-CoV-2 test, hospital and intensive care unit admission from clinical, demographic and blood analysis data that accounts for the missingness that is characteristic for the clinical setting. cache = ./cache/cord-124012-5zxkd2jy.txt txt = ./txt/cord-124012-5zxkd2jy.txt === reduce.pl bib === id = cord-138656-8iyynbup author = Furuyama, Taima N. title = Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3036 sentences = 172 flesch = 61 summary = title: Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant From November 2002 to May 2004, SARS-CoV-1 (Severe Acute Respiratory Syndrome caused by Coronavirus type 1) affected 26 countries worldwide, accounted 8,096 confirmed cases and 774 deaths (9.6% fatality ratio) (Drosten et al., 2003; Ksiazek et al., 2003; Lee et al., 2003; Peiris et al., 2003; Zhong et al., 2003 ; Centers for Disease Control and Prevention -Department of Health and Human Services, 2004; World Health Organization, 2004; Centers for Disease Control and Prevention, 2017) . MERS-CoV (Middle East Respiratory Syndrome caused by Coronavirus) spread to 27 countries around the globe, totalizing 2,519 confirmed cases and 866 deaths (34.4% fatality ratio) continuously since April 2012 (Zaki et al., 2012; Hijawi et al., 2013; Centers for Disease Control and Prevention, 2019; World Health Organization, 2019 , 2020b . If there is a correlation between the D614G variant prevalence and higher SARS-CoV-2 transmission, then the epidemiological data might reveal a significant correlation between D614G prevalence and the growth rate coefficients of epidemic curves globally. cache = ./cache/cord-138656-8iyynbup.txt txt = ./txt/cord-138656-8iyynbup.txt === reduce.pl bib === id = cord-153725-jjefjlx2 author = Sahoo, Suban K title = Computational evidence on repurposing the anti-influenza drugs baloxavir acid and baloxavir marboxil against COVID-19 date = 2020-09-02 pages = extension = .txt mime = text/plain words = 2219 sentences = 116 flesch = 55 summary = In this communication, molecular docking analyses of two influenza antiviral drugs baloxavir acid (BXA) and baloxavir marboxil (BXM) were performed with the three therapeutic target proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp). Considering the need of new potential drugs to repurpose against COVID-19 pandemic, this research was carried out to investigate the effective binding of the drugs BMX and BXA with the three functional proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The molecular docking of the drugs were performed with the therapeutic target proteins and their affinity of binding at the active site was compared. Therefore, to provide computational evidence on the comparative potency of the two influenza antiviral drugs BXA and BXM (Fig. 1) , the molecular docking experiments were performed in Autodock Vina with the therapeutic target proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The blind molecular docking was performed where the grid box was selected to cover the whole protein structure. cache = ./cache/cord-153725-jjefjlx2.txt txt = ./txt/cord-153725-jjefjlx2.txt === reduce.pl bib === id = cord-154170-7pnz98o6 author = Ponciano, Jos'e Miguel title = Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3253 sentences = 175 flesch = 46 summary = Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. Here we show that a multi-model, multi-stages modeling approach helps elucidate i) early epidemic growth in fourteen Latin-American countries ii) the role of poverty in shaping the growth rate of the number of cases and iii) the probability that the number of cases of SARS-CoV-2 exceeds any given amount within arbitrarily defined small windows of time, starting from the present. We draw on prior work in conservation biology, population dynamics and epidemiological theory to complement the current suite of deterministic epidemiological models, characterize the role of urban poverty in shaping the region's SARS-CoV-2 epidemics, and develop a methodology to generate short (5-15 days), sequentially updatable, process-based forecasts. cache = ./cache/cord-154170-7pnz98o6.txt txt = ./txt/cord-154170-7pnz98o6.txt === reduce.pl bib === id = cord-146679-g7qioapl author = Jaimes, Javier A. title = Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses date = 2020-02-14 pages = extension = .txt mime = text/plain words = 3652 sentences = 181 flesch = 55 summary = title: Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses To obtain an initial assessment of shared and/or specific features of the 2019-nCoV spike (S) envelope glycoprotein, a protein sequence alignment was performed to compare the sequence of the Wuhan-Hu-1 strain of the novel coronavirus with that of the closely related human SARS-CoV S strain Tor2 sequence ( Supplementary Fig. 1 ). The relatively high degree of sequence identity for the RBD is consistent with the view that 2019-nCoV, like SARS-CoV, may use ACE2 as its host cell receptor, The composition of residues found at the two known coronavirus S cleavage sites was performed using alignment data ( Fig. 2B and C). cache = ./cache/cord-146679-g7qioapl.txt txt = ./txt/cord-146679-g7qioapl.txt === reduce.pl bib === id = cord-161674-nk0wie0w author = Liu, Zhi title = Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 5137 sentences = 304 flesch = 54 summary = Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). cache = ./cache/cord-161674-nk0wie0w.txt txt = ./txt/cord-161674-nk0wie0w.txt === reduce.pl bib === id = cord-190207-en96o8zo author = Jim'enez-Avalos, Gabriel M. title = High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease date = 2020-08-30 pages = extension = .txt mime = text/plain words = 6206 sentences = 346 flesch = 53 summary = title: High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease Here, a PAIN-filtered flavonoid database was screened against four sites of the protease: a free (normal) conformation of the Substrate Binding Site (NSBS), an induced-fit state of the SBS (ISBS), a Dimerization Site (DS) and a Cryptic Site (CS). In the case of SBS, the top 30 ligands with the lowest binding energies from NSBS and ISBS were contrasted and the ones present in both lists were selected as the final candidates. Each putative binding site had its respective solvent-accessible surface area (SASA) found in PyMol v.2.4 (44) , using as input the hydrogen-curated structure of M PRO obtained before. A previous study on SARS-CoV-1 3CL PRO reported two glycosylated flavonoids as inhibitors, whose sugar moieties interacted with the active sites's S1 and S2 subsites through hydrogen bonds (31) . cache = ./cache/cord-190207-en96o8zo.txt txt = ./txt/cord-190207-en96o8zo.txt === reduce.pl bib === id = cord-189561-jhvwozsn author = Chechetkin, Vladimr R. title = Combining Detection and Reconstruction of Periodic Motifs in Genomic Sequences with Transitional Genome Mapping date = 2020-10-14 pages = extension = .txt mime = text/plain words = 4184 sentences = 268 flesch = 54 summary = A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences. f The distribution of k-mer lengths after TAMGI for the steps within interval 1-500 for the genome of SARS-CoV-2 (shown by crosses) and its comparison with the counterpart distribution for a random reshuffled sequence (shown by circles). The correspondence should be searched between the (generally multiple) elements of icosahedral symmetry and the character of large-scale quasi-periodic segmentation induced by weakly specific cooperative interactions between genomic RNA/DNA and capsid proteins. To sum up, TAMGI method developed in this article is quite general and can be applied to the combined detection/reconstruction of quasi-periodic motifs in the genomic RNA/DNA sequences. cache = ./cache/cord-189561-jhvwozsn.txt txt = ./txt/cord-189561-jhvwozsn.txt === reduce.pl bib === id = cord-167889-um3djluz author = Chen, Jianguo title = A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19 date = 2020-07-04 pages = extension = .txt mime = text/plain words = 12248 sentences = 768 flesch = 50 summary = The progress of CT image inspection based on AI usually includes the following steps: Region Of Interest (ROI) segmentation, lung tissue feature extraction, candidate infection region detection, and COVID-19 classification. Data sources Methods Country/region Huang [82] Yang [231] , WHO [216] CNN, LSTM, MLP, GRU China Hu [80, 81] The Paper [148] , WHO [216] MAE, clustering China Yang [233] Baidu [16] SEIR, LSTM China Fong [51, 52] NHC [139] SVM, PNN China Ai [3] WHO [54, 216] ANFIS, FPA China, USA Rizk [168] WHO [216] ISACL-MFNN USA, Italy, Spain Giuliani [62] Italy [144] EMTMGL Italy Ayyoubzadeh [14] Worldometer [218] , Google [201] LR, LSTM Iran Marini [129, 130] Swiss population Enerpol Switzerland Lai [110] IATA [126] , Worldpop [219] ML Global Punn [155] JHU CSSE [49] SVR, PR, DNN, LSTM, RNN Predicting commercially available antiviral drugs that may act on the novel coronavirus (sars-cov-2) through a drug-target interaction deep learning model cache = ./cache/cord-167889-um3djluz.txt txt = ./txt/cord-167889-um3djluz.txt === reduce.pl bib === id = cord-158628-71n1tgrw author = Russo, Giulia title = In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform date = 2020-05-05 pages = extension = .txt mime = text/plain words = 5596 sentences = 296 flesch = 50 summary = Recently, specific findings about the genome sequencing of SARS-CoV-2 in different countries where cases of infection were registered, revealed its relative intrinsic genomic variability, its virus dynamics and the related host response mechanisms, unveiling interesting knowledge useful for the formulation of innovative strategies for preventive vaccination. Specifically, SARS-CoV-2 sequencing along with its relative intrinsic genomic variability [10] , the presence of minority variants generated during SARS-CoV-2 replication [11] , the involved cellular factors that favors SARS-CoV-2 cell entry [12] , the timing in which viral load peaks (during the first week of illness), its gradual decline (over the second week) and the increasing of both IgG and IgM antibodies (around day 10 after symptom onset) represent some of the relevant insights so far delineated and considered by research community about SARS-CoV-2 virus [13] . UISS is an immune system simulation platform that was designed to be applied to several and different scenarios, especially to carry on in silico trials to predict the efficacy of a specific prophylactic or therapeutic vaccine against a particular disease. cache = ./cache/cord-158628-71n1tgrw.txt txt = ./txt/cord-158628-71n1tgrw.txt === reduce.pl bib === id = cord-171703-n22tr8f2 author = Hanmo, Li title = Robust estimation of SARS-CoV-2 epidemic at US counties date = 2020-10-22 pages = extension = .txt mime = text/plain words = 13227 sentences = 452 flesch = 65 summary = In this work, we propose a robust approach of integrating test data and death toll to estimate COVID-19 transmission characteristics by a Susceptible, Infectious, Resolving (but not infectious), Deceased and reCovered (SIRDC) model initially studied in 7 . We have developed a novel approach to integrate test data and death toll to estimate probability of contracting COVID-19, as well as the time-dependent transmission rate and the number of active infectious individuals at the county level in the US. Furthermore, when we reduce the infectious period by 10% (or equivalently 4.5 days in total), while the transmission rate (β t in SIRDC model) is held the same, the PoC SARS-CoV-2 is reduced by 5 times for 26 counties in Washington and 146 counties in Texas, shown in Extended Data Figure 4 . cache = ./cache/cord-171703-n22tr8f2.txt txt = ./txt/cord-171703-n22tr8f2.txt === reduce.pl bib === id = cord-190540-zf5ksac2 author = Rakshit, Kausik title = An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2065 sentences = 104 flesch = 46 summary = title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. The electrostatic charges accumulated in the layers between the Gr IV Ge is sufficient enough to either fuse or repel the charges of the spike proteins of the RNA, DNA viruses including SARS-Cov-2 (RNA virus) or the aerosols. cache = ./cache/cord-190540-zf5ksac2.txt txt = ./txt/cord-190540-zf5ksac2.txt === reduce.pl bib === id = cord-179749-qdbmpi7j author = Sacks, Daniel W. title = What can we learn about SARS-CoV-2 prevalence from testing and hospital data? date = 2020-08-01 pages = extension = .txt mime = text/plain words = 10732 sentences = 621 flesch = 56 summary = We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on who gets tested, using Indiana data on hospital inpatient records linked to SARS-CoV-2 virological tests. In this paper, we propose a new approach to measuring the point-in-time prevalence of active SARS-CoV-2 infections in the overall population using data on patients who are hospitalized for non-COVID reasons. The combination of these assumptions with linked testinghospital data leads to relatively tight upper and lower bounds on the prevalence of active SARS-CoV-2 infections in the overall population in Indiana in each week from mid-March to mid-June. We maintain the test monotonicity assumption throughout, and we derive upper and lower bounds on prevalence in the population under two alternative assumptions about the representativeness of non-COVID hospitalizations for the broader population. Equivalently, the independence assumption implies that SARS-CoV-2 prevalence is the same among people who are hospitalized for non-COVID conditions and the general population. cache = ./cache/cord-179749-qdbmpi7j.txt txt = ./txt/cord-179749-qdbmpi7j.txt === reduce.pl bib === id = cord-191741-2vuiafv0 author = Schifanella, L. title = Massive viral replication and cytopathic effects in early COVID-19 pneumonia date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1953 sentences = 94 flesch = 46 summary = Here we show that SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes causes focal lung injury in an individual with no history of pulmonary symptoms. Ground glass opacities or patchy infiltrates in the lungs in CT images of asymptomatic SARS-CoV-2 infected individuals [5] [6] [7] suggest that lung infection and associated tissue injury may be detectable in individuals who did not have severe pneumonia or respiratory failure 7 . We have already shown images that suggested that vRNA+ macrophages could acquire vRNA by phagocytosis of infected type II pneumocytes or vRNA released from lysed cells (Fig. 1, 2) , and now show further evidence in support of that conclusion. We show in a SARS-CoV-2 infected individual with ostensibly early infection, who had no known history of pulmonary symptoms, that there was a region of the lung with focal pneumonia in which massive SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes directly contributes to lung pathology. cache = ./cache/cord-191741-2vuiafv0.txt txt = ./txt/cord-191741-2vuiafv0.txt === reduce.pl bib === id = cord-193133-puqcbf8t author = Piplani, Sakshi title = In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3815 sentences = 215 flesch = 51 summary = The devastating impact of the COVID19 pandemic caused by SARS coronavirus 2 (SARSCoV2) has raised important questions on the origins of this virus, the mechanisms of any zoonotic transfer from exotic animals to humans, whether companion animals or those used for commercial purposes can act as reservoirs for infection, and the reasons for the large variations in susceptibilities across animal species. Here we show how computational chemistry methods from structure-based drug design can be used to determine the relative binding affinities of the SARS-CoV-2 spike protein for its receptor, angiotensin converting enzyme (ACE)-2, a critical initiating event for SARS-CoV-2 infection, across multiple common and exotic animal species. 31, 32 Molecular docking was performed on the homology modelled SARS-CoV-2 spike protein with human and animal ACE2 proteins. The molecular dynamics simulation of complexes of SARS-CoV-2 spike protein and ACE2 receptors of various species were performed for 100ns. cache = ./cache/cord-193133-puqcbf8t.txt txt = ./txt/cord-193133-puqcbf8t.txt === reduce.pl bib === id = cord-151024-qe7c2uks author = Koca, Caglar title = Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date = 2020-11-07 pages = extension = .txt mime = text/plain words = 5622 sentences = 353 flesch = 56 summary = We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . cache = ./cache/cord-151024-qe7c2uks.txt txt = ./txt/cord-151024-qe7c2uks.txt === reduce.pl bib === id = cord-196608-k4f79dr4 author = Saha, Sovan title = Computational modeling of Human-nCoV protein-protein interaction network date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4387 sentences = 262 flesch = 51 summary = Our developed computational model of nCoV-Human PPIN contains high quality interactions (HQI) and proteins identified by Fuzzy affinity thresholding and spreadability index validated by SIS model respectively. With the gradual progress of the work, it has been observed that the selected human spreader nodes, identified by our proposed model, emerge as the potential protein targets of the FDA approved drugs for COVID-19. Target proteins of the potential FDA drugs for COVID-19 are found to overlap with the spreader nodes of the proposed computational nCoV-Human protein interaction model. Target proteins of seven potential FDA drugs: Lopinavir 30 , Ritonavir 31 , Hydroxychloroquine 32, 33 , Azithromycin 33 , Remdesivir 34-36 , Favipiravir 37, 38 and Darunavir 39 for COVID-19 as mentioned in the DrugBank white paper 26 overlap with the spreader nodes of the proposed in silico nCoV-Human protein interaction model (see Figure 5 ). cache = ./cache/cord-196608-k4f79dr4.txt txt = ./txt/cord-196608-k4f79dr4.txt === reduce.pl bib === id = cord-193893-rzurz5bj author = Ma, Zhanshan title = Spatiotemporal fluctuation scaling law and metapopulation modeling of the novel coronavirus (COVID-19) and SARS outbreaks date = 2020-03-08 pages = extension = .txt mime = text/plain words = 3683 sentences = 200 flesch = 48 summary = Another TPL parameter (M0) (i.e., infection critical threshold) depends on virus kinds (COVID-19/SARS), time (disease-stages), space (regions) and public-health interventions (e.g., quarantines and mobility control). While TPL can be harnessed to investigate the spatiotemporal fluctuations of coronaviruses, specifically, the scaling (changes) law of coronaviruses infections over space and time, we also aim to understand the spread of the virus infections from both local contagion (endemic) and external migration (epidemic and pandemic) perspectives. Overall, this study sets two primary objectives: (i) to investigate the spatiotemporal fluctuation scaling law and (ii) to obtain an educated guess for the local contagion spread and global migration parameters of the COVID-19 infections. At the community level, the four Taylor's power law extensions (TPLE), can be used to measure the community spatial (temporal) heterogeneity ( on both the general principle of TPL (explained above) and system-or data-specific information (such as the biology of COVID or SARS). cache = ./cache/cord-193893-rzurz5bj.txt txt = ./txt/cord-193893-rzurz5bj.txt === reduce.pl bib === id = cord-184744-oyc2djxk author = Parvez, Md Sorwer Alam title = Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3653 sentences = 224 flesch = 49 summary = The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. The main protease proteins, RNA-dependent RNA polymerase and spike protein of SARS-CoV-2 were employed to molecular docking study with the repurposed drug candidates from plant origin for find out the better drug option towards the COVID-19 pandemic. In the present study, five plantr based therapeutics such as Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were suggested for potential inhibitors for the Main Protease protein, RNA dependent RNA polymerase and Spike protein of SARS-CoV-2 by using molecular docking based virtual screening study. cache = ./cache/cord-184744-oyc2djxk.txt txt = ./txt/cord-184744-oyc2djxk.txt === reduce.pl bib === id = cord-193136-7g6qr73e author = Bhattacharya, Sujit title = Visible Insights of the Invisible Pandemic: A Scientometric, Altmetric and Topic Trend Analysis date = 2020-04-22 pages = extension = .txt mime = text/plain words = 5019 sentences = 273 flesch = 57 summary = (2018) "Google Trends shows the changes in online interest for time series in any selected term in any country or region over a selected time period, for example, a specific year, several years, 3 weeks, 4 months, 30 days, 7 days, 4 hours, 1 hour, or a specified time-frame." They argue that as the internet penetration is increasing web based search activity has become a valid indicator of public behaviour. The paper positions itself in this direction; applying various tools and techniques of scientometrics, Altmetrics and Google Trends to draw meaning from the huge volume of research papers and online activity surrounding this pandemic. The trends observed in measures like lockdown, social distancing and quarantine at global and country level showed the societal increasing concern with these aspects.The findings of this study suggests how the research and public interest has been shaped around this disease. cache = ./cache/cord-193136-7g6qr73e.txt txt = ./txt/cord-193136-7g6qr73e.txt === reduce.pl bib === id = cord-193489-u6ewlh16 author = Wang, Rui title = Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date = 2020-04-29 pages = extension = .txt mime = text/plain words = 6066 sentences = 419 flesch = 62 summary = Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. Genetic identification and characterization of the geographic distribution, intercontinental evolution, and global trends of SARS-CoV-2 is the most efficient approach for studying COVID-19 genomic epidemiology and offer the molecular foundation for region-specific SARS-CoV-2 vaccine design, drug discovery, and diagnostic development [10] . We use K-means methods to cluster SARS-CoV-2 mutations, which provides the updated molecular information for the region-specific design of vaccines, drugs, and diagnoses. Table 5 presents the statistics of single mutations on various SARS-CoV-2 proteins that occurred in the recorded genomes between January 5, 2020, and April 24, 2020. Specifically, nucleocapsid protein has both the highest number of mutations per residues of 0.56 and the highest h-index of 27, suggesting that it is the most non-conservative protein in SARS-CoV-2 genomes. cache = ./cache/cord-193489-u6ewlh16.txt txt = ./txt/cord-193489-u6ewlh16.txt === reduce.pl bib === id = cord-202687-z17knvts author = Angelina, Emilio title = Drug Repurposing to find Inhibitors of SARS-CoV-2 Main Protease date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4110 sentences = 214 flesch = 53 summary = [11] In another study, Jin and colleagues identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of SARS-CoV-2 M pro in complex with this compound. Moreover, another recent crystallographic fragment screening against SARS-CoV-2 M pro that has been deposited in the Protein Data Bank (DOI: 10.2210/pdb5rgj/pdb ) also might help to find structural determinants for ligand anchoring within the enzyme binding cleft. Up to date, more than 100 structures of SARS-CoV-2 M pro with ligands bound at the enzyme binding cleft, have been released. While different fragments bind to different regions of SARS-CoV-2 M pro binding cleft, there are two interaction sites at the enzyme S1 sub-pocket that are targeted by most fragments. In this work we have performed a virtual screening of FDA approved drugs for repurposing as potential inhibitors of SARS-CoV-2 main protease M pro . cache = ./cache/cord-202687-z17knvts.txt txt = ./txt/cord-202687-z17knvts.txt === reduce.pl bib === id = cord-196129-3zfeamgs author = Demertzis, Konstantinos title = Flattening the COVID-19 Curve: The"Greek"case in the Global Pandemic date = 2020-10-09 pages = extension = .txt mime = text/plain words = 5639 sentences = 238 flesch = 46 summary = Focusing on the peculiarities of the disease spreading in Greece, both in epidemiological and in implementation terms, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. Within this context, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. This paper studied the COVID-19 temporal spread in Greece and proposed an innovative, realistic, and highly reliable methodology for forecasting the flattening of the curve, based on the spline and logistic regression algorithm, along with the complex network analysis. cache = ./cache/cord-196129-3zfeamgs.txt txt = ./txt/cord-196129-3zfeamgs.txt === reduce.pl bib === === reduce.pl bib === id = cord-203191-7ftg6bfx author = Guo, Kai title = Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3729 sentences = 184 flesch = 43 summary = title: Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA approved drugs and pre-clinical small-molecule compounds by integrating the gene expression perturbation data by chemicals from the Library of Integrated Network-Based Cellular Signatures (LINCS) project with publically available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We also collected a list of differentially expressed genes (DEGs) in SARS-CoV-2-infected lung BALF using a bulk RNA-Seq analysis to compare against the single-cell-based data. Repurposing analysis in severe COVID-19 patients 60 potent drugs were also selected in severe cases compared to controls (severe vs healthy group) according to their average CS between the replicates, and 25 of them involved in more than one cell subtype ( Figure 2B , Supplementary Tables S8 & S9) . cache = ./cache/cord-203191-7ftg6bfx.txt txt = ./txt/cord-203191-7ftg6bfx.txt === reduce.pl bib === id = cord-221611-eeybl35x author = Vijayan, Ramachandran title = Structure-based inhibitor screening of natural products against NSP15 of SARS- CoV-2 revealed Thymopentin and Oleuropein as potent inhibitors date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3083 sentences = 190 flesch = 48 summary = Here, we screened Selleckchem Natural product database of compounds against the NSP15, Thymopentin and Oleuropein showed highest binding energies. The structure of SARS-CoV-2 NSP15 protein is very similar to other Coronavirus NSP15 monomers, consisting of mainly three regions: the N-terminal domain, a subsequent middle domain, and a catalytic C-terminal nidoviral RNA uridylate-specific endoribonuclease domain. In order to design specific inhibitors against the Non-structural protein 15 (NSP15), Libraries of Selleckchem Natural products (https://www.selleckchem.com/screening/natural-productlibrary.html) were chosen for Virtual screening [24] [25] [26] . After the docking studies, the Molecular dynamic simulation [25] [26] [27] was performed for the top five screened compounds (Thymopentin, Ginsenoside, Oleuropein, Akebia Saponin D and Keampferitrin), to understand the binding stability of the docked complexes. In this study, structure based virtual screening followed by the validation through Molecular dynamic simulation approaches were carried out to find antiviral leads against NSP15 of SARS-CoV-2. cache = ./cache/cord-221611-eeybl35x.txt txt = ./txt/cord-221611-eeybl35x.txt === reduce.pl bib === id = cord-199630-2lmwnfda author = Ray, Sumanta title = Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date = 2020-07-05 pages = extension = .txt mime = text/plain words = 6389 sentences = 379 flesch = 53 summary = Therefore, host-(1) We link existing high-quality, long-term curated and refined, large scale drug/protein -protein interaction data with (2) molecular interaction data on SARS-CoV-2 itself, raised only a handful of weeks ago, (3) exploit the resulting overarching network using most advanced, AI boosted techniques (4) for repurposing drugs in the fight against SARS-CoV-2 (5) in the frame of HDT based strategies. As for (3)-(5), we will highlight interactions between SARS-Cov-2-host protein and human proteins important for the virus to persist using most advanced deep learning techniques that cater to exploiting network data. As per our simulation study, a large fraction, if not the vast majority of the predictions establish true, hence actionable interactions between drugs on the one hand and SARS-CoV-2 associated human proteins (hence of use in HDT) on the other hand. cache = ./cache/cord-199630-2lmwnfda.txt txt = ./txt/cord-199630-2lmwnfda.txt === reduce.pl bib === id = cord-208426-wz3jan5d author = Li, Hongying title = Airborne dispersion of droplets during coughing: a physical model of viral transmission date = 2020-08-05 pages = extension = .txt mime = text/plain words = 4495 sentences = 245 flesch = 57 summary = Using realistic air flow simulation, we model droplet dispersion from coughing and study the transmission risk related to SARS-CoV-2. Notably, numerical methods, such as Computational Fluid Dynamics (CFD) based on Reynolds Averaged Navier-Stokes (RANS) turbulence models 31 produce high resolution flow fields and concentration data, 32 which not only compensate for slow instrumental speeds of analytical techniques, 25 but are also adaptable to different environments and scenarios, such as passengers in an aircraft cabin, 33 and more recently, a cough dispersion study in an outdoor environment under significant wind speeds, 34 whose results are useful in integrated transmission modeling. As detailed in the Supplementary Information, the model cough is inclined downwards at an average of 27·5°, 37 follows a characteristic air flow pattern 33,37 at breath temperature of 36°C, and emits a cluster of droplets with a standard size distribution 11, 38 and viral loading 39 cache = ./cache/cord-208426-wz3jan5d.txt txt = ./txt/cord-208426-wz3jan5d.txt === reduce.pl bib === id = cord-196265-mvnkkcow author = M'esz'aros, B'alint title = Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date = 2020-04-21 pages = extension = .txt mime = text/plain words = 12653 sentences = 666 flesch = 47 summary = We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. Proximity-based mass spectrometry on the MHV replication complex further revealed that the RTC environment repurposes components from the host autophagy, vesicular trafficking and translation machineries (V'kovski et al., 2019) In the present work, we identify a set of conserved SLiM candidates in the ACE2 and integrin proteins, which are likely to act in the cell entry system of SARS-CoV-2. The C-terminal tail of both subunits share a high degree of sequence similarity, and similarly to ACE2, contain several known and candidate SLiMs (see Table 1 and Figure 6 ) that propagate signals in the cytoplasm and regulate integrin activity not just through intracellular pathways, but also changing the structural state of the ectodomains determining ligand binding capacity (Anthis and Campbell, 2011) . cache = ./cache/cord-196265-mvnkkcow.txt txt = ./txt/cord-196265-mvnkkcow.txt === reduce.pl bib === id = cord-197818-asd39zbj author = Wu, Kai title = Magnetic Immunoassays: A Review of Virus and Pathogen Detection Before and Amidst the Coronavirus Disease-19 (COVID-19) date = 2020-07-09 pages = extension = .txt mime = text/plain words = 5625 sentences = 344 flesch = 41 summary = In this review, magnetic biosensors' application in virus and pathogen detection will be summarized and discussed based on the different working principle of the technologies. [69] The key take-away point here is that several experimental demonstrations of the magnetic assays for virus detection based on GMRs and the reported LOD indicate that GMR-based bioassay is one of the promising candidates for onsite, rapid, and sensitive detection of COVID-19. reported the volume-based MPS immunoassay platform utilizing the polyclonal antibodies induced cross-linking of MNPs for one-step, wash-free detection of H1N1 nucleoprotein molecules. In this section, we reviewed some representative works that use magnetic materials are auxiliary tools for high sensitivity virus and pathogen detections, as summarized in Table 3 . We reviewed the magnetic immunoassay literatures prior to COVID-19 and highlighted some promising tools for detecting pathogens as well as viruses with high specificity and sensitivity. Magnetic quantum dot based lateral flow assay biosensor for multiplex and sensitive detection of protein toxins in food samples cache = ./cache/cord-197818-asd39zbj.txt txt = ./txt/cord-197818-asd39zbj.txt === reduce.pl bib === id = cord-203232-1nnqx1g9 author = Canturk, Semih title = Machine-Learning Driven Drug Repurposing for COVID-19 date = 2020-06-25 pages = extension = .txt mime = text/plain words = 5023 sentences = 257 flesch = 52 summary = Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. cache = ./cache/cord-203232-1nnqx1g9.txt txt = ./txt/cord-203232-1nnqx1g9.txt === reduce.pl bib === id = cord-220618-segffkbn author = Bonamassa, Ivan title = Geometric characterization of SARS-CoV-2 pandemic events date = 2020-07-20 pages = extension = .txt mime = text/plain words = 8692 sentences = 452 flesch = 50 summary = Disposing of a robust and comprehensive framework to classify the SARS-CoV-2 pandemic events reported across different countries not only can enhance early [19, 20] public and governmental responses in containing the spreading and/or better absorbing the impact of a rapidly emerging epidemic outbreak, but it can further provide new information to better understand real-world epidemics and to boost the forecasting power of existing models [21] [22] [23] [24] [25] [26] [27] [28] [29] . Moving to a polar representation, we classify the plumes' form through a set of three geometric parameters yielding two complementary rating scales for the SARS-CoV-2 pandemic types: one according to their epidemic magnitude-labeled with roman numbers from I to X for increasing strengths-and measuring the "size" of a national outbreak, and a second one according to their intensity-labeled alphabetically from A to D for increasing speed-quantifying instead the damage inflicted on the population. cache = ./cache/cord-220618-segffkbn.txt txt = ./txt/cord-220618-segffkbn.txt === reduce.pl bib === id = cord-229246-qgp7ksq8 author = Babino, Andres title = Masks and COVID-19: a causal framework for imputing value to public-health interventions date = 2020-06-09 pages = extension = .txt mime = text/plain words = 3605 sentences = 219 flesch = 69 summary = In this paper, we aim to fill this gap by testing the hypothesis that the policy change regarding masks by the CDC (and local governments) decreased the number of positive cases in the states of Connecticut (CT), Massachusetts (MA), New York (NY), Rhode Island (RI), and Virginia (VA). The data from RI is harder to interpret because stay-at-home orders and masks guidelines happened close in time, and data from before April are unreliable (with less than 500 tests a day). The framework that we presented is data-driven, and therefore it relies on only a handful of hypotheses as compared to other methods For example, the counterfactual analysis relies on one hypothesis: the log-odds are piecewise linear (see Eq. 6 in the supplementary material)without the need to assume any of the hypotheses of the SIR model. cache = ./cache/cord-229246-qgp7ksq8.txt txt = ./txt/cord-229246-qgp7ksq8.txt === reduce.pl bib === id = cord-214854-ck61ja2t author = Zhong, Jing title = Rapid and sensitive detection of SARS-CoV-2 with functionalized magnetic nanoparticles date = 2020-10-08 pages = extension = .txt mime = text/plain words = 2059 sentences = 120 flesch = 47 summary = Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and sensitive detection of specific biomolecules, e.g. protein, DNA/RNA and virus. demonstrated the feasibility of wash-free, sensitive and specific assays for the detection of different viruses, e.g. orchid and influenza viruses, with antibody-functionalized MNPs by measuring the reduction in the ac susceptibility in mixed-frequency ac magnetic fields [23] [24] [25] . All these approaches have demonstrated that MNP-based homogeneous biosensing is a wash-free and mix-and-measure approach for rapid and sensitive detection of specific biomolecules. cache = ./cache/cord-214854-ck61ja2t.txt txt = ./txt/cord-214854-ck61ja2t.txt === reduce.pl bib === id = cord-243806-26n22jbx author = Vandelli, Andrea title = Structural analysis of SARS-CoV-2 and prediction of the human interactome date = 2020-03-30 pages = extension = .txt mime = text/plain words = 5252 sentences = 317 flesch = 52 summary = Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . cache = ./cache/cord-243806-26n22jbx.txt txt = ./txt/cord-243806-26n22jbx.txt === reduce.pl bib === id = cord-206006-8l7hrany author = Wang, Rui title = Mutations on COVID-19 diagnostic targets date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1605 sentences = 94 flesch = 56 summary = Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on the genotyping of 7818 SARS-CoV-2 genome samples collected up to May 1, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have had mutations. We further show that SARS-CoV-2 has the most devastating mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been unfortunately used by countries around the world to diagnose COVID-19. It is interesting to note that N-China-F [10] is the most inefficient reagent among all primers/probes and its SARS-CoV-2 target has eight mutations involving samples in all five clusters, which may explain many media reports about the inefficiency of certain COVID-19 diagnostic kits made in China. cache = ./cache/cord-206006-8l7hrany.txt txt = ./txt/cord-206006-8l7hrany.txt === reduce.pl bib === id = cord-218886-lqme2j8n author = Asghari, Aref title = Fast Accurate Point of Care COVID-19 Pandemic Diagnosis Enabled Through Advanced Lab-on-a-Chip Optical Biosensors: Opportunities and Challenges date = 2020-08-01 pages = extension = .txt mime = text/plain words = 6422 sentences = 287 flesch = 46 summary = Primarily, an optical biosensor translates the capture of the target analyte in a measurable alteration of a light property, such as refractive index (RI), intensity or resonance shift, through different methods such as resonators and interferometers ( Fig. 2 ). The sensing transduction signals in Optical label-free biosensing platform functions based on miniscule changes in refractive index resulting from the attachment of biomolecules to the immobilized bioreceptors. On the other hand, by simply depositing a gold layer, the device concept can be used for a surface plasmon resonance, which can improve the LOD even further 71 In order to maximize the sensitivity of the waveguide-based biosensor, the speed of light can be reduced even further. Graphene unique electrical properties has also been exploited effectively to develop different transistor based label-free biosensors including COVID-19 detection system 39 (fig 18.a) . cache = ./cache/cord-218886-lqme2j8n.txt txt = ./txt/cord-218886-lqme2j8n.txt === reduce.pl bib === id = cord-217961-2rczhxp2 author = Chitsaz, Mohsen title = A small molecule drug candidate targeting SARS-CoV-2 main protease date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2298 sentences = 133 flesch = 56 summary = We aligned the inhibitor on the protein and on the initial conformation of the ligand and computed structural deviations RMSDs. To observe the interaction of the inhibitor with the active site and confirming that the inhibitor stays in the active site of SARS-CoV-2 protease, we ran a simulation of 250ns that was 10 times longer than two previous MD simulations. For each of the two complexes, we analyzed the active-site by investigating all hydrophobic, H-bond, ionic and water bridge interactions of the inhibitor with SARS-Cov-2 protease and SARS-CoV protease (see Fig. 5 and Fig. 6 respectively) . We observed that the inhibitor remains in the active site for the entire duration of the simulation and maintains H-bond and water bridge contacts with GLU166 and hydrophobic Pi-Pi stacking contact with HIS41 (see Fig. 13 ). Our primary observation was that the molecule remained in the active site of SARS-CoV-2 protease for the entire duration of the simulation. cache = ./cache/cord-217961-2rczhxp2.txt txt = ./txt/cord-217961-2rczhxp2.txt === reduce.pl bib === id = cord-222664-4qyrtzhu author = Coban, Mathew title = Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date = 2020-07-06 pages = extension = .txt mime = text/plain words = 11220 sentences = 638 flesch = 46 summary = We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors; S/Ace2, Tmprss2, Cathepsins L and K, and Mpro to prevent binding, membrane fusion and replication of the virus, respectively. Using a computational pipeline that aimed to expeditiously identify lead compounds against COVID-19, we combined compound library preparation, molecular modeling, and structure simulations to generate an ensemble of conformations and increase high quality docking outcomes against two essential SARS-CoV-2 viral proteins and their host protein interactions; S/Ace2, Tmprss2, Cathepsin L and K, and M pro that are known to control both viral binding, entry and virus replication (Fig. 1A) . cache = ./cache/cord-222664-4qyrtzhu.txt txt = ./txt/cord-222664-4qyrtzhu.txt === reduce.pl bib === id = cord-228152-k4bw8w5g author = Pyzer-Knapp, Edward O. title = Using Bayesian Optimization to Accelerate Virtual Screening for the Discovery of Therapeutics Appropriate for Repurposing for COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2981 sentences = 140 flesch = 49 summary = The novel Wuhan coronavirus known as SARS-CoV-2 has brought almost unprecedented effects for a non-wartime setting, hitting social, economic and health systems hard.~ Being able to bring to bear pharmaceutical interventions to counteract its effects will represent a major turning point in the fight to turn the tides in this ongoing battle.~ Recently, the World's most powerful supercomputer, SUMMIT, was used to identify existing small molecule pharmaceuticals which may have the desired activity against SARS-CoV-2 through a high throughput virtual screening approach. In this communication, we demonstrate how the use of Bayesian optimization can provide a valuable service for the prioritisation of these calculations, leading to the accelerated identification of high-performing candidates, and thus expanding the scope of the utility of HPC systems for time critical screening It can be seen than on every task the PDTS method of Bayesian optimization outperforms random sampling and thus shows great potential for the efficient prioritisation of HTVS testing of pharmaceuticals for activity against SARS-CoV-2. cache = ./cache/cord-228152-k4bw8w5g.txt txt = ./txt/cord-228152-k4bw8w5g.txt === reduce.pl bib === id = cord-218639-ewkche9r author = Ghavasieh, Arsham title = Multiscale statistical physics of the Human-SARS-CoV-2 interactome date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3175 sentences = 184 flesch = 48 summary = Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing strategies. Similarly, they have been used for characterizing the interactions between viral and human proteins in case of SARS-CoV-2 [13] [14] [15] , providing insights into the structure and function of the virus 16 and identifying drug repurposing strategies 17, 18 . Instead, we model the propagation of perturbations from viral nodes through the whole system, using bio-chemical and regulatory dynamics, to obtain the spreading patterns and compare the average impact of viruses on human proteins. Our results shed light on the unexplored aspects of SARS-CoV-2, from the perspective of statistical physics of complex networks, and the presented framework opens the doors for further theoretical developments aiming to characterize structure and dynamics of virus-host interactions, as well as grounds for further experimental investigation and potentially novel clinical treatments. cache = ./cache/cord-218639-ewkche9r.txt txt = ./txt/cord-218639-ewkche9r.txt === reduce.pl bib === id = cord-235691-en6fgilb author = Althouse, Benjamin M. title = Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4811 sentences = 212 flesch = 47 summary = In Figure 2 we show an example by utilizing a stochastic branching process model with both Poisson and SARS-CoV-1 like NB distribution (k = 0.16) under the same mean R 0 = 2.6 26 , with different population sizes ranging from small clusters of 10 like households to large ones of 10 6 like city-wide. Because they play an important role in the spread of infection, hotspots pose an opportunity for surveillance and control: focusing on facilities and activities known to sustain hotspots, such as healthcare facilities, nursing homes, prisons, meat-packing plants, homeless shelters, schools, mass gatherings, as well as those places with closed, poorly circulated environments, can provide efficient ways to identify potential SSEs before they happen, therefore, potentially reducing a substantial amount of transmission in the population. Multiple lines of evidence at the individual-and population-level strongly indicate the role of SSEs in the transmission dynamics of SARS-CoV-2 and that we should not overlook the heterogeneity in numbers of secondary infections 57 . cache = ./cache/cord-235691-en6fgilb.txt txt = ./txt/cord-235691-en6fgilb.txt === reduce.pl bib === id = cord-245161-xbw72k4m author = Castano, Nicolas title = Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date = 2020-05-23 pages = extension = .txt mime = text/plain words = 11558 sentences = 720 flesch = 44 summary = Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. cache = ./cache/cord-245161-xbw72k4m.txt txt = ./txt/cord-245161-xbw72k4m.txt === reduce.pl bib === id = cord-252232-vgq6gjpx author = Hou, Yuxuan title = Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date = 2010-06-22 pages = extension = .txt mime = text/plain words = 3208 sentences = 159 flesch = 57 summary = Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry. cache = ./cache/cord-252232-vgq6gjpx.txt txt = ./txt/cord-252232-vgq6gjpx.txt === reduce.pl bib === id = cord-249166-0w0t631x author = Booss-Bavnbek, Bernhelm title = Dynamics and Control of Covid-19: Comments by Two Mathematicians date = 2020-08-17 pages = extension = .txt mime = text/plain words = 7251 sentences = 424 flesch = 60 summary = We give an overview of the main branches of mathematics that play a role and sketch the most frequent applications, emphasising mathematical pattern analysis in laboratory work and statistical-mathematical models in judging the quality of tests; demographic methods in the collection of data; different ways to model the evolution of the pandemic mathematically; and clinical epidemiology in attempts to develop a vaccine. A few physicians suggested that every epidemic ends because there are finally not enough people left to be infected, which is a naïve predecessor to the mathematical-epidemiologic concept of Herd Immunity (see Sect. Parallel to the entering the scene of these and other epidemics, and partly motivated by them, basically new mathematical tools of public health emerged in the first part of the 20 th Century, preceded by a few studies in the late 19 th . Dealing with large epidemics mathematically was no longer a matter of demography alone, although that continued to be the main tool for estimating number of cases and deaths. cache = ./cache/cord-249166-0w0t631x.txt txt = ./txt/cord-249166-0w0t631x.txt === reduce.pl bib === id = cord-252292-qz9msrl7 author = Wilder-Smith, Annelies title = Experience of Severe Acute Respiratory Syndrome in Singapore: Importation of Cases, and Defense Strategies at the Airport date = 2006-03-08 pages = extension = .txt mime = text/plain words = 2165 sentences = 107 flesch = 58 summary = METHODS: Information on imported cases of SARS and measures taken at entry points to Singapore was retrieved from the Ministry of Health and the Civil Aviation Authority of Singapore. The large outbreaks in Hong Kong, Toronto, Singapore and Vietnam were initiated by cases that were imported before this new disease had been identified and before appropriate measures had been put in place to prevent transmission. Information on measures taken at the national airport (Changi Airport), seaports and road entry points to reduce the importation of further cases was obtained from the Civil Aviation Authority of Singapore (CAAS) and from the websites of the Ministry of Health, Singapore (http://www.moh.gov.sq/sars/news/chronology.html; accessed 15 June). She became very unwell and breathless on her return flight from Beijing to Singapore on 26 March, but no precautions were taken on the airplane,as her diagnosis was not known.Immediately after arrival, her mother took her in a taxi to Tan Tock Seng Hospital,where she was isolated in the Intensive Care Unit. cache = ./cache/cord-252292-qz9msrl7.txt txt = ./txt/cord-252292-qz9msrl7.txt === reduce.pl bib === id = cord-252005-3ld5e7f5 author = Lewis, Nathaniel M title = Household Transmission of SARS-CoV-2 in the United States date = 2020-08-16 pages = extension = .txt mime = text/plain words = 3039 sentences = 209 flesch = 55 summary = The Centers for Disease Control and Prevention collaborated (CDC) with state and local health departments in the Milwaukee, Wisconsin, and Salt Lake City, Utah, metropolitan areas to identify persons with laboratory-confirmed SARS-CoV-2 infection captured by public health surveillance during March 22-April 25, 2020. The investigation team defined persons identified by local health departments as "index patients." Households were selected by convenience sampling and considered eligible if the index patient was not hospitalized at the time, lived with ≥1 additional person, and tested positive for SARS-CoV-2 rRT-PCR from a nasopharyngeal (NP) swab collected ≤10 days prior to enrollment. One study from China estimated a 28% SIR for spouses of primary patients and 4% for household contacts aged A c c e p t e d M a n u s c r i p t 10 <18 years by SARS-CoV-2 rRT-PCR testing [6] . cache = ./cache/cord-252005-3ld5e7f5.txt txt = ./txt/cord-252005-3ld5e7f5.txt === reduce.pl bib === id = cord-251581-8ubyveyt author = Szymkowiak, Andrzej title = In-store epidemic behavior: scale development and validation date = 2020-05-04 pages = extension = .txt mime = text/plain words = 6038 sentences = 297 flesch = 51 summary = All identified factors significantly correlated with the in-store infection threat which reiterates the importance of providing information revealing the true scale of the pandemic and not leaving space for individuals to create subjective probability judgments. Nonetheless, one must also bear in mind that grocery stores are a place for possible transmission of many bacterial and viral pathogens (Bell et al., 2009; Dalton, New, & Health, 2006; Sinclair, Fahnestock, Feliz, Patel, & Perry, 2018) , causing consumers to undertake various behavioral changes in their approach to shopping. Based on the analysis of this limited quantity of research related to consumer behavioral changes in response to epidemics, it is clear that there is a gap in research on how the fear of contagion and not budgetary limitations can impact consumer willingness to shop at stationery stores. Moreover, the questionnaire was performed during the outbreak of the COVID-19 pandemic which limits the possibility of comparing the results for in-shop behaviors with a time from before the epidemic. cache = ./cache/cord-251581-8ubyveyt.txt txt = ./txt/cord-251581-8ubyveyt.txt === reduce.pl bib === id = cord-252305-rstxyofq author = Tyan, Kevin title = Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting date = 2020-08-31 pages = extension = .txt mime = text/plain words = 2062 sentences = 156 flesch = 49 summary = We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. While this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. Some products on List N do not have an emerging viral pathogen claim but have been included because they 1) demonstrate efficacy against another human coronavirus similar to SARS-CoV-2 or 2) are EPA-approved against select viruses that are harder-to-kill [5] . The publication of the EPA List N was an important step in providing a resource for selecting disinfectants against SARS-CoV-2 and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability. cache = ./cache/cord-252305-rstxyofq.txt txt = ./txt/cord-252305-rstxyofq.txt === reduce.pl bib === id = cord-252428-w6tsf478 author = Hayashi, Takuma title = Highly conserved binding region of ACE2 as a receptor for SARS-CoV-2 between humans and mammals date = 2020-09-29 pages = extension = .txt mime = text/plain words = 2696 sentences = 158 flesch = 52 summary = The multiple sequence alignments of the ACE2 proteins shows high homology and complete conservation of the five amino acid residues: 353-KGDFR-357 with humans, dogs, cats, tigers, minks, and other animals, except for snakes. (B) The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks. The multiple sequence alignments of the sampled ACE2 proteins revealed high homology and high conservation of the five amino acid residues: 353-KGDFR-357 with specific reference to humans, dogs, cats, tigers, minks, and other animals, except for snakes ( Figure 1 (A) and Supplementary Materials). The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks (Figure 1(B) ). cache = ./cache/cord-252428-w6tsf478.txt txt = ./txt/cord-252428-w6tsf478.txt === reduce.pl bib === id = cord-251995-nbqukjzv author = Xiao, Fei title = Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1447 sentences = 94 flesch = 53 summary = title: Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged in China, causing a major outbreak of severe pneumonia and spreading to >200 other countries (1) . A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. The viral load was higher in feces than in respiratory specimens collected at multiple time points (17-28 days after symptom onset) (Appendix Figure, panel D) . We attempted to isolate SARS-CoV-2 virus from 3 of the viral RNA-positive patients. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient cache = ./cache/cord-251995-nbqukjzv.txt txt = ./txt/cord-251995-nbqukjzv.txt === reduce.pl bib === id = cord-252049-rgdynmla author = Tomar, Sakshi title = Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CL(pro)): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS date = 2015-06-08 pages = extension = .txt mime = text/plain words = 11805 sentences = 601 flesch = 56 summary = All coronaviruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the proteolytic activity of the nsp5 protease (also known as 3C-like protease, 3CL(pro)) during virus replication, making it a high value target for the development of anti-coronavirus therapeutics. Therefore, we determined the dependence of the enzymatic activity of MERS-CoV 3CL pro on the total enzyme concentration and compared it with other 3CL pro enzymes from HKU4, HKU5, and SARS coronaviruses (Fig. 2) . The kinetic data for all four 3CL pro enzymes, MERS-CoV, HKU4-CoV, HKU5-CoV, and SARS-CoV, fit well to this model, and the resulting values for the monomer-dimer equilibrium dissociation constant, K d , and apparent turnover number, k cat , for each enzyme are provided in Table 2 . Compound 11 also forms two direct and one water-mediated hydrogen bond interactions with amino acids in the MERS-CoV 3CL pro active site (Fig. 6E) . cache = ./cache/cord-252049-rgdynmla.txt txt = ./txt/cord-252049-rgdynmla.txt === reduce.pl bib === id = cord-252033-43fbfglt author = Plebani, Mario title = Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays? date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2999 sentences = 152 flesch = 44 summary = METHODS: Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Aim of this study was to evaluate different chemiluminescent (CLIA) and enzyme-linked immunosorbent (ELISA) assays for SARS-CoV-2 antibodies in COVID-19 patients and healthcare operators, to identify appropriate cut-offs and evaluate diagnostic accuracy. Donors (only for CLIA assays) and negative autoimmune patients results were included to verify possible analytical interferences and differences with respect to healthcare workers who repeatedly tested negative to nasopharyngeal swab. Rigorous comparative performance data are crucial to understanding the potential clinical usefulness of serological assays, starting from the evaluation of analytical performance characteristics to improve the definition of diagnostic accuracy not only in terms of specificity and sensitivity but also as positive and negative likelihood ratios, in order to provide reliable clinical information in different disease prevalence settings. cache = ./cache/cord-252033-43fbfglt.txt txt = ./txt/cord-252033-43fbfglt.txt === reduce.pl bib === id = cord-252286-377y9aqx author = Gauss, Tobias title = Preliminary pragmatic lessons from the SARS-CoV-2 pandemic from France date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2161 sentences = 132 flesch = 43 summary = Abstract The first wave of the SARS-CoV-2 pandemic required an unprecedented and historic increase in critical care capacity on a global scale in France. The SARS-CoV-2 pandemic requires an unprecedented and historic increase in critical care capacity on a global scale. The ongoing fight against the pandemic and potential resurgence of the virus made it compelling for the authors to share specific concepts for the management of critical care surge capacity. One particularity of any exceptional situation (mass casualty, pandemic, etc.) is the activation of a structured crisis mode during which authority lies within the crisis committee, relying on a chain of command and clearly defined principles of control. ICU/HDU capacities management required conscious effort to preserve protected space for non-SARS-CoV-2 critical care and respond to the evolving situation. Training was essential to prepare healthcare professionals in the first days of the pandemic for PPE use, airway management, cleaning, cardiac arrest, etc. cache = ./cache/cord-252286-377y9aqx.txt txt = ./txt/cord-252286-377y9aqx.txt === reduce.pl bib === id = cord-224516-t5zubl1p author = Daubenschuetz, Tim title = SARS-CoV-2, a Threat to Privacy? date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4799 sentences = 214 flesch = 46 summary = We furthermore discuss the issues with privacy that can occur during a crisis such as this global pandemic and what can be done to ensure information security and hence appropriate data protection. When we are considering the example of doctors treating their patients, we can use the framework of contextual integrity to reason about the appropriate information flow as follows: the patient is both the sender and the subject of the data exchange, the doctor is the receiver, the information type is the patient's medical information, the transmission principle includes, most importantly, doctor-patient confidentiality aside from public health issues. In Germany, the authority for disease control and prevention, the Robert Koch Institute (RKI), made headlines on March 18, 2020, as it became public that telecommunication provider Telekom had shared an anonymized set of mobile phone movement data to monitor citizens' mobility in the fight against SARS-CoV-2. cache = ./cache/cord-224516-t5zubl1p.txt txt = ./txt/cord-224516-t5zubl1p.txt === reduce.pl bib === id = cord-252103-lsaa1nx0 author = Pearks Wilkerson, Alison J title = Coronavirus outbreak in cheetahs: Lessons for SARS date = 2004-03-23 pages = extension = .txt mime = text/plain words = 956 sentences = 52 flesch = 54 summary = To characterize the genomic disposition of the cheetahs' Aju-CoV strain, PCR primers based on alignment of seven coronavirus gene segments (pol1a, pol1b, S, M, N, 7a/7b, and 3′ ′UTR), were used to amplify cDNA from archived cheetah liver and kidney tissues collected during the Winston outbreak. The phylogenetic analyses indicate a close similarity of the Aju-CoV and the FCoV strains, suggesting the cheetah virus is closely related to, if not indistinguishable from, domestic cat isolates. Fourth, while mortality among humans with SARS symptoms and house cats with FCoV is low, around 5-10%, cheetahs with Aju-CoV exhibited the opposite extreme, showing 90% morbidity and over 60% mortality. If this hypothesis is correct, the greater genetic diversity of domestic cats and humans may reduce the severity of the epidemic, and also contribute to the occurrence of rare genetically determined SARS-CoV super-spreaders who can infect with high virulence. cache = ./cache/cord-252103-lsaa1nx0.txt txt = ./txt/cord-252103-lsaa1nx0.txt === reduce.pl bib === id = cord-252761-ro5tj0tx author = Marriott, Deborah title = Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1228 sentences = 92 flesch = 60 summary = title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent's Hospital and associated screening clinics, Sydney, NSW. Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. We report the prevalence of SARS-CoV-2 and other respiratory pathogens including co-infection, and evaluate the A c c e p t e d M a n u s c r i p t 4 temporal pattern of respiratory infections alongside the introduction, and subsequent relaxation, of physical distancing measures. Limited data have been reported on co-infection between SARS-CoV-2 and other respiratory viruses. In conclusion, the introduction of multiple public health measures to minimise SARS-CoV-2 transmission in Australia from mid to late-March 2020 had a major impact on the prevalence of all respiratory viral infections highlighting the effectiveness of this approach. cache = ./cache/cord-252761-ro5tj0tx.txt txt = ./txt/cord-252761-ro5tj0tx.txt === reduce.pl bib === id = cord-252557-f89m6xv5 author = Ong, John title = Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard date = 2020-04-02 pages = extension = .txt mime = text/plain words = 1300 sentences = 97 flesch = 47 summary = title: Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Over 3000 healthcare workers (HCW) in China are suspected of having coronavirus disease 2019 (COVID-19) and over 1700 tested positive. PPE recommendation (general staff): ► All patients to be offered surgical face masks Contingency plan for high-risk patients detected in endoscopy: ► Not stated. PPE recommendation (general staff): ► None stated Contingency plan for high-risk patients detected in endoscopy: ► Not stated. 4 Patient screening undoubtedly is the foremost step at preventing nosocomial transmission; timely detection allows postponement of non-urgent procedures until the infection has resolved, significantly reducing transmission risk to patients and staff. Detecting 'false negatives' that slip through processes allows for the identification of HCWs and patients with infection risk after exposure to asymptomatic or subclinical carriers in the viral incubation period at the time of endoscopy. cache = ./cache/cord-252557-f89m6xv5.txt txt = ./txt/cord-252557-f89m6xv5.txt === reduce.pl bib === id = cord-251961-g0n85kxz author = Li, Guoming title = Safety and efficacy of Artemisinin-Piperaquine for treatment of COVID-19: an open-label, non-randomized, and controlled trial date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3408 sentences = 190 flesch = 53 summary = CONCLUSIONS: In patients with mild to moderate COVID-19, the time to reach undetectable SARS-CoV-2 was significantly shorter in the AP group than that in the control group. According to the "China's Novel Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Seventh Edition) ", COVID-19 patients are usually categorized into mild, moderate, severe, and critical based on their symptoms. Initially, this trial was an open-label randomized parallel-group controlled trial intended to compare the efficacy and safety of AP tablets in comparison with hydroxychloroquine to treat patients with mild to moderate COVID-19. And the rate of patients to undetected SARS-CoV-2 by RT-PCR at day 7, 10, 14, 21, and 28 during drug administration, the CT images results within ten days, the abnormal laboratory index and adverse events would be compared between the two treatments. cache = ./cache/cord-251961-g0n85kxz.txt txt = ./txt/cord-251961-g0n85kxz.txt === reduce.pl bib === id = cord-252234-3txk22yj author = Kaniyala Melanthota, Sindhoora title = Elucidating the microscopic and computational techniques to study the structure and pathology of SARS‐CoVs date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3988 sentences = 226 flesch = 50 summary = Coronavirus replication is initiated with the binding of virion particles to the receptors of the cells, further directing the translation of the viral genome in the cytoplasm and synthesis of membrane-bound proteins. Previous studies have shown the use of a scanning electron microscope (SEM) for obtaining surface information and TEM for revealing inner components of the SARS-CoV particle. Table 1 compares various microscopy techniques for understanding the structure of SARS-CoV and its effect in host cells. The E6 cell lines were subjected to thin-layer electron microscopy and the images revealed typical coronavirus particles within the rough endoplasmic reticulum, specifically in cisternae, as well as in vesicles and several large clusters of extracellular particles were found attached to the surface of the plasma membrane. Apart from studying how the virus enters the cell, immunofluorescence was also used to investigate antibody response to the SARS-CoV and use it as an efficient detection method. cache = ./cache/cord-252234-3txk22yj.txt txt = ./txt/cord-252234-3txk22yj.txt === reduce.pl bib === id = cord-252015-9oiwcn8q author = Niu, Alex title = COVID-19 in allogeneic stem cell transplant: high false-negative probability and role of CRISPR and convalescent plasma date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1278 sentences = 82 flesch = 49 summary = Shortly thereafter, RT-PCR/CRISPR was performed on a blood sample collected on hospital day 36 for clinical purposes and demonstrated strong detection of SARS-CoV-2 RNA (Fig. 1c) . Here, we present two cases of ASCT recipients who presented with respiratory illnesses, initially testing negative for SARS-CoV-2 with conventional RT-PCR, then positive with the more sensitive RT-PCR/CRISPR technique. Our findings suggest that ASCT recipients with negative nasopharyngeal SARS-CoV-2 RT-PCR, but evidence of lower respiratory tract disease, might indeed have COVID-19 that can be detected using a CRISPR-based platform. While safety concerns with performing bronchoscopy remain high with this infection, and COVID-19specific treatments depend on securing a positive test, it may be beneficial to pursue diagnosis with other tissue sources, such as whole blood or plasma. In conclusion, early diagnosis and treatment of COVID-19 is crucial in ASCT recipients, and evaluation regarding the use of other tissue sources for detection of SARS-CoV-2 along with multimodality therapy is required in the continual evolution of this pandemic. cache = ./cache/cord-252015-9oiwcn8q.txt txt = ./txt/cord-252015-9oiwcn8q.txt === reduce.pl bib === id = cord-104501-e5e0xrou author = Bashash, Davood title = The Prognostic Value of Thrombocytopenia in COVID-19 Patients; a Systematic Review and Meta-Analysis date = 2020-09-19 pages = extension = .txt mime = text/plain words = 2752 sentences = 146 flesch = 48 summary = To provide a well-conceptualized viewpoint demonstrating the prognostic value of platelet count in SARS-CoV-2 infection, we performed a meta-analysis of pertinent literature to evaluate whether the emergence of thrombocytopenia could discriminate between severe and non-severe cases. Even though the results of a recent study to establish a prediction model for the prognosis of SARS-CoV-2 infection (19) introduced C reactive protein, lactic dehydrogenase, and lymphocyte count as the most valuable laboratory parameters reflecting COVID-19 severity, articles continuously introducing novel biomarkers with the ability to predict disease outcome are published daily. To provide a clear viewpoint demonstrating the prognostic value of platelet count in this novel infection, we performed a meta-analysis of pertinent literature representing information on the indicated parameter in patients with a clinically validated definition of severe disease. cache = ./cache/cord-104501-e5e0xrou.txt txt = ./txt/cord-104501-e5e0xrou.txt === reduce.pl bib === id = cord-251943-jzaeaxam author = Zhang, Jian‐San title = A serological survey on neutralizing antibody titer of SARS convalescent sera date = 2005-08-24 pages = extension = .txt mime = text/plain words = 2542 sentences = 139 flesch = 50 summary = A seroepidemiologic study was conducted in North China in 2003 to determine the neutralizing antibody titer of severe acute respiratory syndrome (SARS) convalescent sera. A total of 99 SARS convalescent serum samples were collected from patients from the Inner Mongolia Autonomous Region, Hebei Province, and Beijing 35–180 days after the onset of symptoms. To gain a comprehensive understanding of the antibody to SARS-CoV, we report the anti-SARS antibody titer of 87 SARS convalescent sera determined by neutralization assay. These 87 serum samples were confirmed to be positive for anti-SARS antibodies with the combination of ELISA, neutralization, and Western blot, so they were pooled to form a convalescent sera database for the further analysis of neutralizing antibody titer. The anti-SARS neutralizing antibody titer of 87 positive convalescent sera was analyzed quantitatively by the neutralization assay. In our laboratory, a combination of ELISA, neutralization assay, and Western blot were performed on 99 SARS convalescent sera. cache = ./cache/cord-251943-jzaeaxam.txt txt = ./txt/cord-251943-jzaeaxam.txt === reduce.pl bib === id = cord-252574-7oh0k139 author = Nicastro, Emanuele title = A Pediatric Emergency Department Protocol to Avoid Intra-Hospital Dispersal of SARS-CoV-2 during the Outbreak in Bergamo, Italy date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1594 sentences = 88 flesch = 41 summary = In Lombardy, the main outbreak of the infection was located in a community hospital in the Bergamo province, suggesting that the community spread of the infection probably arose from a large cohort of subjects who were in contact with SARS-CoV-2 infected patients attending health care facilities, and who were probably unrecognized at that time., so far pediatric services have not experienced the COVID-19 To address these issues, we developed a protocol addressing reception, risk-management and hospitalization of suspected SARS-CoV-2 cases at the pediatric emergency department and medical-surgical units aimed at containing intra-hospital transmission of the infection, considering that currently our hospital is the largest referral site in the primary outbreak area in Italy. Suspected COVID-19 patients requiring hospitalization are managed by health care personnel (HCP) using personal protective equipment (PPE) (FFP2/N95 respirator + eye protection goggles or face shield + 5 isolation gowns + face mask + gloves), who perform the acquisition of an NP/OP swab for SARS-CoV-2 real time-PCR testing. cache = ./cache/cord-252574-7oh0k139.txt txt = ./txt/cord-252574-7oh0k139.txt === reduce.pl bib === id = cord-252288-klkoerfn author = Zhang, Bicheng title = Immune Phenotyping Based on the Neutrophil-to-Lymphocyte Ratio and IgG Level Predicts Disease Severity and Outcome for Patients With COVID-19 date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3245 sentences = 194 flesch = 57 summary = This disease is initiated by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and uncontrolled cytokine storm, but it remains unknown as to whether a robust antibody response is related to clinical deterioration and poor outcome in COVID-19 patients. Immune response phenotyping based on the late IgG levels and neutrophil-to-lymphocyte ratio (NLR) was characterized to stratified patients into different disease severities and outcomes. Here, we evaluated antibody response within 35 days after symptom onset in laboratory-confirmed cases with COVID-19 as one component of an overall exaggerated immune activation in severe SARS-CoV-2 infection, and developed an immune phenotyping based on the late IgG response and NLR that could help determine disease severity and clinical outcome for COVID-19 patients. Using two immune responserelated indicators NLR and IgG levels detected in sera at late stage, we developed a combined immune response phenotype, which could predict disease severity and the outcome of COVID-19 patients. cache = ./cache/cord-252288-klkoerfn.txt txt = ./txt/cord-252288-klkoerfn.txt === reduce.pl bib === id = cord-232446-vvb2ffhv author = Mongia, Aanchal title = A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date = 2020-07-03 pages = extension = .txt mime = text/plain words = 7123 sentences = 382 flesch = 47 summary = In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. cache = ./cache/cord-232446-vvb2ffhv.txt txt = ./txt/cord-232446-vvb2ffhv.txt === reduce.pl bib === id = cord-252264-d9i19h8q author = Blackburn, Kyle M. title = Post-infectious neurological disorders date = 2020-08-30 pages = extension = .txt mime = text/plain words = 6396 sentences = 384 flesch = 33 summary = In this review, we discuss the proposed mechanisms underlying pathogen-induced autoimmunity, and highlight the clinical presentation and treatment of several post-infectious autoimmune neurological disorders. 2 The role of infections in the pathogenesis of 'classic' neuroimmunological disorders such as multiple sclerosis and Guillain-Barre syndrome (GBS) has been studied extensively. Here, we review the current landscape of post-infectious neurological autoimmunity, discuss proposed immunological mechanisms, highlight specific disorders strongly associated with pathogens, and review treatment considerations. Mimicry-induced autoimmunity may play an important role in GBS cases associated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. 168, 169 Furthermore, a recent systematic review determined that, among 43 post-HSE cases, no patients had experienced recurrence of herpes simplex following treatment for autoimmune encephalitis, despite the use of first and second-line immunotherapy. Guillain-Barre syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study Postinfectious Guillain-Barre syndrome related to SARS-CoV-2 infection: a case report Guillain Barre syndrome associated with COVID-19 infection: a case report cache = ./cache/cord-252264-d9i19h8q.txt txt = ./txt/cord-252264-d9i19h8q.txt === reduce.pl bib === id = cord-252019-tbalg6k5 author = Barra, Gustavo Barcelos title = Analytical Sensitivity and Specificity of Two RT-qPCR Protocols for SARS-CoV-2 Detection Performed in an Automated Workflow date = 2020-10-12 pages = extension = .txt mime = text/plain words = 4900 sentences = 268 flesch = 51 summary = Here, the following analytical performance characteristics of Charité and CDC protocols for SARS-CoV-2 detection were evaluated: (a) analytical specificity, which refers to the qPCR assay detecting the appropriate target sequence rather than other nonspecific targets also present in a sample [17] ; (b) PCR amplification efficiency, which is the increase in amplicon per cycle, and is highly dependent on the primers used [17, 18] ; (c) analytical sensitivity or limit of detection, which refers to the minimum number of nucleic acid copies in a sample that can be detected with 95% probability [17] ; (d) cross-reactivity with other pathogens; (e) on-going accuracy in clinical specimens, which refers to agreement between the test method and another method during the daily routine. cache = ./cache/cord-252019-tbalg6k5.txt txt = ./txt/cord-252019-tbalg6k5.txt === reduce.pl bib === id = cord-252279-0gozdv43 author = Pal, Amit title = Hydroxychloroquine and Covid-19: A Cellular and Molecular Biology Based Update date = 2020-06-10 pages = extension = .txt mime = text/plain words = 3858 sentences = 207 flesch = 39 summary = Without a therapeutic vaccine or specific antiviral drugs, and with a desperate attempt to find a cure against novel Corona Virus Disease 2019 (Covid-19) [1] , the limelight was shifted to hydoxychloroquine (derivative of chloroquine that has antimalarial, antiinflammatory, immunosuppressive and antiautophagy activities [2, 3] ; upon a tweet by US president Mr. Donald J. The main aim of this review is to discuss the mode of action of hydroxychloroquine at cellular and molecular levels, that potentially support the clinical efficacy and few adverse side effects observed in Covid-19 patients treated with hydroxychloroquine, which may further help in improving the clinical outcomes by modifying or altering the drug itself or its restricted use in certain individuals by enforcing strict inclusion and exclusion criteria. Due to its cellular and molecular effects as discussed in previous sections, quite a few clinical trials are studying the effectiveness and safety of hydroxychloroquine (also chloroquine) for Covid-19 (https://clinicaltrials.gov/ct2/ results?cond=%22wuhan?coronavirus%22). cache = ./cache/cord-252279-0gozdv43.txt txt = ./txt/cord-252279-0gozdv43.txt === reduce.pl bib === id = cord-252597-ea78sjcs author = Ramazzotti, Daniele title = VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date = 2020-10-19 pages = extension = .txt mime = text/plain words = 10701 sentences = 502 flesch = 45 summary = Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. The outbreak of coronavirus disease 2019 (COVID19) , which started in late 2019 in Wuhan (China) [1, 2] and was declared pandemic by the World Health Organization, is fueling the publication of an increasing number of studies aimed at exploiting the information provided by the viral genome of SARS-CoV-2 virus to identify its proximal origin, characterize the mode and timing of its evolution, as well as to define descriptive and predictive models of geographical spread and evaluate the related clinical impact [3, 4, 5] . cache = ./cache/cord-252597-ea78sjcs.txt txt = ./txt/cord-252597-ea78sjcs.txt === reduce.pl bib === id = cord-252473-i4pmux28 author = Rogers, Sharon title = Why can't I visit? The ethics of visitation restrictions – lessons learned from SARS date = 2004-08-31 pages = extension = .txt mime = text/plain words = 1908 sentences = 83 flesch = 42 summary = It could be argued that visitation restrictions, in light of a potential outbreak of a contagious disease, are ethically sound because of the compelling need to protect public health. In a health care institution, visitation restrictions not only affect inpatients but also have an impact on ambulatory patients who must come for diagnostic tests or interventions and who, if deprived access, might develop urgent or emergent conditions. Furthermore, to be consistent with expectations of transparency, the criteria by which exceptionality to the rules of visitation restriction exists should also be published openly throughout the organization for staff, patients and visitors. For example, although current policy allows for specific times of visitation and numbers of visitors per day, a sudden outbreak might dictate a quick lockdown of the facility without patients or family members receiving prior notice. It is ethical to accept that public health protection trumps individual rights to liberal visitation. cache = ./cache/cord-252473-i4pmux28.txt txt = ./txt/cord-252473-i4pmux28.txt === reduce.pl bib === id = cord-252550-yaosufpm author = nan title = Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission date = 2020-09-09 pages = extension = .txt mime = text/plain words = 508 sentences = 44 flesch = 54 summary = authors: nan title: Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission SARS-CoV-2 infection down-regulates ACE2 expression and leads to the production of pro-inflammatory mediators, such as IL-6 [1] . As they lose ACE2-mediated protection, Ang-II signaling contributes to the pathological findings observed in COVID-19 patients, such as disseminated coagulopathy and acute tissue damage [4] . Toll-like receptors (TLRs) 3 and TLR 7/8 recognize SARS-CoV-2 RNA and initiate the inflammatory cascade via type I and type II IFN gene expression and NF-κB nuclear translocation [5, 6] . IL-6, an important player in COVID-19, binds IL-6R and gp130 receptors to activate JAK/STAT-3 pathway and then contribute to the CRS observed in COVID-19 patients [13] . Severe respiratory SARS-CoV2 infection: Does ACE2 receptor matter? Toll-like receptor 3 signaling via TRIF contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection cache = ./cache/cord-252550-yaosufpm.txt txt = ./txt/cord-252550-yaosufpm.txt === reduce.pl bib === id = cord-251986-ajlpb9li author = Li, Yan‐Chao title = The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date = 2020-03-11 pages = extension = .txt mime = text/plain words = 2250 sentences = 125 flesch = 47 summary = This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-251986-ajlpb9li.txt txt = ./txt/cord-251986-ajlpb9li.txt === reduce.pl bib === id = cord-252687-7084pfqm author = Szelenberger, Rafal title = Ischemic Stroke among the Symptoms Caused by the COVID-19 Infection date = 2020-08-19 pages = extension = .txt mime = text/plain words = 7334 sentences = 378 flesch = 37 summary = Many clinical studies have shown an association between SARS-CoV-2 infection and hypercoagulability diagnosed on the basis of abnormal coagulation parameters, including activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer and C-reactive protein level. In this review, the potential mechanism and the effect of the SARS-CoV-2 viral infection on the development of ischemic stroke in COVID-19 patients were carefully studied. study, in which most non-survivor COVID-19 patients' (71.4%) blood tests showed prolonged prothrombin time and an increased D-dimer levels, which indicated the state after activation of the plasma coagulation system [14] . The accumulation of immune cells in the vascular wall in response to the viral infection, especially among patients with ischemic risk factors, induces endothelial dysfunction, migration and proliferation of cells, activation of coagulation cascade and production of fibrous plaques. cache = ./cache/cord-252687-7084pfqm.txt txt = ./txt/cord-252687-7084pfqm.txt === reduce.pl bib === id = cord-252600-bvh1o64r author = Galasiti Kankanamalage, Anushka C. title = Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date = 2018-04-25 pages = extension = .txt mime = text/plain words = 4752 sentences = 254 flesch = 54 summary = We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). cache = ./cache/cord-252600-bvh1o64r.txt txt = ./txt/cord-252600-bvh1o64r.txt === reduce.pl bib === id = cord-252506-8u9oiqoc author = Scarfò, Lydia title = COVID-19 severity and mortality in patients with chronic lymphocytic leukemia: a joint study by ERIC, the European Research Initiative on CLL, and CLL Campus date = 2020-07-09 pages = extension = .txt mime = text/plain words = 4023 sentences = 248 flesch = 49 summary = authors: Scarfò, Lydia; Chatzikonstantinou, Thomas; Rigolin, Gian Matteo; Quaresmini, Giulia; Motta, Marina; Vitale, Candida; Garcia-Marco, Jose Antonio; Hernández-Rivas, José Ángel; Mirás, Fatima; Baile, Mónica; Marquet, Juan; Niemann, Carsten U.; Reda, Gianluigi; Munir, Talha; Gimeno, Eva; Marchetti, Monia; Quaglia, Francesca Maria; Varettoni, Marzia; Delgado, Julio; Iyengar, Sunil; Janssens, Ann; Marasca, Roberto; Ferrari, Angela; Cuéllar-García, Carolina; Itchaki, Gilad; Špaček, Martin; De Paoli, Lorenzo; Laurenti, Luca; Levin, Mark-David; Lista, Enrico; Mauro, Francesca R.; Šimkovič, Martin; Van Der Spek, Ellen; Vandenberghe, Elisabeth; Trentin, Livio; Wasik-Szczepanek, Ewa; Ruchlemer, Rosa; Bron, Dominique; De Paolis, Maria Rosaria; Del Poeta, Giovanni; Farina, Lucia; Foglietta, Myriam; Gentile, Massimo; Herishanu, Yair; Herold, Tobias; Jaksic, Ozren; Kater, Arnon P.; Kersting, Sabina; Malerba, Lara; Orsucci, Lorella; Popov, Viola Maria; Sportoletti, Paolo; Yassin, Mohamed; Pocali, Barbara; Barna, Gabor; Chiarenza, Annalisa; dos Santos, Gimena; Nikitin, Eugene; Andres, Martin; Dimou, Maria; Doubek, Michael; Enrico, Alicia; Hakobyan, Yervand; Kalashnikova, Olga; Ortiz Pareja, Macarena; Papaioannou, Maria; Rossi, Davide; Shah, Nimish; Shrestha, Amit; Stanca, Oana; Stavroyianni, Niki; Strugov, Vladimir; Tam, Constantine; Zdrenghea, Mihnea; Coscia, Marta; Stamatopoulos, Kostas; Rossi, Giuseppe; Rambaldi, Alessandro; Montserrat, Emili'; Foà, Robin; Cuneo, Antonio; Ghia, Paolo Of the 190 patients studied, four Spanish cases were previously published in extenso [12] , 47 patients were included in a report describing the impact of SARS-CoV-2 pandemic infection on the practical management of CLL in Italy with only limited clinical data [18] . cache = ./cache/cord-252506-8u9oiqoc.txt txt = ./txt/cord-252506-8u9oiqoc.txt === reduce.pl bib === id = cord-252456-971d0sir author = Hemida, Maged Gomaa title = The SARS-CoV-2 outbreak from a one health perspective date = 2020-03-16 pages = extension = .txt mime = text/plain words = 4824 sentences = 244 flesch = 55 summary = The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . cache = ./cache/cord-252456-971d0sir.txt txt = ./txt/cord-252456-971d0sir.txt === reduce.pl bib === id = cord-252389-xrdbmosj author = Kumar, Mukesh title = Neurological manifestations and comorbidity associated with COVID-19: an overview date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5447 sentences = 265 flesch = 41 summary = In this article, we have reviewed the neurological characteristic features of COVID-19 patients, latent neurotropic mechanisms of SARS-CoV-2 involvement in the comorbidity associated with CNS disorders, and neurological manifestations associated with COVID-19. Therefore, exploring the neurologic manifestations associated with COVID-19 is urgently required for better understanding the SARS-CoV-2 brain infections, inhibiting the additional spread and treating patients affected by this pandemic. The neuronal cells infected with virus, immune systems (microphase, T cells, and monocytes) triggered, and inflammatory system activated leads to cytokine storm, oxidative stress, and associated neurological manifestations neuroinvasiveness of SARS-CoV-2 [11, 35] . In a recent review [51] , authors have categorized the reported neurological findings related to COVID-19 into three categories: a) Central (headache, dizziness, impaired consciousness, acute cerebrovascular disease, ataxia, seizures, and special senses) b) Peripheral (hypogeusia, hyposmia) c) Musculoskeletal (ischemic or hemorrhagic) Apart from the above, increasing evidence indicated that coronaviruses may invade the CNS, causing neurological disorders. cache = ./cache/cord-252389-xrdbmosj.txt txt = ./txt/cord-252389-xrdbmosj.txt === reduce.pl bib === id = cord-252714-idlyl4ga author = Islam, M. Saiful title = Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis date = 2020-05-15 pages = extension = .txt mime = text/plain words = 5654 sentences = 348 flesch = 51 summary = 1,2 Outbreaks of newly emerging or remerging infectious diseases present a unique challenge and a threat to healthcare providers (HCPs) and other frontline responders due to limited understanding of the emerging threat and reliance on infection prevention and control (IPC) measures that may not consider all transmission dynamics of the emerging pathogens. We searched publications in English on 'PubMed' and Google Scholar for the period between January 1 and April 27, 2020, using the following search terms: "2019-nCoV" or "COVID-19" or "2019 novel coronavirus" or "SARS-CoV-2." To identify COVID-19 IPC guidelines, we visited the websites of the international public health agencies such as CDC, ECDC, WHO, as well as the Australian Government Department of Health, the Bureau of Disease Prevention and Control of the National Health Commission of the People's Republic of China, and Public Health England. cache = ./cache/cord-252714-idlyl4ga.txt txt = ./txt/cord-252714-idlyl4ga.txt === reduce.pl bib === id = cord-252528-rgnhfcbx author = Du, Fenghe title = COVID-19: the role of excessive cytokine release and potential ACE2 down-regulation in promoting hypercoagulable state associated with severe illness date = 2020-07-16 pages = extension = .txt mime = text/plain words = 8437 sentences = 359 flesch = 30 summary = • Anti-inflammatory therapies, including tocilizumab, chloroquine, and hydroxychloroquine, which can be promising treatment to control excessive cytokine release in severe COVID-19, have the potential to reduce the risk of vascular thrombotic events, but more clinical data are needed for optimum instruction of drug use and drug selection. By interpreting the pathological mechanisms, we aim to illustrate that excessive pro-inflammatory cytokine release and potential ACE2 down-regulation can promote the hypercoagulable state in severe COVID19 , and propose that the anti-inflammatory medications, as well as ACEI/ARB, can benefit severe COVID-19 patients by reducing the risk of vascular thrombotic events. cache = ./cache/cord-252528-rgnhfcbx.txt txt = ./txt/cord-252528-rgnhfcbx.txt === reduce.pl bib === id = cord-252725-e3pazjdi author = Khalil, Ayman title = The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date = 2020-10-15 pages = extension = .txt mime = text/plain words = 8759 sentences = 338 flesch = 30 summary = In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . cache = ./cache/cord-252725-e3pazjdi.txt txt = ./txt/cord-252725-e3pazjdi.txt === reduce.pl bib === id = cord-252818-1gms4zw3 author = Bouayed, Jaouad title = Behavioural manipulation ‐ key to the successful global spread of the new Coronavirus SARS‐Cov‐2? date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2492 sentences = 131 flesch = 46 summary = The very rapid global spread has raised the issue whether there are further multi‐dimensional consequences of SARS‐CoV‐2 infection on human behaviour, the key of its transmission. In this perspective, we highlight the possibility that COVID‐19 is facilitated by altered human social behaviour that benefits SARS‐CoV‐2 transmission, through showcasing similar virus‐induced changed behaviour by other pathogens and relating this to reports from the grey literature. Interestingly, it was also estimated that 10% of the cases are super-spreaders, resulting in 80% of viral spread, meaning that the majority of SARS-CoV-2 carriers do not appear to unaccountably transmit the virus. In this perspective, we highlighted the possibility that COVID-19 is facilitated by altered human social behaviour that benefits SARS-CoV-2 transmission (Figure 1 ). The scheme highlights the potential manipulative strategy of the novel coronavirus, resulting in viral spread, following an altered behavioural pattern in some COVID-19 patients, as a consequence of a direct impact on brain structure/function, owing to viral infiltration into the CNS, and/or via perturbation of the brain-immune axis or the gut-brain axis. cache = ./cache/cord-252818-1gms4zw3.txt txt = ./txt/cord-252818-1gms4zw3.txt === reduce.pl bib === id = cord-252873-4tazhf40 author = Kruglikov, Ilja L. title = The role of adipocytes and adipocyte‐like cells in the severity of COVID‐19 infections date = 2020-04-27 pages = extension = .txt mime = text/plain words = 2295 sentences = 128 flesch = 47 summary = Coronavirus disease‐2019 (COVID‐19), caused by the highly pathogenic virus SARS‐CoV‐2, demonstrates high morbidity and mortality caused by development of a severe acute respiratory syndrome connected with extensive pulmonary fibrosis (PF). Expression of angiotensin‐converting enzyme 2 (ACE2 ‐ the functional receptor for SARS‐CoV) ‐ is upregulated in adipocytes of obese and diabetic patients, which turns adipose tissue into a potential target and viral reservoir. Similar to the recently established adipocyte‐myofibroblast transition (AMT), pulmonary lipofibroblasts located in the alveolar interstitium and closely related to classical adipocytes, demonstrate the ability to transdifferentiate into myofibroblasts that play an integral part of PF. Recently it was shown that another anti-diabetic drug, metformin, accelerates resolution of pulmonary fibrosis by inducing trans-differentiation of myofibroblasts into lipofibroblasts (18) . Adipose tissue can serve as a viral reservoir, whereas transdifferentiation of pulmonary lipofibroblasts into myofibroblasts can contribute to the development of PF and thus is likely to influence the clinical severity of COVID-19. cache = ./cache/cord-252873-4tazhf40.txt txt = ./txt/cord-252873-4tazhf40.txt === reduce.pl bib === id = cord-252933-bu4oihem author = Xu, Jieqing Jessica title = Renal Infarct in a COVID‐19 Positive Kidney‐Pancreas Transplant Recipient date = 2020-06-01 pages = extension = .txt mime = text/plain words = 1391 sentences = 93 flesch = 38 summary = The novel coronavirus disease 2019 (COVID‐19) is associated with increased risk of thromboembolic events, but the extent and duration of this hypercoagulable state remains unknown. We describe the first case report of renal allograft infarction in a 46‐year‐old kidney‐pancreas transplant recipient with no prior history of thromboembolism, who presented 26 days after diagnosis of COVID‐19. Since we are the first to report this complication, further investigation is required before making recommendations for thromboembolic prophylaxis in all solid organ transplant recipients with COVID-19. In summary, we present the case of a kidney-pancreas transplant recipient with moderate to severe COVID-19 complicated by late kidney allograft segmental infarction. This is the first case of a thromboembolic event in a SARS-CoV-2 positive solid organ recipient. High incidence of venous thromboembolic events in anticoagulated severe CoVID-19 patients Case report of CoVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? cache = ./cache/cord-252933-bu4oihem.txt txt = ./txt/cord-252933-bu4oihem.txt === reduce.pl bib === id = cord-252671-uf96jgig author = Wang, Yi title = The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism date = 2016-02-09 pages = extension = .txt mime = text/plain words = 7390 sentences = 389 flesch = 52 summary = title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. The result of a dual-luciferase assay using the Renilla luciferase gene as a transfection control demonstrated that the SARS-CoV M gene rather than the S and E genes markedly increased IFN-␤ promoter activity (Fig. 1D) , whereas the valineto-alanine alteration at residue 68 of M protein completely abolished this induction, indicating that the specificity of M gene products played a role in this process. Taken together, our data indicate for the first time that SARS-CoV M protein may function as a novel cytosolic PAMP to activate IFN-␤ induction through an intracellular TLR-related signaling pathway in a TRAF3-independent manner. cache = ./cache/cord-252671-uf96jgig.txt txt = ./txt/cord-252671-uf96jgig.txt === reduce.pl bib === id = cord-252980-1e28zj1d author = Zhang, Jiahao title = Insights into the cross-species evolution of 2019 novel coronavirus date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1045 sentences = 75 flesch = 62 summary = 5 Although humans and bats live in different environments, some wildlife species were susceptible to the novel coronaviruses in nature, highlighting that the need of tracing its origin of SARS-CoV-2 in wild animals. The similarity analysis of SARS-CoV-2 and the animal-origin coronaviruses demonstrated that recombination events were likely to occur in bat-and pangolin-origin coronaviruses (Supplementary Figure S1) . Although the S amino acid identities of pangolin-origin coronavirus exhibited lower amino acid identities with bat/RaTG13, it was noteworthy that six amino acids associated with the receptor binding preference of human receptor angiotensin converting enzyme II-464 L, 495F, 502Q, 503S, 510 N, and 514Y (SARS-CoV-2 numbering)-in the pangolin/1 coronavirus were the same as that of SARS-CoV-2 ( Fig. 2 ), but were distinct from that of the bat-origin coronaviruses. Besides, the PRRA-motif insertion was occurred in the S1/S2 junction of SARS-CoV-2; however, the PRRA-motif insertion in the pangolin-and bat-origin coronaviruses was missing (Supplementary Figure S4 ), suggesting that the convergent cross-species evolution of SARS-CoV-2-related coronaviruses. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus cache = ./cache/cord-252980-1e28zj1d.txt txt = ./txt/cord-252980-1e28zj1d.txt === reduce.pl bib === id = cord-252767-as841xo0 author = Fischer, Bastian title = SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, March to June 2020 date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2028 sentences = 110 flesch = 49 summary = We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. To determine an approximation of the actual rate of people who have recovered from COVID-19, representative of the German population, we determined the anti-SARS-CoV-2 IgG seroprevalence of regular blood donors resident in three different German federal states between March and June 2020. The Figure shows the anti-SARS-CoV-2 IgG distribution in blood donors with equivocal (ratio: ≥ 0.8 to < 1.1) and clearly seropositive (ratio: ≥ 1.1) test results. Distribution of anti-SARS-CoV-2 IgG ratios of blood donors with seropositive and equivocal test results, Germany, March-June 2020, (n = 3,186) cache = ./cache/cord-252767-as841xo0.txt txt = ./txt/cord-252767-as841xo0.txt === reduce.pl bib === id = cord-252804-u7tz6xzz author = Ciotti, Marco title = COVID-19 Outbreak: An Overview date = 2020-04-07 pages = extension = .txt mime = text/plain words = 3558 sentences = 186 flesch = 50 summary = Inoculation of bronchoalveolar lavage fluid obtained from patients with pneumonia of unknown origin into human airway epithelial cells and Vero E6 and Huh7 cell lines led to the isolation of a novel coronavirus, SARS-CoV-2, previously named 2019-nCov [1] . As soon as on January 7, 2020, the Chinese health authorities had declared that a novel coronavirus was responsible for this outbreak of pneumonia in Wuhan, a European network of academic and public laboratories designed an rRT-PCR protocol based on the comparison and alignment of previously available SARS-CoV and bat-related coronavirus genome sequences as well as five sequences derived from the novel coronavirus SARS-CoV-2 made available by the Chinese authorities [23] . Regarding the sites under positive selective pressure found on the Spike glycoprotein, the results have shown that amino acid position 536 in COVID-19 has an Asn residue, while the Bat SARS-like coronavirus has a Gln 4 DOI: 10.1159/000507423 residue; the SARS virus, instead, has an Asp residue. Phylogenetic analysis of the SARS-CoV-2 genomes showed that the novel coronavirus responsible for the pneumonia outbreak in Wuhan, China, belongs to the Betacoronavirus genus, subgenus Sarbecovirus [37] . cache = ./cache/cord-252804-u7tz6xzz.txt txt = ./txt/cord-252804-u7tz6xzz.txt === reduce.pl bib === id = cord-252857-vaq0kwln author = Rejdak, Konrad title = Adamantanes might be protective from COVID-19 in patients with neurological diseases: multiple sclerosis, parkinsonism and cognitive impairment date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1227 sentences = 74 flesch = 47 summary = We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson's disease (n=5) or cognitive impairment (n=7). We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson's disease (n=5) or cognitive impairment (n=7). Hereby we report on the result of a questionaire-based study performed to assess whether adamantanes could exert protective antiviral effect against COVID-19 among different neurological disease patients including multiple sclerosis, parkinsonism and cognitive impairment. In this study, twenty-two patients (10 with multiple sclerosis, 5 with Parkinson's disease and 7 with cognitive impairment) who were tested positive for SARS-CoV-2 and were receiving treatment with either amantadine or memantine on stable registered doses (100mg q.d. and 10mg b.i.d, respectively) for at least 3 months prior to the infection exposure, were surveyed on their laboratory results and clinical status (remote contact with verbally received information). cache = ./cache/cord-252857-vaq0kwln.txt txt = ./txt/cord-252857-vaq0kwln.txt === reduce.pl bib === id = cord-253179-pi5uq90z author = Yu, Jing title = SARS-CoV-2 transmission in cancer patients of a tertiary hospital in Wuhan date = 2020-02-25 pages = extension = .txt mime = text/plain words = 1332 sentences = 82 flesch = 53 summary = Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. 3 Among the different disease types, cancer patients are often recalled to the hospital for treatment and disease surveillance, and therefore, they may be at an elevated risk of contracting SARS-CoV-2. https://doi.org/10.1101/2020.02.22.20025320 doi: medRxiv preprint real-time reverse transcription polymerase chain reaction assay for SARS-CoV-2 and eight by the clinical criteria of fever and radiological computed tomography changes; Table 1 ). For cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China cache = ./cache/cord-253179-pi5uq90z.txt txt = ./txt/cord-253179-pi5uq90z.txt === reduce.pl bib === id = cord-252910-7qvnj6c8 author = Li, Xin title = The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date = 2020-09-21 pages = extension = .txt mime = text/plain words = 4180 sentences = 223 flesch = 54 summary = In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Different from these studies, we previously reported several other findings on SARS-CoV-2 for the first time, including the following in particular: (1) the alternative translation of Nankai coding sequence (CDS) that characterize the rapid mutation rate of betacoronavirus at the nucleotide level [2] ; (2) a furin cleavage site (FCS) "RRAR" in the junction region between S1 and S2 subunits (junction FCS) of SARS-CoV-2 that may increase the efficiency of viral entry into cells [3] ; and (3) the use of 5' untranslated-region (UTR) barcoding for the detection, identification, classification and phylogenetic analysis of-though not limited to-CoVs [4] . Using the insertions and deletions (InDels) at six sites, we identified two recently detected betacoronavirus strains RmYN01 and RmYN02 from a bat [6] and discovered that RmYN02 was a recombinant SARS2-like CoV strain. cache = ./cache/cord-252910-7qvnj6c8.txt txt = ./txt/cord-252910-7qvnj6c8.txt === reduce.pl bib === id = cord-252771-6kwfulqe author = Yue, Jing-Li title = Mental health services for infectious disease outbreaks including COVID-19: a rapid systematic review date = 2020-11-05 pages = extension = .txt mime = text/plain words = 7935 sentences = 412 flesch = 41 summary = Group-based cognitive behavioral therapy, psychological first aid, community-based psychosocial arts program, and other culturally adapted interventions were reported as being effective against the mental health impacts of COVID-19, Ebola, and SARS. Specifically, mental health professionals including psychiatrists, psychiatric nurses, and psychologists were deployed to provide psychological counseling and support for vulnerable populations (e.g. frontline healthcare workers, confirmed COVID-19 patients, suspected COVID-19 cases and their families) in China and for people in quarantine in South Korea. For example, group-based CBT (Waterman et al., 2018; Waterman et al., 2019) , PFA, PTL (Decosimo et al., 2019) , culturally adapted interventions such as SMART (Ng et al., 2006) , ultra-brief psychological interventions (Ping et al., 2020) and peer supports (Rastegar Kazerooni et al., 2020) have been reported to effectively mitigate the emotional impacts of COVID-19, EVD, and SARS outbreaks. Culturally-adapted and cost-effective mental health emergency systems based on evidence-based intervention methods integrated into public health emergency responses at the national and global levels are recommended to reduce the psychological impacts of infectious disease outbreaks, especially for COVID-19. cache = ./cache/cord-252771-6kwfulqe.txt txt = ./txt/cord-252771-6kwfulqe.txt === reduce.pl bib === id = cord-253035-tijcxtwx author = Wang, Chen title = A novel coronavirus outbreak of global health concern date = 2020-01-24 pages = extension = .txt mime = text/plain words = 1834 sentences = 92 flesch = 45 summary = Early in the SARS coronavirus outbreak, frontline health workers became infected, which amplified transmission to patients in hospitals where outbreaks were occurring. 4 Early evidence from the initial MERS outbreaks suggested that health workers were likewise being infected, but that their infections were less severe than those of patients in hospitals who became infected and had comorbidities such as diabetes or chronic respiratory disease. 3 In The Lancet, Chaolin Huang and colleagues 7 report clinical features of the first 41 patients admitted to the designated hospital in Wuhan who were confirmed to be infected with 2019-nCoV by Jan 2, 2020. Considering that substantial numbers of patients with SARS and MERS were infected in health-care settings, precautions need to be taken to prevent nosocomial spread of the virus. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected. cache = ./cache/cord-253035-tijcxtwx.txt txt = ./txt/cord-253035-tijcxtwx.txt === reduce.pl bib === id = cord-253006-r2a2ozrc author = Yan, Xiquan title = Duration of SARS-CoV-2 viral RNA in asymptomatic carriers date = 2020-05-24 pages = extension = .txt mime = text/plain words = 493 sentences = 39 flesch = 57 summary = title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers Notably, patient 2 carried SARS-CoV-2 viral for 32 days continuously after exposure to COVID-19 and tested positive for viral RNA in the respiratory sample for 13 days after first positive test onset. The results indicate that asymptomatic human can carry SARS-CoV-2 viral RNA after exposure to COVID-19, and the carriage seems long-lived. Further study is needed to determine the potential for and mode of contagion of asymptomatic carriers to develop more scientific control strategies. The long duration of asymptomatic infection with SARS-CoV-2 may warrant a reassessment of quarantine as the current outbreak. The US Centers for Disease Control and Prevention recommends that contacts of asymptomatic carriers self-isolate for 14 days [4] . Quarantine of asymptomatic carriers and identification of contacts are a crucial part of these control efforts. There is a great need for further studies on the mechanism by which asymptomatic carriers could acquire and carry SARS-CoV-2 that causes COVID-19. cache = ./cache/cord-253006-r2a2ozrc.txt txt = ./txt/cord-253006-r2a2ozrc.txt === reduce.pl bib === id = cord-253238-ptmxkpae author = Kopel, Jonathan title = Clinical Insights into the Gastrointestinal Manifestations of COVID-19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 4148 sentences = 208 flesch = 45 summary = Furthermore, testing stool after a patient has been infected with COVID-19 may be necessary to monitor any GI complications, and the potential for fecal-oral transmission after respiratory symptoms has resolved. Despite the limited information on COVID-19 and its GI symptoms, information from SARS-CoV and MERS-CoV provides some insights on the symptoms and disease severity from other CoVs. The MERS-CoV has shown to infect human primary intestinal epithelial cells, small intestine It is also found to transmit via the fecal-oral route [35] . Physicians should monitor for GI symptoms in COVID-19-infected patients and examine whether the virus continues to remain in their stools after their respiratory symptoms have resolved. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus cache = ./cache/cord-253238-ptmxkpae.txt txt = ./txt/cord-253238-ptmxkpae.txt === reduce.pl bib === id = cord-252922-cdhnlvxv author = West, Erin A. title = Corona Immunitas: study protocol of a nationwide program of SARS-CoV-2 seroprevalence and seroepidemiologic studies in Switzerland date = 2020-10-24 pages = extension = .txt mime = text/plain words = 5479 sentences = 321 flesch = 47 summary = We describe here the protocol of Corona Immunitas, a centrally coordinated research program consisting of repeated cross-sectional and longitudinal seroprevalence and seroepidemiological studies conducted across several regions and populations in Switzerland, whose aim is to generate reliable data to inform policy-making. Specific aims are to: (1) estimate the number of individuals infected with SARS-CoV-2 in the population with or without symptoms at several points in time; (2) compare the seroprevalence between the general population and specific subpopulations; (3) investigate the characteristics, duration, and extent of immunity after infection; (4) assess the association between participant characteristics and behaviors with their risk of infection; and (5) quantify the association between the pandemic and participants' mental and physical health. Corona Immunitas is a research program coordinated by SSPH?, conducting longitudinal, population-based seroprevalence studies covering a number of Swiss Cantons as well as several seroepidemiological studies in specific subpopulations. cache = ./cache/cord-252922-cdhnlvxv.txt txt = ./txt/cord-252922-cdhnlvxv.txt === reduce.pl bib === id = cord-253201-r6vsa0pw author = Nazari, S. title = Central Nervous System Manifestations in COVID-19 Patients: A Systematic Review and Meta-analysis date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3950 sentences = 281 flesch = 49 summary = Despite many studies reporting respiratory infections as the primary manifestations of this illness, an increasing number of investigations have focused on the central nervous system (CNS) manifestations in COVID-19. Based on the results shown in (Table 3 and The highest incidence rate among CNS symptoms of COVID-19 patients was for headache (8.69% with 95% CI: 6.76%-10.82%), followed by Dizziness (5.94%, 95%CI: 3.66%-8.22%), and Impaired consciousness (1.9% with 95% CI: 1%-2.79%). . https://doi.org/10.1101/2020.07.21.20158691 doi: medRxiv preprint CNS: Central nervous system; COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; PHEIC: Public health emergency of international concern; WHO: World health organization; PRISMA: Preferred reporting items for systematic reviews and meta-analyses; PNS: Peripheral nervous system; BBB: Blood brain barrier; ACE2: Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-253201-r6vsa0pw.txt txt = ./txt/cord-253201-r6vsa0pw.txt === reduce.pl bib === id = cord-252919-647zcjgu author = Chen, Yun title = Structure analysis of the receptor binding of 2019-nCoV date = 2020-02-17 pages = extension = .txt mime = text/plain words = 3436 sentences = 185 flesch = 57 summary = We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. In this study, we analyzed the structure of spike glycoprotein RBD of 2019-nCoV and identified a unique feature that potentially allows a high affinity binding to ACE2 in human cells. There are 16 amino acid residues in SARS-CoV RBD that are directly in contact with ACE2, of which 8 are conserved in 2019-nCoV (see Fig. 1B ). Among the 16 amino acid residues in RBD of SARS that are in contact with ACE2, 14, 14, 7, and 8 are shared by SARSv, civet, bat, and 2019-nCoV, respectively (Fig. 1B) . Our study suggests unique structural features of the spike glycoprotein RBD of 2019-nCoV that confers potentially higher affinity binding for its receptor than found with SARS-CoV. cache = ./cache/cord-252919-647zcjgu.txt txt = ./txt/cord-252919-647zcjgu.txt === reduce.pl bib === id = cord-253459-tcn10pho author = Moreau, Gregory Brett title = Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2377 sentences = 154 flesch = 58 summary = 4 A transgenic mouse model to study SARS-CoV-1 infection was developed that expresses the hACE2 gene under the control of the human cytokeratin 18 promoter. To investigate the potential of this transgenic mouse strain as a model for COVID-19 infection, five K18-hACE2 mice were intranasally inoculated with 8 × 10 4 Median Tissue Culture Infectious Dose (TCID50) of SARS-CoV-2, and five mice were mock-infected with sterile Dulbecco's Modified Eagle's Medium (DMEM). In the mouse model expressing hACE2 under the mouse ACE2 promoter, infected mice did not exhibit any clinical symptoms other than maximal weight loss on day 3 postinfection, and those mice recovered. 10 In contrast to these models, in which mice exhibited mild symptoms and recovered, only 60% of the mice survived past day 5 in the mouse strain expressing hACE2 under the lung ciliated epithelial cell HFH4 promoter. cache = ./cache/cord-253459-tcn10pho.txt txt = ./txt/cord-253459-tcn10pho.txt === reduce.pl bib === id = cord-253252-s8fm5rfa author = Jayaweera, Mahesh title = Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy date = 2020-06-13 pages = extension = .txt mime = text/plain words = 14098 sentences = 573 flesch = 45 summary = This review paper intends to outline the literature concerning the transmission of viral-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. There have been myriads of hypotheses corroborating that certain threshold levels of humidity, temperature, sunlight, and ventilation will speed up the virus-laden droplet and aerosol transmission, aggravating the spread of the SARS-CoV disease (Morawska, 2006) . Nevertheless, the effectiveness of the use of masks for the control of SARS-CoV-2-laden aerosol transmission from an infected person to a susceptible host is uncertain and not fully conceivable. Researchers have speculated that both droplets and aerosols generated from non-violent and violent expirations of SARS-CoV-2-infected people may be responsible for the nonnosocomial and nosocomial transmission of COVID-19 disease. cache = ./cache/cord-253252-s8fm5rfa.txt txt = ./txt/cord-253252-s8fm5rfa.txt === reduce.pl bib === id = cord-252965-30pl5tx3 author = Stutt, Richard O. J. H. title = A modelling framework to assess the likely effectiveness of facemasks in combination with ‘lock-down’ in managing the COVID-19 pandemic date = 2020-06-10 pages = extension = .txt mime = text/plain words = 8015 sentences = 341 flesch = 48 summary = The current COVID-19 pandemic, caused by the virus species severe acute respiratory syndromerelated coronavirus, named SARS-CoV-2 [1] , has stimulated considerable controversy over the potential benefits of facemask use by the public and the timing of the initiation and termination of 'lock-down' periods. The currently available control measures to combat SARS-Cov-2, therefore, include: physical distancing, population lock-down periods, good sanitation/hand washing/surface disinfecting, good ventilation, facemask and visor protection, as well as diagnostics followed by contact tracing and quarantine of infected and exposed individuals. We use two complementary modelling approaches to test the effectiveness of facemask wearing by sections of the population in reducing the transmission rate of SARS-Cov-2 and hence in reducing the effective reproduction number, R e (the expected number of new cases caused by a single infectious individual at a given point in the epidemic). cache = ./cache/cord-252965-30pl5tx3.txt txt = ./txt/cord-252965-30pl5tx3.txt === reduce.pl bib === id = cord-253282-zwl0safn author = Plant, Ewan P. title = Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date = 2013-01-18 pages = extension = .txt mime = text/plain words = 5007 sentences = 266 flesch = 55 summary = In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. Here, analyses using synonymous protein coding mutations demonstrate that the region of the genome that harbors the frameshift signal affects the regulation of genomic and subgenomic RNA production without altering protein sequence. Here we describe deletion and mutagenesis experiments with a dual luciferase reporter to show that the effect the sequence between stems 1 and 2 has on frameshifting efficiency is due to structural changes those mutations cause in the pseudoknot. Similar to previously described viruses containing mutations in the slippery site of the frameshift signal [7] , here we show that mutations to the SARS-CoV frameshift stimulating mRNA pseudoknot can also affect the production of viral genomic RNA. cache = ./cache/cord-253282-zwl0safn.txt txt = ./txt/cord-253282-zwl0safn.txt === reduce.pl bib === id = cord-253077-61fmul8c author = Vabret, Nicolas title = Immunology of COVID-19: current state of the science date = 2020-05-06 pages = extension = .txt mime = text/plain words = 20227 sentences = 1120 flesch = 45 summary = Lastly, Nonhuman primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific IgG responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into pro-inflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012; Liu et al., 2019) . Collectively, these data suggest that cross-talk with monocytes might impair NK cell recognition and killing of SARS-CoV-2infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients ( Figure 2 ). However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human coronaviruses, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020) . cache = ./cache/cord-253077-61fmul8c.txt txt = ./txt/cord-253077-61fmul8c.txt === reduce.pl bib === id = cord-252991-gvlyn6j7 author = Silva, V. O. title = PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4148 sentences = 277 flesch = 57 summary = To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. . https://doi.org/10.1101 Professionals from laboratory areas were 25% while workers who had no direct contact with patients (administrative areas, security and cleaning staff) had a higher infection rate, especially in the areas of logistics (Faíco-Filho, et al., 2020) In our study, we chose to use a rapid test for preliminary results, despite the its reported performance (Sensitivity: 86, 43% [95% CI: 82, 51%~89, 58%] and Specificity: 99, 57% [95% CI: 97, 63%~99,92%]).. cache = ./cache/cord-252991-gvlyn6j7.txt txt = ./txt/cord-252991-gvlyn6j7.txt === reduce.pl bib === id = cord-253380-oymg1bba author = Karataş, Ayşe title = Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma date = 2020-07-03 pages = extension = .txt mime = text/plain words = 758 sentences = 52 flesch = 51 summary = title: Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma Herein we report a patient with a history of autologous stem cell transplantation (ASCT) for lymphoma whose RT-PCR test remained positive for SARS-CoV-2 for 74 days. The prolonged RT-PCR positivity, despite convalescent plasma infusion, may suggest that the given antibodies may be ineffective in terms of viral clearance. In patients with hematological malignancies or immunosuppression, such as ASCT, may lead to prolonged viral shedding, and strict isolation is warranted for long-term SARS-CoV-2 infection control. A case whose viral shedding lasted 60 days is reported from China Our patient had also undergone bone ASCT thus, underlying immunosuppression might lead to prolonged shedding. In patients with hematological malignancies or immunosuppression such as ASCT may lead to J o u r n a l P r e -p r o o f prolonged viral shedding and strict medical precautions and isolation rules should be followed for SARS-CoV-2. cache = ./cache/cord-253380-oymg1bba.txt txt = ./txt/cord-253380-oymg1bba.txt === reduce.pl bib === id = cord-253502-v2hh3w3r author = Leung, C.W. title = Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date = 2004-11-05 pages = extension = .txt mime = text/plain words = 8625 sentences = 524 flesch = 45 summary = authors: Leung, C.W.; Chiu, W.K. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children [5] [6] [7] [8] [9] [10] [11] Superspreading events including a major hospital outbreak, in-flight transmission on board commercial PAEDIATRIC RESPIRATORY REVIEWS (2004) Summary Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. cache = ./cache/cord-253502-v2hh3w3r.txt txt = ./txt/cord-253502-v2hh3w3r.txt === reduce.pl bib === id = cord-253178-c41xejo3 author = Neuman, B.W. title = Supramolecular Architecture of the Coronavirus Particle date = 2016-09-15 pages = extension = .txt mime = text/plain words = 7814 sentences = 390 flesch = 46 summary = M proteins in SARS-CoV, FCoV, and MHV virions and virus-like particles (VLPs) form homodimers (Neuman et al., 2011) , which appear to be functionally analogous to the M-GP5 heterodimers of Arteriviridae (de Vries et al., 1995; Faaberg et al., 1995; Snijder et al., 2003) . However, a recent study found that a chimeric MHV with SARS-CoV M and S transmembrane and endodomain was severely deficient in incorporating S into virions, suggesting that cellular localization signals or more complex interactions among the structural proteins may help support S incorporation (Kuo et al., 2016) . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles cache = ./cache/cord-253178-c41xejo3.txt txt = ./txt/cord-253178-c41xejo3.txt === reduce.pl bib === id = cord-253124-s3pa4n8a author = Dhamad, Ahmed E. title = COVID-19: molecular and serological detection methods date = 2020-10-07 pages = extension = .txt mime = text/plain words = 3370 sentences = 188 flesch = 50 summary = Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. And the top keywords that searched were: COVID-19, SARS-CoV-2, coronavirus, genomic RNA, protein structure, ACE2, transmission, symptoms, molecular detection methods, serological detection methods, rRT-PCR, ID NOW COVID-19, isothermal amplification, CRISPR, SARS-CoV-2 DETECTR, LAMP, recombinase polymerase amplification (RPA), Lateral flow assay (LFA) and Enzyme-linked immunosorbent assay (ELISA). In this method (e.g., SARS-CoV-2 DETECTR), the RNA virus is extracted from a specimen and designated regions of N2, E, RP genes are amplified at 62 C for 20 min by specific primes through Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) approach Lamb et al., 2020; Hong et al., 2004) . Unlike molecular methods, serological methods (also called antibody tests) can be applied to detect past and current SARS-CoV-2 infection and monitor the progress of the disease periods and immune response. cache = ./cache/cord-253124-s3pa4n8a.txt txt = ./txt/cord-253124-s3pa4n8a.txt === reduce.pl bib === id = cord-253366-03cg831z author = Chakraborty, Hirak title = Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5024 sentences = 282 flesch = 47 summary = In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes cache = ./cache/cord-253366-03cg831z.txt txt = ./txt/cord-253366-03cg831z.txt === reduce.pl bib === id = cord-253438-k8iqv1jb author = Li, Yujun title = SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig date = 2020-10-27 pages = extension = .txt mime = text/plain words = 5339 sentences = 327 flesch = 60 summary = We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. The RBD of Bat-CoV RaTG13 then showed a binding profile significantly different and narrower than the other three RBDs. Note that human ACE2 and ACE2 orthologs of some domestic animals, including camels, cattle, horses, goats, sheep, cats, and rabbits, support efficient binding to all the four tested RBDs, suggesting that these ACE2 orthologs might be generally functional for supporting cell entry of the four tested viruses. cache = ./cache/cord-253438-k8iqv1jb.txt txt = ./txt/cord-253438-k8iqv1jb.txt === reduce.pl bib === id = cord-253447-4w6caxwu author = Zeng, Xin title = Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date = 2020-04-20 pages = extension = .txt mime = text/plain words = 2866 sentences = 161 flesch = 54 summary = title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. A high-affinity antibody against the target protein can be screened from a phage display antibody library using the standard biopanning process, but its binding epitopes are identified by some extra steps, such as epitope mapping and competitive ELISA. cache = ./cache/cord-253447-4w6caxwu.txt txt = ./txt/cord-253447-4w6caxwu.txt === reduce.pl bib === id = cord-253876-2dc9jq79 author = Pitocco, Dario title = Lack of type 1 diabetes involvement in SARS-COV-2 population: Only a particular coincidence? date = 2020-05-19 pages = extension = .txt mime = text/plain words = 477 sentences = 36 flesch = 56 summary = In 1591 Italian subjects affected by SARS-COV-2, there was a prevalence of 17% of type 2 diabetes. This observation needs to be confirmed and further evaluated, for example in regions with high prevalence of the disease (Scandinavian, Finland or Sardinian), but there could be a number of reasons that justify a low incidence of SARS-COV-2 in subjects with type 1 diabetes. Indeed, we cannot rule out that there are some asymptomatic subjects with SARS-COV-2 infection in type 1 diabetic population. Finally, while the infected population has a high prevalence of hypertension, type 1 diabetes is often characterized by hyperglycemia in the absence of the other cardiovascular risk factors. Prevalence and impact of diabetes among people infected with SARS-CoV-2 All the authors have made substantive contributions to the article and assume full responsibility for its content cache = ./cache/cord-253876-2dc9jq79.txt txt = ./txt/cord-253876-2dc9jq79.txt === reduce.pl bib === id = cord-253468-pf0xubii author = Emara, Mohamed H title = Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients date = 2020-09-02 pages = extension = .txt mime = text/plain words = 986 sentences = 57 flesch = 58 summary = title: Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients We hereby present the data of 3 patients presented to our OPD and were admitted as diabetic ketoacidosis (DKA) and 2-3 days later they developed manifestations suggestive of and proved by swabbing as positive cases. Chest auscultation and chest X ray were unremarkable and hence chest CT scan was requested ( Figure 1 ) and showed picture suggestive of mild-moderate COVID-19, swabbing was done and came positive Case 2: A 51-year-old male, presented by dizziness over last 2-3 days and when examined found to have high RBS and ketonuria, and hence admitted as KDA, and was acidotic (PH 7). A 62-year-old male patient who was not compliant with his medicines over the last 2 months, presented for renewal of medicine without any clinical manifestations, found to have panic RBS measurement, and was positive for urine ketones. cache = ./cache/cord-253468-pf0xubii.txt txt = ./txt/cord-253468-pf0xubii.txt === reduce.pl bib === id = cord-253456-u9num2o9 author = Zhang, Che title = Clinical and epidemiological characteristics of pediatric SARS-CoV-2 infections in China: A multicenter case series date = 2020-06-16 pages = extension = .txt mime = text/plain words = 4540 sentences = 260 flesch = 49 summary = Suspected patients with clinical and/or radiological features of pneumonia were quarantined prior to SARS-CoV-2 nucleic acid detection according to WHO guidelines for cases with suspected infection [8] as well as the instructions from the Pediatric Branch of the Hubei Medical Association for pediatric cases [9] . Specifically, suspected cases of SARS-CoV-2 infection should meet 1 of the following criteria [10] : (1) at least 1 clinical symptom, including fever, expectation, tachypnea, lethargy, poor feeding, cough, vomiting, and diarrhea; (2) chest radiologic abnormalities consistent with viral pneumonia. Patients were discharged when all the following criteria were met [10] : (1) fever had recovered for at least 3 days; (2) upper respiratory symptoms were alleviated; (3) the exudative lesion was alleviated significantly according to radiological evidence; (4) negative results were obtained for SARS-CoV-2 nucleic acid detection in 2 consecutive tests performed with an interval of 24 hours. cache = ./cache/cord-253456-u9num2o9.txt txt = ./txt/cord-253456-u9num2o9.txt === reduce.pl bib === id = cord-253615-qylm0koe author = Müller, Marcel A title = Human Coronavirus NL63 Open Reading Frame 3 encodes a virion-incorporated N-glycosylated membrane protein date = 2010-01-15 pages = extension = .txt mime = text/plain words = 5810 sentences = 305 flesch = 51 summary = In-silico analysis of potential glycosylation sites and membrane topology suggest properties similar to SARS-CoV ORF 3a protein ( Figure 1B and Table 1 ). To analyze the expression of ORF 3 protein during viral replication, colon carcinoma cells (CaCo-2) and Rhesus monkey kidney cells (LLC-MK2) cells were infected with hCoV-NL63 and an immunofluorescence assay (IFA) was done after two and four days, respectively. In contrast to virus-infected cells, cells overexpressing ORF 3 protein from plasmid with an N-terminal FLAG epitope showed only a single band in Western blot whose migration was consistent with the hypothetical unglycosylated form ( Figure 5B, left panel) . Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice Severe acute respiratory syndrome coronavirus 3a protein is released in membranous structures from 3a protein-expressing cells and infected cells cache = ./cache/cord-253615-qylm0koe.txt txt = ./txt/cord-253615-qylm0koe.txt === reduce.pl bib === id = cord-253457-gawn4s9g author = Yau, Kevin title = COVID-19 Outbreak in an Urban Hemodialysis Unit date = 2020-07-15 pages = extension = .txt mime = text/plain words = 2215 sentences = 145 flesch = 47 summary = Patients with SARS-CoV-2 infection including asymptomatic individuals were treated with droplet and contact precautions until confirmation of negative SARS-CoV-2 RT-PCR testing. Nasopharyngeal swabs were performed by physicians, nurse practitioners, and staff from the hospital's COVID-19 Assessment Centre under droplet and contact precautions in the hemodialysis unit with curtains drawn around the dialysis station at which the patient was being swabbed. At the time of testing, six (55%) patients and six (55%) staff positive for SARS-CoV-2 were asymptomatic. Patients with confirmed SARS-CoV-2 infection including asymptomatic individuals were dialyzed in a dedicated room separate from the main hemodialysis unit for the duration of their infection and maintained on droplet and contact precautions. Five hemodialysis staff were allowed to return to work following symptom resolution and documentation of two negative SARS-CoV-2 nasopharyngeal swabs performed 14 days from symptom onset. Infection control authorities concluded that SARS-CoV-2 transmission during an outbreak at the St. Michael's Hospital hemodialysis unit was likely to have originated from two index cases. cache = ./cache/cord-253457-gawn4s9g.txt txt = ./txt/cord-253457-gawn4s9g.txt === reduce.pl bib === id = cord-253656-2x4y403o author = Ren, Wenlin title = Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates date = 2020-06-24 pages = extension = .txt mime = text/plain words = 3645 sentences = 202 flesch = 60 summary = In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. The sera were collected on Day 38 and evaluated by ELISA against SARS-CoV-2 S1-6His protein using HRP-conjugated goat anti-mouse IgG Fc-specific secondary antibodies. As shown in Table 1 and Fig. 5A , immunization of SARS-CoV-2 S1-Fc fusion protein with AD20Gold + as adjuvant also induced very high neutralizing activities with IC50 titers >3000 and IC90 titers around 440-501 in both rabbits on Day 27 after immunizations. Beside high levels of the anti-S1 antibodies elicited, higher neutralizing activities against live SARS-CoV-2 virus and/or pseudovirus from the anti-sera of macaques and rabbits. cache = ./cache/cord-253656-2x4y403o.txt txt = ./txt/cord-253656-2x4y403o.txt === reduce.pl bib === id = cord-253431-fjds5cdr author = Erukainure, Ochuko L. title = Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. (Labiatae) date = 2020-11-03 pages = extension = .txt mime = text/plain words = 6198 sentences = 344 flesch = 46 summary = title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. Ligand-protein interactions between viral protein (SARS-CoV-2 spike protein), the host receptor target (ACE2) and Harpagide 5-O-b-D-glucopyranoside are presented in Figures 5-7 . Harpagide 5-O-b-D-glucopyranoside displayed a good binding in complex with the host receptor target, initiation and termination sequence of the viral spike protein messenger RNA compared to all studied standard drugs with binding affinities of À7.5, À6.4 and 6.3 kcal mol À1 respectively (Table 5) . In the present study, we investigated the epidemiology of COVID-19 and the potentials of harpagide 5-O-b-D-glucopyranoside, a new iridoid glycoside isolated from C. At molecular level, the viral envelope spike (S) protein of SARS-CoV-2 and angiotensin converting enzyme 2 receptor within the host are central to COVID-19 pathogenesis and response to therapeutic interventions among other biological factors . cache = ./cache/cord-253431-fjds5cdr.txt txt = ./txt/cord-253431-fjds5cdr.txt === reduce.pl bib === id = cord-253704-y0t30xw3 author = Lahiri, Durjoy title = COVID-19 Pandemic: A Neurological Perspective date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4348 sentences = 210 flesch = 40 summary = Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to principally affect the respiratory system, neurological involvements have already been reported in some published work. Neurological manifestations can further be subdivided into the central nervous system (headache, dizziness, alteration of the sensorium, ataxia encephalitis, stroke, and seizures) and peripheral nervous system (skeletal muscle injury and peripheral nerve involvement including hyposmia and hypogeusia) symptomatology. Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to mainly affect the respiratory system, neurological involvements have already been reported in some published work. In the present paper, we have reviewed the recently published or pre-print original articles, case reports, and existing open-source data-sets in order to delineate the spectrum of neurological disorders in SARS-CoV-2 positive cases. Another report from China describes a case of acute myelitis, possibly affecting the cervical spinal cord, as evidenced by the clinical features, in a known patient of SARS-CoV-2 infection [22] . cache = ./cache/cord-253704-y0t30xw3.txt txt = ./txt/cord-253704-y0t30xw3.txt === reduce.pl bib === id = cord-253513-zn87f1lk author = Liu, Jia title = Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro date = 2020-03-18 pages = extension = .txt mime = text/plain words = 2370 sentences = 121 flesch = 57 summary = Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Jia Liu 1 , Ruiyuan Cao 2 , Mingyue Xu 1,3 , Xi Wang 1 , Huanyu Zhang 1,3 , Hengrui Hu 1,3 , Yufeng Li 1,3 , Zhihong Hu 1 , Wu Zhong 2 and Manli Wang 1 Dear Editor, The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/2019-nCoV) poses a serious threat to global public health and local economies. To better compare the antiviral activity of CQ versus HCQ, the dose-response curves of the two compounds against SARS-CoV-2 were determined at four different multiplicities of infection (MOIs) by quantification of viral RNA copy numbers in the cell supernatant at 48 h post infection (p.i.). Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment (Supplementary Fig. S2 ). cache = ./cache/cord-253513-zn87f1lk.txt txt = ./txt/cord-253513-zn87f1lk.txt === reduce.pl bib === id = cord-253665-1dn3ek34 author = Vishnubalaji, Radhakrishnan title = Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response date = 2020-07-07 pages = extension = .txt mime = text/plain words = 5427 sentences = 301 flesch = 42 summary = Coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared a global pandemic by the World Health Organization (WHO) on Phenomenal changes in ncRNA expression are also seen within host cells, which can play a major role in respiratory virus pathogenesis, with long non-coding RNAs (lncRNAs) exhibiting higher tissue specificity than coding genes [30] . Disease and function analysis on the differentially expressed genes revealed the most significant enrichment in pathways related to reactive oxygen species, induction of apoptosis and necrosis, as well as activation of neutrophils in SARS-CoV-2 infected NHBE cells (Figure 3a,b) . The top ten activated upstream regulator networks (CST5, IFNG, IFNL1, IFNA2, SPI1, RNY3, PRL, TGM2 , miR-122 and miR-122-5p) in lung tissue derived from COVID-19 patient based on transcriptome and IPA analyses, revealed the enrichment of functions related to immune system associated JAK-STAT cascade, type 1 interferon receptor binding, cytokine receptor binding, and MHC 1 biosynthesis (Figure 6a and Supplementary Table S10 ). cache = ./cache/cord-253665-1dn3ek34.txt txt = ./txt/cord-253665-1dn3ek34.txt === reduce.pl bib === id = cord-253618-bosb7e63 author = Ramteke, Shobhana title = Novel coronavirus disease 2019 (COVID-19) pandemic: considerations for the biomedical waste sector in India date = 2020-08-01 pages = extension = .txt mime = text/plain words = 2732 sentences = 165 flesch = 53 summary = During this epidemic condition, expulsion of biomedical waste created from crisis facilities treating COVID-19 patients in like manner demands unprecedented thought as they can be potential bearers of the disease SARS-CoV-2. During December 2019, a novel Beta-coronavirus temporarily named 2019 novel coronavirus (2019-nCoV), and along these lines authoritatively renamed extreme intense respiratory disorder coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV), causing coronavirus ailment 2019 (or COVID19) , was related with a group of respiratory tract diseases in Wuhan, Hubei Province, China and has quickly spread across main land's [3] . From that point forward, the whole world has been found napping by the clueless increment in the number of new cases because of the exponential increment in the pace of transmission of 2019-nCoV, presently formally alluded to as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) by the International Committee on Taxonomy of Viruses, the causative operator of COVID-19 [5] . cache = ./cache/cord-253618-bosb7e63.txt txt = ./txt/cord-253618-bosb7e63.txt === reduce.pl bib === id = cord-253331-z443e8lk author = Stanhope, Michael J. title = Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV date = 2004-03-31 pages = extension = .txt mime = text/plain words = 2564 sentences = 105 flesch = 44 summary = Based on evolutionary analyses of coronavirus DNA sequences, encompassing an approximately 13kb stretch of the SARS-TOR2 genome, we provide evidence that SARS-CoV has a recombinant history with lineages of types I and III coronavirus. Our results act to both corroborate and extend their findings, adding further support to the idea that SARS has had a recombinant history involving different coronavirus lineages and suggest the possibility that the genome could have arisen through a combination of host jumping and recombination events in a manner analogous to previous outbreaks of influenzae (Gregory et al., 2003; Zhou et al., 1999) . Our results indicate that SARS-CoV recombined with a member of the group III lineage, suggesting that an avian coronavirus was involved, a further point of general agreement between our results and that of Rest and Mindell (2003) . cache = ./cache/cord-253331-z443e8lk.txt txt = ./txt/cord-253331-z443e8lk.txt === reduce.pl bib === id = cord-253422-m18ngwbt author = Trimarchi, Hernán title = COVID-19 and acute kidney injury in pediatric subjects: is there a place for eculizumab treatment? date = 2020-09-29 pages = extension = .txt mime = text/plain words = 976 sentences = 47 flesch = 39 summary = One of the reasons we found this case of particular interest is that it reminds us of a similar experience by one of the authors who observed a dramatic effect of eculizumab in a 4-year-old child with diffuse proliferative lupus nephritis who developed complement-mediated TMA and AKI [6] . She fully recovered but needed chronic eculizumab treatment for atypical hemolytic uremic syndrome (aHUS). In both cases the initial disease was a severe multisystem inflammatory syndrome due to SARS-CoV-2 or systemic lupus erythematosus. He was admitted with severe diffuse bilateral SARS-CoV-2 pneumonia [9] and elevated D-dimer and fibrinogen concentrations, suggesting a pro-coagulant state due to pulmonary microthrombosis, as described in autopsies of subjects with COVID-19 infections [1] , despite ongoing chronic eculizumab treatment. However, while waiting for further follow-up, the present report deserves our utmost interest because it highlights the role of the complement system activation in SARS-COV-2 infection and the pharmacological interventions to attenuate the micro-thrombotic complications associated with COVID-19. Eculizumab, SARS-COV-2 and atypical hemolytic uremic syndrome cache = ./cache/cord-253422-m18ngwbt.txt txt = ./txt/cord-253422-m18ngwbt.txt === reduce.pl bib === id = cord-253851-27nt0op8 author = Koh, David title = SARS: health care work can be hazardous to health date = 2003-06-17 pages = extension = .txt mime = text/plain words = 1451 sentences = 78 flesch = 56 summary = Health care workers (HCWs) are a high-risk group for SARS-CoV infection. As at 4 May, 41% of 203 SARS patients in Singapore and 22% of 1629 cases in Hong Kong [7] were HCWs. The majority of cases in Canada (74.4%) have been attributed to exposure in a hospital or health care setting [8] . That the cluster of cases included housekeepers is also significant-preventive measures need to target much broader groups of HCWs than just the doctors and nurses in direct contact with patients. This was the case in a Singapore hospital [11] , where the experience was reported as: 'We did not see any further transmission from this index patient after we implemented strict infection control measures involving use of N95 masks, gown, gloves, and handwashing before and after patient contact'. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-253851-27nt0op8.txt txt = ./txt/cord-253851-27nt0op8.txt === reduce.pl bib === id = cord-253933-29tedkf8 author = David, Abel P. title = Tracheostomy guidelines developed at a large academic medical center during the COVID‐19 pandemic date = 2020-04-27 pages = extension = .txt mime = text/plain words = 3038 sentences = 163 flesch = 42 summary = 1 As an aerosol-generating procedure (AGP), tracheostomy is associated with high droplet and particle generation, placing health care providers at increased risk for transmission of respiratory viral infections. Factors relevant to our review included optimal timing of tracheostomy, duration of viral shedding in patients with COVID-19, risk to procedural teams from aerosol generation during tracheostomy, ICU capacity, and availability of PPE. In the context of the current pandemic, Tay et al conducted a literature review of tracheostomies performed during the SARS epidemic and concluded the following: (a) proper PPE (N95 mask, surgical cap, gown, goggles, and gloves) is of utmost importance; (b) surgical tracheostomy is preferably performed in a negative pressure ICU room by experienced providers with meticulous planning and seamless communication; (c) aerosol generation should be minimized through patient paralysis, ventilation hold during creation of tracheal window, and utilization of HEPA-filtered suction systems. cache = ./cache/cord-253933-29tedkf8.txt txt = ./txt/cord-253933-29tedkf8.txt === reduce.pl bib === id = cord-253905-zknmfgsh author = Li, Xingguang title = Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 date = 2020-03-11 pages = extension = .txt mime = text/plain words = 3846 sentences = 194 flesch = 49 summary = To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. Homology plot analysis of "dataset_6" also revealed that BetaCoV/bat/Yunnan/ RaTG13/2013 was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378), consistent with phylogenetic analysis ( Figure S5 ). 46, 47 Bayesian analyses with the tip-dating method using a strict clock as well as constant size coalescent tree prior indicated that SARS-CoV-2 is evolving at a rate of 1.24 × 10 −3 substitutions per site per year (Table 1 ), in accordance with our prior research 46, 47 and similar to that found for other human F I G U R E 4 Estimated maximum-clade-credibility tree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using tip-dating method. cache = ./cache/cord-253905-zknmfgsh.txt txt = ./txt/cord-253905-zknmfgsh.txt === reduce.pl bib === id = cord-253844-y6xdcf20 author = Yesudhas, Dhanusha title = COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date = 2020-09-04 pages = extension = .txt mime = text/plain words = 7165 sentences = 422 flesch = 51 summary = In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. SUMMARY: The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs. The sequence similarity between SARS-CoV-2 and SARS-CoV spike proteins explains the possibility of binding to the same receptor angiotensin converting enzyme 2 (ACE2) in the host cell [14] . In this review, we discuss the history of coronaviruses in both humans and animals, their transmissions, mechanism of host cell entry and the structural studies, explaining active and inactive receptor binding of spike protein and the key residues playing an important role in the receptor binding. During viral infection, spike protein (~ 1300 amino acid residues) is cleaved by host proteases into receptor binding subunit S1 and membrane fusion subunit S2. cache = ./cache/cord-253844-y6xdcf20.txt txt = ./txt/cord-253844-y6xdcf20.txt === reduce.pl bib === id = cord-253869-1ouai07v author = Noorimotlagh, Zahra title = A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies date = 2020-10-02 pages = extension = .txt mime = text/plain words = 4151 sentences = 204 flesch = 44 summary = title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies In the current SARS-CoV-2 pandemic, identification of the chemical and/or physical disinfectant that interrupts the virus transmission routes including human-to-human, spreads via respiratory droplets, and contaminated hands or surfaces are of utmost importance. According to finding of the included studies, the SARS-CoV-2 can be easily spread via two main ways in human-tohuman transmission: (1) respiratory droplet and (2) direct and indirect contact with aerosol infected surfaces. In addition to chemical disinfectant, in the present SR, the reviewed studies reported that the efficiency of physical disinfectant including temperature (56°C, 60°C), gamma irradiation using a cobalt-60 source at 1 Mrad, and disinfection of virus in human plasma by amotosalen and ultraviolet A were in effective for inactivating coronavirus in a short contact time. cache = ./cache/cord-253869-1ouai07v.txt txt = ./txt/cord-253869-1ouai07v.txt === reduce.pl bib === id = cord-253777-h8wy0coq author = Afshar, Hale title = Evolution and resolution of brain involvement associated with SARS- CoV2 infection: A close Clinical – Paraclinical follow up study of a case date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1560 sentences = 85 flesch = 46 summary = We report a para-infectious encephalitis patient with clinical, laboratory, and imaging findings during evolution and convalescence phase of coronavirus infection. Herein we report a case with clinical (including respiratory and neurological), laboratory, chest Computed Tomography and Brain Magnetic Resonance Imaging (B-MRI) findings during evolution and convalescence phase which can illuminate the natural history of similar cases. These results led to the diagnosis of para-infectious encephalitis associated with COVID-19 and treatment with IVIg continued to a total dosage of 3g/kg of body weight (250g total) which resulted in considerable improvement in consciousness, but discontinued because of headaches (day 28). Our patient before diagnosis of neurologic involvement had received IVIg (25 g/day for three days) as a part of treatment for COVID-19 severe pulmonary involvement; and after the CNS lesions were established, it was reinstituted and due to very good clinical and radiological response, we decided to continue IVIg therapy until complete recovery, unless there is a complication. cache = ./cache/cord-253777-h8wy0coq.txt txt = ./txt/cord-253777-h8wy0coq.txt === reduce.pl bib === id = cord-254162-tu81j66h author = Bai, Xiyuan title = Hypothesis: alpha-1-antitrypsin is a promising treatment option for COVID-19 date = 2020-11-12 pages = extension = .txt mime = text/plain words = 5512 sentences = 286 flesch = 39 summary = Sixth, AAT inhibition of elastase can antagonize the formation of neutrophil extracellular traps (NETs), a complex extracellular structure comprised of neutrophil-derived DNA, histones, and proteases, and implicated in the immunothrombosis of COVID-19; indeed, AAT has been shown to change the shape and adherence of non-COVID-19-related NETs. Seventh, AAT inhibition of endothelial cell apoptosis may limit the endothelial injury linked to severe COVID-19-associated acute lung injury, multi-organ dysfunction, and pre-eclampsia-like syndrome seen in gravid women. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. cache = ./cache/cord-254162-tu81j66h.txt txt = ./txt/cord-254162-tu81j66h.txt === reduce.pl bib === id = cord-253606-o8a0jhx2 author = Mégarbane, Bruno title = Comment on: Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial date = 2020-08-07 pages = extension = .txt mime = text/plain words = 844 sentences = 58 flesch = 44 summary = 4 Thirdly, using in vitro anti-SARS-CoV-2 activity and drug exposure at the putative target site of action to determine the effective regimen in vivo is misleading. 4 Interestingly, one mechanistic PK/virological/QTc model developed to predict SARS-CoV-2 decline rate and QTc prolongation suggested that only elevated hydroxychloroquine regimens (>400 mg twice daily for 5 days) are predicted to rapidly decrease viral loads, reduce the infected patient proportion and shorten the treatment course, compared with routine regimens (400 mg daily). To conclude, prediction of the effective hydroxychloroquine regimen to treat the SARS-CoV-2-infected patient is doomed due to uncertainties related to the lack of in vitro model reliability and EC 50 pertinence and to the weakness of used PBPK models that did not mirror hydroxychloroquine PK complexity at the intracellular target level. Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial cache = ./cache/cord-253606-o8a0jhx2.txt txt = ./txt/cord-253606-o8a0jhx2.txt === reduce.pl bib === id = cord-254079-pvl44u4d author = Marinella, Mark A. title = COVID-19 pandemic and the stethoscope: don't forget to sanitize date = 2020-04-11 pages = extension = .txt mime = text/plain words = 739 sentences = 46 flesch = 45 summary = Indirect pathogen transmission from inanimate objects is of potential concern not only for the general public, but also for healthcare professionals whose hands come into frequent contact with hard surfaces. Viral pathogens have also been isolated on hard surfaces in the healthcare setting, 3,4 but have not received as much attention as a risk for nosocomial and person-to-person transmission until very recently with the COVID-19 pandemic. 4 The severe fever with thrombocytopenia syndrome (SFTS) virus, an emerging fatal viral hemorrhagic fever in East Asia, has been recovered from stethoscopes and other hard surfaces in patient rooms who were diagnosed with SFTS, also raising concern for nosocomial transmission of highly pathogenic viruses. Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination cache = ./cache/cord-254079-pvl44u4d.txt txt = ./txt/cord-254079-pvl44u4d.txt === reduce.pl bib === id = cord-253245-433mg0ke author = Gao, Zhiru title = A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1854 sentences = 100 flesch = 55 summary = A recent study reported that four medical workers aged 30-36 years who had re-detectable positive (RP) for SARS-CoV-2 within 5-13 days after being cured and discharged, indicating that some of the recovered patients may still be virus carriers, which caused widespread concern (Lan et al., 2020). Although the results of the three nucleic acid tests were negative for the patient, there were viral residue in the lungs, so even if the patient was discharged, we supposed that virus would transfer positive again after a period of time (Yao et al., 2020) . In addition, initial studies reported that the SARS-CoV-2 RNA could be detected in the feces of 81.8% recovered patients (54/66), even in those with negative throat swabs (Ling et al., 2020) . In other words, even if sometimes the virus nucleic acid tested by RT-PCR is positive in the recovery phase of COVID-19, it will not cause a more serious condition, and antiviral therapy may not be required in most patients. cache = ./cache/cord-253245-433mg0ke.txt txt = ./txt/cord-253245-433mg0ke.txt === reduce.pl bib === id = cord-253990-m75xwrz9 author = Wang, Zhiguo title = Covid‐19: From structure to therapeutic targeting in studying approved drugs and local DNA vaccination date = 2020-10-29 pages = extension = .txt mime = text/plain words = 1125 sentences = 62 flesch = 48 summary = The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represent one of the major challenges in controlling the disease severity, keeping to pose a huge threat to the global health. The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represents one of the major challenges in controlling the disease severity and consequences, posing a huge threat to the global health. In this article, we highlight several previously approved drugs for potential effect on combating SARS-CoV-2 coronavirus infection, and modulating pulmonary inflammation and immune response. Despite unprecedented efforts to contain the virus spread and prevent infection, SARS-CoV-2 pneumonitis can still rapidly strike to incapacitate the lung causing severe acute respiratory distress syndrome (ARDS), resulting in severe disease aftermath and sometimes death. cache = ./cache/cord-253990-m75xwrz9.txt txt = ./txt/cord-253990-m75xwrz9.txt === reduce.pl bib === id = cord-253671-g3ypisig author = Otte, Martin Sylvester title = Riechstörungen bei COVID-19 – aktueller Wissensstand date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2511 sentences = 290 flesch = 53 summary = Bislang existiert keine Studie, die mittels validierter Riechtests die tatsächliche Prävalenz von Riechstörungen bei COVID-19-Patienten zu ermitteln versucht hat. In einer retrospektiven Datenauswertung aus San Diego (USA) zeigte sich, dass Riech-und Schmeckstörungen vor allem von SARS-CoV-2-positiven Personen angegeben werden, deren Krankheit eher milde bis moderat verläuft und die ambulant mittels häuslicher Quarantäne behandelt werden können. Dies konnte auch in einer Fragebogenstudie aus Spanien bestätigt werden, in der 35,3 % von 79 Patienten mit PCR-bestätigter COVID-19-Erkrankung die Riechstörung als initiales Symptom angaben. Dies könnte jedoch auch der Tatsache geschuldet sein, dass es sich wie bei den meisten Studien zum Thema bislang um fragebogenbasierte Erhebungen handelt, die vor allem von Patienten mit geringerer Symptomatik beantwortet werden. Nachdem anfängliche Berichte über die SARS-CoV-2-Infektion Riech-und Schmeckstörungen kaum erwähnten, haben mittlerweile mehrere Studien, insbesondere aus Europa und den USA, Wahrnehmungsschwelle, Erkennungsschwelle diese Symptome als Merkmal von COVID-19 bestätigt. cache = ./cache/cord-253671-g3ypisig.txt txt = ./txt/cord-253671-g3ypisig.txt === reduce.pl bib === id = cord-254120-1q8tqeg7 author = Iannone, Primiano title = The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness. date = 2020-04-11 pages = extension = .txt mime = text/plain words = 3240 sentences = 207 flesch = 47 summary = The WHO, ECDC and CDC have issued conflicting guidelines on the use of respiratory filters (N95) by HCWs. Methods We searched PubMed, Embase and The Cochrane Library from the inception to March 21, 2020 to identify randomized controlled trials (RCTs) comparing N95 respirators versus surgical masks for prevention of COVID-19 or any other respiratory infection among HCWs. The grading of recommendations, assessment, development, and evaluation (GRADE) was used to evaluate the quality of evidence. However, wearing N95 respirators can prevent 73 more (95% CI 46-91) clinical respiratory infections per 1000 HCWs compared to surgical masks (2 RCTs; 2594 patients; low quality of evidence). We therefore conducted a systematic review aimed at assessing the efficacy of N95 respirators versus surgical masks for the prevention of respiratory tract infections transmission among HCWs. The evidence from the review can then be used for the development of an appropriate GRADE framework for public health policy guidelines. cache = ./cache/cord-254120-1q8tqeg7.txt txt = ./txt/cord-254120-1q8tqeg7.txt === reduce.pl bib === id = cord-253472-3s142p6u author = Saurabh, Suman title = Author’s reply to correspondence regarding the article ‘Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals’ date = 2020-09-18 pages = extension = .txt mime = text/plain words = 735 sentences = 60 flesch = 57 summary = title: Author's reply to correspondence regarding the article 'Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals' 1 This is since 95% SARS-CoV-2 infected individuals (including both symptomatics and asymptomatics) were found to have virus persistence of up to 20.92 days. 1 Further, they go on to state that 'as per test-based strategy for asymptomatic patients, two respiratory specimens (≥ 24 hours apart) are required to be negative, irrespective of initial date of COVID-19 detection'. Test-based discharge is not practicable with an overwhelming number of SARS-CoV-2 infected individuals and a large proportion of them undergoing home isolation. Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards cache = ./cache/cord-253472-3s142p6u.txt txt = ./txt/cord-253472-3s142p6u.txt === reduce.pl bib === id = cord-253833-0lajhqn5 author = Misra-Hebert, Anita D title = Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system. date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2860 sentences = 133 flesch = 50 summary = [7] [8] [9] 11 A recent prospective study in the United Kingdom and US suggested a ve-fold increased risk for HCW caring for patients with COVID-19 compared to HCW not caring for patients with COVID-19, even with the use of PPE 12 while another study of HCW in a large healthcare system showed a decrease in positive tests for SARS-CoV-2 associated with a universal masking recommendation. In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19 related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. [7] [8] [9] [10] 12 The fact that HCW identi ed as patient-facing had a signi cantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. cache = ./cache/cord-253833-0lajhqn5.txt txt = ./txt/cord-253833-0lajhqn5.txt === reduce.pl bib === id = cord-253987-83h861lp author = Tada, Takuya title = A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date = 2020-09-17 pages = extension = .txt mime = text/plain words = 6830 sentences = 349 flesch = 50 summary = The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. In SARS-CoV-2 entry, the virus attaches to the target cell through the interaction of the spike glycoprotein (S) with its receptor, the angiotensin-converting enzyme 2 (ACE2) (Li, 2015; Li et al., 2005; Li et al., 2003) , a plasma membrane protein carboxypeptidase that degrades angiotensin II to angiotensin-(1-7) [Ang-(1-7)] a vasodilator that promotes sodium transport in the regulation of cardiac function and blood pressure (Kuba et al., 2010; Riordan, 2003; Tikellis and Thomas, 2012) . To determine the relative antiviral activity of soluble ACE2 and the ACE2 microbody proteins, we tested their ability to block the infection SARS-CoV-2 Δ19 S protein pseudotyped GFP/luciferase reporter virus. cache = ./cache/cord-253987-83h861lp.txt txt = ./txt/cord-253987-83h861lp.txt === reduce.pl bib === id = cord-253970-sbj869yy author = Agarwal, Amit title = Neurological emergencies associated with COVID-19: stroke and beyond date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2417 sentences = 149 flesch = 40 summary = There is limited knowledge on the neurologic manifestations of COVID-19 at present, with a wide array of neurological complications reported, ranging from ischemic stroke to acute demyelination and encephalitis. The second subset of neurological presentation involves a response to the cytokine storm and multi-system inflammation including acute demyelination, vasculitis, necrotizing encephalopathy, and posterior reversible encephalopathy syndrome. Table 1 provides a summary of the most common (1) vascular complications with stroke secondary to arterial or venous thrombosis, related to the known hypercoagulable state seen in COVID [4, 5, 14] , and (2) much broader gamut including diffuse leukoencephalopathy, acute demyelination, posterior reversible encephalopathy syndrome (PRES), necrotizing encephalopathy, and focal cytotoxic edema, primarily seen as a consequence of systemic inflammation and cytokine storm seen with COVID-19 [6] [7] [8] [9] [10] [11] [12] [13] . The most common neurological presentation reported has been ischemic stroke, secondary to arterial or venous thrombosis, because of the hypercoagulable state associated with COVID-19. cache = ./cache/cord-253970-sbj869yy.txt txt = ./txt/cord-253970-sbj869yy.txt === reduce.pl bib === id = cord-253968-jtr0p930 author = López, Verónica title = Recomendaciones en el manejo de la pandemia por coronavirus SARS-CoV-2 (Covid-19) en pacientes con trasplante renal date = 2020-04-03 pages = extension = .txt mime = text/plain words = 3627 sentences = 405 flesch = 56 summary = Manejo clínico del COVID-19: tratamiento médico, del 19 de marzo de 2020), los pacientes receptores de un trasplante renal en los que haya sospecha de infección por SARS-CoV-2 tienen indicación de test diagnóstico y valoración de ingreso si el resultado es positivo, así como de inicio de tratamiento específico. Por tanto, dada la escasa experiencia acumulada y la alta probabilidad de evolución tórpida del cuadro clínico en un breve periodo de tiempo, con desarrollo de fracaso multiorgánico y necesidad de soporte ventilatorio, la estrategia inmunosupresora recomendada a priori, al menos en los casos más graves de pacientes trasplantados renales con neumonía por COVID-19, debe consistir en la interrupción temporal de los inmunosupresores e inicio de metilprednisolona a dosis bajas entre 20 y 40 mg/día, para conferir la adquisición en un corto periodo de tiempo de la inmunidad celular necesaria para controlar la infección y evitar así la progresión de la misma y sus complicaciones vitales. cache = ./cache/cord-253968-jtr0p930.txt txt = ./txt/cord-253968-jtr0p930.txt === reduce.pl bib === id = cord-254446-yxqbe1dj author = Ren, Yunzhao R. title = A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19 date = 2020-05-29 pages = extension = .txt mime = text/plain words = 6723 sentences = 426 flesch = 49 summary = The disease name -COVID-19‖ and the associated virus name -SARS-CoV-2‖ were coined by the World Health Organization (WHO) and the Coronavirus Study Group of the International Committee on Virus Taxonomy, respectively, on February 11 1, 2 . Interestingly, pharyngeal swab viral nucleic acid screening results of 2,510 patients between January 23 and February 25 from a hospital fever clinic in Hunan Province (a neighboring province of Hubei) demonstrated that the positive rate of SARS-CoV-2 (1.3%) was lower than that of Influenza A (2.3%) and Influenza B (3.3%) 42 . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-254446-yxqbe1dj.txt txt = ./txt/cord-254446-yxqbe1dj.txt === reduce.pl bib === id = cord-254072-evgw0as5 author = Hsu, Li-Yang title = Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts date = 2003-06-17 pages = extension = .txt mime = text/plain words = 2240 sentences = 129 flesch = 52 summary = title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts We describe the clinical, laboratory, and radiologic features of the index patient and the patient's initial contacts affected with probable SARS. According to the World Health Organization, a suspected case of SARS is defined as documented fever (temperature >38°C), lower respiratory tract symptoms, and contact with a person believed to have had SARS or history of travel to an area of documented transmission. We describe the clinical features of the index patient in Singapore and the patient's initial group of contacts affected with probable SARS. Nine days after admission, the patient began to improve clinically, the laboratory abnormalities returned towards normal, and the chest x-ray abnormalities stabilized and resolved. When the index patient was seen in early March, the clinical features and highly infectious nature of SARS were not known. cache = ./cache/cord-254072-evgw0as5.txt txt = ./txt/cord-254072-evgw0as5.txt === reduce.pl bib === id = cord-253862-jl1zhg13 author = Khalaf, Khalil title = SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date = 2020-10-06 pages = extension = .txt mime = text/plain words = 14595 sentences = 760 flesch = 45 summary = Although this novel virus is less severe than the first SARS-CoV outbreak, human-to-human transmission remains very high and the number of cases continues to rise exponentially in major urban areas, highlighting the urgent need to develop new containment, diagnostic, and treatment protocols. In the case of SARS-CoV-2, viral evasion of the innate immune system leads to an increase in cytokine production and late CD4+/CD8+ response, which then leads to pathogenic inflammation in patients with high viral loads. (ChiCTR2000029308), involving severe SARS-CoV-2 cases, compared lopinavir/ritonavir treatment with standard care alone, and they showed that the antivirals yielded no clinical benefits. In an open-label control study conducted by Cai et al., the antiviral activity of favipiravir + IFN-α was compared to that of lopinavir/ritonavir + IFN-α in patients with confirmed SARS-CoV-2 infection. cache = ./cache/cord-253862-jl1zhg13.txt txt = ./txt/cord-253862-jl1zhg13.txt === reduce.pl bib === id = cord-254395-tu4aqczj author = Froggatt, Heather M. title = Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL(pro) Reporter Assay date = 2020-10-27 pages = extension = .txt mime = text/plain words = 4200 sentences = 254 flesch = 50 summary = This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. With the aim of generating a protease reporter compatible with SARS-CoV-2 and other present and future coronaviruses to support viral inhibitor screening, we selected CoV 3CL pro as our protease target. (C) Quantification of fluorescence from 293T cells 48 h after transfection with each FlipGFP reporter and either the SARS-CoV-2 3CL pro or an influenza virus protein (A/PR8/1834 NP). To observe whether these FlipGFP constructs background fluoresced without CoV 3CL pro activity, we transfected cells with each reporter or a superfolder GFP (sfGFP) expression plasmid. Development of a FlipGFP CoV 3CL pro reporter-based assay for protease inhibitor screening in human cells. cache = ./cache/cord-254395-tu4aqczj.txt txt = ./txt/cord-254395-tu4aqczj.txt === reduce.pl bib === id = cord-254469-7q6xi2xx author = Wang, Fuzhou title = An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4737 sentences = 245 flesch = 48 summary = In March 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US). However, on March 16 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US), conducted by Moderna and the Vaccine Research Center (VRC) of the National Institute of Allergy and Infectious Diseases (NIAID) [12, 13] . Although mRNA vaccines are commencing human clinical trials, due to the rapid global spread of this new viral pandemic, it may not be possible to develop a safe and effective vaccine for SARS-CoV-2 in time to prevent the increasing number of deaths due to this novel RNA virus. cache = ./cache/cord-254469-7q6xi2xx.txt txt = ./txt/cord-254469-7q6xi2xx.txt === reduce.pl bib === id = cord-254821-px4fe7mn author = Infantino, Maria title = Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date = 2020-05-10 pages = extension = .txt mime = text/plain words = 1224 sentences = 67 flesch = 42 summary = Sixty‐one COVID‐19 patients and 64 patients from a control group were tested by iFlash1800 CLIA analyzer for anti‐SARS CoV‐2 antibodies IgM and IgG. The more relaxed rules of the FDA's "Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency" issued on 16 March 2020, 9 has allowed the market easier access to these tests as well as easier and faster diagnostics, but the lack of control in the production process is also dangerous making these tests potentially less reliable. 11 The aim of the this study was to assess the diagnostic performance of a novel fully automated CLIA for the quantitative detection of anti-SARS-CoV-2 IgM and IgG antibodies. 16 As with most existing studies on the diagnostic performance of the SARS-CoV-2 antibodies, our preliminary data showed that most COVID-19 patients have both IgM and IgG, and only few of them have isolated IgG or IgM antibodies. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Assessment of immune response to SARS-CoV-2 with fully-automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays cache = ./cache/cord-254821-px4fe7mn.txt txt = ./txt/cord-254821-px4fe7mn.txt === reduce.pl bib === id = cord-254094-ed1epul1 author = Mayoral, Eduardo Pérez-Campos title = Factors related to asymptomatic or severe COVID-19 infection date = 2020-09-24 pages = extension = .txt mime = text/plain words = 1665 sentences = 98 flesch = 48 summary = In particular, we refer to the TMPRSS2 expression profile, balance of androgen and estrogen, blood group-A and/or B, nonsynonymous mutations in ORF3, and proteins NS7b and NS8 in SARS-CoV-2. In the first months of the COVID-19 pandemic, most authors focused their attention on features such as the high expression of ACE2 in the salivary glands in asymptomatic infection [4] , and the maturity and binding capacity of ACE2 [5, 6] . A higher 2D:4D ratio is associated with COVID-19 severity in men [14] , this means that sex hormones play a role in protection, thus, causing women to develop less serious complications or an asymptomatic COVID-19 Infection [12] . An in-depth study of the factors associated with asymptomatic subjects can provide information to limit severe COVID-19 as much as possible. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated cache = ./cache/cord-254094-ed1epul1.txt txt = ./txt/cord-254094-ed1epul1.txt === reduce.pl bib === id = cord-254017-4a6fs57r author = Pan, Xiu-wu title = Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis date = 2020-03-31 pages = extension = .txt mime = text/plain words = 870 sentences = 52 flesch = 54 summary = Colocalization analysis of ACE2 and TMPRSS genes showed relatively high coexpression in podocytes and proximal straight tubule cells, which were identified as candidate host cells (Fig. 1a, b) . Second, although there was no significant difference in the expression of TMPRSS genes, the expression of the receptor ACE2 in podocytes and proximal straight tubule cells in Occidental donors was more pronounced than that in Asian donors (Fig. S2B) , suggesting that Occidental populations might be at higher risk for developing AKI in COVID-19. In addition, comparative analysis showed that the coexpression of the receptor ACE2 and TMPRSS genes in kidney cells was no less than that in the lung, oesophagus, small intestine and colon (Fig. S2C) , suggesting that the kidney might also be an important target organ for SARS-CoV-2. Based on our findings, we conclude that the cytopathic effects of SARS-CoV-2 on podocytes and proximal straight tubule cells may cause AKI in patients with COVID-19, especially in patients with SARS-CoV-2 infection in blood samples. cache = ./cache/cord-254017-4a6fs57r.txt txt = ./txt/cord-254017-4a6fs57r.txt === reduce.pl bib === id = cord-253993-ynrthadj author = Belhassan, Assia title = Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1766 sentences = 94 flesch = 46 summary = The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Based on all these effects, the study of interactions between chloroquine, hydroxychloroquine and the eighteen imidazole derivatives against the SARS-CoV-2 main protease are recommended. In this paper, the modeling interaction of eighteen imidazole derivatives against novel Coronavirus are performed using the molecular docking method followed by comparison with chloroquine, hydroxychloroquine interactions formed in the same binding site of SARS-CoV-2 main protease. In this study, we have tried to carry out a docking study of chemical compounds reported as potent Antiplasmodial inhibitors of imidazole derivatives based on 7-chloro-4-aminoquinoline and analogues in the active site of SARS-Cov-2 main protease, flowed by comparison with two drugs; chloroquine and hydroxychloroquine. cache = ./cache/cord-253993-ynrthadj.txt txt = ./txt/cord-253993-ynrthadj.txt === reduce.pl bib === id = cord-254318-w8wrn9lx author = Díez, José-María title = Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2687 sentences = 167 flesch = 48 summary = MATERIAL & METHODS: Gamunex(®)-C and Flebogamma(®) DIF (Grifols) intravenous immunoglobulin (IVIG) products were tested using ELISA techniques for antibodies against several antigens of human common betacoronaviruses that may crossreact with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Gamunex R -C (Grifols Therapeutics, Inc., NC, USA) and Flebogamma R DIF (Instituto Grifols S.A., Barcelona, Spain) IVIGs were tested for crossreactivity against several betacoronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 antigens, using ELISA techniques. Even with this uncertainty, in the context of the current health emergency (pandemic), the potential of IVIG as a therapy for COVID-19 is already being evaluated in a number of studies involving patients with severe SARS-CoV-2 viral infections including pneumonia [28] [29] [30] . • This is the first time that currently available intravenous immunoglobulins have been reported to contain antibodies that crossreact against antigens of SARS-CoV-2 and other coronaviruses. cache = ./cache/cord-254318-w8wrn9lx.txt txt = ./txt/cord-254318-w8wrn9lx.txt === reduce.pl bib === id = cord-254478-scc9wee0 author = To, Kelvin Kai-Wang title = Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date = 2020-03-23 pages = extension = .txt mime = text/plain words = 5189 sentences = 294 flesch = 53 summary = title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. We present findings of an observational cohort study of the temporal profile of viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from posterior oropharyngeal saliva samples and serum antibody responses, dated by symptom onset and correlated with clinical findings. cache = ./cache/cord-254478-scc9wee0.txt txt = ./txt/cord-254478-scc9wee0.txt === reduce.pl bib === id = cord-254855-gmy9zyad author = He, Sijia title = PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1700 sentences = 94 flesch = 51 summary = Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. Together, these results demonstrate that PSGL-1 expression in the virus-producer cells severely diminishes the infectivity of virions bearing SARS coronavirus S proteins. We and other previously reported that PSGL-1-mediated inhibition of virion infectivity is through steric hindrance of particle attachment to target cells, which does not depend on the presence of viral envelope glycoproteins (1, 5) . We performed a virion attachment assay and observed that the lentiviral particles pseudotyped with SARS-CoV or SARS-CoV-2 S protein produced from PSGL-1-expressing cells were impaired in their ability to attach to target cells (Fig. 2D) . These results demonstrate that the presence of PSGL-1 on virus particles can structurally hinder virion interaction with the target cells even in the presence of remaining S proteins, consistent with previous studies of PSGL-1 and HIV-1 infection (1, 5) . cache = ./cache/cord-254855-gmy9zyad.txt txt = ./txt/cord-254855-gmy9zyad.txt === reduce.pl bib === id = cord-254419-qw83atrx author = Bhattacharyya, Rajat title = The Interplay Between Coagulation and Inflammation Pathways in COVID-19-Associated Respiratory Failure: A Narrative Review date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5900 sentences = 276 flesch = 33 summary = This narrative review aims to summarize the current available evidence on the interplay between hypercoagulability, thrombo-inflammation, and pulmonary microvascular thrombosis in COVID-19 infection resulting in respiratory failure and how this information can be used to design clinical trials to optimize patient outcomes. ACE2 angiotensin-converting enzyme 2, CRP C-reactive protein, ESR erythrocyte sedimentation rate, LDH lactate dehydrogenase, NETS neutrophil extracellular traps, SARS-COV-2 severe acute respiratory syndrome coronavirus 2, TMPRSS2 transmembrane protease serine 2 shown to be at higher risk of worse outcomes [13] [14] [15] (Fig. 2) . CHD chronic heart disease, CLD chronic lung disease, CKD chronic kidney disease, DOACS direct oral anticoagulants, FDPs fibrinogen degradation products, HTN hypertension, IFN interferon, JAK Janus kinase, LDH lactate dehydrogenase, LMWH low molecular weight heparin, NSAIDS nonsteroidal anti-inflammatory drugs, PT prothrombin time, TNF tumor necrosis factor, VW Ag Von Willebrand antigen and microvascular thrombosis appears to be responsible for the clinical picture that leads to progressive multi-organ failure in a small percentage of patients, ultimately causing fatalities. cache = ./cache/cord-254419-qw83atrx.txt txt = ./txt/cord-254419-qw83atrx.txt === reduce.pl bib === id = cord-254668-szxhlejx author = Brogna, Barbara title = Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1885 sentences = 100 flesch = 43 summary = title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. Spontaneous pneumomediastinum (SPM) and Loculated pneumothorax (LPNX) are both generally rare clinical and radiological conditions associated with Coronavirus Disease 2019 (COVID-19). We report for the first time clinical data and radiological chest CT imaging of two patients affected by COVID-pneumonia associated with early radiological findings of SPM and LPNX. It has been suggested that a dysregulation of the immune response related to SARS-CoV-2, SARS-coV or MERS-CoV infection could lead to lung injury and the clinical and radiological findings typical of ARDS 2, 20 Most of the cases of SPM and PNX described in patients with COVID-19 pneumonia and in those affected by SARS have some features in common, including the absence of smoking history 16, 19 . cache = ./cache/cord-254668-szxhlejx.txt txt = ./txt/cord-254668-szxhlejx.txt === reduce.pl bib === id = cord-254464-6l7fwylu author = Shingare, Ashay title = COVID‐19 in recent kidney transplant recipients date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1712 sentences = 114 flesch = 54 summary = Younger age, absence of other comorbidities and lower dose of anti‐thymocyte globulin (ATG) used as induction possibly contributed to good outcome in our recent LDKT recipients compared with earlier published cases of recent deceased donor kidney transplant recipients with COVID‐19. Sooner or later we would need to restart transplant programs, both LDKT & deceased donor kidney transplant (DDKT), as dust settles on the acute era to a post-COVID-19 new normal, where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will be a possibility. During the further follow-up over next 2 months, 2 of these 7 patients tested positive for SARS-CoV-2 by nasopharyngeal swab real-time reverse transcription polymerase chain reaction (rRT-PCR), 3 tested negative and 2 were not tested as they were asymptomatic. Due to intensive immunosuppression, recent transplant recipients (< 3 months post-transplant) are at increased risk of developing severe disease due to COVID-19. cache = ./cache/cord-254464-6l7fwylu.txt txt = ./txt/cord-254464-6l7fwylu.txt === reduce.pl bib === id = cord-254630-ed5gawoj author = Barron, Sarah P. title = Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy? date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4026 sentences = 180 flesch = 39 summary = Additionally, RFBs pose a risk of nosocomial infection transmission between patients with the identification of human proteins, deoxyribonucleic acid (DNA) and pathogenic organisms on fully reprocessed bronchoscopes despite full adherence to the guidelines. Until now, disposable or single-use flexible bronchoscopes (SUFBs) have primarily been used by anaesthetists in an ICU or peri-operative setting where they perform to an acceptable level in comparison to RFBs [12, 13] combined with the distinct advantage of a reduced risk of infection owing to their sterility [14] . In this review, the risk of infection with standard RFBs will be outlined as will the advantages of SUFBs, with comment on their cost profile compared to RFBs and attempt to suggest a rationale for their use during the COVID-19 pandemic and in a respiratory setting. cache = ./cache/cord-254630-ed5gawoj.txt txt = ./txt/cord-254630-ed5gawoj.txt === reduce.pl bib === id = cord-254825-c5d0wul9 author = Kim, Sei Won title = Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3554 sentences = 205 flesch = 49 summary = In this study, we retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing, contact history, and presence of respiratory symptoms in a single center with a healthcare-associated COVID-19 outbreak. We reviewed the history of patients to assess whether they visited China or other high-risk countries within two weeks prior to the outbreak of healthcare-associated COVID-19, or if they came into contact with confirmed COVID-19 cases. After SARS-CoV-2 infection was confirmed, the Seoul city government announced the closure of the hospital on February 21, 2020, to prevent a healthcare-associated outbreak. After the hospital staff member responsible for transporting patients was confirmed as the first COVID-19 case, people with contact history, fever, or respiratory symptoms were tested for SARS-CoV-2 infection with RT-PCR (Fig 2) . After the first case was reported, epidemiologists from KCDC and the infection control unit of our hospital reviewed electronic medical charts, CCTV, and personal movements to identify individuals with potential contact with confirmed COVID-19 patients. cache = ./cache/cord-254825-c5d0wul9.txt txt = ./txt/cord-254825-c5d0wul9.txt === reduce.pl bib === id = cord-254636-3lr008th author = Shishir, Tushar Ahmed title = In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date = 2020-08-16 pages = extension = .txt mime = text/plain words = 2974 sentences = 171 flesch = 54 summary = We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. We conducted comparative analysis of publicly available genome sequences of SARS-CoV-2 from 27 countries to predict the origin of viruses in Bangladesh by studying a time-4 resolved phylogenetic relationship. Later, we analyzed the variants present in different isolates of Bangladesh to understand the pattern of mutations in relation to the ancestral Wuhan strain, find unique mutations, and possible effect of these mutations on the stability of encoded proteins, and selection pressure on genes. cache = ./cache/cord-254636-3lr008th.txt txt = ./txt/cord-254636-3lr008th.txt === reduce.pl bib === id = cord-254207-uru7bkr4 author = Singanayagam, Anika title = Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2290 sentences = 112 flesch = 51 summary = Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Understanding the duration of infectiousness in persons who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to developing evidence-based public health policies on isolation, contact tracing and return to work. In the first 3 months of the COVID-19 pandemic in the United Kingdom (UK) (late January to early April 2020), we received 754 URT samples from 425 symptomatic cases that tested positive for SARS-CoV-2 by RT-PCR targeting the RNA-dependent RNA polymerase (RdRp) gene [1] and that had a clear record of the dates of symptom onset and sample collection. cache = ./cache/cord-254207-uru7bkr4.txt txt = ./txt/cord-254207-uru7bkr4.txt === reduce.pl bib === id = cord-255365-fog62qdu author = Goldstein, Neal D. title = On the importance of early testing even when imperfect in a pandemic such as COVID-19 date = 2020-08-03 pages = extension = .txt mime = text/plain words = 1482 sentences = 83 flesch = 49 summary = bias in identified cases of SARS-CoV-2 infections will vary in the face of unknown data surrounding test sensitivity and specificity. The true prevalence of COVID-19 will vary in the tested population (e.g., whether a drive-thru public event, clinical referral, group home, etc.), therefore we allowed for a hypothetical range from 0% to 50%. When the true prevalence of COVID-19 infection is low, as at the start of a pandemic, there will be a greater number of false positives, even under excellent specificity. If we assume 25% prevalence of disease in the tested population, we could realistically anticipate between 0 and 75 false positive results, and between 0 and 100 false negative results per 1000 tests. Serosurveys employing antibody assays can thereby inform public health surveillance regarding the extent of the population who have been infected at any point with SARS-CoV-2, and track herd immunity thresholds. cache = ./cache/cord-255365-fog62qdu.txt txt = ./txt/cord-255365-fog62qdu.txt === reduce.pl bib === id = cord-254505-mjj8xrer author = Kannan, Saathvik R. title = Infectivity of SARS-CoV-2: there Is Something More than D614G? date = 2020-09-15 pages = extension = .txt mime = text/plain words = 1917 sentences = 130 flesch = 65 summary = To gain insight into the distribution of mutations in SARS-CoV-2 nonstructural proteins (nsps) and structural proteins, we analyzed protein sequences (n = 7232) from the United States (n = 6302), Europe (n = 420), China (n = 104), and India (n = 406), and determined the mutations with respect to Wuhan-Hu-1 isolate (NCBI Reference Sequence: NC_045512.2). The results of the temporal analysis of the mutation frequency of P323L (nsp12), C241U (5'UTR) and D614G (S-protein) show that P323L was consistently present in the viruses that had D614G mutation and C241U started coevolving with D614G sometime late January 2020 (Fig. 1b) . A mutation of D614 to G614 should result in the loss of these interactions, which could alter the dynamics of S-protein conformational changes during SARS-CoV-2 infection. Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex cell doi The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity cell doi cache = ./cache/cord-254505-mjj8xrer.txt txt = ./txt/cord-254505-mjj8xrer.txt === reduce.pl bib === id = cord-254884-5rmnwcfd author = Ng, S. M. title = Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) date = 2006-01-21 pages = extension = .txt mime = text/plain words = 2218 sentences = 130 flesch = 52 summary = title: Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) The SMART debriefing (1) aimed at boosting resilience and catalyzing transformation among persons undergoing stressful events, (2) adopted a growth-oriented and holistic approach of health promotion, and (3) employed methods drawn from various indigenous sources (e.g. Asian philosophies and Traditional Chinese Medicine). Participants (N=51) were people with chronic diseases recruited about 1 month (August 2003) after the Severe Acute Respiratory Syndrome (SARS) outbreak was eventually under control, after causing widespread panic in Hong Kong. After the one-day group debriefing, participants showed significant decrease in depression level, as measured by Brief Symptom Inventory (Derogatis & Melisaratos, 1983, Psychological Medicine, 13(3), 595–605) and changes in cognitive appraisal towards SARS. We hypothesize the SMART debriefing can promote positive growth among people with chronic diseases and reduce their distress levels at the same time. cache = ./cache/cord-254884-5rmnwcfd.txt txt = ./txt/cord-254884-5rmnwcfd.txt === reduce.pl bib === id = cord-254452-gqqdx2r5 author = Singh, Awadhesh Kumar title = Remdesivir in COVID-19: A critical review of pharmacology, pre-clinical and clinical studies date = 2020-05-12 pages = extension = .txt mime = text/plain words = 3162 sentences = 163 flesch = 47 summary = METHODS: We systematically searched the PubMed, ClinicalTrial.Org and MedRxiv database up till May 5, 2020 using specific key words such as "Remdesivir" or 'GS-5734″ AND "COVID-19" or "SARS-CoV-2" and retrieved all the article published in English language, that have reported the pharmacology and the clinical outcomes of remdesivir in patients with COVID-19. A preliminary report (April 29, 2020) from an interim analysis of an ongoing double-blind randomized controlled trial (RCT) recently suggested that remdesivir had a 31% faster time to recovery, compared to the placebo (p<0.001), in patients with COVID-19 [15] . In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) No evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for COVID-19 infection with oxygen requirement: results of a study using routinely collected data to emulate a target trial cache = ./cache/cord-254452-gqqdx2r5.txt txt = ./txt/cord-254452-gqqdx2r5.txt === reduce.pl bib === id = cord-255264-2kj961en author = Hasan, Syed Shahzad title = Social distancing and the use of PPE by community pharmacy personnel: Does evidence support these measures? date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2233 sentences = 104 flesch = 45 summary = While the United States adopted a universal mask approach and Turkey recommended the use of masks and protective goggles for their pharmacy personnel, almost all of the countries recommended against routine use of face mask and other PPE (gloves or aprons/gowns), except when dealing with suspected COVID-19 patients or performing activities requiring close contact (unable to maintain recommended social distance) with the patients. Though the observation from such case study cannot be regarded as conclusive, the assumption, for now, should be that airborne transmission of SARS-CoV-2 is possible unless being discredited in the future, and therefore we opine that the wearing of appropriate PPE is of utmost importance for healthcare workers, including community pharmacy personnel dealing with individuals may or may not be infected on a day-to-day basis, regardless if they manage to observe social distancing in their workplace or if they perform close contact activities. cache = ./cache/cord-255264-2kj961en.txt txt = ./txt/cord-255264-2kj961en.txt === reduce.pl bib === id = cord-254968-czrgzyr3 author = Zhang, Qiang title = A serological survey of SARS-CoV-2 in cat in Wuhan date = 2020-09-17 pages = extension = .txt mime = text/plain words = 3148 sentences = 180 flesch = 56 summary = Here, we investigated the infection of SARS-CoV-2 in cats during COVID-19 outbreak in Wuhan by serological detection methods. Our data demonstrated that SARS-CoV-2 has infected cats in Wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of COVID-19. Here, we investigated the serological prevalence of SARS-CoV-2 in cats by an indirect ELISA and virus neutralization tests (VNT), and monitored the serum antibody dynamics of cats infected SARS-CoV-2, providing a basis for further understanding the infection of SARS-CoV-2 in cats. In this study, we detected the presence of SARS-CoV-2 antibodies in cats in Wuhan during the COVID-19 outbreak with ELISA, VNT and western blot. Virus neutralization test and Western blot assay of cat serum samples for SARS-CoV-2 (A) Cat#14, Cat#15 and Cat#4 sera were 3-fold serially diluted and mixed with SARS-CoV-2; after incubated at 37°C for 1 h, the mixture was used to infect Vero E6 cells, and replaced with semi-solid media 1 h later. cache = ./cache/cord-254968-czrgzyr3.txt txt = ./txt/cord-254968-czrgzyr3.txt === reduce.pl bib === id = cord-255293-8necodtw author = Phakthanakanok, Krongsakda title = A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism date = 2009-01-30 pages = extension = .txt mime = text/plain words = 3958 sentences = 222 flesch = 63 summary = The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. In order to perform molecular dynamics simulations, three structures of the SARS CoVMpro complexed with the octapeptides obtained from the docking, were prepared. However, one atom of the Na+ was also added in each system of the enzyme-substrate complexed of the octapeptide P3Lys and P3Arg due to it neutralized the amino acid, Lys and Arg. In the simulation, each time step was set to 2 fs and the simulation of the whole system performed for 2,000 ps (2 ns). The structure of the enzyme-substrate complex (SARS CoVMpro-octapeptide) obtained from molecular docking was then subjected to MD simulation. cache = ./cache/cord-255293-8necodtw.txt txt = ./txt/cord-255293-8necodtw.txt === reduce.pl bib === id = cord-255413-8o884nyp author = Hotez, Peter J. title = The Potential Role of Th17 Immune Responses in Coronavirus Immunopathology and Vaccine-induced Immune Enhancement date = 2020-04-17 pages = extension = .txt mime = text/plain words = 1707 sentences = 104 flesch = 35 summary = From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. Beyond direct virus-induced pathology, immune enhancement associated with eosinophilic infiltration and immunopathology is a potential safety concern linked to first-generation vaccines to prevent severe acute respiratory syndrome (SARS) (12) . While vaccinia and other vectored vaccines induce substantial immune enhancement in both the lungs and liver of experimental animals (20) (21) (22) (23) (24) , which in some cases have been linked to viral expression of the N protein (15) , none of these studies specifically examined Th17 responses. A double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge Severe acute respiratory syndrome-associated coronavirus vaccines formulated with delta inulin adjuvants provide enhanced protection while ameliorating lung eosinophilic immunopathology cache = ./cache/cord-255413-8o884nyp.txt txt = ./txt/cord-255413-8o884nyp.txt === reduce.pl bib === id = cord-255101-l5ssz750 author = Daval, Mary title = Efficacy of local budesonide therapy in the management of persistent hyposmia in COVID-19 patients without signs of severity: A structured summary of a study protocol for a randomised controlled trial date = 2020-07-20 pages = extension = .txt mime = text/plain words = 8946 sentences = 919 flesch = 63 summary = Objectif principal: Evaluer l'efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d'odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l'hyposmie 30 jours après le début des symptômes. L'objectif de cet essai randomisé contrôlé, bicentrique, est d'évaluer l'efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d'odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l'hyposmie 30 jours après le début des symptômes. Evaluer l'efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d'odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l'hyposmie 30 jours après le début des symptômes. cache = ./cache/cord-255101-l5ssz750.txt txt = ./txt/cord-255101-l5ssz750.txt === reduce.pl bib === id = cord-254957-jqp1gto6 author = Klann, Kevin title = Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date = 2020-08-11 pages = extension = .txt mime = text/plain words = 7002 sentences = 411 flesch = 50 summary = We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. Additionally, we found carbon 160 metabolism among the pathways showing significantly increased phosphorylation upon SARS-CoV-2 infection (Table S4 ) in addition to previously described changes of total protein levels of enzymes part of glycolysis and carbon metabolism (Bojkova et al., 2020 )( Figure S3 ). We mapped identified members of GFR signaling and their respective phosphorylation differences upon SARS-CoV-2 infection ( Figure 3C ) revealing an extensive overall increase in phosphorylation of the whole pathway, including related components for cytoskeleton remodeling and receptor endocytosis. Growth factor receptor signaling was highly activated upon infection and its inhibition prevented SARS-CoV-2 replication in cells. cache = ./cache/cord-254957-jqp1gto6.txt txt = ./txt/cord-254957-jqp1gto6.txt === reduce.pl bib === id = cord-255170-bp3irxlh author = Mark, John title = SARS coronavirus: Unusual lability of the nucleocapsid protein date = 2008-12-12 pages = extension = .txt mime = text/plain words = 5274 sentences = 355 flesch = 95 summary = The exper i ments used prep a ra tions of recombinant N-pro tein from which the His-tag had not been enzy mat i cally removed; thus, cal cu la tion of the resul tant pro tein/ pep tide masses must take into con sid er ation the pres ence of the His-tag (an addi tional 11 amino acid sequence). A spe cific pro te ol y sis assay was then devel oped using pep tides con tain ing the SR-rich region cor re spond ing to the SARS N-pro tein cleav age site. Taken together, the results from the FITC-labelled casein, the refold ing, and the FRET (EDANS/DAB CYL) detec tion exper i ments strongly sug gest that the SR-spe cific cleav age of N-pro tein is not the result of a con tam i nat ing pro te ase activ ity. Cell type-spe cific cleav age of nucle o cap sid pro tein by effec tor casp as es dur ing SARS coro na vi rus infec tion cache = ./cache/cord-255170-bp3irxlh.txt txt = ./txt/cord-255170-bp3irxlh.txt === reduce.pl bib === id = cord-255446-wddj6hrv author = McDade, T. W. title = High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3121 sentences = 234 flesch = 59 summary = To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. 7 We adapted this ELISA to measure IgG antibodies to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in DBS samples. . https://doi.org/10.1101/2020.06.01.20119602 doi: medRxiv preprint Participants who previously tested positive for SARS-CoV-2 virus were recruited from the community through direct contact. Seroprevalence in 202 samples collected from the community, which includes health care workers and first responders, none of which were confirmed SARS-CoV-2 viral positive. cache = ./cache/cord-255446-wddj6hrv.txt txt = ./txt/cord-255446-wddj6hrv.txt === reduce.pl bib === id = cord-255290-p64apuk1 author = Matheeussen, Veerle title = International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 2121 sentences = 102 flesch = 41 summary = title: International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. Between 6 April and 20 May 2020, each participating laboratory received a blinded panel of eight samples, with five samples containing serial 10-fold dilutions (2.30-5.30 dPCR log10 RNA copies/mL, one duplicated) of non-infectious SARS-CoV-2-positive supernatant obtained from Vero cell culture, two samples with cell culture-derived common human coronavirus (HCoV-NL63, HCoV-OC43) and one negative control with transport medium only. In parallel with the EQA study, laboratories were surveyed to assess their challenges in implementing and executing molecular testing capacity and throughput for SARS-CoV-2 detection, also in April and May 2020. cache = ./cache/cord-255290-p64apuk1.txt txt = ./txt/cord-255290-p64apuk1.txt === reduce.pl bib === id = cord-254777-h8hw4m9f author = Tanner, Tamara title = Hyperinflammation and the utility of immunomodulatory medications in children with COVID-19 date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4731 sentences = 248 flesch = 42 summary = Cytokine storm syndromes include various entities, depending on the inciting factor: primary Hemophagocytic Lymphohistiocytosis [HLH] in children with specific genetic mutations; secondary HLH due to infection or malignancy, macrophage activation syndrome due to rheumatologic disease and cytokine release syndrome (CRS) when hyperinflammation is due to CAR T-cell therapy. Although still under investigation, ADE has been proposed as a potential mechanism underlying the newly described MIS-C, based on the observation that a majority of the patients have evidence of existing antibodies to SARS-CoV-2 and the inflammatory condition seems to lag behind the COVID-19 infection peak by approximately 4-6 weeks. The rationale for use of IL-6 blockade in serious COVID-19 infections is based on the observation that for the subset of patients with severe manifestations, IL-6 is most likely one of the drivers of the cytokine storm, and elevated levels of IL-6 have been consistently shown [14] . cache = ./cache/cord-254777-h8hw4m9f.txt txt = ./txt/cord-254777-h8hw4m9f.txt === reduce.pl bib === id = cord-255284-ffh1jl40 author = Guery, B title = Syndrome respiratoire aigu sévère date = 2003-06-30 pages = extension = .txt mime = text/plain words = 2809 sentences = 291 flesch = 65 summary = Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d'isoler l'agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l'épidémie. Deux éléments notables sont évoqués dans cette publication, tout d'abord le fait que seuls les patients atteints de SARS ont des anticorps témoignant du fait que ce virus circule pour la première fois. À noter que cette faculté existe chez un Coronavirus porcin entraînant des pathologies respiratoires mais, aucun lien de parenté entre ces deux virus n'a été mis en évidence. Dans le cas du SARS, les premières analyses montrent que la contamination nécessite un contact prolongé et répété avec un malade présentant une symptomatologie pulmonaire. ont montré la présente d'ARN du Coronavirus responsable du SARS dans les selles des patients [4] . cache = ./cache/cord-255284-ffh1jl40.txt txt = ./txt/cord-255284-ffh1jl40.txt === reduce.pl bib === id = cord-255252-md0avnqg author = Tang, Julian W. title = Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date = 2007-07-02 pages = extension = .txt mime = text/plain words = 5317 sentences = 326 flesch = 70 summary = SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. Post-mortem tissues were collected with great care from the major organs including heart, kidney, liver, spleen, lung, small bowel, psoas (skeletal) muscle, and bone marrow. Figures 1-6 show the results, using semi-log plots, for each organ: heart, kidney, liver, spleen, lung, and small bowel, respectively, for SARS-CoV, GAPDH and the SARS-CoV/GAPDH RNA ratio. In the organspecific viral load results, the overall picture made up from the data points from the seven different patients with different durations of SARS illness, generally, the SARS-CoV/GAPDH RNA ratio never reached above one in heart, kidney, liver, and spleen tissue for all x-axis parameters analyzed. cache = ./cache/cord-255252-md0avnqg.txt txt = ./txt/cord-255252-md0avnqg.txt === reduce.pl bib === id = cord-255069-9xueqdri author = Leary, Shay title = Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date = 2020-04-11 pages = extension = .txt mime = text/plain words = 1821 sentences = 77 flesch = 43 summary = The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . cache = ./cache/cord-255069-9xueqdri.txt txt = ./txt/cord-255069-9xueqdri.txt === reduce.pl bib === id = cord-255440-ls1l2mlg author = Tindle, Courtney title = Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date = 2020-10-18 pages = extension = .txt mime = text/plain words = 9951 sentences = 525 flesch = 53 summary = Besides the approaches described so far, there are a few more approaches used for modeling COVID-19-(i) 3D organoids from bronchospheres and tracheospheres have been established before (Hild and Jaffe, 2016; Rock et al., 2009; Tadokoro et al., 2016) and are now used in apical-out cultures for infection with SARS-COV-2 (Suzuki et al., 2020); (ii) the most common model used for drug screening is the air-liquid interphase (ALI model) in which pseudo-stratified primary bronchial or small airway epithelial cells are used to recreate the multilayered mucociliary epithelium (Mou et al., 2016; Randell et al., 2011) ; (iii) several groups have also generated 3D airway models from iPSCs or tissue-resident stem cells (Dye et al., 2015; Ghaedi et al., 2013; Konishi et al., 2016; McCauley et al., 2017; Miller et al., 2019; Wong et al., 2012) ; (iv) others have generated AT2 cells from iPSCs using closely overlapping protocols of sequential differentiation starting with definitive endoderm, anterior foregut endoderm, and distal alveolar expression (Chen et al., 2017; Gotoh et al., 2014; Huang et al., 2014; Jacob et al., 2017; Jacob et al., 2019; Yamamoto et al., 2017) . cache = ./cache/cord-255440-ls1l2mlg.txt txt = ./txt/cord-255440-ls1l2mlg.txt === reduce.pl bib === id = cord-255552-k1retwa4 author = Gassen, Nils C. title = Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1208 sentences = 73 flesch = 39 summary = Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Targeting of these pathways by exogenous administration of spermidine, AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS-CoV-2 propagation by 85, 88, and >99%, respectively. In the case of highly pathogenic Middle East respiratory syndrome 57 (MERS)-CoV, we recently showed that autophagy is limited by a virus-induced AKT1-dependent 58 activation of the E3-ligase S-phase kinase-associated protein 2 (SKP2), which targets the key autophagy 59 initiating protein Beclin-1 (BECN1) for proteasomal degradation (10). Direct blocking of the negative BECN1 regulator SPK2 by previously 175 described inhibitors SMIP004, SMIP004-7, valinomycin, and niclosamide (10) showed SARS-CoV-2 176 growth inhibition from 50 (SMIP004, SMIP004-7) to over 99% in case of valinomycin and niclosamide 177 (Figure 4a, lower panel, Figure S3d,e) . cache = ./cache/cord-255552-k1retwa4.txt txt = ./txt/cord-255552-k1retwa4.txt === reduce.pl bib === id = cord-255458-81ugj38k author = Doll, Michelle E. title = Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1169 sentences = 77 flesch = 48 summary = title: Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests Infectious disease physicians designated each patient with high or low probability based on the following clinical criteria consistent with reported literature 7 : (1) exposure to SARS-CoV-2; (2) symptoms of COVID-19, including hypoxia, respiratory or gastrointestinal symptoms, or fever; (3) leukopenia; (4) chest imaging; (5) lack of other explanatory diagnosis. Overall, 70 inpatients with initially negative SARS-CoV-2 testing underwent repeat testing for ongoing clinical concerns between March 2 and April 4, 2020. Early interval retesting of patients with a high pretest probability for SARS-CoV-2 as part of a formal protocol was performed from March 31, 2020, through April 7, 2020. The patient who tested positive 6 days after a negative result was deemed "low probability" when re-evaluated for that repeat test. 3, 4 However, cases of high probability symptomatic patients with false-negative testing early in the course of illness have been reported. cache = ./cache/cord-255458-81ugj38k.txt txt = ./txt/cord-255458-81ugj38k.txt === reduce.pl bib === id = cord-255229-w2xtxo9a author = Edson, Daniel C title = Identification of SARS-CoV-2 in a Proficiency Testing Program date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2048 sentences = 151 flesch = 48 summary = OBJECTIVES: At the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States, testing was limited to the Centers for Disease Control and Prevention–developed reverse transcription polymerase chain reaction assay. METHODS: The American Proficiency Institute sent 2 test samples to 346 clinical laboratories in order to assess the accuracy of SARS-CoV-2 assays. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. In this report we present the results of the first US study of SARS-CoV-2 accuracy by API participant laboratories from the 2020 First Test Event. cache = ./cache/cord-255229-w2xtxo9a.txt txt = ./txt/cord-255229-w2xtxo9a.txt === reduce.pl bib === id = cord-254900-fg5wd0nh author = Havenga, M.J.E. title = Serum‐free transient protein production system based on adenoviral vector and PER.C6 technology: High yield and preserved bioactivity date = 2007-12-13 pages = extension = .txt mime = text/plain words = 7456 sentences = 339 flesch = 48 summary = Because of these features it can be envisioned that the use of adenoviral vectors results in higher protein yields derived from mammalian cells cultured in suspension as compared to current DNA transfection protocols for which processes at scale like cell uptake and nuclear localization, present major technical hurdles. Based on the data obtained thus far it was concluded that an DE1/DE2A adenoviral vector can be efficiently produced at 348C on PER.E2A cells and can subsequently serve as a tranducing agent for PER.C6 cells without inducing viral backbone replication or high level viral capsid protein expression in human A549 indicator cells. As shown in Figure 2C the yield of SARS anti-body produced did not significantly differ demonstrating that cleared vector stock directly harvested from he PER.E2A cell line can be used for production of recombinant protein without compromising yield. cache = ./cache/cord-254900-fg5wd0nh.txt txt = ./txt/cord-254900-fg5wd0nh.txt === reduce.pl bib === id = cord-255631-516epnjw author = Syeda, H. B. title = The Role of Machine Learning Techniques to Tackle COVID-19 Crisis: A Systematic Review. date = 2020-08-25 pages = extension = .txt mime = text/plain words = 6751 sentences = 469 flesch = 46 summary = Results: The 128 publications selected were classified into three themes based on ML applications employed to combat the COVID-19 crisis: Computational Epidemiology (CE), Early Detection and Diagnosis (EDD), and Disease Progression (DP). This study focused on peer-reviewed publications, as well as, preprints that applied ML techniques to analyze and address COVID-19 crisis on different scales including diagnostics, prognostics, disease spread forecast, omics, and drug development. We identified forty studies that primarily focused on diagnosing COVID-19 in patients with suspected infection mostly using chest radiological images such as Computed Tomography (CT), X-Radiation (X-Ray), and Lung Ultrasound (LUS). In our review, we identified one study by Roy et al [126] who used a deep learning model on annotated LUS COVID-19 dataset to predict disease severity. The goal of the study was to develop a decision support tool that integrates readily available lab results from EHRs. The novel coronavirus (COVID-19) pandemic has strained global healthcare systems, especially ICUs, due to hospitalized patients having higher ICU transfer rates [133] . cache = ./cache/cord-255631-516epnjw.txt txt = ./txt/cord-255631-516epnjw.txt === reduce.pl bib === id = cord-255325-tl5fm2yu author = Goletic, Teufik title = Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1726 sentences = 95 flesch = 49 summary = Objectives of this research were: To share obtained sequences of the complete genome of SARS-CoV-2 strains from clinical samples of BiH patients diagnosed with COVID-19, and To contribute to the understanding of the interaction of molecular and classical epidemiology findings of COVID 19 in BH and the whole region and give recommendations for the improvement of prevention and future measures. Livno and Banja Luka samples WGS was performed according to the ARTIC amplicon sequencing protocol for MinION for nCoV-2019, which uses two primer pools to generate the sequence, as described elsewhere [7] . The constructed phylogenetic tree in Figure 2 indicates probable multiple independent introduction events as reflected by clustering of each single BiH sequence in a separate cluster, highlighted with red (Livno, EPI_ISL_462753), green (Banja Luka, EPI_ISL_462990), blue (Sarajevo, EPI_ISL_467300) and purple (Tuzla, EPI_ISL_463893). cache = ./cache/cord-255325-tl5fm2yu.txt txt = ./txt/cord-255325-tl5fm2yu.txt === reduce.pl bib === id = cord-255178-mb784dam author = Velu, P. title = Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2351 sentences = 159 flesch = 60 summary = NP and sputum samples were tested on the altona RealStar® rRT-PCR 145 assay to ensure the absence of SARS-CoV-2 and pooled for use as a matrix for spiking 146 in RNA for LOD studies and accuracy studies. Probit analysis was applied to the NP data after an additional five replicates 187 of testing were performed at 0.8, 0.6, 0.5, 0.4, and 0.2 gene copies/reaction, and 188 narrowed the LOD to 2.7 gene copies/reaction at 95% detection rate (Figure 2) The in silico analysis for inclusivity that was performed by the manufacturer of the kit 197 found 100% homology of the E gene and S gene forward and reverse primers and probes 198 with 563 whole-genome sequences of SARS-CoV-2 published in GISAID and NCBI as of 199 3/16/2020 [9] . cache = ./cache/cord-255178-mb784dam.txt txt = ./txt/cord-255178-mb784dam.txt === reduce.pl bib === id = cord-255476-p0gyyl3c author = Hsu, Albert L. title = Placental SARS‐CoV‐2 in a Pregnant Woman with Mild COVID‐19 Disease date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3310 sentences = 232 flesch = 53 summary = Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality.(1) COVID‐19 manifestations appear similar between pregnant and non‐pregnant women.(2) OBJECTIVES/STUDY DESIGN: We present a case of placental SARS‐CoV‐2 virus in a woman with mild COVID‐19 disease, then review the literature. Evidence of placental COVID‐19 raises concern for placental vasculopathy (potentially leading to fetal growth restriction and other pregnancy complications) and possible vertical transmission – especially for pregnant women who may be exposed to COVID‐19 in early pregnancy. In this case study, we present a case of placental SARS-CoV-2 virus in a woman with an uncomplicated pregnancy and mild COVID-19 disease. To date, there is still no other published work about SARS-CoV-2 virus by immunohistochemistry in the placentas of women with mild COVID-19 disease. Despite her having mild COVID-19 disease in pregnancy, we demonstrate placental vasculopathy and presence of SARS-CoV-2 virus across the placenta. Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of the placenta in pregnancies with COVID-19 positive mothers and neonates at birth cache = ./cache/cord-255476-p0gyyl3c.txt txt = ./txt/cord-255476-p0gyyl3c.txt === reduce.pl bib === id = cord-255474-7fq9culd author = Alifano, Marco title = Renin-angiotensin system at the heart of COVID-19 pandemic date = 2020-04-16 pages = extension = .txt mime = text/plain words = 2599 sentences = 124 flesch = 38 summary = We decided to use the analogy of a play and speculate about the possible impact in this tragedy of 1) air pollution via the interference of nitrogen dioxide on ACE2 expression; 2) the dual role of nicotine; 3) the hypothetical involvement of ACE2 polymorphisms, the relationships of which with ethnic factors and susceptibility to cardiovascular disease seems intriguing; 4) the impact on the severity of infection of hypertension and related medications acting on the renin/angiotensin system, and, finally, 5) the possible helpful role of chloroquine, thanks to its capacity of modifying ACE2 affinity to the viral spike protein by altering glycosylation. 6 Although concurrent cardiovascular disease might explain increased mortality in a severe infection responsible for respiratory failure and deterioration of cardiac function, the observations on hypertension warrant urgent speculation and reflection, while waiting for results of large-scale studies evaluating the independent value of each risk factor. cache = ./cache/cord-255474-7fq9culd.txt txt = ./txt/cord-255474-7fq9culd.txt === reduce.pl bib === id = cord-255371-o9oxchq6 author = Nguyen, Thanh Thi title = Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5640 sentences = 365 flesch = 59 summary = title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. We use 6,324 SARS-CoV-2 genome sequences collected in 45 countries and deposited to the NCBI GenBank so far and create a spreadsheet dataset of all mutations occurred across different genes. In this paper, to evaluate the possible impacts of genomic mutations on the virus functions, we propose the use of the SSpro/ACCpro 5 methods to predict protein secondary structure and relative solvent accessibility [13] . By comparing the prediction results obtained on the reference genome and mutated genomes, we are able to assess whether the detected mutations have the potential to change the protein structure and solvent accessibility, and thus lead to possible changes of the virus characteristics. cache = ./cache/cord-255371-o9oxchq6.txt txt = ./txt/cord-255371-o9oxchq6.txt === reduce.pl bib === id = cord-255738-r8zfdsix author = Ge, Feng title = Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date = 2007-03-30 pages = extension = .txt mime = text/plain words = 5103 sentences = 242 flesch = 49 summary = Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric's group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel's group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. cache = ./cache/cord-255738-r8zfdsix.txt txt = ./txt/cord-255738-r8zfdsix.txt === reduce.pl bib === id = cord-255586-wshvvgxg author = He, Shengyang title = Clinical characteristics of “re-positive” discharged COVID-19 pneumonia patients in Wuhan, China date = 2020-10-15 pages = extension = .txt mime = text/plain words = 2920 sentences = 163 flesch = 45 summary = The demographic features, clinical symptoms, laboratory results, comorbidities, co-infections, treatments, illness severities and chest CT scan results of 267 patients were collected from 1st January to 15th February 2020. | (2020) 10:17365 | https://doi.org/10.1038/s41598-020-74284-6 www.nature.com/scientificreports/ disease progression, no differences were found, suggesting this group of COVID-19 patients could be difficult to detect by using standard clinical data. All raw clinical and laboratory results were collected from electronic medical records system of the Central Hospital of Wuhan, followed by a follow up visit up to 14 days (also known as the discharge quarantine) to test for a re-positive nucleic acid assay. Definition of "re-positive": when a confirmed COVID-19 patient is detected SARS-CoV-2 RNA positive during the 14 days post-discharge quarantine (random test timing). Since understanding of the mechanisms of SARS-CoV-2 infection is still lacking, a careful discharge protocol should be applied (e.g. negative results of the nucleic acid tests of respiratory pathogens for 3 consecutive times), and post-discharge quarantine should be strictly observed, especially for severe and critical COVID-19 patients. cache = ./cache/cord-255586-wshvvgxg.txt txt = ./txt/cord-255586-wshvvgxg.txt === reduce.pl bib === id = cord-255515-7se14455 author = Graudenzi, Alex title = Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date = 2020-07-06 pages = extension = .txt mime = text/plain words = 8275 sentences = 450 flesch = 53 summary = To dissect the mechanisms underlying the observed inflation of variants in SARS-CoV-2 genome, we present the largest up-to-date analysis of intra-host genomic diversity, which reveals that the majority of samples present a complex sublineage architecture, due to the interplay between host-related mutational processes and transmission dynamics. Strikingly, our analysis allowed to identify three non-overlapping mutational signatures, i.e., specific distributions of nucleotide substitutions, which are observed in distinct clusters of samples in a mutually exclusive fashion, suggesting the presence of host-related mutational processes. Finally, the analysis of homoplasies, i.e., (low-frequency) variants shared across distinct viral lineages and unlikely due to infection events, demonstrate that a high number of mutations can independently emerge in multiple samples, due to mutational hotspots often related to signatures or, possibly, to positive (functional) selection. cache = ./cache/cord-255515-7se14455.txt txt = ./txt/cord-255515-7se14455.txt === reduce.pl bib === id = cord-254886-fl5ar971 author = Arav, Y. title = Understanding the indoor pre-symptomatic transmission mechanism of COVID-19 date = 2020-05-17 pages = extension = .txt mime = text/plain words = 2228 sentences = 121 flesch = 54 summary = The model explicitly tracks the dynamics of contact and airborne transmission between individuals indoors, and was validated against the observed fundamental attributes of the epidemic, the secondary attack rate (SAR) and serial interval distribution. We provide evidence that a combination of rather easy to implement measures of frequent hand washing, cleaning fomites and avoiding physical contact decreases the risk of infection by an order of magnitude, similarly to wearing masks and gloves. In fact, pre-symptomatic transmission was recently referred to as the Achilles' heel of COVID-19 pandemic control, as symptom-based detection of infection is less effective in comparison to the control of the SARS epidemic in 2003 (7) . We decided to examine five HBMs: Washing hands, cleaning fomites, maintaining social distancing (i.e avoiding physical contact), wearing a mask and 6 All rights reserved. Frequent hand washing and fomite cleaning coupled with avoiding physical contact result in a similar risk for infection as wearing gloves and a mask. cache = ./cache/cord-254886-fl5ar971.txt txt = ./txt/cord-254886-fl5ar971.txt === reduce.pl bib === id = cord-255495-xnoppq3y author = Elrashdy, Fatma title = On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date = 2020-07-09 pages = extension = .txt mime = text/plain words = 7523 sentences = 353 flesch = 47 summary = It is possible that this "Trojan horse" strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this "silence" time period and then started to re-spread again. The fact that SARS-CoV-2 can be present within the vacuoles or double membrane vesicles (DMVs) within the host cells was proven by the careful post-mortem histopathological analysis of the renal samples of patients with COVID-19 by light microscopy, electron microscopic examination, and immunostaining (Farkash et al., 2020; Su et al., 2020) . Is this "Trojan horse" strategy of the release of the SARS-CoV-2-loaded exosomes or EDMVs represent a reasonable explanation for the appearance of the viral RNA in the recovered COVID-19 patients 7-14 day post discharge? cache = ./cache/cord-255495-xnoppq3y.txt txt = ./txt/cord-255495-xnoppq3y.txt === reduce.pl bib === id = cord-255415-sr81j7my author = Heller, Lindsay K. title = Mustela Vison ACE2 Functions as a Receptor for Sars-Coronavirus date = 2006 pages = extension = .txt mime = text/plain words = 1487 sentences = 97 flesch = 62 summary = However, SARS-CoV-like viruses isolated from palm civets appeared to be under strong selective pressure and are genetically most similar to viruses infecting humans early in the outbreak. Human, palm civet, rat, mouse, chicken, and mink ACE2 were compared to identify differences that are important in species specificity and to discern regions within ACE2 that may impact its function as a SARS-CoV receptor. Expression of ACE2 RNA in SARS-CoV susceptible human (Huh7, HEK293T), African green monkey (VeroE6), and Mv1Lu cell lines 7 was analyzed by RT-PCR (chapter 4.8 this volume). 7 The complete open reading frame of human ACE2 (hACE2) or mvACE2 was amplified from RNA isolated from the Huh7 or Mv1Lu cell line, respectively. Our data demonstrate that mvACE2 RNA is expressed by SARS-CoV susceptible Mv1Lu cells, that it is closely related to palm civet ACE2, and that mvACE2 is a functional receptor for SARS-CoV. cache = ./cache/cord-255415-sr81j7my.txt txt = ./txt/cord-255415-sr81j7my.txt === reduce.pl bib === id = cord-254916-y1rw9q11 author = Ogando, Natacha S. title = SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date = 2020-06-22 pages = extension = .txt mime = text/plain words = 8571 sentences = 423 flesch = 50 summary = The overall level of amino acid sequence identity of viral proteins ranges from about 65 % in the least conserved parts of the S protein to about 95 % in the most conserved replicative enzyme domains, prompting the coronavirus study group of the International Committee on the Taxonomy of Viruses to classify the new agent within the species Severe acute respiratory syndrome-related coronavirus, which also includes the 2003 SARS-CoV [1] . In this report, we describe a comparative study of the basic replication features of SARS-CoV and SARS-CoV-2 in Vero E6 cells, including growth kinetics, virus titres, plaque phenotype and an analysis of intracellular viral RNA and protein synthesis. One of them is the rapid evolution -during virus passaging in Vero cells -of a specific region of the SARS-CoV-2 S protein that contains the so-called furin-like cleavage site. cache = ./cache/cord-254916-y1rw9q11.txt txt = ./txt/cord-254916-y1rw9q11.txt === reduce.pl bib === id = cord-255697-trig04hd author = Cheng, Vincent Chi-Chung title = Viral Infections, an Overview with a Focus on Prevention of Transmission date = 2016-10-24 pages = extension = .txt mime = text/plain words = 6422 sentences = 301 flesch = 42 summary = Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. cache = ./cache/cord-255697-trig04hd.txt txt = ./txt/cord-255697-trig04hd.txt === reduce.pl bib === id = cord-255602-3pzh5ur9 author = Moscadelli, Andrea title = Fake News and Covid-19 in Italy: Results of a Quantitative Observational Study date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4590 sentences = 213 flesch = 51 summary = We used the BuzzSumo application to gather the most shared links on the Internet related to the pandemic in Italy, using keywords chosen according to the most frequent "fake news" during that period. We used the BuzzSumo pplication [38] in order to gather the most shared links or posts on the Internet and social media related to SARS-CoV-2 and the Covid-19 pandemic. The 9 keywords were chosen in a consensus meeting of the research group, since they were the most likely to uncover health-related false information using the BuzzSumo search engine, and specifically fake news that would not meet our exclusion criteria. An article was immediately excluded when the content did not deal specifically with health or science, i.e., the focus may have been on the socioeconomic consequences of the pandemic, which was a topic we excluded from our fake news review. cache = ./cache/cord-255602-3pzh5ur9.txt txt = ./txt/cord-255602-3pzh5ur9.txt === reduce.pl bib === id = cord-255752-ofph98ac author = Chegondi, Madhuradhar title = Coronavirus Disease 2019 (COVID-19) Associated With Febrile Status Epilepticus in a Child date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1615 sentences = 113 flesch = 55 summary = Infection associated with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been named coronavirus disease 2019 (COVID-19). We report the case of a two-year-old child who presented to our pediatric intensive care unit with febrile status epilepticus and was diagnosed to have COVID-19 infection. The emerging literature suggests that the SARS-CoV-2 infection can affect children, including all age groups, predominantly males, and cause milder disease compared to adult patients [2, 3] . We report the case of a two-year-old child who presented to our pediatric intensive care unit (PICU) with febrile status epilepticus and was diagnosed to have COVID-19 infection. A retrospective study from China reported that common neurological symptoms in adult patients with COVID-19 include headache, dizziness, and rarely seizures [12] . Our index case illustrates that SARS-CoV-2 associated COVID-19 can present with febrile seizure and febrile status epilepticus in children. cache = ./cache/cord-255752-ofph98ac.txt txt = ./txt/cord-255752-ofph98ac.txt === reduce.pl bib === id = cord-255498-npk4zv4i author = Harikrishnan, Pandurangan title = Saliva as a Potential Diagnostic Specimen for COVID-19 Testing date = 2020-06-11 pages = extension = .txt mime = text/plain words = 1779 sentences = 113 flesch = 54 summary = Various clinical specimens like blood, pharyngeal swabs, saliva, anal swabs and urine showed the presence of the virus in infected patients. WHO recommends specimens from upper respiratory tract like nasopharyngeal (NP), oropharyngeal (OP) swab or wash in ambulatory patients, and lower respiratory specimens like sputum, endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease for the quantitative assessment of SARS-CoV-2 RNA level through real-time reverse transcription polymerase chain reaction (rRT-PCR). 17 Azzi et al collected saliva from 25 COVID-19 patients (confirmed by NP swabs) through the drooling technique and all were tested positive for the presence of SARS-CoV-2, while there was an inverse association between lactate dehydrogenase (LDH) and Cycle threshold (Ct) values (considered as semiquantitative indicators of viral load). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. cache = ./cache/cord-255498-npk4zv4i.txt txt = ./txt/cord-255498-npk4zv4i.txt === reduce.pl bib === id = cord-255940-chb4iuis author = Walton, David A. title = Facility-Level Approaches for COVID-19 When Caseload Surpasses Surge Capacity date = 2020-06-26 pages = extension = .txt mime = text/plain words = 1801 sentences = 99 flesch = 49 summary = We present two COVID-19 treatment center designs that leverage lessons learned from previous outbreaks of communicable infectious diseases and provide potential solutions when caseload exceeds existing capacity, with and without access to SARS-CoV-2 testing. These designs are intended for settings in which health facilities and testing resources for COVID-19 are surpassed during the pandemic, are adaptable to local conditions and constraints, and mitigate the likelihood of nosocomial transmission while offering an option to care for hospitalized patients. To respond to the immediate crisis facing health workers and patients, we propose a COVID-19 treatment center design ( Figure 1 ) that harnesses lessons learned from other outbreaks and adheres to infection prevention and control principles recommended by the WHO for the novel coronavirus. The design assumes that two thresholds have been reached: first, the health center no longer has space to individually isolate COVID-19 patients, and second, laboratory capacity is limited or surpassed, such that rapid, accurate testing for COVID-19 may not be available, as is the reality facing our colleagues in Haiti. cache = ./cache/cord-255940-chb4iuis.txt txt = ./txt/cord-255940-chb4iuis.txt === reduce.pl bib === id = cord-255755-5jccb3nh author = Saha, Sovan title = Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date = 2020-04-23 pages = extension = .txt mime = text/plain words = 3668 sentences = 212 flesch = 59 summary = title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network The new network attribute spreadability index along with generated SIS values of selected top spreader nodes when compared with the other network centrality based methodologies like Degree centrality (DC), Closeness centrality (CC), Local average centrality (LAC) and Betweeness centrality (BC) is found to perform relatively better than the existing-state-of-art. In the proposed methodology, Protein-protein interaction network (PPIN) has been used as the central component in identification of spreader nodes in SARS-CoV. Once it is formed, spreader nodes are identified in each of SARS-CoV proteins, its level 1 and level 2 of human network by the application of a new network attribute i.e. spreadability index which is a combination of three terminologies: 1) edge ratio [28] 2) neighborhood density [28] and 3) node weight [29] . cache = ./cache/cord-255755-5jccb3nh.txt txt = ./txt/cord-255755-5jccb3nh.txt === reduce.pl bib === id = cord-255791-ghrlj6b2 author = Pruijssers, Andrea J. title = Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date = 2020-04-27 pages = extension = .txt mime = text/plain words = 3444 sentences = 219 flesch = 57 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 μM). These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19. RDV and GS-441524 potently inhibited 110 SARS-CoV-2 replication in a dose-dependent manner in both cell types ( Fig. 2; Table 1 ). Together, these data demonstrate that RDV is potently antiviral 131 against SARS-CoV-2 in primary human lung cultures with a selectivity index of >1000. cache = ./cache/cord-255791-ghrlj6b2.txt txt = ./txt/cord-255791-ghrlj6b2.txt === reduce.pl bib === id = cord-255782-w6nfkdok author = Chikhale, Rupesh V. title = Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach date = 2020-06-22 pages = extension = .txt mime = text/plain words = 5638 sentences = 276 flesch = 51 summary = somnifera in comparison to reference drugs (hydroxychloroquine, lopinavir and remdesivir) against two different protein targets, that is, NSP15 endoribonuclease and prefusion spike RBD from SARS-CoV-2 using in-silico docking simulation and molecular dynamics (MD) study. The top three binding energy scorer ligand to each protein, that is, QGRG, Withanoside X and Ashwagandhanolide for spike RBD and QGRG, Dihydrowithaferin A and Withanolide N for NSP15 Endoribonuclease were selected for further MD study. Therefore, in the present study 100 ns of MD simulations were performed for all selected best six docked complexes to observe how the interaction pattern of the binding site of NSP15 endoribonuclease and spike RBD from SARS CoV-2 adapts to the docked bioactive. The phytochemicals Ashwagandhanolide, QGRG and Withanoside X in complex with the SARS-CoV-2 spike protein (PDB: 6M0J) were selected for the MDS based on molecular docking study results. cache = ./cache/cord-255782-w6nfkdok.txt txt = ./txt/cord-255782-w6nfkdok.txt === reduce.pl bib === id = cord-255734-038xu4hq author = Taylor, Deborah R. title = Obstacles and advances in SARS vaccine development date = 2006-02-13 pages = extension = .txt mime = text/plain words = 5334 sentences = 263 flesch = 44 summary = The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets cache = ./cache/cord-255734-038xu4hq.txt txt = ./txt/cord-255734-038xu4hq.txt === reduce.pl bib === id = cord-255665-srvz2ay0 author = Ferrari, Marco title = COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions date = 2020-10-14 pages = extension = .txt mime = text/plain words = 2481 sentences = 156 flesch = 45 summary = title: COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions The study included all patients undergoing surgery under general anesthesia for HNC at two Italian tertiary referral academic hospitals during the peak of the pandemic diffusion of to an internal "grey zone" of COVID-19 surveillance, submitted to further blood tests, chest CT, and nasal/nasopharyngeal swab while maintaining strict isolation. The following data were extracted from institutional databases: patient-related including the 2-week post-discharge period) was considered as the gold standard evaluation (i.e. patients developing symptoms attributed to COVID-19 through nucleic acid-based test on respiratory secretions in this time frame were considered as "false negative" of the screening; cache = ./cache/cord-255665-srvz2ay0.txt txt = ./txt/cord-255665-srvz2ay0.txt === reduce.pl bib === id = cord-256092-bph9ys72 author = Hussain, Aneela N. title = Role of testosterone in COVID-19 patients - a double-edged sword? date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1574 sentences = 93 flesch = 43 summary = Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Lower levels of testosterone result in the upregulation of ACE2 and TMPRSS2 receptors, facilitating SARS-CoV-1 entry into the alveolar cells, and deregulating a lung-protective pathway (4) . Thereby we hypothesize that low testosterone levels in males have a direct correlation with the severity of disease and a worse outcome in COVID-19. Patients with low testosterone have reportedly developed severe manifestations requiring assisted ventilation because of the upregulation of ACE-2 receptors in lower respiratory cells, increased risk of lung damage, and respiratory muscle catabolism. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China cache = ./cache/cord-256092-bph9ys72.txt txt = ./txt/cord-256092-bph9ys72.txt === reduce.pl bib === id = cord-255907-t7gpi2vo author = Xu, Yifei title = Unveiling the Origin and Transmission of 2019-nCoV date = 2020-02-24 pages = extension = .txt mime = text/plain words = 1330 sentences = 71 flesch = 54 summary = A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Unveiling the Origin and Transmission of 2019-nCoV Yifei Xu 1, * A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Regardless of its initial source, it is likely that 2019-nCoV was introduced into a small cluster of humans from a cluster of infected animals and, from there, the virus acquired the capacity for human-tohuman transmission, spreading in the city before the cluster of patients from the Huanan market was identified. cache = ./cache/cord-255907-t7gpi2vo.txt txt = ./txt/cord-255907-t7gpi2vo.txt === reduce.pl bib === id = cord-256075-fudeaq7y author = Audo, Andrea title = Acute Pulmonary Embolism in SARS-CoV-2 Infection Treated with Surgical Embolectomy date = 2020-04-28 pages = extension = .txt mime = text/plain words = 752 sentences = 40 flesch = 37 summary = We report the first case of SARS-CoV-2 complicated by massive pulmonary embolism underwent successfully surgical embolectomy. We believe that maintaining the same pro-active attitude suggested by current Guidelines might help in reducing morality and improving survival in SARS-COV-2/patients. SARS-CoV-2 infected patients usually experience fever, dry cough, fatigue and worsening dyspnoea with interstitial pneumonia that in up to 3-5% might unfortunately evolve in a severe acute respiratory distress syndrome (ARDS) requiring endotracheal intubation (ETI) and mechanical ventilation. Due to the severe ARDS unresponsive to assisted non-invasive ventilation the patient underwent ETI and was transferred to an isolation ward of the intensive care unit (ICU); the infection of SARS-CoV-2 virus was confirmed thereafter by an RT-PCR assay of a nasal swab. We are now facing this unexpected severe SARS-CoV-2 pandemic, but maintaining the same proactive attitude suggested by current Guidelines or routine standard of care might help in reducing morality rate and improving survival also in SARS-CoV-2 infected patients. cache = ./cache/cord-256075-fudeaq7y.txt txt = ./txt/cord-256075-fudeaq7y.txt === reduce.pl bib === id = cord-255909-m94j1rh4 author = Shree, Priya title = Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5495 sentences = 316 flesch = 49 summary = title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study Molecular docking study showed six probable inhibitors against SARS-CoV-2 M(pro) (Main protease), two from Withania somnifera (Ashwagandha) (Withanoside V [10.32 kcal/mol] and Somniferine [9.62 kcal/mol]), one from Tinospora cordifolia (Giloy) (Tinocordiside [8.10 kcal/mol]) and three from Ocimum sanctum (Tulsi) (Vicenin [8.97 kcal/mol], Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte [8.55 kcal/mol] and Ursolic acid [8.52 kcal/mol]). Active phytoconstituents of Ayurvedic medicinal plants Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) predicted to significantly hinder main protease (M(pro) or 3Cl(pro)) of SARS-CoV-2. Through molecular docking and molecular dynamic simulation study, Withanoside V, Somniferine, Tinocordiside, Vicenin, Ursolic acid and Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte were anticipated to impede the activity of SARS-CoV-2 M(pro). cache = ./cache/cord-255909-m94j1rh4.txt txt = ./txt/cord-255909-m94j1rh4.txt === reduce.pl bib === id = cord-255997-oer5lxxr author = Onodi, Fanny title = SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4209 sentences = 254 flesch = 53 summary = Here, we have studied the interaction of isolated primary SARS-CoV-2 viral strains with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. Importantly, all major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine, including P2and P3-pDC differentiation, the expression of maturation markers, and the production of interferon-α and inflammatory cytokines. Interestingly, pDC responded to SARS-CoV-2 by a complete activation program, including diversification into effector subsets, production of type I and type III IFN, as well as inflammatory cytokines. We also showed that hydroxychloroquine, an antimalarial drug proposed for treatment of COVID-19 patients (Das et al., 2020; Mahévas et al., 2020) , inhibits SARS-CoV-2-induced pDC activation and IFN production in a dose-dependent manner. Following 24 hours of culture, we found that HCQ inhibited pDC diversification in response to SARS-CoV-2, which is similar to the decrease observed with Flu, used as a positive control ( Fig 4A) . cache = ./cache/cord-255997-oer5lxxr.txt txt = ./txt/cord-255997-oer5lxxr.txt === reduce.pl bib === id = cord-255774-ux3c3dzf author = Zhong, H. title = Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients date = 2020-07-05 pages = extension = .txt mime = text/plain words = 2900 sentences = 139 flesch = 48 summary = Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Likewise, metatranscriptomics-detected bacterial or fungal respiratory co-infections were 6 3 defined if the respiratory specimens (at least one sample) of severe patients were mono-dominated (relative abundance >60%) by 6 4 pathogenic microbes known to cause nosocomial infections (appendix 2 p 9: TableS8). Sixty-seven serial 9 7 clinical specimens from the respiratory tract (RT) (n=47, sputum, nasal and throat swab) and gastrointestinal tract (GIT) (n=20, 9 8 anal swab and feces) of these patients were obtained during the same above period for comprehensive assessment of microbial non-rRNA transcripts) varied between different types of specimens, constituting a relatively high fraction of total high-quality 0 6 reads among RT specimens and a low fraction among GIT specimens (appendix 1 p 1: Supplementary figure 1 and appendix 2 0 7 p 4: TableS3). cache = ./cache/cord-255774-ux3c3dzf.txt txt = ./txt/cord-255774-ux3c3dzf.txt === reduce.pl bib === id = cord-255883-mz6nyisw author = Asif, Muhammad title = COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date = 2020-08-14 pages = extension = .txt mime = text/plain words = 5273 sentences = 283 flesch = 44 summary = Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. An in vitro study conducted by Hoffmann and colleagues revealed that SARC-CoV-2 depends on cellular serine protease (TMPRSS2) for S proteins priming which are known to interact with human ACE2 receptors in the lungs and facilitate entry into the cells. The authors opted the following keywords to find relevant studies: "essential oils", "antiviral", "COVID-19", "SARC-CoV-2", "bronchodilation", "immunomodulatory'', "anti-inflammatory'', "corona virus''. Thus, on the basis of these docking and in vitro studies, it is proposed that garlic essential oils and their isolated constituents, especially DAS, have potential to prevent the entry of virus into host cells as well as to activate molecular antioxidant pathways that decrease the secretions of culprit pro-inflammatory cytokines. Essential oils have long been known to have anti-inflammatory, antioxidant, immunomodulatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2. cache = ./cache/cord-255883-mz6nyisw.txt txt = ./txt/cord-255883-mz6nyisw.txt === reduce.pl bib === id = cord-256217-fnjer0e0 author = Neri, Piergiorgio title = COVID-19 and the eye immunity: lesson learned from the past and possible new therapeutic insights date = 2020-04-20 pages = extension = .txt mime = text/plain words = 1928 sentences = 88 flesch = 43 summary = Corona virus represents nowadays the hot topic in the scientific world due to the outbreak of a novel serotype formerly named coronavirus disease (COVID)-19 and now identified as severe acute respiratory syndrome (SARS)-COV-2 [1] . Although ECOR was used to study retinal degeneration specifically, it might represent a possible experimental model for interesting speculations on how to approach severe SARS-COV-2 pulmonary complications. Looking at the ECOR model, it gives the impression that coronavirus creates two different phases: the first is represented by the primary infection which induces the triggering of the immune system, while the second phase is likely to be an autoimmune disease where the role of the severe postviral inflammation represents a severe occurrence worth of prompt intervention. Albeit it is true that anti-IL-6 receptor monoclonal antibody has given promising results for the control of severe SARS-COV-2 pneumonia, it is interesting to notice that retinal degeneration in ECOR is associated with an evident increase in TNF-alpha, as well as soluble TNFR2, inducing an anomaly of TNF-alpha signaling [12] . cache = ./cache/cord-256217-fnjer0e0.txt txt = ./txt/cord-256217-fnjer0e0.txt === reduce.pl bib === id = cord-256109-dkp0fwe3 author = Mazzulli, Tony title = Severe Acute Respiratory Syndrome–associated Coronavirus in Lung Tissue date = 2004-01-17 pages = extension = .txt mime = text/plain words = 2554 sentences = 115 flesch = 53 summary = Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). All patients who met the current World Health Organization case definition of probable SARS and who underwent a postmortem examination in Canada during the March-April 2003 outbreak were included in this study. The clinical description and RT-PCR results for the 11 patients with probable SARS from whom postmortem lung tissue samples were examined are summarized in Table 1 . By using a standardized RT-PCR assay, SARS-CoV has been unequivocally identified in the lung tissue of all patients who died with probable SARS but not in any of the controls. cache = ./cache/cord-256109-dkp0fwe3.txt txt = ./txt/cord-256109-dkp0fwe3.txt === reduce.pl bib === id = cord-256270-7e8zlt3t author = Choy, Ka-Tim title = Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro date = 2020-04-03 pages = extension = .txt mime = text/plain words = 2745 sentences = 147 flesch = 44 summary = We evaluated the in vitro antiviral effect of compounds that were previously reported to inhibit coronavirus replication and compounds that are currently under evaluation in clinical trials for SARS-CoV-2 patients. We report the antiviral effect of remdesivir, lopinavir, homorringtonine, and emetine against SARS-CoV-2 virus in Vero E6 cells with the estimated 50% effective concentration at 23.15 μM, 26.63 μM, 2.55 μM and 0.46 μM, respectively. Among the 16 compounds we tested, remdesivir, lopinavir, homoharringtonine, and emetine dihydrochloride were found to inhibit SARS-CoV-2 replication in Vero E6 cells with EC 50 under 100 μM (Table 1) . Importantly, we observed that some of the compounds currently undergoing clinical trials such as ribavirin, favipiravir, oseltamivir, or baloxavir showed no apparent antiviral effect against the SARS-CoV-2 virus in vitro at concentrations under 100 μM (Table 1) . cache = ./cache/cord-256270-7e8zlt3t.txt txt = ./txt/cord-256270-7e8zlt3t.txt === reduce.pl bib === id = cord-255872-e2b7ox6b author = Sallam, M. title = Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5129 sentences = 380 flesch = 61 summary = This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Similar to other RNA viruses, SARS-CoV-2 can be the subject of phylogenetic analysis due to its high evolutionary rate, and the application of molecular clock analysis might be of value to determine the timing of introductions of large clusters that imply networks of transmission (Duffy et al., 2008; Forster et al., 2020; Pybus and Rambaut, 2009 ). The total number of MENA SARS-CoV-2 S gene sequences that were included in final analysis was 553, distributed as follows: Oman (n=159), KSA (n=140), Egypt (Table 1) . Phylogenetic analysis of the MENA S gene SARS-CoV-2 sequences showed a relatively low level of phylogenetic clustering (15%), which hints to a large number of virus introductions into the region. cache = ./cache/cord-255872-e2b7ox6b.txt txt = ./txt/cord-255872-e2b7ox6b.txt === reduce.pl bib === id = cord-256146-d599uera author = Kuiken, Thijs title = Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date = 2003-07-26 pages = extension = .txt mime = text/plain words = 5686 sentences = 281 flesch = 49 summary = METHODS: We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARSCoV, human metapneumovirus, and other respiratory pathogens. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. . Serial dilutions of the SARS-CoV virus stock and SARS-CoV-infected Vero cells from patient 5688 were made and tested with the NP and polymerase-specific RT-PCRs. Samples from the respiratory tract (nasal swabs, pharyngeal swabs, postmortem trachea, and lung samples) were also monitored for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E), and human metapneumovirus with use of essentially the same RT-PCR methods but with specific primers. Virological examinations of nasal and pharyngeal swabs, and tracheal and lung samples from all four macaques by RT-PCR for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E) and human metapneumovirus were negative. cache = ./cache/cord-256146-d599uera.txt txt = ./txt/cord-256146-d599uera.txt === reduce.pl bib === id = cord-256023-21b5hanj author = Dowdell, A. K. title = Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3829 sentences = 246 flesch = 56 summary = We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Genomic sequencing is rapidly emerging as an orthogonal strategy to RT-PCR for outbreak monitoring as the sequence specificity uncovered in individual SARS-CoV-2 isolates has shown significant utility for the epidemiological investigation of outbreak origins as well as the early identification of possible functional changes to the virus that may affect transmission rates or associated clinical outcomes. In order to assess the heterogeneity of SARS-CoV-2 genomes across OR, a total of 204 nasopharyngeal swab patient specimens (representing 188 unique patients) were sequenced from diverse clinical sites across OR. Next, we sought to determine whether sequence variants in the isolated SARS-CoV-2 genomes were associated with differential clinical manifestation of COVID-19 in the patients. cache = ./cache/cord-256023-21b5hanj.txt txt = ./txt/cord-256023-21b5hanj.txt === reduce.pl bib === id = cord-256156-mywhe6w9 author = Clausen, Thomas Mandel title = SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date = 2020-09-14 pages = extension = .txt mime = text/plain words = 8965 sentences = 562 flesch = 59 summary = We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. In this report, we show that the ectodomain of the SARS-CoV-2 spike (S) protein interacts with cell surface HS through the Receptor Binding Domain (RBD) in the S1 subunit. Adjacent to the ACE2 binding site and exposed in the RBD lies a group of positively-charged amino acid residues that represents a potential site that could interact with heparin or heparan sulfate ( Fig. 1A and Suppl. The SARS-CoV-2 spike protein depends on cellular heparan sulfate for cell binding. Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin cache = ./cache/cord-256156-mywhe6w9.txt txt = ./txt/cord-256156-mywhe6w9.txt === reduce.pl bib === id = cord-256233-k9hdq3z8 author = Lipsky, Martin S. title = Men and COVID-19: A Pathophysiologic Review date = 2020-09-16 pages = extension = .txt mime = text/plain words = 4620 sentences = 233 flesch = 47 summary = The plausible theories underlying these observations include sex-related differences in angiotensin-converting enzyme 2 receptors, immune function, hormones, habits, and coinfection rates.In this review we examine these factors and explore the rationale as to how each may impact COVID-19. Epidemiological evidence from influenza outbreaks and pandemics also reveals a higher morbidity and mortality for menthan that for women in some age groups (Klein et al., 2012) .In animal studies, male animals have poorer immune responses when exposed to the coronavirus and experience more damage to their lungs (Vermillion et al., 2018) .For both SARS and the MERS coronavirus outbreaks, men fared worse than women did. A recent German study found that that critically ill male COVID-19 patients suffer from severe testosterone and dihydrotestosterone deficiencies and concluded that androgens are required to mount a strong antiviral immune response to combat infection in men (Schroeder et al., 2020) . cache = ./cache/cord-256233-k9hdq3z8.txt txt = ./txt/cord-256233-k9hdq3z8.txt === reduce.pl bib === id = cord-255913-430lrbyx author = Brufsky, Adam title = DC/L‐SIGNs of Hope in the COVID‐19 Pandemic date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1518 sentences = 76 flesch = 49 summary = The current pandemic and its pleotropic effects can be explained in part by interaction between SARS‐CoV‐2 spike protein S, the ACE2/L‐SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC‐SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. The current pandemic and its pleotropic effects can be explained in part by interaction between SARS-CoV-2 spike protein S, the ACE2/L-SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC-SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. L-SIGN is expressed on human type II alveolar cells, is associated with ACE2 10 , and can enhance ACE2 mediated binding and cellular entry of viral pseudotypes expressing the spike protein S of SARS-CoV 9 . De-glycosylation reduces infectivity of viral pseudotypes expressing SARS-CoV spike protein 13 and specific asparagine glycosylation sites in three clusters within the SARS-CoV S protein appear critical for DC/L-SIGN mediated, but not ACE2 mediated, SARS Co-V pseudotype entry into cells 13 . cache = ./cache/cord-255913-430lrbyx.txt txt = ./txt/cord-255913-430lrbyx.txt === reduce.pl bib === id = cord-255895-6at9gelt author = Han, Namshik title = Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date = 2020-08-25 pages = extension = .txt mime = text/plain words = 4736 sentences = 269 flesch = 52 summary = We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Importantly, treatment of Calu-3 and Vero E6 cell lines with Proguanil and Sulfasalazine led to a significant downregulation of the mRNA of key cytokines (Figures 4G-J and S8), which are dictated by the p38/MAPK signalling pathway and shown to become elevated during SARS-CoV-2 infection and replication (CXCL3, IFNB1 and TNF-A). Here we have used a series of computational approaches, including bespoke methods for data integration, network analysis, computer simulation and machine learning, to identify novel SARS-CoV-2 induced pathways that could be targeted therapeutically by repurposing existing and approved drugs ( Figure S9 ). cache = ./cache/cord-255895-6at9gelt.txt txt = ./txt/cord-255895-6at9gelt.txt === reduce.pl bib === id = cord-256300-emsvxxs5 author = Tortorici, M. Alejandra title = Structural insights into coronavirus entry date = 2019-08-22 pages = extension = .txt mime = text/plain words = 6535 sentences = 325 flesch = 49 summary = We review here our current understanding of the mechanism used by CoVs to infect host cells based on recent structural and biochemical studies of S glycoprotein ectodomains in prefusion and postfusion states as well as complexes with known receptors or neutralizing antibodies. Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al., 2017; Kirchdoerfer et al., 2018; Song et al., 2018; Walls et al., 2019; Yuan et al., 2017) . Major antigenic determinants of MHV and SARS-CoV S overlap with the fusion peptide region (Daniel et al., 1993; Zhang et al., 2004) and binding of neutralizing antibodies to this site could putatively prevent fusogenic conformational changes, as proposed for influenza virus hemagglutinin or HIV envelope (Corti et al., 2011; Kong et al., 2016; Lang et al., 2017) . cache = ./cache/cord-256300-emsvxxs5.txt txt = ./txt/cord-256300-emsvxxs5.txt === reduce.pl bib === id = cord-256385-g1wcfrfi author = Badraoui, Riadh title = Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 6071 sentences = 332 flesch = 48 summary = title: Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 A better understood of ARDS key features and the pathophysiological injuries of the pulmonary parenchyma are linked to lessons learned from previous severe diseases associated previous coronaviruses outbreaks (especially SARS-CoV and MERS-CoV) and more the ongoing SARS-CoV-2. The novel coronavirus, finally named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and it's inducing Coronavirus Disease 2019 (COVID-19) (Gorbalenya et al., 2020; Khailany et al., 2020) . While SARS-CoV-2 induces mild symptoms in several infected patients (low pathogenic), it can also be associated with a fast onset of widespread infection in the lungs worsened in an acute respiratory distress syndrome (ARDS) . Lessons learned from previous severe diseases caused by coronaviruses outbreaks (SARS-CoV and MERS-CoV) and more recently SARS-CoV-2 lead to a better understood of ARDS key features associated COVID-19. cache = ./cache/cord-256385-g1wcfrfi.txt txt = ./txt/cord-256385-g1wcfrfi.txt === reduce.pl bib === id = cord-256051-87alqfkd author = Revzin, Margarita V. title = Multisystem Imaging Manifestations of COVID-19, Part 1: Viral Pathogenesis and Pulmonary and Vascular System Complications date = 2020-10-01 pages = extension = .txt mime = text/plain words = 8850 sentences = 448 flesch = 39 summary = Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in coronavirus disease 2019 (COVID-19), which was declared an official pandemic by the World Health Organization on March 11, 2020. Although SARS-CoV-2 disease (or coronavirus disease 2019 ) primarily manifests as a lung infection, with symptoms ranging from those of a mild upper respiratory infection to severe pneumonia and acute respiratory distress syndrome (ARDS), other multisystemic manifestations of this disease and related complications are becoming more commonly recognized (3) . Thromboembolic complications, including pulmonary embolism (PE), peripheral venous and arterial thrombosis, and acute stroke (seen also in patients older than 50 years without risk factors) have all been reported (50-57). On the basis of the pattern and distribution of the opacities and the presence or absence of certain clinical signs (such as obesity), the authors developed a chest radiography severity scoring system that could be used as a prognostic factor of outcomes in young adult patients with COVID-19 (Fig 3) . cache = ./cache/cord-256051-87alqfkd.txt txt = ./txt/cord-256051-87alqfkd.txt === reduce.pl bib === id = cord-256152-8wla6ne4 author = Zeng, Xiang title = Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? date = 2020-05-18 pages = extension = .txt mime = text/plain words = 775 sentences = 60 flesch = 54 summary = title: Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? Furthermore, scientists and researchers should always adhere to the conflict-of-interest guidelines during the crisis era. Finally, scientist and researchers need an unbiased interpretation of the findings. For example, while taking care of respiratory emergency is the priority, researchers were also concerned about the damage to the nervous system caused by SARS-CoV-2 infection. 5 Nonetheless, alterations of sex-related hormone levels in reproductive-aged men with SARS-CoV-2 infection may indicate a decline in gonadal function. Such proactive, forward-looking studies render a new perspective on comprehensive understanding of disease and get us prepared for drug discovery, and offer important references for the decision of public health policies. All in all, the scientific community is now taking on new challenges in the era of COVID-19 pandemic. Neurologic features in severe SARS-CoV-2 infection Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study cache = ./cache/cord-256152-8wla6ne4.txt txt = ./txt/cord-256152-8wla6ne4.txt === reduce.pl bib === id = cord-256374-l492w2i2 author = Mackler, Niklas title = Will First-Responders Show Up for Work During a Pandemic? Lessons From a Smallpox Vaccination Survey of Paramedics date = 2007-05-22 pages = extension = .txt mime = text/plain words = 2368 sentences = 144 flesch = 58 summary = Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. The results of this survey indicate that in the event of an outbreak of a contagious disease like smallpox or pandemic influenza, a significant number of paramedics might be unwilling to remain on duty to care for patients without adequate protection against infection. 2, 5 Several recent studies have addressed public health worker and basic and paramedic emergency medical technician (EMT) perceptions about coming to work during a contagious outbreak. cache = ./cache/cord-256374-l492w2i2.txt txt = ./txt/cord-256374-l492w2i2.txt === reduce.pl bib === id = cord-256307-2b1vlda8 author = Bhardwaj, Vijay Kumar title = Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs date = 2020-11-12 pages = extension = .txt mime = text/plain words = 4556 sentences = 292 flesch = 52 summary = RESULTS: The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated deep inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). The selected DSPD molecules (DSPD-1 to 6) were compared on different computational parameters (Docking energy, RMSD, protein-ligand interactions, MM-PBSA binding energy, Contribution energy, and SASA) to repurposed FDA approved antiviral drugs. The inbuilt published tools (ADMET and Toxicity Prediction by Komputer Assisted Technology (TOPKAT) module) and models such as the CYP2D6 Prediction, Hepatotoxic Prediction, PPB Prediction, Solubility Level, Absorption Level, 2D Polar Surface Area, AlogP98, Rat Female NTP Prediction, Rat Male NTP Prediction, Carcinogenic Potency TD50 Rat, Rat Oral LD50, Ames Prediction, DTP Prediction, Skin Irritant, and Skin Sensitization in the discovery J o u r n a l P r e -p r o o f studio package were used to calculate and analyze the pharmacokinetic profiles of DSPD molecules along with the selected FDA approved drugs [31, 32] . cache = ./cache/cord-256307-2b1vlda8.txt txt = ./txt/cord-256307-2b1vlda8.txt === reduce.pl bib === id = cord-255888-znfgh78m author = Fisher, Dale title = Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1816 sentences = 110 flesch = 58 summary = SARS-CoV-2 was detected on workers and environmental samples, including a cutting board used to slice imported salmon. We have assessed the survival of SARS-CoV-2 on refrigerated and frozen meat and salmon over 3 weeks to assess the potential of outbreaks being seeded by imported contaminated food. The clusters of infection of COVID-19 among workers in slaughterhouses and meat processing facilities in many countries can be attributed to factors that promote transmission of virus directly between workers, such as crowding, poor ventilation, and shouting in close proximity due to high ambient noise levels. With a significant burden of virus present in infected workers and the environment then contamination of meat with SARS-CoV-2 is possible during butchering and processing. Our laboratory work has shown that SARS-CoV-2 can survive the time and temperatures associated with transportation and storage conditions associated with international food trade. We believe it is possible that contaminated imported food can transfer virus to workers as well as the environment. cache = ./cache/cord-255888-znfgh78m.txt txt = ./txt/cord-255888-znfgh78m.txt === reduce.pl bib === id = cord-256224-qprj8vlc author = Boixeda, R. title = Is chronic obstructive pulmonary disease a protective factor in SARS-CoV-2 infection? The importance of bronchodilator treatment() date = 2020-09-26 pages = extension = .txt mime = text/plain words = 1402 sentences = 89 flesch = 50 summary = In a systematic review of infections in patients with COPD that required hospital admission, it was observed that the rhinovirus, respiratory syncytial virus (RSV), and influenza virus were the most prevalent agents, followed by parainfluenza and coronavirus. We have analyzed the prevalence of COPD in patients treated for COVID-19 in our center, specifically evaluating their baseline treatment with inhalers as a potential protective factor against SARS-CoV-2 infection. However, the use of tiotropium was significantly lower in patients with COPD who had been hospitalized for COVID-19 in relation to other cohorts of patients with stable COPD and without SARS-CoV-2 infection and controlled in primary care (12% vs. Members of the COCOHMAT (COhorte COvid del Hospital de MATaró) Group Table 1 Treatment with inhaled corticosteroids and anticholinergics in patients with COPD in series of patients hospitalized due to SARS-CoV-2, severe exacerbation of COPD, and patients in the stable phase (primary care) cache = ./cache/cord-256224-qprj8vlc.txt txt = ./txt/cord-256224-qprj8vlc.txt === reduce.pl bib === id = cord-255972-u7v0es5w author = Hashikawa, Andrew title = Child Care in the Time of COVID-19: A Period of Challenge and Opportunity. date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4036 sentences = 229 flesch = 49 summary = Existing CFOC standards do not address the new concerns expressed by ECE workers during the pandemic, which include: determining the risks for ECE workers, establishing whether physical distancing in young children is feasible and effective, providing more details about cleaning and disinfecting, defining new group size requirements, defining the proper use of SARS-CoV-2 screening tests, handling readmission of children with symptoms or positive COVID-19 tests, and establishing guidelines for temperature checks (type of thermometer, fever threshold for exclusion, when to take temperatures after the initial screening). Even though there remain gaps in COVID-19 specific information that need further research, there is an important role for pediatric health experts to provide some structured guidance based on both expert group consensus and best available evidence to assist ECE directors in operating their programs and in providing consistent messaging to parents. cache = ./cache/cord-255972-u7v0es5w.txt txt = ./txt/cord-255972-u7v0es5w.txt === reduce.pl bib === id = cord-256147-lfwytlj3 author = Gabriella, di Mauro title = SARS-Cov-2 infection: response of human immune system and possible implications for the rapid test and treatment date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1645 sentences = 81 flesch = 50 summary = Considering the clinical impact of the new outbreak, it is highly important to study the potential responses of the human immune system during the SARS-CoV-2 infection as well as the role of virus-specific T cells and by B-lymphocytes. In order to apply a rapid test able to detect the presence of specific IgM and IgG for SARS-CoV-2, it is important to consider that the IgM values tend to disappear within 2 weeks since the beginning of the infection. The sensitivity and specificity of these tests were evaluated on 397 blood samples from patients who tested positive for the nasopharyngeal swab for SARS-CoV-2 infection and on 128 patients who tested negative and asymptomatic but potentially at risk of developing the infection based on epidemiological criteria [7] . The results of the study showed that out of 397 blood samples from patients with a SARS-CoV-2 infection, 352 tested positive. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-256147-lfwytlj3.txt txt = ./txt/cord-256147-lfwytlj3.txt === reduce.pl bib === id = cord-256020-wrui3i2l author = Fadaka, Adewale Oluwaseun title = Understanding the epidemiology, pathophysiology, diagnosis and management of SARS-CoV-2 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 7097 sentences = 465 flesch = 49 summary = The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The disease is caused by SARS-CoV-2, a zoonotic pathogen that acquired mutations as it crossed the species barrier from bat to pangolin enabling it to infect humans. 5 The clinical symptoms of COVID-19 include fever, cough, and pneumonia, which makes the disease enormously dangerous with a high case fatality rate. 11 Symptoms of human SARS-CoV-1 infections include headache, fever and respiratory complications such as cough, dyspnea, and pneumonia. 81 The main goal of SARS-CoV-2 diagnosis is to accurately detect the virus and to minimize further transmissions by timely isolation and treatment of infected patients. 112 This implies that variation in ACE-2 expression in COVID-19 patients is likely to affect susceptibility, symptoms and intervention outcomes following SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations cache = ./cache/cord-256020-wrui3i2l.txt txt = ./txt/cord-256020-wrui3i2l.txt === reduce.pl bib === id = cord-256375-f4vrcjr1 author = Cabrera Muras, Antonio title = Bilateral Facial Nerve Palsy associated with COVID‐19 and Epstein‐Barr Virus co‐infection date = 2020-09-30 pages = extension = .txt mime = text/plain words = 580 sentences = 43 flesch = 53 summary = He was diagnosed with right peripheral facial palsy and was treated with prednisone 60 mg/24h with a tapering schedule. This patient presented with severe bilateral facial palsy, evidence of SARS-CoV-2 infection preceded by upper respiratory symptoms, and evidence of coinfection with EBV. EBV infection is responsible for 0.5%-7.5% of peripheral facial palsies, and up to 35% are bilateral [2, 3] . One of the reported patients had isolated bilateral facial palsy and was interpreted as a variant of GBS know as bifacial weakness with paresthesias [6] . SARS-CoV-2 infection should be suspected in patients with facial palsy or any suspicion of GBS in the times of COVID-19 pandemics since it may be the presenting feature in patients with mild respiratory symptoms. Bilateral facial nerve palsy associated with Epstein-Barr virus infection Bilateral facial nerve palsy associated with Epstein-Barr virus infection with a review of the literature Guillain-Barre Syndrome Associated with SARS-CoV-2 cache = ./cache/cord-256375-f4vrcjr1.txt txt = ./txt/cord-256375-f4vrcjr1.txt === reduce.pl bib === id = cord-256508-ce59ovan author = Asselah, Tarik title = COVID-19: discovery, diagnostics and drug development date = 2020-10-08 pages = extension = .txt mime = text/plain words = 9214 sentences = 556 flesch = 46 summary = To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals cache = ./cache/cord-256508-ce59ovan.txt txt = ./txt/cord-256508-ce59ovan.txt === reduce.pl bib === id = cord-256500-nlavfnpt author = Zhang, Dan title = COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome date = 2020-03-26 pages = extension = .txt mime = text/plain words = 3501 sentences = 198 flesch = 50 summary = Background: Excessive monocyte/macrophage activation with the development of a cytokine storm and subsequent acute lung injury, leading to acute respiratory distress syndrome (ARDS) is a feared consequence of infection with COVID-19. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), also known as Corona Virus Disease-19 (COVID-19) is a new coronavirus, first identified in Wuhan, China in December 2019, which frequently induces fatal inflammatory responses and acute lung injury. Herein we describe novel observations in relation to changes in monocyte morphology and activation status, which correlate with the prognosis and severity of COVID-19 infection and which can be readily quantified by flow cytometry with the concurrent measurement of forward scatter (FSC) and (SSC), which measure cell size and complexity, respectively. We have shown that simple assessment of FSC by flow cytometry in the context of COVID-19 infection can rapidly identify those patients with an increasing proportion of large, activated, IL-6 and TNF secreting monocytes, who have severe disease and are at greatest risk of ICU admission. cache = ./cache/cord-256500-nlavfnpt.txt txt = ./txt/cord-256500-nlavfnpt.txt === reduce.pl bib === id = cord-256497-kyer0zjx author = Leyendecker, Pierre title = Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2776 sentences = 169 flesch = 50 summary = title: Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients OBJECTIVES: To retrospectively investigate the incidence of acute adrenal infarction (AAI) in patients who underwent chest CT for severe SARS-CoV-2 infection and to correlate findings with prognosis. Consequently, the purpose of this study is to retrospectively investigate the incidence of AAI in patients with severe SARS-CoV-2 infection and to correlate findings to prognosis data. (a) Severe or critical lung parenchyma lesion characteristics of COVID-19, i.e., involving at least 50% of the total lung parenchyma [10] ; (b) Presence of both entire adrenal glands in the inferior part of the volume of acquisition; (c) Positive RT-PCR for SARS-CoV-2 at the time of chest CT. To conclude, our work demonstrated a high incidence of acute adrenal infarction on initial chest CT of severe COVID-19 (51/219, 23%), which might be a sign of a poorer prognosis. cache = ./cache/cord-256497-kyer0zjx.txt txt = ./txt/cord-256497-kyer0zjx.txt === reduce.pl bib === id = cord-256458-3fyul3k2 author = Kolikonda, Murali Krishnan title = Association of Coronavirus Disease 2019 and Stroke: A Rising Concern date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1167 sentences = 87 flesch = 43 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) causes the coronavirus disease 2019 (COVID-19). Several chemical, mechanical, and/or inflammatory central nervous system pathologies are proposed to explain how this viral infection might induce acute cerebrovascular disease. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus 2019 (COVID19) disease, which quickly became a pandemic [1] . Beyond knowing that bacteria and viruses can be risk factors for cerebrovascular ischemia, the impact of this novel coronavirus on emergency medical issues like acute ischemic stroke remains to be clarified [2] . Although the exact mechanism of SARS-CoV-2 causing cerebrovascular pathology is unclear, there might be a neuroinvasive potential that increases the incidence of stroke, thromboses, and related neuropsychiatric conditions [10] [11] [12] . While coronavirus precautions are being relaxed, acknowledging COVID-19 associations to cerebrovascular disease helps plan health care services and should improve clinical outcomes. cache = ./cache/cord-256458-3fyul3k2.txt txt = ./txt/cord-256458-3fyul3k2.txt === reduce.pl bib === id = cord-256572-sqz8yc7b author = Huo, Jiandong title = Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date = 2020-05-06 pages = extension = .txt mime = text/plain words = 5378 sentences = 313 flesch = 59 summary = The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Potent nanomolar affinity neutralising human monoclonal antibodies against the SARS-CoV RBD have been identified that attach at the ACE2 receptor binding site (including M396, CR3014 and 80R (Ter Meulen et al., 2006; Sui et al., 2004; Zhu et al., 2007) ). We determined the crystal structure of the SARS-CoV-2 RBD-CR3022 Fab complex (see Methods and Table S3 ) to investigate the relationship between the binding epitopes of ACE2 and CR3022. Full interpretation of the detailed interactions between CR3022 and the RBD was enabled by the second crystal form which diffracted to high resolution, 2.4 Å, and the structure of which was refined to give an R-work/R-free of 0.213/0.239 and good stereochemistry (Methods, Table S3, Figure S5 ). cache = ./cache/cord-256572-sqz8yc7b.txt txt = ./txt/cord-256572-sqz8yc7b.txt === reduce.pl bib === id = cord-256303-bpa571ys author = Hotez, Peter J. title = Will COVID-19 become the next neglected tropical disease? date = 2020-04-10 pages = extension = .txt mime = text/plain words = 564 sentences = 32 flesch = 61 summary = The daily World Health Organization (WHO) Coronavirus Situation Reports highlight the rapid spread of COVID-19 across Europe, the United States, and many of the advanced nations in East Asia [1] . If SARS CoV2 becomes a major respiratory virus pathogen in resource-poor countries of the tropics and subtropics, we might envision unprecedented levels of global morbidity and mortality. Accordingly, PLOS Neglected Tropical Diseases will consider articles from the community of scientists and public health experts in Asia, Africa, and Latin America now shifting their efforts to combat the COVID-19 pandemic. However, as John Lennon once said, "life is what happens to you while you're busy making other plans," and on that basis we now invite our community of NTD scientists to submit COVID-19 papers on what may become a global health terror on a scale that rivals or even exceeds some of the world's major neglected tropical diseases. cache = ./cache/cord-256303-bpa571ys.txt txt = ./txt/cord-256303-bpa571ys.txt === reduce.pl bib === id = cord-257008-7q5s1vu1 author = Sharma, Virender K. title = Environmental chemistry is most relevant to study coronavirus pandemics date = 2020-05-20 pages = extension = .txt mime = text/plain words = 1326 sentences = 85 flesch = 42 summary = In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) cache = ./cache/cord-257008-7q5s1vu1.txt txt = ./txt/cord-257008-7q5s1vu1.txt === reduce.pl bib === id = cord-256556-1zea3wa1 author = Lou, Yan title = Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial date = 2020-10-25 pages = extension = .txt mime = text/plain words = 4228 sentences = 225 flesch = 50 summary = The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir marboxil, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. Then, an exploratory single center, open-label, randomized, controlled trial was conducted to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). This trial was an exploratory single center, open-label, randomized, controlled trial to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). The activity against SARS-CoV-2 was tested in vitro for the antiviral drugs used in this trial, including arbidol, ritonavir, lopinavir, darunavir, baloxavir acid, and favipiravir. cache = ./cache/cord-256556-1zea3wa1.txt txt = ./txt/cord-256556-1zea3wa1.txt === reduce.pl bib === id = cord-256351-q8lkhklw author = Di Giorgio, Angelo title = Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1377 sentences = 77 flesch = 48 summary = title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy Twenty-six per cent (n= 39) developed mild/moderate respiratory symptoms likely due to an underlying SARS-CoV-2 infection; however, since the NPS was not carried out, they were classified as suspected cases of COVID-19. cases; the majority of them (3/4 patients, 75%) presented with a mild or moderate clinical phenotype (1 was asymptomatic) whilst 1 patient died ; this patient had risk factors for complicated COVID-19 described in the general population, including old age and associated comorbidities. We previously reported our review of past outbreaks of coronavirus infections and our preliminary experience with these patients followed in our center, and we suggested that immunocompromised patients (adults and children) are not at increased risk of COVID-19 complicated course compared to the general population (3). However we recently reported the uneventful course of patients with inflammatory bowel disease who were under IS or immunomodulating drugs, including antimetabolites, during the SARS-CoV-2 epidemic (4). cache = ./cache/cord-256351-q8lkhklw.txt txt = ./txt/cord-256351-q8lkhklw.txt === reduce.pl bib === id = cord-256893-3sh87h2x author = Yang, Li title = COVID-19: immunopathogenesis and Immunotherapeutics date = 2020-07-25 pages = extension = .txt mime = text/plain words = 5347 sentences = 300 flesch = 42 summary = The recent novel coronavirus disease (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is seeing a rapid increase in infected patients worldwide. SARS-CoV-2 not only activates antiviral immune responses, but can also cause uncontrolled inflammatory responses characterized by marked pro-inflammatory cytokine release in patients with severe COVID-19, leading to lymphopenia, lymphocyte dysfunction, and granulocyte and monocyte abnormalities. The number of people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is rapidly increasing worldwide. The effect of elevated cytokine production on clinical manifestations Increasing evidence shows that viral infection can induce severe syndromes of shock and organ failure; 8,57 this phenomenon was also investigated for COVID-19. Treg cell-based therapy The dysregulated inflammatory processes caused by SARS-CoV-2 in patients with severe COVID-19 are partially due to the dysfunction of Tregs, which are responsible for inhibiting inflammation. cache = ./cache/cord-256893-3sh87h2x.txt txt = ./txt/cord-256893-3sh87h2x.txt === reduce.pl bib === id = cord-257140-ge15qrqg author = Perkmann, T. title = Increasing both specificity and sensitivity of SARS-CoV-2 antibody tests by using an adaptive orthogonal testing approach date = 2020-11-07 pages = extension = .txt mime = text/plain words = 3949 sentences = 255 flesch = 51 summary = Methods To increase sensitivity, cut-offs of three commercially available SARS-CoV-2 automated assays (Roche, Abbott, and DiaSorin) were reduced according to published values in a pre-pandemic specificity cohort (n=1117) and a SARS-CoV-2 positive cohort (n=64). In our cohort, regardless of whether the assays were used for screening or confirmation, combining Roche and Abbott delivered the best overall performance (+~10% sensitivity compared to the single tests and 100% specificity). The disadvantage of this test strategy, which was recently shown in a study for the SARS-CoV-2 antibody tests from Abbott, Roche, and DiaSorin (19) , is that the gain in specificity usually comes at the expense of sensitivity and therefore increases the number of false negatives of individual tests. The Abbott Anti-SARS-CoV-2 IgG test, in contrast, reached 100.0% specificity only when followed by the Roche assay; in the other combinations, it remained slightly below, as a few false-positives persisted (99.8-99.9%). cache = ./cache/cord-257140-ge15qrqg.txt txt = ./txt/cord-257140-ge15qrqg.txt === reduce.pl bib === id = cord-256737-ptjng78b author = McBride, Corrin E. title = Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date = 2010-09-01 pages = extension = .txt mime = text/plain words = 8233 sentences = 414 flesch = 58 summary = The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step. cache = ./cache/cord-256737-ptjng78b.txt txt = ./txt/cord-256737-ptjng78b.txt === reduce.pl bib === id = cord-256961-935r7w01 author = Lu, S. title = Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis date = 2020-04-22 pages = extension = .txt mime = text/plain words = 5136 sentences = 465 flesch = 57 summary = We included RCTs and cohort studies evaluating the effectiveness and safety of glucocorticoids in children and adults with COVID-19, SARS and MERS, and conducted meta-analyses of the main indicators that were identified in the studies. We used the following search: ("COVID-19" OR "SARS-CoV-2" OR "2019 novel coronavirus" OR "2019-nCoV" OR "Wuhan coronavirus" OR "novel coronavirus" OR "Wuhan seafood market pneumonia virus" OR "Wuhan virus" OR "MERS" OR "SARS" OR "Severe Acute Respiratory Syndrome" OR "Middle East Respiratory Syndrome Coronavirus" OR "Influenza") AND ("adrenal cortex hormones" OR " betamethasone valerate " OR " glucocorticoids" OR " methylprednisolone" OR "Cortisone" OR "Dexamethasone" OR "Cortodoxone" OR "Hydrocortisone"). Five cohort studies (one on COVID-19, three on SARS, one on severe MERS) with a total of 5872 patients assessed the duration of hospital stay (29, 31, 35, 37, 41 Figure 9 ). cache = ./cache/cord-256961-935r7w01.txt txt = ./txt/cord-256961-935r7w01.txt === reduce.pl bib === id = cord-256888-tdx12ccj author = Bradley, Benjamin T title = Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series date = 2020-07-16 pages = extension = .txt mime = text/plain words = 5006 sentences = 300 flesch = 45 summary = To date, documentation of the histopathological features in fatal cases of the disease caused by SARS-CoV-2 (COVID-19) has been scarce due to sparse autopsy performance and incomplete organ sampling. 8 Post-mortem studies have shown pulmonary, renal, and small vessel injury, with particles resembling virus observed in the kidney by electron microscopy. By electron microscopy, aggregates of uniform, round enveloped particles ranging in size from around 70 nm to 100 nm with peripheral spike-like projections consistent with the morphology described for SARS-CoV-2 were observed in the lung, trachea, kidney, and large intestine of patient 8 and patient 13. [9] [10] [11] [12] We present a case series of autopsy findings in 14 patients who died after SARS-CoV-2 infection. The major histopathological observation in our series of patients who died with COVID-19 was diffuse alveolar damage-type lung injury in the acute or organising phases (12 [86%] of 14 patients). cache = ./cache/cord-256888-tdx12ccj.txt txt = ./txt/cord-256888-tdx12ccj.txt === reduce.pl bib === id = cord-257265-lkzytud0 author = Zheng, Fang title = SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date = 2020-08-03 pages = extension = .txt mime = text/plain words = 4181 sentences = 236 flesch = 53 summary = According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. cache = ./cache/cord-257265-lkzytud0.txt txt = ./txt/cord-257265-lkzytud0.txt === reduce.pl bib === id = cord-256872-jekx1czw author = Singh, Manvendra title = A single-cell RNA expression map of human coronavirus entry factors date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4554 sentences = 6938 flesch = 74 summary = To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell transcriptomics across various healthy human tissues. Evidence of impaired gonadal function in male COVID-19 patients was also recently presented The high level of TMPRSS2, ACE2 and other coronavirus receptors such as ANPEP in the trophectoderm, which gives rise to the placenta, combined with low levels of IFITMs in this lineage (Figure 2A and Figure S1A ) raises the possibility that the developing placenta may be vulnerable to SARS-CoV-2 infection. Our study, along with several others (Table S1 ) have tapped into vast amount of publicly available scRNA-seq data to profile the expression of host factors thought to be important for entry of SARS-CoV-2 in healthy tissues. cache = ./cache/cord-256872-jekx1czw.txt txt = ./txt/cord-256872-jekx1czw.txt === reduce.pl bib === id = cord-257105-vrwuaknf author = Davies, Julie title = Neuropilin-1 as a new potential SARS-CoV-2 infection mediator implicated in the neurologic features and central nervous system involvement of COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2642 sentences = 141 flesch = 47 summary = Preclinical studies have suggested that neuropilin-1 (NRP1), which is a transmembrane receptor that lacks a cytosolic protein kinase domain and exhibits high expression in the respiratory and olfactory epithelium, may also be implicated in COVID-19 by enhancing the entry of SARS-CoV-2 into the brain through the olfactory epithelium. This study presents a detailed in silico analysis of the expression of nrP1 in the human brain, highlighting the potential role of nrP1 as an additional SarS-coV-2 infection mediator in the CNS via NRP1-expressing cells. Given this newly identified role of nrP1 in enhancing SarS-coV-2 entry into the cnS, characterizing the precise expression of nrP1 in the human brain becomes important in the context of the neurologic involvement of coVid-19. Finally, the parolfactory gyri which receive inputs from the olfactory bulb and provide input to the limbic system, also exhibit nrP1 expression, and so their potential involvement in the SarS-coV-2 infection of the cnS merits further research. cache = ./cache/cord-257105-vrwuaknf.txt txt = ./txt/cord-257105-vrwuaknf.txt === reduce.pl bib === id = cord-256761-rjss51sq author = Caputo, Leonardo title = Repurposing therapeutic agents and herbal medicines to defeat viral nemesis date = 2020-03-30 pages = extension = .txt mime = text/plain words = 1085 sentences = 69 flesch = 43 summary = After a deep analysis and exhaustive illustration of both the rationale behind this tentative approach and related safety concern, Gurwitz suggested that data mining of clinical patient records survived to COVID-19 epidemic might be useful to assess the feasibility of sartans' repurposing as therapeutic treatment to decrease acute respiratory distress syndrome (ARDS) and reduce the aggressiveness from severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. Obviously, repurposing old drugs for COVID-19 may start from therapeutic agents with proven efficacy against other lethal viral infections. On the other hand, the use of traditional Chinese remedies as a therapeutic approach for combating SARS-CoV has been well publicized (World Health Organization [WHO], 2003) and it was recently proposed for prevention of COVID-19 (Luo et al., 2020) . Whatever sources of drugs (natural, synthetic, or repurposed) are suggested to be used for COVID-19, their efficacy should be proven through a valid clinical trial. cache = ./cache/cord-256761-rjss51sq.txt txt = ./txt/cord-256761-rjss51sq.txt === reduce.pl bib === id = cord-256537-axbyav1m author = Kimball, Ann Marie title = Emergence of Novel Human Infections: New Insights and New Challenges date = 2016-10-24 pages = extension = .txt mime = text/plain words = 4979 sentences = 283 flesch = 50 summary = In reviewing the new challenges posed by these emergent events, new technologies promise some answers; however, global health security against pandemic threats, particularly given the uneven distribution of global resources for prevention, detection, and response, remains a critical area of challenge. Specifically: (1) it is now well appreciated that influenza can migrate directly from avian sources to humans, and the appreciation of the actual directness of 'species jumping' has moved forward; (2) new infections have also introduced uncertainty in transmission dynamics with emphasis on super-spreader events as well as nosocomial transmission; (3) infectious particles are not confined to those organisms which contain genetic material; (4) a new paradigm such as 'Planetary Health' may be necessary for defining these trends; and (5) global preparedness and response is not in place for the next pandemic. To summarize, the recent episodes of respiratory infectious diseases related to influenza, SARS-CoV, and MERS-CoV have demonstrated increasingly direct links between animal and human infections, agile intercontinental geographic spread, and complex transmission dynamics including 'superspreader' events. cache = ./cache/cord-256537-axbyav1m.txt txt = ./txt/cord-256537-axbyav1m.txt === reduce.pl bib === id = cord-256702-lwxt4587 author = Song, Lingjie title = A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date = 2020-04-06 pages = extension = .txt mime = text/plain words = 2037 sentences = 144 flesch = 57 summary = title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. Although the nucleic acid test was negative or single-target positive, the low number of white blood cells and lymphocytes in laboratory tests, and GGO in the lungs by CT examination indicated SARS-CoV-2 infection. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. We report the epidemiological history and clinical information of a patient with negative (or single-target positive) SARS-CoV-2 infection with multiple RT-PCR tests. cache = ./cache/cord-256702-lwxt4587.txt txt = ./txt/cord-256702-lwxt4587.txt === reduce.pl bib === id = cord-257022-6vw88jib author = SHANG, Lei title = Polymorphism of SARS-CoV Genomes date = 2006-04-30 pages = extension = .txt mime = text/plain words = 2739 sentences = 144 flesch = 61 summary = Abstract In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. In this work, the genome of one SARS-CoV isolated directly from the stool sample of a SARS patient was completely sequenced. We aligned 116 complete genome sequences of SARS-CoV (including BJ202 ) to analyze their single nucleotide polymorphism (SNPs). The 21.9-23.9 kb region, which falls into OrfS, had the third highest mutation frequency, in which 39 polymorphic sites were found in the nearly 2 kb stretch of genomic sequence (1 9.5 SNPs in 1 kb). Although it was reported that the in vitro mutation rate of the SARS-CoV in Vero cell passage was negligible['81, there might be difference between the genomic sequences obtained directly from clinical samples and from isolates of the cell culture. In this work, we completed the sequencing of SARS-CoV genome directly from the stool sample and analyzed the polymorphism of the SARS-CoV genome. cache = ./cache/cord-257022-6vw88jib.txt txt = ./txt/cord-257022-6vw88jib.txt === reduce.pl bib === id = cord-256808-lxlerb13 author = Lim, W.S title = Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004 date = 2004-06-02 pages = extension = .txt mime = text/plain words = 2426 sentences = 167 flesch = 55 summary = Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS. During 2003 Severe Acute Respiratory Syndrome caused by a novel coronavirus (SARS-CoV) emerged as an infectious disease with a significant inhospital mortality and posed a considerable occupational risk for healthcare workers. Please discuss the classification of SARS patients with the Health Protection Agency's Communicable Disease Surveillance Centre (CDSC) Duty doctor (Tel.: 0208-200-6868) and complete a standard SARS report form and fax to your local Consultant in Communicable Disease Control (CCDC) and CDSC (details at: http://www.hpa.org.uk/infections/ topics_az/SARS/forms.htm). Inform the local Health Protection Team/CCDC regarding the hospital discharge of patients to ensure follow-up in the community. Severe acute respiratory syndrome (SARS): infection control cache = ./cache/cord-256808-lxlerb13.txt txt = ./txt/cord-256808-lxlerb13.txt === reduce.pl bib === id = cord-257399-p6of5fno author = Gentry, Chris A title = Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date = 2020-09-21 pages = extension = .txt mime = text/plain words = 4529 sentences = 196 flesch = 42 summary = METHODS: This retrospective cohort study included de-identified information of all veterans in the US Veterans Health Administration clinical administrative database aged 18 years or older with rheumatoid arthritis, systemic lupus erythematosus, or associated rheumatological conditions (based on International Classification of Diseases, 10th edition, diagnostic codes) who were alive on March 1, 2020. We aimed to examine whether patients with rheuma tological conditions receiving chronic hydroxy chloroquine therapy are at less risk of developing SARS-CoV-2 infection compared with a propensity-matched group of patients not receiving hydroxychloroquine. Our study takes advantage of a setting in which a specific group of patients has been receiving chronic hydroxy chloroquine over several months to years as a novel virus emerges among the population, setting up an ideal premise to test the hypothesis that hydroxychloroquine might be effective in preventing SARS-CoV-2 infection. cache = ./cache/cord-257399-p6of5fno.txt txt = ./txt/cord-257399-p6of5fno.txt === reduce.pl bib === id = cord-256940-yuja99jg author = Wei, Bo title = Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date = 2020-07-20 pages = extension = .txt mime = text/plain words = 1994 sentences = 136 flesch = 56 summary = title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. However, some COVID-19 patients have been reported to have long-term positivity for SARS-CoV-2 ribonucleic acid (RNA). On April 5, after three consecutive negative nucleic acid test results, he was discharged and transferred to another hospital for further treatment of comorbidities. Thus, DNVr may be a potential antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. cache = ./cache/cord-256940-yuja99jg.txt txt = ./txt/cord-256940-yuja99jg.txt === reduce.pl bib === id = cord-257310-wqu7t44n author = Maideniuc, Catalina title = Acute necrotizing myelitis and acute motor axonal neuropathy in a COVID-19 patient date = 2020-08-09 pages = extension = .txt mime = text/plain words = 1091 sentences = 78 flesch = 51 summary = A 61-year-old woman with COVID 19 infection developed acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. Here we present a unique case of COVID 19 patients with acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. However, MRI Cervical spine showed patchy T2 hyperintensities within the central cord extending from below the foreman magnum, proximal Electronic supplementary material The online version of this article (https ://doi.org/10.1007/s0041 5-020-10145 -6) contains supplementary material, which is available to authorized users. The patient had a spinal fluid analysis that showed a hemorrhagic tap (red blood cells 312/mm 3 ) with normal white blood cells (3/mm 3) elevated protein (87 mg/ dl) and glucose (73 mg/dl). Acute necrotizing encephalitis, myelitis and variants of GBS such as axonal, demyelinating, and Miller Fisher Syndrome have been reported with the COVID 19 [2] [3] [4] [5] . cache = ./cache/cord-257310-wqu7t44n.txt txt = ./txt/cord-257310-wqu7t44n.txt === reduce.pl bib === id = cord-257398-fmkfo5ju author = Meng, Qing-Bin title = Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3231 sentences = 190 flesch = 49 summary = In the present study, we collected clinical data from 652 suspected COVID-19 patients and 206 non-COVID-19 patients to investigate the diagnostic value of SARS-CoV-2 IgM/IgG antibody test kits with colloidal gold immunoassays and nucleic acid RT-PCR test kits. As recently reported, a rapid IgM/IgG October 6, 2020 Volume 8 Issue 19 combined antibody test was used for the diagnosis of SARS-CoV-2 infection, showing 88.66% sensitivity and 90.63% specificity [15] . Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. cache = ./cache/cord-257398-fmkfo5ju.txt txt = ./txt/cord-257398-fmkfo5ju.txt === reduce.pl bib === id = cord-256904-uq6gy24x author = Bartolini, A. title = Immunochromatographic assays for COVID-19 epidemiological screening: our experience date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2684 sentences = 147 flesch = 49 summary = We submitted to serological screening by two different immunochromatographic (IC) rapid testing for detection of IgG and IgM against SARS-CoV-2, 151 asymptomatic or minimally symptomatic healthcare workers previously tested positive for SARS-CoV-2 RT-PCR in order to evaluate the performance of rapid assays. Results showed discrepancies between molecular and IC results, and an inconsistency of immunoglobulins positivity patterns when compared to ELISA/CLIA results, highlighting the absolute necessity of assays performance validation before their marketing and use, in order to avoid errors in the results evaluation at both clinical and epidemiological level. Our aim was to evaluate the performances of two different IC assays, submitting to serological testing the 151 healthcare workers previously tested positive for SARS-CoV-2 RT-PCR and trying to find a correlation between the molecular method, that is considered the gold standard and rapid IC tests actually available. cache = ./cache/cord-256904-uq6gy24x.txt txt = ./txt/cord-256904-uq6gy24x.txt === reduce.pl bib === id = cord-257191-u5xnmsv8 author = Farshi, Esmaeil title = Investigation of immune cells on elimination of pulmonary‐Infected COVID‐19 and important role of innate immunity, phagocytes date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2540 sentences = 128 flesch = 53 summary = [4] [5] [6] [7] [8] Lethal disease in BALB/c mice infected with a mouse-adapted strain of SARS-CoV, MA15, showed a lack of activation of innate immune response, resulting in a barely detectable antivirus T cell response. 8 On the other hand, aged BALB/c mice that were infected with a human clinical isolate of SARS-CoV (Urbani strain) successfully eliminated the invasive virus within 1 week post-infection; these mice exhibited high and prolonged levels of viral replication, signs consistent with clinical symptoms, and pathologic changes in the lung resembling those seen in elderly SARS patients. In this study, we attempted to identify the types of immune cells that contribute to clearing COVID-19 during the acute phase of the infection in mice models plus human. Cellular immune responses to severe acute respiratory syndrome coronavirus (SARS-CoV) infection in senescent BALB/c mice: CD4+ T cells are important in control of SARS-CoV infection cache = ./cache/cord-257191-u5xnmsv8.txt txt = ./txt/cord-257191-u5xnmsv8.txt === reduce.pl bib === id = cord-257206-av2k44ig author = Chen, Ruey title = Effects of a SARS prevention programme in Taiwan on nursing staff's anxiety, depression and sleep quality: A longitudinal survey date = 2006-02-28 pages = extension = .txt mime = text/plain words = 5064 sentences = 278 flesch = 59 summary = Abstract The aim of this research is to determine the levels of anxiety, depression, and sleep quality a severe acute respiratory syndrome (SARS) nursing staff experienced before and after a SARS prevention program. Using general estimating equations (GEE) statistical analysis to control possible for affecting factors, we found that the nursing staff's anxiety and depression along with sleep quality started to improve 2 weeks after the initiation of SARS prevention controls. This research is to describe the anxiety level, depression level, and sleep quality of nursing staff who cared for SARS patients during a sweeping epidemic and the effects of a SARS prevention program. Tables 2 and 3 show the effects of the SARS prevention program on nursing staff through their self-reported levels of anxiety and depression as well as sleep quality. cache = ./cache/cord-257206-av2k44ig.txt txt = ./txt/cord-257206-av2k44ig.txt === reduce.pl bib === id = cord-257403-jujrazsr author = Yin, Changchuan title = Genotyping coronavirus SARS-CoV-2: Methods and implications date = 2020-04-27 pages = extension = .txt mime = text/plain words = 2614 sentences = 179 flesch = 53 summary = Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. In this study, we use the Jaccard distance of the SNP mutations of SARS-CoV-2 genomes to measure the dissimilarity of virus isolates. From the SNP profiles of SARS-CoV-2 strain, high-frequency mutations predominate in the virus isolations, therefore, these high-frequency mutations probably contribute to increased transmissibility. This study employs the substitutions variants in genotyping for understanding the evolution and transmission of SARS-CoV-2, however, structural variants including insertions, deletions, and copy number variation are critical for virus pathogenicity [40] and human pathology [41, 42] . In this study, the complete genomes of SARS-CoV-2 are used for SNP genotype calling. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-257403-jujrazsr.txt txt = ./txt/cord-257403-jujrazsr.txt === reduce.pl bib === id = cord-257135-xt4w0baw author = Li, Zhengqian title = The brain, another potential target organ, needs early protection from SARS-CoV-2 neuroinvasion date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1112 sentences = 61 flesch = 44 summary = Based on the existing evidence and lessons from SARS outbreak in 2003, our attention should not be confined to the general organs whose dysfunctions were relatively easy to be observed or examined such as lung, kidney, and liver; at the same time, the brain should not be neglected due to the potential neuroinvasion of SARS-CoV-2, which prompts us to keep an alert on the onset of neurological symptoms, early diagnostics, and neuroprotection. So far, no direct evidence of entry of SARS-CoV-2 into the CNS has been reported in any international peer-reviewed journal, although some researchers have proposed that the neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients cache = ./cache/cord-257135-xt4w0baw.txt txt = ./txt/cord-257135-xt4w0baw.txt === reduce.pl bib === id = cord-257584-v38tjof3 author = Fahmi, Muhamad title = Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date = 2020-03-03 pages = extension = .txt mime = text/plain words = 2933 sentences = 180 flesch = 49 summary = Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45). cache = ./cache/cord-257584-v38tjof3.txt txt = ./txt/cord-257584-v38tjof3.txt === reduce.pl bib === id = cord-257556-lmws8eed author = Rafiq, Danish title = Three months of COVID‐19: A systematic review and meta‐analysis date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3195 sentences = 223 flesch = 50 summary = 2 While several other human coronaviruses such as HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1 cause mild respiratory disease, others like the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV tend to have a higher fatality rate 6 (summarized in Table 1 ). Typical of respiratory viruses like influenza virus, SARS-CoV-2019 can spread through large droplets (with a transmission risk restricted tõ 6 ft from the patient). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: a data-driven Modelling analysis of the early outbreak Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: a data driven analysis in the early phase of the outbreak cache = ./cache/cord-257556-lmws8eed.txt txt = ./txt/cord-257556-lmws8eed.txt === reduce.pl bib === id = cord-256633-vls23fu5 author = Dimeglio, Chloé title = The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1336 sentences = 88 flesch = 63 summary = We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. Our statistical model for predicting the spread of SARS-CoV-2 in France is based on a diffusion and transmission coefficient that varies with an individual's age, the likelihood of contagion, and two administration parameters (confinement and quarantine). Figures 1.b, 1 .c, 1.d, 1.e showed predictions of new cases per day depending on the SARS-CoV-2 seroprevalence before and after the containment phase. Our data indicate that seroprevalence must reach approximately 50% after total deconfinement on May 11 or a gradual exit phase over several months starting on May 11 if an infection rebound is to be avoided (Figure 1 .d, 1.e and Figure 2 .b). cache = ./cache/cord-256633-vls23fu5.txt txt = ./txt/cord-256633-vls23fu5.txt === reduce.pl bib === id = cord-257258-hu9oxea1 author = Chabner, Bruce A. title = Taking the Longer View of COVID‐19 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1810 sentences = 88 flesch = 39 summary = In the absence of a vaccine or effective antivirals, social distancing is currently the primary public health strategy for containing the epidemic and has been successful in South Korea and China, where it was stringently employed. Regarding the chances of creating an effective vaccine against SARS-CoV-2 infection, in the U.S. the Biomedical Advanced Research and Development Authority (BARDA) of the Department of Health and Human Services is devoting significant support for two currently approved trials: a lipid nanoparticle vaccine that contains mRNAs directing the synthesis of the SARS-CoV-2 spike protein (Moderna) and an adenovirus construct of virus material co-supported by Johnson & Johnson [1] . However, vaccine development and its worldwide implementation, coupled with effective antiviral treatment, will be required to control COVID-19 and prevent another pandemic. In order to be ready for the next iteration of COVID-19, the worldwide medical community will need to cooperate in conducting extensive clinical trials of vaccines, antivirals, and immune therapies on an accelerated time scale. cache = ./cache/cord-257258-hu9oxea1.txt txt = ./txt/cord-257258-hu9oxea1.txt === reduce.pl bib === id = cord-256688-yy7abob9 author = Chavez, Summer title = Coronavirus Disease (COVID-19): A primer for emergency physicians date = 2020-03-24 pages = extension = .txt mime = text/plain words = 6416 sentences = 374 flesch = 48 summary = DISCUSSION: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing COVID-19, is primarily transmitted from person-to-person through close contact (approximately 6 ft) by respiratory droplets. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), previously referred to as 2019-nCoV, is the virus responsible for causing Coronavirus Disease 2019 (COVID-19) [3] [4] [5] [6] [7] . An emergency medicine approach to COVID-19 should focus on identifying and isolating patients at risk for infection, informing hospital infection prevention and local public health authorities, and engaging infectious disease and other specialists early in care. Emergency physicians should obtain a detailed travel history from all patients and suspect COVID-19 in patients presenting with symptoms of an acute upper respiratory illness and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Home care for patients with suspected novel coronavirus (nCoV) infection presenting with mild symptoms and management of contacts cache = ./cache/cord-256688-yy7abob9.txt txt = ./txt/cord-256688-yy7abob9.txt === reduce.pl bib === id = cord-256699-d2tf2g7f author = Brochot, Etienne title = Comparison of different serological assays for SARS-CoV-2 in real life date = 2020-08-02 pages = extension = .txt mime = text/plain words = 1860 sentences = 118 flesch = 55 summary = Using 168 samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections, we evaluated the clinical performance of 5 serological assays widely used worldwide (WANTAI®, BIORAD®, EUROIMMUN®, ABBOTT® and LIAISON®). Thus, we evaluated five commercial serological tests widely used worldwide on samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections. The assays were validated using serum samples from (i) patients hospitalized for COVID-19 (n=20), non-hospitalized patients but PCR confirmed with SARS-CoV-2 (n= 58), patients participating in screening campaigns (n= 62), and samples from patients with a history of other seasonal coronavirus infections (n= 28). For the first group, with 20 patients hospitalized for COVID-19 with a positive nasopharyngeal SARS-CoV-2 PCR, all samples were positive with these serological assays evaluated ( Figure 1A ). cache = ./cache/cord-256699-d2tf2g7f.txt txt = ./txt/cord-256699-d2tf2g7f.txt === reduce.pl bib === id = cord-257468-woyycghi author = Basso, Trude title = Transmission of infection from non-isolated patients with COVID-19 to health care workers date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1824 sentences = 114 flesch = 59 summary = This study evaluated transmission of infection from a symptomatic patient with COVID-19 to 60 HCWs exposed ≤2 m for ≥15 minutes, or during aerosol generating procedures. Following ≥106 unique high-risk contacts, none of the HCWs tested positive for SARS-CoV-2 RNA or had developed antibodies. These results were in accordance with other reports and should reassure HCWs and further stimulate a broader evaluation of the foundation for the current practice of home-quarantine of non-symptomatic HCWs. During the Coronavirus Disease-19 (COVID-19) pandemic, the proportion of health care workers (HCWs) amongst verified, infected individuals, has been reported somewhere between 10 and 20 % [1, 2] . In this study we found that ≥106 unique close contact exposures, including 12 contacts during AGPs with a nonisolated patient with COVID-19, resulted in no SARS-CoV-2 transmissions from patient to HCWs. With one exception, all included HCWs were certain or quite certain that their adherence to the hand hygiene procedure had been proper at the time of exposure. cache = ./cache/cord-257468-woyycghi.txt txt = ./txt/cord-257468-woyycghi.txt === reduce.pl bib === id = cord-257169-1lk737lw author = Lau, C. S. title = Performance of an automated chemiluminescence SARS-COV-2 IG-G Assay date = 2020-09-08 pages = extension = .txt mime = text/plain words = 4265 sentences = 230 flesch = 53 summary = Methods We assessed assay precision, sensitivity, specificity, positive/negative predictive values (PPV/NPV), cross-reactivity (influenza/dengue/hepatitis B and C/rheumatoid factor/anti-nuclear/double-stranded DNA/syphilis) and sample throughput in samples from real-time polymerase chain reaction (RT-PCR) positive patients/healthcare workers (HCWs)/pre-pandemic samples. A lower COI limit for reactivity (≥0.55, using the 99th percentile COI of our controls and ROC analysis) improved diagnostic sensitivity, especially at 0-6 days POS (45.9% to 55.8%), with a small decrease in specificity (98.9%). We report on our evaluation of the Abbott Architect chemiluminescent immunoassay for SARS-CoV-2-IgG including deriving an optimised cut-off index that may be useful in testing early Covid-19 samples. An optimized COI limit for reactive samples (COI ≥0.55) (concordant values between 99th percentile of healthy controls and ROC analysis) improved the sensitivity of the assay in early infection (45.9% to 55.8% in subjects 0-6 days POS) but with a small decrease in specificity (99.8% to 98.9%). cache = ./cache/cord-257169-1lk737lw.txt txt = ./txt/cord-257169-1lk737lw.txt === reduce.pl bib === id = cord-256750-5m7psxri author = Park, Hye Yoon title = Posttraumatic stress disorder and depression of survivors 12 months after the outbreak of Middle East respiratory syndrome in South Korea date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4564 sentences = 196 flesch = 48 summary = Acute infectious outbreaks of Emerging Infectious Diseases (EIDs) are known to influence the physical as well as the mental health of affected patients, as observed during similar events such as the Severe Acute Respiratory Syndrome (SARS) outbreak [3] , which was associated with such issues during the acute phase [4] and the long-term follow-up phase [5, 6] . Thus, the present study explored mental health issues and related factors in MERS survivors 12 months after the outbreak to determine the long-term psychological outcomes of this population. The univariate analysis revealed that several factors were significantly associated with PTSD, including previous psychiatry history, having a family member who died from MERS, depression and anxiety during the MERSaffected period, greater perceived stigma currently and during the illness, and negative coping strategies (Table S2) . Our study showed that nearly half the assessed MERS survivors experienced significant mental health problems, including PTSD and depression, at 12 months post-MERS. cache = ./cache/cord-256750-5m7psxri.txt txt = ./txt/cord-256750-5m7psxri.txt === reduce.pl bib === id = cord-257600-0plhquk9 author = Calles, Antonio title = Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6981 sentences = 353 flesch = 47 summary = Differences in health-care systems, in the incidence and prevalence of SARS-CoV-2 infection by geographic regions, and patient access to intensive support care -including MVand treatment with antivirals or anti-IL6/IL1 agents may ultimately influence outcomes in patients with lung cancer affected by COVID-19. We aimed to describe the clinical characteristics of lung cancer patients with COVID-19 attended in a tertiary hospital in Madrid, one of the most hit regions by coronavirus in the world so far, and analyze factors associated with worse outcome, including type of treatment receiving at the time of COVID-19 diagnosis. We performed SARS-CoV-2 RT-PCR to every suspicious case and included all lung cancer patients attended at our hospital (emergency room, hospitalization, ambulatory office, day care area). Data from Wuhan, in China, showed that active cancer treatment received in the 14 days before SARS-CoV-2 infection had an increase on the risk of severe outcomes of COVID-19 (HR 4.079, 95%CI, 1.086-15.322; p = 0.037) (9) . cache = ./cache/cord-257600-0plhquk9.txt txt = ./txt/cord-257600-0plhquk9.txt === reduce.pl bib === id = cord-257663-i7wrqh2g author = Principi, Nicola title = Effects of Coronavirus Infections in Children date = 2010-02-17 pages = extension = .txt mime = text/plain words = 4205 sentences = 176 flesch = 49 summary = The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The identifi cation of SARS-CoV and the isolation of 2 novel HCoVs in humans (HCoV-NL63 and HCoV-HKU1) (5,6) have led to several studies of the epidemiology and clinical and socioeconomic effects of HCoV infections, which were greatly facilitated by the availability of modern molecular biology methods that enable direct viral identifi cation in respiratory secretions (7) (8) (9) (10) (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) . cache = ./cache/cord-257663-i7wrqh2g.txt txt = ./txt/cord-257663-i7wrqh2g.txt === reduce.pl bib === id = cord-257766-z7vcdtcq author = Varadhachary, Atul title = Salivary anti-SARS-CoV-2 IgA as an accessible biomarker of mucosal immunity against COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 8470 sentences = 455 flesch = 50 summary = To minimize risk to lab personnel of exposure to SARS-CoV-2, our clinical study was limited to salivary samples collected from individuals who were at least a month post-symptom onset, so we cannot report on when IgA levels first appear in saliva, though that work is currently underway. Individual Immunity and Clinical Implications: Our observations that (i) we see a large variation in salivary IgA titer, even in pre-COVID-19 samples; (ii) elevated IgA levels appear to persist for at least 2-3 months; and (iii) individuals may develop mucosal IgA without an overt SARS-CoV-2 infection, each raise intriguing questions. . https://doi.org/10.1101/2020.08.07.20170258 doi: medRxiv preprint Community Surveillance and Herd Immunity: Reports that systemic IgA may be detectable earlier than IgG or IgM, 22,23 as early as two days after symptom onset are consistent with the early-response role played by IgA, as well as with our anecdotal observations that individuals can muco-convert to positive salivary IgA contemporaneously with viral detection by PCR. cache = ./cache/cord-257766-z7vcdtcq.txt txt = ./txt/cord-257766-z7vcdtcq.txt === reduce.pl bib === id = cord-256982-t6urqus7 author = Wellinghausen, Nele title = Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date = 2020-09-16 pages = extension = .txt mime = text/plain words = 2514 sentences = 131 flesch = 51 summary = The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. A comparison of five commercial immunoassays in serum samples taken at least ten days after onset of symptoms from 51 PCR-confirmed COVID-19 outpatients revealed an overall sensitivity of the assays from 74.5% to 88.2%. cache = ./cache/cord-256982-t6urqus7.txt txt = ./txt/cord-256982-t6urqus7.txt === reduce.pl bib === id = cord-257142-q79yy6o5 author = Wambier, Carlos Gustavo title = Androgen sensitivity gateway to COVID‐19 disease severity date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3188 sentences = 172 flesch = 43 summary = Similarly, we believe that shorter CAG repeats in the androgen receptor gene may be associated with increased COVID-19 disease severity and mortality. A spectrum of androgenic activity would imply in polar pauciviral COVID-19 (e.g., children < 7), with null airway/fecal transmission potential, women with normal androgen activity would have low transmission potential (borderline pauciviral COVID-19), male teenagers and adults would have high transmission potential (borderline multiviral , and infected individuals with abnormally high androgen receptor activity (genetic or acquired) would represent the multiviral COVID-19 pole of the spectrum, with extremely high transmission To further test this hypothesis, it would be interesting to observe for severe COVID cases in female patients who present with increase androgens, for example, females with metabolic syndrome, or whom are using birth control methods with progestogen hormones that bind to androgen receptor. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated cache = ./cache/cord-257142-q79yy6o5.txt txt = ./txt/cord-257142-q79yy6o5.txt === reduce.pl bib === id = cord-257408-ejhhk1iu author = Goss, Matthew B. title = The Pediatric Solid Organ Transplant Experience with COVID‐19: An Initial Multi‐Center, Multi‐Organ Case Series date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2294 sentences = 146 flesch = 46 summary = CONCLUSIONS: Our multi‐institutional experience suggests the prognoses of pediatric transplant recipients infected with COVID‐19 may mirror those of immunocompetent children, with infrequent hospitalization and minimal treatment, if any, required. Many adult centers (2) (3) (4) have suggested that transplant recipients are at particular risk for an arduous clinical course given their immunocompromised state, though highly associated comorbidities exist as confounders and appear to play a significant role in COVID-19 outcomes for the transplant subpopulation (5) . Data were collected via institutions' respective electronic medical record systems and were reviewed for patient characteristics, history of recent exposure, timing of presentation, symptomatology, laboratory values, immunosuppression management, antiviral treatment strategies, and clinical outcomes. To date, the bulk of the literature examining COVID-19 following transplant is adult focused, with pediatric reports limited to single patient experiences. Comorbidities associated with a severe COVID-19 clinical phenotype among adult transplant recipients, e.g. hypertension, obesity, and diabetes, (14) are less prevalent in the pediatric population. cache = ./cache/cord-257408-ejhhk1iu.txt txt = ./txt/cord-257408-ejhhk1iu.txt === reduce.pl bib === id = cord-257533-i85dyg8n author = Henn, Wolfram title = Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity date = 2020-06-23 pages = extension = .txt mime = text/plain words = 1070 sentences = 60 flesch = 45 summary = title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity Although healthcare systems around the world currently are fully absorbed with the day-today challenge of slowing down the spread of the SARS-CoV-2 virus, ongoing research makes it very likely that a protective vaccine will be developed within a rather short period of time [1, 2] . Given the unprecedented public attention to the issue, these criteria must be medically adequate, socially fair, transparent, verifiable, and easily understandable for non-experts, in order to bridge thehopefully short but anyway relevant-initial shortage of vaccine supply without creating social discomfort or even unrest. As current data clearly show that COVID-19 mortality is strongly associated with age [7] , it should be the leading and also easily verifiable medical parameter for the distribution of the expected vaccine during an initial scarcity. cache = ./cache/cord-257533-i85dyg8n.txt txt = ./txt/cord-257533-i85dyg8n.txt === reduce.pl bib === id = cord-257719-5s6acr7m author = Poh Ng, Lisa Fong title = The Virus That Changed My World date = 2003-12-22 pages = extension = .txt mime = text/plain words = 1510 sentences = 74 flesch = 61 summary = In the three months that Singapore was labelled as a "SARS country" by the World Health Organization (WHO), over 200 cases of SARS were reported, and 33 people died. Referring to the high standards of medical care and the societal measures put in place, Dr David Mansoor of WHO said that if not even Singapore could contain the outbreak, it was going to be very hard for other countries to prevent SARS from spreading (Chua 2003 I was to be part of the diagnostic team, and work began almost immediately. Data obtained from this work were significant for further understanding of coronavirus replication and pathogenesis, but never had I imagined that I would be able to use this knowledge in designing the SARS-CoV diagnostic kit with Roche. The months working on SARS opened my mind, as it did my heart, about the importance of research and of keeping our faith and motivation even in the toughest times. cache = ./cache/cord-257719-5s6acr7m.txt txt = ./txt/cord-257719-5s6acr7m.txt === reduce.pl bib === id = cord-257792-m7nij17v author = Ng, Oi-Wing title = Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection date = 2016-04-12 pages = extension = .txt mime = text/plain words = 4237 sentences = 203 flesch = 56 summary = In this study, the screening for the presence of SARS-specific T cells in a cohort of three SARS-recovered individuals at 9 and 11 years post-infection was carried out, and all memory T cell responses detected target the SARS-CoV structural proteins. As shown in Fig. 1 , higher frequencies of IFN␥producing SFUs were observed for in vitro-expanded PBMCs from SARS subject 1 compared to the healthy individual, suggesting the presence of SARS-specific memory T cells at 9 years post-infection. In another study looking at SARSspecific memory T cell responses in SARS-recovered individuals at 4 years post-infection, 28.75% of them presented T cell responses to M peptides [22] , further supporting the role of M protein in eliciting dominant cellular immunity during SARS-CoV infection. In SARS subject 1 at 6 years post-infection, a HLA-B*1525-restricted memory CD8 + T cell response targeting the N53 peptide, corresponding to residues 261-275 of N protein, was detected. cache = ./cache/cord-257792-m7nij17v.txt txt = ./txt/cord-257792-m7nij17v.txt === reduce.pl bib === id = cord-257456-15bm9psj author = Arumugam, Arunkumar title = A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5286 sentences = 294 flesch = 59 summary = Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. To further improve the speed of a diagnostic assay, we and others tested using untreated or heat-inactivated samples added directly to one-step RT-PCR master mixes without an RNA extraction step [6, [13] [14] [15] [16] [17] [18] [19] . Prior to COVID-19 emerged as a global pandemic, we have tested the feasibility of circumventing the sample preparation steps by adding a few microliters of the unprocessed sample (in VTM) directly into the RT-qPCR assay master mix targeting InfA, InfB, and RSV. cache = ./cache/cord-257456-15bm9psj.txt txt = ./txt/cord-257456-15bm9psj.txt === reduce.pl bib === id = cord-257732-3xuy6tbn author = Azzi, Lorenzo title = Saliva is a reliable tool to detect SARS-CoV-2 date = 2020-04-14 pages = extension = .txt mime = text/plain words = 3510 sentences = 201 flesch = 56 summary = OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. At present, Real Time reverse transcription Polymerase Chain Reaction (rRT-PCR) on respiratory specimens represents the gold standard test for detection of SARS-CoV-2 infection. 10 , 11 Sputum and oropharyngeal secretions have recently been suggested as a possible target for the molecular diagnosis of COVID-19, 12 and salivary droplets represent the main source of the human-to-human transmission of the SARS-CoV-2 infection when social distance is less than 2 m. There were not significant differences regarding the clinical and anamnestic history between males and females, with the only exception of the values of serum LDH, which were higher in the female patients' haematochemical analyses carried out on the day of saliva collection ( p = 0.025). cache = ./cache/cord-257732-3xuy6tbn.txt txt = ./txt/cord-257732-3xuy6tbn.txt === reduce.pl bib === id = cord-257809-bq9ha4d0 author = Mukaino, Masahiko title = Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-04-08 pages = extension = .txt mime = text/plain words = 708 sentences = 46 flesch = 45 summary = title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection T he recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a pandemic. Here, therefore, we introduce a preliminary attempt to use a telerehabilitation system to deliver exercise opportunities to individuals isolated because of SARS-CoV-2 infection. Four hospitalized individuals (aged 19-66 yrs, median age = 53 yrs, 2 male individuals), who were infected with SARS-CoV-2 during the outbreak on the Diamond Princess cruise ship, participated in the program. Using videoconferencing (Zoom by Zoom Video Communications Inc, San Jose, CA) and remote control software (TeamViewer; TeamViewer GmbH, Göppingen, Germany), a physical therapist guided each individual in a 20-min exercise program (Fig. 1) . With the pandemic spread of SARS-CoV-2, the number of isolated individuals is expected to increase. cache = ./cache/cord-257809-bq9ha4d0.txt txt = ./txt/cord-257809-bq9ha4d0.txt === reduce.pl bib === id = cord-257729-s0vo7dlk author = Bauer, Melissa title = Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4278 sentences = 212 flesch = 38 summary = T he management of obstetric patients infected with Coronavirus Disease 2019 (COVID19) due to human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires quite unique considerations-from caring for critically ill pregnant and postpartum women to protecting health care workers from exposure during the delivery hospitalization (health care providers, personnel, family members, and beyond). 4 An additional manifestation noted among patients with COVID-19 infection is the sudden loss (or reduction) of the sense of smell and taste, which is currently recommended by the American Academy of Otolaryngology-Head With increasing numbers of Coronavirus Disease 2019 (COVID 19) cases due to efficient human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United States, preparation for the unpredictable setting of labor and delivery is paramount. cache = ./cache/cord-257729-s0vo7dlk.txt txt = ./txt/cord-257729-s0vo7dlk.txt === reduce.pl bib === id = cord-257058-wf6oxzrk author = Kim, Sinae title = The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene date = 2020-10-26 pages = extension = .txt mime = text/plain words = 3332 sentences = 237 flesch = 61 summary = The S gene of SARS-CoV, which encodes for the spike glycoprotein on the viral envelope, recognizes a receptor on the membrane of specific host cells. The present study with novel mutations in critical RBD of S gene may explain the high pathogenicity of SARS-CoV2 through precise biochemistry result with recombinant spike proteins as well as cell infectivity experiment. The alignment of four SARS-CoV2 spike amino acid sequences compared to the wild type sequence revealed that there are two additional mutations in the critical RBD and another mutation in subdomain (SD) 2, which is very close to the known mutation residue D614G (Figs. A recent study reported a single point mutation in which amino acid residue aspartic acid 614 replaced by glycine (D614G) in S gene, resulting in enhanced infectivity of SARS-CoV2 (18) . However, two novel mutations in S gene of Korean COVID-19 in the Korean patients were present in RBD (Fig. 6 , green bar), a site that is important for binding to ACE2 receptor on the host cell membrane. cache = ./cache/cord-257058-wf6oxzrk.txt txt = ./txt/cord-257058-wf6oxzrk.txt === reduce.pl bib === id = cord-257611-z0sng9sx author = Kalantari, Hamidreza title = Determination of COVID-19 prevalence with regards to age range of patients referring to the hospitals located in western Tehran, Iran date = 2020-10-07 pages = extension = .txt mime = text/plain words = 2796 sentences = 148 flesch = 61 summary = We decided to examine suspected samples of pneumonia outbreak caused by the new coronavirus SARS-CoV-2 and provide information about the mortality rate due to this infection in different age groups in Iran. In this descriptive-cross-sectional study, a total of 784 samples of naso/oropharyngeal swabs of suspected patients with COVID-19 symptoms who had referred to Imam Khomeini, Shahid Fayaz-Bakhsh and Modarres hospitals in Tehran from February 24, 2020 to March 24, 2020 were examined by RT-PCR method. Therefore, in this study, we aimed at targeting these three genes using real-time RT-PCR method to examine suspected samples of COVID-19 and to determine the mortality rate due to this infection in different age groups in Iran. This was in accordance with the results of the present study, in which the highest number of deaths and positive cases were reported in people in the age group of >70 years. cache = ./cache/cord-257611-z0sng9sx.txt txt = ./txt/cord-257611-z0sng9sx.txt === reduce.pl bib === id = cord-257802-vgizgq2y author = Uttamchandani, Mahesh title = Applications of microarrays in pathogen detection and biodefence date = 2008-11-12 pages = extension = .txt mime = text/plain words = 6568 sentences = 305 flesch = 35 summary = Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC's list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] . cache = ./cache/cord-257802-vgizgq2y.txt txt = ./txt/cord-257802-vgizgq2y.txt === reduce.pl bib === id = cord-258113-mnou31j3 author = Wang, Yaping title = Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date = 2020-05-19 pages = extension = .txt mime = text/plain words = 3898 sentences = 215 flesch = 54 summary = title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. [5] studied the clinical features of 99 patients with COVID-19 and found that SARS-Cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ARDS). Among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, PCT, LDH, CK, ALB, AST, and D-dimer were associated with disease severity. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-258113-mnou31j3.txt txt = ./txt/cord-258113-mnou31j3.txt === reduce.pl bib === id = cord-257613-o0q7hvn3 author = Shafiee, Abbas title = Coronavirus disease 2019: A tissue engineering and regenerative medicine perspective date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3427 sentences = 199 flesch = 43 summary = To date, numerous studies have been conducted to evaluate the safety and efficacy of tissue engineering and regenerative medicine (TERM) products, including mesenchymal stem cells (MSCs), and their derivatives (eg, exosomes) for coronavirus infections, which could be applied for the COVID‐19. Over the COVID-19 outbreak, the funding for many TERM projects is being cut, which has a significant impact on the present and future of Current clinical trials highlight the potential benefits of stem cell therapies for COVID-19 patients. Effective multi-institutional collaboration and adequate funding from government and nongovernment sources are also needed to collect and analyze the data from ongoing and new human trials, to better understand the potential benefits of stem cell therapies for COVID-19 patients. Clinical study of mesenchymal stem cell treating acute respiratory distress syndrome induced by epidemic Influenza A (H7N9) infection, a hint for COVID-19 treatment. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial cache = ./cache/cord-257613-o0q7hvn3.txt txt = ./txt/cord-257613-o0q7hvn3.txt === reduce.pl bib === id = cord-257876-nzjp1hrz author = Yang, Wenzhong title = Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality date = 2020-09-14 pages = extension = .txt mime = text/plain words = 3319 sentences = 192 flesch = 55 summary = Genomic annotation of the BLAST hits also showed that viruses from geographic regions with severe infections tended to have more dynamic genomic regions in the SARS-CoV-2 receptor-binding domain (RBD) and receptor-binding motif (RBM) of the spike protein (S protein). We collected all available raw sequencing data for SARS-CoV-2 from the four sequencing platforms (Illumina, BGI, Ion-Torrent and Nanopore) deposited in the National Center for Biotechnology Information (NCBI) Short Reads Archive (SRA) database as of 15 April 2020 (Supplementary Table S1 ). The BLAST hit score (BHS) is a metric based on the similarity between a high-quality read of a SARS-CoV-2 sample and each assembled genome in the coronavirus databases (Methods). To investigate the dynamic binding between RBM and ACE2, we implemented protein structure dockings between the modeled S proteins (with and without the 'hidden mutations' in the alignments of 4I.C1) and human ACE2 protein using HDOCK [26] The threshold for the high-quality reads from BGI and Illumina platforms is 0.9 (marked by a dash line) and that for Ion-Torrent and Nanopore is 0.2 (marked by a dash line). cache = ./cache/cord-257876-nzjp1hrz.txt txt = ./txt/cord-257876-nzjp1hrz.txt === reduce.pl bib === id = cord-257820-4qmajxtb author = Abate, Giulia title = Impact of COVID-19 on Alzheimer’s Disease Risk: Viewpoint for Research Action date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4086 sentences = 241 flesch = 45 summary = On the other hand, we cannot exclude that, in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) positive subjects, the virus infection could have long-term consequences, leading to chronic medical conditions such as dementia and neurodegenerative disease. Based on the belief that the tissue distribution of host receptors are generally consistent with the tropism of the virus [35] , ACE2 expression and its modulation in CNS might aid in dissecting the invasion rate and distribution of SARS-CoV-2 in the brain area. Recently, in the UK Biobank Community Cohort (n = 451,367), the ApoE e4e4 (homozygous) genotype was also found associated with an increased risk of severe COVID-19 infection, independent of preexisting dementia, cardiovascular disease, and type-2 diabetes [81] . All of these hypotheses about the theoretical impact of SARS-CoV-2 brain infection on Alzheimer's disease risk are summarized Table 1 . Theoretical impact of SARS-CoV-2 brain infection on Alzheimer's disease risk. AD, Alzheimer's disease; Aβ, Beta-amyloid; ACE2, Angiotensin-Converting Enzyme 2; NO, nitric oxide. cache = ./cache/cord-257820-4qmajxtb.txt txt = ./txt/cord-257820-4qmajxtb.txt === reduce.pl bib === id = cord-257487-xanqvdhn author = Carbajo-Lozoya, Javier title = Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date = 2012-02-10 pages = extension = .txt mime = text/plain words = 2945 sentences = 191 flesch = 49 summary = Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. Knockdown of the cellular FK506binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. To examine whether FK506 exerts an inhibitory activity on other human coronaviruses, CaCo2 cells were infected with HCoV-NL63 at MOI = 0.004 (Herzog et al., 2008) in the presence of increasing inhibitor concentrations. In order to examine whether the cellular FK506-binding proteins FKBP1A and FKBP1B are required for virus replication, CaCo2 knockdown cell lines were established using lentiviral expression of shRNA (Sirion GmbH, Martinsried, Germany). cache = ./cache/cord-257487-xanqvdhn.txt txt = ./txt/cord-257487-xanqvdhn.txt === reduce.pl bib === id = cord-258067-par61wwh author = Di Martino, Marcello title = Elective Surgery During the SARS-CoV-2 Pandemic (COVID-19): A Morbimortality Analysis and Recommendations on Patient Prioritisation and Security Measures date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3464 sentences = 178 flesch = 42 summary = Conclusions The patients undergoing the surgical procedures showed high rates of COVID-19 infection and postoperative complications, especially the patients with oncological diseases. The following variables were analysed: age; sex; functional status (defined according to the ECOG scale) (21); personal background; diagnosis; type of surgical intervention; the timing of SARS-CoV-2 infection; the treatment required (Table 1) ; the severity of the respiratory infection (according to the BRCSS) (20) ; and postoperative complications (according to the Dindo-Clavien classification) (19) . Ten (16.9%) of the oncological patients, one (1%) of those operated on electively for benign diseases and four (7%) of the urgent surgery group presented with a SARS-CoV-2 infection, with statistically significant differences in the infection rate of the three groups (p = 0.004) ( Table 2) . Patients undergoing elective surgery before and during the peak of the COVID-19 pandemic showed a high rate of postoperative complications, with a SARS-CoV-2 infection rate of up to 16% in patients undergoing oncologic surgical procedures. cache = ./cache/cord-258067-par61wwh.txt txt = ./txt/cord-258067-par61wwh.txt === reduce.pl bib === id = cord-257789-pdybfft6 author = Diamond, Betty title = SARS-CoV-2 and interferon blockade date = 2020-11-09 pages = extension = .txt mime = text/plain words = 3583 sentences = 200 flesch = 43 summary = We propose that SARS-CoV-2 activates the innate immune system through the renin-angiotensin and kallikrein-bradykinin pathways, blocks interferon production and reduces an effective adaptive immune response. Here we propose that the systemic inflammation seen in Covid-19 patients results from the activation of two intersecting systems, the renin-angiotensin system (RAS) and the kallikrein-bradykinin system (Diamond 2020) . The engagement of these pathways helps explain how severe Covid-19 infection is characterized by massive inflammation in multiple target organs, a poor anti-viral response with little production of interferon, and little participation of the adaptive immune system. As we have hypothesized that some of the inflammation induced in severe, and perhaps even moderate, Covid-19 is the result of dysregulation of the RAS and kallikrein-bradykinin pathways, the associated players serve as potential therapeutic targets ( Fig. 1 ) As mentioned above, ACE inhibitors and AT1 blockers (ARBs) are approved and safe drugs. cache = ./cache/cord-257789-pdybfft6.txt txt = ./txt/cord-257789-pdybfft6.txt === reduce.pl bib === id = cord-257698-ed2tqn35 author = Wong, Raymond S.M. title = Index Patient and SARS Outbreak in Hong Kong date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1495 sentences = 86 flesch = 53 summary = During the global outbreak of severe acute respiratory syndrome (SARS) in 2003, treatment was empiric. We report the case history of the index patient in a hospital outbreak of SARS in Hong Kong. Other laboratory tests were performed, including blood, sputum, and urine cultures, nasopharyngeal aspirate for influenza and parainfluenza, indirect immunofluorescence for respiratory syncytial viral antigen detection, and atypical pneumonia titer (for adenovirus, Chlamydia psittaci, Q fever, influenza A and B, and Mycoplasma). Our patient was identified as the index case-patient 5 days after the onset of this large outbreak at the Prince of Wales Hospital, as he was the first patient who had the characteristic clinical, radiologic, and laboratory features of SARS and had epidemiologic links with other infected persons. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-257698-ed2tqn35.txt txt = ./txt/cord-257698-ed2tqn35.txt === reduce.pl bib === id = cord-257994-i6hut28h author = Nogee, Daniel title = Covid-19 and the N95 respirator shortage: Closing the gap date = 2020-04-13 pages = extension = .txt mime = text/plain words = 592 sentences = 36 flesch = 35 summary = Due to extreme shortages of personal protective equipment caused by the COVID-19 pandemic, many healthcare workers will be forced to recycle protective masks intended for disposal after a single use. We propose investigating the use of ultraviolet germicidal irradiation to sterilize masks of SARS-CoV-2 for safer reuse. The Centers for Disease Control and Prevention has published guidelines for optimizing supply to extend stocks through limiting use, reuse at the patient and provider levels, and alternative personal protective equipment recommendations. Although further work will be needed to determine dosages of UVGI to effectively sterilize SARS-CoV-2 contaminated FFRs, UVGI provides a potential avenue for greatly extending the limited FFR supply in the face of the ongoing COVID-19 pandemic in a simple, cost-effective, and rapidly deployable manner. A pandemic influenza preparedness study: use of energetic methods to decontaminate filtering facepiece respirators contaminated with H1N1 aerosols and droplets Ultraviolet germicidal irradiation of influenza-contaminated N95 filtering facepiece respirators No financial support was provided relevant to this article. cache = ./cache/cord-257994-i6hut28h.txt txt = ./txt/cord-257994-i6hut28h.txt === reduce.pl bib === id = cord-258360-fqrn02lr author = Lee, Jimmy title = No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2833 sentences = 151 flesch = 52 summary = In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our 'upstream' market chain samples suggests that these detections in 'downstream' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. Our negative findings across five viral families associated with emerging and re-emerging zoonotic diseases in recent decades contrast with reports of the detection of parainfluenza virus (Wang et al., 2018) , coronaviruses and Sendai virus (Liu et al., 2019; Zhang et al., 2020) , and SARSr-CoVs (Lam et al., 2020; Xiao et al., 2020) in Sunda pangolins. We therefore conclude that the detections of SARS-CoV-2 related viruses in pangolins are more plausibly a result of their exposure to infected people, wildlife or other animals after they entered the trade network. cache = ./cache/cord-258360-fqrn02lr.txt txt = ./txt/cord-258360-fqrn02lr.txt === reduce.pl bib === id = cord-258011-19yfwvki author = Deprest, Jan title = SARS‐CoV2 (COVID‐19) infection: is fetal surgery in times of national disasters reasonable? date = 2020-04-22 pages = extension = .txt mime = text/plain words = 2087 sentences = 123 flesch = 48 summary = 10 From a fetal intervention perspective, we need to appreciate that doing an invasive procedure in a SARS-CoV2 positive woman potentially increases the risk of vertical transmission, similar to what was observed in HIV positive women prior to the introduction of antiviral therapies. With open fetal surgery, the risk of mother-child transmission is likely higher than with needle and fetoscopic procedures as the fetus is exposed to more maternal blood and the fetal skin integrity is usually breached in these interventions. SARS-CoV2 negative patients planned to undergo fetal intervention should be informed that exposure to healthcare professionals, other patients or hospital staff increases their risk of contracting the virus. 5 The risk for an asymptomatic SARS-CoV2-positive pregnant mother to progress to overt COVID-19 disease is unknown, though most sources quote it as 'low' and not higher than health-and age-equivalent women. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-258011-19yfwvki.txt txt = ./txt/cord-258011-19yfwvki.txt === reduce.pl bib === id = cord-258152-3udtsvga author = Dawood, Ali Adel title = Tunicamycin, an anticancer drug and inhibitor of N- linked glycosylation proteins is reliable to treat COVID-19 date = 2020-10-20 pages = extension = .txt mime = text/plain words = 2965 sentences = 174 flesch = 50 summary = The glycans in some proteins play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. SARS-CoV is one of the viruses contain N-linked glycoproteins which are glycosylated by the transfer of core oligosaccharides from a dolichol pyrophosphate carrier to asparagine residues on the polypeptide [2] . Furthermore, HE protein of MHV was found to be modified by N-linked glycosylation and was inhibited by tunicamycin but not monensin. The inhibition Nlinked glycosylation of SARS-CoV 8ab protein by tunicamycin is not completely understood [33, 34] . HE and 8ab proteins of SARS-CoV glycosylation are inhibited by tunicamycin. Since tunicamycin has long been used as an anti-cancer and can inhibit glycoproteins of coronaviruses, we recommend using this drug to treat the SARS-CoV-2. cache = ./cache/cord-258152-3udtsvga.txt txt = ./txt/cord-258152-3udtsvga.txt === reduce.pl bib === id = cord-258307-nsdhvc8w author = Maki, Dennis G. title = SARS Revisited: The Challenge of Controlling Emerging Infectious Diseases at the Local, Regional, Federal, and Global Levels date = 2011-10-20 pages = extension = .txt mime = text/plain words = 5019 sentences = 252 flesch = 48 summary = The most recent and perhaps most fearsome emerging infections are the appearance of West Nile virus encephalitis in New York City in 1999 and its rapid spread westward 6 ; inhalation anthrax, deriving from use of Bacillus anthracis spores as a biologic weapon against the US civilian population in 2001 7 ; the global outbreak of severe acute respiratory syndrome (SARS) in 2003 8 ; and the looming threat of pandemic influenza, especially global disease caused by the highly virulent avian subtype A (H5N1). If it is not, the effort will not have been wasted because it is likely that all the planning and resource allocation will prove invaluable for controlling the spread of natural emerging pathogens, such as SARS-CoV or a new strain of influenza virus, which are probably far more likely to pose a serious threat to human and animal health in the United States and worldwide. cache = ./cache/cord-258307-nsdhvc8w.txt txt = ./txt/cord-258307-nsdhvc8w.txt === reduce.pl bib === id = cord-258281-gxwk8jq9 author = Wenling, Yao title = Pregnancy and COVID-19: management and challenges date = 2020-08-31 pages = extension = .txt mime = text/plain words = 5015 sentences = 263 flesch = 46 summary = Based on recently published literature and official documents, this review provides an introduction to the pathogenesis, pathology, and clinical features of COVID-19 and has focused on the current researches on clinical features, pregnancy outcomes and placental histopathological analysis from pregnant women infected with SARS-CoV-2 in comparison with SARS-CoV and MERS-CoV. Although there is no unequivocal evidence to support the fetal infection by intrauterine vertical transmission of SARS, MERS and SARS-CoV-2 so far, more and more articles began to report maternal deaths due to COVID-19. There were no cases of vertical transmission identified among pregnant women infected with SARS 44-49 so far, but SARS during pregnancy is associated with high incidences of spontaneous miscarriage, preterm delivery, intrauterine growth restriction, endotracheal intubation and admission to the neonatal intensive care unit [44] [45] [46] . This is a review on pregnant women infected by SARS-CoV-2, SARS, and MERS, including their pathogenesis, clinical manifestations and pregnancy outcomes. Middle East respiratory syndrome coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature cache = ./cache/cord-258281-gxwk8jq9.txt txt = ./txt/cord-258281-gxwk8jq9.txt === reduce.pl bib === id = cord-258160-v08cs51n author = Wang, Lin-Fa title = Review of Bats and SARS date = 2006-12-17 pages = extension = .txt mime = text/plain words = 3793 sentences = 171 flesch = 50 summary = Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Although in 1 live animal market, 3 species were found to be infected by viruses related to SARS-CoV (9), all subsequent studies have focused mainly on palm civets, possibly because the rate of detection was higher in civets or because the number of civets traded in southern People's Republic of China exceeds that of other wildlife groups. cache = ./cache/cord-258160-v08cs51n.txt txt = ./txt/cord-258160-v08cs51n.txt === reduce.pl bib === id = cord-257751-n7w1psr4 author = Halperin, Daniel T. title = Coping With COVID-19: Learning From Past Pandemics to Avoid Pitfalls and Panic date = 2020-06-30 pages = extension = .txt mime = text/plain words = 6378 sentences = 386 flesch = 57 summary = As we wrestle with how best to mitigate COVID-19, it is imperative to concur on the likely main drivers of transmission (notably, infection clusters resulting from prolonged indoor respiratory exposure) in order to clearly explain risk and to determine the most effective, realistic behavioral and other means to reduce illness and mortality. What is clear, based on evidence from several countries (and despite media attention to statistically anomalous cases of healthy and younger victims), is that severe outcomes and deaths from COVID-19 are overwhelmingly associated with preexisting (and especially multiple) serious illnesses such as diabetes and heart disease, [14] [15] [16] more so in men and particularly when exacerbated by obesity and smoking. Moreover, the fact that between 96% (in the United States 16 ) and more than 99% (in Italy 14 ) of COVID-19-related deaths, at any age, have occurred in persons with preexisting conditions could suggest that even very old but otherwise healthy people may not be at greatly elevated risk of dying from the disease. cache = ./cache/cord-257751-n7w1psr4.txt txt = ./txt/cord-257751-n7w1psr4.txt === reduce.pl bib === id = cord-257958-yehnlabq author = Barh, Debmalya title = Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date = 2020-10-10 pages = extension = .txt mime = text/plain words = 5431 sentences = 364 flesch = 43 summary = In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). cache = ./cache/cord-257958-yehnlabq.txt txt = ./txt/cord-257958-yehnlabq.txt === reduce.pl bib === id = cord-258167-jqm3qyfm author = Zhou, Peng title = Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date = 2009-09-18 pages = extension = .txt mime = text/plain words = 2309 sentences = 118 flesch = 57 summary = Studies using wild bat sera revealed that it is highly likely that the immunodominant epitopes overlap with the major neutralizing sites of the SL-CoV S protein. Our previous studies showed that the SL-CoV and SARS-CoV shared similar genomic organization and highly conserved gene products, with the exception of the spike protein (S protein), which had a low sequence identity, especially in the receptor binding domain (RBD) located at the N-terminal region of the S proteins. In this study, the immunogenicity and immunodominant region of S SL was determined using sera generated from DNA immunization and naturally infected bats. Hyperimmune mouse sera were generated by DNA immunizations with plasmids pcDNA 3.1(+) containing the codon-optimized fulllength S gene of SARS-CoV BJ01, SL-CoV Rp3, and two chimeric plasmids CS 310-518 and CS 259-518 (see Fig. 1 for diagrams). In this study, DNA constructs expressing four different S proteins, SARS-CoV BJ01, SL-CoV Rp3 S and two chimeras, were used to generate hyperimmune sera in mice via DNA immunization. cache = ./cache/cord-258167-jqm3qyfm.txt txt = ./txt/cord-258167-jqm3qyfm.txt === reduce.pl bib === id = cord-257805-pcp3qgn0 author = Mehta, Harsh title = Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date = 2020-05-16 pages = extension = .txt mime = text/plain words = 2222 sentences = 148 flesch = 50 summary = title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Since its first reported case in China, more than 4 Coronaviruses are known pathogens and have previously been responsible for epidemics caused by severe acute respiratory syndrome coronavirus (SARS-CoV1) and We report a case of a high-risk pregnant woman who developed respiratory failure associated with COVID-19, and had a favorable outcome postdelivery. A repeat chest X-ray showed worsening bilateral pulmonary infiltrates, raising concern for development of acute respiratory distress syndrome (ARDS). In the data available in pregnant patients from the previous coronavirus outbreaks, no vertical transmission was reported [4] . cache = ./cache/cord-257805-pcp3qgn0.txt txt = ./txt/cord-257805-pcp3qgn0.txt === reduce.pl bib === id = cord-258255-hzmcrenk author = Jiang, Xuejun title = Asymptomatic SARS‐CoV‐2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days date = 2020-04-24 pages = extension = .txt mime = text/plain words = 553 sentences = 35 flesch = 49 summary = Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs([1]), but the presence of SARS‐CoV‐2 RNA in feces of COVID‐19 patients indicates the possibility of transmission via fecal‐oral route([2‐4]). Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs [1] , but the presence of SARS-CoV-2 RNA in feces of COVID-19 patients indicates the possibility of transmission via fecal-oral route [2] [3] [4] . Herein, we report the distinctive clinical characteristics of an asymptomatic case in which SARS-CoV-2 viral nucleotide detection was positive in anal swabs but negative in nasopharyngeal swabs for such a long period (42 days). This case will further provide the new information that, besides confirmed COVID-19 patients, the asymptomatic SARS-CoV-2 infected case can be persistently tested positive in the stool samples but negative in nasopharyngeal swabs for a long time. Detectable SARS-CoV-2 viral RNA in feces of three children during recovery period of COVID-19 pneumonia cache = ./cache/cord-258255-hzmcrenk.txt txt = ./txt/cord-258255-hzmcrenk.txt === reduce.pl bib === id = cord-258382-ep73us0e author = Braga, Cássia L. title = The renin–angiotensin–aldosterone system: Role in pathogenesis and potential therapeutic target in COVID‐19 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 2990 sentences = 195 flesch = 46 summary = 8, 9 According to Zhou et al, SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor to invade and infect cells. These proteins bud into the endoplasmic reticulum-Golgi intermediate compartment (ERGIC); new viral particles are then assembled and released to infect new target cells comes from the observation that endosomal alkalization induced by ammonium chloride inhibited SARS-CoV-2 replication. Once a hypertensive patient is infected with SARS-CoV-2, sensitization of the immune system toward an overactivation of the inflammatory response could be associated with subsequent development of cytokine storm. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS cache = ./cache/cord-258382-ep73us0e.txt txt = ./txt/cord-258382-ep73us0e.txt === reduce.pl bib === id = cord-258576-ywbyflas author = Bösmüller, Hans title = The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3628 sentences = 207 flesch = 44 summary = We present the pulmonary findings in four cases of fatal COVID-19 with a spectrum of lung pathology reflecting disease course and duration, invasive therapies, and laboratory features. Based on conventional criteria, respiratory insufficiency therefore might be considered unlikely direct cause of death, but this case and recently published autopsy data indicate that pulmonary microvascular changes are an important and distinguishing feature of COVID-19 and may contribute to hypoxemia and acute cardiac insufficiency. Irrespective of the severity of pulmonary changes, however, all 4 patients showed SARS-CoV-2 RNA in lung tissues but failed to show detectable levels of viral RNA in other organs studied. The laboratory findings observed in patients 2 and 3 reflect common risk factors of fatal outcome, namely, lymphopenia; increased D-dimers; evidence of massive systemic inflammation including high levels of CRP, procalcitonin, and IL-6 during acute disease; and in the final stages massive ALT/AST elevation [1, 3, 4, 7, 11, 20] . cache = ./cache/cord-258576-ywbyflas.txt txt = ./txt/cord-258576-ywbyflas.txt === reduce.pl bib === id = cord-258242-xblxjlb5 author = Liu, Tengwen title = Systems Pharmacology and Verification of ShenFuHuang Formula in Zebrafish Model Reveal Multi-Scale Treatment Strategy for Septic Syndrome in COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 5215 sentences = 310 flesch = 44 summary = Recent studies reported that many critically ill COVID-19 patients developed typical septic syndrome, including inflammatory injury, immune dysfunction, coagulation disorder, and multiple organ failure (Bellinvia et al., 2020; Coronado et al., 2020; . Current studies reported that severe COVID-19 patients with septic syndrome mainly showed abnormal pathological features, including virus infection and tissue damage, excessive inflammation in early stage but immune suppression in late stage, and coagulation dysfunction . Since the data of systems pharmacology illustrated that SFH may regulate several key targets and biological processes of sepsis, such as PPARG in inflammatory response, GSK3b and MAPK14 in cell proliferation, and PTGS2 in coagulation, we hypothesized that SFH improves the condition of critically ill COVID-19 patients with septic syndrome by ameliorating lung injury, suppressing excessive inflammation but enhancing the capacity of pathogen phagocytosis and killing, and improving the function of blood coagulation. cache = ./cache/cord-258242-xblxjlb5.txt txt = ./txt/cord-258242-xblxjlb5.txt === reduce.pl bib === id = cord-258435-lhn34tc4 author = Tracy, C Shawn title = Public perceptions of quarantine: community-based telephone survey following an infectious disease outbreak date = 2009-12-16 pages = extension = .txt mime = text/plain words = 3724 sentences = 180 flesch = 47 summary = CONCLUSION: To engender strong public support for quarantine and other restrictive measures, government officials and public health policy-makers would do well to implement a comprehensive system of supports and safeguards, to educate and inform frontline public health workers, and to engage the public at large in an open dialogue on the ethical use of restrictive measures during infectious disease outbreaks. In view of the evidence of potential adverse effects on individual well-being and psychosocial health, and owing to the critical necessity of high compliance in the event of a major infectious disease outbreak, it is increasingly important to understand how quarantine is perceived by the general public. The data reported in this paper are derived from a subset of 15 survey items specifically designed to measure public attitudes towards the use of quarantine during infectious disease outbreaks. cache = ./cache/cord-258435-lhn34tc4.txt txt = ./txt/cord-258435-lhn34tc4.txt === reduce.pl bib === id = cord-258681-66ct8nod author = Warnock, David G. title = Clinical Trials during the SARS-CoV-2 Pandemic date = 2020-04-14 pages = extension = .txt mime = text/plain words = 731 sentences = 43 flesch = 52 summary = The primary outcome measures of this trial include the incidence of active COVID-19-related disease at 14 days post-enrollment, and a COVID-19 Disease Severity Scale self-reported by participants at 14 days post-enrollment: no COVID-19-related disease (score of 1); COVID-19-related disease with no hospitalization (score of 2); or COVID-19-related disease with hospitalization or death (score of 3).The goal is to enroll and randomize 1,500 subjects into each of the active-drug and placebo arms, followed by a 6-day treatment course with hydroxychloroquine. Secondary outcome measures include 14-day incidence of hospitalization, 14-day incidence of confirmed SARS-CoV-2 infection, the number of participants in each arm who discontinue or withdraw from the protocol, and 90-day incidence of death related to COVID-19-related disease. The trial includes a chartered Data Safety Monitoring Board with defined stopping rules for clinical futility or statistically significant improvement in the primary outcome measures comparing the active-drug group to the placebo group (personal communication, March 22, 2020: covid19faq COVID-1-Post-Exposure Prophylaxis FAQ Account). cache = ./cache/cord-258681-66ct8nod.txt txt = ./txt/cord-258681-66ct8nod.txt === reduce.pl bib === id = cord-258548-1u7v1nlr author = Mansueto, Gelsomina title = Can COVID 2019 disease induces a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? date = 2020-06-26 pages = extension = .txt mime = text/plain words = 5924 sentences = 280 flesch = 35 summary = Only one case of cardiac tamponade in a 47-year-old man SARS-CoV-2 infected without cardiovascular risk is reported in the literature as a complication of myocarditis and pericarditis (29) . Large and more recent studies have reported that previous myocardial infarction, diabetes, J o u r n a l P r e -p r o o f dyslipidaemias, hypertension, and other cardiovascular risk factors can predispose to an acute ischemic event in respiratory virus infections such as recently reported during the pandemic COVID-19 disease (34, 35, 36) . It is known that patients with cardiovascular disease have a higher risk of a thrombo-embolic event as it is known that all viral infections have a potential role in disseminated intravascular coagulation J o u r n a l P r e -p r o o f (DIC) The endothelial damage, the blood flow turbulence, and hypercoagulability are the basis of the mechanism. There is no substantial data to say that anti-RAAS, ACE inhibitors, statins increase the risk of cardiovascular damage in COVID patients. cache = ./cache/cord-258548-1u7v1nlr.txt txt = ./txt/cord-258548-1u7v1nlr.txt === reduce.pl bib === id = cord-258019-njky7v5x author = Kinaret, Pia A.S. title = Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1359 sentences = 79 flesch = 40 summary = However, similarities between the responses to SARS-CoV-2 and certain nanomaterials suggest fibrotic pulmonary disease as a concern for public health in the next future. Also rigid multi-walled carbon nanotubes (rMWCNT), among other nanomaterials, induce innate immune response by activation of NF-κB, STAT3 and HIF-1/2, and consequent cytokine cascade [15, 16] . As the Covid-19 disease progresses, massive damage of the pulmonary tissue occurs by induction of an uncontrolled innate immune response, mainly mediated by M1 pro-inflammatory macrophages and granulocytes. Moreover, up-regulation of antigen processing pathways, RIG-1 and several viral-induced human disease pathways have been reported consequently to carbon nanomaterial exposure, both in vitro [23] and in murine lung in vivo [19, 24] . On the other hand, certain nanoparticles might induce lung fibrosis by a combination of metabolic tissue damage and primary activation of the innate immune cells. Here we summarized noticeable cellular and molecular similarities between the acute responses to both SARS-CoV-2 infection and certain nanomaterials exposure. cache = ./cache/cord-258019-njky7v5x.txt txt = ./txt/cord-258019-njky7v5x.txt === reduce.pl bib === id = cord-258221-pn8gh73b author = Rocha, José Lucas Martins title = Mesenchymal Stromal Cells in Viral Infections: Implications for COVID-19 date = 2020-09-07 pages = extension = .txt mime = text/plain words = 8950 sentences = 487 flesch = 42 summary = Abbreviations: ANG, Angiogenin; ANGPT1, Angiopoietin 1; bFGF, Basic fibroblast growth factor; BV/BR, Biliverdin and Bilirubin; COX2, Cyclooxygenase-2; DAMPs, Damage-associated molecular pattern; EGF, Epidermal growth factor; ESM1, Endothelial Cell Specific Molecule 1; FAS/FASL, apoptosis antigen 1 receptor and ligand; HGF, Hepatocyte growth factor; HLA-G, Human leukocyte antigen G; HO-1, Heme oxygenase 1; IDO, Indoleamine 2,3-dioxygenase; ISGs, Interferon-stimulated genes; Kyn, Kynurenin; LIF, Leukemia inhibitory factor; LPS, Lipopolysaccharide; miRNAs, micro RNA; MMPs, Matrix metalloproteinases; MSC-EV, Extracellular vesicles from MSC; PAMPs, Pathogen-associated molecular pattern; PGE2, Prostaglandin E2; PD-1/PD-L1, Programmed death receptor and ligand; ROS, Reactive oxygen species; SOD, Superoxide dismutase; sHLA-G, Soluble human leukocyte antigen G; sPD-L1/2, Soluble Programmed death ligands 1 and 2; TGF-β, Transforming growth factor β; TLR, Toll-like receptor; TNF-α, Tumor necrosis factor α; Trp , Tryptophan; TSG-6, TNFstimulated gene 6 Similarly, long-lasting FASL interactions enable MSCs to induce T cell apoptosis [39] . cache = ./cache/cord-258221-pn8gh73b.txt txt = ./txt/cord-258221-pn8gh73b.txt === reduce.pl bib === id = cord-258701-jyzxu9nk author = Kaushal, Darwin title = Endoscopy in Otorhinolaryngology During Corona Outbreak: A Proposal for Safe Practice date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2464 sentences = 184 flesch = 54 summary = In this article, we propose essential steps that can be implemented at the departmental and institutional levels to do endoscopic diagnostic procedures effectively during COVID-19 outbreak and to break the transmission chain. Coronavirus disease 2019 (COVID-19) is a type of viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Person-toperson transmission is thought to occur among close contacts mainly via respiratory droplets produced when an infected person coughs or sneezes, which is very common in endoscopic procedures in Otorhinolaryngology. • Deep cleaning and fumigation of the room should be performed when a reverse transcriptase-polymerase chain reaction COVID-19 positive patient undergoes a procedure. • When possible, procedures on COVID-19 suspect/positive patients should be performed as the last procedure, and the endoscopy room should be thoroughly ventilated for at least 1 h before the next procedure by using blowers or natural ventilation. cache = ./cache/cord-258701-jyzxu9nk.txt txt = ./txt/cord-258701-jyzxu9nk.txt === reduce.pl bib === id = cord-258722-1o6zhnnj author = Gbinigie, Kome title = Should azithromycin be used to treat COVID-19? A rapid review date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3320 sentences = 193 flesch = 50 summary = In vivo and in vitro studies were included assessing the safety and effectiveness of azithromycin for treatment of COVID-19, and/or the activity of azithromycin against SARS-CoV-2. In another pre-print, Andreania and colleagues 13 report the results of an in vitro study assessing the activity of azithromycin and hydroxychloroquine against SARS-CoV-2. In vivo research effectiveness Only one trial was identified on the effectiveness of azithromycin for the treatment of COVID-19, conducted by Gautret and colleagues in France and reported in a pre-print 14 (see Table 1 ). The same research team that conducted the in vivo study included in this review conducted a singlearm trial of 80 patients who tested positive for SARS-CoV-2 and showed mild symptoms, 17 to further assess the effectiveness of the combined hydroxychloroquine/azithromycin treatment regime. No in vivo studies were identified assessing the safety or effectiveness of azithromycin as a standalone treatment for COVID-19. cache = ./cache/cord-258722-1o6zhnnj.txt txt = ./txt/cord-258722-1o6zhnnj.txt === reduce.pl bib === id = cord-258725-z79gel8h author = Wood, R. title = Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5315 sentences = 272 flesch = 53 summary = Methods Using a Scotland-wide record-linkage based occupational cohort comprising healthcare workers and members of their households, we examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalisation with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). Similar, but slightly stronger associations were found when the analysis was restricted to households where at least one member of staff had a patient-facing role (fully adjusted model, HR per child 0.83; 95% CI 0.68-1.02, Supplementary Table S3), a group with greater occupational exposure to SARS-CoV-2 than non-patient facing healthcare workers, although on formally testing for an interaction between patient facing and non-patient facing groups, the coefficient included the null, (P-value for interaction = 0.80). cache = ./cache/cord-258725-z79gel8h.txt txt = ./txt/cord-258725-z79gel8h.txt === reduce.pl bib === id = cord-258614-7unadw41 author = Ogidigo, Joyce Oloaigbe title = Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach date = 2020-10-25 pages = extension = .txt mime = text/plain words = 8459 sentences = 416 flesch = 47 summary = Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M(pro)) SARS-CoV-2. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; −41.1 and −43.4 kcal/mol) against the M(pro) of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Thus, among the 86 phytocompounds and 3 antiviral drugs screened (Supplementary material Table S1 ), 6 phyto ligands exhibited appreciable binding energies against the SARS-CoV-2 M pro and strong interactions within the binding pocket. Analysis of the per-residue additional showed that studied compounds interact with these key amino acid residues in the active site of the main protease, suggesting that these phytocompounds could emerge as ideal candidate's inhibitors against SARS-CoV-2 M pro and another virus protease. cache = ./cache/cord-258614-7unadw41.txt txt = ./txt/cord-258614-7unadw41.txt === reduce.pl bib === id = cord-258844-b4d79m1f author = Denning, M. title = DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY date = 2020-07-18 pages = extension = .txt mime = text/plain words = 3793 sentences = 237 flesch = 49 summary = Methods From 22nd March 2020 to 18th June 2020, healthcare workers from the United Kingdom, Poland, and Singapore were invited to participate using a self-administered questionnaire comprising the Safety Attitudes Questionnaire (SAQ), Oldenburg Burnout Inventory (OLBI) and Hospital Anxiety and Depression Scale (HADS) to evaluate safety culture, burnout and anxiety/depression. Significant predictors of burnout included patient-facing roles: doctor (OR 2.10; 95% CI 1.49-2.95), nurse (OR 1.38; 95% CI 1.04-1.84), and other clinical staff (OR 2.02; 95% CI 1.45-2.82); being redeployed (OR 1.27; 95% CI 1.02-1.58), bottom quartile SAQ score (OR 2.43; 95% CI 1.98-2.99), anxiety (OR 4.87; 95% CI 3.92-6.06) and depression (OR 4.06; 95% CI 3.04-5.42). This study aims to describe the prevalence and predictors of burnout, anxiety and depression in healthcare workers during the Covid-19 pandemic. The survey consisted of four parts; demographic questions followed by 3 validated psychometric instruments; the Safety Attitudes Questionnaire, Oldenburg Burnout Inventory and Hospital Anxiety and Depression Scale. cache = ./cache/cord-258844-b4d79m1f.txt txt = ./txt/cord-258844-b4d79m1f.txt === reduce.pl bib === id = cord-258624-041cf99j author = Ahmad, Sajjad title = Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date = 2020-05-23 pages = extension = .txt mime = text/plain words = 8187 sentences = 434 flesch = 48 summary = title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. In order to estimate the MMPBSA binding free energies for the receptors and multi-epitope peptide vaccine construct, the MMPBSA.py module [56] of AMBER16 was castoff. The B-cell epitopes predicted for the vaccine candidates were in the following order: nine for Nsp8 and 3C-like proteinase, five for Nsp9, eight for Nsp10, 34 for spike glycoprotein and surface glycoprotein, and four for ORF1ab polyprotein| partial. Molecular interactions and binding conformation of the designed MEPVC with TLR3 and TLR4 innate immune receptors were deciphered via a protein-peptide docking approach. The dynamic simulations of the human immune system in response to the designed vaccine construct were deciphered through C-immsim server [40] . cache = ./cache/cord-258624-041cf99j.txt txt = ./txt/cord-258624-041cf99j.txt === reduce.pl bib === id = cord-258708-da6x5rxa author = Hafiane, Anouar title = SARS-CoV-2 and the cardiovascular system date = 2020-07-16 pages = extension = .txt mime = text/plain words = 4033 sentences = 253 flesch = 43 summary = The coronavirus disease COVID-19 is a public health emergency caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In COVID-19, particular attention has been given to the role of angiotensin-(Ang) converting enzyme 2 (ACE2), and the binding site for SARS-CoV-2 cellular entry (3). One of the clinical features of patients infected with SARS-CoV-2 included abnormal features such as acute cardiac injury (12%) (22) . Significance of the SARS-CoV-2 infection in the CV system is reflected through incidences of acute myocardial injury, arrhythmias, ACS, sepsis, septic shock, viral myocarditis, and heart failure. Coronavirus Disease 2019 (COVID-19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin-Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection 19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin‐Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection cache = ./cache/cord-258708-da6x5rxa.txt txt = ./txt/cord-258708-da6x5rxa.txt === reduce.pl bib === id = cord-258630-mvz2l3yj author = Liu, Tiantian title = A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date = 2020-11-10 pages = extension = .txt mime = text/plain words = 11041 sentences = 596 flesch = 57 summary = We compared seven different library construction protocols and specifically evaluated the cross-protocol performance in sequencing read mappability, viral genome coverage percentage and uniformity, effect of sequence depth, SNV calling concordance (reproducibility), precision (positive predictive value), and sensitivity (proportion of consensus variants identified at different sequencing depths and viral copy number inputs) across protocols. Here, we compared seven WGS protocols for SARS-CoV-2 using clinical samples from infected patients, benchmarking the performances of these protocols in several aspects including the sequencing read mappability, genome coverage (percentage and uniformity, minimum sequences required); sample storage condition; effects of viral input, sequencing depth, length and platform; sensitivity, reproducibility and precision of SNV calling and related assay factors (e.g., amount of viral input, sequencing depth and bioinformatics pipeline). cache = ./cache/cord-258630-mvz2l3yj.txt txt = ./txt/cord-258630-mvz2l3yj.txt === reduce.pl bib === id = cord-258905-0hgdtalg author = Bond, Katherine title = Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3663 sentences = 176 flesch = 44 summary = METHODS: Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). A testing panel was specifically developed to test PoCT devices for this study (Supplementary Material), consisting of 3 patient populations: (1) sera from 91 patients with SARS-CoV-2 detected by RT-PCR from upper and/or lower respiratory tract specimens; (2) sera from 36 patients with seasonal coronavirus infections or other acute infections (eg, dengue, cytomegalovirus, Epstein-Barr virus); and (3) serum from a random cohort (56 patients) of the Australian population obtained in 2018. In this study, we assessed the performance characteristics of 5 serological PoCT, a commercial ELISA, and a commercial novel sVNT against a large serum panel from a cohort of over 100 patients with RT-PCR-confirmed SARS-CoV-2. cache = ./cache/cord-258905-0hgdtalg.txt txt = ./txt/cord-258905-0hgdtalg.txt === reduce.pl bib === id = cord-258250-zueo1xfa author = Hirotsu, Yosuke title = Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3105 sentences = 184 flesch = 55 summary = title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . cache = ./cache/cord-258250-zueo1xfa.txt txt = ./txt/cord-258250-zueo1xfa.txt === reduce.pl bib === id = cord-258084-nkr3lrov author = Juthani, Prerak title = Coronavirus Disease 2019 (COVID-19) Manifestation as Acute Myocardial Infarction in a Young, Healthy Male date = 2020-07-11 pages = extension = .txt mime = text/plain words = 1753 sentences = 91 flesch = 48 summary = In this case report, we describe a 29-year-old nonobese hospital food service associate who presented with diffuse abdominal and chest pain; he was found to be positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significantly elevated levels of troponin T and multiple acute phase reactants; his EKG demonstrated ST-elevations consistent with anterolateral infarction. In this case report, we discuss a young patient who tested positive for SARS-CoV-2 and subsequently developed significant cardiovascular complications. We believe that this case is unique because this was a young, athletic patient with minimal risk factors for coronary disease who tested positive for COVID-19 and developed an acute MI with STEMI and required stent placement. It is a reminder to us that cardiovascular complications must be considered in the COVID-19 population, even in those patients with minimal risk factors for heart disease. cache = ./cache/cord-258084-nkr3lrov.txt txt = ./txt/cord-258084-nkr3lrov.txt === reduce.pl bib === id = cord-258859-iaiosjlu author = Wang, Jiao title = Mask use during COVID-19: A risk adjusted strategy() date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2683 sentences = 159 flesch = 53 summary = In the context of Coronavirus Disease (2019) (COVID-19) cases globally, there is a lack of consensus across cultures on whether wearing face masks is an effective physical intervention against disease transmission. This study 1) illustrates transmission routes of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); 2) addresses controversies surrounding the mask from perspectives of attitude, effectiveness, and necessity of wearing the mask with evidence that the use of mask would effectively interrupt the transmission of infectious diseases in both hospital settings and community settings; and 3) provides suggestion that the public should wear the mask during COVID-19 pandemic according to local context. The mask is generally used 278 by general public, while the respirator or a filtering face piece, which is designed to 279 protect the wearer from exposure to airborne contaminants, is mainly used by health care 280 workers especially during AGP (European Centre for Disease Prevention and Control, 281 2020). cache = ./cache/cord-258859-iaiosjlu.txt txt = ./txt/cord-258859-iaiosjlu.txt === reduce.pl bib === id = cord-258128-qtmjgrml author = Mirjalili, Mahtabalsadat title = Coronavirus Disease 2019 (COVID-19) and Transplantation: Pharmacotherapeutic Management of Immunosuppression Regimen date = 2020-07-03 pages = extension = .txt mime = text/plain words = 6450 sentences = 369 flesch = 38 summary = 12 In one case report regarding the successful treatment of a kidney transplant recipient with pneumonia caused by SARS-CoV-2 in China, all the immunosuppressants were stopped and the patient received 5 g intravenous immunoglobulin (IVIG) on the first day and then 10 g/day for the next 11 days, with 40 mg/day methylprednisolone for 12 days and 5 million units/day interferon as atomization inhalation. 17, 18 Considering that adverse clinical outcomes and increased mortality and morbidity following the administration of corticosteroids in patients with respiratory infections caused by respiratory syncytial virus (RSV), influenza, SARS-CoV-1, or MERS-CoV may be due to an increased risk of secondary bacterial infections, their use for the prevention of disease progression or its treatment remains under discussion. So far, few studies have been conducted regarding the use of this drug in liver and kidney transplant patients, but if it is administered to this population, its adverse effects and interactions with immunosuppressants and other medications used in transplant patients, such as fluoroquinolones for the treatment of Gram-negative infections, should be considered. cache = ./cache/cord-258128-qtmjgrml.txt txt = ./txt/cord-258128-qtmjgrml.txt === reduce.pl bib === id = cord-258223-8dhtwf03 author = Chow, Cristelle title = The Next Pandemic: Supporting COVID-19 Frontline Doctors Through Film Discussion date = 2020-09-05 pages = extension = .txt mime = text/plain words = 4749 sentences = 185 flesch = 41 summary = Themes derived from the film included preparedness, blame, and the impact on healthcare workers and public, which were further discussed to include concerns regarding current local readiness levels given global connectivity, the need for international cooperation, and the effects of blame such as racism and prejudice. These rich discussions demonstrate the pivotal role health humanities has in times of uncertainty such as an emerging infectious disease outbreak by providing timely pandemic education and supporting reflective learning. Hence, as the world experiences the current COVID-19 pandemic situation, this study aims to describe the use of a short film and post-film discussion to educate and support frontline doctorsin-training during an acute emerging infectious disease outbreak. While the focus of this study was on the implementation of a timely film screening and discussion, the themes that emerged from the guided reflections were insightful and can inform future pandemic-preparedness efforts for frontline healthcare staff. cache = ./cache/cord-258223-8dhtwf03.txt txt = ./txt/cord-258223-8dhtwf03.txt === reduce.pl bib === id = cord-258792-4lakgpxp author = Yoon, Sung‐Won title = Sovereign Dignity, Nationalism and the Health of a Nation: A Study of China's Response in Combat of Epidemics date = 2008-04-08 pages = extension = .txt mime = text/plain words = 7935 sentences = 341 flesch = 50 summary = Unless and until the Chinese leadership examines the nationalistic element embedded in their approach towards growing disease Sung-Won Yoon: Sovereign Dignity, Nationalism and the Health of a Nation epidemics and globalising health challenges, China's ascendance to great power status will actually be harmed rather than helped. A major factor behind the government's recent change in its attitude towards the AIDS epidemic seemed to be the outbreak of SARS in China in Studies in Ethnicity and Nationalism: Vol. 8, No. 1, 2008 2003, which exposed the dangers of not reacting to emerging infectious diseases. It is argued that global health governance may influence the nation's response to the threats posed by emerging infectious diseases such as SARS or AIDS as a mode of building political compromises but does not considerably alter the nation's behaviour, at least for China. cache = ./cache/cord-258792-4lakgpxp.txt txt = ./txt/cord-258792-4lakgpxp.txt === reduce.pl bib === id = cord-258431-8zgwj2fa author = Strafella, Claudia title = Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications date = 2020-07-03 pages = extension = .txt mime = text/plain words = 4055 sentences = 203 flesch = 42 summary = The eQTLs analysis located in and targeting ACE2 revealed a high distribution of eQTL variants in different brain tissues, suggesting a possible link between ACE2 genetic variability and the neurological complications in patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. Moreover, they found a higher allelic frequency of eQTL variants, which is associated with higher ACE2 expression in tissues, suggesting a different susceptibility or response to SARS-Cov-2 infection with respect to other populations under similar conditions [28] . cache = ./cache/cord-258431-8zgwj2fa.txt txt = ./txt/cord-258431-8zgwj2fa.txt === reduce.pl bib === id = cord-258268-7ypq0t3d author = Zanin, Luca title = SARS-CoV-2 can induce brain and spine demyelinating lesions date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1481 sentences = 113 flesch = 47 summary = On January 24, 2020, a new virus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been identified, quickly gaining worldwide attention [21] . Similarly to other Coronavirus, SARS-CoV-2 can attack the olfactory bulb and then affect the central nervous system (CNS) through the olfactory tract in the early stages of infection [5] . Neurological impairment and demyelinating reaction appear as complications in case of severe Coronavirus Disease 2019 (COVID-19) [10] . Our patient showed symptoms consistent with a neurological involvement consequent to SARS-CoV-2 infection. In SARS-CoV-2 infection, neurological impairment was observed only in case of severe COVID-19 [10] . SARS-CoV-2 was not detected in the CSF probably because the neurological damage was sustained by a delayed immune response that occurred after the viremia. Sudden neurological impairment with seizures in COVID-19 patients may be sustained by CNS involvement and demyelinating lesions. Neurologic features in severe SARS-CoV-2 infection cache = ./cache/cord-258268-7ypq0t3d.txt txt = ./txt/cord-258268-7ypq0t3d.txt === reduce.pl bib === id = cord-258595-bk35vxlr author = Westhaus, Sandra title = Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4965 sentences = 305 flesch = 57 summary = Inoculation of differentiated Caco-2 cells for ten days with purified and concentrated wastewater (P2, P5, P11, and P12) did not result in the production of infectious SARS-CoV-2 particles (data not shown), which suggests that treated sewage appears to be non-infectious even though viral RNA fragments can be detected. Inter-comparing these nine catchment areas, we plotted the estimated cumulative and the acute prevalence against the measured SARS-CoV-2 load (Figure 8 ), the latter calculated from RT-qPCR measured M-gene copy concentration ( Figure 4 ) and the actual wastewater flow Q actual on the day of sampling (Table 2) . In contrast, plotting the incidence against SARS-CoV-2 concentration did not yield a conclusive correlation (not shown), likely because the precision of the qPCR employed was not sufficient to discriminate relatively minor differences in the incidence prevailing in the studied catchment areas at the time of sampling, ranging from 30 to 174 cases per 100,000 residents (less than an order of magnitude, Figure 8C and D). cache = ./cache/cord-258595-bk35vxlr.txt txt = ./txt/cord-258595-bk35vxlr.txt === reduce.pl bib === id = cord-258312-3v5t4k8d author = Majachani, Nicole title = A Case of a Newborn Baby Girl Infected with SARS-CoV-2 Due to Transplacental Viral Transmission date = 2020-10-25 pages = extension = .txt mime = text/plain words = 1962 sentences = 131 flesch = 51 summary = Patient: Female, 31-year-old Final Diagnosis: COVID-19 • SARS-CoV-2 Symptoms: Asymptomatic Medication:— Clinical Procedure: — Specialty: Pediatrics and Neonatology OBJECTIVE: Unusual clinical course BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious virus and is responsible for the current pandemic. CASE REPORT: 31-year-old Hispanic woman in the final week of pregnancy developed mild respiratory symptoms of COVID-19 pneumonia and tested positive for SARS-CoV-2 infection. In response to the potential risks to both the mother and fetus, the American College of Obstetricians and Gynecologists, the American Academy of Pediatrics, and the Centers for Disease Control have developed guidelines which provide a framework for detecting infections early and preventing potential transmission of SARS-CoV-2. Although similar viruses like severe acute respiratory syndrome coronavirus 1 have not demonstrated the ability to cause fetal infection, SARS-CoV-2 is able to bind ACE2 with much higher affinity [11] , thus increasing the probability of transplacental transmission. cache = ./cache/cord-258312-3v5t4k8d.txt txt = ./txt/cord-258312-3v5t4k8d.txt === reduce.pl bib === id = cord-259185-qg4jwbes author = Vadlamani, B. S. title = Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date = 2020-09-09 pages = extension = .txt mime = text/plain words = 3988 sentences = 249 flesch = 51 summary = In this work, we report the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor and its efficacy for rapid detection of spike glycoprotein of SARS-CoV-2 by examining S-RBD protein as the reference material. Our manuscript reports the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor for rapid detection of spike glycoprotein of SARS-CoV-2. . https://doi.org/10.1101/2020.09.07.20190173 doi: medRxiv preprint asymptomatic individuals are needed, which is feasible only after the development of a simple, portable and rapid point-of-use sensor for the detection of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data showed that cobalt functionalized TNTs could selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~ 30 secs. cache = ./cache/cord-259185-qg4jwbes.txt txt = ./txt/cord-259185-qg4jwbes.txt === reduce.pl bib === id = cord-258172-p54j4zzo author = Barker, Harlan title = Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date = 2020-10-28 pages = extension = .txt mime = text/plain words = 8453 sentences = 409 flesch = 48 summary = Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . cache = ./cache/cord-258172-p54j4zzo.txt txt = ./txt/cord-258172-p54j4zzo.txt === reduce.pl bib === id = cord-259084-lwh3rww4 author = Anderson, Cole title = Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1002 sentences = 66 flesch = 52 summary = title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations. This protocol allows for 35 the rapid detection of SARS-CoV-2 RNA from clinical specimens such as, nasopharyngeal and 36 oropharyngeal swabs, sputum, bronchoalveolar lavage, and tracheal aspirates. 43 In this study, we examined the feasibility of pooling nasopharyngeal swab specimens submitted 44 for COVID-19 testing using the CDC 2019-nCoV RT-PCR diagnostic panel without compromising 45 Specimens were submitted to 54 the Virology laboratory at Landstuhl Regional Medical Center for routine SARS-CoV-2 testing 55 using the CDC 2019-nCoV RT-PCR assay. Pooling nasopharyngeal/throat swab specimens to increase testing 176 capacity for influenza viruses by PCR cache = ./cache/cord-259084-lwh3rww4.txt txt = ./txt/cord-259084-lwh3rww4.txt === reduce.pl bib === id = cord-258902-h0wrs01h author = Liu, Xianglei title = Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5015 sentences = 268 flesch = 52 summary = title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice The cell-cell fusion assay results correlated well with the virus neutralization potency and could be used for high-throughput screening of large panels of anti-SARS-CoV-2 antibodies and vaccines without the requirement of live virus infection in BSL3 containment. Based on its highly homology to SARS-CoV, SARS-CoV-2 RBD is corroborated to contain immune dominant epitopes capable of eliciting antibodies that can neutralize viral infection and block viral entry by competing hACE2 Pseudovirus neutralization assay was then performed by incubation of SARS-CoV-2 pseudovirus with serially diluted mice serum for 1h at 37 °C, followed by addition of the mixture into pre-seeded 293T-ACE2 cells. On day 0 (pre-immunization), day 13 and day 27, mouse sera were collected and analyzed for RBD binding, pseudovirus and live virus neutralization, and cell-cell fusion inhibition. cache = ./cache/cord-258902-h0wrs01h.txt txt = ./txt/cord-258902-h0wrs01h.txt === reduce.pl bib === id = cord-258873-l9oxmqdp author = Baker, D. title = COVID‐19 vaccine‐readiness for anti‐CD20‐depleting therapy in autoimmune diseases date = 2020-08-01 pages = extension = .txt mime = text/plain words = 6017 sentences = 323 flesch = 44 summary = It appears that the innate immune response, and perhaps later anti-viral CD8 T cell responses, could eliminate the SARS-CoV2 before significant antibody responses have developed [20, 28, 33] (Fig. 1) , suggesting that most MS treatments that largely exhibit limited persistent effects on the innate immune and CD8 T cell responses would have limited influence on COVID-19. The suggestion that rituximab treatment may increase risk of infection should be considered in the context of possible sampling biases, although this Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells in the lung and the gut via the angiotensin-converting enzyme 2 (ACE2). If COVID-19-related vaccine responses become a key concern among people with MS or other autoimmune diseases choosing treatment options, the selection of B cell-depleting agents that allow quick repopulation of B cells may be relevant for optimum vaccine readiness. cache = ./cache/cord-258873-l9oxmqdp.txt txt = ./txt/cord-258873-l9oxmqdp.txt === reduce.pl bib === id = cord-259200-65b267ic author = Harypursat, Vijay title = Six weeks into the 2019 coronavirus disease outbreak: it is time to consider strategies to impede the emergence of new zoonotic infections date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1705 sentences = 77 flesch = 47 summary = Subsequent to the severe acute respiratory syndrome (SARS) outbreak in China 2003, and the Middle East respiratory syndrome (MERS) outbreak in the Middle East in 2012, global concerns regarding the pathogenicity and epidemic/pandemic potential of novel human coronaviruses began to emerge, with some experts predicting that novel coronaviruses could likely again cross the species barrier and present humans with future pandemic-potential infections. 2019-nCoV is the seventh coronavirus species that is now known to infect humans, is also zoonotic in origin, and is the causative organism for the current viral pneumonia epidemic in China. The complete ban on market trading and sale of wild game meat in China on January 26th, 2020 will help prevent zoonotic transmission of 2019-nCoV in the current epidemic and, to a certain degree, help prevent emergence of new zoonotic infections. cache = ./cache/cord-259200-65b267ic.txt txt = ./txt/cord-259200-65b267ic.txt === reduce.pl bib === id = cord-258533-gds7sdc9 author = Lytras, Theodore title = High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries date = 2020-04-16 pages = extension = .txt mime = text/plain words = 357 sentences = 28 flesch = 50 summary = title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries Passengers on repatriation flights to Greece from the UK, Spain and Turkey were screened with oropharyngeal swabs on arrival for SARS-CoV-2 infection. Despite almost all passengers being asymptomatic, many tested positive (3.6% from UK, 6.3% from Spain and 6.3% from Turkey), indicating widespread transmission of SARS-CoV-2 in these countries. Even more remarkably, the infection prevalence in these passengers was much higher than in the repatriation flights from Wuhan during the peak of the epidemic there, which was reported as <1%. Estimating infection prevalence in Wuhan City from repatriation flights Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries Estimating the ascertainment rate of SARS-CoV-2 infection in Wuhan, China: implications for management of the global outbreak cache = ./cache/cord-258533-gds7sdc9.txt txt = ./txt/cord-258533-gds7sdc9.txt === reduce.pl bib === id = cord-259223-6b07qiw2 author = Feitosa, Eduardo L title = COVID-19: Rational discovery of the therapeutic potential of Melatonin as a SARS-CoV-2 main Protease Inhibitor date = 2020-07-30 pages = extension = .txt mime = text/plain words = 6844 sentences = 322 flesch = 40 summary = Molecular docking studies described the binding sites and the interaction energies of 74 Mpro-ligand complexes deposited in the Protein Data Bank (PDB). The search for structural similarity used the 10 hit molecules that presented the best interaction energies (Kcal/mol) measured in the docking study among all 74 ligand-Mpro complexes from PDB. The selected hits (top 10 best-scored compounds identified by previous docking study), as well as their respective similar binders, were docked into SARS-CoV-2 main protease (Mpro) with unliganded active site (PDB id: 6Y84). The interaction between melatonin and Mpro (Figure 4) improved the values of binding energy and created a new perspective for a molecule with high therapeutic potential over the COVID-19 pathology to act, so far, only in more severe cases of the disease. To understand the need to clinically evaluate melatonin against Cov-2, we should make a brief introduction to infectious and physiopathological characteristics related mainly to the viral cycle and host immune response in the COVID-19 ( Figure 5) . cache = ./cache/cord-259223-6b07qiw2.txt txt = ./txt/cord-259223-6b07qiw2.txt === reduce.pl bib === id = cord-258724-1qhen1bj author = Young, Barnaby E title = Viral dynamics and immune correlates of COVID-19 disease severity date = 2020-08-28 pages = extension = .txt mime = text/plain words = 3612 sentences = 253 flesch = 52 summary = METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). In this multi-pronged study, we describe the serologic evolution, inflammatory response and pattern of viral shedding and viability in patients with virologically confirmed COVID-19 in Singapore, and analyse the contributions these make to severe infections. Serum collected during the acute and convalescent phases of infection were tested for SARS-CoV-2 receptor binding domain specific IgM and IgG using capture ELISA (details in Supplementary Appendix). The central role of the immune response to SARS-CoV-2 in COVID-19 was evident from the strong correlation between disease severity and levels of IgG/IgM and inflammatory immune mediators in our cohort. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study cache = ./cache/cord-258724-1qhen1bj.txt txt = ./txt/cord-258724-1qhen1bj.txt === reduce.pl bib === id = cord-259261-fmuozy3w author = Bickler, Stephen W. title = AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2039 sentences = 130 flesch = 55 summary = title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. We also asked the question if the differentially expressed genes between the oldest and youngest age groups encode proteins that interact with SARS-CoV-2 (see "Methods" section). Our analysis revealed eleven differentially expressed genes between the oldest and youngest age groups that encode proteins known to interact with SARS-CoV-2 (Fig. 3d) . Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts we show that expression of PRR genes and ACE2, the receptor for SARS-CoV-2 vary with age. cache = ./cache/cord-259261-fmuozy3w.txt txt = ./txt/cord-259261-fmuozy3w.txt === reduce.pl bib === id = cord-259238-n2uuaof6 author = Zhang, Bao-Zhong title = SARS-CoV-2 infects human neural progenitor cells and brain organoids date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1887 sentences = 136 flesch = 51 summary = To explore the direct involvement of SARS-CoV-2 in the CNS in physiologically relevant models, we assessed SARS-CoV-2 infection in induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and brain organoids. Importantly, extensive SARS-CoV-2 antigen was detected in the infected samples at 72 hpi (Fig. 1f) , indicating that SARS-CoV-2 directly infected the brain organoids. The results demonstrated SARS-CoV-2 RdRp gene copy number increased in a timedependent manner, suggesting active release of progeny virus particles from infected brain organoids (Fig. 1g, left) . Plaque assays performed on supernatant samples from brain organoids infected with SARS-CoV-2 showed that the infectious virus titer peaked at 24 hpi and were continuously detected at 48 and 72 hpi. h Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and TUJ1. i Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and NESTIN. cache = ./cache/cord-259238-n2uuaof6.txt txt = ./txt/cord-259238-n2uuaof6.txt === reduce.pl bib === id = cord-259572-8n12n6ym author = Bogensperger, Christina title = Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report date = 2020-07-22 pages = extension = .txt mime = text/plain words = 931 sentences = 62 flesch = 46 summary = title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. Here we present the case of a liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine preservation (NMP), which we have recently established as a routine in liver transplantation (6). cache = ./cache/cord-259572-8n12n6ym.txt txt = ./txt/cord-259572-8n12n6ym.txt === reduce.pl bib === id = cord-259523-92hz534s author = Pullen, Lara C. title = COVID‐19: transplant works toward adaptation date = 2020-09-29 pages = extension = .txt mime = text/plain words = 1642 sentences = 93 flesch = 52 summary = These recommendations state that during the COVID-19 pandemic, deceased donor kidney transplantations should be performed only if it is possible to transplant a SARS-CoV-2 negative organ into a SARS-CoV-2 negative patient, and that renal transplantation should be prioritized for recipients facing urgent clinical conditions "because frequent healthcare contact due to the severity of their underlying disease means that these patients will remain at high risk for acquiring SARS-CoV-2, a risk that might be greater than the risk of SARS-CoV-2 acquisition through successful transplantation," says Dr. Remuzzi. Currently, the American Society of Transplantation and the ISOT do not recommend the use of organs from living donors who are SARS-CoV-2 positive or classifi ed as high risk after screening. Recently, colleagues at Dr. Remuzzi's institution reported the presence of SARS-CoV-2 in the kidney, and the potential for donor-derived COVID-19 infection remains unknown. Dr. Potena estimates that in a typical winter, 20 to 25% of the transplant center's patients have COVID-like symptoms. cache = ./cache/cord-259523-92hz534s.txt txt = ./txt/cord-259523-92hz534s.txt === reduce.pl bib === id = cord-259033-op94wuy4 author = Wendling, Daniel title = Can SARS-CoV-2 trigger reactive arthritis? date = 2020-10-27 pages = extension = .txt mime = text/plain words = 1193 sentences = 73 flesch = 42 summary = The potential mechanisms at the origin of arthritis in a context of viral infection by SARS-CoV-2 remain at the hypothesis stage. The mechanism of reactive arthritis is plausible, due to the clinical presentation, the delay between the onset (or diagnosis) of COVID and the onset of rheumatological manifestations, the usual negativation of nasopharyngeal RT-PCR at the time of onset of rheumatological involvement. However, cases of symptomatic SARS-CoV-2 infection have been reported in patients treated with an anti IL-17 monoclonal antibody for spondyloarthritis [19] . Arthritis may be reactive to a masked pulmonary or digestive infection as a consequence of COVID [13] , or it may be a non-specific consequence of the "cytokine storm" that accompanies the symptomatic forms of the disease [20] . This new infectious disease may induce rheumatological manifestations, with the possibility of reactive arthritis. Patient-reported Disease Activity in an Axial Spondyloarthritis Cohort during the COVID-19 Pandemic. A Case of Reactive Arthritis Secondary to Coronavirus Disease 2019 Infection Case of acute arthritis following SARS-CoV-2 infection cache = ./cache/cord-259033-op94wuy4.txt txt = ./txt/cord-259033-op94wuy4.txt === reduce.pl bib === id = cord-259585-mjtxiu0t author = Occhipinti, Vincenzo title = Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date = 2020-04-21 pages = extension = .txt mime = text/plain words = 2803 sentences = 122 flesch = 46 summary = Every possible effort was made to quickly increase the capacity of intensive care units (ICUs) to accommodate the alarming numbers of very sick CoViD-19 patients, including constructing new units in unused areas of the hospital or converting surgical rooms into ICUs. These drastic measures were implemented in a very short period of time, and although necessary to counteract the devastation brought about by the outbreak, they also posed tremendous challenges to the care of patients with GI conditions, including those with inflammatory bowel diseases (IBD). However, for patients on biologic therapies, we have implemented a mandatory phone call-in the day before any planned hospital visit to screen for possible CoViD-19 symptoms or contact with infected individuals and to reassure patients that all possible precautions are being taken by the IBD center to reduce the risk of infection. cache = ./cache/cord-259585-mjtxiu0t.txt txt = ./txt/cord-259585-mjtxiu0t.txt === reduce.pl bib === id = cord-259267-trpo5w11 author = Vilibic-Cavlek, Tatjana title = Severe acute respiratory syndrome coronavirus 2 seroprevalence among personnel in the healthcare facilities of Croatia, 2020 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 1490 sentences = 94 flesch = 48 summary = From April 25 to May 24, 2020, when the COVID-19 epidemic curve was approaching the end of the first wave in Croatia, a total of 592 serum samples from HCWs and allied/auxiliary HCWs were tested for the presence of SARS-CoV-2 antibodies. Two studies from the United Kingdom showed that 18% of symptomatic HCWs 6 and 3% of asymptomatic HCWs tested RT-PCR-positive for SARS-CoV-2 7 . Data are limited on the seroprevalence of COVID-19 among HCWs. In this study, using ELISA, SARS-CoV-2 IgG antibodies were detected in 2.7% of participants, while neutralizing antibodies were detected in 1.5% of participants, indicating a low seroprevalence among HCWs in Croatia. In the present study, three seropositive HCWs reported experiencing COVID-19-consistent clinical symptoms, while six were asymptomatic. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients cache = ./cache/cord-259267-trpo5w11.txt txt = ./txt/cord-259267-trpo5w11.txt === reduce.pl bib === id = cord-259347-3acsko74 author = Cheng, Qi title = Infectivity of human coronavirus in the brain date = 2020-05-28 pages = extension = .txt mime = text/plain words = 3981 sentences = 185 flesch = 42 summary = A new strain of human coronaviruses (hCoVs), Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has been identified to be responsible for the current outbreak of the coronavirus disease 2019 (COVID-19). Data from multiple hACE2 transgenic mouse models has revealed that SARS-CoV detection in the brain is significantly delayed compared to that within the lung, consistent with the initial establishment of infection within the respiratory system before dissemination to the CNS [21À23]. In addition, the detection of SARS-CoV in CSF of patients with neurological manifestation has also provided direct evidence for the neuroinvasion and neurovirulence of hCoVs. However, the role of the virus in the process of the disease in acute phase as well as in the long term still remains elusive. Severe acute respiratory syndrome coronavirus infection of mice transgenic for the human Angiotensin-converting enzyme 2 virus receptor cache = ./cache/cord-259347-3acsko74.txt txt = ./txt/cord-259347-3acsko74.txt === reduce.pl bib === id = cord-259852-skhoro95 author = Oboh, Mary Aigbiremo title = Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1661 sentences = 69 flesch = 42 summary = In addition to the Regional Disease Surveillance Systems Enhancement fund (US$600 million) provided by the World Bank for strengthening health systems and disease surveillance, each country should further establish an epidemic emergency fund for epidemic preparedness and response. Given the various epidemic events that have previously oc-curred in Africa, from Ebola virus disease (EVD) [4] to yellow fever, cholera, measles and Lassa fever [5] , it would almost be safe to assume that African governments have prepared proactive measures against possible future epidemics. A measure could have been applied to restrict travel even from countries with fewer than 100 confirmed SARS-CoV-2 cases given that the virus is highly transmissible, with a high reproductive number [3] . In addition to the REDISSE fund (US$600 million) created by the World Bank for strengthening health systems and disease surveillance, each country should further map out an epidemic emergency fund that will be used to address situations such as this in the future. cache = ./cache/cord-259852-skhoro95.txt txt = ./txt/cord-259852-skhoro95.txt === reduce.pl bib === id = cord-259593-shrd1s7r author = Qin, Zhao-ling title = siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date = 2007-06-27 pages = extension = .txt mime = text/plain words = 4603 sentences = 255 flesch = 56 summary = title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. cache = ./cache/cord-259593-shrd1s7r.txt txt = ./txt/cord-259593-shrd1s7r.txt === reduce.pl bib === id = cord-259471-lsdodl0a author = Pagliano, Pasquale title = Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date = 2020-03-24 pages = extension = .txt mime = text/plain words = 626 sentences = 29 flesch = 39 summary = In contrast, no similar effect on early phases of coronavirus infection has been reported for other drugs proposed for SARS-CoV-2 treatment, which are able to interfere only after cell infection, affecting protease cleavage (protease inhibitors) or viral genome replication (remdesivir or ribavirin). Hydroxychloroquine, the HIV protease inhibitors (particularly lopinavir), ribavirin, and remdesivir are the most promising drugs proposed for coronavirus disease 2019 (COVID-19) treatment, but currently no drug has been proposed for postexposure or preexposure prophylaxis for those accidently exposed to SARS-CoV-2 [6] . Hydroxychloroquine's effectiveness profile, its ability to inhibit lung viral replication for a 10-day period after only a 5-day cycle of therapy, and the large amounts of knowledge in term of safety deriving from its use for malaria prophylaxis and rheumatologic diseases lead us to recommend its preexposure or postexposure use for those performing procedures at high risk of viral diffusion in patients with COVID-19 pneumonia. cache = ./cache/cord-259471-lsdodl0a.txt txt = ./txt/cord-259471-lsdodl0a.txt === reduce.pl bib === id = cord-259396-vmc2q1bi author = Periyasamy, Petrick title = Aerosolized SARS-CoV-2 transmission risk: Surgical or N95 masks? date = 2020-09-15 pages = extension = .txt mime = text/plain words = 1527 sentences = 96 flesch = 51 summary = WHO underlines the use of N95 respirators or equivalent as part of personal protective equipment (PPE) for healthcare workers (HCW) managing COVID-19 positive patients when aerosolised-generating-procedures (AGP) are being conducted.This retrospective observational study describes the result of COVID-19 reverse transcriptase polymerase chain reaction (RT-PCR) in health care workers (HCW) wearing different form of personal protective equipment (PPE) who had had close contact with a confirmed COVID-19 patient during performing such procedures. Little is known about the effectiveness of different types of personal protective equipment (PPE) for preventing SARS-CoV-2 in HCWs. We describe the clinical outcome of HCWs exposed to sudden acute respiratory infection patient before the diagnosis of COVID-19 was known. This retrospective observational study describes the result of reverse-transcriptase polymerase chain reaction (RT-PCR) testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in HCWs wearing different form of PPE who had close contact with a confirmed COVID-19 patient during performing AGPs. All HCWs were quarantined for 14 days after the exposure. cache = ./cache/cord-259396-vmc2q1bi.txt txt = ./txt/cord-259396-vmc2q1bi.txt === reduce.pl bib === id = cord-259668-nwezszhj author = Ortiz, Alberto title = Complement and protection from tissue injury in COVID-19 date = 2020-10-04 pages = extension = .txt mime = text/plain words = 2618 sentences = 129 flesch = 37 summary = Finally, preclinical studies in endotoxaemia, another hyperinflammation syndrome characterized by lung and kidney injury, suggest that cilastatin, an inexpensive drug already in clinical use, may provide tissue protection against hyperinflammation in COVID-19. In any case, this report suggests that assessing complement peptides may eventually contribute to define clusters of COVID-19 patients, as has been done for C3 glomerulopathies/immune complex-mediated membranoproliferative glomerulonephritis [11, 12] . In non-controlled case series and case reports, relatively positive results have been reported for the anti-C5 monoclonal antibody eculizumab, for C3 inhibitor AMY-101, for the mannan-binding lectin-associated serine protease 2 blocker narsoplimab (OMS721), for aliskiren and for nafamostat mesylate, a US Food and Drug Administration-approved anticoagulant agent that has broad-spectrum serine protease inhibitory activity, including for C1 esterase [2, [19] [20] [21] [22] [23] [24] [25] [26] . [3] emphasize, the fact that the SARS-CoV-2 cellular receptor ACE2 is expressed in lipid rafts may provide two mechanisms by which cilastatin may protect from severe COVID-19: (i) stabilizing ACE2 at the cell surface lipid rafts and preventing virus/ACE2 internalization and (ii) preventing hyperinflammation-induced tissue injury as observed in rat endotoxemia. cache = ./cache/cord-259668-nwezszhj.txt txt = ./txt/cord-259668-nwezszhj.txt === reduce.pl bib === id = cord-259907-yqmi0cqy author = Maxwell, Cynthia title = Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 date = 2009-10-31 pages = extension = .txt mime = text/plain words = 3419 sentences = 211 flesch = 49 summary = title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 Labour triage and antenatal hospital admission Actions • Assessment is made as to whether the patient has suspected or probable SARS [1, 14] • Upon arrival in the labour and delivery triage unit, pregnant patients presenting with fever N38°C and respiratory symptoms and one of the associated symptoms (cough, unexplained hypoxia, shortness of breath, or dyspnea) and history of an exposure to an individual with probable SARS are immediately transferred to the designated isolation room, which is equipped with negative pressure ventilation. • Parents and family are counselled to look for symptoms and signs of SARS in the mother and newborn, especially in the first 10 days following delivery, and to report to any findings to the health care team Summary SARS, a life-threatening respiratory illness caused by a novel coronavirus, was responsible for a worldwide outbreak in 2003. cache = ./cache/cord-259907-yqmi0cqy.txt txt = ./txt/cord-259907-yqmi0cqy.txt === reduce.pl bib === id = cord-259340-1ir19s25 author = Das, Rohit Pritam title = Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1640 sentences = 128 flesch = 51 summary = Here the authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The B-cell epitopic regions present in SARS-CoV-2 S protein were identified using BcePred prediction server (https://webs.iiitd.edu.in/cgibin/bcepred/) [17] . Molecular docking was performed between the predicted peptides and MHC representative structures using PatchDock web server [22, 23, 24] . Interaction of both TLR2 and TLR4 structures with the predicted peptides were performed using PatchDock web server [22, 23, 24] . This study is focused on the prediction of effective epitopes from Spike protein of SARS-CoV-2. cache = ./cache/cord-259340-1ir19s25.txt txt = ./txt/cord-259340-1ir19s25.txt === reduce.pl bib === id = cord-259620-qigfstxt author = Yang, Chen title = Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date = 2020-10-10 pages = extension = .txt mime = text/plain words = 3373 sentences = 205 flesch = 54 summary = Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Studies have indicated direct infection of SARS-CoV-2 in kidney in addition to lung 5, 31 , however, ACE2 remains the only confirmed receptor which may mediate this invasion. Notably, our results suggest that SARS-CoV-2-RBD binds KIM1 and ACE2 via two distinct pockets, implicating that KIM1 and ACE2 may synergistically mediate the invasion of SARS-CoV-2 in kidney cells; which may explain the strong renal tropism, as well as the high incidence of acute kidney injury in COVID-19 patients 5 . ACE2 is the most well-studied receptor for SARS-CoV-2 so far, yet it is not an ideal therapeutic target for COVID-19 since it is widely expresses in multiple organs, and plays crucial roles in regulating blood pressure and preventing heart/kidney injury 36, 37 . cache = ./cache/cord-259620-qigfstxt.txt txt = ./txt/cord-259620-qigfstxt.txt === reduce.pl bib === id = cord-259558-remrzrq1 author = LeBlanc, Jason J. title = A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1458 sentences = 96 flesch = 52 summary = Low viral loads are known to occur in the early and late stages of COVID-19 illness [4] [5] [6] [11] [12] [13] [14] [15] [16] [17] [18] [19] , and false negative results can arise from differences in analytical sensitivity between methods (Table S1 ) [20, 21] , the variability in specimen collection, or factors influencing specimen stability or recovery of SARS-CoV-2 RNA during specimen transport, storage or processing. [4, 13] For example, three different SARS-CoV-2 targets were detected between the various PCR methods used for testing of J o u r n a l P r e -p r o o f specimens from patient 1, yet high Ct values were observed for these targets (Table 1) . cache = ./cache/cord-259558-remrzrq1.txt txt = ./txt/cord-259558-remrzrq1.txt === reduce.pl bib === id = cord-259935-xyo2pe4g author = Wang, Ching-Ying title = SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date = 2017-05-02 pages = extension = .txt mime = text/plain words = 4628 sentences = 259 flesch = 52 summary = To examine the association of SARS-CoV PLpro-induced TGF-β1 production with the collagen up-regulation, A549 lung epithelial cells transiently transfected with pcDNA3.1 and pSARS-PLpro were analyzed the production of TGF-β1 and type I collagen using Western blot, realtime RT-PCR and Sirius red staining assays (Fig. 1) . To examine whether SMAD-dependent pathways involve in TGF-β1mediated up-regulation of Type I collagen in response SARS-CoV PLpro, subcellular localization of receptor-regulated SMAD3 and inhibitory SMAD7 in transfected cells were detected using the immunofluorescent and DAPI staining (Fig. 4) . To examine the possible pathways involved in TGF-β1-dependent up-regulation of Type I collagen by SARS-CoV PLpro, the profiles of ubiquitin-conjugated proteins in transfected cells with vector control and pSARS-PLpro were determined using immune-precipitation and nanoLC-MS/MS. Subcellular localization analysis demonstrated that SMAD3 was predominant in cytoplasmic, but not in the nucleus in transfected cells with pSARS-PLpro compared to vector control (Fig. 4) , revealing that canonical Smad-dependent signaling pathway was not involved in PLpro-induced TGF-β1-dependent upregulation of Type I collagen. cache = ./cache/cord-259935-xyo2pe4g.txt txt = ./txt/cord-259935-xyo2pe4g.txt === reduce.pl bib === id = cord-259619-sco0d5cc author = Ludvigsson, Johnny title = Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2498 sentences = 129 flesch = 51 summary = title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society We suggest here that more selective assisted isolation of vulnerable populations would reduce the predictable increase in hospital admissions and more rapidly alleviate the fallout from total lockdown measures. Even though COVID19 sometimes leads to need for treatment at intensive care units (ICU) also for younger individuals, the virus appears most dangerous for a selected group of the most vulnerable people. We must consider diverting our major efforts to protect the vulnerable-elderly and patients with preexisting comorbidities-by providing safe and assisted isolation and care; not least now that lockdown rules start to be relaxed. However, these measures have isolated subjects at risk, but have not increased immunization of the population with so called herd immunity through the transient infection of the less vulnerable. cache = ./cache/cord-259619-sco0d5cc.txt txt = ./txt/cord-259619-sco0d5cc.txt === reduce.pl bib === id = cord-259660-x9sobzyw author = Mohakud, Nirmal K title = An Assumed Vertical Transmission of SARS-CoV-2 During Pregnancy: A Case Report and Review of Literature date = 2020-09-26 pages = extension = .txt mime = text/plain words = 1435 sentences = 90 flesch = 56 summary = In the present report, we describe a premature newborn, who was born to a primigravida mother with HELLP (hemolysis, elevated liver enzymes, and low platelet count) syndrome and moderate COVID-19 pneumonia. The newborn tested positive at 12 hours of life for COVID-19 by real-time polymerase chain reaction (RT-PCR) of the tracheal aspirate sample [9] . The authors in one review reported 179 cases of newborns tested positive at birth, whose mothers were infected in the third trimester of pregnancy [5] . The authors of one study described that three newborns born to mothers with COVID-19 infection had positive antibodies (IgM and IgG) at birth [7, 8] . In the present report, the index newborn was tested positive at 12 hours of life without any features of symptomatic COVID-19 infection [9] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn A neonate born to mother with COVID-19 during pregnancy & HELLP syndrome: a possible vertical transmission cache = ./cache/cord-259660-x9sobzyw.txt txt = ./txt/cord-259660-x9sobzyw.txt === reduce.pl bib === id = cord-259863-ndclxrm7 author = Cooke, William R. title = SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases date = 2020-05-15 pages = extension = .txt mime = text/plain words = 728 sentences = 69 flesch = 56 summary = title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases We present our experience of managing two cases of SARS-CoV-2 infection in very preterm pregnancy. SARS-CoV-2 infection causing type 1 respiratory failure was presumed. A multidisciplinary (obstetric, anaesthetic and intensivist) decision was made for delivery by caesarean section, to facilitate invasive ventilation of the woman. SARS-CoV-2 RNA swab from the patient was positive, and from the baby was negative. SARS-CoV-2 RNA swab from the mother was positive, and from the baby was negative. To date 3 cases of severe SARS-CoV-2 infection in very preterm pregnancy (<32 weeks) have been published; all underwent caesarean section for maternal resuscitation; one woman died [1] [2] [3] . 1. Both women deteriorated within 24 hours of presentation: we recommend early administration of corticosteroids for fetal maturation. A case of 2019 Novel Coronavirus in a pregnant woman with preterm delivery cache = ./cache/cord-259863-ndclxrm7.txt txt = ./txt/cord-259863-ndclxrm7.txt === reduce.pl bib === id = cord-259566-qtlq7a6l author = Guraya, Salman Yousuf title = Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2421 sentences = 150 flesch = 39 summary = title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article Benefits of delaying elective and non-urgent surgery outweighs the risk of performing surgical procedures on patients with asymptomatic or active COVID-19 disease. Limiting the number of operating room personnel, use of disposable instruments, small trocar incisions, negative pressure environment, and setting energy devices at low modes can help reduce disease transmission during laparoendocsopic procedures. This write up provides a brief account of the impact of the COVID-19, big data analytics of response of medical personnel in curtailing and understanding the disease process and the consensus guidelines for carrying out laparoscopic and endoscopic procedures. -Limiting the number of operating room personnel, use of disposable instruments, negative pressure air flow, and setting electrocautery energy devices at low modes can possibly reduce disease transmission during laparoendocsopic procedures. cache = ./cache/cord-259566-qtlq7a6l.txt txt = ./txt/cord-259566-qtlq7a6l.txt === reduce.pl bib === id = cord-258914-g6pv8zz9 author = Proud, Pamela C. title = Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date = 2020-09-25 pages = extension = .txt mime = text/plain words = 1191 sentences = 90 flesch = 51 summary = title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19. The TLRs are key microbe-recognition receptors with a crucial role in 97 activation of host defence and protection from infections and therefore attractive drug 98 targets against infectious diseases [12] [13] [14] To determine whether TLR2/6 agonists are also active against SARS-CoV-2, we used In life samples were taken at days 1, 3, 5, 7, 10 and 12, with scheduled culls at days 137 3 (n=6) and end of study days 12-14 (n=18) (Fig 1A) . cache = ./cache/cord-258914-g6pv8zz9.txt txt = ./txt/cord-258914-g6pv8zz9.txt === reduce.pl bib === id = cord-259925-g28sx9qu author = Saleemi, Mansab Ali title = Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date = 2020-10-06 pages = extension = .txt mime = text/plain words = 6875 sentences = 375 flesch = 51 summary = The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. Up to date, it is unclear how SARS-CoV-2 interacts with the host antiviral immunity, hence lessons can be learned from previous studies of other members of the coronavirus family and also human pathogenic viruses, such as human immunodeficiency viruses and severe acute respiratory syndrome (SARS) CoV known as human CoVs (HCoVs) due to their ability to cause human infections (Andersen et al., 2020) . cache = ./cache/cord-259925-g28sx9qu.txt txt = ./txt/cord-259925-g28sx9qu.txt === reduce.pl bib === id = cord-259869-kwzsdhrr author = Baghizadeh Fini, Maryam title = Oral saliva and CVID-19 date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2440 sentences = 134 flesch = 49 summary = Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable. Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable in a dental office. The analysis of saliva in COVID-19 cases can help to explain the pathogenesis because epithelial oral cavity cells demonstrated ample expression of the Angiotensin-Converting Enzyme 2 (ACE2) receptor that plays a critical role in allowing SARS-CoV-2 to enter the cells [4] . SARS-CoV-2 in the lower and upper respiratory tract reaches the oral cavity along with the liquid droplets; SARS-CoV-2 in the blood may enter the mouth through the gingival crevicular fluid; and major and minor infection of the salivary gland, with the ensuing release of particles into the saliva through salivary ducts [7] . Detection of SARS-CoV-2 in Saliva and Characterization of Oral Symptoms in COVID-19 Patients. cache = ./cache/cord-259869-kwzsdhrr.txt txt = ./txt/cord-259869-kwzsdhrr.txt === reduce.pl bib === id = cord-260310-0gkoanrg author = Kim, Jin Yong title = Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea date = 2020-02-20 pages = extension = .txt mime = text/plain words = 2171 sentences = 118 flesch = 58 summary = In this patient, the initial test was performed on day 14 of symptom onset and SARS-CoV-2 was detected in both URT and LRT specimens. Although the viral load and CXR findings in these two patients may not represent the whole spectrum of SARS-CoV-2 illness, our report will provide many important findings and opportunity to understand this newly discovered virus infection in human. First, unlike SARS-CoV infection, 8 we found that viral load was highest during the early phase of the illness (3-5 days from first symptom onset, fever and myalgia were the only symptoms in Patient 1) and continued to decrease until the end of the second week. Second, even in a patient with mild disease, if visible infiltration on CXR is observed, virus is still detected in both URT and LRT specimens even at the end of second week after symptom onset. cache = ./cache/cord-260310-0gkoanrg.txt txt = ./txt/cord-260310-0gkoanrg.txt === reduce.pl bib === id = cord-259747-sl9q63oc author = Remmelink, Myriam title = Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4541 sentences = 244 flesch = 48 summary = BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). In this post-mortem study, we included the first 17 adult patients (> 18 years) who died in our hospital (either in a COVID-19 unit or an intensive care unit) from March 13, 2020, with confirmed SARS-CoV-2 infection (i.e., positive RT-PCR assay on nasopharyngeal swab and/or bronchoalveolar lavage specimen). This post-mortem study showed several histopathological abnormalities in COVID-19 non-survivors; however, none of the findings was specific for direct viral injury, even though SARS-CoV-2 was detected in all examined organs using RT-PCR. cache = ./cache/cord-259747-sl9q63oc.txt txt = ./txt/cord-259747-sl9q63oc.txt === reduce.pl bib === id = cord-259229-e8m8m4ut author = Samidurai, Arun title = Cardiovascular Complications Associated with COVID-19 and Potential Therapeutic Strategies date = 2020-09-16 pages = extension = .txt mime = text/plain words = 10768 sentences = 530 flesch = 38 summary = Emerging evidence reveals a direct interplay between COVID-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. Respiratory illness and acute cardiac injury are major clinical manifestations observed in patients infected with SARS-CoV-2 during the late stage complications of the disease [38] . Based on the available clinical data, potential myocardial injury is a relevant challenge among hospitalized patients with COVID-19 with increased risk of mortality; therefore, it is essential for multidisciplinary assessment, including blood pressure control in hypertensive patients as well as cardiovascular evaluation and therapy to reduce the morality for COVID-19 infection. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China cache = ./cache/cord-259229-e8m8m4ut.txt txt = ./txt/cord-259229-e8m8m4ut.txt === reduce.pl bib === id = cord-259808-82drb14x author = Andrews, Paul L R title = COVID‐19, nausea, and vomiting date = 2020-10-05 pages = extension = .txt mime = text/plain words = 7911 sentences = 404 flesch = 46 summary = Considering the likely effects of SARS-CoV-2 on the digestive tract (discussed further), a relationship between symptoms such as nausea/vomiting and diarrhea would not be unexpected but identifying the time of onset of each postinfection is essential to assessing their relative relevance for diagnosis. There are no formal studies at present so we have reviewed the effects of SARS-CoV-2 (and other coronaviruses) on the digestive tract in the light of knowledge of the established mechanisms of nausea and vomiting; this is the same approach that has been used to understand the pathogenesis of other symptoms (e.g. diarrhoea 10 ). We hypothesize that SARS-CoV-2 would induce acute (first few days postinfection) nausea and vomiting by causing the release of key hormones from the enteroendocrine cells (EECs) in the mucosa of the upper GI tract or after gaining direct entry into the blood, by acting directly within the brainstem. cache = ./cache/cord-259808-82drb14x.txt txt = ./txt/cord-259808-82drb14x.txt === reduce.pl bib === id = cord-259603-bh198xgl author = Snijder, E.J. title = The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date = 2016-09-14 pages = extension = .txt mime = text/plain words = 24187 sentences = 1090 flesch = 50 summary = Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein's importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V'Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme's activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. cache = ./cache/cord-259603-bh198xgl.txt txt = ./txt/cord-259603-bh198xgl.txt === reduce.pl bib === id = cord-260402-9b1ltcf1 author = Lang, Adam Edward title = More Than Meets the Eye: The Similarities Between COVID-19 and Smoking date = 2020-08-11 pages = extension = .txt mime = text/plain words = 584 sentences = 42 flesch = 54 summary = To the Editor: Research shows that cigarette smoking upregulates ACE2, the receptor by which SARS-CoV-2 gains entry to the host resulting in COVID-19, in the lungs and therefore potentially leads to increased morbidity [1] . As part of a tobacco treatment campaign implemented at the beginning of the pandemic at McDonald Army Health Center, the authors performed a literature search and found that SARS-CoV-2 and smoking both contribute to myocarditis, thrombosis, immune impairment, and increased inflammation. SARS-CoV-2 and smoking upregulate this cytokine release and lead to an increased risk of coagulopathy [4, 5] . The upregulation of ACE2 in smokers may predispose this population to an increased risk of SARS-CoV-2 infection. The host cell transmembrane protease, serine 2 (TMPSRSS2), which primes the SAR-CoV-2 S protein for entry, may also be upregulated in smokers [6] , which would further increase the odds of viral infectivity. Smoking-Mediated Upregulation of the Androgen Pathway Leads to Increased SARS-CoV-2 Susceptibility cache = ./cache/cord-260402-9b1ltcf1.txt txt = ./txt/cord-260402-9b1ltcf1.txt === reduce.pl bib === id = cord-259993-hlsvu1cg author = Qiu, Wuqi title = The Impacts on Health, Society, and Economy of SARS and H7N9 Outbreaks in China: A Case Comparison Study date = 2018-06-28 pages = extension = .txt mime = text/plain words = 3417 sentences = 178 flesch = 56 summary = AIMS: This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country's economy, its society, and its place in the global community. In the past 15 years China has experienced numerous public health crises caused by disease outbreaks including Severe Acute Respiratory Syndromes (SARS) in 2003 and Influenza A Virus Subtype H7N9 (H7N9) in 2013. This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country's economy, its society, and its place in the global community. cache = ./cache/cord-259993-hlsvu1cg.txt txt = ./txt/cord-259993-hlsvu1cg.txt === reduce.pl bib === id = cord-259933-ggx4v0bz author = Dalan, Rinkoo title = The ACE-2 in COVID-19: Foe or Friend? date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4187 sentences = 225 flesch = 44 summary = The SARS-CoV-2, a positive strand RNA virus, has been seen to infect humans through the angiotensin converting enzyme -2 (ACE-2) receptor [9] . In individuals with hypertension, diabetes, and other cardiovascular disorders with vascular complications, the renin angiotensin system (RAS) is known to be activated with an increase in ACE activity and a downregulation of ACE-2. Therefore, it may be assumed that the inherent downregulation of the ACE-2-Ang-(1-7)-Mas axis (as seen in metabolic conditions) is exacerbated in the COVID-19 state because (i) the virus uses the peptidase domain of the enzyme for entry into the cells and (ii) there is a decrease in ACE-2 with an increase in ACE [9] . Individuals with underlying hypertension, type 2 diabetes, or cardiovascular disease are at higher risk for respiratory failure and mortality in COVID-19. cache = ./cache/cord-259933-ggx4v0bz.txt txt = ./txt/cord-259933-ggx4v0bz.txt === reduce.pl bib === id = cord-260054-iihgc5nr author = Cavallo, Luigi title = D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date = 2020-06-08 pages = extension = .txt mime = text/plain words = 4062 sentences = 210 flesch = 59 summary = 3D structures are now available from the Protein Data Bank (PDB) (21) for the SARS-CoV-2 S protein in the pre-fusion conformation, also bound to the ACE2 receptor (22) (23) (24) (25) (26) (27) (28) , and for the post-fusion core of its S2 subunit in the postfusion conformation (29) . We downloaded all the SARS-CoV-2 genomic sequences from the GISAID resource on April 21 st 2020, extracted from them 7,692 complete S protein sequences and identified all the point mutations occurring in at least two identical sequences (see Methods). When looking at the post-fusion conformation of the SARS-CoV-2 spike protein S2 subunit, these mutations appear more revealing. Based on a thorough analysis of the S protein sequences, that we extracted from the genomic sequences of SARS-CoV-2 reported in GISAID on April 21 st , we identified the fusion core of the HR1 as a mutational hotspot. cache = ./cache/cord-260054-iihgc5nr.txt txt = ./txt/cord-260054-iihgc5nr.txt === reduce.pl bib === id = cord-259699-48jg7ci7 author = González-Calatayud, Dra Mariel title = Observational study of the suspected or confirmed cases of sars COV-2 infection needing emergency surgical intervention during the first months of the pandemic in a third level hospital: Case series date = 2020-10-24 pages = extension = .txt mime = text/plain words = 2797 sentences = 131 flesch = 46 summary = METHOD: We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial biomarkers (first five days of hospitalization), days of hospital stay, days in the Intensive Care Unit and reason for discharge. We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial laboratory tests (first five days of hospitalization): ferritin, D-dimer, total leucocyte count, total lymphocyte count, lymphocytes (%), platelets, lactate dehydrogenase, fibrinogen, and procalcitonin; we also considered days of hospital stay (DOHS), days in the Intensive Care Unit (ICU), and reason for discharge. Indeed, it has been decided to reduce elective surgical treatment, we have also observed that patients undergoing emergency surgery with suspicion or confirmation of SARS-Cov-2 infection have significant mortality depending on the performed surgical procedure, without relevant findings regarding biomarkers. cache = ./cache/cord-259699-48jg7ci7.txt txt = ./txt/cord-259699-48jg7ci7.txt === reduce.pl bib === id = cord-260132-lqpk3ig7 author = Quartuccio, Luca title = Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome date = 2020-04-19 pages = extension = .txt mime = text/plain words = 2463 sentences = 116 flesch = 39 summary = Currently, the humanized monoclonal antibody anti-interleukin-6 receptor (anti-IL-6R), namely tocilizumab, appears as a promising tool to turn off the cytokine storm, which dramatically complicates the course of the infection in some patients, causing a rapidly fatal acute respiratory distress syndrome. Importantly, SARS-CoV patients admitted to the Intensive Care Unit showed higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, creatine kinase, and creatine, emphasizing the role of the systemic inflammation downstream the virus infection, and the transformation of the infectious disease into a systemic immunological and inflammatory disease. Lung pathology in 2003 SARS-CoV patients showed epithelial cell proliferation and desquamation, hyaline membranes formation along alveolar walls and cells infiltration (lymphocytes, neutrophils, and monocytes) during the early stage of the disease, while, of note, increased fibrosis and multinucleated epithelial giant cells formation at a later stage, highlighting the existence of a two-phase lung injury. cache = ./cache/cord-260132-lqpk3ig7.txt txt = ./txt/cord-260132-lqpk3ig7.txt === reduce.pl bib === id = cord-260238-2p209g2p author = Peiris, J S M title = Severe acute respiratory syndrome date = 2004-11-30 pages = extension = .txt mime = text/plain words = 6296 sentences = 317 flesch = 40 summary = Severe acute respiratory syndrome (SARS) was caused by a previously unrecognized animal coronavirus that exploited opportunities provided by 'wet markets' in southern China to adapt to become a virus readily transmissible between humans. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Characterization of severe acute respiratory syndrome-associated coronavirus (SARS CoV) spike glycoprotein-mediated viral entry Severe acute respiratory syndrome associated coronavirus (SARS CoV) infection inhibition using spike protein heptad repeat-derived peptides Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAB to S1 protein that blocks receptor association cache = ./cache/cord-260238-2p209g2p.txt txt = ./txt/cord-260238-2p209g2p.txt === reduce.pl bib === id = cord-260034-a1y0enrg author = Karsulovic, Claudio title = mTORC inhibitor Sirolimus deprograms monocytes in “cytokine storm” in SARS-CoV2 secondary hemophagocytic lymphohistiocytosis- like syndrome date = 2020-07-13 pages = extension = .txt mime = text/plain words = 930 sentences = 61 flesch = 44 summary = title: mTORC inhibitor Sirolimus deprograms monocytes in "cytokine storm" in SARS-CoV2 secondary hemophagocytic lymphohistiocytosislike syndrome Human M1 monocytes in vitro were able to express higher levels of IL-6 and IL-1β after LPS stimulation (8) (Fig. 1) . When monocytes are treated in vitro with sirolimus, and mTORC blocker, they are unable to express M1 proteins even in presence of LPS. With this data and previous reports of its use in influenza pneumonia (13) , it seems reasonable to think that the SARS-CoV2 induced sHLH-Like syndrome could be successfully slowed or terminated by sirolimus, due to its action blocking the migration of monocytes to lung tissue. We propose at least compassionate use of sirolimus in SARS-CoV2 patients who are classified as high risk of ominous progression or are currently using tocilizumab, corticosteroids and/or J o u r n a l P r e -p r o o f protease inhibitors and Hscore shows high probability of sHLH. cache = ./cache/cord-260034-a1y0enrg.txt txt = ./txt/cord-260034-a1y0enrg.txt === reduce.pl bib === id = cord-260550-ld9eieik author = Ng, Man Wai title = The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date = 2007-06-01 pages = extension = .txt mime = text/plain words = 2839 sentences = 164 flesch = 63 summary = title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese In this study, we investigated the single nucleotide polymorphisms (SNPs) of inflammatory chemokine genes, i.e. RANTES, IP-10 and monokine induced by gamma interferon gene (Mig) in two Chinese cohorts from Hong Kong and Beijing and found that the RANTES -28 G allele was associated with disease susceptibility and severity of SARS. Among them, 20 patients were classified as severe group, which were identified by their admissions to intensive care units or deaths from SARS (mean ± SD age = 39.45 ± 12.8, 11 male and 9 female). After correction by Bonferroni method, the significant P value should be less than 0.007 This study showed that RANTES -28 G allele was a risk factor that associated with severe clinical outcomes in both Hong Kong and Beijing Chinese SARS patients. cache = ./cache/cord-260550-ld9eieik.txt txt = ./txt/cord-260550-ld9eieik.txt === reduce.pl bib === id = cord-260180-kojb8efv author = Elsoukkary, Sarah S. title = Autopsy Findings in 32 Patients with COVID-19: A Single-Institution Experience date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4600 sentences = 269 flesch = 49 summary = METHODS: We report the clinicopathologic findings from 32 autopsy studies conducted on patients who died of COVID-19 including routine gross and microscopic examination with applicable special and immunohistochemical staining techniques. The purpose of this study is to describe clinical and pathologic findings in major organ systems of patients who died from SARS-CoV-2 infection. In this study, we described the unique and multisystem clinical and pathologic findings in 32 autopsies of patients who died from the novel coronavirus, SARS-CoV-2. On histologic examination, we observed findings secondary to the patients' preexisting conditions in the heart, lungs, liver, and kidneys, as well as changes secondary to SARS-CoV-2 infection such as various stages of DAD and multiple thromboemboli in large and small vessels in multiple organs. While the lung findings are most significant for the majority of those infected, other organ systems are frequently involved including with widespread microscopic thromboses in numerous organs, as well as liver, kidney, and lymph node pathology. cache = ./cache/cord-260180-kojb8efv.txt txt = ./txt/cord-260180-kojb8efv.txt === reduce.pl bib === id = cord-260191-0u0pu0br author = Haas, W. title = „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date = 2004-05-29 pages = extension = .txt mime = text/plain words = 2431 sentences = 335 flesch = 51 summary = Abstract Some emerging infectious diseases have recently become endemic in Germany.Others remain confined to specific regions in the world.Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms.Several of these emerging infections will be explained.HIV is an example for an imported pathogen which has become endemic in Germany.SARS and avian influenza are zoonoses with the potential to spread from person to person.Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain.Outbreaks of dengue fever in endemic areas are reflected in increased infec-gehäuften Erkrankungen bei Rückkehrern wieder.West-Nil-Virus-Erkrankungen kommen derzeit nur als importierte Erkrankungen in Deutschland vor.Wichtig ist,diese Erkrankungen frühzeitig in die differenzialdiagnostischen Überlegungen des Klinikers einzubeziehen,um die erforderlichen Maßnahmen zur Diagnostik,Therapie und zum Infektionsschutz rechtzeitig einleiten zu können.Dies erfordert ein gutes Zusammenspiel mit dem Labor und dem öffentlichen Gesundheitsdienst. cache = ./cache/cord-260191-0u0pu0br.txt txt = ./txt/cord-260191-0u0pu0br.txt === reduce.pl bib === id = cord-260062-qajk0ov4 author = Mocchegiani, Federico title = Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area date = 2020-09-10 pages = extension = .txt mime = text/plain words = 667 sentences = 40 flesch = 54 summary = title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area reported 200 LTRs with 3 tested positive patients for SARS-CoV-2, none developed a clinical pulmonary disease [3] . reported three deaths among 111 long-term adult liver transplant survivors (transplanted more than 10 years ago) following severe COVID-19 while 3 of 40 recently transplanted (ie, within the past 2 years) patients who were found SARS-CoV-2 positive experienced an uneventful course of the disease [4] . reported an incidence of confirmed COVID-19 infection of 1.25% in the population of LTRs of one Milan transplant centre of whom none developed such a severe disease to require invasive ventilation [5] . During the outbreak of COVID-19, in Marche region the infection rate of SARS-Cov-2 has been of 0.44% [1], similar to that observed in our LTRs population. cache = ./cache/cord-260062-qajk0ov4.txt txt = ./txt/cord-260062-qajk0ov4.txt === reduce.pl bib === id = cord-260247-akujsk0s author = Hamed, Ehab title = Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar date = 2020-11-02 pages = extension = .txt mime = text/plain words = 962 sentences = 79 flesch = 56 summary = title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar The group suggested recurrent positive rt-PCR results of more than 21 days following the resolution of symptoms as criteria for reinfection. Utilising the criteria set by the COCOREC study group, this record-based study reports on the cases with recurrent positive RT-PCR nasopharyngeal swab for SARS-CoV-2 results in primary health care corporation (PHCC) settings in Qatar. The study population included patients attending with documented SARS-CoV-2 rt-PCR results during the study period. What are the rates of recurrent rt-PCR SARS-CoV-2 positive results of more than 21 days, and what are the population characteristics? No previous studies reported to the rates of recurrent positive rt-PCR for SARS-CoV-2 infections. Given the extensive reporting of the SARS-CoV-2 infections, the number of case reports of recurrent positive and reinfection to date is extremely low, which agrees with our findings. cache = ./cache/cord-260247-akujsk0s.txt txt = ./txt/cord-260247-akujsk0s.txt === reduce.pl bib === id = cord-259968-cr3zf4oa author = Harb, Roa title = Evaluation of Three Commercial Automated Assays for the Detection of anti-SARS-CoV-2 Antibodies date = 2020-08-06 pages = extension = .txt mime = text/plain words = 255 sentences = 29 flesch = 49 summary = key: cord-259968-cr3zf4oa cord_uid: cr3zf4oa The Diasorin assay detects IgG antibodies to the S1 and S2 subunits of the spike protein and the signal is expressed in arbitrary units (AU/mL). The Roche assay detects total antibodies to the nucleocapsid protein and the signal is reported as a cutoff index (COI). Cutoffs for positive samples by the Abbott, Diasorin, and Roche assays are ≥ 1.4, ≥ 15 AU/mL, and ≥ 1.0 COI, respectively. Clinical performance of the roche sars-cov-2 serologic assay Clinical performance of the elecsys electrochemiluminescent immunoassay for the detection of sars-cov-2 total antibodies Performance characteristics of four high-throughput immunoassays for detection of igg antibodies against sars-cov-2 Middle, values for Diasorin SARS-CoV-2 IgG for expected negative (n=344) and expected positive (n=65) specimens. Right, values for Roche SARS-CoV-2 total antibodies for expected negative (n=141) and expected positive (n=65) specimens. B) Distribution of anti-SARS-CoV-2 antibody results in expected positive specimens at 0-11 (n=12) cache = ./cache/cord-259968-cr3zf4oa.txt txt = ./txt/cord-259968-cr3zf4oa.txt === reduce.pl bib === id = cord-260048-yis26g81 author = McNamara, Ryan P. title = High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date = 2020-10-20 pages = extension = .txt mime = text/plain words = 2272 sentences = 156 flesch = 55 summary = The 154 number of reads aligned varied depending on the viral load, as determined by real-time qPCR using 155 CDC primer N1, but not total RNA, as determined using RNAse P, of the samples ( Figure 1B) . At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 158 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 159 and coverage was more variable. This data is consistent with the 187 astonishingly high reported genome copy numbers of SARS-CoV-2 in some cases 188 and demonstrates the principal suitability of "testing by sequencing" as a diagnostic option for SARSCoV-2 and other rapidly evolving viruses. In sum, this study generated exhaustive SNV information representing the introduction and 276 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 277 from symptomatic cases and the majority of genomes clustered with variants that predominate the 278 outbreak in the U.S., rather than Europe or China. cache = ./cache/cord-260048-yis26g81.txt txt = ./txt/cord-260048-yis26g81.txt === reduce.pl bib === id = cord-260508-z11exbyu author = Wang, Hongru title = Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date = 2020-10-12 pages = extension = .txt mime = text/plain words = 4698 sentences = 272 flesch = 58 summary = Phylogenetic analyses (Fig. 2 ) in genomic regions with all recombination tracts 6 (Supplementary Table 5 ) masked using Maximum-likelihood (Fig. 2a) and Neighbor-joining 7 based on synonymous (Fig. 2b ) or non-synoymous (Fig. 2c ) mutation distance metrics, 8 consistently support RmYN02 as the nearest outgroup to human SARS-CoV-2, in contrast to 9 previous analyses before the discovery of RmYN02, which instead found RaTG13 to be the 10 nearest outgroup ). Notice that the divergences 14 between human SARS-CoV-2 and the bat viral sequences, RaTG13 and RmYN02, in most 15 regions of the genome, are quite low compared to the other comparisons. While the overall divergence in the S gene encoding the spike protein could suggest the 10 presence of recombination in the region, previous study ) reported that the tree 11 based on synonymous substitutions supported RaTG13 as the sister taxon to the human SARS-12 cache = ./cache/cord-260508-z11exbyu.txt txt = ./txt/cord-260508-z11exbyu.txt === reduce.pl bib === id = cord-260057-2m6jdvtc author = Pandey, Preeti title = Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date = 2020-09-23 pages = extension = .txt mime = text/plain words = 7756 sentences = 409 flesch = 51 summary = To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking–based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. The selected docking conformations of NSP6 in complex with haloperidol and dextromethorphan were sampled by 100-ns MD simulation, and the dynamic stability of the complex was elucidated by calculating the Cα-RMSD values of the protein as the function of simulation time ( Figure S3A ). In conclusion, the study elucidated the detailed interaction mechanism of dextromethorphan and haloperidol to NSP6 protein and the associated structural and dynamical changes upon drug binding. cache = ./cache/cord-260057-2m6jdvtc.txt txt = ./txt/cord-260057-2m6jdvtc.txt === reduce.pl bib === id = cord-260376-29ih5c9v author = Guo, Jian-Ping title = SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date = 2004-07-01 pages = extension = .txt mime = text/plain words = 2994 sentences = 168 flesch = 57 summary = title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera. cache = ./cache/cord-260376-29ih5c9v.txt txt = ./txt/cord-260376-29ih5c9v.txt === reduce.pl bib === id = cord-260077-xf4sofyc author = Sawalha, Amr H. title = Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients date = 2020-04-08 pages = extension = .txt mime = text/plain words = 2598 sentences = 143 flesch = 45 summary = title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Examining whole-genome DNA methylation data generated using an array-based approach, we observe significant hypomethylation in the ACE2 gene in this T cell subset compared to KIR − CD11a low T cells isolated from the same lupus patients (Fig. 1A) . Therefore, it is reasonable to suggest the possibility that the DNA methylation defect in lupus patients, exacerbated by oxidative stress generated from SARS-CoV-2 infection, will further enhance viral entry in lupus patients through epigenetic de-repression of ACE2 and increased ACE2 expression. cache = ./cache/cord-260077-xf4sofyc.txt txt = ./txt/cord-260077-xf4sofyc.txt === reduce.pl bib === id = cord-260412-yjr83ef6 author = Hotez, Peter J. title = Developing a low-cost and accessible COVID-19 vaccine for global health date = 2020-07-29 pages = extension = .txt mime = text/plain words = 2322 sentences = 117 flesch = 43 summary = Our group is developing a two-pronged approach to advance recombinant protein-based vaccines to prevent COVID-19 caused by SARS-CoV-2 and other coronavirus infections. One vaccine is based on a yeast-derived (Pichia pastoris) recombinant protein comprised of the receptor-binding domain (RBD) of the SARS-CoV formulated on alum and referred to as the CoV RBD219-N1 Vaccine. In addition to their low cost and suitability for use in public immunization programs in lowand middle-income countries, we pursued RBD recombinant protein-based vaccines as a technology to maximize safety relative to other platforms, such as virus vectors that have previously been found to induce immune enhancement. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1), a SARS Vaccine Candidate Potential for developing a SARS-CoV receptor-binding domain (RBD) recombinant protein as a heterologous human vaccine against coronavirus infectious disease (COVID)-19 Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1) Formulated with Alum Induces Protective Immunity and Reduces Immune Enhancement cache = ./cache/cord-260412-yjr83ef6.txt txt = ./txt/cord-260412-yjr83ef6.txt === reduce.pl bib === id = cord-260225-bc1hr0fr author = Sirpilla, Olivia title = SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date = 2020-07-20 pages = extension = .txt mime = text/plain words = 8918 sentences = 582 flesch = 44 summary = Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). cache = ./cache/cord-260225-bc1hr0fr.txt txt = ./txt/cord-260225-bc1hr0fr.txt === reduce.pl bib === id = cord-260257-phmd0u6d author = Siegler, Aaron J title = Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3710 sentences = 237 flesch = 54 summary = METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. 8, 9 Calls for home-based specimen collection or drive-through specimen collection models to address SARS-CoV-2 virus test scale-up have cogently argued that these approaches have the benefit of (1) avoiding burdening hospitals at a critical time, (2) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), (3) likely lowering costs, and (4) potentially achieving rapid scale-up due to laboratory centralization. We conducted an online survey to assess patient willingness to use the following SARS-CoV-2 testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. Across a diverse sample of 1,435 participants, one-third more persons reported that they would be willing to collect specimens at home for SARS-CoV-2 testing if they experienced illness, compared to clinic-based testing. cache = ./cache/cord-260257-phmd0u6d.txt txt = ./txt/cord-260257-phmd0u6d.txt === reduce.pl bib === id = cord-260365-neili1bd author = Silverstein, Jenna S. title = Acute Respiratory Decompensation Requiring Intubation in Pregnant Women with SARS-CoV-2 (COVID-19) date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2205 sentences = 134 flesch = 50 summary = Data from China suggest that pregnant women with COVID-19 have favorable maternal and neonatal outcomes, with rare cases of critical illness or respiratory compromise. However, we report two cases of pregnant women diagnosed with COVID-19 in the late preterm period admitted to tertiary care hospitals in New York City for respiratory indications. 8 We report here two pregnant women with no medical comorbidities, one under 18 years of age, diagnosed with COVID-19 at 34 and 36 weeks of gestation, respectively, who rapidly decompensated and underwent caesarean delivery under general anesthesia followed by prolonged mechanical ventilation. The risks and benefits of delivery in pregnant patients with critical respiratory illness from COVID-19 infections are not yet known, but prior experience with maternal acute respiratory distress syndrome (ARDS) and viral 2009/H1N1 influenza requiring mechanical ventilation in pregnancy reveals increased risk of fetal HR abnormalities, as well as fetal and neonatal mortality. cache = ./cache/cord-260365-neili1bd.txt txt = ./txt/cord-260365-neili1bd.txt === reduce.pl bib === id = cord-260429-5wsj003j author = Kenyon, Chris title = Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study date = 2020-04-06 pages = extension = .txt mime = text/plain words = 2260 sentences = 160 flesch = 61 summary = title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV1. Methods At a country level, linear regression was used to assess the association between COVID19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID19 epidemic and testing intensity. Conclusion Whilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections. /2020 In this ecological study we found that countries that promoted widespread face mask 185 usage had lower cumulative numbers of COVID-19 diagnosed after controlling for 186 testing intensity and age of the epidemic. cache = ./cache/cord-260429-5wsj003j.txt txt = ./txt/cord-260429-5wsj003j.txt === reduce.pl bib === id = cord-260315-uau554jj author = Ramirez, Santseharay title = Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date = 2020-10-04 pages = extension = .txt mime = text/plain words = 2269 sentences = 122 flesch = 54 summary = title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. Importance The cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. 137 We performed a comparative titration in various cells of the P2 VeroE6 and the P5 Huh7.5 viruses ( Figure 138 1b) and found that the infectivity titers in Huh7.5 cells after culture adaptation had increased by more 139 than 3 logs (mean of 4.7 and 8.0 Log 10 TCID 50 /mL, respectively). cache = ./cache/cord-260315-uau554jj.txt txt = ./txt/cord-260315-uau554jj.txt === reduce.pl bib === id = cord-260624-rqjeacow author = Gu, Jiang title = Multiple organ infection and the pathogenesis of SARS date = 2005-08-01 pages = extension = .txt mime = text/plain words = 5320 sentences = 271 flesch = 51 summary = SARS viral particles and genomic sequence were detected in a large number of circulating lymphocytes, monocytes, and lymphoid tissues, as well as in the epithelial cells of the respiratory tract, the mucosa of the intestine, the epithelium of the renal distal tubules, the neurons of the brain, and macrophages in different organs. In situ hybridization demonstrated SARS viral sequences in the cytoplasm of a large number of intact and degenerating epithelial cells of the lungs as well as in the scanty infiltrating lymphocytes and clustered macrophages ( Fig. 1, C and D) . (C) In situ hybridization of SARS genomic sequence of the lung from a SARS victim who died 62 d after the onset of high fever detected a large number of pulmonary epithelial cells (small arrows) that contained the virus. In the autopsy samples, in situ hybridization and EM demonstrated virus-infected immune cells in the circulating blood, spleen, lymph nodes, and lymphoid tissue of various organs. cache = ./cache/cord-260624-rqjeacow.txt txt = ./txt/cord-260624-rqjeacow.txt === reduce.pl bib === id = cord-260729-b12v3c8c author = de Lang, Anna title = Functional Genomics Highlights Differential Induction of Antiviral Pathways in the Lungs of SARS-CoV–Infected Macaques date = 2007-08-10 pages = extension = .txt mime = text/plain words = 6800 sentences = 335 flesch = 51 summary = As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. In order to elucidate early host responses during the acute phase of SARS-CoV infection, we infected cynomolgus macaques with SARS-CoV and used macaque-specific microarrays and real-time (RT)-PCR techniques to study host gene expression profiles. In this study, we simultaneously examined virus replication and host-response gene expression profiles in macaque lungs during the acute phase of SARS to gain more insight into the early events that take place after SARS-CoV infection. In order to visualize the host response in the lungs of SARS-CoV-infected macaques, IFN-b production and translocation of phosphorylated STAT1 was studied using immunohistochemistry. The expression of IFN-b, which strongly correlated to the amount of virus present, continued throughout day 4 and was confirmed using immunohistochemistry; IFN-b-positive cells could be detected in the lungs of the SARS-CoV-infected macaques. cache = ./cache/cord-260729-b12v3c8c.txt txt = ./txt/cord-260729-b12v3c8c.txt === reduce.pl bib === id = cord-260503-yq4dtf8n author = SAMARANAYAKE, LAKSHMAN P. title = Severe acute respiratory syndrome and dentistry A retrospective view date = 2004-09-30 pages = extension = .txt mime = text/plain words = 6836 sentences = 383 flesch = 54 summary = Objectives The authors trace the emergence of the SARS outbreak from southern China and its spread worldwide, discuss the viral etiology of the infection and its clinical features, and review the infection control guidelines issued during the outbreak by the health authorities in Hong Kong, the Centers for Disease Control and Prevention, the World Health Organization and the American Dental Association. Conclusions and Clinical Implications Researchers believe that a combination of factors, including the universal infection control measures that the dental community has implemented and/or the low degree of viral shedding in the prodromal phase of SARS, may have obviated the spread of the disease in dental settings. Interim domestic infection control precautions for aerosol-generating procedures on C L I N I C A L P R A C T I C E patients with severe acute respiratory syndrome (SARS) cache = ./cache/cord-260503-yq4dtf8n.txt txt = ./txt/cord-260503-yq4dtf8n.txt === reduce.pl bib === id = cord-260673-gf028lf6 author = Bottemanne, Hugo title = Does the Coronavirus Epidemic Take Advantage of Human Optimism Bias? date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3397 sentences = 150 flesch = 45 summary = Building on evidence from past epidemics and three decades of research in psychology suggesting that various cognitive biases influence beliefs about life hazards, we propose that such cognitive biases have contributed to the discrepancy between early warnings about the danger of SARS-CoV-2 and slow growth of consideration for these warnings. Importantly, data collected in Western countries during the peak of the COVID 19 pandemic provides direct evidence favoring the hypothesis that unrealistic optimism has played a role in the apparent discrepancy between official warnings and individual beliefs about the consequences of the pandemic for oneself: When getting infected and infecting others became frequent events as the number of cases and deaths sharply increased, citizens in the US, Europe and the United Kingdom estimated their probability of getting infected with the virus and of subsequently infecting others as lower for themselves than for someone else (Dolinski et al., 2020; Kuper-Smith et al., 2020) . cache = ./cache/cord-260673-gf028lf6.txt txt = ./txt/cord-260673-gf028lf6.txt === reduce.pl bib === id = cord-260559-n8i52e8q author = Peiris, Malik title = What can we expect from first-generation COVID-19 vaccines? date = 2020-09-21 pages = extension = .txt mime = text/plain words = 1355 sentences = 87 flesch = 41 summary = A popular assumption is that these vaccines will provide population immunity that can reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and lead to a resumption of pre-COVID-19 "normalcy". The immunological correlates of protection from SARS-CoV-2 infection and COVID-19 have yet to be elucidated. Pre-existing neutralising antibody seemed to have afforded protection against re-infection in people on board a fishing vessel where there was an outbreak of SARS-CoV-2 with a high infection attack rate. 20 Alongside the risks of severe morbidity and mortality and of disease transmission, this framework stipulates two additional criteria for equitable vaccine allocation-namely, risks of acquiring infection and of negative societal impact. If COVID-19 vaccines have acceptable effectiveness in reducing morbidity and mortality in high-risk groups, they would have an important role, irrespective of impact on transmission and population immunity. cache = ./cache/cord-260559-n8i52e8q.txt txt = ./txt/cord-260559-n8i52e8q.txt === reduce.pl bib === id = cord-260854-v7wgb6mr author = Colafrancesco, Serena title = COVID-19 gone bad: A new character in the spectrum of the hyperferritinemic syndrome? date = 2020-05-05 pages = extension = .txt mime = text/plain words = 3340 sentences = 160 flesch = 37 summary = The severe form of COVID-19 share several clinical and laboratory features with four entities gathered under the term "hyperferritinemic syndrome" and including macrophage activation syndrome (MAS), adult-onset Still's disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS) and septic shock. COVID-19 systemic inflammatory reaction and "hyperferritinemic syndromes" are all characterized by high serum ferritin and a life-threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi-organ failure. In this review, we analyze the possible epidemiological and molecular mechanisms responsible for hyper-inflammation in patients with severe COVID-19 and we underline the similarities between this condition and "hyperferritinemic syndromes" which would allow considering this entity as the fifth member of the spectrum of inflammatory conditions. The umbrella term "hyperferritinemic syndrome" encompasses four clinical conditions, macrophage activation syndrome (MAS), adult-onset Still's disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS), and septic shock, all characterized by high serum ferritin and a life -threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi -organ failure [1] . cache = ./cache/cord-260854-v7wgb6mr.txt txt = ./txt/cord-260854-v7wgb6mr.txt === reduce.pl bib === id = cord-260407-jf1dnllj author = Tang, Catherine So-kum title = Factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult Chinese in Hong Kong date = 2004-06-11 pages = extension = .txt mime = text/plain words = 4503 sentences = 219 flesch = 47 summary = This study aimed to determine factors associating with individuals' practice of the target SARS preventive behavior (facemask wearing). Three of the five components of the Health Belief Model, namely, perceived susceptibility, cues to action, and perceived benefits, were significant predictors of facemask-wearing even after considering effects of demographic characteristics. Overall, perceived benefits, perceived barriers, and perceived susceptibility are the three most powerful components of the Health Belief Model in influencing whether individuals practice different preventive behaviors [21, 29, 30] . A logistic regression with odds ratios was conducted to test the efficacy of the Health Belief Model in predicting the wearing of facemasks to prevent SARS. Similar to previous research [15 -26] , this study found the Health Belief Model useful in identifying major determinants of the wearing of facemasks to prevent contracting and spreading SARS. The remaining two components of the Health Belief Model, perceived severity and perceived barriers, were found to be nonsignificant determinants of the target SARS preventive behavior in this study. cache = ./cache/cord-260407-jf1dnllj.txt txt = ./txt/cord-260407-jf1dnllj.txt === reduce.pl bib === id = cord-260871-dtn5t8ka author = Silva, Marcus Tulius T. title = SARS-CoV-2: Should We Be Concerned about the Nervous System? date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4110 sentences = 263 flesch = 43 summary = Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system cache = ./cache/cord-260871-dtn5t8ka.txt txt = ./txt/cord-260871-dtn5t8ka.txt === reduce.pl bib === id = cord-260618-k0y0fz7k author = Belli, Simone title = Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? date = 2020-07-01 pages = extension = .txt mime = text/plain words = 9640 sentences = 417 flesch = 51 summary = Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. (2004) , and collected 256 articles indexed in the Science Citation Index (SCI) in the period March-July 2003, analyzing traditional indicators (authorship, collaboration, journals, language, document type, organization, times cited, etc.). We offer a general search in all databases available at Web of Science (WoS) platform and a deeper bibliometric analysis of recent coronavirus scientific publications indexed in its Core Collection. For the 2001-2020 period (Table 1) , the value of the TLS in proportion to the number of documents provided is especially low in countries such as Japan, South Korea, Taiwan or Brazil, with 0.46, 0.35, 0.28 and 0.38 links per document and 35.87%, 25.81%, 19.89% and 31.79% of documents resulted from international collaboration respectively. cache = ./cache/cord-260618-k0y0fz7k.txt txt = ./txt/cord-260618-k0y0fz7k.txt === reduce.pl bib === id = cord-260772-n5q2yi7j author = Ji, Dong title = Reply to: ‘No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease’ date = 2020-05-06 pages = extension = .txt mime = text/plain words = 405 sentences = 34 flesch = 57 summary = title: Reply to: 'No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease' Secondly, this is in keeping to our hypothesis that dysregulated hepatic innate immunity in patients with MAFLD contribute to the pathogenesis of COVID-19. 2 The liver is enriched with innate immune cells (such as macrophages, natural killer, natural killer T, and γδ T cells) 3 and due to its rich blood supply from the small bowel, circulation of the virus via the hepatic reticular system is expected. Hepatic innate immunity populations are potent cytokine producers and there are reports that obesity and NAFLD were associated with increased production of pro-inflammatory cytokines like TNF-α by adipose cells and Kupffer cells. No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease of the link between the dysregulated hepatic innate immunity and COVID-19. cache = ./cache/cord-260772-n5q2yi7j.txt txt = ./txt/cord-260772-n5q2yi7j.txt === reduce.pl bib === id = cord-260886-v1ei9im8 author = Baggett, Travis P. title = COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1103 sentences = 78 flesch = 56 summary = Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. In mid-March, 2020, Boston Health Care for the Homeless Program (BHCHP), in partnership with city and state public health agencies and community partners, created a COVID-19 response strategy that included front-door symptom screening at area shelters, expedited referrals for SARS-CoV-2 testing and isolation for those with respiratory symptoms, dedicated treatment settings for COVID-positive individuals, and detailed contact tracing of confirmed cases. With support from the Massachusetts Department of Public Health (MDPH), BHCHP rapidly conducted polymerase chain reaction (PCR) testing for SARS-CoV-2 along with focused symptom assessments among all guests residing at the shelter over a 2-day period. cache = ./cache/cord-260886-v1ei9im8.txt txt = ./txt/cord-260886-v1ei9im8.txt === reduce.pl bib === id = cord-260565-cdthfl5f author = Burkle, Frederick M. title = Declining Public Health Protections within Autocratic Regimes: Impact on Global Public Health Security, Infectious Disease Outbreaks, Epidemics, and Pandemics date = 2020-04-02 pages = extension = .txt mime = text/plain words = 8816 sentences = 516 flesch = 53 summary = While China is seeking to adhere as much as possible to the underlying norms and rules of global institutions," reemphasizing that China after SARS "perhaps [needs] to reframe health as a global public good that is available to each and every individual of the world, rather than merely as an issue of concern to nation-states." 37 In a rare openness, rarely seen before, the normally secretive Xi admitted at a meeting to coordinate the fight against the virus that China must learn from "obvious shortcomings exposed during its response." Yet given the second-guessing that always surfaces in these tragedies, "it cannot be denied that the Chinese government tried to control the narrative, another sign of irrational hubris, and as a result, the contagion was allowed to spread, contributing to equally irrational fear." A China researcher for Human Rights Watch (New York USA) noted: "authorities are as equally, if not more, concerned with silencing criticism as with containing the spread of the coronavirus. cache = ./cache/cord-260565-cdthfl5f.txt txt = ./txt/cord-260565-cdthfl5f.txt === reduce.pl bib === id = cord-260644-5moccf8c author = Hashemi, Seyed Ahmad title = Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date = 2020-11-07 pages = extension = .txt mime = text/plain words = 2174 sentences = 149 flesch = 67 summary = title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Some researchers evaluated and compared the whole genome sequence of SARS-CoV-2 isolated in various parts of the world and identified some mutations. The high-frequency mutations of the SARS-CoV-2 genome were seen in nsp6, RNA polymerase, helicase, membrane glycoprotein, RNA primase, nucleocapsid phosphoprotein, and spike protein genes (Yin, 2020) . In the first step, we used the sequence of S protein of SARS-CoV-2, published in Gene bank with accession number MT252819.1, for appropriate restriction endonuclease selection and primer design. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity cache = ./cache/cord-260644-5moccf8c.txt txt = ./txt/cord-260644-5moccf8c.txt === reduce.pl bib === id = cord-260925-puuqv6zk author = Wen, Feng title = Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 date = 2020-03-05 pages = extension = .txt mime = text/plain words = 1171 sentences = 70 flesch = 56 summary = title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 The sequences NC_004718.3 of SARS coronavirus 6 genes were utilized to define the protein products of SARS-CoV-2. First, the protein sequences of SARS-CoV-2 were compared with RaTG13, human SARS (NC_004718.3), bat SARS (DQ022305.2), and human MERS (NC_019843.3) by calculating the similarity in a given sliding window ( Fig. 1 A) . These results suggested that there had probably been no hyper-variable genomic hotspot in the SARS-CoV-2 population until now. The hyper-variable genomic hotspot has been established in the SARS-CoV-2 population at the nucleotide but not the amino acid level, suggesting that there have been no beneficial mutations. mutations in nsp1, nsp3, nsp15, and gene S that identified in this study would be associated with the SARS-CoV-2 epidemic and was worthy of further study. The genome sequence of the SARS-associated coronavirus cache = ./cache/cord-260925-puuqv6zk.txt txt = ./txt/cord-260925-puuqv6zk.txt === reduce.pl bib === id = cord-260866-bzdd4f5h author = Barceló, Damià title = Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date = 2020-09-14 pages = extension = .txt mime = text/plain words = 4676 sentences = 249 flesch = 50 summary = Paper-based devices would be certainly one of the best measurement solutions for the rapid and onsite detection of COVID-19 in sewage waters and humans as well [2, 16] and also the use of other biomarkers of exposure [1] . Detection of SARS-CoV-2 in sewage has been employed as a complementary method to clinical test .It is an early warning indicator of virus spreading in communities, covering both symptomatic and asymptomatic cases. Hopefully at certain moment applications to detect SARS-CoV-2 and other viruses in wastewater will be developed based on these LOC/POCT systems that will enable simple, fast and sensitive virus detection. PCR platforms like RT-qPCR are still the most widely used methods for SARS-Cov-2 detection in waste waters. Sewage sensors, such as paper-based and smartphones for SARS-CoV2 detection at the population level have as well a clear potential for early warning of COVID-19 pandemic. cache = ./cache/cord-260866-bzdd4f5h.txt txt = ./txt/cord-260866-bzdd4f5h.txt === reduce.pl bib === id = cord-261025-y49su5uc author = Sampathkumar, Priya title = SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date = 2003-07-31 pages = extension = .txt mime = text/plain words = 3952 sentences = 200 flesch = 49 summary = Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-261025-y49su5uc.txt txt = ./txt/cord-261025-y49su5uc.txt === reduce.pl bib === id = cord-260697-oepk0b1d author = Huang, J. title = COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches date = 2020-08-01 pages = extension = .txt mime = text/plain words = 5734 sentences = 353 flesch = 50 summary = We applied the Synthetic Minority Oversampling Technique (SMOTE) to overcome the rare recurring events in certain age groups and performed Virtual Twins (VT) analysis facilitated by random forest regression for medical treatment-recurrence classification. Here, we report the clinical, radiological, laboratory, and drug treatment findings of 93 recurring patients from 414 patients in Shenzhen, along with our machine learning approaches for identifying the best drug combinations that reduce recurring rates in all population, different age groups and obese patients. The interaction among age, hospitalization delay and drug treatment on SARS-CoV-2 recurring rate is shown in Figure 3 . Interestingly, we found out that the combination of anti-influenza virus drug, oseltamivir, with Interferon/Lopinavir/Ritonavir/Arbidol, has very good outcome (recurring rate of 0.172), supporting the hypothesis of co-infection of influenzas and SARS-CoV-2. . https://doi.org/10.1101/2020.07.29.20164699 doi: medRxiv preprint Supplement Table Table S1 : Clinical characteristics, laboratory findings, treatments, and outcomes of Covid-19 patients with and without recurrence of SARS-CoV-2 PCR positivity during hospitalization. cache = ./cache/cord-260697-oepk0b1d.txt txt = ./txt/cord-260697-oepk0b1d.txt === reduce.pl bib === id = cord-261180-w62mynqb author = Ling, L. title = Infection control in non‐clinical areas during the COVID‐19 pandemic date = 2020-04-19 pages = extension = .txt mime = text/plain words = 482 sentences = 35 flesch = 54 summary = SARS-CoV-2 is easily transmissible as each person with COVID-19 infects approximately 2.2 close contacts, and asymptomatic transmission has been reported [2,3]. Therefore, we believe non-clinical areas are potentially high-risk for transmission between healthcare workers, and often neglected by infection prevention and control protocols. To alert others to this risk and how it may be reduced, we describe our non-clinical workplace infection prevention and control measures that have been modified from those originally developed during the 2003 severe acute respiratory syndrome epidemic [5] . Infographics are displayed on walls as reminders to perform hand hygiene when entering offices, after contact with respiratory secretions, before and after eating or drinking, and donning and doffing of masks. Designated bins for mask disposal are placed in communal areas. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Transmission of SARS to healthcare workers. cache = ./cache/cord-261180-w62mynqb.txt txt = ./txt/cord-261180-w62mynqb.txt === reduce.pl bib === id = cord-261110-cnj0e0s9 author = Debarnot, Claire title = Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date = 2011-02-25 pages = extension = .txt mime = text/plain words = 2656 sentences = 169 flesch = 64 summary = This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. We present X-ray diffraction data from these SARS-CoV nsp10-nsp16 crystals. The purified SARS-CoV nsp10-nsp16 complex was analyzed by 12% SDS-PAGE and stained using Coomassie Blue. Lane MK, molecular-weight markers; lane 1, 2 mg nsp10-nsp16 protein complex eluted from the Strep-Tactin column. The nsp10-nsp16 complex eluted from the Strep-Tactin column was analyzed on a 16/60 S200 gel-filtration column and the elution of protein and nucleic acid was followed by measuring the absorption at 280 nm (blue) and 260 nm (orange), respectively. The purified SARS-CoV nsp10-nsp16 complex was loaded onto a 4-12% NuPAGE gel and stained using Coomassie Blue. We have crystallized a complex of the SARS-CoV nsp10 and nsp16 proteins. cache = ./cache/cord-261110-cnj0e0s9.txt txt = ./txt/cord-261110-cnj0e0s9.txt === reduce.pl bib === id = cord-261405-n05wjimk author = Lui, Grace title = Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19 date = 2020-04-18 pages = extension = .txt mime = text/plain words = 1157 sentences = 81 flesch = 56 summary = reported in this journal that viral shedding of SARS-CoV-2 in nasal swabs was longer in intensive care unit (ICU) patients compared with non-ICU patients with Coronavirus Disease 2019 (COVID-19). 3 We collected serial upper (pooled nasopharyngeal and throat swabs, N=75) and lower respiratory tract samples (sputum and tracheal aspirate, N=43), peripheral blood plasma (N=50), urine (N=43) and stool (N=43) samples from all participants, and monitored SARS-CoV-2 viral loads in these samples. In all five participants with severe/critical and three with moderate disease, viral loads in respiratory tract samples continued to rise and peaked in the second week of illness (range 5.57-9.66 log copies/mL). In this study of patients with COVID-19 across a wide spectrum of severity, we observed that viral shedding in the respiratory tract lasting longer than 14 days was common. In more severe disease, viral load appeared to peak in the second week of illness in both upper and lower respiratory tract. cache = ./cache/cord-261405-n05wjimk.txt txt = ./txt/cord-261405-n05wjimk.txt === reduce.pl bib === id = cord-261193-960th627 author = Ohnishi, Kouji title = Evaluation of a non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold as a SARS 3CL protease inhibitor date = 2019-01-15 pages = extension = .txt mime = text/plain words = 6061 sentences = 348 flesch = 70 summary = A non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold was evaluated as a novel inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)). The synthesized decahydroisoquinolin inhibitors showed about 2.4 times potent inhibitory activities for SARS 3CL(pro) when combined with a non-prime site substituent. The residue was purified by silica gel column chromatography (hexane/EtOAc = 5:1) to give a title alcohol ( TPAP (tetra-n-propyl ammonium perrutenate, 316 mg, 0.9 mmol) was added to a solution of above alcohol (10.5 g, 47.5 mmol) and NMO (N-methylmorphline-N-oxide, 21.1 g, 180 mmol) in CH 2 Cl 2 (180 mL) at 0°C. After being stirred for 30 min, the reaction mixture was filtered through a silica gel layer and the filtrate was concentrated. The filtrate was concentrated and resulting residue was purified by silica gel column chromatography (hexane/ EtOAc = 10:1) to afford 15 (640 mg, 50%). cache = ./cache/cord-261193-960th627.txt txt = ./txt/cord-261193-960th627.txt === reduce.pl bib === id = cord-261173-lnjh56ts author = Misra-Hebert, Anita D. title = Impact of the COVID-19 Pandemic on Healthcare Workers’ Risk of Infection and Outcomes in a Large, Integrated Health System date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3574 sentences = 166 flesch = 47 summary = In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19-related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. 23 For the outcomes of hospital and intensive care unit (ICU) admission of COVID-19 testpositive patients, the propensity score covariates are those that were found associated with COVID-19 hospitalization outcome in our previous work including age, race, ethnicity, gender, smoking history, body mass index, median income, population per housing unit, presenting symptoms (including fever, fatigue, shortness of breath, diarrhea, vomiting), comorbidities (including asthma, hypertension, diabetes, immunosuppressive disease), medications (including immunosuppressive treatment, nonsteroidal anti-inflammatory drugs [NSAIDs]), and laboratory values (including pre-testing platelets, aspartate aminotransferase, blood urea nitrogen, chloride, and potassium). [7] [8] [9] [10] 12 The fact that HCW identified as patient facing had a significantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. cache = ./cache/cord-261173-lnjh56ts.txt txt = ./txt/cord-261173-lnjh56ts.txt === reduce.pl bib === id = cord-260793-bb4h255w author = Brann, David H. title = Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date = 2020-05-18 pages = extension = .txt mime = text/plain words = 11985 sentences = 604 flesch = 53 summary = It has recently been demonstrated through single cell RNA sequencing analysis (referred to herein as scSeq) that cells from the human upper airway -including nasal RE goblet, basal and ciliated cells -express high levels of ACE2 and TMPRSS2, suggesting that these RE cell types may serve as a viral reservoir during CoV-2 infection (33) . The presence of Ace2 and Tmprss2 transcripts in mouse WOM and their (near total) absence in purified OSNs suggest that the molecular components that enable CoV-2 entry into cells are expressed in non-neuronal cell types in the mouse nasal epithelium. An independent mouse scSeq data set (obtained using the 10x Chromium platform, see Methods) revealed that olfactory sensory neurons did not express Ace2 (2 of 28769 mature OSNs were positive for Ace2), while expression was observed in a fraction of Bowman's gland cells and HBCs ( Figure S4 , see methods). cache = ./cache/cord-260793-bb4h255w.txt txt = ./txt/cord-260793-bb4h255w.txt === reduce.pl bib === id = cord-261059-rcpx4god author = Brenner, Steven Robert title = Erythropoietin Induced Hemoglobin Sub‐Unit Beta may Stimulate Innate Immune RNA Virus Pattern Recognition, Suppress Reactive Oxygen Species, Reduce ACE2 Viral Doorway Opening and Neutrophil Extracellular Traps against Covid‐19 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 869 sentences = 55 flesch = 34 summary = Erythropoietin may stimulate innate immunity against RNA viruses, such as Covid‐19, through hemoglobin sub‐unit Beta acting on the retinoic acid inducible gene I (RIG‐1) and melanoma differentiation associated gene 5 (MDA5) viral pattern recognition receptors, causing interferon production and also maintains the vascular endothelium, a major target of SARS‐CoV‐2, possibly reducing thrombotic events which are becoming increasingly recognized complications of COVID19. Possibly hemoglobin (HB), especially subunit beta also contributed to recovery, since HB participates in innate immunity through differentially regulating the retinoic acid inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5), which are involved in viral recognition and mobilizing an interferon response. (Assessment of Endothelial and Haemostatic Changes During Severe SARS-CoV-2 Infection (Covid-Thelium), including syndecan-1, a marker of degradation of glycocalyx, D-dimers plasma levels association with thrombotic events, and von Willibrandt Factor, Viscoelastic testing and Vascular endothelial Growth Factor Receptor type 1. cache = ./cache/cord-261059-rcpx4god.txt txt = ./txt/cord-261059-rcpx4god.txt === reduce.pl bib === id = cord-261029-befymalm author = Sultan, Keith title = Review of inflammatory bowel disease and COVID-19 date = 2020-10-07 pages = extension = .txt mime = text/plain words = 3257 sentences = 153 flesch = 48 summary = Early reports of the virus, now known as severe acute respiratory syndrome coronavirus 2, and its clinical disease coronavirus disease 2019 (COVID-19), has shown higher rates of morbidity and mortality in the elderly and those with pre-existing medical conditions. The authors also reported that there had been no cases of IBD/SARS-CoV-2 infected patients in the three largest tertiary IBD centers in Wuhan (Tongji Hospital, Union Hospital, and Zhongnan Hospital) at the time their manuscript was prepared, March 8, 2020. Rodriguez-Lago et al [29] reported on 40 cases of IBD (21 hospitalized) with confirmed positive tests for SARS-CoV-2 from 5 sites in the Basque Country (Spain), median age 59 years, 60% male, 32% Crohn's disease (CD), with 28% on immune therapy, 18% biologic, and 10% systemic corticosteroids. To date, the largest national case reporting has come from a combined 24 IBD referral centers in Italy, affiliated with the Italian Group for the Study of Inflammatory Bowel Disease (IG-IBD) [32] . cache = ./cache/cord-261029-befymalm.txt txt = ./txt/cord-261029-befymalm.txt === reduce.pl bib === id = cord-261253-btwx2vxo author = Yip, Timothy T. C. title = Application of ProteinChip Array Profiling in Serum Biomarker Discovery for Patients Suffering From Severe Acute Respiratory Syndrome date = 2007 pages = extension = .txt mime = text/plain words = 3836 sentences = 310 flesch = 66 summary = By protein chip array profiling technology, a number of serum biomarkers that might be useful in monitoring the clinical course of SARS patients were identified. The serum profiling spectra in SARS patients were acquired, baseline subtracted and analyzed in parallel with those from the control subjects by Ciphergen ProteinChip Software 3.0.2 with their peak intensities compared by a nonparametric two sample Mann-Whitney-U test. More than twelve peaks were differentially expressed in SARS patients with one at m/z of 11,695 (later identified to be serum amyloid A protein), which had increase in peak intensity correlating with the extent of SARS-coronavirus induced pneumonia as defined by a serial chest X-ray opacity score. In a recent article, the discovery of 12 upor downregulated serum biomarkers were reported in SARS patients by a novel protein chip array profiling approach (1014) with one biomarker appears to be useful in monitoring the extent of pneumonia (15) . cache = ./cache/cord-261253-btwx2vxo.txt txt = ./txt/cord-261253-btwx2vxo.txt === reduce.pl bib === id = cord-261307-qmh3wtqo author = Evans, Scott E. title = Inducible Epithelial Resistance against Coronavirus Pneumonia in Mice date = 2020-10-17 pages = extension = .txt mime = text/plain words = 658 sentences = 38 flesch = 44 summary = , a single PUL-042 treatment significantly improved survival of otherwise lethal SARS-CoV infection and significantly reduced the lung MERS-CoV burden 3 days after challenge, congruent with our prior work demonstrating a consistent correlation between survival advantage and reduced pathogen burden. Although it is suspected that a second pandemic wave may arise concurrently with seasonal influenza, a patient with a virus-like illness can be preemptively treated with PUL-042 with the expectation that she or he will appreciate a benefit, whether the syndrome results from SARS-CoV-2, influenza A, both viruses, or another pathogen. The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents the latest threat to global health security, and the pressure to identify effective therapeutics during this pandemic is immense. After an early report of a "cytokine storm" in patients with coronavirus disease (COVID-19) , there is increased interest in anti-IL-6 therapy as a treatment option, with ill-defined criteria for use (1). Inducible epithelial resistance against acute Sendai virus infection prevents chronic asthma-like lung disease in mice cache = ./cache/cord-261307-qmh3wtqo.txt txt = ./txt/cord-261307-qmh3wtqo.txt === reduce.pl bib === id = cord-261111-g1qxo01i author = Kowalewski, Joel title = Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space date = 2020-08-06 pages = extension = .txt mime = text/plain words = 6029 sentences = 349 flesch = 58 summary = There are subsequently unmet needs in COVID-19 research, including identification of compounds that target the relevant SARS-CoV-2 human proteins from (1) approved drugs, (2) FDA registered chemicals or (3) a large repository of~14 million purchasable chemicals from the ZINC 15 database [18] , which we computed additional properties for such as mammalian toxicity, vapor pressure, and logP. For 65 human protein targets that SARS-CoV-2 interacts with that had publicly available bioassay and chemical data [6] , we first generated a database of predictions based on structural similarity to chemicals that interact with the targets and then machine learning models (34) . Accordingly, we used the machine learning models to predict activities of 100,000 FDA registered chemicals (UNII database) [19] as well as the DrugBank [20] and Therapeutic Targets [21, 22] databases, which include information on drug interactions, pathways, and approval status. cache = ./cache/cord-261111-g1qxo01i.txt txt = ./txt/cord-261111-g1qxo01i.txt === reduce.pl bib === id = cord-260981-647wfa8z author = Torti, Lorenza title = Impact of SARS CoV-2 in Hemoglobinopathies with Immune Disfunction and Epidemiology. A Protective Mechanism from Beta Chain Hemoglobin Defects? date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1291 sentences = 83 flesch = 54 summary = A novel coronavirus (SARS-CoV-2) has rapidly overspread infecting in few months all continents and representing a medical emergency, with 20% of patients with severe clinical manifestations. 2 The transcribed, non-structural SARS-CoV-2 proteins ORF 8, 3a, and 10 play critical roles during infection (viral replication) and disease pathogenesis (stimulate NF-kB mediated inflammation and immune responses). Of the 105 patients who were in contact with the infected staff, only 7 reported symptoms, all mild, in the two months surveillance, and only 1 of the 7 tested positive on the swab. The SARS-CoV-2 positive patient, a female aged 59 with Beta-Thalassemia Major(TM)(IVS-6/745) received a transfusion on March 5, and after being notified, called the hospital on March 21 reporting mild temperature (37 o C). So, our case of SARS-CoV-2 infection in TM patient was revealed during an endemic outbreak, which involved 24 symptomatic HCPs out of a staff of 52. Recently a multicentric Iranian experience of 18350 Beta-thalassemic patients (only fifteen confirmed cases) reported mild to moderate disease of COVID-19. cache = ./cache/cord-260981-647wfa8z.txt txt = ./txt/cord-260981-647wfa8z.txt === reduce.pl bib === id = cord-261414-vqvctafm author = Ian Gallicano, G. title = Molecular targeting of vulnerable RNA sequences in SARS CoV-2: identifying clinical feasibility date = 2020-11-12 pages = extension = .txt mime = text/plain words = 3032 sentences = 230 flesch = 58 summary = Here we show that siRNAs and miRNAs inhibit SARS CoV-2 spike protein production in a dose-dependent manner in both HEK293 cells and a primary human airway tracheal cell line. Two cell types, HEK293 cells and primary human tracheal cells (hpTCs) were employed to test the hypothesis that siRNAs or miRNAs could suppress SARS CoV-2 spike expression. As a result, electroporation was used to introduce spike cDNA into hpTCs. Twenty four hours after electroporation of spike plasmid, 200 nM of each small RNA (the concentration seen to virtually completely suppress spike in HEK293 cells) was transfected resulting in marked reduction in spike protein expression in both siRNA1 + 2 and miRNA1 + 2 samples (Fig. 3A) . The data in Fig. 3B , C reveal that siRNA1/NT (non-transfection reagent) suppressed spike protein production in a dose-dependent manner in HEK293 cells (Fig. 3B ). cache = ./cache/cord-261414-vqvctafm.txt txt = ./txt/cord-261414-vqvctafm.txt === reduce.pl bib === id = cord-261075-wqtxhiy8 author = Zhang, Meng title = The nervous system——a new territory being explored of SARS-CoV-2 date = 2020-10-28 pages = extension = .txt mime = text/plain words = 3716 sentences = 216 flesch = 41 summary = However, there is growing evidence that SARS-CoV-2 can result in a broad spectrum of neurologic diseases (6) (7) (8) (9) , which is not surprising, as neurological manifestations have been reported in other respiratory viral infections, including coronavirus, but the nervous system manifestations of COVID-19 are more common and disabling, raising the worldwide concerns about its potential long-term complications to humans (10, 11) . In particular, we focused on its neurological manifestations and specific pathogenesis, as well as its comparison with other viral respiratory infections.Finally, we further summarized the significance of the neuroinvasion and the follow-up issues that need to be paid attention to by scientists, so as to help neurologists understand the influence of SARS-CoV-2 on nervous system better and promote the accurate diagnosis and efficient treatment of COVID-19. cache = ./cache/cord-261075-wqtxhiy8.txt txt = ./txt/cord-261075-wqtxhiy8.txt === reduce.pl bib === id = cord-261297-kbcsa9zj author = Chang, Shan-Chwen title = Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) date = 2005-03-31 pages = extension = .txt mime = text/plain words = 1040 sentences = 68 flesch = 50 summary = title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) Severe acute respiratory syndrome (SARS) is a new infectious disease in humans caused by SARS-associated coronavirus (SARS-CoV). Liu et al reported clinical characteristics, management, and analysis of prognostic factors in patients with probable SARS who were treated at a specially designated hospital in Taipei City during the SARS epidemic from late April to July 2003. A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Clinical characteristics, management and prognostic factors in patients with probable severe acute respiratory syndrome (SARS) in a SARS center in Taiwan Temporal relationship of viral load, ribavirin, interleukin (IL)-6, IL-8, and clinical progression in patients with severe acute respiratory syndrome cache = ./cache/cord-261297-kbcsa9zj.txt txt = ./txt/cord-261297-kbcsa9zj.txt === reduce.pl bib === id = cord-261279-6mef38eo author = Chu, Daniel K W title = Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date = 2020-01-31 pages = extension = .txt mime = text/plain words = 2971 sentences = 178 flesch = 54 summary = RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. cache = ./cache/cord-261279-6mef38eo.txt txt = ./txt/cord-261279-6mef38eo.txt === reduce.pl bib === id = cord-261415-qxl14j2m author = Fu, Yajing title = Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools date = 2020-03-03 pages = extension = .txt mime = text/plain words = 2594 sentences = 140 flesch = 41 summary = In addition, given that uncontrolled pulmonary inflammation is likely a leading cause of fatality in SARS-CoV-2 infection, we also attempt to speculate possible therapeutic interventions that may be applied to attenuate inflammatory responses in order to reduce mortality (Fig. 2) . In SARS-CoV infection, viroporin 3a has also been shown to trigger the activation of NLRP3 (NOD-like receptor protein 3) inflammasome and the secretion of IL-1b in bone marrowderived macrophages, suggesting the induction of cell pyroptosis , which can cause the release of large amounts of proinflammatory factors (Fink and Cookson 2005) . However, previous studies in animal models have shown that in SARS-CoV infection, such anti-S protein-neutralizing antibodies (anti-S-IgG) can also cause severe lung injury by altering inflammatory responses (Liu et al. This animal study suggests that despite viral suppression, the presence of anti-spike protein antibody at the acute stage of SARS-CoV infection can actually cause severe acute lung injury that persists until the late stages. cache = ./cache/cord-261415-qxl14j2m.txt txt = ./txt/cord-261415-qxl14j2m.txt === reduce.pl bib === id = cord-261470-sqxdwu6j author = Weichmann, Franziska title = Projected supportive effects of Pycnogenol® in patients suffering from multi-dimensional health impairments after a SARS-CoV2 infection date = 2020-10-09 pages = extension = .txt mime = text/plain words = 5918 sentences = 308 flesch = 38 summary = Two London based hospitals also found increasing numbers of patients with Kawasaki-like symptoms in communities with high rates of COVID 19, which was provisionally called pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) [68] [70] . Another double-blind, placebo-controlled study reported similar effects when supplementing type II diabetes and hypertensive patients, taking ACE inhibitor medication together with 125 mg Pycnogenol ® daily for 3 months. Regarding endotheliitis, Pycnogenol ® studies offer good evidence for potential beneficial effects for patients suffering from COVID-19 by improving endothelial function. As Pycnogenol ® offers antioxidant and anti-inflammatory activities and positively influences endothelial cell function as well as microcirculation and platelet reactivity, a supplementation might support the management of COVID-19 patients. We hypothesize possible additional beneficial effects of Pycnogenol ® in patients infected with the new coronavirus SARS-CoV2 and those who suffer from abiding health problems, when complemented to the standard treatment also upon the first day of symptoms or infection. cache = ./cache/cord-261470-sqxdwu6j.txt txt = ./txt/cord-261470-sqxdwu6j.txt === reduce.pl bib === id = cord-261634-vfe1lawl author = Riddell, Shane title = The effect of temperature on persistence of SARS-CoV-2 on common surfaces date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4210 sentences = 224 flesch = 55 summary = Currently, there are conflicting reports on the survivability of SARS-CoV-2, with data ranging from 3 to 14 days at room temperature for a single surface type, stainless steel Open Access *Correspondence: Shane.Riddell@csiro.au Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia [5, 11] . At 20 °C, infectious SARS-CoV-2 virus was still detectable after 28 days post inoculation, for all non-porous surfaces tested (glass, polymer note, stainless steel, vinyl and paper notes). The present study has demonstrated that in controlled conditions, SARS-CoV-2 at a starting viral load and in a fluid matrix equivalent to that typically excreted by infected patients, remains viable for at least 28 days when dried onto non-porous surfaces at 20 °C and 50% relative humidity. It is important to note that after 28 days, infectious SARS-CoV-2 was also recovered from stainless steel, vinyl and glass, suggesting survivability on paper or polymer banknotes was not very different from the other non-porous surfaces studied. cache = ./cache/cord-261634-vfe1lawl.txt txt = ./txt/cord-261634-vfe1lawl.txt === reduce.pl bib === id = cord-261834-x5ltmj30 author = Guo, Cheng-Xian title = Epidemiological and clinical features of pediatric COVID-19 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3438 sentences = 195 flesch = 48 summary = METHODS: A retrospective study was conducted on children with a definite diagnosis of COVID-19 in mainland China using the web crawler technique to collect anonymous COVID-19 updates published by local health authorities. In this report, we conducted a retrospective review of COVID-19 features in 341 pediatric patients with ages between 0 and 14 years with the overall goal of providing data that could help in the development of guidelines for the prevention and treatment of pediatric COVID-19. This retrospective review was conducted in children aged 0-14 years with a definite diagnosis of COVID-19 from local health authorities between January 15, 2020, and March 15, 2020, in mainland China. Although there is relatively ample information available for adult COVID-19 patients, our knowledge and analysis of the epidemiology and clinical characteristics of pediatric COVID-19 is quite limited. The data was obtained from local China health authorities thus unable to compare the epidemiological and clinical data from US and European studies in children with COVID-19. cache = ./cache/cord-261834-x5ltmj30.txt txt = ./txt/cord-261834-x5ltmj30.txt === reduce.pl bib === id = cord-261750-6b1y7yxg author = Kwek, Seow-Khee title = Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge date = 2006-05-31 pages = extension = .txt mime = text/plain words = 2795 sentences = 179 flesch = 58 summary = title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge Method Postal survey comprising Health-Related Quality of Life (HRQoL) questionnaires and anxiety and depression measures was sent to them at 3 months' postdischarge. Hence, in this study, we undertook to ascertain systematically the quality of life and psychological well-being of SARS survivors 3 months' postdischarge from the acute episode. The responders and the nonresponders were comparable on demographic parameters, duration of hospital stay, preillness health status, as well as the proportion of patients admitted to the intensive care unit ( Table 2 ). The health care workers appeared to be more adversely affected than nonstaff based on both the HRQol SF-36 scores (Fig. 1 , see staff-SARS) and the mean scores for IES, and the HADS Depression and Anxiety scores, although these were not significant. cache = ./cache/cord-261750-6b1y7yxg.txt txt = ./txt/cord-261750-6b1y7yxg.txt === reduce.pl bib === id = cord-261921-c97ygxq2 author = Souders, Colby P. title = Considerations for Bedside Urologic Procedures in Patients with Severe Acute Respiratory Syndrome Coronavirus-2 date = 2020-04-24 pages = extension = .txt mime = text/plain words = 1826 sentences = 94 flesch = 42 summary = METHODS: Urologic trainees and attending physicians at our institution, who are familiar with existing safety recommendations and guidelines regarding the care of infected patients, were queried regarding their experiences to determine an expert consensus on best practices for bedside procedures for SARS-CoV-2 positive patients. RESULTS: Our team developed the following general recommendations for urologic interventions on SARS-CoV-2 positive patients: maximize use of telehealth (even for inpatient consults), minimize in-room time, use personal protective equipment appropriately, enlist a colleague to assist, and acquire all supplies that may be needed and maintain them outside the room. Our aim is to share our experiences performing bedside urologic procedures on SARS-CoV-2positive patients and offer considerations to maximize the safety of the patients and providers involved and conserve supplies while maintaining a high standard of care. Outlined above are our experiences with inpatient consultations and bedside procedures in SARS-CoV-2 patients and how we have attempted to address urologic challenges that have emerged with this pandemic. cache = ./cache/cord-261921-c97ygxq2.txt txt = ./txt/cord-261921-c97ygxq2.txt === reduce.pl bib === id = cord-261877-4y37676n author = Xu, Cong title = Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date = 2020-06-30 pages = extension = .txt mime = text/plain words = 8754 sentences = 505 flesch = 60 summary = Recent cryoelectron microscopy (cryo-EM) studies on the stabilized ectodomain of SARS-CoV-2 S protein revealed a closed state of S trimer with three RBD domains in "down" conformation (Walls et al., 2020) , as well as an open state with one RBD in the "up" conformation, corresponding to the receptor-accessible state (Walls et al., 2020; Wrapp et al., 2020) . To gain a thorough picture on how the receptor ACE2 binding induces conformational dynamics of the SARS-CoV-2 S trimer and triggers transition towards the postfusion state, we determine the cryo-EM structure of SARS-CoV-2 S trimer in complex with human ACE2 PD domain to 3.8 Å resolution (termed SARS-CoV-2 S-ACE2, Figs. Based on the data, we put forward a mechanism of ACE2 binding-induced conformational transitions of SARS-CoV-2 S trimer from the tightly closed ground prefusion state transforming towards the postfusion state (Fig. 6) . Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding cache = ./cache/cord-261877-4y37676n.txt txt = ./txt/cord-261877-4y37676n.txt === reduce.pl bib === id = cord-261959-pvufajw4 author = Karathanou, Konstantina title = A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 9192 sentences = 455 flesch = 59 summary = Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. The surface of the Severe Acute Respiratory Syndrome (SARS)-CoV-2 virion is decorated with large membrane-anchored spike proteins S (Figure 1 ) that bind to Angiotensin Converting Enzyme 2 (ACE2) receptor of the host cell (Briefing, 2020; Hoffmann et al., 2020; Li et al., 2003; Xiao et al., 2003; Zhou et al., 2020) . To derive clues about intra-molecular interactions with potential role in shaping structural dynamics of protein S, we computed two-dimensional graphs of all Hbonds of protein S in structures proposed for the closed, open, and pre-fusion conformation, and for ACE2 bound to an RBD fragment. cache = ./cache/cord-261959-pvufajw4.txt txt = ./txt/cord-261959-pvufajw4.txt === reduce.pl bib === id = cord-261662-d0tg9i90 author = Andres, Cristina title = Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date = 2020-06-08 pages = extension = .txt mime = text/plain words = 4673 sentences = 214 flesch = 52 summary = title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. Because of the importance of the S protein, we carried out a deep-sequencing study of the S gene in upper respiratory tract samples from 18 patients with mild or severe SARS-CoV-2 disease. The fact that the truncated S protein was present in only a low percentage of the entire viral quasispecies suggests that natural selection may have designed a favorable equilibrium in which a limited number of deleted virions are generated to balance virus production with infection of new cells during disease progression. cache = ./cache/cord-261662-d0tg9i90.txt txt = ./txt/cord-261662-d0tg9i90.txt === reduce.pl bib === id = cord-261718-zqoggwnk author = Pietschmann, Jan title = Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date = 2020-06-03 pages = extension = .txt mime = text/plain words = 1188 sentences = 76 flesch = 45 summary = Available point-of-care diagnostic systems as lateral flow assays have high potential for fast and easy on-site antibody testing but are lacking specificity, sensitivity or possibility for quantitative measurements. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. For magnetic immuno-detection, immunofiltration columns were coated with a SARS-CoV-2 spike protein peptide. After addition of 176 biotinylated GaR and subsequent labelling with streptavidin-AP, the ELISA plate was read out at 177 405 nm and obtained measuring values were used to generate calibration curves for SARS-CoV-2 178 specific antibody concentrations in PBS (Fig 1, black curve) and in human serum samples (Fig 1, red 179 curve). Same calibration measurements employing dilutions of SARS-CoV-2 specific antibody were 211 done with our PoC MInD-based setup (Fig 2 and 3) . Comparable to laboratory-based ELISA, the same 212 dilutions of SARS-CoV-2 spike protein peptide specific antibody in PBS-buffer (Fig 3, black cache = ./cache/cord-261718-zqoggwnk.txt txt = ./txt/cord-261718-zqoggwnk.txt === reduce.pl bib === id = cord-262104-oig3qrr7 author = Brüssow, Harald title = COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date = 2020-06-08 pages = extension = .txt mime = text/plain words = 7118 sentences = 365 flesch = 53 summary = Very similar information was reported in data describing household transmission in Wuhan, where children showed a 4% infection rate compared with 17% in adults. 1.6 million tests were used to identify 1'400 SARS-CoV-2-positive cases; 1000 patients had had exposure to infected people from Hubei. In Wuhan, 105 index cases of patients suffering from moderate COVID-19 symptoms (fever, cough, fatigue) were investigated for secondary transmission to 392 household contacts. The control measures that stopped the epidemic locally have included: intense infection surveillance of incoming travelers; isolation of COVID-19 cases in hospitals; contact tracing and quarantine in holiday camps; and school closure but no lock-down, thus preventing the crisis from having a negative economic impact. Model calculations showed that the containment measures (the quarantine of exposed, and the isolation of infected persons) which depleted the number of susceptible individuals for the virus, reproduced the actually observed case development. cache = ./cache/cord-262104-oig3qrr7.txt txt = ./txt/cord-262104-oig3qrr7.txt === reduce.pl bib === id = cord-261941-xf1k5uj1 author = Stackhouse, Robin A. title = Severe acute respiratory syndrome and tuberculosis date = 2005-03-01 pages = extension = .txt mime = text/plain words = 5420 sentences = 306 flesch = 55 summary = Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients cache = ./cache/cord-261941-xf1k5uj1.txt txt = ./txt/cord-261941-xf1k5uj1.txt === reduce.pl bib === id = cord-261472-qcu73sdu author = Yao, Yong Xiu title = Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date = 2004-07-01 pages = extension = .txt mime = text/plain words = 3851 sentences = 159 flesch = 47 summary = Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. The possible use of insect cell-displayed S protein for diagnostic application was assessed by examining fragment reactivity with serum samples from patients infected with human CoV 229E and also with serum from a patient with suspected but clinically unconfirmed SARS (serum sample 3118). Of the 2 assay formats we used, nondenatured S protein present on the cell surface provided the most sensitive detection of antibodies, with clear shifts in fluorescence for serum samples from patients with suspected but clinically unconfirmed SARS. cache = ./cache/cord-261472-qcu73sdu.txt txt = ./txt/cord-261472-qcu73sdu.txt === reduce.pl bib === id = cord-262000-k32cb9ym author = Li, Xue-Ting title = Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1911 sentences = 94 flesch = 44 summary = title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 Angiotensin converting enzyme 2 (ACE2) has garnered widespread interest as the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19 pandemic, providing a critical link among COVID-19, inflammatory storm, ACE2 and cardiovascular disease 1,2 . Remarkably, recombinant human ACE2 (rhACE2), sACE2, ACE2-Fc, and ACE2-Ig are thought to be promising therapeutic approaches for COVID-19 patients with SARS-CoV-2 infection through competitive inhibiting the binding of viral Spike protein to mACE2 4 . Intriguingly, circulating Ang II level was obviously elevated in COVID-19 patients with lung injury (Table 1) 9 which further upregulates ADAM-17 activity by interacting with AT1 receptors, leading to more shedding of ACE2 and thereby accelerating renin-angiotensin-aldosterone system (RAAS)-mediated injury including severe cardiopulmonary damage (Fig. 1) (Table 1) 10 . cache = ./cache/cord-262000-k32cb9ym.txt txt = ./txt/cord-262000-k32cb9ym.txt === reduce.pl bib === id = cord-261435-wcn4bjnw author = Ren, Xianwen title = Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date = 2020-10-29 pages = extension = .txt mime = text/plain words = 8495 sentences = 468 flesch = 57 summary = Notably, the percentages of megakaryocytes 207 and monocytes in PBMCs were elevated, particularly in severe COVID-19 patients during 208 the disease progression stage (Figure 2A) The increased plasma B cells in peripheral blood appeared to be derived from active 231 proliferation of plasmablasts and transitions from memory B cells based on the paired BCR 232 sequencing analyses. Similarly, the clonal expansion of 398 a central memory CD4+ T cell cluster highly expressing AQP3 (T_CD4_c02-AQP3) was 399 also associated with the triad interaction by disease severity, age, and sex ( SARS-CoV-2 detected in multiple epithelial and immune cell types with 414 interferon response phenotypes 415 The enrichment of plasma B and proliferative T cells in BALF and the elevation of these 416 cells in PBMCs of COVID-19 patients highlighted the roles of these cells in combating 417 SARS-CoV-2 infection. cache = ./cache/cord-261435-wcn4bjnw.txt txt = ./txt/cord-261435-wcn4bjnw.txt === reduce.pl bib === id = cord-262068-9ixq8hwb author = Gottardi, Andrea De title = Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1773 sentences = 119 flesch = 49 summary = The data that support the findings of this study are available from the corresponding author, upon Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection SUMMARY We present here the case of a 62-year-old man, who was referred to the emergency department with fever and cough for 3 days. Therefore, due to the potential clinical efficacy for COVID-19 patients [11] and based on SARS clinical cases in 2003 [12] , and before the publication of the LOTUS China trial [13] , we started a treatment with lopinavir 200 mg and ritonavir 50 mg 2-0-2, and hydroxychloroquine 200 mg twice daily. Clinical data available so far indicate that up to 53% of the patients with COVID-19 present increased levels of transaminases during the infection and that liver injury is apparently associated with the severity of respiratory symptoms [14, 15] . cache = ./cache/cord-262068-9ixq8hwb.txt txt = ./txt/cord-262068-9ixq8hwb.txt === reduce.pl bib === id = cord-261619-31jk1vh6 author = Lindholm, David A title = Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2176 sentences = 112 flesch = 47 summary = Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. Mitigation of the coronavirus disease 2019 (COVID-19) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] . During the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (PPE) use [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . The electronic medical record was reviewed (1) for comorbid conditions in positive cases and (2) for additional SARS-CoV-2 testing and BAMC hospital admission within 14 days of screening for all patients. Nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. However, none of the screen-only patients later tested positive or were hospitalized for COVID-19 within 14 days. cache = ./cache/cord-261619-31jk1vh6.txt txt = ./txt/cord-261619-31jk1vh6.txt === reduce.pl bib === id = cord-261688-njlxrxv6 author = Yang, Ziwei title = Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date = 2020-08-12 pages = extension = .txt mime = text/plain words = 2508 sentences = 166 flesch = 52 summary = Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA. Based on our existing experimental data, we propose a simple working model to illustrate how NSP8 218 negatively regulates innate immune responses by inhibiting MDA5 K63-linked polyubiquitination (Fig.5c) . cache = ./cache/cord-261688-njlxrxv6.txt txt = ./txt/cord-261688-njlxrxv6.txt === reduce.pl bib === id = cord-262180-t4akem15 author = Cheruiyot, Isaac title = Comment on “Encephalopathy in patients with COVID‐19: A review” date = 2020-07-11 pages = extension = .txt mime = text/plain words = 269 sentences = 29 flesch = 42 summary = key: cord-262180-t4akem15 title: Comment on "Encephalopathy in patients with COVID‐19: A review" cord_uid: t4akem15 I read with great interest the article by Garg and colleagues on "Encephalopathy in patients with COVID-19: A review". The authors performed a review of published reports on COVID-19-associated encephalitis and encephalopathy. Encephalopathy in patients with COVID-19: a review Status of SARS-CoV-2 in cerebrospinal fluid of patients with COVID-19 and stroke Facial diplegia, a possible atypical variant of Guillain-Barré Syndrome as a rare neurological complication of SARS-CoV-2 Guillain-Barré syndrome after SARS-CoV-2 infection Guillain-Barré syndrome associated with leptomeningeal enhancement following SARS-CoV-2 infection A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 Sars-Cov-2: underestimated damage to nervous system COVID-19 encephalopathy: detection of antibodies against SARS-CoV-2 in CSF Encephalopathy and encephalitis associated with cerebrospinal fluid cytokine alterations and coronavirus disease How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis? cache = ./cache/cord-262180-t4akem15.txt txt = ./txt/cord-262180-t4akem15.txt === reduce.pl bib === id = cord-262020-ygl8xlhk author = McDermott, Aoibhinn title = Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection date = 2020-05-16 pages = extension = .txt mime = text/plain words = 300 sentences = 30 flesch = 55 summary = authors: McDermott, Aoibhinn; O'Kelly, John; de Barra, Eoghan; Fitzpatrick, Fidelma; Little, Dilly M.; Davis, Niall F. title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection To date, many urological centres have prioritised their patients for urgent surgical intervention because of a reduction in operating theatre availability and the risk of hospital-acquired SARS-CoV-2 infection [1, 2] . Here we present our perioperative outcomes for patients undergoing urological surgery during the initial stage of the SARS-CoV-2 pandemic in Ireland (between March 16 and May 1, 2020, inclusive). Our hospital has an onsite microbiology laboratory that performs daily SARS-CoV-2 realJ o u r n a l P r e -p r o o f Elective surgery was prioritised according to recent European guidelines and patients were then placed on a centralised departmental theatre waiting list [1] . cache = ./cache/cord-262020-ygl8xlhk.txt txt = ./txt/cord-262020-ygl8xlhk.txt === reduce.pl bib === id = cord-261566-fn08b0y2 author = Mudgal, Rajat title = Prospects for mucosal vaccine: shutting the door on SARS-CoV-2 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 7060 sentences = 413 flesch = 38 summary = 15 The disease severity and lung damage in the case of SARS-CoV-2 infection can be directly correlated with the dysregulated immune response at 7-10 days after symptom onset and is characterized by exuberant production of cytokines including IL-2, IL-7, IL-10, MIP-1A, IP-10, and TNF-α. 53, [98] [99] [100] [101] [102] Ferrets are a suitable animal model for SARS-CoV vaccine evaluation as they support viral replication in the respiratory tract, develop similar disease symptoms, and display severe lung pathology. Potential ADE and waning of vaccine-induced immune response represent other obstacles in the development of a mucosal vaccine against SARS-CoV-2. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Effect of mucosal and systemic immunization with virus-like particles of severe acute respiratory syndrome coronavirus in mice cache = ./cache/cord-261566-fn08b0y2.txt txt = ./txt/cord-261566-fn08b0y2.txt === reduce.pl bib === id = cord-262149-qrjprsv5 author = Sarode, Gargi S. title = Clinical status determines the efficacy of salivary and nasopharyngeal samples for detection of SARS-CoV-2 date = 2020-10-12 pages = extension = .txt mime = text/plain words = 824 sentences = 67 flesch = 58 summary = To draw a meaningful conclusion in this regard, the most important study design would be a comparative cross-sectional analysis of salivary and nasopharyngeal samples (NPSs) in the detection of SARS-CoV-2 RNA with a cycle threshold value. (Table 1 ) All the studies projected saliva as potential sampling material for the detection and diagnosis of SARS-CoV-2 RNA using RT-PCR. In asymptomatic cases, the sensitivity and detection rate was more in salivary samples as compared to NPS [2, 7] . On the contrary, in asymptomatic cases, NPS could not be a representative sample (probably due to absent or limited viral localization) for the detection of SARS-CoV-2. Looking at this discriminative trend, prescription of saliva samples for asymptomatic cases and NPS for symptomatic cases would be a valuable recommendation subject to validation in future randomized prospective studies. A direct comparison of enhanced saliva to nasopharyngeal swab for the detection of SARS-CoV-2 in symptomatic patients cache = ./cache/cord-262149-qrjprsv5.txt txt = ./txt/cord-262149-qrjprsv5.txt === reduce.pl bib === id = cord-262029-zzn74cjr author = Kang, Chang Kyung title = In vitro activity of lopinavir/ritonavir and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2 at concentrations achievable by usual doses date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2575 sentences = 151 flesch = 52 summary = We examined the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2, at concentrations which can be used to treat coronavirus-19 patients with little concern of toxicity. Its in vitro antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19, has been recently suggested [4] . Therefore, the screening of poten-tial antivirals to fight COVID-19 is urgently needed and led us to assess the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2 at clinically administrable doses. We examined the in vitro activity of the oral antivirals lopinavir/ritonavir and hydroxychloroquine against SARS-CoV-2 at their patient administrable doses. In conclusion, this in vitro experimental study showed that lopinavir/ritonavir, at its clinically relevant concentration, showed significant anti-SARS-CoV-2 activity when it was administered following viral infection. 1. Lopinavir/ritonavir showed significant anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity both in terms of the prevention of cytotoxicity and reducing the viral load at plasma concentrations achievable by usual doses. cache = ./cache/cord-262029-zzn74cjr.txt txt = ./txt/cord-262029-zzn74cjr.txt === reduce.pl bib === id = cord-262145-i29e3fge author = Huang, Kuan-Ying A. title = Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date = 2020-10-19 pages = extension = .txt mime = text/plain words = 2949 sentences = 207 flesch = 61 summary = A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. The MAbs with 161 strong anti-RBD binding have a relatively long heavy chain CDR3 length (50% 162 binding concentration <0.5 µg/ml versus >0.5 µg/ml, p=0.03, two-tailed Mann-163 Whitney test; Supplemental Figure 3 The 32 anti-spike glycoprotein MAbs were systematically examined by plaque 173 reduction neutralisation (PRNT) assay for neutralisation of wild type SARS-CoV-2 174 virus (see methods; summarised in Table 1 ). Potent neutralising antibodies to the RBD of SARS-CoV-2 spike glycoprotein were 188 identified and we thus analyse the blockade of the ACE2-RBD interaction by anti-189 RBD antibodies in two assays ( Figure 3 , Table 1 The structure of VHH72-Fc bound to RBD is known (17) and its footprint on the 198 RBD does not overlap that of ACE2, so inhibition is thought to occur by steric 199 hindrance. cache = ./cache/cord-262145-i29e3fge.txt txt = ./txt/cord-262145-i29e3fge.txt === reduce.pl bib === id = cord-262268-gm99cadh author = Wang, Jingqiang title = Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date = 2003-12-01 pages = extension = .txt mime = text/plain words = 4027 sentences = 189 flesch = 49 summary = Consequently, we thoroughly investigated the immunoreactivities with patient sera of a series of synthesized peptides from SARS-coronavirus structural proteins. Results: Four epitopic sites, S599, M137, N66, and N371-404, located in the SARS-coronavirus S, M, and N proteins, respectively, were detected by screening synthesized peptides. The peptides representing the COOH terminus of the N protein, in particular N371 and N385, had high absorbance/cutoff value ratios with the highest positive detection rate and the lowest hydrophobicity score among all of the synthesized peptides (Fig. 1C, and Fig. 3 in the online Data Supplement). The other 17 peptides reacted only slightly with the sera from SARS patients and gave low detection rates, suggesting that the regions of the S protein covered by these peptides have no epitopic site. The patient sera preincubated with 4 mg/L S599 or N385 gave a 25-30% lower response in the ELISA (data not shown), suggesting that the two peptides could compete with SARS coronavirus for binding to the antibodies in SARS serum. cache = ./cache/cord-262268-gm99cadh.txt txt = ./txt/cord-262268-gm99cadh.txt === reduce.pl bib === id = cord-261952-xq6qney7 author = Mazzulli, Tony title = Proteomics and Severe Acute Respiratory Syndrome (SARS): Emerging Technology Meets Emerging Pathogen date = 2005-01-01 pages = extension = .txt mime = text/plain words = 1471 sentences = 75 flesch = 49 summary = This approach was hampered, however, by the fact that clinical and laboratory features did not distinguish patients with SARS from those with other respiratory illnesses and that there was no reliable rapid diagnostic test (1) (2) (3) . Characterizing the proteins that make up SELDI-TOF profiles in this manner not only provides insight into the pathophysiology of the disease, but may also lead to the development of more direct diagnostic tools and novel therapeutic targets relevant to SARS-CoV. In addition, in both studies (7, 8 ) , the patients with SARS were well characterized in terms of timing of specimen collection and severity of disease. (8 ) chose to apply SELDI-TOF to the diagnosis of SARS, there are many other, more common infectious diseases, such as influenza, that would also benefit from more rapid and reliable diagnostic and prognostic tests. cache = ./cache/cord-261952-xq6qney7.txt txt = ./txt/cord-261952-xq6qney7.txt === reduce.pl bib === id = cord-262184-uxyb4vih author = Jockusch, Steffen title = A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses that Cause SARS and COVID-19 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 6488 sentences = 395 flesch = 54 summary = We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. Using the criteria above, our study examines 11 nucleotide analogues with sugar or base modifications (structures shown in Fig. 1 ) for their ability to inhibit the SARS-CoV-2 or SARS-CoV RdRps: Ganciclovir 5'-triphosphate, Carbovir 5'-triphosphate, Cidofovir diphosphate, Stavudine 5'-triphosphate, Entecavir 5'-triphosphate, 2'-O-methyluridine-5'-triphosphate (2'-OMe-UTP), 3'-O-methyluridine-5'triphosphate (3'-OMe-UTP), 2'-fluoro-2'-deoxyuridine-5'-triphosphate (2'-F-dUTP), desthiobiotin-16aminoallyl-uridine-5'-triphosphate (Desthiobiotin-16-UTP), biotin-16-aminoallyl-2'-deoxyuridine-5'triphosphate (Biotin-16-dUTP) and 2'-amino-2'-deoxyuridine-5'-triphosphate (2'-NH 2 -dUTP). We then performed polymerase extension assays with the library of nucleoside triphosphate analogues (Fig. 1) either alone or in combination with natural nucleotides: 2'-OMe-UTP, 3'-OMe-UTP, 2'-F-dUTP, 2'-NH 2 -dUTP, Biotin-UTP, desthiobiotin-16-UTP, Sta-TP, Cid-DP + UTP + ATP, Car-TP + UTP + ATP + CTP, Gan-TP + UTP + ATP + CTP, or Ent-TP + UTP + ATP + CTP, following the addition of a pre-annealed RNA template and primer to a pre-assembled mixture of the SARS-CoV and/or SARS-CoV-2 RdRp (nsp12) and the two cofactor proteins (nsp7 and nsp8). cache = ./cache/cord-262184-uxyb4vih.txt txt = ./txt/cord-262184-uxyb4vih.txt === reduce.pl bib === id = cord-262159-8y0q45gr author = Ciorba, Andrea title = Don’t forget ototoxicity during the SARS-CoV-2 (Covid-19) pandemic! date = 2020-07-10 pages = extension = .txt mime = text/plain words = 956 sentences = 59 flesch = 41 summary = Aim of this communication is to remind clinical professionals to be aware of ototoxic side effects of several specific drugs proposed for the treatment of the new virus SARS-CoV-2 (Covid-19). In particular, chloroquine and hydroxychloroquine have been widely promoted and used during the pandemic; 2,3 however, in the past, data in the literature have suggested that in many treated cases side effects such as sensorineural hearing loss, tinnitus, and/or persistent imbalance were common. However, ototoxicity has been reported among the possible side effects of the adenosine nucleotide analogues; 5, 6 specifically, data in the literature report that patients may develop irreversible unilateral or bilateral hearing loss and tinnitus due to the use of these drugs, usually after a few weeks of administration. 7, 8 Lopinavir, a nucleoside reverse-transcriptase inhibitor, proposed in the treatment of SARS-CoV-2 infections, has been related to the onset of sensorineural hearing loss, 9 after several weeks of administration. cache = ./cache/cord-262159-8y0q45gr.txt txt = ./txt/cord-262159-8y0q45gr.txt === reduce.pl bib === id = cord-261876-7rsc803x author = Kaslow, David C. title = Certainty of success: three critical parameters in coronavirus vaccine development date = 2020-05-25 pages = extension = .txt mime = text/plain words = 6462 sentences = 305 flesch = 36 summary = In considering the "certainty of success" in development of human coronavirus vaccines, particularly SARS-CoV-2, a third, related critical parameter is proposed—infectious inoculum intensity, at an individual-level, and force of infection, at a population-level. Reducing the infectious inoculum intensity (and force of infection, at a population-level) is predicted to lengthen the incubation period, which in turn is predicted to reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. The one factor that emerges for consideration in SARS-CoV-2 vaccine development and implementation is reducing the infectious inoculum intensity (and force of infection, at a populationlevel) to lengthen the incubation period, reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. cache = ./cache/cord-261876-7rsc803x.txt txt = ./txt/cord-261876-7rsc803x.txt === reduce.pl bib === id = cord-261615-p81l6zvz author = Grabbe, Stephan title = Systemische Immunsuppression in Zeiten von COVID‐19: Müssen wir umdenken? date = 2020-08-21 pages = extension = .txt mime = text/plain words = 2089 sentences = 202 flesch = 36 summary = Über eine mögliche therapeutische Wirksamkeit von Chloroquin oder Hydroxychloroquin bei einer COVID-19-Erkrankung wurde bereits in der Laienpresse spekuliert, sodass diese Substanzen vielfach als unkritisch für die Dauerbehandlung von Patienten mit Autoimmunerkrankungen angesehen werden. In der Klinik scheint jedoch die langfristige therapeutische Einnahme von Hydroxychloroquin in Patienten mit systemischem LE nicht vor einer Covid-19-Erkrankung oder einem schweren Verlauf zu schützen [30, 31] . Somit gibt es derzeit keine Hinweise, dass die Therapie mit Chloroquin oder Hydroxychloroquin negative oder schützende Effekte auf eine SARS-CoV-2-Infektion hat oder den Infektionsverlauf ändert. Grundsätzlich gibt es derzeit keine Datenlage für eine generelle Reduktion oder Pausierung einer Immunsuppression bei Patienten mit Autoimmunerkrankungen, da das Risiko einer Untertherapie dieser zumeist schweren Erkrankungen deutlich höher als das eines aggravierten Infektionsverlaufs einer COVID-19-Erkrankung ist. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-261615-p81l6zvz.txt txt = ./txt/cord-261615-p81l6zvz.txt === reduce.pl bib === id = cord-262090-nbxzyjvf author = Acharya, Arpan title = SARS-CoV-2 Infection Leads to Neurological Dysfunction date = 2020-05-23 pages = extension = .txt mime = text/plain words = 3434 sentences = 213 flesch = 50 summary = A number of neurological disease complications have been seen following infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Such central nervous system (CNS) signs and symptoms linked to laboratory-confirmed SARS-CoV-2 infection is often life threatening. As cardio-respiratory impairments could reflect brainstem dysfunction it may, in part, be responsible for ARDS as frequently occurs as a cause of COVID-19 mortality among SARS-CoV-2 infected patients (Netland et al. As the impaired ability to smell and test are a common manifestation of respiratory neurotropic viral invasion of the olfactory system, we suspect there is a possibility that SARS-CoV-2 can infect the olfactory system and may enter the CNS using the olfactory pathway. A retrospective study substantiates this, wherein, 36.4% of patients out of 214 confirmed cases of SARS-CoV-2 have been documented to present with varying degree of neurological manifestations that include skeletal muscle injury, delirium and acute cerebrovascular disease (Fig. 2) . cache = ./cache/cord-262090-nbxzyjvf.txt txt = ./txt/cord-262090-nbxzyjvf.txt === reduce.pl bib === id = cord-262250-o7qhncic author = Habel, J. R. title = Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype date = 2020-08-19 pages = extension = .txt mime = text/plain words = 6206 sentences = 308 flesch = 57 summary = Using peptide-HLA-I tetramers, we performed direct ex vivo tetramer enrichment to define the frequency and activation profiles of the responding SARS-CoV2-specific CD8 + T-cells in acute and convalescent COVID-19 patients and in prepandemic PBMCs, tonsil and lung tissues from uninfected donors. 17.20176370 doi: medRxiv preprint To further probe the the responsiveness of A2/SARS-CoV-2 CD8 + T-cells from uninfected versus convalescent COVID-19 donors, PBMCs or tonsil cells were stimulated with the S 269 and Orf1ab 3183 peptides and cultured in vitro for 10 days. Our findings show that, while 'early memory' CD8 + T-cells can be detected in convalescent HLA-A*02:01 COVID-19 patients at frequencies ∼5-fold higher than those from pre-pandemic samples, the SARS-CoV-2-specific response was ∼10-fold lower than that found regularly for CD8 + T-cells directed at IAV or EBV epitopes. Even so, it is the case that SARS-CoV-2-specific CD8 + T-cells were found in all COVID-19 acute and convalescent donors, and in stored pre-pandemic PBMC and tonsil samples (but not lung tissues) from HLA-A*02:01 children, mature adults and the elderly. cache = ./cache/cord-262250-o7qhncic.txt txt = ./txt/cord-262250-o7qhncic.txt === reduce.pl bib === id = cord-262043-66qle52a author = Basit, Abdul title = Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date = 2020-05-20 pages = extension = .txt mime = text/plain words = 4866 sentences = 275 flesch = 55 summary = Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. We designed a truncated version (tACE2) of ACE2 receptor covering the binding residues and performed protein-protein docking and molecular dynamic simulations to analyze its binding affinity for RBD and complex stability. Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) . cache = ./cache/cord-262043-66qle52a.txt txt = ./txt/cord-262043-66qle52a.txt === reduce.pl bib === id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2735 sentences = 147 flesch = 41 summary = To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. cache = ./cache/cord-261961-u4d0vvmq.txt txt = ./txt/cord-261961-u4d0vvmq.txt === reduce.pl bib === id = cord-262119-s6hc7fxs author = Ostaszewski, Marek title = COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date = 2020-10-27 pages = extension = .txt mime = text/plain words = 12332 sentences = 742 flesch = 38 summary = title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms cache = ./cache/cord-262119-s6hc7fxs.txt txt = ./txt/cord-262119-s6hc7fxs.txt === reduce.pl bib === id = cord-262107-qso8ewi9 author = Kim, In-Cheol title = Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned date = 2020-05-22 pages = extension = .txt mime = text/plain words = 429 sentences = 37 flesch = 56 summary = title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned procurement team from the city (Daegu) where the COVID-19 outbreak was prevalent due to the concern of SARS-CoV-2 spread. Our procurement team decided to take a nasopharyngeal swab to prove negative of SARS-CoV-2 infection before the departure. Algorithm of the SARS-CoV-2 Test Strategy for the brain death donor and candidate for heart transplantation during COVID-19 outbreak. Brain death donors should be tested for SARS-CoV-2 infection (preferably rRT-PCR assay from upper and/or lower respiratory tract specimens). When the heart transplantation recipient has symptoms suggesting viral infection, unknown cause of fever, or close contact history with the SARS-CoV-2 infected patients prior 14 days, test for SARS-CoV-2 infection should be performed and proceed heart transplantation when the result is negative. Confirmation of the negative SARS-CoV-2 result need to be ensured according to the strategy of each hospital organ procurement organization. If the symptom of SARS-CoV-2 infection is highly suggested, repeated test need to be performed for the suspicious result. cache = ./cache/cord-262107-qso8ewi9.txt txt = ./txt/cord-262107-qso8ewi9.txt === reduce.pl bib === id = cord-262266-m0fjt483 author = Peddu, Vikas title = Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1847 sentences = 110 flesch = 53 summary = METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Eight unique patient samples consisting of six positive and two negative cases of suspected SARS-CoV-2 were sequenced using RNA extracted for a qRT-PCR diagnostic assay. Despite our reference database not containing any SARS-CoV-2 genomes, the six samples that were positive for SARS-CoV-2 by qRT-PCR had reads classified to Table 2) . Phylogenetic analysis revealed that the six SARS-CoV-2 sequences found cluster within two clades representing the Washington state and European outbreaks. cache = ./cache/cord-262266-m0fjt483.txt txt = ./txt/cord-262266-m0fjt483.txt === reduce.pl bib === id = cord-262192-w86qc3fq author = Balkhair, Abdullah A. title = COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1103 sentences = 85 flesch = 54 summary = According to the World Health Organization (WHO), the world has witnessed the emergence of several disease outbreaks and epidemics caused by more than 20 infectious agents over the past decade. 3 Over the past two decades, the emergence of coronavirus-associated diseases (SARS and MERS) inflicted global challenges to public health systems. This is exemplified by the current COVID-19 pandemic where the appearance of a seemingly limited cluster of cases of pneumonia linked to a sea food market in Wuhan, China 7 has become one of the worst pandemics in human history with a staggering number of more than 1.4 million infections in 177 countries and more than 85 000 deaths globally as of 9 April 2020. The quest for a vaccine against SARS-CoV-2 is an urgent priority, and its development and global availability is a prerequisite for ending the COVID-19 pandemic. The current COVID-19 pandemic and its dreadful global impact is a reminder of the potential detriment of emerging infectious diseases. cache = ./cache/cord-262192-w86qc3fq.txt txt = ./txt/cord-262192-w86qc3fq.txt === reduce.pl bib === id = cord-262412-bs7quwov author = Kaya, Gürkan title = Clinical and Histopathological Features and Potential Pathological Mechanisms of Skin Lesions in COVID-19: Review of the Literature date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3358 sentences = 189 flesch = 37 summary = Clinical manifestations are as follows (see Table 1 ): generalized or localized rash (erythematous, papulovesicular, maculopapular, petechial, morbilliform, symmetrical drug-related intertriginous and flexural exanthema (SDRIFE)-like, digitate papulosquamous pityriasis rosea-like), generalized urticaria, varicelliform rash, herpes lesions (zoster), purpuric lesions (retiform purpura), livedoid lesions (livedo reticularis, livedo racemosa), acro-ischemic lesions (dry gangrene, blisters, cyanosis), erythema multiforme-like, chilblain-like lesions (COVID toes) and other lesions such as urticarial vasculitis, acute generalized exanthematous pustulosis (AGEP)-like rash, eosinophilic panniculitis, COVID mask, periorbital dyschromia, oral ulcers and COVID red half-moon nail sign. In a recent report, the postmortem histology of COVID-19 patients revealed lymphocytic endotheliitis in lung, heart, kidney, liver and small intestine, a pathological picture reminiscent of what is seen in skin lesions, suggesting that SARS-CoV-2 infection facilitates the induction of endothelial inflammation in several organs as a direct consequence of viral involvement and of host inflammatory response [61] . cache = ./cache/cord-262412-bs7quwov.txt txt = ./txt/cord-262412-bs7quwov.txt === reduce.pl bib === id = cord-262328-q7mt0xve author = Wajnberg, Ania title = Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4419 sentences = 216 flesch = 54 summary = In this observational study, we ran an outreach programme in the New York City (NY, USA) area, including parts of Connecticut and New Jersey, to identify people who had recovered from SARS-CoV-2 infection for nasopharyngeal PCR (cobas 6800; Roche Diagnostics, Indianapolis, IN, USA) and serum IgG titre measurement (ELISA; Icahn School of Medicine at Mount Sinai, New York, NY, USA). We did not find reports of ELISA antibody assays as large as this one from areas with major COVID-19 hotspots, and found mixed and growing reports of IgG response to and PCR positivity for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over time. In the 584 participants for whom both nasopharyngeal PCR testing and serum antibody testing was available, SARS-CoV-2 RNA was detected in 249 (43%) at a median of 20 days (IQR 18-23) from symptom onset and 12 days (9-14) from symptom resolution. cache = ./cache/cord-262328-q7mt0xve.txt txt = ./txt/cord-262328-q7mt0xve.txt === reduce.pl bib === id = cord-262428-erlmyzwn author = CABARKAPA, Sonja title = The psychological impact of COVID-19 and other viral epidemics on frontline healthcare workers and ways to address it: A rapid systematic review date = 2020-09-17 pages = extension = .txt mime = text/plain words = 5588 sentences = 329 flesch = 53 summary = The search strategy included terms for HCWs (e.g., nurse and doctor), mental health (e.g., wellbeing and psychological), and viral outbreaks (e.g., epidemic and pandemic). In terms of mental health impact of epidemics, HCWs represent a particularly vulnerable group due to the high risk of infection, increased work stress and fear of spreading to their families. The following search terms were used: 'health worker', 'health care worker', 'medical', 'doctor', 'nursing', 'nurse', 'allied health', 'pandemic', 'outbreak', 'mental health', 'mental illness', 'psychiatric', 'psychological', 'coping', 'psychosocial', 'COVID-19', 'coronavirus', 'SARS', 'MERS' and 'Ebola'. 36, 51 At the early stages of the COVID-19 pandemic, a Wuhan study 28 found that 34.4% (342 of 994) of medical and nursing staff had mild mental health disturbances while 6.2% (62) had severe disturbances, while in another study 24 of 1,521 Chinese HCWs 14.1% had psychological abnormalities. Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 novel coronavirus disease outbreak: A cross-sectional study. cache = ./cache/cord-262428-erlmyzwn.txt txt = ./txt/cord-262428-erlmyzwn.txt === reduce.pl bib === id = cord-262454-bccrvapy author = Szente Fonseca, Silvia Nunes title = Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis date = 2020-10-31 pages = extension = .txt mime = text/plain words = 4700 sentences = 249 flesch = 53 summary = With all that, we developed a protocol for early recognition and treatment of high-risk patients (in our population, age greater than 40 years because of generally poorer health standards, or with comorbidities) who would come to our outpatient network of emergency rooms with influenza-like symptoms: fever, cough, myalgia and headache, among others, and receive early treatment, provided to patients at the first doctor visit, using physician discretion from among HCQ, azithromycin, ivermectin, oseltamivir, zinc sulfate, nitazoxanide and prednisone (the last starting on day-6 of symptoms). On March 28, 2020, the FDA issued an emergency use authorization for remdesivir and HCQ for patients in both clinical trials and with severe hospitalized disease (31) . We found early outpatient use of HCQ and prednisone, both as individual prescriptions and used together, to lower the risk of hospitalization in symptomatic high-risk COVID-19 patients presenting for primary care at the emergency rooms of our large HMO in Brazil. cache = ./cache/cord-262454-bccrvapy.txt txt = ./txt/cord-262454-bccrvapy.txt === reduce.pl bib === id = cord-262282-9xh51cd1 author = Serwer, Philip title = Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4323 sentences = 260 flesch = 57 summary = Without going into details concerning live vaccine production via eukaryotic viruses, I think it reasonable to assume that eukaryotic virus production is more difficult, more expensive and less rapid than the production of phages. However, current efforts to human-engineer improved antigens for anti-RNA virus vaccines have shown that neutralizing antibodies typically react with viral proteins that are in states that are context dependent and unstable [12, 13, 15, 20] . I take the liberty of responding here to the obvious objection that no membrane-covered, single-stranded RNA phage has ever been isolated [21] and that the pandemic viruses include influenza, Zika-type and coronaviruses, all in this category. A non-specialist observer reasonably concludes that DNA and RNA vaccines, when viewed in the context of our overall objective, are examples of type 2 strategy options. Given that eukaryotic viruses have doubling times much greater than those of phages (2-5 min for typical coliphages), meeting this objective implies that a live virus vaccine has to be already present in the environment. cache = ./cache/cord-262282-9xh51cd1.txt txt = ./txt/cord-262282-9xh51cd1.txt === reduce.pl bib === id = cord-262361-3f09z5pf author = Agbelele, Penance title = Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case date = 2020-07-30 pages = extension = .txt mime = text/plain words = 1759 sentences = 100 flesch = 48 summary = title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case The authors present the case of a young man victim of a traffic accident during the SARS-CoV-2 confinement, having presented a fracture of the femoral shaft that was soon complicated by respiratory failure with oxygen desaturation. This case demonstrates the difficulty of differential interpretation of CT images between fatty embolism and SARS-CoV-2 infection. However, no study has investigated the specific features of CT scans to differentiate fat embolism syndrome from SARS-Cov-2 infection. His condition was further complicated by acute respiratory failure with CT images that may suggest either SARS-Cov-2 infection or a fatty embolism or both. Upon our patient's arrival during the pandemic, he presented with fever (38°C) and oxygen desaturation (88%) strongly suggestive of a SARS-CoV-2 infection, especially since the signs of fat embolism occur on average at H39 [11, 12] . cache = ./cache/cord-262361-3f09z5pf.txt txt = ./txt/cord-262361-3f09z5pf.txt === reduce.pl bib === id = cord-262415-cj4pjuuc author = Eiros, R. title = Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers date = 2020-07-14 pages = extension = .txt mime = text/plain words = 4634 sentences = 282 flesch = 49 summary = title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers The present study was designed to search for evidence of pericardial and myocardial involvement after past SARS-CoV-2 infection comprehensively studied by clinical assessment, laboratory tests, electrocardiography and cardiac magnetic resonance (CMR) imaging. Overall, the drug therapy aimed at Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. 10 This study examined the prevalence of pericarditis and of myocarditis in a cohort of SARS-CoV-2 positive health-care workers in Salamanca, Spain. However, the strength of this study is the addition of non-hospitalized participants and also the inclusion of participants diagnosed of past SARS-CoV-2 infection through serology, who also had a high prevalence of pericarditis and myocarditis. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. cache = ./cache/cord-262415-cj4pjuuc.txt txt = ./txt/cord-262415-cj4pjuuc.txt === reduce.pl bib === id = cord-262441-slh52nxm author = Sakai, Yusuke title = Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date = 2017-07-21 pages = extension = .txt mime = text/plain words = 6120 sentences = 261 flesch = 52 summary = To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3. cache = ./cache/cord-262441-slh52nxm.txt txt = ./txt/cord-262441-slh52nxm.txt === reduce.pl bib === id = cord-262556-gpnp06je author = Behrens, Estuardo title = COVID-19: IFSO LAC Recommendations for the Resumption of Elective Bariatric Surgery date = 2020-08-22 pages = extension = .txt mime = text/plain words = 3197 sentences = 178 flesch = 46 summary = RESULTS: The resumption of elective BMS must be a priority maybe similar to oncological surgery, when hospitals reach phase I or II, treating obesity patients in a NON-COVID area, avoiding inadvertent intrahospital contagion from healthcare provider, patients, and relatives. On December 2019, Wuhan, China, reported an outbreak of the coronavirus SARS-CoV-2 (COVID19) , an RNA virus that affects the respiratory system and has a high fatality rate especially in adults over the age of 60 and patients suffering obesity and its comorbidities [1] [2] [3] . Currently, the most effective treatment against obesity available is bariatric and metabolic surgery, which further resolves or improves the related comorbidities that are the same risk factors in developing a severe case of SARS-CoV-2. It is recommended that elective bariatric surgery be performed in medical facilities with the necessary infrastructure to treat obesity patients in a NON-COVID area. cache = ./cache/cord-262556-gpnp06je.txt txt = ./txt/cord-262556-gpnp06je.txt === reduce.pl bib === id = cord-262420-vw7fnguu author = Moey, Melissa Y.Y. title = Electrocardiographic Changes and Arrhythmias in Hospitalized Patients With COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 733 sentences = 53 flesch = 37 summary = Subgroup analysis was performed by gender, race, intensive care unit (ICU) admission, troponin-I levels, and SARS-CoV-2 specific therapy (hydroxychloroquine, azithromycin, tocilizumab). Patients had significant lengthening of their QTc intervals during hospitalization regardless of whether they received SARS-CoV-2 specific therapy. Ours is the first report of electrocardiographic changes in patients hospitalized with SARS-CoV-2 showing significant prolongation of PR, QRS, and QTc intervals. PR interval prolonged significantly in all patients admitted with SARS-CoV-2 infection regardless of medication status or troponin elevation. Critically ill patients with SARS-CoV-2 admitted to ICU and those with elevated troponin-I levels had a significantly wider QRS at the time of admission and during the hospital course. Interestingly, we observed significant QTc lengthening during hospitalization in the small subgroup of patients (n=25) not receiving hydroxychloroquine or azithromycin, suggesting an additional unknown mechanism responsible for QTc prolongation in patients with SARS-CoV-2. Observational study of hydroxychloroquine in hospitalized patients with COVID-19 cache = ./cache/cord-262420-vw7fnguu.txt txt = ./txt/cord-262420-vw7fnguu.txt === reduce.pl bib === id = cord-262470-nkql7h9x author = Muus, Christoph title = Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date = 2020-04-20 pages = extension = .txt mime = text/plain words = 17577 sentences = 869 flesch = 50 summary = title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. To assess the association of age, sex, and smoking status with the expression of ACE2, TMPRSS2, and CTSL, we aggregated 22 scRNA-seq datasets of healthy human nasal and lung cells, as well as fetal samples. cache = ./cache/cord-262470-nkql7h9x.txt txt = ./txt/cord-262470-nkql7h9x.txt === reduce.pl bib === id = cord-262499-68vmdqky author = Bordi, Licia title = Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay date = 2020-10-20 pages = extension = .txt mime = text/plain words = 5037 sentences = 311 flesch = 56 summary = We evaluated the use of commercial Simplexa™ COVID-19 Direct assay on OF samples from hospitalized COVID-19 patients, for identification of SARS-CoV-2 RNA, duration of viral shedding, and determining the assay specificity and sensitivity on OF samples compared to NPS and BAL samples. The first performance evaluation on clinical specimen was done by testing 41 consecutive OF samples, including 9 samples from SARS-CoV-2-negative patients, with the Simplexa™ COVID-19 Direct assay and comparing results with that obtained using RT-PCR method established by Corman VM. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. Second, results from testing on paired OF, NPS and BAL samples by Simplexa™ COVID-19 Direct assay showed almost perfect concordance for virus detection, and high correlation of Ct values. cache = ./cache/cord-262499-68vmdqky.txt txt = ./txt/cord-262499-68vmdqky.txt === reduce.pl bib === id = cord-262485-sx2q5ol4 author = Davda, Jayeshkumar Narsibhai title = An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3255 sentences = 193 flesch = 59 summary = The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. cache = ./cache/cord-262485-sx2q5ol4.txt txt = ./txt/cord-262485-sx2q5ol4.txt === reduce.pl bib === id = cord-262338-ipvzugo8 author = Choi, Jun-Yong title = The pathogenesis and alternative treatment of SARS-CoV2 date = 2020-05-03 pages = extension = .txt mime = text/plain words = 1153 sentences = 69 flesch = 55 summary = The scientific community has identified the culprit of the shock wave as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) (1). Since 2002, however, newly merged hCoV causes fever, dyspnea, and often organ failure, which bestow SARS (severe acute respiratory syndrome) to otherwise benign hCoV (5) . During the MERS-CoV and SARS-CoV outbreaks, most patients died of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS), a severe case of ALI (11) . Fortunately, the mortality of SARS-CoV2 infection, which is related to ALI or ARDS, is lower than those of the other two outbreaks (13) . As yet, however, no evidence is available that, if administered to patients on the principles of traditional Asian medicine, the medicinal herbs show effectiveness against ALI caused by SARS-CoV2 infection. The time comes to examine whether antiinflammatory medicinal herbs give a medical benefit to patients infected by SARS-CoV2. cache = ./cache/cord-262338-ipvzugo8.txt txt = ./txt/cord-262338-ipvzugo8.txt === reduce.pl bib === id = cord-262640-4vr4cm1s author = Nguyen, N. N. title = Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2 date = 2020-07-08 pages = extension = .txt mime = text/plain words = 2744 sentences = 208 flesch = 54 summary = This paper highlights the analytical characteristic of an ELISA based assay by AnshLabs and three random access immunoassay (RAIA) by DiaSorin, Roche, and Abbott that have been approved for emergency use authorization (EUA), at a tertiary academic center in a low disease-prevalence area. All discrepant samples that were positive by AnshLabs and negative by RAIA tested positive by all-in-one step SARS-CoV-2 Total (COV2T) assay performed on the automated Siemens Advia Centaur XPT analyzer. The Elecsys Anti-SARS-CoV-2 assay is performed on the Roche cobas e601 analyzer for total antibodies 126 specific for IgG, IgM and IgA which target nucleocapsid protein, in human serum or plasma. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint Table 4 shows the concordance between ELISA and RAIA results for samples that were confirmed 174 positive for SARS-CoV-2 by rtPCR. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint non-specific binding in AnshLabs ELISA assay 320 All rights reserved. cache = ./cache/cord-262640-4vr4cm1s.txt txt = ./txt/cord-262640-4vr4cm1s.txt === reduce.pl bib === id = cord-262760-mf1pn587 author = Weber, Stefanie title = Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4664 sentences = 264 flesch = 59 summary = By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). cache = ./cache/cord-262760-mf1pn587.txt txt = ./txt/cord-262760-mf1pn587.txt === reduce.pl bib === id = cord-262467-epqqd8n8 author = Chen, Jun title = COVID-19 infection: the China and Italy perspectives date = 2020-06-08 pages = extension = .txt mime = text/plain words = 7596 sentences = 384 flesch = 47 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 disease as originally shown in Wuhan, China, as early as documented from 1 December 2019 (ref. A recent prospective study failed to find antiviral activity or clinical benefit of this combination for the treatment of our hospitalized patients with severe COVID-19 (ref. More recently, a randomized, controlled study conducted in Wuhan, China also failed to identify beneficial effect of LPV/r beyond standard therapy in hospitalized patients with severe Covid-19 (ref. Clinical trials also showed that in patients with severe H1N1 influenza A, in the 2009 pandemic, therapy with convalescent plasma from patients who recovered, especially within 5 days of symptom onset, resulted in a lower viral load and lower mortality 66, 67 . The duration from onset of symptoms to viral clearance is significantly longer in severe and critical ill SARS-CoV-2infected patients compared with that in the mild cases 48 . cache = ./cache/cord-262467-epqqd8n8.txt txt = ./txt/cord-262467-epqqd8n8.txt === reduce.pl bib === id = cord-262276-5nue46dm author = Roussel, Yanis title = SARS-CoV-2: fear versus data date = 2020-03-19 pages = extension = .txt mime = text/plain words = 1860 sentences = 119 flesch = 55 summary = The first, severe acute respiratory syndrome (SARS) coronavirus, had very little impact on global morbidity and mortality, with more than 80 0 0 recognized cases and 774 deaths [15 , 16] . Among the Organisation for Economic Co-operation and Development (OECD) countries, 7476 patients have tested positive for SARS-CoV-2, with 96 deaths (mortality rate 1.3%) ( Table 3 ). In France, 191 people have tested positive for SARS-CoV-2, with three deaths (mortality rate 1.6%). If the extrapolation of deaths in AP-HM hospitals is correct, in metropolitan France, this would represent 543/0.8 * 100 = 67 875 cases of patients hospitalized with a respiratory infection with common coronaviruses in 2 months, which is almost as many cases as for SARS-CoV-2 worldwide. Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China cache = ./cache/cord-262276-5nue46dm.txt txt = ./txt/cord-262276-5nue46dm.txt === reduce.pl bib === id = cord-262783-uhfnv532 author = Yamamoto, Fumiichiro title = Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1683 sentences = 107 flesch = 52 summary = title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression The ABO blood group polymorphism was previously shown to influence the susceptibility to SARS with individuals in groups A and O having a higher and lower risk, respectively [6] . Since 11 March 2020, several papers reported the association between ABO blood groups and SARS-CoV-2/COVID-19. The authors compared ABO blood group distribution among 265 SARS-CoV-2-infected patients and 3,694 healthy controls. The SARS-CoV-2 viruses produced in individuals of groups A, B, AB and O express A, B, A and B antigens, and none, respectively. For example, SARS-CoV-2 viruses produced in group A individuals may express A antigens and infect group A or AB individuals without such antigen-antibody reactions. Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies Association between ABO blood groups and risk of SARS-CoV-2 pneumonia ABO blood groups and SARS-CoV-2 infection. cache = ./cache/cord-262783-uhfnv532.txt txt = ./txt/cord-262783-uhfnv532.txt === reduce.pl bib === id = cord-262726-lfuxhlki author = Diallo, Aïssatou Bailo title = Daytime variation in SARS-CoV-2 infection and cytokine production date = 2020-09-11 pages = extension = .txt mime = text/plain words = 1156 sentences = 77 flesch = 51 summary = Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. Importance The implication of circadian rhythm (CR) in pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recently anticipated. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. cache = ./cache/cord-262726-lfuxhlki.txt txt = ./txt/cord-262726-lfuxhlki.txt === reduce.pl bib === id = cord-262550-oip5m9br author = Kumar, S. Udhaya title = The Rise and Impact of COVID-19 in India date = 2020-05-22 pages = extension = .txt mime = text/plain words = 2866 sentences = 179 flesch = 58 summary = The coronavirus disease (COVID-19) pandemic, which originated in the city of Wuhan, China, has quickly spread to various countries, with many cases having been reported worldwide. The Ministry of Health and Family Welfare of India has raised awareness about the recent outbreak and has taken necessary actions to control the spread of COVID-19. The recent outbreak of COVID-19 in several countries is similar to the previous outbreaks of SARS and Middle East respiratory syndrome (MERS) that emerged in 2003 and 2012 in China and Saudi Arabia, respectively (8) (9) (10) . A recent study reported that affected family members had not visit the Wuhan market in China, suggesting that SARS-CoV-2 may spread without manifesting symptoms (21) . The Ministry of Health and Family Welfare (MOHFW), India, has raised awareness about the recent outbreak and taken necessary action to control COVID-19. The impacts on health, society, and economy of SARS and H7N9 outbreaks in China: a case comparison study cache = ./cache/cord-262550-oip5m9br.txt txt = ./txt/cord-262550-oip5m9br.txt === reduce.pl bib === id = cord-262575-06i2nv0t author = Caracciolo, Massimo title = Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2163 sentences = 139 flesch = 40 summary = title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome Severe cases of COVID-19 present with serious lung inflammation, acute respiratory distress syndrome and multiorgan damage. SARS-CoV-2 infection is associated with high cytokine levels, including interleukin-6 and certain subsets of immune cells, in particular, NK, distinguished according to the cell surface density of CD56. Cytokine levels are inversely correlated with lymphocyte count, therefore cytokine release syndrome may be an impediment to the adaptive immune response against SARS-CoV-2 infection. An 85 year old male presenting in our hospital with COVID-19, whose condition was complicated by acute respiratory distress syndrome and cardiac and renal failure (with oliguria) after 25 days of hospitalization, was intubated and received canakinumab for compassionate use. The immune response, including the release of pro-inflammatory cytokines and activation of T cells, are essential for controlling the viral spread, inflammation, and tissue renewal (5, 6) . cache = ./cache/cord-262575-06i2nv0t.txt txt = ./txt/cord-262575-06i2nv0t.txt === reduce.pl bib === id = cord-262786-otxpc46a author = Mohammadi, Soheil title = Understanding the Immunologic Characteristics of Neurologic Manifestations of SARS-CoV-2 and Potential Immunological Mechanisms date = 2020-09-01 pages = extension = .txt mime = text/plain words = 6290 sentences = 334 flesch = 38 summary = Here, we review the currently available evidence to discuss the plausible immunologic pathways that may contribute to the development of COVID-19 neurological complications, namely Alzheimer's disease, Parkinson's disease, stroke, multiple sclerosis, Guillain-Barre syndrome, seizure, and brainstem involvement. Although the virus, also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mainly manifests as an acute respiratory infection [2] , recent evidence suggests that 36% of affected patients exhibit neurological sequelae [3] . Systemic inflammatory response syndrome (SIRS) is defined as excessive host immune response against noxious stimuli (e.g., viral infection), through which the primary protective role of cytokine release turns into a detrimental response against host tissues, leading to impaired integrity of capillary walls and end-organ dysfunction [22] . We hypothesize that not only the persistent systemic inflammation caused by SARS-CoV-2 may act as a trigger for microglial activation but also large amounts of pro-inflammatory cytokines secreted in response to this viral infection may aggravate neurodegeneration leading to AD. cache = ./cache/cord-262786-otxpc46a.txt txt = ./txt/cord-262786-otxpc46a.txt === reduce.pl bib === id = cord-263031-cco2vh0f author = Vultaggio, Alessandra title = Considerations on Biologicals for Patients with allergic disease in times of the COVID‐19 pandemic: an EAACI Statement date = 2020-06-05 pages = extension = .txt mime = text/plain words = 2870 sentences = 177 flesch = 41 summary = We discuss immunological and clinical considerations for patients on biologic agents (biologicals)targeting the type 2 inflammatory response due to difficult-to-treat allergic diseases in the context of COVID-19. In other coronavirus infections such as severe acute respiratory syndrome (SARS), type I IFN are critical for the initiation of immune response and virus clearance. In line with a paucity of mechanistic data on COVID-19 in the context of type 2 inflammation, knowledge on the disease course in patients treated with biologicals targeting type 2 inflammation due to severe asthma or other atopic diseases, such as CSU, AD and CRSwNP, is scarce to absent. In the past years, new biological therapies for severe asthma, atopic dermatitis (AD), chronicrhinosinusitis with nasal polyps (CRSwNP) and chronic spontaneous urticaria (CSU) have been developed targeting different aspects of the type 2 immune response. cache = ./cache/cord-263031-cco2vh0f.txt txt = ./txt/cord-263031-cco2vh0f.txt === reduce.pl bib === id = cord-262841-nr42rs8f author = Li, Lanjuan title = SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date = 2003-12-31 pages = extension = .txt mime = text/plain words = 2124 sentences = 107 flesch = 58 summary = Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, "replicative intermediates") and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Although the virus has been identified Abbreviations: BNIBernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany; BSL3biosafety level 3; CoVcoronavirus; MHVmouse hepatitis virus; PCRpolymerase chain reaction; minus -RNAreplicative negative-stranded RNA; plus -RNApositive-stranded genomic RNA; RTreverse transcription; SARSsevere acute respiratory syndrome; SCAsodium citrate anticoagulant. In order to evaluate (i) whether SARS-CoV can infect peripheral blood mononuclear cells (PBMCs) of infected persons, (ii) whether the virus can replicate in their PBMCs, and (iii) to reveal any dynamic changes to the virus during the course of the disease, we carried out follow-up investigations on the plusand minus-RNA forms in SARS patients. cache = ./cache/cord-262841-nr42rs8f.txt txt = ./txt/cord-262841-nr42rs8f.txt === reduce.pl bib === id = cord-262766-ndn6iwre author = Easom, Nicholas title = 68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit date = 2020-03-06 pages = extension = .txt mime = text/plain words = 2964 sentences = 145 flesch = 45 summary = Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. In addition, many mild respiratory viral infections were managed as influenza 10 , with significant resource implications, both for healthcare services and patients Here we describe our experience of the first 68 patients we have tested for SARS-CoV-2 at a Regional Infectious Diseases unit (RIDU) in the UK. Specialist Infectious Diseases consultant-delivered assessment of a group of patients who predominantly have mild illness is unlikely to be sustainable, especially as the case-definition broadens to include a wider geographical area and/or COVID-19 patients requiring inpatient care becomes more common in the UK. cache = ./cache/cord-262766-ndn6iwre.txt txt = ./txt/cord-262766-ndn6iwre.txt === reduce.pl bib === id = cord-262796-syu4wbpi author = Wei, Xiao-Shan title = Diarrhea is associated with prolonged symptoms and viral carriage in COVID-19 date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2863 sentences = 174 flesch = 57 summary = Abstract Background & Aims We compared clinical, laboratory, radiological, and outcome features of patients with SARS-CoV-2 infection (COVID-19) with pneumonia, with vs without diarrhea. Methods We performed a retrospective, single-center analysis of 84 patients with SARS-CoV-2 pneumonia in Wuhan Union Hospital, China, from January 19 through February 7, 2020. Of 76 patients with a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039). On admission to hospital, all confirmed COVID patients were tested for SARS-CoV-2 RNA from stool samples. Of 76 COVID-19 patients who had a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039) ( Table 5) . cache = ./cache/cord-262796-syu4wbpi.txt txt = ./txt/cord-262796-syu4wbpi.txt === reduce.pl bib === id = cord-262635-fdwd99ah author = Hajra Martínez, Ismael El title = Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus date = 2020-08-07 pages = extension = .txt mime = text/plain words = 238 sentences = 25 flesch = 63 summary = key: cord-262635-fdwd99ah title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus cord_uid: fdwd99ah abdominal CT scan, a thickening of the terminal ileum was observed suggesting the presence of acute ileitis. The patient received empirical treatment with ciprofloxacin and metronidazole without any improvement. Microbiological stool examinations were negative, also for SARS-CoV-2 rRT-PCR test. April 29 th , the study was completed with an ileo-colonoscopy with ileal biopsy. The mucosa of ileum and colon was macroscopically normal, and the biopsy showed no damage. However, RT-PCR test on ileal tissue was positive for SARS-CoV-2 RNA. We repeated the SARS-CoV-2 rRT-PCR test on nasopharyngeal swab and it again came back negative. The patient improved over the next few days without any specific treatment. Evidence for Gastrointestinal Infection of SARS-CoV-2 Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis cache = ./cache/cord-262635-fdwd99ah.txt txt = ./txt/cord-262635-fdwd99ah.txt === reduce.pl bib === id = cord-262863-f07v5uk8 author = Bertocchi, Ilaria title = The hidden role of NLRP3 inflammasome in obesity‐related COVID‐19 exacerbations: lessons for drug repurposing date = 2020-08-09 pages = extension = .txt mime = text/plain words = 5438 sentences = 252 flesch = 30 summary = We and others have demonstrated that NLRP3 inflammasome over-activation is involved not only in the pathogenesis of diabesity, but also in the exacerbation of related cardiovascular injuries, including myocardial infarction, and this process is associated to an increase in the local inflammatory response. Similarly, the diabesityrelated basal activation of the NLRP3 inflammasome cascade, leading to increase in either gastrointestinal or vascular permeability, may contribute to exacerbate SARS-CoV-2 systemic diffusion and enhance the intricate mechanisms of intracellular cross talk operational in the pathogenesis of COVID-19. Up to nowadays six clinical trials (NCT04347980, NCT04325061, NCT04395105, NCT04344730, NCT04360876, NCT04327401), reported on clinicaltrials.gov are recruiting patients to test the efficacy of the corticosteroid dexamethasone, whose beneficial effects in airway inflammation has been recently demonstrated to involve lung inhibition of the activity of NLRP3 inflammasome and the release of IL-1β and IL-18 (Guan, Ma, Fan, Chen, Miao & Wu, 2020) . cache = ./cache/cord-262863-f07v5uk8.txt txt = ./txt/cord-262863-f07v5uk8.txt === reduce.pl bib === id = cord-262911-e9z00y3b author = Delpino, M. Victoria title = SARS-CoV-2 Pathogenesis: Imbalance in the Renin-Angiotensin System Favors Lung Fibrosis date = 2020-06-12 pages = extension = .txt mime = text/plain words = 2806 sentences = 132 flesch = 38 summary = In addition to its functions in regulating blood pressure, AngII plays a pivotal role in signaling cellular and molecular events that are considered critical in the pathogenesis of pulmonary fibrosis, such as: (i) inflammation (promoting production of proinflammatory cytokines such as IL-6, and IL-8 by macrophages), (ii) the production of reactive oxygen species (ROS) among infected-alveolar epithelial cells followed by its apoptosis, and (iii) the proliferation, migration, and differentiation of fibroblasts to myofibroblasts capable of synthesize smooth muscle alpha-actin (α-SMA) and produce extracellular matrix (collagen and fibronectin) through a mechanism mediated by autocratic trans-activation of TGF-β in the fibroblast itself (Wolf et al., 1992; Kagami et al., 1994; Jia, 2016) . In contrast, the Ang1-7 peptide, after interacting with its cellular receptor Mas, exhibits the ability to inhibit proapoptotic signaling in alveolar epithelial cells, promote autophagy, andtogether with the ACE2 receptor-counteract the profibrotic effects, reducing both TGF-β mediated collagen expression, as well as the transition from fibroblasts to myofibroblasts (Iwata et al., 2005; Zeng et al., 2009; Zhou et al., 2016) . cache = ./cache/cord-262911-e9z00y3b.txt txt = ./txt/cord-262911-e9z00y3b.txt === reduce.pl bib === id = cord-263292-qjfe2t9v author = Sansone, A. title = Addressing male sexual and reproductive health in the wake of COVID-19 outbreak date = 2020-07-13 pages = extension = .txt mime = text/plain words = 3912 sentences = 210 flesch = 39 summary = Despite being a trivial matter for patients in intensive care units (ICUs), erectile dysfunction (ED) is a likely consequence of COVID-19 for survivors, and considering the high transmissibility of the infection and the higher contagion rates among elderly men, a worrying phenomenon for a large part of affected patients. Testicular function in COVID-19 patients requires careful investigation for the unclear association with testosterone deficiency and the possible consequences for reproductive health. However, independently of whether testosterone is a friend or foe for COVID-19, it should be acknowledged that the testis is a target for SARS-CoV-2 and the possibility for long-lasting consequences on the endocrine function exists, even for recovered patients. Drugs such as β-blockers and antihypertensive agents, routinely used in COVID-19 patients, have the potential to impair sexual function [41] ; therefore, both the cardiovascular consequences and their treatment might ease progression from subclinical to a clinically overt ED [42, 43] . cache = ./cache/cord-263292-qjfe2t9v.txt txt = ./txt/cord-263292-qjfe2t9v.txt === reduce.pl bib === id = cord-262936-yo6jf3ng author = Deng, Jia-gang title = Carry forward advantages of traditional medicines in prevention and control of outbreak of COVID-19 pandemic date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2941 sentences = 131 flesch = 39 summary = This paper manly reviews the achievements of the implementation of the epidemic prevention and control plan, advances of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. After the outbreak of COVID-19, the research team of GXUCM responded actively, and the application for two special science and technology projects to prevent and control pneumonia caused by SARS-CoV-2 in Guangxi in 2020 was approved, including Sino-Singapore cooperation for evaluating the effectiveness and application of Guangxi Zhuang/Yao medicines against In summary, this paper manly contents achievements of the implementation of the epidemic prevention and control plan, advance of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. cache = ./cache/cord-262936-yo6jf3ng.txt txt = ./txt/cord-262936-yo6jf3ng.txt === reduce.pl bib === id = cord-262730-1dxeg8ci author = Barón-Sánchez, J. title = Smell and taste disorders in Spanish patients with mild COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3510 sentences = 244 flesch = 54 summary = [12] [13] [14] The olfactory alterations associated with SARS-COV-2 infection present sudden onset, are generally not accompanied by rhinorrhoea or nasal obstruction with mucus, and are of variable intensity, although patients frequently report complete loss of the sense of smell. V a r i a b l e s Participants meeting the inclusion criteria were asked to complete a questionnaire, which gathered the following data: sex; age; medical history; characteristics of olfactory/gustatory alterations (complete loss of the sense of smell/taste [anosmia/ageusia], decreased sense of smell [hyposmia], altered sense of taste [dysgeusia]); date of onset and resolution of the alterations; symptom progression; associated symptoms; close contact with a patient with COVID-19 (confirmed by PCR testing); and PCR results for COVID-19, if the test was performed. In our study, only 8.4% of individuals with olfactory/gustatory alterations undergoing PCR testing were negative for SARS-CoV-2; this supports the hypothesis that these symptoms are highly prevalent in patients with mild COVID-19. cache = ./cache/cord-262730-1dxeg8ci.txt txt = ./txt/cord-262730-1dxeg8ci.txt === reduce.pl bib === id = cord-262673-j2ot35lt author = Ahmed-Hassan, Hanaa title = Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date = 2020-08-18 pages = extension = .txt mime = text/plain words = 8591 sentences = 472 flesch = 41 summary = Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells cache = ./cache/cord-262673-j2ot35lt.txt txt = ./txt/cord-262673-j2ot35lt.txt === reduce.pl bib === id = cord-263279-afdmegq0 author = Uhteg, Katharine title = Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date = 2020-04-26 pages = extension = .txt mime = text/plain words = 3175 sentences = 186 flesch = 51 summary = Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. cache = ./cache/cord-263279-afdmegq0.txt txt = ./txt/cord-263279-afdmegq0.txt === reduce.pl bib === id = cord-262598-zk192s0x author = Tatu, Laurent title = Guillain–Barré syndrome in the COVID-19 era: another occasional cluster? date = 2020-06-23 pages = extension = .txt mime = text/plain words = 702 sentences = 51 flesch = 55 summary = entitled 'Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster?' [1] . The authors reported an unusual cluster of seven patients affected by Guillain-Barré syndrome (GBS) in an Italian region (Friuli Venezia-Giulia), which coincided with the descending curve of the COVID-19 pandemic. In the public health crisis of March-April 2020, we encountered an unusually high number of GBS cases, admitting seven patients. Some authors report a possible correlation between acute symptomatic COVID-19 infection and GBS [4, 5] . Nevertheless, the issue raised by Gigli's cases and those in this series is different: an abnormally high frequency of GBS amid the SARS-CoV-2 pandemic in patients without a COVID infection. Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster? Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré syndrome related to COVID-19 infection cache = ./cache/cord-262598-zk192s0x.txt txt = ./txt/cord-262598-zk192s0x.txt === reduce.pl bib === id = cord-263090-29n9tsk9 author = Roy, Susmita title = Dynamical asymmetry exposes 2019-nCoV prefusion spike date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4573 sentences = 331 flesch = 57 summary = In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. A number of Cryo-EM structures captured the 'up' and 'down' conformations of the RBD domain of spike proteins of other coronaviruses including SARS-CoV-2 where the S1 subunit undergoes a hinge-like conformational movement prerequisite for receptor binding (Fig. 2C) (7, 8, 10, 17) . Analysis of all the simulations yields the 2-D free energy landscape of the trimeric spike protein of SARS-CoV-2 ( Fig 3B) with its all possible conformations. This generates a homo-trimeric SARS-CoV-2 spike where this initial structure has important components in terms of intra and inter-chain contacts (interaction) leading to an 'S1-head-up' and an 'S1-head-down' conformation for each protomer. cache = ./cache/cord-263090-29n9tsk9.txt txt = ./txt/cord-263090-29n9tsk9.txt === reduce.pl bib === id = cord-263002-f3itn0sb author = Wagener, Frank A. D. T. G. title = Targeting the Heme-Heme Oxygenase System to Prevent Severe Complications Following COVID-19 Infections date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3943 sentences = 248 flesch = 39 summary = Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. These predisposing conditions, and inflammation in general, downregulate HO-1 expression and activity [67, 74, [100] [101] [102] [103] [104] [105] [106] , further supporting that this compromised protection and diminished tolerance against inflammatory and oxidative stress promotes adverse clinical outcome in COVID-19 patients. Since dexamethasone reduces hemolysis and induces HO-1 in macrophages [113] , it is tempting to speculate that this increased protection against free heme attenuates the severity of disease in COVID-19 patients. cache = ./cache/cord-263002-f3itn0sb.txt txt = ./txt/cord-263002-f3itn0sb.txt === reduce.pl bib === id = cord-263438-9ra94uda author = Snowden, Frank M. title = Emerging and reemerging diseases: a historical perspective date = 2008-09-19 pages = extension = .txt mime = text/plain words = 14393 sentences = 608 flesch = 47 summary = Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. In 1996, in addition, President Bill Clinton (28) issued a fact sheet entitled 'Addressing the Threat of Emerging Infectious Diseases' in which he declared them 'one of the most significant health and security challenges facing the global community.' There were also highly visible hearings on emerging infections in the US Congress (29) . The Rand Corporation intelligence report The Global Threat of New and Reemerging Infectious Diseases: Reconciling U.S. National Security and Public Health Policy (53) had two leading themes. cache = ./cache/cord-263438-9ra94uda.txt txt = ./txt/cord-263438-9ra94uda.txt === reduce.pl bib === id = cord-262844-qeheeqe3 author = Xia, Xuhua title = Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date = 2020-04-14 pages = extension = .txt mime = text/plain words = 3305 sentences = 204 flesch = 53 summary = The zinc finger antiviral protein (ZAP, known as ZC3HAV1 in mammals or hZAP in human), a key component in mammalian interferon-mediated immune response, binds specifically to CpG dinucleotides in viral RNA genomes via its RNA-binding domain (Meagher et al., 2019) . If a coronavirus infects a different host tissue with different ZAP abundance, then its RNA genome will experience different selection pressure against its CpG. The most striking pattern in Fig. 1 is an isolated but dramatic shift in the lineage leading to BatCoV RaTG13 which was reported (Zhou et al., 2020) (Theys et al., 2018) , but also in experimentally CpG dinucleotide-enriched viral genomes (Antzin-Anduetza et al., 2017; Burns et al., 2009; Fros et al., 2017; Trus et al., 2019; Tulloch et al., 2014; Wasson et al., 2017) . To search for a mammalian host with the potential to select viral lineages with low Poder, 2011; Pratelli, 2006) , have genomic ICpG and GC% values similar to those observed in SARS-CoV-2 and BatCoV RaTG13 (Fig. 3A) . cache = ./cache/cord-262844-qeheeqe3.txt txt = ./txt/cord-262844-qeheeqe3.txt === reduce.pl bib === id = cord-263450-v6vdg8os author = Shegogue, Daniel title = Object-oriented biological system integration: a SARS coronavirus example date = 2005-05-15 pages = extension = .txt mime = text/plain words = 4930 sentences = 260 flesch = 38 summary = Results: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. In addition, applying a well-defined software engineering process and object-oriented methodology provide an effective means to capture specifications from experimental data and integrate the biological system information. Finally, this process provides a guideline for the development of an integrated biological system, represented as an object-oriented software architecture, in a widely accepted objectoriented modeling language (such as UML), which can facilitate communication about complex systems among software engineers, biologists and other users. To demonstrate the efficacy of a well-defined software engineering process in the translation of a biological system to a model grounded in object-oriented principles, we used UML in the development of a severe acquired respiratory syndrome-coronavirus (SARS-CoV) model. cache = ./cache/cord-263450-v6vdg8os.txt txt = ./txt/cord-263450-v6vdg8os.txt === reduce.pl bib === id = cord-263179-uvq3hzga author = Malik, Zohra R title = A Case of a COVID-19-positive Patient date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1558 sentences = 106 flesch = 60 summary = Virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) or the 2019 novel coronavirus (2019-nCoV) belong to the broad family of coronaviruses (subgenus Sarbecovirus). The HCoV (human coronavirus) is responsible for up to 10% -30% of the upper respiratory tract infections globally [2] . Historically, HCoV's were only responsible for mild infections until 2002, with the emergence of the severe acute respiratory syndrome (SARS) that started in the Guangdong province of China. Based on available data of SARS and MERS, the Centers for Disease Control and Prevention (CDC) has estimated an incubation period for the COVID-19 to be between two and 14 days [6] . There have been reported cases involving large populations showing people with varying incubation periods and the severity of symptoms based on age and immune status. The patient was placed on airborne, droplet, and contact isolation because of the high suspicion of coronavirus infection. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease cache = ./cache/cord-263179-uvq3hzga.txt txt = ./txt/cord-263179-uvq3hzga.txt === reduce.pl bib === id = cord-262958-tmp6yxlv author = Pinto, Dora title = Structural and functional analysis of a potent sarbecovirus neutralizing antibody date = 2020-04-09 pages = extension = .txt mime = text/plain words = 2241 sentences = 147 flesch = 55 summary = The SARS-CoV-2 spike (S) glycoprotein 26 promotes entry into host cells and is the main target of neutralizing antibodies. None of the mAbs studied bound to 97 prefusion OC43 S or MERS-CoV S ectodomain trimers, indicating a lack of cross-98 reactivity outside the sarbecovirus subgenus (Extended Data Fig.1) . The structural data explain the S309 cross-reactivity between SARS-CoV-2 and 148 SARS-CoV as 19 out of 24 residues of the epitope are strictly conserved ( Fig. 2f and 149 Extended Data Fig. 6a To further investigate the mechanism of S309-mediated neutralization, we 175 compared side-by-side transduction of SARS-CoV-2-MLV in the presence of either 176 S309 Fab or S309 IgG. This analysis 208 identified at least four antigenic sites within the S B domain of SARS-CoV targeted by 209 our panel of mAbs. The receptor-binding motif, which is targeted by S230, S227 and 210 S110, is termed site I. cache = ./cache/cord-262958-tmp6yxlv.txt txt = ./txt/cord-262958-tmp6yxlv.txt === reduce.pl bib === id = cord-263509-wi0um8cm author = Rivera, Victor M title = Actitudes Terapéuticas Hacia La Esclerosis Múltiple En Centroamérica Y El Caribe Frente A La Pandemia De Sars-Cov-2 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 921 sentences = 96 flesch = 53 summary = Esclerosis Múltiple (EM) en Centroamérica y el Caribe (CAC) mantiene una baja prevalencia¹ mientras que el impacto socioeconómico ejercido por esta enfermedad en los sistemas de salud de la región es severo considerando el nivel de crecimiento económico de estos países. A pesar de esta limitación, en años recientes la mayoría de los sistemas de seguridad social y algunos de atención pública en esta zona, han dedicado una gran porción de sus presupuestos a la adquisición de las variadas y onerosas terapias aprobadas por agencias internacionales para el manejo de EM². La teórica posibilidad que pacientes con EM pudieran ser especialmente vulnerables a la infección con SARS-CoV-2 considerando presencia de discapacidad neurológica y uso de tratamientos que afectan al sistema inmune, varios medicamentos de hecho causando persistente depleción linfocitaria, conllevó al Foro Centroamericano y del Caribe de Esclerosis Múltiple (FOCEM) a explorar actitudes terapéuticas en la región hispanoparlante encarando la pandemia. cache = ./cache/cord-263509-wi0um8cm.txt txt = ./txt/cord-263509-wi0um8cm.txt === reduce.pl bib === id = cord-263308-q0iriid8 author = Piano, Carla title = An Italian Neurology Outpatient Clinic Facing SARS-CoV-2 Pandemic: Data From 2,167 Patients date = 2020-05-29 pages = extension = .txt mime = text/plain words = 3561 sentences = 169 flesch = 36 summary = Methods: Patients with chronic neurologic diseases routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for symptoms suggestive of SARS-CoV-2 infection in the pandemic period, consequences of social restrictions, and neurological disease features, concomitant medical conditions, current medical and disease-specific treatments. Specifically, the survey assessed: (1) Demographic and clinical characteristics, including age at onset, duration of illness, and disability measures (ADL/IADL) (8); (2) COVID-19 related questions, including history of recent travel in endemic areas, direct contacts with COVID-19 confirmed cases (COVID-19+), symptoms suggestive of COVID-19 infection started or worsened in the last 3 months (fever, cough/sore throat, asthenia, dyspnea, myalgia, and hyposmia/hypogeusia), and confirmatory testing for COVID-19 (nasal/pharyngeal swab test results); (3) information related to the impact of COVID-19 on disease burden, including subjective worsening of neurological symptoms, compliance with restrictions and specific effects of restriction measures on the perception of illness (need of urgent neurological care, discontinuation of pharmacological treatment or physiotherapy, difficulties in finding drugs). cache = ./cache/cord-263308-q0iriid8.txt txt = ./txt/cord-263308-q0iriid8.txt === reduce.pl bib === id = cord-263167-es806qhz author = Rogers, Thomas F. title = Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model date = 2020-06-15 pages = extension = .txt mime = text/plain words = 4512 sentences = 249 flesch = 53 summary = We showed that passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters, as revealed by maintained weight and low lung viral titers in treated animals. Donor plasma were tested for binding to recombinant SARS-CoV-2 and SARS-CoV-1 S and receptor binding domain (RBD) proteins, for binding to cell surface expressed spikes and for neutralization in both live replicating virus and pseudovirus assays (Fig. 2, B to D, and fig. The bulk-transformed ligation products for both the heavy chain and light chain were transfected and tested for binding to RBD and S protein, and for neutralization in the SARS-CoV-2 pseudovirus assay using HeLa-ACE2 target cells ( fig. To investigate the relationship between in vitro neutralization and protection in vivo against SARS-CoV-2, we selected two mAbs for passive transfer/challenge experiments in a Syrian hamster animal model based on a summary of the nAb data (table S3 and fig. cache = ./cache/cord-263167-es806qhz.txt txt = ./txt/cord-263167-es806qhz.txt === reduce.pl bib === id = cord-263224-osf0tkzr author = Maunder, Robert G. title = Long-term Psychological and Occupational Effects of Providing Hospital Healthcare during SARS Outbreak date = 2006-12-17 pages = extension = .txt mime = text/plain words = 4091 sentences = 171 flesch = 42 summary = To identify factors that might explain variance in adverse outcome, between-group differences in traumatic stress symptoms, psychological distress, and burnout were tested for the following categories: gender; duration of healthcare experience; job type; regular work during the SARS outbreak in emergency department, intensive care unit, or SARS isolation unit; indicators of the frequency and intensity of contact with SARS patients; and exposure to quarantine. For this analysis, the functional impact of SARS experience was operationalized as the number of adverse outcomes experienced by a person (from 0 to 7) of the following 7 outcomes: posttraumatic stress (IES >26); psychological distress (K10 >16); burnout (MBI-EE >27); decrease in face-to-face patient contact since SARS; decrease in work hours since SARS; increase in smoking, alcohol, or other problematic behavior since SARS; and >4 shifts missed because of stress or illness in the 4 months before the survey. cache = ./cache/cord-263224-osf0tkzr.txt txt = ./txt/cord-263224-osf0tkzr.txt === reduce.pl bib === id = cord-263350-i02z0hgx author = Nagata, Noriyo title = Pathological and Virological Analyses of Severe Acute Respiratory Syndrome–Associated Coronavirus Infections in Experimantal Animals date = 2006 pages = extension = .txt mime = text/plain words = 982 sentences = 56 flesch = 52 summary = To determine the pathological features of SARS-CoV infection in experimental animals, its clinical, pathological, and virological features were investigated in cynomolgus monkeys, BALB/c mice, and F344 rats. In monkeys, following intranasal inoculation with 10 6 TCID 50 of SARS-CoV, the virus was isolated from throat and nasal swabs, and the viral genome was detected in rectal swabs collected between 2 and 7 days postinoculation (p.i.). Angiotensin-converting enzyme 2 (ACE2, a receptor for SARS-CoV 2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium in the lung of monkeys ( Figure 1A , B, and C). In BALB/c mice, the virus was detected in nasal and lung washes on days 3 and 5 after intranasal inoculation with 10 6 TCID 50 of SARS-CoV. In these experimental animals, ACE2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium (Table 1 ). cache = ./cache/cord-263350-i02z0hgx.txt txt = ./txt/cord-263350-i02z0hgx.txt === reduce.pl bib === id = cord-263039-uoxaem82 author = Perchetti, Garrett A. title = Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection date = 2020-07-23 pages = extension = .txt mime = text/plain words = 664 sentences = 42 flesch = 58 summary = Nucleic acid degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can compromise the accuracy of molecular detection methods. It has been demonstrated that nasopharyngeal specimens containing SARS-CoV-2 can be stored in phosphate-buffered saline (PBS) as a substitute for viral transport medium (VTM) for up to 7 days (3). Here, we evaluate the stability of differing viral loads of SARS-CoV-2 over 28 days stored at room temperature, 4°C, -20°C, or -80°C. For the high concentration of SARS-CoV-2, regardless of storage conditions, 100% of samples were detected by qRT-PCR through day 28. For lower concentrations of virus, storage at room temperature was associated with reductions of positivity beginning at day 7, and by day 28, 0% of samples were detected for N1. At viral loads of Ͼ5,000 copies/ ml-corresponding to Ͼ75% of positive samples recovered in our clinical lab to date-different storage temperatures did not have a substantial impact on our ability to detect SARS-CoV-2 when stored in PBS. cache = ./cache/cord-263039-uoxaem82.txt txt = ./txt/cord-263039-uoxaem82.txt === reduce.pl bib === id = cord-263471-u3su9loz author = Lam, Meylin Caballeros title = Cardiac magnetic resonance characterization of COVID-19 myocarditis date = 2020-07-04 pages = extension = .txt mime = text/plain words = 934 sentences = 67 flesch = 49 summary = 1 Myocardial injury may occur at different phases of COVID-19 disease (ie, viral, pulmonary, inflammatory, and recovery phase), even late after the onset of symptoms. SARS-CoV-2 viral particles have been identified by real-time polymerase chain reaction (PCR) testing in cardiac tissue, providing evidence that direct cardiotoxicity might occur. Since more than 7.5% of myocardial cells have positive ACE2 expression, this could mediate SARS-CoV-2 entry into cardiomyocytes and cause direct cardiotoxicity. The CMR study performed on a 1.5T system (Magnetom Aera, Siemens Healthineers, Erlangen, Germany) showed normal biventricular function, no regional wall motion abnormalities, slightly increased T2 (54 ms, normal < 52 ms) and native T1 values (1110 ms, CMR allows targeting of several features of myocarditis, such as contractile dysfunction, inflammatory edema, and necrosis, and has become the gold standard for the noninvasive assessment of the disease. The role of cardiovascular imaging for myocardial injury in hospitalized COVID-19 patients cache = ./cache/cord-263471-u3su9loz.txt txt = ./txt/cord-263471-u3su9loz.txt === reduce.pl bib === id = cord-263452-y2ral8nx author = Watanabe, Yasunori title = Site-specific glycan analysis of the SARS-CoV-2 spike date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2073 sentences = 121 flesch = 50 summary = To resolve the site-specific glycosylation of SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo-electron microscopy (cryo-EM) structure, albeit without glycan processing blockade using kifunensine (4). The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27) , influenza HA (28, 29) , and LASV GPC (24). For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34) . This suggests that SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies. SARS-CoV-2 spike site-specific N-linked glycan analysis cache = ./cache/cord-263452-y2ral8nx.txt txt = ./txt/cord-263452-y2ral8nx.txt === reduce.pl bib === id = cord-263538-0wozg085 author = Cooch, P. B. title = Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date = 2020-10-23 pages = extension = .txt mime = text/plain words = 4440 sentences = 259 flesch = 52 summary = Conclusions: Supervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, paired with infection mitigation strategies (e.g., masking, physical distancing, stable cohorts, and hand hygiene), comprise a comprehensive strategy for safe school reopening. We hypothesized that supervised self-collection of anterior nares and saliva samples for the purpose of SARS-CoV-2 surveillance would be acceptable and feasible for kindergarten through 8 th grade children, their household contacts, and camp staff, and that camp staff could assist with collection supervision. 17 To our knowledge, this is the first study to describe self-collected anterior nares SARS-CoV-2 testing among children, or any participants in a school-like setting. In conclusion, we demonstrated excellent feasibility and acceptability of a serial surveillance SARS-CoV-2 testing approach with supervised anterior nares self-collection in 5-14 year-old children, their household contacts, and staff, during indoor summer camp. cache = ./cache/cord-263538-0wozg085.txt txt = ./txt/cord-263538-0wozg085.txt === reduce.pl bib === id = cord-263245-2qub96mz author = Singh, D. title = Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4779 sentences = 234 flesch = 41 summary = This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . cache = ./cache/cord-263245-2qub96mz.txt txt = ./txt/cord-263245-2qub96mz.txt === reduce.pl bib === id = cord-263123-5y8cc5eb author = Bian, Jingwei title = Anti-RAS drugs and SARS-CoV-2 infection date = 2020-04-28 pages = extension = .txt mime = text/plain words = 770 sentences = 56 flesch = 56 summary = authors: Bian, Jingwei; Zhao, Rongsheng; Zhai, Suodi; Li, Zijian In addition, ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAS) and plays a key role in cardiovascular disease, especially Here, we present a completely different perspective on the relationship between SARS-CoV-2 infection and ACEI/ARB drugs. Firstly, there is no sufficient evidence to support that ACEIs and ARBs can upregulate the protein expression level of ACE2. Therefore, there is no adequate evidence to support that ACEIs/ARBs increase the risk of the SARS-CoV-2 infection by up-regulating ACE2 protein level. In addition, liver/lymph node-specific and dendritic In summary, there is currently no clear evidence indicating that anti-RAS drugs (ACEIs and ARBs) increase the risk of SARS-CoV-2 infection, as well as target organ injury. There is still no need to recommend the discontinuation of ACEIs/ARBs for hypertensive patients with or at high risk of SARS-CoV-2 infection, or the change to other antihypertensive drugs. Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19 cache = ./cache/cord-263123-5y8cc5eb.txt txt = ./txt/cord-263123-5y8cc5eb.txt === reduce.pl bib === id = cord-263365-ymnbktm5 author = Dube, Geoffrey K. title = COVID‐19 infection in pancreas transplant recipients date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2494 sentences = 168 flesch = 51 summary = 1 Clinical manifestations of COVID-19, the disease caused by SARS-CoV-2, range from asymptomatic infection to mild upper respiratory tract symptoms or viral pneumonia. We present here the first four cases of COVID-19 disease reported in PT recipients, with one case being a presumptive diagnosis based on suggestive symptoms and known nosocomial exposure in the absence of confirmatory PCR testing for SARS-CoV-2. First, the main presenting symptoms in our PT recipients (fever in 100%, cough in 75%) were similar to what is reported in the non-transplant population. The clinical deterioration of patient 3 after 10 days highlights the importance of close monitoring of suspected or confirmed COVID-19 in PT recipients followed in the outpatient setting until complete symptom resolution. When our patients informed us of symptoms consistent with COVID-19 infection, we held mycophenolate in 3 of our patients and temporarily held tacrolimus in 1 patient on monotherapy, a strategy similar to that employed in other solid organ transplant recipients at our center. cache = ./cache/cord-263365-ymnbktm5.txt txt = ./txt/cord-263365-ymnbktm5.txt === reduce.pl bib === id = cord-263481-w5ytp1q7 author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3013 sentences = 171 flesch = 54 summary = MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. cache = ./cache/cord-263481-w5ytp1q7.txt txt = ./txt/cord-263481-w5ytp1q7.txt === reduce.pl bib === id = cord-263844-ixgejst2 author = Majdic, Gregor title = Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1702 sentences = 87 flesch = 49 summary = title: Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? If there is a sex difference in the expression of ACE2 in the lung, this could theoretically explain the gender disparity in COVID-19 disease. Epidemiological data show that a much larger number of men are severely affected by the disease, and there is an even more substantial gender difference in the mortality of patients with COVID-19. Here, I propose a novel hypothesis that not only addresses the significant gender differences in morbidity and mortality due to COVID-19 but also potentially tackles the low morbidity and especially the low mortality in children infected by the SARS-CoV-2 virus. Therefore, I propose the hypothesis that the expression of ACE2 protein is different between males and females and that this sex difference contributes to the gender disparity in morbidity and mortality from the COVID-19 disease. cache = ./cache/cord-263844-ixgejst2.txt txt = ./txt/cord-263844-ixgejst2.txt === reduce.pl bib === id = cord-262735-xj9md751 author = Li, Lian Yong title = Digestive system involvement of novel coronavirus infection: Prevention and control infection from a gastroenterology perspective date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1280 sentences = 71 flesch = 43 summary = In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. Gastrointestinal manifestation in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection above, by adopting single-cell RNA-sequencing technology from two cohort samples, a recent study has shown that ACE2 is highly expressed in cholangiocytes rather than the hepatocytes or other interstitial cells. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-262735-xj9md751.txt txt = ./txt/cord-262735-xj9md751.txt === reduce.pl bib === id = cord-263576-pn2zieek author = Das, Sourav title = An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study date = 2020-05-13 pages = extension = .txt mime = text/plain words = 5000 sentences = 266 flesch = 54 summary = Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. Hydroxychloroquine, a promising candidate for the treatment of the current pandemic due to SARS-CoV-2 (Gautret et al., 2020) , has been found to bind within the active site of the protease through p-sulphur interaction with MET165, p-sigma with GLN189, alkyl hydrophobic with LEU167 and PRO168, and van der Waals interactions with other residues as shown in Figure 2c . Curcumin, a potent bioactive molecule binds in the active site of SARS-CoV-2 M pro (Figure 3a ) through hydrogen bonding with GLY143 and GLN192, p-sulphur, p-sigma interactions with CYS145 and PRO168, respectively, along with other non-covalent interactions such as van der Waals interactions with other residues as shown in the 2 D plot (Figure Table 1 . cache = ./cache/cord-263576-pn2zieek.txt txt = ./txt/cord-263576-pn2zieek.txt === reduce.pl bib === id = cord-263456-lqe1yckv author = Craney, Arryn R. title = Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2902 sentences = 177 flesch = 54 summary = We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. On 4 February 2020, the Centers for Disease Control and Prevention (CDC) received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for an RT-PCR assay to detect SARS-CoV-2 in a range of respiratory specimens (5) . In this study, we compared the diagnostic performances of the cobas 6800 and Panther Fusion high-throughput RT-PCR systems for the detection of SARS-CoV-2 RNA in 389 NP swab specimens, the predominant specimen type employed for SARS-CoV-2 RT-PCR (4). However, to the best of our knowledge, no study has evaluated the performance characteristics of the Panther Fusion SARS-CoV-2 RT-PCR assay or directly compared two high-throughput systems. In conclusion, the cobas 6800 and Panther Fusion systems and their associated SARS-CoV-2 tests are comparable in terms of their performance characteristics in the clinical setting. cache = ./cache/cord-263456-lqe1yckv.txt txt = ./txt/cord-263456-lqe1yckv.txt === reduce.pl bib === id = cord-263583-a1zon98c author = Fabbris, Cristoforo title = Is oro/nasopharyngeal swab for SARS-CoV-2 detection a safe procedure? Complications observed among a case series of 4876 consecutive swabs date = 2020-10-13 pages = extension = .txt mime = text/plain words = 760 sentences = 52 flesch = 52 summary = In this paper we present the complications encountered in a series of healthworkers who underwent oro/nasopharyngeal swab for detection of SARS-CoV-2. All patients underwent sampling with a sterile collection Citoswab® (Citotest Labware Manufacturing Co., LTD) All reports, possible complications and clinical information were noted from registries of the infectious disease units and medical records. One patient, affected by diabetes mellitus and neutropenia, developed septal abscess (case 2) and another, who later was observed to have septal deviation, had severe anterior and posterior bleeding from an arterial point of the olfactory area, possibly arising from the anterior ethmoidal artery (case 3) requiring surgical cauterization. However arterial rupture can give catastrophic bleed as seen in one patient: we suspect the septal deviation may have misled the swabbing process to the upper part of nares where trauma to the anterior ethmoidal artery may have occurred. In conclusion, oro/nasopharyngeal swabs are safe procedures to detect SARS-CoV-2 infection. cache = ./cache/cord-263583-a1zon98c.txt txt = ./txt/cord-263583-a1zon98c.txt === reduce.pl bib === id = cord-262904-0b0ljjq1 author = Lon, Jerome Rumdon title = Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5006 sentences = 263 flesch = 53 summary = It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. On this basis, we predicted the linear and conformational B cell epitopes, analyzed the conservation of the epitopes, the adaptability and other evolutionary characteristics of the surface protein, which provided a theoretical basis for the vaccine development and prevention of SARS-CoV-2. With the amino acid sequences of the surface protein of SARS-CoV-2 of NC_045512.2 as templates, we predicted the 3D structure of E and M protein through the online server SWISS-MODEL [10] based on homology modeling method, selected the optimal structure based on the template identity and GMQE value [10] , and the rationality of the structure was evaluated by Ramachandran plot [11] with PDBsum server. cache = ./cache/cord-262904-0b0ljjq1.txt txt = ./txt/cord-262904-0b0ljjq1.txt === reduce.pl bib === id = cord-263764-2ewz8ok4 author = Kutter, Jasmin S title = Transmission routes of respiratory viruses among humans date = 2018-01-17 pages = extension = .txt mime = text/plain words = 4392 sentences = 242 flesch = 40 summary = We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . cache = ./cache/cord-263764-2ewz8ok4.txt txt = ./txt/cord-263764-2ewz8ok4.txt === reduce.pl bib === id = cord-264042-4hc2i25r author = Chim, Harvey title = Severe Acute Respiratory Syndrome in a Naval Diver date = 2006-06-17 pages = extension = .txt mime = text/plain words = 2133 sentences = 132 flesch = 50 summary = In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive. S evere acute respiratory syndrome (SARS) is an emerging infectious disease that was first reported in Guangdong Province in southern China in November 2002 and subsequently caused outbreaks in Singapore, Hong Kong, Southeast Asia, and Canada. In the week following diagnosis of SARS in this patient, only essential personnel in the diving unit were required to report to work to prevent the possible spread of SARS. cache = ./cache/cord-264042-4hc2i25r.txt txt = ./txt/cord-264042-4hc2i25r.txt === reduce.pl bib === id = cord-264012-q2quyijg author = Lim, Su Bin title = ACE2-expressing endothelial cells in aging mouse brain date = 2020-07-11 pages = extension = .txt mime = text/plain words = 2133 sentences = 106 flesch = 48 summary = Further, scRNA-seq dataset specifically derived from brain vasculature in young adult and aged mice (T3) confirms the elevated ACE2 expression in subsets of the three identified cell types, which consist of 32.8% of the cell populations ( Fig. 1 C) . While our study provides a foundation for a more refined level of analysis of EC and vascular PC, a cell type that remains poorly understood despite its key roles in immune response and microvascular stability [17] , our analyses are limited only to the normal aging mouse and human brains, lacking the context of COVID-19 neuropathology. Despite the works that failed to identify direct signs of SARS-CoV-2 infection in the brains of COVID-19 patients [12, 13] , other lines of evidence support the neurotropism of the virus, as evidenced by experimental platforms leveraging human induced pluripotent stem cell (iPSC)derived dopaminergic neurons [22] and an organotypic brain model [23] . cache = ./cache/cord-264012-q2quyijg.txt txt = ./txt/cord-264012-q2quyijg.txt === reduce.pl bib === id = cord-263532-q044i7ym author = Goyal, Bhupesh title = Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy date = 2020-05-13 pages = extension = .txt mime = text/plain words = 6017 sentences = 402 flesch = 54 summary = In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M(pro) on its dimerization and, thus, catalytic activity. The individual monomers of SARS-CoV M pro are enzymatically inactive, and two strategies have been employed to develop inhibitors against this enzyme: (i) molecules targeting the substrate binding pocket to block the catalytic activity, and (ii) dimerization inhibitors. 14, 15 In the present review, literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M pro on its dimerization and, thus, catalytic activity are compiled. The various mutation analyses, N-terminal truncation studies, and MD simulation studies that highlighted key residues of SARS-CoV M pro involved in the stabilization of the catalytically active dimeric structure of the enzyme are listed in Table 2 and are arranged in chronological order. cache = ./cache/cord-263532-q044i7ym.txt txt = ./txt/cord-263532-q044i7ym.txt === reduce.pl bib === id = cord-263801-01goni72 author = Sobral, Marcos Felipe Falcão title = Association between climate variables and global transmission oF SARS-CoV-2 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 2957 sentences = 173 flesch = 46 summary = In this study, we aimed at analyzing the associations between transmission of and deaths caused by SARS-CoV-2 and meteorological variables, such as average temperature, minimum temperature, maximum temperature, and precipitation. On the basis of the assumption that different climatic conditions play a significant role in the course of COVID-19, it is essential to identify associations between environmental factors, such as average, maximum, and minimum temperatures; precipitation; and demographic density, and SARS-CoV-2 transmission and COVID-19 mortality in humans. Even with the complete specification that includes two binary variables capturing specific effects for the months of the year and controlling for population density, the results suggest that an increase in temperature is associated with a decrease in the number of infections. This study aimed to identify the associations between environmental variables and SARS-CoV-2 transmission/COVID-19 mortality. We examined the associations between climatic variables and SARS-CoV-2 transmission and COVID-19 mortality. cache = ./cache/cord-263801-01goni72.txt txt = ./txt/cord-263801-01goni72.txt === reduce.pl bib === id = cord-263594-jd9ako6c author = Kang, Sisi title = A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2517 sentences = 181 flesch = 56 summary = Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Severe acute 57 respiratory distress syndrome-associated coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein 58 is a highly immunopathogenic and multifunctional viral protein (14) (15) (16) (17) (18) (19) , which elicited high titers 59 of binding antibodies in humoral immune responses (20) (21) (22) . Herein, 66 we report a human mAb derived from COVID-19 convalescent, with specific targeting to SARS-67 CoV-2 N protein and functionally compromising complement hyper-activation ex vivo. Isolation of N protein-directed mAbs 69 To profile antibody response to SARS-CoV-2 N protein in early recovered patients, we collected 70 six convalescent blood samples at seven to 25 days after the onset of the disease symptoms. cache = ./cache/cord-263594-jd9ako6c.txt txt = ./txt/cord-263594-jd9ako6c.txt === reduce.pl bib === id = cord-263508-row2mn17 author = Chan, Jasper Fuk-Woo title = The emerging novel Middle East respiratory syndrome coronavirus: The “knowns” and “unknowns” date = 2013-07-21 pages = extension = .txt mime = text/plain words = 4344 sentences = 202 flesch = 43 summary = Ten years after the devastating epidemic of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV), which resulted in a total of 774 deaths among more than 8000 confirmed cases in over 30 countries, the world is facing a new challenge posted by a "SARS-like" infection caused by another novel coronavirus emerging from the Middle East, which was originally named human coronavirus EMC/2012 (HCoV-EMC) and recently renamed by the Coronavirus Study Group of the International Committee for Taxonomy of Viruses as Middle East respiratory syndrome coronavirus (MERS-CoV). 6,7,10e14 Although the number of laboratory-confirmed cases remains limited, the severe clinical manifestations with an unusually high mortality rate of over 50%, the spread of the infection beyond the geographical confinement in the Middle East, and the epidemiological evidence of human-to-human transmission arising from the recent clusters of cases in a family in the United Kingdom (Cases 10 to 12), and in hospitals in KSA (Cases 18 to 30, 32 and 33) and France (Cases 31 and 34), have raised significant concerns on the possible emergence of another SARS-like epidemic in the near future. cache = ./cache/cord-263508-row2mn17.txt txt = ./txt/cord-263508-row2mn17.txt === reduce.pl bib === id = cord-263719-a9mnjr3s author = Lee, A. title = Wuhan novel coronavirus (COVID-19): why global control is challenging? date = 2020-02-29 pages = extension = .txt mime = text/plain words = 1276 sentences = 101 flesch = 56 summary = At this stage, the global spread of COVID-19 acute respiratory disease continues to grow, and the full extent and severity of this outbreak remains to be seen. 7 Once the pathogen has landed in a new country, the likelihood of contagion and spread is dependent on local transmission pathways and the strength of local health protection systems. 8 High-income countries such as the United States and United Kingdom have well-developed health protection systems to detect and respond to communicable disease threats. The other component of well-developed health protection systems are strong infectious disease surveillance systems. The current concerns then regarding the 2019-nCoV outbreak must be for low-and middle-income countries where health protection systems tend to be weaker. In these settings, laboratory resources may be lacking, notification of infectious diseases are often not timely or complete, and their public health infrastructure is often weak. Global infectious disease surveillance and health intelligence cache = ./cache/cord-263719-a9mnjr3s.txt txt = ./txt/cord-263719-a9mnjr3s.txt === reduce.pl bib === id = cord-263738-8g5ujfaf author = Qian, Jing-Yi title = Acute Kidney Injury in the 2019 Novel Coronavirus Disease date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3509 sentences = 189 flesch = 49 summary = COVID-19 is characterized by acute respiratory disease, with 80% of patients presenting mild like flu-like symptoms; however, 20% of patients may have a severe or critical clinical presentation, which likely causes multiple organ injuries (e.g., kidney, heart, blood, and nervous system). Novel coronavirus disease (COVID-19) is a newly discovered acute infectious disease caused by the SARS-CoV-2 virus, which is mainly manifested as acute respiratory diseases characterized by acute interstitial and alveolar pneumonia and can affect multiple organs such as the kidneys, the heart, the digestive tract, and blood [1] . In another study of 99 patients with COVID-19, seven cases developed various degrees of kidney injury with elevated serum creatinine (Scr) and/or blood urea nitrogen (BUN) levels, and 3 of them were diagnosed with AKI [4] . These results provide direct evidence that the SARS-CoV-2 virus can directly infect the renal tubular epithelium and podocytes, which may induce AKI in COVID-19 patients [17] . cache = ./cache/cord-263738-8g5ujfaf.txt txt = ./txt/cord-263738-8g5ujfaf.txt === reduce.pl bib === id = cord-263616-igprqlqr author = Hamid, Hytham K. S. title = Considerations for transanal surgery during COVID‐19 pandemic date = 2020-07-15 pages = extension = .txt mime = text/plain words = 148 sentences = 19 flesch = 56 summary = key: cord-263616-igprqlqr authors: Hamid, Hytham K. title: Considerations for transanal surgery during COVID‐19 pandemic date: 2020-07-15 journal: J Surg Oncol DOI: 10.1002/jso.26085 sha: doc_id: 263616 cord_uid: igprqlqr nan To the Editor, Elective colorectal cancer surgery at the oncologic hub of Lombardy inside a pandemic COVID-19 area Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis Prolonged presence of SARS-CoV-2 viral RNA in faecal samples Evidence for gastrointestinal infection of SARS-CoV-2 Detection of SARS-CoV-2 in different types of clinical specimens Isolation of 2019-nCoV from a stool specimen of a laboratory-confirmed case of the coronavirus disease 2019 (COVID-19) Detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child Coronavirus disease (COVID-19) in a paucisymptomatic patient: epidemiological and clinical challenge in settings with limited community transmission cache = ./cache/cord-263616-igprqlqr.txt txt = ./txt/cord-263616-igprqlqr.txt === reduce.pl bib === id = cord-263840-1t4ykc01 author = Altay, Ozlem title = Current status of COVID-19 therapies and drug repositioning applications date = 2020-06-20 pages = extension = .txt mime = text/plain words = 2099 sentences = 140 flesch = 44 summary = Summary The rapid and global spread of a new human coronavirus (SARS-CoV-2) has produced an immediate urgency to discover promising targets for treatment of COVID-19. Here, we review current information concerning the global health issue of COVID-19 including promising approved drugs and ongoing clinical trials for prospective treatment options. At the genome 60 level, SARS-CoV-2 has 79·5% homology to SARS CoVCoV-2 and other coronaviruses, and its relative ease of sample acquisition and study, it has been widely 75 accepted that drug repositioning is a promising approach to make available an effective, safety-assured 76 treatment in a timely manner. In this review, we summarize diagnosis approaches, risk groups, available 77 treatment options, and drug repositioning studies related to COVID-19. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 525 2019 (COVID-19): The experience of clinical immunologists from China cache = ./cache/cord-263840-1t4ykc01.txt txt = ./txt/cord-263840-1t4ykc01.txt === reduce.pl bib === id = cord-263874-q0egnzwf author = Khan, Md. Arif title = Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study date = 2020-07-22 pages = extension = .txt mime = text/plain words = 2991 sentences = 166 flesch = 52 summary = Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. Also, researchers have currently reported using the drug repurposing approach based on the molecular docking and dynamics study where the key target proteins are 3CL protease, RNA dependent RNA polymerase (RdRp), and spike proteins (Elfiky, 2020b; Muralidharan et al., 2020; Smith & Smith, 2020; Tahir Ul Qamar et al., 2020; Yu et al., 2020) . In this ground, it is clearly seen that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions among the 23 potential inhibitors against SARS-CoV-19 main protease and those results pave the way in drug discovery although it has to be further validated by in vitro and in vivo investigations. cache = ./cache/cord-263874-q0egnzwf.txt txt = ./txt/cord-263874-q0egnzwf.txt === reduce.pl bib === id = cord-263970-9w6ciglv author = Marquez-Miranda, Valeria title = Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date = 2020-10-22 pages = extension = .txt mime = text/plain words = 2882 sentences = 166 flesch = 53 summary = SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. Here we used this dimeric structure to perform full atom molecular dynamic simulations and electrostatic potential calculations to ask questions concerning the dimers' stability and whether ions could be populating specific regions of the channel. To assess the impact of the ion occupancies described above, we obtained the electrostatic potential maps for the ORF3a channel for the initial configuration, and the last frame, at the end of a trajectory of 500 ns of the molecular dynamics simulations, by employing the Poison-Boltzmann approach implemented in the APBS package [12] . This analysis shows that the entry of Cl-ions through the inter-subunit tunnel into the central polar cavity and the accumulation of K+ ions at the cytosolic domain's surface changed the channel's electrostatic profile. cache = ./cache/cord-263970-9w6ciglv.txt txt = ./txt/cord-263970-9w6ciglv.txt === reduce.pl bib === id = cord-264045-h0vt3r9j author = Pallett, Scott J C title = Serological assays for delayed SARS-CoV-2 case identification – Author's reply date = 2020-09-14 pages = extension = .txt mime = text/plain words = 644 sentences = 34 flesch = 46 summary = We read with interest the insightful comments put forward by Kay Weng Choy, raising important considerations for clinicians planning to use pointof-care serological assays for delayed case identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in response to those presented in our Article. Our study was designed specifically to evaluate the use of point-ofcare assays for frontline health-care workers directly involved in the clinical care of patients with SARS-CoV-2 infection; therefore, it was not possible to evaluate any difference in detection of SARS-CoV-2 IgG in young or older people. 4 An evaluation of the potential effect of immunodeficiency on assay performance was beyond the scope of our study; however, we strongly agree that this is an important issue for future studies where consideration can be given to testing in different populations. Pointof-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study cache = ./cache/cord-264045-h0vt3r9j.txt txt = ./txt/cord-264045-h0vt3r9j.txt === reduce.pl bib === id = cord-263739-xoum5e0k author = Zhang, X.-Y. title = Analysis of the effect of proton pump inhibitors on the course of common COVID-19 date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2581 sentences = 179 flesch = 66 summary = In the proton pump inhibitors group and the control group, the duration of SARS-CoV-2 clearance were 7(6-9) and 7(6-11) days, and the duration of hospital stay was 21(16-25) and 20(15-26) days, respectively. Case exclusion criteria: (1) the patients used drugs to inhibit the secretion of 179 gastric acid within 30 days before admission; (2) Specimens used for SARS-CoV-180 2 nucleic acid testing were collected at an interval of more than 48 hours; (3) 181 The demographic and clinical data included age and sex of the patients, The nucleic acid test specimens of SARS-CoV-2 in this study were 209 The cumulative probability of SARS-CoV-2 clearance or discharge from 224 COVID-19 cases were conducted through Kaplan-Meier statistics, and the 225 difference was examined by Log-rank test. Cumulative probability of SARS-CoV-2 clearance and discharge in COVID-19 676 patients between PPIs group and control group by 1:1 PS-matching analysis cache = ./cache/cord-263739-xoum5e0k.txt txt = ./txt/cord-263739-xoum5e0k.txt === reduce.pl bib === id = cord-263847-kyak5cy4 author = Shi, Tzu-Hau title = Andrographolide and its fluorescent derivative inhibit the main proteases of 2019-nCoV and SARS-CoV through covalent linkage date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3093 sentences = 162 flesch = 45 summary = We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (AndroNBD), suppressed the main protease (M(pro)) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys(145) of either 2019-nCoV M(pro) or SARS-CoV M(pro). Moreover, lopinavir/ritonavir, previously identified as HIV protease inhibitors and found to exhibit anti-SARS-CoV activity in vitro and in clinical, have been proposed to bind 2019-nCoV M pro and are being investigated for COVID-19 treatments [6, 7] . Lopinavir/ritonavir, the HIV protease inhibitors previously identified with anti-SARS-CoV activity in vitro and in clinical, was proposed to bind 2019-nCoV M pro and thus has been investigated for COVID-19 treatments [6, 7] . In this study, we revealed that andrographolide and its derivative inhibits the activity of main protease and thus likely to impair the replication of SARS-CoV and 2019-nCoV. cache = ./cache/cord-263847-kyak5cy4.txt txt = ./txt/cord-263847-kyak5cy4.txt === reduce.pl bib === id = cord-264057-z5arb1k5 author = Goel, S. title = Preparations and limitations for prevention of severe acute respiratory syndrome in a tertiary care centre of India date = 2007-05-18 pages = extension = .txt mime = text/plain words = 2753 sentences = 190 flesch = 59 summary = This short-term observational study of infection control practice was performed in the medical emergency outpatient department (EMOPD) of a tertiary-care hospital in India when threatened by an outbreak of severe acute respiratory syndrome (SARS). Infection control measures such as fumigation and cleaning were noted, as was the EMOPD laboratory function, use of personnel protection and display of information on infectious diseases. The EMOPDs in key hospitals need be able to screen for infectious diseases, especially in view of the threats from SARS and Avian influenza. The need to screen all patients with suspected infectious disease in the medical emergency outpatient department (EMOPD), and for control and prevention of infection, was recognized. In addition, the patient/attendant load, patient flow, and medical staff practice were observed, and information displayed on SARS or other infectious diseases was noted. cache = ./cache/cord-264057-z5arb1k5.txt txt = ./txt/cord-264057-z5arb1k5.txt === reduce.pl bib === id = cord-264052-uph136sn author = Wilson, Mitchell P title = Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature date = 2020-04-23 pages = extension = .txt mime = text/plain words = 2110 sentences = 141 flesch = 44 summary = title: Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature A search of MEDLINE, J o u r n a l P r e -p r o o f EMBASE, Scopus, and the Cochrane Library (including the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and the Cochrane Special Collections) from inception to April 7, 2020 was performed in order to identify articles evaluating both COVID-19 and neurology or neurosurgery. A total of 10 articles including 4 articles discussing clinical symptomatology and/or the neuroinvasive potential of SARS-CoV-2 (5-8) and 6 articles discussing recommendations for modified neurosurgical (9-11), stroke (12) , and spine (13) (14) practices during the COVID-19 crisis. Thus far, early experience and recommendations in neurosurgical (9) (10) (11) 33) , stroke (12) , and spine (13, 14) practices have been reported (Table 2) As an early scoping review of available literature to date, this study has certain limitations. cache = ./cache/cord-264052-uph136sn.txt txt = ./txt/cord-264052-uph136sn.txt === reduce.pl bib === id = cord-264461-nzvuugls author = Li, Jing title = Puzzle of highly pathogenic human coronaviruses (2019-nCoV) date = 2020-02-22 pages = extension = .txt mime = text/plain words = 2048 sentences = 101 flesch = 48 summary = The immunosuppressive drug CsA prevents the nucleocapsid protein of the virus from binding to cyclophilin A (CypA) of the host cell, which has a peptidyl prolyl cis/trans isomerase (PPIase) activity, and a combination of interferon and CsA has been shown previously to significantly inhibit the replication and tissue damage caused by coronavirus infection in bronchi and lungs of humans. reported a mathematical model for simulating the transmission of the novel Wuhan Coronavirus, which is a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source to the humans (Chen et al., 2020a) . They estimated the transmissibility of 2019-nCoV via the basic reproduction number based on only the data from the early stages of the outbreak (Zhao et al., 2020a) . From SARS-CoV to Wuhan 2019-nCoV outbreak: similarity of early epidemic and prediction of future trends Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin cache = ./cache/cord-264461-nzvuugls.txt txt = ./txt/cord-264461-nzvuugls.txt === reduce.pl bib === id = cord-264266-6xvj9zey author = Chakrabarti, Sankha Shubhra title = COVID-19 in India: Are Biological and Environmental Factors Helping to Stem the Incidence and Severity? date = 2020-05-09 pages = extension = .txt mime = text/plain words = 3845 sentences = 175 flesch = 46 summary = Apart from SARS-CoV and MERS-CoV which caused severe respiratory diseases following outbreaks in 2003 and 2012, there are four endemic human corona viruses, HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1 in populations that are responsible for various types of respiratory illness which are generally self-limiting in young and immunecompetent persons [8] . It can be assumed that some degrees of sequence homology or conformational similarities among the structural proteins, especially the S protein, of SARS-CoV-2 and the endemic corona viruses (HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1) may result in cross-reactive immunity (circulating antibodies or primed T-cells) in persons with prior exposure to the latter viruses, and this may modulate the course and outcome of COVID-19. Thus, the possibility of a protective cross-immunity in the Indian population against COVID-19 cannot be ignored in explaining a rather mild effect of the current coronavirus pandemic in India in comparison to that in Europe and the USA. Therefore, cross-reactive antibodies generated as a result of infections from other human corona viruses may have a protective role in a population affected by COVID-19. cache = ./cache/cord-264266-6xvj9zey.txt txt = ./txt/cord-264266-6xvj9zey.txt === reduce.pl bib === id = cord-264051-ps0x2es1 author = Li, Wei title = Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date = 2020-11-05 pages = extension = .txt mime = text/plain words = 8939 sentences = 450 flesch = 51 summary = Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Besides, these virus fragments containing HIS can increase the H3K27 acetylation (H3K27ac) enrichment at their corresponding regions of the human genome in different mammalian cells and activate the expression of adjacent and distant genes associated with inflammation. Collectively, we identified HIS in SARS-CoV-2 genome, and the targeted human genome loci enriched with cytokines genes suggested that HIS may underly the clinical characteristics of COVID-19 patients and serve as a vital player in the pathological progression. cache = ./cache/cord-264051-ps0x2es1.txt txt = ./txt/cord-264051-ps0x2es1.txt === reduce.pl bib === id = cord-264260-8p6pvjkn author = Peng, Hongbing title = A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report date = 2020-07-16 pages = extension = .txt mime = text/plain words = 3163 sentences = 161 flesch = 49 summary = title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report We note that the intravenous infusion of CP and MSCs for the treatment of severe COVID-19 patients may have synergistic characteristics in inhibiting cytokine storm, promoting the repair of lung injury, and recovering pulmonary function. We reviewed a case of severe COVID-19 cured successfully with convalescent plasma-umbilical cord mesenchymal stem cells and observed and analyzed the change of clinical symptoms and laboratory data before and after treatment. From admission to discharge, the researchers continue to observe and evaluate patients' dynamic changes in clinical symptoms and laboratory results, especially after receiving plasma and stem cell therapy. Intravenous infusion of human umbilical cord Wharton's jelly-derived mesenchymal stem cells as a potential treatment for patients with COVID-19 pneumonia cache = ./cache/cord-264260-8p6pvjkn.txt txt = ./txt/cord-264260-8p6pvjkn.txt === reduce.pl bib === id = cord-264360-eroqjkoh author = Risku, Minna title = Detection of human coronaviruses in children with acute gastroenteritis date = 2010-03-15 pages = extension = .txt mime = text/plain words = 2364 sentences = 154 flesch = 60 summary = STUDY DESIGN: 878 stool specimens from children with acute gastroenteritis and 112 from control children were tested by RT-PCR to detect HCoV groups 1B, 2A and SARS. On the basis of this study, the significance of coronaviruses as gastrointestinal pathogens in children appears minor, since most of the coronavirus findings were co-infections with known gastroenteritis viruses. Our study shows that human coronaviruses OC43, HKU1, 229E and NL63 can be found in stool samples of children with acute gastroenteritis. 10 In our study one of the 36 healthy control patients had coronavirus detected in stool specimen and thus, there was no difference in the HCoV detection rate between the cases of acute gastroenteritis and control children. Future studies should investigate such mild cases for HCoVs. In conclusion, non-SARS human coronaviruses can be found in stool samples of children with acute gastroenteritis. cache = ./cache/cord-264360-eroqjkoh.txt txt = ./txt/cord-264360-eroqjkoh.txt === reduce.pl bib === id = cord-264326-teahway7 author = Eleftheriou, Phaedra title = In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus date = 2020-05-29 pages = extension = .txt mime = text/plain words = 5403 sentences = 256 flesch = 50 summary = According to docking analysis the most promising results were found for HCV protease, DPP-4, α-thrombin and coagulation Factor Xa known inhibitors, with several of them exhibiting estimated free binding energy lower than −8.00 kcal/mol and better prediction results than reference compounds. Since the 3D structure of the active site of the enzyme is crucial for catalytic activity, we proceeded to a comparison of the SARS-CoV-2 main protease, Mpro, with the HIV-1 protease, the HCV protease (NS3 protein) and the human proteases DPP-4, thrombin, Factor Xa, renin and ACE, which constitute known drug targets with approved inhibitors. The structural similarity between the SARS-CoV-2 protease and some of the selected proteases, in combination with the existence of the same amino acids at certain positions of the substrate cleavage site, such as Ser at the P1' position of the recognition sequence of the HCV protease and thrombin are promising features in the effort to identify effective SARS-CoV-2 protease inhibitors among the approved drugs of the selected proteases. cache = ./cache/cord-264326-teahway7.txt txt = ./txt/cord-264326-teahway7.txt === reduce.pl bib === id = cord-264477-2onwu92a author = Brida, Margarita title = The globe on the spotlight: Coronavirus disease 2019 (Covid-19) date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1972 sentences = 91 flesch = 46 summary = Our world, however, failed to learn necessary lessons from the SARS-CoV and MERS-CoV outbreaks and to invest on essential global research on ways of preventing the spread of infectious disease. The paper by Tan and Aboulhosn published in the current issue of the Journal, summarizes current knowledge regarding Covid-19 disease pandemic and its potential cardiovascular involvement, with a reference to adult congenital heart disease (ACHD) [8] . However, we are currently lacking ACHD specific data and a strict policy of social distancing employed in other parts of the world, seems to have had a positive response during the first phase of this pandemic in reducing the spread of disease and allowing for health care systems to prepare and somewhat cope with the unprecedented need. There are emerging publications regarding models of care of cardiovascular patients with infectious disease, which however are short of specific ACHD experience at present [14, 15] . cache = ./cache/cord-264477-2onwu92a.txt txt = ./txt/cord-264477-2onwu92a.txt === reduce.pl bib === id = cord-263803-0n41gylj author = Villoutreix, Bruno O. title = Prevention of COVID-19 by drug repurposing: rationale from drugs prescribed for mental disorders date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1287 sentences = 72 flesch = 49 summary = We also compared these 18 drugs with published molecules known to have in vitro antiviral activities [1, 2] using various chemoinformatics strategies (e.g., computation of molecular descriptors and compounds clustering carried out on J o u r n a l P r e -p r o o f about 300 molecules with in vitro antiviral activities on various viruses including SARS-CoV-2). Overall, our analysis suggests that the most commonly prescribed psychotropic drugs, including some antihistamine agents used as anxiolytics, possess in vitro antiviral activity ( Table 1 ). In summary, we propose that some of the drugs commonly prescribed to psychiatric patients could protect them from SARS-CoV-2 infection via the modulation of the endo-lysosomal pathway, membrane fusion and yet to be characterized interactions with specific receptors (e.g., nAChR, ACE2 and Sigma receptors, Fig. 1 ). Based upon the above analysis, we suggest that one of these CAD molecules or a combination could be used as preventive treatment against SARS-CoV-2 infection, especially drugs with reduced adverse effects (e.g., low dosage nicotine patch associated with an antihistamine agent). cache = ./cache/cord-263803-0n41gylj.txt txt = ./txt/cord-263803-0n41gylj.txt === reduce.pl bib === id = cord-264031-0y7xbgun author = Wierbowski, Shayne D. title = A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date = 2020-10-13 pages = extension = .txt mime = text/plain words = 5066 sentences = 291 flesch = 42 summary = title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. Further, we explore the utility of our interactome modeling approach in identifying key 99 interactions undergoing evolution along viral protein interfaces, highlighting population variants on 100 human interfaces that could modulate the strength of viral-host interactions to confer protection from or 101 susceptibility to COVID-19, and prioritizing drug candidates predicted to bind competitively at viral-102 human interaction interfaces. cache = ./cache/cord-264031-0y7xbgun.txt txt = ./txt/cord-264031-0y7xbgun.txt === reduce.pl bib === id = cord-264614-2x7cdul3 author = Díaz-Guio, Diego Andrés title = COVID-19: Biosafety in the Intensive Care Unit date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3857 sentences = 228 flesch = 49 summary = PURPOSE OF REVIEW: COVID-19 is a new, highly transmissible disease to which healthcare workers (HCWs) are exposed, especially in the intensive care unit (ICU). This article aims to show the different strategies to prevent the widespread of the disease to critical care healthcare workers based on the review of the recent literature and the author's experience with the personal protective equipment (PPE) in the care of patients with COVID-19 and work on human factors in crisis management. Nonetheless, to date, there is no robust evidence that medical masks are inferior to N95/FFP2 respirators for protecting healthcare workers against laboratory-confirmed COVID-19 during patients care and non-AGPs [31] . While personal protective equipment is an essential part of safety to prevent SARS-CoV-2 transmission, it must be employed appropriately, together with frequent hand hygiene, and mastering specific techniques and non-technical skills like awareness, closed-loop communication, leadership, team working, appropriate resource management, and cognitive aids [14, 34] . cache = ./cache/cord-264614-2x7cdul3.txt txt = ./txt/cord-264614-2x7cdul3.txt === reduce.pl bib === id = cord-264261-98h1bmb2 author = Caruana, Giorgia title = Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1417 sentences = 99 flesch = 48 summary = It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients cache = ./cache/cord-264261-98h1bmb2.txt txt = ./txt/cord-264261-98h1bmb2.txt === reduce.pl bib === id = cord-264646-d7qexyav author = Raza, Syed Shadab title = Mesenchymal Stem Cells: A new front emerge in COVID19 treatment: Mesenchymal Stem Cells therapy for SARS-CoV2 viral infection date = 2020-07-15 pages = extension = .txt mime = text/plain words = 2773 sentences = 143 flesch = 43 summary = Currently, treating coronavirus disease 2019 (COVID19) patients, particularly those afflicted with severe pneumonia, is challenging, as no effective pharmacotherapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exists. Based on results from preliminary clinical investigations, one predicts that MSCs therapy for SARS-CoV-2 infected patients is safe and effective although multiple clinical trials with a protracted follow-up will be necessary to determine the long term effects of the treatment on COVID19 patients. Further, MSCs exhibit broad immune regulatory function, which makes them suitable for anti-viral therapy as safety and effectiveness of these cells have been documented in clinical trials of severe lung infections [9, 10, 11] . The first study was a case report [12] , in which a critically ill 65-year-old female with severe pneumonia, respiratory failure, moderate anemia, hypertension, and multiple organ failure received three infusions of umbilical cord MSCs (UCMSCs, 5X10 7 cells/infusion), three days apart. cache = ./cache/cord-264646-d7qexyav.txt txt = ./txt/cord-264646-d7qexyav.txt === reduce.pl bib === id = cord-264013-8jnae6ig author = Tsilingiris, Dimitrios title = Telomere length, epidemiology, and pathogenesis of severe COVID‐19 date = 2020-08-09 pages = extension = .txt mime = text/plain words = 1905 sentences = 115 flesch = 46 summary = Cohen et al reported that in a relatively selected population of healthy adults aged between 18 and 55 years, following experimental exposure to Rhinovirus 39 (a single-stranded RNA virus), a shorter telomer length in PBMCs, total lymphocytes, as well as CD4+ and CD8+ Tlymphocyte subsets was associated with an increased probability of upper respiratory infection 23 . A diminishing telomere length in human lymphocytes is related to the process of their replicative senescence (or biological "aging") 26 . 29 Conversely, CD8+ lymphocyte senescence associated with critical telomere shortening induces a state of "hyper-function" with evasion of apoptosis, increased secretion of pro-inflammatory cytokines such as Tumor Necrosis Factor-alpha and interleukin-6 and loss of surface CD28, a co-stimulatory receptor necessary for the mobilization of targeted T-cell immune responses. We further speculate that this observation is driven by a complex immune dysregulation tracing back to immune cell senescence associated with telomere shortening, leading to increased susceptibility to infection and clinical disease (particularly pneumonia) by SARS-CoV-2, as well as unfavorable disease progression potentially marked by cytokine storm syndrome. cache = ./cache/cord-264013-8jnae6ig.txt txt = ./txt/cord-264013-8jnae6ig.txt === reduce.pl bib === id = cord-263945-yli5suxb author = Iancu, Gabriela Mariana title = Viral exanthema as manifestation of SARS-CoV-2 infection: A case report date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2216 sentences = 142 flesch = 47 summary = RATIONALE: The clinical manifestations of the SARS-CoV-2 infection are mainly respiratory but the virus can cause a variety of symptoms. PATIENT CONCERNS: We present the case of SARS-CoV-2 infection in a previously healthy woman who presented with respiratory symptoms and developed anosmia, diarrhea, and an erythematous maculo-papular rash on day 15 from symptom onset. [6] Pathogenetically, the appearance of cutaneous lesions during the SARS-CoV-2 infection can be explained by an immune response initiated by the viral nucleotides which activate Langerhans cells with the secondary involvement of keratinocytes (maculopapular, urticarial and chicken pox-like rashes), by microthrombi formation and cutaneous vasculopathy (chilblain lesions, livedo reticularis, erythema multiforme-like rash, gangrene), or by reaction to the medication administered (urticaria, erythroderma, erythema multiforme, etc.). [7, 8] We report a case of disseminated exanthema that appeared after 15 days of treatment for SARS-CoV-2 infection in a patient without other medical and dermatological problems in the past. cache = ./cache/cord-263945-yli5suxb.txt txt = ./txt/cord-263945-yli5suxb.txt === reduce.pl bib === id = cord-264333-mgeicojq author = Chiotos, Kathleen title = Multisystem Inflammatory Syndrome in Children During the Coronavirus 2019 Pandemic: A Case Series date = 2020-05-28 pages = extension = .txt mime = text/plain words = 2490 sentences = 165 flesch = 51 summary = On 6 May 2020, authors from London, England, reported clinical and laboratory features of a cluster of 8 children with hyperinflammatory shock, all of whom tested positive for SARS-CoV-2 antibodies [1] . To evaluate for incomplete Kawasaki disease/Kawasaki disease shock syndrome, an echocardiogram was performed on HD 6 that demonstrated normal biventricular systolic function (shortening fraction [SF], 38%; normal, 28%-45%) but identified right coronary artery dilation (Boston z score, 3.15). A 12-year-old male with no chronic medical conditions presented to an outside facility with a 6-day history of fever, Nasopharyngeal SARS-CoV-2 PCR was negative. Her lowest documented blood pressure within 24 hours of her PICU admission was 92/50 mm Hg. A repeat SARS-CoV-2 nasopharyngeal PCR was positive with a high cycle threshold (37.54). Further, for some patients, fever and gastrointestinal symptoms preceded the development of other "classic" clinical features of Kawasaki disease, including rash, conjunctivitis, mucous membrane changes, and extremity edema, which were variably present in our cohort. cache = ./cache/cord-264333-mgeicojq.txt txt = ./txt/cord-264333-mgeicojq.txt === reduce.pl bib === id = cord-264515-nle4axad author = Vlachos, J. title = School closures and SARS-CoV-2. Evidence from Sweden's partial school closure date = 2020-10-14 pages = extension = .txt mime = text/plain words = 7580 sentences = 407 flesch = 56 summary = To study the broad impact of school closures on the transmission of the virus, we estimate differences in infection rates between parents exposed to lower and upper secondary students. We estimate differences in infections among parents, teachers, and teachers' partners who were differently exposed to lower (open) and upper (online) secondary schools using linear probability models (OLS) and logistic regressions. We find that parental exposure to open rather than closed schools is associated with a somewhat higher rate of PCR-confirmed SARS-CoV-2 infections The positive association for PCR-confirmed cases could partly reflect other behavioral differences between households with slightly younger and older children, but if treated as a causal the estimates indicate that a hypothetical closure of lower secondary schools in Sweden would have resulted in 341 fewer detected cases among the 312 575 parents in our sample. cache = ./cache/cord-264515-nle4axad.txt txt = ./txt/cord-264515-nle4axad.txt === reduce.pl bib === id = cord-264924-ds6jv5ek author = Tambyah, Paul A title = Severe acute respiratory syndrome from the trenches, at a Singapore university hospital date = 2004-11-30 pages = extension = .txt mime = text/plain words = 5458 sentences = 274 flesch = 53 summary = Summary The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The severe acute respiratory syndrome (SARS) coronavirus is a novel pathogen that emerged in southern China at the end of 2002 and because of a single event in a hotel in Hong Kong one night in February 2003, spread to three continents. Mild illness associated with severe acute respiratory syndrome coronavirus infection: lessons from a prospective seroepidemiologic study of health-care workers in a teaching hospital in Singapore cache = ./cache/cord-264924-ds6jv5ek.txt txt = ./txt/cord-264924-ds6jv5ek.txt === reduce.pl bib === id = cord-263457-puf8gjir author = Jayarangaiah, Apoorva title = COVID-19-Associated Coagulopathy: An Exacerbated Immunothrombosis Response date = 2020-07-31 pages = extension = .txt mime = text/plain words = 5552 sentences = 374 flesch = 34 summary = Activated leukocytes potentiate a procoagulant state via release of intravascular tissue factor, platelet activation, NETosis, and inhibition of anticoagulant mechanisms. 4, 5 The predominant underlying mechanism in COVID-19-related mortality is hypothesized to be widespread tissue damage and endothelial injury from an overactivated immune system via exaggerated T-cell responses and increased cytokine secretion, leading to a cytokine storm. 70 In conclusion, a viral-mediated coagulant state culminates in the presence of endothelial injury and dysfunction and cytokine-driven inflammatory conditions, leading to activation of TF-mediated thrombosis. The current COVID-19 pandemic has resurrected the concept of immunothrombosis as it is a relevant model to demonstrate the potentiating effects of the immune system and the coagulation system and the detrimental effects associated with their unrestrained activation, as evidenced by microthrombi and overt venous and arterial thrombi (Figure 4 ). A procoagulant state in COVID-19 is the result of a direct viral-related endothelial injury, leukocyte-and cytokinemediated platelet activation, TF release, and NETosis augmented by an unchecked activation of the complement system. cache = ./cache/cord-263457-puf8gjir.txt txt = ./txt/cord-263457-puf8gjir.txt === reduce.pl bib === id = cord-264916-c4n0kyog author = Zimmerman, Keith title = Natural protection of ocular surface from viral infections – a hypothesis date = 2020-07-09 pages = extension = .txt mime = text/plain words = 4671 sentences = 225 flesch = 46 summary = A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. cache = ./cache/cord-264916-c4n0kyog.txt txt = ./txt/cord-264916-c4n0kyog.txt === reduce.pl bib === id = cord-264974-hspek930 author = Timmis, Kenneth title = The COVID‐19 pandemic: some lessons learned about crisis preparedness and management, and the need for international benchmarking to reduce deficits date = 2020-05-03 pages = extension = .txt mime = text/plain words = 7222 sentences = 275 flesch = 35 summary = If, despite the explicit warning of the World Health Organization in 2011 that 'The world is ill-prepared to respond to a severe influenza pandemic or to any similarly global, sustained and threatening public-health emergency' (https://apps.who.int/gb/ebwha/pdf_files/WHA64/A64_10en.pdf), it was not apparent to those in charge, and to the general public-i.e., those suffering from COVID-19 infections and the funders of health services (tax/insurance payers)-that existing health systems had inherent vulnerabilities which could prove to be devastating when seriously stressed, the SARS-CoV-2 pandemic (e.g., see Brüssow, 2020 ) has brutally exposed it now. International benchmarking is mandatory, because it has become clear that there is a wide range of effectiveness in the ability of different countries with developed economies to respond to this crisis (and probably others), and the tax-paying public has no compelling reason to tolerate perpetuation of factors underlying poor responses to crises. cache = ./cache/cord-264974-hspek930.txt txt = ./txt/cord-264974-hspek930.txt === reduce.pl bib === id = cord-264828-6w13xo2a author = Albini, Adriana title = The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies date = 2020-05-19 pages = extension = .txt mime = text/plain words = 3662 sentences = 172 flesch = 40 summary = Older COVID-19-affected patients with cardiovascular comorbidities exhibit a more severe clinical course and a worse prognosis, with many of them being also treated with ARBs or ACE-Is. Another confounding factor is cigarette smoking, which has been reported to increase ACE-2 expression in both experimental models and humans. 4. Renin-angiotensin-aldosterone system (RAAS)-interfering drugs are likely to affect ACE-2 receptor-SARS-CoV-2 interaction dynamics within lung, heart, vascular, kidney and gut tissues [5, 19] , while it is still not completely elucidated how such interactions are relevant to the clinical course of cardiovascular comorbidities in patients with COVID-19 [29] . Consequently, the up-regulation of human ACE-2 induced by RAAS-antagonists in SARS-CoV-2-infected patients could be clinically useful, due to the cardiovascular protection elicited by the increased activity of angiotensin(1-7), thereby attenuating angiotensin II effects on vasoconstriction and sodium retention [31, 34] . cache = ./cache/cord-264828-6w13xo2a.txt txt = ./txt/cord-264828-6w13xo2a.txt === reduce.pl bib === id = cord-263965-i8yutik6 author = Relf, Michael V. title = What's Old is New! Similarities Between SARS-CoV-2 and HIV date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1787 sentences = 97 flesch = 61 summary = In time, I anticipate analysts examining the domestic and global response to this pandemic will evaluate if the use of Covid-19, in an effort to reduce global anxiety and fear associated with SARS, helped or hindered governmental responses and the initial public awareness about the emerging threat. As I witness the unfolding of the Covid-19 pandemic, I continue to think back to the early years of the HIV epidemic. Today, the SARS-CoV-2 pandemic, like the HIV epidemic of the 1980s and 1990s, is a metamorphosis described as "invading the society, and efforts to reduce mortality … are called a fight, a struggle, a war" (Sontag, 1989, p. The U.S. Centers for Disease Control and Prevention (CDC) has published a great resource document, entitled COVID-19: What people with HIV should know (CDC, 18 March 2020), which is available at https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/hiv.html. cache = ./cache/cord-263965-i8yutik6.txt txt = ./txt/cord-263965-i8yutik6.txt === reduce.pl bib === id = cord-264497-7xz97awb author = Przedlacki, Jerzy title = Patients’ and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic date = 2020-07-27 pages = extension = .txt mime = text/plain words = 1000 sentences = 58 flesch = 56 summary = title: Patients' and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic One mandatory swab test in all patients and dialysis unit HCP taken at a "time zero", followed by swabs taken in the presence of clinical indications only (as in answer 1) 3. The members of the healthcare team had an additional option: (4) as in answer 1 plus testing "on demand", in the case of even weak clinical suspicion of SARS-CoV-2 infection. Eventually, all patients were asked to report their sense of safety related to the risk of contracting SARS-CoV-2 while attending the dialysis unit during the COVID-19 pandemic. All participants were informed that an increased frequency of screening tests is not an alternative to self-isolation or to the use of personal protective equipment during dialysis. In summary, the perception of safety in the context of the COVID-19 pandemic can be related to the availability of the SARS-CoV-2 screening test. cache = ./cache/cord-264497-7xz97awb.txt txt = ./txt/cord-264497-7xz97awb.txt === reduce.pl bib === id = cord-264709-p835wf4f author = Menezes, A. M. B. title = High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3169 sentences = 174 flesch = 55 summary = Using data from the most recent wave of the EPICOVID19 study, a nationwide household-based survey including 133 cities from all states of Brazil, we estimated the proportion of people with and without antibodies for SARS-CoV-2 who were asymptomatic, which symptoms were most frequently reported, the number of symptoms reported and the association between symptomatology and socio-demographic characteristics. Symptoms change in smell or taste, fever and myalgia were most likely to predict positive test results as suggested by recursive partitioning tree analysis. 62 63 Using data from the most recent wave of the EPICOVID19 study, a nationwide 64 household-based survey including 133 cities from all states of Brazil, 7 we estimate the 65 proportion of people with and without antibodies for SARS-CoV-2 who were 66 asymptomatic. The above results from the third wave of the study confirmed a high prevalence of 232 symptoms using a 4-month recall period; only 12.1% positive subjects were 233 asymptomatic, compared to 42.2% of those without antibodies. cache = ./cache/cord-264709-p835wf4f.txt txt = ./txt/cord-264709-p835wf4f.txt === reduce.pl bib === id = cord-264968-ctx39vhi author = Woo, Patrick CY title = Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia date = 2004-03-13 pages = extension = .txt mime = text/plain words = 3570 sentences = 171 flesch = 47 summary = An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. Assessment of recombinant nucleocapsid protein ELISA Serum samples from 149 healthy blood donors who donated blood 3 years previously (aged 18 years or older) and 106 patients with pneumonia positive for antibodies against SARS-CoV detected by our indirect immunofluorescence assay 1 were used for the assessment of the ELISA-based IgG antibody test. cache = ./cache/cord-264968-ctx39vhi.txt txt = ./txt/cord-264968-ctx39vhi.txt === reduce.pl bib === id = cord-265111-d44ireu5 author = D’Ardes, Damiano title = Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3103 sentences = 148 flesch = 45 summary = A longer duration of COVID-19 with delayed clinical healing (symptom-free) occurred in patients presenting at admission a lower PaO(2)/FiO(2) ratio (p < 0.001), a more severe clinical presentation (p = 0.001) and a lower lymphocyte count (p = 0.035). All adult patients were diagnosed with COVID-19 according to World Health Organization (WHO) interim guidance: they had clinical symptoms of COVID-19 and confirmation of SARS-CoV-2 infection through instrumental signs and a positive result on RT-PCR assays of nasopharyngeal swab specimens. The specific inclusive criteria were as follows: (1) patients confirmed by positive detection of SARS-CoV-2 RNA from nasopharyngeal/throat swabs by RT-PCR with clinical data suggesting for COVID-19, (2) patients aged more than 18 years old and (3) patients with a known date of performing different RT-PCR assays. Disease severity and lower lymphocyte levels at admission also predict longer SARS-CoV-2 viral shedding. cache = ./cache/cord-265111-d44ireu5.txt txt = ./txt/cord-265111-d44ireu5.txt === reduce.pl bib === id = cord-264915-g5ar0pwb author = Abrams, Rory M.C. title = Severe rapidly progressive Guillain-Barré syndrome in the setting of acute COVID-19 disease date = 2020-07-27 pages = extension = .txt mime = text/plain words = 1596 sentences = 88 flesch = 41 summary = There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS). We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss diagnostic and management issues and complications that may warrant special consideration in similar patients. There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS) (Guidon and Amato 2020) . We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss management dilemmas that may warrant special attention in similar patients. cache = ./cache/cord-264915-g5ar0pwb.txt txt = ./txt/cord-264915-g5ar0pwb.txt === reduce.pl bib === id = cord-265191-unk6rt7u author = Durrani, Muhammad title = Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1818 sentences = 109 flesch = 40 summary = title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report Among the respiratory viral pathogens, the Coronaviridae family and its genera coronaviruses have been implicated as having neurotropic and neuroinvasive capabilities in human hosts.1 Despite previous strains of coronaviruses exhibiting neurotropic and neuroinvasive capabilities, little is known about the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its involvement with the central nervous system (CNS). CONCLUSION: The patient underwent further workup and treatment with intravenous corticosteroids with improvement of symptoms and a discharge diagnosis of ATM secondary to SARS-CoV-2. 11 Additionally, the first case report of acute infectious myelitis associated with concurrent SARS-CoV-2 was only recently described. Our patient met the inclusion criteria for diagnosis of ATM based on bilateral motor symptoms and autonomic dysfunction with bladder incontinence along with evidence of CSF lymphocytic pleocytosis and characteristic MRI findings while ruling out other infectious, autoimmune, and connective tissue etiologies. cache = ./cache/cord-265191-unk6rt7u.txt txt = ./txt/cord-265191-unk6rt7u.txt === reduce.pl bib === === reduce.pl bib === id = cord-264970-232stxxo author = Testa, Sophie title = Switch from oral anticoagulants to parenteral heparin in SARS-CoV-2 hospitalized patients date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1421 sentences = 67 flesch = 28 summary = The development of COVID-19 syndrome in anticoagulated patients, and especially their admission to intensive-care units with acute severe respiratory syndrome (SARS-CoV-2), expose them to specific problems related to their therapy, in addition to those associated with the acute viral infection. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral heparin to avoid the risk of over/under treatment. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease, and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral low-molecular-weight heparin (LMWH) or unfractionated heparin (UH) to avoid the risk of over/under treatment. cache = ./cache/cord-264970-232stxxo.txt txt = ./txt/cord-264970-232stxxo.txt === reduce.pl bib === id = cord-264976-6n9cdex6 author = Corse, Tanner title = Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date = 2020-10-18 pages = extension = .txt mime = text/plain words = 6080 sentences = 266 flesch = 41 summary = The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. cache = ./cache/cord-264976-6n9cdex6.txt txt = ./txt/cord-264976-6n9cdex6.txt === reduce.pl bib === id = cord-264421-799n9wqj author = Novelli, Antonio title = Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3316 sentences = 197 flesch = 52 summary = Several studies suggested that genetic variants in the ACE2 gene may influence the host susceptibility or resistance to SARS-CoV-2 infection according to the functional role of ACE2 in human pathophysiology. We therefore investigated the occurrence of ACE2 variants in a cohort of 131 Italian unrelated individuals clinically diagnosed with COVID-19 and in an Italian control population, to evaluate a possible allelic association with COVID-19, by direct DNA analysis. METHODS: As a pilot study, we analyzed, by whole-exome sequencing, genetic variants of ACE2 gene in 131 DNA samples of COVID-19 patients hospitalized at Tor Vergata University Hospital and at Bambino Gesù Children's Hospital, Rome. Indeed, several studies inferred that genetic variants in ACE2 gene may influence the individual susceptibility or resistance to SARS-CoV-2 according to the functional role of ACE2 in human pathophysiology [12] . In this study, we, therefore, investigated the occurrence of ACE2 variants in a cohort of 131 Italian SARS-CoV-2-positive patients, extracting data on ACE2 variants by direct DNA analysis. cache = ./cache/cord-264421-799n9wqj.txt txt = ./txt/cord-264421-799n9wqj.txt === reduce.pl bib === id = cord-265128-i0d4lxko author = Gurung, Arun Bahadur title = Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M(pro) enzyme through in silico approach date = 2020-05-22 pages = extension = .txt mime = text/plain words = 2234 sentences = 168 flesch = 57 summary = Among coronaviruses, the main protease (M(pro)) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 M(pro) enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 M(pro), SARS-CoV M(pro) and MERS-CoV M(pro) were studied using molecular docking. Structure-based drug design primarily relies on molecular docking to identify lead molecules against the target proteins from chemical libraries [12, 13] . The natural products such as traditional medicines and plant-derived compounds (phytochemicals) are the rich sources of promising antiviral drugs [14] . The binding energies and inhibition constants of the phytochemicals with the SARS-CoV-2 M pro enzyme were compared with that of a set of twelve FDA approved antiviral drugs-a) Viral cache = ./cache/cord-265128-i0d4lxko.txt txt = ./txt/cord-265128-i0d4lxko.txt === reduce.pl bib === id = cord-264772-v3a2qmj5 author = Harada, Kouji H. title = Letter to the Editor on “An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)”, Back to Basics date = 2020-06-18 pages = extension = .txt mime = text/plain words = 509 sentences = 37 flesch = 48 summary = authors: Harada, Kouji H.; Harada Sassa, Mariko; Yamamoto, Naomichi Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)" highlights an imperative need for research on SARS-CoV-2 in environmental sciences. Here we highlight research showing the importance of basic sanitations to control the spread of infectious diseases applicable to the prevention of COVID-19. 4 The aerosol transmission route for SARS-CoV-2 in aerosols 5 means effective ventilation, including both natural and mechanical ventilation, is an important, easy and basic way to reduce risk of transmission. 8 A case study of the nosocomial spread of SARS in a Vietnam hospital with 33 SARS patients during the 2003 SARS outbreak demonstrated the effectiveness of face masks, gloves, hand sanitizer, and cross-ventilation in the hospital in reducing cross-infection rates. Although comparisons of the cost-effectiveness of basic versus advanced technologies are not yet available, COVID-19 cases in low-and middle-income countries are rapidly rising. cache = ./cache/cord-264772-v3a2qmj5.txt txt = ./txt/cord-264772-v3a2qmj5.txt === reduce.pl bib === id = cord-265329-bsypo08l author = van Dorp, Lucy title = Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4915 sentences = 270 flesch = 49 summary = Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1 ) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk). In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. The genomic diversity of the global SARS-CoV-2 population being recapitulated in multiple countries points to extensive worldwide transmission of COVID-19, likely from extremely early on in the pandemic. cache = ./cache/cord-265329-bsypo08l.txt txt = ./txt/cord-265329-bsypo08l.txt === reduce.pl bib === id = cord-265221-qtkwciym author = Bahadur, Gulam title = SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3261 sentences = 182 flesch = 49 summary = It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. raising equal concerns for embryo and fetal development (Colaco et al., 2020) .In males, ACE2 receptor sites have been reported in testicular tissue which then have the capability to harbour SARS-CoV-2 virus and eventual shedding into the semen and hence its implication in sexual transmission, early pregnancy or early in utero embryonic development. Studies analysing SARS-CoV-2 in seminal fluid or testicular biopsies have so far lacked appropriate controls and patients suffered from predominantly mild infections and tested several weeks after the infection, thereby increasing the complexity of result interpretation. Also no SARS-CoV-2 was detected in expressed prostatic secretion (EPS) of 18 confirmed Covid-19 infected patients and 5 strongly suspected cases but absent semen analyses. cache = ./cache/cord-265221-qtkwciym.txt txt = ./txt/cord-265221-qtkwciym.txt === reduce.pl bib === id = cord-265170-yv04ijsm author = Ceccarelli, Giancarlo title = Probiotics and COVID-19 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 1124 sentences = 69 flesch = 36 summary = SARS-CoV-2 has been postulated to affect gut inflammation both directly and indirectly, infecting intestinal epithelial cells through the angiotensin-converting enzyme 2 (ACE2) receptor and transmembrane protease serine 2, and inducing proinflammatory chemokine and cytokine release. 7 Given this evidence, bacteriotherapy could represent a complementary resource for the prevention and restoration of SARS-CoV-2 intestinal mucosa damage through the modulation of gut microbiota and decreasing related inflammation. In other infections, such as HIV, in which intestinal inflammation and related microbiota impairment can affect gut epithelial barrier function, bacteriotherapy (through microbiota surface compounds and metabolites) to exist between different probiotic bacterial species and strains. 8, 9 We believe that studies of bacteriotherapy in SARS-CoV-2 are needed to evaluate the potential effects on intestinal mucosal inflammation and microbiome homoeostasis. In the absence of a vaccine or effective therapy for COVID-19, we agree that probiotics represent a complementary approach for the prevention and restoration of SARS-CoV-2-induced mucosal damage or inflammation through the modulation of gut microbiota. cache = ./cache/cord-265170-yv04ijsm.txt txt = ./txt/cord-265170-yv04ijsm.txt === reduce.pl bib === id = cord-264814-v4wnmg03 author = Flanagan, Katie L. title = Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date = 2020-10-02 pages = extension = .txt mime = text/plain words = 15130 sentences = 700 flesch = 44 summary = Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure. cache = ./cache/cord-264814-v4wnmg03.txt txt = ./txt/cord-264814-v4wnmg03.txt === reduce.pl bib === id = cord-265262-r01u4jr6 author = Cannarella, Rossella title = Systemic effects of the hormonal treatment of male hypogonadism with preliminary indications for the management of COVID-19 patients date = 2020-10-13 pages = extension = .txt mime = text/plain words = 8737 sentences = 471 flesch = 47 summary = Furthermore, recent findings on novel coronavirus disease (COVID-19) epidemiology have shown a greater mortality in male compared with female patients and a role of T in promoting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection of the host cells has been demonstrated. To accomplish the aims of the study, we performed a search on PubMed, Scopus, Ovid and Science Direct, and the following keywords were used: hypogonadism, TD, TRT, blood pressure, hypertension, ischemic heart disease, heart failure, stroke, obesity, insulin, diabetes, metabolic disorders, prostatic hyperplasia, prostate cancer, COVID-19, and SARS-CoV2. 45 In 2017, a meta-analysis including 39 randomized controlled trials (RCTs) and 10 observational studies with a total of about 5500 patients did not find any significant association between TRT and myocardial infarction, stroke, or mortality, even if the quality of the evidence was low. cache = ./cache/cord-265262-r01u4jr6.txt txt = ./txt/cord-265262-r01u4jr6.txt === reduce.pl bib === id = cord-264653-ms6zrrnd author = Bhatnagar, Tarun title = Lopinavir/ritonavir combination therapy amongst symptomatic coronavirus disease 2019 patients in India: Protocol for restricted public health emergency use date = 2020-04-28 pages = extension = .txt mime = text/plain words = 2709 sentences = 163 flesch = 48 summary = In view of the earlier evidence about effectiveness of repurposed lopinavir/ritonavir against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as preliminary docking studies conducted by the ICMR-National Institute of Virology, Pune, the Central Drugs Standard Control Organization approved the restricted public health use of lopinavir/ritonavir combination amongst symptomatic COVID-19 patients detected in the country. Hospitalized adult patients with laboratory-confirmed SARS-CoV-2 infection with any one of the following criteria will be eligible to receive lopinavir/ritonavir for 14 days after obtaining written informed consent: (i) respiratory distress with respiratory rate ≥22/min or SpO(2) of <94 per cent; (ii) lung parenchymal infiltrates on chest X-ray; (iii) hypotension defined as systolic blood pressure <90 mmHg or need for vasopressor/inotropic medication; (iv) new-onset organ dysfunction; and (v) high-risk groups age >60 yr, diabetes mellitus, renal failure, chronic lung disease and immunocompromised persons. cache = ./cache/cord-264653-ms6zrrnd.txt txt = ./txt/cord-264653-ms6zrrnd.txt === reduce.pl bib === id = cord-265164-ybh5yljw author = Zhao, Bin title = Numerical study of the transport of droplets or particles generated by respiratory system indoors date = 2004-11-24 pages = extension = .txt mime = text/plain words = 2613 sentences = 152 flesch = 56 summary = The drift flux model, which considers the settling of particles or droplets under the effect of gravitational sedimentation, is adopted to simulate the droplets transport and distribution indoors during respiration and sneezing or coughing process, while the simplified model for solving the continuous fluid flow is combined. The results show that droplets or particles generated by normal breathing process transport a relatively short distance, while droplets or particles generated during coughing or sneezing may travel much longer distances, which may pose adverse effect on human bodies for defending the SARS or other infectious diseases. To calculate the three-dimensional and non-isothermal airflow inside ventilated rooms, a well validated simplified methodology combined with N-point air supply opening model [4] , a zero equation turbulence model [5] is applied. Numerical studies on the transport and distribution of particles or droplets generated by normal respiration and sneezing or coughing indoors result in the following conclusions: cache = ./cache/cord-265164-ybh5yljw.txt txt = ./txt/cord-265164-ybh5yljw.txt === reduce.pl bib === === reduce.pl bib === id = cord-265350-k9yus2sv author = Han, Guan-Zhu title = Pangolins Harbor SARS-CoV-2-Related Coronaviruses date = 2020-04-06 pages = extension = .txt mime = text/plain words = 1217 sentences = 94 flesch = 59 summary = Several recent studies identified SARS-CoV-2-related viruses in Malayan pangolins (Manis javanica), providing new insights into the host distribution and evolution of SARS-CoV-2-related viruses [3] [4] [5] [6] [7] . SARS-CoV and SARS-CoV-2 have been taxonomically classified into a single viral species, Severe acute respiratory syndrome-related coronavirus [8] . Whereas SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), two highly contagious CoVs that emerged in humans during the past two decades, might ultimately have bat origins, both of them were introduced into human populations through intermediate hosts [9] . Phylogenetic analysis based on the synonymous sites of RBD, whose evolution is less likely to be influenced by natural selection, shows that RaTG13 is more closely related to SARS-CoV-2 than are the GD pangolin CoVs (Figure 1B) , indicating that the high amino acid similarity between the GD pangolin CoVs and SARS-CoV-2 in the RBD might be due to convergent evolution [3] . cache = ./cache/cord-265350-k9yus2sv.txt txt = ./txt/cord-265350-k9yus2sv.txt === reduce.pl bib === id = cord-265322-3854ddb9 author = Vavougios, George D. title = A data-driven hypothesis on the epigenetic dysregulation of host metabolism by SARS coronaviral infection: potential implications for the SARS-CoV-2 modus operandi date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1252 sentences = 72 flesch = 41 summary = Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host's metabolism as part of its lifecycle. In the literature, SARS-CoV has been known to cause de novo diabetes by ACE2-dependent uptake on pancreatic isle cells, and furthermore dysregulate lipid autophagy in favor of the viral lifecycle. Their study provided the foundation for a hypothesis put forth by Fang and colleagues indicating that diabetic and hypertensive patients exposed to ACE2 inhibitors may be at an increased risk of more severe COVID-19 (7) . In another study, SARS-CoV was shown to cause diabetes by ACE2-dependent infection of pancreatic isle cells (10) . Future studies should determine SARS-CoV-2 interaction and effect on the human transcriptome, further identifying drug targets using pharmacogenomic enrichment analyses. Natural small molecules as inhibitors of coronavirus lipid-dependent attachment to host cells: a possible strategy for reducing SARS-COV-2 infectivity? cache = ./cache/cord-265322-3854ddb9.txt txt = ./txt/cord-265322-3854ddb9.txt === reduce.pl bib === id = cord-265277-ymvrserl author = Crooke, Stephen N. title = Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date = 2020-05-14 pages = extension = .txt mime = text/plain words = 4620 sentences = 249 flesch = 52 summary = A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. cache = ./cache/cord-265277-ymvrserl.txt txt = ./txt/cord-265277-ymvrserl.txt === reduce.pl bib === id = cord-265617-e91s6xo8 author = Jouali, Farah title = SARS-CoV-2 Genome Sequence from Morocco, Obtained Using Ion AmpliSeq Technology date = 2020-07-30 pages = extension = .txt mime = text/plain words = 933 sentences = 55 flesch = 55 summary = This study describes a genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sampled from a male patient with SARS-CoV-2 who was likely infected in Casablanca, Morocco. As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here, we present the sequence of a SARS-CoV-2 genome that was obtained from a mildly symptomatic Moroccan patient. The five patients were found to be PCR positive for SARS-CoV-2 after a real-time reverse transcriptase PCR (RT-PCR) assay using a Da An gene kit (Sun Yat-sen University, China). The SARS-CoV-2 viral genome sequencing was performed manually using the Ion AmpliSeq technology and the Ion Torrent personal genome machine (PGM). The libraries were prepared using the Ion AmpliSeq library kit version 2.0 (Life Technologies) and Ion AmpliSeq SARS-CoV-2 research assay panel according to the manufacturer's instructions. The genome sequence was compared to the complete genome of the SARS-CoV-2 Wuhan-Hu-1 isolate using the Betacoronavirus BLAST tool and showed 99.8% similarity. cache = ./cache/cord-265617-e91s6xo8.txt txt = ./txt/cord-265617-e91s6xo8.txt === reduce.pl bib === id = cord-265022-p5cab562 author = Kotfis, Katarzyna title = COVID-19: ICU delirium management during SARS-CoV-2 pandemic date = 2020-04-28 pages = extension = .txt mime = text/plain words = 5426 sentences = 256 flesch = 34 summary = Indeed, patients with COVID-19 are at accelerated risk for delirium due to at least seven factors including (1) direct central nervous system (CNS) invasion, (2) induction of CNS inflammatory mediators, (3) secondary effect of other organ system failure, (4) effect of sedative strategies, (5) prolonged mechanical ventilation time, (6) immobilization, and (7) other needed but unfortunate environmental factors including social isolation and quarantine without family. Given early insights into the pathobiology of the virus, as well as the emerging interventions utilized to treat the critically ill patients, delirium prevention and management will prove exceedingly challenging, especially in the intensive care unit (ICU). Many hospitalized patients with COVID-19 will develop delirium, and given early insights into the pathobiology of this virus indicating invasion into the brain stem, as well as the emerging interventions utilized to treat these critically ill patients, delirium prevention and management may prove exceedingly challenging, especially in the intensive care unit (ICU). cache = ./cache/cord-265022-p5cab562.txt txt = ./txt/cord-265022-p5cab562.txt === reduce.pl bib === id = cord-265682-yac7kzaf author = Eden, John-Sebastian title = An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1847 sentences = 99 flesch = 53 summary = Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is directly linked to the Iranian epidemic, from where genomic data are currently lacking. cache = ./cache/cord-265682-yac7kzaf.txt txt = ./txt/cord-265682-yac7kzaf.txt === reduce.pl bib === id = cord-265278-wf5pbvvt author = Fishman, Jay A. title = Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation date = 2020-09-17 pages = extension = .txt mime = text/plain words = 5266 sentences = 317 flesch = 40 summary = In transplant recipiAfter infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viral replication ensues in the respiratory epithelium, followed by viremia and systemic spread to organs by means of the angiotensin-converting-enzyme 2 receptor. 22 Graft rejection and toxic effects from calcineurin inhibitors may be difficult to distinguish from The varied presentation of SARS-CoV-2 infection reflects diversity in host immune responses, notably in immunosuppressed transplant recipients. Although the use of antiinflammatory drugs (e.g., high-dose glucocorticoids or interleukin-6 receptor antagonists) in solid-organ transplant recipients may have the additional benefit of protecting against rejection among patients who are receiving tapering courses of the immunosuppressive agents, especially when calcineurin inhibitors are discontinued because of severe disease, their efficacy in the context of solidorgan transplantation warrants testing in clinical trials. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection cache = ./cache/cord-265278-wf5pbvvt.txt txt = ./txt/cord-265278-wf5pbvvt.txt === reduce.pl bib === id = cord-265595-55s19mr1 author = Brug, Johannes title = Risk Perceptions and Behaviour: Towards Pandemic Control of Emerging Infectious Diseases: International Research on Risk Perception in the Control of Emerging Infectious Diseases date = 2009-01-06 pages = extension = .txt mime = text/plain words = 2318 sentences = 113 flesch = 46 summary = Three papers [5] [6] [7] were the result of a European Commission funded project, called SARS-Control that was partly dedicated to exploring risk perceptions and risk communications related to SARS and other emerging infectious diseases. Effective management of new epidemic infectious disease risks in the phase that no treatment or vaccination is yet possible is largely dependent on precautionary behaviour of the population. Four of the papers present empirical mostly explorative original research on risk perceptions, knowledge, beliefs and other issues related to SARS during or after the SARS outbreak in 2003. Given the clear and present danger of newly emerging infectious disease outbreaks in the near future and the importance of the public response and precautionary actions to control the spread, additional research on risk perceptions and other behavioural determinants is warranted. Perceived threat, risk perception and efficacy beliefs related to SARS and other (emerging) infectious diseases: results of an international survey cache = ./cache/cord-265595-55s19mr1.txt txt = ./txt/cord-265595-55s19mr1.txt === reduce.pl bib === id = cord-265260-n6wm54wz author = Cuong, Hoang Quoc title = Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-09-25 pages = extension = .txt mime = text/plain words = 2074 sentences = 120 flesch = 56 summary = RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. In this study, the assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master showed positive results from a single reaction of triplicate in the three days of 4.8 copies/reaction ( Table 3) . In this study, we reported the comparative analysis of laboratory screening for SARS-CoV-2 among three primer-probe sets in two different master mixes (Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master). cache = ./cache/cord-265260-n6wm54wz.txt txt = ./txt/cord-265260-n6wm54wz.txt === reduce.pl bib === id = cord-265599-903w782b author = Woods, R. title = Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection date = 2020-10-21 pages = extension = .txt mime = text/plain words = 2254 sentences = 188 flesch = 58 summary = title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection Conclusion: Inaccurate specimen collection from poor swab technique could contribute to false negative rate of testing for SARS-CoV-2. 8, 9 A study was performed to assess nasopharyngeal swab technique of staff in a major academic institution. Accurate specimen collection is critical to ensure optimal sensitivity of testing for SARS-CoV-2 but depends on the skill of the person performing the swab.  There is little evidence on the accuracy of swabbing technique in peer-reviewed published medical literature  This study uses a novel tool to evaluate a crucial aspect of public health measures to control the spread of SARS-CoV-2  The low success rate of accurately swabbing the nasopharynx implies that better training is necessary  Better training may improve specimen collection and sensitivity of testing for SARS-CoV-2  Standardised training videos with description of the relevant anatomy would likely be useful to improve testing . cache = ./cache/cord-265599-903w782b.txt txt = ./txt/cord-265599-903w782b.txt === reduce.pl bib === id = cord-265242-y8t37p0b author = Cui, Wei title = Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date = 2003-09-15 pages = extension = .txt mime = text/plain words = 1782 sentences = 112 flesch = 64 summary = title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS. means ‫ע‬ SD The differences in the mean values between patients with SARS and healthy control subjects were estimated with Student's t test, with a limit of significance of 0.05. The mean lymphocyte count of patients with SARS was significantly lower than that of healthy control subjects ( ; table 1) . The results of lymphocyte immunophenotyping demonstrated that the absolute counts of all lymphocyte subsets declined in patients with SARS (table 2) . Our study shows that the absolute counts of CD4 + T cells and CD8 + T cells have clinical significance in patients with SARS and that surveillance of lymphocytes and lymphocyte subsets is helpful in the diagnosis and treatment of SARS. cache = ./cache/cord-265242-y8t37p0b.txt txt = ./txt/cord-265242-y8t37p0b.txt === reduce.pl bib === id = cord-265473-ju81kiyw author = Balmeh, Negar title = Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2854 sentences = 160 flesch = 49 summary = Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Approximately 377 predicted and valid targets of hsa-miR-1307 which were predicted The best herbal compounds for ACE2, TMPRSS2, GRP78, and AT1R receptors were identified based on their binding energy. The molecular docking results of the ACE2, TMPRSS2, GRP78, and AT1R receptors with medicinal herbal compounds are presented in Supplementary Table 2 . Increased expression of hsa-miR-1307-3p may lead to a reduction in SARS-CoV-2 replication through binding to the 3'UTR site of the virus genome. It has been confirmed that endocytosis and exocytosis are associated with virus entry and spread, therefore, controlling these pathways by hsa-miR-1307-3p could be an effective strategy for SARS-CoV-2 infection. cache = ./cache/cord-265473-ju81kiyw.txt txt = ./txt/cord-265473-ju81kiyw.txt === reduce.pl bib === id = cord-265598-4h3wx81q author = Hasan, Abdulkarim title = Histopathology Laboratory Paperwork as a Potential Risk of COVID-19 Transmission among the Lab Personnel date = 2020-08-06 pages = extension = .txt mime = text/plain words = 2230 sentences = 121 flesch = 50 summary = Methods We tracked paper-based forms from time of test ordering till the release of the pathology report by calculating the time taken for the papers to reach the lab and the exposure of each staff group to the received papers from both high and moderate COVID-19 risk areas. Conclusion More than 80% of the manual paper request forms will take less than 24 hours to be handled by laboratory personnel; carrying a high potential risk for viral transmission. In this study we focused on defining the major hospital departments that request histopathology (by frequency and percent), measuring the time from handling the paper by clinician staff till handling by laboratory personnel, and comparing the possibility of COVID-19 transmission by paperwork to laboratory personnel, according to their exposure time to these papers. More studies are required to detect stability of the SARS-COV-2 on different surfaces and the potential risk of COVID-19 transmission through papers. cache = ./cache/cord-265598-4h3wx81q.txt txt = ./txt/cord-265598-4h3wx81q.txt === reduce.pl bib === id = cord-265418-yqe9vdj1 author = Kumar, Nilesh title = Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date = 2020-04-11 pages = extension = .txt mime = text/plain words = 5288 sentences = 363 flesch = 54 summary = Integrated interactome-transcriptome analysis to generate Calu-3-specific humanIt is likely that the outcome of SARS-CoV-2 infection can largely be determined by the interaction patterns of host proteins and viral factors. By integrating this Calu-3 co-expression network with SIPs-derived PPI subnetwork, we generated Calu-3-specific human-SARS-CoV-2 Interactome (CSI) that contains 214 SIPs interacting with their first and second neighbors make a network of 4,123 nodes and 14,650 edges (Fig. 1c, Supplementary Data 1) . We showed that CSI follows a power law degree distribution with a few nodes harboring increased connectivity, and thus exhibits properties of a scale-free network (r 2 = 0.91; (Fig. 1d , Supplementary Data 1), similar to the previously generated other human-viral interactomes 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . In conclusion, we generated a human-SARS-CoV-2 interactome, integrated virusrelated transcriptome to interactome, discover COVID-19 pertinent structural and functional modules, identify high-value viral targets, and perform dynamic transcriptional modeling. cache = ./cache/cord-265418-yqe9vdj1.txt txt = ./txt/cord-265418-yqe9vdj1.txt === reduce.pl bib === id = cord-265723-6k8196p2 author = Yu, Chengjun title = Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2622 sentences = 136 flesch = 41 summary = title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis Therefore, we conducted this updated systematic review and meta-analysis to recapitulate relevant studies to evaluate the safety, efficacy, tolerability and treatment-related outcomes of type I IFNs for coronavirus infection in clinical practice, with expectation to provide more robust evidence whether IFNs should be served as first-line agents for coronavirus infection, including the SARS-CoV-2. Each included article was thoroughly reviewed, and the following baseline information were extracted (Table 1) : first author, publication year, region, study type, participants, diagnostic method of coronavirus, data collection method, time from admission to treatment start, time from diagnosis to treatment start, primary endpoints, and treatment-related adverse effects. Critically ill defined as coronavirus-infected patients with other severe comorbidities, respiratory distress or failure, directly or indirectly transferred to ICU, needing intubation, mechanical ventilation, or extracorporeal membrane oxygenation (ECMO), when admitted to primary treatment. cache = ./cache/cord-265723-6k8196p2.txt txt = ./txt/cord-265723-6k8196p2.txt === reduce.pl bib === id = cord-265366-vmuqbpkk author = Leibowitz, Jill title = Comparison of Clinical and Epidemiologic Characteristics of Young Febrile Infants with and without SARS-CoV-2 Infection date = 2020-10-09 pages = extension = .txt mime = text/plain words = 2626 sentences = 142 flesch = 54 summary = 7, 8, 9, 10, 11, 12, 13 The largest case series to date describes 18 infants younger than 90 days of age who tested positive for SARS-CoV-2, 14 of whom were febrile. 9 The objective of this study was to compare the clinical and demographic characteristics and hospital course of febrile infants who presented to Cohen Children's Medical Center (CCMC) during March and April of 2020, the time period of peak COVID-19 incidence in our region, to febrile infants treated in CCMC during March and April of previous years. The key findings of our study are that during the peak of the COVID-19 pandemic in New York, SARS-CoV-2 was the predominant pathogen identified among febrile infants younger than 57 days of age, and the disease was self-limited in all infants with COVID-19. 26 Infants with COVID-19 presented with lethargy and feeding difficulty more with SARS-CoV-2 infection among infants younger than 90 days of age. cache = ./cache/cord-265366-vmuqbpkk.txt txt = ./txt/cord-265366-vmuqbpkk.txt === reduce.pl bib === id = cord-265740-wjdeps3h author = Radbel, Jared title = Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2250 sentences = 121 flesch = 51 summary = Given that SARS-CoV-2 viral RNA has demonstrated stability, we posited that phosphate buffered saline (PBS) may be a viable transport medium, as an alternative to VTM), for clinical qPCR testing. We assessed the intraand inter-individual reliability of SARS-CoV-2 qPCR in clinical endotracheal secretion samples transported in VTM or PBS, evaluating the stability of the RT-qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that using PBS as a transport medium has high intra-and inter-individual reliability, maintains viral stability, and is comparable to VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. SARS-CoV-2 detection using standard testing of upper airway secretions requires a nasopharyngeal (NP) or oropharyngeal (OP) swab that is transported to a clinical laboratory using viral transport media (VTM) (https://www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testingsars-cov-2#offeringtests, last accessed April 29 2020). cache = ./cache/cord-265740-wjdeps3h.txt txt = ./txt/cord-265740-wjdeps3h.txt === reduce.pl bib === id = cord-265155-jbvrcjx8 author = Aroniadis, Olga C. title = Current Knowledge and Research Priorities in the Digestive Manifestations of COVID-19 date = 2020-04-22 pages = extension = .txt mime = text/plain words = 1606 sentences = 85 flesch = 39 summary = Herein we discuss the known digestive manifestations of COVID-19 and their potential implications, important questions that remain unanswered, and what gastroenterologists should know to care for affected patients and contribute to extinguishing the pandemic. This is based on: 1) a high incidence (in some reports) of digestive symptoms among infected patients, 1-4 2) expression of Angiotensin Converting Enzyme 2 (ACE2) receptors -the viral target for cellular entry -throughout the digestive system, 1,2 3) presence of viral RNA in the stool of infected patients [1] [2] [3] 5 , and 4) prior experience with the 2003 SARS-coronavirus and the 2012 Middle Eastern Respiratory Syndrome (MERS)-coronavirus, both of which are known to infect and injure the GI tract. Multiple studies have confirmed the presence of SARS-nCoV-2 RNA in the stool of COVID-19 patients, including some who never tested positive in the upper respiratory tract. Digestive Symptoms in COVID-19 Patients with Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes cache = ./cache/cord-265155-jbvrcjx8.txt txt = ./txt/cord-265155-jbvrcjx8.txt === reduce.pl bib === id = cord-265697-bbvlowyo author = Sang, Eric R. title = Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date = 2020-08-31 pages = extension = .txt mime = text/plain words = 7298 sentences = 333 flesch = 46 summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. (C) We also detected several short ACE2 isoforms (underlined) in the domestic animals including dog, pig, goat and cattle, which have an N-terminal truncation spanning 10-13 key residues in the contacting network to S-RBD but keeping the enzyme active sites (indicated by Yellow triangles), thus resulting in little engagement by the viral S protein and predicting an unexpected evolutionary advantage for relieving potential COVID-19 risk caused by the viral engagement and functional distortion on the classical long ACE2 isoforms in these animal species. cache = ./cache/cord-265697-bbvlowyo.txt txt = ./txt/cord-265697-bbvlowyo.txt === reduce.pl bib === id = cord-265353-xwpdq8wo author = Ramzy, Danny title = Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. date = 2020-09-15 pages = extension = .txt mime = text/plain words = 174 sentences = 21 flesch = 54 summary = key: cord-265353-xwpdq8wo title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. cord_uid: xwpdq8wo In December 2019, an outbreak of pneumonia traced to a wet market in Wuhan, China, proliferated into a global pandemic with seemingly exponential vehemence and in just eight months spread globally with over 800, 000 deaths 1,2 . Coronavirus Disease 2019 (COVID 19), is caused by the novel betacoronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which is characterized by extreme virulence and a complex spectrum of pathologies ranging in severity from mild constitutional symptoms to multi-organ failure 3 A Novel Coronavirus from Patients with Pneumonia in China The outbreak of COVID-19: An overview COVID-19 Illness in Native and Immunosuppressed States: A Clinical-Therapeutic Staging Proposal Pneumatocele and cysts in a patient with SARS-CoV-2 infection Spontaneous tension pneumothorax and acute pulmonary emboli in a patient with COVID-19 infection COVID-19 Complicated by Spontaneous Pneumothorax cache = ./cache/cord-265353-xwpdq8wo.txt txt = ./txt/cord-265353-xwpdq8wo.txt === reduce.pl bib === id = cord-265877-dund6unq author = Yang, Q. title = Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3757 sentences = 237 flesch = 52 summary = We extracted data from eligible studies to summarize the clinical manifestations and laboratory indexes of kidney injury on COVID-19 infection patients and further compared the prevalence of acute kidney injury (AKI) and the mean differences of three biomarkers between in ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint "SARS-CoV-2", "clinical", "laboratory", "kidney", "Acute Kidney Injury", "proteinuria" and "hematuria". To identify the risk factors for critical illnesses of COVID-19 patients, we then analyzed the relevance of the AKI and the three laboratory indexes with the clinical severity through comparing the incidences of AKI and mean differences of those biomarkers between ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint Due to the restriction of clinic information and most of the studies did not include in the death cases and the mortality of COVID-19, the association between kidney impairment and COVID-19-induced death was not be analyzed in our meta-analysis. cache = ./cache/cord-265877-dund6unq.txt txt = ./txt/cord-265877-dund6unq.txt === reduce.pl bib === id = cord-265887-g5zhoyo9 author = Mukherjee, Shruti title = Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date = 2020-08-11 pages = extension = .txt mime = text/plain words = 9085 sentences = 538 flesch = 41 summary = (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. cache = ./cache/cord-265887-g5zhoyo9.txt txt = ./txt/cord-265887-g5zhoyo9.txt === reduce.pl bib === id = cord-265813-2onv9mvl author = Criado, Paulo Ricardo title = Are the cutaneous manifestations during or due to SARS-CoV-2 infection/COVID-19 frequent or not? Revision of possible pathophysiologic mechanisms date = 2020-06-02 pages = extension = .txt mime = text/plain words = 5143 sentences = 262 flesch = 39 summary = RESULTS: The pathophysiology of the disease is multifactorial: association with innate immune response, hypercoagulability state, lung tissue damage, neurological and/or gastrointestinal tract involvement, monocytic/macrophage activation syndrome, culminating in exaggerated cytokine secretion, called "cytokine storm", which leads to worsening and death. Until the present day, the cardinal points in severe COVID-19 are upregulated innate immune human response; hypercoagulable state; polymorphous clinical manifestations, due to pulmonary tissue damage, neurological and/ or gastrointestinal tract involvement; and fatal outcome in severe cases of macrophage activation syndrome-like (MAS) [102] . Excessive activation of inflammatory mediators creating a "cytokine storm", leading to damage to the endothelium; formation of multiple thromboses in the microvasculature of the skin; changes in the cellular component of immunity with activation of the complement system, as well as, the possibility of direct entry of SARS-CoV-2 entry via receptor ACE2 and protease TMPRSS2 in the human endothelial cell in dermal blood vessels cannot be excluded such as possible mechanisms if the possibility of virus circulation in the blood is proved. cache = ./cache/cord-265813-2onv9mvl.txt txt = ./txt/cord-265813-2onv9mvl.txt === reduce.pl bib === id = cord-266033-gbx48scp author = Xu, Yu-Huan title = Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 date = 2020-02-25 pages = extension = .txt mime = text/plain words = 3082 sentences = 153 flesch = 55 summary = Based on the fifth edition of the China Guidelines for the Diagnosis and Treatment Plan of Novel Coronavirus (2019-nCoV) Infection by the National Health Commission (Trial Version 5), 6 the NCP was classified into four types: mild with slight clinical symptoms but no imaging presentations of pneumonia; common with fever, respiratory symptoms and imaging presentations of pneumonia; severe type with any of the following: respiratory distress with RR > 30 times/minutes, oxygen saturation at rest < 93%, or PaO2/FiO2 < 300 mmHg (1 mmHg = 0.133 kPa); critically severe type with any of the following: respiratory failure needing mechanical ventilation, shock, or combination with other organ failure needing ICU intensive care. Fifty patients with NCP caused by infection of the SARS-CoV-2 virus were enrolled and had high-resolution pulmonary CT scanning, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three ( Table 1 ). cache = ./cache/cord-266033-gbx48scp.txt txt = ./txt/cord-266033-gbx48scp.txt === reduce.pl bib === id = cord-265228-afbkp3wm author = Fomsgaard, Anna S. title = An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020 date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1797 sentences = 103 flesch = 57 summary = The comparison of the SensiFAST Probe No-ROX One-Step Real-time PCR results using the simplified workflow to both NA purification systems is shown in Table 1 , Table 2 Comparison of results obtained with the SensiFAST Probe No-ROX One-Step Real-time PCR a assay on clinical samples, which were prior subjected to various minimal processing methods or nucleic acid extractions b , Denmark, 2020 (n = 87 patient samples c ) SARS-CoV-2 positive and negative oropharyngeal swab-samples heat-processed for 5 min at 98 °C before the RT-qPCR reaction showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy compared with MagNA Pure 96 purified samples when using the SensiFAST assay ( Table 1 ). Due to the alarmingly low accessibility to NA purification reagents and kits, we show an alternative to the MagNA Pure purification step with simple heating for 5 min at 98 °C that results in a sensitivity, specificity, and accuracy of 97.4% (95% CI: 86.2-99.9), 100.0% (95% CI: 84.6-100.0) and 98.3% (95% CI: 91.1-99.9), respectively, using the SensiFAST SARS-CoV-2 RT-qPCR assay (Supplementary Data). cache = ./cache/cord-265228-afbkp3wm.txt txt = ./txt/cord-265228-afbkp3wm.txt === reduce.pl bib === id = cord-265724-fdt00qw1 author = Varadarajan, Saranya title = EMMPRIN/BASIGIN as a biological modulator of oral cancer and COVID-19 interaction: novel propositions date = 2020-07-09 pages = extension = .txt mime = text/plain words = 1761 sentences = 105 flesch = 39 summary = Apart from ACE-2, recently EMMPRIN, has been regarded as a target for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attachment and entry into the host cell. Since one of the routes of entry for the virus is the oral cavity, it becomes imperative to percept oral comorbidities such oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMDs) in terms of EMMPRIN as a target for SARS-CoV-2. 1 Angiotensin-Converting Enzyme 2 (ACE-2) on the host cells is the attachment protein for the spike receptor present on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [4] [5] [6] Apart from ACE-2, recently extracellular matrix metalloproteinase inducer (EMMPRIN), which is also called BASIGIN/CD147, has been regarded as a target for SARS-CoV-2 attachment and its entry into the host cell. OSCC, by the virtue of upregulation of EMMPRIN expression (potential and alternative site for 'S' receptor), increases the susceptibility to SARS-CoV-2 infection. cache = ./cache/cord-265724-fdt00qw1.txt txt = ./txt/cord-265724-fdt00qw1.txt === reduce.pl bib === id = cord-266016-555e3ndo author = Hildenwall, Helena title = Paediatric COVID‐19 admissions in a region with open schools during the two first months of the pandemic date = 2020-06-21 pages = extension = .txt mime = text/plain words = 969 sentences = 53 flesch = 54 summary = While it appears that most children get mild symptoms if they become infected with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) (1), there have been concerns that they may present with high viral loads and contribute to asymptomatic transmission (2) . We carried out a two-month review of paediatric admissions aged 0-17 years who tested positive for SARS-CoV-2 in the Stockholm region, where approximately 514,000 (24%) of all Swedish children live. A total of 63 admitted children aged 0-17 years tested positive for SARS-CoV-2 during the study period. Infants represented more than half of all symptomatic admissions (16/30, 53%) whereas the proportion of all SARS-CoV-2 positive admitted children Paediatric admissions accounted for a minor part of the total admissions due to COVID-19 as a primary diagnosis during the first two months of the pandemic in Stockholm (30/4347, 0.7%). cache = ./cache/cord-266016-555e3ndo.txt txt = ./txt/cord-266016-555e3ndo.txt === reduce.pl bib === id = cord-266150-wox7pnkr author = Torres, Juan Pablo title = SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4202 sentences = 222 flesch = 53 summary = Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. cache = ./cache/cord-266150-wox7pnkr.txt txt = ./txt/cord-266150-wox7pnkr.txt === reduce.pl bib === id = cord-265899-skpkuzyu author = Pryzdial, Edward L. G. title = Antiviral anticoagulation date = 2020-07-06 pages = extension = .txt mime = text/plain words = 5658 sentences = 354 flesch = 36 summary = 129 Although known as the cold sore virus and typically not life threatening, there are numerous correlations between HSV1 and other members of the herpesvirus family to cardiovascular disease, 130, 131 suggesting links to TF: (i) HSV1 seropositivity is associated with a 2-fold increase in myocardial infarction incidence and death due to coronary heart disease 113 ; (ii) fibrin deposits in the microvasculature are linked to HSV1 infection 132, 133 ; (iii) DIC in neonates may occur during severe HSV1 infection 134 ; (iv) HSV2 is linked to ischemic and hemorrhagic stroke due to DIC 107, 135 ; (v) a history of CMV infection is linked to subclinical and clinical arterial thickening [136] [137] [138] ; (vi) CMV is strongly correlated to accelerated atherosclerosis in immunosuppressed organ transplant recipients [139] [140] [141] [142] ; and (vii) CMV infection is a strong risk factor for restenosis after angioplasty. cache = ./cache/cord-265899-skpkuzyu.txt txt = ./txt/cord-265899-skpkuzyu.txt === reduce.pl bib === id = cord-266348-tbr2ynx0 author = Stroemer, A. title = Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera date = 2020-06-17 pages = extension = .txt mime = text/plain words = 2893 sentences = 215 flesch = 61 summary = Here, we compare the diagnostic accuracy of six commercially available SARS-CoV-2 IgG (Abbott SARS-CoV-2 IgG; Diasorin Liaison SARS-CoV-2 S1/2 IgG; Epitope EDI Novel Coronavirus COVID-19 IgG ELISA Kit; Euroimmun Anti-SARS-CoV-2 ELISA (IgG); Mikrogen recomWell SARS-CoV-2 IgG) or total SARS-CoV-2 antibody assays (Roche Elecsys Anti-SARS-CoV-2). The majority of assay results were confirmed in a laboratory-developed plaque reduction neutralization test and by a SARS-CoV-2 IgG-specific line assay including measurement of generally low IgG avidities (Mikrogen recomLine Coronavirus IgG [Aviditaet], prototype). Out 132 of the remaining 34 samples, only one serum (#20; Figure 1 ) which was obtained ten days after a positive 133 RT-PCR was tested negative for SARS-CoV-2 IgG/total antibodies in the six assays. Six of them -including three family members of a 153 confirmed COVID-19 case (#22; Figure 1 ) -were classified SARS-CoV-2 IgG/total antibody positive by the 154 majority of the tests. cache = ./cache/cord-266348-tbr2ynx0.txt txt = ./txt/cord-266348-tbr2ynx0.txt === reduce.pl bib === id = cord-266036-qhlo99l7 author = Axell-House, Dierdre B. title = The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date = 2020-08-31 pages = extension = .txt mime = text/plain words = 5760 sentences = 318 flesch = 47 summary = OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. cache = ./cache/cord-266036-qhlo99l7.txt txt = ./txt/cord-266036-qhlo99l7.txt === reduce.pl bib === id = cord-265529-0n9xxa9h author = John Hann, Angus title = Controversies regarding shielding and susceptibility to COVID‐19 disease in liver transplant recipients in the United Kingdom date = 2020-06-17 pages = extension = .txt mime = text/plain words = 774 sentences = 46 flesch = 49 summary = The objective of this case series is to report on SARS-CoV-2 infection in liver transplant recipients and discuss the role of immunosuppression, comorbidities and shielding. In the UK, transplant recipients were classified as individuals vulnerable to SARS-CoV-2 infection due to immunosuppression. A report from a high incidence area of northern Italy did not see fatalities in SARS-CoV-2-infected liver transplant patients, unless they were elderly and comorbid. 6 Therefore, these authors suggest that immunosuppression alone is not a risk factor for development of severe SARS-CoV-2 disease. We highlight three contrasting cases of SARS-CoV-2 infection in liver transplant recipients from the early stages of the pandemic in the UK (Table 1) . We suggest that liver transplant recipients are at high risk for severe SARS-CoV-2 infection and should continue to undergo strict isolation until the pandemic has passed, or robust evidence proves a lack of risk. cache = ./cache/cord-265529-0n9xxa9h.txt txt = ./txt/cord-265529-0n9xxa9h.txt === reduce.pl bib === id = cord-266090-f40v4039 author = Gao, Wei title = New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system date = 2020-08-03 pages = extension = .txt mime = text/plain words = 2737 sentences = 177 flesch = 51 summary = title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system According to the report presented by the World Health Organization, a new member of viruses, namely, coronavirus, shortly 2019-nCoV, which arised in Wuhan, China, on January 7, 2020, has been introduced to the literature. Whereas the obtained results show the effectiveness of the theoretical method considered for the governing system, the results also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. The obtained results show the effectiveness of the theoretical method considering the governing system and also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. In this subsection, by using VIM we numerically investigate the Bats-Hosts-Reservoir-People coronavirus model. Modeling the dynamics of novel coronavirus (2019-nCov) with fractional derivative Application of variational iteration method to nonlinear differential equations of fractional order cache = ./cache/cord-266090-f40v4039.txt txt = ./txt/cord-266090-f40v4039.txt === reduce.pl bib === id = cord-266175-4jyltfus author = Brendish, Nathan J title = Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5468 sentences = 243 flesch = 47 summary = METHODS: We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. [5] [6] [7] [8] The aim of this trial was to assess the clinical impact and real-world diagnostic accuracy of point-of-care testing using the QIAstat-Dx Respiratory SARS-CoV-2 Panel (Qiagen, Hilden, Germany) in adults presenting with suspected COVID-19 during the first wave of the pandemic in the UK. This prospective, non-randomised, controlled trial of routine point-of-care testing for COVID-19 in hospital shows the feasibility of point-of-care testing with the QIAstat-Dx Respiratory SARS-CoV-2 Panel, and shows clinical benefits across a range of outcome measures including time to results, infection control measures, and recruitment into clinical trials compared with a control group tested by centralised laboratory PCR. cache = ./cache/cord-266175-4jyltfus.txt txt = ./txt/cord-266175-4jyltfus.txt === reduce.pl bib === id = cord-266113-3fp46sov author = Dashti‐Khavidaki, Simin title = Considerations for Statin Therapy in Patients with COVID‐19 date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1352 sentences = 88 flesch = 42 summary = Current coronavirus pandemic named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third coronavirus outbreak during the current century after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses.1 Acute respiratory distress syndrome (ARDS) is an immunopathologic event and main cause of death following COVID-19. The main mechanism of ARDS is uncontrolled systemic inflammatory response and cytokine storm following release of proinflammatory cytokines (such as interferons (IFN), interleukines (IL), tumor necrosis factor (TNF)-α) and chemokines.2-3 So, some Chinese researchers proposed or used anti-inflammatory agents in the treatment regimen of patients with COVID-19.3-4. The current coronavirus pandemic is an outbreak of coronavirus disease 2019 (COVID19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2, 23 Thus, initiating statins in patients with COVID-19 may increase the risk and severity of myopathies and acute kidney injury. cache = ./cache/cord-266113-3fp46sov.txt txt = ./txt/cord-266113-3fp46sov.txt === reduce.pl bib === id = cord-265233-v5sq5epy author = Cassorla, Lydia title = Decontamination and Reuse of N95 Filtering Facepiece Respirators: Where Do We Stand? date = 2020-10-15 pages = extension = .txt mime = text/plain words = 6246 sentences = 470 flesch = 47 summary = P ersistent shortages of filtering facepiece respirators (FFR) to protect health care workers (HCW) 1 during the current coronavirus disease 2019 (COVID-19) pandemic 2,3 has driven interest in decontamination and reuse. 8 While FFR are not superior to surgical masks for protection of HCW from seasonal flu, [9] [10] [11] [12] [13] [14] retrospective studies showed increased protection from severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1). [28] [29] [30] [31] [32] [33] [34] In 2006, the Institute of Medicine, now the National Academy of Medicine, convened a "Committee on the Development of Reusable Facemasks for Use during an Influenza Pandemic." Highlighting unpreparedness, 2 reports recommended "expeditious research and policy action" to develop personal protective equipment (PPE) designed to withstand decontamination, evidence-based performance standards, and improved coordination among regulatory agencies. Best available evidence supports moist heat, low T autoclave, MWGS, and HP-based decontamination as effective methods for SARS-CoV-2 without causing significant damage to FFR for 2-5 cycles. cache = ./cache/cord-265233-v5sq5epy.txt txt = ./txt/cord-265233-v5sq5epy.txt === reduce.pl bib === id = cord-266135-jbc9nml0 author = Princiotta Cariddi, Lucia title = Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1141 sentences = 78 flesch = 41 summary = title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient Besides pneumonia, it has been demonstrated that SARS-CoV-2 infection affects multiple organs, including brain tissues, causing different neurological manifestations, especially acute cerebrovascular disease (ischemic and hemorrhagic stroke), impaired consciousness and skeletal muscle injury. To our knowledge, among neurological disorders associated with SARS-CoV2 infection, no Posterior Reversible Encephalopathy Syndrome (PRES) has been described yet. Herein, we report a case of a 64-year old woman with COVID19 infection who developed a PRES, and we suggest that it could be explained by the disruption of the blood brain barrier induced by the cerebrovascular endothelial dysfunction caused by SARS-CoV-2. Brain CT and CTA were consistent with hemorrhagic Posterior Reversible Encephalopathy Syndrome (PRES; Fig. 1a, b) . Posterior reversible encephalopathy syndrome in infection, sepsis, and shock Posterior reversible encephalopathy syndrome (PRES) and infection: a systematic review of the literature Hemorrhagic posterior reversible encephalopathy syndrome as a manifestation of COVID-19 infection cache = ./cache/cord-266135-jbc9nml0.txt txt = ./txt/cord-266135-jbc9nml0.txt === reduce.pl bib === id = cord-266450-g9vihgbk author = Tran, Michael title = SARS-CoV-2 and pulmonary embolism: who stole the platelets? date = 2020-09-03 pages = extension = .txt mime = text/plain words = 1498 sentences = 93 flesch = 38 summary = Careful attention to his daily platelet count suggested the possibility of immune mediated heparin-induced thrombocytopenia (HIT) which was confirmed by laboratory testing and resolved when anticoagulation was switched to a direct thrombin inhibitor. CONCLUSIONS: Since excessive platelet activation and in situ thrombosis occur in HIT, this case underscores the need to consider that thrombocytopenia in patients with SARS-CoV-2—most of whom receive heparinoids—may be unrecognized HIT. Emerging reports suggest the possibility of HIT developing in SARS-CoV-2 patients receiving heparin anticoagulation [4, 5] . The patient's platelet count decreased from 487 k/uL to a nadir of 91 k/uL over the following 4 days, raising the concern for heparin induced thrombocytopenia (HIT) with an intermediate pretest probability by the 4Ts score of 4 ( Table 1 ). Platelet count and time points for anticoagulation administration and laboratory testing COVID-19 patients receiving heparin-involved treatment. cache = ./cache/cord-266450-g9vihgbk.txt txt = ./txt/cord-266450-g9vihgbk.txt === reduce.pl bib === id = cord-266324-uvsmbrbf author = Zhang, Hu title = Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2336 sentences = 131 flesch = 48 summary = title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases A cohort study of 140 COVID-19 patients showed that gastrointestinal symptoms were observed in 39.6% of the patients, including nausea (17.3%), diarrhoea (12.9%) and vomiting (5.0%) [4] . Therefore, we determined that a retrospective analysis of cases might be useful for clinicians to identify the clinical characteristics of COVID-19 patients with gastrointestinal symptoms. In this study, red and white blood cells were not identified in the faeces of patients who experienced gastrointestinal symptoms, a finding characteristic of viral infections. Second, this study was the lack of the result of SARS-CoV-2 RNA in the stool of COVID-19 patients, so we did not determine the hypothesis that the severity of gastrointestinal symptoms may be related to the presence of viral replication in stool. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan cache = ./cache/cord-266324-uvsmbrbf.txt txt = ./txt/cord-266324-uvsmbrbf.txt === reduce.pl bib === id = cord-266350-yybunc6z author = Sinha, Saurabh K. title = An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3180 sentences = 165 flesch = 48 summary = From the binding energy and interaction studies, the Saikosaponins U and V showed the best affinity towards both the proteins suggesting them to be future research molecule as they mark the desire interaction with NSP15, which is responsible for replication of RNA and also with 2019-nCoV spike glycoprotein which manage the connection with ACE2. The docking simulation study of total 23 Saikosaponins (Supplementary file) was performed on the 1.9 A crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the complex with a citrate (PDB ID: 6W01) and prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up (PDB ID: 6VSB) which was retrieved from protein data bank (https://www.rcsb.org). Our observations revealed that, the Saikosaponin V having two oxane rings substituted with 3 hydroxyl group and the side chain contains 4 hydroxyl and an ester linkage showed very high binding with active site having a furrow between the two b-sheets, carries amino acids Lys290, Thr341, Tyr343 and Ser29. cache = ./cache/cord-266350-yybunc6z.txt txt = ./txt/cord-266350-yybunc6z.txt === reduce.pl bib === id = cord-266104-xqvwht7c author = Mu, Chenglin title = Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2149 sentences = 137 flesch = 52 summary = title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology Here using TCMSP and Swiss Target Prediction databases to sort out the potential targets of the main chemical components and GenCLiP3, NCBI, and GeneCard databases to search for COVID-19 related targets, the chemical compound-target-pathway network was analyzed. Moreover, modern and ancient pharmacological records showed that Rhizoma Polygonati has a wide pharmacological function in antibacterial, antiviral, immunity enhancement, anti-ageing, anti-cancer, anti-diabetes, anti-fatigue, and anti-heart Network pharmacology in TCM combines with multidisciplinary technologies, such as systems biology, and computational biology in order to build a complex network between drug-target-diseases, and elucidate the mechanism of drugs in treatment (Luo et al., 2020) . Therefore, to explore the active ingredients and mechanism of different species of Rhizoma Polygonati based on their active compounds concentration in the treatment of pulmonary symptoms caused by the new coronavirus will help to precisely apply TCM for anti-virus. cache = ./cache/cord-266104-xqvwht7c.txt txt = ./txt/cord-266104-xqvwht7c.txt === reduce.pl bib === id = cord-266313-b518n9dx author = Cao, Yu-chen title = Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence date = 2020-04-02 pages = extension = .txt mime = text/plain words = 5542 sentences = 262 flesch = 48 summary = China has also taken immediate action to put remdesivir into clinical trials with the purpose of applying it into clinical therapeutics for Corona Virus Disease 2019 (COVID-19). When we set our sights on the broad-spectrum antiviral drugs, we found that a drug unlisted, remdesivir, has demonstrated strength in trials related to MERS-CoV and Ebola virus infection. This article starts from the structure, immunogenicity, and pathogenesis of infection of the SARS-CoV-2, and then analyzes the feasibility of conducting trials and putting into clinical use of COVID-19 from the pharmacological characteristics and successful cases of remdesivir. Remdesivir (GS-5734) is a nucleoside analogues drug (Fig. 3B ) with extensive antiviral activity and effective treatment of lethal Ebola and Nipah virus infections in nonhuman primates [21] . The need of treatment on COVID-19 is urgent, so if the results of clinical trials prove it has the potential to benefit the treatment, according to China's "Compassionate Use", remdesivir will be more immediately used in patients with severe illness. cache = ./cache/cord-266313-b518n9dx.txt txt = ./txt/cord-266313-b518n9dx.txt === reduce.pl bib === id = cord-266022-aco5kpaj author = Matusiak, Magdalena title = Expression of SARS-CoV-2 entry receptors in the respiratory tract of healthy individuals, smokers and asthmatics date = 2020-09-29 pages = extension = .txt mime = text/plain words = 1837 sentences = 122 flesch = 48 summary = We analyzed publicly available RNA microarray datasets for SARS-CoV-2 entry receptors and cofactors ACE2, TMPRSS2, BSG (CD147) and FURIN. Furthermore, respiratory epithelia were negative for ACE-2 and TMPRSS2 protein expression while positive for BSG and furin, suggesting a possible alternative entry route for SARS-CoV-2. First, by plotting the first 2 principal components computed on ACE2, TMPRSS2, BSG and FURIN expression across smokers' and asthmatics' datasets, we verified that there were no detectable batch effects within each of the six microarray datasets we sought to analyze (Figs. We next examined four RNA microarray datasets for ACE2, TMPRSS2, BSG and FURIN expression in airway epithelia from patients with a common respiratory disease, asthma. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; COVID-19: Coronavirus disease 2019; ACE-2: Angiotensin I converting enzyme 2; TMPRSS2: Transmembrane serine protease 2; BSG: Basigin; XIST: X inactive specific transcript; RPS4Y1: Ribosomal protein S4 Y-linked 1 SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues cache = ./cache/cord-266022-aco5kpaj.txt txt = ./txt/cord-266022-aco5kpaj.txt === reduce.pl bib === id = cord-266168-hxu5u5op author = Grimaud, Emilie title = Delayed acute bronchiolitis in infants hospitalized for COVID‐19 date = 2020-07-10 pages = extension = .txt mime = text/plain words = 406 sentences = 33 flesch = 48 summary = To the Editor, Because of the infant's history, a chest X-ray was performed and returned normal. A term eutrophic male with otherwise unremarkable neonatal history was referred for poorly tolerated high fever at age 2 months. The respiratory and clinical examination findings including hemodynamics were normal. RT-PCR testing of a nasopharyngeal swab was positive for SARS-CoV-2 but negative for RSV and IV. The chest X-ray was normal, and no lung ultrasonography was performed. These two cases of COVID-19 in infants hospitalized for poorly tolerated high fever and neurological symptoms in whom acute bronchiolitis developed following a delay of 2 to 8 days suggest that SARS-CoV-2 infection may cause acute bronchiolitis in the absence of a viral coinfection such as RSV. Pneumonia is the most common respiratory illness among symptomatic children with COVID-19. Infection and rapid transmission of SARS-CoV-2 in Ferrets Wheezing rhinovirus illnesses in early life predict asthma development in high-risk children cache = ./cache/cord-266168-hxu5u5op.txt txt = ./txt/cord-266168-hxu5u5op.txt === reduce.pl bib === id = cord-266156-xmf4emln author = Miller, Tyler E. title = Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4329 sentences = 221 flesch = 45 summary = Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. The goal of this study is to examine the clinical sensitivity and provide insights into the interpretation of the two most common SARS-CoV-2 diagnostic test modalities: polymerase chain reaction (PCR) and serology. Serologic analysis of IgM, IgA and IgG status was performed in a subset of the above SARS-CoV-2 PCR-positive patients for which we had excess material in the MGH core laboratories for clinical validation studies. To assess the sensitivity of our serology assay over time, we tested for IgM, IgG, and IgA antibodies against the RBD of SARS-CoV-2 spike protein in 157 SARS-CoV-2 PCR-positive patients using an in-house ELISA (Table 1) . cache = ./cache/cord-266156-xmf4emln.txt txt = ./txt/cord-266156-xmf4emln.txt === reduce.pl bib === id = cord-266480-u8o4eitu author = Colubri, Andrés title = Preventing outbreaks through interactive, experiential real-life simulations date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3167 sentences = 173 flesch = 45 summary = Operation Outbreak (OO) is an educational curriculum and simulation platform that uses Bluetooth to spread a virtual "pathogen" in real-time across smartphones in close proximity. The app-generated data from these simulations represented the "ground truth" of the mock outbreaks, captured several essential features of SARS-CoV-2, and allowed us to observe behavioral changes among participants--many of which are now being mirrored in real life. Our 2018 SMA Ebola simulation first showed how student social-distancing could affect an "outbreak's" trajectory ( Figure 2A More detailed data from the 2019 simulation allowed us to reconstruct transmission chains over time and identify important features of the outbreak, such as the existence of two super-spreaders causing 4 and 5 secondary infections early in the game ( Figure 2C ). We envision OO as playing two key roles: (1) as a pedagogical platform for teaching fundamentals of pandemic response that are vital for the public to understand and (2) as a novel system for simulating outbreaks and evaluating real-world mitigation strategies, including those needed to restart in-person education. cache = ./cache/cord-266480-u8o4eitu.txt txt = ./txt/cord-266480-u8o4eitu.txt === reduce.pl bib === id = cord-266307-w56rii2p author = Acheampong, Desmond Omane title = Male Predisposition to Severe COVID-19: Review of Evidence and Potential Therapeutic Prospects date = 2020-09-09 pages = extension = .txt mime = text/plain words = 8837 sentences = 467 flesch = 46 summary = The sex hormones, estrogens and androgens which exist in varying functional levels respectively in females and males are cited as the underlying cause for the differential immune response to COVID-19. In this review efforts are made to expand understanding and explain the possible roles of the immune system, the sex hormones and the angiotensin-converting enzyme (ACE) systems in male bias to severe COVID-19. Hence, females known for producing high-level estrogen will be better protected against infections including COVID-19 compared to their male counterparts. Hence, women are better protected against viral infections and for that matter the severe COVID-19 due to the over-expression of TLR7 in females compared to their male counterparts. This explains J o u r n a l P r e -p r o o f why prolong inflammation is very common in males infected with SARS-CoV-2 virus compared to females, and could be one of the factors that promote severe COVID-19 in men. cache = ./cache/cord-266307-w56rii2p.txt txt = ./txt/cord-266307-w56rii2p.txt === reduce.pl bib === id = cord-266648-962r0vm8 author = Grossberg, Laurie B title = Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3613 sentences = 234 flesch = 50 summary = title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic Although data in patients with IBD contracting COVID-19 are still limited, both providers and patients have particular concerns regarding the risk of infection with SARS-CoV-2 and how to manage their medications during the COVID-19 pandemic. Information regarding risk factors, prevention, routine care (including office visits, testing, endoscopy, and surgery), and medication management of patients with IBD in the setting of COVID-19 was collected from each reference and is summarized in the Results. 10, 11 Other organizations, including the American Gastroenterological Association doi: 10.1093/ibd/izaa174 Published online 3 July 2020 (AGA), the Gastroenterological Society of Australia, and the European Crohn's and Colitis Organisation (ECCO), agree that there are no data to support an increased risk of infection among patients with IBD. cache = ./cache/cord-266648-962r0vm8.txt txt = ./txt/cord-266648-962r0vm8.txt === reduce.pl bib === id = cord-266558-vd41u2t1 author = Verdecchia, Paolo title = The pivotal link between ACE2 deficiency and SARS-CoV-2 infection date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4690 sentences = 316 flesch = 48 summary = Clinical reports of patients infected with SARS-CoV-2 show that several features associated with infection and severity of the disease (i.e., older age, hypertension, diabetes, cardiovascular disease) share a variable degree of ACE2 deficiency. The entry of SARS-CoV-2 into cells is mediated by the efficient binding of the spike (S) viral protein, a 1273 amino acid long protein which belongs to the viral envelope and protrudes outwards with a 'corona' like appearance, to the angiotensin converting enzyme 2 (ACE2) receptors. In the current pandemic of SARS-CoV-2 infection with associated pulmonary inflammation and Acute Respiratory Distress Syndrome (ARDS), it is interesting to note that angiotensin II also interferes with adaptive immunity by activating machrophages [24] and other cells of the immune system, with consequent increased production of IL-6, [25] TNFα and other inflammatory citokynes. The authors found that even the isolated spike viral protein induced down-regulation of ACE2 receptors with concomitant increase of angiotensin II in the lung tissue and precipitation of severe pulmonary inflammatory lesions. cache = ./cache/cord-266558-vd41u2t1.txt txt = ./txt/cord-266558-vd41u2t1.txt === reduce.pl bib === id = cord-266512-xh6zed03 author = Scala, Enrico title = Atopic statusprotects from severe complications of COVID‐19 date = 2020-08-16 pages = extension = .txt mime = text/plain words = 1297 sentences = 70 flesch = 44 summary = In infection, the Th2 response counteractsthe microbicidal Th1 response, which could limit the tissue damage induced by Th1-mediated inflammation (4) on one hand, but also cause a less efficient anti-virus response, as shown in a study on experimental Coronavirus 229E infection in healthy volunteers, where atopy appeared to be associated with a more severe rhinitis score (5) .Further, atopic subjects show a reduced expression of ACE2, the SARS-CoV-2 receptor, which could be associated with reduced susceptibility to the virus (6) . The multiple logistic regression analysis(details in supplementary material) confirmed a significant association between atopic status andmilder COVID-19;non-atopic patients had a significantly higher risk of having severe Covid-19 (OR adj 3.0, 95% CI 1.6-5.7, p =0.001) ( Table 1) In severe SARS-CoV-2 infection hyper-expressed cytokines include IFN-gamma, TNF-alpha, and IL-6, which cause fever, fatigue, flu-like symptoms, vascular leakage due to endothelial dysfunction, cardiomyopathy, hypotension, lung injury, activation of the coagulation cascade, and diffuse intravascular coagulation (7) . cache = ./cache/cord-266512-xh6zed03.txt txt = ./txt/cord-266512-xh6zed03.txt === reduce.pl bib === id = cord-265855-zf52vl11 author = Mayor-Ibarguren, Ander title = A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5324 sentences = 283 flesch = 47 summary = Zinc deficiency may increase ACE-2 receptor activity on type 2 pneumocytes and other cells that are infected by SARS-COV-2, mainly in the lower respiratory tract. Although there are no specific data regarding zinc in this pathway for SARS-CoV-2, zinc may limit infection through upregulation of IFN-alpha production and an increase in its antiviral activity (77, 78) . Thus, patients with IL-6-174 GG polymorphism (C-carriers) may be susceptible to developing a severe infection due to SARS-CoV-2, leading to an increase in IL-6 levels that produce a cytokine storm related to impaired zinc homeostasis. We believe there is enough evidence to further investigate how zinc status or homeostasis is involved in the pathogenesis of severe illness produced by SARS-CoV-2 infection, and its potential role as an active treatment should be assessed in clinical trials. cache = ./cache/cord-265855-zf52vl11.txt txt = ./txt/cord-265855-zf52vl11.txt === reduce.pl bib === id = cord-266511-g5h4tazp author = Deslandes, A title = SARS-COV-2 was already spreading in France in late December 2019 date = 2020-05-03 pages = extension = .txt mime = text/plain words = 1369 sentences = 93 flesch = 58 summary = We report here a case of a patient hospitalized in December 2019 in our intensive care, of our hospital in the north of Paris, for hemoptysis with no etiological diagnosis and for which RT-PCR was performed retrospectively on the stored respiratory sample which confirmed the diagnosis of COVID-19 infection. After its onset in December 2019 in China, the new coronavirus (SARS-COV-2) spreads widely in several countries, causing COVID-19 illness. 8 Clinical symptomatology between COVID-19 and ILIis similar,we therefore decided retrospectively to look for SARS-COV2 in respiratory samples collected in the intensive care units (ICUs) of our hospital near Paris. We reviewed medical record of ICUs patients admitted for ILI between December 2, 2019 and January 16, 2020, with a negative RT-PCR performed at admission. Samples taken from patients with both ILI symptoms (fever higher than 38.5°C, cough, rhinitis, sore throat or myalgia) and ground glass opacity according to their medical record underwent SARS-COV-2 RT-PCR. cache = ./cache/cord-266511-g5h4tazp.txt txt = ./txt/cord-266511-g5h4tazp.txt === reduce.pl bib === id = cord-266616-boeb1xcp author = Liu, Yu title = Regulatory T cells: A potential weapon to combat COVID‐19? date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4158 sentences = 233 flesch = 49 summary = This review discusses the clinical and pathological features of COVID‐19, the roles of immune cells in pathological processes, and the possible avenues for induction of immunosuppressive T regulatory cells attenuating lung inflammation due to viral infection. 13, 19, 37, 38 In a mouse model study by Fulton et al, 38 evaluating the balance between virus clearance and immunopathology, Foxp3 + CD4 + regulatory T cells were shown to accumulate in mediastinal lymph nodes and the lungs of infected animals and to reduce immunopathology by regulating the responses of CD8 effector T cell during infection of respiratory syncytial virus. 38 IL-10 and TGF-β, antiinflammatory cytokines, could suppress the activity of NK cells, macrophage, cytotoxic CD8 T cells, and T helper cells 1 to reduce inflammatory storm caused by those during virus infection (Figure 1 ). Current pathology reports have revealed that the lung tissues in people infected with SARS-CoV-2 were prominently infiltrated with multinucleated giant cells and inflammatory cells. cache = ./cache/cord-266616-boeb1xcp.txt txt = ./txt/cord-266616-boeb1xcp.txt === reduce.pl bib === id = cord-266034-811lov8f author = Benameur, Karima title = Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 2447 sentences = 123 flesch = 43 summary = CSF analysis also showed markedly increased levels of interleukin (IL)-6, IL-8, and IL-10, but severe acute respiratory syndrome coronavirus 2 was not identified in any CSF sample. Because MRI changes seen in these patients could be caused by hypercoagulability (15) or metabolic encephalopathy (16) , we propose that CSF investigation can improve the distinction between neurologic involvement of SARS-CoV-2 (or neuro-COVID) and neurologic symptoms caused by other COVID-related causes. The failure to detect CSF SARS-CoV-2 RNA does not diminish the likelihood of direct CNS infection because it is only recovered from blood in 1% of the actively infected cases (18) , and increased levels CSF IgM are also more commonly found as evidence for CNS infection than viral recovery in other encephalitides, including those for infection with Japanese encephalitis virus (19) , dengue virus (20) , human parvovirus 4 (21) , and rabies virus (22) . cache = ./cache/cord-266034-811lov8f.txt txt = ./txt/cord-266034-811lov8f.txt === reduce.pl bib === id = cord-266444-rw94yls8 author = Dominguez Andres, Ana title = SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date = 2020-08-19 pages = extension = .txt mime = text/plain words = 5639 sentences = 305 flesch = 44 summary = The interactome and proteome studies identified cellular processes affected by SARS-CoV-2 infection or specific viral proteins, notably innate immune signaling (19, 20, 23, (28) (29) (30) , ubiquitin ligase activities (19, 20, 23, (28) (29) (30) , p38 mitogenactivated protein kinase (MAPK) signaling (19, 20, 23, (28) (29) (30) . To assess if there were notable differences in the intensity of the changes in protein abundance in response to proteasome inhibition, we calculated relative changes in protein abundance between control and ORF9c-expressing cells from both the DMSO and MG132 conditions for proteins associated with IFN signaling or the ubiquitin proteasome (UBP) system and antigen presentation (Fig. 2D ). In contrast to the proteomic results that revealed predominant downregulation of proteins following ORF9c expression, RNA-seq analysis showed a similar number of transcripts were increased or decreased in the presence or absence of MG132 (Fig. 3A, table S2 ). cache = ./cache/cord-266444-rw94yls8.txt txt = ./txt/cord-266444-rw94yls8.txt === reduce.pl bib === id = cord-266308-fjpq1ljp author = Mondal, Priya title = Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation date = 2020-11-05 pages = extension = .txt mime = text/plain words = 6882 sentences = 383 flesch = 50 summary = Binding energies (BEs; kcal/mol) of selected bioactives from medicinal plants with SARS-CoV-2 M pro , S-protein and human ACE2 and their chemical interactions with the binding site. Among the standard drugs, nelfinavir, an anti-retroviral and protease inhibitor, has shown a stronger affinity towards all three targets of SARS-CoV-2 with the BE of À8.3 kcal/mol for M pro , À6.6 kcal/mol for S-protein and À6.4 kcal/mol for ACE2 (Supporting Information Table S1 ). In our current study, the selected bioactives from medicinal plants as well as standard drugs have shown interaction towards the key residues of the S-protein receptor-binding motif, as shown in Supporting Information Fig. S4 and S5 . The interactions of the standard drugs and medicinal plant bioactives were also similar towards hotspot residues of the ACE2 receptor as shown in Supporting Information Fig. S7 and S8. cache = ./cache/cord-266308-fjpq1ljp.txt txt = ./txt/cord-266308-fjpq1ljp.txt === reduce.pl bib === id = cord-266775-4npowkkz author = Xu, Jun title = Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date = 2005-10-15 pages = extension = .txt mime = text/plain words = 3449 sentences = 167 flesch = 46 summary = In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . cache = ./cache/cord-266775-4npowkkz.txt txt = ./txt/cord-266775-4npowkkz.txt === reduce.pl bib === id = cord-266052-rcuzi70u author = Liu, Lilong title = Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19 date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5743 sentences = 275 flesch = 53 summary = As pit latrines and the use of untreated excreta as fertilizer were common in rural China, we surveyed 27 villages of Jiangxi and Hubei provinces and found that pit latrines could be a potential source of SARS-CoV-2 water pollution. Another study showed that infectious SARS-CoV-2 virus were successfully isolated from 2 of 3 patients with viral RNA-positive, indicating that infectious virus in feces was a common manifestation of COVID-19 and confirmed the potential of fecal-oral or fecal-respiratory transmission (Xiao et al., 2020b) . Coupled with the fact that villagers usually use untreated excreta as agricultural fertilizer, we believe that the use of pit latrines in rural China and other low-income countries increases the possibility of SARS-CoV-2 contaminating the surrounding natural environment and ultimately harms human health. We proposed this hypothesis to illustrate the mechanism that SARS-COV-2 might spread from the excreta of infected humans in pit latrines to potential animal hosts and then become a sustainable source of infection in rural China and other low-income countries. cache = ./cache/cord-266052-rcuzi70u.txt txt = ./txt/cord-266052-rcuzi70u.txt === reduce.pl bib === id = cord-266885-a5fdeuvv author = Dlotko, P. title = Covid-19 clinical data analysis using Ball Mapper date = 2020-04-15 pages = extension = .txt mime = text/plain words = 2957 sentences = 207 flesch = 64 summary = In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. Our target will be to locate any clusters of patients with particularly high value of variable 2 (positively of SARS-Cov-2 result), patients that have been admitted to a regular ward, semi intensive or intensive care unit. Our task is to present how the predictive variables 2, 3, 4 and 5 (SARS-Cov-2 result, standard ward, semi intensive care and intensive care admission) changes over P by examining how they change over the obtained Ball Mapper graph. The obtained Ball Mapper graph suggest that the patients, which are likely to have positive result for SARS-Cov2, have quite similar values coming from the blood tests. . Figure 6 : Ball Mapper graph for normalized data colored by the patients who required Intensive Care Unit. cache = ./cache/cord-266885-a5fdeuvv.txt txt = ./txt/cord-266885-a5fdeuvv.txt === reduce.pl bib === id = cord-266696-w9sb038q author = Zhou, Yi-Hua title = Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date = 2004-03-15 pages = extension = .txt mime = text/plain words = 1306 sentences = 67 flesch = 56 summary = [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China cache = ./cache/cord-266696-w9sb038q.txt txt = ./txt/cord-266696-w9sb038q.txt === reduce.pl bib === id = cord-266695-ktbgm0p9 author = Dawson, Liza title = SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date = 2020-06-04 pages = extension = .txt mime = text/plain words = 1452 sentences = 109 flesch = 50 summary = have recently argued that researchers should consider conducting SARS-CoV-2 human challenge studies to hasten vaccine development [1] . However, we disagree that SARS-CoV-2 challenge studies are ethically appropriate at this time, for three reasons: 1) current scientific knowledge of SARS-CoV-2 infection is insufficient to manage risks; 2) autonomous decision-making, while necessary, does not override concerns about risk; and 3) undertaking challenge studies now would imperil confidence in the research enterprise, potentially undermining the global response to the COVID-19 pandemic. Current scientific knowledge is insufficient to manage the risks of severe disease or death of volunteers in SARS-CoV-2 human challenge studies, especially in terms of selecting low risk volunteers [2] . It is not obvious that the possible benefits of developing a successful vaccine in less time justify the risks SARS-CoV-2 challenge studies, as Eyal and colleagues suggest. However, conducting SARS-CoV-2 human challenge trials now unjustifiably threatens both the well-being of volunteers and confidence in the research enterprise. cache = ./cache/cord-266695-ktbgm0p9.txt txt = ./txt/cord-266695-ktbgm0p9.txt === reduce.pl bib === id = cord-266031-tlrsco40 author = Haghani, Milad title = Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCoV literature date = 2020-09-21 pages = extension = .txt mime = text/plain words = 7993 sentences = 356 flesch = 51 summary = To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. The decision on which general database to use (e.g. Web of Science (WoS) or Scopus) was mainly made on the basis of the number of indexed Covid-19 studies in particular, as the sector of the coronavirus literature that is currently emerging (compared to the literatures on SARS and MERS that have already stabilised). In this cluster, one can observe terms such as those associated with general public health including "wold health organisation", "public health", "public The map of keyword co-occurrences associated with the Covid-19 literature health service", "global health", as well as those associated with disease outbreaks including "emergency", "health risk" "epidemics", "pandemic", "outbreak", "viral diseases", "virus infection", "communicable disease", "transmission", "travel". cache = ./cache/cord-266031-tlrsco40.txt txt = ./txt/cord-266031-tlrsco40.txt === reduce.pl bib === id = cord-266536-4frv2vb7 author = Martel, Jan title = Could nitric oxide help to prevent or treat COVID-19? date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2067 sentences = 110 flesch = 44 summary = In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. During the 2002-2003 severe acute respiratory syndrome (SARS) epidemic, also caused by a coronavirus, inhaled NO was tested in six SARS patients, producing beneficial effects that include decreased pulmonary hypertension, improved arterial oxygenation, and reduced spread and density of lung infiltrates [5] . In addition, limiting the lifestyle factors that reduce endogenous NO levels in the airways-such as mouth breathing and smoking-may also help to reduce SARS-CoV-2 viral load and symptoms of COVID-19 pneumonia by promoting more efficient antiviral defense mechanisms in the respiratory tract. cache = ./cache/cord-266536-4frv2vb7.txt txt = ./txt/cord-266536-4frv2vb7.txt === reduce.pl bib === id = cord-266755-y2lf7ssp author = Yehualashet, Awgichew Shewasinad title = ACEIs and ARBs and Their Correlation with COVID-19: A Review date = 2020-09-16 pages = extension = .txt mime = text/plain words = 4160 sentences = 221 flesch = 46 summary = 21, 22 Both ACE-1 and ACE-2 cleave angiotensin peptides in that ACE-1 cleaves angiotensin I and generating angiotensin (Ang) II, which causes vasoconstriction, bronchoconstriction, increases vascular permeability, inflammation, and fibrosis and enhance the development of acute respiratory disease syndrome (ARDS) and lung failure in patients infected with SARS-CoV-2. 36 The probable rational proposed for the possible relation between the use of ACEIs/ARBs, and progression to ARDS in COVID-19 is the increased availability of ACE-2 attached to surface in the lung endothelium, an inherent effect of these two classes, leading to enhanced coupling of SARS-CoV2 to ACE-2 and its consequent cell entry. Based on prior animal studies, it was suggested that proposed ACEIs and ARBs can enhance ACE2 activity and thereby increase infectivity of COVID-19 virus. 48 In severe lung injury animal models, preclinical studies have showed that ACE2 is significantly downregulated and it has been shown that the inhibition of the angiotensin type 1 receptor by ARB like losartan reduces severe acute lung injury in mice administered with the spike glycoprotein of SARS-CoV. cache = ./cache/cord-266755-y2lf7ssp.txt txt = ./txt/cord-266755-y2lf7ssp.txt === reduce.pl bib === id = cord-266930-a1mzxmsb author = Rigatti, S. J. title = SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2620 sentences = 167 flesch = 52 summary = Using state population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. Conclusions: The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. cache = ./cache/cord-266930-a1mzxmsb.txt txt = ./txt/cord-266930-a1mzxmsb.txt === reduce.pl bib === id = cord-266948-n7sltd1b author = Ahamed, Jasimuddin title = Severe aortic stenosis patient risk during the COVID-19 pandemic date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1314 sentences = 85 flesch = 46 summary = The patient risk assessment typically includes patient age and surgical risk; however, given the increased general risk of the procedure and that SARS-CoV-2 infection can be an additional and very dangerous comorbidity, suggesting the less invasive TAVR should be considered. 5 AS patients therefore may have increased risk for developing thromboembolic complications during the valve replacement procedure or during subsequent hospitalisation and recovery if they are infected with SARS-CoV-2. In fact, a recent study showed that a prosthetic aortic graft thrombosis patient died from COVID-19 and that anticoagulant and thrombectomy procedure were unsuccessful. 5 Therefore, direct thrombin inhibitors should be considered for AS patients who test positive for SARS-CoV-2, since both COVID-19 and AS procedure can increase the risk of thrombosis. Studies in animals have suggested that inhibitors of this system can upregulate ACE2 expression, which led some investigators to postulate that patients receiving those inhibitors may be at high risk of contracting a SARS-CoV-2 infection, which needs to be validated experimentally. cache = ./cache/cord-266948-n7sltd1b.txt txt = ./txt/cord-266948-n7sltd1b.txt === reduce.pl bib === id = cord-266820-exl36jt3 author = Rivera, Frida title = Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date = 2020-08-19 pages = extension = .txt mime = text/plain words = 873 sentences = 76 flesch = 61 summary = title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. cache = ./cache/cord-266820-exl36jt3.txt txt = ./txt/cord-266820-exl36jt3.txt === reduce.pl bib === id = cord-266888-ryvk6mte author = Cai, Guoshuai title = Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2 date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1444 sentences = 83 flesch = 53 summary = In addition, we analyzed three microarray data sets of samples derived from healthy subjects and patients with chronic obstructive pulmonary disease (COPD), including small airway epithelium samples from current smokers (from GSE5058, n = 26 [7] ), bronchial airway epithelium samples from current and former smokers (GSE37147, n = 238 [9] ), and lung samples from white patients (n = 438) who underwent lung cancer surgery at the Institut Universitaire de Cardiologie et de Pneumologie de Québec (10). We identified upregulation of pulmonary ACE2 gene expression in ever-smokers compared with nonsmokers in all data sets, irrespective of tissue subset or COPD status (Figure 1) . The significant effect of smoking on ACE2 pulmonary expression identified in this study may suggest an increased risk for viral binding and entry of SARS-CoV and SARS-CoV-2 in lungs of smokers. We further evaluated the effect of smoking on ACE2 pulmonary expression in single bronchial epithelial cells from six never-smokers and six current smokers. cache = ./cache/cord-266888-ryvk6mte.txt txt = ./txt/cord-266888-ryvk6mte.txt === reduce.pl bib === id = cord-266903-lxtxqdst author = Lee, Jong-Hwan title = A novel rapid detection for SARS-CoV-2 spike 1 antigens using human angiotensin converting enzyme 2 (ACE2) date = 2020-10-15 pages = extension = .txt mime = text/plain words = 2514 sentences = 147 flesch = 62 summary = In this study, we designed and developed a novel rapid detection method for SARS-CoV-2 spike 1 (S1) protein using the SARS-CoV-2 receptor ACE2, which can form matched pairs with commercially available antibodies. ACE2 and S1-mAb were paired with each other for capture and detection in a lateral flow immunoassay (LFIA) that did not cross-react with SARS-CoV Spike 1 or MERS-CoV Spike 1 protein. To decrease the non-specific interaction between capture probes in test lines and 20 detection probes, the nitrocellulose membrane was treated with the blocking solution (10 mM 2-21 amino-2-methyl-1-propanol (pH 9.0), 0.5% BSA, 0.5% β-Lactose, 0.05% Triton X-100, 0.05% 22 sodium azide) for 1 hour in a vacuum oven (37°C). -The human ACE2 and commercial antibody were paired with each other as capture and detection probes in a lateral flow immunoassay that was not cross-reactive with SARS-CoV S1 and MERS-CoV S1 proteins. cache = ./cache/cord-266903-lxtxqdst.txt txt = ./txt/cord-266903-lxtxqdst.txt === reduce.pl bib === id = cord-266914-3eatplc2 author = Wang, Yongjin title = Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date = 2010-06-02 pages = extension = .txt mime = text/plain words = 4005 sentences = 220 flesch = 53 summary = The group II coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis coronavirus (MHV) encode a number of proteins that antagonize host innate immunity. Innate immune signal transduction was stimulated by NDV infection in cells transfected with plasmids-expressing nsp1 from HCoV-229E, HCoV-NL63 or SARS-CoV, or with a control plasmid. Luciferase reporter assays showed that synthesis of the innate immune promoter IFN-band ISG15-driven genes was suppressed by 5-20-folds in HCoV-229E and HCoV-NL63 nsp1-expressing 293 cells (Fig. 4A) . Synthesis of non-immune promoter-driven genes, including for SV40, HSV-TK and CMV promoters, was inhibited to a similar extent by the two group I coronavirus nsp1 proteins (Fig. 4B) . These results indicate that group I coronaviruses have evolved a mechanism strikingly similar to SARS-CoV for antagonizing host cell proliferation and innate immunity using nsp1. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells cache = ./cache/cord-266914-3eatplc2.txt txt = ./txt/cord-266914-3eatplc2.txt === reduce.pl bib === id = cord-267013-nbwrl4g3 author = Ruan, R title = Subacute Thyroiditis might be a complication triggered by SARS-CoV-2 date = 2020-10-13 pages = extension = .txt mime = text/plain words = 884 sentences = 81 flesch = 66 summary = The actual coronavirus disease 2019 (COVID-19) pandemia, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached more than 16 million confirmed cases worldwide, being the United Kingdom, Spain and Italy the most affected countries in Europe. We describe a clinical case of SAT following SARS-CoV-2 infection. Thyroid scintigraphy with 5.73 mCi of 99m Tc-pertechnetate was performed on May 26th, which showed absence of uptake in the gland (figure 1). To date, four cases of subacute thyroiditis during or shortly after SARS-CoV2 infection have been reported 2-5 . SAT is a clinical entity that must be suspected in patients that experience a sudden onset of neck pain and tenderness, during or after COVID-19 disease. Subacute thyroiditis in a patient infected with SARS-COV-2: an endocrine complication linked to the COVID-19 pandemic Hormones (Athens) A case of subacute thyroiditis associated with Covid-19 infection SARS-CoV-2: a potential trigger for subacute thyroiditis? Subacute Thyroiditis After Sars-COV-2 Infection cache = ./cache/cord-267013-nbwrl4g3.txt txt = ./txt/cord-267013-nbwrl4g3.txt === reduce.pl bib === id = cord-266866-z98x80zj author = Sohpal, Vipan Kumar title = Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA date = 2020-09-24 pages = extension = .txt mime = text/plain words = 2027 sentences = 139 flesch = 53 summary = Hence the purpose of the present work is to assess the genomic relationship on the basis of statistical techniques between MERS-CoV, SARS-CoV, and SARS-CoV-2 with an objective to (1) maximized value of likelihood function of nucleotide substitution models, (2) transition/transversion bias and frequencies computation using maximum likelihood (ML) technique, (3) analyze the probability rate of substitution using ML. ML of different nucleotide substitution models BIC and AICc are the most important parameters for statistical analysis of ML to analyze the biological data. It indicates ML method accurately fits of 24 different nucleotide substitution models for biological data of SARS-CoV-2, MERS-CoV, and SARS-CoV under neutral evolution. In broad, the transitional/transversional varies from 0.57 (GTR model) to 0.89 (T92 + G + I), higher values indicate proportion of invariable sites (+I) and/or rate of variation across sites (+G) are more dominating in T92 model for SARS-CoV-2, SARS-CoV, and MERSCoV biological sequence. Six different nucleotide substitution models were simulated for biological sequence data of SARS-CoV, MERS-CoV and SARS-CoV-2. cache = ./cache/cord-266866-z98x80zj.txt txt = ./txt/cord-266866-z98x80zj.txt === reduce.pl bib === id = cord-266896-unb9yvjr author = Nihei, Yoshihito title = Continuous extracorporeal treatments in a dialysis patient with COVID-19 date = 2020-10-04 pages = extension = .txt mime = text/plain words = 2821 sentences = 127 flesch = 44 summary = Inflammatory cytokine storm caused by SARS-CoV-2 infection has been reported to play a central role in COVID-19; therefore, treatments for suppressing cytokines, including extracorporeal treatments, are considered to be beneficial. The cytokine storm caused by SARS-CoV-2 infection, primarily characterised by elevated plasma concentrations of interleukin 6 (IL-6), plays a central role in COVID-19 [2] ; therefore, its suppression is considered a key treatment approach in patients with COVID-19. Especially, CHDF is reported to continually suppress inflammatory cytokines and has been used in critically ill patients, including those with septic shock, ARDS and infections with viruses such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus [5] . We herein present a patient on PD who became critically ill due to COVID-19 and was treated with several extracorporeal treatments including PE, PMX-DHP and CHDF to suppress the cytokine storm. cache = ./cache/cord-266896-unb9yvjr.txt txt = ./txt/cord-266896-unb9yvjr.txt === reduce.pl bib === id = cord-266996-knwpkyg6 author = Kipkorir, Vincent title = Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1050 sentences = 89 flesch = 57 summary = title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test 2 Recently, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has also been isolated from anal/rectal swabs and stool specimens 3, 4 , raising concerns of potential alternative routes of viral transmission. Thereafter, a pooled analysis incorporating only cohort studies or case series with sample ≥10 patients was conducted to calculate pooled prevalence estimates (PPE) of prolonged SARS-CoV-2 RNA detection in anal/rectal swabs and stool samples after negative conversion in nasopharyngeal RT-PCR using the MetaXL (software Version 5.3, EpiGear International Pty Ltd., Sunrise Beach, Australia). In the pooled analysis of 8 cohort studies/ case series (n= 315), the pooled prevalence estimate (PPE) for prolonged rectal/anal/stool SARS-CoV-2 RNA was 32% (95% CI 22-44) (Figure 1 ). cache = ./cache/cord-266996-knwpkyg6.txt txt = ./txt/cord-266996-knwpkyg6.txt === reduce.pl bib === id = cord-266564-imj1lcy9 author = Liu, Yangli title = Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy date = 2020-03-05 pages = extension = .txt mime = text/plain words = 698 sentences = 47 flesch = 52 summary = Given the maternal physiologic and immune function changes in pregnancy [2] , pregnant individuals might face greater risk of getting infected by SARS-CoV-2 and might have more complicated clinical events. We described epidemiological, clinical characteristics, pregnancy and perinatal outcomes of all hospitalized pregnant patients diagnosed with COVID-19 in China. We identified all hospitalized pregnant patients with laboratory-confirmed SARS-CoV-2 infection between December 8, 2019, and February 25, 2020 officially reported by the central government, in areas outside Wuhan, China. We reported 13 pregnant COVID-19 patients in China, indicating pregnant women also susceptible to SARS-CoV-2. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China cache = ./cache/cord-266564-imj1lcy9.txt txt = ./txt/cord-266564-imj1lcy9.txt === reduce.pl bib === id = cord-266710-3wdy16tw author = Fintelman-Rodrigues, Natalia title = Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production date = 2020-09-21 pages = extension = .txt mime = text/plain words = 4822 sentences = 298 flesch = 55 summary = Molecular dynamics analysis revealed that the root mean square deviation (RMSD) for the SARS-CoV-2 Mpro backbone presented different conformations in complex with ATV or LPV (see Fig. S3 ). As a control, the activity of SARS-CoV-2 Mpro in fractions from infected cells was evaluated by treatment with RTV, which inhibited activity in the molecular range of 31 to 38 kDa without a change in the 70-kDa region (Fig. 2 , RTV lanes). Since the results regarding the pharmacologic activity of ATV and ATV/RTV against SARS-CoV-2 replication in Vero cells were promising, we next investigated whether the proposed drug therapies could inhibit virus replication in a human epithelial pulmonary cell line (A549). We highlight ATV and ATV/RTV because our assay readout to quantify infectious virus particles reveals (i) a good profile of antiviral activity, (ii) higher potencies in respiratory cells, and (iii) the ability to reduce levels of proinflammation mediator in monocytes. cache = ./cache/cord-266710-3wdy16tw.txt txt = ./txt/cord-266710-3wdy16tw.txt === reduce.pl bib === id = cord-266869-fs8dn7ir author = Kim, So Young title = Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date = 2020-04-15 pages = extension = .txt mime = text/plain words = 3813 sentences = 217 flesch = 54 summary = title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs might be involved in host cell entry of SARS-CoV-2. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. Using a modified version of Autodock Vina tuned for use with carbohydrates (Vina-Carb) [20, 21] , we performed blind docking on the trimeric SARS-CoV-2 SGP model to discover objectively the preferred binding GAG-binding sites on the SGP protein surface. cache = ./cache/cord-266869-fs8dn7ir.txt txt = ./txt/cord-266869-fs8dn7ir.txt === reduce.pl bib === id = cord-266988-72uvawth author = Barth, Rolf F. title = The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 date = 2020-07-14 pages = extension = .txt mime = text/plain words = 2504 sentences = 115 flesch = 43 summary = title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 COVID-19 disease is caused by a novel coronavirus, which has been named "Severe Acute Respiratory Syndrome Corona virus-2 (SARS-CoV-2)" [2] . Our current understanding of the pathology and the pathogenesis of COVID-19 disease and SARS-CoV-2 transmission is at an early stage and much still remains to be learned [5, 6] . Therefore, the total number of autopsies performed is miniscule compared to the number of deaths, but nevertheless they are both very revealing and important in order to better understand the multi-organ involvement associated with COVID-19 infection and for the development of better treatment strategies [1, 3] . The autopsy reports that already have been published provide a solid base for a better understanding of the consequences of COVID-19 infection but much more remains to be learned about this complex disease in order to develop better treatment strategies. cache = ./cache/cord-266988-72uvawth.txt txt = ./txt/cord-266988-72uvawth.txt === reduce.pl bib === id = cord-266702-6oxtlzqo author = Cristelo, Cecília title = SARS-CoV-2 and Diabetes: New Challenges for the Disease date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4054 sentences = 241 flesch = 47 summary = Emerging evidence demonstrates that the correct management of diabetes in those patients infected with SARS-CoV-2 is of utmost importance for the viral disease progression, therefore, the importance of blood glucose control will also be addressed. In vitro and in vivo studies showed that angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for SARS-CoV virus [7, 8] . It has been confirmed in some clinical studies that the long-term use of ACEIs or ARBs by patients is not associated with an increased risk of SARS-CoV-2 infection, neither of developing severe COVID-19 or even with a higher risk of in-hospital death [40] [41] [42] . In the case of SARS-CoV-2 the same transient damage in the pancreas has already been documented [44] , and given its higher infectivity and affinity for the ACE2 receptor, there is increased concern relative to the complications caused by hyperglycemia, as well as the long-term effects of the infection on recovered patients. cache = ./cache/cord-266702-6oxtlzqo.txt txt = ./txt/cord-266702-6oxtlzqo.txt === reduce.pl bib === id = cord-267115-6jqdi417 author = Giobbe, Giovanni Giuseppe title = SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date = 2020-06-24 pages = extension = .txt mime = text/plain words = 8080 sentences = 408 flesch = 47 summary = Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . cache = ./cache/cord-267115-6jqdi417.txt txt = ./txt/cord-267115-6jqdi417.txt === reduce.pl bib === id = cord-266923-hd1tjj6b author = Padroni, Marina title = Guillain-Barré syndrome following COVID-19: new infection, old complication? date = 2020-04-24 pages = extension = .txt mime = text/plain words = 1146 sentences = 70 flesch = 38 summary = Taking together all these findings, the causal association between GBS and COVID-19 remains speculative, but more probable, given that GBS and Bickerstaff's encephalitis have been already described as postinfectious complications of other coronavirus, sharing similarities with SARS-CoV-2 (Middle East respiratory syndrome, MERS-CoV) [11] . If our hypothesis will be confirmed in larger case series, neurologists and other clinicians should be aware of the important early recognition and treatment of the potential neuromuscular and autonomic worsening leading to cardio-respiratory failure in patients with GBS and mild or controlled pulmonary COVID-19 Notwithstanding the causative relationship remains unproved, we believe that our case description provide further evidence to the heterogenous and multi-systemic complications associated with SARS-CoV-2. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS CoV-2 infection: causality or coincidence Toscana virus associated with Guillain-Barré syndrome: a case-control study cache = ./cache/cord-266923-hd1tjj6b.txt txt = ./txt/cord-266923-hd1tjj6b.txt === reduce.pl bib === id = cord-266983-hpwebkbi author = Mallhi, Tauqeer Hussain title = Risks of Zoonotic Transmission of COVID-19 During Eid-Ul-Adha in Pakistan date = 2020-07-27 pages = extension = .txt mime = text/plain words = 946 sentences = 54 flesch = 53 summary = P akistan is expected to celebrate Eid-ul-Adha, an annual religious festival during which millions of farm animals, including sheep, goats, cows, buffalo, and camels are sacrificed, in the end of July or early August this year. 2 Since a recent investigation found the potential of zoonotic transmission of coronavirus disease (COVID-19) by farm animals, 3 we felt inclined to underscore the risks of virus transmission from humans to animals due to various activities surrounded by the festive celebration in Pakistan. It is pertinent to mention that ACE2s in animals, which are abundantly sacrificed during the Eid-Ul-Adha, have the ability to contract SARS-CoV-2, like humans. We believe that risks of zoonotic transmission of COVID-19 should be considered during the preparation of festive celebrations, and immediate measures must be taken to avoid any possible surge in COVID-19 cases during the Eid-Ul-Adha. cache = ./cache/cord-266983-hpwebkbi.txt txt = ./txt/cord-266983-hpwebkbi.txt === reduce.pl bib === id = cord-266987-ikt8r2o1 author = Loeffelholz, Michael J. title = Laboratory diagnosis of emerging human coronavirus infections – the state of the art date = 2020-03-30 pages = extension = .txt mime = text/plain words = 4734 sentences = 269 flesch = 46 summary = The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. It must be appreciated that no matter how accurate and fast laboratory testing methods are, the diagnosis of viral pneumonias such as caused by SARS-CoV-2 involves collecting the correct specimen from the patient at the right time. The authors recommended to use serology to facilitate the diagnosis of SARS-CoV-2 infections when an NP swab specimen was collected inappropriately and the molecular assays were performed unsatisfactorily [42] . Several RT-PCR protocols for detection of SARS-CoV-2 RNA have been posted by the World Health Organization at https://www.who.int/emergencies/ diseases/novel-coronavirus-2019/technical-guidance/ laboratory-guidance. Considering the increased levels of mortality and infectivity associated with three novel-coronavirus outbreaks, these random-access, safe and simple tests, which offer fast and accurate detection and identification, are likely to have an immediate impact on prompt clinical and epidemiological decisions [7, 63] . cache = ./cache/cord-266987-ikt8r2o1.txt txt = ./txt/cord-266987-ikt8r2o1.txt === reduce.pl bib === id = cord-267261-8z4aqfff author = Su, John R. title = Emerging viral infections date = 2005-03-01 pages = extension = .txt mime = text/plain words = 6882 sentences = 400 flesch = 45 summary = In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients cache = ./cache/cord-267261-8z4aqfff.txt txt = ./txt/cord-267261-8z4aqfff.txt === reduce.pl bib === id = cord-267308-rgqjolue author = Crovetto, F. title = SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1432 sentences = 91 flesch = 52 summary = Introduction: Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. We evaluated the seroprevalence and clinical presentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pregnant women in the first and third trimester. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. cache = ./cache/cord-267308-rgqjolue.txt txt = ./txt/cord-267308-rgqjolue.txt === reduce.pl bib === id = cord-267134-5gz2dotn author = Sallenave, Jean-Michel title = Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 5347 sentences = 239 flesch = 39 summary = The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus cache = ./cache/cord-267134-5gz2dotn.txt txt = ./txt/cord-267134-5gz2dotn.txt === reduce.pl bib === id = cord-267246-hq7g62p5 author = Huang, Su-Hua title = Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism date = 2015-07-31 pages = extension = .txt mime = text/plain words = 3422 sentences = 190 flesch = 41 summary = title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism METHODS: This study identified SARS-CoV ORF6-interacting proteins using the phage displayed human lung cDNA libraries, and examined the association of ORF6–host factor interaction with Type I IFN antagonism. RESULTS: The highest affinity clone to ORF6 displayed the C-terminal domain of NPIPB3 (nuclear pore complex interacting protein family, member B3; also named as phosphatidylinositol-3-kinase-related kinase SMG-1 isoform 1 homolog). The nucleotide sequences of the C terminus (amino acid residues 936e1050) of NPIPB3 (Accession Number Q92617) fused with the coat protein of ORF6-interacting phage clone 40 was amplified using PCR, and then cloned into bacterial expression vector pET32a for coimmunoprecipitation in vitro and mammalian expression vector pDsRed1-C (BD Biosciences Clontech) for colocalization assay. cache = ./cache/cord-267246-hq7g62p5.txt txt = ./txt/cord-267246-hq7g62p5.txt === reduce.pl bib === id = cord-267307-kyh0xsrp author = Kasting, Monica L. title = Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 4343 sentences = 230 flesch = 54 summary = Public health efforts should focus on increasing perceived severity and threat of SARS-CoV-2-related disease, while promoting NPI as effective in reducing threat. A six-item measure was used to assess participants' perceptions of the effectiveness of NPIs to prevent SARS-CoV-2 infection and spread. Three of the six items measured the perceived effectiveness of preventing yourself from spreading COVID-19 to others and included: 1) wearing a mask anytime you leave the house to go out in public, 2) practicing social distancing by leaving at least six feet between you and other people (this does not include people you live with), and 3) covering your mouth when you cough. Any variable that was significant at p<0.01 in bivariate comparisons was included in an adjusted logistic regression model with the binary lower/ higher perceived effectiveness of COVID-19 prevention measures as the outcome. cache = ./cache/cord-267307-kyh0xsrp.txt txt = ./txt/cord-267307-kyh0xsrp.txt === reduce.pl bib === id = cord-267388-jz5mm91w author = Cheung, Szeya title = Recurrent Acute Pancreatitis in a Patient with COVID-19 Infection date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1555 sentences = 102 flesch = 44 summary = Patient: Male, 38-year-old Final Diagnosis: Recurrent idiopathic acute pancreatitis with COVID-19 Symptoms: Nausea • severe abdominal pain • fever • vomiting Medication:— Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases • General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: The novel COVID-19 disease has infected more than 2 million people worldwide, causing more than 120 000 deaths. CONCLUSIONS: The temporal relationship between clinical presentation of acute pancreatitis and SARS-CoV-2 infection in this patient with no precipitating risk factors for pancreatitis suggests COVID-19-associated acute pancreatitis. Our review of the literature showed a few case studies that described the presentation of idiopathic acute pancreatitis in patients with concurrent SARS-CoV-2 infection [5] [6] [7] [8] [9] [10] . It is also important to note that while respiratory symptoms improve in patients with COVID-19 infection, these patients can still test positive for SARS-CoV-2 and are at risk for developing acute pancreatitis. cache = ./cache/cord-267388-jz5mm91w.txt txt = ./txt/cord-267388-jz5mm91w.txt === reduce.pl bib === id = cord-267476-j59tm40d author = Yong, Sarah Ee Fang title = Connecting clusters of COVID-19: an epidemiological and serological investigation date = 2020-04-21 pages = extension = .txt mime = text/plain words = 3562 sentences = 187 flesch = 49 summary = We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection. Serological testing had a crucial role in establishing a link between clusters, showing its use in identifying convalescent COVID-19 cases and supporting epidemiological investigations. In our epidemiological investigation, we used RT-PCR and serological testing to diagnose cases of COVID-19 and establish links between clusters. This investigation shows how SARS-CoV-2 serological analysis (ELISA detecting IgG and VNT detecting neutralising antibodies), in addition to use of traditional epidemiological methods, was important in establishing links among locally transmitted COVID-19 cases and tracing the transmission chain to an imported source. cache = ./cache/cord-267476-j59tm40d.txt txt = ./txt/cord-267476-j59tm40d.txt === reduce.pl bib === id = cord-267373-nzxbogga author = Antinori, Spinello title = Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3468 sentences = 149 flesch = 49 summary = title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status This prospective (compassionate), open-label study of remdesivir, which was conducted at Luigi Sacco Hospital, Milan, Italy, between February 23 and March 20, 2020, involved patients with SARS-CoV-2 pneumonia aged ≥18 years undergoing mechanical ventilation or with an oxygen saturation level of ≤94% in air or a National Early Warning Score 2 of ≥4. Patients were eligible to receive remdesivir for compassionate use if they were a male or non-pregnant female aged >18 years, had SARS-CoV-2 infection confirmed by a positive reverse-transcriptase polymerase chain reaction (RT-PCR) test of a respiratory tract sample and pneumonia confirmed by a chest X-ray or computed tomography (CT) scan, and were mechanically ventilated or had an oxygen saturation (SaO2) level of <94% in room air or a National Early Warning Score (NEWS)2 of  4 [19] . cache = ./cache/cord-267373-nzxbogga.txt txt = ./txt/cord-267373-nzxbogga.txt === reduce.pl bib === id = cord-267124-8efdzlc0 author = Wichmann, Dominic title = Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4062 sentences = 240 flesch = 50 summary = In response to the pandemic spread of SARS-CoV-2, the authorities of the German federal state of Hamburg ordered mandatory autopsies in all patients dying with a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR). During autopsy, tissue samples for histology were taken from the following organs: heart, lungs, liver, kidneys, spleen, pancreas, brain, prostate and testes (in males), ovaries (in females), small bowel, saphenous vein, common carotid artery, pharynx, and muscle. In this autopsy study of 12 consecutive patients who died of COVID-19, we found a high incidence of deep venous thrombosis (58%). In studies that examined deceased patients with COVID-19 without relying on autopsy, no increased rates of pulmonary embolism were observed clinically. To our knowledge, only 3 case reports have been published on patients with COVID-19 who have undergone complete autopsy and a few more in which only lung tissue was examined (7, 8) . cache = ./cache/cord-267124-8efdzlc0.txt txt = ./txt/cord-267124-8efdzlc0.txt === reduce.pl bib === id = cord-267402-kca05rvz author = South, Kieron title = Preceding infection and risk of stroke: An old concept revived by the COVID-19 pandemic date = 2020-07-24 pages = extension = .txt mime = text/plain words = 6248 sentences = 335 flesch = 41 summary = What follows herein is a detailed summary of the current literature surrounding COVID-19, encompassing the immune and inflammatory responses to infection, thrombotic manifestations and vascular consequences of infection with a focus on possible mechanisms by which these elements may contribute to acute stroke events. 89 This is not the case in COVID-19 (and the previous SARS outbreak) and a recent retrospective cohort study has suggested an incidence of stroke 7-8 times higher in patients hospitalized with COVID-19 infection compared with those hospitalized by influenza, 90 supporting the possibility of a SARS-CoV-2-driven hyper-coagulant state. [91] [92] [93] Obesity, in particular, is emerging as a prominent risk factor in the development of severe COVID-19 disease and is generally associated with increased incidence and increased severity of respiratory viral infection. Notably, the cytokine IL-33 is persistently elevated in obese individuals and is capable of stimulating endothelial cells to release pro-coagulant tissue factor 97 which may expose them to more severe COVID-19 disease and/or stroke. cache = ./cache/cord-267402-kca05rvz.txt txt = ./txt/cord-267402-kca05rvz.txt === reduce.pl bib === id = cord-267397-b7ogeokm author = Smith, E. R. title = Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods date = 2020-11-12 pages = extension = .txt mime = text/plain words = 5612 sentences = 401 flesch = 53 summary = Given the scarcity of COVID data in pregnancy, differences in data collection protocols globally, and potential risks for severe illnesses in this population, there is an urgent need to rapidly generate high quality information to make evidence-based decisions and create guidelines on the prevention and treatment of COVID-19 illness in pregnant women and infants. We updated the data modules in September 2020 to reflect evolving understanding of SARS-CoV-2 infection in newborns and to reflect and an updated generic protocol developed by WHO for COVID-related pregnancy cohort studies (Supplementary File 3) . Studies will be eligible to contribute data to the PMA when they have accrued at least 25 confirmed cases with completed follow up including obtaining maternal and neonatal outcomes. Given the current state of limited, high-quality evidence to inform public health guidance and healthcare strategies for pregnant women and newborn, the proposed study will contribute timely and necessary evidence-based data for decision-making in the context of COVID-19 and maternal and neonatal health. cache = ./cache/cord-267397-b7ogeokm.txt txt = ./txt/cord-267397-b7ogeokm.txt === reduce.pl bib === id = cord-267744-asjvf123 author = Lee, Yu-Ching title = Chicken single-chain variable fragments against the SARS-CoV spike protein date = 2007-07-23 pages = extension = .txt mime = text/plain words = 4057 sentences = 212 flesch = 52 summary = Following the immunization of chickens with these recombinant spike proteins, two single-chain variable fragment (scFv) antibody libraries were established with short or long linkers to contain 5 × 10(7) and 9 × 10(6) transformants, respectively. In a comparison of nucleotide sequences with the chicken germline gene, we found that all clones varied in the complementarity-determining regions, that two scFv antibodies reacted significantly with SARS-CoV-infected Vero cells, and that those two specific scFv antibodies recognized the same region of the spike protein spanning amino acid residues 750–1000. The current study aimed to show that monoclonal IgY scFv antibodies which bind specifically to the S protein and SARS-CoV-infected Vero cells can be isolated from chickens immunized with Escherichia coli-derived S proteins. Cellular lysates containing single-chain variable fragment (scFv) antibodies from various Ssc (A) and Lsc (B) library clones were examined for their binding to SARS-CoV-infected cell lysates using a commercially available kit. cache = ./cache/cord-267744-asjvf123.txt txt = ./txt/cord-267744-asjvf123.txt === reduce.pl bib === id = cord-267136-1abp6oom author = Lan, Yu-Ching title = Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan date = 2004-12-07 pages = extension = .txt mime = text/plain words = 3106 sentences = 173 flesch = 63 summary = Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. To better understand evolutionary relationships between SCoVs isolated in Taiwan and those isolated in other parts of the world, we constructed phylogenetic trees with two different methods using full-length genomic sequences from 45 human (12 Taiwanese) and two civet SCoVs. Tree topologies were consistent for the NJ (Fig. 1a) and Pars (Fig. 1b) methods. Pairwise comparison methods were used to analyze nucleotide sequence variation within the full-length genomes of 20 human SCoVs (7 from early epidemic and 13 from late epidemic) (Fig. 2) . cache = ./cache/cord-267136-1abp6oom.txt txt = ./txt/cord-267136-1abp6oom.txt === reduce.pl bib === id = cord-267579-gkvd0fol author = Yang, Xiaoyu title = Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period date = 2020-07-27 pages = extension = .txt mime = text/plain words = 470 sentences = 37 flesch = 52 summary = title: Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period The 2019 novel coronavirus disease (COVID-19) causing acute infectious pneumonia has widely spread in China and other countries in the world. Studies have documented that novel coronavirus spread through human-to-human transmission in hospital and family setting 2,3 . Nevertheless, the transmission of the novel coronavirus from an asymptomatic carrier should be considered as a source of the infection of COVID-19 as well 4 . Therefore, it is of significance to identify and isolate asymptomatic carriers as well as patients with mild symptoms to prevent the spread of the virus. Clinical Characteristics of Coronavirus Disease 2019 in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients cache = ./cache/cord-267579-gkvd0fol.txt txt = ./txt/cord-267579-gkvd0fol.txt === reduce.pl bib === id = cord-267458-uofy7jyx author = Jiang, Xiao-Lin title = Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China date = 2020-04-22 pages = extension = .txt mime = text/plain words = 1622 sentences = 124 flesch = 59 summary = title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China We report a three-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Herein, we report a 3-family cluster study of eight patients associated with asymptomatic and pauciasymptomatic (one mild symptom only) SARS-CoV-2 transmission in Shandong Province, China. The first positive SARS-CoV-2 patients in this cluster were identified on January 21, 2020 triggering an epidemiological investigation by the local center for disease control and prevention. Our findings show that the transmission of SARS-CoV-2 by individuals with asymptomatic or paucisymptomatic infections is possible. Patient 5 (asymptomatic) was identified to be infected with SARS-CoV-2 after frequent contact with Patients 3 and 4 during work and home visits. In this study, we detected SARS-CoV-2 in two environmental swabs from the household of Patient 3. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period cache = ./cache/cord-267458-uofy7jyx.txt txt = ./txt/cord-267458-uofy7jyx.txt === reduce.pl bib === id = cord-267587-hag6qydb author = Lau, Susanna K.P. title = Engineering Coronaviruses to Evaluate Emergence and Pathogenic Potential date = 2016-04-16 pages = extension = .txt mime = text/plain words = 1977 sentences = 107 flesch = 46 summary = A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. [1] and another similar study in Nature Medicine published in December 2015 by the same group [2] reported the use of existing sequence data with reverse genetics to engineer SARS-related CoVs and evaluate their potential of emergence and pathogenicity. In order to predict whether a SARS-related bat CoV, named WIV1-CoV, discovered in Chinese horseshoe bats in Yunnan [6] , had the potential to emerge in humans, Menachery et al. employed can be used for evaluating the emergence and pathogenic potential of other CoVs. Before the SARS epidemic, fewer than 10 CoVs with complete genome sequences were available. cache = ./cache/cord-267587-hag6qydb.txt txt = ./txt/cord-267587-hag6qydb.txt === reduce.pl bib === id = cord-267426-3eu9umx5 author = Yao, Hangping title = Patient-derived mutations impact pathogenicity of SARS-CoV-2 date = 2020-04-19 pages = extension = .txt mime = text/plain words = 4615 sentences = 314 flesch = 62 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously referred to as 32 2019-nCoV), associated with the ongoing outbreak of atypical pneumonia, has already 33 caused a global pandemic, despite China's extensive systematic effort to contain the 34 All rights reserved. 75 To address this, we characterized 11 SARS-CoV-2 viral isolates from patients (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.04.14.20060160 doi: medRxiv preprint 16 sequences and Taijima's D is -2.8874 with a nucleotide diversity (π) of 0.000641 (p < 229 0.05 according to simulations performed in (Tajima, 1989) , indicating that the 230 SARS-CoV-2 genome has an excess of low-frequency alleles due to recent population 231 expansions, consistent with the repeated bottlenecking events during viral infections. cache = ./cache/cord-267426-3eu9umx5.txt txt = ./txt/cord-267426-3eu9umx5.txt === reduce.pl bib === id = cord-267436-mivxm8oh author = Groneberg, David A title = Treatment and vaccines for severe acute respiratory syndrome date = 2005-03-10 pages = extension = .txt mime = text/plain words = 5913 sentences = 317 flesch = 44 summary = The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. 31 The results of a randomised clinical study in Guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose (400-600 mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. Search terms were "severe acute respiratory syndrome", "SARS", "treatment", "coronavirus", "infection", "SARS coronavirus", "vaccination", and "antiviral". Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus cache = ./cache/cord-267436-mivxm8oh.txt txt = ./txt/cord-267436-mivxm8oh.txt === reduce.pl bib === id = cord-267666-i7uuf3ck author = Sarkar, Bishajit title = Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach date = 2020-11-11 pages = extension = .txt mime = text/plain words = 1873 sentences = 129 flesch = 50 summary = Therefore, in this study, immunoinformatics methods were exploited to design a novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. Thereafter, several in silico validations i.e., the molecular docking, molecular dynamics simulation (including the RMSF and RMSD studies), and immune simulation studies were also performed which predicted that the designed vaccine should be quite safe, effective, and stable within the biological environment. The MHC class-I and class-II epitopes were predicted from the target protein sequences for 503 constructing the vaccine. Exploring Leishmania secretory proteins 1232 to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach Immunoinformatics approaches 1236 to explore Helicobacter Pylori proteome (Virulence Factors) to design B and T cell multi-epitope 1237 subunit vaccine. Immunoinformatics-guided designing of 1405 epitope-based subunit vaccine against the SARS Coronavirus-2 (SARS-CoV-2) cache = ./cache/cord-267666-i7uuf3ck.txt txt = ./txt/cord-267666-i7uuf3ck.txt === reduce.pl bib === id = cord-267588-ruuzr6l1 author = Garnett, Lauren title = Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date = 2020-08-08 pages = extension = .txt mime = text/plain words = 3093 sentences = 156 flesch = 51 summary = This study aimed to examine the efficacy of six different swabs that are commonly found in hospital settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima), along with more readily available alternative transport mediums (DMEM, PBS, 100% ethanol, 0.9% normal saline and VTM) for their use in molecular detection of SARS-CoV-2. Therefore, our results suggest that the cotton and wood For the portion of the study focusing on alternative transport media, we assessed the ability of DMEM, PBS, 0.9% Normal Saline, and 100% ethanol compared to VTM to be used as medium for the preservation and recovery of viral RNA to be quantified by molecular detection. Despite finding similar levels of viral RNA collected using different swabs and transport media, there is variation when evaluating different respiratory clinical samples while testing for SARS-CoV-2. cache = ./cache/cord-267588-ruuzr6l1.txt txt = ./txt/cord-267588-ruuzr6l1.txt === reduce.pl bib === id = cord-267845-18hb5ndr author = Resende, Paola Cristina title = SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date = 2020-05-01 pages = extension = .txt mime = text/plain words = 1616 sentences = 89 flesch = 48 summary = Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. Despite those limitations, we developed a sequencing protocol that successfully obtained whole genomes from SARS-CoV-2 positive samples referred to the National Reference laboratory at FIOCRUZ in Brazil. The tiling amplicon multiplex PCR method has been previously used for virus sequencing directly from clinical samples to obtain consensus genome sequences (3). Here, we describe three protocols using a primer set designed to sequence SARS-CoV-2 directly from total RNA extracted from clinical samples, which were initially diagnosed using real-time RT-PCR (7, 8) . Here we introduce a versatile sequencing protocol to recover the complete SARS-CoV-2 genome based on reverse transcription plus an overlapping long amplicon multiplex PCR strategy, and associated with pipelines to report the data, and recover the consensus files. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples cache = ./cache/cord-267845-18hb5ndr.txt txt = ./txt/cord-267845-18hb5ndr.txt === reduce.pl bib === id = cord-267831-uu883ofc author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1257 sentences = 80 flesch = 44 summary = We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry cache = ./cache/cord-267831-uu883ofc.txt txt = ./txt/cord-267831-uu883ofc.txt === reduce.pl bib === id = cord-267511-tb69dwg8 author = Talebian, Sepehr title = Why Go NANO on COVID-19 Pandemic? date = 2020-09-02 pages = extension = .txt mime = text/plain words = 1964 sentences = 100 flesch = 46 summary = This will be essential to find viral particles in an efficient way and target them for destruction by developing NANOvaccines involved in host cell protection and immune and immunity response and/or anti-viral NANOagents, involved in inhibiting viral attachment, cell entry, and systemic infection (Figure 1 ). 6 Hence, one could imagine the realization of an oral multi-modal NANOvaccine for targeted delivery of a synthetic mRNA of the virus to the respiratory tract, with the purpose of enhancing the immunostimulatory activity of the vaccine, by simply including antibodies or small molecules that could target the interaction sites between ACE2 and SARS-CoV. Considering that viruses could be phylogenetically unrelated and structurally different, and given that most vaccines are virus specific, a promising approach would be that of developing broad-spectrum anti-viral NANOparticles to fight COVID-19 and future pandemics. Potential Therapeutic Approaches by which NANOtechnology Can Contribute against COVID-19 cache = ./cache/cord-267511-tb69dwg8.txt txt = ./txt/cord-267511-tb69dwg8.txt === reduce.pl bib === id = cord-267610-bzbr9ios author = Anastassopoulou, Cleo title = SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2472 sentences = 107 flesch = 43 summary = In agreement with this reasoning, data suggest that SARS-CoV-2 infections in children involve the upper rather than the lower respiratory tract, the typical site of severe COVID-19 disease where ACE2 receptors are more abundant [29] . In this respect, a large prospective NIH-funded study of 6000 people from 2000 US families in 11 cities, called human epidemiology and response to SARS-CoV-2, will help determine the incidence of novel coronavirus infection in children in the USA and whether rates differ between children who have asthma or other allergic conditions and children who do not [45] . School children are nonetheless anticipated to contribute to the community transmission of SARS-CoV-2 through their large numbers of daily social contacts, some of which are intergenerational, with older age groups where the risk for more severe illness is increased. cache = ./cache/cord-267610-bzbr9ios.txt txt = ./txt/cord-267610-bzbr9ios.txt === reduce.pl bib === id = cord-267566-gdjl0qmu author = Kweon, Oh Joo title = Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date = 2020-10-22 pages = extension = .txt mime = text/plain words = 3599 sentences = 232 flesch = 51 summary = This study aims to assess the serologic profiles and time kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with COVID-19 using two immunoassays. METHODS: A total of 97 samples serially collected from 17 patients with COVID-19 and 137 negative control samples were analyzed for IgM and IgG against SARS-CoV-2 using the AFIAS COVID-19 Ab (Boditech Med Inc., Chuncheon, Republic of Korea) and the EDI(™) Novel Coronavirus COVID-19 ELISA Kit (Epitope Diagnostics, Inc., San Diego, CA). The diagnostic sensitivities of IgM/IgG for ≤14d PSO were 21.4%/35.7~57.1% and increased to 41.2~52.9%/88.2~94.1% at >14 d PSO with specificities of 98.5%/94.2% for AFIAS COVID-19 Ab and 100.0%/96.4% for EDI(™) Novel Coronavirus COVID-19 ELISA Kit. Among 137 negative controls, 12 samples (8.8%) showed positive or indeterminate results. cache = ./cache/cord-267566-gdjl0qmu.txt txt = ./txt/cord-267566-gdjl0qmu.txt === reduce.pl bib === id = cord-267762-mzon01fd author = Ferreira, A. title = Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection. date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2939 sentences = 167 flesch = 51 summary = Methods: By analyzing the Portuguese anonymized data on private and public based medical prescriptions we have identified all cases chronically receiving HCQ for the management of diseases such as systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. Cross linking the two sets of data has allowed us to compare the proportion of HCQ chronic treatment (at least 2 grams per month) in laboratory confirmed cases of SARS-CoV-2 infection with laboratory confirmed negative cases. Several in vitro studies have shown chloroquine phosphate and hydroxychloroquine sulphate (HCQ) to be effective in both preventing and treating SARS-CoV-2 infection in isolated cells (1) (2) (3) . By analyzing these sets of data, we were able to detect all patients with SARS-CoV-2 confirmed infections and all clinically suspected but non-confirmed patients between Mars 2, 2020 (the date of the first Portuguese case) and the moment of the analysis. The proportion of HCQ chronic treatment was higher in negative patients is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-267762-mzon01fd.txt txt = ./txt/cord-267762-mzon01fd.txt === reduce.pl bib === id = cord-267533-nmgtan4e author = Hu, Zhigang title = Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date = 2020-10-29 pages = extension = .txt mime = text/plain words = 3605 sentences = 214 flesch = 46 summary = By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin. cache = ./cache/cord-267533-nmgtan4e.txt txt = ./txt/cord-267533-nmgtan4e.txt === reduce.pl bib === id = cord-267887-ntwvquqz author = Yang, Ren title = Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1308 sentences = 81 flesch = 51 summary = title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro Previously, researchers had developed a pseudotyped virus system for SARS-CoV and MERS-CoV, based on HIV-1 core, bearing virus spike protein. Furthermore, the neutralization results for ppSARS-2 were consistent with those of live SARS-CoV-2 and determined using the serum samples from convalescent patients. In conclusion, we have developed an easily accessible and reliable tool for studying the neutralizing efficiency of antibodies against SARS-CoV-2 and the entry process of the virus in a BSL-2 laboratory. Development and optimization of a sensitive pseudovirus-based assay for HIV-1 neutralizing antibodies detection using A3R5 cells A safe and convenient pseudovirus-based inhibition assay to detect neutralizing antibodies and screen for viral entry inhibitors against the novel human coronavirus MERS-CoV Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig cache = ./cache/cord-267887-ntwvquqz.txt txt = ./txt/cord-267887-ntwvquqz.txt === reduce.pl bib === id = cord-267723-loj718vd author = Kloc, Małgorzata title = Macrophages in diabetes mellitus (DM) and COVID-19: do they trigger DM? date = 2020-10-17 pages = extension = .txt mime = text/plain words = 2305 sentences = 128 flesch = 47 summary = We also describe the DM-related changes in the monocyte/macrophages functions, how they could lead to the severe outcome of SARS-CoV-2 infection, and importantly, if and how they could initiate DM in DM-susceptible patients. Preclinical and clinical studies indicate that the increased numbers of innate immune cells, and produced by them inflammatory factors have causative and detrimental effects on the islets and β-cells in diabetes (Böni-Schnetzler and Meier 2019). As we wrote above, SARS-CoV-2 infects many types of cells expressing ACE2 receptors, including the macrophages and β-cell in the pancreas. One possibility is that, similar to the effect of SARS-CoV-2 in the lungs, the infection of pancreatic macrophages causes inflammatory cytokine and chemokines storm in the pancreas. Although, this scenario seemed the least likely because the direct damage to the pancreatic islets should result in higher than the reported incidence of COVID-19-induced diabetes, however, recent data presented in Nature News indicate that indead, the SARS-CoV-2 may cause direct damage to the insulin producing β-cells (Mallapaty 2020) . cache = ./cache/cord-267723-loj718vd.txt txt = ./txt/cord-267723-loj718vd.txt === reduce.pl bib === id = cord-267856-t3ksa18w author = Funk, Colin D. title = A Novel Strategy to Mitigate the Hyperinflammatory Response to COVID-19 by Targeting Leukotrienes date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4340 sentences = 232 flesch = 43 summary = We offer a simple treatment paradigm using two generic drugs targeting the hyperinflammatory response that characterizes the turning point from mild to severe/critical COVID-19 by targeting leukotriene biosynthesis with zileuton (Zyflo(®) controlled release formulation) and antagonism of the cysteinyl leukotriene 1 receptor with montelukast (Singulair(®)). By targeting vascular permeability, immune modulating and general inflammation-dampening effects at the CysLT 1 level with montelukast (Dahleń et al., 1981; Maeba et al., 2005; Capra et al., 2007; Tahan et al., 2008; Khodir et al., 2014) and LT biosynthesis with the 5-lipoxygenase inhibitor zileuton, to block both arms of the LT pathway ( Figure 2 ) and remove ligands for another key receptor regulating vascular permeability, CysLT 2 (Moos et al., 2008) , as well as inflammatory cell recruitment and endothelial cell adhesion via BLT 1 receptor (Ford-Hutchinson et al., 1980; Tager et al., 2003; Taube et al., 2006; Sasaki and Yokomizo, 2019) , there is a sound scientific basis for alleviating disease progression from mild to severe-critical stages of COVID-19 (Figures 1 and 2) . cache = ./cache/cord-267856-t3ksa18w.txt txt = ./txt/cord-267856-t3ksa18w.txt === reduce.pl bib === id = cord-267770-ik1ib3zb author = Koo, Hyun Jung title = RadioGraphics Update: Radiographic and CT Features of Viral Pneumonia date = 2020-06-05 pages = extension = .txt mime = text/plain words = 2754 sentences = 145 flesch = 46 summary = In this updated review, we expand on the information presented in our 2018 article (4) and focus on the clinical features and chest CT findings of SARS-CoV-2 pneumonia to help radiologists detect the disease at its early stage. A reverse transcription-polymerase chain reaction (RT-PCR) test of an upper respiratory tract specimen (obtained with nasopharyngeal swab and/or oropharyngeal swab) and/or sputum sample is the standard diagnostic tool for determining hospitalization and isolation of patients with SARS-CoV infection. After 13 days of conservative management, her respiratory symptoms ameliorated, and a negative RT-PCR test result for SARS-CoV-2 was obtained. On the basis of this suggestion and experience managing patients with COVID-19, we provide a brief clinical setting to show the use of chest CT to facilitate the diagnosis of SARS-CoV-2 pneumonia (Fig 5) . For the management of patients with respiratory symptoms in endemic areas, an RT-PCR test is the primary diagnostic tool used for discriminating SARS-CoV-2-positive cases. cache = ./cache/cord-267770-ik1ib3zb.txt txt = ./txt/cord-267770-ik1ib3zb.txt === reduce.pl bib === id = cord-267482-afqfymbq author = Ryu, Seungjin title = Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date = 2020-09-12 pages = extension = .txt mime = text/plain words = 8189 sentences = 476 flesch = 49 summary = Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs. Also, initial studies that employ lung ciliated epithelial cell-specific HFH4/FOXJ1 promoter driven hACE2 transgenic mice show SARS-CoV-2 infection induces weight loss, lung inflammation and approximately 50% mortality rate, suggesting the usefulness of this model to understand the mechanism of immune dysregulation (Jiang et al., 2020) . Moreover, given our recent findings that ketogenesis inhibits inflammation and expands tissue resident ϒδ T cells (Goldberg et al., 2019) while SARS-CoV-2 infection in patients is associated with depletion of ϒδ T cells (Lei et al., 2020; Rijkers et al., 2020) , we next tested whether elevating BHB by feeding a ketogenic diet (KD) protects against mCoV-A59-driven inflammatory damage in aged mice. cache = ./cache/cord-267482-afqfymbq.txt txt = ./txt/cord-267482-afqfymbq.txt === reduce.pl bib === id = cord-268075-kbislbx0 author = Song, Limin title = Cardiovascular Changes in Patients With COVID-19 From Wuhan, China date = 2020-09-02 pages = extension = .txt mime = text/plain words = 4052 sentences = 224 flesch = 44 summary = Alternatively, ascending aortic dilation and LA enlargement might be present before infection but characterized the patient at risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Epidemiological studies have demonstrated that acute pneumonia is associated with an increased risk for cardiac complications at all levels of infection severity (4) . In this study, we retrospectively collected and analyzed detailed clinical data from patients with laboratory-confirmed COVID-19 who were admitted to the Union Hospital (Wuhan, China). Myocardial injury associated with the SARS-CoV-2 occurred in five of the first 41 patients diagnosed with COVID-19 in Wuhan, which mainly manifested as an increase in high-sensitivity cardiac troponin I levels (2) . In summary, we have shown that hypertension is a common comorbidity among hospitalized patients with COVID-19 in Wuhan, China, and cardiac injury was the most common complication. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China cache = ./cache/cord-268075-kbislbx0.txt txt = ./txt/cord-268075-kbislbx0.txt === reduce.pl bib === id = cord-267509-w7nfbnbb author = Tian, Yuan title = Review article: gastrointestinal features in COVID‐19 and the possibility of faecal transmission date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1577 sentences = 107 flesch = 52 summary = METHODS: We have reviewed gastrointestinal features of, and faecal test results in, COVID‐19 from case reports and retrospective clinical studies relating to the digestive system published since the outbreak. 7, 11, 17 Gastrointestinal symptoms were also present in critically ill children, 28 Early studies indicated that individuals infected with SARS-CoV-2 might shed and spread the virus while they were pre-symptomatic or asymptomatic. Manifestations of digestive system in hospitalized patients with novel coronavirus pneumonia in Wuhan, China: a single-center, descriptive study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-267509-w7nfbnbb.txt txt = ./txt/cord-267509-w7nfbnbb.txt === reduce.pl bib === id = cord-267690-g0kesgjm author = Mueller, Sarina K. title = Considerations for Continuing Semielective and Emergency Otolaryngological Procedures During the COVID-19 Pandemic date = 2020-09-07 pages = extension = .txt mime = text/plain words = 2802 sentences = 154 flesch = 51 summary = The objective of this study was to analyze procedures and outcomes of continuing semielective and emergency surgeries during the COVID-19 pandemic. CONCLUSIONS: Continuing selected otorhinolaryngological surgeries is crucial for patients' health, survival, and long-time quality of life, yet, the protection of the medical personnel has to be granted. In case of a negative SARS-CoV-2 test, the scheduled surgery was performed the following day without special protective equipment ( Figure 1A) . If the SARS-CoV-2 test result could not be awaited due to the condition of the patient, the surgery was performed with full protective equipment consisting of a FFP2 or FFP3 (filtering face piece mask), a gown, a face shield, and double gloves. If the SARS-CoV-2 test result was positive, surgery was also performed with the full protective equipment. If the SARS-CoV-2 test was negative, surgery was performed as in the semi-elective cases without the above named protective equipment ( Figure 1B ). cache = ./cache/cord-267690-g0kesgjm.txt txt = ./txt/cord-267690-g0kesgjm.txt === reduce.pl bib === id = cord-267735-y3832u9e author = Sun, Wuping title = Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3073 sentences = 178 flesch = 40 summary = title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic It has been reported that hyper-immunity individuals have received treatment with immunosuppressive or modulatory agents; these approaches may increase the possibility of SARS-CoV-2 infection (Cai et al., 2020) . These results demonstrated that SARS-CoV-2 infection-induced immune alteration in COVID-19 patients. These studies suggested that SARS-CoV-2 infection-induced immune alteration could further result in the concurrence of chronic pain since it affects the nervous system. Acquired immune deficiency syndrome (AIDS) is associated with various infection symptoms, and peripheral neuropathic pain is the most common and severe neurological manifestation that has been reported in HIV-positive, immunocompromised individuals (Amaniti et al., 2019) . Chronic pain patients have received limited treatment and discounted services during the COVID-19 outbreak due to limit the spread of SARS-CoV-2 infection. Chronic pain patients may also have increased infection risks to SARS-CoV-2 due to complicated reasons. cache = ./cache/cord-267735-y3832u9e.txt txt = ./txt/cord-267735-y3832u9e.txt === reduce.pl bib === id = cord-267815-4fw7xgnt author = Peña, Juan A. title = A Survey of Labor and Delivery Practices in New York City during the COVID-19 Pandemic date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2888 sentences = 170 flesch = 54 summary = We therefore developed an internet-based survey to elucidate the practices put into place to guide the care of obstetrical patients during the COVID-19 pandemic. We found that all sites made changes to their practices, and that there appeared to be agreement with screening and testing for COVID-19, as well as labor and delivery protocols, for SARS-CoV-2-positive patients. One center performed SARS-CoV-2 PCR testing for all support persons either on admission to labor and delivery (L&D), or 24 to 48 hours prior to a scheduled admission. For half of the sites, after 34 weeks, the risks of continued expectant management of a patient with COVID-19 seemed to outweigh the risks of prematurity, and these centers would forgo testing and recommend delivery. Here we report on the obstetrical practices and protocols from four academic medical centers in NYC at the height of the COVID-19 pandemic. cache = ./cache/cord-267815-4fw7xgnt.txt txt = ./txt/cord-267815-4fw7xgnt.txt === reduce.pl bib === id = cord-267917-belkwihy author = Peters, Alexandra title = Putting some context to the aerosolization debate around SARS-CoV-2 date = 2020-04-30 pages = extension = .txt mime = text/plain words = 887 sentences = 54 flesch = 60 summary = 1 The experiments reported in this letter compared the stability of SARS-CoV-2 and SARS-CoV-1 in aerosols and on a number of different surfaces. The work showed that "SARS-CoV-2 remained viable in aerosols throughout the duration of (the) experiment (3 hours), with a reduction in infectious titer from 10 3.5 to 10 2.7 TCID50 per liter of air. [2] [3] [4] These media articles' assertions include that SARS-Co V-2 can last "three hours after being coughed out into the air", 4 and that the van Doremalen et al. 2 The media even went as far as suggesting that the aerosols generated by the three-jet Collison nebulizer "duplicated the microscopic droplets created in a cough or a sneeze". It is for these reasons that the WHO and infection prevention specialists continue to support assertion that transmission of SARS-CoV-2 is primarily through droplets and contact (including indirect contact with contaminated surfaces). cache = ./cache/cord-267917-belkwihy.txt txt = ./txt/cord-267917-belkwihy.txt === reduce.pl bib === id = cord-268034-7id7sfsu author = Auerswald, Heidi title = Assessment of Inactivation Procedures for SARS-CoV-2 date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1620 sentences = 100 flesch = 47 summary = This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10. The buffers used in this lysis step yield varying results [11, 13, 15, 16] ; however, unlike 224 previous studies [11] , this study found that AVL buffer alone was successfully able to fully 225 inactivate up to 5 log10 of virus from three different primary isolates of SARS-CoV-2. Previous 234 studies have shown that GITC-lysis buffers are able to inactivate SARS-CoV-2 samples [11, 12] ; 235 however, the addition of Triton-X may be necessary for complete inactivation [11] . Therefore, formaldehyde treatment does not appear to be a 247 solution for increased molecular SARS-CoV-2 testing; however, it does remain a viable alternative 248 for sample inactivation or disinfection. cache = ./cache/cord-268034-7id7sfsu.txt txt = ./txt/cord-268034-7id7sfsu.txt === reduce.pl bib === id = cord-267613-hsc2x36j author = Dittmar, Mark title = Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 7558 sentences = 452 flesch = 50 summary = Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. Previous studies found that the antiviral drug remdesivir, which was developed against the RNA-dependent RNA polymerase of Ebola virus, was also active against SARS-CoV-2 in vitro, with promising results in clinical trials (5) (6) (7) . Both cepharanthine and tetrandrine were previously shown to have antiviral activity against the human coronavirus OC43 and in recent studies on SARS-CoV-2 in Vero cell screens (13, 62, 63) . Strikingly, the activities of all of these drugs is similar in the two cell lines suggesting the same target and mechanism-of-action and that Cyclosporine would block SARS-CoV-2 in diverse infected tissues in vivo. cache = ./cache/cord-267613-hsc2x36j.txt txt = ./txt/cord-267613-hsc2x36j.txt === reduce.pl bib === id = cord-267971-xgwmda8e author = Tan, Shing Cheng title = Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients date = 2020-04-07 pages = extension = .txt mime = text/plain words = 2851 sentences = 204 flesch = 57 summary = Background: Numerous groups have reported the clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) cases; however, the data remained inconsistent. Understanding the clinical and 46 epidemiological characteristics of the disease is important for informing public health decision 47 making, which would enable improvement of surveillance and effective planning of treatment. (4) found that the male-to-female ratio among the 81 patients included 56 was close to 1:1, indicating that both genders were equally susceptible to 57 the World Health Organization (WHO) has declared COVID-19 a global pandemic and the 58 contagion shows no sign of slowing down (13). In this 60 study, a systematic review and pooled analysis was performed to characterize the clinical and 61 epidemiological features of COVID-19 patients. In this work, a systematic review and pooled analysis was 137 performed to combine data from 69 previous reports, in order to yield a more accurate summary 138 of the clinical and epidemiological characteristics of COVID-19 patients. cache = ./cache/cord-267971-xgwmda8e.txt txt = ./txt/cord-267971-xgwmda8e.txt === reduce.pl bib === id = cord-268140-s5lailkp author = Atal, Shubham title = IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising Therapy? date = 2020-06-13 pages = extension = .txt mime = text/plain words = 5174 sentences = 258 flesch = 41 summary = Considering the proven role of cytokine dysregulation in causing this hyperinflammation in the lungs with IL-6 being a key driver, particularly in seriously ill COVID-19 patients, it is crucial to further explore selective cytokine blockade with drugs like the IL-6 inhibitors tocilizumab, sarilumab, and siltuximab. Considering the proven role of cytokine dysregulation in serious COVID-19 and interleukin (IL)-6 being the key driver of this hyperinflammation, which can cause multi-organ failure, a series of clinical trials with IL-6 inhibitors like tocilizumab, sarilumab and siltuximab are underway. Another Italian Phase II open-label trial (NCT04315480) with tocilizumab 8 mg/kg single dose is being conducted in patients with severe multifocal interstitial pneumonia due to COVID-19 to evaluate its role in the virus-induced cytokine storm, in blocking deterioration of lung function or even promoting a rapid improvement of clinical conditions, preventing naso-tracheal intubation and/or death [51] . cache = ./cache/cord-268140-s5lailkp.txt txt = ./txt/cord-268140-s5lailkp.txt === reduce.pl bib === id = cord-267782-4pjfnund author = Lan, Fan-Yun title = Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA date = 2020-10-30 pages = extension = .txt mime = text/plain words = 5048 sentences = 272 flesch = 46 summary = Therefore, we conducted this study aiming to investigate: 1) SARS-CoV-2 infection rate, transmission and exposure risks among grocery retail employees, 2) their use of personal protective equipment (PPE) and perception on COVID-19 and 3) their mental health state during the COVID-19 pandemic. ► This is the first study to demonstrate the significant asymptomatic infection rate, exposure risks and associated psychological distress of grocery retail essential workers during the pandemic, which supports the policy recommendations that employers and government officials should take actions on implementing preventive strategies and administrative arrangements, such as methods to reduce interpersonal contact, repeat and routine SARS-CoV-2 employee testing, to ensure the health and safety of essential workers. 13 14 In fact, a pioneering study conducted in the Table 3 Characteristics of retail essential employees in a single grocery store in Massachusetts, USA presented for SARS-CoV-2, the virus causing COVID-19, RT-PCR assay testing by Patient Health Questionnaire-9 (PHQ-9) screening score for depression These are in contrast to positions mainly dealing with consumer goods or the environment, such as stocker, backroom, receiving and maintenance. cache = ./cache/cord-267782-4pjfnund.txt txt = ./txt/cord-267782-4pjfnund.txt === reduce.pl bib === id = cord-268065-mxvbbkc4 author = Wei, Maoti title = Epidemiology of Coronavirus Disease 2019 (COVID-19) Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-05-18 pages = extension = .txt mime = text/plain words = 4409 sentences = 246 flesch = 57 summary = Shortly after the virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the epidemic of coronavirus disease 2019 (COVID-19) broke out, and an information storm occurred. Based on information of SARS, Middle East respiratory syndrome (MERS), and COVID-19, the components of the epidemic (the sources, the routes of infection, and the susceptible population) will be discussed, as well as the role of natural and social factors involved. S ince the end of 2019, a novel coronavirus, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID19) , appeared in Wuhan, Hubei Province, China. Recent results showed that SARS-CoV-2 persists longer with a higher viral load and peaks later in the respiratory tissue of patients with severe disease; this phenomenon highlights the need for the prevention and control of the epidemic. Some experts commented that people with mild or asymptomatic SARS-CoV-2 infection were not identified by epidemic prevention measures, thus accelerating the spread of the disease. cache = ./cache/cord-268065-mxvbbkc4.txt txt = ./txt/cord-268065-mxvbbkc4.txt === reduce.pl bib === id = cord-268169-xry3nhzt author = Couturier, Aymeric title = Indirect effects of severe acute respiratory syndrome coronavirus 2 on the kidney in coronavirus disease patients date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3084 sentences = 175 flesch = 47 summary = Among patients hospitalized for novel coronavirus disease (COVID-19), between 10 and 14% develop an acute kidney injury and around half display marked proteinuria and haematuria. Collapsing glomerulopathy is a peculiar form of focal segmental glomerulosclerosis (FSGS) [6] that has been well characterized in patients infected by human immunodeficiency virus (HIV) type 1 [7] . In order to better characterize the relationship between SARS-CoV-2 infection and collapsing FSGS, we performed an RT-PCR assay on the renal tissue specimen from Patient 1. Our results are in line with a recent inpress report that describes the presence of collapsing glomerulopathy and tubulointerstitial lesions in living COVID-19 patients of African origin, homozygous for APOL1 risk allele G1 and evidence of chronicity on kidney biopsy [12] . Although our findings do not definitely rule out a direct infection of kidney cells by SARS-CoV-2, COVID-19-related collapsing FSGS appears to be related to a viral-induced inflammatory response against a peculiar genetic background. cache = ./cache/cord-268169-xry3nhzt.txt txt = ./txt/cord-268169-xry3nhzt.txt === reduce.pl bib === id = cord-268329-apl6n6jl author = Antunes, Douglas Eulálio title = Will cases of leprosy reaction increase with COVID-19 infection? date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1508 sentences = 79 flesch = 45 summary = The coronavirus disease 2019 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus (betaCoV)-emerged for the first time as an outbreak of pneumonia in Wuhan, China, and it is now spreading to several countries around the world [1] . Some studies of SARS-CoV-2 infection have reported the presence of a cytokine storm syndrome and a subgroup of patients who progressed to severe forms of the disease, expressing a pro-inflammatory profile in plasma with IL-2, IL-7, TNF-α, and others as significant complications, such as occurs in T1R [10, 11] . In both reactions, we warn of the possible effect that COVID-19 infection may have on the number of cases of these immunological events because the presence of infection is an important risk factor for triggering leprosy reactions [8] . Another disturbing factor, which may contribute to the susceptibility of those affected by leprosy reactions, are the treatments implemented during these events that interfere with the inflammatory response of these patients. cache = ./cache/cord-268329-apl6n6jl.txt txt = ./txt/cord-268329-apl6n6jl.txt === reduce.pl bib === id = cord-267960-r5m7o9dp author = Hourdel, Véronique title = Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4466 sentences = 211 flesch = 51 summary = In this study, we aimed at implementing an ampliconbased sequencing approach to obtain SARS-CoV-2 consensus genomes directly from clinical specimens, adaptable into the field conditions, with the two easily manageable nextgeneration sequencers, the nanopore MinION and the Illumina iSeq100 TM system. Sputum specimens and respective isolates RNA extracts were tested with the SARS-CoV-2 real-time RdRP gene duplex reverse transcription (RT)-PCR developed by the French National Reference Center for Respiratory Viruses and the real-time E gene RT-PCR from the Charité protocol (see WHO Coronavirus disease COVID-19 technical guidance: Laboratory testing for 2019-nCoV in humans, available from https://www.who. Globally, using our amplicon-based approach, combined with the MinION platform, we were able to obtain the near fulllength genome of the studied viral specimens in around 8 h, from samples to sequences data. Viral consensus genomic sequences were rapidly and easily obtained for the two SARS-CoV-2 clinical specimens and their respective isolates, by using the two different sequencing platforms, MinION and iSeq100 TM system. cache = ./cache/cord-267960-r5m7o9dp.txt txt = ./txt/cord-267960-r5m7o9dp.txt === reduce.pl bib === id = cord-268211-egy8rgtl author = Barrasa, Helena title = SARS-Cov-2 in Spanish Intensive Care: Early Experience with 15-day Survival In Vitoria date = 2020-04-09 pages = extension = .txt mime = text/plain words = 2681 sentences = 181 flesch = 53 summary = Methods: We identified patients from the two public hospitals in Vitoria who were admitted to ICU with confirmed infection by SARS-CoV-2. Conclusion: This early experience with SARS-CoV-2 in Spain suggests that a strategy of right oxygenation avoiding non-invasive mechanical ventilation was life-saving. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring mechanical ventilation. Because of mortality reports in Wuhan [5] suggesting a close association, we assessed correlation between plasma procalcitonin at ICU admission and 7-day mortality. Our findings suggest that an oxygenation strategy emphasising optimisation of oxygenation, intubation based on clinical criteria of hyperventilation and avoiding ventilator-induced lung injury associated with non-invasive mechanical ventilation would be life-saving in a significant proportion of patients. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring prolonged mechanical ventilation. cache = ./cache/cord-268211-egy8rgtl.txt txt = ./txt/cord-268211-egy8rgtl.txt === reduce.pl bib === id = cord-268049-7xqln70d author = Montrief, Tim title = COVID-19 respiratory support in the emergency department setting date = 2020-08-08 pages = extension = .txt mime = text/plain words = 5197 sentences = 337 flesch = 45 summary = DISCUSSION: Patients presenting with SARS-CoV-2 infection are at high risk for acute respiratory failure requiring airway management. [29] [30] [31] [32] Based on currently available evidence, the WHO states that "HFNC and NIV systems with good interface fitting do not create widespread dispersion of exhaled air and therefore should be associated with [a] low risk of airborne transmission." 15 The risk of respiratory pathogen transmission when using HFNC is subject to a variety of factors, including the duration of support, maximal flow rate, patient sneezing or coughing, cannula fit, and patient cooperation. 35 Many guidelines, including those by Australian and New Zealand Intensive Care Society (ANZICS), the WHO, and the Surviving Sepsis Campaign recommend the use of HFNC in COVID-19 patients presenting with acute hypoxemic respiratory failure unresponsive to conventional oxygen therapy. 20 Notably, the SCCM guidelines on the management of critically ill patients with COVID-19 recommend "a trial of NIV with close monitoring and shortinterval assessment for worsening of respiratory failure" if HFNC is not available and there is no urgent indication for intubation. cache = ./cache/cord-268049-7xqln70d.txt txt = ./txt/cord-268049-7xqln70d.txt === reduce.pl bib === id = cord-268074-9mact9br author = Bi, Qifang title = Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study date = 2020-04-27 pages = extension = .txt mime = text/plain words = 5307 sentences = 238 flesch = 51 summary = We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We characterise differences in demographics and severity between cases identified through symptom-based surveillance and monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterise SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval, and observed reproductive number (R). This study is, to our knowledge, the first analysis of SARS-CoV-2 transmission and COVID-19 natural history based on a large primary dataset of cases and close contacts, for which the mode of surveillance (ie, symptom-based versus contact-based) was sufficiently documented and RT-PCR testing was nearly universal. Between Jan 14 and Feb 12, 2020, the Shenzhen CDC confirmed 391 cases of SARS-CoV-2 infection ( of 87) than were those detected through contact-based surveillance (tables 1, 2). cache = ./cache/cord-268074-9mact9br.txt txt = ./txt/cord-268074-9mact9br.txt === reduce.pl bib === id = cord-268340-xwj8ge5t author = Ozaki, Masayuki title = Reducing Aerosol Generation During Ventilator Weaning in a Coronavirus Disease 2019 Patient Using a Supraglottic Airway: A Case Report date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1034 sentences = 79 flesch = 47 summary = Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. We conducted a weaning procedure from mechanical ventilation in advance of emergence from sedation in a patient with COVID-19 by exchanging the tracheal tube to a supraglottic airway (SGA), which is associated with fewer coughs. Reducing patients' coughing cases-anesthesia-analgesia.org a & a pRaCtICe and avoiding this aerosol-generating procedure during tracheal extubation may reduce occupational infection. To reduce the risk of occupational infection with SARS-CoV-2 at the time of weaning from mechanical ventilation, we propose replacing the tracheal tube with an SGA such as i-gel before emergence from sedation to reduce environmental distribution of the virus. cache = ./cache/cord-268340-xwj8ge5t.txt txt = ./txt/cord-268340-xwj8ge5t.txt === reduce.pl bib === id = cord-268324-86a0n0dc author = Charitos, Ioannis A title = Special features of SARS-CoV-2 in daily practice date = 2020-09-26 pages = extension = .txt mime = text/plain words = 6117 sentences = 279 flesch = 42 summary = The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia. cache = ./cache/cord-268324-86a0n0dc.txt txt = ./txt/cord-268324-86a0n0dc.txt === reduce.pl bib === id = cord-268098-71g1w1mc author = Beckman, M. F. title = Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date = 2020-09-15 pages = extension = .txt mime = text/plain words = 4203 sentences = 316 flesch = 49 summary = Visualization of protein-protein interaction networks was completed using STRINGv11.0 [31] program by testing different confidence levels to identify ontologies of biological significance for the significant pathways associated with comorbidities. Possible comorbidity significant associated gene sets/pathways were checked for quality control by generating Quantile-Quantile (Q-Q) plots using observed quantiles and residual Z-scores of genes within the gene set, based on the MAGMAv1.07b publicly available Rv3.6.2 script (posthoc_qc_107a.r) [32, 33] . . https://doi.org /10.1101 was used to test the top 250 human mRNA gene expressions for each comorbidity based on available human data using NCBI GEO[39] , by only including comorbidities that had significant pathways identified by MAGMAv1.07b and VEP STRING analyses. For each comorbidity, human mRNA gene expression data corresponding to average log-fold change (aLFC) were formatted for clustering of genes identified by MAGMAv1.07b and VEP and subsequently matched to STRING protein-protein interactions. cache = ./cache/cord-268098-71g1w1mc.txt txt = ./txt/cord-268098-71g1w1mc.txt === reduce.pl bib === id = cord-268085-vpzrk8u7 author = Mandal, Amrendra title = Gastrointestinal Manifestations in COVID-19 Infection and Its Practical Applications date = 2020-06-21 pages = extension = .txt mime = text/plain words = 3106 sentences = 163 flesch = 43 summary = This outbreak is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is also commonly known as COVID-19. We reviewed the mechanisms, clinical manifestation, impact on pre-existing liver diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. This article aims to review the mechanisms, clinical manifestation, impact on pre-existing digestive diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. Clinical characteristics of hospitalized patients with SARS-CoV-2 and hepatitis B virus co-infection Exploring the mechanism of liver enzyme Abnormalities in patients with novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. cache = ./cache/cord-268085-vpzrk8u7.txt txt = ./txt/cord-268085-vpzrk8u7.txt === reduce.pl bib === id = cord-268071-ow2aijmj author = Pachetti, Maria title = Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4449 sentences = 236 flesch = 53 summary = Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. Naturally occurring mutations in critical residues for drug efficacy can lead to drug resistance phenomena, with a significant loss in the binding affinity of these molecules to the RdRp. We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. Among all mutation sites analyzed, RdRp mutant is particularly interesting given that the enzyme is directly involved in viral replication and its fidelity determines the mutagenic capabilities of SARS-CoV-2. In the present work we have compared the SARS-CoV-2 reference genome to those exported from the GISAID database with the aim of gaining important insights into virus mutations, their occurrence over time and within different geographic areas. cache = ./cache/cord-268071-ow2aijmj.txt txt = ./txt/cord-268071-ow2aijmj.txt === reduce.pl bib === id = cord-268283-eja8fkwv author = Iftikhar, Hafsa title = Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach date = 2020-06-09 pages = extension = .txt mime = text/plain words = 4811 sentences = 235 flesch = 45 summary = In this regard, several recent studies have been conducted using computational methods to screen libraries of approved drugs or drug-like molecules to identify potential inhibitors of different viral proteins, particularly, RdRp and 3CL-protease [13] [14] [15] [16] [17] . Here, we applied a computer aided drug discovery approach by targeting three important enzymes (RdRp, 3CL-protease and helicase) of SARS-CoV-2 and identified three FDA-approved drugs and three other drug-like molecules as potential therapeutics. In this study, we used a virtual screening based strategy to identify already approved drugs or drug-like molecules that can bind to any of the three key viral enzymes, 3CL-protease, RdRp and helicase, and potentially inhibit the function of these enzymes. In our studies we performed computational screening by targeting three important enzymes of SARS-CoV-2 including RdRp, 3CL-protease and helicase, to identify not only the already approved drugs for repurposing but also the drug candidates or lead structures that can be chemically modified to develop potential drugs. cache = ./cache/cord-268283-eja8fkwv.txt txt = ./txt/cord-268283-eja8fkwv.txt === reduce.pl bib === id = cord-268193-xwptzgvl author = Wang, Tzong-Luen title = Establishing a clinical decision rule of severe acute respiratory syndrome at the emergency department() date = 2003-12-29 pages = extension = .txt mime = text/plain words = 3218 sentences = 157 flesch = 50 summary = Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Methods: According to the clinical characteristics and initial laboratory findings of 175 suspected cases defined by the WHO criteria (20 confirmed as cases of SARS) in 3 university teaching hospitals in Taipei between March 1 and April 20, 2003, the scoring system for SARS was designed by multivariate analysis and stepwise logistic regression as the simple arithmetic sum of point values assigned to 7 parameters. cache = ./cache/cord-268193-xwptzgvl.txt txt = ./txt/cord-268193-xwptzgvl.txt === reduce.pl bib === id = cord-268335-mfcjldu3 author = Dimeglio, Chloé title = Children are protected against SARS-CoV-2 infection date = 2020-05-20 pages = extension = .txt mime = text/plain words = 556 sentences = 38 flesch = 56 summary = Chloé Dimeglio 1,2* , Jean-Michel Mansuy 2 , Sandrine Charpentier 3,4 , Isabelle Claudet 4,5 , and Jacques Izopet 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. As infants and young children infected with respiratory tract viruses are particularly at risk of hospitalization (3) the paucity of pediatric patients with COVID-19 has raised many questions for clinicians, epidemiologists and scientists. The study previously published by Lancet Infectious Disease has important implications for the clinical management of these patients and the social distancing needed to prevent virus transmission (4). The abovementioned study has found that children are susceptible to SARS-CoV-2 infection, but rarely display any physical signs of the disease. The most important finding emerging from this analysis is the clear evidence that children are less susceptible to SARS-CoV-2 infection than adults. While children have been regarded as facilitators of virus transmission, we now need to identify the mechanism which protects them, at least partially, against SARS-CoV-2 infection. cache = ./cache/cord-268335-mfcjldu3.txt txt = ./txt/cord-268335-mfcjldu3.txt === reduce.pl bib === id = cord-268224-5tbb8df1 author = Di Gioacchino, Andrea title = The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date = 2020-08-27 pages = extension = .txt mime = text/plain words = 7109 sentences = 412 flesch = 62 summary = Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven, in the N protein coding region, both by the viral codon bias and by the high value of the CpG content, leading to a loss in CpG. Finally we use a model of the viral gene evolution under human host pressure, characterized by the CpG force, to study synonymous mutations, and in particular those which change CpG content, observed since the SARS-CoV-2 entered the human population (Sec. 2.3). We first compute the global force on CpG dinucleotides for SARS-Cov-2 and a variety of other viruses from the Coronaviridae family affecting humans or other mammals (bat, pangolin), see Fig. 1a , using as null model the nucleotide usage calculated from human genome [22] (see Methods Sec. 4.2) 1 . cache = ./cache/cord-268224-5tbb8df1.txt txt = ./txt/cord-268224-5tbb8df1.txt === reduce.pl bib === id = cord-268468-036i1082 author = Asif, Muhammad title = The role of biosensors in COVID-19 outbreak date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3204 sentences = 189 flesch = 43 summary = In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. In this outbreak, three different types of diagnosis tests are being used including (i) chest CT scan along with clinical indications, (ii) RNA detection using RT-PCR assay and (iii) lateral flow assays, full automatic chemiluminescence method, enzyme-linked immunosorbent assay (ELISA) for the determination of antibodies [5] . In this review, we have summarized the biosensor based technologies which are able to detect SARS-CoV-2 effectively. The peptide monolayer was successfully coated on SPR biosensor and further functionalized with virus nucleocapsid protein which was finally able to detect SARS-CoV-2 antibodies at nanomolar level. The sensing aptitude of the biosensor was evaluated employing antigen protein, self-cultured virus, and nasopharyngeal swab samples taken from people infected with COVID-19 pneumonia. cache = ./cache/cord-268468-036i1082.txt txt = ./txt/cord-268468-036i1082.txt === reduce.pl bib === id = cord-268406-3v309r41 author = Grajewski, Rafael S. title = A missing link between SARS‐CoV‐2 and the eye?: ACE2 expression on the ocular surface date = 2020-06-12 pages = extension = .txt mime = text/plain words = 668 sentences = 53 flesch = 53 summary = We applaud Lange et al.1 for their extensive efforts to analyse entry factors for severe acute respiratory syndrome coronavirus (SARS-CoV-2) into conjunctival epithelial cells covering the ocular surface, which is an important albeit controversially discussed issue1,2 . A missing link between SARS-CoV-2 and the eye?: ACE2 expression on the ocular surface Before incubation with the primary antibody, tissue was subjected to heat-induced epitope retrieval using Target Retrieval Solution pH 9 (catalog #S2367; Dako). The location of ACE2 expression at the ocular surface enables direct contact of SARS-CoV-2 with conjunctival cells, raising the question how often this occurs and if protective mechanisms of tears and conjunctiva might prevent conjunctivitis to happen more frequently. 6 In summary, our results provide an important addition to the results of Lange et al 1 and other works by clearly demonstrating specific ACE2 expression in conjunctival epithelial cells, providing the receptor for direct entry of SARS-CoV-2. cache = ./cache/cord-268406-3v309r41.txt txt = ./txt/cord-268406-3v309r41.txt === reduce.pl bib === id = cord-268339-jxm69ndw author = Karamitros, Timokratis title = SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date = 2020-03-28 pages = extension = .txt mime = text/plain words = 3755 sentences = 217 flesch = 51 summary = We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify smalland large-scale intra-host variations in the viral genome. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays. Here, we explore intra-host genomic variants and low-frequency polymorphic quasispecies in Next Generation Sequencing (NGS) data derived from patients infected by SARS-CoV-2. The S1 subunit consists of a signal peptide and the NT and receptor binding (RB) domains, with the latter sharing only 40% amino acid identity with other SARS-related CoVs. Our analysis revealed that similarly to other genomic regions, the S1 subunit hosts many low-frequency SNVs, characterized by higher density compared to the rest of the S gene sequence (Figure 1-E) . cache = ./cache/cord-268339-jxm69ndw.txt txt = ./txt/cord-268339-jxm69ndw.txt === reduce.pl bib === id = cord-268390-npuvodd4 author = Rehman, Aziz ul title = The role of primary and secondary bio-molecules in optical diagnosis of pandemic COVID-19 outbreak date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1277 sentences = 64 flesch = 42 summary = • Raman and fluorescence signature of ACE-2 specific proteins is the basis for real time detection of COVID-19. This letter to the editor aims to introduce primary and secondary biomarkers whose reflectance, transmittance and fluorescence signals can be used for optical diagnosis of COVID-19 to the scientific community and persuade to build portable, cost effective, label free and real time optical devices for its detection. Keeping in view the epidemic nature of COVID-19, we need early stage, cost effective, real time diagnosis and portable devices to detect this disease so that treatment can be started to save the vulnerable population. Similarly, nucleic acid and protein bound coenzymes molecules like NADH, FAD have their own specific fluorescence biomarkers when excited with UV-A light [13] and can be used for label free detection of COVID-19 on early stages employing portable optical detection systems. cache = ./cache/cord-268390-npuvodd4.txt txt = ./txt/cord-268390-npuvodd4.txt === reduce.pl bib === id = cord-268144-maa8c4a4 author = Zhang, Yuan title = Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization date = 2007-02-17 pages = extension = .txt mime = text/plain words = 2548 sentences = 129 flesch = 44 summary = The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. As an envelope glycoprotein, the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) plays a key role in the viral entry and neutralization (Bartlam et al., 2005; Denison, 2004; Lau and Peiris, 2005; Xu and Gao, 2004; Zhu, 2004) . Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association cache = ./cache/cord-268144-maa8c4a4.txt txt = ./txt/cord-268144-maa8c4a4.txt === reduce.pl bib === id = cord-268254-1mg7a17c author = Liu, Li title = High neutralizing antibody titer in intensive care unit patients with COVID-19 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 3475 sentences = 200 flesch = 53 summary = This study determined the seroprevalence of 733 non-COVID-19 individuals from April 2018 to February 2020 in the Hong Kong Special Administrative Region and compared the neutralizing antibody (NAb) responses of eight COVID-19 patients admitted to the intensive care unit (ICU) with those of 42 patients not admitted to the ICU. In this study, the absence of NAb in the serum of over 733 HKSAR residents indicates that SARS-CoV-2 is unlikely to have spread silently in Hong Kong before its emergence in COVID-19 patients. During our manuscript revision, a preprint paper indicated that SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease [26] . Neutralizing antibodies responses to SARS-CoV-2 in COVID-19 inpatients and convalescent patients. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. cache = ./cache/cord-268254-1mg7a17c.txt txt = ./txt/cord-268254-1mg7a17c.txt === reduce.pl bib === id = cord-268425-xg8xnjf9 author = DiNicolantonio, James J. title = Harnessing Adenosine A2A Receptors as a Strategy for Suppressing the Lung Inflammation and Thrombotic Complications of COVID-19: Potential of Pentoxifylline and Dipyridamole date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3891 sentences = 251 flesch = 41 summary = 5 Importantly, neutrophils, whose activation and transit into lung interstitial tissue and alveolar space is a key mediator of the respiratory distress syndrome associated with COVID-19, are highly responsive to the functionally suppressive effects of A2AR, as are the endothelial cells whose activation attracts and enables transendothelial passage of activated neutrophils. Most studies with DIP have focused on its platelet-stabilizing effects -which presumably could provide some protection from SARS-CoV-2's pro-thrombotic effects -but experimental studies also show that DIP can act on neutrophils to suppress superoxide production, adhesion to endothelial cells, and, in a mouse model of anti-phospholipid syndrome (a sometime feature of COVID-19), NETosis formation. 79 Supplemental glucosamine may likewise up-regulate the type 1 interferon responses to viruses, while exerting anti-inflammatory effects that render it protective in rodent models of sepsis and lung inflammation induced by LPS or cigarette smoke. cache = ./cache/cord-268425-xg8xnjf9.txt txt = ./txt/cord-268425-xg8xnjf9.txt === reduce.pl bib === id = cord-268483-joiajgs4 author = Shah, Vibhuti Kumar title = Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past date = 2020-08-07 pages = extension = .txt mime = text/plain words = 10644 sentences = 477 flesch = 43 summary = As there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like SARS, MERS, HIV, ebola, malaria, and tuberculosis are being given to COVID-19 patients, and clinical trials for many such drugs have already begun. An ELISA-based time kinetics study to detect the COVID-19 specific humoral immune response showed that the patients produced IgM and IgG antibodies that did not cross-react with other human coronaviruses except SARS-CoV. A case study on pediatric patients reports that 5 out of 6 children showed a protective humoral response, with neutralizing IgG and IgM antibodies targeting the N and S-RBD proteins of SARS-CoV-2 (65) . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice cache = ./cache/cord-268483-joiajgs4.txt txt = ./txt/cord-268483-joiajgs4.txt === reduce.pl bib === id = cord-268206-ino9srb6 author = Hamed, Manal A. title = An overview on COVID-19: reality and expectation date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6067 sentences = 330 flesch = 46 summary = Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. In the current SARS-COV-2 pandemic, Wu and McGoogan (2020) showed that patients with chronic diseases, including diabetes, were at higher risk for severe COVID-19 infection and mortality. The former (S) is the wild type which is milder while the latter (L) is the novel one which resulted in high binding affinity between SARS-COV-2 virus with angiotensin-converting enzyme 2 receptor in human cells. The use of convalescent plasma was recommended before as an important treatment during outbreaks of Ebola virus, Middle East respiratory syndrome coronavirus, SARS-COV-1, H5N1 avian influenza, and H1N1 influenza (Zhou et al. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. cache = ./cache/cord-268206-ino9srb6.txt txt = ./txt/cord-268206-ino9srb6.txt === reduce.pl bib === id = cord-268501-z4oztgi0 author = Palatnik-de-Sousa, Clarisa B. title = What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date = 2020-08-26 pages = extension = .txt mime = text/plain words = 6331 sentences = 280 flesch = 46 summary = In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . cache = ./cache/cord-268501-z4oztgi0.txt txt = ./txt/cord-268501-z4oztgi0.txt === reduce.pl bib === id = cord-268453-87b298uk author = Ibáñez, Sebastián title = Hydroxychloroquine and chloroquine in COVID-19: should they be used as standard therapy? date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3500 sentences = 150 flesch = 48 summary = In the absence of a vaccine and specifically designed antivirals, the medical community has proposed the use of various previously available medications in order to reduce the number of patients requiring prolonged hospitalizations, oxygen therapy, and mechanical ventilation and to decrease mortality from coronavirus disease 2019 (COVID-19). HCQ was, in vitro, at least as effective as chloroquine in inhibiting SARS-CoV-2 infection, although it should be noted that studies on its mechanisms of action are not as extensive as with CQ [30] . The evidence for the use of hydroxychloroquine or chloroquine in COVID-19 is not good so far, not only because of the negative results of most of the studies but also because of their design, when publishing results of a very low number of patients, when reporting favorable results but without having a control group that allows comparison, when choosing results for which it will be very difficult to find significant differences, such as mortality, or for which their clinical relevance is uncertain. cache = ./cache/cord-268453-87b298uk.txt txt = ./txt/cord-268453-87b298uk.txt === reduce.pl bib === id = cord-268330-mo5myrz4 author = Gentile, Pietro title = Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4618 sentences = 239 flesch = 47 summary = title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia [1] , reported exceptional outcomes in improved pulmonary functional activity, into seven patients who suffered Coronavirus Disease 2019 (COVID19) after an intravenous administration of clinical-grade mesenchymal stem cells (MSCs). [1] , 7 SARS-CoV-2 positive patients, with COVID-19 pneumonia (study group), showed a great improving pulmonary functional activity after an intravenous administration of clinical-grade MSCs [1] . The rationale of the present work is to suggest the possibility to use autologous or allogeneic adipose-derived stromal stem cells (ASCs) (in the last case after decellularization and with good manufacturing practices -GMPlaboratory approval) intravenously or directly through a ventilation mask (aerosol). In the last case, it could be possible to donate human adipose tissue to GMP, EMA, or FDA Laboratory or bank to isolate SVFs and ASCs and re-infuse the cellular product obtained, as certified drugs, in COVID-19 patients. cache = ./cache/cord-268330-mo5myrz4.txt txt = ./txt/cord-268330-mo5myrz4.txt === reduce.pl bib === id = cord-268561-vq1uhj5i author = da Silva, Severino Jefferson Ribeiro title = Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19 date = 2020-08-04 pages = extension = .txt mime = text/plain words = 9916 sentences = 594 flesch = 47 summary = 11 The causative agent was identified as a novel CoV, eventually named SARS-CoV-2, and the respiratory syndrome associated with the infection was designated as coronavirus disease-2019 (COVID-19) by the World Health Organization (WHO). In direct tests, the clinical sample is examined directly for the presence of particles, virus antigens, or viral nucleic acids, whereas indirect methods detect the serological response against the infection (Figure 2 ). 11 Culture-based methods for SARS-CoV-2 detection have been used in research and public health laboratories in different parts of the world, but virus isolation is not recommended as a routine diagnostic procedure because it has low sensitivity, it is time-consuming, and it requires BSL-3 containment. 11 In addition to unequivocally confirming the diagnosis of a SARS-CoV-2 infection, regular sequencing of a percentage of patient samples from clinical cases can be used to monitor changes in the viral genome over time and trace transmission patterns. cache = ./cache/cord-268561-vq1uhj5i.txt txt = ./txt/cord-268561-vq1uhj5i.txt === reduce.pl bib === id = cord-268661-a56u5e2o author = Nadeau, S. A. title = The origin and early spread of SARS-CoV-2 in Europe date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5407 sentences = 289 flesch = 55 summary = Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions. Here, we fit a phylodynamic model with geographic structure to full-length SARS-CoV-2 genomes to (i) estimate the early patterns of SARS-CoV-2 spread into and across Europe, (ii) weigh genomic evidence for competing hypotheses about the geographic origin of the predominant A2a lineage in Europe, (iii) report on the epidemiological parameters, and (iv) compare the rate of new cases arising from within-region transmission versus migration during the early epidemic. cache = ./cache/cord-268661-a56u5e2o.txt txt = ./txt/cord-268661-a56u5e2o.txt === reduce.pl bib === id = cord-268476-3lxsh1zz author = Skoog, Hunter title = Tracheotomy in the SARS‐CoV‐2 pandemic date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1504 sentences = 91 flesch = 44 summary = The severe acute respiratory syndrome (SARS)‐CoV‐2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. The severe acute respiratory syndrome (SARS)-CoV-2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. Our priorities in establishing these guidelines included: optimal patient care, protection of medical personnel, minimizing further spread of the virus and preservation of important resources (ICU beds, ventilators, and PPE). Due to the paucity of data regarding the current SARS-CoV-2 epidemic, the literature from the SARS epidemic of In Canada, 43% of cases occurred in health care workers as a result of AGPs. 1,2 One instance involved a difficult intubation of a patient who was under investigation for SARS. There are multiple reports 3,4 of safely performing tracheotomy on patients with SARS without infecting health care workers. cache = ./cache/cord-268476-3lxsh1zz.txt txt = ./txt/cord-268476-3lxsh1zz.txt === reduce.pl bib === id = cord-268653-mje0rysp author = Chen, Miaomiao title = Changes in physiology and immune system during pregnancy and coronavirus infection: a review date = 2020-10-16 pages = extension = .txt mime = text/plain words = 2922 sentences = 167 flesch = 47 summary = We explained why pregnant women are susceptible to coronavirus in terms of their adaptive changes in physiology and immune system during pregnancy, and described the associations between maternal clinical symptoms, perinatal outcomes and coronavirus infections. Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been labeled as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) on January 30, 2020 [1] [2] . Pregnant women are suspected to aspiration pneumonia because of the decreased sphincter tone in the lower esophagus, which is thought to be associated with high levels of progesterone [30] , which can reduce both pro-inflammatory and cytotoxic T cell responses. As mentioned earlier, pregnant women in their first and third trimester of pregnancy are both at the pro-inflammatory state, and the cytokine storm induced by SARS-CoV-2 in these periods may exacerbate the severity of inflammatory J o u r n a l P r e -p r o o f state, following the obstetric adverse outcomes. cache = ./cache/cord-268653-mje0rysp.txt txt = ./txt/cord-268653-mje0rysp.txt === reduce.pl bib === id = cord-268760-31i0mpvn author = Zhang, Qian title = Anosmia and Ageusia as the Only Indicators of Coronavirus Disease 2019 (COVID-19) date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2109 sentences = 125 flesch = 54 summary = There is currently a lack of published case reports describing COVID-19 patients with the sole symptoms of anosmia and ageusia in the United States of America. This case report details a 60year-old woman with the chief complaint of right-sided headache along with anosmia and ageusia but was eventually found to be SARS-COV-2 positive. The most common COVID-19 symptoms include fever (43.8% on initial presentation and 88.7% during hospitalization), cough (67.8%), nasal congestion (4.8%), nausea or vomiting (5.0%), and diarrhea (3.8%) based on a research study of 1099 patients from China. Our patient had a very low clinical suspicion of COVID-19 infection, as she was afebrile along with no respiratory symptoms despite having anosmia and ageusia in the setting of headache caused by trigeminal neuralgia. Awareness of a possible COVID-19 infection should be raised in patients with the sole presentation of anosmia and ageusia despite the lack of published case reports or research findings on its exact mechanisms of action. cache = ./cache/cord-268760-31i0mpvn.txt txt = ./txt/cord-268760-31i0mpvn.txt === reduce.pl bib === id = cord-268370-kfjujs4z author = Huang, Yu-Tung title = Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study date = 2009-05-31 pages = extension = .txt mime = text/plain words = 3292 sentences = 173 flesch = 48 summary = title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study The purpose of this study was to explore the effect of the SARS outbreak on hospitalization for chronic ambulatory-care-sensitive conditions (ACSCs) in Taiwan. Methods We applied a population-based interrupted time series study design and used the time series auto-regressive integrated moving-average model to compare the actual and predicted admission rates of seven selected chronic ACSCs. The analyses were based on National Health Insurance hospital inpatient claims data from 1997 to 2003. We applied a population-based interrupted time series design to compare the actual with predicted hospitalization for ACSCs after the SARS outbreak, to identify conditions with increased hospitalization that might have been caused by untimely or inappropriate primary care during the SARS outbreak. We found that the actual hospitalization rates for six selected ACSCs, particularly respiratory conditions, were significantly lower than their predicted rates for at least 1 month during the SARS period. cache = ./cache/cord-268370-kfjujs4z.txt txt = ./txt/cord-268370-kfjujs4z.txt === reduce.pl bib === id = cord-268572-uhak283t author = Woo, Marcel S. title = Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients date = 2020-07-11 pages = extension = .txt mime = text/plain words = 1304 sentences = 92 flesch = 51 summary = title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients However, few details about the effect of individual immunotherapies have been reported, which could instruct us about the immunological control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we report on two individuals with underlying neuroimmunological diseases who were under stable rituximab therapy-a B cell-depleting monoclonal antibody [6, 7] -when confirmed COVID-19 developed. Patient 2 was a 68-year-old female with neuromyelitis optica spectrum disorder (NMOSD, diagnosed 2014, EDSS 6.0), who was directly admitted to our intensive care unit (ICU) on March 29th, 2020 with progressive respiratory failure and infection of the urinary tract. She had a B cell count of 25/µL (Ref. 80-500/µL, Supplementary Table 2) at the day of admission and tested negative for SARS-CoV-2-specific antibodies (3.5 AU/mL; Ref. In summary, we report on two patients who developed COVID-19 while under treatment with rituximab due to neuroimmunological diseases. Antibody responses to SARS-CoV-2 in patients with COVID-19 cache = ./cache/cord-268572-uhak283t.txt txt = ./txt/cord-268572-uhak283t.txt === reduce.pl bib === id = cord-268894-amfv3z2y author = Nguyen-Contant, Phuong title = S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4632 sentences = 269 flesch = 56 summary = Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Approximately one-third of non-SARS-CoV-140 2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N 141 proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs ( Figure 1A ). In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E 192 and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-193 exposed subjects, consistent with the higher levels of serum IgG against these antigens ( Figure 2E -194 2H) . cache = ./cache/cord-268894-amfv3z2y.txt txt = ./txt/cord-268894-amfv3z2y.txt === reduce.pl bib === id = cord-268540-wrjzr3ws author = Park, You Jeong title = Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date = 2020-08-13 pages = extension = .txt mime = text/plain words = 16363 sentences = 868 flesch = 45 summary = A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . cache = ./cache/cord-268540-wrjzr3ws.txt txt = ./txt/cord-268540-wrjzr3ws.txt === reduce.pl bib === id = cord-268484-hf4zflsy author = Davanzo, Riccardo title = Breast feeding at the time of COVID-19: do not forget expressed mother’s milk, please date = 2020-04-06 pages = extension = .txt mime = text/plain words = 726 sentences = 49 flesch = 57 summary = In the context of the coronavirus disease (COVID-19) prevention and cure, a remarkable issue, particularly in maternity hospitals, is represented by the risk of mother to child transmission by a breastfeeding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive woman. Moreover, Chinese colleagues who have recently coped with COVID-19 just do not consider the breast feeding option, nor the use of expressed breast milk for newborn infants. Thus, the author seems to implicitly endorse the use of expressed mother's milk, although in the flow chart contained in the online supplementary appendix, he contradictorily warns just against breast feeding for all SARS-CoV-2-positive mothers at delivery. In conclusion, protocols applied in maternity hospitals to prevent COVID-2 should consider, as far as possible, the promotion of breast feeding, without disregarding the feasible option of expressing mother's milk. cache = ./cache/cord-268484-hf4zflsy.txt txt = ./txt/cord-268484-hf4zflsy.txt === reduce.pl bib === id = cord-268750-kox3uah2 author = Wong, S. F. title = Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures date = 2004-01-08 pages = extension = .txt mime = text/plain words = 1584 sentences = 87 flesch = 55 summary = When the operations were performed, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga., USA) had not yet prepared guidelines for the prevention of SARS transmission during Caesarean sections. For the three Caesarean sections performed on mothers with SARS, the number of healthcare workers was limited to a minimum, with only those personnel essential to carry out the operation, neonatal resuscitation, and cleanup being involved (i.e., 2 senior obstetricians, 2 senior neonatologists, 1 senior anaesthetist, 1 theatre assistant, a team of 4 senior midwives, and 2 cleansing staff). The participating HCWs wore appropriate PPE according to the hospital's guidelines prior to the arrival of the patient from the intensive care unit. In conclusion, the procedures described above were sufficient to prevent our healthcare workers from contracting SARS while performing these very high-risk operations. cache = ./cache/cord-268750-kox3uah2.txt txt = ./txt/cord-268750-kox3uah2.txt === reduce.pl bib === id = cord-268740-ldz5366v author = Sun, Mei title = Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2389 sentences = 132 flesch = 47 summary = title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients We propose anal swabs as the potentially optimal specimen for SARS-CoV-2 detection for evaluation of hospital discharge of COVID-19 patients. In this study, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of a few cured patients, which challenges the current standards for discharge and termination of compulsory isolation for COVID-19 patients. In summary, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of several cured patients. • SARS-CoV-2 detection is positive in anal swabs but negative in throat swabs and sputum swabs of a few discharged patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. cache = ./cache/cord-268740-ldz5366v.txt txt = ./txt/cord-268740-ldz5366v.txt === reduce.pl bib === id = cord-268645-5op2m7pu author = Wu, Zhiqiang title = Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date = 2015-08-11 pages = extension = .txt mime = text/plain words = 5949 sentences = 277 flesch = 49 summary = However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . cache = ./cache/cord-268645-5op2m7pu.txt txt = ./txt/cord-268645-5op2m7pu.txt === reduce.pl bib === id = cord-268755-13xmmin1 author = Meltzer, Martin I. title = Multiple Contact Dates and SARS Incubation Periods date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1522 sentences = 85 flesch = 50 summary = Many severe acute respiratory syndrome (SARS) patients have multiple possible incubation periods due to multiple contact dates. I present a simple spreadsheet-based method that uses multiple contact dates to calculate the possible incubation periods of SARS. I present a simple method that allows a simulation of the frequency distribution, including confidence intervals, of the possible incubation periods (in days) for SARS. The method can also be used to calculate when infectious persons are most likely to have transmitted SARS to susceptible persons, even when multiple days of possible transmission exist. Simulation of frequency distribution of incubation period of severe acute respiratory syndrome. Many of the patients included in the database had multiple possible incubation periods (see Table) , resulting in the confidence intervals displayed for each day. The method readily "accepts" data in which patients have multiple possible incubation periods. cache = ./cache/cord-268755-13xmmin1.txt txt = ./txt/cord-268755-13xmmin1.txt === reduce.pl bib === id = cord-268970-uz7q6z2f author = Ott, Isabel M. title = Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date = 2020-08-04 pages = extension = .txt mime = text/plain words = 2790 sentences = 181 flesch = 58 summary = Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes. Following RNA extraction 9 and RT-qPCR 10 testing for SARS-CoV-2 on the day of saliva collection 2 , the remaining sample volumes (n=20) were aliquoted and stored at -80°C, room temperature (recorded as ~19°C) and 30°C. Moreover, SARS-CoV-2 RNA remained relatively stable in saliva samples left for up to 25 days at room temperature (~19°C; Ct increase of 0.027, 95% CI: -0.019, 0.071) ( Figure 1B) . cache = ./cache/cord-268970-uz7q6z2f.txt txt = ./txt/cord-268970-uz7q6z2f.txt === reduce.pl bib === id = cord-268895-m97zsodx author = Duan, Ping title = Safety considerations during return to work in the context of stable COVID-19 epidemic control: an analysis of health screening results of all returned staff from a hospital date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3217 sentences = 161 flesch = 45 summary = In total, 4729 returned staff from Zhongnan Hospital of Wuhan University, Wuhan, China were examined for COVID-19, and the basic information, radiology and laboratory test results were obtained and systematically analysed. The 4729 returned staff, all from Zhongnan Hospital of Wuhan University, underwent comprehensive SARS-CoV-2 screening, including SARS-CoV-2 nucleic acid test, antibody detection, chest CT scan, body temperature measurement and recording of infection characteristics. Among 172 people with abnormal first physical examination results, we observed that 170 cases (98.84%) were negative in the first SARS-CoV-2 nucleic acid test, but one of which was positive by RT-PCR at the time of reexamination. In summary, we efficiently identified asymptomatic infections through extensive health screening of all returned staff from a hospital in a short period of time, combined with a variety of inspection methods (including nucleic acid test for SARS-CoV-2, antibody detection and chest CT scan), and emphasising the presence of asymptomatic infections in the general population. cache = ./cache/cord-268895-m97zsodx.txt txt = ./txt/cord-268895-m97zsodx.txt === reduce.pl bib === id = cord-268492-0rbmqarx author = Alberer, Martin title = Cats and kids: how a feline disease may help us unravel COVID-19 associated paediatric hyperinflammatory syndrome date = 2020-09-02 pages = extension = .txt mime = text/plain words = 1533 sentences = 79 flesch = 44 summary = The RCPCH and CDC have published a case definition and scientists refer to this novel but still very rare severe clinical condition in children as "paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2" (PIMS-TS). While reflecting on this syndrome and its characteristic features, some interesting similarities come to mind when comparing the clinical course of PIMS-TS cases and the specific features of a disease in cats called feline infectious peritonitis (FIP) caused by the feline coronavirus (FCoV), an alphacoronavirus [2] . On this note, it would be of great interest to see whether mutations in the viral genome, particularly in regions affecting the S-protein of SARS-CoV-2, could lead to a change in cell tropism enabling the virus to more effectively infect and replicate within human monocytes/macrophages subsequently leading to the clinical picture of PIMS-TS. cache = ./cache/cord-268492-0rbmqarx.txt txt = ./txt/cord-268492-0rbmqarx.txt === reduce.pl bib === id = cord-269001-m4mpcoab author = Zullo, Fabrizio title = COVID-19 Antibody Testing in Pregnancy date = 2020-05-18 pages = extension = .txt mime = text/plain words = 586 sentences = 38 flesch = 54 summary = 1, 2 Almost all patients with COVID-19 infection test positive for 23 antiviral immunoglobulin-G (IgG) within about 10-20 days after symptom onset (Figure 1 ), but the 24 clinical value of antibody testing has not yet been completely elucidated, either in non-pregnant or 25 even more pregnant patients. Testing pregnant women for antibody response to COVID-19 may have different advantages, 33 including identifying: 1. Women still at risk for COVID-19 infection (e.g. IgM and IgG negative). Those tested positive to either IgM 69 or IgG at the rapid combined antibody test, have NP swab offered, and the outpatient appointment is 70 postponed, as shown in Figure 2B . In summary, we recommend testing for antibody response to SARS-CoV-2 for pregnant women Development and Clinical Application of A Rapid IgM-IgG Combined Antibody 111 Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-269001-m4mpcoab.txt txt = ./txt/cord-269001-m4mpcoab.txt === reduce.pl bib === id = cord-268718-tt07cwrf author = Tan, Heng Wee title = Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date = 2020-06-30 pages = extension = .txt mime = text/plain words = 6346 sentences = 400 flesch = 52 summary = 54 Virus infectivity study has indicated that the SARS-CoV-2 is able to utilize ACE2 of human, Chinese horseshoe bats, civet, and pig but was not able to use mouse ACE2. The roles of ACE2 expression in SARS-CoV-2 pathogenesis and human COVID-19 susceptibility are largely unknown. B, ACE2 expression in lung cancer patients with different smoking histories analyzed using similar methods as described previously 106 other symptoms in addition to respiratory symptoms, suggesting that SARS-CoV-2 could perhaps infect other organs (Figure 3 ). 118 In addition to sputum, SARS-CoV-2 RNA has been detected in the stools of a COVID-19 patient, 119 F I G U R E 3 Tissue distribution of angiotensin-converting enzyme 2 (ACE2) expression and potential COVID-19 susceptibility. Expression of elevated levels of proinflammatory cytokines in SARS-CoV-infected ACE2 + cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS cache = ./cache/cord-268718-tt07cwrf.txt txt = ./txt/cord-268718-tt07cwrf.txt === reduce.pl bib === id = cord-269130-zsem29ss author = Lingappan, K. title = Understanding the age divide in COVID-19: why are children overwhelmingly spared? date = 2020-07-01 pages = extension = .txt mime = text/plain words = 3121 sentences = 163 flesch = 45 summary = The differences in the clinical course are highlighted by the lack of progression of the SARS-CoV-2 infection beyond mild symptoms in a majority of children, whereas in adults the disease progresses to acute lung injury and an acute respiratory distress syndrome (ARDS)-like phenotype with high mortality. The pathophysiological mechanisms leading to decreased lung injury in children may involve the decreased expression of the mediators necessary for viral entry into the respiratory epithelium and differences in the immune system responses in children. On the other hand, the heightened immune response to the virus in many adult patients can lead to the worsening of lung disease with SARS-CoV-2 infection (37) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice cache = ./cache/cord-269130-zsem29ss.txt txt = ./txt/cord-269130-zsem29ss.txt === reduce.pl bib === id = cord-268939-ws74xprt author = Ozoner, Baris title = Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic date = 2020-05-28 pages = extension = .txt mime = text/plain words = 5138 sentences = 391 flesch = 46 summary = The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. [5] [6] [7] In neurosurgery practice, intensive modifications were required in surgical scheduling, administration of inpatient and outpatient clinics, management of emergency cases, and even academic & educational activities. 26 A recent study from Wuhan City, China reported that some severe COVID-19 patients developed neurologic manifestations, such as acute cerebrovascular diseases (5.7%), and impaired consciousness (14.8%). 76, 80 Also, a patient with a mass lesion in the sellar region that underwent endonasal endoscopic surgery in Neurosurgery Department, Tongji Medical College, Wuhan City, China was diagnosed with COVID-19 after surgery, and disease was confirmed in 14 healthcare professionals in the same clinic afterwards. cache = ./cache/cord-268939-ws74xprt.txt txt = ./txt/cord-268939-ws74xprt.txt === reduce.pl bib === id = cord-268886-mpceglk1 author = Bourne, T. title = ISUOG Consensus Statement on rationalization of gynecological ultrasound services in context of SARS‐CoV‐2 date = 2020-04-08 pages = extension = .txt mime = text/plain words = 3086 sentences = 198 flesch = 46 summary = Given the challenges of the current coronavirus (SARS-CoV-2) pandemic and to protect both patients and ultrasound providers (physicians, sonographers, allied professionals), the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) has compiled the following expert-opinion-based guidance for the rationalization of ultrasound investigations for gynecological indications. While these are extremely troublesome conditions, patients and healthcare providers should consider delaying ultrasound evaluation until resolution of the COVID-19 pandemic. Although associated symptoms (mass effect leading to pressure, bladder/bowel symptoms) are not usually acute or life-threatening, they may signal advanced ovarian cancer, in which case, it may be reasonable to recommend that ultrasound assessment should be carried out by an expert soon and appropriate treatment commenced. • Abdominopelvic 'mass' without associated symptoms (SOON or LATER): the healthcare provider may consider delaying the ultrasound evaluation until the resolution of the pandemic if there is a known history of pelvic pathology, such as leiomyoma. cache = ./cache/cord-268886-mpceglk1.txt txt = ./txt/cord-268886-mpceglk1.txt === reduce.pl bib === id = cord-269009-0i2bvt77 author = D’Souza, Rohan title = A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID‐19 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3295 sentences = 205 flesch = 36 summary = Should patients develop coronavirus disease (COVID‐19) pneumonia requiring hospital admission for treatment of hypoxia, the risk for thromboembolic complications increases greatly. 2 As pregnancy is a prothrombotic state, the possibility of an increased risk of thrombosis in pregnant women with COVID-19 has become an area of concern, and a number of international organiPatients with severe COVID-19 may be at risk for pulmonary thromboembolic complications through at least two distinct mechanisms -immunothrombosis and hospital-associated venous thromboembolism (VTE). 12 A recent study of patients with severe COVID-19 demonstrated a correlation between IL-6 and fibrinogen levels, 3 further supporting the theory that massive activation of the acute phase response, with increased production of coagulation factors, appears to be the predominant prothrombotic mechanism in COVID-19. A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID-19 cache = ./cache/cord-269009-0i2bvt77.txt txt = ./txt/cord-269009-0i2bvt77.txt === reduce.pl bib === id = cord-269213-tsm6zoe3 author = Slaughter, Laura title = A framework for capturing the interactions between laypersons’ understanding of disease, information gathering behaviors, and actions taken during an epidemic date = 2005-01-30 pages = extension = .txt mime = text/plain words = 8435 sentences = 449 flesch = 52 summary = This paper provides a description of a methodological framework designed to capture the inter-relationships between the lay publics' understanding of health-related processes, information gathering behaviors, and actions taken during an outbreak. This methodological framework, based on narrative analysis, is a tool for learning about how laypersons use information to build representations of an epidemic situation and how the results of this process influence their decisions to act. For example, the interview texts also result in a list of information needs expressed by the lay public concerning an outbreak as well as a general list of actions taken for SARS prevention. The arrangement of the interview into time periods (before, during, and upcoming events related to the epidemic) facilitates the data analysis when looking at the interactions and influences between informa-tion received, lay understanding, and actions taken. cache = ./cache/cord-269213-tsm6zoe3.txt txt = ./txt/cord-269213-tsm6zoe3.txt === reduce.pl bib === id = cord-269114-mdsiv6tr author = Pattabiraman, C. title = Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka date = 2020-07-11 pages = extension = .txt mime = text/plain words = 3141 sentences = 203 flesch = 62 summary = A comprehensive study of circulating variants of the virus in Iceland, which included over 580 complete genomes in combination with epidemiological information (travel history and contact tracing) revealed that while the initial importation of the virus was from China and Southeast Asia subsequent importations were from different parts of Europe 8 . While these studies have added valuable information on circulating lineages of SARS-CoV-2 in India, they have not comprehensively linked genomic data with epidemiological information. Here we report 47 full-length SARS-CoV-2 genome sequences obtained from individuals who tested positive for the virus by RT-PCR and present an analysis of epidemiological information combined with genomic data to elucidate the introduction and spread of the virus in the state. The data from this study using a combination of genomic epidemiology and contact tracing provides evidence for multiple introductions of the virus into the state, with sustained local transmission. cache = ./cache/cord-269114-mdsiv6tr.txt txt = ./txt/cord-269114-mdsiv6tr.txt === reduce.pl bib === id = cord-268827-qwcbvtna author = Ibanez, Agustin title = COVID-19 in older people with cognitive impairment in Latin America date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1465 sentences = 88 flesch = 49 summary = 9 If SARS-CoV-2 can impair proteostasis through ORF8 binding and cause dysregulated endoplasmic reticulum protein traffick ing, then α-synuclein could aggregate uncontrollably. The COVID-19 pandemic in Latin America and Caribbean countries (LACs) has failed to capture the attention exiguous. 7 Many hospitals in LACs have inadequate protective equipment and there is scarce support for health-care workers who become sick. implemented control measures, is third highest among LACs. The public health conditions in these countries are complex and pose unique challenges; one underlying explanation for the surge in cases might be a large informal economy, in which workers need to leave their house every day to clean other households or to stand, for instance, at crowded traffic corners to sell their goods or shine shoes. For instance, with 20% of over 11 000 health workers in Mexico ill with COVID-19-one of the highest rates in the world-hospital staffing is and attract the resources necessary to control it. cache = ./cache/cord-268827-qwcbvtna.txt txt = ./txt/cord-268827-qwcbvtna.txt === reduce.pl bib === id = cord-269071-jbxbknyt author = Giorgianni, Andrea title = Transient acute-onset tetraparesis in a COVID-19 patient date = 2020-06-02 pages = extension = .txt mime = text/plain words = 785 sentences = 44 flesch = 42 summary = Since the main organic, infectious, and immunomediated causes of acute-onset flaccid tetraparesis have been excluded from the anamnestic, neuroradiological, and laboratory data recorded, we can hypothesize that SARS-CoV-2 had a promoter role in the onset of the tetraparetic clinical presentation. A first-reported case of postinfective acute transverse myelitis has been described in the literature [2] , suggesting that spinal cord can be the target of SARS-CoV-2 infection. Therefore, we can deduce that the neuro-shocking and neuro-irritative effect of SARS-CoV-2, in addition to hyperglycemic neuro-stress, can have a promoting and synergistic role in the manifestation of the tetraparetic transient acute clinic. As described in this case, the neuroinvasive and neurotrophic potential of SARS-CoV-2 could have a synergistic and promoter role in determining neuro-irritative and neuro-shocking effects, without necessarily causing neuroimaging evident organic damage. Acute myelitis after SARS-CoV-2 infection: a case report cache = ./cache/cord-269071-jbxbknyt.txt txt = ./txt/cord-269071-jbxbknyt.txt === reduce.pl bib === id = cord-269021-juh2qkm0 author = Bai, Zhihua title = The Rapid Assessment and Early Warning Models for COVID-19 date = 2020-04-01 pages = extension = .txt mime = text/plain words = 4599 sentences = 226 flesch = 48 summary = Human beings have experienced a serious public health event as the new pneumonia (COVID-19), caused by the severe acute respiratory syndrome coronavirus has killed more than 3000 people in China, most of them elderly or people with underlying chronic diseases or immunosuppressed states. In the case of a gradually improved infectious disease surveillance system, the research on forecasting and early warning of epidemics based on models has become the focus of the public health system. In response to the current epidemic of SARS-CoV-2, many researchers have developed mathematical models with varying degrees of complexity, aiming to assess the capacity of pathogen transmission and which interventions are most likely to be effective (Fig. 2) . Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven Modelling analysis of the early outbreak cache = ./cache/cord-269021-juh2qkm0.txt txt = ./txt/cord-269021-juh2qkm0.txt === reduce.pl bib === id = cord-268817-wx96wwpg author = Karp, Donna Grace title = Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3600 sentences = 182 flesch = 47 summary = Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. 6 In this study, we report the development and validation of a highly sensitive and specific SARS-CoV-2 total antibody assay on a Hamilton MicroLab STAR liquid-handling platform (Fig. 1) , based on the ADAP STAR assay-ready workstation. The successful implementation of the automated high-throughput ADAP SARS-CoV-2 total antibody assay solution as described herein can help meet the surge in demand for COVID-19 infection testing. To evaluate the assay's sensitivity, 57 serum specimens from COVID-19 patients were subjected to the ADAP SARS-CoV-2 total antibody analysis. cache = ./cache/cord-268817-wx96wwpg.txt txt = ./txt/cord-268817-wx96wwpg.txt === reduce.pl bib === id = cord-268809-plgip4h6 author = Bielecki, Michel title = Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2609 sentences = 170 flesch = 56 summary = We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. To our knowledge, it is unknown if lowering the viral inoculum during infection with SARS-CoV-2 or altering the mode of infection by physical means can affect the clinical course of the disease. Here, we present an outbreak at a Swiss Army Base with two very similar groups infected prior and after the implementation of stringent social distancing and hygiene A c c e p t e d M a n u s c r i p t measures (SDHMs). We describe an outbreak of SARS-CoV-2 infections in young, healthy soldiers in two spatially separated groups with almost identical baseline characteristics but different clinical courses. cache = ./cache/cord-268809-plgip4h6.txt txt = ./txt/cord-268809-plgip4h6.txt === reduce.pl bib === id = cord-269025-2j37561h author = Pratelli, Annamaria title = Canine coronavirus inactivation with physical and chemical agents date = 2007-05-21 pages = extension = .txt mime = text/plain words = 6155 sentences = 325 flesch = 53 summary = The methods for CCoV inactivation could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure of researchers to pathogens during routine laboratory procedures. To examine the ability of heat to inactivate CCoV, 500 lL aliquots of virus samples were incubated in duplicate in a 15 mL polypropylene conical tube (Falcon, Becton Dickinson Labware) for increasing periods of time at three different temperatures: +56°C, +65°C and +75°C. To examine formaldehyde and glutaraldehyde inactivation of CCoV, aliquots of virus and aldehyde samples, each at two different dilutions, were incubated at +4°C, +25°C and +37°C, respectively, for up to 3 days. Despite the differences in stability during heat treatment at 56°C between SARS-CoV and CCoV, the several methods of CCoV inactivation, including inhibition of viral entry, could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure to the virus through unsafe laboratory practices. cache = ./cache/cord-269025-2j37561h.txt txt = ./txt/cord-269025-2j37561h.txt === reduce.pl bib === id = cord-268935-4obwu75u author = Lepak, Alexander J. title = Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) date = 2020-10-12 pages = extension = .txt mime = text/plain words = 963 sentences = 57 flesch = 45 summary = title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) Adoption of the infection control bundle described may be helpful to prevent SARS-CoV-2 spread within healthcare institutions. Notably, repeated inpatient testing of individuals was, in general, directed toward those undergoing procedures, those in whom signs or symptoms suggested possible COVID-19, those with acute changes in status requiring intensive care unit (ICU) or intermediate (IMC) care, and/or based on provider judgment. For the single positive inpatient without a prior history of SARS-CoV-2, chart review revealed that this adult patient lived in a community setting, had mild symptoms (sinus congestion, eye pain, and cough) that started 10 days prior to admission, and was self-isolating at home. We believe that infection was present from community exposure prior to admission; therefore, we did not find any laboratory-confirmed cases suggestive of possible nosocomially acquired SARS-CoV-2 infection despite a substantial inpatient population with and without COVID-19. cache = ./cache/cord-268935-4obwu75u.txt txt = ./txt/cord-268935-4obwu75u.txt === reduce.pl bib === id = cord-269202-re2djjrc author = Sapino, Anna title = The autopsy debate during the COVID-19 emergency: the Italian experience date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1140 sentences = 63 flesch = 48 summary = "in patients dying with SARS-CoV-2 infection, the autopsies can confirm laboratory and radiological findings and can contribute to an accurate diagnosis and to a better understanding of mechanisms of the disease." In the meantime, the SIAPC Board accepted to collaborate with the Scientific Society of Hospital Forensic Medicine of the National Health System (COMLAS) to produce a joint document, which was available on the SIAPEC web site on March 22 [2] . In addition, in cases of autopsies without apparent SARS-CoV-2 infection, we recommend (i) to discuss with the clinicians the reason why the post-mortem examination is requested; (ii) and if available, to perform nasal-oropharyngeal swabs on corpses This article is part of the Topical Collection on Quality in Pathology * Mattia Barbareschi mattia.barbareschi@apss.tn.it within 2 h of death to assess the presence of SARS-CoV-2 infection to implement the safety measures [3] . cache = ./cache/cord-269202-re2djjrc.txt txt = ./txt/cord-269202-re2djjrc.txt === reduce.pl bib === id = cord-269143-8j3m03gc author = Brindisi, Giulia title = Pills to think about in allergic rhinitis children during COVID‐19 era date = 2020-07-05 pages = extension = .txt mime = text/plain words = 632 sentences = 39 flesch = 45 summary = Allergic rhinitis (AR) is a common pediatric disease, that involves up to the 25% of children worldwide. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection in children is uncommon and often asymptomatic or mild. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children is uncommon and often asymptomatic or mild 1 . So far, we do not have data demonstrating a higher risk in the development of Coronavirus disease-19 (COVID-19) in allergic children, except for those with uncontrolled symptoms. This could help to detect affected children even with mild symptoms and limit SARS-CoV2 transmission. Instead it can be continued, as usual, in allergic children without clinical symptoms of COVID-19 and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Intranasal corticosteroids in allergic rhinitis in COVID-19 infected patients: An ARIA-EAACI statement cache = ./cache/cord-269143-8j3m03gc.txt txt = ./txt/cord-269143-8j3m03gc.txt === reduce.pl bib === id = cord-268622-3jireyep author = Babadaei, Mohammad Mahdi Nejadi title = The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets date = 2020-06-01 pages = extension = .txt mime = text/plain words = 4071 sentences = 247 flesch = 53 summary = Researchers have reported some useful information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leading to CoV disease 2019 (COVID-19). Indeed, these outcomes have elucidated the principal mechanism that the oral cavity is basically in higher risk to SARS-CoV-2 infection and showed a piece of conformation for the ongoing inhibition approach in clinical implementation It has been also revealed that in addition to causing fever and respiratory symptoms, COVID-19 resulted in gastrointestinal disorders including diarrhoea, vomiting and some pains in abdominal part . Figure 2C also shows the SARS-CoV-2 infection-related sensitive organs which can explain about the non-respiratory symptoms identified in COVID-19 patients . According to a report from China, the fatality is observed in older people as well as patients with hypertension, chronic lung disease, diabetes, and CVDs. One of the most likely mechanisms by which COVID-19 can causes lung and cardiac damage is through the SARS-CoV-2 binding to ACE2 receptors. cache = ./cache/cord-268622-3jireyep.txt txt = ./txt/cord-268622-3jireyep.txt === reduce.pl bib === id = cord-269470-emzr3dzb author = Menéndez, Cintia A. title = Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease date = 2020-09-11 pages = extension = .txt mime = text/plain words = 4729 sentences = 252 flesch = 56 summary = In addition, the authors considered the potential mutability of residues belonging to the M pro catalytic site and explained that the development of drug resistance associated with the natural evolution of M pro could wipe out efforts that target this protein for COVID-19 treatment. Apart from these residues, ebselen bound at both sites shows the lowest  factor values; however, at this specific point, this system exhibits as high flexibility as M pro -apo protein (Fig. 3A , green line). A total of more than 6 s of classical MD simulations of SARS-CoV-2 M pro -apo state and M pro -ebselen complex were run using the AMBER18 (29) simulation package (3 s, ebselen as a molecular probe; 2.4 s, shear strain analysis; 100 ns, water structure and flux analysis; 990 ns, free energy analysis). cache = ./cache/cord-269470-emzr3dzb.txt txt = ./txt/cord-269470-emzr3dzb.txt === reduce.pl bib === id = cord-268874-ldja6aa4 author = Park, Sun Hee title = Personal Protective Equipment for Healthcare Workers during the COVID-19 Pandemic date = 2020-06-24 pages = extension = .txt mime = text/plain words = 6754 sentences = 330 flesch = 44 summary = Although no study has conclusively linked SARS-CoV-2 transmission to contaminated environmental surfaces, indirect contact with fomites is considered a possible route based on the evidence of heavy environmental contamination in healthcare settings, objects used by COVID-19 patients [26, 27] , and the finding that the virus remains viable on plastic surfaces for as long as 3 days [28] . Initially, the Korea Center for Disease Control and Prevention (KCDC) guidelines recommended coveralls with shoe covers for contact precautions, goggles/face shields for eye protection, N95 or equivalent respirators for respiratory protection, and powered airpurifying respirators (PAPRs) when AGPs are performed [46] . PPE for droplet and contact precautions, such as surgical masks with eye protection, gowns, and gloves, are recommended for HCWs in contact with suspected or confirmed COVID-19 patients, and N95 or equivalent respirators should to be worn by HCWs whenever AGPs are performed. cache = ./cache/cord-268874-ldja6aa4.txt txt = ./txt/cord-268874-ldja6aa4.txt === reduce.pl bib === id = cord-269283-jm18lj5t author = Uddin, Md Bashir title = Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2736 sentences = 169 flesch = 50 summary = Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. As the outbreak of the 2019 novel coronavirus (COVID-19 [SARS-CoV-2]) is expanding rapidly, analysis of epidemiological data of COVID-19 is necessary to explore the measures of burden associated with the disease and to simultaneously gather information on determinants and interventions. Moreover, the conservancy study of immunogenic peptides predicted from the SARS-CoV-2 proteins was also compared against other human coronavirus strains (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1 and MERS-CoV). Cross-checked conservancy analysis of COVID-19 antigenic epitopes with SARS-CoV proteins showed that conservancy when crosschecked with other coronaviruses, including BufCoV-HKU26 of Bangladesh origin, was not significant ( Table 3) . cache = ./cache/cord-269283-jm18lj5t.txt txt = ./txt/cord-269283-jm18lj5t.txt === reduce.pl bib === id = cord-269087-f9hyntvf author = Li, X. title = A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19 date = 2020-04-04 pages = extension = .txt mime = text/plain words = 4280 sentences = 236 flesch = 49 summary = Results: We included 25 published literature references related to the epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. The risk factors which may suggest severe or critical progress for children are: Fast respiratory rate and/or; lethargy and drowsiness mental state and/or; lactate progressively increasing and/or; imaging showed bilateral or multi lobed infiltration, pleural effusion or rapidly expending of lesions in a short period of time and/or; less than 3 months old or those who underly diseases. To help better understand how it would affect children and what is the latest specific clinical and research finding on children with it, we provide a mini-review based on 25 literature references covering the fields of epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. According to the current literature on the pediatric cases, children confirmed with COVID-19 mostly had good prognosis, with considerably less severe to critical progress (5.9%) as compared to adult patients (18.5%). cache = ./cache/cord-269087-f9hyntvf.txt txt = ./txt/cord-269087-f9hyntvf.txt === reduce.pl bib === id = cord-269275-b7xxk48t author = Tang, Xiaojia title = Neurological manifestations in COVID-19 and its possible mechanism date = 2020-09-27 pages = extension = .txt mime = text/plain words = 4631 sentences = 260 flesch = 44 summary = SARS-CoV-2 has been reported to be associated with Guillain-Barré syndrome, rhabdomyolysis, acute cerebrovascular disease, central nervous system infections and other neurological diseases. Four formal reports have described neurological problems in SARS patients, including polyneuropathy [35] , myopathy and rhabdomyolysis [36] , large artery ischemic stroke [37] and central nervous system infections [38] . In a study by Mao et al., 214 patients diagnosed with COVID-19 were enrolled, and six (2.80%) of them developed acute cerebrovascular disease (five cases of ischemic stroke and one case of cerebral hemorrhage). Strokes are not uncommon in critically ill patients with multiple comorbidities, so SARS-CoV-2 infections in humans may increase the risk of stroke. Since some COVID-19 patients have complained of headaches, nausea etc, care providers should be alert for central nervous system infections caused by SARS-CoV-2 if such patients also exhibit symptoms such as a fever, epilepsy and disturbances of consciousness. cache = ./cache/cord-269275-b7xxk48t.txt txt = ./txt/cord-269275-b7xxk48t.txt === reduce.pl bib === id = cord-269206-160ddfsc author = Ceylan, Rahmiye Figen title = Historical evidence for economic effects of COVID-19 date = 2020-06-04 pages = extension = .txt mime = text/plain words = 4555 sentences = 268 flesch = 51 summary = Yet, the contagious diseases having global effects had forgotten long time ago even if there appeared some recent encounters in the past 20 The differentiating features of COVID-19 or SARS-COV2 from the recent encounters are its geographical dispersion in terms of contagion and its causalities. In an earlier attempt to comment on prospective COVID-19 effects, Barro and his friends estimated growth of national income and consumption expenditures of 42 countries between 1901 and 1929 on human capital loss due to the WWI. Due to changing labour market composition and economic conditions during and after the influenza, both productivity and overall income had declined and savings and investment potential were affected negatively. Confirming previous research on SARS, Lionello [26] indicated that rising social fear and reduction in social contact resulted in reduced supplies and reduced labour demand specifically in the services sector between 20 and 70%. Especially, shrinking services and industries facing lower labour supplies and reducing demand are expected to downsize all economic structures. cache = ./cache/cord-269206-160ddfsc.txt txt = ./txt/cord-269206-160ddfsc.txt === reduce.pl bib === id = cord-269289-6uog10j4 author = Mabillard, Holly title = Electrolyte Disturbances in SARS-CoV-2 Infection date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5684 sentences = 289 flesch = 44 summary = These include additional respiratory complications (pulmonary fibrosis -reported in 21% of those hospitalised with SARS-CoV-2 9 months post-discharge in one study 3 ) 7 , cardiovascular complications (acute cardiac injury (7% 8 ), cardiomyopathy (1/3 patients 9 ), cardiac tamponade, heart failure, dysrhythmias (17% 8 ) and venous thromboembolic events (20% 10 )) 11 , neurological complications (myopathy, acute stroke (5.7% of those with severe infection 12 ), Guillain-Barre syndrome (0.4% hospitalised patients 11 ) and encephalopathy) 13 , acute liver and/or pancreatic injury (29% and 17% respectively in one cohort) 14 , cytokine storm syndrome, septic shock, DIC, diarrhoea, Kawasaki-like disease 14 and renal complications (acute tubular injury, rhabdomyolysis, proteinuria, secondary focal segmental glomerulosclerosis and possible renin-angiotensinaldosterone system activation) 15 . The study reported that the degree of hypokalaemia correlated with severity of SARS-CoV-2 symptoms and they suggested that hypokalaemia can be difficult to correct as seen in two patients because the renal potassium wasting persists until clinical recovery from the virus. cache = ./cache/cord-269289-6uog10j4.txt txt = ./txt/cord-269289-6uog10j4.txt === reduce.pl bib === id = cord-269101-7altkx5u author = Jakhmola Mani, Ruchi title = Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study date = 2020-10-28 pages = extension = .txt mime = text/plain words = 4934 sentences = 270 flesch = 50 summary = title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study An amazing herb, Nigella sativa, having antiviral, antihypertensive, antidiarrhoeal, analgesics, and anti-bacterial properties, needs to be explored for its efficacy against SARS-CoV-2, the causative agent of COVID-19. sativa bioactive constituents were similar to the pathways followed in SARS-COV-2 pathology, like renin-angiotensin system, kidney functions, regulation of blood circulation, blood vessel diameter, etc. To study the effectiveness of N.sativa against SARS-CoV-2, protein interactions studies were carried out for receptors predicted via swiss target prediction for this plant's bioactive constituents, to understand their beneficial effect on SARS-CoV-2 in humans. sativa bioactive constituents by protein interaction and docking studies as well as proven their binding efficiency with ACE2 receptor and now this can be studied further in wet lab and be formulated as the medicine to combat the deadly disease COVID-19. cache = ./cache/cord-269101-7altkx5u.txt txt = ./txt/cord-269101-7altkx5u.txt === reduce.pl bib === id = cord-269408-6qncy0nd author = Khonyongwa, Kirstin title = Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date = 2020-10-13 pages = extension = .txt mime = text/plain words = 4131 sentences = 233 flesch = 54 summary = AIMS: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a Teaching Hospital NHS Trust in London, England. Factors studied included the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity (DRP), selfreported COVID-19 sickness absence among hospital staff, total hospital bed occupancy, community incidence of COVID-19 (CIC19) and the change in incidence of other significant hospital-acquired bacterial infections (HAB). When a HA-COVID-19 case was identified, actions included staff refresher training for correct PPE usage, rapid transfer of patients to a COVID-19 positive cohort ward, deep cleaning (washing walls and carpets) followed by increasing the cleaning frequency until no further transmission was seen (defined as no new symptom onset within 2 weeks of last known case and in haematology and geriatrics a CNTS was tested for SARS-CoV-2 RNA twice weekly for all contacts up to 2 weeks from last positive case regardless of symptoms). cache = ./cache/cord-269408-6qncy0nd.txt txt = ./txt/cord-269408-6qncy0nd.txt === reduce.pl bib === id = cord-269187-lt0uo7q3 author = Saha, Indrajit title = Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date = 2020-07-11 pages = extension = .txt mime = text/plain words = 2305 sentences = 142 flesch = 58 summary = Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. Based on this information, they developed an SNP-based PCR assay to show differentiation between To address the above facts, we have analyzed publicly available 566 Indian complete or near complete SARS-CoV-2 genomes in order to find the mutation points as substitution, deletion J o u r n a l P r e -p r o o f and insertion. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs. The genomic sequences of Indian SARS-CoV-2 virus was collected from Global Initiative on Sharing All Influenza Data (GISAID) 1 in fasta format on 11th June 2020. cache = ./cache/cord-269187-lt0uo7q3.txt txt = ./txt/cord-269187-lt0uo7q3.txt === reduce.pl bib === id = cord-269568-vwkawh6x author = Ten Hulzen, Richard D. title = Impact of Hearing Loss and Universal Face Masking in the COVID-19 Era. date = 2020-08-03 pages = extension = .txt mime = text/plain words = 1084 sentences = 65 flesch = 48 summary = Abbreviations: COVID-19 = coronavirus disease 2019; dB = decibel; ED = Emergency Department; FFP = filtering face piece; FM = frequency modulation; Hz = Hertz; ICU = Intensive Care Unit; N95 mask = a particulate-filtering face mask that filters at least 95% of airborne particles; PPE = personal protective equipment; PSAPs -personal sound amplification products; SARS-CoV-2 = severe acute respiratory syndrome-coronavirus-2. We'd like to call attention to the negative impacts of universal masking and social distancing in both health-care and community settings for individuals with hearing loss. Social Healthcare professionals should recognize that, with the loss of visual cues (i.e., lip reading) and support systems (e.g., family members), current COVID-19 policies such as universal masking, social distancing, and unaccompanied patients may "unmask" significant hearing loss-related issues that previously had been diminished or ignored. cache = ./cache/cord-269568-vwkawh6x.txt txt = ./txt/cord-269568-vwkawh6x.txt === reduce.pl bib === id = cord-269553-d3hozs14 author = Khan, Suliman title = The spread of novel coronavirus has created an alarming situation worldwide date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1491 sentences = 83 flesch = 48 summary = The COVID-19 epidemic became a serious challenge for the healthcare authorities, scientific community, and the infections controlling agencies across China, in terms of spread, treatment, and prevention. In the current scenario of the outbreak in Wuhan, healthcare workers are at the highest risk of contracting an infection. This indicates that a large number of medical staffs is suspected to have contracted the infection and their confirmation may create an alarming situation for healthcare authorities. Therefore, the increasing numbers of infected and suspected doctors and nurses are creating an additional significant shortage of working medical staff, thus, increasing an additional working and mental pressure on the normal health workers [6] . The medical staff resisted to provide treatment services to the suspected individual, fearing the possible transmission of the infection. Beside this, hospitals in developing or underdeveloped countries should be equipped on urgent basis for providing effective services to the individuals infected by novel coronavirus. cache = ./cache/cord-269553-d3hozs14.txt txt = ./txt/cord-269553-d3hozs14.txt === reduce.pl bib === id = cord-269383-1tyorrb0 author = Lai, Christopher K C title = Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date = 2020-08-01 pages = extension = .txt mime = text/plain words = 2845 sentences = 186 flesch = 57 summary = METHODS: We performed a prospective study in two regional hospitals in Hong Kong RESULTS: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep-throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. International authorities recommend laboratory diagnosis of SARS-CoV-2 infection should base on real-time PCR (RT-PCR) detection of viral RNA in respiratory specimens [2, 3] . In another study by the same research group [23] , they tested archived nasopharyngeal swabs and posterior oropharyngeal saliva specimens from 58 confirmed COVID-19 patients using Xpert® Xpress SARS-CoV-2 assay. To date, our current study provides the largest number of patients with prospectively collected saliva specimens throughout the clinical course and with head-to-head comparison of DTS to both upper and lower tract respiratory samples. DTS contains lower viral RNA concentration and is less sensitive in detecting SARS-CoV-2 infection than sputum and pooled NP and throat swabs. cache = ./cache/cord-269383-1tyorrb0.txt txt = ./txt/cord-269383-1tyorrb0.txt === reduce.pl bib === id = cord-269377-ylgyvxtd author = Matos, Ana R. title = COVID-19 Associated Central Nervous System Vasculopathy date = 2020-06-02 pages = extension = .txt mime = text/plain words = 939 sentences = 57 flesch = 38 summary = Stroke in the setting of viral vasculopathy has been described with other viruses, such as varicella zoster virus (VZV) or 1 ; more recently, it has also been associated with other coronavirus, namely, Middle East respiratory syndrome coronavirus, during the outbreak in Saudi Arabia in 2012. The imaging presentation of multiple lesions involving deep and subcortical white matter, as well as deep gray nuclei, with marked restricted diffusion of some, has been described in the setting of VZV vasculopathy. Primary angiitis of the central nervous system was also considered, but the absence of obvious large vessel irregularities, normal CSF cellular count, and concomitant SARS-CoV-2 infection led us consider a COVID-19-related vasculopathy as the most probable diagnosis, potentially induced by misdirected immune mediated-vasoconstriction of medium-/ small-sized arteries; we believe this represents a new imaging presentation of a SARS-CoV-2-related complication. cache = ./cache/cord-269377-ylgyvxtd.txt txt = ./txt/cord-269377-ylgyvxtd.txt === reduce.pl bib === id = cord-269726-z0frgm7s author = Gidari, Anna title = Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date = 2020-10-10 pages = extension = .txt mime = text/plain words = 6678 sentences = 441 flesch = 54 summary = Criteria for patients' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . cache = ./cache/cord-269726-z0frgm7s.txt txt = ./txt/cord-269726-z0frgm7s.txt === reduce.pl bib === id = cord-269555-29t956ik author = Zaconeta, Alberto title = Letter to the editor“SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?” date = 2020-09-22 pages = extension = .txt mime = text/plain words = 187 sentences = 24 flesch = 55 summary = key: cord-269555-29t956ik title: Letter to the editor"SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?" journal: Placenta DOI: 10.1016/j.placenta.2020.09.063 cord_uid: 29t956ik transmission of SARS-CoV-2. After discussing anatomical and molecular differences between 36 the alveolar-capillary and syncytium-capillary barriers, the authors presented the well-37 considered hypothesis that the absence of caveolin expression in the syncytium is one of the 38 most important mechanisms preventing the transplacental passage of this virus (1) . their masterful analysis, we would like to extend the discussion to another important risk factor 40 for vertical transmission, namely viral load in blood. Factors preventing 55 materno-fetal transmission of SARS-CoV-2 Detection of SARS-CoV-2 in 58 different types of clinical specimens Clinical features of patients 61 infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not 65 associated with infectious virus The trinity of COVID-19: immunity, 68 inflammation and intervention cache = ./cache/cord-269555-29t956ik.txt txt = ./txt/cord-269555-29t956ik.txt === reduce.pl bib === id = cord-269496-tnw7sxlh author = Sen Gupta, Parth Sarthi title = Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date = 2020-10-28 pages = extension = .txt mime = text/plain words = 4910 sentences = 246 flesch = 53 summary = Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). Together, being conserved and a necessary component for the replication of coronavirus, a multi-functional protein, Nsp13-helicase, is another vital SARS-COV-2 target (Jia et al., 2019) , which can be considered further for antiviral drug discovery provided a very small number of Nsp13 inhibitors reported to date . Molecular docking of Ivermectin with twelve SARS-COV-2's targets along with Importin-a was carried out, followed by binding mechanism exploration and structural stability analysis using molecular dynamics (MD) simulation through the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g ), and binding free energy of the complexes of Ivermectin with the best targets. cache = ./cache/cord-269496-tnw7sxlh.txt txt = ./txt/cord-269496-tnw7sxlh.txt === reduce.pl bib === id = cord-269488-7fy6exsd author = Zhen, Wei title = Development of a New Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection date = 2020-09-19 pages = extension = .txt mime = text/plain words = 1421 sentences = 73 flesch = 56 summary = A LOD study with inactivated virus exhibited equal performance to the modified CDC assay with a final LOD of 1,301 ± 13 genome equivalents/ml for the Northwell Health Laboratories laboratory developed test (NWHL LDT) vs. The results demonstrate that the NWHL LDT multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and can be used as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2. The findings demonstrate that the NWHL LDT has comparable clinical performance for the specific detection of SARS-CoV-2 RNA in NP specimens and is more efficient and cost effective in comparison to the modified CDC assay. In summary, The NWHL LDT has comparable analytical sensitivity and accuracy for specific detection of SARS-CoV-2 RNA and also showed superior efficiency and cost-effectiveness when compared to the modified CDC assay. cache = ./cache/cord-269488-7fy6exsd.txt txt = ./txt/cord-269488-7fy6exsd.txt === reduce.pl bib === id = cord-268795-tjmx6msm author = Sardar, Rahila title = Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date = 2020-03-21 pages = extension = .txt mime = text/plain words = 2257 sentences = 128 flesch = 47 summary = title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Our analysis shows unique host-miRNAs targeting SARS-CoV2 virus genes. CELLO2GO (7)server was used to infer biological function for each protein of SARS-CoV2 genome with their localization prediction. Assembled SARS-CoV2 genomes sequences in FASTA format from India, USA, China, Italy and Nepal used for coronavirus typing tool analysis. For the phylogenetic analysis, we compared the sequences of 6 SARS-CoV2 isolates from different countries namely, Wuhan, India, Italy, USA and Nepal along with other corona virus species ( Figure 1 ). cache = ./cache/cord-268795-tjmx6msm.txt txt = ./txt/cord-268795-tjmx6msm.txt === reduce.pl bib === id = cord-269521-vq2m4c8q author = Lucchese, Guglielmo title = Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons date = 2020-05-01 pages = extension = .txt mime = text/plain words = 815 sentences = 59 flesch = 43 summary = Brainstem involvement has been proposed as a possible cause of respiratory failure in SARS-CoV-2 infection, given that the virus appears to have potential for inducing neurological damage, a number of neurological symptoms have been described, and SARS-CoV has been reported to massively infect the brainstem in both patients and experimental animals [3] . Indeed, the proteome of the virus (https://www.ncbi.nlm.nih.gov/nuccore/ MN908947) shares three sequences of six amino acids (GSQASS, LNEVAK, and SAAEAS) with three proteins, namely DAB1, AIFM, and SURF1 (as catalogued at www.uniprot.org) that are present in the human brainstem preBötC (Table 1 ) and are part of experimentally validated epitopes [10] . In the context of this peptide sharing between the preBötc, and SARS-CoV-2, it appears possible that immunological targeting of DAB1, AIFM1, and SURF1 might contribute to brainstem-related respiratory failure in COVID-19 patients and that a therapeutic benefit might come from immunomodulatory agents. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-269521-vq2m4c8q.txt txt = ./txt/cord-269521-vq2m4c8q.txt === reduce.pl bib === id = cord-269564-r5mmsnbx author = Hans, Diana title = Rapidly Fatal Infections date = 2008-05-31 pages = extension = .txt mime = text/plain words = 7549 sentences = 426 flesch = 46 summary = Reports have suggested a mortality rate of 30% to 70% despite aggressive treatment [35] TSS is most commonly caused by Staphylococcus aureus and group A streptococcus. Unfortunately, complicated group A streptococcus infections are shown to have a high mortality rate despite aggressive antibiotic therapy, and penicillin has been shown to have limited effects if not initiated early in the disease. Fifty-three percent of the patients were positive for MRSA, and the risk factors associated with colonization included recent antibiotic use (within 3 months), hospitalization within the past year, skin or soft tissue infection on admission, and HIV infection [68] . PVL-positive S aureus pneumonia typically occurred in younger patients (median age, 14.8 years) who were previously healthy, and 75% were found to have had a viral infection in the preceding days. Two deadly viral infections that have emerged in recent years include severe acute respiratory syndrome (SARS) and influenza A (H5N1), also known as avian influenza or bird flu. cache = ./cache/cord-269564-r5mmsnbx.txt txt = ./txt/cord-269564-r5mmsnbx.txt === reduce.pl bib === id = cord-269526-3npk3u5t author = Dehghanbanadaki, Hojat title = Bibliometric analysis of global scientific research on Coronavirus (COVID-19) date = 2020-05-23 pages = extension = .txt mime = text/plain words = 3305 sentences = 174 flesch = 52 summary = Methods: We extracted all COVID-19 documents indexed in the Scopus from December 1, 2019, to April 1, 2020, without any language limitation and determined their bibliometric characteristics, including document type, open accessibility status, citation counting, H-index, top cited documents, the most productive countries, institutions and journals, international collaboration, the most frequent terms and keywords, journal bibliographic coupling and cocitations. The most frequent terms were COVID (n = 983 repeats), patient (n = 741 repeats), SARS-CoV (n = 593 repeats), China (n = 497 repeats), case (n = 464 repeats), nCoV (n = 417 repeats), outbreak (n = 355 repeats), infection (n = 344 repeats), novel coronavirus (n = 324 repeats), Wuhan (n = 269 repeats), Coronavirus (n =243 repeats), virus (n = 204 repeats), pneumonia (n = 195 repeats), Coronavirus disease (n = 170 repeats), treatment (n = 162 repeats), transmission (n = 158 repeats), study (n = 156 repeats), data (n = 151 repeats), country (n = 137 repeats), and epidemic (n = 136 repeats). cache = ./cache/cord-269526-3npk3u5t.txt txt = ./txt/cord-269526-3npk3u5t.txt === reduce.pl bib === id = cord-269474-94c1mudi author = Nasef, Nehad title = Lessons from SARS: A retrospective study of outpatient care during an infectious disease outbreak date = 2010-07-20 pages = extension = .txt mime = text/plain words = 3171 sentences = 154 flesch = 52 summary = In response, a decision was made by the neonatal neuro-developmental follow up (NNFU) clinic staff to select patients with scheduled appointments to have a mail/telephone assessment using Ages and Stages Questionnaire (ASQ) or to postpone/skip their visit. The objective of this study was to compare the developmental assessment and its outcome in two groups of NNFU clinic patients, SARS versus non-SARS, over three standard clinic appointments. The objective of this retrospective study was to compare the developmental assessment and its' outcome in two groups of NNFU clinic patients, SARS versus non-SARS over an assessment trajectory of 3 booked clinic appointments (labeled before, during and after according to the time of clinic closure during SARS). Of 30 patients diagnosed with developmental delay at the before visit in the SARS group, 8 were contacted by mail or telephone and 22 were never contacted during the period of clinic closure. cache = ./cache/cord-269474-94c1mudi.txt txt = ./txt/cord-269474-94c1mudi.txt === reduce.pl bib === id = cord-269045-i7vijtol author = Martínez‐Murcia, A. title = Comparative in silico design and validation of GPS™ CoVID‐19 dtec‐RT‐qPCR test date = 2020-07-29 pages = extension = .txt mime = text/plain words = 3889 sentences = 239 flesch = 59 summary = An illustration of the mismatching of primers/probe sequences of the GPS CoVID-19 dtec-RT-qPCR Test, respect of the SARS-CoV-2, Bat SARS-like-CoV, SARS-CoV, Bat-CoV, and Pangolin-CoV groups is shown in Fig. 2 . Finally, the results obtained in the diagnostic validation of the GPS TM CoVID-19 dtec-RT-qPCR Test, carried out by the Instituto de Salud Carlos III (ISCIII), are shown in Table 3 . As the number of genomes available rapidly expanded during last January, the GPS TM CoVID-19 dtec-RT-qPCR test was based on a more specific target for SARS-CoV-2 detection, being this company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. Finally, the kit GPS TM COVID-19 dtec-RT-qPCR Test showed the highest number of mismatches (i.e. 19-48) for all coronavirus sequences described so far, including these of Pangolin-CoV, which showed a range of 19-31 mismatches. cache = ./cache/cord-269045-i7vijtol.txt txt = ./txt/cord-269045-i7vijtol.txt === reduce.pl bib === id = cord-269519-8hr8wyrr author = Hirotsu, Yosuke title = Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date = 2020-07-07 pages = extension = .txt mime = text/plain words = 1599 sentences = 113 flesch = 54 summary = Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. cache = ./cache/cord-269519-8hr8wyrr.txt txt = ./txt/cord-269519-8hr8wyrr.txt === reduce.pl bib === id = cord-269537-h3lzl1un author = Banerjee, Aditi title = Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 2937 sentences = 189 flesch = 39 summary = Viral infections including SARS-CoV are associated with increased levels of reactive oxygen species, disturbances of Ca(++) caused by unfolded protein response (UPR) mediated by endoplasmic reticulum (ER) stress and is due to the exploitation of virus's own protein i.e., viroporins into the host cells. Considering the properties of both compounds in terms of anti-inflammatory, antioxidant, anti-pyrogenic, anti-viral and ER stress modulation and computational approaches revealing andrographolide docks with the SARS-CoV2 binding site, we predict that this combination therapy may have potential utility against COVID-19. Accumulating evidence suggests that ER stress and sustained UPR signaling are major contributors to the pathogenesis of several diseases, including inflammatory disorders and viral infections [15] and can increase the severity of these events [16] . Endoplasmic reticulum stress and IRE-1 signaling cause apoptosis in colon cancer cells in response to andrographolide treatment cache = ./cache/cord-269537-h3lzl1un.txt txt = ./txt/cord-269537-h3lzl1un.txt === reduce.pl bib === id = cord-269522-38dhwggn author = Hong, Xia title = Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() date = 2009-08-27 pages = extension = .txt mime = text/plain words = 4269 sentences = 243 flesch = 56 summary = title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() OBJECTIVE: To measure the incidence and impact of posttraumatic stress disorder (PTSD) in a cohort of 70 subjects with severe acute respiratory syndrome (SARS). To study the impact of PTSD, we used the Impact of Event Scale (IES), Zung Self-Rating Anxiety Scale (SAS), Zung Self-Rating Depression Scale (SDS), Symptom Checklist 90 (SCL-90), Short Form-36 (SF-36 Health Survey) and Social Disability Screening Schedule (SDSS). In one study of 63 survivors of SARS at 3 months postdischarge from hospital in Singapore, the rate of possible PTSD, inferred from an Impact of Event Scale (IES) Score of N26, was 41.7% [15] . In a study of 195 survivors of SARS at 1 month postdischarge from hospital in Hong Kong, 10% to 18% of them reported symptoms related to PTSD [16] . cache = ./cache/cord-269522-38dhwggn.txt txt = ./txt/cord-269522-38dhwggn.txt === reduce.pl bib === id = cord-269234-8twdx4g2 author = Koyama, Takahiko title = Variant analysis of SARS-CoV-2 genomes date = 2020-07-01 pages = extension = .txt mime = text/plain words = 4025 sentences = 321 flesch = 66 summary = OBJECTIVE: To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here we analysed the SARS-CoV-2 genome from 10 022 samples to understand the variability in the viral genome landscape and to identify emerging clades. Finally, we carefully Objective To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Given the evolving nature of the SARS-CoV-2 genome, drug and vaccine developers should continue to be vigilant for emergence of new variants or sub-strains of the virus. Variant analysis of SARS-CoV-2 genomes [data repository cache = ./cache/cord-269234-8twdx4g2.txt txt = ./txt/cord-269234-8twdx4g2.txt === reduce.pl bib === id = cord-269465-3fdjqnhb author = Leth-Larsen, Rikke title = The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages date = 2007-05-15 pages = extension = .txt mime = text/plain words = 7168 sentences = 404 flesch = 61 summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) infects host cells with its surface glycosylated spike-protein (S-protein). Macrophages, DCs, 293T and Vero cells were harvested, incubated for 30 min with 20% (v/v) goat serum, and then stained for 45 min on ice with a mouse monoclonal anti-ACE2 antibody. Cells were washed twice with the binding buffer and then incubated with the myc antibody followed by goat anti-mouse IgG and analyzed by flow cytometry as above. To examine whether S-protein expressed in this study is recognized by ACE2, Vero cells were incubated with the purified S-protein and bound S-protein was detected by flow cytometry using a myc antibody. Blocking of Binding of S-protein to macrophages and DCs: (A) macrophages and DCs were cultured from monocytes and, upon washing, incubated with a mouse anti-human ACE2 monoclonal antibody (solid lines) or, as a control, isotype IgG (solid histograms). cache = ./cache/cord-269465-3fdjqnhb.txt txt = ./txt/cord-269465-3fdjqnhb.txt === reduce.pl bib === id = cord-269612-pmzdovna author = Pennington, Hugh title = Politics, media and microbiologists date = 2004 pages = extension = .txt mime = text/plain words = 3821 sentences = 177 flesch = 52 summary = Studies on the SARS outbreak in Hong Kong 1 -after the exclusion of two 'superspread' events where special circumstances allowed index cases to infect many individuals (at the Prince of Wales Hospital and at the Amoy Gardens estate) -gave an estimated R 0 value of 2.7. From analyses of samples taken from Vietnam, Singapore and Hong Kong, laboratories in the network ruled out the possibility of infection by any of the known influenza virus strains or other established causes of pneumonia, and concluded that SARS was new. It meant that the Hong Kong Department of Health, Hospital Authority and laboratory surveillance facility 11 , and the WHO, were particularly well prepared to respond to the SARS outbreak. In March 1997, an outbreak of avian influenza caused by the A virus subtype H5N1 killed several thousand chickens in three rural Hong Kong chicken farms. cache = ./cache/cord-269612-pmzdovna.txt txt = ./txt/cord-269612-pmzdovna.txt === reduce.pl bib === id = cord-269902-sbp18486 author = Springer, Steffen title = Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin date = 2020-05-06 pages = extension = .txt mime = text/plain words = 790 sentences = 54 flesch = 63 summary = title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin tigris) in the Bronx Zoo were reported [Gollakner & Capua, 2020] , corresponding peaks were revealed in search queries by Google Trends, in particular for the unusual transmission to lions and tigers (figure 1). For the Pearson correlation coefficient, a high correlation between the search terms "CoViD-19" and "tiger" (r = 0.669, p < 0.05) was found for the period from 1 st January 2020 to 24 th April 2020. For the search term "palm civet" a low Pearson correlation coefficient was found (r=0.148; p < 0.05). Our data support that the main interest of the population is currently rather in the medical therapeutic direction and, apart from anecdotal individual reports (e.g. Bronx Zoo cats), there is less interest in possible virus carriers or the animal origin and reservoir. cache = ./cache/cord-269902-sbp18486.txt txt = ./txt/cord-269902-sbp18486.txt === reduce.pl bib === id = cord-269454-9gthf2jl author = Kulkarni, Rajesh title = Early-onset symptomatic neonatal COVID-19 infection with high probability of vertical transmission date = 2020-08-02 pages = extension = .txt mime = text/plain words = 1778 sentences = 109 flesch = 59 summary = RESULTS: A COVID-19 suspected mother, who tested negative by RT-PCR for COVID, but tested positive for SARS-CoV-2 by serology, delivered a term baby. CONCLUSION: This report highlights a very strong possibility of vertical transmission of COVID-19 from a mildly symptomatic, RT-PCR negative but antibody-positive mother with significant symptomatic, early—onset neonatal infection. This report describes the clinical course and laboratory findings in a neonate born in Pune, India in whom infection with SARS-CoV-2 very likely occurred via vertical transmission. NPA from baby, cord stump, and placenta (which were collected as per national guidelines at birth) were reported as positive for SARS-CoV2 at 12 h of life. Two neonates with positive RT-PCR testing as early as 30 h after delivery have been reported; however, these cases lacked sufficient clinical data or precise information regarding isolation methods, and perinatal transmission could not be ruled out [7, 8] . cache = ./cache/cord-269454-9gthf2jl.txt txt = ./txt/cord-269454-9gthf2jl.txt === reduce.pl bib === id = cord-269973-sntnmqqd author = To, Kelvin Kai-Wang title = Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1860 sentences = 139 flesch = 63 summary = However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. cache = ./cache/cord-269973-sntnmqqd.txt txt = ./txt/cord-269973-sntnmqqd.txt === reduce.pl bib === id = cord-269718-e1mxmo3a author = Wang, Jingquan title = Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China date = 2020-11-13 pages = extension = .txt mime = text/plain words = 862 sentences = 59 flesch = 49 summary = title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China Considering the live SARS-CoV-2 was detected and isolated from the excrement and urine of infected patients, the potential public health risk of its waterborne transmission should be paid broad and close attention. The purpose of the current study is to investigate the associations between COVID-19 incidences and hydrological factors such as lake area, river length, precipitation and volume of water resources in 30 regions of China. Based on the results of descriptive analysis and nonlinear regression analysis, positive associations with COVID-19 confirmed numbers were observed for migration scale index (MSI), river length, precipitation and volume of water resources, but negative associations for population density. length, precipitation and volume of water resources, but negative associations for 21 population density. Impact of meteorological factors on the COVID-19 transmission: 435 A multi-city study in China Water transmission oF SARS-CoV-2 cache = ./cache/cord-269718-e1mxmo3a.txt txt = ./txt/cord-269718-e1mxmo3a.txt === reduce.pl bib === id = cord-270015-5gtxfkoz author = Mahmood Shah, Sayed Mustafa title = Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1003 sentences = 70 flesch = 49 summary = title: Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health 6 This comes at a time when many Muslim majority countries are stilling struggling with the public health crisis posed by COVID-19, with variable success in controlling the transmission of the virus. 7 A structural analysis of ACE-2 receptor in vertebrates has shown artiodactyl mammals (which include domesticated cattle, sheep and goats) express ACE-2 receptors and were classified as medium score for binding to SARS-CoV-2 Spike protein. 7 This finding has been reiterated in a comparative x-ray structural analysis of SARS-CoV-2 spike protein receptor binding domain to ACE-2 receptors in humans and putative intermediate hosts. Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts SARS-CoV-2: structural diversity, phylogeny, and potential animal host identification of spike glycoprotein cache = ./cache/cord-270015-5gtxfkoz.txt txt = ./txt/cord-270015-5gtxfkoz.txt === reduce.pl bib === id = cord-269766-arjoemla author = Dutescu, R. Michael title = Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2141 sentences = 124 flesch = 57 summary = title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. To clarify this, we tested the tear fluid of confirmed hospitalized SARS-CoV-2 patients by PCR using a method not previously used for the collection of tear samples. In this study, we could confirm SARS-CoV-2 RNA positive tear samples by PCR in as many as 28% of determined SARS-CoV-2 patients by oropharyngeal swabs. 13 In a more recent cross-sectional study, only 1 (1.38%) conjunctival swab of 72 confirmed SARS-CoV-2 cases was tested positive. cache = ./cache/cord-269766-arjoemla.txt txt = ./txt/cord-269766-arjoemla.txt === reduce.pl bib === id = cord-269825-k685efoh author = Hu, Parker title = Early comprehensive testing for COVID-19 is essential to protect trauma centers date = 2020-07-01 pages = extension = .txt mime = text/plain words = 3286 sentences = 177 flesch = 48 summary = We recorded the daily number of trauma patients diagnosed with SARS-CoV-2 infection, the presence of clinical symptoms or radiological signs of COVID-19, and the results of verbal symptom screen (for new admissions). Positive verbal screen results, presence of ground glass opacities on admission chest CT, and presence of clinical symptoms were not significantly different in patients with or without SARS-CoV-2 infection (p > 0.05). [14] [15] [16] While the position is becoming well defined for those patients with known, established disease, there is little available data to guide trauma centers that may be required to treat significant numbers of asymptomatic infected new patients during this ongoing crisis. The screening and testing procedure in the trauma bay subsequently identified four additional SARS-CoV-2-infected patients. All new trauma patients should be regarded as SARS-CoV-2 positive until testing can be completed to minimize exposures to staff and limit nosocomial spread of disease. cache = ./cache/cord-269825-k685efoh.txt txt = ./txt/cord-269825-k685efoh.txt === reduce.pl bib === id = cord-269563-2979u47a author = Caetano Silva-Filho, José title = The influence of ABO blood groups on COVID-19 susceptibility and severity: a molecular hypothesis based on carbohydrate-carbohydrate interactions date = 2020-08-02 pages = extension = .txt mime = text/plain words = 4614 sentences = 218 flesch = 40 summary = Based on this survey, we hypothesize that the correlation between the ABO blood system and susceptibility to SARS-CoV-2 infection can be presumably explained by the modulation of sialic acid-containing receptors distribution on host cell surface induced by ABO antigens through carbohydrate-carbohydrate interactions, which could maximize or minimize the virus Spike protein binding to the host cell. to cell receptors, as well as (ii) the biochemical aspects of ABO blood group system and its association to infection and some circulatory conditions, we hypothesize that the influence of blood type on COVID-19 severity relies on the differential clustering of glycoproteins receptors to SARS-CoV-2 on host cell surface, induced by ABH antigens through carbohydrate-carbohydrate interactions with the glycan portions of these receptors, which could modulate virus binding to the target cell. cache = ./cache/cord-269563-2979u47a.txt txt = ./txt/cord-269563-2979u47a.txt === reduce.pl bib === id = cord-269756-tid8a464 author = Basso, Luis G. M. title = SARS-CoV fusion peptides induce membrane surface ordering and curvature date = 2016-11-28 pages = extension = .txt mime = text/plain words = 12194 sentences = 532 flesch = 49 summary = Although membrane fusion promoted by class I viral glycoproteins, such as SARS-CoV Spike, human immunodeficiency virus (HIV) gp160 or influenza virus hemagglutinin (HA), has been broadly studied in recent years [16] [17] [18] [19] , many aspects of the molecular mechanism behind the virus-host cell membrane fusion remain unknown, including conformational changes of the lipid bilayers during peptide-membrane interactions. In the present study, we investigated the effects of two putative fusion peptides from SARS-CoV S glycoprotein, corresponding to residues 770-788 (SARS FP ) and 873-888 (SARS IFP ) 13, 15, 22, 23 , on the structural dynamics, physicochemical properties, and thermotropic phase behavior of lipid model membranes by differential scanning calorimetry (DSC), continuous wave (CW) and pulsed electron spin resonance (ESR) along with nonlinear least-squares (NLLS) spectral fitting 24 . cache = ./cache/cord-269756-tid8a464.txt txt = ./txt/cord-269756-tid8a464.txt === reduce.pl bib === id = cord-269946-zb7gcw0m author = Boscolo-Rizzo, Paolo title = New onset of loss of smell or taste in household contacts of home-isolated SARS-CoV-2-positive subjects date = 2020-05-24 pages = extension = .txt mime = text/plain words = 1766 sentences = 85 flesch = 53 summary = PURPOSE: To estimate the prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. To better estimate the burden of smell and taste impairment during COVID-19 pandemic, we searched for the prevalence of these symptoms in subjects at high risk for SARS-CoV-2 infection, i.e. household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. We previously reported the prevalence of loss of the sense of smell or taste as well as other COVID-19 symptoms in a case series of 202 home-isolated mildly symptomatic confirmed cases of SARS-CoV-2 infection [8] . The prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients was 1.5%, 22.3%, and 63.0% in subjects tested negative, non-tested, and tested positive for SARS-CoV-2 infection, respectively. However, this study showed that smell or taste impairment is quite common in not-tested household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. cache = ./cache/cord-269946-zb7gcw0m.txt txt = ./txt/cord-269946-zb7gcw0m.txt === reduce.pl bib === id = cord-270116-r2rnnsfh author = Lippi, Giuseppe title = Current laboratory diagnostics of coronavirus disease 2019 (COVID-19) date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4742 sentences = 192 flesch = 37 summary = As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized especially by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. Recent studies have also been published on the possibility to use rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for SARS-CoV-2 detection, but additional evidence is needed at this point in time for validating their routine usage in COVID-19 diagnostics (38, 39) . As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. cache = ./cache/cord-270116-r2rnnsfh.txt txt = ./txt/cord-270116-r2rnnsfh.txt === reduce.pl bib === id = cord-270112-o2exvfy5 author = Ferrarese, Carlo title = An Italian multicenter retrospective-prospective observational study on neurological manifestations of COVID-19 (NEUROCOVID) date = 2020-05-19 pages = extension = .txt mime = text/plain words = 2465 sentences = 103 flesch = 31 summary = We report here the description of a multicenter retrospective-prospective observational study promoted by the Italian Society of Neurology (SIN), involving the Italian Neurological Departments, who will consecutively recruit patients with neurological symptoms and/or signs, occurred at the onset or as a complication of COVID-19. A comprehensive data collection, in the form of electronic case report form (eCRF), will register all possible neurological manifestations involving central nervous systems, peripheral nerves, and muscles, together with clinical, laboratory (including cerebrospinal fluid, if available), imaging, neurological, neurophysiological, and neuropsychological data. More specifically, the aims are to gather data on the following: (1) the appearance of neurologic symptoms and/or signs at COVID-19 onset or during the disease course, (2) the exams performed for the diagnosis of the neurological involvement, (3) the clinical course of both the COVID-19 infection and the neurological events, but also the occurrence of possible long-term neurological complications within a 6-month period of follow-up. cache = ./cache/cord-270112-o2exvfy5.txt txt = ./txt/cord-270112-o2exvfy5.txt === reduce.pl bib === id = cord-270218-578lsck9 author = Gentile, Davide title = Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study date = 2020-04-23 pages = extension = .txt mime = text/plain words = 5872 sentences = 300 flesch = 46 summary = On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pro (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pr (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. To further validate the pharmacophore model descriptors, validate the poses and binding energies, and comprehensively investigate the interactions of the new ligands within the catalytic site of the protease, we conducted a parallel docking study, with Autodock4, and MD simulations on those compounds (1-17) that showed a better affinity (Table 1) . cache = ./cache/cord-270218-578lsck9.txt txt = ./txt/cord-270218-578lsck9.txt === reduce.pl bib === id = cord-270122-xijsj0d8 author = Hogan, Robert Edward title = COVID-19 in Patients With Seizures and Epilepsy: Interpretation of Relevant Knowledge of Presenting Signs and Symptoms date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1636 sentences = 92 flesch = 42 summary = Realizing the need for current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and clinical presentation of COVID-19, especially in relationship to patients with seizures and epilepsy. Overall, findings indicate seizures and epilepsy are rare, especially in mild COVID-19 cases, but may occur in more severe cases later in the disease course. Realizing both the need for and limitation of current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and COVID-19, especially in relationship to patients with seizures and epilepsy. 27 As compared to population-based studies of the initial clinical presentation of COVID-19, studies in patients with seizures and epilepsy are lacking. While a neuroinvasive mechanism of SARS-CoV-2 virus CNS infection remains a postulated cause of clinical neurological disease, 16 investigation of new-onset neurological impairments associated with COVID-19 found lack of evidence for direct acute insult of SARS-CoV-19 virus to the CNS. cache = ./cache/cord-270122-xijsj0d8.txt txt = ./txt/cord-270122-xijsj0d8.txt === reduce.pl bib === id = cord-270019-er70ehk4 author = Yang, Kunyu title = Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study date = 2020-05-29 pages = extension = .txt mime = text/plain words = 4268 sentences = 242 flesch = 48 summary = title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study METHODS: We did a retrospective, multicentre, cohort study of 205 patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and with a pathological diagnosis of a malignant tumour in nine hospitals within Hubei, China, from Jan 13 to March 18, 2020. Multivariable regression analysis showed that receiving chemotherapy within 4 weeks before symptom onset (odds ratio [OR] 3·51 [95% CI 1·16–10·59]; p=0·026) and male sex (OR 3·86 [95% CI 1·57–9·50]; p=0·0033) were risk factors for death during admission to hospital. 5 In particular, male sex and receiving chemotherapy within 4 weeks before symptom onset were identified as risk factors for death in patients with cancer who were diagnosed with COVID-19. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-270019-er70ehk4.txt txt = ./txt/cord-270019-er70ehk4.txt === reduce.pl bib === id = cord-269723-gm65p1op author = Tzeng, Nian-Sheng title = What could we learn from SARS when facing the mental health issues related to the COVID-19 outbreak? A nationwide cohort study in Taiwan date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4370 sentences = 198 flesch = 46 summary = There were several studies about the psychiatric and mental health issues related to the severe adult respiratory syndrome (SARS) outbreak in 2003, however, the association between SARS and the overall risk of psychiatric disorders and suicides has, as yet, to be studied in Taiwan. A total of 285 patients with SARS and 2850 controls without SARS (1:10) matched for sex, age, insurance premium, comorbidities, residential regions, level of medical care, and index date were selected between February 25 and June 15, 2003 from the Inpatient Database Taiwan's National Health Insurance Research Database. To the best of our knowledge, this is the first study on the association between SARS and increased risk in developing psychiatric disorders and suicide, in a 12-year follow-up, from a nationwide, population-based database. cache = ./cache/cord-269723-gm65p1op.txt txt = ./txt/cord-269723-gm65p1op.txt === reduce.pl bib === id = cord-269909-1cso5cl4 author = Amatya, Shaili title = Management of newborns exposed to mothers with confirmed or suspected COVID-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5552 sentences = 278 flesch = 44 summary = The unexpectedly high asymptomatic carrier rates reported from other institutions as well as prolonged face-to-face patient care required during labor and delivery drove this decision, allowing for judicious personal protective equipment (PPE) use and decreased potential exposure for both healthcare workers and newborns. Several reports, based on expert opinion, have recommended that DCC not be performed in neonates born to mothers with confirmed or suspected COVID-19 in order to reduce the risk of secondary transmission [15, 47, 49] . For resuscitation of premature, high-risk, and newborns with anomalies born to mothers with cinfirmed or suspected COVID-19, a fully donned neonatal resuscitation team enters the room upon delivery. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Neonatal resuscitation and postresuscitation care of infants born to mothers with suspected or confirmed SARS-CoV-2 infection cache = ./cache/cord-269909-1cso5cl4.txt txt = ./txt/cord-269909-1cso5cl4.txt === reduce.pl bib === id = cord-269707-titu9lm4 author = Hsieh, Ching-Lin title = Structure-based design of prefusion-stabilized SARS-CoV-2 spikes date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2125 sentences = 122 flesch = 50 summary = Here, we characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting ~10-fold higher expression than its parental construct and the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2. In addition to salt bridges, filling loosely packed hydrophobic cores that allow the protein to refold can help stabilize the prefusion state, as shown by previous cavity-filling substitutions in RSV F and HIV-1 Env (12, 20, 22) . Adding one disulfide (S884C/A893C) to a single proline variant (F817P) also reduced the expression level, although the quaternary structure of the spikes was well maintained (table S2, Combo40). HexaPro expressed 9.8-fold higher than S-2P, had ~5°C increase in Tm, and retained the trimeric prefusion conformation (Fig. 3D) . cache = ./cache/cord-269707-titu9lm4.txt txt = ./txt/cord-269707-titu9lm4.txt === reduce.pl bib === id = cord-270355-5mljrk1h author = Fontanet, Arnaud title = Les enseignements du SRAS date = 2007-02-28 pages = extension = .txt mime = text/plain words = 2339 sentences = 166 flesch = 61 summary = Points essentiels Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l'homme; d'où l'importance d'une détection précoce par la surveillance des foyers épidémiques inhabituels. Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l'homme ; d'où l'importance d'une détection précoce par la surveillance des foyers épidémiques inhabituels. Un même scénario est plausible dans le contexte de la grippe aviaire, où les virus directement contractés au contact des volailles n'ont heureusement pas encore (ou exceptionnellement) été à l'origine de transmission interhumaine [11] . Modes de transmission, durée d'incubation et période de contagiosité ont été rapidement connus [12] , avant même que l'agent infectieux ne soit identifié, ce qui a permis d'instaurer des mesures de prévention efficaces associant protection contre les germes respiratoires, isolement des cas, quarantaine des contacts, et restriction des déplacements. cache = ./cache/cord-270355-5mljrk1h.txt txt = ./txt/cord-270355-5mljrk1h.txt === reduce.pl bib === id = cord-270348-5804ffwx author = Angelino, Andrew F. title = Design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 positive patients. date = 2020-07-02 pages = extension = .txt mime = text/plain words = 5818 sentences = 334 flesch = 59 summary = To prevent COVID-19 outbreaks in our units, we next decided to require universal nasal swab testing for SARS-CoV-2 for all medically asymptomatic patients being admitted to psychiatric units 3 . Second, we realized that we needed to decide where to care for SARS-CoV-2 positive, medically asymptomatic patients with mental illnesses who required hospitalization-those without symptoms of COVID-19. In light of the above, we concluded it would best serve our patients if we developed an inpatient psychiatric unit capable of accepting SARS-CoV-2 infected patients without COVID-19 symptoms, or with mild enough symptoms that they would not require medical hospitalization. Further, it is highly beneficial for continuity of care if the patient requires transfer to a medical COVID-19 unit that the psychiatrist be able to follow them there and maintain the psychiatric treatments as indicated. cache = ./cache/cord-270348-5804ffwx.txt txt = ./txt/cord-270348-5804ffwx.txt === reduce.pl bib === id = cord-269862-krcu3hfa author = Wang, Shui-Mei title = APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date = 2009-05-25 pages = extension = .txt mime = text/plain words = 6895 sentences = 379 flesch = 58 summary = We previously demonstrated that HIV-1 Gag mutants containing severe acute respiratory syndrome coronavirus nucleocapsid (SARS-CoV N) coding sequences as NC substitutes can effectively assemble VLPs . Given that SARS-CoV N possesses a RNA-binding property, it is likely that assembly-competent chimeras containing a replacement of HIV-1 NC by an SARS-CoV N sequence may support the incorporation of hA3G into VLPs. Here we demonstrate that the carboxyl-terminal half of the SARS-CoV or human coronavirus 229E (HCoV-229E) N protein not only enables efficient VLP production, but also confers the ability to efficiently package human APOBEC3G (hA3G) when substituted for HIV-1 NC. As the results in Fig. 6B indicate, the carboxyl-terminal half of HCoV-229E N (which also contains a putative self-association domain) (Tswen-Kei Tang, 2005) was capable of replacing the HIV-1 NC function with respect to VLP assembly and hA3G packaging-that is, substantial amounts of VLPs and hA3G were detected in NC(229EN2) transfectant supernatant (lane 4). cache = ./cache/cord-269862-krcu3hfa.txt txt = ./txt/cord-269862-krcu3hfa.txt === reduce.pl bib === id = cord-270257-5f95gve3 author = Jeon, Sangeun title = Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date = 2020-03-28 pages = extension = .txt mime = text/plain words = 1145 sentences = 79 flesch = 53 summary = Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. In near future, these already FDA-approved drugs could be further developed following clinical trials in order to provide additional therapeutic options for patients with COVID-19. We screened approximately 3,000 FDA-and IND-approved drug library against SARS-CoV to identify antiviral drug candidates (manuscript in preparation). Among the 48 drugs that were evaluated in our study, 24 drugs showed potential antiviral activities against SARS-CoV-2 with IC 50 values in Second, ciclesonide is another interesting drug candidate for further development although its antiviral potency was much lower (IC 50 = 4.33 µM) than niclosamide. Prior to our evaluation of 48 drugs against SARS-CoV-2 infection, we also tested antiviral activity of several other drugs based on the cytopathic effect of the virus in the presence of each drug ( Figure 2 ). cache = ./cache/cord-270257-5f95gve3.txt txt = ./txt/cord-270257-5f95gve3.txt === reduce.pl bib === id = cord-269939-8nvrt5y7 author = Tan, Boon Fei title = Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1927 sentences = 109 flesch = 53 summary = title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore Abstract COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. On 23 January 2020, Singapore reported its first imported case of the novel coronavirus infection, officially named COVID-19, [AQ1]which was later declared a global pandemic by the World Health Organization (WHO) [1] . The division serves about 61% of the country's population who require radiotherapy, treating about 280-300 patients per day, including inpatients from SGH and other hospitals within the healthcare cluster. Should any patient who is quarantined for 14 days due to close contact with confirmed COVID-19 cases or those with a Stay Home Notice (SHN) due to recent entry from abroad as of 20 March 2020 require radiotherapy, it will be conducted in a highly controlled manner with close collaboration with the Ministry of Health. cache = ./cache/cord-269939-8nvrt5y7.txt txt = ./txt/cord-269939-8nvrt5y7.txt === reduce.pl bib === id = cord-269835-mz7i66qp author = Furfaro, Federica title = SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date = 2020-06-11 pages = extension = .txt mime = text/plain words = 7275 sentences = 295 flesch = 38 summary = The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with inflammatory bowel disease (IBD) who need to undergo endoscopic procedures. In particular, recommendations regarding the use of personal protective equipment to prevent COVID-19 transmission, both for patients and health-care professionals, are proposed and different scenarios in endoscopic IBD management are evaluated to suggest when endoscopy could be rescheduled and replaced by alternative biomarkers. The panel of experts con sidered possible aerosolization during colonoscopy, in particular during the insertion and removal of instruments through the biopsy channel and the presence of the virus in the stool and advised on the use of N95 masks for lower gastrointestinal procedures as a precautionary measure to protect the endoscopist from the risk of possible COVID-19 transmission from the patient if infected by SARS-CoV-2 (ref. cache = ./cache/cord-269835-mz7i66qp.txt txt = ./txt/cord-269835-mz7i66qp.txt === reduce.pl bib === id = cord-270049-54t3w94z author = Campione, Elena title = Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date = 2020-08-17 pages = extension = .txt mime = text/plain words = 2029 sentences = 113 flesch = 53 summary = We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. 222 We performed the same analysis over the evaluated human lactoferrin (hLF)-Spike complex, 223 obtaining a binding pose superimposable to that observed for the bovine protein (Fig. 5B) . Clinical trial 397 We performed a randomized, prospective, interventional study to assess the efficacy of a liposomal Blood parameters obtained at T0 in COVID-19 group and control group were compared using t-test. cache = ./cache/cord-270049-54t3w94z.txt txt = ./txt/cord-270049-54t3w94z.txt === reduce.pl bib === id = cord-270035-1e1wzdri author = Cazzaniga, Marco title = SARS-COV-2 Infection and Kawasaki Disease: Case Report of a Hitherto Unrecognized Association date = 2020-07-03 pages = extension = .txt mime = text/plain words = 2076 sentences = 109 flesch = 43 summary = The association of Kawasaki disease and COVID-19 infection has to our knowledge been reported only once (5), we report a second case from Italy, currently the third most affected country in the world with regard to number of proven SARS-COV-2 infections. We were then contacted as reference Center for Kawasaki Disease (KD) in our Pediatric Immunology Unit: considering the clinical history (fever lasting more than 5 days, erythematous rash, labial, and conjunctival hyperemia) and the result of laboratory tests we confirmed the diagnostic suspicion of atypical/incomplete KD without coronary involvement, and started treatment with high dose intravenous immunoglobulins (IVIG) 2 g/kg and high dose acetylsalicylic acid (ASA 50 mg/kg/day). In the setting of COVID-19 there are several reports of using corticosteroids for Acute Respiratory Disease Syndrome (ARDS), but considering the not severe clinical course and presentation in our patient we did not start steroid therapy. cache = ./cache/cord-270035-1e1wzdri.txt txt = ./txt/cord-270035-1e1wzdri.txt === reduce.pl bib === id = cord-270123-m8utyd1m author = Enmozhi, Sukanth Kumar title = Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach date = 2020-05-05 pages = extension = .txt mime = text/plain words = 3873 sentences = 187 flesch = 49 summary = This paper evaluates the compound Andrographolide from Andrographis paniculata as a potential inhibitor of the main protease of SARS-COV-2 (Mpro) through in silico studies such as molecular docking, target analysis, toxicity prediction and ADME prediction. And upon certain in vitro and some clinical data chloroquine phosphate and hydroxychloroquine sulphate was advised to be the treatment for COVID-19 and enough randomized trials on these compounds to be provided and allowed the administration of the above drugs to be used for emergency (https://www.fda.gov/emergency-use-authori-zation#covidtherapeutics). Though there are many targets are found for the treatment of COVID-19, the main protease (M pro ) of SARS-CoV-2 was chosen due to interest of treating infected patients, to stop the multiplication of virus within the cells, through which M pro was involved in the release of polypeptides which are functional extensive proteolysis and cleavage of the enzyme itself from the sites of genome, pp1a and ppa1ab . cache = ./cache/cord-270123-m8utyd1m.txt txt = ./txt/cord-270123-m8utyd1m.txt === reduce.pl bib === id = cord-270458-7imgvale author = Franchini, Massimo title = The impact of the SARS‐CoV‐2 outbreak on the safety and availability of blood transfusions in Italy date = 2020-04-13 pages = extension = .txt mime = text/plain words = 1525 sentences = 78 flesch = 50 summary = The CNS has already released since 22 January 2020 a recommendation outlining preventative measures for the transmission of SARS-CoV-2 by transfusion of labile blood components related to travels from the People's Republic of China. On 2 March 2020, following the recommendations of the European Centre for Disease Prevention and Control (ECDC) [9] and reflecting the decrees of the Italian government, the CNS updated the prevention measures, reducing the period of temporary deferral of donors from the previous 28 to 14 days. Following the declaration of the government of the widespread dissemination of the SARS-CoV-2 infection in Italy, the last update of the CNS on 10 March 2020 extended these measures to the whole national territory of Italy. In Fig. 1 , the trend of positive cases for SARS-CoV-2 infection in Italy, updated on 20 March 2020, is reported with a concise chronology of the main documents released and the trend of blood donations in the same period. cache = ./cache/cord-270458-7imgvale.txt txt = ./txt/cord-270458-7imgvale.txt === reduce.pl bib === id = cord-270064-hidirfkv author = Tort, Fernando L. title = A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date = 2020-04-12 pages = extension = .txt mime = text/plain words = 4314 sentences = 257 flesch = 61 summary = In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. In order to gain insight into the emergence, evolution, adaptation and spread of the SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. To gain insight into the biology and evolution of emerging SARS-CoV-2, a comprehensive analysis of genome composition, codon and amino acid usage of βCoV strains isolated in China from humans, bats, civets and ferret hosts was performed, including SARS-CoV-2 strains recently isolated from current outbreak. The results of these studies revealed that SARS-CoV-2 strains enrolled in these analyses have a distinct genome composition in relation to other βCoV strains isolated from human (SARS-CoV), bats, civets and ferrets (see Fig. 1 ). cache = ./cache/cord-270064-hidirfkv.txt txt = ./txt/cord-270064-hidirfkv.txt === reduce.pl bib === id = cord-270462-d9l3agr0 author = Zeng, Zhi title = Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2734 sentences = 186 flesch = 54 summary = title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion The aim of this study was to explore pulmonary pathology of early phase COVID‐19 pneumonia in a patient with a benign lung lesion. METHODS AND RESULTS: We analyzed the pathological changes of lung tissue from a 55‐year‐old female patient with early phase SARS‐CoV‐2 infection. CONCLUSION: The results highlighted the pulmonary pathological changes of early phase SARS‐CoV‐2 infection and suggested a role of immune dysfunction in the pathogenesis of COVID‐19 pneumonia. [8] [9] [10] However, the pathological changes in the lungs caused by SARS-CoV-2, especially in the early stage of infection, have seldom been described. Combining epidemiological characteristics, clinical presentation, nucleic acid testing and intracytoplasmic viral-like inclusions, it is reasonable to speculate that this case represents an early stage of lung injury secondary to SARS-CoV-2 infection. Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer cache = ./cache/cord-270462-d9l3agr0.txt txt = ./txt/cord-270462-d9l3agr0.txt === reduce.pl bib === id = cord-270329-t60t639i author = Schloer, Sebastian title = Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date = 2020-10-16 pages = extension = .txt mime = text/plain words = 1053 sentences = 77 flesch = 52 summary = title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. While drugs 87 directly acting on virus structures are much more likely to completely eliminate the 88 pathogens in shorter treatment time, emerging viral resistance to these antivirals is a major 89 concern, as observed with the influenza neuraminidase inhibitor oseltamivir (Kim et al., itraconazole antiviral activity in SARS-CoV-2 infected Vero cells (Fig. 1b) . cache = ./cache/cord-270329-t60t639i.txt txt = ./txt/cord-270329-t60t639i.txt === reduce.pl bib === id = cord-270533-s2d3q4ob author = Lau, Yu-Lung title = SARS: future research and vaccine date = 2004-11-05 pages = extension = .txt mime = text/plain words = 3000 sentences = 167 flesch = 47 summary = Severe acute respiratory syndrome (SARS), a newly emerged infectious disease of humans in the 21st century, appeared in Guangdong Province in Southern China in November 2002 and spread to 26 countries on five continents along international air travel routes, causing large scale outbreaks in Hong Kong, Singapore and Toronto in early 2003. This novel CoV has satisfied Koch's postulates for causation by its consistent isolation from SARS patients, viral isolation, reproduction of disease in non-human primates after inoculation and the presence of specific antibody response against the virus in both patients and experimentally infected primates 8 . Indeed, sporadic reemergence of cases have been reported in Guangdong Province as well as from research laboratories Summary Severe acute respiratory syndrome (SARS) is a new infectious disease of the 21st century that has pandemic potential. The high morbidity and mortality of this potentially pandemic infection demands a rapid research response to develop effective antiviral treatment and vaccine. cache = ./cache/cord-270533-s2d3q4ob.txt txt = ./txt/cord-270533-s2d3q4ob.txt === reduce.pl bib === id = cord-269771-hffxb7bm author = Cheung, Ka Shing title = Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date = 2020-04-03 pages = extension = .txt mime = text/plain words = 4797 sentences = 263 flesch = 51 summary = title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. The proportion of patients with detectable stool viral RNA was higher among those with diarrhea than those without diarrhea Table 2 including the hospital admission period, places in which the patients were recruited, sample size, age, sex, disease severity, non-gastrointestinal symptoms (fever and respiratory symptoms) on presentation, and gastrointestinal symptoms (anorexia, nausea/vomiting, diarrhea and abdominal pain/discomfort). In this meta-analysis of 4,243 COVID-19 patients from six countries, the pooled prevalence of all gastrointestinal symptoms (including anorexia, nausea/vomiting, diarrhea or abdominal pain) was 17.6%. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-269771-hffxb7bm.txt txt = ./txt/cord-269771-hffxb7bm.txt === reduce.pl bib === id = cord-270645-tzctvs9q author = Martelletti, Luigi title = Air Pollution and the Novel Covid-19 Disease: a Putative Disease Risk Factor date = 2020-04-15 pages = extension = .txt mime = text/plain words = 946 sentences = 58 flesch = 50 summary = This study analyzed the correlation between the increment of the API (Air Pollution Index) and the rate of fatality due to SARS across 5 regions in China. In 2017, Ciencewicki and Jaspers conducted an epidemiological analysis regarding air pollution and respiratory viral infections which noted positive correlation between the high level of particulate matter (PM) in some urban areas and mortality due to cardiovascular and respiratory conditions. A recent study from the SIMA (Società Italiana di Medicina Ambientale) reported that the specificity of the high spread of the contagious virus in some areas of Northern Italy is likely to be linked to air pollution conditions. The above studies show that air pollutants, such as particulate matter, nitrogen dioxide, and carbon monoxide, are most likely direct to facilitate the longevity of virus particles in favorable climate conditions. Air pollution and case fatality of SARS in the People's Republic of China: an ecologic study cache = ./cache/cord-270645-tzctvs9q.txt txt = ./txt/cord-270645-tzctvs9q.txt === reduce.pl bib === id = cord-270278-d61n3v90 author = Choi, S.M.Y. title = Enhancing legal preparedness for the prevention and control of infectious diseases: Experience from severe acute respiratory syndrome in Hong Kong date = 2009-03-31 pages = extension = .txt mime = text/plain words = 4224 sentences = 193 flesch = 45 summary = This article shares Hong Kong's experience in reforming its public health legislation to: (1) update terminology and re-organize provisions in accordance with modern public health disease control principles and control mechanisms for disease; (2) enhance responsiveness for better preparedness and flexibility in handling emergent infections; (3) ensure appropriate checks and balances to coercive powers; and (4) introduce emergency powers for the handling of public health emergencies. During the outbreak of SARS in 2003, the Quarantine and Prevention of Disease Ordinance 2 (QPDO) of the laws of Hong Kong was the legal tool that provided the legal framework for the prevention and control of infectious diseases of public health importance in Hong Kong. This article shares Hong Kong's experience in reforming its public health legislation, leading to the passing of the Prevention and Control of Disease Ordinance 4 in order to strengthen the capacity of law to support strategy in the control of infectious diseases. cache = ./cache/cord-270278-d61n3v90.txt txt = ./txt/cord-270278-d61n3v90.txt === reduce.pl bib === id = cord-270474-jaurhjvr author = Xiang, Zhen title = Glucocorticoids improve severe or critical COVID-19 by activating ACE2 and reducing IL-6 levels date = 2020-06-27 pages = extension = .txt mime = text/plain words = 4417 sentences = 258 flesch = 46 summary = We verified the efficacy of nine chemicals on regulating ACE2 expression in human GES-1, an upper digestive tract epithelial cell line, and THP-1, a human monocyte cell line, and found that several glucocorticoids imparted activating effects on ACE2 in both cell lines. We retrospectively analyzed the therapeutic efficacy of nine severe or critical patients from a cohort of 90 COVID-19 cases, who received medium to small doses of glucocorticoids from our integrated medical team in Wuhan. This study provides experimental and clinical evidence that medium-to-low-dose glucocorticoids may play a protective role in the respiratory and digestive systems by activating ACE2 and suppressing cytokine storm. Because the epithelial cells of the respiratory and digestive tracts are susceptible targets of SARS-CoV-2, we verified the regulatory effects of several candidate agonists of ACE2 expression on available normal human epithelial cells. Compared to the blank control, hydrocortisone revealed the strongest activating effect on ACE2 expression, followed by prednisolone, dexamethasone, and methylprednisolone. cache = ./cache/cord-270474-jaurhjvr.txt txt = ./txt/cord-270474-jaurhjvr.txt === reduce.pl bib === id = cord-270635-l8380adr author = Maggi, Enrico title = COVID-19: unanswered questions on immune response and pathogenesis date = 2020-05-08 pages = extension = .txt mime = text/plain words = 880 sentences = 64 flesch = 60 summary = It is generally accepted that only achieving a better understanding of the interactions between the virus and host immune response and of the pathogenesis of infection is crucial to identify valid therapeutic tools to control virus entry, replication and spread as well as to impair its lethal effects. On this basis, we also touch important aspects regarding the immune response in asymptomatic subjects, the immune-evasion of SARS-CoV-2 in severe patients and differences in disease severity by age and gender. This implies to be able to answer many questions on the virus itself, on the pathogenesis of infection, on the 81 host immune response and to identify therapeutic tools to control virus entry into the cells, its replication and 82 spread as well as its lethal effects. Humoral Immune Responses SARS-CoV 3 -Seroconversion few days after the disease onset and specific IgG detectable in most patients by 14 days. cache = ./cache/cord-270635-l8380adr.txt txt = ./txt/cord-270635-l8380adr.txt === reduce.pl bib === id = cord-270399-yfko8mpc author = Foster, Allison title = It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3390 sentences = 210 flesch = 47 summary = title: It's complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury In this report, we discuss a unique case of an HIV-positive patient in New York City who presented with a 2-week history of worsening fatigue, cough, dyspnea, and myalgias and was found to have COVID-19 pneumonia and acute kidney injury. The pathophysiologic mechanisms of acute kidney injury, SARS-CoV-2 renal tropism, and the impact of highly active antiretroviral therapy on COVID-19 pneumonia are discussed. 20 Whether directly through involvement of SARS-CoV-2 interaction with ACE-2 receptor or indirectly from causing hypotension from an undetermined mechanism, this patient's decline in renal function can be attributed to his acute infection with COVID-19. [24] [25] [26] Our patient's exceptional clinical course despite having HIV lends to the idea that his HAART regimen as well as his azithromycin use prior to presentation may have decreased the total amount of SARS-CoV-2 viral replication in both the renal parenchyma and pulmonary tissue resulting in a rapid recovery and subsequent hospital discharge. cache = ./cache/cord-270399-yfko8mpc.txt txt = ./txt/cord-270399-yfko8mpc.txt === reduce.pl bib === id = cord-270788-w0pewq52 author = Chou, Chih-Fong title = A novel cell-based binding assay system reconstituting interaction between SARS-CoV S protein and its cellular receptor date = 2004-11-05 pages = extension = .txt mime = text/plain words = 4759 sentences = 241 flesch = 64 summary = A binding epitope with lesser degree of glycosylation and native conformation was localized by using rabbit anti-sera raised against five denatured recombinant S protein fragments expressed in Escherichia coli. Cells were washed once with PBS and three times with PBS containing 500 mM NaCl. To test whether the anti-sera from SARS patients or raised against S protein fragments can block the binding between CHO-SG and Vero E6, dislodged CHO-SG cells were preincubated with the anti-serum to be tested at 4 • C for 1 h. The CHO-G cells resisted the PBS wash but were detached by the solutions containing supplemented NaCl. In contrast, the binding between CHO-SG and Vero E6 could resist up to 1M NaCl. We sought to investigate the binding specificity of this interaction by testing whether the serum from a recovered SARS patient (P8 in Tan et al., 2004a ) and a goat anti-ACE2 antibody could block the interaction. cache = ./cache/cord-270788-w0pewq52.txt txt = ./txt/cord-270788-w0pewq52.txt === reduce.pl bib === id = cord-270515-bfjdvfuq author = Deng, Chu-Xia title = The global battle against SARS-CoV-2 and COVID-19 date = 2020-03-15 pages = extension = .txt mime = text/plain words = 1052 sentences = 52 flesch = 54 summary = Compared with its close related coronavirus family member SARS-CoV and MERS-CoV, which infected 8096 and 2494 people in year 2003 and year 2012, respectively, the outbreak of COVID-19 is much more serious with its high virulence. Zheng indicated that SARS-CoV-2 is an emerging new coronavirus that causes a global threat, and summarized the key events occurred during the early outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients, the possible transmission pathways of the virus, the Zhou and Zhao pointed out the great importance of using therapeutic neutralizing antibodies (NAbs) to control the spread and re-emergence of SARS-CoV-2 and assert that the development of NAbs therefore should be a high priority in near future [5] . Understanding the knowledge, attitudes and behaviors of residents towards COVID-19 during the early stage of disease outbreak could help the authority effectively implement preventive and control measures. Traditional Chinese Medicine in the Treatment of Patients Infected with 2019-New Coronavirus (SARS-CoV-2): A Review and Perspective cache = ./cache/cord-270515-bfjdvfuq.txt txt = ./txt/cord-270515-bfjdvfuq.txt === reduce.pl bib === id = cord-270591-0szbkhiz author = Shi, Chen title = Comprehensive Landscape of Heparin Therapy for COVID-19 date = 2020-10-22 pages = extension = .txt mime = text/plain words = 6198 sentences = 354 flesch = 41 summary = Clinical observations found that systemic symptoms caused by SARS-CoV-2 infection are attenuated when using the anticoagulant agent heparin, indicating that heparin may play other roles in managing COVID-19, in addition to prevention of pulmonary thrombosis. This review discusses the pharmacological mechanisms of heparin regarding its anticoagulant, anti-inflammatory and direct antiviral activities, providing current evidence concerning the effectiveness and safety of heparin therapy for this major public health emergency. In addition to its anticoagulant and anti-inflammatory activity, heparin may possess a direct antiviral effect to SARS-CoV-2, based on the preclinical studies for other viral infections. There are both preclinical evidence and clinical data to demonstrate the benefits of heparin therapy for SARS-CoV-2 infection.With anticoagulant and anti-inflammatory effects, heparin can offer supportive treatment and alleviate the systematic symptoms of COVID-19. cache = ./cache/cord-270591-0szbkhiz.txt txt = ./txt/cord-270591-0szbkhiz.txt === reduce.pl bib === id = cord-270606-r46pbaf0 author = Rashed, Mohamed Z. title = Rapid detection of SARS-CoV-2 antibodies using electrochemical impedance-based detector date = 2020-10-07 pages = extension = .txt mime = text/plain words = 3135 sentences = 152 flesch = 42 summary = Here, we demonstrate rapid label-free electrochemical detection of SARS-CoV-2 antibodies using a commercially available impedance sensing platform. A 16-well plate containing sensing electrodes was pre-coated with receptor binding domain (RBD) of SARS-CoV-2 spike protein, and subsequently tested with samples of anti-SARS-CoV-2 monoclonal antibody CR3022 (0.1 [Formula: see text] g/ml, 1.0 [Formula: see text] g/ml, 10 [Formula: see text] g/ml). In this study, we report a non-faradic capacitive immunosensing assay using a commercially-available impedance detection system that uses specialized well-plates that have integrated sensing electrodes from ACEA Biosciences ( Figure 1 ). Coating the wells with anti-SARS-CoV-2 antibodies instead of spike RBD antigen may enable rapid EIS detection of viral particles in patient samples, although further testing is needed to determine the limit of detection for that approach. An alternative medical Rapid Detection of SARS-CoV-2 Antibodies Figure S1 : Measurements with greater time resolution were acquired with a different impedance analyzer (Agilent 4294A, 10 kHz, 0.5 V), demonstrating improved resolution. cache = ./cache/cord-270606-r46pbaf0.txt txt = ./txt/cord-270606-r46pbaf0.txt === reduce.pl bib === id = cord-270613-vnjuubt4 author = Poon, Terence C.W. title = Proteomic analysis reveals platelet factor 4 and beta‐thromboglobulin as prognostic markers in severe acute respiratory syndrome date = 2012-06-28 pages = extension = .txt mime = text/plain words = 3358 sentences = 176 flesch = 49 summary = The data on 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count) from 38 SARS patients before treatment were subjected to forward stepwise multiple logistic regression (SPSS, v18, IBM) for prediction of the ICU admission and/or supplemental oxygen administration in the later period. Among the 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count), multiple logistic regress analyses identified four proteomic features (m/z 6634, m/z 7769, m/z 8635, m/z 8865) as statistically significant prognostic markers for supplemental oxygen administration or ICU admission in the later period. To confirm the differential patterns and the identities of the m/z 7769 and m/z 8865 proteomic features, serum samples were subjected to Western blot analysis using specific antibodies against PF4 and beta-TG. cache = ./cache/cord-270613-vnjuubt4.txt txt = ./txt/cord-270613-vnjuubt4.txt === reduce.pl bib === id = cord-270665-z4l3lq39 author = Tian, Qing title = Endoscopic mask innovation and protective measures changes during the COVID‐19 pandemic: experience from a Chinese hepato‐biliary‐pancreatic unit date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1833 sentences = 115 flesch = 44 summary = However, due to the distinctive epidemiological characteristics of SARS‐CoV‐2 (the virus causing COVID‐19), healthcare providers are exposed to the patient's respiratory and gastrointestinal fluids, rendering endoscopy a high risk for transmitting a nosocomial infection. This article introduces preventive measures for endoscopic treatment enacted in our medical center during COVID‐19, including the adjustment of indications, the application of endoscope protective equipment, the design and application of endoscopic masks and splash‐proof films, and novel recommendations for bedside endoscope pre‐sterilization. During the COVID-19 pandemic, due to the distinctive epidemiological characteristics of SARS-CoV-2, endoscopy poses a high risk of nosocomial infection, since healthcare providers are exposed to the patient's respiratory and gastrointestinal fluids 6 . 6) All medical personnel who a) have fever or respiratory symptoms, b) had contact with suspected or confirmed COVID-19 patients, c) live in or had contact with individuals residing in areas where the disease is prevalent, or d) recently returned from a high-pandemic area or country should undergo self-isolation for 14 days. cache = ./cache/cord-270665-z4l3lq39.txt txt = ./txt/cord-270665-z4l3lq39.txt === reduce.pl bib === id = cord-269871-w41o1krr author = Aggarwal, Shyam title = High Viral Load and Poor Ventilation: Cause of High Mortality From COVID-19 date = 2020-07-25 pages = extension = .txt mime = text/plain words = 835 sentences = 50 flesch = 57 summary = Low viral load in the nasal cavity due to open air ventilation is a plausible reason for this difference. As a result, people living in developed countries tend to build up high viral load in their nasal cavity and nasopharynx. These factors indicate a strong association between high viral load and poor ventilation, which, in turn, leads to high mortality from COVID-19 in developed Western nations. In this article, we have tried to explain that poor ventilation and subsequent buildup of high viral load could be a reason for such a drastic difference in mortality rates among these two groups of countries. 2 These studies suggest an association of high viral load in nasal cavity and nasopharynx with the severity of the disease. For this reason, the viral load in the nasal cavity and the nasopharynx could be lower and result in a less severe disease. cache = ./cache/cord-269871-w41o1krr.txt txt = ./txt/cord-269871-w41o1krr.txt === reduce.pl bib === id = cord-270550-if748w2n author = Bailey, Adam L. title = SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date = 2020-11-05 pages = extension = .txt mime = text/plain words = 5808 sentences = 440 flesch = 49 summary = To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. cache = ./cache/cord-270550-if748w2n.txt txt = ./txt/cord-270550-if748w2n.txt === reduce.pl bib === id = cord-270510-z6qg48nz author = Lauro, A. title = Emergency Endoscopy During the SARS-CoV-2 Pandemic in the North of Italy: Experience from St. Orsola University Hospital—Bologna date = 2020-04-22 pages = extension = .txt mime = text/plain words = 1669 sentences = 87 flesch = 42 summary = We report our experience with emergency endoscopies in the COVID-19 era; the goal was to sustain a full emergency endoscopic capability despite the hospital overload due to SARS-CoV-2-infected patients. Instead, emergency endoscopies were performed on SARS-CoV-2-negative and positive patients; a negative-pressure room outside the endoscopy department was planned, but, at the beginning of the pandemic, the only practical possibility was to create a separate suite for SARS-CoV-2-positive patients needing Editor's Note: This report is one of a series documenting the impact of the pandemic caused by the SARS-CoV-2 virus with resultant morbidity and mortality due to COVID-19. In our hospital, trainees are essential to the management of the burden among patients infected by SARS-CoV-2, but, regarding endoscopy, our policy was to stop training in the urgent endoscopy suite in order to reduce the numbers of inside operators and their use of PPE. cache = ./cache/cord-270510-z6qg48nz.txt txt = ./txt/cord-270510-z6qg48nz.txt === reduce.pl bib === id = cord-270377-lfcoy8n1 author = Novazzi, Federica title = SARS-CoV-2 positivity in rectal swabs implication for possible transmission date = 2020-07-02 pages = extension = .txt mime = text/plain words = 422 sentences = 37 flesch = 62 summary = Currently, the diagnosis is based on molecular detection of SARS-CoV-2 RNA in respiratory samples such as nasal swab (NS) [1] . However, the evidence that NS in patients with pneumoniae were sometimes negative highlight the needed to collect alternative clinical specimens in whom SARS-CoV-2 RNA could be detected. From the past coronavirus epidemics (SARS-CoV and MERS-CoV) we learned that viral RNA could be also detected in several clinical specimens such as rectal swab (RS) other than respiratory samples [2] . In this perspective, we explored the potential diagnostic role of SARS-CoV-2 real-time RT-PCR performed in biological specimens different from respiratory samples. However, the very low rate of SARS-CoV-2 positivity in samples different from respiratory specimens suggest a limited J o u r n a l P r e -p r o o f Detection of SARS-CoV-2 in Different Types of Clinical Specimens cache = ./cache/cord-270377-lfcoy8n1.txt txt = ./txt/cord-270377-lfcoy8n1.txt === reduce.pl bib === id = cord-270495-2u072mtp author = Lokida, Dewi title = Diagnosis of COVID-19 in a Dengue-Endemic Area date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1750 sentences = 110 flesch = 53 summary = When SARS-CoV-2 is negative and clinical indication is present (at least fever and thrombocytopenia), DENV NS1 antigen and/or IgM/IgG antibody testing may be performed. Clinicians from Singapore reported two COVID-19 cases that were misdiagnosed as dengue among patients who presented with clinical manifestations and hematology profiles, suggesting dengue infection and false-positive DENV IgM antibody using a rapid diagnostic test (RDT). COVID-19 cases were defined as inpatients who met the COVID-19 criteria based on a predetermined combination of symptoms, laboratory testing, imaging, and risk exposure at Tangerang District Hospital, Indonesia (see Supplemental Table 1 ), and had a positive nasopharyngeal or oropharyngeal real-time RT-PCR for SARS-CoV-2. None of the 42 subjects was positive for dengue NS1 or showed seroconversion or increasing DENV IgM and IgG index values, suggesting no acute DENV infection among these COVID-19 cases. The third patient did not recall having a fever before acute COVID-19 illness, suggesting asymptomatic or mild dengue, the most common presentation of DENV infection. cache = ./cache/cord-270495-2u072mtp.txt txt = ./txt/cord-270495-2u072mtp.txt === reduce.pl bib === id = cord-270622-aofva2ab author = Li, Qizhang title = Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 2830 sentences = 165 flesch = 55 summary = title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 Based on the "steric-clashes alleviating receptor (SCAR)" strategy developed in our lab recently, we screened the library of clinic and investigational drugs, and identified nine drugs that might be repurposed as covalent inhibitors of the priming proteases (cathepsin B, cathepsin L, and TMPRSS2) of the spike protein of SARS-CoV-2. After careful filtering and 79 evaluation, we identified five (trapoxin B, neratinib, HKI-357, domatinostat and (Z)-dacomitinib) 80 potential covalent inhibitors for CatB, three (neratinib, HKI-357 and (Z)-dacomitinib) for CatL Although the docked poses 160 were slightly different on these two proteins, the warheads of these drugs were also at the positions 161 suitable for covalent bonding (Figure 3F-H) Taken together, using our SCARdock protocol, we identified nine drugs that might be repurposed as 229 the covalent inhibitors of the priming proteases of the S protein of SARS-CoV-2. cache = ./cache/cord-270622-aofva2ab.txt txt = ./txt/cord-270622-aofva2ab.txt === reduce.pl bib === id = cord-270837-xvauo76d author = Hui, David S. title = The 1-Year Impact of Severe Acute Respiratory Syndrome on Pulmonary Function, Exercise Capacity, and Quality of Life in a Cohort of Survivors date = 2005-10-31 pages = extension = .txt mime = text/plain words = 5821 sentences = 284 flesch = 54 summary = Our assessment included: lung volume (total lung capacity [TLC], vital capacity, residual volume, functional residual capacity), spirometry (FVC, FEV1), diffusing capacity of the lung for carbon monoxide (Dlco), inspiratory and expiratory respiratory muscle strength, 6-min walk distance (6MWD), chest radiographs (CXRs), and HRQoL by Medical Outcomes Study 36-Item Short-Form General Health Survey questionnaire. The lung function tests at 12 months showed significantly lower percentage of predicted FVC, VC, TLC, RV, and Dlco in survivors who required ICU support than those who were treated on medical wards, although no significant difference was noted for 6MWD and respiratory muscle strength between the two groups ( Table 5) . The 1-year lung function indexes (percentage of predicted FVC, VC, TLC, RV, and Dlco) in survivors who required ICU support were remarkably lower than those of patients who were treated on medical wards, although no significant differences were noted for 6MWD, respiratory muscle strength, and health status between the two groups. cache = ./cache/cord-270837-xvauo76d.txt txt = ./txt/cord-270837-xvauo76d.txt === reduce.pl bib === id = cord-270475-mkpn9tz6 author = Requena, Manuel title = COVID-19 and Stroke: incidence and etiological description in a high-volume center. date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2426 sentences = 137 flesch = 49 summary = Although COVID-19 pandemic has produced an enormous collateral damage over stroke systems of care leading to a drop of mild strokes admissions and late arrival of severe strokes, only incidental cases of large vessel occlusion (LVO) in young adults infected by SARS-CoV-2 have been reported without a clear causative relationship (4) . The presence of SARS-CoV-2 infection has been associated with worse functional outcome and higher mortality among patients with acute stroke (11) ; in parallel, history of stroke has also been associated with more severe clinical symptoms and poorer outcomes in patients with COVID-19 (12) . From March 2 nd to April 30 th , 2050 patients were admitted to our center with RT-PCR confirmed SARS-CoV-2 infection; of them 21 (1.02%) presented an acute ischemic stroke 21 and 4 (0.2%) suffered an ICH. Our study shows that the frequency of acute stroke in patients with COVID-19 requiring hospital admission is low (1%) and in most cases a usual cause of stroke was identified. cache = ./cache/cord-270475-mkpn9tz6.txt txt = ./txt/cord-270475-mkpn9tz6.txt === reduce.pl bib === id = cord-270909-wb7mwklo author = Cheng, Vincent C.C. title = Absence of nosocomial transmission of coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in the pre-pandemic phase in Hong Kong date = 2020-05-24 pages = extension = .txt mime = text/plain words = 2262 sentences = 111 flesch = 46 summary = BACKGROUND: To describe the infection control strategy to achieve zero nosocomial transmission of symptomatic coronavirus disease (COVID-19) due to SARS-CoV-2 during the pre-pandemic phase (the first 72 days after announcement of pneumonia cases in Wuhan) in Hong Kong. Pandemic infection of a coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) was declared by World Health Organization (WHO) on 11 March 2020, which is 72 days after announcement of a cluster of patients with community acquired pneumonia in Wuhan, Hubei Province by National Health Commission of the People's Republic of China (NHCPRC), on 31 December 2019 (day 1) [1] . Up to 11 March 2020 (day 72 after the official announcement of a cluster of pneumonia of unknown etiology in Wuhan, Hubei Province, a total of 130 cases of SARS-CoV-2 infection were confirmed in Hong Kong, while the first 42 patients were reported previously [9] . cache = ./cache/cord-270909-wb7mwklo.txt txt = ./txt/cord-270909-wb7mwklo.txt === reduce.pl bib === id = cord-270866-olc5r2yx author = Mallet, Jasmina title = Addictions in the COVID-19 era: Current evidence, future perspectives a comprehensive review date = 2020-08-12 pages = extension = .txt mime = text/plain words = 6839 sentences = 392 flesch = 53 summary = RESULTS: Overall, pathophysiological data showed an increased risk of infections for individuals with Substance Use Disorders (SUD) and a possible protective role of nicotine. An electronic search was conducted in Medline (PubMed interface), using the MESH (Medical Subject Headings) search terms ("coronavirus 2019" OR "COVID-19" OR "2019-nCoV" OR "SARS-CoV-2") AND "substance use" OR "SUD" OR "tobacco smoking" OR "cigarette "OR "smoking" OR "nicotine" / "alcohol" / "cannabis" OR "THC" /"opiates" OR "opioid"; between 2019 and the present time (i.e., June 4, 2020), with language restriction (English or French). Heavy alcohol use (assessed several years before) was not associated with an increased risk of COVID-19 infection or COVID-19 related hospitalization (OR=1.12 (0.93-1.35)). Finally, as all past economic crises were associated with increased long-term alcohol-related problems (especially for men and low socio-economic strata) (de Goeij et al., 2015) , we might expect important effects of the COVID-19 pandemic in the next decade. Prevalence, Severity and Mortality associated with COPD and Smoking in patients with COVID-19: A Rapid Systematic Review and Meta-Analysis cache = ./cache/cord-270866-olc5r2yx.txt txt = ./txt/cord-270866-olc5r2yx.txt === reduce.pl bib === id = cord-270886-m9na7cbm author = Quadeer, Ahmed Abdul title = Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges date = 2020-08-15 pages = extension = .txt mime = text/plain words = 1216 sentences = 60 flesch = 37 summary = Serological assays can also assist in detecting a large number of subclinical infections in the community arising largely due to the high proportion of asymptomatic COVID-19 cases, and in identifying donors with highly reactive antibodies for convalescent plasma therapy. In the current issue of EBioMedicine, Ng and colleagues attempt to address the above limitations of current serological assays by presenting a novel linear B cell immunodominant epitopes based assay for detecting exposure to SARS-CoV-2 [5] . Specifically, they identified a set of five immunodominant linear B cell epitopes from a peptide library of SARS-CoV-2 structural proteins by performing IgG reactivity test on pooled plasma samples of COVID-19 infected patients from Singapore. Consistent with multiple recent reports (e.g., [7, 8] ), the authors also found that the magnitude of IgG responses in COVID-19 patients against the identified epitopes correlated with disease severity. Second, the usefulness of serological assays in detecting prior exposure relies on the stimulation and persistence of SARS-CoV-2-specific antibody responses in infected patients. cache = ./cache/cord-270886-m9na7cbm.txt txt = ./txt/cord-270886-m9na7cbm.txt === reduce.pl bib === id = cord-270661-e83xe4sp author = Falahi, Shahab title = Transmission routes for SARS-COV-2 infection: Review of Evidence date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1274 sentences = 90 flesch = 57 summary = Subsequent studies have shown that the virus is also present in saliva; given the evidence of virus transmission from asymptomatic individuals(1) and the presence of the virus in saliva, it has been suggested that even secretory droplets during normal speeching may be a route to transmit SARS-COV-2 (2). In a number of studies, the SARS-CoV-2 genome was identified in blood samples from a number of patients with COVID-19 (15, 16) , and subsequently raised the question: Is SARS-CoV-2 transmitted through transfusion? In a study, all blood samples of asymptomatic people with COVID-19 were negative for SARS-COV-2 PCR and RNAemia was detected in severe and symptomatic cases. Sexual transmission: SARS-COV-2 is present in saliva and feces, and in theory it is possible to transmit through oral-anal intercourse (17) but this sexual habit is not common, so it is unlikely that this route will be a significant mean of transmission. cache = ./cache/cord-270661-e83xe4sp.txt txt = ./txt/cord-270661-e83xe4sp.txt === reduce.pl bib === id = cord-270588-c9rxmo44 author = Algarroba, Gabriela N. title = Visualization of SARS-CoV-2 virus invading the human placenta using electron microscopy date = 2020-05-13 pages = extension = .txt mime = text/plain words = 825 sentences = 61 flesch = 50 summary = We present a case of rapid clinical deterioration in a woman at 28 weeks' gestation due to 36 severe COVID-19 infection. Using electron microscopy to evaluate for potential viral transmission in the 37 placenta, we visualized and identified coronavirus virions invading into syncytiotrophoblasts in placental 38 All placentas from COVID-19 positive mothers are submitted for gross and histologic 70 evaluation in our institution. In this case, the placenta was submitted to the pathology laboratory 71 without fixative; fresh tissue was taken, using appropriate personal protective gear, under the Fisher 72 Ten representative, 3 mm thick tissue sections were 76 submitted from the placental parenchyma, membranes and umbilical cord for histologic evaluation. Preterm delivery 125 in pregnant woman with critical COVID-19 pneumonia and vertical transmission Clinical characteristics and intrauterine 130 vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective 131 review of medical records Evidence for and against 133 vertical transmission for SARS-CoV-2 (COVID-19) cache = ./cache/cord-270588-c9rxmo44.txt txt = ./txt/cord-270588-c9rxmo44.txt === reduce.pl bib === id = cord-270858-ozvdz9ew author = Altmann, Daniel M title = What policy makers need to know about COVID-19 protective immunity date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1563 sentences = 90 flesch = 49 summary = Strategies in various countries that aim to stagger return to work on the basis of disease severity risk and age do not take account of how exposing even lower-risk individuals, such as young people with no comorbidities, to the virus so as to increase herd immunity can still result in pandemic spread. A caveat is that most studies, either of SARS survivors or of COVID-19 patients, have focused on people who were hospitalised and had severe, symptomatic disease. Anecdotal reports of reinfection from China and South Korea should be regarded with caution because some individuals who seemed to have cleared SARS-CoV-2 infection and tested negative on PCR might nevertheless have harboured persistent virus. 16 On the basis of this estimated R 0 , the herd immunity calculation suggests that at least 60% of the population would need to have protective immunity, either from natural infection or vaccination. cache = ./cache/cord-270858-ozvdz9ew.txt txt = ./txt/cord-270858-ozvdz9ew.txt === reduce.pl bib === id = cord-270743-yyl50z94 author = Haseli, Sara title = Reply to “MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss” date = 2020-06-10 pages = extension = .txt mime = text/plain words = 619 sentences = 40 flesch = 47 summary = title: Reply to "MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss" We read with great interest the letter by Eliezer and Hautefort discussing our recent report in Academic Radiology of magnetic resonance imaging (MRI) findings in a patient with coronavirus disease-2019 (Covid-19) and enumerating the possible mechanisms of SARS-CoV-2-induced anosmia 1 . In the apparent absence of anatomical changes on MRI and to assess a putative loss of neuronal function in anosmia of Covid-19, we performed 18 FDG PET/CT scan in a patient with isolated anosmia under neutral olfactory condition, which revealed hypoactivity of the left orbitofrontal cortex, thus suggesting a probable neuroinvasive mechanism for anosmia of Covid-19 8 . MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. cache = ./cache/cord-270743-yyl50z94.txt txt = ./txt/cord-270743-yyl50z94.txt === reduce.pl bib === id = cord-270683-982eqtog author = Pavel, Shaikh Terkis Islam title = Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date = 2020-09-16 pages = extension = .txt mime = text/plain words = 5515 sentences = 318 flesch = 61 summary = We determined that the Vero E6 and MA-104 cell lines are suitable for supporting SARS-CoV-2 that supports viral replication, development of cytopathic effect (CPE) and subsequent cell death. Phylogenetic analyses of the whole genome sequences showed that the hCoV-19/Turkey/ERAGEM-001/2020 strain clustered with the strains primarily from Australia, Canada, England, Iran and Kuwait and that the cases in the nearby clusters were reported to have travel history to Iran and to share the common unique nucleotide substitutions. For whole genome sequencing of hCoV-19/Turkey/ERAGEM-001/2020, Vero E6 cells infected with the virus were used for RNA extraction. The growth kinetics study showed that SARS-CoV-2 replicated rapidly and efficiently and could be detected within 6 h post-infection in Vero E6 and MA-104 cells (Fig 6A and 6B ). Immunoblotting analysis also confirmed that only Vero E6 and MA-104 cell lines infected with SARS-CoV-2 showed the expression of the virus specific proteins expression (Fig 5) . cache = ./cache/cord-270683-982eqtog.txt txt = ./txt/cord-270683-982eqtog.txt === reduce.pl bib === id = cord-270951-6nq3jwgr author = Amerio, Paolo title = COVID‐19 and psoriasis: Should we fear for patients treated with biologics? date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2258 sentences = 154 flesch = 53 summary = One of question is if psoriasis patients treated with immunomodulating and immunosuppressive drugs have to discontinue their treatment in the midst of fears for the infection and its consequences. Previous coronaviruses outbreaks reports, current published evidences on pathogenesis and on clinical reports of COVID infection in immunosuppressed patients are used to make a scientifically based decision. 3 Recently some concern over the possibility that cytokine directed immunosuppressive treatment may be a risk factor for SARS-CoV-2 infection in psoriasis patients has been expressed. Given the potential role of proinflammatory cytokines in the pathogenesis of SARS and MERS severe disease, also ant inflammatory drugs have been suggested as novel treatments in these diseases. High levels of IL-2, IL-7, GM-CSF, MIP1-α, and TNF-α have also been correlated with disease severity in SARS-CoV-2 infected patients. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): the perspectives of clinical immunologists from China cache = ./cache/cord-270951-6nq3jwgr.txt txt = ./txt/cord-270951-6nq3jwgr.txt === reduce.pl bib === id = cord-270528-3rsv3jlh author = Yazdanpanah, Fereshteh title = The immune system and COVID-19: Friend or foe? date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3134 sentences = 192 flesch = 48 summary = The pathogenesis of this virus is not yet clearly understood, but there is evidence of a hyper-inflammatory immune response in critically ill patients, which leads to acute respiratory distress syndrome (ARDS) and multi-organ failure. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID19) , and has affected people's lives globally, since first observed in Wuhan, China in the last days of 2019 (1, 2) . On the other hand, the hyper-inflammatory and cytokine release syndrome (CRS) typical of COVID-19 causes tissue damage to the lung epithelium and ARDS (32); therefore, immunosuppressive drugs may be useful as there is some evidence that an anti-IL-6 approach is effective in critically ill patients in the ICU (33) . Also, due to the overexpression of ACE2 in islet cells of the pancreas, SARS-CoV-2 may be a diabetogenic virus that causes severe instability in the blood glucose levels of diabetes patients, which worsens the inflammatory imbalance (37) . cache = ./cache/cord-270528-3rsv3jlh.txt txt = ./txt/cord-270528-3rsv3jlh.txt === reduce.pl bib === id = cord-270888-8j17ul7k author = Fernández-González, Sara Mª title = ¿Infección Por Sars-Cov-2 Como Desencadenante De Un Síndrome Inflamatorio Sistémico? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 862 sentences = 90 flesch = 50 summary = Desde entonces este síndrome se ha conocido con diferentes nomenclaturas y, desde Mayo, se conoce como Paediatric inflammatory multisystem syndrome temporally associated with severe J o u r n a l P r e -p r o o f acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PIMS-TS) [3] [4] [5] . Presentamos el caso de un niño de 4 años con síndrome de respuesta inflamatoria sistémica e IgG positiva para SARS-CoV-2 con IgM y reacción en cadena de la polimerasa (PCR) sobre muestra de frotis nasofaríngeo negativas. Tras 24 horas de inicio de tratamiento presentó una mejoría clínica progresiva con desaparición del exantema, edema e hiperemia conjuntival, así como normalización de constantes (frecuencia cardiaca 71 lpm y tensión arterial 97/52 mmHg, p50) y parámetros analíticos, a excepción de trombocitosis reactiva (plaquetas 579000/L) Estuvo ingresado durante 9 días en planta de hospitalización, hasta completar 7 días de antibioterapia intravenosa en espera de resultados de cultivos y mejoría de parámetros analíticos, manteniéndose estable a nivel hemodinámico y respiratorio sin necesitar soporte vasoactivo ni respiratorio. cache = ./cache/cord-270888-8j17ul7k.txt txt = ./txt/cord-270888-8j17ul7k.txt === reduce.pl bib === id = cord-270935-t9pym9k0 author = Dumyati, Ghinwa title = Does Universal Testing for COVID-19 Work for Everyone? date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2681 sentences = 179 flesch = 55 summary = Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. Dr. Jump reports support for this work in part through the Cleveland Geriatric Research 50 While there is general agreement that increased access to testing is important for personal and 23 public health, the selection and use of diagnostic tests to mitigate COVID-19 infections in post-24 acute and long-term care settings is complex and should be tailored to individual sites. Because he met the nursing 36 home's enhanced screening criteria for COVID-19 (Table 1) , 1 he was placed on transmission-37 based precautions and a laboratory test for SARS-CoV-2 was ordered. cache = ./cache/cord-270935-t9pym9k0.txt txt = ./txt/cord-270935-t9pym9k0.txt === reduce.pl bib === id = cord-270698-9w3ap3gz author = Guo, Hua title = Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2496 sentences = 142 flesch = 59 summary = title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. Consistent results were observed by binding affinity assays between SARSand SARSr-CoV spike proteins and receptor molecules from bats and humans. In a host-virus arms race situation, the genes involved tend to display dN/dS ratios Codon-based analysis of molecular evolution 536 Bat ACE2 and SARSr-CoV spike sequences were analyzed for positive selection. Identification of key amino acid 671 residues required for horseshoe bat angiotensin-I converting enzyme 2 to function as a 672 receptor for severe acute respiratory syndrome coronavirus cache = ./cache/cord-270698-9w3ap3gz.txt txt = ./txt/cord-270698-9w3ap3gz.txt === reduce.pl bib === id = cord-270880-azslipmp author = Cozzupoli, Grazia Maria title = Possible Retinal Impairment Secondary to Ritonavir Use in SARS-CoV-2 Patients: A Narrative Systematic Review date = 2020-08-22 pages = extension = .txt mime = text/plain words = 2813 sentences = 153 flesch = 44 summary = Seven single cases and one case series, reporting a total of 10 patients affected by retinal changes secondary to long-term ritonavir treatment, were included in the review. Although a recent randomized trial [3] involving hospitalized adult patients with confirmed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection has not shown significant benefits with lopinavir/ritonavir treatment beyond standard care, this protease inhibitor association is used in worldwide hospitals [4] . us, we conducted a narrative systematic review of the published reports describing the clinical features and imaging signs associated with ritonavirinduced retinal toxicity. Anyway, it is not illogical to hypothesize that the retinal toxic effects of both long-term hydroxychloroquine [32] and ritonavir therapies might appear also after short-term treatments, as in the case of SARS-CoV-2 patients, enhanced by the deterioration of renal and hepatic clearance function, respectively. e authors report a case of bull's eye maculopathy pattern in an HIV-positive patient, being treated with ritonavir for 13 years. cache = ./cache/cord-270880-azslipmp.txt txt = ./txt/cord-270880-azslipmp.txt === reduce.pl bib === id = cord-270776-oulnk1b3 author = Chau, Tai-nin title = Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome date = 2004-08-15 pages = extension = .txt mime = text/plain words = 2775 sentences = 142 flesch = 45 summary = title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome Purpose To determine whether the initial chest radiograph is helpful in predicting the clinical outcome of patients with severe acute respiratory syndrome (SARS). Results Bilateral disease and involvement of more than two zones on the initial chest radiograph were associated with a higher risk of liver impairment and poor clinical outcome. Together with the clinical characteristics of SARS, such as fever and chest symptoms, and a recent history of contact with a suspected or confirmed SARS patient, radiographic evidence of infiltrates consistent with pneumonia or acute respiratory distress syndrome is important in establishing the diagnosis (5) . Studies involving patients with community-acquired pneumonia (10) , acute interstitial pneumonia (11) , or idiopathic pulmonary fibrosis (12) have shown that quantitative and qualitative changes on chest radiographs might predict clinical outcome. cache = ./cache/cord-270776-oulnk1b3.txt txt = ./txt/cord-270776-oulnk1b3.txt === reduce.pl bib === id = cord-271014-xzpvupms author = Erikstrup, Christian title = Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2366 sentences = 177 flesch = 57 summary = title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. cache = ./cache/cord-271014-xzpvupms.txt txt = ./txt/cord-271014-xzpvupms.txt === reduce.pl bib === id = cord-271174-886xc1n3 author = Lipworth, Brian title = Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2344 sentences = 136 flesch = 38 summary = High-risk patients requiring hospitalization for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are those over 60 years old, males, obese, smokers, and those with common comorbidities including hypertension, cardiovascular disease, diabetes, and chronic lung disease. The cytokine cascade resulting from acute severe SARS-CoV-2 infection, with downstream IL-6 activation considered to be a hallmark feature in terms of progression of COVID-19 pneumonia to hyperinflammation and ARDS. Also shown are the putative mechanisms of action for bromhexine and hydroxychloroquine in attenuating upstream SARS-CoV-2 tissue binding, the effect of antivirals on replication, azithromycin as an antiviral and immunomudulator, nonspecific cytokine suppression by corticosteroids, together with the selective downstream effect of IL-6 blockade with tocilizumab or sarilumab and effects of anti-TNF and interferon beta-1-a. Patients with eosinophilic asthma and COPD should continue to use ICS-containing therapy to maintain optimal control and protect against viral insults including SARS-CoV-2 infection. cache = ./cache/cord-271174-886xc1n3.txt txt = ./txt/cord-271174-886xc1n3.txt === reduce.pl bib === id = cord-270919-0hldozml author = Cortey, Martí title = SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date = 2020-05-17 pages = extension = .txt mime = text/plain words = 1063 sentences = 73 flesch = 56 summary = title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%. 54 The aim of the present study was to determine the amino acid substitutions in viral 55 proteins that were widely present in available sequences of SARS-CoV-2, relating them 56 to the known chronology of the pandemic. cache = ./cache/cord-270919-0hldozml.txt txt = ./txt/cord-270919-0hldozml.txt === reduce.pl bib === id = cord-271188-ewlxy5po author = Liu, Wei title = Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4237 sentences = 245 flesch = 42 summary = Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 cache = ./cache/cord-271188-ewlxy5po.txt txt = ./txt/cord-271188-ewlxy5po.txt === reduce.pl bib === id = cord-271338-v2k9zn87 author = Pujadas, E. title = SARS-CoV-2 Viral Load Predicts COVID-19 Mortality date = 2020-06-12 pages = extension = .txt mime = text/plain words = 1007 sentences = 72 flesch = 57 summary = We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). To date, few studies have reported on SARS-CoV-2 viral loads, and no studies have assessed viral load and mortality in large patient cohorts. 2, 3, 4, 5 This letter is the first to report SARS-CoV-2 viral load at the time of diagnosis as an independent predictor of COVID-19 mortality in a large hospitalized cohort (n=1,145) within the Mount Sinai Health System in New York City. . https://doi.org/10.1101/2020.06.11.20128934 doi: medRxiv preprint Transforming front-line qualitative testing into a quantitative viral load will assist clinicians in risk-stratifying patients who should be admitted and closely monitored versus those who may safely convalesce at home. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients cache = ./cache/cord-271338-v2k9zn87.txt txt = ./txt/cord-271338-v2k9zn87.txt === reduce.pl bib === id = cord-271404-tu8u1b1d author = Gaunkar, Ridhima B title = COVID-19 in Smokeless Tobacco Habitués: Increased Susceptibility and Transmission date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3088 sentences = 154 flesch = 49 summary = Smokeless tobacco (SLT) consumption is of particular concern in countries in South Asia with high population densities, as it facilitates exposure to SARS-CoV-2 within or between communities by the act of public spitting. SLT-induced higher expression of angiotensin-converting enzyme 2 receptors along with the presence of furin in the oral mucosa and dysfunctional immune responses among SLT habitués increase viral dissemination and an individual's susceptibility to COVID-19. There has not been much research on the increased risk of contracting COVID-19 for smokeless tobacco (SLT) users, although the use of these products is widely prevalent in South Asia and the Western Pacific region. The known action of the enzyme furin and the nicotine-induced increased expression of the ACE2 receptor result in COVID-19 viral tropism to the oral mucosal tissues in smokeless tobacco habitués [11] [12] [13] [14] [15] [16] [17] [18] [19] . cache = ./cache/cord-271404-tu8u1b1d.txt txt = ./txt/cord-271404-tu8u1b1d.txt === reduce.pl bib === id = cord-271495-5906wju4 author = Beldomenico, Pablo M. title = Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1995 sentences = 107 flesch = 53 summary = Data and modelling supported the existence of 'superspreaders' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. cache = ./cache/cord-271495-5906wju4.txt txt = ./txt/cord-271495-5906wju4.txt === reduce.pl bib === id = cord-271027-4omocd8q author = Fronza, R. title = Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak date = 2020-05-01 pages = extension = .txt mime = text/plain words = 5723 sentences = 309 flesch = 55 summary = While it is possible to reason that observed variation in the number and severity of cases stem from the initial number of infected individuals, the difference in the testing policies and social aspects of community transmissions, the factors that could explain high discrepancy in areas with a similar level of healthcare still remain unknown. A generalized Poisson model was fitted to estimate the association among the data showing the number of infected cases per million and the atmospheric factors. Binary classifier based on an artificial neural network (ANN) was implemented to test the capacity of the atmospheric variables to predict the epidemic escalation of the number of positive cases per million on the basis of a combination of where l= PM2.5, PM10, NH 3 dM A l and O 3 . The expected number of infected cases in the total of 107 Italian provinces were predicted for the months of March (Spring), June (Summer), September (Autumn) and December (Winter) using the real measured values for PM2.5 and O 3 atmospheric factors from 2018 seasonal datasets. cache = ./cache/cord-271027-4omocd8q.txt txt = ./txt/cord-271027-4omocd8q.txt === reduce.pl bib === id = cord-271701-tx0lqgff author = te Velthuis, Aartjan J.W. title = The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date = 2011-10-29 pages = extension = .txt mime = text/plain words = 7357 sentences = 367 flesch = 56 summary = Commonly, its core subunit is a single RNA-dependent RNA polymerase (RdRp) that drives the production of template strands for replication, new genome molecules, and-in many RNA virus groupsalso subgenomic (sg) mRNAs. This canonical RdRp is structurally conserved among RNA viruses and widely accepted to drive catalysis of phosphodiester bond formation via a well-established reaction mechanism involving two metal ions that are coordinated by aspartate residues in its motifs A and C (3) (4) (5) . Interestingly, both nsp8 and nsp(7+8) are able to extend the RNA primers beyond template length in the presence of heparin ( Figure 4D and Supplementary Figure S2B ), suggesting that these extensions result from terminal transferase activity and not from template switching, as was previously observed for poliovirus 3D pol (20) . Subsequent alanine substitution of the N-terminal D/ ExD/E motif, composed of D50 and D52 in SARS-CoV, greatly affected primer extension activity on the CU 10 template as shown in Figure 5C . cache = ./cache/cord-271701-tx0lqgff.txt txt = ./txt/cord-271701-tx0lqgff.txt === reduce.pl bib === id = cord-270994-1mmqfp7g author = ul Qamar, Muhammad Tahir title = Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants date = 2020-03-26 pages = extension = .txt mime = text/plain words = 2019 sentences = 139 flesch = 55 summary = title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants Therefore, herein, we analysed the 3CL(pro) sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. On January 21, the first article related to 2019-nCoV was 27 published, which revealed that 2019-nCoV belongs to the beta-coronavirus group, sharing 28 ancestry with bat coronavirus HKU9-1, similar to SARS-coronaviruses, and despite sequence 29 diversity its spike protein interacts strongly with the human ACE2 receptor [1] . Structure-based activity analyses and high-57 throughput studies have identified potential inhibitors for SARS-CoV and MERS-CoV 3CL pro 58 Our analyses identified nine novel non-toxic, 171 druggable natural compounds that are predicted to bind with the receptor binding site and 172 catalytic dyad (Cys-145 and His-41) of SARS-CoV-2 3CL pro ( Table 2 ; Fig. S5 ). cache = ./cache/cord-270994-1mmqfp7g.txt txt = ./txt/cord-270994-1mmqfp7g.txt === reduce.pl bib === id = cord-271469-lozvq3y6 author = Shaikh, Faiq title = Current landscape of Imaging and the potential role for Artificial intelligence in the management of COVID-19 date = 2020-06-27 pages = extension = .txt mime = text/plain words = 3042 sentences = 171 flesch = 42 summary = The clinical presentation of COVID-19 COVID-19 is primarily a respiratory tract infection caused by the SARS-CoV2 virus. Currently, the imaging features related to the neurologic complications of the virus are consistent with stroke related to large vessel occlusion and encephalopathy (Fig. 5) with reported leptomeningeal enhancement and cranial nerve palsies [25, 26] , which in the vast majority are seen in subjects with severe alternate manifestations of Covid-19 infection [27, 28] . Given that it has been shown to be useful for imaging lung infections, such as tuberculosis and atypical pneumonia [33] , its potential role in COVID19 management, albeit small may be extrapolated (Fig. 6) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response Severity assessment of coronavirus disease 2019 (COVID-19) using quantitative features from chest CT images cache = ./cache/cord-271469-lozvq3y6.txt txt = ./txt/cord-271469-lozvq3y6.txt === reduce.pl bib === id = cord-271211-frkk6w0a author = Han, Yu title = The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID‐19): A Chinese perspective date = 2020-03-12 pages = extension = .txt mime = text/plain words = 2110 sentences = 139 flesch = 55 summary = The Chinese government has taken emergency measures to control the outbreak and has undertaken initial steps in the diagnosis and treatment of 2019 novel coronavirus infection disease (COVID‐19). A study in South Korea showed that many environmental surfaces of patients with MERS were contaminated by MERS-CoV, and virus RNA was detected from environmental surfaces within 5 days after the last positive PCR of patients' respiratory samples. 12 Guangzhou CDC also found SARS-CoV-2 in the house of a confirmed patient, 13 which serves as evidence of contact transmission. 20 The Lancet also reminded doctors not to ignore SARS-CoV-2 transmission via ocular surfaces as infected droplets and bodily fluids may easily contaminate the human conjunctival epithelium. 27 A study showed that during the outbreak of SARS-CoV, of all exposed health care workers, 7.5% were asymptomatic SARSpositive cases. SARS-CoV-2 viral load in upper respiratory specimens of infected patients cache = ./cache/cord-271211-frkk6w0a.txt txt = ./txt/cord-271211-frkk6w0a.txt === reduce.pl bib === id = cord-271371-qs7zge3l author = Gao, Jia title = Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2217 sentences = 139 flesch = 57 summary = As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligandand protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (M(pro)) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of M(pro). We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 M(pro). Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs. Nevertheless, using this fragment-based approach is a feasible strategy for repurposing low-molecular-weight drugs targeting SARS-CoV-2 M pro . cache = ./cache/cord-271371-qs7zge3l.txt txt = ./txt/cord-271371-qs7zge3l.txt === reduce.pl bib === id = cord-271419-v6dfel3l author = Adachi, Shun title = Commentary: Origin and evolution of pathogenic coronaviruses date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1211 sentences = 77 flesch = 51 summary = Among viruses, some coronaviruses (CoVs) are notorious for causing the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The said article has successfully predicted today's COVID-19 outbreak by pointing out that novel pathogenic variants will readily emerge from very diversified severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) of the bat origin through their close coexistence and high genetic recombination ability (Figure 1) . Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. Thus, to consider the origin of new pathogens and the prevention of their transmission to humans, and control of the viruses, not only studies on SARS-CoV, MERS-CoV, and SARS-CoV-2, but also those on their relatives SARSr-CoVs and MERSr-CoVs are recommendable for bats tracked for the ecology and evolution. cache = ./cache/cord-271419-v6dfel3l.txt txt = ./txt/cord-271419-v6dfel3l.txt === reduce.pl bib === id = cord-271411-h3k7r2ia author = Pelletier, Jesse S. title = Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination date = 2020-08-26 pages = extension = .txt mime = text/plain words = 1330 sentences = 82 flesch = 46 summary = title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination We believe that, additionally, nasal and oral decontamination measures may be implemented to reduce viral aerosolization before it reaches barriers, surfaces, and fomites. Nasal and oral decontamination is currently a routine step used to reduce postoperative infectious contamination across many surgical subspecialties. Povidone-iodine (PVP-I) is nearly universally virucidal and has recently shown rapid in vitro inactivation of SARS-CoV-2. Clinical studies of PVP-I in vivo support a durable, protective effect against bacteria and possibly SARS-CoV-2. 12 Nasal and oral decontamination strategy should be effective and convenient for use in outpatient ophthalmic clinics and ambulatory surgery centers (ASCs) in both developed and developing countries alike. Rapid in-vitro inactivation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using povidone-iodine oral antiseptic rinse Is povidone iodine mouthwash effective against SARS-CoV-2? cache = ./cache/cord-271411-h3k7r2ia.txt txt = ./txt/cord-271411-h3k7r2ia.txt === reduce.pl bib === id = cord-271090-91lzr4tz author = Edwards, Kathryn M. title = Anticipating SARS-CoV-2 Vaccine Testing, Licensure, and Recommendations for Use date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2694 sentences = 142 flesch = 47 summary = Because of concerns raised about enhanced disease after wild virus infection in animal studies following vaccination against severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and Middle East respiratory syndromecoronavirus (MERS-CoV) (9, 10), experts have met and proposed immunologic criteria to be evaluated in animals and humans to detect and consequently reduce the risk of enhanced disease (11) . Some of the Phase 1 studies evaluating SARS-CoV-2 vaccines have also included individuals >65 years of age to assess safety and immunogenicity in this population, which is at greater risk for severe COVID-19 disease. With SARS-CoV-2 vaccines, Phase 2 studies are planned to expand the safety profile and to assess immune responses in larger numbers of subjects. The Phase 3 efficacy trials planned for SARS-CoV-2 vaccines in the United States are expected to enroll 20,000 to 30,000 individuals, the numbers projected to be necessary to determine whether the vaccines will prevent significant disease over a period of 6 months follow-up. cache = ./cache/cord-271090-91lzr4tz.txt txt = ./txt/cord-271090-91lzr4tz.txt === reduce.pl bib === id = cord-271505-eot38721 author = Wang, Hongliang title = Molecular pathogenesis of severe acute respiratory syndrome date = 2006-09-28 pages = extension = .txt mime = text/plain words = 4959 sentences = 229 flesch = 48 summary = demonstrated that the angiotensin-converting enzyme 2 (ACE2) is a functional cellular receptor of SARS-CoV, by using coimmunoprecipitation of the virus glycoprotein (S1) with lysates from cells that are susceptible to virus infection (Vero E6 cells) followed by mass spectrometry analysis [7] . In the case of SARS, apoptosis was observed in patients' lung epithelial cells; thus, SARS-CoV induced apoptosis would certainly have a deleterious pathogenic role, leading to severe tissue damage [26] . This model system allowed us to avoid possible secondary effects resulting from viral replication or infections in vivo and to directly test whether SARS-CoV spike protein might adversely affect acute lung injury through modulation of ACE2. SARS-CoV infection or spike protein treatment can down-regulate the expression of ACE2, and thus aggravate lung injury. Nabel, pH-dependent entry of severe acute respiratory syndrome coronavirus is mediated by the spike glycoprotein and enhanced by dendritic cell transfer through DC-SIGN cache = ./cache/cord-271505-eot38721.txt txt = ./txt/cord-271505-eot38721.txt === reduce.pl bib === id = cord-271751-46oo9xv5 author = Ingraham, Nicholas E. title = Shining a light on the evidence for hydroxychloroquine in SARS-CoV-2 date = 2020-04-28 pages = extension = .txt mime = text/plain words = 1112 sentences = 77 flesch = 51 summary = Chloroquine and hydroxychloroquine seem effective in killing SARS-CoV in vitro [1, 3] . Recent reports show it also may be effective at killing SARS-CoV-2-infected cells in vitro [4] . To date, no pre-clinical studies have evaluated the efficacy of hydroxychloroquine in the current SARS-CoV-2 pandemic. A recent article published in Chinese found no benefit with chloroquine in a 1:1 randomized trial with 30 patients [6] . Until data from randomized controlled trials are available, we suggest caution utilizing hydroxychloroquine off label for patients with COVID-19. There are currently no evidence supporting hydroxychloroquine as prophylaxis, but unfortunately these data are being extrapolated to the indication potentially resulting in drug shortages for patients with rheumatic diseases who require this medication. Preliminary study of hydroxychloroquine sulfate in treating common coronavirus disease (COVID-19) patients in 2019 Hydroxychloroquine and azithromycin as a treatment of COVID-19: preliminary results of an open-label nonrandomized clinical trial cache = ./cache/cord-271751-46oo9xv5.txt txt = ./txt/cord-271751-46oo9xv5.txt === reduce.pl bib === id = cord-271243-8cfyen86 author = Xiao, Y. title = Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus date = 2008-05-31 pages = extension = .txt mime = text/plain words = 3375 sentences = 179 flesch = 52 summary = title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus Summary Masked palm civets are highly susceptible to infection with the severe acute respiratory syndrome coronavirus (SARS-CoV). The present study describes the spectrum of histopathological changes in the lung, spleen, lymph node, liver, small intestine, kidney and cerebrum of civets infected experimentally with SARS-CoV. One animal from each group was sacrificed at 3, 13, 23, 34 and 35 days post-infection (dpi), and lung, spleen, lymph node, small intestine, kidney, trachea, cerebrum, pancreas, sex glands, stomach and heart were collected from each animal. In summary, the data presented in this study further corroborate previous findings (Wu et al., 2005) in demonstrating that civets are more susceptible to SARS-CoV infection than other animals, as implied by their clinical symptoms, pathological changes and virus distribution within tissues. cache = ./cache/cord-271243-8cfyen86.txt txt = ./txt/cord-271243-8cfyen86.txt === reduce.pl bib === id = cord-270964-kxze0470 author = Lau, Kwok-Kwong title = Possible Central Nervous System Infection by SARS Coronavirus date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1556 sentences = 93 flesch = 57 summary = On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). In our patient, the occurrence of generalized convulsion with a positive RT-PCR for SARS-CoV in the CSF suggests possible infection of the central nervous system by SARS-CoV. The findings from our patient are not compatible with multiple sclerosis, and the PCR result suggests that the central nervous system (CNS) is affected by SARS-CoV. The possibility also remains that infection of the CNS never occurred, as suggested by the lack of focal neurologic deficit, normal CSF pressure, cell count, and biochemistry. Besides involvement of the lungs and possibly the CNS, no good alternative explanation exists for acute renal failure in this patient. Renal failure could possibly be caused by SARS-CoV involving the kidneys. Additionally, our patient had diarrhea from day 3 to day 20, with positive RT-PCR for SARS-CoV in stool specimens, suggesting involvement of the gastrointestinal tract as well. cache = ./cache/cord-270964-kxze0470.txt txt = ./txt/cord-270964-kxze0470.txt === reduce.pl bib === id = cord-271920-1dzkgt6w author = Carpenter, Christopher R. title = Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date = 2020-06-16 pages = extension = .txt mime = text/plain words = 7248 sentences = 523 flesch = 48 summary = 3 As waves of COVID-19 patients present to ED's in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient's exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. cache = ./cache/cord-271920-1dzkgt6w.txt txt = ./txt/cord-271920-1dzkgt6w.txt === reduce.pl bib === id = cord-271504-t3y1w9ef author = Luo, Zichao title = Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date = 2020-06-16 pages = extension = .txt mime = text/plain words = 14361 sentences = 795 flesch = 42 summary = A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . cache = ./cache/cord-271504-t3y1w9ef.txt txt = ./txt/cord-271504-t3y1w9ef.txt === reduce.pl bib === id = cord-270857-8424oq4x author = Hui, David S. title = Exhaled Air Dispersion During Oxygen Delivery Via a Simple Oxygen Mask date = 2007-08-31 pages = extension = .txt mime = text/plain words = 4034 sentences = 186 flesch = 50 summary = We studied the dispersion of exhaled air through a simple oxygen mask applied to a human patient simulator (HPS) during the delivery of different oxygen flow in a room free of air currents. 7 As part of our influenza pandemic preparedness, we studied the safety of oxygen therapy by examining exhaled air dispersion from a simple oxygen mask attached to a human patient simulator (HPS) during the delivery of oxygen at different levels of flow. 33 Using a laser visualization technique and a mathematical model that was different from the one used in the current study for data analysis, we have previously shown a maximal dispersion distance of approximately 0.4 m during the application of oxygen at 4 L/min via a simple mask to the HPS, which was programmed at a respiratory rate of 12 breaths/min and a tidal volume of 0.5 L. cache = ./cache/cord-270857-8424oq4x.txt txt = ./txt/cord-270857-8424oq4x.txt === reduce.pl bib === id = cord-271723-8qoozmgk author = Gelman, Ram title = Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents date = 2020-06-18 pages = extension = .txt mime = text/plain words = 6269 sentences = 304 flesch = 37 summary = title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents The ongoing severe acute respiratory syndrome pandemic caused by the novel coronavirus 2 (SARS-CoV-2) is associated with high morbidity and mortality rates, and it has created a pressing global need for effective antiviral therapies against it. Potential therapeutic approaches have been proposed to target various steps in the viral infectious process, including a SARS-CoV-2 S-protein-based vaccine, a TMPRSS2 inhibitor aiming to block the priming of the viral S protein, an anti-ACE2 antibody to block the surface receptor, and a soluble ACE2 analogue which competitively binds with SARS-CoV-2 to slow viral entry into cells and decrease viral spread [27] . receptor, which may also be associated with the antiviral immune response Dipeptidyl peptidase 4 (DPP4), also known as CD26, is a 110 kDa transmembrane glycoprotein expressed on the surface of a wide variety of epithelial cells and some lymphocytes. cache = ./cache/cord-271723-8qoozmgk.txt txt = ./txt/cord-271723-8qoozmgk.txt === reduce.pl bib === id = cord-271871-8grkln6o author = Singer, J. S. title = Low Prevalence (0.13%) of COVID-19 Infection in Asymptomatic Pre-operative/Pre-procedure Patients at a Large Academic Medical Center Informs Approaches to Perioperative Care date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2842 sentences = 158 flesch = 43 summary = Abstract Background The COVID-19 pandemic has resulted in reduced performance of elective surgeries and procedures at medical centers across the U.S. Awareness of the prevalence of asymptomatic disease is critical for guiding safe approaches to operative/procedural services. Conclusions These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to inform perioperative protocols during the COVID-19 pandemic. These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic 117 population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to 118 inform perioperative protocols during the COVID-19 pandemic. As a large urban referral center, we adopted the CDC and ACS recommendations early in the pandemic, 327 suspending elective surgical and interventional procedures, and later relaxing those suspensions while 328 balancing local/regional COVID-19 epidemiology, data regarding our pre-operative/pre-procedure 329 testing results, and health system resources and priorities. cache = ./cache/cord-271871-8grkln6o.txt txt = ./txt/cord-271871-8grkln6o.txt === reduce.pl bib === id = cord-271551-bj2db91j author = Tomczyk, Samuel title = Social Distancing and Stigma: Association Between Compliance With Behavioral Recommendations, Risk Perception, and Stigmatizing Attitudes During the COVID-19 Outbreak date = 2020-08-11 pages = extension = .txt mime = text/plain words = 5338 sentences = 242 flesch = 37 summary = Latent class analysis examined patterns of compliance, and subsequent multinomial logistic regression models tested sociodemographic (age, gender, country of origin, level of education, region, and number of persons per household) and psychosocial (knowledge about preventive behaviors, risk perception, stigmatizing attitudes) predictors. However, to our knowledge, only one study applied latent class analysis to population behaviors following a novel virus outbreak [i.e., influenza A (H7N9)] in Hong Kong (Liao et al., 2015) , despite the method's statistical advantages in modeling behavioral patterns (e.g., flexibility, integration of measurement error). Via an online survey, a community sample of 157 German adults [80% female; M (SD) age = 27.82 (11.01)] provided information about their knowledge of preventive measures, risk perception, intentions to comply with official behavioral recommendations and guidelines as well as their stigmatizing attitudes toward people suffering from COVID-19. cache = ./cache/cord-271551-bj2db91j.txt txt = ./txt/cord-271551-bj2db91j.txt === reduce.pl bib === id = cord-272179-wvw5mmy3 author = Calderaro, Adriana title = Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date = 2020-10-02 pages = extension = .txt mime = text/plain words = 1095 sentences = 70 flesch = 53 summary = title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children cache = ./cache/cord-272179-wvw5mmy3.txt txt = ./txt/cord-272179-wvw5mmy3.txt === reduce.pl bib === id = cord-271849-wxmr8eki author = Meysman, Pieter title = Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date = 2020-09-09 pages = extension = .txt mime = text/plain words = 2924 sentences = 166 flesch = 58 summary = In this paper, we demonstrate the use of machine learning to classify SARS-CoV-2 epitope specific T-cell clonotypes in T-cell receptor (TCR) sequencing data. We apply these models to public TCR data and show how they can be used to study T-cell longitudinal profiles in COVID-19 patients to characterize how the adaptive immune system reacts to the SARS-CoV-2 virus. No other epitopes present in TCRex (including the 49 non-SARS-CoV-2 models) were predicted to have a single TCR target within this data set. Once established, these models can be applied to any TCR repertoire data and thus can be used to study putative SARS-CoV-2 reactive T cells in the currently available COVID-19 data. In addition, using such models on longitudinal data reveals a potential difference in temporal dynamics between T cells predicted to react against epitopes that are unique to SARS-CoV-2 and those that are shared among other coronaviruses. cache = ./cache/cord-271849-wxmr8eki.txt txt = ./txt/cord-271849-wxmr8eki.txt === reduce.pl bib === id = cord-271919-pbs95hy0 author = Desenclos, Jean-Claude title = Introduction of SARS in France, March–April, 2003 date = 2004-02-17 pages = extension = .txt mime = text/plain words = 3412 sentences = 145 flesch = 56 summary = For patients who fulfilled the definition of a probable case, respiratory secretion specimens were taken from the nose, throat, or sputum to detect for SARS-associated coronovirus (CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (7) at the National Reference Center for Influenza (Northern France), Institut Pasteur, Paris. As recommended by WHO, this follow-up included the passengers who sat within two rows of a SARS case-patient on the Air France Hanoi-Paris flight of March 22 and 23, 2003 (14) . Passengers on a flight in which a person with a symptomatic probable case had traveled were informed publicly through the media and mail of the potential exposure and advised to call the emergency service phone number to be evaluated and admitted to the closest university-affiliated infectious disease ward if a fever of >38°C developed within 10 days of the flight. cache = ./cache/cord-271919-pbs95hy0.txt txt = ./txt/cord-271919-pbs95hy0.txt === reduce.pl bib === id = cord-271781-cfv0ta10 author = Patel, Kishan P. title = Transmission of SARS-CoV-2: an update of current literature date = 2020-07-07 pages = extension = .txt mime = text/plain words = 4469 sentences = 232 flesch = 47 summary = To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] . cache = ./cache/cord-271781-cfv0ta10.txt txt = ./txt/cord-271781-cfv0ta10.txt === reduce.pl bib === id = cord-271998-hdkmwihu author = Rabenau, H. F. title = SARS-coronavirus (SARS-CoV) and the safety of a solvent/detergent (S/D) treated immunoglobulin preparation date = 2005-06-30 pages = extension = .txt mime = text/plain words = 3071 sentences = 170 flesch = 49 summary = SARS-CoV viraemia does not seem to reach high titres, however, it has to be excluded that virus transmission may occur via blood transfusion or application of therapeutic plasma products, e.g. fresh-frozen plasma or single components derived thereof. On the basis of existing validation data for enveloped viruses, it can be anticipated that the inactivation/ removal steps incorporated into manufacturing processes for plasma-derived medicinal products will also be effective for SARS-CoV. Therefore, the inactivation of SARS-CoV by SD treatment was investigated in the laboratory scale at lowered concentration of solvent and detergent (75% of standard SD concentration) and at a shortened process time (30 min). In conclusion, the results obtained in our investigation demonstrated that the process conditions specified for the SD treatment of OCTAGAM are very sufficient to inactivate enveloped viruses such as SARS-CoV to below the limit of detection. cache = ./cache/cord-271998-hdkmwihu.txt txt = ./txt/cord-271998-hdkmwihu.txt === reduce.pl bib === id = cord-271930-9a18h2tr author = Licari, Amelia title = Allergy and asthma in children and adolescents during the COVID outbreak: What we know and how we could prevent allergy and asthma flares date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1177 sentences = 83 flesch = 47 summary = The Center for Disease Control and Prevention (CDC) initially proposed that patients with chronic lung diseases, including moderate-severe asthma, and allergy may have a higher risk of developing severe COVID-19 than otherwise healthy people (https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/asthma.html). Allergic children had a significantly higher (P < .0001) eosinophil count than COVID-19 patients. However, it has been recently commented that chronic respiratory diseases, including COPD and asthma, seem to be underrepresented in the comorbidities of COVID-19 patients. On the other hand, children and adolescents with allergy and asthma should be adequately managed during this COVID-19 pandemic, also considering the restrictive rules released by governmental authorities that impose a strict limitation on movements. 10 In summary, the rapid spread of SARS-CoV-2 infection and the lack of specific antiviral therapies and vaccines currently require additional medical efforts to prevent COVID-19 and mostly protect patients with chronic diseases. Association of respiratory allergy, asthma, and expression of the SARS-CoV-2 receptor, ACE2 Do chronic respiratory diseases or their treatment affect the risk of SARS-CoV-2 infection? cache = ./cache/cord-271930-9a18h2tr.txt txt = ./txt/cord-271930-9a18h2tr.txt === reduce.pl bib === id = cord-272414-oo8kcuf3 author = Chiocchetti, Roberto title = ACE2 Expression in the Cat and the Tiger Gastrointestinal Tracts date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3005 sentences = 161 flesch = 52 summary = Although the evidence of ACE2-IR in the feline GIT does not necessarily indicate the possibility of viral replication and SARS-CoV-2 spread with stool, the findings in the present study could serve as an anatomical basis for additional studies considering the risk of the SARS-CoV-2 fecal-oral transmission between cats/felids, and between cats/felids and humans. Since the necessary condition for the enteric multiplication of SARS-CoV-2 is represented by the expression of its election receptor on the host cells, the present study immunohistochemically investigated the localization of ACE2 in the GIT of feline domestic (cat) and wild (tiger) species. The present study described the expression of the ACE2 receptor in the stomach and intestine of the cat and tiger for the first time and highlighted the GIT as a potential site of SARS-CoV-2 replication. cache = ./cache/cord-272414-oo8kcuf3.txt txt = ./txt/cord-272414-oo8kcuf3.txt === reduce.pl bib === id = cord-271648-m2c5bvuj author = Ashour, Hossam M. title = Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date = 2020-03-04 pages = extension = .txt mime = text/plain words = 7536 sentences = 401 flesch = 56 summary = Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model cache = ./cache/cord-271648-m2c5bvuj.txt txt = ./txt/cord-271648-m2c5bvuj.txt === reduce.pl bib === id = cord-271544-i20105lq author = Poston, Daniel title = Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection date = 2020-10-11 pages = extension = .txt mime = text/plain words = 1366 sentences = 87 flesch = 53 summary = Cross-reactive immune responses elicited by seasonal coronaviruses might impact SARS-CoV-2 susceptibility and disease outcomes. We measured neutralizing activity against SARS-CoV-2 in pre-pandemic sera from patients with prior PCR-confirmed seasonal coronavirus infection. One hypothesis is that cross reactive immune responses, elicited by prior 46 infection with seasonal coronaviruses impacts the course of SARS-CoV-2 infection, perhaps 47 providing a degree of protection against severe COVID-19 disease. The numbers of rVSV/SARS-2/GFP was assessed by flow cytometric detection of 92 GFP expression as described previously To assess whether prior infection by seasonal coronaviruses could elicit antibodies with 104 neutralization activity against SARS-CoV-2, we identified 37 serum samples collected prior to 105 the COVID19 pandemic from patients who were diagnosed using PCR with a seasonal 106 coronavirus 11-291 days (median 80 = days) prior to serum sample collection. . https://doi.org/10.1101/2020.10.08.20209650 doi: medRxiv preprint neutralize rVSV/SARS-CoV-2/GFP with NT50 values ranging from 96 to 5400. cache = ./cache/cord-271544-i20105lq.txt txt = ./txt/cord-271544-i20105lq.txt === reduce.pl bib === id = cord-272019-4uua0zgp author = Sun, Wei title = Changes in coagulation and fibrinolysis of post-SARS osteonecrosis in a Chinese population date = 2006-03-18 pages = extension = .txt mime = text/plain words = 2231 sentences = 125 flesch = 46 summary = The purpose of this study was to detect changes in coagulation and fibrinolysis of post-severe acute respiratory syndrome (SARS) Chinese patients with osteonecrosis, investigate the aetiology of post-SARS osteonecrosis (ON), and select the sensitive molecular markers for identifying the susceptible population. Of 88 patients with post-SARS, 78 (88.64%) were found to have at least one coagulopathy versus 36.54% of controls (p<0.01); PC, APC-R, AT-III, PAI, and PLG were significantly different between the two groups (Tables 1 and 2 ). [28] studied risk factors for pulmonary emboli after total hip or knee arthroplasty, 21 serological measures and five genes associated with thrombophilia and/or hypofibrinolysis were assessed: 13 of 27 (48%) in the control group also had at least one abnormality. In this study, we did not detect any coagulation abnormalities in a small proportion of the patients; this may reflect limitations in our understanding of the causes of thrombosis and hypofibrinolysis. Risk factors potentially activating intravascular coagulation and causing nontraumatic osteonecrosis cache = ./cache/cord-272019-4uua0zgp.txt txt = ./txt/cord-272019-4uua0zgp.txt === reduce.pl bib === id = cord-272405-jmwn8pdn author = Parvez, Mohammad K. title = Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date = 2017-08-04 pages = extension = .txt mime = text/plain words = 4192 sentences = 210 flesch = 43 summary = Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. cache = ./cache/cord-272405-jmwn8pdn.txt txt = ./txt/cord-272405-jmwn8pdn.txt === reduce.pl bib === id = cord-271815-yr1dq258 author = Hulkower, Rachel L. title = Inactivation of surrogate coronaviruses on hard surfaces by health care germicides date = 2011-06-30 pages = extension = .txt mime = text/plain words = 4178 sentences = 222 flesch = 47 summary = Methods The efficacy of health care germicides against 2 surrogate coronaviruses, mouse hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), was tested using the quantitative carrier method on stainless steel surfaces. This study was undertaken using the carrier method to evaluate 6 chemical germicides commonly used in health care settings for their efficacy in reducing infectivity of coronaviruses on environmental surfaces. The efficacy of 6 hospital surface germicides was tested against 2 coronaviruses, MHV and TGEV, used as surrogates for SARS-CoV. 3, 15, 17, 24 The results of this study show that, of the commonly used hospital germicides tested, only the ethanol-based germicides were able to achieve this level of reduction of infectious virus after 1 minute of contact time. Studies of hospital germicide efficacy against adenovirus 8 using the same carrier-based method with 1-minute contact times found greater log 10 reduction factors by OPA (4.37) than were observed in this study for TGEV (2.27) and MHV (1.71). cache = ./cache/cord-271815-yr1dq258.txt txt = ./txt/cord-271815-yr1dq258.txt === reduce.pl bib === id = cord-272113-j82z4q8x author = Akaji, Kenichi title = Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease date = 2020-08-27 pages = extension = .txt mime = text/plain words = 6459 sentences = 281 flesch = 45 summary = Instead of an exhaustive survey of the inhibitors [21] , we provide an overview of several typical inhibitors, and our recent efforts for the rational design of new scaffolds are discussed based on the inhibitory mechanism and structural interactions with SARS-CoV 3CL pro . Following the interaction with the active center of the SARS-CoV 3CL pro , the nucleophilic Cys145 thiolate generated by a proton-withdrawing effect caused by His41 at the catalytic dyad promotes a typical 1,4-addition to the α,β-unsaturated structure of the Michael acceptor ( Figure 3 ). These data also indicate that the corresponding S1 pocket of the SARS-CoV 3CL pro might accept a simple ring structure containing heteroatoms at this specific interaction site, which provides a clue to our design of a potent substrate-based inhibitor described later in this review. cache = ./cache/cord-272113-j82z4q8x.txt txt = ./txt/cord-272113-j82z4q8x.txt === reduce.pl bib === id = cord-271536-pscw933i author = Guo, Zhen-Dong title = Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1685 sentences = 100 flesch = 61 summary = To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. Furthermore, we found that rates of positivity differed by air sampling site, which reflects the distribution of virus-laden aerosols in the wards ( Figure 2 , panel A). SARS-CoV-2 aerosol was detected at all 3 sampling sites; rates of positivity were 35.7% (5/14) near air outlets, 44.4% (8/18) in patients' rooms, and 12.5% Figure 2 (1/8) in the doctors' office area. First, SARS-CoV-2 was widely distributed in the air and on object surfaces in both the ICU and GW, implying a potentially high infection risk for medical staff and other close contacts. cache = ./cache/cord-271536-pscw933i.txt txt = ./txt/cord-271536-pscw933i.txt === reduce.pl bib === id = cord-272423-o5yinjcz author = Mao, Xiao-Yuan title = iPSCs-Derived Platform: A Feasible Tool for Probing the Neurotropism of SARS-CoV-2 date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1219 sentences = 76 flesch = 46 summary = In a recent article, Yuen and colleagues present the first experimental evidence of SARS-CoV-2 infection in the human central nervous system using induced pluripotent stem cells (iPSCs)-derived platform including human neural progenitor cells, neurospheres, and three-dimensional brain organoids (Yuen, K.Y., and Huang, J.D. et al. Recently, Yuen and colleagues used induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and three-dimensional (3D) brain organoids for evaluation of SARS-CoV-2 infection in the brain. provided the first experimental evidence showing that SARS-CoV-2 could replicate in hNPCs and neurospheres and also the novel virus could productively infect cortical neurons and NPCs in 3D brain organoids ( Figure 1 ). In summary, the data provided by Yuen and colleagues offer useful experimental evidence supporting that SARS-CoV-2 can infect the human brain using an iPSCs-derived platform including hNPCs, neurospheres, and 3D human organoids. cache = ./cache/cord-272423-o5yinjcz.txt txt = ./txt/cord-272423-o5yinjcz.txt === reduce.pl bib === id = cord-272292-k0ugjb6f author = Liu, Shih-Jen title = Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates date = 2006-04-12 pages = extension = .txt mime = text/plain words = 4957 sentences = 261 flesch = 57 summary = The recombinant nucleocapsid (rN) protein of the coronavirus (CoV) responsible for severe acute respiratory syndrome (SARS) was cloned and expressed in Escherichia coli, extracted from cell lysates containing 6 M urea, then purified by Ni(2+)-affinity chromatography. To identify the B-cell immunodominant epitopes of the rN protein in the mouse and monkey, the reactivities of antisera raised against purified rN proteins formulated in ISA-51/CpG were tested with a panel of overlapping synthetic peptides covering the entire N protein sequence. We also only observed that peptides corresponding to residues 336–350 were capable of stimulating IFN-γ production in T-cell cultures derived from peripheral blood mononuclear cells (PBMCs) of macaques immunized with the rN protein emulsified in ISA/CpG adjuvant. cache = ./cache/cord-272292-k0ugjb6f.txt txt = ./txt/cord-272292-k0ugjb6f.txt === reduce.pl bib === id = cord-272445-0xauff51 author = Naaber, Paul title = Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date = 2020-10-27 pages = extension = .txt mime = text/plain words = 2751 sentences = 150 flesch = 50 summary = title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients' clinical data and the time-point the test was performed. Our study aimed to compare the performance characteristics of seven commercial and two in-house IgG/total Ab tests, which analyze the reactivity to several target proteins, and to correlate the results with the patients' clinical data (with different symptoms score and age), and time from disease onset. cache = ./cache/cord-272445-0xauff51.txt txt = ./txt/cord-272445-0xauff51.txt === reduce.pl bib === id = cord-272653-01wck9f3 author = Isaacs, David title = Apocalypse perhaps date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1894 sentences = 133 flesch = 59 summary = The exact starting date of the novel coronavirus pandemic COVID-19 will never be known, but China informed the World Health Organization (WHO) about the disease on New Year's Eve, 31 December 2019. Transmission of severe acute respiratory syndrome (SARS)-CoV-2, the virus that causes COVID-19, was accelerated by traditional travel of 3 billion people for 40 days before the Chinese New Year on 25 January 2020. 2,3 When the Australian Chief Medical Officer activated the pandemic emergency response plan, weeks before the World Health Organization declared a pandemic, the Government was legally obliged to act. 12 The authors conclude that staff were being infected through community transmission and that PPE was effective in protecting front-line health-care workers. At a time when world leaders want to blame each other for aspects of the COVID-19 pandemic, the war metaphor is particularly menacing. Managing mental health challenges faced by healthcare workers during covid=19 pandemic cache = ./cache/cord-272653-01wck9f3.txt txt = ./txt/cord-272653-01wck9f3.txt === reduce.pl bib === id = cord-272573-wxqly479 author = Maia Chagas, Andre title = Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5074 sentences = 317 flesch = 55 summary = Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. Community and commercial open source efforts in diagnostic technology to date have focused on four areas: i) open platforms for scaling reactions as exemplified by Opentrons ( Fig 3A) [28] , an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona; ii) trying to fill gaps where less attention is being paid by clinical diagnostics companies, such as Chia Bio's Open qPCR (Fig 3B) environmental test kit for surveillance via surface swabs [111] ; iii) distributed reproduction of rapidly-published, lab-scale protocols, seen within the OpenCOVID initiative hosted by Just One Giant Lab [39] which involves many community labs worldwide; iv) initiatives such as the Open Enzyme Collection [93] , Free Genes [94] and Biomaker Challenge [112] which are investigating new approaches to foundational technologies such as reagents and instrumentation, with a view to building capacity and resources or global science and medicine to face a future pandemic. cache = ./cache/cord-272573-wxqly479.txt txt = ./txt/cord-272573-wxqly479.txt === reduce.pl bib === id = cord-272450-8a3ir06y author = Iwen, Peter C title = Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-19 pages = extension = .txt mime = text/plain words = 1732 sentences = 68 flesch = 40 summary = The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. cache = ./cache/cord-272450-8a3ir06y.txt txt = ./txt/cord-272450-8a3ir06y.txt === reduce.pl bib === id = cord-271259-6kkzh1tp author = Chen, Shuai title = Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode date = 2010-01-01 pages = extension = .txt mime = text/plain words = 7826 sentences = 352 flesch = 56 summary = Therefore, the N-terminal auto-processing of M(pro) appears to require only two "immature" monomers approaching one another to form an "intermediate" dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. These results indicate that N-terminal autocleavage of SARS-CoV M pro from the polyproteins only requires two "immature" proteases approaching one another to form an "intermediate" dimer structure and does not depend on the active dimer conformation existing in the mature protease. Since mutation of either of these two residues were reported to completely abolish the dimer of mature M pro , our finding raises the intriguing question of how the E290R and R298E mutants can auto-process their N-terminal GST tags when they are unable to form the active dimer structure. cache = ./cache/cord-271259-6kkzh1tp.txt txt = ./txt/cord-271259-6kkzh1tp.txt === reduce.pl bib === id = cord-271813-nroflfmc author = Deng, Wang title = Positive results for patients with COVID-19 discharged form hospital in Chongqing, China date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2423 sentences = 145 flesch = 46 summary = METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Among them, 61 patients had positive results of SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (RT-PCR) test, which provided the important information and clinical evidence for the improved management of patients recovered from COVID-19. The study revealed the clinical features of recovered patients with the recurrence of positive results of SARS-CoV-2.Multi-site screening including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. cache = ./cache/cord-271813-nroflfmc.txt txt = ./txt/cord-271813-nroflfmc.txt === reduce.pl bib === id = cord-271915-nvilxnzl author = Adachi, D. title = Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date = 2004-12-01 pages = extension = .txt mime = text/plain words = 3591 sentences = 152 flesch = 54 summary = The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada. This single-tube RT-PCR is based on consensus primers targeting conserved regions of coronavirus genome sequences and allows for the detection and species identification of several coronaviruses including SARS-HCoV, with high analytical sensitivity. Aliquots of a 10-fold serial RNA dilution prepared from a lung biopsy sample of a patient with SARS (see Section 2) were used to compare our assay with the RealArt HPA coronavirus RT-PCR (Artus GmbH). cache = ./cache/cord-271915-nvilxnzl.txt txt = ./txt/cord-271915-nvilxnzl.txt === reduce.pl bib === id = cord-272654-hh29olk7 author = Bošnjak, Berislav title = Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID-19 convalescent patients revealed by two different detection methods date = 2020-11-02 pages = extension = .txt mime = text/plain words = 6111 sentences = 414 flesch = 54 summary = We used a surrogate virus neutralization test (sVNT) and SARS-CoV-2 S protein-pseudotyped vesicular stomatitis virus (VSV) vector-based neutralization assay (pVNT) to assess the degree to which serum antibodies from coronavirus disease 2019 (COVID-19) convalescent patients interfere with the binding of SARS-CoV-2 S to ACE2. Similarly, anti-SARS-CoV-2 S IgA antibodies were present in 33/37 (89.2%) of the tested sera; two samples were diagnosed as borderline positive and two as negative Fig. 1 Qualitative analysis of serum total IgG (A) and IgA (B) antibodies against SARS-CoV-2 S1 in convalescent patients with mild or severe COVID-19 and healthy controls (HC) determined by ELISA. The median sVNT titer of the mildly affected convalescent cohort was 1:180, indicating that patients with mild COVID-19 produce relatively low amounts of SASRS-CoV-2 neutralizing antibodies (Fig. 2H ). This hypothesis is further supported by a positive correlation between the duration of symptoms and total anti-SARS-CoV-2 IgG, but not IgA, antibodies in convalescent patients with mild disease (Fig. 5A, B) . cache = ./cache/cord-272654-hh29olk7.txt txt = ./txt/cord-272654-hh29olk7.txt === reduce.pl bib === id = cord-272009-yxjhfg7m author = Cui, Jie title = Evolutionary Relationships between Bat Coronaviruses and Their Hosts date = 2007-10-17 pages = extension = .txt mime = text/plain words = 3543 sentences = 190 flesch = 55 summary = Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. cache = ./cache/cord-272009-yxjhfg7m.txt txt = ./txt/cord-272009-yxjhfg7m.txt === reduce.pl bib === id = cord-272211-nkv6irr7 author = Hagan, Liesl M. title = Mass Testing for SARS-CoV-2 in 16 Prisons and Jails — Six Jurisdictions, United States, April–May 2020 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3012 sentences = 143 flesch = 41 summary = To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. In May 2020, CDC requested data from 15 jurisdictions (the Federal Bureau of Prisons [BOP], 10 state prison systems, and four city or county jails), describing SARS-CoV-2 mass testing events † and cases identified before mass testing. High SARS-CoV-2 prevalence detected during mass testing events in a convenience sample of correctional and detention facilities suggests that symptom-based testing underestimates the number of COVID-19 cases in these settings. cache = ./cache/cord-272211-nkv6irr7.txt txt = ./txt/cord-272211-nkv6irr7.txt === reduce.pl bib === id = cord-272602-rywg9mek author = Allison, James R title = Evaluating aerosol and splatter following dental procedures: addressing new challenges for oral healthcare and rehabilitation date = 2020-09-23 pages = extension = .txt mime = text/plain words = 4942 sentences = 266 flesch = 49 summary = A number of authors have used microbiological methods to study bacterial contamination from aerosol and splatter following dental procedures, either by air sampling 21, 32, 33 , swabbing of contaminated surfaces 34, 35 , or most commonly, by collection directly onto culture media [36] [37] [38] [39] . Many studies are small and report only one repetition of a single procedure, and some have only examined contamination of the operator and assistant; a number of studies which have measured spatial distribution of aerosol and splatter have only done so to a limited distance from the source. We present initial data on three dental procedures (high-speed air-turbine, ultrasonic scaler, and 3-in-1 spray use) and examine the effect of dental suction and the presence of an assistant on aerosol and splatter distribution. cache = ./cache/cord-272602-rywg9mek.txt txt = ./txt/cord-272602-rywg9mek.txt === reduce.pl bib === id = cord-272318-8yfg1j0o author = Reddy, Sujan T. title = Cerebrovascular Disease in Patients with COVID-19: A Review of the Literature and Case Series date = 2020-06-11 pages = extension = .txt mime = text/plain words = 3392 sentences = 197 flesch = 41 summary = To further characterize cerebrovascular disease (CVD) in COVID-19, we review the current literature of published cases and additionally report the clinical presentation, laboratory and diagnostic testing results of 12 cases with COVID-19 infection and concurrent CVD from two academic medical centers in Houston, TX, USA, between March 1 and May 10, 2020. To date, few studies have reported cerebrovascular complications in COVID-19 [3, 4] and 4 small case series have described the clinical and laboratory findings in patients with COVID-19 and concurrent stroke [5] [6] [7] [8] . We review the current literature of published cases and describe our experience of 12 cases with COVID-19 infection and concurrent cerebrovascular disease (CVD) to highlight the clinical presentation and proposed mechanisms of central nervous system (CNS) involvement by SARS-CoV-2. Additionally, we performed a retrospective chart review of all hospitalized cases with confirmed COVID-19 infection (SARS-CoV-2 RT-PCR positive) and CVD (ischemic and hemorrhagic stroke) between March 1 and May 10, 2020 seen at two comprehensive stroke centers in Houston, TX, USA. cache = ./cache/cord-272318-8yfg1j0o.txt txt = ./txt/cord-272318-8yfg1j0o.txt === reduce.pl bib === id = cord-271339-wt5o9sgm author = Chen, Chao-Ju title = Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2084 sentences = 122 flesch = 57 summary = The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To ensure the whole process of the COVID-19 diagnostic testing took place without a problem, we simultaneously added primers and a probe of human RNase P gene (RP gene) as an internal control in the same well with the RdRp gene assay according to the protocol from the U.S. CDC [6] (Figure 3 ). In the present report, we demonstrated our experience of relying on a protocol template from the Taiwan CDC to establish an optimized COVID-19 molecular diagnostic test within our routine services in a public health emergency. cache = ./cache/cord-271339-wt5o9sgm.txt txt = ./txt/cord-271339-wt5o9sgm.txt === reduce.pl bib === id = cord-272241-2fwz8z8n author = Kumar, Amit title = Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4608 sentences = 281 flesch = 49 summary = title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach Hence, in this study, we have used immunoinformatic approaches to predict highly antigenic epitopes from SARS-CoV-2 structural proteins that would evoke a strong immune response in humans. For this purpose, we have used the structural proteins: Spike, Envelope, and nucleocapsid to predict B-cell, cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes for construction of vaccine. We have also performed the docking and molecular dynamic simulations (MDS) between the vaccine and human Toll-like Receptor-3 (TLR-3) to study their binding stability. The VaxiJen 2.0 server predicts the antigenicity of the multi-epitope vaccine peptide based on the physicochemical properties of the input protein. Whereas, ANTIGENpro server predicts the antigenicity of the multi-epitopic vaccine based on the protein microarray data analysis of the target organism. Three structural proteins (spike glycoprotein, nucleocapsid, and envelope) were selected to construct a multi-epitope vaccine, which is capable of eliciting the humoral and cell-mediated immune response. cache = ./cache/cord-272241-2fwz8z8n.txt txt = ./txt/cord-272241-2fwz8z8n.txt === reduce.pl bib === id = cord-272734-kawim93f author = Freire-Paspuel, Byron title = Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1243 sentences = 92 flesch = 60 summary = title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies The CDC designed 2019-nCoV CDC EUA kit (IDT, USA) is based on N1 and N2 probes to detect SARS-CoV-2 that have received positive evaluation on recent reports (1) (2) (3) , and and RNase P as an RNA extraction quality control. Other kit avalaible in the market is nCoV-QS (MiCo BioMed; South Corea) that include probes "ORF3a" and "N" probes for SARS-CoV-2 detection but no probe for RNA extraction quality control, with no EUA approval neither from FDA (USA) nor from Korean CDC (4,5,6). Both CoV-QS and 2019-nCoV CDC EUA kits were used at SARS-CoV-2 diagnosis laboratory "LabGal" at "Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos" at Puerto Ayora in Galapagos Islands (Ecuador), where we considered this validation necessary to guarantee the sensibility of SARS-CoV-2 during the surveillance. cache = ./cache/cord-272734-kawim93f.txt txt = ./txt/cord-272734-kawim93f.txt === reduce.pl bib === id = cord-272681-u3p0hsla author = Vargas-Gandica, Jair title = Ageusia and anosmia, a common sign of COVID-19? A case series from four countries date = 2020-07-14 pages = extension = .txt mime = text/plain words = 1508 sentences = 84 flesch = 53 summary = As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to evolve, novel signs and symptoms continue to emerge and expand the clinical manifestations of coronavirus disease 2019 (COVID-19) (Rodriguez-Morales et al. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. As we observed in our patients, deficits in olfactory and taste function were usually of acute onset and at early stages of the disease, presenting for most cases as the initial clinical manifestation throughout the first days (Beltran-Corbellini et al. Anosmia as a presenting symptom of SARS-CoV-2 infection in healthcare workers -a systematic review of the literature, case series, and recommendations for clinical assessment and management cache = ./cache/cord-272681-u3p0hsla.txt txt = ./txt/cord-272681-u3p0hsla.txt === reduce.pl bib === id = cord-272902-kdkyzfjv author = Naghibzadeh, Mahmoud title = Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5406 sentences = 322 flesch = 61 summary = An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. Therefore, this research follows two objectives, development of a general microsatellite discoverer which can be used for different genomes, and analysis of the structures of both SARS-CoV-1 and that of Coronavirus-Covid-19 using this tool and revealing their differences. The properties and novelties of the presented method, which is named Fast MicroSatellite Discoverer (FMSD), for finding all microsatellites of a given gene, DNA, RNA, or other genome sequences including the Novel Coronavirus (GenBabk 2019) and SARS (Rota et al. Section 5 details the evaluation, reports the comparison results, and highlights the structural differences with respect to microsatellites between SARS and Coronavirus-Covid-19 as a case study. A software tool called mreps is develop to detect all tandem repeats, including microsatellites, in DNA as well as whole genome. cache = ./cache/cord-272902-kdkyzfjv.txt txt = ./txt/cord-272902-kdkyzfjv.txt === reduce.pl bib === id = cord-272419-y3ebt4jm author = Monari, Caterina title = A Focus on the Nowadays Potential Antiviral Strategies in Early Phase of Coronavirus Disease 2019 (Covid-19): A Narrative Review date = 2020-08-09 pages = extension = .txt mime = text/plain words = 6476 sentences = 318 flesch = 46 summary = Possible inhibition of SARS-CoV-2 3-chymotrisyn-like (3CL)-protease and papain-like protease Lopinavir is excreted in the gastrointestinal (GI) tract, and thus coronavirus-infected enterocytes might be exposed to higher concentrations of the drug LPV/r tab 200/50 mg: 2 tab BID LPV/r oral sol 80/20 mg: 5 mL BID DRV/cobi tab 800/150 mg: 1 tab QD Gastrointestinal: diarrhea, nausea, vomiting, increased amylase, lipase, total cholesterol and triglycerides (risk factor for pancreatitis) Hepatotoxicity: increasing in GGT, AST, ALT, total bilirubin, hepatitis Cardiological: QT-and PR-interval prolongation, hypertension, bradyarrhytmias; torsade de pointes have been reported in patients treated with LPV/r Metabolical: hyperglycemia and diabetes mellitus, increased uric acid Recently, a randomized, controlled, open-label trial comparing the efficacy of LPV/r versus standard of care was conducted in 199 hospitalized adult patients with severe COVID-19: no significant difference between the two groups neither in the time of clinical improvement (hazard ratio [HR] 1.31; 95% CI 0.95-1.80; p 0.09), nor in the 28-day mortality rate (19.2% versus 25.0%; 95% CI −17.3 to 5.7) was observed [40] . cache = ./cache/cord-272419-y3ebt4jm.txt txt = ./txt/cord-272419-y3ebt4jm.txt === reduce.pl bib === id = cord-272690-r8lv1zzx author = St. John, Ronald K. title = Border Screening for SARS date = 2005-01-17 pages = extension = .txt mime = text/plain words = 2643 sentences = 139 flesch = 51 summary = With the rapid international spread of severe acute respiratory syndrome (SARS) from March through May 2003, Canada introduced various measures to screen airplane passengers at selected airports for symptoms and signs of SARS. Because of the continuing outbreak in Toronto, domestic spread in other affected countries in Southeast Asia, and international spread to other countries, Health Canada intensified its initial response by instituting both inbound and outbound passenger screening to identify persons with symptoms or signs compatible with SARS. In parallel to these measures, Health Canada initiated a pilot study on May 8, 2003 , on the use of infrared thermal scanning machines to detect temperatures >38°C in selected international arriving and departing passengers at Vancouver's International and Toronto's Pearson International airports. Careful analysis of the travel histories of suspected and probable SARS patients who traveled to Canada showed that persons became ill after arrival and would not have been detected by airport screening measures. cache = ./cache/cord-272690-r8lv1zzx.txt txt = ./txt/cord-272690-r8lv1zzx.txt === reduce.pl bib === id = cord-273035-sewfb3q8 author = Kang, Xixiong title = Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome date = 2005-01-01 pages = extension = .txt mime = text/plain words = 4128 sentences = 177 flesch = 50 summary = Background: Definitive early-stage diagnosis of severe acute respiratory syndrome (SARS) is important despite the number of laboratory tests that have been developed to complement clinical features and epidemiologic data in case definition. Results: The discriminatory classifier with a panel of four biomarkers determined in the training set could precisely detect 36 of 37 (sensitivity, 97.3%) acute SARS and 987 of 993 (specificity, 99.4%) non-SARS samples. We established a decision tree algorithm consisting of four unique biomarkers for acute SARS in the training set and subsequently validated the accuracy of this classifier by use of a completely blinded test set. To identify the serum biomarkers that could distinguish SARS from non-SARS samples, we used a training set of specimens (37 SARS acute and 74 controls; Tables 1 and 2) and constructed the decision tree classification algorithm using 10 989 peaks [99 peaks ϫ (37 ϩ 74) spectra] of statistical significance identified in the low energy readings (see Materials and Methods). cache = ./cache/cord-273035-sewfb3q8.txt txt = ./txt/cord-273035-sewfb3q8.txt === reduce.pl bib === id = cord-272010-kc0gi3cj author = Anand, Sai Priya title = Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3661 sentences = 216 flesch = 56 summary = The viral entry of SARS-CoV-2 depends on an interaction between the receptor-binding domain of its trimeric spike glycoprotein and the human angiotensin-converting enzyme 2 (ACE2) receptor. One potential therapeutic target receiving significant attention is the interaction between the SARS-CoV-2 spike (S) glycoprotein and its receptor, human angiotensin-converting enzyme 2 (ACE2). To better understand the interactions between membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins with their receptor, human ACE2, we sought to determine the cooperativity of ACE2 within the respective trimers. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 cache = ./cache/cord-272010-kc0gi3cj.txt txt = ./txt/cord-272010-kc0gi3cj.txt === reduce.pl bib === id = cord-271978-j5enftje author = Zoltán, Köntös title = In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date = 2020-11-10 pages = extension = .txt mime = text/plain words = 2910 sentences = 153 flesch = 52 summary = Conclusion Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients. Enthused by promising findings from a recent study by Pelletier and colleagues (12) , the present study was interested in Essential Iodine Drops (EID) for oral/nasal decontaminant in known or suspected cases of COVID-19 as a potentially better alternative to PVP-I. Briefly, the three dilutions of Essential Iodine Drops (EID) containing SARS-CoV-2 virus solution (1:1; 2:1 and 3:1) were tested in triplicates for virucidal activity as described by Pelletier and colleagues (12) . In vitro virucidal assay in the present study has indeed demonstrated that 75% and 50% of Essential Iodine Drops (EID) solution reduced SARS-CoV-2 virus titre after 60 seconds and 90 seconds of incubation by an LRV of 2.0 (99%). cache = ./cache/cord-271978-j5enftje.txt txt = ./txt/cord-271978-j5enftje.txt === reduce.pl bib === id = cord-272135-a09bf50o author = Brouqui, Philippe title = Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease date = 2009-04-22 pages = extension = .txt mime = text/plain words = 6629 sentences = 370 flesch = 48 summary = However, because the modes of infectious agent transmission are often underestimated, as was recently reported for infl uenza and SARS, 55 and because tuberculosis cannot be identifi ed without biological testing, EUNID recommends that droplet precaution should be upgraded to airborne precaution each time Situations in which a patient would need to be admitted to an HLIU • Patients with an unknown human-to-human transmittable or a potentially transmittable epidemic febrile illness that is native or imported from abroad • Patients with a known infectious disease caused by a group 3 or 4 agent* At admission of patients with HID to an emergency department • Systematically apply standard precautions and cough and respiratory etiquette • Set up at least one single room with a dedicated route and direct access, or an isolation room as recommended by EUNID for a referral hospital, † if HLIU cannot be used for ruling out HID diagnoses • Off er special training to the emergency department team • Retain close relationships with the HLIU team of the referral hospital cache = ./cache/cord-272135-a09bf50o.txt txt = ./txt/cord-272135-a09bf50o.txt === reduce.pl bib === id = cord-273367-gl266pvt author = Gunawardana, M. title = Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5731 sentences = 417 flesch = 59 summary = Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. Subject 557 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on 558 symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but 559 tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A) . cache = ./cache/cord-273367-gl266pvt.txt txt = ./txt/cord-273367-gl266pvt.txt === reduce.pl bib === id = cord-272626-bw9lbzvt author = Pizzorno, Andrés title = Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date = 2020-04-02 pages = extension = .txt mime = text/plain words = 2051 sentences = 116 flesch = 40 summary = Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Developed from biopsies of nasal or bronchial cells differentiated in the air/liquid interphase, these models reproduce with high fidelity most of the main structural, functional and innate immune features of the human respiratory epithelium that play a central role 70 in the early stages of infection and constitute robust surrogates to study airway disease mechanisms and for drug discovery (10) . Comparably, daily treatment with 20 µM remdesivir resulted in 7.3 log10 and 7.9 log10 reductions of intracellular SARS-CoV-2 viral titers at 48 hpi in nasal and bronchial HAE, respectively (Fig. 4D, upper panel) . cache = ./cache/cord-272626-bw9lbzvt.txt txt = ./txt/cord-272626-bw9lbzvt.txt === reduce.pl bib === id = cord-272986-ebgusf3o author = Cao, Yipeng title = Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date = 2020-05-17 pages = extension = .txt mime = text/plain words = 4339 sentences = 267 flesch = 56 summary = title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel. We tried to use potential mean force (PMF) to reveal the permeability of different physiological ions and water molecules in the pores of the E protein pentamer. Figure 3A shows the PMF of ions and water molecules permeating through the SARS-CoV-2 E protein pentamer pore. The free energy calculation of the ions permeating through the SARS-CoV-2 pentameric E protein channel strongly suggests that the pore has selection permeability for monovalent ions. cache = ./cache/cord-272986-ebgusf3o.txt txt = ./txt/cord-272986-ebgusf3o.txt === reduce.pl bib === id = cord-272633-2vmdf9j6 author = Wong, Gary W.K. title = Out of the East – Emerging infections date = 2006-06-05 pages = extension = .txt mime = text/plain words = 1364 sentences = 106 flesch = 51 summary = Severe Acute respiratory syndrome (SARS) originated from southern China and rapidly spread to many countries in early 2003 with over 8000 cases worldwide. 1 Human infection due to a highly pathogenic avian influenza A (H5N1) virus was first described in a mini-outbreak from Hong Kong in 1997. The first outbreak of human disease of avian influenza occurred in 1997 with 18 cases and 6 deaths. 2 Unlike SARS, human disease of avian influenza has a high mortality in both adults and children. Epidemiology of severe acute respiratory syndrome (SARS): adults and children Avian influenza virus infections in humans Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus Outbreak of avian influenza A (H5N1) virus infection in Hong Kong in 1997 Pathology of fatal human infection associated with avian influenza A H5N1 virus cache = ./cache/cord-272633-2vmdf9j6.txt txt = ./txt/cord-272633-2vmdf9j6.txt === reduce.pl bib === id = cord-272501-byfxqsbu author = Motta, Juan Camilo title = Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report date = 2020-08-22 pages = extension = .txt mime = text/plain words = 1507 sentences = 92 flesch = 48 summary = title: Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report We report a case of SARS-Cov2 and adenovirus coinfection, which further developed into acute respiratory distress syndrome. The exact time of coinfection could not be established, and additional poor prognostic factor to the development of severe disease added to patient's comorbidities and reported tests [1, 6] . Although coinfection is not common, in cases with severe disease or CT findings that are not explained by COVID-19 infection [11, 14, 15] , additional studies such as nested PCR for respiratory germs are required to detect potentially treatable pathogens, such as mycoplasma or influenza virus [14] . Larger and better designed prospective analytical studies are required to determine further risk factors, clinical impact, prognosis, and the prevalence of SARS-Cov2 and another respiratory pathogen coinfection. Coinfection with SARS-CoV-2 and other respiratory pathogens in COVID-19 patients in Guangzhou cache = ./cache/cord-272501-byfxqsbu.txt txt = ./txt/cord-272501-byfxqsbu.txt === reduce.pl bib === id = cord-271944-oxtus5vb author = Joseph, Rudman title = Seizure And COVID-19: Association and Review of Potential Mechanism date = 2020-10-13 pages = extension = .txt mime = text/plain words = 2360 sentences = 166 flesch = 48 summary = Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, this highly transmissible virus has since spread rapidly around the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a novel coronavirus that causes Coronavirus Disease of 2019 (COVID19) , a disease that can present with a variety of symptoms [1] . The most common symptoms at the onset of COVID-19 illness are fever, cough, and fatigue; in severe cases, patients may develop severe pneumonia, acute respiratory distress syndrome, and organ failure [4] . This article presents a review of the current literature on seizures linked with SARS-COV 2 infection and describes possible underlying mechanisms. describes the demographic data, time to onset of neurological symptoms, diagnostic criteria, intervention, and outcomes from 11 studies of seizures associated with SARS-COV-2 infection. cache = ./cache/cord-271944-oxtus5vb.txt txt = ./txt/cord-271944-oxtus5vb.txt === reduce.pl bib === id = cord-273451-xnce010o author = Salisbury-Afshar, Elizabeth M. title = Vulnerable Populations: Weathering the Pandemic Storm date = 2020-04-22 pages = extension = .txt mime = text/plain words = 1658 sentences = 97 flesch = 47 summary = Yet, even with awareness that all individuals deserve access to services, and that supporting marginalized populations will slow the spread of SARS-CoV-2, resource limitations will demand difficult allocation determinations. 3 Many individuals experiencing homelessness with SARS-CoV-2 will not meet hospitalization criteria and will be discharged into the general population. 11 In response to SARS-CoV-2, the Substance Abuse and Mental Health Services Administration has developed emergency regulations to support medication for opioid use disorder via telehealth, 12 and temporarily waived the requirement for in-person physical exam to be able to initiate buprenorphine. These often forgotten populations-people incarcerated, homeless, or using drugs-are likely to experience higher risk of exposure to SARS-CoV-2 because of their social circumstances. Planning should incorporate dedicated efforts, funding, and policies/guidelines specific to individuals who experience homelessness, are incarcerated, or are coping with substance use disorders both because these populations deserve care and services, and because not doing so poses great risk to the broader community. cache = ./cache/cord-273451-xnce010o.txt txt = ./txt/cord-273451-xnce010o.txt === reduce.pl bib === id = cord-273253-rgqvdzna author = Skowronski, D. M. title = Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 4173 sentences = 265 flesch = 50 summary = title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 The goal of these serial snapshots was to establish baseline and early pandemic sero-prevalence for future attack rate comparison; to estimate cumulative incidence, residual susceptibility and the extent to which community transmission was suppressed; and to assess surveillance underascertainment across the winter-spring 2020 period in BC. Two of 869 sera were dual-assay positive at the March snapshot giving a crude seroprevalence of 0.23% (95%CI=0.03-0.83) and age-standardized sero-prevalence of 0.28% (95%CI=0.03-0.95). We estimated sero-prevalence based on dual-assay positivity and report cumulative incidence of 0.28% by the start of first wave population-level measures in March. Results of SARS-CoV-2 sero-survey screening by chemiluminescent assay for antibodies to spike (S1) and nucleocapsid proteins, by age group, March and May 2020 snapshots, Lower Mainland, BC, Canada Table 2 . cache = ./cache/cord-273253-rgqvdzna.txt txt = ./txt/cord-273253-rgqvdzna.txt === reduce.pl bib === id = cord-273074-k8m917i4 author = Fu, Chao-Yang title = Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens date = 2005-12-01 pages = extension = .txt mime = text/plain words = 1662 sentences = 91 flesch = 50 summary = title: Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot and neutralization test results showed that the IgY obtained was of a high purity and had a strong reactive activity with a neutralization titer of 1:640. In this study, we have successfully immunized specific pathogen-free (SPF) chickens, and then purified a high-titer anti-SARS coronavirus yolk immunoglobulin (IgY) with neutralizing activity against SARS coronavirus. The activity of IgY in sera and yolks diluted at 1:200 in phosphate buffer saline (PBS) from immunized animals was assessed using an indirect ELISA assay as described previously (Huang et al., 2005) (Fig. 1) . The development of high-titer anti-SARS coronavirus IgY described in this study would appear to have potential as a new anti-SARS biological product for passive immunization, as it effectively neutralized the SARS coronavirus. cache = ./cache/cord-273074-k8m917i4.txt txt = ./txt/cord-273074-k8m917i4.txt === reduce.pl bib === id = cord-273626-zy8qjaai author = Gong, Shu‐ran title = The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models date = 2018-07-28 pages = extension = .txt mime = text/plain words = 3257 sentences = 183 flesch = 56 summary = This illness has been named Middle East respiratory syndrome and the pathogen (MERS-CoV) has been shown to be a type of coronavirus that is highly related to SARS-CoV. Another suitable and well-established model is the common marmoset (Saguinus mystax), which can show more severe clinical signs than rhesus macaques when infected with MERS-CoV. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Middle East Respiratory Syndrome Coronavirus (MERS-CoV) origin and animal reservoir Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques Studies of severe acute respiratory syndrome coronavirus pathology in human cases and animal models Infection, replication, and transmission of middle east respiratory syndrome Coronavirus in Alpacas cache = ./cache/cord-273626-zy8qjaai.txt txt = ./txt/cord-273626-zy8qjaai.txt === reduce.pl bib === id = cord-273351-vq3budip author = Farré, Núria title = Prolonged QT Interval in SARS-CoV-2 Infection: Prevalence and Prognosis date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4368 sentences = 238 flesch = 51 summary = A prolonged QTc was independently associated with a higher mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. QTc prolongation was defined as an increase of at least one millisecond in QTc compared to baseline QTc. According to the protocol at our center at the time of the study, treatment with hydroxychloroquine and azithromycin was recommended to all patients. The variables included in the model were age, baseline QTc > 480 ms, chronic kidney disease, treatment with azithromycin and hydroxychloroquine, ischemic chronic disease, atrial fibrillation or flutter, heart failure, and the presence of any cardiovascular risk factor. Although these differences could be due to a more severe presentation in a group of elderly comorbid patients, SARS-CoV-2 infection could be the cause of this prolonged QTc interval, either as a direct effect of the virus or through systemic inflammation. A prolonged QTc was independently associated with a higher risk of mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. cache = ./cache/cord-273351-vq3budip.txt txt = ./txt/cord-273351-vq3budip.txt === reduce.pl bib === id = cord-273604-0w5shxmf author = Psevdos, George title = Halting a SARS-CoV-2 Outbreak in a U.S. Veterans Affairs Nursing Home date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1241 sentences = 76 flesch = 51 summary = Faced with a dwindling supply of PPE, the Infection Control team distributed supplies saved for a possible Ebola outbreak; A COVID unit was created within the nursing home facilitating the geographic isolation of cases; universal testing of residents and employees allowed for the implementation of proper quarantine measures. 7 Although nationally the virus spreads like wildfire in nursing homes (among residents and working staff), the Department of Veterans Affairs (VA) reported lower COVID-19 rates in their affiliated nursing homes in a U.S. Congressional hearing. Swift detection by rapid RT-PCR testing of all asymptomatic carriers (residents and employees via universal testing) and implementation of strict infection control and isolation measures are pivotal in containing and thus eliminating a COVID-19 outbreak. Universal and Serial Laboratory Testing for SARS-CoV-2 at a Long-Term Care Skilled Nursing Facility for Veterans Hospital affiliated long term care facility COVID-19 containment strategy by using prevalence testing and infection control practices cache = ./cache/cord-273604-0w5shxmf.txt txt = ./txt/cord-273604-0w5shxmf.txt === reduce.pl bib === id = cord-272759-dqkjofw2 author = Small, Michael title = Super-spreaders and the rate of transmission of the SARS virus date = 2006-03-15 pages = extension = .txt mime = text/plain words = 7581 sentences = 508 flesch = 62 summary = The main conclusions of this study are: (i) "super-spreaders" may occur even if the infectiousness of all infected individuals is constant; (ii) consistent with previous reports, extended exposure time beyond 3–5 days (i.e. significant nosocomial transmission) was the key factor in the severity of the SARS outbreak in Hong Kong; and, (iii) the spread of SARS can be effectively controlled by either limiting long range links (imposing a partial quarantine) or enforcing rapid hospitalisation and isolation of symptomatic individuals. 1 Two characteristic features were observed during the SARS outbreak in Hong Kong in 2003 (see Fig. 1 ) [3, 4] : so-called super-spread events (SSE), in which a single individual initiates a large number of cases; and persistent transmission within the community. In this paper, we apply these methods to the modelling of the spread of SARS in Hong Kong; transmission is only allowed to occur along a limited number of direct links between individuals. cache = ./cache/cord-272759-dqkjofw2.txt txt = ./txt/cord-272759-dqkjofw2.txt === reduce.pl bib === id = cord-273314-p1dlzoh1 author = Gadiparthi, Chiranjeevi title = Gastrointestinal Bleeding in Patients with Severe SARS-CoV-2 date = 2020-06-04 pages = extension = .txt mime = text/plain words = 1464 sentences = 88 flesch = 45 summary = Gastrointestinal symptoms are common and frequently reported in Coronavirus Disease-2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, GIB in COVID-19 patients poses unique challenges to patients due to high-risk of concomitant respiratory failure and to endoscopy personnel due to risk of airborne transmission during endoscopic procedures. GI bleeding (GIB) in patients with SARS-CoV-2 poses unique challenges, especially for endoscopists and other procedural staff because of the potential for aerosol spread. In this article, we report 3 hospitalized patients with SARS-CoV-2 infection with GIB and acute blood loss anemia with focus on management strategies. She tested positive for SARS-CoV-2 by RT-PCR assay and developed acute hypoxic respiratory failure requiring supplemental oxygen of 15 L per minute via a nonrebreather mask. On hospital day 5, the patient developed recurrent GIB with a large amount of melena and bright red blood per rectum with hemodynamic instability requiting intensive care unit (ICU) transfer. cache = ./cache/cord-273314-p1dlzoh1.txt txt = ./txt/cord-273314-p1dlzoh1.txt === reduce.pl bib === id = cord-273064-c58nf9vb author = Hallowell, Benjamin D. title = Severe Acute Respiratory Syndrome Coronavirus 2 Prevalence, Seroprevalence, and Exposure among Evacuees from Wuhan, China, 2020 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 3519 sentences = 168 flesch = 47 summary = At arrival in the United States and again at the quarantine facility, evacuees were asked to complete a US Traveler's Health Declaration form disclosing any symptoms; they were also screened for illness and fever, asked about symptoms in the past 72 hours, and asked about any high-risk exposures (including working in or visiting healthcare settings; caring for or visiting persons with fever, respiratory illness, or a confirmed COVID-19 diagnosis; or visiting any live animal markets) in Wuhan in the past 14 days. The survey captured information on demographics, clinical signs/ symptoms, travel outside of Hubei Province, face mask use, limitation of time spent in public, and past high-risk exposures (including contact with confirmed COVID-19 case-patients; persons with fever, acute respiratory illness, or both; healthcare and laboratory facilities; and animals and live animal markets). cache = ./cache/cord-273064-c58nf9vb.txt txt = ./txt/cord-273064-c58nf9vb.txt === reduce.pl bib === id = cord-272702-7uc4ozjy author = Graham, T. G. W. title = Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date = 2020-09-18 pages = extension = .txt mime = text/plain words = 8061 sentences = 483 flesch = 59 summary = We therefore tested whether we could detect SARS-CoV-2 RNA by adding 1 μ l of each swab sample to 20 μ l TaqPath reactions containing the N1, N2, and RNase P (RP) probes ( Fig 2A) . Taken together, these results show that RT-qPCR with BEARmix can detect SARS-CoV-2 in clinical samples, either using purified RNA or by direct addition of swab samples, albeit with somewhat less sensitivity than commercial TaqPath master mix. To evaluate a complete protocol in which swab samples are collected into PK solution and then added directly to BEARmix RT-PCRs, we prepared contrived swab samples in which live virus was mixed with pathogenfree human nasal fluid prior to dilution into either DNA/RNA Shield, VCM containing 0.4 mg/ml proteinase K, or a solution of 0.4 mg/ml proteinase K in water (Fig 6) . Here we have developed simple, academic laboratory-derived methods for RNA extraction, direct sample addition, and RT-PCR detection that provide low-cost alternatives to the use of commercial kits (Fig 8) . cache = ./cache/cord-272702-7uc4ozjy.txt txt = ./txt/cord-272702-7uc4ozjy.txt === reduce.pl bib === id = cord-273505-pcsw3vmx author = Liu, Xiaosheng title = High-Dose Intravenous Immunoglobulins in the Treatment of Severe Acute Viral Pneumonia: The Known Mechanisms and Clinical Effects date = 2020-07-14 pages = extension = .txt mime = text/plain words = 10764 sentences = 515 flesch = 35 summary = Based on the previous clinical experience in China, it was proposed that early initiation of high-dose intravenous immunoglobulins (IVIg) and low-molecular-weight heparin might be effective in improving the prognosis of severe and critically ill COVID-19 patients (16, 17) . The substantial increase in IgG concentration may saturate FcRn and reduce the half-life of pathogenic antibodies, contributing to the anti-inflammatory mechanism of high-dose IVIg. A balance between activating and inhibitory FcγRs is critical for a well-regulated immune response, and a disbalance markedly influences immunopathology in autoimmune and infectious diseases. Based on these potential supportive F(ab) ′ 2 and Fc mediated mechanisms and the known clinical effects in treating severe virus pneumonia such as SARS, MERS, influenza, and RSV disease, the early application of high-dose IVIg therapy may be considered in the management of severe COVID-19 patients. cache = ./cache/cord-273505-pcsw3vmx.txt txt = ./txt/cord-273505-pcsw3vmx.txt === reduce.pl bib === id = cord-273182-djb0ozrt author = Díez, José María title = Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4326 sentences = 260 flesch = 50 summary = Recently, we reported cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2 and MERS-CoV with Flebogamma R DIF 5 and 10% and Gamunex R -C, two currently available intravenous IGs (IVIG) [23] . Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2 and MERS-CoV by: ELISA techniques; and well-established neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT 50 titers ranging from 4.5 to >5 (Figure 2 ). This neutralizing activity correlates with the cross-reactivity to different coronavirus antigens observed in ELISA-binding assays with IVIG, as shown in a previous study [23] . • Intravenous immunoglobulin products were tested against severe acute respiratory syndrome coronavirus 2 in cell culture neutralization assays. cache = ./cache/cord-273182-djb0ozrt.txt txt = ./txt/cord-273182-djb0ozrt.txt === reduce.pl bib === id = cord-273114-eanwxkvt author = Perrone, Serafina title = Report of a series of healthy term newborns from convalescent mothers with COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1666 sentences = 106 flesch = 53 summary = A further case series described 7 women with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), all of whom required oxygen therapy and received Caesarean section at term; only 3 neonates were tested, of whom one was positive. Here we report a series of cases of healthy term newborns whose mother developed COVID-19 infection during the third trimester of pregnancy and were convalescent with negative test at the time of delivery. Moreover, birth date, mode of delivery, gestational age, birth weight (g), anthropometric data, Apgar score 1'-5', amniotic fluid, mother-child contact, clinical signs or symptoms and swab results was collected by newborns. Her husband suffered from COVID-19 infection and RT-PCR assay on her nasopharyngeal swab was positive for SARS-CoV-2. We reported four cases of healthy neonates born from mothers with previous SARS-CoV-2 pneumonia in the third trimester of pregnancy. cache = ./cache/cord-273114-eanwxkvt.txt txt = ./txt/cord-273114-eanwxkvt.txt === reduce.pl bib === id = cord-272566-rtnhndw3 author = Robertson, M. title = A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort date = 2020-05-04 pages = extension = .txt mime = text/plain words = 5158 sentences = 323 flesch = 55 summary = Following baseline questionnaire completion, study participants will be contacted monthly (for 6 months) to complete assessments of engagement in non-pharmaceutical interventions (e.g., use of cloth masks, avoiding large gatherings); COVID-19 symptoms; SARS/COV2 testing and diagnosis; hospitalizations; healthcare access; and uptake of health messaging. 2, 3 In response to the COVID-19 pandemic the CUNY Institute for Implementation Science in Population Health (ISPH) launched the Communities, Households and SARS/COV-2 Epidemiology (CHASING) COVID Cohort "C 3 " study on March 28, 2020 . For analyses to assess subsequent disease after Month 1, incident COVID-19 disease will be defined as development of new COVID-like symptoms > 7 days after the first (positive or negative) SARS/COV2 serologic test result. The C 3 cohort is geographically and socio-demographically diverse, and includes participants from many active hotspots during the recruitment period (March 28-April 20, 2020), as well as frontline health care workers and other essential employees, and individuals who are vulnerable to severe outcomes associated with SARS/COV2 infection. cache = ./cache/cord-272566-rtnhndw3.txt txt = ./txt/cord-272566-rtnhndw3.txt === reduce.pl bib === id = cord-273645-czh3zfb3 author = Lu, Shuaiyao title = Comparison of SARS-CoV-2 infections among 3 species of non-human primates date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2197 sentences = 171 flesch = 65 summary = In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Here, to establish the COVID-19 model, two families including 3 species of non-human primates, which are widely used for animal models with their own advantages and disadvantages, were experimentally infected with SARS-CoV-2, followed by comparisons of clinical symptoms, hematology, biochemical indexes, immunology and histopathology among 3 species. Given that host factors may be involved in viral pathogenesis, we designed an experiment in the present study to investigate whether host genetics, age and gender affect SARS-CoV-2 infection in non-human primates ( Figure 1 ). To know dynamics of viral replication and virus shedding, samples of nasal swabs, throat swabs, anal swabs, feces, blood and tissues were collected at the indicated time points, and SARS-CoV-2 genomes were quantitated by RT-qPCR. cache = ./cache/cord-273645-czh3zfb3.txt txt = ./txt/cord-273645-czh3zfb3.txt === reduce.pl bib === id = cord-273251-k3ltbpnb author = Phipps, Meaghan M. title = Acute Liver Injury in COVID‐19: Prevalence and Association with Clinical Outcomes in a Large US Cohort date = 2020-05-30 pages = extension = .txt mime = text/plain words = 4025 sentences = 204 flesch = 50 summary = In multivariable analysis, peak ALT was significantly associated with death or discharge to hospice (OR 1.14, p=0.044), controlling for age, body mass index, diabetes, hypertension, intubation, and renal replacement therapy. (18) Patients with a positive test for SARS-CoV-2 were evaluated in subsequent analyses, categorized into those with peak ALT consistent with no/mild liver injury (<2 times ULN), moderate liver injury (2) (3) (4) (5) times ULN) and severe liver injury (>5 times ULN). Although initial alkaline phosphatase levels were similar across all categories of ALT, median peak value was higher in patients with severe liver injury (p<0.001), however it was only mildly elevated. In this cohort with 2273 cases and 1108 controls, we demonstrate that initial and peak ALT are higher in those who test positive for SARS-CoV-2 compared to those who test negative with a similar clinical presentation. Higher peak ALT values were also significantly associated with overall disease severity and measured clinical outcomes. cache = ./cache/cord-273251-k3ltbpnb.txt txt = ./txt/cord-273251-k3ltbpnb.txt === reduce.pl bib === id = cord-273373-5elel6qo author = Wang, Haofeng title = Recent progress in the discovery of inhibitors targeting coronavirus proteases date = 2016-02-19 pages = extension = .txt mime = text/plain words = 3083 sentences = 165 flesch = 50 summary = The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. Structural analyses revealed that the substrate-binding pockets of various CoV M pro s are highly conserved, which led to the concept of "widespectrum inhibitors" for targeting all CoVs. Through a structure-based drug design, we have identified a lead compound named N3 with potent inhibitory activity against all M pro s tested ( Figure 2D) . Structurebased design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome-coronavirus papain-like protease Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Papain-like protease 2 (PLP2) from severe acute respiratory syndrome coronavirus (SARS-CoV): expression, purification, characterization, and inhibition cache = ./cache/cord-273373-5elel6qo.txt txt = ./txt/cord-273373-5elel6qo.txt === reduce.pl bib === id = cord-272603-nbosceoz author = Lin, Qiuyuan title = Microfluidic Immunoassays for Sensitive and Simultaneous Detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1882 sentences = 98 flesch = 42 summary = Facing the emergence of this pandemic, we established a portable microfluidic immunoassay system for easy-to-use, sensitive, rapid (<15 min), multiple, and on-site detection of IgG/IgM/Antigen of SARS-CoV-2 simultaneously. This integrated method was successfully applied for detecting SARS-CoV-2 IgM and IgG antibodies in clinical human serum as well as SARS-CoV-2 antigen in pharyngeal swabs from 26 patients with COVID-19 infection and 28 uninfected people. 26 To meet the challenge of the large epidemic, we describe the development of a point-of-care microfluidic platform integrating a homemade fluorescence detection analyzer ( Figure 1A ), SARS-CoV-2 diagnostic microchips ( Figure 1B) , and multiple immunoassays ( Figure 1C ) for detecting three biomarkers (IgG, IgM, and antigen). This robust microfluidic immunoassay system can provide a useful tool for SARS-CoV-2 diagnosis in public health laboratories as well as for timely screening potentially infected patients to monitor and prevent the epidemic owning to its capability of easy, fast, cost-effective, and point-of-care detection. cache = ./cache/cord-272603-nbosceoz.txt txt = ./txt/cord-272603-nbosceoz.txt === reduce.pl bib === id = cord-273685-oxvfxmtr author = Fan, Qihong title = Anal swab findings in an infant with COVID‐19 date = 2020-03-17 pages = extension = .txt mime = text/plain words = 1250 sentences = 89 flesch = 61 summary = In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in pharyngeal swab and anal swab were compared. In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in pharyngeal swab and anal swab were compared. The oropharyngeal specimen showed negative result for SARS-CoV-2 on the 14th day after onset of the illness. However, the anal swab was still positive for SARS-CoV-2 on the 28th day after the onset of the illness. COVID-19, Anal swab, SARS-CoV-2, Fecal-oral transmission confirmed in China with at least 3042 reported deaths. Several reports noted that the stool specimens from the patients with COVID-19 were positive for the novel SARS-CoV-2. However, the anal swabs remained positive for SARS-CoV-2 on the 28th day after the onset of the illness (Table 1) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-273685-oxvfxmtr.txt txt = ./txt/cord-273685-oxvfxmtr.txt === reduce.pl bib === id = cord-273492-i483r91m author = Fulzele, Sadanand title = COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile date = 2020-05-09 pages = extension = .txt mime = text/plain words = 3637 sentences = 233 flesch = 51 summary = In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Based on the above reports, we did in silico analysis of miRNAs targeting SARS and COVID-19 (recent isolates from different regions) to understand the pathophysiology and identify novel therapeutic targets. In a previous report, host cellular miRNAs-181 binds to the ORF-4 region at the viral genome of porcine reproductive and respiratory syndrome virus (PRRSV) to inhibit its replication [17] . Both KEGG and GO pathway analysis revealed that COVID-19 targeting human cellular miRNAs are involved in the number of age-related complications. cache = ./cache/cord-273492-i483r91m.txt txt = ./txt/cord-273492-i483r91m.txt === reduce.pl bib === id = cord-273553-xp4nfnq3 author = Ramatillah, D. L. title = TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA date = 2020-10-16 pages = extension = .txt mime = text/plain words = 3967 sentences = 217 flesch = 54 summary = Conclusion: The most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine.The higher the patient's average treatment duration, the lower the average survival rate for COVID-19 patients. Samples used in this study were patients with confirmed COVID-19 who were undergoing treatment and receiving antiviral agent therapy. Patients receiving the combination Oseltamivir + Chloroquine therapy had an average survival rate of about 17% after about 23 days of treatment. Meanwhile, patients who received combination therapy Favipiravir + Oseltamivir + Chloroquine had an average survival rate of about 10% after undergoing treatment for about 39 days. Based on the Chi-Square test, it was found that there was a significant relationship between COVID-19 antiviral agent therapy and the clinical outcome of COVID-19 patients (p = 0.025). Based on the Chi-Square test, there was no significant effect between gender (p = 0.174) and age (p = 0.065) on the clinical outcome of COVID-19 patients. cache = ./cache/cord-273553-xp4nfnq3.txt txt = ./txt/cord-273553-xp4nfnq3.txt === reduce.pl bib === id = cord-273613-cpiveo7j author = Cao, Xia title = Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3505 sentences = 178 flesch = 46 summary = Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Affinity maturation of STI-1499 resulted in identification of STI-2020, an antibody with a 35-fold increased affinity for the SARS-CoV-2 Spike receptor-binding domain (RBD) leading to a greater than 50-fold increase in virus neutralization potency against live WA-1/2020 and 2020001 viruses in vitro. In this study, we detail the initial discovery and profiling of a SARS-CoV-2 nAb isolated from a phage display antibody library derived from the B-cell repertoire of over 600 healthy normal individuals. Candidate nAbs were characterized for binding of Spike S1 subunit and neutralization of related clinical SARS-CoV-2 isolates. cache = ./cache/cord-273613-cpiveo7j.txt txt = ./txt/cord-273613-cpiveo7j.txt === reduce.pl bib === id = cord-273614-qmp2tqtb author = Tahir, Faryal title = Cardiac Manifestations of Coronavirus Disease 2019 (COVID-19): A Comprehensive Review date = 2020-05-08 pages = extension = .txt mime = text/plain words = 7164 sentences = 413 flesch = 53 summary = However, multiple studies that highlight the clinical features, laboratory findings, and prognosis of acute myocardial injury (AMI) in COVID-19-affected individuals have been published. The study concluded that severe respiratory illness with 2019n-CoV infection with deteriorating complications was associated with ICU admission and a higher mortality rate [24] . This study concluded that patients with very severe COVID-19 have a higher percentage of increased cTnI levels and their mortality rate can be improved by protecting them from myocardial injury [40] . The study concluded that cardiac injury is a prevalent condition among hospitalized patients with COVID-19 in Wuhan, China, and it is associated with a higher risk of in-hospital mortality [41] . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study (Epub ahead of print) Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China (Epub ahead of print) cache = ./cache/cord-273614-qmp2tqtb.txt txt = ./txt/cord-273614-qmp2tqtb.txt === reduce.pl bib === id = cord-273764-itu39mln author = Li, Taisheng title = Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date = 2006-12-20 pages = extension = .txt mime = text/plain words = 2660 sentences = 120 flesch = 49 summary = In this report, we have sequentially monitored 30 recovered patients over a two-year period to characterize temporal changes in SARS-CoV-specific antibody responses as well as cytotoxic T cell (CTL) responses. As show in Fig. 1 , recovered patients clearly experienced two distinct phases of cell restoration in the peripheral blood; an initial rapid phase for all the cell populations studied in the first 3 months after the onset of symptoms followed by a significant slower phase during the subsequent months. To study the sequential changes in CTL responses against SARS-CoV, we used ELISPOT-based technique to quantify the number of INF-c releasing cells in the peripheral blood against peptide pools covering the entire N protein derived from the Urbani strain [3] . We have shown for the first time that recovered patients have persistent and robust binding as well as neutralizing antibody and CTL responses throughout the study period with a moderate decline one year after the onset of symptoms. cache = ./cache/cord-273764-itu39mln.txt txt = ./txt/cord-273764-itu39mln.txt === reduce.pl bib === id = cord-273126-gceffbfp author = Yuan, Kehu title = Suppression of SARS-CoV entry by peptides corresponding to heptad regions on spike glycoprotein date = 2004-07-02 pages = extension = .txt mime = text/plain words = 3263 sentences = 174 flesch = 58 summary = Subsequently, the highly conserved heptad repeat (HR) regions (HR1 and HR2) in the glycoprotein interact with each other to form a six-helix bundle structure, which facilitates the juxtaposition of the virus and cell membranes, leading to membrane fusion [9] . Based on the fusion mechanism described above, we used an approach that was successfully used for studying other enveloped viruses, such as HIV-1 and MHV, to identify the potent inhibitor for virus entry [16, 18, 19, 25] . Screened through the pseudotyped virus infection assay [7, [26] [27] [28] and validated with wild-typed virus infection, two peptides were identified, HR1-1 and HR2-18, which were able to inhibit the SARS-CoV entry process. Although we designed a series of peptides overlapping the HR2 region, only one peptide HR2-18 was identified to inhibit the entry of SARS-CoV with low inhibitor activity. cache = ./cache/cord-273126-gceffbfp.txt txt = ./txt/cord-273126-gceffbfp.txt === reduce.pl bib === id = cord-273859-tr4s5i7h author = Luis García Garmendia, José title = DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1379 sentences = 139 flesch = 61 summary = En las formas clínicas menos graves, la detección de ARN viral es máxima durante las dos primeras semanas desde el inicio de los síntomas(4), y a partir de los 7-10 días se produce respuesta inmunológica de IgM y después de IgG (5) . El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). A estos pacientes se les hicieron 2 determinaciones de rRT-PCR de Coronavirus a partir de 21 días del inicio de síntomas, separadas por 24 h, para comprobar si persistía eliminación del virus. La detección del ARN viral mediante técnicas de rRT-PCR parece ser una forma adecuada de determinar la necesidad de aislamiento de los pacientes con SARS-CoV-2(8, 12). Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. cache = ./cache/cord-273859-tr4s5i7h.txt txt = ./txt/cord-273859-tr4s5i7h.txt === reduce.pl bib === id = cord-273349-penb65x7 author = Zhang, Chao title = Liver injury in COVID-19: management and challenges date = 2020-05-31 pages = extension = .txt mime = text/plain words = 1541 sentences = 82 flesch = 44 summary = The severity, mortality, and incidence of complications in these patients, including secondary infection, hepatic encephalopathy, upper gastrointestinal bleeding, and liver failure, need to be examined in large-cohort clinical studies. As the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread from China to other countries, governments and the medical community are taking steps to prevent transmission, from common sense recommendations to radical quarantine measures. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalised patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-273349-penb65x7.txt txt = ./txt/cord-273349-penb65x7.txt === reduce.pl bib === id = cord-273426-55vu6b3u author = Iba, Toshiaki title = Coagulopathy of Coronavirus Disease 2019 date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4536 sentences = 257 flesch = 31 summary = Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. (Crit Care Med 2020; XX:00-00) Key Words: coagulopathy; coronavirus; coronavirus disease 2019; disseminated intravascular coagulation; hypercoagulability; thromboembolism I ncreasing communications worldwide have reported that hospitalized, critically ill coronavirus disease 2019 (COVID-19) patients are frequently developing laboratory abnormalities compatible with hypercoagulability and clinically a high prevalence of thromboembolic events (1). cache = ./cache/cord-273426-55vu6b3u.txt txt = ./txt/cord-273426-55vu6b3u.txt === reduce.pl bib === id = cord-272956-0yumc7em author = Gnavi, Roberto title = Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1772 sentences = 90 flesch = 51 summary = Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. cache = ./cache/cord-272956-0yumc7em.txt txt = ./txt/cord-272956-0yumc7em.txt === reduce.pl bib === id = cord-273675-0oiq44gl author = Wu, Di title = To alert coinfection of COVID-19 and dengue virus in developing countries in the dengue-endemic area date = 2020-05-04 pages = extension = .txt mime = text/plain words = 568 sentences = 38 flesch = 66 summary = At the meantime, dengue was endemic in the Southeast Asia and South America, and a part of the patients shared the same symptoms, so, we write this paper to alert the clinicians to distinguish these two diseases. 1 Gabriel Yan et al 2 reported 2 cases of COVID-19 patients coinfected with dengue fever in Singapore. Joob et al 3 also reported a patient coinfected with SARS-CoV-2 and dengue virus in Thailand. These 3 cases raise concern that patients with fever can be infected with both SARS-CoV-2 and dengue at the same time in dengue-endemic areas such as Singapore, Thailand, and Malaysia in Southeast Asia and Brazil in South America. Some patients present only with fever when infected with SARS-CoV-2. Therefore, measures should be taken to distinguish patients with fever and headache from dengue fever and COVID-19, and these atypical symptoms should trigger alerts, especially in developing countries with a high incidence of dengue fever, as in Southeast Asia and South American. cache = ./cache/cord-273675-0oiq44gl.txt txt = ./txt/cord-273675-0oiq44gl.txt === reduce.pl bib === id = cord-273083-xrydkiu4 author = Pahmeier, Felix title = A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date = 2020-09-01 pages = extension = .txt mime = text/plain words = 999 sentences = 64 flesch = 49 summary = Here, we describe the generation and characterization of a reporter system to visualize dengue virus and SARS-CoV-2 replication in live cells. The system is based on viral protease activity causing cleavage and nuclear translocation of an engineered fluorescent protein that is expressed in the infected cells. Here we describe a reporter system that takes advantage of virus-encoded proteases that are expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. In order to generate a reporter system that can specifically indicate virus infection, we 219 designed a construct expressing a GFP fusion protein that could selectively be cleaved 220 by viral proteases. However, since no fluorescent 304 protein coding sequence is incorporated into the construct, expression of the DENV 305 polyprotein cannot be followed by live cell imaging. cache = ./cache/cord-273083-xrydkiu4.txt txt = ./txt/cord-273083-xrydkiu4.txt === reduce.pl bib === id = cord-273913-xem3alih author = Marraha, Farah title = A Review of the Dermatological Manifestations of Coronavirus Disease 2019 (COVID-19) date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4225 sentences = 234 flesch = 48 summary = In this review, we discuss these various cutaneous manifestations and skin problems related to personal protective equipment, as well as different cutaneous anti-COVID-19 drug-associated reactions. e first case infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was reported in Wuhan, China, in late November 2019. ese skin lesions can guide clinicians for diagnosis if the patients present other COVID-19 symptoms; however, viral infection cannot be the only cause; mediated inflammatory responses and drug reactions can also be suspected. e aim of our literature review is to report the various cutaneous manifestations described to date associated with COVID-19, the skin problems related to personal protective equipment, and the different cutaneous anti-COVID-19 drug reactions [6, 7] . e frequency of the skin lesions associated with COVID-19 infection varies according to the series; in a Chinese study of 1099 positive cases, the incidence was only 0.2%, while in an Italian series of 88 patients it was 20.4% [42] . cache = ./cache/cord-273913-xem3alih.txt txt = ./txt/cord-273913-xem3alih.txt === reduce.pl bib === id = cord-273408-jtpaue0z author = Romeyke, Tobias title = COVID-19 Case Report: An 84-Year-Old Man with Exacerbation of Multiple Comorbidities Due to COVID-19 Managed by a Multidisciplinary Team Using Patient-Reported Outcomes date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3045 sentences = 201 flesch = 48 summary = Patient: Male, 84-year-old Final Diagnosis: Acute bronchitis • chronic multiple pain with spondylosis with radiculopathy: lumbar region • chronic renal failure CKD 4 • derailed type 2 diabetes mellitus • diabetes mellitus type 2 • eart failure • hyperuricaemia • progressive aortic stenosis • pulmonary hypertension • SARS-CoV2 Symptoms: Appetite loss • fever • pain • sore throat Medication: — Clinical Procedure: — Specialty: General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: When treating patients with comorbidities who are infected with severe acute respiratory syndrome as a result of SARS-CoV-2, it is crucial to offer multidisciplinary treatment that takes into consideration all of the health conditions with which they have been diagnosed. We collected clinical and patient-reported data on quality of life, physical functions, the sensation of pain, psychological well-being, and symptoms while taking into account the degree of chronicity of the conditions, the level of the patient's pain, and his hospitalization in an isolation ward. cache = ./cache/cord-273408-jtpaue0z.txt txt = ./txt/cord-273408-jtpaue0z.txt === reduce.pl bib === id = cord-273311-dl9u85nh author = Boscolo‐Rizzo, Paolo title = Challenges in interpreting the diagnostic performance of symptoms to predict COVID‐19 status: the case of anosmia date = 2020-06-25 pages = extension = .txt mime = text/plain words = 430 sentences = 34 flesch = 54 summary = Consequently, several studies have tried to estimate the sensitivity and specificity as well as the positive predictive value of self-reported new onset of smell and/or taste impairment for COVID-19 in populations of patients with flu-like symptoms. The first is that the standard diagnostic tool for diagnosis of SARS-CoV-2 infection, i.e. This article is protected by copyright. While the pooled sensitivity was 61% (95% CI, 55-68%), the pooled specificity reached 87% (95% CI, 80-92%); publication bias is possible (Figure 1b In conclusion, despite we believe that the new onset of smell and/or taste loss during COVID-19 pandemic should be considered a manifestation of SARS-CoV-2 infection until proven otherwise, sufficient to justify testing, self-isolation and the use of personal protective equipment by medical personnel interacting with these subjects, taken into account the above considerations, diagnostic performance of single symptoms should be fully understood and considered with caution when predicting SARS-CoV-2 infection in patients with flu-like symptoms. cache = ./cache/cord-273311-dl9u85nh.txt txt = ./txt/cord-273311-dl9u85nh.txt === reduce.pl bib === id = cord-273382-7w8fli6w author = Guderian, Daniela B. title = In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling date = 2020-09-07 pages = extension = .txt mime = text/plain words = 3941 sentences = 242 flesch = 45 summary = title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling Five typical surgical intervention techniques (mechanical stress with a passive instrument with and without suction, CO(2) laser treatment, drilling and bipolar electrocoagulation) were examined and compared regarding resulting particle release. The aim of the presented study was therefore to develop an experimental setup for the simultaneous assessment of aerosol and particle formation in various typical ENT interventions. Similarly, no particle or aerosol formation was detected during mechanical impact by use of a passive instrument in direct tissue contact with additional suction (cf. The laser treatment of the tissue did not lead to a detectable particle formation at any of the three points in time of the analysis (see Fig. 3 , third line). cache = ./cache/cord-273382-7w8fli6w.txt txt = ./txt/cord-273382-7w8fli6w.txt === reduce.pl bib === id = cord-273784-sr6afv60 author = Cazares, Lisa H. title = Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5793 sentences = 299 flesch = 54 summary = The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. To determine the feasibility of targeted MS for SARS-CoV-2 diagnostics, we developed a method for the detection and quantitation of the S and NP, which employs parallel reaction monitoring (PRM) using a high-resolution Orbitrap instrument, thereby providing very high specificity. To test the ability of the PRM assay to detect S protein and NP in a relevant sample type, we spiked inactivated SARS CoV-2 virions into in vitro derived mucus. (B) PRM assay was then used to quantitate the SARS-CoV-2 protein levels in a mock sample that was created by adding an inactivated virus sample to in vitro derived mucus. Using the calibration curve from the best performing peptide for NP (DQVILLNK), the low and high SARS-CoV-2 mock samples contained on average 227 and 422 amol of NP, respectively, on column (see Figure 5A ). cache = ./cache/cord-273784-sr6afv60.txt txt = ./txt/cord-273784-sr6afv60.txt === reduce.pl bib === id = cord-273751-61eeykj1 author = Yang, Zhenwei title = The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis date = 2020-04-10 pages = extension = .txt mime = text/plain words = 3003 sentences = 204 flesch = 52 summary = title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis The inclusion criteria in this meta-analysis were as follows: (1) subjects in each study were patients with coronavirus infection; (2) the patients were divided into the experimental group using corticosteroids and the control group not using corticosteroids; (3) the outcomes included the use of corticosteroids in critical and noncritical patients, mortality, length of stay (LOS) and adverse reactions to corticosteroids. We extracted the following variables: the authors, the publication year, the study design, viral type, population, treatment details (including corticosteroid use, types and doses of corticosteroids, and other treatments), and outcome measures such as the use of corticosteroids in critical and non-critical patients, mortality, LOS and adverse reactions to corticosteroids (including bacterial infection, hyperglycemia, hypocalcemia and hypokalemia). In this systematic review and meta-analysis, the result indicated that patients with severe conditions were more likely to require corticosteroids therapy. cache = ./cache/cord-273751-61eeykj1.txt txt = ./txt/cord-273751-61eeykj1.txt === reduce.pl bib === id = cord-273882-tqdcb3oo author = Pratibha, title = Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1958 sentences = 122 flesch = 62 summary = title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. These ubiquitous forbidden orders (UFO) are unique structures of the viruses that may provide an insight into viruses' chemical behavior and the folding patterns of the proteins. Next, we analyzed protein sequences of 26 viruses (Figures 2, 3 , and Supplementary Figures 1 -4) to search for a ubiquitous forbidden order in each one of them. Among the 26 viruses studied, we noted that the forbidden order BPAB is unique to SARS CoV-2, Rubella, and Avian IB (Figure 3) . We found that at R-group classified sequences of N, B, A, and P in these two samples are identical up to level 4 of the amino acid ordering in the protein structures (Figures 4a, d, g) . cache = ./cache/cord-273882-tqdcb3oo.txt txt = ./txt/cord-273882-tqdcb3oo.txt === reduce.pl bib === id = cord-273891-7w334xgt author = Kirchdoerfer, Robert N. title = Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date = 2018-03-31 pages = extension = .txt mime = text/plain words = 3300 sentences = 170 flesch = 55 summary = The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. Subsequent studies of the highly pathogenic human coronavirus S proteins of SARS-64 CoV 15,22 and MERS-CoV 17,22 showed that these viral S1 RBD do indeed sample an 'up' 65 conformation where the receptor-binding site is accessible. 70 To examine the hypothesized conformational transitions induced by proteolysis and 71 receptor binding, we used single-particle cryo-EM to determine structures of S in uncleaved, 72 S1/S2 cleaved and ACE2-bound states. Three-dimensional classification of the S1 RBD 73 positions and corresponding atomic protein models revealed that neither ACE2-binding nor 74 trypsin cleavage at the S1/S2 boundary induced substantial conformational changes in the CoV may use a distinct mechanism of FP2 membrane insertion. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein 381 reveal a prerequisite conformational state for receptor binding cache = ./cache/cord-273891-7w334xgt.txt txt = ./txt/cord-273891-7w334xgt.txt === reduce.pl bib === id = cord-273893-3nd6ptrg author = Lu, Guangwen title = Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 date = 2013-07-07 pages = extension = .txt mime = text/plain words = 4674 sentences = 260 flesch = 56 summary = Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. cache = ./cache/cord-273893-3nd6ptrg.txt txt = ./txt/cord-273893-3nd6ptrg.txt === reduce.pl bib === id = cord-273726-24mi50rv author = Aaroe, Ashley title = Potential Neurologic and Oncologic Implications of the Novel Coronavirus date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1091 sentences = 79 flesch = 54 summary = It is one of seven coronaviruses that are known to infect humans, along with SARS-CoV1, MERS-CoV, and four endemic species that cause cold-like symptoms (229E, OC43, NL63 and HKU1). Human coronavirus species have been detected in CNS samples of patients with MS as early as the 1980s in autopsy studies [3] , and also in the CSF of children with acute disseminated encephalomyelitis. A similar phenomenon may be evident in SARS-CoV2, as an estimated 63% of COVID-19 patients develop lymphopenia, and recent data shows a trend to worsened lymphopenia in patients with CNS symptoms compared with those without [5] . A preliminary report describes a case of acute myelitis following SARS-CoV2 infection [9] . Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. Acute myelitis after SARS-CoV-2 infection: a case report. The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients cache = ./cache/cord-273726-24mi50rv.txt txt = ./txt/cord-273726-24mi50rv.txt === reduce.pl bib === id = cord-274028-dvsvtsn0 author = Del Brutto, Oscar H. title = SARS-CoV-2-related mortality in a rural Latin American population date = 2020-08-08 pages = extension = .txt mime = text/plain words = 1217 sentences = 74 flesch = 60 summary = Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . cache = ./cache/cord-274028-dvsvtsn0.txt txt = ./txt/cord-274028-dvsvtsn0.txt === reduce.pl bib === id = cord-273723-srfypn7j author = Omar, Sarah title = Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2932 sentences = 135 flesch = 46 summary = title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis As far as we are aware, there are currently no published data on the duration of RNA positivity in the upper respiratory of patients with mild COVID-19 that could inform a public health assessment of RT-qPCR as a tool for monitoring home isolation. At 14 days after onset, the earliest moment to discontinue home isolation currently recommended in Germany [18] , 53.5% of COVID-19 patients still had detectable SARS-CoV-2 RNA (Figure 2) . Duration of SARS-CoV-2-RNA positivity in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 (n = 537) For cases where laboratory monitoring is indispensable, knowledge of the RT-qPCR threshold cycle may improve our judgement on whether a positive result indicates infectiousness or not [20] . cache = ./cache/cord-273723-srfypn7j.txt txt = ./txt/cord-273723-srfypn7j.txt === reduce.pl bib === id = cord-273828-557vlq9d author = Brito, Carlos Antunes title = Mechanisms and consequences of COVID-19 associated liver injury: What can we affirm? date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3095 sentences = 166 flesch = 50 summary = Since the first reports of coronavirus disease 2019 (COVID-19) cases in December 2019 in China, numerous papers have been published describing a high frequency of liver injury associated with severe acute respiratory syndrome coronavirus 2 infection, many of them proposing a link between these findings and patient outcomes. Recently, many papers have been published reporting gastrointestinal manifestations, including acute liver injury, with increased levels of aminotransferases, in COVID-19 patients; these manifestations have been reported more frequently in patients with severe forms of this disease. Liver injury related to SARS-CoV-2 disease has been defined by increased liver enzyme serum levels, mainly aminotransferases and bilirubin, during the infection course in patients with or without previous liver disease [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] . Wide variability in deviations of liver enzyme serum levels from normal values is observed in infected patients, with an elevation frequency ranging from 16% to 62% for aminotransferases and from 5% to 21% for bilirubin. cache = ./cache/cord-273828-557vlq9d.txt txt = ./txt/cord-273828-557vlq9d.txt === reduce.pl bib === id = cord-274007-zndtddty author = Rasmussen, Sonja A. title = Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date = 2020-02-24 pages = extension = .txt mime = text/plain words = 5912 sentences = 330 flesch = 50 summary = For Middle East respiratory syndrome, there were 13 case reports in pregnant women, of which 2 were asymptomatic, identified as part of a contact investigation; 3 patients (23%) died. Principles of management of coronavirus disease 2019 in pregnancy include early isolation, aggressive infection control procedures, oxygen therapy, avoidance of fluid overload, consideration of empiric antibiotics (secondary to bacterial infection risk), laboratory testing for the virus and coinfection, fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations. General principles regarding management of COVID-10 during pregnancy include early isolation, aggressive infection control procedures, testing for SARS-CoV-2 and coinfection, oxygen therapy as needed, avoidance of fluid overload, empiric antibiotics (because of secondary bacterial infection risk), fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations (Box 2). cache = ./cache/cord-274007-zndtddty.txt txt = ./txt/cord-274007-zndtddty.txt === reduce.pl bib === id = cord-273906-s7l0yxc0 author = Ranga, Vipin title = Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date = 2020-07-23 pages = extension = .txt mime = text/plain words = 7046 sentences = 354 flesch = 53 summary = Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] . cache = ./cache/cord-273906-s7l0yxc0.txt txt = ./txt/cord-273906-s7l0yxc0.txt === reduce.pl bib === id = cord-274008-p3st70u3 author = Mann, E. R. title = Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis date = 2020-06-16 pages = extension = .txt mime = text/plain words = 6004 sentences = 359 flesch = 49 summary = Here we report the outcome of a longitudinal immune profiling study in hospitalised patients during the peak of the COVID-19 pandemic in the UK and show the relationship between immune responses and severity of the clinical presentation. Although, as reported previously 4 , a higher neutrophil to lymphocyte ratio (NLR) on hospital admission was observed in those patients whose disease trajectory was ultimately severe, whereas there were no appreciable differences observed in monocytes (figure 1A, 1B and table 1). Longitudinal analysis revealed that in the majority of patients (70%) (irrespective of severity) T cell frequencies in whole blood increased prior to hospital discharge, while neutrophil frequencies reciprocally decreased (figure 1E). Severe COVID-19, on the other hand, was associated with monocytes displaying increased expression of the cell cycle marker, Ki67 (normally <5% in healthy peripheral blood), irrespective of whether monocytes were stimulated or not (figure 3C and appendix 6C), which strongly correlated with hospital data for CRP (figure 3C). cache = ./cache/cord-274008-p3st70u3.txt txt = ./txt/cord-274008-p3st70u3.txt === reduce.pl bib === id = cord-274090-eab7i4f6 author = Gaspari, Valeria title = Can Covid‐19 be a sexually transmitted disease? Posterity will judge date = 2020-05-24 pages = extension = .txt mime = text/plain words = 566 sentences = 31 flesch = 47 summary = The knowledge of all possible modes of transmission of SARS-CoV-2 infection is the key to improving both the identification of the asymptomatic population and the necessary isolation measures in order to further flatten the curve. The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients (66.67%) has already been demonstrated in recent studies in Wuhan, without being statistically related to gastrointestinal symptoms and/or disease severity. Moreover, the positivity for SARS-CoV-2 on vaginal swab raises the possibility of both sexual and mother-to-child transmission 7 , although further studies are needed on these issues since no definitive proofs have been found. A further step would be adding SARS-CoV-2 serology, pharyngeal, anal and vaginal swabs to our usual STD screening also in the asymptomatic population, in order to identify positive cases and to confirm the SARS-CoV-2 orogenital route of transmission. SARS-CoV-2 possible contamination of genital area: implications for sexual and vertical transmission routes cache = ./cache/cord-274090-eab7i4f6.txt txt = ./txt/cord-274090-eab7i4f6.txt === reduce.pl bib === id = cord-274053-406dfdih author = Srivastava, Kamna title = Association between COVID-19 and cardiovascular disease date = 2020-07-14 pages = extension = .txt mime = text/plain words = 2574 sentences = 166 flesch = 46 summary = SARS-CoV-2 infects host cells through ACE2 receptors, leading to COVID-19-related pneumonia. Search methods and strategies for identification of studies Literature search was performed in WHO reports, PubMed, Scopus, Science Direct and also in American Heart Association journals, Nature, JAMA, BMJ and THE LANCET journals using following terms:ACE2, coronavirus, COVID-19 and 2019-nCoV, COVID-19 and CVD, Cardiovascular Risk and Diseases to find articles published from January 05 to May 20, 2020. SARS-CoV-2 shares both high sequence similarity and the use of the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV). In another study [43] , we have reported the role of Angiotensin type I receptor in patients with essential hypertension and normal healthy controls as pathological and physiological differential expression at mRNA and protein levels. In a report by Huang et al [3] myocardial injury associated with the SARS-CoV-2 was found in 5 of the first 41 patients diagnosed with COVID-19 in Wuhan. cache = ./cache/cord-274053-406dfdih.txt txt = ./txt/cord-274053-406dfdih.txt === reduce.pl bib === id = cord-273918-knlc3bxh author = Holmes, Emily A title = Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science date = 2020-04-15 pages = extension = .txt mime = text/plain words = 10279 sentences = 452 flesch = 35 summary = 1,2 Furthermore, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, might infect the brain or trigger immune responses that have additional adverse effects on brain function and mental health in patients with Research funders and researchers must deploy resources to understand the psychological, social, and neuroscientific effects of the COVID-19 pandemic. We use the term mental health sciences to reflect the many different disciplines, including, but not limited to, psychology, psychiatry, clinical medicine, behavioural and social sciences, and neuroscience, that will need to work together in a multidisciplinary fashion together with people with lived experience of mental health issues or COVID-19 to address these research priorities. cache = ./cache/cord-273918-knlc3bxh.txt txt = ./txt/cord-273918-knlc3bxh.txt === reduce.pl bib === id = cord-274122-n9jnu2ah author = Mielech, Anna M. title = MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date = 2014-02-01 pages = extension = .txt mime = text/plain words = 4845 sentences = 242 flesch = 51 summary = Coronaviruses encode papain-like proteases (PLpro) that are often multifunctional enzymes with protease activity to process the viral replicase polyprotein and deubiquitinating (DUB)/deISGylating activity, which is hypothesized to modify the innate immune response to infection. Further, we compared the ability of MERS-CoV PLpro and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) PLpro to block innate immune signaling of proinflammatory cytokines. In this study, we demonstrate the deISGylating and deubiquitinating (DUB) activities of the papain-like protease from MERS-CoV, and provide new information on the potential role of coronavirus protease/DUBs to inhibit the innate immune response. Our results suggest that PLpro might contribute to the modulation of innate immune responses upon SARS-CoV and MERS-CoV infection, however, the exact mechanism and the role of coronavirus PLPs and their associated DUB and deISGylating activities in these processes remains to be determined. cache = ./cache/cord-274122-n9jnu2ah.txt txt = ./txt/cord-274122-n9jnu2ah.txt === reduce.pl bib === id = cord-274459-781by93r author = Khalifa, Shaden A. M. title = Comprehensive Overview on Multiple Strategies Fighting COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 5466 sentences = 311 flesch = 51 summary = Our review aims to evaluate strategies of the most affected countries from different continents all over the world (China, Italy, Germany, France, Spain, America, Canada, Brazil, UK, India, Japan, Singapore, Iran, Korea, and Australia) for confronting the epidemic as it explains the best practices that could help other countries to overcome current or any upcoming pandemic. Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . cache = ./cache/cord-274459-781by93r.txt txt = ./txt/cord-274459-781by93r.txt === reduce.pl bib === id = cord-273961-ja8xggnd author = Nakagawara, Kensuke title = Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date = 2020-07-26 pages = extension = .txt mime = text/plain words = 784 sentences = 54 flesch = 58 summary = title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . cache = ./cache/cord-273961-ja8xggnd.txt txt = ./txt/cord-273961-ja8xggnd.txt === reduce.pl bib === id = cord-273898-i7icvsg1 author = Parcell, B. title = Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1755 sentences = 99 flesch = 60 summary = title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland Scotland recently began reporting staff absence rates in the health and social care sector showing that at the time of writing 1 in 20 staff were absent as a direct result of Current UK guidance for social distancing and self-isolation requires that HSCWs experiencing symptoms of a respiratory infection, such as cough or fever, should be absent from work for 7 days, while if a household contact is unwell, the staff member should be absent from work for 14 days to account for the incubation period of the virus. The results show a striking save of over 8000 lost working days for health and social care staff over a period of just 3 weeks which is likely to have a significant impact on the ability of health systems to respond to the SARS-CoV-2 pandemic. cache = ./cache/cord-273898-i7icvsg1.txt txt = ./txt/cord-273898-i7icvsg1.txt === reduce.pl bib === id = cord-274141-vujx538o author = Chinsembu, Kazhila C. title = Coronaviruses and Nature’s Pharmacy for the Relief of Coronavirus Disease 2019 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 11338 sentences = 676 flesch = 53 summary = De Clercq (2005 suggested that it was feasible to develop SARS-CoV fusion inhibitors analogous to enfuvirtide, a linear 36-amino acid synthetic peptide marketed under the trade name Fuzeon, an approved anti-HIV drug that inhibits the entry of the virus into cells. It was hypothesized that specific flavonoids, such as quercetin, hesperetin, and myricetin (7) and their glycosylated derivatives, may play an effective role in inhibiting SARS-CoV entry into host cells, specifically by binding with high affinity to the spike protein, helicase, and protease sites on the ACE receptor (Ngwa et al. Although the ongoing SARS-CoV-2 global pandemic should remind scientists that current options for treating life-threatening zoonotic coronavirus infections are very limited , medicinal plants offer a strong pipeline for the discovery of novel lead compounds that can be converted into new drugs to treat COVID-19. cache = ./cache/cord-274141-vujx538o.txt txt = ./txt/cord-274141-vujx538o.txt === reduce.pl bib === id = cord-274184-hm516x6p author = Elli, Luca title = Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4843 sentences = 280 flesch = 50 summary = From the abovementioned reasons we must deduce that: -in high SARS-CoV-2 incidence areas where PCR assays are not extensively performed, Covid-19 cannot be ruled out by simple clinical examination or epidemiological link; -the greatest amount of efforts and precautions are required to minimize the spread of the disease and to preserve medical staff from infection. In our current situation, which is characterized by high incidence of Covid-19 and relative scarcity of surveillance assays in asymptomatic subjects, for the abovementioned reasons we recommend different modalities of individual protection based on a strict clinical and epidemiological stratification of patients with potential SARS-CoV-2 infection undergoing endoscopic examination. In this setting, regardless of the classification of patients (high/low-risk, , in order to prevent the medical staff from becoming infected, we suggest high-performance personal protection equipment, i.e. a N95 or FFP2/FFP3 respirator, a hairnet, a double pair of gloves, a disposable waterproof surgical gown, a face shield (which we prefer because it allows to protect, and then spare, respirators) or goggles, and work safety clogs (Table 1) . cache = ./cache/cord-274184-hm516x6p.txt txt = ./txt/cord-274184-hm516x6p.txt === reduce.pl bib === id = cord-274097-11hvriqy author = Katz, Louis M. title = Is SARS‐CoV‐2 transfusion transmitted? date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2023 sentences = 132 flesch = 51 summary = The few studies of SARS-CoV-2 RNA in donors or of donors developing COVID-19 after giving blood are a mix of small series wherein prospectively test-positive units were quarantined and not transfused or involved units quarantined after donation to permit the donor time to get ill before units are distributed. In a lookback to recipients of 17 transfused components from seven South Korean donors who developed COVID-19 6 to 15 days after donation, there was no associated clinical morbidity in the recipients; however, archived samples tested by PCR after the donors reported their illnesses were negative. 21 Precise estimates of the prevalence of asymptomatic/presymptomatic infection and especially of whether RNA-emia or, more germane to this topic, viremia occur in the absence of illness (especially in healthy donors or the larger well population who might be qualified to donate) are among the key missing data needed to inform our debate about any risk of TTI and subsequent TTD. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations cache = ./cache/cord-274097-11hvriqy.txt txt = ./txt/cord-274097-11hvriqy.txt === reduce.pl bib === id = cord-274343-y9zqbefu author = Petersen, Irene title = Three Quarters of People with SARS-CoV-2 Infection are Asymptomatic: Analysis of English Household Survey Data date = 2020-10-08 pages = extension = .txt mime = text/plain words = 2197 sentences = 151 flesch = 57 summary = We estimated sensitivity, specificity, the proportion of asymptomatic cases (1 – sensitivity), positive predictive value (PPV) and negative predictive value (NPV) of COVID-19 symptoms as a marker of infection using results of the SARS-CoV-2 test as the "gold standard". 8 In this analysis of data from a large representative study by the English Office for National Statistics we aimed to understand the value of COVID-19 symptoms as a marker for SARS-CoV-2 infection. We estimated the sensitivity, specificity, positive and negative predictive values of COVID-19 symptoms for SARS-CoV-2 infections as well as the proportion of asymptomatic cases (1 -sensitivity). We estimated the sensitivity, specificity, and positive and negative predictive values of COVID-19 symptoms as a marker of infection by using the results of the SARS-CoV-2 test as the "gold standard". To our knowledge, the Office for National Statistics Coronavirus (COVID-19) Infection Survey pilot is the largest population survey carried out to date including information on the association between COVID-19 symptoms and SARS-CoV-2 test results. cache = ./cache/cord-274343-y9zqbefu.txt txt = ./txt/cord-274343-y9zqbefu.txt === reduce.pl bib === id = cord-274396-l611eisi author = Park, Su-Jin title = Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4355 sentences = 208 flesch = 46 summary = While the lopinavir-ritonavir-, hydroxychloroquine sulfate-, or emtricitabine-tenofovir-treated group exhibited lower overall clinical scores than the phosphate-buffered saline (PBS)-treated control group, the virus titers in nasal washes, stool specimens, and respiratory tissues were similar between all three antiviral-candidate-treated groups and the PBS-treated control group. Compared to the PBS-treated control group, azathioprine-immunosuppressed ferrets exhibited a longer period of clinical illness, higher virus titers in nasal turbinate, delayed virus clearance, and significantly lower serum neutralization (SN) antibody titers. In order to determine the antiviral efficacies of lopinavir-ritonavir, hydroxychloroquine (HCQ) sulfate, or emtricitabine-tenofovir for treatment of SARS-CoV-2 infection, SARS-CoV-2 antibody-free ferrets (10/group) were inoculated with 10 5.8 50% tissue culture infective doses (TCID 50 )/ml of an NMC-nCoV02 strain through the intranasal (i.n.) route ( Fig. 1 ). Therefore, although clinical symptoms were attenuated in ferret groups treated with antiviral candidates, we also evaluated virus titers in respiratory and gastrointestinal tracts using nasal washes and stool samples, respectively, from SARS-CoV-2-infected ferrets. cache = ./cache/cord-274396-l611eisi.txt txt = ./txt/cord-274396-l611eisi.txt === reduce.pl bib === id = cord-274114-fglyfz8p author = Minervina, Anastasia A. title = Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date = 2020-10-01 pages = extension = .txt mime = text/plain words = 5557 sentences = 297 flesch = 56 summary = In this study we use longitudinal TCRalpha and TCRbeta repertoire sequencing to quantitatively track T cell clones that significantly expand and contract after recovery from a mild COVID-19 infection, and determine their phenotype. We reveal the dynamics and the phenotype of the memory cells formed after infection, identify pre-existing T cell memory clones participating in the response, and describe public TCR sequence motifs of SARS-CoV-2-reactive clones, suggesting a response to immunodominant epitopes. At the time of writing, no data on TCR sequences specific to MHC-II class epitopes exist to map specificities of CD4+ T-cells in a similar way as we did with MIRA-specific TCRs. However, a recently published database of 1414 bulk TCRbeta repertoires from COVID-19 patients allowed us to confirm the SARS-CoV-2 specificity of contracting clones indirectly. Public TCRbeta sequences that can recognize SARS-CoV-2 epitopes are expected to be clonally expanded and thus sampled more frequently in the repertoires of COVID-19 patients than in control donors. cache = ./cache/cord-274114-fglyfz8p.txt txt = ./txt/cord-274114-fglyfz8p.txt === reduce.pl bib === id = cord-274366-t138l6px author = Benetti, Elisa title = ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4525 sentences = 247 flesch = 49 summary = Taking advantage of the Network of Italian Genomes (NIG), a consortium established to generate a public database (NIG-db) containing aggregate variant frequencies data for the Italian population (http://www.nig.cineca.it/), here we describe the genetic variation of ACE2 in the Italian population, one of the newly affected countries by the SARS-CoV-2 outbreak causing COVID-19. In order to shed light on the role of ACE2 variants on interindividual variability and susceptibility to COVID-19 in Italian population we performed WES analysis on a cohort of 131 patients and 258 controls who agreed in participating to the study (see "Materials and methods"). These variants which surround residual essentials for the SARS-CoV-2 spike protein binding were predicted to likely affect the cleavage-dependent virion intake, such as the polymorphic c.2158A>G p.(Asn720Asp) (allele frequency 0.011) which lies four amino acids from the cleavage sequence of TMPRSS2 or to have a substantial impact on protein structure and spike protein interaction by MD simulation (Fig. 3a) . cache = ./cache/cord-274366-t138l6px.txt txt = ./txt/cord-274366-t138l6px.txt === reduce.pl bib === id = cord-274439-y9jrdg5n author = Aoyama, Kazuyoshi title = Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model date = 2020-07-27 pages = extension = .txt mime = text/plain words = 593 sentences = 38 flesch = 45 summary = title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model A Through the interface, users can define inputs such as surgical statistics, including percent change of surgical caseload, and constraint on the number of available N95 respirators to model expected resource utilization at the individual hospital level, community level, or provincial level. Beginning on 16 March 2020, our quaternary-care children's hospital performed only emergent and urgent surgeries (e.g., cancer surgery), including 236 cases during the first three weeks after the pandemic was declared. We estimated that cancelling elective surgeries during those three weeks reduced the cumulative incidence of SARS-CoV-2 transmission to an anesthesiologist by more than six times (2.1% with cancellation compared with 13.5% without cancellation) (Figure) . 5 Although we considered aerosol transmission and environmental contamination of SARS-CoV-2 in the model, we did not account for transmission risks among HCWs in operating rooms, which is our future work. The user can tune the transmission risk in the model when new data emerge. SARS-CoV-2 Infection in children cache = ./cache/cord-274439-y9jrdg5n.txt txt = ./txt/cord-274439-y9jrdg5n.txt === reduce.pl bib === id = cord-274521-u8p5lz9o author = Lee, Abby C. title = Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation date = 2020-07-31 pages = extension = .txt mime = text/plain words = 5720 sentences = 308 flesch = 51 summary = In this study, we mined three independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. Both smoking and use of nicotine and flavor-containing e-cigs led to upregulation of pro-inflammatory cytokines and inflammasome-related genes. Current data indicate that patients who have cardiovascular and chronic respiratory conditions, including those caused by tobacco use, are at higher risk of developing severe COVID-19 symptoms and have significantly increased fatality [1] . The GSE138326 dataset, from Song et al., details gene expression in the bronchial epithelial cells of patients who smoked flavor-less and nicotine-less e-cigs vs. The GSE112073 dataset, from Corbett et al., details gene expression in bronchial cells of patients who smoked nicotine-containing e-cigs of any flavor vs. The upregulation of a significant number of inflammatory cytokines in smokers and nicotine/flavor-containing e-cig users and the association of smoking with IL-1B prompted us to examine inflammasome activation in smokers and e-cig users ( Table 2 ). cache = ./cache/cord-274521-u8p5lz9o.txt txt = ./txt/cord-274521-u8p5lz9o.txt === reduce.pl bib === id = cord-274286-07arhrv9 author = Hosier, H. title = First case of placental infection with SARS-CoV-2 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 3935 sentences = 237 flesch = 50 summary = Conclusion: This case demonstrates, for the first time, SARS-CoV-2 invasion of the placenta, highlighting the potential for severe morbidity among pregnant women with Covid-19. Levels of anti-SARS-CoV-2 IgG and IgM antibodies in the case study patient were among the highest observed in 56 Covid-19 + patients admitted to Yale New Haven Hospital. This report describes a case of second-trimester Covid-19 associated with preeclampsia and SARS-CoV-2 infection of the placenta. Further studies of placenta from women with Covid-19 may help address whether this is a histological feature associated with placental SARS-CoV-2 infection. RNA was extracted from homogenized placenta, umbilical cord, fetal lungs, heart kidney tissues (27-160 mg; stored in formalin) and maternal oral, nasal, and rectal swabs, saliva, urine, plasma, and serum post-operatively and tested for the presence of SARS-CoV-2 and human RNase P using the US CDC qRT-PCR assay as described 7 . cache = ./cache/cord-274286-07arhrv9.txt txt = ./txt/cord-274286-07arhrv9.txt === reduce.pl bib === id = cord-274680-6pui91uu author = Gao, Chun title = Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date = 2020-10-14 pages = extension = .txt mime = text/plain words = 2206 sentences = 151 flesch = 52 summary = 5 Many studies have found that older patients have a higher risk of having a severe case and they have a higher death rate from COVID-19, which may be related to a weaker host immune response for antiviral defense and an uncontrolled proinflammatory cytokine storm. [10] [11] Therefore, this retrospective study aimed to analyze the clinical characteristics of COVID-19 patients who experienced prolonged viral shedding and to investigate the contributing risk factors. This is a comprehensive report of 112 COVID-19 patients investigating the distinct characteristics and risk factors for prolonged SARS-CoV-2 viral RNA shedding. In our study, we found that COVID-19 patients with prolonged viral shedding were older (p<0.001) and presented with a higher rate of hypertension (p<0.001). This study focused on investigating the risk factors for COVID-19 patients with prolonged viral shedding. In summary, in this study, we investigated the distinct dynamics of the inflammatory response in COVID-19 patients with prolonged viral RNA shedding. cache = ./cache/cord-274680-6pui91uu.txt txt = ./txt/cord-274680-6pui91uu.txt === reduce.pl bib === id = cord-274231-2s7ki6g7 author = Ziebuhr, John title = SARS – Unprecedented global response to a newly emerging disease date = 2003-12-31 pages = extension = .txt mime = text/plain words = 1214 sentences = 57 flesch = 51 summary = 293, 229 ± 231 (2003) ¹ Urban & Fischer Verlag http://www.urbanfischer.de/journals/ijmm Editorial SARS ± Unprecedented global response to a newly emerging disease Severe acute respiratory syndrome (SARS) is a life-threatening form of pneumonia that is characterized by fever, chills, myalgia, dry cough, and progressing lung infiltrates (Nicholls et al., 2003; Peiris et al., 2003a) . Only few weeks after the outbreak, the concerted global efforts have resulted in the identification of first coronavirus enzyme inhibitors (Anand et al., 2003; Xiong et al., 2003) that are hoped to be useful for the development of anti-SARS drugs. SARS Working Group: A novel coronavirus associated with severe acute respiratory syndrome SARS study group: Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome cache = ./cache/cord-274231-2s7ki6g7.txt txt = ./txt/cord-274231-2s7ki6g7.txt === reduce.pl bib === id = cord-274508-nigru1o8 author = Lally, Michelle title = Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 date = 2020-10-26 pages = extension = .txt mime = text/plain words = 937 sentences = 64 flesch = 41 summary = title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 Design Retrospective cohort study Setting and Participants: 775 nursing home residents infected with SARS-CoV-2 who resided in one of the 134 Community Living Centers (CLC) of the Veterans Health Administration (VHA) during March 1, 2020 to May 13, 2020 were included. Results Relative to those not receiving diabetes medications, residents taking metformin were at significantly reduced hazard of death (adjusted HR 0.48, 95%CI 0.28, 0.84) over the subsequent 30 days from COVID-19 diagnosis. Conclusions and Implications Our data suggests a reduction in 30-day mortality following SARS-CoV-2 infection in residents who were on metformin-containing diabetes regimens. These findings suggest a relative survival benefit in nursing home residents on metformin, potentially through its mTOR inhibition effects. A recent focus on potential treatment for SARS-CoV-2 42 infection includes a pathway not usually considered for its "antiviral" property, the mammalian 43 target of rapamycin (mTOR) pathway. cache = ./cache/cord-274508-nigru1o8.txt txt = ./txt/cord-274508-nigru1o8.txt === reduce.pl bib === id = cord-274513-0biyfhab author = Baumgartner, M. T. title = Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19 date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5076 sentences = 249 flesch = 46 summary = In this study, we used an individual-based age-structured network model to assess the effective roles of different healthcare protocols such as the use of personal protection equipment and social distancing at neighborand city-level scales. Our results revealed that the model was more sensitive to changes in the parameter representing the rate of contact among people from different neighborhoods, which defends the social distancing at the city-level as the most effective protocol for the control of the disease outbreak. By varying model parameters related to these protocols, we were able to discuss better scenarios considering the delay in the infection peak and lower numbers of cases, as well as activities with a low potential to boost the outbreak. Given the specified model structure, those results forecasting early wave peaks emerged under moderate to high probabilities of the individual-level exposure to SARS-CoV-2 virus (high β), in combination with higher encountering rates among people (v and k) ( Figure 1 ; Table S1 ). cache = ./cache/cord-274513-0biyfhab.txt txt = ./txt/cord-274513-0biyfhab.txt === reduce.pl bib === id = cord-274156-c0c4rjfa author = Chau, J.P.C. title = Infection control practices among hospital health and support workers in Hong Kong date = 2010-08-31 pages = extension = .txt mime = text/plain words = 3104 sentences = 150 flesch = 49 summary = We examined compliance with isolation precautions and infection control guidelines, including proper wearing of a mask, goggles/face shield, or gown; handling patient care equipment, linen, and laundry; routine and terminal cleaning; and terminal cleaning of an isolation room. Activities were recorded using an observation checklist for two patient care activities: direct (physical examination, basic and technical nursing care) and indirect (computer data entry and disinfection of equipment); and for compliance with isolation precautions and infection control guidelines laid down by the Centers for Disease Control and Prevention (CDC) and the Hong Kong Hospital Authority (HKHA). The support workers who performed this work demonstrated good compliance, though one was found not to wear a gown during the terminal cleaning of bedside equipment of a patient requiring contact precaution, and some failed to clean and disinfect environmental surfaces such as doorknobs, faucet handles and floors. cache = ./cache/cord-274156-c0c4rjfa.txt txt = ./txt/cord-274156-c0c4rjfa.txt === reduce.pl bib === id = cord-274409-4ugdxbmy author = Laskar, Rezwanuzzaman title = Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3300 sentences = 190 flesch = 57 summary = title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India Further, constitution of 'Disease' mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. With a definitive possibility of India becoming the most affected country by SARS-CoV-2 in near future and the demographic burden involved, its pertinent to be analyze the accumulating variations in the genome accounting for possible changes in protein and their potential to alter the virus in any manner. Herein we extend our study using the same congregation of sequences to analyze the nature and composition of the observed mutations and their impact on proteins of SARS-CoV-2. The distribution of Disease and Neutral variants across the different genes of SARS-CoV-2 has been shown in Table 4 and Supplementary file 5. cache = ./cache/cord-274409-4ugdxbmy.txt txt = ./txt/cord-274409-4ugdxbmy.txt === reduce.pl bib === id = cord-274280-x5s4l0pp author = Yang, Jinsung title = Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor date = 2020-09-11 pages = extension = .txt mime = text/plain words = 7278 sentences = 403 flesch = 56 summary = Here, we analyze the biophysical properties of the SARS-CoV-2 S-glycoprotein binding, on model surfaces and on living cells, to ACE2 receptors using force-distance (FD) curve-based atomic force microscopy (FD-curve-based AFM) (Fig. 1c) . used FD-curve-based AFM to evaluate at the single-molecule level the binding strength of the interaction established between the glycosylated S1 subunit and ACE2 receptors on model surfaces (Fig. 2a) . To investigate the properties of the binding complex, force-distance (FD) curves were recorded by repeatedly approaching and withdrawing the S1 subunit or RBD-functionalized tip from the ACE2 model surface (Fig. 2a, b) . To this end, we synthetized four different peptides (sequences provided in Supplementary Fig. 9 ), which have been selected to mimic the regions of ACE2 that interact with the S1 subunit as determined by the crystal structure 29 , and we tested their binding inhibition properties using our single-molecule force spectroscopy approach (Fig. 4a, b) . cache = ./cache/cord-274280-x5s4l0pp.txt txt = ./txt/cord-274280-x5s4l0pp.txt === reduce.pl bib === id = cord-274205-e2r38v29 author = Tsunetsugu-Yokota, Yasuko title = Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen date = 2007-11-28 pages = extension = .txt mime = text/plain words = 2170 sentences = 165 flesch = 66 summary = title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen In general, a whole virion serves as a simple vaccine antigen and often essential material for the analysis of immune responses against virus infection. In order to develop an effective vaccine and diagnostic tools, we prepared UV-inactivated SARS coronavirus on a large scale under the strict Biosafety Level 3 (BSL3) regulation. We have demonstrated that subcutaneously administered UV-inactivated SARS-CoV elicits a high level of IgG-type neutralizing antibodies and weak T-cell responses in mice (4). Here we describe our protocol for the largescale preparation of UV-inactivated SARS-CoV virion under the strict Biosafety Level 3 (BSL3) regulation. In order to increase the safety of this UV-inactivated SARS-CoV, we inactivated the virion vaccine using both UV and formalin. Severe acute respiratory syndrome (SARS) coronavirus: application of monoclonal antibodies and development of an effective vaccine cache = ./cache/cord-274205-e2r38v29.txt txt = ./txt/cord-274205-e2r38v29.txt === reduce.pl bib === id = cord-274341-vrwmxwvm author = Frank, Carlos Henrique Michiles title = Guillain–Barré Syndrome Associated with SARS-CoV-2 Infection in a Pediatric Patient date = 2020-07-12 pages = extension = .txt mime = text/plain words = 1744 sentences = 96 flesch = 42 summary = We report the case of a 15-year-old male patient presenting frontal headaches with retro-orbital pain accompanied by fever evolving to weakness and pain of the lower limbs, which ascended to upper limbs. Here, we report a pediatric case involving a progressive acute symmetrical paralysis of the lower and upper limbs, with an upward evolution, which was possibly related to SARS-CoV-2 infection. Given the patient's clinical history of a rapidly progressive symmetrical weakness with supporting electroneurography findings, a recent SARS-CoV-2 infection confirmed through the PCR test, negative microbiologic results for other etiologies in CSF and normal MRI, a diagnosis of GBS associated with COVID-19 was made. According to the most recently published systematic review on neurological manifestations in patients with COVID-19, studies have shown data ranging from common, non-specific symptoms to more complex and life-threatening conditions, such as cerebrovascular diseases, encephalopathies and GBS [5] . cache = ./cache/cord-274341-vrwmxwvm.txt txt = ./txt/cord-274341-vrwmxwvm.txt === reduce.pl bib === id = cord-274399-cd7cmpoj author = Barzin, Amir title = SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3304 sentences = 189 flesch = 47 summary = This is one of the first published seroprevalence studies from North Carolina and included multicenter, primary care, and emergency care facilities serving a low-density, suburban and rural population since description of the North Carolina state index case introducing the SARS-CoV-2 respiratory pathogen to this population. Asymptomatic infection by SARS-CoV-2 (with no clinical symptoms) was examined using an Emergency Use Authorization (EUA)-approved antibody test (Abbott) for the presence of SARS-CoV-2 IgG. This study identifies a very limited seroprevalence of SARS-CoV-2 among asymptomatic individuals accessing the UNC Health system. This study employed an EUA assay performed in a CLIA-certified laboratory on a venous blood sample, with demonstrated specificity to detect antibodies only to SARS-CoV-2, not to seasonal coronaviruses. Upon arrival for SARS-CoV-2 Seroprevalence in North Carolina ® routine care or scheduled visits for enrollment into the study, patients performed a consent procedure that included reviewing recent COVID-19 clinical history using UNC IRB-approved questionnaires. cache = ./cache/cord-274399-cd7cmpoj.txt txt = ./txt/cord-274399-cd7cmpoj.txt === reduce.pl bib === id = cord-274326-msbdrp3e author = Ren, Xiaohan title = Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 4897 sentences = 291 flesch = 46 summary = title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 We hypothesized that in critically ill patients, an inflammatory cytokine storm could directly attack specific cells in the kidney and testis due to their high expression of ACE2 and cytokine receptors, leading to injury of the urinary tract. Compared with the control group, patients with pulmonary arterial hypertension, chronic kidney disease, and diabetic Infection and Drug Resistance 2020:13 submit your manuscript | www.dovepress.com DovePress 3979 nephropathy, as well as smokers, exhibited higher expression levels of ACE2 in their affected tissues (kidneys or lungs) ( Figure 3A -D). 48 Considering the high level of IL6 in severe COVID-19 patients and the enrichment of the IL6 receptor in various testicular cells, this might be a reason for the potential orchitis caused by SARS-CoV-2 infection. cache = ./cache/cord-274326-msbdrp3e.txt txt = ./txt/cord-274326-msbdrp3e.txt === reduce.pl bib === id = cord-274313-mrvk9r4w author = Li, Hui title = SARS-CoV-2 and viral sepsis: observations and hypotheses date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2428 sentences = 138 flesch = 44 summary = With evidence collected from autopsy studies on COVID-19 and basic science research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV, we have put forward several hypotheses about SARS-CoV-2 pathogenesis after multiple rounds of discussion among basic science researchers, pathologists, and clinicians working on COVID-19. Whether SARS-CoV-2 is able to directly attack vascular endothelial cells expressing high levels of ACE2, 13 and then lead to abnormal coagulation and sepsis, still needs to be explored. On the basis of observations from COVID-19 patients, we hypothesise that in mild cases, resident macrophages initiating lung inflammatory responses were able to contain the virus after SARS-CoV-2 infection; both innate and adaptive immune responses were efficiently established to curb the viral replication so that the patient would recover quickly. Meanwhile, the direct attack on other organs by disseminated SARS-CoV-2, the immune pathogenesis caused by the systemic cytokine storm, and the microcirculation dysfunctions together lead to viral sepsis (figure). cache = ./cache/cord-274313-mrvk9r4w.txt txt = ./txt/cord-274313-mrvk9r4w.txt === reduce.pl bib === id = cord-274279-f99nd3dx author = Fantini, Jacques title = Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection date = 2020-04-03 pages = extension = .txt mime = text/plain words = 4442 sentences = 271 flesch = 56 summary = Using a combination of structural and molecular modelling approaches, this study showed that chloroquine (CLQ), one of the drugs currently under investigation for SARS-CoV-2 treatment, binds sialic acids and gangliosides with high affinity. A ganglioside-binding site in the Nterminal domain (NTD) of the spike (S) glycoprotein of SARS-CoV-2 was identified, and CLQ was shown to be a potential blocker of the S-ganglioside interaction which occurs in the first step of the viApril 10, 2020; 14:43 ] ral replication cycle (i.e. attachment to the surface of respiratory cells, mediated by the S protein). At this stage, attachment of the NTD to the ganglioside-rich microdomain involved the whole interface (i.e. Table 1 Energy of interaction of each amino acid residue of SARS-CoV-2 spike protein in contact with GM1 molecules. As CLQ and CLQ-OH are potential therapies for SARS-CoV-2 infection, it is important to check whether the amino acid residues identified as critical for ganglioside binding are conserved among clinical isolates. cache = ./cache/cord-274279-f99nd3dx.txt txt = ./txt/cord-274279-f99nd3dx.txt === reduce.pl bib === id = cord-274252-h4occy7h author = de Lima Menezes, Gabriela title = Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) date = 2020-07-13 pages = extension = .txt mime = text/plain words = 4147 sentences = 262 flesch = 56 summary = After main pocket validation using two control drugs and the main conformations of nsp1, molecular docking based on virtual screening were performed to identify novel potential inhibitors from DrugBank database. Three of them was ranked as the best compounds among them and showed better energy score than control molecules that have in vitro activity against nsp1 from SARS-CoV-2. Due to lack of active site information a blind docking using two cyclophilin inhibitors described as potential CoV suppressors (Carbajo-Lozoya et al., 2014; Kamitani et al., 2009; Pfefferle et al., 2011) were performed by AutoDock Vina (Morris et al., 2009 ) with nsp1 conformations in order to define the best pocket for virtual screening. After that, based on AutoDock Vina energy scores, it was possible to identify the main residues/regions involved in the interactions and thus define the target pockets to be used in the virtual screening simulations with DrugBank database. cache = ./cache/cord-274252-h4occy7h.txt txt = ./txt/cord-274252-h4occy7h.txt === reduce.pl bib === id = cord-274708-w6gmscv4 author = Mathewson, Alison C. title = Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 date = 2008-11-17 pages = extension = .txt mime = text/plain words = 2800 sentences = 135 flesch = 60 summary = Although in different groups, the coronaviruses severe acute respiratory syndrome-coronavirus (SARS-CoV) and NL63 use the same receptor, angiotensin converting enzyme (ACE)-2, for entry into the host cell. (2007) showed that incubation of a tagged form of the RBD with cell lines expressing a number of natural and synthetic ACE-2 variants indicated that the ACE-2 contact residues critical for binding both SARS-CoV and NL63 S overlap (Li et al., 2007) . To investigate CoV S protein binding to ACE-2 in a unified format, we produced soluble and cell-bound versions of the two S proteins through the use of baculovirus expression vectors designed for secretion of proteins as Fc-tagged fusion proteins (Chen et al., 2007) or, separately, displayed on the insect cell surface following tagging with the VSV G protein transmembrane (TM) domain (Chapple & Jones, 2002 ) (see Supplementary Fig. S1 , available in JGV Online). Identification of residues in the receptor-binding domain (RBD) of the spike protein of human coronavirus NL63 that are critical for the RBD-ACE2 receptor interaction cache = ./cache/cord-274708-w6gmscv4.txt txt = ./txt/cord-274708-w6gmscv4.txt === reduce.pl bib === id = cord-274648-e0daf8w6 author = Madeddu, Paolo title = Cardiovascular complications of COVID-19: evidence, misconceptions, and new opportunities date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1940 sentences = 95 flesch = 41 summary = The virus binds with its spike protein to the surface receptor angiotensin converting enzyme 2 (ACE2) to unlock human cells and begin infection. Likewise, it remains to be established whether repeated exposures or a single contact with massive doses of the virus, like in the case of clinical staff caring patients who are not known to be infected, can increase the risk of developing severe forms of the disease. The binding of SARS-CoV-2 to ACE2 is stronger than previous coronaviruses, due to difference in key amino acid residues allowing for enhanced interactions between the virus and human cells. Therefore, when considering severity of COVID-19, the low ACE2 levels observed in elderly people and those with cardiovascular disease seem to facilitate rather than protect from the disease (9) . The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts cache = ./cache/cord-274648-e0daf8w6.txt txt = ./txt/cord-274648-e0daf8w6.txt === reduce.pl bib === id = cord-274474-u2fdicgz author = Majumder, Joydeb title = Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus date = 2020-10-13 pages = extension = .txt mime = text/plain words = 10098 sentences = 634 flesch = 46 summary = The present review summarizes recent advances in the development of nanocarrier based therapeutics for local and targeted delivery of drugs, nucleic acids and imaging agents for diagnostics and treatment of various diseases such as cancer, cystic fibrosis, and coronavirus. [1, 2] Therefore, methods of developing new therapeutic solutions as well as improving the current therapies for the common lung diseases such as asthma, cystic fibrosis, chronic obstructive pulmonary disease, lung cancer, and coronavirus infections remain the main focus in the fields of targeted drug delivery. In this review, we will summarize recent reports on the development of lipid and polymer based nanocarriers for targeted delivery of drugs and nucleic acids for the treatment of lung cancer. In a similar study, we used a complex liposomal drug delivery system containing anticancer drug doxorubicin and both MRP1 and BCL2 targeting antisense oligonucleotides for inhalation treatment in lung cancer cells. cache = ./cache/cord-274474-u2fdicgz.txt txt = ./txt/cord-274474-u2fdicgz.txt === reduce.pl bib === id = cord-274284-mi4n7xty author = Pang, Khang Wen title = Frequency and Clinical Utility of Olfactory Dysfunction in COVID-19: a Systematic Review and Meta-analysis date = 2020-10-13 pages = extension = .txt mime = text/plain words = 4402 sentences = 254 flesch = 50 summary = Meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if OD symptoms were explicitly asked in questionnaires or interviews or if smell tests were performed. RESULTS: The pooled frequency of OD in COVID-19 positive patients (17,401 patients, 60 studies) was 0.56 (0.47–0.64) but differs between detection via smell testing (0.76 [0.51–0.91]) and survey/questionnaire report (0.53 [0.45–0.62]), although not reaching statistical significance (p = 0.089). To investigate the estimated frequency of OD amongst COVID-19 patients, meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if smell tests were performed or if OD symptoms were explicitly asked in questionnaires or interviews. Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Self-reported olfactory and taste disorders in patients With severe acute respiratory coronavirus 2 infection: a cross-sectional study cache = ./cache/cord-274284-mi4n7xty.txt txt = ./txt/cord-274284-mi4n7xty.txt === reduce.pl bib === id = cord-274416-bmvazgj7 author = Trevisanuto, Daniele title = Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3761 sentences = 219 flesch = 49 summary = title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection. Although it is unlikely that neonates born from SARS-CoV-2-infected mothers require an intensive care management related to the maternal infection [18, 19] , coronaviruses may result in adverse outcomes for the fetus and infant (intrauterine growth restriction, preterm delivery, admission to the neonatal intensive care unit (NICU), spontaneous abortion and perinatal death) [16, 17, 25] . Our designated approach for the management of women with suspected or confirmed CO-VID-19 and their infants before, during, and after delivery provides cues to reduce the chance of neonatal infection and therefore potential negative outcomes in the newborn. cache = ./cache/cord-274416-bmvazgj7.txt txt = ./txt/cord-274416-bmvazgj7.txt === reduce.pl bib === id = cord-274707-mxh38hwd author = Laureano, Ana Flávia Santarine title = The different tests for the diagnosis of COVID-19 - A review in Brazil so far date = 2020 pages = extension = .txt mime = text/plain words = 3736 sentences = 204 flesch = 50 summary = The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor's Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-274707-mxh38hwd.txt txt = ./txt/cord-274707-mxh38hwd.txt === reduce.pl bib === id = cord-274536-fv7mltj7 author = Tong, Yongqing title = Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3120 sentences = 188 flesch = 59 summary = RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn't be detected in other types of specimen in this study. Firstly, we analyzed the possible sites of infection in hospitalized patients with COVID-19 by detecting viral RNA with 12 different types of specimens, including nasopharyngeal swab, oropharyngeal swab, sputum, bronchoalveolar lavage fluid (BALF), stool, anal swab, urine, peritoneal dialysis fluid (PDF), blood, sweat, cerebrospinal fluid (CSF) and corneal secretion. The 20 discharged cases of COVID-19, the criteria [12] for which was the SARS-CoV-2 virus RNA detection negative in two consecutive respiratory specimens (at least 1 day of time interval of sampling) for patients who have reached the standards of isolation period (14 days) after clinical cured, during the isolation period were selected to detect SARS-CoV-2 RNA with multiple specimens including nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and blood. cache = ./cache/cord-274536-fv7mltj7.txt txt = ./txt/cord-274536-fv7mltj7.txt === reduce.pl bib === id = cord-274520-c674wkmt author = Moelling, Karin title = Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection date = 2020-05-28 pages = extension = .txt mime = text/plain words = 6725 sentences = 370 flesch = 47 summary = title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection e authors concluded that there was likely no risk for contracting infectious diseases from pollutant-associated microbes, but they recommended fixing soil by vegetation to reduce the amount of airborne microbes originating from fecal and terrestrial sources, including potential allergens [31] . As observed in the New York City subway, bacterial communities showed significant similarities with those of outdoor air samples, with some human skin-associated bacteria also being present. ere is evidence that people exposed to severe air pollution are more susceptible to infection with the present SARS-CoV-2 pandemic virus and experience stronger symptoms, not only in large cities of China but also in other parts of the world [46] [47] [48] [49] [50] [51] . Potential human pathogens are typically below the detection limit in air samples even from closed environments such as subway systems, which means that there is not likely a significant risk for infection [31, 32, [34] [35] [36] [37] . cache = ./cache/cord-274520-c674wkmt.txt txt = ./txt/cord-274520-c674wkmt.txt === reduce.pl bib === id = cord-274510-fo7p98np author = Spadera, Lucrezia title = Potential Role of GcMAF in suppressing the severity of COVID-19-induced immune responses: lesson learned from HIV date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4050 sentences = 217 flesch = 40 summary = Based on the aforementioned findings and on documented analogies between SARS-CoV-2 and HIV [13] , we hypothesized that the reduced conversion activity of the Gc protein (human groupspecific component (Gc)) into the macrophage activating factor (MAF) could have a key role in the dysregulate immune response induced by SARS-CoV-2, just like for HIV infected patients [14] [15] . In particular, based on their antiviral activity [68] , chloroquine and hydroxychloroquine, initially conceived as antimalarial therapeutics, were proposed to treat patients hospitalized with COVID-19, better if associated to azithromycin, showing promising efficacy in "inhibiting the exacerbation of pneumonia, improving lung imaging findings, promoting a virus negative conversion and shortening the disease course" [69] [70] . So, in sight of this, given its multifunctional properties, we believe that GcMAF could have a very important role in the pathophysiology of organ damage induced by SARS-CoV-2, providing explanations which are consistent with the clinical, radiological and histopathological findings observed in patients with COVID-19. Effects of vitamin D(3)-binding protein-derived macrophage activating factor (GcMAF) on angiogenesis cache = ./cache/cord-274510-fo7p98np.txt txt = ./txt/cord-274510-fo7p98np.txt === reduce.pl bib === id = cord-274602-q9i2k304 author = Iqbal, Yousaf title = Psychiatric presentation of patients with acute SARS-CoV-2 infection: a retrospective review of 50 consecutive patients seen by a consultation-liaison psychiatry team date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3717 sentences = 231 flesch = 45 summary = BACKGROUND: Reports of psychiatric morbidity associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection tend to be limited by geography and patients' clinical status. AIMS: To describe the psychiatric morbidity associated with SARS-CoV-2 infection (confirmed by real-time polymerase chain reaction) in referrals to a consultation-liaison psychiatry service in Qatar. 12 Finally, all current studies in hospital settings have restricted themselves to symptomatic patients with COVID-19, although psychiatric consultation-liaison services will also be referred patients who have tested positive for SARS-CoV-2 but are physically asymptomatic. The current study aimed to complement existing data by characterising the psychiatric morbidity associated with acute SARS-CoV-2 infection in patients referred to a consultation-liaison psychiatry service in Qatar. As such it offers a broad clinical picture of the psychiatric problems associated with acute SARS-CoV-2 infection, occurring in a general hospital setting, and including patients who are symptomatic and asymptomatic for COVID-19 infection. cache = ./cache/cord-274602-q9i2k304.txt txt = ./txt/cord-274602-q9i2k304.txt === reduce.pl bib === id = cord-274945-6p5de7o2 author = Clevers, Hans title = COVID-19: organoids go viral date = 2020-06-01 pages = extension = .txt mime = text/plain words = 1375 sentences = 86 flesch = 51 summary = Indeed, enterocytes generated in ASC derived, small intestinal organoid cultures allowed cultivation of multiple human norovirus strains. There is no robust in vitro model beyond the use of ex vivo bronchus explant cultures for assessing the infectivity of emerging flu viruses in humans. Penninger and colleagues 7 demonstrated that SARS CoV2 could directly infect capillary organoids and kidney organoids, both established from human iPSCs. These observations may explain the spread of the virus through the body and the loss of kidney function in severely ill individuals. All three studies reported that the most common cell type of the intestinal epithelium, the enterocyte, is readily infected, suggesting that the intestine is a poten tial site of SARS CoV2 replication. Differentiated human airway organoids to assess infectivity of emerging influenza virus TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes Infection of bat and human intestinal organoids by SARS-CoV-2 cache = ./cache/cord-274945-6p5de7o2.txt txt = ./txt/cord-274945-6p5de7o2.txt === reduce.pl bib === id = cord-274542-fpzk5k79 author = Patti, Giuseppe title = Questions and Answers on Practical Thrombotic Issues in SARS-CoV-2 Infection: A Guidance Document from the Italian Working Group on Atherosclerosis, Thrombosis and Vascular Biology date = 2020-11-03 pages = extension = .txt mime = text/plain words = 5628 sentences = 239 flesch = 32 summary = UFH should be limited to patients with CrCl < 30 mL/min An invasive "catheter"-based therapy for PE is indicated in selected cases with contraindication to anticoagulant drugs, recurrent events despite adequate anticoagulation, or when systemic fibrinolysis cannot be performed For the risk stratification of patients with VTE, monitoring of the following parameters is useful: troponin, BNP, D-dimer, blood cell count, fibrinogen, prothrombin time, activated partial thromboplastin time, and degradation products of fibrin After the initial approach, DOACs may represent an option for in-hospital treatment of a VTE episode in patients with clinical stability and decreasing inflammation After a VTE episode, DOACs should represent the therapy of choice at discharge The use of imaging techniques in diagnosing a VTE episode is complex, because of the risk of viral transmission to other patients and to healthcare workers, and must be regulated by specific in-hospital protocols aimed at limiting such risk. cache = ./cache/cord-274542-fpzk5k79.txt txt = ./txt/cord-274542-fpzk5k79.txt === reduce.pl bib === id = cord-274834-24v2b509 author = Lima, Rosiane title = Establishment of a pediatric COVID-19 biorepository: unique considerations and opportunities for studying the impact of the COVID-19 pandemic on children date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5588 sentences = 268 flesch = 40 summary = Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. METHODS: A COVID-19 biospecimen collection study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. Specific questions that must be addressed revolve around the role children play in viral transmission, differences in pediatric viral susceptibility and immune responses, which could guide potential therapies for adults, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the development of severe hyperinflammatory shock and cardiac damage seen in Multisystem Inflammatory Syndrome in Children (MIS-C). In order to capture the full range of SARS-CoV-2 infection in the pediatric population, a COVID-19 biospecimen collection study was designed and implemented, including patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2-infected mothers, and asymptomatic children. cache = ./cache/cord-274834-24v2b509.txt txt = ./txt/cord-274834-24v2b509.txt === reduce.pl bib === id = cord-274591-p34kk4up author = Horby, Peter W, title = Prospects for Emerging Infections in East and Southeast Asia 10 Years after Severe Acute Respiratory Syndrome date = 2013-06-17 pages = extension = .txt mime = text/plain words = 4265 sentences = 156 flesch = 36 summary = The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The SARS epidemic provided a dramatic demonstration of the weaknesses in national and global capacities to detect and respond to emerging infectious diseases, and it was in many ways a watershed event that had a transformative effect on many of the clinical, public health, and other professionals involved. Surveillance and response capacities have improved in the last decade, and East and Southeast Asia are far better prepared to detect and respond to emerging infectious diseases. cache = ./cache/cord-274591-p34kk4up.txt txt = ./txt/cord-274591-p34kk4up.txt === reduce.pl bib === id = cord-274668-lh7c9izt author = Wang, Chaofu title = Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4584 sentences = 253 flesch = 45 summary = BACKGROUND: The novel coronavirus pneumonia COVID-19 caused by SARS-CoV-2 infection could lead to a serious of clinical symptoms and severe illness, including acute respiratory distress syndrome (ARDS) and fatal organ failure. INTERPRETATION: Infection of Alveolar macrophage by SARS-CoV-2 might be drivers of the "cytokine storm", which might result in damages in pulmonary tissues, heart and lung, and leading to the failure of multiple organs . One case report showed the pathological characteristics of a patient who died from severe infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by postmortem biopsies. Moreover, type II alveolar epithelial cells and macrophages in alveoli and pulmonary hilum lymphoid tissue were infected by SARS-CoV-2, as revealed by immunohistochemistry using Rp3-NP specific antibodies (Figs. [10] In the case of COVID-19, the viral infection of aggregated alveolar macrophages was obvious from early phase to the late stage, according to our study and the results in recent reports of pulmonary pathology [17, 20] . cache = ./cache/cord-274668-lh7c9izt.txt txt = ./txt/cord-274668-lh7c9izt.txt === reduce.pl bib === id = cord-275111-38hgg0jz author = Kumar, Abhishek title = Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients date = 2020-10-06 pages = extension = .txt mime = text/plain words = 2300 sentences = 171 flesch = 60 summary = title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients AIM: To analyse the liver function in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. 91 patients admitted with confirmed SARS-CoV-2 infection were included in this study and divided into asymptomatic, mild, moderate and severe groups. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. In this study, we aimed to analyse the liver function abnormalities in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. [16, 21, 22] In our study, the levels of AST and ALP between different groups of disease severity was highly significant which is consistent with a previous report. cache = ./cache/cord-275111-38hgg0jz.txt txt = ./txt/cord-275111-38hgg0jz.txt === reduce.pl bib === id = cord-274528-mr81o9cu author = Li, Fei title = Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date = 2020-09-12 pages = extension = .txt mime = text/plain words = 6428 sentences = 416 flesch = 53 summary = Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Notably, in addition to prostate, other essential 40 organs, including lung, kidney and liver, which are permissive for SARS-CoV-2 infection in human, were 41 characterized with Tmprss2-postive epithelial cells ( Fig. 1b and Extended Data Fig. 1c ). Consistently, 25 enzalutamide significantly decreased TMPRSS2 expression and inhibited SARS-CoV-2 infection in human 26 prostate cancer cells (Fig. 2) . cache = ./cache/cord-274528-mr81o9cu.txt txt = ./txt/cord-274528-mr81o9cu.txt === reduce.pl bib === id = cord-275128-620wf0pb author = White, J. R. title = PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2388 sentences = 173 flesch = 47 summary = We performed a statistical evaluation of in vitro gene expression profiles reflecting exposure to 1,835 drugs, and found topoisomerase inhibitors and PI3K/mTOR pathway inhibitors among the strongest candidates for reduced expression of ACE2, a host gene associated with SARS-CoV-2 infection. We next performed a retrospective review of clinical records to evaluate the frequency of SARS-CoV-2 infection in patients on these ACE2-associated antineoplastics. Retrospective data was obtained from an IRB-approved study of adult cancer patients tested for SARS-CoV-2 receiving active antineoplastic therapy at Memorial Sloan Kettering Cancer Center (MSKCC) during the COVID-19 epidemic period (n=4,040 patients; Table S2 ). Patients receiving ACE2-associated therapies demonstrated a lower univariate odds ratio (0.65, 95% CI 0.00-0.98, P=0.04) for a positive SARS-CoV-2 test during active antineoplastic therapy compared to patients on other agents (Table S3) . Cancer patients taking these potential ACE2-associated agents showed lower rates of a positive SARS-CoV-2 test compared to patients taking other forms of active antineoplastic therapy. cache = ./cache/cord-275128-620wf0pb.txt txt = ./txt/cord-275128-620wf0pb.txt === reduce.pl bib === id = cord-275360-uphdzj5l author = Sahajpal, Nikhil Shri title = Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date = 2020-07-30 pages = extension = .txt mime = text/plain words = 1675 sentences = 92 flesch = 49 summary = Herein, we propose a mass population screening approach, based on sample pooling strategy for rapid and wide-scale population screening that may be adopted by laboratories currently using RT-PCR based methods to test for SARS-CoV-2. The strategy we propose leverages on existing high throughput systems that employ high analytically sensitive [limit of detection (LOD) 5-20 copies/ml] real-time PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. 6 The advantages of this approach include the potential to catch up with huge testing deficits, reducing turnaround times and most importantly ensuring enormous savings through the most efficient use of RNA extraction and/or testing kits, which even today are in significant short supply. The strategy we propose leverages existing high throughput systems which employ analytically high sensitive RT-PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. cache = ./cache/cord-275360-uphdzj5l.txt txt = ./txt/cord-275360-uphdzj5l.txt === reduce.pl bib === id = cord-275023-0z219rcy author = Cerofolini, Linda title = Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date = 2020-07-29 pages = extension = .txt mime = text/plain words = 3485 sentences = 198 flesch = 44 summary = title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. In this manuscript we apply a very simple method based on a unitedresidue modelling of protein-surface interactions, to specifically address the problem of determining the orientation of the SARS-CoV-2 Spike protein Receptor Binding Domain (RBD) on a few prototypical surfaces for biomedical use. In this work, we describe the use of united-residue modelling for the prediction of the orientation of the receptor binding domain of the spike protein of the novel coronavirus SARS-CoV-2, a protein of high immunological relevance at the most commonly used surfaces for the preparation of lateral-flow immunochemical devices. cache = ./cache/cord-275023-0z219rcy.txt txt = ./txt/cord-275023-0z219rcy.txt === reduce.pl bib === id = cord-274841-rcdoewwv author = Tay, Matthew Zirui title = The trinity of COVID-19: immunity, inflammation and intervention date = 2020-04-28 pages = extension = .txt mime = text/plain words = 7186 sentences = 383 flesch = 43 summary = Monoclonal antibodies targeting the When severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells expressing the surface receptors angiotensin-converting enzyme 2 (ACE2) and TMPRSS2, the active replication and release of the virus cause the host cell to undergo pyroptosis and release damageassociated molecular patterns, including ATP, nucleic acids and ASC oligomers. While there are no clinical trials specifically testing these drugs against COVID-19 at the time of writing, when camostat mesylate was tested on SARS-CoV-2 isolated from a patient, it prevented entry of the virus into lung cells 44, 50 . Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Neutralizing antibodies in patients with severe acute respiratory syndrome-associated Nature reviews | Immunology coronavirus infection cache = ./cache/cord-274841-rcdoewwv.txt txt = ./txt/cord-274841-rcdoewwv.txt === reduce.pl bib === id = cord-274715-dcs1rgd0 author = Mani Mishra, Pushpendra title = Serum albumin-mediated strategy for the effective targeting of SARS-CoV-2 date = 2020-04-24 pages = extension = .txt mime = text/plain words = 2145 sentences = 121 flesch = 45 summary = Novel coronavirus (NCoV-19), also known as SARS CoV-2, is a pathogen causing an emerging infection that rapidly increases in incidence and geographic range, is associated with the ever-increasing morbidity and mortality rates, and shows sever economic impact worldwide. We are suggesting here a strategy for the COVID-19 treatment that could be effective in curing the patients in the current scenario when no efficient medicine or Vaccine is currently available, and Clinicians solely depend upon the performing trials with drugs with known antiviral activities. If the albumin is used to stabilize and deliver the EGCG and Curcumin for targeting the intracellular virus components in combination with the drug that could block the virus fusion and/or entry to a cell, this strategy might represent an effective way of treating the SARS CoV-2 infection. cache = ./cache/cord-274715-dcs1rgd0.txt txt = ./txt/cord-274715-dcs1rgd0.txt === reduce.pl bib === id = cord-275004-qzg03dvg author = Veras, Flavio Protasio title = SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology date = 2020-09-14 pages = extension = .txt mime = text/plain words = 6380 sentences = 383 flesch = 51 summary = The concentration of NETs was augmented in plasma, tracheal aspirate, and lung autopsies tissues from COVID-19 patients, and their neutrophils released higher levels of NETs. Notably, we found that viable SARS-CoV-2 can directly induce the release of NETs by healthy neutrophils. The well-known similarities between sepsis and key events involved in the COVID-19 pathophysiology, such as cytokine overproduction (Mehta et al., 2020) , microthrombosis (Magro et al., 2020; Dolhnikoff et al., 2020) , and acute respiratory distress syndrome (Lai et al., 2020) , led us to hypothesize that NETs are triggered during SARS-CoV-2 infection and might contribute to tissue injury in COVID-19 patients. In summary, in the present study, we demonstrated that in COVID-19 patients, circulating and lung-infiltrating neutrophils are releasing higher levels of NETs. We also showed that SARS-CoV-2 directly stimulates neutrophils to release NETs in mechanisms dependent on ACE2 and serine protease activity axis and effective viral replication. cache = ./cache/cord-275004-qzg03dvg.txt txt = ./txt/cord-275004-qzg03dvg.txt === reduce.pl bib === id = cord-274750-fynxciwg author = Peterson, Danielle title = Calm before the storm: understanding the role of JAK inhibitors in COVID-19 date = 2020-04-25 pages = extension = .txt mime = text/plain words = 462 sentences = 40 flesch = 51 summary = Based on these 51 considerations, we believe there is insufficient evidence to recommend continuing JAK inhibitors in 52 patients who are acutely infected with SARS-CoV-2. 53 54 Napolitano et al suggest that baricitinib and upadacitinib might be useful in treating the cytokine 55 release syndrome (CRS) that can occur in SARS-CoV-2 infection. Furthermore, there is 58 evidence in both rhesus macaques and mice infected with the original SARS virus, SARS-CoV, that a 59 suboptimal early anti-viral type I interferon response may predispose to this late manifestation. In summary, we believe there is insufficient evidence to recommend that JAK inhibitors be continued in 70 all patients taking these medications who are acutely infected with SARS-CoV-2. While JAK inhibitors 71 may prove useful in the treatment of SARS-CoV-2-associated CRS, this is a separate consideration of a 72 relatively uncommon manifestation of this viral infection that occurs late in disease course. cache = ./cache/cord-274750-fynxciwg.txt txt = ./txt/cord-274750-fynxciwg.txt === reduce.pl bib === id = cord-275108-snqbrxgr author = Daverio, Marco title = Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date = 2020-05-22 pages = extension = .txt mime = text/plain words = 505 sentences = 31 flesch = 51 summary = We read with interest the article by Cowling and Aiello [1] about the use of proactive public health measures to help slow the spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over the world. Furthermore, the numbers of individuals infected are difficult to estimate, owing to the presence of both SARS-CoV-2-positive asymptomatic individuals and symptomatic, self-isolating individuals in whom nasopharyngeal swab samples were not obtained. It may seem a waste of resources but knowing people's serological status regarding SARS-CoV-2 could allow those who were previously infected to return to work and restart the world economy before the entire pandemic is over. We therefore suggest, along with all the necessary public preventive measures, performing target testing for SARS-CoV-2 antibodies in particular subpopulations, for example, young and healthy persons who can actively work. cache = ./cache/cord-275108-snqbrxgr.txt txt = ./txt/cord-275108-snqbrxgr.txt === reduce.pl bib === id = cord-275420-zkxyxiv5 author = Crabtree, Scott J. title = The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1190 sentences = 67 flesch = 50 summary = title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States This case study highlights the role of a multidisciplinary Infection Prevention team in the identification of the first community-transmitted SARS-CoV-2 case at a large, tertiary referral center in the United States. By rounding on the hospital units such teams can serve vital infection prevention, antibiotic stewardship, and disease surveillance functions. Through the coordinated efforts of UCD's multidisciplinary infection prevention (IP) program, the patient was identified as a possible COVID-19 case and obtained SARS-CoV-2 testing. During rounds, each patient is reviewed through the electronic medical record and via discussion with the bedside nurse to evaluate for possible infection prevention and antimicrobial stewardship interventions. The patient's case was discussed with her bedside nurse, who confirmed that SARS-CoV-2 was considered by her primary team, but given the absence of exposures, testing for this agent was not pursued. cache = ./cache/cord-275420-zkxyxiv5.txt txt = ./txt/cord-275420-zkxyxiv5.txt === reduce.pl bib === id = cord-274824-kaefedl1 author = Turski, Waldemar A. title = AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5928 sentences = 284 flesch = 36 summary = as pro viral factor TiPARP, and to the modulation of cytokine gene expression, specifically, interleukin 1␤ (IL-1␤), IL-10, and TNF-␣ ( Fig. 1) , which is consistent with the role for AhR activation in the host response to CoV infection Grunewald, Shaban, Mackin, Fehr, & Perlman, 2020; Neavin, Liu, Ray, & Weinshilboum, 2018) . Since CoV persistently activate AhRs, this may lead to up-regulation of multiple sets of downstream effectors resulting in different pathologies (Fig. 2) depending on time after infection, individuals overall state of health, comorbidities, and environmental factors affecting AhRs. We believe it is therefore appropriate to describe this disease as a systemic AhR activation syndrome (SAAS), which can manifest in an acute (current pandemic), and perhaps later, in a chronic form, in survivors. cache = ./cache/cord-274824-kaefedl1.txt txt = ./txt/cord-274824-kaefedl1.txt === reduce.pl bib === id = cord-274761-c2hgkbg6 author = Rosenberg, Eli S. title = Cumulative incidence and diagnosis of SARS-CoV-2 infection in New York date = 2020-06-17 pages = extension = .txt mime = text/plain words = 3431 sentences = 178 flesch = 44 summary = SARS-CoV-2 cumulative incidence was estimated from antibody reactivity by first post-stratification weighting then adjusting by antibody test characteristics. CONCLUSIONS: From the largest US serosurvey to date, we estimated > 2 million adult New York residents were infected through late March, with substantial disparities, although cumulative incidence remained below herd immunity thresholds. Cumulative incidence among non-institutionalized adults, by geographic and demographic features, was estimated from weighted reactivity rates that were adjusted for validated test characteristics. We estimated SARS-Cov-2 cumulative incidence from observed antibody reactivity using two sequential steps: 1) post-stratification weighting to standardize to the New York State population and 2) adjustment by estimated antibody test characteristics. Test-characteristic adjusted cumulative incidence values were multiplied by the one-and two-way non-institutionalized adult populations (e.g. excluding settings such as prisons and nursing homes) from the American Community Survey 2014-2018 Public Use Microdata Sample file [23] . cache = ./cache/cord-274761-c2hgkbg6.txt txt = ./txt/cord-274761-c2hgkbg6.txt === reduce.pl bib === id = cord-274802-7ioiwsd8 author = Varghese, Praveen Mathews title = Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies date = 2020-08-19 pages = extension = .txt mime = text/plain words = 19657 sentences = 1033 flesch = 42 summary = Proteomic and transcriptomic studies on bronchoalveolar lavage (BAL) samples from COVID-19 patients have also revealed considerable insights into the expression of SARS-CoV-2 receptors, co-receptors, immune responses, as well as risk factors for severe disease e.g. age and co-morbidities. Furthermore, treatment with a recombinant C5a antibody on 2 male COVID-19 patients aged 54 and 67 years showed significant benefit in suppressing complement hyperactivation, which contributes to the excessive immune response causing aggravated inflammatory lung injury, a hallmark of SARS-CoV-2 pathogenesis and lethality (242) . Consistent with endothelial injury, the significantly elevated levels of von Willebrand factor found in the patient with severe COVID-19 has led to the idea that the infection of the ACE2 expressing endothelium by SARS-CoV-2 induces injury and activates the complement , which sets up a feedback loop that maintains a state of inflammation (243, (268) (269) (270) . Initial clinical studies in China involving 100 SARS-CoV-2 infected patients, who were treated with Chloroquine, showed amelioration of pneumonia, shortened disease progression, increased resolution of lung lesions on CT, and a better virus-negative conversion (313, 314) . cache = ./cache/cord-274802-7ioiwsd8.txt txt = ./txt/cord-274802-7ioiwsd8.txt === reduce.pl bib === id = cord-274852-84m62t4x author = Hogan, Catherine A. title = Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019 date = 2020-10-17 pages = extension = .txt mime = text/plain words = 1083 sentences = 62 flesch = 46 summary = To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. The study period corresponded to the onset of the 2019-2020 respiratory virus season, during which the number of cases of influenza A, influenza B, and respiratory syncytial virus increased and the frequency To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. Our pooled screening strategy for investigating local community transmission of SARS-CoV-2 in the San Francisco Bay area of California during late 2019 during the onset of the respiratory virus season identified no COVID-19 cases. cache = ./cache/cord-274852-84m62t4x.txt txt = ./txt/cord-274852-84m62t4x.txt === reduce.pl bib === id = cord-274788-oyk8js16 author = Bae, Sanghyuk title = Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3249 sentences = 184 flesch = 58 summary = BACKGROUND: In February 2020, a coronavirus disease 2019 (COVID-19) outbreak was reported in fitness centers in Cheonan, Korea. We determined the epidemiological characteristics of confirmed cases of SARS-CoV-2 infection, and estimated the time-dependent reproduction number to assess the transmission dynamics of the infection. In this report, we describe the epidemiological characteristics of the COVID-19 outbreak at fitness centers in Cheonan, Korea, based on the official epidemiological investigation, and document the effectiveness of contact tracing and isolation at containing the outbreaks. In the present study, we described epidemiological characteristics of a COVID-19 outbreak in fitness centers in Cheonan, Korea from February 24 to March 13, 2020. A previous epidemiological investigation of an outbreak in a single call center in Seoul, Korea reported that 99.8% of traced contacts had been tested. cache = ./cache/cord-274788-oyk8js16.txt txt = ./txt/cord-274788-oyk8js16.txt === reduce.pl bib === id = cord-275348-jna496x7 author = Kapadia, Sagar U. title = SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date = 2008-06-20 pages = extension = .txt mime = text/plain words = 5982 sentences = 317 flesch = 53 summary = A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells. cache = ./cache/cord-275348-jna496x7.txt txt = ./txt/cord-275348-jna496x7.txt === reduce.pl bib === id = cord-274948-ze6scnae author = Segondy, Michel title = Les Coronavirus humains date = 2020-10-31 pages = extension = .txt mime = text/plain words = 2469 sentences = 262 flesch = 64 summary = Toutefois, à côté de ces infections à coronavirus endémiques, ont récemment émergé chez l'homme, à partir de réservoirs animaux, des coronavirus responsables de syndromes respiratoires sévères avec un taux de mortalité élevé [2] . Ce sont des virus enveloppés dont le génome est un ARN de polarité positive d'une taille de l'ordre de 30 kilobases, ce qui en fait le génome le plus grand chez les virus à ARN [3] . Des coronavirus génétiquement très proches du Mers-CoV ont été identifiés chez des chauves-souris qui représentent le réservoir de virus [29] . Bien que le plus souvent inapparente ou bénigne chez le jeune enfant, l'infection par le Sars-CoV-2 peut être à l'origine d'un syndrome hyper inflammatoire similaire à la maladie de Kawasaki [38] . ◗t Les coronavirus émergents sont responsables d'infections respiratoires sévères avec une mortalité élevée. En moins de vingt ans, ce sont trois coronavirus responsables d'infections respiratoires sévères avec une mortalité élevée qui ont émergé dans la population humaine. cache = ./cache/cord-274948-ze6scnae.txt txt = ./txt/cord-274948-ze6scnae.txt === reduce.pl bib === id = cord-275452-ymimvoq9 author = Ameen, Fuad title = Covid-19 pandemic outburst in Saudi Arabia: A Glimpse date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2456 sentences = 142 flesch = 47 summary = This short review report very briefly highlights covid-19 syndromes; propagation; Middle East outburst, natural products as cure for viral diseases, probable psychosomatic effects, protective measures and Islamic wisdom. Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. -q (2020) Traditional Chinese medicine is a resource for drug discovery against 2019 novel coronavirus (SARS-CoV-2) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-275452-ymimvoq9.txt txt = ./txt/cord-275452-ymimvoq9.txt === reduce.pl bib === id = cord-274839-r4jg6wac author = Azam, Faizul title = An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5156 sentences = 254 flesch = 46 summary = Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing −5.30 kcal/mol and −84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. Therefore, in this study, molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) and molecular dynamics protocols have been exploited to investigate the binding interactions between IVM and 15 potential drug targets associated with COVID-19 as well as IMPa co-crystallized with NS5 fragment. cache = ./cache/cord-274839-r4jg6wac.txt txt = ./txt/cord-274839-r4jg6wac.txt === reduce.pl bib === id = cord-275199-y7b12vml author = Suárez-Fariñas, Mayte title = Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date = 2020-09-25 pages = extension = .txt mime = text/plain words = 5683 sentences = 331 flesch = 47 summary = The RISK cohort 18 : ACE2 and TMPRSS2 in treatment-free pediatric CD (<17 years of age) patients was studied using RNA-seq expression profiles from GSE57945, which includes ileal biopsies from endoscopically defined inflamed samples (n=160), non-inflamed (n=53) and non-IBD controls (n=42). Genes differentially expressed in blood 22 , lung NHBE/A549 23 or human small intestinal organoids 24 (hSIO) following SARS-CoV-2 infection; IBD inflammation; or response to medications were separately projected onto various BGRNs allowing for 1 or 2 nearest neighbors depending on the signature sizes. The expression of ACE2 and TMPRSS2 was similar when comparing active smokers to non-smokers, either between healthy controls or IBD patients (data not shown) and no significant interactions with inflammation status, region or other covariates were found. We observed that genes: up-regulated with inflammation, or positively associated with macroscopic or microscopic measures of disease, or associated with the risk of IBD, were significantly enriched with genes up-regulated by SARS-CoV2 infection of lung epithelial cells ( Figure S10e ). cache = ./cache/cord-275199-y7b12vml.txt txt = ./txt/cord-275199-y7b12vml.txt === reduce.pl bib === id = cord-275340-q8d7rvnj author = Sun, JingKang title = Advances in the use of chloroquine and hydroxychloroquine for the treatment of COVID-19 date = 2020-06-21 pages = extension = .txt mime = text/plain words = 6629 sentences = 285 flesch = 47 summary = CQ/HCQ may synergistically exert antiviral and immunomodulatory effects on COVID-19 through multiple mechanisms including hindering the receptor recognition process by influencing the affinity of ACE2 and S protein, and the affinity for sialic acid and ganglioside; inhibiting the membrane fusion process by suppressing endolysosome acidification; suppressing the p38 activation and affecting host defense machinery, and preventing MHC class II expression (block expression of CD154 on the surface of CD4 + T cell) and TLR signaling and reducing the production of cytokines through inhibiting the activation of T cells and B cells. ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; CQ, chloroquine; HCQ, hydroxychloroquine; CoVs, coronaviruses; MAPK, mitogen-activated protein kinase; MHC-II, major histocompatibility complex class II; TLR, toll-like receptor; cGAS, cyclic GMP-AMP synthase; IFN, interferon; IL, interleukin; TNF-α, tumor necrosis factor-α. The authors deemed that the anti-inflammatory effect of low-dose HCQ and the activity of inhibiting viral replication may have important significance in critically ill patients with COVID-19. cache = ./cache/cord-275340-q8d7rvnj.txt txt = ./txt/cord-275340-q8d7rvnj.txt === reduce.pl bib === id = cord-275404-hv3y4x4g author = Zumla, Alimuddin title = Infection control and MERS-CoV in health-care workers date = 2014-05-20 pages = extension = .txt mime = text/plain words = 1527 sentences = 80 flesch = 48 summary = 1 The WHO Emergency Committee concluded that the increase in cases reported among health-care workers from hospitals in Jeddah was amplifi ed due to overcrowding and inadequate infection control measures. 11 On the basis of analysis of data in a case-control study that involved 124 medical wards in 26 hospitals in Guangzhou, China, and Hong Kong, the risk factors for super-spreading events of SARS-CoV in the hospital setting were: close separation between beds of less than 1 m; performance of resuscitation; staff working while experiencing symptoms; and patients requiring oxygen or non-invasive ventilation therapy. A systematic review of fi ve case-control and fi ve retrospective cohort studies identifi ed tracheal intubation, tracheotomy, and manual ventilation before intubation as procedures associated with risk of transmission of SARS-CoV to health-care workers. Interim infection prevention and control recommendations for hospitalized patients with Middle East respiratory syndrome coronavirus (MERS-CoV) cache = ./cache/cord-275404-hv3y4x4g.txt txt = ./txt/cord-275404-hv3y4x4g.txt === reduce.pl bib === id = cord-275250-ilmgy7ce author = Xia, Yong title = Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date = 2020-05-17 pages = extension = .txt mime = text/plain words = 728 sentences = 52 flesch = 63 summary = As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. cache = ./cache/cord-275250-ilmgy7ce.txt txt = ./txt/cord-275250-ilmgy7ce.txt === reduce.pl bib === id = cord-275173-ely3aen3 author = Pickering, Brad S. title = Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1917 sentences = 107 flesch = 52 summary = The work reported here aims to determine whether domestic swine are susceptible to 63 SARS-CoV-2 infection, providing critical information to aid public health risk assessments. The data presented in 66 this study provides evidence live SARS-CoV-2 virus can persist in swine for at least 13 days 67 following experimental inoculation. Two pigs (20-10, 20-11) displayed low 237 levels of viral RNA by RT-qPCR at 3 DPI (Table 2, Detection of SARS-CoV-2 was also attempted from whole blood by RT-qPCR, following 253 the sampling schedule outlined in Table 1 . To identify potential target tissues or gross lesions consistent with SARS-CoV-2 disease, 261 necropsy was performed on two animals starting at 3 DPI and every other day up to day 15; with 262 an additional two pigs necropsied at both 22 and 29 DPI (Table 1) (Table 2) . The results presented in this study define domestic swine as a susceptible species albeit at 293 low levels to SARS-CoV-2 viral infection. cache = ./cache/cord-275173-ely3aen3.txt txt = ./txt/cord-275173-ely3aen3.txt === reduce.pl bib === id = cord-275252-4e3cn50u author = Rad SM, Ali Hosseini title = Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date = 2020-05-16 pages = extension = .txt mime = text/plain words = 4368 sentences = 302 flesch = 53 summary = In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. cache = ./cache/cord-275252-4e3cn50u.txt txt = ./txt/cord-275252-4e3cn50u.txt === reduce.pl bib === id = cord-275216-dnt88ycw author = Zhang, Xue-Yan title = Biological, clinical and epidemiological features of COVID-19, SARS and MERS and AutoDock simulation of ACE2 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 4893 sentences = 259 flesch = 51 summary = This review is intended to summarize the research on this new coronavirus, to analyze the similarities and differences between COVID-19 and previous outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and to provide guidance regarding new methods of prevention, diagnosis and clinical treatment based on autodock simulations. Given that the epidemic is still spreading and the evidence that there are similarities among the three coronaviruses in terms of their biological, clinical and epidemiological features, a comparison among the three is very helpful to guide the improvement of treatment and prevention measures, and the similarities and differences among the three are likely to provide the key to addressing the COVID-19 epidemic. In 2002-2003, SARS-CoV caused an epidemic of severe acute respiratory diseases in China; MERS-CoV was found in the Middle East in 2012 [9, 10] . cache = ./cache/cord-275216-dnt88ycw.txt txt = ./txt/cord-275216-dnt88ycw.txt === reduce.pl bib === id = cord-275552-ijxxeo27 author = Yen, Zui-Shen title = How much would you be willing to pay for preventing a new dangerous infectious disease: A willingness-to-pay study in medical personnel working in the emergency department date = 2007-10-10 pages = extension = .txt mime = text/plain words = 2704 sentences = 166 flesch = 56 summary = The objective of this study was to estimate the median amount of money ED personnel would be willing to pay for preventing nosocomial severe acute respiratory syndrome (SARS). 9 In this study, CVM was used to estimate the median amount emergency medical personnel would be willing to pay for a hypothetical vaccine to prevent developing nosocomial SARS. We used this study as an example to demonstrate that medical personnel would be willing to pay substantial monetary amounts to avert the risk of nosocomial SARS infection. However, we found that the median amount medical personnel in the ED would be willing to pay for a SARS vaccine was US $1,762, which was exceedingly high compared to the usual cost of a vaccine and equal to 14% of the 2002 Taiwan gross domestic product per capita (US $12,588). cache = ./cache/cord-275552-ijxxeo27.txt txt = ./txt/cord-275552-ijxxeo27.txt === reduce.pl bib === id = cord-275438-drywzvx8 author = Satış, Hasan title = Prognostic value of interleukin-18 and its association with other inflammatory markers and disease severity in COVID-19 date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3539 sentences = 212 flesch = 46 summary = Serum IL-18 levels were remarkably higher in COVID-19 patients compared to healthy subjects with being highest in severe pneumonia group (p < 0.001). According to the disease course, COVID-19 patients may be roughly divided into two groups; asymptomatic or mild cases that usually recover and severe cases that develop multi organ failure, primarily respiratory failure, requiring intensive care unit (ICU) admission [5, 6] . In this study, we found that both IL-6 and serum IL-18 concentrations are remarkably increased in patients with COVID-19 and correlated with other inflammatory markers and disease severity. There are differences in cytokine production among COVID-19 patients, such as men are more susceptible to SARS-CoV-2 infection than women and children, in whom it could present as Kawasaki disease [29, 30] , as well as serum cytokine levels tend to be higher in men explaining their worse prognosis [29] . cache = ./cache/cord-275438-drywzvx8.txt txt = ./txt/cord-275438-drywzvx8.txt === reduce.pl bib === id = cord-275482-ncrhb75f author = Jia, Hong Peng title = Infection of Human Airway Epithelia by Sars Coronavirus is Associated with ACE2 Expression and Localization date = 2006 pages = extension = .txt mime = text/plain words = 2141 sentences = 110 flesch = 42 summary = In contrast with results in polarized epithelia, poorly differentiated primary human tracheobronchial epithelia or A549 cells grown on tissue culture plastic expressed little ACE2 mRNA or protein. (D) β-galactosidase levels determined in primary human airway epithelia cultured under ALI or resubmerged conditions that were infected from the apical with SARS-S protein pseudotyped FIV. These results indicated that SARS-CoV infects undifferentiated human airway epithelial cells poorly or not at all, while well-differentiated conduction airway epithelia are susceptible. Our studies revealed the novel observation that SARS-CoV infection of human airway epithelia is dependent upon the state of epithelial differentiation and ACE2 mRNA and protein expression. In conclusion, studies in models of human airway epithelial differentiation and polarity reveal that SARS-CoV infects well-differentiated cells from the apical surface and preferentially exits from the apical side. cache = ./cache/cord-275482-ncrhb75f.txt txt = ./txt/cord-275482-ncrhb75f.txt === reduce.pl bib === id = cord-275521-dlp055z8 author = Goldman, Emanuel title = Exaggerated risk of transmission of COVID-19 by fomites date = 2020-07-03 pages = extension = .txt mime = text/plain words = 737 sentences = 42 flesch = 58 summary = A clinically significant risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission by fomites (inanimate surfaces or objects) has been assumed on the basis of studies that have little resemblance to real-life scenarios. The longest survival (6 days) of severe acute respiratory syndrome coronavirus (SARS-CoV) on surfaces was done by placing a very large initial virus titre sample (10⁷ infectious virus particles) on the surface being tested. 1 Another study that claimed survival of 4 days used a similarly large sample (10⁶ infectious virus particles) on the surface. 3 Yet another study found long survival (5 days) of human coronavirus 229E on surfaces with what I would still consider a substantially large viral load (10³ plaque-forming units) in a cell lysate. For example, in the studies that used a sample of 10⁷, 10⁶, and 10⁴ particles of infectious virus on a small surface area, 1-3 these concentrations are a lot higher than those in droplets in real-life situations, with the amount of virus actually deposited on surfaces likely to be several orders of magnitude smaller. cache = ./cache/cord-275521-dlp055z8.txt txt = ./txt/cord-275521-dlp055z8.txt === reduce.pl bib === id = cord-275336-lnhkux0m author = Marino Gammazza, Antonella title = Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1935 sentences = 104 flesch = 41 summary = title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the cause of COVID-19 disease, has the potential to elicit autoimmunity because mimicry of human molecular chaperones by viral proteins. We compared viral proteins with human molecular chaperones, many of which are heat shock proteins, to determine if they share amino acid-sequence segments with immunogenic-antigenic potential, which can elicit cross-reactive antibodies and effector immune cells with the capacity to damage-destroy human cells by a mechanism of autoimmunity. We identified the chaperones that can putatively participate in molecular mimicry phenomena after SARS-CoV-2 infection, focusing on those for which endothelial cell plasma-cell membrane localization has already been demonstrated. We compared the amino acid sequences of all the SARS-CoV-2 proteins with the sequences of human chaperones to determine if they share segments with immunogenic-antigenic potential that might be causing autoimmunity. cache = ./cache/cord-275336-lnhkux0m.txt txt = ./txt/cord-275336-lnhkux0m.txt === reduce.pl bib === id = cord-275604-5u4kikov author = Feehan, Amy K. title = Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 date = 2020-11-17 pages = extension = .txt mime = text/plain words = 1417 sentences = 88 flesch = 51 summary = Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. We estimated SARS-CoV-2 infections in Orleans and Jefferson Parishes, Louisiana, USA, and determined the COVID-19-related IFR by race. io) considered >50 characteristics, including social determinants of health and US Census population Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. Study participants for whom either or both tests were positive were considered to be infected with SARS-CoV-2. Our study found the overall SARS-CoV-2 exposure rate in this area to be 7.8% and confirmed a recent report of overrepresentation of Black persons with COVID-19 in the New Orleans area (5) . cache = ./cache/cord-275604-5u4kikov.txt txt = ./txt/cord-275604-5u4kikov.txt === reduce.pl bib === id = cord-275357-yx8lsfdv author = Lu, J. title = Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2348 sentences = 130 flesch = 56 summary = The Limits of Detection of two sets of RT-PCR assays, the TaqPath Multiplex RT-PCR COVID-19 Kit (Thermo) and the PrimerDesign COVID-19 assay, were determined using different viral RNA and reaction volumes ( Supplementary Table 1 ). In the Helix lab, a miniaturized 5 uL input RNA (10 uL total reaction volume) TaqPath assay was performed on a Quantstudio 7 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 6.25 viral copies. In the UCSD lab, a miniaturized 2 uL input RNA (3 uL total reaction volume) TaqPath assay was performed on a Quantstudio 5 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 3.125 viral copies. RNA was extracted from the NPS VTM and Saliva samples and analyzed using the PrimerDesign and TaqPath assays at the sites shown in Table 2 (full dataset with Ct values for each viral target sequence and internal control sequences are shown in Supplementary Table 2 ). cache = ./cache/cord-275357-yx8lsfdv.txt txt = ./txt/cord-275357-yx8lsfdv.txt === reduce.pl bib === id = cord-275257-upj8mvzn author = Hwang, E. Shelley title = Surgical Oncologists and the COVID-19 Pandemic: Guiding Cancer Patients Effectively through Turbulence and Change date = 2020-06-14 pages = extension = .txt mime = text/plain words = 8495 sentences = 389 flesch = 40 summary = Perspectives are provided on: (1) maintaining a safe environment for surgical oncology care; (2) redirecting the multidisciplinary model to guide surgical decisions; (3) harnessing telemedicine to accommodate requisite physical distancing; (4) understanding interactions between SARS CoV-2 and cancer therapy; (5) considering the ethical impact of professional guidelines for surgery prioritization; and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. The panel provides perspectives on: (1) creating a safe environment for surgical oncology care, (2) redirecting the multidisciplinary model to guide surgical decisions, (3) harnessing telemedicine to accommodate requisite physical distancing, (4) understanding interactions between SARS CoV-2 and cancer therapy, (5) considering the ethical impact of professional guidelines for surgery prioritization, and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. cache = ./cache/cord-275257-upj8mvzn.txt txt = ./txt/cord-275257-upj8mvzn.txt === reduce.pl bib === id = cord-275191-lgze4zex author = Al-Sadeq, Duaa W. title = The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3287 sentences = 221 flesch = 48 summary = AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. cache = ./cache/cord-275191-lgze4zex.txt txt = ./txt/cord-275191-lgze4zex.txt === reduce.pl bib === id = cord-275185-9br8lwma author = Zeng, Hao title = The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date = 2020-10-06 pages = extension = .txt mime = text/plain words = 6613 sentences = 360 flesch = 53 summary = Following CP transfusion, six out of eight patients showed improved oxygen support status; chest CT indicated varying degrees of absorption of pulmonary lesions in six patients within 8 days; the viral load was decreased to a negative level in five patients who had the previous viremia; other laboratory parameters also tended to improve, including increased lymphocyte counts, decreased C-reactive protein, procalcitonin, and indicators for liver function. Herein, we performed a retrospective observational study involving eight critical or severe patients with COVID-19 from four designated hospitals in the southwest region of China, aiming to explore the potential efficacy and safety of CP therapy, and to provide more evidence for the quality control of donated plasma and reasonable clinical application of CP transfusion. 23 Assessing the effects of neutralizing activity of CP on the patients' clinical efficacy, we found that patients treated by CP with high NAT50 (>1:640) had more obvious improvement than patients receiving low NAT50 value (≤1:640) of CP, including shorter negative conservation time of viral RNA, and higher increment of IgG level after CP transfusion. cache = ./cache/cord-275185-9br8lwma.txt txt = ./txt/cord-275185-9br8lwma.txt === reduce.pl bib === id = cord-275495-h60x89zi author = Bocksberger, S. title = Temporäre Hyposmie bei COVID-19-Patienten date = 2020-05-25 pages = extension = .txt mime = text/plain words = 1291 sentences = 145 flesch = 58 summary = CONCLUSION: The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1–3 weeks after the onset of COVID-19 symptoms. Die im Dezember 2019 erstmalig in Wuhan, China, aufgetretene Coronaviruserkrankung (COVID-19) wird durch die Infektion mit SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), einem neuartigen RNA-β-Coronavirus, hervorgerufen und verursacht in einer Vielzahl von Fällen eine akute Atemwegsinfektion [1] . The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1-3 weeks after the onset of COVID-19 symptoms. cache = ./cache/cord-275495-h60x89zi.txt txt = ./txt/cord-275495-h60x89zi.txt === reduce.pl bib === id = cord-275439-cdlcv1c9 author = Iwasaki, S. title = Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1850 sentences = 130 flesch = 66 summary = We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in nine COVID-19 patients. SARS-CoV-2 was detected in saliva in 8 of 9 (89%) patients and in all 11 samples taken within 2 weeks after disease onset. The diagnosis of COVID-19 is made by PCR testing of samples collected by nasopharyngeal or oropharyngeal swabs, with the nasopharyngeal route being the standard with a sensitivity for the virus in the range of 52-71% [1] [2] [3] [4] [5] . demonstrated the saliva to be more sensitive for SARS-CoV-2 detection patients than nasopharyngeal swabs 14 . We prospectively compared SARS-CoV-2 detection between nasopharyngeal samples and saliva samples in 9 patients with COVID-19. Our results were consistent to these data; the virus was detected in all the saliva samples taken within 2 weeks after symptom onset. Data are shown as mean ± SD (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-275439-cdlcv1c9.txt txt = ./txt/cord-275439-cdlcv1c9.txt === reduce.pl bib === id = cord-275088-wbqznzj7 author = Garrido, Pablo F. title = The Lord of the NanoRings: cyclodextrins and the battle against SARS-CoV-2 date = 2020-07-25 pages = extension = .txt mime = text/plain words = 9649 sentences = 535 flesch = 44 summary = This includes the encapsulation and transport of specific drugs, as adjuvants to stabilize proteins, vaccines or other molecules involved in the infection, as cholesterol trappers to destabilize the virus envelope, as carriers for RNA therapies, as direct antiviral drugs and even to rescue blood coagulation upon heparin treatment. Modified Cyclodextrins in general antiviral formulations Not only native CDs but also CD derivates have been studied as potential drugdelivery platforms to treat several viral diseases. The inclusion conjugates release sACE2 after entering the body via atomization or other drug delivery means, and the released sACE2 would combine with SARS-CoV-2 S-proteins to block the virus's ability to infect and destroy human cells. Recently, we discuss the mechanism and production of cyclodextrin-soluble angiotensin-converting enzyme 2 (CD-sACE2) inclusion compounds in the treatment of SARS-CoV-2 infections by blocking S-proteins. cache = ./cache/cord-275088-wbqznzj7.txt txt = ./txt/cord-275088-wbqznzj7.txt === reduce.pl bib === id = cord-275569-i5y23mmz author = de Bernardis, E. title = A putative role for the tobacco mosaic virus in smokers’ resistance to COVID-19 date = 2020-07-31 pages = extension = .txt mime = text/plain words = 1500 sentences = 69 flesch = 41 summary = Though it is intuitively tempting, on the basis of physiopathological common knowledge, to predict a greater risk of contracting the SARS-CoV-2 infection in tobacco smokers, an analysis of studies from various countries shows that hospitalized COVID-19 patients have a lower, and apparently inversely proportional, rate of current tobacco smoking, in comparison with the respective general population, although once the disease has developed meta-analyses suggest that smoking is associated with a worse prognosis [1] . Incidentally, this behavior reminds the proposed effects of tobacco smoking, protective against initial SARS-CoV-2 infection and deleterious in the florid phase of the COVID-19 disease. Taken together, all these elements suggest that the oral use of tobacco, continuously exposing to non-pathogenic but immunogenic TMV particles, and chronically stimulating a natural antiviral response, may induce a state of resistance to the initial SARS-CoV-2 infection. cache = ./cache/cord-275569-i5y23mmz.txt txt = ./txt/cord-275569-i5y23mmz.txt === reduce.pl bib === id = cord-275708-17cz3agx author = Babyn, Paul S. title = Severe acute respiratory syndrome (SARS): chest radiographic features in children date = 2003-11-18 pages = extension = .txt mime = text/plain words = 5761 sentences = 296 flesch = 47 summary = CONCLUSION: In pediatric cases, SARS manifests with nonspecific radiographic features making radiological differentiation difficult, especially from other commonly encountered childhood respiratory viral illnesses causing airspace disease. This article presents the initial chest radiographic findings collated from 62 children diagnosed as probable or suspect SARS cases during the recent SARS outbreak in Toronto, Singapore, and Hong Kong. Keywords Chest AE Severe acute respiratory syndrome (SARS) AE Radiography AE CT AE Children the following signs and symptoms: fever, chills, body ache, cough, sore throat, rhinorrhea, dyspnea, tachypnea, crackles, headache, dizziness, hypoxemia, malaise, myalgia, rigor, lethargy, and gastrointestinal symptoms including vomiting and diarrhea. In general, fever and cough were the most common clinical presentation amongst younger pediatric SARS cases (age<10 years), whereas, in addition to these symptoms, headache, myalgia, sore throat, chills, and/or rigor were reported in older patients (age ‡10 years). cache = ./cache/cord-275708-17cz3agx.txt txt = ./txt/cord-275708-17cz3agx.txt === reduce.pl bib === id = cord-275746-3sgbpn13 author = Shimamoto, Yasuhiro title = Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors date = 2015-02-15 pages = extension = .txt mime = text/plain words = 6600 sentences = 347 flesch = 66 summary = After the reaction mixture was cooled to room temperature, water was added and the whole was extracted with AcOEt. The organic layer was washed with 1 M HCl and brine, dried over MgSO 4 , filtered, and concentrated. After the mixture was stirred for 12 h, the reaction was quenched with saturated aqueous NH 4 Cl and the whole was extracted with AcOEt. The organic layer was washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by silica gel column chromatography (hexane/AcOEt = 3:1) to give a title alcohol ( 21 .0 mmol) in CH 2 Cl 2 (50 mL), and the mixture was stirred for 8 h at room temperature. The residue was purified by silica gel column chromatography (hexane/AcOEt = 6:1) to give 32 ( Tris-HCl buffer pH 7.5 containing 7 mM DTT) was incubated with the R188I SARS 3CL pro28 (56 nM) at 37°C for 60 min in the presence of various inhibitor concentrations at 37°C for 60 min. cache = ./cache/cord-275746-3sgbpn13.txt txt = ./txt/cord-275746-3sgbpn13.txt === reduce.pl bib === id = cord-275454-an8xvow3 author = Clark, Andrew E title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1607 sentences = 87 flesch = 48 summary = We read with interest the study appearing in this issue by Li et al, who utilized a pooled sample strategy and a point-of-care (POC) reverse transcriptase-polymerase chain reaction (RT-PCR) assay for screening asymptomatic airline passengers arriving from areas of high SARS-CoV-2 prevalence. At the time of this writing, 2 reference laboratories in the United States (Quest Diagnostics and LabCorp) have received emergency use authorizations from the US Food and Drug Administration to use pooled specimens for SARS-CoV-2 detection [2] . In this work, pooling was performed in a 10:1 ratio, meaning 10 patient specimens were combined and tested using a single SARS-CoV-2 assay. At our institution, we are aware of patients who underwent preprocedure SARS-CoV2 screening utilizing the same assay deployed in this work, only to be diagnosed with active, symptomatic COVID-19 within 5 days of testing. cache = ./cache/cord-275454-an8xvow3.txt txt = ./txt/cord-275454-an8xvow3.txt === reduce.pl bib === id = cord-275862-1aqtqaod author = Yang, Xiaodong title = A case of COVID-19 patient with the diarrhea as initial symptom and literature review date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1316 sentences = 93 flesch = 57 summary = authors: Yang, Xiaodong; Zhao, Jie; Yan, Qiang; Zhang, Shangxin; Wang, Yigao; Li, Yongxiang Here we reported a case of 2019 novel coronavirus-infected patient (NCIP) with diarrhea as the initial symptom. Laboratory examination shows that the absolute number of leukocytes, neutrophils and lymphocytes decrease in most patients, while CRP increases significantly and procalcitonin is usually normal [7] . In our case, the patient suffered from diarrhea as the initial symptom, which was relatively rare in NCIP. In conclusion, we reported the clinic feature and laboratory examination of a NCIP patient with diarrhea as the initial symptom. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China cache = ./cache/cord-275862-1aqtqaod.txt txt = ./txt/cord-275862-1aqtqaod.txt === reduce.pl bib === id = cord-275960-1m6poddy author = Thieme, C. J. title = The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3244 sentences = 217 flesch = 52 summary = Analyzing a cohort of COVID-19 patients with moderate, severe, and critical disease severity, we show that overlapping peptide pools (OPP) of all three proteins can activate SARS-CoV-2-reactive T-cells with a stronger response of CD4+ compared to CD8+ T-cells. Accordingly, very recent studies identified SARS-CoV-2 S-protein reactive T cell responses in patients suffering from moderate, severe, and critical COVID-19 4, 10 . Surprisingly, and in contrast to the endemic SARS-CoV infection, we detected the highest magnitude of CD4 + and CD8 + T cells reactive to S-, M-, and N-proteins in critical COVID-19 (Fig. 3) . Polyfunctional T cells showed higher frequencies in critical COVID-19 patients compared to moderate and severe cases (Fig. 3e ,f,n,o). In line with data showing an association between polyfunctionality and the stage of phenotypic differentiation 17 , we observed higher frequencies of CD8 + T cells with effector memory (TEM)/TEMRA phenotype in critical COVID-19 patients compared to moderate and severe cases (Fig S4) . cache = ./cache/cord-275960-1m6poddy.txt txt = ./txt/cord-275960-1m6poddy.txt === reduce.pl bib === id = cord-275784-n6jv72l7 author = Spina, Alfio title = The Management Of Neurosurgical Patients During The Covid-19 Pandemic date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2228 sentences = 131 flesch = 45 summary = An adequate management protocol can reduce hospital viral spread, improving safety both for patients and healthcare professionals. 1 The management of an ever-increasing number of patients, particularly those suffering from coronavirus disease 2019 (COVID-19) pneumonia has deeply affected the organization of healthcare facilities. 11 In a single-center Chinese case series of 138 hospitalized patients, presumed hospitalrelated infection of COVID-19 was suspected in 41% of patients, with a reported mortality of 4.3% and an intensive care unit admission rate of 26%. 12 Furthermore, COVID-19 transmission rate to healthcare worker was reported up to 20% 13 These data suggest that, inadequate hospital setting may represent a relevant route of SARS-CoV-2 spread both for patients and healthcare professionals. Whenever possible, elective surgery for confirmed cases (i.e. Group 1) should be rescheduled, because of this class of patients show higher risks of intensive care need and death. cache = ./cache/cord-275784-n6jv72l7.txt txt = ./txt/cord-275784-n6jv72l7.txt === reduce.pl bib === id = cord-275946-ofd2ipvs author = Cheng, Matthew P. title = Serodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review date = 2020-06-04 pages = extension = .txt mime = text/plain words = 5277 sentences = 282 flesch = 38 summary = Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation. Appropriately designed seroepidemiologic studies will play an essential part in the public health response to the COVID-19 pandemic by characterizing transmission dynamics, refining disease burden estimates, and providing insight into the kinetics of humoral immunity to SARS-CoV-2. Serologic surveillance studies can also assess the accumulation of persons with antibody responses over time to estimate incidence of SARS-CoV-2 infection (57, 58) and can track age-and jurisdiction-specific disease susceptibility and identify at-risk populations (59) . cache = ./cache/cord-275946-ofd2ipvs.txt txt = ./txt/cord-275946-ofd2ipvs.txt === reduce.pl bib === id = cord-275979-cx2h5bsw author = Scutelnic, Adrian title = Vascular Events, Vascular Disease and Vascular Risk Factors—Strongly Intertwined with COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 6747 sentences = 342 flesch = 46 summary = According to the INTERSTROKE study, the 10 most frequent modifiable vascular risk factors are arterial hypertension, physical inactivity, overweight, dyslipidaemia, smoking, unhealthy diet, cardiac pathologies, diabetes mellitus, stress/depression and overconsumption of alcohol. Also, a higher rate of infection with COVID-19, severe COVID-19 and bad outcome has been demonstrated in patients with pre-existing vascular disease and vascular risk factors. A higher rate of infection with COVID-19, severe COVID-19, and worse outcome has been demonstrated in patients with pre-existing vascular disease and risk factors, compared with young and healthy persons [1, 6, 8-11, 28, 29] . Several potential mechanisms increasing this risk of COVID-19 in patients with diabetes mellitus have been proposed: (1) higher affinity of cellular binding of SARS-CoV-2 and higher levels of circulating furin facilitating virus entry, (2) increased ACE2 expression in the lungs, (3) decreased viral clearance, (4) diminished T cell function, (5) increased susceptibility to inflammation and cytokine storm syndrome and (6) co-existence of vascular disease and risk factors [5] . cache = ./cache/cord-275979-cx2h5bsw.txt txt = ./txt/cord-275979-cx2h5bsw.txt === reduce.pl bib === id = cord-275506-3t5gf66c author = Agbuduwe, Charles title = Hematolological Manifestations of COVID‐19: From Cytopenia to Coagulopathy date = 2020-07-14 pages = extension = .txt mime = text/plain words = 4280 sentences = 265 flesch = 39 summary = [45] A retrospective study of COVID-19 patients admitted to ICU identified DVT in 25% with advanced age, lower lymphocyte counts and elevated D-dimers being significant risk factors. [63] Currently, the evidence base for the clinical management of COVID-19 is mostly limited to case series and other relatively small observational studies of hospitalised patients. Similar to findings in SARS patients, [64] lymphopenia is the most commonly reported hematological abnormality in COVID-19 and recent data shows that it can be predictive of disease severity. The use of convalescent plasma may, in addition, provide neutralising antibodies against SARS-CoV-2 and a small-scale clinical trial has reported modest but encouraging results in severely-ill but not in critical COVID-19 patients. In view of the increased thrombotic risk associated with COVID-19, prophylactic anticoagulation with low Accepted Article molecular weight heparin is recommended for all hospitalised patients with the disease and clinical trials are needed to investigate the role of more intensive anticoagulation and other experimental therapies. cache = ./cache/cord-275506-3t5gf66c.txt txt = ./txt/cord-275506-3t5gf66c.txt === reduce.pl bib === id = cord-275565-xerr4vki author = Kumar, Manish title = Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3456 sentences = 230 flesch = 58 summary = For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. Thus, there still remains questions pertaining to: i) capability of conventional WWTPs to reduce the abundance of SARS-CoV-2 RNA, ii) better understanding of the protocol, virus J o u r n a l P r e -p r o o f Journal Pre-proof precipitation through PEG and filtration which one is better methods for concentrating the samples before RNA isolation. Appraising the genetic loading reduction through Upflow Anaerobic Sludge Blanket (UASB) systems, and iii) Comparing the performances between PEG and filtration as virus concentration methods in terms of SARS-CoV-2 RNA sensitivity and inhibition removal. cache = ./cache/cord-275565-xerr4vki.txt txt = ./txt/cord-275565-xerr4vki.txt === reduce.pl bib === id = cord-275690-83nrzfon author = Stanifer, Megan L. title = Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date = 2020-04-24 pages = extension = .txt mime = text/plain words = 4696 sentences = 256 flesch = 52 summary = title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, and in agreement with the results observed in cells depleted of the type III IFN receptor, this increase in infectivity was also associated with an increase in infectious denovo virus particle production ( Fig. 3G ). All together, these results strongly support a model where the type III IFN mediated signaling controls SARS-CoV-2 infection in human intestinal epithelial cells. All together these results show that human colon organoids can support SARS-CoV-2 infection, replication and spread and that the type III IFN response plays a critical role in controlling virus replication. cache = ./cache/cord-275690-83nrzfon.txt txt = ./txt/cord-275690-83nrzfon.txt === reduce.pl bib === id = cord-275894-puwaty70 author = Wajnberg, A. title = SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2493 sentences = 190 flesch = 61 summary = Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. In order to determine if antibodies induced against the spike protein exert neutralizing activity, we 111 performed a well-established, quantitative microneutralization assay (18) based on authentic 112 SARS-CoV-2 with 120 samples of known ELISA titers ranging from 'negative' to 1:2880. . https://doi.org/10.1101/2020.07.14.20151126 doi: medRxiv preprint with authentic SARS-CoV-2 virus, and the vast majority of individuals with antibody titers of 1:320 167 or higher show neutralizing activity in their serum. cache = ./cache/cord-275894-puwaty70.txt txt = ./txt/cord-275894-puwaty70.txt === reduce.pl bib === id = cord-275888-6u1o6414 author = Tan, Kian Teo title = N95 acne date = 2004-06-29 pages = extension = .txt mime = text/plain words = 2073 sentences = 146 flesch = 52 summary = 1 The giant porokeratosis lesion on the left hand of our patient was totally excised and grafted. A diagnosis of sarcoidosis involving the central nervous system, lacrimal gland, nasal septum, vocal cord, lung and scalp was made, and the patient was treated with 20 mg of methylprednisone on alternate days with intralesional triamcinolone injection for skin lesions. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. cache = ./cache/cord-275888-6u1o6414.txt txt = ./txt/cord-275888-6u1o6414.txt === reduce.pl bib === id = cord-275760-hi9sj0d7 author = Ng, Siew C title = Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification date = 2020-04-22 pages = extension = .txt mime = text/plain words = 644 sentences = 39 flesch = 59 summary = title: Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification We read with interest the Correspondence by Christopher Green and colleagues 1 suggesting the need for a molecular test to screen faecal microbiota transplant (FMT ) donors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to prevent the potential risk of transmission. 5 As described by Green and colleagues, 1 the University of Birmingham Microbiota Treatment Centre (Birmingham, UK) is not actively processing new donors until a validated SARS-CoV-2 stool test is available. As per the diagnostic protocol of our local health authority, all COVID-19 cases had been confirmed by two RT-PCR tests targeting different regions of the RdRp gene in respiratory specimens. Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward cache = ./cache/cord-275760-hi9sj0d7.txt txt = ./txt/cord-275760-hi9sj0d7.txt === reduce.pl bib === id = cord-275993-isff6lp2 author = Han, Dong P title = Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date = 2004-08-15 pages = extension = .txt mime = text/plain words = 5598 sentences = 308 flesch = 52 summary = Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. S-protein of coronaviruses, which is thought to function as a trimer (Delmas and Laude, 1990) , is responsible for both binding to cellular receptors and inducing membrane fusion for virus entry into target cells (Collins et al., 1982; Godet et al., 1994; Kubo et al., 1994) . Despite difficulties in detecting S-protein directly by immunoassays, proteins expressed from both pcDNA-S and pHCMV-S constructs were able to pseudotype MuLV particles to produce SARS pseudoviruses that could readily infect Vero E6 cells (Fig. 3A) . To assess whether SARS pseudoviruses we generated could be used to quantify virus-neutralizing antibodies, we examined their susceptibility to convalescent sera from SARS-CoV-infected patients. Pseudotyping of murine leukemia virus with the envelope glycoproteins of HIV generates a retroviral vector with specificity of infection for CD4-expressing cells cache = ./cache/cord-275993-isff6lp2.txt txt = ./txt/cord-275993-isff6lp2.txt === reduce.pl bib === id = cord-276345-xsjh3766 author = Arshad, Yasir title = Detection of SARS-CoV-2 in ophthalmic secretions in Pakistan: A preliminary report date = 2020-08-25 pages = extension = .txt mime = text/plain words = 667 sentences = 54 flesch = 62 summary = All 35 oropharyngeal swab samples were detected positive for SARS CoV-2, however out of total 35 conjunctival swab samples, 3(8.5%) were detected positive by using real-time RT-PCR. There was no ocular manifestation observed among patients with positive conjunctival specimens and similar information has already been reported by the previous study [4] . Results of the present study support the evidence that ophthalmic secretions may not be the main source of transmission for the novel SARS-CoV-2, but the role of eye in the transmission of this highly contagious virus must not be ignored. In 2004, SARScoronavirus was detected from tear samples in 37.5% positive cases and in another study, positivity of SARS-CoV-2 from conjunctival swabs was 16.6% which contributed to the evidence of eye as a carrier [6, 7] . SARS-CoV-2 in the ocular surface of COVID-19 patients. New evidence of SARS-CoV-2 transmission through the ocular surface. Evaluation of ocular symptoms and tropism of SARS-CoV-2 in patients confirmed with COVID-19 cache = ./cache/cord-276345-xsjh3766.txt txt = ./txt/cord-276345-xsjh3766.txt === reduce.pl bib === id = cord-276057-427ji6ze author = Effenberger, Maria title = Faecal calprotectin indicates intestinal inflammation in COVID-19 date = 2020-04-20 pages = extension = .txt mime = text/plain words = 907 sentences = 56 flesch = 52 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-RNA was detected in the faeces in ~50% of patients with COVID-19 3 5 6 ; SARS-CoV-2 viral particles were observed by electron microscopy in stool samples from two patients without diarrhoea 2 ; and one study reported SARS-CoV-2 infection of the oesophagus, stomach, duodenum and rectum. 7 In this pilot study, we explored a relation between GI symptoms, intestinal inflammation (determined by FC) and faecal SARS-CoV-2-RNA in hospitalised patients with COVID-19 who did not require intensive care measures. We report evidence that SARS-CoV-2 infection in patients with COVID-19 indeed instigates an inflammatory response in the gut, as evidenced by diarrhoea, elevated FC (largely expressed by neutrophil granulocytes 7 ) and a systemic IL-6 response. Faecal SARS-CoV-2 RNA was not detected during acute diarrhoea but could be detected in asymptomatic patients with or without previous diarrhoeal symptoms. cache = ./cache/cord-276057-427ji6ze.txt txt = ./txt/cord-276057-427ji6ze.txt === reduce.pl bib === id = cord-275846-7onenxg7 author = Kamikubo, Yasuhiko title = Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2 date = 2020-03-27 pages = extension = .txt mime = text/plain words = 2302 sentences = 150 flesch = 62 summary = Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here, we developed the world's first influenza-based epidemiological method as a useful proxy to detect the spread of SARS-CoV-2 and the establishment of partial herd immunity in countries. These results prompted us to hypothesize that (i) S type SARS-CoV-2 exit Wuhan or other epicenter in China earlier than L type virus without recognition by infectious disease surveillance systems of China and other countries; (ii) the infection by S type induced herd immunity that provides at least partial protection against spread of SARS-CoV-2. cache = ./cache/cord-275846-7onenxg7.txt txt = ./txt/cord-275846-7onenxg7.txt === reduce.pl bib === id = cord-275926-rj23z7po author = Fontanella, Marco M. title = Neurosurgical practice during the SARS-CoV-2 pandemic: a worldwide survey date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4013 sentences = 234 flesch = 52 summary = 3. Institutional plans for the SARS-CoV-2 outbreak: any special measures adopted for SARS-CoV-2 positive neurosurgical patients were investigated, i.e. their screening rate and method, any changes in surgical indications, planning and activity for oncologic procedures, non-emergency surgeries, and subarachnoid hemorrhages (SAHs). The same correlation was found with regards to the medical perception of disease activity (Q2) in different countries, and only few respondents (3%) claimed their country was not facing the outbreak during the time period studied: among them, neurosurgeons from Germany were probably the most "wrong", since their country had between 10 4 to 10 5 SARS-CoV2 patients during the study period (Fig. 4A) . 5 India and Pakistan have been reported to be the world's best respondents to the SARS-COV-2 pandemic, 22-24 thus reflecting high rates of neurosurgical activity reorganizations. cache = ./cache/cord-275926-rj23z7po.txt txt = ./txt/cord-275926-rj23z7po.txt === reduce.pl bib === id = cord-276058-1mpp7sbt author = Shlomai, A. title = Global versus focused isolation during the SARS-CoV-2 pandemic-A cost-effectiveness analysis date = 2020-04-01 pages = extension = .txt mime = text/plain words = 3798 sentences = 232 flesch = 56 summary = Objective: To compare the cost-effectiveness of global isolation of the whole population to focused isolation of individuals at high risk of being exposed, augmented by thorough PCR testing. We used R0=2.4 (range 1.4-3.9) (13), we assumed that the recovery time is 26 days, thus the transmission rate from infected (carrier) patients to susceptible population (β) was 0.09 (range 0.031 to 0.186)(13). In strategy 1, r1_HR_c represents the proportion of the population under relaxed isolation due to a high risk of contact with SARS-CoV-2 patients (0.7%). We next tested our model with a strategy of strict isolation of all infected individuals, relaxed isolation for two weeks of the high-risk group and a global quarantine of the susceptible population (strategy 1). https://doi.org/10.1101/2020.03.30.20047860 doi: medRxiv preprint each high-risk individual during the 14 days of isolation, and therefore ~10,000-15,000 tests will be needed daily for a country the size of Israel. cache = ./cache/cord-276058-1mpp7sbt.txt txt = ./txt/cord-276058-1mpp7sbt.txt === reduce.pl bib === id = cord-276139-l13hbucu author = Hashem, A. M. title = Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients date = 2020-09-23 pages = extension = .txt mime = text/plain words = 4628 sentences = 272 flesch = 57 summary = Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Here, we studied the kinetics of SARS-CoV-2 specific antibodies to S1 and N viral proteins in blood samples collected between 4 to 70 days post-symptoms onset from a cohort of 87 COVID-19 patients with different disease presentations (i.e. mild, moderate or severe) or outcomes (i.e. survival vs death). Comparing the kinetics of antibody response in COVID-19 patients who had fatal outcomes to those who survived the infection also showed that early induction of anti-N IgG and IgM during the first 15 days post-disease onset is indicative of fatal outcomes (Figure 4c) . In this study we studied the characteristics and kinetics of SARS-CoV-2 specific antibody response (nAbs, IgG and IgM) in a series of serum samples collected from a total of 87 confirmed COVID-19 hospitalized patients over a period of 70 days post-symptoms onset. cache = ./cache/cord-276139-l13hbucu.txt txt = ./txt/cord-276139-l13hbucu.txt === reduce.pl bib === id = cord-276017-2375ipkk author = Chen, Dongsheng title = Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date = 2020-06-14 pages = extension = .txt mime = text/plain words = 4132 sentences = 365 flesch = 70 summary = Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Previous studies have proposed that animal tissues show high heterogeneity in terms of cellular composition and gene expression profiles 15 , and ACE2 is only expressed in a small proportion of specific cell populations 16 , making single cell analysis of SARS-CoV-2 target cells an attracting field to investigate. Here, we constructed the single cell atlas for livestock, poultry, pets and wildlife, then screened putative SARS-CoV-2 target cells (indicated by the co-expression patterns of SARS-CoV-2 entry receptor ACE2 and SARS-CoV-2 entry activator TMPRSS2) and systematically evaluated their susceptibility, with the aim to understand the virus transmission routes and provide clues to fight against COVID-19. cache = ./cache/cord-276017-2375ipkk.txt txt = ./txt/cord-276017-2375ipkk.txt === reduce.pl bib === id = cord-276013-8dhqa2gj author = Luo, Yung-Hung title = Overview of coronavirus disease 2019: Treatment updates and advances date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3764 sentences = 232 flesch = 47 summary = 7, 11 Patients with severe symptoms may have unfavorable disease Abstract: In late December 2019, several cases of pneumonia with unknown cause were reported in Wuhan, China, and this new type of pneumonia spread rapidly to across provinces during the subsequent weeks. Clinical trials on baricitinib demonstrated at least some effects in selective patient populations with COVID-19 acute respiratory disease. On March 17, 2020, the National Medical Products Administration of China approved favipiravir as the first coronavirus drug with evidence from clinical trials showing efficacy for the treatment of COVID-19 infection. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-276013-8dhqa2gj.txt txt = ./txt/cord-276013-8dhqa2gj.txt === reduce.pl bib === id = cord-275858-46jzw94p author = Leung, Janice M. title = COVID-19 and COPD date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3024 sentences = 166 flesch = 42 summary = Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study Risk factors associated with clinical outcomes in 323 COVID-19 hospitalized patients in Wuhan, China Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: a retrospective single center analysis A preliminary study on serological assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 238 admitted hospital patients Epidemiological, clinical, and virological characteristics of 465 hospitalized cases of coronavirus disease 2019 (COVID-19) from Zhejiang province in China. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China cache = ./cache/cord-275858-46jzw94p.txt txt = ./txt/cord-275858-46jzw94p.txt === reduce.pl bib === id = cord-276394-s9y11oep author = Liang, W. title = Hindsight: A re-analysis of the severe acute respiratory syndrome outbreak in Beijing date = 2007-10-31 pages = extension = .txt mime = text/plain words = 2970 sentences = 140 flesch = 54 summary = Summary Objective To review the severe acute respiratory syndrome (SARS) epidemic in Beijing using basic epidemiological principles omitted from the original analysis. Previously excluded cases were included for plotting on an epidemic curve, and basic spot mapping for distribution of cases was used from attack rates recalculated for age, gender, occupation, residential location, date of onset of illness and demographics. If a spot map of incidence density rates was used during the early phase of the outbreak, the inner city might have been identified as a major risk factor requiring rapid quarantining. 8 Re-analysis included an epidemic curve for 'probable' SARS cases only and calculations of the Beijing population-based rate, stratified by age and sex, using the Fifth General Census of China (version 2000). The import phase of the Beijing epidemic occurred rapidly, between 1 and 10 March, with 14 cases admitted with an acute pneumonia of unknown cause without history taken for exposure to a case of respiratory illness or environmental contact. cache = ./cache/cord-276394-s9y11oep.txt txt = ./txt/cord-276394-s9y11oep.txt === reduce.pl bib === id = cord-276090-n8c2jpr6 author = Patel, Hiren N. title = Cerebellar Infarction Requiring Surgical Decompression in patient with COVID 19 Pathological Analysis, Brief Review date = 2020-07-29 pages = extension = .txt mime = text/plain words = 2871 sentences = 162 flesch = 41 summary = CONCLUSION: A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. angiography, CXR denotes chest X-ray, FiO2 denotes fraction of inspired oxygen, SARS-COV-2 denotes severe acute respiratory syndrome coronavirus 2, STAT denotes statum which is Latin meaning immediately, t-PA denotes tissue plasminogen activator, WHO denotes World Health Organization. A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. COVID-19 complicated with cerebral and large vessel vasculitis and its treatment will require a need for randomized clinical trials showing benefit in outcomes and mortality. This is a report of a patient with COVID-19 immune dysregulation who developed an acute cerebellar ischemic stroke secondary to vertebral artery thrombosis. cache = ./cache/cord-276090-n8c2jpr6.txt txt = ./txt/cord-276090-n8c2jpr6.txt === reduce.pl bib === id = cord-275978-pezm1tnw author = Riccardo, Flavia title = Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic date = 2020-04-11 pages = extension = .txt mime = text/plain words = 5549 sentences = 310 flesch = 55 summary = Methods We analysed data from the national case-based integrated surveillance system of all RT-PCR confirmed COVID-19 infections as of March 24th 2020, collected from all Italian regions and autonomous provinces. However, once interventions are introduced or the susceptibility in the population decreases, the transmission potential at a given time t is measured as the net reproduction number Rt. In this paper, we estimated both R0 and Rt for Italian regions in different epidemiological situations (high, intermediate and low age-adjusted attack rates), selected among those with highest data robustness. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. cache = ./cache/cord-275978-pezm1tnw.txt txt = ./txt/cord-275978-pezm1tnw.txt === reduce.pl bib === id = cord-276034-a8pixbuc author = Zhi, Yan title = Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein date = 2005-04-25 pages = extension = .txt mime = text/plain words = 6210 sentences = 298 flesch = 49 summary = Overlapping peptides were used to identify major histocompatibility complex class I-restricted epitopes in mice immunized with vectors encoding codon-optimized SARS-CoV spike protein. The optimized recombinant adenoviral vaccine vectors encoding spike can generate robust antigen-specific cellular immunity in mice and may potentially be useful for control of SARS-CoV infection. Therefore, several versions of replication-defective adenoviral vectors expressing spike protein were created to induce spike-specific T cell responses in mice and to screen for CD8 T-cell epitopes using an overlapping peptide library spanning the entire spike protein in IFN-g ELISPOT and intracellular IFN-g staining assays. More importantly, a single administration of the optimized SARS-CoV spike vaccine vectors based on replication-defective human and simian adenovirus can generate strong spikespecific CD8 T-cell responses in mice. More importantly, a single administration of an optimized SARS-CoV spike vaccine vector based on a replication-defective simian adenovirus can generate strong spike-specific CD8 T-cell responses in mice. cache = ./cache/cord-276034-a8pixbuc.txt txt = ./txt/cord-276034-a8pixbuc.txt === reduce.pl bib === id = cord-276267-77903fld author = Al‐Ani, Aysha H. title = Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5481 sentences = 355 flesch = 42 summary = 6 Consequently, there is a concern that IBD patients are at greater risk of developing COVID-19 and at increased risk of progressing to a more severe clinical course or even death compared to the general population. 18 Furthermore, there is a recent case report of a possible SARS-CoV-2 gastrointestinal infection causing acute haemorrhagic colitis and signalling COVID-19 disease. Clinical assessment of risk factors for infection in inflammatory bowel disease patients Protection of 318 inflammatory bowel disease patients from the outbreak and rapid spread of COVID-19 infection in Wuhan Risk of infection with methotrexate therapy in inflammatory diseases: a systematic review and meta-analysis Comparative risk of serious infections with biologic and/or immunosuppressive therapy in patients with inflammatory bowel diseases: a systematic review and meta-analysis Infection-related hospitalizations are associated with increased mortality in patients with inflammatory bowel diseases Respiratory tract infections in patients with inflammatory bowel disease: safety analyses from vedolizumab clinical trials cache = ./cache/cord-276267-77903fld.txt txt = ./txt/cord-276267-77903fld.txt === reduce.pl bib === id = cord-276335-e1xlwcvc author = Poh, W.P. title = Characterization of cytotoxic T‐lymphocyte epitopes and immune responses to SARS coronavirus spike DNA vaccine expressing the RGD‐integrin‐binding motif date = 2009-05-27 pages = extension = .txt mime = text/plain words = 6046 sentences = 326 flesch = 52 summary = Significant cell‐mediated immune responses were characterized by cytotoxic T‐lymphocyte (51)Cr release assay and interferon‐gamma secretion ELISPOT assay against RMA‐S target cells presenting predicted MHC class I H2‐Kb epitopes, including those spanning residues 884–891 and 1116–1123 within the S2 subunit of SARS‐CoV spike protein. The production of antigen-specific antibody induced by the SARS-CoV spike DNA vaccinations was assessed For the MHC-peptide binding assay, the mean fluorescence increase (MFI) was calculated as the ratio of the fluorescence of peptide-loaded RMA-S cells to the fluorescence of unloaded RMA-S cells. Mouse IFN-g ELISPOT for splenocytes of C57BL/6 mice immunized with selected S-His and S-RGD/His DNA vaccines to confirm T-cell epitopes of spike protein. This study demonstrated that prime-boost immunization of mice with SARS-CoV spike DNA vaccine constructs S-His and S-RGD/His induced significant antigen-specific cellular immune responses, IFN-g stimulation, and CTL activation. cache = ./cache/cord-276335-e1xlwcvc.txt txt = ./txt/cord-276335-e1xlwcvc.txt === reduce.pl bib === id = cord-276147-30buoweg author = Avancini, Joao title = Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil date = 2020-09-15 pages = extension = .txt mime = text/plain words = 278 sentences = 25 flesch = 61 summary = authors: Avancini, Joao; Miyamoto, Denise; Arnone, Marcelo; Villas-Boas Gabbi, Tatiana; Ferreira, Paula Silva; Neta, Cyro Festa; Sanches, Jose Antonio title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil cord_uid: 30buoweg Contents of the manuscript have not been previously published and are not currently submitted elsewhere. All listed authors have seen and approved of the manuscript and will sign off on any subsequent manuscript revisions. To the editor: We read with interest the letters from the New York City report regarding the absence of COVID toes lesions on their patients and the recommendation of caution when concluding that cutaneous findings are specifically due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cutaneous manifestations in patients with COVID-19: a preliminary review of an emerging issue Classification of the cutaneous manifestations of COVID-19: a rapid prospective nationwide consensus study in Spain with 375 cases cache = ./cache/cord-276147-30buoweg.txt txt = ./txt/cord-276147-30buoweg.txt === reduce.pl bib === id = cord-276132-tv5y1eqc author = Ray, Upasana title = COVID-19: The Impact in Oncology Care date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5696 sentences = 243 flesch = 39 summary = The COVID-19 pandemic has imposed a critical challenge to the current oncology care and practices including late diagnoses, delayed anti-cancer treatment, and static clinical trials. Delaying anti-cancer treatment in the ongoing pandemic cannot be recommended as a sensible choice to reduce the associated infection risk in patients. The American Society of Clinical Oncology (ASCO) recommends that in cancer patients diagnosed with the infection, the immunosuppressive therapies should be withheld until the symptoms resolve like complete remission of fever without use of antipyretics along with a negative COVID-19 test. Nevertheless, contact limitation and physical distancing guidelines continue to be an important part of the cancer treatment strategies during the pandemic in order to protect the patients, health-care personnel and non-COVID-19 patients being treated in the same organization. A practical approach to the management of cancer patients during the novel coronavirus disease 2019 (COVID-19) pandemic: an international collaborative group Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan cache = ./cache/cord-276132-tv5y1eqc.txt txt = ./txt/cord-276132-tv5y1eqc.txt === reduce.pl bib === id = cord-276316-7ot9ds34 author = Lei, Chunliang title = Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China date = 2020-10-14 pages = extension = .txt mime = text/plain words = 2375 sentences = 160 flesch = 57 summary = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in respiratory tract, blood samples and digestive tract was detected and lymphocyte subsets were tested periodically. 270 patients were detected for SARS-CoV-2 RNA in anal swabs and/or blood samples, and the overall positive rate was 23.0 % (62/270), higher in severe/critical cases than in mild/moderate cases (52.0 % vs. Detectable SARS-CoV-2 RNA in anal swabs and/or blood samples, as well as higher CD4/CD8 ratio were independent risk factors of respiratory failure and ICU admission. A total of 270 patients were detected for SARS-CoV-2 RNA in anal swabs J o u r n a l P r e -p r o o f 8 / 25 and/or blood samples, and the overall positive rate was 23.0% (62/270), higher in severe/critical cases than in mild/moderate cases (52.0% vs. cache = ./cache/cord-276316-7ot9ds34.txt txt = ./txt/cord-276316-7ot9ds34.txt === reduce.pl bib === id = cord-276487-8vkrh70j author = Kang, Sisi title = Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4092 sentences = 248 flesch = 52 summary = title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2. In this study, we report the crystal structure of SARS-CoV-2 nucleocapsid N-terminal domain (termed as SARS-CoV-2 N-NTD) as a model for understanding the molecular interactions that govern SARS-CoV-2 N-NTD binding to ribonucleotides. Since full-length SARS-CoV-2 N protein aggregated status were found in our expression and purification studies (Supporting Information Fig. S2 ), as well as previously reported data on other coronavirus nucleocapsid protein, we next investigated the structural studies on N-terminal region of SARS-CoV-2 N protein (termed as SARS-CoV-2 N-NTD). cache = ./cache/cord-276487-8vkrh70j.txt txt = ./txt/cord-276487-8vkrh70j.txt === reduce.pl bib === id = cord-276234-2nkeq4ud author = Siedlecki, Jakob title = COVID-19: Ophthalmological Aspects of the SARS-CoV 2 Global Pandemic date = 2020-05-06 pages = extension = .txt mime = text/plain words = 3702 sentences = 227 flesch = 46 summary = Indeed, ophthalmologists seem to rank among the medical specialties with the highest risk for COVID-19 infection, probably due to close patient contact during examination, e.g., at the slit lamp [4] , and possible conjunctival involvement during the course of the disease [5, 6] . In this paper, a systematic review of current COVID-19 literature relevant for ophthalmological practice is performed, with a special focus on modes of transmission, the prevention thereof, structural adjustments of clinical care required during the pandemic, and possible ocular manifestations of this novel disease. The novel coronavirus SARS-CoV 2, currently causing the COVID-19 pandemic, has severe implications for ophthalmologybe it because the eyes represent an important route of infection, most probably through lacrimal drainage into the nasal mucosa, or because of ocular manifestations, which, even if rather rare, can represent the first symptoms of this novel disease [29] . cache = ./cache/cord-276234-2nkeq4ud.txt txt = ./txt/cord-276234-2nkeq4ud.txt === reduce.pl bib === id = cord-276358-so390gp4 author = Nieto-Torres, Jose L. title = Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome date = 2015-11-30 pages = extension = .txt mime = text/plain words = 7169 sentences = 396 flesch = 49 summary = title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome In this report, we demonstrate that SARS-CoV E protein forms protein–lipid channels in ERGIC/Golgi membranes that are permeable to calcium ions, a highly relevant feature never reported before. Previously, we reported that SARS-CoV E protein showed mild selectivity for cations (Na þ and K þ ) when reconstituted in ERGIC/ Golgi membranes, mostly conferred by the negative charges of the lipids (Verdia-Baguena et al., 2012 . Synthetic peptides representing the full-length SARS-CoV E protein, or its transmembrane domain (amino acids 7-38) containing point mutations that inhibited ion channel activity (N15A and V25F), were generated by standard phase synthesis and purified by HPLC, as previously described (Verdia-Baguena et al., 2012) . Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis cache = ./cache/cord-276358-so390gp4.txt txt = ./txt/cord-276358-so390gp4.txt === reduce.pl bib === id = cord-276061-7b8h2sjw author = Zammit, M title = A rise in facial nerve palsies during the coronavirus disease 2019 pandemic date = 2020-10-01 pages = extension = .txt mime = text/plain words = 2478 sentences = 146 flesch = 56 summary = OBJECTIVE: An increase in spontaneous lower motor neuron facial nerve (VIIth cranial nerve) palsies was seen during the severe acute respiratory syndrome coronavirus 2 outbreak in our emergency clinic. • There was an increased incidence of spontaneous lower motor neuron facial nerve palsy in our emergency ENT clinic • Only two prior case reports have referenced an association between VIIth cranial nerve palsy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) • Facial nerve palsy incidence of 3.5 per cent was seen in clinic during 2020, 2.7 times higher than the previous year at 1.3 per cent • A SARS-CoV-2 incidence of 11.8 per cent was seen in our cohort, contrasting with that of the Liverpool population of 0.5 per cent • It is important for clinicians to be aware that facial nerve palsy may be an initial presentation of the disease cache = ./cache/cord-276061-7b8h2sjw.txt txt = ./txt/cord-276061-7b8h2sjw.txt === reduce.pl bib === id = cord-276350-lcl9jn35 author = Acharya, Dhiraj title = Dysregulation of type I interferon responses in COVID-19 date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1608 sentences = 83 flesch = 40 summary = In a mouse model of SARS-CoV infection, local IFN responses in the lungs were delayed relative to peak viral replication, which impeded virus clearance and was associated with the development of CRS 5 . By contrast, IFNAR inhibition enhanced the recruitment of neutrophils to the lungs in MERS-CoV-infected mice, leading to elevated production of pro-inflammatory cytokines 6 . While patients with severe COVID-19 showed profound depletion and functional exhaustion of NK cells 8 , it is unclear whether this NK cell dysfunction is due to dysregulation of IFN responses. It is thus tempting to speculate that the deficient or dysregulated IFN responses elicited by SARS-CoV-2 infection may influence the generation of T reg cells during the recovery phase of COVID-19. Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice cache = ./cache/cord-276350-lcl9jn35.txt txt = ./txt/cord-276350-lcl9jn35.txt === reduce.pl bib === id = cord-276209-5999g9gp author = Poland, Gregory A. title = Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine development date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1607 sentences = 105 flesch = 55 summary = Very soon thereafter, the causative agent was identified as the now-named SARS-CoV-2 virus-a betacoronavirus that had crossed the species barrier to infect humans. There is no question that a vaccine against this virus, and other as-yet-to-come coronaviruses, is imperative to protect human health and to quickly respond to future viral introductions, epidemics, and pandemics. These pathways, informed by science and the past history of successes and failures, are designed to maximize the chances of efficacy and safety. Further mutations could conceivably lead to issues of original antigenic sin with resultant disease enhancement after exposure or to vaccines that simply are not effective into the future. In addition to safety issues, I raise concern over ''S-only" vaccine approaches for the mid-to long-term control of this RNA virus. We need a vaccine-and we need it as quickly as one can be developed-that demonstrates safety and efficacy in adequately powered studies. cache = ./cache/cord-276209-5999g9gp.txt txt = ./txt/cord-276209-5999g9gp.txt === reduce.pl bib === id = cord-276784-8lmg97zc author = Boziki, Marina Kleopatra title = COVID-19 Immunopathology and the Central Nervous System: Implication for Multiple Sclerosis and Other Autoimmune Diseases with Associated Demyelination date = 2020-06-04 pages = extension = .txt mime = text/plain words = 4769 sentences = 225 flesch = 33 summary = Moreover, the management of chronic neurological diseases, such as Multiple Sclerosis (MS), underwent guided modifications, such as an Extended Interval Dose (EID) of Disease-Modifying Treatment (DMT) administration, in order to minimize patients' exposure to the health system, thus reducing the risk of SARS-CoV-2 infection. In this review, we summarize existing evidence of key immune pathways that the SARS-CoV-2 modifies during COVID-19 and the relevant implication for MS and other autoimmune diseases with associated demyelination (such as Systemic lupus erythematosus and Antiphospholipid syndrome), including the context of potential neuroinvasion by SARS-Cov-2 and the alterations that DMT induces to the immune system. In this respect, the clinical implication of SARS-CoV-2 infection in PwMS needs to be carefully evaluated in long-term prospective studies that assess not only physical disability measurements but also cognition, patient-reported outcomes, and quality of life, thus aiming to elucidate COVID-19-related long-term effects on MS-related neurological status and beyond. cache = ./cache/cord-276784-8lmg97zc.txt txt = ./txt/cord-276784-8lmg97zc.txt === reduce.pl bib === id = cord-276980-k8xi2zvh author = Koh, David title = Occupational Health Response to SARS date = 2005-01-17 pages = extension = .txt mime = text/plain words = 1120 sentences = 69 flesch = 48 summary = detected severe acute respiratory syndrome-associated coronavirus (SARS-CoV) from throat wash and saliva specimens and suggested that these specimens have advantages over other specimens, including ease of procurement and safety for medical personnel (1) . To the Editor: Severe acute respiratory syndrome (SARS), an occupational disease risk for healthcare workers, warrants an occupational health response, as clearly described by Esswein et al. The occupational health audits included site inspections and reviews of work processes of those areas where actual transmission of SARS had occurred and where triage of febrile patients was taking place. Occupational health physicians subsequently served on hospital SARS debriefing committees that reviewed institutional shortcomings and recommended new measures for future outbreaks. Clinical specimens were retrieved, and RT-PCR was performed to specifically amplify a genomic segment of SARS-CoV encompassing the deletion site. Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) cache = ./cache/cord-276980-k8xi2zvh.txt txt = ./txt/cord-276980-k8xi2zvh.txt === reduce.pl bib === id = cord-276995-b003vcdc author = Wiese, Andrew D title = Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date = 2020-06-20 pages = extension = .txt mime = text/plain words = 818 sentences = 54 flesch = 39 summary = And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. cache = ./cache/cord-276995-b003vcdc.txt txt = ./txt/cord-276995-b003vcdc.txt === reduce.pl bib === id = cord-276414-kicu0tv5 author = Bahadur Gurung, Arun title = In silico screening of FDA approved drugs reveals ergotamine and dihydroergotamine as potential coronavirus main protease enzyme inhibitors date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2423 sentences = 138 flesch = 58 summary = Interestingly, the anti-migraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. In the present study, we have explored the possibilities of FDA approved drugs as potential inhibitors of the coronavirus main protease, a therapeutically important drug target playing a salient role in the maturation and processing of the viral polyproteins and are vital for viral replication and transcription. Interestingly, the antimigraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. cache = ./cache/cord-276414-kicu0tv5.txt txt = ./txt/cord-276414-kicu0tv5.txt === reduce.pl bib === id = cord-276327-wyevh4xv author = Sheng, Calvin C title = Canakinumab to reduce deterioration of cardiac and respiratory function in SARS‐CoV‐2 associated myocardial injury with heightened inflammation (canakinumab in Covid‐19 cardiac injury: The three C study) date = 2020-08-24 pages = extension = .txt mime = text/plain words = 3239 sentences = 192 flesch = 37 summary = We designed a proof‐of‐concept randomized controlled trial to evaluate whether treatment with canakinumab prevents progressive respiratory failure and worsening cardiac dysfunction in patients with SARS‐CoV2 infection, myocardial injury, and high levels of inflammation. The three C Study is a prospective, IRB approved, blinded randomized-controlled Phase II study designed to evaluate whether treatment with canakinumab prevents progressive heart and respiratory failure in patients with Covid-19 associated myocardial injury and increased inflammation. This blinded randomized controlled trial is designed as a proof of concept study to demonstrate whether IL-1β antagonism can dampen the deleterious autoinflammatory response to SARS-CoV2 infection in patients with myocardial injury and heightened inflammation. In evaluating this hypothesis, the Three C study will help inform whether targeting inappropriate activation of the innate immune system should be investigated in larger clinical trials to improve survival in patients with Covid-19 and myocardial injury. cache = ./cache/cord-276327-wyevh4xv.txt txt = ./txt/cord-276327-wyevh4xv.txt === reduce.pl bib === id = cord-276769-th7iou21 author = Khan, Suliman title = Coronaviruses disease 2019 (COVID-19): causative agent, mental health concerns, and potential management options date = 2020-07-25 pages = extension = .txt mime = text/plain words = 3375 sentences = 173 flesch = 45 summary = Despite physical health consequences, COVID-19 pandemic has created stress and anxiety, as result there is an increased risk of mental illnesses both in the infected and normal individuals. Although bats are thought to be the source of origin for SARS-CoV-2, the intermediate animal that caused the transmission of virus to humans, is still unknown [3] . The individuals at higher risk of developing severe disease after contracting the infection should be give the priority for treatment and providing the mangeemtn and health servicesConsidering the importance of COVID-19 in the aspects of the asymptomatic spread of the virus and adverse health impacts, it is deemed necessary to investigate the factors associated with the rate of infectiousness and severity of symptoms. After originating in bats, SARS-CoV-2 emerged in Wuhan, spread all over the world through human to human transmission, and infected millions of individuals. cache = ./cache/cord-276769-th7iou21.txt txt = ./txt/cord-276769-th7iou21.txt === reduce.pl bib === id = cord-276820-l7bd5y8y author = So, Winnie K.W. title = The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong date = 2004-11-30 pages = extension = .txt mime = text/plain words = 4507 sentences = 225 flesch = 55 summary = authors: So, Winnie K.W.; Chan, Sophia S.C.; Lee, Angel C.K.; Tiwari, Agnes F.Y. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong Abstract The study aims to examine the knowledge and the practice of the precautionary measures taken by older adults in Hong Kong against the outbreak of severe acute respiratory syndrome (SARS). The aim of the study is to describe the knowledge about SARS and precautionary measures taken by older adults in Hong Kong. Understanding older adults' knowledge level and adherence to the government's recommended precautionary measures to prevent transmission of SARS is an essential step in being able to design similar promotion programmes for this population in the future. (1) What demographic variables influenced older adults' knowledge level, beliefs, and precautionary measures taken to prevent transmission of SARS? cache = ./cache/cord-276820-l7bd5y8y.txt txt = ./txt/cord-276820-l7bd5y8y.txt === reduce.pl bib === id = cord-276361-77cylm1o author = Yamamoto, Norio title = HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus date = 2004-06-04 pages = extension = .txt mime = text/plain words = 2267 sentences = 129 flesch = 55 summary = title: HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus Here we report that the HIV-1 protease inhibitor, nelfinavir, strongly inhibited replication of the SARS coronavirus (SARS-CoV). Experiments with various timings of drug addition revealed that nelfinavir exerted its effect not at the entry step, but at the post-entry step of SARS-CoV infection. We found that nelfinavir, a widely used HIV-1 protease inhibitor, could inhibit SARS-CoV replication efficiently. We screened our chemical library and found that nelfinavir could inhibit SARS-CoV replication in Vero E6 cells. Nelfinavir clearly inhibited the cytopathic effect (CPE) induced by infection with SARS-CoV (Fig. 1A) . Nelfinavir significantly inhibited SARS-CoV replication when used before infection (Figs. The other protease inhibitors including ritonavir had no effect on replication of SARS-CoV CC 50 , cytotoxic concentration of the compound that reduced cell viability to 50%. Our studies have clearly shown that nelfinavir can strongly inhibit the replication of SARS-CoV in Vero E6 cells. cache = ./cache/cord-276361-77cylm1o.txt txt = ./txt/cord-276361-77cylm1o.txt === reduce.pl bib === id = cord-276957-pk33dl8q author = Hu, Xuejiao title = Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5649 sentences = 287 flesch = 47 summary = To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. The detection results obtained using the RT-LAMP assay showed good concordance with those obtained using the RT-qPCR In Cohort I, 35 of 37 nasopharyngeal swabs from 24 COVID-19 patients were confirmed to be SARS-CoV-2 positive according to the criteria of RT-qPCR (28 samples) and NGS confirmation (7 samples) (see Table S3 in the supplemental material). Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on serial upper respiratory samples from an asymptomatic carrier, and the inconsistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. cache = ./cache/cord-276957-pk33dl8q.txt txt = ./txt/cord-276957-pk33dl8q.txt === reduce.pl bib === id = cord-276857-i948aq4b author = Chung, Grace TY title = A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date = 2005-10-18 pages = extension = .txt mime = text/plain words = 2331 sentences = 129 flesch = 50 summary = We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [8, 12] . In this study, we demonstrate the feasibility of the adoption of allelic discrimination assays based on the use of fluorogenic oligonucleotide probes for the genotyping of SARS-CoV isolates. Our study has clearly demonstrated the feasibility of using allelic discrimination assays as a method for genetic characterization of SARS-CoV genotypes in patients. Genotype of SARS-CoV culture isolates from 30 patients determined by Taqman Allelic Discrimination assays Petric M, Skowronski DM cache = ./cache/cord-276857-i948aq4b.txt txt = ./txt/cord-276857-i948aq4b.txt === reduce.pl bib === id = cord-276548-bh3w7oas author = Ramkumar, K. title = Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1114 sentences = 81 flesch = 51 summary = title: Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. Furthermore, SARS-CoV-2 infection reduces ACE2 expression and shifts cells to a more mesenchymal phenotype with loss of EPCAM and upregulation of ZEB1 and other EMT-associated genes. Methods: We analyzed mRNA expression of AXL and other TAM family members as well as angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor, in treatment-naïve (n¼1016) and previously treated (n¼239) NSCLC tumors and in a panel of NSCLC cell lines (n¼70). Notably, expression of ACE2 was downregulated while that of AXL and ZEB1, an EMT transcription factor, were upregulated in NSCLC cells infected with SARS-CoV-2 as compared to mock infected cells, suggesting a shift to a more mesenchymal phenotype. D. Gibbons: Advisory/Consultancy, Research grant/Funding (self Advisory/Consultancy: Synta; Research grant/Funding (self): Bayer. L.A. Byers: Advisory/Consultancy, Research grant/Funding (self cache = ./cache/cord-276548-bh3w7oas.txt txt = ./txt/cord-276548-bh3w7oas.txt === reduce.pl bib === id = cord-276403-yomjm2gg author = Woo, Patrick CY title = Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections date = 2006-10-30 pages = extension = .txt mime = text/plain words = 3636 sentences = 178 flesch = 50 summary = title: Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections In this review, these two severe zoonotic viral infections transmitted by the respiratory route, with pandemic potential, are used as models to illustrate the role of Chinese wet-markets in their emergence, amplification and dissemination. The outbreak of avian influenza A H5N1 virus human infections in Hong Kong in 1997, with 18 cases and six deaths [6] , serves as another excellent example to illustrate the role of Chinese wet-markets in the emergence of zoonotic severe respiratory viral infections (Fig. 4) . China, with one-quarter of the world's population, 16 of the 20 most polluted cities of the world and a huge diversity of animals closely associated with the human population, is one of the countries with the greatest potential for the emergence and spread of infectious diseases, such as SARS and avian influenza. cache = ./cache/cord-276403-yomjm2gg.txt txt = ./txt/cord-276403-yomjm2gg.txt === reduce.pl bib === id = cord-276870-gxtvlji7 author = Bobrowski, Tesia title = Learning from history: do not flatten the curve of antiviral research! date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5089 sentences = 219 flesch = 49 summary = Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. However, despite many experimental and clinical studies, no effective drugs or treatments have emerged to treat the previous six epidemics of bird flu, SARS, swine flu, MERS, Ebola, and Zika as well as, thus far, COVID-19. We evaluated the number of publications (in both peer-reviewed journals and ArXiv preprint servers) and the number of clinical trials performed over the course of the epidemic to estimate the engagement and success of the scientific community in response to the seven major outbreaks of the past two decades: bird flu, SARS, swine flu, MERS, Ebola, Zika, and COVID-19. cache = ./cache/cord-276870-gxtvlji7.txt txt = ./txt/cord-276870-gxtvlji7.txt === reduce.pl bib === id = cord-276481-os1nf3cs author = Ishizaki, Tatsuro title = Estimation of the impact of providing outpatients with information about SARS infection control on their intention of outpatient visit date = 2004-09-30 pages = extension = .txt mime = text/plain words = 4930 sentences = 171 flesch = 38 summary = Abstract To examine the effect of provision of information about the infection control in the specific infection disease treatment unit in a city hospital on the outpatient's intention of outpatient service use, respondents who underwent outpatient medical care at the hospital (N = 821) were asked whether or not they intended to continue the outpatient visit at the hospital if a severe acute respiratory syndrome (SARS) patient was admitted to the unit. This study examined the effect of providing outpatients with information about SARS infection control in the infectious disease treatment unit in a community hospital on their intention to continue outpatient visits, and estimated the cumulative total number of outpatients as well as the cumulative total expenditures for outpatient care at the hospital during a 180-day period after the admission of a SARS patient to the hospital. cache = ./cache/cord-276481-os1nf3cs.txt txt = ./txt/cord-276481-os1nf3cs.txt === reduce.pl bib === id = cord-276908-9jthjf24 author = Gupta, Akanksha title = COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date = 2020-07-06 pages = extension = .txt mime = text/plain words = 5174 sentences = 385 flesch = 57 summary = In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. cache = ./cache/cord-276908-9jthjf24.txt txt = ./txt/cord-276908-9jthjf24.txt === reduce.pl bib === id = cord-276402-ymxvtyll author = Wei, Jia title = SARS-CoV-2 infection in immunocompromised patients: humoral versus cell-mediated immunity date = 2020-07-29 pages = extension = .txt mime = text/plain words = 3517 sentences = 212 flesch = 49 summary = BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic placed unprecedented pressure on various healthcare systems, including departments that use immunotherapies such as chimeric antigen receptor (CAR) T-cell therapy and immunosuppression therapy in organ transplantation units. The true impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on immunocompromised CAR T-cell therapy recipients and kidney transplant recipients (KTRs) has not yet been established. His virus clearance failure and life-threating cytokine storm during SARS-CoV-2 infection suggested that any decision to proceed CAR T-cell therapy during COVID-19 pandemics will require extensive discussion of potential risks and benefits. 3 Coronavirus disease 2019 (COVID-19) is a heterogeneous disease population, of which most patients exhibit mild to moderate symptoms, however approximately 15% progress to severe pneumonia, while 5% were eventually admitted to intensive care units (ICU) due to the resultant acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure. cache = ./cache/cord-276402-ymxvtyll.txt txt = ./txt/cord-276402-ymxvtyll.txt === reduce.pl bib === id = cord-277076-yvsyo4l9 author = Berger, A. title = SARS date = 2019-09-12 pages = extension = .txt mime = text/plain words = 4349 sentences = 215 flesch = 45 summary = Measures including source isolation of patientswho only became infectious after onset of clinical symptomsstrict infection control in health care facilities, timely identification and quarantining of exposed contacts, and perhaps also measures to increase social distance, such as travel warnings and screening of travelers, had led to this remarkable and remarkably rapid success. A further, small SARS outbreak occurred again in Guangdong in late 2003/early 2004; molecular analysis of virus isolates from human cases and animals sampled at the same place and time confirmed that this was zoonotically acquired from Paguma larvata. The laboratory diagnosis of SARS remains a challenge; in fact, despite the rapid identification of SARS-CoV as the etiological agent, testing contributed little to the successful control of the 2003 outbreak. A negative antibody test result later than 21 days after the onset of illness is likely to indicate that no infection with SARS-CoV has taken place. cache = ./cache/cord-277076-yvsyo4l9.txt txt = ./txt/cord-277076-yvsyo4l9.txt === reduce.pl bib === id = cord-276991-gv1k7u7j author = Zhang, Xu title = Strategies to trace back the origin of COVID-19 date = 2020-04-08 pages = extension = .txt mime = text/plain words = 745 sentences = 49 flesch = 58 summary = The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2, had raised great concern. Chinese authorities originally announced that the first infection case was reported on December 31, 2019, and many of the initial cases were linked directly to Huanan seafood market in Wuhan, in the Hubei province. The hypothesis that the outbreak originated at the market, with its initial transmission from live animals to human beings followed by rapid human-to-human transmission, is suggested to be most likely and convincing. Emergence of SARS-like coronavirus poses new challenge in China Novel coronavirus disease (Covid-19): the first two patients in the UK with person to person transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Emergence of SARS-like coronavirus in china: an update cache = ./cache/cord-276991-gv1k7u7j.txt txt = ./txt/cord-276991-gv1k7u7j.txt === reduce.pl bib === id = cord-276969-mdry8qzv author = Chirumbolo, Salvatore title = Might the many positive COVID19 subjects in Italy have been caused by resident bat‐derived zoonotic β‐coronaviruses instead of the Wuhan (China) outbreak? date = 2020-03-27 pages = extension = .txt mime = text/plain words = 865 sentences = 57 flesch = 50 summary = Might the many positive COVID19 subjects in Italy have been caused by resident bat-derived zoonotic β-coronaviruses instead of the Wuhan (China) outbreak? The same authors concluded that the SARS-CoV2 in Italy might be present at least since September and October 2019, much before the claimed Wuhan outbreak. Questions may be raised, therefore, if, taking into account the genomic distance (or similarity) and the RNA-virus mutation rate, the "Italian" SARS-CoV2 might be the evolutionary balanced genotype (or strain) from a resident zoonotic spillover. 3 This should suggest that the cross-talk between evolution and epidemiology is closely intertwined, causing that the maintenance of an onward transmission might be crucially asThe issue of human coronaviruses virulence was recently addressed for SARS-CoV and MERS-CoV and some reports have outlined the role of coronavirus E protein in triggering an inflammatory response, cytokine storm, and/or inhibition of the innate immunity with dampening Th1 interferon-γ signaling. cache = ./cache/cord-276969-mdry8qzv.txt txt = ./txt/cord-276969-mdry8qzv.txt === reduce.pl bib === id = cord-277014-iz8jo44e author = Hu, Weihua title = Disorders of sodium balance and its clinical implications in COVID-19 patients: a multicenter retrospective study date = 2020-10-16 pages = extension = .txt mime = text/plain words = 3643 sentences = 202 flesch = 43 summary = This study indicates that severity of the disease, the length of stay in the hospital of surviving patients, and mortality were higher among COVID-19 patients with sodium balance disorders. CONCLUSION: Sodium balance disorder, particularly hyponatremia, is a common condition among hospitalized patients with COVID-19 in Hubei, China, and it is associated with a higher risk of severe illness and increased in-hospital mortality. reported hyponatremia to be much common (50%) amongst hospitalized COVID-19 patients in the United States [13] , and recently study further suggested that serum sodium concentration was inversely correlated with IL-6, and hyponatremia was associated with a more severe outcome of COVID-19 disease [14] . The associative disorders of serum sodium balance, their clinical characteristics, severity, and outcomes in SARS-CoV-2 infected patients have not been established. It was revealed that disease severity, the length of hospital stay for surviving patients, and mortality were high among COVID-19 patients with sodium balance disorders. cache = ./cache/cord-277014-iz8jo44e.txt txt = ./txt/cord-277014-iz8jo44e.txt === reduce.pl bib === id = cord-276493-hoaxv5e0 author = Jeong, Gi Uk title = Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5687 sentences = 363 flesch = 56 summary = With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. cache = ./cache/cord-276493-hoaxv5e0.txt txt = ./txt/cord-276493-hoaxv5e0.txt === reduce.pl bib === id = cord-277239-cedoi5jr author = Bray, R. A. title = Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4446 sentences = 246 flesch = 50 summary = This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. The data demonstrate that while most individuals have significant IgG responses to community coronaviruses, all pre-COVID-19 samples tested negative against the SARS-CoV-2 targets as well as to SARS and MERS S1 proteins. . https://doi.org/10.1101/2020.09.02.20185199 doi: medRxiv preprint multiplexed, solid phase assay compared to other platforms (e.g., ELISA) include the ability to assay multiple viral targets simultaneously (and thereby provide internal assay controls for coronavirus specificity), the capacity to incorporate additional SARS-CoV-2 proteins in the future, a relatively short assay time, high throughput and semiquantitative assessment of the antibody response. cache = ./cache/cord-277239-cedoi5jr.txt txt = ./txt/cord-277239-cedoi5jr.txt === reduce.pl bib === id = cord-276619-6ndkz1da author = Perrone, Serafina title = Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum date = 2020-06-02 pages = extension = .txt mime = text/plain words = 912 sentences = 68 flesch = 56 summary = title: Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum Lack of viral transmission to preterm newborn from a COVID-19 positive breastfeeding mother at 11 days postpartum In this paper, we reported the case of a mother who presented clinical symptoms of respiratory tract infection 10 days after the spontaneous delivery of a preterm newborn. Since birth, the newborn was fed with both breastfeeding and expressed maternal milk, and received Kangaroo Mother Care sessions. Postnatal horizontal COVID-19 infection occurred in newborns but expressed breast milk analysis did not reveal traces of the virus, so breastfeeding continued and the dyad was not separate. 9, 10 Here we describe a case of preterm baby breastfeeding mother at 11 days postpartum COVID-19 affected, in a NICU setting. Clinical characteristics of novel coronavirus disease 2019 (COVID-19) in newborns, infants and children cache = ./cache/cord-276619-6ndkz1da.txt txt = ./txt/cord-276619-6ndkz1da.txt === reduce.pl bib === id = cord-276874-9rjbmsvb author = Ng, M.L. title = Topographic Changes in SARS Coronavirus–infected Cells at Late Stages of Infection date = 2004-11-17 pages = extension = .txt mime = text/plain words = 3172 sentences = 188 flesch = 52 summary = Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome–associated coronavirus at the cell surface. Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome-associated coronavirus at the cell surface. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. The aim of this study was to use scanning electron and atomic force microscopes to investigate changes in the surface topography of SARS-CoV-infected cells at late infection. Scanning electron microscopy of Vero E6 cells infected with severe acute respiratory syndrome-associated coronavirus at 24 h after infection. cache = ./cache/cord-276874-9rjbmsvb.txt txt = ./txt/cord-276874-9rjbmsvb.txt === reduce.pl bib === id = cord-276797-86hc3lbi author = Jamieson, Denise J. title = Emerging infectious disease outbreaks: Old lessons and new challenges for obstetrician-gynecologists date = 2006-06-30 pages = extension = .txt mime = text/plain words = 7263 sentences = 417 flesch = 50 summary = Objective The purpose of this study was to summarize 3 recent high-profile infectious disease threats that have affected the United States: severe acute respiratory syndrome, West Nile virus, and anthrax. Results The 3 emerging infectious diseases pose very different threats: Severe acute respiratory syndrome is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. This systematic review summarizes 3 recent, highprofile infectious disease threats that have affected the United States: (1) SARS, (2) West Nile virus, and (3) anthrax. The 3 emerging infectious disease threats that are described in this systematic review pose very different and novel health threats: SARS is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. cache = ./cache/cord-276797-86hc3lbi.txt txt = ./txt/cord-276797-86hc3lbi.txt === reduce.pl bib === id = cord-277197-njy99jh4 author = Song, Fang title = COVID‐19: Recommended sampling sites at different stage of the disease date = 2020-04-16 pages = extension = .txt mime = text/plain words = 545 sentences = 45 flesch = 49 summary = At present, it mainly relies on Real‐time RT‐PCR to detect SARS‐CoV‐2 virus nucleic acid collected from the clinical specimens of patients as the standard for diagnosis, discontinuation of quarantine and discharge.(1,2) This article is protected by copyright. 13 Different from the suspected cases with typical clinical characteristics, the diagnosis rate can be improved by detecting the nucleic acid in fecal samples, the latest discharge standards in China still requires only the collection of respiratory specimens 1 . But it has been emphasized in the discharge standard to collect "nasal swab, sputum" and other upper and lower respiratory tract specimens at the same Based on the improvement of clinical symptoms and CT imaging, the guidelines require only two consecutive negative nucleic acid tests (≥24 hours) before discharge can be considered. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan cache = ./cache/cord-277197-njy99jh4.txt txt = ./txt/cord-277197-njy99jh4.txt === reduce.pl bib === id = cord-277025-gmy51dx4 author = Pfefferle, Susanne title = Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date = 2020-06-04 pages = extension = .txt mime = text/plain words = 949 sentences = 59 flesch = 56 summary = title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany. A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China, as the alleged cause of a cluster of severe pneumonia cases (1) . Here, we describe the full-genome sequence of a SARS-CoV-2 strain (SARS-CoV-2/ human/DEU/HH-1/2020) isolated from a female patient with COVID-19. The isolate was obtained from an upper respiratory tract specimen (oropharyngeal swab) from a 62-year-old woman who was part of a small local cluster of COVID-19 cases, originating from a household contact who likely acquired the virus while traveling in Italy. The samples after trimming contained 18,369,904 high-quality paired-end reads, with 61,312 ϫ 2 reads (e.g., 122,624 reads) mapping to the reference Wuhan-Hu-1 sequence (GenBank accession number NC_045512.2) (6). cache = ./cache/cord-277025-gmy51dx4.txt txt = ./txt/cord-277025-gmy51dx4.txt === reduce.pl bib === id = cord-277278-lg38l5gh author = Tang, Olive title = Outcomes of nursing home COVID-19 patients by initial symptoms and comorbidity: Results of universal testing of 1,970 residents date = 2020-10-14 pages = extension = .txt mime = text/plain words = 2160 sentences = 125 flesch = 53 summary = Residents who were positive for COVID-19 and had multiple symptoms at the time of testing had the highest risk of mortality (HR 4.44; 95% CI: 2.97, 6.65) and hospitalization (SHR 2.38; 95% CI: 1.70, 3.33), even after accounting for comorbidity burden. Of 52 SARS-CoV-2 positive residents who were asymptomatic at the time of testing and were closely monitored for 14 days at one facility, only 6 (11.6%) developed symptoms. Conclusions and Implications Asymptomatic infection with SARS-CoV-2 in the nursing home setting was associated with increased risk of death suggesting a need for closer monitoring of these residents, particularly those with underlying cardiovascular and respiratory comorbidities. A 78 cohort of all residents at one facility who were asymptomatic at the time of testing were closely 79 monitored by nursing home staff for development of symptoms over a 14 day period; this was 80 documented in a dedicated line list and included as a sub-analysis. cache = ./cache/cord-277278-lg38l5gh.txt txt = ./txt/cord-277278-lg38l5gh.txt === reduce.pl bib === id = cord-276758-k2imddzr author = Siegel, Jane D. title = 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date = 2007-12-07 pages = extension = .txt mime = text/plain words = 46228 sentences = 2479 flesch = 35 summary = Activities currently assigned to ICPs in response to emerging challenges include (1) surveillance and infection prevention at facilities other than acute care hospitals (eg, ambulatory clinics, day surgery centers, LTCFs, rehabilitation centers, home care); (2) oversight of employee health services related to infection prevention (eg, assessment of risk and administration of recommended treatment after exposure to infectious agents, tuberculosis screening, influenza vaccination, respiratory protection fit testing, and administration of other vaccines as indicated, such as smallpox vaccine in 2003); (3) preparedness planning for annual influenza outbreaks, pandemic influenza, SARS, and bioweapons attacks; (4) adherence monitoring for selected infection control practices; (5) oversight of risk assessment and implementation of prevention measures associated with construction and renovation; (6) prevention of transmission of MDROs; (7) evaluation of new medical products that could be associated with increased infection risk (eg, intravenous infusion materials); (8) communication with the public, facility staff, and state and local health departments concerning infection control-related issues; and (9) participation in local and multicenter research projects. cache = ./cache/cord-276758-k2imddzr.txt txt = ./txt/cord-276758-k2imddzr.txt === reduce.pl bib === id = cord-276895-p85obwp2 author = Carriazo, Sol title = Kidney disease and electrolytes in COVID-19: more than meets the eye date = 2020-07-16 pages = extension = .txt mime = text/plain words = 3633 sentences = 197 flesch = 43 summary = The current issue of Clinical Kidney Journal presents 15 articles on COVID-19 and kidney disease from three continents, providing a global perspective of the impact of severe acute respiratory syndrome coronavirus 2 on electrolytes and different kidney compartments (glomeruli, tubules and vascular compartments) and presenting clinically as a syndrome of inappropriate antidiuretic hormone secretion, acute kidney injury, acute kidney disease, collapsing glomerulopathy and thrombotic microangiopathy, among others, in the context of a brand-new cardiorenal syndrome. The present issue of Clinical Kidney Journal (ckj) contains reports from the most affected countries (Figure 1 ) that illustrate the impact of SARS-CoV-2 on electrolytes and the kidneys, the different possibilities for acute renal replacement therapy (RRT) and the impact of COVID-19 in patients with pre-existing chronic kidney disease (CKD) and on chronic RRT, with emphasis on preventive measures and providing insights into therapy. cache = ./cache/cord-276895-p85obwp2.txt txt = ./txt/cord-276895-p85obwp2.txt === reduce.pl bib === id = cord-277210-xaj2623u author = Weinkove, Robert title = Managing haematology and oncology patients during the COVID‐19 pandemic: interim consensus guidance date = 2020-05-13 pages = extension = .txt mime = text/plain words = 6044 sentences = 315 flesch = 38 summary = • Adopt measures within cancer centres to reduce risk of nosocomial SARS-CoV-2 acquisition; support population-wide social distancing; reduce demand on acute services; ensure adequate staffing; and provide culturally safe care. Patients with cancer could be at elevated risk of severe COVID-19, while delivery of cancer therapies could be disrupted by quarantines, social distancing measures, and interruption of routine health care delivery by the pandemic. 38 Community spread of COVID-19 has the potential to diminish the donor pool, to threaten the capacity of cancer services to provide routine transfusion support, and to increase the risks that transfusion-dependent patients will come into contact with other individuals with SARS-CoV-2. We present interim guidance for clinicians caring for patients with cancer who may be particularly vulnerable both to severe COVID-19 and the potential impact of the pandemic on the provision of cancer investigations and treatment. cache = ./cache/cord-277210-xaj2623u.txt txt = ./txt/cord-277210-xaj2623u.txt === reduce.pl bib === id = cord-277357-lpurk7pe author = González-González, Everardo title = Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3999 sentences = 211 flesch = 49 summary = title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. cache = ./cache/cord-277357-lpurk7pe.txt txt = ./txt/cord-277357-lpurk7pe.txt === reduce.pl bib === id = cord-277110-e27lm7rr author = Iria, Neri title = Major cluster of pediatric “ true ” primary chilblains during the COVID‐19 pandemic: a consequence of lifestyle changes due to lockdown date = 2020-06-13 pages = extension = .txt mime = text/plain words = 2903 sentences = 181 flesch = 52 summary = We reported demographical, laboratory and clinical features, history of close contact with COVID‐19 patients, presence of similar skin lesions in other family members, precipitating and risk factors for chilblain onset. All rights reserved In April 2020, we observed a growing number of chilblain-like manifestations similar to coldinduced lesions during the pandemic, with the opportunity to study 8 cases, 2 children and 6 adolescents, and report here our results. The aim of this study is to verify whether the chilblain-like lesions were a cutaneous clue for SARS-CoV-2 infection or due to other causes. All rights reserved -PCR-assay on blood samples for Parvovirus B19 DNA and Enterovirus RNA -PCR-assay on skin biopsy for Parvovirus B19, Mycoplasma pneumoniae and SARS-CoV-2 was performed in a single patient (12.5%). Various cutaneous findings were observed in adults infected with COVID-19 and, simultaneously, a marked increase of chilblain-like lesions occurred worldwide among children during the COVID-19 pandemic 10, 11 In our cases we exclude SARS-CoV-2 infection. cache = ./cache/cord-277110-e27lm7rr.txt txt = ./txt/cord-277110-e27lm7rr.txt === reduce.pl bib === id = cord-277039-yo5ojr0s author = Mendenhall, Ian H. title = Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date = 2019-04-17 pages = extension = .txt mime = text/plain words = 2419 sentences = 133 flesch = 55 summary = In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. The zoonotic SARS-coronavirus (SARS-CoV) outbreak originated in southern China from horseshoe bats, where wet markets permitted atypical contact between species, including subsequent spillover to humans [9] . On the other hand, camels are the putative natural reservoir for MERS-coronavirus, although recent phylogenetic analysis indicated that bats harbor coronaviruses that are ancestral to the MERS-CoV lineage [11] . In this study, we collected fresh bat guano from three caves at different locations in Kazakhstan and conducted molecular screening for coronaviruses. To further understand the evolutionary relationships of these viruses, we analyzed novel bat coronavirus sequences in combination with 2811 RdRp sequences of coronavirus from different host species worldwide, representing the three genera: Alpha-, Beta-, and Gamma-coronaviruses. The Alpha-CoV genus comprises a large number of coronaviruses from diverse hosts, including bats, shrews, dogs, cats, ferrets, pigs, and humans. cache = ./cache/cord-277039-yo5ojr0s.txt txt = ./txt/cord-277039-yo5ojr0s.txt === reduce.pl bib === id = cord-277113-pykf7iw1 author = Wang, Xingyu title = The Clinical Features and Outcomes of Discharged Coronavirus Disease 2019 Patients：A Prospective Cohort Study date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3565 sentences = 232 flesch = 57 summary = By gathering detailed information of symptoms and treatments, reexamined outcomes, distribution of quarantine locations and close contact history post hospitalization, we aimed to track the course of clinical outcomes of COVID-19 patients after discharge, and to evaluate their transmissibility during the period of observation, therefore to make improvement on post-discharge management if necessary. All of the discharged COVID-19 patients met the discharge criteria as follows: afebrile for at least three days, respiratory symptoms significantly improved, improvement in the radiological abnormalities on chest radiograph or CT, and two consecutive negative SARS-CoV-2 tests more than 24 hours apart [6] . However, the clinical characteristics of Patient 2 was not in line with other 7 patients, who retested with positive SARS-CoV-2 but were only associated with mild symptoms as dry cough or intermittent fever and ultimately pronounced negative tests and improved chest CT during 4 weeks of follow-up period. cache = ./cache/cord-277113-pykf7iw1.txt txt = ./txt/cord-277113-pykf7iw1.txt === reduce.pl bib === id = cord-276630-qci7khki author = Lima, William Gustavo title = The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3727 sentences = 214 flesch = 49 summary = Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus. cache = ./cache/cord-276630-qci7khki.txt txt = ./txt/cord-276630-qci7khki.txt === reduce.pl bib === id = cord-277186-sj8ngpk8 author = He, Qigai title = Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA date = 2005-04-19 pages = extension = .txt mime = text/plain words = 4192 sentences = 234 flesch = 54 summary = Specific binding of the MAb S-A5D5 to both purified N195 and SARS CoV nucleocapsid antigen was effectively inhibited by human SARS positive serum and guinea pig anti-N195 serum. The monoclonal antibodies were characterized by SARS CoV-infected Vero cells and nucleocapsid-spike fusion protein-based IFA, Western blot, and N195 proteinbased ELISA. The isotype of the promising monoclonal antibody, designated as S-A5D5, was determined and was further applied to develop a specific and sensitive antigen capture ELISA for the detection of SARS CoV. The specific reactivity of the MAb S-A5D5 with purified N195 protein (Fig. 3A ) was identical to that of the human SARS positive serum (Fig. 3B) , while no reaction was observed when non-antibody secreting hybridoma was tested (Fig. 3C) . Therefore, this antigen capture ELISA, based on MAb to N protein, might provide a more sensitive method for early detection of SARS CoV infection. cache = ./cache/cord-277186-sj8ngpk8.txt txt = ./txt/cord-277186-sj8ngpk8.txt === reduce.pl bib === id = cord-277188-t33nw4zb author = Fang, Jie title = Efficacy of Early Combination Therapy With Lianhuaqingwen and Arbidol in Moderate and Severe COVID-19 Patients: A Retrospective Cohort Study date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4641 sentences = 227 flesch = 46 summary = RESULTS: The early combined usage of LHQW and Arbidol can significantly accelerate the recovery of patients with moderate COVID-19 by reducing the time to conversion to nucleic acid negativity, the time to chest CT improvement, and the length of hospital stay. One case report of four patients with mild or severe COVID-19 in Shanghai (China) found that combining antiviral drugs (lopinavir/ ritonavir or Arbidol) with TCM (Shufengjiedu capsule) resulted in a significant improvement in clinical symptoms . In conclusion, this retrospective study demonstrated that the early administration of LHQW + Arbidol combination therapy could significantly accelerate recovery in patients with moderate COVID-19 by reducing the time to conversion to nucleic acid Frontiers in Pharmacology | www.frontiersin.org September 2020 | Volume 11 | Article 560209 negativity, the time to chest CT improvement and the length of hospital stay. cache = ./cache/cord-277188-t33nw4zb.txt txt = ./txt/cord-277188-t33nw4zb.txt === reduce.pl bib === id = cord-277260-7se220oz author = Gosain, Rohit title = COVID-19 and Cancer: a Comprehensive Review date = 2020-05-08 pages = extension = .txt mime = text/plain words = 5926 sentences = 306 flesch = 39 summary = Since the emergence of the first case in Wuhan, China, in December 2019, tremendous research efforts have been underway to understand the mechanisms of infectivity and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a fatal virus responsible for abysmal survival outcomes. Data from China thus far have shown that cancer patients infected with COVID-19 are at 3.5 times the risk of requiring mechanical ventilation or ICU admission, compared to the general population [9•] . The CALAVI trial will be initiated as a randomized global clinical trial to assess the potential of acalabrutinib in the treatment of the cytokine storm associated with severely ill COVID-19 patients [86] . An exploratory meta-analysis of 32 studies showed evidence of reduced mortality after receiving various doses of convalescent plasma in patients with severe acute respiratory infections of viral etiology [92] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China cache = ./cache/cord-277260-7se220oz.txt txt = ./txt/cord-277260-7se220oz.txt === reduce.pl bib === === reduce.pl bib === id = cord-277137-k3jj5vom author = Anand, Praveen title = SARS-CoV-2 strategically mimics proteolytic activation of human ENaC date = 2020-05-26 pages = extension = .txt mime = text/plain words = 2707 sentences = 144 flesch = 53 summary = We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site, absent in any previous coronavirus sequenced, resulting in the striking mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). Although the furin-like cleavage motifs can be found in other viruses (Coutard et al., 2020) , the exact mimicry of human ENaC-a cleavage site raises the specter that SARS-CoV-2 may be hijacking the protease network of ENaC-a for viral activation. The overlap of the cell-types expressing ACE2 and ENaC-a, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. SARS-CoV-2 then exploits enzymes called proteases to cut, or cleave, its spikes at a specific site which allows the virus to infiltrate the host cell. show that the spike proteins on SARS-CoV-2 may have the same sequence of amino acids at its cut site as a human epithelial channel protein called ENaC-a. cache = ./cache/cord-277137-k3jj5vom.txt txt = ./txt/cord-277137-k3jj5vom.txt === reduce.pl bib === id = cord-277342-40d24mvm author = Chen, Yu title = SARS-CoV-2: virus dynamics and host response date = 2020-03-23 pages = extension = .txt mime = text/plain words = 804 sentences = 57 flesch = 53 summary = In The Lancet Infectious Diseases, Kelvin To and colleagues 4 report the viral load and antibody profiles of a cohort of 23 patients admitted to hospital with COVID-19. First, the high viral load during the early phase of illness suggests that patients could be most infectious during this period, and it might account for the high transmissibility of SARS-CoV-2. Second, age was associated with viral load in this study, which could explain the high degree of severe disease in older patients with SARS-CoV-2. 5, 6 The high viral load in elderly patients is associated not only with low immunity but also with high expression of the ACE2 receptor (the cellentry receptor for SARS-CoV-2) in older adults. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore cache = ./cache/cord-277342-40d24mvm.txt txt = ./txt/cord-277342-40d24mvm.txt === reduce.pl bib === id = cord-277307-wabruzfs author = Gu, Wei title = Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1096 sentences = 79 flesch = 66 summary = In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region cache = ./cache/cord-277307-wabruzfs.txt txt = ./txt/cord-277307-wabruzfs.txt === reduce.pl bib === id = cord-277313-5f5lrn3c author = Hayakawa, Satoshi title = Covid‐19 pandemic and pregnancy date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4622 sentences = 280 flesch = 51 summary = 20 However, fortunately, clinical data suggest no deleterious outcomes of pregnant women who are infected with COVID-19 during pregnancy compared with those infected with SARS-CoV or MERS. In another report from Wuhan, of 13 pregnant women who developed COVID-19 during pregnancy, one woman delivered a dead fetus at 34 weeks of gestation, but the cause of fetal death was speculated to be severe maternal pneumonia and multiple organ failure rather than viral infection of the fetus. 22 Another report showed that 3 of 33 pregnant women who developed COVID-19 during pregnancy in Wuhan showed evidence of intrauterine infection by cord blood PCR test. While early studies showed no evidence of vertical transmission of SARS-CoV-2 from mother-to-child in late pregnancy, 21 recent reports have shown possible in utero transmission. Coronavirus disease 2019 (COVID-19) in pregnant women: A report based on 116 cases cache = ./cache/cord-277313-5f5lrn3c.txt txt = ./txt/cord-277313-5f5lrn3c.txt === reduce.pl bib === id = cord-277486-12uah5qi author = Kopp, Kristen title = Interdisciplinary Model for Scheduling Post-discharge Cardiopulmonary Care of Patients Following Severe and Critical SARS-CoV-2 (Coronavirus) Infection date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3178 sentences = 146 flesch = 32 summary = As Covid-19 can severely implicate the respiratory and cardiovascular systems, potential pulmonary, and/or cardiovascular sequelae may be anticipated in patients following severe and critical SARS-CoV-2 infection meriting coordinated post-discharge management to identify residual effects and to mitigate potential worsening of pre-existing conditions. The WHO report Interim Guidance: Clinical Management of Covid 19, released 27 May 2020 however anticipates potential sequelae in patients with severe and critical SARS-CoV-2 infection following treatment with mechanical ventilation, sedation, and/or prolonged bed rest based on evidence from general critical care populations. A coordinated post-discharge care concept for patients surviving Covid-19 is therefore warranted to identify any cardiopulmonary sequelae and to mitigate possible worsening of preexisting disease following severe and critical SARS-Cov-2 infection. Short, intermediate and long-term effects following severe and critical SARS-CoV-2 infection are unknown, and significant sequelae may be expected, especially in patient populations experiencing ARDS, sepsis, and/or multiple organ dysfunction, as well as patients with exacerbation or progression of preexisting pulmonary or cardiovascular disease. cache = ./cache/cord-277486-12uah5qi.txt txt = ./txt/cord-277486-12uah5qi.txt === reduce.pl bib === id = cord-277399-0w8is9xm author = Esteves, Sandro C. title = SARS‐CoV‐2 pandemic and repercussions for male infertility patients: A proposal for the individualized provision of andrological services date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4160 sentences = 216 flesch = 38 summary = The prolonged lockdown of health facilities providing non‐urgent gamete cryopreservation—as currently recommended by many reproductive medicine entities and regulatory authorities due to the SARS‐CoV‐2 pandemic will be detrimental for subgroups of male infertility patients. These groups include infertility patients (eg, azoospermic and cryptozoospermic) undergoing medical or surgical treatment to improve sperm quantity and quality, as well as males of reproductive age affected by inflammatory and systemic auto‐immune diseases who are about to start treatment with gonadotoxic drugs or who are under remission. Sperm banking should be considered in men with HH who respond to therapy, that is, have viable spermatozoa in the ejaculate, in particular, when the continuation of gonadotropin therapy during the SARS-CoV-2 pandemic is neither possible (eg, due to economic or logistic reasons), nor desired. We propose remedies to mitigate the consequences of a prolonged cessation of andrological services due to the SARS-CoV-2 pandemic to vulnerable subgroups of male infertility patients. cache = ./cache/cord-277399-0w8is9xm.txt txt = ./txt/cord-277399-0w8is9xm.txt === reduce.pl bib === id = cord-277731-thazunob author = Smith, Matthew L. title = Biosurfactants: A Covid-19 Perspective date = 2020-06-09 pages = extension = .txt mime = text/plain words = 4700 sentences = 207 flesch = 38 summary = In this case, the use of biosurfactants in dealing with this pandemic justifies extensive study with their potential applications being in the prevention of viral spread; dealing with the symptoms that develop after the incubation period; directly targeting viral infected cells and preventing the spread of the virus throughout the host, all in addition to also acting as potential drug delivery systems and cleaning agents. The use of biosurfactants will therefore be considered in handwashes and cleaning agents to prevent the spread of the virus; targeting and relieving the symptoms after infection; acting as drug delivery systems and additionally their use in other important areas with a key example being the production reliable antiviral facemasks. This structure will be significant in directly targeting the virus, impacting its overall emulsification activity, while also being crucial in our application of biosurfactants in drug delivery. cache = ./cache/cord-277731-thazunob.txt txt = ./txt/cord-277731-thazunob.txt === reduce.pl bib === id = cord-277705-6lgt2i7f author = Luan, Junwen title = A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1149 sentences = 89 flesch = 64 summary = An RGD motif (403-405) was identified in SARS-CoV-2 S protein ( Figure 1A ). These results suggested that RGD/KGD integrin-binding motif is conserved in several coronaviruses including SARS-CoV-2 and SARS-CoV. To investigate whether RGD/KGD motif in S proteins from SARS-CoV-2 We identified a KGD motif in 353-355 of ACE2 (BAB40370.1), which is a key region for binding S protein ( Figure 1F ). Integrin associates with ACE2 through its KGD motif including K353, which is one of key AAs for S protein recognition. Integrin associates with S protein by its RGD/KGD motif, which would shield the space of RBM for contacting with ACE2. Because RGD recognized a broader spectrum of integrins than KGD, more integrins could block receptor binding of SARS-CoV-2 S than that of SARS-CoV S. In conclusion, we identified an RGD/KGD integrin-binding motif in S proteins from SARS-CoV-2 and SARS-CoV. cache = ./cache/cord-277705-6lgt2i7f.txt txt = ./txt/cord-277705-6lgt2i7f.txt === reduce.pl bib === id = cord-277490-xrgnt6l5 author = Huang, Zhongwei title = Optimal temperature zone for the dispersal of COVID-19 date = 2020-05-16 pages = extension = .txt mime = text/plain words = 424 sentences = 33 flesch = 57 summary = Abstract It is essential to know the environmental parameters within which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can survive to understand its global dispersal pattern. Our findings suggest that there is an optimal climatic zone in which the concentration of SARS-CoV-2 markedly increases in the ambient environment (including the surfaces of objects). The aerodynamic characteristics and propagation of SARS-CoV-2 in aerosols have been reported (Liu et al., 2020) . Therefore, it is essential to understand the survival of SARS-CoV-2 in the ambient environment to prevent COVID-19. Transmission of a 2009 Pandemic Influenza Virus Shows a Sensitivity to Temperature and Humidity Similar to That of an H3N2 Seasonal Strain Evidence that higher temperatures are associated with lower incidence of COVID-19 in pandemic state, cumulative cases reported up to Association between ambient temperature and COVID-19 infection in 122 cities from China cache = ./cache/cord-277490-xrgnt6l5.txt txt = ./txt/cord-277490-xrgnt6l5.txt === reduce.pl bib === id = cord-277440-9nehpbg2 author = Grimm, Christian title = Could an endo-lysosomal ion channel be the Achilles heel of SARS-CoV2? date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1326 sentences = 82 flesch = 55 summary = Genetic ablation of TPCs or TPC blockers have been previously shown to affect trafficking of both viruses and bacterial toxins through the endo-lysosomal system, reducing infectivity, including, e.g. cholera toxin, diphtheria toxin, Pasteurella multocida toxin, Anthrax toxin, Ebola virus, and MERS-CoV [5] [6] [7] . Indeed, it has been demonstrated before that SARS-CoV, like EBOV, displays late cell entry kinetics and that transport to NPC1+ (Niemann-Pick C1 protein) late endo-lysosomes is a rate-defining step [9] . The two-pore channels (TPC1, TPC2) are required by viruses such as EBOV (Ebola virus), MERS-CoV and SARS-CoV, orchestrating the interplay of virus and endolysosomal milieus such as trafficking from early to late endosomes, fusion of late endosomes with lysosomes, and facilitating releasing of viral RNA into the cytoplasm. cache = ./cache/cord-277440-9nehpbg2.txt txt = ./txt/cord-277440-9nehpbg2.txt === reduce.pl bib === id = cord-277498-hdhq99k2 author = Chua, Melvin L.K. title = Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3345 sentences = 158 flesch = 45 summary = title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic These scenarios would be considered high-risk for SARS-CoV-2 transmission, and the HCW consulting the patient would require full personal protection equipment (PPE) consisting of N95 mask, surgical gowns, gloves, and goggles/face shields 16 . Following the completion of treatment any patient with direct contact with a SARS-CoV-2 infected individual or who has personally tested positive or has symptoms of COVID-19 should not be seen in an oncology clinic for a follow-up visit. When it is challenging to distinguish between post-treatment edema and residual tumor on imaging, a detailed physical exam including endoscopy may be required, and as aforementioned, full PPE is required to protect the HCW from transmission of SARS-CoV-2 through aerosolization during NPL. Herein, we focused on the impact of this pandemic on the management of head and neck cancer patients who are undergoing or have completed radiation treatment. cache = ./cache/cord-277498-hdhq99k2.txt txt = ./txt/cord-277498-hdhq99k2.txt === reduce.pl bib === id = cord-277735-a9gkath5 author = Leung, Danny Tze Ming title = Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date = 2004-07-15 pages = extension = .txt mime = text/plain words = 4010 sentences = 192 flesch = 55 summary = We examined serum samples obtained from 46 patients with SARS, 40 patients with non-SARS pneumonia, and 38 healthy individuals, by use of Western blotting (WB), enzyme-linked immunoassay (ELISA), and immunofluorescence assay, using both native and bacterially produced antigens of the virus. Both the humoral and cellular arms of the adaptive immune response are presumed to be important in controlling 2 or preparation U reacted with a serum sample from a patient with SARS showing the highly reactive antigens-nucleocapsid (N) 1, N2, and N3-in the former. Second, we made a recombinant antigen of the N-terminal half of the N protein (rNa), and, when it was used in an IgG ELISA, we found results almost identical to those found with the crude viral extract (89% sensitivity and 94%-95% specificity), including 4 negative cases in common ( figure 2) . cache = ./cache/cord-277735-a9gkath5.txt txt = ./txt/cord-277735-a9gkath5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-277253-vy0mvzeb author = Liu, Hongbo title = Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date = 2020-04-11 pages = extension = .txt mime = text/plain words = 2265 sentences = 154 flesch = 52 summary = title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors. Inspired by the previous studies, several covalent inhibitors were experimentally identified to inhibit the 3CL pro activity and viral replication of SARS-CoV-2, and some of the complex crystal structures were solved [14, 15] . baicalensis inhibits SARS-CoV-2 3CL pro activity and the most active ingredient baicalein exhibits an IC50 of 0.39 M. We also identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CL pro activity at microM concentration. baicalensis and tested its inhibitory activity against SARS-CoV-2 3CL pro . baicalensis extract at different concentrations on SARS-CoV-2 3CL pro activity were 6 shown in Figure 1A . cache = ./cache/cord-277253-vy0mvzeb.txt txt = ./txt/cord-277253-vy0mvzeb.txt === reduce.pl bib === id = cord-277509-khvuiwl1 author = Hashemi, Seyyed Alireza title = Ultra-sensitive viral glycoprotein detection NanoSystem toward accurate tracing SARS-CoV-2 in biological/non-biological media date = 2021-01-01 pages = extension = .txt mime = text/plain words = 5375 sentences = 283 flesch = 52 summary = The working electrode of developed sensor is activated upon coating a layer of coupled graphene oxide (GO) with sensitive chemical compounds along with gold nanostars (Au NS) that can detect the trace of viruses in any aquatic biological media (e.g., blood, saliva and oropharyngeal/ nasopharyngeal swab) through interaction with active functional groups of their glycoproteins. Herein, we have addressed this demand via developing a rapid and highly sensitive diagnostic kit that do not require any extraction or biological marker and can detect trace of different kinds of pathogenic animal/human viruses such as SARS-CoV-2, infectious bronchitis virus (IBV), avian influenza and Newcastle Disease Virus (LaSota and V4 strains) via active functional groups of their viral glycoproteins upon demonstration of differentiable fingerprints of each virus at diverse voltage positions. cache = ./cache/cord-277509-khvuiwl1.txt txt = ./txt/cord-277509-khvuiwl1.txt === reduce.pl bib === id = cord-277549-sg7tzhdm author = Stanley, Kate E. title = Coronavirus disease (COVID-19) and fertility: viral host entry protein expression in male and female reproductive tissues date = 2020-05-08 pages = extension = .txt mime = text/plain words = 5364 sentences = 249 flesch = 47 summary = Single cell RNA sequencing (scRNAseq) in human and non-human primate respiratory tissues have shown co-expression of ACE2 and TMPRSS2 in pneumocytes in the lungs and goblet secretory cells in the nose (6) , indicating that these cell types may serve as foci for infection and potentially explaining the range of respiratory symptoms associated with COVID-19. Cell-type specific expression patterns of genes that produce viral host entry proteins, and identification of potential loci of infection within the reproductive system, are therefore necessary in order to predict whether SARS-CoV-2 is likely to have any impact on fertility. Categorizations for protein expression correspond to the categorizations given by the Human Protein Atlas and the Human Proteome Map. Published scRNAseq datasets in human testicular (18) and non-human primate ovarian (19) tissue were used to assess the cell-type specific expression pattern of SARS-CoV-2 entry receptor ACE2 and entry-associated protease TMPRSS2 and their coexpression. cache = ./cache/cord-277549-sg7tzhdm.txt txt = ./txt/cord-277549-sg7tzhdm.txt === reduce.pl bib === id = cord-277345-bbgerem6 author = Pan, A. title = Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area date = 2020-08-22 pages = extension = .txt mime = text/plain words = 4219 sentences = 271 flesch = 44 summary = Disparate racial and ethnic burdens of the Coronavirus Disease 2019 (COVID-19) pandemic may be attributable to higher susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or to factors such as differences in hospitalization and care provision. In our cross-sectional analysis of lab-confirmed COVID-19 cases from a tertiary, eight-hospital healthcare system (Houston Methodist) across greater Houston, multivariable logistic regression models were fitted to evaluate the odds of hospitalization and mortality for non-Hispanic Blacks (NHBs) vs. Models adjusted for demographics, vital signs, laboratory parameters, hospital complications, and ICU admission demonstrated non-significantly lower likelihoods of in-hospital mortality among NHBs and Hispanics, aOR (CI): 0.65 (0.40-1.03) and 0.89 (0.59-1.31), respectively. Given our prior data, we hypothesized that Black race and Hispanic ethnicity will be independently associated with a higher hospitalization rate and in-hospital mortality in the population of COVID-19 patients across HM. cache = ./cache/cord-277345-bbgerem6.txt txt = ./txt/cord-277345-bbgerem6.txt === reduce.pl bib === id = cord-277760-i4xjk61t author = Castillo, Andrés E. title = Phylogenetic analysis of the first four SARS‐CoV‐2 cases in Chile date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1208 sentences = 79 flesch = 59 summary = To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this report, we present the sequence analysis for the first four complete genomes for SARS-CoV-2 isolates on Chilean patients. Also, a phylogenetic study was performed with worldwide SARS-CoV-2 sequences and the full genomes from Chilean isolates, to identify their genetic similarity. cache = ./cache/cord-277760-i4xjk61t.txt txt = ./txt/cord-277760-i4xjk61t.txt === reduce.pl bib === id = cord-277774-kec1o4ys author = Wang, Shangqian title = The need for urogenital tract monitoring in COVID-19 date = 2020-04-20 pages = extension = .txt mime = text/plain words = 1528 sentences = 84 flesch = 48 summary = Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, which invades a cell through binding to the ACE2 receptor and TMPRSS2 priming. Most patients with severe COVID-19 present with pneumonia-related symptoms, but some patients with severe disease could develop serious urinary complications including acute kidney injury (AKI), which requires continuous renal replacement therapy (CRRT) 1 . Furthermore, male reproductive systems are vulnerable to infection; dramatic changes in sex hormones in patients with COVID-19 have been observed, suggesting gonadal function impairment 2 . Similar findings were also observed in autopsy kidney samples from patients with MERS-CoV infection 4 , which showed degeneration of the renal tubules, including ectasia changes and necrosis, sloughing, and loss of brush surface in the proximal tubular epithelial cells. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection cache = ./cache/cord-277774-kec1o4ys.txt txt = ./txt/cord-277774-kec1o4ys.txt === reduce.pl bib === id = cord-277443-mv7sk5aa author = Kumaki, Yohichi title = Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol(®) (Poly IC:LC), in a lethal SARS-CoV-infected BALB/c mouse model date = 2016-12-09 pages = extension = .txt mime = text/plain words = 10048 sentences = 686 flesch = 62 summary = Hiltonol(®) at 5, 1, 0.5 or 0.25 mg/kg/day by intranasal (i.n.) route resulted in significant survival benefit when administered at selected times 24 h prior to challenge with a lethal dose of mouse-adapted severe acute respiratory syndrome coronavirus (SARS-CoV). In other studies, treatment with an interferon inducer, polyriboinosinicpolyribocytidylic acid stabilized with poly-L-lysine and carboxymethyl cellulose (poly IC:LC), given by the intranasal route, was effective in protecting mice against a lethal infection with mouseadapted SARS-CoV and reduced viral lung titers (Kumaki et al., 2010) . These treated, SARS-CoVinfected mice receiving the various Hiltonol ® dosing regimens were also significantly protected against weight loss due to virus infection (Table 1 , p < 0.05-p<0.001) from days 0e3 post virus exposure when the greatest weight loss occurred in this mouse model. cache = ./cache/cord-277443-mv7sk5aa.txt txt = ./txt/cord-277443-mv7sk5aa.txt === reduce.pl bib === id = cord-277763-ihg3te63 author = Moynan, David title = The role of healthcare staff COVID-19 screening in infection prevention & control date = 2020-06-25 pages = extension = .txt mime = text/plain words = 654 sentences = 51 flesch = 51 summary = While HCW can acquire infections and contribute to cross-transmission during hospital outbreaks such as influenza or norovirus, asymptomatic staff are usually not routinely screened as part of the outbreak control measures. In March and April 2020, on three wards with two or more positive COVID-19 patients after three days of admission (designated as potential nosocomial infection), we implemented universal staff SARS-CoV-2 testing on that ward as part of outbreak management. As asymptomatic (or indeed, pre-symptomatic) HCW may have similar viral loads and may be capable of transmission as much as symptomatic individuals 9 , their detection and subsequent exclusion from work is an important aspect of a hospital's COVID-19 strategy. In conclusion, as hospitals begin to reopen to routine non-COVID-19 services, HCW SARS-CoV-2 testing irrespective of symptoms should be considered, particularly as part of outbreak management to rapidly prevent onward transmission to patients and other staff. COVID-19: PCR Screening of Asymptomatic Health-Care Workers at London Hospital cache = ./cache/cord-277763-ihg3te63.txt txt = ./txt/cord-277763-ihg3te63.txt === reduce.pl bib === id = cord-277529-z2r14w2k author = Stella, Alessandro title = Familial Mediterranean Fever and COVID-19: Friends or Foes? date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3634 sentences = 194 flesch = 42 summary = We were intrigued by the remarkable overlap between these clinical manifestations and some of the typical manifestations of Familial Mediterranean Fever (FMF), a largely recessively inherited monogenic inflammasomopathy (autoinflammatory disorder involving the inflammasome) caused by mutations in the MEFV gene that is particularly prevalent in the Mediterranean basin (14) . It is tempting to speculate that FMF patients carrying V726A and R761H variants-which represents the wild type residues in all bats and pangolin sequences-might modulate better their cytokine response to SARS-CoV-2 infection. Thus, the severity of COVID-19 disease in FMF patients, once infected, might be influenced, at least partially, depending on specific MEFV genotypes which shows country-specific differences. FMF, in which Pyrin activity and consequent ASC oligomerization are increased because of MEFV pathogenic variants, may therefore represent a unique opportunity as a disease model to investigate the regulation of the inflammatory response to novel emerging viruses. cache = ./cache/cord-277529-z2r14w2k.txt txt = ./txt/cord-277529-z2r14w2k.txt === reduce.pl bib === id = cord-277640-vy7ex5lv author = Calderaro, Adriana title = SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1171 sentences = 63 flesch = 52 summary = The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. cache = ./cache/cord-277640-vy7ex5lv.txt txt = ./txt/cord-277640-vy7ex5lv.txt === reduce.pl bib === id = cord-277679-sc9hugxr author = Khateb, Mohamed title = Coronaviruses and Central Nervous System Manifestations date = 2020-06-23 pages = extension = .txt mime = text/plain words = 4204 sentences = 245 flesch = 41 summary = This minireview scans the literature regarding the involvement of the CNS in coronavirus infections in general, and in regard to the recent SARS-CoV-2, specifically. In December 2019, the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged in Wuhan, China. Accumulating evidence implies a possible link between infection with the novel SARS-CoV-2 and acute ischemic stroke (AIS). Accumulating evidence from the current SARS-CoV-2 pandemic, together with literature on other coronaviruses, suggest that infection with coronaviruses may be related to CNS manifestations or complications, including anosmia, acute ischemic strokes, viral meningoenchephalitis, acute necrotizing encephalopathy, acute flaccid paralysis, and other presumably post/para-infectious syndromes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome cache = ./cache/cord-277679-sc9hugxr.txt txt = ./txt/cord-277679-sc9hugxr.txt === reduce.pl bib === id = cord-277619-83bve5z0 author = Huang, Victoria W. title = Head and neck survivorship care in the times of the SARS‐CoV‐2 pandemic date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2306 sentences = 127 flesch = 49 summary = In this present commentary, we discuss the unique mental health challenges and burdens of patients with head and neck cancer in the times of the SARS‐CoV‐2 pandemic and approaches to mitigate these stressors through telemedicine to reduce future burdens to the patient and the health care system. With the uncertainties of the SARS-CoV-2 pandemic and a head and neck cancer (HNC) diagnosis, the potential mental health consequences of such delays to treatment warrant further discussion. 24 With HNC patients already a vulnerable population, delaying treatment in the times of the SARS-CoV-2 pandemic can place additional strain on the mental health and QOL of patients, resulting in future burdens on the health care system. With examples of utilizing technology from China, providers need to address the mental health burden of a HNC diagnosis for patients who are being asked to delay treatment to ensure comprehensive cancer care. cache = ./cache/cord-277619-83bve5z0.txt txt = ./txt/cord-277619-83bve5z0.txt === reduce.pl bib === id = cord-277860-vzyrcmu4 author = Pizzorno, Andrés title = In vitro evaluation of antiviral activity of single and combined repurposable drugs against SARS-CoV-2 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 960 sentences = 71 flesch = 45 summary = In vitro evaluation of antiviral activity of single and combined repurposable drugs 1 against SARS-CoV-2 2 3 Authors: Andrés Pizzorno a , Blandine Padey a,b , Julia Dubois a , Thomas Julien a,c , Aurélien 4 Traversier a , Victoria Dulière a,c , Pauline Brun a,c , Bruno Lina a,d , Manuel Rosa-Calatrava a,c* † , 5 Olivier Terrier a* † 6 7 Author affiliations: Abstract: 27 In response to the current pandemic caused by the novel SARS-CoV-2, identifying and 28 validating effective therapeutic strategies is more than ever necessary. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. cache = ./cache/cord-277860-vzyrcmu4.txt txt = ./txt/cord-277860-vzyrcmu4.txt === reduce.pl bib === id = cord-277873-4819g00y author = Matson, M. Jeremiah title = Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1418 sentences = 82 flesch = 52 summary = We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. We describe SARS-CoV-2 stability in human nasal mucus and sputum under different environmental conditions. The t 1/2 we report here for SARS-CoV-2 in surface nasal mucus and sputum at 21°C/40% (Table) is considerably shorter than what we found in culture media under similar conditions (t 1/2 6.8 [95% CI 5.6-8.2] hours) (3). Nevertheless, with our experimental protocol and initial titer, we predicted that SARS-CoV-2 would remain infectious in nasal mucus and sputum on surfaces for >10-12 hours even in warm, humid conditions. In addition, reduced surface stability of SARS-CoV-2 in human nasal mucus and sputum in warmer and more humid conditions might result in decreased virus transmission, and climatic influence on SARS-CoV-2 transmission rates might eventually drive seasonal outbreak dynamics in a postpandemic period (7) , similar to other respiratory viruses (e.g., influenza A virus or human coronavirus OC43). cache = ./cache/cord-277873-4819g00y.txt txt = ./txt/cord-277873-4819g00y.txt === reduce.pl bib === id = cord-277564-x5qfxag3 author = Kim, Si-Hyun title = Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea date = 2020-10-24 pages = extension = .txt mime = text/plain words = 1310 sentences = 78 flesch = 47 summary = title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea Patients with findings suggestive of COVID-19 should be placed in a negative-pressure isolation room in the ED until the results of the rRT-PCR test for SARS-CoV-2 are confirmed as negative. However, patients requiring emergency surgery before confirmed negative SARS-CoV-2 rRT-PCR test results are evaluated for the risk of transmission by infectious disease specialists and the infection control team based on 3 criteria: clinical signs or symptoms, epidemiological risk, and chest radiological findings (Fig. 1 ). Patients who still have unconfirmed SARS-CoV-2 rRT-PCR test at the end of the surgery are transferred to the cohort ward, a single room, or a negative-pressure isolation room according to their risk. cache = ./cache/cord-277564-x5qfxag3.txt txt = ./txt/cord-277564-x5qfxag3.txt === reduce.pl bib === id = cord-277812-4cz2hziz author = Sieni, Elena title = Favourable outcome of coronavirus disease 2019 in a 1‐year‐old girl with acute myeloid leukaemia and severe treatment‐induced immunosuppression date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1345 sentences = 75 flesch = 48 summary = Since the beginning of coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults.1 Few cases of infection in children with cancer are described; also in these patients, except for one reported case,2 the disease was largely asymptomatic.3 Nevertheless, the management of COVID-19 in young patients with comorbidities, particularly cancer, remains a challenge for the clinician; further data are required to optimize the clinical approach to these cases. Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults. On day 18, routine laboratory testing further improved (WBC 2080 cells/µl with 48% neutrophils, Hb 112 g/l, PLTs correspondence 297 000/µl, negative CRP), and she was finally discharged, despite persistent positivity for SARS-CoV-2 at nasal swab, with oral prophylactic anti-microbial therapy. cache = ./cache/cord-277812-4cz2hziz.txt txt = ./txt/cord-277812-4cz2hziz.txt === reduce.pl bib === id = cord-277496-9ss09g6h author = Thaweerat, Wajana title = Current evidence on pancreatic involvement in SARS-CoV-2 infection date = 2020-05-27 pages = extension = .txt mime = text/plain words = 945 sentences = 66 flesch = 42 summary = SARS-CoV-2, the infectious agent of COVID-19, attached to angiotensin-converting enzyme 2 (ACE2) at cell surface which act as a receptor for viral entry into host cells. 5 Chinese case series reported 9 patients with mild elevation of pancreatic enzymes less than triple of upper limit of normal which does not reach the cut-point for diagnosis and did not provide other supported evidence to fulfill the criteria of diagnosing acute pancreatitis such as characteristics of abdominal pain or imaging findings. 8 Acute pancreatitis in severe COVID-19 patients may result from direct attack of SARS-CoV-2 to pancreatic acinar cells or uncontrollable systemic inflammatory response from cytokine storm syndrome leading to multi-organ dysfunction including pancreatic injury. 14 Therefore, further autopsy of COVID-19 cases still required to provide histological evidence of SARS-CoV-2 infection in pancreatic cells. In conclusion, current evidence of pancreatic manifestation in COVID-19 patients are limited which further investigation is essential to unravel consequences of SARS-CoV-2 infection to both endocrine and exocrine function of pancreas. cache = ./cache/cord-277496-9ss09g6h.txt txt = ./txt/cord-277496-9ss09g6h.txt === reduce.pl bib === id = cord-277611-3iynrfzq author = Buetti, Niccolò title = Risk factors for SARS-CoV-2 detection in blood of critically ill patients date = 2020-09-02 pages = extension = .txt mime = text/plain words = 810 sentences = 86 flesch = 68 summary = In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . cache = ./cache/cord-277611-3iynrfzq.txt txt = ./txt/cord-277611-3iynrfzq.txt === reduce.pl bib === id = cord-277410-lt19mijb author = Salvatore, Phillip P title = Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3282 sentences = 206 flesch = 52 summary = METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). Given the paucity of data examining associations of these factors with Ct value at the time of diagnosis, we sought to identify relationships between Ct values and time since onset, demographic factors, and symptoms among laboratory-confirmed COVID-19 cases identified in a multistate investigation of SARS-CoV-2 household transmission. Cycle threshold (Ct) values for SARS-CoV-2 rRT-PCR target probes N1 and N2 are plotted against the time elapsed between symptom onset and NP specimen collection in panel 1A. cache = ./cache/cord-277410-lt19mijb.txt txt = ./txt/cord-277410-lt19mijb.txt === reduce.pl bib === id = cord-278256-dmrtsxik author = Qiu, Haiyan title = Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study date = 2020-03-25 pages = extension = .txt mime = text/plain words = 3458 sentences = 199 flesch = 50 summary = title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study INTERPRETATION: Although all paediatric patients in our cohort had mild or moderate type of COVID-19, the large proportion of asymptomatic children indicates the difficulty in identifying paediatric patients who do not have clear epidemiological information, leading to a dangerous situation in community-acquired infections. All children with COVID-19 had been infected either by close contact with adults infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or by exposure to the epidemic area. By contrast with findings in adults, children with COVID-19 had milder clinical manifestations; nearly half of paediatric patients were asymptomatic (ie, no fever and no cough). When compared with children with SARS, paediatric patients with COVID-19 had much milder disease in terms of the prevalence of fever, cough, pneumonia, and severe case type. cache = ./cache/cord-278256-dmrtsxik.txt txt = ./txt/cord-278256-dmrtsxik.txt === reduce.pl bib === id = cord-277491-q18b88lm author = Cao, Ying-Li title = Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date = 2011-02-11 pages = extension = .txt mime = text/plain words = 3988 sentences = 210 flesch = 53 summary = title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus Nucleocapsid (N) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a major pathological determinant in the host that may cause host cell apoptosis, upregulate the proinflammatory cytokine production, and block innate immune responses. In the current study, we compared the N gene sequences derived from 16 different isolates of SARS-CoV and selected three novel siRNA targeting sites in the N gene, including one targeting the 3' terminus of the gene. Overall, the above results provide strong evidence to show that all three novel siRNAs (si-N213, si-N863 and si-N1240) are specific and effective inhibitors to block the isolated SARS-CoV N gene expression. Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles Small interfering RNA effectively inhibits the expression of SARS coronavirus membrane gene at two novel targeting sites cache = ./cache/cord-277491-q18b88lm.txt txt = ./txt/cord-277491-q18b88lm.txt === reduce.pl bib === id = cord-277911-x916hsg6 author = Wu, Di title = Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) date = 2020-04-13 pages = extension = .txt mime = text/plain words = 615 sentences = 50 flesch = 56 summary = title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated from Wuhan in China and has now spread globally. However, despite the concern focused on SARS-CoV-2, influenza virus continues to circulate and cause disease. The SARS-COV-2 outbreak in late December of 2019 in Wuhan, China, has caused many infections and deaths globally. 1 In China, several respiratory viruses are also now active including influenza, parainfluenza virus, respiratory syncytial virus, adenovirus, and now SARS-COV-2. The current World Health Organization (WHO)/ECDC definition of suspected case is not focused on pediatric population. Considering the large number of patients referring to pediatric hospital because of acute respiratory infections in winter season, the strict adoption of WHO/ECDC criteria can lead to a congestion of our hospitals. Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia cache = ./cache/cord-277911-x916hsg6.txt txt = ./txt/cord-277911-x916hsg6.txt === reduce.pl bib === id = cord-277683-9cg90zbo author = Panettieri, Reynold A. title = Asthma and COVID: What are the Important Questions? date = 2020-06-22 pages = extension = .txt mime = text/plain words = 946 sentences = 60 flesch = 49 summary = However, critical questions remain about the biologic and 40 clinical features that predispose to CSS and critical illness, including underlying comorbidities 41 such as asthma and the medications used to treat them. Older age and comorbidities, especially heart disease, hypertension, chronic obstructive 43 pulmonary disease (COPD), diabetes and obesity, are reported risk factors for the development 44 and progression of COVID-19 (3). However, controversy exists as to whether patients with 45 asthma manifest high or elevated rates of COVID-19 incidence. Inhaled steroids 62 have also been associated with decreased expression of angiotensin-converting enzyme 2 63 (ACE2), the co-receptor for SARS-CoV-2 raising the question of whether these drugs could Future studies should address whether inhaled steroids in patient with asthma and/or allergic 68 rhinitis increase or decrease risks of SARS-CoV-2 infection, and whether these effects different 69 across inhaled steroid types. Changes in medication 115 adherence among patients with asthma and COPD during the COVID-19 pandemic cache = ./cache/cord-277683-9cg90zbo.txt txt = ./txt/cord-277683-9cg90zbo.txt === reduce.pl bib === id = cord-278106-ev1nx60h author = Cancarevic, Ivan title = Coronavirus Disease 2019 (COVID-19) in Cancer Patients date = 2020-04-26 pages = extension = .txt mime = text/plain words = 2479 sentences = 130 flesch = 50 summary = The Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the most talked-about clinical entity in early 2020. Management presents its own set of challenges, including but not limited to, deciding whether postponing cancer treatment until the infection resolves is going to benefit the patient and how to organize all aspects of patient care when social contact is as limited as it is for patients newly diagnosed with COVID-19. found that the prevalence of cancer among patients infected with SARS-CoV-2 (COVID-19) was higher than in the general population [12] . We would strongly encourage clinicians to keep reporting any cases of cancer patients infected with SARS-CoV-2, their management, and the outcome in order to further our understanding of this complex issue. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges The treatment and outcome of a lung cancer patient infected with SARS-CoV-2 cache = ./cache/cord-278106-ev1nx60h.txt txt = ./txt/cord-278106-ev1nx60h.txt === reduce.pl bib === id = cord-277841-7sp8ftbc author = Kumari, Pratibha title = Potential diagnostics and therapeutic approaches in COVID-19 date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4873 sentences = 279 flesch = 45 summary = Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. COVID-19 is a contagious disease, caused by a novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2). In this article, we evaluated literature for reports informing various diagnostic methods, potential antiviral chemical therapeutics, and effective treatment strategies towards clinical management of COVID-19 patients. Molecular diagnostic methods target to detect either specific regions of the viral genome or RNA-dependent RNA polymerase (RdRP) and/or structural proteins of SARS-CoV-2 (Table 1) . Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2. Table 2: Primers and probes for targeting SARS-Cov-2 genes in an RT-PCR test for COVID-19 diagnosis. cache = ./cache/cord-277841-7sp8ftbc.txt txt = ./txt/cord-277841-7sp8ftbc.txt === reduce.pl bib === id = cord-278249-vvhq9vgp author = Blot, Mathieu title = CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDS date = 2020-11-02 pages = extension = .txt mime = text/plain words = 6238 sentences = 346 flesch = 45 summary = In addition, since most patients need to undergo mechanical ventilation in this context, ventilator-induced lung injury (VILI) could exacerbate tissue damage as well as local and systemic inflammation, thus acting as a "second hit." Our team has previously shown that mitochondrial alarmins (i.e., mitochondrial DNA) are released by human epithelial cells submitted to cyclic stretch, and these alarmins are also recovered from bronchoalveolar lavage (BAL) fluid obtained from either ventilated rabbits or ARDS patients. This comprehensive evaluation of systemic and pulmonary immune response showed that the higher CXCL10 concentrations in both the systemic and alveolar compartments of patients with COVID-19 ARDS were associated with a longer duration of mechanical ventilation. Finally, in both COVID-19 and non-COVID-19 patients, higher mitochondrial DNA concentrations in the plasma and ELF compartment were highly correlated with alveolar inflammation, as assessed by BALF cell count and ELF IL-8 and IL-1β concentrations. cache = ./cache/cord-278249-vvhq9vgp.txt txt = ./txt/cord-278249-vvhq9vgp.txt === reduce.pl bib === id = cord-277870-o79wph9r author = Han, Yanqiang title = Potential inhibitors for the novel coronavirus (SARS-CoV-2) date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3814 sentences = 171 flesch = 45 summary = In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. In this study, we chose 3CL Mpro as the therapeutic target to ab initio investigate its inhibition mechanism and binding ability of these most promising drug molecules by ligand-protein docking program (Rosetta) and molecular dynamics (MD) simulations. Through molecular docking and kinetic analysis, we found that for repurposed drugs, the Chloroquine molecule has the strongest interaction with the 3CL Mpro, indicating that Chloroquine is the best potential inhibitor for SARS-CoV-2, followed by Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir. For docking and binding analysis, seven clinically approved inhibitors (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) were selected from previous reported virtual screening works or were found to be highly effective in the control of SARS-CoV-2 infection in vitro [6, 12] . cache = ./cache/cord-277870-o79wph9r.txt txt = ./txt/cord-277870-o79wph9r.txt === reduce.pl bib === id = cord-277539-xt2nt11e author = Kochhar, Anuraj Singh title = Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date = 2020 pages = extension = .txt mime = text/plain words = 4502 sentences = 296 flesch = 50 summary = Despite the avalanche of information that has exploded in relation to this rapidly spreading disease, there is a lack of consolidated information to guide dentists regarding clinical management including precautions to take materials to use and postprocedure care, during and after the COVID-19 pandemic. This review aims to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan can be formulated and adapted to the circumstances of each dental practice during the pandemic and the times to follow. The purpose of this review is to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan of measures can be formulated and adapted according to the circumstances of each dental practice during the pandemic and the times to follow. cache = ./cache/cord-277539-xt2nt11e.txt txt = ./txt/cord-277539-xt2nt11e.txt === reduce.pl bib === id = cord-277759-zbmzjsvs author = Wang, Luwen title = Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China date = 2020-03-31 pages = extension = .txt mime = text/plain words = 3233 sentences = 190 flesch = 53 summary = BACKGROUND: Whether the patients with coronavirus disease 19 (COVID-19) infected by severe acute respiratory syndrome (SARS)-CoV-2 would commonly develop acute kidney injury (AKI) is an important issue worthy of clinical attention. This study aimed to explore the effects of SARS-CoV-2 infection on renal function through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. As shown in Table 2 , 111 COVID-19-confirmed patients without CKD did not develop obvious abnormal renal function after infection with SARS-CoV-2 and during the treatment of pneumonia. SARS-CoV-2 RNA in urine sediments of COVID-19-confirmed 53 patients, including 5 CKD cases, enrolled in this study was examined by real-time RT-PCR. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. cache = ./cache/cord-277759-zbmzjsvs.txt txt = ./txt/cord-277759-zbmzjsvs.txt === reduce.pl bib === id = cord-278050-wl83d6gs author = Morgenstern, Birgit title = Ribavirin and interferon-β synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines date = 2005-01-28 pages = extension = .txt mime = text/plain words = 2390 sentences = 127 flesch = 50 summary = Abstract Initial in vitro investigations demonstrated type I interferons (IFNs: IFN-α, IFN-β) to inhibit replication of SARS coronavirus (SARS-CoV), but found the nucleoside analogue ribavirin ineffective in Vero cells. In this report, ribavirin was shown to inhibit SARS-CoV replication in five different cell types of animal or human origin at therapeutically achievable concentrations. The influence of the infectious dose on the anti-SARS-CoV activity of ribavirin was investigated in Caco2 cells infected at different MOIs by measurement of virus titre. For example, in Caco2 cells infected with SARS-CoV FFM1 strain (MOI 0.01), ribavirin concentrations inhibiting virus production in combination with IFN-b were at least 10-fold lower when compared with cultures receiving single treatment with ribavirin. These clinical findings together with the observation of antiviral activity in different SARS-CoV-infected cell lines encourage the testing of treatment strategies using ribavirin in combination with other antiviral agents such as IFNs to increase inhibitory effects on virus replication and subsequently minimised immunopathological damages. cache = ./cache/cord-278050-wl83d6gs.txt txt = ./txt/cord-278050-wl83d6gs.txt === reduce.pl bib === id = cord-277830-6fsz9iy7 author = Saikatendu, Kumar Singh title = Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date = 2005-11-08 pages = extension = .txt mime = text/plain words = 6555 sentences = 344 flesch = 56 summary = The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. A view of the proposed active site of SARS ADRP along with the superimposed structures of AF1521 and yeast Ymx7 are shown in Figure 4B , highlighting the interactions that are likely between residues of the protein with the ligand. cache = ./cache/cord-277830-6fsz9iy7.txt txt = ./txt/cord-277830-6fsz9iy7.txt === reduce.pl bib === id = cord-278362-pwi48i20 author = Khan, Abbas title = Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) date = 2020-06-18 pages = extension = .txt mime = text/plain words = 5136 sentences = 287 flesch = 55 summary = title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) Furthermore, results from molecular dynamics simulation and total binding free energy revealed that Saquinavir and TCM5280805 target the catalytic dyad (His41 and Cys145) and possess stable dynamics behavior. In this study, the protein of SARS-COV-2 (3CLpro, also named 3-chymotrypsin-like protease) was subjected to drug repurposing and virtual screening for potent drug identification followed by molecular dynamics simulation and binding free energy calculation. In the current study, the repurposing of anti-HIV drugs against the SARS-COV-2 main protease was carried out using structure-based screening methods. In this study, based on the results of bioinformatics analysis, we targeted 3CLpro from SARS-COV-2 using drugs repurposing (anti-HIV drugs) virtual drugs screening (TCM) approaches to shortlist the most potent compounds for the possible treatment. cache = ./cache/cord-278362-pwi48i20.txt txt = ./txt/cord-278362-pwi48i20.txt === reduce.pl bib === id = cord-278129-bpuyrsza author = De Haan, Cornelis A. M. title = Hosting the severe acute respiratory syndrome coronavirus: specific cell factors required for infection date = 2006-06-27 pages = extension = .txt mime = text/plain words = 4481 sentences = 216 flesch = 47 summary = As with all viruses, the severe acute respiratory syndrome coronavirus (SARS‐CoV) utilizes specific host cell factors during its infection cycle. In this short review we focus on the severe acute respiratory syndrome coronavirus (SARS-CoV) describing what is currently known of the cell's contributions during the successive phases of the infection cycle, i.e. entry, replication and assembly (Fig. 1) . Amino acids 270-510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensinconverting enzyme 2 Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry cache = ./cache/cord-278129-bpuyrsza.txt txt = ./txt/cord-278129-bpuyrsza.txt === reduce.pl bib === id = cord-278522-e4qa19o6 author = Park, Se Yoon title = Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1605 sentences = 106 flesch = 56 summary = There are limited data on the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory specimens after resolution of coronavirus disease 2019 (COVID-19)-associated symptoms/signs. Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs Se Yoon Park 1 , Soon Gyu Yun 2 , Jeong Won Shin 2 , Bo Young Lee 3 , Hyo-Ju Son 1 , Seungjae Lee 1 , Eunjung Lee 1 , and Tae Hyong Kim 1 Since the first case of coronavirus disease 2019 (COVID-19) was reported in Wuhan, China in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than three million people in 211 countries. Few studies have investigated the duration of SARS-CoV-2 detection during the patients' recovery phase after resolution of COVID-19-associated symptoms/signs. SARS-CoV-2 shedding continued for about 4 weeks after resolution of COVID-19-associated symptoms/signs, with the longest period being 48 days. In conclusion, we found that SARS-CoV-2 virus shedding can persist for more than three weeks after resolution of COVID-19-associated symptoms/signs. cache = ./cache/cord-278522-e4qa19o6.txt txt = ./txt/cord-278522-e4qa19o6.txt === reduce.pl bib === id = cord-277874-cr53ycrm author = Neault, N. title = SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date = 2020-09-03 pages = extension = .txt mime = text/plain words = 7079 sentences = 372 flesch = 49 summary = We believe MPAD based SARS-CoV-2 protein quantitation represents a promising epidemiological tool with a sensitivity sufficiently superior to viral RNA measurement that, in addition to enabling early detection and population tracking of COVID-19 load, will also open the way to effective infection surveillance of specific facilities, schools and residences. Primary sludge and PEG precipitated influent fractions, collected from the contiguous cities of Ottawa and Gatineau in April through June 2020, were analysed for the presence of four SARS-CoV-2 structural proteins, N (nucleocapsid), M (membrane), S (spike), and E (envelope), by western blot. Next, in order to assure specificity for detection of SARS-CoV-2 proteins, we used MPAD with an expanded panel to simultaneously measure three viral proteins, N, S and M, along with six fecal content control proteins in PEG precipitated "influent solids" samples drawn from the Ottawa WRRF during the study period ( Fig 5) . cache = ./cache/cord-277874-cr53ycrm.txt txt = ./txt/cord-277874-cr53ycrm.txt === reduce.pl bib === id = cord-278238-w1l8h8g8 author = Okba, Nisreen MA title = Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches date = 2017-04-13 pages = extension = .txt mime = text/plain words = 5086 sentences = 226 flesch = 39 summary = Nisreen MA Okba, V Stalin Raj and Bart L Haagmans Middle East respiratory syndrome coronavirus (MERS-CoV) is a cause of severe respiratory infection in humans, specifically the elderly and people with comorbidities. The other candidate MVA-S, a viral-vector-based vaccine, induced systemic neutralizing antibodies and mucosal immunity which conferred protection against MERS-CoV challenge and reduced virus shedding in vaccinated camels [52 ] Therefore, this vaccine candidate may provide a means to prevent zoonotic transmission of the virus to the human population. Prophylaxis with a Middle East respiratory syndrome coronavirus (MERS-CoV)-specific human monoclonal antibody protects rabbits from MERS-CoV infection T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice The recombinant Nterminal domain of spike proteins is a potential vaccine against Middle East respiratory syndrome coronavirus (MERS-CoV) infection cache = ./cache/cord-278238-w1l8h8g8.txt txt = ./txt/cord-278238-w1l8h8g8.txt === reduce.pl bib === id = cord-278182-75u57fw1 author = Goh, Gerard Kian-Meng title = Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids date = 2020-03-31 pages = extension = .txt mime = text/plain words = 4613 sentences = 253 flesch = 58 summary = A model to classify and predict the levels of respective respiratory and fecal-oral transmission potentials of the various viruses was built before the outbreak of MERS-CoV using AI and empirically-based molecular tools to predict the disorder level of proteins. Using the percentages of intrinsic disorder (PID) of the nucleocapsid (N) and membrane (M) proteins of CoV, the model easily clustered the viruses into three groups with the SARS-CoV (M PID = 8%, N PID = 50%) falling into Category B, in which viruses have intermediate levels of both respiratory and fecal-oral transmission potentials. In 2011-2012, just before the outbreak of the Middle Eastern Respiratory Syndrome (MERS-CoV), we built an empirically-based model that measures the percentage of intrinsic disorder (PID) of the membrane (M) and nucleocapsid (N) proteins in viruses [5, 6] . cache = ./cache/cord-278182-75u57fw1.txt txt = ./txt/cord-278182-75u57fw1.txt === reduce.pl bib === id = cord-277659-afysef1e author = Hamilton, F. title = Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date = 2020-07-04 pages = extension = .txt mime = text/plain words = 3096 sentences = 203 flesch = 53 summary = Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCW's). In this paper, we report the kinetics and performance of this assay in three populations: confirmed (PCR +ve) and suspected COVID-19 patients, confirmed (PCR +ve) healthcare workers, and pre-pandemic controls with respiratory infection. The sensitivity of the Abbott SARS-CoV-2 IgG assay was estimated with 95% Confidence Intervals at different time points post symptom onset (DISCOVER patients) or first PCR positive result (healthcare workers). cache = ./cache/cord-277659-afysef1e.txt txt = ./txt/cord-277659-afysef1e.txt === reduce.pl bib === id = cord-277889-8u685f45 author = Costela-Ruiz, Víctor J. title = SARS-CoV-2 infection: the role of cytokines in COVID-19 disease date = 2020-06-02 pages = extension = .txt mime = text/plain words = 9212 sentences = 552 flesch = 49 summary = The majority of patients infected with COVID-19 have normal or reduced white cell counts and lymphocytopenia, and those with severe disease have shown significantly elevated levels of neutrophils, dimer-D, and urea in blood, with a continuing decrease in lymphocytes. detected elevated levels of the antagonistic receptor of IL-1 (IL-1Ra) in 14 severe cases of COVID-19, and this marker has been associated with increased viral load, loss of pulmonary function, lung damage, and mortality risk [55] . observed that its expression during infection with an influenza virus had negative effects on CD8 + memory T cells [71] .Various studies of COVID-19 patients have detected elevated IL-4 levels as part of the cytokine storm associated with severe respiratory symptoms [16, 17, 43, 72] . Elevated IL-17 levels have been reported in patients with SARS-CoV-2 as part of the cytokine storm [17] , and they have been associated with the viral load and disease severity [56] . cache = ./cache/cord-277889-8u685f45.txt txt = ./txt/cord-277889-8u685f45.txt === reduce.pl bib === id = cord-277669-uujny2dm author = Lumpuy-Castillo, Jairo title = Cardiovascular Damage in COVID-19: Therapeutic Approaches Targeting the Renin-Angiotensin-Aldosterone System date = 2020-09-04 pages = extension = .txt mime = text/plain words = 7443 sentences = 476 flesch = 40 summary = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can differentially infect multiple tissues (i.e., lung, vessel, heart, liver) in different stages of disease, and in an ageand sex-dependent manner. In particular, treatments with angiotensin-converting enzyme inhibitors (ACEi) and angiotensin-receptor blockers (ARB) may help to reduce hyperinflammation and viral propagation, while infusion of soluble ACE2 may trap plasma viral particles and increase cardioprotective Ang-(1–9) and Ang-(1–7) peptides. SARS-CoV-2 infection initiates in the respiratory system, when the S protein of its external layer binds the angiotensin-converting enzyme-2 (ACE2) at the plasma membrane of host cells [5] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . cache = ./cache/cord-277669-uujny2dm.txt txt = ./txt/cord-277669-uujny2dm.txt === reduce.pl bib === id = cord-278406-n5e3a09i author = Macauley, Precious title = CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1492 sentences = 79 flesch = 39 summary = Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). cache = ./cache/cord-278406-n5e3a09i.txt txt = ./txt/cord-278406-n5e3a09i.txt === reduce.pl bib === id = cord-277585-evw3pu87 author = Malavolta, Marco title = Exploring the Relevance of Senotherapeutics for the Current SARS-CoV-2 Emergency and Similar Future Global Health Threats date = 2020-04-08 pages = extension = .txt mime = text/plain words = 4183 sentences = 211 flesch = 36 summary = Drugs targeting IL-6 have been included among the potential strategies to inhibit the deleterious consequences of the senescence-associated secretory phenotype (SASP), the secretome produced by senescent cells [31, 32] . The evidence that patients with cancer, hypertension or with smoking habits (conditions associated with a pathological role of cellular senescence) experienced worse outcomes from COVID-19 [71] , further supports the hypothesis that an accumulation of senescent cells may favor the development of severe events during SARS-CoV-2 infection. In the case of dengue virus infection, cellular senescence seems to exert an anti-viral function [64] but other viruses, such as IFV, have evolved mechanisms to increase replication in senescent cells [68] . Clarifying the role of cellular senescence in SARS-CoV infection may additionally provide a strong rationale for the use of senotherapeutics, such as SASP inhibitors, in the management of elderly patients affected by COVID-19. cache = ./cache/cord-277585-evw3pu87.txt txt = ./txt/cord-277585-evw3pu87.txt === reduce.pl bib === id = cord-278457-yrm5hi3v author = Sung, Heungsup title = Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea date = 2020-10-17 pages = extension = .txt mime = text/plain words = 3722 sentences = 187 flesch = 45 summary = EQAs using pooled respiratory samples spiked with inactivated cultured SARS-CoV-2 had indicated the possible effects of these variations on assay performance, thereby allowing External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. cache = ./cache/cord-278457-yrm5hi3v.txt txt = ./txt/cord-278457-yrm5hi3v.txt === reduce.pl bib === id = cord-278271-rpq62xhl author = Lyu, Jinglu title = Reflection on lower rates of COVID-19 in children: does childhood immunizations offer unexpected protection? date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4641 sentences = 230 flesch = 46 summary = The frequent childhood vaccinations and repeated pathogens infections might be resulting in trained immunity of innate immune cells, immune fitness of adaptive immune cells or cross-protection of antibodies in the children. Candida isolated from 4 airway specimens in a case report of patients with new coronavirus pneumonia Compared with adult cases, children tend to have milder symptoms, shorter disease course and generally better prognosis. found that memory lymphocytes can also mediate longer-term cross-protection as a byproduct of adaptive immunity: CD8 + memory T cells can be activated by cytokines (IL-12 and IL-18) in early stages of infection in an antigen-independent manner, leading to the production of IFN-γ and enhanced response to subsequent infectious agents (45) . Equipping confirmed COVID-19 patients with these vaccinations as emergent prophylaxis may prevent severe illness caused by secondary infection, in the meantime, it may mobilize the host's lymphocyte response to the opposite direction in response to SARS-CoV-2. cache = ./cache/cord-278271-rpq62xhl.txt txt = ./txt/cord-278271-rpq62xhl.txt === reduce.pl bib === id = cord-278123-mq56em3z author = Hasan, Mohammad Rubayet title = Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date = 2020-07-24 pages = extension = .txt mime = text/plain words = 3924 sentences = 259 flesch = 58 summary = Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. cache = ./cache/cord-278123-mq56em3z.txt txt = ./txt/cord-278123-mq56em3z.txt === reduce.pl bib === id = cord-278176-o9glkhyv author = Houng, Huo-Shu H title = Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date = 2004-09-01 pages = extension = .txt mime = text/plain words = 4782 sentences = 226 flesch = 54 summary = The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. It was demonstrated that the RT-PCR assay with 91% amplification efficiency could be used for consistent detect ion of the SARS-CoV viral RNA extracted from samples containing as little as 0.005 pfu per reaction with an anticipated C T value of 40 cycles (data not shown). It was demonstrated in this study that the cloned pHCV1 plasmid could be used to replace viral cDNA as a stable and rational SARS-CoV copy number standard for the SARS-CoV RT-PCR assay. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-278176-o9glkhyv.txt txt = ./txt/cord-278176-o9glkhyv.txt === reduce.pl bib === id = cord-278509-k62bsk9b author = Manikandan, Natesan title = Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? date = 2020-09-12 pages = extension = .txt mime = text/plain words = 589 sentences = 50 flesch = 48 summary = title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? 7 In a new modeling study in Singapore, Joel R Koo and colleagues found that the combined approach of physical distancing interventions, quarantine, school closure, and workplace distancing, is the most effective at reducing the transmission of SARS-CoV-2. 8 A report from the United States suggested that social distancing interventions can give communities vital time to mitigate the spread of COVID-19 pandemic. Nevertheless, to overcome this global threat, combination of preventive measures like social distancing, hand washing and wearing face masks are the important key practices to mitigate the transmission of COVID-19 in the community. The role of community-wide wearing of face mask for control of Coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2 Impact of self-imposed prevention measures and short-term governmentimposed social distancing on mitigating and delaying a COVID-19 epidemic: A modelling study cache = ./cache/cord-278509-k62bsk9b.txt txt = ./txt/cord-278509-k62bsk9b.txt === reduce.pl bib === id = cord-277816-ncdy9qgb author = Wang, Ji-gan title = Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3600 sentences = 202 flesch = 48 summary = title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis In order to understand the clinical manifestations and incidence of gastrointestinal symptoms of coronavirus disease (COVID-19) in children and discuss the importance of fecal nucleic acid testing.We retrospectively analyzed studies on gastrointestinal symptoms and fecal nucleic acid detection in pediatric COVID-19 patients from January 1, 2020 to August 10, 2020, including prospective clinical studies and case reports. Stata12.0 software was used for meta-analysis.The results showed that the most common gastrointestinal symptoms in children with COVID-19 were vomiting and diarrhea, with a total incidence of 17.7% (95% Cl 13.9–21.5%). At present, there is no relevant study on whether there is a difference in the positive rate of fecal nucleic acid testing in COVID-19 children with and without diarrhea. Clinical features of 33 cases in children infected with SARS-CoV-2 in Anhui Province, China: a multi-center retrospective cohort study. cache = ./cache/cord-277816-ncdy9qgb.txt txt = ./txt/cord-277816-ncdy9qgb.txt === reduce.pl bib === id = cord-277907-x6387i7b author = Tham, Sai Meng title = Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020 date = 2020-11-17 pages = extension = .txt mime = text/plain words = 922 sentences = 59 flesch = 50 summary = Coronavirus disease (COVID-19) and tuberculosis (TB) developed in 4 foreign workers living in dormitories in Singapore during April–May 2020. Clinical manifestations and atypical radiographic features of COVID-19 led to the diagnosis of TB through positive interferon-gamma release assay and culture results. Pleural fluid analysis revealed a lymphocytic exudative effusion with an adenosine deaminase (ADA) level of 130 U/L (reference range <40 U/L), but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 112 U/L and interleukin-6 (IL-6) level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 62 U/L and an IL-6 level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. tuberculosis and SARS-CoV-2 in patients with atypical radiographic features of COVID-19. cache = ./cache/cord-277907-x6387i7b.txt txt = ./txt/cord-277907-x6387i7b.txt === reduce.pl bib === id = cord-277739-eb4z3u66 author = Hu, Ke title = Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3665 sentences = 195 flesch = 48 summary = title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial In the latest publication, Lianhuaqingwen (LH) capsule (Shijiazhuang Yiling Pharmaceutical Co. Ltd., Shijiazhuang, China) was a manufactured product of the traditional Chinese medicine formula marketed in China that could significantly inhibit SARS-CoV-2 replication, alter the viral morphology and confer anti-inflammatory activity in vitro . On the basis of usual treatment, we sought to explore the safety and efficacy of LH capsules in patients with Covid-19 by conducting a multicenter randomized controlled trial in mainland China. Eligibility criteria consisted of the following: 1) Laboratory-confirmed cases with according to the Protocol for Diagnosis and Treatment of Novel Coronarvirus Pneumonia (4 th edition) which was issued by the National Health Commission (General Office Of The National Health And Health Commission, 2020) (Panel 1); 2) Being symptomatic (either having fever, coughing, or fatigue) plus radiologic abnormalities consistent with pneumonia; 3) Patients aged 18 years or greater of either sex. cache = ./cache/cord-277739-eb4z3u66.txt txt = ./txt/cord-277739-eb4z3u66.txt === reduce.pl bib === id = cord-278491-cnqxsno8 author = Wang, K. title = Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3139 sentences = 216 flesch = 57 summary = Methods Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. 9, 10 However, the dynamics and roles of SARS-CoV-2specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Our study may provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases and aid in the development of vaccines against SARS-CoV-2. 15, 16 The short-term humoral immune response in COVID-19 patients is also highly consistent with that observed in patients infected with SARS-CoV and MERS-CoV, 17, 18 who show a rapid decrease in virus-specific antibody titers within 3-4 months. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. cache = ./cache/cord-278491-cnqxsno8.txt txt = ./txt/cord-278491-cnqxsno8.txt === reduce.pl bib === id = cord-278045-hr3r17mz author = Yokota, Isao title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-09-25 pages = extension = .txt mime = text/plain words = 2271 sentences = 156 flesch = 52 summary = METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (NPS and self-collected saliva) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. cache = ./cache/cord-278045-hr3r17mz.txt txt = ./txt/cord-278045-hr3r17mz.txt === reduce.pl bib === id = cord-278951-vxrwrzlj author = Huang, Hsien-Hao title = Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak date = 2006-12-31 pages = extension = .txt mime = text/plain words = 2736 sentences = 128 flesch = 56 summary = title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak Background The immediate and long-term impact of severe acute respiratory syndrome (SARS) outbreak on emergency department (ED) visits and hospital expenditures for these visits has not been thoroughly investigated. 14 This study found that a substantial mean reduction in the number of ED visits occurred during the SARS epidemic, with a peak of 51.6% and a mean of 32.1% (95% CI of the mean difference, 27.6-36.6%) during the 4-month (April-July) epidemic period in a designated SARS hospital in Taiwan ( Figure 1 ). The higher total cost for each patient during the SARS epidemic was primarily attributed to increases in the number of laboratory investigations, radiographic examinations, ancillary procedures and medications required ( Figure 5 ). cache = ./cache/cord-278951-vxrwrzlj.txt txt = ./txt/cord-278951-vxrwrzlj.txt === reduce.pl bib === id = cord-278370-fuu20ae7 author = Palao, M. title = Multiple Sclerosis following SARS-CoV-2 infection date = 2020-07-07 pages = extension = .txt mime = text/plain words = 1544 sentences = 93 flesch = 44 summary = However, available information about demyelinating complications of the central nervous system (CNS) is limited with only one report of acute disseminated encephalomyelitis (ADEM) in a severe COVID-19 patient being published to date 5 and a single case of meningo-encephalitis 6 , the latter with the presence of SARS-CoV-2 in the cerebrospinal fluid (CSF) confirmed by PCR. As viral infections have been linked to the development of demyelinating diseases 7 it would be interesting to know if this relationship also exists in the case of SARS-CoV-2. We present a case of first presentation of demyelinating disease in the form of optic neuritis following SARS-CoV-2 infection. In our case, the patient presented symptoms attributed to COVID-19 infection (anosmia and dysgeusia) prior to the visual manifestations. In this case, SARS-CoV-2 may have acted as a precipitating factor rather than multiple sclerosis being a direct consequence of the infection. cache = ./cache/cord-278370-fuu20ae7.txt txt = ./txt/cord-278370-fuu20ae7.txt === reduce.pl bib === id = cord-278325-ykcd7d59 author = Cheung, Carmen Ka Man title = Coronavirus Disease 2019 (COVID-19): A Haematologist's Perspective date = 2020-07-28 pages = extension = .txt mime = text/plain words = 7672 sentences = 379 flesch = 39 summary = Two meta-analyses showed that a lower platelet count is associated with an increased risk of severe disease and mortality in patients with COVID-19 and may serve as a marker for progression of illness [53, 54] . Experience from previous SARS patients, caused by SARS-CoV-1, suggested that coronavirus could cause thrombocytopenia by direct viral infection of bone marrow haematopoietic stem cells via CD13 or CD66a, formation of auto-antibodies and immune complexes, disseminated intravascular coagulopathy (DIC), and consumption of platelet in lung epithelium [61, 62] . The International Society on Thrombosis and Haemostasis (ISTH) suggested all patients (including non-critically ill) who require hospital admission for COVID-19 infection should receive a prophylactic dose of LMWH unless contraindicated (Table 2 ) [102] . Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 cache = ./cache/cord-278325-ykcd7d59.txt txt = ./txt/cord-278325-ykcd7d59.txt === reduce.pl bib === id = cord-278540-gy65bvot author = Chen, I-Yin title = Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date = 2019-01-29 pages = extension = .txt mime = text/plain words = 4645 sentences = 256 flesch = 50 summary = A recent study shows that the SARS-CoV E protein, which comprise only 76 amino acids, forms Ca 2+ -permeable ion channels and activates the NLRP3 inflammasome (Nieto-Torres et al., 2015) . To this end, we substituted amino acids Cys-127, Cys-130, and Cys-133 within the cysteine-rich domain of the SARS-CoV 3a protein with serine to generate a lentivirus expressing the ion channel activity-loss mutant, 3a-CS (Chan et al., 2009; Figure 2A) . Together, these data provide evidence that the ion channel activity of the SARS-CoV 3a protein is essential for triggering the NLRP3 inflammasome. Since mitochondrial ROS are important for NLRP3 inflammasome activation (Nakahira et al., 2011; Zhou et al., 2011) , we next stimulated BMMs with extracellular ATP or lentiviruses expressing the SARS-CoV E or 3a proteins in the presence or absence of the antioxidant, Mito-TEMPO, a scavenger that is specific for mitochondrial ROS Trnka et al., 2009) . cache = ./cache/cord-278540-gy65bvot.txt txt = ./txt/cord-278540-gy65bvot.txt === reduce.pl bib === id = cord-278055-v2ed3tei author = Sia, Sin Fun title = Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date = 2020-05-14 pages = extension = .txt mime = text/plain words = 5396 sentences = 292 flesch = 56 summary = Previous study of SARS-CoV (Urbani strain) in 5-weeks-old golden Syrian hamsters showed robust viral replication with peak viral titers detected in the lungs on 2 dpi, followed by rapid viral clearance by 7 dpi, but without weight loss or evidence of disease in the inoculated animals 20 . Our results indicate that the golden Syrian hamster is a suitable experimental animal model for SARS-CoV-2, as there is apparent weight loss in the inoculated and naturally-infected hamsters and evidence of efficient viral replication in the nasal mucosa and lower respiratory epithelial cells. c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. e, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one donor on 6 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. cache = ./cache/cord-278055-v2ed3tei.txt txt = ./txt/cord-278055-v2ed3tei.txt === reduce.pl bib === id = cord-278440-vti6xp9v author = Paraiso, Ines L title = Potential use of polyphenols in the battle against COVID-19 date = 2020-09-09 pages = extension = .txt mime = text/plain words = 2338 sentences = 124 flesch = 45 summary = The present mini-review aims to report in silico and in vitro evidence of the potential of polyphenols as anti-SARS-CoV-2 agents. Screening by molecular docking of 33 molecules including natural products, antivirals, antifungals and antiprotozoal agents revealed that rutin (a citrus flavonoid) could bind to the active site of the SARS-CoV-2 3CL pro (PDB: 6Y84) with the highest affinity among the molecules screened [44] . •This study demonstrates that SARS-CoV-2 uses ACE2 as receptor for host-cell entry and the S protein needs the serine protease TMPRSS2 for priming. A: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: An in-silico analysis cache = ./cache/cord-278440-vti6xp9v.txt txt = ./txt/cord-278440-vti6xp9v.txt === reduce.pl bib === id = cord-278260-3o91v72a author = Halstead, Scott B title = COVID 19 Vaccines: Should we fear ADE? date = 2020-08-12 pages = extension = .txt mime = text/plain words = 2331 sentences = 178 flesch = 44 summary = Within months large numbers of vaccinated children developed a severe breakthrough disease, called "atypical measles." [6] A similar outcome, "vaccine associated enhanced respiratory disease (VAERD)," was observed in infants, 4 -12 months of age, who were given formalininactivated respiratory syncytial virus (RSV) and a few months later infected by RSV. The biological behavior of some coronaviruses in non-human species together with evidence that human coronavirus antibodies enhanced infection of SARS or MERS CoVs in Fc receptor-bearing cells, in vitro, have led to speculations that ADE contributes to disease severity in humans. [11] It has been reported that high levels of SARS CoV-1 IgG antibodies circulated in severe SARS cases and that anti-S IgG neutralizing antibody (NAb) responses developed significantly faster after the onset of clinical symptoms in fatal compared with recovered cases leading some to attribute enhanced tissue damage to ADE. With others, we conclude that the differences in clinical, epidemiological and pathological features of SARS and DENV diseases suggest that iADE does not contribute to the severity of natural human coronavirus infections. cache = ./cache/cord-278260-3o91v72a.txt txt = ./txt/cord-278260-3o91v72a.txt === reduce.pl bib === id = cord-278093-0twnkv93 author = Perveen, Shagufta title = Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3149 sentences = 162 flesch = 56 summary = Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. cache = ./cache/cord-278093-0twnkv93.txt txt = ./txt/cord-278093-0twnkv93.txt === reduce.pl bib === id = cord-278649-ge9ike2c author = Makaronidis, Janine title = Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4278 sentences = 232 flesch = 58 summary = title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study The study aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a community-based population with acute loss of smell and/or taste and to compare the frequency of COVID-19 associated symptoms in participants with and without SARS-CoV-2 antibodies. • Recruited participants completed online questionnaires regarding demographics, their loss of smell and/or taste, and other COVID-19 symptoms, before they had a telemedicine consultation with a healthcare professional who confirmed the history of their symptoms and supervised a test to find out if they had SARS-CoV-2 antibodies. In this community-based cohort study, undertaken during the peak of the COVID-19 outbreak in London, the seroprevalence of SARS-CoV-2 antibodies in participants with new onset loss of sense of smell and/or taste, was 77.6%. cache = ./cache/cord-278649-ge9ike2c.txt txt = ./txt/cord-278649-ge9ike2c.txt === reduce.pl bib === id = cord-278169-elhz77ek author = Zhou, Dapeng title = Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics date = 2020-06-10 pages = extension = .txt mime = text/plain words = 4216 sentences = 237 flesch = 51 summary = In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1–4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1. The receptor-binding domain region of the SARS-CoV-1spike protein is densely covered by glycans except FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ, which overlaps with a previously identified "Achilles heel" (i.e., vulnerable spot) for antibody binding (Berry, et al. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on Severe Acute Respiratory Syndrome Coronavirus Neutralization Escape and Fitness cache = ./cache/cord-278169-elhz77ek.txt txt = ./txt/cord-278169-elhz77ek.txt === reduce.pl bib === id = cord-278812-5jps95q9 author = Edwards, Sarah J L title = Anthroponotic risk of SARS-CoV-2, precautionary mitigation, and outbreak management date = 2020-07-02 pages = extension = .txt mime = text/plain words = 658 sentences = 52 flesch = 57 summary = Following early reports of anthroponotic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and mixed messages over anthroponotic risk, some pets were reportedly abandoned to fend for them selves or killed. Evidence of infection of animals with SARS-CoV-2 has been shown experimentally both in vivo and in vitro for mammals including monkeys, cats, ferrets, rabbits, foxes, and hamsters, while bioinformatic studies also predict infectivity of pigs and wild boar among other mammals. 6 Additional experimental inoculation of animals would not help because small sample sizes and bioinformatic studies alone cannot confirm that a whole species is incapable of being infected by SARS-CoV-2. Sufficient evidence exists of anthroponosis of SARS-CoV-2 on which to base precautionary steps to mitigate the risks it poses. Infection and rapid transmission of SARS-CoV-2 in ferrets Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Potential fecal transmission of SARS-CoV-2: current evidence and implications for public health SARS-CoV-2 infection in farmed minks, the Netherlands cache = ./cache/cord-278812-5jps95q9.txt txt = ./txt/cord-278812-5jps95q9.txt === reduce.pl bib === id = cord-278467-c0jw9dkw author = Tulchinsky, Mark title = The American College of Nuclear Medicine Guidance on Operating Procedures for a Nuclear Medicine Facility During COVID-19 Pandemic date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2101 sentences = 147 flesch = 45 summary = During the COVID-19 pandemic, 5 scheduling of examinations should be judicious, equipment disinfection should be practiced before each patient, medical service sustainability should be optimized, all aerosol-generating tests must be avoided, and time of staff-patient contact should be minimized for each test in order to contain the contagion. 3. Provide to the patient and/or guardian as much information as possible by phone in advance of arrival to an NMF, including screening questions for COVID-19 risk and explanation of the test or therapy to be performed, in order to minimize the time spent in close in-person contact. Although the outlined principles are universal, their practical applications and implementation are dependent on prevalence dynamics of COVID-19 at specific locations and resources available to individual NMFs. A novel coronavirus from patients with pneumonia in China Incidental findings suggestive of COVID-19 in asymptomatic patients undergoing nuclear medicine procedures in a high-prevalence region cache = ./cache/cord-278467-c0jw9dkw.txt txt = ./txt/cord-278467-c0jw9dkw.txt === reduce.pl bib === id = cord-278678-ivye1qao author = Calvez, R. M. title = Molecular detection of SARS-CoV-2 using a reagent-free approach date = 2020-05-02 pages = extension = .txt mime = text/plain words = 3223 sentences = 186 flesch = 55 summary = Optimisation of the heat-treatment method and inhibitory properties of UTM In a preliminary study to evaluate the best assay conditions, a range of SARS-CoV-2-positive and negative samples was selected and heat-treated at different temperatures and for different times. Each heat-treated sample was then subject to SARS-CoV-2 testing using our in-house assay derived from the CDC resource website (targeting the N-gene and using the TaqMan® Fast Virus 1-Step RT-qPCR kit from ABI). As shown in table 2 below, the ABI TaqMan® One-Step RT-qPCR mix systematically failed to detect SARS-CoV-2 in swab samples resuspended in UTM (COPAN swabs) even in the presence of viral loads greater than 1×10 6 copies/mL (003850 and 003862). Although heat-treatment of respiratory samples prior to RT-qPCR showed an attractive methodology compared to a conventional nucleic acid extraction method, the addition of an internal control is critical for quality control and successful detection of this virus if present in the patient samples. cache = ./cache/cord-278678-ivye1qao.txt txt = ./txt/cord-278678-ivye1qao.txt === reduce.pl bib === id = cord-278945-q5lzf5o4 author = Hashemi, Seyed Ahmad title = Report of death in children with SARS‐CoV‐2 and Human metapneumovirus (hMPV) co‐infection: is hMPV the trigger? date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1285 sentences = 88 flesch = 55 summary = To investigate the presence of other respiratory viruses, we performed a panel of virus detection through PCR and RT‐PCR tests to detect influenza virus, parainfluenza virus, Human metapneumovirus, Human bocavirus, adenovirus, and respiratory syncytial virus on nasopharyngeal swabs of all 74 SARS‐CoV‐2 positive dead patients. Although surveys confirmed that children could be infected with SARS-CoV-2 (1-3), there is evidence showing people more than 50 years old are more susceptible to the COVID-19. Case presentation Blood tests, including blood cell differential count, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) were performed for all patients admitted to the hospital with suspicion of infection with SARS-CoV-2. Besides, all patients underwent a chest CT scan that is the most sensitive test for COVID-19 identification (5, 6) , and SARS-COV-2 detection was performed using real-time PCR. We found the influenza virus, Human bocavirus, respiratory syncytial virus, parainfluenza virus, and hMPV in some SARS-CoV-2 positive samples. cache = ./cache/cord-278945-q5lzf5o4.txt txt = ./txt/cord-278945-q5lzf5o4.txt === reduce.pl bib === id = cord-278839-uu2wlpmp author = Alberca, Ricardo Wesley title = Pregnancy, Viral Infection, and COVID-19 date = 2020-07-07 pages = extension = .txt mime = text/plain words = 7237 sentences = 368 flesch = 43 summary = In 2009, during the H1N1 flu pandemic, an increased ratio of female to male cases was verified, in which pregnant women developed more complications, as severe acute respiratory syndrome, and higher mortality compared to the general population (30, 31) . Additionally, infection by the Lassa virus in pregnant women shows high levels of placental replication, and the risk of maternal-fetal mortality increases with the duration of pregnancy (38, 39) . At first, contagion occurred through contact with some infected animals but, soon there were the first reports of human-to-human transmission (93), The virus was identified as belonging to the coronaviridae family and was designated SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) (94). Chen and collaborators, verified alteration in calcium and albumin levels in the blood of pregnant women with SARS-CoV-2 infection (124) , which could potentially increase the severity in COVID-19 (125) . cache = ./cache/cord-278839-uu2wlpmp.txt txt = ./txt/cord-278839-uu2wlpmp.txt === reduce.pl bib === id = cord-278618-7tu5c7m1 author = Romano-Bertrand, Sara title = Sustainability of SARS-CoV-2 in aerosols: Should we worry about airborne transmission? date = 2020-06-12 pages = extension = .txt mime = text/plain words = 1340 sentences = 70 flesch = 45 summary = This is based on previous knowledge [1] and the doctrine that: a patient positive for SARS-CoV-2 is contagious by respiratory secretions (>10μm in size) that disseminate only on short distance (<1m); SARS-CoV-2 carried on large droplets settles onto local surfaces and is not stable in the air; SARS-CoV-2 aerosol dispersion is possible during AGPs which extensively expose HCWs and therefore HCWs need to wear a respirator for a higher respiratory protection during AGPs. However, an experimental study of van Doremalen et al, [2] assessed the sustainability of SARS-CoV-2 in aerosols (<5μm at 65% of hygrometry (expressed in %RH for relative humidity)) performed using a high-powered machine that does not reflect normal cough conditions (https://www.who.int/publications-detail/modes-of-transmission-of-virus-causing-covid-19-implicationsfor-ipc-precaution-recommendations). They showed that SARS-CoV-2 remained viable and infective at least 3 hours in aerosols, which opened the debate on SARS-CoV-2 transmission through longdistance aerosols (>1m), and questioned the appropriateness of respiratory protection for HCWs. An individual who is well, emits 10 to 10 4 particles per liter of expired air, including 95% of <1μm-size particles [3] . cache = ./cache/cord-278618-7tu5c7m1.txt txt = ./txt/cord-278618-7tu5c7m1.txt === reduce.pl bib === id = cord-279105-e2zjxjox author = Lee, Cheryl Yi-Pin title = Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3872 sentences = 212 flesch = 44 summary = With the limitations of qRT-PCR, immunoassays may offer another FIGURE 2 | Schematic illustration on the window period of detection for either viral RNA or antibodies in SARS-CoV-2-infected individuals. However, interestingly, one study demonstrated that longitudinal profiling of both antibodies in a population of 63 COVID-19 patients showed no specific chronological order in terms of IgM and IgG seroconversion (10) , which was also observed in patients infected with SARS-CoV and another human coronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV) (22, 23) . These findings on SARS-CoV-2-specific antibodies seroconversion against the S viral protein suggest the importance to test for both IgM and IgG antibodies to confirm a positive infection. With the availability of immunoassays utilizing various coronavirus structural proteins, the use of more than one different antigen-based serological approach may be essential to establish a true positive SARS-CoV-2 infection. cache = ./cache/cord-279105-e2zjxjox.txt txt = ./txt/cord-279105-e2zjxjox.txt === reduce.pl bib === id = cord-279001-l5ogbl5p author = Wilder-Smith, Annelies title = Can we contain the COVID-19 outbreak with the same measures as for SARS? date = 2020-03-05 pages = extension = .txt mime = text/plain words = 4387 sentences = 241 flesch = 53 summary = COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. In November, 2002, the severe acute respiratory syn drome coronavirus (SARSCoV) emerged in China causing global anxiety as the outbreak rapidly spread, and by July, 2003, had resulted in over 8000 cases in 26 countries. In the absence of vaccines and specific treatment, the only available public health tools to control persontoperson transmittable diseases are isolation and quarantine, social distancing, and community containment measures. Isolation, quarantine, social distancing and community containment: pivotal role for oldstyle public health measures in the novel coronavirus (2019nCoV) outbreak Public health measures to control the spread of the severe acute respiratory syndrome during the outbreak in Toronto cache = ./cache/cord-279001-l5ogbl5p.txt txt = ./txt/cord-279001-l5ogbl5p.txt === reduce.pl bib === id = cord-278225-d0gxb6bx author = Meng, Yifan title = Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients date = 2020-04-30 pages = extension = .txt mime = text/plain words = 900 sentences = 68 flesch = 56 summary = title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients It has been emphasized that diagnostic testing for SARS-CoV-2 was an especially important tool in the diagnosis and management of patients with COVID-19. All patients included in the present study were verified as positive for SARS-CoV-2 infection by reverse transcriptase polymerase chain reaction (RT-PCR). At present clinical practice, patients with improved respiratory symptoms, improved pulmonary imaging, and nucleic acid tests negative twice consecutively (sampling interval ≥ 24 hours) can be discharged. reported that potential false-negative nucleic acid testing results for SARS-CoV-2 could be caused by thermal inactivation of samples with low viral loads. Value of Diagnostic Testing for SARS-CoV-2/COVID-19 Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19 Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads cache = ./cache/cord-278225-d0gxb6bx.txt txt = ./txt/cord-278225-d0gxb6bx.txt === reduce.pl bib === id = cord-278923-u4gv2e7w author = da Silva, Joyce Kelly R. title = Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation date = 2020-05-12 pages = extension = .txt mime = text/plain words = 6372 sentences = 408 flesch = 50 summary = A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 M(pro)), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). One study evaluated the in vitro antiviral effect against influenza type A (H1N1) of commercial essential oils that included cinnamon (Cinnamomum zeylanicum), bergamot (Citrus bergamia), lemongrass (Cymbopogon flexuosus), thyme (Thymus vulgaris), and lavender (Lavandula angustifolia). In this work, we carried out a molecular docking analysis of the major components of essential oils that exhibit antiviral activity (Tables 1 and 2 ) with known SARS-CoV-2 protein targets. Docking scores, normalized for molecular weight (DS norm , kJ/mol), of essential oil components with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular targets. cache = ./cache/cord-278923-u4gv2e7w.txt txt = ./txt/cord-278923-u4gv2e7w.txt === reduce.pl bib === id = cord-278542-vqp6ec6e author = Coyne, Carolyn title = Recommendations for future university pandemic responses: What the first COVID-19 shutdown taught us date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2562 sentences = 148 flesch = 45 summary = Successes and failures along the way highlighted how the autonomous nature of the American academic research enterprise and skillsets normally required of university leaders were ill-suited to mounting an emergency response. Here, as faculty from medical centers in the United States, we draw lessons from these experiences and apply them as we plan for the next possible COVID-19-induced shutdown as well as other large-scale pandemics and emergencies at universities in the United States and throughout the world. In addition, students (and faculty) with children or other dependents required homeschooling and alternative care plans that conflicted with classes they either were enrolled in or taught. Other swiftly implemented decisions included accommodating research groups who possessed expertise to work on SARS-CoV-2 while creating protocols such as social distancing and PPE use for their safety. In addition, institutions need to consider the needs of laboratory staff and trainees and include them in the decision-making process. cache = ./cache/cord-278542-vqp6ec6e.txt txt = ./txt/cord-278542-vqp6ec6e.txt === reduce.pl bib === id = cord-278960-3xw4qjoy author = Evangelista, A. T. title = The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3833 sentences = 170 flesch = 51 summary = The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. In temperate regions of the globe, the incidence of respiratory enveloped viruses, such as influenza and endemic human coronaviruses peak in winter months, usually in January and February, which is considered due to indoor social crowding with droplet and contact transmission and the added effect of low indoor relative humidity (RH). cache = ./cache/cord-278960-3xw4qjoy.txt txt = ./txt/cord-278960-3xw4qjoy.txt === reduce.pl bib === id = cord-278987-3s5p9yw6 author = Hirotsu, Yosuke title = Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship date = 2020-04-17 pages = extension = .txt mime = text/plain words = 517 sentences = 45 flesch = 55 summary = title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship The patient stayed in room A for 3 days, during which he had the SARS-CoV-2 infection. SARS-CoV-2 is detectable in several types of clinical samples including bronchial lavage fluid, nasopharyngeal swab, pharyngeal swab, sputum, saliva, and feces. 4, 5 Transmission of SARS-CoV-2 via surfaces in hospitals is of great concern to medical staff and patients. 6 A recent study showed that environmental contamination can occur via contact with patients with SARS-CoV-2 and upper respiratory tract symptoms. Double-quencher probes improved the detection sensitivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by one-step RT-PCR Surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient All authors report no conflicts of interest relevant to this article. cache = ./cache/cord-278987-3s5p9yw6.txt txt = ./txt/cord-278987-3s5p9yw6.txt === reduce.pl bib === id = cord-279132-florvm7z author = K., Branimir title = From apparent to true – from frequency to distributions (II) date = 2020-08-17 pages = extension = .txt mime = text/plain words = 2390 sentences = 113 flesch = 45 summary = According to Roda et al (2) , one of the main reasons for the variability in predicting the COVID-19 epidemic is the lack of data on the actual dynamics of the infection spread, which results in so-called nonidentifiability in model calibration. The authors determined the model parameters using the Bayesian approach and Markov chain Monte Carlo, and concluded that the COVID-19 epidemics in Wuhan and Seattle had likely been spreading for several weeks before they became apparent and were far more extensive than initially reported. Feroze (7) used Bayesian structural time series models to investigate the pattern of SARS-CoV-2 spread in India, Brazil, USA, Russia, and the UK between March 1 and June 29, 2020 to assess the impact of mitigation measures and predict the dynamics of the epidemic over the next 30 days. Dehning et al (9) used the SIR epidemiological model framework in combination with Bayesian inference to analyze the effective growth rate of the number of new cases over time. cache = ./cache/cord-279132-florvm7z.txt txt = ./txt/cord-279132-florvm7z.txt === reduce.pl bib === id = cord-278759-pykihnup author = Koh, Yiwen title = Nurses' perceptions of risk from emerging respiratory infectious diseases: A Singapore study date = 2012-03-21 pages = extension = .txt mime = text/plain words = 4899 sentences = 277 flesch = 53 summary = Another significant finding of this study is that the government's, organizations' and nurses' perceptions of new emerging respiratory infectious diseases were influenced by their previous experience with SARS. 16 It can be seen from this discussion that there is a substantial amount of research examining how HCWs perceive the risks of Emerging Acute Respiratory Infectious Diseases such as H1N1 and SARS; 17, 25 however, few studies have focused specifically on nurses. 41, 42 With the resurgence of emerging acute respiratory infectious diseases such as SARS and pandemic influenza in the 21st century, research investigating nurses' risk perceptions towards their exposure is more than ever pertinent. The data show that the nurses in this study have similar concerns to previous research on HCW's perceptions of risk from SARS and other emerging acute respiratory infectious diseases in that these nurses were concerned about risks to their personal health (from patients, from colleagues and visitors to the organization). cache = ./cache/cord-278759-pykihnup.txt txt = ./txt/cord-278759-pykihnup.txt === reduce.pl bib === id = cord-278721-g5zqebju author = Jakhmola, Shweta title = Comorbidity Assessment Is Essential During COVID-19 Treatment date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3748 sentences = 233 flesch = 45 summary = Our study revealed that deaths associated with cardiovascular diseases and diabetes are highly significant (p < 0.0001) compared to hospitalized in countries like Italy, France, and Spain unlike the Netherlands. Deaths from kidney diseases (Italyp < 0.0001; Swedenp < 0.0001; Netherlandsp = 0.0001; Francep = 0.0033) and neurological ailments (Francep = 0.0001; Netherlandsp < 0.0001) are significantly higher than the total hospitalized patients affected by the particular comorbidity. The information about numbers of hospitalized or deceased COVID-19 patients with associated comorbidities from individual countries was already provided in their respective reports. The death proportions due to Heart Diseases including, cardiovascular diseases and hypertension, were significantly higher (p < 0.0001) compared to the total hospitalized patients in Italy, Sweden, and Spain. Notably we found that heart diseases, including hypertension along with cardiovascular diseases, are the most frequent association with SARS-CoV2 infection in most countries (Italy, France, Spain, and Sweden) except the Netherlands. cache = ./cache/cord-278721-g5zqebju.txt txt = ./txt/cord-278721-g5zqebju.txt === reduce.pl bib === id = cord-279334-j0i9ozsz author = McCreary, Erin K title = Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date = 2020-03-23 pages = extension = .txt mime = text/plain words = 8269 sentences = 363 flesch = 44 summary = Most existing preclinical and clinical data on antiviral therapy are derived from other viruses, including SARS-CoV-1 (first reported in 2003), Middle East respiratory syndrome coronavirus ([MERS-CoV] first reported in 2012), and non-coronaviruses (eg, Ebola virus disease). The use of 500 mg of chloroquine by mouth twice daily as the reference for efficacy is rational given initial reports from China [16] , but it is important to note that this dosing still requires validation, and the improved R LTEC values reported are largely driven by the finding that hydroxychloroquine was 7.6 times more potent than chloroquine in vitro. Given this finding, the small numbers in this study, the lack of clinical outcomes presented, the potential for additive toxicity with hydroxychloroquine and azithromycin, and the desperate need to practice good antimicrobial stewardship during the COVID-19 pandemic, we would caution clinicians against using these data to support combination therapy. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-279334-j0i9ozsz.txt txt = ./txt/cord-279334-j0i9ozsz.txt === reduce.pl bib === id = cord-279290-wtnnlp4i author = Solorio-Pineda, Saúl title = Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? date = 2020-09-25 pages = extension = .txt mime = text/plain words = 1370 sentences = 95 flesch = 50 summary = title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? BACKGROUND: In December 2019, in Wuhan, a new virus emerged, causing severe acute respiratory syndrome (SARS) secondary to infection by a type of coronavirus, causing coronavirus disease (COVID-19). A new virus emerged, causing severe acute respiratory syndrome (SARS) originated in the city of Wuhan, China, in December 2019. [6, 9] We decided to present the following remarkable case from a patient with pituitary tumor apoplexy infected with SARS-CoV-2. Unfortunately, given the patient's condition and his timely isolation in the coronavirus disease (COVID-19) floor, it was not possible to perform a brain MRI scan. e CNS involvement in COVID-19 infection includes cerebrovascular events due to endothelial dysfunction, with pituitary apoplexy being an unusual presentation, a situation that should be confirmed in the future. Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? cache = ./cache/cord-279290-wtnnlp4i.txt txt = ./txt/cord-279290-wtnnlp4i.txt === reduce.pl bib === id = cord-278453-ogbmaw3o author = Spiller, Tobias R. title = Development of health care workers' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1502 sentences = 101 flesch = 58 summary = title: Development of health care workers' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies BACKGROUND: Virus outbreaks such as the current SARS-CoV-2 pandemic are challenging for health care workers (HCWs), affecting their workload and their mental health. Since both, workload and HCW's well-being are related to the quality of care, continuous monitoring of working hours and indicators of mental health in HCWs is of relevance during the current pandemic. METHODS: We conducted two cross-sectional online studies among Swiss HCWs assessing working hours, depression, anxiety, and burnout. With this study, we aimed to assess changes in working hours and mental health (assessed as symptoms of anxiety, depression, and burnout) in Swiss HCWs at the height of the SARS-CoV-2 pandemic (T1) and again after its flattening (T2). In the conducted network analyses burnout and anxiety were both independently related to lower perceived support by the employer in both studies, a well-described association also in non-pandemic contexts (Shanafelt & Noseworthy, 2017) . cache = ./cache/cord-278453-ogbmaw3o.txt txt = ./txt/cord-278453-ogbmaw3o.txt === reduce.pl bib === id = cord-279255-v861kk0i author = Dhama, Kuldeep title = Coronavirus Disease 2019–COVID-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 23862 sentences = 1164 flesch = 44 summary = Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . Health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel CoV (originally named 2019-nCoV), which was first identified in Wuhan City, Hubei Province, China, on 12 December 2019. cache = ./cache/cord-279255-v861kk0i.txt txt = ./txt/cord-279255-v861kk0i.txt === reduce.pl bib === id = cord-279172-d2algx16 author = Zheng, Kewen title = Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme date = 2006-11-02 pages = extension = .txt mime = text/plain words = 6381 sentences = 284 flesch = 58 summary = During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 Å, which agrees well with the experimental observations made by X‐ray crystallography; (ii) His163 and Glu166 form the "tooth" conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate‐binding pocket formed by loop 140–146 and loop 184–197 is large enough to accommodate the substrate analog. In this research, by comparing the process of the MD simulation of monomer with dimer, our aim is to (i) find the structural variations and dynamics of the active site residues in SARS M pro monomer in contrast to the dimer, which result in an inactive monomer and provide useful information for receptor based drug design; (ii) investigate the detailed specific interactions involving the two monomers within the dimer and its functional roles in maintaining the activity of the dimer, which provides insights for the design of specific protease inhibitors using the interface of the dimer as a new target. cache = ./cache/cord-279172-d2algx16.txt txt = ./txt/cord-279172-d2algx16.txt === reduce.pl bib === id = cord-279260-tdvb0fhv author = Lv, Huibin title = COVID‐19 vaccines: knowing the unknown date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1476 sentences = 98 flesch = 46 summary = It is also important to note that T-cell immunity was found to be elicited by SARS-CoV or MERS-CoV DNA vaccines (both express trimeric spike protein) [7, 9] . Determining which adjuvants can enhance protective vaccine response to SARS-CoV-2 will be important. For example, the MF59-adjuvanted influenza vaccine, Fluad, is only licensed and approved for adults aged 65 years and older, to elicit a higher protective immune response in the elderly This article is protected by copyright. To accelerate vaccine development, animal infection models for SARS-CoV-2 are needed. Although macaques show COVID-19-like disease upon SARS-CoV-2 infection, the non-human primate model is usually not readily accessible to most laboratories [27] . Expressing hACE2 through adenoviral transduction may provide another possible approach to generate a mouse model for SARs-CoV-2 infection. For example, a conserved CD4 T-cell epitope can mediate cross-reactive protection between SARS-CoV and MERS-CoV [38] . cache = ./cache/cord-279260-tdvb0fhv.txt txt = ./txt/cord-279260-tdvb0fhv.txt === reduce.pl bib === id = cord-279476-h7zi82a8 author = Wang, Xueliang title = Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) date = 2020-04-13 pages = extension = .txt mime = text/plain words = 596 sentences = 35 flesch = 57 summary = title: Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) To cope with the COVID-19 epidemic, the China National Medical Products Administration (NMPA) approved six RT-PCR kits for SARS-CoV-2, and some of which subsequently received CE marking. To verify its applicability, the viral RNA was tested with the six kits provided by Shanghai Liferiver Bio-tech Co., Ltd, Wuhan Huada Bio-tech Co., Ltd, Shanghai GeneoDx Biotech Co., Ltd, DAAN Gene Co., Ltd of Sun Yat-sen University, Sansure Biotech Inc., and Shanghai BioGerm Medical Co., Ltd. The different target genes ( Table 1 ) produced typical S-shaped amplification curves, indicating that the RNA could be used in the six kits to evaluate their LoDs. The viral RNA concentration was determined with RT-droplet digital PCR (RT-ddPCR), which allows the absolute quantification of viral RNA by counting single molecules, without reference to an external standard curve. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR We acknowledge the six manufacturers for providing the SARS-CoV-2 RT-PCR detection kits. cache = ./cache/cord-279476-h7zi82a8.txt txt = ./txt/cord-279476-h7zi82a8.txt === reduce.pl bib === id = cord-279316-xz7aawem author = MIZUTANI, T. title = Signal Transduction in SARS‐CoV‐Infected Cells date = 2007-04-23 pages = extension = .txt mime = text/plain words = 3156 sentences = 171 flesch = 45 summary = Recent studies regarding SARS and SARS‐CoV have clarified that activation of mitogen‐activated protein kinases (MAPKs) plays important roles in upregulation of cytokine expression and apoptosis both in vitro and in vivo. For example, mitogen-activated protein kinases (MAPKs) are well-known signal transducers that respond to extracellular stimulation by cytokines, growth factors, viral infection, and stress, and in turn regulate cell differentiation, proliferation, survival, and apoptosis. Extracellular signal-regulated kinase (ERK) 1/2 was phosphorylated in SARS-CoV-infected Vero E6 cells, 27 whereas ERK1/2 was downregulated in N protein-expressing COS-1 cells as described below. Activation of the p38 MAPK signaling pathway and dephosphorylation of STAT3 via p38 MAPK induced by SARS-CoV infection have partially proapoptotic roles in Vero E6 cells. Importance of Akt signaling pathway for apoptosis in SARS-CoV-infected Vero E6 cells cache = ./cache/cord-279316-xz7aawem.txt txt = ./txt/cord-279316-xz7aawem.txt === reduce.pl bib === id = cord-279550-7u2hksxm author = Wang, Kai title = Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date = 2020-08-03 pages = extension = .txt mime = text/plain words = 2656 sentences = 190 flesch = 56 summary = METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. Thus, serological testing, especially to detect NAbs, is essential in determining the onset of the serological immune response, evaluating the potential capacity of the host body for viral clearance, and identifying donors for passive antibody therapy trials. 12, 13 However, the dynamics and roles of SARS-CoV-2-specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Furthermore, to determine if there was a statistical correlation between NAb levels and virus-specific IgG levels in COVID-19 patients, serum samples were grouped by time (weeks) after symptom onset. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. cache = ./cache/cord-279550-7u2hksxm.txt txt = ./txt/cord-279550-7u2hksxm.txt === reduce.pl bib === id = cord-279106-3ffa9djf author = Syatila Ab Ghani, Nur title = Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6970 sentences = 404 flesch = 52 summary = In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed. 33 In this work, amino acid side chain similarity searching was utilized to propose alternative target sites in 34 SARS-CoV-2 protein structures for drug repositioning. cache = ./cache/cord-279106-3ffa9djf.txt txt = ./txt/cord-279106-3ffa9djf.txt === reduce.pl bib === id = cord-278682-s4gfbsqy author = Chan, W-M title = Precautions in ophthalmic practice in a hospital with a major acute SARS outbreak: an experience from Hong Kong date = 2005-04-29 pages = extension = .txt mime = text/plain words = 4131 sentences = 218 flesch = 47 summary = The ultimate infectivity of the tears secretion and ocular discharge from SARS patients may bring impacts on not only the daily ophthalmic practice but also the universal infection control measures practiced by general public and health-care workers. Discard gloves, wash or alcohol-rub the hands and then put on new gloves in-between case Wear glove in high-risk procedure General categories: for all patients attending the ophthalmic outpatients in which the SARS status is not certain. In a case-control study among 254 Hong Kong health-care workers with documented exposure to SARS patients, none of the 69 staff reporting use of four infection control measures, namely mask, gloves, gowns, and hand washing, was infected. Hospital Authority guideline on infection control of Severe Acute Respiratory Syndrome (SARS) cache = ./cache/cord-278682-s4gfbsqy.txt txt = ./txt/cord-278682-s4gfbsqy.txt === reduce.pl bib === id = cord-278939-z6kiee09 author = Mani, Janice S. title = Natural product-derived phytochemicals as potential agents against coronaviruses: a review date = 2020-04-30 pages = extension = .txt mime = text/plain words = 8148 sentences = 435 flesch = 46 summary = As previous work has highlighted the potential of traditional Chinese medicines as a source of potential novel drugs (Ling, 2020) , we have not included details on such studies investigating the antiviral activity of remedies comprising portions of numerous plant species in this review. (2020) virtually screened 83 compounds found in Chinese traditional medicines for activity against the RNA-dependent RNA polymerase of SARS-CoV-2, identifying theaflavin, an antioxidant polyphenol, as a potential inhibitor. Several authors have utilised virtual computer docking models to screen for potential compounds that could bind to and inhibit key proteins present in SARS-CoV (Liu and Zhou, 2005; Toney et al., 2004; Wang et al., 2007) , highlighting the potential antiviral activity of compounds such as sabadinine and aurantiamide acetate. Several large in vitro screening studies searching for inhibitory activity of naturally occurring compounds against SARS-CoV have been performed, mainly on Chinese medicinal herbs (Li et al., 2005; Wang et al., 2003) . cache = ./cache/cord-278939-z6kiee09.txt txt = ./txt/cord-278939-z6kiee09.txt === reduce.pl bib === id = cord-278648-hkvurb2k author = Menachery, Vineet D. title = Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis date = 2017-11-15 pages = extension = .txt mime = text/plain words = 5195 sentences = 263 flesch = 47 summary = While the absence of 2′O-MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Generation of mutants with changes in the NSP16 KDKE active site resulted in IFN-mediated in vitro and in vivo attenuation of both mouse hepatitis virus (MHV) and SARS-CoV (9, 10) . While a more rapid CPE following both WT and dNSP16 mutant MERS-CoV infections precluded an equivalent finding at late time points, the SARS-CoV results suggest that the absence of NSP16 activity eventually initiates host response changes that contribute to attenuation at late time points. cache = ./cache/cord-278648-hkvurb2k.txt txt = ./txt/cord-278648-hkvurb2k.txt === reduce.pl bib === id = cord-279563-4lu1n0s7 author = Gorzalski, Andrew J. title = High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1720 sentences = 116 flesch = 47 summary = The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). CONCLUSIONS: The higher analytical sensitivity may explain the assay's ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. To assess differences in analytical sensitivity between real-time PCR and TMA, we performed a limit-ofdetection (LoD) study by creating a dilution series of purified / quantified SARS-CoV-2 genomic material either in VTM or APTIMA collection matrix. Noting the sensitivity difference demonstrated by the LoD study, we sought to assess the performance of TMA on specimens previously tested by RT-PCR for SARS-CoV-2. The Hologic Panther SARS-CoV-2 transcription mediated amplification test showed higher analytical sensitivity when compared to real time PCR for the detection of SARS-CoV-2. cache = ./cache/cord-279563-4lu1n0s7.txt txt = ./txt/cord-279563-4lu1n0s7.txt === reduce.pl bib === id = cord-279158-dsnniuo6 author = Luo, Y. title = Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3903 sentences = 200 flesch = 47 summary = title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study Through a systematic review, meta-analysis and retrospective cohort study, we found that the low blood sodium population may significantly increase the risk and severity of SARS-CoV-2 infection. In this study, we aimed to find a key risk factor for SARS-CoV-2 epidemic by investigating the relationship between the blood sodium concentration and the severity of patients with COVID-19 through a systematic reviews, meta-analysis and retrospective cohort study. For the systematic review and meta-analysis, median or mean values of serum sodium, chloride and potassium concentrations from each report were considered as an independent variable for statistical analysis, and an unpaired t-test was used to compare the differences between the groups related to the severity of disease. In this study, we found that the patients infected by SARS-CoV-2 on admission have presented the low blood sodium levels (hyponatremia) that were related to the disease severity. cache = ./cache/cord-279158-dsnniuo6.txt txt = ./txt/cord-279158-dsnniuo6.txt === reduce.pl bib === id = cord-279180-xad53zht author = Kumaravel, Santhosh Kumar title = Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies date = 2020-08-17 pages = extension = .txt mime = text/plain words = 11396 sentences = 653 flesch = 54 summary = The COVID-19 is a respiratory disease that spreads at a maximum rate through droplets of the infected people through the air (World Health Organisation 2020a). • In addition, the incorporation of lockdown with other treatment and prevention measures such as school closures, travel restrictions, and social distancing has had a greater impact on spread prevention, cases requiring critical care beds, and deaths compared with quarantine alone. Machine learning has the potential to support clinicians' work processing and management of large amounts of medical data contained in electronic health records and used in clinical applications which includes recognizing high-risk patients in need of ICU, the identification of early signs of lung cancer, determination of patient's respiratory status from X-rays in the chest, such deep learning approaches employ neural networks to predict the input-output data relationship. cache = ./cache/cord-279180-xad53zht.txt txt = ./txt/cord-279180-xad53zht.txt === reduce.pl bib === id = cord-279115-eyk8sxk7 author = Cecconi, Maurizio title = Ten things we learned about COVID-19 date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1621 sentences = 106 flesch = 51 summary = The infection starts with the competition between the SARS-CoV-2 virions arrived in the respiratory mucosa that express high levels of ACE2 receptors and the barrier made by mucus secreted by goblet cells and moved by hair-like cilia and innate immunity reactions. Evidence from SARS-CoV-1 suggests that these viruses may block interferon-mediated antiviral immunity (Fig. 1 ). Inflammation plays a key role in the development of COVID-19 from a SARS-CoV-2 infection. Unsurprisingly for a disease characterised by an inflammatory state in response to a viral infection, venous and arterial thromboembolic complications are common in hospitalised patients [6] . Given the timing and characteristics of the antibody response (see above), appropriately validated assays are instrumental for epidemiological studies, evaluation of plasma donations (see below), assessment of memory and response to vaccine, and as a companion diagnostic in RT-PCR-negative patients. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region cache = ./cache/cord-279115-eyk8sxk7.txt txt = ./txt/cord-279115-eyk8sxk7.txt === reduce.pl bib === id = cord-279363-4almssg6 author = Crespo, Roland Mojica title = Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión date = 2020-05-16 pages = extension = .txt mime = text/plain words = 5181 sentences = 512 flesch = 59 summary = En ese momento, a este nuevo coronavirus se le llamó 2019-nCoV (del inglés: 2019-novel coronavirus) y fue identificado por las autoridades sanitarias chinas como el agente causal de estos casos de neumonía atípica 1,3,4 . Hacia final de mes, el día 30 de enero la OMS declaró la enfermedad causada por el nuevo coronavirus como una emergencia de salud pública de preocupación internacional, ya que para aquel momento se habían reportado casos en todas las regiones de la OMS en solo un mes 9,11 . Concretamente la RNVE en su informe n°29 del día 7 de mayo enumera los principales síntomas presentados por el conjunto de la población española, hasta la fecha y a base de una muestra de 217,543 casos, de la siguiente manera: Entre estos hallazgos, es comúnmente observar la leucopenia y linfopenia, siendo esta última característica de COVID-19. cache = ./cache/cord-279363-4almssg6.txt txt = ./txt/cord-279363-4almssg6.txt === reduce.pl bib === id = cord-279435-ffgd2ets author = ALBalawi, Hani B title = COVID-19: Precautionary Guidelines for Ophthalmologists date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3183 sentences = 148 flesch = 49 summary = Healthcare providers, particularly ophthalmologists, are at high risk of a COVID-19 infection through unprotected contact with eye secretions during routine ophthalmic examinations that involve the use of direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that allows for close doctor-patient contact. In fact, ophthalmologists are at high risk of contracting the COVID-19 virus through unprotected eye contact with secretions during routine ophthalmic examinations with direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that has close doctor-patient contact. A three-stage control measure to reduce the transmission of the virus in the ophthalmology department in Hong Kong was based on text messaging to reschedule refill visits [6] ; a triage to identify patients with fever, conjunctivitis, and respiratory symptoms; asking those who recently traveled to areas infected with the virus to postpone their ophthalmology visits for 14 days; and the avoidance of micro-aerosol generating procedures, nasal endoscopy, and operations under general anesthesia. cache = ./cache/cord-279435-ffgd2ets.txt txt = ./txt/cord-279435-ffgd2ets.txt === reduce.pl bib === id = cord-279629-t1xjy12y author = Nazneen Akhand, Mst Rubaiat title = Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date = 2020-04-15 pages = extension = .txt mime = text/plain words = 6717 sentences = 379 flesch = 47 summary = The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Hence, the study was designed to develop a chimeric recombinant vaccine against COVID-19 by targeting four major structural proteins of the pathogen, while revealing the evolutionary history of different species of coronavirus based on whole genome and protein domain-based phylogeny. Apart from the human coronaviruses, we introduced other coronaviruses which choose different species of bats, whale, turkey, rat, mink, ferret, swine, camel, rabbit, cow and others as host (Supplementary TableDomain analysis of spike protein of coronaviruses reveals that they contain mainly one signature domains namely, coronavirus S2 glycoprotein (IPR002552), which is present in all the candidates. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. cache = ./cache/cord-279629-t1xjy12y.txt txt = ./txt/cord-279629-t1xjy12y.txt === reduce.pl bib === id = cord-279642-0j5828ah author = Stafford, Emma G. title = Pharmacovigilance in Patients with Diabetes: A Data-Driven Analysis Identifying Specific RAS Antagonists with Adverse Pulmonary Safety Profiles That Have Implications for COVID-19 Morbidity and Mortality date = 2020-06-01 pages = extension = .txt mime = text/plain words = 1918 sentences = 97 flesch = 48 summary = Angiotensin converting enzyme inhibitors (ACEIs) and angiotensin-II receptor blockers (ARBs) are considered first-line agents in diabetics due to their nephroprotective effects but administration of these drugs leads to upregulation of angiotensin-converting-enzyme-2 (ACE2), responsible for viral entry of severe-acute-respiratory-distress-syndrome, coronavirus-2 (SARS-CoV-2). In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. cache = ./cache/cord-279642-0j5828ah.txt txt = ./txt/cord-279642-0j5828ah.txt === reduce.pl bib === id = cord-279346-7del8d2p author = Callendret, Benoît title = Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date = 2007-07-05 pages = extension = .txt mime = text/plain words = 10731 sentences = 471 flesch = 49 summary = title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared. cache = ./cache/cord-279346-7del8d2p.txt txt = ./txt/cord-279346-7del8d2p.txt === reduce.pl bib === id = cord-279765-sb1ifyfx author = Isakova-Sivak, Irina title = A promising inactivated whole-virion SARS-CoV-2 vaccine date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1083 sentences = 52 flesch = 44 summary = In this regard, the study by Shengli Xia and colleagues 7 is timely because it provides valuable evidence for the safety and immunogenicity of a β-propiolactone inactivated aluminium hydroxideadjuvanted whole-virion SARS-CoV-2 vaccine candidate developed by China National Biotec Group and the Beijing Institute of Biological Products (BBIBP-CorV), which was tested in randomised, double-blind, placebocontrolled phase 1/2 clinical trials in healthy individuals aged 18 years and older. Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Effect of an inactivated vaccine against SARS-CoV-2 on safety and immunogenicity outcomes: interim analysis of 2 randomized clinical trials Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBIBP-CorV: a randomised, double-blind, placebo-controlled, phase 1/2 trial cache = ./cache/cord-279765-sb1ifyfx.txt txt = ./txt/cord-279765-sb1ifyfx.txt === reduce.pl bib === id = cord-279443-2e4gz2bo author = Khan, Suliman title = Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns date = 2020-06-09 pages = extension = .txt mime = text/plain words = 4939 sentences = 245 flesch = 43 summary = To identify and select the papers in this review we searched the published research and review articles relevant to origin and outbreaks of three human coronaviruses, and features, transmission, spread, entry mechanisms, infectiousness, control strategies, and animals hosts for SARS-CoV-2. Although it is important to know about the symptoms' appearance and severity, however, understanding the transmission of the infection to healthy individuals from COVID-19 patients and zoonotic sources can be of great importance in the aspects of developing strategies to prevent and control the spread of COVID-19. This outbreak was reported to be caused by SARS-CoV, originated from market civets before its transmission and infection in humans (17) . Early claims came FIGURE 2 | The SARS-CoV-2 transmission from bats via unknown intermediate to humans causes infectiousness known as COVID-19 disease. According to the CDC report on coronavirus disease, individuals with underlying chronic medical conditions are at higher risk for contracting COVID-19 infection. cache = ./cache/cord-279443-2e4gz2bo.txt txt = ./txt/cord-279443-2e4gz2bo.txt === reduce.pl bib === id = cord-279766-s3ms5f56 author = Ye, Zhongde title = A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis date = 2008-07-28 pages = extension = .txt mime = text/plain words = 3408 sentences = 181 flesch = 46 summary = title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis All these data suggest that ORF-6 induces apoptosis via Caspase-3 mediated, ER stress and JNK-dependent pathways. We observed that ORF-6 was able to induce apoptosis when overexpressed in Vero E6 and COS-7 cells (Fig. 1A and B) . The death rates were comparable to the rates caused by the overexpression of Bax, a well-known pro-apoptotic member of the Bcl-family, and ORF-7a, a SARS protein that has been shown to induce apoptosis [19] . Our observation suggests that overexpression of ORF-6 induced apoptosis via a Caspase-3-dependent pathway. One of the possible mechanisms for SARS protein-induced cell death is via the JNK pathway. Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells G0/G1 arrest and apoptosis induced by SARS-CoV 3b protein in transfected cells cache = ./cache/cord-279766-s3ms5f56.txt txt = ./txt/cord-279766-s3ms5f56.txt === reduce.pl bib === id = cord-279750-if9vphb2 author = Savić, Dragan title = Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report date = 2020-07-27 pages = extension = .txt mime = text/plain words = 2041 sentences = 138 flesch = 50 summary = title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report We are presenting a case of a 13-year-old girl with a ruptured cerebral pseudoaneurysm of the left middle cerebral artery (M2 segment) with severe intracerebral hemorrhage as the earliest manifestation of COVID-19 infection. There are rare case reports of adult patients (the youngest was a 31-year-old male, other patients over 60 years old) with COVID-19 infection and ruptured cerebral aneurysm with subarachnoid hemorrhage [1, 16, 19] . In this paper, we present an adolescent girl with COVID-19 infection, who developed an intracerebral hematoma due to cerebral pseudoaneurysm rupture. As far as we know, this is the first reported case of an adolescent with ruptured cerebral pseudoaneurysm as the initial presentation of COVID-19 infection. As a consequence of the infection, a multisystem inflammatory syndrome or the direct damage by the virus has resulted in severe brain hemorrhage attributable to the ruptured pseudoaneurysm. cache = ./cache/cord-279750-if9vphb2.txt txt = ./txt/cord-279750-if9vphb2.txt === reduce.pl bib === id = cord-279616-8gtumtxb author = Wu, Kitty K. title = Posttraumatic Stress after SARS date = 2005-08-17 pages = extension = .txt mime = text/plain words = 1746 sentences = 86 flesch = 55 summary = We used 2 Chinese self-report measures to examine features of PTSD, anxiety, and depression in 131 survivors of severe acute respiratory syndrome at 1 month and 3 months after discharge from the hospital. The first category included pre-SARS variables: sex, age, education level, family income, availability of emotional support as indicated by the number of persons with whom one could talk and share worries, and whether one was a healthcare worker. The measures used in the study include the Chinese versions of the Impact of Event Scale -Revised (IES-R) (7, 8) and the Hospital Anxiety and Depression Scale (HADS) (8) (9) (10) . Results of Pearson correlations (Table 2) showed that the level of SaO 2 , the number of persons with whom one could talk and share worries, and the rating on perceived threat were significantly related to various IES-R and HADS subscale scores. cache = ./cache/cord-279616-8gtumtxb.txt txt = ./txt/cord-279616-8gtumtxb.txt === reduce.pl bib === id = cord-279131-1unb0z79 author = Buijsers, Baranca title = Beneficial non-anticoagulant mechanisms underlying heparin treatment of COVID-19 patients date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3989 sentences = 219 flesch = 30 summary = Here, we summarise potential beneficial, non-anticoagulant mechanisms underlying treatment of COVID-19 patients with heparin/LMWH, which include: (i) Inhibition of heparanase activity, responsible for endothelial leakage; (ii) Neutralisation of chemokines, and cytokines; (iii) Interference with leukocyte trafficking; (iv) Reducing viral cellular entry, and (v) Neutralisation of extracellular cytotoxic histones. In addition to functioning as anticoagulants, heparins have other therapeutic functions that are relevant for the treatment of COVID-19-associated clinical manifestations, i.e. neutralisation of inflammatory chemokines, and cytokines, such as CXCL-1, IL-6, and IL-8 that play a key role in ARDS; neutralisation of extracellular cytotoxic histones and by interfering with leukocyte trafficking [20] . Data for this review were identified by searches of PubMed, and preprint servers, and references from relevant articles using the search terms "COVID-19", "Heparin", "Non-anticoagulant functions of heparin", "Low molecular weight heparin", "ARDS", "Kidney dysfunction", "Endothelial barrier dysfunction", "Heparanase", "Heparan sulphate", "Viral entry", "Heparanase inhibition", "Inflammation", "Complement system", and "Neutrophil extracellular traps". cache = ./cache/cord-279131-1unb0z79.txt txt = ./txt/cord-279131-1unb0z79.txt === reduce.pl bib === id = cord-279439-h4ji0ttm author = Viotti, Manuel title = HUMAN PRE-IMPLANTATION EMBRYOS ARE PERMISSIVE TO SARS-COV-2 ENTRY date = 2020-09-30 pages = extension = .txt mime = text/plain words = 517 sentences = 41 flesch = 49 summary = DESIGN: Assessment of expression levels of SARS-CoV-2 entry mediators in human embryo biopsies by RNAseq analysis, and infection of cultured embryos with SARS-CoV-2 Spike glycoprotein pseudotyped reporter virions expressing green fluorescent protein (GFP). MATERIALS AND METHODS: Trophectoderm biopsies from blastocyst-stage embryos (n¼24) were processed for RNAseq using a commercial kit and sequenced; results were analyzed for expression of factors implicated in SARS-CoV-2 cellular entry. For viral infection experiments, blastocyst-stage embryos (n¼94) were hatched from zonas mechanically, and infected by spinoculation with GFP-reporter virions pseudotyped with the SARS-CoV-2 Spike glycoprotein (required for SARS-CoV-2 entry). RESULTS: Cells collected from blastocyst-stage embryos robustly expressed the canonical SARS-CoV-2 entry receptor ACE2 and the putative activator protease TMPRSS2, in addition to other reported entry factors. Embryos exposed to reporter virions pseudotyped with SARS-CoV-2 Spike glycoprotein displayed robust GFP signal, often in numerous cells with cytoplasmic localization. CONCLUSIONS: Our results indicate that cells present in preimplantation embryos are permissive to the canonical Spike-ACE2 viral entry mechanism utilized by SARS-CoV-2. cache = ./cache/cord-279439-h4ji0ttm.txt txt = ./txt/cord-279439-h4ji0ttm.txt === reduce.pl bib === id = cord-279861-gk8cow8k author = Glasser, John W. title = Modeling and public health emergency responses: Lessons from SARS date = 2011-01-28 pages = extension = .txt mime = text/plain words = 4361 sentences = 196 flesch = 40 summary = By overestimating the potential of managing contacts versus cases, moreover, we may even have inadvertently contributed to a lingering misunderstanding of means by which this epidemic was controlled that will affect their future responses to newly-emerging infectious diseases. Given the assumptions outlined above, together with a gamma distribution, these results suggest that for a disease with ℜ 0 = 3, isolation that was 100% effective in blocking transmission could prevent ℜ 0 − 1 infections (and thus lead to epidemic control) if implemented up to 5.2 days after symptom onset, on average (Fig. 1) . Knowledgeable public health practitioners might have cautioned against overestimating the potential impact of managing contacts of SARS patients, and interpreted observations suggesting that infected people were not particularly infectious until acutely ill as an indication for managing cases instead. cache = ./cache/cord-279861-gk8cow8k.txt txt = ./txt/cord-279861-gk8cow8k.txt === reduce.pl bib === id = cord-279223-qvih5qas author = Hascoët, Jean-Michel title = Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3057 sentences = 165 flesch = 50 summary = Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Thus, although the mother was considered cleared at 6 weeks after the onset of infection, which was confirmed by negative nasopharyngeal and stool SARS-CoV-2 RT-PCR tests after delivery, we tested stool and pharynx swab samples from asymptomatic baby-girl D. Two additional babies and their mothers were tested at birth because the mothers had symptomatic infection, documented with positive SARS-CoV-2 RT-PCR results, at 28 and 31 days before delivery, respectively. Despite the first newborn was asymptomatic and the screening performed as part of routine systematic testing, SARS-CoV-2 RNA detection through early nasopharyngeal sampling and the persistent detection of virus in stool strongly suggest possible vertical maternofetal infection. cache = ./cache/cord-279223-qvih5qas.txt txt = ./txt/cord-279223-qvih5qas.txt === reduce.pl bib === id = cord-279584-9x1d1kp1 author = Anderson, E. M. title = Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection date = 2020-11-10 pages = extension = .txt mime = text/plain words = 2949 sentences = 206 flesch = 54 summary = Finally, we completed a series of studies using 36 serum collected from COVID-19 patients to determine if antibodies reactive to hCoVs are 37 boosted upon SARS-CoV-2 infections. We completed ELISAs to quantify levels of pre-pandemic SARS-CoV-2-reactive IgG 42 antibodies in 204 human serum samples collected in 2017. We completed ELISAs to quantify levels of pre-pandemic hCoV-reactive IgG antibodies 69 in all 204 human serum samples collected in 2017. We 74 completed full antibody titrations to directly compared levels of hCoV antibodies in a subset of 75 pre-pandemic samples from individuals who either did (n=12) or did not (n=51) possess cross-76 reactive SARS-CoV-2 antibodies (Figure 1f-h) . Our study demonstrates that ~23% of individuals possessed SARS-CoV-2 cross-reactive 137 serum antibodies prior to the COVID-19 pandemic. We compared antibody titers in 296 pre-pandemic serum samples from individuals who did and did not have a subsequent PCR-297 confirmed SARS-CoV-2 infection. cache = ./cache/cord-279584-9x1d1kp1.txt txt = ./txt/cord-279584-9x1d1kp1.txt === reduce.pl bib === id = cord-279725-d82sj80v author = Ströher, Ute title = Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date = 2004-04-01 pages = extension = .txt mime = text/plain words = 2235 sentences = 126 flesch = 52 summary = We evaluated the susceptibility of the SARS-related coronavirus (SARS CoV) to ribavirin and interferon (IFN)-α in vitro by use of cytopathic effect, plaque assay, and immunoblot analysis. To support the search for effective antiviral treatments, we evaluated the susceptibility of SARS CoV isolates (detailed studies were performed with the Tor2 isolate [Toronto, Canada]) to ribavirin and interferon (IFN)-a-2b in vitro. Our data indicate that ribavirin does not inhibit the virus at concentrations attainable in human serum but that IFN-a-2b may be useful and deserves further evaluation as a therapeutic agent. To quantify the effect of IFN-a-2b on the replication of the SARS CoV, Vero E6 cells were infected at an MOI of 0.001 and were incubated in the presence IFN-a-2b (0-5000 IU/mL), as described above. Whether combined therapy with IFN-a-2b and ribavirin would inhibit the replication of the SARS CoV in vitro has not yet been evaluated; the combination is more effective than either agent used alone for the treatment of HCV infection in humans. cache = ./cache/cord-279725-d82sj80v.txt txt = ./txt/cord-279725-d82sj80v.txt === reduce.pl bib === id = cord-279576-wt4crton author = Fajardo, Álvaro title = Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date = 2020-05-13 pages = extension = .txt mime = text/plain words = 4842 sentences = 263 flesch = 54 summary = Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . cache = ./cache/cord-279576-wt4crton.txt txt = ./txt/cord-279576-wt4crton.txt === reduce.pl bib === id = cord-280147-xvzi1i0v author = Consoli, Letizia title = 2019 novel coronavirus (COVID-19) pneumonia complications: the importance of lung ultrasound date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1386 sentences = 76 flesch = 46 summary = Herein, we report a case of a patient affected by COVID-19 pneumonia referred in the emergency department of our institution on April 4, 2020, with peculiar lung ultrasound findings. In January 2020, Chinese scientists isolated a novel coronavirus from patients affected by viral pneumonia, denominated severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), and in February 2020, the World Health Organization designated as COVID-19 the coronavirus disease caused by SARS-COV-2. As indicated in a report from the Chinese Center for Disease Control and Prevention on 44,500 SARS-COV-2 patients, severe respiratory symptoms were found in 14% of cases, characterized by dyspnea, hypoxia, or > 50% lung involvement on imaging. On the other hand, ultrasound may produce a real-time and dynamic evaluation, even in Convex array probe showed the absence pleural sliding at the left lung with a "barcode sign" at the M-mode evaluation cases with critical complications of severe COVID-19 pneumonia, such as pneumothorax. cache = ./cache/cord-280147-xvzi1i0v.txt txt = ./txt/cord-280147-xvzi1i0v.txt === reduce.pl bib === id = cord-279754-95zawygq author = Hsu, Yu-Chen title = Risk and Outbreak Communication: Lessons from Taiwan's Experiences in the Post-SARS Era date = 2017-04-01 pages = extension = .txt mime = text/plain words = 3387 sentences = 161 flesch = 46 summary = After the SARS outbreak, Taiwan's Centers for Disease Control (Taiwan CDC) followed the WHO outbreak communication guidelines on trust, early announcements, transparency, informing the public, and planning, in order to reform its risk communication systems. After the SARS outbreak, Taiwan's Centers for Disease Control (CDC) followed the WHO outbreak communication guidelines-on trust, announcing early, transparency, informing the public, and planning-to reform its risk communication systems. In order to analyze the efficiency of risk communication on influenza vaccination, Taiwan CDC has monitored the toll-free hotline to identify topics that are of most concern to the public (eg, who are the target population, where to get the shot, adverse event reporting). The government of Taiwan has demonstrated considerable improvement in its risk communication practices during public health emergencies since the SARS outbreak in 2003. cache = ./cache/cord-279754-95zawygq.txt txt = ./txt/cord-279754-95zawygq.txt === reduce.pl bib === id = cord-280043-bm0qkrod author = Esagian, Stepan M. title = Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic date = 2020-06-04 pages = extension = .txt mime = text/plain words = 4217 sentences = 214 flesch = 38 summary = As the coronavirus disease 2019 (COVID-19) outbreak has rapidly evolved into a global pandemic, abdominal organ transplantation programs are currently facing multiple challenges. According to the report of the first case series from China, a significant proportion of patients (23.7%) suffered from comorbidities, which are commonly seen in abdominal transplant candidates, including hypertension (15.0%), diabetes mellitus (7.2%), hepatitis B infection (2.1%), cancer (0.9%), chronic kidney disease (0.7%) and immunodeficiency (0.2%) (7) . Although data for abdominal organ transplant candidates and recipients are still limited, emerging reports have indicated that these patients may present with atypical COVID-19 manifestations. These guidelines address three potential standpoints the epidemic confronts transplantation systems with; first, the risk of donor-derived SARS-CoV-2 infection, which although has not been reported thus far in neither organ or blood product recipients, extensive donor screening protocols have been implemented in many transplant centers in pandemic areas. cache = ./cache/cord-280043-bm0qkrod.txt txt = ./txt/cord-280043-bm0qkrod.txt === reduce.pl bib === id = cord-279406-wwdqh9qs author = Guzman, Norberto A. title = A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy date = 2020-07-30 pages = extension = .txt mime = text/plain words = 17172 sentences = 835 flesch = 33 summary = To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses. It would be beneficial to have a sample processing method before separation, to isolate and concentrate the intended viruses or EVs. Immunoaffinity capillary electrophoresis has already been proven to be a useful technology to isolate, separate, and quantify cell-free molecules of biological interest based on the specificity and selectivity not only of antibody reagents, but also of lectin and aptamer reagents, quantifying molecules ranging from microgram/milliliter to femtogram/milliliter [25, 54, 55, 57, 75] . cache = ./cache/cord-279406-wwdqh9qs.txt txt = ./txt/cord-279406-wwdqh9qs.txt === reduce.pl bib === id = cord-280025-4hmecfi0 author = Korber, B title = Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 11173 sentences = 524 flesch = 54 summary = We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. Over the past two months, the HIV database team at Los Alamos National Laboratory has turned to developing an analysis pipeline to track in real time the evolution of the SARS-CoV-2 Spike (S) protein in the COVID-19 pandemic, using the Global Initiative for Sharing All Influenza Data GISAID SARS-CoV-2 sequence database as our baseline (Sup. Item 1 is the GISAID acknowledgments table, listing all the groups who contribute sequences to this global effort) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) . GISAID is the primary SARS-CoV-2 sequence database resource, and our intent is to complement what they provide with visualizations and summary data specifically intended to support the immunology and vaccine communities, and to alert the broader community to changes in frequency of mutations that might signal positive selection and a change in either viral phenotype or antigenicity. cache = ./cache/cord-280025-4hmecfi0.txt txt = ./txt/cord-280025-4hmecfi0.txt === reduce.pl bib === id = cord-279932-bilr71ay author = Plotkin, Stanley A title = The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date = 2020-07-16 pages = extension = .txt mime = text/plain words = 1119 sentences = 61 flesch = 52 summary = A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development cache = ./cache/cord-279932-bilr71ay.txt txt = ./txt/cord-279932-bilr71ay.txt === reduce.pl bib === id = cord-279474-c5y2lygj author = Bozzo, Caterina Prelli title = IFITM proteins promote SARS-CoV-2 infection of human lung cells date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1110 sentences = 90 flesch = 55 summary = Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) restrict numerous viral pathogens and are thought to prevent infection by severe acute respiratory syndrome coronaviruses (SARS-CoVs). In striking contrast, however, endogenous IFITM expression promoted genuine SARS-CoV-2 infection in human lung cells both in the presence and absence of interferon. Taken together, our results show that all three IFITMs prevent SARS-CoV-2 S/ACE2-mediated attachment and membrane fusion in single round pseudotype infection assays. Notably, titration experiments showed that IFITMs do not promote genuine SARS-CoV-2 247 infection in HEK239T cells over a broad range of expression levels ( Figure S4E ). (F) Quantification of the entry of VSV(luc)ΔG*-SARS-CoV-2-S by luciferase activity in HEK293T cells transiently expressing indicated proteins (IFITM mutants) and infected 24 h post-transfection with the VSVpp (MOI 0.025) for 16 h. (G) Quantification of the entry of HIV(Fluc)Δenv*-SARS-CoV-2-S by luciferase activity in HEK293T cells stably expressing indicated proteins (IFITM mutants) and ACE2 cache = ./cache/cord-279474-c5y2lygj.txt txt = ./txt/cord-279474-c5y2lygj.txt === reduce.pl bib === id = cord-279519-4ad8ubrt author = Poochi, Saravana Prabha title = Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein date = 2020-07-06 pages = extension = .txt mime = text/plain words = 2363 sentences = 146 flesch = 50 summary = title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein Angiotensin converting enzyme 2 (ACE2) and main protease (M(Pro)) are significant target proteins, mainly involved in the attachment of viral genome to host cells and aid in replication of severe acute respiratory syndrome‐coronaviruses or SARS‐CoV genome. In the present study, we identified 11 potent bioactive compounds from ethanolic leaf extract of Ipomoea obscura (L.) by using GC‐MS analysis. These potential bioactive compounds were considered for molecular docking studies against ACE2 and M(Pro) target proteins to determine the antiviral effects against SARS‐COV. In this investigation we performed in silico docking by applying Glide 5.5 (Dik-Lung, Daniel, & Chung, 2011; Glide, 2009 ), against respiratory therapeutic target ACE2 exhibited in human and M Pro in SARS-CoV-2. Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS-CoV-2 main protease and ACE2 protein cache = ./cache/cord-279519-4ad8ubrt.txt txt = ./txt/cord-279519-4ad8ubrt.txt === reduce.pl bib === id = cord-279518-z3k7zaw4 author = Xue, Xiaotong title = High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 1506 sentences = 89 flesch = 52 summary = High ACE2 expression was identified in the type II alveolar cells (AT2), bronchial transient secretory cells, small intestinal epithelium cells and the oral epithelial cells in accordance with respiratory clinical manifestations and rare clinical manifestations such as gastrointestinal symptoms, suggesting the respiratory droplet, digestive ２ and fecal-oral transmission routes of SARS-CoV-2 (Lukassen et al., 2020; Liang et al., 2020; Xu et al., 2020a) . Therefore, we hypothesized that the expression and distribution of ACE2 in human organs and tissues could reflect the potential infection routes of SARS-CoV-2. However, scRNA-seq has not yet been applied to examine the ACE2 expression in the cells of skin tissues, and the transmission of this virus by percutaneous routes remains unclear. In conclusion, the high expression of ACE2 on keratinocytes in human skin indicated that percutaneous transmission might be a potential risk route for SARS-CoV-2 infection, especially in condition of skin barrier dysfunction. cache = ./cache/cord-279518-z3k7zaw4.txt txt = ./txt/cord-279518-z3k7zaw4.txt === reduce.pl bib === id = cord-279520-zccd1mq5 author = Christian, Michael D. title = Possible SARS Coronavirus Transmission during Cardiopulmonary Resuscitation date = 2004-02-17 pages = extension = .txt mime = text/plain words = 4047 sentences = 199 flesch = 45 summary = Infection of healthcare workers with the severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to occur primarily by either contact or large respiratory droplet transmission. We investigated a possible cluster of SARS-CoV infections in healthcare workers who used contact and droplet precautions during attempted cardiopulmonary resuscitation of a SARS patient. On the basis of the results of this investigation and previous reports of SARS transmission during aerosol-generating procedures, a systematic approach to the problem is outlined, including the use of the following: 1) administrative controls, 2) environmental engineering controls, 3) personal protective equipment, and 4) quality control. However, despite the use of infection control precautions and personal protective equipment designed to prevent contact and droplet transmission, episodes of SARS-CoV transmission to health-care workers have continued to occur under certain circumstances. We present the results of an investigation of the first reported transmission of SARS-CoV to healthcare workers that occurred during attempted cardiopulmonary resuscitation of a completely unresponsive SARS patient. cache = ./cache/cord-279520-zccd1mq5.txt txt = ./txt/cord-279520-zccd1mq5.txt === reduce.pl bib === id = cord-279989-swsxez0a author = Sokolov, Elisaveta title = Non-convulsive status epilepticus: COVID-19 or clozapine induced? date = 2020-10-04 pages = extension = .txt mime = text/plain words = 2664 sentences = 165 flesch = 54 summary = We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We highlight seizure disorders as a possible manifestation of SARS-CoV2 infection and describe the complexity of these presentations in the intensive care setting, especially in the context of atypical antipsychotics such as Clozapine. These two scans were done when the Findings that shed new light on the possible pathogenesis of a disease or an adverse effect patient was noted not to be waking following extubation, first as she was quadriplegic at this time and second to consider if there were any MRI features known to be associated with COVID-19. cache = ./cache/cord-279989-swsxez0a.txt txt = ./txt/cord-279989-swsxez0a.txt === reduce.pl bib === id = cord-280029-g1k3zlax author = Gabutti, Giovanni title = Coronavirus: Update Related to the Current Outbreak of COVID-19 date = 2020-04-08 pages = extension = .txt mime = text/plain words = 5006 sentences = 271 flesch = 53 summary = The World Health Organization (WHO) has officially named the infection coronavirus disease 2019 (COVID-19), and the virus has been classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS is caused by a virus that emerged in southern China in November 2002 and led to [ 8000 human infections and 774 deaths in 37 countries in the 2002-2003 period [3] ; MERS is related to a virus detected for the first time in Saudi Arabia in 2012, responsible for 2494 laboratoryconfirmed cases of infection and 858 deaths since September 2012 [4] . On January 11 and 12, 2020, the WHO received further details and information from the Chinese National Health Commission regarding the possible association of this epidemic with exposure in a fish market in Wuhan, and the Chinese authorities shared the genetic sequence of a new coronavirus, subsequently identified as SARS-CoV-2 [14] . cache = ./cache/cord-280029-g1k3zlax.txt txt = ./txt/cord-280029-g1k3zlax.txt === reduce.pl bib === id = cord-280050-fktc778q author = Tahir, Shumaila title = Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan date = 2020-06-17 pages = extension = .txt mime = text/plain words = 3423 sentences = 182 flesch = 53 summary = Methods We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. The primary aim of this retrospective observational study was to report the epidemiological features and statistics of individuals infected with COVID-19 from February 26 to April 24 from East Karachi, Pakistan, and contribute towards an accurate collection of figures from the country. The suspected or confirmed cases were clinically classified as asymptomatic, mild, moderate, severe, and critical, according to the National Institute of Health, Pakistan guidelines and are defined below in Table 1 [9]. Candidates with fever, symptoms of lower respiratory illness, and a travel history to Wuhan, China or other countries with uncontrolled COVID-19 cases or who have been in contact with an individual suspected of COVID-19 or with laboratory-confirmed COVID-19 in the preceding 14 days should be isolated and tested for the infection promptly [19] . cache = ./cache/cord-280050-fktc778q.txt txt = ./txt/cord-280050-fktc778q.txt === reduce.pl bib === id = cord-280003-ndpuezpo author = Lou, Bin title = Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date = 2020-03-27 pages = extension = .txt mime = text/plain words = 3024 sentences = 190 flesch = 57 summary = Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. In order to answer some of the questions, we investigated the characteristics of antibody responses in 80 Covid-19 patients during their hospitalization periods, through detecting total antibody, IgM and IgG using immunoassays. A total of 80 Covid-19 patients and 100 to 300 healthy people were tested for antibodies against SARS-CoV-2 using different immunoassays. The present data showed that the sensitivity of total antibody detection was higher than that of IgM and IgG (p<0.001) while the specificities are overall comparable when the same testing technic (ELISA, CLMA or LFIA) is used. cache = ./cache/cord-280003-ndpuezpo.txt txt = ./txt/cord-280003-ndpuezpo.txt === reduce.pl bib === id = cord-279569-289fu2yb author = Lei, Yu title = Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area date = 2020-03-13 pages = extension = .txt mime = text/plain words = 2291 sentences = 152 flesch = 57 summary = title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area Abstract Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in Epidemiological, clinical laboratory and radiological characteristics, chronic medical histories, clinical symptoms, treatment and outcome data were obtained from electronic medical records and analysed by two independent researchers. With advancing time, the medical history associated with case exposure to SARS-CoV-2 infected patients from Wuhan has become less obvious. In conclusion, imported cases of SARS-CoV-2 infection in Tibetan patients were generally mild in this high-altitude area. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan cache = ./cache/cord-279569-289fu2yb.txt txt = ./txt/cord-279569-289fu2yb.txt === reduce.pl bib === id = cord-279976-juz9jnfk author = Xie, Mingxuan title = Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date = 2020-04-01 pages = extension = .txt mime = text/plain words = 3863 sentences = 228 flesch = 50 summary = METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". cache = ./cache/cord-279976-juz9jnfk.txt txt = ./txt/cord-279976-juz9jnfk.txt === reduce.pl bib === id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 pages = extension = .txt mime = text/plain words = 9036 sentences = 483 flesch = 43 summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). cache = ./cache/cord-279691-v5kpmk0b.txt txt = ./txt/cord-279691-v5kpmk0b.txt === reduce.pl bib === id = cord-280198-bhjw6xc5 author = Olaleye, Omonike A. title = Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1814 sentences = 112 flesch = 49 summary = title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 Spike Protein Interaction In Vitro Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effect in vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. Therefore, targeting 106 the interaction between human ACE2 receptor and the RBD in S protein of SARS-CoV-2 could 107 serve as a promising approach for the development of effective entry inhibitors for potential 108 prevention and/or treatment of COVID-19. Activity of Clioquinol (CLQ) and Analogues against ACE2 Exopeptidase Activity and 725 ACE2 and SARS-CoV-2 Spike (RBD) Protein Interaction cache = ./cache/cord-280198-bhjw6xc5.txt txt = ./txt/cord-280198-bhjw6xc5.txt === reduce.pl bib === id = cord-279940-i2rgjpxf author = Comentale, Giuseppe title = Sars-Cov-2 interference in HEME production: is it the time for an early predictive biomarker? date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1348 sentences = 65 flesch = 43 summary = In particular, thrombosis seems to drive the entire disease course: Sars-Cov-2 infection triggers a large thrombophilic response that results in diffuse occlusion of the smaller vessels, especially in the lungs where the result is a wide thrombotic microangiopathy [5] explaining the radiologic "ground glass" pattern. Furthermore, as IL-1 was shown to be a major culprit in the development of many cardiovascular diseases [11] , its involvement in the Sars-Cov-2 infection could explain the high mortality and morbidity rate among cardiopathic patients. Identifying the mechanisms by which Sars-Cov-2 damages the human body, focusing on the structural proteins, could be a possible strategy to finding an effective solution. From this point of view, Sars-Cov-2 seems to be very similar to malaria: many clinical and scientific reports have shown that Covid-19, not only can be successfully treated with chloroquine but also, like malaria, appears to be diagnosed much more frequently in blood group A patients [14] . cache = ./cache/cord-279940-i2rgjpxf.txt txt = ./txt/cord-279940-i2rgjpxf.txt === reduce.pl bib === id = cord-280350-ay4cnzn5 author = Chan, Jasper F.W. title = Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus date = 2013-10-03 pages = extension = .txt mime = text/plain words = 5156 sentences = 259 flesch = 45 summary = We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. Given the limited time available to develop novel anti-MERS-CoV agents in this evolving epidemic, we attempted to provide an alternative solution by identifying potential broad-spectrum antiviral agents against MERS-CoV and influenza A viruses by a small compound-based forward chemical genetics approach using chemical libraries consisting of 1280 drug compounds already marketed or having reached clinical trials in the United States, Europe, or Asia (Microsource Discovery Systems, USA). 25 We then assessed the anti-MERS-CoV activities of the identified drug compounds in cell culture by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction assay (PRA) assays, as well as drug cytotoxicity. cache = ./cache/cord-280350-ay4cnzn5.txt txt = ./txt/cord-280350-ay4cnzn5.txt === reduce.pl bib === id = cord-280454-etf32afd author = Moustaqil, Mehdi title = SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date = 2020-06-05 pages = extension = .txt mime = text/plain words = 10152 sentences = 562 flesch = 56 summary = title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts Direct cleavage of IRF3 by NSP3 could explain the blunted TypeI IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. In this report, we show that the viral proteases PLpro and 3CLpro of SARS-CoV2 lead to the in-vitro proteolytic cleavage of three important proteins of the host immune response: IRF3, TAB1 and NLRP12 (Fig. 1B) . The presence of the five human-like cleavage sites for IRF3, TAB1 and NLRP12 in a single species shows that it is possible that the SARS viruses could have gained the new functionality of cleaving these Human Innate Immune Proteins in a single reservoir host, potentially in Myotis Davidii. cache = ./cache/cord-280454-etf32afd.txt txt = ./txt/cord-280454-etf32afd.txt === reduce.pl bib === id = cord-280001-y7pvj2l1 author = Patel, Robin title = Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date = 2020-03-26 pages = extension = .txt mime = text/plain words = 1785 sentences = 77 flesch = 46 summary = If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness. cache = ./cache/cord-280001-y7pvj2l1.txt txt = ./txt/cord-280001-y7pvj2l1.txt === reduce.pl bib === id = cord-280392-ij5gtesw author = Gultom, Mitra title = Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date = 2020-11-10 pages = extension = .txt mime = text/plain words = 2253 sentences = 140 flesch = 50 summary = In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. The AEC 131 cultures from 12 different species (rhesus macaque, cat, ferret, dog, rabbit, pig, cattle, goat, llama, 132 camel, and two neotropical bats) were inoculated with 10.000 TCID50 of either IAV or IDV and incubated 133 at 33°C and 37°C. For IDV we observed 137 antigen-positive cells in all AEC model, except for rhesus macaque and one of the neotropical bat 138 species, indicating that the AEC cultures were all well-differentiated and susceptible to virus infection. In the viral sequences in the 96 hpi samples from virus-infected 156 rhesus macaque and cat AEC cultures, we observed no obvious signs of nucleotide transitions that lead 157 to nonsynonymous mutations compared to the respective inoculums ( Fig. 3) , irrespective of 158 temperature and animal species. cache = ./cache/cord-280392-ij5gtesw.txt txt = ./txt/cord-280392-ij5gtesw.txt === reduce.pl bib === id = cord-280423-v3r7vo0o author = Desmazes‐Dufeu, Nadine title = Discordant courses of COVID‐19 in a cohabiting couple of lung transplant recipients date = 2020-07-31 pages = extension = .txt mime = text/plain words = 1771 sentences = 107 flesch = 52 summary = Solid organ transplant recipients are perceived to be at increased risk of severe COVID‐19 due to their chronic use of immunosuppressive drugs (ISDs) and to their associated conditions. We report here two cases of COVID‐19 in a cohabiting couple of lung transplant recipients for cystic fibrosis, who had different ISDs management and who developed discordant courses of their disease. We report here two cases of synchronic COVID-19 in a cohabiting couple of lung transplant recipients for cystic fibrosis but who had discordant courses of their disease. 13 While lymphopenia and lower CD4 + and CD8 + lymphocytes count have been associated with worst outcome and prolonged viral shedding in the general population of COVID-19 patients, 14 other reports suggested that ISDs per se might diminish the "cytokine storm" underlying the development of acute respiratory distress syndrome (ARDS) and subsequent mortality. cache = ./cache/cord-280423-v3r7vo0o.txt txt = ./txt/cord-280423-v3r7vo0o.txt === reduce.pl bib === id = cord-280621-tph5n7ak author = Kim, Yunjeong title = Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor date = 2016-03-30 pages = extension = .txt mime = text/plain words = 7417 sentences = 354 flesch = 52 summary = Shifts in tissue or cell tropism and resulting changes in virulence have also been reported for coronaviruses; porcine respiratory coronavirus causes mild respiratory infection in pigs and presumably arose from transmissible gastroenteritis virus (TGEV), the etiologic agent of gastroenteritis in young pigs with a high fatality, by spontaneous mutations and/or deletions in its genome [9] . Effective treatment intervention for coronavirus infections with an immunopathological component, such as SARS, MERS and FIP, is speculated to involve the judicious use of immunomodulatory agents to enhance protective host immunity and decrease pathological immune responses and antiviral drugs to directly inhibit viral replication. These results on viral titers show that FIPV 3CLpro is a valid target for FIPV antiviral drugs and GC376 can effectively reduce the virus load in the macrophages from the ascites and the omentum of cats with FIP. cache = ./cache/cord-280621-tph5n7ak.txt txt = ./txt/cord-280621-tph5n7ak.txt === reduce.pl bib === id = cord-280408-0ze1lfnf author = Leon, A. title = SARS-CoV-2 infection may mask another infection date = 2020-05-16 pages = extension = .txt mime = text/plain words = 147 sentences = 22 flesch = 48 summary = key: cord-280408-0ze1lfnf authors: Leon, A.; Debry, C.; Renaud, M. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 journal: Eur Ann Otorhinolaryngol Head Neck Dis DOI: 10.1016/j.anorl.2020.05.005 sha: doc_id: 280408 cord_uid: 0ze1lfnf nan Brain CT, axial scan with bone window setting. Presence of a bone defect of the lateral wall of the left sphenoid sinus (arrow). MRI, gadolinium-enhanced T1-weighted sequence, coronal section through the cavernous sinus. Intense enhancement of the fluid-filled sphenoid sinus (solid arrow) and the walls of the lateral sellar compartment (*) with inflammatory stenosis of the intracavernous segment of the internal carotid arteries (dotted arrow). Neurological Complications of Acute and Chronic Sinusitis Neurologic Features in Severe SARS-CoV-2 Infection Incidence of thrombotic complications in critically ill ICU patients with COVID-19 European Position Paper on Rhinosinusitis and Nasal Polyps Intraoperative bacterial analysis in nasal polyposis: Clinical and functional impact cache = ./cache/cord-280408-0ze1lfnf.txt txt = ./txt/cord-280408-0ze1lfnf.txt === reduce.pl bib === id = cord-280231-jo3grxd5 author = Hardenberg, Jan‐Hendrik title = Covid‐19, ACE2 and the kidney date = 2020-08-02 pages = extension = .txt mime = text/plain words = 3901 sentences = 285 flesch = 55 summary = Corona-virus disease 2019 (Covid-19) is a global pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 15 A cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter collectrin (also known as B 0 AT1), with or without the receptor SARS-CoV2 binding domain (RBD), of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 F I G U R E 1 Evolution of the "anginotensin converting enzyme" (ACE) family. 25 That Covid-19 patients develop acute kidney injury (AKI) would not be a surprise. Progressive respiratory failure, not renal failure, is the primary T A B L E 1 A brief overview of Covid-19 patients, acute kidney injury (AKI) and renal-replacement therapies (RRT) Stepwise multivariate binary logistic regression analyses showed that severity of pneumonia was the risk factor most commonly associated with lower odds of proteinuric or haematuric remission and recovery from AKI. cache = ./cache/cord-280231-jo3grxd5.txt txt = ./txt/cord-280231-jo3grxd5.txt === reduce.pl bib === id = cord-280518-2tl0mtb8 author = Xia, Jianhua title = Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection date = 2020-03-12 pages = extension = .txt mime = text/plain words = 1359 sentences = 108 flesch = 60 summary = title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. On 7 January 2020, the Chinese Center for Disease Control and Prevention isolated and confirmed this pathogen as a novel type of coronavirus through a throat swab. Study Group of the International Committee on Taxonomy of Viruses named 2019-nCoV severe acute respiratory syndrome-related coronavirus 2, or SARS-CoV-2. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection cache = ./cache/cord-280518-2tl0mtb8.txt txt = ./txt/cord-280518-2tl0mtb8.txt === reduce.pl bib === id = cord-280062-1qrav1d5 author = McClenaghan, Elliot title = The global impact of SARS-CoV-2 in 181 people with cystic fibrosis date = 2020-11-04 pages = extension = .txt mime = text/plain words = 1707 sentences = 95 flesch = 62 summary = Whilst outcomes in this large cohort are better than initially feared overall, possibly due to a protective effect of the relatively younger age of the CF population compared to other chronic conditions, SARS-CoV-2 is not a benign disease for all people in this patient group. The characteristics of the 149 people in the non-transplant cohort were; median age 24 years (range 0-74 years), 48% male, 36% were homozygous and 37% were heterozygous for F508del, 24% had CFrelated diabetes (CFRD), 43% were taking CFTR modulator therapy, and median best FEV 1 prior to infection was 73% predicted, (range 18-123%) ( Table 1) . One of the seven deaths, in a non-transplant patient, was reported by the clinical team as being related to advanced cystic fibrosis, not SARS-CoV-2. In the non-transplant cohort, 4 deaths were recorded, 2 of which had a best FEV1 the year prior to infection of <40% predicted and 2 with 40-70% predicted. cache = ./cache/cord-280062-1qrav1d5.txt txt = ./txt/cord-280062-1qrav1d5.txt === reduce.pl bib === id = cord-280528-7ivw72l0 author = TUFAN, Abdurrahman title = COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs date = 2020-04-21 pages = extension = .txt mime = text/plain words = 7053 sentences = 364 flesch = 42 summary = In this review, to gain better information about appropriate anti-inflammatory treatments, mostly used in rheumatology for COVID-19, we have focused the attention on the structural features of SARS-CoV-2, the host immune response against SARS-CoV-2 and its association with the cytokine storm. The effective antiviral responses of the host innate and adaptive immunity, including the production of various proinflammatory cytokines, the activation of T cells, CD4 and CD8+ T cells, are essential for controlling the viral replication, limiting the spread of virus, inflammation and cleaning the infected cells [31, 32] . Few retrospective studies have revealed that the lung injury reported with Murray score is strongly associated with the level of IL-1α, IL-1ra, IL-2, IL-7, IL-10, IL-17, IFN-ɣ, inducible interferon protein (IP)-10, G-CSF, and MCP-3 and these cytokines and chemokines excluding MCP-3 are positively related to SARS-CoV-2 viral load 2 [7] . cache = ./cache/cord-280528-7ivw72l0.txt txt = ./txt/cord-280528-7ivw72l0.txt === reduce.pl bib === id = cord-280280-9jr7ekbu author = Bertoncelli, Deborah title = COVID19: potential cardiovascular issues in pediatric patients date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3393 sentences = 181 flesch = 36 summary = Ongoing studies and accumulated data are detailing the features and the effects of the new coronavirus disease 19 (COVID 19) in the adult population, and cardiovascular involvement is emerging as the most significant and life-threatening complication, with an increased risk of morbidity and mortality in patients with underlying cardiovascular disease. At present, though the limited data on the effects of COVID 19 in pediatric patients, children seem to count for a little proportion of SARS-COV 2 infection, and present with less severe disease and effects However infants and toddlers are at risk of developing critical course. Coronavirus disease 19 (COVID-19) is a severe acute respiratory syndrome for which the etiologic agent is the novel beta coronavirus SARS-CoV-2, first described in December 2019 in China in a cluster of patients presenting with pneumonia. The main presenting clinical feature of the disease is pneumonia, ranging from asymptomatic or mildly symptomatic to severe acute respiratory distress syndrome, but cardiovascular involvement is emerging as one of the most significant and life-threatening complications of SARS-CoV-2 infection (1, 2) . cache = ./cache/cord-280280-9jr7ekbu.txt txt = ./txt/cord-280280-9jr7ekbu.txt === reduce.pl bib === id = cord-280172-6o1gqe8v author = Sanami, Samira title = Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5835 sentences = 307 flesch = 55 summary = In this research, first, the CTL, HTL, and B-cell epitopes of the S protein were predicted using ProPred-1, ProPred, and ABCPred servers, respectively, and then were selected base on antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Next, the physicochemical properties of the construct were investigated, the 3D structure of the protein was predicted, and finally, its affinity to the MHC I and II molecules was investigated through docking, following that, was performed the molecular dynamics (MD) simulation of docking complexes. The antigenicity of the epitopes were calculated by VaxiJen v2.0 server (http://www.ddgpharmfac.net/vaxijen/VaxiJen/VaxiJen.html), which is based on the transformation of the protein sequences auto cross-covariance (ACC) into uniform vectors of main amino acid properties. selected N, M, and S proteins as the target antigen for the prediction of T and B-cell epitopes and designed a multi-epitope vaccine against SARS-CoV-2 [48] . cache = ./cache/cord-280172-6o1gqe8v.txt txt = ./txt/cord-280172-6o1gqe8v.txt === reduce.pl bib === id = cord-280068-rszu1c48 author = Twomey, Julianne D. title = COVID-19 update: The race to therapeutic development date = 2020-10-24 pages = extension = .txt mime = text/plain words = 6195 sentences = 331 flesch = 42 summary = We highlight two major lines of therapeutic strategies for COVID-19 treatment: 1) repurposing the existing drugs for use in COVID-19 patients, such as antiviral medications (e.g., remdesivir) and immunomodulators (e.g., dexamethasone) which were previously approved for other disease conditions, and 2) novel biological products that are designed to target specific molecules that are involved in SARS-COV-2 viral entry, including neutralizing antibodies against the spike protein of SARS-COV-2, such as REGN-COV2 (an antibody cocktail) and LY-COV555, as well as recombinant human soluble ACE2 protein to counteract SARS-COV-2 binding to the transmembrane ACE2 receptor in target cells. The current review highlights the potential therapeutic strategies for the treatment of COVID-19, including small molecule drugs and therapeutic proteins to target the SARS-CoV-2 viral entry, viral amplification or the host immune responses. cache = ./cache/cord-280068-rszu1c48.txt txt = ./txt/cord-280068-rszu1c48.txt === reduce.pl bib === id = cord-280821-kc0ut4oy author = Venturini, Elisabetta title = Treatment of children with COVID-19: position paper of the Italian Society of Pediatric Infectious Disease date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5481 sentences = 315 flesch = 45 summary = The Italian Society of Pediatric Infectious Diseases steering and scientific committee developed a position paper on treatment of children with COVID-19, reviewing the current literature on this topic and providing indications based on the available literature data. Currently, American guidelines on COVID-19 treatment published in May 2020, recommend both in children and adults to use lopinavir/ritonavir only in the context of clinical trials, given the lack of effectiveness reported now in literature [9, 12] . The latest Chinese guidelines on SARS-Cov-2 pneumoniae do not recommend the use of a specific antiviral for the treatment of COVID-19, and nevertheless include lopinavir/ritonavir among the available therapeutic options for hospitalized patients [29] . In May 2020, following an assessment of the emergency use authorization criteria and available scientific evidence, the FDA issued an emergency use authorization allowing for the administration of remdesivir intravenously by health care providers for the treatment of COVID-19 suspected or laboratoryconfirmed in adults and pediatric patients hospitalized with severe disease [34] . cache = ./cache/cord-280821-kc0ut4oy.txt txt = ./txt/cord-280821-kc0ut4oy.txt === reduce.pl bib === id = cord-280662-gakayv6e author = Bian, Jingwei title = Angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 receptor and RAS modulator date = 2020-10-13 pages = extension = .txt mime = text/plain words = 5251 sentences = 308 flesch = 49 summary = Angiotensin-converting enzyme 2 (ACE2) was rapidly identified as the critical functional receptor for SARS-CoV-2. Given that ACE2 functions as both a SARS-CoV-2 receptor and a RAS modulator, the treatment for COVID-19 presents a dilemma of how to limit virus entry but protect ACE2 physiological functions. We propose five novel working modes for functional receptor for SARS-CoV-2 infection and the routes of ACE2-mediated virus entering host cells, as well as its regulatory mechanism. SARS-CoV-2 has been shown to share the same functional receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV) 4, 5 . SARS-CoV S-protein binding facilitates ADAM17-dependent ACE2 shedding and has been shown to induce viral entry into the cell 52 . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-280662-gakayv6e.txt txt = ./txt/cord-280662-gakayv6e.txt === reduce.pl bib === id = cord-280628-ok62havd author = Groß, Sonja title = SARS-CoV-2 receptor ACE2-dependent implications on the cardiovascular system: From basic science to clinical implications date = 2020-04-30 pages = extension = .txt mime = text/plain words = 4453 sentences = 252 flesch = 43 summary = COVID-19 requires the collaboration of nearly 200 countries to curb the spread of SARS-CoV-2 while gaining time to explore and improve treatment options especially for cardiovascular disease (CVD) and immunocompromised patients, who appear to be at high-risk to die from cardiopulmonary failure. Since the coronavirus disease (COVID19) is still an emerging pandemic with more than 2.1 million confirmed cases worldwide [1] , special focus is currently directed towards the understanding of why people are hospitalized, receive intensive care, and frequently die as a consequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. While higher mortality rates among CVD patients are also associated with other respiratory diseases (especially influenza virus-induced flu or previous SARS epidemics), the question was put forward, whether people treated for heart-related illness are more prone to SARS-CoV-2 viral infection, based on first epidemiological evidence, but particularly based on the presumed upregulation of the SARS-CoV-2 entry receptor. cache = ./cache/cord-280628-ok62havd.txt txt = ./txt/cord-280628-ok62havd.txt === reduce.pl bib === id = cord-280544-1rhu478r author = Korte, Wolfgang title = SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on date = 2020-08-25 pages = extension = .txt mime = text/plain words = 822 sentences = 50 flesch = 55 summary = title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on antibodies rapidly decline early on 1, 3 Wolfgang Korte*, 2,3 Marija Buljan, 2,3 Matthias Rösslein, 2,3 Peter Wick, 1 Valentina Golubov, 1 Jana Jentsch, 1 Michael Reut, 3, 4 Karen Peier, 3 Brigitte Nohynek, 3 Aldo Fischer, 3 Raphael Stolz, 3 This cohort study included patients with a history of a positive SARS-CoV-2 PCR test. Results of the antibody course in 159 participants (52·2% females, 47·8% males), effectively spanning the time frame of two to ten weeks after a positive SARS-CoV-2 PCR test, are provided. The decline is statistically significant for anti-SP and anti-NC IgG at weeks 8-10 ( Figure 1) ; this is remarkable, as a continued IgG response for more than 34 weeks was seen with the SARS-CoV(-1) outbreak 6 . Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-280544-1rhu478r.txt txt = ./txt/cord-280544-1rhu478r.txt === reduce.pl bib === id = cord-280697-tovty20e author = Rodríguez‐Martínez, Carlos E. title = Efficacy, safety and cost‐effectiveness of hydroxychloroquine in children with COVID‐19: A call for evidence date = 2020-06-03 pages = extension = .txt mime = text/plain words = 929 sentences = 55 flesch = 48 summary = Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including pediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for pediatric patients) at present time (2). 1 Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including paediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for paediatric patients) at present time. We would therefore encourage nations where the undertaking of high-quality clinical trials in children during the current SARS-CoV-2 pandemic is possible, to ensure that putative treatments that would be available and affordable in low-to middle-income countries (LMICs), such as hydroxychloroquine, are included wherever possible. At a time of great uncertainty, evidence is urgently needed to inform treatment options, and therefore, randomised controlled trials are necessary to clarify further the clinical benefit of HCQ in paediatric patients with SARS-CoV-2 infections. cache = ./cache/cord-280697-tovty20e.txt txt = ./txt/cord-280697-tovty20e.txt === reduce.pl bib === id = cord-280627-dfnc9g2c author = Wang, Xiong title = Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date = 2020-04-18 pages = extension = .txt mime = text/plain words = 1846 sentences = 111 flesch = 53 summary = The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). cache = ./cache/cord-280627-dfnc9g2c.txt txt = ./txt/cord-280627-dfnc9g2c.txt === reduce.pl bib === id = cord-280427-smqc23vr author = Singla, Rubal title = Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date = 2020-09-14 pages = extension = .txt mime = text/plain words = 7194 sentences = 381 flesch = 58 summary = The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. cache = ./cache/cord-280427-smqc23vr.txt txt = ./txt/cord-280427-smqc23vr.txt === reduce.pl bib === id = cord-280774-r2xm164s author = Gallizzi, Romina title = Management of pernio‐like cutaneous manifestations in children during the outbreak of covid‐19. date = 2020-09-19 pages = extension = .txt mime = text/plain words = 2083 sentences = 128 flesch = 47 summary = The increased number of cases of pernio-like lesions compared to the cases per year we usually observe, the mild temperatures of those months in Southern Italy and the concomitant lockdown, led us to hypothesize a possible correlation with SARS-CoV-2 infection. This is useful to highlight, as in our case, the D-dimer of our patients was weakly increased, a condition perfectly correlated with the mild symptoms of SARS-CoV-2 putative infection presented. In a report of 19 adolescent patients with a clinical diagnosis of pernio-like lesions nasopharyngeal swab and IgG serology for SARS-CoV-2 nucleocapsid protein were negative. Why some children who come into contact with the SARS-CoV-2 do not develop striking respiratory symptoms but present pernio-like lesions with negativity on diagnostic tests? This pathogenic mechanism could explain the appearance of pernio-like lesions due to SARS-CoV-2 infection. In conclusion, we think there is a correlation between pernio-like lesions and SARS-CoV-2 infection, but further studies are needed to prove it. cache = ./cache/cord-280774-r2xm164s.txt txt = ./txt/cord-280774-r2xm164s.txt === reduce.pl bib === id = cord-280915-yk872yaz author = Flaherman, Valerie J title = Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1528 sentences = 98 flesch = 54 summary = In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. cache = ./cache/cord-280915-yk872yaz.txt txt = ./txt/cord-280915-yk872yaz.txt === reduce.pl bib === id = cord-280914-6k8gpp4y author = Alpaslan Kocamemi, B. title = First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2156 sentences = 147 flesch = 62 summary = SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2, Covid-19, sewage, wastewater, RT-qPCR, virus concentration, PEG SARS-CoV-2 virus titers of manhole were higher than inlet of WWTPs. Terkos wastewater sample has the highest Case number (person)/WWTP flow (m3/d), but SARS-CoV-2 virus was not detected. So far, ultracentrifugation [6] , Polyethylene glycol 8000 (PEG 8000) adsorption [5] , electronegative membrane [3] and ultrafiltration [3, 4, 8] methods were used for SARS-CoV-2 concentration from wastewater samples. Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases cache = ./cache/cord-280914-6k8gpp4y.txt txt = ./txt/cord-280914-6k8gpp4y.txt === reduce.pl bib === id = cord-280961-fka8c69p author = Zhang, Rui title = CT features of SARS-CoV-2 pneumonia according to clinical presentation: a retrospective analysis of 120 consecutive patients from Wuhan city date = 2020-04-11 pages = extension = .txt mime = text/plain words = 3651 sentences = 211 flesch = 50 summary = METHODS: This was a retrospective analysis of the clinical and thoracic CT features of 120 consecutive patients with confirmed SARS-CoV-2 pneumonia admitted to a tertiary university hospital between January 10 and February 10, 2020, in Wuhan city, China. (c) Unenhanced axial CT images of a 27-year-old male doctor with a history of exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), nonproductive cough, dyspnea, and myalgia (c1) who progressed to a severe case requiring oxygen supplementation (c2). (d) Unenhanced axial CT images of a 52-year-old male doctor with asthma and exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), non-productive cough, dyspnea, and myalgia who rapidly progressed to a severe form requiring mechanical ventilation. In this study, we reported the clinical characteristics and chest CT findings at presentation for all types of SARS-CoV-2 pneumonia severity. cache = ./cache/cord-280961-fka8c69p.txt txt = ./txt/cord-280961-fka8c69p.txt === reduce.pl bib === id = cord-280819-z6ucnwk0 author = Achilonu, Ikechukwu title = Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach date = 2020-09-02 pages = extension = .txt mime = text/plain words = 5411 sentences = 301 flesch = 52 summary = title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach The SARS-CoV-2 main protease (M(pro)) is an attractive target towards discovery of drugs to treat COVID-19 because of its key role in virus replication. Using 6Y2G and the prior knowledge that protease inhibitors could eradicate COVID-19, we designed a computational study aimed at identifying FDA-approved drugs that could interact with M(pro). We used HTVS, induced-fit ligand docking and molecular dynamics simulation studies to identify additional classes of plausible FDA-approved drugs as possible drug candidate to treat COVID-19. In conclusion, we have used a computational approach which includes HTVS, IFD, MM/GBSA free binding energy calculations and MD simulation to study potential drug candidates for COVID-19. Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach Ikechukwu Achilonu 1 * cache = ./cache/cord-280819-z6ucnwk0.txt txt = ./txt/cord-280819-z6ucnwk0.txt === reduce.pl bib === id = cord-280970-gy0kfhy6 author = Peng, Fujun title = Management and Treatment of COVID-19: The Chinese Experience date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2618 sentences = 188 flesch = 48 summary = Since mid-December 2019, there has been a worldwide outbreak of COronaVIrus Disease 90 (COVID)-19, caused by SARS-CoV-2 (formerly 2019-nCoV or and first detected in 91 Wuhan, China. 52 However, 421 a single-center in Wuhan shared that early, low-dose and short-term (1-2mg/kg/d for 5-7 days) 422 corticosteroids was associated with a faster improvement of clinical symptoms and absorption of 423 focal lung lesions in severe cases of COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Early, low-dose and short-term application of corticosteroid treatment in patients with severe COVID-19 pneumonia: single-center experience from Wuhan, China. cache = ./cache/cord-280970-gy0kfhy6.txt txt = ./txt/cord-280970-gy0kfhy6.txt === reduce.pl bib === id = cord-280671-0b1qcdwk author = Calderone, Alba title = Selective Estrogen Receptor Modulators in COVID-19: A Possible Therapeutic Option? date = 2020-07-15 pages = extension = .txt mime = text/plain words = 1555 sentences = 82 flesch = 37 summary = In particular, susceptibility to SARS-CoV-2 infection is almost similar in both genders, but higher severity and mortality are observed in male patients (Wenham et al., 2020) . The previous severe acute respiratory syndromes caused by SARS-CoV and MERS-CoV were often associated with rapid viral replication, huge infiltration of inflammatory cells, and excessive production of proinflammatory cytokines (cytokine storm syndrome), leading to lung injury and respiratory distress syndrome . Moreover, pro-inflammatory cytokines, including IL-1b and IL-6, are directly induced by SARS-CoV-2 by interaction between viral components (probably nucleocapsid proteins) and toll like receptors of the host cells. Besides their potential effects on proinflammatory cytokine expression (mediated by ERs), some SERMs seem to play broader roles in inhibiting viral replication by ER-independent mechanisms. Anti-inflammatory effect of selective estrogen receptor modulators (SERMs) in microglial cells cache = ./cache/cord-280671-0b1qcdwk.txt txt = ./txt/cord-280671-0b1qcdwk.txt === reduce.pl bib === id = cord-281241-k1adcls8 author = Döhla, M. title = Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date = 2020-04-18 pages = extension = .txt mime = text/plain words = 1991 sentences = 127 flesch = 59 summary = Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. We therefore evaluated a rapid antibody IgG/IgMebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. Thirty-nine randomly selected individuals at the centre were tested simultaneously using the SARS-CoV-2 rapid test and the gold standard RT-qPCR method (Altona Diagnostics). The rapid test used for evaluation is a qualitative IgG/IgM detection system to test for a current or past infection of SARS-CoV-2. cache = ./cache/cord-281241-k1adcls8.txt txt = ./txt/cord-281241-k1adcls8.txt === reduce.pl bib === id = cord-280922-w6a5ec06 author = Sen, Sanjana title = Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4134 sentences = 289 flesch = 55 summary = Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Furthermore, a recent review on antibody-dependent enhancement of SARS-CoV-2 stated, "At present, there are no known clinical findings, immunological assays or biomarkers that can differentiate any severe infection from immune-enhanced disease, whether by measuring antibodies, T cells or intrinsic host responses (7) ." This conclusion inspired our study. The results demonstrate that Abs to a specific epitope from N protein plus disease risk factors strongly correlate with COVID-19 disease severity. The DRFS of patients with αEp9 Abs strongly correlates with COVID-19 disease severity (Pearson's r = 0.72, p-value <0.0001, and R 2 = 0.52) (Fig. 4A) . cache = ./cache/cord-280922-w6a5ec06.txt txt = ./txt/cord-280922-w6a5ec06.txt === reduce.pl bib === id = cord-280924-g6062fwk author = Hachim, Mahmood Yaseen title = Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2851 sentences = 147 flesch = 42 summary = title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. To effectively address the ongoing COVID-19 pandemic, there is a recognized need for a framework for rapid identification of novel targets for diagnostic and therapeutic interventions as well as determine clinically approved drugs with high potential for repurposed use against SARS-CoV-2. In this study, we have applied this approach, and our findings have identified IFITM3 as an early upregulated gene and indicate that valproic acid enhances IFITM3 mRNA expression and antiviral action. Our toxicogenomic analysis showed that valproic acid increased the mRNA expression of IFITM3, supporting a new report that the SARS-CoV-2-human protein-protein interaction map showed that valproic acid might be a potential repurposing drug for COVID-19 (34) . cache = ./cache/cord-280924-g6062fwk.txt txt = ./txt/cord-280924-g6062fwk.txt === reduce.pl bib === id = cord-281005-6gi18vka author = Singh, Praveen Kumar title = Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3161 sentences = 203 flesch = 57 summary = title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. In this study, we aimed to predict the mutations in the spike protein (S) of SARS-CoV-2 genomes available in the database (whole genome sequences as well as partial coding sequences of spike protein) and analyze the effect of each mutation on the antigenicity of the predicted epitopes. cache = ./cache/cord-281005-6gi18vka.txt txt = ./txt/cord-281005-6gi18vka.txt === reduce.pl bib === id = cord-280958-36ytqapi author = Decker, Summer J title = 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3513 sentences = 266 flesch = 63 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. cache = ./cache/cord-280958-36ytqapi.txt txt = ./txt/cord-280958-36ytqapi.txt === reduce.pl bib === id = cord-280994-w8dtfjel author = Peng, Qi title = Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date = 2020-04-23 pages = extension = .txt mime = text/plain words = 2105 sentences = 135 flesch = 55 summary = Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities cache = ./cache/cord-280994-w8dtfjel.txt txt = ./txt/cord-280994-w8dtfjel.txt === reduce.pl bib === id = cord-281248-z2gisufl author = Buonsenso, Danilo title = A Pediatric Strategy for the Next Phase of the SARS–CoV-2 Pandemic date = 2020-10-09 pages = extension = .txt mime = text/plain words = 2972 sentences = 124 flesch = 42 summary = Considering that most of these conditions present several overlaps with SARS-CoV-2 (Figure 1 ), this will pose challenges to pediatricians and health system to appropriately manage all these conditions and properly allocate resources, because COVID-19 will need to be considered until exclusion, in order to reduce nosocomial transmission and new outbreaks. In light of new evidences and the need to reduce as much as possible the diffusion of infectious diseases among children during the next season (because this would lead to include all cases in the differential diagnosis with COVID-19 because of similar symptoms), a reorganization of school environments should be a priority for policy makers. Therefore, even though the direct clinical impact of the SARS-COV-2 virus on children has been limited with a very low mortality rate, and the COVID-19-related pediatric inflammatory multisystem syndrome remains a relatively rare consequence of the disease, pediatricians will still need to include SARS-CoV-2 in the differential diagnosis. cache = ./cache/cord-281248-z2gisufl.txt txt = ./txt/cord-281248-z2gisufl.txt === reduce.pl bib === id = cord-281106-vzb5xzza author = Zerwes, S. title = COVID-19-Infektion – Risiko für thrombembolische Komplikationen date = 2020-09-01 pages = extension = .txt mime = text/plain words = 1929 sentences = 204 flesch = 38 summary = According to current data, the risk of thromboembolic events in hospitalized COVID-19 patients is significantly increased, making thrombosis prophylaxis with low molecular weight or unfractionated heparin necessary. Neben den bekannten Ursachen der Thromboseentstehung, wurden bei der COVID-Erkrankung spezielle Pathomechanismen beobachtet, die zur Bildung von Thrombosen sowohl im venösen als auch im arteriellen System beitragen können. Auch wenn die Mechanismen noch nicht in Ihrer Gesamtheit erfasst sind, so ist bereits jetzt ersichtlich, dass die thrombembolischen Komplikationen im Zusammenhang mit dem SARS-CoV-2-Virus auf eine exzessive Inflammationsreaktion, Veränderung von Blutflusseigenschaften, direkte virusbedingte Thrombozytenaktivierung und Endothelschädigung zurückzuführen sind [3] . Diese Hypothese wird von nahezu allen bisher publizierten Arbeiten zu thrombembolischen Ereignissen bei COVID-19-Patienten postuliert und könnte eine Erklärung für die deutlich erhöhte Anzahl von TVT bieten [1, 7, 17, 28, 39] . Eine einheitliche Nomenklatur besteht noch nicht, die Pu-blikationmitdergrößtenSerie benennt es als "Pediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2" (PIMS-TS) [36] . cache = ./cache/cord-281106-vzb5xzza.txt txt = ./txt/cord-281106-vzb5xzza.txt === reduce.pl bib === id = cord-281101-gv1sgbk1 author = Shin, Gu-Choul title = Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date = 2006-08-30 pages = extension = .txt mime = text/plain words = 5929 sentences = 279 flesch = 52 summary = Severe acute respiratory syndrome-coronavirus nucleocapsid (SARS-CoV N) protein has been found to be important to the processes related to viral pathogenesis, such as virus replication, interference of the cell process and modulation of host immune response; detection of the antigen has been used for the early diagnosis of infection. Reactivity of SARS-N mAbs with SARS-CoV infected cells was determined by immunofluorescence assay, performed according to the instructions of the manufacturer (Euroimmun, Germany). To further assess the specificity of the mAbs, antigen-capture ELISA was performed with human coronavirus-infected cell lysates and BrSARS-N protein as positive control (Fig. 6B) . (B) Cross-reactivity of SARS-N mAbs was examined by antigen-capture ELISA using human coronavirus OC43 lysates (256 HA unit), BrSARS-N protein (500 ng/well) and PBST buffer with 1% BSA as control. These mAbs were available for use in detecting SARS-CoV N protein by various diagnostic methods, such as immunoblot assay, immunofluorescence assay and antigen-capture ELISA (Table 3) . cache = ./cache/cord-281101-gv1sgbk1.txt txt = ./txt/cord-281101-gv1sgbk1.txt === reduce.pl bib === id = cord-281081-rifr5uub author = Deng, Junhua title = Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1515 sentences = 86 flesch = 55 summary = In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. The results showed that no SARS-CoV-2-specific antibodies were detected in above species of animals including pangolin which has been reported as an intermediate host of SARS-CoV-2 (Kangpeng Xiao, 2020) . After confirming the specificity, sensitivity and suitability of SARS-CoV-2 ELISA kit for different species of experimental animals, clinical serum samples from domestic livestock (pig, cow, sheep, horse), poultry (chicken, duck, goose), experimental animal (mice, rat and rhesus monkey), companion animal (dog and cat) and wild animals (camel, fox, mink, alpaca, ferret, bamboo rat, peacock, eagle, tiger rhinoceros, pangolin, leopard cat, jackal, giant panda, masked civet, porcupine, bear, yellow-throated marten, weasel, red pandas and wild boar) were used for antibody detection. cache = ./cache/cord-281081-rifr5uub.txt txt = ./txt/cord-281081-rifr5uub.txt === reduce.pl bib === id = cord-281254-x7ivjvti author = Chang, Zhijie title = Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date = 2012-08-16 pages = extension = .txt mime = text/plain words = 3803 sentences = 256 flesch = 56 summary = The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. Since SARS-CoV rep-To address the issue related to delivery of siRNAs into cells or lication also requires certain host proteins, genes from host cells living organisms, researchers have used several approaches, ininvolved in viral replication can also be selected as targets. Therefore, RNA interference this coronavirus family), siRNAs targeting different genes of can be a tool for down-regulation of gene expression in cultured SARS-CoV were used by various groups to inhibit virus gene cells as well as in living organisms. cache = ./cache/cord-281254-x7ivjvti.txt txt = ./txt/cord-281254-x7ivjvti.txt === reduce.pl bib === id = cord-280996-anq680a1 author = Agarwal, Arnav title = High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission date = 2020-06-15 pages = extension = .txt mime = text/plain words = 7117 sentences = 383 flesch = 42 summary = title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission Review 1: we synthesized results from randomized-controlled trials (RCTs) comparing HFNC to conventional oxygen therapy (COT) in critically ill patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. We conducted two rapid systematic reviews commissioned by the WHO to summarize the evidence for the efficacy, safety, and risk of aerosol generation and infection transmission during HFNC use among patients with acute hypoxemic respiratory failure due to COVID-19. cache = ./cache/cord-280996-anq680a1.txt txt = ./txt/cord-280996-anq680a1.txt === reduce.pl bib === id = cord-281113-t450ccnq author = Mattar, Rejane title = Breath tests for gastrointestinal diseases - will it be safe to conduct breath tests after the COVID-19 pandemic? date = 2020-06-16 pages = extension = .txt mime = text/plain words = 756 sentences = 53 flesch = 55 summary = Viral RNA was detected in respiratory droplets and aerosols from coronavirus-, influenza virus-, and rhinovirus-infected patients (9) . The test carries risks of contamination to the healthcare worker collecting the breath samples and to the patients, as the ultrafine aerosol droplets may also carry SARS-CoV-2 and remain airborne for long periods, and could be inhaled (5) . pylori infection diagnosis, the patient blows into a plastic mouthpiece attached to an aluminized bag. Although the test lasts 20 minutes, it carries the risk of contamination by SARS-CoV-2 in the aerosol droplets generated by the exhaled air (5) . Other analytical assays for SARS-CoV-2 diagnosis include antigen detection by lateral flow assays that are fast and low cost; nonetheless, these tests lack good sensitivity early in the infection stage (11) . Digestive Symptoms in COVID-19 Patients With Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes cache = ./cache/cord-281113-t450ccnq.txt txt = ./txt/cord-281113-t450ccnq.txt === reduce.pl bib === id = cord-281281-knelqmzx author = Villas-Boas, Gustavo R. title = The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date = 2020-09-07 pages = extension = .txt mime = text/plain words = 15780 sentences = 708 flesch = 42 summary = The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. cache = ./cache/cord-281281-knelqmzx.txt txt = ./txt/cord-281281-knelqmzx.txt === reduce.pl bib === id = cord-280979-0vaarrji author = Gauttier, V. title = Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date = 2020-08-14 pages = extension = .txt mime = text/plain words = 4302 sentences = 227 flesch = 40 summary = These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Altogether, these data showed that optimized peptide vaccination against selected SARS-CoV-2 epitopes elicits robust and broad Th1-biased immunogenicity against several structural (S, M, N) and non-structural proteins in HLA-A2 expressing mice and that several peptides induce viral-specific memory CD8 T cells displaying all characteristics of T lymphocyte sentinels in barrier tissues. Using sequence design through reverse vaccinology selection approach based on previous CoVs knowledge on immunodominant epitopes and computational immunology optimization, we developed a combination of 12 CD8 T cell synthetic peptides originating from 11 SARS-CoV-2 structural and non-structural proteins capable to cover HLA polymorphism with high coverage globally and to induce immunogenicity to different proteins independently of HLA alleles expression. cache = ./cache/cord-280979-0vaarrji.txt txt = ./txt/cord-280979-0vaarrji.txt === reduce.pl bib === id = cord-280939-d478p8u6 author = Abe, Kento T. title = A simple protein-based surrogate neutralization assay for SARS-CoV-2 date = 2020-10-02 pages = extension = .txt mime = text/plain words = 7576 sentences = 380 flesch = 53 summary = Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). SARS-CoV-2 ELISAs are performed by immobilizing a recombinantly produced viral antigen (such as the spike trimer or RBD) ( Figure 1B and Supplemental Figures 1 and 2; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.142362DS1) (see Methods) onto multiwell plastic plates that are then incubated with diluted patient serum or plasma samples. cache = ./cache/cord-280939-d478p8u6.txt txt = ./txt/cord-280939-d478p8u6.txt === reduce.pl bib === id = cord-281346-bjhdy8mg author = Palacios Cruz, M. title = COVID-19, a worldwide public health emergency() date = 2020-04-21 pages = extension = .txt mime = text/plain words = 3481 sentences = 190 flesch = 51 summary = This new species of coronavirus has been termed 2019-nCoV and has caused a considerable number of cases of infection and deaths in China and, to a growing degree, beyond China, becoming a worldwide public health emergency. 2019-nCoV has high homology to other pathogenic coronaviruses, such as those originating from bat-related zoonosis (SARS-CoV), which caused approximately 646 deaths in China at the start of the decade. 17 Moreover, a recently published study estimated that 95% of the cases of 2019-nCoV infections in Wuhan showed symptoms before the 12th of January 2020, 18,19 a fact that, combined with the virus' incubation period, suggests a high possibility of the disease's travelrelated propagation. According to the WHO, a suspected case involves a patient with severe acute respiratory infection (fever, cough, requiring hospitalization) and with no other etiology that completely explains the clinical presentation, as well as a history of travel or residence in China during the 14 days before symptom onset. cache = ./cache/cord-281346-bjhdy8mg.txt txt = ./txt/cord-281346-bjhdy8mg.txt === reduce.pl bib === id = cord-281216-7t647fww author = Goldust, Mohamad title = Performing dermoscopy in the COVID‐19 pandemic date = 2020-05-05 pages = extension = .txt mime = text/plain words = 499 sentences = 43 flesch = 56 summary = A novel coronavirus (SARS-CoV-2) that has recently emerged from China in late 2019 has become a global pandemic. Recent data has suggested that SARS -COV2 can remain viable in aerosols for multiple hours. However, cross-infection is a significant concern with contact dermoscopy especially during a viral pandemic. to disinfect hands with 60-70% isopropyl alcohol, provide verbal consents, and wear surgical masks before entering procedure rooms. It is advisable to wear adequate eye protection (goggles or visor) considering that exposed mucous membranes and unprotected eyes can increase the risk of SARS-CoV2 transmission. 4 Mucous membrane dermoscopy should only be performed when the examination has fundamental significance for therapeutic decisions. Aerosol and Surface Stability of SARSCoV-2 as Compared with SARS-CoV-1 Identifying gram-positive cocci on dermatoscopes and smartphone adapters using MALDI-TOF MS: a cross-sectional study 2019-nCoV transmission through the ocular surface must not be ignored cache = ./cache/cord-281216-7t647fww.txt txt = ./txt/cord-281216-7t647fww.txt === reduce.pl bib === id = cord-281141-ouno4jpl author = Mahajan, Swapnil title = Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date = 2020-11-05 pages = extension = .txt mime = text/plain words = 6208 sentences = 307 flesch = 52 summary = A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . cache = ./cache/cord-281141-ouno4jpl.txt txt = ./txt/cord-281141-ouno4jpl.txt === reduce.pl bib === id = cord-281501-ca9oxl7f author = Khan, Shumayila title = Neuropathogenesis of SARS-CoV-2 infection date = 2020-07-30 pages = extension = .txt mime = text/plain words = 3208 sentences = 163 flesch = 43 summary = Emerging reports of encephalopathies and similar ailments with the detection of the virus in the CSF has elicited an urgent need for investigating the possibility of neuroinvasiveness of the virus, which cannot be ruled out given the expression of low levels of ACE2 receptors in the brain. One study from Japan which described the first case of COVID-19-associated encephalitis where the patient was admitted for convulsions accompanied by unconsciousness reported that although the patient tested negative for SARS-CoV-2 in a nasopharyngeal swab, the viral RNA was surprisingly detected in the CSF, and the patient MRI exhibited abnormalities of the medial temporal lobe and hippocampus (Moriguchi et al., 2020) . The preliminary reports which hint towards the involvement of the CNS imply an urgent need for more studies, and a systematic collection and preservation of CSF samples along with associated clinical data, at least in patients displaying extrapulmonary or neurological symptoms, to examine the neuronal aspect of COVID-19. cache = ./cache/cord-281501-ca9oxl7f.txt txt = ./txt/cord-281501-ca9oxl7f.txt === reduce.pl bib === id = cord-281500-5mm1nnwv author = Spadera, Lucrezia title = Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3619 sentences = 184 flesch = 51 summary = The questionnaire was composed of five sections: (a) respondents' workplace, age, and sex of the patient; (b) general information about the risk of exposure to COVID-19, asking to specify if the patient is a healthcare professional; (c) clinical information: onset of symptoms, grade of olfactory loss (OL) with three subjective levels (mild, moderate, and severe/complete), presence or absence of: ageusia, hypogeusia and/or dysgeusia gathered together under the name of "taste symptoms"; nasal discharge and/or congestion, other accompanying symptoms (e.g., fever, fatigue, dry cough, dyspnoea, and myalgia), comorbidities and complications; d) execution and results of nasopharyngeal (NP)/oropharyngeal (OP) swab; e) short description about the clinical case. The mean time of SOL onset before or after the first typical COVID-19 symptom (fever, dry cough, and dyspnoea) was 2.4 days (SD ± 2.7); anosmia/hyposmia occurred as the first symptom in 46.7% of cases, as sole symptom in 16.7% of cases or in association with other clinical manifestations in 31.2% of patients. cache = ./cache/cord-281500-5mm1nnwv.txt txt = ./txt/cord-281500-5mm1nnwv.txt === reduce.pl bib === id = cord-281528-xy8j5jiv author = Di Paola, Luisa title = The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date = 2020-06-17 pages = extension = .txt mime = text/plain words = 6715 sentences = 402 flesch = 56 summary = All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein. We also provided biophysical evidence based on the elastic network modeling (ENM) approach, combined with perturbation-response scanning (PRS) 36 that AMRs in both viruses acted as a mediator of intermolecular allostery between the S protein and ACE2. The map of the participation coefficient projected onto the ribbon structure of the SARS-CoV/ACE2 complex ( Figure 1C ) shows an active region (P > 0) in the junction between the fusion peptide and the trimeric bulk phase of the spike protein. cache = ./cache/cord-281528-xy8j5jiv.txt txt = ./txt/cord-281528-xy8j5jiv.txt === reduce.pl bib === id = cord-281294-dnaith3a author = Röhr, Susanne title = Psychosoziale Folgen von Quarantänemaßnahmen bei schwerwiegenden Coronavirus-Ausbrüchen: ein Rapid Review date = 2020-04-27 pages = extension = .txt mime = text/plain words = 3068 sentences = 424 flesch = 47 summary = Im April 2020 unterstand weltweit mehr als ein Drittel der Menschheit Quarantänemaßnahmen, um die Ausbreitung des neuartigen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) einzudämmen. Die durch die Infektion mit SARS-CoV-2 ausgelöste Atemwegserkrankung Corona Virus Disease 2019 (COVID19) wurde erstmals im Dezember 2019 in der chinesischen Millionenstadt Wuhan beschrieben und entwickelte sich bereits im Januar 2020 zur Epidemie in China [1] . Evidenz über psychosoziale Folgen von Quarantänemaßnahmen im Zusammenhang mit den genannten Ausbrüchen können Grundlage für entsprechende Untersuchungsansätze und Handlungsempfehlungen im Rahmen der COVID-19-Pandemie sein. Insgesamt konnten 13 Studien identifiziert werden, die konsistent psychosoziale Folgen von Quarantäne-und Isolationsmaßnahmen bei der SARS-Pandemie 2002/2003 und lokalen MERS-CoV-Ausbrüchen in den Zehnerjahren beschrieben, darunter Depressivität, Ängstlichkeit, Wut, Stress, Schlafstörungen, Sorgen, soziale Isolation, Einsamkeit und Stigmatisierung. Erste Fallstudien aus Deutschland bestätigen erhöhte psychische Belastungen infolge von COVID-19 und unterstreichen den Bedarf für eine Public-Health-Agenda, die Maßnahmen zum Schutz der psychosozialen Gesundheit während der Massenquarantäne hierzulande forciert [46] . cache = ./cache/cord-281294-dnaith3a.txt txt = ./txt/cord-281294-dnaith3a.txt === reduce.pl bib === id = cord-281161-u896icp9 author = Wang, Jing title = The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date = 2012-05-17 pages = extension = .txt mime = text/plain words = 6854 sentences = 317 flesch = 49 summary = We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. As shown in Table 2 , similar IgG1 and IgG2a humoral immune responses against the influenza viruses were induced in the mice vaccinated previously with rRBD plus rOv-ASP-1 adjuvant and those administered with PBS only. As shown in Table 3 , all of the NHPs vaccinated with rRBD protein plus 50 mg (n = 2), 100 mg rOv-ASP-1 (n = 2) or 500 mg CpG (n = 1) as the adjuvant developed RBDspecific IgG antibody response with increasing antibody level after each boost. Secondly, using two concentration of the rOv-ASP-1 adjuvant, 50 or 100 mg, and rRBD as the vaccine antigen, we were able to induce after three immunizations high titers of neutralizing antibodies (1:3,500-1:6,392) that much exceed what is needed for protection against SARS-CoV infection in vivo (.1:500) [56] . cache = ./cache/cord-281161-u896icp9.txt txt = ./txt/cord-281161-u896icp9.txt === reduce.pl bib === id = cord-281508-zl2url8z author = Pearce, N. title = Is death from Covid-19 a multistep process? date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4997 sentences = 245 flesch = 53 summary = The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope (indicating a smaller number of steps); in contrast, seasonal and pandemic influenza showed quite different agepatterns. These findings are consistent with a multistep model of disease involving a six-step process that in the case of SARS-COV-2 is probably defined by comorbidities and age producing immune-related susceptibility. cache = ./cache/cord-281508-zl2url8z.txt txt = ./txt/cord-281508-zl2url8z.txt === reduce.pl bib === id = cord-281551-0aj2zwx8 author = Schlagenhauf, Patricia title = Repurposing antimalarials and other drugs for COVID-19 date = 2020-04-02 pages = extension = .txt mime = text/plain words = 1433 sentences = 80 flesch = 50 summary = A French paper reporting on the use of drug combinations in infected patients highlighted the possibility that hydroxychloroquine is effective in the treatment of COVID-19 patients [4] particularly in combination with azithromycin. For instance, teicoplanin was proposed as a potential treatment in COVID-19 patients and has already shown inhibitory effects on cell entry of Ebola virus, SARS-CoV and MERS-CoV in the past. However, it has to be acknowledged that in this and other cases, it is a long, expensive and time-consuming way, even if there is an accelerated avenue to expedite promising developments, from in vitro assays indicative of antiviral effects to the initiation steps of safety and efficacy assessments in humans, Finding compounds that can block the entry of the virus into the cell could be an important approach to find potential therapies for COVID-19. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-281551-0aj2zwx8.txt txt = ./txt/cord-281551-0aj2zwx8.txt === reduce.pl bib === id = cord-281393-96j70n2z author = Capai, L. title = Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020. date = 2020-09-30 pages = extension = .txt mime = text/plain words = 3684 sentences = 262 flesch = 60 summary = A minimum sample size of 1814 was calculated assuming an a priori 5% IgG anti-SARS-CoV-2 seroprevalence (Salje et al., 2020) , a confidence in the estimate of 95%, a maximum allowable error in the prevalence of 1%, and a Corsican population size of 344,679 habitants based on the latest French census data (INSEE, 2020). Residual sera obtained from persons of all ages were tested for the presence of anti-SARS-CoV-2 IgG using the EUROIMMUN enzyme immunoassay kit for semiquantitative detection of IgG antibodies against S1 domain of viral spike protein (ELISA-S) (reference: In all samples with a ratio ≥ 0.8, neutralizing antibodies were detected using a VNT as previously described (Gallian et al., 2020) . To the best of our knowledge this is the first study describing the prevalence of SARS-CoV-2 antibodies in a representative sample of Corsican patients having carried out a blood analysis in biological laboratories after the COVID19 epidemic period. cache = ./cache/cord-281393-96j70n2z.txt txt = ./txt/cord-281393-96j70n2z.txt === reduce.pl bib === id = cord-281699-pxof67pl author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3089 sentences = 169 flesch = 55 summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are not under selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene, and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors ( Fig. 1) . cache = ./cache/cord-281699-pxof67pl.txt txt = ./txt/cord-281699-pxof67pl.txt === reduce.pl bib === id = cord-281285-5g1rw202 author = Simonis, Alexander title = A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date = 2020-11-03 pages = extension = .txt mime = text/plain words = 9501 sentences = 504 flesch = 46 summary = Based on its MOA, repurposed drugs with anti-SARS-CoV-2 activity can be divided into substances that prevent viral entry into host cells (1-2) and inhibit viral proteases (3) and inhibitors of viral replicase (4). The disappointing clinical results might be related to sub-therapeutic levels for inhibition of SARS-COV-2 because application of 400/100 mg of lopinavir/ritonavir twice daily was shown to yield median serum concentrations of 7.2 mg/l (11.5 µM) in patients with HIV (van der Lugt et al, 2009), which is significantly lower than the observed EC 50 in the in vitro studies. In this comparative review, we focus on repurposed drugs with antiviral effects against SARS-CoV-2 in cell-based assays as those substances offer great opportunities for a treatment early in the course of COVID-19 by inhibition of viral replication and might be even suitable for preventive strategies as shown for neuraminidase inhibitors in case of influenza (Jefferson et al, 2014) . cache = ./cache/cord-281285-5g1rw202.txt txt = ./txt/cord-281285-5g1rw202.txt === reduce.pl bib === id = cord-281487-x0a9qgjs author = Kim, Min Young title = General Approach to the Clinical Care of Solid Organ Transplant Recipients with COVID-19 Infection: Management for Transplant Recipients date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5908 sentences = 296 flesch = 36 summary = The coronavirus disease 2019 (COVID19) pandemic has led to unique challenges in solid organ transplantation as centers balance the risk of caring for immunosuppressed patients with the best timing and urgency of transplantation. Patients hospitalized with COVID-19 pneumonia were included Abbreviations: CHF, congestive heart failure; Because renal abnormalities are associated with a high risk of in-hospital death and appear to be more prevalent in transplant recipients [36] , serum creatinine and urinalysis should be monitored closely. Figure 1 shows a model for the management of solid organ transplant recipients during COVID-19 pandemic, based on recommendations of the Centers for Disease Control and Prevention (CDC) and the American Society of Transplantation (AST) [52, 61] . Transplant recipients with direct contact (< 6 ft for ≥ 15 min) with a COVID-19 infected individual should be quarantined for 14 days and consider testing for SARS-CoV-2 after exposure or if they develop symptoms [49, 52] . cache = ./cache/cord-281487-x0a9qgjs.txt txt = ./txt/cord-281487-x0a9qgjs.txt === reduce.pl bib === id = cord-281536-8y7yxcp4 author = Lim, Hocheol title = Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3527 sentences = 178 flesch = 55 summary = title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method In this work, to find common hot spot amino acids on the interfaces between the RBD domain and hACE2 of the three complexes, RBD-SARS-CoV-2/hACE2 (twelve experimental structural data), RBD-SARS-CoV-1/ hACE2 (four experimental structural data), and RBD-HCoV-NL63/hACE2 (one experimental structural data), we performed FMO-DFTB3/D/PCM calculations. Consequently, we summarized the FMO-DFTB3/D/PCM/3D-SPIEs results as interaction maps and found the hot spot regions in RBD-SARS-CoV-2 and hACE2 at a QM level. In order to narrow down the hot spot regions between hACE2 and RBD-SARS-CoV-1, we performed FMO calculations on four RBD-SARS-CoV-1/antibody complexes (Supplementary Table S14-S19). In order to find common hot spot amino acids in RBD-SARS-CoV-1 against hACE2 and SARS-CoV-1 antibodies, we illustrated the FMO results with a 3D-SPIEs-based map. cache = ./cache/cord-281536-8y7yxcp4.txt txt = ./txt/cord-281536-8y7yxcp4.txt === reduce.pl bib === id = cord-281686-edpyn8fd author = Dalamaga, Maria title = 19 treatment regimens? date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1448 sentences = 89 flesch = 35 summary = These agents could attenuate ARDS and help control SARS-CoV-2 via multiple mechanisms including: 1) inhibition of viral replication; 2) decrease of iron availability; 3) upregulation of B cells; 4) improvement of the neutralizing anti-viral antibody titer; 5) inhibition of endothelial inflammation and 6) prevention of pulmonary fibrosis and lung decline via reduction of pulmonary iron accumulation. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. It could also be reasonable to speculate that iron chelators may prevent the development of pulmonary fibrosis and lung function decline following COVID-19 infection. cache = ./cache/cord-281686-edpyn8fd.txt txt = ./txt/cord-281686-edpyn8fd.txt === reduce.pl bib === id = cord-281679-xmbnpawj author = Meekins, David A. title = Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date = 2020-08-16 pages = extension = .txt mime = text/plain words = 3402 sentences = 191 flesch = 46 summary = In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Cats, hamsters, and ferrets are highly susceptible to SARS-CoV-2 infection, demonstrate varying clinical and pathological disease manifestations, readily transmit the virus to naïve animals, and mount a virusspecific immune response [22] [23] [24] [25] [26] [27] [28] . Pigs are therefore unlikely to play an important role in the COVID-19 pandemic as a virus reservoir or as a pre-clinical animal model to study SARS-CoV-2 pathogenesis or develop novel countermeasures. cache = ./cache/cord-281679-xmbnpawj.txt txt = ./txt/cord-281679-xmbnpawj.txt === reduce.pl bib === id = cord-281677-pspmmrq7 author = Schulze-Koops, Hendrik title = Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie e. V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1199 sentences = 117 flesch = 43 summary = V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Daten aus COVID-19-Registern, Fallserien und Fallberichten legen aber nach derzeitigem Wissensstand nahe, dass Patienten mit ERE im Vergleich zur nicht rheumatisch erkrankten Bevölkerung kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 aufweisen [7] [8] [9] [10] [11] . unten) -die medikamentöse antirheumatische Therapie ein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt [11] . Abstract A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Aktuelle Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie für die Betreuung von Patienten mit rheumatischen Erkrankungen während der SARS-CoV-2/Covid 19-Pandemie cache = ./cache/cord-281677-pspmmrq7.txt txt = ./txt/cord-281677-pspmmrq7.txt === reduce.pl bib === id = cord-281561-r10y2sgb author = Tiwari, Nidhi title = Novel β-Coronavirus (SARS-CoV-2): Current and Future Aspects of Pharmacological Treatments date = 2020-08-27 pages = extension = .txt mime = text/plain words = 6877 sentences = 384 flesch = 45 summary = Another invitro study reported that Ribavirin, analogue of guanosine nucleotide having wide spectrum of antiviral activity, used along with LPV/RTV to treat SARS-COV-2 viral infection in china (ChiCTR2000029387) . reported remdesivir shows possible efficacy better as compared to placebo group in hospitalized patients for the treatment of SARS-CoV-2 virus. The effectiveness and safety concern of darunavir/cobicistat combination is being evaluated under development of clinical trials phase 3 by enrolling 30 COVID-19 patients and estimated completion of study on December 31, 2020. Recently, retrospective cohort study showed high dose of anakinra (5 mg/kg, BD,iv) produces beneficial and efficacious effects in 72% Covid-19 infected patients associated with ARDS (Cavalli et al., 2020) . Based on case study of patients with SARS-CoV2 infection and also confirmed severe pneumonia and ARDS treated with i.v. infusion of eculizumab along with anticoagulant therapy (Enoxaparin 4000 IU/day s.c), antiviral therapy (LPV 800 mg/day + RTV 200 mg/day), hydroxychloroquine 400 mg/day, ceftriaxone 2 g/day IV, vitamin C 6 g/day for 4 days. cache = ./cache/cord-281561-r10y2sgb.txt txt = ./txt/cord-281561-r10y2sgb.txt === reduce.pl bib === id = cord-281512-79g22dk6 author = Aguirre, A. Alonso title = Illicit Wildlife Trade, Wet Markets, and COVID‐19: Preventing Future Pandemics date = 2020-07-05 pages = extension = .txt mime = text/plain words = 3829 sentences = 188 flesch = 54 summary = This article will explore the connections among the current pandemic, live-animal markets, the spread of animal-related diseases, and the illicit wildlife trade and will include a set of policy recommendations prescribed to prevent future outbreaks stemming from these issues. It further explains "the identification of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in civet cats and other wild animals in live animal markets suggests that this novel human pathogen emerged as a result of an interspecies transmission" (Poon et al., 2005 (Poon et al., , p. The devastation resulting from the spread of COVID-19 could potentially serve as a future warning for what is to come, if practices such as illicit wildlife trade and wet markets are allowed to continue on a global scale. Research must focus on the central causes of the spread of zoonotic diseases such as illicit wildlife trade and wet markets. cache = ./cache/cord-281512-79g22dk6.txt txt = ./txt/cord-281512-79g22dk6.txt === reduce.pl bib === id = cord-281793-tj4m01s4 author = Ho, Mitchell title = Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3745 sentences = 203 flesch = 51 summary = Crossreactive antibodies (e.g., 47D11, S309, and VHH-72) that bind highly conserved epitopes on the RBDs of SARS-CoV and SARS-CoV-2 could have broad neutralization activities against viral infection. The receptor binding domain (RBD) of the SARS-CoV-2 S protein contains several novel residues that might be introduced through recombination with the pangolin coronavirus, indicating a possible critical step in the evolution of the ability of SARS-CoV-2 to infect humans [10] . isolated a human monoclonal antibody (named "rRBD-15") that inhibits the interaction of the RBD of SARS-CoV-2 and the ACE2 and neutralizes the pseudovirus infection [5] . The structure complex of 47D11 and the RBD (or the S1/S protein) would reveal a novel conserved site on the RBD for broad-neutralizing antibodies against SARSr-CoVs. In addition to 47D11, another human antibody (S309) isolated from memory B cells of a SARS survivor infected in 2003 neutralizes SARS-CoV-2 [18] . cache = ./cache/cord-281793-tj4m01s4.txt txt = ./txt/cord-281793-tj4m01s4.txt === reduce.pl bib === id = cord-281391-0qkku2jd author = Miller-Handley, Hilary title = Treatment Options for COVID-19 in Patients with Reduced or Absent Kidney Function date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4720 sentences = 276 flesch = 47 summary = COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, was first identified in the Hubei Province of China in late 2019. Because of these findings, chloroquine and hydroxychloroquine were used as early therapies in the treatment of COVID-19, and its use was further propagated by a small, retrospective, biased study from France with 36 patients which showed decrease in viral burden, and improved outcomes in patients treated with hydroxychloroquine [17] . A retrospective study from the Veterans Affairs, looked at hospitalized patients who received hydroxychloroquine and showed no evidence that use of hydroxychloroquine reduced the risk of progression of disease including mechanical ventilation and death [20] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-281391-0qkku2jd.txt txt = ./txt/cord-281391-0qkku2jd.txt === reduce.pl bib === id = cord-282133-5dzzm9s8 author = Watzky, Manon title = Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry date = 2020-10-15 pages = extension = .txt mime = text/plain words = 5706 sentences = 337 flesch = 50 summary = In here, exploiting a large panel of publicly available genome-wide data, we investigated whether the human receptor ACE2 and human proteases TMPRSS2, FURIN and CATHEPSINs (B, L and V), which are involved in SARS-CoV-2 cell entry, are transcriptionally regulated by environmental cues. We queried the comparative toxicogenomics database (CTD) to identify studies reporting changes in expression levels of human genes encoding receptor and proteases J o u r n a l P r e -p r o o f important for SARS-CoV-2 cell entry upon chemical exposure (Davis et al., 2019) . Using these criteria, we identified several chemical exposures regulating the expression of receptor ACE2 and human proteases TMPRSS2, FURIN and Cathepsins genes in human cells and tissues (Figure 2; Supplementary Table S2 ). Our analysis suggests that expression of human receptor and proteases of SARS-CoV-2 spike S glycoprotein are not directly regulated by cigarette smoke at the transcriptional level in lung cells, nor that PIR and ACE2 are coregulated upon cigarette smoke exposure. cache = ./cache/cord-282133-5dzzm9s8.txt txt = ./txt/cord-282133-5dzzm9s8.txt === reduce.pl bib === id = cord-281754-auqh3vtr author = nan title = EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date = 2017-09-12 pages = extension = .txt mime = text/plain words = 3626 sentences = 229 flesch = 49 summary = As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] . cache = ./cache/cord-281754-auqh3vtr.txt txt = ./txt/cord-281754-auqh3vtr.txt === reduce.pl bib === id = cord-282043-cs1oyohu author = Giustino, Gennaro title = Coronavirus and Cardiovascular Disease, Myocardial Injury, and Arrhythmia: JACC Focus Seminar date = 2020-10-27 pages = extension = .txt mime = text/plain words = 1923 sentences = 114 flesch = 27 summary = Both direct viral infection and indirect injury resulting from inflammation, endothelial activation, and microvascular thrombosis occur in the context of coronavirus disease 2019. Although originally believed to be a syndrome characterized by acute lung injury, respiratory failure, and death, it is now apparent that severe coronavirus disease 2019 (COVID-19) is further characterized by exuberant cytokinemia, with resultant endothelial inflammation, microvascular thrombosis, and multiorgan failure (2) . Myocardial injury can be detected in w25% of hospitalized patients with COVID-19 and is associated with an increased risk of mortality. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Acute myocardial injury in patients hospitalized with COVID-19 infection: a review Characteristics and clinical significance of myocardial injury in patients with severe coronavirus disease 2019 cache = ./cache/cord-282043-cs1oyohu.txt txt = ./txt/cord-282043-cs1oyohu.txt === reduce.pl bib === id = cord-282045-pf08iakf author = Chen, Haoyan title = Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1676 sentences = 105 flesch = 60 summary = title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production The percentage of these five SARS-CoV-2 entry genes was similar as ACE2, which is gradually increased in epithelial cells from normal control, CRA to CRC samples (Supplementary Fig. S3d ). Strikingly, pathways associated with virus infection, inflammation and cytokine signaling were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) . Given that IL-6 and TNF pathways were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) , we compared the IL-6 and TNF-alpha levels in peripheral blood from mild (n = 102) and severe (n = 50) COVID-19 pneumonia patients Table S3 ). Here, we first proved that the six SARS-CoV-2 entry genes, including ACE2 and TMPRSS2, are expressed in the colon epithelial cells of Chinese adults. In a word, the expression of additional five SARS-CoV-2 entry genes, virus infection, and inflammatory pathways are significantly enriched in colon epithelia cells with ACE2-positive expression. cache = ./cache/cord-282045-pf08iakf.txt txt = ./txt/cord-282045-pf08iakf.txt === reduce.pl bib === id = cord-282058-it0ojdk3 author = Yu, Yuanqiang title = Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review date = 2020-05-15 pages = extension = .txt mime = text/plain words = 7461 sentences = 389 flesch = 50 summary = References for this review were identified through searches of PubMed for articles published from January 1, 2003, to May 1, 2020, by use of the terms "coronavirus, " "neonate, " "children, " "COVID19, " and "SARS-CoV-2." Relevant articles published between 2003 and 2020 were identified through searches in the authors' personal files. The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The symptoms of COVID-19 appear to be less severe in infants and children than in adult patients, similar to the SARS-CoV infection (15) (16) (17) . Of the 34 pregnant women who were confirmed with the SARS-CoV-2 infection in multiple hospitals in Wuhan, including one pregnant woman with a negative nucleic acid test result, 30 had a fever and 16 had a cough (54) (55) (56) (57) . cache = ./cache/cord-282058-it0ojdk3.txt txt = ./txt/cord-282058-it0ojdk3.txt === reduce.pl bib === id = cord-281552-zfjy3m3i author = Alsaadi, Entedar A. J. title = Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date = 2020-09-22 pages = extension = .txt mime = text/plain words = 4781 sentences = 205 flesch = 49 summary = Here, we test E-derived peptides for membrane binding activity in vitro and confirm those identified as positive in the context of the full length protein expressed in two different cell types. Relative densitometry of the HSP and LSP bands revealed significant differences among the mutants with regard to their localisation to the different membrane fractions of E expressing insect cells ( Figure 5B ) and confirmed a role for the amphipathic MHV CoV E 50-64 peptide in membrane interaction. An amphipathic helix, EPTM, detected in the post-TM region of E, was suggested by bioinformatics analysis and assessed for direct membrane interaction in vitro by binding to GUVs. For comparison, the predicted E protein TM domain, ETM, and an established membrane active peptide from the influenza M2 protein were also included. Following expression of the complete E protein with mutations in the same identified peptide, altered membrane binding in two distinct cell types, mammalian and insect, was apparent. cache = ./cache/cord-281552-zfjy3m3i.txt txt = ./txt/cord-281552-zfjy3m3i.txt === reduce.pl bib === id = cord-281860-zjvrohgg author = Peng, Jing title = Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2493 sentences = 122 flesch = 51 summary = Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. To address this, we treated clinical sputum specimens with four commonly used reagents-saline, NALC, PK, and DTT, prior to NA extraction, and compared their performance in diagnosing COVID-19 in real practice. With the sputum samples collected from the 47 patients having non-COVID-19 diseases, no amplification curves were observed for either the ORF1ab or N gene under any treatment conditions (saline, NALC, PK, and DTT), suggesting no SARS-CoV-2 in these samples. According to the positive criteria described in the methods section, pretreatment of sputum samples with NALC, PK, and DTT increased the detection of SARS-CoV-2 + cases to 85.7% (18/21), 95.2% (20/21), and 95.2% (20/21), respectively, as compared to the 52.4% (11/21) obtained with saline pretreated sputum (see Table 1 ). cache = ./cache/cord-281860-zjvrohgg.txt txt = ./txt/cord-281860-zjvrohgg.txt === reduce.pl bib === id = cord-282318-890mltl8 author = Richard, Mathilde title = Factors determining human-to-human transmissibility of zoonotic pathogens via contact date = 2017-02-28 pages = extension = .txt mime = text/plain words = 3647 sentences = 173 flesch = 44 summary = We used the following examples to illustrate these four modes of contact transmission: Treponema pallidum pertenue (TPE) for skin contact transmission, human immunodeficiency virus type 1 (HIV-1) for sexual contact transmission, coronaviruses (CoV) for respiratory contact transmission and Ebola virus for contact transmission via multiple routes. Other pathogen factors that have contributed to the 'success' of HIV-1 M strain as a human pathogen, despite its relatively low infectivity (risk estimate of 1 in 1000 exposures for heterosexual transmission; [9] ), include its extraordinary propensity to evolve its genome through recombination and low-fidelity replication, allowing immune and therapeutic escape [20] , the nature of its long, 'latent', often sub-clinical infection, during which patients can transmit the virus [21] , and high viral load. Amongst the pathogen factors that promote H2H transmission of Ebola virus is the high virus load in secreted bodily fluids combined with a very low infectious dose, as low as 10 plaque forming units as measured in experimental infection studies in nonhuman primates [56] . cache = ./cache/cord-282318-890mltl8.txt txt = ./txt/cord-282318-890mltl8.txt === reduce.pl bib === id = cord-282530-55lhjfm8 author = Carsana, Luca title = Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3429 sentences = 160 flesch = 41 summary = [6] [7] [8] [9] We describe the lung histopathological findings from a large series of patients who died from COVID-19 in northern Italy, with the aim of reporting the main micro scopic pulmonary lesions associated with SARS-CoV-2 infection and severe respiratory failure. To our knowledge, these data represent the first relevant provisional information regarding tissue damage specifically induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), besides the previously described diffuse alveolar damage, a feature that characterises interstitial pneumonia regardless of infectious agent. 3, 4, 11, 14 In two autopsy studies of patients who died from SARS (eight cases from Singapore 11 and 20 cases from Toronto), 3 the predominant pattern of lung injury was diffuse alveolar damage, including the exudative and proliferative phases. In a case report of a patient who died from COVID-19 in China, the histological findings in the lungs included desquamation of pneumocytes, diffuse alveolar damage, and oedema. cache = ./cache/cord-282530-55lhjfm8.txt txt = ./txt/cord-282530-55lhjfm8.txt === reduce.pl bib === id = cord-282338-u01qv3uc author = Cherry, James. D. title = The chronology of the 2002–2003 SARS mini pandemic date = 2004-11-05 pages = extension = .txt mime = text/plain words = 3528 sentences = 176 flesch = 55 summary = SARS-CoV disease should be considered at a minimum in the differential diagnoses for persons requiring hospitalisation for pneumonia confirmed radiographically or acute respiratory distress syndrome without identifiable aetiology and who have one of the following risk factors in the 10 days before the onset of illness: (1) Travel to mainland China, Hong Kong, or Taiwan, or close contact with an ill person with a history of recent travel to one of these areas, or; (2) Employment in an occupation associated with a risk for SARS-CoV exposure (e.g. healthcare worker with direct patient contact or worker in a laboratory that contains live SARS-CoV) or; (3) Part of a cluster of cases of atypical pneumonia without an alternative diagnosis. cache = ./cache/cord-282338-u01qv3uc.txt txt = ./txt/cord-282338-u01qv3uc.txt === reduce.pl bib === id = cord-282449-7mxp3sdy author = A, Amouroux title = Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1511 sentences = 95 flesch = 55 summary = Abstract COVID-19 can severely affect pregnant women and the issue of vertical transmission of sars-cov-2 has also emerged. Sars-cov-2 could be recovered by real-time (RT) PCR from nasal and throat swabs, sputum and feces of symptomatic patients including neonates but not from vaginal swabs, amniotic fluid, placenta, cord blood, neonatal blood or breast milk. Detection rates of real-time PCR and the interpretation of IgM and IgG antibodies levels in cord and neonatal blood are discussed in relation with the immaturity of the fetal and neonatal immune system. Based upon RT-PCR identification of SARS-CoV-2 virus, early reports from China suggested that intrauterine vertical transmission was unlikely 1 . Total (Ab) and IgG antibodies seem to be acquired over 2 weeks' in infected individuals from the onset of symptoms and the introduction of SARS-CoV-2 serology is a rapidly evolving field of research and much-needed aid in the management of the pandemic. cache = ./cache/cord-282449-7mxp3sdy.txt txt = ./txt/cord-282449-7mxp3sdy.txt === reduce.pl bib === id = cord-282177-8l7zukg4 author = Lin, Yi-Chun title = A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date = 2020-05-26 pages = extension = .txt mime = text/plain words = 370 sentences = 31 flesch = 55 summary = title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 cache = ./cache/cord-282177-8l7zukg4.txt txt = ./txt/cord-282177-8l7zukg4.txt === reduce.pl bib === id = cord-282108-hhnnloxp author = Heister, Paula M. title = Pharmacological hypothesis: TPC2 antagonist tetrandrine as a potential therapeutic agent for COVID‐19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 4037 sentences = 253 flesch = 49 summary = The putative mechanism of action of tetrandrine that underlies its potential use as a coronavirus disease 2019 (COVID-19) treatment is its ability to block the two-pore channel 2 (TPC2) in host cells and thus inhibit virus replication at low micromolar concentrations. While this paper was in preparation, a large-scale study exploring SARS-CoV-2 human protein-protein interactions to identify potential therapeutic candidates identified verapamil as a contender, but initial in vitro screening did not show a promising effect at the concentrations used. If indicated by the above, clinical trials to investigate tetrandrine's potential, using an established oral dose, as an acute therapeutic or prophylactic agent against SARS-CoV-2 infection, provided safety can be confirmed for the particular length of use. 7. If indicated by the above, clinical trials to investigate the potential role of established calcium channel blockers as therapeutic agents in SARS-CoV-2 infection. cache = ./cache/cord-282108-hhnnloxp.txt txt = ./txt/cord-282108-hhnnloxp.txt === reduce.pl bib === id = cord-281727-elartlro author = Sun, Jing title = Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient date = 2020-05-18 pages = extension = .txt mime = text/plain words = 974 sentences = 60 flesch = 58 summary = title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. A novel coronavirus SARS-CoV-2 emerged to cause a major outbreak of severe pneumonia in humans in China and has spread to over 100 other countries [1] . Although viral RNA can be detected in multiple organs in COVID-19 patients, infectious SARS-CoV-2 has only been isolated from respiratory specimens [3, 4] . The urine sample tested positive for SARS-CoV-2 RNA on day 12 post infection (p.i.) (February 5th) for the first time and had periodically showed positive results in RT-PCR test until March 6th. Although it is hard to determine whether the kidney, the testis or the bladder were infected and produced infectious virus from current study, isolation of infectious SARS-CoV-2 in urine raises the possibility of fecal/urine-respiratory transmission. cache = ./cache/cord-281727-elartlro.txt txt = ./txt/cord-281727-elartlro.txt === reduce.pl bib === id = cord-282576-mcx0xq0w author = Boutin, Catherine-Audrey title = Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument date = 2020-09-04 pages = extension = .txt mime = text/plain words = 1363 sentences = 94 flesch = 63 summary = title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. We evaluated the concordance between the two-target cobas SARS-CoV-2 test (Roche Molecular Diagnostics, Laval, Canada) on the fully automated cobas 8800 platform authorized by Health Canada and a laboratory-developed (LD) standardized RT-PCR test using widely used primer set and probe (2, 3) in samples submitted at the diagnostic laboratory for patient care at the Centre Hospitalier de l'Université de Montréal. The correlation between Ct values obtained in the LD RT-PCR test and cobas SARS CoV-2 ORF-1 target for positive samples in both assays was good (r 2 = 0.82, data not shown). cache = ./cache/cord-282576-mcx0xq0w.txt txt = ./txt/cord-282576-mcx0xq0w.txt === reduce.pl bib === id = cord-282372-nmii30mc author = Youk, Jeonghwan title = Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5124 sentences = 294 flesch = 53 summary = Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . cache = ./cache/cord-282372-nmii30mc.txt txt = ./txt/cord-282372-nmii30mc.txt === reduce.pl bib === id = cord-282433-p6jl9gxf author = Tu, Xinyi title = Functional polymorphisms of the CCL2 and MBL genes cumulatively increase susceptibility to severe acute respiratory syndrome coronavirus infection date = 2015-03-27 pages = extension = .txt mime = text/plain words = 4611 sentences = 213 flesch = 45 summary = RESULTS: Both the high-CCL2-producing GG genotype and the low-MBL-producing B allele were consistently associated with increased risks of SARS-CoV infection in all 4 case–control populations (joint P = 1.6 × 10(−4) and 4.9 × 10(−8), for CCL2 and MBL respectively), with no interaction between polymorphisms could be detected. 3À10 In particular, our previous two independent association studies have implicated that a functional polymorphism at codon 54 in exon 1 (rs1800450, G230A, denoted as A/B variant) of mannose binding lectin (MBL), which encodes a protein belonging to the family of collectin and plays a critical role in the innate immune response, conferred a significantly increased susceptibility to SARS-CoV infection. Taken together, the large size of the investigation, the consistency of the observations in 4 independent caseecontrol series and the low P values distinguish our study from previous studies investigating the influence of different other polymorphisms on the development of SARS, and strengthen the association between the CCL2 G-2518A and MBL codon 54 variant (A/B) and susceptibility to SARS-CoV infection. cache = ./cache/cord-282433-p6jl9gxf.txt txt = ./txt/cord-282433-p6jl9gxf.txt === reduce.pl bib === id = cord-282272-wy8do2z6 author = Nelson, Atiba title = Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks date = 2020-07-06 pages = extension = .txt mime = text/plain words = 952 sentences = 56 flesch = 48 summary = title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. 2, 3 We conducted environmental sampling to assess the extent of surface contamination with SARS-CoV-2 virus within long-term care facilities with declared COVID-19 outbreaks. Environmental contamination with SARS-CoV-2 virus was detected at each of three COVID-19 outbreak facilities sampled in this study, including surfaces of five frequently used medical devices transferred between patient rooms, and one high-touch surface used by care staff This study contains limitations. Our findings suggest medical equipment is a potential environmental route for transmission of SARS-CoV-2 virus in long-term care facilities. cache = ./cache/cord-282272-wy8do2z6.txt txt = ./txt/cord-282272-wy8do2z6.txt === reduce.pl bib === id = cord-282371-39qo9afy author = Khulood, Daulat title = Convalescent plasma appears efficacious and safe in COVID-19 date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3095 sentences = 218 flesch = 52 summary = Convalescent plasma (CP) therapy is a classic adaptive immunotherapy which has been in use for more a century to prevent and treat infections including SARS, Middle East respiratory syndrome (MERS), and H1N1 pandemic. Despite its promising beneficial effects in patients severely ill with COVID-19, CP therapy requires further evaluation in randomized clinical trials (RCTs) as a lack of satisfactory efficacy data from this area certainly enhances the hesitancy with regard to employing this treatment. Although CP therapy showed satisfactory efficacy in treating patients with severe COVID-19, 41 this approach requires evaluation in randomized clinical trials (RCTs) 38 as lack of data from this area certainly enhances the hesitation with regard to employing this treatment. 46 Recently, the FDA has approved use of CP to treat critically ill patients while a clinical trial of plasma therapy for COVID-19 has been approved in the UK. Treatment with convalescent plasma for critically ill patients with SARS-CoV-2 infection. cache = ./cache/cord-282371-39qo9afy.txt txt = ./txt/cord-282371-39qo9afy.txt === reduce.pl bib === id = cord-282750-d9sb7o63 author = Benhadou, F. title = Improvement of SARS‐CoV2 symptoms following Guselkumab injection in a psoriatic patient date = 2020-05-07 pages = extension = .txt mime = text/plain words = 550 sentences = 28 flesch = 44 summary = We read with great interest the publication of Messina et al (1) reporting the first case of SARS‐CoV2 infection in a young patient of 32‐year‐old suffering from psoriasis and psoriatic arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)‐23(2).The patient contracted the SARS‐CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)-23 2 .The patient contracted the SARS-CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. These findings support the potential role of IL-23p19 inhibitors to counteract the « cytokine storm » triggered by the SARS-CoV2 and which is potentially implicated in the severity of the symptoms 3 . cache = ./cache/cord-282750-d9sb7o63.txt txt = ./txt/cord-282750-d9sb7o63.txt === reduce.pl bib === id = cord-281571-vob1bu9c author = Tam, Theresa W.S title = The Canadian Pandemic Influenza Plan: an evolution to the approach for national communicable disease emergencies date = 2004-06-30 pages = extension = .txt mime = text/plain words = 1843 sentences = 77 flesch = 34 summary = The general concepts incorporated into the CPIP may be utilised in the contingency planning for a bioterrorism event or other communicable disease emergencies, including: a national, coordinated approach in planning; an emergency management structure to conduct the response; the use of common terminology to facilitate communication and response coordination, and the establishment of specific technical, communications and operational response groups and networks in advance. After the Hong Kong influenza A/H5N1 incident in 1997, the pandemic plan evolved to include a more comprehensive approach, incorporating the following key components: surveillance, vaccine programs, and use of antivirals, health services, emergency services, public health measures and communications. The general concepts incorporated into the CPIP that may be utilised in the contingency planning for other infectious disease emergencies include: a national, coordinated approach to planning; an emergency management structure to coordinate and conduct the response; the need for common terminology (e.g. using the same response phases), and the need to have specific technical, communications and operational response groups and networks formed in advance. cache = ./cache/cord-281571-vob1bu9c.txt txt = ./txt/cord-281571-vob1bu9c.txt === reduce.pl bib === id = cord-281684-m3m4mhye author = Fagre, Anna C. title = A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3707 sentences = 212 flesch = 47 summary = title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. However, to date, there has been only a gross histological analysis of the lung pathological changes following infection and the impact of SARS-CoV-2 neutralizing antibody clones on lung immune infiltrates has yet to be fully assessed. Those antibody clones that blocked the interaction of the RBD with ACE2 and bound to native spike protein were then tested for neutralization of SARS-CoV-2 in a cytopathic effect (CPE) assay with Vero E6 cells. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity cache = ./cache/cord-281684-m3m4mhye.txt txt = ./txt/cord-281684-m3m4mhye.txt === reduce.pl bib === id = cord-281619-fhyamruq author = Burlacu, Alexandru title = Unpuzzling COVID-19 Prothrombotic State: Are Preexisting Thrombophilic Risk Profiles Responsible for Heterogenous Thrombotic Events? date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2016 sentences = 112 flesch = 32 summary = 1 The similarity between these 2 conditions is sustained by autopsy studies findings, documented immune pathogenesis, and microcirculation dysfunctions, the ability of SARS-CoV-2 to disseminate the infection in other organs and by the fact that many critically ill COVID-19 patients developed clinical symptoms of shock following a process called "viral sepsis." 2 A recent paper dealing with SARS-CoV-2 and "viral sepsis" raised alarm signals that despite the huge percentage of 71,4% of non-survivors of COVID-19 who matched the grade of overt disseminated intravascular coagulation, the concrete mechanisms of vascular thrombosis are not yet known. The hypercoagulation state consequent to SARS-COV-2 infection seems to manifest not only as pulmonary embolism, but also as other thrombotic events such as deep vein thrombosis, myocardial infarction, or ischemic stroke, 31 suggesting that the most plausible explanation has to be a pattern concerning either the patients or the virus. cache = ./cache/cord-281619-fhyamruq.txt txt = ./txt/cord-281619-fhyamruq.txt === reduce.pl bib === id = cord-281717-kzd9vvci author = Digard, Paul title = Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date = 2020-05-08 pages = extension = .txt mime = text/plain words = 4473 sentences = 266 flesch = 53 summary = CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . cache = ./cache/cord-281717-kzd9vvci.txt txt = ./txt/cord-281717-kzd9vvci.txt === reduce.pl bib === id = cord-282009-a83mun7u author = Pundir, Hemlata title = Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors date = 2020-10-20 pages = extension = .txt mime = text/plain words = 6213 sentences = 360 flesch = 53 summary = To identify possible inhibitors against SARS-CoV-2, we applied the Pharmacophore-based virtual screening method following Chou's 5-step rule [16] , molecular docking, drug-like analysis, and toxicity prediction (Fig. 1) . After the pharmacophore-based screening using Chou's 5-steps rule, we performed the molecular docking of all screened compounds with crystal structure of SARS-CoV-2 Mpro. After successful completion of MDS, the MD trajectories were used to calculate root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R g ), hydrogen bonds, solvent accessible surface area (SASA) [28] , principal component analysis (PCA) [29] , and distance to analyze the stability of Mpro and Mpro-ligand complex. Pharmacophore-based screening by Chou's 5-steps rule X77 binds to the active site of SARS-CoV-2 Mpro with binding energy − 8.4 kcal/mol as shown in Fig. 2 . cache = ./cache/cord-282009-a83mun7u.txt txt = ./txt/cord-282009-a83mun7u.txt === reduce.pl bib === id = cord-281887-b511bjdy author = Ribeiro, Reitan title = Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date = 2020-09-26 pages = extension = .txt mime = text/plain words = 4739 sentences = 234 flesch = 45 summary = DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. CONCLUSIONS: We present a protocol, focused on the patients' outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Our objective was to present the Brazilian Society of Surgical Oncology (BSSO) protocol for rational use of resources and for reducing the risk of surgical cancer patients being operated on during the coronavirus incubation period, in the context of areas with limited resources, and focused on patient outcomes. In light of all the previous considerations, Table 3 presents our suggested protocol for the rational use of resources to reduce the risk of surgical cancer patients from being operated on during the COVID-19 incubation period, in the context of areas with limited resources. cache = ./cache/cord-281887-b511bjdy.txt txt = ./txt/cord-281887-b511bjdy.txt === reduce.pl bib === id = cord-282965-xguotf4m author = O’Callaghan-Gordo, Cristina title = COVID-19: The Disease of the Anthropocene date = 2020-05-15 pages = extension = .txt mime = text/plain words = 1585 sentences = 66 flesch = 47 summary = Since the emergence of AIDS, many other epidemic infectious diseases, such as Ebola, SARS and MERS to name the most recent, have been caused by the transmission of viruses from wild animal species to humans as shown in 2008 by Jones et al. The complete causal sequences and impacts of these ecological changes are still poorly understood, but frequently these emerging zoonosis appear and spread in circumstances that denote the effects of an economic and commercial practices that destroys natural habitats and animal populations, including those of humans living there, in the absence of effective protection and regulatory policies. The destruction of natural habitats and the extinction of species, the poorly regulated capture, marketing and consumption of non-human animals, the influence of lobbies to nullify or delay measures to protect natural and social systems, the limitation of current scientific knowledge and the contempt by governments and companies of the available evidence, have all worked in an orchestrated sequence to facilitate the current COVID-19 pandemic. cache = ./cache/cord-282965-xguotf4m.txt txt = ./txt/cord-282965-xguotf4m.txt === reduce.pl bib === id = cord-282817-vtzpf2wr author = Byrne, Hannah title = A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications date = 2013-10-02 pages = extension = .txt mime = text/plain words = 8419 sentences = 417 flesch = 34 summary = Despite significant positive clinical results, especially in the case of hematological malignancies, adverse clinical outcomes and animal studies have highlighted underlying limitations of mAbs. Accordingly, many strategies have been developed in order to improve the specificity and control the functions of antibodies. The BiTE format potentially overcomes several limiting factors relating to the biological activity of tumor-directed bsAbs. BiTEs combine the minimal binding domains (Fv fragments) of two different mAbs fused together by a short flexible linker that allows free rotation of the two arms, and thus facilitates optimal antibody:antigen interaction [28] . bsAbs are attractive in such assays because they simplify the detection steps and are currently used for the development of simple, rapid, and highly sensitive immunoassays for the detection of bacterial and viral infectious diseases and in cancer diagnostics. CD40-targeted adenoviral gene transfer to dendritic cells through the use of a novel bispecific single-chain Fv antibody enhances cytotoxic T cell activation cache = ./cache/cord-282817-vtzpf2wr.txt txt = ./txt/cord-282817-vtzpf2wr.txt === reduce.pl bib === id = cord-282560-tofppr3b author = Henderson, Jack A. title = Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors date = 2020-09-21 pages = extension = .txt mime = text/plain words = 6242 sentences = 332 flesch = 56 summary = Here, we report the pK(a) calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. 14, 15 Our previous work employing the hybrid-solvent based continuous constant pH molecular dynamics (CpHMD) simulations 16 demonstrated that the elucidation of proton-coupled conformational dynamics offers a deeper understanding of the structure-dynamics-function relationships 17 and inhibition mechanisms 18-20 of aspartyl proteases. We performed pH replica-exchange CpHMD simulations to estimate the pKa values of Asp/Glu/His/Cys/Lys side chains and assess possible proton-coupled dynamics in SARS-CoV, SARS-CoV-2, and MERS-CoV PLpros. To provide support for the protonation states determined by GB-CpHMD titrations and test the proton-coupled dynamics of the BL2 loop, we performed conventional all-atom fixed-charge MD simulations of SARS-CoV-2 PLpro with the catalytic side chains fixed in the charged states and Cys270 fixed in the protonated or deprotonated state. cache = ./cache/cord-282560-tofppr3b.txt txt = ./txt/cord-282560-tofppr3b.txt === reduce.pl bib === id = cord-282106-7k088cqv author = Yang, Zhi-yong title = A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice date = 2004 pages = extension = .txt mime = text/plain words = 3739 sentences = 193 flesch = 48 summary = Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Immunization and challenge were performed in mice as described previously 18 , and viral replication (mean log 10 TCID 50 per g tissue with standard error) in the lower (a) and upper (b) respiratory tract after challenge with SARS-CoV was measured for five immunized animals inoculated with SDCD, SDTM or empty plasmid vector control. cache = ./cache/cord-282106-7k088cqv.txt txt = ./txt/cord-282106-7k088cqv.txt === reduce.pl bib === id = cord-282821-qvtvpnrr author = Thijsen, Steven title = Elevated nucleoprotein-induced interferon-γ release in COVID-19 patients detected in a SARS-CoV-2 enzyme-linked immunosorbent spot assay date = 2020-06-12 pages = extension = .txt mime = text/plain words = 784 sentences = 45 flesch = 58 summary = (2) (3) (4) The objective of the present study was to determine the functional T-cell responses to SARS-CoV-2 antigens (mosaic surface protein and nucleoprotein), by using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay, in patients with RT-PCR confirmed COVID-19 (n=27) and healthy controls (n=16). Our results show that the SARS-CoV-2-specific T-cell response measured in the ELISpot versus the dps induced by the mosaic surface protein and the nucleoprotein showed different patterns. In all but one of the 27 COVID-19 cases the T-cell response against the mosaic surface protein was absent or weak, as shown by the ELISpot results which were lower than 20 spot forming cells (SFC). In contrast, the Tcell response against the nucleoprotein measured by the ELISpot assay was elevated (10-150 SFC) in 12 of 19 patients (63%) that were sampled at ≥14 dps ( Fig. 1b) . cache = ./cache/cord-282821-qvtvpnrr.txt txt = ./txt/cord-282821-qvtvpnrr.txt === reduce.pl bib === id = cord-282724-zzkqb0u2 author = Moore, Jason H. title = Ideas for how informaticians can get involved with COVID-19 research date = 2020-05-12 pages = extension = .txt mime = text/plain words = 7588 sentences = 315 flesch = 33 summary = Some key considerations and targets of research include: (1) feature engineering, transforming raw data into features (i.e. variables) that ML can better utilize to represent the problem/target outcome, (2) feature selection, applying expert domain knowledge, statistical methods, and/or ML methods to remove 'irrelevant' features from consideration and improve downstream modeling, (3) data harmonization, allowing for the integration of data collected at different sites/institutions, (4) handling different outcomes and related challenges, e.g. binary classification, multi-class, quantitative phenotypes, class imbalance, temporal data, multi-labeled data, censored data, and the use of appropriate evaluation metrics, (5) ML algorithm selection for a given problem can be a challenge in itself, thus strategies to integrate the predictions of multiple machine learners as an ensemble are likely to be important, (6) ML modeling pipeline assembly, including critical considerations such as hyper-parameter optimization, accounting for overfitting, and clinical interpretability of trained models, and (7) considering and accounting for covariates as well as sources of bias in data collection, study design, and application of ML tools in order to avoid drawing conclusions based on spurious correlations. cache = ./cache/cord-282724-zzkqb0u2.txt txt = ./txt/cord-282724-zzkqb0u2.txt === reduce.pl bib === id = cord-281948-xv7vuypd author = Hoang, Ansel title = COVID-19 in 7780 pediatric patients: A systematic review date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4065 sentences = 235 flesch = 47 summary = We included published or in press peer-reviewed cross-sectional, case series, and case reports providing clinical signs, imaging findings, and/or laboratory results of pediatric patients who were positive for COVID-19. Data collected included the type of article (e.g., case series), country of origin, number of pediatric patients, demographic information, and all clinical symptoms (e. Compared to that review and other COVID-19 pediatric systematic reviews, [18À21] this manuscript has several key advantages: (1) we summarize 131 studies that includes 7780 children from 26 different countries, (2) this report synthesizes underlying pediatric medical conditions and delineates bacterial and viral coinfections, (3) we quantitatively describe clinical symptoms and imaging findings, (4) herein, we conglomerate the mean and standard deviation of frequently used laboratory analytes in COVID-19 positive children, (5) our report presents antiviral therapies by specific agents, and (6) our systematic review offers a preliminary comparison of patients with/without MIS-C. cache = ./cache/cord-281948-xv7vuypd.txt txt = ./txt/cord-281948-xv7vuypd.txt === reduce.pl bib === id = cord-281726-s1o5l7ns author = Yu, Ignatius T. S. title = Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date = 2005-05-01 pages = extension = .txt mime = text/plain words = 3528 sentences = 181 flesch = 56 summary = We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Layout of the ward where the index case patient with severe acute respiratory syndrome (SARS) was hospitalized, showing the location of beds, air supply diffusers, and exhaust grilles. The relationships between SARS and bed location, date of exposure, duration of exposure, smoking To explore the possible roles of HCWs in the outbreak of infection, all nurses working on the ward during the study period were interviewed in person between 28 March and 8 April with a questionnaire to collect information on symptoms, contacts, and working practices. The analysis of the temporal-spatial spread of SARS from the index case patient to other inpatients in the ward suggested that airborne spread through virus-laden aerosols possibly played an important role. cache = ./cache/cord-281726-s1o5l7ns.txt txt = ./txt/cord-281726-s1o5l7ns.txt === reduce.pl bib === id = cord-282732-qym6wji7 author = McLaughlin, Katie-May title = COVID-19-Related Coagulopathy—Is Transferrin a Missing Link? date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2895 sentences = 164 flesch = 46 summary = To identify gene products that may contribute to COVID-19-related coagulopathy, we analyzed the expression of genes associated with the Gene Ontology (GO) term "blood coagulation" in the Genotype-Tissue Expression (GTEx) database and identified four procoagulants, whose expression is higher in males and increases with age (ADAMTS13, F11, HGFAC, KLKB1), and two anticoagulants, whose expression is higher in females and decreases with age (C1QTNF1, SERPINA5). Thus, gene products that (1) are involved in coagulation, (2) change with age, (3) differ in their levels between females and males, and (4) are regulated in response to SARS-CoV-2 infection represent candidate factors that may contribute to COVID-19-related coagulopathy and disease severity. To identify such candidate factors that may be involved in COVID-19-related coagulopathy, we here performed a combined analysis of a proteomics dataset derived from SARS-CoV-2-infected cells [10] , of a dataset of host cell proteins found to bind to SARS-CoV-2 proteins [11] , and of human gene expression data from the Genotype-Tissue Expression (GTEx) database [12] . cache = ./cache/cord-282732-qym6wji7.txt txt = ./txt/cord-282732-qym6wji7.txt === reduce.pl bib === id = cord-282862-kve6fa49 author = Pastick, Katelyn A title = A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3313 sentences = 206 flesch = 47 summary = Clinicaltrials.gov was searched for relevant studies, using the preprogrammed search terms "COVID-19," "SARS-CoV-2," "2019-nCoV," "2019 novel coronavirus," and "severe acute respiratory syndrome coronavirus 2." Inclusion and exclusion criteria were examined to determine whether pregnant and/or breastfeeding patients were excluded from the study. Of the actively ongoing interventional clinical trials investigating the use of a drug (including dietary supplements and biologic agents) that did not report the exclusion of pregnant or breastfeeding women, the first author contacted study personnel for each of these studies by email to discern whether or not pregnant or breastfeeding women were eligible to be enrolled. Despite available safety data in pregnancy for hydroxychloroquine and lopinavir/ritonavir, we were surprised to find 68% and 80% of the respective clinical trials had excluded pregnant or breastfeeding persons. Our review of the literature was timely and is the first study (to our knowledge) to systematically examine and compile the available data related to treatment and outcomes of COVID-19 in pregnancy and related clinical trials. cache = ./cache/cord-282862-kve6fa49.txt txt = ./txt/cord-282862-kve6fa49.txt === reduce.pl bib === id = cord-282895-85if4mnu author = Xiao, Xiaodong title = The SARS-CoV S glycoprotein: expression and functional characterization date = 2003-12-26 pages = extension = .txt mime = text/plain words = 3819 sentences = 182 flesch = 54 summary = Fragments containing the N-terminal amino acid residues 17–537 and 272–537 but not 17–276 bound specifically to Vero E6 cells and purified soluble receptor, ACE2, recently identified by M. Here we report cloning, expression, and characterization of the SARS-CoV fulllength S glycoprotein and various soluble fragments, demonstration of its fusogenic function at neutral pH, development of a quantitative cell fusion reporter gene-based assay, and localization of the RBD in the N-terminal 303-537 residues. We have not observed measurable cytopathic effects in cells transfected with any of the constructs we developed (data not shown) indicating the possibility that the full-length and soluble fragments of the S glycoprotein may not have direct cytopathic effects. In an attempt to localize the receptor-binding domain (RBD) of the S glycoprotein prior to the identification of the SARS-CoV receptor, we developed an assay based on the binding of various soluble fragments to receptor expressing Vero E6 cells. cache = ./cache/cord-282895-85if4mnu.txt txt = ./txt/cord-282895-85if4mnu.txt === reduce.pl bib === id = cord-281937-yztlb0fn author = Sheahan, Timothy P title = The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2456 sentences = 120 flesch = 54 summary = A new paradigm for human coronavirology was born with the emergence of severe acute respiratory syndrome CoV (SARS-CoV) in November 2002 in Guangdong Province, China. The epidemic strain of SARS-CoV, is believed to have emerged from a bat reservoir through a civet intermediate host in live animal markets and then spilled over into humans 2 . This notion of CoV emergence was further solidified with discovery of the novel highly pathogenic Middle East respiratory syndrome CoV (MERS-CoV) in 2012, which also likely emerged from an ancestral bat-CoV but through a camel intermediate host which continues to seed human MERS-CoV infections to this day 2,3 . Given the diversity and prevalence of CoV circulating among wild birds and mammals, it is not surprising that the potential for emerging CoV to cause severe disease outbreaks and epidemics is not limited to humans. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence cache = ./cache/cord-281937-yztlb0fn.txt txt = ./txt/cord-281937-yztlb0fn.txt === reduce.pl bib === id = cord-282795-kje7rn57 author = Zheng, Yue title = Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date = 2020-09-21 pages = extension = .txt mime = text/plain words = 487 sentences = 36 flesch = 58 summary = To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. Pseudotyped MLV viruses were tested on HEK293FT, HEK293T-ACE2, Huh7 and SupT1 cells. To test for specificity of neutralization, we asked whether neutralizing antibodies from SARSCoV-2 patients would exhibit cross-reactivity against a pseudotype expressing SARS-CoV-1 ( Figure 112 4). Characterization of 162 spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with 163 SARS-CoV Veesler D: Structure, Function, and 165 Antigenicity of the SARS-CoV-2 Spike Glycoprotein The 167 D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases 168 infectivity High-efficiency gene 170 transfer into CD34+ cells with a human immunodeficiency virus type 1-based retroviral 171 vector pseudotyped with vesicular stomatitis virus envelope glycoprotein G Pseudotyping Viral Vectors With Emerging Virus Envelope 177 Proteins cache = ./cache/cord-282795-kje7rn57.txt txt = ./txt/cord-282795-kje7rn57.txt === reduce.pl bib === id = cord-282738-aqc9gxlw author = Liu, Anding title = Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date = 2020-10-23 pages = extension = .txt mime = text/plain words = 179 sentences = 22 flesch = 64 summary = key: cord-282738-aqc9gxlw authors: Liu, Anding; Li, Ying; Wan, Zhengce; Wang, Wenjie; Lei, Xiaomei; Lv, Yongman title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 cord_uid: aqc9gxlw This cross-sectional study examines the seropositive prevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, by sex and age group. Nasal swab specimens were obtained to test for SARS-CoV-2 by real-time RT-PCR. Total RNAs from nasal swab specimens was extracted by a viral nucleic acid kit The 95% CI of the seroprevalence was calculated from binomial probabilities using Wilson's methods. Chisquare test was used for comparison of seroprevalence between groups, and logistic Association of Public Health Interventions With the Epidemiology of the COVID-19 Outbreak in Wuhan, China Antibody responses to SARS-CoV-2 in patients with COVID-19 Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely correlated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients cache = ./cache/cord-282738-aqc9gxlw.txt txt = ./txt/cord-282738-aqc9gxlw.txt === reduce.pl bib === id = cord-283193-8qj41kpp author = Chak-Yiu Lee, Andrew title = Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2326 sentences = 139 flesch = 51 summary = title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters Utilizing Syrian hamster model, we demonstrate that the severity of pneumonia induced by intranasal inhalation of SARS-CoV-2 increases with virus inoculum. By 4 dpi, the hamsters infected with 10 2 or 10 3 PFU of SARS-90 CoV-2 also developed lung parenchymal damage which were milder than those observed in the 91 hamsters infected with 10 4 or 10 5 PFU of virus ( Figure 1D including both arteries and veins. The 133 intranasally infected hamsters had significantly higher viral load in oesophagus and stomach, but 134 no detectable virus in small intestinal tissues (n=3, Figure 2C ). In order to quantitatively compare the severity of lung damage after oral and intranasal 196 inoculation, we performed semi-quantitative histopathological evaluation of the bronchioles, 197 alveoli and blood vessels using a method modified from our previous influenza infection mouse 198 model and a reported hamster infection model (Table S1 ). cache = ./cache/cord-283193-8qj41kpp.txt txt = ./txt/cord-283193-8qj41kpp.txt === reduce.pl bib === id = cord-282142-76jr4p7n author = Wang, Yun title = Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date = 2020-08-07 pages = extension = .txt mime = text/plain words = 5495 sentences = 292 flesch = 47 summary = Pregnant women are susceptible to respiratory pathogens and the development of severe pneumonia, suggesting the urgent need to assess the potential maternal and infant outcome of pregnancy with COVID-19. Therefore, the effect of SARS-CoV-2 infection on maternal and infant outcomes needs to be explored, especially the intrauterine vertical transmission potential of COVID-19. SARS-CoV infection during pregnancy was associated with a risk of adverse maternal and neonatal complications, including intrauterine growth restriction, preterm delivery, spontaneous miscarriage, severe maternal illnesses, such as, admission to the intensive care unit (ICU), renal failure, and disseminated intravascular coagulopathy, and death (4, 6, 13, (42) (43) (44) (45) (46) . The samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples from six patients tested negative for SARS-CoV-2 (5), suggesting no intrauterine vertical transmission of SARS-CoV-2 in the nine pregnant COVID-19 patients. cache = ./cache/cord-282142-76jr4p7n.txt txt = ./txt/cord-282142-76jr4p7n.txt === reduce.pl bib === id = cord-283116-ib5c3lbi author = Koh, David title = Occupational health responses to COVID‐19: What lessons can we learn from SARS? date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3389 sentences = 204 flesch = 58 summary = Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. coronavirus, COVID-19, health care, occupational health, outbreaks, public health, SARS-CoV-2 confirmed cases and over 62 000 deaths spread over 200 countries and territories. cache = ./cache/cord-283116-ib5c3lbi.txt txt = ./txt/cord-283116-ib5c3lbi.txt === reduce.pl bib === id = cord-282964-dmc8mlxu author = Wathore, Roshan title = Understanding air and water borne transmission and survival of coronavirus: Insights and way forward for SARS-CoV-2 date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3366 sentences = 176 flesch = 44 summary = This has spurred efforts to characterize the coronavirus and understand the factors impacting its transmission and survival such as aerosols, air quality, meteorology, chemical compositions and characteristics of particles and surfaces, which are directly or indirectly associated with coronaviruses infection spread. Nonetheless, many peer-reviewed articles have studied these aspects but mostly in isolation; a complete array of coronavirus survival and transmission from an infected individual through airand water-borne channels and its subsequent intractions with environmental factors, surfaces, particulates and chemicals is not comprehensively explored. Finally, this study outlines probable air and water borne routes and suggest a way forward highlighting the need for investigating the effect of particulate matter characteristics on survival and transmission of SARS-CoV-2 due to the prominent presence of PM in ambient, spaces, and on the surfaces. cache = ./cache/cord-282964-dmc8mlxu.txt txt = ./txt/cord-282964-dmc8mlxu.txt === reduce.pl bib === id = cord-282384-qbcqbhk4 author = Savastano, Alfonso title = Peripapillary Retinal Vascular Involvement in Early Post-COVID-19 Patients date = 2020-09-08 pages = extension = .txt mime = text/plain words = 3740 sentences = 227 flesch = 44 summary = Furthermore, we performed an additional analysis within the post-COVID-19 group correlating the primary outcome measures with the other examined variables to detect potential risk factors for RPCP impairment in post SARS-CoV-2 patients. Spearman's Test revealed a statistically significant linear correlation between RNFL average thickness and both RPCP perfusion density (p < 0.001) ( Figure 3 ) and RPCP flow index (p < 0.001) (Figure 4) within the post-COVID-19 group. Our study examined this aspect outlining the correlation of the RPCP perfusion density and RPCP flow index with the RNFL average thickness also in early post-COVID-19 patients. In this regard, it is interesting to notice that patients in the post-COVID-19 group showed a lower mean age, a lower prevalence of diabetes and systemic arterial hypertension, and a higher prevalence of females (typically affected by milder manifestations of the disease) compared to the reported SARS-CoV-2 epidemiologic data [38] . cache = ./cache/cord-282384-qbcqbhk4.txt txt = ./txt/cord-282384-qbcqbhk4.txt === reduce.pl bib === id = cord-283152-wav0d0ws author = Patel, Sanjay K. S. title = Deploying Biomolecules as Anti-COVID-19 Agents date = 2020-06-09 pages = extension = .txt mime = text/plain words = 3094 sentences = 166 flesch = 50 summary = Severe acute respiratory syndrome coronavirus (SARS-CoV-2) known as COVID-19 has emerged as a major threat to human existence. The emergence of a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, renamed as COVID19) in 2019 from Wuhan, China has led to a global crisis and it has been declared as a pandemic emergency by World Health Organization (WHO) due to its fast rate of transmission among human beings [1, 2] . Coronaviruses (CoVs) are a group of genetically distinct viruses, which originated from broad ranges of hosts, including animal and bird species, and primarily cause respiratory and intestinal infections to humans and animals [1, [5] [6] [7] [8] . Transmission of COVID-19 possibly involved an adaptive evolution through an intermediate host (bat) before infecting humans. Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective cache = ./cache/cord-283152-wav0d0ws.txt txt = ./txt/cord-283152-wav0d0ws.txt === reduce.pl bib === id = cord-282920-s4yixzuy author = Rubin, Elizabeth S. title = Detection of COVID-19 in a Vulvar Lesion date = 2020-07-02 pages = extension = .txt mime = text/plain words = 969 sentences = 54 flesch = 49 summary = While current research suggests COVID-19 viral antigen is not found in vaginal secretions, its detectability in the female lower genital tract may have clinical implications for obstetric and gynecologic care for women. While vertical transmission has largely not been reported, the presence of detectable virus in the female lower genital tract makes this a continued possibility and area of study. Given her other reported symptoms, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nasopharyngeal test was also ordered, and the patient was instructed to have the test performed at an offsite outpatient testing site specifically designated for this purpose. This patient represents the first reported case of SARS-CoV-2 viral shedding detected in a vulvar lesion. [4] [5] [6] Finally, while vertical transmission of COVID-19 to fetuses and newborns has not been definitively shown, 7-9 the presence of detectable virus in the lower genital tract should prompt continued studies into this possibility. SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection cache = ./cache/cord-282920-s4yixzuy.txt txt = ./txt/cord-282920-s4yixzuy.txt === reduce.pl bib === id = cord-283196-laerx0n2 author = Bedford, Juliet title = Living with the COVID-19 pandemic: act now with the tools we have date = 2020-10-08 pages = extension = .txt mime = text/plain words = 1695 sentences = 81 flesch = 40 summary = The Strategic and Technical Advisory Group for Infectious Hazards (STAG-IH), the independent advisory group to the WHO Health Emergencies Programme, has reviewed information from countries around the world and has concluded that the most sound approach on the basis of current understanding is to deploy long-term strategies with a focus on preventing amplification of transmission, protecting those most at risk of severe illness, and supporting research to better understand the virus, the disease, and people's responses to them. 2 This approach is based on three principles: understanding, trust, and participation by all population groups; decreased transmission of SARS-CoV-2 using basic epidemiological and public health interventions; and acknowledging that any potential COVID-19 vaccines and treatments will only be part of the solution and that they will best perform in conjunction with a longterm overall public health strategy. With current knowledge, even in the absence of COVID-19 vaccines or treatments and comprehensive knowledge of the immune response to SARS-CoV-2, countries can navigate pathways to reduced transmission, decreased severe illness and mortality, and less economic disruption in the short and longer term. cache = ./cache/cord-283196-laerx0n2.txt txt = ./txt/cord-283196-laerx0n2.txt === reduce.pl bib === id = cord-283138-18q23z8l author = Balasubramanian, S. title = Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date = 2020-04-09 pages = extension = .txt mime = text/plain words = 3464 sentences = 205 flesch = 44 summary = Pediatric coronavirus disease-19 (COVID-19) infection is relatively mild when compared to adults, and children are reported to have a better prognosis. Clinical features of COVID-19 in children include fever and cough, but a large proportion of infected children appears to be asymptomatic and may contribute to transmission. It remains unclear why children and young adults are less severely affected than older individuals, but this might involve differences in immune system function in the elderly and/or differences in the expression/function of the cellular receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)Angiotensin converting enzyme 2 (ACE2). This review additionally considers COVID-19 in immunosuppressed children, and also suggests a management algorithm for the few children who appear to present with life threatening infection, including the potential use of antiviral and immunomodulatory treatment. Asymptomatic, mild and moderate infections comprise over 90% of all children who have tested positive for COVID-19 with fewer severe and critical cases (5.9%) compared to adults (18.5%) [13] . cache = ./cache/cord-283138-18q23z8l.txt txt = ./txt/cord-283138-18q23z8l.txt === reduce.pl bib === id = cord-283197-jjye8t6j author = Ingraham, Nicholas E. title = Fact Versus Science Fiction: Fighting Coronavirus Disease 2019 Requires the Wisdom to Know the Difference date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1870 sentences = 107 flesch = 42 summary = This commentary uses a recent study of hydroxychloroquine to demonstrate the dire need for randomized clinical trials, but more importantly, to explore the potential consequences of misinformation, how fear fuels its impact, and offer guidance to maintain scientific integrity without relinquishing hope. As of March 25, there remains no randomized control trial in humans with evidence that chloroquine or hydroxychloroquine is beneficial in SARS-CoV or SARS-CoV-2. Premature acceptance of efficacy is not new (swine flu vaccination [10] or recombinant human activated protein C [11] ), but it is these prior experiences that influence current standards to require high quality and often multiple randomized control trials to change practice. However, despite warnings from healthcare leaders and public health agencies, there continues to be a premature adoption of hydroxychloroquine as treatment based on limited preclinical data and misinformed interpretation of a nonrandomized study. cache = ./cache/cord-283197-jjye8t6j.txt txt = ./txt/cord-283197-jjye8t6j.txt === reduce.pl bib === id = cord-283127-jetmocvk author = Wang, Denong title = Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date = 2015-03-12 pages = extension = .txt mime = text/plain words = 3983 sentences = 212 flesch = 45 summary = In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). One intriguing question is whether human viruses of distinct phylogenetic origins, such as HIV-1 and SARS-CoV, may display conserved glycan targets that are suitable for broad virus neutralization. Subsequently, we performed a comparative carbohydrate microarray analysis to characterize the glycan-binding profiles of 2G12 and GNA and to pinpoint specific glyco-epitopes they recognize. To support exploration of the potential GNA glyco-epitopes in this study, we produced a set of comprehensive antigen microarrays, which include a large-panel of carbohydrates, lipids/liposomes, and protein antigens (Supplementary Table S1 ). Using carbohydrate microarrays and ELISA-based viral glycan-profiling analysis, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and lectin GNA. cache = ./cache/cord-283127-jetmocvk.txt txt = ./txt/cord-283127-jetmocvk.txt === reduce.pl bib === id = cord-282317-k9mtf6yl author = Srivastava, Vivek title = Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2 date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3964 sentences = 190 flesch = 51 summary = The main objective of the present study is to carry out molecular docking analysis of Glycyrrhiza glabra active compounds, Glycyrrhizic acid, Liquiritigenin and Glabridin against the main protease (M pro ) one by one followed by molecular interaction study (hydrogen bond prediction between target and drugs), drug-likeness behaviour and ADMET prediction to confirm the efficiency and efficacy of these active compound against SARS-CoV2. The molecular docked pose of the minimum binding affinity conformer of the Gg active compounds that is glycyrrhizic acid, Glabridin and Liquiritigenin demonstrated that they also firmly goes and bind to the active site of the M pro protein of the SARS-CoV-2 ( figure 4 and table 2 ). Molecular docking indicated that the three active compounds of Glycyrrhiza glabra namely glycyrrhizic acid, Liquiritigenin, and Glabridin successfully docked with the amino acid molecule at the catalytic site of the M pro with a high negative binding affinity and formed several molecular interaction with the main protease of SARS-CoV2. cache = ./cache/cord-282317-k9mtf6yl.txt txt = ./txt/cord-282317-k9mtf6yl.txt === reduce.pl bib === id = cord-282571-ilf73g71 author = Ni, Wentao title = Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5424 sentences = 287 flesch = 46 summary = Both SARS-CoV-2 and SARS-CoV enter host cells via the angiotensin-converting enzyme 2 (ACE2) receptor, which is expressed in various human organs. In addition to the direct viral effects and inflammatory and immune factors associated with COVID-19 pathogenesis, ACE2 downregulation and the imbalance between the RAS and ACE2/angiotensin-(1–7)/MAS after infection may also contribute to multiple organ injury in COVID-19. Autopsies of SARS patients showed that SARS-CoV infection can cause injury to multiple organs, such as the heart, kidney, liver, skeletal muscle, central nervous system, and adrenal and thyroid glands, besides the lungs [30, 31] . Several studies have shown that SARS-CoV infection can downregulate ACE2 expression on cells, thereby disrupting the physiological balance between ACE/ACE2 and Ang-II/angiotensin-(1-7) and subsequently causing severe organ injury [44] [45] [46] [47] . Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS cache = ./cache/cord-282571-ilf73g71.txt txt = ./txt/cord-282571-ilf73g71.txt === reduce.pl bib === id = cord-283413-xapzer5s author = Chan, A. K. M. title = Social media for rapid knowledge dissemination: early experience from the COVID‐19 pandemic date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1213 sentences = 63 flesch = 36 summary = During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2], while a recent study from Wuhan, China reported that 1716 healthcare workers were infected with COVID-19, representing 3.8% of confirmed cases [3]. During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2] . Known risks of non-peer-reviewed materials disseminated via social medial include the application of context-specific resources to unsuitable situations; engagement with biased knowledge within echo chambers' (groups consisting of only like-minded individuals) and algorithm-driven filter bubbles that selectively display information based on user preferences [15] ; and insufficient source information available to Box 1 Criteria for the responsible use of social media disseminated information. In the current COVID-19 pandemic, social media has the potential, if responsibly and appropriately used, to provide rapid and effective dissemination routes for key information. cache = ./cache/cord-283413-xapzer5s.txt txt = ./txt/cord-283413-xapzer5s.txt === reduce.pl bib === id = cord-282899-kp114q7n author = Biswas, Saurav title = Blood clots in COVID-19 patients: Simplifying the curious mystery date = 2020-11-06 pages = extension = .txt mime = text/plain words = 2501 sentences = 138 flesch = 38 summary = Considering the above facts and recent unusual reports, a hypothesis develops for the blood clots formation in the COVID-19 patients (Figure 1) , states that "Due to an internal injury in the endothelium of blood vessels, either directly by SARS-CoV-2 infection (coexpression and binding of the spike protein with the ACE2) or my virus-mediated inflammatory immune response, may result in vasoconstriction and the activation of coagulation and blood clotting pathways, resulting in the formation of blood clots". During COVID-19 infection, SARS-CoV-2 enters into the systemic circulation and binds with the ACE2 expressing endothelial cells (endothelium) lining the blood vessels. SO, in COVID-19 patients, the SARS-CoV-2 mediated endothelial inflammation, thrombin generation, platelet, and leukocyte recruitment, complement activation, and the initiation of innate and adaptive immune responses, forming clots, culminate in immunothrombosis, ultimately resulting in thrombotic complications, stroke, and finally death. cache = ./cache/cord-282899-kp114q7n.txt txt = ./txt/cord-282899-kp114q7n.txt === reduce.pl bib === id = cord-282421-yialyuav author = Alcoba-Florez, Julia title = Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date = 2020-08-01 pages = extension = .txt mime = text/plain words = 1049 sentences = 69 flesch = 55 summary = In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. cache = ./cache/cord-282421-yialyuav.txt txt = ./txt/cord-282421-yialyuav.txt === reduce.pl bib === id = cord-283109-ka3n9pft author = Arumugam, Arunkumar title = The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1725 sentences = 103 flesch = 58 summary = Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. Using Inf and RSV clinical specimens, we successfully performed RT-qPCR reactions by simply adding a few microliters of the unprocessed sample in viral transport medium (VTM) directly into the RT-qPCR assay master mix. We next tested whether the RNA from SARS-CoV-2 can be detected by directly spiking samples of the non-replicative recombinant virus particles (SeraCare AccuPlex SARS-CoV-2 reference material) in VTM to master mix without an extraction step. As shown in Fig. 3 , the SARS-CoV-2 RNA from directly spiked samples was successfully detected by the RT-qPCR reaction without a nucleic acid extraction step (N1 target shown). cache = ./cache/cord-283109-ka3n9pft.txt txt = ./txt/cord-283109-ka3n9pft.txt === reduce.pl bib === id = cord-283034-ebely0rx author = Brunet, E title = Ileitis as the exclusive manifestation of covid-19. The first reported case date = 2020-10-19 pages = extension = .txt mime = text/plain words = 449 sentences = 47 flesch = 50 summary = The patient did not report any respiratory symptoms. Two nasopharyngeal and oropharyngeal swab specimens performed before admission had been negative for SARS-CoV-2. Respiratory auscultation was strictly normal, and pain was noted on the palpation of the right lower abdominal quadrant. The patient was admitted to the gastroenterology unit after a confirmatory negative SARS-CoV-2 NAAT The patient recovered completely, with normalization of the previous blood test abnormalities. A SARS-CoV-2 control NAAT in rectal swab was negative before discharge from hospital. To our knowledge, our report is the first well-documented case of SARS-CoV-2 intestinal infection without evidence of pulmonary involvement. The multiple negative nasopharyngeal swabs plus the normal chest X-ray and CT findings rule out pulmonary infection. We report a patient with SARS-CoV-2 infection apparently limited to the bowel. In conclusion, SARS-CoV-2 may occur with an exclusive intestinal symptoms. Abdominal Pain: A Real Challenge in Novel COVID-19 Infection cache = ./cache/cord-283034-ebely0rx.txt txt = ./txt/cord-283034-ebely0rx.txt === reduce.pl bib === id = cord-283376-6wolrfvk author = Yin, M. title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study date = 2020-04-11 pages = extension = .txt mime = text/plain words = 4109 sentences = 301 flesch = 56 summary = For this retrospective cohort study, we reviewed clinical records, laboratory findings, and chest CT scans from 31 pregnant women and 35 non-pregnant women from Jan 28 to Feb 28, 2020 to evaluate the effects of SARS-CoV-2 infection during pregnancy. 4, [7] [8] [9] Although numerous studies have illuminated the clinical characteristics and outcomes of general population with COVID-19, 2, 8 little has been reported about the effects of SARS-CoV-2 infection on pregnant women. Considering that inflammatory cytokine storm was the main lethal factor of infectious pneumonia such as SARS and Middle East Respiratory Syndrome (MERS), 18-21 we compared the levels of interleukin (IL)-6 and some inflammatory indices including NLR, LMR, PLR, SII, ANRI and APRI, in pregnant and non-pregnant patients ( author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 12 However, we found a shorter interval from onset to hospitalization and severer COVID-19 in pregnant patients than non-pregnant patients with SARS-CoV-2 infection. cache = ./cache/cord-283376-6wolrfvk.txt txt = ./txt/cord-283376-6wolrfvk.txt === reduce.pl bib === id = cord-283372-c20i99qa author = Sanchis-Gomar, Fabian title = Amiodarone in the COVID-19 Era: Treatment for Symptomatic Patients Only, or Drug to Prevent Infection? date = 2020-08-01 pages = extension = .txt mime = text/plain words = 2612 sentences = 126 flesch = 37 summary = Amiodarone, one of the most widely prescribed antiarrhythmic drugs to treat both ventricular and supraventricular arrhythmias, has been identified as a candidate drug for use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We present the rationale of using amiodarone in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe coronavirus disease 2019 (COVID-19), based on current evidence. However, amiodarone is not free of secondary adverse effects, contraindications and interactions with other drugs, including the potential to cause pulmonary toxicity and fibrosis, thyroid disease, hepatic toxicity, increased creatine levels, QT interval prolongation, and bradyarrhythmia [9] . We present here the rationale for amiodarone use in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe COVID-19, based on current evidence. cache = ./cache/cord-283372-c20i99qa.txt txt = ./txt/cord-283372-c20i99qa.txt === reduce.pl bib === id = cord-283310-5wam14aa author = Bevova, M. R. title = The New Coronavirus COVID-19 Infection date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4812 sentences = 248 flesch = 52 summary = Later, the pneumonia was associated with a new coronavirus; in February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus causing it. In February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus. The estimation of the case-fatality rate (portion of deaths divided by the total number of cases) for the disease varies from 1 to 7% [24, 25] depending on the sex and age composition of the population; strategies of testing, diagnostics, and treatment; bureaucratic peculiarities of healthcare in a particular country; and congestion of healthcare systems. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-283310-5wam14aa.txt txt = ./txt/cord-283310-5wam14aa.txt === reduce.pl bib === id = cord-283699-c4jjdj5o author = Eslami, Gholamali title = The impact of sofosbuvir/daclatasvir or ribavirin in patients with severe COVID-19 date = 2020-08-19 pages = extension = .txt mime = text/plain words = 3476 sentences = 188 flesch = 51 summary = With the national standard COVID-19 treatment protocol at the time being lopinavir/ritonavir 200/50 mg two tablets every 12 h plus hydroxychloroquine 400 mg daily, it was decided to conduct a two-arm trial where both arms would receive the standard protocol in addition to either ribavirin or sofosbuvir/ daclatasvir. In this open-label trial, the effects of sofosbuvir/daclatasvir and ribavirin in patients with severe COVID-19 were measured. The time required before observing clinical improvement was significantly less in patients treated with sofosbuvir/daclatasvir, and the side effects of the medication, such as GI bleeding and anaemia, were lower than in the group receiving ribavirin. In this open-label study, treatment of patients with severe COVID-19 with sofosbuvir/daclatasvir was significantly more effective than ribavirin through improved clinical symptoms, lower mortality rates, a shorter duration of both ICU and hospital stays, and fewer side effects. cache = ./cache/cord-283699-c4jjdj5o.txt txt = ./txt/cord-283699-c4jjdj5o.txt === reduce.pl bib === id = cord-283439-hqdq2qrh author = Rahman, Mohammad Tariqur title = Can Zn Be a Critical Element in COVID-19 Treatment? date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5248 sentences = 315 flesch = 50 summary = The suggested treatments for COVID-19 are, but not limited to, the use of (i) convalescent plasma for COVID-19 treatment [63] [64] [65] ; (ii) ribavirin, a nucleoside analogue in combination with recombinant interferon showed inhibition of MERS-CoV replication [66] ; (iii) lopinavir/ritonavir-a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus infection [67] ; (iv) remdesivir, a nucleotide analogue that inhibit RNA polymerase with a broad spectrum of anti-viral activities; in inhibition of human and zoonotic coronavirus [15, 68, 69] ; (v) favipiravir (also known as T-705, Avigan or favilavir) is a pyrazinecarboxamide derivative known to inhibit RNA polymerase [70] . In the current pandemic of SARS-CoV-2, Zn supplement could play an important role to treat COVID-19 patients such as (i) added immune boosting effects with anti-viral drugs and (ii) stopping SARS-CoV-2 replication in infected cells, if combined with chloroquine. cache = ./cache/cord-283439-hqdq2qrh.txt txt = ./txt/cord-283439-hqdq2qrh.txt === reduce.pl bib === id = cord-282853-l0c69uul author = Massad, Eduardo title = Forecasting versus projection models in epidemiology: The case of the SARS epidemics date = 2005-03-30 pages = extension = .txt mime = text/plain words = 3085 sentences = 173 flesch = 56 summary = In this work we propose a simple mathematical model for the analysis of the impact of control measures against an emerging infection, namely, the severe acute respiratory syndrome (SARS). The model provides a testable hypothesis by considering a dynamical equation for the contact parameter, which drops exponentially with time, simulating control measures. In contrast, with control measures, which reduce the contact rate to about 25% of its initial value, the expected final number of cases is reduced to 1778 in Hong Kong and 226 in Toronto (Canada). The aim of this work is to provide a projection of what would have happened with the course of severe acute respiratory syndrome (SARS) epidemic if the universal procedures to reduce contact were not implemented in the affected areas. The model projects that, in the absence of control, the final number of cases would be 320,000 in Hong Kong and 36,900 in Toronto (Canada). cache = ./cache/cord-282853-l0c69uul.txt txt = ./txt/cord-282853-l0c69uul.txt === reduce.pl bib === id = cord-282839-3ii79g6j author = Moreno-Fernández Ayala, Daniel J. title = Age-related mitochondrial dysfunction as a key factor in COVID-19 disease date = 2020-11-07 pages = extension = .txt mime = text/plain words = 10245 sentences = 560 flesch = 37 summary = Thus, it seems clear that mitochondrial dysfunction is an important factor in the proinflammatory profile caused by the release of inflammatory cytokines produced by activation of NLRP3 inflammasome and other mechanisms over-activated in aging and in metabolic diseases. It seems clear that, mitochondrial dysfunction in diabetic patients contributes importantly to the low-grade inflammatory profile associated with this disease that is aggravated during aging and has been associated with higher severity in COVID-19 infection. Mediterranean diet, rich in plant foods, is associated with reduced risk of developing age-J o u r n a l P r e -p r o o f related chronic diseases by inducing protection against oxidative stress and improving mitochondrial activity that could be the cause of a reduced inflammation level (Tosti et al., 2018) . Mitochondrial dysfunction releases many damage signals to cytosol that end in the activation of inflammasome and the release of inflammatory cytokines that cause the chronic inflammation associated with aging and age-related diseases. cache = ./cache/cord-282839-3ii79g6j.txt txt = ./txt/cord-282839-3ii79g6j.txt === reduce.pl bib === id = cord-283823-8n1cy0hj author = Parikh, Bijal A. title = The Brief Case: “Not Positive” or “Not Sure”—COVID-19-Negative Results in a Symptomatic Patient date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1618 sentences = 84 flesch = 49 summary = The diagnosis of SARS-CoV-2 has relied almost exclusively on molecular testing of upper and lower respiratory specimens. As of 7 April 2020 (when the BAL fluid sample for this patient was sent to a reference laboratory for testing), 28 of the 29 commercially available assays approved by the FDA for emergency use were for testing on nasopharyngeal swabs (Table 1 ). Case reports of SARS-CoV-2 detection in sputum, tracheal aspirate, and BAL fluid specimens suggest that these specimens may be positive when NP swabs are negative, though large-scale studies have yet to be published (5) . It has become clear that negative NP swabs alone do not rule out SARS-CoV-2 infection, and as of now, there is no single "ideal" specimen for the diagnosis of COVID-19 (5) . Updated IDSA (Infectious Diseases Society of America) guidelines for COVID-19 diagnosis describe an algorithmic approach based on patient symptomatology, suspicion for infection, hospitalization status, and availability of lower respiratory specimens (6) . SARS-CoV-2 viral load in upper respiratory specimens of infected patients cache = ./cache/cord-283823-8n1cy0hj.txt txt = ./txt/cord-283823-8n1cy0hj.txt === reduce.pl bib === id = cord-283430-k1ex9fes author = Smithgall, Marie C. title = Third Trimester Placentas of SARS‐CoV‐2‐Positive Women: Histomorphology, including Viral Immunohistochemistry and in Situ Hybridization date = 2020-07-21 pages = extension = .txt mime = text/plain words = 1277 sentences = 100 flesch = 39 summary = CONCLUSIONS: In this study, third trimester placentas from SARS‐CoV‐2‐positive women were more likely to show evidence of maternal/fetal vascular malperfusion; however, no evidence of direct viral involvement or vertical transmission was noted by ISH and IHC. Studies to date regarding SARS-CoV-2 and placental pathology have been limited by the number of SARS-CoV-2 positive cases, 4, 5 and only one with a sample size of 5 cases has utilized in-situ hybridization (ISH) and immunohistochemistry (IHC) analyses. 6 In our study, we compared placental histopathology from 51 SARS-CoV-2-positive and 25 SARS-CoV-2negative women in their third-trimesters presenting to L&D, and tested placentas from SARS-CoV-2-positive mothers using ISH and/or IHC. Placentas from SARS-CoV-2-positive women showed non-specific evidence of maternal/fetal vascular malperfusion, including subchorionic thrombi (Fig.1A) , intervillous thrombi (Fig.1B) , infarction (Fig.1C) , chorangiosis, segmental avascular-villi (Fig.1D) , fetal thrombotic vasculopathy (Fig.1E) , and villous agglutination (Fig.1F ). cache = ./cache/cord-283430-k1ex9fes.txt txt = ./txt/cord-283430-k1ex9fes.txt === reduce.pl bib === id = cord-283512-qly8iclf author = Na, Ki Ryang title = Acute Kidney Injury and Kidney Damage in COVID-19 Patients date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3170 sentences = 206 flesch = 60 summary = METHODS: From February 21 to April 24, 2020, 66 patients diagnosed with COVID-19 at Chungnam National University Hospital were analyzed; all patients underwent routine urinalysis and were tested for serum creatinine, urine protein to creatinine ratio (PCR), and urine albumin to creatinine ratio (ACR). In this study, the clinical data of 66 patients diagnosed with COVID-19 were analyzed, and the effects of SARS-CoV-2 infection on renal function and its complications were explored. Data were collected, including age, gender, initial and follow-up SCr and eGFR (chronic kidney disease [CKD]-epidemiology collaboration), routine urinalysis with microscopy, urine PCR, urine ACR, underlying disease (diabetes mellitus [DM], hypertension, CKD, and cardiovascular disease), and whether mechanical ventilation, extracorporeal membrane oxygenation (ECMO), or renal replacement therapy was implemented. In our study, there was a lower percentage of patients with AKI (4.5%) and moderately to severely increased proteinuria (30.3%) than in previous human coronavirus infections. cache = ./cache/cord-283512-qly8iclf.txt txt = ./txt/cord-283512-qly8iclf.txt === reduce.pl bib === id = cord-282539-skzosh6u author = Casadevall, Arturo title = Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1588 sentences = 75 flesch = 45 summary = The article by Wang et al in this issue of Clinical Infectious Diseases reports that neutralizing antibody titers to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus peak 4-5 weeks after the onset of symptoms and decline by 3 months [1] . The decline in neutralizing antibody titers measured by Wang et al [1] in 93.5% of the patients studied is concerning for it raises the possibility that like other coronaviruses, COVID-19 may not result in the establishment of long lasting immunity. Whereas implications of the kinetics of the antibody response to SARS-CoV-2 for long-lasting and vaccine-mediated immunity are uncertain, the results of Wang et al [1] are important for the development and use of antibody therapies. The finding that SARS-CoV-2 neutralizing titers declined relatively quickly in the Wang et al study [1] means that efforts to collect convalescent plasma with high titers of neutralizing antibody for therapy and hyper-immune globulin preparation need to be highly organized such that potential donors are contacted early in the weeks following COVID-19. cache = ./cache/cord-282539-skzosh6u.txt txt = ./txt/cord-282539-skzosh6u.txt === reduce.pl bib === id = cord-283411-40ojqv1y author = Ben-Shmuel, Amir title = Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1174 sentences = 91 flesch = 56 summary = title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. cache = ./cache/cord-283411-40ojqv1y.txt txt = ./txt/cord-283411-40ojqv1y.txt === reduce.pl bib === id = cord-283705-ia65pade author = de Gabory, Ludovic title = Le virus influenza, le SARS-CoV2 et les voies aériennes : mise au point pour l’Otorhinolaryngologiste date = 2020-06-05 pages = extension = .txt mime = text/plain words = 3386 sentences = 319 flesch = 69 summary = L'objectif de cet article est de faire une mise au point sur les mécanismes de production et de pénétration des gouttelettes de sécrétions, émises lors de tous les phénomènes expiratoires, susceptibles de transporter ces virus et venir au contact de la muqueuse respiratoire. Si ces ARNs sont détectables autour des patients, sur les surfaces et dans l'air ambiant à des distances variables selon les études (de 0,5 m jusqu'au-delà de la chambre du patient) cela ne préjuge pas du caractère infectieux (viabilité) du virus et de la dose minimale infectieuse. L'objectif de cette mise au point était d'analyser les données objectives de contagiosité des patients lors du transport des virus par le produit des sécrétions et leur possibilité de pénétration dans les voies aériennes. En pratique le pourcentage de VI infectieux dans les gouttelettes produites lors de la toux ou de l'expiration variaient de 5 à 42 % pour des particules de 0,3 à 8 µm de diamètres lorsque les patients ont les signes cliniques depuis 2 jours [47, 49, 54, 55] . cache = ./cache/cord-283705-ia65pade.txt txt = ./txt/cord-283705-ia65pade.txt === reduce.pl bib === id = cord-282771-iwpx02v3 author = Dietzel, Steffen title = A joint action in times of pandemic: the German BioImaging recommendations for operating imaging core facilities during the SARS‐Cov‐2 emergency date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2242 sentences = 140 flesch = 55 summary = To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS‐CoV‐2 between users and staff. The outcome of this workshop, the first version of the "German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic" was published on the GerBI-GMB website a few days after the meeting. The aim of these recommendations is to help protecting users and staff working in a low-safety environment (mostly biosafety level 1) from accidental contagion by yet unidentified, asymptomatic SARS-CoV-2 carriers, and are based on our current still fragmentary knowledge of this virus. Thus, all surfaces that might get touched by different users during operating a microscope are to be disinfected before and after each usage to avoid potential spread of SARS-CoV-2 via this route. German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic cache = ./cache/cord-282771-iwpx02v3.txt txt = ./txt/cord-282771-iwpx02v3.txt === reduce.pl bib === id = cord-283590-xvnv17zy author = Chen, Dabiao title = Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date = 2020-03-05 pages = extension = .txt mime = text/plain words = 1499 sentences = 96 flesch = 48 summary = Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People's Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). cache = ./cache/cord-283590-xvnv17zy.txt txt = ./txt/cord-283590-xvnv17zy.txt === reduce.pl bib === id = cord-282990-qb4wk4yb author = Chen, Zhuo title = Safety considerations in the bioanalytical laboratories handling specimens from coronavirus disease 2019 patients date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1971 sentences = 113 flesch = 48 summary = Since blood specimen is one of the most commonly analyzed sample types, viral load of SARS-CoV-2 in blood is a key issue for laboratory biosafety. Besides the above three studies, other recently published papers also demonstrated that the detection rates of SARS-CoV-2 RNA in blood from COVID-19 patients were generally low as: five of 48 (10%) [1] , two of 9 (22%) [2] and six of 41 (15%) [3] . Despite the relatively low SARS-CoV-2 viral load detected in the blood and urine of COVID-19 patients, scientists have yet to draw conclusions about the infectivity of these specimens. The Centers for Disease Control and Prevention (CDC) has issued the interim laboratory biosafety guidelines for handling COVID-19 specimens, which recommends virus inactivation prior to sample processing to reduce the risk of infection [10] . Nevertheless, only the protocol of heating at 92 • C for 15 min completely inactivated SARS-CoV-2 in respiratory specimens with much higher viral load. cache = ./cache/cord-282990-qb4wk4yb.txt txt = ./txt/cord-282990-qb4wk4yb.txt === reduce.pl bib === id = cord-283818-4m9p717r author = Yan, Chao title = Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1589 sentences = 119 flesch = 60 summary = title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase 23 chain reaction (RT-PCR). The main findings of this study is that we established a rapid, sensitive, and 199 specific assay for SARS-CoV-2 detection by RT-LAMP. Rapid and sensitive detection of 311 novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated 312 isothermal amplification combined with a lateral-flow device A real-time 326 reverse transcription loop-mediated isothermal amplification assay for the rapid 327 detection of yellow fever virus cache = ./cache/cord-283818-4m9p717r.txt txt = ./txt/cord-283818-4m9p717r.txt === reduce.pl bib === id = cord-283779-mudwcypl author = Lauretani, Fulvio title = Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date = 2020-05-11 pages = extension = .txt mime = text/plain words = 9727 sentences = 500 flesch = 42 summary = The chronic increase in inflammatory cytokines, augmented by COVID-19 infection, may explain the higher tendency for "the cascade leading to pulmonary fibrosis and insufficiency and activation of clotting" and poorer clinical prognosis, especially in multimorbid older persons (4) . In case of persistent fever, higher than 37.5°C for a time longer than 3 days and peripheral oxygen level lower than 95% after starting therapy, we should consider and proceed to hospitalization especially in multimorbid older patients with cardiac, respiratory diseases and diabetes. First, patients at risk for poor outcomes and higher mortality following infection with SARS-CoV-2, namely older adults and multimorbid individuals, should be checked for malnutrition through screening and assessment. Older patients infected by COVID-19 often experience atypical and less severe symptoms in older persons, side-effects of the drugs and require specific nutritional and motor treatment for avoiding disability and death. cache = ./cache/cord-283779-mudwcypl.txt txt = ./txt/cord-283779-mudwcypl.txt === reduce.pl bib === id = cord-282878-8qgsq2km author = Fignani, Daniela title = SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date = 2020-10-23 pages = extension = .txt mime = text/plain words = 7565 sentences = 359 flesch = 43 summary = Finally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the β-cell line EndoC-βH1 and in primary human pancreatic islets. To address this question, we screened the ACE2 expression pattern in human pancreata obtained from adult non-diabetic multiorgan donors and in the insulin-producing human β-cell line EndoC-βH1, using different methodologies, multiple reagents, and publicly available or in-house generated RNA sequencing datasets. Here, we adopted multiple technologies and reagents to thoroughly analyse presence of ACE2, both at mRNA and protein level, in order to evaluate its expression and localization in pancreatic tissue samples obtained from adult non-diabetic multiorgan donors from the INNODIA EUnPOD biobank collection, in enzymatic-and LCM-isolated primary adult human pancreatic islets and in human β-cell line EndoC-βH1. Importantly, a recent report showed that human pancreatic islets can be infected in vitro by SARS-CoV-2 (23), supporting our observations of a specific tropism of the virus due to ACE2 expression. cache = ./cache/cord-282878-8qgsq2km.txt txt = ./txt/cord-282878-8qgsq2km.txt === reduce.pl bib === id = cord-282858-zikoui4h author = Graudenz, Gustavo Silveira title = SARS-CoV-2. Long Distance Airborne Transmission and its Public Health Implications date = 2020-11-02 pages = extension = .txt mime = text/plain words = 1665 sentences = 87 flesch = 42 summary = Its predecessor, SARS-CoviD-1, the agent that caused Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003, showed strong evidence of opportunistic airborne transmission in different environments, such as collective housing environments (8) , indoor environments such as airplanes (9), and health service institutions (10) . (12) that suggested transmission of SARS-CoV-2 through infected surfaces and contaminated individual protection equipment as well as long distance environment contamination. In health care settings, the Center for Disease Control's recommendations for prevention of airborne transmission include maintaining a negative pressure environment, fine filtering of exhaust air from infected patients' rooms, maintaining high air exchange rates (12 air exchanges per hour), shutting recirculation ducts, and establishing pressure cascades (2) in these settings until further evidence of long distance transmission is obtained Unfortunately, these precautionary measures have not yet been applied in most health care facilities in Brazil. Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus cache = ./cache/cord-282858-zikoui4h.txt txt = ./txt/cord-282858-zikoui4h.txt === reduce.pl bib === id = cord-283716-tleh9323 author = Amatore, F. title = SARS‐CoV‐2 infection presenting as a febrile rash date = 2020-05-27 pages = extension = .txt mime = text/plain words = 828 sentences = 53 flesch = 48 summary = The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide.1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide. 1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. [3] [4] [5] [6] [7] [8] [9] Herein, we describe a febrile rash as the only clinical manifestation of SARS-CoV-2 infection in a patient free from pulmonary symptoms. Firstly, Covid-19 disease can present with a distinctive rash, which is histologically similar but clinically different to classic viral exanthemata. cache = ./cache/cord-283716-tleh9323.txt txt = ./txt/cord-283716-tleh9323.txt === reduce.pl bib === id = cord-283786-d65njv7b author = Toptan, Tuna title = Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date = 2020-06-20 pages = extension = .txt mime = text/plain words = 5258 sentences = 235 flesch = 53 summary = The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). Therefore, we additionally compared the performance of two research kits (New England Biolabs, Ipswich, MA, USA) and one In conclusion, our M-gene-based qRT-PCR detection of SARS-CoV-2 RNA was at least as specific as the RdRP PCR recommended for confirmation by the WHO but showed a significantly higher sensitivity. cache = ./cache/cord-283786-d65njv7b.txt txt = ./txt/cord-283786-d65njv7b.txt === reduce.pl bib === id = cord-282635-ffq8kpij author = Tierraseca, Melody Sánchez title = MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) date = 2020-05-11 pages = extension = .txt mime = text/plain words = 535 sentences = 64 flesch = 50 summary = title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) Como se describe en el manuscrito al que hace referencia el título, así como series publicadas desde enero de 2020, la mayoría de los niños infectados por SARS-CoV-2 presentan clínica respiratoria leve 2,3 . Aún no disponemos de suficiente información de la clínica gastrointestinal exclusiva por SARS-CoV-2 y los protocolos actuales están dirigidos al manejo de las manifestaciones respiratorias quedando muchas incógnitas sobre otras manifestaciones. Sin embargo, se ha descrito la posibilidad de su transmisión por la excreción fecal 2,3 por la detección del ARN viral en las heces de pacientes infectados, incluso varias semanas tras su negativización en muestras respiratorias. Actualización de la situación epidemiológica de la infección por SARS-CoV-2 en España. Infección por coronavirus(COVID-19) en Anales de Pediatría Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and cache = ./cache/cord-282635-ffq8kpij.txt txt = ./txt/cord-282635-ffq8kpij.txt === reduce.pl bib === id = cord-282867-kbyxdegu author = Shah, Sayed Zulfiqar Ali title = Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date = 2020-08-26 pages = extension = .txt mime = text/plain words = 4542 sentences = 247 flesch = 39 summary = The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living. cache = ./cache/cord-282867-kbyxdegu.txt txt = ./txt/cord-282867-kbyxdegu.txt === reduce.pl bib === id = cord-282604-xp71rkxc author = Nikolaev, EN title = Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date = 2020-05-25 pages = extension = .txt mime = text/plain words = 2181 sentences = 114 flesch = 53 summary = title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. We have performed a pilot study on nasopharynx epithelial swabs already collected from patients with CODIV-19 for RT-qPCR and showed confident identification of the N protein of the SARS CoV-2 virus by mass-spectrometry with the use of a very basic sample preparation procedure. Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients cache = ./cache/cord-282604-xp71rkxc.txt txt = ./txt/cord-282604-xp71rkxc.txt === reduce.pl bib === id = cord-284028-l0r7f9sr author = Lee, Chi-Wei title = A loophole in international quarantine procedures disclosed during the SARS crisis date = 2004-12-30 pages = extension = .txt mime = text/plain words = 2797 sentences = 130 flesch = 47 summary = This phenomenon revealed a loophole in the control mechanisms of international quarantine procedures, letting travelers carrying a highly contagious virus slip by undetected and causing possible multi-country outbreaks of communicable diseases. Reasons for its rapid global spread were the highly contagious nature of the virus with its air-borne route of infection, the busy links between affected countries, and probably inadequacies in international quarantine procedures. As shown in Tables 1 and 2, although none of the six patients were eventually diagnosed wild SARS, this observed phenomenon disclosed a very important loophole in the control aspect of international quarantine procedures: the inability to prevent persons with a highly contagious virus from slipping past undetected and thus preventing the further spread of epidemics like SARS on international travel routes. In this study, we identified that there were loopholes in the international quarantine system for controlling the international spread of contagious disease like SARS, especially when travelers lack a strong motivation to cooperate with national health authorities. cache = ./cache/cord-284028-l0r7f9sr.txt txt = ./txt/cord-284028-l0r7f9sr.txt === reduce.pl bib === id = cord-283895-1p5uog38 author = Trottier, J. title = Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date = 2020-07-09 pages = extension = .txt mime = text/plain words = 1925 sentences = 125 flesch = 61 summary = Indeed, several reports indicate that SARS-CoV-2 RNA was readily detected in wastewater, and it is proposed that such approach could anticipate the occurrence of novel COVID-19 outbreaks in low prevalence regions , La Rosa et al., 2020 , Medema et al., 2020 , Orive et al., 2020 , Randazzo et al., 2020 . First, we showed that the Ebola standard (Ebo Std) primer/probe set was not detecting RNA from SARS-CoV-2-infected Vero E6 cells (Table 1) . . https://doi.org/10.1101/2020.07.08.20148882 doi: medRxiv preprint Next, we measured the SARS-CoV-2 RNA levels using N1 and N3 primer/probe sets in wastewater collected upstream of the main WWTP of the Montpellier metropolitan area on May 7 th , 18 th , 26 th , June 4 th , 15 th and 25 th (Figure 2A ). This intriguing result is reminiscent of a recent Spanish study, in which the authors could detect SARS-CoV-2 RNA in wastewater weeks before the first COVID-19 cases were reported (Randazzo et al., 2020) . cache = ./cache/cord-283895-1p5uog38.txt txt = ./txt/cord-283895-1p5uog38.txt === reduce.pl bib === id = cord-282947-3hgku2e4 author = Wong, Hui Hui title = Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date = 2017-12-30 pages = extension = .txt mime = text/plain words = 8714 sentences = 423 flesch = 46 summary = title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins. cache = ./cache/cord-282947-3hgku2e4.txt txt = ./txt/cord-282947-3hgku2e4.txt === reduce.pl bib === id = cord-283984-jch0ja1o author = Loizzo, Monica R. title = Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species date = 2008-03-20 pages = extension = .txt mime = text/plain words = 1495 sentences = 97 flesch = 59 summary = title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species oxycedrus oil, in which α‐pinene and β‐myrcene were the major constituents, revealed antiviral activity against HSV‐1 with an IC (50) value of 200 μg/ml and a SI of 5. In this study, we report the antiviral activity of seven essential oils obtained from berry, fruits, and leaves of different species collected in Lebanon. nobilis berries oil exhibited an IC 50 value of 120 mg/ml against SARS-CoV with a selectivity index (SI; TC 50 /IC 50 ) of 4.2. oxycedrus oil exhibited the highest activity against HSV-1 with a IC 50 value of 200 mg/ml and a SI of 5. P. palaestina essential oil was inactive against SARS-CoV (IC 50 > 1000 mg/ml) and less active against HSV-1 (IC 50 500 mg/ml). nobilis oil against SARS-CoV, and we also reported the interesting anti-herpetic activity of J. cache = ./cache/cord-283984-jch0ja1o.txt txt = ./txt/cord-283984-jch0ja1o.txt === reduce.pl bib === id = cord-284163-3jmqzemf author = Seffer, Malin-Theres title = Heparin 2.0: A New Approach to the Infection Crisis date = 2020-07-02 pages = extension = .txt mime = text/plain words = 2982 sentences = 156 flesch = 43 summary = This narrative review will give a brief overview regarding some of the extracorporeal devices that could be used to treat COVID-19 patients, including the Seraph® 100 Microbind® Affinity Blood Filter, produced by ExThera Medical (Martinez, CA, USA), first licensed in the European Economic Area in 2019. Bacteria, viruses, fungi, and toxins have been shown to bind to the immobilized heparin in a similar way to the interaction with heparan sulfate on the cell surface. Of note, it has recently been demonstrated that SARS-CoV-2 attaches to heparin through its surface protein Spike 1 receptor-binding domain [21] . The Seraph ® 100 Microbind ® Affinity Blood Filter is an extracorporeal hemoperfusion device whose functional core, that is, polyethylene beads (diameter of 0.3 mm) with immobilized heparin bound to it, mimics a naturally mammalian cell surface (Fig. 1) . Cytokines in blood from septic patients interact with surface-immobilized heparin cache = ./cache/cord-284163-3jmqzemf.txt txt = ./txt/cord-284163-3jmqzemf.txt === reduce.pl bib === id = cord-283948-rb9rrkxb author = Gavriilidis, Paschalis title = The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1595 sentences = 105 flesch = 48 summary = title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series Currently, the first articles reporting outcomes of liver transplant recipients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are published. The aim of the present study was to summarise the reported evidence of liver transplant recipients infected by SARS-CoV-2 during the global pandemic. A systematic literature search of articles published from inception until April 2020 performed in EMBASE, MED-LINE (PubMed), Cochrane Library, and Google Scholar databases using free text and MeSH terms (corona virus, COVID-19, liver transplantation, liver transplant recipients, global pandemic of COVID-19, severe acute respiratory syndrome, SARS). Of note, D'Antiga reported that children liver transplant recipients although immunosuppressed were not at increased risk to develop severe COVID-19 compared with the general population [7] . cache = ./cache/cord-283948-rb9rrkxb.txt txt = ./txt/cord-283948-rb9rrkxb.txt === reduce.pl bib === id = cord-284008-vlwdtjbe author = Li, Na title = The Application of Corticosteroids in COVID-19: A Two-edged Sword date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3092 sentences = 189 flesch = 48 summary = Their study revealed that proper corticosteroid treatment resulted in lower mortality and shorter hospitalization stay in patients with critical SARS with an oxygenation index (OI) of <300 mm Hg, and it was not associated with significant secondary lower respiratory infection and other complications. [21] described the effect of different doses of adjuvant corticosteroid therapy on 30-or 60-day mortality of patients with influenza A (H1N1) pdm09 viral pneumonia through a retrospective analysis. The results of stratified analysis based on the doses of corticosteroids showed that only treatment with low-to moderate-dose corticosteroid could reduce 30-and 60-day mortality of patients with severe infection with PaO2/FiO2 <300 mm Hg. However, corticosteroids at any dose increased the 60-day mortality of patients with mild infection with PaO2/FiO2 >300 mm Hg. Cao et al. [25] reported the clinical characteristics and treatment of patients with COVID-19 with ARDS in a study available on the medRxiv preprint server. cache = ./cache/cord-284008-vlwdtjbe.txt txt = ./txt/cord-284008-vlwdtjbe.txt === reduce.pl bib === id = cord-284302-odvv2yn3 author = Minagorre, Pedro J. Alcalá title = CAMBIOS A PARTIR DE LA COVID-19. UNA PERSPECTIVA DESDE LA PEDIATRÍA INTERNA HOSPITALARIA date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3134 sentences = 297 flesch = 49 summary = Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Pero ante el impacto anual del VRS y la gripe en las unidades de críticos (15, 16) y los posibles rebrotes de COVID-19, se ha de proveer una adecuada disponibilidad de recursos para el conjunto de pacientes afectados. El notable incremento del número de niños con patología crónica compleja en los últimos años obliga a todos los centros a disponer de planes asistenciales específicos para este grupo de pacientes, también en situaciones excepcionales como esta pandemia por COVID-19. cache = ./cache/cord-284302-odvv2yn3.txt txt = ./txt/cord-284302-odvv2yn3.txt === reduce.pl bib === id = cord-284045-scd3f8vk author = Pape, Constantin title = Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date = 2020-10-07 pages = extension = .txt mime = text/plain words = 5627 sentences = 300 flesch = 53 summary = Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay which complements the portfolio of SARS-CoV-2 serological assays. The dsRNA co-localizing pattern 213 observed for sera from the negative control cohort is by definition non-specific for SARS-CoV-2, 214 but would be classified as a positive hit based on staining intensity alone. The high information content of the IF data (differential staining patterns) 363 together with a machine learning-based approach [45] and the implementation of stable cell lines 364 expressing selected viral antigens in the IF assay will provide additional parameters for 365 classification of patient sera and further improve sensitivity and specificity of the presented IF 366 assay. cache = ./cache/cord-284045-scd3f8vk.txt txt = ./txt/cord-284045-scd3f8vk.txt === reduce.pl bib === id = cord-284398-rhfwbyav author = Aboubakr, Hamada A. title = Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date = 2020-07-14 pages = extension = .txt mime = text/plain words = 6425 sentences = 341 flesch = 54 summary = In another study, aerosolized SARS-CoV-2 retained its infectivity for a period of 16h at room temperature and the authors concluded that the virus can be considered as an airborne pathogen (Fears et al., 2020 and was infectious after 72 hr of aerosolization (Ijaz, Brunner, Sattar, Nair, & Johnson-Lussenburg, 1985) . In the first study, SARS-CoV-2 retained its infectivity for 4 days but was completely decayed after 7 days on plastic surface at room temperature and 65% RH (Chin et al., 2020) . Although this study reported longer virus survival, it has been shown that the survivability of SARS-CoV-1 on plastic surface is drastically affected by increases in temperature and RH as described below. In another study, a this virus with a higher initial load (5.5 log TCID 50 ) retained its infectivity for 4 days and was completely inactivated after 7 days on stainless steel at room temperature and RH of 65% (Chin et al., 2020) . cache = ./cache/cord-284398-rhfwbyav.txt txt = ./txt/cord-284398-rhfwbyav.txt === reduce.pl bib === id = cord-284091-1dj4yxkz author = Duart, Gerard title = SARS-CoV-2 envelope protein topology in eukaryotic membranes date = 2020-09-09 pages = extension = .txt mime = text/plain words = 2892 sentences = 155 flesch = 45 summary = In this report, we studied the E protein topology from the new SARS-CoV-2 virus both in microsomal membranes and in mammalian cells. Computer-assisted analysis of the SARS-CoV-2 E protein amino acid sequence using seven popular prediction methods showed that all membrane protein prediction algorithms except MEMSAT-SVM suggested the presence of one transmembrane (TM) segment located roughly around amino acids 12 to 39 (table 1) , which is not predicted as a cleavable signal sequence according to SignalP-5.0 [7] . Since multiple topologies have been reported for previous coronavirus E proteins [13] [14] [15] [16] [17] , SARS-CoV-2 E protein insertion into the microsomal membranes in two opposite orientations cannot be discounted, but according to our data being dominant an Nt lum /Ct cyt orientation. As shown in figure 2c, E protein (NST) was efficiently glycosylated when microsomal membranes were added to the translation mixture cotranslationally (lane 4). Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells cache = ./cache/cord-284091-1dj4yxkz.txt txt = ./txt/cord-284091-1dj4yxkz.txt === reduce.pl bib === id = cord-283491-y6t64pux author = Brzezinski, Dariusz title = Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date = 2020-09-27 pages = extension = .txt mime = text/plain words = 3182 sentences = 166 flesch = 45 summary = Understandably, firstline research findings, including molecular structure determinations, depositions in the Protein Data Bank (PDB), 1 and related results, are often made public on BioRxiv 2 or MedRxiv 3 before formal peer review. In this paper, we present covid-19.bioreproduciblity.org, a web resource that organizes SARS-CoV-2 related structural information in a way that should be understandable and useful for a wider scientific community, and not only for structural biologists. Finally, the structures are evaluated by a team of expert structural biologists who use a combination of the mined data, validation reports, and manual inspection of the protein models and associated electron density to examine potential problems. If raw diffraction data are available, the results of automatic processing of images by HKL-3000auto are examined to verify that the structure was determined in the correct space group and at optimal resolution. cache = ./cache/cord-283491-y6t64pux.txt txt = ./txt/cord-283491-y6t64pux.txt === reduce.pl bib === id = cord-284464-avriske3 author = Liu, Tao title = Recurrent positive SARS‐CoV‐2: Immune certificate may not be valid date = 2020-06-09 pages = extension = .txt mime = text/plain words = 295 sentences = 32 flesch = 58 summary = key: cord-284464-avriske3 cord_uid: avriske3 The presence of SARS-CoV-2 in COVID-19 patients is usually confirmed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) method.2 This article is protected by copyright. Statistical analyses were conducted using SAS software version 9.4 (SAS Institute; Carey, NC). A two-sided P < .05 was considered statistically significant. Among 150 patients who were recovering from COVID-19, 11 (7.3%, 95% confidence interval: 3.1%-11.6%) tested positive again for SARS-CoV-2 in throat swabs. Positive rates for SARS-CoV-2 did not differ by sex or age. There were no differences in the prevalence of IgM or IgG to SARS-CoV-2 ( Figure S1 ) or serum levels of these antibodies (Table 1) Detection of SARS-CoV-2 in different types of clinical specimens Positive RT-PCR test results in patients recovered from COVID-19 Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis cache = ./cache/cord-284464-avriske3.txt txt = ./txt/cord-284464-avriske3.txt === reduce.pl bib === id = cord-283120-hyzk59qv author = Sharma, Ashish title = Liver disease and outcomes among COVID-19 hospitalized patients- a systematic review and meta-analysis date = 2020-10-16 pages = extension = .txt mime = text/plain words = 2630 sentences = 157 flesch = 48 summary = In this meta-analysis, we aim to study the occurrence and association of liver injury, comorbid liver disease and elevated liver enzymes in COVID-19 confirmed hospitalizations with outcomes. MATERIALS AND METHODS: Data from observational studies describing comorbid chronic liver disease, acute liver injury, elevated aspartate aminotransferase (AST), alanine aminotransferase (ALT) levels and outcomes of COVID-19 hospitalized patients from December 1, 2019, to June 30, 2020 was extracted following PRISMA guidelines. The aim of the study is to evaluate the role of the comorbid chronic liver disease (CM-CLD), elevated liver enzymes and COVID-19 associated acute liver injury (COVID-19 ALI) in predicting the outcomes in confirmed COVID-19 hospitalized patients. The Maentel-Haenszel formula was used to calculate dichotomous variables to obtain odds ratios (ORs) along with its 95% confidence intervals to describe the association of comorbid liver disease, elevated liver enzymes, acute liver injury and outcomes of COVID-19 patients in each study. cache = ./cache/cord-283120-hyzk59qv.txt txt = ./txt/cord-283120-hyzk59qv.txt === reduce.pl bib === id = cord-284444-mgxxbm0u author = Reychler, G. title = Nebulization: A potential source of SARS-CoV-2 transmission date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1122 sentences = 68 flesch = 54 summary = authors: Reychler, G.; Vecellio, L.; Dubus, J.C. title: Nebulization: A potential source of SARS-CoV-2 transmission However, the Aerosoltherapy workgroup (GAT) of the Société de Pneumologie de Langue Franç aise decided at SARS-CoV2 pandemic preparedness to suggest avoiding a drug delivery via nebulization to reduce the risk of spreading the virus by this way. Indeed, some arguments suggested that the aerosol generated from the patient during the nebulization or from the nebulizer can directly exposes mucosae and eyes of the health care workers and contaminate surfaces with potentially infective droplets. One can suppose that the particles generated by the nebulizer and those exhaled by the patient will have optimal sizes to transmit the SARS-CoV2 to the healthcare workers. Based on these three elements, we think reasonable to avoid delivery of drugs via nebulization to SARS CoV2 patients for reducing the risk of exposure of the healthcare workers. cache = ./cache/cord-284444-mgxxbm0u.txt txt = ./txt/cord-284444-mgxxbm0u.txt === reduce.pl bib === id = cord-283249-pk5sc2ca author = Yoshida, Wataru title = Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers date = 2006-09-15 pages = extension = .txt mime = text/plain words = 5356 sentences = 235 flesch = 56 summary = The structural change of the enzyme-inhibiting aptamer site induces a change in the inhibitory activity of the AES, which enables us to detect a target molecule by measuring the enzymatic activity of the whole aptameric complex in a homogeneous solution without bound/free separation. The stem-and-loop structure bearing the probe DNA sequence was inserted into the 3 0 -end T-T loop of the G-quartet structure of the 31-mer thrombin-inhibiting aptamer. We also inserted two additional T bases between the thrombin-inhibiting aptamer and the stem-and-loop structure in all AESs except AES 1, since the diameter of the DNA double helix is different from the distance between two Gs of the G-quartet structure (approximately 17 and 20 Å , respectively). For the measurement of the CD spectra of AES SARS 1, a stem-and-loop structure to be inserted into the 31-mer thrombin-inhibiting aptamer on AES SARS 1 was synthesized. cache = ./cache/cord-283249-pk5sc2ca.txt txt = ./txt/cord-283249-pk5sc2ca.txt === reduce.pl bib === id = cord-284038-93s3ffoy author = Keyhanian, Kiandokht title = SARS-CoV-2 and nervous system: From pathogenesis to clinical manifestation date = 2020-11-07 pages = extension = .txt mime = text/plain words = 11701 sentences = 592 flesch = 42 summary = Since the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a growing body of evidence indicates that besides common COVID-19 symptoms, patients may develop various neurological manifestations affecting both the central and peripheral nervous systems as well as skeletal muscles. Growing number of case reports and/or series indicate that a variety of neurological conditions and post-viral triggered autoimmune complications, as we discuss below, occur in association with SARS-CoV-2 infection which mainly include Guillain-Barré syndromes (GBSs) (table 2), myopathy and rhabdomyolysis (table 2) , encephalopathy, meningoencephalitis, encephalomyelitis, and myelitis (table 3) . Moreover, two cases of acute necrotizing encephalopathy (ANE) in patients with COVID-19 positivity from nasopharyngeal and oropharyngeal swab, but without CSF PCR for SARS-CoV-2 data, were reported in the literature (Poyiadji, Shahin, 2020 , Radmanesh et al. cache = ./cache/cord-284038-93s3ffoy.txt txt = ./txt/cord-284038-93s3ffoy.txt === reduce.pl bib === id = cord-283367-azzy2t1a author = Rahman, Asma title = Neurological manifestations in COVID-19: A narrative review date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4426 sentences = 364 flesch = 54 summary = Some patients show neurological manifestations such as headache, dizziness, cerebrovascular disease, peripheral nerve and muscle symptoms and smell and taste impairment. Sarma and Bilello 41 1 Acute transverse myelitis A 28-year-old female patient with SARS-CoV-2 presenting lower back pain, bilateral symmetric upper, and lower extremity numbness. 50 None of the patients with post-COVID-19 GBS tested positive for SARS-CoV-2 in the CSF, 51 points to an immune mechanism such as inflammation secondary to a cytokine storm as a possible cause. During the COVID-19 pandemic, if a patient has neurological symptoms such as loss of the sense of smell and taste or delirium, testing for SARS-CoV-2 should be considered irrespective of them not having the other typical symptoms. Stroke in patients with SARS-CoV-2 infection: case series Acute myelitis after SARS-CoV-2 infection: a case report. Self-reported olfactory and taste disorders in patients with severe acute respiratory coronavirus 2 infection: a cross-sectional study cache = ./cache/cord-283367-azzy2t1a.txt txt = ./txt/cord-283367-azzy2t1a.txt === reduce.pl bib === id = cord-283253-qdq4mfz3 author = Davlantes, Elizabeth title = Notes from the Field: COVID-19 Prevention Practices in State Prisons — Puerto Rico, 2020 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 657 sentences = 42 flesch = 43 summary = These results followed implementation in mid-March of a protocol (2) for the diagnosis, management, and prevention of COVID-19 in all Puerto Rico Department of Correction and Rehabilitation prisons based on CDC's interim guidance on management of COVID-19 in correctional and detention facilities (3) . To minimize SARS-CoV-2 transmission from newly incarcerated persons, all state prison intakes in Puerto Rico now occur at a single location, in the municipality of Bayamon. During March 16-July 31, 2020, 1,340 persons entered Puerto Rico Department of Correction and Rehabilitation prisons, and two (0.1%) had positive SARS-CoV-2 RT-PCR test results. If any group member exhibits COVID-19 symptoms, which are defined according to CDC guidelines (4), the symptomatic person is isolated in the prison's medical facility, and the entire group is quarantined until the symptomatic person receives a negative SARS-CoV-2 RT-PCR result. cache = ./cache/cord-283253-qdq4mfz3.txt txt = ./txt/cord-283253-qdq4mfz3.txt === reduce.pl bib === id = cord-284625-to6w5hm2 author = Duan, Xiaopei title = A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3347 sentences = 183 flesch = 55 summary = Given the concept of the early diagnosis and treatment of SARS-CoV-2, this article mainly focused on the 25 initial laboratory-confirmed patients in the Luoyang area, discussing their imaging features and clinical characteristics. From January 10 to February 8, 2020, 25 patients with laboratory-confirmed SARS-CoV-2 infection in the area of Luoyang, Henan Province, China, were enrolled in the study. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. A woman who is the wife of the patient 3 and mother of patient 22 had two negative PCR results, but the lesions in her lung had the same progression, and the blood test also confirmed the SARS-CoV-2 infection. cache = ./cache/cord-284625-to6w5hm2.txt txt = ./txt/cord-284625-to6w5hm2.txt === reduce.pl bib === id = cord-283380-l60yyr6l author = Grabbe, Stephan title = Systemic immunosuppression in times of COVID‐19: Do we need to rethink our standards? date = 2020-08-02 pages = extension = .txt mime = text/plain words = 2577 sentences = 123 flesch = 35 summary = However, it is also currently under discussion whether patients under immunosuppressive therapy also have a higher risk of suffering a severe course of the COVID-19 disease. However, in clinical practice, long-term therapeutic use of hydroxychloroquine in patients with systemic lupus erythematosus does not appear to protect against covid-19 disease or a severe course of the disease [30, 31] . Therefore, the authors recommend that this therapy option should be considered especially in patients with other risk factors for a severe course of SARS-CoV-2 infection. Essentially, there is currently no data available for a general reduction or pause of immunosuppression in patients with autoimmune diseases, since the risk of an insufficient therapy of these mostly severe diseases is clearly higher than that of an aggravated course of COVID-19 disease. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-283380-l60yyr6l.txt txt = ./txt/cord-283380-l60yyr6l.txt === reduce.pl bib === id = cord-284791-bgodmbru author = Whitworth, Carrie title = Persistence of Bacteriophage Phi 6 on Porous and Nonporous Surfaces and the Potential for Its Use as an Ebola Virus or Coronavirus Surrogate date = 2020-08-18 pages = extension = .txt mime = text/plain words = 5152 sentences = 250 flesch = 55 summary = The persistence of phi 6 was evaluated as a surrogate for Ebola virus (EBOV) and coronaviruses on porous and nonporous hospital surfaces. Under these laboratory-simulated Western indoor hospital conditions, we assessed the suitability of phi 6 as a surrogate for environmental persistence research related to enveloped viruses, including EBOV and coronaviruses. This study evaluated the persistence of phi 6 in the presence of artificial test soil (ATS) as a potential surrogate for EBOV or coronaviruses at two absolute humidity (AH) conditions on four potential fomites: nonporous stainless steel (SS) and plastic (PL) and two types of porous hospital curtain fabrics. found that the Phi 6 was shown here in the current study to be a conservative surrogate for EBOV in a laboratory-simulated Western hospital room condition of 3.0 g/m 3 AH, persisting longer than the Makona-C05 variant (AH ϭ 3.3 g/m 3 ), with decay rates of 0.06 log 10 /d and 0.79 log 10 /h, respectively (Table 1 ). cache = ./cache/cord-284791-bgodmbru.txt txt = ./txt/cord-284791-bgodmbru.txt === reduce.pl bib === id = cord-284102-rovyvv45 author = Wagner, Teresa R. title = NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date = 2020-09-28 pages = extension = .txt mime = text/plain words = 2910 sentences = 190 flesch = 53 summary = Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Considering that Nbs targeting diverse epitopes within the RBD:ACE2 interface are beneficial 201 in both reducing viral infectivity and preventing mutational escape, we next combined the most 202 potent inhibitory and neutralizing candidates derived from Nb-Set1 (NM1226, NM1228) and 203 We incubated our previously generated color-coded beads 232 comprising RBD, S1 domain or homotrimeric spike with serum samples from patients or non-233 infected individuals, in addition to dilution series of the combinations NM1226/ NM1230 or 234 NM1228/ NM1230 and used this to detect patient-derived IgGs bound to the respective 235 antigens. As a result, we modified our previously described multiplex immunoassay 303 (MULTICOV-AB, 20 ) and developed a novel diagnostic test called NeutrobodyPlex to monitor 304 the presence and the emergence of neutralizing antibodies in serum samples of SARS-CoV-2 305 infected individuals. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block 681 interaction with ACE2 cache = ./cache/cord-284102-rovyvv45.txt txt = ./txt/cord-284102-rovyvv45.txt === reduce.pl bib === id = cord-284449-z7r4n0w7 author = Ma, L. title = Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study date = 2020-03-24 pages = extension = .txt mime = text/plain words = 2847 sentences = 181 flesch = 53 summary = This study provides the first direct evidence about the influence of medical condition of COVID-19 on male sex hormones, alerting more attention to gonadal function evaluation among patients recovered from SARS-CoV-2 infection, especially the reproductive-aged men. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. cache = ./cache/cord-284449-z7r4n0w7.txt txt = ./txt/cord-284449-z7r4n0w7.txt === reduce.pl bib === id = cord-284498-54j6ys8s author = Ihsanullah, Ihsanullah title = Coronavirus 2 (SARS-CoV-2) in water environments: Current status, challenges and research opportunities date = 2020-10-16 pages = extension = .txt mime = text/plain words = 5702 sentences = 398 flesch = 47 summary = Some of the significant challenges and research opportunities are the development of standard techniques for the detection and quantification of SARS-CoV-2 in the water phase, assessment of favorable environments for its survival and decay in water; and development of effective strategies for elimination of the novel virus from water. Development of effective standard techniques for the detection and quantification of SARS-CoV-2 in water, assessment of the existing water purification technologies and development of novel advanced water treatment systems are major challenges and open research opportunities. Furthermore, careful surveillance of water and wastewater to be used as an early warning tool for such outbreaks in future, understanding the survival and decay mechanism of the novel virus in water and wastewater, analysis of potential pathways of SARS-CoV-2 into water bodies are other potential research opportunities for environmental researchers [40] [41] [42] [43] [44] . cache = ./cache/cord-284498-54j6ys8s.txt txt = ./txt/cord-284498-54j6ys8s.txt === reduce.pl bib === === reduce.pl bib === id = cord-283749-j4600733 author = Itoyama, Satoru title = ACE1 polymorphism and progression of SARS date = 2004-10-22 pages = extension = .txt mime = text/plain words = 2975 sentences = 152 flesch = 53 summary = Angiotensin converting enzyme (ACE1) insertion/deletion (I/D) polymorphism was previously reported to show association with the adult respiratory distress syndrome, which is also thought to play a key role in damaging the lung tissues in SARS cases. Despite the small sample size, the frequency of the D allele was significantly higher in the hypoxemic group than in the non-hypoxemic group (p =0.013), whereas there was no significant difference between the SARS cases and controls, irrespective of a contact history. Genotypic distribution and allele frequency of the ACE I/D polymorphism in SARS cases and controls with or without contact history to SARS patients were compared (Table 4 ). The ACE insertion/deletion polymorphism has also been reported to be a risk factor of the diseases mentioned above [17] and this might be associated with systemic angiopathy and influence progression of SARS in the lung. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore cache = ./cache/cord-283749-j4600733.txt txt = ./txt/cord-283749-j4600733.txt === reduce.pl bib === id = cord-283485-xit6najq author = Van Damme, Wim title = The COVID-19 pandemic: diverse contexts; different epidemics—how and why? date = 2020-07-27 pages = extension = .txt mime = text/plain words = 9627 sentences = 633 flesch = 53 summary = Since its emergence in Wuhan, China, in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 4 It was soon discovered that the virus is easily transmitted, can cause Summary box ► Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 88 Box 2 On the use of mathematical models during epidemics A dominant way of studying the transmission dynamics of an infectious disease such as COVID-19, and predicting the amplitude and peak of the epidemic in a population (city, province, country) and analysing the effect of control measures is using mathematical models. cache = ./cache/cord-283485-xit6najq.txt txt = ./txt/cord-283485-xit6najq.txt === reduce.pl bib === id = cord-284526-a5kgo4ct author = Gavriilaki, Eleni title = Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses date = 2020-08-27 pages = extension = .txt mime = text/plain words = 6004 sentences = 319 flesch = 32 summary = Experience from previous coronaviruses has triggered hypotheses on the role of endothelial dysfunction in the pathophysiology of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which are currently being tested in preclinical and clinical studies. Recent evidence suggests that signs and symptoms of severe coronavirus disease-2019 (COVID-19) infection resemble the clinical phenotype of endothelial dysfunction and share mutual pathophysiological mechanisms [1] . Experience from previous coronaviruses has triggered studies testing hypotheses on the role of the endothelial dysfunction in patients with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Α high rate of VTE (43%, mainly PE) overall was reported in another series of 150 ICU patients in which patients with COVID-19associated acute respiratory distress syndrome (ARDS) had higher rates of thrombotic complications compared with non-COVID-19-ARDS [65] . Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection cache = ./cache/cord-284526-a5kgo4ct.txt txt = ./txt/cord-284526-a5kgo4ct.txt === reduce.pl bib === id = cord-283432-od5nnxvg author = Morawska, Lidia title = How can airborne transmission of COVID-19 indoors be minimised? date = 2020-05-27 pages = extension = .txt mime = text/plain words = 5052 sentences = 246 flesch = 41 summary = We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. While evidence for airborne transmission of COVID-19 is currently incomplete, several hospital-based studies have performed air-sampling for SARS-COV-2, including one published paper (Ong et al. cache = ./cache/cord-283432-od5nnxvg.txt txt = ./txt/cord-283432-od5nnxvg.txt === reduce.pl bib === id = cord-283486-ji0e8yoo author = Radulesco, Thomas title = Safety and Impact of Nasal Lavages During Viral Infections Such as SARS-CoV-2 date = 2020-08-27 pages = extension = .txt mime = text/plain words = 1600 sentences = 122 flesch = 46 summary = 8 Regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Carrouel et al found the use of a mouth rinses with local nasal applications that contain b-cyclodextrins combined with flavonoids agents reduce the viral load of saliva and nasopharyngeal microbiota, including potential SARS-CoV-2 carriage. Nasal mucosa have high viral loads and include cells expressing proteases responsible for virus entry (such as angiotensinconverting enzyme 2 and TMPRSS2 for SARS-CoV-2), 19, 20 The upper airway has shown to be a reservoir for descending bacterial or viral infection to the lung. 3, 23, 24 Given the potential benefits summarized above, nasal saline irrigation may enhance recovery in patients known to be infected with COVID-19. 26 The potential direct antiviral actions and reduction in viral load have led to proposals that use in patients with COVID-19 may reduce risk of nosocomial transmission. Copper enhanced nasal saline irrigations: a safe potential treatment and protective factor for COVID-19 infection? cache = ./cache/cord-283486-ji0e8yoo.txt txt = ./txt/cord-283486-ji0e8yoo.txt === reduce.pl bib === id = cord-283579-aejbfk3l author = Hilda, Awoyelu Elukunbi title = Phyloevolutionary analysis of SARS-CoV-2 in Nigeria date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1708 sentences = 112 flesch = 49 summary = Conclusion The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. Knowledge on the outbreak and spread of SARS-CoV-2 in Nigeria would help in providing preventive measures and reduce transmission among populations at risk. Comparative analysis of strains within clades was performed on Geneious Prime (https://www.geneious.com/) based on statistical analysis to determine positions in the genomic sequences from Nigeria that significantly differ between other strain. Figures 2a -g showed consensus similarities and variants between 3 strains from Wuhan, China and Nigeria, including human SARS-CoV-2 human genome. Comparative analysis of the strain from Nigeria, 2 strains from Wuhan sharing the same clade and the reference human SARS-CoV-2 genome was done. The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. cache = ./cache/cord-283579-aejbfk3l.txt txt = ./txt/cord-283579-aejbfk3l.txt === reduce.pl bib === id = cord-283352-0l1ggmhx author = Javelot, H title = Panic and pandemic: narrative review of the literature on the links and risks of panic disorder as a consequence of the SARS-CoV-2 pandemic date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4437 sentences = 191 flesch = 36 summary = Abstract Although the 'panic' word has been abundantly linked to the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic in the press, in the scientific literature very few studies have considered whether the current epidemic could predispose to the onset or the aggravation of panic attacks or panic disorder. The current SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic is likely to induce, beyond its potentially dramatic impact on health, serious psychological consequences, particularly in terms of the often reported "panic" state it triggered, and the medical disorder potentially linked to this state, i.e., panic disorder [1] [2] [3] [4] [5] . In this review, we propose to address : (i) the way in which the international literature has used to date the terminology of "panic" in relation to the SARS-CoV-2 pandemic, (ii) the very concept of panic attack, panic disorder and the specificity of the respiratory component frequently associated with it, (iii) and finally, a synthesis of the links and risk factors between COVID-19 and "respiratory" panic disorder. cache = ./cache/cord-283352-0l1ggmhx.txt txt = ./txt/cord-283352-0l1ggmhx.txt === reduce.pl bib === id = cord-284559-g9szoh3g author = Bartoloni, Elena title = Hypertension and SARS-Cov-2 infection: is inflammation the missing link? date = 2020-09-23 pages = extension = .txt mime = text/plain words = 616 sentences = 50 flesch = 33 summary = The dramatic emergence of the pandemic coronavirus disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised significant medical and public health concerns for the high disease mortality rate ranging from 1% to more than 5%. 2 In fact, pre-existing cardiovascular comorbidities, including hypertension (HTN), diabetes mellitus, cerebrovascular and coronary heart disease, enhance susceptibility to SARS-CoV-2 infection and are associated with increased risk of severe disease, myocardial injury and short-term mortality rate. 4 However, due to the high prevalence of hypertension in the general population, concerns raised as to whether hypertension represents merely a concomitant risk factor or a pivotal pathogenic trigger of cardiac injury in patients with SARS-CoV2 infection. In this setting, it may be hypothesized that COVID-19associated PAMPs may act as exogenous triggers of TLR4 signalling pathway leading to inflammasome activation and inflammatory cytokine release, including interleukin-1 (Figure) . cache = ./cache/cord-284559-g9szoh3g.txt txt = ./txt/cord-284559-g9szoh3g.txt === reduce.pl bib === id = cord-283850-kt8n6pg2 author = Steardo, Luca title = Psychiatric face of COVID-19 date = 2020-07-30 pages = extension = .txt mime = text/plain words = 7886 sentences = 374 flesch = 32 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similarly to other coronaviruses demonstrate neurotropism; the viral infection of the brain stem may complicate the course of the disease through damaging central cardio-respiratory control. Post-mortem analysis of nervous tissue from tissue of a 54 years-old man who died from severe respiratory failure associated with COVID-19 identified SARS-COV-2 viral particles in the olfactory nerve, in the gyrus rectus and in the brainstem with signs of profound damage to all elements of the tissue including glial cells, neurones, their axons and myelin 37 . Infection with SARS-CoV-2 (even in moderate clinical cases) thus promotes cognitive disorders with emergence of delirium, acute psychosis, exacerbation of mild cognitive impairment or with accelerating of dementia associated with various neurodegenerative conditions, including Alzheimer's disease (AD) 85, 86 . Patients with COVID-19 could present with a wide range of neuropsychiatric symptoms, which result from systemic inflammation, CNS effects of cytokines, infection of neural cells by SARS-COV-2, neuroinflammation, glial dysfunction or aberrant epigenetic modifications of stress-related genes. cache = ./cache/cord-283850-kt8n6pg2.txt txt = ./txt/cord-283850-kt8n6pg2.txt === reduce.pl bib === id = cord-284862-nhihxog0 author = Kroemer, Marie title = COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1043 sentences = 63 flesch = 49 summary = Although the existence of SARS-CoV-2 specific T-cells has been described 2,3 , the frequency and the intensity of SARS-CoV-2 specific T-cell responses among mild illness and severe pneumonia convalescent COVID-19 patients remains to be investigated. In this prospective study, 60 patients who had COVID-19 were enrolled in a two cohorts study that were entitled mild illness (n=30) and severe pneumonia (n=30) at least 21 days after the first symptoms of ; Table 1 for CoV-N) might be explained by the sequence homology between structural proteins from various coronavirus suggesting the existence of cross reactive memory T-cells 5 . We observed that all patients with severe pneumonia had a positive serology index and most of them had at least one specific cellular response for SARS-CoV-2 proteins (28 out of 30). Specific T-cell responses for S, M and N proteins were simultaneously shown for 70.0% of severe pneumonia patients while only for 37.9% of mild illness patients (P=0.0191) (Fig. 1E) . cache = ./cache/cord-284862-nhihxog0.txt txt = ./txt/cord-284862-nhihxog0.txt === reduce.pl bib === id = cord-283956-zgrtux7i author = Amin, Sk. Abdul title = Fight against novel coronavirus: A perspective of medicinal chemists date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5095 sentences = 356 flesch = 52 summary = Like other RNA viruses, the functional significance of this Mpro or chymotrypsin-like protease (3CLpro) of SARS-CoV-2 emerges as an attractive drug target for the development of anti-viral agents. A group of scientists from the Cairo University, Egypt predicted COVID-19 spike binding site to a cell-surface receptor namely Glucose Regulated Protein 78 (GRP78) by employing structural bioinformatics in combination with protein-protein docking [55] . An early virtual screening (VS) study of FDA approved drugs (retrieved from Selleckchem Inc.) against the first resolved SARS-CoV-2 Mpro crystal structure (PDB: 6LU7) was performed. In another study, Elfiky [67] reported SARS-CoV-2 RdRp targeted molecular docking study of some anti-polymerase drugs which have been approved for use against various viruses. This study deals with the information currently available on potential targets for therapeutic invention and screening of new compounds or drug repurposing against SARS-CoV-2 (Figure 8 ). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 cache = ./cache/cord-283956-zgrtux7i.txt txt = ./txt/cord-283956-zgrtux7i.txt === reduce.pl bib === id = cord-284841-flhfagp3 author = Nicol, Thomas title = Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech) date = 2020-06-15 pages = extension = .txt mime = text/plain words = 2806 sentences = 214 flesch = 58 summary = METHODS: Two automated immunoassays (Abbott SARS-CoV-2 CLIA IgG and Euroimmun Anti-SARS-CoV-2 ELISA IgG/IgA assays) and one lateral flow immunoassay (LFIA NG-Test® IgG-IgM COVID-19) were tested. The aim of the study was to assess the clinical performance of CE marked assays available in Europe to detect SARS-CoV-2 antibodies: two automated immunoassays (Euroimmun and Abbott assays) targeting two different proteins and also one lateral flow immunoassay (NG Biotech). On May, 2020, the French Health Authority (Haute Autorité de Santé) and Infectious Diseases Society of America recommended that patients with symptoms consistent with COVID-19 but having a positive result for SARS-CoV-2 by RT-PCR may be diagnosed by serological tests [22, 23] . Here, we did not observe any significant difference between sensitivity of IgA ELISA and IgM LFIA In conclusion, our study showed equivalent clinical performance for IgG of three immunoassays (ELISA, CLIA and LFIA) >14 days after symptoms onset. cache = ./cache/cord-284841-flhfagp3.txt txt = ./txt/cord-284841-flhfagp3.txt === reduce.pl bib === id = cord-284702-reu77suz author = Lau, Suet-Ting title = Tachycardia amongst subjects recovering from severe acute respiratory syndrome (SARS) date = 2005-04-08 pages = extension = .txt mime = text/plain words = 734 sentences = 51 flesch = 46 summary = This study to identify the possible causes for the tachycardia excluded active disease, thyroid dysfunction, haematological, cardiac, autonomic and significant pulmonary defect at 2 months from onset of disease. Possible causes are deconditioning [2] , impaired pulmonary function, impaired cardiac function, cardiac arrhythmia, thyroid dysfunction, anaemia, autonomic dysfunction [3] and anxiety state. Chest radiography findings, haemoglobin level, length of hospital stay, time elapsed after discharge, presence of complications, WHO Quality of Life (QOL) score and Monitored Functional Task Evaluation (MFTE) score [4] are shown in Table 2 . Mild residual CXR changes, minor lung function impairment and normal blood gas makes pulmonary defect unlikely to be a significant cause of sinus tachycardia during normal activity. Deconditioning and anxiety state causes tachycardia in the daytime but not at night, and is compatible with the pattern observed in this cohort. In the absence of significant cardiac, pulmonary, thyroid and haematological dysfunction, we believe that sinus tachycardia is attributable to physical deconditioning and contributed by impaired psychological well-being. cache = ./cache/cord-284702-reu77suz.txt txt = ./txt/cord-284702-reu77suz.txt === reduce.pl bib === id = cord-284376-plwyjhl8 author = Fu, Xinmiao title = Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date = 2020-05-31 pages = extension = .txt mime = text/plain words = 14726 sentences = 782 flesch = 49 summary = All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In contrast, corticosteroid use within the month before sampling was not different between The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis. cache = ./cache/cord-284376-plwyjhl8.txt txt = ./txt/cord-284376-plwyjhl8.txt === reduce.pl bib === id = cord-285179-26ey3fm8 author = Chan, Kwok-Hung title = Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests date = 2013-04-10 pages = extension = .txt mime = text/plain words = 5270 sentences = 278 flesch = 52 summary = title: Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests We conducted a seroprevalence study on archived sera from 94 game-food animal handlers at a wild life market, 28 SARS patients, and 152 healthy blood donors in Southern China to assess the zoonotic potential and evidence for intrusion of HCoV-EMC and related viruses into humans. 12 In order to further substantiate the hypothesis of HCoV-EMC being a zoonotic agent and elicit evidence for intrusion of HCoV-EMC and its related viruses into humans, we studied the antibody titers using immunofluorescence (IF) as screening and neutralization as confirmatory tests in at-risk groups working in a wild life market in Guangzhou of Southern China who were constantly exposed to a wide range of game food animals, SARS patients who might have acquired their infection directly from wild animals, and healthy blood donors. cache = ./cache/cord-285179-26ey3fm8.txt txt = ./txt/cord-285179-26ey3fm8.txt === reduce.pl bib === id = cord-285168-qkadqohe author = Delatorre, Edson title = Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries date = 2020-04-23 pages = extension = .txt mime = text/plain words = 2551 sentences = 149 flesch = 55 summary = Here, we estimate the probable onset date of the community spread of SARS-CoV-2 from the cumulative number of deaths reported during the early stage of the epidemic in Western Europe and the Americas. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analyzed between the middle of January and early February 2020, thus long before community transmission was officially recognized and control measures were implemented. In some countries (Italy and Netherlands) community transmission was traced long before (2-4 weeks) the first confirmed SARS-CoV-2 infection case; while in others (Spain, France, United Kingdom, Germany, and Belgium) the onset date roughly coincides with the time of detection of the first imported cases (Figure 1 ). That quite long period of cryptic community transmission (> 4 weeks) in all analyzed countries draws attention to the great challenge of tracking the early global spread of SARS-CoV-2 and supports that control measures should be adopted at least as soon as first imported cases are detected in a new geographic region. cache = ./cache/cord-285168-qkadqohe.txt txt = ./txt/cord-285168-qkadqohe.txt === reduce.pl bib === id = cord-283440-8du0s33p author = Ciuca, Ioana M title = COVID-19 in Children: An Ample Review date = 2020-06-25 pages = extension = .txt mime = text/plain words = 5636 sentences = 313 flesch = 45 summary = The aim of this review was to describe the current knowledge about coronavirus disease 2019 (COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) in children, from epidemiological, clinical, and laboratory perspectives, including knowledge on the disease course, treatment, and prognosis. This review highlights that COVID-19 in children is similar to the disease in the adult population, but with particularities regarding clinical manifestations, laboratory test results, chest imaging, and treatment. It started at the end of 2019, when many adult patients with a new form of pneumonia that was frequently fatal were admitted to Chinese hospitals; this illness was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [11] [12] [13] This study aimed to review the current data on SARS-CoV-2 infection in children, from epidemiological, clinical, and laboratory perspectives, including data on the disease course, treatment, and prognosis. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-283440-8du0s33p.txt txt = ./txt/cord-283440-8du0s33p.txt === reduce.pl bib === id = cord-284829-dge21g0g author = Dinakaran, Damodharan title = Neuropsychiatric aspects of COVID-19 Pandemic: A Selective Review date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2288 sentences = 174 flesch = 38 summary = In this selective review, the authors present the neuropsychiatric manifestations and postulated mechanisms of COVID-19. Though the most common presentation is a self limiting viral illness with fever and dry cough, severe infection is reported in 15-20% of the affected population (26) . In about 5% of the severely ill patients, Acute Respiratory Distress Syndrome (ARDS), Multi organ involvement and septic shock leads to further clinical deterioration. Acute polyradiculopathy (Guillain Barre Syndrome -GBS) has been reported related to SARS-CoV-2 infection (41) (42) (43) (44) (45) (46) . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain Barre syndrome associated with COVID-19 infection: A case report cache = ./cache/cord-284829-dge21g0g.txt txt = ./txt/cord-284829-dge21g0g.txt === reduce.pl bib === id = cord-285362-7dc2gox0 author = Jacot, Damien title = Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1229 sentences = 86 flesch = 59 summary = title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses We analyzed SARS-CoV-2 viral loads from 22'323 RT-PCR results according to samples types, gender, age, and health units. Quantitative reverse transcription polymerase chain reaction (RT-PCR) represents a 24 key diagnostic tool for patients with suspected SARS-CoV-2 infection. The report of RT-PCR SARS-CoV-2 viral loads raised also several 38 questions regarding the use of this information for the laboratory as an internal quality assessment 39 tool, as well as (i) to predict contagiousness of patients and hence to guide epidemiological 40 decisions, especially for hospitalized patients and (ii) to predict the patient prognosis and assess for the E-gene PCR was those described by Corman and colleague (4) . Clinical progression and 218 viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study SARS-CoV-2 Viral Load in Upper 224 Respiratory Specimens of Infected Patients cache = ./cache/cord-285362-7dc2gox0.txt txt = ./txt/cord-285362-7dc2gox0.txt === reduce.pl bib === id = cord-284573-w0sk622m author = Caduff, Carlo title = What Went Wrong: Corona and the World after the Full Stop date = 2020-07-21 pages = extension = .txt mime = text/plain words = 9277 sentences = 517 flesch = 58 summary = Published by a group of experts without peer review on an institutional website, the report compared Covid-19 with the great pandemic of 1918, which killed over 50 million people worldwide and suggested, without any evidence, that SARS-CoV-2 was "a virus with comparable lethality to H1N1 influenza in 1918." 1 Most frightening in all this was not so much the lethality of the SARS-CoV-2 virus but the license to rush forward with predictions, abandon basic standards of science, and make dramatic claims to scare people. This extreme and unprecedented blanket approach systematically imposed on entire populations was driven by a number of factors that variously prevailed in different countries across the world: a growing sense of panic, constant media sensationalism, deep authoritarian longings, increasing political pressure to contain the spread of the virus, disturbing accounts of overwhelmed hospitals unable to cope with the surge of patients, misleading mortality calculations, and, most importantly, a trust in the power of mathematical disease modeling. cache = ./cache/cord-284573-w0sk622m.txt txt = ./txt/cord-284573-w0sk622m.txt === reduce.pl bib === id = cord-285557-my16g91c author = Berger, A. title = Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date = 2004-01-31 pages = extension = .txt mime = text/plain words = 6381 sentences = 291 flesch = 47 summary = This strengthened the case for the novel coronavirus being the cause of SARS, but only after it had been shown to cause a similar illness in artificially infected macaques could it be regarded as fulfilling all four of Koch's postulates ; World Health Organisation Multicentre Collaborative Networks for Severe Acute Respiratory Syndrome Diagnosis, 2003) . Nevertheless, and despite considerable progress in this field, much remains to be done until laboratory tests become a useful tool for the management of SARS cases (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003) . An enzyme-linked immunosorbent assay (ELISA) was developed that detects antibodies in the serum of SARS patients and reliably yields positive results at around day 21 after the onset of illness (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003). cache = ./cache/cord-285557-my16g91c.txt txt = ./txt/cord-285557-my16g91c.txt === reduce.pl bib === id = cord-284925-vy2li9lz author = Lam, Dennis Shun Chiu title = COVID-19: Special Precautions in Ophthalmic Practice and FAQs on Personal Protection and Mask Selection date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4717 sentences = 268 flesch = 52 summary = We also endeavor to answer the key frequently asked questions in areas of the coronaviruses, COVID-19, disease transmission, personal protection, mask selection, and special measures in ophthalmic practices. Ophthalmologists are at risk of COVID-19 infection, since routine ophthalmic examinations are usually performed in a setting with close doctor-patient contact. We have also shared the precautions and strategies that we have implemented in our ophthalmic practice, based on our previous and current successful experiences in preventing severe acute respiratory syndrome (SARS) in 2003 and the current COVID-19 outbreaks in Hong Kong. For healthcare workers, surgical masks should be worn when performing sterile procedures, or as general protection against droplets infections. The close proximity of patients and doctors during eye examination, the presence of tears and liquids for anesthesia and dilation, or the potential aerosol or droplets from "air puff" tonometry, all pose a high risk for infective transmission. Interim infection prevention and control recommendations for patients with suspected or confirmed Coronavirus Disease 2019 (COVID-19) in healthcare settings cache = ./cache/cord-284925-vy2li9lz.txt txt = ./txt/cord-284925-vy2li9lz.txt === reduce.pl bib === id = cord-284873-m1ehdydr author = Cadegiani, Flavio A. title = Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2536 sentences = 158 flesch = 38 summary = title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 At the onset of the COVID-19 pandemic, mortality following infection of severe acute respiratory coronavirus (SARS-CoV-2) was thought to be solely associated with aging and pre-existing conditions; however, as the pandemic ensued, several large scale epidemiological observations eluded to additional atypical risk factors, particularly hypertension, obesity, and male gender (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) . The Renin-Angiotensin-Aldosterone System (RAAS) has been shown to be central in COVID-19, since three of the key modulators of SARS-CoV-2 infectivity-angiotensin 1-7, ACE2, and AT1-belong to the RAAS, in addition to the TMPRSS2 expression (12) (13) (14) (15) (16) (17) (18) (19) . Abnormal ACE2 expression, angiotensin II and angiotensin 1-7 imbalance, and TMPRSS2 androgen-mediated overactivity seem to be key regulators of SARS-CoV-2 infectivity, in accordance with epidemiological observations of hypertension, obesity, and male sex as being major risk factors. cache = ./cache/cord-284873-m1ehdydr.txt txt = ./txt/cord-284873-m1ehdydr.txt === reduce.pl bib === id = cord-284042-awl5bb0j author = Carrascosa, J.M. title = Cutaneous Manifestations in the Context of SARS-CoV-2 Infection (COVID-19)() date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3952 sentences = 216 flesch = 45 summary = From the pathogenic point of view, the immune response triggered by infection with SARS-CoV-2 may result in harmful effects, such as endothelial cell dysfunction and activation of J o u r n a l P r e -p r o o f coagulation pathways; this may explain the cardiovascular and thrombotic complications that affect a subgroup of patients. 19 Vesicular lesions, usually monomorphic, appear early on and may at times precede other symptoms (in 15% of patients), 11 although in most cases, up to 79.2% in a series of 24 patents reported by Fernandez-Nieto et al., 20 they occur at the onset of other symptoms. 21 reported the case of a female patient who developed an urticarial rash, accompanied by odynophagia and arthralgia, before developing the full clinical manifestations of COVID-19. cache = ./cache/cord-284042-awl5bb0j.txt txt = ./txt/cord-284042-awl5bb0j.txt === reduce.pl bib === id = cord-284879-sjkni2uc author = Song, Suk-Kyoon title = IgG Seroprevalence of COVID-19 among Individuals without a History of the Coronavirus Disease Infection in Daegu, Korea date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2559 sentences = 146 flesch = 51 summary = METHODS: Serologic testing for immunoglobulin G antibody based on immunochromatographic assay was conducted in 103 patients and 95 guardians aged 18 to 82 years without any history of COVID-19 diagnosis, who visited outpatient clinics of a single university-affiliated hospital from May 25 to June 5, 2020. 4-15 However, a significant fraction of the population has developed antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suggesting that the infection is much more pervasive than implied by the number of confirmed cases. Next, we compared seroprevalence among subgroups stratified by characteristics of study subjects, including age (< 40, 40-59, ≥ 60 years), gender, body mass index (BMI) (< 25, ≥ 25 kg/m 2 ), smoking history (current, previous, never), history of doctor-diagnosed diabetes or hypertension (yes, no), reason for the current hospital visit (patient, guardian), and the presence of COVID-19 confirmed cases among close contacts (yes, no). cache = ./cache/cord-284879-sjkni2uc.txt txt = ./txt/cord-284879-sjkni2uc.txt === reduce.pl bib === id = cord-285053-ah9z9luw author = Freedman, David O title = In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks date = 2020-09-25 pages = extension = .txt mime = text/plain words = 2057 sentences = 106 flesch = 58 summary = This review presents a comprehensive table summarizing all peer-reviewed or public health publication of flights with likely, possible or unproven in-flight SARS-CoV-2 transmission from 24 January 2020 to 21 September 2020. Two likely secondary cases (one seated in Row 40 with 5 index cases) had negative Day 0 PCR testing and were PCR+ on Day 14; pre-flight transmission shortly before the relatively short flight cannot be ruled out. A number of these flights have carried COVID-19 cases, 5 but no national databases or unified international registries documenting evacuation flights or their passenger loads are publicly available, and few data have been published to date. On flights N-R with the rigid masking policies (meals served) of Emirates Airlines, no secondary cases were identified on Day 14 screening despite 58 passengers who were PCR+ on a total of 5 flights of 8 hours each with ∼1500-2000 passengers. cache = ./cache/cord-285053-ah9z9luw.txt txt = ./txt/cord-285053-ah9z9luw.txt === reduce.pl bib === id = cord-284867-p4jgyusp author = Schöler, Lara title = A Novel In-Cell ELISA Assay Allows Rapid and Automated Quantification of SARS-CoV-2 to Analyze Neutralizing Antibodies and Antiviral Compounds date = 2020-10-09 pages = extension = .txt mime = text/plain words = 4328 sentences = 235 flesch = 42 summary = Altogether, the SARS-CoV-2 icELISA test allows rapid (<48 h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs and antiviral drugs using reagents and equipment present in most routine diagnostics departments. The fact that the infection and the resulting icELISA signal were neutralized by NAbs present in immune sera indicated that the fast and automated icELISA format is applicable for icNTs. Although most SARS-CoV-2 NTs have not been formally validated and certified, classic plaque reduction neutralization tests (PRNT) are currently considered to represent the gold standard for the detection of SARS-CoV-2-specific NAbs. Various commercially available IgM, IgA, and IgG ELISAs have been compared to PRNTs [e.g., (30) ]. Given the excellent signal-to-noise ratio between infected and uninfected cells, the test was applicable to quantify the efficacy of antiviral compounds, here shown for IFNb, and SARS-CoV-2-specific NAbs present in immune sera. cache = ./cache/cord-284867-p4jgyusp.txt txt = ./txt/cord-284867-p4jgyusp.txt === reduce.pl bib === id = cord-285430-o086q2qa author = Gribble, Karleen title = Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date = 2020-07-25 pages = extension = .txt mime = text/plain words = 2622 sentences = 150 flesch = 51 summary = BACKGROUND: In an effort to prevent infants being infected with SARS-CoV-2, some governments, professional organisations, and health facilities are instituting policies that isolate newborns from their mothers and otherwise prevent or impede breastfeeding. WEIGHING OF RISKS IS NECESSARY IN POLICY DEVELOPMENT: Such policies are risky as was shown in the early response to the HIV pandemic where efforts to prevent mother to child transmission by replacing breastfeeding with infant formula feeding ultimately resulted in more infant deaths. In the COVID-19 pandemic, the risk of maternal SARS-CoV-2 transmission needs to be weighed against the protection skin-to-skin contact, maternal proximity, and breastfeeding affords infants. However, mothers and infants present a special situation as the risk of mother-to-child transmission of SARS-CoV-2 needs to be weighed against the protection from infectious diseases and the support for bonding and caregiving provided by close maternal proximity and breastfeeding. cache = ./cache/cord-285430-o086q2qa.txt txt = ./txt/cord-285430-o086q2qa.txt === reduce.pl bib === id = cord-284037-nj5jo1ev author = Kwee, Thomas C. title = Chest CT in COVID-19: What the Radiologist Needs to Know date = 2020-10-23 pages = extension = .txt mime = text/plain words = 7662 sentences = 363 flesch = 41 summary = Chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available. According to the Fleischner Society consensus statement, chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available (59) . In cases of clinical worsening, chest imaging is advised to assess for COVID-19 progression or secondary cardiopulmonary complications such as acute respiratory distress syndrome (ARDS), PE, superimposed pneumonia, or heart failure that can potentially be secondary to COVID-19-induced cardiac injury (59) . cache = ./cache/cord-284037-nj5jo1ev.txt txt = ./txt/cord-284037-nj5jo1ev.txt === reduce.pl bib === id = cord-283912-ha2xwjzy author = Zheng, Meijuan title = Serum inflammatory factors are positively correlated with the production of specific antibodies in coronavirus disease 2019 patients date = 2020-09-22 pages = extension = .txt mime = text/plain words = 1523 sentences = 78 flesch = 46 summary = 5 Thus, a detailed characterization of the associations between humoral immune responses and inflammatory factors could result in a better understanding of SARS-CoV-2-host interactions in COVID-19 patients. In the current study, the levels of RBD-specific IgG, RBD-specific IgA, and the frequencies of ASCs and ICOS+ T follicular helper (TFH) cells were found to be higher in severely affected COVID-19 patients than those in nonseverely affected patients. Collectively, these results indicated that severe COVID-19 illness induced strong humoral immune responses, which is consistent with previous studies showing higher IgG titers in severe patients than in nonsevere patients. Our study showed that the severely affected patients displayed higher levels of anti-RBD antibodies, increased frequencies of ASCs and ICOS + TFH cells, and elevated levels of CXCL13. Effective control of SARS-CoV-2 requires further investigation of the mechanism underlying the correlations between humoral immunity and inflammatory factors in severe COVID-19, and the results of such studies could be used to guide immunotherapy with passive antibodies while controlling hyperinflammation. cache = ./cache/cord-283912-ha2xwjzy.txt txt = ./txt/cord-283912-ha2xwjzy.txt === reduce.pl bib === id = cord-284734-qioy7eso author = Pourahmad, Ramtin title = Efficacy of Plasmapheresis and Immunoglobulin Replacement Therapy (IVIG) on Patients with COVID-19 date = 2020-07-31 pages = extension = .txt mime = text/plain words = 3073 sentences = 168 flesch = 45 summary = According to recent observations about different modalities in treatment of patients infected with COVID-19, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection. According to the medical experiences in the treatment of patients infected with other members of coronavirus family such as SARS-CoV and MERS-CoV, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection [1] [2] [3] [4] [5] [6] [7] . As the world confronting a pandemic due to SARS-CoV-2, immunoglobulin replacement therapy (IVIG) could be an ideal option for prevention and treatment of COVID-19 disease. According to the reports, China has used immunoglobulin replacement therapy on several COVID-19 patients during the outbreak of this novel coronavirus which showed promising results [46] . The use of convalescent plasma therapy and remdesivir in the successful management of a critically ill obstetric patient with novel coronavirus 2019 infection: a case report. cache = ./cache/cord-284734-qioy7eso.txt txt = ./txt/cord-284734-qioy7eso.txt === reduce.pl bib === id = cord-284234-9cd2v6bt author = Sebastian, S title = Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date = 2020-06-10 pages = extension = .txt mime = text/plain words = 4483 sentences = 256 flesch = 44 summary = Understandable concerns have been raised on the safety of steroids, immunosuppressive drugs, and biologics used in patients for a variety of indications including immune mediated inflammatory disease such as inflammatory bowel diseases (IBD), which do increase the risk of opportunistic bacterial, viral and fungal infections (5) . Therefore, continuing concerns remain both from IBD patients and the A c c e p t e d M a n u s c r i p t clinicians managing them, regarding the potential of IBD related drugs causing more frequent infections by SARS-CoV2, and increased risk of severe complications from COVID-19 (13) . Corticosteroids are thought to have a divergent effect on viral infections including SARS COV viruses; on one hand they inhibit host immune response acting on migration and chemokines production leading to impaired viral clearance and the resultant prolonged Moreover, a prospective, randomized double-blinded, placebo-controlled trial compared early hydrocortisone treatment (before day seven of the illness) with a placebo and found that early hydrocortisone therapy was associated with a higher subsequent plasma viral load (61) . cache = ./cache/cord-284234-9cd2v6bt.txt txt = ./txt/cord-284234-9cd2v6bt.txt === reduce.pl bib === id = cord-284589-j1609xlu author = Sedova, Mayya title = Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence date = 2020-05-29 pages = extension = .txt mime = text/plain words = 1302 sentences = 85 flesch = 55 summary = RESULTS: Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context. At the same time, with the exception of the spike protein mutations, there are no publicly available resources that provide analysis for all the other structurally characterized regions of the SARS-CoV-2 proteins. For commercial re-use, please contact journals.permissions@oup.com MN908947.3), with information on boundaries of the predicted proteins, currently available SARS-CoV-2 structures and a histogram of the aminoacid mutation frequency. The first of the lower level panels (Figure 1b) provides interactive visualization of the selected structure or model, with an option for coloring the chain according to the mutation frequency. The Coronavirus3D server was designed to provide users with information and tools to carry out their own analysis of how mutations in the SARS-CoV-2 proteins may affect their 3D-structures and their functions. cache = ./cache/cord-284589-j1609xlu.txt txt = ./txt/cord-284589-j1609xlu.txt === reduce.pl bib === id = cord-283824-c7y9zf7o author = Opitz, Sven title = Regulating epidemic space: the nomos of global circulation date = 2015-02-20 pages = extension = .txt mime = text/plain words = 8618 sentences = 492 flesch = 46 summary = The first concerns the referent object of governmental practice: the regulatory effort to secure global public health does not focus on human life so much as it does on post-human materialities of global traffic. Most importantly, the key passages of the IHR read like a clear-cut manifestation of the liberal government of circulation: 'The purpose and scope of these Regulations are to prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which avoid unnecessary interference with international traffic and trade.' (IHR, Article 2) The mobility of disease and the mobility of goods and people are conjoined in this problem space. These bodies of transmission belong to a governmental vision that pictures the world as a space of universal traffic and that focuses on routes and material means of global circulation. cache = ./cache/cord-283824-c7y9zf7o.txt txt = ./txt/cord-283824-c7y9zf7o.txt === reduce.pl bib === id = cord-284950-qqje5s04 author = Venkataraman, Thiagarajan title = The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis date = 2017-07-31 pages = extension = .txt mime = text/plain words = 6622 sentences = 335 flesch = 45 summary = In this article, we summarize pulmonary fibrotic changes observed after a SARS-CoV infection, discuss the extent to which other respiratory viruses induce fibrosis, describe available animal models to study the development of SARS-CoV induced fibrosis and review evidence that pulmonary fibrosis is caused by a hyperactive host response to lung injury mediated by epidermal growth factor receptor (EGFR) signaling. In this article, we summarize observations of pulmonary fibrosis during and after the SARS epidemic, note the extent to which fibrosis occurs after other pulmonary viral infections, describe efforts to recapitulate fibrotic changes in mouse models of SARS, and review evidence that the condition represents a hyperactive response to lung injury, driven by proinflammatory mediators acting through epidermal growth factor receptor (EGFR) signaling. After an illness lasting 1e2 weeks, most patients resolve the infection, however about one-third develop severe pulmonary complications leading to acute lung injury and acute respiratory distress syndrome (ARDS), resulting in intubation and prolonged hospitalization (Tsui et al., 2003) . cache = ./cache/cord-284950-qqje5s04.txt txt = ./txt/cord-284950-qqje5s04.txt === reduce.pl bib === id = cord-285018-l26px1bc author = Ong, David S.Y. title = Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1492 sentences = 90 flesch = 55 summary = title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? OBJECTIVES: The aim of this study was to assess the diagnostic performance of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2. RealAmp Kit on the sample-to-result InGenius® platform in comparison to the national reference standard in the Netherlands, and to determine the added value of nucleoprotein (N) gene detection to establish the diagnosis of COVID-19. Patients were sampled from the oral cavity and subsequently from the nasal cavity using the same nasopharyngeal swab, which was tested by a validated in-house NAT assay on the presence of COVID-19 envelope protein (E) gene and RNA dependent RNA polymerase (RdRp) gene according to a reference method that was established after international collaboration [5] . cache = ./cache/cord-285018-l26px1bc.txt txt = ./txt/cord-285018-l26px1bc.txt === reduce.pl bib === id = cord-284478-c1uj3jra author = Schub, David title = High levels of SARS-CoV-2–specific T cells with restricted functionality in severe courses of COVID-19 date = 2020-10-15 pages = extension = .txt mime = text/plain words = 7277 sentences = 364 flesch = 48 summary = RESULTS: Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2–specific T cells as compared with convalescent individuals. So far, mainly nonspecific general changes in the number and functionality of blood cells have been described, whereas specific T cell immunity directed against SARS-CoV-2 has as yet not been studied as extensively (7) (8) (9) (10) (11) , especially in patients with different disease severity. As shown in Figure 3A , the percentage of multifunctional, SARS-CoV-2-specific CD4 + T cells with the ability to simultaneously produce all 3 cytokines was significantly lower in patients with severe courses as compared with convalescent individuals. Nevertheless, the SEB-reactive and SARS-CoV-2-specific cytokine profiles exhibited similar differences between patients with severe disease and convalescent individuals ( Figure 3A ). We also analyzed expression of cytotoxic T lymphocyte antigen 4 (CTLA-4) on SARS-CoV-2-specific and SEB-reactive T cells as phenotypical correlates of altered functionality commonly observed during active infections. cache = ./cache/cord-284478-c1uj3jra.txt txt = ./txt/cord-284478-c1uj3jra.txt === reduce.pl bib === id = cord-283861-kcv1bmyx author = Zou, J. title = Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents date = 2020-05-06 pages = extension = .txt mime = text/plain words = 3192 sentences = 175 flesch = 63 summary = We quantitated anti-SARS/CoV-2 IgG and IgM by ELISA in self-collected blood samples (n=142) in arbitrarily-selected metro Atlanta residents, primarily acquaintances of the authors' lab members from 4/17-4/27, 2020. While we do not claim this small immune survey is 49 broadly representative of metro Atlanta, and we have greater confidence in the IgG results, 50 which had only 2.4% positivity, it nonetheless demonstrates that persons with antibodies to 51 SARS/CoV-2, who've not suspected they'd been exposed to this virus, can readily be found in 52 various Atlanta area neighborhoods (9 positives were in 8 zip codes). Nonetheless, our quantitative approaches enabled seemingly readily and 74 reliable discernment that about 3 and 6 of 127 arbitrarily subjected Atlanta area residents 75 displayed SARs/CoV-2-specific IgG and IgM, respectively, which likely reflects that they have 76 been exposed to this virus. cache = ./cache/cord-283861-kcv1bmyx.txt txt = ./txt/cord-283861-kcv1bmyx.txt === reduce.pl bib === id = cord-284068-sbon3aes author = Mok, Chee Keng title = Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1798 sentences = 104 flesch = 49 summary = Validation assays to determine changes in infectious virus titres upon treatment was carried out by testing selected hit compounds in dose-dependent assays in Vero E6 to confirm the primary screen observation and also in the human hepatocarcinoma HuH7 cell line as the latter cell line expresses high levels of the ACE2 receptor (10) and supports replication of coronaviruses (11) . While recent data has shown that vitamin D levels are negatively associated with morbidity and mortality of COVID-19 cases (13, 14) , this is the first report of a direct inhibitory effect of calcitriol on SARS-CoV-2. The authors speculated that vitamin D supplementation could protect against SARS-CoV-2 infection and improve patient disease outcomes (16) , and our finding certainly provides credence to this hypothesis. Given the high transmissibility of SARS-CoV-2 globally (23), if these findings can be replicated in clinical trials, calcitriol may certainly prove to be an effective tool in the effort to control the pandemic while waiting for an effective vaccine to be rolled out globally. cache = ./cache/cord-284068-sbon3aes.txt txt = ./txt/cord-284068-sbon3aes.txt === reduce.pl bib === id = cord-284387-cjziykrz author = Garcia-Castrillo, Luis title = European Society For Emergency Medicine position paper on emergency medical systems’ response to COVID-19 date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2346 sentences = 125 flesch = 44 summary = Second, protective measures by health services, especially in public and open environments like emergency departments (EDs) where isolation of potentially infected patients is a real challenge or clinical wards is vital [10] . Clinical care of suspected patients with COVID-19 should focus on early recognition, and immediate isolation, as well as appropriate infection prevention measures and control measures with care taken to optimise supportive care. (1) An informative, coordinated campaign for public and healthcare professionals, focused on mechanisms of contagion [4] , personal protection equipment (PPE) use, and a clinical pathway for the suspected patients infected with COVID-19. (5) The development and implementation of cleaning protocols, considering that coronavirus has been isolated on inanimate objects, and healthcare workers were infected by SARS, even without direct contact with sick patients [15] . The patient, relative or general practitioner may alert the emergency number indicating that a potential case of SARS-CoV-2 infection with severe symptoms is seeking care. cache = ./cache/cord-284387-cjziykrz.txt txt = ./txt/cord-284387-cjziykrz.txt === reduce.pl bib === id = cord-285467-uxfk6k3c author = Ragni, Enrico title = Management of osteoarthritis during COVID‐19 pandemic date = 2020-05-21 pages = extension = .txt mime = text/plain words = 7077 sentences = 353 flesch = 37 summary = Since an effective immune response against viral infections depends on cytotoxic T cells activation (25) , experimental evidence supports the observation that overexpression of inflammatory cytokines like IL-6 during the viral immune response might be associated with a decreased viral clearance by impairing the polarization and functionality of Th1 and CD8 cells (26), contributing to the worsening of the COVID-19 symptoms, and their management may appear an intriguing therapeutical approach. Overall, the administration of drugs for the control of inflammation, inhibiting the response of the immune system, may be detrimental in the initial phases of the viral infection, reducing the ability of the body to react to the presence of SARS-CoV-2, as observed in patients chronically treated for rheumatoid arthritis (27) . All rights reserved This shall prompt orthopaedics and clinicians in general to evaluate with extreme care the clinical conditions of OA patients not only under the perspective of OA symptoms management but also for undercurrent comorbidities, naturally occurring or OA-treatment-related, that, in the era of COVID-19 pandemic, may strongly affect patients outcomes more than the net combination of SARS-CoV-2 infection and OA. cache = ./cache/cord-285467-uxfk6k3c.txt txt = ./txt/cord-285467-uxfk6k3c.txt === reduce.pl bib === id = cord-284429-d7qxfo6d author = Trezza, Alfonso title = An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors date = 2020-08-17 pages = extension = .txt mime = text/plain words = 4720 sentences = 244 flesch = 47 summary = We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein – ACE2 interaction inhibitor. By combining molecular dynamics simulations (MD), Supervised MD (SuMD), Steered MD (SMD) and interaction energy calculations, we showed that Simeprevir and Lumacaftor bind RDB with high affinity and prevent ACE2 interaction. In order to identify possible PPI inhibitors the transient pocket that contained key residues involved in hACE2 recognition and binding (Fig. 1A ) was selected and used for the virtual screening of 1582 FDA-approved drugs. In order to understand if Simeprevir and Lumacaftor are able to interfere and prevent the binding between the S glycoprotein and ACE2, we ran a Supervised Molecular Dynamics (SuMD) simulations. Using SuMD it is possible to simulate the full binding process of ACE2 to RBD in presence of Simeprevir or Lumacaftor in an unbiased way (i.e. independently from starting relative positions), taking into account hydration patterns and drug binding-unbinding events. cache = ./cache/cord-284429-d7qxfo6d.txt txt = ./txt/cord-284429-d7qxfo6d.txt === reduce.pl bib === id = cord-285527-1mceq6v0 author = Kinloch, Natalie N title = Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1910 sentences = 127 flesch = 55 summary = To investigate suboptimal sample collection as a possible cause of false-negative test results, we quantified human DNA levels recovered on nasopharyngeal swabs submitted to a single laboratory for COVID-19 testing, hypothesizing that human DNA could serve as a stable molecular marker of specimen collection quality. Human DNA levels were quantified using droplet digital PCR (ddPCR), a technique where each sample is fractionated into 20,000 nanolitre-sized water-in-oil droplets prior to PCR amplification with sequence-specific primers and fluorescent probes, and where Poisson detection sensitivity compared to the original real-time RT-PCR assay, we re-tested the 40 suspected false-negative specimens by nested RT-PCR. Overall, we observed significantly lower human DNA levels in the suspected false-negative nasopharyngeal swab samples compared to a panel of consecutive samples submitted for testing during the same period, though overlap between groups was still substantial (Figure 1, p<0.001) . Our observations strongly support suboptimal biological sampling, but not PCR sensitivity for SARS-CoV-2 RNA detection, as a contributing cause of false-negative COVID-19 test results. cache = ./cache/cord-285527-1mceq6v0.txt txt = ./txt/cord-285527-1mceq6v0.txt === reduce.pl bib === === reduce.pl bib === id = cord-285449-frft2h85 author = Guillon, Patrice title = Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies date = 2008-09-25 pages = extension = .txt mime = text/plain words = 6026 sentences = 293 flesch = 54 summary = Severe acute respiratory syndrome coronavirus (SARS-CoV) is a highly pathogenic emergent virus which replicates in cells that can express ABH histo-blood group antigens. We observed that the S protein/angiotensin-converting enzyme 2-dependent adhesion of these cells to an angiotensin-converting enzyme 2 expressing cell line was specifically inhibited by either a monoclonal or human natural anti-A antibodies, indicating that these antibodies may block the interaction between the virus and its receptor, thereby providing protection. We present data indicating that the S protein/ACE2-mediated adhesion between cells expressing ACE2 and cells coexpressing the S protein and the A histo-blood group antigen can be specifically blocked by anti-A antibodies. To further evaluate the potential effect of the ABO polymorphism on the epidemiology of SARS, we present a model of its transmission dynamics that takes into account the effect of the protection by anti-histo-blood group natural antibodies. cache = ./cache/cord-285449-frft2h85.txt txt = ./txt/cord-285449-frft2h85.txt === reduce.pl bib === id = cord-285254-8a1cia8s author = Parry, Nicola M.A. title = COVID-19 and pets: When pandemic meets panic date = 2020-12-31 pages = extension = .txt mime = text/plain words = 3624 sentences = 206 flesch = 57 summary = Concern also rapidly emerged among pet owners and the general public in late February 2020, when a dog in Hong Kong tested positive for the novel coronavirus. Although the dog had no clinical signs, he was taken to a nearby animal quarantine facility where oral, nasal, and rectal swab specimens were collected from him for SARS-CoV-2 testing. In late March 2020, health officials in Belgium reported that a cat from Liège province had also tested positive for SARS-CoV-2, about 1 week after its owner was diagnosed with COVID-19. Thus, the positive RT-PCR results in these pets do not necessarily indicate the presence of viable virus that was infectious and could potentially have put other people (or animals) at risk of SARS-CoV-2 infection. cache = ./cache/cord-285254-8a1cia8s.txt txt = ./txt/cord-285254-8a1cia8s.txt === reduce.pl bib === id = cord-285315-7r44j3q9 author = Bein, Berthold title = SARS-CoV-2/COVID-19: Empfehlungen zu Diagnostik und Therapie date = 2020-04-09 pages = extension = .txt mime = text/plain words = 2244 sentences = 280 flesch = 48 summary = Die Case Fatality Rate (Zahl der Infizierten, die verstirbt; Letalität) von SARS-CoV-2 beträgt aktuellen Berechnungen nach nur 1,4 %, wobei das Risiko für eine symptomatische Infektion mit zunehmendem Alter ansteigt (ca. Die Surviving Sepsis Campaign (SSC) zitiert in ihren kürzlich publizierten Empfehlungen zur Behandlung von Patienten mit COVID-19 eine aktuelle Metaanalyse, in der keine Überlegenheit von speziellen "respiratory masks" (analog unseren FFP2/FFP3-Masken) gegenüber konventionellem Mund-Nasen-Schutz bezüglich einer Ansteckung von medizinischem Personal, das infektiöse Patienten betreut hatte, gefunden werden konnte [30] . Das bedeutet konkret, dass die Behandlung von Patienten mit COVID-19 zuallererst auf "Best Standard Care" beruht, also auf einer optimalen Anwendung evidenzbasierter Therapieempfehlungen, die für die Therapie des akuten Lungenversagens (Acute respiratory Distress Syndrome, ARDS) erarbeitet wurden [33] . cache = ./cache/cord-285315-7r44j3q9.txt txt = ./txt/cord-285315-7r44j3q9.txt === reduce.pl bib === id = cord-284627-qvz63m93 author = Banerjee, Shuvam title = Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date = 2020-04-09 pages = extension = .txt mime = text/plain words = 3691 sentences = 336 flesch = 67 summary = The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. 12, 14 In this study, we comprehensively analyzed the whole genome sequence homology from the available patient data uploaded by affected countries in NCBI Virus database, identified the mutations developed by different strains from the ancestor strain and studied the impact of those mutations at functional level. In summary, the present study reveals that the fatality rate increases with not only the number of mutations but also depending on its allelic rarity as well as functional alteration of protein. cache = ./cache/cord-284627-qvz63m93.txt txt = ./txt/cord-284627-qvz63m93.txt === reduce.pl bib === id = cord-284978-vh1x6pg9 author = Jang, Hongje title = Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date = 2013-02-18 pages = extension = .txt mime = text/plain words = 2968 sentences = 160 flesch = 53 summary = Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . cache = ./cache/cord-284978-vh1x6pg9.txt txt = ./txt/cord-284978-vh1x6pg9.txt === reduce.pl bib === id = cord-284366-snajbvr9 author = Han, Zhiyong title = Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2017 sentences = 133 flesch = 61 summary = [3] [4] [5] The diagnosis of COVID-19 considers clinical symptoms, GGO lesions in chest CT or Xray images, and positive RT-PCR test results for the presence of SARS-CoV-2 RNA in patient samples. For example, the guidelines of the National Health Commission of China state that patients must meet the following 4 benchmarks before they can be discharged: (i) be afebrile for at least 3 consecutive days, (ii) have significantly improved respiratory function, (iii) produce two negative SARS-CoV-2 RT-PCR test results at least 24 hours apart, and (iv) have significant improvement in lung GGO lesions determined by chest CT or X-ray imaging. In Table 1 , we summarize the information about patients who tested positive for SARS-CoV-2 RNA in post-discharge, follow-up examinations in China as described in the 12 published reports. Our analysis indicates that many of the discharged patients tested positive for SARS-CoV-2 RNA when feces or anal swabs were employed, even though they tested negative at the same time when nasopharyngeal or oropharyngeal or sputum samples were examined. cache = ./cache/cord-284366-snajbvr9.txt txt = ./txt/cord-284366-snajbvr9.txt === reduce.pl bib === id = cord-284191-05djnz4p author = Bert, Nina Le title = Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date = 2020-05-27 pages = extension = .txt mime = text/plain words = 1944 sentences = 103 flesch = 53 summary = To study SARS-CoV-2 specific T cells associated with viral clearance, we collected peripheral blood of 24 individuals who recovered from mild to severe COVID-19 (demographic, clinical and virological information are summarized in Extended Data Table 1 ) and studied the T cell response against selected structural (nucleocapsid protein-NP) and non-structural proteins (NSP7 and NSP13 of ORF1) of the large SARS-CoV-2 proteome ( Figure 1A) . To confirm and further delineate the multispecificity of the NP-specific T cell response detected ex vivo in COVID-19 recovered patients, we defined in nine individuals, the distinctive sections of NP targeted by T cells. This is consistent with the findings of Grifoni et al 11 : using selected peptides, they detected ORF-1 specific T preferentially in some SARS-CoV-2 unexposed donors while T cells of COVID-19 recovered donors preferentially recognized structural proteins. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals cache = ./cache/cord-284191-05djnz4p.txt txt = ./txt/cord-284191-05djnz4p.txt === reduce.pl bib === id = cord-285569-ei9w19i7 author = Shah, Aditya title = Guide to Understanding the 2019 Novel Coronavirus date = 2020-02-28 pages = extension = .txt mime = text/plain words = 2060 sentences = 141 flesch = 53 summary = A cluster of cases of pneumonia caused by a novel coronavirus, COVID-19, was first reported in Wuhan in the Hubei province in China in late December 2019. 1 Beta coronaviruses include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the coronavirus variant COVID-19 virus first described in Wuhan. SARS-CoV disproportionately impacted health care workers (HCWs) in countries with the most reported cases. Similar to SARS-CoV, presentation is typically fever with symptoms of lower respiratory tract infection and radiographic evidence of pneumonia or ARDS. 16 The Centers for Disease Control and Prevention (CDC) has issued interim guidance for HCWs. 17 Novel coronavirus should be suspected if patients meet the criteria described in Table 1 . Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-285569-ei9w19i7.txt txt = ./txt/cord-285569-ei9w19i7.txt === reduce.pl bib === id = cord-285111-qjclp51i author = Davanzo, Riccardo title = Breastfeeding and coronavirus disease‐2019: Ad interim indications of the Italian Society of Neonatology endorsed by the Union of European Neonatal & Perinatal Societies date = 2020-04-26 pages = extension = .txt mime = text/plain words = 3616 sentences = 209 flesch = 53 summary = The Italian Society on Neonatology (SIN) after reviewing the limited scientific knowledge on the compatibility of breastfeeding in the COVID‐19 mother and the available statements from Health Care Organizations has issued the following indications that have been endorsed by the Union of European Neonatal & Perinatal Societies (UENPS). • If a breastfeeding mother and her newborn infant are managed jointly, measures aimed at preventing the transmission of the viral infection should be put in place: avoid kissing the neonate, protect him from adult coughing and respiratory secretions (wear a mask during feeding and intimate contact with the baby), wash hands, in particular, before feeding, suspend visits. We recognize that this guidance might be subject to change in the future when further knowledge will be acquired about the COVID-19 pandemic, its perinatal transmission, and clinical characteristics of cases of neonatal SARS-CoV-2 infection. cache = ./cache/cord-285111-qjclp51i.txt txt = ./txt/cord-285111-qjclp51i.txt === reduce.pl bib === id = cord-285469-b61y9ezi author = Hernández-Fernández, Francisco title = Cerebrovascular disease in patients with COVID-19: neuroimaging, histological and clinical description date = 2020-07-09 pages = extension = .txt mime = text/plain words = 7007 sentences = 368 flesch = 42 summary = The aim of our study is to describe the clinical characteristics, laboratory findings, neuroimaging and available pathological anatomy data, as well as the presentation, therapeutic management and clinical outcomes of patients with acute CVD in a healthcare setting with a high incidence of transmission of this virus. We registered all hospitalized patients with COVID-19 reported during this period, and included all patients diagnosed with acute CVD, both ischaemic and haemorrhagic, treated consecutively by neurology, neurosurgery and the intensive care unit. Bivariates studies were designed to contrast the main variables among CVD patients, between ischaemic/haemorrhagic subtypes within the COVID-19 group, and to assess clinical prognosis. The other three haemorrhagic cases were detected on varying days of clinical evolution because having been intubated, sedated and treated for SARS-CoV-2 infection, the neurological manifestations were masked prior to tracheal extubation, when difficulty arousing these patients was observed. cache = ./cache/cord-285469-b61y9ezi.txt txt = ./txt/cord-285469-b61y9ezi.txt === reduce.pl bib === id = cord-284954-uuqchon4 author = Plebani, Mario title = SARS-CoV-2 antibody-based SURVEILLANCE: New light in the SHADOW date = 2020-11-05 pages = extension = .txt mime = text/plain words = 963 sentences = 48 flesch = 44 summary = The paper by Perico and coworkers, published in this issue of EBioMedicine, is a comprehensive analysis of the prevalence of SARS-CoV-2 infection in the Bergamo province, an area of Italy that experienced a massive COVID-19 outbreak, with its epicenter in the whole Lombardy region. Furthermore, in a study performed in Iceland on the measurement of SARS-CoV-2 antibodies, it is estimated that 44% of individuals infected with the virus were not diagnosed by quantitative polymerase-chain-reaction (qPCR) thus confirming the risk of under-diagnosis on using molecular testing alone [2] . The paper by Perico and colleagues is welcome for several reasons: first, it confirms the usefulness of SARS-CoV-2 antibody assay for a better knowledge of the spread of the infection in a specific population or subpopulation, and for avoiding the risk of under-diagnosis when using rRT-PCR testing alone. cache = ./cache/cord-284954-uuqchon4.txt txt = ./txt/cord-284954-uuqchon4.txt === reduce.pl bib === id = cord-285603-f4572w5m author = Ortega, Joseph T. title = Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date = 2020-06-24 pages = extension = .txt mime = text/plain words = 5994 sentences = 348 flesch = 47 summary = In order to gain a deeper understanding if the pharmacokinetic parameters of the SARS-CoV2 protease inhibitors could be related to positive outcomes in the therapy, we analyzed the ADME parameters of famotidine and compared with several known antiviral drugs such as ribavirin, lopinavir, and nafamostat, which were evaluated against SARS-CoV2. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Altogether, in this study, we showed that famotidine could be used as an antiviral agent against SARS-CoV2, targeting proteases involved in the virus replication, mostly the main protease, as well as the viral PLpro and human host Tmprss2. cache = ./cache/cord-285603-f4572w5m.txt txt = ./txt/cord-285603-f4572w5m.txt === reduce.pl bib === id = cord-285787-xvi5miqw author = Bell, Jennifer AH title = SARS and hospital priority setting: a qualitative case study and evaluation date = 2004-12-19 pages = extension = .txt mime = text/plain words = 3099 sentences = 177 flesch = 50 summary = The purpose of this study is to describe and evaluate priority setting in a hospital in response to SARS using the ethical framework 'accountability for reasonableness'. CONCLUSIONS: 'Accountability for reasonableness' is a framework that can be used to guide fair priority setting in health care organizations, such as hospitals. 'Accountability for reasonableness' is an explicit ethical framework for legitimate and fair priority setting in health care [2] . The purpose of this study was to describe priority setting in a hospital in response to SARS and evaluate it using 'accountability for reasonableness'. In this section we describe one hospital's priority setting in response to SARS by focusing on the types of decisions, the decision making process, and the supportive reasoning. 'Accountability for reasonableness' is a framework that can be used to guide legitimate and fair priority setting in health care organizations, such as hospitals. Priority setting in a hospital critical care unit: qualitative case study cache = ./cache/cord-285787-xvi5miqw.txt txt = ./txt/cord-285787-xvi5miqw.txt === reduce.pl bib === id = cord-285203-ilxd0ih9 author = Paradiso, Angelo Virgilio title = Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date = 2020-04-06 pages = extension = .txt mime = text/plain words = 3073 sentences = 174 flesch = 49 summary = Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint All the 191 subjects enrolled in the study had a SARS-CoV-2 RT-PCR test and RapidIgG/IgM test performed. The design of our study allowed us to specifically analyze two aspects of the open issue: the concordance of the rapid serological test with standard molecular testing; the trend of immunoglobulinsIgG/IgMexpression with respect to the onset of clinical symptoms. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint symptom appearance is accompanied by an improvement in serological test sensitivity compared to standard molecular testing Our study has some important limitations. Our study analyzed theclinical performance of the rapid serological test, Viva-Diag TM and confirmedthe test's limited applicability for the diagnosis of SARS-CoV-2 infection when compared to standard molecular testing. cache = ./cache/cord-285203-ilxd0ih9.txt txt = ./txt/cord-285203-ilxd0ih9.txt === reduce.pl bib === id = cord-285162-srkd3wh0 author = Jung, F. title = How we should respond to the Coronavirus SARS-CoV-2 outbreak: A German perspective date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4634 sentences = 256 flesch = 61 summary = Figure 1 shows that until March 20 (day 80), the daily cases of new confirmed infections increased with doubling times between 1-5 days, showing a strong exponential rise of positive tests for SARS-CoV-2 infections in Germany. Common elements of these Asian states were the immediate action of governments to implement certain social distancing strategies and the wearing of face masks in public to reduce the number of new cases, which has proven to be effective to prevent transmission from infected individuals [15] . This led to a longer phase of exponential growth of SARS-CoV-2 infections and deaths in Germany, France and Italy and caused cumulative case numbers to grow significantly higher in comparison to the East-Asian countries (Fig. 2) . Until the end of March (day 91), Japan, however, has managed to stabilize these at under 5,000 confirmed cases, while Germany had almost 71,000 and France almost 52,000 confirmed SARS-Cov-2 infections. cache = ./cache/cord-285162-srkd3wh0.txt txt = ./txt/cord-285162-srkd3wh0.txt === reduce.pl bib === id = cord-285755-zblitbo0 author = Zhang, F. title = Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study date = 2020-03-24 pages = extension = .txt mime = text/plain words = 3069 sentences = 164 flesch = 42 summary = [Results] A total of 110 patients with confirmed (n=80) or suspected (n=30) COVID-19 were screened and 48 patients (female 31.3%, mean age 70.58{+/-}13.38 year old) among them with high-sensitivity cardiac troponin I (hs-cTnI) test within 48 hours after admission were included, of whom 17 (17/48, 35.4%) died in hospital while 31 (31/48, 64.6%) were discharged or transferred to other hospital. [Conclusions] Cardiac injury defined by hs-cTnI elevation and elevated d-dimer on admission were risk factors for in-hospital death, while higher SpO2 could be seen as a protective factor, which could help clinicians to identify patients with adverse outcome at the early stage of COVID-19. Short-term prognosis of COVID-19 patients are discrepancy and in-hospital mortality risk are high in severe cases[1] [2] Although previous study had indicated that several risk factors were independently associated with short-term mortality, such as elevated d-dimer, older age and higher Sequential Organ Failure Assessment (SOFA) score [2] , few studies focused on cardiac injury with COVID-19 patients. cache = ./cache/cord-285755-zblitbo0.txt txt = ./txt/cord-285755-zblitbo0.txt === reduce.pl bib === === reduce.pl bib === id = cord-285440-srtkqr13 author = Zhang, Jianguo title = Web-based electronic patient records for collaborative medical applications date = 2004-12-20 pages = extension = .txt mime = text/plain words = 3525 sentences = 169 flesch = 46 summary = We developed a web-based system to interactively display electronic patient records (EPR), such as DICOM images, graphics, and structure reports and therapy records, for intranet and internet collaborative medical applications. Second, we present a new design of web-based interactive system architecture and its major components, which support EPR display and manipulation and operate in a central mode for collaborative applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. cache = ./cache/cord-285440-srtkqr13.txt txt = ./txt/cord-285440-srtkqr13.txt === reduce.pl bib === id = cord-285426-iyl12ber author = Ghavami, Shaghayegh Baradaran title = IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date = 2020-09-08 pages = extension = .txt mime = text/plain words = 1967 sentences = 111 flesch = 47 summary = Interestingly, in the recent pandemic of coronavirus disease (COVID19) , and the SARS-CoV epidemic in 2003, while the fecal samples of these patients were positive for the virus, they did not present any severe respiratory distress syndrome (4). Remarkably, the angiotensin-converting enzyme-2 (ACE2) is the receptor for SARS-CoV-2 and it is expressed in different organs including the lungs, testis and ileum. showed that when rheumatoid arthritis patients were treated with anti-TNF-α biologicals (infliximab, adalimumab, and certolizumab pegol), the expression of IFN-α-regulated genes was increased in the peripheral blood mononuclear cell (PBMC) compared to the control group. Besides, in IBD patients, particularly those who are under anti-TNF-α treatment, the host innate immune system interferes more efficiently with viral replication cycle and the clinical presentations are more moderate (9, 12) . Are patients with inflammatory bowel disease at increased risk for Covid-19 infection? cache = ./cache/cord-285426-iyl12ber.txt txt = ./txt/cord-285426-iyl12ber.txt === reduce.pl bib === id = cord-285739-0enn5bzn author = Gutiérrez Rodríguez, José title = Variables asociadas a mortalidad en una población de pacientes mayores de 80 años y con algún grado de dependencia funcional hospitalizados por COVID-19 en un Servicio de Geriatría date = 2020-07-16 pages = extension = .txt mime = text/plain words = 3924 sentences = 356 flesch = 52 summary = Ese mismo día, tras un gran esfuerzo organizativo se abren las plantas para pacientes con COVID-19 en nuestro centro hospitalario: un total de 38 camas destinadas a pacientes mayores de 80 años con infección por coronavirus, que precisan hospitalización por presentar insuficiencia respiratoria aguda o descompensación de patología de base y que, en caso de empeoramiento clínico, no serían subsidiarios de beneficio de ingreso en UCI por sufrir algún grado de dependencia funcional y/o deterioro cognitivo 22 . En este ámbito asistencial, los objetivos de este trabajo han sido: a) estudiar las características epidemiológicas, clínica, analíticas y radiológicas de pacientes mayores de 80 años con algún grado de dependencia funcional y/o deterioro cognitivo ingresados con COVID-19 confirmado por diagnóstico de laboratorio, b) determinar la tasa de mortalidad, c) analizar las variables clínicas, terapéuticas, funcionales y mentales que se asocian a mayor riesgo de mortalidad. cache = ./cache/cord-285739-0enn5bzn.txt txt = ./txt/cord-285739-0enn5bzn.txt === reduce.pl bib === id = cord-285580-gq7400tq author = Pieretti, Joana C. title = Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date = 2020-10-18 pages = extension = .txt mime = text/plain words = 4877 sentences = 281 flesch = 49 summary = In this mini-review, we discuss recent progress concerning the antivirus activity of NO in clinical, pre-clinical and research settings, and its beneficial effects in the treatment of clinical complications in patients infected with coronaviruses and other respiratory viral diseases, including COVID-19. Although positive biological effects have been reported for the administration of NO donors, further studies are required to better evaluate the levels of inflammatory mediators and the activity of important heme-containing enzymes, such as indoleamine 2,3-dioxygenase (IDO), directly involved in the inflammatory responses in respiratory viral infections (Anderson and Russel, 2020) . In other words, NO demonstrates potential for the treatment of patients infected with COVID-19 both in severe and nonsevere conditions, improving oxygenation and antiviral mechanisms, and preventing aggravation of the disease (Ferrari et al., 2020; Parikh et al., 2020) . Protocol of a randomized controlled trial testing inhaled nitric oxide in mechanically ventilated patients with severe acute respiratory syndrome in COVID-19 (SARS-CoV-2) cache = ./cache/cord-285580-gq7400tq.txt txt = ./txt/cord-285580-gq7400tq.txt === reduce.pl bib === id = cord-285159-gytebbua author = Eydoux, Cecilia title = A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3603 sentences = 215 flesch = 59 summary = Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). cache = ./cache/cord-285159-gytebbua.txt txt = ./txt/cord-285159-gytebbua.txt === reduce.pl bib === id = cord-285636-cs26uuwx author = Singh, N. K. title = Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer date = 2020-09-25 pages = extension = .txt mime = text/plain words = 7858 sentences = 486 flesch = 53 summary = In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads as benchmarked by RT-qPCR within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). The major hurdle in repurposing a glucometer for direct detection of SARS-CoV-2 is that the target biomarkers (e.g., protein N and S) are present at low concentrations in biological samples The average CoVID-19 viral load in nasal/throat, sputum, and saliva samples is 3×10 6 , 7.50×10 5 , and 3.5×10 7 copies/ml 24, 25 , respectively, necessitating signal amplification to generate product (i.e. glucose) in quantities similar to physiological levels in human blood (i.e. 10-600 mg/dL or 0.6-33 mM) 21, 26 . To transduce antigen binding SARS-CoV-2 N or S protein specific biotinylated aptamer is conjugated to streptavidin coated magnetic bead (MB) and pre-hybridized with a complementary antisense oligonucleotide strand that is covalently attached to an invertase enzyme. cache = ./cache/cord-285636-cs26uuwx.txt txt = ./txt/cord-285636-cs26uuwx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-285486-99trkti1 author = Abd-Elsalam, Sherief title = Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2928 sentences = 166 flesch = 53 summary = Univariate logistic regression analysis showed that HCQ treatment was not significantly associated with decreased mortality in COVID-19 patients. So, adding HCQ to standard care did not add significant benefit, did not decrease the need for ventilation, and did not reduce mortality rates in COVID-19 patients. 1. Hydroxychloroquine group: This group included 97 patients who received HCQ 400 mg twice daily (in day 1) followed by 200 mg tablets twice daily added to the standard of care treatment adopted by the Egyptian MOH for 15 days. 18 Although cardiac toxicity is a known adverse event requiring monitoring during treatment, HCQ showed promise in treating SARS-CoV-2-infected patients with multiple comorbidities including coronary artery disease. 12 studied the change in symptom severity over 14 days in nonhospitalized patients between HCQ and control groups and did not find any significant difference (P = 0.12). cache = ./cache/cord-285486-99trkti1.txt txt = ./txt/cord-285486-99trkti1.txt === reduce.pl bib === id = cord-285848-37dmv4ep author = Fu, Xiao-Wei title = Review of possible psychological impacts of COVID-19 on frontline medical staff and reduction strategies date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4405 sentences = 195 flesch = 42 summary = A large number of studies have reported that infectious epidemic diseases, such as severe acute respiratory syndrome (SARS), induce considerable psychological pressure that continues to impact frontline medical personnel a full year after such incidences [1] . In this paper, we present the findings of a review of studies that have investigated the psychological pressure and causes of stress associated with previous outbreaks of infectious diseases, such as SARS and influenza A (H1N1). The association between nurses' perceived Stress from SARS and their corresponding 13 Chan et al [15] Hong Kong Questionnaires A total of 8 of the 42 Hong Kong public hospitals Perceived health status during the SARS epidemic 14 Kim et al [18] Seoul and in Kyung-gi province psychological interventions targeting frontline medical staff prior to the outbreak of epidemic infectious diseases in the future to reduce or avoid the pressures and impacts of these epidemics on them. cache = ./cache/cord-285848-37dmv4ep.txt txt = ./txt/cord-285848-37dmv4ep.txt === reduce.pl bib === id = cord-285711-2utcn0hw author = Elliott, Robert title = COVID-19 Related Mortality During Management of a Hepatic Abscess date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2071 sentences = 102 flesch = 48 summary = Declared a pandemic by the World Health Organization on March 11th, 2020, COVID-19 has challenged healthcare systems to limit the spread of community and hospital-acquired of disease. In the setting of an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), healthcare systems have been challenged to limit in-hospital transmission of the virus; a task noted to be incredibly difficult given the suggestion of what appears to be fairly high viral transmissibility (3, 4) . We presented a case of a patient death from SARS-CoV-2 infection prior to the implementation of universal masking. In addition, now having lived this experience with universal masking, we question: (1) if there might be a survival advantage to short-interval masking during the height of seasonal influenza activity and (2) if there may be a benefit to expanded use of N95 respirators in the IR suite during AGP-type interventions performed on individuals presenting with respiratory infections not limited to Covid-19. cache = ./cache/cord-285711-2utcn0hw.txt txt = ./txt/cord-285711-2utcn0hw.txt === reduce.pl bib === id = cord-285647-9tegcrc3 author = Estrada, Ernesto title = Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 9179 sentences = 533 flesch = 59 summary = By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19. 25, 26 Therefore, we assume here that perturbations produced by SARS-CoV-2 proteins on the human PPI network are propagated by means of diffusive processes. Here, we propose the use of a time-fractional diffusion model on the PPI network of proteins targeted by SARS-CoV-2. We now consider how a perturbation produced by SARS-CoV-2 on a protein mainly expressed in the lungs can be propagated to proteins mainly located in other tissues (see Table S4 in the supplementary material) by a subdiffusive process. Here, we have studied the particular case in which the time-fractional diffusion equation produces a subdiffusive regime, with the use of α = 3/4 in the network of human proteins targeted by SARS-CoV-2. cache = ./cache/cord-285647-9tegcrc3.txt txt = ./txt/cord-285647-9tegcrc3.txt === reduce.pl bib === id = cord-285822-b5itedu3 author = Carlos Marín-Gabriel, José title = Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 date = 2020-05-27 pages = extension = .txt mime = text/plain words = 7445 sentences = 774 flesch = 52 summary = Promover la participación de los residentes de Aparato Digestivo en los procedimientos endoscópicos en pacientes con bajo riesgo de infección por SARS-CoV-2, siempre y cuando se disponga de los recursos necesarios que garanticen la seguridad del procedimiento. En la situación actual de alto riesgo de transmisión de la infección por SARS-CoV-2 en el entorno hospitalario, es crítico revisar los protocolos de la UE en relación con la circulación de los pacientes y acompañantes, las estrategias de cribado de COVID-19, la disponibilidad de EPI y las medidas de desinfección de las salas y equipos de endoscopia. Las sociedades firmantes de este documento se posicionan a favor de que los residentes en Aparato Digestivo continúen realizando procedimientos bajo supervisión directa en pacientes de bajo riesgo de infección por SARS-CoV-2. Para los pacientes con alta sospecha o infección confirmada por SARS-CoV2, es recomendable una desinfección en profundidad de la sala después de cada endoscopia 6 , 27 . cache = ./cache/cord-285822-b5itedu3.txt txt = ./txt/cord-285822-b5itedu3.txt === reduce.pl bib === id = cord-285758-c18arb6s author = Jiang, Shibo title = SARS Vaccine Development date = 2005-07-17 pages = extension = .txt mime = text/plain words = 2305 sentences = 106 flesch = 39 summary = The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. (30) reported that mucosal immunization of African green monkeys with an attenuated parainfluenza virus expressing S protein resulted in production of neutralizing antibodies and protected animals from infection by challenge with SARS-CoV. These findings suggest that RBD contains the major neutralizing epitopes in the S protein and is an ideal SARS vaccine candidate because RBD contains the receptor-binding site, which is critical for virus attachment to the target cell for infection (15, (17) (18) (19) . Epitope mapping and biological function analysis of antibodies produced by immunization of mice with an inactivated Chinese isolate of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine cache = ./cache/cord-285758-c18arb6s.txt txt = ./txt/cord-285758-c18arb6s.txt === reduce.pl bib === id = cord-286001-pu1fetq7 author = Zang, Ruochen title = TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date = 2020-04-23 pages = extension = .txt mime = text/plain words = 2049 sentences = 145 flesch = 50 summary = In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. Importantly, we found that 160 expression of TMPRSS4 but not ST14 also resulted in a significant increase in the levels of viral RNA and infectious virus titers in the presence of ACE2 ( Fig. 3B and S3C) . Collectively, we have shown that TMPRSS2 and TMPRSS4 activate SARS-CoV-2 S and 187 enhance membrane fusion and viral endocytosis into host cells. Importantly, abrogating TMPRSS4 expression led 209 to a 4-fold reduction in SARS-CoV-2 chimera virus replication in human enteroid, even 210 more significant than TMPRSS2 knockout (Fig. 4B) , highlighting its importance in 211 mediating virus replication in primary cells. It is possible that in the 293 small intestine, whereas SARS-CoV-2 is relatively stable, additional proteases such as 294 trypsin likely enhance viral pathogenesis by triggering more robust IEC fusion (Fig. S2A) . cache = ./cache/cord-286001-pu1fetq7.txt txt = ./txt/cord-286001-pu1fetq7.txt === reduce.pl bib === id = cord-286038-a62k3lma author = Klimke, A. title = Hydroxychloroquine as an aerosol might markedly reduce and even prevent severe clinical symptoms after SARS-CoV-2 infection date = 2020-04-27 pages = extension = .txt mime = text/plain words = 2336 sentences = 104 flesch = 45 summary = The antimalarial drugs chloroquine phosphate (CQ) and hydroxychloroquine (HCQ) impair in vitro the terminal glycosylation of ACE2 without significant change of cell-surface ACE2 and, therefore, might be potent inhibitors of SARS-CoV-2 infections. We hypothesize that HCQ especially as an aerosol application will prevent or at least markedly reduce the replication rate of the SARS-CoV-2 virus in the early phase of the infection and subsequently substantially lower the number of severe pneumonias and casualties. This hypothesis is new since the major assumption in ongoing clinical studies and actual recommendations is that HCQ and CQ should be used in oral application form in patients with severe covid-19 pneumonia and only when other treatment strategies have failed. If our hypothesis is true, HCQ as an aerosol might not only reduce the side effect potential of the oral application form but can also be clinically used as an efficient antiviral agent in the early phase of COVID-19 and eventually lower the rate of severely ill patients and fatalities. cache = ./cache/cord-286038-a62k3lma.txt txt = ./txt/cord-286038-a62k3lma.txt === reduce.pl bib === id = cord-285806-363ivs67 author = Magro, Giuseppe title = SARS-CoV-2 and COVID-19: is interleukin-6 (IL-6) the 'culprit lesion' of ARDS onset? What is there besides Tocilizumab? SGP130Fc date = 2020-05-14 pages = extension = .txt mime = text/plain words = 5157 sentences = 257 flesch = 41 summary = In a humanized transgenic mouse MERS-CoV infection model, Remdesivir (a drug already being used against SARS-CoV-2 in patients with severe and moderate disease, GS-US-540-5773/4 Studies) showed more activity and efficacy in prophylactic and therapeutic use then the combination of Lopinavir/Ritonavir and Interferon beta 9 , this points towards the necessity to explore other options regarding immune system modulation and how control of viraemia is also essential. More evidence suggests that critically ill patients with severe respiratory failure and SARS-CoV-2 have either immune dysregulation or macrophage-activation syndrome, both of which are characterized by pro-inflammatory cytokines. This is another evidence of the pro-inflammatory role of the trans-signaling pathway and it could also be the explanation as to why some patients show a higher inflammatory response mediated by IL-6, similarly to what is happening with SARS-CoV-2 infection. cache = ./cache/cord-285806-363ivs67.txt txt = ./txt/cord-285806-363ivs67.txt === reduce.pl bib === id = cord-285490-tpsf05ca author = Solís, José Gabriel title = Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm date = 2020-07-29 pages = extension = .txt mime = text/plain words = 1793 sentences = 130 flesch = 39 summary = title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm He developed acute kidney injury requiring renal replacement therapy without reversibility, despite optimal treatment. 2 We report the case of a patient with confirmed SARS-CoV-2 infection who presented with rhabdomyolysis as a cardinal manifestation, discuss the possible mechanisms, and propose a diagnostic-therapeutic algorithm. Laboratory tests revealed grade 3 acute kidney injury (AKI) with a creatinine level of 11 mg/dL (basal value 0.7 mg/dL); increased blood levels of creatine kinase (CK) (> 400,000 U/L), lactate dehydrogenase (LDH), aspartate aminotransferase, alanine aminotransferase; and electrolyte disturbances with hyperkalemia, hyperphosphatemia, hypocalcemia, and severe metabolic acidosis. The underlying cause of muscle injury must be identified and treated, which is difficult in patients with COVID-19 because there is no specific therapy. Kidney disease is associated with in-hospital death of patients with COVID-19 Acute kidney injury due to rhabdomyolysis and renal replacement therapy: a critical review cache = ./cache/cord-285490-tpsf05ca.txt txt = ./txt/cord-285490-tpsf05ca.txt === reduce.pl bib === id = cord-285944-8lapwnuw author = Suwanwongse, Kulachanya title = Hyperpyrexia in COVID‐19 patients date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2171 sentences = 124 flesch = 39 summary = We propose three possible underlying mechanisms based on our current knowledge: 1) direct brain injury from SARS-CoV-2, 2) persistent immune dysfunction and dysregulation of cytokines, and 3) vascular thrombosis. According to our case series, the lack of normal daily temperature variation in patient 4 and 5, and the presence of hypothermia in patient 1 and 5 support the hypothesis that direct brain injury from SARS-CoV-2 leads to hyperpyrexia. SARS-CoV-2 may cause injury to the brain-stem respiratory center explaining why COVID-19 patients often report lesser perception of dyspnea than the actual degree of hypoxia and the extent of lung pathology [15] . Our case series also highlights the need to determine underlying mechanisms of hyperpyrexia in COVID-19 patients as each cause requires different management. The underlying mechanisms of hyperpyrexia in COVID-19 are unknown but may be a result of SARS-CoV-2 related brain injury, exuberant immune response, and thrombus formation. cache = ./cache/cord-285944-8lapwnuw.txt txt = ./txt/cord-285944-8lapwnuw.txt === reduce.pl bib === id = cord-285896-lb8toc1m author = Beurton, Alexandra title = Limiting positive end-expiratory pressure to protect renal function in SARS-CoV-2 critically ill patients date = 2020-07-10 pages = extension = .txt mime = text/plain words = 1013 sentences = 66 flesch = 55 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related pneumonia is a risk factor for acute respiratory distress syndrome (ARDS) and acute kidney injury (AKI) [1, 2] . Herein, we report our experience in SARS-CoV-2 critically ill patients before and after having modified our practices in the view of the high occurrence of AKI that needed renal replacement therapy (RRT) in the first cases we managed. During "period 1" (between 04 and 15 March 2020), all mechanically ventilated patients with confirmed SARS-CoV-2 admitted to our intensive care unit received volume-controlled ventilation with a tidal volume of 6 ml/kg of ideal body weight and PEEP stepwise increased to reach a plateau pressure below 28 cmH 2 O. Our findings suggest that changing our practices was associated with a decreased need for RRT and a lower proportion of patients with AKI KDIGO 3. cache = ./cache/cord-285896-lb8toc1m.txt txt = ./txt/cord-285896-lb8toc1m.txt === reduce.pl bib === id = cord-285852-ocu69od2 author = Luqman, Zubair title = Disinfection of corona virus in histopathology laboratories date = 2020-06-25 pages = extension = .txt mime = text/plain words = 599 sentences = 40 flesch = 46 summary = Severe acute respiratory syndrome (SARS CoV‐2/COVID‐19) is a highly contagious and deadly disease caused by a virus belonging to the coronaviridae family. Researchers working in histopathology laboratories, dealing with morbid samples, are particularly vulnerable to infection unless they have very strong immunity. The current review highlights the biological and physical agents that can be used to inactivate the virus and disinfect the surrounding environment in the laboratory. Severe acute respiratory syndrome, also termed SARS-CoV, was first (Lim et al., 2004; Rachael, 2004; World Health Organization [WHO], 2003 , 2006 . Severe acute respiratory syndrome (SARS CoV-2/COVID-19) is a highly communicable and lethal virus (WHO, 2020). Scientists working in histopathology laboratories, handling morbid samples, can be infected with this dangerous virus and are more likely to be susceptible to it regardless of well-functioning immune systems. Severe Acute Respiratory Syndrome (SARS) Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Laboratory-acquired severe acute respiratory syndrome cache = ./cache/cord-285852-ocu69od2.txt txt = ./txt/cord-285852-ocu69od2.txt === reduce.pl bib === id = cord-285748-us5do6c2 author = Cheng, Yongqian title = SARS-CoV-2-Related Kidney Injury: Current Concern and Challenges date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5322 sentences = 295 flesch = 48 summary = Currently, the diagnosis and treatment of SARS-CoV-2 infection in patients with chronic kidney disease (CKD) are still unclear. Here, we review the recent findings of characteristics of COVID-19 in CKD patients and highlight the possible mechanisms of kidney injury caused by SARS-CoV-2 infection. Controversial results also exist like another study [18] indicating that SARS-CoV-2 infection was not found significantly correlated with incremental acute renal injury or aggravate chronic kidney failure in the COVID-19 patients. Therefore, SARS-CoV-2 infection in kidney transplant patients from this study showed that such cases may be severe enough requiring intensive care admission and these patients are in high risk of disease progression and death. Another study based on single-cell analysis by Lin and colleagues [28] also found that ACE2 was enriched in proximal tubular cells which may indicate that the kidney is more susceptible to SARS-CoV-2 infection. cache = ./cache/cord-285748-us5do6c2.txt txt = ./txt/cord-285748-us5do6c2.txt === reduce.pl bib === id = cord-285960-1zuhilmu author = Conly, John title = Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4921 sentences = 209 flesch = 41 summary = The report by the World Health Organization (WHO) Joint Mission on Coronavirus Disease 2019 (COVID-19) in China supports person-to-person droplet and fomite transmission during close unprotected contact with the vast majority of the investigated infection clusters occurring within families, with a household secondary attack rate varying between 3 and 10%, a finding that is not consistent with airborne transmission. Based on the scientific evidence accumulated to date, our view is that SARS-CoV-2 is not spread by the airborne route to any significant extent and the use of particulate respirators offers no advantage over medical masks as a component of personal protective equipment for the routine care of patients with COVID-19 in the health care setting. The findings from multiple systematic reviews and meta analyses over the last decade have not demonstrated any significant difference in the clinical effectiveness of particulate respirators compared to the use of medical masks when used by HCWs in multiple health care settings for the prevention of respiratory virus infections, including influenza [57] [58] [59] . cache = ./cache/cord-285960-1zuhilmu.txt txt = ./txt/cord-285960-1zuhilmu.txt === reduce.pl bib === id = cord-285965-mar8zt2t author = Su, Liang title = The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19 date = 2020-03-25 pages = extension = .txt mime = text/plain words = 2751 sentences = 160 flesch = 57 summary = This study aims to analyze the different clinical characteristics between children and their families infected with severe acute respiratory syndrome coronavirus 2. Here, we report the clinical manifestations, laboratory test results, imaging characteristics, and treatment regimen of nine SARS-CoV-2 infected children and their families in Jinan, Shandong province to increase awareness of this disease, especially in children. A retrospective review was conducted of the clinical, lab tests, and radiologic findings for nine children and their families admitted to the Jinan Infectious Diseases Hospital identified to be nucleic acid-positive for SARS-CoV-2 from 24 January 2020 to 24 February 2020. All the patients were recorded with basic information and epidemiological histories [4] including (1) History of travel or residence in Wuhan and surrounding areas or other reported cases within 14 days of onset; (2) History of contact with new coronavirus infection (nucleic acid-positive) 14 days before onset; (3) history of contact with patients with fever or respiratory symptoms from Wuhan and surrounding areas, or from communities with case reports within 14 days before onset; (4) Cluster onset, along with disease condition changes. cache = ./cache/cord-285965-mar8zt2t.txt txt = ./txt/cord-285965-mar8zt2t.txt === reduce.pl bib === id = cord-286029-rafcdzhm author = Bogaards, Johannes Antonie title = The potential of targeted antibody prophylaxis in SARS outbreak control: A mathematic analysis() date = 2006-05-05 pages = extension = .txt mime = text/plain words = 5574 sentences = 291 flesch = 46 summary = METHOD: We developed a mathematical model to investigate the effects of hospital admission and targeted antibody prophylaxis on the reproduction number R, defined as the number of secondary cases generated by an index case, during different SARS outbreak scenarios. RESULTS: Assuming a basic reproduction number R(0)=3, admission of patients to hospital within 4.3 days of symptom onset is necessary to achieve outbreak control without the need to further reduce community-based transmission. Based on our model, we derived an expression for the effective reproduction number of SARS to study conditions for containment and we explored how the size and duration of an outbreak depend on the efficacy of control. Given functions for the distribution of onset-to-admission time and transmission rate before the implementation of public health measures, we define the basic reproduction number R 0 as the average number of secondary cases before intervention is in place. cache = ./cache/cord-286029-rafcdzhm.txt txt = ./txt/cord-286029-rafcdzhm.txt === reduce.pl bib === id = cord-285865-1gsy43a0 author = Wu, Guang title = Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species date = 2004-12-09 pages = extension = .txt mime = text/plain words = 4309 sentences = 214 flesch = 53 summary = Randomly predictable present type of amino-acid pair with unpredictable frequency There are 84 alanines (A) in the spike glycoprotein from human SARS-CoV. In view of the unpredictable portion whose actual value is smaller than its predicted value (left panel), the spike glycoproteins have the largest percentages in both unpredictable type and frequency among different coronavirus proteins. With respect to the second line of evidence, we find that the spike glycoprotein has a larger percentage of unpredictable types and frequencies whose actual values are smaller than the predicted values in Fig. 2 . Comparison with the first nine proteins in Table 2 (columns V, VI, VII and VIII in Table 2 , similar to Fig. 3) shows that the difference between actual and predicted values is statistically larger in spike glycoproteins regarding unpredictable types and is statistically smaller regarding unpredictable frequency. cache = ./cache/cord-285865-1gsy43a0.txt txt = ./txt/cord-285865-1gsy43a0.txt === reduce.pl bib === id = cord-286015-oonfpa0c author = Verbeure, Birgit title = Patent pools and diagnostic testing date = 2006-01-27 pages = extension = .txt mime = text/plain words = 4328 sentences = 187 flesch = 42 summary = Recent studies have reported on the licensing practices of the owners of patents for genetic inventions [3] [4] [5] [6] , and concerns have been raised that patent thickets, resulting in royalty stacking (see Glossary), block access to patented technology through the accumulated license fees that a downstream inventor has to pay to upstream patent holders. In the late 1990s, several patent pools were formed in the electronics and telecommunications industries, starting with the moving picture experts group (MPEG)-2 pool in 1997 for inventions relating to the MPEG-2 standard (see Klein [15] and the Guidelines on the Application of Article 81 of the EC Treaty to Technology Transfer Agreements [16] . The Organization for Economic Co-operation and Development (OECD; www.oecd.org) considers the concept of a patent pool to be an interesting one for biotechnology but has some doubts as to whether the technologies and markets for genetic inventions are amenable to patent pools [20] . cache = ./cache/cord-286015-oonfpa0c.txt txt = ./txt/cord-286015-oonfpa0c.txt === reduce.pl bib === id = cord-286130-4f7otdx1 author = Xavier, Joilson title = The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4670 sentences = 233 flesch = 50 summary = title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing To better understand the recent epidemic in the second most populous state in southeast Brazil Minas Gerais (MG) we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Initial phylogenetic analysis using the first two SARS-CoV-2 complete genomes isolated in São Paulo from travellers returning from Italy revealed two independent introductions into the country relative to the data set available at that time [13] . Herein, we present a summary of epidemiological data and the generation and analysis of 40 new SARS-CoV-2 genome sequences isolated from clinical samples of confirmed cases from MG. cache = ./cache/cord-286130-4f7otdx1.txt txt = ./txt/cord-286130-4f7otdx1.txt === reduce.pl bib === id = cord-285700-9q6vwoct author = Grzelak, Ludivine title = SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. date = 2020-04-24 pages = extension = .txt mime = text/plain words = 6520 sentences = 392 flesch = 53 summary = title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. Here, we performed a pilot study to assess the levels of anti-SARS-CoV-2 antibodies in samples taken from 491 preepidemic individuals, 51 patients from Hopital Bichat (Paris), 209 pauci-symptomatic individuals in the French Oise region and 200 contemporary Oise blood donors. To avoid redundancy, we focused LIPS analysis to N, selecting it for its sensitivity regarding an intracellular viral protein not targeted by NAbs and S1 as it is described as a target of most NAbs. To establish the specificity of the assay, we first analyzed the same series of 40 sera we used for S-Flow and found all of the sera to be negative (Fig. S3 ). Sera from pre-epidemic individuals sampled between 2017 and 2019 (first row), hospitalized cases with confirmed COVID-19 (second row), paucisymptomatics individual from the Crépy-en-Vallois epidemic cluster (third row) and healthy blood donors (last row) were surveyed for anti-SARS-Cov-2 antibodies using four serological assays. cache = ./cache/cord-285700-9q6vwoct.txt txt = ./txt/cord-285700-9q6vwoct.txt === reduce.pl bib === id = cord-285979-ha5nszxi author = Rojas, Manuel title = Convalescent plasma in Covid-19: Possible mechanisms of action date = 2020-05-05 pages = extension = .txt mime = text/plain words = 5818 sentences = 334 flesch = 44 summary = CP early administered after symptoms onset showed a reduction in mortality compared with placebo or no therapy in severe acute respiratory infections of viral etiology like influenza and SARS-CoV, however, a similar response in Ebola disease was not observed [20, 25] . This was demonstrated in B cells, where the upregulation of FCRIIB was associated with treatment efficacy for acute rejection after kidney transplantation [81] , and was J o u r n a l P r e -p r o o f a key determinant for IVIg response in patients with Kawasaki disease [82] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection cache = ./cache/cord-285979-ha5nszxi.txt txt = ./txt/cord-285979-ha5nszxi.txt === reduce.pl bib === id = cord-286014-cc99e24x author = Jang, T.-N title = Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases date = 2003-11-05 pages = extension = .txt mime = text/plain words = 3025 sentences = 201 flesch = 56 summary = To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). The first probable SARS patient in Taiwan returned from China via Hong Kong early in the global outbreak in February 2003. 7 We analyse the clinical, laboratory, and radiological features of patients with probable SARS who were seen at the Shin Kong Wu Ho-Su Memorial Hospital (SKMH) in Taipei, Taiwan. 16 In our study, SARS-associated coronavirus RNA was detected in oropharyngeal swabs by RT-PCR in 16 (55.1%) of 29 patients at initial presentation. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome in Singapore: clinical features of index patient and initial contacts Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China cache = ./cache/cord-286014-cc99e24x.txt txt = ./txt/cord-286014-cc99e24x.txt === reduce.pl bib === id = cord-286168-019rcbpg author = Vindegaard, Nina title = COVID-19 pandemic and mental health consequences: systematic review of the current evidence date = 2020-05-30 pages = extension = .txt mime = text/plain words = 4106 sentences = 217 flesch = 45 summary = Out of these, only two studies evaluated patients with confirmed COVID-19 infection, whereas 41 evaluated the indirect effect of the pandemic (2 on patients with preexisting psychiatric disorders, 20 on medical health care workers, and 19 on the general public). 23, 24 We aimed to systematically review the literature in order to provide an overview of the psychiatric complications to COVID-19 infection (direct effect) and how COVID-19 are currently affecting mental health among psychiatric patients and general public (indirect effect) alongside with factors altering the risk of psychiatric symptoms in both groups. A variety of factors were associated with higher risk of psychiatric symptoms and/or low psychological well-being of the general public including female gender, front-line health care workers, and poor self-rated health. From previous studies of the SARS CoV-1 epidemic it is known that health care workers are at risk of anxiety and depressive symptoms, which the current studies indicate also is the case of COVID19 . cache = ./cache/cord-286168-019rcbpg.txt txt = ./txt/cord-286168-019rcbpg.txt === reduce.pl bib === id = cord-286217-3uklf2u2 author = Jiang, He-wei title = SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date = 2020-07-14 pages = extension = .txt mime = text/plain words = 6829 sentences = 423 flesch = 54 summary = Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We detected the SARS-CoV-2-specific IgG and IgM proteins bound to the array using fluorescent-labeled anti-human antibodies, thereby generating a global assessment of each patient's humoral antibody response. All of the samples and the controls were probed on the proteome microarray, and after data filtering and normalization, we constructed the IgG and IgM profile for each serum and performed clustering analysis to generate heatmaps (Figs. To statistically analyze the IgG responses against SARS-CoV-2 proteins, we calculated the p-values followed by multiple testing correction (or q-values), and applied significant analysis of microarray (SAM) to identify significant positive proteins (Supplementary Fig. 7 and Data 2). cache = ./cache/cord-286217-3uklf2u2.txt txt = ./txt/cord-286217-3uklf2u2.txt === reduce.pl bib === id = cord-286466-scokdxp2 author = Tani, Hideki title = Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date = 2020-08-23 pages = extension = .txt mime = text/plain words = 2558 sentences = 155 flesch = 54 summary = The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The neutralization values of the serum 31 samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative 32 donors against the pseudotyped virus infection evaluated by the CRNT were compared with 33 was designated as pCAG-SARS-CoV-2. Vero cells were treated with serially diluted sera or whole blood of convalescent patients with 145 COVID-19 or PCR-negative donors and then inoculated with Sfullpv, St19pv, or VSVpv. To 146 remove hematopoietic cells from whole blood samples, centrifugation was performed at 2,000 × g 147 for 5 min. To determine the specificity of infection of Sfullpv and St19pv, a neutralization assay of the 183 pseudotyped viruses was performed using sera of two hospitalized COVID-19 patients. cache = ./cache/cord-286466-scokdxp2.txt txt = ./txt/cord-286466-scokdxp2.txt === reduce.pl bib === id = cord-285907-xoiju5ub author = Chang, Shang-Miao title = Comparative study of patients with and without SARS WHO fulfilled the WHO SARS case definition date = 2005-05-31 pages = extension = .txt mime = text/plain words = 3607 sentences = 192 flesch = 59 summary = Abstract To differentiate severe acute respiratory syndrome (SARS) from non-SARS illness, we retrospectively compared 53 patients with probable SARS and 31 patients with non-SARS who were admitted to Mackay Memorial Hospital from April 27 to June 16, 2003. SARS patients with an initially normal chest X-ray study developed infiltrates at a mean of 5 ± 3.44 days after onset of fever (21/22 SARS vs. Severe acute respiratory syndrome (SARS) is a rapidly progressive disease caused by a novel coronavirus. Initial chest X-ray studies were normal in 22 of 53 SARS patients (41%) and 5 of 31 non-SARS patients (16%) ( Table 4 ). All except 1 of the 22 SARS patients with an initially normal chest X-ray study eventually developed abnormalities (mean FD 5 Ϯ 3.44). No non-SARS patient with an initially negative chest X-ray developed abnormalities on follow-up films. cache = ./cache/cord-285907-xoiju5ub.txt txt = ./txt/cord-285907-xoiju5ub.txt === reduce.pl bib === id = cord-286365-fy0a8mb4 author = ElHawary, Hassan title = Bibliometric Analysis of Early COVID-19 Research: The Top 50 Cited Papers date = 2020-10-13 pages = extension = .txt mime = text/plain words = 2619 sentences = 157 flesch = 48 summary = CONCLUSION: By highlighting the characteristics of the top 50 cited COVID-19-related articles, the authors hope to disseminate information that could assist researchers to identify the important topics, study characteristics, and gaps in the literature. To that end, the goal of this study was to present a bibliometric analysis to identify and dissect the characteristics of the top 50 cited COVID-19-related articles published early on following the outbreak. 62 The majority of the highly cited research assessed COVID-19's clinical presentation and disease description while only 7 papers discussed potential treatment. While this limitation is present with any bibliometric analysis, the main goal of this study was to highlight the characteristics of the highly cited research articles early during the COVID-19 pandemic and the dynamic nature of citation count should not diminish the value of the information presented here. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-286365-fy0a8mb4.txt txt = ./txt/cord-286365-fy0a8mb4.txt === reduce.pl bib === id = cord-286301-7sjw5ci7 author = Sadasivan, Jibin title = Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date = 2017-04-18 pages = extension = .txt mime = text/plain words = 6243 sentences = 289 flesch = 48 summary = SARS-S-Y was absent from surface in most of the cells and localized at the intracellular compartments (figure 5a), and OC43-S protein was mainly localized in distinct puncta that could represent endocytic structures following internalization from the plasma membrane (figure 5b). Our studies clearly demonstrated that the KXHXX motif is the major intracellular localization signal of the full-length SARS-S protein and the C-terminal proximity is not essential. Our alanine mutation studies on the KXHXX motif confirm the importance of the lysine and histidine in the full-length wild-type HCoV-SARS S protein; the mutant protein showed localization in plasma membrane instead of the usual ER and ERGIC. In contrast, Lysosomal acid phosphatase, also a type I membrane protein with a cytosolic tail GYXXØ motif located 7 residues from both transmembrane domain and the carboxy termini (Tm-RMQAQPPGYRHVADGEDHA) delivered mainly via the cell surface (Braun et al. cache = ./cache/cord-286301-7sjw5ci7.txt txt = ./txt/cord-286301-7sjw5ci7.txt === reduce.pl bib === id = cord-286084-2275xvxb author = Dixit, Alok title = Ivermectin: Potential Role as Repurposed Drug for COVID-19 date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2238 sentences = 113 flesch = 45 summary = Currently there is no effective treatment for coronavirus infection; major effort is to develop vaccine against the virus and development of therapeutic drugs for the disease. IVM is shown to be effective in vitro against RNA and deoxyribonucleic acid (DNA) viruses, including human immunodeficiency virus-1 (HIV-1), dengue virus (DENV), influenza, Venezuelan equine encephalitis virus (VEEV) and Zika virus (14) . Currently, remdesivir is a promising potential therapy for COVID-19 due to its broad-spectrum and potent in vitro activity against several novel coronavirus (nCoVs), including SARS-CoV-2 with EC 50 (half maximal effective concentration) and EC 90 (concentration to induce 90% maximal response) values of 0.77 μM and 1.76 μM, respectively (8). IVM which is a widely used as antiparasitic drug has shown to have antiviral activity in in vitro studies against HIV, dengue, influenza, VEEV and Zika virus. Studies are available for its use against RNA virus and have also been tested for its effectiveness against SARS-CoV-2 in vitro. cache = ./cache/cord-286084-2275xvxb.txt txt = ./txt/cord-286084-2275xvxb.txt === reduce.pl bib === id = cord-286072-kgpvdb42 author = Sa Ribero, Margarida title = Interplay between SARS-CoV-2 and the type I interferon response date = 2020-07-29 pages = extension = .txt mime = text/plain words = 7026 sentences = 360 flesch = 43 summary = While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection. IFN, interferon; IFNAR, interferon alpha and beta receptor; IκB, inhibitor of nuclear factor κB; IKKε, IκB kinase-ε; IRF, IFN regulatory factor; ISG, IFN-stimulated gene; JAK, Janus kinase; M, membrane; MAVS, mitochondrial antiviral signaling protein; MDA5, melanoma differentiation-associated gene 5; N, nucleocapsid; Nsp, nonstructural protein; ORF, open reading frame; P, phosphate; PLP, papain-like protease; RIG-I, retinoic acid-inducible gene 1; SARS-CoV, severe acute respiratory syndrome coronavirus; STAT, signal transducer and activator of transcription; TANK, TRAF family member associated NF-κB activator; TBK1, TANK-binding kinase 1; TRAF3, tumor necrosis factor receptor-associated factor 3; TYK2, tyrosine kinase 2. cache = ./cache/cord-286072-kgpvdb42.txt txt = ./txt/cord-286072-kgpvdb42.txt === reduce.pl bib === id = cord-286429-voem879q author = Shao, Yi‐Ming title = Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors date = 2007-08-23 pages = extension = .txt mime = text/plain words = 2043 sentences = 100 flesch = 49 summary = Optimization of TL-3 as an inhibitor against the 3CL protease by replacement of the peripheral Val-Ala residues or the two central phenyl groups was based on the rationale that the binding mode of TL-3 in the protein-ligand complex mainly involves at least a dipeptide scaffold. We thus synthesized two compounds to test the binding mode hypothesis: one with two Trp groups adjacent to the central diol (4, Scheme 1) and the other with two additional Val-Ala residues as in 9. The consensus complex structure was compared with the differential density map, which shows the superimposition of the differential electron density map and the modeled binding mode of compound 4. The ligand-protein complex shown in Figure 1 B was different from the top-ranked Trp-Trp binding mode predicted from the preliminary modeling task (for differences see Figure S2 ). The subsequent refinement of the complex structure significantly improved the accuracy of the binding model, and provided a working model for further optimization of the lead compounds. cache = ./cache/cord-286429-voem879q.txt txt = ./txt/cord-286429-voem879q.txt === reduce.pl bib === id = cord-286390-ytgw3j4s author = Case, James Brett title = Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1659 sentences = 103 flesch = 47 summary = An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We engineered an infectious molecular clone of vesicular 83 stomatitis virus (VSV) to encode the SARS-CoV-2 S protein in place of the native envelope 84 glycoprotein (G) and rescued an autonomously replication-competent virus bearing the spike. Evaluation of a novel vesicular stomatitis virus pseudotype-based assay for detection of 641 neutralizing antibody responses to SARS-CoV Vesicular stomatitis virus pseudotyped with severe acute 645 respiratory syndrome coronavirus spike protein Retroviruses pseudotyped with the severe acute respiratory 722 syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting 723 enzyme 2 cache = ./cache/cord-286390-ytgw3j4s.txt txt = ./txt/cord-286390-ytgw3j4s.txt === reduce.pl bib === id = cord-286121-ltaxmp3u author = Xu, Ke title = Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date = 2009-06-05 pages = extension = .txt mime = text/plain words = 5289 sentences = 287 flesch = 56 summary = In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein. cache = ./cache/cord-286121-ltaxmp3u.txt txt = ./txt/cord-286121-ltaxmp3u.txt === reduce.pl bib === id = cord-286343-s8n1ldol author = Martin, Javier title = Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date = 2020-10-09 pages = extension = .txt mime = text/plain words = 5925 sentences = 340 flesch = 53 summary = We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory (data not shown). cache = ./cache/cord-286343-s8n1ldol.txt txt = ./txt/cord-286343-s8n1ldol.txt === reduce.pl bib === id = cord-286269-vrjyj2y1 author = Sagheb, Setareh title = Two seriously ill neonates born to mothers with COVID-19 pneumonia- a case report date = 2020-09-21 pages = extension = .txt mime = text/plain words = 2778 sentences = 168 flesch = 61 summary = They evaluated cord blood, amniotic fluid and even breast milk samples of mothers diagnosed with COVID-19 pneumonia, but SARS-COV-2 tests were negative in all cases. Consequently, because of performing all the aforementioned droplet and contact precautions during hospitalization, having high LDH, lymphopenia and SIADH soon after birth may be due to early-onset infection of SARS-COV-2. Furthermore, another study conducted on a limited number of patients showed a high level of SARS-COV-2 IgM in neonates born from COVID-19 infected mothers within 2 first hours of their birth [7] , which may indicate infection transmission from mother to fetus. It is worth noting that, although our neonates' RT-PCR tests' results for SARS-COV-2 were negative 1 hour after their birth, they tested positive on day 7 and 12. Neonatal Early-Onset Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in Wuhan, China cache = ./cache/cord-286269-vrjyj2y1.txt txt = ./txt/cord-286269-vrjyj2y1.txt === reduce.pl bib === id = cord-286006-t5gj0k54 author = Nicholas, David B. title = Pediatric epidemic crisis: Lessons for policy and practice development date = 2008-12-31 pages = extension = .txt mime = text/plain words = 5026 sentences = 283 flesch = 44 summary = Methods Qualitative interviews were conducted with 23 participants representing key stakeholder groups: (a) pediatric patients with probable or suspected SARS, (b) their parents, and (c) health care professionals providing direct care to SARS patients. Semi-structured, qualitative interviews were conducted with 23 participants from key stakeholder groups affected by pediatric SARS as follows: pediatric patients between the ages of 5 and 17 years (n = 5), their parents (n = 10), and frontline pediatric health care providers (n = 8). The majority of health care providers (88%) recognized the importance of their work, yet grappled with concerns related to personal vulnerability and the impact of SARS policies on patients and families. Accordingly findings speak clearly to the need for: systematic and well-orchestrated information flow; communication strategies in responding and disseminating relevant information; means to ease vulnerability among stakeholders; strategies for ensuring effective and responsive leadership; and the development of practice and policy guidelines for treatment and contingency planning for an unknown patient care path. cache = ./cache/cord-286006-t5gj0k54.txt txt = ./txt/cord-286006-t5gj0k54.txt === reduce.pl bib === id = cord-286298-pn9nwl64 author = Helmy, Yosra A. title = The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date = 2020-04-24 pages = extension = .txt mime = text/plain words = 9290 sentences = 516 flesch = 51 summary = Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. cache = ./cache/cord-286298-pn9nwl64.txt txt = ./txt/cord-286298-pn9nwl64.txt === reduce.pl bib === id = cord-286573-k4khwvt7 author = Peng, Michael title = The Role of the Ocular Tissue in SARS-CoV-2 Transmission date = 2020-10-02 pages = extension = .txt mime = text/plain words = 4362 sentences = 305 flesch = 54 summary = Here, we reviewed both clinical and research evidence on the ocular manifestations associated with COVID-19, the presence of SARS-CoV-2 in ocular surface tissues and tears, and the potential role of the eye in contracting SARS-CoV-2. For this review, relevant studies that emphasized ocular manifestations of COVID-19 or SARS-CoV-2, viral detection of SARS-CoV-2 in ocular surface secretions or tears, and ACE2 presence in ocular tissues were included. 29 Zhang et al also reported that one of the two COVID-19 patients with conjunctivitis was SARS-CoV-2 RNA positive in the tear sample. Similarly, in a cross sectional study of 33 COVID-19 patients, most of the ocular samples were collected more than 7 days of symptom onset, and Xie et al found only 2 cases with positive ocular SARS-CoV-2 RNA results. 44 Recent studies have attempted to determine ACE2 in ocular surface tissues, such as the conjunctiva and cornea, which are exposed to the external environment and are potential entry points for SARS-CoV-2 infection. cache = ./cache/cord-286573-k4khwvt7.txt txt = ./txt/cord-286573-k4khwvt7.txt === reduce.pl bib === id = cord-286631-3fmg3scx author = Pormohammad, Ali title = Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis date = 2020-06-05 pages = extension = .txt mime = text/plain words = 3669 sentences = 212 flesch = 47 summary = title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis The trigger for rapid screening and treatment of COVID-19 patients is based on clinical symptoms, laboratory, and radiographic findings that are similar to SARS and MERS infections. In this study, we attempted to distinguish the clinical symptoms, laboratory findings, radiographic signs, and outcomes of confirmed COVID-19, SARS, and MERS patients. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Clinical aspects and outcomes of 70 patients with Middle East respiratory syndrome coronavirus infection: a single-center experience in Saudi Arabia Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection Middle East respiratory syndrome coronavirus: a case-control study of hospitalized patients cache = ./cache/cord-286631-3fmg3scx.txt txt = ./txt/cord-286631-3fmg3scx.txt === reduce.pl bib === id = cord-286555-rz88g3ze author = Petrovan, Vlad title = Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date = 2020-07-11 pages = extension = .txt mime = text/plain words = 3527 sentences = 156 flesch = 55 summary = The most widely used molecular method approved by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) to detect SARS-CoV-2 is the real-time reverse transcription polymerase chain reaction (qRT-PCR) [4] . The protocol for the COVID-19 PCR Diatheva Detection Kit used with Fast Gene Probe One Step Mix uses 5 µL of mix 1 mixed with 0.625 µL of mix 2, 9.375 µL of primer/probe mix, and 5 µL of RNA template, with a total volume of 20 µL. An initial interlaboratory validation was performed by the Molecular Pathology Laboratory from the University Emergency Hospital Bucharest, using the PowerCheck 2019-nCoV Real-Time PCR Kit. This study was conducted as part of a surveillance program for COVID-19 implemented by the Romanian government. To determine the analytical sensitivity of the COVID-19 commercial assays used in Romanian hospitals (PowerCheck Kogene 2019-nCoV, COVID-19 PCR Diatheva Detection Kit, and 2019-nCoV CDC EUA), we first evaluated their limit of detection (LOD) by performing 10-fold serial dilutions of the controls provided by the kits. cache = ./cache/cord-286555-rz88g3ze.txt txt = ./txt/cord-286555-rz88g3ze.txt === reduce.pl bib === id = cord-286919-fny060vk author = Lahfaoui, M title = Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1019 sentences = 78 flesch = 64 summary = Les auteurs déclarent ne pas avoir de liens d'intérêts Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson L'émergence et la propagation d'un nouveau coronavirus (SARSCoV-2) à partir de Wuhan, en Chine, sont devenues une urgence de santé publique de portée internationale, désignée par l'Organisation mondiale de la santé [1]. Nous rapportons un cas d'un nourrisson, de sexe féminin âgée de 17 mois, de Berkan, Maroc, admis initialement pour prise en charge d'une anémie, puis un tableau de sepsis sévère, le body-scan a objectivé des lésions pulmonaire bilatérale d'allure virale, le RT-PCR a confirmé le diagnostic de SARS-COV-2, la patiente a été décédé après 24H suite à un syndrome de détresse respiratoire aigüe. A la date du 10 mars 2020, ce nouveau coronavirus (SRAS-CoV-2) est déjà responsable de plus de 110000 infections et de 4 000 décès dans le monde, mais les données concernant les caractéristiques épidémiologiques et cliniques des enfants cache = ./cache/cord-286919-fny060vk.txt txt = ./txt/cord-286919-fny060vk.txt === reduce.pl bib === id = cord-286341-16tghl48 author = CONCHA-MEJIA, A. title = CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia date = 2020-07-24 pages = extension = .txt mime = text/plain words = 2012 sentences = 125 flesch = 50 summary = In Colombia, the first case was diagnosed on March 6, 2020 , with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Results: We included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). In this study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Bogota, Colombia, with special emphasis on the presence of gastrointestinal symptoms. cache = ./cache/cord-286341-16tghl48.txt txt = ./txt/cord-286341-16tghl48.txt === reduce.pl bib === id = cord-286290-85l99l13 author = Goddard, N.L. title = Lessons learned from SARS: The experience of the Health Protection Agency, England date = 2005-11-16 pages = extension = .txt mime = text/plain words = 3393 sentences = 155 flesch = 44 summary = Lessons learned from mounting a UK response to SARS included: the importance of international collaboration; formation of a UK-wide, multidisciplinary Task Force; flexible case reporting mechanisms; integration of surveillance and laboratory data; generation of prompt and web-accessible guidance and advice; availability of surge capacity; and contingency planning. The global response to SARS provided new opportunities for the UK to collaborate with WHO (Geneva and Western Pacific Region), a number of public health organisations in south east Asia, as well as national public health centres such as the Centers for Disease Control and Prevention in the USA and Health Canada. Surveillance arrangements were revised during the outbreak to encourage initial alerting to HPA Regional Offices and ensure that local public health authorities were aware of the potential cases. 3. Flexible case reporting mechanisms need to be implemented at central, regional and local level during an evolving outbreak to inform appropriate public health measures. cache = ./cache/cord-286290-85l99l13.txt txt = ./txt/cord-286290-85l99l13.txt === reduce.pl bib === id = cord-286441-nl3kuqw3 author = Murray, D. D. title = Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative date = 2020-11-12 pages = extension = .txt mime = text/plain words = 5560 sentences = 303 flesch = 48 summary = Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. cache = ./cache/cord-286441-nl3kuqw3.txt txt = ./txt/cord-286441-nl3kuqw3.txt === reduce.pl bib === id = cord-286638-bqxyb61p author = Singh, Awadhesh Kumar title = Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations date = 2020-04-09 pages = extension = .txt mime = text/plain words = 4824 sentences = 281 flesch = 46 summary = The disease burden of coronavirus infectious disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) has been increasing continuously with more than a million confirmed patients and more than 45 thousand deaths globally [1] . Emerging data suggests that COVID-19 is common in patients with diabetes, hypertension, and cardiovascular disease (CVD), although the prevalence rate varied in different studies as well in country-wise data. Evolving data also suggest that patients of COVID-19 with diabetes are more often associated with severe or critical disease varying from 14 to 32% in different studies [15e18, 20, 22, 24] . Though there is limited data about the association of blood glucose levels with disease course in COVID-19 at present, data from other infections like SARS and influenza H1N1 has shown that patients with poor glycemic control have increased risk of complications and death [60, 61] . cache = ./cache/cord-286638-bqxyb61p.txt txt = ./txt/cord-286638-bqxyb61p.txt === reduce.pl bib === id = cord-286854-0s7oq0uv author = Jin, Xi title = Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site date = 2020-07-03 pages = extension = .txt mime = text/plain words = 6012 sentences = 322 flesch = 54 summary = title: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes. Sequence alignment analysis indicated 38 mutation sites for ZJ01 compared with other SARS-CoV-2 family members ( Figure 2(A) ). Further comparative alignment analysis of GZ02 (SARS viral strain), Wuhan-Hu-1 (the earliest sequenced SARS-CoV-2), RaTG13, HKU9-1 (the potential ancestor of SARS and SARS-CoV-2), HKU-1 and OC43 showed that the variation of FCS sequence had certain regularity in coronavirus evolution ( Figure 4(B) ). We speculated that, despite the gene similarity between ZJ01 and Wuhan-Hu-1, the mutation near the FCS changed the protein structure conformation and surface electrostatic potential of ZJ01, which further influenced its binding capacity with Furin. cache = ./cache/cord-286854-0s7oq0uv.txt txt = ./txt/cord-286854-0s7oq0uv.txt === reduce.pl bib === id = cord-286537-7ri2p5b8 author = Lee, Ting-Wai title = Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide date = 2005-11-11 pages = extension = .txt mime = text/plain words = 7020 sentences = 365 flesch = 61 summary = authors: Lee, Ting-Wai; Cherney, Maia M.; Huitema, Carly; Liu, Jie; James, Karen Ellis; Powers, James C.; Eltis, Lindsay D.; James, Michael N.G. title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. In contrast, in protomer A of the M pro CAðK1Þ :APE complex, the benzyl group of APE squeezes into and thereby widens the S4 specificity pocket of the peptidase, so that it is snugly accommodated in this enlarged pocket now formed by the residues 165 to 168, Phe185, Gln192 and the main-chain atoms of Val186 (Figures 3(b) and 4(c)). cache = ./cache/cord-286537-7ri2p5b8.txt txt = ./txt/cord-286537-7ri2p5b8.txt === reduce.pl bib === id = cord-286703-ipoj13va author = de Wilde, Adriaan H. title = Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date = 2017-01-15 pages = extension = .txt mime = text/plain words = 3343 sentences = 165 flesch = 48 summary = Data from cell culture infection models (Chan et al., 2013a (Chan et al., , 2013b de Wilde et al., 2013b; Falzarano et al., 2013a; Kindler et al., 2013; Zielecki et al., 2013) and experiments in rhesus macaques (Falzarano et al., 2013b) and marmosets (Chan et al., 2015) suggested that interferons (IFNs) are potent inhibitors of MERS-CoV replication. As ribavirin has previously been reported to inhibit MERS-CoV replication (Falzarano et al., 2013a) and ALV and ribavirin have been used together during clinical trials for hepatitis C treatment (Pawlotsky et al., 2015) , this combination was tested in LLC-MK2 cells. (e, f) SARS-CoV-infected (e) Vero or (f) VeroE6 cells (MOI 0.01) were treated with various concentrations of ALV from 1 h p.i. onwards, and virus titers in the culture medium at 32 h p.i. were determined by plaque assay. cache = ./cache/cord-286703-ipoj13va.txt txt = ./txt/cord-286703-ipoj13va.txt === reduce.pl bib === id = cord-286472-pqtem19t author = McFee, R.B. title = MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5364 sentences = 291 flesch = 47 summary = This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol cache = ./cache/cord-286472-pqtem19t.txt txt = ./txt/cord-286472-pqtem19t.txt === reduce.pl bib === id = cord-287100-xkp8a9b9 author = López-Díaz, Álvaro title = COVID-19 Infection During Pregnancy and Risk of Neurodevelopmental Disorders in Offspring: Time for Collaborative Research date = 2020-10-31 pages = extension = .txt mime = text/plain words = 1390 sentences = 68 flesch = 28 summary = Cohorts of COVID-19-infected pregnant women may currently provide biological (e.g., umbilical cord and placenta samples) and clinical (e.g., maternal serum samples and neonatal filter paper blood samples) data that would enable the acquisition of very valuable genetic, metabolic, and immunological information. Such information would help determine the extent to which maternal infection, in addition to genetic vulnerability, contributes to an increased risk of neuropsychiatric disturbance in the offspring, and would improve our understanding of the role of immune-inflammatory mechanisms during pregnancy in the etiology of neurodevelopmental disorders (10). Such populationbased birth cohort studies of SARS-CoV-2-infected pregnant women should involve detailed systematic clinical and biological examinations during pregnancy and delivery along with an extended follow-up of the offspring, including neurocognitive, neuroimaging, and electrophysiological examination. Large-scale and long-term prospective population-based birth cohort studies of COVID-19-infected and unaffected pregnant women are needed to unravel the complex interactions between maternal infection and risk of neurodevelopmental disorders in offspring. cache = ./cache/cord-287100-xkp8a9b9.txt txt = ./txt/cord-287100-xkp8a9b9.txt === reduce.pl bib === id = cord-286655-5vorrnq3 author = Vivek-Ananth, R.P. title = In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection date = 2020-08-22 pages = extension = .txt mime = text/plain words = 12942 sentences = 693 flesch = 55 summary = Lastly, we filtered the subset of phytochemicals whose binding energy in the best docked pose with TMPRSS2 (respectively, cathepsin L) is ≤−8.5 kcal/mol (respectively, ≤−8.0 In the third stage, we performed protein-ligand docking using AutoDock Vina [34] . Finally, in the fifth stage, for the top three inhibitors of TMPRSS2 namely, T1 (qingdainone), T2 (edgeworoside C) and T3 (adlumidine), and of cathepsin L namely, C1 (ararobinol), C2 ((+)-oxoturkiyenine) and C3 (3α,17α-cinchophylline), their respective protein-ligand complexes were analyzed using 180 ns MD simulation (Section 3; Figures 8 and 9; Supplementary Figures S1 and S2) and their interaction binding energy was computed using MM-PBSA method (Section 3; Table 3 ). As mentioned above, we have identified 96 potential natural product inhibitors of TMPRSS2 by computational screening of 14,011 phytochemicals produced by Indian medicinal plants, and these 96 compounds labelled T1-T96 are listed in Supplementary Table S1 along with their PubChem identifier, common name, IUPAC name and structure in SMILES format. cache = ./cache/cord-286655-5vorrnq3.txt txt = ./txt/cord-286655-5vorrnq3.txt === reduce.pl bib === id = cord-286870-92eckkhk author = Gul, Seref title = In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials date = 2020-08-05 pages = extension = .txt mime = text/plain words = 6577 sentences = 387 flesch = 50 summary = title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials The FDA-approved drug library was used to screen for the identification of molecules with high affinity to the active site of 3CL pro and nsp8 binding site of RdRp ( Figure 1 ). We also determined critical residues responsible for the high binding affinity of drugs to the protease, which may help to develop novel inhibitor molecules through rational drug design and quantitative structure-activity relationship (QSAR) studies. Conservation of these interactions during MD simulations and their contribution to BFE suggests that ergotamine can stably interact with the nsp8 binding site of RdRp. These results indicate that ergotamine and dihydroergotamine are possible candidates for further in vitro testing and clinical evaluation as an anti-SARS-CoV-2 agents. cache = ./cache/cord-286870-92eckkhk.txt txt = ./txt/cord-286870-92eckkhk.txt === reduce.pl bib === id = cord-286713-14i38xtt author = Guarner, Jeannette title = Three Emerging Coronaviruses in Two Decades: The Story of SARS, MERS, and Now COVID-19 date = 2020-02-13 pages = extension = .txt mime = text/plain words = 1179 sentences = 71 flesch = 58 summary = As a matter of fact, the characteristic electron microscopy appearance was the clue to amplify and sequence nucleic acids from Dr Urbani's (one of the health care providers who died of severe acute respiratory syndrome [SARS] in 2003) respiratory specimen using a consensus coronavirus primer. The virus was ultimately named SARS-CoV, as febrile patients had severe acute respiratory syndrome and could present with pneumonia and lower respiratory symptoms such as cough and dyspnea. Nine years later, a new coronavirus that causes respiratory disease appeared in the Middle East, thus the name of MERS-CoV. Symptoms of MERS-CoV are nonspecific, but many patients end up with severe acute respiratory distress. SARS-CoV-2 will cause many more deaths than its predecessors, even though the mortality rate is lower than MERS-CoV infections, because there have been so many more cases. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-286713-14i38xtt.txt txt = ./txt/cord-286713-14i38xtt.txt === reduce.pl bib === id = cord-286923-o4fj8kx0 author = Berhan, Yifru title = What immunological and hormonal protective factors lower the risk of COVID-19 related deaths in pregnant women? date = 2020-07-18 pages = extension = .txt mime = text/plain words = 4536 sentences = 212 flesch = 34 summary = The immunological changes predominantly inclining to anti-inflammatory state, which is augmented by placental hormones' immune modulating action, looks against with COVID-19 inflammatory reaction leading to cytokine storm and multiple organ failure. As discussed hereunder, accumulating evidence from other infections and autoimmune diseases shows that immune modulating hormones, cytokines and other anti-inflammatory endogenous ligands are determinant factors in reducing the severity of several diseases during pregnancy; which could also be the most plausible explanation for the less severity and mortality of Covid-19 in pregnant women. Despite serious concern for patients with autoimmune disease, taking their immune suppression and medications, at least 110 individuals (79% females) with rheumatoid arthritis and got infected with SARS CoV-2 (from six continents) were not as such at higher risk of mortality, probably as they were on anti-inflammatory medication; only 6(5%) persons died of COVID-19 [89] . cache = ./cache/cord-286923-o4fj8kx0.txt txt = ./txt/cord-286923-o4fj8kx0.txt === reduce.pl bib === id = cord-286895-i3g4ad4z author = Panciani, Pier Paolo title = SARS-CoV-2: “Three-steps” infection model and CSF diagnostic implication date = 2020-05-05 pages = extension = .txt mime = text/plain words = 772 sentences = 61 flesch = 52 summary = Dear Editor, An increasing number of Coronavirus Disease 2019 (COVID-19) patients shows neurological symptoms, but currently few studies have systematically analyzed the impact of SARS-CoV-2 on the Central Nervous System (CNS). (Bertran Recasens et al., 2020) In our Department we observed 3 different clinical pictures in SARS-CoV-2 infection with neurological impairment: cerebral thrombosis (CTh) with hemorrhagic infarction, demyelinating lesions and encephalopathy. SARS-CoV-2 may lead to Neuro-COVID through three phases ( Fig.1) : neuroinvasion, CNS clearance and immune response. Negative results could also be explained by the lack of apoptosis and/or necrosis as observed in pre-clinical models (Netland et al., 2008) , the lowsensitivity of the method and the CSF clearance of SARS-CoV-2 that lead to a low viral below the sensitivity of currently available instrumentation. In the last phase, the respiratory system is severely affected leading to potential hypoxia with subsequent brain damage. cache = ./cache/cord-286895-i3g4ad4z.txt txt = ./txt/cord-286895-i3g4ad4z.txt === reduce.pl bib === id = cord-286683-mettlmhz author = Ortiz-Prado, Esteban title = Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date = 2020-05-30 pages = extension = .txt mime = text/plain words = 13299 sentences = 726 flesch = 45 summary = Interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in SARS [59] and MERS diseases [60] were also reported in the early study of 41 patients with COVID-19 in Wuhan [41] . A recently published case report of a patient with mild-to-moderate COVID-19 revealed the presence of an increased activated CD4+ T cells and CD8+ T cells, antibody-secreting cells (ASCs), follicular helper T cells (TFH cells), and anti-SARS-CoV-2 IgM and IgG antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [82] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series cache = ./cache/cord-286683-mettlmhz.txt txt = ./txt/cord-286683-mettlmhz.txt === reduce.pl bib === id = cord-287205-k64svq6n author = Pollet, Jeroen title = SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date = 2020-11-05 pages = extension = .txt mime = text/plain words = 4245 sentences = 282 flesch = 56 summary = title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. The modified SARS-CoV-2 antigen, 264 RBD219-N1C1, when formulated on Alhydrogel ® , was shown to induce virus-neutralizing antibodies 265 in mice, equivalent to those levels elicited by the wild-type (RBD219-WT) recombinant protein 266 counterpart. Here we report on a yeast-expressed SARS-CoV-2 RBD219-N1C1 protein and its potential as a 397 vaccine candidate antigen for preventing COVID-19. In a mouse virus challenge model for the SARS CoV RBD recombinant protein vaccine, we 422 found that Alhydrogel ® formulations induced high levels of protective immunity but did not 423 stimulate eosinophilic immune enhancement, suggesting that Alhydrogel ® may even reduce immune The selection of the P. cache = ./cache/cord-287205-k64svq6n.txt txt = ./txt/cord-287205-k64svq6n.txt === reduce.pl bib === id = cord-286901-whvq8y1p author = Vidali, Sofia title = D-dimer as an indicator of prognosis in SARS-CoV-2 infection: a systematic review date = 2020-07-13 pages = extension = .txt mime = text/plain words = 4272 sentences = 228 flesch = 37 summary = This study aims to highlight the correlation between elevated D-dimer (an indirect thrombosis marker) and the increased rate of poor prognosis-associated conditions, and to introduce D-dimer-labelled anticoagulant administration as a potentially useful tool to prevent complications and positively influence coronavirus disease 2019 (COVID-19) course. The keywords and their variants (differently combined) used for the search were "COVID-19", "2019-nCoV", "2019 novel coronavirus", "SARS-CoV-2", "D-dimer", "coagulation", "hypercoagulative state", "laboratory analysis", "ARDS", "haemostasis", "thrombosis", "pulmonary embolism", "disseminated intravascular coagulation (DIC)", "heparin" and "anti-coagulation". The alterations of coagulation factors during SARS-CoV-2 infection and specifically that of D-dimer are, as documented in the clinical experiences described here, severe, constant and correlated with prognosis, complications and CEP rates. Among the factors that were demonstrated to be connected to the clinical outcome of COVID-19 patients, the presence of comorbidities may represent a confounding factor for the interpretation of D-dimer and other coagulation parameter alterations, especially considering the heterogeneous aetiology of thrombotic and thrombophilic states. cache = ./cache/cord-286901-whvq8y1p.txt txt = ./txt/cord-286901-whvq8y1p.txt === reduce.pl bib === id = cord-287043-53oy5w34 author = Reyes‐Bueno, José Antonio title = Miller‐Fisher syndrome after SARS‐CoV‐2 infection date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1423 sentences = 91 flesch = 49 summary = The neurophysiological study carried out on April 14 th showed F-wave anomalies such as asymmetric latency for the lower limbs and low A-wave amplitude on the left leg, alteration of bilateral R1 responses in the Blink-Reflex and in the intermediary standard electromyography poor activity in right rectus-anterior femoral muscle and little spontaneous denervation activity in left rectus-anterior femoral (RAF) muscle; all of this was compatible with an acute Guillain-Barre type demyelinating polyneuropathy in a very early stage. In the papers reviewed, the presence of anosmia and/or ageusia was only present in one case of Guillain-Barré syndrome (11) and in the two patients described with Miller-Fisher syndrome (5) . Our case would be the 3rd patient with MFS associated with COVID-19 as far as we know. Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré Syndrome Associated with SARS-CoV-2 Guillain Barre syndrome associated with COVID-19 infection: A case report cache = ./cache/cord-287043-53oy5w34.txt txt = ./txt/cord-287043-53oy5w34.txt === reduce.pl bib === id = cord-287156-3plpi6i9 author = Lassandro, Giuseppe title = Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date = 2020-07-01 pages = extension = .txt mime = text/plain words = 8021 sentences = 535 flesch = 43 summary = Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission cache = ./cache/cord-287156-3plpi6i9.txt txt = ./txt/cord-287156-3plpi6i9.txt === reduce.pl bib === id = cord-287210-sars5dmi author = Woo, Patrick C. Y. title = Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia date = 2005-12-01 pages = extension = .txt mime = text/plain words = 3345 sentences = 206 flesch = 56 summary = However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. All prospectively collected NPAs from patients with community-acquired pneumonia that were sent to the clinical microbiology laboratories of 4 hospitals in Hong Kong during a 12-month period (22 March 2003 [the beginning of the SARS epidemic in Hong Kong] to 21 March 2004) for detection of SARS-CoV and were found to be negative for SARS-CoV RNA, by reverse-transcription polymerase chain reaction (RT-PCR) [20] , were included in the study. Sequence analysis revealed 0%-2% nucleotide differences between the sequences of the fragments and the sequence of the pol gene from The epidemiological, clinical, and radiological characteristics of the 10 patients with CoV-HKU1-associated community-acquired pneumonia are summarized in table 2. cache = ./cache/cord-287210-sars5dmi.txt txt = ./txt/cord-287210-sars5dmi.txt === reduce.pl bib === id = cord-287228-0qm939ve author = Hong, Ke title = Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date = 2020-10-27 pages = extension = .txt mime = text/plain words = 3616 sentences = 192 flesch = 51 summary = In one study including 70 patients with COVID-19, 21% clinically recovered patients with two consecutive negative results of nucleic acid detection experienced a later positive testing for SARS-CoV-2, and the longest duration of viral RNA positivity in this study was 45 days following infection [4] . A total of 2860 COVID-19 patients were hospitalized and followed in this hospital since the epidemic, and those with persistent or intermittent viral RNA positivity in respiratory samples (including the nasopharyngeal, oropharyngeal and sputum samples) for at least 4 weeks were included in our study, regardless of the age and their clinical status. However, in most of these studies, PCR testing was used as a marker to indicate the existence of virus, and patients with positive viral RNA was considered infectious though they have been infected for months without further clinical symptoms. cache = ./cache/cord-287228-0qm939ve.txt txt = ./txt/cord-287228-0qm939ve.txt === reduce.pl bib === id = cord-287101-k3zq75zc author = Micheli, V. title = Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase date = 2020-07-24 pages = extension = .txt mime = text/plain words = 2400 sentences = 149 flesch = 51 summary = The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. A dataset of 41 genome assemblies of Sars-Cov-2 strains isolated in Italy between 20 February 2020 and 30 March 2020 were retrieved from GISAID database 12 , (see Supplementary Table 1 for details). All patients were resident in Lombardy Region, distributed in different provinces, as reported in table X: in particular, the category 'Milano' contains also patients hospitalized for non-COVID-19 disease, for whom SARS-CoV-2 hospital acquisition was supposed; in addition, HSacco-20, in 'Other' category, was a nurse living in Bergamo and working at Lodi Hospital. cache = ./cache/cord-287101-k3zq75zc.txt txt = ./txt/cord-287101-k3zq75zc.txt === reduce.pl bib === id = cord-287091-a3nieh5p author = Kumar, Anuj title = Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches date = 2020-06-04 pages = extension = .txt mime = text/plain words = 5544 sentences = 314 flesch = 51 summary = In the current study, we report novel natural metabolites namely, ursolic acid, carvacrol and oleanolic acid as the potential inhibitors against main protease (M(pro)) of COVID-19 by using integrated molecular modeling approaches. Besides the uses of various FDA-approved antiviral compounds as mentioned above, there are many in-silico studies have been performed to screen the novel phytochemical molecules as a potential inhibitors of main protease of SARS-CoV-2 or develop new drugs against COVID-19 (Adem et al., 2020; Chandel et al., 2020; Gentile et al., 2020; Gonzalez-Paz et al., 2020; Khaerunnisa et al., 2020; Khan et al., 2020; Qamar et al., 2020; Sharma & Kaur, 2020; Sun et al., 2020) . In the present study, we have targeted the protease of SARS-CoV-2 virus using available molecular modelling based methods and studied the interactions with selected natural compounds (ursolic acid, carvacrol and oleanolic acid) by molecular docking and molecular dynamics simulations followed by molecular mechanic/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) validation. cache = ./cache/cord-287091-a3nieh5p.txt txt = ./txt/cord-287091-a3nieh5p.txt === reduce.pl bib === id = cord-287289-zgehbwve author = Schmidt, M. title = FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2381 sentences = 154 flesch = 60 summary = title: FACTFrankfurt adjusted COVID-19 testinga novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity We applied a novel protocol to NAT testing of respiratory swabs for SARS-CoV-2: First, to evaluate for suitability of different mini-pool sizes, swabs were contaminated with a defined SARS-CoV-2 virus concentration of 1x10 4 copies/ml, and then placed in a series of 10 tubes with lysis buffer for 5 minutes each. P-value for individuals sample and mini pool NAT was 0.299 and 0.354 for the ORF region and E-gene, respectively, which we consider not statistically significant. Ct-values did not differ significantly between mini-pool and the single sample testing (p-value for the ORF region and E gene were 0.44 and 0.46, respectively) (table 4). Here, we present an alternate protocol (FACT) that is based on incubation of a respiratory swab first in a single sample tube, and then again in a mini-pool tube. cache = ./cache/cord-287289-zgehbwve.txt txt = ./txt/cord-287289-zgehbwve.txt === reduce.pl bib === id = cord-287372-ya5uvoki author = Böszörményi, Kinga P. title = Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date = 2020-11-05 pages = extension = .txt mime = text/plain words = 3973 sentences = 249 flesch = 58 summary = This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. cache = ./cache/cord-287372-ya5uvoki.txt txt = ./txt/cord-287372-ya5uvoki.txt === reduce.pl bib === id = cord-287172-h8zoplkm author = Ghobrial, Moheb title = The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date = 2020-10-21 pages = extension = .txt mime = text/plain words = 7020 sentences = 315 flesch = 55 summary = To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. Notably, the top regulated pathways included inflammation, angiogenesis, coagulation, cell-extracellular matrix interaction, viral-host interaction, vascular metabolism, blood-brain-barrier permeability, and reactive oxygen species (ROS) in both the adult and the fetal brain endothelium ( Together, these data reveal that CTSB is highly expressed in various endothelial cell clusters of the fetal and adult human brain and that pathways downstream of CTSB might provide a suggestive explanation of some of the neurovascular symptoms observed in COVID-19 cache = ./cache/cord-287172-h8zoplkm.txt txt = ./txt/cord-287172-h8zoplkm.txt === reduce.pl bib === id = cord-287256-hgqz1bcs author = Magurano, Fabio title = SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date = 2020-11-05 pages = extension = .txt mime = text/plain words = 1177 sentences = 76 flesch = 60 summary = title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID 50 viral titre of 0,67 and 0,25 log10 respectively. cache = ./cache/cord-287256-hgqz1bcs.txt txt = ./txt/cord-287256-hgqz1bcs.txt === reduce.pl bib === id = cord-287304-h6wj7m8u author = Keil, Roger title = Governing the Sick City: Urban Governance in the Age of Emerging Infectious Disease date = 2007-12-07 pages = extension = .txt mime = text/plain words = 11689 sentences = 450 flesch = 45 summary = While there has been much attention in recent years on the significance of global city regions in the new world economy (Brenner and Keil 2006) and while the governance and regulation of these regions has captured the imagination of academics and policymakers alike (Buck et al 2005; Harding 2005; Heinelt and Kübler 2005; Kantor and Savitch 2005; Scott 2001) , little has been said specifically about the growing pressures posed by the potential threat of infectious disease through the global network on urban governance. 2 For the area of urban planning and governance a more or less critical literature has begun to explore the spaces that cities have to maneuver in the rather open field of infectious disease preparedness planning and public health since the onset of the "new normal" after the attacks of 9/11 Malizia 2006; Matthew and Macdonald 2006) . cache = ./cache/cord-287304-h6wj7m8u.txt txt = ./txt/cord-287304-h6wj7m8u.txt === reduce.pl bib === id = cord-287447-5lzzobl3 author = Keyaerts, Els title = In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date = 2004-10-08 pages = extension = .txt mime = text/plain words = 2159 sentences = 130 flesch = 53 summary = Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Glycyrrhizin (an active component of liquorice roots), niclosamide (an antihelminthic drug), nelfinavir (a human immunodeficiency deficiency virus (HIV) protease inhibitor), and SNAP (a nitric oxide donor) were reported to have an antiviral effect against SARS-CoV [12] [13] [14] [15] . In this study we report the in vitro antiviral activity of chloroquine against SARS-CoV Frankfurt 1 strain infection. The IC 50 of chloroquine inhibition of SARS-CoV replication in Vero E6 cells, 8.8 lM, is below (1000-fold) the plasma concentrations of chloroquine that are reached in human plasma, following treatment with chloroquine (for acute malaria) at a dose of 25 mg/kg over three days [27] . Our results show that chloroquine inhibits the replication of SARS-CoV in Vero E6 cells. cache = ./cache/cord-287447-5lzzobl3.txt txt = ./txt/cord-287447-5lzzobl3.txt === reduce.pl bib === id = cord-287222-wojyisu0 author = Zhou, Min title = Coronavirus disease 2019 (COVID-19): a clinical update date = 2020-04-02 pages = extension = .txt mime = text/plain words = 5683 sentences = 276 flesch = 35 summary = Of the first 99 laboratory-confirmed patients, 49 (49%) had been exposed to HSWM, which was reported to be the possible initial source of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [5] . New Coronavirus Infection Diagnosis and Treatment Scheme (Trial Version) published by Military Support Hubei Medical Team also put forward that for mild to moderate COVID-19 patients, corticosteroids should not be given principally and highdose corticosteroid pulse therapy was not recommended. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical pathology of critical patient with novel coronavirus pneumonia (COVID-19) cache = ./cache/cord-287222-wojyisu0.txt txt = ./txt/cord-287222-wojyisu0.txt === reduce.pl bib === id = cord-287410-boxxlopy author = Devi, Arpita title = In silico designing of multi-epitope vaccine construct against human coronavirus infections date = 2020-08-10 pages = extension = .txt mime = text/plain words = 7189 sentences = 446 flesch = 60 summary = Band T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. To predict the probable immune response of the designed multi-epitope vaccine construct in human immune system, in silico immune simulations were conducted using the C-ImmSim server (http://150.146.2.1/C-IMMSIM/index.php) (Rapin et al., 2010) . C-ImmSim is a novel in silico approach for the study of the mammalian immune system The tool is a combination of a mesoscopic scale simulator of the immune system with machine learning techniques for molecular-level predictions of major histocompatibility complex (MHC)-peptide-binding interactions, linear B-cell epitope discovery, and protein-protein potential estimation. The antigenicity of the vaccine construct including the adjuvant sequence and His-tag was predicted by the VaxiJen 2.0 server to be 0.6452 with a bacteria model at a threshold of 0.4. cache = ./cache/cord-287410-boxxlopy.txt txt = ./txt/cord-287410-boxxlopy.txt === reduce.pl bib === id = cord-287497-93oiiqqi author = Tagliamento, Marco title = Italian survey on managing immune checkpoint inhibitors in oncology during COVID‐19 outbreak date = 2020-06-14 pages = extension = .txt mime = text/plain words = 3228 sentences = 199 flesch = 49 summary = The objectives of this survey were to examine the impact of COVID-19 outbreak on the perception of Italian physicians involved in the administration of ICIs about SARS-CoV-2 related risks in cancer patients receiving these therapies, and their attitudes towards the management of ICIs in oncology. The perception of respondents regarding the potential increased risk of severe events related to SARS-CoV-2 infection in cancer patients treated with ICIs is displayed in Figure 1B . 17 Moreover, besides the overlapping between cancer-related signs/symptoms or side effects of oncological treatments (including irAEs) and COVID-19 manifestations, additional issues could emerge from the differential diagnosis between radiological findings of lung involvement from SARS-CoV-2 and pneumonitis induced by ICIs. 9, 24 To the best of our knowledge, this is the first study exploring the perception of physicians towards these unsolved issues, and whether the outbreak has modified the clinical practice in managing the treatment with ICIs in oncology. cache = ./cache/cord-287497-93oiiqqi.txt txt = ./txt/cord-287497-93oiiqqi.txt === reduce.pl bib === id = cord-287349-1zcq7kzx author = Chen, James title = Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2959 sentences = 215 flesch = 53 summary = title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. The analogous structural 234 arrangement leads us to propose that the SARS-CoV-2 RdRp may backtrack, generating a single-235 stranded RNA segment at the 3'-end that would extrude out the RdRp secondary channel 236 Table S1 ; Video S1). This aspect of helicase function could provide the NTP-296 dependent motor activity necessary to backtrack the RdRp. In cellular organisms, DdRp 297 backtracking plays important roles in many processes, including the control of pausing during 298 transcription elongation, termination, DNA repair, and fidelity (Nudler, 2012) . Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase cache = ./cache/cord-287349-1zcq7kzx.txt txt = ./txt/cord-287349-1zcq7kzx.txt === reduce.pl bib === id = cord-287054-zmxpuynv author = Li, Ning title = Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date = 2020-08-25 pages = extension = .txt mime = text/plain words = 6747 sentences = 356 flesch = 37 summary = Since March 3, 2020, three methods have been used for the diagnosis of novel coronavirus pneumonia: i) Detection of positive 2019-nCoV nucleic acids by RT-PCR; ii) viral gene sequencing to detect known 2019-nCoV sequences; and iii) the identification of positive 2019-nCoV-specific IgM and IgG antibodies in serum (15) . The China National Medical Products Administration has approved a gene sequencing system (ultra-high-throughput sequencer DNBSEQ-T7), supporting analysis software and nucleic acid detection kits (Table Ⅲ ), which can identify and diagnose coronaviruses, including 2019-nCoV and other infectious respiratory pathogens and enable rapid detection of viral sequences (22) . The clinical application of the total antibody detection can improve limitations, including slow speed of nucleic acid detection in suspected patients, complex sampling, low sensitivity and the requirement for high-level biosafety measures for the control and prevention of the current 2019-nCoV epidemic (74) . cache = ./cache/cord-287054-zmxpuynv.txt txt = ./txt/cord-287054-zmxpuynv.txt === reduce.pl bib === id = cord-287499-zcizdc7s author = Thompson, Hayley A title = SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1399 sentences = 72 flesch = 46 summary = title: SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China Highlight: We estimated SARS-CoV-2 infection prevalence in cohorts of repatriated citizens from Wuhan to be 0.44% (95% CI: 0.19%-1.03%). Although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in Wuhan City, China, in the absence of large-scale population testing early in the epidemic. By focusing on flights where all passengers were tested for SARS-CoV-2 infection with real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR), regardless of symptoms, a more accurate estimate of infection prevalence can be obtained compared to relying on symptomatic surveillance testing alone. 8 The repatriation flights we considered represent a globally diverse population of foreign nationals who were residing in Wuhan City leading up to the outbreak for variable periods of time and for a variety of reasons: students, work-related travel, visiting friends and families and tourism. High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries cache = ./cache/cord-287499-zcizdc7s.txt txt = ./txt/cord-287499-zcizdc7s.txt === reduce.pl bib === id = cord-287338-pws42iay author = Gendelman, Omer title = Continuous hydroxychloroquine or colchicine therapy does not prevent infection with SARS-CoV-2: Insights from a large healthcare database analysis date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2016 sentences = 107 flesch = 46 summary = As such, in this study, we investigated whether a chronic baseline use of anti-inflammatory medications (namely, hydroxychloroquine and colchicine) could provide a potentially beneficial effect in preventing or, at least partially, mitigating the burden of the SARS-CoV-2 infection. In the present study, we have utilized "real-world data" to explore the associations between subjects positive for SARS-COV-2, different underlying co-morbidities and medications, which were not administered for anti-viral treatment purposes. In a population-based study evaluating the clinical characteristics of 1,482 patients hospitalized with COVID-19 in the USA [19] the majority of patients were males (54.4%) with a similar pattern of underlying comorbidities, most commonly hypertension (49.7%), followed by obesity (48.3%), DM (28.3%), and cardiovascular disease (27.8%). Concerning the alleged anti-viral activities of hydroxychloroquine [23] and its potential protective role against infections [24] , the existing scholarly literature reports contrasting findings even though to date no RCT has shown an unequivocal advantage in preventing or improving the major outcomes in COVID-19 patients [25, 26] . cache = ./cache/cord-287338-pws42iay.txt txt = ./txt/cord-287338-pws42iay.txt === reduce.pl bib === id = cord-287477-aios0h8s author = Sicari, Daria title = Role of the early secretory pathway in SARS-CoV-2 infection date = 2020-07-28 pages = extension = .txt mime = text/plain words = 6483 sentences = 359 flesch = 44 summary = CoV-2 infection starts when its spike (S) protein binds to angiotensin I-converting enzyme 2 (ACE2) receptors on the host cell membrane (Lake, 2020; Letko et al., 2020) . Thus, virion spread critically depends on recruiting the most efficient secretory machineries of host cells (Su et al., 2016; Proteins of the early secretory pathway bound by SARS-CoV-2 As the entire world asks for ways to stop CoV-2, many laboratories are investigating the virus's Achilles heel(s). The role of glycosylation and protein quality control in SARS-CoV-2 infections Most CoVs bud at the ERGIC level ( Fig. 1) and are then transported along the exocytic pathway (Klumperman et al., 1994; Stertz et al., 2007) . We observed enrichment for five host-derived virus-interacting proteins (GOLGB1, PDE4DIP, TOR1A, HMOX1, and HYOU1) involved in different processes and related to quality control and ER-Golgi homeostasis maintenance. cache = ./cache/cord-287477-aios0h8s.txt txt = ./txt/cord-287477-aios0h8s.txt === reduce.pl bib === id = cord-287604-w0ktwl8q author = Patel, Chirag N. title = Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4840 sentences = 259 flesch = 46 summary = We selected HE as a target in this study to identify potential inhibitors using a combination of various computational approaches such as molecular docking, ADMET analysis, dynamics simulations and binding free energy calculations. Virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin as potential HE inhibitors with better binding energy. In this study, we employed virtual screening approach to screen NPACT (Naturally occurring Plant-based Anti-cancer Compound activity-Target database) compounds against HE target [32, 35] and the best-scoring molecules were validated using molecular dynamics simulations analysis to better understand the interactions and conformational changes to inhibit HE target [36, 37] . Different molecular modeling techniques were employed in this study viz, molecular docking, Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) prediction, molecular dynamics simulations, and binding free energy calculations to obtain new leads from NPACT compounds [38] . cache = ./cache/cord-287604-w0ktwl8q.txt txt = ./txt/cord-287604-w0ktwl8q.txt === reduce.pl bib === id = cord-287653-69nfi379 author = Lacy, J. Matthew title = COVID-19: POSTMORTEM DIAGNOSTIC AND BIOSAFETY CONSIDERATIONS date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5202 sentences = 304 flesch = 45 summary =  Prosect cases in negative pressure isolation suite with at least 6-12 air changes per hour  Doff contact and droplet precaution PPE, as well as N95 respirator or PAPR  Limit personnel in the isolation suite to the minimum necessary to perform the examination  Employ splash and aerosol reduction techniques during prosection; oscillating saws are discouraged but if used should have vacuum shroud attachment  Use caution when handling sharps; allow only one person to prosect at a given time  Ensure a technician is outside isolation room to monitor procedure and provide support as needed  Procure synthetic nasopharyngeal (+/-lung) respiratory swabs in sterile tubes of 2-3 ml of viral transport media for SARS-CoV-2 testing as needed  Carefully decontaminate morgue surfaces and outer body bag following autopsy  Ensure body is fully enclosed in a secure bag, tag as infectious and ensure funeral home is informed  Consider modifying release procedures to prevent bag being opened in morgue for identification  Perform hand hygiene after doffing PPE A C C E P T E D cache = ./cache/cord-287653-69nfi379.txt txt = ./txt/cord-287653-69nfi379.txt === reduce.pl bib === id = cord-287321-1ro10ujr author = Alpaydin, Aylin Ozgen title = Clinical and Radiological Diagnosis of Non‐SARS‐CoV‐2 Viruses in the Era of Covid‐19 Pandemic date = 2020-08-08 pages = extension = .txt mime = text/plain words = 3288 sentences = 197 flesch = 48 summary = INTRODUCTION: Following the announcement of first coronavirus disease 2019 (COVID‐19) case on March 11, 2020, in Turkey we aimed to report the co‐infection rates, and the clinical, laboratory, radiological distinctive features of viral pneumonia caused by viruses other than severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The spectrum of SARS-CoV-2 originated human disease named as coronavirus disease 2019 (COVID19) changes from little to no symptoms to severe pneumonia and acute respiratory distress syndrome 4 . Under these conditions; it was aimed to report the co-infection rates, the prevalence, clinical, laboratory and radiological characteristics of non-SARS-CoV-2 respiratory pathogens in a teaching hospital organized as a pandemic hospital immediately at the beginning of the pandemic in Turkey. Radiological assessments for the more frequently identified Non-SARS-CoV-2 pathogens (both metapneumovirus and rhinovirus) were compatible with indeterminate or atypical for COVID-19 disease. Some clinical, laboratory and especially radiological findings may aid in the differential diagnosis of non-SARS-CoV-2 pathogens from COVID-19. cache = ./cache/cord-287321-1ro10ujr.txt txt = ./txt/cord-287321-1ro10ujr.txt === reduce.pl bib === id = cord-287220-mpnuhqwg author = Giuliani, C. title = Breastfeeding during the COVID-19 pandemic: suggestions on behalf of Woman Study Group of AMD date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2758 sentences = 161 flesch = 50 summary = Woman Study Group of AMD, after reviewing current knowledge about COVID-19 vertical transmission and the compatibility of breastfeeding in COVID-19 mother, the available recommendations from Health Care Organizations and main experts opinions, issued the following suggestions on breastfeeding during the COVID-19 pandemic, addressed both to mothers with and without diabetes It should be considered that following suggestions may change in the future when more evidence is acquired regarding SARS-Cov2 infection. Chen Y et al 5 reported four cases of live born infants, born to pregnant women with the COVID-19 infection in Wuhan: newborns had no clinical signs of disease and were tested negative for the virus at delivery. 14 Moreover, some experts speculate that, similar to the 2002-2003 SARS-Co-V epidemic 15 , specific SARS-CoV-2 antibodies pass via the breast milk from the COVID-19 mother to the infant within a few days after the onset of the disease, possibly moderating the clinical expression of infant's infection 16 . cache = ./cache/cord-287220-mpnuhqwg.txt txt = ./txt/cord-287220-mpnuhqwg.txt === reduce.pl bib === id = cord-287247-vv0zc0gd author = Gutman, Julie R. title = Malaria and Parasitic Neglected Tropical Diseases: Potential Syndemics with COVID-19? date = 2020-06-01 pages = extension = .txt mime = text/plain words = 4248 sentences = 236 flesch = 41 summary = With many LMICs implementing movement restrictions or ordering their populations to stay at home to limit SARS-CoV-2 transmission, the threat to essential health services is likely to be immediate, causing delays to diagnosis and treatment for other diseases, including malaria and NTDs. During the Ebola epidemic in West Africa, there were substantial reductions in all-cause outpatient visits and patients treated with antimalarial drugs 2 ; modeling the potential for similar disruptions in malaria control due to COVID-19 suggests that there could be up to an estimated 769,000 deaths due to malaria in 2020 (approximately double the number seen in 2018), mostly among children younger than 5 years. 58 Thus, coinfection with parasitic NTDs could result in altered risks and severity of clinical manifestations of SARS-CoV-2 infection, with the potential for decreased development of immunity with increased viral loads. cache = ./cache/cord-287247-vv0zc0gd.txt txt = ./txt/cord-287247-vv0zc0gd.txt === reduce.pl bib === id = cord-287459-k9x3z2h1 author = Abu-Farha, Mohamed title = The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date = 2020-05-17 pages = extension = .txt mime = text/plain words = 4822 sentences = 253 flesch = 41 summary = Since lipids play a crucial function in the viral life cycle, we asked whether drugs targeting lipid metabolism, such as statins, can be utilized against SARS-CoV-2 and other viruses. Similarly, increased expression of age-dependent phospholipase A2 group IID (PLA2G2D), an enzyme that usually contributes to anti-inflammatory/pro-resolving lipid mediator expression, resulted in worsened outcomes in aged mice infected with SARS-CoV, suggesting that inhibition of such factor could represent a potential therapeutic option [36] . Of high relevance to this review and the ongoing COVID-19 pandemic is the role of lipid rafts in viral entry into the host cells. Taken together, these studies suggest a beneficial impact for statins and potentially other lipid-lowering drugs such as PCSK9 inhibitors for treatment of COVID-19, especially that of the most severely infected people which are suffering from cardiovascular disease and diabetes [55] . cache = ./cache/cord-287459-k9x3z2h1.txt txt = ./txt/cord-287459-k9x3z2h1.txt === reduce.pl bib === id = cord-287658-c2lljdi7 author = Lopez-Rincon, Alejandro title = Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4766 sentences = 253 flesch = 55 summary = The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. cache = ./cache/cord-287658-c2lljdi7.txt txt = ./txt/cord-287658-c2lljdi7.txt === reduce.pl bib === id = cord-287628-lzqsh3jf author = Gomersall, Charles D. title = Transmission of SARS to healthcare workers. The experience of a Hong Kong ICU date = 2006-02-25 pages = extension = .txt mime = text/plain words = 2608 sentences = 151 flesch = 58 summary = CONCLUSIONS: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff exposure times and a sub-standard physical environment. Conclusions: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff If our protective measures were effective when fully developed and rigorously applied, then the logical con-clusion is that intensive care units should have strategies in place to prevent infection of healthcare workers; all staff should be fully aware of the procedures and be fully trained in the use of protective equipment. In summary, our data indicate that, with infection control measures, the risk to ICU healthcare workers of acquiring SARS is low, despite prolonged exposure to patients with SARS. cache = ./cache/cord-287628-lzqsh3jf.txt txt = ./txt/cord-287628-lzqsh3jf.txt === reduce.pl bib === id = cord-287644-ay0vv27m author = Blackall, Douglas title = Rapid Establishment of a COVID‐19 Convalescent Plasma Program in a Regional Healthcare Delivery Network date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3764 sentences = 215 flesch = 49 summary = Overall, 6 major implementation "themes" were addressed: (1) registration of individual hospitals and principle investigators with a national investigational new drug research protocol, (2) collaboration with a regional blood donor center, (3) targeted recruitment of convalesced donors, (4) information technology issues related to all aspects of CCP ordering, distribution, and transfusion, (5) prioritization of patients to receive CCP, and (6) evaluation of CCP products including antibody characteristics and patient response to therapy. The Mayo IND provides specific criteria for patient inclusion in the protocol; namely, that they have positive molecular testing for SARS-CoV-2, are an adult (≥ 18 years of age), and have met defined clinical criteria qualifying them as having severe or life-threatening COVID-19. randomized controlled study, this protocol provided the infrastructure to initiate a convalescent plasma transfusion program in the SSM-STL network, which is the basis for this report. cache = ./cache/cord-287644-ay0vv27m.txt txt = ./txt/cord-287644-ay0vv27m.txt === reduce.pl bib === id = cord-288146-xqxznv1r author = Kohyama, Shunsuke title = Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date = 2009-09-11 pages = extension = .txt mime = text/plain words = 6140 sentences = 347 flesch = 59 summary = title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a As shown in Fig. 2 , significant numbers of IFN-␥-producing CD8 + T cells (p < 0.01) were detected in mice immunized with syngeneic cells pulsed with each of nine pp1aderived peptides including pp1a-2187, -2207, -2340, -2546, -2755, -2990, -3444, -3687, and -3709 , suggesting that these nine peptides may be HLA-A*0201-restricted CTL epitopes derived from SARS-CoV pp1a protein. After HHD mice were immunized once with one of the nine liposomal peptides, spleen cells of them were prepared, stimulated with a relevant synthetic peptide, and stained for their expression of surface CD8 and intracellular IFN-␥. In summary, we have identified seven HLA-A*0201-restricted CTL epitopes derived from pp1a protein of SARS-CoV using computational algorithms, HLA-A*0201 transgenic mice and the surface-linked liposomal peptide. cache = ./cache/cord-288146-xqxznv1r.txt txt = ./txt/cord-288146-xqxznv1r.txt === reduce.pl bib === id = cord-288051-wp8v2mc5 author = Sánchez-González, Álvaro title = What Should Be Known by a Urologist About the Medical Management of COVID-19’s Patients? date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3616 sentences = 267 flesch = 47 summary = Seven days after the clinical onset, the risk of transmission decreases in mildsymptomatic patients, but it may be extended over 24 days in severe cases [11•, 15] . The clinical spectrum of SARS-CoV-2 infection varies widely, including asymptomatic infection, mild upper respiratory tract illness, severe viral pneumonia with respiratory failure, and even death [9, 11•] (Fig. 1) . Corticosteroids are recommended in the treatment of septic shock, exacerbation of chronic obstructive respiratory disease and these COVID-19's patients with respiratory deterioration and quick radiological progression associated with sings of cytokine storm (cytopenia, maintained fever, an increase of inflammatory reactants: D-dimer > 1000 ng/mL, ferritin > 1000 ng/mL, fibrinogen > 100 ng/mL, IL-6 > 40 pg/mL) [6, 23••] . Results from 237 patients, 158 assigned to remdesivir, showed no differences in time to clinical improvement, 28day mortality, oxygen support, hospitalization, or viral load. Clinical management of severe acute respiratory infection (SARI) when COVID-19 disease is suspected. Effective treatment of severe COVID-19 patients with tocilizumab cache = ./cache/cord-288051-wp8v2mc5.txt txt = ./txt/cord-288051-wp8v2mc5.txt === reduce.pl bib === id = cord-287682-97fquq16 author = Daubin, Cédric title = Is a COPD patient protected against SARS-CoV-2 virus? date = 2020-10-03 pages = extension = .txt mime = text/plain words = 745 sentences = 55 flesch = 50 summary = In addition, cigarette smoke and COPD were reported to up-regulate Angiotensin-converting enzyme 2 (ACE-2) expression, which plays a key role in the pathogenesis of SARS-CoV-2 in lower airways [2] . Considering a significant inverse relationship between ACE-2 gene expression and the severity of COPD [2] , one hypothesis could be that COPD protects against SARS-CoV-2 through a TMPRSS2 inhibitor activity or by an a downregulation of the inflammatory pathway limiting severe forms of infection. Interestingly, as reported by Halpin et al., inhaled corticosteroids, used by COPD patients can reduce the risk of viral infection. Therefore, inhaled corticosteroids in combination with bronchodilators could limit expression or activity of transmenbrane serine protease TMPRSS2 which facilitates SARS-CoV-2 entry in cells. Surprisingly current smokers (i.e., a large part of COPD patients) could be protected against SARS-CoV-2 infection [4] . Sin DD (2020) ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19 cache = ./cache/cord-287682-97fquq16.txt txt = ./txt/cord-287682-97fquq16.txt === reduce.pl bib === id = cord-288484-qy619tfg author = Bernard‐Valnet, R. title = Two patients with acute meningoencephalitis concomitant with SARS‐CoV‐2 infection date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1138 sentences = 73 flesch = 40 summary = We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. Patient 1 was a 64-year-old woman without psychiatric history, known to have had contact with SARS-CoV-2 (her husband tested positive 15 days before) and presenting for 5 days with flu-like symptoms (mild asthenia, myalgia, cough) without fever, acutely developed psychotic symptoms. Cerebral magnetic resonance imaging was normal, but her lumbar puncture was compatible with viral meningoencephalitis (Table 1) and SARS-CoV-2 was detected in her nasopharyngeal swab. A 67-year-old woman, already diagnosed with SARS-CoV-2 infection for 17 days with mild respiratory symptoms, presented an intense wake-up headache. However, CSF SARS-CoV-2 and viral/bacterial pathogen polymerase chain reaction tests were negative (Table 1 ). To conclude, we report the first temporal association between acute SARS-CoV-2 infection and aseptic encephalitis with focal neurological symptoms and signs. cache = ./cache/cord-288484-qy619tfg.txt txt = ./txt/cord-288484-qy619tfg.txt === reduce.pl bib === id = cord-288070-qwax5tg9 author = Robilotti, E. V. title = Determinants of Severity in Cancer Patients with COVID-19 Illness date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2652 sentences = 166 flesch = 48 summary = Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. On multivariate analysis, age ≥ 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. In this study, we report on the epidemiology of COVID-19 illness experienced at our cancer center over the last month, during the height of incident cases in New York City, and offer an analysis of risk factors for severe infection that is pertinent to cancer patient populations. cache = ./cache/cord-288070-qwax5tg9.txt txt = ./txt/cord-288070-qwax5tg9.txt === reduce.pl bib === id = cord-287847-rmhvc5n5 author = Miles, Brett A. title = Tracheostomy during SARS‐CoV‐2 pandemic: Recommendations from the New York Head and Neck Society date = 2020-04-20 pages = extension = .txt mime = text/plain words = 3458 sentences = 166 flesch = 38 summary = Patients with significant medical comorbidities, acute respiratory distress syndrome/severe respiratory failure and a low chance of recovery who are infected with SARS-CoV-2 should be carefully evaluated, and discussions with family members, consultants, institutional ethics committees and the treating team should focus on overall prognosis and goals of care prior to performing tracheostomy as a routine matter of care. Although there are limited data on the current pandemic to fully inform personal protective equipment (PPE) recommendations, performing tracheostomy in an actively infected SARS-CoV-2 patient is certainly a high-risk procedure for health care workers. Techniques to manage the acute airway with endotracheal intubation, video laryngoscope for example, should be utilized if possible to avoid emergent tracheostomy in SARS-CoV-2 patients due to the high risk of unsafe conditions and health care worker contaminations. • When clinically appropriate, delay of tracheostomy procedures is recommended to allow for reduced viral load and to decrease the risk of nosocomial infection to critical health care providers. cache = ./cache/cord-287847-rmhvc5n5.txt txt = ./txt/cord-287847-rmhvc5n5.txt === reduce.pl bib === id = cord-288010-i9zrojoo author = Jia, Yuanyuan title = Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China date = 2020-05-15 pages = extension = .txt mime = text/plain words = 1132 sentences = 64 flesch = 58 summary = title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China 6 However, limited studies on full-length genome characterization of SARS-CoV-2 from COVID-19 cases imported from abroad. Here, we characterized the genotype and mutation characteristics of SARS-CoV-2 isolated from eight imported cases from abroad in Yunnan, China. To further characterize the characteristics of virus variation, the sequence analyses based on SARS-CoV-2 full-length nucleotide and amino acid sequences was performed using the strain Wuhan-Hu-1 (Genbank no. Moreover, three novel mutations, including D1962V in nsp3 from the strain YN_Im03, L1375F in nsp3 and A829T in S protein from the isolate YN_Im04 were first identified in this study according to the comparison with 11,231 genomic sequences available at GISAID on 4/26/2020. In summary, we characterized the full-length genomes of SARS-CoV-2 strains from eight COVID-19 cases imported from abroad in Yunnan, China. cache = ./cache/cord-288010-i9zrojoo.txt txt = ./txt/cord-288010-i9zrojoo.txt === reduce.pl bib === id = cord-288255-p8uzrsbd author = Goossens, Gijs H. title = Obesity and COVID-19: A Perspective from the European Association for the Study of Obesity on Immunological Perturbations, Therapeutic Challenges, and Opportunities in Obesity date = 2020-08-13 pages = extension = .txt mime = text/plain words = 7043 sentences = 333 flesch = 36 summary = authors: Goossens, Gijs H.; Dicker, Dror; Farpour-Lambert, Nathalie J.; Frühbeck, Gema; Mullerova, Dana; Woodward, Euan; Holm, Jens-Christian Evidence from studies in humans indicates that people with obesity are characterized by systemic low-grade inflammation, higher susceptibility to infections, dampened immune response to infectious agents, as well as higher morbidity and mortality associated with infections, and demonstrate an impaired immune response to vaccinations and antimicrobial treatment [25] [26] [27] [28] . Together, these findings imply that evaluation of cytokine profiles and immune cell subsets in patients with SARS-CoV-2 infection, and a deeper understanding of the underlying processes, will significantly contribute to better treatment strategies and clinical management of COVID-19 [37] . At the same time, the rapidly emerging clinical data require ongoing scrutiny to understand not only the risks and benefits of single drugs to tackle COVID-19, but also the interaction with pharmacological agents commonly used in people with obesity and related NCDs, including type 2 diabetes and cardiovascular diseases, who are especially at risk of or hospitalized with SARS-CoV-2 infection. cache = ./cache/cord-288255-p8uzrsbd.txt txt = ./txt/cord-288255-p8uzrsbd.txt === reduce.pl bib === id = cord-287488-h102xn29 author = Araujo, Danielle Bastos title = SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date = 2020-10-23 pages = extension = .txt mime = text/plain words = 3927 sentences = 223 flesch = 53 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. cache = ./cache/cord-287488-h102xn29.txt txt = ./txt/cord-287488-h102xn29.txt === reduce.pl bib === id = cord-287758-da11ypiy author = Mônica Vitalino de Almeida, Sinara title = COVID-19 therapy: what weapons do we bring into battle? date = 2020-09-10 pages = extension = .txt mime = text/plain words = 17412 sentences = 1034 flesch = 45 summary = The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. cache = ./cache/cord-287758-da11ypiy.txt txt = ./txt/cord-287758-da11ypiy.txt === reduce.pl bib === id = cord-287448-hwsr1804 author = Bigaut, Kévin title = Guillain-Barré syndrome related to SARS-CoV-2 infection date = 2020-05-27 pages = extension = .txt mime = text/plain words = 903 sentences = 62 flesch = 54 summary = Twenty-one days after the beginning of respiratory symptoms, he presented with in a rapidly progressive manner paraesthesia, hypoesthesia, and distal weakness in the lower limbs. CSF results showed normal cell count (1 × 10 6 /L), increased protein level (0.94 g/L), and negative SARS-CoV-2 on RT-PCR assay. CSF results showed subnormal cell count (6 × 10 6 /L), increased protein level (1.06 g/L), and negative SARS-CoV-2 on RT-PCR assay. We reported here 2 cases of GBS related to SARS-CoV-2 infection with neurologic improvement on IVIg, adding to few cases of GBS, one case of Miller Fisher syndrome, and one case of polyneuritis cranialis already published. 3 However, previous reports and our cases suggest that GBS associated with SARS-CoV-2 infection could start between 5 and 21 days after the SARS-CoV-2 clinical symptoms. 4 It could follow a postinfectious profile as reported on Middle East respiratory syndrome coronavirus infection in 4 patients with Bickerstaff's encephalitis overlapping with GBS. cache = ./cache/cord-287448-hwsr1804.txt txt = ./txt/cord-287448-hwsr1804.txt === reduce.pl bib === id = cord-288017-f9b3t0ts author = Kabeerdoss, Jayakanthan title = Understanding immunopathological fallout of human coronavirus infections including COVID‐19: Will they cross the path of rheumatologists? date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4281 sentences = 280 flesch = 46 summary = High risks for fatal disease in COVID‐19 include older age, metabolic syndrome, male gender, and individuals who develop delayed type I IFN response. 54 In a macaque model of SARS-CoV infection too, aged macaques had more severe lung pathology, lower expression of type I IFN and higher expression of pro-inflammatory cytokines as compared to younger macaques. 80 to patients with COVID-19 that it is a mild immunomodulatory F I G U R E 2 Hydroxychloroquine (HCQ) inhibits SARS-CoV-2 entry and inhibits virus-induced type I interferon (IFN) signaling and proinflammatory cytokines production. While male gender, older age and people with metabolic syndrome seem to be at a higher risk of contracting more severe SARS-CoV-2 infection, younger females of African and Asian ancestry have higher risk for developing SLE; male gender among lupus patients, however, is an independent risk factor for severe disease. Evasion by stealth: inefficient immune activation underlies poor T cell response and severe disease in SARS-CoV-infected mice cache = ./cache/cord-288017-f9b3t0ts.txt txt = ./txt/cord-288017-f9b3t0ts.txt === reduce.pl bib === id = cord-287742-y1j9x5ne author = Lee, Kai Wei title = Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis date = 2020-10-06 pages = extension = .txt mime = text/plain words = 6545 sentences = 292 flesch = 45 summary = Therefore, we performed a systematic review and meta-analysis of currently available epidemiological, clinical, and laboratory data related to both stroke and COVID-19 infection. We, therefore, performed a systematic review and metaanalysis involving the epidemiological, clinical presentation, imaging characteristics, and laboratory finding related to both stroke and COVID-19 infection. The following data were extracted from every study: the last name of the first author, year of publication, country, severity status, study design, patient characteristics (ethnicity composition, gender, and mean age), comorbidities (diabetes, hyperlipidemia, hypertension, ischemic heart disease, heart failure, previous stroke, chronic kidney disease/end-stage renal disease, number of stroke patients per overall participants, any information relevant to strokes such as the location of stroke [arterial or venous]), types of stroke (ischemic or haemorrhagic), classification of stroke, mortality rate, and blood parameters. The aim of this current study is to perform a systematic review and meta-analysis concerning the epidemiological, clinical presentation, imaging characteristics, and laboratory findings related to both stroke and COVID-19 infection. cache = ./cache/cord-287742-y1j9x5ne.txt txt = ./txt/cord-287742-y1j9x5ne.txt === reduce.pl bib === id = cord-288153-2qsh2dlk author = Hays, Priya title = Clinical sequelae of the novel coronavirus: does COVID-19 infection predispose patients to cancer? date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4322 sentences = 225 flesch = 41 summary = Major signaling pathways implicated in aberrant cellular growth are activated, the ensuing cytokine storm weakens the immune system response to tumors, and patients may develop cancer as a result of superimposed mutagenic and/or carcinogenic events. There may be a distinct association between novel coronavirus infection and the onset of cancer through the activation of the MAPK and JAK-STAT signaling pathways and the NF-κB transcription factor. The turning on of oncogenic signaling pathways and the acute inflammatory response that results upon coronavirus infection can be hypothesized as being cancer inducing, or leading to the risk of developing cancer, especially if the patient has a superimposed mutagenic or carcinogenic event occurring concomitantly, even if the virus does not cause a chronic infection like viruses such as HCV, HCV and EBV. Oncologic sequelae of the novel coronavirus • Viral infection induces a robust immune response, a 'cytokine storm' leading to tissue damage and inflammation, which may predispose to cancer. cache = ./cache/cord-288153-2qsh2dlk.txt txt = ./txt/cord-288153-2qsh2dlk.txt === reduce.pl bib === id = cord-288231-vg8bwed9 author = Haagmans, Bart L. title = The Application of Genomics to Emerging Zoonotic Viral Diseases date = 2009-10-26 pages = extension = .txt mime = text/plain words = 3406 sentences = 146 flesch = 35 summary = Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. cache = ./cache/cord-288231-vg8bwed9.txt txt = ./txt/cord-288231-vg8bwed9.txt === reduce.pl bib === id = cord-288651-bgo8istm author = SHI, Yi title = Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date = 2005-03-17 pages = extension = .txt mime = text/plain words = 3062 sentences = 242 flesch = 62 summary = RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. The results show that all siRNA duplexes specifically reduced SARS-CoV genes expression to different extents compared with the control (Fig. 1) . Kinetic study results (Fig. 2B ) revealed a continuous increase in the specific inhibition of SARS-CoV genes expression by No. 5, No. 6, and No. 16 siRNA from 24 to 72 h after transfection. cache = ./cache/cord-288651-bgo8istm.txt txt = ./txt/cord-288651-bgo8istm.txt === reduce.pl bib === id = cord-288632-2aliqy8p author = Phillips, Nicole title = The Perfect Storm: COVID-19 Health Disparities in US Blacks date = 2020-09-23 pages = extension = .txt mime = text/plain words = 4575 sentences = 210 flesch = 36 summary = Specifically, Fig. 1 illustrates a conceptual model through which psychological influences (stress, anxiety, depression), pre-existing/comorbid disease (e.g., HTN, T2DM), and COVID-19 interconnect on the basis of known and unknown genetic variations that translate into human health outcomes and molecular modes of viral pathogenesis. Importantly, it is the interplay between key environmental exposures (stress; social determinants of health, SDH) and genetic predisposition for aspects of viral pathogenesis and/or comorbid disease (e.g., type 2 diabetes mellitus, T2DM; hypertension, HTN) that ultimately converges on COVID-19 manifestation and affects mortality . While there is conflicting data regarding the effects of variants in all three of the candidate genes discussed here, the remarkable relevance of associated phenotypes to COVID-19 pathophysiology together implies that genetic polymorphisms which regulate immune and stress responses may interact to affect underlying disease risk and, simultaneously, SARS-CoV-2 pathogenicity. cache = ./cache/cord-288632-2aliqy8p.txt txt = ./txt/cord-288632-2aliqy8p.txt === reduce.pl bib === id = cord-288584-wql253d8 author = Rivera-Oyola, Ryan title = Dermatologic findings in two patients with COVID-19 date = 2020-04-28 pages = extension = .txt mime = text/plain words = 362 sentences = 28 flesch = 46 summary = Cutaneous involvement was observed both at symptom onset (8 patients) and after hospitalization (10 patients).(4) A study from Thailand described a dengue-like rash in a COVID-19 patient who was initially misdiagnosed with dengue.(5) Additionally, a recent letter reported a COVID-19 patient who simultaneously developed a non-pruritic, diffuse body rash, myalgia and cephalgia. (6) It is worth noting the variability in clinical presentation of cutaneous findings following SARS-CoV-2 infection. Similarly, we observed a diversity of morphological presentations and variability in time to onset of cutaneous manifestations in the literature (4) (5) (6) . It is unlikely that our patients' rashes were due to a medication reaction as there had been no changes to their medication regimen, the rashes had an acute onset following COVID-19 symptom onset, and, in Case 1, the biopsy did not illustrate tissue eosinophilia. At present, there is limited data regarding the cutaneous manifestations following SARS-CoV-2 infection. COVID-19 should be considered in the initial differential diagnosis for a patient with acute skin changes following flu-like symptoms. cache = ./cache/cord-288584-wql253d8.txt txt = ./txt/cord-288584-wql253d8.txt === reduce.pl bib === id = cord-288025-skkpkqw6 author = Eslami, Hadi title = The role of environmental factors to transmission of SARS-CoV-2 (COVID-19) date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4860 sentences = 269 flesch = 54 summary = Human-to-human transmission of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs most often when people are in the incubation stage of the disease or are carriers and have no symptoms. Therefore, in this study, was discussed the role of environmental factors and conditions such as temperature, humidity, wind speed as well as food, water and sewage, air, insects, inanimate surfaces, and hands in COVID-19 transmission. This study aimed to investigate the effect and role of various factors, including environmental factors (climate change, water transfer, air, and food), disinfection of surfaces, and hands in the transmission and prevalence of COVID-19 pandemics. The most well-known methods of surface disinfection to remove SARS-CoV-2 virus are, in short, the use of ethyl alcohol (62-70%), or hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%, dilution ratio 1 to 50) with a contact time of 1 min (Henwood 2020; WHO 2014) . cache = ./cache/cord-288025-skkpkqw6.txt txt = ./txt/cord-288025-skkpkqw6.txt === reduce.pl bib === id = cord-288500-ko4eda9w author = Zheng, Ruijun title = Prevalence and associated factors of depression and anxiety among nurses during the outbreak of COVID-19 in China: A cross-sectional study date = 2020-10-23 pages = extension = .txt mime = text/plain words = 4678 sentences = 260 flesch = 52 summary = The results indicated that COVID-19-related stress, relationship quality with family, and demographic characteristics were associated with depression, anxiety, and perceived health status. A study reported that health care workers at high risk of contracting SARS were more likely to have a higher prevalence of depression and anxiety, and develop post-traumatic stress during the SARS epidemic (McAlonan et al., 2007) . In this study, we hypothesize that COVID-19-related stress, relationship quality with family, and perceived health status are associated with the risk of depression and anxiety. The questionnaire contained ten main items: unknown origin of COVID-19, fear of infection, lack of effective treatment, poor patient compliance, nursing workload, poor social support, parent-child relationship quality, couple relationship quality, relationship quality with other family members, and perceived health status. The main findings indicated that nurses experiencing COVID-19-related stress and poor relationship quality with family were more likely to develop depression and anxiety symptoms and have health concerns. cache = ./cache/cord-288500-ko4eda9w.txt txt = ./txt/cord-288500-ko4eda9w.txt === reduce.pl bib === id = cord-288284-fghu8ouc author = Hawryluck, Laura title = Clinical review: SARS – lessons in disaster management date = 2005-01-13 pages = extension = .txt mime = text/plain words = 4269 sentences = 182 flesch = 45 summary = Infectious diseases, whether they be natural (e.g. SARS [severe acute respiratory syndrome] and influenza) or the result of bioterrorism, have the potential to create a large influx of critically ill into our already strained hospital systems. Core to any disaster management plan are leaders with clear responsibilities to coordinate efforts and develop policies to contain the disease; to coordinate resource allocation and manpower; to advise and share information regarding infection control and treatment; to share data and research endeavours; to maintain staff morale; and to provide information to various levels of government, health care institutions, front-line workers and the public [1, 13] . The model we propose (Fig. 1 ) is one of a Central Critical Care Crisis Team, composed of leaders of different subteams of multidisciplinary professionals responsible for domains of crucial importance: clinical management, infection control, education, communication, team morale, manpower and system thinking, data collection, research and, finally, lobbying to ensure resources are available to meet critical care needs. cache = ./cache/cord-288284-fghu8ouc.txt txt = ./txt/cord-288284-fghu8ouc.txt === reduce.pl bib === id = cord-287991-10jz1dz2 author = Goshen-Lago, Tal title = The Potential Role of Immune Alteration in the Cancer–COVID19 Equation—A Prospective Longitudinal Study date = 2020-08-26 pages = extension = .txt mime = text/plain words = 4497 sentences = 235 flesch = 47 summary = Conclusion: Our results indicate a similar rate of asymptomatic COVID19 infection in cancer patients and healthcare workers in a longitudinal study throughout the pandemic time. During the study interval, there was no documented symptomatic case of COVID19 among the recruited participants, nor in the general patient population of the cancer center or in the healthcare workers cohort. Furthermore, when analyzing the myeloid lineage, we found a substantial increase in myeloid cells in cancer patients compared to healthcare workers (both SARS-CoV-2 IgG-), in line with previous studies [11, 12] . Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. cache = ./cache/cord-287991-10jz1dz2.txt txt = ./txt/cord-287991-10jz1dz2.txt === reduce.pl bib === id = cord-288660-z0k2ui3y author = Edler, Alice A. title = Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology date = 2006-02-28 pages = extension = .txt mime = text/plain words = 2409 sentences = 135 flesch = 48 summary = Abstract Avian flu, influenza A subtype H5N1, is an emergent and virulent disease that poses a threat to the health and safety of the world community. Avian flu is responsible for the current outbreak in Asia; H5N1 has now displayed probable human-to-human transmission; it could be a harbinger of a global epidemic. Subtype H5N1, currently known as avian or bird flu, is of particular interest because of its increasing pathogenicity and ability to form a new viral subtype to which there is no native immunity in human hosts. However, if individuals are infected, the current case-fatality rate for avian flu is thought to be greater than 50% in humans [2] and greater than 90% in birds and other mammals. The key to addressing the threat of avian flu in all populations, including anesthesiologists, is prevention of the disease and containment of its spread through traditional, public health preparedness: basic hygiene, Universal Precautions, and special procedures designed to prevent exposure and contain infection in health-care settings. cache = ./cache/cord-288660-z0k2ui3y.txt txt = ./txt/cord-288660-z0k2ui3y.txt === reduce.pl bib === id = cord-288066-sh6n2c3n author = Mohamed, Mohamed S. title = Sex differences in COVID-19: the role of androgens in disease severity and progression date = 2020-11-11 pages = extension = .txt mime = text/plain words = 2489 sentences = 155 flesch = 41 summary = Variants in the androgen receptor gene correlate with androgen sensitivity and are implicated in diseases like androgenetic alopecia and prostate cancer, conditions that have been associated with worse COVID-19 outcomes and hospitalization. The proposed mechanism behind this effect is based on the idea that androgen receptor and, subsequently, TMPPRSS2 expression affects the SARS-COV2 virus ability to enter host cells and its spike proteins affinity to bind ACE2 receptors (Fig. 1 ). SARS-CoV2 spike proteins are then primed by TMPRSS2, allowing the interaction with ACE2 receptors to enter host cells Fig. 2 Theoretical mechanisms suggesting CAG repeats length and associated androgen sensitivity as a predictor for COVID-19 disease severity lack of control groups or testosterone levels prior to infection, the results warrant consideration. Increased androgen receptor expression might lead to a higher risk of acquiring a severe COVID-19 disease by promoting TMPRSS2 transcription (Fig. 2) . Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men cache = ./cache/cord-288066-sh6n2c3n.txt txt = ./txt/cord-288066-sh6n2c3n.txt === reduce.pl bib === id = cord-288357-3mqoexcr author = Liu, Pei title = Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds date = 2020-08-01 pages = extension = .txt mime = text/plain words = 1882 sentences = 148 flesch = 61 summary = title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds We identified several N-substituted isatin compounds as potent SARS-CoV-2 3C-like protease inhibitors. [4, [9] [10] [11] [12] To date, several potential SARS-CoV-2 3CL pro inhibitors have been reported from compound library screening, [8] rational design [8, 13] , [14] and testing of ingredients from traditional Chinese medicine. Previously, we reported a series of N-substituted 5-carboxamide-isatin compounds as inhibitors of SARS CoV 3CL pro . [12] Apparently, the isatin scaffold with derivatization may also provide a good starting point for SARS CoV-2 3CL pro inhibitor development, because the two proteases share high sequence identity and the same active site. In conclusion, we have tested the inhibition activity of 29 N-substituted isatin derivatives against SARS-CoV-2 3CL pro . Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors substituted isatin compounds are potent SARS-CoV-2 3C-like protease inhibitors. cache = ./cache/cord-288357-3mqoexcr.txt txt = ./txt/cord-288357-3mqoexcr.txt === reduce.pl bib === id = cord-288644-ywaefpe8 author = Rodon, Jordi title = Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date = 2020-10-20 pages = extension = .txt mime = text/plain words = 7571 sentences = 449 flesch = 50 summary = We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. cache = ./cache/cord-288644-ywaefpe8.txt txt = ./txt/cord-288644-ywaefpe8.txt === reduce.pl bib === id = cord-288553-fez60jyn author = Colaneri, Marta title = Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. date = 2020-03-19 pages = extension = .txt mime = text/plain words = 537 sentences = 37 flesch = 53 summary = title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. Health care workers are at increased risk of acquiring COVID-19 infection, possibly due to direct contact with the patients. In this regard, studies suggest that surfaces and suspensions can carry HCoVs, increasing the risk of contact transmission that could lead to hospital acquired HCoVs infections [4, 5] Since February 21, 2020, when the first autochthonous case in Italy was confirmed, an overwhelming number of SARS-CoV-2 infections is continuously being detected, exceeding 8,000 cases at the time of writing. Fondazione IRCCS Policlinico San Matteo, Pavia, is a 1,300-bed tertiary teaching hospital in Northern Italy and a national SARS-CoV-2 referral center. Survival of human coronaviruses 229E and OC43 in suspension and after drying on surfaces: A possible source of hospital-acquired infections Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination cache = ./cache/cord-288553-fez60jyn.txt txt = ./txt/cord-288553-fez60jyn.txt === reduce.pl bib === id = cord-288824-sygnmiun author = Lam, SD title = SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date = 2020-08-19 pages = extension = .txt mime = text/plain words = 7353 sentences = 412 flesch = 54 summary = To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We correlated changes in the energy of the complex with changes in the structure of ACE2, chemical properties of residues in the binding interface, and experimental COVID-19 infection phenotypes from in vivo and in vitro animal studies. We used multiple methods to assess the relative change in binding energy (ΔΔG) of the SARS-CoV-2 S-protein:ACE2 complex following mutations in DC residues and DCEX residues that are likely to influence binding. Irrespective of host, the SARS-CoV-2 spike receptor binding domain is conserved (Fig. 4b) across tested human and animal associated SARS-CoV-2, suggesting mutations in the RBD are not required for infections observed in non-human species to date. cache = ./cache/cord-288824-sygnmiun.txt txt = ./txt/cord-288824-sygnmiun.txt === reduce.pl bib === id = cord-288692-v471648u author = Yip, Shea Ping title = Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date = 2005-10-01 pages = extension = .txt mime = text/plain words = 2387 sentences = 117 flesch = 51 summary = title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus We designed a 1-step real-time quantitative RT-PCR assay for SARS-CoV with the use of 2 TaqMan probes, instead of 1 probe, hybridizing to the same PCR product to further improve the sensitivity. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Quantitation of severe acute respiratory syndrome coronavirus genome by real-time polymerase chain reaction assay using minor groove binder DNA probe technology Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested-polymerase chain reaction cache = ./cache/cord-288692-v471648u.txt txt = ./txt/cord-288692-v471648u.txt === reduce.pl bib === id = cord-288398-vnra553x author = Yogeswaran, Athiththan title = Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1166 sentences = 78 flesch = 54 summary = authors: Yogeswaran, Athiththan; Gall, Henning; Tello, Khodr; Grünig, Ekkehard; Xanthouli, Panagiota; Ewert, Ralf; Kamp, Jan C.; Olsson, Karen M.; Wißmüller, Max; Rosenkranz, Stephan; Klose, Hans; Harbaum, Lars; Lange, Tobias J.; Opitz, Christian F.; Waelde, Andrea; Milger, Katrin; Sommer, Natascha; Seeger, Werner; Ghofrani, Hossein Ardeschir; Richter, Manuel J. title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study This multi-centre study provides evidence for a negative influence of these restrictions on patient care in pulmonary hypertension expert referral centres. The impact of SARS-CoV-2 associated restrictions on PH out-patient departments in Germany, however, has not been systematically evaluated. This study provides evidence for the significant impact of SARS-CoV-2 and the related restrictions on the medical care of patients with (suspected and subsequently confirmed) PH in Germany. Of note, the relative fraction of patients with subsequently initiated PH-specific therapy remained constant during the SARS-CoV-2 pandemic. cache = ./cache/cord-288398-vnra553x.txt txt = ./txt/cord-288398-vnra553x.txt === reduce.pl bib === id = cord-288558-rthnj6wd author = Cheng, V. C. C. title = Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date = 2004-02-15 pages = extension = .txt mime = text/plain words = 3801 sentences = 201 flesch = 46 summary = The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. In this retrospective study, we attempt to correlate the virus load of SARS coronavirus shedding from the nasopharynx, the upper end of the aerodigestive tract, with the presence of diarrhea in a cohort of patients with SARS. cache = ./cache/cord-288558-rthnj6wd.txt txt = ./txt/cord-288558-rthnj6wd.txt === reduce.pl bib === id = cord-288197-drto66xt author = Chen, Huijun title = Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records date = 2020-02-12 pages = extension = .txt mime = text/plain words = 3927 sentences = 225 flesch = 54 summary = METHODS: Clinical records, laboratory results, and chest CT scans were retrospectively reviewed for nine pregnant women with laboratory-confirmed COVID-19 pneumonia (ie, with maternal throat swab samples that were positive for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) who were admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from Jan 20 to Jan 31, 2020. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy. Evidence of vertical transmission was assessed by testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in amniotic fluid, cord blood, breastmilk, and neonatal throat swab samples from six of nine patients. Based on data from this small group of patients, there is currently no evidence of vertical transmission in pregnant women who develop COVID-19 pneumonia in the third trimester. cache = ./cache/cord-288197-drto66xt.txt txt = ./txt/cord-288197-drto66xt.txt === reduce.pl bib === id = cord-288403-m6qe57he author = Abbas, K. M. title = Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa date = 2020-05-26 pages = extension = .txt mime = text/plain words = 7098 sentences = 317 flesch = 45 summary = First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month Covid-19 risk period without catch-up campaigns. Specifically, we conducted a benefit-risk analysis of vaccine-preventable deaths averted by sustaining routine childhood immunisation in comparison to excess Covid-19 deaths from SARS-CoV-2 infections acquired by visiting routine vaccination service delivery points. The central estimates for benefit-risk ratio at the household level show the child deaths averted by continuing the routine childhood immunisation programmes (1-dose MCV1, RCV1, MenA, YFV for 9-month-old children) per excess Covid-19 death caused by SARS-CoV2 infections acquired in the vaccination service delivery points. cache = ./cache/cord-288403-m6qe57he.txt txt = ./txt/cord-288403-m6qe57he.txt === reduce.pl bib === id = cord-288271-p074ffpt author = Mathies, D. title = A Case of SARS‐CoV‐2‐pneumonia with successful antiviral therapy in a 77‐year‐old male with heart transplant date = 2020-04-21 pages = extension = .txt mime = text/plain words = 2473 sentences = 155 flesch = 52 summary = In this report, we present a 77‐year old patient with a heart transplant under relevant immunosuppressive therapy who was tested positive for SARS‐CoV‐2 after several days of dyspnoea, dry cough and light general symptoms. All rights reserved Diagnosis: SARS-CoV-2-Infection with viral pneumonia in a patient with heart transplant due to coronary artery disease with ischemic cardiomyopathy In this case the combination of radiologic signs of viral pneumonia and the supposed high-risk state of severe immunosuppression led to the decision to start an antiviral therapy immediately after receiving the positive rtPCR-results although the patient presented only mild symptoms. [13] A second question is whether patients with a solid organ transplant who receive immunosuppressive medication are at greater risk for a severe manifestation of a SARS-CoV 2-Infection or might even benefit from a reduced immunologic reaction. For SARS-CoV 2 we found two cases of patients with a heart transplant of which one had only mild manifestations and one required mechanical ventilation but survived [9] . cache = ./cache/cord-288271-p074ffpt.txt txt = ./txt/cord-288271-p074ffpt.txt === reduce.pl bib === id = cord-288670-1vlowf2n author = Yang, Naidi title = Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19 date = 2020-03-15 pages = extension = .txt mime = text/plain words = 4511 sentences = 207 flesch = 45 summary = As a result, the endocytic pathway including endosome and lysosome has become important targets for development of therapeutic strategies in combating diseases caused by CoVs. In this mini-review, we will focus on the importance of the endocytic pathway as well as the autophagy process in viral infection of several pathogenic CoVs inclusive of SARS-CoV, MERS-CoV and the new CoV named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and discuss the development of therapeutic agents by targeting these processes. Further studies also demonstrated that either ATG5 or ATG7, two of the key autophagy proteins in control of autophagosome biogenesis, is not required for viral replication in cells infected by MHV [28, 29] or by SARS-CoVs [30] . Taken together, establishing the role of endocytic pathway in viral entry is a major breakthrough in the mechanistic understanding of the CoVs infection, which offers great opportunity in development of novel therapeutic strategies for treatment of diseases such as SARS and COVID-19. cache = ./cache/cord-288670-1vlowf2n.txt txt = ./txt/cord-288670-1vlowf2n.txt === reduce.pl bib === id = cord-287501-7it4kh0e author = Roh, Changhyun title = A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date = 2012-05-03 pages = extension = .txt mime = text/plain words = 2964 sentences = 153 flesch = 45 summary = We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. 33 In this study, we report a novel approach for the inhibitor screening of SARS-CoV N protein using a quantum dots (QDs)-conjugated oligonucleotide system with wide applicability for facile and sensitive imaging analysis on a biochip. To the best of our knowledge, this is the first report on the inhibition effects of (-)-catechin gallate and (-)-gallocatechin gallate on SARS-CoV N protein using an optical nanoparticle-based RNA oligonucleotide platform. Among the polyphenolic compounds screened, (-)-catechin gallate and (-)-gallocatechin gallate showed high anti-SARS-CoV N protein activity. At a concentration of 0.05 µg mL -1 , (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a QDs-RNA oligonucleotide biochip platform. cache = ./cache/cord-287501-7it4kh0e.txt txt = ./txt/cord-287501-7it4kh0e.txt === reduce.pl bib === id = cord-289255-qwzg7prx author = Seligman, Stephen J. title = Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date = 2007-02-15 pages = extension = .txt mime = text/plain words = 642 sentences = 43 flesch = 55 summary = title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants have reported data on a 386-nt deletion in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) [1] . Because 1 patient had both the L386del variant and the wild-type variant in the same specimen, they raised the possibility that SARS-CoV exists as a quasi species, at least in some patients. Previous authors studying single-nucleotide variants from Beijing-area isolates in 2003 [2] and from the Singapore 2004 outbreak [3] have also found multiple viral sequences in the same sample that they attributed to quasi species. Although these 3 studies clearly establish the presence of a diversity of SARS-CoV genomes in individual patients, the issue of whether SARS-CoV quasi species exists remains open, particularly with respect to the 386-nt deletion. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? SARS-associated coronavirus quasispecies in individual patients cache = ./cache/cord-289255-qwzg7prx.txt txt = ./txt/cord-289255-qwzg7prx.txt === reduce.pl bib === id = cord-289101-ko1knslk author = Fu, Weihui title = An open-label, randomized trial of the combination of IFN-κ plus TFF2 with standard care in the treatment of patients with moderate COVID-19 date = 2020-09-20 pages = extension = .txt mime = text/plain words = 6194 sentences = 315 flesch = 48 summary = Our previous clinical pilot study indicated that aerosol inhalation of IFN-k plus TFF2 is a safe treatment and is able to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby resulting in an early release from hospitalization without induction of a proinflammatory response [20] . This study demonstrated that the combination inhalation of IFN-k and TFF2 is able to shorten the time of viral RNA negative conversion and CT improvement, and facilitating patients early discharge from the hospital, in the absence of induction of a proinflammatory response and treatment-related adverse events. The primary endpoint was a significantly shorter time (Mean 3¢80 days, 95% CI 2¢07À5¢53) from the start of the study treatment to viral RNA negative conversion for SARS-CoV-2 in all clinical samples, including nasopharyngeal swabs, throat swabs and stool swabs, in experimental group than in control group (7¢40 days, 95% CI 4¢57À10¢23) (p = 0¢031), and difference between means was 3¢60 days (Fig. 2A) . cache = ./cache/cord-289101-ko1knslk.txt txt = ./txt/cord-289101-ko1knslk.txt === reduce.pl bib === id = cord-288731-x2cwyvb7 author = Puenpa, Jiratchaya title = Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4207 sentences = 275 flesch = 57 summary = In the current study associations between SARS-CoV-2 gene variation and exposure history during the first wave of the outbreak in Thailand between January and May 2020 were investigated. In Thailand the Ministry of Public Health reported the first laboratory-confirmed case of SARS-CoV-2 in a 61-year-old Chinese traveller who had arrived from Wuhan on 12 January 2020. Based on the genome sequences available in GIASID, nucleotide variation in four regions of the SARS-CoV-2 genome was used to conduct viral tracking and identify sites of origin of outbreaks in Thailand. One sample in the current study collected in January 2020 was closely related to the SARS-CoV-2 strain circulating in China at that time identified as type L. A new cohort of imported cases identified in May 2020 included a group of migrant workers in the southern part of Thailand 24 with type G2 SARS-CoV-2. cache = ./cache/cord-288731-x2cwyvb7.txt txt = ./txt/cord-288731-x2cwyvb7.txt === reduce.pl bib === id = cord-288758-onis9xmo author = Peng, Z. title = Exhaled CO2 as COVID-19 infection risk proxy for different indoor environments and activities date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3167 sentences = 191 flesch = 58 summary = Contrary to some earlier recommendations setting a single indoor CO2 threshold, we show that the CO2 level corresponding to a given infection risk varies by over 2 orders of magnitude for different environments and activities. Although large uncertainties, mainly from virus exhalation rates, are still associated with our infection risk estimates, our study provides more specific and practical recommendations for low-cost CO2-based indoor infection risk monitoring. In this study, we derive the analytical expressions of the probability of indoor COVID-19 infection through room-level aerosol transmission only (i.e., assuming social distance is kept so that close proximity aerosol and droplet pathways are eliminated; fomite transmission is not included), human-exhaled CO2 concentration, and subsequently a few CO2-based quantities as infection risk proxies. where N is number of occupants, Ep is the SARS-CoV-2 exhalation rate by an infector (quanta h -1 ), mex mask filtration efficiency for exhalation, V indoor environment volume (m 3 ), and λ firstorder virus loss rate coefficient (h -1 ) that includes the ventilation with outdoor air and all other virus removal and deactivation processes. cache = ./cache/cord-288758-onis9xmo.txt txt = ./txt/cord-288758-onis9xmo.txt === reduce.pl bib === id = cord-288920-xkfcc2dx author = Broxmeyer, L title = SARS: Just another viral acronym? date = 2003-08-31 pages = extension = .txt mime = text/plain words = 2362 sentences = 115 flesch = 47 summary = Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. CDC began supporting the World Health Organization (WHO) in the investigation of a multi-country outbreak of the atypical pneumonia of unknown etiology (1), referred to as severe acute respiratory syndrome (SARS). Although high fever, nonproductive cough, low blood oxygen saturation, and varying degrees of respiratory distress, all found in SARS, are nothing new to the clinical picture of tuberculosis (11) , the number of TB cases in which people in the Orient die of adult respiratory distress syndrome (ARDS) is definitely on the rise (12), the same ARDS that often provokes the 'crazypaving' appearance at thin-section CT (13). cache = ./cache/cord-288920-xkfcc2dx.txt txt = ./txt/cord-288920-xkfcc2dx.txt === reduce.pl bib === id = cord-288998-0by0bkgs author = Colarusso, Chiara title = A lesson from a saboteur: high molecular weight kininogen (HMWK) impact in COVID‐19 date = 2020-06-04 pages = extension = .txt mime = text/plain words = 3857 sentences = 211 flesch = 45 summary = In the attempt to understand how the virus spreads and how to pharmacologically abolish it, it was highlighted that SARS‐CoV‐2 infects human cells by means of angiotensin converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2) and SARS‐CoV‐2 main protease (M(pro)). Our attention has been focused on the role of ACE2 in that its blockade by the virus increases Bradykinin and its metabolites, well known to facilitate inflammation in the lung (responsible for cough and fever), facilitate both the coagulation and complement system, three mechanisms that are typical of angioedema, cardiovascular dysfunction and sepsis, pathologies which symptoms occur in COVID‐19 patients. Once SARS-CoV-2 binds to ACE2 , the enzyme is blocked, therefore, leading to what we are actually assisting in terms of high blood pressure in COVID-19 patients and pulmonary edema up to angioedema, which underlies the fact that physiologically ACE2 cleaves several bioactive peptides, among which [des-Arg 9 ]bradykinin ([des-Arg 9 ]BK) (Vickers et al. cache = ./cache/cord-288998-0by0bkgs.txt txt = ./txt/cord-288998-0by0bkgs.txt === reduce.pl bib === id = cord-289003-vov6o1jx author = Burdet, C. title = Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals date = 2018-02-28 pages = extension = .txt mime = text/plain words = 8327 sentences = 327 flesch = 46 summary = Abstract We present here the proceedings of the 5th seminar on emerging infectious diseases, held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows: encourage research on the prediction, screening and early detection of new risks of infection; develop research and surveillance concerning transmission of pathogens between animals and humans, with their reinforcement in particular in intertropical areas ("hot-spots") via public support; pursue aid development and support in these areas of prevention and training for local health personnel, and foster risk awareness in the population; ensure adapted patient care in order to promote adherence to treatment and to epidemic propagation reduction measures; develop greater awareness and better education among politicians and healthcare providers, in order to ensure more adapted response to new types of crises; modify the logic of governance, drawing from all available modes of communication and incorporating new information-sharing tools; develop economic research on the fight against emerging infectious diseases, taking into account specific driving factors in order to create a balance between preventive and curative approaches. cache = ./cache/cord-289003-vov6o1jx.txt txt = ./txt/cord-289003-vov6o1jx.txt === reduce.pl bib === id = cord-289038-15yp9uqy author = Chow, Jonathan Tak-Sum title = Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5312 sentences = 445 flesch = 62 summary = The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. Another recent study used a high-throughput reporter screen of miRNA from human and mouse respiratory epithelial cells to identify hsa-miR-127-3p, hsa-miR-486-5p, and hsa-miR-593-5p as contributors to the antiviral defence against influenza A virus by targeting the genomes of the H3N2 and attenuated PR8 (H1N1) viral strains [16] . Given the wealth of evidence supporting a role for miRNA in host cell antiviral defence mechanisms, we sought to identify human miRNA that have the potential to target the SARS-CoV-2 genome. DEA of Calu3 cells infected with SARS-CoV revealed that only hsa-miR-155-3p (upregulated) and hsa-let-7a-3p (downregulated) out of the 128 miRNA we identified in this study, were differentially expressed ( Figure 4B ). cache = ./cache/cord-289038-15yp9uqy.txt txt = ./txt/cord-289038-15yp9uqy.txt === reduce.pl bib === id = cord-289079-m417oxpc author = Waggershauser, Constanze H. title = Letter: immunotherapy in IBD patients in a SARS‐CoV‐2 endemic area date = 2020-08-14 pages = extension = .txt mime = text/plain words = 405 sentences = 35 flesch = 58 summary = Editors, With interest, we read the article of Taxonera et al on symptoms and the risk of COVID-19 in inflammatory bowel disease (IBD). 1 We would like to provide data from our IBD centre during the outbreak of SARS-CoV-2 concerning patients receiving immunotherapies. 2 Therefore, soon two questions raised great concern: are IBD patients who receive immunotherapies more susceptible to SARS-CoV-2 infections than the general population and are infected patients exposed to a more severe course? Since the estimated number of silent SARS-CoV-2 infections is high 7 and most individuals show only moderate symptoms of respiratory tract infection, we called or invited our patients to fill-in a questionnaire, 8 Our data confirm the recommended practice that immunotherapies should not be stopped or delayed during the COVID-19 crisis. Daniel Szokodi has served as a speaker for Pfizer. 2019 novel coronavirus disease (COVID-19) in patients with inflammatory bowel diseases cache = ./cache/cord-289079-m417oxpc.txt txt = ./txt/cord-289079-m417oxpc.txt === reduce.pl bib === id = cord-289064-435bp4rt author = Muniangi-Muhitu, Hermine title = Covid-19 and Diabetes: A Complex Bidirectional Relationship date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5744 sentences = 290 flesch = 43 summary = Identified risk factors for disease severity and death from SARS-Cov2 infection include older age, male sex, diabetes, obesity and hypertension. We consider roles for the immune system, the observed phenomenon of microangiopathy in severe Covid-19 infection and the potential for direct viral toxicity on metabolically-relevant tissues including pancreatic beta cells and targets of insulin action. (18) , patients with diabetes and hypertension who had been treated with ACE inhibitors or angiotensin receptor blockers (ARB) had a high number of ACE2 receptors in the lung, and could therefore be at higher risk of developing severe symptoms, if infected with Covid-19. With respect to the glycemic deterioration seen in patients with preexisting T2D during Covid-19, a very recent report (63) provides the intriguing observation that ACE2 expression at both the mRNA and protein is increased substantially in human beta cells in response to response to inflammatory cytokines, presumably rendering these cells more susceptible to infection. cache = ./cache/cord-289064-435bp4rt.txt txt = ./txt/cord-289064-435bp4rt.txt === reduce.pl bib === id = cord-289144-d6fgs8qg author = Sieńko, Jerzy title = COVID-19: The Influence of ACE Genotype and ACE-I and ARBs on the Course of SARS-CoV-2 Infection in Elderly Patients date = 2020-07-21 pages = extension = .txt mime = text/plain words = 5129 sentences = 320 flesch = 49 summary = Moreover, there is evidence that ACE genotype affects the outcomes of acute respiratory distress syndrome (ARDS) treatment, the most severe consequence of SARS-CoV-2 infection. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 63 This upregulation of the ACE2 receptor causes an increase in SARS-CoV-2 binding sites, which can lead to COVID-19 infection. Association of inpatient use of angiotensin converting enzyme inhibitors and angiotensin II receptor blockers with mortality among patients with hypertension hospitalized with COVID-19 cache = ./cache/cord-289144-d6fgs8qg.txt txt = ./txt/cord-289144-d6fgs8qg.txt === reduce.pl bib === id = cord-288639-wy07nao0 author = Earnest, Arul title = Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore date = 2005-05-11 pages = extension = .txt mime = text/plain words = 2797 sentences = 152 flesch = 50 summary = title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore BACKGROUND: The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make real-time predictions on the number of beds occupied in Tan Tock Seng Hospital, during the recent SARS outbreak. The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make realtime predictions on the number of beds occupied in TTSH during the SARS outbreak, starting from 14 Mar 2003, when the CDC was activated, to 31 May 2003 when Singapore was declared SARS free. To the best of our knowledge, this is the first study to suggest the application of a known statistical method such as the ARIMA model, to predict and monitor the utilization of hospital isolation beds during the recent SARS outbreak in Singapore, for which Tan Tock Seng Hospital was the Admissions, predicted and actual number of beds occupied cache = ./cache/cord-288639-wy07nao0.txt txt = ./txt/cord-288639-wy07nao0.txt === reduce.pl bib === id = cord-289349-imkgpwn0 author = Qiu, Li title = Strong immunity in the early two years of age links to frequent immunization of routine vaccines date = 2020-08-08 pages = extension = .txt mime = text/plain words = 2040 sentences = 121 flesch = 52 summary = In this retrospective study, 25 patients under 10 years old were selected from a total of 186 laboratory-confirmed COVID-19 patients (Materials and methods, Fig. S1 , and Table S1 online). The patient age distribution revealed that children of all ages are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (Fig. 1a) . Because pediatric COVID-19 patients aged under 2 years were found to have shorter recovery times, we next further analyzed the clinical differences between children under and over 2 years old; several variables were compared between these two groups (Table S7 online). However, a previous epidemiological study revealed that the incidence of seasonal coronavirus infection in children under one year old is not significantly different from that in older children [15] . Pre-existing cross-reactive T-cell immunity to infections or vaccinations alters subsequent T-cell responses to antigens of unrelated pathogens [18] [19] [20] , thus frequently contributing to a protective or pathogenic role in infectious diseases [18, 20] . cache = ./cache/cord-289349-imkgpwn0.txt txt = ./txt/cord-289349-imkgpwn0.txt === reduce.pl bib === id = cord-289076-8iymevqm author = Marjanovic, Zdravko title = The relevance of psychosocial variables and working conditions in predicting nurses’ coping strategies during the SARS crisis: An online questionnaire survey date = 2007-08-31 pages = extension = .txt mime = text/plain words = 4581 sentences = 210 flesch = 42 summary = Three multiple regression analysis revealed that the model we evolved—including higher levels of vigor, organizational support, and trust in equipment/infection control initiative; and lower levels of contact with SARS patients, and time spent in quarantine—predicted to lower levels of avoidance behavior, emotional exhaustion, and state anger. We hypothesized that greater vigor, organizational support, and trust in equipment/infection control, and less contact with SARS patients and time spent in quarantine, would predict to lower levels of emotional exhaustion, state anger, and avoidance behavior. The five independent measures (predictors) were three psychosocial variables, vigor, organizational support, and trust in equipment/ infection control initiatives; and two working conditions variables, contact with SARS patients, and time spent in quarantine. State anger was positively correlated to avoidance behavior, contact with SARS patients, and greater time in quarantine; and negatively related to vigor, organizational support, and trust in equipment/ infection control initiatives. cache = ./cache/cord-289076-8iymevqm.txt txt = ./txt/cord-289076-8iymevqm.txt === reduce.pl bib === id = cord-289134-ne3tjt5g author = Xing, Yue title = Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1628 sentences = 93 flesch = 58 summary = By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. From 45828 SARS-CoV-2 genome sequences available in the GISAID database as of June 13, 2020, 103 strains of SARS-CoV-2 1 https://www.ncbi.nlm.nih.gov/Class/Structure/aa/aa_explorer.cgi carried various DNA mutations including 25 unique ones that may affect the furin cleavage site located at the amino acid residual positions 680-689 (S1/S2 region) (Coutard et al., 2020; Wang et al., 2020; Zhang et al., 2020) of the SARS-CoV-2 spike protein (Figure 1 , Table 1, and Supplementary Table 1) . We uncovered 103 SARS-CoV-2 strains from multiple geographic regions, 81 of which carried 25 unique mutations that may affect the furin cleavage site in the spike glycoprotein. cache = ./cache/cord-289134-ne3tjt5g.txt txt = ./txt/cord-289134-ne3tjt5g.txt === reduce.pl bib === id = cord-288818-6uvb4qsk author = Tanveer, Faouzia title = Ethics, pandemic and environment; looking at the future of low middle income countries date = 2020-10-15 pages = extension = .txt mime = text/plain words = 6998 sentences = 322 flesch = 45 summary = From the restrictions on public freedom and burgeoning socio-economic impacts to the rationing of scarce medical resources, the spread of COVID-19 is an extraordinary ethical dilemma for resource constrained nations with less developed health and research systems. International regimes are on high alert to stop its spread, however, as far as the global scenario is concerned, countries and governments are clueless in stopping the expanding pandemic as not much is known about SARS-CoV-2, while left only with implementing nationwide lock downs and curfews which opened new economic fronts and social challenges. COVID-19 has presented itself as a test case for the humanity in terms of global fraternity, decision making, technology and expertise sharing, rapid pandemic response mechanisms, stability, crises management and policy making. cache = ./cache/cord-288818-6uvb4qsk.txt txt = ./txt/cord-288818-6uvb4qsk.txt === reduce.pl bib === id = cord-289282-4oz6r7op author = Hon, Kam Lun title = Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date = 2020-06-01 pages = extension = .txt mime = text/plain words = 3558 sentences = 269 flesch = 58 summary = title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS cache = ./cache/cord-289282-4oz6r7op.txt txt = ./txt/cord-289282-4oz6r7op.txt === reduce.pl bib === id = cord-288756-r96izsyq author = Wu, Zhiqiang title = ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date = 2016-02-15 pages = extension = .txt mime = text/plain words = 2253 sentences = 108 flesch = 55 summary = title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus Several lineage B betacoronaviruses termed severe acute respiratory syndrome (SARS)–like CoVs (SL-CoVs) were identified from Rhinolophus bats in China. The nucleotide sequences in the ORF1ab, E, M, and N genes in these bat-borne lineage B beta-CoVs are 89%-93% similar to those in the SARS-CoVs from humans. Furthermore, genetic evidence for the identical ORF8 is needed to trace the origin of SARS-CoVs to bat SL-CoVs. All genome sequences were submitted to GenBank. In this study, a systematic survey of bat-borne CoVs was performed using bat virome data from throughout China, described in our previous report [6] , to obtain genetic evidence indicating the source of SARS-CoVs. Fifteen SL-CoVs were identified from 9 bat species in 11 provinces ( Figure 1A ) [6] . sinicus have nearly identical ORF8s and similar backbone genes to those in SARS-CoVs in Yunnan and Guangxi provinces. cache = ./cache/cord-288756-r96izsyq.txt txt = ./txt/cord-288756-r96izsyq.txt === reduce.pl bib === id = cord-289490-u0f0zyad author = Lumba, Rishi title = Neonate Born to a Mother with a Diagnosis of Suspected Intra-Amniotic Infection versus COVID-19 or Both date = 2020-07-18 pages = extension = .txt mime = text/plain words = 1444 sentences = 73 flesch = 44 summary = In this report, we detail a case of a newborn born to a mother with a clinical diagnosis of intra-amniotic infection with maternal fever and fetal tachycardia, who was then found to be SARS-CoV-2 positive on testing. Due to the varying presentation of COVID-19, this case illustrates the low threshold needed to test mothers for SARS-CoV-2 in order to prevent horizontal transmission to neonates and to healthcare providers. e current recommendations made by the American College of Obstetricians and Gynecologists (ACOG) are that the diagnosis of suspected intraamniotic infection be made on clinical criteria, which include maternal intrapartum fever and one or more of the following: maternal leukocytosis, purulent cervical drainage, or fetal tachycardia. Although a clinical diagnosis of Triple I was made by the obstetrics team, given maternal fever, testing for SARS-CoV-2 was included as well. cache = ./cache/cord-289490-u0f0zyad.txt txt = ./txt/cord-289490-u0f0zyad.txt === reduce.pl bib === id = cord-288862-upcsvjuo author = Wang, Junmei title = Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4369 sentences = 269 flesch = 54 summary = Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson–Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Flexible docking and MM-PBSA-weighted solvent-accessible surface area (WSAS) were applied as the first and second filters, respectively, to improve the efficiency and accuracy of HVS in inhibitor identification for SARS-CoV-2 main protease. MD simulations were first performed for a docking hit for two purposes: (1) studying the relative stability of the ligand residing in the binding pocket; (2) sampling a set of conformations for MM-PBSA-WSAS binding free energy calculations and MM-GBSA residue−ligand binding free energy decomposition analysis. cache = ./cache/cord-288862-upcsvjuo.txt txt = ./txt/cord-288862-upcsvjuo.txt === reduce.pl bib === id = cord-289332-hvakv08t author = Chen, Guoqian title = Pathogenic role of HMGB1 in SARS? date = 2004-04-30 pages = extension = .txt mime = text/plain words = 1670 sentences = 90 flesch = 37 summary = High mobility group box 1 protein (HMGB1) is released by necrotic cells or activated macrophages/monocytes, and functions as a late mediator of lethal systemic and local pulmonary inflammation. In light of observations that three Chinese herbal formulations recommended for treatment of severe acute respiratory syndrome (SARS) specifically inhibited the release of HMGB1 from innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. High mobility group box 1 protein (HMGB1, formerly known as HMG-1 or amphoterin) has recently been identified as a new proinflammatory cytokine and a late mediator of inflammation, sepsis, and acute lung injury. In light of observations that several Chinese herbal remedies recommended for treatment of SARS specifically inhibited the release of HMGB1 from activated innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. cache = ./cache/cord-289332-hvakv08t.txt txt = ./txt/cord-289332-hvakv08t.txt === reduce.pl bib === id = cord-289216-g4kqi560 author = Malecki, M. title = Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1927 sentences = 127 flesch = 51 summary = title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. In this study, two diagnostic laboratories of a tertiary care hospital equipped with different PCR systems validated the available kits on the respective systems for SARS-CoV-2 testing. In order to evaluate the performance of analytical components used for SARS-CoV-2 diagnostic we compared three commercially available RT-PCR kits, six extraction kits and four PCR cyclers in all possible combinations using predefined EQA samples. cache = ./cache/cord-289216-g4kqi560.txt txt = ./txt/cord-289216-g4kqi560.txt === reduce.pl bib === id = cord-289599-7vsynfgn author = Kostoff, Ronald N. title = COVID-19 vaccine safety date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2715 sentences = 153 flesch = 45 summary = The present article examines whether short-term, mid-term, and long-term vaccine safety can be achieved under such an accelerated schedule, given the myriad vaccine-induced mechanisms that have demonstrated adverse effects based on previous clinical trials and laboratory research. It is uncertain as to whether any of the drugs, vaccines, foods or radiation exposures of our predecessors, which were not tested for transgenerational effects, are adversely affecting human life at present. Of note, the question remains whether humanity is currently willing to pass on potential devastating diseases to future generations due to the present need for the speedy development of a vaccine, bypassing adequate long-term and transgenerational safety testing. The vaccine costs in this discussion are the potential adverse health effects from a cOVId-19 vaccine, particularly for the mid-and long-term. This least vulnerable demographic population would have to bear the brunt of any potential mid-and long-term adverse health impacts that may result from a vaccine inadequately tested for these effects. cache = ./cache/cord-289599-7vsynfgn.txt txt = ./txt/cord-289599-7vsynfgn.txt === reduce.pl bib === id = cord-289476-8wh3hn0n author = Leiker, Brenna title = COVID - 19 BRIEF INTRODUCTION IN MENTAL HEALTH CONSIDERATIONS FOR HEALTH CARE WORKERS AND PATIENTS date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3754 sentences = 208 flesch = 48 summary = This document describes five categories of people for SARS-CoV-2 testing with viral tests (i.e., nucleic acid or antigen tests) [the following are hot links to CDC resources]:  Testing individuals with signs or symptoms consistent with COVID-19  Testing asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 to control transmission  Testing asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings  Testing to determine resolution of infection (i.e., test-based strategy for Discontinuation of Transmission-based Precautions, HCP Return to Work, and Discontinuation of Home Isolation)  Public health surveillance for SARS-CoV-2 Generally, viral testing for SARS-CoV-2 is considered to be diagnostic when conducted among individuals with symptoms consistent with COVID-19 or among asymptomatic individuals with known or suspected recent exposure to SARS-CoV-2 to control transmission, or to determine resolution of infection. Testing is considered to be surveillance when conducted among asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification, or to detect transmission hot spots or characterize disease trends. cache = ./cache/cord-289476-8wh3hn0n.txt txt = ./txt/cord-289476-8wh3hn0n.txt === reduce.pl bib === id = cord-289364-p31gt533 author = AlFehaidi, Alanoud title = A case of SARS-CoV-2 re-infection date = 2020-10-25 pages = extension = .txt mime = text/plain words = 965 sentences = 73 flesch = 56 summary = Different reports have proposed the reactivation of SARS-CoV-2 infection, with 2 RT-PCR positive results following resolving symptoms and interim RT-PCR negative results [4] [5] [6] [7] [8] [9] [10] [11] . Early studies reported that re-detectable positive virus nucleic acid among patients with SARS-CoV-2 with an average duration of 15 days from discharge to a re-positive results 13 . Patients in those early reports did not show signs of infection with the second positive results and had negative swab results within one week later. The COCOREC (Collaborative study COvid RECurrences) study suggested that recurrence of infection is likely if the patient has two confirmed SARS-CoV-2 RT-PCR positive results over 15 days apart with one major clinical sign and no other cause to explain the symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report cache = ./cache/cord-289364-p31gt533.txt txt = ./txt/cord-289364-p31gt533.txt === reduce.pl bib === id = cord-288733-c51lfwd6 author = Kavanagh, Oisín title = Inhaled Hydroxychloroquine to Improve Efficacy and Reduce Harm in the Treatment of COVID-19 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 769 sentences = 51 flesch = 55 summary = An analysis of clinical trials registered on ClinicalTrials.gov revealed that this may continue as many studies combine HCQ with agents that prolong the QT interval. Here we describe an inhaled formulation of HCQ which has passed safety studies in clinical trials for the treatment of asthma and discuss how this approach may reduce side-effects and improve efficacy. Chloroquine and hydroxychloroquine (HCQ) were two of the earliest drugs to 33 receive attention as possible repurposable treatment options for COVID-19 3 . Concerns associated with severe side effects 41 are such that the FDA and EMA now formally recommend against taking HCQ for COVIDEffects of chloroquine on 178 viral infections: An old drug against today's diseases? FDA Drug Safety Communication: FDA cautions 199 against use of hydroxychloroquine or chloroquine for COVID-19 outside of the 200 hospital setting or a clinical trial due to risk of heart rhythm problems Optimizing hydroxychloroquine 210 dosing for patients with COVID-19: An integrative modeling approach for effective 211 drug repurposing cache = ./cache/cord-288733-c51lfwd6.txt txt = ./txt/cord-288733-c51lfwd6.txt === reduce.pl bib === id = cord-289711-4ab3d00h author = Yarmarkovich, Mark title = Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date = 2020-06-08 pages = extension = .txt mime = text/plain words = 5290 sentences = 252 flesch = 46 summary = Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 cache = ./cache/cord-289711-4ab3d00h.txt txt = ./txt/cord-289711-4ab3d00h.txt === reduce.pl bib === id = cord-289520-i6pv90s9 author = Harris, Carlyn title = An evidence-based framework for priority clinical research questions for COVID-19 date = 2020-03-31 pages = extension = .txt mime = text/plain words = 4699 sentences = 282 flesch = 46 summary = RESULTS: From the research objectives for SARS-CoV and MERS-CoV, ten themes in the literature were identified: Clinical characterisation, prognosis, diagnosis, clinical management, viral pathogenesis, epidemiological characterisation, infection prevention and control/transmission, susceptibility, psychosocial, and aetiology. Outbreaks, especially of novel agents, create a pressing need to collect data on clinical characterization, treatment, and validation of new diagnostics to inform rapid public health response. We compared our findings to the 2018 systematic review on SARS and MERS to determine which questions have already been addressed, what information is lacking, and provide recommendations for data sharing and clinical study designs to be conducted during the current outbreak. These observational studies are practical in the fast-paced outbreak setting, as they are easier than randomised controlled The First Few X (FFX) WHO Protocol https://www.who.int/publications-detail/the-first-few-x-(ffx)-cases-and-contact-investigation-protocol-for-2019-novel-coronavirus-(2019-ncov)-infection) What are the risk factors for death or severe illness? cache = ./cache/cord-289520-i6pv90s9.txt txt = ./txt/cord-289520-i6pv90s9.txt === reduce.pl bib === id = cord-289890-sf2uxubd author = Rushworth, S. A. title = Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay date = 2020-06-12 pages = extension = .txt mime = text/plain words = 3954 sentences = 195 flesch = 52 summary = We evaluated the FDA approved SARS-CoV-2 immunoassay (developed at Mount Sinai, by Krammer and colleagues) for the identification of COVID-19 seroconversion and potential cross-reactivity of the assay in a United Kingdom (UK) National Health Service (NHS) hospital setting. In summary, we report that the Mount Sinai IgG ELISA assay is highly sensitive test for SARS-Cov-2 infection, however modification of thresholding was required to minimise false positive results. Figure 2A shows that 42/47 samples from this group were established as negative for SARS-CoV-2 IgG antibody in the first RBD screening test step, and 5/47 required confirmatory assessment with the second dilution assay. On testing of the control group, 70/72 patient samples were identified as being negative for SARS-CoV-2 IgG antibody following the RBD step of the assay using the 5 SD threshold. To conclude, here we report that the Mount Sinai IgG ELISA assay is highly sensitive and apparent cost-effective test for SARS-Cov-2 infection in a UK NHS acute hospital laboratory setting. cache = ./cache/cord-289890-sf2uxubd.txt txt = ./txt/cord-289890-sf2uxubd.txt === reduce.pl bib === id = cord-289377-2vqqabum author = Yubero, P. title = Evidence for immunity to SARS-CoV-2 from epidemiological data series date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4972 sentences = 268 flesch = 53 summary = We then estimate the capacity of EAKF techniques to infer the duration of this memory and then apply this approach to mortality time series from New York City, discerning immunity times against SARS-CoV-2 with reasonable accuracy. (B) The value of the synthetic infection rate β synth (dotted line) is captured by the protocol β model (blue) after some data assimilation steps, and prior to the pandemic peak. . https://doi.org/10.1101/2020.07.22.20160028 doi: medRxiv preprint uity of a strong reduction of the infection rate during the initial days of the epidemic in all data sets that we studied (results of Belgium, Spain and France are available in Fig. S4 ). In our case, the time-dependent state variables are the infection rate β , the immunity memory τ and the population in each compartment of the model. cache = ./cache/cord-289377-2vqqabum.txt txt = ./txt/cord-289377-2vqqabum.txt === reduce.pl bib === id = cord-289522-7u3d6nfc author = Ebrahimi, Mina title = COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population date = 2020-10-17 pages = extension = .txt mime = text/plain words = 2460 sentences = 161 flesch = 45 summary = title: COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population This review compared coronavirus disease 2019 (COVID-19) laboratory findings, comorbidities, and clinical outcomes in patients from the general population versus medical staff to aid diagnosis of COVID-19 in a more timely, efficient, and accurate way. Two reviewers separately extracted the data from included studies, considering key characteristics including author, publication year, country, type of study, sample size, laboratory findings, comorbidities, and final clinical outcomes. Further analysis revealed the frequency of clinical manifestations in infected medical staff were similar to patients in the general public (Table 3) . The findings of this COVID-19 meta-analysis review revealed that the normal or abnormal outcome of a patient's laboratory results may shed light on the stage of the disease and its progression. Laboratory findings, signs and symptoms, clinical outcomes of Patients with COVID-19 Infection: An updated systematic review and meta-analysis cache = ./cache/cord-289522-7u3d6nfc.txt txt = ./txt/cord-289522-7u3d6nfc.txt === reduce.pl bib === id = cord-289114-ifnk41oq author = Singh, Angaraj title = Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date = 2020-10-28 pages = extension = .txt mime = text/plain words = 6894 sentences = 470 flesch = 54 summary = The SARS-CoV-2 infected patients with the cardiovascular problem have a higher fatality rate as compared to general COVID-19 patients. The ACE-2 has been suggested as a medicine for the treatment of diabetes because it reduces inflammation .Therefore, the diabetes and COVID-19 patients treated with ACE-2 have higher risk of infection (Zachary, 2020) . Although, the specific drug for SARS-CoV-2 is not discovered till date, the medical observers are attempting with different antiviral drugs for the treatment of COVID-19 infection . All rights reserved patients demonstrated that the combination of a new antiviral drug remdesivir and chloroquine slowed down the growth of SARS-CoV-2 (Abdul et al., 2017) . Convalescent plasma therapy has been observed as a better alternative for the treatment of severely infected COVID-19 patients. A research report suggested that plasma treatment is more effective at the initial stage (within 14 days of symptoms) of COVID-19 infection. cache = ./cache/cord-289114-ifnk41oq.txt txt = ./txt/cord-289114-ifnk41oq.txt === reduce.pl bib === id = cord-290056-x74cq2k5 author = Delgado-Roche, Livan title = Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1910 sentences = 103 flesch = 43 summary = title: Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection Some authors suggest that the onset of severe lung injury in SARS-CoV infected patients depends on activation of the oxidative stress machinery that is coupled with innate immunity and activates transcription factors, such as NF-κB, resulting in an exacerbated proinflammatory host response (14) . Activation of the PI3K/Akt signaling pathway may lead to a delay in Oxidative stress -NF-kB -toll-like receptor (mainly TL4) signaling pathways, triggered by viral pathogens like SARS-CoV, may further amplify the host inflammatory response, ultimately leading to acute lung injury. In conclusion, literature evidence suggests that oxidative stress and chronic low-grade inflammation in the lungs are associated with aging and may contribute to age-related immune dysfunction and mortality risk in aged patients affected by respiratory virus infections, such as SARS-CoV-2. cache = ./cache/cord-290056-x74cq2k5.txt txt = ./txt/cord-290056-x74cq2k5.txt === reduce.pl bib === id = cord-289574-engwi8h3 author = An, Peng-jiao title = Biochemical indicators of coronavirus disease 2019 exacerbation and the clinical implications date = 2020-05-23 pages = extension = .txt mime = text/plain words = 3188 sentences = 220 flesch = 39 summary = Accumulating evidence suggested that the progression of COVID-19 is associated with lymphopenia and excessive inflammation, and a subset of severe cases might exhibit cytokine storm triggered by secondary hemophagocytic lymphohistiocytosis (sHLH). Previously, it has been found that the serum levels of pro-inflammatory cytokines [IFN-γ, IL-1, IL-6, IL-12, and transforming growth factor-β (TGF-β)], and chemokines (CCL2, CXCL9, CXCL10, and IL-8) in SARS-CoV infected patients were higher than those in healthy individuals. Procalcitonin (PCT), released by bacterial infectious tissues under the irritation of pro-inflammatory cytokines, is a more specific marker of serious bacterial infection compared to C-reactive protein (CRP) and IL-6 [111] PCT-based strategy has been applied to guide antibiotic use in ICU or emergency wards, since the serum PCT levels in patients with severe bacterial infections are much higher than those with simple viral infections or non-specific inflammatory diseases [111] [112] [113] . The definition and risks of Cytokine Release Syndrome-Like in 11 COVID-19-Infected Pneumonia critically ill patients: Disease Characteristics and Retrospective Analysis cache = ./cache/cord-289574-engwi8h3.txt txt = ./txt/cord-289574-engwi8h3.txt === reduce.pl bib === id = cord-289813-kq3ayyip author = Arnaez, Juan title = The Impact of the Current SARS-CoV-2 Pandemic on Neonatal Care date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1965 sentences = 90 flesch = 41 summary = These changes mainly impact several key points: (1) the organization and workflow of the neonatal unit, (2) parent-infant bonding and family-centered care, and (3) stress-related consequences in health professionals (Figure 1) . The contingency plans required by the circumstances in the current SARS-CoV-2 outbreak scenario must not let us forget that restrictions on parental contact and interventions in the care of infants may entail costs to the families in addition to the loss of opportunities for the newborn to adapt to the extrauterine environment and advance in neurodevelopment. Importantly, health-workers should rely positively on the contingency plans and help parents to reduce their fear and encourage them to participate in their children's care. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes A contingency plan for the management of the 2019 novel coronavirus outbreak in neonatal intensive care units cache = ./cache/cord-289813-kq3ayyip.txt txt = ./txt/cord-289813-kq3ayyip.txt === reduce.pl bib === id = cord-289598-t8upoq9a author = Yoon, Jane C title = COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2980 sentences = 197 flesch = 56 summary = BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. Risk of SARS-CoV-2 infection, the virus that causes COVID-19, may be higher among people experiencing homelessness (PEH) because of challenges in preventing respiratory disease transmission in congregate shelter settings. Our finding of decreased prevalence in four shelters during repeat testing is consistent with reports from skilled nursing facilities and correctional facilities, supporting the use of universal (facility-wide) testing for early identification and isolation of those with positive SARS-CoV-2 as a strategy to interrupt transmission in congregate settings [23] [24] [25] . cache = ./cache/cord-289598-t8upoq9a.txt txt = ./txt/cord-289598-t8upoq9a.txt === reduce.pl bib === id = cord-289740-nsiycudn author = Smithgall, Marie C. title = Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2 date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2230 sentences = 141 flesch = 57 summary = OBJECTIVE: This study aimed to compare two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2, to the Roche cobas SARS-CoV-2 assay for samples with low, medium, and high viral concentrations. STUDY DESIGN: A total of 113 nasopharyngeal swabs from remnant patient samples were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. CONCLUSIONS: While Xpert showed high agreement with cobas across a wide range of viral concentrations, this study highlights an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Utilizing the high volume of patient testing performed at our medical center in New York City, we sought to evaluate and compare the performance of these two rapid assays across a wide range of clinical samples. Deidentified remnant patient samples that underwent routine clinical testing with the cobas SARS-CoV-2 assay on the 6800 platform (Roche Diagnostics, Indianapolis, IN) were used to evaluate the Xpert and ID Now assays. cache = ./cache/cord-289740-nsiycudn.txt txt = ./txt/cord-289740-nsiycudn.txt === reduce.pl bib === id = cord-289612-4x5t4c5u author = Alsuliman, Tamim title = COVID-19 paraclinical diagnostic tools: Updates and future trends date = 2020-06-20 pages = extension = .txt mime = text/plain words = 7353 sentences = 387 flesch = 48 summary = Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases cache = ./cache/cord-289612-4x5t4c5u.txt txt = ./txt/cord-289612-4x5t4c5u.txt === reduce.pl bib === id = cord-289407-8fje16z1 author = Moore, G. title = Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4720 sentences = 328 flesch = 59 summary = Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. 6 Air samples taken during tracheostomy procedures, high flow nasal oxygen treatment, non-invasive ventilation and nebulisation have not contained SARS-CoV-2 RNA 7 and HCWs exposed to unrecognised COVID-19 patients undergoing similar high-risk AGPs have not become infected. . https://doi.org/10.1101/2020.09.24.20191411 doi: medRxiv preprint Several studies, utilising a range of air and surface sampling methods, have been carried out to determine the presence and prevalence of SARS-CoV-2 in the healthcare environment. [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients cache = ./cache/cord-289407-8fje16z1.txt txt = ./txt/cord-289407-8fje16z1.txt === reduce.pl bib === id = cord-289716-nleql08z author = Tsitsilonis, Ourania E. title = Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report date = 2020-09-21 pages = extension = .txt mime = text/plain words = 3225 sentences = 143 flesch = 44 summary = Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. According to the manufacturer's package insert, Elecsys ® Anti-SARS-CoV-2 exhibits high overall clinical specificity of 99.81% with no cross-reactivity to the common cold coronaviruses; clinical sensitivity, determined by testing a total of 204 samples from 69 symptomatic patients with a PCR-confirmed SARS-CoV-2 infection, is 100% for samples collected ≥14 days after PCR confirmation in this collective; these values were verified in our study by measuring 25 RT-qPCR SARS-CoV-2 positive and 25 negative samples. cache = ./cache/cord-289716-nleql08z.txt txt = ./txt/cord-289716-nleql08z.txt === reduce.pl bib === id = cord-289852-4uxb70rh author = Kassem, Dina H. title = Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis date = 2020-09-30 pages = extension = .txt mime = text/plain words = 6959 sentences = 342 flesch = 44 summary = Thus, harnessing the immunomodulatory properties of mesenchymal stem cells (MSCs) to ameliorate that cytokine-storm can indeed provide a golden key for the treatment of COVID-19 patients, especially severe cases. In fact, MSCs transplantation can improve the overall outcome of COVID-19 patients via multiple mechanisms; first through their immunomodulatory effects which will help to regulate the infected patient inflammatory response, second via promoting tissue-repair and regeneration, and third through their antifibrotic effects. Similar studies are also warranted to compare the therapeutic benefit of a certain MSCs type, and its derived EVs. Antimicrobial activity of mesenchymal stem cells: current status and new perspectives of antimicrobial peptide-based therapies Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ILL COVID-19 patients: the case for compassionate use Human umbilical cord-derived mesenchymal stem cell therapy in patients with COVID-19: a phase 1 clinical trial cache = ./cache/cord-289852-4uxb70rh.txt txt = ./txt/cord-289852-4uxb70rh.txt === reduce.pl bib === id = cord-289588-n61gz7pi author = Samudrala, Pavan Kumar title = Virology, pathogenesis, diagnosis and in-line treatment of COVID-19 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3898 sentences = 253 flesch = 56 summary = Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. As far as safety is a major concern, 424 Gilead Sciences announced phase III clinical trial of remdesivir to prove its safety and 425 efficacy in COVID-19 infection (Keown, 16 .03.2020). Epidemiology, causes, clinical manifestation and 687 diagnosis, prevention and control of coronavirus disease (COVID-19) during the early 688 outbreak period: a scoping review First known person-to-784 person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 785 the USA Clinical 803 features of patients infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 (COVID-19) Vaccine Development and Production: An 817 Severe acute respiratory 845 syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The 846 epidemic and the challenges Unique epidemiological and clinical features 949 of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control 950 measures cache = ./cache/cord-289588-n61gz7pi.txt txt = ./txt/cord-289588-n61gz7pi.txt === reduce.pl bib === id = cord-287819-qzg4bhoy author = Priftis, Konstantinos title = COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1164 sentences = 81 flesch = 47 summary = title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke COVID-19 following infection by SARS-CoV-2 can affect the brain causing confusion, depression, and dementia-like signs. We report on LA, a patient who was affected by a left-hemisphere ischemic stroke, probably because of SARS-CoV-2. The patient showed a highly specific neuropsychological profile characterized by severe agraphia and some signs of conduction aphasia. Therefore, in the present study, we aimed to investigate, more in depth, the specific and focal neuropsychological consequences of SARS-CoV-2, in a patient affected by lefthemisphere stroke. LA had a largely intact neuropsychological profile, except for the presence of severe agraphia and some signs of conduction aphasia. We suggest that patients affected by SARS-CoV-2 and stroke might not only show diffuse neurocognitive and neurobehavioural signs (e.g. confusion, agitation, psychosis), but they can also present with highly focal neuropsychological disorders, such as agraphia and conduction aphasia. cache = ./cache/cord-287819-qzg4bhoy.txt txt = ./txt/cord-287819-qzg4bhoy.txt === reduce.pl bib === id = cord-290378-h4cof32m author = Guy, Tiphaine title = High-flow nasal oxygen: a safe, efficient treatment for COVID-19 patients not in an ICU date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1389 sentences = 77 flesch = 54 summary = SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. Patients infected with SARS-CoV-2 can develop severe pneumonia and respiratory failure, which often require treatment in intensive care units (ICU) in Western European countries (2) . This report describes the use of HFNO to manage SARS-CoV-2 infected patients with respiratory failure on the pulmonology ward rather than in an ICU. The theoretical risk of virus aerosolization resulted in early published reports of critically ill SARS-CoV-2-infected patients in China not recommending the use of HFNO or non-invasive ventilation until the patient had been cleared of COVID-19 (4). While these results should be confirmed in larger studies, we believe that our data strongly suggest that SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. cache = ./cache/cord-290378-h4cof32m.txt txt = ./txt/cord-290378-h4cof32m.txt === reduce.pl bib === id = cord-289535-srrfr1es author = Tregoning, J. S. title = Vaccines for COVID‐19 date = 2020-10-18 pages = extension = .txt mime = text/plain words = 14329 sentences = 793 flesch = 44 summary = One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial cache = ./cache/cord-289535-srrfr1es.txt txt = ./txt/cord-289535-srrfr1es.txt === reduce.pl bib === id = cord-290123-scd9u8ix author = Mustafa, Mujahed I. title = Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors date = 2020-09-23 pages = extension = .txt mime = text/plain words = 3551 sentences = 202 flesch = 47 summary = title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors In this review, we will focus on cytokine storm in COVID-19 patients, their impact on the body organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. However, novel coronavirus still gains entry into humans by targeting ACE2 receptor that is found on lung cells, which destroy human lungs through cytokine storms, and this leads to hyperinflammation, forcing the immune cells to destroy healthy cells, which could be the reason behind COVID-19 patients' frequent intensive care admission [28] . This review deals with cytokine storm in COVID-19 patients, their impact on the organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. COVID-19 triggers cytokine storm in many stages of its pathological course that causes lung fibrosis, acute respiratory distress syndrome, and eventually leads to multiorgan failure [34, 54, 61] . cache = ./cache/cord-290123-scd9u8ix.txt txt = ./txt/cord-290123-scd9u8ix.txt === reduce.pl bib === id = cord-289905-dvl2pud2 author = Gan, Rosemary title = COVID-19 as a Viral Functional ACE2 Deficiency Disorder with ACE2 Related Multi-organ Disease date = 2020-06-23 pages = extension = .txt mime = text/plain words = 4355 sentences = 215 flesch = 33 summary = Appreciating the clear differences between SARS and COVID-19 in presentation, poor prognostic indicators related to individuals' co-morbid status, and biochemical and radiologic profiles, a novel disease model may assist in: 1) the early recognition of atypical (non-respiratory) presentations of disease; 2) early prophylactic treatment intervention for individuals at risk of severe and critical disease which could take place 6 in the community; 3) revised management of pulmonary complications including those related to prone posturing and ventilation protocols; 4) allowing better utilisation of data collated at a global level in the absence of an evidence-based disease model at this time; 5) identification of different markers of disease progression in at-risk individuals. An upregulation of ACE2 expressing cells related to chronic ATII elevation [18] or treatment with ACEinhibitors [19] , may increase the infective potential of SARS-CoV-2 in this group as a consequence of the duality of ACE2 functioning as both a receptor for viral entry to cells and as an enzyme. cache = ./cache/cord-289905-dvl2pud2.txt txt = ./txt/cord-289905-dvl2pud2.txt === reduce.pl bib === id = cord-290429-0d34abdo author = Elengoe, Asita title = COVID-19 Outbreak in Malaysia date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1332 sentences = 105 flesch = 61 summary = The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic outbreak emerged in December 2019 from Wuhan City, Hubei Province, China and spread to the rest of the world. They reported that the virus had 96.3% genetic similarity with a Yunnan bat coronavirus RaTG13 and 70% homology with severe acute respiratory syndrome coronavirus (SARS-CoV) [2] . On the 12 th January 2020, the World Health Organization (WHO) announced the cause of this epidemic outbreak was a novel coronavirus discovered in 2019 (2019-nCoV) or SARS-CoV-2 and named the disease coronavirus disease 2019 (COVID-19) [3] . Coronavirus COVID-19 cases spiked across Asia after a mass gathering in Malaysia. The origin, transmission, and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak -An update on the status Epidemiology, causes, clinical manifestation and diagnosis, prevention, and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review cache = ./cache/cord-290429-0d34abdo.txt txt = ./txt/cord-290429-0d34abdo.txt === reduce.pl bib === id = cord-290254-m9l8ntur author = Rodriguez-Manzano, J. title = A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date = 2020-06-30 pages = extension = .txt mime = text/plain words = 5622 sentences = 340 flesch = 54 summary = In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Currently, reverse transcriptase polymerase chain reaction using real-time benchtop platform (RT-qPCR) is considered the gold standard for COVID-19 diagnosis due to its capability to detect the presence of SARS-CoV-2 RNA close to the onset of symptomatic illness which is critical for isolation. In this paper, we combined LAMP with an in-house LoC device to develop a rapid PoC diagnostic test (< 20 min) for the detection of SARS-CoV-2 RNA from extracted samples. cache = ./cache/cord-290254-m9l8ntur.txt txt = ./txt/cord-290254-m9l8ntur.txt === reduce.pl bib === id = cord-290290-wyx9ib7s author = Sinegubova, Maria V. title = High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date = 2020-11-05 pages = extension = .txt mime = text/plain words = 5978 sentences = 304 flesch = 49 summary = title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. Previously we have developed the plasmid vector p1.1, containing large fragments of non-coding DNA from the EEF1A1 gene of the Chinese hamster and fragment of the Epstein-Barr virus long terminal repeat concatemer [21] and employed it for unusually high-level expression of various proteins in CHO cells, including blood clotting factors VIII [22] , IX [23] , and heterodimeric follicle-stimulating hormone [24] . We have proposed that SARS-CoV-2 RBD, suitable for in vitro diagnostics use, may be expressed in large quantities by stably transfected CHO cells, bearing the EEF1A1-based plasmid. cache = ./cache/cord-290290-wyx9ib7s.txt txt = ./txt/cord-290290-wyx9ib7s.txt === reduce.pl bib === id = cord-289719-64ugdvfe author = Tenforde, Mark W. title = Characteristics of Adult Outpatients and Inpatients with COVID-19 — 11 Academic Medical Centers, United States, March–May 2020 date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3166 sentences = 148 flesch = 46 summary = During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. To explore the spectrum of illness across health care settings and potential community SARS-CoV-2 exposures after issuance of national social distancing guidelines on March 16, 2020 (4), 11 academic medical centers in nine states conducted telephone-based surveys of a sample of patients with positive SARS-COV-2 test results during April 15-May 24, 2020 (testing dates = March 31-May 10, 2020). cache = ./cache/cord-289719-64ugdvfe.txt txt = ./txt/cord-289719-64ugdvfe.txt === reduce.pl bib === id = cord-290209-gkx57lyq author = Losurdo, Pasquale title = Impact of lockdown for SARS-CoV-2 (COVID-19) on surgical site infection rates: a monocentric observational cohort study date = 2020-09-14 pages = extension = .txt mime = text/plain words = 4094 sentences = 207 flesch = 45 summary = At multivariate analysis, the measures to reduce the SARS-CoV-2 spread (OR 0.368; p 0.05) were independently associated with the reduction for total, superficial and deep SSIs. Moreover, the presence of drains (OR 4.99; p 0.009) and a Type III–IV of SWC (OR 1.8; p 0.001) demonstrated a worse effect regarding the primary endpoint. The presence of a drain and a contaminated or dirty type of surgery (according to SWC) could increase the overall rate of SSIs, but the presence of a drain did not demonstrate an increased risk of superficial and/or deep SSIs. On the other hand, protection with surgical masks for both patient and surgeon during the post-operative period in the surgical unit and the absence of visitors, dramatically reduced superficial and deep SSIs. These two simple precautions emerged as independently associated with the reduction of both superficial and deep SSIs. Quality improvement initiatives aimed at reducing SSI rates are often hindered by limited or even conflicting evidence for proposed interventions to reduce SSI [33] . Surgery and the postoperative management of surgical wound carries a non-negligible risk of SSIs. In this study, we provided important insights into the superficial and deep surgical site infection risk assessment for patients who underwent surgery. cache = ./cache/cord-290209-gkx57lyq.txt txt = ./txt/cord-290209-gkx57lyq.txt === reduce.pl bib === id = cord-290758-kz0qfy3r author = Hui, David S. title = The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China date = 2020-02-29 pages = extension = .txt mime = text/plain words = 1305 sentences = 68 flesch = 51 summary = title: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -The latest 2019 novel coronavirus outbreak in Wuhan, China The 2019-nCoV infection in Wuhan appears clinically milder than SARS or MERS overall in terms of severity, case fatality rate and transmissibility, which increases the risk of cases remaining undetected. The rapid identification and containment of a novel coronavirus virus in a short period of time is a reassuring and a commendable achievement by China's public health authorities and reflects the increasing global capacity to detect, identify, define and contain new outbreaks. The latest analysis show that the Wuhan CoV cluster with the SARS CoV.10 (Novel coronavirus -China (01) Whilst several important aspects of MERS-CoV epidemiology, virology, mode of transmission, pathogenesis, diagnosis, clinical features, have been defined, there remain many unanswered questions, including source, transmission and epidemic potential. cache = ./cache/cord-290758-kz0qfy3r.txt txt = ./txt/cord-290758-kz0qfy3r.txt === reduce.pl bib === id = cord-290066-umthoftd author = Jia, Xingwang title = False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 518 sentences = 41 flesch = 55 summary = title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 We read with interest that antibody testing using a rapid immunochromatographic assay is reliable in the diagnosis of severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ) infection 1 . positive antibody results could be eliminated after five times dilution with normal human serum, when the RF level was lower than 10 IU/mL. The false positive antibody results could also be eliminated after 5 times dilution with normal human serum. Although the RT-PCR test has become the standard method for the diagnosis of SARS-CoV-2 infection, false-negative rates have been reported. Therefore, the combination of serum IgM/IgG antibody detection, the nucleic acid test, CT scan and clinical features improves the accuracy of COVID-19 diagnosis. Reliability and usefulness of a rapid IgM-IgG antibody test for the diagnosis of SARS-CoV-2 infection: A preliminary report cache = ./cache/cord-290066-umthoftd.txt txt = ./txt/cord-290066-umthoftd.txt === reduce.pl bib === id = cord-290068-s1gdbsfx author = Hon, KLE title = Clinical presentations and outcome of severe acute respiratory syndrome in children date = 2003-05-17 pages = extension = .txt mime = text/plain words = 1900 sentences = 117 flesch = 55 summary = title: Clinical presentations and outcome of severe acute respiratory syndrome in children In addition, we treated patients who had moderate symptoms of high fluctuating fever and notable malaise with intravenous ribavirin (20 mg/kg daily, given in three doses) and hydrocortisone (2 mg/kg every 6 h) immediately after admission. Lymphopenia (0·3-3·0ϫ10 9 /L) was reported in all patients, but the teenagers were generally more severely affected than the younger children. 2, 3 Ribavirin is a broad-spectrum antiviral agent and has been used for treatment of severe respiratory syncytial virus infection in We noted two distinct patterns of clinical presentation among the children we studied. On this basis, we did an open-label study in which oral gabapentin 300 mg thrice daily was given for every other chemotherapy treatment in nine patients with breast cancer. The patient reported severe nausea after the first two chemotherapy treatments. cache = ./cache/cord-290068-s1gdbsfx.txt txt = ./txt/cord-290068-s1gdbsfx.txt === reduce.pl bib === id = cord-290472-w77cmljm author = Sharon, Donald title = Systems Biology Approaches to Disease Marker Discovery date = 2010-06-09 pages = extension = .txt mime = text/plain words = 8665 sentences = 393 flesch = 39 summary = These markers, such as protein (including autoantibodies, which are antibodies specific to self-antigens [43] ), hormonal markers (such as lack of insulin in Type I diabetic patients [89] ), and genetic/genomic markers (such as BRCA1 mutation in breast cancer patients [52] ), enable clinicians to diagnose the disease while it is still at early stages, to ensure appropriate surgical intervention, efficient drug treat-ment and monitoring, and to predict an individual's risk of developing specific diseases before they experience symptoms. Scientists, such as the group led by Gil Mor at Yale University, recruited proteomics-based approaches using antibody-based protein microarrays to identify new serum biomarkers, which, in combination with CA-125, may enhance the early detection of ovarian cancer [48, 66, 110] . To date, no studies that attempt to identify novel breast cancer markers have been performed using high-density protein microarrays. cache = ./cache/cord-290472-w77cmljm.txt txt = ./txt/cord-290472-w77cmljm.txt === reduce.pl bib === id = cord-290001-603qy8ml author = Pimentel, Lígia L. title = Cholesterol, inflammation, and phospholipids: COVID-19 share traits with cardiovascular disease date = 2020-10-17 pages = extension = .txt mime = text/plain words = 1836 sentences = 92 flesch = 44 summary = COVID-19, the severe acute respiratory syndrome produced by the coronavirus SARS-CoV-2, has resulted to date in more than 27 million infected cases and 900000 deaths worldwide since the first reported cases in December 2019 at the Chinese city of Wuhan (for updated information readers can consult https://covid19.who.int/). Moreover, total counts of white blood cells (WBC) were significantly higher in patients in critical condition [1] and those with severe respiratory failure showed macrophage activation syndrome [4], confirmed by the presence of monocyte recruiting chemokines in bronchoalveolar fluid [2] . Furthermore, plasma lipidomic analyses have revealed a close relationship between the severity of COVID-19 and circulating lipids: a combination of larger levels of atherogenic diglycerides (DG 16:0/20:2/20:0) and triglycerides (TG 14:0/22:1/22:3), alterations of the phosphatidylinositol (PI) signalling system with decreased concentrations of phosphatidylcholine (PC) [7] and sphingosine-1-phosphate (S1P) [8] . Thus, it was observed in SARS-CoV-2 positive subjects that anticardiolipin antibodies (aCL IgG) profile (>15 U/mL) was associated to disease severity (i.e.respiratory distress) while those patients have not a previous record history of thrombosis [11] . cache = ./cache/cord-290001-603qy8ml.txt txt = ./txt/cord-290001-603qy8ml.txt === reduce.pl bib === id = cord-290277-ndfoppoq author = Bahl, Prateek title = Airborne or droplet precautions for health workers treating COVID-19? date = 2020-04-16 pages = extension = .txt mime = text/plain words = 3496 sentences = 207 flesch = 58 summary = World Health Organization (WHO) has issued guidelines for contact and droplet precautions for Healthcare Workers (HCWs) caring for suspected COVID-19 patients, whilst the US Centre for Disease Control (CDC) has recommended airborne precautions. We aimed to review the evidence for horizontal distance travelled by droplets and the guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) on respiratory protection for COVID-19. We aimed to review the evidence supporting the rule of 1 m (≈3 ft) spatial separation for droplet precautions in the context of guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) for HCWs on respiratory protection for COVID-19. Interim Infection Prevention and Control Recommendations for Hospitalized Patients with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) cache = ./cache/cord-290277-ndfoppoq.txt txt = ./txt/cord-290277-ndfoppoq.txt === reduce.pl bib === id = cord-290445-vb53bih9 author = Ahmed, Shiek SSJ title = Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date = 2020-04-23 pages = extension = .txt mime = text/plain words = 3793 sentences = 208 flesch = 42 summary = Secondly, the viral replication machinery network from SET-B with 332 seed proteins extended to 1486 neighboring proteins with 11438 interacting edges which representing the mechanism attributed to evasion of the SARS-CoV2 genome into the host. Similarly, the viral replication machinery network was acquired with 1522 proteins with 9747 interacting edges showing the complex SARS-CoV-2 mechanism in the human lungs. These common molecules represent the inter-connecting mechanism involved in the transcription machinery, immune response, cell growth and/or maintenance, transport, metabolism, protein metabolism, cell communication and signal transduction that activated upon virus binding and has been subsequently utilized for viral replication process (S5 Table) Also mapping with other viral infection dataset, 50 hub proteins of the replication machinery network have noticed in influenza virus infection (S4 Table) , which suggests SARS-CoV2 and influenza may have a similar mode of host infection machinery [17] . The molecular pathways of interconnecting protein hubs could be the intermediate phase that connects the receptor activation mechanism and viral replication process (Fig 10) . cache = ./cache/cord-290445-vb53bih9.txt txt = ./txt/cord-290445-vb53bih9.txt === reduce.pl bib === id = cord-289947-z2dw2eaz author = Wong, River Chun-Wai title = Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay date = 2020-08-16 pages = extension = .txt mime = text/plain words = 800 sentences = 75 flesch = 64 summary = title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens. The overall performance of Xpert Xpress SARS-CoV-2 assay was satisfactory when tested with DTS and LRT specimens. To our knowledge, this is the first report to evaluate the use of PBS for sample homogenization of DTS prior to testing with Xpert Xpress SARS-CoV-2 assay. These procedures can minimize the mucus and viscous substances among non-validated specimen types and broaden the testing scope of Xpert Xpress SARS-CoV-2 assay. cache = ./cache/cord-289947-z2dw2eaz.txt txt = ./txt/cord-289947-z2dw2eaz.txt === reduce.pl bib === id = cord-290170-s6wjitfo author = Kuhrt, Katy title = Placental abruption in a twin pregnancy at 32 weeks’ gestation complicated by COVID-19, without vertical transmission to the babies. date = 2020-05-08 pages = extension = .txt mime = text/plain words = 304 sentences = 33 flesch = 64 summary = key: cord-290170-s6wjitfo title: Placental abruption in a twin pregnancy at 32 weeks' gestation complicated by COVID-19, without vertical transmission to the babies. cord_uid: s6wjitfo Other coronavirus spectrum infections have been 31 associated with miscarriage, preterm birth, preeclampsia, caesarean delivery, perinatal death, 32 fetal growth restriction, and placental abruption. She gave a one-day history of cough, fever and 100 5 mild shortness of breath. An echocardiogram performed the same day showed a mild pericardial 102 effusion, and NT-BNP was 28pg/ml (normal <100pg/ml) (done to rule out cardiac failure or 103 cardiomyopathy). Outcome 186 of Coronavirus spectrum infections (SARS, MERS, COVID 1 -19) during 187 pregnancy: a systematic review and meta-analysis MERS-CoV Infection in a Pregnant Woman in Korea Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in 198 Possible Vertical Transmission 202 of SARS-CoV-2 From an Infected Mother to Her Newborn Placental 210 abruption in twin pregnancies, risk factors and perinatal outcomes cache = ./cache/cord-290170-s6wjitfo.txt txt = ./txt/cord-290170-s6wjitfo.txt === reduce.pl bib === id = cord-290796-x9xqqcj6 author = Stefanelli, P. title = Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento date = 2020-11-13 pages = extension = .txt mime = text/plain words = 3142 sentences = 212 flesch = 55 summary = All individuals above ten years of age resident in 5 municipalities of the Autonomous Province of Trento, northern Italy, who resulted IgG positive for anti-SARS-CoV-2 nucleocapsid (NC) antibodies in a serosurvey conducted on May 2020 were retested after 4 months. The duration of protection against infection with common human coronaviruses appears to be rather short 2, 3 , and there are studies showing declines in IgG antibodies against SARS-CoV-2 among both symptomatic and asymptomatic individuals 4, 5 . In order to evaluate the persistence of SARS-CoV-2 antibodies, we repeated a serosurvey in five municipalities of the Autonomous Province (AP) of Trento, Italy, recruiting those individuals who had resulted positive in a large population-based seroprevalence study conducted 4 months before 14 . The analyser automatically calculates SARS-CoV-2 NC IgG antibody concentration expressed as an is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint cache = ./cache/cord-290796-x9xqqcj6.txt txt = ./txt/cord-290796-x9xqqcj6.txt === reduce.pl bib === id = cord-290218-dvyeg5fk author = Jiang, Yi title = RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date = 2020-09-04 pages = extension = .txt mime = text/plain words = 2249 sentences = 143 flesch = 53 summary = Interestingly, the structure of complexed nsp12 is almost identical to nsp12 in apo RdRp, with an RMSD of 0.5 Å [17] , coinciding with the high processivity of the viral RNA polymerase, which does not need to consume extra energy for conformation changes in the active site during the replication cycle (Fig. 3B ). These "sliding poles" are stabilized by interactions formed between the positively charged residues at the extended N-terminal of nsp8 and bases in RNA backbones ( Fig. 3E ) and reported to account for the known processivity of the RdRp, which is required for replicating the long coronavirus genomes [39] . Although the sequence identity of nsp12 across the RNA viruses is low, the polymerase active site is structurally highly conserved, suggesting that RdRp inhibitors may serve as a potential J o u r n a l P r e -p r o o f broad-spectrum antiviral drug against RNA viruses. cache = ./cache/cord-290218-dvyeg5fk.txt txt = ./txt/cord-290218-dvyeg5fk.txt === reduce.pl bib === id = cord-290802-761wqgbe author = Zhao, Zheng title = Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3890 sentences = 237 flesch = 51 summary = title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. In sum, structurally, SARS-CoV-2 has high global/ core structural similarity to the RDRP catalytic domains of all other RNA viruses, which provides an opportunity for structure-based COVID-19 drug design and repurposing, noting that keys differences lie in the subtle details. According to the similarity of functionsite interaction fingerprints over all complexes, it was possible to divide the binding modes into four classes, where each class contains multiple PDB structures from different kinds of viruses (Table 1) . cache = ./cache/cord-290802-761wqgbe.txt txt = ./txt/cord-290802-761wqgbe.txt === reduce.pl bib === id = cord-290195-8uaai9nv author = Stebbing, Justin title = Mechanism of baricitinib supports artificial intelligence‐predicted testing in COVID‐19 patients date = 2020-05-30 pages = extension = .txt mime = text/plain words = 6584 sentences = 326 flesch = 46 summary = Furthermore, baricitinib treatment resulted in a significant reduction (p<0.05) from baseline in plasma IL-6 at week 12 in patients with active RA who had an inadequate response to methotrexate from a phase 2b (Tanaka, Emoto et al., 2016) , randomized, placebo-controlled, dose-ranging study (Fig. 1B) . As shown in Figure 3A , all four patients showed improvement with baricitinib treatment in signs and symptoms such as cough, fever, and reduction in plasma IL-6 levels, along with a reduction in the SARS-CoV-2 RNA viral load, as detected by the real-time reverse-transcriptase-polymerase chain reaction (RT-PCR) signal from the nasopharyngeal carriage. Therefore, the impact of baricitinib on the subsequent development of protective humoral and cell-mediated anti-viral immunity in COVID-19 patients must be evaluated in randomized clinical trials (Ottoviani & Stebbing, 2020) . The finding that baricitinib is a potent AAK1/BIKE/GAK inhibitor that may reduce host cell infectivity, along with reaffirmation of its anti-cytokine profile, provide reasons to study this intervention in randomized clinical trials. cache = ./cache/cord-290195-8uaai9nv.txt txt = ./txt/cord-290195-8uaai9nv.txt === reduce.pl bib === id = cord-290428-zrlqzbss author = de Faria Coelho-Ravagnani, Christianne title = Dietary recommendations during the COVID-19 pandemic date = 2020-07-12 pages = extension = .txt mime = text/plain words = 6419 sentences = 348 flesch = 45 summary = Since to date there is no vaccine or evidence-based treatment for COVID-19, the optimization of nutrient intake through well-balanced meals and the use of good hygiene practices in food selection, preparation, and conservation is probably the most effective approach for managing the continuous risk of viral infection. There is no evidence that COVID-19 is spread through eating or touching raw fruits or vegetables; Prior to consumption, fresh fruits and vegetables should be washed or scrubbed under cold, running, potable tap water; While there are no special precautions for storing food, handwashing after putting away purchased food and before preparing food is recommended; Hands should be washed before and after food containers are washed EUFIC (2020) 19 Appropriate intakes of copper, folate, iron, selenium, zinc, and vitamins A, B 6 , B 12 , C, and D play an important role in the immune system; In general, these nutrients should be obtained through foods Supplements can be used to add nutrients to the diet in individuals who have specific challenges in meeting dietary requirements cache = ./cache/cord-290428-zrlqzbss.txt txt = ./txt/cord-290428-zrlqzbss.txt === reduce.pl bib === id = cord-290148-6cxndab8 author = Rossi, Gian Paolo title = Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients date = 2020-04-06 pages = extension = .txt mime = text/plain words = 3145 sentences = 156 flesch = 46 summary = The discovery of angiotensin converting enzyme-2 (ACE-2) as the receptor for SARSCoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) has implicated the renin-angiotensin-aldosterone system in acute respiratory distress syndrome (ARDS) and respiratory failure in patients with coronavirus disease-19 (COVID-19). However, they differ markedly: ACE-1 cleaves the dipeptide His-Leu from angiotensin I, thus generating angiotensin (Ang) II, which causes vaso-and broncho-constriction, increases vascular permeability, inflammation, and fibrosis and thereby promotes the development of ARDS and lung failure in patients infected with the SARS-CoV and SARS-CoV-2 (Yang et al., 2015) (Figure 1, panel B) . In one commentary ACE-2 was suggested to be secreted at higher amounts in patients with cardiovascular disease than in healthy individuals, and in another, it was also stated that 'ACE-2 levels can be increased by the use of ACEIs' , albeit no evidence of this occurring in the lungs Mechanisms of COVID-19 by which the SARS-COV-2 virus infects the lower airway cells and modalities to increase circulating soluble ACE-2 for therapeutic use. cache = ./cache/cord-290148-6cxndab8.txt txt = ./txt/cord-290148-6cxndab8.txt === reduce.pl bib === id = cord-290851-1e5e033r author = Gerlier, Denis title = Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date = 2011-06-12 pages = extension = .txt mime = text/plain words = 2742 sentences = 153 flesch = 45 summary = Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection cache = ./cache/cord-290851-1e5e033r.txt txt = ./txt/cord-290851-1e5e033r.txt === reduce.pl bib === id = cord-289892-yh1lioyz author = Bai, Bingke title = Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date = 2008-07-16 pages = extension = .txt mime = text/plain words = 5451 sentences = 300 flesch = 55 summary = Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. In addition, because in vitro infection model of bat SL-CoV has not so far been established, we intended to use VLPs as an alternative to study the immune responses induced in DCs. Therefore, we compared the phenotypic and functional changes of immature DCs inoculated with BVLPs or with SARS CoV VLPs. The S-specific immune activation was further confirmed in mice using S DNA vaccines. Combining the flow cytometry results in Fig. 2 , it is reasonable to draw a conclusion that the structure of BVLPs, not LPS contamination, contributed to cytokine production in BVLPs-treated DCs. We previously constructed SARS CoV VLPs and investigated the humoral and cellular immune responses induced by SARS CoV VLPs in mice [29] . cache = ./cache/cord-289892-yh1lioyz.txt txt = ./txt/cord-289892-yh1lioyz.txt === reduce.pl bib === id = cord-290414-8i8g0xdc author = Chuan, Ong Sze title = Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? date = 2020-06-21 pages = extension = .txt mime = text/plain words = 398 sentences = 32 flesch = 62 summary = title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? Unlike face masks which provided some protection against both aerosols and droplets, slit lamp shields conferred protection only against direct large droplet transmission, with a limited role in reducing aerosol transmission risk. The SARS-CoV-2 is primarily transmitted via respiratory droplets, contact with 1 contaminated surfaces, or free-floating aerosols. We attempted to replicate the 5 spread of infected aerosols and large droplets in the clinical setting of a slit lamp 6 examination, to evaluate the efficacy of protective equipment in reducing the risk of viral 7 4 The experimental setup ( Figure S1 , available online at 12 www.aaojournal.org) consisted of a slit lamp (B900 Slit Lamp, Haag-Streit Holding AG, 13 Switzerland), a mannequin face which represented the ophthalmologist, and a spray bottle at 14 the chin rest which represented respiratory particle production from the patient. cache = ./cache/cord-290414-8i8g0xdc.txt txt = ./txt/cord-290414-8i8g0xdc.txt === reduce.pl bib === id = cord-290257-2u228xe9 author = Hsu, Chih-Cheng title = Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan date = 2006-05-05 pages = extension = .txt mime = text/plain words = 3081 sentences = 170 flesch = 51 summary = title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan This paper assesses factors related to public health nurses' confidence in managing community SARS control programs. The third section contained questions (using 10-point Likert scale: 1 5 the worst to 10 5 the best) about the effectiveness of the nurse's institution in managing the SARS epidemic, including the nurse's assessment of (1) the institutional functioning on community home quarantine, (2) the quality of training received for controlling infectious disease outbreaks, and (3) the adequacy of support (for both manpower and financing) received from superior health agencies force commander said the epidemic situation was stable and advised people to return to their routine. In summary, public health nurses' confidence in the control of a SARS outbreak and people's compliance with quarantine measures are 2 major factors that can affect the success of a SARS-control program. cache = ./cache/cord-290257-2u228xe9.txt txt = ./txt/cord-290257-2u228xe9.txt === reduce.pl bib === id = cord-290333-996tmrgo author = Chiu, Cheng-Hsun title = Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1051 sentences = 74 flesch = 54 summary = title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic 7 Soon on March 23, the US Food and Drug Administration (FDA) responded that the following actions be taken: donor screening with questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2 and testing donors and/ or donor stool for SARS-CoV-2, to ensure the safety of FMT. 8e12 In addition to the recommended testing procedures, all the screening protocols include questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2. Safety alert regarding use of fecal microbiota for transplantation and additional safety protections pertaining to SARS-CoV-2 and COVID-19 Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward Additional safety protections relating to COVID-19 for faecal microbiota transplant (FMT) products Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification cache = ./cache/cord-290333-996tmrgo.txt txt = ./txt/cord-290333-996tmrgo.txt === reduce.pl bib === id = cord-290792-ggcz1zfw author = Qutob, N. title = Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study date = 2020-09-01 pages = extension = .txt mime = text/plain words = 2051 sentences = 129 flesch = 54 summary = Serological tests for the 2455 serum samples were done using an Immunoassay for the qualitative detection of antibodies against SARS-CoV-2 .The random sample of Palestinians living in the West Bank yielded 0% seroprevalence with 95% CI [0,0.0036], while the lab referrals sample yielded 4 positive cases. Most authorities rely on PCR testing results to estimate number of COVID-19 cases and make up-to-date decisions 6 . The proportion of the population who have overcome the infection without being noticed can probably be approximated by testing for antibodies against SARS-CoV-2. The study included 2491 individuals (1355 from randomly selected households and 1136 from laboratory referrals; was designed to be representative by cities and used Elecsys ® Anti-SARS-CoV-2 testing. We estimated seroprevalence as the proportion of individuals who had a positive result in the total SARS-CoV-2 antibodies in the immunoassay. Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from cache = ./cache/cord-290792-ggcz1zfw.txt txt = ./txt/cord-290792-ggcz1zfw.txt === reduce.pl bib === id = cord-290813-6ylwj5je author = Ng, Enders K. O. title = Molecular Diagnosis of Severe Acute Respiratory Syndrome date = 2006 pages = extension = .txt mime = text/plain words = 3125 sentences = 179 flesch = 53 summary = To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Subsequently, together with the improvement of viral RNA extraction in which plasma or serum requires no ultracentrifugation, two real-time quantitative RT-PCR assays, one aimed toward the polymerase region and the other toward the nucleocapsid region of the virus genome ( Fig. 1) , were developed for measuring the concentration of SARS-CoV RNA in serum/plasma samples from SARS patients (13, 14) . With the use of the real-time quantitative RT-PCR assay, SARS-CoV RNA has recently been shown to be detectable in the plasma samples of pediatric patients during different stages of SARS (Fig. 4) (14) . Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome cache = ./cache/cord-290813-6ylwj5je.txt txt = ./txt/cord-290813-6ylwj5je.txt === reduce.pl bib === id = cord-290598-wquwtovs author = li, s. title = Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1766 sentences = 126 flesch = 51 summary = Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases. In this study, we assay the IgG and IgM antibodies in ocular disease patients undiagnosed COVID-19 (people have no symptom of COVID-19 and negative result for viral RNA testing) to estimate the seropositivity rate in different type of ocular disease. We enrolled 1331 individuals with different ocular diseases but negative to SARS-CoV-2 RNA testing in Eye and ENT Hospital of Fudan University from February 2020 to May 2020. We conducted a serological survey testing the IgG and IgM antibodies against SARS-CoV-2 antigens in each participant of different ocular disease. Our study evaluated the seroprevalence in patients with different ocular diseases, including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others. cache = ./cache/cord-290598-wquwtovs.txt txt = ./txt/cord-290598-wquwtovs.txt === reduce.pl bib === id = cord-290776-l6ajq6vp author = Frithiof, Robert title = Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients date = 2020-09-29 pages = extension = .txt mime = text/plain words = 986 sentences = 71 flesch = 58 summary = title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients Patients infected with SARS-CoV-2 requiring intensive care due to coronavirus disease 2019 (COVID-19) frequently develop acute kidney injury (AKI) [1] , but the underlying mechanisms are poorly explored. In this report, SARS-CoV-2 RNA levels were prospectively investigated in urine of patients with upper or lower airway swab test PCR-verified COVID-19, admitted to a Swedish intensive care unit (ICU, n = 81). Nucleic acid was extracted from urine samples using NucliSENS® eMAG® (bioMerieux), and the amount of viral RNA was quantitated by detection of SARS-CoV-2 E and N-genes using real-time RT-PCR according to previously described protocols [5, 6] . In this cohort, SARS-CoV-2 RNA was not more frequently detected in urine of patients that died or developed acute kidney injury. cache = ./cache/cord-290776-l6ajq6vp.txt txt = ./txt/cord-290776-l6ajq6vp.txt === reduce.pl bib === id = cord-290904-ngvhk0qy author = Zheng, Zhiqiang title = Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date = 2020-07-16 pages = extension = .txt mime = text/plain words = 4471 sentences = 246 flesch = 57 summary = In this study, we aim to verify if the sequence of the immunogen used to generate mAb 1A9, as well as three other mAbs, is conserved in different coronaviruses and if these mAbs bind to the S protein of SARS-CoV-2 expressed in mammalian cell lines. IF analysis performed on transiently transfected COS-7 cells showed binding of the four mAbs to this S protein fragment of SARS-CoV-2 ( Figure 2B ). Utility of monoclonal antibody 1A9 for detection of S protein in a sandwich ELISA format and in SARS-CoV-2 infected cells Based on indirect ELISA data, mAb 1A9 has the strongest binding to S protein when compared with the other three mAbs. Hence, a sandwich ELISA was performed to determine if it can be paired with the human mAb CR3022 which is known to bind to the S1 subunit of SARS-CoV-2. cache = ./cache/cord-290904-ngvhk0qy.txt txt = ./txt/cord-290904-ngvhk0qy.txt === reduce.pl bib === id = cord-290690-53t7df81 author = Roberts, David J. title = Life in Times of COVID‐19 date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1448 sentences = 69 flesch = 60 summary = The articles by CK Lee from Hong Kong 2 and Dana Devine 3 from Canada describe how blood services in two very different epidemiological settings responded to the epidemic. However, the measures implemented for SARS in Hong Kong in 2003, namely social distancing, use of personal protective equipment and screening of donors, laid the foundation for many blood services' response to this current epidemic. Similarly, the methods developed by Dr Lee in the SARS epidemic in 2002 described in this issue, have enable Hong Kong to maintain the blood supply in this COVID-19 pandemic and have been shared by webinar and have helped many blood services cope with the current crisis (https://education.isbtweb.org/isbt/#!*menu=8*browseby=8*sortby=2*label=19776) (Accessed 1st May 2020). Perhaps the wider lesson from the experience of Hong Kong and Canada was that very real threat posed by SARS in 2003 prompted improved pandemic planning. cache = ./cache/cord-290690-53t7df81.txt txt = ./txt/cord-290690-53t7df81.txt === reduce.pl bib === id = cord-290845-bf1q4k6t author = Bouchghoul, Hanane title = Do pregnant women have protective immunity against COVID‐19? date = 2020-06-24 pages = extension = .txt mime = text/plain words = 474 sentences = 35 flesch = 51 summary = Thornton, in which the author relates that coronavirus disease 2019 (COVID-19) is less severe in pregnancy than the two previous coronavirus infections, SARS and Middle East respiratory syndrome. Furthermore, as SARS-CoV-2 infection can activate innate and adaptive immune responses with severe consequences, pregnant women could be preserved by the state of immunomodulation during pregnancy. In the most severe SARS-CoV-2 infections we report uncontrolled inflammatory innate responses and impaired adaptive immune responses that may lead to harmful tissue damage, both locally and systemically. 3 A cytokine profile has been reported in most severe SARS-CoV-2 infections, characterised by increased levels of cytokines and chemokines. As in patients infected with SARS-CoV-2, the serious complication is acute respiratory distress syndrome and ventilation of the mother may be difficult in the third trimester of pregnancy; it is certainly possible that the decision to delivery by an elective caesarean section was influenced by the understandable anxiety towards the potential consequences. COVID19 during pregnancy: a systematic review of reported cases cache = ./cache/cord-290845-bf1q4k6t.txt txt = ./txt/cord-290845-bf1q4k6t.txt === reduce.pl bib === id = cord-290950-v28kilvn author = Peyrony, Olivier title = Surfaces and equipment contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Emergency Department at a university hospital date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3158 sentences = 168 flesch = 57 summary = METHODS: We performed multiple samples from different sites in ED patients care and non-patient care areas with sterile premoistened swabs and used real-time reverse transcriptase polymerase chain reaction (RT-PCR) to detect the presence of SARS-CoV-2 ribonucleic acid (RNA). CONCLUSIONS: Our findings suggest that surfaces and equipment contamination by SARS-CoV-2 RNA in an ED during the COVID-19 outbreak is low and concerns exclusively patients' examination and monitoring rooms, preserving non-patient care areas. In this study, we aimed to assess the surface and equipment contamination by SARS-CoV-2 of an ED during the COVID-19 outbreak depending on patient care and non-patient care areas. In our study, a sample was considered positive if either both ORF1a/b and E genes were Also, we did not detect any presence of SARS-CoV-2 RNA on the different surfaces of the patients' registration desk or COVID-19 patients' waiting room. cache = ./cache/cord-290950-v28kilvn.txt txt = ./txt/cord-290950-v28kilvn.txt === reduce.pl bib === id = cord-291047-mpahl77t author = Alm, Erik title = Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3698 sentences = 124 flesch = 42 summary = We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. In this report, we applied the available nomenclatures to the European subset of the GISAID dataset to describe broad geographical and temporal trends in the distribution of SARS-CoV-2 genetic clades during the first half of 2020 and we discuss potential genomic surveillance objectives at the European level. cache = ./cache/cord-291047-mpahl77t.txt txt = ./txt/cord-291047-mpahl77t.txt === reduce.pl bib === id = cord-290687-kc7t1y5o author = Ray, Soumi title = Susceptibility and Sustainability of India against CoVid19: a multivariate approach date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4768 sentences = 303 flesch = 60 summary = Materials and Methods: Data of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. Conclusions: Though depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation. We have considered life expectancy also to inspect its impact on the number of infected cases and deaths. In This article, the data of Bacillus Calmette-Guérin (BCG) vaccination has been compared with present death rate of different countries. These diseases have shown an impact on death rate in many countries which are badly affected by coronavirus. Negative minimum temperature, a specific range of maximum temperature, lack of BCG vaccination and tendency of other lungs diseases have shown some positive impact in increasing the number of CoVid19 cases and death. cache = ./cache/cord-290687-kc7t1y5o.txt txt = ./txt/cord-290687-kc7t1y5o.txt === reduce.pl bib === id = cord-290863-f0wpsaip author = Tenforde, Mark W. title = Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 date = 2020-07-31 pages = extension = .txt mime = text/plain words = 2969 sentences = 146 flesch = 51 summary = During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. At 14-21 days from the test date, CDC personnel interviewed the randomly sampled patients or their proxies by telephone to obtain self-reported baseline demographic, socioeconomic, and underlying health information, including the presence of chronic medical conditions. cache = ./cache/cord-290863-f0wpsaip.txt txt = ./txt/cord-290863-f0wpsaip.txt === reduce.pl bib === id = cord-291024-9g4om4sf author = Isakbaeva, Elmira T. title = SARS-associated Coronavirus Transmission, United States date = 2004-02-17 pages = extension = .txt mime = text/plain words = 3669 sentences = 160 flesch = 53 summary = To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. To that end, we obtained serial biologic specimens and clinical and exposure data for 5 to 10 weeks after onset of illness from seven laboratory-confirmed U.S. SARS patients and their household contacts. We detected SARS-CoV in fecal and respiratory specimens and found that SARS case-patients may have high concentrations of virus in stools during the 2nd week of illness and continue to shed the virus in feces until at least 26 days after onset of symptoms. All upper respiratory specimens in the first 2 weeks after onset were negative for SARS-CoV by RT-PCR; this finding differs from a report in Hong Kong, where viral RNA was detected in nasopharyngeal aspirates of 68% of case-patients at day 14 (21) . cache = ./cache/cord-291024-9g4om4sf.txt txt = ./txt/cord-291024-9g4om4sf.txt === reduce.pl bib === id = cord-290671-6p23qxb8 author = Jiang, Shibo title = An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies date = 2020-01-31 pages = extension = .txt mime = text/plain words = 1113 sentences = 55 flesch = 45 summary = We have recently designed and engineered a pan-CoV fusion inhibitor, EK1 peptide, which could inhibit infection of five human coronaviruses, including SARS-CoV and MERS-CoV, and three bat-SL-CoVs [7] . Intranasal application of EK1 peptide before or after viral challenge, EK1 peptide can protect human DPP4-transgenic mice from MERS-CoV infection, suggesting its potential prophylactic and therapeutic effect against 2019-nCoV infection. The recently developed SARS-CoV and MERS-CoV neutralizing monoclonal antibodies (mAbs) and nanobodies with protective efficacy are specific to the S1 subunit of S protein, particularly the RBD [5, [8] [9] [10] . One of the rapid approaches is to evaluate the currently available SARS-CoV neutralizing antibodies with cross-neutralizing and protection activity against 2019-nCoV infection. The spike protein of SARS-CoV-a target for vaccine and therapeutic development A novel neutralizing monoclonal antibody targeting the N-terminal domain of the MERS-CoV spike protein cache = ./cache/cord-290671-6p23qxb8.txt txt = ./txt/cord-290671-6p23qxb8.txt === reduce.pl bib === id = cord-290895-tb0xald0 author = Indu, Purushothaman title = Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach date = 2020-10-26 pages = extension = .txt mime = text/plain words = 2632 sentences = 155 flesch = 53 summary = title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. RESULTS: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥ -8 kcal/mol. In this study, FDA J o u r n a l P r e -p r o o f approved small molecule antiviral drugs were screened against protein targets of SARS-CoV-2 using a computational based approach. In our study, other screened antiviral drugs such as Indinavir, Tipranavir, and Pibrentasvir showed dock energy value more than -8 kcal/mol and these drugs might also serve as an inhibitors of Mpro target of SARS-CoV-2. cache = ./cache/cord-290895-tb0xald0.txt txt = ./txt/cord-290895-tb0xald0.txt === reduce.pl bib === id = cord-290993-bsnja161 author = McAuliffe, Josephine title = Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date = 2004-12-05 pages = extension = .txt mime = text/plain words = 4548 sentences = 203 flesch = 52 summary = Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. cache = ./cache/cord-290993-bsnja161.txt txt = ./txt/cord-290993-bsnja161.txt === reduce.pl bib === id = cord-290443-naulq6q7 author = Battistoni, Allegra title = Might renin–angiotensin system blockers play a role in the COVID-19 pandemic? date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2219 sentences = 128 flesch = 50 summary = 15, 16 Therefore, the higher ACE2 expression due to chronically medicating SARS-CoV-2-infected patients with ARB may protect them against acute lung injury by blocking the deleterious effect of angiotensin II, as well as by decreasing the production of angiotensin II by up-regulating ACE2, which in turn increases the production of angiotensin (1-7). 33-36 Moreover, even though ACEIs and ARBs might increase ACE2 levels in the lungs, this might not be relevant to SARS-CoV-2 infection. [38] [39] [40] [41] [42] [43] For the second aim, not only case series, but also autoptic exams should investigate the expression and activation of RAS components in different organs during COVID-19 infection in patients treated or not with an ACEI/ARB, also investigating ACE2 polymorphisms which could impact the affinity for the spike protein of SARS-CoV-2. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury cache = ./cache/cord-290443-naulq6q7.txt txt = ./txt/cord-290443-naulq6q7.txt === reduce.pl bib === id = cord-290677-3gdcyrrz author = De Virgiliis, Francesco title = Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19 date = 2020-08-25 pages = extension = .txt mime = text/plain words = 6108 sentences = 278 flesch = 34 summary = In line with these findings, virus-induced airway hyperresponsiveness in humans seems to be mediated by the vagus nerve 53 , raising the possibility that the dyspnoea and respiratory failure observed in patients with severe COVID-19 is exacerbated by neuroimmune crosstalk in the lungs. A plausible hypothesis is that these NAMs act in concert with neuronal cells to control inflammation, and that malfunctioning of this system in older or immunocompromised people could contribute to the cytokine storm and ARDS in patients with severe COVID-19 or other respiratory virus infections. In the context of SARS-CoV-2 infection, specific tissueresident macrophages that are involved in modulating inflammation following viral infection are in close contact with vagal fibres innervating the lungs, and this 'neuroimmune synapse' could be one of the keys to controlling aberrant inflammation in patients with severe COVID-19. cache = ./cache/cord-290677-3gdcyrrz.txt txt = ./txt/cord-290677-3gdcyrrz.txt === reduce.pl bib === id = cord-291194-cl3nu5cm author = DURDAĞI, Serdar title = Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target date = 2020-06-21 pages = extension = .txt mime = text/plain words = 2146 sentences = 136 flesch = 54 summary = One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC's NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. The small molecules from NCGC-NIH Chemical Genomics Center Pharmaceutical Collection (i.e. NPC library) were used in virtual screening studies at the active site of developed TMPRSS2 model target protein. Interestingly, benzquercin was also found as potent hit compounds in our previous virtual screening study using same protocol against another important cellentry target of SARS-CoV-2 Spike/ACE2 (Durdagi et al., 2020) . In this study, a virtual drug repurposing study was performed to identify new compounds against TMPRSS2 which is an important target for the entry of the SARS-CoV-2 to the host cell. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike Receptor-Binding Domain Bound with ACE2 COVID19 Target Proteins: A Virtual Drug Repurposing Study cache = ./cache/cord-291194-cl3nu5cm.txt txt = ./txt/cord-291194-cl3nu5cm.txt === reduce.pl bib === id = cord-290978-e7imc11r author = Shevachman, M. title = A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic date = 2020-08-07 pages = extension = .txt mime = text/plain words = 4777 sentences = 283 flesch = 51 summary = A long-lasting sanitizing skin protectant that can effectively inactivate SARS-CoV-2 and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. Hence, development of an effective hand sanitizer that can generate long-lasting protective effects can offer significant benefits in minimizing rampant viral transmissions and maximize virus inactivation in a pandemic situation like SARS-CoV-2 outbreak [15, [17] [18] [19] . In order to determine the prolonged protective effects of IonLAST TM in contrast to the currently marketed products containing 70% ethyl alcohol, an in-vitro efficacy study was conducted using E. We evaluated the virucidal effects of IonLAST TM gel and the active CG-101 (5% w/w in purified water) against human Coronavirus strain 229E (hCoV229E) using a virucidal suspension test (in-vitro time-kill method) based on industry/regulatory-relevant global standardized methodologies (ASTM E1052-20). cache = ./cache/cord-290978-e7imc11r.txt txt = ./txt/cord-290978-e7imc11r.txt === reduce.pl bib === id = cord-290744-m0vpizuh author = Kindler, E. title = Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date = 2016-09-09 pages = extension = .txt mime = text/plain words = 7229 sentences = 399 flesch = 52 summary = Here, we will summarize the insights gathered so far on an important aspect of virulence and host adaptation, the interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells. The broad antiviral activity of IFNs occurs on several levels, namely virus entry, viral polymerase function, host cell translation, RNA availability, RNA stability, particle budding, apoptosis, or general boosting of innate and adaptive immune responses. Crystal structure of the middle east respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response cache = ./cache/cord-290744-m0vpizuh.txt txt = ./txt/cord-290744-m0vpizuh.txt === reduce.pl bib === id = cord-291028-ejidqmpm author = Montero Feijoo, A. title = Recomendaciones prácticas para el manejo perioperatorio del paciente con sospecha o infección grave por coronavirus SARS-CoV-2 date = 2020-03-17 pages = extension = .txt mime = text/plain words = 4603 sentences = 443 flesch = 51 summary = Debe de estar compuesto por: mascarilla N95 o preferiblemente FFP3, protección ocular ajustada de montura integral o facial completa, bata impermeable, doble guante, gorro y calzas impermeables La higiene de manos debe ser realizada por el personal antes y después de todo contacto con el paciente, particularmente antes de ponerse y después de quitarse el EPI Se deben minimizar los procesos que generen aerosoles y en el caso de ser necesarios usar siempre las medidas de protección recomendadas En el caso de ser necesaria la intubación traqueal se recomienda debe ser realizada por el profesional más experimentado disponible, realizar una inducción de secuencia rápida, evitar la ventilación manual, usar videolaringoscopio y preferiblemente tubo endotraqueal con aspiración subglótica Iniciar de forma precoz el tratamiento de soporte a los pacientes con compromiso respiratorio (taquipnea, hipoxemia) o shock séptico El uso de gafas nasales de alto flujo o ventilación mecánica no invasiva debe ser evitado en la medida de lo posible y reservado para pacientes muy concretos, puesto que son dispositivos que generan aerosoles La administración de antimicrobianos no está recomendada inicialmente, tan solo si existe sospecha de sepsis asociada o sobreinfección bacteriana. cache = ./cache/cord-291028-ejidqmpm.txt txt = ./txt/cord-291028-ejidqmpm.txt === reduce.pl bib === id = cord-291052-nstfe15a author = Cag, Yasemin title = A novel approach to managing COVID-19 patients; results of lopinavir plus doxycycline cohort date = 2020-08-27 pages = extension = .txt mime = text/plain words = 1930 sentences = 125 flesch = 54 summary = This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. Second, moderate to severe cases were hospitalized and prescribed with a regimen of lopinavir plus doxycycline plus ceftriaxone for 5 days. We hospitalized moderate to severe cases and administered lopinavir combined with doxycycline and ceftriaxone to 343 patients, among whom 161 had positive PCR test results (161/343, 46.9%). We administered hydroxychloroquine to mild cases isolated at home, lopinavir plus doxycycline to hospitalized moderate to severe cases, and favipiravir in the salvage treatment. We concluded that home isolation of mild cases is an effective means to manage the burden of disease, while lopinavir plus doxycycline is an alternative to current treatment regimens for COVID-19. cache = ./cache/cord-291052-nstfe15a.txt txt = ./txt/cord-291052-nstfe15a.txt === reduce.pl bib === id = cord-290948-cuu78cvl author = Imbert, Isabelle title = The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date = 2008-02-05 pages = extension = .txt mime = text/plain words = 7091 sentences = 356 flesch = 53 summary = Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. cache = ./cache/cord-290948-cuu78cvl.txt txt = ./txt/cord-290948-cuu78cvl.txt === reduce.pl bib === id = cord-291012-y0ufzx93 author = Ye, Qing title = SARS-CoV-2 infection causes transient olfactory dysfunction in mice date = 2020-11-10 pages = extension = .txt mime = text/plain words = 1846 sentences = 125 flesch = 51 summary = Robust viral nucleocapsid (N) protein was detected in the 89 lung from SARS-CoV-2 infected hACE2 mice, but not from the control animals 90 ( Figure S1B ). Remarkably, a significantly increased latency (152.8 s v.s. 81.8 s; p=0.022) to locate 103 food pellets was observed in SARS-CoV-2 infected mice as compared with the control 104 animals on 2 dpi ( Figure 1D ). Further RT-qPCR assay showed a dozen of 211 OR genes were significantly down regulated in response to SARS-CoV-2 infection 212 ( Figure 5E ), which may also attribute to the observed olfactory dysfunction. Interestingly, SARS-CoV-2 positive signals were also observed in mOSNs and HBCs 245 of infected animals, although we didn't detect any hACE2 expression in these cells. A) Representative multiplex immunofluorescent staining shows SARS-CoV-2 674 (SARS-CoV-2 N protein-positive) infects sustentacular cells (CK8-positive, yellow 675 arrows), Bowman's gland cells (Sox9/CK8-positive, white arrows), microvillar cells 676 (CD73/CK8-positive, cyan arrows), HBCs (CK5-postitive, gold arrows) and iOSNs 677 (GAP43-positive cache = ./cache/cord-291012-y0ufzx93.txt txt = ./txt/cord-291012-y0ufzx93.txt === reduce.pl bib === id = cord-291149-j70b7kyi author = Leuzinger, K. title = Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5480 sentences = 369 flesch = 55 summary = Aim: To cross-validate manual and automated high-throughput (Roche-cobas6800-Target1/Target2) testing for SARS-CoV-2-RNA, to describe detection rates following lockdown and relaxation, and to evaluate SARS-CoV-2-loads in different specimens. As comprehensive real-life data are scarce, we analyze the epidemiology of SARS-CoV-2detection following lockdown and relaxation measures and investigate the quantitative relationship of the different assays and explore SARS-CoV-2-loads in follow-up NOPS and in time-matched lower respiratory fluids, and in plasma samples. Basel-S-gene RT-QNAT was used for SARS-CoV-2 genome quantification in 936 follow-up NOPS from 261 patients with a positive Roche-Cobas-Target1/Target2 screening result, in 95 NOPS and time-matched lower respiratory fluids (tracheal aspirates, bronchial-alveolar lavage, or sputum) or in 259 NOPS and time-matched plasma samples from COVID-19 patients. To follow the SARS-CoV-2-detection rates after introducing more stringent lockdown measures in Switzerland in calendar week 12 (https://www.bag.admin.ch/bag/en/home/dasbag/aktuell/medienmitteilungen.msg-id-78454.html), we identified all NOPS from 12'363 symptomatic adults and children tested for SARS-CoV-2 from calendar week 14 to 24 (Follow-up cohort-1; Table 1 ) including 270 (2%) confirmed infections ( Figure 3A) . cache = ./cache/cord-291149-j70b7kyi.txt txt = ./txt/cord-291149-j70b7kyi.txt === reduce.pl bib === id = cord-291014-cfnoxhtd author = Zheng, Jian title = Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host date = 2018-02-28 pages = extension = .txt mime = text/plain words = 4394 sentences = 261 flesch = 32 summary = In one example, our studies of mice infected with SARS-CoV showed that the severity of SARS correlated with the ability to develop a virus-specific immune response, while inhibitory alveolar macrophages and inefficient activation of dendritic cells (DCs) delayed this process and aggravated disease [1] . The CoV endonuclease, nsp15, efficiently prevented activation of host cell dsRNA sensors including melanoma differentiation-associated protein 5 (Mda5), 2 0 -5 0 oligoadenylate synthetase (OAS) and PKR [93, 94 ] , while coronavirus-encoded proteases countered innate immunity, including the IFN response, through diverse pathways [95] . Glycosylation of the HA protein not only mediated virus entry into host cells [115] [116] [117] , but also modulated IAV replication and transmission [118] , and the immune response against the virus [119] [120] [121] , thus representing a potential target for vaccine and drug development [122, 123 ] . cache = ./cache/cord-291014-cfnoxhtd.txt txt = ./txt/cord-291014-cfnoxhtd.txt === reduce.pl bib === id = cord-291323-kbjyd5g3 author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5258 sentences = 266 flesch = 49 summary = We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We have constructed chimeric forms of vesicular stomatitis virus (VSV) bearing the fusion proteins of Zaire ebolavirus (ZEBOV) or SARS coronavirus 2 (SARS-CoV-2) and shown that two small-molecule inhibitors of an endosomal lipid kinase (PIKfyve) inhibit viral infection by preventing release of the viral contents from endosomes. cache = ./cache/cord-291323-kbjyd5g3.txt txt = ./txt/cord-291323-kbjyd5g3.txt === reduce.pl bib === id = cord-291361-2vn1o7ag author = Li, Jing title = Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China date = 2020-07-06 pages = extension = .txt mime = text/plain words = 3619 sentences = 185 flesch = 53 summary = title: Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China The epidemiological and clinical characteristics of the family cluster patients were analysed and compared with those of 43 contemporaneous sporadic cases. In terms of epidemiological characters and clinical symptoms, no significant differences were observed between the family cluster and sporadic cases. In this study, we aimed to investigate the epidemiological and clinical characteristics of these three family clusters of COVID-19 cases by comparing them with sporadic cases, which would provide insights for epidemic control in the context of the current serious situation worldwide. This study revealed that sporadic cases had lower levels of albumin and lymphocyte counts than family cluster cases; otherwise, there were no significant differences in terms of other epidemiological characters and clinical features between the two groups. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-291361-2vn1o7ag.txt txt = ./txt/cord-291361-2vn1o7ag.txt === reduce.pl bib === id = cord-291113-iizj932l author = Cumbo, Enzo title = Alternative Methods of Sterilization in Dental Practices Against COVID-19 date = 2020-08-08 pages = extension = .txt mime = text/plain words = 7441 sentences = 273 flesch = 40 summary = It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. cache = ./cache/cord-291113-iizj932l.txt txt = ./txt/cord-291113-iizj932l.txt === reduce.pl bib === id = cord-291374-1bpcj9dw author = Pernazza, Angelina title = Early histologic findings of pulmonary SARS-CoV-2 infection detected in a surgical specimen date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1652 sentences = 83 flesch = 41 summary = Here we describe the pathologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who developed SARS-CoV-2 infection soon after surgery. The main histologic findings observed were pneumocyte damage, alveolar hemorrhages with clustering of macrophages, prominent and diffuse neutrophilic margination within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T lymphocytes. Here we describe the histologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who later developed SARS-CoV-2 infection. A recent autopsy report highlights the finding of diffuse alveolar damage as the major lung feature also in severe SARS-CoV-2 infection [4] . Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore cache = ./cache/cord-291374-1bpcj9dw.txt txt = ./txt/cord-291374-1bpcj9dw.txt === reduce.pl bib === id = cord-291248-0kuc9jv9 author = Al-Sehemi, Abdullah G. title = Potential of NO donor furoxan as SARS-CoV-2 main protease (M(pro)) inhibitors: in silico analysis date = 2020-07-08 pages = extension = .txt mime = text/plain words = 4973 sentences = 293 flesch = 49 summary = Herein, we evaluated the phenyl furoxan, a well-known exogenous NO donor to identify the possible potent inhibitors through in silico studies such as molecular docking as per target analysis for candidates bound to substrate binding pocket of SARS-COV-2 M(pro). In the present study to validate the molecular docking, MD simulation and MM-PBSA results, crystal structure of M(pro) bound to experimentally known inhibitor X77 was used as control and the obtained results are presented herein. Docking analysis of the studied furoxan derivatives were found to have similar binding ability to SARS-CoV-2 M pro as compared to reported inhibitors. Residue wise decomposition results confirms that the interacting residues from binding pocket of SARS-CoV-2 M pro as obtained from docking analysis (Table 1 ) also shows significantly higher energetic contribution in binding with potent furoxan derivatives 22, 26 in comparison to control ( Figure 10A -C). cache = ./cache/cord-291248-0kuc9jv9.txt txt = ./txt/cord-291248-0kuc9jv9.txt === reduce.pl bib === id = cord-291315-y40s45iv author = Logunov, Denis Y title = Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia date = 2020-09-04 pages = extension = .txt mime = text/plain words = 5697 sentences = 282 flesch = 50 summary = title: Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). INTERPRETATION: The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong humoral and cellular immune responses in participants. These findings of two open, phase 1/2 non-randomised studies of a heterologous prime-boost COVID-19 vaccine based on recombinant adenoviral vectors rAd26-S and rAd5-S show that the vaccine is safe, well tolerated, and induces strong humoral and cellular immune responses in 100% of healthy participants. In our study, despite formation of neutralising antibodies to recombinant adenoviruses after vaccination with rAd26 and rAd5, formation of a humoral immune response to target antigen (SARS-CoV-2 glycoprotein S) in vaccinated volunteers was not affected. cache = ./cache/cord-291315-y40s45iv.txt txt = ./txt/cord-291315-y40s45iv.txt === reduce.pl bib === id = cord-291222-n8kgsz2e author = Park, Benjamin J. title = Lack of SARS Transmission among Healthcare Workers, United States date = 2004-02-17 pages = extension = .txt mime = text/plain words = 2399 sentences = 125 flesch = 45 summary = We conducted an investigation of healthcare workers exposed to laboratory-confirmed SARS patients in the United States to evaluate infection-control practices and possible SARS-associated coronavirus (SARS-CoV) transmission. Due to the importance of healthcare facilities in transmission of SARS worldwide, state and local health departments, together with the Centers for Disease Control and Prevention (CDC), conducted a review of U.S. healthcare workers exposed to patients positive for SARS-associated coronavirus (SARS-CoV). In the United States, potential droplet-and aerosol-generating procedures were infrequent: only one patient required mechanical ventilation, and few healthcare workers reported administering aerosolized medication or performing 1 0 (0) 0 (0) a SARS, severe acute respiratory syndrome; HCWs, healthcare workers; NA, not available due to incomplete reporting. Unprotected exposures in healthcare workers exposed to laboratory-confirmed SARS patients after full infection-control procedures were initiated (n = 43) a Exposure type n (%) Any unprotected exposure 21 (49) Without eye protection 18 (42) Without N95 or higher respirator 6 (14) Direct contact without gloves 6 (14) a SARS, severe acute respiratory syndrome. cache = ./cache/cord-291222-n8kgsz2e.txt txt = ./txt/cord-291222-n8kgsz2e.txt === reduce.pl bib === id = cord-291190-f6km3c7z author = Nasi, Aikaterini title = Reactive oxygen species as an initiator of toxic innate immune responses in retort to SARS-CoV-2 in an ageing population, consider N-acetylcysteine as early therapeutic intervention date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2999 sentences = 155 flesch = 42 summary =  SARS-CoV has been reported to modulate PARP function and thereby NAD+ biosynthesis  Cellular homeostasis and redox imbalances by SARS-CoV2 can cause stress responses  Antioxidants such as NAC could limit ROS mediated tissue damage during COVID-19 Hereby, based on literature review from the current pandemic and previous outbreaks with corona viruses we analyze the impact of the virus infection on cell stress responses and redox balance. PLA2G2D expression was shown to be increased in the lungs of middle aged mice, resulting in decreased survival and impaired T cell responses upon infection with SARS-CoV1 [20] . Interestingly, NAC administration to aged mice, diminished PLAG2D expression in both lung cells and CD11c+ DCs. In addition, increased levels of oxidized phospholipidsare a common feature associated with acute respiratory distress syndrome (ARDS) caused by viruses including SARS and H5N1. cache = ./cache/cord-291190-f6km3c7z.txt txt = ./txt/cord-291190-f6km3c7z.txt === reduce.pl bib === id = cord-291264-akuvt5ig author = Schnichels, Sven title = Kann SARS-CoV-2 das Auge infizieren? – Ein Überblick über den Rezeptorstatus in okularem Gewebe date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2764 sentences = 326 flesch = 61 summary = At the time of the research, angiotensin-converting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV‑2. Auch in dieser Studie war die exprimierte Menge von ACE2 in der epithelialen Kornea zwischen 5-und 20-mal geringer als in den anderen untersuchten Geweben (Hoden, Dünndarm, Herz) [22] . Des Weiteren wurde TMPRSS2 auch in Proben der Konjunktiva und Hornhaut nachgewiesen, mit einem im Vergleich zu ACE2 ubiquitäreren Färbungsmuster. At the time of the research, angiotensinconverting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV-2. Aufgrund der geringeren ACE2-und TMPRSS2-Expression ist das Auge nicht als Hochrisikogewebe anzusehen. Expression of SARS coronavirus S protein functional receptor-Angiotensin-converting enzyme 2 in human cornea and conjunctiva cache = ./cache/cord-291264-akuvt5ig.txt txt = ./txt/cord-291264-akuvt5ig.txt === reduce.pl bib === id = cord-291393-iht5zndl author = De Angelis, Giulia title = Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features date = 2020-10-19 pages = extension = .txt mime = text/plain words = 2704 sentences = 133 flesch = 47 summary = METHODS: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Because of substantial pneumonia-related morbidity and mortality [3] , testing for SARS-CoV-2 infection of patients who meet the suspected-case definition for COVID-19 [4] is central for their management. We comparatively explored the clinical features of 165 patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia admitted to COVID-19 wards of the Fondazione Policlinico A. We tested the hypothesis that negative patients did not differ from SARS-CoV-2 RNA positive patients by comparing features of 165 cases with clinically diagnosed 2019-nCoV pneumonia in our hospital. cache = ./cache/cord-291393-iht5zndl.txt txt = ./txt/cord-291393-iht5zndl.txt === reduce.pl bib === id = cord-291076-p350i54m author = Wang, Renxi title = The role of C5a in acute lung injury induced by highly pathogenic viral infections date = 2015-05-06 pages = extension = .txt mime = text/plain words = 5790 sentences = 373 flesch = 42 summary = Unregulated complement activation is likely to play a crucial role in the pathogenesis of acute lung injury (ALI) induced by highly pathogenic virus including influenza A viruses H5N1, H7N9, and severe acute respiratory syndrome (SARS) coronavirus. [1] [2] [3] In addition, the complement system has been implicated in the development of acute lung diseases induced by highly pathogenic viruses including influenza A virus H1N1, 4 H5N1, 5 H7N9, 6 severe acute respiratory syndrome coronavirus (SARS-Cov), 7 Middle East respiratory syndrome coronavirus (MERS-Cov). C5a-mediated release of reactive oxygen species C5a is a strong chemoattractant for neutrophils and monocytes; it then activates these cells to generate oxidative burst with release of 10 A study demonstrated that ROS are primary pathogenic molecules in pneumonia from mice infected with influenza virus. Inhibition of Complement Activation Alleviates Acute Lung Injury Induced by Highly Pathogenic Avian Influenza H5N1 Virus Infection cache = ./cache/cord-291076-p350i54m.txt txt = ./txt/cord-291076-p350i54m.txt === reduce.pl bib === id = cord-291436-cu5o8ipw author = Martínez-Hernández, Fernando title = Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals date = 2020-10-05 pages = extension = .txt mime = text/plain words = 2947 sentences = 176 flesch = 57 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect animals, however, the whole range of potential hosts is still unknown. This work makes an assessment of wildlife susceptibility to SARS-CoV-2 by analyzing the similarities of Angiotensin Converting Enzyme 2 (ACE2) and Transmembrane Protease, Serine 2 (TMPRSS2) —both recognized as receptors and protease for coronavirus spike protein— and the genetic variation of the viral protein spike in the recognition sites. Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is causing the biggest pandemic 52 of this century, and could potentially infect between 30 to 40% of the world's populations (De 53 Soto et al., 2020) . Due to its high transmission rate and mortality, researches around the world 54 are trying to get some insight about its origin through the analysis of related-virus genes 55 sequences in humans and animals (Lu R et al., 2020) , and looking for Angiotensin-Converting 56 cache = ./cache/cord-291436-cu5o8ipw.txt txt = ./txt/cord-291436-cu5o8ipw.txt === reduce.pl bib === id = cord-291388-tt9eq7e0 author = Wang, Jann-Tay title = Clinical Manifestations, Laboratory Findings, and Treatment Outcomes of SARS Patients date = 2004-05-17 pages = extension = .txt mime = text/plain words = 4355 sentences = 226 flesch = 50 summary = Previous reports have described some major clinical findings of SARS, including the temporal progression of clinical symptoms and chest radiography, the outcomes, suggested treatment protocol, and risk factors for death (4, 5) . We report on the clinical features of our SARS patients with pneumonia, with emphasis on temporal progression of laboratory findings, treatment outcome, and risk factors for poor prognosis. Methylprednisolone was usually administered in the second week of the disease if any of the following occurred: a flare of fever, progression of clinical symptoms (such as dyspnea or diarrhea), a surge or resurge of CRP level, or rapid deterioration of chest radiographic findings (development of new infiltration). A previous study reported the temporal progression of clinical and radiologic findings in SARS patients and indicated that several parameters would become more severe in the second and third week of disease (5). cache = ./cache/cord-291388-tt9eq7e0.txt txt = ./txt/cord-291388-tt9eq7e0.txt === reduce.pl bib === id = cord-291176-evb6yt0r author = Giorgi Rossi, Paolo title = Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date = 2020-08-27 pages = extension = .txt mime = text/plain words = 4559 sentences = 213 flesch = 46 summary = In this report, based on the cohort of all residents in the province of Reggio Emilia who were SARS-CoV-2-positive at nasal and pharyngeal swab and with symptoms (COVID-19 cases) since the inception of the epidemic, we describe patient characteristics and explore their role as putative prognostic factors in predicting the occurrence of hospital admission or death. We considered the following patient characteristics: age, sex, place of birth (Italy or abroad), time span (in days) from symptom onset to diagnosis/ hospitalization, and comorbidities, whose prognostic role was explored both singly (chronic obstructive pulmonary disease, arrhythmia, diabetes, coronary heart disease, heart failure, vascular diseases, obesity) and by computing the Charlson Comorbidity Index, which provides an overall measure of an individual patient's complexity [12] . While in this study we focused on the risk of hospitalization and death in a cohort of COVID-19 patients diagnosed during the epidemic in Northern Italy, it also provided us with the opportunity to describe the pattern of distribution of the disease in the whole population. cache = ./cache/cord-291176-evb6yt0r.txt txt = ./txt/cord-291176-evb6yt0r.txt === reduce.pl bib === id = cord-291360-z19ri377 author = Lan, Fan-Yun title = COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4339 sentences = 251 flesch = 52 summary = Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system's estimated total HCW population (n = 4600). cache = ./cache/cord-291360-z19ri377.txt txt = ./txt/cord-291360-z19ri377.txt === reduce.pl bib === id = cord-291523-4dtk1kyh author = Nguyen, Thanh Thi title = Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date = 2020-07-01 pages = extension = .txt mime = text/plain words = 5361 sentences = 313 flesch = 62 summary = Outcomes of a phylogenetic analysis suggest that the virus belongs to the genus Betacoronavirus, sub-genus Sarbecovirus, which includes many bat SARS-like CoVs and SARS CoVs. Another study in [5] confirms this finding by analysing genomes obtained from three adult patients admitted to a hospital in Wuhan on December 27, 2019. With the cut-off parameter C is set equal to 0.7, the hierarchical clustering algorithm separates the reference sequences into 6 clusters in which cluster "5" comprises all examined viruses of the Sarbecovirus sub-genus, including many SARS CoVs, bat SARS-like CoVs and pangolin CoVs (Fig. 7A) . With the results obtained in Fig. 7D (and also in the experiments with the DBSCAN method presented next), we support a hypothesis that bats or pangolins are the probable origin of SARS-CoV-2. In this Appendix, we first present results of the hierarchical clustering method applied to the dataset that combines Set 1 of reference sequences (Table 1 ) with all 334 SARS-CoV-2 sequences (see Fig. 9 ). cache = ./cache/cord-291523-4dtk1kyh.txt txt = ./txt/cord-291523-4dtk1kyh.txt === reduce.pl bib === id = cord-291156-zxg3dsm3 author = Bernasconi, Anna title = Empowering Virus Sequences Research through Conceptual Modeling date = 2020-05-01 pages = extension = .txt mime = text/plain words = 4600 sentences = 206 flesch = 38 summary = We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. cache = ./cache/cord-291156-zxg3dsm3.txt txt = ./txt/cord-291156-zxg3dsm3.txt === reduce.pl bib === id = cord-291281-ygrh8ces author = Durner, J. title = Critical Questions when Interpreting Coronavirus PCR Diagnostics date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1912 sentences = 121 flesch = 57 summary = In contrast to other PCR examinations, or laboratory medical analyses, currently SARS-CoV-2 diagnostic information about the device or the detection limit / sensitivity is not usually provided by the laboratory. Using a protocol without purification of viral RNA, i.e. the Munich Extraction Protocol (MEP) [2] , we could show that the type of transport medium had little influence on the detection sensitivity of SARS-CoV-2 in the PCR (Table 1) . By using this system, the sensitivity could be increased by at least one more dilution step compared to the use of commercial purification methods in PCR (Table 3) . . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 1 Comparison of different types of transport media for their influence on the detectability of SARS-CoV-2. . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 2 Comparison of different purification systems for their influence on the detectability of SARS-CoV-2 (Cp = crossing point). cache = ./cache/cord-291281-ygrh8ces.txt txt = ./txt/cord-291281-ygrh8ces.txt === reduce.pl bib === id = cord-291356-df5n5v09 author = Verma, Saguna title = ACE2 receptor expression in testes: implications in coronavirus disease 2019 pathogenesis date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1279 sentences = 71 flesch = 49 summary = Expression of angiotensin-converting enzyme 2, receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is high in the testes, therefore SARS-CoV-2 infection and its association with male reproductive health should be investigated in male coronavirus disease 2019 patients. SARS-CoV-2 infection is robust in cells expressing angiotensinconverting enzyme 2 (ACE2) receptor, a type I integral membrane protein that controls cardiac and kidney functions by negatively regulating renin-angiotensin systems [2] . High ACE2 expression may augment virus infection in the lung, heart, and small intestine that might explain the pathophysiology of acute lung and myocardial injury, and gastrointestinal symptoms reported in COVID-19 patients [1] . Cytokines and chemokines induced by SARS-CoV-2 entry into the LC and SC may recruit peripheral immune cells including macrophages and virus-specific T cells that may further potentiate inflammation and orchitis in accordance with reported symptoms from 19% of patients in study by Pan et al. cache = ./cache/cord-291356-df5n5v09.txt txt = ./txt/cord-291356-df5n5v09.txt === reduce.pl bib === id = cord-291467-vv2lrx2p author = Qing, Huiling title = The possibility of COVID‐19 transmission from eye to nose date = 2020-03-18 pages = extension = .txt mime = text/plain words = 526 sentences = 41 flesch = 62 summary = T he Coronavirus Disease 2019 , caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not only spreading throughout China but has reached more than 20 countries and has already posed threats to global health and economy. The reason is that although a small number of COVID-19 patients have conjunctivitis, not all of them show positive test of SARS-CoV-2 nucleic acid in conjunctival sac swabs. In addition, some patients did not have conjunctivitis despite positive test results for the SARS-CoV-2 nucleic acid in their conjunctiva sac swabs (Dr. Yanping Song from Wuhan City, China, the outbreak area in China, unpublished paper). Studies show that, like the severe acute respiratory syndrome coronavirus (SARS-CoV) that caused SARS, SARS-CoV-2 binds to human angiotensin-enzyme II (ACE2), using it as a cell entry receptor to invade respiratory and lung epithelium through the spike (S) protein (Zhou et al., 2020a (Zhou et al., ,2020b . cache = ./cache/cord-291467-vv2lrx2p.txt txt = ./txt/cord-291467-vv2lrx2p.txt === reduce.pl bib === id = cord-291517-ifei60ly author = Dixon, Luke title = COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1835 sentences = 118 flesch = 43 summary = title: COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia OBJECTIVE: To describe a novel case of coronavirus disease 2019 (COVID-19)-associated acute necrotizing encephalopathy (ANE) in a patient with aplastic anemia where there was early brain stem-predominant involvement. Nasopharyngeal swab testing for severe acute respiratory syndrome coronavirus (SARS-CoV-2) was positive, and CT during admission demonstrated diffuse swelling of the brain stem. 2 Here, we report a further case of possible COVID-19-related necrotizing hemorrhagic encephalopathy associated with early brain stem involvement. Extensive abnormal signal and microhemorrhage were found in a symmetrical distribution within the dorsolateral putamina, ventrolateral thalamic nuclei, subinsular regions, splenium of the corpus callosum, cingulate gyri, and subcortical Glossary ANE = acute necrotizing encephalopathy; COVID-19 = coronavirus disease 2019; GCS = Glasgow Coma Score; GTCS = generalized tonic-clonic seizure; SARS-CoV-2 = severe acute respiratory syndrome coronavirus 2. cache = ./cache/cord-291517-ifei60ly.txt txt = ./txt/cord-291517-ifei60ly.txt === reduce.pl bib === id = cord-291588-tp89j1kk author = Dorche, Maryam Sharifian title = Neurological complications of coronavirus infection; a comparative review and lessons learned during the COVID-19 pandemic date = 2020-08-07 pages = extension = .txt mime = text/plain words = 5579 sentences = 431 flesch = 42 summary = During the current pandemic, 370 patients with SARS-CoV-2 infection out of 37 studies (Table 3) were reported to suffer from AIS or transient ischemic attack (TIA). (145) Acute Necrotizing Encephalopathy(ANE) which was reported in 8 patients (Table 3) with COVID-19 is a distinct entity defined as rapid onset of neurological symptoms often secondary to a viral infection such as herpes viruses and influenza. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series Evolution and resolution of brain involvement associated with SARS-CoV2 infection: A close Clinical -Paraclinical follow up study of a case EEG Findings in Acutely Ill Patients Investigated for SARS-CoV-2/COVID-19: A Small Case Series Preliminary Report. Guillain-Barré syndrome in a patient infected with SARS-CoV-2, a case report Guillain-Barré Syndrome as a Neurological Complication of Novel COVID-19 Infection: A Case Report and Review of the Literature cache = ./cache/cord-291588-tp89j1kk.txt txt = ./txt/cord-291588-tp89j1kk.txt === reduce.pl bib === id = cord-291513-vpehn6nx author = Minich, Jeremiah title = Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date = 2020-08-18 pages = extension = .txt mime = text/plain words = 6429 sentences = 326 flesch = 55 summary = Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. Here we characterize the suitability of detecting SARS-CoV-2 RNA in experimental conditions as well as COVID-19 patient and built-environment samples using viral-inactivating storage solutions and alternative medical-grade and consumer-grade swabs. In a subset of seven COVID-19 patient nares samples stored in 95% EtOH, we also detected signi cantly higher SARS-CoV-2 viral load in RNA extracted from the swab head versus eluent ( Fig. 1b ; one-tailed paired Student's t-test p = 0.03). Based on the results from these initial experiments, we conducted a proof-of-concept study in the clinical setting by performing RT-qPCR for the SARS-CoV-2 N1 amplicon and human RNase P gene on RNA extracted from the swab head of nasal samples collected using TMI and/or CGp swabs alongside the recommended SYN swabs. cache = ./cache/cord-291513-vpehn6nx.txt txt = ./txt/cord-291513-vpehn6nx.txt === reduce.pl bib === id = cord-291420-40xsypzt author = Nelson-Sathi, Shijulal title = Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date = 2020-10-01 pages = extension = .txt mime = text/plain words = 2274 sentences = 145 flesch = 54 summary = title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. The structural analysis of the mutated spike glycoprotein of SARS-CoV-2 RBD domain was done to assess the impact of interface amino acid residue mutations on binding affinity towards the human ACE2 (hACE2) receptor. Comparative analysis of structures showed key differences in all three binding clusters of SARS-CoV-2 RBD wild type and mutant interfaces with human or mouse ACE2 (Figure 2C, 2D and Table S1 ). cache = ./cache/cord-291420-40xsypzt.txt txt = ./txt/cord-291420-40xsypzt.txt === reduce.pl bib === id = cord-291561-sxvgue36 author = Haixu, Liang title = Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date = 2019-11-25 pages = extension = .txt mime = text/plain words = 10271 sentences = 543 flesch = 50 summary = A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. cache = ./cache/cord-291561-sxvgue36.txt txt = ./txt/cord-291561-sxvgue36.txt === reduce.pl bib === id = cord-291642-xfkdxnfb author = Howley, Fergal title = Late presentation of ‘Lemierre’s syndrome’: how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic date = 2020-10-10 pages = extension = .txt mime = text/plain words = 2575 sentences = 148 flesch = 42 summary = title: Late presentation of 'Lemierre's syndrome': how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic We describe an atypical case of Lemierre's syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe an atypical case of Lemierre's syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe a severe case of Lemierre's syndrome, requiring ICU admission and intubation, where presentation and initiation of treatment were delayed by the SARS-CoV-2 pandemic. cache = ./cache/cord-291642-xfkdxnfb.txt txt = ./txt/cord-291642-xfkdxnfb.txt === reduce.pl bib === id = cord-291363-re45w37d author = Sanville, Bradley title = A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date = 2020-03-30 pages = extension = .txt mime = text/plain words = 1308 sentences = 86 flesch = 53 summary = title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . cache = ./cache/cord-291363-re45w37d.txt txt = ./txt/cord-291363-re45w37d.txt === reduce.pl bib === id = cord-291677-zcbyhsf1 author = Wilamowski, M. title = Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date = 2020-08-16 pages = extension = .txt mime = text/plain words = 5348 sentences = 308 flesch = 56 summary = To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex cache = ./cache/cord-291677-zcbyhsf1.txt txt = ./txt/cord-291677-zcbyhsf1.txt === reduce.pl bib === id = cord-291397-look6ddt author = Roberto, Palumbo title = Current treatment of COVID-19 in renal patients: hope or hype? date = 2020-09-28 pages = extension = .txt mime = text/plain words = 5827 sentences = 326 flesch = 46 summary = Given the lack of specific therapy about the ongoing SARS-CoV-2 infection, we conducted a brief review to summarize the mechanism of action and the potentially side effects of the treatment currently available, focusing on the effects of the drugs on renal disease at different stages in terms of therapeutic management and survival. A randomized clinical trial, handled by a Chinese group, suggested that in hospitalized adult patients with severe infection, no benefit was observed with lopinavir/ritonavir beyond standard care in terms of time to clinical improvement, reduction of mortality and safety (side effects and discontinuation of treatment) [29, 30] . Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial cache = ./cache/cord-291397-look6ddt.txt txt = ./txt/cord-291397-look6ddt.txt === reduce.pl bib === id = cord-291459-m56dy8us author = Hraiech, Sami title = Lack of viral clearance by the combination of hydroxychloroquine and azithromycin or lopinavir and ritonavir in SARS-CoV-2-related acute respiratory distress syndrome date = 2020-05-24 pages = extension = .txt mime = text/plain words = 1152 sentences = 64 flesch = 52 summary = In order to evaluate these results in intensive care unit (ICU) patients, we retrospectively assessed in moderate-to-severe ARDS the efficacy of hydroxychloroquine-azithromycin combination regarding viral disappearance at both day 6 of the treatment and day 6 of evolution of ARDS as compared with patients treated with lopinavir-ritonavir and a control group without any anti-viral treatment. Negative nasopharyngeal PCR for SARS-CoV-2 at day 6 following the initiation of treatment were observed in 5 (38%) patients from the lopinavir-ritonavir group as compared with 3 (18%) patients from the hydroxychloroquine-azithromycin group and 2 (20%) from the control group (p = 0.39). At day 6 following ARDS onset, PCR was negative in only 9 patients, 5 from the lopinavir-ritonavir group, 2 from the hydroxychloroquine-azithromycin group and 2 from the control group. cache = ./cache/cord-291459-m56dy8us.txt txt = ./txt/cord-291459-m56dy8us.txt === reduce.pl bib === id = cord-291710-ixun0c8g author = Su, Haixia title = Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2572 sentences = 154 flesch = 53 summary = A crystal structure of SARS-CoV-2 3CLpro in complex with baicalein, the first non-covalent, non-peptidomimetic small-molecule inhibitor, was also determined, revealing a unique binding mode of this natural product with the protease. To validate the binding of baicalin and baicalein with SARS-CoV-2 3CLpro and exclude the suspicion of being the pan-assay interference compounds (PAINS) (15) , their binding affinities with the protease were measured by isothermal titration calorimetry (ITC), widely known as an invaluable tool used to determine thermodynamic parameters of protein-ligand interactions such as Kd (Fig. 1, A and B ; Table 1 ). Moreover, the ITC profiles in combination with their chemical structures suggest that baicalin and baicalein act as noncovalent inhibitors of SARS-CoV-2 3CLpro with a high ligand binding efficiency. The mode of action of baicalein and the structural determinants associated with its binding with SARS-CoV-2 3CLpro were further explored using X-ray protein crystallography. cache = ./cache/cord-291710-ixun0c8g.txt txt = ./txt/cord-291710-ixun0c8g.txt === reduce.pl bib === id = cord-291595-8241pjpe author = Mahmudpour, Mehdi title = COVID-19 cytokine storm: The anger of inflammation date = 2020-05-30 pages = extension = .txt mime = text/plain words = 5842 sentences = 351 flesch = 43 summary = The virus-mediated down-regulation of ACE2 causes a burst of inflammatory cytokine release through dysregulation of the renin-angiotensin-aldosterone system (ACE/angiotensin II/AT1R axis), attenuation of Mas receptor (ACE2/MasR axis), increased activation of [des-Arg9]-bradykinin (ACE2/bradykinin B1R/DABK axis), and activation of the complement system including C5a and C5b-9 components. Because Ang-(1-7) exerts a critical role in counteracting the pro-inflammatory effect of RAAS, protecting from endothelial cell activation and resulting lung damage from inflammatory mediators in the cytokine storm, the administration of Ang-(1-7) or one of its similar agents to patients with COVID-19 pneumonitis has been suggested [35, 66] . We suggested ACE2/Bradykinin/DABK may be involved in the inflammatory response of SARS CoV-2; therefore, blockade of this axis by inhibiting BKB1R may ameliorate a part of the cytokine storm which occurs in COVID-19 infection. cache = ./cache/cord-291595-8241pjpe.txt txt = ./txt/cord-291595-8241pjpe.txt === reduce.pl bib === id = cord-291552-qv6koo6g author = KWAN, AMBROSE CHI‐PONG title = Severe acute respiratory syndrome‐related diarrhea date = 2005-02-23 pages = extension = .txt mime = text/plain words = 2840 sentences = 189 flesch = 65 summary = Background: Severe acute respiratory syndrome (SARS) is an emerging infectious disease and diarrhea has been reported in up to 76% of cases. The purpose of the present paper was to carry out a retrospective study of the clinical and demographic data of SARS patients with diarrhea in Princess Margaret Hospital. Patient data, need of ventilatory care, survival, number of bowel movements per day, total potassium supplement, lowest serum potassium and lowest serum albumin level were retrieved from the records and entered into a database for further analysis. described the clinical course of 75 patients in United Christian Hospital in Hong Kong and reported that 73% had watery diarrhea 7.5 ± 2.3 days after the onset of symptoms. We noted that female patients and residents of Amoy Gardens Estate were associated with diarrhea, and loglinear analysis showed that there was no significant interaction between these two factors. Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens cache = ./cache/cord-291552-qv6koo6g.txt txt = ./txt/cord-291552-qv6koo6g.txt === reduce.pl bib === id = cord-291738-nak5357h author = Padoan, Andrea title = Clinical performances of an ELISA for SARS-CoV-2 antibody assay and correlation with neutralization activity date = 2020-08-18 pages = extension = .txt mime = text/plain words = 1111 sentences = 66 flesch = 49 summary = Here we describe the clinical performances of an ELISA (Novalisa NovaTec Immunodiagnostica, Dietzenbach, Germany) for the detection of SARS-CoV-2 IgA, IgM and IgG and the comparison of results with the neutralization activity. A total of 171 leftover serum samples from 41 SARS-CoV-2 negative subjects (20 healthcare workers, 13 autoimmune patients, 8 pregnant women) and 130 COVID-19 patients (9 asymptomatic/mildly symptomatic recovered at home with supportive care and isolation, and 121 hospitalized, classified with moderate or severe disease following WHO interim guidance [5] ) were included in the study. As expected, when the time frame < 12 days was considered, the diagnostic sensitivity of the three assays was very limited and the best performances were found for IgA with a sensitivity equal to 65%, thus confirming our previously reported findings, as in most patients increased antibody levels should be detected only after 6-7 days post symptom onset (PSO) [7] [8] [9] . Evaluation of an ELISA for SARS-CoV-2 antibody testing: clinical performances and correlation with plaque reduction neutralization titer cache = ./cache/cord-291738-nak5357h.txt txt = ./txt/cord-291738-nak5357h.txt === reduce.pl bib === id = cord-291613-pfgy9ztl author = Farshidpour, Maham title = A brief review of liver injury in patients with Corona Virus Disease-19 during the pandemic date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1536 sentences = 77 flesch = 40 summary = Corona Virus Disease (COVID)-19 is a respiratory viral infection caused by a newly emergent coronavirus, Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2), which started in Wuhan, China, in December 2019 and has since evolved into a pandemic with a global risk to human health [1] . Although abnormal liver enzymes were regularly described as an extrapulmonary clinical feature, and almost one half of patients experienced grades of hepatic injury [6] [7] [8] [9] , liver damage in patients with SARS infections was primarily manifested in the mild and moderate elevation of alanine and/or aspartate aminotransferases (ALT and AST) with some degree of hypoalbuminemia and hyperbilirubinemia during the early stage of the illness [10, 11] . In this brief review article, we summarized the characteristics and mechanism of liver injury in patients with SARS-CoV-2 infection, with the hope of guiding further study on this important topic. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: a retrospective study cache = ./cache/cord-291613-pfgy9ztl.txt txt = ./txt/cord-291613-pfgy9ztl.txt === reduce.pl bib === id = cord-291505-vt5vpp60 author = Rusconi, Chiara title = SARS-CoV-2 Interstitial Pneumonia Treated With Tocilizumab in a Patient Affected by Classical Hodgkin Lymphoma date = 2020-09-01 pages = extension = .txt mime = text/plain words = 1769 sentences = 111 flesch = 40 summary = [5] [6] [7] We therefore report a case of SARS-CoV-2 interstitial pneumonia in a patient with classical Hodgkin Lymphoma (cHL) successfully treated with tocilizumab. 6, 7 More recently, a series of hematological cancer patients SARS-CoV-2 infected has been described: 3 out of 25 patients received tocilizumab, in 2 cases together with steroids, and a successful outcome has been reported for two of them. The first cHL patient affected by COVID-19 has been described by O'Kelly and colleagues: at symptoms onset, a PD-1 inhibitors induced pneumonitis was suspected, and treatment against SARS-CoV-2 was started after NPS test resulted positive. 14 To the best of our knowledge, this is the first extended report on successful tocilizumab treatment for a lymphoma patient affected by COVID-19; immunocompromised subjects may mount an antibody response and overcome SARS-CoV-2 infection, even in case of severe interstitial pneumonia. cache = ./cache/cord-291505-vt5vpp60.txt txt = ./txt/cord-291505-vt5vpp60.txt === reduce.pl bib === id = cord-291687-kwu0otpi author = Judson, Gregory L. title = Cardiovascular Implications and Therapeutic Considerations in COVID-19 Infection date = 2020-06-13 pages = extension = .txt mime = text/plain words = 5569 sentences = 273 flesch = 40 summary = A review of 44,672 confirmed COVID-19 cases from Wuhan, China, demonstrated increased mortality in patients with cardiovascular disease (10.5%), diabetes (7.3%), and hypertension (6%), which was significantly higher than the overall case-fatality rate of 2.3% [22] . These initial cases series have shown a similar relationship between underlying cardiac comorbidities with a higher prevalence of hypertension, diabetes, coronary artery disease, and obesity in patients requiring mechanical ventilation [24] . Early studies reported a prevalence of acute cardiac injury of 12% in the entire cohort as defined by either high sensitivity troponin (Hs Tn) or the MB fraction of creatinine kinase (CK-MB) [ 99 th percentile or new echocardiographic or electrocardiographic abnormalities with greater elevations in cardiac biomarkers among patients requiring ICU care [1, 20] . Case cohort studies included data in patients for whom the outcome and illness course helped further elucidate the role of cardiac injury in COVID-19 disease. cache = ./cache/cord-291687-kwu0otpi.txt txt = ./txt/cord-291687-kwu0otpi.txt === reduce.pl bib === id = cord-291577-nf80kih2 author = Baluku, Joseph Baruch title = HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1727 sentences = 129 flesch = 59 summary = From Wuhan, China, Zhu et al., reported a severe case of a newly diagnosed HIV/SARS-CoV-2 co-infected male with diabetes who presented with fever, hypoxemia, lymphopenia and chest computed tomography (CT) abnormalities, who was managed on oxygen therapy, the HIV antiviral agent lopinavir/ritonavir, moxifloxacin, gamma-globulin and methyl prednisone (5) . also reported 5 cases of HIV/SARS-CoV-2 co-infection -of whom 4 were virologically suppressed on antiretroviral therapy (ART) -from Spain, who invariably presented with cough and fever (6) . In a case series from Spain, all HIV/SARS-CoV-2 co-infected patients had cough and fever (6) . Also, similar to this patient, the HIV co-infected patient who had good adherence to ART and a suppressed viral load, presented with weakness and non-bloody diarrhoea with no significant clinical signs and laboratory abnormalities in a case series from Turkey (11) The presentation with chest pain, tachypnea, normal auscultation findings and tachycardia raises the possibility of alternative diagnoses that could mimic COVID -19. cache = ./cache/cord-291577-nf80kih2.txt txt = ./txt/cord-291577-nf80kih2.txt === reduce.pl bib === id = cord-291923-jvbehgb7 author = Rajoli, R. K. title = Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4442 sentences = 286 flesch = 55 summary = The present study used physiologically-based pharmacokinetic (PBPK) modelling to inform optimal doses of nitazoxanide capable of maintaining plasma and lung tizoxanide exposures above the reported nitazoxanide 90% effective concentration (EC90) against SARS-CoV-2. Methods: A whole-body PBPK model was constructed for oral administration of nitazoxanide and validated against available tizoxanide pharmacokinetic data for healthy individuals receiving single doses between 500 mg SARS-CoV-2 4000 mg with and without food. The model predicted optimal doses of 1200 mg QID, 1600 mg TID, 2900 mg BID in the fasted state and 700 mg QID, 900 mg TID and 1400 mg BID when given with food, to provide tizoxanide plasma and lung concentrations over the reported in vitro EC90 of nitazoxanide against SARS-CoV-2. The model and the reported dosing strategies provide a rational basis for the design (optimising plasma and lung exposures) of future clinical trials of nitazoxanide in the treatment or prevention of SARS-CoV-2 infection. cache = ./cache/cord-291923-jvbehgb7.txt txt = ./txt/cord-291923-jvbehgb7.txt === reduce.pl bib === id = cord-291719-1ku6cmwj author = Hajjo, Rima title = A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date = 2020-10-06 pages = extension = .txt mime = text/plain words = 6493 sentences = 315 flesch = 41 summary = METHODS: We developed and employed a systems biology workflow capable of identifying small-molecule antiviral drugs and vaccines that can boast immunity and affect a wide variety of viral disease pathways to protect from the fatal consequences of emerging viruses. RESULTS: Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. Herein, we describe a unique drug and vaccine repurposing workflow, and list high confidence proteins and pharmacological classes of compounds, that work as BCG mimics at the system level by inducing beneficial long lasting trained immune response. Earlier studies suggested that the documented beneficial off-target effects of BCG in protecting from non-TB infections, including perhaps COVID-19, involve a potentiation of innate immune responses through epigenetic mechanisms (56) (57) (58) . cache = ./cache/cord-291719-1ku6cmwj.txt txt = ./txt/cord-291719-1ku6cmwj.txt === reduce.pl bib === id = cord-291590-24psoaer author = Ogando, Natacha S. title = The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4299 sentences = 228 flesch = 52 summary = In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. cache = ./cache/cord-291590-24psoaer.txt txt = ./txt/cord-291590-24psoaer.txt === reduce.pl bib === id = cord-291624-fod0eyuj author = Malone, Robert W. title = COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms date = 2020-06-22 pages = extension = .txt mime = text/plain words = 6496 sentences = 354 flesch = 43 summary = We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H (2) activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. Patients with COVID-19 disease can present with a range of mild to severe non-speci c clinical signs and symptoms which develop two to fourteen days after exposure to SARS-CoV-2. The most likely mechanisms of actions include: via antiviral activity, via novel human targets, or via the on-target mechanism described in the current FDA market authorization-famotidine is a histamine receptor H 2 antagonist (and inverse agonist). To assess the possibility that famotidine may inhibit SARS-CoV-2 infection by other routes, a Vero E6 cell-based assay was performed to compare median tissue culture infectious doses (TCID50/mL) of famotidine, remdesivir, and hydroxychloroquine ( Figure 2 ). In both of these studies, the observed non-in ammatory edema in early-stage COVID-19 pulmonary disease is consistent with histamine release by mast cells. cache = ./cache/cord-291624-fod0eyuj.txt txt = ./txt/cord-291624-fod0eyuj.txt === reduce.pl bib === id = cord-291790-z5rwznmv author = Li, Qianqian title = The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4884 sentences = 362 flesch = 66 summary = We first tested the infectivity of 106 pseudotyped viruses (80 natural variants and 26 129 glycosylation mutants) in 293T-hACE2 cells, where a difference by 4 -fold in RLU compared 130 with the reference Wuhan-1 strain (GenBank: MN908947) was deemed as being significant 131 ( Figure S1 ). Notably, some RBD variants such as A475V 283 and F490L have been confirmed to have decreased sensitivity to both human sera and multiple 284 neutralizing mAbs. A475V reduced the sensitivity to 6 mAbs out of the 13 mAb used in this study, 285 while F490L reduced the sensitivity to neutralization by 3 mAbs. It is possible that antibodies in 286 14 convalescent sera are able to neutralize these critical epitopes targeted by these mAbs that are 287 known to disrupt the binding of the S protein to hACE2 receptor (Ju et Serial dilutions of mAb preparations were pre-incubated with the pseudotyped viruses at 37°C for 355 one hour before they were added to Huh-7 cells. cache = ./cache/cord-291790-z5rwznmv.txt txt = ./txt/cord-291790-z5rwznmv.txt === reduce.pl bib === id = cord-291644-5y0ioety author = Akiyama, Tomohiro title = The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond date = 2020-08-29 pages = extension = .txt mime = text/plain words = 5835 sentences = 306 flesch = 45 summary = title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond Since the long-term continuous measurement of intravascular NO was impossible, complementary tests were conducted to determine whether IFMC could increase the surface temperature, blood flow rate, velocity and vessel diameter in the human body. The present study confirmed that the natural-mineral-based novel nanomaterial IFMC, with a size of tens of nanometres (Figure 1 ), could induce an increase of intravascular NO (Figure 3) , vasodilation (vessel diameter) and blood flow rate in a living body (Figure 4) , as well as an increase of the surface temperature of a hand including fingers ( Figure 5 ). To summarise, our inter-and trans-disciplinary approach revealed that the natural-mineral-based novel nanomaterial IFMC can induce an increase of intravascular NO, vasodilation and blood flow rate, as well as an increase of hand surface temperature in a living body. cache = ./cache/cord-291644-5y0ioety.txt txt = ./txt/cord-291644-5y0ioety.txt === reduce.pl bib === id = cord-291655-l7mg5a0z author = Ku, C. W. title = Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 4332 sentences = 311 flesch = 62 summary = Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods. In order to validate the use of buccal swabs and saliva specimen as alternative diagnostic tests for SARS-CoV-2, our group performed a cross-sectional study of NPS, self-collected buccal swabs and saliva specimens collected concurrently in order to determine the positive percent agreement (PPA), negative percent agreement (NPA), overall agreement (OA), positive and negative predictive values. In this study, we have shown that saliva tests and buccal swabs were comparable to each other and were in moderate agreement with NPS for the detection of SARS-CoV-2, with PPA between 56 and 66% and PPV 95 to 100%. cache = ./cache/cord-291655-l7mg5a0z.txt txt = ./txt/cord-291655-l7mg5a0z.txt === reduce.pl bib === id = cord-291729-4l4v9jxd author = de Salazar, Adolfo title = Sample pooling for SARS-COV-2 RT-PCR screening date = 2020-09-10 pages = extension = .txt mime = text/plain words = 2641 sentences = 124 flesch = 50 summary = CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. Our objective in this study has been to evaluate the efficacy of sample pooling in a multicentre way compared to the individual analysis for the detection of COVID-19 by using different commercial platforms available for genomic extraction and amplification by RT -PCR in real time. Here we report on the high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. In summary, we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. cache = ./cache/cord-291729-4l4v9jxd.txt txt = ./txt/cord-291729-4l4v9jxd.txt === reduce.pl bib === id = cord-291747-3du4jluy author = Habashy, Noha H. title = The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking date = 2020-11-11 pages = extension = .txt mime = text/plain words = 1341 sentences = 91 flesch = 57 summary = title: The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking We evaluated the predicted anti-SARS-CoV-2 effect of major royal jelly protein (MRJP)2 and MRJP2 isoform X1, which recently showed high efficacy against other enveloped RNA-viruses (HCV and HIV). Since the end of 2019 to the present, severe acute respiratory syndrome 47 coronavirus 2 (SARS-CoV-2) has caused widespread infection and is considered 48 a threat to public health security. SARS-CoV-2, severe 865 acute respiratory syndrome-related coronavirus; nsps, non-structural proteins. Structural and 661 molecular modelling studies reveal a new mechanism of action of 662 chloroquine and hydroxychloroquine against SARS-CoV-2 infection The potential antiviral effect of major royal jelly protein2 and its 835 isoform X1 against severe acute respiratory syndrome coronavirus 2 836 (SARS-CoV-2): Insight on their sialidase activity and molecular 837 docking cache = ./cache/cord-291747-3du4jluy.txt txt = ./txt/cord-291747-3du4jluy.txt === reduce.pl bib === id = cord-291965-9r9ll83m author = Pfefferle, Susanne title = Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date = 2009-09-17 pages = extension = .txt mime = text/plain words = 4306 sentences = 245 flesch = 56 summary = Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc. cache = ./cache/cord-291965-9r9ll83m.txt txt = ./txt/cord-291965-9r9ll83m.txt === reduce.pl bib === id = cord-291920-gtzc69lc author = Meyers, Kristin J. title = A cross‐sectional community‐based observational study of asymptomatic SARS‐CoV‐2 prevalence in the greater Indianapolis area date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1466 sentences = 91 flesch = 45 summary = The Asymptomatic novel CORonavirus iNfection (ACORN) study was designed to investigate the prevalence of SARS‐CoV‐2 infection in the asymptomatic adult population of the Indianapolis metropolitan area, to follow individuals testing positive for the development of symptoms, and to understand duration of positive test results. A nested longitudinal study for participants who test positive for SARS-CoV-2 is ongoing to investigate symptom development at approximately 2 weeks post-index testing. Further, participants who test positive are invited to return for repeat testing at approximately 2-week intervals until the nasopharyngeal swab result is negative for SARS-CoV-2 infection (for a maximum of 3 additional tests). Baseline characteristics, medical history, and overall infection risk factors were generally consistent between SARS-CoV-2 positive and negative participants (Table I) . The identified prevalence of asymptomatic SARS-CoV-2 infection in the community from the ACORN study, the high This article is protected by copyright. cache = ./cache/cord-291920-gtzc69lc.txt txt = ./txt/cord-291920-gtzc69lc.txt === reduce.pl bib === id = cord-292025-dr611nse author = Kam, Kai-qian title = Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1648 sentences = 104 flesch = 52 summary = From 23 March 2020 to 3 April 2020, all inpatient pediatric confirmed COVID-19 cases diagnosed via positive SARS-CoV-2 polymerase chain reaction (PCR) from nasopharyngeal swabs using the real-time reverse transcription (rRT)-PCR assay for the E gene were included in this study. In the 9 infected children with detectable SARS-CoV-2 in buccal specimens, the mean difference of Ct values between buccal and nasopharyngeal specimens for all infected patients was 10.7 (range, 6.1-16.1), and this was statistically significant (P < .001). Our findings confirm that SARS-CoV-2 can be detected in buccal specimens of infected children and that the viral load is the highest in the first week of illness or diagnosis. In our study, the average viral loads of buccal SARS-CoV-2 were consistently lower than the respective nasopharyngeal specimens, with substantial differences between the average Ct values. Two COVID-19-infected children had negative buccal specimens despite detectable nasopharyngeal viral load. cache = ./cache/cord-292025-dr611nse.txt txt = ./txt/cord-292025-dr611nse.txt === reduce.pl bib === id = cord-291809-b7sosrc7 author = Iacovoni, Attilio title = A case series of Novel-Coronavirus infection in heart transplantation from two centers in the pandemic area in the North of Italy date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2482 sentences = 163 flesch = 53 summary = BACKGROUND Little is known about the coronavirus SARS-CoV-2 disease (COVID-19) in solid organ transplanted patients. (5) It has been speculated that 10 SARS-CoV-2 damages the host through two overlapping mechanisms, the first is the direct damage 11 of the virus itself, the second is an abnormal host response that may lead to a cytokine storm Aim of this study is to report a series of heart transplanted patients with SARS-CoV-2 infection 3 from two Heart Transplant Centers in the North of Italy describing clinical characteristics, 4 prognosis and the impact of COVID-19 on heart transplant programs. The high case fatality rate observed in heart transplanted patients may be due 3 to the characteristics of the cohort evaluated in the analysis. These characteristics may therefore explain the 12 higher incidence SARS-CoV-2 infection, the more severe clinical presentation and the higher 13 mortality rate in transplanted patients. Case report of COVID-19 in a kidney transplant recipient: Does 21 immunosuppression alter the clinical presentation? cache = ./cache/cord-291809-b7sosrc7.txt txt = ./txt/cord-291809-b7sosrc7.txt === reduce.pl bib === id = cord-291991-on70zzn0 author = Jaimes, Javier A. title = Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1700 sentences = 93 flesch = 58 summary = Here we provide context and clarify the role of the novel SARS-CoV-2 S1/S2 cleavage site in virus 90 emergence and infection, and perform a direct assessment of the proteases cleaving this site by use of 91 biochemical assays. To directly address the proteases cleaving the SARS-CoV-2 S1/S2 site, we used a biochemical peptide 95 cleavage assay (Jaimes et al., 2019), which was previously used to screen emerging influenza viruses 96 (Straus and Whittaker, 2017) . The comparative data with SARS-CoV S1/S2 site reveals that the acquisition of the 4 109 amino acid insert distinctively broadens the activating protease repertoire of the SARS-CoV-2 S1/S2 110 cleavage site to all major classes of proteolytic enzymes known to potentially activate coronavirus S 111 proteins. Activation of the SARS coronavirus spike 195 protein via sequential proteolytic cleavage at two distinct sites A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at 258 the S1/S2 cleavage site of the spike protein cache = ./cache/cord-291991-on70zzn0.txt txt = ./txt/cord-291991-on70zzn0.txt === reduce.pl bib === id = cord-291847-x3b6j5d0 author = Chan, K. H. title = The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus date = 2011-10-01 pages = extension = .txt mime = text/plain words = 2305 sentences = 122 flesch = 47 summary = The dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22–25°C and relative humidity of 40–50%, that is, typical air-conditioned environments. The better stability of SARS coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as Hong Kong) during the spring and in air-conditioned environments. Thus, information on the survival of the SARS coronavirus (SCoV) in the environment at different temperature and humidity conditions is of significant interest to understanding virus transmission. A recent study using surrogate coronaviruses (transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHC)) has investigated the effect of air 2 Advances in Virology (21) temperature and relative humidity on coronavirus survival on surface [18] . SARS CoV can retain its infectivity up to 2 weeks at low temperature and low humidity environment, which might facilitate the virus transmission in community as in Hong Kong which locates in subtropical area (Table 2(e)). cache = ./cache/cord-291847-x3b6j5d0.txt txt = ./txt/cord-291847-x3b6j5d0.txt === reduce.pl bib === id = cord-292002-g0v0xc21 author = Yang, Wenjing title = The role of imaging in 2019 novel coronavirus pneumonia (COVID-19) date = 2020-04-15 pages = extension = .txt mime = text/plain words = 4642 sentences = 228 flesch = 45 summary = Imaging features of multiple patchy areas of ground glass opacity and consolidation predominately in the periphery of the lungs are characteristic manifestations on chest CT and extremely helpful in the early detection and diagnosis of this disease, which aids prompt diagnosis and the eventual control of this emerging global health emergency. • Among the infected patients, characteristic findings on CT imaging include multiple, patchy, ground-glass opacity, crazy-paving pattern, and consolidation shadows, mainly distributed in the peripheral and subpleural areas of both lungs, which are very helpful for the frontline clinicians. The typical chest CT imaging characteristics of COVID-19 include multiple, peripheral, bilateral, patchy, sub-segmental, or segmental ground glass opacities and areas of consolidation, which are mostly distributed along the bronchovascular bundles and subpleural space. Furthermore, in the currently available reports, the most common chest CT findings in COVID-19 patients are the peripheral areas of ground glass opacity/consolidation (without subpleural sparing) which are bilateral in distribution [21] [22] [23] . cache = ./cache/cord-292002-g0v0xc21.txt txt = ./txt/cord-292002-g0v0xc21.txt === reduce.pl bib === id = cord-291954-wormplcu author = Sakulkonkij, Parichart title = A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date = 2020-08-08 pages = extension = .txt mime = text/plain words = 4424 sentences = 304 flesch = 48 summary = A novel betacoronavirus, the seventh member of coronaviruses, which is shown to infect humans and lately named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an ongoing outbreak of respiratory illness that began in December 2019 in China called coronavirus disease 2019 . On admission, a nasopharyngeal and throat swabs for SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) revealed a positive result, other laboratory findings included white blood cell count (WBC) 2480 cells/mm 3 , lymphocyte (L) 18%, neutrophil (N) 78%, and C-reactive protein (CRP) 62.7 mg/L. Although acute hypoxemic respiratory failure from COVID-19 in elderly and KT recipients in our cohort seemed to be prominent, early investigation in high-risk populations, prompt initiation of potential therapy, and intensive supportive care are important to prevent adverse consequences and mortality. Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? cache = ./cache/cord-291954-wormplcu.txt txt = ./txt/cord-291954-wormplcu.txt === reduce.pl bib === id = cord-291627-5dqwyd9r author = Yadav, Rakhee title = SARS-CoV-2-host dynamics: Increased risk of adverse outcomes of COVID-19 in obesity date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4361 sentences = 269 flesch = 48 summary = 11 Many recent studies are now reporting obesity as one of the risk factors for severity of COVID-19 in USA, Brazil, UK, Italy, Spain and France [12] [13] [14] [15] [16] [17] [18] 67 (summarised in the In the current scenario, since USA has become the epi-centre of the COVID-19 pandemic; the dynamics of patient characteristics in terms of associated complications is showing a difference from the initial data put out by China. During the present pandemic, till now, it has been well established that cardiovascular diseases and diabetes are the major risk factors for poor outcomes but considering a higher BMI to be a forerunner for both these co-morbidities, the inclusion of obesity and overweight individuals as candidates for poor COVID-19 outcomes becomes very important. 58 Thus, the interaction between ACE2-RAS system, adipose tissue and the SARS-CoV-2 could, at least partially, explain the higher morbidity and mortality risk of COVID-19 in obese patients. cache = ./cache/cord-291627-5dqwyd9r.txt txt = ./txt/cord-291627-5dqwyd9r.txt === reduce.pl bib === id = cord-291726-8670s4st author = Che, Xiao-yan title = A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date = 2006-07-01 pages = extension = .txt mime = text/plain words = 2584 sentences = 102 flesch = 46 summary = Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. cache = ./cache/cord-291726-8670s4st.txt txt = ./txt/cord-291726-8670s4st.txt === reduce.pl bib === id = cord-292152-gmru83ac author = Makrinioti, Heidi title = Intussusception in two children with SARS-CoV-2 infection in children date = 2020-08-08 pages = extension = .txt mime = text/plain words = 1752 sentences = 109 flesch = 45 summary = This report compares intussusception as likely associated with SARS-CoV-2 infection in infants that presented in Wuhan and London. Based on the data so far, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in children is shown to run a milder course with lower reported mortality rates (1, 2) . However, as the definition of suspected cases does not include presentations with gastrointestinal symptoms only, there is still no clear answer to the question "should we screen for SARS-CoV-2 infection in children who require admission to hospital with gastrointestinal symptoms?". In addition to the fact that most of the presentations of the infection in children are atypical, there is very recent evidence showing that the highest viral shedding is taking place 2 to 3 days before onset of symptoms (https://www.nature.com/articles/s41591-020-0869-5). This brief report describes two cases of intussusception in infants found to be positive with SARS-CoV-2. This report describes two infants with intussusception and SARS-CoV-2 infection. cache = ./cache/cord-292152-gmru83ac.txt txt = ./txt/cord-292152-gmru83ac.txt === reduce.pl bib === id = cord-292015-pfvgpf7v author = Brouwer, A. F. title = SARS-CoV-2 surveillance in decedents in a large, urban medical examiner's office date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2914 sentences = 184 flesch = 54 summary = We found large racial disparities in test results: despite no statistical difference in the racial distribution between those flagged and not, SARS-CoV-2 positive decedents were substantially more likely to be Black (89% vs 51%). Since mid-March (shortly after surveillance networks began detecting positive cases [7] ), WCME has been piloting daily SARS-CoV-2 surveillance by testing nasopharyngeal swabs of decedents, including both COVID-19 suspects and nonsuspects. In this analysis we compare percent positivity in WCME's piloted SARS-Cov-2 surveillance among decedents-distinguishing between those flagged by a COVID-19 checklist and those that were not-to the percent positivity of tests among people in the surrounding catchment area. The percent positivity for SARS-CoV-2 infection among decedents flagged for testing by a COVID-19 checklist in large, urban medical examiner's office closely mirrored percent positivity among tests in the catchment population. . https://doi.org/10.1101/2020.08.03.20162883 doi: medRxiv preprint CoV-2 test results among decedents not flagged by the COVID-19 checklist. cache = ./cache/cord-292015-pfvgpf7v.txt txt = ./txt/cord-292015-pfvgpf7v.txt === reduce.pl bib === id = cord-292004-9rpoll7y author = Mitchell, Hugh D. title = The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections date = 2019-09-20 pages = extension = .txt mime = text/plain words = 8357 sentences = 373 flesch = 43 summary = The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The same relationships between network topology, viral pathogenicity, and gene expression that were observed for influenza virus were also noted when we used a similar dataset of SARS-CoV infections, thus further validating our analysis and demonstrating that these relationships appear to apply to respiratory viruses in general. cache = ./cache/cord-292004-9rpoll7y.txt txt = ./txt/cord-292004-9rpoll7y.txt === reduce.pl bib === id = cord-292050-x3isowrt author = Ackerman, Emily E. title = Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning date = 2020-09-26 pages = extension = .txt mime = text/plain words = 6948 sentences = 384 flesch = 44 summary = Based on network topology and controllability, 16 proteins involved in translation, cellular transport, cellular stress, and host immune response are predicted as regulators of the SARS-CoV-2 infected cell. Screenings of experimentally verified SARS-CoV-2 interacting host proteins [7] have elucidated key infection mechanisms which, when compared to drug databases, have predicted a range of possible targets for repurposing. To assess whether the robust controllability classifications of the driver and virus interacting proteins are a result of the network's connectivity structure, a randomization analysis was performed as developed in previous work [11] . The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. cache = ./cache/cord-292050-x3isowrt.txt txt = ./txt/cord-292050-x3isowrt.txt === reduce.pl bib === id = cord-291916-5yqc3zcx author = Hozhabri, Hossein title = The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date = 2020-08-05 pages = extension = .txt mime = text/plain words = 16737 sentences = 847 flesch = 45 summary = cache = ./cache/cord-291916-5yqc3zcx.txt txt = ./txt/cord-291916-5yqc3zcx.txt === reduce.pl bib === id = cord-291987-zpkzzldu author = To, Kelvin KW title = False-positive SARS-CoV-2 serology in three children with Kawasaki disease date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1397 sentences = 98 flesch = 53 summary = Recent reports showed that children with KD-like disease from KD low prevalence regions had positive SARS-CoV-2 serology despite a negative SARS-CoV-2 polymerase chain reaction (PCR) in respiratory samples. To describe three paediatric Kawasaki Disease patients with false positive SARS-CoV-2 serology. We aim to describe three paediatric Kawasaki Disease patients diagnosed during the COVID-19 outbreak with false positive SARS-CoV-2 serology. Blood (5 mL) was collected from each patient and serum was obtained for the detection of IgG against SARS-CoV-2 nucleoprotein (NP) and spike protein receptor binding domain (RBD) using a microsphere-based antibody assay as described previously. Three Chinese children, who had no epidemiological links with COVID-19 patients were diagnosed with typical KD during the peak of COVID-19 outbreak in Hong Kong (Table 1) 10 11 We believe the false positive SARS-CoV-2 serology results were unrelated to the administration of IVIG for treating KD. cache = ./cache/cord-291987-zpkzzldu.txt txt = ./txt/cord-291987-zpkzzldu.txt === reduce.pl bib === id = cord-292030-cjz4nuag author = Qiu, Guangyu title = Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection date = 2020-04-13 pages = extension = .txt mime = text/plain words = 5689 sentences = 305 flesch = 48 summary = In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. 26−29 In this work, we developed a dual-functional LSPR biosensor through combining the photothermal effect and plasmonic sensing transduction for SARS-CoV-2 viral nucleic acid detection. The plasmonic chip with the twodimensional distribution of nanoabsorbers (AuNIs) is capable to generate the local PPT heat and transduce the in situ hybridization for highly sensitive and accurate SARS-CoV-2 detection. According to the phase-sensing diagram in Figure 4b and S6a, the LSPR response of the dual-functional AuNI biosensor started to increase when the RdRp-COVID genes were injected into the microfluidic chamber at about 200 s and attained the maximum phase value after about 800 s hybridization. cache = ./cache/cord-292030-cjz4nuag.txt txt = ./txt/cord-292030-cjz4nuag.txt === reduce.pl bib === id = cord-292173-95t89yee author = Villani, Federico Alcide title = COVID-19 and Dentistry: Prevention in Dental Practice, a Literature Review date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4583 sentences = 260 flesch = 49 summary = Several authors have highlighted the importance of telephone triage and/or clinic questionnaires, body temperature measurement, usage of personal protective equipment, surface disinfection with ethanol between 62% and 71%, high-speed instruments equipped with an anti-retraction system, four-handed work, and large-volume cannulas for aspiration. The aim of this narrative review is to investigate preventive measures in dental practice by assessing the operator and patient health protection during the new COVID-19 emergency by considering past experiences in terms of prevention, as the virus was only recently discovered. In addition, a second search was made: "masks" OR "disinfectants" OR "PPE" OR "dental equipment" AND "Covid-19" OR "coronavirus" OR "SARS-CoV-2". instead obtained diametrically opposing results; they showed, through a randomized controlled clinical study on 3591 subjects, that health workers who used N95 masks continuously during the shift or in situations considered to be at high risk, presented an 85% chance of not contracting a viral infection transmitted via droplets [36] . cache = ./cache/cord-292173-95t89yee.txt txt = ./txt/cord-292173-95t89yee.txt === reduce.pl bib === id = cord-292041-a65kfw80 author = Orienti, Isabella title = Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19 date = 2020-05-27 pages = extension = .txt mime = text/plain words = 6110 sentences = 334 flesch = 34 summary = At present, there is no vaccine or effective standard treatment for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (or coronavirus disease-19 (COVID-19)), which frequently leads to lethal pulmonary inflammatory responses. Therefore, due to its poly-pharmacology, fenretinide administration by pulmonary formulations may be expected to be protective against acute lung injury (ALI)/ acute respiratory distress syndrome (ARDS) caused by SARS-CoV infection and could represent a useful tool in a multimodal therapy aimed at establishing a rapid anti-inflammatory and antiviral effect. Pulmonary delivery of fenretinide could be a valuable tool in COVID-19 due to the possibility of obtaining a very high drug concentration in the airway and alveolar epithelia, thus triggering a rapid onset of local anti-inflammatory response. Moreover, the pulmonary administration of fenretinide, in combination with the drugs that are currently used in SARS-CoV-2 infection, could represent a new, effective tool in COVID-19 treatment. cache = ./cache/cord-292041-a65kfw80.txt txt = ./txt/cord-292041-a65kfw80.txt === reduce.pl bib === id = cord-292236-eudcs9t2 author = Wang, Yishan title = Asymptomatic cases with SARS‐CoV‐2 infection date = 2020-05-22 pages = extension = .txt mime = text/plain words = 901 sentences = 60 flesch = 43 summary = On 31 March 2020, Chinese Health Authorization announced that numbers of asymptomatic cases with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection will be made to the public daily. Currently, asymptomatic cases are not included in the confirmed patients in everyday-report according to the "Novel Coronavirus Pneumonia Diagnosis and Treatment Protocol (7th edition, trial)." Another study reported that the asymptomatic ratio was estimated at 30.8% among evacuees tested positive for SARS-CoV-2 using the information on Japanese nationals that were evacuated from Wuhan, China. Studies from single-center reported 4% to 6% cases with SARS-CoV-2 did not develop any symptom during the course of the disease. Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data. Alert for non-respiratory symptoms of Coronavirus Disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection cache = ./cache/cord-292236-eudcs9t2.txt txt = ./txt/cord-292236-eudcs9t2.txt === reduce.pl bib === id = cord-292250-jjhpwgfa author = Heinz, Nicole title = A case of an Infant with SARS‐CoV‐2 hepatitis early after liver transplantation date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1294 sentences = 80 flesch = 45 summary = We present a case of a pediatric liver transplant recipient diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection four days after receiving a living donor liver allograft from her mother. The team decision to proceed with the transplant contemplated the rate of progression of chronic liver failure, the risk of patient mortality before the epidemic abated, the perceived lower risk at the onset of the epidemic compared to the weeks/months ahead and the fact that neither the donor nor recipient demonstrated signs or symptoms of SARS-CoV-2 infection. Follow-up evaluation in the outpatient clinic on POD 30 was notable for resolution of all symptoms including diarrhea, but liver enzymes were again elevated in the setting of a subtherapeutic tacrolimus trough (Table 1, Figure 2) . On POD 36 the patient remained clinically well, liver enzymes had improved and tacrolimus trough was at target. A case of an Infant with SARS-CoV-2 hepatitis early after liver transplantation cache = ./cache/cord-292250-jjhpwgfa.txt txt = ./txt/cord-292250-jjhpwgfa.txt === reduce.pl bib === id = cord-292337-74c69z28 author = Tsai, Shin-Han title = Transporting Patient with Suspected SARS date = 2004-07-17 pages = extension = .txt mime = text/plain words = 1471 sentences = 90 flesch = 57 summary = Because medical facilities are limited on these islands, the Department of Health authorized the National Aeromedical Consultation Center (NACC), a physician-based 24-hour control center that coordinates all aeromedical transport of critically ill or injured patients within Taiwan, to coordinate transporting these patients to designated SARS hospitals in Taipei. When leaving the pre-isolation room, the physician and the PIU were sprayed with a sodium hypochloride solution before the first layer of personal protective equipment was removed. Although one report by Christopher and Eitzen (2) suggested the value of an aeromedical team to evacuate patients with suspected lethal, infectious diseases, limited evidence supported a safer means of transportation that would possibly reduce transmission of SARS to persons taking part in the mission. Interim guidance: air medical transport for severe acute respiratory syndromes (SARS) patients cache = ./cache/cord-292337-74c69z28.txt txt = ./txt/cord-292337-74c69z28.txt === reduce.pl bib === id = cord-292209-d1ty9etr author = Horta, Bernardo L title = Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4330 sentences = 247 flesch = 53 summary = Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. The present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in 133 sentinel cities throughout Brazil, as part of the EPICOVID-19 study (www.epicovid19brasil.org). In summary, the analyses of the three waves of national serological surveys in Brazil showed important inequalities in the prevalence of antibodies against SARS-CoV-2 according to family wealth, education and ethnic groups. Yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against SARS-CoV-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. cache = ./cache/cord-292209-d1ty9etr.txt txt = ./txt/cord-292209-d1ty9etr.txt === reduce.pl bib === id = cord-292274-upwn9o2m author = Ghaffari, Abdi title = COVID-19 Serological Tests: How Well Do They Actually Perform? date = 2020-07-04 pages = extension = .txt mime = text/plain words = 4648 sentences = 244 flesch = 44 summary = While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . Typically, RDT test strips use a drop of blood to detect the presence of patient antibodies (IgG, IgM, or IgA) produced against a specific SARS-CoV-2 antigen ( Figure 2 ). Critics point to gaps in our understanding of immune response to COVID-19 infection, including the ability of serological tests to detect neutralizing antibodies and the capacity of the immune system to provide long-term immunity against SARS-CoV-2. cache = ./cache/cord-292274-upwn9o2m.txt txt = ./txt/cord-292274-upwn9o2m.txt === reduce.pl bib === id = cord-292578-co5essuw author = Johnson, Marina title = Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date = 2020-08-02 pages = extension = .txt mime = text/plain words = 2111 sentences = 121 flesch = 52 summary = OBJECTIVES: The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS: A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). CONCLUSION: Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality. In summary, the MSD multiplexed coronavirus panel assay evaluated in this study is highly reproducible, specific and sensitive for the detection of anti-SARS-CoV-2 antibody over 14 days since the onset of COVID-19 symptoms. cache = ./cache/cord-292578-co5essuw.txt txt = ./txt/cord-292578-co5essuw.txt === reduce.pl bib === id = cord-292045-pnid9dmq author = Kumar, Manish title = First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3037 sentences = 183 flesch = 58 summary = While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. Consistency between abundance of SARS-CoV-2 genetic materials and number of confirmed cases was observed in the previous reports in Australia, France, Italy, Spain and Japan Further, referring to the limitations of the present study owing to lockdown scenario, we recommend that although based MPC analysis, the efficiency of RNA extraction and RT-PCR is considered high for all the wastewater samples collected for this study, the efficiency of PEG method could have been better established. The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 cache = ./cache/cord-292045-pnid9dmq.txt txt = ./txt/cord-292045-pnid9dmq.txt === reduce.pl bib === id = cord-292423-jupcit75 author = Narkhede, Rohan R. title = Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences date = 2020-06-17 pages = extension = .txt mime = text/plain words = 2709 sentences = 134 flesch = 47 summary = With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. We proposed some natural products including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene as potential candidate for exerting the antiviral activity against SARS-CoV-2 infection using molecular docking study. The results acquired after docking analysis in terms of ligand binding affinity (kcal/mol), the interaction of natural products with the COVID-19 main protease, and the drug-like properties were shown in (Table 1 ). A promising binding to the COVID-19 main protease was observed in the case of rhein and berberine where both natural products were found to exhibit an affinity of − 8.9 and − 8.1 kcal/mol respectively. cache = ./cache/cord-292423-jupcit75.txt txt = ./txt/cord-292423-jupcit75.txt === reduce.pl bib === id = cord-292350-cmrtg91a author = Mondal, Samhati title = Thromboembolic disease in COVID-19 patients: A brief narrative review date = 2020-09-14 pages = extension = .txt mime = text/plain words = 4000 sentences = 207 flesch = 29 summary = Table 1 & 2 summarize the various thrombotic complications noted in COVID-19 patients as published as of June 6 th , 2020 obtained by a literature search on PubMed and EMBASE using combinations of the following MeSH terms: COVID-19, SARS-COV2, novel corona virus, thrombosis, thromboembolic complications, pulmonary embolism. Clinical signs and symptoms of thrombosis such as cutaneous manifestations ("COVID toe") [84] , overt line thrombosis, arterial or venous clots, unexplained increase in oxygen requirement, or organ dysfunction should raise suspicion and prompt further investigation and/or discussion about therapeutic intervention [7] As new information becomes available, it appears increasingly important to routinely monitor platelet count, PT/aPTT, d-dimer, and fibrinogen to assist in anticipating and managing thrombotic complications. ICU patients positive for COVID-19 with elevated d-dimer levels and/or clinico-radiological suspicion for thrombosis as noted above should be considered for therapeutic anticoagulation only after careful assessment of their bleeding risk. cache = ./cache/cord-292350-cmrtg91a.txt txt = ./txt/cord-292350-cmrtg91a.txt === reduce.pl bib === id = cord-292462-zbjig3pt author = Backhaus, Andreas title = Common Pitfalls in the Interpretation of COVID-19 Data and Statistics date = 2020-06-07 pages = extension = .txt mime = text/plain words = 3163 sentences = 158 flesch = 58 summary = Daily data releases on confi rmed COVID-19 cases and deaths provide information on the course of the pandemic. In its simplest form, the case fatality rate divides the total number of confi rmed deaths by COVID-19 by the to-Forum hence be lower than the IFR (and the CFR). Recall that the computation of the CFR only requires the total number of confi rmed deaths by COVID-19 and the total number of confi rmed cases of infections with SARS-CoV-2. Italy and South Korea are among those countries that have published demographic characteristics of their confi rmed cases comparatively early and consistently over the course of the pandemic. Consequently, the IFR divides the total number of confi rmed deaths by COVID-19 by the total number of infections with SARS-CoV-2. cache = ./cache/cord-292462-zbjig3pt.txt txt = ./txt/cord-292462-zbjig3pt.txt === reduce.pl bib === id = cord-292367-ocbsmmt6 author = El-Masri, Maher M. title = Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date = 2012-02-29 pages = extension = .txt mime = text/plain words = 3089 sentences = 134 flesch = 49 summary = Such comparison is intended to provide a surrogate measure of the influence that strict enforcement of infection control strategies during the SARS outbreak may have had on the risk of HAIs. Methods A retrospective chart review was conducted on the medical records of 400 intensive care patients who were admitted to the ICU three months before and during the 2003 SARS outbreak. The intent of such comparison is to provide a surrogate measure of the influence that strict enforcement of infection control guidelines might have had on the risk of developing HAIs. A retrospective chart review was conducted on the medical records of 400 patients who were admitted to the intensive care unit of a community-based hospital in Southwestern Ontario. cache = ./cache/cord-292367-ocbsmmt6.txt txt = ./txt/cord-292367-ocbsmmt6.txt === reduce.pl bib === id = cord-292561-iy06b9h9 author = Miesbach, Wolfgang title = COVID-19: Coagulopathy, Risk of Thrombosis, and the Rationale for Anticoagulation date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4889 sentences = 262 flesch = 45 summary = The novel coronavirus infection (COVID-19) is caused by the new coronavirus SARS-CoV-2 and is characterized by an exaggerated inflammatory response that can lead to severe manifestations such as adult respiratory syndrome, sepsis, coagulopathy, and death in a proportion of patients. 5 While most patients show only mild symptoms, 6 a characteristic feature of COVID-19 is that a proportion of patients develop severe complications within a short time after infection, such as adult respiratory syndrome (ARDS) or disseminated intravascular coagulation (DIC), sepsis followed by organ failure, and death. 15 These laboratory changes are consistent with previous studies which showed that hypoalbuminemia, lymphopenia, and C-reactive protein 4 mg/dL were the predictive factors for the progression of pneumonia to respiratory failure in MERS-CoV-infected patients and that elevated lactate dehydrogenase (LDH) levels were associated with hospital-acquired infection with SARS-CoV. cache = ./cache/cord-292561-iy06b9h9.txt txt = ./txt/cord-292561-iy06b9h9.txt === reduce.pl bib === id = cord-292347-d7xq7x5g author = Carter, Linda J. title = Assay Techniques and Test Development for COVID-19 Diagnosis date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3426 sentences = 227 flesch = 51 summary = 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. cache = ./cache/cord-292347-d7xq7x5g.txt txt = ./txt/cord-292347-d7xq7x5g.txt === reduce.pl bib === id = cord-292544-m7jyydf1 author = Grau-Pujol, Berta title = Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4575 sentences = 257 flesch = 50 summary = OBJECTIVES: The aim of this study is to assess the efficacy of the use of pre-exposure prophylaxis (PrEP) with hydroxychloroquine against placebo in healthcare workers with high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in reducing their risk of coronavirus disease 2019 (COVID-19) disease during an epidemic period. As secondary endpoints, we will obtain: i) the SARS-CoV-2 seroconversion in the PrEP group compared to placebo during the 6 months of follow-up in healthcare workers with negative serology at day 0; ii) the occurrence of any adverse event related with hydroxychloroquine treatment; iii) the incidence of SARS-CoV-2 infection and COVID-19 among healthcare workers in the non-PrEP group, among the total of healthcare workers included in the non-PrEP group during the study period; iv) the risk ratio for the different clinical, analytical and microbiological conditions to develop COVID-19; v) a repository of serum samples obtained from healthcare workers confirmed COVID-19 cases for future research on blood markers to predict SARS-CoV-2 infection. cache = ./cache/cord-292544-m7jyydf1.txt txt = ./txt/cord-292544-m7jyydf1.txt === reduce.pl bib === id = cord-292256-jp80u828 author = Moriguchi, Takeshi title = A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1742 sentences = 121 flesch = 53 summary = We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient's nasopharyngeal specimen is negative. cache = ./cache/cord-292256-jp80u828.txt txt = ./txt/cord-292256-jp80u828.txt === reduce.pl bib === id = cord-292650-i95upz10 author = Marafini, Irene title = LOW FREQUENCY OF COVID-19 IN INFLAMMATORY BOWEL DISEASES date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1053 sentences = 56 flesch = 53 summary = The risk of infection or death due to Covid-19 in patients with inflammatory bowel diseases (IBD) is unknown at this stage. We here examined the frequency of symptoms/signs suggestive of Covid-19 in IBD patients and assessed the risk of SARS-CoV-2 infection in IBD. Cumulative incidence of SARS-CoV-2 infection in IBD was calculated dividing the positive cases by the overall population of IBD patients enrolled for the study. Although, we need more robust epidemiological data to draw a conclusion regarding the incidence rate of Covid-19 in IBD, our findings suggest that IBD patients are not at increased risk of Covid-19 as compared with the general population. It is likely that the incidence of SARS-CoV-2 infection in our IBD population is underestimated as the majority of the patients did not underwent rhino-pharyngeal swab. published recently by Norsa and colleagues, who reported no case of SARS-CoV-2 infection in a cohort of IBD patients living in a high-risk area of Northern Italy (7). cache = ./cache/cord-292650-i95upz10.txt txt = ./txt/cord-292650-i95upz10.txt === reduce.pl bib === id = cord-292386-hfbgigj6 author = Borges, Lysandro Pinto title = Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3897 sentences = 219 flesch = 49 summary = In order to support the ongoing public health response, all participants who tested positive for SARS-CoV-2 antibodies were contacted by phone by staff from the designated authorities to track the infection. The importance of NPIs on reducing the infection rate was observed in Vo, Italy, where prevalence estimates showed a significant decrease after a period of lockdown, suggesting that viral transmission could be effectively suppressed by combining the early isolation of detected cases with social distancing total assessed cases in that city [CI, 11.5% -21.4%]) and 12 (5.9% of the total assessed cases in that city [CI, 3.1% -10.1%]) cases; Itabaiana, that presented 55 (14.8% of the total assessed cases in that city [CI, 11.4 -18.9]) and 17 of the total assessed cases in that city (5.4% [CI, 3.1% -8.4%]) cases, being the three cities with the highest seroprevalence of SARS-CoV-2 in the state. cache = ./cache/cord-292386-hfbgigj6.txt txt = ./txt/cord-292386-hfbgigj6.txt === reduce.pl bib === id = cord-292387-2xv3wgaq author = D′Agostino, Armando title = Brief Psychotic Disorder During the National Lockdown in Italy: An Emerging Clinical Phenomenon of the COVID-19 Pandemic date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4555 sentences = 240 flesch = 44 summary = Approximately 2 months after the COVID-19 outbreak in Lombardy and 50 days into national lockdown, we began to hospitalize patients with brief psychotic episodes at a remarkable rate. We report a case series of all consecutive patients admitted to the 2 psychiatric inpatient units of the San Paolo University Hospital who were discharged with a diagnosis of BPD during the COVID-19 pandemic lockdown in Milan, Italy (March 9 to May 18). In order to standardize the evaluation criteria, the following set of instruments was employed: the Brief Psychiatric Rating Scale (BPRS) 20 was performed as a global measure of psychopathology upon admission and at discharge; the presence of stressful life events in the 12 months before the lockdown was assessed using Paykel's interview for recent life events 21 ; the Structured Clinical Interview for DSM (SCID-II) 22 was performed to evaluate the presence of a personality disorder; and the Temperament and Character Inventory-240 items (TCI-240) 23 was administered to investigate personality dimensions. cache = ./cache/cord-292387-2xv3wgaq.txt txt = ./txt/cord-292387-2xv3wgaq.txt === reduce.pl bib === id = cord-292416-3hhi4wps author = Sarid, Ronit title = Investigating an Emerging Virus During a Sudden Pandemic Outbreak date = 2020-07-31 pages = extension = .txt mime = text/plain words = 4869 sentences = 230 flesch = 41 summary = Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. cache = ./cache/cord-292416-3hhi4wps.txt txt = ./txt/cord-292416-3hhi4wps.txt === reduce.pl bib === id = cord-292751-tk1oggi9 author = Hosseini, Elahe Seyed title = The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3784 sentences = 222 flesch = 46 summary = Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-292751-tk1oggi9.txt txt = ./txt/cord-292751-tk1oggi9.txt === reduce.pl bib === id = cord-292580-caxb9ob9 author = Chang, Z title = RNAi therapeutics: Can siRNAs conquer SARS? date = 2005-11-10 pages = extension = .txt mime = text/plain words = 1311 sentences = 95 flesch = 60 summary = The epidemic of the severe acute respiratory syndrome (SARS) [1] [2] [3] in 2003 heightened the necessity for us to develop strategies to cope with emerging infectious diseases. Recent work has also shown that selected siRNAs can effectively inhibit SARS-CoV replication in cultured cells. This new study provided, for the first time, the evidence that siRNAs have a significant effect on suppression of SARS-like symptoms in a macaque model. The authors' results indicated that the SARS-CoV-infected monkeys had attenuated SARS-like symptoms when the animals were treated with siRNA duplexes. Rhesus macaque is a good model for studying human SARS-CoV infections. Although this approach is obviously not a cure for SARS since the treated animals also developed SARS symptoms, it can be used as a complementary strategy to reduce the severity of the disease and to low the viral load in patients. cache = ./cache/cord-292580-caxb9ob9.txt txt = ./txt/cord-292580-caxb9ob9.txt === reduce.pl bib === id = cord-292972-p7ifetgw author = Jiang, Xuan title = Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS? date = 2020-02-24 pages = extension = .txt mime = text/plain words = 1010 sentences = 64 flesch = 54 summary = However, based on our analysis of a larger dataset available so far, we find there is no observable difference between the incubation time for SARS-CoV-2, severe acute respiratory syndrome coronavirus (SARS-CoV), and middle east respiratory syndrome coronavirus (MERS-CoV), highlighting the need for larger and well-annotated datasets. The symptom onset date of the first identified patient infected by SARS-CoV-2 was December 1st, 2019, which is about 14 days before the subsequent reported cases. 3 The first estimate of mean incubation time was based on the exposure information of 10 confirmed early SARS-CoV-2 infected cases in Wuhan, China and was predicted to be 5. The reported estimate of the SARS-CoV-2 incubation time was based on limited case data. For the MERS datasets, for example, we found only five reports published with accessible raw data, but one report had several patients with incubation times ranged from 0 to 21 days. cache = ./cache/cord-292972-p7ifetgw.txt txt = ./txt/cord-292972-p7ifetgw.txt === reduce.pl bib === id = cord-292657-gq3965se author = Das, Piyanki title = Decoding the global outbreak of COVID-19: the nature is behind the scene date = 2020-06-22 pages = extension = .txt mime = text/plain words = 5030 sentences = 221 flesch = 43 summary = The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. cache = ./cache/cord-292657-gq3965se.txt txt = ./txt/cord-292657-gq3965se.txt === reduce.pl bib === id = cord-292675-tkyngspy author = Qi, Furong title = Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses date = 2020-03-19 pages = extension = .txt mime = text/plain words = 3513 sentences = 217 flesch = 50 summary = For this purpose, we collected single cell gene expression matrices from 13 relatively normal human tissues, consisting of lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] from published literatures. We analyzed the single cell co-expression profiles of 51 known ssRNA viral receptors and 400 membrane proteins, including ACE2, in the identified 119 cell types across the 13 human tissues. Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] (Table S1) . cache = ./cache/cord-292675-tkyngspy.txt txt = ./txt/cord-292675-tkyngspy.txt === reduce.pl bib === id = cord-293059-2iwzieqm author = Tao, Huaqiang title = Dysimmunity and inflammatory storm: Watch out for bone lesions in COVID-19 infection date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1818 sentences = 104 flesch = 38 summary = It has been approved that inflammation-induced pathogenesis in COVID-19 infection has a strong correlation with incidence of cardiovascular metabolic diseases and gastrointestinal injury (1) . However, studies on the correlation between pro-inflammatory cytokine responses and bone metabolism in COVID-19 patients are still lacking. In this special background, will inflammatory disorder and immune imbalance affect bone metabolism after COVID-19 infection? Simultaneously, hypoxia inducible factor (HIF-1) was proven to facilitate osteoclast differentiation by overexpressing RANKL and nuclear factor of activated T cells cytoplasmic 1 (NFATc1) (14) . As osteoblasts and osteoclasts exist in approach with immune cells in medullary cavity, it's no wonder that immune system shares massive regulatory cytokines, signaling molecules and transcription factors with bone biology. Apart from that, NF-κB and AP-1 stimulate the expression of many elements which required for inflammatory cytokines, driving up osteoclast activity and usually implicated inhibition on proliferation and differentiation of osteoblasts (22) . cache = ./cache/cord-293059-2iwzieqm.txt txt = ./txt/cord-293059-2iwzieqm.txt === reduce.pl bib === id = cord-292874-6zjqflhz author = SØRENSEN, MORTEN DRÆBY title = Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date = 2006-05-10 pages = extension = .txt mime = text/plain words = 1560 sentences = 110 flesch = 54 summary = abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV. In February 2003, the new and previously unknown deadly coronavirus causing severe acute respiratory syndrome (SARS-CoV) was brought to the attention of the World Health Organization (WHO) by Dr. Carlo Urbani and his colleagues. Creation of immune phage-display libraries for immunized donors has shown a particular efficiency in selecting neutralizing antibodies (NABs) against different viruses, for example, rabies, 39 varicella-zoster, 40 hepatitis A 41 and E, 42 measles, 43 and respiratory syncytial virus. cache = ./cache/cord-292874-6zjqflhz.txt txt = ./txt/cord-292874-6zjqflhz.txt === reduce.pl bib === id = cord-292600-mgvrbfzd author = Ly, T. D. A. title = Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020. date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2220 sentences = 125 flesch = 52 summary = In March-April, we enrolled 411 homeless individuals, 77 asylum-seekers, 58 people living in precarious conditions, and 152 employees working in these accommodation centres and collected nasal samples. In this study, we present the results of SARS-CoV-2 screening campaigns conducted among sheltered homeless individuals, in comparison with asylum-seekers, other persons living in precarious conditions, and employees working in the accommodation centres. . https://doi.org/10.1101/2020.05.05.20091934 doi: medRxiv preprint Table 3 shows SARS-CoV-2 positivity rates among homeless people according to the time of screening, demographics and housing facility, using univariate analysis. We found an overall 7.0% SARS-CoV-2 positivity rate, with most infected individuals among homeless people and employees working in homeless facilities, while no cases were found in asylum-seekers and in other people also living in precarious conditions. Grey cells: four groups in study : Homeless people (N=411); other specific population living in precarious conditions (N=58), asylum seekers (N=77), and employees (N=152) and SARS-CoV-2 prevalence in each group. cache = ./cache/cord-292600-mgvrbfzd.txt txt = ./txt/cord-292600-mgvrbfzd.txt === reduce.pl bib === id = cord-292985-w62xaa4f author = Römer, Rudolf A. title = Flexibility and mobility of SARS-CoV-2-related protein structures date = 2020-07-12 pages = extension = .txt mime = text/plain words = 5201 sentences = 341 flesch = 61 summary = We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. cache = ./cache/cord-292985-w62xaa4f.txt txt = ./txt/cord-292985-w62xaa4f.txt === reduce.pl bib === id = cord-293080-b4pxjrcj author = Zhang, Chunyan title = Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4173 sentences = 190 flesch = 55 summary = Immunological diagnosis of COVID-19 is mainly achieved through testing specific antibody IgM and IgG responses after human infection with SARS-CoV-2 and is based on antigen-antibody capturemethods. Such methods include lateral flow assays and provide the advantages of easy operation, quick test results, no need of a special laboratory site with (complex) instruments, and high sensitivity and specificity, and is suitable for carrying out large-scale SARS-CoV-2 infection/screening as point-of-care sites [7] . Based on the process of SARS-CoV-2 infection and the production of specific antibody responses, a diagnostic IgG and IgM detection assay would be the most useful method to diagnosis the occurrence of COVID-19 and development of pulmonary disease. In the present study, the recombinant protein and test strip for detecting the SARS-CoV-2 antibody by the antigen capturing method, and its preparation method were provided, supporting a new method for SARS-CoV-2 infection screening, diagnosis, disease monitoring and prognosis evaluation. cache = ./cache/cord-293080-b4pxjrcj.txt txt = ./txt/cord-293080-b4pxjrcj.txt === reduce.pl bib === id = cord-292880-zegtr19k author = Hu, Fuying title = Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3794 sentences = 242 flesch = 52 summary = title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 Here, we reviewed medical records of patients with laboratory-confirmed COVID-19 in Tianmen, a city in Hubei province adjacent to Wuhan, to describe the clinical features, epidemiological characteristics and risk factors associated with prolonged viral shedding of COVID-19. Time from illness onset to hospital admission (P < 0.001), radiographic extent (P = 0.002), lymphocyte count (P = 0.038), albumin (P = 0.046), hs-CRP (P = 0.010), and prescription of antibiotics (P < 0.001), arbidol (P = 0.020), oseltamivir (P <0.001), corticosteroid (P < 0.001) and immunoglobulin (P < 0.001) were also associated with prolonged viral shedding. In the present study, we described the epidemiological and clinical characteristics of patients in Tianmen city, Hubei province, and concluded that delayed admission, and prescription of corticosteroid and oseltamivir were significantly associated with prolonged viral shedding. cache = ./cache/cord-292880-zegtr19k.txt txt = ./txt/cord-292880-zegtr19k.txt === reduce.pl bib === id = cord-293167-3bd3adip author = Nepal, Gaurav title = Neurological manifestations of COVID-19: a systematic review date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5534 sentences = 311 flesch = 44 summary = Most patients infected by SARS-CoV-2 have presented with a mild clinical course: beginning with fever and dry cough, progressing to a form of mild or moderate respiratory disease, and resolving without specific treatment [2] . A retrospective observational study from Wuhan, China, reported that six (2.8%) patients, out of the 214 reviewed COVID-19 cases, developed ischemic stroke. A retrospective observational study from a different center in Wuhan, China, found eleven (5.0%) patients, out of 221 reviewed COVID-19 cases, developed acute ischemic stroke. Those who had COVID-19 infection with new onset of ischemic stroke were more likely to have a severe SARS-CoV-2 presentation, an advanced age (71.6 ± 15.7 years versus 52.1 ± 15.3 years), and preexisting cardiovascular risk factors including hypertension, diabetes, and previous cerebrovascular disease. A retrospective observational study from Wuhan, China, reported one (0.45%) patient, out of 221 reviewed COVID-19 cases, who developed intracerebral hemorrhage. cache = ./cache/cord-293167-3bd3adip.txt txt = ./txt/cord-293167-3bd3adip.txt === reduce.pl bib === id = cord-292673-00s3wgem author = Buonaguro, Luigi title = SARS-CoV-2 RNA polymerase as target for antiviral therapy date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2062 sentences = 120 flesch = 50 summary = In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. Journal of Translational Medicine *Correspondence: l.buonaguro@istitutotumori.na.it 1 Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy Full list of author information is available at the end of the article SARS-CoV-2 is a positive-sense RNA virus belonging to the Orthocoronavirinae (coronavirus, CoV) family and, in particular, to the genus beta (group 2) together with the other two new human coronaviruses SARS-CoV and MERS-CoV. However, all three of them have been developed for negative-sense RNA viruses which show a significant difference in the RdRp sequence and structure compared to the positive-sense SARS-CoV-2 RNA virus. In conclusion, as for all RNA viruses, the RdRp of the newly identified positive-sense human SARS-CoV-2 RNA virus represents the most optimal target for an antiviral drug. cache = ./cache/cord-292673-00s3wgem.txt txt = ./txt/cord-292673-00s3wgem.txt === reduce.pl bib === id = cord-293367-0fe62h2f author = Henderson, Lauren A. title = American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS‐C) Associated with SARS‐CoV‐2 and Hyperinflammation in COVID‐19. Version 1 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 6229 sentences = 333 flesch = 41 summary = Since its initial description in December 2019 in Wuhan China, coronavirus disease 2019 , caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly evolved into a worldwide pandemic affecting millions of lives.(1) Unlike adults, the vast majority of children with COVID-19 have mild symptoms. Reports in the literature and unpublished observations by members of the panel both note that some patients with MIS-C can decompensate rapidly; however, the risk factors that predispose patients to such severe and progressive illness have not been identified.(10, 13) Accordingly, children with abnormal vital signs, concerning physical examination findings, significantly elevated inflammatory markers, or signs of cardiac involvement will need to be admitted to the hospital for supportive care while Tier 2 testing is completed. cache = ./cache/cord-293367-0fe62h2f.txt txt = ./txt/cord-293367-0fe62h2f.txt === reduce.pl bib === id = cord-292733-dya40tln author = Lancman, Guido title = Severe COVID-19 virus reactivation following treatment for B cell acute lymphoblastic leukemia date = 2020-10-02 pages = extension = .txt mime = text/plain words = 1377 sentences = 84 flesch = 51 summary = She was initially hospitalized with COVID-19 in April and developed a high antibody titer with two negative nasal polymerase chain reaction (PCR) swabs for SARS-CoV-2 on discharge. She developed a severe COVID-19 pneumonia with lymphopenia, high inflammatory markers, and characteristic bilateral ground-glass opacities on chest CT, requiring high-flow nasal cannula and transfer to the intensive care unit. Given the short time frame from leukemia treatment to PCR positivity and the low case rate in mid-June in New York City, reinfection appears to have been unlikely and SARS-CoV-2 reactivation is a possible explanation. This case illustrates the risks of treating recently recovered COVID-19 patients with immunosuppressive therapy, particularly lymphocyteand antibody-depleting therapy, and raises new questions about the potential of SARS-CoV-2 reactivation. Here, we report a case of severe COVID-19 virus reactivation following chemotherapy, including rituximab, cytarabine, and dasatinib for B cell acute lymphoblastic leukemia (B-ALL). cache = ./cache/cord-292733-dya40tln.txt txt = ./txt/cord-292733-dya40tln.txt === reduce.pl bib === id = cord-292988-q1yz9y8k author = Zumla, Alimuddin title = Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3157 sentences = 174 flesch = 39 summary = title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . cache = ./cache/cord-292988-q1yz9y8k.txt txt = ./txt/cord-292988-q1yz9y8k.txt === reduce.pl bib === id = cord-293382-uyat0w58 author = Walker, Susanne N. title = SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4793 sentences = 274 flesch = 55 summary = title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients The first assay is surface plasmon resonance (SPR) based and can quantitate both antibody binding to the SARS-CoV-2 spike protein and blocking to the Angiotensin-converting enzyme 2 (ACE2) receptor in a single experiment. The second assay is enzyme-linked immunosorbent assay (ELISA) based and can measure competition and blocking of the ACE2 receptor to the SARS-CoV-2 spike protein with antispike antibodies. Four of the six guinea pigs immunized against SARS-CoV-2 spike showed statistically significant ACE2 blocking, and importantly, the pooled sera was comparable to the average AUC from all six serum samples (Fig. 3F, Fig. S2D ). First, we showed that an ELISA-based assay could be employed to measure receptor blocking antibodies in animals vaccinated with the SARS-CoV-2 spike protein. cache = ./cache/cord-293382-uyat0w58.txt txt = ./txt/cord-293382-uyat0w58.txt === reduce.pl bib === id = cord-293315-kx4x2g24 author = Colmenero, I. title = SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases date = 2020-06-20 pages = extension = .txt mime = text/plain words = 2530 sentences = 162 flesch = 43 summary = title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases CONCLUSIONS: Although the clinical and histopathological features were similar to other forms of chilblains, the presence of viral particles in the endothelium and the histological evidence of vascular damage, support a causal relation of the lesions with SARS‐CoV‐2. 4 Most patients have been negative for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) when tested by PCR of nasopharyngeal and oropharyngeal swabs, and less than 50% have a history of exposure to positive household contacts or previous history of mild upper respiratory or gastrointestinal symptoms. Lymphocytic vascular damage was the hallmark feature in biopsies from our 7 patients with COVID-19 related chilblains. 25 We have demonstrated the presence of viral particles within endothelial cells in lesional skin biopsies from patients presenting with chilblains during the COVID-19 pandemic. Chilblain-like lesions: a case series of 41 patients during the COVID-19 pandemic cache = ./cache/cord-293315-kx4x2g24.txt txt = ./txt/cord-293315-kx4x2g24.txt === reduce.pl bib === id = cord-292883-7hvq9qaj author = Nguyen-Contant, Phuong title = S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date = 2020-09-25 pages = extension = .txt mime = text/plain words = 5334 sentences = 264 flesch = 51 summary = RBD-binding MBCs sampled in the convalescent phase of SARS-CoV-2 infection expressed Abs with relatively low numbers of V gene mutations, suggesting that this component of the response largely reflected naive B cell activation by novel epitopes (20) . Approximately one-third of non-SARS-CoV-2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs (Fig. 1A) . Since the healthy donor samples in our analysis were collected 6 to 10 years before the emergence of SARS-CoV-2, we considered the possibility that a recently circulating HCoV was responsible for the higher anti-OC43 S IgG titers in the convalescent subjects. In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-exposed subjects, consistent with the higher levels of serum IgG against these antigens (Fig. 2E to H) . cache = ./cache/cord-292883-7hvq9qaj.txt txt = ./txt/cord-292883-7hvq9qaj.txt === reduce.pl bib === id = cord-293169-rd12xwvl author = Black, Margaret A. title = Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples date = 2020-11-07 pages = extension = .txt mime = text/plain words = 3000 sentences = 155 flesch = 51 summary = OBJECTIVES: We validate the use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. Herein, we describe clinical validation of a new lateral flow immunoassay (LFI) test intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood. Plasma, serum, whole blood, and capillary blood (finger stick) samples from patients diagnosed with COVID-19 by PCR were tested with the 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) (Biolidics Ltd.), and the results were correlated with those obtained by enzyme-linked immunosorbent assay (ELISA), the gold standard for serologic detection of antibodies. Furthermore, we show J o u r n a l P r e -p r o o f that capillary whole blood obtained by finger stick shows comparable sensitivity for detecting anti-SARS-CoV-2 IgM and IgG antibodies as venous blood samples. cache = ./cache/cord-293169-rd12xwvl.txt txt = ./txt/cord-293169-rd12xwvl.txt === reduce.pl bib === id = cord-292742-mio4przi author = McAloose, Denise title = From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date = 2020-10-13 pages = extension = .txt mime = text/plain words = 6364 sentences = 309 flesch = 47 summary = KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4). cache = ./cache/cord-292742-mio4przi.txt txt = ./txt/cord-292742-mio4przi.txt === reduce.pl bib === id = cord-293180-f1ulk9ce author = Li, R W K title = Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs date = 2004-08-14 pages = extension = .txt mime = text/plain words = 4289 sentences = 295 flesch = 51 summary = Special management protocols and modified measures that regulate droplet and aerosol contamination in a dental setting have to be introduced and may include the reduction or avoidance of droplet/aerosol generation, the disinfection of the treatment field, application of rubber dam, pre-procedural antiseptic mouthrinse and the dilution and efficient removal of contaminated ambient air. In the first part of this two-part article an account of the epidemiology, virology, pathology and management of Severe Acute Respiratory Syndrome (SARS) was provided together with public health issues and general aspects of infection control. On the other hand smaller droplets (or aerosols, generally under 10 µm in size) or small-particle residue of evaporated droplets are usually airborne and are entrained in the air for a lengthy period • SARS is a highly infectious disease and dental personnel are likely to be at risk because of the nature of their profession, working in close proximity to the patient. cache = ./cache/cord-293180-f1ulk9ce.txt txt = ./txt/cord-293180-f1ulk9ce.txt === reduce.pl bib === id = cord-292836-1o2ynvy3 author = Ogimi, Chikara title = What’s New With the Old Coronaviruses? date = 2020-04-21 pages = extension = .txt mime = text/plain words = 5194 sentences = 267 flesch = 44 summary = In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] . cache = ./cache/cord-292836-1o2ynvy3.txt txt = ./txt/cord-292836-1o2ynvy3.txt === reduce.pl bib === id = cord-293127-c27qh5y7 author = Monteleone, Pedro AA title = A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments date = 2020 pages = extension = .txt mime = text/plain words = 4508 sentences = 224 flesch = 47 summary = In this review, we summarize the latest research progress related to COVID-19 epidemiology and the reported data of pregnant women, and discuss the current evidence of COVID-19 infections during pregnancy and its potential consequences for assisted reproductive treatments. The current outbreak of the novel 2019 coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China in December 2019 and subsequently spread to many other countries. Coronaviruses are a large family of viruses known to cause symptoms ranging from a common cold to more severe diseases, such as the severe acute respiratory syn A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments Pedro AA Monteleone 1,2 , Mayra Nakano 1,2 , Victor Lazar 1 , Alecsandra P Gomes 1 , (Drosten et al., 2003; Ksiazek et al., 2003) , and MERS coronavirus (MERS-CoV) was the pathogen responsible for severe respiratory disease outbreaks in the Middle East in 2012 (Zaki et al., 2012) . cache = ./cache/cord-293127-c27qh5y7.txt txt = ./txt/cord-293127-c27qh5y7.txt === reduce.pl bib === id = cord-293544-nemw29r7 author = Valdivia, Arantxa title = Qualitative assessment of SARS‐CoV‐2‐specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay date = 2020-08-02 pages = extension = .txt mime = text/plain words = 765 sentences = 57 flesch = 45 summary = Here, we carried out qualitative assessment of SARS‐CoV‐2‐specific antibody avidity using an urea (6M) dissociation test performed on a lateral flow immunochromatographic IgG/IgM device. 2 Although serology testing is mainly aimed at identifying individuals who have previously been exposed to SARS-CoV-2, it may also aid in diagnosis of ongoing COVID-19, particularly in RT-PCR negative patients who present at relatively late times after infection. 3 Knowledge of the precise timing of infection may be of clinical and epidemiological relevance as viral shedding in the upper respiratory tract seems to continue up to 7 to 9 days after onset of symptoms in patients presenting with mild or moderate COVID-19. T A B L E 2 Qualitative assessment of SARS-CoV-2-specific antibody avidity in serial serum samples from patients with COVID Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay cache = ./cache/cord-293544-nemw29r7.txt txt = ./txt/cord-293544-nemw29r7.txt === reduce.pl bib === id = cord-293557-jcgc93it author = Recalde, Borja title = Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients date = 2020-08-23 pages = extension = .txt mime = text/plain words = 1412 sentences = 93 flesch = 47 summary = title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients In December 2019, an outbreak of severe acute respiratory syndrome associated to SARS-CoV2 was reported in Wuhan, China. To date, little is known on histopathological findings in patients infected with the new SARS-CoV2. Postmortem multiorgan biopsies in 10 patients who died with SARS COV-2 infection were performed after oral authorisation of a first-degree relative. In this report, we describe the histopathology of lung damage in COVID-19 with DAD in all lung samples, associated with medium size arterial thrombosis in four cases, and the presence of viral RNA in all organs. It is remarkable that 9 out of the 10 patients had at least one organ with significant amount of SARS-CoV2 RNA, being most prevalent in lung tissue. Pathological findings of COVID-19 associated with acute respiratory distress syndrome cache = ./cache/cord-293557-jcgc93it.txt txt = ./txt/cord-293557-jcgc93it.txt === reduce.pl bib === id = cord-293304-kakxmc14 author = Achutha, A. S. title = Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5877 sentences = 369 flesch = 58 summary = The interactions with the active site residues especially with Cys145 and His41, which are involved in catalytic diad for proteolysis, make these compounds potent main protease inhibitors. Molecular docking studies with the 3CL pro protein were performed to analyze the drug likeness as well as to correlate the binding energy of the docked complex with various physicochemical properties of the active molecules, which will aid in the design of new anti-COVID-19 medicatives. By using the formulated regression Model 2, we predicted the binding energy of some primaquine analogs obtained from the literature and PubChem database and then carried out their molecular docking studies on 3CL pro target to check the inhibitory potency of the ligands, given in Table 4 . Thirty molecules that showed lower binding energies were subjected to molecular docking analysis to identify the potent 3CL pro inhibitors (Supplementary Figure S5) . cache = ./cache/cord-293304-kakxmc14.txt txt = ./txt/cord-293304-kakxmc14.txt === reduce.pl bib === id = cord-293517-8derad2p author = Fischer, Johannes C. title = Correction to: The role of passive immunization in the age of SARS-CoV-2: an update date = 2020-10-30 pages = extension = .txt mime = text/plain words = 191 sentences = 21 flesch = 70 summary = key: cord-293517-8derad2p authors: Fischer, Johannes C.; Zänker, Kurt; van Griensven, Martijn; Schneider, Marion; Kindgen-Milles, Detlef; Knoefel, Wolfram Trudo; Lichtenberg, Artur; Tamaskovics, Balint; Djiepmo-Njanang, Freddy Joel; Budach, Wilfried; Corradini, Stefanie; Ganswindt, Ute; Häussinger, Dieter; Feldt, Torsten; Schelzig, Hubert; Bojar, Hans; Peiper, Matthias; Bölke, Edwin; Haussmann, Jan; Matuschek, Christiane title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update journal: Eur J Med Res cord_uid: 8derad2p High activity natural killer cell during target attack. Footprint of previously attached natural killer cell can be identified by patchy membrane residuals on the target cell surface. When will NK-cells join the cellular immune cascade to fight SARS-CoV-2? The role of passive immunization in the age of SARS-CoV-2: an update Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Fischer et al. Eur J Med Res (2020) 25:53 cache = ./cache/cord-293517-8derad2p.txt txt = ./txt/cord-293517-8derad2p.txt === reduce.pl bib === id = cord-293136-lfwqzf8m author = Escosa‐García, Luis title = Ten key points about COVID‐19 in children: the shadows on the wall date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3631 sentences = 241 flesch = 52 summary = It was initially named Pediatric multisystem inflammatory syndrome (PIMS) temporally associated with COVID-19 by the Royal College of Paediatrics and Child Health (RCPCH) 18 To date, some cases of neonatal SARS-CoV-2 infection have been reported 27 28 . Recent data from a German study indicate that viral loads in the very young (age group 0-6 years) do not significantly differ from those of adults 44 To put it briefly, SARS-CoV-2 PCR of nasopharyngeal swab is considered the gold standard diagnostic test for acute COVID-19 disease. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center's observational study Characteristics and Outcomes of Children With Coronavirus Disease 2019 (COVID-19) Infection Admitted to US and Canadian Pediatric Intensive Care Units cache = ./cache/cord-293136-lfwqzf8m.txt txt = ./txt/cord-293136-lfwqzf8m.txt === reduce.pl bib === id = cord-293082-fw7deem8 author = Zhang, Guangzhi title = Animal coronaviruses and SARS‐CoV‐2 date = 2020-08-16 pages = extension = .txt mime = text/plain words = 2068 sentences = 157 flesch = 48 summary = As of April 7, just four months since its first outbreak, more 48 than 3.4 million confirmed cases and 238,000 deaths have been recorded in 215 countries, areas, 49 and territories, and moreover it seems that severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2) that causes COVID-19 will probably continue to circulate around the globe 51 (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/). The health 52 authorities and governments of affected countries have paid attention to current pandemic and 53 have taken immediate measures to block COVID-19 transmission, including utilization of personal 54 protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis 55 and sharing, public health education, maintaining social distance, the creation of diagnostics, 56 therapeutics, and vaccines, etc (Xiao and Torok 2020) . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain cache = ./cache/cord-293082-fw7deem8.txt txt = ./txt/cord-293082-fw7deem8.txt === reduce.pl bib === id = cord-293259-o51fnvuw author = Sinaei, Reza title = Why COVID-19 is less frequent and severe in children: a narrative review date = 2020-09-25 pages = extension = .txt mime = text/plain words = 7043 sentences = 359 flesch = 44 summary = Thus far, only a small number of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection have involved children, so that they have accounted for only 1-5% of total patients [2, [6] [7] [8] [9] [10] . Severe SARS-CoV-2 infection is characterized by a hyperproinflammatory response or cytokine storm state that results to acute respiratory distress syndrome (ARDS) and multisystem inflammatory syndrome (MIS). The search strategy was constructed based on searching terms 2019 novel coronavirus, COVID-19, SARS-CoV-2 with using and/or, also the terms of child, pediatric, newborn, infant, adolescence, adult, age, age groups, severity, epidemiology, prevalence, difference, immune system, etiology, reasons in title, abstract, and key words. The first results stem from some considerations that children have a less vigorous immune response to the virus than adults because the cytokine storm is thought to be important in the pathogenesis of severe SARS-CoV-2 infections [28] . cache = ./cache/cord-293259-o51fnvuw.txt txt = ./txt/cord-293259-o51fnvuw.txt === reduce.pl bib === id = cord-293265-qqxlwpju author = Zeng, Yong title = Clinical characteristics of 9 cancer patients with SARS-CoV-2 infection date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1370 sentences = 89 flesch = 51 summary = D-dimmer rise, infection index rise, and chest CT(computed tomography) progression may be clinical warning indicators for severe patients, in our study, more 50% of patients had elevated levels of these indicators, but only 44% (including the dead) of patients had received treatment in the intensive care unit. Cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may be effective in the prevention and treatment of novel coronavirus-infected pneumonia (NICP). Studies [10] found that the combination of traditional Chinese medicine and western medicine was effective in the prevention and treatment of NICP in all stages, and the response rate of symptoms such as fever, cough and fatigue were significantly increased in ordinary patients after taking lianhua qingwen granules. By analyzing 9 cancer patients with SARS-CoV-2 infection, cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may cache = ./cache/cord-293265-qqxlwpju.txt txt = ./txt/cord-293265-qqxlwpju.txt === reduce.pl bib === id = cord-293056-kz3w0nfh author = Indes, Jeffrey E. title = Early Experience with Arterial Thromboembolic Complications in Patents with COVID-19 date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1933 sentences = 125 flesch = 51 summary = A retrospective case-control study design was used to identify, characterize and evaluate potential risk factors for arterial thromboembolic disease in SARS-CoV-2 positive patients. Although not statistically significant, in patients with arterial thromboembolism, patients who were SARS-CoV-2 positive compared to those testing negative or not tested tended to be male (66.7 % v. Treatment of arterial thromboembolic disease in the COVID-19 positive patients included open thromboembolectomy in 6 patients (40%), anticoagulation alone in 4 (26.7%) and 5 (33.3%) did not require or their overall illness severity precluded additional treatment. The SARS-CoV-2 positive group included patients with a range of COVID-19 16 symptomatology (mild to severe) as well as those tested as part of routine preoperative 17 preparation. Patients with arterial thrombosis who were SARS-CoV-10 2 positive had significantly higher D-dimer levels, BMI, were younger, and less often on 11 antiplatelet medications as compared to patients who were SARS-CoV-2 negative or not tested. cache = ./cache/cord-293056-kz3w0nfh.txt txt = ./txt/cord-293056-kz3w0nfh.txt === reduce.pl bib === id = cord-293710-f1tzt6jb author = Karolyi, M. title = Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1424 sentences = 85 flesch = 49 summary = SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Studies showed reduced mortality in hospitalized COVID-19 patients treated vs not treated with anticoagulants in patients with a sepsis-induced-coagulopathy (SIC) score ≥ 4 or D-Dimer > 6 times upper limit of normal [4] . We describe a case series of four outpatients with proven SARS-CoV-2 infection who developed pulmonary embolism (PE) with a delay of 2-4 weeks after symptom onset with complete resolution of initial symptoms. The characteristics of outpatients who are suitable for anticoagulation have to be determined.In conclusion, new onset of dyspnea and tachycardia after initial resolution of COVID-19 symptoms ("disease trajectory characterised by two peaks") should raise suspicion of PE and a CT scan should be considered. cache = ./cache/cord-293710-f1tzt6jb.txt txt = ./txt/cord-293710-f1tzt6jb.txt === reduce.pl bib === id = cord-293579-w5sub348 author = Che, Xiao-yan title = Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date = 2005-06-15 pages = extension = .txt mime = text/plain words = 2564 sentences = 115 flesch = 49 summary = By use of Western blot analysis, indirect immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA), antigenic cross-reactivity between severe acute respiratory syndrome (SARS)—associated coronavirus (SARS-CoV) and 2 HCoVs (229E and OC43) was demonstrated in immunized animals and human serum. In the present study, we cloned the nucleocapsid genes of SARS-CoV, HCoV-229E, and HCoV-OC43 and produced specific animal antisera to determine if the nucleocapsid protein is responsible for the observed antigenic cross-reactivity. The serum samples from patients with SARS had antibody responses to SARS-CoV as well as to HCoV-229E and HCoV-OC43 when nucleocapsid proteins were used in the Western blot analysis and when CoV-infected cells were used in the IFA. Furthermore, antibodies to SARS-CoV could be detected in only 1 serum sample from a healthy donor by either IFA or nucleocapsid protein-based Western blot analysis, even though patients with SARS had antibodies to HCoV-229E and HCoV-OC43. cache = ./cache/cord-293579-w5sub348.txt txt = ./txt/cord-293579-w5sub348.txt === reduce.pl bib === id = cord-293890-thfros7x author = Carbo, Ellen C. title = Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness date = 2020-08-21 pages = extension = .txt mime = text/plain words = 2315 sentences = 129 flesch = 49 summary = METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. Additionally, the efficacy of detection of novel coronaviruses using capture probes targeting vertebrate viruses [10] [11] known before the current pandemic was analyzed using a SARS-CoV-2 clinical sample. After extraction of human reads, FASTQ files generated for SARS-CoV-2 samples (with and without viral enrichment) were uploaded for classification and de novo assembly by the commercial webbased tool Genome Detective v1.120 (www.genomedetective.com, accessed 2020-05-11) [9] , using a reference database (generated 2019-09-21). In this study, we evaluated the performance of a metagenomic sequencing protocol for the identification of emerging viruses using clinical samples in combination with a simulated reference database. cache = ./cache/cord-293890-thfros7x.txt txt = ./txt/cord-293890-thfros7x.txt === reduce.pl bib === id = cord-293615-f1e6hs11 author = Dockery, Dominique M. title = The Ocular Manifestations and Transmission of COVID-19; Recommendations for Prevention date = 2020-05-08 pages = extension = .txt mime = text/plain words = 903 sentences = 48 flesch = 52 summary = Abstract Background Coronavirus disease-2019 (COVID-19), caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been linked to ocular signs and symptoms in several case reports. Research has demonstrated that SARS-CoV-2 is spread primarily through close contact via respiratory droplets, but there is the possibility for ocular transmission with the conjunctiva as a conduit as well as a source of infection. Discussion Ocular manifestations of SARS-CoV-2 include follicular conjunctivitis and have been repeatedly noted as an initial or subsequent symptom of COVID-19 positive patients. Particularly in patients with ocular manifestations, there is evidence that the virus may present in tears based on the detection of SARS-CoV-2 in conjunctival swab samples via reverse transcription polymerase chain reaction (RT-PCR). The conjunctivitis was noted to resolve at day 20 and the patient continued to have daily viral 109 SARS-CoV-2 RNA detection in ocular samples until day 21. cache = ./cache/cord-293615-f1e6hs11.txt txt = ./txt/cord-293615-f1e6hs11.txt === reduce.pl bib === id = cord-293415-u9onutny author = Amendola, A. title = Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression date = 2020-11-10 pages = extension = .txt mime = text/plain words = 3522 sentences = 214 flesch = 50 summary = title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression Our findings indicate that human cardiac stromal cells have a susceptibility to SARS-CoV-2 infection and produce variable viral yields depending on the extent of cellular ACE2 receptor expression. The susceptibility of the myocardial tissue to SARS-CoV-2 infection Tavazzi et al., 2020) has been inferred based on the expression of the Angiotensin-Converting Enzyme-2 (ACE2) receptor in various cardiac cell types (Zou et al., 2020) , and the evidence that the virus interacts with this receptor via the Spike (S) protein, as a main cellular docking/internalization site . Together, these results highlight an additional cardiac pathogenesis mechanism by SARS-CoV-2 independent of ACE2 expression, consisting of substantial upregulation of genes involved in response to viral infection, intercellular virus transmission and related to innate immunity signaling and fibrotic activation. cache = ./cache/cord-293415-u9onutny.txt txt = ./txt/cord-293415-u9onutny.txt === reduce.pl bib === id = cord-293503-e7be12qb author = Xiang, Chao title = CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation date = 2020-08-15 pages = extension = .txt mime = text/plain words = 3312 sentences = 193 flesch = 50 summary = COVID-19 leads to respiratory infections similar to those of SARS and MERS, causing pneumonia, severe acute respiratory syndrome, kidney failure, and even death. The CT image characteristics were recorded as follows: (a) lesion's location (segment), (b) morphology (patchy, nodular, and linear), (c) distribution (single or multiple, peripheral or/and central), (d) type (ground-glass opacity, consolidation, and linear opacity), (e) pattern (reticulation, parenchymal bands, crazy-paving, and interlobular thickening), (f) atelectasis, (g) cavitation, (h) pleural effusion, (i) hilar or mediastinal lymphadenopathy, (j) bronchiectasis, and (k) air bronchogram. Although a patient with exposure history may be asymptomatic and obtained negative results of CT findings and viral nucleic acid test at initial presentation, the potential infection cannot be totally excluded, and performing repeating CT scan and coronavirus RNA test is needed. Ground-glass opacity and consolidation with multiple, bilateral, and lower lobe distribution are the main features of COVID-19 pneumonia at initial CT scan. cache = ./cache/cord-293503-e7be12qb.txt txt = ./txt/cord-293503-e7be12qb.txt === reduce.pl bib === id = cord-293274-ysr1l557 author = Perisé-Barrios, Ana Judith title = Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date = 2020-09-22 pages = extension = .txt mime = text/plain words = 4140 sentences = 267 flesch = 54 summary = Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. cache = ./cache/cord-293274-ysr1l557.txt txt = ./txt/cord-293274-ysr1l557.txt === reduce.pl bib === id = cord-293826-2p7dqacd author = Lee, Cheryl Yi-Pin title = Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date = 2020-10-09 pages = extension = .txt mime = text/plain words = 1314 sentences = 84 flesch = 54 summary = Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Overall, our study shows that the D614G mutation on the S protein does not 150 impact SARS-CoV-2 neutralization by the host antibody response, nor confer viral 151 resistance against the humoral immunity. cache = ./cache/cord-293826-2p7dqacd.txt txt = ./txt/cord-293826-2p7dqacd.txt === reduce.pl bib === id = cord-293559-c78wcr8m author = Rego, Gabriel N. A. title = Current Clinical Trials Protocols and the Global Effort for Immunization against SARS-CoV-2 date = 2020-08-25 pages = extension = .txt mime = text/plain words = 9752 sentences = 506 flesch = 53 summary = Two purified inactivated SARS-CoV-2 vaccine candidates, an mRNA-based vaccine mRNA1273, and the chimpanzee adenoviral vaccine ChAdOx1 are currently in phase III clinical trials in the respective countries Brazil, the United Arab Emirates, the USA, and the United Kingdom. Thus, during the pandemic caused by COVID-19, several vaccine candidates with attenuated virus, encoding, or presenting SARS-CoV-2 antigens have been developed globally, reaching clinical trial phases I or II for the evaluation of their safety and immunogenicity. Six protocols are developing phase II and/or III clinical trials using the chimpanzee adenoviral vector ChAdOx1 [50] [51] [52] , purified inactivated SARS-CoV-2 vaccine [53, 54] , and mRNA-1273 vaccine [55] . A Phase I Clinical Trial to Evaluate the Safety, Tolerance and Preliminary Immunogenicity of Different Doses of a SARS-CoV-2 mRNA Vaccine in Population Aged 18-59 Years and 60 Years and Above cache = ./cache/cord-293559-c78wcr8m.txt txt = ./txt/cord-293559-c78wcr8m.txt === reduce.pl bib === id = cord-293655-2ab7wdsk author = Mandic-Rajcevic, S. title = Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy) date = 2020-05-08 pages = extension = .txt mime = text/plain words = 6602 sentences = 327 flesch = 56 summary = Objective To study the source, symptoms, and duration of infection, preventive measures, contact tracing and their effects on SARS-CoV-2 epidemic among healthcare workers (HCW) in 2 large hospitals and 40 external healthcare services in Milan (Italy) to propose effective measures to control the COVID-19 epidemic among healthcare workers. Most prominent symptoms include fever, dry cough, headache, sore throat and sneezing, although a growing number of reports underline asymptomatic and patients with mild symptoms having the same viral load as symptomatic patients and spreading the infection in the general population and among healthcare workers (HCW) (2) (3) (4) (5) . A much smaller sample of workers (N=10), commonly found among close contacts but absent from the hospital for other reasons, reported their daily symptoms even in the days leading to the positive NF swab. cache = ./cache/cord-293655-2ab7wdsk.txt txt = ./txt/cord-293655-2ab7wdsk.txt === reduce.pl bib === id = cord-293389-3h9vsc1a author = Risitano, Antonio M. title = Complement as a target in COVID-19? date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1069 sentences = 53 flesch = 34 summary = Most patients who become critically ill following infection with SARS-CoV-2, the causative agent of COVID-19, develop acute respiratory distress syndrome (ARDS) 1 . The prominent decrease in lung-infiltrating neutrophils and the reduced levels of both intrapulmonary and plasma IL-6 seen in SARS-CoV-infected C3-deficient mice suggests the potential of combining C3 inhibitors with anti-IL-6 regimens. A recent preprint study reported that lung biopsy samples from patients with severe COVID-19 showed widespread complement activation, characterized by C3a generation and C3-fragment deposition 6 . Proximal complement inhibitors (which target C3 or its upstream activators) could be more effective, but these are still in clinical development, and none has yet been approved, although limited data from phase II clinical trials are available. However, the combination of clinical indicators of ARDS progression with known biomarkers of inflammation (C-reactive protein, plasma IL-6 levels and ferritin) would allow identification of patients that could benefit from complement inhibition. cache = ./cache/cord-293389-3h9vsc1a.txt txt = ./txt/cord-293389-3h9vsc1a.txt === reduce.pl bib === id = cord-293301-7bmj8qsv author = Buonanno, Giorgio title = Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment date = 2020-04-17 pages = extension = .txt mime = text/plain words = 4387 sentences = 195 flesch = 49 summary = The quanta emission rates of an asymptomatic SARS-CoV-2 infected subject, with a viral load in the mouth of 108 copies mL-1, were 10.5 quanta h-1 and 320 quanta h-1 for breathing and speaking respiratory activities, respectively, at rest. The findings in terms of quanta emission rates were then adopted in infection risk models to demonstrate its application by evaluating the number of people infected by an asymptomatic SARS-CoV-2 subject in Italian indoor microenvironments before and after the introduction of virus containment measures. In particular, airborne transmission of SARS-CoV-2 by an asymptomatic 76 subject within pharmacies, supermarkets, restaurants, banks, and post offices were simulated, and 77 the reduction in the average number of infected people from one contagious person, R0, was 78 estimated. The quanta emission rate used in the simulation of the scenario represents the average value 220 obtained from the four expiratory activities (whispered counting, voiced counting, speaking, and 221 breathing); the data are reported and discussed in the result sections. cache = ./cache/cord-293301-7bmj8qsv.txt txt = ./txt/cord-293301-7bmj8qsv.txt === reduce.pl bib === id = cord-293692-t5rfvyvj author = Kazi, Sajida title = The delights and perils of publishing, knowledge-sharing and critique during a pandemic: Observations from COVID-19 coagulopathies date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1958 sentences = 102 flesch = 40 summary = Despite the limited data, the high-stakes milieu and risk of litigation have led several institutions to adopt a more aggressive approach of using intermediate or full-dose anticoagulation for most of their critically ill COVID-19 patients admitted to the Intensive Care Unit [22] . The dissemination of knowledge during times of international crisis is guided by the principles first set out in the World Health Organization's 2016 statement on data-sharing during public health emergencies, which incorporated lessons from the Ebola and Zika outbreaks, and was undersigned by many notable foundations and journals [23] . These principles have been adopted for use in the current pandemic through a call to share "research data and findings relevant to the novel coronavirus (COVID19) outbreak" in the same fashion [24] . Sharing research data and findings relevant to the novel coronavirus (COVID-19) outbreak cache = ./cache/cord-293692-t5rfvyvj.txt txt = ./txt/cord-293692-t5rfvyvj.txt === reduce.pl bib === id = cord-293688-g6kag5ij author = Nora, Holtmann title = Assessment of SARS-CoV-2 in human semen - a cohort study date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2231 sentences = 146 flesch = 57 summary = OBJECTIVE: To investigate the presence of viral RNA in human semen of severe-acute-respiratory syndrome coronavirus 2 (SARS-CoV-2) recovered and positive patients and to evaluate its presence and relevance on semen parameters. SARS-CoV-2 RNA could not be detected in semen of recovered and acute COVID-19 positive males. SARS-CoV-2 RNA could neither be detected in semen samples from recovered nor from acute infected subjects. On another note, it is of interest, that although it was described before in the literature that viral infections have a negative impact on semen parameters like 306 volume, number of spermatozoa and motility we could not detect a negative influence of the SARS-CoV-2 infection in respect of the aforementioned sperm count parameters in recovered subjects with mild symptoms. We found no evidence of SARS-CoV-2 shedding in semen of recovered males or patients with an acute COVID-19 infection after a recovery time of 32,7 days on average. cache = ./cache/cord-293688-g6kag5ij.txt txt = ./txt/cord-293688-g6kag5ij.txt === reduce.pl bib === id = cord-293481-bmfj50fb author = Malin, Jakob J. title = Remdesivir against COVID-19 and Other Viral Diseases date = 2020-10-14 pages = extension = .txt mime = text/plain words = 9097 sentences = 428 flesch = 42 summary = Remdesivir or GS-5734 is a prodrug of a nucleoside analog with direct antiviral activity against several single-stranded RNA viruses, including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, preliminary data from a randomized placebo-controlled clinical trial showed that remdesivir reduces the time to recovery in patients with COVID-19 (5) , leading to an emergency-use authorization (EUA) by the U.S. Food and Drug Administration (FDA) only 2 days after the first press release from the National Institute of Allergy and Infectious Diseases (NIAID) (6) . There were strong arguments for the antiviral effect of remdesivir against coronaviruses emerging from multiple cell-based in vitro models, including primary human airway epithelial (HAE) cell cultures (25) , and, for MERS-CoV, from a mouse model of pulmonary infection (28) . After the outbreak of SARS-CoV-2 in January 2020, remdesivir was rapidly tested in a Vero E6 cell-based model that made use of direct viral quantification by rtPCR along with the antimalaria and immune-modulating drug chloroquine and known antivirals such as ribavirin and penciclovir. cache = ./cache/cord-293481-bmfj50fb.txt txt = ./txt/cord-293481-bmfj50fb.txt === reduce.pl bib === id = cord-293543-87ulnpdm author = Shalhoub, Sarah title = Interferon beta-1b for COVID-19 date = 2020-05-10 pages = extension = .txt mime = text/plain words = 957 sentences = 57 flesch = 53 summary = 8 In The Lancet, Ivan Fan-Ngai Hung and colleagues 9 present the results of an open-label, randomised, phase 2 trial that examined the effect of a triple combination regimen of interferon beta-1b 8 million international units (0·25 mg) on alternate days, lopinavir 400 mg plus ritonavir 100 mg every 12 h, and ribavirin 400 mg every 12 h, compared with lopinavir 400 mg plus ritonavir 100 mg every 12 h alone. However, as the authors acknowledge, future studies to examine the efficacy of interferon beta-1b alone or in combination with other drugs to treat severe or critically ill patients with confirmed COVID-19 compared with placebo are warranted. Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study Triple combination of interferon beta-1b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial cache = ./cache/cord-293543-87ulnpdm.txt txt = ./txt/cord-293543-87ulnpdm.txt === reduce.pl bib === id = cord-293547-29i3u83s author = Pfaar, O title = COVID‐19 pandemic: Practical considerations on the organization of an allergy clinic – an EAACI/ARIA Position Paper date = 2020-06-12 pages = extension = .txt mime = text/plain words = 8811 sentences = 512 flesch = 42 summary = RESULTS: Based on diagnostic and treatment standards developed by EAACI, on international information regarding COVID‐19, on guidelines of the World Health Organization (WHO) and other international organizations as well as on previous experience, a panel of experts including clinicians, psychologists, IT experts and basic scientists along with EAACI and the "Allergic Rhinitis and its Impact on Asthma (ARIA)" inititiative have developed recommendations for the optimal management of allergy clinics during the current COVID‐19 pandemic. CONCLUSIONS: This international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients whilst ensuring necessary safety in the current COVID‐19 pandemic. In the current SARS-CoV-2 pandemic, the European Task Force on Atopic Dermatitis (ETFAD) recommends to continue all immune-modulating treatment since exacerbations of underlying diseases can have a large negative impact on the patient's immunity [30] . cache = ./cache/cord-293547-29i3u83s.txt txt = ./txt/cord-293547-29i3u83s.txt === reduce.pl bib === id = cord-293578-yu2i0u2h author = Kusadasi, Nuray title = A Pathophysiological Perspective on the SARS-CoV-2 Coagulopathy date = 2020-08-10 pages = extension = .txt mime = text/plain words = 3914 sentences = 259 flesch = 38 summary = The potential role of plasma kallikrein in case of SARS-CoV-2 infection may be summarized as (1) the activation of FXII with the end-product thrombin (coagulation system) (2) the generation of bradykinin with subsequent vascular permeability and leakage (kallikrein-kinin system), (3) the activation of the renin-angiotensin system through conversion of renin from pre-renin leading to a pro-inflammatory state through increased angiotensin 1 receptor activation and (4) the activation of C5, in part through activation of C1 via FXII and in part through activation of C3 via plasmin (complement system). 54, 55 Since prekallikrein is seen as a potential regulator in the fibrin clot formation through FXII activation and is involved in the pathogenesis of thrombosis, there might be an important role for controlling the hypercoagulable state of the patients infected with SARS-CoV-2 as a therapeutic target. Taken together, all these mechanisms may contribute to the complex hypercoagulable state of the critically ill patients infected with SARS-CoV-2 having severe hypoxia and ongoing endothelial activation. cache = ./cache/cord-293578-yu2i0u2h.txt txt = ./txt/cord-293578-yu2i0u2h.txt === reduce.pl bib === id = cord-293564-6xtg8uqt author = Hara, Tasuku title = Infection risk in a gastroenterological ward during a nosocomial COVID‐19 infection event date = 2020-04-22 pages = extension = .txt mime = text/plain words = 453 sentences = 35 flesch = 48 summary = A case of presumably nosocomial COVID‐19 was detected in the gastroenterological ward; however, appropriate precautions against contact and droplet prevented a subsequent infection cluster. To assess the risk of COVID-19 infection, the exposure-risk category and underlying conditions and their relationship with a positive PCR result were examined. Exposure-risk categories, which is based on whether patients and healthcare professionals use personal protective equipment, were assessed using Interim U.S. Guidance for Risk The basic reproduction number (R0: the number of people a single patient is expected to infect) for COVID-19 is estimated at 2.2 (1.4-3.9). 6,7 Therefore, the CCI was used in this study to assess the risk conferred by underlying diseases for COVID-19. No patient in the low-exposure risk category or with high-risk underlying conditions was infected with SARS-CoV-2 at this hospital. The authors thank all members of the Department of Gastroenterology and Hepatology, Fukuchiyama City Hospital. cache = ./cache/cord-293564-6xtg8uqt.txt txt = ./txt/cord-293564-6xtg8uqt.txt === reduce.pl bib === id = cord-293736-nyvwv31m author = Méry, Geoffroy title = COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella date = 2020-07-21 pages = extension = .txt mime = text/plain words = 5746 sentences = 268 flesch = 39 summary = Here we seek to explore what underlies the link between immune response and respiratory failure in CoV infections on the one hand, and the current observation of obesity as a risk factor for severe outcome in COVID-19 on the other. Indeed, during COVID-19 infection, most patients exhibit a specific cytokine profile, associating innate immunity chemokines (such as monocyte chemoattractant protein 3 and interferon gamma-induced protein 10 (IP-10), which are suggestive of macrophage activation and epithelial suffering), and pro-inflammatory macrophage-produced cytokines such as IL-6 (45). We suggest that the tampering with such pathways could also lead to abnormalities in the inflammatory response observed in severe CoV infections through their influence on immune regulation and cytokine production. Besides suffering from a pro-inflammatory environment, which favors macrophage activation and neutrophil production, obese patients exhibit abnormal responses to viral infection. cache = ./cache/cord-293736-nyvwv31m.txt txt = ./txt/cord-293736-nyvwv31m.txt === reduce.pl bib === id = cord-293946-4bquxdqa author = Huong, Nguyen Quynh title = Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 6229 sentences = 292 flesch = 51 summary = In this study we investigated the presence and diversity of coronavirus sequences in the field rat trade distribution chain, wildlife farms specializing in raising rodents for human consumption, and bat guano "farms" and roosts near human dwellings to better understand the natural hosts of coronaviruses and the risk for these interfaces to facilitate spillover into humans. Out of 70 sites, coronavirus positives were detected at 58 including 100% (24/24) of live rat trade sites, 60.7% (17/28) of rodent wildlife farm sites, 94.1% (16/17) of bat guano farm sites, and at the one natural pteropid bat roost. Significant findings of this study are the high proportion of coronavirus positive wildlife (bats and rodents) and the increasing proportion of positives found along the rat trade supply chain from sub-interfaces close to the capture site (rat traders) to restaurants. cache = ./cache/cord-293946-4bquxdqa.txt txt = ./txt/cord-293946-4bquxdqa.txt === reduce.pl bib === id = cord-294028-pcc6mucj author = Caussy, Cyrielle title = Obesity is Associated with Severe Forms of COVID‐19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 747 sentences = 42 flesch = 56 summary = which reports a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2) requiring invasive mechanical ventilation. (1) , which reported a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation (IMV). The findings (1) reporting a higher IMV in severe obesity (BMI ≥ 35) versus lean patients (BMI < 25) from Lille University Center in France may not be generalizable to other centers in France or in other countries, depending on the criteria implemented for the indication of IMV in other centers (2) . However, our data tend to confirm the observation from Lille University Center of a higher requirement for IMV in severe obesity (BMI ≥ 35) compared with lean patients (81.8% vs. High prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation cache = ./cache/cord-294028-pcc6mucj.txt txt = ./txt/cord-294028-pcc6mucj.txt === reduce.pl bib === id = cord-293765-xpc4yizb author = Huang, Jia-Ling title = Th2 predominance and CD8+ memory T cell depletion in patients with severe acute respiratory syndrome() date = 2005-02-24 pages = extension = .txt mime = text/plain words = 5149 sentences = 250 flesch = 53 summary = To define the dynamics of the immune spectrum in SARS, serum levels of cytokines, chemokines, immunoglobulins, complement and specific antibodies against SARS-associated coronavirus (SARS-CoV) were assayed by enzyme-linked immunosorbent assay (ELISA), and phenotypes of peripheral lymphocytes were analyzed by flow cytometry in 95 SARS-infected patients. IL-10 levels in the serum of SARS patients were continuously elevated for the 5 months observed in this study (2.47-4 .57 times that of normal control levels; Fig. 1C , P < 0.001, correlation coefficient = 0.514, one-way ANOVA; minimum detectable dose < 3.9 pg/ml). In this study, we found that infection with SARS-CoV triggered vigorous immune disturbances characterized by the following: (1) typical anti-viral nonspecific and specific humoral responses; (2) perturbation of cytokine and chemokine levels; and (3) severe impairment of cellular immunity, including lymphopenia in acute phase and loss of CD8+ memory T cells in convalescent phase. cache = ./cache/cord-293765-xpc4yizb.txt txt = ./txt/cord-293765-xpc4yizb.txt === reduce.pl bib === id = cord-294212-nlekz39f author = Wang, Dongliang title = Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date = 2020-07-03 pages = extension = .txt mime = text/plain words = 6072 sentences = 305 flesch = 54 summary = Linear B-cell epitopes of the SARS-CoV-2 S protein were predicted by BepiPred 2.0 in IEDB (BepiPred 2.0., Immune Epitope Database and Analysis Resource, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA) with a threshold of 0.55 (corresponding specificity > 0.817 and sensitivity < 0.292), and only the epitopes with more than 8 residues were considered for subsequent antigenicity analysis. Discontinuous B-cell epitopes were predicted via the DiscoTope 2.0 server tool in IEDB with a default threshold of −3.7 (corresponding specificity > 0.75 and sensitivity < 0.47), based on the 3-dimensional (3D) structures of the SARS-CoV-2 S protein (PDB ID: 6VYB, B chain) and the SARS-CoV-2 S protein RBD (PDB ID: 6M0J, B chain). It is worth noting that one epitope ( 786 QILPDPLKPTKRSFIEDLLFNKVTLA 811 ) located in the S2 subunit of the SARS-CoV S protein is an important linear B-cell epitope capable of eliciting the production of a neutralizing antibody (NAb) identified in patients who recovered from SARS-CoV infection (Table S2 ) [13] . cache = ./cache/cord-294212-nlekz39f.txt txt = ./txt/cord-294212-nlekz39f.txt === reduce.pl bib === id = cord-293991-x5zdo8t2 author = Wheatley, A. K. title = Evolution of immunity to SARS-CoV-2 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4622 sentences = 333 flesch = 56 summary = While SARS-CoV-2 specific B and T cell responses are readily induced by infection, the longitudinal dynamics of these key memory populations remains poorly resolved. We find that binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection, as expected, with a similar decline in S-specific CD4+ and circulating T follicular helper (cTFH) frequencies. Serum inhibition of RBD-ACE2 binding and S1-specific IgG 106 responses in early infection were also well correlated with neutralisation titre in late 107 convalescence (Spearman rho=0.79, 0.81, respectively; Extended Data Fig 3) . S-specific cTFH and conventional CD4+ 152 and CD8+ memory T cells (Tmem), were quantified using activation induced marker 153 (AIM) assays 19,22 (Methods) following stimulation with overlapping S (split into S1 154 or S2) peptide pools (Fig. 3A, 3B ). SARS-CoV-2 infection induces sustained humoral immune 623 responses in convalescent patients following symptomatic COVID-19. cache = ./cache/cord-293991-x5zdo8t2.txt txt = ./txt/cord-293991-x5zdo8t2.txt === reduce.pl bib === id = cord-294073-65h2mkdy author = Ke, Jia title = Strategies and recommendations for the management of gastrointestinal surgery during the COVID-19 pandemic: experience shared by Chinese surgeons date = 2020-07-03 pages = extension = .txt mime = text/plain words = 4150 sentences = 234 flesch = 43 summary = We also recommend that each hospital should establish a group of diagnostic experts with responsibilities for risk stratification, especially for patients under investigation who need urgent surgery. • It is known that fever is one of the most common symptoms of COVID-19 and that patients with certain GI diseases (e.g. acute appendicitis, gastric perforation, intestinal obstruction) who required urgent care with emergency GI surgery often present with high fever as well. COVID-19-positive patients with GI bleeding with hemodynamic stability should undergo conservative treatments first, including angioembolization, before endoscopic treatment due to the high risk of endoscopy being an aerosol-generating procedure. For confirmed/high-risk COVID-19 patients and PUIs, diagnostic and therapeutic GI endoscopies should be performed in a negative-pressure room with Level Three precautions. For all surgical personnel involved in GI surgery for confirmed/ high-risk COVID-19 patients or for PUIs for COVID-19, we recommend the following protective measures (Figure 1 ). cache = ./cache/cord-294073-65h2mkdy.txt txt = ./txt/cord-294073-65h2mkdy.txt === reduce.pl bib === id = cord-293858-dk4snw9r author = Yang, Lin title = Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date = 2019-02-14 pages = extension = .txt mime = text/plain words = 4083 sentences = 195 flesch = 46 summary = Annual excess rates of mortality or hospitalization associated with influenza in the older population were estimated for the pre-SARS (reference period), post-SARS and post-pandemic period, respectively. We constructed time series segmented regression models to estimate cause-specific mortality or hospitalization risks associated with influenza in the older population during the pre-SARS, post-SARS, and post-pandemic periods for Hong Kong and Brisbane. Compared to Hong Kong, during the study period Brisbane had higher mortality rates for all-cause (81.7 vs 66.5 per 100,000 population), cardiorespiratory diseases (CRD, 42.1 vs 33.8), stroke (9.5 vs 6.5) and ischemic heart diseases (IHD, 17.0 vs 7.5), but a lower rate for pneumonia and influenza (P&I, 2.8 vs 9.9), and a comparable rate for chronic obstructive pulmonary disease (COPD, 3.9 vs 4.2) (Additional file 1: Appendix 3). In this study, we estimated excess rates of mortality or hospitalizations attributable to influenza in different periods (pre-SARS, post-SARS, and post-pandemic) for two subtropical cities Hong Kong and Brisbane. cache = ./cache/cord-293858-dk4snw9r.txt txt = ./txt/cord-293858-dk4snw9r.txt === reduce.pl bib === id = cord-293701-u4ntxo0y author = Su, Shan title = Learning from the past: development of safe and effective COVID-19 vaccines date = 2020-10-16 pages = extension = .txt mime = text/plain words = 8201 sentences = 390 flesch = 40 summary = In this Perspective, we summarize examples of vaccine-associated disease enhancement in the history of developing vaccines against respiratory syncytial virus, dengue virus, SARS-CoV and Middle East respiratory syndrome coronavirus, which highlight the importance of a robust safety and efficacy profile, and present recommendations for preclinical and clinical evaluation of COVID-19 vaccine candidates as well as for vaccine design and optimization. One month later, five more candidates had also entered phase I clinical trials, and more than 100 COVID-19 vaccine candidates were in results, all of these vaccines induced antibodies against the spike protein (S protein) and the receptor-binding domain (RBD), including antibodies that neutralized pseudotyped and live SARS-CoV-2. We summarize examples of VADE in the history of the development of vaccines against respiratory syncytial virus (RSV), dengue virus (DENV), SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), each of which provides clues for safe COVID-19 vaccine development and highlights the need for rigorous preclinical and clinical safety testing. cache = ./cache/cord-293701-u4ntxo0y.txt txt = ./txt/cord-293701-u4ntxo0y.txt === reduce.pl bib === id = cord-293860-6kz0iws6 author = Qutayba Almerie, Muhammad title = The Association between Obesity and Poor Outcome after COVID-19 Indicates a Potential Therapeutic Role for Montelukast date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2801 sentences = 139 flesch = 41 summary = HYPOTHESIS: Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. With its prominent effect in reducing leukotriene-mediated cytokine release montelukast would have the potential to moderate the background inflammation associated with obesity and the body's inflammatory response to SARS-CoV2. The strong association between the pro-inflammatory state found in metabolic syndrome and obesity and a more aggressive clinical course in COVID-19 suggests a potential treatment role for drugs that inhibit cytokine release and macrophage activation. cache = ./cache/cord-293860-6kz0iws6.txt txt = ./txt/cord-293860-6kz0iws6.txt === reduce.pl bib === id = cord-293831-28ddm9um author = Qian, Mengcen title = Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey date = 2020-02-20 pages = extension = .txt mime = text/plain words = 4851 sentences = 304 flesch = 51 summary = Objective: To investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China Design: Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020 Setting: Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan) Participants: Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18 Main outcome measures: Anxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). 18.20024448 doi: medRxiv preprint We found that higher perceived risk and severity of contracting the novel coronavirus, higher perceived relative transmissibility and harm to body to SARS, and more confusion about information reliability were all significantly and positively associated with reported moderate or severe anxiety during the outbreak (Table 3 ). cache = ./cache/cord-293831-28ddm9um.txt txt = ./txt/cord-293831-28ddm9um.txt === reduce.pl bib === id = cord-294199-o8w35pdy author = Zhang, Qiangzhe title = Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity date = 2020-06-17 pages = extension = .txt mime = text/plain words = 2222 sentences = 132 flesch = 48 summary = Inspired by the fact that the infectivity of SARS-CoV-2 relies on its binding with the protein receptors, either known or unknown, on the target cells, we create cellular nanosponges as a medical countermeasure to the coronavirus. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) and CD147 expressed on the host cells, such as human alveolar epithelial type II cells, as receptors for cellular entry. To further verify that the inhibition was indeed due to epithelial cell or macrophage membrane coating, control nanosponges made from membranes of red blood cells (denoted "RBC-NS") were also tested in parallel for viral inhibition but were not effective in neutralizing SARS-CoV-2 infection of Vero E6 cells ( Figure 3C ). In principle, as long as the target of the virus remains the identified host cell, the nanosponges will be able to neutralize the infection, providing a broad-acting countermeasure resistant to mutations and protection against this and other emerging coronaviruses. cache = ./cache/cord-294199-o8w35pdy.txt txt = ./txt/cord-294199-o8w35pdy.txt === reduce.pl bib === id = cord-293852-r72c6584 author = Greco, S. title = Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date = 2020-10-31 pages = extension = .txt mime = text/plain words = 8163 sentences = 468 flesch = 40 summary = Different studies found that the values of cardiac Troponins were increased in COVID-19 patients with more severe disease [4, 5, [68] [69] [70] , indicating an association of SARS-CoV-2 with myocardial damage. Moreover, the single-cell RNA-sequencing (scRNAseq) approach has been used to profile the SARS-CoV-2 host-response in the PBMCs of COVID-19 patients, and to comprehensively characterize the immunological changes [124] [125] [126] [127] [128] [129] [130] . However, SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) induced cytotoxic effects and RNA-seq findings highlighted significant transcriptional changes in gene pathways related to cellular metabolism and immune response [131] [132] [133] . This analysis also revealed several host-derived lncRNAs differentially expressed in COVID-19 patient-derived lung tissue, and in SARS-CoV-2 infected epithelial cells, including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and NEAT1 (nuclear-enriched autosomal transcript 1) [151] (Fig. 5) . cache = ./cache/cord-293852-r72c6584.txt txt = ./txt/cord-293852-r72c6584.txt === reduce.pl bib === id = cord-293732-rxd1lyi7 author = Manoj, M.G. title = Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date = 2020-08-01 pages = extension = .txt mime = text/plain words = 4180 sentences = 210 flesch = 49 summary = Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. cache = ./cache/cord-293732-rxd1lyi7.txt txt = ./txt/cord-293732-rxd1lyi7.txt === reduce.pl bib === id = cord-294392-a8s66g96 author = Zhang, Shuai title = Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date = 2020-09-07 pages = extension = .txt mime = text/plain words = 985 sentences = 65 flesch = 46 summary = title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. 12 Two studies showed that tracheal intubation procedure was related to increased risk of 120 transmission SARS-CoV-1 and SARS-CoV-2 to HCWs. 13,14 Face mask and eye protection especially 121 N95 respirators were most consistently with reduced COVID-19 infection among HCWs. 14,15 Face 122 mask was also reported to be associated with asymptomatic SARS-CoV-2 infection based on several 123 uncontrolled reports. The univariable logistic regression analysis showed worked in high-risk departments, 169 hand washing consistently and consistent use of isolation gown, N95 respirators, gloves, hair cover, 170 and eye protection were associated with an increased likelihood of asymptomatic infection (Table S1) . cache = ./cache/cord-294392-a8s66g96.txt txt = ./txt/cord-294392-a8s66g96.txt === reduce.pl bib === id = cord-294120-8fxrqorg author = Guebre-Xabier, Mimi title = NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date = 2020-08-19 pages = extension = .txt mime = text/plain words = 866 sentences = 78 flesch = 64 summary = title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. And, hACE2 receptor 158 inhibition titers of 649, 1,410, and 1,320 in 2.5, 5, and 25 µg NVX-CoV2373 dose groups 159 respectively were 5.2 -11.2-fold higher than in convalescent sera ( Figure 1C) . Finally, 160 SARS-CoV-2 GMT neutralization antibody titers of 17,920 -23,040 CPE 100 in 161 immunized macaques, were 7.9 -10.1-fold higher than in convalescent sera ( Figure 162 1D) . To evaluate the potential efficacy of NVX-CoV2373 vaccine, macaques were 165 challenged with SARS-CoV-2 virus in upper and lower airways. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 214 elicits immunogenicity in baboons and protection in mice These interests do not alter the authors adherence to policies on 209 sharing data and materials. cache = ./cache/cord-294120-8fxrqorg.txt txt = ./txt/cord-294120-8fxrqorg.txt === reduce.pl bib === id = cord-294385-6dlgv3tb author = Tong, Xin title = Surveillance of SARS‐CoV‐2 infection among frontline health care workers in Wuhan during COVID‐19 outbreak date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1380 sentences = 92 flesch = 58 summary = The radiological analysis revealed that there was no typical chest CT scan of COVID‐19 among 222 HCWs. Consistently, anti‐SARS‐CoV‐2 IgM or IgG was also found to be negative among 191 HCWs. CONCLUSIONS: There was no nosocomial infection of SARS‐CoV‐2 among our cohort of the frontline HCWs, suggesting that zero occupational infection is an achievable goal with appropriate training, strict compliance, and psychological support for the frontline HCWs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging infectious disease, first described in Wuhan, China, has rapidly spread throughout worldwide. 2 The ever-increasing number of COVID-19 cases, overwhelming workload, the depletion of personal protection equipment (PPE), physical fatigue, and psychological stress during the early outbreak has resulted in at least 22 073 cases of COVID-19 among HCWs. 3 A study from China Center for Disease Control and Prevention (CDC) showed that as of 17 February 2020, 3.8% confirmed COVID-19 cases were among HCWs. 4 A report from Italy revealed 11% of COVID-19 cases were HCWs. 5 All the evidence suggested a high risk of occupational infection of SARS-CoV-2. cache = ./cache/cord-294385-6dlgv3tb.txt txt = ./txt/cord-294385-6dlgv3tb.txt === reduce.pl bib === id = cord-293988-f5gvwjyh author = Musso, Nicolò title = New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3223 sentences = 186 flesch = 54 summary = The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat's pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2. cache = ./cache/cord-293988-f5gvwjyh.txt txt = ./txt/cord-293988-f5gvwjyh.txt === reduce.pl bib === id = cord-293938-40zyv1h8 author = Jonsdottir, Hulda R. title = Coronaviruses and the human airway: a universal system for virus-host interaction studies date = 2016-02-06 pages = extension = .txt mime = text/plain words = 5533 sentences = 288 flesch = 41 summary = The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. Given the documented history of coronaviruses overcoming the species barrier and causing severe disease in humans, it is important to investigate the zoonotic potential of close evolutionary relatives of common HCoVs in a culture model that recapitulates the aspects of the human airway, e.g. morphology and receptor distribution. The establishment of transgenic animal models for human disease is attainable when either the virus receptor has been identified, which is not the case for all HCoVs, or when viruses can be adapted to a different host. cache = ./cache/cord-293938-40zyv1h8.txt txt = ./txt/cord-293938-40zyv1h8.txt === reduce.pl bib === id = cord-294335-qnu19ru5 author = Yousaf, Anna R title = A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3221 sentences = 179 flesch = 50 summary = We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . cache = ./cache/cord-294335-qnu19ru5.txt txt = ./txt/cord-294335-qnu19ru5.txt === reduce.pl bib === id = cord-294295-sd5893ii author = Badua, Christian Luke D.C. title = Genomic and Proteomic Mutation Landscapes of SARS‐CoV‐2 date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3432 sentences = 193 flesch = 57 summary = The overall frequency and densities of mutations in the genes and proteins of SARS‐CoV‐2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. Altogether, approximately similar proportions of nucleotide change types were observed between genomes among the geographical areas collected from December-March 2020 versus December-May 2020 ( Figure 3B , 3C). All in all, the ORF7b gene/protein was observed to have no mutations in all geographical region and between the study timepoints, therefore this gene may be potentially conserved in SARS-CoV-2. In conclusion, this study highlights the importance of the characterization of both nucleotide and amino acid mutation landscape in SAR-CoV-2 to identify hotspots and coldspots that may be significant in the effectivity of diagnostic tools and treatment options for COVID-19, over the different areas worldwide as the pandemic continues. cache = ./cache/cord-294295-sd5893ii.txt txt = ./txt/cord-294295-sd5893ii.txt === reduce.pl bib === id = cord-294410-iy57tjx5 author = Zhang, Shengnan title = (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain date = 2010-12-23 pages = extension = .txt mime = text/plain words = 1013 sentences = 60 flesch = 65 summary = title: (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain The main protease (M(pro)) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. Here, we reported the NMR assignments of the SARS-CoV M(pro) N-terminal domain alone, which are essential for its solution structure determination. The backbone resonance chemical shift assignments were based on 2D 1 H-15 N HSQC, 3D HNCA, HN(CO)CA, HNCACB, CBCA(CO)HN, HNCO, HN(CA)CO and HBHA(CO)NH NMR spectra. The side chain resonance chemical shift assignments were based on 3D HCCH-COSY, HCCH-TOCSY, (H)CCH-COSY, and (H)CCH-TOCSY NMR experiments data. Without its n-finger, SARS-CoV main protease can form a novel dimer through its C-terminal domain C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer cache = ./cache/cord-294410-iy57tjx5.txt txt = ./txt/cord-294410-iy57tjx5.txt === reduce.pl bib === id = cord-293715-lipme817 author = Hutchison, Lisa title = Neuropsychiatric Symptoms in an Adolescent Boy with Multisystem Inflammatory Syndrome in Children (MIS-C) date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3230 sentences = 175 flesch = 44 summary = BACKGROUND: Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID-19) is an emergent syndrome affecting children globally in the wake of the SARS-CoV-2 pandemic. METHOD: This case describes a 14-year-old boy who developed prominent neuropsychiatric symptoms including delirium followed by impairments in executive functioning in the context of MIS-C with positive SARS-CoV-2 antibodies. The recent SARS-CoV-2 pandemic has been associated with emergence of a new syndrome referred to as Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID19) . Given the paucity of knowledge concerning this syndrome's effect on the nervous system, the intent of this case report is to describe the neuropsychiatric symptoms in one 14-year-old boy presenting with multisystem inflammatory syndrome and positive SARS-CoV-2 antibodies. Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicenter cohort cache = ./cache/cord-293715-lipme817.txt txt = ./txt/cord-293715-lipme817.txt === reduce.pl bib === id = cord-294122-ou3wj4rz author = Hwang, Stephen W title = Population mortality during the outbreak of Severe Acute Respiratory Syndrome in Toronto date = 2007-05-29 pages = extension = .txt mime = text/plain words = 2944 sentences = 177 flesch = 51 summary = BACKGROUND: Extraordinary infection control measures limited access to medical care in the Greater Toronto Area during the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak. The objective of this study was to determine if the period of these infection control measures was associated with changes in overall population mortality due to causes other than SARS. METHODS: Observational study of death registry data, using Poisson regression and interrupted time-series analysis to examine all-cause mortality rates (excluding deaths due to SARS) before, during, and after the SARS outbreak. An interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak. The interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak in 2003, as indicated by the fact that the observed rates remained almost entirely within the 95% CI for the predicted rates. cache = ./cache/cord-294122-ou3wj4rz.txt txt = ./txt/cord-294122-ou3wj4rz.txt === reduce.pl bib === id = cord-294069-7zr77r71 author = Hu, Xiaowen title = The distribution of SARS-CoV-2 contamination on the environmental surfaces during incubation period of COVID-19 patients date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2527 sentences = 136 flesch = 50 summary = In this study, we sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the environmental surfaces during the incubation period of coronavirus disease 2019 (COVID-19) patients. In addition, we synchronously sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the SARS-CoV-2 distribution on the environmental surfaces during the incubation period of COVID-19 patients. Then, medical staffs stayed in hotel immediately sampled their nasopharyngeal swabs and environmental surfaces, and transferred them to the hospital for further diagnosis Additionally, the frequency of washing behaviors of patients at the quarantine room, including face washing, hands washing, tooth brushing, bathing and excrement, were shown in Table 2 . Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient cache = ./cache/cord-294069-7zr77r71.txt txt = ./txt/cord-294069-7zr77r71.txt === reduce.pl bib === id = cord-294262-yvbufnf4 author = Fernandez-Nieto, D. title = Comment on: “To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out. Characterization of herpetic lesions in hospitalized COVID-19 patients.” date = 2020-06-22 pages = extension = .txt mime = text/plain words = 538 sentences = 40 flesch = 59 summary = All 15 patients presented typical clinical lesions and symptoms of herpes 39 simplex/zoster. In spite of performing PCR tests for SARS-CoV-2 from the 42 content of the vesicles in only three patients, the results were all negative. Regarding vesicular rashes or varicella-like COVID-19 exanthems 3 , we previously 44 reported four cases in which we performed both PCR multiplex for herpesvirus and rt-45 PCR for SARS-CoV-2, directly from the content of the vesicles. This reasonably rules out a role of herpes 47 viruses 3 , and a potential infective ability of SARS-CoV-2 through the vesicles. In our current experience, the diagnosis of 55 herpesvirus infection in COVID-19 patients does not usually involve diagnostic doubts, 56 due to the clinical presentation and reported symptoms being typical of the disease, 57 even when lesions are extensive (Figure 1) . cache = ./cache/cord-294262-yvbufnf4.txt txt = ./txt/cord-294262-yvbufnf4.txt === reduce.pl bib === id = cord-294592-zwvr57a0 author = Mukherjee, Moumita title = Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 6099 sentences = 371 flesch = 57 summary = title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. There are experimentally validated evidences of human RBPs binding to the regulated signals within the untranslated region of SARS-CoV RNA in order to control the viral RNA synthesis and turnover. cache = ./cache/cord-294592-zwvr57a0.txt txt = ./txt/cord-294592-zwvr57a0.txt === reduce.pl bib === id = cord-294558-cqa58db8 author = Wang, Yubo title = Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date = 2020-05-22 pages = extension = .txt mime = text/plain words = 2858 sentences = 214 flesch = 57 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. cache = ./cache/cord-294558-cqa58db8.txt txt = ./txt/cord-294558-cqa58db8.txt === reduce.pl bib === id = cord-294115-7t7kubf6 author = Miralles, Oriol title = Unmet needs, health policies, and actions during the COVID-19 pandemic: a report from six European countries date = 2020-10-15 pages = extension = .txt mime = text/plain words = 7255 sentences = 343 flesch = 48 summary = The information collected from the six national reports was pulled together and discussed following the key priorities for action outlined in the UN Policy Brief: (1) Right to health and the participation in the decision-making process; (2) Social inclusion and solidarity under conditions of physical distancing; (3) Necessity of adequate, correctly funded care and support services for older adults; and (4) Need to expand participation by older adults, share good practice and harness knowledge and data [4] . In the Frenchspeaking region, the "Plan d'Urgence Hospitalier" was launched on 14th March and focused on ensuring distribution of hospital equipment, including personal protective equipment (PPE), and human resources (e.g., by reduction/ Impact of COVID-19 on health inequity: On 25th May, Belgium had reported 5734 people with confirmed SARS-CoV-2 infection in long-term care facilities (LTCF). cache = ./cache/cord-294115-7t7kubf6.txt txt = ./txt/cord-294115-7t7kubf6.txt === reduce.pl bib === id = cord-294237-6hovffso author = Cherry, James D title = SARS: The First Pandemic of the 21(st) Century date = 2004 pages = extension = .txt mime = text/plain words = 3477 sentences = 192 flesch = 56 summary = SARS (severe acute respiratory syndrome) was a new disease in the fall of 2002, which first occurred in Guangdong Province, China and spread to 29 countries with 8422 cases and 916 fatalities (1) (2) (3) . Moreover, cataloging the genome from human cases assisted in the search for the origin of this disease, when viruses related to the SARS-CoV were identified in animals [Himalayan palm civets (Paguma larvata) and raccoon dogs (Nyctereutes procyonoides)] in a live animal market in Shenzhen, China (12) . On the one hand, in the initial phases of the spread of SARS in Hong Kong, Singapore, and Toronto, a disproportionate number of health care workers became ill and apparent "superspreader" cases were noted (2-4, 6, 11, 14 -18) . Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens, Kowloon Bay, Hong Kong, main findings of the investigation Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong cache = ./cache/cord-294237-6hovffso.txt txt = ./txt/cord-294237-6hovffso.txt === reduce.pl bib === id = cord-294440-zd0arwmr author = Sacco, Guillaume title = COVID-19 in seniors: Findings and lessons from mass screening in a nursing home date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3981 sentences = 216 flesch = 52 summary = CONCLUSIONS: The pauci-symptomatic expression of COVID-19 in older residents, together with the high prevalence of asymptomatic forms in caregivers, justifies mass screening in nursing homes, possibly prioritizing residents with suggestive combinations of clinical signs including dyspnea, falls, anorexia and/or altered consciousness. The objective of the present study was to clarify symptoms and chronological aspects of the propagation of the SARS-CoV-2 in a nursing home, both in residents and staff members. The study consisted in a five-week retrospective observational cohort study in a middle-sized nursing home in Maine-et-Loire, West of France, having performed COVID-19 mass screening of residents (n=87) and staff members (n=92). The present report of COVID-19 mass screening in a nursing home showed a high prevalence of asymptomatic infected staff members, and confirmed that older residents exhibit few and mainly nonspecific symptoms. cache = ./cache/cord-294440-zd0arwmr.txt txt = ./txt/cord-294440-zd0arwmr.txt === reduce.pl bib === id = cord-294363-bv6xa8v8 author = Zhou, Hong title = Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 8902 sentences = 456 flesch = 46 summary = Several studies demonstrated angiotensin converting enzyme 2 (ACE2) as an important therapeutic target of SARS-CoV-2 entry and infection, and many potential targets were subsequently proposed, such as the spike (S) protein and transmembrane serine protease 2 (TMPRSS2). Therefore, accelerating research for potential therapeutic target confirmation, promising drug discovery, and clinical verification development will speed up efforts to combat SARS-CoV-2. In addition to inhibiting the virus directly, ASOs are also expected to target the disease-related proteins involved in the inflammatory cytokine storm process, which could be considered a promising therapeutic strategy for combating SARS-CoV-2 . Although many strategies have been used to block the attachment, entry, replication and release processes to inhibit SARS-CoV-2 infection, how to prevent viral evasion from host immune responses and virus-induced cytopathic effects is considered one of the most urgent problems that need to be solved in SARS-CoV-2-induced pneumonia-associated respiratory syndrome (PARS) patients. cache = ./cache/cord-294363-bv6xa8v8.txt txt = ./txt/cord-294363-bv6xa8v8.txt === reduce.pl bib === id = cord-294527-fct2y5vn author = Guadarrama-Ortiz, Parménides title = Neurological Aspects of SARS-CoV-2 Infection: Mechanisms and Manifestations date = 2020-09-04 pages = extension = .txt mime = text/plain words = 8820 sentences = 441 flesch = 37 summary = The human infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern that has caused more than 16.8 million new cases and 662,000 deaths as of July 30, 2020. Although coronavirus disease 2019 (COVID-19), which is associated with this virus, mainly affects the lungs, recent evidence from clinical and pathological studies indicates that this pathogen has a broad infective ability to spread to extrapulmonary tissues, causing multiorgan failure in severely ill patients. In this context, SARS-CoV-2 can also cause viral meningitis and encephalitis, as demonstrated by a recent report of a 64-yearold patient with laboratory-confirmed COVID-19 who presented neurologic manifestations during the infection, including lethargy, clonus, and pyramidal signs in the lower limbs as well as stiff neck and Brudzinski sign (76) . Future studies are required to evaluate the serologic features of anti-glycolipid antibodies in patients with COVID-19 to elucidate possible mechanisms underlying the association between SARS-CoV-2 infection and Guillain-Barré syndrome. cache = ./cache/cord-294527-fct2y5vn.txt txt = ./txt/cord-294527-fct2y5vn.txt === reduce.pl bib === id = cord-294644-xuafsnxm author = Herrmann, Burkhard L. title = Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1028 sentences = 121 flesch = 55 summary = title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten Patients with newly diagnosed COVID-19 (coronavirus disease 2019) develop antibodies against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The prevalence of 1.2% of SARS-CoV-2-IgG-antibodies and consequently the rate of infection in asymptomatic outpatients in Northrhine-Westfalia (Germany) is low. Inwiefern sich im Rahmen einer ambulanten Vorstellung (Einzugsgebiet Nordrhein-Westfalen [NRW], Deutschland) SARS-CoV-2-IgG-AK im Screening nachweisen lassen, wurde in einer monozentrischen prospektiven Erhebung an 415 Patienten ohne zurückliegenden wissentlichen Kontakt mit SARS-CoV-2 oder COVID-19 untersucht. Alle Patienten willigten in die Untersuchung ein und gaben an, zum Zeitpunkt der Abnahme unter keinen Symptomen einer akuten Infektion wie Husten, Fieber oder Dyspnoe zu leiden. Alle Patienten wurden durch den Autor eigenständig anamnestiziert und verneinten einen Kontakt mit Menschen, die positiv auf SARS-CoV-2 getestet wurden oder an COVID-19 erkrankt sind. Mit einer Prävalenz von 1,2% wurden SARS-CoV-2-AK in der Studienpopulation (ambulante, asymptomatische Patienten) nachgewiesen. cache = ./cache/cord-294644-xuafsnxm.txt txt = ./txt/cord-294644-xuafsnxm.txt === reduce.pl bib === id = cord-294372-pec1886j author = Greene, Dina N. title = Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1698 sentences = 103 flesch = 60 summary = Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. In the United States, surveillance data suggest that mean age of infected patients is decreasing compared to the early stages of the COVID-19 pandemic. We used SARS-CoV-2 testing data from a national reference laboratory to characterize the age distribution of detected cases between March and July of 2020. Surveillance data in the United States have shown a trend toward decreasing age among persons with laboratory-confirmed SARS-CoV-2 infection. This study found a similar pattern among patients tested by a national reference laboratory, with the median age among patients testing positive being five years lower in June and early July compared to March and April. cache = ./cache/cord-294372-pec1886j.txt txt = ./txt/cord-294372-pec1886j.txt === reduce.pl bib === id = cord-294304-9w6zt778 author = Doanvo, Anhvinh title = Machine Learning Maps Research Needs in COVID-19 Literature date = 2020-09-16 pages = extension = .txt mime = text/plain words = 5506 sentences = 283 flesch = 50 summary = The projection values of COVID-19 abstracts on PC2 were lower and associated with 11 emergent COVID-19 clinical-, modeling-or field-based (CMF) research -such as observational, 12 clinical, and epidemiological studies -exemplified by stem terms "patient", "pandem", "estim", 13 and "case". 14 Furthermore, we developed a framework that improves upon existing bibliometric studies 15 in three key ways; namely, our approach (1) maps connections between publications by relying 16 directly on the abstracts instead of the narrow information gained from metadata as in other 17 bibliometric analyses, including those from other fields 9,10 ; (2) uses ML to explore latent 18 semantic information of vast scale and complexity to identify hidden trends; and (3) does not 19 rely on any a priori knowledge of what topics we expect coronavirus literature to cover but 20 rather highlights them without any preconceived assumptions. cache = ./cache/cord-294304-9w6zt778.txt txt = ./txt/cord-294304-9w6zt778.txt === reduce.pl bib === id = cord-294136-e69ao8j0 author = Han, Dongsheng title = COVID-19: Insight into the asymptomatic SARS-COV-2 infection and transmission date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5215 sentences = 263 flesch = 42 summary = successfully isolated SARS-CoV-2 from throat swabs of two asymptomatic patients in a cell culture of Caco-2 cells, suggesting the potential for presymptomatic transmission [16] ; (5) Increasing studies show clear epidemiological evidence of human-to-human asymptomatic spread of COVID-19 (described in the following section); (6) Asymptomatic infection tends to be, but is not only, identified among young people (<20 years old) [14, 15, [17] [18] [19] ; And (7) the majority (>90%) of asymptomatic patients appears to have a milder clinical course during hospitalization [15] , but the severity of the symptoms of the secondary patients infected by SARS-COV-2 from asymptomatic patients varies based on their physical constitution [2, 20] . As the transmission of SARS-COV-2 may occur in the early course of infection and a high viral load in respiratory samples could be detected [13] , RT-PCR testing for this virus is more suitable for screening at earlier stages of infection in key populations, such as patients with obvious symptoms and close contacts of asymptomatic patients [35] . cache = ./cache/cord-294136-e69ao8j0.txt txt = ./txt/cord-294136-e69ao8j0.txt === reduce.pl bib === id = cord-294677-l1b4mw9d author = Prashantha, C.N. title = Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date = 2020-10-13 pages = extension = .txt mime = text/plain words = 2409 sentences = 147 flesch = 48 summary = (2) Coronavirus S2 glycoprotein (662-1270) is translated as a large polypeptide that is subsequently cleaved to S1 and S2 domains from Molecular docking plays vital role in computer-aided drug discovery to predict best active molecules to the target protein. Using AutoDock 4.2 and AutoDock Vina to predict the best drug binding sites towards the affinity of active site amino acids are screened based on binding energy and number of hydrogen bonds formed to the target amino acids. • Computational Approaches to build the 3D structure of protein • Drug selection for preclinical trials to study the efficacy and disease treatment • Molecular docking approaches to screen the compounds based on binding energy cache = ./cache/cord-294677-l1b4mw9d.txt txt = ./txt/cord-294677-l1b4mw9d.txt === reduce.pl bib === id = cord-294498-fv545rfa author = Spiegel, Martin title = The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein date = 2004-07-31 pages = extension = .txt mime = text/plain words = 1276 sentences = 83 flesch = 59 summary = title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein In this study, we demonstrated that multiplication of SARS-CoV in cell culture can be strongly inhibited by pretreatment with interferon-beta. In this study, we investigated the potential of different IFNs to inhibit replication of SARS-CoV in cell culture and determined whether the human MxA protein contributes to the antiviral effect of type I IFNs. African green monkey kidney (Vero) cells were grown in Dulbecco's modified Eagle's medium containing 10% fetal calf serum. We investigated the inhibitory effect of type I and II IFNs on SARS-CoV multiplication in cell culture. Therefore, we tested growth of SARS-CoV in Vero cell lines which stably express MxA (Frese et al., 1995) . Thus, the search for antiviral effects against SARS-CoV should focus on other IFN-induced proteins such as PKR or RNase L. cache = ./cache/cord-294498-fv545rfa.txt txt = ./txt/cord-294498-fv545rfa.txt === reduce.pl bib === id = cord-294427-6eiligyy author = Salimi, Ali title = The North American Layman's Understanding of COVID-19: Are We Doing Enough? date = 2020-07-03 pages = extension = .txt mime = text/plain words = 5699 sentences = 217 flesch = 46 summary = Methods: In this cross-sectional observational study, an online survey targeted to North Americans focused on the public's knowledge of COVID-19, risk perception, and precautionary behaviors taken in response to this pandemic. The results of this study highlight that this relatively young and educated sample of North Americans had a high level of knowledge about COVID-19 and a large proportion of them were taking the precautionary measures against this pandemic. To that end, this study aimed to compare and contrast the level of knowledge, risk perception, and precautionary measures taken in response to COVID-19, between populations of the United States of America (US) and Canada. To date, the US has reported the highest rate of COVID-19 positive cases in the world and therefore, by understanding the public's attitude and risk perception toward the current pandemic, we hope to provide valuable information to help develop adequate populationtailored communication protocols that are effective in disease prevention and containment. cache = ./cache/cord-294427-6eiligyy.txt txt = ./txt/cord-294427-6eiligyy.txt === reduce.pl bib === id = cord-294696-pm6pfeeb author = Kunz, Y. title = Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag date = 2020-10-13 pages = extension = .txt mime = text/plain words = 3216 sentences = 392 flesch = 43 summary = Ausgelöst wird diese Infektionskrankheit durch das Virus SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), das zur Familie der β-Coronaviridiae bzw. Das SARS-CoV-2 wird im Wesentlichen via Tröpfcheninfektion -und somit über Aerosole -von symptomatischen COVID-19-Patienten übertragen. Es wurde eine Literatursuche in PubMed, bioRxiv und medRxiv sowie den Datenbanken der WHO und des CDC über SARS-CoV-2 und chirurgisches Prozedere bei infizierten Patienten durchgeführt. Das Prostatagewebe scheint demgegenüber nicht von SARS-CoV-2 befallen zu werden, zumindest konnte eine chinesische Gruppe in einer kleinen Studie keine Virus-RNA im Prostatasekret nachweisen [29] . Da basierend auf der oben angesprochenen Studienlage eine SARS-CoV-2-Übertragung mittels Urin denkbar ist, muss bei COVID-19-Patienten und unklaren Verdachtsfällen zusätzlich zur gängigen Schutzkleidung im Operationssaal auf FFP-2-Masken und Schutzbrillen zurückgegriffen werden. Da Aerosole nicht nur während der Operation, sondern bereits zuvor im Rahmen einer OP-Einleitung entstehen können, sollte laut aktuellen Empfehlungen unbedingt auf FFP-2-Masken im Falle eines zu behandelnden Patienten mit Verdacht auf oder einer bestätigten COVID-19-Infektion zurückgegriffen werden. cache = ./cache/cord-294696-pm6pfeeb.txt txt = ./txt/cord-294696-pm6pfeeb.txt === reduce.pl bib === id = cord-294134-o9bx1gn7 author = Brecher, Stephen M. title = Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 745 sentences = 44 flesch = 51 summary = One early issue in the validation/ evaluation of antibody tests for evidence of SARS-CoV-2 infection is the possibility of cross-reacting antibodies from the plasma of patients who had been infected with one or more of the common cold coronaviruses (coronavirus 229E, HKU1, NL63, and OC43). It also ties in with issues outlined in the Infectious Diseases Society of America (IDSA) guidelines (4) and in a commentary in Lancet (5) on how to best utilize antibody test data, especially when there could be false-positive results, including cross-reacting antibodies to the four common cold coronaviruses. Although the sample size was minimal, these data are reassuring that at least for the Abbott Architect SARS-CoV-2 antibody test, plasma from patients with documented positive PCRs for these four common cold coronaviruses did not test positive for the SARS-CoV-2 IgG antibody. However, this multisite study, including data from 3 regional Veterans Affairs (VA) institutions (MA, CT, and VT) suggests that cross-reacting antibodies are not detected when testing for SARS-CoV-2 IgG antibody. cache = ./cache/cord-294134-o9bx1gn7.txt txt = ./txt/cord-294134-o9bx1gn7.txt === reduce.pl bib === id = cord-294429-isivkz8b author = Grifoni, Alba title = Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals date = 2020-05-20 pages = extension = .txt mime = text/plain words = 10250 sentences = 589 flesch = 55 summary = To test for the generation of SARS-CoV-2 CD4 + and CD8 + T cell responses following infection, we initially recruited 20 adult patients who had recovered from COVID-19 disease ( Table 1) . Initial definition and assessment of human antigen-specific SARS-CoV-2 T cell responses are best made with direct ex vivo T cell assays using broad-based epitope pools, such as MPs, and assays capable of detecting T cells of unknown cytokine polarization and functional attributes. Data from both the epitope MPs and protein peptide pool experiments can be interpreted in the context of previously reported T cell response immunodominance patterns observed for other coronaviruses, particularly the SARS and MERS viruses, which have been studied in humans, HLA-transgenic mice, wild-type mice and other species. (C) Correlation of SARS-CoV-2−specific CD4 + T cells detected using the epitope prediction approach (CD4_R MP) compared against the sum total of all antigen pools of overlapping peptides (excluding spike), run with samples from the same donors in two different experiment series. cache = ./cache/cord-294429-isivkz8b.txt txt = ./txt/cord-294429-isivkz8b.txt === reduce.pl bib === id = cord-294108-uvnh0s9r author = Dube, Taru title = Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date = 2020-10-25 pages = extension = .txt mime = text/plain words = 13885 sentences = 845 flesch = 44 summary = [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. cache = ./cache/cord-294108-uvnh0s9r.txt txt = ./txt/cord-294108-uvnh0s9r.txt === reduce.pl bib === id = cord-294692-qfz6a1kc author = Ortega, Karem L. title = SARS-CoV-2 and dentistry date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1014 sentences = 56 flesch = 49 summary = The identification that the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a virus transmitted through airways or by direct contact with the mucosas [2] has prompted the dental community to become alert. They concluded that human coronavirus on inanimate surfaces could be inactivated by using ethanol (62-71%), hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%) for 1 min, whereas other substances such as benzalkonium chloride (0.05% and 0.2%) and chlorhexidine digluconate (0.02%) were less effective. The authors also pointed out that although no study had tested the virucidal capacity of those agents against SARS-CoV-2, they expected a similar effect against this virus [5] . However, the suggestion to use mouthwash with 1% hydrogen peroxide or 0.2% povidone in order to decrease the viral load in saliva, based on the idea that SARS-CoV-2 would be vulnerable to oxidation, does not seem to be based on scientific evidence to date. cache = ./cache/cord-294692-qfz6a1kc.txt txt = ./txt/cord-294692-qfz6a1kc.txt === reduce.pl bib === id = cord-294537-wpq1492g author = Ritschl, Paul V. title = Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach date = 2020-05-10 pages = extension = .txt mime = text/plain words = 2530 sentences = 176 flesch = 46 summary = title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach 6 As no consensus guidelines or international recommendations have been published on coronavirus disease 2019 (COVID19) and organ transplant, the aim of this study was to offer a consensus-based approach to manage transplant programs until reliable data on risk and benefits of conducting organ transplants in times of a viral pandemic are available. the United Kingdom recommend a low threshold for SARS-CoV-2testing in transplant patients after contact with a positively tested person or subject to a broader spectrum of COVID-19-associated symptoms. Although SARS-CoV-2 nasopharyngeal PCR shows reasonable sensitivity, a recently published study demonstrates that of 51 COVID-19 patients only 36 were initially positive in NAT. Until now, no solid organ transplant procedure has reportedly been performed on a SARS-CoV-2-infected patient. Solid organ transplantation programs facing lack of empiric evidence in the COVID-19 pandemic: A By-proxy Society Recommendation Consensus approach cache = ./cache/cord-294537-wpq1492g.txt txt = ./txt/cord-294537-wpq1492g.txt === reduce.pl bib === id = cord-294349-ps3qlho2 author = Al-Sharif, Eman title = Ocular tropism of coronavirus (CoVs): a comparison of the interaction between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye date = 2020-09-03 pages = extension = .txt mime = text/plain words = 7053 sentences = 340 flesch = 43 summary = PURPOSE: Several studies have reported conflicting results on ocular manifestations and transmission of coronavirus disease 2019 (COVID-19) whose causative virus, SARS-CoV-2, belongs to the coronavirus family, the seventh recognized as a human pathogen and the third causing a severe clinical syndrome. Coronavirus disease 2019, known as COVID-19, is an emerging infection which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first reported in Wuhan city, China, late in December 2019 [4] . Clinical ocular manifestations were absent in all SARS-CoV-1 patients, and viral RNA was detected in the conjunctival secretions and tears in three cases out of 120 (2.5%) with a range of 0-8% [6] [7] [8] [9] . Similarly, a small study testing the conjunctival secretions and tears (collected twice over 2-3 days) of 30 confirmed COVID-19 patients demonstrated the presence of viral RNA (in both samples) in one patient only who also showed clinical signs of conjunctivitis [12] . cache = ./cache/cord-294349-ps3qlho2.txt txt = ./txt/cord-294349-ps3qlho2.txt === reduce.pl bib === id = cord-294590-1niaplc2 author = Schrag, Stephanie J. title = SARS Surveillance during Emergency Public Health Response, United States, March–July 2003 date = 2004-02-17 pages = extension = .txt mime = text/plain words = 4720 sentences = 214 flesch = 44 summary = In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003 , a total of 398 (27%) met clinical and epidemiologic SARS case criteria. On March 14, 2003 , the U.S. Centers for Disease Control and Prevention (CDC) launched an emergency public health response and established national surveillance for SARS to identify case-patients in the United States and determine if domestic transmission was occurring. cache = ./cache/cord-294590-1niaplc2.txt txt = ./txt/cord-294590-1niaplc2.txt === reduce.pl bib === id = cord-294571-qd0qjo3y author = Rothan, Hussin A. title = Molecular Aspects of COVID-19 Differential Pathogenesis date = 2020-07-06 pages = extension = .txt mime = text/plain words = 3246 sentences = 173 flesch = 43 summary = Angiotensin-converting enzyme-2 (ACE2) represents the primary SARS-CoV-2 entry receptor, and its physiological role is crucial in the progress of COVID-19 illness. Previous studies on SARS-CoV-1 reported that the binding of viral spike (S) protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . The levels of ACE2 expression, which could be sex-and age-dependent, have a protective role against lung and kidney injuries that could impact the severity of COVID-19 illness in male vs. The susceptibility of cardio-metabolic patients to develop severe COVID-19 illness and the high mortality rate could be linked to the ACE2 function during SARS-CoV-2 infection and the cardio-metabolic treatments that may interfere with ACE2-virus interaction. Previous studies on SARS-COV-1 reported that the binding of viral S protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . cache = ./cache/cord-294571-qd0qjo3y.txt txt = ./txt/cord-294571-qd0qjo3y.txt === reduce.pl bib === id = cord-294275-pp0vlaye author = Li, Jingjing title = Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date = 2020-06-03 pages = extension = .txt mime = text/plain words = 2367 sentences = 152 flesch = 55 summary = Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. Here, we use nanopore Flongle workflow combined with LAMP reaction to propose a faster and more convenient method to detect SARS-CoV-2 and other respiratory viruses in two hours. This study presents a LAMP based method combined with nanopore Flongle rapid realtime sequencing workflow to detect COVID-19 as low as 3.25×10^2 copies/mL of SARS-CoV-2 in both laboratory and wild-caught environment. To test the limit of detection, the amplification products of dilution gradient 3.25×10^4, 3.25 × 10^3, 1.1 × 10^3, 6.5 × 10^2, 3.25 × 10^2 copies/mL and negative control total 12 samples were constructed another barcoding library (Oxford Nanopore, SQK-RBK004) as described above and sequenced using a PromethION flowcell to achieve more data. The study design ( Figure 2 ) for SARS-CoV-2 detection is based on LAMP rapid amplification of specific genes and sequenced by nanopore Flongle workflow. cache = ./cache/cord-294275-pp0vlaye.txt txt = ./txt/cord-294275-pp0vlaye.txt === reduce.pl bib === id = cord-294501-1nf98mpb author = Bonafè, Massimiliano title = Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes date = 2020-05-03 pages = extension = .txt mime = text/plain words = 3745 sentences = 197 flesch = 40 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by a high mortality of elderly men with age-related comorbidities. Consistent with this finding, the ability of DCs and macrophages to elicit CD8 + T cell response and proliferation and to release antiviral cytokines is impaired in elderly individuals [34] ; in parallel, these subjects are characterized by a reduced activity of plasmacytoid DCs, the main sources of type I IFNs, which underpin the antiviral response and provide the first-line sentinels in immune surveillance, also in the lung [35] . 4. In older men with age-related diseases, the aging-dependent reduction in ACE2 activity worsens SARS-CoV-2 infection outcomes Angiotensin-converting enzyme (ACE)2, the main SARS-CoV2 host cell receptor, plays a crucial role in virus entry into the cell, as previously demonstrated in SARS and NL63 human coronaviruses [41] . In these individuals, acute SARS-CoV-2 infection compounds their chronic, subclinical, aging-related proinflammatory state (inflamm-aging) which, together with immune senescence and the age-and gender-specific distribution of ACE2 in the airway epithelia, could blunt the antiviral response to inflammation. cache = ./cache/cord-294501-1nf98mpb.txt txt = ./txt/cord-294501-1nf98mpb.txt === reduce.pl bib === id = cord-294704-prizmksg author = Lateef, Fatimah title = New paradigm for protection:: The emergency ambulance services in the time of severe acute respiratory syndrome date = 2004-06-16 pages = extension = .txt mime = text/plain words = 2579 sentences = 144 flesch = 56 summary = Severe acute respiratory syndrome (SARS) is a newly emerging and highly infectious form of atypical pneumonia with a high rate of transmission, especially among health care workers. With SARS, certain policies had to be implemented rapidly by the emergency ambulance services and the Ministry of Health to support and protect all personnel adequately. The authors hope to share their experience in the implementation of these strategies by the Singapore Civil Defence Force and stress the importance of the psychological preparedness of the paramedics and prehospital care providers worldwide in this era of SARS. To date, a total of seven probable and five suspected cases were conveyed by the EAS out of a total of 204 patients with SARS-like signs and symptoms. With the declaration of the SARS outbreak in Singapore, the Ministry of Health designated Tan Tock Seng Hospital (TTSH), one of the public hospitals, as the ''SARS hospital.'' All suspected and probable cases were sent and managed there. cache = ./cache/cord-294704-prizmksg.txt txt = ./txt/cord-294704-prizmksg.txt === reduce.pl bib === id = cord-294788-9usyb1nn author = Baek, Woong Kee title = A Comprehensive Review of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-05-03 pages = extension = .txt mime = text/plain words = 4459 sentences = 231 flesch = 46 summary = Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus strain that causes coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China in December 2019. It is suspected that the acute respiratory distress syndrome (ARDS)-like picture in SARS-CoV-2-infected patients is precipitated and worsened by the excess monocytes in response to GM-CSF, which is released by rapidly activated CD4+T-cell lineage [17] . have reported that the cytokine profile and the trend of the inflammatory markers of SARS-CoV-2-infected patients present similarly to the secondary hemophagocytic lymphohistiocytosis (sHLH), whose severe clinical presentation is related to the cytokine storm [23] . There is no consensus yet on how to treat SARS-CoV-2-infected patients who present with a wide spectrum of clinical symptoms and severity. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Epub ahead of print) cache = ./cache/cord-294788-9usyb1nn.txt txt = ./txt/cord-294788-9usyb1nn.txt === reduce.pl bib === id = cord-294861-inlaz4od author = Liu, Chen title = Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3240 sentences = 167 flesch = 51 summary = title: Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series METHODS: We retrospectively analyzed the diagnosis and treatment of six gynecological cancer patients infected with SARS-CoV-2 in Tongji Hospital in Wuhan from January 30 to March 25, 2020. RESULTS: We observed a high rate of nosocomial SARS-CoV-2 infection among these six gynecological cancer patients, who were in a low immune state. reported a case in which a lung cancer patient infected with SARS-CoV-2 recovered from pneumonia while continuing initial targeted therapy (10) . After antivirus and anti-infection treatment, combined with G-CSF (Recombinant Human Granulocytestimulating Factor) and immunity enhancing drugs, she was finally discharged from hospital after 35 days (Figure 1) . Moreover, cancer patients showed a state of low immunity after surgery or radio-/chemo-therapy treatment, so they became more susceptible to COVID-19 (12) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-294861-inlaz4od.txt txt = ./txt/cord-294861-inlaz4od.txt === reduce.pl bib === id = cord-294551-s3nsiano author = Muller, M. P. title = Early diagnosis of SARS: lessons from the Toronto SARS outbreak date = 2006-04-04 pages = extension = .txt mime = text/plain words = 3638 sentences = 160 flesch = 47 summary = To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Patients were classified as confirmed SARS if they had a compatible clinical illness (fever or nonproductive cough or dyspnea), an exposure to SARS (direct contact with a known SARS case or travel to a SARS-endemic area or time spent at an institution where SARS transmission was occurring, within 12 days of symptom onset), and a positive microbiological test (positive acute or convalescent serology, or positive PCR from clinical or pathological specimens). Findings associated with a confirmed diagnosis included direct exposure to a known case (OR, 2.34; 95%CI, 1.01-5.40), symptomatic fever as an initial symptom (OR, 5.07; 95%CI, 2.24-11.50), a documented temperature of 38.0°C on admission to hospital (OR, 2.6; 95%CI, 1.14-5.92), and the presence of a pulmonary infiltrate by the time of admission (OR, 2.46; 95%CI, 1.09-5.56). cache = ./cache/cord-294551-s3nsiano.txt txt = ./txt/cord-294551-s3nsiano.txt === reduce.pl bib === id = cord-294700-pb5k21da author = Dulek, Daniel E title = Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute COVID-19 in Pediatric Patients date = 2020-08-18 pages = extension = .txt mime = text/plain words = 14522 sentences = 835 flesch = 38 summary = Although the majority of SARS-CoV-2 infections in pediatric populations result in minimal or mild COVID-19 in the acute phase of infection, a small subset of children develop severe and even critical disease in this phase with concomitant inflammation that may benefit from immunomodulation. The framework presented herein offers an approach to decision-making regarding immunomodulatory therapy for severe or critical pediatric COVID-19 and is informed by currently available data, while awaiting results of placebo-controlled randomized clinical trials. Given the lack of available results from randomized-controlled trials of immunomodulatory therapy in children with COVID-19, the risk-benefit ratio for most pediatric patients points toward supportive care as the key management strategy. In the absence of such opportunity, and recognizing that definitive evidence is lacking, consideration for use of immunomodulatory agents in cases of SARS-CoV-2 infection with clinical and biochemical evidence of cytokine storm physiology (e.g., features of secondary HLH) should be limited to patients with clear evidence of critical COVID-19 disease and risk for multi-organ failure. cache = ./cache/cord-294700-pb5k21da.txt txt = ./txt/cord-294700-pb5k21da.txt === reduce.pl bib === id = cord-294789-07hto8qn author = Schoch-Spana, Monica title = The public’s role in COVID-19 vaccination: human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5808 sentences = 272 flesch = 37 summary = Members of the working group-listed as authors on this paper-included national figures in public health and social science with research, policy, and practice expertise in vaccinology, vaccine hesitancy/confidence, health disparities, infectious disease, bioethics, epidemiology, bioinformatics, public health law, pandemic mitigation, public health preparedness, mass vaccination campaigns, community engagement, and crisis and emergency risk communication. A combination of literature reviews on vaccination, pandemic planning, and health crisis communication; an assessment of current news and social media trends regarding COVID-19 vaccines; and key informant interviews with each working group member focusing on their respective expertise formed the basis of the research presented in this article. To ensure a successful COVID-19 vaccination campaign, it is necessary for sponsors to invest in time-critical investigations on human factors related to vaccine acceptance, and for public health authorities and other stakeholders to act on the social and behavioral findings of this research. cache = ./cache/cord-294789-07hto8qn.txt txt = ./txt/cord-294789-07hto8qn.txt === reduce.pl bib === id = cord-294441-nehorqhi author = O’Brien, Stephen J. title = Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS date = 2006-08-31 pages = extension = .txt mime = text/plain words = 6767 sentences = 390 flesch = 50 summary = A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach. Representing carnivores, the cat family Felidae offers numerous examples of reduced genetic var-iation in natural populations common to endangered species including Asian lion (Panthera leo persica) (Gilbert et al., 1991) , cheetah (Acinonyx jubatus) (Menotti-Raymond and O'Brien, 1993) , tiger (P. Our ongoing research into host-pathogen interactions in the cat family Felidae offers additional insights on how the application of molecular genomic technologies to non-human animal species not traditionally studied in research laboratories holds real promise in conservation. cache = ./cache/cord-294441-nehorqhi.txt txt = ./txt/cord-294441-nehorqhi.txt === reduce.pl bib === id = cord-294666-xlyuhzo9 author = Arguin, Paul M. title = Health Communication during SARS date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1493 sentences = 67 flesch = 44 summary = Timely health communication, along with surveillance, quarantine, isolation, and travel restrictions, figured prominently among the tools the Centers for Disease Control and Prevention (CDC) used to help contain the outbreak. By the end of September 1994, CDC had produced six documents to distribute to public health officials: an outbreak notice; a plague advisory for travelers to India; a plague alert notice handed to passengers arriving from India, which described the symptoms of plague and urged them to seek medical attention if they developed a febrile illness within 7 days; recommendations for treatment and prophylaxis; guidelines for diagnosis and biosafety; and a review article in the Morbidity and Mortality Weekly Report. Kennedy International Airport on flights from India), the departments of health in New York City and New York State supplemented CDC's surveillance plan by using two approaches to disseminate information to heighten awareness of plague, focusing on emergency department physicians. cache = ./cache/cord-294666-xlyuhzo9.txt txt = ./txt/cord-294666-xlyuhzo9.txt === reduce.pl bib === id = cord-294582-flkjekyo author = Hijikata, Atsushi title = Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs date = 2020-05-25 pages = extension = .txt mime = text/plain words = 4238 sentences = 232 flesch = 49 summary = In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Among these methods, SBDR is the most promising to find Abbreviations ACE2, angiotensin I-converting enzyme 2; MERS, Middle East respiratory syndrome; RBD, receptor-binding domain; SARS-CoV, severe acute respiratory syndrome coronavirus; SBDR, structure-based drug repositioning; WHO, World Health Organization. Also, the structural models of the complexes between SARS-CoV-2 proteins and potential drugs were proposed by comparing the ligand molecules of the proteins and approved, experimental, or natural drugs. A total of 11 ligand molecules were matched to 21 approved/experimental and 5 natural drugs, and the complex models of the SARS-CoV-2 proteins with several promising drugs, those with high similarity score or placed in higher ranking, were constructed as follows. cache = ./cache/cord-294582-flkjekyo.txt txt = ./txt/cord-294582-flkjekyo.txt === reduce.pl bib === id = cord-294854-rvrgcugn author = Hu, Biying title = The cytokine storm and COVID‐19 date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2781 sentences = 187 flesch = 47 summary = An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread throughout the world 1 . It has been reported that a cytokine storm is Accepted Article associated with the deterioration of many infectious diseases, including severe acute respiratory syndrome (SARS) 3 and Middle East respiratory syndrome (MERS) 4 . It is considered to be the main cause of disease severity and death in Accepted Article COVID-19 patients 5 , and is related to high levels of circulating cytokines, severe lymphopenia, thrombosis, and massive mononuclear cell infiltration in multiple organs 21 . Anakinra, an IL-1 receptor antagonist that blocks the activity of pro-inflammatory cytokines IL-1α and IL-1β, has been reported to improve respiratory function and increase the survival rate of COVID-19 patients 73 . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of Accepted Article coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) cache = ./cache/cord-294854-rvrgcugn.txt txt = ./txt/cord-294854-rvrgcugn.txt === reduce.pl bib === id = cord-294921-h44tct43 author = Greninger, Alexander L. title = The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2744 sentences = 121 flesch = 55 summary = Dr. Greninger was working in his research lab, assembling data for an early February grant for funding to understand the function of his favorite coronavirus gene (orf3a) in SARS-CoV-2, while Dr. Jerome continued splitting time between clinical virology and his work at the Fred Hutchinson Cancer Research Center on gene therapies for persistent viruses. From mid-January until the end of February, we received respiratory specimens from about 15 different persons under investigation for COVID-19 for respiratory virus panel testing, but each of them tested negative for SARS-CoV-2, not only at the CDC but also in our lab as we continued the evaluation of our assay. We could not report results from our assay development and validation studies, but our clinicians soon became disappointed by the 5-to 7-day turnaround time for clinical results from the CDC, during which patients waited in isolation for test results. cache = ./cache/cord-294921-h44tct43.txt txt = ./txt/cord-294921-h44tct43.txt === reduce.pl bib === id = cord-294910-gnc04ax1 author = Nogueira, Paulo Jorge title = The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4935 sentences = 251 flesch = 42 summary = The risk factors for increased odds of death by COVID-19 were: sex (male: OR = 1.47, ref = female), age ((56–60) years, OR = 6.01; (61–65) years, OR = 10.5; (66–70) years, OR = 20.4; (71–75) years, OR = 34; (76–80) years, OR = 50.9; (81–85) years, OR = 70.7; (86–90) years, OR = 83.2; (91–95) years, OR = 91.8; (96–104) years, OR = 140.2, ref = (0–55)), Cardiac disease (OR = 2.86), Kidney disorder (OR = 2.95), and Neuromuscular disorder (OR = 1.58), while condition (None (absence of precondition); OR = 0.49) was associated with a reduced chance of dying after adjusting for other variables of interest. The data retrieved include individuals' demographic characteristics (age, sex, region), COVID-19 disease information (death, recovery, still in treatment, hospitalization, intensive care, respiratory support), and preconditions (Asthma, Cancer, Cardiac disease, Hematological disorder, Diabetes, HIV and other immune deficiency, Kidney disorder, Liver disorder, Neuromuscular disorder, Other precondition and None (absence of precondition)). cache = ./cache/cord-294910-gnc04ax1.txt txt = ./txt/cord-294910-gnc04ax1.txt === reduce.pl bib === id = cord-294812-nnlzwaf1 author = Desforges, Marc title = Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date = 2014-03-12 pages = extension = .txt mime = text/plain words = 7096 sentences = 318 flesch = 36 summary = However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . cache = ./cache/cord-294812-nnlzwaf1.txt txt = ./txt/cord-294812-nnlzwaf1.txt === reduce.pl bib === id = cord-294698-mtfrbn87 author = Kim, H. K. title = Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date = 2016-05-23 pages = extension = .txt mime = text/plain words = 2682 sentences = 169 flesch = 62 summary = In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential. cache = ./cache/cord-294698-mtfrbn87.txt txt = ./txt/cord-294698-mtfrbn87.txt === reduce.pl bib === id = cord-294931-a77g9rjo author = Zhang, Linqi title = Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals date = 2005-11-18 pages = extension = .txt mime = text/plain words = 4013 sentences = 193 flesch = 52 summary = While there is no systematic evaluation of cytotoxic T-cell (CTL) activity in infected patients, there are some reports showing detection of binding antibodies to nucleocapsid (N) and spike (S) glycoprotein after about 2 weeks, remaining detectable for as long as 210 days after the onset of symptoms [Shi et al., 2003 Huang et al., 2004; Leung et al., 2004; Liu et al., 2004; Nie et al., 2004a; Temperton et al., 2005] . In this report, using both the ELISA-based and pseudotyped retrovirus-based neutralization systems, we characterized temporal changes in N protein-specific antibody and S glycoprotein-specific Nab responses in infected patients who have either recovered from or succumb to SARS-CoV infection. Since the 293/ACE2 cell line is the most susceptible to entry of the pseudotyped retrovirus bearing S glycoprotein, we chose this cell line for studies of neutralization antibody (Nab) activities of serum samples collected from SARS-CoV-infected patients. cache = ./cache/cord-294931-a77g9rjo.txt txt = ./txt/cord-294931-a77g9rjo.txt === reduce.pl bib === id = cord-294718-n3gx862b author = Tam, Patrick C K title = Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1606 sentences = 135 flesch = 61 summary = title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. cache = ./cache/cord-294718-n3gx862b.txt txt = ./txt/cord-294718-n3gx862b.txt === reduce.pl bib === id = cord-295029-zki5ac2g author = Pena, Robert C.F. title = In Reply to the Letter to the Editor Regarding “Coronavirus Neurosurgical/Head and Neck Drape to Prevent Aerosolization of Coronavirus Disease 2019 (COVID-19): The Lenox Hill Hospital/Northwell Health Solution” date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1647 sentences = 93 flesch = 38 summary = 1 This simple, cost-effective method can be easily assembled and is flexible with minimal disruption of the surgery being performed, while offering the ability to shield essential personnel in the operating room during procedures involving drilling of air-cells potentially harboring SARS-CoV-2 virions. 1,10 This draping method may therefore provide additional protection to surgeons against multiple viruses aerosolized by a wide range of drill settings, although further research should be conducted regarding COVID-19 aerosol generation in relation to drill speed in neurosurgical and otolaryngology-based procedures. Finally, whereas other researchers have proposed various methods of mask modification or alternate materials to provide barrier protection against COVID-19 aerosol transmission, 9 this and prior draping techniques may offer additional simple, easy to assemble, and cost-effective intraoperative protection. Specifically, this method provides protection to neurosurgical staff during high-speed drilling in the posterior fossa, whereas previously described drapes focus more on the restricted dissemination of COVID-19-laden aerosols during intubation, extubation, positive pressure ventilation, and endonasal endoscopic procedures. cache = ./cache/cord-295029-zki5ac2g.txt txt = ./txt/cord-295029-zki5ac2g.txt === reduce.pl bib === id = cord-294912-xl0wzi16 author = Alteri, Claudia title = Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date = 2020-09-08 pages = extension = .txt mime = text/plain words = 3630 sentences = 216 flesch = 49 summary = Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72–345). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients. In this study, the presence of SARS-CoV-2 genome was evaluated in 55 SARS-CoV-2 rtPCR negative nasopharyngeal swabs from COVID-19 suspected patients thanks to a quantitative ad hoc designed assay based on ddPCR. This proof-of-concept study shows that an in-house ddPCR-based assay can allow an efficient detection of SARS-CoV-2 at low copy number in symptomatic cases resulted negative by standard rtPCR. cache = ./cache/cord-294912-xl0wzi16.txt txt = ./txt/cord-294912-xl0wzi16.txt === reduce.pl bib === id = cord-295034-em6z8mlu author = Daverey, Achlesh title = COVID-19: Eco-friendly hand hygiene for human and environmental safety date = 2020-11-11 pages = extension = .txt mime = text/plain words = 1896 sentences = 125 flesch = 40 summary = Frequent handwashing with soap and the use of alcohol-based hand sanitizers is recommended by WHO for hand hygiene and to prevent the spread of COVID-19. However, there are safety concerns associated with the use of soaps and alcohol-based hand sanitizers. Therefore, the review aims to highlight the health and environmental concerns associated with the frequent use of soaps/detergents and alcohol-based hand sanitizers amid COVID-19. The potential of some of the natural detergents and sanitizing agents as eco-friendly alternatives to petrochemical-based soaps and alcohol-based hand rubs for hand hygiene are discussed. Overall, all these properties of plant-derived natural soaps and detergents have the potential to replace the synthetic detergents and alcohol-based sanitizers. Economical production of biosurfactants and extraction of bioactive antimicrobial agents from the plants will play a crucial role in their commercial application and sustainability as eco-friendly soaps and hand sanitizers and therefore further research is needed in this direction. cache = ./cache/cord-295034-em6z8mlu.txt txt = ./txt/cord-295034-em6z8mlu.txt === reduce.pl bib === id = cord-294856-eeh2a0t8 author = Lambert, Paul-Henri title = Consensus Summary Report for CEPI/BC March 12-13, 2020 Meeting: Assessment of Risk of Disease Enhancement with COVID-19 Vaccines date = 2020-05-25 pages = extension = .txt mime = text/plain words = 5236 sentences = 251 flesch = 40 summary = Therefore, CEPI and the Brighton Collaboration Safety Platform for Emergency vACcines (SPEAC) convened a scientific working meeting https://brightoncollaboration.us/brighton-collaboration-cepi-covid-19-web-conference/) on March 12 and 13, 2020 of experts in the field of vaccine immunology and coronaviruses to discuss current knowledge that could form the basis for the assessment of the risk of enhanced disease during SARS-CoV-2 vaccine development. Ferret models of SARS-CoV-1 also demonstrate virus replication in respiratory tracts with induction of a neutralizing antibody response but also demonstrated little evidence of clinical disease [13] . Efficacy of several SARS-CoV-1 vaccines was evaluated in these models with spike (S) protein based vaccines demonstrating neutralizing antibody and protection against pulmonary replication of the challenge virus in mice and hamsters [16] . There is evidence for disease enhancement in vaccinated animals after challenge with live virus in multiple studies with SARS-CoV-1 vaccine candidates as summarized in Table. Chinese macaques immunized with a modified vaccinia virus expressing S protein then challenged with SARS-CoV-1 did not develop clinical disease, but histopathology showed lung injury. cache = ./cache/cord-294856-eeh2a0t8.txt txt = ./txt/cord-294856-eeh2a0t8.txt === reduce.pl bib === id = cord-295061-58tj4csz author = Wilder‐Smith, Annelies title = Short communication: Low risk of transmission of severe acute respiratory syndrome on airplanes: the Singapore experience date = 2003-10-22 pages = extension = .txt mime = text/plain words = 1321 sentences = 60 flesch = 57 summary = The risk of transmission of severe acute respiratory syndrome (SARS) on airplanes is of major concern to the public and airline industry. Seven airplanes with nine passengers on board later diagnosed as suffering from probable SARS (based on WHO criteria) arrived in Singapore between 25 February and 31 May 2003: three were from Hong Kong (with five cases of SARS), one from Beijing, one from New York, one from East Malaysia and one from Indonesia. However, only three airplanes (with four passengers) had symptomatic cases of SARS on board, whereas the passengers of the other flights developed symptoms within the first 2 days after arrival in Singapore. The third flight with one passenger with severe symptoms of SARS (fever, cough, shortness of breath) arrived after the Infectious Disease Act had been invoked: all crew members and 46 of 47 passengers were contactable and quarantined with active surveillance for 10 days; none developed SARS. cache = ./cache/cord-295061-58tj4csz.txt txt = ./txt/cord-295061-58tj4csz.txt === reduce.pl bib === id = cord-294831-pem059zk author = Zhang, Ling-Pu title = Focus on a 2019-novel coronavirus (SARS-CoV-2) date = 2020-06-11 pages = extension = .txt mime = text/plain words = 6173 sentences = 378 flesch = 54 summary = A report of five patients in a family cluster who traveled to Wuhan and were infected with SARS-CoV-2 was the first report directly illustrating that the virus is capable of person-to-person transmission in hospital and family settings [23] . Xiao and colleagues showed that 53.42% of 73 hospitalized COVID-19 patients had SARS-CoV-2 RNA in stool specimens, and the duration time of positive stool results ranged from 1 to 12 days [27] . In a study published in The Lancet, 41 of 41 patients who were identified as positive for SARS-CoV-2 infection presented with pneumonia and abnormal chest computed tomography (CT) [6] . An article reported in Science shows that SARS-CoV-2 can replicate in the upper respiratory tract of ferrets, indicating that ferrets represent an ideal animal model for evaluating antiviral drugs or vaccine candidates against COVID-19 [64] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-294831-pem059zk.txt txt = ./txt/cord-294831-pem059zk.txt === reduce.pl bib === id = cord-294800-akr4f5p8 author = Kabir, Md. Tanvir title = nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date = 2020-07-10 pages = extension = .txt mime = text/plain words = 14084 sentences = 700 flesch = 44 summary = They also summarized that as viral load is quite high during the time of hospital admissions, use of potent antiviral agents at an early stage might prove Abbreviations: ACE2, angiotensin converting enzyme 2; AP, antigen presentation; APCs, antigen presentation cells; APN, aminopeptidase N, ARBs, angiotensin II receptor blockers; ARDS, acute respiratory distress syndrome; CDC, Centers for Disease Control; nCOVID-19, novel coronavirus disease 2019; CoVs, coronaviruses; DPP4, dipeptidyl peptidase 4; dsRNA, double-strand RNA; EC 50 , half maximal effective concentration; ED, emergency department; ELISA, enzymelinked immunosorbent assay; EUA, emergency use authorization; FDA, Food and Drug Administration; GGO, ground-glass opacity; HCV, hepatitis C virus; HIV, human immunodeficiency virus;, MHC, major histocompatibility complex; or HLA, human leukocyte antigen; ICU, intensive care unit; IL-6, interleukin 6; LPV/r, lopinavir/ritonavir; mAbs, monoclonal antibodies; MERS, Middle East respiratory syndrome; N7-MTase, N7-methyltransferase; NSAIDs, nonsteroidal anti-inflammatory drugs; PRRs, pattern recognition receptors; PUI, patient under investigation; RdRp, RNA-dependent RNA polymerase; RSV, respiratory syncytial virus; S protein, spike protein; SAM, S-adenosyl-methionine; SARS, severe acute respiratory syndrome; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; WHO, World Health Organization. cache = ./cache/cord-294800-akr4f5p8.txt txt = ./txt/cord-294800-akr4f5p8.txt === reduce.pl bib === id = cord-295302-vwrxentv author = Shivarov, Velizar title = Potential SARS-CoV-2 Preimmune IgM Epitopes date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2397 sentences = 118 flesch = 50 summary = While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. For the present study, the degrees of the vertices representing the natural SARS-CoV-2 epitopes, all of which belonged to the giant component, were used as the number of adjacent mimotopes parameter. A simple comparison for exact matches to peptides from the SARS-CoV-2 proteome yielded 3 heptapeptides-two in the open reading frame 1ab ( 3518 AQTGIAV 3524 and 5198 TKGPHEF 5204 ) and one in the spike protein ( 108 TTLDSKT 114 ). This loop is adjacent to the loop representing the epitope of the neutralizing antibody LCA60 on the SARS-CoV spike (8, 9) . Thus, it is quite possible that the SARS-CoV-2 spike epitope TTLDSKT is bound by B cells that will contribute to the induced immune response. cache = ./cache/cord-295302-vwrxentv.txt txt = ./txt/cord-295302-vwrxentv.txt === reduce.pl bib === id = cord-295142-5sqkdpi8 author = Han, Y. title = The active lung microbiota landscape of COVID-19 patients date = 2020-08-23 pages = extension = .txt mime = text/plain words = 3028 sentences = 199 flesch = 47 summary = The bronchoalveolar lavage fluid (BALF), containing microenvironment information on bronchioles and lung alveoli from the lower respiratory tract, is one of key sample types for characterizing the host inflammatory response and microbiota of COVID-19 patients as lung is one of main organs for the infection of SARS-CoV-2 (7, 8) . In this study, we systematically profiled the transcriptionally active microbiota landscape in BALF from COVID-19 patients and healthy individuals, identified microorganism composition in healthy individuals and COVID-19 patients, found disease-specific active microbes in the COVID-19 patient group, revealed the interaction between several bacteria or viruses and SARS-CoV-2. The diversity analysis revealed that the infection of SARS-CoV-2 probably caused a different lung microbiota composition in the COVID-19 patient group compared with the healthy group. Our study provides insight into the active microbiota in the lungs of COVID-19 patients and will contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. cache = ./cache/cord-295142-5sqkdpi8.txt txt = ./txt/cord-295142-5sqkdpi8.txt === reduce.pl bib === id = cord-294933-oc2glu4a author = Cinesi Gómez, César title = Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date = 2020-06-19 pages = extension = .txt mime = text/plain words = 5643 sentences = 337 flesch = 45 summary = The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations. cache = ./cache/cord-294933-oc2glu4a.txt txt = ./txt/cord-294933-oc2glu4a.txt === reduce.pl bib === id = cord-295559-yc8q62z8 author = Qian, Zhaohui title = Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date = 2013-10-03 pages = extension = .txt mime = text/plain words = 7303 sentences = 303 flesch = 50 summary = Coronavirus S proteins are Class I viral fusion proteins like the HIV envelope (env), influenza hemagglutinin (HA) and paramyxovirus fusion (F) glycoproteins [17] , which typically require protease cleavage between the S1 and S2 domains ( Figure 1A ) to permit conformational changes in S2, activated by receptor binding and/or low pH, that mediate membrane fusion leading to virus entry and syncytia formation [3, 17, 18] . In addition to entry by endocytosis, we showed that, like SARS-CoV [21, 22] , MERS pseudovirions could enter susceptible Vero E6 cells at the plasma membrane if virions were first bound to cell surface receptors at 4°C at neutral pH in the presence of NH 4 Cl to inhibit acidification of endosomes, and also treated briefly at room temperature with trypsin to cleave the viral S protein. cache = ./cache/cord-295559-yc8q62z8.txt txt = ./txt/cord-295559-yc8q62z8.txt === reduce.pl bib === id = cord-295051-upyar7en author = Ahmadian, Elham title = Covid‐19 and kidney injury: Pathophysiology and molecular mechanisms date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4859 sentences = 321 flesch = 45 summary = The SARS‐CoV‐2‐induced kidney damage is expected to be multifactorial; directly it can infect the kidney podocytes and proximal tubular cells and based on an angiotensin‐converting enzyme 2 (ACE2) pathway it can lead to acute tubular necrosis, protein leakage in Bowman's capsule, collapsing glomerulopathy and mitochondrial impairment. 6, 7 The initial impact might be the direct role of the virus on the renal parenchyma mediated by activating the angiotensin-converting enzyme 2 (ACE2), which functions as a SARS-CoV-2 receptor. 22 Altogether, these reports clarify that kidney cells are targeted by SARS-CoV-2 and new strategies are needed to treat Covid-19 to prevent organ infection and dysfunction. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Coronavirus disease 19 infection does not result in acute kidney injury: an analysis of 116 hospitalized patients from Wuhan, China Acute kidney injury in SARS-CoV-2 infection: direct effect of virus on kidney proximal tubule cells cache = ./cache/cord-295051-upyar7en.txt txt = ./txt/cord-295051-upyar7en.txt === reduce.pl bib === id = cord-295075-cqbayzat author = Rajnarayanan, Rajendram V. title = “Teaching old drugs to kill new bugs”: structure-based discovery of anti-SARS drugs date = 2004-08-20 pages = extension = .txt mime = text/plain words = 3675 sentences = 208 flesch = 50 summary = Several old drugs that bind to SARS 3CLpro active site were selected and in silico derivatized to generate covalent irreversible inhibitors with enhanced affinity. Structural conclusions from active site similarity within the coronavirus family and virtual screening on homology models have provided some clues regarding the class of compounds that could interact with SARS protease. The present study employs in silico derivatization as a method to ''teach old drugs to kill new bugs.'' We have designed irreversible covalent inhibitors by selective derivatization of top non-covalent leads, which includes several old drugs especially a class of HIV inhibitors identified from virtual screening. The side chains of His163 and Phe140 and the main-chain atoms of Met165, Glu166, and His172 form the S1 subsite, which confers specificity towards Gln. Thus, specific covalent inhibitors of SARS 3CLpro could be designed by substituting the amino acid at the P1 0 position with a thiol specific reactive organic moiety like chloromethyl ketone. cache = ./cache/cord-295075-cqbayzat.txt txt = ./txt/cord-295075-cqbayzat.txt === reduce.pl bib === id = cord-295257-iguhy1z8 author = Calcagnile, Matteo title = ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date = 2020-04-24 pages = extension = .txt mime = text/plain words = 4785 sentences = 253 flesch = 49 summary = SARS-CoV-2 and respiratory syndrome corona virus (SARS-CoV) Spike proteins share very high phylogenetic similarities (99%), and, indeed, both viruses exploit the same human cell receptor namely angiotensin-converting enzyme 2 (ACE2), a transmembrane enzyme whose expression dominates on lung alveolar epithelial cells 6, 15, 16 . In this study we have used a combination of in silico tools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 Spike glycoprotein. Results indicate that some residues of the ACE2 interface, which are involved in the interaction with SARS-CoV-2 Spike glycoprotein can actually fluctuate (Fig. 5cd ). Indeed, in the rodent blockade of the renin-angiotensin-aldosterone system limits the acute lung injury induced by the SARS-CoV-1 spike protein 49 , suggesting that if ACE2 function is preserved (because of increased baseline expression, as especially seen in pre-menopausal women), clinical course of infection might be less severe. cache = ./cache/cord-295257-iguhy1z8.txt txt = ./txt/cord-295257-iguhy1z8.txt === reduce.pl bib === id = cord-295041-5vpawtef author = Jakhmola, Shweta title = SARS-CoV-2, an Underestimated Pathogen of the Nervous System date = 2020-09-28 pages = extension = .txt mime = text/plain words = 5012 sentences = 310 flesch = 39 summary = Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. cache = ./cache/cord-295041-5vpawtef.txt txt = ./txt/cord-295041-5vpawtef.txt === reduce.pl bib === id = cord-294999-a5x8bmfr author = Plotkin, Stanley A title = The New Coronavirus, the Current King of China date = 2020-02-21 pages = extension = .txt mime = text/plain words = 1185 sentences = 82 flesch = 54 summary = There are several candidate vaccines against MERS being developed by an international organization, the Coalition for Epidemic Preparedness (CEPI; see below) [13] . Although yet to be confirmed at this writing, it is likely that SARS-CoV-2 originated from infections transferred from small mammals in the Wuhan market to humans. Aside from the development of vaccines against SARS-CoV-2, a step the Chinese government should take is to ban the sale of small mammals in their markets to prevent the introduction of other coronaviruses or, for that matter, pathogens in general that could adapt to humans. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study A synthetic consensus anti-spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates A double-inactivated whole virus candidate SARS coronavirus vaccine stimulates neutralising and protective antibody responses cache = ./cache/cord-294999-a5x8bmfr.txt txt = ./txt/cord-294999-a5x8bmfr.txt === reduce.pl bib === id = cord-295455-km0qcmlh author = Fehr, Anthony R. title = Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date = 2018-07-31 pages = extension = .txt mime = text/plain words = 5467 sentences = 309 flesch = 46 summary = The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Originally described as ADP-ribose-1 00 -phosphatases, both cellular and viral macrodomains enzymatically remove mono-and poly-ADP-ribose from proteins, supporting the notion that protein ADP-ribosylation is a component of the antiviral response. It was unclear how these mutations affected this protein, as neither mutant affected PAR binding and it was unknown whether alphaviruses' macrodomains had de-ADP-ribosylating activity. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites The conserved macrodomains of the nonstructural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases cache = ./cache/cord-295455-km0qcmlh.txt txt = ./txt/cord-295455-km0qcmlh.txt === reduce.pl bib === id = cord-295548-o877eog6 author = Antonio, G.E title = Imaging in Severe Acute Respiratory Syndrome (SARS) date = 2003-10-21 pages = extension = .txt mime = text/plain words = 2481 sentences = 136 flesch = 48 summary = HRCT is an important tool for early diagnosis in patients with a high clinical suspicion and a negative initial chest radiograph [8] . (1) the majority (108/138, 78%) of patients had air-space opacification of various extent on the chest radiograph at presentation, (2) the right lung was more affected than the left (82/108, 76% versus 67/108, 62%), (3) the lower zone (70/108, 65%) and peripheral lung fields (81/108, 75%) were commonly involved, (4) unifocal involvement (59/108, 55%) was more common at presentation, high fever (.388C), AND cough or breathing difficulty, AND one or more of the following exposures during the 10 days prior to onset of symptoms: close contact with a person who is a suspect or probable case of SARS; history of travel, to an area with recent local transmission of SARS; residing in an area with recent local transmission of SARS. cache = ./cache/cord-295548-o877eog6.txt txt = ./txt/cord-295548-o877eog6.txt === reduce.pl bib === id = cord-295545-ruxz77i8 author = Hennighausen, Lothar title = Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1660 sentences = 108 flesch = 55 summary = The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2. A study in pneumocytes demonstrated that ACE2 expression is induced by interferons (Ziegler, 2020) , possibly through the transcription factors Signal Transducer and Activator of Transcription (STAT) 1 and 2, as the authors suggest. Ace2 mRNA levels vary widely between cell types, with high expression detected in lactating mammary and intestinal tissues ( Figure 1A -B) and Type II Pneumocytes (Ziegler, 2020) . To explore the possibility that Ace2 gene expression in SARS-CoV-2 target cells is regulated not only by interferons but also by a range of cytokines through the family of STAT transcription factors, we mined available scRNA-seq data (Ziegler, 2020) (Table 1) . cache = ./cache/cord-295545-ruxz77i8.txt txt = ./txt/cord-295545-ruxz77i8.txt === reduce.pl bib === id = cord-295742-d11ty5ed author = van Dam, Peter A. title = High mortality of cancer patients in times of SARS-Cov-2: do not generalize! date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1118 sentences = 59 flesch = 51 summary = This is an important issue as in times limited of resources, the label "cancer with COVID-19" can compromise the access of intensive care (ICU) and outcome of patients dramatically in overwhelmed health care systems due to the outbreak of the SARS-CoV-2 pandemic. 4 The OpenSAFELY study, looking at factors associated with 5683 COVID-19-related hospital deaths in the linked electronic health records of 17 million adult NHS patients clearly showed that male gender (HR 1.99; 95% CI 1.80-2.10), age (with a very strong gradient), ethnicity (adjusted HR 1.71; 95% CI 1.44-2.02), uncontrolled diabetes (HR 2.26 95% CI: 2.18-2.56), obesity (with a very strong gradient) and various other medical conditions often had a higher impact on the probability to die of SARS-CoV-2 then cancer. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR cache = ./cache/cord-295742-d11ty5ed.txt txt = ./txt/cord-295742-d11ty5ed.txt === reduce.pl bib === id = cord-295800-w0dup04b author = So, Loletta K-Y title = Development of a standard treatment protocol for severe acute respiratory syndrome date = 2003-05-10 pages = extension = .txt mime = text/plain words = 2401 sentences = 140 flesch = 50 summary = Add combination treatment with ribavirin and methylprednisolone when: q Extensive or bilateral chest radiographic involvement q Or persistent chest radiographic involvement and persistent high fever for 2 days q Or clinical, chest radiographic, or laboratory findings suggestive of worsening q Or oxygen saturation <95% in room air Standard corticosteroid regimen for 21 days q Methylprednisolone 1 mg/kg every 8 h (3 mg/kg daily) intravenously for 5 days q Then methylprednisolone 1 mg/kg every 12 h (2 mg/kg daily) intravenously for 5 days q Then prednisolone 0·5 mg/kg twice daily (1 mg/kg daily) orally for 5 days q Then prednisolone 0·5 mg/kg daily orally for 3 days q Then prednisolone 0·25 mg/kg daily orally for 3 days q Then off Ribavirin regimen for 10-14 days q Ribavirin 400 mg every 8 h (1200 mg daily) intravenously for at least 3 days (or until condition becomes stable) q Then ribavirin 1200 mg twice daily (2400 mg daily) orally Pulsed methylprednisolone q Give pulsed methylprednisolone if clinical condition, chest radiograph, or oxygen saturation worsens (at least two of these), and lymphopenia persists q Give as methylprednisolone 500 mg twice daily intravenously for 2 days, then back to standard corticosteroid regimen Ventilation q Consider non-invasive ventilation or mechanical ventilation if oxygen saturation <96% while on >6 L per min oxygen or if patient complains of increasing shortness of breath conditioning) was increased to 10-12 changes per h. cache = ./cache/cord-295800-w0dup04b.txt txt = ./txt/cord-295800-w0dup04b.txt === reduce.pl bib === id = cord-295130-e7j7kac0 author = Moreno-Contreras, Joaquín title = Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2906 sentences = 122 flesch = 58 summary = In this study, we compared the RT-qPCR results from 253 paired samples obtained from saliva and swabs of ambulatory patients; the RNA in the swab samples was extracted using a commercial RNA purification kit, and the saliva samples were directly mixed with a lysis buffer, boiled, and used for the RT-qPCR protocol. To evaluate if saliva is a good source of viral RNA for the RT-qPCR, we determined the presence of the SARS-CoV-2 genome in paired saliva and swab samples from 253 ambulatory patients. Direct lysis of nasopharyngeal or oropharyngeal swab samples in viral transport medium using the QE buffer has been reported as a suitable method for direct RT-qPCR for SARS-CoV-2 detection, with rates similar to those of methods based on column purification (11, 15) . cache = ./cache/cord-295130-e7j7kac0.txt txt = ./txt/cord-295130-e7j7kac0.txt === reduce.pl bib === id = cord-295121-4xemmaqt author = Ferreira, Eliane de Oliveira title = Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date = 2020-09-29 pages = extension = .txt mime = text/plain words = 2301 sentences = 117 flesch = 40 summary = The outbreak caused by the novel coronavirus SARS-CoV-2 and its associated symptoms, termed COVID-19 disease, originally in Wuhan, China in 2019, has rapidly become a global pandemic (Park, 2020) . Although some of those risk factors for CDI are also related to higher probability rates of mortality in severe SARS-CoV-2 infection, the limited number of CDI cases reported among COVID-19 patients is somewhat surprising. The authors emphasized that when CDI is present as a co-infection with COVID-19 and the diarrhea persists, therapy can be difficult because of the SARS-CoV-2 infection. The dearth of studies regarding secondary infections, such as Clostridioides difficile, in COVID-19 patients makes it difficult to measure the effect of the pandemic on antimicrobial stewardship programs and on long term antimicrobial resistance. In conclusion, it seems highly likely that cases of CDI are being under-reported among COVID-19 patients and the increased use of antibiotics may, in part, be responsible. cache = ./cache/cord-295121-4xemmaqt.txt txt = ./txt/cord-295121-4xemmaqt.txt === reduce.pl bib === id = cord-295508-yhdj5m0e author = Yang, Li-Tao title = Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients date = 2006-06-16 pages = extension = .txt mime = text/plain words = 4422 sentences = 241 flesch = 64 summary = title: Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients In this study, we found that memory T-cell responses against the spike (S) protein were persistent for more than 1 year after SARS-CoV infection by detecting the production of IFN-γ using ELISA and ELISpot assays. In this study, we analyzed CD4 + and CD8 + T-cell responses in peripheral blood of recovered SARS patients to a pool of 169 overlapping SARS-CoV S peptides and characterized the phenotype of memory T-cell subpopulations. In this study, we performed phenotypic characterization of antiviral T-cell responses specific for SARS-CoV S peptides on the basis of their ability to secrete IFN-g and the expression of CD45RO, CCR7 and CD62L. Consistent with observations in HIV infection, we showed that SARS-CoV S-specific CD8 + T cells produced IFN-g but not IL-2 and predominantly displayed CD45RO À CCR7 À phenotype which might represent terminally differentiated effector memory T cells [25] . cache = ./cache/cord-295508-yhdj5m0e.txt txt = ./txt/cord-295508-yhdj5m0e.txt === reduce.pl bib === id = cord-295433-olmein3q author = Banerjee, Arinjay title = Bats and Coronaviruses date = 2019-01-09 pages = extension = .txt mime = text/plain words = 5655 sentences = 298 flesch = 52 summary = Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . cache = ./cache/cord-295433-olmein3q.txt txt = ./txt/cord-295433-olmein3q.txt === reduce.pl bib === id = cord-295973-41jqgsv0 author = Singh, Awadhesh Kumar title = Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries date = 2020-03-26 pages = extension = .txt mime = text/plain words = 3461 sentences = 163 flesch = 50 summary = In this review article, we have systematically searched the medical data base until and collated all the available evidences that have emerged so far on the efficacy of chloroquine and hydroxychloroquine, in the treatment of patients with COVID19 , with or without diabetes and present a perspective on both these compounds. A Chinese study involving more than 100 patients of COVID-19 found chloroquine superior to the control group in reducing symptom duration, exacerbation of pneumonia including radiological improvement and promoting virus-negative seroconversion without any severe side effects [18] . The expert consensus from the Department of Science and Technology and Health Commission of Guangdong province published on 20th February (based on in vitro evidence and still unpublished clinical experience) chloroquine phosphate tablet at a dose of 500 mg twice per day for 10 days for patients diagnosed as mild, moderate and severe cases of SARS-CoV-2 pneumonia in the absence of contraindication to the drug [21] . cache = ./cache/cord-295973-41jqgsv0.txt txt = ./txt/cord-295973-41jqgsv0.txt === reduce.pl bib === id = cord-295274-gzkfy70s author = Mecham, Jeffrey C. title = Utility of Tracheostomy in Patients With COVID‐19 and Other Special Considerations date = 2020-05-12 pages = extension = .txt mime = text/plain words = 2901 sentences = 160 flesch = 37 summary = METHODS: We explore current literature and recommendations for tracheostomy in patients with COVID‐19 and look back at previous data from severe acute respiratory syndrome coronavirus 1 (SARS‐CoV‐1), the virus responsible for the SARS outbreak of 2003. RESULTS: Given the severity and clinical uncertainty of patients with COVID‐19 and the increased risk of transmission to clinicians, careful consideration should be taken prior to performing tracheostomy. One concern for healthcare professionals managing the airways of COVID-19 patients is the risk of viral exposure during aerosol-generating procedures, including intubation and tracheostomy. There is a plausible risk for increased intraprocedural viral exposure via secretions and aerosolized particles when tracheostomy is performed percutaneously because this technique requires additional manipulation of the airway with multiple, repetitive dilations. Given the severity and uncertain clinical outcome of patients with COVID-19, in addition to the increased risk of transmission to clinicians during aerosol generating procedures, careful consideration should be taken prior to performing tracheostomy. cache = ./cache/cord-295274-gzkfy70s.txt txt = ./txt/cord-295274-gzkfy70s.txt === reduce.pl bib === id = cord-295375-nakxfhxk author = Yu, Yang title = Assessment of the quality of systematic reviews on COVID‐19: A comparative study of previous coronavirus outbreaks date = 2020-04-28 pages = extension = .txt mime = text/plain words = 2455 sentences = 143 flesch = 48 summary = In this comparative study, we investigated the present status of conducting SRs on COVID-19, MERS, and SARS, appraised the methodological quality of these SRs using the a measurement tool to assess systematic reviews (AMSTAR 2), and performed a preliminary examination of the potential risk factors associated with the quality of SRs, with the aim of providing suggestions from the aspects of methodological quality for conducting and using SRs during the COVID-19 pandemic. AMSTAR, a measurement tool to assess systematic reviews; MA, meta-analysis quality of most SRs is unsatisfactory, and those on COVID-19 have higher risks of poor quality, despite the rapid actions taken to conduct SRs. Teams that may want to conduct a SR should focus on the study design and focus on improving the quality of the SR. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis cache = ./cache/cord-295375-nakxfhxk.txt txt = ./txt/cord-295375-nakxfhxk.txt === reduce.pl bib === id = cord-295523-5pv7kw6i author = Picchianti Diamanti, Andrea title = Cytokine Release Syndrome in COVID-19 Patients, A New Scenario for an Old Concern: The Fragile Balance between Infections and Autoimmunity date = 2020-05-08 pages = extension = .txt mime = text/plain words = 7905 sentences = 390 flesch = 39 summary = However, in about 20% of patients, the infection progresses to severe interstitial pneumonia and can induce an uncontrolled host-immune response, leading to a life-threatening condition called cytokine release syndrome (CRS). We critically review the rationale for the adoption of immunosuppressive agents, commonly used in autoimmune diseases, in the treatment of SARS-CoV-2 infection and report current knowledge of ongoing studies. The exacerbated reaction to infections or to biological therapy is caused by the rapid recruitment of macrophages and neutrophils, which produce pro-inflammatory cytokines and alter the fragile balance between a controlled immune response and a host-damaging reaction. As of now, four clinical trials are recruiting patients with COVID-19, severe acute respiratory failure, and CRS, aiming at evaluating the safety and effectiveness of anakinra alone or in combination with anti-IL-6 agents (NCT04330638, NCT0432402, NCT04357366, NCT04339712). High disease activity is associated with an increased risk of infection in patients with rheumatoid arthritis cache = ./cache/cord-295523-5pv7kw6i.txt txt = ./txt/cord-295523-5pv7kw6i.txt === reduce.pl bib === id = cord-295733-f3rt1fyk author = Ge, Tianxiang title = Evaluation of disinfection procedures in a designated hospital for COVID-19 date = 2020-08-22 pages = extension = .txt mime = text/plain words = 2492 sentences = 142 flesch = 49 summary = When compared with previous study, more places that could be potentially contaminated by COVID-19 patients were sampled for viral RNA detection, such as the flush button of the toilet bowl, medical refuse transfer trolley, elevators, and the examination rooms for these patients. These areas could not be used for non-COVID-19 patients until all the environmental samples collected were negative for SARS-CoV-2 RNA detection. In this study, surface samples collected from the examination rooms were all negative for SARS-CoV-2 RNA detection, and the samples collected from isolation wards and other places were also negative for viral RNA detection, which indicated that the terminal disinfection was effective. Other researches had revealed the presence of SARS-CoV-2 RNA in aerosol, which indicated the air could be contaminated by the virus, and patients could be infected in the isolation wards [12, 28] . Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients cache = ./cache/cord-295733-f3rt1fyk.txt txt = ./txt/cord-295733-f3rt1fyk.txt === reduce.pl bib === id = cord-295792-hajvtzj9 author = Álvez, Fernando title = SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date = 2020-07-03 pages = extension = .txt mime = text/plain words = 4504 sentences = 196 flesch = 46 summary = In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice cache = ./cache/cord-295792-hajvtzj9.txt txt = ./txt/cord-295792-hajvtzj9.txt === reduce.pl bib === id = cord-296031-r6iqiy1n author = Tattan-Birch, H. title = COVID-19, smoking, vaping and quitting: A representative population survey in England date = 2020-06-30 pages = extension = .txt mime = text/plain words = 5196 sentences = 343 flesch = 59 summary = Aims: To explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home. Conclusions: In a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In this study, we will use a representative population sample of adults in England to estimate: 1) associations between suspected SARS-CoV-2 infection and smoking status, e-cigarette use and NRT use; . https://doi.org/10.1101/2020.06.29.20142661 doi: medRxiv preprint A1: Logistic regression was used to estimate the association between suspected SARS-CoV-2 infection and (i) smoking status, (ii) e-cigarette use and (iii) NRT use, with and without adjustment for potential confounders. cache = ./cache/cord-296031-r6iqiy1n.txt txt = ./txt/cord-296031-r6iqiy1n.txt === reduce.pl bib === id = cord-295525-emrwcx0m author = To, Kelvin Kai-Wang title = Consistent Detection of 2019 Novel Coronavirus in Saliva date = 2020-02-12 pages = extension = .txt mime = text/plain words = 1912 sentences = 110 flesch = 55 summary = The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. cache = ./cache/cord-295525-emrwcx0m.txt txt = ./txt/cord-295525-emrwcx0m.txt === reduce.pl bib === id = cord-295846-quhnesbr author = Li, Huan title = Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2788 sentences = 185 flesch = 45 summary = In conclusion, corticosteroid use in subjects with SARS-CoV-2, SARS-CoV, and MERS-CoV infections delayed virus clearing and did not convincingly improve survival, reduce hospitalization duration or ICU admission rate and/or use of mechanical ventilation. Because of the overlapping genetic and clinical feature of SARS-CoV-2, SARS-CoV, and MERS-CoV, we performed a meta-analysis of safety and efficacy of corticosteroid use in these coronavirus infections. Our meta-analysis focus on the effects of corticosteroids on virus clearing and mortality in persons infected with SARS-CoV-2, SARS-CoV, or MERS-CoV. Inclusion criteria included: (1) research articles including observational studies and clinical trials but excluding reviews or case reports on the use of corticosteroids in persons with SARS-CoV-2, SARS-CoV, and MERS-CoV infections; (2) reported outcomes of virus clearance and/or death; and (3) published in English and/or Chinese. To test impact of corticosteroid use on duration of hospitalization we included 3 studies [12, 13, 16] involving 828 subjects (SARS, N = 519; MERS, N = 309). cache = ./cache/cord-295846-quhnesbr.txt txt = ./txt/cord-295846-quhnesbr.txt === reduce.pl bib === id = cord-295144-tyyc81uc author = Stradner, Martin H. title = Rheumatic Musculoskeletal Diseases and COVID-19 A Review of the First 6 Months of the Pandemic date = 2020-10-09 pages = extension = .txt mime = text/plain words = 9901 sentences = 442 flesch = 39 summary = In this review, we summarize the published cases of COVID-19 infections in RMD patients, including patients with inflammatory arthritis and connective tissue diseases as well as anti-phospholipid syndrome and Kawasaki syndrome. It also reviews the general risk of viral infections in patients with RMD, the impact of disease modifying anti-rheumatic drugs (DMARDs) on the outcome of infections, and gives a comparison between present and previous coronavirus pandemics. This argues against a protective role of HCQ (in the usually administered dose for RMD patients) in SARS-CoV-2 infection, which is also supported by pharmacological in vitro data describing a much higher level needed for effective viral inhibition (61) . In conclusion, data published in the first 6 months do not consistently describe a higher risk for infection with SARS-CoV-2 or a more severe course of COVID-19 in patients with either inflammatory arthritis or connective tissue diseases. cache = ./cache/cord-295144-tyyc81uc.txt txt = ./txt/cord-295144-tyyc81uc.txt === reduce.pl bib === id = cord-296128-kjoi54ea author = Balestri, Riccardo title = Do we have serological evidences that chilblain‐like lesions are related to SARS‐CoV‐2? A review of the literature date = 2020-08-26 pages = extension = .txt mime = text/plain words = 1631 sentences = 105 flesch = 51 summary = Our review demonstrated a high prevalence of negative serological results in CLL: antibodies were observed only in a few patients, that are even less excluding those with positive IgA, not clearly involved in the pathogenesis of the disease. The outbreak of chilblain-like lesions (CLL) coincidentally to the COVID-19 pandemic is a topic of great concern 1 SARS-CoV-2 was hypothesized as the etiologic agent of CLL, initially on the basis of the temporal correlation between the "burst" of skin manifestations and the viral pandemic. However, it has been shown that CLL are not related to an acute infection, since real-time reverse transcription polymerase chain reaction (rt-PCR) tests from nasopharyngeal swabs seldom resulted positive 1-9Therefore, dermatologists' attention shifted to the search for specific SARS-CoV-2 antibodies. The search was limited to articles published in English We included only case series, clearly declaring that a search for SARS-CoV-2 specific antibodies had been performed. Chilblain-like lesions during COVID-19 pandemic: a serological study on a case series cache = ./cache/cord-296128-kjoi54ea.txt txt = ./txt/cord-296128-kjoi54ea.txt === reduce.pl bib === id = cord-295946-p9enjxiq author = Hattori, Shin-ichiro title = GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection date = 2020-08-20 pages = extension = .txt mime = text/plain words = 7044 sentences = 390 flesch = 54 summary = We assessed various newly generated compounds that target the main protease (M(pro)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. When VeroE6 cells were exposed to SARS-CoV-2 WK-521 at a multiplicity of infection (MOI) of 0.05 and cultured in the presence of various concentrations of the two indole chloropyridinyl esters GRL-0820 and GRL-0920, the compounds were found to be highly potent against SARS-CoV-2 WK-521 with 50% effective concentration (EC 50 ) values of 15 Ϯ 18 and 2.8 Ϯ 0.3 M, respectively, using RNA-qPCR (Table 1) . When VeroE6 TMPRSS2 cells were exposed to SARS-CoV-2 WK-521 and cultured in the presence of various concentrations of lopinavir and nelfinavir, many virus-infected cells were seen at 1 and 10 M and stained in green, indicating that these two compounds had no detectable antiviral activity in the assay. cache = ./cache/cord-295946-p9enjxiq.txt txt = ./txt/cord-295946-p9enjxiq.txt === reduce.pl bib === id = cord-296095-onereai5 author = Vardhan, Seshu title = In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5483 sentences = 274 flesch = 48 summary = Considering the published literature on medicinal importance, 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). In this manuscript, 154 phytochemicals from limonoids and triterpenoids were selected by considering their known medicinal importance to search potential hits for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). Our recent molecular docking study on searching inhibitors for COVID-19 revealed that the phytochemical limonin known for inhibiting the replication of retroviruses like HTLV-I and HIV-1 showed the higher dock score towards the protein targets RdRp and ACE2 of SARS-CoV-2, and comparatively higher than the drug hydroxychloroquine [17] . cache = ./cache/cord-296095-onereai5.txt txt = ./txt/cord-296095-onereai5.txt === reduce.pl bib === id = cord-295957-s17z2ccf author = Bordi, Licia title = Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1923 sentences = 108 flesch = 52 summary = BACKGROUND: So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. CONCLUSIONS: The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients. Moreover, to evaluate the performance of the test in a different clinical specimen, a total of 33 Broncho-Alveolar Lavage (BAL) collected for COVID-19 diagnosis between 20 March and 03 April 2020 were also analysed in parallel with the Simplexa™ COVID-19 Direct assay and the routine laboratory method, based on the WHO protocols (7, 8) , using the Abbot m2000 extraction platform. cache = ./cache/cord-295957-s17z2ccf.txt txt = ./txt/cord-295957-s17z2ccf.txt === reduce.pl bib === id = cord-295765-c7o2ukm6 author = Silvas, Jesus A. title = Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2234 sentences = 145 flesch = 53 summary = VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. As SARS-CoV-2 replication 174 damages the cell monolayer, impedance measurements decrease over time, providing a detailed 175 assessment of infection kinetics. Based on the toxicity window of 1-20 221 h.p.t. determined with the VPS34 inhibitors, neither Triacsin C nor Orlistat induced early 222 cytotoxic effects, even at the highest concentrations of 50uM and 500uM, respectively ( Figure 223 3A and 3C). Here, we demonstrate that two VPS34 inhibitors, Orlistat, and Triacsin C each have clear effects 308 on SARS-CoV-2 replication and the morphology of viral replication centers. In contrast, the compounds did not exhibit any activity against 384 SARS-CoV-2 in Vero E6 cells whereas Triacsin C did. cache = ./cache/cord-295765-c7o2ukm6.txt txt = ./txt/cord-295765-c7o2ukm6.txt === reduce.pl bib === id = cord-295514-vhymj0rw author = Lim, Peter A title = Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: Severe acute respiratory syndrome date = 2004-08-01 pages = extension = .txt mime = text/plain words = 5277 sentences = 244 flesch = 43 summary = Severe acute respiratory syndrome (SARS) is a new respiratory viral epidemic that originated in China but has affected many parts of the world, with devastating impact on economies and the practice of medicine and rehabilitation. Rehabilitation was significantly affected by SARS, because strict infection control measures run counter to principles such as multidisciplinary interactions, patients encouraging and learning from each other, and close physical contact during therapy. Rehabilitation medicine was increasingly affected by everstricter infection control measures regarding close contacts and interactions between health care workers. Rehabilitation medicine was directly affected when the entire neurology ward, including patients and health care staff, were transferred out to TTSH for isolation and observation because of suspicious clusters of fevers that involved both patients and staff. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-295514-vhymj0rw.txt txt = ./txt/cord-295514-vhymj0rw.txt === reduce.pl bib === id = cord-296020-kje1wiah author = Patoulias, Dimitrios title = Diabetes mellitus and SARS-CoV-2-related mortality: the impact of acute hyperglycemic crises and some further considerations date = 2020-08-20 pages = extension = .txt mime = text/plain words = 604 sentences = 27 flesch = 42 summary = We would like to emphasize on another aspect of SARS-CoV-2 infection among patients with DM, the triggering of acute hyperglycemic crises, either diabetic ketoacidosis (DKA) or hyperosmolar hyperglycemic state (HHS). described the presentation and clinical course of 6 patients with DM who developed DKA and HHS in the context of SARS-CoV-2 infection [2] . However, according to a recent retrospective analysis from the UK, patients with DM who develop DKA due to disease are more likely to survive compared to those patients that are not complicated by an acute hyperglycemic crisis [5] . Therefore, it would be interesting to know in future, large, observational studies the proportion of patients that developed DKA/HHS in the context of SARS-CoV-2 infection, the underlying treatment and the outcome of disease. Clinical characteristics and outcome in patients with combined diabetic ketoacidosis and hyperosmolar hyperglycemic state associated with COVID-19 :a retrospective, hospital-based observational case series cache = ./cache/cord-296020-kje1wiah.txt txt = ./txt/cord-296020-kje1wiah.txt === reduce.pl bib === id = cord-295431-p9iy7uaf author = Atangana, Ernestine title = Facemasks simple but powerful weapons to protect against COVID-19 spread: Can they have sides effects? date = 2020-09-30 pages = extension = .txt mime = text/plain words = 9778 sentences = 441 flesch = 53 summary = Climatic factors including climate temperature, humidity, wind speed have played some crucial role in respect to the transition of the ongoing pandemic COVID-19, caused by the severe acute respiratory syndrome coronavirus2 (SARS-COV-2) and patient's recovery and the death rate across the globe. With all these results in hand, there is a clear evidence that the wind could be a carrier of droplets containing concentration of COVID-19, while some case studied have been done for indoor and outdoor exposure with a wind speed of 2km/h, no mathematical model has been suggested to see in general how far such droplets could be transported. It was also observed that the transport followed a crossover behaviour, where during the first period, the transport followed a fading memory process but later a power law behaviour, with no steady state, this was very interesting as this shows that, when the COVID-19 infected person sneezed there were no wind effect, thus concentration released in the air with initial speed was able to spread like in the results described in [66] see Figure 8 below. cache = ./cache/cord-295431-p9iy7uaf.txt txt = ./txt/cord-295431-p9iy7uaf.txt === reduce.pl bib === id = cord-296148-za3j19k5 author = Rosenzweig, Ivana title = Does damage to hypothalamic paraventricular nucleus underlie symptoms of ultradian rhythm disorder and an increased anxiety in coronavirus disease 2019? date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1706 sentences = 80 flesch = 34 summary = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may directly target parts of the brain, more specifically the hypothalamus and its paraventricular nucleus, and possibly lead to increased prevalence of anxiety disorders. Any changes in the PVN circuitries, due to their major control over most of neuro-endocrine axes and neuronal autonomic centers, may cause robust alteration in homeostatic regulation, and through influence on regulatory brain centers impact on sleep and wakefulness, increased propensity to affective disorders and anxiety, and alteration of ultradian rhythms. We correspondingly argue a direct SARS-CoV-2 effect on the specific part of the brain's hypothalamic paraventricular nucleus (PVN) circuitry ( Figure 1 ) as a neurologic mechanism that may, at least in part, underlie previously reported ultradian disruption, and that may lead to an increased anxiety symptomatology (7) . We propose that SARS-CoV-2 may target the distinct ACE2-tagged part of the PVN-subcircuitry (8), via a direct monosynaptic subfornical route (Figure 1 ), leading to the pleomorphic dysautonomic ultradian presentation, which is further compounded with nocturnal sleep fragmentation. cache = ./cache/cord-296148-za3j19k5.txt txt = ./txt/cord-296148-za3j19k5.txt === reduce.pl bib === id = cord-296187-nnv2e7gr author = Mulgaonkar, Nirmitee title = Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4943 sentences = 306 flesch = 57 summary = The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. This study utilizes in silico methodology followed by in vitro experimental validation to screen existing FDA-approved small molecule drugs specific to the RBD of the spike protein of SARS-CoV-2 to identify repurposable drugs targeting further clinical validation. cache = ./cache/cord-296187-nnv2e7gr.txt txt = ./txt/cord-296187-nnv2e7gr.txt === reduce.pl bib === id = cord-296214-xeezt6f7 author = Sabatino, Jolanda title = Women's perspective on the COVID-19 pandemic: Walking into a post-peak phase date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2699 sentences = 160 flesch = 49 summary = Therefore, we discussed the impact of COVID-19 pandemic on women, children and young patients, particularly those with underlying cardiovascular comorbidities or congenital heart disease. Although the so far evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is likely to have a lower fatality rate in women, the course of the disease during pregnancy is not fully understood. Indeed, in rat lungs a higher expression of ACE2 has been observed in younger females animals than in adult males [26] Despite adult patients with cardiovascular co-morbidities have a worse course of the disease, and higher mortality rate, when we look at children infected by SARS-CoV-2 with concomitant congenital heart disease (CHD), they seem to have the same clinical trend and mortality of peers without CHD. An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes cache = ./cache/cord-296214-xeezt6f7.txt txt = ./txt/cord-296214-xeezt6f7.txt === reduce.pl bib === id = cord-295864-kwdvais7 author = Flahault, Antoine title = Has China faced only a herald wave of SARS-CoV-2? date = 2020-03-27 pages = extension = .txt mime = text/plain words = 271 sentences = 24 flesch = 63 summary = key: cord-295864-kwdvais7 journal: The Lancet cord_uid: kwdvais7 Serosurveys should be seen as polls before elections; they can be repeated several times, 3 week after week, to monitor the epidemic precisely. There is no reason to wait for the end of the epidemic before doing serosurveys. The results would be tremendously informative to China, first and foremost, and to the entire international community, on the risk of big secondary epidemic waves. The attack rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) calculated by mathe matical models, from estimates of the basic reproduction number, R0, of 2-3, suggests that 50-60% of the population should eventually be infected because the population seems to be entirely naive to the new virus. COVID-19) advice for the public Director-General's opening remarks at the media briefing on COVID-19 -28 A WHO-UNICEF-Lancet Commission cache = ./cache/cord-295864-kwdvais7.txt txt = ./txt/cord-295864-kwdvais7.txt === reduce.pl bib === id = cord-296007-1gsgd22t author = Mohseni, Amir Hossein title = Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date = 2020-09-12 pages = extension = .txt mime = text/plain words = 2327 sentences = 110 flesch = 64 summary = Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV N proteins prefers the 2 2 1 hydrophobic amino acid residues (e.g. Ile, Leu, Met, and Phe), and the second position of these hit peptides 2 2 2 is an hydrophobic amino acid residue Pro forming five strong VDW forces with residues Y99, V67, M45, 2 2 3 Y7, and F9 and two H-bonds with residues K66 and E63 on MHC molecule ( Figure S2A , left). Visualization of interactions in the atomic level structure of a TCR-pMHC complex in the hit peptide of 2 4 9 SARS-CoV-2 N protein for HLA-E ( Figure S3C ) within 20 and 8 Å was generated on-the-fly using of the homologous peptide antigens of all queries has no detectable binding to both MHC and TCR. cache = ./cache/cord-296007-1gsgd22t.txt txt = ./txt/cord-296007-1gsgd22t.txt === reduce.pl bib === id = cord-296054-s8pibdeg author = Hanson, K. E. title = Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 date = 2020-10-21 pages = extension = .txt mime = text/plain words = 2452 sentences = 125 flesch = 51 summary = title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 We prospectively compared health care worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of coronavirus disease 2019 (COVID-19) in 354 patients. More cases were detected by the use of NPS (n = 80) and saliva (n = 81) than by the use of ANS (n = 70), but no single specimen type detected all severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Larger studies that compare the performance of patient self-collected ANS and straight saliva to health care worker-collected NPS for SARS-CoV-2 detection are needed. Therefore, we performed a prospective comparative study to evaluate the performance of patient self-collected ANS and saliva versus that of health care providercollected NPS for SARS-CoV-2 diagnostic testing. This study represents one of the largest prospective comparisons of specimen types to date and demonstrates excellent agreement between provider-collected NPS and patient self-collected saliva and ANS. cache = ./cache/cord-296054-s8pibdeg.txt txt = ./txt/cord-296054-s8pibdeg.txt === reduce.pl bib === id = cord-296147-yfcp0xf2 author = Mairesse, Antoine title = High clinical performance and quantitative assessment of antibody kinetics using a dual recognition assay for the detection of SARS-CoV-2 IgM and IgG antibodies date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3217 sentences = 226 flesch = 56 summary = This study aims at assessing the analytical and clinical performances of the iFlash® anti-SARS-CoV-2 chemiluminescence assay for the detection of both IgM and IgG antibodies. The determination of anti-SARS-CoV-2 IgG antibodies from 28 days since symptom onset was associated with high sensitivity, especially using optimized cut-offs (i.e. 100%). The aim of this study was to evaluate the analytical and clinical performances of the iFlash ® SARS-CoV-2 antibodies (IgM and IgG) chemiluminescence assay (CLIA). Clinical sensitivity for SARS-Cov-2 serological test depending on the onset of COVID-19 symptoms was carried out with the manufacturer's cut-off (>10 AU/mL for both IgM and IgG) and with ROC curve adapted cut-offs (2.81 AU/mL for IgM; 4.86 AU/mL for IgG). The aims of the present study were to evaluate the analytical and clinical performances of the iFlash ® anti-SARS-CoV-2 CLIA assay for IgM and IgG antibodies with a large cohort of COVID-19 patients, to provide an external validation of this test and to evaluate the antibody kinetics since symptom onset. cache = ./cache/cord-296147-yfcp0xf2.txt txt = ./txt/cord-296147-yfcp0xf2.txt === reduce.pl bib === id = cord-295850-nb6miso7 author = Zhang, Chuan-hai title = Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain date = 2005-05-02 pages = extension = .txt mime = text/plain words = 2930 sentences = 161 flesch = 55 summary = title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain The immunogenicity of a candidate-inactivated vaccine prepared from SARS-CoV F69 strain was evaluated in Balb/c mice. The present study was performed with the objective of determining the immunogenicity of a candidate-inactivated SARS-CoV vaccine made from F69 strain in Balb/c mice. In test groups, anti-SARS-CoV specific IgM antibodies were induced by the inactivated vaccine. The results showed that SARS-CoV F69 strain inactivated vaccine could induce potent humoral immune responses in Balb/c mice. In present study, the specificity of serum antibodies induced by F69 strain inactivated vaccine was identified by Western blot assay. A convalescent serum of SARS patient was used, and the same positive result was obtained (lane 3, Fig. 4) , which further demonstrated the specificity of the antibodies induced with the inactivated vaccine produced from F69 strain. cache = ./cache/cord-295850-nb6miso7.txt txt = ./txt/cord-295850-nb6miso7.txt === reduce.pl bib === id = cord-296195-m2wwlvgx author = Chen, Chung-Jen title = Toona sinensis Roem tender leaf extract inhibits SARS coronavirus replication date = 2008-10-30 pages = extension = .txt mime = text/plain words = 2541 sentences = 156 flesch = 66 summary = RESULTS: Only TSL-1, the extract from tender leaf of Toona sinensis Roem was found to have an evident effect against SARS-CoV with selectivity index 12∼17. In the third study, five TCM formulae included Yin-Chiau-San, Pu-Zhi-Siau-Du-Yien, Ger-Gern-Hwang-Lein, Sang-Zhiu-Yien and Huang-Lein-Zhei-Du-Tang as well as Toona sinensis Roem tender leaf extract TSL-1 and TSL-1nm were tested against SARS-CoV. Much different from a lot of previously identified components or drugs against SARS-CoV, the tender leaf of Toona sinensis Roem has been used as a popular vegetable by Chinese people in both mainland China and Taiwan with high level of safety. To our knowledge, this is the first report to show extract from the tender leaf of Toona sinensis Roem against SARS-CoV. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. cache = ./cache/cord-296195-m2wwlvgx.txt txt = ./txt/cord-296195-m2wwlvgx.txt === reduce.pl bib === id = cord-296109-kco85lqn author = Vanuytsel, Kim title = Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date = 2020-05-19 pages = extension = .txt mime = text/plain words = 2499 sentences = 132 flesch = 47 summary = Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. In the United States, significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate COVID-19 patient care and public health management of the pandemic (Sharfstein et al., 2020) , impacting the timely mapping of the dynamics of viral spread in the general population, and more topically, the conservation of personal protective equipment. Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). cache = ./cache/cord-296109-kco85lqn.txt txt = ./txt/cord-296109-kco85lqn.txt === reduce.pl bib === id = cord-296219-zzg9hds0 author = Battaglini, Denise title = Neurological Manifestations of Severe SARS-CoV-2 Infection: Potential Mechanisms and Implications of Individualized Mechanical Ventilation Settings date = 2020-08-12 pages = extension = .txt mime = text/plain words = 7486 sentences = 369 flesch = 33 summary = Within this Abbreviations: ACE2, angiotensin-converting enzyme-2; ANE, acute necrotizing encephalopathy; ARDS, acute respiratory distress syndrome; BALF, bronchoalveolar lavage fluid; BBB, blood brain-barrier; CA, Ammon's horn; CD, cluster of differentiation; CI, confidence interval; CNS, central nervous system; CoV, coronavirus; COVID-19, coronavirus disease 2019; CT, computed tomography; CXCR, chemokine receptor; DIC, disseminated intravascular coagulation; DO 2 , oxygen delivery; DPP4, dipeptidyl dipeptidase-4; ECMO, extracorporeal membrane oxygenation; FiO 2 fraction of inspired oxygen; FOX, forkhead box; HLH, hemophagocytic lymphohistiocytosis; ICAM, intracellular adhesion molecule; ICH, intracerebral hemorrhage; ICP, intracranial pressure; IFN, interferon; MERS, Middle East respiratory syndrome; MHV, mouse hepatitis virus; MRI, magnetic resonance images; nCoV, novel coronavirus; OR, odds ratio; PaCO 2 , partial pressure of carbon dioxide; PaO 2 partial pressure of oxygen; PbtO 2 brain tissue oxygenation tension; PCR, polymerase chain reaction; PEEP, positive end-expiratory pressure; PRES posterior reversible encephalopathy syndrome; RM, recruitment maneuvers; RNA, ribonucleic acid; SARS, severe acute respiratory syndrome; TLRs, toll-like receptor; TMPRSS2 transmembrane serine protease 2; TNF, tumor necrosis factor; WHO, World Health Organization. cache = ./cache/cord-296219-zzg9hds0.txt txt = ./txt/cord-296219-zzg9hds0.txt === reduce.pl bib === id = cord-295603-mk9oartb author = Yu, Xiaoqi title = Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness date = 2020-07-05 pages = extension = .txt mime = text/plain words = 1991 sentences = 97 flesch = 49 summary = However, it is unclear whether there has been cryptic transmission before these early officially confirmed cases, we therefore retrospectively screened for the SARS-CoV-2 RNA in 1271 nasopharyngeal swab samples, as well as the prevalence of IgM, IgG, and total antibodies against SARS-CoV-2 in 357 matched serum samples collected from hospitalized patients with influenza-like illness between 1 December 2018 and 31 March 2020 in Shanghai Ruijin Hospital. Additionally, among 6662 patients with influenza-like illness from 1 December 2017 to 31 March 2020, the overall number of patients positive for influenza and other respiratory viruses during the COVID-19 period decreased significantly when compared with that in the same period of the last two years, reflecting that public health interventions can effectively control the spread of common respiratory viruses. The nasopharyngeal swab samples for this study were collected from 1271 hospitalized patients with influenza-like illness from 1 December 2018 to 31 March 2020 in Ruijin Hospital (Shanghai, China). cache = ./cache/cord-295603-mk9oartb.txt txt = ./txt/cord-295603-mk9oartb.txt === reduce.pl bib === id = cord-296043-jc74soom author = Butterfield, T. R. title = Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica date = 2020-09-29 pages = extension = .txt mime = text/plain words = 1650 sentences = 121 flesch = 57 summary = Serum samples collected [≥]14 days after onset of symptoms, or [≥]14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. For all assays examined, SARS-CoV-2 real-36 time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive 37 were significantly different for samples testing antibody positive versus negative. CoV-2 antibody assays: Roche Elecsys ® Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 53 preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. When moderate, severe and 109 critical disease was grouped, for each assay there was a significant association between this 110 group and testing antibody positive: Elecsys ® Anti-SARS-CoV-2 (χ 2 =19.03, p=0.001), Architect 111 SARS-CoV-2 IgG (χ 2 =15.72, p=0.003), Euroimmun SARS-CoV-2 IgA (χ 2 =21.11, p=0.007), 112 All rights reserved. cache = ./cache/cord-296043-jc74soom.txt txt = ./txt/cord-296043-jc74soom.txt === reduce.pl bib === id = cord-296259-4kdblf4z author = Oudit, Gavin Y title = Plasma angiotensin-converting enzyme 2: novel biomarker in heart failure with implications for COVID-19 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1811 sentences = 102 flesch = 44 summary = This editorial refers to 'Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors' † , by I.E. Sama et al., on page 1810. Angiotensin-converting enzyme 2 (ACE2) has emerged as the negative regulator of the renin-angiotensin system (RAS) and was more recently identified as the SARS-CoV-2 receptor responsible for the current COVID-19 pandemic. [3] [4] [5] Direct clinical evidence came from SARS and the current COVID-19 pandemic, where there is down-regulation of tissue ACE2 through endocytosis and proteolytic processing which leads to a corresponding increase in plasma angiotensin II (Ang II) levels as seen in COVID-19 patients (linearly correlated with SARS-CoV-2 viral load), thus providing a direct link between the tissue and systemic RAS. obtained in heart failure patients in the pre-COVID-19 period offer supporting evidence to continue ACE inhibitors or ARBs in patients at risk for SARS-CoV-2 infection. cache = ./cache/cord-296259-4kdblf4z.txt txt = ./txt/cord-296259-4kdblf4z.txt === reduce.pl bib === id = cord-296306-xcomjvaa author = Rivett, Lucy title = Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date = 2020-05-11 pages = extension = .txt mime = text/plain words = 6500 sentences = 350 flesch = 48 summary = Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Table 3 outlines the total number of SARS-CoV-2 tests performed in each screening group (HCW asymptomatic, HCW symptomatic, and HCW symptomatic household contact) categorised according to the ward with the highest anticipated risk of exposure to high; 'amber', medium; 'green', low; . Three subgroups of SARS-CoV-2 positive asymptomatic HCW Each individual in the HCW asymptomatic screening group was contacted by telephone to establish a clinical history, and COVID-19 probability criteria ( Table 1) were retrospectively applied to categorise any symptoms in the month prior to testing ( Figure 2 ). 12/30 (40%) individuals from the HCW asymptomatic screening group reported symptoms > 7 days prior to testing, and the majority experiencing symptoms consistent with a high probability of COVID-19 had appropriately self-isolated during that period. cache = ./cache/cord-296306-xcomjvaa.txt txt = ./txt/cord-296306-xcomjvaa.txt === reduce.pl bib === id = cord-295830-1sbnewog author = Kim, Sung-Jae title = A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2371 sentences = 133 flesch = 50 summary = Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this study. The region containing this mutation point was confirmed as a B-cell epitope located in the S1 domain, and SARS-CoV-2b strains exhibited severe reduced antigenic indexes compared to SARS-CoV-2a in this area. Generally, several types of coronavirus are divided into subtypes depending on amino acid mutations in S gene sequences, and molecular analysis based on the S gene can provide insights into antigenicity, immunogenicity, or evolutionary trends [2, 4, 10, 12, 13] . Vaccines 2020, 8, 220 3 of 8 change alters the conformation of these immunogenic determinants; consequently, this region is expected to no longer act as a B-cell epitope in SARS-CoV-2b. The results of the antigenic index analysis showed severely reduced indexes of amino acids 615-617 in the SARS-CoV-2b strains compared to SARS-CoV-2a; it is predicted that the change of D614G affects the antigenicity of this region ( Figure 1F ). cache = ./cache/cord-295830-1sbnewog.txt txt = ./txt/cord-295830-1sbnewog.txt === reduce.pl bib === id = cord-296319-fwn97wds author = Juno, J. A. title = Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5331 sentences = 383 flesch = 59 summary = In 139 summary, antibody responses against both S and the RBD are consistently elicited in 140 SARS-CoV-2 infected individuals, the endpoints titres of which correlate significantly 141 with neutralising activity (r=0.55 and r=0.61 respectively) and ACE2 binding 142 inhibition (r=0.72 and r=0.72 respectively) in the plasma ( Figure S2) . 143 144 B cell responses to S antigens following SARS-CoV-2 infection 145 We next examined the frequency and specificity of class-switched B cells in 146 convalescent subjects using SARS-CoV-2 spike or RBD proteins as flow cytometric 147 probes. Clear antigen-specific populations of CD19 + IgD -B cells (gating in Figure S3 ) 148 binding spike, spike and RBD or RBD alone could be resolved in our cohort of 149 recovered from SARS-CoV-2 subjects, with minimal background staining in 150 uninfected controls (Figure 2A ; Figure S4 ). cache = ./cache/cord-296319-fwn97wds.txt txt = ./txt/cord-296319-fwn97wds.txt === reduce.pl bib === id = cord-296227-dm1wkpnv author = Liao, L. title = Can N95 respirators be reused after disinfection? And for how many times? date = 2020-04-07 pages = extension = .txt mime = text/plain words = 5343 sentences = 272 flesch = 56 summary = We found that heating (<100 {degrees}C) under various humidities (up to 100% RH at 75 {degrees}C) and ultraviolet (UV) irradiation were the most promising candidates for mask reuse in the modern hospital infrastructure (up to 20 cycles), when tested on a fabric with particle filtration efficiency [≥]95%. For dangerous airborne particulates, including viral aerosols during the current COVID-19 pandemic, the United States Centers for Disease Control and Prevention (CDC) recommends the usage of N95 filtering facepiece respirators (FFR) as personal protective equipment for healthcare professionals [18] [19] [20] . We applied these treatments (see methods for details) to a meltblown fabric (20 g/m 2 ) that has an initial efficiency of ≥95%, which may be integrated into N95 FFRs. We evaluated the filtration efficiency and pressure drop of these treated fabrics via industry standard equipment, Automated Filter Tester 8130A (TSI), with a flow rate of 32 L/min. cache = ./cache/cord-296227-dm1wkpnv.txt txt = ./txt/cord-296227-dm1wkpnv.txt === reduce.pl bib === id = cord-296356-qkvafy69 author = Garman, Elspeth title = SARS Proteomics Reveals Viral Secrets date = 2005-11-30 pages = extension = .txt mime = text/plain words = 1306 sentences = 74 flesch = 51 summary = The structure of the mutagenic base pair in the confines of a closed polymerase complex exposes some of those strategies. (2005) In a worldwide cooperative research effort involving a multidisciplinary approach, structural and functional characterization of the SARS virus and its host interactions has been swiftly pursued. By sequence alignment and structural comparison with all known H2A domains, as well as examination of functional data, the authors conjecture that proteins from this superfamily form an emerging group of nucleotide phosphatases, all with similar functionality. This has two pivotal consequences for understanding the biology of the virus: A systematic approach is essential, and, even more importantly, a deeper structural and functional knowledge of the many complexes that the SARS CoV proteins form with one another and with proteins of the host organisms will be required-research that is still in its infancy. cache = ./cache/cord-296356-qkvafy69.txt txt = ./txt/cord-296356-qkvafy69.txt === reduce.pl bib === id = cord-296362-9vi8xwu7 author = Wang, Jian-Min title = Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function date = 2008-09-12 pages = extension = .txt mime = text/plain words = 3490 sentences = 199 flesch = 57 summary = title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. For in-depth study of functions of different viral proteins and regulatory sequence elements by reverse genetics, full-length infectious cDNA clones have been established using various techniques including bacterial artificial chromosome (BAC) vector [23] [24] [25] and SARS-CoV replicon cell lines [26] , which can also be used for antiviral drug screening. Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis cache = ./cache/cord-296362-9vi8xwu7.txt txt = ./txt/cord-296362-9vi8xwu7.txt === reduce.pl bib === id = cord-296268-kb7fgfaq author = Mendonça, Luiza title = SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date = 2020-11-05 pages = extension = .txt mime = text/plain words = 2647 sentences = 161 flesch = 57 summary = Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Understanding the genome 27 replication, assembly and egress of SARS-CoV-2, a multistage process that involves different 28 cellular compartments and the activity of many viral and cellular proteins, is critically Krios to identify each individual infected cell (39.2 % for MOI of 0.1 and 45.4% for MOI 124 0.5) where cryoET tilt series were collected at the cell periphery. The grids were then 125 transferred to a FIB/SEM dualbeam instrument and the same infected cells were subjected to 126 either serial cryoFIB/SEM volume imaging (Zhu et al., 2021) or cryoFIB milling of cellular 127 lamellae where additional cryoET tilt series were collected (Sutton et al., 2020) . cache = ./cache/cord-296268-kb7fgfaq.txt txt = ./txt/cord-296268-kb7fgfaq.txt === reduce.pl bib === id = cord-296426-upwsdgso author = Virmani, Sarthak title = Identifying a Kidney Transplant Recipient COVID Phenotype to Aid Test Utilization in the Setting of Limited Testing Availability - Does One Exist? date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4402 sentences = 222 flesch = 49 summary = While it is true that other non-novel viruses tend to cause more severe disease in immunocompromised patients [1] , no conclusive data is available to suggest an increased susceptibility or severity of SARS-Cov-2 infection in immunosuppressed kidney transplant recipients (KTRs). This was a single center, retrospective chart review performed as a QAPI project to assess similarities in kidney transplant recipients who tested positive for SARS-CoV-2 as compared to those who tested negative, and guide testing recommendations in the setting of limited testing availability during the COVID-19 pandemic. We did not observe any significant association between patient gender, level of education, or history of diabetes on the SARS-CoV-2 test result. Our cohort of KTRs showed no significant difference in ALC between patients who tested positive and negative for SARS-CoV-2 (Table 3 ). Though statistically significant in our small patient cohort, larger studies of KTRs with COVID-19 disease and a history of BKV will be required to confirm and better understand this association. cache = ./cache/cord-296426-upwsdgso.txt txt = ./txt/cord-296426-upwsdgso.txt === reduce.pl bib === id = cord-296232-6zj99nuw author = Talukdar, Jayanta title = Potential of natural astaxanthin in alleviating the risk of cytokine storm in COVID-19 date = 2020-10-16 pages = extension = .txt mime = text/plain words = 7622 sentences = 435 flesch = 41 summary = We present reports where ASX is shown to prevent against oxidative damage and attenuate exacerbation of the inflammatory responses by regulating signaling pathways like NF-ĸB, NLRP3 and JAK/STAT. Studies including human trials have shown that ASX effectively regulates immunity and disease etiology, suggesting its wide array of potential therapeutic and nutritional support in prevention and treatment of various pathogenic diseases and metabolic disorders, all of which have elements of oxidative stress and/or inflammation in the pathogenesis [8, 10, 17] . [9] found that the administration of ASX provides both preventive and curative anti-inflammatory effects against LPS-induced inflammation in the human gingival keratinocyte line NDUSD-1 by suppressing the production of IL-6 via inhibiting activation of the NF-ĸB signaling pathway. Evidence from these studies suggest that ASX is a potent antioxidant and a natural anti-inflammatory compound having efficient immunomodulatory action that exerts potential therapeutic benefits against oxidative and inflammation induced tissue damage. cache = ./cache/cord-296232-6zj99nuw.txt txt = ./txt/cord-296232-6zj99nuw.txt === reduce.pl bib === id = cord-296331-i4hyzqcv author = Adapa, Sreedhar title = COVID-19 Pandemic Causing Acute Kidney Injury and Impact on Patients With Chronic Kidney Disease and Renal Transplantation date = 2020-06-04 pages = extension = .txt mime = text/plain words = 5086 sentences = 289 flesch = 49 summary = COVID-19 infection causes acute kidney injury (AKI) and is an independent risk factor for mortality. The impact of COVID-19 infection on chronic kidney disease (CKD) and renal transplant patients is also discussed in the manuscript. Acute kidney injury (AKI) was seen in 5-15% of the cases infected with SARS-CoV and MERS-CoV, and had a higher mortality rate of 60-90% as per the literature [12] . We summarized the finding from multiple studies including patient characteristics, co-morbidities, incidence of AKI in general as well as ICU/severely ill patients, number of patients requiring continuous renal replacement therapy (CRRT), extracorporeal membrane oxygenation (ECMO) and mortality in Table 2 [9-11, 13, 19, 22-24, 26-32] . Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-296331-i4hyzqcv.txt txt = ./txt/cord-296331-i4hyzqcv.txt === reduce.pl bib === id = cord-295794-glcg36si author = Seghers, Victor J. title = After the initial COVID-19 surge: a phased radiology departmental re-opening plan date = 2020-08-22 pages = extension = .txt mime = text/plain words = 4747 sentences = 201 flesch = 37 summary = Social distancing, stay home/work safe orders, protective measures for vulnerable individuals (e.g., immunocompromised patients), masking protocols, visitation policies, testing and many more measures resulted in an accelerated but necessary ramping down of elective hospital services [4] [5] [6] [7] [8] [9] . While the radiologist-in-chief also participates in daily meetings with other clinical service chiefs and executive leadership for the hospital, the radiologist-in-chief is an integral member of the systemwide "Phased Recovery and Redesign Team" as well, which includes team captains for infection control, surgery, anesthesia, emergency and urgent care centers, radiology, pathology, ambulatory medicine, specialty care centers, e-health, revenue cycle and billing, and marketing and public relations. This can include patient-directed online scheduling and expanded access to imaging, offering same-day service with hours and locations adapted to the patient and family lifestyle; improved use of virtual dashboards to more easily track various metrics including MR efficiency, sedation utilization, and length of patient stay in the imaging department; and investment in Table 2 Radiology: the opportunity to re-design operations post COVID-19 cache = ./cache/cord-295794-glcg36si.txt txt = ./txt/cord-295794-glcg36si.txt === reduce.pl bib === id = cord-296339-23yi8so0 author = Mok, Wendy title = Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens date = 2007-09-26 pages = extension = .txt mime = text/plain words = 1395 sentences = 75 flesch = 43 summary = We used computational methods to examine the extent to which this practice can result in inaccurate 'retrodiction.' Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance. Herein, we show that adopting molecular clock assumptions can yield inaccurate estimated origin times, considering as an example data from the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) infection in humans. Recognizing that this change in substitution rate would violate a molecular clock assumption and could cause pairwise genetic distances to yield inaccurate evolutionary divergence estimates (especially if genetic distance calculations were performed with respect to a reference sequence representing an hypothetical common ancestor), we quantifi ed the extent to which failing to account for dynamic SARS-CoV evolution might affect estimating an origin time. cache = ./cache/cord-296339-23yi8so0.txt txt = ./txt/cord-296339-23yi8so0.txt === reduce.pl bib === id = cord-296375-gf0mgz5x author = Zhang, Xi title = Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3275 sentences = 164 flesch = 53 summary = CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. Therefore, in this study, by collecting the daily numbers of newly confirmed COVID-19 and SARS cases during the two epidemics, we aimed to determine the spatial behavior and temporal features of the COVID-19 spread in mainland China and compared them with respective features from the SARS epidemic using spatiotemporal analysis. Incident cases infected by COVID-19 were extracted from the daily briefings on novel coronavirus cases from January 20 to March 4, 2020, provided on the official website of the National Health Commission of the People's Republic of China [5] . Incident cases of SARS were extracted from daily situation reports for mainland China from April 21 to August 3, 2003 , which were posted by China.org.cn (in Chinese) and were also provided by the National Health Commission. cache = ./cache/cord-296375-gf0mgz5x.txt txt = ./txt/cord-296375-gf0mgz5x.txt === reduce.pl bib === id = cord-296483-x95lwwnm author = Kranke, Peter title = Geburtshilfliche Anästhesie während der SARS-CoV-2-Pandemie: Übersicht der Handlungsempfehlungen date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1995 sentences = 241 flesch = 43 summary = Diese Annahmen stützten sich möglicherweise auf den Umstand, dass die Morbidität Schwangerer bei saisonaler Influenza höher ist als in einem Vergleichskollektiv [4 -6] und im beschriebenen Kollektiv zu einer gegenüber einem Vergleichskollektiv überproportionalen Frühgeburtlichkeit von 24-25 % führte [7] . In Bezug auf die vertikale Übertragung (Übertragung von der Mutter auf das Kind prä-oder intrapartal) zeigen nahezu alle publizierten Fallberichte aus China keine Hinweise für eine Übertragung auf den Fetus [9, 15 -17] . Einschränkend sollte berücksichtigt werden, dass es sich bislang nur um einen einzigen Fallbericht handelt und es im Rahmen der systemischen Inflammation möglicherweise zu einem erhöhten Transfer von Antikörpern kommen könnte. Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 (23.03.2020). cache = ./cache/cord-296483-x95lwwnm.txt txt = ./txt/cord-296483-x95lwwnm.txt === reduce.pl bib === id = cord-296556-fr8x8j3i author = Chaccour, Carlos title = Ivermectin and COVID-19: Keeping Rigor in Times of Urgency date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1400 sentences = 91 flesch = 47 summary = 10 recently reported that ivermectin is a potent inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication in vitro. 13 However, even with this dose, which is 10-fold greater than those approved by the US Food and Drug Administration, the C max values reported were ∼250 ng/mL, 13 one order of magnitude lower than effective in vitro concentrations against SARS-CoV-2. Very recently, preliminary findings on a potential effect of hydroxychloroquine combined with azithromycin against SARS-CoV-2 were widely publicized, 15 leading to a surge in demand and self-medication, which resulted in serious harm in some cases and a stock shortage that jeopardized drug availability for other critical conditions for which hydroxychloroquine or chloroquine is the standard of care, that is, vivax malaria, rheumatoid arthritis, and systemic lupus erythematosus. 20, 21 Second, boosted antiretrovirals such as lopinavir/ritonavir and darunavir/cobicistat, which have been widely used against SARS-CoV-2 based on limited evidence, and a number of other drugs, are potent inhibitors of cytochrome P 450 3A4, the main metabolic pathway for ivermectin. cache = ./cache/cord-296556-fr8x8j3i.txt txt = ./txt/cord-296556-fr8x8j3i.txt === reduce.pl bib === id = cord-296388-ayfdsn07 author = Maziarz, Mariusz title = Agent‐based modelling for SARS‐CoV‐2 epidemic prediction and intervention assessment: A methodological appraisal date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4560 sentences = 240 flesch = 41 summary = CONCLUSIONS: Given this, we claim that the best epidemiological ABMs are models of actual mechanisms and deliver both mechanistic and difference‐making evidence. While the 2009 swine flu pandemic was the motivation for constructing AceMod, the model was not intended to accurately represent the outbreak of the H1N1 strain, but rather as a generalized framework for studying how an infectious disease spreads through the social interactions of Australians. In cases like the current pandemic, effective interventions may best be aimed at the societal level and therefore mechanistic models that integrate social factors, human behaviour and biological aspects (something that the ABM discussed here attempts to do) are arguably best suited for providing understanding and suggesting policy decisions. 10 Our claim that AceMod calibrated for SARS-CoV-2 bears similarity to the actual mechanism of the epidemic depends on the accuracy of the empirical results used as an input for this model. Agent-based modelling for SARS-CoV-2 epidemic prediction and intervention assessment: A methodological appraisal cache = ./cache/cord-296388-ayfdsn07.txt txt = ./txt/cord-296388-ayfdsn07.txt === reduce.pl bib === id = cord-296250-7ln7p715 author = Wang, Sheng-Fan title = The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 4962 sentences = 302 flesch = 43 summary = Increasing evidence showed potential therapeutic agents directly acting against SARS-CoV-2 virus, such as interferon, RNA-dependent RNA polymerase inhibitors, protease inhibitors, viral entry blockers, neuraminidase inhibitor, vaccine, antibody agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitor. Increasing evidence reveals potential therapeutic agents acting directly against SARS-CoV-2, such as interferon (IFN), RdRp inhibitors, protease inhibitors, coronaviral protease inhibitor, viral entry blocker, neuraminidase inhibitor, vaccine, antibody, agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitors. The novel specific anti-SARS-CoV-2 agents might comprise inhibitors interfering with the viral replication cycle, antibody targeting the host receptor and virus S protein, and inhibitors of host cellular proteases involved in the virus endocytosis pathway. 33, 34 Moreover, evidence showed that diarylheptanoids, the natural products derived from Japanese alder (Alnus japonica), can inhibit the papain-like protease and restore the host innate immunity response against SARS-CoV through maintaining the function of IFNs. 31 Therefore, specific coronaviral proteases might be good candidate targets for developing new drugs to fight COVID-19. cache = ./cache/cord-296250-7ln7p715.txt txt = ./txt/cord-296250-7ln7p715.txt === reduce.pl bib === id = cord-296494-6kn4mr04 author = Saban-Ruiz, J. title = COVID-19: A Personalized Cardiometabolic Approach for Reducing Complications and Costs. The Role of Aging Beyond Topics date = 2020-05-12 pages = extension = .txt mime = text/plain words = 6444 sentences = 326 flesch = 50 summary = Bearing this in mind, it is quite likely, that if we have fewer complications, particularly severe ones (cardiac arrest, ventricular tachyarrhythmia, acute heart failure, acute coronary syndrome, haemorrhagic or massive ischaemic stroke), this integrated approach could cut down the elevated mortality in the highest risk group (cancer, COPD and oldest subjects with comorbidities), usually preceded by a multi-organ failure. In aged COVID-19 patients or with history of coronary artery disease (CAD) an acute coronary syndrome (ACS) can also be seen for plaque vulnerability in the presence of a pro-inflammatory state with cytokine release (71) but from the experience in animals, could it be plausible that any of them could be due to arteritis? The third aspect would be the combination of T2DM and Heart failure (HF) (the most frequent cardiac complication in any of the phases of the disease), which is present in a high percentage of patients, especially those at higher risk. cache = ./cache/cord-296494-6kn4mr04.txt txt = ./txt/cord-296494-6kn4mr04.txt === reduce.pl bib === id = cord-296378-ki93iltt author = Smith, Joan C. title = Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract date = 2020-05-16 pages = extension = .txt mime = text/plain words = 10042 sentences = 595 flesch = 54 summary = Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination. In total, our results demonstrate that exposure to cigarette smoke increases the expression of the coronavirus receptor ACE2 in rodent and human respiratory tissue, and this upregulation is potentially reversible. To investigate a potential link between inflammation and the expression of the host factors required for coronavirus infections, we first examined the levels of ACE2 in published datasets of respiratory epithelial cells challenged with different viruses. To further verify these results, we re-analyzed a published gene expression dataset of airway epithelial cells exposed to IFN-β, and we found a similar increase in ACE2 levels following interferon treatment ( Figure 5H ) (Rusinova et al., 2013; Shapira et al., 2009) . cache = ./cache/cord-296378-ki93iltt.txt txt = ./txt/cord-296378-ki93iltt.txt === reduce.pl bib === id = cord-296237-i9cti2ok author = Díez, José-María title = Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3741 sentences = 220 flesch = 51 summary = Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. Recently, cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2, and MERS-CoV has been reported with currently available intravenous immunoglobulins (IVIG) such as Gamunex-C and Flebogamma DIF 19 . In this study, the neutralization capacity of the IVIG products Gamunex-C and Flebogamma DIF against these epidemic human coronaviruses -SARS-CoV, SARS-CoV-2, and MERS-CoV-was evaluated. Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2, and MERS-CoV by: i) ELISA techniques; and ii) well-stablished neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT50 titers ranging from 4.5 to >5 (Figure 2 ). cache = ./cache/cord-296237-i9cti2ok.txt txt = ./txt/cord-296237-i9cti2ok.txt === reduce.pl bib === id = cord-296271-85io9yvy author = Chong, Woon H. title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) date = 2020-07-28 pages = extension = .txt mime = text/plain words = 784 sentences = 54 flesch = 54 summary = title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) 1 A study of 701 SARS-CoV-2 patients by Cheng and colleagues demonstrated that in-hospital mortality increased by almost three-fold in those who had AKI. 2 We report a patient with SARS-CoV-2 who developed AKI likely secondary to rhabdomyolysis and discuss the possible association between cytokine storm as the etiology. A case series of SARS-CoV-related rhabdomyolysis showed the development of AKI with peak CK levels ranging from 7,500 to 340,000 IU/L. 3 Jin and colleagues were the first to describe a 60-year-old man who was admitted with RT-PCR confirmed SARS-CoV-2 pneumonia and developed rhabdomyolysis on day 9 th of hospital admission. A retrospective study of 171 SARS-CoV-2 patients showed that CK of more than 185 IU/L, AKI, and requirement of RRT was associated with an increase in mortality. cache = ./cache/cord-296271-85io9yvy.txt txt = ./txt/cord-296271-85io9yvy.txt === reduce.pl bib === id = cord-296619-uhhndp0a author = Kondo, Yuki title = Coinfection with SARS-CoV-2 and influenza A virus date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1689 sentences = 118 flesch = 53 summary = We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We report a case of coinfection with SARS-CoV-2 and influenza A virus in a patient with pneumonia in Japan. The patient with both COVID-19 and influenza virus infection presented similar clinical characteristics with COVID-19 only. Initial considerations for this patient who presented acutely with fever and cough include infection with a common virus (rhinoviruses, non-SARS-CoV-2 coronaviruses and influenza virus) and communityacquired pneumonia. 3 The clinical characteristics of patients with both COVID-19 and influenza virus infection were similar to those of COVID-19 cases. ► There was no significant difference in rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with and without other pathogens. The clinical characteristics of pneumonia patients coinfected with 2019 novel coronavirus and influenza virus in Wuhan cache = ./cache/cord-296619-uhhndp0a.txt txt = ./txt/cord-296619-uhhndp0a.txt === reduce.pl bib === id = cord-296551-efqt3tw2 author = Fukushi, Shuetsu title = Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry Mediated by SARS Coronavirus Spike Proteins date = 2007-11-28 pages = extension = .txt mime = text/plain words = 1670 sentences = 100 flesch = 56 summary = Severe acute respiratory syndrome (SARS) coronavirus (CoV) contains a spike (S) protein that binds to a receptor molecule (angiotensin-converting enzyme 2; ACE2), induces membrane fusion, and serves as a neutralizing epitope. To study the functions of the S protein, we describe here the generation of SARS-CoV S protein-bearing vesicular stomatitis virus (VSV) pseudotype using a VSV∆G∗/GFP system in which the G gene is replaced by the green fluorescent protein (GFP) gene (VSV-SARS-CoV-St19/GFP). Thus, VSV pseudotyped with SARS-CoV S protein is useful for developing a rapid detection system for neutralizing antibody specific for SARS-CoV infection as well as studying the S-mediated cell entry of SARS-CoV. In addition to a significant advantage of the VSV-SARS-St19/GFP for safe and rapid analyses of infection, the VSV⌬G*/SEAP system, in which the G gene is replaced with the secreted alkaline phosphatase (SEAP) gene, may be superior to high-throughput quantitative analysis of S-mediated cell entry. Mix serially diluted VSV-SARS-St19/GFP with DMEM-5%FCS and inoculate the mixture into Vero E6 cells seeded in 96-well culture plates. cache = ./cache/cord-296551-efqt3tw2.txt txt = ./txt/cord-296551-efqt3tw2.txt === reduce.pl bib === id = cord-296588-q2716lda author = Hanson, Kimberly E title = Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 10179 sentences = 681 flesch = 47 summary = OBJECTIVE: The IDSA's goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. cache = ./cache/cord-296588-q2716lda.txt txt = ./txt/cord-296588-q2716lda.txt === reduce.pl bib === id = cord-296392-2u9mz6d3 author = Sarıgül, Figen title = Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3891 sentences = 209 flesch = 51 summary = title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic This value being higher than 0.73 coefficient obtained through comparison of RdRps of the two kits only, showed that inclusion of a secondary biomarker by Diagnovital improved the correlation of different kits. In this study, we investigated the compatibility between the two different SARS-CoV-2 PCR kits produced in Turkey during the COVID-19 pandemic. Nevertheless, the strong correlation of the two kit results suggested that two different RNA targeting gene assays were appropriate as suggested by WHO in the diagnosis of COVID-19 disease [20] . showed that similar results were found; the PCR kit with two different genes of the SARS-CoV-2 had a higher yield than the other two kits performing one gene analysis [21] . cache = ./cache/cord-296392-2u9mz6d3.txt txt = ./txt/cord-296392-2u9mz6d3.txt === reduce.pl bib === id = cord-296492-knofua00 author = Qiu, L. title = Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province date = 2020-07-07 pages = extension = .txt mime = text/plain words = 2889 sentences = 201 flesch = 54 summary = Lung transplantation recipients (LTx) were susceptible to severe acute respiratory syndrome-corona virus-2 (SARS-Cov-2) and suffered a higher mortality risk than healthy subjects. In this study, the clinical characteristics, laboratory testing and epidemiology survey results of 10 LTx recipients undergoing allograft lung transplantation surgeries in the First Affiliated Hospital of Zhengzhou University during the COVID-19 pandemic were collected. In this work, we collected characteristics of these LTx recipients and designed an epidemiology questionnaire to obtain the information of SARS-CoV-2 infection condition and after-discharge preventive measures of LTx recipients who underwent surgeries in the hospital accepting COVID-19 patients during the COVID-19 pandemic. Consistent with previous reports [12, 13] , the key reasons for the zero SARS-CoV-2 infective rate of LTx recipients in our study may be due to the good performance of hand hygiene, wearing masks and indoor disinfection, and even isolation from family members. cache = ./cache/cord-296492-knofua00.txt txt = ./txt/cord-296492-knofua00.txt === reduce.pl bib === id = cord-296517-414grqif author = Wong, Gary title = MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease date = 2015-10-14 pages = extension = .txt mime = text/plain words = 2880 sentences = 129 flesch = 50 summary = In September 2012, Middle East Respiratory Syndrome coronavirus (MERS-CoV) emerged as a novel virus that can result in severe respiratory disease with renal failure, with a case fatality rate of up to 38%. Notably, between May and July 2015, an outbreak of MERS-CoV centered in South Korea killed 36 people out of 186 confirmed cases (Promedmail.org, 2015) , with thousands quarantined as health authorities attempted to control virus spread. The 2015 MERS-CoV outbreak in South Korea began from an imported case, a 68-year-old male with a recent travel history to several Middle Eastern countries, including Bahrain, the United Arab Emirates, Saudi Arabia, and Qatar. Thus, the MERS-CoV outbreak in South Korea was driven primarily by three infected individuals, and approximately 75% of cases can be traced back to three super-spreaders who have each infected a disproportionately high number of contacts ( Figure 1A ). cache = ./cache/cord-296517-414grqif.txt txt = ./txt/cord-296517-414grqif.txt === reduce.pl bib === id = cord-296579-oa67njov author = d’Ettorre, Gabriella title = Analysis of type I IFN response and T cell activation in severe COVID-19/HIV-1 coinfection: A case report date = 2020-09-04 pages = extension = .txt mime = text/plain words = 2745 sentences = 155 flesch = 51 summary = Hence, this study aims to compare type I IFN response and T cell activation levels between a SARS-CoV-2/HIV-1-coinfected female patient and age-matched HIV-1-positive or uninfected women. LESSONS: These results indicate that SARS-CoV-2 infection in HIV-1-positive female patient was associated with increased levels of IFNα/β-mRNAs and T cell activation compared to healthy individuals. [1] Despite high number of people living with human immunodeficiency virus (HIV)-1 globally (about 37 million) and higher severity impact for certain viral infections in this category, [2] severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)/HIV-1 coinfection has been described in few cases. This study reports a severe case of SARS-CoV-2 in a black female patient co-infected by HIV-1 under protease inhibitors (PI) regimen, who was treated with hydroxychloroquine. Because of the key role of chronic immune activation and persistent IFN-I response in driving HIV-1 disease, [8, 9] we evaluated IFNa and IFNb gene expression and T cell activation levels in patient with SARS-CoV-2/HIV-1 coinfection. cache = ./cache/cord-296579-oa67njov.txt txt = ./txt/cord-296579-oa67njov.txt === reduce.pl bib === id = cord-296605-p67twx7a author = LAU, Arthur Chun-Wing title = Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date = 2004-03-10 pages = extension = .txt mime = text/plain words = 4846 sentences = 247 flesch = 38 summary = title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS) cache = ./cache/cord-296605-p67twx7a.txt txt = ./txt/cord-296605-p67twx7a.txt === reduce.pl bib === id = cord-296390-jv86w4j9 author = Shao, Chen title = Evolution of SARS-Co-2 RNA test results in a fatal Covid-19 patient: a case report date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1436 sentences = 99 flesch = 53 summary = On day 9 after admission, chest CT scan showed diffuse ground-glass shadows in patient's bilateral lungs. How SARS-CoV-2-infected patients progress to critical disease is a key issue in clinical practice. He was confirmed as Covid-19 positive in February 2 nd by qPCR analysis for SARS-CoV-2RNA of samples collected by nasopharyngeal swabs. He progressed to septic shock, severe metabolic acidosis and respiratory acidosis occurred successively and then, the patient died on February 14 th . It is worthy to note that the patient received SARS-CoV-2 RNA tests by nasopharyngeal swabs six times ( Table 1 ). Since February 6 th , four times SARS-CoV-2 RNA testing by nasopharyngeal swabs were negative (Table 1) . Given the missed diagnosis of the potential bacterial infection, antibiotics treatment was started too later in this patient, which might have resulted in multi-organ failure due to a septic shock. Clinical manifestation and lung histological alteration showed that this patient suffered from SARS-CoV-2 viral pneumonia. cache = ./cache/cord-296390-jv86w4j9.txt txt = ./txt/cord-296390-jv86w4j9.txt === reduce.pl bib === id = cord-296657-mymndjvd author = Higuchi, Yusuke title = High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date = 2020-09-16 pages = extension = .txt mime = text/plain words = 3509 sentences = 195 flesch = 51 summary = The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. Three cycles of screening resulted in an identification of mutant ACE2 clones with more than 100-fold higher binding affinity to the RBD and lower half-maximal inhibitory concentration (IC50) for SARS-CoV-2 pseudotyped lentivirus as well as authentic virus. We engineered ACE2 to bind the RBD of the SARS-CoV-2 spike protein with the combination of surface display of mutagenized library and fluorescence-activated cell sorting (FACS) to perform the evolution in 293T human cells. cache = ./cache/cord-296657-mymndjvd.txt txt = ./txt/cord-296657-mymndjvd.txt === reduce.pl bib === id = cord-296692-t5p09le8 author = Elgin, T.G. title = The changing landscape of SARS-CoV-2: Implications for the maternal-infant dyad date = 2020-09-07 pages = extension = .txt mime = text/plain words = 5325 sentences = 303 flesch = 47 summary = In December of 2019 cases of an unknown viral pneumonia were reported from Wuhan, Hubei, China Although much uncertainty remains, regarding the natural history and demographics of COVID19 , the virus appears to primarily cause infection in adults over 51 with case fatality rates increasing dramatically with age [5] . There are, however, emerging case reports of pregnant mothers who test positive for COVID-19 infection and who remain either completely asymptomatic [23] and or manifest mild symptoms in the subsequent 24 hours following delivery. Although clinical evidence is lacking, the case numbers to date of COVID-19 in pregnancy remain very low [32] and case reports of two neonates who tested positive for SARS-CoV-2 shortly after birth lends some credence to the concern. Vertical transmission of coronavirus disease 19 (COVID-19) from infected pregnant mothers to neonates: A review An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-296692-t5p09le8.txt txt = ./txt/cord-296692-t5p09le8.txt === reduce.pl bib === id = cord-296649-h6oyjz56 author = Scherf-Clavel, Oliver title = Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date = 2020-11-06 pages = extension = .txt mime = text/plain words = 5076 sentences = 263 flesch = 53 summary = In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. The value obtained from our experiments falls in that range and is comparable to the V z obtained in mice from blood concentrations and to plasma V z measured in humans (see Table 4 ). cache = ./cache/cord-296649-h6oyjz56.txt txt = ./txt/cord-296649-h6oyjz56.txt === reduce.pl bib === id = cord-296676-2anl2agl author = Goldberg, Michael F. title = Neuroradiologic manifestations of COVID-19: what the emergency radiologist needs to know date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4158 sentences = 213 flesch = 43 summary = Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global pandemic with a wide spectrum of clinical signs and symptoms. These neurologic manifestations were more common in severely affected patients, tended to occur early in the disease course, and could be the initial, presenting clinical evidence of COVID-19 [4] . Lastly, the authors note that ECMO alone (in the absence of SARS-CoV-2 infection) is a risk factor for intracranial hemorrhage, further limiting the generalizability of this small case series. Regardless, prior studies that evaluated neuroimaging findings of patients infected with other members of the Betacoronavirus genus have also demonstrated significant abnormalities, including intracranial hemorrhage and evidence of acute disseminated encephalomyelitis (ADEM), which could represent sequelae of inflammatory response and/or direct CNS infection [50, 51] . On behalf of the CoCo Neurosciences study group (2020) Retrospective observational study of brain magnetic resonance imaging findings in patients with acute SARS-CoV-2 infection and neurological manifestations cache = ./cache/cord-296676-2anl2agl.txt txt = ./txt/cord-296676-2anl2agl.txt === reduce.pl bib === id = cord-296602-19noki6p author = Law, Helen KW title = Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells date = 2009-06-08 pages = extension = .txt mime = text/plain words = 4427 sentences = 230 flesch = 53 summary = In this study, we focussed on the gene expression of toll-like receptors (TLRs), chemokine receptors (CCRs) and death receptor ligands in SARS-CoV infected DCs. We also compared adult and cord blood (CB) DCs to find a possible explanation for the age-dependent severity of SARS. There was also strong induction of TNF-related apoptosis-inducing ligand (TRAIL), but not Fas ligand gene expression in SARS-CoV infected DCs. Interestingly, the expressions of most genes studied were higher in CB DCs than adult DCs. CONCLUSION: The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. Interestingly, the SARS-CoV infected DCs showed low expression of antiviral cytokines (IFN-α, IFN-β, IFN-γ and IL-12p40), moderate upregulation of proinflammatory cytokines (TNF-α and IL-6) but significant upregulation of inflammatory chemokines (macrophage inflammatory protein (MIP)-1α/CCL3, regulated upon activation, normal T cell expressed and secreted (RANTES)/CCL-5, interferon-inducible protein of 10 kD (IP-10)/CXCL10 and monocyte chemotactic protein (MCP)-1/CCL2. cache = ./cache/cord-296602-19noki6p.txt txt = ./txt/cord-296602-19noki6p.txt === reduce.pl bib === id = cord-296917-yk574m99 author = Kumar, Sathish title = Aerosol‐mediated transmission of SARS‐Cov‐2 or COVID‐19 in the cardiac surgical operating room date = 2020-07-11 pages = extension = .txt mime = text/plain words = 738 sentences = 44 flesch = 40 summary = The coronavirus disease-2019 (COVID-19) virus spreads predominantly through droplet and aerosol routes and blood-borne infection is not considered a major source of transmission. As a result, while contact is necessary for droplet infections and thereby handwashing and gloves are highly effective against contact transmission, viral particles transmitted though aerosol is absorbed via the respiratory mucosa and potentially across the conjunctivae, other measures are required to prevent transmission. However, because of the smaller size, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 as it is popularly known as, can spread across larger areas and has been shown to remain viable in aerosols even at 3 hours. 7 The highest viral load of the virus causing COVID-19 is in sputum and upper airway secretions and endotracheal intubation is the commonest and most relevant aerosol-generating procedure in cardiac surgery. Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review cache = ./cache/cord-296917-yk574m99.txt txt = ./txt/cord-296917-yk574m99.txt === reduce.pl bib === id = cord-296440-18vpg419 author = Beurnier, Antoine title = Characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who require hospitalisation date = 2020-07-30 pages = extension = .txt mime = text/plain words = 3554 sentences = 206 flesch = 49 summary = The objective of this study was to investigate the characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who required hospitalisation during the spring 2020 outbreak in Paris, France. As the world faces the coronavirus disease 2019 (COVID-19) pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, concerns have arisen about a possible increased risk of asthma exacerbations. In Wuhan, authors pointed out a rate of 0.9% [3] , markedly lower than that in the local population; in another study investigating the clinical characteristics and allergy status of 140 patients infected by SARS-CoV-2 in Wuhan, no patient were reported as being asthmatic [3] . All adult patients hospitalized from March 15, 2020 to April 15, 2020 with a diagnosis of SARS-CoV-2 infection and reporting a history of asthma were included. Moreover, obesity, hypertension and diabetes were the most common comorbidities observed in our cohort of hospitalized asthmatics with COVID-19, which is consistent with earlier research in other patient groups [4] [23] . cache = ./cache/cord-296440-18vpg419.txt txt = ./txt/cord-296440-18vpg419.txt === reduce.pl bib === id = cord-296672-i267t23m author = Wang, Shui-Mei title = Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain date = 2008-07-01 pages = extension = .txt mime = text/plain words = 5504 sentences = 300 flesch = 52 summary = We replaced the HIV-1 nucleocapsid (NC) domain with different N-coding sequences to test SARS-CoV nucleocapsid (N) self-interaction capacity, and determined the capabilities of each chimera to direct virus-like particle (VLP) assembly. Each mutant was transiently transfected into 293T cells and subjected to Western immunoblotting to determine its ability to assemble and release VLPs. As shown in Fig. 2b , chimeric proteins with predicted molecular weights corresponding to Pr55 gag containing a SARS-CoV N coding sequence insertion in the NC region were readily detected. The above results suggest that HIV-1 Gag containing a large sequence of approximately 200-400 residues inserted into the NC region is still capable of assembling and releasing VLPs. Since the cultured 293T transfectant supernatant was centrifuged through 20% sucrose cushions for 40 min, we believe the recovered viral proteins in the pelleted medium are virus-associated. cache = ./cache/cord-296672-i267t23m.txt txt = ./txt/cord-296672-i267t23m.txt === reduce.pl bib === id = cord-296977-yzhsdz9c author = Soares, R. R. G. title = Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date = 2020-11-06 pages = extension = .txt mime = text/plain words = 6533 sentences = 391 flesch = 55 summary = ; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 . cache = ./cache/cord-296977-yzhsdz9c.txt txt = ./txt/cord-296977-yzhsdz9c.txt === reduce.pl bib === id = cord-296950-9dldbs6o author = El-Zein, Rayan S title = COVID-19-associated meningoencephalitis treated with intravenous immunoglobulin date = 2020-09-06 pages = extension = .txt mime = text/plain words = 1832 sentences = 122 flesch = 43 summary = Neurologic manifestations in patients infected with SARS-CoV-2 have been reported such as anosmia, ageusia, ataxia, seizures, haemorrhagic necrotising encephalopathy, and Guillain-Barré syndrome. The SARS-CoV-2 CSF PCR was negative; however, a high index of suspicion remained due to the temporal relationship of his current symptoms and the recent COVID-19 pneumonia. Our report describes a case of encephalitis associated with SARS-CoV-2 which showed clinical improvement with IVIg therapy. Moriguchi et al 5 described what appears to be the first case of COVID-19-associated meningoencephalitis presenting with convulsions and confirmed with a positive SARS-CoV-2 CSF PCR; their patient had abnormal MRI findings of the medial temporal lobe and was treated with favipiravir. Paniz-Mondolfi et al 6 reported a case of COVID-19-associated pneumonia in a 74 years old with Parkinson's who succumbed to his illness on day 11; however, SARS-CoV-2 was found in the brain capillary endothelium and neuronal cell bodies on postmortem examination. cache = ./cache/cord-296950-9dldbs6o.txt txt = ./txt/cord-296950-9dldbs6o.txt === reduce.pl bib === id = cord-296986-8fuj072z author = Kumar, Manish title = A chronicle of SARS-CoV-2: Part-I - Epidemiology, diagnosis, prognosis, transmission and treatment date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4465 sentences = 308 flesch = 52 summary = The review explicitly covers the aspects like genome and pedigree of SARS-CoV-2; epidemiology, prognosis, pathogenesis, symptoms and diagnosis of COVID-19 in order to catalog the right information on transmission route, and influence of environmental factors on virus transmissions, for the robust understanding of right strategical steps for proper COVID-19 management. We have explicitly highlighted several useful information and facts like: i) No established relationship between progression of SARS-CoV-2 with temperature, humidity and/or both, ii) The underlying mechanism of SARS-CoV-2 is not fully understood, iii) Respiratory droplet size determines drop and airborne-based transmission, iv) Prognosis of COVID-19 can be done by its effects on various body organs, v) Infection can be stopped by restricting the binding of S protein and AE2, vi) Hydroxychloroquine is believed to be better than chloroquine for COVID-19, vii) Ivermectin with Vero-hSLAM cells is able to reduce infection by ~5000 time within 2 days, and viii) Nafamostat mesylate can inhibit SARS-CoV-2 S protein-initiated membrane fusion. Outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): increased transmission beyond China-fourth update cache = ./cache/cord-296986-8fuj072z.txt txt = ./txt/cord-296986-8fuj072z.txt === reduce.pl bib === id = cord-296762-sc6crkkw author = Ali, Fedaa title = ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date = 2020-08-20 pages = extension = .txt mime = text/plain words = 808 sentences = 59 flesch = 60 summary = title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity Here, we combined ACE2 coding variants analysis in different populations and computational chemistry calculations to probe the effects on SARS-CoV-2/ACE2 interaction. Furthermore, the structure of ACE2 was trimmed by removing residues from P733 to the end of The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-108 2/ACE2 were compared between single mutated and WT protein at pH =7 ( Fig. 2A) . Based on our calculations, G211R mutant is shown to induce the largest increase 112 in the binding energy between SARS-CoV-2 and ACE2, where the binding is more favorable by 113 ~ 7.6 Kcal/mol than the WT. SARS-CoV-2/ACE2 interface in the 123 WT protein and corresponding mutants is showed to be a dominated by van der Waals 124 interactions, which accounts for more than 60% of the interaction energy. cache = ./cache/cord-296762-sc6crkkw.txt txt = ./txt/cord-296762-sc6crkkw.txt === reduce.pl bib === id = cord-296881-2g81sjnl author = Nabil, Ahmed title = Current coronavirus (SARS-CoV-2) epidemiological, diagnostic and therapeutic approaches: An updated review until June 2020 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 4802 sentences = 253 flesch = 43 summary = On May 7, 2020, Gilead Sciences, announced that the Japanese Ministry of Health, Labour and Welfare (MHLW) has granted regulatory approval of Veklury® (Remdesivir) as a treatment for SARS-CoV-2 infection, the virus that causes COVID-19 acute respiratory syndrome, under an exceptional approval pathway. In COVID-19 infection, a massive number of T-lymphocytes and mononuclear macrophages are activated, emitting different cytokines such as interleukin-6 (IL-6), which binds to the IL-6 receptor on its target cells, causing the cytokine storm and severe inflammatory responses in most organs including lungs, liver, kidney and other tissues and organs. Moreover, in July 2020 the WHO discontinued clinical trials with hydroxychloroquine and lopinavir/ritonavir treatment arms for COVID-19 (WHO, 2020b), where both therapies produced little and no reduction in the mortality of hospitalized SARS-CoV-2 cases when compared to standard of care. COVID-19 infection and treatment with hydroxychloroquine cause severe haemolysis crisis in a patient with glucose-6-phosphate dehydrogenase deficiency cache = ./cache/cord-296881-2g81sjnl.txt txt = ./txt/cord-296881-2g81sjnl.txt === reduce.pl bib === id = cord-296767-mgr32ftl author = Große, Karsten title = SARS‐CoV‐2 as an extrahepatic precipitator of acute‐on‐chronic liver failure date = 2020-05-29 pages = extension = .txt mime = text/plain words = 295 sentences = 27 flesch = 45 summary = key: cord-296767-mgr32ftl cord_uid: mgr32ftl We read with great interest the report by Qiu and colleages reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. As ACLF following hepatic versus extrahepatic insults may differ in presentation, course, and prognosis, we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. To the Editor We read with great interest the report by Qiu et al 1 reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. 1 As ACLF following hepatic vs extrahepatic insults may differ in presentation, course and prognosis, 2 we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. Acute on chronic liver failure from novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acute-on-chronic liver failure precipitated by hepatic injury is distinct from that precipitated by extrahepatic insults Multiorgan and renal tropism of SARS-CoV-2 cache = ./cache/cord-296767-mgr32ftl.txt txt = ./txt/cord-296767-mgr32ftl.txt === reduce.pl bib === id = cord-296981-tded20ih author = Gilmore, Kerry title = In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 3162 sentences = 174 flesch = 50 summary = We report in vitro efficacy of Artemisia annua extracts as well as artemisinin, artesunate, and artemether against SARS-CoV-2. Subsequent concentration-response studies using a high-throughput antiviral assay, based on immunostaining of SARS-CoV-2 spike glycoprotein, revealed that pretreatment and treatment with extracts, artemisinin, and artesunate inhibited SARS-CoV-2 infection of VeroE6 cells. The selectivity index (SI), calculated based on treatment and cell viability assays, was highest for artemisinin (54), and roughly equal for the extracts (5-10), artesunate (6) and artemether (<7). annua extracts, as well as pure artemisinin, artesunate, and artemether are active against SARS-CoV-2 in vitro. To initially screen whether extracts and pure artemisinin were active against SARS-CoV-2, their antiviral activity was tested by pretreating VeroE6 cells at different time points during 120 minutes with selected concentrations of the extracts or compounds prior to infection with the first European SARS-CoV-2 isolated in München (SARS-CoV-2/human/Germany/BavPat 1/2020). cache = ./cache/cord-296981-tded20ih.txt txt = ./txt/cord-296981-tded20ih.txt === reduce.pl bib === id = cord-297072-f5lmstyn author = Struck, Anna-Winona title = A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 date = 2012-01-16 pages = extension = .txt mime = text/plain words = 5088 sentences = 302 flesch = 61 summary = title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 Peptide (438)YKYRYL(443) is part of the receptor-binding domain (RBD) of the spike protein of SARS-CoV. The interaction of SARS-CoV with its receptor ACE2 is an attractive drug target as epitopes of the RBD on the spike protein may serve as leads for the design of effective entry inhibitors (Du et al., 2009) . This method allows the determination of the binding specificity, as Table 2 Synthetic peptide library of fourteen 6mer peptides comprising RBD-residues N435-E452 and A471-S500 of SARS-CoV spike protein. We found a hexapeptide in the receptor-binding domain (RBD) of the S protein of SARS-CoV that carries a significant portion of the binding affinity of the virus to the human cell. Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein cache = ./cache/cord-297072-f5lmstyn.txt txt = ./txt/cord-297072-f5lmstyn.txt === reduce.pl bib === id = cord-296997-ba7f2mf3 author = Sikora, Mateusz title = Map of SARS-CoV-2 spike epitopes not shielded by glycans date = 2020-07-03 pages = extension = .txt mime = text/plain words = 5818 sentences = 371 flesch = 55 summary = To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. Our simulation system contained four membrane-embedded SARS-CoV-2 S proteins assembled from resolved structures where available and models for the missing parts (SI Appendix, Fig. S5 ). In the ray analysis, we illuminated the protein model by diffuse light; in the Fab docking analysis, we performed rigid body Monte Carlo simulations of S and the SARS-CoV-2 antibody CR3022 Fab to determine the steric accessibility to an antibody Fab. To account for protein and glycan mobility, we performed both analyses individually for 4 × 193 snapshots taken at 10 ns time intervals from the 1.93 µs MD simulation with four glycosylated S proteins. cache = ./cache/cord-296997-ba7f2mf3.txt txt = ./txt/cord-296997-ba7f2mf3.txt === reduce.pl bib === id = cord-297023-0qlo0mun author = Park, Sung‐Soo title = Mass screening of healthcare personnel for SARS-CoV-2 in the northern emirates date = 2020-10-17 pages = extension = .txt mime = text/plain words = 753 sentences = 57 flesch = 66 summary = While healthcare personnel (HCP) potentially has an increased risk of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the era of the pandemic [1] , the approach to testing HCP for the virus has not been uniform [2] . Given the significant percentage of asymptomatic coronavirus disease 2019 (COVID-19) infection [3] , universal testing of HCP could allow infected workers to be identified and isolated early, reduce in-hospital transmission, mitigate potential workforce depletion, and enhance healthcare workers' safety [4] . This study aimed to evaluate the effectiveness of the universal staff screening for COVID-19 and identify any risk factor for viral infection. The staff were encouraged to notify the occupational health nurse for SARS-CoV-2 test any time if they had any suspicious symptoms of COVID-19 or close contact with COVID-19 patients. Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 COVID-19: the case for healthcare worker screening to prevent hospital transmission cache = ./cache/cord-297023-0qlo0mun.txt txt = ./txt/cord-297023-0qlo0mun.txt === reduce.pl bib === id = cord-297197-klr208kp author = Weizman, Yehuda title = Use of Wearable Technology to Enhance Response to the COVID-19 Pandemic date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1361 sentences = 73 flesch = 50 summary = ABSTRACT Introduction As part of the COVID-19 outbreak response, numerous technology-based solutions have been created to enable contact tracing, track movements of the population and ensure social control. The bracelet would facilitate 3 functions; screening on a population level, digital contact tracing and real-time immunity status tracking. The bracelet would employ the IoT to transfer data over a network to an interactive web-based dashboard that tracks COVID-19 in real-time. If an individual then tested positive for SARS-CoV-2, the database could automatically trace back anyone they had come in contact with in the past 14 days using a GPS feature (described below). In this instance, the biometric bracelet's GPS feature would continuously track movements of individuals within a geographical area and communicate back to the Covid-19 database platform saving input on the population whereabouts at each timepoint. As the coronavirus pandemic continues to spread, some Privacy Commissioners are lifting data restrictions for health officials to keep track of the outbreak. cache = ./cache/cord-297197-klr208kp.txt txt = ./txt/cord-297197-klr208kp.txt === reduce.pl bib === id = cord-297168-t6zf5k99 author = Brüssow, Harald title = The Novel Coronavirus – A Snapshot of Current Knowledge date = 2020-03-06 pages = extension = .txt mime = text/plain words = 4136 sentences = 207 flesch = 50 summary = While bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the Huanan food market in Wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. W. Tan and colleagues, who now constitute the China Novel Coronavirus Investigating and Research Team, described subsequently the isolation of further coronaviruses from three patients in Wuhan who tested negative for 18 viral and four bacterial respiratory pathogens. Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients Outside Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-297168-t6zf5k99.txt txt = ./txt/cord-297168-t6zf5k99.txt === reduce.pl bib === id = cord-297202-oup8ptya author = Beer, Martin title = SARS‐CoV‐2 vaccination—A plea for fast and coordinated action date = 2020-07-01 pages = extension = .txt mime = text/plain words = 449 sentences = 30 flesch = 56 summary = If we assume that the level of herd immunity to halt the spread follows the 1 − 1/R 0 rule (Anderson, Heesterbeek, Klinkenberg, & Hollingsworth, 2020) and given conservative estimates for the basic reproduction number R 0 = 3 (Sanche et al., 2020) at least two-thirds of the world's population must mount an effective immune response against the virus to prevent recurrent outbreaks. Yes, an R t < 0.2 would halt the spread of SARS-CoV-2 in a given population at time t, but any re-introduction of the virus could catapult us back to where we were. Unless serological surveys suggest a much higher-than-expected silent exposure of the human population to SARS-CoV-2, there is no reasonable scenario to reach the required level of herd immunity under the 'reduce spread' paradigm that many countries have emulated. cache = ./cache/cord-297202-oup8ptya.txt txt = ./txt/cord-297202-oup8ptya.txt === reduce.pl bib === id = cord-297127-nhgm09db author = Hasseli, Rebecca title = National registry for patients with inflammatory rheumatic diseases (IRD) infected with SARS-CoV-2 in Germany (ReCoVery): a valuable mean to gain rapid and reliable knowledge of the clinical course of SARS-CoV-2 infections in patients with IRD date = 2020-09-02 pages = extension = .txt mime = text/plain words = 4093 sentences = 218 flesch = 45 summary = OBJECTIVES: Patients with inflammatory rheumatic diseases (IRD) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be at risk to develop a severe course of COVID-19. 2 In this situation, patients with inflammatory rheumatic diseases (IRD) may face a particular risk as their disease, especially when clinically active, and their immunomodulatory treatment may impact the course of COVID-19 infection. However, firm knowledge of the course of SARS-CoV-2 infection in patients with IRD is missing, and therefore, evidence-based recommendations for the management of COVID-19 in patients with rheumatic disorders and antirheumatic treatments are lacking. As necessary data cannot be extracted from clinical charts or health insurance records, the DGRh and the Justus-Liebig University Giessen decided to establish a web-based registry, which allows a rapid and timely collection of IRD cases with confirmed SARS-CoV-2 infections in Germany to analyse the clinical course of SARS-CoV-2 infections in patients with IRD and to develop guidance for the management of patients with IRD during the COVID-19 pandemic. cache = ./cache/cord-297127-nhgm09db.txt txt = ./txt/cord-297127-nhgm09db.txt === reduce.pl bib === id = cord-297217-pe6mehjv author = Simpson, A. Hamish R. W. title = COVID-19: potential transmission through aerosols in surgical procedures and blood products date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1324 sentences = 73 flesch = 48 summary = A six-fold increased risk of transmission of viral diseases, such as severe acute respiratory syndrome (SARS) has been reported during anaesthetic procedures such as endotracheal intubation. 2 no definite transmission has been reported due to surgical procedures, however unlike other viral diseases such as SARS and middle east respiratory syndrome (meRS), CoVid-19 appears to be both severe and highly transmissible and therefore could pose a far higher risk to surgeons and operating room staff. 9, 11 in comparison to SARS, in which only very low plasma levels of virus have been reported, 12 the blood of CoVid-19 patients is likely to have a higher potential for aerosols produced during surgical procedures to carry the virus. there is increasing evidence that a significant number of potentially up to 50% or more of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) are asymptomatic. cache = ./cache/cord-297217-pe6mehjv.txt txt = ./txt/cord-297217-pe6mehjv.txt === reduce.pl bib === id = cord-297132-lhfa9fl5 author = Aghagoli, Ghazal title = Neurological Involvement in COVID-19 and Potential Mechanisms: A Review date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5940 sentences = 280 flesch = 36 summary = In this review, we synthesize a range of clinical observations and initial case series describing potential neurologic manifestations of COVID-19 and place these observations in the context of coronavirus neuro-pathophysiology as it may relate to SARS-CoV-2 infection. The novel 2019 coronavirus disease (COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) results in a variety of symptoms including fever, cough, and fatigue [1] . The Kawasaki-like syndrome that is now described in young patients following COVID-19 infection and associated with a hyper-inflammatory state is further suggestive of a vascular inflammatory potential of SARS-CoV-2 [48, 49] . Once established in the CNS, SARS-CoV, the virus responsible for Severe Acute Respiratory Syndrome (SARS), has been shown to be capable of inducing rapid transneuronal spread and death of infected neurons in transgenic mice models expressing human ACE2 receptors [63] . cache = ./cache/cord-297132-lhfa9fl5.txt txt = ./txt/cord-297132-lhfa9fl5.txt === reduce.pl bib === id = cord-297326-n0fpu8s3 author = ÁLVAREZ, E. title = New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date = 2015-01-16 pages = extension = .txt mime = text/plain words = 4995 sentences = 244 flesch = 47 summary = Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. These equations involve three stocks (SUSCEPTIBLE, LATENT, INFECTED), three auxiliary variables (prevalence, contagion rate, recovery rate) and three parameters (incubation period, case fatality, disease duration). The simulation output for the variable 'sick per day' fit the data reported by the Hong Kong authorities (Fig. 4a) , suggesting that the model was able to reproduce the epidemic curve. These results are consistent with a previous report showing the basic reproductive numbers for different SARS epidemic curves, which supports the notion that our model is able to largely replicate the disease outbreak in Hong Kong [31] . Under these conditions, the model output fits the epidemic curve observed in the Hong Kong SARS-CoV outbreak (Fig. 4) . cache = ./cache/cord-297326-n0fpu8s3.txt txt = ./txt/cord-297326-n0fpu8s3.txt === reduce.pl bib === id = cord-297208-f4ob3ox6 author = Pisano, Antonio title = Cardiothoracic surgery at the time of COVID-19 pandemic: lessons from the East (and from a previous epidemic) for western battlefields date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1376 sentences = 62 flesch = 39 summary = 1 Evidently, countries which faced the severe acute respiratory syndrome (SARS) outbreak, the first coronavirus pandemic of the current century which affected more than 8000 people (mainly in China, Vietnam, Singapore and Canada) in 2003 7 , were much more prepared, both culturally and in terms of facilities and equipment, as compared with western countries (many of which had to face, in the initial stages of the emergency, the shortage of even simple and cheap devices such as surgical masks). cache = ./cache/cord-297208-f4ob3ox6.txt txt = ./txt/cord-297208-f4ob3ox6.txt === reduce.pl bib === id = cord-296661-6ndn2qxc author = Lu, Dingnan title = Primary concentration – The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review date = 2020-07-25 pages = extension = .txt mime = text/plain words = 6214 sentences = 304 flesch = 42 summary = This review provides new insights into the primary concentration methods that have been adopted by the eighteen recently reported COVID-19 wastewater detection studies, along with a brief discussion of the mechanisms of the most commonly used virus concentration methods, including the PEG-based separation, electrostatically charged membrane filtration, and ultrafiltration. The PEG-based separation is the most used technique (7 out of 18) among all concentration methods, and all four studies that adopted this concentration method showed positive results regarding the SARS-CoV-2 detection in wastewater samples (Bar Or et al., 2020; Hata et al., 2020; La Rosa et al., 2020b; Wu et al., 2020) . As previously mentioned, using electrostatically charged membranes filtration to concentrate viruses from turbid water, such as raw wastewater, can be subject to a significant reduction of virus recovery efficiency due to the presence of organic matter and high turbidity, which can lead to a preferential attachment to the charged filters and raise the risk of detrimental clogging. cache = ./cache/cord-296661-6ndn2qxc.txt txt = ./txt/cord-296661-6ndn2qxc.txt === reduce.pl bib === id = cord-297256-i9468t8v author = Cesari, Matteo title = Geriatric Medicine in Italy in the Time of Covid-19 date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1645 sentences = 92 flesch = 58 summary = In fact, although current data indicate that persons aged 70 years and older contribute to about the 85% of the death events in Italy, it cannot be overlooked the fact that Japan has substantially smaller figures despite being the oldest country in the world. To keep the healthcare machine running and support the colleagues overwhelmed in the management of COVID patients, there have been pediatricians working with older patients, or surgeons taking care of internal medicine issues... Geriatric medicine has produced substantial evidence showing that frail older persons require adaptations in the clinical approach, and that the environment plays a critical role for the wellbeing of the aging individual (5,6). Many older persons (with their chronic conditions and care needs) remained isolated after the SARS-CoV-2 outbreak. The same human interaction between the patient and his/her physician is lost behind the burdening personal protective equipment in COVID-19 facilities. cache = ./cache/cord-297256-i9468t8v.txt txt = ./txt/cord-297256-i9468t8v.txt === reduce.pl bib === id = cord-297439-xg0pkjrh author = Gao, Jing title = The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China date = 2020-04-22 pages = extension = .txt mime = text/plain words = 2030 sentences = 120 flesch = 62 summary = Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and lasting positive nucleic acid test result in patients recovered from pneumonia. The CT image is used to assess the disease progress, whereas the continued two times of negative results from SARS-CoV-2 nucleic acid detection had been considered as a criterion for ending antiviral treatment. Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and showed the suspected SARS-CoV-2 carrier. On day 16, the 4th result of nucleic acid in throat swab changed to negative, whereas it was positive in sputum ( Fig. 1) , thus continued the antiviral treatment with interferon inhalation and lopinavir/ ritonavir. On day 8 and day 10, SARS-CoV-2 nucleic acid in throat swab were shown the negative at that two time, and the repeated chest CT image showed that the infection range was declined a lot (Fig. 1) . cache = ./cache/cord-297439-xg0pkjrh.txt txt = ./txt/cord-297439-xg0pkjrh.txt === reduce.pl bib === id = cord-297324-me5ff1pb author = Zeng, Rong title = Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date = 2004-07-30 pages = extension = .txt mime = text/plain words = 4579 sentences = 223 flesch = 57 summary = Analysis of the genomic organization of SARS-CoV showed that a gene locus containing ORF3a and 3b located between the S and E genes, 6 -8 is frequently found in different members of the coronavirus family (see Figure 4A ). According to the genomic sequence information for SARS-CoV, ORF 3a encoded a putative 31 kDa protein containing 274 amino acid residues. 6, 7 In order to confirm the result by shot-gun assay, the collected cytosol of SARS-CoV-infected Vero E6 cells was separated with SDS-PAGE, and then the gel slice around the 31 kDa region was excised and analyzed by capillary liquid chromatography electrospray tandem mass spectrometry (mLC-ESI-MS/MS). Interestingly, comparison with S protein sequences of the coronavirus family also shows a cysteinerich region overlapping the junction of the membrane-spanning domain and the cytoplasmic tail, which is a conserved motif of spike proteins in all analyzed coronaviruses (see Figure 3 of Marra et al. cache = ./cache/cord-297324-me5ff1pb.txt txt = ./txt/cord-297324-me5ff1pb.txt === reduce.pl bib === id = cord-297423-iefq0fh0 author = Bushman, Dena title = Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2739 sentences = 152 flesch = 50 summary = At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS) § who had negative test results for influenza and, in some instances, other respiratory pathogens. cache = ./cache/cord-297423-iefq0fh0.txt txt = ./txt/cord-297423-iefq0fh0.txt === reduce.pl bib === id = cord-297323-l3f12hg4 author = Amor, Sandra title = Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date = 2020-09-26 pages = extension = .txt mime = text/plain words = 4982 sentences = 304 flesch = 43 summary = Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. These subsequently induce expression of type I IFNs (IFNα/β) and interferon stimulated genes (ISGs) [figure 2] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. Likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to SARS-CoV-2 infection, [ Table 4 ; (101) (102) (103) (104) (105) (106) (107) (108) (109) (110) (111) (112) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection cache = ./cache/cord-297323-l3f12hg4.txt txt = ./txt/cord-297323-l3f12hg4.txt === reduce.pl bib === id = cord-297209-84gs67bn author = Livanos, A. E. title = Gastrointestinal involvement attenuates COVID-19 severity and mortality date = 2020-09-09 pages = extension = .txt mime = text/plain words = 7509 sentences = 496 flesch = 54 summary = In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first time in vivo but failed to obtain culturable virus. . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint (nausea, vomiting and diarrhea) was associated with less severe disease (p<0.02 Fisher's exact 188 test) and lower mortality (p<0.001 Fisher's exact test) (Fig. 1a) . . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint CoV-2 nucleocapsid protein in small intestinal enterocytes of COVID-19 patients ( Fig. 4i,n, CD8 + T cells, the dominant IEL 388 population, showed an increase (2.6-fold) in COVID-19 cases compared to controls but the 389 difference did not reach statistical significance (p=0.4) ( Supplementary Table 12a ), likely owing 390 to inter-patient variability, also observed by light microscopy. cache = ./cache/cord-297209-84gs67bn.txt txt = ./txt/cord-297209-84gs67bn.txt === reduce.pl bib === id = cord-297178-moxhk2e0 author = Novaes Rocha, Vinicius title = Viral replication of SARS-CoV-2 could be self-limitative - the role of the renin-angiotensin system on COVID-19 pathophysiology date = 2020-10-01 pages = extension = .txt mime = text/plain words = 3272 sentences = 184 flesch = 46 summary = Caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus disease 2019 (COVID-19) is provoking devastating consequences on economic and social fields throughout all continents. Amongst the components of rennin-angiotensin system (RAS), the angiotensin-converting enzyme 2 (ACE2) has gained great prominence for being directly associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the coronavirus related to COVID-19 [4, 5] . ACE2 is a fundamental piece in the pathophysiology of COVID-19, since the high replication capacity of SAR-CoV-2 is directly related to the coupling to ACE2 and cell infection. The ACE2 level reduction caused by SARS-CoV-2 infection may be directly related to the pathogenesis of COVID-19 [26] . The reduction in ACE2 expression may be related to pulmonary inflammation and subsequent cytokine storm seen in patients with severe COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severeacute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensinconverting enzyme-2 (ACE2) cache = ./cache/cord-297178-moxhk2e0.txt txt = ./txt/cord-297178-moxhk2e0.txt === reduce.pl bib === id = cord-297432-2edncbgn author = Helleberg, Marie title = Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2390 sentences = 139 flesch = 46 summary = A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. cache = ./cache/cord-297432-2edncbgn.txt txt = ./txt/cord-297432-2edncbgn.txt === reduce.pl bib === id = cord-297418-36j840wm author = Carneiro Leão, Jair title = Coronaviridae ‐ old friends, new enemy! date = 2020-05-31 pages = extension = .txt mime = text/plain words = 3978 sentences = 263 flesch = 53 summary = However, in recent years, coronaviruses have given rise to significant diseases such as severe acute respiratory syndrome (SARS-CoV) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) SARS-CoV infected 8,000 people, from 2002 to 2003 and had a mortality rate of approximately 10% (Marra et al., 2003) . On the other hand, evolutionary analysis based on the ORF1a / 1b, S and N genes suggests that SARS-CoV-2 is more likely to be a new coronavirus that has been introduced independently from animals to humans due to the inherent mutation property of coronaviruses in nature (Lam et al., 2020) . Severe acute respiratory syndrome (SARS) is a human disease associated with severe pneumonia and as noted above is caused by SARS-Coronavirus (SARS-CoV) (Drosten et al., 2003) . The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges cache = ./cache/cord-297418-36j840wm.txt txt = ./txt/cord-297418-36j840wm.txt === reduce.pl bib === id = cord-297236-wnuvofwr author = Zhang, Si title = SARS-CoV-2 binds platelet ACE2 to enhance thrombosis in COVID-19 date = 2020-09-04 pages = extension = .txt mime = text/plain words = 10404 sentences = 646 flesch = 50 summary = SARS-CoV-2 and its Spike protein directly enhanced platelet activation such as platelet aggregation, PAC-1 binding, CD62P expression, α granule secretion, dense granule release, platelet spreading, and clot retraction in vitro, and thereby Spike protein enhanced thrombosis formation in wild-type mice transfused with hACE2 transgenic platelets, but this was not observed in animals transfused with wild-type platelets in vivo. However, similar to the results from the SARS-CoV-2 virus experiments, we were able to demonstrate that the Spike protein dose-dependently enhanced platelet aggregation and ATP release (Additional file 1: Online Figure 6 ). In addition, the Spike protein potentiated platelet aggregation and ATP release in response to agonists in vitro and enhanced thrombosis formation in vivo on hACE2 transgenic mice, while it had no effect on wild-type mice ( Fig. 6c and Additional file 1: Online Figure 8 ). cache = ./cache/cord-297236-wnuvofwr.txt txt = ./txt/cord-297236-wnuvofwr.txt === reduce.pl bib === id = cord-297327-19dfgfz6 author = Drożdżal, Sylwester title = COVID-19: Pain Management in Patients with SARS-CoV-2 Infection—Molecular Mechanisms, Challenges, and Perspectives date = 2020-07-20 pages = extension = .txt mime = text/plain words = 5672 sentences = 319 flesch = 41 summary = Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, nonPutative mechanisms of myalgia and headache during viral infection. Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, non-steroidal inflammatory drugs or analgosedation [52] . Recently, concerns about the possible higher frequency of adverse effects and exacerbation of symptoms of viral respiratory tract infections, such as COVID-19, in patients treated with NSAIDs have been raised [67] . There are reports of a significantly higher use of opioids because of sedation requirements during respiratory failure caused by SARS-CoV-2, which highlights the importance of undertaking a study aiming to determine efficacious and safe procedures of pain management in patients with COVID-19. cache = ./cache/cord-297327-19dfgfz6.txt txt = ./txt/cord-297327-19dfgfz6.txt === reduce.pl bib === id = cord-297630-eabtzfd0 author = Manganaro, Marco title = First considerations on the SARS-CoV-2 epidemic in the Dialysis Units of Piedmont and Aosta Valley, Northern Italy date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1285 sentences = 70 flesch = 53 summary = No SARS-COV-2 cases were observed in the only Paediatric Nephrology Unit in the Region (having in charge 4 hemodialysis, 4 peritoneal dialysis, and 35 transplanted The members of the Working group of the Piedmont and Aosta Valley Section of the SIN are listed in "Acknowledgements" section. In adults, 156 SARS-COV-2 cases were recorded: 130 RRT patients including 98 in hemodialysis, 4 in peritoneal dialysis, 26 transplanted, and 2 waiting for transplantation, and 26 health care workers (6 physicians, 18 nurses and 2 members of auxiliary staff). This is much higher than the rates for the general population in Piedmont and Aosta Valley (7782 subjects affected by SARS-CoV-2, i.e., 0.17% of the population), with an odds ratio of 13.43, 95% CI 11.27 to 16.00; z score p < 0.0001 for RRT patients, and of 12.80 (95% CI 8.67 to 18.89; z score p < 0.0001) for staff. cache = ./cache/cord-297630-eabtzfd0.txt txt = ./txt/cord-297630-eabtzfd0.txt === reduce.pl bib === id = cord-297365-11es4w0u author = Peng, Hui title = Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1697 sentences = 113 flesch = 56 summary = METHODS: We retrospectively summarized the characteristics, treatment and outcomes of pediatric cases in Wuhan children's hospital which was the only designated hospital for children with COVID-19 in Hubei Province. In December 2019, a cluster of cases caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Wuhan, Hubei The observed cases were pediatric patients who were discharged from the Wuhan Children's Hospital from December 8, 2019 to February 29, 2020 and diagnosed with COVID-19. Chinese Center for Disease Control and Prevention has analyzed the illness severity of 44415 adult and pediatric patients, and found that severe and critical cases accounted for nearly 20% [9] . A epidemiological study in Chinese children with COVID-19 (n=2143) showed that severe and critical illness accounted for J o u r n a l P r e -p r o o f 5.8% [10, 11] . Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study cache = ./cache/cord-297365-11es4w0u.txt txt = ./txt/cord-297365-11es4w0u.txt === reduce.pl bib === id = cord-297381-1upz6dsy author = Sánchez‐Duque, Jorge A. title = Are we now observing an increasing number of coinfections between SARS‐CoV‐2 and other respiratory pathogens? date = 2020-05-29 pages = extension = .txt mime = text/plain words = 1015 sentences = 83 flesch = 60 summary = Then, we would like to take the opportunity to discuss some of them, 1-10 as there are not yet reviews on this emerging issue of Currently, the evidence suggests that the coinfection rates between SARS-CoV-2 and other respiratory pathogens would be higher than initially expected, which represents a challenge for the diagnosis and treatment. Of patients with confirmed SARS-CoV-2 infection, 20.7% (n=24) were positive for one or more additional pathogens, of which the most common were rhinovirus/enterovirus (6.9%; n=8), respiratory syncytial virus (5.2%; n=6) and other Coronaviruses (4.3%; n=5). 2 Another study by Ding et al., 3 included 115 patients with SARS-CoV-2 infection, 4.35% (n=5) had influenza coinfection (3 for influenza A; 2 for influenza B) 9 . 6 Arashiro et al., 4 published a case report of a patient who debuted with severe acute respiratory distress associated with This article is protected by copyright. cache = ./cache/cord-297381-1upz6dsy.txt txt = ./txt/cord-297381-1upz6dsy.txt === reduce.pl bib === id = cord-297652-ut6e1ysz author = Vanden Eynde, Jean Jacques title = COVID-19: A Brief Overview of the Discovery Clinical Trial date = 2020-04-10 pages = extension = .txt mime = text/plain words = 3140 sentences = 191 flesch = 58 summary = The study is entitled "Trial of Treatments for COVID-19 in Hospitalized Adults (DisCoVeRy)" (NCT04315948) [4] . In a MERS-CoV mouse model, the combination lopinavir/ritonavir/interferon β-1a, used as prophylactic and curative treatments, revealed no significant decrease in the viral load [9] . The results of an ongoing clinical trial (NCT Pharmaceuticals 2020, 13, 65 5 of 8 02845843 [4]), entitled "MERS-CoV infection treated with a combination of lopinavir/ritonavir and interferon Beta-1b", are eagerly awaited, but will not be disclosed before 2021. On March 28, the FDA issued an Emergency Use Authorization for use of hydroxychloroquine and chloroquine for patients who do not have access to the drugs via clinical trials [36] . The first cases of COVID-19 emerged in Wuhan, China, in late 2019, and to date there is no approved specific drug to cure patients infected by SARS-CoV-2. In Vitro Antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-297652-ut6e1ysz.txt txt = ./txt/cord-297652-ut6e1ysz.txt === reduce.pl bib === id = cord-297684-9q3oopaz author = Dobaño, Carlota title = Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5198 sentences = 226 flesch = 41 summary = The Receptor-Binding Domain (RBD) of the spike (S) glycoprotein of SARS-CoV-2, the leading vaccine candidate target, was selected as the primary antigen to develop the initial qSAT assay because (i) S is one of the most immunogenic surface proteins together with the nucleocapsid protein (N) (20) (ii) RBD is the fragment of the virus that mediates binding to the host receptor ACE2 in the lung cells (21) (iii) antibodies to RBD correlate with neutralizing antibodies (20)(22) that could be associated with protection based on studies of other coronaviruses and animal models (23) (24) (25) (26) , and (iv) an ELISA based on this same protein has received FDA approval for COVID-19 serology (11) . We developed three novel multiplex immunoassays for quantifying IgM, IgA and IgG to eight SARS-CoV-2 protein constructs and evaluated by machine learning classification algorithms the performance of several isotype/antigen combinations to detect any positive antibody response to infection, obtaining specificities of 100% and sensitivities of 94.94% (≥14 days since symptoms onset) or 96.08% (≥21 days since symptoms onset), and very high predictability (AUC ≥0.99). cache = ./cache/cord-297684-9q3oopaz.txt txt = ./txt/cord-297684-9q3oopaz.txt === reduce.pl bib === id = cord-297332-rzf0cw1x author = Wang, Qidi title = Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates date = 2016-04-11 pages = extension = .txt mime = text/plain words = 8688 sentences = 431 flesch = 56 summary = 15 Other observations include evidence of ADE reported here for the first time induced by an inactivated SARS-CoV vaccine in rhesus macaques ( Figure 1 ) and by antisera from SARS patients (Table S1) , as well as ADE in other coronavirus infections. Herein, we discovered that a peptide of the viral sequence simultaneously elicits the antibodies of disparate functions in protection and enhancement against SARS-CoV infection by the studies with host Vero E6 cells in vitro and in non-human primates. In contrast, the immunized monkeys in the Vac3 group had a strongly increased ability to control SARS-CoV infection in association with induction of high levels of anti-S 604−625 antibodies ( Figure 7E ). 44 This study demonstrates for the first time that an antibody (mAb43-3-14) targeting a specific linear epitope (S 597−603 ) of the SARS-CoV spike protein can mediate enhancement of virus infection both in vitro and in non-human primates via an epitope sequence-dependent mechanism. cache = ./cache/cord-297332-rzf0cw1x.txt txt = ./txt/cord-297332-rzf0cw1x.txt === reduce.pl bib === id = cord-297599-y4lu8m4k author = Luo, Hua title = Anti-COVID-19 drug screening: Frontier concepts and core technologies date = 2020-10-28 pages = extension = .txt mime = text/plain words = 7665 sentences = 373 flesch = 44 summary = This paper thoroughly summarizes interdisciplinary notions and techniques, including disease model, biochip, network pharmacology, and molecular docking technology, etc., providing a reference for researchers in the screening of drugs for COVID-19 prevention and treatment. Some researchers are currently using mice as an animal model to test drugs and vaccines and to investigate the nature of the infection of SARS-CoV-2 [49] [50] [51] . In fact, in a study led by Qin Chuan on SARS, engineered mice that could express human ACE2 protein was successfully established, leading this Chinese team pioneered the establishment of a SARS-CoV-2 infected hACE2 transgenic mouse model [54] . For example, an effective and convenient novel mouse model in evaluating in vivo protective capacity of the SARS-CoV-2 vaccines was developed through stitching the human gene for ACE2 into an adenovirus by Perlman et al. cache = ./cache/cord-297599-y4lu8m4k.txt txt = ./txt/cord-297599-y4lu8m4k.txt === reduce.pl bib === id = cord-297826-2nruf2g7 author = Tian, Jing-Hui title = SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date = 2020-06-30 pages = extension = .txt mime = text/plain words = 2660 sentences = 171 flesch = 60 summary = In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). Mice 171 immunized with 10 μg dose of NVX-CoV2373/Matrix-M induced antibodies that blocked 172 hACE2 receptor binding to S-protein and virus neutralizing antibodies 21-28-days after 173 a single priming dose ( Fig. 4B and 4C ). Importantly, we found the frequency 254 of IFN-γ + , TNF-α + , and IL-2 + cytokine-secreting CD4 + and CD8 + T cells was 255 significantly higher (p <0.0001) in spleens from the NVX-CoV2373/Matrix-M immunized 256 mice compared to mice immunized without adjuvant ( Fig. 6B and 6C) . Anti-S protein IgG titers were detected within 21-days of a single priming immunization 288 in animals immunized with NVX-CoV2373/Matrix-M across all the dose levels (GMT = 289 1,249-19,000). cache = ./cache/cord-297826-2nruf2g7.txt txt = ./txt/cord-297826-2nruf2g7.txt === reduce.pl bib === id = cord-297702-vxcj25sn author = Chen, Yuxin title = A comprehensive, longitudinal analysis of humoral responses specific to four recombinant antigens of SARS-CoV-2 in severe and non-severe COVID-19 patients date = 2020-09-10 pages = extension = .txt mime = text/plain words = 5253 sentences = 250 flesch = 46 summary = We continuously monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the nucleoprotein (NP), receptor binding domain (RBD), S1 protein, and ectodomain (ECD) of the spike protein among non-severe and severe COVID-19 patients for seven weeks since disease onset. In this retrospective study, we successively monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the NP protein, RBD protein, S1 protein, and ECD protein in 19 non-severe and 7 severe COVID-19 patients during the disease progression. The severe patients and non-severe patients had comparable reduced fold of IgM, IgG, and IgA binding titer specific to RBD, ECD, S1, and NP protein and neutralization activities. Furthermore, 80.7% of the convalescent sea from COVID-19 patients displayed varying levels of neutralization activities against SARS-CoV-2, which correlated with S1-specific and ECD-specific IgA responses in non-severe patients. cache = ./cache/cord-297702-vxcj25sn.txt txt = ./txt/cord-297702-vxcj25sn.txt === reduce.pl bib === id = cord-297463-mmmwi8de author = Hsu, You-Ren title = Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors date = 2013-03-15 pages = extension = .txt mime = text/plain words = 934 sentences = 61 flesch = 58 summary = title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect the SARS coronavirus (SARS-CoV) nucleocapsid protein interaction without fluorescent labeling. We demonstrated AlGaN/GaN was highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleic acid-protein interaction. Here, we demonstrated using the AlGaN/GaN HEMT-based sensors to detect the SARS-CoV CTD s protein. Here, we demonstrated that the AlGaN/GaN HEMTs also have the capability of detecting nucleic acid-protein interaction with high sensitivity. The detection limit of AlGaN/GaN HEMTs sensor for SARS-CoV N protein of dsDNA immobilized device was 0.003 nM, and two orders lower than AMPs immobilized nanowire FET 17 . In summary, AlGaN/GaN HEMTs can detect the nucleic acid binding protein at a low detection limit. cache = ./cache/cord-297463-mmmwi8de.txt txt = ./txt/cord-297463-mmmwi8de.txt === reduce.pl bib === id = cord-297451-p5rlquym author = Luz María Trujillo, G title = Relación Entre Covid-19 Y Síndrome De Guillain-Barre En Adultos.Revisión Sistemática date = 2020-07-24 pages = extension = .txt mime = text/plain words = 1737 sentences = 141 flesch = 52 summary = Se han reportado varios casos en distintos centros de salud, de ingreso de pacientes que presentan Síndrome de Guillain-Barré (SGB) y son COVID-19 positivo activos o cursaron con la enfermedad, por lo que se ha planteado la asociación entre ambas patologías. Encefalopatía infecciosa Aguda/tóxica, descrita como síndrome de disfunción cerebral reversible causado por cuadros tóxicos sistémicos, trastornos metabólicos e hipoxia durante un período de infección aguda; y por último, la Enfermedad cerebrovascular aguda (Ataque cerebrovascular) que en los últimos meses ha sido ampliamente atribuida al SARS-CoV-2, debido a que este virus causa una cascada de citoquinas proinflamatorias, encontrándose también niveles elevados de Dímero-D y bajos niveles de plaquetas, pudiendo presentarse un Ataque cerebrovascular 4 . Los estudios analizados demuestran una clara tendencia de asociación entre ambas patologías, donde el virus SARS-CoV-2, sería el potencial gatillador del SGB. Guillain-Barré Syndrome associated with SARS-CoV-2 infection Guillain-Barré Syndrome associated with SARS-CoV-2 infection cache = ./cache/cord-297451-p5rlquym.txt txt = ./txt/cord-297451-p5rlquym.txt === reduce.pl bib === id = cord-297786-jz1d1m2e author = Hasan, Md. Mahbub title = Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3271 sentences = 187 flesch = 54 summary = Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Then, we studied the variants present in different isolates of Bangladesh to investigate the pattern of mutations, identify UMs, and discuss the pseudo-effect of these mutations on the structure and function of encoded proteins, with their role in pathogenicity. To understand the SARS-CoV-2 viral transmission in Bangladesh, we performed phylogenetic analysis on the selected 207 viral genomes reported from different districts of Bangladesh along with selected 467 globally submitted sequences as reported from 42 countries and 6 continents ( Figure 1 ). cache = ./cache/cord-297786-jz1d1m2e.txt txt = ./txt/cord-297786-jz1d1m2e.txt === reduce.pl bib === id = cord-297470-lx3xwg92 author = Pan, Yunbao title = Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date = 2020-10-07 pages = extension = .txt mime = text/plain words = 1600 sentences = 97 flesch = 51 summary = title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Hence, Wuhan launched a population-scale, massive SARS-CoV-2 testing campaign for detecting viral nucleic acid and antibodies in residents to further prevent viral transmission, screen out infected patients who were in the incubation period or were asymptomatic virus carriers, and map the epidemiological sero-distribution of this infectious disease in the epicenter. The present study described the screening results of 61,437 community members in Wuchang District, Wuhan. Most of the recent studies showed detectable SARS-CoV-2 anti-IgM antibodies after one to two months (10, 11) . Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China cache = ./cache/cord-297470-lx3xwg92.txt txt = ./txt/cord-297470-lx3xwg92.txt === reduce.pl bib === id = cord-297708-uocs65sl author = Alders, N. title = COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected date = 2020-08-22 pages = extension = .txt mime = text/plain words = 3415 sentences = 216 flesch = 48 summary = Four distinct groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile illnesses with or without extra-pulmonary organ dysfunction (21%). The relative paucity of data describing SARS-CoV-2 in the paediatric population mandates a broad-arching approach to pandemic planning with preparations put in place to manage a heterogeneous population of patients presenting with a range of single and multi-organ pathology of varying severity. . https://doi.org/10.1101/2020.08.20.20178541 doi: medRxiv preprint Methods All patients aged ≤ 18 years with positive respiratory or nasal SARS-CoV-2 RT-PCR and/or serum IgG (Epitope Diagnostics Inc. TM ) up to 19 th May 2020. Four distinct clinical groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile/viral illness with or without single organ dysfunction (21%). cache = ./cache/cord-297708-uocs65sl.txt txt = ./txt/cord-297708-uocs65sl.txt === reduce.pl bib === id = cord-297832-picpuzvo author = Salazar, Rafael title = Decreased Mortality in Patients With Severe Bronchospasm Associated With SARS-CoV-2: An Alternative to Invasive Mechanical Ventilation date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1768 sentences = 110 flesch = 47 summary = The number of patients with acute episodes of severe bronchospasm needing intubation and ventilatory support has increased rapidly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus disease 2019 (COVID-19) pandemic. Anteroposterior chest X-ray at the time of acute bronchospasm with Radiographic Assessment of Lung Edema (RALE) score 2 The initial management comprised placing the patient in the prone position and administering oxygen at high flow through a non-rebreather mask with flow between 10 and 15 liters per minute until reaching 100% FiO 2 . To improve ventilatory mechanics and ultimately postpone the need for IMV due to acute bronchospasm in patients diagnosed with COVID-19, we put in place a therapeutic approach consisting of early respiratory therapy and pharmacological bronchospasm rescue approach. The therapeutic bundle of early respiratory therapy, consisting of deep inspiration with inspiratory hold, and pharmacological bronchospasm rescue decreased the need for invasive mechanical ventilation in patients with bronchospasm associated with SARS-CoV-2 and reduced the mortality rate. cache = ./cache/cord-297832-picpuzvo.txt txt = ./txt/cord-297832-picpuzvo.txt === reduce.pl bib === id = cord-297671-3d3gcn6k author = Venn, April M.R. title = A case series of pediatric croup with COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2360 sentences = 153 flesch = 59 summary = We describe three previously healthy children, admitted from our emergency department (ED) to our free-standing children's hospital, as the first documented cases of croup as a manifestation of SARS-CoV-2 infection. All three cases (ages 11 months, 2 years, and 9 years old) presented with non-specific upper-respiratory-tract symptoms that developed into a barky cough with associated stridor at rest and respiratory distress. The novel 2019 coronavirus SARS-CoV-2, responsible for COVID-19 disease, commonly presents in children with fever, cough or shortness of breath. [7] After an electronic health record database review, we describe this ca 1 se series of our ED's only three cases, between March 1, 2020 and July 31, 2020, of children who received nebulized racemic epinephrine (NRE) and had a positive SARS-CoV-2 infection. [15] Pediatric croup patients who received ≥3 NRE in one children's hospital were more likely to need intensive care management. cache = ./cache/cord-297671-3d3gcn6k.txt txt = ./txt/cord-297671-3d3gcn6k.txt === reduce.pl bib === id = cord-297842-hkr1wm3k author = Tilley, Kimberly title = A Cross-Sectional Study Examining the Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in a University Student Population date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3894 sentences = 197 flesch = 43 summary = PURPOSE: The aim of the study was to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in a university student population. METHODS: This was a cross-sectional survey study based on the World Health Organization population-based seroepidemiological investigational protocol for SARS-CoV-2 conducted between April 29, 2020, and May 8, 2020, examining SARS-CoV-2 antibody prevalence among 790 university students in Los Angeles, CA. With the goal of having the sample distributions match distributions in the population, these strata were selected based on internal university data, indicating that females are more likely to participate in health-related research projects compared with males, and fewer undergraduates (36.4%) spent the end of the Spring 2020 semester in Los Angeles relative to graduate students (76.5%). Seroprevalence of SARS-CoV-2 antibodies in a Los Angeles university student population as of May 8, 2020, was estimated to be 4.0%. cache = ./cache/cord-297842-hkr1wm3k.txt txt = ./txt/cord-297842-hkr1wm3k.txt === reduce.pl bib === id = cord-297691-w4cdfwv0 author = Nikaeen, Ghazal title = Application of nanomaterials in treatment, anti-infection and detection of coronaviruses date = 2020-05-07 pages = extension = .txt mime = text/plain words = 4537 sentences = 228 flesch = 39 summary = In this special report, different strategies of using nanoparticles in dealing with coronaviruses are discussed in three parts: applications in nano-based vaccines, antiviral activity and development of diagnostic sensors. Meanwhile, as nanoparticles have been proven to have immunostimulatory effects [28] , a great deal of attention has been given to development of nano-based therapeutic agent or vaccines against different types of coronaviruses. evaluated the protective immune response stimulated by the administration of gold nanoparticles (Au NPs) conjugated with a type of coronavirus known as swine transmissible gastroenteritis virus (TGEV) in immunized mice and rabbits [29] . Recent applications of nanoparticles in developing coronaviruses sensors based on different analytical techniques and related limit of detections. The above studies on the recent applications of NPs in developing sensors based on different analytical techniques for coronaviruses and their related limit of detections are compared in Table 3 . cache = ./cache/cord-297691-w4cdfwv0.txt txt = ./txt/cord-297691-w4cdfwv0.txt === reduce.pl bib === id = cord-297747-kifqgskc author = Lupala, Cecylia S. title = Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date = 2020-03-27 pages = extension = .txt mime = text/plain words = 4522 sentences = 231 flesch = 57 summary = Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. When this study was started, neither the crystal structure of the SARS-CoV-2 spike protein nor the RBD segment were determined, so the homology modeling approach was applied to construct the model of the SARS-CoV-2 spike RBD in complex with the human ACE2 binding domain (denoted as CoV2-RBD/ACE2 in the following). Although the crystal structure and the predicted model of the CoV2-RBD/ACE2 complex provide important information about the binding interactions at the molecular interfaces, MD simulations can extend the knowledge to a dynamics regime in a fully solvated environment. cache = ./cache/cord-297747-kifqgskc.txt txt = ./txt/cord-297747-kifqgskc.txt === reduce.pl bib === id = cord-297884-a6yrtuwf author = Burke, R. M. title = Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States date = 2020-05-03 pages = extension = .txt mime = text/plain words = 7343 sentences = 341 flesch = 49 summary = To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with ≥ 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members. Among 49 HCP who provided care to or came into contact with the infectious fluids of travelassociated case patients and who had at least one set of respiratory samples collected and tested for SARS-CoV-2, the secondary attack rate was 0% (95% CI: 0 -7%). cache = ./cache/cord-297884-a6yrtuwf.txt txt = ./txt/cord-297884-a6yrtuwf.txt === reduce.pl bib === id = cord-297878-c4cq92x8 author = Ali, Mohammed title = ST-Elevation Myocardial Infarction in a 27-Year-Old Male With COVID-19 date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2098 sentences = 128 flesch = 53 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that led to a global public health emergency causing coronavirus disease 2019 (COVID-19). Here we present a case of a very young 27-year-old patient without any past history of hypertension, coronary artery disease, or any risk factors for coronary artery disease except obesity, who developed STEMI while in the hospital. Here we present a case of ST-elevation myocardial infarction (STEMI) in a very young 27-year-old African American patient who was admitted for respiratory 1 2 1 3, 4 failure secondary to COVID-19. revealed that STEMI was the presenting clinical manifestation in 24 out of 28 COVID-19 patients who were diagnosed with an STEMI. COVID-19 has now been associated with increased cardiovascular injury and even more so in patients with severe disease. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Cardiac involvement in a patient with coronavirus disease 2019 (COVID-19) cache = ./cache/cord-297878-c4cq92x8.txt txt = ./txt/cord-297878-c4cq92x8.txt === reduce.pl bib === id = cord-297693-lqyc49t6 author = Samec, Matthew J title = 80-year-old man with dyspnoea and bilateral groundglass infiltrates: an elusive case of COVID-19 date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2821 sentences = 177 flesch = 48 summary = COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a 'crazy paving' pattern on chest CT imaging and a negative initial infectious workup. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a 'crazy paving' pattern on chest CT imaging and a negative initial infectious workup. The case was reviewed with the institutional infection prevention and control team who recommended repeating SARS-CoV-2 PCR 48 hours from the initial test. 14 There have been three published case reports of initially negative COVID-19 PCR tests in patients subsequently new disease determined to have COVID-19 infection. cache = ./cache/cord-297693-lqyc49t6.txt txt = ./txt/cord-297693-lqyc49t6.txt === reduce.pl bib === id = cord-297641-bgmib6xb author = Meng, Xiujuan title = Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China date = 2020-04-07 pages = extension = .txt mime = text/plain words = 638 sentences = 47 flesch = 56 summary = title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China 1 The virus causing COVID-19, designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is closely related to SARS-CoV. 2 In 2003, a SARS-CoV outbreak at Amoy Gardens in Hong Kong led to 329 confirmed cases of infection and 42 deaths. 3 Subsequent studies suggested that the plumbing and ventilation systems at Amoy Gardens interacted to allow transmission of the SARS virus and that high concentrations of viral aerosols in the plumbing were the primary mode of transmission in this outbreak. Based on these characteristics, SARS-CoV-2 is prone to cause outbreaks in the community, particularly in rural areas. In concentrated areas, residents mainly use flush toilets, which can generate huge quantities of aerosols; the ventilation and plumbing systems in these places are not effective for maximal hygiene. The feces may form high concentrations of viral aerosols that travel through the air to cause infection. cache = ./cache/cord-297641-bgmib6xb.txt txt = ./txt/cord-297641-bgmib6xb.txt === reduce.pl bib === id = cord-298036-2zurc60t author = Imre, Gergely title = Cell death signalling in virus infection date = 2020-09-12 pages = extension = .txt mime = text/plain words = 8002 sentences = 414 flesch = 37 summary = Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . cache = ./cache/cord-298036-2zurc60t.txt txt = ./txt/cord-298036-2zurc60t.txt === reduce.pl bib === id = cord-297918-840thddt author = Yilmaz, Umut title = COVID-19: neurologische Manifestationen: Was wir bisher wissen date = 2020-09-02 pages = extension = .txt mime = text/plain words = 1333 sentences = 172 flesch = 48 summary = So wurde in einer ersten Studie mit 214 COVID-19-Patienten aus Wuhan eine neurologische Beteiligung in 36,4 % der Fälle beschrieben [1] . Eine Studie mit 58 aufgrund eines akuten Lungenversagens ("acute respiratory distress syndrome", ARDS) intensivmedizinisch behandelten COVID-19-Patienten aus Straßburg berichtet von neurologischen Komplikationen in 84 % der Fälle. Im weiteren Verlauf der Pandemie sind in den letzten Monaten zahlreiche Fallberichte und Fallserien publiziert worden, die von unterschiedlichen neurologischen Manifestationen bei CO-VID-19-Patienten berichten. Daher wurden in einer aktuellen Metaanalyse von Fallberichten und Studien zu neurologischen Komplikationen standardisierte Falldefinitionen für die Wahrscheinlichkeit eines Zusammenhangs zur COVID-19-Infektion gefordert [7] . Eine PCR-Analyse des Liquors auf SARS-CoV-2 wurde in 4 Fällen durchgeführt und fiel bei einem Patienten positiv aus. In einer europäischen Studie mit 417 Patienten wird von Störungen des Geruchs-oder Geschmackssinnes in über 85 % der Fälle mit bestätigter Infektion berichtet [2] . Saggese und Kollegen berichten von einem 62-jährigen COVID-19-positiven Patienten mit multiplen vaskulären Risikofaktoren, der aufgrund eines Schlaganfalls behandelt wurde. cache = ./cache/cord-297918-840thddt.txt txt = ./txt/cord-297918-840thddt.txt === reduce.pl bib === id = cord-297800-hnx213kp author = Bi, Qifang title = Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts date = 2020-03-04 pages = extension = .txt mime = text/plain words = 5363 sentences = 279 flesch = 54 summary = We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We characterize differences in demographics and severity between cases identified through symptom-based surveillance and the monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterize SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval and observed reproductive number. Based on 48 pairs of cases with a clear infector-infectee relationship and time of symptom onset, we estimate that the serial interval is gamma distributed with mean 6.3 days (95% CI 5.2,7.6) and a standard deviation of 4.2 days (95% CI, 3.1,5.3) ( Figure 2B , Table S2 ). This analysis of early SARS-CoV-2 cases and their close contacts in Shenzhen China, provides insights into the natural history, transmission and control of this disease. cache = ./cache/cord-297800-hnx213kp.txt txt = ./txt/cord-297800-hnx213kp.txt === reduce.pl bib === id = cord-298056-svwtfshi author = Fabio, Ciceri title = Early predictors of clinical outcomes of COVID-19 outbreak in Milan, Italy date = 2020-06-12 pages = extension = .txt mime = text/plain words = 3319 sentences = 169 flesch = 46 summary = Multivariable analysis showed older age, coronary artery disease, cancer, low lymphocyte count and high RALE score as factors independently associated with an increased risk of mortality. CONCLUSION: In a large cohort of COVID-19 patients of European origin, main risk factors for mortality were older age, comorbidities, low lymphocyte count and high RALE. 14 In this report we describe the demographical, clinical, radiological and laboratory characteristics, as well as the clinical outcomes and the risk factors for mortality, of the first 500 patients with COVID-19 admitted to San Raffaele Scientific Institute, a tertiary care academic hospital in Milan, Italy. With a clinical observation longer than one months from the last patient admitted, w e were able to identify early predictors of mortality related to patient characteristics, radiological and laboratory findings at hospital admission for COVID-19. cache = ./cache/cord-298056-svwtfshi.txt txt = ./txt/cord-298056-svwtfshi.txt === reduce.pl bib === id = cord-297942-6wdwrttn author = Li, Taisheng title = Diagnosis and clinical management of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection: an operational recommendation of Peking Union Medical College Hospital (V2.0): Working Group of 2019 Novel Coronavirus, Peking Union Medical College Hospital date = 2020-03-14 pages = extension = .txt mime = text/plain words = 1825 sentences = 99 flesch = 42 summary = To standardize the clinical diagnosis and treatment, Peking Union Medical College Hospital (PUMCH) has established a working group and formulated the following operational recommendation regarding "Diagnosis and Clinical Management of Severe Acute Respiratory Syndrome Coronavirus 2 Infection" (V2.0). According to the definition of the National Health Commission [1] , patients in accordance with one of the following standards should be hospitalized and transferred to Beijing designated medical institution as soon as possible; (1) respiratory rate increased (≥30 per min) or dyspnoea; (2) oxygen saturation ≤ 95% when breathing ambient air, or arterial oxygen tension (PaO₂) over inspiratory oxygen fraction (FIO₂) of less than 300 mm Hg (1 mm Hg equals to 0.133 kPa); (3) lung imaging indicating multilobular lesions or progression of lesions over 50% within 48 h; (4) quick sequential organ failure assessment (qSOFA) score ≥2; (5) community-acquired pneumonia-65 (CURB-65) score ≥ 1; (6) combined pneumothorax; (7) other clinical conditions that require hospitalization. cache = ./cache/cord-297942-6wdwrttn.txt txt = ./txt/cord-297942-6wdwrttn.txt === reduce.pl bib === id = cord-297787-t9neub6d author = Fu, Ziyang title = Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date = 2020-07-18 pages = extension = .txt mime = text/plain words = 2152 sentences = 149 flesch = 64 summary = The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19. The in-vitro 85 IC50 of GRL0617 against SARS-COV-2 PLpro was 2.1 ± 0.2 μM, suggesting a promising lead 86 compound and therefore it was subjected to further structural and mechanistic studies ( Fig. 2A) . Taken together, our NMR and X-ray analysis indicates that GRL0617 162 is a potent PPI (protein-protein interaction) inhibitor for PLpro blocking the binding of ISG15. Our co-crystal structure of PLpro C111S in complex with the potent 175 inhibitor GRL0617 validated that SARS-COV-2 PLpro is a druggable target. Based on the structure, GRL0617 resides in the S3/S4 site of PLpro, naturally it will also 179 inhibit the processing of viral polyproteins of SARS-CoV-2 since these viral polyproteins share the 180 same substrate cleavage sequence with Ub and ISG15. The SARS-coronavirus papain-like 257 protease: structure, function and inhibition by designed antiviral compounds cache = ./cache/cord-297787-t9neub6d.txt txt = ./txt/cord-297787-t9neub6d.txt === reduce.pl bib === id = cord-297974-sduz0j35 author = Bokelmann, L. title = Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4761 sentences = 307 flesch = 55 summary = Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp. cache = ./cache/cord-297974-sduz0j35.txt txt = ./txt/cord-297974-sduz0j35.txt === reduce.pl bib === id = cord-298067-awo3smgp author = Li, Huanjie title = Transmission Routes Analysis of SARS-CoV-2: A Systematic Review and Case Report date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4853 sentences = 268 flesch = 51 summary = Through associating infection symptoms with the transmission routes of virus and the patient course of the disease, we expect to provide guidelines for clinical diagnosis and the basis for suppressing the spread of the virus and antiviral treatment. On February 1, 2020, respiratory samples of four patients were confirmed SARS-CoV-2 infections by real-time PCR in Jinan Central Hospital, Shandong province, China. Summarizing the published articles, including SARS-CoV and SARS-CoV-2, we combined with epidemiological and clinical data to analyze the possible routes of asymptomatic patients with virus infection in order to provide the basis for suppressing the spread of the virus, and antiviral treatment and advice for the protection of medical staff. The study found that the detection of SARS-CoV-2 nucleic acid positive in a few feces of patients with confirmed COVID-19 cases indicated the presence of a live virus. cache = ./cache/cord-298067-awo3smgp.txt txt = ./txt/cord-298067-awo3smgp.txt === reduce.pl bib === id = cord-297681-m0cckidw author = Na, Joo-Young title = [Secondary Publication] Standard Operating Procedure for Post-mortem Inspection in a Focus on Coronavirus Disease-19: the Korean Society for Legal Medicine date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2813 sentences = 139 flesch = 48 summary = The Korean Society for Legal Medicine, a highly specialized organization responsible for post-mortem examination and death investigation, aims to protect multiple staff-related post-mortem examinations and prevent the spread of COVID-19 in medical institutions and communities to improve social stability through this guideline for COVID-19 post-mortem inspections. The risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during post-mortem inspection of a dead body is relatively lower than that in the case of medical procedures or treatments because dead bodies do not cough and spread droplets. Due to the nature of postmortem inspection, in most cases, there is no or insufficient ante-mortem information, so collaboration with investigative agencies, local governments, and relevant public health centers is essential to determine the possibility of SARS-CoV-2 infection. 1) After confirming the identity of the deceased, if it is necessary to confirm whether he or she has the possibility of infection with COVID-19, request confirmation to the public health center through the police in charge, and proceed with the post-mortem inspection. cache = ./cache/cord-297681-m0cckidw.txt txt = ./txt/cord-297681-m0cckidw.txt === reduce.pl bib === id = cord-298216-iq7fenxm author = Jiang, Chao title = Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1618 sentences = 114 flesch = 44 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to sweep the world, causing infection of millions and death of hundreds of thousands. The respiratory disease that it caused, COVID-19 (stands for coronavirus disease in 2019), has similar clinical symptoms with other two CoV diseases, severe acute respiratory syndrome and Middle East respiratory syndrome (SARS and MERS), of which causative viruses are SARS-CoV and MERS-CoV, respectively. This is a discussion and comparison of the virus structures, transmission characteristics, clinical symptoms, diagnosis, pathological changes, treatment and prevention of the two kinds of viruses, CoVs and IAVs. It hopes to provide information for practitioners in the medical field during the epidemic season. In December 2019, a novel coronavirus, SARS-CoV-2, caused a pneumonia epidemic 44 in Wuhan, Hubei province of China. Lung pathology of severe 567 acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Molecular pathology analyses of two fatal 572 human infections of avian influenza A(H7N9) virus cache = ./cache/cord-298216-iq7fenxm.txt txt = ./txt/cord-298216-iq7fenxm.txt === reduce.pl bib === id = cord-297941-7yut9vt4 author = Haq, M. title = Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2709 sentences = 210 flesch = 61 summary = In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV2 antibodies and the risk factors of COVID 19 in healthcare-workers but little is known from developing countries. Methods: This cross-sectional study was conducted on prevalence of SARS CoV2 antibody and risk factors for seropositivity in HCWs in tertiary care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan. To our knowledge this is the first study of assessing SARS-CoV-2 antibodies of HCWs form both public and private tertiary care hospitals in Peshawar, Pakistan. To our knowledge this is the first study on prevalence of SARS CoV-2 antibodies in HCW of tertiary care hospitals in Pakistan. The risk of becoming positive for SARS-CoV-2 antibodies did not increase with history of direct contact with COVID patients within or outside the hospital. cache = ./cache/cord-297941-7yut9vt4.txt txt = ./txt/cord-297941-7yut9vt4.txt === reduce.pl bib === id = cord-297859-p57pl45i author = Mahlke, Lutz title = Chirurgie in der SARS-CoV-2-Pandemie: Empfehlungen zum operativen Vorgehen date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2374 sentences = 329 flesch = 49 summary = authors: Mahlke, Lutz; Flohé, Sascha; Matthes, Gerrit; Paffrath, Thomas; Wagner, Frithjof; Wölfl, Christoph Die Virusinfektion mit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ist hochkontagiös, daher besteht auch für die Mitarbeiter des Krankenhauses ein hohes Risiko [1] . Über die persönliche Schutzausrüstung (PSA) für Mitarbeiter der Anästhesie sind in einer kürzlich erschienenen Publikation sehr detailliert das Vorgehen und das notwendige Equipment beschrieben worden [2] , sodass hier v. Sofern es Personalschlüssel und Ausbildungsstand der Abteilung erlauben, ist die Schaffung von speziell geschulten "COVID-19"-OP-Teams sinnvoll. Auch die bisherigen Virusnachweise im Darm und im Stuhl lassen keine hohe Viruslast erkennen [13] , zumal unklar ist, ob es sich hierbei noch um ein infektiöses Virus handelt [14] . Even patients infected by SARS-CoV-2 or COVID-19 may need operative procedures. Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 cache = ./cache/cord-297859-p57pl45i.txt txt = ./txt/cord-297859-p57pl45i.txt === reduce.pl bib === id = cord-297870-m7n43k4p author = Azevedo, Rafael Bellotti title = Covid-19 and the cardiovascular system: a comprehensive review date = 2020-07-27 pages = extension = .txt mime = text/plain words = 5108 sentences = 211 flesch = 30 summary = Moreover, as in other respiratory infections, preexisting CV diseases and risk factors can increase the severity of COVID-19, leading to the aggravation and decompensation of chronic underlying cardiac pathologies as well as acute-onset of new cardiac complications [3] , highlighting that myocardial injury can be present in approximately 12% of hospitalized patients with SARS-CoV-2 infection [1] . Within the CV manifestations of COVID-19, we can highlight four different aspects: (a) CV risk factors and established CV disease is associated with a worse prognosis, (b) appearance of acute CV complications in previously healthy individuals, (c) promising therapies with antimalarials and antivirals present important CV side effects, and (d) questioning the safety of the use of renin-angiotensin-aldosterone system (RAAS) inhibitors regarding an increased risk of COVID-19 [1] . cache = ./cache/cord-297870-m7n43k4p.txt txt = ./txt/cord-297870-m7n43k4p.txt === reduce.pl bib === id = cord-297879-6xb25uhx author = Moncunill, G. title = SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5546 sentences = 320 flesch = 56 summary = A follow-up survey one month after the baseline (April-May 2020) measured SARS-CoV-2 infection by real time reverse-transcriptase polymerase chain reaction (rRT-PCR) and IgM, IgA, IgG and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein by Luminex. We found that 9.3% (95% CI: 7.1-12.0) of the participants were seropositive and the cumulative prevalence of SARS-CoV-2 infection (considering a past or current positive result to either antibody testing or rRT-PCR) was 11.2% (95% CI: 8.8-14.1). We measured IgM, IgG, and IgA isotypes and subclasses, and assessed the factors associated with new infections as well as levels and kinetics of antibodies. Levels (median fluorescence intensity, MFI) of IgM, IgG, and IgA against receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein stratified by asymptomatic participants and participants who reported COVID-19 compatible symptoms at recruitment (month 0, M0), month 1 (M1) or at both visits (M0&M1). cache = ./cache/cord-297879-6xb25uhx.txt txt = ./txt/cord-297879-6xb25uhx.txt === reduce.pl bib === id = cord-297775-ug4ovsws author = Hosie, Margaret J title = Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1997 sentences = 118 flesch = 54 summary = High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. Recent reports from Dutch mink farms of both mink-to-cat and mink-tohuman transmission of the virus provide support for this scenario (5, 9) We used a range of laboratory techniques to show that two domestic cats from households with suspected cases of COVID-19, and which displayed either mild or severe respiratory disease, were infected with SARS-CoV-2. As we do not have the owner's virus sequence, we cannot determine whether the observed mutations in cat 2's viral genome arose in a human prior to transmission. Table 1 details the SNPs observed in the cat 2 viral genome, and their frequency in the existing UK human population and among existing feline SARS-CoV-2 sequences. cache = ./cache/cord-297775-ug4ovsws.txt txt = ./txt/cord-297775-ug4ovsws.txt === reduce.pl bib === id = cord-297989-4grwa4ab author = Li, Yunjin title = Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2 date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1616 sentences = 89 flesch = 46 summary = Since the expression profile of ACE2, a crucial cell entry receptor for SARS‐CoV‐2, could indicate the susceptibility to SARS‐CoV‐2 infection, here we systematically dissected ACE2 expression using large‐scale multi‐omics data from 30 organs/tissues, 33 cancer types and some common chronic diseases involving >28 000 samples. Furthermore, the patients with common chronic diseases regarding angiocardiopathy, type 2 diabetes, liver, pneumonia and hypertension were also with higher ACE2 expression compared to related controls, which were validated using independent data sets. Collectively, our study may reveal a novel important mechanism that the patients with certain cancers and chronic diseases may express higher ACE2 expression compared to the individuals without diseases, which could lead to their higher susceptibility to multi‐organ injury of SARS‐CoV‐2 infection. Here, we systematically analysed ACE2 expression using largescale multi-omics data from a variety of organs/tissues and cancer types, as well as the common chronic diseases of heart, liver, diabetes, pneumonia and hypertension involving a total of >28 000 samples. cache = ./cache/cord-297989-4grwa4ab.txt txt = ./txt/cord-297989-4grwa4ab.txt === reduce.pl bib === id = cord-298372-4pw1y404 author = Koch, Lionel title = Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? date = 2020-08-18 pages = extension = .txt mime = text/plain words = 6206 sentences = 286 flesch = 42 summary = The last Ebola outbreak in 2014 in West Africa was regarded as a paradigm of the issues caused by emerging infectious diseases nowadays: this extremely deadly pathogen has naturally emerged in a large new area, and its overwhelming spread has subsequently impacted Europe and the United States [3] . At the same time, some natural outbreaks were caused by naturally altered pathogens like the Escherichia coli O104:H4 in Europe in 2011, a strain that acquired and combined unusual virulence factor and drug resistance genes [25] or in 2003 the new human coronavirus (SARS-CoV) identified with surprise in front of severe acute respiratory syndrome cases [26] . Indeed, even if the substantial remaining risk in the case of an attack is the possibility of secondary actions aiming to maximise damages to the emergency infrastructure [38] , the real challenge for global safety remains the early detection, the accurate characterisation and the establishment of specific measures, whatever the outbreak origin [39, 40] . cache = ./cache/cord-298372-4pw1y404.txt txt = ./txt/cord-298372-4pw1y404.txt === reduce.pl bib === id = cord-298242-iuskpoug author = Yu, Alvin title = A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date = 2020-10-02 pages = extension = .txt mime = text/plain words = 3604 sentences = 204 flesch = 47 summary = Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. In this paper, we construct a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion from the currently available structural and atomistic simulation data on SARS-CoV-2 proteins. In this work, we detail several of our CG methods used to iteratively develop a CG model for the full SARS-CoV-2 virion, in which molecular interactions between CG particles are derived using a combination of phenomenological, experimental, and atomistic simulation approaches. In recent cryo-EM images of SARS-CoV-2 particles, the S1 domain of the S protein was found to transiently open and close in order to bind the ACE-2 receptor (3, 5) , which are subtle conformational changes that are difficult to sample in atomistic simulations. cache = ./cache/cord-298242-iuskpoug.txt txt = ./txt/cord-298242-iuskpoug.txt === reduce.pl bib === id = cord-298227-av1ev8ta author = Kähler, Christian J. title = Fundamental protective mechanisms of face masks against droplet infections date = 2020-06-28 pages = extension = .txt mime = text/plain words = 7149 sentences = 376 flesch = 58 summary = Many governments have instructed the population to wear simple mouth-and-nose covers or surgical face masks to protect themselves from droplet infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in public. First of all, we show that the masks protect people in the surrounding area quite well, since the flow resistance of the face masks effectively prevents the spread of exhaled air, e.g. when breathing, speaking, singing, coughing and sneezing. Thirdly, we show that even simple mouth-and-nose covers made of good filter material cannot reliably protect against droplet infection in contaminated ambient air, since most of the air flows through gaps at the edge of the masks. However, if the distance rules cannot be observed and the risk of inhalation-based infection becomes high because many people in the vicinity are infectious and the air exchange rate is small, improved filtration efficiency masks are needed, to take full advantage of the three fundamental protective mechanisms these masks provide. cache = ./cache/cord-298227-av1ev8ta.txt txt = ./txt/cord-298227-av1ev8ta.txt === reduce.pl bib === id = cord-298172-iyxyennq author = Guo, Youjia title = Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date = 2020-10-02 pages = extension = .txt mime = text/plain words = 4557 sentences = 295 flesch = 49 summary = Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Among them, two antibodies were shown to attenuate the interaction of spike proteins with ACE2 and neutralized infection of VeroE6/TMPRSS2 cells by SARS-CoV-2. Mice were immunized with these recombinant spike proteins to generate antibodies against the SARS-CoV-2 virus, followed by cell fusion to generate a hybridoma-producing antibody. The performance of our antibodies in IP experiments prompted us to examine whether they were capable of inhibiting spike-ACE2 binding or even neutralizing SARS-CoV-2 infection. Our antibodies, S1D7 and S3D8, have been shown to attenuate the interaction of spike proteins with ACE2 and neutralize infection of VeroE6/TM2 cells by SARS-CoV-2. cache = ./cache/cord-298172-iyxyennq.txt txt = ./txt/cord-298172-iyxyennq.txt === reduce.pl bib === id = cord-298321-8871aifz author = Laamarti, Meriem title = Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2142 sentences = 123 flesch = 58 summary = The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes. Our recent study (13) based on the analysis of 30,983 genomes of SARS-CoV-2 variants belonging to 80 countries, revealed 5.67% of total mutations with a frequency greater than 1% of all the sequences analyzed suggesting that this virus is not yet adapted to its host. In all Moroccan SARS-CoV-2 genomes, the analysis of genetic variants revealed 61 mutations compared to the reference sequence (Fig 1) , including 29 non-syn(Fig 2A) . cache = ./cache/cord-298321-8871aifz.txt txt = ./txt/cord-298321-8871aifz.txt === reduce.pl bib === id = cord-298343-nvuc1j7t author = Ma, J. title = Exhaled breath is a significant source of SARS-CoV-2 emission date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2791 sentences = 170 flesch = 64 summary = Here, 35 COVID-19 subjects were recruited; exhaled breath condensate (EBC), air samples and surface swabs were collected and analyzed for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). COVID-19 patients were shown to exhale SARS-CoV-2 into the air at an estimated rate of 103-105 RNA copies/min; while toilet and floor surfaces represented two important SARS-CoV-2 reservoirs. Surface swabs from the cell phone and hands of one patient(ITA-YL1) tested negative for the virus, but the SARS-CoV-2 was present on the toilet pit surface in that patient's hotel room (Fig. 1C ). Although EBC samples from two patients (ITA-YW2 and UK-YJ1) were shown to 20 contain SARS-CoV-2, surface swabs from their cell phones, hands, and toilet surfaces were negative for the virus. . https://doi.org/10.1101/2020.05.31.20115154 doi: medRxiv preprint Out of 242 surface swab samples, 13 were positive for SARS-CoV-2 ( Fig. 3 and Table S4 ). cache = ./cache/cord-298343-nvuc1j7t.txt txt = ./txt/cord-298343-nvuc1j7t.txt === reduce.pl bib === id = cord-298079-hgdyxk98 author = Hsu, Jeffrey J. title = Heart Transplantation in the Early Phase of the COVID‐19 Pandemic: A Single‐Center Case Series date = 2020-07-12 pages = extension = .txt mime = text/plain words = 2096 sentences = 126 flesch = 53 summary = Here, we describe our center's experience with orthotopic heart transplantation (OHT) in one of the country's pandemic epicenters, where we performed eight OHTs in the first two months after community spread began in late February 2020. 3 Further, the effects of SARS-CoV-2 in highly immunosuppressed patients in the early post-transplant period are currently unclear. Current recommendations from the International Society of Heart and Lung Transplantation (ISHLT) is for all potential donors to undergo PCR-based testing for SARS-CoV-2. In our eight cases performed during the period of pandemic onset (Table) , none have become infected with SARS-CoV-2 to date, despite the growing number of cases in Los Angeles (Figure 1) . Similarly, the impact of SARS-CoV-2 infection in a patient with a newly transplanted cardiac graft is unclear, as to our knowledge, there are have yet to be any cases reported at the time of this communication. More evidence is needed to determine the risks of SARS-CoV-2 infection in newly transplanted patients. cache = ./cache/cord-298079-hgdyxk98.txt txt = ./txt/cord-298079-hgdyxk98.txt === reduce.pl bib === id = cord-298083-4h3tg6hg author = Ho, Tin-Yun title = Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein date = 2004-01-23 pages = extension = .txt mime = text/plain words = 3557 sentences = 208 flesch = 56 summary = In order to analyze the antigenicity and receptor-binding ability of SARS-CoV S protein, we expressed the S protein in Escherichia coli using a pET expression vector. By biotinylated ELISA and Western blot using biotin-labeled S protein as the probe, we identified 130-kDa and 140-kDa proteins in Vero cells that might be the cellular receptors responsible for SARS-CoV infection. Taken together, these results suggested that recombinant S protein exhibited the antigenicity and receptor-binding ability, and it could be a good candidate for further developing SARS vaccine and anti-SARS therapy. These data suggested that comparison of primary amino acid sequences does not provide insight into the receptor-binding specificity or antigenic properties of SARS-CoV S protein. To analyze the antigenicity of recombinant S protein, we performed Western blot and ELISA using sera from SARS patients or from spike-immunized rabbits. cache = ./cache/cord-298083-4h3tg6hg.txt txt = ./txt/cord-298083-4h3tg6hg.txt === reduce.pl bib === id = cord-298301-p1zj6jg9 author = Dey, Lopamudra title = Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date = 2020-09-03 pages = extension = .txt mime = text/plain words = 6298 sentences = 387 flesch = 49 summary = title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins A total of 1326 potential human target proteins of SARS-CoV-2 have been predicted by the proposed ensemble model and validated using gene ontology and KEGG pathway enrichment analysis. In this article, we have tried to predict the target human proteins of the SARS-CoV-2 virus based on their protein sequences combining amino acid composition, pseudo amino acid composition, and conjoint triad features using machine learning techniques. Subsequently, after feature reduction, we have used some popular supervised learning algorithms such as Support Vector Machine (SVM), Naive Bayes (NB), Random Forest (RF) and K-Nearest Neighbor (KNN) along with a deep multi-layer perceptron model and ensemble techniques (Voting classifier, XGBoost, AdaBoost) for classification and prediction. A total of 3 sets of sequence-based features, namely, amino acid composition, conjoint triad, and pseudo amino acid composition of the human proteins are considered to train the machine learning models. cache = ./cache/cord-298301-p1zj6jg9.txt txt = ./txt/cord-298301-p1zj6jg9.txt === reduce.pl bib === id = cord-298156-d0pb1kik author = Cheval, Sorin title = Observed and Potential Impacts of the COVID-19 Pandemic on the Environment date = 2020-06-10 pages = extension = .txt mime = text/plain words = 11027 sentences = 569 flesch = 47 summary = Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. The concept of disaster has evolved over time, and here we use an adapted Intergovernmental Panel on Climate Change (IPCC) definition: a disaster is an event, which severely alters the functioning of a community due to hazardous physical, biological or human related impacts leading to widespread adverse effects on multiple scales and systems (environment, economic, social). While negative impacts on the economy and society in general are probably huge, it is very likely that the global-scale reduction of economic activities due to the COVID-19 crisis triggers a lot of sensible improvements in environmental quality and climatic systems. cache = ./cache/cord-298156-d0pb1kik.txt txt = ./txt/cord-298156-d0pb1kik.txt === reduce.pl bib === id = cord-298490-p1msabl5 author = Obukhov, Alexander G. title = SARS-CoV-2 Infections and ACE2: Clinical Outcomes Linked With Increased Morbidity and Mortality in Individuals With Diabetes date = 2020-07-15 pages = extension = .txt mime = text/plain words = 6493 sentences = 319 flesch = 41 summary = As suggested by the recent reports regarding the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), upon entry into the host, this virus binds to the extracellular domain of ACE2 in nasal, lung, and gut epithelial cells through its spike glycoprotein subunit S1. In this Perspective, we bring attention to specific factors that may complicate COVID-19 in individuals with diabetes including 1) the presence of bone marrow changes (myeloidosis) that predispose those with diabetes to an excessive proinflammatory response (cytokine storm) and contribute to insulin resistance and reduced vascular repair, and worsening function of the heart, kidney, and systemic vasculature as a whole; 2) increased circulating furin levels that could cleave the spike protein and increase infectivity of SARS-CoV-2; 3) dysregulated autophagy that may promote replication and/or reduce viral clearance; and 4) gut dysbiosis that leads to widespread systemic inflammation, increased gut glucose and sodium absorption, and reduced tryptophan and other key amino acid absorption needed for incretin secretion and glucose homeostasis. cache = ./cache/cord-298490-p1msabl5.txt txt = ./txt/cord-298490-p1msabl5.txt === reduce.pl bib === id = cord-298406-7wfdwou8 author = Sun, Haifang title = Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus date = 2003-12-31 pages = extension = .txt mime = text/plain words = 2678 sentences = 161 flesch = 60 summary = title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus To facilitate the studies regarding the functions and structures of SARS_3CLpro, in this report the synthetic genes encoding 3CLpro of SARS_CoV were assembled, and the plasmid was constructed using pQE30 as vector and expressed in Escherichia coli M15 cells. In our previous work [24, 25] , we reported a 3D model of SARS_3CL pro and its inhibitor design by virtual screening, as well as the cloning, expression, and purification of the E protein of SARS_CoV. In this article, we would like to present the results describing the molecular cloning, expression and purification of 3CL pro of SARS_CoV, and the preliminary study on its mass spectrometric characterization is also reported. Expression and purification of SARS_3CL pro Escherichia coli M15 cells transformed with the plasmid pQE30-SARS_3CL pro were grown in 100 ml LB medium containing ampicillin (100 mg/L) and kanamycin (25 mg/L) at 37°C overnight and then inoculated into 1 L LB supplemented with both the antibiotics. cache = ./cache/cord-298406-7wfdwou8.txt txt = ./txt/cord-298406-7wfdwou8.txt === reduce.pl bib === id = cord-298098-4dfqlebp author = Xu, Ruodan title = Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System date = 2020-07-30 pages = extension = .txt mime = text/plain words = 3326 sentences = 173 flesch = 53 summary = In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Construction of SARS-CoV-2 VLPs was performed by co-transfecting cells with S, M, E, and N with molar ratio at 8:6:8:3 as shown in Figure 1 . To get better understanding of the secretory features of four SARS-CoV-2 structural proteins, we first transfected HEK-293T and Vero E6 cells with vectors expressing S, M, E, or N, respectively. In the current study, we described the efficient construction of SARS-CoV-2 VLPs by plasmid-driven transfection of viral structural proteins in mammalian cells. cache = ./cache/cord-298098-4dfqlebp.txt txt = ./txt/cord-298098-4dfqlebp.txt === reduce.pl bib === id = cord-298327-j04nyg5y author = Lv, Zhihua title = Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study date = 2020-05-18 pages = extension = .txt mime = text/plain words = 1892 sentences = 118 flesch = 51 summary = Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Preliminary analysis indicated that higher white blood cell and 129 neutrophil counts, as well as higher levels of D-dimer, IL-6, IL-10, CRP and PCT were found 130 in male patients compared to those of females, which was similar to patients in critical and 131 severe groups compared with those of mild groups (Table 2) . Higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, IL-6, 155 IL-10, CRP and PCT were observed in patients co-infected with other respiratory pathogens 156 than those of infected with SARS-CoV-2 homogeneously (Table 2) . cache = ./cache/cord-298327-j04nyg5y.txt txt = ./txt/cord-298327-j04nyg5y.txt === reduce.pl bib === id = cord-298725-da71febn author = Okuhama, Ayako title = Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan date = 2020-11-17 pages = extension = .txt mime = text/plain words = 1433 sentences = 100 flesch = 46 summary = title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Reports have been published on COVID-19 among patients receiving hemodialysis (2), but none have evaluated whether HD effluent is infectious. We report detection of SARS-CoV-2 RNA in hemodialysis effluent from a patient with COVID-19 pneumonia and prolonged inflammation. PCR results showed SARS-CoV-2 RNA of 157.9 copies/μL with cycle threshold (C t ) values of 38.3 at 1 hour after starting hemodialysis but were negative on effluent collected at 2 hours. In conclusion, we report positive qRT-PCR results for SARS-CoV-2 RNA from hemodialysis effluent in a patient receiving renal dialysis. cache = ./cache/cord-298725-da71febn.txt txt = ./txt/cord-298725-da71febn.txt === reduce.pl bib === id = cord-298679-w0yp4u19 author = Iftimie, Simona title = Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3587 sentences = 184 flesch = 48 summary = Logistic regression analyses showed that fever, pneumonia, acute respiratory distress syndrome, diabetes mellitus and cancer were the variables that showed independent and statistically significant associations with mortality. This is one of the first studies to describe the factors associated with mortality in patients infected with SARS-CoV-2 in Spain, and one of the few in the Mediterranean area. The objective of the present study has been to characterize our patients' epidemiology and to identify the risk factors associated with mortality for this disease in our geographical area. Logistic regression analyses showed that the presence of fever, pneumonia, acute respiratory distress syndrome, type 2 diabetes mellitus and cancer were the only variables that showed an independent and statistically significant association with mortality when they were adjusted for differences in age, gender, smoking status and alcohol intake (Tables 2 and 3) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-298679-w0yp4u19.txt txt = ./txt/cord-298679-w0yp4u19.txt === reduce.pl bib === id = cord-298696-rsifxvtj author = Lim, Meng-Kin title = Global response to pandemic flu: more research needed on a critical front date = 2006-10-13 pages = extension = .txt mime = text/plain words = 2257 sentences = 100 flesch = 50 summary = Given that air transportation is the one feature that most differentiates present day transmission scenarios from those in 1918, our present inability to prevent spread of influenza by international air travel, as reckoned by the World Health Organization, constitutes a major weakness in the current global preparedness plan against pandemic flu. Alas, the 2005 WHO report Avian influenza: assessing the pandemic has dismally concluded that "If only a few countries are affected, travel-related measures, such as exit screening for persons departing from affected areas, might delay international spread somewhat, but cannot stop it. Against a conservatively estimated US$800 billion a year that a human pandemic of avian influenza could cost the global economy [24] , not to mention the incalculable cost in terms of human lives [25] , it seems incredible that the aviation lessons of SARS have not led to an acceleration of scientific research and health policy evaluation aimed at strengthening public health defenses on the air transportation front. cache = ./cache/cord-298696-rsifxvtj.txt txt = ./txt/cord-298696-rsifxvtj.txt === reduce.pl bib === id = cord-298281-wkje5jyt author = Chan, Vinson Wai-Shun title = A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3492 sentences = 271 flesch = 54 summary = Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Primary outcomes of our study included urological manifestations of COVID-19, detection rates of SARS-CoV-2 viral RNA in urine and stool samples, and special considerations in urological conditions. For the urological manifestations and viral RNA detection rates, data were pool analysed using MetaXL and Microsoft Excel when there are two or more studies with at least four patients reporting the same outcome under the same definition. There were a total of 11 studies that reported the number of patients who had their urine tested for SARS-CoV-2 viral RNA. Our meta-analysis included 12 studies that reported the number of patients with stools tested for SARS-CoV-2 viral RNA. Our study showed that 5.74% of the COVID-19 patients had positive viral RNA in urine samples. cache = ./cache/cord-298281-wkje5jyt.txt txt = ./txt/cord-298281-wkje5jyt.txt === reduce.pl bib === id = cord-298440-0pb8ssj2 author = Rascón-Ramírez, Fernando J title = Supra and infratentorial massive strokes in previously healthy young patients with SARS-CoV-2. The role of neurosurgery date = 2020-09-06 pages = extension = .txt mime = text/plain words = 1428 sentences = 94 flesch = 50 summary = COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). Keywords: Cerebrovascular disease; COVID-19; Coronavirus; stroke; decompressive craniectomy; Cerebellar; SARS-CoV-2. We present two massive supra and infratentorial strokes in people of young age with no known risk factors and with the severe acute respiratory syndrome (SARS-CoV-2), requiring Endotracheal Intubation (ETI). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. cache = ./cache/cord-298440-0pb8ssj2.txt txt = ./txt/cord-298440-0pb8ssj2.txt === reduce.pl bib === id = cord-298350-pq1dcz3a author = Ryan, Jeffrey R. title = Category C Diseases and Agents date = 2016-03-25 pages = extension = .txt mime = text/plain words = 7266 sentences = 451 flesch = 57 summary = Specific examples explored in this chapter include Nipah virus, hantavirus, West Nile fever virus, and the coronaviruses that cause severe acute respiratory syndrome and Middle East respiratory syndrome. Remarkably, researchers noted that human case patients had an association with infected animals from a concurrent and severe outbreak of respiratory disease in pigs and that there was a notable absence of illness in children. Research shows that many HPS case patients acquired the virus after having been in frequent contact with rodents or their droppings for long periods (Centers for Disease Control and Prevention, Special Pathogens Branch, 2007) . Initially, Saint Louis encephalitis virus was believed to be the cause of the human infections until WNV was isolated from the human and animal specimens. Patients infected with the SARS-coronavirus disease are likely to present to health-care facilities. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia cache = ./cache/cord-298350-pq1dcz3a.txt txt = ./txt/cord-298350-pq1dcz3a.txt === reduce.pl bib === id = cord-298639-v9yg80jw author = Chen, Yuxin title = High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients date = 2020-06-04 pages = extension = .txt mime = text/plain words = 3369 sentences = 178 flesch = 51 summary = Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. Briefly, 96-well plates were coated with 500 ng/mL of recombinant RBD or NP protein overnight, incubating with diluted were also collected and the nasopharyngeal swab samples from these patients have been repeatedly tested as negative for SARS-CoV-2 RNA at least twice at a two-day apart. Our study proved that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. cache = ./cache/cord-298639-v9yg80jw.txt txt = ./txt/cord-298639-v9yg80jw.txt === reduce.pl bib === id = cord-298505-r7ihqb96 author = Górski, Andrzej title = Sepsis, Phages, and COVID-19 date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3735 sentences = 226 flesch = 47 summary = In fact, in addition to data obtained in experimental animals, there are already reports of successful phage therapy in patients with sepsis [2] . Phage therapy efficacy has also been studied in a mouse model of neonatal sepsis caused by Escherichia coli, Klebsiella pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Citrobacter freundii and Moraxella catarrhalis. High effectiveness of phage therapy in the treatment of experimental sepsis induced by multidrug resistant P. Further progress in phage therapy of sepsis has recently been achieved by introducing engineered phages used to treat a patient with a disseminated drug resistant mycobacterial infection. In recent years, a number of reports derived from experimental studies in animals and human clinics have suggested the potential value of phage therapy in the treatment of sepsis. The anti-inflammatory and the immunomodulating properties of phages could also be useful in the treatment of severe COVID-19 syndrome including viral sepsis (Table 2) . cache = ./cache/cord-298505-r7ihqb96.txt txt = ./txt/cord-298505-r7ihqb96.txt === reduce.pl bib === id = cord-298482-r7lallv0 author = De Maio, Flavio title = Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis date = 2020-09-04 pages = extension = .txt mime = text/plain words = 1739 sentences = 86 flesch = 54 summary = title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. The amino acid sequence of the SARS-CoV-2 Envelope protein was extracted, and the NMR structure of the 119 homologous protein of SARS-CoV (PDB code: 2MM4) was used as a template. In Figure 1B and 1C, the two predicted monomeric E full length protein structure models have been 159 constructed and show N-terminal (blue), transmembrane (green), C-terminal domains (red) as well as the 160 amino acid variants (yellow). In order to verify the potential implications of the altered amino acid sequence, the binding pose of the two 174 C-terminus octapeptides belonging to SARS-CoV and SARS-CoV-2 were determined and compared with 175 the crystallographic structure of the complex PALS1-CRB1[31]. cache = ./cache/cord-298482-r7lallv0.txt txt = ./txt/cord-298482-r7lallv0.txt === reduce.pl bib === id = cord-298693-x25r0gtt author = Advani, Sonali D. title = Are we forgetting the “universal” in universal masking? Current challenges and future solutions date = 2020-07-16 pages = extension = .txt mime = text/plain words = 844 sentences = 53 flesch = 49 summary = Overall, HCP compliance with protective measures such as universal masking often correlates with the level of risk they perceive. Earlier this year, public health authorities pointed out a lack of evidence related to the use of universal masking by the general public to prevent acquisition of SARS-CoV-2. Inconsistent, contradictory and unclear advice from public health authorities has contributed to widespread confusion about the utility of universal masking in preventing the spread of SARS-COV-2 (response efficacy). COVID-19 fatigue, a term that describes drift in following preventative measures as this pandemic goes on, is an important cause of poor compliance with policies related to universal masking. Finally, we need clear, simple, and consistent messaging from public health authorities for successful implementation of universal masking policies. Our goal should be to focus on the simple message of universal masking to prevent the transmission of SARS-CoV-2. cache = ./cache/cord-298693-x25r0gtt.txt txt = ./txt/cord-298693-x25r0gtt.txt === reduce.pl bib === id = cord-298894-t5hyfum3 author = Rifino, Nicola title = Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital, Bergamo, Italy date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4682 sentences = 247 flesch = 44 summary = Neurological manifestations were classified as: (a) cerebrovascular disease [53 pts (38.7%)] including 37 ischemic and 11 haemorrhagic strokes, 4 transient ischemic attacks, 1 cerebral venous thrombosis; (b) peripheral nervous system diseases [31 (22.6%)] including 17 Guillain–Barrè syndromes; (c) altered mental status [49 (35.8%)] including one necrotizing encephalitis and 2 cases with RT-PCR detection of SARS-Cov-2 RNA in CSF; (d) miscellaneous disorders, among whom 2 patients with myelopathy associated with Ab anti-SARS-CoV-2 in CSF. COVID-19 diagnosis was confirmed: (1) by real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) on nasopharyngeal specimens [13] ; or (2) by RT-PCR on bronchoalveolar lavage (BAL) obtained by bronchoscopy in case of high clinical suspicion of SARS-CoV-2 infection and negative test results on at least two nasopharyngeal swabs performed at least 24 h apart; or (3) in the presence of characteristic radiological interstitial pneumonia associated with typical symptoms (fever, dry cough, dyspnea), even with negative RT-PCR, with no other possible aetiologic explanation. cache = ./cache/cord-298894-t5hyfum3.txt txt = ./txt/cord-298894-t5hyfum3.txt === reduce.pl bib === id = cord-298669-g2up0cfi author = Pollock, David D title = Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 3261 sentences = 158 flesch = 52 summary = Nevertheless, the evolutionary reasons for low GC content are still debated in even exceptionally well-studied systems with unquestioned animal origins (2020) points out, the mammalian zinc finger antiviral protein (ZAP) binds to CpG dinucleotides in viral RNA genomes and inhibits viral replication and mediates viral degradation (Ficarelli et al., 2020; Ficarelli et al., 2019; Meagher et al., 2019; Takata et al., 2017) . Despite this, Xia (2020) speculated that low viral genomic CpG levels in SARS-CoV-2 required evolutionary time in a previous host species and tissue that more actively selected for CpG depletion than do bats. In addition to being unsupported by positive evidence, Xia's (2020) hypothesis for dogs as intermediate hosts of ancestral viruses giving rise to SARS-CoV-2 requires an unlikely history of cross-species viral transmission (see Fig. 2 for potential hypotheses) for which there is no evidence. cache = ./cache/cord-298669-g2up0cfi.txt txt = ./txt/cord-298669-g2up0cfi.txt === reduce.pl bib === id = cord-298777-hit7rs6q author = Zhang, Linjie title = What we know so far about Coronavirus Disease 2019 in children: A meta‐analysis of 551 laboratory‐confirmed cases date = 2020-06-10 pages = extension = .txt mime = text/plain words = 3869 sentences = 250 flesch = 58 summary = We conducted this systematic review and meta-analysis of currently available studies to summarize what we know so far about the epidemiological, clinical, radiological, and laboratory features, as well as therapeutic and prognostic aspects, of COVID-19 in children. To be included in this review, studies needed to meet the following criteria: (a) Study design: randomized trials, observational studies (cross-sectional, cohort and case-control), case series or case reports, and research letters; (b) Participants: children up to 18 years of age with laboratory-confirmed COVID-19; (c) Variables: epidemiological and demographic characteristics, clinical, radiological and laboratory findings, treatments, and prognosis. Thus, 46 articles [7] [8] [9] 14, 15, reporting 551 laboratory-confirmed cases of COVID-19 in children were included in the review (Figure 1 ). A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study cache = ./cache/cord-298777-hit7rs6q.txt txt = ./txt/cord-298777-hit7rs6q.txt === reduce.pl bib === id = cord-298461-tyhtdawb author = Zhao, L. title = COVID-19: Effects of weather conditions on the propagation of respiratory droplets date = 2020-05-25 pages = extension = .txt mime = text/plain words = 7832 sentences = 475 flesch = 55 summary = This study investigates the influence of weather conditions including temperature, humidity and wind velocity, on the transmission of SARS-CoV-2-containing respiratory droplets. We suggest that the current pandemic may not ebb over the summer without continuous and proper public health intervention, because (1) in hot and dry weather, respiratory droplets more easily evaporate into aerosol particles capable of long-range transmission; (2) infectious PM2.5 that can infiltrate deeply into our lung has a longer suspension time in hot and dry weather; (3) many public spaces implement air-conditioning systems that can still operate at temperature and humidity setpoints that favor droplet transport. . https://doi.org/10.1101/2020.05.24.20111963 doi: medRxiv preprint Key parameters considered in the model include the distribution of initial droplet size d0, initial velocity v0, environmental temperature T ∞ , relative humidity RH, air velocity Vair, whose values are given here. cache = ./cache/cord-298461-tyhtdawb.txt txt = ./txt/cord-298461-tyhtdawb.txt === reduce.pl bib === id = cord-298075-lzuxlzb0 author = Mao, Kang title = Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology? date = 2020-03-23 pages = extension = .txt mime = text/plain words = 1095 sentences = 52 flesch = 46 summary = However, an alternative method utilizing wastewater-based epidemiology (WBE), may provide an effective approach to predict the potential spread of the infection by testing for infectious agents in wastewater, which has been approved as an effective way to trace illicit drugs, and obtain information on health, disease, and pathogens. Therefore, it is critical to develop efficient transportable and robust analytical tools to accurately and quickly trace low-level SARS-CoV-2 sources through WBE to confirm these suspected cases and screen asymptomatic infected cases without centralized laboratories. We believe that in the case of asymptomatic infections in the community or people are not sure whether they are infected or not, rapid and real-time community sewage detection through paper analytical devices can determine whether there are SARS-CoV-2 carriers in the area in a timely manner to enable rapid screening, quarantine, and prevention. The potentially infected patient will also benefit from paper analytical device tracing SARS-CoV-2 sources with WBE, providing information for the correct and timely treatment of COVID-19. cache = ./cache/cord-298075-lzuxlzb0.txt txt = ./txt/cord-298075-lzuxlzb0.txt === reduce.pl bib === id = cord-298426-hhly45md author = Zhang, Shan-Yan title = Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China date = 2020-07-08 pages = extension = .txt mime = text/plain words = 3726 sentences = 207 flesch = 52 summary = title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China CONCLUSIONS: Clinicians should pay close attention to these features in patients with COVID-19 including older age, male, fever, cough, hemoptysis, gastrointestinal symptoms and hypertension to identify the severity of illness as early as possible. Hence, the aim of our study is to summarize the epidemiologic and clinical characteristics, laboratory and radiograph findings, treatments, and outcomes of different subtypes of patients with COVID-19 in Zhejiang Province. We conducted a retrospective study investigating on the epidemiological, clinical, laboratory, radiograph, treatments and outcomes characteristics of confirmed cases of COVID-19 in Zhejiang Province from 17 January to 12 February 2020. Several risk factors for the severity of illness in patients with COVID-19 were identified in our study including male, fever, cough, hemoptysis, gastrointestinal symptoms, hypertension, and higher age-grading. cache = ./cache/cord-298426-hhly45md.txt txt = ./txt/cord-298426-hhly45md.txt === reduce.pl bib === id = cord-298886-xidaim04 author = Leszczyński, Piotr title = COVID-19: a short message to rheumatologists date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1571 sentences = 71 flesch = 42 summary = In the treatment of cytokine storm in COVID-19, there is a possibility of using a TNF alpha inhibitor (adalimumab) or IL-6 receptor inhibitors (tocilizumab, sarilumab) [6] [7] [8] , which are currently being studied in randomized clinical trials in SARS-CoV-2 infected patients with signs and symptoms of rapidly progressing pneumonia. Our own experience with the combined use of chloroquine and azithromycin or ceftriaxone (n = 34) and tocilizumab (n = 1) in the treatment of severe pneumonia in the course of COVID-19 disease is very good, although it should only be considered as a series of cases (Figs. In accordance with some clinical concerns of rheumatologists, patients with rheumatic diseases treated with disease-modifying drugs (DMARDs) should have a higher risk of SARS-CoV-2 infection. Patient with pharmacologically treated rheumatic disease after close contact (staying at a distance of less than 2 m, for more than 15 minutes, in the last 7 days) with a person with confirmed SARS-CoV-2 infection without clinical symptoms of COVID-19: cache = ./cache/cord-298886-xidaim04.txt txt = ./txt/cord-298886-xidaim04.txt === reduce.pl bib === id = cord-298991-5qae0ege author = Aiello, Francesco title = Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3143 sentences = 183 flesch = 50 summary = SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients' conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. This systematic review will firstly attempt to analyse the current knowledge on SARS-CoV-2 colonization of ocular and periocular tissues and secretions (i.e., cornea, conjunctiva, lacrimal sac, and tears), in order elucidate if conjunctival transmission occurs, and secondarily aims to propose a potential diagnostic tool in the evaluation of suspected, infected patients. Due to the scant evidence, both original articles, editorials, letters, and reviews providing evidence (i.e., prevalence, anecdotal report) about SARS-CoV-2 colonization of ocular and periocular tissues and secretions were all included in the study. This systematic review analysed 252 SARS-CoV-2infected patients globally who underwent conjunctival swab, and demonstrates the prevalence of ocular conjunctivitis complicating the course of COVID-19 to be as high as 32% (12 patients out 38) , differently as what Lu et al. cache = ./cache/cord-298991-5qae0ege.txt txt = ./txt/cord-298991-5qae0ege.txt === reduce.pl bib === id = cord-298866-dzatps7b author = Licskai, Christopher title = Key highlights from the Canadian Thoracic Society’s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1545 sentences = 94 flesch = 48 summary = title: Key highlights from the Canadian Thoracic Society's Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic In general, asthma maintenance and exacerbation management should continue according to national and international guidelines during the COVID-19 pandemic, however treatment decisions should be individualized based on patient characteristics. 6, 7, 8 Are patients with asthma at risk of having an exacerbation triggered by SARS-CoV-2 (COVID 19)? The Centers for Disease Control identify people with asthma as a group that may be at higher risk for severe illness from COVID-19. No. Asthma patients should restart or continue their prescribed inhaled corticosteroid or inhaled corticosteroid steroid plus long-acting beta 2 -agonist maintenance therapy to improve disease control and to reduce the severity of exacerbations, including exacerbations that may be caused by SARS-CoV-2. Yes. There is no evidence that inhaled corticosteroids increase the risk of acquiring COVID-19 or that inhaled corticosteroids increase the severity of infection. cache = ./cache/cord-298866-dzatps7b.txt txt = ./txt/cord-298866-dzatps7b.txt === reduce.pl bib === id = cord-298773-vnmc6nqd author = Pfeiffer, Julie K. title = Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? date = 2015-01-20 pages = extension = .txt mime = text/plain words = 1713 sentences = 87 flesch = 50 summary = title: Is the Debate and "Pause" on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? This letter is about the potential impact of the debate and pause on graduate students and postdoctoral fellows and how their future plans may be affected. To gain initial insight into how the debate and research pause have affected trainees, I created an informal survey 2 days before the National Academy of Sciences meeting. These projects involve a subset of "gain of function" experiments designed to create mouse adapted viral strains, generate drug resistant viruses to understand drug mechanisms of action, understand host immunity by analyzing viruses with resistance to certain host immune pathways, and to study factors that influence transmission by the respiratory route (which was made famous by work from the Kawaoka and Fouchier labs in 2012). Third, the debate and research pause are influencing future plans of virology trainees. cache = ./cache/cord-298773-vnmc6nqd.txt txt = ./txt/cord-298773-vnmc6nqd.txt === reduce.pl bib === id = cord-298722-rmibv5z7 author = Abdel-latif, Rania G title = Statin therapy and SAR-COV-2: an available and potential therapy? date = 2020-05-07 pages = extension = .txt mime = text/plain words = 712 sentences = 49 flesch = 39 summary = 4 In fact, some observational data suggest that moderate dose statin therapy was associated with lower mortality among patients with influenza pneumonia. 9 Host ACE2 receptors utilized by SARS-CoV-2 might be potential targets for viral therapeutic intervention. 10 Clinical studies are encouraged to investigate the effect of ACE2 expression in protection against respiratory distress and the role of statin therapy for this postulated hypothesis. Further clinical studies are warranted to evaluate the efficacy of statin therapy against COVID-19 and determine the effective therapeutic dose. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region, Italy Cardiovascular implications of fatal outcomes of patients with coronavirus disease 2019 (COVID-19) Statins reduce the expression of proinflammatory cytokines in influenza A virus infected CrFK cells A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury cache = ./cache/cord-298722-rmibv5z7.txt txt = ./txt/cord-298722-rmibv5z7.txt === reduce.pl bib === id = cord-298716-pubhq564 author = Bryche, Bertrand title = Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3558 sentences = 212 flesch = 56 summary = title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. We measured the OE thickness, the OSN cilia quality (based on Golf staining) and the immune cell infiltration of the olfactory mucosa (based on the Iba1 staining) on 6 images per animal taken from 3 different slides spread along the nasal cavity. Two recent reports indicate that olfactory neurons in hamster (Sia et al., 2020) and respiratory cells in ferret (Ryan et al., 2020) may be the target of SARS-CoV-2 but these studies did not focus on the nasal cavity and they did not use double staining to clearly identify the infected cells in the OE. cache = ./cache/cord-298716-pubhq564.txt txt = ./txt/cord-298716-pubhq564.txt === reduce.pl bib === id = cord-298902-afek8kgr author = Li, Xingguang title = Transmission dynamics and evolutionary history of 2019‐nCoV date = 2020-02-14 pages = extension = .txt mime = text/plain words = 2020 sentences = 104 flesch = 46 summary = To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019‐nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. 19 In the present study, we investigated the time origin and genetic diversity of 2019-nCoV in humans based on 32 genomes of virus strains sampled from China, Thailand, and the USA with known sampling dates between 24 December 2019 and 23 January 2020. Likelihood-mapping analysis of "dataset_14" revealed that 100% of the quartets were distributed in the center of the triangle, indicating a strong star-like topology signal reflecting a novel virus, which may be due to exponential epidemic spread ( Figure 1A) . Of note, the strong star-like signal (100% of quartets were distributed in the center of the triangle) from "dataset_14" at the beginning of the virus outbreak suggests that 2019-nCoV initially exhibited low genetic divergence, with recent and rapid human-tohuman transmission. cache = ./cache/cord-298902-afek8kgr.txt txt = ./txt/cord-298902-afek8kgr.txt === reduce.pl bib === id = cord-298899-lkrmg5qr author = Xie, Yewei title = Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date = 2020-08-31 pages = extension = .txt mime = text/plain words = 6242 sentences = 368 flesch = 53 summary = To fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, CT results, and risk factors of the COVID-19. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study cache = ./cache/cord-298899-lkrmg5qr.txt txt = ./txt/cord-298899-lkrmg5qr.txt === reduce.pl bib === id = cord-298850-tgxfki7n author = Figuero-Pérez, Luis title = Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1027 sentences = 84 flesch = 49 summary = title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab Several studies have proposed that anti-IL-6 receptor antibodies, such as tocilizumab, play an important role in the treatment of severe acute respiratory infection associated with SARS-CoV-2. We present a case report of a 51-year-old man diagnosed with severe respiratory infection associated with SARS-CoV-2 that was refractory to antiviral and anti-IL-6 treatment, with a favourable clinical outcome and analytical improvement after treatment with anti-IL-1 (anakinra). We present the case of a 51-year-old patient with bilateral pneumonia secondary to SARS-CoV-2 infection refractory to treatment with tocilizumab who showed improvement after treatment with anakinra. The "cytokine storm" secondary to SARS-CoV-2 infection determines severe COVID-19 disease. 3 The use of anti-IL-6 antibodies in the treatment of SARS-CoV-2 infection is currently under study, being one of the current pillars of COVID-19 disease treatment. cache = ./cache/cord-298850-tgxfki7n.txt txt = ./txt/cord-298850-tgxfki7n.txt === reduce.pl bib === id = cord-298989-qk0k2lmz author = , Umesh title = Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3226 sentences = 179 flesch = 52 summary = title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. SARS-CoV-2 main protease, a potential drug target, crystal structure (PDB-ID: 6Y84) was available and used for docking simulation and identification of potential drug molecule form Indian spices. Details of various kinds of interaction shown between the amino acids near the active site of SARS-CoV-2 main protease along with their respective inhibitor constant (Ki) and biological source and binding energy. Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study cache = ./cache/cord-298989-qk0k2lmz.txt txt = ./txt/cord-298989-qk0k2lmz.txt === reduce.pl bib === id = cord-299422-s5evsj96 author = Abdollahi, Alireza title = The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types date = 2020-05-23 pages = extension = .txt mime = text/plain words = 2909 sentences = 139 flesch = 50 summary = CONCLUSION: Similar to several previous studies about other viral diseases' association with ABO histo-blood groups, we have concluded that an individual's ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. Previous researches have proved the potential role of ABO blood groups on a host's genetic susceptibility to various viral diseases such as influenza, Ebola, enteric viruses, and SARS-CoV infections (8) (9) (10) (11) (12) . In the present study, 397 COVID-19 patients and 500 normal controls were analyzed to evaluate the association of the ABO histo-blood group phenotypes with COVID-19 disease in the Iranian population. Further studies are required to determine the exact mechanism through which ABO blood group influences COVID-19 susceptibility, which could be helpful in patient management and disease control. However, our results were discordant regarding the ABO histo-blood antigens which make people susceptible to COVID-19 (AB versus A histo-blood group phenotype in Iran and China, respectively). cache = ./cache/cord-299422-s5evsj96.txt txt = ./txt/cord-299422-s5evsj96.txt === reduce.pl bib === id = cord-298920-1lc2xf7u author = Bello-Perez, Melissa title = Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date = 2020-07-05 pages = extension = .txt mime = text/plain words = 6863 sentences = 326 flesch = 40 summary = Along this line, the generation of these coronavirus-induced autophagosomes requires the PtdIns3P-enrichment of the ER membrane outer leaflet, and the recruitment of ZFYVE1/DFCP1 (a key protein in omegasome formation), WIPI1/2, ATG5 and LC3-II (all components of the autophagic machinery), and SQSTM1/p62 (a receptor protein for selective autophagy) [31, 50, 51] . Briefly, chloroquine, apart from disorganizing the Golgi, induces lysosomal alkalinization, which prevents amphisome/autophagosome-lysosome fusion and blocks the vesicle trafficking system [53] [54] [55] 93] , which potentially affects the replication cycle of coronavirus systemically, including their entry, which is mediated by pH-dependent endocytosis and requires a low pH for the S protein to trigger its membrane fusion activity [94, 95] . Nitazoxanide is another late-stage autophagy blocker [96] that shows high anti-SARS-CoV-2 activity in cell cultures (IC 50 : 2.12 µM) [97] , although it should be considered that its main metabolite, tizoxanide, induces autophagy by inhibiting the PI3K-AKT-MTOR pathway [98] . cache = ./cache/cord-298920-1lc2xf7u.txt txt = ./txt/cord-298920-1lc2xf7u.txt === reduce.pl bib === id = cord-298967-vjyh1xvh author = Bertossi, Dario title = Safety guidelines for non‐surgical facial procedures during covid‐19 outbreak date = 2020-06-07 pages = extension = .txt mime = text/plain words = 2005 sentences = 130 flesch = 51 summary = METHODS: A virtual meeting was conducted with the members (n=12) of the European Academy of Facial Plastic Surgery Focus Group to outline the safety protocol for the non‐surgical facial aesthetic procedures for aesthetic practices in order to protect the clinic staff and the patients from SARS‐CoV‐2 infection. While many medical Accepted Article practices are being run with online consultations 10 , some countries have recently decided to allow the opening of practices requiring one-on-one contact like dental, physiotherapy, for emergencies provided they strictly follow the guidelines detailing the infection control measures [12] [13] . In our largely elective field, both staff and resources should ideally be allocated through careful protocols in order to prevent COVID-19 infection. In response to this pandemic, our focus group has developed a process to stratify procedures and clinical levels with protocols that aim to minimize the risk of contagion and the diffusion of COVID-19 infection. cache = ./cache/cord-298967-vjyh1xvh.txt txt = ./txt/cord-298967-vjyh1xvh.txt === reduce.pl bib === id = cord-299156-1dwsm3ie author = Shemer, Asaf title = Ocular involvement in coronavirus disease 2019 (COVID-19): a clinical and molecular analysis date = 2020-09-14 pages = extension = .txt mime = text/plain words = 3509 sentences = 214 flesch = 56 summary = The aim of this study was to assess the clinical and molecular ocular involvement among patients with confirmed COVID-19 admitted to a tertiary care facility. CONCLUSIONS: Among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was noted in one out of five cases, and was associated with loss of smell and taste. Among patients with COVID-19, active conjunctival injection was associated with loss of smell and loss of taste as part of the clinical presentation (66.7% vs 7.7%, p = 0.018). In this study, we evaluated the ocular signs and symptoms, as well as the presence of SARS-CoV-2 in conjunctival swab samples among patients with COVID-19 in one tertiary referral center during March and April of 2020. To conclude, among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was present in 19% of cases and was associated with loss of smell and taste as part of the clinical presentation. cache = ./cache/cord-299156-1dwsm3ie.txt txt = ./txt/cord-299156-1dwsm3ie.txt === reduce.pl bib === id = cord-299449-226dd23u author = Bernhardt, Denise title = Neuro-oncology Management During the COVID-19 Pandemic With a Focus on WHO Grade III and IV Gliomas date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4200 sentences = 221 flesch = 45 summary = It is acknowledged that the SARS-CoV-2 pandemic will require center specific discussions of appropriate resource allocation that considers patient and provider safety, resource constraints, and a realistic evaluation of the impact of therapy upon Incurable brain tumors. This international multidisciplinary group of experts in HGG provides a risk-adapted framework for decisions in both pandemic scenarios, considering both ethical issues and resource constraints, in order to minimize the irreparable damage associated with withholding necessary treatments. We recognize that during the pandemic the challenges of ICU capacity, conservation of PPE, availability of health care professional expertise and the risk for patients' exposure to SARS-CoV-2 may reduce the ability to provide optimal surgical management. Patients and caregivers should be included in the decision-making process as much as possible, and this should include all relevant data on chemotherapy and radiotherapy, as well as the individual risk profile associated with a potential SARS-CoV-2 infection. cache = ./cache/cord-299449-226dd23u.txt txt = ./txt/cord-299449-226dd23u.txt === reduce.pl bib === id = cord-299432-lbv69du4 author = Franklin, Alan B. title = Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen date = 2020-05-12 pages = extension = .txt mime = text/plain words = 2104 sentences = 126 flesch = 56 summary = Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal waste water treatment plants into the natural aquatic environment where potential wildlife hosts become infected. Here, we propose a plausible mechanism where SARS-CoV-2, the pathogen causing the disease COVID-19, could spillover from infected humans into novel wildlife hosts in North America. While the primary risk associated with the current COVID-19 outbreak appears to be humanto-human transmission of SARS-CoV-2, we believe the existing evidence also supports the plausibility of novel coronaviruses, such as SARS-CoV-2, spilling over to new wildlife hosts through fecal shedding by infected humans and introduction to the natural aquatic environment via the waste water treatment system. cache = ./cache/cord-299432-lbv69du4.txt txt = ./txt/cord-299432-lbv69du4.txt === reduce.pl bib === id = cord-299354-rmjohbse author = Chen, Fu-Lun title = Co-infection with an atypical pathogen of COVID-19 in a young date = 2020-05-21 pages = extension = .txt mime = text/plain words = 126 sentences = 20 flesch = 70 summary = key: cord-299354-rmjohbse authors: Chen, Fu-Lun; Wang, Cheng-Hui; Hung, Ching-Sheng; Su, Ying-Shih; Lee, Wen-Sen title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.05.007 sha: doc_id: 299354 cord_uid: rmjohbse nan Dear Editor: The article by Jean et al. Treatment options for COVID-19: The reality and challenges Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV Recommendations and guidelines for the treatment of pneumonia in Taiwan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical characteristics of coronavirus disease 2019 in China cache = ./cache/cord-299354-rmjohbse.txt txt = ./txt/cord-299354-rmjohbse.txt === reduce.pl bib === id = cord-299105-3ivzmiqn author = Cheng, Yi‐Qiang title = Deciphering the Biosynthetic Codes for the Potent Anti‐SARS‐CoV Cyclodepsipeptide Valinomycin in Streptomyces tsusimaensis ATCC 15141 date = 2006-03-01 pages = extension = .txt mime = text/plain words = 3774 sentences = 221 flesch = 52 summary = Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors d‐α‐hydroxyisovaleric acid and l‐lactic acid. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors D-a-hydroxyisovaleric acid and L-lactic acid. The respective adenylation domains in these two modules contain novel substrate-specificity-conferring codes that might specify for a class of hydroxyl acids for the biosynthesis of the depsipeptide natural products. The key element of this approach is to sequence a certain number of random genomic clones and to identify candidate gene(s) involved in natural product biosynthesis. cache = ./cache/cord-299105-3ivzmiqn.txt txt = ./txt/cord-299105-3ivzmiqn.txt === reduce.pl bib === id = cord-299133-09mbiqrr author = Smither, Sophie J. title = Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1391 sentences = 81 flesch = 57 summary = title: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity In this study, the ability of SARS-CoV-2 to survive in the dark, at two different relative humidity values and within artificial saliva, a clinically relevant matrix, was investigated. SARS-CoV-2 was found to be stable, in the dark, in a dynamic small particle aerosol under the four experimental conditions we tested and viable virus could still be detected after 90 minutes. A recent study has shown the Washington variant of SARS-CoV-2 remains viable in a small particle aerosol for long periods [2] . Here we extend that research to look at a UK variant of SARS-CoV-2 in aerosols, at different relative humidity values, and in artificial saliva. SARS-CoV-2 England-2 variant was aerosolised in tissue culture media or in artificial saliva and maintained in a dynamic aerosol at medium RH (40-60%) or high RH (68-88%) (Supplementary Material: Table 1 ). cache = ./cache/cord-299133-09mbiqrr.txt txt = ./txt/cord-299133-09mbiqrr.txt === reduce.pl bib === id = cord-299443-nggl87u6 author = Stockman, Lauren J. title = Coronavirus Antibodies in Bat Biologists date = 2008-06-17 pages = extension = .txt mime = text/plain words = 1009 sentences = 55 flesch = 59 summary = To address the possibility that the antibodies from this serum sample were not specifi c to SARS-CoV, we tested it against recombinant N proteins of human CoVs, HCoV-229E, HCoV-OC43, NL63, and HKU-1. If the antibodies were induced by a SARS-like CoV infection, we would expect to have also detected antibodies against recombinant S protein (9) or recombinant fragments representing antigenically distinct regions of the N protein of SARS-CoV. We did not detect either; instead, we detected antibodies against the antigenically distinct N fragments from group 1 and 2 human CoVs. Thus, this survey of a sample of bat biologists, who were exposed primarily to North American bats but also to bats from Asia and Africa, showed no evidence of SARSlike CoV infection. Recombinant protein-based assays for detection of antibodies to severe acute respiratory syndrome coronavirus spike and nucleocapsid proteins. Antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (SARS) coronavirus and polyclonal antisera of antigenic group I animal coronaviruses: implication for SARS diagnosis cache = ./cache/cord-299443-nggl87u6.txt txt = ./txt/cord-299443-nggl87u6.txt === reduce.pl bib === id = cord-299024-jkqdzt87 author = Mangner, Norman title = Paraneoplastic syndrome and SARS-CoV-2 – incremental effect of two thrombogenic conditions? date = 2020-10-21 pages = extension = .txt mime = text/plain words = 1071 sentences = 65 flesch = 40 summary = We present the case of a patient with a non-bacterial thrombotic aortic valve endocarditis experiencing severe thromboembolic complications and an acute right internal carotid artery occlusion in the context of a paraneoplastic syndrome and an asymptomatic SARS-CoV-2 infection, despite treatment with different and overlapping anticoagulant medication. This case describes a patient with non-bacterial thrombotic aortic valve endocarditis that developed despite treatment with a factor-Xa-inhibitor and who subsequently suffered a myocardial infarction and two strokes within a short period of time in the context of a paraneoplastic syndrome and asymptomatic SARS-CoV-2 infection. Paraneoplastic syndromes are often linked to increased thrombogenicity; however, non-bacterial thrombotic aortic valve endocarditis is rare even in the situation of cancer. 3 This case highlights the many-sided effects of paraneoplastic syndromes and SARS-CoV-2 infection in patients being already at increased risk for thrombotic complications due to underlying disease. cache = ./cache/cord-299024-jkqdzt87.txt txt = ./txt/cord-299024-jkqdzt87.txt === reduce.pl bib === id = cord-298734-h286m32c author = Xia, Siyu title = Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4766 sentences = 302 flesch = 53 summary = title: Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury In this study, we successfully established long term cultures of normal human kidney proximal tubule epithelial cells (KPTECs) in 2D and 3D culture systems using conditional reprogramming (CR) and organoids techniques. Due to the lack of specific detection of ACE2 mRNA and protein expression in human kidney tubule cells, it is hard to confirm the direct infection of SARS-CoV-2. In this study, we firstly established long term cell cultures of KPTECs using 2D CR and 3D organoids technologies, which maintained the lineage function, and the ability to differentiate and repair DNA damage. In terms of the questions above, we need model systems to study infection of SARS-CoVs in ACE2 expressing cell types, especially in kidney epithelial cells (Hamming et al. cache = ./cache/cord-298734-h286m32c.txt txt = ./txt/cord-298734-h286m32c.txt === reduce.pl bib === id = cord-299082-s8bm40vy author = Wang, Yueying title = Cardiac arrhythmias in patients with COVID‐19 date = 2020-07-26 pages = extension = .txt mime = text/plain words = 3714 sentences = 247 flesch = 40 summary = 5, 6, 9, 10, [12] [13] [14] [15] Several investigators have reported cardiac function and structural abnormalities in patients with SARS-CoV-2 infection, including acute heart failure (HF), 3,10,16 takotsubo syndrome, 17 ,18 viral myocarditis, 19 and acute myocardial infarction. In addition to exacerbating the previous cardiomyopathy and conduction disorders, inducing arrhythmia events, SARS-CoV-2 may also induce electrophysiological abnormalities in patients with no previous history of heart disease under a variety of mechanisms. Clinical features and mechanism of heart injury in patients suffered from severe acute respiratory syndrome. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial Risk of QT interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease 2019 (COVID-19) cache = ./cache/cord-299082-s8bm40vy.txt txt = ./txt/cord-299082-s8bm40vy.txt === reduce.pl bib === id = cord-299122-djfj4262 author = Yu, Hua title = Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date = 2007-03-15 pages = extension = .txt mime = text/plain words = 5459 sentences = 273 flesch = 52 summary = title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown). cache = ./cache/cord-299122-djfj4262.txt txt = ./txt/cord-299122-djfj4262.txt === reduce.pl bib === id = cord-299148-uge5uodk author = Wang, Qiang title = A Method To Prevent SARS-CoV-2 IgM False Positives in Gold Immunochromatography and Enzyme-Linked Immunosorbent Assays date = 2020-05-26 pages = extension = .txt mime = text/plain words = 2874 sentences = 124 flesch = 47 summary = We set out to investigate the interference factors that led to false-positive novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgM detection results using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions. GICA and ELISA were used to detect SARS-CoV-2 IgM in 86 serum samples, including 5 influenza A virus (Flu A) IgM-positive sera, 5 influenza B virus (Flu B) IgM-positive sera, 5 Mycoplasma pneumoniae IgM-positive sera, 5 Legionella pneumophila IgM-positive sera, 6 sera of HIV infection patients, 36 rheumatoid factor IgM (RF-IgM)-positive sera, 5 sera from hypertensive patients, 5 sera from diabetes mellitus patients, and 14 sera from novel coronavirus infection disease 19 (COVID-19) patients. At a urea dissociation concentration of 4 mol/liter and with affinity index (AI) levels lower than 0.371 set to negative, SARS-CoV-2 IgM results were positive in 3 mid-to-high-level-RF-IgM-positive sera and in 14 COVID-19 patient sera detected using ELISA. cache = ./cache/cord-299148-uge5uodk.txt txt = ./txt/cord-299148-uge5uodk.txt === reduce.pl bib === id = cord-299093-zp07aqpm author = Harrison, Andrew G. title = Mechanisms of SARS-CoV-2 transmission and pathogenesis date = 2020-10-14 pages = extension = .txt mime = text/plain words = 6389 sentences = 385 flesch = 46 summary = Thus, evasion of IFN signaling by SARS-CoV-2 and impaired IFN production in J o u r n a l P r e -p r o o f human peripheral blood immune cells might contribute to the productive viral replication, transmission, and severe pathogenesis during COVID-19, although further testing is warranted to fully dissect these putative evasion pathways [95] . For instance, Krt18-hACE2 and betaactin-hACE2-transgenic mice rapidly succumb to SARS-CoV-2 infection with lung infiltration of inflammatory immune cells inducing severe pulmonary disease, accompanied by evident thrombosis and anosmia, which partially recapitulate human COVID-19 [114] [115] . Furthermore, upon viral challenge, lymphocytes have expanded in rhesus macaque models around 5 dpi with complementary B-cell responses against SARS-CoV-2 Spike appearing 10-15 dpi in blood samples [125] ; expansion of these adaptive immune compartments was analogous to those observed in COVID-19 patients [37, 125, [132] [133] [134] . cache = ./cache/cord-299093-zp07aqpm.txt txt = ./txt/cord-299093-zp07aqpm.txt === reduce.pl bib === id = cord-299333-qu0bmov5 author = Reddy, Gireesh B. title = Clinical Characteristics and Multisystem Imaging Findings of COVID-19: An Overview for Orthopedic Surgeons date = 2020-08-17 pages = extension = .txt mime = text/plain words = 4412 sentences = 235 flesch = 37 summary = Since December 2019, infections with severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), a novel betacoronavirus strain responsible for coronavirus disease 2019 (COVID19) , rapidly progressed from an isolated cluster of cases in the Hubei province of east central China to a pandemic, with significant global health and economic repercussions [4, 5, 10, 24, 25, 27, 28, 44, 58, 80, 91] . Early reports from Italy and China indicated that although pulmonary diseases including ARDS and diffuse pneumonia comprise the predominant lethal complications of COVID-19, patients have also presented with or developed significant cardiac signs and symptoms [50] . COVID-19 musculoskeletal and neurologic manifestations are being reported with increased frequency, particularly in patients with more severe respiratory disease, indicating coronavirus neurotropism possibly directly related with higher viral loads, which are now detectable in cerebrospinal fluid [20] . cache = ./cache/cord-299333-qu0bmov5.txt txt = ./txt/cord-299333-qu0bmov5.txt === reduce.pl bib === id = cord-299308-gza1pwx6 author = Laxminarayan, Ramanan title = Is Gradual and Controlled Approach to Herd Protection a Valid Strategy to Curb the COVID-19 Pandemic? date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1557 sentences = 80 flesch = 52 summary = Most pandemics in the twentieth and twentyfirst centuries have been caused by virusesinfluenza, chikungunya, HIV/AIDS and now the coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients reportedly acquire COVID-19 either through close contact with infected family members (89%), exposure to endemic areas (33%), or both (22%); with the majority (53%) showing moderate symptoms and no severe or critical cases [2] . We do not endorse the idea of letting the epidemic a free hand in order to create sufficient herd immunity to end the epidemic;as it would entail an enormous burden on the healthcare system -United Kingdom, at first, considered a different approach -of unrestricted spread of disease without any brakes applied, but public health experts were able to convince the government to accept the more reasonable mitigation approach. The proportion of the population that should be exposed to the virus for herd immunity to be effective is calculated as 1-1/Ro. In the absence of serological studies, the true extent of spread of SARS-COV-2 in India is unknown. cache = ./cache/cord-299308-gza1pwx6.txt txt = ./txt/cord-299308-gza1pwx6.txt === reduce.pl bib === id = cord-299346-f13xly6q author = Awad, Mohamed E. title = Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic date = 2020-04-10 pages = extension = .txt mime = text/plain words = 4216 sentences = 254 flesch = 42 summary = title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic To reduce the occupational risk in treating suspected or confirmed COVID-19 urgent orthopaedic patients, recommended precautions and preventive actions (triage area, ED consultation room, induction room, operating room, and recovery room) are reviewed. HCPs in high-risk areas should adhere to infection prevention and control practices, which includes the appropriate use of engineering controls (negative pressure rooms), administrative controls, and personal protective equipment (PPE) ( 6 Per CDC recommendations, a clinically suspected/ confirmed COVID-19 patient should wear a cloth face covering, over nose, and mouth and a surgical mask should be reserved for HCP and first responders. It is recommended for an environmental services worker to increase the Flowchart demonstrating the the recommended use of personal protective equipment for different activities at various settings managing suspected/clinically Coronavirus disease 2019 patients. cache = ./cache/cord-299346-f13xly6q.txt txt = ./txt/cord-299346-f13xly6q.txt === reduce.pl bib === id = cord-299520-2khjhows author = Dalla Volta, Alberto title = The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures date = 2020-08-18 pages = extension = .txt mime = text/plain words = 2422 sentences = 115 flesch = 50 summary = title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures We conducted a surveillance for SARS-CoV-2 infection among the staff members of the Medical Oncology Unit of ASST Spedali Civili in Brescia, one of the Italian areas most affected by the SARS-CoV-2 pandemic. Since last February 24, 2020, the Medical Oncology Unit of ASST Spedali Civili in Brescia put in place most of the protective measures that were subsequently acknowledged to be effective in preventing viral infection among healthcare professionals (HCPs) and patients (3) (4) (5) . The Medical Oncology Unit of ASST Spedali Civili of Brescia is located in one of the Italian areas that were most affected by the SARS-CoV-2 infection, and the hospital had to allocate the majority of its beds to patients with severe virus-related diseases. cache = ./cache/cord-299520-2khjhows.txt txt = ./txt/cord-299520-2khjhows.txt === reduce.pl bib === id = cord-299491-8rfm0jxh author = Xiao, Shenglan title = Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date = 2017-07-20 pages = extension = .txt mime = text/plain words = 4765 sentences = 218 flesch = 53 summary = Like many other respiratory viruses, the SARS-CoV is suspected to spread from an infected person to the susceptible via three basic transmission routes, i.e., the long-range airborne, close contact and fomite routes [14] [15] [16] , as shown in Fig 1. Several studies have proposed probable evidence for the airborne spread of the SARS-CoV based on the consistencies between bio-aerosol concentration distributions and reported attack rates [19] [20] [21] , but no mechanism-based investigations exist for the fomite route. To investigate the role the fomite route plays in SARS-CoV transmission, we conducted a detailed modelling study of the largest hospital outbreak in Hong Kong [20] , in which the distribution of reported attack rates of inpatients showed a statistically significant spatial pattern. A multi-agent model ( Fig 2) was developed to simulate the possible spread of the viruses from the index patient to the susceptible by air flow and surface touching, and to calculate the possible exposure doses and infection risks for each hypothesis. cache = ./cache/cord-299491-8rfm0jxh.txt txt = ./txt/cord-299491-8rfm0jxh.txt === reduce.pl bib === id = cord-298441-77w86l8q author = Lombardi, Andrea title = Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1438 sentences = 67 flesch = 52 summary = To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). cache = ./cache/cord-298441-77w86l8q.txt txt = ./txt/cord-298441-77w86l8q.txt === reduce.pl bib === id = cord-299472-pmqqemku author = Yang, Naibin title = In-flight Transmission Cluster of COVID-19: A Retrospective Case Series date = 2020-03-30 pages = extension = .txt mime = text/plain words = 3591 sentences = 279 flesch = 66 summary = No data were available about the risk of SARS-CoV-2 transmission on aircraft and clinical characteristics and outcomes of these COVID-19 patients. We conducted a retrospective study focused on the clinical characteristics of ten patients with COVID-19 successively admitted to Xiaoshan First People's Hospital after having been on a flight. Epidemiology data were collected by interviewing each patient including exposure history, dates of illness onset, hospital admissions and All rights reserved. Patients were discharged from hospital when the results of two RT-PCR tests taken 24 hours apart were negative for SARS-CoV-2 and symptoms improved obviously according to China guidelines 10 . . https://doi.org/10.1101/2020.03.28.20040097 doi: medRxiv preprint SARS-CoV-2 transmission on aircraft were similar to those without in-flight history, as previously reported [4, 7, 14] . Notably, the symptoms of COVID-19 patients infected in this flight were relatively mild, outcomes were inclined to be better, and the risk to passengers was higher compared with transmission of SARS on aircraft [15-17]. cache = ./cache/cord-299472-pmqqemku.txt txt = ./txt/cord-299472-pmqqemku.txt === reduce.pl bib === id = cord-299116-1agfnjvq author = Bunders, Madeleine title = Implications of sex differences in immunity for SARS-CoV-2 pathogenesis and design of therapeutic interventions date = 2020-08-17 pages = extension = .txt mime = text/plain words = 6250 sentences = 333 flesch = 45 summary = Emerging knowledge on the basic biological pathways that underlie differences in immune responses between women and men needs to be incorporated into research efforts on SARS-CoV-2 pathogenesis and pathology to identify targets for therapeutic interventions aimed at enhancing antiviral immune function and lung airway resilience while reducing pathogenic inflammation in COVID-19. The current Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic highlights the clinical consequences of these sex differences in antiviral immunity and tissue resilience Scully et al., 2020) , with in particular older men suffering from severe Coronavirus disease 2019 (COVID-19) and experiencing higher case mortality rates (Docherty et al., 2020; Grasselli et al., 2020; Jin et al., 2020; Salje et al., 2020) . In the following, we will address the different stages of SARS-CoV-2 pathogenesis, including viral entry and sensing, induction of antiviral immune responses and inflammation, and immune-mediated tissue-repair, in the context of critical differences in immune responses that exist between the sexes and contribute to the male-bias in development of severe COVID-19. cache = ./cache/cord-299116-1agfnjvq.txt txt = ./txt/cord-299116-1agfnjvq.txt === reduce.pl bib === id = cord-299544-r3cqvf0c author = de Souza, T. H. title = Clinical Manifestations of Children with COVID-19: a Systematic Review date = 2020-04-03 pages = extension = .txt mime = text/plain words = 2582 sentences = 216 flesch = 56 summary = Study Selection: Inclusion criteria were: (1) studied patients younger than 18 years old; (2) presented original data from cases of COVID-19 confirmed by reverse-transcription polymerase chain reaction; and (3) contained descriptions of clinical manifestations, laboratory tests or radiological examinations. https://doi.org/10.1101/2020.04.01.20049833 doi: medRxiv preprint children infected with SARS-CoV-2 may not meet all the criteria required in the suspected case definition. The following data were extracted, when available, from each elected article: first author, publication year, study design, number of cases, gender, age, clinical manifestations, laboratory tests, radiological examinations and outcomes (discharged, still hospitalized or death). In our study, we described the main clinical, laboratorial and radiological characteristics of children infected with SARS-CoV-2 reported in the literature. A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study cache = ./cache/cord-299544-r3cqvf0c.txt txt = ./txt/cord-299544-r3cqvf0c.txt === reduce.pl bib === id = cord-299810-e57pwgnx author = Martelloni, Gabriele title = Modelling the downhill of the Sars-Cov-2 in Italy and a universal forecast of the epidemic in the world date = 2020-07-01 pages = extension = .txt mime = text/plain words = 3022 sentences = 180 flesch = 62 summary = Finally we study the behavior of the ratio infected over swabs for Italy, Germany and USA, and we show as studying this parameter we recover the generalized Logistic model used in [1] for these three countries. The parameters r 0 represents the rates of growth of epidemic, K is the carrying capacity for the classical logistic model, α is a constant in order to have a power low initial growth before LD, β is the exponent of the second term of equation 1 that represents the influence of asymptomatic; δ,a correction of the quadratic term of logistic, and γ are the constant parameters considering the influence of the government measures 1 , K f is a proportionality constant between deaths and total number of infected, while t d and t r are the delays of deaths and recoveries respect to infected respectively; the constant A represents the contribution of asymptomatic people as introduced in [1] and finally t 0 is the time of LD start. cache = ./cache/cord-299810-e57pwgnx.txt txt = ./txt/cord-299810-e57pwgnx.txt === reduce.pl bib === id = cord-299470-sqqer16k author = Chappell, J. G. title = Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4491 sentences = 206 flesch = 46 summary = In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. Initial SARS-CoV-2 RT-PCR testing in the UK was offered via referral to Public Health England (PHE) national and regional diagnostic laboratories, and required strict epidemiological and clinical criteria to be met, specifically a recent travel history to Hubei province or contact with a known case and 1 or more of fever, shortness of breath or new and persistent dry cough. We describe the detection of SARS-CoV-2 from 8 patients admitted to hospital with severe respiratory distress who were not tested at the time because they had no travel history or contact with someone infected and therefore did not meet the case definition applied at the time. cache = ./cache/cord-299470-sqqer16k.txt txt = ./txt/cord-299470-sqqer16k.txt === reduce.pl bib === id = cord-299480-mehwd0dk author = Liu, Zheng-Xue title = Identification of single-chain antibody fragments specific against SARS-associated coronavirus from phage-displayed antibody library date = 2005-04-08 pages = extension = .txt mime = text/plain words = 4261 sentences = 225 flesch = 62 summary = Abstract To develop early diagnostic reagents, effective vaccines, and even drugs against SARS-associated coronavirus (SARS-CoV), the human single fold single-chain antibody fragments, (scFv) libraries I+J (Tomlinson I+J) were used to identify novel scFvs, which can specifically bind to SARS-CoV. Interestingly, two scFvs (B5 and B9) exhibited higher binding specificity to SARS-CoV with the OD450 value 0.608 and 0.545, respectively, and their coding sequences shared the identical sequence composed of VH gene (351bp) and VL gene (327bp), so the two scFvs were uniformly named as SA59B and chosen for further analysis. Hence, single-chain antibody fragments specific against SARS-CoV from phage-displayed antibody library have potential for exploitation as diagnostic or even antiviral therapeutic reagents. The ELISA plates coated with purified SARS-CoV lysate, positive and negative sera were provided by Military Medical Science Academic and HuaDa Gene Company (Beijing, China). The panning procedure was performed on a 96-well flexible assay plate coated with purified SARS-CoV lysate, which was blocked directly with MPBS (PBS containing 4% skimmed milk powder) at room temperature for 2 h. cache = ./cache/cord-299480-mehwd0dk.txt txt = ./txt/cord-299480-mehwd0dk.txt === reduce.pl bib === id = cord-299940-nvlcwcz8 author = Rastrelli, Giulia title = Low testosterone levels predict clinical adverse outcomes in SARS‐CoV‐2 pneumonia patients date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3458 sentences = 187 flesch = 47 summary = OBJECTIVES: To estimate the association between T level and SARS‐CoV‐2 clinical outcomes (defined as conditions requiring transfer to higher or lower intensity of care or death) in a cohort of patients admitted in the respiratory intensive care unit (RICU). 16, 17 Thereof, we sought to estimate the association between the T levels and the SARS-CoV-2 infection clinical outcomes (defined as conditions requiring to transfer to a higher or lower intensity of care units or even death) as well as the biochemical prognostic predictors of severe and fatal SARS-CoV-2 infection in a cohort of patients admitted in the respiratory intensive care unit (RICU) of a single Hospital in Mantua, one of the epicenter of the global SARS-CoV-2 pandemic in Italy. Discussion and conclusion: Our study demonstrates for the first time that lower baseline levels of TT and cFT levels predict poor prognosis and mortality in SARS-CoV-2-infected men admitted to RICU. cache = ./cache/cord-299940-nvlcwcz8.txt txt = ./txt/cord-299940-nvlcwcz8.txt === reduce.pl bib === id = cord-299565-shlhreve author = Sweileh, Waleed M. title = Global research trends of World Health Organization’s top eight emerging pathogens date = 2017-02-08 pages = extension = .txt mime = text/plain words = 6058 sentences = 393 flesch = 52 summary = According to WHO, the list of pathogens, which required urgent attention for research and development pertaining to preparedness, included "Crimean Congo haemorrhagic fever, Ebola virus, Marburg, Lassa fever, Middle East respiratory syndrome (MERS) and Severe acute respiratory syndrome (SARS) coronavirus diseases, Nipah, and Rift Valley fever" [1] . ( TITLE ( "Crimean-Congo" OR ebola OR "Middle East Respiratory Syndrome" OR "Severe acute respiratory syndrome" OR lassa OR nipah OR "Rift valley" OR marburg OR mers OR merscov OR sars OR ebolavirus OR crimean ) AND TITLE-ABS ( virus OR viral OR fever OR hemorrhagic OR haemorrhagic OR corona* OR coronavirus OR infection OR infectious ) AND TITLE ( vaccin* ) ) AND PUBYEAR > 1995 AND PUBYEAR < 2016 AND ( LIMIT-TO ( SRCTYPE , "j" ) ) AND ( EXCLUDE ( DOCTYPE , "er" ) ) N = 472 cache = ./cache/cord-299565-shlhreve.txt txt = ./txt/cord-299565-shlhreve.txt === reduce.pl bib === id = cord-299552-rgrm8dil author = Bianchi, Martina title = Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2082 sentences = 134 flesch = 52 summary = In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. In this report, a structural comparison between the Sars-CoV-2 surface proteins from different isolates with homologous proteins from closely related viruses such as those from Bat and Pangolin is described. Sars-CoV-2 E sequences differ from the homologous proteins also at positions 55-56, where the dyad Ser-Phe replaces Thr-Val (except in Bat coronavirus isolate BtKY72, accession code KY352407). In this paper, E and M proteins from 797 Sars-CoV-2 genomes have been compared to the counterparts taken from the most closely related virus also to evaluate the potential role of amino acid mutations in the epizootic origin of COVID-19. cache = ./cache/cord-299552-rgrm8dil.txt txt = ./txt/cord-299552-rgrm8dil.txt === reduce.pl bib === id = cord-299679-6z9e5gi6 author = Rello, Jordi title = Clinical phenotypes of SARS-CoV-2: implications for clinicians and researchers date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1961 sentences = 112 flesch = 37 summary = Many intubated patients present with phenotype 4, characterised by pulmonary hypoxic vasoconstriction, being associated with severe hypoxaemia with "normal" (>40 mL·cmH(2)O(−1)) lung compliance and likely representing pulmonary microvascular thrombosis. Phenotype 5 is often associated with high plasma procalcitonin and has low pulmonary compliance, Which is a result of co-infection or acute lung injury after noninvasive ventilation. The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad, ranging from asymptomatic infection to flu-like illness (sometimes with digestive disturbances) to viral pneumonia. Phenotype 2 represents 80% of hospitalisations and is characterised by the presence of hypoxaemia or small opacities on chest radiographs and these patients should be referred for close respiratory monitoring ( particularly respiratory rate and oxygen saturation measure by pulse oximetry) because they are at risk of rapid deterioration progressing to death if intubation is not timely instituted. cache = ./cache/cord-299679-6z9e5gi6.txt txt = ./txt/cord-299679-6z9e5gi6.txt === reduce.pl bib === id = cord-300046-orlga9qf author = Gomes da Silva, J. title = Health literacy of inland population in the mitigation phase 3.2. of COVID-19's pandemic in Portugal - a descriptive cohort study date = 2020-05-14 pages = extension = .txt mime = text/plain words = 5399 sentences = 273 flesch = 48 summary = Globally, younger individuals, females, graduates and the Non-Risk Group presented higher relative frequencies of the correct answer along COVID-19's Questionnaire. However, three exceptions were observed: the Undergraduate Group and the Risk-Group had a high relative frequency stating that COVID-19 has a cure and in mentioning "Social Isolation" as an important preventive measure to adopt when compared to the Graduate Group and the Non-Risk Group, respectively. Males have higher relative frequency in answering the correct number of SNS24 and in stating that children can get sick and transmit the infection by SARS-CoV-2 when compared to females ( Table 2 -Supplementary information). Nonparametric tests reveal a statistically significant association regarding variable "Age", "Gender" and "Risk Factor", with younger individuals, females and individuals from Risk-Group stating more often the correct answer. Nonparametric tests reveal a statistically significant association regarding variable "Gender" and "Risk Factor", with males and individuals from Non-Risk Group answering the correct number. cache = ./cache/cord-300046-orlga9qf.txt txt = ./txt/cord-300046-orlga9qf.txt === reduce.pl bib === id = cord-299853-pvugij9l author = Patil, Uday P. title = Newborns of COVID-19 mothers: short-term outcomes of colocating and breastfeeding from the pandemic’s epicenter date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1217 sentences = 67 flesch = 54 summary = Newborns are at high risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from their infected mothers who delivered during this period; however, data remains limited [3] . Data regarding demographic and clinical characteristics, SARS-CoV-2 test results, symptoms and signs of COVID-19, colocation (rooming-in), breastfeeding, and newborn follow-up were obtained from review of electronic medical records. During the early period of the pandemic, our center tested only symptomatic pregnant women for SARS-CoV-2 and newborns of infected mothers were placed in isolation rooms based on the available literature at that time [6] . However, due to the dramatic surge in the number of SARS-CoV-2 positive mothers delivering at our center after initiation of universal screening of all pregnant women admitted for delivery, the limited isolation spaces for the newborns, early postpartum discharges, the crowded housing conditions in our community and the desire to promote breastfeeding, we utilized shared decision-making and offered rooming-in of mothers with their newborns [7] . cache = ./cache/cord-299853-pvugij9l.txt txt = ./txt/cord-299853-pvugij9l.txt === reduce.pl bib === id = cord-299711-m5gb03is author = Udrea, Ana-Maria title = Laser irradiated phenothiazines: New potential treatment for COVID-19 explored by molecular docking date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2191 sentences = 153 flesch = 54 summary = In this study we predict, using molecular docking, the binding affinity of 15 phenothiazines (antihistaminic and antipsychotic drugs) when interacting with the main protease (M(pro)) of SARS-CoV-2. For identifying a treatment of COVID-19 disease, we used molecular docking procedure to predict the inhibitory activity (against SARS-CoV-2) M pro of some compounds from phenothiazines drug class. To simulate the interaction between SARS-CoV-2 and drugs from the class of phenothiazines including TZ and CPZ photoproducts we have used the virus M pro from RCSB Protein Data Bank: PDB code 6LU7 [15] . The 2D/3D chemical structure of compounds from Phenothiazines class and TZ and CPZ photoproducts that resulted during laser irradiation; 2D chemical structure, lowest EFEB (kcal/mol) for each compound resulted after 100 runs using molecular docking simulation, predicted KI (nM) and pKI values are also presented. Our results suggest that TZ and TZ photoproducts obtained by laser irradiation, have significant biological activity on SARS-CoV-2 M pro and could be used in a potent treatment in COVID-19 disease. cache = ./cache/cord-299711-m5gb03is.txt txt = ./txt/cord-299711-m5gb03is.txt === reduce.pl bib === id = cord-299781-9d5g5xaw author = Hrusak, Ondrej title = Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment date = 2020-04-07 pages = extension = .txt mime = text/plain words = 2377 sentences = 128 flesch = 49 summary = title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment While we should not underestimate the risk of developing a more severe course of COVID-19 than observed here, the intensity of preventive measures should not cause delays or obstructions in oncological treatment. The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causing the Coronavirus Disease (COVID-19) pandemic in 2020 was identified in December, 2019. 11 To evaluate this, we used a flash survey to determine whether there was current evidence that pediatric patients with cancer in SARS-CoV-2 affected areas had been tested for this virus or had developed severe COVID-19 disease. More research is needed to better understand the epidemiology of SARS-CoV-2 infection and COVID-19 in pediatric patients with cancer or other immunocompromised children. cache = ./cache/cord-299781-9d5g5xaw.txt txt = ./txt/cord-299781-9d5g5xaw.txt === reduce.pl bib === id = cord-299560-np6nfvf2 author = Hendaus, Mohamed A. title = Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2789 sentences = 166 flesch = 53 summary = Replication of SARS-CoV-2 depends on the viral RNAdependent RNA polymerase (RdRp) (Elfiky & Azzam, 2020) which is the most probable target of the investigational nucleotide analogue remdesivir (RDV) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . RDV exhibits broad-spectrum antiviral activity against RNA viruses, and former studies with RdRps from Ebola virus (EBOV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have shown that delayed chain-termination is RDV's conceivable mechanism of action ( Figure 2 ) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . On April 29, 2020, Gilead revealed results from the openlabel, Phase 3 SIMPLE trial evaluating 5-day and 10-day dosing durations of the investigational antiviral remdesivir in hospitalized patients with severe manifestations of COVID-19 disease. cache = ./cache/cord-299560-np6nfvf2.txt txt = ./txt/cord-299560-np6nfvf2.txt === reduce.pl bib === id = cord-299635-bxdf27sv author = Squire, M. M. title = Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions date = 2020-08-24 pages = extension = .txt mime = text/plain words = 5088 sentences = 317 flesch = 47 summary = The objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. Hence, hospital operations require the assessment of energy efficiency when evaluating Coronavirus Disease 2019 (COVID19) intervention measures, due to COVID-19 being caused by the Severe Acute Respiratory Disease Coronavirus-2 (SARS-CoV-2). As potential infection control interventions for COVID-19 are considered, information that pertains to energy consumption at hospitals provides additional context on costs related to implementation of mitigation strategies for person-to-person transmission, as well as environmental contamination. This paper evaluates the energy implications and impact of NP and XP-UV infection control measures on decreasing secondary transmission of SARS-CoV-2 in acute care hospitals. 21.20178855 doi: medRxiv preprint This study seamlessly combines projections of COVID-19 hospitalizations, evaluation of energy use, and the impact of infection control measures among three different hospital sizes. cache = ./cache/cord-299635-bxdf27sv.txt txt = ./txt/cord-299635-bxdf27sv.txt === reduce.pl bib === id = cord-299911-v95pf3eg author = El-Ghiaty, Mahmoud A. title = Cytochrome P450-mediated drug interactions in COVID-19 patients: current findings and possible mechanisms date = 2020-06-26 pages = extension = .txt mime = text/plain words = 5319 sentences = 272 flesch = 37 summary = Based on the conclusions drawn from the currently rapidly evolving knowledge about COVID-19, our hypothesis is built on the potential modulation of CYPs activity by the inflammatory environment provoked by SARS-CoV-2 infection, as well as the pathologic involvement of the liver which harbors the majority of the drug metabolizing enzymes (DMEs). Systemic inflammation and immune response represent a substantial element in many acute and chronic diseases which is strongly implicated in altering drug pharmacokinetics through, mainly, modulating the expression and activity of DMEs. As a main contributor to the metabolic biotransformation of most drugs, CYPs are widely involved in such disease-drug interactions [19] . For decades, IL-6 has been recognized as the major inflammatory element that provokes a significant repressive effect on the expression and activity of different CYPs. Human recombinant interleukin 6 (rhIL-6) has shown concentration-dependent blocking of phenobarbital-mediated induction of CYP2B1/2 mRNA and activity in rat hepatocytes [48] . cache = ./cache/cord-299911-v95pf3eg.txt txt = ./txt/cord-299911-v95pf3eg.txt === reduce.pl bib === id = cord-300024-169g2ih5 author = Flemming, S. title = Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date = 2020-05-26 pages = extension = .txt mime = text/plain words = 299 sentences = 24 flesch = 52 summary = key: cord-300024-169g2ih5 title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 cord_uid: 169g2ih5 Abdominal fluid (ascites), bile, liver and gall bladder samples were collected during emergency cholecystectomy of a critically ill patient suffering from COVID-19. Tracheal secretion and throat swab samples were collected immediately prior to surgery as positive controls. All samples were tested for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (PCR) using validated primers 5 . PCR tests revealed strongly positive results for SARS-CoV-2 RNA in tracheal secretion as well as in throat swab samples, with cycle threshold values of 20 and 25, respectively. The remaining samples all tested negative for SARS-CoV-2 suggesting that the virus does not spread to the abdominal cavity, bile and abdominal organs. A stool sample obtained one day after surgery also tested negative. Recommendations for general surgery activities in a pandemic scenario (SARS-CoV-2) cache = ./cache/cord-300024-169g2ih5.txt txt = ./txt/cord-300024-169g2ih5.txt === reduce.pl bib === id = cord-299783-8ti6r0eh author = Bruni, M. title = Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date = 2020-08-01 pages = extension = .txt mime = text/plain words = 3283 sentences = 188 flesch = 47 summary = Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. The performances of these ELISA assays were assessed for the different viral antigens and classes of antibodies by determining ROC curves using i) a cohort of 56 sera from COVID-19 patients collected between April and June 2020 and tested positive for nasopharyngeal swabs, and ii) 436 pre-COVID-19 sera, collected between 2012 and 2015 (Supplementary Table 1 and Figure S1 ). Non-hospitalized COVID-19 subjects manifested a lower antibody titer as compared to severe ICU patients for all the tested antibody classes and viral antigens ( Figure 1B-D) . cache = ./cache/cord-299783-8ti6r0eh.txt txt = ./txt/cord-299783-8ti6r0eh.txt === reduce.pl bib === id = cord-300149-djclli8n author = Ruan, Yijun title = Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection date = 2003-05-24 pages = extension = .txt mime = text/plain words = 4355 sentences = 226 flesch = 54 summary = title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection METHODS: We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations. All genetic variations of Singapore isolates identified when compared with available SARS-CoV genome sequences were further confirmed by primer extension genotyping technology (Sequenom, San Diego, CA, USA). These sequences showed that the genomes of SARS-CoV isolated in Singapore are comprised of 29 711 bases, with the exception of a five-nucleotide deletion in strain SIN2748 and a six-nucleotide deletion in SIN2677. cache = ./cache/cord-300149-djclli8n.txt txt = ./txt/cord-300149-djclli8n.txt === reduce.pl bib === id = cord-299899-is815pol author = He, Jingjing title = Proportion of asymptomatic coronavirus disease 2019 (COVID‐19): a systematic review and meta‐analysis date = 2020-07-21 pages = extension = .txt mime = text/plain words = 2576 sentences = 191 flesch = 46 summary = The pooled proportion of asymptomatic infection among 1152 COVID‐19 children from 11 studies is 27.7% (95% CI: 16.4–42.7%), which is much higher than patients from all aged groups. However, patients infected with SARS-CoV-2 could also be asymptomatic, confirmed by positive Nucleic acid testing results during the illness. While a variety of studies on asymptomatic infection have been reported, the proportion of asymptomatic patients in confirmed COVID-19 cases is not well characterized. Original articles reporting asymptomatic infection in confirmed COVID-19 patients were included for meta-analysis. Noticeably, one study from Wuhan showed that 98/1021(9.6%) nucleic acid testing negative patients had lgG positive results, suggesting possible recovery from asymptomatic SARS-CoV-2 infection 54 . Characteristics of asymptomatic patients with SARS-CoV-2 infection in Jinan, China. Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha, China. Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection cache = ./cache/cord-299899-is815pol.txt txt = ./txt/cord-299899-is815pol.txt === reduce.pl bib === id = cord-299927-ixuvy2g4 author = Frontera, Jennifer title = Global Consortium Study of Neurological Dysfunction in COVID-19 (GCS-NeuroCOVID): Study Design and Rationale date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4851 sentences = 229 flesch = 30 summary = As the COVID-19 pandemic evolves worldwide, reports of a spectrum of mild to severe neurological syndromes among patients infected with SARS-CoV-2 are emerging, including headache, anosmia, ageusia, seizures, coma, encephalitis, Guillain-Barre syndrome, and acute cerebrovascular events including ischemic stroke, intracerebral hemorrhage, and cerebral venous sinus thromboses [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] . [15] reported that 84% (49/58) of patients with severe SARS-CoV-2 infection and acute respiratory distress syndrome had neurological symptoms including encephalopathy, agitation and confusion, and corticospinal tract signs. We established the Global Consortium to Study Neurological dysfunction in COVID-19 patients (GCS-NeuroCOVID) and promptly launched a tiered research program with an early, pragmatic, and nimble design to enable successful implementation during a global pandemic crisis when healthcare systems are stressed. The primary outcome in Tier 1 is the prevalence of new clinical neurological syndromes in SARS-CoV-2 patients including: new onset headache, anosmia/ageusia, clinical seizures/status epilepticus, strokes (ischemic and hemorrhagic), meningitis/encephalitis, hypoxic/ischemic injury, acute encephalopathy, coma, myelopathy, neuropathy, and dysautonomia/sympathetic storming. cache = ./cache/cord-299927-ixuvy2g4.txt txt = ./txt/cord-299927-ixuvy2g4.txt === reduce.pl bib === id = cord-299499-66qh3r75 author = Guilamo-Ramos, Vincent title = Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date = 2020-09-07 pages = extension = .txt mime = text/plain words = 4199 sentences = 218 flesch = 42 summary = In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. cache = ./cache/cord-299499-66qh3r75.txt txt = ./txt/cord-299499-66qh3r75.txt === reduce.pl bib === id = cord-300040-rvrp5zvv author = Dutta, Noton Kumar title = Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine date = 2008-06-15 pages = extension = .txt mime = text/plain words = 4681 sentences = 255 flesch = 54 summary = We constructed eukaryotic expression plasmid encoding N [(N1 (nucleotide: 1-1269), N2 (nucleotide: 1-327), and N3 (nucleotide: 328-1296)) gene fragments of the SARS-CoV and compared their individual potential immune responses in BALB/c mice for use in the development of SARS vaccine candidates. In this report, we detected SARS-Cov N1 and N3 protein-specific immune response induced by pVAX-N1 and N3 DNA vaccination, respectively, and found significantly high titres of specific antibody and specific cell mediated immunity compared to control. These results indicate that N protein, which naturally exists in virus particles after binding of viral RNA, was able to induce strong humoral and cellular immune responses when induced by DNA vaccine, and it might be a prospective candidate gene for development of SARS-CoV vaccine. showed that expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization. The expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization cache = ./cache/cord-300040-rvrp5zvv.txt txt = ./txt/cord-300040-rvrp5zvv.txt === reduce.pl bib === id = cord-299999-jra1yu6a author = Tattar, R. title = COVID PDPs date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1630 sentences = 94 flesch = 48 summary = However, a structure needs to be developed to account for the disruption in training COVID-19 has caused and facilitate the progression of the trainees without compromising the quality and integrity of the respected specialities. The New England Journal of Medicine case report of the first COVID-19 patient in the USA detected high SARS-CoV-2 viral load in their stool sample. At present, PDPs are not a routine part of the undergraduate curricula 3 and as such, newly qualified dentists will be faced with the new challenge of having to proactively plan their CPD to fulfil outstanding competencies from their current training course. Whilst CPD cycles are five years, the need to complete certain key foundation skills to ensure adequate competence and baseline knowledge to facilitate progression through postgraduate training pathways will result in trainees having to meet such objectives sooner. Urgent dental care for patients during the COVID-19 pandemic Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic cache = ./cache/cord-299999-jra1yu6a.txt txt = ./txt/cord-299999-jra1yu6a.txt === reduce.pl bib === id = cord-300018-3uzau7if author = Mak, Gannon C.K. title = The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date = 2020-07-24 pages = extension = .txt mime = text/plain words = 649 sentences = 54 flesch = 61 summary = authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong In an attempt to understand the relevance of D614G substitution among COVID-19 patients in Hong Kong, full length S gene sequences from severe and non-severe cases were examined. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 The SARS-CoV-2 Spike Protein D614G cache = ./cache/cord-300018-3uzau7if.txt txt = ./txt/cord-300018-3uzau7if.txt === reduce.pl bib === id = cord-300272-95o8yd7h author = Thépaut, Michel title = DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date = 2020-08-10 pages = extension = .txt mime = text/plain words = 6862 sentences = 356 flesch = 53 summary = In the context of the current COVID-19 pandemic, attention is now focused on the SARS-CoV-2 virus Zhou et al., 2020) .Coronaviruses use a homotrimeric glycosylated spike (S) protein protruding from their viral envelope to interact with cell membranes and promote fusion upon proteolytic activation. Additionally, in the case of SARS-CoV-2, a new paradigm is needed to untangle the complex clinical picture, resulting in a vast range of possible symptoms and in a spectrum of disease severity associated on one hand with active viral replication and cell infection through interaction with ACE2 along the respiratory tract, and, on the other hand, to the development of excessive immune activation, i.e. the so called "cytokine storm", that is related to additional tissue damage and potential fatal outcomes. These observations prompted us to investigate the potential interaction of C-type lectins receptors, notably DC/L-SIGN with SARS-CoV-2, through glycan recognition of the spike envelope glycoprotein, as well at their potential role in SARS-CoV-2 transmission. cache = ./cache/cord-300272-95o8yd7h.txt txt = ./txt/cord-300272-95o8yd7h.txt === reduce.pl bib === id = cord-299989-p59u6qa0 author = Zhang, Lei title = Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1282 sentences = 69 flesch = 49 summary = title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. Interestingly, our finding that ACE2 was highly expressed in breast appears to be in contrast to a retrospective study on nine pregnant women with COVID-19 in the third trimester, in which the colostrum from six patients tested negative for SARS-CoV-2 (H. cache = ./cache/cord-299989-p59u6qa0.txt txt = ./txt/cord-299989-p59u6qa0.txt === reduce.pl bib === id = cord-300041-1d9xu4ts author = Chen, Sharon C-A title = Focus on SARS-CoV-2 and COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 1024 sentences = 60 flesch = 52 summary = In contrast, more recent pandemics have been dominated by viruses such as influenza H1N1 and H3N2, localised epidemics by Ebola virus, severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1), MERS-CoV, and now, SARS-CoV-2, the causative agent of COVID-19. However, by having a single edition, with broad focus on human pathology of SARS-CoV-2 infection, we aim to provide the readers of Pathology with insights from different areas of COVID-19 diagnosis. 2 Substantive progress continues to be made in the arena of diagnostic tests for SARS-CoV-2 infection with improvements in molecular diagnostics, rapid antigen detection tests and serological assays. We continue to be faced by the risk of pandemics and we must learn from our observations at present with SARS-CoV-2 infection, and resulting COVID-19 disease. Virus isolation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnostic and research purposes Rapid deployment of pathology services to a remote Australian quarantine setting during the COVID-19 pandemic cache = ./cache/cord-300041-1d9xu4ts.txt txt = ./txt/cord-300041-1d9xu4ts.txt === reduce.pl bib === id = cord-299835-92karhpl author = Ho, Khek Y. title = Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date = 2004-02-17 pages = extension = .txt mime = text/plain words = 3524 sentences = 163 flesch = 52 summary = title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. cache = ./cache/cord-299835-92karhpl.txt txt = ./txt/cord-299835-92karhpl.txt === reduce.pl bib === id = cord-300117-rlpzejjt author = Coutard, B. title = The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade date = 2020-02-10 pages = extension = .txt mime = text/plain words = 3021 sentences = 146 flesch = 50 summary = In the case of human-infecting coronaviruses such as HCoV-OC43 (Le Coupanec et al., 2015) , MERS-CoV (Millet and Whittaker, 2014) , and HKU1 (Chan et al., 2008) the spike protein has been demonstrated to be cleaved at an S1/S2 cleavage site (Fig. 2) generating the S1 and S2 subunits. The furin-like S2′ cleavage site at KR↓SF with P1 and P2 basic residues and a P2′ hydrophobic Phe (Seidah and Prat, 2012) , downstream of the IFP is identical between the 2019-nCoV and SARS-CoV (Fig. 2) . However, in the other less pathogenic circulating human CoV, the S2′ cleavage site only exhibits a monobasic R↓S sequence (Fig. 2) with no basic residues at either P2 and/or P4 needed to allow furin cleavage, suggesting a less efficient cleavage or higher restriction at the entry step depending on the cognate proteases expressed by target cells. cache = ./cache/cord-300117-rlpzejjt.txt txt = ./txt/cord-300117-rlpzejjt.txt === reduce.pl bib === id = cord-300300-jqi4ylrx author = Lin, Ray Junhao title = From SARS to COVID‐19: the Singapore journey date = 2020-05-31 pages = extension = .txt mime = text/plain words = 2611 sentences = 159 flesch = 50 summary = The 2003 severe acute respiratory syndrome (SARS) outbreak challenged the nation's public health system and now the coronavirus disease 2019 (COVID-19) pandemic is presenting a greater challenge. This framework serves as the foundation for the national responses to any outbreak and is divided into four levels of incremental severity (green, yellow, orange and red), based on risk assessment of the public health impact of the disease and the current disease situation in Singapore (Box 1). Workers who tested positive were transferred to community isolation facilities if they had mild symptoms, or to the NCID and public hospitals for further treatment and isolation. Health care workers in direct contact with COVID-19 patients who developed fever or symptoms of acute respiratory infection were encouraged to declare their symptoms to their superiors and present themselves to the screening centre, to be managed based on their exposure risk (Box 4). cache = ./cache/cord-300300-jqi4ylrx.txt txt = ./txt/cord-300300-jqi4ylrx.txt === reduce.pl bib === id = cord-300138-1s87msv2 author = Jang, Youngeun title = Olfactory and taste disorder: The first and only sign in a patient with SARS-CoV-2 pneumonia date = 2020-04-20 pages = extension = .txt mime = text/plain words = 706 sentences = 47 flesch = 55 summary = 3 Recently, Giacomelli et al 4 reported that 20 of 59 (33.9%) of SARS-CoV-2-positive hospitalized patients had an olfactory or taste disorder. 4 SARS-CoV-2 can be transmitted in the asymptomatic or paucisymptomatic stages; therefore, olfactory and taste disorders can be significant signs for its early detection to control transmission. He had been self-quarantined for 14 days since March 12 due to close contact with a confirmed SARS-CoV-2-positive patient, who was his cohabitant. Although he had no clinical symptoms or signs of COVID-19 such as fever, myalgia, cough, and sore throat, on March 26 (the final day of his quarantine) he was confirmed positive based on a polymerase chain reaction (PCR) test (Rdrp gene, cycle threshold value of 30.28 on sputum and 33.47 on nasopharyngeal and oropharyngeal swab). This case of a SARS-CoV-2-positive patient with radiologically proven pneumonia on chest CT, who presented with only olfactory and taste disorders and no other clinical manifestations, suggests that previous cases with asymptomatic infections could have been misclassified. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study cache = ./cache/cord-300138-1s87msv2.txt txt = ./txt/cord-300138-1s87msv2.txt === reduce.pl bib === id = cord-300156-ags07bc5 author = Zhou, Yunyun title = Ocular Findings and Proportion with Conjunctival SARS-COV-2 in COVID-19 Patients date = 2020-04-21 pages = extension = .txt mime = text/plain words = 823 sentences = 50 flesch = 52 summary = The 1 patient with ocular symptoms and positive SARS-CoV-2 conjunctival swab results was classified as a severe or critical case. Two patients without ocular symptoms showed positive results for conjunctival SARS-CoV-2, with one of them classified as a severe or critical case and another classified as a mild or moderate case. Of 3 patients who showed positive results for conjunctival SARS-CoV-2, 2 were severe or critical cases and 1 was a mild or moderate case. The finding of ocular symptoms was not associated significantly with the results of conjunctival SARS-CoV-2 detection (Table S2, Our study has several limitations. In conclusion, this study characterizes the ocular symptoms in COVID-19 patients, reports the proportion of samples with positive conjunctival and nasopharyngeal RT-PCR results from patients with COVID-19, and incorporates the duration of disease into the analysis. The appearance of symptoms and penlight findings or the results of positive conjunctival swab analysis were not correlated significantly with the duration of disease. cache = ./cache/cord-300156-ags07bc5.txt txt = ./txt/cord-300156-ags07bc5.txt === reduce.pl bib === id = cord-300174-5pt9jmyz author = Deng, Wei title = Therapeutic efficacy of Pudilan Xiaoyan Oral Liquid (PDL) for COVID-19 in vitro and in vivo date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1242 sentences = 84 flesch = 56 summary = 4 Twelve SARS-CoV-2infected hACE2 mice were randomly assigned to the two groups, PDL-treated group and model control group. Next, the viral RNA copies of lung were significantly reduced in SARS-CoV-2-infected hACE2 mice with PDL treatment compared with model control group at 3 dpi (****p < 0.0001, t = 27.94, df = 4) and 5 dpi (p = 0.0021) (Fig. 1c) . These data indicated that PDL had a potent inhibitory effect against SARS-CoV-2 in vitro and in vivo, as well as improved the weight loss caused by the viral replication. To evaluate the efficacy of PDL against pneumonia caused by SARS-CoV-2 infection, the histopathological changes were observed in PDL-treated mice and control mice. These data indicated that the pneumonia in SARS-CoV-2-infected hACE2 mice was relieved after PDL treatment. cache = ./cache/cord-300174-5pt9jmyz.txt txt = ./txt/cord-300174-5pt9jmyz.txt === reduce.pl bib === id = cord-300194-nsp53lv6 author = Rath, Soumya Lipsa title = Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date = 2020-06-19 pages = extension = .txt mime = text/plain words = 4302 sentences = 226 flesch = 54 summary = Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. and S2 domains individually, with respect to the starting structure, to understand the ause for higher R S values o served at and igure The R S values of S1 domain at and were found to e around nm nearly nm more than simulations at 1 and respe tively similar trend was o served in the R S of S domain ut the differen e in values was only 1 nm lthough in this study we haven't considered the bilayer lipid membrane of the SARS-COV-2 envelope inside which the Spike 9 glycoprotein resides, the S2 domain shows remarkable stability in its RMSD values ( Figure 2 ). cache = ./cache/cord-300194-nsp53lv6.txt txt = ./txt/cord-300194-nsp53lv6.txt === reduce.pl bib === id = cord-298535-wmxlu3l1 author = Agnihothram, Sudhakar title = Evaluation of Serologic and Antigenic Relationships Between Middle Eastern Respiratory Syndrome Coronavirus and Other Coronaviruses to Develop Vaccine Platforms for the Rapid Response to Emerging Coronaviruses date = 2013-11-18 pages = extension = .txt mime = text/plain words = 5036 sentences = 235 flesch = 43 summary = In this article, we use alphavirus replicon vaccine vectors to express a panel of recombinant S and N proteins from distantly related alphacoronaviruses and betacoronaviruses, including MERS-CoV and other subgroup 2c CoVs. Using mouse polyclonal antisera and recombinant proteins, we compare the cross-reactivity and neutralization titers of these antisera between distantly related human and bat CoVs. Our results indicate that the S glycoprotein but not the N protein is the major determinant of the neutralizing antibody response to MERS-CoV; that the N proteins of CoVs only cross-react within but not between subgroups; that little if any cross-neutralization or cross-reactivity exists between the S proteins of CoVs within subgroup 2c or any other subgroup; and that cross-neutralization and cross-reactive patterns were validated with the convalescent-phase serum sample from a patient infected with MERS-CoV Hu/England-N1/2012 and a donor panel of human antisera against 3 different HCoVs. Our approach provides critical reagents, antisera, and recombinant virus vaccines that allow for rapid diagnosis of and intervention against MERS-CoV and other zoonotic CoVs that emerge in the future. cache = ./cache/cord-298535-wmxlu3l1.txt txt = ./txt/cord-298535-wmxlu3l1.txt === reduce.pl bib === id = cord-300078-svu06v9c author = Haghani, Milad title = Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6365 sentences = 298 flesch = 52 summary = To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. Figures A1 and A2 in the Appendix illustrate the map associated with the SARS literature overlaid respectively with the average year of publication and average number of citations associated with the studies where these keywords have occurred. Maps of term occurrences based on the analysis of the title and abstract of studies on SARS, MERS and Covid-19 have also been presented in Figures 7, 8 and 9 respectively. An inspection of the maps overlaid with the average year of publications for SARS and MERS in Figures A1 and A3 in the Appendix suggests that, on average, this cohort of studies are generally the last to emerge in the published domain compared to the two other major clusters, but they receive relatively high citations on average (according to Figures A2, A4 and A6). cache = ./cache/cord-300078-svu06v9c.txt txt = ./txt/cord-300078-svu06v9c.txt === reduce.pl bib === id = cord-300532-4d6fnjt8 author = Wang, Jiao title = Disinfection technology of hospital wastes and wastewater: Suggestions for disinfection strategy during coronavirus Disease 2019 (COVID-19) pandemic in China date = 2020-04-24 pages = extension = .txt mime = text/plain words = 6421 sentences = 331 flesch = 38 summary = For each ward and restroom of an infectious disease hospital or the infectious disease area of a general Table 1 Comparison of Disinfection technologies for hospital wastewater (Fan et al., 2017; Kühn et al., 2003; Kleinb€ ohl et al., 2018; Messerle et al., 2018; Yu et al., 2013 The ability of decoloring and deodorizing and quick decomposition of microorganisms High operation costs and hazardous by-products hospital, 1 kg of bleaching powder containing 25% of available chlorine per 10 beds should be added 3 to 4 times before further disinfection. From the perspective of investment and operation costs as well as economic and social benefits, high temperature incineration is still one of the most valuable hospital waste disinfection technology in China. Recently, RNA of SARS-CoV-2 has been found in feces of patients, which triggered concern to the disinfection of wastes and wastewater of designated hospitals during COVID-19 pandemic in China. cache = ./cache/cord-300532-4d6fnjt8.txt txt = ./txt/cord-300532-4d6fnjt8.txt === reduce.pl bib === id = cord-300319-9k8zseao author = Cinatl Jr., J. title = Infection of cultured intestinal epithelial cells with severe acute respiratory syndrome coronavirus date = 2004 pages = extension = .txt mime = text/plain words = 3017 sentences = 159 flesch = 42 summary = To identify a model for the study of intestinal pathogenesis of severe acute respiratory syndrome (SARS) we tested the sensitivity of six human intestinal epithelial cell lines to infection with SARS coronavirus (SARS-CoV). In both cell lines, SARS-CoV infection deregulated expression of cellular genes which may be important for the intestinal pathogenesis of SARS. To investigate whether ACE2 is a functional receptor for SARS-CoV in intestinal epithelial cell cultures, the cells were pre-treated for 60 min at 37°C with goat antibody directed against the human ACE2 ectodomain (R&D Systems; Wiesbaden-Nordenstadt, Germany). SARS-CoV infection of Caco-2 cells up-regulated OAS2 and MXA but not PKR genes. The discrepancy between transcriptional activation of IFN-induced genes and the ability of SARS-CoV to replicate in Caco-2 cells could be explained by the existence of a specific viral mechanism for escaping IFNinduced anti-viral effects common to most viruses [28] . This justifies the use of intestinal cell lines as a model to study the direct effects of SARS-CoV infection on gene expression in permissive human cells. cache = ./cache/cord-300319-9k8zseao.txt txt = ./txt/cord-300319-9k8zseao.txt === reduce.pl bib === id = cord-300324-95fty9yi author = Ni Lochlainn, M. title = Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4271 sentences = 247 flesch = 51 summary = Conclusions: Being older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. Visit to hospital as outcome were fit to test for association between i) self-reported obesity and ii) chronic lung disease and asthma, heart disease, diabetes and kidney disease in the following groups: 1) self-reported COVID-19 infection with classical symptoms (SR-COVID19); 2) self-reported positive COVID-19 test results (T-COVID19); 3) imputed/predicted COVID-19 infection based on symptomatology (I-COVID19) Imputation for testing positive for COVID was performed using the data at day of maximum sum of symptoms and applying a logistic regression using coefficients defined previously (2) . In this study we found that age, obesity, diabetes and pre-existing lung, renal and cardiac disease, were risk factors for a hospital visit with COVID-19 amongst a large but relatively young, community-based population of app users. cache = ./cache/cord-300324-95fty9yi.txt txt = ./txt/cord-300324-95fty9yi.txt === reduce.pl bib === id = cord-300423-q2i328sz author = Bai, Lei title = Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date = 2020-10-14 pages = extension = .txt mime = text/plain words = 1470 sentences = 106 flesch = 64 summary = Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. The results demonstrate that the pre-infection of 57 IAV strongly enhances the infectivity of SARS-CoV-2 by boosting viral entry in the cells 58 and by elevating viral load plus more severe lung damage in infected mice. We 75 further tested more cell lines to show that the enhancement of the pSARS-CoV-2 infectivity 76 by IAV was a general effect although the increased folds were different (lower basal level 77 of infectivity, higher enhancement fold) (Fig.1D ). We found that the pre-infection of IAV 80 strongly increased the copy numbers of the SARS-CoV-2 genome (E and N genes) in both 81 cell lysates and supernatants of A549 (~15 folds) (Fig.1F) . The histological data in Fig. 2D further illustrated that IAV and 98 SARS-CoV-2 co-infection induced more severe lung pathologic changes with massive 99 infiltrating cells and obvious alveolar necrosis as compared to SARS-CoV-2 single 100 infection or mock infection. cache = ./cache/cord-300423-q2i328sz.txt txt = ./txt/cord-300423-q2i328sz.txt === reduce.pl bib === id = cord-300445-qzu4gz2d author = Zhang, Xiao-lei title = Pharmacological and cardiovascular perspectives on the treatment of COVID-19 with chloroquine derivatives date = 2020-09-23 pages = extension = .txt mime = text/plain words = 7247 sentences = 376 flesch = 37 summary = Chloroquine phosphate and its derivative hydroxychloroquine, which have been used in the treatment and prevention of malaria and autoimmune diseases for decades, were found to inhibit SARS-CoV-2 infection with high potency in vitro and have shown clinical and virologic benefits in COVID-19 patients. However, chloroquine phosphate and its derivative hydroxychloroquine, which have been used for decades in the treatment and prevention of malaria and chronic inflammatory diseases such as rheumatoid arthritis and systemic lupus erythematosus, were discovered to have a high inhibitory potency against SARS-CoV-2 infection in vitro [2] [3] [4] [5] and favorable clinical and virologic benefits in COVID-19 patients [6] [7] [8] [9] [10] , and they have emerged as important therapies for COVID-19 in several countries, including China, France, USA, and India, although the mechanisms of their anti-COVID-19 effects remain unclear. cache = ./cache/cord-300445-qzu4gz2d.txt txt = ./txt/cord-300445-qzu4gz2d.txt === reduce.pl bib === id = cord-300063-5jemq8nm author = Rane, Jitendra Subhash title = Targeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 5786 sentences = 301 flesch = 49 summary = Because of the enormous therapeutic importance, we selected some well-characterized pyrimidine substituted phenols (Kumar & Rao, 2018; Table S1 , supplementary material) to investigate their efficiency in binding to the interface of the hACE2-S protein complex and modulate the pattern of infectivity of the SARS-CoV-2 virus. In this study, we aim to identify diaryl pyrimidine derivatives as a potential lead molecule which may bind at the interface of the hACE2-S protein complex with high affinity. The study presented here, using molecular docking tool, revealed significant binding interaction of diaryl pyrimidines with the interface of the hACE2-S receptor complex (hACE2-spike protein complex: PDB ID 6VW1) (Table 1) . To examine the spatial stability and mechanistic aspects of conformational dynamics underlying the molecular interaction of diaryl pyrimidine derivatives, AP-NP, AP-3-OMe-Ph and AP-4-Me-Ph with hACE2-S protein complex, we performed MD simulation in an aqueous environment for the period of 100 ns, at physiological temperature (300 K). cache = ./cache/cord-300063-5jemq8nm.txt txt = ./txt/cord-300063-5jemq8nm.txt === reduce.pl bib === id = cord-300322-koqm5yxq author = Li, Fang title = Interactions Between Sars Coronavirus and its Receptor date = 2006 pages = extension = .txt mime = text/plain words = 1711 sentences = 103 flesch = 60 summary = The SARS-CoV RBD is sufficient for tight binding to ACE2, and thus it is the most important determinant of virus-receptor interactions, viral host range, and tropism. 8 The final model of the complex contains the N-terminal peptidase domain of human ACE2 (residues 19-615) and the spike RBD of human SARS-CoV (residues 323-502, missing residues 376-381). The structure reveals important residue changes at the binding interface that determine the species specificity of SARS-CoV. 6, 7 Detailed structural analysis sheds light on the significance of these residues in virus-receptor interactions (Figure 4 ). Rat ACE2 does not support SARS-CoV Leu472 on the RBD has a hydrophobic interaction with Met82 on ACE2. On rat ACE2, residue 82 is glycosylated, preventing the binding of SARS-CoV. In summary, the crystal structure of SARS-CoV spike RBD in complex with ACE2 has revealed detailed interactions between the virus and its receptor. Structure of SARS coronavirus spike receptor-binding cache = ./cache/cord-300322-koqm5yxq.txt txt = ./txt/cord-300322-koqm5yxq.txt === reduce.pl bib === id = cord-300191-vpc7p0d6 author = Bektaş, Osman title = The relationship between severe acute respiratory syndrome coronavirus 2 (SARS - COV - 2) pandemic and fragmented QRS date = 2020-07-22 pages = extension = .txt mime = text/plain words = 1925 sentences = 139 flesch = 57 summary = OBJECTIVE: The aim of the study is to determine the frequency of fragmented QRS (FQRS) in patients with SARS COV 2. [7] In a study, evaluating patients with coronary artery disease (CAD), those with FQRS had significantly higher all cause mortality and higher frequency of adverse cardiovascular outcomes (myocardial infarction, sudden cardiac death, revascularization) [8] . The requirement for intensive care unit incresed with increasing levels of troponin in patients with SARS-COV-2 (p<0.000, Table 3 ). Moreover, a significant positive correlation was detected between serum CRP levels,heart rate and frequency of FQRS in patients with SARS-COV-2 (r=0.204, p=0.024, r=0.187 p=0.029) Lineer regression analyses revealed that serum CRP levels and heart rate were the independent predictors of presence of FQRS (Table 4 ). Fragmented QRS on a 12-lead ECG: a predictor of mortality and cardiac events in patients with coronary artery disease cache = ./cache/cord-300191-vpc7p0d6.txt txt = ./txt/cord-300191-vpc7p0d6.txt === reduce.pl bib === id = cord-300608-eju7wnb9 author = Sheervalilou, Roghayeh title = COVID‐19 under spotlight: A close look at the origin, transmission, diagnosis, and treatment of the 2019‐nCoV disease date = 2020-05-26 pages = extension = .txt mime = text/plain words = 7391 sentences = 384 flesch = 47 summary = 2.1 | Respiratory system SARS-CoV-2 tends to infect the respiratory tract, thus, pneumonia is a primary clinical finding in patients with COVID-19 Li, Guan, et al., 2020; Zhu et al., 2020) . A number of investigations recently conducted on COVID-19 have reported that IL-6 levels was actually higher in the patients with severe disease (Cai, 2020; Chen, Liu, et al., 2020; Xiang et al., 2020) . Impaired liver function tests have been reported for a number of patients with SARS-CoV-2 infection, suggesting hepatic damage as an extrapulmonary complication of COVID-19 in almost one half of the patients (Chen, Zhou, et al., 2020; Wang, Hu, et al., 2020) . Since H7N9 and SARS-CoV-2 can result in similar complications, for example, ARDS and respiratory failure, MSC-based therapy might lead to a new path in treatment of COVID-19-associated pneumonia . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-300608-eju7wnb9.txt txt = ./txt/cord-300608-eju7wnb9.txt === reduce.pl bib === id = cord-300625-fvirvpyl author = Srinivasan, Suhas title = Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date = 2020-03-25 pages = extension = .txt mime = text/plain words = 5902 sentences = 285 flesch = 41 summary = In addition to the global structural genomics, an initiative that focuses on determining the 3D structures of individual proteins on a genome scale [34] , as well as to the specific efforts aimed at rapid structural characterization of proteins in emerging viruses [35] [36] [37] [38] , multiple works have used comparative modeling to predict the structures of protein-protein interaction complexes [39] [40] [41] , facilitate structure-based drug discovery [33, 42, 43] , infer protein functions [44] , determine the macromolecular interaction network [45] [46] [47] [48] , and provide molecular insights into the viral evolution [49] [50] [51] . To do so, we structurally characterized individual proteins as well as intra-viral and human-virus protein complexes, extracted the information on their interaction interfaces and ligand binding, and superposed the evolutionary difference and conservation information with the binding information. cache = ./cache/cord-300625-fvirvpyl.txt txt = ./txt/cord-300625-fvirvpyl.txt === reduce.pl bib === id = cord-300320-07tdrd4w author = Siordia, Juan A. title = Systematic and Statistical Review of Coronavirus Disease 19 Treatment Trials date = 2020-07-15 pages = extension = .txt mime = text/plain words = 4829 sentences = 372 flesch = 44 summary = Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, tocilizumab, favipiravir, heparin, and dexamethasone. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Medical therapies investigated included lopinavir/ritonavir, arbidol, hydroxychloroquine, remdesivir, favipiravir, heparin, glucocorticoids, interferon, ivermectin, and convalescent plasma. Key words included COVID-19, SARS-CoV2, randomized, This article is part of the Topical Collection on Covid-19 controlled, human, retrospective, prospective, trial, chloroquine, hydroxychloroquine, lopinavir, ritonavir, arbidol, umifenovir, tocilizumab, favipiravir, steroids, dexamethasone, glucocorticoids, interferon, ivermectin, remdesivir, azithromycin, heparin, and low-molecular weight heparin. Lopinavir/ritonavir, arbidol, hydroxychloroquine, favipiravir, remdesivir, and heparin are medications that have been tested in human controlled trials for COVID-19 treatment. In human trials, arbidol shows no significant positive-negative conversion rate or recovery time compared to standard therapy or lopinavir/ritonavir [4, 9] . Combining T, treatment group (remdesivir); C, control group all the hydroxychloroquine human trials showed no benefit with reducing COVID-19 viral shedding time. cache = ./cache/cord-300320-07tdrd4w.txt txt = ./txt/cord-300320-07tdrd4w.txt === reduce.pl bib === id = cord-300685-bcjnujlj author = Poon, Leo L M title = Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date = 2003-06-01 pages = extension = .txt mime = text/plain words = 2425 sentences = 115 flesch = 54 summary = The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. cache = ./cache/cord-300685-bcjnujlj.txt txt = ./txt/cord-300685-bcjnujlj.txt === reduce.pl bib === id = cord-300458-jeuwaj50 author = Maisch, Bernhard title = COVID-19—What we know and what we need to know: There are more questions than answers date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1156 sentences = 73 flesch = 57 summary = COVID-19-What we know and what we need to know: There are more questions than answers This collection of short statements from the editors of HERZ/Cardiovascular Diseases is a strong signal to the readers of our journal in critical times. But we also fear that with a low herd immunity a second wave of infection might follow, since no proven antiviral treatment for COVID-19 exists and vaccination is not yet available [3] . Pulmonology demonstrates with every ventilated patient that COVID-19 is a potentially lethal lung disease. The first reported Chinese patient with suspected myocarditis from SARS-CoV-2 was treated with ventilation, methylprednisolone, i.v. immunoglobulins and inotropics and survived [4] . A total of 55 authors (!) have described in an observational study with 66 COVID-19 patients without a control group a beneficial effect in the New England Journal of Medicine [5] . 2020) compassionate use of remdesivir for patients with severe Covid-19 cache = ./cache/cord-300458-jeuwaj50.txt txt = ./txt/cord-300458-jeuwaj50.txt === reduce.pl bib === id = cord-300640-9pvhaz8q author = Parackova, Zuzana title = Disharmonic Inflammatory Signatures in COVID-19: Augmented Neutrophils’ but Impaired Monocytes’ and Dendritic Cells’ Responsiveness date = 2020-09-29 pages = extension = .txt mime = text/plain words = 5975 sentences = 344 flesch = 47 summary = We demonstrate the impaired functionality of COVID-19 dendritic cells and monocytes, particularly their low expression of maturation markers, increased PD-L1 levels, and their inability to upregulate phenotype upon stimulation. Ex vivo stimulation of peripheral whole blood with lipopolysaccharide (LPS) led to a rapid increase in surface degranulation markers CD11b and CD66b, and decrease in CD62L, a lectin involved in granulocyte trafficking, on both patient and healthy donor neutrophils ( Figure 1C and Figure S1C ). Only the COVID-19, but not the healthy neutrophils, were able to increase the production of IL-1β and TNFα upon ssRNA stimulation in comparison with untreated cells ( Figure 2B ) indicating a pro-inflammatory bias, possibly due to priming with SARS-CoV-2 or excessive cytokine/chemokine stimulation. In contrast to monocytes and DCs, COVID-19 neutrophils expressed significantly decreased levels of PD-L1 and their stimulation with ssRNA led to elevated production of proinflammatory cytokines. cache = ./cache/cord-300640-9pvhaz8q.txt txt = ./txt/cord-300640-9pvhaz8q.txt === reduce.pl bib === id = cord-300697-p96i25uc author = Chen, Taojiang title = A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report date = 2020-09-29 pages = extension = .txt mime = text/plain words = 2182 sentences = 128 flesch = 43 summary = title: A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report CASE PRESENTATION: We herein described a case of severe SARS-CoV-2 infected patient with several risk factors for poor prognosis, including male, hypertension, old age, mixed bacterial infection and multilobular infiltration on radiological imaging. After improvement of respiratory status, the onset of gastrointestinal bleeding occurred, probably resulting from direct viral invasion as evidenced by the positive findings for SARS-CoV-2 in the repeat stool specimens. Additionally, despite the clinical manifestations of coronavirus disease 2019 (COVID-19) are dominated by respiratory symptoms, evidences from recent studies have suggested that SARS-CoV-2 has the ability to actively infect and replicate in the gastrointestinal tract [3] . Herein, we described an old-aged COVID-19 patient with multiple risk factors for severe disease and ultimately died from massive GIB at Wuhan Union Hospital. cache = ./cache/cord-300697-p96i25uc.txt txt = ./txt/cord-300697-p96i25uc.txt === reduce.pl bib === id = cord-300627-7x4me5lx author = Ng, W. F. title = The placentas of patients with severe acute respiratory syndrome: a pathophysiological evaluation date = 2006-06-30 pages = extension = .txt mime = text/plain words = 4396 sentences = 293 flesch = 57 summary = Summary Aims The pathology of the placentas delivered from pregnant women who had severe acute respiratory syndrome (SARS) in Hong Kong was studied. In three placentas delivered in the acute stage of SARS, there were increases in intervillous or subchorionic fibrin which might be related to disturbances in maternal placental blood flow due to the hypoxic respiratory disease. Extensive fetal thrombotic vasculopathy (FTV) with sharply demarcated zones of avascular fibrotic villi was noted in the placentas of two patients convalescent from SARS in the third trimester. Wong also showed that pregnant SARS patients had a higher rate of respiratory failure and drew an analogy with the more severe clinical course of epidemic influenza in pregnant women. This study was undertaken to examine the pathology of the placentas delivered from women who contracted SARS during pregnancy and to correlate the findings with the clinical and obstetric course and the neonatal outcome. cache = ./cache/cord-300627-7x4me5lx.txt txt = ./txt/cord-300627-7x4me5lx.txt === reduce.pl bib === id = cord-300399-21xozruq author = Jayamohan, Harikrishnan title = SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date = 2020-10-18 pages = extension = .txt mime = text/plain words = 13003 sentences = 770 flesch = 44 summary = This review paper examines current molecular diagnostic tools (Fig. 1) , such as amplification-based (including CRISPR-Cas based), antibody and antigen tests, and sequencing, utilized for the detection of SARS-CoV-2. In addition, we also discuss sample preparation aspects that are relevant to wider utilization and point-of-care (POC) deployment of COVID-19 diagnostic tests (PCR, isothermal amplification, and sequencing-including library preparation). RT-PCR broadly involves four steps-lysis of SARS-CoV-2 in the sample, purification of the viral RNA, reverse transcription to complementary DNA (cDNA), and amplification of specific regions of the cDNA, and finally, optical detection of the amplified cDNA. The assay can detect the virus from respiratory swab samples with sensitivity comparable to that of the US Centers for Disease Control and Prevention (CDC) SARS-CoV-2 real-time RT-PCR assay in 30-40 min. Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples cache = ./cache/cord-300399-21xozruq.txt txt = ./txt/cord-300399-21xozruq.txt === reduce.pl bib === id = cord-300395-87bl6e38 author = Behrmann, Ole title = Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification date = 2020-10-14 pages = extension = .txt mime = text/plain words = 1017 sentences = 140 flesch = 61 summary = As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplifi cation (RT-RPA) technology. DOI: 10.1007/s12268-020-1458-3 © Die Autoren 2020 ó Die derzeitigen Protokolle zur Diagnose von SARS-CoV-2-Infektionen beruhen auf der quantitativen reversen Transkriptions-PCR (RT-qPCR) für den Direktnachweis der viralen RNA [1] . Alternativ sind seit einigen Jahren isotherme Verfahren -wie die loop-mediated isothermal amplifi cation (LAMP) [2] oder die recombinase polymerase amplification (RPA) [3] -verfügbar, welche der PCR hinsichtlich Sensitivität und Spezifi tät gleichwertig sind. Aufbauend auf vorhergehenden Arbeiten, in welchen der Nachweis anderer Coronaviren wie MERS-CoV [4] und Bovines Coronavirus (BCoV) [5] mittels RPA demonstriert wurde, stellen wir in diesem Artikel die Entwicklung eines RPA-Assays für den Schnellnachweis von SARS-CoV-2 vor. cache = ./cache/cord-300395-87bl6e38.txt txt = ./txt/cord-300395-87bl6e38.txt === reduce.pl bib === id = cord-300466-sk9iilum author = Kong, Wen-Hua title = Serologic Response to SARS-CoV-2 in COVID-19 Patients with Different Severity date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2461 sentences = 135 flesch = 52 summary = According to the Chinese Centers for Disease Prevention and Control (CDC) report, among 72,314 COVID-19 cases in China's mainland most of cases (81%) presented only mild illness or moderate pneumonia, yet 14% developed severe symptoms such as dyspnea, high respiratory frequency and low blood oxygen saturation, and another 5% were in critical conditions like respiratory failure, septic shock, and multiple organ dysfunction/failure (Epidemiology Working Group for NCIP Epidemic Response and Chinese CDC, 2020; Wu and McGoogan 2020) . In this study, we, compared the results of serologic tests and nucleic acid test (NAT) from a group of COVID-19 patients in Wuhan, and analyzed the serologic IgM and IgG antibody level of patients with different disease severity. In summary, this study supported the combination of serologic testing and NAT in routine COVID-19 diagnosis and provided evidence on the temporal profile of antibody response against SARS-CoV-2 in patients with different disease severity. cache = ./cache/cord-300466-sk9iilum.txt txt = ./txt/cord-300466-sk9iilum.txt === reduce.pl bib === id = cord-300850-59j1m2tm author = Peron, Jean Pierre Schatzmann title = Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE) date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3267 sentences = 171 flesch = 44 summary = Toward this, we raise two main points, i) increased ACE-2 expression in pulmonary and heart tissues in users of chronic angiotensin 1 receptor (AT1R) blockers; and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. Toward this, we raise two main points of discussion, i) the increased angiotensin-converting enzyme-2 (ACE-2) expression in pulmonary and heart tissues of hypertensive patients with chronic use of AT1R blockers and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. SARS-CoV-2 spike proteins bind to angiotensin-converting enzyme-2 (ACE-2), which is expressed in the epithelial cells of the lungs (8, 9) . We believe that i) increased expression of ACE-2 in hypertensive patients being treated with ACE inhibitors and AT1R blockers and ii) previous exposure to circulating coronaviruses with low neutralizing capacity to SARS-CoV-2 may greatly contribute to the increased susceptibility of the elderly patients to COVID-19. cache = ./cache/cord-300850-59j1m2tm.txt txt = ./txt/cord-300850-59j1m2tm.txt === reduce.pl bib === id = cord-300604-xx2d1s41 author = Li, Juyi title = Association between ABO blood groups and risk of SARS‐CoV‐2 pneumonia date = 2020-05-26 pages = extension = .txt mime = text/plain words = 795 sentences = 47 flesch = 58 summary = In December, 2019, a cluster of acute respiratory illness caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred in Wuhan, China.1,2 Epidemiological, clinical characteristics, risk factors for mortality of patients infected with SARS-CoV-2, and risk factors in the susceptibility to SARS-CoV-2 included age and chronic disease have been reported. 32Á2 %, P < 0Á01) in blood group A was much higher than that in the control group; however, there is currently no literature supporting that hypertension and hepatitis increase the risk of infection of SARS-CoV-2. 7 We still find that the proportion of blood group A in patients infected with SARS-CoV-2 was significantly higher than that in healthy controls (38Á0 % vs. 32Á2 %, P < 0Á001), while the proportion of blood group O in SARS-CoV-2 infected patients was significantly lower than in healthy controls (25Á7 % vs. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-300604-xx2d1s41.txt txt = ./txt/cord-300604-xx2d1s41.txt === reduce.pl bib === id = cord-300696-alpztpzw author = Dilek, Tugce Damla title = THE IMPACT OF SARS-COV 2 ON THE ANXIETY LEVELS OF SUBJECTS AND ON THE ANXIETY AND DEPRESSION LEVELS OF THEIR PARENTS date = 2020-10-26 pages = extension = .txt mime = text/plain words = 4238 sentences = 215 flesch = 60 summary = This study was conducted to evaluate the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety depression status of their parents. In this study, we aimed to evaluate the the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety -depression status of their parents. Disease flares, problems about reaching the hospitals, and medication, any history of contact with confirmed SARS-CoV2 infections of self or family members, encounters with digital screen, workout program, caring about diet, use of vitamins, direct exposure to sunlight, obeying the 14 rules recommended by the Ministry of Health and similar issues were questioned in the survey. The patient and control groups were compared according to STAI scores to investigate the anxiety status during SARS-CoV2 pandemic. cache = ./cache/cord-300696-alpztpzw.txt txt = ./txt/cord-300696-alpztpzw.txt === reduce.pl bib === id = cord-300707-k9uk14b3 author = Bouwman, Kim M. title = Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date = 2020-09-04 pages = extension = .txt mime = text/plain words = 2328 sentences = 176 flesch = 59 summary = Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues. The results demonstrate 104 that fully glycosylated trimeric SARS-CoV-2 RBD proteins reveal the 105 differences in ACE2 expression between cell cultures and tissue sections. A similar trend of binding intensities was observed for 214 monomeric, trimeric, and different N-glycosylated SARS-CoV-RBD proteins 215 fused to mOrange2 ( Fig S3A) . 226 227 To confirm our observations of different binding on tissues, we quantified the 228 intensities of the ACE2 antibody and SARS-CoV-1 and -2 RBD proteins, except 229 for the monomeric GnTI derived proteins as these were almost at the 230 background ( Fig 4D) . cache = ./cache/cord-300707-k9uk14b3.txt txt = ./txt/cord-300707-k9uk14b3.txt === reduce.pl bib === id = cord-300791-417tzufc author = Austin, Zubin title = Pharmacy practice in times of civil crisis: The experience of SARS and “the blackout” in Ontario, Canada date = 2007-10-16 pages = extension = .txt mime = text/plain words = 6544 sentences = 398 flesch = 65 summary = OBJECTIVES: The objectives were to describe and analyze the impact of 2 major crises (the severe acute respiratory syndrome [SARS] outbreak, and the electrical system failure ["blackout"]) on pharmacy practice and pharmacists in Toronto, Canada. RESULTS: Five key themes emerged from this research: (1) during times of crisis, pharmacies become frontline health care facilities, (2) a vacuity of leadership/lack of utility of emergency preparedness guidelines and policies, (3) role of and reliance on experience and professional judgment, (4) importance of documentation, and (5) the importance of "teamness" in enabling successful adaptation during times of crisis. In order to participate in this study, pharmacists were required to have been practicing as a pharmacist in a direct patient-care setting in Toronto for at least 25 h/wk during March 2003 to June 2003 (SARS) and August 2004 (blackout). cache = ./cache/cord-300791-417tzufc.txt txt = ./txt/cord-300791-417tzufc.txt === reduce.pl bib === id = cord-300774-5mrkmctl author = Hernández-Mora, Miguel Górgolas title = Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date = 2020-10-25 pages = extension = .txt mime = text/plain words = 4340 sentences = 230 flesch = 50 summary = INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . cache = ./cache/cord-300774-5mrkmctl.txt txt = ./txt/cord-300774-5mrkmctl.txt === reduce.pl bib === id = cord-300793-tuq8z6gm author = Weiss, Robin A title = Social and environmental risk factors in the emergence of infectious diseases date = 2004 pages = extension = .txt mime = text/plain words = 5853 sentences = 273 flesch = 47 summary = About 30 new diseases have been identified, including Legionnaires' disease, human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS), hepatitis C, bovine spongiform encephalopathy (BSE)/variant Creutzfeldt-Jakob disease (vCJD), Nipah virus, several viral hemorrhagic fevers and, most recently, severe acute respiratory syndrome (SARS) and avian influenza. Emerging infectious diseases in humans comprise the following: first, established diseases undergoing increased incidence or geographic spread, for example, Tuberculosis and Dengue fever; second, newly discovered infections causing known diseases, for example, hepatitis C and Helicobacter pylori; and third, newly emerged diseases, for example, HIV/AIDS and SARS. Although some of the apparent increase in infectious disease may be attributable to better diagnostic methods and surveillance, there seems little doubt that more incidents are occurring, and have the potential to spread more widely than 50 years ago, as outbreaks and spread of infections like Nipah virus and SARS would not have passed unnoticed. cache = ./cache/cord-300793-tuq8z6gm.txt txt = ./txt/cord-300793-tuq8z6gm.txt === reduce.pl bib === id = cord-300716-urmogf97 author = Briguglio, Matteo title = Disentangling the Hypothesis of Host Dysosmia and SARS-CoV-2: The Bait Symptom That Hides Neglected Neurophysiological Routes date = 2020-06-05 pages = extension = .txt mime = text/plain words = 9889 sentences = 460 flesch = 42 summary = The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. Keywords: smell, olfactory bulb, coronavirus, SARS-CoV-2, COVID-19, infections, virulence, host pathogen interactions THE SNIFFING OUT OF CORONAVIRUSES Named after their crown-like spikes, coronaviruses are large non-segmented single-stranded positive-sense enveloped RNA viruses that may spill out from animals to infect humans and cause respiratory diseases. It is urgent to discuss whether SARS-CoV-2 can gain access to the central nervous system through a nasal-nervous pathway or other routes and if the fatal respiratory failure may be associated with a neuronal injury in critical brain areas of the host. cache = ./cache/cord-300716-urmogf97.txt txt = ./txt/cord-300716-urmogf97.txt === reduce.pl bib === id = cord-300848-0igfcixy author = Meijers, Björn title = The clinical characteristics of coronavirus-associated nephropathy date = 2020-09-02 pages = extension = .txt mime = text/plain words = 1687 sentences = 109 flesch = 52 summary = While a minority of SARS-CoV patients did develop acute kidney injury (AKI), this was attributed to critical illness with acute tubular necrosis in post-mortem kidney tissue. In kidney tissue obtained at autopsy of 26 critically ill patients with COVID-19, diffuse proximal tubule injury also was the main finding on light microscopy [9] . This puts SARS-CoV-2 in an expanding list of other viruses with proven kidney tropism, including hantavirus [14] , the Middle East respiratory syndrome coronavirus [15] , polyomavirus (polyomavirus-associated nephropathy) [16] and the human immunodeficiency virus (HIV-associated nephropathy) [17] . To date, kidney histology of COVID-19 patients with a less severe clinical course has not been reported. In this issue of Nephrology Dialysis Transplantation, data from a large European cohort study of patients with COVID-19 are reported [3] . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-300848-0igfcixy.txt txt = ./txt/cord-300848-0igfcixy.txt === reduce.pl bib === id = cord-300763-3ateeei3 author = Vannabouathong, Christopher title = Novel Coronavirus COVID-19: Current Evidence and Evolving Strategies date = 2020-05-06 pages = extension = .txt mime = text/plain words = 6137 sentences = 308 flesch = 52 summary = The term PHEIC is defined as 27 : "an extraordinary event which is determined to constitute a public health risk to other States through the international spread of disease; and to potentially require a coordinated international response." Also, according to the WHO 28 , "This definition implies a situation that is serious, unusual, or unexpected; carries implications for public health beyond the affected state's national border; and may require immediate international action." Eleven days later, on February 10, 2020, there were, cumulatively, 40,554 confirmed cases and 910 deaths globally across 25 countries, and the majority were identified in the People's Republic of China 29 . In a cross-sectional analysis that included 1,023 COVID-19-related deaths in the People's Republic of China, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team 43 found that >80% were patients ‡60 years of age; when extending this range to those who were ‡50 years of age, this number increased to >90% 44 . cache = ./cache/cord-300763-3ateeei3.txt txt = ./txt/cord-300763-3ateeei3.txt === reduce.pl bib === id = cord-300784-4jeaqqn9 author = Ma, Huan title = COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3493 sentences = 203 flesch = 56 summary = Here, we aimed to develop a more quantitative and sensitive serological test for COVID-19 diagnosis, monitoring and clinical investigation, based on the detection of antigen-specific IgA as well as IgM and IgG in blood in response to SARS-CoV-2 infection. Methods In this investigation, we report the development of a set of validated diagnostic kits for detecting serum IgA, IgM, and IgG specific to SARS-CoV-2 nucleocapsid protein (NP) and receptor-binding domain (RBD) of the spike protein by chemi-luminescence immuno-analysis. . https://doi.org/10.1101/2020.04.17.20064907 doi: medRxiv preprint Based on the clinical RT-qPCR diagnosis results of SARS-CoV-2 infection, receiver operating 208 characteristic (ROC) analysis was conducted using MedCalc software to determine the optimal cut-off 209 value (criterion) and evaluate the diagnostic value of NP-or RBD-specific IgA, IgM, and IgG kits. Nonetheless, we showed that our serological kits based on SARS-CoV-2 spike 322 protein RBD as an immobilized antigen provide a high sensitivity and specificity for detecting IgA, IgM, 323 and IgG in a quantitative manner. cache = ./cache/cord-300784-4jeaqqn9.txt txt = ./txt/cord-300784-4jeaqqn9.txt === reduce.pl bib === id = cord-301025-cf2jcw6x author = Musca, Serban C. title = A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine's Prophylactic Effect Against Infection With SARS-CoV-2 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 4364 sentences = 190 flesch = 54 summary = title: A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine's Prophylactic Effect Against Infection With SARS-CoV-2 We propose to use data from patients with rheumatic diseases (RA, SLR) who have been chronically taking HCQ medication since before the COVID-19 outbreak (hereafter: HCQpa), in order to evaluate the potential of HCQ for preventing infection with SARS-CoV-2. If HCQ has no prophylactic effect against infection with SARS-CoV-2, COVID-19 prevalence in HCQpa will not be statistically different from that in the general population (all comers who do not take HCQ medication; hereafter: pop gen ). HCQ having a prophylactic effect against SARS-CoV-2 infection would manifest itself by a COVID-19 prevalence in HCQpa that is lower than the COVID-19 prevalence in the general population. cache = ./cache/cord-301025-cf2jcw6x.txt txt = ./txt/cord-301025-cf2jcw6x.txt === reduce.pl bib === id = cord-300950-ag0sql4i author = Lin, John title = Potential therapeutic options for coronavirus disease 2019: using knowledge of past outbreaks to guide future treatment date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1899 sentences = 104 flesch = 50 summary = Several case reports including the first report of SARS outbreak described the use of the anti-viral drug ribavirin and a corticosteroid in patients with contradictory clinical outcomes. In several studies, lopinavir/ritonavir was shown to have anti-CoV effects in vitro, in MERS-infected primate models, and in SARS-infected humans. Furthermore, in a single MERS patient, a triple-combination therapy of ribavirin, IFN and lopinavir/ ritonavir resolved viremia in 2 days following initiation of treatment. [7] [8] [9] In two reports from China and Korea, the use of lopinavir/ritonavir in patients with COVID-19 improved recovery and reduced viral load. [7, 8] However, Chen et al [9] showed that lopinavir/ ritonavir and the anti-influenza treatment Arbidol had no clinically significant improvement in 134 people with mild COVID-19. [17] In an effort to combat inflammation and improve clinical outcome, corticosteroid use has been described in SARS, MERS, and COVID-19. cache = ./cache/cord-300950-ag0sql4i.txt txt = ./txt/cord-300950-ag0sql4i.txt === reduce.pl bib === id = cord-301151-f6vya3qh author = Zhu, Xiaojuan title = Co-infection with respiratory pathogens among COVID-2019 cases date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2599 sentences = 180 flesch = 61 summary = In this study, the clinical features of COVID-19 patients were analyzed, then 39 respiratory pathogens in their throat swab were detected by specific real-time RT-PCR. 257 patients were diagnosed with the SARS-CoV-2 infection and their clinical severity was classified according to National Health Commission of the People's Republic of China revised criteria for diagnosis and treatment of novel coronavirus infection pneumonia (trial version fifth, revised version). Below 15 years of age, a total of 11 (4.3 %) were diagnosed with the SARS-CoV-2 infection and there were no case in severe/critical category. In our study, 94.2 % of COVID-19 patients could be co-infected with one or more other pathogens, including 9 viruses, 11 bacteria and 4 fungi. Along with the course of disease, both the rates and pathogen species of co-infection among COVID-19 patients were decreased significantly, which may due to the treatment X. cache = ./cache/cord-301151-f6vya3qh.txt txt = ./txt/cord-301151-f6vya3qh.txt === reduce.pl bib === id = cord-300866-cso6l6ze author = Bao, Yi title = Clinical Features of COVID-19 in a Young Man with Massive Cerebral Hemorrhage—Case Report date = 2020-05-23 pages = extension = .txt mime = text/plain words = 4252 sentences = 217 flesch = 50 summary = Both SARS-CoV-2 nucleic acid tests were negative (24 h interval), Fig. 2 The treatment of COVID-19 patients with intracerebral hemorrhage suggesting that antiviral treatment was effective. On February 29, the patient did not have high fever again, the results of the cerebrospinal fluid review showed that it was light red, no clot, protein decreased to 0.8 g/L, sugar increased to 4.45 mmol/L, and white blood cells decreased to 37 × 10 6 G/L, of which monocytes accounted for 74%. The patient's cerebrospinal fluid showed improvement, and since the two re-examinations of SARS-CoV-2 nucleic acid test was negative, and the antiviral treatment with Abidol, Ribavirin, and Oseltamivir had reached the course of treatment, so it was discontinued. However, in combination with the patient's high fever, lymphocytopenia, increased neutrophils, and poor antibacterial treatment effect, the clinical manifestations conform to the COVID-19 characteristics, and nucleic acid detection is required. cache = ./cache/cord-300866-cso6l6ze.txt txt = ./txt/cord-300866-cso6l6ze.txt === reduce.pl bib === id = cord-300968-dtaasxk1 author = Kliger, Yossef title = From genome to antivirals: SARS as a test tube date = 2005-03-01 pages = extension = .txt mime = text/plain words = 5104 sentences = 272 flesch = 46 summary = Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. This strategy seems promising in developing anti-viral therapeutic peptides to other viruses that possess type 1 viral fusion proteins [e.g. measles virus and respiratory syncytial virus (RSV)], which share some structural motifs with HIV. Similar to HIV, binding of the viral spike glycoprotein to some receptor(s) on host cells is the first step in SARS-CoV infection. HIV entry involves the binding of the viral envelope glycoproteins (comprising gp120 and gp41, which are the homologous of SARS-CoV S1 and S2, respectively) to CD4 on the host cell plasma membrane. Following the rule: formation of the 6-helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoproteinmediated viral entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeatderived peptides cache = ./cache/cord-300968-dtaasxk1.txt txt = ./txt/cord-300968-dtaasxk1.txt === reduce.pl bib === id = cord-300783-pvn2qq0f author = Sadykov, Mukhtar title = Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date = 2020-08-07 pages = extension = .txt mime = text/plain words = 933 sentences = 91 flesch = 61 summary = title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins. One such 34 mechanism is the CpG dinucleotide reduction observed in many single-stranded RNA 35 fraction of the observed C>U changes represent multiple, independent events ( Figure S3 ). CpG Dinucleotides in SARS-CoV-2 Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host 396 antiviral defense Multi-site co-398 mutations and 5'UTR CpG immunity escape drive the evolution of SARS-CoV-2 cache = ./cache/cord-300783-pvn2qq0f.txt txt = ./txt/cord-300783-pvn2qq0f.txt === reduce.pl bib === id = cord-301167-101lnq4f author = Liu, Quanjun title = Microarray-in-a-Tube for Detection of Multiple Viruses date = 2007-02-01 pages = extension = .txt mime = text/plain words = 3248 sentences = 177 flesch = 48 summary = Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube. cache = ./cache/cord-301167-101lnq4f.txt txt = ./txt/cord-301167-101lnq4f.txt === reduce.pl bib === id = cord-300923-5cyxr98s author = Younger, David S title = Postmortem Neuropathology in Covid‐19 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 631 sentences = 46 flesch = 42 summary = This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid‐19) due to severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) from among 250 reported patients succumbing to Covid‐19 illness (1‐7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid‐19 illness, and are important in the development of effective treatment strategies. This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid-19) due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from among 250 reported patients succumbing to Covid-19 illness (1-7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid-19 illness, and are important in the development of effective treatment strategies. As shown in Table 1 , older age, male gender, increased serum cytokine and pro-coagulation markers, and critical care hospitalization for ≤10 days prior to death characterized the cohort. Neuropathologic features of four autopsied COVID-19 patients The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 cache = ./cache/cord-300923-5cyxr98s.txt txt = ./txt/cord-300923-5cyxr98s.txt === reduce.pl bib === id = cord-301079-n1nytr6k author = Tan, Li title = Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date = 2020-07-27 pages = extension = .txt mime = text/plain words = 3556 sentences = 205 flesch = 60 summary = Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. cache = ./cache/cord-301079-n1nytr6k.txt txt = ./txt/cord-301079-n1nytr6k.txt === reduce.pl bib === id = cord-301183-k39e12cq author = Pham, Tho D. title = SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution date = 2020-07-17 pages = extension = .txt mime = text/plain words = 289 sentences = 26 flesch = 55 summary = title: SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution than 1 month after symptom resolution is concerning in light of current guidelines, which do not recommend SARS-CoV-2 screening in the general allogeneic donor population (5) . In this case, plasma viral RNA was reproducibly detected at a time point that exceeded recommendations for deferral based on time since symptom resolution (14 days). Of importance, these results are unlikely to be false-positive given that 2 different regions of the SARS-CoV-2 genome were detected in separate specimens collected on the day of donation and that quality control passed on all runs, including the absence of amplification in the negative controls. Of note, however, the infectivity of SARS-CoV-2 from blood remains unknown and, to date, we are not aware of cases of transfusion-transmitted COVID-19. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations cache = ./cache/cord-301183-k39e12cq.txt txt = ./txt/cord-301183-k39e12cq.txt === reduce.pl bib === id = cord-300963-1n1f8mf2 author = Gajendran, Mahesh title = Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date = 2020-10-12 pages = extension = .txt mime = text/plain words = 6681 sentences = 350 flesch = 46 summary = Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient's age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. cache = ./cache/cord-300963-1n1f8mf2.txt txt = ./txt/cord-300963-1n1f8mf2.txt === reduce.pl bib === id = cord-301106-qskwujpa author = Gambato, Martina title = Clinical implications of COVID-19 in patients with chronic liver disease and liver tumor date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1665 sentences = 81 flesch = 44 summary = On March 31st of this year, the World Health Organization (WHO) declared a pandemic infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing 2019 coronavirus disease (COVID-19). A single case of acute chronic liver failure secondary to SARS-CoV-2 infection in a decompensated alcoholic cirrhotic patient was recently reported. Overall, the reported data are not yet enough for us to know the risk of infection in patients with existing chronic liver disease, or the impact of COVID-19 on their liver status and outcomes. Patients with liver cancer are another special population often coming to the hospital for treatment and monitoring, who may be at higher risk of contracting COVID-19, especially if they are receiving chemotherapy or immunotherapy. In conclusion, liver damage during SARS-CoV-2 infection has been reported quite frequently, especially in patients who developed severe COVID-19 disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan cache = ./cache/cord-301106-qskwujpa.txt txt = ./txt/cord-301106-qskwujpa.txt === reduce.pl bib === id = cord-300978-busx8w6s author = Apetrii, Mugurel title = A brand-new cardiorenal syndrome in the Coronavirus Disease- 2019 (COVID-19) setting date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2999 sentences = 151 flesch = 40 summary = Although the pandemic outbreak of coronavirus disease-2019 (COVID-19) targets preferentially patient's lungs, recent data have documented that COVID-19 causes myocarditis, acute myocardial infarction, exacerbation of heart failure and acute kidney injury. Studies show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similar to its predecessor SARS-CoV, engages angiotensin-converting enzyme 2 (ACE2) as the entry receptor. In patients with SARS-CoV-2 infection, the most important features that suggest myocardial injury are electrocardiogram changes and troponin elevation coupled with echocardiography showing signs of subclinical left ventricular diastolic impairment or even reduced ejection fraction (EF) in severe cases [11] , with a higher likelihood of the need for mechanical ventilation in those with reduced EF, as was seen during previous coronavirus outbreaks [9] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection cache = ./cache/cord-300978-busx8w6s.txt txt = ./txt/cord-300978-busx8w6s.txt === reduce.pl bib === id = cord-300899-yi2mx91a author = Kaur, Satinder title = Understanding COVID-19 transmission, health impacts and mitigation: timely social distancing is the key date = 2020-07-18 pages = extension = .txt mime = text/plain words = 5347 sentences = 337 flesch = 55 summary = COVID-19 is a highly infectious disease caused by SARS-CoV-2, first identified in China and spread globally, resulting into pandemic. Various measures are undertaken to prevent infection such as maintaining hygiene, using facemasks, isolation/quarantine, social/physical distancing, in extreme cases lockdown (restricted movement except essential services) in hot spot areas or throughout the country. Python programming is conducted for change point analysis (CPA) using Bayesian probability approach for understanding the impact of restrictions and mitigation methods in terms of either increase or stagnation in number of COVID-19 cases for eight countries. COVID-19 is caused by novel strain of virus SARS-CoV-2 emerged from China and now declared as pandemic due to its presence across the continents in more than 213 countries. Rise in number of cases in different weeks is presented in Table 1 where it can be observed that India, France and Japan had experienced increase in fifth week, that in USA and Spain in the fourth week, Italy in the third week except for Iran and China in second week. cache = ./cache/cord-300899-yi2mx91a.txt txt = ./txt/cord-300899-yi2mx91a.txt === reduce.pl bib === id = cord-301080-xr7kl573 author = Sakanashi, Daisuke title = Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1623 sentences = 102 flesch = 54 summary = title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Therefore, the present study aimed to compare nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19. Among them, five patients had been diagnosed with COVID-19 by reverse transcription real-time polymerase chain reaction (rRT-PCR) of nasopharyngeal swabs and were hospitalized before the first collection of paired specimens, whereas seven were outpatients suspected to have COVID-19 based on their clinical symptoms. cache = ./cache/cord-301080-xr7kl573.txt txt = ./txt/cord-301080-xr7kl573.txt === reduce.pl bib === id = cord-301026-spgidqh3 author = Das, Shaoli title = In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data date = 2020-06-30 pages = extension = .txt mime = text/plain words = 4169 sentences = 190 flesch = 43 summary = Next, using the available drug perturbational data sets from the Broad Institute Connectivity map (CMAP project 14 , we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. To get a pathway-based estimation instead of individual genes, we calculated ssGSEA scores for the differentially enriched pathways in COVID-19 or SARS infection for all drug-treated cell lines at different dose/time points. Thereafter, combining the potential human interactome of SARS-CoV-2 from a recently published study 9 and SARS-CoV-1-interacting proteins curated in another publication 8 with drug target databases 10, 11 , drug perturbational data sets 14 , and drug sensitivity screening data sets 15 , we propose a map of the drugs that can be effective in COVID-19 treatment. Next, using the available drug perturbational data sets from the Broad Institute CMAP project, we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. cache = ./cache/cord-301026-spgidqh3.txt txt = ./txt/cord-301026-spgidqh3.txt === reduce.pl bib === id = cord-300991-ipy24zxp author = Khan, Amira Sayed title = Obesity and COVID-19: Oro-Naso-Sensory Perception date = 2020-07-08 pages = extension = .txt mime = text/plain words = 5971 sentences = 314 flesch = 47 summary = Through a recent upsurge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, the clinical assessment of most of the coronavirus disease 19 (COVID-19) patients clearly presents a health condition with the loss of oro-naso-sensory (ONS) perception, responsible for the detection of flavor and savor. Hence, obesity represents a great risk factor for SARS-CoV-2 infection, as it may hide the viral-associated altered ONS symptoms, thus leading to a high mortality rate in these subjects. Moreover, the number of immunosuppressive T-regulatory, Treg (CD4 + CD25 + Foxp3 + ) cells and concentrations of IL-6, IL-10, and C-reactive protein (CRP) were upregulated in patients with severe COVID-19 [18] , suggesting that SARS-CoV-2 infection may lead to "over-immunosuppression" in the case of obesity ( Figure 1 ). SARS-CoV-2 infection may further aggravate the ONS functions; mask the obesity-induced inflammation, including loss of taste and smell; and render the obese subjects more vulnerable and prone to severe pathophysiological consequences such as RTI, leading to death. cache = ./cache/cord-300991-ipy24zxp.txt txt = ./txt/cord-300991-ipy24zxp.txt === reduce.pl bib === id = cord-300964-knc0ruou author = Hoffman, Tove title = Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2546 sentences = 139 flesch = 54 summary = We evaluated a commercially available test developed for rapid (within 15 minutes) detection of SARS-CoV-2-specific IgM and IgG by 29 PCR-confirmed COVID-19 cases and 124 negative controls. In the present study, we evaluated a commercially available assay, the COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China), developed for detection of SARS-CoV-2-specific antibodies. None of the 24 healthy volunteers, without any known history of SARS-CoV-2 infection/COVID-19, tested positive for IgM or IgG. In this study we evaluated a commercial rapid test for detection of SARS-CoV-2-specific IgM and IgG. If this was the case for one or more of the included patients, the actual sensitivities should be higher, i.e. when evaluated only on samples known to contain detectable levels of SARS-CoV-2-specific IgM and/or IgG. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis cache = ./cache/cord-300964-knc0ruou.txt txt = ./txt/cord-300964-knc0ruou.txt === reduce.pl bib === id = cord-300847-ycuiso0g author = Li, Wei title = Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2801 sentences = 172 flesch = 55 summary = We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. By using phage display we have previously identified a number of potent fully human mAbs (m396, m336, m102.4) against emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV) (4) , Middle East respiratory syndrome coronavirus (MERS-CoV) (5) and henipaviruses (6, 7) , respectively, which are also highly effective in animal models of infection (8) (9) (10) (11) ; one of them was administered on a compassionate basis to humans exposed to henipaviruses and successfully evaluated in a clinical trial (12) . Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak. cache = ./cache/cord-300847-ycuiso0g.txt txt = ./txt/cord-300847-ycuiso0g.txt === reduce.pl bib === id = cord-301216-a0rkpez7 author = Perez, Adriana title = Presentation of SARS-CoV-2 Infection As Cholestatic Jaundice in Two Healthy Adolescents date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1667 sentences = 117 flesch = 49 summary = Liver abnormalities in severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, including hepatitis and cholestasis, have been observed in adults and is associated with worse outcomes. As of June 25, 2020, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) resulted in >9.4 million confirmed cases worldwide and > 482,000 deaths worldwide, including > 2.3 million cases and > 121,000 deaths reported in the US, among which were 84 pediatric deaths in persons < 24 years of age by June 13 2020. The incidence of liver injury in adult patients with COVID-19 has been ranges from 14.8% -53%(, being more significant in severe cases and ranging up to 78% among fatal cases.(10) Liver abnormalities described included elevation of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST), mildly elevated bilirubin levels, high gamma-glutamyl transferase (GGT) and low albumin levels (2.6-3.3 g/L) (10, 11) . We present two cases of acute hepatitis with clinically apparent jaundice and cholestasis without biliary obstruction associated with SARS-CoV-2 infection. cache = ./cache/cord-301216-a0rkpez7.txt txt = ./txt/cord-301216-a0rkpez7.txt === reduce.pl bib === id = cord-301303-44sk478e author = Wu, Vin-Cent title = Renal hypouricemia is an ominous sign in patients with severe acute respiratory syndrome date = 2008-02-21 pages = extension = .txt mime = text/plain words = 3128 sentences = 193 flesch = 54 summary = Conclusion: One fourth of patients with SARS developed hypouricemia, which might result from a defect in renal UA handling and was associated with a high serum IL-8 level. Serum levels of the proinflammatory cytokines IL-6, IL-8, and TNF-␣ were measured in 16 patients (6 hypouricemic, 10 normouricemic) during their UA excretion studies. The inverse correlation between serum UA level and FE UA indicates that the hypouricemia in patients with SARS resulted from an abnormal increase in UA excretion during SARS-CoV infection. 27 Our study showed that the lowest serum UA level occurred days 7 to 9 after fever onset, when the cytokine storm of patients with SARS usually occurred. 19 The present study shows that hypouricemic patients with SARS had a poor outcome, especially in terms of respiratory failure, compared with normouricemic patients. In summary, hypouricemia resulting from abnormal renal urate handling is not rare in patients with SARS-CoV infection and may reflect the severity of disease and predict poor patient outcomes. cache = ./cache/cord-301303-44sk478e.txt txt = ./txt/cord-301303-44sk478e.txt === reduce.pl bib === id = cord-301251-6f2nzvhz author = Cheemarla, N. R. title = Host response-based screening to identify undiagnosed cases of COVID-19and expand testing capacity date = 2020-06-05 pages = extension = .txt mime = text/plain words = 3393 sentences = 215 flesch = 64 summary = Based 25 on previous work, we hypothesized that an elevated level of the interferon inducible protein 26 CXCL10 in the nasopharynx could serve as a sensitive screen for patients with an active 27 respiratory virus infection including SARS-CoV2 2 . Protein measurements lend themselves to 30 rapid, high throughput, and point-of care diagnostic methodologies 3,4 , so this combined strategy 31 offers the potential to have a first step which is sensitive and convenient (CXCL10 assay) 32 followed by a more specific test (PCR) for a subset of screen-positive patients. . https://doi.org/10.1101/2020.06.04.20109306 doi: medRxiv preprint Previously, we found that the CXCL10 level in the NP swab viral transport medium was a useful 45 indicator of infection with many common respiratory viruses 2 , suggesting that this measurement 46 could be used to indicate which of these 376 samples were most likely to contain a virus not 47 detected by the RVP. cache = ./cache/cord-301251-6f2nzvhz.txt txt = ./txt/cord-301251-6f2nzvhz.txt === reduce.pl bib === id = cord-301115-sedfbjlw author = Han, Mingfeng title = Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4577 sentences = 255 flesch = 53 summary = title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity The results of our analysis demonstrated that the initial SARS-CoV-2 RNA loads varied in patients, but were comparable in different patient groups stratified by age, gender, comorbidities and disease severity. We compared the measured SARS-CoV-2 RNA levels in sputum specimens from COVID-19 patients at admission among groups divided according to age, sex, underlying diseases and disease severity (Fig. 2a) . a, b The measured SARS-CoV-2 RNAs levels in sputum (a) and throat swab (b) specimens from COVID-19 patients at admission were compared according to the age, sex, comorbidity, and the disease severity. In this study, we analyzed the clinical features including SARS-CoV-2 RNA load and immunological characteristics of peripheral blood in a patient cohort with COVID-19 from Anhui Province, China. cache = ./cache/cord-301115-sedfbjlw.txt txt = ./txt/cord-301115-sedfbjlw.txt === reduce.pl bib === id = cord-301292-yaii6e16 author = Kuk, Anthony Y. C. title = The estimation of SARS incubation distribution from serial interval data using a convolution likelihood date = 2005-07-12 pages = extension = .txt mime = text/plain words = 4354 sentences = 252 flesch = 60 summary = By constructing a convolution likelihood based on the serial interval data, we are able to estimate the incubation distribution which is assumed to be Weibull, and justifications are given to support this choice over other distributions. The indirect estimate obtained using the method of convolution likelihood is validated by means of comparison with a direct estimate obtained directly from a subset of patients for whom the incubation time can be ascertained. Despite its name, the proposed indirect estimate is actually more precise than the direct estimate because serial interval data are recorded for almost all patients, whereas exact incubation times can be determined for only a small subset. By constructing a convolution likelihood based on the serial interval data in Singapore, we are able to estimate the incubation distribution parametrically. It is possible to obtain a combined estimate that makes use of the incubation times for the 50 patients in the ascertained subset and the serial intervals for the remaining 148 cases. cache = ./cache/cord-301292-yaii6e16.txt txt = ./txt/cord-301292-yaii6e16.txt === reduce.pl bib === id = cord-301324-2tyl1r2l author = Zhan, Jing title = Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() date = 2020-09-09 pages = extension = .txt mime = text/plain words = 543 sentences = 43 flesch = 45 summary = title: Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() The emergence of a novel coronavirus named by SARS-CoV-2 during December, 2019, has caused the global outbreak of coronavirus disease 2019 (COVID-19), which is officially announced to be a pandemic by the World Health Organization (WHO). Understanding the transmission, survival, and evolution of the virus in the environment will assist in the prevention, control, treatment and eradication of its infection. Herein, we aimed to elucidate the environmental impacts on the transmission and evolution of SARS-CoV-2, based on briefly introducing this respiratory virus. This review should be of great help to prevent and control the epidemics caused by emerging respiratory coronaviruses (CoVs). Summary: More knowledge on the transmission and evolution of SARS-CoV-2 in the environment is urgently needed. High infectivity and pathogenicity of influenza A 620 virus via aerosol and droplet transmission cache = ./cache/cord-301324-2tyl1r2l.txt txt = ./txt/cord-301324-2tyl1r2l.txt === reduce.pl bib === id = cord-301157-tu3iig9o author = Felsenstein, Susanna title = Presentation, Treatment Response and Short-Term Outcomes in Paediatric Multisystem Inflammatory Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS) date = 2020-10-14 pages = extension = .txt mime = text/plain words = 7843 sentences = 455 flesch = 45 summary = Whilst most children and young people develop mild symptoms, recent reports suggest a novel paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS). Since the advent of the Coronavirus Disease 2019 (COVID-19) pandemic, dominated by respiratory disease and evolution of acute respiratory distress syndrome (ARDS), cardiovascular compromise, excessive systemic inflammation and coagulopathy in adults [1] [2] [3] , several countries affected by the coronavirus disease [4] pandemic have reported an unusually high number of cases of children hospitalized due to a multisystem inflammatory condition, at times requiring intensive care (Table S1) . Temporal distribution of paediatric inflammatory multisystem syndrome temporally associated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (PIMS-TS) cases of this cohort, in relation to COVID-19 like presentations to hospitals in England. The peak of presentations of children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 followed the peak of presentations of patients, adult and paediatric, to English Emergency Departments, with a lag of 4-6 weeks (Figure adapted from https://www.gov.uk/government/news/weekly-covid-19-surveillance-report-published; week 30). cache = ./cache/cord-301157-tu3iig9o.txt txt = ./txt/cord-301157-tu3iig9o.txt === reduce.pl bib === id = cord-301313-9595vm0k author = OKBA, NISREEN M.A. title = SARS-CoV-2 specific antibody responses in COVID-19 patients date = 2020-03-20 pages = extension = .txt mime = text/plain words = 4271 sentences = 248 flesch = 55 summary = Here, we describe development of serological assays for the detection of virus neutralizing antibodies and antibodies to the nucleocapsid (N) protein and various spike (S) domains including the S1 subunit, and receptor binding domain (RBD) of SARS-CoV-2 in ELISA format. Using a wellcharacterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house as well as a commercial platform. We evaluated SARS-CoV-2 specific antibody responses in severe and mild cases using serum samples collected at different times post-disease onset from three French PCR-confirmed CoVID-19 patients. We tested sera for SARS-CoV-2 specific antibodies using different ELISAs. Following infections, all three patients seroconverted between days 13 and 21 post onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S and S1 subunit including the N-terminal (S1 A ) domain and the receptor binding domain (RBD). cache = ./cache/cord-301313-9595vm0k.txt txt = ./txt/cord-301313-9595vm0k.txt === reduce.pl bib === id = cord-301227-ica5x0r1 author = Sun, Yi-Sheng title = A SARS-CoV-2 variant with the 12-bp deletion at E gene date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4410 sentences = 236 flesch = 65 summary = In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. In this paper, we isolated two SARS-CoV-2 strains with both wild-type and mutant E genes from the same sample using plaque purification. To explore whether other clinical samples contained a similar SARS-CoV-2 strain lacking a 12-bp sequence in the E gene, we used RT-PCR to detect the mutant E gene specifically. Our results indicated that both the F8 and 8X strains can infect Vero cells, however, the S protein content of the F8 viral culture was higher than that of 8X. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. cache = ./cache/cord-301227-ica5x0r1.txt txt = ./txt/cord-301227-ica5x0r1.txt === reduce.pl bib === id = cord-301233-nenw0f81 author = Naydenova, Katerina title = Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4059 sentences = 217 flesch = 51 summary = Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. cache = ./cache/cord-301233-nenw0f81.txt txt = ./txt/cord-301233-nenw0f81.txt === reduce.pl bib === id = cord-301454-ayf42grs author = Phyu Khin, Phyu title = A potential therapeutic combination for treatment of COVID-19: synergistic effect of DPP4 and RAAS suppression date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1762 sentences = 105 flesch = 45 summary = A recent study proved that coronavirus SARS-CoV-2 also uses dipeptidyl peptidase-4 (DPP4, also known as adenosine deaminase complexing protein 2, CD26) as a co-receptor when entering cells. In particular, SARS-CoV-2 is able to infect T lymphocytes despite their very low expression level of ACE-2, implying an alternate receptor for viral entry [5, 6] . Among elderly patients (average age: 80 years) infected with SARS-CoV-2 in Italy in early 2020, the mortality rate was highest in patients with hypertension (69%), followed by those with type 2 diabetes (31%), and those with ischemic heart diseases (27%) [5] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients With Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China cache = ./cache/cord-301454-ayf42grs.txt txt = ./txt/cord-301454-ayf42grs.txt === reduce.pl bib === id = cord-301226-hmc2wmst author = Randazzo, Walter title = Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date = 2020-04-27 pages = extension = .txt mime = text/plain words = 2158 sentences = 127 flesch = 52 summary = Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Here, we show that SARS-CoV-2 can be reproducibly detected by RT-qPCR in longitudinal samples from sewage treatment plants that receive wastewaters from over one million inhabitants in the metropolitan area of Valencia, Spain. Following concentration of viral content by flocculation, a standard RT-qPCR procedure allowed us to detect SARS-CoV-2 RNA in 12/12 samples collected from March 9 to April 14, 2020, with Ct values ranging between 34•00 and 37•84, correspondingly revealing between 5•22 and 5•99 log 10 genomic copies (gc)/L (Table 1) . Interestingly, we consistently detected SARS-CoV-2 RNA in samples collected on March 9 and March 11, when only 50 and 76 cumulative cases were declared in the entire Region of Valencia. cache = ./cache/cord-301226-hmc2wmst.txt txt = ./txt/cord-301226-hmc2wmst.txt === reduce.pl bib === id = cord-301388-p3juk2vv author = Yen, Muh-Yong title = Recommendations for protecting against and mitigating the COVID-19 pandemic in long-term care facilities date = 2020-04-10 pages = extension = .txt mime = text/plain words = 3933 sentences = 225 flesch = 47 summary = 5, 6 It is therefore essential that the health care community develop infection control guidelines on prevention measures to address pandemic preparedness and response in LTCFs. 7, 8 Here we offer recommendations based on what we consider the "gold standard" for pandemic preparedness and response in LTCFs. However, we recognize that the ideal response we describe is likely not an option for LTCFs in the midst of the current COVID-19 pandemic. 18 Given the significant vulnerability of LTCF residents and staff to the COVID-19 pandemic, here we recommend adopting eTCB, and adapting it to LTCFs. Enhanced TCB protects LTCF staff and residents from droplet, contact and fomite transmission through a process including triage prior to entering the facility, separate zones of risk within the facility and checkpoint hand hygiene throughout. cache = ./cache/cord-301388-p3juk2vv.txt txt = ./txt/cord-301388-p3juk2vv.txt === reduce.pl bib === id = cord-301484-y9l2hmqf author = MASSAROTTI, Claudia title = Asymptomatic SARS‐CoV‐2 infections in pregnant patients in an Italian city during complete lockdown date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1102 sentences = 64 flesch = 47 summary = Data from both New York and London report a high prevalence of the asymptomatic SARS‐CoV‐2 infection in pregnant patients admitted for delivery, raising questions on the possible correlated dangers (i.e. contacts with healthcare workers; the possible creation of an intra‐hospital outbreak at birth; conflicting evidences on vertical transmission). For this study, results from SARS‐CoV‐2 screening via nasopharyngeal swab from maternity wards of the four hospitals of Genoa, Italy were collected during a month of complete lockdown, from April 1 to April 30, 2020. Early detection and isolation of asymptomatic SARS-CoV-2 positive patients is a crucial public safety action [1] , but a screening of the entire population is difficult to be This article is protected by copyright. The incidence of positive SARS-CoV-2 nasopharyngeal swabs in asymptomatic pregnant women were 13.5 and 6.2% in two reported screened cohort in New York and London [2, 3] . Since the implementation of the universal screening, all pregnant women admitted for delivery were tested for SARS-CoV-2. cache = ./cache/cord-301484-y9l2hmqf.txt txt = ./txt/cord-301484-y9l2hmqf.txt === reduce.pl bib === id = cord-301590-70qmpccs author = Campos, António title = The Paradigm Shift of Ophthalmology in the COVID-19 Era date = 2020-09-14 pages = extension = .txt mime = text/plain words = 3010 sentences = 164 flesch = 52 summary = CONCLUSION: It was possible to keep the ophthalmological activity during the pandemic outbreak due to the existence of a pre-scheduled fixed regimen for IVI and to the availability of personal protective equipment. We are facing a different sort of challenge now: how to accommodate the usual huge number of patients previous to the COVID-19 outbreak in the waiting rooms, while respecting the new demands from the healthcare authorities to reduce the number of waiting patients to a half or one-third. 9 Issues such as the use of personal protective equipment, the size of waiting rooms, ventilation, adherence to disinfection protocols, choose of whom to treat based on the disease natural evolution and the need to prioritize treatment visits over monitoring visits, were addressed recently. Symptomatic patients, SARS-CoV-2 positive patients and contacts, were postponed until they were RT-PCR negative, except for emergency surgeries that were performed in a COVID-dedicated OR (one room with negative pressure and special requirements 12 cache = ./cache/cord-301590-70qmpccs.txt txt = ./txt/cord-301590-70qmpccs.txt === reduce.pl bib === id = cord-301547-d4wt9dqp author = Seng, J. J. B. title = Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics date = 2020-05-11 pages = extension = .txt mime = text/plain words = 5400 sentences = 296 flesch = 49 summary = Study selection Studies which evaluated health literacy related to novel coronavirus disease 2019 (COVID-19), Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS) Data extraction Data on the characteristics of study designs, instruments, participants and level of health literacy were collected. Keywords employed in the search strategy included terms related to health literacy as well as the viruses and syndromes implicated in the three coronavirus pandemics which were namely COVID-19, MERS and SARS. Studies which evaluated health literacy related to COVID-19, SARS or MERS among adult participants aged ≥ 18 years old from the general population, healthcare sectors and infected patients were included. Questions from instruments used across included studies were classified into three main themes, which were 1) knowledge, 2) attitudes and 3) practices, to help guide future development of standardised COVID-19 and pandemic health literacy tools. cache = ./cache/cord-301547-d4wt9dqp.txt txt = ./txt/cord-301547-d4wt9dqp.txt === reduce.pl bib === id = cord-301556-f3m9gwvo author = Huang, Jessie title = SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response date = 2020-09-18 pages = extension = .txt mime = text/plain words = 6737 sentences = 319 flesch = 49 summary = Serially passaging these epithelial spheres generated >10 30 iAT2s per starting sorted tdTomato+ cell over 225 days in culture (Hurley et al., 2020) , generating cells that maintained expression of AT2 marker genes including surfactants as shown by single cell RNA sequencing (scRNA-Seq) ( Figure 1C -D, Figure S1 ) and providing a stable source of human primary-like AT2 cells for viral infection disease modeling. Compared to other published datasets of SARS-CoV-2 infection models in Calu-3, J o u r n a l P r e -p r o o f A549-ACE2, and primary (non-alveolar) normal human bronchial epithelium (NHBE) (Blanco-Melo et al., 2020) , iAT2s were able to uniquely capture the downregulation of AT2-specific programs, such as decreased surfactant gene expression and loss of lamellar body gene ontology (GO) terms (comparative gene set enrichment based on lung-related GO biological processes; Figure S3 ). cache = ./cache/cord-301556-f3m9gwvo.txt txt = ./txt/cord-301556-f3m9gwvo.txt === reduce.pl bib === id = cord-301633-t8s4s0wo author = Gralinski, Lisa E. title = Return of the Coronavirus: 2019-nCoV date = 2020-01-24 pages = extension = .txt mime = text/plain words = 3938 sentences = 186 flesch = 51 summary = Similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections, patients exhibited symptoms of viral pneumonia including fever, difficulty breathing, and bilateral lung infiltration in the most severe cases [1] . A range of disease has been observed highlighted by fever, dry cough, shortness of breath, and leukopenia; patients have included mild cases needing supportive care to severe cases requiring extracorporeal membrane oxygenation; however, compared to SARS-CoV (10% mortality) and MERS-CoV (35% mortality), the 2019-nCoV appears to be less virulent at this point with the exception of the elderly and those with underlying health conditions. In the early part of the outbreak, the absence of infection in health care workers argued for inefficient human to human spread and distinguished 2019-nCoV from both SARS-CoV and MERS-CoV. cache = ./cache/cord-301633-t8s4s0wo.txt txt = ./txt/cord-301633-t8s4s0wo.txt === reduce.pl bib === id = cord-301622-mn59vszt author = Jomah, Shahamah title = Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review date = 2020-08-03 pages = extension = .txt mime = text/plain words = 6281 sentences = 405 flesch = 50 summary = However, several agents are included in Infectious Diseases Society of America (IDSA) Management Guidelines for treatment of COVID-19 patients; including antimalaria (chloroquine, hydroxychloroquine), antivirals (lopinavir/ritonavir), antibacterial (azithromycin, and immunomodulators (Tocilizumab) based on their beneficial role reported by practicing physicians or small scale clinical trials. Additional keywords such as treatment", "antiviral", "protease inhibitors", "lopinavir ritonavir", "ribavirin", Remdesivir", "arbidol",Östalmovir", "Favipiravir", human studies, randomized controlled trials (RCT), prospective or retrospective cohort designs, case-control designs, case series and case report, with COVID-19 produced more than 300 trails. A randomized control trial including 199 severe COVID-19 patients revealed that lopinavir group had significantly shorter time for clinical improvement compared to standard therapy. Prospective, randomized, controlled, open-label multicenter trial [27] • 236 moderate/severe confirmed COVID-19 cases randomized; 116 to receive Favipiravir for 10 days and 120 to receive Umifenovir (Arbidol) for 10 days and all patients received conventional therapy. cache = ./cache/cord-301622-mn59vszt.txt txt = ./txt/cord-301622-mn59vszt.txt === reduce.pl bib === id = cord-301535-eui41zyg author = Chandler-Brown, Devon title = A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date = 2020-04-10 pages = extension = .txt mime = text/plain words = 4143 sentences = 228 flesch = 52 summary = This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). cache = ./cache/cord-301535-eui41zyg.txt txt = ./txt/cord-301535-eui41zyg.txt === reduce.pl bib === id = cord-301638-2f8r37ns author = Bonney, Glenn Kunnath title = SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? date = 2020-05-29 pages = extension = .txt mime = text/plain words = 709 sentences = 55 flesch = 54 summary = title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? The rapid spread of a novel coronavirus disease (COVID-19) caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) has triggered a global pandemic. [2] The severity of AP observed varies from mild [1, 2] to severe,[43 but unfortunately accepted diagnostic criteria [4] was not used in these studies, raising the possibility that the elevated pancreatic enzymes may be due to other causes including increased gut permeability with SARS-CoV-2 infection. A study from 2010 using immunostaining found ACE2 to be highly expressed in islet cells and postulated that binding of SARS-CoV caused islet cell injury and hyperglycaemia in infected patients. [9] It is not known whether SARS-CoV-2 causes AP, whether the AP is a consequence of severe systemic inflammation and microvascular thrombosis from COVID-19 infection, or whether it is just an epiphenomenon. ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection Coronavirus Disease-19 (COVID-19) associated with severe acute pancreatitis: Case report on three family members cache = ./cache/cord-301638-2f8r37ns.txt txt = ./txt/cord-301638-2f8r37ns.txt === reduce.pl bib === id = cord-301641-epr1sct6 author = Kumar, Durgesh title = Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures date = 2020-05-04 pages = extension = .txt mime = text/plain words = 4095 sentences = 204 flesch = 49 summary = Herein, MM-GBSA method was to calculate the change in enthalpy and the change in free energy for the formation of complex, number of hydrogen bonds (HBs) are determined to study the binding of the hit molecule with the protease of SARS-CoV-2 for COVID-19. However, the designed molecules were filtered against the protease of SARS-CoV-2 for COVID-19 based on total energy or binding energy (kcal/mol) of drug-target complex using iGEMDOCK Singh et al., 2019; Zhao et al., 2019) . Herein, MM-GBSA method is used to determine the change in enthalpy and change in free energy for the formation of complex, number of HBs to understand the binding of screened noscapines with the protease of SARS-CoV-2 of COVID-19 (Al-Anazi et al., 2018; Chaudhari & Pahelkar, 2019; Chinnasamy et al., 2019; Du et al., 2011) . Further, the detailed analysis of newly formed drug-target complex through root-mean-square fluctuation (RMSF) versus the residue number of protease of coronavirus for COVID-19 for top hit molecule is represented in Figure 7 . cache = ./cache/cord-301641-epr1sct6.txt txt = ./txt/cord-301641-epr1sct6.txt === reduce.pl bib === id = cord-301693-3hsu2u1k author = He, Yuwen title = Value of Viral Nucleic Acid in Sputum and Feces and Specific IgM/IgG in Serum for the Diagnosis of Coronavirus Disease 2019 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3551 sentences = 184 flesch = 53 summary = To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We undertook a study on the viral nucleic acids of SARS-CoV-2 in swabs (nasal, pharyngeal), sputum and feces, as well as antibodies in the serum of COVID-19 patients admitted to the First Affiliated Hospital of Guangzhou Medical University, China. cache = ./cache/cord-301693-3hsu2u1k.txt txt = ./txt/cord-301693-3hsu2u1k.txt === reduce.pl bib === id = cord-301677-b6mnn27h author = Soleimanian, Saeede title = Harnessing Memory NK Cell to Protect Against COVID-19 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 9746 sentences = 462 flesch = 42 summary = In this regard, Natural Killer (NK) cells as essential front-line responders to many viral infections in humans have been proposed for a suitable therapeutic approach in severe COVID-19 patients, and several clinical trials have begun (Market et al., 2020) . In this line, Type I IFNs have a critical role in concert with pattern PRR signaling to prime innate and adaptive antiviral responses such as stimulating natural killer (NK) cells, macrophages, and production of proinflammatory cytokines (Samuel, 2001; Murira and Lamarre, 2016) . The detection of both SARS-CoV-2 nucleic acid and specific antibodies to viral proteins have thus far become significant for primary diagnosis infection and immunity in COVID-19 patients, respectively. in a pneumonia model of SARS in mice, mimicking features of the human disease, illustrated that mice depleted of both CD4 and CD8T cells, had the ability to control SARS-CoV replication in the lungs, suggesting an immune mechanism independent of T cells, and a role for innate antiviral response and NK cells, in viral clearance. cache = ./cache/cord-301677-b6mnn27h.txt txt = ./txt/cord-301677-b6mnn27h.txt === reduce.pl bib === id = cord-301811-ykpiorgo author = Tanaka, Takuma title = Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5530 sentences = 296 flesch = 55 summary = title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing We estimated the numbers of undiagnosed symptomatic patients and the lower bound of the number of total infected individuals per diagnosed patient before and after the declaration of the state of emergency in Hokkaido, Japan. The present analysis uses the distributions of the cluster size and patients' time from onset to diagnosis, which are released by the health officials, to estimate the model parameters. At the same time, the nodes in the connected component containing the diagnosed node are also removed from the network, which corresponds to the contact tracing of the infected individuals (Fig 2, gray open circles) . In this paper, we have formulated a model to describe the spreading of infection and the quarantine of infected individuals, and estimated the number of undiagnosed symptomatic and asymptomatic COVID-19 patients in Hokkaido. cache = ./cache/cord-301811-ykpiorgo.txt txt = ./txt/cord-301811-ykpiorgo.txt === reduce.pl bib === id = cord-301603-gdxvbspx author = Sokouti, Massoud title = Comparative Global Epidemiological Investigation of SARS-CoV-2 and SARS-CoV Diseases Using Meta-MUMS Tool Through Incidence, Mortality, and Recovery Rates date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1884 sentences = 113 flesch = 57 summary = In this meta-analysis, a random effect model of relations of incidence, mortality, and recovery rates of COVID-19 and SARS world infections were determined. The meta-analysis and forest plots of two viral world infections showed that the incidence rate of COVID-19 infection is more than SARS infections, while recovery and mortality event rates of SARS-CoV are more than COVID-19 infection. In the current study, the comparisons between incidence and mortality, as well as recovery and death rates among the countries for COVID-19 and SARS-CoV with the higher incidence rates, were performed using the meta-analysis approach developed in the Meta-MUMS tool. The incidence event rates of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 1A , showing the relationships between two infectious diseases. Recovery event rate of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 2A , showing the relations between both diseases. cache = ./cache/cord-301603-gdxvbspx.txt txt = ./txt/cord-301603-gdxvbspx.txt === reduce.pl bib === id = cord-301823-fbeb1nw1 author = Sridhar, Sushmita title = A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6118 sentences = 309 flesch = 51 summary = Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. cache = ./cache/cord-301823-fbeb1nw1.txt txt = ./txt/cord-301823-fbeb1nw1.txt === reduce.pl bib === id = cord-302015-z2k6wuhm author = Bonardel, Claire title = Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1021 sentences = 90 flesch = 43 summary = authors: Bonardel, Claire; Bonnerot, Mathieu; Ludwig, Marie; Vadot, Wilfried; Beaune, Gaspard; Chanzy, Bruno; Cornut, Lucie; Baysson, Hélène; Farines, Magali; Combes, Isabelle; Macheda, Gabriel; Bing, Fabrice title: Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by Covid-19. Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case Abstract In time of SARS-Cov2 pandemic, neurologists need to be vigilant for cerebrovascular complications of Covid-19. We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by . A first brain MRI performed one hour after clinical onset showed bilateral and asymmetric acute occipito-temporal infarction without visibility of the P3 segments of the posterior cerebral arteries (PCA) (Figure 2A to C). cache = ./cache/cord-302015-z2k6wuhm.txt txt = ./txt/cord-302015-z2k6wuhm.txt === reduce.pl bib === id = cord-301942-ppa7gb95 author = Neuman, Benjamin W. title = Ultrastructure of SARS-CoV, FIPV, and MHV Revealed by Electron Cryomicroscopy date = 2006 pages = extension = .txt mime = text/plain words = 1189 sentences = 78 flesch = 47 summary = The current understanding of coronavirus ultrastructure relies heavily on transmission electron microscopy of negatively stained images. Each virus appeared approximately round in cryo-EM images, with a fringe of spikes protruding from the viral membrane and a region of lower density near the virion center ( Fig. 1A-B) . Spike-depleted SARS-CoV particles appeared similar to spike-depleted MHV particles in negative stain, but were produced in lower yield, not suitable for effective cryo-EM imaging. The arrangement of spike densities near the center of some particles approximates a rhombus, which would not be inconsistent with a paracrystalline organization of spikes as observed in the virions of pleomorphic arenavirus particles, 17 or a local hexagonal close-packing of structural proteins as observed in retroviral particles. Fine structure of influenza A virus observed by electron cryo-microscopy Cryo-electron microscopy reveals ordered domains in the immature HIV-1 particle Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: implications for retroviral assembly mechanisms cache = ./cache/cord-301942-ppa7gb95.txt txt = ./txt/cord-301942-ppa7gb95.txt === reduce.pl bib === id = cord-302111-kg0dmgq0 author = Darden, Dijoia B. title = The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4492 sentences = 257 flesch = 34 summary = Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. cache = ./cache/cord-302111-kg0dmgq0.txt txt = ./txt/cord-302111-kg0dmgq0.txt === reduce.pl bib === id = cord-301947-b6nwaost author = Millán-Oñate, José title = Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3699 sentences = 205 flesch = 48 summary = We report here the clinical features and therapeutic course of the first reported patient with confirmed COVID-19 pneumonia that recovered in Colombia, after the use of chloroquine and clarithromycin. It is essential to acknowledge that no good controlled data are supporting the use of any of these agents, except for a recent randomized, controlled, open-label trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection, that showed no benefit with lopinavir-ritonavir (LPV/RTV) treatment beyond standard care [13] . We present a confirmed case of COVID-19 from Buga, Valle del Cauca, Colombia, that successful recovered of SARS-CoV-2 infection after receiving chloroquine. Although that just based in one case, we cannot recommend the use of these drugs, our patient improved significantly, and his clinical manifestations ceased, including becoming negative for the SARS-CoV-2 infection, as observed in the rRT-PCR test. cache = ./cache/cord-301947-b6nwaost.txt txt = ./txt/cord-301947-b6nwaost.txt === reduce.pl bib === id = cord-301730-flv5lnv8 author = Pandey, Anamika title = Natural Plant Products: A Less Focused Aspect for the COVID-19 Viral Outbreak date = 2020-10-15 pages = extension = .txt mime = text/plain words = 7101 sentences = 346 flesch = 50 summary = Despite the previous positive reports of plant-based medications, no successful clinical trials of phyto-anti-COVID drugs could be conducted to date. Medicinal plant extracts have been reported to impede the replication of several viruses including human immunodeficiency virus (HIV), hepatitis B virus (HBV), poxvirus, severe acute respiratory syndrome (SARS) virus, and herpes simplex virus type 2 (HSV-2) (Vermani and Garg, 2002; Kotwal et al., 2005; Huang et al., 2006) . Different researchers are investigating diverse plant forms based on ethnopharmacological data to find effective anti-CoV drugs with novel action mechanisms especially targeting viral replication. Moreover, creating an effective phyto-anti-COVID drug during this pandemic may provide an idea on the duration and the strategy required for the development of potent plant-based therapeutics in case of such random viral outbreaks (Figure 1) . cache = ./cache/cord-301730-flv5lnv8.txt txt = ./txt/cord-301730-flv5lnv8.txt === reduce.pl bib === id = cord-301978-9uu318tp author = Yin, Xiaoping title = A mild type of childhood Covid-19 - A case report date = 2020-03-27 pages = extension = .txt mime = text/plain words = 1216 sentences = 85 flesch = 56 summary = This case is about a 9-year-old child diagnosed with COVID-19, with a history of epidemiology; SARS-CoV-2 nucleic acids testing was positive, while chest CT examination was negative. Because the child had lived in Wuhan two weeks before the onset of the disease and had a fever, SARS-CoV-2 infection was not excluded. Children and teenagers infected with SARS-CoV-2 have mild clinical symptoms and radiological manifestations [4] , and are rarely severe or critical. If children and adolescents have a history of living or traveling in epidemic areas within one to two weeks, or they have had contact with confirmed or suspected cases, or stay in an aggregated disease environment, the possibility of their infection with SARS-CoV-2 cannot be ruled out, even when their clinical symptoms are mild and there is no typical chest imaging manifestation. SARS-CoV-2 nucleic acid or gene testing is required for these patients. Preliminary study on clinical imaging features of 2019 novel coronavirus (2019-nCoV) pneumonia in Wuhan. cache = ./cache/cord-301978-9uu318tp.txt txt = ./txt/cord-301978-9uu318tp.txt === reduce.pl bib === id = cord-301771-43fl2gwp author = Ouassou, Hayat title = The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention date = 2020-07-10 pages = extension = .txt mime = text/plain words = 3866 sentences = 179 flesch = 45 summary = The causative virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the World Health Organization (WHO) named the new epidemic disease Coronavirus Disease (COVID-19). Several coronaviruses can infect humans, like the globally endemic human coronaviruses HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43 that tend to cause mild respiratory disease, and the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that have a higher case fatality rate [2] . After the diagnosis of SARS-Cov2 infection was made, the prevention and quarantine are considered as the most way to stop the fast spreading of the virus, because there is no effective vaccine, drugs, or antiviral to prevent and treat this disease despite the great efforts made by the scientists and researchers around the world to develop vaccines and treatments of coronavirus. cache = ./cache/cord-301771-43fl2gwp.txt txt = ./txt/cord-301771-43fl2gwp.txt === reduce.pl bib === id = cord-301828-qux5hvcw author = Khalifa, Ibrahim title = Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2519 sentences = 146 flesch = 43 summary = We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS‐CoV‐2 by assembling with the catalytic dyad residues of its 3CL(pro) using molecular operating environment (MOE 09). Likewise, tannin-type compounds, such as epiacutissimins A and B, castalin, vescalin, chebulagic acid, and punicalagin showed anti-herpesvirus activity via targeting viral glycoprotein-glycosaminoglycan binding to inhibit access and cell-to-cell feast (Lin et al., 2011; Aires, 2020 The current study was designed to find out a potent inhibitor against COVID-19 from 19 structural different hydrolysable tannins which could target the main protease of SARS-CoV-2 using in silico approaches (molecular docking and drug-likeness scan). Among these hydrolysable tannins, pedunculagin, strongly interacted with the catalytic dyad residues (Cys-145 and His-41) of SARS-CoV-2-3CL pro , with sense binding affinity, docking score, and ADMET properties. Herein, we screened the structural relationship activity of 19 hydrolysable tannins as potential antiviral components and we chose the top three hits that may inhibit the main protease of SARS-CoV-2 and hence virus copying. cache = ./cache/cord-301828-qux5hvcw.txt txt = ./txt/cord-301828-qux5hvcw.txt === reduce.pl bib === id = cord-301626-7ow1jja4 author = Li, Shih-Wen title = SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6 date = 2016-05-05 pages = extension = .txt mime = text/plain words = 3733 sentences = 183 flesch = 47 summary = Severe acute respiratory syndrome coronavirus (SARS-CoV) papain-like protease (PLPro) reportedly inhibits the production of type I interferons (IFNs) and pro-inflammatory cytokines in Toll-like receptor 3 (TLR3) and retinoic acid-inducible gene 1 (RIG-I) pathways. The decrease in the activated state of TRAF3 and TRAF6 correlated with the inactivation of TBK1 in response to IMQ by PLPro. The results revealed that the antagonism of SARS-CoV PLPro on TLR7-mediated innate immunity was associated with the negative regulation of TRAF3/6-TBK1-IRF3/NF-κB/AP1 signals. To examine whether SARS-CoV PLPro modulates the TLR7 signaling pathway, stable transfected promonocyte cells expressing PLPro and vector control cells were established, treated with TLR7 agonist (imiquimod (IMQ)), then further analyzed for activation of type I IFN production ( Figure 1 ). To examine the inhibitory mechanism of TLR7 antagonism by SARS-CoV PLPro, differential profiles of ubiquitin-conjugated proteins in the vector control and PLPro-expressing cells in the absence or presence of IMQ were analyzed using immune-precipitation ( Figure 5A,B) . cache = ./cache/cord-301626-7ow1jja4.txt txt = ./txt/cord-301626-7ow1jja4.txt === reduce.pl bib === id = cord-301779-y07xjnpe author = Fox, Sharon E title = Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3284 sentences = 174 flesch = 44 summary = INTERPRETATION: We identify key pathological states, including thrombotic and microangiopathic pathology in the lungs, that contributed to death in patients with severe COVID-19 and decompensation in this demographic. Evidence before this study We reviewed the single study of autopsy in a COVID-19 positive patient by Z Xu and colleagues, published in this journal, and reports of pathology from severe acute respiratory syndrome (SARS) coronavirus and similar viral infections by J Nicholls. Previous evidence [10] [11] [12] [13] [14] reports viral infection causing activation of both maladaptive cytokine pathways and a platelet response, and our findings suggest that these immune functions might be related to severe forms of COVID-19. We do not have evidence of direct infection of megakaryocytes by SARS-CoV-2, but the abundance of these cells in the lungs at autopsy is probably related to the abundance of small, sometimes platelet-rich thrombi, and foci of haemorrhage. cache = ./cache/cord-301779-y07xjnpe.txt txt = ./txt/cord-301779-y07xjnpe.txt === reduce.pl bib === id = cord-302115-r39ser2c author = Matricardi, Paolo Maria title = The first, holistic immunological model of COVID‐19: implications for prevention, diagnosis, and public health measures date = 2020-05-02 pages = extension = .txt mime = text/plain words = 3738 sentences = 237 flesch = 46 summary = We propose here the first model, explaining how the outcome of first, crucial 10‐15 days after infection, hangs on the balance between the cumulative dose of viral exposure and the efficacy of the local innate immune response (natural IgA and IgM antibodies, Mannose Binding Lectin ). The delayed and strong adaptive immune response (high affinity IgM and IgG antibodies) that follows, causes severe inflammation and triggers mediator cascades (complement, coagulation, and cytokine storm) leading to complications often requiring intensive therapy and being, in some patients, fatal. All rights reserved We focused on humoral components and, in particular on natural antibodies and MBL, to ascertain whether these players of the innate immunity fit all the epidemiological and clinical pre-conditions presented in the last three months by SARS-CoV-2. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for Accepted Article This article is protected by copyright. cache = ./cache/cord-302115-r39ser2c.txt txt = ./txt/cord-302115-r39ser2c.txt === reduce.pl bib === id = cord-302075-ctd9sutv author = Tetro, Jason A. title = Is COVID-19 receiving ADE from other coronaviruses? date = 2020-02-22 pages = extension = .txt mime = text/plain words = 1267 sentences = 70 flesch = 44 summary = One of the most perplexing questions regarding the current COVID-19 coronavirus epidemic is the discrepancy between the severity of cases observed in the Hubei province of China and those occurring elsewhere in the world. ADE also requires prior exposure to similar antigenic epitopes, presumably circulating in local viruses, making it a possible explanation for the observed geographic limitation of severe cases and deaths. Notably, these observations in COVID-19 patients are similar to those who suffered from severe acute respiratory syndrome (SARS) during the 2003 epidemic [4] . Based on this information and the similarity of symptoms to SARS, COVID-19 appears to constitute a major threat to human health justifying the World Health Organization's declaration of a Public Health Emergency of International Concern. Cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis Anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a pH-and cysteine protease-independent FcgR pathway cache = ./cache/cord-302075-ctd9sutv.txt txt = ./txt/cord-302075-ctd9sutv.txt === reduce.pl bib === id = cord-302146-51hof7it author = Cross, Thomas J. title = Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3668 sentences = 196 flesch = 50 summary = Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery. Molecular modeling is an important tool for guiding inhibitor discovery, making it possible to evaluate large numbers of candidate drugs in silico to select experimental targets; however, standard approaches screen against only one version of the protein, typically the reference or wild-type (WT) sequence. Here we characterize all 79 known variants of M pro as of 29 April, 2020, and analyze trends in amino acid substitutions and the resulting structural changes using network analysis and molecular modeling. Analysis of active site networks (ASN) from M pro variants suggests differences in active site flexibility and cohesion that may serve to guide the design of robust, mutation-resistant inhibitors. cache = ./cache/cord-302146-51hof7it.txt txt = ./txt/cord-302146-51hof7it.txt === reduce.pl bib === id = cord-302160-4yfvspaq author = Ruetalo, Natalia title = Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date = 2020-10-07 pages = extension = .txt mime = text/plain words = 1853 sentences = 108 flesch = 56 summary = Strikingly, short exposure of high titer surface dried virus (3*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total reduction of SARS-CoV-2 infectivity. We hence conducted a "real-life" application approach simulating the 66 inactivation of dried surface residing infectious SARS-CoV-2 by a mobile handheld UV-C 67 emitting device and an UV-C box designed to decontaminate medium-size objects. Simulating the situation that exhaled droplets or aerosols from infected 115 individuals contaminate surfaces, we produced a high-titer SARS-CoV-2 infectious stock and 116 dried 35µL of this stock corresponding to ~4*10^6 IU/ml in each well of a 6-well plate. Of note, even short UV-C treatment of the dried virus in the context of the moving "fast" 135 regimen completely inactivated SARS-CoV-2, as no infected cells were detected based on 136 fluorescence protein expression (Fig. 1b) . Altogether, our data 143 demonstrate that UV-C regimens that expose high-titer SARS-CoV-2 to doses down to 16 144 mJ/cm² are sufficient to achieve complete inactivation of the virus. cache = ./cache/cord-302160-4yfvspaq.txt txt = ./txt/cord-302160-4yfvspaq.txt === reduce.pl bib === id = cord-301744-rx7ywew5 author = Kelleni, Mina T. title = SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality date = 2020-08-15 pages = extension = .txt mime = text/plain words = 373 sentences = 30 flesch = 59 summary = title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality have reported SARS-CoV-2 viral load at diagnosis as an independent predictor of mortality. In a trial to explain the apparent contradictory results found in different studies as well as the lack of a distinct boundary between the viral loads that might be associated with a higher mortality rate or a higher recover rate; the author would like to suggest that SARS CoV-2 viral load should be only considered as a personalized reflection to the immune response to COVID-19 as well as to the genetic polymorphisms in SARS CoV-2 receptors 3 . ACE2 polymorphisms might be a better field of study than SARS CoV-2 viral load wishing to develop a genetic test that might predict and exempt, if possible, from COVID-19 related duty those who are more vulnerable to complications and mortality 4 SARS-CoV-2 viral load predicts COVID-19 mortality cache = ./cache/cord-301744-rx7ywew5.txt txt = ./txt/cord-301744-rx7ywew5.txt === reduce.pl bib === id = cord-301876-d2j9wpqk author = Kalita, Parismita title = Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2 date = 2020-05-04 pages = extension = .txt mime = text/plain words = 3449 sentences = 212 flesch = 49 summary = Few groups have designed subunit vaccines against SARS-CoV-2; however, their workflow involved either use of single protein for vaccine design [24, 25] or used only CTL epitopes without considering the importance of B-cell or HTL epitopes [26] . B-cell epitopes for the screened SARS-CoV-2 proteins were predicted using the ABCPred server (http://crdd.osdd.net/raghava/abcpred/). A total of 6 HTLs, 18 CTLs, and 9 B-cell epitopes derived from the three proteins were used to design the subunit vaccine (566 amino acid residues) against SARS-CoV-2 (Supplementary Figure 1) . Based on extensive bioinformatics analysis, we used three proteins to design a multi-epitope subunit vaccine against novel coronavirus SARS-CoV-2. Computational studies suggest that our multi-epitope based subunit vaccine has a probability of showing good protective efficacy and safety against SARS-CoV-2 infection in humans. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach cache = ./cache/cord-301876-d2j9wpqk.txt txt = ./txt/cord-301876-d2j9wpqk.txt === reduce.pl bib === id = cord-302020-ypsh3rjv author = Kim, Dongwan title = The Architecture of SARS-CoV-2 Transcriptome date = 2020-04-23 pages = extension = .txt mime = text/plain words = 6092 sentences = 403 flesch = 57 summary = In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. (A) Read counts from nanopore direct RNA sequencing of total RNA from Vero cells infected with SARS-CoV-2. We further discovered RNA modification sites and measured the poly(A) tail length of gRNAs and sgRNAs. To delineate the SARS-CoV-2 transcriptome, we first performed DRS runs on a MinION nanopore sequencer with total RNA extracted from Vero cells infected with SARS-CoV-2 (Be-taCoV/Korea/KCDC03/2020). To unambiguously investigate the modifications, we generated negative control RNAs by in vitro transcription of the viral sequences and performed a DRS run on these unmodified controls ( Figure S4A ). cache = ./cache/cord-302020-ypsh3rjv.txt txt = ./txt/cord-302020-ypsh3rjv.txt === reduce.pl bib === id = cord-301946-erzh30mt author = Kwak-Kim, Joanne title = COVID-19 and immunomodulation treatment for women with reproductive failures date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5604 sentences = 335 flesch = 42 summary = With the Coronavirus Disease 2019 (COVID-19) pandemic, patient care has been significantly challenged not only for the COVID-19 cases but for the others, including pregnant women with a history of reproductive failures (RF), such as recurrent pregnancy losses (RPL), repeated implantation failures (RIF), with immune etiologies including autoimmune diseases, cellular immune dysfunction, and rheumatic conditions. SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus), which caused the SARS outbreak in 2003, infects macrophages and T cells (Perlman and Dandekar 2005) and induces various cytokines, such as type I IFN, TNF-α, IL-1, etc., and B cell-related antibodies (Prompetchara et al. With the currently available data, it is unlikely that the use of IVIg in patients with RFI will impact the chances of contracting the disease or negatively affect the clinical course in women with COVID-19 infection during pregnancy. cache = ./cache/cord-301946-erzh30mt.txt txt = ./txt/cord-301946-erzh30mt.txt === reduce.pl bib === id = cord-302163-0jav84zw author = Anastassopoulou, Cleo title = Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity date = 2020-10-22 pages = extension = .txt mime = text/plain words = 4823 sentences = 212 flesch = 41 summary = We searched PubMed/MEDLINE for all Englishlanguage original articles or reviews reporting on potential associations between human genetic factors and susceptibility to SARS-CoV-2 infection or COVID-19 severity, up to August 12, 2020 (with updating as of September 11, 2020, during the revision of the manuscript). The search was performed using all combinations of terms related to the novel coronavirus and the disease (e.g., "SARS-CoV-2," "2019-nCoV," and "COVID-19") on the one hand, and terms concerning susceptibility to infection or disease severity (e.g., "polymorphisms," "allelic variation," "genetic predisposition," "genotype," "clinical outcome") as well as the names of individual genes in which relevant polymorphisms were found (e.g., "TLR7," "ACE2"), on the other. A recently published comparative genetic analysis of approximately 81,000 human genomes across different populations suggested possible associations of coding region variants of ACE2 and TMPRSS2 with COVID-19 susceptibility, severity, and clinical outcomes [49] . cache = ./cache/cord-302163-0jav84zw.txt txt = ./txt/cord-302163-0jav84zw.txt === reduce.pl bib === id = cord-302125-96w0nh9q author = Péré, Hélène title = Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date = 2020-09-03 pages = extension = .txt mime = text/plain words = 370 sentences = 27 flesch = 58 summary = title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Running title: Sequential SARS-CoV-2 serology testing in health-workers Hélène Péré 1,2,3 , Maxime Wack 4 , Benoit Védie 5 , Nathalie Demory Guinet 6 , Kassis Chikani Najiby 7 , Laurence Janot 6 , Laurent Bélec 1,2,3 , David Veyer 1, 8 surface protein, with the high-throughput UniCel DxI 800 Access Immunoassay System (Beckman Coulter), to increase hospital productivity in SARS-CoV-2 IgG serology testing. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients The authors are also grateful to Beckman Coulter, France, for providing the ACCESS SARS-CoV-2 IgG kits for the study.J o u r n a l P r e -p r o o f cache = ./cache/cord-302125-96w0nh9q.txt txt = ./txt/cord-302125-96w0nh9q.txt === reduce.pl bib === id = cord-301974-4wn40ivq author = Berry, Jody D title = Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus date = 2004-09-01 pages = extension = .txt mime = text/plain words = 5877 sentences = 293 flesch = 51 summary = A total of 15 l of SARS-CoV antigen (infected Vero cell lysate) or 5 g of highly purified virus is coated (per spot) for 1 h at 37 • C. c Protein specificity tests shown here were determined by Western immunoblot with purified virus and infected cell lysate under denaturing conditions (Fig. 1) . The four Western immunoblot negative, virus-neutralising mAbs were tested for their ability to bind native SARS-CoV in infected cells by immunofluorescence assay. While purified virus is clearly the optimal antigen tested in this series of experiments, the lower quality SARS-CoV-infected Vero cell lysates are, however, much easier to prepare for diagnostic assays. This paper describes the development of murine mAbs which recognise SARS-CoV antigens in ELISA, immuno-dotblot, Western immunoblot, on the surface of infected cells, and in neutralisation assays. cache = ./cache/cord-301974-4wn40ivq.txt txt = ./txt/cord-301974-4wn40ivq.txt === reduce.pl bib === id = cord-301943-qdtfjdxr author = Javelot, H title = Panique et pandémie: revue de la littérature sur les liens entre le trouble panique et l'épidémie à SARS-CoV-2 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 4740 sentences = 393 flesch = 53 summary = Résumé L'état de panique associé à la pandémie liée au SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) incite à s'interroger sur les troubles anxieux que cette situation pourrait générer ou aggraver. D'éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d'hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l'infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. D'éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d'hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l'infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. cache = ./cache/cord-301943-qdtfjdxr.txt txt = ./txt/cord-301943-qdtfjdxr.txt === reduce.pl bib === id = cord-301921-i1o18nmw author = Sernicola, Alvise title = How to Deal With Post-viral Cutaneous Eruptions in the Era of Coronavirus Infection date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1144 sentences = 53 flesch = 41 summary = In our routine clinical practice during the COVID-19 outbreak, we are observing a growing number of post viral cutaneous eruptions in apparently healthy individuals in the second or third decade of life that we feel is remarkable compared to the usual local epidemiology of this season. A dermatopathologist from our country has shared the report of skin biopsies performed on two patients with COVID-19 disease, matching the histology of Giannotti-Crosti syndrome, that is a non-specific manifestation of a viral infection (11) . These observations hint at the possible role of specific genetic factors that, while a predisposition to the development of skin eruptions, may protect from severely symptomatic presentations of coronavirus infection. In our current cases of atypical skin eruptions, in which a relationship with conventional viral agents has been ruled out by laboratory testing and clinical history, molecular testing with PCR could be performed on pharynx swabs to support the hypothesis of a possible association with the novel coronavirus. cache = ./cache/cord-301921-i1o18nmw.txt txt = ./txt/cord-301921-i1o18nmw.txt === reduce.pl bib === id = cord-302166-tah3jdw0 author = Zhang, Shen-Ying title = Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity? date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1601 sentences = 88 flesch = 41 summary = We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. Studies since 1996 have identified a number of monogenic inborn errors of immunity (IEIs) underlying life-threatening infectious diseases, including specific viral diseases, in previously healthy patients 1,3-6 . The search for monogenic IEIs conferring predisposition to severe COVID-19 in previously healthy children and young or even middle-aged adults should therefore involve the genome-wide, agnostic testing of genetic hypotheses (see also COVID Human Genetic Effort) 10 . The discovery of monogenic IEIs to SARS-CoV-2 should help unravel the mechanistic basis of the immunopathogenesis of severe COVID-19 in young, previously healthy individuals. A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection cache = ./cache/cord-302166-tah3jdw0.txt txt = ./txt/cord-302166-tah3jdw0.txt === reduce.pl bib === id = cord-302316-raf5rlkq author = Brüssow, Harald title = COVID‐19: From pathogenesis models to the first drug trials date = 2020-06-23 pages = extension = .txt mime = text/plain words = 6944 sentences = 350 flesch = 44 summary = US researchers studied the viral and cellular transcriptional response upon infection of cell cultures and in animal models with different respiratory viruses including influenza A virus and SARS-CoV-2. A French study randomizing 181 COVID-19 patients with pneumonia on hydroxychloroquine or placebo, observed, however, no significant effect of treatment on transfer to ICU, mortality, or in the prevention of development of acute respiratory distress syndrome (Mah evas et al., 2020). A total of 86 COVID-19 cases of patients from China with mild/moderate disease were randomized on the antiviral lopinavir (an inhibitor of HIV protease combined with ritonavir, which prolongs the presence of drugs in the body) or the antiviral arbidol (an influenza virus fusion inhibitor only registered in Russia) or in a control group in a 2:2:1 ratio. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial cache = ./cache/cord-302316-raf5rlkq.txt txt = ./txt/cord-302316-raf5rlkq.txt === reduce.pl bib === id = cord-302527-n53d5en0 author = Dadlani, Shashi title = SARS-CoV-2 Transmission in a Dental Practice in Spain: After the Outbreak date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2425 sentences = 148 flesch = 54 summary = SARS-CoV-2 is a human-to-human viral infection [4, 5] transmitted through airborne droplets from talking, coughing, or sneezing [6] or by touching or coming into contact with contaminated surfaces that are then transmitted to oral, nasal, and mucosal membranes [7] . During the coronavirus outbreak, dentists in Spain and other countries were recommended to only attend dental emergencies under strict measures wearing specific professional protection equipment to minimize the risk and maintain social distancing [12] . SARS-CoV-2 has been identified in the saliva of infected patients [14] , suggesting that the aerosols generated during dental procedures from an infected person can be extremely contagious. ese droplets can remain in the area even after the patient has left the clinic, leading to infection of dental professionals via contaminated surfaces [15] . e inhalation of airborne particles and aerosol particles during dental treatments on patients with SARS-CoV-2 is a very high-risk procedure where dentists can be exposed to the virus. cache = ./cache/cord-302527-n53d5en0.txt txt = ./txt/cord-302527-n53d5en0.txt === reduce.pl bib === id = cord-302381-oujsmf8d author = Rankin, John title = Godzilla in the corridor: The Ontario SARS crisis in historical perspective date = 2006-06-30 pages = extension = .txt mime = text/plain words = 5098 sentences = 252 flesch = 61 summary = The following evaluation of yellow fever, cholera and the Spanish influenza will illustrate a continuity in epidemic nurses' feelings of fear and isolation from the mid-19th to the early 20th century. The five submissions studied were: the Canadian Nursing Association Brief to the National Advisory Committee on SARS and Public Health On 5 March 2003, SARS claimed its first Ontario victim when Sui-chu Kwan, a 78-year-old woman who had returned from a trip to Hong Kong, died of the disease. Instead, the silencing of nurses proved deadly as the SARS virus continued to spread placing both the public and health care workers at heightened risk. It is evident that nurses had little knowledge of previous public health crises and no context in which to place the SARS epidemic. That is they reacted to health care crisis of unknown epidemiology with much fear and, due to the nature of nursing during these crises, are prone to feelings of isolation. cache = ./cache/cord-302381-oujsmf8d.txt txt = ./txt/cord-302381-oujsmf8d.txt === reduce.pl bib === id = cord-302393-hrz3bypr author = Omrani, Ali S. title = The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date = 2020-10-19 pages = extension = .txt mime = text/plain words = 4533 sentences = 269 flesch = 52 summary = Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. In this study, we describe 60-day outcomes of a nationwide COVID-19 cohort from Qatar, and explore patient characteristics associated with the need for admission to an intensive care unit (ICU). In the multivariable logistic regression, we found that older age, male sex, co-existing diabetes or chronic kidney disease, and higher BMI were all independently associated with increased risk of need for ICU admission ( Table 2) . cache = ./cache/cord-302393-hrz3bypr.txt txt = ./txt/cord-302393-hrz3bypr.txt === reduce.pl bib === id = cord-302358-vou46eie author = Fomsgaard, Anna S title = An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage date = 2020-03-30 pages = extension = .txt mime = text/plain words = 1720 sentences = 114 flesch = 58 summary = With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98°C prior to the RT-qPCR reaction. Analysis of SARS-CoV-2 positive and negative oropharyngeal swaps using the SensiFAST TM kit showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy when samples were heat-processed for 5 min. Analysis of the clinical samples using the RealStar® SARS-CoV-2 RT-PCR kit showed significant inhibition of the RT-qPCR reaction (Figure 1 ) except when the MagNA Pure and QIACube purified samples were used. Moreover, this positive result could not be confirmed by any other NA purification method or SARS-CoV-2 specific RT-qPCR assay and therefore we cannot confirm if this patient sample is truly positive for COVID-19 using the QIACube purification system or false negative using the MagNA Pure system. cache = ./cache/cord-302358-vou46eie.txt txt = ./txt/cord-302358-vou46eie.txt === reduce.pl bib === id = cord-302414-g5onwhg1 author = Tahir ul Qamar, Muhammad title = Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6780 sentences = 434 flesch = 47 summary = Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches. cache = ./cache/cord-302414-g5onwhg1.txt txt = ./txt/cord-302414-g5onwhg1.txt === reduce.pl bib === id = cord-302147-6r67g5zk author = Kayaaslan, Bircan title = Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact date = 2020-10-16 pages = extension = .txt mime = text/plain words = 370 sentences = 35 flesch = 62 summary = title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact The author emphasizes that even if semen has a very low possibility for transmission of the virus, the disease can be transmitted by the respiratory route due to the very close contact between partners. We think that even if severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is detected in a patient's semen sample, it is quite difficult to say that the transmission between partners has solely been through semen. However, sexual contact carries a high risk in terms of SARS-CoV-2 transmission between partners through the respiratory secretions, not semen. Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 No evidence of severe acute respiratory syndrome-coronavirus 2 in semen of males recovering from coronavirus disease 2019 Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection cache = ./cache/cord-302147-6r67g5zk.txt txt = ./txt/cord-302147-6r67g5zk.txt === reduce.pl bib === id = cord-302485-hhsa76k8 author = Wu, Yuntao title = SARS-CoV-2 is an appropriate name for the new coronavirus date = 2020-03-06 pages = extension = .txt mime = text/plain words = 853 sentences = 51 flesch = 59 summary = be significantly attenuated to the point of becoming a new low-pathogenic or non-patho genic virus, such attenuated viral isolates could be named as lowpathogenic human coronaviruses, such as LPH-CoV. We believe that the naming of SARS-CoV-2 by the Coronavirus Study Group is aligned with the goals of the International Committee on Taxonomy of Viruses to facilitate good practice and scientific exchange. We have read with great interest the Correspondence by Shibo Jiang and colleagues, 1 in which they propose a name change for the newly emerged coronavirus, 2 which was recently designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. 4 Through DivErsity pArtitioning by hieRarchical Clustering-based analyses, 5 the newly emerged coronavirus was deemed not sufficiently novel but is a sister virus to SARS-CoV, the primary viral isolate defining the species. cache = ./cache/cord-302485-hhsa76k8.txt txt = ./txt/cord-302485-hhsa76k8.txt === reduce.pl bib === id = cord-302409-40ktyt5q author = Wang, Jie title = SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2771 sentences = 166 flesch = 51 summary = OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. cache = ./cache/cord-302409-40ktyt5q.txt txt = ./txt/cord-302409-40ktyt5q.txt === reduce.pl bib === id = cord-302195-25gjbyi1 author = Al Huraimel, Khalid title = SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date = 2020-07-15 pages = extension = .txt mime = text/plain words = 7089 sentences = 386 flesch = 50 summary = This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. There is no conclusive evidence for aerosol or faecal-oral transmission of SARS-CoV-2 despite several researchers considering them as plausible routes that may explain the high infectivity and global spread of COVID-19 (Chen et al., 2020; van Doremalen et al., 2020; Wang et al., 2020a) . From the literature studied, concerns of COVID-19 infection through environmental contact pertain mainly to areas that lack proper sanitation and wastewater treatment, lack adequate solid waste management infrastructure, in areas where raw sewage is discharged directly into natural water bodies, and in cities where air pollution is problematic.  Robust evidence is needed to assess impact of air pollution, solid waste management, and sewage contamination of water bodies on COVID-19 spread and infectivity. cache = ./cache/cord-302195-25gjbyi1.txt txt = ./txt/cord-302195-25gjbyi1.txt === reduce.pl bib === id = cord-302238-l8j1vy0y author = Shah, Prakesh S. title = Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates date = 2020-04-21 pages = extension = .txt mime = text/plain words = 943 sentences = 55 flesch = 42 summary = title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. Vertical transmission of coronavirus Disease 19 (COVID-19) from infected pregnant mothers to neonates: a review Neonatal early-onset infection with SARS-CoV-2 in 33 neonates born to mothers with COVID-19 in Wuhan, China. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn cache = ./cache/cord-302238-l8j1vy0y.txt txt = ./txt/cord-302238-l8j1vy0y.txt === reduce.pl bib === id = cord-302584-fwdpzv85 author = Zhu, Ying title = Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date = 2005-01-01 pages = extension = .txt mime = text/plain words = 3429 sentences = 170 flesch = 54 summary = title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates Despite the fact that the SARS-CoV can cause an atypical and fatal form of pneumonia, the genome structure, gene expression pattern, and protein profiles of the virus are similar to those of other conventional coronaviruses [17] , which are only responsible for mild respiratory tract infections in a wide range of animals including humans, pigs, cows, mice, cats, and birds [10, 19] . In this report, we described the isolation of a new SARS-CoV strain (WHU) from a patient in Hubei Province, China during the late period of SARS outbreak. Comparative study of genetic characterization and nucleotide variation of all known SARS-CoV offers insights into understanding functions of the viral genes and revealing the evolution trends of the virus. cache = ./cache/cord-302584-fwdpzv85.txt txt = ./txt/cord-302584-fwdpzv85.txt === reduce.pl bib === id = cord-302228-n5o6jfs2 author = Lodise, Thomas P. title = COVID‐19: Important Therapy Considerations and Approaches in this Hour of Need date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1935 sentences = 113 flesch = 50 summary = A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients.1-3 However, optimal drug therapy decisions for those with moderate to severe COVID-19 infections are extremely challenging at this time as evidence is limited. A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified, and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients. If data are amassed on COVID-19 patients, it is important that detailed information is collected on the outcomes associated with the treatment strategies used at our respective institutions. Despite data suggesting that lopinavir-ritonavir was active against SARS-CoV-2 infection, no benefit was observed with lopinavir-ritonavir treatment versus standard care in a study of hospitalized adult patients with severe COVID-19. cache = ./cache/cord-302228-n5o6jfs2.txt txt = ./txt/cord-302228-n5o6jfs2.txt === reduce.pl bib === id = cord-302541-0upiu6iq author = Gupta, Abhishek title = Lockdown—the only solution to defeat COVID-19 date = 2020-05-06 pages = extension = .txt mime = text/plain words = 575 sentences = 35 flesch = 62 summary = As it is a new strain of coronavirus and little is known about its behaviour except its potential for transmission while being asymptomatic during an incubation period of up to 14 days and its sensitivity to heat, Sophie Bushwick, technology editor at Scientific American, a science magazine, stated on 20 March 2020 that asymptomatic people with COVID-19 have a higher viral load. A lockdown period depends upon the virus' faster decay rate which is directly related to the melting point of the outer protective lipid bilayers of SARS-CoV2. In the case of SARS-CoV2 being zoonotic, it is presumed that the melting point of its lipid layer should be around 40°C, resulting in its faster decay during the summer. Because coronavirus is transmitted from host to host only, keeping it away from a host for longer than its incubation period through a lockdown can cause its own death and defeat COVID-19. cache = ./cache/cord-302541-0upiu6iq.txt txt = ./txt/cord-302541-0upiu6iq.txt === reduce.pl bib === id = cord-302616-1uwrcvjx author = Steenblock, Charlotte title = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis date = 2020-05-07 pages = extension = .txt mime = text/plain words = 3872 sentences = 201 flesch = 41 summary = title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis Furthermore, it has to be considered that certain therapies impacting expression of ACE2 might also influence the RAAS and the neuroendocrine stress axis, which may lead to long-term consequences, as prolonged exposure to stressors increases the risk to develop major depressive, anxiety and post-traumatic stress disorders [42] . In addition to contributing to the progression of the immune response against viral infection, cytokines activate the HPA axis, resulting in the release of adrenal glucocorticoids [43] . In relation to coronavirus infections, it was shown that pulmonary stem/progenitor cells that express ACE2 are targeted by SARS-CoV in primary cultures [73] . Increasing brain angiotensin converting enzyme 2 activity Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis decreases anxiety-like behavior in male mice by activating central Mas receptors cache = ./cache/cord-302616-1uwrcvjx.txt txt = ./txt/cord-302616-1uwrcvjx.txt === reduce.pl bib === id = cord-302576-fv2ib5vc author = Barisione, Emanuela title = Fibrotic progression and radiologic correlation in matched lung samples from COVID-19 post-mortems date = 2020-09-28 pages = extension = .txt mime = text/plain words = 5448 sentences = 238 flesch = 37 summary = This study uses an innovative cryobiopsy approach for the post-mortem sampling of lung tissues from COVID-19 patients demonstrating the progression of fibrosis in time and correlation with computed tomography features. The main findings of this study include the following: (1) the identification of a chronological evolution of lesions from an early exudative phase with hyaline membranes to a mid-phase characterized by intra-alveolar fibrinous exudate and early fibroblastic interstitial fibrosis to a late phase with alveolar obliteration by fibrosis and possible micro-honeycombing; (2) mild degree of inflammatory infiltrates; and (3) correlation of histologic patterns with lung CT alterations. Immunohistochemistry for SARS-CoV-2 nucleocapsid protein also showed modification during disease progression as intense immunostaining was seen in early exudative phase Fig. 4 Histology and radiology of late/organizing phase of DAD pattern: aspects of progressive derangement/obliteration of alveolar structure by interstitial fibroblast proliferation. cache = ./cache/cord-302576-fv2ib5vc.txt txt = ./txt/cord-302576-fv2ib5vc.txt === reduce.pl bib === id = cord-302608-fw4pmaoc author = Huang, Jiao-Mei title = Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-19 pages = extension = .txt mime = text/plain words = 1890 sentences = 125 flesch = 57 summary = However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. The host specificity of virus particle is determined by amino acid sequence of RBD and is usually dissimilar among different CoVs. Therefore, RBD is a core determinant for tissue tropism and host range of CoVs. This article presents SARS-CoV-2 phylogenetic trees, comparison and analysis of genome, spike protein, and RBD amino acid sequences of different CoVs, deducing source and etiology of COVID-19 and evolutionary relationship among SARS-CoV-2 in human. The S-protein amino acid sequence identity between SARS-CoV-2 and related beta-CoVs showed that bat/Yunnan/RaTG13 shares highest similarity of 97.43%. cache = ./cache/cord-302608-fw4pmaoc.txt txt = ./txt/cord-302608-fw4pmaoc.txt === reduce.pl bib === id = cord-302442-jhio7mrl author = Chrzanowski, Wojciech title = Can Stem Cells Beat COVID-19: Advancing Stem Cells and Extracellular Vesicles Toward Mainstream Medicine for Lung Injuries Associated With SARS-CoV-2 Infections date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4158 sentences = 180 flesch = 38 summary = Stem cell therapies and, more recently, their secreted extracellular vesicles (EVs), are emerging as new promising treatments, which could attenuate inflammation but also regenerate the lung damage caused by COVID-19. In this review article, we outline the mechanisms of cytokine storm and lung damage caused by SARS-CoV-2 virus leading to COVID-19 disease and how mesenchymal stem cells (MSCs) and their secreted EVs can be utilized to tackle this damage by harnessing their regenerative properties, which gives them potential enhanced clinical utility compared to other investigated pharmacological treatments. The safety profile and efficacy of MSCs are well-established based on the results from a number of completed clinical studies investigating the therapeutic potential of these therapies in lung diseases such as ARDS (Matthay et al., 2019; and bronchopulmonary dysplasia (Namba, 2019) , cardiovascular diseases (Kim et al., 2015; Suvakov et al., 2020) , diabetes (Thakkar et al., 2015; Cho et al., 2018) , and spinal cord injury (Xu and Yang, 2019) . cache = ./cache/cord-302442-jhio7mrl.txt txt = ./txt/cord-302442-jhio7mrl.txt === reduce.pl bib === id = cord-302733-rfuyd041 author = Dellicour, Simon title = A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date = 2020-10-21 pages = extension = .txt mime = text/plain words = 3727 sentences = 165 flesch = 41 summary = At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. We generated a time-scaled phylogenetic tree using a rapid maximum likelihood approach 16 and subsequently ran a preliminary discrete phylogeographic analysis along this tree to identify internal nodes and descending clades that likely correspond to distinct introductions into the Belgian territory ( Fig. 1, S2 ). We used the continuous diffusion model 13 available in BEAST 1.10 14 to perform a spatially-explicit (or "continuous") phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. cache = ./cache/cord-302733-rfuyd041.txt txt = ./txt/cord-302733-rfuyd041.txt === reduce.pl bib === id = cord-302786-ibt7mupq author = Suwanwongse, Kulachanya title = Fatal Outcome in a Kidney-Pancreas Transplant Recipient With COVID-19 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2229 sentences = 138 flesch = 47 summary = Despite a growing report on clinical characteristics and prognosis of patients with COVID-19, the data in the special population, including transplant recipients, is still limited. We proposed that the pre-existing T-cell dysfunction from the long-term use of immunosuppressive agents in organ transplant recipients adversely affects COVID-19 prognosis and worsens COVID-19 mortality. However, impaired immune functions may paradoxically protect transplant patients from the hyper-inflammatory response to SARS-CoV-2 and thus dampen the disease severity. Long-term immunosuppressive therapy in organ transplant recipients may alter clinical features and outcomes of COVID-19. The long-term use of immunosuppressive medications in organ transplant recipients is associated with the decrease in T-cell number and function; TAC and MMF preferentially inhibit T-cell response. However, in this report, immunosuppressive agents were discontinued in patients with severe disease, presumably with high mortality risks. Preexisting T-cell immune response deficits from long-term use of immunosuppressive agents may worsen the prognosis of COVID-19 in transplant recipients. cache = ./cache/cord-302786-ibt7mupq.txt txt = ./txt/cord-302786-ibt7mupq.txt === reduce.pl bib === id = cord-303173-q88zdf03 author = Panchaud, Alice title = An international registry for emergent pathogens and pregnancy date = 2020-04-27 pages = extension = .txt mime = text/plain words = 530 sentences = 29 flesch = 43 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) pandemic is no exception. 3 To tweak resources, we have adjusted the Zika virus international web registry 9 to create COVI-Preg, a structured data collection tool available to any facility assessing pregnant patients for SARS-CoV-2 infection. For the ongoing SARS-CoV-2 pandemic, we hypothesise that the collected data will allow researchers and health-care professionals to better characterise the disease course and spectrum, quantitatively estimate associated risks, and identify specific risk factors that can be used to define screening strategies in pregnant women and adequate prevention meas ures, and to direct specific and early clinical management of women and fetuses at risk. Clinical analysis of pregnancy in second and third trimesters complicated severe acute respiratory syndrome An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-303173-q88zdf03.txt txt = ./txt/cord-303173-q88zdf03.txt === reduce.pl bib === id = cord-302813-963ypqow author = Tegally, H. title = Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3543 sentences = 200 flesch = 59 summary = Through the unprecedented sharing of SARS-CoV-2 sequences during this pandemic, including from one of the first cases in Wuhan, China (MN908947.3) 2 , genomic epidemiology investigations globally are playing a major role in characterizing and understanding this emerging virus [4] [5] [6] [7] [8] [9] . The profile of SARS-CoV-2 epidemiological progression in South Africa was largely influenced by the implementation of lockdown measures in the early phases of the epidemic and the subsequent easing of these measures. We focused on the three largest monophyletic lineage clusters (C.1, B.1.1.54, B.1.1.56,) that spread in South Africa during lockdown and then grew into large transmission clusters during the peak infections phase of the epidemic (Fig 1C) . Our analysis therefore shows that a number of SARS-CoV-2 lineages, each with unique mutations, emerged within localized epidemics during lockdown even as the introduction of new lineages from outside South Africa was being curbed. cache = ./cache/cord-302813-963ypqow.txt txt = ./txt/cord-302813-963ypqow.txt === reduce.pl bib === id = cord-303384-bgvagdft author = Bilinska, Katarzyna title = Anosmia in COVID-19: A Bumpy Road to Establishing a Cellular Mechanism date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2173 sentences = 124 flesch = 49 summary = Several very recent papers contributed to explaining the key cellular steps occurring in the olfactory epithelium leading to anosmia/hyposmia (collectively known as dysosmia) initiated by SARS-CoV-2 infection. Initial hospital observations and early studies have suggested several possible mechanisms for the development of anosmia in COVID-19, including olfactory cleft syndrome, nasal obstruction and rhinorrhea, cytokine storm, direct damage to olfactory receptor neurons (ORNs), and impairment of the olfactory perception centers in the brain. The current model of olfactory dysfunction in COVID-19 is based on the already proven observation that SUS cells are the primary target of the virus and that SUSs infection initiates a series of events leading to dysosmia. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. cache = ./cache/cord-303384-bgvagdft.txt txt = ./txt/cord-303384-bgvagdft.txt === reduce.pl bib === id = cord-302939-z0071rwa author = Erdeve, Ömer title = The Turkish Neonatal Society proposal for the management of COVID-19 in the neonatal intensive care unit date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3955 sentences = 203 flesch = 48 summary = • NICUs should prepare emergency plans for COVID-19 to ensure the optimal management of potential victims • The assigned team should coordinate the hospitalization and maintenance of the patient with suspected COVID-19 • In the presence of high-risk factors, it is recommended that the newborn should be admitted and taken into an isolation ward in the NICU as soon as possible • Samples of the patient should be taken by staff that is trained and designated by the NICU • Newborns may be born prematurely and the most common non-specific initial symptoms include respiratory distress, shortness of breath, cyanosis, increased heart rate, lethargy, fever, feeding intolerance and vomiting • The SARS-CoV-2 has not been detected in breast milk, but the choice to breastfeed should be the mother's and the families • There is no effective anti-coronavirus treatment yet and treatment is generally supportive cache = ./cache/cord-302939-z0071rwa.txt txt = ./txt/cord-302939-z0071rwa.txt === reduce.pl bib === id = cord-303027-r2jgu2be author = Lu, Yen-Ta title = Viral load and outcome in SARS infection: The role of personal protective equipment in the emergency department date = 2006-01-24 pages = extension = .txt mime = text/plain words = 4579 sentences = 234 flesch = 57 summary = Both specific droplet and rigorous universal precautions were thus recommended for healthcare workers (HCWs) taking care of patients with severe acute respiratory syndrome (SARS) (4) . We designed this study to explore the relationship between personal protective equipment (PPE) used by HCWs and the clinical course, outcome, and viral load in both HCWs and non-HCWs involved in a SARS cluster stemming from exposure to a single index case in our Emergency Department. Differences between the quantitative RT-PCR values for SARS-CoV in nasopharyngeal swab and HRCT scores in HCWs and non-HCWs were tested for significance using the Mann-Whitney U test. We have described a better clinical outcome after SARS in 4 HCWs compared with 12 non-HCWs; despite all having been involved in a cluster related to one index patient, with 13 apparently directly infected by that patient and 3 others by secondary transmission. cache = ./cache/cord-303027-r2jgu2be.txt txt = ./txt/cord-303027-r2jgu2be.txt === reduce.pl bib === id = cord-302902-34vftqt9 author = Law, Brenda Hiu Yan title = Effect of COVID-19 Precautions on Neonatal Resuscitation Practice: A Balance Between Healthcare Provider Safety, Infection Control, and Effective Neonatal Care date = 2020-08-18 pages = extension = .txt mime = text/plain words = 2901 sentences = 157 flesch = 33 summary = Adaptations have been proposed for resuscitation of infants born to women with COVID-19, to protect health care providers, maintain infection control, and limit post-natal transmission. Changes especially impact respiratory procedures, personal protective equipment (PPE) use, resuscitation environments, teamwork, and family involvement. Adaptations have been proposed for resuscitation of infants born to women with suspected or confirmed COVID-19, to protect health care providers (HCPs), limit post-natal transmission, and maintain infection control (7) . Neonatal resuscitation may be especially impacted by changes in (i) respiratory support, (ii) personal protective equipment (PPE), (iii) resuscitation environment, (iv) team-based activities, and (v) family involvement ( Table 1) . Modifications to ventilation practices during neonatal resuscitation have been proposed to protect HCPs during AGPs, based on limited evidence on vertical transmission and aerosolization of SARS-CoV-2 (7, 9) . General COVID-19 resuscitation guidelines recommend the use of viral filters on mask ventilation devices to decrease risks to HCPs (9) . cache = ./cache/cord-302902-34vftqt9.txt txt = ./txt/cord-302902-34vftqt9.txt === reduce.pl bib === id = cord-302983-3v5bc80z author = Matterne, Uwe title = Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review date = 2020-10-10 pages = extension = .txt mime = text/plain words = 5446 sentences = 296 flesch = 46 summary = title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review OBJECTIVE: The aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). METHODS: We searched major databases and included publications of quantitative and qualitative studies in English and German on any type of research on the functional, critical and communicative domains of HL conducted in the context of the three outbreaks in the general population. Therefore, the aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). cache = ./cache/cord-302983-3v5bc80z.txt txt = ./txt/cord-302983-3v5bc80z.txt === reduce.pl bib === id = cord-302707-cap2rgf7 author = Ng, Dianna L. title = SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4364 sentences = 224 flesch = 50 summary = Here, we present data validating the use of the EUA authorized Abbott Architect SARS-CoV-2 IgG test for antibody detection in two populations in March 2020, a hospitalized COVID-19 patient cohort at a tertiary care hospital in San Francisco and a cohort of blood donors from the San Francisco Bay Area. These studies demonstrate that SARS-CoV-2 seroprevalence in the San Francisco Bay Area was very low, suggesting limited circulation of the virus in the community as of early March, and that IgG and IgM titers are predictive of neutralizing activity, with high positive percent agreement. To evaluate assay sensitivity, we assembled a cohort of 38 hospitalized patients and 5 outpatients at University of California, San Francisco (UCSF) Medical Center and the San Francisco Veterans Affairs (SFVA) Health Care System, all of whom received care at adult inpatient units or clinics and were real-time polymerase chain reaction (RT-PCR) positive for SARS-CoV-2 from nasopharyngeal and/or oropharyngeal swab testing ( Fig. 1a and Supplementary Table 1 ). cache = ./cache/cord-302707-cap2rgf7.txt txt = ./txt/cord-302707-cap2rgf7.txt === reduce.pl bib === id = cord-303017-4zx94rm6 author = Barbieri, Antonio title = Can Beta-2-Adrenergic Pathway Be a New Target to Combat SARS-CoV-2 Hyperinflammatory Syndrome?—Lessons Learned From Cancer date = 2020-09-30 pages = extension = .txt mime = text/plain words = 3539 sentences = 191 flesch = 41 summary = This hypothesis relies on different pieces of evidence: IL-6, TNFa, and IL-1b promote Th17 response and are associated with inflammatory symptoms including fever, and the two latter are also associated with vascular permeability and leakage; IL-17 has a broad inflammatory effect and together with GM-CSF is involved in inflammatory and autoimmune disease; Covid-19 patients have a significantly increased number of CCR6+ Th17 cells (4) ; elevated TH17 and IL-17 related pathways are increased in SARS-CoV, MERS-CoV, and H1N1 influenza virus patients (14) (15) (16) ; In MERS-CoV patients, IL-17 and low IFNg are associated with worse prognosis (14) . Targeting beta-2adrenergic pathway was shown to reduce inflammatory cytokine and Th17 response in different settings such as cancer and autoimmune diseases. Two different reports on cancer patients show that propranolol treatment reduces inflammatory cytokines including IL-6 and TNFa, inflammation-related transcription factors such as NFkB and STAT3 and reduces the activation of Treg lymphocytes (36, 37) . cache = ./cache/cord-303017-4zx94rm6.txt txt = ./txt/cord-303017-4zx94rm6.txt === reduce.pl bib === id = cord-302912-aqutzlx4 author = Liu, Ziteng title = The Inhibitory Effect of Curcumin on Virus-Induced Cytokine Storm and Its Potential Use in the Associated Severe Pneumonia date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5738 sentences = 286 flesch = 42 summary = The development of coronavirus-evoked pneumonia is associated with excessive inflammatory responses in the lung, known as "cytokine storms," which results in pulmonary edema, atelectasis, and acute lung injury (ALI) or fatal acute respiratory distress syndrome (ARDS). Therefore, in this review, we summarize the mounting evidence obtained from preclinical studies using animal models of lethal pneumonia where curcumin exerts protective effects by regulating the expression of both proand anti-inflammatory factors such as IL-6, IL-8, IL-10, and COX-2, promoting the apoptosis of PMN cells, and scavenging the reactive oxygen species (ROS), which exacerbates the inflammatory response. As part of a robust immune response in severe cases, the virus triggers overaction of immune systems, producing a large number of inflammatory factors, which causes severe damage to the lung and manifests acute respiratory distress syndrome (ARDS), resulting in high mortality. Such an inflammatory response, including overproduction of immune cells and pro-inflammatory cytokines, is defined as the cytokine storm that usually occurs in viral infection and causes acute lung injury (ALI) and ARDS. cache = ./cache/cord-302912-aqutzlx4.txt txt = ./txt/cord-302912-aqutzlx4.txt === reduce.pl bib === id = cord-303111-iv4lzpev author = Almazán, Fernando title = Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date = 2014-12-19 pages = extension = .txt mime = text/plain words = 7071 sentences = 314 flesch = 42 summary = Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. cache = ./cache/cord-303111-iv4lzpev.txt txt = ./txt/cord-303111-iv4lzpev.txt === reduce.pl bib === id = cord-303022-9hqoq7tf author = Madapusi Balaji, Thodur title = Oral cancer and periodontal disease increase the risk of COVID 19? A mechanism mediated through furin and cathepsin overexpression date = 2020-06-01 pages = extension = .txt mime = text/plain words = 888 sentences = 54 flesch = 47 summary = In addition to furin, another protease cathepsin L is also elevated in chronic periodontitis and oral cancer, which in turn could be a result of the interleukin 6 mediated activation of the caveolin -1 mediated JNK-AP-1 signaling pathway [8] [9] [10] . 3) Following binding of the S1 subunit to the ACE-2 receptors, the virus fuses with the host cell in two mechanisms: (a) endosomal fusion which is mediated by cysteine proteases cathepsin B/L and (b) plasma membrane fusion mediated by the serine protease TMPRSS2. Based on the above-mentioned data, it can be hypothesized that the increased protease levels in chronic periodontitis and oral cancer could potentially increase the risk of an oral mucosa mediated SARS-corona virus-2 infection (figure 1). In addition to increasing proteases, chronic periodontitis, and oral cancer patients have also reported having a low melatonin level [14, 15] . cache = ./cache/cord-303022-9hqoq7tf.txt txt = ./txt/cord-303022-9hqoq7tf.txt === reduce.pl bib === id = cord-302821-b9ikg0xy author = Gawałko, Monika title = COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3685 sentences = 209 flesch = 34 summary = Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. The pathophysiology of COVID-19 related AF is not well understood and proposed putative mechanisms include a reduction in angiotensin-converting enzyme 2 (ACE2) receptor availability, CD147-and sialic acid-spike protein interaction, enhanced inflammatory signalling eventually culmination in inflammatory cytokine storm, direct viral endothelial damage, electrolytes and acid-base balance abnormalities in the acute phase of severe illness and increased adrenergic drive.(28) (Fig. 1) . cache = ./cache/cord-302821-b9ikg0xy.txt txt = ./txt/cord-302821-b9ikg0xy.txt === reduce.pl bib === id = cord-303056-bdse9o26 author = Okada, Masaji title = Development of vaccines and passive immunotherapy against SARS corona virus using SCID-PBL/hu mouse models date = 2007-04-20 pages = extension = .txt mime = text/plain words = 1290 sentences = 81 flesch = 56 summary = The production of neutralizing antibodies against SARS CoV was observed in the serum from mice immunized with S DNA vaccine SARS (M) DNA vaccine and N DNA vaccine induced murine T cell responses against SARS [4] . Human neutralizing antibodies were induced from SCID-PBL/hu mice vaccines with SARSS [6] and M DNA vaccines (Fig. 2) . Titer of neutralizing antibody in the serum from SCID-PBL/hu mice immunized with SARS (M) DNA vaccine was 1:10. SARS S DNA vaccine which elicits effective neutralizing antibody responses that generate protective immunity in a mouse model [9] . Furthermore, SARS M DNA as well as SARSS DNA vaccine induce human neutralizing antibodies against SARS CoV by the SCID-PBL/hu model. Therefore, the effect of combination immunization with such SARS vaccines (M vaccine and S vaccine) and the specificity of human monoclonal neutralizing antibodies are now being studied. A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice cache = ./cache/cord-303056-bdse9o26.txt txt = ./txt/cord-303056-bdse9o26.txt === reduce.pl bib === id = cord-302735-zal2gr28 author = Priyanka title = Aerosol transmission of SARS-CoV-2: The unresolved paradox date = 2020-09-04 pages = extension = .txt mime = text/plain words = 218 sentences = 25 flesch = 59 summary = key: cord-302735-zal2gr28 title: Aerosol transmission of SARS-CoV-2: The unresolved paradox cord_uid: zal2gr28 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the aetiological agent 18 of coronavirus disease 2019 , has led to a global pandemic defying the 19 geographical borders and putting the lives of billions at risk. The commonly evident 20 symptoms include fever, altered sense of smell and/or taste, cough, sputum expectoration, 21 sore throat, dyspnoea, fatigue and myalgia; whereas the uncommon symptoms include 22 confusion, dizziness, headache, conjunctivitis, rhinorrhoea, nasal congestion, hemoptysis, 23 chest pain, bronchial breath sounds, tachypnoea, crackles/rales on auscultation, cutaneous The transmission of respiratory pathogens have been associated with three primary modes 30 known as "contact," "droplet," and "airborne" transmission. These modes are also being 31 speculated in the context of SARS-CoV-2, but the existing research-based literature and the 32 consequent guidance from the leading public health agencies are still paradoxical. Viable 117 SARS-CoV-2 in the air of a hospital room 1 with COVID-19 patients. Aerosol transmission of SARS-CoV-2? cache = ./cache/cord-302735-zal2gr28.txt txt = ./txt/cord-302735-zal2gr28.txt === reduce.pl bib === id = cord-303539-gimz41yb author = Goudouris, Ekaterini S. title = Laboratory diagnosis of COVID-19() date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3605 sentences = 220 flesch = 45 summary = DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. 25 Some studies report patients with mild (or even asymptomatic) COVID-19 present lower levels of SARS-CoV-2-specific antibodies or may even do not develop detectable levels, while patients with more severe conditions have higher levels of these. 38 The data presented suggest that the diagnosis of COVID-19 should be based on clinical manifestations, contact history, imaging tests, laboratory tests, and not only on serological tests and the search for the genetic material of the virus. The gold standard for the diagnosis of SARS-CoV-2 infection is the identification of viral genetic material by RT-PCR, in different samples, with greater sensitivity in bronchoalveolar lavage and nasopharyngeal swab. cache = ./cache/cord-303539-gimz41yb.txt txt = ./txt/cord-303539-gimz41yb.txt === reduce.pl bib === id = cord-303407-n7j56sci author = Popofsky, Stephanie title = Impact of Maternal SARS-CoV-2 Detection on Breastfeeding Due to Infant Separation at Birth date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4364 sentences = 204 flesch = 45 summary = CONCLUSION: In the setting of COVID-19, separation of mother–newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following discharge compared with unseparated mothers and infants. In the setting of COVID-19, separation of mother-newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following J o u r n a l P r e -p r o o f 3 discharge compared with unseparated mothers and infants. The Centers for Disease Control and Prevention (CDC) [4] and American Academy of Pediatrics (AAP) [5] each published interim guidelines for management of neonates born to mothers with confirmed or suspected COVID-19, including recommendations for temporary separation of these dyads. To assess the impact of our policy change surrounding mother-newborn dyad separation on breastfeeding rates, we evaluated mothers' pre-delivery plans for feeding, and compared these with actual outcomes of breastfeeding during perinatal admission and following discharge. cache = ./cache/cord-303407-n7j56sci.txt txt = ./txt/cord-303407-n7j56sci.txt === reduce.pl bib === id = cord-303061-vvzkpetn author = Olyaee, Mohammad Hossein title = RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1343 sentences = 110 flesch = 59 summary = title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation Utilizing chaos game representation (CGR) as well as recurrence quantification analysis (RQA) as a powerful nonlinear analysis technique, we proposed an effective process to extract several valuable features from genomic sequences of SARS-CoV-2.  The dataset involves features that enable us to compare genomic sequences with different lengths. In this work, according to the diagram represented in Fig. 1 , several recurrencequantification-based features are extracted from the nucleotide sequences. In this paper, we introduce a new dataset which involves efficient nonlinear features related to genomic sequences of SARS-CoV-2. In the final step, by applying recurrence quantification analysis (RQA), from each extracted coordinate series, 9 features are provided and totally 18 ( ) features will be extracted. • Extract features from coordinate series by applying recurrence quantification analysis measure gives the probability that two neighbors of any state are also neighbors and is obtained as below: cache = ./cache/cord-303061-vvzkpetn.txt txt = ./txt/cord-303061-vvzkpetn.txt === reduce.pl bib === id = cord-303143-4sksz6xz author = Wu, Y. P. title = Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients date = 2009-03-19 pages = extension = .txt mime = text/plain words = 4222 sentences = 243 flesch = 50 summary = title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients The diagnosis was further confirmed using the ELISA assay for plasma SARS-CoV protein N IgG measurement (described below). Anti-SARS-CoV N protein IgG levels were [median (95% CI)] 0.97 (0.81-1.58) versus 0.05 (0.04-0.06) and 0.05 (0.04-0.07) units (OD450) in patients with SARStype pneumonia, patients with CAP (S. A significant correlation between plasma SP-D and anti-SARS-CoV N protein IgG measured in SARS patients was observed using linear regression (r 2 = 0.5995, P = 0.02) (Fig. 5) . This was further confirmed by the measures of lung injury reported in the present study showing no significant differences in pulmonary infiltrate, chest radiographic score, thrombocytopenia and leucocytopenia between SARS patients and the bacterial-type pneumonia patients. Plasma surfactant protein levels and clinical outcomes in patients with acute lung injury cache = ./cache/cord-303143-4sksz6xz.txt txt = ./txt/cord-303143-4sksz6xz.txt === reduce.pl bib === id = cord-303135-rx21ajiw author = Jian, Li title = Perspective: COVID-19, implications of nasal diseases and consequences for their management date = 2020-05-01 pages = extension = .txt mime = text/plain words = 1723 sentences = 82 flesch = 47 summary = This leads us to the question whether treatment in patients with allergic rhinitis, normally INCS, or in severe patients with CRSwNP, nowadays including biologics to suppress type 2 immune reactions, should be continued in case of a SARS-CoV-2 infection. SARS-CoV-2 may also infect patients with severe asthma and CRSwNP, who might be under treatment with a type 2 biologic drug such as dupilumab, omalizumab, or mepolizumab. However, we begin to recognize that diseases of the upper airways or their management by corticosteroids and biologics do not seem to increase the risk of infection nor the risk for severe COVID-19. In research perspective, because the airway passage of nose and nasopharynx is the main entry for respiratory viruses including the SARS-CoV 2, the expression and its regulation of the ACE2 receptor and the TMPRSS2 protease are key topics for research and targets for interventions. SARS-CoV-2 entry genes are most highly expressed in nasal goblet and ciliated cells within human airways cache = ./cache/cord-303135-rx21ajiw.txt txt = ./txt/cord-303135-rx21ajiw.txt === reduce.pl bib === id = cord-303330-zh8wzza5 author = Magleby, Reed title = Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3557 sentences = 204 flesch = 51 summary = In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. cache = ./cache/cord-303330-zh8wzza5.txt txt = ./txt/cord-303330-zh8wzza5.txt === reduce.pl bib === id = cord-303069-ss6g3jkg author = Jakhar, Renu title = An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3379 sentences = 202 flesch = 52 summary = A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. The aim of this study is to analyze envelope protein strains using in silico approaches looking for the conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine [22, 23, 24] . Envelope protein from the SARS-CoV-2 was analyzed using the IEDB MHC-1 binding prediction tool to predict the T cell epitope suggested interacting with different types of MHC Class I alleles. Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus cache = ./cache/cord-303069-ss6g3jkg.txt txt = ./txt/cord-303069-ss6g3jkg.txt === reduce.pl bib === id = cord-303054-s1clwunc author = Velly, Lionel title = Guidelines: Anaesthesia in the context of COVID-19 pandemic date = 2020-06-05 pages = extension = .txt mime = text/plain words = 9239 sentences = 471 flesch = 42 summary = Operating theatre 12 R1.3.1 -Experts suggest that healthcare professionals involved in airway management (intubation, extubation, supraglottic airway insertion and/or removal…), or those who could be brought to do so in some given situations, wear a fit tested respirator mask (Respirator N95 or FFP2 standard, or equivalent) in addition to a disposable face shield or at least, in the absence of the latter, safety goggles, regardless of the patient's COVID-19 status (Table 1) The presence of major (i.e., very frequent or relatively characteristic) and/or minor (i.e. more inconsistent and/or less specific) symptoms allows to orient the preoperative COVID-19 status assessment, and then to estimate the benefit/risk balance of maintaining or postponing the surgery, taking into account the risk of contamination of health personnel and others patients within the care structure. cache = ./cache/cord-303054-s1clwunc.txt txt = ./txt/cord-303054-s1clwunc.txt === reduce.pl bib === id = cord-302920-jkr438p9 author = Gasser, Romain title = Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date = 2020-10-09 pages = extension = .txt mime = text/plain words = 423 sentences = 31 flesch = 48 summary = key: cord-302920-jkr438p9 title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 cord_uid: jkr438p9 Characterization of the humoral response to SARS-CoV-2, the etiological agent of Covid-19, is essential to help control the infection. In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. In this study, we selected plasma from a cohort of Covid-19 convalescent patients and selectively depleted immunoglobulin A, M or G before testing the remaining neutralizing capacity of the depleted plasma. This observation may help design efficient antibody-based COVID-19 therapies and may also explain the increased susceptibility to SARS-CoV-2 of autoimmune patients receiving therapies that impair the production of IgM. Decline of humoral 409 responses against SARS-CoV-2 Spike in convalescent individuals Potent neutralizing 413 antibodies from COVID-19 patients define multiple targets of vulnerability cache = ./cache/cord-302920-jkr438p9.txt txt = ./txt/cord-302920-jkr438p9.txt === reduce.pl bib === id = cord-303363-uu9hb1c9 author = Karimi, Mehran title = Implications of SARSr-CoV 2 infection in thalassemias: Do patients fall into the “high clinical risk” category? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3271 sentences = 174 flesch = 42 summary = We're all flying blind regarding coronavirus, but it's fair to think if thalassemic patients are particularly vulnerable to SARS-COV-2 infection or are at potential higher risk of complications from COVID-19 than normal population, specially when they become older. Therefore, it is recommended that patients with diabetes maintain a good glycemic control, because it might help reduce the risk of infection itself and may also modulate the severity of the clinical expression of the disease (39) . Hemoglobin disorders including thalassemias are generally not associated with respiratory diseases but anemia and iron-overload involving the heart, lungs (pulmonary hypertension), liver disease, diabetes and even the immune system, can encounter these patients to have higher risk of complications from SARS-COV-2 infection than normal population, specially when they become older. The few reported cases of SARS-CoV-2 infection in people with thalassemias might reflect the efforts to minimise social contacts or other unclarified reasons, such as lower beta globin protein as a possible target of COVID-19 in these patients (51) . cache = ./cache/cord-303363-uu9hb1c9.txt txt = ./txt/cord-303363-uu9hb1c9.txt === reduce.pl bib === id = cord-303377-lkewcf8a author = Dimke, H. title = Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4112 sentences = 205 flesch = 52 summary = Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. A total of 87 clinical sample specimens were chosen based on SARS-CoV-2 status from the Cobas ® 6800 system and used to evaluate the analytical sensitivity, specificity and accuracy of our in-house SARS-CoV-2 RT-qPCR assay after RNA purification using the Maxwell ® RSC 48 and AGPC methods. The AGPC method delivers high analytical sensitivity, specificity and accuracy for SARS-CoV-2 testing To evaluate whether conventional AGPC based extraction of RNA could serve as a viable alternative to automated systems with respect to reliability and accuracy, we isolated RNA using the AGPC method from 87 clinical specimens (oropharyngeal or nasopharyngeal swabs) with known SARS-CoV-2 status (57 positive and 30 negative), and performed a side-by-side comparison with the identical samples extracted on a Maxwell ® RSC 48 instrument. cache = ./cache/cord-303377-lkewcf8a.txt txt = ./txt/cord-303377-lkewcf8a.txt === reduce.pl bib === id = cord-302806-1e99cygs author = Bozkurt, Banu title = The COVID-19 Pandemic: Clinical Information for Ophthalmologists date = 2020-04-29 pages = extension = .txt mime = text/plain words = 3685 sentences = 228 flesch = 55 summary = 27 published in the journal Ophthalmology last week, viral culture and RT-PCR analysis of 64 tear samples collected simultaneously with nasopharyngeal swabs from 17 COVID-19 patients between 3 and 20 days after initial symptom onset failed to demonstrate the presence of 2019-CoV. 34 The Turkish Ministry of Health, in a guidance report entitled "Evaluation of Healthcare Workers with Patient Contact" published on March 25, 2020, identified ophthalmologic examination as a procedure requiring intensive contact, and recommended prophylaxis with hydroxychloroquine for a total of 3 days (400 mg twice on day 1, 200 mg twice daily on days 2 and 3) and 5 days of home isolation followed by a PCR test in the event of high-risk contact with COVID-19 patients without the use of personal protective equipment. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Assessing Viral Shedding and Infectivity of Tears in Coronavirus Disease 2019 (COVID-19) Patients. cache = ./cache/cord-302806-1e99cygs.txt txt = ./txt/cord-302806-1e99cygs.txt === reduce.pl bib === id = cord-303018-3ka72y3p author = Ng, Siew C title = COVID-19 and the gastrointestinal tract: more than meets the eye date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1646 sentences = 98 flesch = 54 summary = COVID-19 and the gastrointestinal tract: more than meets the eye Siew C Ng , 1 Herbert Tilg 2 An outbreak of coronavirus disease 2019 , caused by severe acute respiratory syndrome (SARS-CoV-2), has rapidly spread from China to almost all over the world affecting over 800,000 people across 199 countries. 5 In GUT several articles report on GI symptoms, detection of the virus in faeces and potential pathophysiological aspects including viral receptor expression in the GI tract. In about 50% of COVID-19 cases, the presence of SARS-CoV-2 in faecal samples and detection of SARS-CoV-2 in intestinal mucosa of infected patients suggest that enteric symptoms could be caused by invasion of ACE2 expressing enterocytes and the GI tract may be an alternative route of infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-303018-3ka72y3p.txt txt = ./txt/cord-303018-3ka72y3p.txt === reduce.pl bib === id = cord-303216-1pbuywz6 author = Das, Gaurav title = Neurological Insights of COVID-19 Pandemic date = 2020-04-22 pages = extension = .txt mime = text/plain words = 2872 sentences = 155 flesch = 54 summary = If scientific reports relevant to the SARS-CoV-2 virus are noted, it can be seen that the virus owes much of its killer properties to its unique structure that has a stronger binding affinity with the human angiotensin-converting enzyme 2 (hACE2) protein, which the viruses utilize as an entry point to gain accesses to its hosts. The intriguing part though is that recently reported studies have noted altered mental health in some COVID-19 patients showing symptoms like anosmia and ageusia thereby indicating a neuroinvasive nature of the virus. The neurological manifestations of SARS-CoV-2 have been recently recognized from CT scan images and MRI scan of the brain of a patient who contracted COVID-19 and showed symptoms of necrotizing hemorrhagic encephalopathy. The brain reportedly, like most other organs, expresses the hACE2 considered to be the entry point of the SARS-CoV-2 viruses in humans and is therefore not immune to viral infection. cache = ./cache/cord-303216-1pbuywz6.txt txt = ./txt/cord-303216-1pbuywz6.txt === reduce.pl bib === id = cord-303659-mzez7v4d author = Elsayed, Sarah M title = The Possibility and Cause of Relapse After Previously Recovering From COVID-19: A Systematic Review date = 2020-09-05 pages = extension = .txt mime = text/plain words = 3203 sentences = 195 flesch = 54 summary = There are reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial clearance of the virus. There have been reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial documented clearance of the virus. The publications included COVID-19 positive patient data and the relapse of disease was confirmed by PCR; the full text was available for these publications. Data were collected in the following categories when available: Study design; Study country; Patient demographics; Clinical signs and symptoms; Laboratory findings; Imaging studies; Dynamics of the oropharyngeal swab test; Treatment of the first presentation; The clinical picture of relapse; Day of a positive result after confirmed negative We tabulated the data using Microsoft Excel (2010, Microsoft Corp, Redmond, WA). The study reports a total of 11 patients (6 females and 5 males), all from China, who tested positive for COVID-19. cache = ./cache/cord-303659-mzez7v4d.txt txt = ./txt/cord-303659-mzez7v4d.txt === reduce.pl bib === id = cord-303506-rqerh2u3 author = Patel, V. title = A call for governments to pause Twitter censorship: a cross-sectional study using Twitter data as social-spatial sensors of COVID-19/SARS-CoV-2 research diffusion date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2933 sentences = 187 flesch = 56 summary = Objectives: To determine whether Twitter data can be used as social-spatial sensors to show how research on COVID-19/SARS-CoV-2 diffuses through the population to reach the people that are especially affected by the disease. Mapping of worldwide data illustrated that high Twitter activity was related to high numbers of COVID-19/SARS-CoV-2 deaths, with tweets inversely weighted with number of publications. • Using Twitter data used as social-spatial sensors, we demonstrated that Twitter activity was significantly positively correlated to the numbers of COVID-19/SARS-CoV-2 deaths, when holding the country's number of publications constant. Mapping of worldwide data illustrated that high Twitter activity was related to high Conclusions: This study shows that Twitter can play a crucial role in the rapid research response during the COVID-19/SARS-CoV-2 global pandemic, especially to spread research with prompt public scrutiny. cache = ./cache/cord-303506-rqerh2u3.txt txt = ./txt/cord-303506-rqerh2u3.txt === reduce.pl bib === id = cord-303297-fiievwy7 author = Oberemok, Volodymyr V. title = SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date = 2020-04-30 pages = extension = .txt mime = text/plain words = 4082 sentences = 174 flesch = 49 summary = In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. cache = ./cache/cord-303297-fiievwy7.txt txt = ./txt/cord-303297-fiievwy7.txt === reduce.pl bib === id = cord-303171-u5jrbsii author = Yang, Gee-Gwo title = SARS-associated Coronavirus Infection in Teenagers date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1226 sentences = 83 flesch = 66 summary = On April 28, when a student (case-patient 1) visited the school nurse on the first day that he had a fever, an infection specialist from affiliated Tzu-Chi Medical Center immediately responded. All nine schoolmates underwent chest x-ray examinations and were tested for SARS-associated coronavirus (SARS -CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (4) and DNA sequencing. Six schoolmates were positive for SARS-CoV by RT-PCR, confirmed later by DNA sequencing for replicase. No new cases of fever have occurred in Tzu-Chi High School in the 2 months since these patients' isolation. Six schoolmates with fever were confirmed by real-time RT-PCR and DNA sequences to have SARS-CoV infection. Worldwide, SARS-CoV infection has been clinically severe, characterized by respiratory distress and a 15% average mortality rate (6) (7) (8) . Our teenagers with presumed SARS-CoV infection had very mild courses. The benign course of SARS-CoV infection in our teenage students supports the WHO finding of less-severe disease in younger persons. cache = ./cache/cord-303171-u5jrbsii.txt txt = ./txt/cord-303171-u5jrbsii.txt === reduce.pl bib === id = cord-303517-8971aq02 author = Cajamarca-Baron, Jairo title = SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression date = 2020-10-16 pages = extension = .txt mime = text/plain words = 9096 sentences = 459 flesch = 45 summary = 27, 28 Among other comorbidities, chronic kidney disease is associated with in-hospital mortality, as are cancer and cerebrovascular disease, demonstrated through two meta-analyses that included over fifteen thousand patients ( Table 2) ; studies suggest that superficial fungal infections and psoriasis confer vulnerability to COVID-19; a body mass index (BMI) > 40 kg/m2 is an independent risk factor for complications from the infection; and there are discouraging results regarding underlying neurological disease and SARS-CoV-2. It is even possible that such disease-modifying therapies and their immunosuppressive effect may play a protective role during 19-COVID infection by preventing or dampening hyperimmune activity that, in some cases, could lead to clinical deterioration; there is even a report of a patient with primary progressive multiple sclerosis receiving treatment with ocrelizumab and becoming infected with SARS-CoV-2, in the context of lymphopenia and hypogammaglobulinema expected for this type of treatment, without generating major clinical complications, this hypothesis is obviously limited for now only to academic deductions and limited information. cache = ./cache/cord-303517-8971aq02.txt txt = ./txt/cord-303517-8971aq02.txt === reduce.pl bib === id = cord-303868-aes92l6s author = Steffen, Tara L. title = The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date = 2020-08-22 pages = extension = .txt mime = text/plain words = 6098 sentences = 300 flesch = 46 summary = In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. This suggests that polyclonal antibody binding to the RBD domain of the spike protein represents the key target of neutralizing antibody to SARS-CoV-2 after natural infection. Most importantly, our antigen-specific antibody depletion approach demonstrated that the RBD domain of the spike protein is responsible for 70% +/-18.9% of the human polyclonal neutralizing antibody activity to spike after natural SARS-CoV-2 infection. Although our study shows that the dominant target of IgG neutralizing antibody response after natural SARS-CoV-2 infection is the RBD domain of the spike protein, we have evaluated a limited number (n=10) of patients by antigen-specific antibody depletion. cache = ./cache/cord-303868-aes92l6s.txt txt = ./txt/cord-303868-aes92l6s.txt === reduce.pl bib === id = cord-303787-dx1n8jap author = Vonck, Kristl title = Neurological manifestations and neuro‐invasive mechanisms of the severe acute respiratory syndrome coronavirus type 2 date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3806 sentences = 208 flesch = 42 summary = RESULTS: Neurological manifestations potentially related to COVID‐19 have been reported in large studies, case series and case reports and include acute cerebrovascular diseases, impaired consciousness, cranial nerve manifestations and auto‐immune disorders such as Guillain‐Barré Syndrome often present in patients with more severe COVID‐19. Neurological symptoms were more common in patients with severe infection according to their respiratory status (45.5% vs 30.2% in non-severe cases) and fell into 3 categories: central nervous system (CNS) manifestations (dizziness, headache, impaired consciousness, acute cerebrovascular disease, ataxia, and seizure), cranial and peripheral nervous system manifestations (taste impairment, smell impairment, vision impairment, and neuropathy), and skeletal muscular injury manifestations. This is illustrated by a recent report of a COVID-19 patient with an acute necrotizing encephalopathy, a rare complication observed in infections with viruses including influenza, and related to a cytokine storm in the brain without direct viral invasion 26 . cache = ./cache/cord-303787-dx1n8jap.txt txt = ./txt/cord-303787-dx1n8jap.txt === reduce.pl bib === id = cord-303665-l57e54hu author = Lahrich, S. title = Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date = 2020-09-10 pages = extension = .txt mime = text/plain words = 5849 sentences = 329 flesch = 48 summary = Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. cache = ./cache/cord-303665-l57e54hu.txt txt = ./txt/cord-303665-l57e54hu.txt === reduce.pl bib === id = cord-304031-poh3te9j author = Leder, K. title = Respiratory infections during air travel date = 2005-01-13 pages = extension = .txt mime = text/plain words = 4521 sentences = 241 flesch = 50 summary = Issues regarding cabin air quality and the potential risks of transmission of respiratory infections during flight have been investigated and debated previously, but, with the advent of severe acute respiratory syndrome and influenza outbreaks, these issues have recently taken on heightened importance. Confined space, limited ventilation, prolonged exposure times and recirculating air, all common to air travel, are demonstrated risk factors for the transmission of upper respiratory tract infections in other settings and create the potential for the spread of respiratory pathogens during flight. Aspects of the aircraft cabin environment that influence the potential transmission of respiratory pathogens on airplanes will be outlined here and then the Internal Medicine Journal 2005; 35: 50-55 evidence for the occurrence of outbreaks of respiratory illness among airline passengers will be reviewed. The majority of patients (68%) had recently completed a series of commercial aircraft flights, and the authors concluded that air travel played a role in the transmission of disease among the 60 infected persons. cache = ./cache/cord-304031-poh3te9j.txt txt = ./txt/cord-304031-poh3te9j.txt === reduce.pl bib === id = cord-302382-eifh95zm author = Owji, Hajar title = Immunotherapeutic approaches to curtail COVID-19 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 11312 sentences = 606 flesch = 40 summary = Active immunization through vaccines, interferon administration, passive immunotherapy by convalescent plasma or synthesized monoclonal and polyclonal antibodies, as well as immunomodulatory drugs, are different immunotherapeutic approaches that will be mentioned in this review. Nevertheless, the similarity of severe respiratory failure induced by SARS-CoV-2 to acute respiratory distress syndrome (ARDS) and the deterioration of patients' conditions in around a week following the first symptoms implicate the role of immunity dysregulation in COVID-19 profile [6] . Subsequently, plasma transfusion was recommended as a safe and effective way for the prevention or treatment of the Ebola virus in 2014 and also several other severe viral infections, including MERS, SARS-CoV, and avian influenza A [35, 36] . CP extracted from the SARS-COV-2 survivors may be a promising approach for the protection of COVID-19 patients with antibody deficiency before the development of an effective vaccine [44] . cache = ./cache/cord-302382-eifh95zm.txt txt = ./txt/cord-302382-eifh95zm.txt === reduce.pl bib === id = cord-303745-wx3udkee author = Martinez-Fleta, P. title = SARS-Cov-2 cysteine-like protease (Mpro) is immunogenic and can be detected in serum and saliva of COVID-19-seropositive individuals date = 2020-07-18 pages = extension = .txt mime = text/plain words = 5031 sentences = 328 flesch = 57 summary = Using ELISA tests, coating several SARS-CoV-2 proteins produced in vitro, we describe that COVID-19 patients make high titre IgG, IgM and IgA antibody responses to the Cys-like protease from SARS-CoV-2, also known as 3CLpro or Mpro, and it can be used to identify individuals with positive serology against the coronavirus. Since this study evaluated, for the first time, whether coronavirus-infected individuals could 121 generate an antibody response against the Cys-like protease, MPro, other SARS-CoV-2 122 proteins, commonly used in serology tests, were produced, for comparison. 1101 individuals with high specificity and sensitivity 153 A cohort of 36 COVID-19 patients (PCR+) and 33 healthy donors was recruited at La Princesa 154 University Hospital, Madrid (Table 1 ) and ELISA assays were performed to detect Mpro-, as 155 well as RBD-and NP-, specific antibodies of the IgG, IgA and IgM subclasses in sera ( Figure 156 3). cache = ./cache/cord-303745-wx3udkee.txt txt = ./txt/cord-303745-wx3udkee.txt === reduce.pl bib === id = cord-303960-86mukxg1 author = Rahimi, Farid title = Tackling the COVID-19 Pandemic date = 2020-04-24 pages = extension = .txt mime = text/plain words = 1754 sentences = 111 flesch = 54 summary = Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. cache = ./cache/cord-303960-86mukxg1.txt txt = ./txt/cord-303960-86mukxg1.txt === reduce.pl bib === id = cord-303692-py908dt8 author = Langley, Caroline title = Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement date = 2019-01-01 pages = extension = .txt mime = text/plain words = 6198 sentences = 316 flesch = 55 summary = title: Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement davidii ISG15, we use this protease as a biochemical tool; specifically, as a tool to illuminate the importance of the hydrophobic interdomain interface of ISG15 and how residue variation in this region between different species of ISG15s leads to biochemical differences in ISG15-protein engagement. With the exception of Pro38, which is a histidine residue in hISG15, all of these positions are conserved between bISG15 and the ISG15s from mice and humans. Taking the ITC data as a whole, the impact of mutations at Phe40 in bISG15 and its counterparts highlights the importance of ISG15 interdomain interactions in the effective binding of ISG15 by a protein that engages more than one domain of ISG15. cache = ./cache/cord-303692-py908dt8.txt txt = ./txt/cord-303692-py908dt8.txt === reduce.pl bib === id = cord-303609-9217t0ui author = Baselga, María Trinidad title = Trombosis y COVID-19: revisión de alcance date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3233 sentences = 320 flesch = 53 summary = Esta revisión de alcance (scoping review) resume y evalúa críticamente la evidencia sobre la relación entre la trombosis y el COVID-19, y se basa en una búsqueda bibliográfica sistemática de todos los artículos publicados hasta el 5 de mayo de 2020 e incluidos en las bases de datos PubMed, Scopus, Cochrane y Clinicaltrials.gov. En otros estudios se estandarizó el uso de ecografía para la detección de las complicaciones J o u r n a l P r e -p r o o f DISCUSIÓN Esta es la primera scope review que revisa los artículos que relacionan la infección por SARS-CoV-2 y las alteraciones en la coagulación, incluyendo sus repercusiones clínicas y radiológicas; en orden cronológico desde el 1 de diciembre de 2019 hasta el 5 mayo de 2020. cache = ./cache/cord-303609-9217t0ui.txt txt = ./txt/cord-303609-9217t0ui.txt === reduce.pl bib === id = cord-303880-zv4nbz9p author = Tsikala Vafea, Maria title = Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 5485 sentences = 328 flesch = 42 summary = RESULTS: Key focus areas include the applications of artificial intelligence, the use of Big Data and Internet of Things, the importance of mathematical modeling for predictions, utilization of technology for community screening, the use of nanotechnology for treatment and vaccine development, the utility of telemedicine, the implementation of 3D-printing to manage new demands and the potential of robotics. The technologies in this review include: artificial intelligence (AI), machine learning and deep learning, nanomedicine, novel technologies for vaccines development and therapeutics, novel mathematical modeling, big data, internet of things (IoT), telemedicine, robots, and 3D printing technology. Mei et al proposed an AI system based on machine learning and deep learning models that combines demographic (age, sex) and clinical information (laboratory test results, reported symptoms, history of exposure etc.) with chest imaging findings for rapid identification of patients with COVID-19. cache = ./cache/cord-303880-zv4nbz9p.txt txt = ./txt/cord-303880-zv4nbz9p.txt === reduce.pl bib === id = cord-303959-e1654g5j author = Vitiello, Antonio title = COVID-19 Patients with Pulmonary Fibrotic Tissue: Clinical Pharmacological Rational of Antifibrotic Therapy date = 2020-08-27 pages = extension = .txt mime = text/plain words = 1917 sentences = 89 flesch = 38 summary = In this direction, the use of a pharmacological approach to reduce or prevent fibrotic status, with antifibrotic agents such as pirfenidone, used with demonstrated clinical efficacy in idiopathic pulmonary fibrosis [4] can be a valuable aid in the prevention of serious or fatal complications from COVID-19 in patients with ongoing infection, or in those already healed with residual fibrotic lung lesions [5] . Although many patients who develop SARS-CoV-2 respiratory distress syndrome survive the acute phase of the Fig. 1 Antifibrotic therapy, pleiotropic effects of Pirfenidone disease, data have shown that some of them die from progressive pulmonary fibrosis [19] . Several reports suggest, however, that there are differences between IPF and COVID-19-induced pulmonary fibrosis, diversity in the rapid evolution of the fibrotic and inflammatory state, and a highly developed procoagulant effect in SARS-CoV-2 viral infection [22, 23] . cache = ./cache/cord-303959-e1654g5j.txt txt = ./txt/cord-303959-e1654g5j.txt === reduce.pl bib === id = cord-304088-xkg0ylz8 author = Zhu, Han title = Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date = 2020-04-21 pages = extension = .txt mime = text/plain words = 5532 sentences = 236 flesch = 38 summary = While limited data exist, potential mechanisms of cardiac injury include direct viral entry through the angiotensin-converting enzyme 2 (ACE2) receptor and toxicity in host cells, hypoxia-related myocyte injury, and immune-mediated cytokine release syndrome. The increased incidence of cardiac injury among those with severe systemic inflammatory response syndromes (SIRS) and shock in the setting of COVID-19 also highlights an important relationship between the immune response to the virus and the cardiovascular system. Of note, SARS-CoV-2 also contains an RNA-dependent RNA polymerase which is the target of the anti-viral agent remdesivir, currently being studied randomized clinical trials for use against COVID-19 disease [26] . A recent retrospective, multi-center study of 150 patients confirmed that inflammatory markers, including elevated ferritin (mean 1297.6 ng/ml in non-survivors vs 614.0 ng/ml in survivors, p < 0.001) and IL-6 (p < 0.0001) were associated with more severe COVID-19 infection, suggesting that systemic inflammation may be a significant driver of multi-organ damage [18, 64] . cache = ./cache/cord-304088-xkg0ylz8.txt txt = ./txt/cord-304088-xkg0ylz8.txt === reduce.pl bib === id = cord-303585-8py6joh6 author = Verma, Surjeet title = Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19) date = 2020-09-25 pages = extension = .txt mime = text/plain words = 10884 sentences = 562 flesch = 50 summary = The objective of this review was to collate information regarding the potential of plants and natural products to inhibit coronavirus and targets associated with infection in humans and to highlight known drugs, which may have potential activity against SARS-CoV-2. Finally, this review discusses the potential use of Southern African medicinal plants, which have traditionally been used for the treatment of symptoms related to respiratory viral infections, and influenza, to inhibit SARS-CoV-2. The selective index (SI) values of compounds 1-6 were found to be 58, >510, 111, 193, 180 , and >667, respectively, indicating that these plants were able to inhibit viral replication without having a cytotoxic effect on the host cells. A chalcone, xanthoangelol E (8), isolated from the ethanolic leaf extract of Angelica keiskei (Miq.) Koidz., showed inhibitory activity against SARS-CoV 3CL pro and a papain-like protease (PL pro ) with IC 50 values of 11.4 and 1.2 µM, respectively, using cell-free assays. cache = ./cache/cord-303585-8py6joh6.txt txt = ./txt/cord-303585-8py6joh6.txt === reduce.pl bib === id = cord-303651-fkdep6cp author = Thompson, Robin N. title = Key questions for modelling COVID-19 exit strategies date = 2020-08-12 pages = extension = .txt mime = text/plain words = 11567 sentences = 587 flesch = 40 summary = This leads to a roadmap for future research (figure 1) made up of three key steps: (i) improve estimation of epidemiological parameters using outbreak data from different countries; (ii) understand heterogeneities within and between populations that affect virus transmission and interventions; and (iii) focus on data needs, particularly data collection and methods for planning exit strategies in low-to-middle-income countries (LMICs) where data are often lacking. Three key steps are required: (i) improve estimates of epidemiological parameters (such as the reproduction number and herd immunity fraction) using data from different countries ( §2a-d); (ii) understand heterogeneities within and between populations that affect virus transmission and interventions ( §3a-d); and (iii) focus on data requirements for predicting the effects of individual interventions, particularly-but not exclusively-in data-limited settings such as LMICs ( §4a-c). cache = ./cache/cord-303651-fkdep6cp.txt txt = ./txt/cord-303651-fkdep6cp.txt === reduce.pl bib === id = cord-303941-3lg1bzsi author = Han, Hui-Ju title = Bats as reservoirs of severe emerging infectious diseases date = 2015-07-02 pages = extension = .txt mime = text/plain words = 4679 sentences = 244 flesch = 56 summary = Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Currently, bats have been considered to be natural reservoirs of SARS-CoV, MERS-CoV, NiV, HeV, Ebola virus, and Marburg viruses. The viruses discussed above tend to be restricted to certain geographic regions with a particular bat reservoir, such as HeV and NiV associated with flying foxes in Australia and Southeast Asia and Ebola virus associated with Egyptian fruit bats in Africa. Bats have been proposed as the natural reservoirs of viruses causing severe diseases in humans, such as NiV and HeV in Southeast Asia and Australia, Ebola and Marburg viruses in Africa, SARS-CoV in Asia and MERS-CoV in Middle East. cache = ./cache/cord-303941-3lg1bzsi.txt txt = ./txt/cord-303941-3lg1bzsi.txt === reduce.pl bib === id = cord-303741-1ou0cy5k author = Stafstrom, Carl E. title = COVID-19: Neurological Considerations in Neonates and Children date = 2020-09-10 pages = extension = .txt mime = text/plain words = 7035 sentences = 369 flesch = 40 summary = An especially apropos case demonstrated maternal viremia, placental infection shown by immunohistochemistry, and high placental viral load with subsequent neonatal viremia, implying transplacental transfer of SARS-CoV-2 from pregnant mother to fetus [24] ; this newborn presented with neurological symptoms as discussed in Section 3. The lack of unequivocal reports of SARS-CoV-2 being recovered from the CSF of individuals affected with presumed neurological involvement nor in brain tissue from the limited number of autopsied cases strengthens the possibility that the virus does not often directly cause the symptoms but rather, that the neurological sequelae are secondary to hypoxia, cytokine involvement, or some other non-direct mechanism (see Section 6). Finally, 4 of 27 children with COVID-19 associated MIS-C developed new neurologic symptoms including encephalopathy, headache, weakness, ataxia, and dysarthria [81] ; two patients had lumbar punctures and CSF was negative for SARS-CoV-2 in both. cache = ./cache/cord-303741-1ou0cy5k.txt txt = ./txt/cord-303741-1ou0cy5k.txt === reduce.pl bib === id = cord-303832-1kcqhgjw author = Dai, Manman title = Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date = 2020-09-06 pages = extension = .txt mime = text/plain words = 834 sentences = 49 flesch = 66 summary = Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. ABSTRACT 21 Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that 22 fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. In this study, we detected the titer (50% tissue culture infectious dose/mL, TCID 50 /mL) of 35 viable SARS-CoV-2 attached on salmon or untreated SARS-CoV-2 in culture medium stored at 36 4°C, the temperature in refrigerators or cold rooms for the temporary storage of fish, or 25°C, the 37 regular room temperature, respectively, using end-point titration assay on Vero E6 cells as 38 described previously (8). As shown in Figure A and B, salmon-attached SARS-CoV-2 remained 39 viable at 4°C and 25°C for 8 and 2 days, respectively, while the untreated SARS-CoV-2 in 40 culture medium remained infectious at 4°C and 25°C for more than 8 days. cache = ./cache/cord-303832-1kcqhgjw.txt txt = ./txt/cord-303832-1kcqhgjw.txt === reduce.pl bib === id = cord-303934-8gh3q7p3 author = Sungnak, Waradon title = SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways date = 2020-03-13 pages = extension = .txt mime = text/plain words = 3044 sentences = 170 flesch = 47 summary = To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA-sequencing (scRNA-seq) datasets from healthy individuals generated by the Human Cell Atlas consortium. To clarify the expression patterns of ACE2 and TMPRSS2 and analyze the expression of the other potential genes associated with SARS-CoV-2 pathogens at cellular resolution, we interrogated single-cell transcriptome expression data from published scRNA-seq datasets from healthy donors generated by the Human Cell Atlas consortium 24 . While we cannot rule out the possibility that the virus uses alternative proteases for entry in such contexts, or that lung fetal tissue expresses the relevant genes, these results are at least consistent with early reports that fail to detect evidence of intrauterine infection through vertical transmission in women who develop COVID-19 pneumonia in late pregnancy 38 . cache = ./cache/cord-303934-8gh3q7p3.txt txt = ./txt/cord-303934-8gh3q7p3.txt === reduce.pl bib === id = cord-304073-f3iwclkm author = Mullick, Jhinuk Basu title = Animal Models to Study Emerging Technologies Against SARS-CoV-2 date = 2020-07-27 pages = extension = .txt mime = text/plain words = 5315 sentences = 322 flesch = 50 summary = Animal models are indispensable to understand these processes and develop and test emerging technologies; however, the mechanism of infection for SARS-CoV-2 requires certain similarities to humans that do not exist in common laboratory rodents. Here, we review important elements of viral infection, transmission, and clinical presentation reflected by various animal models readily available or being developed and studied for SARS-CoV-2 to help bioengineers evaluate appropriate preclinical models for their emerging technologies. Non-human primates, Syrian hamsters, ferrets, cats, and engineered chimeras mimic the human infection more closely and hold strong potential as animal models of SARS-CoV-2 infection and progression of resulting human disease. Overall, the studies show that the Syrian hamster is a useful animal model for SARS-CoV-2 infection especially to study viral replication, shedding, and transmission through the respiratory tract. In all studies, animals developed NAbs. Overall, the rhesus macaque model has been similar in many aspects to the human COVID-19 pathogenesis. cache = ./cache/cord-304073-f3iwclkm.txt txt = ./txt/cord-304073-f3iwclkm.txt === reduce.pl bib === id = cord-304016-4o2bpedp author = Hanage, William P. title = COVID-19: US federal accountability for entry, spread, and inequities—lessons for the future date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5701 sentences = 249 flesch = 49 summary = In this article we assess the impact of missteps by the Federal Government in three specific areas: the introduction of the virus to the US and the establishment of community transmission; the lack of national COVID-19 workplace standards and enforcement, and lack of personal protective equipment (PPE) for workplaces as represented by complaints to the Occupational Safety and Health Administration (OSHA) which we find are correlated with deaths 16 days later (ρ = 0.83); and the total excess deaths in 2020 to date already total more than 230,000, while COVID-19 mortality rates exhibit severe—and rising—inequities in race/ethnicity, including among working age adults. Finally, despite the initial federal failure to report COVID-19 data by race/ethnicity [6] , a combination of specific studies, state reporting, investigative journalism, and data trackers has revealed that a persistent feature of the pandemic has been the existence of racial/ethnic inequities in cases, hospitalizations, and mortality, especially with regard to increased risk among US Black, Latinx, and American Indian/Alaska Native populations compared to the US white non-Hispanic population [3-5, 7, 8, 69, 70] . cache = ./cache/cord-304016-4o2bpedp.txt txt = ./txt/cord-304016-4o2bpedp.txt === reduce.pl bib === id = cord-303661-etb19d6y author = Shin, Hyoung-Shik title = Empirical Treatment and Prevention of COVID-19 date = 2020-06-22 pages = extension = .txt mime = text/plain words = 4019 sentences = 212 flesch = 42 summary = Though the COVID-19 showed pandemic spread and unexpected clinical manifestations characterized by various symptoms throughout the whole body, SARS-CoV-2 seems to be less virulent especially in children and adolescents, in whom the disease mimics common cold caused by seasonal coronaviruses [7] . At the early stage of the epidemic, it had been recommended to apply the treatment regimen of middle east respiratory syndrome coronavirus (MERS-CoV) in the case of the patients with severe symptoms [23] . Considering that the infection can be asymptomatic and as it can rapidly spread across national borders, studies-to elucidate the life cycle of SARS-CoV-2, innate and adaptive immune responses to the virus, and side effects of medicationsshould be conducted on a global scale; this would help in developing appropriate treatment strategies. cache = ./cache/cord-303661-etb19d6y.txt txt = ./txt/cord-303661-etb19d6y.txt === reduce.pl bib === id = cord-303917-2tu707ng author = Zhang, Lei title = Potential interventions for novel coronavirus in China: A systematic review date = 2020-03-03 pages = extension = .txt mime = text/plain words = 5433 sentences = 369 flesch = 46 summary = We suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children's RNA‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. In addition, Semba et al 12 had reported that vitamin A supplementation reduced morbidity and mortality in different infectious diseases, such as measles, diarrheal disease, measles-related pneumonia, human immunodeficiency virus (HIV) infection, and malaria. 15 The mechanism by which vitamin A and retinoids inhibit measles replication is upregulating elements of the innate immune response in uninfected bystander cells, making them refractory to productive infection during subsequent rounds of viral replication. Remdesivir (RDV), a nucleoside analog GS-5734, had been reported to inhibit human and zoonotic coronavirus in vitro and to restrain severe acute respiratory syndrome coronavirus (SARS-CoV) in vivo. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association cache = ./cache/cord-303917-2tu707ng.txt txt = ./txt/cord-303917-2tu707ng.txt === reduce.pl bib === id = cord-304101-b9na3yf6 author = Yong, Suh Kuan title = Molecular Targets for the Testing of COVID‐19 date = 2020-05-18 pages = extension = .txt mime = text/plain words = 1777 sentences = 97 flesch = 46 summary = This diagnostic panel is working with Applied Biosystems 7500 Fast DX Real-Time PCR Instrument with SDS 1.4 software; 2) "New coronavirus nucleic acid assay" which targeted on ORF1ab and N genes was developed by Chinese National Institute for Viral Disease Control and Prevention; 3) Molecular test kits from four companies such as Seegene Inc., Kogene Biotech Co. Ltd., Sd Biosensor Inc., and Solgent Co. were approved by Ministry Food and Drug Safety and Korea Centers for Disease Control and Prevention which are now widely being used in South Korea. A probe, usually a specific antibody, is needed before a successful viral protein detection method can be developed. As aforementioned, the serology testing of COVID-19 is not targeting the virus itself but the antibodies such as immunoglobulin M (IgM) and immunoglobulin G (IgG) induced following viral infection. Serology testings targeting on viral-induced antibodies are given different information as those for viral RNA and proteins from SARS-CoV-2. cache = ./cache/cord-304101-b9na3yf6.txt txt = ./txt/cord-304101-b9na3yf6.txt === reduce.pl bib === id = cord-304013-nzigx0k0 author = Lipinski, Tom title = Review of ventilation strategies to reduce the risk of disease transmission in high occupancy buildings date = 2020-09-13 pages = extension = .txt mime = text/plain words = 12834 sentences = 557 flesch = 47 summary = This paper will discuss the factors affecting air particle properties in-terms of flow dynamics and critically analyse current ventilation strategies and mechanisms and identify areas for improvement in the search for the reduction of indoor infections. The study by the University of Oregon [54, 58] observed that Natural Ventilation with a plentiful supply of fresh air dilutes and removes contaminated air much more effectively than fan driven, recirculated air movement, significantly reducing the risk of infection, as shown in Figure 17 . Displacement ventilation with a generously sized natural inlet is preferred as it can move stale, contaminated air directly to the exhaust of the room in a laminar fashion whilst the concentration of small droplets and airborne particles in the indoor air is significantly reduced. cache = ./cache/cord-304013-nzigx0k0.txt txt = ./txt/cord-304013-nzigx0k0.txt === reduce.pl bib === id = cord-304139-ya3d7u9b author = Bosmann, Markus title = Complement Activation during Critical Illness: Current Findings and an Outlook in the Era of COVID-19 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 2000 sentences = 104 flesch = 35 summary = 230-240) report on the association between alternative complement pathway activity and better survival in patients with critical illness (3). The alternative pathway hemolytic assay (AH50) and total complement activity (CH50) tests were retrospectively analyzed in a single-center heterogeneous cohort of n = 321 patients with acute respiratory distress syndrome (33%), with suspected sepsis (63%), and on mechanical ventilation (96%). Inappropriate complement activity may result in the unloading of harmful effector functions on host cells, with the consequence of disease-causing tissue injury and organ dysfunction during critical illness. Complement activation may occur early during SARS-CoV-2 infection by the direct interaction of viral proteins with the MBL (mannose-binding lectin) and ficolin pathway, rather than the alternative pathway. In another experimental study, the host transcriptional response in SARS-CoV-2-infected A549 human lung epithelial cells included the differential expression of C3, C1R, and other complement proteins (10) . Increased alternative complement pathway function and improved survival during critical illness cache = ./cache/cord-304139-ya3d7u9b.txt txt = ./txt/cord-304139-ya3d7u9b.txt === reduce.pl bib === id = cord-304058-i8cywew0 author = Pfefferle, Susanne title = Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date = 2009-08-24 pages = extension = .txt mime = text/plain words = 9548 sentences = 514 flesch = 53 summary = title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). cache = ./cache/cord-304058-i8cywew0.txt txt = ./txt/cord-304058-i8cywew0.txt === reduce.pl bib === id = cord-304115-xs54f295 author = Zamaniyan, Marzieh title = Preterm delivery in pregnant woman with critical COVID‐19 pneumonia and vertical transmission date = 2020-04-17 pages = extension = .txt mime = text/plain words = 1793 sentences = 98 flesch = 51 summary = Given the patient's history and fever and cough, two nasal and throat swab samples were taken and tested to be positive for SARS-CoV-2 with SuperScript III Platinum, Quantitive Real-time PCR system Kits (Invitrogen company, USA) 4 . The RT-PCR tests was positive for amniotic fluid and neonate, suggesting the infant might have been affected intrauterine by COVID-19; therefore, once more, it raised the concerns regarding possible vertical transmission of the virus in mothers with serious illness. In some previous studies, the authors reported 21 healthy babies delivered by infected mothers to COVID-19, but they could not detect the virus in any of the feto-maternal parts namely placenta, amniotic fluid and cord blood [9] [10] [11] . The current case study, once again, raises concerns regarding possible vertical transmission of COVID-19 in pregnant women infected by SARS CoV-2 in contrast to the findings reported in some small studies published previously. cache = ./cache/cord-304115-xs54f295.txt txt = ./txt/cord-304115-xs54f295.txt === reduce.pl bib === id = cord-304271-vyayyk50 author = Qin, Yuan-Yuan title = Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial date = 2020-03-05 pages = extension = .txt mime = text/plain words = 3984 sentences = 228 flesch = 42 summary = title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial [9] During the SARS epidemic of 2003, therapeutic systemic glucocorticoids were widely administered in patients who were infected with the severe acute respiratory syndrome coronavirus (SARS-COV), and who subsequently developed severe respiratory disease. [12] In addition, a further retrospective observational study found that glucocorticoid therapy in patients with MERS was associated with delayed Middle East respiratory syndrome coronavirus (MERS-CoV) RNA clearance. [13, 20, 21] Glucocorticoid therapy was used in the treatment of severe SARS because early anecdotal experience supported it, and radiologic findings and histologic features of critically ill patients with SARS were similar to those of patients with acute respiratory distress syndrome (ARDS). Factors associated with psychosis among patients with severe acute respiratory syndrome: a case-control study Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial cache = ./cache/cord-304271-vyayyk50.txt txt = ./txt/cord-304271-vyayyk50.txt === reduce.pl bib === id = cord-304201-fziv9a9k author = Chiang, Chi-Huei title = Eight-Month Prospective Study of 14 Patients With Hospital-Acquired Severe Acute Respiratory Syndrome date = 2004-11-30 pages = extension = .txt mime = text/plain words = 4220 sentences = 229 flesch = 47 summary = CONCLUSION The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. Although several case series of SARS have been reported, 7-9 to our knowledge, a prospective clinical study including long-term follow-up assessment by chest radiography, chest high-resolution computed tomography (HRCT), and pulmonary function testing has not been reported, particularly for hospital-acquired cases. cache = ./cache/cord-304201-fziv9a9k.txt txt = ./txt/cord-304201-fziv9a9k.txt === reduce.pl bib === id = cord-304263-5kddk5fa author = C., Selvaa Kumar title = Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3768 sentences = 252 flesch = 56 summary = In summary, nicotine showed a profound binding affinity for the sACE2-INS1 complex than the sACE2 alone paving for the clinical trials to validate its therapeutic efficacy as a bitter compound against the SARS-CoV-2 virulence. Research studies unveiled the interaction between the structural spike 1 (S1) protein of SARS-CoV-2 with the nicotinic acetylcholine receptors (nAChRs) that are likely to intervene with its biological function (20, 21) . Thus, the insilico study performed to unveil the nicotine's urge for binding with the soluble ACE2 with or without SARS-CoV-2 in compliance with its interaction with the known human neuronal alpha4-beta2 nicotine-acetylcholine receptor (nN-AChR). We found the reported structural protein template of ACE2-SARS-CoV-2 complex with the enlisted PDB ID: 6VW1 (24) incomplete with numerous missing amino acid residues. Structural binding characteristics of nicotine with the soluble angiotensinconverting enzyme 2 (sACE2)-SARS-CoV-2 complex in the context of its interaction with the neuronal nicotinic acetylcholine receptor (nN-AChR). cache = ./cache/cord-304263-5kddk5fa.txt txt = ./txt/cord-304263-5kddk5fa.txt === reduce.pl bib === id = cord-304372-6eqnr52t author = Stolle, Claudia title = Bedarfe der Langzeitpflege in der COVID-19-Pandemie date = 2020-10-28 pages = extension = .txt mime = text/plain words = 2696 sentences = 359 flesch = 46 summary = Hier wiesen die Befragten auf eine Lücke bei notwendigen Informationen und Verfah-renshinweisen im Umgang mit kognitiv beeinträchtigten und verhaltensveränderten Pflegebedürftigen während der COVID-19-Pandemie hin. 70 % der Befragten, zusammengefasst in der Unterkategorie SARS-CoV-2-Testungen, forderten die Durchführung von "systematischen" und "regelmäßigen" Reihentestungen (n = 72) zum einen beim Personal der Einrichtungen und zum anderen bei den Pflegebedürftigen. 22 % der Befragten gaben an, dass entsprechende Kontaktpersonen nicht immer ausreichend qualifiziert erschienen, um mit praxisnahen Problemlösungen in den Einrichtungen weiterhelfen zu können, sodass ein Bedarf an einer fachlich "kompetenten Beratung" bestehe (n = 16). Dazu äußerten die Befragten einen konkreten Bedarf an "Beratung zur Umsetzung" (n = 12) der Vorgaben und Empfehlungen in den Einrichtungen. Mit der Dynamik und den steigenden Erkenntnissen in der Pandemie wurden auch die Empfehlungen zum Umgang SARS-CoV-2 in den Pflegeeinrichtungen seitens des RKI angepasst. Um die vulnerable Gruppe der Pflegebedürftigen und die Mitarbeitenden von Pflegeeinrichtungen in der aktuellen Situation vor SARS-CoV-2-Infektionen zu schützen, ergeben sich aus den Ergebnissen v. cache = ./cache/cord-304372-6eqnr52t.txt txt = ./txt/cord-304372-6eqnr52t.txt === reduce.pl bib === id = cord-304282-om2xc4bs author = Berhan, Yifru title = Will Africa be Devastated by Covid-19 as Many Predicted? Perspective and Prospective date = 2020-05-17 pages = extension = .txt mime = text/plain words = 5345 sentences = 235 flesch = 57 summary = Since the novel coronavirus disease 2019 (Covid-19 or SARS CoV-2 infection) has been declared as pandemic, several mathematicians and statisticians have developed different trajectory curves for Africa, with the assumption that the virus can have an exponential pattern of transmission. A very important argument is; had the Covid-19 transmission been as contagious as in Europe and USA, by this time, every health facility in Africa and other tropical countries could have been flooded with severely ill patients and deaths. The other side of the coin is; the overwhelming cases and deaths experienced in Europe and USA is despite the fact that they started to report Covid-19 confirmed cases almost same time or later than many of the countries in the tropical climate zone. An important observation was that, like the currently observed Covid-19 pandemic, the morbidity and mortality of the aforementioned influenza outbreaks were not that much spreading and killing outside the temperate zone, at least in Africa. cache = ./cache/cord-304282-om2xc4bs.txt txt = ./txt/cord-304282-om2xc4bs.txt === reduce.pl bib === id = cord-304355-y3fagw3t author = Pan, Boyu title = Chinese herbal compounds against SARS-CoV-2: puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor date = 2020-11-11 pages = extension = .txt mime = text/plain words = 4390 sentences = 212 flesch = 45 summary = Here, we identified puerarin (PubChem CID: 5281807), quercetin (PubChem CID: 5280343) and kaempferol (PubChem CID: 5280863) as potential compounds with binding activity to ACE2 by using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). In this study, we first screened out puerarin as the candidate compound targeting human ACE2 from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and identified the potential effective herbs containing puerarin through TCMSP analysis platform. The possible interaction of these compounds with ACE2 was further investigated by molecular docking and surface plasmon resonance assays, and the results support the view that puerarin and quercetin could significantly impair the binding of viral S-protein to its human ACE2 receptor, shedding light on CHM-based new drug discovery against COVID-19 (See workflow scheme in Figure 1 ). To screen the potential CHM compounds targeting human ACE2 receptor, Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was employed. cache = ./cache/cord-304355-y3fagw3t.txt txt = ./txt/cord-304355-y3fagw3t.txt === reduce.pl bib === id = cord-304176-yloqrblw author = Tunesi, S. title = Prescribing COVID-19 treatments: what we should never forget date = 2020-05-13 pages = extension = .txt mime = text/plain words = 701 sentences = 42 flesch = 51 summary = authors: Tunesi, S.; Bourgarit, A. COVID-19-induced proinflammatory status looks to trigger most severe SARS-CoV-2 forms (2). Many drugs have been hypothesized to be directly active against COVID-19 only because of a supposed antiviral activity: remdesivir, a molecule originally tested against Ebola virus, shows in vivo activity against MERS-CoV (5) but there is actually no real evidence of in vivo activity against COVID-19; lopinavir/ritonavir, a well-known protease inhibitor used in HIV treatment, has been widely used before randomized clinical trials showed his inefficacy in mortality reduction (6); chloroquine and hydroxychloroquine, which are largely used in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) treatment, show modest antiviral effects, but mortality due to QT elongation-related cardiac events is a matter of concern (7). Conversely, preliminary data about a potential role of ACE inhibitors in favouring the onset of severe forms of SARS-CoV-2 infection induced a massive change in antihypertensive drugs prescription that caused the onset of severe cardiovascular events (9). cache = ./cache/cord-304176-yloqrblw.txt txt = ./txt/cord-304176-yloqrblw.txt === reduce.pl bib === id = cord-304321-y177sqee author = Cho, Ryan H. W. title = Pearls of experience for safe and efficient hospital practices in otorhinolaryngology—head and neck surgery in Hong Kong during the 2019 novel coronavirus disease (COVID-19) pandemic date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4375 sentences = 192 flesch = 43 summary = We hope that our experiences will serve as pearls for otolaryngologists and other healthcare personnel working in institutes that serve large numbers of patients every day, particularly with regard to the sharing of clinical and administrative tasks during the COVID-19 pandemic. In 2003 outbreak of SARS in Hong Kong, the initial phase of outbreak began in Prince of Wales Hospital with a carrier of coronavirus in a medical ward causing widespread infection to patients and medical staff through the use of nebulizer for bronchodilators which facilitated the transmission of the virus through aerosol spread. Health seminars on COVID-19, which were organized by the infection control team to all hospital staff on daily basis across the whole month, provided a direct platform from which to educate healthcare personnel about the virus, its mode of transmission, the course of the disease, management and the mortality rate. cache = ./cache/cord-304321-y177sqee.txt txt = ./txt/cord-304321-y177sqee.txt === reduce.pl bib === id = cord-304295-3mpymd8a author = Khan, Muhammad Muzamil title = Emergence of novel coronavirus and progress toward treatment and vaccine date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2935 sentences = 210 flesch = 48 summary = 10 Favipiravir was effectively used against influenza and has the potential to inhibit viral RNA synthesis and a new study also supports its activity against SARS-CoV-2. 15 In another recent study, Gao et al found that chloroquine phosphate reduced the symptoms of pneumonia in SARS-CoV-2 patients and shortening the duration of disease. 67 Different technologies are being utilized to F I G U R E 1 Mechanism of action of HCQ and CQ by blocking binding of virus with ACE-2 receptors and increasing endosomal pH and preventing fusion with the cell develop potential vaccine for SARS-CoV-2 including DNA and mRNAbased nanoparticles. Clinical study for safety and efficacy of favipiravir in the treatment of novel coronavirus pneumonia (COVID-19) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-304295-3mpymd8a.txt txt = ./txt/cord-304295-3mpymd8a.txt === reduce.pl bib === id = cord-304340-9mrtic2k author = Karacan, Ilker title = The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2988 sentences = 181 flesch = 54 summary = Although SARS-CoV-2 has a lower mutation rate than expected [18] , real-time tracking of the virus isolates in populations may help epidemiological understanding of the disease and early detection of important mutational or recombination events. Herein, we analyzed full-length SARS-CoV-2 genomes from three patients in Istanbul together with their clinical findings. Sample Collection: Nasopharyngeal swabs were collected from unrelated patients and tested for SARS-CoV-2 presence as a standard care protocol for routine diagnosis in Umraniye Training and Research Hospital (UEAH), Istanbul. The physical examination in the emergency department revealed a body temperature of 36.8°C, blood pressure of 120/70 mm Hg, the pulse of 100 beats per minute, respiratory rate of 20 breaths per minute, and oxygen saturation of 97% while the patient was breathing ambient air. Herein, we report three virus genomes isolated in Istanbul for the first time together with patients' clinical findings. cache = ./cache/cord-304340-9mrtic2k.txt txt = ./txt/cord-304340-9mrtic2k.txt === reduce.pl bib === id = cord-304280-2a84u4tm author = Masic, Izet title = Public Health Aspects of COVID-19 Infection with Focus on Cardiovascular Diseases date = 2020-03-17 pages = extension = .txt mime = text/plain words = 4693 sentences = 196 flesch = 43 summary = METHODS: We used method of descriptive analysis of the published papers with described studies about Corona virus connected with CVD, and, also, Guidelines proposed by World Health Organization (WHO) and European Society of Cardiology (ESC), and some other international associations which are included in global fighting against COVID-19 infection. Early COVID-19 case reports suggest that patients with underlying conditions are at higher risk for complications or mortality -up to 50% of hospitalized patients have a chronic medical illness (40% cardiovascular or cerebrovascular disease). The clinical effects of pneumonia have been linked to increased risk of CVD up to 10-year follow-up (11) and it is likely that cases infected via respiratory virus outbreaks will experience similar adverse outcomes. The European Medicines Agency (EMA) has issued a statement advising that patients continue treatment with angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs), despite widely circulated reports that the agents could worsen coronavirus disease (20) . cache = ./cache/cord-304280-2a84u4tm.txt txt = ./txt/cord-304280-2a84u4tm.txt === reduce.pl bib === id = cord-304232-c0cpx2q3 author = Opriessnig, Tanja title = Update on possible animal sources for COVID‐19 in humans date = 2020-06-17 pages = extension = .txt mime = text/plain words = 988 sentences = 75 flesch = 54 summary = 7 In support of these early results, an ongoing study conducted at the Friedrich Loeffler Institute in Germany further confirmed that pigs and chickens are not susceptible to intranasal infection with SARS-CoV-2 (https://prome dmail.org/prome d-post/?id=7196506). 7 Natural infection, as evidenced by the presence of antibodies, SARS-CoV-2 RNA or both, has been identified in selected dogs in close contact with COVID-19 patients (Table 3) . A recent French study, which investigated nine cats and 12 dogs in close contact with a cluster of COVID-19 patients, was unable to detect evidence of SARS-CoV-2 infection in any of the animals. Moreover, animal-to-human SARS-CoV-2 infection as well as natural animal-to-animal transmission has yet to be confirmed and none of the species considered to be susceptible to the virus at this point are presently used for xenotransplantation. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 cache = ./cache/cord-304232-c0cpx2q3.txt txt = ./txt/cord-304232-c0cpx2q3.txt === reduce.pl bib === id = cord-304487-ycvu5l5f author = Wertheim, Joel O title = A glimpse into the origins of genetic diversity in SARS-CoV-2 date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1202 sentences = 74 flesch = 43 summary = Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. cache = ./cache/cord-304487-ycvu5l5f.txt txt = ./txt/cord-304487-ycvu5l5f.txt === reduce.pl bib === id = cord-304457-8g36h1bz author = Idelsis, E.-M. title = Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date = 2020-08-01 pages = extension = .txt mime = text/plain words = 5862 sentences = 330 flesch = 47 summary = Conclusions: In a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly negativized the virus on day 4 of treatment when comparing with IFN-alpha2b. The RT-PCR after treatment with IFNs on day 14 for hospital discharges was negative to SARS-CoV-2 in 100% and 91% of patients of HeberFERON and control cohorts, respectively. These results confirm the validity of early intervention with the treatment of IFNs in patients with COVID-19, whereas demonstrated in the trial, the combination of type I and type II IFNs impacts strongly in the reduction of the risk for a severe disease likely through the efficient implementation of a timely controlled inflammatory antiviral response against the SARS-CoV-2 infection. Evaluation of the Effect and Safety of HeberFERON vs Heberon Alpha in Patients Infected with Corona Virus SARS-CoV-2 (Study ESPERANZA/HOPE): TRIALS cache = ./cache/cord-304457-8g36h1bz.txt txt = ./txt/cord-304457-8g36h1bz.txt === reduce.pl bib === id = cord-304306-rxjahqwh author = Vlachakis, Dimitrios title = Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date = 2020-10-08 pages = extension = .txt mime = text/plain words = 8517 sentences = 459 flesch = 48 summary = The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response cache = ./cache/cord-304306-rxjahqwh.txt txt = ./txt/cord-304306-rxjahqwh.txt === reduce.pl bib === id = cord-304388-pth2d40p author = Lai, Chih-Cheng title = Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths date = 2020-03-04 pages = extension = .txt mime = text/plain words = 4374 sentences = 284 flesch = 53 summary = Abstract Since the emergence of coronavirus disease 2019 (COVID-19) (formerly known as the 2019 novel coronavirus [2019-nCoV]) in Wuhan, China in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 75,000 cases have been reported in 32 countries/regions, resulting in more than 2000 deaths worldwide. 11, 15 Similarly, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team in China reported that 66.7% (n Z 29,798) of 44,672 cases of COVID-19 of varying degrees of severity were between 20 and 60 years of age. First, the clinical manifestation of COVID-19 ranges from the asymptomatic carrier state to severe pneumonia; however, most early reports only showed the findings of SARS-CoV-2 pneumonia, in which the ratio of male patients was much larger than that of female patients, there were no pediatric cases, and the mortality rate was high. cache = ./cache/cord-304388-pth2d40p.txt txt = ./txt/cord-304388-pth2d40p.txt === reduce.pl bib === id = cord-304356-jyp9gjh9 author = Grant, Rogan A. title = Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date = 2020-08-05 pages = extension = .txt mime = text/plain words = 7453 sentences = 427 flesch = 44 summary = We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. cache = ./cache/cord-304356-jyp9gjh9.txt txt = ./txt/cord-304356-jyp9gjh9.txt === reduce.pl bib === id = cord-304574-03s404s5 author = Luciani, Lorenzo G. title = Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. Urinary Frequency as a Possible Overlooked Symptom in COVID-19 Patients: Does SARS-CoV-2 Cause Viral Cystitis? Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection date = 2020-06-12 pages = extension = .txt mime = text/plain words = 174 sentences = 25 flesch = 67 summary = key: cord-304574-03s404s5 authors: Luciani, Lorenzo G.; Gallo, Fabrizio; Malossini, Gianni title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection journal: Eur Urol DOI: 10.1016/j.eururo.2020.06.006 cord_uid: 03s404s5 Mumm et al [1] reported that urinary frequency might be a symptom of SARS-CoV-2. This assumption is based on the finding that the bladder urothelium, as well as the kidney, harbors cells expressing ACE2, the receptor for the viral spike protein [2,3]. Our experience appears to confirm their suspicion, further suggesting that the urinary tract may become the target of life-threatening involvement by SARS-CoV-2. We report three cases of gross hematuria admitted to two hospitals in Northern Italy between The authors have nothing to disclose. Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Eur Urol Eur Urol cache = ./cache/cord-304574-03s404s5.txt txt = ./txt/cord-304574-03s404s5.txt === reduce.pl bib === id = cord-304379-4mfyxp6h author = Wang, Jin title = Mathematical models for COVID-19: applications, limitations, and potentials date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1561 sentences = 77 flesch = 35 summary = (5) conducted computational modeling of potential epidemic trajectories to estimate the outbreak size in Wuhan, China, and their results indicated that control measures need to block well over 60% of transmission to be effective in containing the outbreak. Incorporating such an environment-tohuman route into mathematical modeling may better characterize the transmission dynamics of COVID-19 and potentially gain deeper understanding of its epidemic patterns. For example, many countries (China in particular) implemented strong disease control measures, including large-scale quarantine, intensive tracking of movement and contact, strict isolation of infected individuals, expanded medical facilities, and social distancing, which can effectively (and, in some places, rapidly) reduce the transmissibility of the virus. Mathematical epidemic models are well positioned to incorporate the economic impact of COVID-19, to quantify the interaction of epidemiological and economic factors, and to suggest an optimal balance between the pandemic control and economic development. cache = ./cache/cord-304379-4mfyxp6h.txt txt = ./txt/cord-304379-4mfyxp6h.txt === reduce.pl bib === id = cord-304418-k9owyolj author = Le Maréchal, M. title = COVID-19 in clinical practice: a narrative synthesis date = 2020-09-29 pages = extension = .txt mime = text/plain words = 6288 sentences = 367 flesch = 49 summary = Plasmatic detection of SARS-CoV-2 has been reported but only with low viral titers, and mainly in clinically severe cases [44] ; bloodstream infectivity has yet to be demonstrated. The first large clinical trial published on LPV/RTV on SARS-CoV-2 compared 99 patients receiving the antiviral vs 100 receiving SoC alone [124] ; there was no difference between the 2 groups regarding the primary end point (time to improvement) (15 vs 16 days, p=0.09). Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China cache = ./cache/cord-304418-k9owyolj.txt txt = ./txt/cord-304418-k9owyolj.txt === reduce.pl bib === id = cord-304479-uxp1kg86 author = Goodarzi, Pedram title = Coronavirus disease 2019 (COVID-19): Immunological approaches and emerging pharmacologic treatments date = 2020-08-08 pages = extension = .txt mime = text/plain words = 8098 sentences = 434 flesch = 41 summary = Finally, recently, a case report study from Japan shows that orally inhaled ciclesonide alleviates the local inflammation in the lung of patients with COVID-19 pneumonia and inhibits the propagation of the virus by antiviral activity [60] . In the same way, a recent case-report study showed that the adoptive transfer therapy of human umbilical cord blood derived-mesenchymal stem cells (hUCMSCs) to a Chinese female patient afflicted with acute COVID19 syndromes improved her laboratory tests and CT images [69] . In vitro evidence of activity against SARS-CoV-2 in infected Vero E6 cells reported with high concentrations of the drug [104, 105, 142] FPV significantly improved the latency to relief for pyrexia and cough [99] FPV in patients with COVID-19 led to decrease of viral load and significant improvement in chest imaging compared with the control arm [98] cache = ./cache/cord-304479-uxp1kg86.txt txt = ./txt/cord-304479-uxp1kg86.txt === reduce.pl bib === id = cord-304498-ty41xob0 author = Denison, Mark R title = Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date = 2011-03-01 pages = extension = .txt mime = text/plain words = 7332 sentences = 345 flesch = 38 summary = Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. cache = ./cache/cord-304498-ty41xob0.txt txt = ./txt/cord-304498-ty41xob0.txt === reduce.pl bib === id = cord-304254-67brxejx author = Wei, Ping title = The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase date = 2006-01-20 pages = extension = .txt mime = text/plain words = 4577 sentences = 240 flesch = 47 summary = As we have reported previously, the peptide cleavage assay shows that the specific activity for proteolysis decreases linearly with the decrease of enzyme concentration, suggesting that the dimer is the major form for biological activity and that the dimeric interface could be targeted for structural-based drug design against SARS 3CL proteinase [18] . The crystal structure of SARS 3CL proteinase indicates that the N-finger fragment plays an important role in the dimerization and maintenance of the active form of the enzyme [16] . The dimer dissociation constants of the SARS 3CL proteinase and N-terminal mutants were determined by sedimentation velocity and equilibrium methods. In summary, we have carried out a mutational study on the N-finger of SARS 3CL proteinase and determined the dimer dissociation constants for the wild-type protein and the mutants using sedimentation velocity and equilibrium techniques. cache = ./cache/cord-304254-67brxejx.txt txt = ./txt/cord-304254-67brxejx.txt === reduce.pl bib === id = cord-304544-tqtdjh2m author = Enes, Ak title = Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3745 sentences = 189 flesch = 49 summary = Comparison of transcriptome of NHBE cells 24 hours after mock-infection and SARS-CoV-2 infection demonstrated that most genes that respond to infection were upregulated (320 genes) rather than being downregulated (115 genes).While upregulated genes were enriched in signalling pathways related to virus response, downregulated genes are related to kidney development. Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. Upregulated MMPs and chemokines demonstrate the response generated by NHBE cells to trigger the immune system, these two subgroups of genes are further discussed below comparatively in SARS-CoV-2 and H1N1 infection. Interestingly, none of the IL-17 ligands were expressed in detectable amounts in NHBE cells, and none of the ligands or receptors were upregulated in response to virus infection, therefore the positive feedback loop is likely to be initiated by activation of NFκB via other signalling pathways. cache = ./cache/cord-304544-tqtdjh2m.txt txt = ./txt/cord-304544-tqtdjh2m.txt === reduce.pl bib === id = cord-304660-w7rs2dvt author = Bharadwaj, Shiv title = SARS-CoV-2 M(pro) inhibitors: identification of anti-SARS-CoV-2 M(pro) compounds from FDA approved drugs date = 2020-11-05 pages = extension = .txt mime = text/plain words = 4854 sentences = 242 flesch = 46 summary = The top 10 screened potential compounds against SARS-CoV-2 M(pro) were then studied by re-docking, binding affinity, intermolecular interaction, and complex stability via 100 ns all atoms molecular dynamics (MD) simulation followed by post-simulation analysis, including end point binding free energy, essential dynamics, and residual correlation analysis against native crystal structure ligand N3 inhibitor. Hence, comparative molecular docking analysis of screened FDA approved drugs against N3 inhibitor suggested the potential of selected drugs to inhibit SARS-CoV-2 M pro by formation of hydrogen and non-covalent interaction with its catalytic dyad and substrate binding residues. Based on the combinatorial computational analysis, including structure-based virtual screening, molecular docking, binding free energy calculations, MD simulation and post-MD simulation analysis for the screened FDA drugs with viral protease, suggested the drugs, R428, Teniposide, VS-5584, and Setileuton with comparatively higher stability and affinity with SARS-CoV-2 M pro against N3 inhibitor via strong intermolecular interactions formation as well disturbing the conformation of viral protease active pocket. cache = ./cache/cord-304660-w7rs2dvt.txt txt = ./txt/cord-304660-w7rs2dvt.txt === reduce.pl bib === id = cord-304480-azosg1tt author = Hu, Donghua title = Studies on the interactions of Ti-containing polyoxometalates (POMs) with SARS-CoV 3CL(pro) by molecular modeling date = 2006-09-05 pages = extension = .txt mime = text/plain words = 2363 sentences = 162 flesch = 62 summary = The ligand-receptor interaction of POMs/3CL pro generally causes energy decreasing and conformation changing; accordingly these changes should influence the enzyme catalytic activity of the SARS-CoV 3CL pro . What is more, during the course of POMs/SARS-CoV 3CL pro complex formation, the atom charge loading properties and the electrostatic characteristic are very vital elements that keep the enzyme-inhibitor interaction. The investigation results show that: (1) POMs interact with the 3CL pro receptor in enzyme active site region, with several polarized residues including the enzyme catalyst residues of His41/Cys145; (2) The total binding energies of the five POM/SARS-CoV 3CL pro complexes lead to the following order of complex stability: 1,2-PTi 2 /3CL pro > 1,4-PTi 2 /3CL pro > 1,5-PTi 2 /3CL pro > 1,6-PTi 2 /3CL pro > 1,11-PTi 2 /3CL pro . (3) Electrostatic energy and hydrogen bond interaction contribute much to the enzyme-inhibitor complex formation between POMs and SARS-CoV 3CL pro . cache = ./cache/cord-304480-azosg1tt.txt txt = ./txt/cord-304480-azosg1tt.txt === reduce.pl bib === id = cord-304724-luql6159 author = Paderno, Alberto title = Smell and taste alterations in Covid‐19: a cross‐sectional analysis of different cohorts date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3347 sentences = 207 flesch = 50 summary = The study aims to estimate the different characteristics of OD and GD in hospitalized patients and home-quarantined subjects with a nasal/pharyngeal swab positive for SARS-CoV-2 in an epidemic area. All subjects with positive nasal/pharyngeal swab for SARS-CoV-2 were home-quarantined or Patients were not informed about the specific study aim to minimize confirmation bias. The study describes a sample of more than 500 cases with confirmed SARS-CoV-2 infection, distinguishing between hospitalized patients and home-quarantined subjects. All cases with OD and GD reported an acute onset and a significant degree of dysfunction, without solid connection with other symptoms suggestive of upper airway infection (i.e., pharyngodynia and nasal congestion). # Patients affected by olfactory and gustatory dysfunction reported these complains as delayed symptom of presentation of the infection with SARS-CoV-2 in 231 (81.6%) and 264 (82.2%) cases, respectively. cache = ./cache/cord-304724-luql6159.txt txt = ./txt/cord-304724-luql6159.txt === reduce.pl bib === id = cord-304839-lesa5u2n author = Jiang, Fang title = Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19) date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1896 sentences = 152 flesch = 57 summary = In late December 2019, a cluster of cases with 2019 Novel Coronavirus pneumonia (SARS-CoV-2) in Wuhan, China, aroused worldwide concern. On January 7, 2020, researchers rapidly isolated a novel coronavirus (SARS-CoV-2, also referred to as 2019-nCoV) from confirmed infected pneumonia patients. 3 We reviewed the published clinical features, symptoms, complications, and treatments of patients with COVID-19 to help health workers around the world combat the current outbreak. Keywords used were "COVID-19," "2019 novel coronavirus," "SARS-CoV-2," "2019-nCoV," "Wuhan coronavirus," and "Wuhan seafood market pneumonia virus." After careful screening, six published articles with confirmed cases were identified and included in this review. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan cache = ./cache/cord-304839-lesa5u2n.txt txt = ./txt/cord-304839-lesa5u2n.txt === reduce.pl bib === id = cord-304792-8sdxqmkb author = Khan, Md. Abdullah-Al-Kamran title = SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2983 sentences = 207 flesch = 48 summary = title: SARS-CoV-2 proteins exploit host's genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. We have utilized KEGG mapper tool (Kanehisa and Sato, 2020) for the mapping of 197 deregulated genes SARS-CoV-2 interacting host proteins in different cellular pathways. cache = ./cache/cord-304792-8sdxqmkb.txt txt = ./txt/cord-304792-8sdxqmkb.txt === reduce.pl bib === id = cord-304550-6j1pb1pu author = Yongchen, Zhang title = Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2032 sentences = 108 flesch = 43 summary = Here, we conducted a serial investigation on 21 individuals infected with SARS-CoV-2 in two medical centres from Jiangsu Province, including 11 non-severe COVID-19 patients, and 5 severe COVID-19 patients and 5 asymptomatic carriers based on nucleic acid test and clinical symptoms. In this respective study, we serially analysed the virus RNA test results in swab samples, along with anti-SARS-CoV-2 IgM and IgG responses among 21 COVID-19 patients at the Second Hospital of Nanjing and the Affiliated Hospital of Xuzhou Medical University in Jiangsu Province, China. Our serial SARS-CoV-2 RNA testing identified a prolonged viral shedding for asymptomatic cases compared to COVID-19 patients, suggesting the importance of early identification and timely quarantine for these asymptomatic carriers. It is possible that significantly high level of SARS-CoV-2 viral load observed in severe cases [8, 9] drives an early antibody response produced by immediate activation of extrafollicular B cells during acute infection [10, 11] . cache = ./cache/cord-304550-6j1pb1pu.txt txt = ./txt/cord-304550-6j1pb1pu.txt === reduce.pl bib === id = cord-304734-r0k1rfmt author = Moreno-Casbas, María Teresa title = Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI date = 2020-05-25 pages = extension = .txt mime = text/plain words = 3237 sentences = 343 flesch = 60 summary = La población diana está constituida por profesionales de la salud de todas las Comunidades Autónomas de España, con actividad en cualquier centro que atienda a pacientes con COVID-19 y que sean un caso confirmado de infección por SARS-CoV-2 por laboratorio. Laborales y epidemiológicas: lugar y unidad de trabajo, tiempo trabajado en los últimos 10 años, elementos de protección (disponibilidad, utilización y percepción del uso correcto), métodos y frecuencia de la higiene de manos y de otras medidas higiénicas en el trabajo, carga de trabajo en la última jornada, existencia de protocolos de protección, motivo de realización del test y responsable de indicarlo, fechas de inicio de síntomas, de test positivo y test negativo, contactos previos al test, aislamiento y sus características y reincorporación al trabajo. En relación a la percepción de los profesionales, en las primeras semanas de la pandemia, de la disponibilidad de medidas de protección en la categoría "siempre/frecuentemente" fue: para mascarilla FPP1 57,3%, guantes 89,5%, jabón 95% y solución hidroalcohólica 91,5%. cache = ./cache/cord-304734-r0k1rfmt.txt txt = ./txt/cord-304734-r0k1rfmt.txt === reduce.pl bib === id = cord-304791-wv4qu9xm author = Carfora, Vincenzo title = Anticoagulant treatment in COVID-19: a narrative review date = 2020-08-18 pages = extension = .txt mime = text/plain words = 3568 sentences = 193 flesch = 41 summary = Besides the respiratory involvement, COVID 19 patients frequently develop a pro-coagulative state caused by virus-induced endothelial dysfunction, cytokine storm and complement cascade hyperactivation. [11] enrolled 183 consecutive COVID-19 patients and performed routine coagulation tests [PT, [8] In COVID-19-patients it is common to observe increased fibrinogen and D-Dimer levels Chen, 2020 [9] In COVID-19-patients it is common to observe variable levels of prothrombin time (PT), activated partial thromboplastin time (aPTT) and International standardized ratio (INR) Qin, 2020 [15] In COVID-19 the hyperinflammation mediated by IL-1, TNF-alfa and IL-6 leads to an increase of plasma concentrations of fibrinogen and plasminogen activator inhibitor-1 (PAI-1) Campbell, 2020 [19] In a murine model of MERS-CoV infection, increased concentrations of C5a and C5b-9 were found in sera and lung tissues. Moreover, patients with cardiovascular disease and dyslipidemia have high levels of circulating asymmetric di-methyl-arginine (ADMA) [28] , an analogue of L-arginine that inhibits NOS-3 activity [29] , and this leads to lower NO levels; this explains why endothelial dysfunction and the pro-coagulant state are more severe in this cohort of patients. cache = ./cache/cord-304791-wv4qu9xm.txt txt = ./txt/cord-304791-wv4qu9xm.txt === reduce.pl bib === id = cord-304718-w469n0o8 author = Wang, Yan title = Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection date = 2009-05-01 pages = extension = .txt mime = text/plain words = 2595 sentences = 161 flesch = 51 summary = One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. A few case-control studies have reported an association between SARS susceptibility and human leucocyte antigen (HLA) and MBL [8] [9] [10] [11] . With regard to SARS-CoV infection, the codon 54 variant of the MBL gene has been shown to be associated with infection susceptibility but not with disease severity [11] . As the downstream protein of MBL, variants of the MASP2 gene may be associated with SARS-CoV infection. Genomic DNA from 30 individuals with SARS was chosen for analysis of MASP2 gene polymorphisms. cache = ./cache/cord-304718-w469n0o8.txt txt = ./txt/cord-304718-w469n0o8.txt === reduce.pl bib === id = cord-304787-fohgekp4 author = Prazuck, Thierry title = Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1126 sentences = 75 flesch = 62 summary = 1 Herein, we describe the epidemiological, clinical and biological characteristics of 30 households in close contact with SARS-CoV-2-infected members, living in a confined environment during the French national lockdown. During the 5 days before the French national lockdown, both families moved from their usual Parisian residence to a closed property in the countryside, composed by 3 neighboring houses (A, B and C) in a park. House A was inhabited by 8 persons from a single family, including 3 couples who shared their bed for at least 4 days after the onset of symptoms. The first diagnosed case was a 67-year-old man (resident #1) living in the house A and referring to the Infectious Diseases outpatient clinic on March 17 for cough, fever and asthenia for 4 days. No transmission occurred between husbands and wives in house A although couples moved to separated rooms only 4 days after the onset of symptoms of the index case. cache = ./cache/cord-304787-fohgekp4.txt txt = ./txt/cord-304787-fohgekp4.txt === reduce.pl bib === id = cord-304742-ytf2ilw4 author = Albini, Adriana title = The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based antihypertensive therapies—reply date = 2020-07-14 pages = extension = .txt mime = text/plain words = 1187 sentences = 52 flesch = 41 summary = The transmembrane protease serine 2 TMPRSS2, an androgendependent enzyme, acts in reinforcing the ACE-2 receptor activity in allowing cell entry to a number of viral pathogens as well as to SARS-CoV-2 as reported in our Point of View [2] . Yet in trisomy 21 individuals a TMPRSS2 protease overexpression has been documented, as mentioned in the comment of Dr De Cauwer [1] , with this leading to an increased viral infection's rate of susceptible host's cells and tissues. In conclusion, the interesting comment by Dr De Cauwer points out the complex interactions between ACE-2 and TMPRSS2 with reference to the clinical course of CoViD-19 as well as to SARS-CoV-2 infection's pathogenic evolution and severity degree in given population segments of infected individuals, like male individuals and Down syndromeaffected patients [1] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACEinhibitor-and angiotensin II receptor blocker-based cardiovascular therapies: comment The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies cache = ./cache/cord-304742-ytf2ilw4.txt txt = ./txt/cord-304742-ytf2ilw4.txt === reduce.pl bib === id = cord-304626-ffao7vka author = Mellors, Jack title = Viral Evasion of the Complement System and Its Importance for Vaccines and Therapeutics date = 2020-07-09 pages = extension = .txt mime = text/plain words = 11744 sentences = 539 flesch = 34 summary = A better understanding of this virus-host interplay and its contribution to pathogenesis has previously led to: the identification of genetic factors which influence viral infection and disease outcome, the development of novel antivirals, and the production of safer, more effective vaccines. Infected host cells which present viral antigens on the cell surface membrane can activate the classical pathway, as the antigens bind IgM/IgG to induce complement dependent cytotoxicity (CDC). Non-neutralizing antibodies can still bind the viral target with the potential to cross-link with Fc receptors, or activate complement and interact with complement receptors, to enhance viral infection of host cells (241) . Use of the non-neutralizing influenza virus M2 extracellular vaccine in mice required functional C3 to confer protection and induce effective humoral and cell-mediated immune responses (245) . cache = ./cache/cord-304626-ffao7vka.txt txt = ./txt/cord-304626-ffao7vka.txt === reduce.pl bib === id = cord-304617-5ozf18lg author = Al-Khafaji, Khattab title = Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4367 sentences = 227 flesch = 51 summary = The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. The got protein-drug complex structures from covalent docking were submitted to MD simulations (saquinavir, ritonavir, and remdesivir with SARS-CoV-2 Mpro). The effect of drug-protein interactions upon dynamics of biological system is a fundamental in drug discovery thereby we used RMSD to investigate the influence of saquinavir, ritonavir, and remdesivir upon the stability of SARS-CoV-2 Mpro. One of the more noteworthy findings in this study is that MD simulation analysis that saquinavir, ritonavir, and remdesivir can form stable interaction inside the binding site of SARS-CoV-2 Mpro. cache = ./cache/cord-304617-5ozf18lg.txt txt = ./txt/cord-304617-5ozf18lg.txt === reduce.pl bib === id = cord-304871-gva617yp author = Zheng, Ting title = Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2576 sentences = 162 flesch = 53 summary = title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China The objective of this study is to compare clinical characteristics and outcomes between patients with and without GI symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan. This retrospective study included 1320 patients with confirmed COVID-19 infection admitted to Jianghan Fangcang Shelter Hospital from February 5, 2020, to March 9, 2020. Multivariable logistic regression analysis showed Accepted Article that GI symptoms (p=0.045), male gender (p<0.001), and elevated CRP (p=0.008) were independent risk factors for patient transfer to a tertiary hospital ( Table 3) . Potential risk factors for developing GI symptoms, male gender, and increased CRP may help clinicians predict clinical worsening in COVID-19 patients. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-304871-gva617yp.txt txt = ./txt/cord-304871-gva617yp.txt === reduce.pl bib === id = cord-304584-jxha3rz8 author = Giacomo, Di title = SARS-COV-2 infection in cancer patients undergoing checkpoint blockade: clinical course and outcome date = 2020-05-03 pages = extension = .txt mime = text/plain words = 425 sentences = 35 flesch = 51 summary = The potential interplay between Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) infection and treatment with immune-checkpoint inhibitors (ICI) of cancer patients is presently unknown. Two subsequent swabs tested negative on April 3 and 4 for SARS-CoV-2 infection ( Figure 1) ; thus, the patient was considered cured from COVID-19 and she will resume ICI-therapy shortly. Undoubtedly, no general conclusion can be drawn from the positive outcome of these two patients on the reciprocal interplay between ICI therapy and SARS-CoV-2 infection. Nevertheless, these findings seem to suggest that treatment with ICI is a doable approach during the COVID-19 pandemic, and that SARS-CoV-2 infection does not seem to represent an obstacle to grant cancer patients the best treatment according to their clinical setting. SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerasechain-reaction (rRT-PCR) testing positive (★) or negative (✪). SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerase-chainreaction (rRT-PCR) testing positive (★) or negative (✪). cache = ./cache/cord-304584-jxha3rz8.txt txt = ./txt/cord-304584-jxha3rz8.txt === reduce.pl bib === id = cord-304898-he57l0y7 author = Belghmaidi, Sarah title = Third Cranial Nerve Palsy Presenting with Unilateral Diplopia and Strabismus in a 24-Year-Old Woman with COVID-19 date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1666 sentences = 104 flesch = 49 summary = Patient: Female, 24-year-old Final Diagnosis: Third cranial nerve palsy in a women presenting COVID-19 Symptoms: Ophthalmoplegia Medication:— Clinical Procedure: — Specialty: Ophthalmology OBJECTIVE: Rare disease BACKGROUND: Coronavirus disease (COVID 19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is the causative agent of a serious disease that is of great global public health concern. We describe the case of a patient with an incomplete palsy of the left third cranial nerve sparing the pupils in the context of SARS-CoV-2 virus infection. CASE REPORT: We report the case of a 24-year-old woman with confirmed COVID-19, which presented with acute onset of diplopia and strabismus of the left eye that occurred 3 days after the start of general symptoms. A previously healthy 24-year-old woman, with no medical history (such as diabetes, high blood pressure, dyslipidemia, vasculitis, smoking, obesity, familial neurological disease, or other risk factors for ischemic ophthalmoplegia), presented to the Emergency Department for acute onset of strabismus and diplopia of the left eye, evolving for 3 days. cache = ./cache/cord-304898-he57l0y7.txt txt = ./txt/cord-304898-he57l0y7.txt === reduce.pl bib === id = cord-305025-pqye1ebh author = Sharifi, Majid title = Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3583 sentences = 226 flesch = 44 summary = The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 637 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 638 RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Rapid COVID-19 detection causative virus (SARS-CoV-2) in human 933 nasopharyngeal swab specimens using field-effect transistor-based biosensor cache = ./cache/cord-305025-pqye1ebh.txt txt = ./txt/cord-305025-pqye1ebh.txt === reduce.pl bib === id = cord-304815-3datxv8j author = Gronvall, Gigi Kwik title = The Scientific Response to a Pandemic date = 2006-02-24 pages = extension = .txt mime = text/plain words = 1522 sentences = 92 flesch = 49 summary = More than 150 scientists and public health practitioners from 25 countries gathered in Lyon, France, to hear speakers from the WHO, the European Commission, scientific journals, Interpol, and public health networks-many of the institutions and individuals who will likely play key roles in the global response to the next pandemic. By discussing the biosafety and biosecurity challenges presented by past epidemics such as SARS, participants recognized the importance of scientific and public health collaboration in combating disease-and the need to plan. Researchers will need to share biological samples between laboratories, sometimes internationally; decision makers and journalists will want the latest information, which may not be peer reviewed; and researchers will risk contracting the disease they research, which could then spread outside of the laboratory. Scientists need access to samples from patients and laboratories in order to conduct research and public health surveillance, as well as to develop diagnostic tests. cache = ./cache/cord-304815-3datxv8j.txt txt = ./txt/cord-304815-3datxv8j.txt === reduce.pl bib === id = cord-305091-tfn2pyc6 author = Tripathi, Praveen Kumar title = Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2 date = 2020-12-01 pages = extension = .txt mime = text/plain words = 4026 sentences = 240 flesch = 52 summary = We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL(Pro) of SARS-CoV-2. COVID-19 is an infectious disease caused by a newly discovered positive-sense single-stranded RNA virus called the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The involvement of H-bond donors and acceptors around hydrophobic sites compel the Teicoplanin molecule to interact within the inhibitor binding pocket of the 3CL Pro protease. In a recent MD simulation study, it was reported that Teicoplanin in complex with SARS-CoV-2 main protease has stable ligand-protein complex and intermolecular interactions during the simulated trajectory [21] . We report Teicoplanin as an effective drug against 3CL Pro which works at a micromolar concentration of 1.5 µM (Fig. 2) and acts by blocking the active site of the protease (Fig. 4F) . cache = ./cache/cord-305091-tfn2pyc6.txt txt = ./txt/cord-305091-tfn2pyc6.txt === reduce.pl bib === id = cord-305134-s7h6bpof author = Mackman, Nigel title = Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses date = 2020-07-13 pages = extension = .txt mime = text/plain words = 6412 sentences = 443 flesch = 41 summary = It is likely that multiple systems contribute to thrombosis in COVID-19 patients, such as activation of coagulation, platelet activation, hypofibrinolysis, endothelial cell dysfunction, inflammation, neutrophil extracellular traps, and complement. 60, 82 Taken together, these results indicate that most COVID-19 patients have an activated coagulation system that is associated with increased levels of d-dimer; however, it is unlike classic DIC since there is little change in PT and the thrombocytopenia is generally mild. [95] [96] [97] [98] [99] There is clear evidence for activation of different cell types, such as lung epithelial cells, macrophages, neutrophils, endothelial cells, and platelets, as well as different systems, such as coagulation, inflammation, and complement, in the lungs of COVID-19 patients (Figure) . We found that plasma levels of extracellular vesicle TF activity were increased in severe influenza virus patients and were associated with mortality. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infects lung epithelial cells and endothelial cells (ECs), which leads to the recruitment of a variety of immune cells, such as macrophages and neutrophils. cache = ./cache/cord-305134-s7h6bpof.txt txt = ./txt/cord-305134-s7h6bpof.txt === reduce.pl bib === id = cord-305059-8z54lw2d author = Qu, Jie-Ming title = Chapter 4 Diagnosis of COVID-19 date = 2021-12-31 pages = extension = .txt mime = text/plain words = 5054 sentences = 271 flesch = 45 summary = If any one of the following pathogenic or serological tests is positive, the patient is confirmed as COVID-19: (1) positive RT-PCR results for SARS-CoV-2 nucleic acid; (2) viral gene sequencing highly homologous to the known SARS-CoV-2; or (3) serum samples positive for SARS-CoV-2-specific IgM and IgG antibodies. The fifth edition of the program was specially designed for Hubei to establish the diagnostic criteria of "clinical diagnosis cases," which include clinical compliance with the characteristics of viral pneumonia, such as corresponding clinical symptoms and imaging CT findings, especially the multiple lobes exudative ground-glass shadow and intermittent consolidation, normal or decreased total count of white blood cells in laboratory examination, and reduced lymphocyte count. The methods are: (1) real-time fluorescence RT-PCR detection of SARS-CoV-2 nucleic acid positive and (2) viral gene sequencing, highly homologous with the known novel coronavirus. cache = ./cache/cord-305059-8z54lw2d.txt txt = ./txt/cord-305059-8z54lw2d.txt === reduce.pl bib === id = cord-305054-4d84b2g6 author = Liu, Yuan title = The selection of reference genome and the search for the origin of SARS-CoV-2 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2166 sentences = 140 flesch = 60 summary = The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts. Zhang, Wu, and Zhang [13] re-analyzed the RNA-Seq reads from two pangolins carrying coronavirus using reference-guided de novo assembly method, with Wuhan-Hu-1 as the reference genome. They also performed RNA sequencing in five archived pangolins samples from Guangdong, and assembled the genomes using WIV04, another SARS-CoV-2 genome from human, as reference genome. Using de novo assembly method, they obtained viral genome that showed 90.32% and 90.24% of whole genome identify to Wuhan-Hu-1and Bat-CoV RaTG13, respectively. RaTG13, which is a bat CoV, had 1,287 reads mapped to it, and the resulting assembly has total length of 21,925 and N50 of 1,428. cache = ./cache/cord-305054-4d84b2g6.txt txt = ./txt/cord-305054-4d84b2g6.txt === reduce.pl bib === id = cord-305104-jk6ai1od author = Escribese, María M title = Cross‐sectional pilot study exploring the feasibility of a rapid SARS‐CoV‐2 immunization test in health and non‐healthcare workers date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1265 sentences = 70 flesch = 52 summary = All rights reserved Cross-sectional pilot study exploring the feasibility of a rapid SARS-CoV-2 immunization test in healthcare and non-healthcare workers To the Editor: We aimed to generate an immune response map to SARS-CoV-2 in a very specific population of a Medical School were both healthcare workers and non-healthcare workers cohabit, and elucidate the main risk factors that can be associated with COVID-19 diagnosis in each population. Additionally, this pilot study provides the knowledge and the positive controls (healthcare workers with positive RT-PCR) for the development of future methodological strategies aiming to set up new immunological tests for herd immunity follow-up (ELISA, neutralization assays, etc.).This will be helpful if we take into account the shortage of commercial kits for SARS-CoV-2 immunological tests during the pandemic, and the limitations of these tests in terms of specificity and sensitivity (5, 6)(). cache = ./cache/cord-305104-jk6ai1od.txt txt = ./txt/cord-305104-jk6ai1od.txt === reduce.pl bib === id = cord-304899-vruq4r7z author = Guihot, Amélie title = Syndrome respiratoire aigu sévère : une épidémie singulière de pneumonie virale date = 2004-03-31 pages = extension = .txt mime = text/plain words = 2706 sentences = 261 flesch = 63 summary = L'agent infectieux étiologique a rapidement été identifié comme étant un nouveau Coronavirus, baptisé Coronavirus associé au Sras (Sras-CoV).La transmission du virus est interhumaine, par les particules respiratoires principalement. n Chine du Sud-Est, au début de l'année 2003, une épidémie de pneumopathie hautement contagieuse et potentiellement mortelle a été signalée par les autorités sanitaires chinoises.Cette entité clinique d'étiologie inconnue a été baptisée Syndrome respiratoire aigu sévère (Sras) par l'Organisation mondiale de la santé (OMS). La ribavirine est un analogue nucléosidique utilisé comme anti-viral dans le traitement de l'hépatite C chronique (Rébétol ® ), en association avec l'interféron α .La ribavirine possédant une activité in vitro contre plusieurs virus respiratoires (virus syncytial respiratoire, virus de la grippe), elle a été utilisée empiriquement par plusieurs équipes chez des patients atteints de Sras. cache = ./cache/cord-304899-vruq4r7z.txt txt = ./txt/cord-304899-vruq4r7z.txt === reduce.pl bib === id = cord-305274-mcsdem7y author = Beniac, Daniel R. title = Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date = 2007-10-24 pages = extension = .txt mime = text/plain words = 5463 sentences = 254 flesch = 51 summary = We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. The structures of ACE2 bound to a fragment of the SARS spike containing the receptor-binding domain and the pre-and postfusion configurations of the fusion core heptad repeats of the spike have been solved to atomic resolution [2, 3, [24] [25] [26] . In addition, the atomic resolution structures of two neutralizing antibodies bound to the SARS spike receptor-binding domain have been solved [27, 28] showing that blocking of the receptor binding domain, preventing attachment of virions to cell-surface ACE2, is the likely mechanism of virus neutralization by these antibodies. cache = ./cache/cord-305274-mcsdem7y.txt txt = ./txt/cord-305274-mcsdem7y.txt === reduce.pl bib === id = cord-305093-og4k3fc7 author = Konno, Yoriyuki title = SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant date = 2020-09-04 pages = extension = .txt mime = text/plain words = 3192 sentences = 210 flesch = 62 summary = Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Although 177 three additional ORF3b proteins of SARS-CoV-related viruses from bats (HKU3-2, 178 GX2013 and Yunnan2011) were shorter than 39 amino acids in length, they did not 179 exhibit anti-IFN-I activity, most likely because of their poor expression and/or 180 stability (Figures 2C and S2B) . mean values of three independent experiments with SEM are shown, 648 and statistically significant differences (P < 0.05) compared to the SeV-infected 649 empty vector-transfected cells (#) and the same amount of the SARS The mean values of three independent 753 experiments with SEM are shown, and statistically significant differences (P < 0.05) 754 compared to the SeV-infected empty vector-transfected cells (#) and the same 755 amount of the SARS-CoV-2 ORF3b WT cache = ./cache/cord-305093-og4k3fc7.txt txt = ./txt/cord-305093-og4k3fc7.txt === reduce.pl bib === id = cord-305139-851v2qr3 author = Peys, Elise title = Haemoptysis as the first presentation of COVID-19: a case report date = 2020-10-22 pages = extension = .txt mime = text/plain words = 2555 sentences = 172 flesch = 53 summary = This case emphasises the added value of bronchoscopy with BAL in the diagnostic work-up in case of high clinical suspicion and negative serial NPS in patients presenting with severe symptoms. Here, we report an unusual case of a man who presented with life-threatening haemoptysis as the first and unique symptom of COVID-19. According to the institutional guidelines during the current COVID-19 pandemic, nasopharyngeal swab (NPS) samples on two consecutive days were obtained and tested for SARS-CoV-2 using real-time polymerase chain reaction (RT-PCR), which repeatedly returned negative. Unusually, in this case, haemoptysis was the initial and unique symptom of SARS-CoV-2 infection in a patient with underlying emphysema. [7] , haemoptysis was the only clinical symptom during the first ten days of the disease course, whereas Casey and co-workers presented a case of COVID-19 associated with acute segmental pulmonary emboli which eventually caused haemoptysis [8] . cache = ./cache/cord-305139-851v2qr3.txt txt = ./txt/cord-305139-851v2qr3.txt === reduce.pl bib === id = cord-305341-nokybn2a author = Zeng, Fanya title = Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments date = 2004-03-19 pages = extension = .txt mime = text/plain words = 3954 sentences = 192 flesch = 51 summary = title: Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments Another interesting finding was that mouse antibodies elicited separately by plasmids encoding S1 and S2 subunits cooperatively neutralized SARS-CoV but neither the S1 nor S2 specific antibodies did, suggesting the possible role of both S1 and S2 subunits in host cell docking and entry. Animals vaccinated with DNA encoding secreting form of E2 glycoprotein of classical swine fever virus (CSFV) showed both CSFV specific antibody response and protection upon viral challenge though the native E2 was anchor membrane protein ( [28, 29] and Zeng et al., unpublished data). In the mice experiment, it was demonstrated that SARS-CoV specific antibodies could be induced by immunization with plasmids encoding S1, S2 and fragment of S1 subunit. The first paper on immunizing masques with structural genes of SARS-CoV, however, reported that co-delivery of three viral genes encoding S1, nucleocapsid (N), and membrane (M) protein could elicit a high titer of neutralizing antibody and T-cell response [24] . cache = ./cache/cord-305341-nokybn2a.txt txt = ./txt/cord-305341-nokybn2a.txt === reduce.pl bib === id = cord-305270-vos341i1 author = Conte, Luana title = Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2455 sentences = 152 flesch = 39 summary = title: Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection 16 Targeting the gut-lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection keywords: anti-inflammatory effects, COVID-19 infection, gut-lung microbiota aixs, high-fibre diet, probiotics, SARS-CoV-2 Among dietary supplements, potential new treatments against COVID-19 infection could be based on probiotics, 17, 22 which might not only reduce colonisation by pathogenic species but also increase commensal bacterial growth in the respiratory tract. Although there is no clinical evidence that targeting the gut-lung microbiota axis would play a therapeutic role in COVID-19 infection, we believe that the manipulation of microbial patterns through the use of probiotics, prebiotics and a high-fibre diet may help to reduce cell inflammation, maintain a healthy gut microbial diversity and strengthen the immune system. cache = ./cache/cord-305270-vos341i1.txt txt = ./txt/cord-305270-vos341i1.txt === reduce.pl bib === id = cord-305511-gdpxvqkk author = Dave, Gaurav S. title = High affinity interaction of Solanum tuberosum and Brassica juncea residue smoke water compounds with proteins involved in coronavirus infection date = 2020-08-11 pages = extension = .txt mime = text/plain words = 3194 sentences = 222 flesch = 48 summary = Phytoconstituents that possess remarkable pharmacological activity were selected as reported from Solanum tuberosum and Brassica juncea residue smoke water (Dave et al., 2018) and Ligand library was prepared of potential molecules to be used for the docking study with human, SARS-CoV and SARS-CoV-2 proteins as given in Table 1 (Sakai et al., 2014) , SARS-CoV-S in complex with ACE2 (PDB: 2AJF) (Li et al., 2005; Micholas & Jeremy, 2020) , PLpro (PDB: 3E9S) , SARS-CoV-2 3CLpro (PDB: 6LU7) , SARS-CoVRdRp (PDB: 6NUR) (Elfiky, 2020) , SARS-CoV-2 spike glycoprotein structure (SARS-CoV-2-S) (PDB: 6VSB) (Grifoni et al., 2020) , binding complex of human ACE2 and RBD (PDB: 6VW1) (Qiu et al., 2020) , SARS-CoV-2-S (closed) (PDB: 6VXX) (Walls et al., 2020) , SARS-CoV-2-S with one S B (open) (PDB: 6VYB) (Walls et al., 2020) and Human angiotensin-converting enzyme 2 (ACE2) (PDB: 1R42) (Jia et al., 2009) are selected for the present study as target proteins ( Figure 1 ). cache = ./cache/cord-305511-gdpxvqkk.txt txt = ./txt/cord-305511-gdpxvqkk.txt === reduce.pl bib === id = cord-305130-vz72ldbo author = Keil, Shawn D. title = Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3457 sentences = 173 flesch = 52 summary = title: Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment CONCLUSION: Riboflavin and UV light effectively reduced the titre of SARS‐CoV‐2 in both plasma and platelet products to below the limit of detection in tissue culture. The author of MERS-CoV study also indicated that they were not able to recover infectious virus from those patient samples using cell culture, suggesting that transfusion transmission is a low risk [15] . As with the plasma study, the virus titre was reduced to the limit of detection (≤0Á25 log PFU/ml) in all three donor platelet units. Riboflavin and UV light effectively reduced the titre of SARS-CoV-2 in both human platelet and plasma products to below the limit of detection using an in vitro plaque assay. Inactivation of Middle East respiratory syndrome coronavirus (MERS-CoV) in plasma products using a riboflavinbased and ultraviolet light-based photochemical treatment cache = ./cache/cord-305130-vz72ldbo.txt txt = ./txt/cord-305130-vz72ldbo.txt === reduce.pl bib === id = cord-305263-fgwf6wy3 author = Wang, Ben X. title = The yin and yang of viruses and interferons date = 2012-02-07 pages = extension = .txt mime = text/plain words = 6285 sentences = 294 flesch = 38 summary = IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. cache = ./cache/cord-305263-fgwf6wy3.txt txt = ./txt/cord-305263-fgwf6wy3.txt === reduce.pl bib === id = cord-305262-23qylbmg author = Rowan, Neil J. title = Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic – Implications for efficacy, re-use and sustainable waste management date = 2020-09-10 pages = extension = .txt mime = text/plain words = 9978 sentences = 575 flesch = 46 summary = Important countermeasures for preventing COVID-19 transmission include mitigating potential high risk aerosol transmission in healthcare setting using medical PPE (such as filtering facepiece respirators (FFRs)) and the appropriate use of face coverings by the general public that carries a lower transmission risk. Given that disposable, plastic-based, PPE (gowns, eye protection, gloves, face masks, filtering facepiece respirators (FFRs)) are heat sensitive, existing healthcare technologies were considered to be either not available, unsuitable or not configured for reprocessing of PPE in healthcare for emergency use (Rowan and Laffey, 2020) . However, potential solutions for effective reprocessing of PPE that considered virus inactivation, material compatibility and device functionality (filtration efficacy, penetration, fit test and so forth) post processing included use of low temperature hydrogen peroxide vapour (VH2O2), ultraviolet germicidal light (UVGI), moist heat, and use of weak bleach for liquid decontamination (Rowan and Laffey, 2020; CDC, 2020) . cache = ./cache/cord-305262-23qylbmg.txt txt = ./txt/cord-305262-23qylbmg.txt === reduce.pl bib === id = cord-304943-thg4fqi2 author = Noor, Aziz Ullah title = Epidemiology of CoViD-19 Pandemic: Recovery and mortality ratio around the globe date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3237 sentences = 217 flesch = 57 summary = SARS-CoV-1 disease was originated in Guangzhou city of China and the start of 2020 was again a challenging year for this country because of extremely contagion 2019-novel coronavirus (2019-nCoV) disease outbreak. Chinese health ministry took immediate action to investigate and control the disease, including quarantine measures, continuous observation of contacts, clinical and epidemiological data collection from infected people and development of diagnostic tools and efficient treatment protocols. 9 Previous study revealed that wet markets of southern China including Wuhan and Guangzhou cities have the greater risk of spreading novel corona viruses, because of wild animal trading and the absence of biosecurity measures. In-vitro studies indicated that Remdesivir has been successful in the termination of viral RNA replication, 30, 32 and showed effectiveness against the MERS-CoV, SARS-CoV and other bat originated coronaviruses. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-304943-thg4fqi2.txt txt = ./txt/cord-304943-thg4fqi2.txt === reduce.pl bib === id = cord-305223-go75cs6r author = Wang, Yafei title = Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3218 sentences = 180 flesch = 52 summary = title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China OBJECTIVES: The aim of this study was to explore the clinical characteristics and risk factors of severe pneumonia caused by the SARS-CoV-2 in Wuhan, China. SPSS was used for data analysis to explore the clinical characteristics and risk factors of patients with severe pneumonia caused by SARS-CoV-2. Statistical analysis showed that advanced age, increased D-Dimer, and decreased lymphocytes were characteristics of the patients with severe pneumonia. Severe pneumonia usually progresses rapidly, and many clinical indicators can change in a short time, especially lymphocyte count, D-Dimer and serum albumin values, and chest CT manifestations. The result suggests that advanced age, lymphocyte decline, and D-dimer elevation are independent risk factors for patients with severe COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China cache = ./cache/cord-305223-go75cs6r.txt txt = ./txt/cord-305223-go75cs6r.txt === reduce.pl bib === id = cord-305234-nclk7bbo author = Do, Mytrang H. title = Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date = 2020-06-27 pages = extension = .txt mime = text/plain words = 146 sentences = 19 flesch = 58 summary = key: cord-305234-nclk7bbo authors: Do, Mytrang H.; Minkis, Kira; Petukhova, Tatyana A.; Lipner, Shari R. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.06.983 sha: doc_id: 305234 cord_uid: nclk7bbo nan . Furthermore, the patient's mouth and nose are often exposed We hope that these suggestions provide the best possible protection for dermatologic efficiency particle air, RT-PCR, reverse transcription-polymerase chain reaction, SARS-CoV-2, 81 severe acute respiratory syndrome coronavirus 2 Head and neck surgery is a high-risk procedure for COVID-19 87 transmission and there is a need for a preventive strategy to protect professionals Detection of SARS-CoV-2 in Different Types of Clinical 4. American College of Surgeons. COVID-19: Considerations for Optimum Surgeon 19/clinical-guidance/surgeon-protection American Academy of Dermatology. Reopening the dermatologic surgery office in the cache = ./cache/cord-305234-nclk7bbo.txt txt = ./txt/cord-305234-nclk7bbo.txt === reduce.pl bib === id = cord-305496-t8ykkekl author = Stone, E. Taylor title = Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date = 2020-08-21 pages = extension = .txt mime = text/plain words = 7227 sentences = 391 flesch = 60 summary = One such tool for evaluating neutralizing antibody response is a 88 plaque/focus neutralization reduction test (PRNT/FRNT), which evaluates the ability of polyclonal 89 sera samples to prevent or reduce infection of a cell monolayer in vitro. We examined the impact of cell density on foci formation for both Vero WHO and Vero E6 cells 144 by plating identical dilutions of SARS-CoV-2 virus stocks on 96-well plates seeded with differing 145 numbers of WHO or E6 cells (3 × 104, 1.5 × 104 or 3 × 104 cells/well) one day prior to infection 146 of the cell monolayer. To determine the optimal time frame for infection of SARS-CoV-2 on a Vero WHO cell 172 monolayer to form individual foci, we tested a variety of incubation times. The FFA relies on an immunostaining protocol of an infected cell monolayer in order to 197 quantify infectious virus titer and is therefore dependent upon SARS-CoV-2-specific antibody 198 cache = ./cache/cord-305496-t8ykkekl.txt txt = ./txt/cord-305496-t8ykkekl.txt === reduce.pl bib === id = cord-305591-ir3wz6nr author = Ji, Danyang title = Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 5138 sentences = 315 flesch = 55 summary = We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). We confirm Gquadruplex structure forming in the top-ranked PQSs by multiple spectroscopic assays in vitro and characterize the crosstalk between G-quadruplexes and viral helicase by microscale thermophoresis (MST) and molecular docking. Our analysis of Gquadruplex-forming sequences in SARS-CoV-2 provides insights into the design of anti-viral treatment by targeting the viral helicase and G-quadruplex structures. Interestingly, PQSs at positions 13385 and 24268 with the highest G-scores indicating high probability to adopt G-quadruplex structures only share high sequence similarity to the bat CoVs (see Supplementary Information S1 available online at https://academic.oup.com/bib and Table 2 ). In comparison, our G-quadruplex search across the genome of SARS-CoV-2 also identified a number of GG PQSs. PQS at position 13385 was confirmed to adopt G-quadruplex structures, which also contains a [GAAAG] sequence in the middle ( Table 1 ). cache = ./cache/cord-305591-ir3wz6nr.txt txt = ./txt/cord-305591-ir3wz6nr.txt === reduce.pl bib === id = cord-305581-0bqxwh1o author = Hassan, Sk. Sarif title = Molecular phylogeny and missense mutations of envelope proteins across coronaviruses date = 2020-09-12 pages = extension = .txt mime = text/plain words = 2000 sentences = 109 flesch = 57 summary = The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations. In the Table 1 , total number of available CoV genomes of respective hosts as well as distinct number of envelope proteins are presented. It is noted that the envelope (E) protein of the CoVs of Pangolin and Chimpanzee are found to be 100% conserved as presented in Table 1 and consequently no mutation was found over there. Among 79 available complete CoV genomes of Bat, twenty-five sequences possess various mutations in the three domains of the E protein as presented in the Fig.2 . Based on mutation characteristics and amino acid conservations over the E proteins across various host CoVs, this report predicts potential close kins of human SARS-CoV2 as the Pangolin-CoV and Bat-CoV which was also reported in a recent study [21] . cache = ./cache/cord-305581-0bqxwh1o.txt txt = ./txt/cord-305581-0bqxwh1o.txt === reduce.pl bib === id = cord-305534-936peb1n author = Johnson, Kemmian D. title = Pulmonary and Extra-Pulmonary Clinical Manifestations of COVID-19 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 6712 sentences = 346 flesch = 43 summary = The severe acute respiratory syndrome coronavirus−2 (SARS-CoV-2) has been recently identified as the culprit of the highly infectious, outbreak named coronavirus disease 2019 (COVID-19) in China. While it is known that COVID-19 manifests similarly to the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2012 Middle East Respiratory Syndrome (MERS), primarily affecting the pulmonary system, the impact of the disease extends far beyond the respiratory system and affects other organs of the body. In the severe disease state, the patient's clinical course is complicated by the development of pneumonia with ARDS, acute hypoxic respiratory failure, and/or death (7) . Several retrospective studies have consistently reported pulmonary manifestations in patients with COVID-19, which include cough, shortness of breath, sputum production, respiratory failure, and ARDS (Table 1) (5, 7, (9) (10) (11) (12) (13) (14) (15) (16) (17) . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-305534-936peb1n.txt txt = ./txt/cord-305534-936peb1n.txt === reduce.pl bib === id = cord-305589-ofpna4k1 author = Schubert, Katharina title = SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date = 2020-07-07 pages = extension = .txt mime = text/plain words = 4090 sentences = 229 flesch = 55 summary = By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. Based on these results we assembled in vitro a 40S-Nsp1 complex and determined its structure at 2.8 Å resolution using cryo-EM (Extended Data Fig. 2 ). As observed in the high-resolution structure of the 40S-Nsp1 complex, the C-terminal part of Nsp1 in the mRNA entrance channel (Fig. 1e ) folds into two helices that interact with h18 of the 18S rRNA as well as proteins uS3 in the head and uS5 and eS30 in the body, respectively ( Fig. 1f; Fig. 2a ). Our structural data suggest that SARS-CoV-2 Nsp1 inhibits translation by sterically occluding the entrance region of the mRNA channel and interfering with binding of cellular mRNAs (Fig. 4a,b) . cache = ./cache/cord-305589-ofpna4k1.txt txt = ./txt/cord-305589-ofpna4k1.txt === reduce.pl bib === id = cord-305266-fuaq4ujb author = Gong, Yue title = Early Research on COVID-19: A Bibliometric Analysis date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2118 sentences = 125 flesch = 44 summary = In this review, we found that because of the rapid response of researchers worldwide, the number of COVID-19-related publications showed a high growth trend in the first ten days of February; among these, the largest number of studies originated in China, the country most affected by pandemic in its early stages. The Coronavirus Study Group 4 (CSG) of the International Committee on Taxonomy of Viruses designated the causative 5 virus as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease, 6 which subsequently spread globally, was named coronavirus disease of 2019 7 COVID-19, covering topics such as etiology, diagnosis, epidemiology, treatment, 24 prognosis, nursing, prevention and control, were available in the PubMed and China 25 national knowledge infrastructure (CNKI) databases. Escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in Hong Kong cache = ./cache/cord-305266-fuaq4ujb.txt txt = ./txt/cord-305266-fuaq4ujb.txt === reduce.pl bib === id = cord-305582-3hmsknon author = Li, Lei title = Therapeutic strategies for critically ill patients with COVID-19 date = 2020-04-20 pages = extension = .txt mime = text/plain words = 6155 sentences = 310 flesch = 39 summary = In the present article, we have summarized the promising drugs, adjunctive agents, respiratory supportive strategies, as well as circulation management, multiple organ function monitoring and appropriate nutritional strategies for the treatment of COVID-19 in the ICU based on the previous experience of treating other viral infections and influenza. According to the latest version of diagnosis and treatment guidelines, confirmed cases infected with 2019-nCoV are classified to have severe illness once complying with one of the following symptoms: (1) anhelation, respiratory rate ≥ 30 times/min; (2) oxygen saturation at rest ≤ 93%; (3) PaO2/FiO2 ≤ 300 mmHg; and classified to be the critical/life-threatening illness once complying with one of the following symptoms: (1) respiratory failure, mechanical ventilation needed; (2) shock; (3) other organ dysfunction syndrome and requirement of intensive care unit admission. cache = ./cache/cord-305582-3hmsknon.txt txt = ./txt/cord-305582-3hmsknon.txt === reduce.pl bib === id = cord-305742-wf6qxplf author = Gomez, Santiago A. title = Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3457 sentences = 176 flesch = 53 summary = In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. cache = ./cache/cord-305742-wf6qxplf.txt txt = ./txt/cord-305742-wf6qxplf.txt === reduce.pl bib === id = cord-305616-2obemy16 author = Montes, Maria Teresa title = Neonatal nursing in the COVID-19 pandemic: can we improve the future? date = 2020-07-10 pages = extension = .txt mime = text/plain words = 3520 sentences = 162 flesch = 46 summary = Contingency plans due to the covid-19 pandemic have impacted on three key areas: 1) the organization and workflow of neonatal units, 2) perinatal and neonatal care, including breastfeeding, and 3) communicationcollaboration with parents. Many centres have adopted very restrictive policies to care for pregnant women who are positive for SARS-CoV-2 in the maternal area, as well as in the NUs, in order to control the spread of the virus and protect health professionals. Initial recommendations to the management regarding the SARS-CoV-2-positive puerperant supported changes to delivery plans by introducing restrictions, both in vaginal deliveries and caesarean sections on the presence of the other parent at childbirth and postpartum unit, early skin-to-skin contact, and late-cord clamping . In addition to frequent hand-washing, cleaning of the breast before breastfeeding and skin-to-skin contact, and wearing face masks, the risk to others can be reduced, for example, by testing parents and health professionals for SARS-CoV-2 and restricting their access to where their child is placed. cache = ./cache/cord-305616-2obemy16.txt txt = ./txt/cord-305616-2obemy16.txt === reduce.pl bib === id = cord-305587-xtqvtleb author = Ma, Cuiqing title = From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2310 sentences = 122 flesch = 40 summary = Identification and characterization of novel neutralizing epitopes in the 506 receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic determinants in inactivated 507 SARS-CoV vaccine Intranasal vaccination of recombinant adeno-associated virus 533 encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces 534 strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of SARS-CoV spike protein induces highly 556 potent neutralizing antibodies: implication for developing subunit vaccine Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies 613 primarily targeting the receptor binding region Receptor-binding domain of severe acute respiratory syndrome coronavirus 621 spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies. Cross-neutralization of human and palm civet severe acute 636 respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein cache = ./cache/cord-305587-xtqvtleb.txt txt = ./txt/cord-305587-xtqvtleb.txt === reduce.pl bib === id = cord-305610-v1hn934x author = Kerslake, Rachel title = Co-expression of peripheral olfactory receptors with SARS-CoV-2 infection mediators: Potential implications beyond loss of smell as a COVID-19 symptom date = 2020-06-17 pages = extension = .txt mime = text/plain words = 3002 sentences = 141 flesch = 41 summary = Using Gene Expression Profiling Interactive Analysis, The Cancer Genome Atlas, Genotype-Tissue Expression, cBioPortal and Shiny Methylation Analysis Resource Tool, we highlight the expression of peripheral ORs in both healthy and malignant tissues, and describe their co-expression with key mediators of SARS-CoV-2 infection, such as ACE2 and TMPRSS2, as well as cathepsin L (CTSL; another cellular protease mediating SARS-CoV-2 infection of host cells). The present study aimed to identify, both in normal and cancer tissues, the co-expression profile of a number of ORs which are known to be expressed in peripheral tissues in relationship to key mediators of the SARS-coV-2 infection, namely AcE2, TMPRSS2 and cTSL. In conclusion, the present study offers new data regarding the expression of ORs in peripheral tissues and their co-expression pattern with key mediators of SARS-coV-2 cell entry and infection (i.e., AcE2, TMPRSS2, and cTSL). cache = ./cache/cord-305610-v1hn934x.txt txt = ./txt/cord-305610-v1hn934x.txt === reduce.pl bib === id = cord-305521-lkou3ycu author = Michel, W. title = A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay date = 2020-09-27 pages = extension = .txt mime = text/plain words = 1072 sentences = 104 flesch = 65 summary = title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay Conclusions: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. A meta-53 analysis of different SARS-CoV-2 studies showed the highest detection rates in Expected shortages of swabs led us to assess alternative diagnostic specimens. In 59 this study, we compared test performance when using mouthwash or a combined oro-60 nasopharyngeal swab. This may limit its use in patients 144 to minimize exposure of health-care personel.In conclusion, SARS-CoV2 detection 145 with mouthwash showed a low sensitivity compared to oro-nasopharyngeal swabs. cache = ./cache/cord-305521-lkou3ycu.txt txt = ./txt/cord-305521-lkou3ycu.txt === reduce.pl bib === id = cord-305422-t8azymo7 author = Yi, Ye title = COVID-19: what has been learned and to be learned about the novel coronavirus disease date = 2020-03-15 pages = extension = .txt mime = text/plain words = 8300 sentences = 446 flesch = 53 summary = The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. The virus is highly homologous to the coronavirus (CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003; thus, it was named SARS-CoV-2 by the World Health Organization (WHO) on February 11, 2020, and the associated disease was named CoV Disease-19 (COVID-19) [1] . Whenever possible, we will try to compare COVID-19 with SARS and another CoV-caused disease, Middle East respiratory syndrome (MERS, an outbreak in 2012). Due to the lack of experience with the novel CoV, physicians can mainly provide supportive care to COVID-19 patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other CoVs such as SARS-CoV and MERS-CoV and other viral diseases ( Table 2) . cache = ./cache/cord-305422-t8azymo7.txt txt = ./txt/cord-305422-t8azymo7.txt === reduce.pl bib === id = cord-305330-mklkugj5 author = Moiseev, Sergey title = Cancer in intensive care unit patients with COVID-19 date = 2020-05-28 pages = extension = .txt mime = text/plain words = 489 sentences = 35 flesch = 49 summary = susceptible to severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection and complications, although data on COVID-19 and malignancies remain limited. noted that patients with cancer were more likely to experience severe sequelae of SARS-CoV-2 infection, such as intensive care admission, invasive ventilation or death. 2 However, Wang and Zhang argued that the most important morbidity factor is exposure to an infection source, whereas worse outcomes from SARS-CoV-2 infection could be associated (at least partly) with older age of patients with cancer 3 . In a nationwide study, we evaluated the prevalence of malignancies among 1307 intensive care unit (ICU) patients with SARS-CoV-2 pneumonia who required respiratory support. However, our data suggest that other factors, such as older age and comorbidities, contribute significantly to the more severe course of SARS-CoV-2 infection in cancer patients. cache = ./cache/cord-305330-mklkugj5.txt txt = ./txt/cord-305330-mklkugj5.txt === reduce.pl bib === id = cord-305632-xbji6g5x author = Uccelli, Matteo title = COVID-19 and Obesity: Is Bariatric Surgery Protective? Retrospective Analysis on 2145 Patients Undergone Bariatric-Metabolic Surgery from High Volume Center in Italy (Lombardy) date = 2020-10-31 pages = extension = .txt mime = text/plain words = 2889 sentences = 167 flesch = 49 summary = There are also emerging data indicating that obesity is an independent predictor of intensive care unit (ICU) admission, mechanical ventilation, and death [6, 11, 12] , and in a recent report from a large cohort of COVID-19 patients in New York, obesity was found to be one of the most common associated comorbidities in hospitalized patients [13, 14] . We therefore analyzed a significant number of patients to evaluate the spread and the effects of the SARS-CoV-2 infection in a population of patients who had undergone bariatric surgery. Therefore, our data are encouraging, considering that these patients were obese: bariatric surgery and the consequent weight loss seem to significantly lower the risk of serious consequences due to COVID infection. Bariatric surgery, therefore, can be considered a protective factor with respect to the onset of severe respiratory disease resulting from infection with SARS-CoV-2. cache = ./cache/cord-305632-xbji6g5x.txt txt = ./txt/cord-305632-xbji6g5x.txt === reduce.pl bib === id = cord-305763-160heazx author = Lai, Chih-Cheng title = Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date = 2020-10-09 pages = extension = .txt mime = text/plain words = 4257 sentences = 264 flesch = 61 summary = One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. cache = ./cache/cord-305763-160heazx.txt txt = ./txt/cord-305763-160heazx.txt === reduce.pl bib === id = cord-305788-z75yv88e author = Agergaard, Charlotte Nielsen title = Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date = 2020-09-28 pages = extension = .txt mime = text/plain words = 727 sentences = 64 flesch = 61 summary = Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. cache = ./cache/cord-305788-z75yv88e.txt txt = ./txt/cord-305788-z75yv88e.txt === reduce.pl bib === id = cord-305703-ypeibwje author = Veronese, Nicola title = Use of Corticosteroids in Coronavirus Disease 2019 Pneumonia: A Systematic Review of the Literature date = 2020-04-24 pages = extension = .txt mime = text/plain words = 2878 sentences = 144 flesch = 37 summary = For each article, we extracted data regarding authors, year of publication, country, city or region in which the study was conducted, the period of observation, how the diagnosis of COVID-19 was obtained, the stage of COVID-19 infection (asymptomatic forms, pneumonia, acute respiratory distress syndrome (ARDS), requiring intensive care unit, ICU; convalescent), sample size included, number of males and females, mean age and its standard deviation (or similar information such as median and range), the percentage of people treated with corticosteroids in the sample as a whole, and, if possible, the route of administration and type of corticosteroid considered. Overall, two studies reported negative findings regarding these medications, one reported no significant association between corticosteroids and clinical outcomes, and one concluded that methylprednisolone was associated with a significant reduction of mortality in patients with COVID-19 pneumonia developing ARDS. cache = ./cache/cord-305703-ypeibwje.txt txt = ./txt/cord-305703-ypeibwje.txt === reduce.pl bib === id = cord-305755-6jup93v4 author = Gouveia, Duarte title = Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date = 2020-07-22 pages = extension = .txt mime = text/plain words = 6708 sentences = 328 flesch = 50 summary = In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analyzed by MS/MS with a short gradient. To foster the development of alternative detection methods for SARS-CoV-2, we performed a proof-of-concept study to assess the potential of MS/MS for proteotyping SARS-CoV-2: (i) in simulated nasal swabs containing different quantities of viral peptides and (ii) in nasopharyngeal swabs from COVID-19 diagnosed patients. cache = ./cache/cord-305755-6jup93v4.txt txt = ./txt/cord-305755-6jup93v4.txt === reduce.pl bib === id = cord-305704-grzrkff9 author = Almutairi, Abdulelah title = Dermatological Manifestations in Patients With SARS-CoV-2: A Systematic Review date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2289 sentences = 134 flesch = 46 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been initially defined as a disease of the respiratory tract; however, with the increasing number of patients and announcing that the virus became a pandemic, new systemic clinical manifestations are observed, including dermatological manifestations. The following step was filtering the results to include only original research studies investigating the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. The results were then filtered to include only original research studies examining the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. After searching the abstracts and reviewing the eligibility criteria in identified potential abstracts, a total of seven studies [14] [15] [16] [17] [18] [19] [20] were considered as eligible to be included in the present systematic review, covering a total of 555 patients with SARS-CoV-2 who had dermatological symptoms in the form of skin lesions. cache = ./cache/cord-305704-grzrkff9.txt txt = ./txt/cord-305704-grzrkff9.txt === reduce.pl bib === id = cord-305931-0pgu2gvh author = Janus, Scott E title = COVID19: a case report of thrombus in transit date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1431 sentences = 85 flesch = 43 summary = In view of the fact that the utility of tissue plasminogen activator in this population is not well studied, we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. 4 Although the utility of tissue plasminogen activator (TPA) for thrombus in transit in other clinical settings has previously been reported, 5 the literature regarding cardiovascular events in SARS-CoV-2 remains scarce; we therefore describe the case of a 64-year-old male who presented with Learning points SARS-CoV-2 pneumonia, who was found to have extensive clot in transit on echocardiography and underwent successful lytic therapy. In view of the fact that the utility of TPA in this population is not well studied, 10 we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. cache = ./cache/cord-305931-0pgu2gvh.txt txt = ./txt/cord-305931-0pgu2gvh.txt === reduce.pl bib === id = cord-305770-xygg4lxu author = Busetto, Gian Maria title = SARS-CoV-2 Infection and High-Risk Non-Muscle-Invasive Bladder Cancer: Are There Any Common Features? date = 2020-06-09 pages = extension = .txt mime = text/plain words = 6963 sentences = 343 flesch = 40 summary = Most severe cases of COVID-19 and high-risk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). Most severe cases of COVID-19 and highrisk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). When compared with COVID-19 patients without ARDS, patients with ARDS are generally older and have a higher proportion of comorbidities, and there are more observations of neutrophilia associated with lymphocytopenia, neutrophil-to-lymphocyte ratio (NLR) increase, increase in several inflammation indices (including interleukins, IL-2 and IL-6, tumor necrosis factor α, C-reactive protein and many other cytokines), elevated coagulation function and alteration of other organ dysfunction indices (liver, kidney, etc.) [4] . The following terms were the most commonly used: SARS-CoV-2, COVID-19, bladder cancer, risk factors, diabetes, obesity, aging, inflammation, cytokine, interleukin (IL), IL-6, smoking. cache = ./cache/cord-305770-xygg4lxu.txt txt = ./txt/cord-305770-xygg4lxu.txt === reduce.pl bib === id = cord-305798-7b8rua4z author = Rivas-García, S title = Rhabdomyolysis as the main manifestation of coronavirus disease 2019 date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1133 sentences = 76 flesch = 53 summary = Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China in the late December 2019. Recent patient case series published in the setting of COVID-19 infection in China have described myalgia and elevated CK as frequent findings. High levels of CK-MB (muscle and brain isoform) were found in 4.5% of a 201 patient case series in Wuhan, [3] showing a significant association with acute respiratory syndrome distress development. Muscle weakness and elevated serum CK levels were also commonly found in coronavirus case series reported in the 2003 outbreak of SARS and the 2012 outbreak of Middle East respiratory syndrome (MERS) [4] . Even if myalgia and CK elevation are relatively frequent, rhabdomyolysis symptoms have been rarely reported in SARS-CoV-2 outbreaks. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China cache = ./cache/cord-305798-7b8rua4z.txt txt = ./txt/cord-305798-7b8rua4z.txt === reduce.pl bib === id = cord-305640-tgowzrqo author = Li, Yong-Hua title = Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: Comparison with results of other viral markers date = 2005-07-15 pages = extension = .txt mime = text/plain words = 3688 sentences = 174 flesch = 59 summary = A capture enzyme-enhanced chemiluminescence immunoassay (ECLIA) based on three specific monoclonal antibodies to detect the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in the serial serum samples from SARS patients was developed. The N protein is an extensively phosphorylated, highly basic protein, which interacts with viral RNA and makes up the viral core and nucleocapsid (Lai, 2003 the diagnosis of SARS depends basically upon detecting SARS-CoV RNA by RT-PCR and/or testing specific antibodies directed against SARS-CoV by assays based on cultured virus or recombinant viral antigens. In the present study, a capture ECLIA was developed based on three monoclonal antibodies directed against the N protein of SARS-CoV, and the N protein in the longitudinal serum samples from the SARS patients were detected with this method. The detection of the N protein of SARS-CoV in serum samples by ECLIA appears to be superior to the detection of the viral RNA by RT-PCR in rapid diagnosis of SARS patients. cache = ./cache/cord-305640-tgowzrqo.txt txt = ./txt/cord-305640-tgowzrqo.txt === reduce.pl bib === id = cord-306373-61snvddh author = Xu, Xiao-Wei title = Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series date = 2020-02-19 pages = extension = .txt mime = text/plain words = 3594 sentences = 204 flesch = 56 summary = OBJECTIVE: To study the clinical characteristics of patients in Zhejiang province, China, infected with the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) responsible for coronavirus disease 2019 (covid-2019). Since the outbreak of covid-19, strict precautionary measures have been implemented in Zhejiang province, including the creation of fever clinics that exclusively receive patients with suspected SARS-Cov-2 infection, defined as presenting with a fever or any respiratory symptoms, including dry cough, and especially in those with a history of travel to Wuhan or exposure to infected people within two weeks before the onset of illness since January 2020. The incubation period was defined as the time from exposure to the onset of illness, which was estimated among patients who could provide the exact date of close contact with individuals from Wuhan with confirmed or suspected SARS-Cov-2 infection. cache = ./cache/cord-306373-61snvddh.txt txt = ./txt/cord-306373-61snvddh.txt === reduce.pl bib === id = cord-306108-ja0wyr5w author = B K, Anupama title = A Review of Acute Myocardial Injury in Coronavirus Disease 2019 date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4754 sentences = 219 flesch = 34 summary = Although SARS-CoV-2 infection predominantly causes pulmonary complications, such as pneumonia and ARDS, the disease has also been associated with a variety of cardiovascular complications, including acute myocardial injury, myocarditis, arrhythmia, heart failure, and venous thromboembolism [6] . Hence, one potential explanation for the higher likelihood of acquiring infection, and the increased risk of severe disease and adverse outcomes in patients with COVID-19 with pre-existing CVD, maybe the elevated secretion of ACE2 in these patients, thus making them more susceptible to direct viral damage to cardiac myocytes [33] ; but, this has not yet been demonstrated in pathology studies. In a single-center, retrospective cohort study including 188 patients with COVID-19 in Wuhan, China, conducted to explore whether heart injury occurred during COVID-19 on admission and later increased mortality, approximately 11.2% of patients had high-sensitivity cardiac troponin I (hs-TnI) exceeding the clinical upper normal limit on admission. cache = ./cache/cord-306108-ja0wyr5w.txt txt = ./txt/cord-306108-ja0wyr5w.txt === reduce.pl bib === id = cord-305745-9lngdjow author = Solnier, Julia title = Flavonoids: A complementary approach to conventional therapy of COVID-19? date = 2020-09-18 pages = extension = .txt mime = text/plain words = 9494 sentences = 469 flesch = 48 summary = Chalcones isolated from Angelica keiskei were shown to inhibit both SARS-CoV proteases PLpro and 3CLpro in enzymatic, FRET-based (Table 2) and molecular docking studies (Park et al. As Table 2 demonstrates, the compounds showed generally higher inhibitory potential against SARS-CoV PLpro than when tested against the other viral proteases using fluorogenic methods, which is likely related to genomic variations in the single amino acid sequences. In particular, herbacetin, quercetin and isobavachalcone (Fig. 3) were identified as promising antiviral leads against SARS-and MERS-CoV based on their broad-spectrum activity against the viral proteases 3CL and PL of both CoVs, the number of relevant literature data, and the availability of the compounds from different plant sources. However, despite some promising inhibitory activities of flavonoids against SARS-and MERS-CoV in vitro, none of these compounds have been tested in vivo using animal and/or human cell models. cache = ./cache/cord-305745-9lngdjow.txt txt = ./txt/cord-305745-9lngdjow.txt === reduce.pl bib === id = cord-305956-l02xdq87 author = Alqahtani, Saleh A title = Liver injury in COVID-19: The current evidence date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3062 sentences = 198 flesch = 44 summary = These reports highlighted that beyond severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a complicated course of the disease or even viral infection itself can lead to involvement of other organs and multiorgan failure. The current review summarizes the pathophysiology and potentially specific role of COVID-19 in liver disease based on the available data and case series published, ahead of print and non-peer-reviewed preprints as of 2 April. In this study, 47.3% of the discharged patients showed elevated LFTs at baseline, and 23.7% developed abnormalities during hospitalization, suggesting emerging liver injury from drugs or during the course of the infection. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: A single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series cache = ./cache/cord-305956-l02xdq87.txt txt = ./txt/cord-305956-l02xdq87.txt === reduce.pl bib === id = cord-305564-dj3vj4tk author = DeDiego, Marta L. title = PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date = 2008-07-01 pages = extension = .txt mime = text/plain words = 6065 sentences = 287 flesch = 53 summary = All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR cache = ./cache/cord-305564-dj3vj4tk.txt txt = ./txt/cord-305564-dj3vj4tk.txt === reduce.pl bib === id = cord-306390-pzzev8hd author = Reisinger, Emil C. title = Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1531 sentences = 180 flesch = 57 summary = title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest Somit kann die Bestimmung der Antikörper gegen SARS-CoV-2 bei Müttern indirekt Auskunft über den Infektionsstatus bei deren Kindern geben. Für den in dieser Studie verwendeten ELISA-Test zum Nachweis von SARS-CoV-2-Antikörpern (Euroimmun) wird in der Literatur eine hohe Sensitivität und Spezifität angegeben [6] . In dieser Pilotstudie wurden 401 Mütter von Kindern im Alter von 1-10 Jahren als Sentinel untersucht, um die Prävalenz der Infektion mit SARS-CoV-2 auch bei Kindern abzuschätzen. Die Aussagekraft dieser Studie zur Prävalenz der Infektion mit SARS-CoV-2 bei Müttern ist durch die relativ geringe Fallzahl (5 % der Mütter mit schulpflichtigen Kindern in Rostock) limitiert. Da in dieser Studie durch die indirekte Immunfluoreszenz weder das positive Ergebnis des ELISA für IgG, noch die 11 positiven und 3 grenzwertigen Ergebnisse des ELISA für IgA bestätigt wurden, empfehlen wir, positive SARS-CoV-2-Antikörperbefunde in den hier verwendeten ELISA-Tests mittels Bestätigungstests (z. cache = ./cache/cord-306390-pzzev8hd.txt txt = ./txt/cord-306390-pzzev8hd.txt === reduce.pl bib === id = cord-305858-gp1u4kh7 author = Song, Xiang title = High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date = 2020-07-19 pages = extension = .txt mime = text/plain words = 4896 sentences = 268 flesch = 49 summary = To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. To determine whether platelets were directly targeted by SARS-CoV-2 or trigged by viral inflammatory reactions, we examined the ACE2 expression on the highly-purified CD41b + CD42a + platelets from human peripheral blood ( Figure 3A Our previous work established that platelets could release mitochondria contributing to the immune modulation and islet b-cell regeneration [13] . Thus, the virus-infected alveolar macrophages play a critical role in the pathogenesis of COVID-19 and SARS [28] [29] [30] and may recruit the lung infiltration of additional immune cells through predominantly releasing cytokines and chemokines [31, 32] , resulting in pulmonary edema and hypoxemia: the hallmark of acute respiratory distress syndrome (ARDS) ( Figure 6 ). cache = ./cache/cord-305858-gp1u4kh7.txt txt = ./txt/cord-305858-gp1u4kh7.txt === reduce.pl bib === id = cord-305856-xt3zxajf author = Shanmugam, Chandrakumar title = COVID-2019 – A comprehensive pathology insight date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4597 sentences = 325 flesch = 46 summary = Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. The current pandemic of corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2) led to complete lockdown in many countries contributing to major socio-economic crisis and irreparable recession, globally. [22, 31, 32, 33] Similar to SARS CoV, a recent study reported non-O blood group specifically group A had higher infection and death rates due to COVID-19 owing to absence of protective anti-A IgM antibodies. Pulmonary pathology of early phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer The clinical pathology of severe acute respiratory syndrome (SARS): a report from China cache = ./cache/cord-305856-xt3zxajf.txt txt = ./txt/cord-305856-xt3zxajf.txt === reduce.pl bib === id = cord-306308-zjq6cscm author = de Moura, Ronald Rodrigues title = Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2514 sentences = 175 flesch = 54 summary = Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. cache = ./cache/cord-306308-zjq6cscm.txt txt = ./txt/cord-306308-zjq6cscm.txt === reduce.pl bib === id = cord-305816-06lddk87 author = Musarrat, Farhana title = The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3227 sentences = 189 flesch = 52 summary = title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections A systematic screening of several drugs including cardiac glycosides and kinase inhibitors and inhibitors of human immunodeficiency virus (HIV) entry revealed that only the FDA‐approved HIV protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S‐n‐ and S‐o‐mediated cell fusion with complete inhibition at a 10‐μM concentration. 26 In addition to its potent activity against the HIV protease, nelfinavir mesylate was found to produce multiple effects on cellular processes including the induction of apoptosis and necrosis as well as induction of cell-protective mechanisms, including cell cycle retardation and the unfolded protein response. HRP, horseradish peroxidase; SARS CoV, severe acute respiratory syndrome coronavirus; Sn, S-new Recently, it was shown that a peptide that targeted the S-n HR1 domain S inhibited SARS-CoV-2 virus replication, virus entry, and virus-induced cell fusion. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides cache = ./cache/cord-305816-06lddk87.txt txt = ./txt/cord-305816-06lddk87.txt === reduce.pl bib === id = cord-306351-ka6asw3m author = Alsuliman, Tamim title = A review of potential treatments to date in COVID-19 patients according to the stage of the disease date = 2020-05-30 pages = extension = .txt mime = text/plain words = 6057 sentences = 374 flesch = 48 summary = Several trials of Remdesivir treatment on few patients in the United States have shown early promising benefits in cases with severe pneumonia [33, 34] . On the other hand, data emerging from other ongoing Chinese trials have demonstrated that CQ phosphate is superior to a control treatment in the following areas: pneumonia exacerbation inhibition, imaging findings improvement, virus negative conversion promoting, and disease course shortening [62] . For example, clinical data from reliable randomized controlled studies are still missing, and data published to date lacks homogeneity in terms of recommended dose concentration, treatment duration, and severity of patient illness [58] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The experience of clinical immunologists from China cache = ./cache/cord-306351-ka6asw3m.txt txt = ./txt/cord-306351-ka6asw3m.txt === reduce.pl bib === id = cord-306085-gnrnsxej author = Hassan, Sk. Sarif title = SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences date = 2020-07-05 pages = extension = .txt mime = text/plain words = 963 sentences = 69 flesch = 67 summary = The envelope protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane domain and (C)-terminus in 15 (0.414%) genomes among 3617 available SARS-CoV2 genomes. Here, we present the non-synonymous mutations of the envelope protein over the available 3617 SARS-CoV2 genomes (Table 1) . It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contain the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes.  In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617 on which the present study of mutation over the envelope protein is made. More precisely, it is to be mentioned that 10(0.386\%) out of 2588 genomes from the USA, 3(0.806\%) from Asia, 1 (0.348\%) from Europe and 1 (0.274\%) from Oceania contain the missense mutations over the envelope proteins of SARS-CoV2 genomes. cache = ./cache/cord-306085-gnrnsxej.txt txt = ./txt/cord-306085-gnrnsxej.txt === reduce.pl bib === id = cord-306438-db2rqz4d author = Kalathiya, Umesh title = Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date = 2020-05-14 pages = extension = .txt mime = text/plain words = 6921 sentences = 354 flesch = 49 summary = An important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. These findings identify a novel small molecule binding-site formed by the spike protein oligomer, that might assist in future drug discovery programs aimed at targeting the coronavirus (CoV) family of viruses. Our current study focuses on understanding the variability of the trimer spike glycoprotein in SARS-CoV-2 with respect to the genomes from other coronavirus strains, and identifying the changes in the molecular properties due to conformational flexibility in the spike protein. Our data suggest a mechanism whereby Chitosan (and possibly its derivatives), as well as macrolide type molecules, might bind to a pocket formed by the spike protein trimer and provide a novel domain to focus on for future drug discovery projects. cache = ./cache/cord-306438-db2rqz4d.txt txt = ./txt/cord-306438-db2rqz4d.txt === reduce.pl bib === id = cord-306465-7kevsl1z author = Agarwal, Krishna Mohan title = Study and Overview of the Novel Corona Virus Disease (COVID-19) date = 2020-09-06 pages = extension = .txt mime = text/plain words = 2645 sentences = 170 flesch = 59 summary = In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. The current global pandemic is caused by the "novel coronavirus disease (2019-nCoV) or severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) popularly known as COVID19 Hunan seafood market was sealed, on 7 th January roughly a week after China's notification of a possible outbreak the disease was confirmed to be the novel coronavirus disease or COVID-19 which has more than 95% homology with bat coronavirus and almost 70% similarity to the SARS CoV-1 Flatten the curve is a statement used during healthcare emergencies, its basic concept is to limit the spread of the virus such that at any given time during a pandemic the total number of patients required to be hospitalized is less than the maximum capacity of the state's health infrastructure. cache = ./cache/cord-306465-7kevsl1z.txt txt = ./txt/cord-306465-7kevsl1z.txt === reduce.pl bib === id = cord-306017-4wf4yhyz author = d'Aloja, Ernesto title = COVID-19 and medical liability: Italy denies the shield to its heroes date = 2020-07-24 pages = extension = .txt mime = text/plain words = 1005 sentences = 56 flesch = 54 summary = As well known, Italy is one of the Countries in a worldwide context more severely affected by the SARS-CoV-2 pandemic and some of the northern regions paid the highest price in terms of deaths among health care workers (HCWs).The 'Istituto Nazionale Assicurazione Infortuni sul Lavoro' (INAIL), the Italian public insurance body that protects workers in the event of accidents and occupational diseases, reported that 40% of the 236 filedfatal cases involved HCWs [1] . From a negligent pandemic point of view, this may mean that if the hospital À even a no-COVID one -does not provide for all these measures, and one or more cases of SARS-COV-2 positive patients are detected in the healthcare facility, a presumption of liability may be enough to pursuing a negligent pandemic crime (article 452, Italian penal code). cache = ./cache/cord-306017-4wf4yhyz.txt txt = ./txt/cord-306017-4wf4yhyz.txt === reduce.pl bib === id = cord-306332-ug6pare2 author = Chen, Ze-Liang title = From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2008 sentences = 123 flesch = 53 summary = title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends [1, 2] The 2019 novel coronavirus (2019-nCoV) caused a pneumonia outbreak, which is spreading around the country and has affected 32 provinces and regions of China as of January 27, 2020. [14, 15] Subsequent case investigations also showed that SARS-CoV had the capability to multiply and continuously undergo human-to-human transmission [Supplementary Figure 2C , http://links.lww.com/CM9/ A209]; at least four generations of cases were identified from one original patient. [18] On January 19, 2020, a cluster of cases, including 15 healthcare workers, were confirmed to have been infected via patients, confirming that 2019-nCoV also has humanto-human transmission capability. Transmission and epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected pneumonia (COVID-19): preliminary evidence obtained in comparison with 2003-SARS cache = ./cache/cord-306332-ug6pare2.txt txt = ./txt/cord-306332-ug6pare2.txt === reduce.pl bib === id = cord-306365-7cydmgn2 author = Ami, Yasushi title = Co‐infection of respiratory bacterium with severe acute respiratory syndrome coronavirus induces an exacerbated pneumonia in mice date = 2008-04-01 pages = extension = .txt mime = text/plain words = 5090 sentences = 250 flesch = 55 summary = Our results show that both low-virulent Pp infection, and administration of LPS derived from Escherichia coli, induced elastase in the lungs and enhanced the replication of SARS-CoV, resulting in exacerbation of the respiratory disease caused by SARS-CoV infection and a high mortality rate. Thus, mice co-infected with Pp + Fr-mo developed severe respiratory disease, suggesting the possibility that elastase produced by Pp infection exacerbated infection by SARS-CoV adapted to mice. An important condition for sustaining high titers beyond four days p.i. would be that of high replication in the lungs in an early phase of infection, which could be facilitated by elastase induced by Pp. These data suggest that severe respiratory disease caused by co-infection of Pp and mouse-adapted SARS-CoV is attributable to the high replication of virus in the lungs, for which the elastase produced by Pp infection is probably responsible. cache = ./cache/cord-306365-7cydmgn2.txt txt = ./txt/cord-306365-7cydmgn2.txt === reduce.pl bib === id = cord-306414-2dv3qced author = Gutierrez, Lucas title = Deciphering the TCR Repertoire to Solve the COVID-19 Mystery date = 2020-06-20 pages = extension = .txt mime = text/plain words = 6993 sentences = 368 flesch = 42 summary = Advances in sequencing technologies and single-cell immune profiling can be leveraged to monitor adaptive immune responses in COVID-19 patients and guide future SARS-CoV-2 immunotherapy and biomarker development. Whether the aged and less diverse TCR repertoire impacts the ability to generate a sufficiently robust T cell response against SARS-CoV-2 in older patients remains to be studied. The development of faster and cheaper sequencing technologies, augmented by the advances in computational tools, support the feasibility of using TCR analyses not only to track SARS-CoV-2specific T cell expansion post-COVID-19 infection or in the course of treating patients with COVID-19, but also to establish certain features of the TCR repertoire architecture as predictive biomarkers for patients' clinical outcome. Thus, a comprehensive characterization of the dynamics and composition of the TCR repertoires to SARS-CoV-2 infection can largely contribute to the evolving understanding of the functional and mechanistic involvement of the adaptive immune cell response and potentially guide the design of effective treatment. cache = ./cache/cord-306414-2dv3qced.txt txt = ./txt/cord-306414-2dv3qced.txt === reduce.pl bib === id = cord-306177-5wefp31y author = Iheagwam, Franklyn Nonso title = Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants date = 2020-09-12 pages = extension = .txt mime = text/plain words = 4804 sentences = 251 flesch = 42 summary = e Unites States Food and Drug Administration-(USFDA-) approved drugs [26] , drugbank [27, 28] , traditional Ayurvedic, Chinese and natural medicine [20, [28] [29] [30] [31] , dark chemical matter, and fooDB [25] are some of the ZINC database subsets that have been rigourously screened for molecules to combat SARS-CoV-2 with main protease, RNA-dependent RNA polymerase, and angiotensin-converting enzyme-2 as the major therapeutic targets. Hence, this study analysed a plethora of natural products (NPs) from African medicinal plants with known bioactivities in human as therapeutic candidates targeting and inhibiting SARS-CoV-2 RNA synthesis, replication, structural protein function, and host-specific receptors/enzymes. In the course of drug discovery, structure-based virtual screening is a computational approach utilised to identify promising novel small chemical ligands from curated chemical compound databases with potential activity against drug targets [48] . cache = ./cache/cord-306177-5wefp31y.txt txt = ./txt/cord-306177-5wefp31y.txt === reduce.pl bib === id = cord-306486-y6a4u0vh author = Wang, Bin title = Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients date = 2020-05-05 pages = extension = .txt mime = text/plain words = 847 sentences = 52 flesch = 50 summary = 5 To fulfill the pressing need, we examined antibody generation and virus clearance in 26 patients with SARS-CoV-2-induced COVID-19. Thus, this is the first report to state that innate immunity plays an essential role in SARS-CoV-2 clearance, which The disease severity and fatality were increased with age in COVID-19 patients, which may be explained by the augmentation of proinflammatory responses and the reduction of antiviral cytokines in elder individuals. Taken together, we showed that SARS-CoV-2 could coexist with virus-specific IgG antibodies in COVID-19 patients for an unexpectedly long time and, without adaptive immunity, innate immunity may still be powerful enough to eliminate SARS-CoV-2. The long-term coexistence of IgG with SARS-CoV-2 in the human body raises the question of whether patients with antibodies are still at risk for reinfection, which may make COVID-19 "immunity passports" Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients cache = ./cache/cord-306486-y6a4u0vh.txt txt = ./txt/cord-306486-y6a4u0vh.txt === reduce.pl bib === id = cord-305959-x061q8t7 author = Davoudi-Monfared, Effat title = A Randomized Clinical Trial of the Efficacy and Safety of Interferon β-1a in Treatment of Severe COVID-19 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4733 sentences = 280 flesch = 50 summary = As the primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 ± 5.8 versus 8.3 ± 4.9 days, respectively, P = 0.95). The vital signs at the time of hospital admission were not statistically different, except respiratory rate was significantly higher in the IFN group (22 versus 20, respectively, P ϭ 0.009). As a primary outcome, the time to clinical response was not significantly different between the IFN and control groups (9.7 Ϯ 5.8 versus 8.3 Ϯ 4.9 days, respectively, P ϭ 0.95), which is shown in the Kaplan-Meier plot (Fig. 2) . On day 0, there was no significant difference between the groups in terms of the components Interferon ␤-1a in Treatment of Severe COVID19 Antimicrobial Agents and Chemotherapy of this scale. The present study was the first randomized, open-label, controlled trial that assessed the efficacy and safety of IFN ␤-1a in the treatment of patients diagnosed with severe COVID-19. cache = ./cache/cord-305959-x061q8t7.txt txt = ./txt/cord-305959-x061q8t7.txt === reduce.pl bib === id = cord-306675-kwrm8whn author = Crespo Sabarís, R title = “SARS-CoV-2: una presentación peculiar” date = 2020-05-08 pages = extension = .txt mime = text/plain words = 813 sentences = 77 flesch = 63 summary = El 27 de marzo se contacta con el paciente que refiere seguir con algunas lesiones y prurito, pero no se modifica tratamiento, aunque el día 30 acude muy nervioso y desde la consulta de enfermería se envían las fotografías 1 y 2 (figuras 1 y 2) al médico titular, que está haciendo teletrabajo, y al apreciar en las mismas componente inflamatorio y lesiones de rascado, se indica administrar metilprednisolona y dexcloreniramina parenterales, con mejoría en menos de una hora, y se pautan 5 días de tratamiento con prednisona de 30 mg, se aumenta la hidroxicina cambiándose cetirizina por rupatadina. Se sabe que estas lesiones, además de por la propia infección vírica, se pueden observar tras los tratamientos para la COVID19, pero esto no se cumple en el caso que nos ocuoa, por lo que hay una relación directa entre la propia infección y las lesiones, como en diversas infecciones víricas 6 , aunque todavía no se conoce su patogenia exacta. cache = ./cache/cord-306675-kwrm8whn.txt txt = ./txt/cord-306675-kwrm8whn.txt === reduce.pl bib === id = cord-306748-i9ndb71n author = Kobia, Francis title = COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness? date = 2020-04-17 pages = extension = .txt mime = text/plain words = 3218 sentences = 148 flesch = 51 summary = In fact, this strategy is being used by Senegal, which together with UK collaborators, is developing an affordable COVID-19 RDT (expected to cost $1 per test) for home use in African countries (Financial Times, 2020b). The authors contend that most African countries lack the capacity to administer mass screening to ascertain the extent of the disease spread, and call for support toward the development of homegrown RDTs and POCTs as a strategy to achieve mass screening of COVID-19 in Africa The present review by the authors provides important information on diagnostic challenges facing African countries in their combat against the ongoing COVID-19 pandemic. Specific to the present COVID-19 case, would it be faster and cheaper importing the diagnostic tools, as is already being done by some countries?The authors may wish to put " " section before " COVID-19 point of care testing strategies " section, for consistency with the conclusion. cache = ./cache/cord-306748-i9ndb71n.txt txt = ./txt/cord-306748-i9ndb71n.txt === reduce.pl bib === id = cord-306581-g3d0lqxp author = Khattab, Mohamed H. title = Early detection of SARS-CoV-2 from staging PET-CT date = 2020-09-29 pages = extension = .txt mime = text/plain words = 1214 sentences = 78 flesch = 45 summary = METHODS: Here, we present a case study of a mildly symptomatic patient with anal cancer diagnosed with SARS-CoV-2 from a staging PET-CT scan. Given the ongoing COVID-19 pandemic, a nasopharyngeal swab with polymerase chain reaction (PCR) was obtained and was confirmed positive for the potentially lethal SARS-CoV-2 viral infection. In geographic regions with a Fig. 1 Screening positron emission tomography fused with computed tomography demonstrating fluorodeoxyglucose-avid multifocal, rounded, peripheral ground-glass nodules, some demonstrating the reversed halo sign, within the right lower, right middle, and left lower lung lobes concerning for an infectious process significant and increasing COVID-19 case burden, routine PCR testing in the absence of clinical or radiologic findings may be indicated in patients undergoing chemoradiation or radiation, and it is our institutional practice to test all patients receiving any chemotherapy or greater than 10 days of radiation. In the setting of asymptomatic or mildly symptomatic patients with confirmed SARS-CoV-2 infection, multidisciplinary discussion with oncology and infectious disease teams is important to ascertain the risks and benefits of delaying cancer therapy. cache = ./cache/cord-306581-g3d0lqxp.txt txt = ./txt/cord-306581-g3d0lqxp.txt === reduce.pl bib === id = cord-306034-1u29o2id author = Cazzolla, Angela P. title = Taste and Smell Disorders in COVID-19 Patients: Role of Interleukin-6 date = 2020-08-04 pages = extension = .txt mime = text/plain words = 4014 sentences = 193 flesch = 47 summary = [Image: see text] The rapid recovery of smell and taste functions in COVID-19 patients could be attributed to a decrease in interleukin-6 levels rather than central nervous system ischemic injury or viral damage to neuronal cells. To correlate interleukin-6 levels in COVID-19 patients with olfactory or gustatory dysfunctions and to investigate the role of IL-6 in the onset of these disorders, this observational study investigated 67 COVID-19 patients with taste or smell disorders or both, who did not require intensive care admission, admitted at COVID Hospital of Policlinico of Bari from March to May 2020. Interleukin-6 levels in COVID-19 patients in relation to olfactory or gustatory disorders were correlated from the time of their admission to the time of swab negativization. The aim was to monitor and to correlate IL-6 levels in laboratory-confirmed COVID-19 patients with olfactory or gustatory disorders from the time of their admission to the time of swab negativization. cache = ./cache/cord-306034-1u29o2id.txt txt = ./txt/cord-306034-1u29o2id.txt === reduce.pl bib === id = cord-306749-qetf3uur author = Caves, N.D. title = Attitudes to basic life support among medical students following the 2003 SARS outbreak in Hong Kong() date = 2005-10-10 pages = extension = .txt mime = text/plain words = 4318 sentences = 177 flesch = 49 summary = This study seeks to explore whether this epidemic has altered the willingness of Hong Kong medical students to perform basic life support and mouth-to-mouth ventilation during an out-of-hospital cardiac arrest. The survey was conducted during July and August 2003, approximately two months after Hong Kong was removed from the World Health Organisation SARS Infected Areas list, and was designed to examine student confidence in BLS skills, their perceptions of the risks associated with performing BLS and their willingness to perform BLS in varying situations. Many of the previous studies investigating this issue have indicated that respondees are more reluctant to perform mouth-to-mouth ventilation than chest compressions, and have highlighted rescuers' fears regarding transmission of the human immunodeficiency virus (HIV) in particular as a reason for not performing BLS. cache = ./cache/cord-306749-qetf3uur.txt txt = ./txt/cord-306749-qetf3uur.txt === reduce.pl bib === id = cord-306733-df36w6l7 author = Rosales-Mendoza, Sergio title = What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date = 2020-04-14 pages = extension = .txt mime = text/plain words = 8591 sentences = 420 flesch = 39 summary = Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. cache = ./cache/cord-306733-df36w6l7.txt txt = ./txt/cord-306733-df36w6l7.txt === reduce.pl bib === id = cord-306508-xpwluph5 author = Nkengasong, John title = China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response date = 2020-01-27 pages = extension = .txt mime = text/plain words = 1452 sentences = 68 flesch = 56 summary = It shows a marked departure from public health policies that, during the SARS outbreak in 2002, contributed to the deaths of 774 people, spread of the disease to 37 countries and an economic loss of over US$40 billion over a period of 6 months 6, 7 . As of 20 January 2020, the Chinese government reported 136 new cases of infection with this virus over the weekend that were spreading to other cities in the country, bringing the total cumulative cases worldwide to over 200 (ref. There is also a need for closer coordination of efforts between the Africa Centres for Disease Control and Prevention, based in Addis Ababa, Ethiopia, and China CDC for sharing information on potential people suspected of being infected who are traveling from China to Africa. China's political openness to reporting in a timely manner and the emergence of the novel virus 2019-nCoV, coupled with the rapid sequencing and public sharing of the sequences, represents a new dawn for global health security and international health diplomacy. cache = ./cache/cord-306508-xpwluph5.txt txt = ./txt/cord-306508-xpwluph5.txt === reduce.pl bib === id = cord-306431-r83n27la author = Chan, Chak-Ming title = The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function date = 2009-05-04 pages = extension = .txt mime = text/plain words = 4794 sentences = 276 flesch = 55 summary = title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function Consistent with the Vero E6 cells data (Fig. 2) , our in vivo results further validate the importance of cysteine-rich, Yxx and diacidic domains of 3a (Fig. 1A) in 3a's pro-apoptotic function. In this study, we generated mutant 3a constructs, 3a-CS, 3a-YA and 3a-DE (Fig. 1A) , and investigated the functional significance of the cysteine-rich, Yxx and diacidic domains on 3a's pro-apoptotic activity. We previously reported caspase-8 activation in 3a-WTexpressing Vero E6 cells , and our in vivo data also showed that cytochrome c can modulate 3a-WT-induced apoptosis . Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway cache = ./cache/cord-306431-r83n27la.txt txt = ./txt/cord-306431-r83n27la.txt === reduce.pl bib === id = cord-307109-nz8qvuw6 author = Martinez, Miguel Angel title = Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus date = 2020-04-21 pages = extension = .txt mime = text/plain words = 3758 sentences = 201 flesch = 42 summary = The previous epidemics of infections by high-morbidity human coronaviruses, such as SARS-CoV in 2003 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, prompted the characterization of compounds that could be potentially active against the currently emerging novel coronavirus, SARS-CoV-2. In addition, a combination of the human immunodeficiency virus type 1 (HIV-1) protease inhibitors lopinavir/ritonavir and interferon beta (LPV/RTV–IFN-β) was shown to be effective in patients infected with SARS-CoV. To predict new zoonotic coronavirus jumps across species and to understand the rate of virus spread among people, it is crucial to determine whether SARS-CoV-2 is mutating to improve its binding to human receptors for infection. Clinical observations in animals and humans showed that MERS-CoV infections were mediated by both virus replication and host inflammatory responses. However, therapeutic treatment with human monoclonal antibodies did not protect against the severe disease or the loss of lung function induced by MERS-CoV in animal models (20) . cache = ./cache/cord-307109-nz8qvuw6.txt txt = ./txt/cord-307109-nz8qvuw6.txt === reduce.pl bib === id = cord-306826-vbfdxoc2 author = Solerte, Sebastiano Bruno title = Dipeptidyl peptidase-4 (DPP4) inhibition in COVID-19 date = 2020-06-06 pages = extension = .txt mime = text/plain words = 2251 sentences = 112 flesch = 41 summary = CONCLUSIONS: The use of DPP4 inhibitors, such as gliptins, in patients with COVID-19 with, or even without, type 2 diabetes, may offer a simple way to reduce the virus entry and replication into the airways and to hamper the sustained cytokine storm and inflammation within the lung in patients diagnosed with COVID-19 infection. The novel beta-coronavirus 2019 (SARS-CoV-2) has recently emerged as a threat for human kind, causing severe respiratory syndrome , associated with other systemic complications (i.e., intestinal infections, renal and heart failure) and with a relative high mortality [1] . The co-expression of ACE2 and DPP4/CD26 as receptors of spike glycoproteins could hypothesize that different human coronaviruses (CoVs) target similar cell types across different human tissues and explain the presence of similar clinical features in patients infected with different CoVs. In another case, it was shown that DPP4 acted for CoV co-receptor, thus suggesting a potential similar mechanism of entry for SARS-CoV-2 [5] . cache = ./cache/cord-306826-vbfdxoc2.txt txt = ./txt/cord-306826-vbfdxoc2.txt === reduce.pl bib === id = cord-306832-w8s282nq author = Tarragón, Blanca title = FRACASO RENAL AGUDO EN PACIENTES HOSPITALIZADOS POR COVID-19 date = 2020-10-09 pages = extension = .txt mime = text/plain words = 3471 sentences = 362 flesch = 59 summary = La mediana de estancia fue de 12 días (RIC 9-23), y el 22% fallecieron-Los pacientes que desarrollaron FRA durante el ingreso presentaron valores más altos de proteína C-reactiva, LDH o dímero D, una afectación pulmonar más grave, más necesidad de ingreso en UCI, más tratamiento con lopinavir/ritonavir y fármacos biológicos y mayor necesidad de TSR. Además, esta afectación en pacientes COVID-19 no es uniforme según lo comunicado por los hospitales chinos y puede estar condicionada por la estrategia de detección de casos de cada sistema de salud, la política de ingresos de cada hospital, la definición de daño renal e incluso los factores genéticos y ambientales de las diversas poblaciones afectadas. El FRA se ha definido como factor de peor pronóstico y mayor mortalidad en pacientes ingresados con infección por SARS-Cov-2 9,10 . cache = ./cache/cord-306832-w8s282nq.txt txt = ./txt/cord-306832-w8s282nq.txt === reduce.pl bib === id = cord-306424-gf0bglm0 author = Scutigliani, Enzo Maxim title = Interaction of the innate immune system with positive-strand RNA virus replication organelles date = 2017-06-27 pages = extension = .txt mime = text/plain words = 8320 sentences = 382 flesch = 36 summary = Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus cache = ./cache/cord-306424-gf0bglm0.txt txt = ./txt/cord-306424-gf0bglm0.txt === reduce.pl bib === id = cord-307070-tqxvu3pu author = Iqbal, Phool title = Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date = 2020-09-20 pages = extension = .txt mime = text/plain words = 2758 sentences = 150 flesch = 49 summary = However, improvement was observed in the clinical condition of the patients who were managed as per COVID-19 protocol based upon the clinical signs and symptoms after correlating with diagnostic chest imaging studies. The infectious disease team advised testing with COVID-19 serology (immunoglobulin (Ig) M and IgG antibodies through lateral flow assay), the results of which were positive, indicating recent infection. The infectious disease team was consulted and based upon his clinical presentation and previous investigations, the patient was maintained on the local management protocol for COVID-19 infection. Moreover, biomarkers such as CRP, ferritin, lymphocyte counts, lactate dehydrogenase, and N-terminal pro b-type natriuretic peptide, along with radiological findings in CXR or features such as unilateral or bilateral pneumonia, ground-glass opacities, or consolidations in a chest CT scan, can suggest COVID-19 infection even in such patients where RT-PCR alone is negative [4] . cache = ./cache/cord-307070-tqxvu3pu.txt txt = ./txt/cord-307070-tqxvu3pu.txt === reduce.pl bib === id = cord-307044-4czeehkq author = Liu, Jiaye title = Longitudinal Changes of Liver Function and Hepatitis B Reactivation in COVID‐19 Patients with Pre‐existing Chronic HBV Infection date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3520 sentences = 178 flesch = 50 summary = However, to the best of our knowledge, no studies had been carried out on the impact of chronic HBV infection on the disease progression and liver function changes of COVID-19 patients, and how the SARS-CoV-2 infection in turn affects the course of chronic HBV infection. 16 The factors for propensity score calculation include age, gender, body mass index (BMI), time intervals between COVID-19 onset to hospital admission, number of comorbidities except for CHB, liver biochemistries (ALT, AST, GGT, TBIL), PaO2/FIO2 ratio, chest CT score, CRP, lymphocyte count, and platelet count at baseline. As the median of testing/assessing time intervals and follow-up durations were 3 days and 14 days for liver biochemistries (ALT, AST, GGT, TBIL), we compared the dynamic levels of these indicators within/between the two groups at baseline, 3, 6, 9, 12, 15 days during hospitalization. The median levels of liver biochemistries over time were no significant difference between two groups ( Figure 3 ; Wilcoxon signed-rank test, ALT: p=0.56, AST: p=0.58, GGT: p=0.43, TBIL: p=0. cache = ./cache/cord-307044-4czeehkq.txt txt = ./txt/cord-307044-4czeehkq.txt === reduce.pl bib === id = cord-306819-otabtxin author = Asensio-Samper, JM title = Recomendaciones Prácticas Para El Manejo Del Paciente Con Dolor Crónico Durante La Pandemia De COVID-19 date = 2020-09-02 pages = extension = .txt mime = text/plain words = 5168 sentences = 491 flesch = 52 summary = Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. En las Unidades de Tratamiento del Dolor, los casos en los que se establece la necesidad de manejo preferente de pacientes en situación de crisis sanitaria, incluyendo pandemia COVID-19, son aquellos casos no subsidiarios de atención mediante telemedicina, es decir, aquellos casos refractarios a tratamiento médico convencional que requieran evaluación clínica especializada y alta probabilidad de realización de procedimiento invasivo para control del dolor, el cual podrá ser realizado en formato de "acto único". cache = ./cache/cord-306819-otabtxin.txt txt = ./txt/cord-306819-otabtxin.txt === reduce.pl bib === id = cord-306718-7wp5jmxe author = Remaeus, Katarina title = Characteristics and short‐term obstetric outcomes in a case series of 67 women tested positive for SARS‐CoV‐2 in Stockholm, Sweden date = 2020-09-27 pages = extension = .txt mime = text/plain words = 2558 sentences = 154 flesch = 57 summary = For the care of pregnant women positive for SARS-CoV-2, National Swedish guidelines were published early in the pandemic and recommended individualized antenatal care, mode of delivery based on obstetric considerations, and no routine separation of the mother and newborn after birth. Here, we want to report a case series of 67 women with a positive test for SARS-CoV-2, who gave birth from March 19 until April 26, 2020 in the Stockholm region, Sweden. In this case series of 67 SARS-CoV-2 test-positive delivered women with varying clinical presentation ranging from asymptomatic to manifest COVID19 disease, the majority had a vaginal, term birth and delivered a healthy normal weight neonate that did not test positive for SARS-CoV-2. In this case series of 67 test-positive women few women presented with severe COVID-19 illness, a majority had a vaginal birth at term with a healthy neonate that were test-negative for SARS-CoV-2. cache = ./cache/cord-306718-7wp5jmxe.txt txt = ./txt/cord-306718-7wp5jmxe.txt === reduce.pl bib === id = cord-306598-xe0pq0ik author = Zhou, Mi title = Re-emergence of SARS-CoV2 in a discharged COVID-19 case date = 2020-04-02 pages = extension = .txt mime = text/plain words = 608 sentences = 50 flesch = 72 summary = title: Re-emergence of SARS-CoV2 in a discharged COVID-19 case Re-emergence of SARS-CoV2 in a discharged COVID-19 case Dear Editor: Since December 2019, novel coronavirus (SARS-CoV2) infected disease (now nominated as COVID-19) has soon emerged as a global health concern. Here we report a case of COVID-19 who met the criteria for discharge but was tested positive for SARS-CoV2 again 10 days after discharge. There her nasal swab was obtained, and SARS-CoV2 was tested positive with real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) assay targeting ORF1ab and N gene of virus genome. RT-PCR examination for SARS-CoV-2 was performed on day 10, 11 and 14, and all 3 tests were negative. Her symptom was not relieved on day 25, so her nasal swab was obtained and the test for SARS-CoV-2 was positive again. Previous study on SARS-CoV showed that virus load could be detected for more than 10 weeks after disease onset. cache = ./cache/cord-306598-xe0pq0ik.txt txt = ./txt/cord-306598-xe0pq0ik.txt === reduce.pl bib === id = cord-306835-juitltpi author = Babaei, Fatemeh title = Curcumin (a constituent of turmeric): New treatment option against COVID‐19 date = 2020-09-06 pages = extension = .txt mime = text/plain words = 6226 sentences = 363 flesch = 45 summary = The keywords used for the search were as follows: coronavirus-19, COVID-19, SARS-CoV-2, curcumin, Curcuma longa, turmeric, curcumin and antiviral, curcumin and anti-inflammatory, curcumin and antipyretic, curcumin and lung, curcumin and acute lung injury, curcumin and fatigue, curcumin and antioxidant, curcumin and ARDS, curcumin and bradykinin, curcumin and fibrosis, curcumin and Interleukin-6 (IL-6), curcumin and tumor necrosis factor-alpha (TNF-α), curcumin and NF-κB, curcumin and Toll-like receptors (TLRs), curcumin and antiapoptotic. AA: arachidonic acid, ALI: acute lung injury, AP-1: activator protein 1, BK: bradykinin, ACE2: angiotensin-converting enzyme 2, Ang II: angiotensin II, ARDS: acute respiratory distress syndrome, Cas-3: caspase 3, COX: cyclooxygenase, CXCL: chemokine (C-X-C motif) ligand, 12-HPETE: 12-hydroperoxyeicosatetraenoic acid, JNK: c-Jun N-terminal kinase, 12 LOX: 12-lipoxygenase, MMP: matrix metalloproteinase NF-κB: nuclear factor kappa-light-chain-enhancer of activated B cells, MAPK: mitogen-activated protein kinase, PAI-1: plasminogen activator inhibitor-1, PLA2: phospholipase A2, PG: prostaglandin, SMAD3: mothers against decapentaplegic homolog 3, TGF-β1: transforming growth factor-beta 1, TNF-α: tumor necrosis factor-α, TLR: Toll-like receptor, TRPA1: transient receptor potential channel subfamily vanilloid member 1, TRPV1: transient receptor potential channel subfamily A member 1 mechanisms that curcumin may be useful to prevent or treat the ARDS. cache = ./cache/cord-306835-juitltpi.txt txt = ./txt/cord-306835-juitltpi.txt === reduce.pl bib === id = cord-306901-uuwgpuhw author = Roy, Sylvie title = Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date = 2020-09-16 pages = extension = .txt mime = text/plain words = 4215 sentences = 251 flesch = 58 summary = title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. High amounts of SARS-CoV-2 DS protein are incorporated into MLV VLPs released 142 from stable producer cells. A VLP-derived SARS CoV-2 vaccine will be a viable option if 143 sufficient amounts of S protein are incorporated at the surface of the released particles. In conclusion, we have developed and characterized a new MLV VLP platform that can 243 efficiently incorporate the S protein from SARS-CoV-2, and that has the potential to produce a pan-244 coronavirus vaccine. cache = ./cache/cord-306901-uuwgpuhw.txt txt = ./txt/cord-306901-uuwgpuhw.txt === reduce.pl bib === id = cord-307303-9mzs5dl4 author = Barnett, Daniel J. title = The Application of the Haddon Matrix to Public Health Readiness and Response Planning date = 2005-02-02 pages = extension = .txt mime = text/plain words = 4303 sentences = 184 flesch = 44 summary = However, in practice, public health preparedness requires additional models and tools to provide a framework to better understand and prioritize emergency readiness and response needs, as well as to facilitate solutions; this is particularly true at the local health department level. By breaking a larger problem into smaller, more manageable components, the Haddon matrix provides a practical, efficient decisionmaking and planning tool that health department leaders can use to better understand current and emerging threats, perform vulnerability assessments, prioritize and allocate readiness and response resources, and maintain institutional agility in responding to an array of public health emergencies. Applying the Haddon matrix to the threat of a dirty bomb illustrates the value of this injury prevention model as a public health readiness and response tool, even when focusing exclusively on environmental issues. cache = ./cache/cord-307303-9mzs5dl4.txt txt = ./txt/cord-307303-9mzs5dl4.txt === reduce.pl bib === id = cord-307113-mu3ow7m4 author = Colmenero, I. title = SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors date = 2020-09-30 pages = extension = .txt mime = text/plain words = 415 sentences = 33 flesch = 53 summary = title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors The size and shape of the particle shown in our paper fit with other descriptions of SARS‐CoV‐2, but there may be a bias in interpretation. The size and shape of the particle shown in our paper fit with other descriptions of SARS-CoV-2, but there may be a bias in interpretation. After the publication of our series, new evidence is rising favouring a causal role for SARS-CoV-2 in COVID chilblains. Positive immunohistochemistry for SARS-CoV has been reported by different authors in cutaneous biopsies of COVID chilblains using antibodies directed against different parts of the virus, 3, 4 and SARS-CoV-2 RNA-positive cells have been demonstrated by RNAscope. SARS-CoV-2 endothelial infection causes COVID-19 chilblains: histopathological, immunohistochemical and ultrastructural study of seven paediatric cases Chilblains and COVID-19: why SARS-CoV-2 endothelial infection is questioned. cache = ./cache/cord-307113-mu3ow7m4.txt txt = ./txt/cord-307113-mu3ow7m4.txt === reduce.pl bib === id = cord-307208-tw6mwa5v author = Cabrera Villegas, Antonio title = [(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2 date = 2020-09-16 pages = extension = .txt mime = text/plain words = 3341 sentences = 167 flesch = 50 summary = The aim of this study was to retrospectively analyse the incidence of suspicious imaging findings of COVID-19 in PET/CT performed in asymptomatic patients referred to our Department with oncologic indications. Inclusion criteria were the following: (a) outpatients referred to Nuclear Medicine for whole-body PET/CT, (b) with [ 18 F]-FDG or [ 18 F]-fluorocholine, (c) referral was due only to oncologic indications, and (d) patients were asymptomatic for SARS-CoV-2 infection. The limitations in the diagnosis of COVID-19, together with the fact that most of the patients infected with SARS-CoV-2 are asymptomatic or present scarce symptoms, were the reason for initiating this retrospective study analysing patients scanned with PET/CT in which there were suspicious lung findings for SARS-CoV-2 infection. Our results confirm that the prevalence of SARS-CoV-2 infection is higher than the known figures, due to the relevant proportion of asymptomatic patients, some of them with lung disease, which can be diagnosed in a presymptomatic phase based on the incidental imaging findings in imaging procedures performed for completely different clinical indications. cache = ./cache/cord-307208-tw6mwa5v.txt txt = ./txt/cord-307208-tw6mwa5v.txt === reduce.pl bib === id = cord-307036-n44yml79 author = Ng, Oi-Wing title = Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date = 2014-07-14 pages = extension = .txt mime = text/plain words = 8528 sentences = 392 flesch = 57 summary = Next, to determine if mAb 1A9 exhibits cross-neutralizing activity, S-pseudotyped virus particles, or S-pps, carrying the human SARS-CoV S or the various RBD-modified chimeric S of civet SARS-CoV SZ3 strain and bat SL-CoV Rp3 and Rf1 strains were generated and used to infect CHO-ACE2 cells in the absence or presence of different concentrations (100, 150 and 200 mg/ml) of mAb 1A9. Wild-type S, substitution S mutants, namely D1128A, N1056K, and that containing both D1128A and N1056K, were then expressed in 293 FT cells and Western Blot analysis was performed to determine the effects of these mutations on the binding of the S protein to mAb 1A9. (A) S-pp expressing S protein of humans SARS-CoV HKU39849, civet SARS-CoV SZ3, bat SL-CoV Rp3 and Rf1 and (B) S-pp containing wild-type or mutant D1128A, N1056K or D1128A/ N1056K S were generated and used to infect CHO-ACE2 cells at equal amount (as quantitated using P24 ELISA). cache = ./cache/cord-307036-n44yml79.txt txt = ./txt/cord-307036-n44yml79.txt === reduce.pl bib === id = cord-307148-k1uo3fxm author = Bradshaw, Patrick C. title = COVID-19: Proposing a Ketone-Based Metabolic Therapy as a Treatment to Blunt the Cytokine Storm date = 2020-09-09 pages = extension = .txt mime = text/plain words = 20788 sentences = 1093 flesch = 40 summary = R-BHB activates anti-inflammatory GPR109A signaling and inhibits the NLRP3 inflammasome and histone deacetylases, while a ketogenic diet has been shown to protect mice from influenza virus infection through a protective γδ T cell response and by increasing electron transport chain gene expression to restore energy metabolism. Others have also suggested that increasing systemic ketone levels may aid host defenses against respiratory viral infection, in part, by decreasing inflammation [1, 2] , including a recent comprehensive review [3] , while a clinical trial of the effects of a ketogenic diet on intubated SARS-CoV-2 patients has recently been registered (NCT04358835). Coronaviruses have been shown to increase the oxidation of phospholipids, which stimulate toll-like receptor 4 (TLR4) signaling on macrophages, leading to cytokine production and acute lung injury [163] , so HDAC inhibition with R-BHB appears to be a viable treatment to decrease cytokine levels and inflammation. cache = ./cache/cord-307148-k1uo3fxm.txt txt = ./txt/cord-307148-k1uo3fxm.txt === reduce.pl bib === id = cord-307229-wjx90xki author = da Silveira, Matheus Pelinski title = Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date = 2020-07-29 pages = extension = .txt mime = text/plain words = 8418 sentences = 362 flesch = 34 summary = Additionally, elevations of IL-1β, IFN-γ, IP10 and MCP1 in infections by the novel coronavirus were associated with the Th1 response; however, an increase in interleukins of the T helper type 2 (Th2) profile, such as IL-4, IL-5, IL10, which suppress the inflammation, was also associated with a greater severity of COVID-19, which may demonstrate an imbalance in immune regulation and an attempt to minimize tissue inflammatory damage [35, 40] . In addition, obesity is an important factor for the development of T2DM-especially when associated with low levels of physical activity and poor physical conditioning-and as mentioned, both diseases are related to higher expression of ACE2, increasing the risk of advanced infection by SARS-CoV-2 [43] . Similarly, regular exercise practices at moderate levels favor the function of the human body's immune surveillance against pathogens, as they stimulate an exchange of white blood cells between the circulatory system and tissues, a fact that reduces morbidity and mortality from acute respiratory disease and infections viral. cache = ./cache/cord-307229-wjx90xki.txt txt = ./txt/cord-307229-wjx90xki.txt === reduce.pl bib === id = cord-306760-05my504t author = Turner, Dan title = Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date = 2020-03-31 pages = extension = .txt mime = text/plain words = 3832 sentences = 209 flesch = 46 summary = METHODS: An electronic reporting system of children with IBD infected with SARS-CoV-2 has been circulated among 102 PIBD centres affiliated with the Porto and Interest-group of ESPGHAN. Standard IBD treatments including biologics should continue at present through the pandemic, especially in children who generally have more severe IBD course on one hand, and milder SARS-CoV-2 infection on the other. In light of the hyperinflammatory immune response seen in patients with COVID-19 it is highly relevant that blockade of IL-6R with tocilizumab resulted in clinical improvement associated with normalisation of fever, lymphocyte counts, and CRP in a retrospective group of 21 adults with severe SARS-CoV-2 infection (20) . Therefore, uninfected children should generally continue their medical treatment, including immunomodulators and biologic therapies, as the risk of a disease flare outweighs any estimated risk of SARS-CoV2 infection. cache = ./cache/cord-306760-05my504t.txt txt = ./txt/cord-306760-05my504t.txt === reduce.pl bib === id = cord-307536-qeo5dfxg author = Feng, Ye title = Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date = 2020-06-30 pages = extension = .txt mime = text/plain words = 998 sentences = 69 flesch = 58 summary = title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19. Based on both the epitope counts and HLA score, we 250 eventually selected 13 T-cell epitopes-only vaccine peptides. cache = ./cache/cord-307536-qeo5dfxg.txt txt = ./txt/cord-307536-qeo5dfxg.txt === reduce.pl bib === id = cord-307489-2liu4anc author = Elavia, Nasha title = An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia date = 2020-05-23 pages = extension = .txt mime = text/plain words = 1321 sentences = 72 flesch = 43 summary = title: An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia Clinical presentation and severity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) varies greatly amongst patients, as supported by recent literature. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) presenting with atypical gastrointestinal symptoms in a patient with SARS-CoV-2 infection. This atypical presentation of PE is unique to our case and highlights the significance of a high index of clinical suspicion for SARS-CoV-2 and its associated thrombogenic effect, even in patients with atypical symptoms. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) in a patient with SARS-CoV-2 pneumonia who mainly presented with gastrointestinal symptoms. Our patient however presented mainly with gastrointestinal symptoms, which have been reported with SARS-CoV-2; however, with significant hypoxia in the absence of a respiratory viral syndrome although with a low pretest probability for PE, we decided to further evaluate the patient for hypoxia. cache = ./cache/cord-307489-2liu4anc.txt txt = ./txt/cord-307489-2liu4anc.txt === reduce.pl bib === id = cord-307227-x6xketcn author = Martin, William R. title = Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3999 sentences = 219 flesch = 52 summary = Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19. 2, 3 In our initial network-based drug repurposing study, 4 we identified toremifene, another selective estrogen receptor modulator (SERM), as a strong candidate for the potential treatment of COVID-19. A drug repurposing study for SARS-CoV-1 5 indicated a low 50% effective concentration (EC 50 ) for toremifene, and noted that estrogen signaling may not be involved in the inhibitory pathway, similar to that of inhibition of Ebola. Future work will be needed to confirm these results; optimally, the determination of a cocrystal structure with Journal of Proteome Research pubs.acs.org/jpr Article NSP14 and/or the spike glycoprotein from SARS-CoV-2 with toremifene would be solved. cache = ./cache/cord-307227-x6xketcn.txt txt = ./txt/cord-307227-x6xketcn.txt === reduce.pl bib === id = cord-307160-1vz0gw1w author = Morais-Almeida, Mário title = COVID-19, asthma, and biologic therapies: What we need to know date = 2020-05-16 pages = extension = .txt mime = text/plain words = 3561 sentences = 160 flesch = 41 summary = Ongoing prospective cohort studies (SARP, NHLBI and others) provide a unique opportunity to examine the effects of COVID-19 on severe asthma and potential interactions with therapy, including inhaled and oral corticosteroids, as well as targeted treatment with biologics. It was believed that low eosinophil counts in peripheral blood would be related to the infection with the SARS-CoV-2 virus itself, and not necessarily an indicator that treatments which reduce eosinophil counts in patients with asthma would be associated with more severe COVID-19 disease. As in the placebo controlled trials with omalizumab, mepolizumab, benralizumab, reslizumab and dupilumab in asthmatic patients, no risk of increased infection susceptibility or immunosuppressive effect was reported to date and, in the case of omalizumab, there is a possible anti-infectious effect; hence we do not need to discontinue these treatments during the current pandemic. cache = ./cache/cord-307160-1vz0gw1w.txt txt = ./txt/cord-307160-1vz0gw1w.txt === reduce.pl bib === id = cord-307556-k2lavvca author = Jang, Hongje title = Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date = 2013-02-18 pages = extension = .txt mime = text/plain words = 2983 sentences = 154 flesch = 53 summary = Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . cache = ./cache/cord-307556-k2lavvca.txt txt = ./txt/cord-307556-k2lavvca.txt === reduce.pl bib === id = cord-306770-hjzlj8k3 author = Mick, Paul title = Aerosol-generating otolaryngology procedures and the need for enhanced PPE during the COVID-19 pandemic: a literature review date = 2020-05-11 pages = extension = .txt mime = text/plain words = 6318 sentences = 332 flesch = 43 summary = During the coronavirus disease 2019 (COVID-19) pandemic, personal protective equipment (PPE) worn by health care workers is critical for reducing transmission of the infection in health care settings, particularly when aerosol-generating medical procedures (AGMP) are being performed. For example, Givi et al and the Canadian Society of Otolaryngology-Head and Neck Surgery [2] call for airborne precautions when performing AGMP on patients for whom the index of suspicion for COVID-19 infection is not high, whereas the World Health Organization, the U.S. Centers for Disease Control, and the Public Health Agency of Canada do not [3, 14, 15] . Measuring the level of aerosolized viral particles in rooms where AGMPs are being performed on patients with COVID-19 would provide indirect evidence of the degree to which these procedures put health care workers at risk of aerosolized transmission, and whether exposure concentration affects risk of infection and/or severity of disease. cache = ./cache/cord-306770-hjzlj8k3.txt txt = ./txt/cord-306770-hjzlj8k3.txt === reduce.pl bib === id = cord-307248-8e34ndn4 author = Klimek, Ludger title = Handling of allergen immunotherapy in the COVID‐19 pandemic: An ARIA‐EAACI statement date = 2020-04-24 pages = extension = .txt mime = text/plain words = 2109 sentences = 128 flesch = 36 summary = Allergen‐specific immunotherapy (AIT) is one of the most important treatment options for IgE‐mediated allergies and is based on immunological effects on the diseased patient Allergen-specific immunotherapy (AIT) is one of the most important treatment options for IgE-mediated allergies and is based on immunological effects on the diseased patient. The highest risk of healthcare-associated transmission occurs in the absence of standard precautions, when primary infection prevention and control measures for respiratory infections are not in place, and when handling patients whose COVID-19 diagnoses is yet to be confirmed. Eventhough it is well established that allergic airway diseases are associated with an Highly active antiretroviral treatment has improved the immune function and life expectancy in HIV-infected patients whose respiratory allergic incidence is similar to that of the general population (33) . In patients, who recovered from COVID-19 or who are found to have a sufficient SARS-CoV-2 antibody response after (asymptomatic) disease (14), AIT can be started or continued as planned. cache = ./cache/cord-307248-8e34ndn4.txt txt = ./txt/cord-307248-8e34ndn4.txt === reduce.pl bib === id = cord-307596-0bbxyyea author = Parhar, Harman S. title = Topical preparations to reduce SARS‐CoV‐2 aerosolization in head and neck mucosal surgery date = 2020-04-25 pages = extension = .txt mime = text/plain words = 2377 sentences = 129 flesch = 42 summary = AIM: The COVID‐19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has put health care workers at risk when exposed to aerosolized viral particles during upper airway mucosal surgery. 12, 13 There has been very little published, however, regarding whether there exist any topical agents that could be utilized preoperatively to potentially lower the viral load in the upper aerodigestive tract thereby mitigating any risk of viral aerosolization in persons undergoing head and neck mucosal surgery. 14 While studies on virucidal activity of PVP-I have not yet been performed specifically on SARS-CoV-2, there have been numerous in vitro studies demonstrating its effectiveness against multiple viruses including related coronaviruses. Though no topical therapies have been studied to specifically reduce the viral load and potential aerosolization of SARS-CoV-2 during upper airway mucosal surgery, PVP-I solutions have demonstrated effective virucidal activity against related coronaviruses in numerous studies. cache = ./cache/cord-307596-0bbxyyea.txt txt = ./txt/cord-307596-0bbxyyea.txt === reduce.pl bib === id = cord-307213-i8yijbiu author = Ip, Jonathan Daniel title = Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date = 2020-11-02 pages = extension = .txt mime = text/plain words = 1043 sentences = 82 flesch = 58 summary = title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. A total of 28 serial respiratory specimens from 12 patients were successfully sequenced 49 using nanopore and Illumina sequencing. Temporal profiles of 310 viral load in posterior oropharyngeal saliva samples and serum antibody responses during 311 infection by SARS-CoV-2: an observational cohort study A neutralizing human antibody 370 binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Viral load dynamics and disease 397 severity in patients infected with SARS-CoV-2 in Zhejiang province, China cache = ./cache/cord-307213-i8yijbiu.txt txt = ./txt/cord-307213-i8yijbiu.txt === reduce.pl bib === id = cord-307504-cogk5kig author = Zhu, Yuanmei title = Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date = 2020-03-28 pages = extension = .txt mime = text/plain words = 1946 sentences = 107 flesch = 51 summary = title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. Taken together, these results suggested that 128 SARS-CoV-2 might evolve an increased interaction between the HR1 and HR2 domains in 129 the S2 fusion protein thus critically determining its high fusogenic activity. Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: 354 implications for virus fusogenic mechanism and identification of fusion inhibitors Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition 368 using spike protein heptad repeat-derived peptides Heptad repeat-derived peptides block protease-mediated direct entry from the cell surface of 371 severe acute respiratory syndrome coronavirus but not entry via the endosomal pathway cache = ./cache/cord-307504-cogk5kig.txt txt = ./txt/cord-307504-cogk5kig.txt === reduce.pl bib === id = cord-307263-znuqdzdp author = Sun, Niuniu title = A Qualitative Study on the Psychological Experience of Caregivers of COVID-19 Patients date = 2020-04-08 pages = extension = .txt mime = text/plain words = 4478 sentences = 250 flesch = 50 summary = Previous studies have shown that during sudden natural disasters and infectious diseases, nurses will sacrifice their own needs to actively participate in the anti-epidemic work and make selfless contributions out of moral and professional responsibility [7] . Previous studies have shown that when nurses are in close contact with patients with emerging infectious diseases such as SARS [9] , MERS-Cov [10, 11] , Ebola [12] , H1N1 [13] , they will suffer from loneliness, anxiety, fear, fatigue, sleep disorders, and other physical and mental health problems. This study explored the psychological experience of caregivers of patients with COVID-19 using phenomenological methods and we summarised our findings into four themes: significant amounts of negative emotions at an early stage, self-coping styles, growth under stress, and positive emotions that occur simultaneously or progressively with negative emotions. cache = ./cache/cord-307263-znuqdzdp.txt txt = ./txt/cord-307263-znuqdzdp.txt === reduce.pl bib === id = cord-307490-b4un4703 author = Chan, Sophia S.C. title = Improving older adults’ knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study date = 2007-09-30 pages = extension = .txt mime = text/plain words = 3757 sentences = 190 flesch = 51 summary = title: Improving older adults' knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study Objectives To assess the effectiveness of delivering a telephone health education programme dealing with anxiety levels, and knowledge and practice of measures to prevent transmission of SARS among a group of older adults with low SES. This is the first systematic study to assess the effectiveness of delivering telephone health education to older adults during the outbreak of SARS in Hong Kong. Results of the study supported that telephone health education was effective in relieving anxiety and improving knowledge of the main transmission routes of SARS in older adults, but not fostering practice of preventing SARS. This is the first systematic study to assess the effectiveness of telephone health education in improving older adults' knowledge and practice of preventive measures during the SARS epidemic. cache = ./cache/cord-307490-b4un4703.txt txt = ./txt/cord-307490-b4un4703.txt === reduce.pl bib === id = cord-307436-qcdlcxyb author = Bui, L. V. title = Estimation of the incubation period of SARS-CoV-2 in Vietnam date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2468 sentences = 158 flesch = 52 summary = Methods: Only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset and clearly defined window of possible SARS-CoV-2 exposure were included. To assure the reliability of analysis, we selected only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset (including fever, cough, and shortness of breath) and clearly defined window of possible SARS-CoV-2 exposure. We estimated the incubation period of Vietnamese confirmed COVID-19 cases from public reported data with three parametric models, including Weibull, Gamma and Lognornal . The estimated mean of incubation period for 19 Vietnamese confirmed COVID-19 cases using Weibull distribution model is higher than that of SARS in Hong Kong and Beijing [14] and in MERS [15, 16] . Our study has several strengths, including being the first effort to estimate SAR-CoV-2 incubation period using data from Vietnamese locally transmitted cases. cache = ./cache/cord-307436-qcdlcxyb.txt txt = ./txt/cord-307436-qcdlcxyb.txt === reduce.pl bib === id = cord-306881-wrd2rhjz author = Gehrie, Eric title = Transfusion Service Response to the COVID-19 Pandemic date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3296 sentences = 140 flesch = 44 summary = In this article, we highlight "best practices" that have emerged during the pandemic, focusing on management of blood supply and blood bank operations, rapid incorporation of COVID-19 convalescent plasma into blood bank inventory, and changes to the approach to the patient requiring therapeutic apheresis. Extrapolation from previous experience with SARS-CoV, Middle Eastern respiratory syndrome, and influenza, and with the strong backing of statements by AABB, the Centers for Disease Control and Prevention, and the Food and Drug Administration (FDA), as well as the preliminary experience of other areas that were afflicted by COVID-19 prior to its wide spread in the United States, blood bankers were able to convince most stakeholders that the true risk to the blood supply was not SARS-CoV-2 itself, but rather social distancing practices resulting in an interruption to the critically needed blood supply. cache = ./cache/cord-306881-wrd2rhjz.txt txt = ./txt/cord-306881-wrd2rhjz.txt === reduce.pl bib === id = cord-307285-bxy0zsc7 author = Dar Odeh, Najla title = COVID-19: Present and Future Challenges for Dental Practice date = 2020-04-30 pages = extension = .txt mime = text/plain words = 4708 sentences = 227 flesch = 44 summary = Realizing the severity of outcomes associated with this disease and its high rate of transmission, dentists were instructed by regulatory authorities, such as the American Dental Association, to stop providing treatment to dental patients except those who have emergency complaints. In vitro studies have shown that azithromycin is active against Zika and Ebola viruses, [18] [19] [20] and is able to prevent severe respiratory tract infections when administrated to patients suffering viral infection [12] However, the efficacy of azithromycin in combination with hydroxychloroquine in the treatment of COVID-19 patients has not been confirmed yet [21, 22] , and more studies are needed to further investigate its clinical effects. Following the recommended cross-infection control procedures, spreading awareness based on evidence and not misconceptions, identifying emergency cases indicated for dental treatment, and practicing effective tele-dentistry when needed can all be helpful for dental patients and community as a whole. cache = ./cache/cord-307285-bxy0zsc7.txt txt = ./txt/cord-307285-bxy0zsc7.txt === reduce.pl bib === id = cord-307406-59yh48tt author = de Loyola, Mariana Braccialli title = Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5739 sentences = 408 flesch = 47 summary = 2, 3 A1AT is an inhibitor of SARS-CoV-2 infection and two of the most important proteases in the pathophysiology of Covid-19: the transmembrane serine protease 2 (TMPRSS2) and the disintegrin and metalloproteinase 17 (ADAM17), as was well as an inhibitor of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. [4] [5] [6] Moreover, recent data indicate that lower IL-6:A1AT levels are related to worse prognosis in This review addresses the interplay between A1AT, TMPRSS2, ADAM17, and inflammatory molecules during SARS-CoV-2 infection with the aim of identifying new avenues for effective treatments against Covid-19. In order to achieve a more comprehensive understanding of A1AT in Covid-19, is important to address the following concerns: The evidence presented in this review highlights the relevance of the A1AT as a host protective factor, which can inhibit the TMPRSS2-mediated SARS-CoV-2 infection, modulate the deleterious effect of ADAM17 activation and the activity of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. cache = ./cache/cord-307406-59yh48tt.txt txt = ./txt/cord-307406-59yh48tt.txt === reduce.pl bib === id = cord-307242-e20gtx0z author = Jegouic, Sophie M. title = Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3454 sentences = 177 flesch = 52 summary = Similar western blot analysis of total protein extracts following induction of logarithmic phase E.coli cultures with IPTG confirmed the expression of His-tagged S antigen of the predicted molecular weight in all cases ( Figure 3 , upper panel). Nevertheless, we found that S protein fragments prepared for gel electrophoresis using non-reducing loading buffer could be used successfully for epitope mapping of 2 S reactive monoclonal antibodies, 3G9, an unpublished mouse mAb generated to SARS S, and CR3022, a human mAb also isolated originally to SARS [19] but shown to cross-react with SARS-CoV-2. To provide an additional level of validation and to add epitope specificity to the data, 2 of the sera scoring positive by S1 ELISA were used as probes on western blots using full length S expressed in insect cells (cf. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain ( RBD219-N1 ), a SARS Vaccine Candidate cache = ./cache/cord-307242-e20gtx0z.txt txt = ./txt/cord-307242-e20gtx0z.txt === reduce.pl bib === id = cord-307702-n74wvika author = Durant, Thomas J S title = Impact of COVID-19 Pandemic on Laboratory Utilization date = 2020-07-14 pages = extension = .txt mime = text/plain words = 2811 sentences = 162 flesch = 44 summary = METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. cache = ./cache/cord-307702-n74wvika.txt txt = ./txt/cord-307702-n74wvika.txt === reduce.pl bib === id = cord-307287-zpq6byml author = Poulsen, Nadia Nicholine title = Cyclosporine and COVID‐19: Risk or Favorable? date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4455 sentences = 235 flesch = 39 summary = A letter by Russel et al suggests that there is tantalizing in vitro evidence for cyclosporine as an anti-coronavirus agent as well as a potential disease-modifying role through inhibition of Severe Acute Respiratory Syndrome (SARS) coronavirus-mediated IL-2 induction and authors advocate that a trial of cyclosporine should be considered in the event of a future SARS epidemic 22 . The Immunonephrology Working Group of the European Renal Association-European Dialysis and Transplant Association has published recommendations for the management of patients with immune-mediated kidney disease during this current pandemic, and authors point out that patients with mild COVID-19 might continue low dose of cyclosporine due to the in vitro evidence of inhibition of coronavirus replication 84 . We are still awaiting robust data from COVID-19 patients actively treated with calcineurin inhibitors due to transplantation or autoimmune diseases but so far there is no evidence that use of cyclosporine possess an additional risk for severe COVID-19 in addition to the co-morbidities such as diabetes, smoking, hypertension and obesity that often co-exist in these patients. cache = ./cache/cord-307287-zpq6byml.txt txt = ./txt/cord-307287-zpq6byml.txt === reduce.pl bib === id = cord-307671-f9l2l8fi author = Said, Mohammed title = The Forgotten Element in the Resumption of Elective Bariatric Surgery During the COVID-19 Pandemic: the Patient Consent! date = 2020-09-19 pages = extension = .txt mime = text/plain words = 2199 sentences = 123 flesch = 39 summary = The aim was to assess their knowledge and expectations regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A total of 233 (87.6%) candidates believed that they were prone to a higher risk of severe SARS-CoV-2 infection, and 24.4% of them believed that bariatric surgery, during the pandemic, would improve their immunity. The present study aims to help in answering these questions through an assessment of patients' concepts regarding bariatric surgery resumption after the peak of the COVID-19 pandemic. The following four questions assessed the patient opinion regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Bariatric teams need to ensure that candidates for surgery share the required knowledge regarding the methods of transmission of SARS-CoV-2 infection and are willing to follow the protective measures. cache = ./cache/cord-307671-f9l2l8fi.txt txt = ./txt/cord-307671-f9l2l8fi.txt === reduce.pl bib === id = cord-307853-m1q1sjr4 author = Majumder, Satyabrata title = Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model date = 2020-10-16 pages = extension = .txt mime = text/plain words = 3048 sentences = 176 flesch = 57 summary = title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model In this study we have examined the intrinsic dynamics of the prefusion, lying state of trimeric S protein of these viruses through Normal Mode Analysis using Anisotropic Network Model. MERS-CoV spike shows unique dynamical motion compared to the other two S protein indicated by low RMSIP, spectral overlap and cosine correlation value. A detailed study to explore the intrinsic dynamical motion of the prefusion lying state spike protein trimer is needed for proper understanding of its function from conformation perspective. RMSIP computes quantitative comparison value between the sets of normal modes and expressed as: Structural alignments of the models were done using PyMol. We have computed the eigenvalues of first hundred non-zero normal modes of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike (S) proteins in the lying state ( Fig. 1 ). cache = ./cache/cord-307853-m1q1sjr4.txt txt = ./txt/cord-307853-m1q1sjr4.txt === reduce.pl bib === id = cord-307653-nyr6mtj1 author = Palmeira, Patricia title = Why is SARS-CoV-2 infection milder among children? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3455 sentences = 163 flesch = 40 summary = As with SARS-CoV, COVID-19 is believed to be initiated by the binding of the SARS-CoV-2 envelope-anchored spike protein to the outer surface of the angiotensin-converting enzyme 2 (ACE2) catalytic domain (13) , promoting endocytosis where viral and host membranes fuse and consequent entry of the virus into the host cell. (16) reported that ACE2 pulmonary expression is concentrated mainly in type II alveolar cells, which express many other genes that could favor viral replication, thus offering an explanation for the severe alveolar damage associated with SARS-CoV-2 infection. In agreement with the hypothesis that ACE2 expression levels have a significant role in acute respiratory distress syndrome (ARDS), which also occurs in COVID-19, an experimental mouse model of H5N1 virus-induced lung injury and death showed ACE2 downregulation following infection (25) . cache = ./cache/cord-307653-nyr6mtj1.txt txt = ./txt/cord-307653-nyr6mtj1.txt === reduce.pl bib === id = cord-307701-fujejfwb author = Gaurav, Shubham title = Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date = 2020-06-07 pages = extension = .txt mime = text/plain words = 2069 sentences = 111 flesch = 54 summary = Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the cause of the novel human Corona Virus Disease COVID-19, first reported on November 17 th , 2019 in Wuhan, China [12] . In addition to structural and NSPs, SARS-CoV-2 genome also codes for at least two other viroporin candidates (other than the E protein), namely ORF3a and ORF8 [3] . Moreover, the 29-nucleotide deleted SARS CoV-1 strain had a 23-fold less viral replication as compared to its wild type, suggesting that this mutation effectively attenuated the virus. cache = ./cache/cord-307701-fujejfwb.txt txt = ./txt/cord-307701-fujejfwb.txt === reduce.pl bib === id = cord-307460-v6xgkg1p author = Hsu, Yu-Lung title = Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan date = 2020-06-13 pages = extension = .txt mime = text/plain words = 220 sentences = 26 flesch = 64 summary = key: cord-307460-v6xgkg1p authors: Hsu, Yu-Lung; Lin, Hsiao-Chuan; Wei, Hsiu-Mei; Lai, Huan-Cheng; Hwang, Kao-Pin title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan cord_uid: v6xgkg1p Therefore, we believe that, all things being equal, the transmission of SARS CoV-2 differs 32 between tropical and non-tropical regions. This is because countries greatly 34 differ with respect to population density, disease burden, health care quality, infection control Stability of SARS coronavirus in human specimens and 42 environment and its sensitivity to heating and UV irradiation Epidemiology and clinical 45 presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 46 3 years using a novel multiplex real-time PCR method The pediatric burden of human coronaviruses 49 evaluated for twenty years Coronaviruses in the Pediatric Population Hsu 57 and Hsiao-Chuan Lin interpreted data Distribution of COVID-19 patients around the world 64 Distribution of local cases of COVID-19 in Taiwan cache = ./cache/cord-307460-v6xgkg1p.txt txt = ./txt/cord-307460-v6xgkg1p.txt === reduce.pl bib === id = cord-307815-reg04lpt author = Brancatella, Alessandro title = Is subacute thyroiditis an underestimated manifestation of SARS-CoV-2 infection? Insights from a case series date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2296 sentences = 174 flesch = 58 summary = After our initial description of a patient experiencing subacute thyroiditis (SAT) associated with SARS-CoV-2 infection (1), three additional case have been reported (2) (3) (4) . On March 1 st , a 38 year-old-woman underwent oropharyngeal swab for SARS-CoV-2 because of symptoms suspected for COVID-19 (Table 1) . At last evaluation (on May 10 th ), while taking prednisone 15 mg/d, patient was asymptomatic and thyroid function tests and inflammatory markers were in the normal range (Table 1) . At last evaluation (on May 18 th ), while taking 15 mg/d of prednisone, patient was asymptomatic, inflammatory markers were in the normal range, whereas thyroid function tests was consistent with subclinical hypothyroidism (Table 1) . In the present series, as well as in our previous report (1), patients experienced SAT after the resolution of distinctive symptoms of SARS-CoV-2 infection. cache = ./cache/cord-307815-reg04lpt.txt txt = ./txt/cord-307815-reg04lpt.txt === reduce.pl bib === id = cord-307463-bheq9p5w author = Rödel, Franz title = Low-dose radiation therapy for COVID-19 pneumopathy: what is the evidence? date = 2020-05-09 pages = extension = .txt mime = text/plain words = 2006 sentences = 97 flesch = 43 summary = Due to the current lack of effective pharmacological concepts, this situation has caused interest in (re)considering historical reports on the treatment of patients with low-dose radiation therapy for pneumonia. Although these historical reports are of low-level evidence per se, hampering recommendations for decision-making in the clinical setting, they indicate effectiveness in the dose range between 0.3 and 1 Gy, similar to more recent dose concepts in the treatment of acute and chronic inflammatory/degenerative benign diseases with, e.g., a single dose per fraction of 0.5 Gy. This concise review aims to critically review the evidence for low-dose radiation treatment of COVID-19 pneumopathy and discuss whether it is worth investigating in the present clinical situation. This situation has caused interest in (re)considering the historical treatment of patients with low-dose radiation therapy for pneumonia. This review on 15 reports covers 863 patients with severe pneumonia of K different pathogeneses, including two studies of viral origin treated with low doses of kilovoltage X-rays. cache = ./cache/cord-307463-bheq9p5w.txt txt = ./txt/cord-307463-bheq9p5w.txt === reduce.pl bib === id = cord-307605-8zgyar7e author = Klimek, Ludger title = Management von Anaphylaxie-gefährdeten Patienten während der Covid-19-Pandemie: Ein Positionspapier des Ärzteverbandes Deutscher Allergologen (AeDA)A, der Deutschen Gesellschaft für Allergologie und klinische Immunologie (DGAKI)B, der Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)C und des Deutschen Allergie- und Asthmabundes (DAAB)D date = 2020-11-09 pages = extension = .txt mime = text/plain words = 3716 sentences = 485 flesch = 38 summary = Schlussfolgerung: Die Beratung, die Entwicklung von Strategien zur Expositionsprophylaxe und die Notfalltherapie von Patienten mit Anaphylaxie ist in der aktuellen Covid-19-Pandemie bei gefährdeten Patienten sehr wichtig. Die Selbstapplikation der Notfallmedikation ist gerade unter den Bedingungen einer möglichen Quarantäne oder Isolation zu bevorzugen und auch die Verordnung eines zweiten Adrenalin-Autoinjektors sollte großzügig Patientenindividuell geprüft werden. Der globale Ausbruch einer Pandemie von Infektionen mit dem neuartigen Coronavirus SARS-CoV-2 wurde als "Coronavirus-Krankheit 2019" ( Covid19) benannt und stellt die Gesundheitssysteme weltweit vor große Herausforderungen. Bei einer großen Zahl von Patienten führt die Infektion nach der Inkubationszeit zu einer Erkrankung der oberen und unteren Atemwege oder seltener anderer Organsysteme (NerAngiotensin-converting-enzyme-2 Fall zum Multiorganversagen und respiratorischer Insuffizienz führt, wie dies auch für andere Coronavirus-Infektionen (SARS-CoV-1, MERS-CoV) beschrieben wurde [4, 5, 6] . Unter Berücksichtigung der aktuellen Leitlinien zur Anaphylaxie-Behandlung wie auch der WHO-und RKI-Empfehlungen zu Covid-19 schlussfolgern wir, dass Anaphylaxie-Patienten mit vermuteter oder diagnostizierter SARS-CoV-2-Infektion weiterhin nach den aktuellen Richtlinien behandelt werden sollten. cache = ./cache/cord-307605-8zgyar7e.txt txt = ./txt/cord-307605-8zgyar7e.txt === reduce.pl bib === id = cord-308021-cnf4xljc author = Kohns Vasconcelos, Malte title = SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date = 2020-10-13 pages = extension = .txt mime = text/plain words = 1981 sentences = 99 flesch = 47 summary = Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Paediatric departments of 23 mostly tertiary care hospitals in 12 European countries (Belgium, Germany, France, Italy, Poland, Portugal, the UK, the Netherlands, Greece, Spain, Lithuania and Switzerland) participated in the surveys (response rate 29%). This changed by April at all three sites, so that afterwards detection of another pathogen that could explain the respiratory symptoms no longer excluded a patient from being a suspect case and from undergoing SARS-CoV-2 testing. In the early stages of the COVID-19 pandemic, paediatric emergency departments implemented standardised case definitions, testing guidelines and infection control measures rapidly. cache = ./cache/cord-308021-cnf4xljc.txt txt = ./txt/cord-308021-cnf4xljc.txt === reduce.pl bib === id = cord-307502-vuju89lc author = Leipe, J. title = SARS-CoV-2 & Rheuma: Konsequenzen der SARS-CoV-2-Pandemie für Patienten mit entzündlich rheumatischen Erkrankungen. Ein Vergleich der Handlungsempfehlungen rheumatologischer Fachgesellschaften und Risikobewertung verschiedener antirheumatischer Therapien date = 2020-08-26 pages = extension = .txt mime = text/plain words = 1854 sentences = 220 flesch = 45 summary = V. (DGRh) bereits zu Beginn der COVID-19-Pandemie im März 2020 erste Handlungsempfehlungen zum Management von Patienten mit entzündlich rheumatischen Erkrankungen (ERE) unter dem Aspekt der SARS-CoV-2/COVID-19-Bedrohung herausgegeben hat [13] , wurden diese im Juli 2020 durch ein Update aktualisiert und erweitert (im Folgenden DGRh-Update) [14] . Bezüglich der Risikoeinschätzung für schwere COVID-19-Verläufe wurde in den Empfehlungen der DGRh, EULAR und ACR postuliert, dass Patienten mit ERE kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 oder eines schweren Verlaufes für COVID-19 aufweisen. a. basierend auf teilweise kurz davor publizierten Daten, davon aus, dass auch die medikamentöse antirheumatische Therapie kein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt, mit Ausnahme von Glukokortikoiden in einer Dosierung von 10 mg Prednisolonäquivalent/Tag und mehr [4] . Im DGRh-Update wurde, basierend auf aktuell publizierten Daten zu SARS-CoV-2 und Erkenntnissen aus früheren Studien zum allgemeinen Infektionsrisiko, von einem erhöhten Risiko für einen schweren COVID-19-Verlauf bei unzureichend eingestellten ERE ausgegangen [3] . cache = ./cache/cord-307502-vuju89lc.txt txt = ./txt/cord-307502-vuju89lc.txt === reduce.pl bib === id = cord-307770-1igydu3y author = Rawson, Timothy M title = Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2998 sentences = 266 flesch = 45 summary = title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. cache = ./cache/cord-307770-1igydu3y.txt txt = ./txt/cord-307770-1igydu3y.txt === reduce.pl bib === id = cord-308080-1heu9vuv author = Simulundu, Edgar title = First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1714 sentences = 99 flesch = 52 summary = title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient's SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. cache = ./cache/cord-308080-1heu9vuv.txt txt = ./txt/cord-308080-1heu9vuv.txt === reduce.pl bib === id = cord-308071-1bk3xuwf author = Lang, Christian title = Lung transplantation for COVID-19-associated acute respiratory distress syndrome in a PCR-positive patient date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2432 sentences = 128 flesch = 46 summary = Herein, we report the first case of lung transplantation for a patient with a persistently positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR test result. This decision was based on the following considerations: (1) virus culture was negative and real-time RT-PCR Ct values were high; (2) it was more than 5 weeks since the start of the SARS-CoV-2 infection; (3) no alternative treatment options were available; (4) the case was a single-organ failure in a young patient; (5) it was a preseptic condition originating from the lungs; and (6) there were no other obvious barriers for long-term recovery. To our knowledge, available evidence for lung transplant ation in COVID-19 is limited to two preliminary reports from China, suggesting that this treatment might be an option for SARS-CoV-2 PCR-negative patients. 11, 12 The case we present here extends the reports from China by showing that lung transplantation can be done in patients with positive RT-PCR results, provided that Vero cell cultures confirm non-infectivity. cache = ./cache/cord-308071-1bk3xuwf.txt txt = ./txt/cord-308071-1bk3xuwf.txt === reduce.pl bib === id = cord-307842-7q2jd0mf author = Fox, Alisa title = Robust and specific secretory IgA against SARS-CoV-2 detected in human milk date = 2020-10-26 pages = extension = .txt mime = text/plain words = 467 sentences = 40 flesch = 58 summary = The SARS-CoV-2 immune response in human milk has not yet been examined, though protecting infants and young children from COVID-19 is critical for limiting community transmission, and preventing serious illness and death. Milk samples were initially evaluated for IgA binding reactivity by human IgA-specific ELISA to the 88 full trimeric SARS-CoV-2 Spike (Fig. 1) . It was evident that all samples obtained from COVID-19-89 recovered donors (100%), in undiluted form, exhibited binding activity significantly above that of the 90 pre-pandemic control milk samples, which did exhibit some low-level non-specific or cross-reactive 91 activity (Fig. 1a) . It was found 92 that all COVID-19-recovered samples exhibited endpoint titers significantly higher than control samples evident that most of the samples contained SARS-CoV-2-reactive IgA without necessarily containing 146 measurable IgG and/or IgM, which particularly in the case of IgG, would likely be derived in large part 147 from the serum. cache = ./cache/cord-307842-7q2jd0mf.txt txt = ./txt/cord-307842-7q2jd0mf.txt === reduce.pl bib === id = cord-308123-eu0azqfu author = Lee, Yun Young title = Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5002 sentences = 315 flesch = 54 summary = title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm Our findings suggest that exogenously administered long-acting nanoparticulate DNase-1 can effectively reduce cfDNA levels and neutrophil activities and may be used as a potential therapeutic intervention for life-threatening SARS-CoV-2-mediated illnesses. We showed that an intravenous administration of DNase-1-coated polydopamine-poly (ethylene glycol) nanoparticulates, named long-acting DNase-1 (Scheme 1), effectively inhibited NETosis factors in blood samples of patients with COVID-19 and also improve survival in a sepsis model. We also observed markedly reduced NET levels, MPO activity, and NE levels in neutrophils of COVID-19 patients with sepsis upon treatment of the DNase-1 formulations (Fig. 4C-E) . patients with sepsis, the long-acting DNase-1 significantly reduced cfDNA levels and increased the activity of the DNase-1 ( Fig. S6A and B) . (C) NET ratio of SARS-CoV-2 Sepsis patient PBMCs was suppressed after free DNase-1 or long-acting DNase-1 treatment. cache = ./cache/cord-308123-eu0azqfu.txt txt = ./txt/cord-308123-eu0azqfu.txt === reduce.pl bib === id = cord-307885-butuv3n1 author = Galvani, Alison P. title = Emerging Infections: What Have We Learned from SARS? date = 2004-07-17 pages = extension = .txt mime = text/plain words = 1195 sentences = 71 flesch = 44 summary = As is typical of an emerging disease, no vaccines or drugs to combat SARS existed, making quarantine, patient isolation, travel restrictions, and contact precautions the only means of limiting transmission. Previously, similar models had guided public health policy, for example, in halting an outbreak of hoof and mouth disease in the United Kingdom in 2001 (5, 6) . The case-fatality rate is a key determinant of the public health impact of an emerging disease and was high for SARS at approximately 15% (11) . The success with which WHO coordinated the global collaboration in containing SARS galvanized the World Health Assembly to grant WHO greater authority to verify outbreaks, conduct investigations of outbreak severity, and evaluate the adequacy of control measures. Transmission dynamics of the etiological agent of severe acute respiratory syndrome (SARS) in Hong Kong: the impact of public health interventions Infectious diseases of humans: dynamics and control cache = ./cache/cord-307885-butuv3n1.txt txt = ./txt/cord-307885-butuv3n1.txt === reduce.pl bib === id = cord-308093-m40czdsr author = Matthews, M. M. title = COVID-19 serological survey using micro blood sampling date = 2020-10-13 pages = extension = .txt mime = text/plain words = 3542 sentences = 249 flesch = 60 summary = During August 2020, we carried out a serological survey among students and employees at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, testing for the presence of antibodies against SARS-CoV-2, the causative agent of COVID-19. We used a FDA-authorized 2-step ELISA protocol developed by the Krammer Lab in combination with at-home self-collection of blood samples using a custom low-cost finger prick-based capillary blood collection kit. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. . https://doi.org/10.1101/2020.10.09.20209858 doi: medRxiv preprint 48 Serological surveys which detect the presence of antibodies against SARS-CoV-2 49 antigens can provide important information to the government for issuing health care 50 guidelines. cache = ./cache/cord-308093-m40czdsr.txt txt = ./txt/cord-308093-m40czdsr.txt === reduce.pl bib === id = cord-308356-ojx3tasi author = Schwarz, Silke title = Corona bei Kindern: Die Co-Ki Studie: Relevanz von SARS-CoV-2 in der ambulanten pädiatrischen Versorgung in Deutschland date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1258 sentences = 172 flesch = 64 summary = Hintergrund Die aktuelle Studienlage deutet darauf hin, dass Kinder und Jugendliche eine geringere Rate symptomatischer SARS-CoV-2-Infektionen (COVID-19) aufweisen als Erwachsene und mehrheitlich keine oder nur milde Symptome entwickeln [1] [2] [3] . Darüber hinaus ist leider nicht bekannt, wie viele der vom RKI erfassten Kinder symptomatisch waren, und ob ihre etwaigen Symptome auf SARS-CoV-2 zurückzuführen sind. Diese KJÄ meldeten insgesamt 9803 Kinder und Jugendliche, die aufgrund eines Verdachts der Eltern oder eines Kontaktes mit einem SARS-CoV-2-Infizierten in der Sprechstunde vorgestellt wurden. Die KJÄ ihrerseits hatten den klinischen Verdacht auf eine SARS-CoV-2-Infektion bei 3654 Kindern, wobei einzelne KJÄ mehr eigene Verdachtsfälle als Vorstellungen mit Verdacht meldeten, und das Wort "ebenfalls" in Frage 4 wohl ignorierten, weshalb die 3654 nicht eine reine Teilmenge von den 9803 sind. Die höhere Rate an Antikörperpositivität hängt mit der Tatsache zusammen, dass mehr Kinder getestet wurden, die zuvor Symptome und/oder einen positiven PCR-Test hatten. cache = ./cache/cord-308356-ojx3tasi.txt txt = ./txt/cord-308356-ojx3tasi.txt === reduce.pl bib === id = cord-308288-3ewdy5l3 author = Domingues, Renan Barros title = First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1163 sentences = 67 flesch = 48 summary = However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74–100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs. The viral genome was demonstrated by RT-PCR technique in cerebrospinal fluid sample (CSF), suggesting that the virus has the ability to infect central nervous system (CNS) [1] . However, no case has been described of an association between SARS-COV-2 and CNS demyelinating disease so far. This case report suggests a possible association between CNS focal symptoms compatible with demyelinating disease and SARS-COV-2 infection. cache = ./cache/cord-308288-3ewdy5l3.txt txt = ./txt/cord-308288-3ewdy5l3.txt === reduce.pl bib === id = cord-308075-1ftswsm8 author = Segura, Patricia Sanz title = Involvement of the digestive system in COVID-19. A review date = 2020-10-09 pages = extension = .txt mime = text/plain words = 4829 sentences = 247 flesch = 47 summary = 4 Recent studies have indicated detection of SARS-CoV-2 by PCR in the faeces of infected patients, with a higher prevalence in those with gastrointestinal symptoms, in particular diarrhoea. Moreover, the cohort studies that have analysed the course of COVID-19 in patients with viral hepatitis (hepatitis B) 41 and those that have assessed the impact of non-alcoholic fatty liver disease on the disease due to the novel coronavirus, especially in the absence of obesity, have concluded that there is a higher risk of developing a serious form of pneumonia and having more prolonged hospital stays, 42 although the available data in this regard remain insufficient. cache = ./cache/cord-308075-1ftswsm8.txt txt = ./txt/cord-308075-1ftswsm8.txt === reduce.pl bib === id = cord-307942-t8165mdx author = Zwald, Marissa L. title = Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1619 sentences = 71 flesch = 43 summary = On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). During the investigation period, 226 patients seen at one of the four urgent care centers met the inclusion criteria (i.e., Santa Clara County resident, respiratory symptoms, no recent travel, and no known close contact with a patient with confirmed COVID-19) and were tested for evidence of influenza virus infection; among those, 53 (23%) had positive test results for influenza. cache = ./cache/cord-307942-t8165mdx.txt txt = ./txt/cord-307942-t8165mdx.txt === reduce.pl bib === id = cord-307858-274a699i author = Hotez, Peter J. title = COVID-19 vaccines: neutralizing antibodies and the alum advantage date = 2020-06-04 pages = extension = .txt mime = text/plain words = 1331 sentences = 64 flesch = 40 summary = A chemically inactivated virus vaccine (PiCoVacc) and a recombinant proteinbased vaccine (CoV-RBD219N1) were recently shown to elicit high levels of protective immunity in rhesus macaques or in mice against homologous virus challenge with SARS-CoV-2 or SARS-CoV, respectively 2,3 . Similarly, mice vaccinated with CoV-RBD219N1, based on the recombinant RBD protein of SARS-CoV, which is now investigated as a COVID-19 vaccine candidate, exhibited virus-neutralizing antibody titres between 640 and 1,280 upon SARS-CoV homologous viral challenge 3 . Therefore, an emerging story in COVID-19 vaccine development is the potential importance of inducing high levels of neutralizing antibodies to the S protein or its RBD. A key finding so far is that aluminium adjuvant formulations, such as those used for PiCoVacc and CoV-RBD219N1, appear to promote high titres of neutralizing antibody. A potential concern about the use of aluminium adjuvants is based on the claim that T H 2-type immune responses might promote vaccine-enhanced respiratory disease (VAERD) 9 . cache = ./cache/cord-307858-274a699i.txt txt = ./txt/cord-307858-274a699i.txt === reduce.pl bib === id = cord-307811-6e3j0pn7 author = Hao, Wei title = Binding of the SARS-CoV-2 Spike Protein to Glycans date = 2020-07-02 pages = extension = .txt mime = text/plain words = 5665 sentences = 299 flesch = 54 summary = Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. Previous studies of many other viruses suggested that SARS-CoV-2 S protein may use other molecules on host cell surface as attachment factors to facilitate binding to the high-affinity receptor ACE2. 36 A recent study suggested that HS may bind to the receptor binding domain (RBD, the C-terminal region of the S1 subunit, Fig. 2 ) of the SARS-CoV-2 spike protein and change its conformation. 38 In this study, we systematically examined and compared the binding of the SARS-CoV-2 S protein subunits, full-length molecule and its trimer to different HS using microarray experiments (Fig. 2) . In addition to binding protein-based receptors, many viruses can interact with cell surface glycans, including GAGs and sialic acid-containing oligosaccharides. cache = ./cache/cord-307811-6e3j0pn7.txt txt = ./txt/cord-307811-6e3j0pn7.txt === reduce.pl bib === id = cord-308066-lrbi5198 author = Childs, James E. title = Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date = 2007 pages = extension = .txt mime = text/plain words = 15698 sentences = 714 flesch = 41 summary = The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). cache = ./cache/cord-308066-lrbi5198.txt txt = ./txt/cord-308066-lrbi5198.txt === reduce.pl bib === id = cord-308279-gsk4qel5 author = Suzuki, Yuichiro J. title = The viral protein fragment theory of COVID-19 pathogenesis date = 2020-09-11 pages = extension = .txt mime = text/plain words = 1397 sentences = 70 flesch = 44 summary = I herein propose the viral protein fragment theory of COVID-19 pathogenesis based on my observations in cultured human vascular cells that SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I hypothesize that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling without the rest of the viral components. This hypothesis is based on my experimental observations in cultured human vascular cells that the recombinant full length S1 subunit of SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I propose a scenario that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling. cache = ./cache/cord-308279-gsk4qel5.txt txt = ./txt/cord-308279-gsk4qel5.txt === reduce.pl bib === id = cord-308077-hbxpn5a1 author = Siepmann, Timo title = Variability of symptoms in neuralgic amyotrophy following infection with SARS‐CoV‐2 date = 2020-10-01 pages = extension = .txt mime = text/plain words = 493 sentences = 38 flesch = 46 summary = The report of Cacciavillani and colleagues contributes to the discussion of the possibility of peripheral nerve involvement in coronavirus disease 2019 (COVID-1 9) and adds to our observation of neuralgic amyotrophy following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Interestingly, research prior to the COVID-19 pandemic showed that earlier coronaviruses such as hemagglutinating encephalomyelitis virus may first enter peripheral nerve terminals before traveling to the central nervous system (CNS) via synapse-connected routes. In fact, peripheral nerve damage might occur in almost 10% of patients hospitalized for SARS-CoV-2 infection. Whether peripheral nervous system complications following COVID-19 such as neuralgic amyotrophy result from direct neuroinvasion or from an auto-immune post-infectious mechanism needs to be elucidated. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-308077-hbxpn5a1.txt txt = ./txt/cord-308077-hbxpn5a1.txt === reduce.pl bib === id = cord-307932-7t41wvw3 author = Guo, Xiaoqin title = Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers date = 2020-02-14 pages = extension = .txt mime = text/plain words = 1854 sentences = 115 flesch = 58 summary = title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers METHODS: A long-term prospective cohort study followed 34 SARS-CoV-infected healthcare workers from a hospital with clustered infected cases during the 2002-2003 SARS outbreak in Guangzhou, China, with a 13-year follow-up. Non-linear exponential decay models were used to estimate the average decay rates of the antibody CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In our cohort, we found that two healthcare workers might have been misdiagnosed with 236 SARS, as the IgG antibodies against both the whole virus and N199 antigen was persistently 237 lower than the cutoff value, for these two patients. Collectively, based on our results, we can infer that the IgG against SARS-CoV can persist at CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-307932-7t41wvw3.txt txt = ./txt/cord-307932-7t41wvw3.txt === reduce.pl bib === id = cord-308234-4obggisp author = Ford, Nathan title = Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID‐19: initial assessment date = 2020-04-15 pages = extension = .txt mime = text/plain words = 2845 sentences = 137 flesch = 45 summary = RESULTS: From an initial screen of 433 titles, two randomized trials and 24 observational studies provided clinical outcome data on the use of antiretroviral drugs; most studies reported outcomes using LPV/r as treatment. The use of lopinavir/ritonavir (LPV/r) has been supported by data from in vitro studies, animal models and positive clinical outcomes when LPV/r was given to patients infected with severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) diseases also caused by coronaviruses [2] [3] [4] [5] . Lopinavir/ritonavir (LPV/r) is included in rapid guidance issued by researchers from Wuhan University based on clinical use during prior epidemics of severe acute respiratory syndrome (SARS) and MERS coronavirus (CoV) infections [6] . This systematic review identified two randomized trials and 21 observational studies provided clinical outcome data on the use of LPV/r for the treatment of COVID-19, SARS and MERS. cache = ./cache/cord-308234-4obggisp.txt txt = ./txt/cord-308234-4obggisp.txt === reduce.pl bib === id = cord-308142-3x3n6cpt author = Lee, Nelson title = Chikungunya Fever, Hong Kong date = 2006-11-17 pages = extension = .txt mime = text/plain words = 1722 sentences = 85 flesch = 46 summary = aureus isolated from active lesions were not available for testing, the recovery of identical PVL-positive organisms from nasal cultures strongly suggests the presence of a pathogenic clone that probably caused the recurrent infections in the 6 affected family members. Serum specimens taken on days 2 and 6 were positive for chikungunya virus RNA by in-house reverse transcription (RT)-PCR at the Public Health Laboratory Service (PHLS) (targeting the nonstructural protein-1 [NSP-1] gene) and PWH laboratory (targeting both NSP-1 and the envelope glycoprotein [E1] gene). The most striking finding from the cytokine analysis (Table) is the high level of interferon-γ (IFN-γ)-inducible protein-10 (IP-10/CXCL-10), up to 26 and 16 times the upper limit of the normal range at days 2 and 6 after disease onset, respectively. In severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (4, 5) and H5N1 influenza (6) infections, very high blood levels of CXCL10 and moderately high CCL2, CXCL9, and CXCL8 concentrations, or their enhanced expressions in vitro, have been reported. cache = ./cache/cord-308142-3x3n6cpt.txt txt = ./txt/cord-308142-3x3n6cpt.txt === reduce.pl bib === id = cord-308224-cqi1x92w author = Wu, Lianhua title = Clinical study on the related markers of blood coagulation in the patients with ANFH after SARS date = 2007-10-01 pages = extension = .txt mime = text/plain words = 1634 sentences = 96 flesch = 54 summary = The expression of CD31, CD61, CD62p, CD63 and PAC-1 on platelet membrane was measured respectively by flowcytometry, and the plasma prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and fibrinogen (Fbg) were measured by blood clotting instrument in 26 patients with ANFH after SARS and in 17 healthy adults. When patients experienced discomfort or pain at the site of hip-joint four to six months after administration of hormone, their blood samples were taken intravenously under the condition of fasting to measure CD31, CD61, CD62P, CD63, PAC-1 on platelet membrane and coagulation four indices including PT, APTT, Fbg and TT. It was found that, in these patients with ANFH after SARS, the expression of glycoprotein CD31, CD61, CD62P, CD63 and PAC-1 on platelet membrane decreased; coagulation four indices including PT, APTT and TT time were all normal. cache = ./cache/cord-308224-cqi1x92w.txt txt = ./txt/cord-308224-cqi1x92w.txt === reduce.pl bib === id = cord-308100-tvk47fd7 author = Soetikno, Roy title = Considerations in performing endoscopy during the COVID-19 pandemic date = 2020-03-27 pages = extension = .txt mime = text/plain words = 2705 sentences = 224 flesch = 54 summary = Based on experiences and the literature, our objective is to provide practical suggestions for performing endoscopy in the setting of COVID-19 pandemic. 6 It is unknown how much of the risk was related to the direct care of infected patients or to the inadequate use of personal protective equipment (PPE). 9 With numbers of COVID-19 cases continuing to rise in North America and Europe, we aim to provide practical suggestions to potentially avoid the transmissions of COVID-19 in the endoscopy unit. Possible routes of SARS-CoV-2 transmission include (1) person-to-person, (2) respiratory droplets, (3) aerosols generated during endoscopy, and (4) contact with contaminated surroundings and body fluids. 13 Recently, the World Health Organization (WHO) has published an extensive guideline on the rational use of personal protective equipment (PPE) for COVID-19 and provided specific instructions for healthcare workers performing AGP on patients with COVID-19. 17 Note that as an AGP, endoscopy of PUI/COVID patients requires the use of respiratory protection. cache = ./cache/cord-308100-tvk47fd7.txt txt = ./txt/cord-308100-tvk47fd7.txt === reduce.pl bib === id = cord-308358-2bap7iih author = Friedland, Robert P title = The role for the metagenome in the pathogenesis of COVID-19 date = 2020-10-07 pages = extension = .txt mime = text/plain words = 1126 sentences = 57 flesch = 39 summary = A common factor associated with aging and other COVID-19 risk factors is the dysbiosis of gut microbiota and resulting low grade inflammation with loss of epithelial barrier function [5] . Germ free animals have defective immune systems and the gut microbiota influences pathogen dissemination, inflammation, organ damage and mortality in murine pneumonia [9] . Changes in diet with aging may well influence short chain fatty acid production, affecting immune homeostasis, barrier function and severity of COVID-19. However, in cases of severe disease of COVID-19, it is the innate response and not the unregulated adaptive immune response via T cells that results in morbidity and death. The influence of the microbiota on immune processes in COVID19 infection may be assessed with metagenomic analysis of nasal, oral and intestinal communities, as well as metabolomics. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals cache = ./cache/cord-308358-2bap7iih.txt txt = ./txt/cord-308358-2bap7iih.txt === reduce.pl bib === id = cord-308302-5yns1hg9 author = Wu, Gang title = A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings date = 2020-08-20 pages = extension = .txt mime = text/plain words = 2966 sentences = 202 flesch = 48 summary = We used machine learning for processing laboratory findings of 110 patients with SARS-CoV-2 pneumonia (including 51 non-survivors and 59 discharged patients). Thus it is feasible to establish an accurate prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings. Laboratory tests for SARS-CoV-2 pneumonia included: blood routine test, serum biochemical (including glucose, renal and liver function, creatine kinase, lactate dehydrogenase, and electrolytes), coagulation profile, cytokine test, markers of myocardial injury, infection-related makers, and other enzymes. 68 discharged patients with SARS-CoV-2 pneumonia whose age and gender matched the non-survivors were selected (46 male, median age 66 years). A number of laboratory features were compared between non-survivors and discharged patients with SARS-CoV-2 pneumonia. With machine learning methods previously used in radiomics, a prediction model combining seven out of thirty-eight laboratory features was built for predicting the outcome of SARS-CoV-2 pneumonia. cache = ./cache/cord-308302-5yns1hg9.txt txt = ./txt/cord-308302-5yns1hg9.txt === reduce.pl bib === id = cord-307860-iqk1yiw4 author = Ionescu, Mihaela Ileana title = An Overview of the Crystallized Structures of the SARS-CoV-2 date = 2020-10-24 pages = extension = .txt mime = text/plain words = 9856 sentences = 668 flesch = 57 summary = Structures retrieved from PDB (August 12, 2020) were analyzed for relevant information on COVID-19 infection, synthesis of new inhibitors, SARS-CoV-2 interaction with host receptors, and the neutralizing antibodies interactions with spike glycoprotein. The first X-ray structure found (PDB ID 6LU7) belongs to the nonstructural protein 5 (3C-like protease) of the SARS-CoV-2 in complex with the Michael acceptor-based inhibitor N3 (PRD_002214). There is a cryo-EM crystal structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp12/nsp8/nsp7) with the antiviral drug remdesivir (PDB ID 7BV2) [37] . Previous studies on the crystal structures of SARS-CoV S glycoprotein mutants neutralized by 80R-specific antibodies have been considered a hope for the immunotherapeutic Fig. 8 The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites cache = ./cache/cord-307860-iqk1yiw4.txt txt = ./txt/cord-307860-iqk1yiw4.txt === reduce.pl bib === id = cord-308576-iw8oobbe author = Wuxing, Dai title = Expression and purification of SARS coronavirus membrane protein date = 2004 pages = extension = .txt mime = text/plain words = 1785 sentences = 130 flesch = 67 summary = To construct a recombinant plasmid Pet23a-M, the gene encoding severe acute respiratory syndrome (SARS) coronavirus membrane protein was amplified by RT-PCR and cloned into the expression plasmid Pet23a. To screen and prepare effective SARS virus vaccine and diagnostic antigens, we designed a pair of primers to amplify the gene encoding SARS coronavirus membrane protein and cloned it into an expression plasmid Pet23a. Coli BI.21 ( D E 3 ) and induced by I P T G , Western-blot showed that the expressed 27 kD protein which was characterized by SDS-PAGE and purified by metal chelated chromatography could react with antibodies in sera of SARS patients during convalescence, demonstrating the recombinant protein possessed the biological activity of membrane protein. cache = ./cache/cord-308576-iw8oobbe.txt txt = ./txt/cord-308576-iw8oobbe.txt === reduce.pl bib === id = cord-308256-jy20xtwx author = Wells, P. M. title = Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date = 2020-07-30 pages = extension = .txt mime = text/plain words = 4262 sentences = 235 flesch = 52 summary = Methods: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. cache = ./cache/cord-308256-jy20xtwx.txt txt = ./txt/cord-308256-jy20xtwx.txt === reduce.pl bib === id = cord-308231-1t70vkxm author = Childs, S. J. title = Could Deficiencies in South African Data Be the Explanation for Its Early SARS-CoV-2 Peak? date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3167 sentences = 191 flesch = 64 summary = It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, while the second is that of an imperceptible, pre-existing, immune fraction of the population. This fact, alone, is nonetheless unable to reasonably explain the SARS-CoV-2 threshold observed in the South African data, without contemplating improbably-high, though not impossible, values. It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, denoted a, while the second is that of an imperceptible, pre-existing, immune fraction of the population, denoted b. The phenomenon of infections having been underestimated by a multiplicative factor, alone, is unable to comprehensively explain the SARS-CoV-2 peak observed in the South African data, without contemplating improbably-high values. cache = ./cache/cord-308231-1t70vkxm.txt txt = ./txt/cord-308231-1t70vkxm.txt === reduce.pl bib === id = cord-308424-crvnzr44 author = Mascarenhas, Victor Hugo Alves title = Care recommendations for parturient and postpartum women and newborns during the COVID-19 pandemic: a scoping review date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4494 sentences = 276 flesch = 49 summary = Normal childbirth: • Mild clinical conditions; • There are no contraindications, especially due to a lack of evidence on vertical transmissions; • If pregnant women infected with SARS-CoV-2* present spontaneous labor and good cervical conditions, normal childbirth is advised, provided that the health service has the apparatus necessary to promote appropriate precautions; • To shorten the duration of the second stage of labor, directed pushing is recommended and parturient women are supposed to wear a surgical mask. This decision should be taken together with the mother and health workers involved in care delivery; • There is a risk of mothers transmitting SARS-CoV-2* to their NB † through respiratory droplets at the time of breastfeeding, even when wearing a surgical mask; • Women who opt not to breastfeed during the period of the disease should be encouraged to express breast milk to feed their NB † ; cache = ./cache/cord-308424-crvnzr44.txt txt = ./txt/cord-308424-crvnzr44.txt === reduce.pl bib === id = cord-308408-aciaj30k author = Paneesha, S. title = Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2069 sentences = 129 flesch = 60 summary = It is likely that patients who undergo immuno-chemotherapy as part of disease management will be at increased risk of clinical complications following SARS-CoV-2 infection. As such, the clinical outcome of SARS-CoV-2 infection in patients with therapy-naive CLL is an area of considerable importance. These findings suggest that SARS-CoV-2 infection in patients with therapy-naive CLL may be associated with considerably greater clinical risk than seen in the general population and argue for strict enforcement of quarantine conditions. At clinic one month prior to final admission the blood count showed Hb 85 g/l, WBC 274 x10 9 /l and platelets 127 x10 9 /l. Clinically, it is important to recognise that this is a feature of acute SARS-CoV-2 infection in patients with CLL and that the lymphocytosis can resolve quickly. Covid-induced lymphocytosis The peripheral lymphocyte count is shown for each patient at the most recent outpatient clinic prior to onset of SAR-CoV-2 infection and also the peak value during Covid-19 infection. cache = ./cache/cord-308408-aciaj30k.txt txt = ./txt/cord-308408-aciaj30k.txt === reduce.pl bib === id = cord-308110-cco3aq4n author = Okamoto, Mika title = The chemokine receptor antagonist cenicriviroc inhibits the replication of SARS-CoV-2 in vitro date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2689 sentences = 148 flesch = 51 summary = In this study, CVC was examined for its inhibitory effect on the replication of SARS-CoV-2, the causative agent of COVID-19, in cell cultures and found to be a selective inhibitor of the virus. The 50% effective concentrations of CVC were 19.0 and 2.9 μM in the assays based on the inhibition of virus-induced cell destruction and viral RNA levels in culture supernatants of the infected cells, respectively. Considering the fact that the regulation of excessive immune activation is required to treat COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. Since not only the inhibition of viral replication but also the control of excessive immune activation is mandatory to save COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. cache = ./cache/cord-308110-cco3aq4n.txt txt = ./txt/cord-308110-cco3aq4n.txt === reduce.pl bib === id = cord-308715-uo6h1h2e author = Chandra, Aman title = Personal protective equipment (PPE) for vitreoretinal surgery during COVID-19 date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1836 sentences = 104 flesch = 43 summary = SARS-CoV-2 is the recently discovered virus which has resulted in the pandemic illness known as coronavirus disease 2019 (COVID-19) [1] . Estimates for the proportion of asymptomatic patients infected with SARS-CoV-2 in different populations range between 7 and 80% [10] [11] [12] , with a substantial proportion of transmission occurring prior to illness onset [13, 14] . Gloves, disposable aprons, eye protection, fluid resistant type IIR surgical masks and slit lamp guards are recommended as personal protective equipment (PPE) for ophthalmic clinic assessment by the Royal College of Ophthalmologists [17] . Symptomatic patients with SARS tend to develop lower respiratory tract infections, suggesting aerosol transmission is important [25] . Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed Coronavirus Disease 2019 (COVID-19) in Healthcare Settings Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review cache = ./cache/cord-308715-uo6h1h2e.txt txt = ./txt/cord-308715-uo6h1h2e.txt === reduce.pl bib === id = cord-308428-zw26usmh author = Walter, Justin D. title = Highly potent bispecific sybodies neutralize SARS-CoV-2 date = 2020-11-10 pages = extension = .txt mime = text/plain words = 10526 sentences = 580 flesch = 54 summary = Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. However, binders of the isolated RBD may not effectively engage the aforementioned pre-fusion conformation of the spike protein, which could account for the poor neutralization ability of recently described single-domain antibodies that were raised against the RBD of SARS-CoV-2 spike protein [29] . Since Sb#15 and Sb#68 can bind simultaneously to the RBD and the full-length spike protein, we mixed Sb#15 and Sb#68 together to investigate potential additive or synergistic neutralizing activity of these two independent sybodies. To gain structural insights into how Sb#15 and Sb#68 recognize the RBD, we performed single particle cryo-EM analysis of the spike protein in complex with the sybodies. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 cache = ./cache/cord-308428-zw26usmh.txt txt = ./txt/cord-308428-zw26usmh.txt === reduce.pl bib === id = cord-308499-xqmguqyi author = Ahmed, Sakir title = Reply to Rheumatologists’ perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? date = 2020-05-09 pages = extension = .txt mime = text/plain words = 678 sentences = 47 flesch = 43 summary = title: Reply to Rheumatologists' perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? Heparin has multiple possible mechanisms of action which may support its use for COVID-19. SARS coronavirus strain HSR1 multiplication can be directly inhibited by heparin as evidenced by reduction of viral plaques by 50% on addition of heparin to Vero cell cultures [3] . One of the mechanisms of inhibition of cellular entry of SARS coronavirus is via lactoferrin binding [4] . SARS-CoV-2 entry into a cell via the ACE2 receptor leads to shedding of this receptor [6] . Furthermore, RAAS (renin-angiotensin-aldosterone system) activation is linked to thrombosis by multiple mechanisms [9] . Therefore, ACE2 downregulation by SARS-CoV-2 may lead to enhanced thrombosis. To summarize, SARS-CoV-2 can possibly activate the RAAS axis via ACE2 shedding and promote thrombosis. The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 receptor binding domain undergoes conformational change upon heparin binding. cache = ./cache/cord-308499-xqmguqyi.txt txt = ./txt/cord-308499-xqmguqyi.txt === reduce.pl bib === id = cord-308501-z3eiac25 author = Zhu, Chengliang title = nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk date = 2020-06-04 pages = extension = .txt mime = text/plain words = 847 sentences = 70 flesch = 57 summary = An emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) pandemic, imposes a great threat to global public health 1 . The transmission and pathophysiology of SARS-CoV-2 gradually known among various populations, but public health effects of COVID-19 on women and their outcomes should not be ignored 1, 2 . In pregnant and perinatal women, vertical transmission of SARS-CoV-2 from infected mother to her newborn is a controversial issue [2] [3] [4] . Here, we represent clinical characteristics of COVID-19 pneumonia in puerperal women and evidence of SARS-CoV-2 shedding in her breastmilk. Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection. cache = ./cache/cord-308501-z3eiac25.txt txt = ./txt/cord-308501-z3eiac25.txt === reduce.pl bib === id = cord-308400-8wihm63b author = Kanellopoulou, A. title = Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort date = 2020-11-13 pages = extension = .txt mime = text/plain words = 4420 sentences = 312 flesch = 58 summary = Background: To assess the level of knowledge and trust in the policy decisions taken regarding the coronavirus disease (COVID-19) pandemic among Epirus Health Study (EHS) participants. Variables assessing knowledge and beliefs towards the pandemic were summarized overall and by gender, age group (25-39, 40-49, 50-59, 60+ years) and period of report (before the lifting of lockdown measures in Greece: March 30th to May 3rd, and two post-lockdown time periods: May 4th to June 31st, July 1st to August 31st). Therefore, the primary objective of this 123 study was to investigate the levels of knowledge and beliefs on the COVID-19 pandemic and the magnitude 124 of trust upon Greek authorities and how these measures differed according to age, gender and time period 125 among the participants of an ongoing Greek cohort study, the Epirus Health Study (EHS). cache = ./cache/cord-308400-8wihm63b.txt txt = ./txt/cord-308400-8wihm63b.txt === reduce.pl bib === id = cord-308310-wtmjt3hf author = Zha, Lisha title = Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2012 sentences = 110 flesch = 54 summary = Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. The receptor binding domain (RBD) of the SARS spike protein binds to ACE2 and is an important target for neutralizing antibodies [5] [6] [7] . Hence, the RBD-CuMVTT vaccine candidate is able to induce high levels of SARS-CoV-2 neutralizing antibodies. Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine cache = ./cache/cord-308310-wtmjt3hf.txt txt = ./txt/cord-308310-wtmjt3hf.txt === reduce.pl bib === id = cord-308252-qwoo7b1l author = Cardinale, Vincenzo title = Intestinal permeability changes with bacterial translocation as key events modulating systemic host immune response to SARS-CoV-2: A working hypothesis date = 2020-09-16 pages = extension = .txt mime = text/plain words = 4596 sentences = 229 flesch = 36 summary = During the course of severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and 2 (SARS-CoV-2) infection, this pathway is unbalanced due to intestinal involvement and systemic inflammatory response. This review provides evidence on gut-liver axis involvement in Covid-19 as well as insights into the hypothesis that intestinal endotheliitis and permeability changes with bacterial translocation are key pathophysiologic events modulating systemic inflammatory response. Since inflammation seems to upregulate ACE2 expression [17] , it is important to understand whether patients with inflammatory bowel disease (IBD) are more susceptible to Covid-19 and the cytokine release syndrome (CRS) associated with lung injury and fatal outcome [21] . While the risk of SARS-CoV-2 infection in IBD patients depends on several universal risk factors, including social distancing [22] , older age and comorbidities have been associated with a negative outcome in IBD, whereas IBD treatments have not, highlighting that acute IBD flare prevention and inflammation reduction may avoid severe Covid-19 [23] . cache = ./cache/cord-308252-qwoo7b1l.txt txt = ./txt/cord-308252-qwoo7b1l.txt === reduce.pl bib === id = cord-308342-ycdok8fc author = Shutler, J. title = Risk of SARS-CoV-2 infection from contaminated water systems date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3147 sentences = 196 flesch = 57 summary = Collectively this evidence suggests that SARS-CoV-2 virus can survive 45 within water and the viral loads within untreated sewage effluent are likely high in countries 46 of high infection rates, a portion of which is viable virus, and therefore water contaminated 47 We note that adenoviruses are 122 known to be particularly resilient, and therefore likely to represent an upper estimate, but 123 also that our selected range is consistent with the 10 -3 value used elsewhere for assessing 124 viral risk in water systems (eg 14 ), including one assessment for SARS CoV-2 transmission 125 risk to wastewater workers 18 . Collectively this means that if a drinking water source 156 was to become infected with SARS-CoV-2 the standard virus removal and disinfection 157 approaches of ultraviolet exposure and chlorination may not reduce the virus below 158 detectable limits. cache = ./cache/cord-308342-ycdok8fc.txt txt = ./txt/cord-308342-ycdok8fc.txt === reduce.pl bib === id = cord-308800-b8gtwdxc author = Goldhaber-Fiebert, Sara N. title = Low-flow Nasal Cannula and Potential Nosocomial Spread of COVID-19 date = 2020-05-18 pages = extension = .txt mime = text/plain words = 573 sentences = 46 flesch = 53 summary = 8 Even with single-occupancy rooms, healthcare providers could be exposed to or spread SARS-CoV-2 after touching contaminated surfaces surrounding unsuspected COVID-19 patients presenting for other reasons. Some institutions have begun covering low-flow nasal cannula, at least in certain contexts, 10 11 though discussions with peers across specialities and institutions suggest that practice is far from uniform and is often limited to known COVID-19 patients. 11 By a conservative estimate, if 10% of the occupants of the roughly one-million hospital beds in the US are on low-flow nasal cannula oxygen on any given day, that translates into 100,000 patients in US hospitals whose treatment may also be adding to nosocomial spread of SARS-CoV-2. With many governments currently encouraging everyone to wear cloth masks in public to decrease spread, our healthcare systems should likewise consider the potential risks from the constant blowing of uncovered, loose-fitting, low-flow nasal cannula oxygen. cache = ./cache/cord-308800-b8gtwdxc.txt txt = ./txt/cord-308800-b8gtwdxc.txt === reduce.pl bib === id = cord-308786-e6rv5csl author = Alamri, Mubarak A. title = Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1483 sentences = 94 flesch = 47 summary = In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL(pro), that can be further developed as potential pan-PL(pro) based broad-spectrum antiviral drugs. Conclusively, the reported SARS-CoV-2 PL(pro) specific compounds could serve as seeds for developing potent pan-PL(pro) based broad-spectrum antiviral drugs against deadly human coronaviruses. Interestingly, the functionally 176 well-conserved catalytic triad residues within the catalytic pockets of PL pro among SARS183 Integrated computational methods comprising virtual high throughput screening, molecular 184 docking, and MD simulation are a significant approach for the exploration of potential 185 inhibitors against a target protein [22, 28, 78, 86] . Pharmacoinformatics and 655 molecular dynamics simulation studies reveal potential covalent and FDA-approved 656 inhibitors of SARS-CoV-2 main protease 3CLpro An integrated structure-based computational approach identified potential inhibitors of SARS-CoV-2 PL pro cache = ./cache/cord-308786-e6rv5csl.txt txt = ./txt/cord-308786-e6rv5csl.txt === reduce.pl bib === id = cord-308615-4fobikeh author = AKTAS, Busra title = Gut-lung axis and dysbiosis in COVID-19 date = 2020-06-21 pages = extension = .txt mime = text/plain words = 4221 sentences = 216 flesch = 45 summary = Although SARS-CoV-2 mainly causes lung infection, gastrointestinal symptoms described in COVID-19 patients and detection of the viral RNA in feces of infected patients drove attentions to a possible fecal-oral transmission route of SARS-CoV-2. This review points out the role of dysbiosis of the gut microbiota involving in sepsis, on the severity of SARS-CoV-2 infection. Due to the common symptoms, indicating respiratory tract disease, of patients infected with SARS-CoV-2, the main organ effected by the COVID-19 seems to be lung. In addition to the data detecting viral RNA in feces previously, these results suggest that SARS-CoV-2 infection does not remain with the respiratory tract only and the gastrointestinal system contribute to the course of the disease as well. However, with the limited data until today, it is hard to propose a fecal-oral transmission route to explain the enteric symptoms in COVID-19 patients and claim that SARS-CoV-2 pass through stomach and reach intestine to infect the intestinal cells as enteric viruses accomplish. cache = ./cache/cord-308615-4fobikeh.txt txt = ./txt/cord-308615-4fobikeh.txt === reduce.pl bib === id = cord-308451-pmwmfl3w author = Chiang, Shu-Fen title = SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells date = 2010-07-27 pages = extension = .txt mime = text/plain words = 6273 sentences = 345 flesch = 51 summary = In this report, we showed that spike protein of SARS virus could induce phenotypic conversion of human B cells, either from peripheral blood or B lymphoma cells, to macrophage-like cells that were steadily losing the B-cell marker CD19 and in turn expressing the macrophage-specific marker Mac-1. In conclusion, our results suggest that conversion of B cells to macrophage-like cells, similar to a pathophysiological response, could be mediated by a devastating viral ligand, in particular spike protein of SARS virus, or in combination with severe local hypoxia, which is a condition often observed in afflicted lungs of SARS patients. Our results show that spike protein of SARS displayed on recombinant baculovirus or prolonged exposure to hypoxia can trigger the conversion of peripheral B cells and B lymphoma cells into Mac-1 positive macrophage-like cells. As determined by microarray analysis, expression of CD86 (B7-2) gene was rapidly induced in B lymphoma cells within 12 h of SSDRB treatment (Fig. 4B) . cache = ./cache/cord-308451-pmwmfl3w.txt txt = ./txt/cord-308451-pmwmfl3w.txt === reduce.pl bib === id = cord-308740-06jr58kz author = Lazaridis, Charalampos title = Involvement of Cardiovascular System As The Critical Point in Coronavirus Disease 2019 (COVID-19) Prognosis and Recovery date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2536 sentences = 173 flesch = 42 summary = All cases were linked to a seafood market in the same city 2 and were confirmed to be associated with a novel RNA betacoronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3,4 . A recent study in patients with heart failure found that circulating levels of ACE2 were higher in men than in women, suggesting increased ACE2 tissue expression which could contribute to susceptibility to SARS-CoV-2 infection and disease progress 49 . Remarkably, severe COVID-19 has been associated with hypokalemia and higher blood pressure, supporting suggestions of decreased ACE2 function and augmented levels of angiotensin II after SARS-CoV-2 infection 96 . The participation of ACE2 in the pathogenesis of COVID-19, acting as a cell receptor for SARS-CoV-2 13 has caused increasing concern about the role of antihypertensive therapy with angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II Chloroquine, an antimalarial agent with known anti-viral effects 141 Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan cache = ./cache/cord-308740-06jr58kz.txt txt = ./txt/cord-308740-06jr58kz.txt === reduce.pl bib === id = cord-308994-4nljzm8a author = Tang, Zhongmin title = Insights from nanotechnology in COVID-19 treatment date = 2020-11-04 pages = extension = .txt mime = text/plain words = 3239 sentences = 177 flesch = 36 summary = We focus specifically on SARS-CoV-2 and the detailed role that nanotechnology can play in addressing this pandemic, including i) using FDA-approved nanomaterials for drug/vaccine delivery, including further exploration of the inhalation pathway; ii) introducing promising nanomaterials currently in clinical trials for drug/vaccine delivery; iii) designing novel biocompatible nanomaterials to combat the virus via interfering in its life cycle; and iv) promoting the utilization of nanomaterials in pneumonia treatment. To summarize, the advantages of nanotechnology in antiviral research include the following: 1) promotes the delivery of water-insoluble drugs; [39] 2) enhances the circulation time of drugs in vivo; [40] 3) achieves co-delivery of drugs; [40] 4) improves drug utilization efficiency and reduce side effects through targeting antibody modification; [41] 5) protects DNA and mRNA vaccines, overcoming bottlenecks for in vivo applications; [42] and 6) the physicochemical properties of nanomaterials can also be employed directly against viruses. cache = ./cache/cord-308994-4nljzm8a.txt txt = ./txt/cord-308994-4nljzm8a.txt === reduce.pl bib === id = cord-308857-otsrexqu author = Goel, Saurav title = Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date = 2020-05-28 pages = extension = .txt mime = text/plain words = 10608 sentences = 526 flesch = 47 summary = This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. cache = ./cache/cord-308857-otsrexqu.txt txt = ./txt/cord-308857-otsrexqu.txt === reduce.pl bib === id = cord-308760-xonuu04p author = Clerici, Bianca title = A case of newly diagnosed immune thrombocytopenia in the COVID-19 era date = 2020-11-12 pages = extension = .txt mime = text/plain words = 2165 sentences = 116 flesch = 47 summary = First-line treatment options for ITP include corticosteroids and intravenous immunoglobulin (IvIg); of the two, corticosteroids induce a more persistent increase in platelet count, and appear more suitable in this case. In this patient, the benefits of a rapid increase in platelet count must be weighed against the risk of deterioration of the ongoing viral infection, of superimposed hospital-acquired infections, of liver impairment, and of venous thromboembolic events, which might be favored by ITP itself [6, 7] , the treatment with a TPO-RA [8] , the suspected presence of a neoplasm, the length of hospitalization and SARS-CoV-2 infection [9, 10] . The impact of the anti-CD20 activity of Rituximab on the course of SARS-CoV-2 infection in a patient on steroid treatment was unknown and particularly worrisome given the crucial role of humoral immunity in infection contrast [11, 12] . cache = ./cache/cord-308760-xonuu04p.txt txt = ./txt/cord-308760-xonuu04p.txt === reduce.pl bib === id = cord-308752-uylvtqlu author = Miao, Y. title = First case of acute pancreatitis related to SARS‐CoV‐2 infection date = 2020-06-03 pages = extension = .txt mime = text/plain words = 401 sentences = 38 flesch = 55 summary = title: First case of acute pancreatitis related to SARS‐CoV‐2 infection Indeed, we have made similar observations: abdominal pain mimicking surgical disease is frequent during the first days of COVID-19, specifically pancreatitis-like presentation. We report the first case of symptomatic acute pancreatitis associated with SARS-CoV-2 without pulmonary symptoms. Blood tests revealed leucocytes 5960/mm 3 , haemoglobin 13⋅7 g/dl, neutrophils 3650/mm 3 , lymphocytes 1580/mm 3 , eosinophils 30/mm 3 , platelets 242 000/mm 3 , lipase at 211 U/l (3⋅5 N), gamma-glutamyl transferase 65 UI/l, alcaline phosphatase level 83 U/l, lactate dehydrogenase 170 U/l and C-reactive protein at 13⋅8 mg/l. Lipase level peaked on day 4 (430 U/l = 7 N). 4 reported elevated lipase or amylase in 17 per cent of a Chinese cohort without mentioning abdominal pain. Covid-19-related pancreatic injury Pancreatic injury patterns in patients with COVID-19 pneumonia Binding of SARS coronavirus to its receptor damages islets and causes acute diabetes cache = ./cache/cord-308752-uylvtqlu.txt txt = ./txt/cord-308752-uylvtqlu.txt === reduce.pl bib === id = cord-308667-6jr3z9wx author = Papachristodoulou, Eleni title = Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1768 sentences = 82 flesch = 51 summary = Furthermore, data from SARS-CoV suggest that the duration of immunity may not be sufficiently significant, while the immunity response against SARS-CoV-2 may not be efficiently effective in all patients, as relapses have already been reported. In conclusion, the development of an effective vaccine is an urgent necessity, as long-term natural immunity to SARS-CoV-2 may not be sufficient for the control of the current and future outbreaks. Information from follow-up studies of patients recovered from other coronaviruses may provide a background regarding the possible long-term immune response of SARS-CoV-2 infection. (2011) reported that antibody titers were undetectable in 21/23 patients at six years post-infection, while SARS-CoV antigen-specific memory B-cell response was undetectable in all 23 patients. As a consequence, the increasing number of individuals recovered from COVID-19 may not be able to provide effective herd immunity during subsequent post-pandemic waves of infection by mutant variants (Biswas et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered 1 patient cohort and their implications cache = ./cache/cord-308667-6jr3z9wx.txt txt = ./txt/cord-308667-6jr3z9wx.txt === reduce.pl bib === id = cord-308912-2pd801t1 author = Bensimon, Cécile M. title = A qualitative study of the duty to care in communicable disease outbreaks date = 2007-12-31 pages = extension = .txt mime = text/plain words = 6458 sentences = 290 flesch = 52 summary = He continued, stating that on the whole, institutions have a responsibility to provide resources and set up mechanisms with respect to ''anything that would impact on potentially impairing healthcare workers from carrying out their duties.'' A nurse echoed this view, stating his expectation that, ''if I'm going to be involved in dealing with patients with some type of infectious disease, I want to know that my employer has instituted policies and procedures that are protecting my rights.'' Many other participants agreed that ''HCPs have the right to adequate protection,'' and if such is not the case, ''they should have the right to opt out, legally and ethically.'' While many participants shared this view, several participants added the qualifier that ''in a situation where the institution fulfills its obligation to protect these individuals, yat that point [they] can no longer respect [providers'] voluntary decision to withdraw from work and stay home.'' A nurse stated that if someone is protected with proper equipment, ''I don't think you should be given a choice of saying no,'' thus suggesting, as many others did, that HCPs ought not be able to refuse to provide care if supports are in place. cache = ./cache/cord-308912-2pd801t1.txt txt = ./txt/cord-308912-2pd801t1.txt === reduce.pl bib === id = cord-308583-vtmwv8zl author = Du, Qishi title = Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase date = 2005-02-15 pages = extension = .txt mime = text/plain words = 3856 sentences = 225 flesch = 63 summary = In this research we study the cleavage mechanism, the properties of the relevant chemical bonds, and the catalytic interactions between the octapeptides and the SARS CoV M pro using molecular mechanical and quantum chemical simulations to provide useful insights for the chemical modification. The docking calculation between SARS CoV M pro and the octapeptide AVLQSGFR was performed using the molecular although still bound to the active site, the peptide has lost its cleavability after its scissile bond was modified from a hybrid peptide bond to a strong bond. Fig. 5B is the contour map of differential electronic density of the peptide bond Gln-Ser in the octapeptide AVLQSGFR, obtained by subtracting the electron density in the gaseous phase from the electron density in the background [23] of SARS CoV M pro and solvent water molecules. For the peptide inhibitor of proteinase, the chemical modification to cleavable octapeptide should focus on the scissile peptide bond between R 1 and R 1 0 to be cleaved by SARS CoV M pro . cache = ./cache/cord-308583-vtmwv8zl.txt txt = ./txt/cord-308583-vtmwv8zl.txt === reduce.pl bib === id = cord-309370-g8d3w7it author = Insausti-García, Alfredo title = Papillophlebitis in a COVID-19 patient: Inflammation and hypercoagulable state date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2083 sentences = 119 flesch = 40 summary = We believe that the inflammatory reaction and the coagulation alteration present in our patient due to Sars-Cov2 coronavirus may have acted as risk factors for the development of papillophlebitis. It has been suggested to result from idiopathic inflammation of retinal vascular and, possibly of the capillaries of the optic disc; however it is mandatory to work out a hypercoagulable state (hereditary or acquired thrombophilia factors), vasculitic syndromes, blood hyperviscosity, and other recognized systemic vascular inflammatory disorders. On left eye fundus examination, and color and red free retinographies, severe inflammation of the optic nerve head was observed accompanied by retinal venous vasodilatation and tortuosity, cotton-wool spots and moderate superficial hemorrhages in all four quadrants. 8 In addition to the respiratory tract infection and to these acute ocular manifestations, the current pandemic caused by the SARS-CoV-2 is associated with coagulation activation and a disproportionate systemic inflammatory response. cache = ./cache/cord-309370-g8d3w7it.txt txt = ./txt/cord-309370-g8d3w7it.txt === reduce.pl bib === id = cord-308736-kpz0o1ag author = Heßling, Martin title = Ultraviolet irradiation doses for coronavirus inactivation – review and analysis of coronavirus photoinactivation studies date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2826 sentences = 156 flesch = 45 summary = Methods: Coronavirus inactivation experiments with ultraviolet light performed in the past were evaluated to determine the UV radiation dose required for a 90% virus reduction. To answer the important question regarding SARS-CoV-2 and other coronaviruses as to which irradiation doses are needed for inactivation, the existing coronavirus photoinactivation results of the last 60 years have been reviewed and analyzed in this study. In most studies, the authors did not intend to investigate the log-reduction doses of coronaviruses, but rather virus inactivation in various applications. Most authors did not measure the UVC absorption properties of their biological materials because it was of no importance for their research task; thus, it is almost impossible to extract the role of the absorption in the calculation of the necessary irradiation doses for a 90% virus reduction. To date, UVC radiation has been effective against all coronaviruses in all published investigations, although the absorption properties of the sample media reduced inactivation success. cache = ./cache/cord-308736-kpz0o1ag.txt txt = ./txt/cord-308736-kpz0o1ag.txt === reduce.pl bib === id = cord-308597-ieju8gd8 author = de Carvalho, Renata Cristina title = The interference of COVID-19 in the male reproductive system: Important questions and the future of assisted reproduction techniques date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1152 sentences = 58 flesch = 49 summary = If the presence of SARS-Cov-2 in semen is confirmed, the methods of assisted human reproduction conduct should be modified, ensuring the timely safety of couples; however, current information about the virus raises other issues, such as: if seminal transmission exists, should a couple avoid sexual intercourse or use a barrier method if the male partner is known to be positive for the coronavirus disease 2019 (COVID-19)? If there is SARS-Cov-2 in an infected male's semen, is double sperm washing effective in isolating the virus as it is for HIV and hepatitis C? In addition, even with the absence of the virus in the seminal sample, a study has reported the presence of orchialgia in men diagnosed with COVID-19 (16) , which is indicative of testicular damage. Absence of 2019 novel coronavirus in semen and testes of COVID-19 patients Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease cache = ./cache/cord-308597-ieju8gd8.txt txt = ./txt/cord-308597-ieju8gd8.txt === reduce.pl bib === id = cord-308370-9av7qw10 author = Islam, Rajib title = A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 date = 2020-05-12 pages = extension = .txt mime = text/plain words = 5675 sentences = 333 flesch = 49 summary = To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. The aim of this study is to explore and identify the binding affinities and interactions of these antiviral phytochemicals against the main protease of SARS-CoV-2 using computational and statistical tools. In this study, a-ketoamide-11r is considered as a control ligand because it is recently reported as a good inhibitor against main protease , which shows binding affinity of -7.8 kcal/mol. Among the studied 40 phytochemicals, hypericin, cyanidin 3-glucoside, baicalin, glabridin, and a-ketoamide-11r show the highest binding affinity and strong interactions with both or at least one of the catalytic residues (Cys145 and His41) of the main protease. cache = ./cache/cord-308370-9av7qw10.txt txt = ./txt/cord-308370-9av7qw10.txt === reduce.pl bib === id = cord-308833-ei1faruy author = Zheng, Xiaohong title = Experimental investigation of integrated air purifying technology for bioaerosol removal and inactivation in central air-conditioning system date = 2004 pages = extension = .txt mime = text/plain words = 2763 sentences = 158 flesch = 54 summary = In this research, high voltage static electricity and ultraviolet technologies were integrated to an air purifying device which can be used to trap and kill airborne bacteria and viruses in central air-conditioning systems. This provides a basis for using this particular phage strain as a viral simulant in place of SARS CoV and other airborne viruses in the tests for evaluation of bioaerosol removal and inactivation by different types of air purifiers. Fig. 4(a) shows that the plaques formed on a GSM plate were used to sample the airflow containing phage aerosol generated with a source suspension with 10 5 pfu/mL when the integrated air purifier was turned off. In addition to particle removal test, airborne bacteria were also sampled in the experimental room with the integrated air purifier. Based upon the integrated technology of high voltage electric field, ultraviolet ray, composite silver material, and activated carbon fibers, an air purifying device has been developed to prevent airborne bacteria and virus spread through central air-conditioning system. cache = ./cache/cord-308833-ei1faruy.txt txt = ./txt/cord-308833-ei1faruy.txt === reduce.pl bib === id = cord-309043-dlmx12vt author = von Brunn, Albrecht title = Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date = 2007-05-23 pages = extension = .txt mime = text/plain words = 6706 sentences = 341 flesch = 52 summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. cache = ./cache/cord-309043-dlmx12vt.txt txt = ./txt/cord-309043-dlmx12vt.txt === reduce.pl bib === id = cord-309304-glcxrh7t author = Flemming, Sven title = Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 596 sentences = 37 flesch = 43 summary = title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 Nevertheless, these recommendations should be critically challenged since only the transmission of human papillomavirus from patient to surgeon by surgical smoke (aerosols) has been reported in a very small number of cases. Several recent studies have shown that fecal samples of COVID-19 patients can be positive for SARS-CoV-2, suggesting potential fecal oral transmission and thus a higher risk for gastrointestinal surgeons 3 . The purpose of our case report was to share actual clinical observations and results from a critically ill patient suffering from COVID-19 pneumonia who required emergency surgical treatment. These results have since been supported by a second case report showing negative PCR of peritoneal fluid in a COVID-19 patient who needed emergency surgery due to acute appendicitis. cache = ./cache/cord-309304-glcxrh7t.txt txt = ./txt/cord-309304-glcxrh7t.txt === reduce.pl bib === id = cord-308945-i2agpvhk author = Phipps, William S title = SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3167 sentences = 174 flesch = 50 summary = METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. Long et al 8 have described a variable antiviral IgM and IgG immune response to SARS-CoV-2 infection in a Chinese population in which seroconversion in a group of 285 patients from 3 hospitals showed IgG positivity for all cases beyond 17 to 19 days. The goals of this study were to ascertain key performance metrics of analytical specificity and cross-reactivity for a SARS-CoV-2 IgG serologic assay, perform a detailed cross-sectional and serial assessment of IgG and IgM antibody responses in suspected COVID-19 patients, and determine their relation to disease severity. SARS-CoV-2 IgG antibody results agreed with the PCR-negative samples for 96 of 97 (99%) of cases, including 55 instances of patients with new or acute-on-chronic symptoms suspicious for COVID-19 and with known time of onset. cache = ./cache/cord-308945-i2agpvhk.txt txt = ./txt/cord-308945-i2agpvhk.txt === reduce.pl bib === id = cord-308831-u5bj1sod author = Chaung, Jenna title = Coinfection with COVID‐19 and Coronavirus HKU1 – the critical need for repeat testing if clinically indicated date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1008 sentences = 70 flesch = 54 summary = COVID-19 is the latest global pandemic caused by the severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2). We describe a case of endemic HCoV co-infection with SARS-CoV-2 in a patient with COVID-19. Nasopharyngeal swabs were sent on day 1 of admission, one was positive for HCoV-HKU1 on the FilmArray Respiratory Panel (RP) (BioFire Diagnostics, bioMerieux) but another was negative for SARS-CoV-2 by RT-PCR (in-house-laboratorydeveloped test detecting the N and ORF1ab genes by primers, with LightCycler 2.0 instrument from Roche, RotKreuz, Switzerland a ) 6 . Hence, we believe that our patient experienced co-infection with both endemic HCoV-HKU1 and pandemic SARS-CoV-2. Our case illustrates the importance of maintaining a high degree of suspicion and to note that positivity for a known virus on any respiratory multiplex assay does not exclude the possibility of co-infection with SARS-CoV-2 in a patient with a compatible clinical presentation and epidemiological history. cache = ./cache/cord-308831-u5bj1sod.txt txt = ./txt/cord-308831-u5bj1sod.txt === reduce.pl bib === id = cord-309317-cgs0sui7 author = Galeotti, Caroline title = Autoimmune and inflammatory diseases following COVID-19 date = 2020-06-04 pages = extension = .txt mime = text/plain words = 1624 sentences = 80 flesch = 44 summary = Emerging reports show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection precedes the appearance of various autoimmune and autoinflammatory diseases, including paediatric inflammatory multisystemic syndrome (PIMS) or multisystem inflammatory syndrome in children (MIS-C), thus adding to the growing mystery of this virus and raising questions about the nature of its link with autoimmune and autoinflammatory sequelae. Several emerging reports show that coronavirus disease 2019 (COVID-19), a pandemic respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), could lead to autoimmune and autoinflammatory diseases, such as paedi atric inflammatory multisystemic syndrome (PIMS; which includes Kawasaki-like disease, Kawasaki disease shock syndrome, toxic shock syndrome, myocarditis and macrophage activation syndrome) in children [1] [2] [3] [4] [5] [6] . In the USA, the New York City Health Department on 4 May 2020 reported that 15 children aged 2-15 years had presented with symptoms of MIS-C, including persistent fever and increased levels of inflammatory markers, and many also had rash, abdominal pain, vomiting or diarrhea; ten of the 15 child ren were positive for SARS-CoV-2 infection 6 . cache = ./cache/cord-309317-cgs0sui7.txt txt = ./txt/cord-309317-cgs0sui7.txt === reduce.pl bib === id = cord-309360-cpis1l4u author = Barrios-López, J. M. title = Ischaemic stroke and SARS-CoV-2 infection: A causal or incidental association? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 3152 sentences = 235 flesch = 42 summary = Results: The association between COVID-19 and stroke was probably causal in 2 patients, who presented cortical infarcts and had no relevant arterial or cardioembolic disease, but did show signs of hypercoagulability and systemic inflammation in laboratory analyses. A recent study described the cases of 3 patients with COVID-19 who presented ischaemic stroke and antiphospholipid antibodies, in addition to elevated D-dimer levels and laboratory markers of systemic inflammation. 7 A recent study reported 3 cases of severe COVID-19 and ischaemic stroke; these patients presented antiphospholipid antibodies and laboratory findings compatible with systemic inflammation and coagulopathy. 19 In patients 1 and 2 of our series (Table 1) , the likelihood of a causal relationship between COVID-19 and stroke is high, as these patients presented laboratory markers of systemic inflammation and hypercoagulability and the aetiological study found no evident cause for ischaemic stroke. cache = ./cache/cord-309360-cpis1l4u.txt txt = ./txt/cord-309360-cpis1l4u.txt === reduce.pl bib === id = cord-308507-hp6m6qrn author = Gan, Yi-Ru title = Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase date = 2005-10-19 pages = extension = .txt mime = text/plain words = 1570 sentences = 98 flesch = 62 summary = The results demonstrate that, compared with other compounds reported so far, AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus, and that no detectable toxicity is observed on Vero cells under the condition of experimental concentration. These authors had done studies of docking the octapeptide to SARS-CoV M pro based on the three-dimensional structure of SARS coronavirus main proteinase obtained by Anand et al. The binding results obtained through docking study [10] and structural bioinformatics [7] show that the octapeptide AVLQSGFR is bound to the SARS proteinase through six hydrogen bonds. The present study was initiated in an attempt to conduct an in-depth examination of the antiviral activity of the octapeptide AVLQSGFR against SARS-associated coronavirus by biochemical experimental approaches. We also detected the effect of the octapeptide AVLQSGFR on replication of SARS-associated coronavirus in Vero cells (Fig. 2) . cache = ./cache/cord-308507-hp6m6qrn.txt txt = ./txt/cord-308507-hp6m6qrn.txt === reduce.pl bib === id = cord-309138-44qpk2vf author = Khanna, Kanika title = Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date = 2020-10-03 pages = extension = .txt mime = text/plain words = 6385 sentences = 354 flesch = 43 summary = Moreover, AYUSH has recommended certain preventive and medicinal plants for prevention and prophylactic of COVID-19 including warm extracts of Tinospora cordifolia (advised for chronic fever), Andrograhis paniculata (advised for fever and cold), Cydonia oblonga, Zizyphus jujube and Cordia myxa (enhancing antioxidant, immune-modulatory, anti-allergic, smooth muscle relaxant, anti-influenza activity) and Ever since, has been elucidated that, PAK1 tends to cause cancers, viral diseases like HIV, Hepatitis, pappiloma, influenza, ebola, SARS and corona virus along with immune system suppression of hosts, henceforth, propolis would be quintessential in blocking COVID/coronavirus curbed fibrosis in respiratory tract and boosting the immunity of an individual (Maruta, 2014) . Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study Molecular mechanism of action of repurposed drugs and traditional Chinese medicine used for the treatment of patients infected with COVID-19: A systematic review Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective cache = ./cache/cord-309138-44qpk2vf.txt txt = ./txt/cord-309138-44qpk2vf.txt === reduce.pl bib === id = cord-309319-si5c14e8 author = Cao, Chunxiang title = Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China date = 2016-08-15 pages = extension = .txt mime = text/plain words = 4693 sentences = 255 flesch = 44 summary = Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The Bayesian Maximum Entropy (BME) approach of modern geostatistics incorporates higher-order statistical estimation for space-time epidemic phenomena and has shown more accurate mapping results than those derived from linear kriging geostatistics [19] . BME provides an effective stochastic method, based on a cogent theoretical and technological strategy, to analyze relationships of SARS outbreaks in the composite space-time domain. (2) BME considers spatial heterogeneity in SARS outbreaks, which broadens the traditional epidemic research field from the temporal to space-time domain. In the case of the SARS outbreaks, we used the observations to explore general structural characteristics of the SARS S/TRF, that is, the existence of mean (or surface) trends in the space-time domain, and to explore the underlying temporal and spatial structure of the S/TRF with suitable covariance functions. cache = ./cache/cord-309319-si5c14e8.txt txt = ./txt/cord-309319-si5c14e8.txt === reduce.pl bib === id = cord-309206-kq77whdx author = Yan, Victoria C. title = Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2300 sentences = 155 flesch = 49 summary = 13 Seeing that the enzymes involved in McGuigan prodrug hydrolysis are hardly expressed in the lungs undermines its utility in the context of a primarily respiratory disease such as Covid-19. 4−6 For the fleeting duration of time that remdesivir is in the blood (prior to hydrolysis to GS-441524), the expression of bioactivating enzymes for McGuigan prodrugs suggests that the highest concentrations of NTP formation by remdesivirrather than GS-441524 would occur in cell types with high expression of CES1/ CTSA/HINT1. 26 At the time of publication, a study by Agostini and colleagues is the only report that has compared the antiviral activities of GS-441524 and remdesivir in primary human airway epithelial (HAE) cells, the most clinically relevant in vitro model of the lung, infected with either SARS-CoV or MERS-CoV. 1 Above all else, premature hydrolysis of the McGuigan prodrug, followed by dephosphorylation in serum such that GS-441524 is the predominant metabolite 4,5,29 compels studies investigating its utility in patients with Covid-19. cache = ./cache/cord-309206-kq77whdx.txt txt = ./txt/cord-309206-kq77whdx.txt === reduce.pl bib === id = cord-309091-te15ahvw author = Larson, Derek title = A Case of Early Re-infection with SARS-CoV-2 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 498 sentences = 57 flesch = 63 summary = A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus cache = ./cache/cord-309091-te15ahvw.txt txt = ./txt/cord-309091-te15ahvw.txt === reduce.pl bib === id = cord-309302-n6cd2fc3 author = Wang, Li title = Clinical management of lung cancer patients during the outbreak of COVID-19 epidemic date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5674 sentences = 318 flesch = 46 summary = In this review, we focus on the epidemiological characteristics, early diagnosis, patient management and mental health of lung cancer patients during the COVID-19 epidemic. According to China's New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), drugs with potential antiviral effects should be used early in the course of the disease, and it is recommended to focus on patients with high risk factors for severe illness patients. However, hydroxychloroquine or combined azithromycin is not recommended for COVID-19 patients base on China's New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). In addition, convalescent plasma is suitable for patients with rapid disease progression, severe and critically ill patients base on China's New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). According to China's New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), Tocilizumab can be tried for patients with extensive lung disease and elevated IL-6 levels in the laboratory. cache = ./cache/cord-309302-n6cd2fc3.txt txt = ./txt/cord-309302-n6cd2fc3.txt === reduce.pl bib === id = cord-309074-pys4aa60 author = Huang, Victoria W. title = Telehealth in the times of SARS-CoV-2 infection for the Otolaryngologist date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2644 sentences = 154 flesch = 48 summary = OBJECTIVE: In response to the American Academy of Otolaryngology – Head and Neck Surgery's recommendations to limit patient care activities in the times of SARS-CoV-2, many elective surgeries have been canceled without patient clinics transitioning to virtual visits. In response to these evolving needs, the American Academy of Otolaryngology -Head and Neck Surgery (AAO-HNS) telemedicine committee has put forth new recommendations to prioritize novel applications of telehealth to help limit coronavirus disease pandemic spread while maintaining quality care 8 . As testing in the U.S. becomes more available in this era of SARS-CoV-2, telemedicine continues to take the main role of "forward triage", evaluating patients with respiratory symptoms before they arrive in hospitals 23 With the AAO-HNS recommending all otolaryngologists to limit patient care activities to time-sensitive, urgent, and emergent medical conditions, elective surgeries have been canceled with many outpatient clinics rescheduling appointments and transitioning to virtual visits 7, 8 . cache = ./cache/cord-309074-pys4aa60.txt txt = ./txt/cord-309074-pys4aa60.txt === reduce.pl bib === id = cord-309200-t2xugb8l author = Asadi, Sima title = The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? date = 2020-04-03 pages = extension = .txt mime = text/plain words = 2077 sentences = 108 flesch = 45 summary = (2005) established that hospitalized patients infected with SARS during the 2003 epidemic emitted viable aerosolized virus into the air. Recent work on influenza (another viral respiratory disease) has established that viable virus can indeed be emitted from an infected individual by breathing or speaking, without coughing or sneezing (Yan et al. In regard to virology, information is required about the average viral titer in the respiratory fluid and the emitted aerosol particles, as well as the minimum infectious dose for COVID-19 in susceptible individuals. But given the large numbers of expiratory particles known to be emitted during breathing and speech, and given the clearly high transmissibility of COVID-19, a plausible and important hypothesis is that a face-to-face conversation with an asymptomatic infected individual, even if both individuals take care not to touch, might be adequate to transmit Note that the key word in the last sentence was "might." Many urgent questions about aerosol transmission and COVID-19 must be answered. cache = ./cache/cord-309200-t2xugb8l.txt txt = ./txt/cord-309200-t2xugb8l.txt === reduce.pl bib === id = cord-309517-yh4d414y author = Yu, Chao title = Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3498 sentences = 188 flesch = 38 summary = In addition, some asymptomatic patients can develop symptoms during hospitalization [6] , and the characteristics of these presymptomatic patients and their independent risk factors have not been addressed yet. Therefore, in the present study, we investigated 79 asymptomatic patients to analyze their clinical characteristics, disease progression, and recurrence of positive SARS-CoV2 RNA after discharge. No intergroup differences were observed in other radiographic characteristics, and patchy shadowing was the most common abnormality Meanwhile, the asymptomatic carriers had normal levels of other markers related to liver damage, renal dysfunction, inflammation, and coagulation, which were comparable with those of the symptomatic patients. Although the presymptomatic patients developed symptoms during hospitalization, these patients had similar viral RNA shedding duration compared with the asymptomatic carriers (14 days [IQR 7-25 days] vs. In our study, the recurrence rate of positive SARS-CoV-2 nucleic acid in the asymptomatic carriers after discharge was lower than that in the symptomatic patients (10.12% vs. cache = ./cache/cord-309517-yh4d414y.txt txt = ./txt/cord-309517-yh4d414y.txt === reduce.pl bib === id = cord-309513-dleo9rpl author = Zhang, Huilan title = Histopathologic Changes and SARS–CoV-2 Immunostaining in the Lung of a Patient With COVID-19 date = 2020-03-12 pages = extension = .txt mime = text/plain words = 609 sentences = 44 flesch = 51 summary = Biopsy lung sections were analyzed with hematoxylineosin staining, and immunostaining for SARS-CoV-2 was conducted as reported elsewhere (1) . In contrast, viral protein expression was minimally detectable on blood vessels ( Figure 2 , B, dashed black line) or in the interstitial areas between alveoli (Figure 2, B, bottom panel, blue arrows) . Immu-nostaining of Huh7 cells infected with SARS-CoV and of lung sections from an HIV-positive patient who died of fungal infection served as positive and negative staining controls, respectively (Figure 2, C) . A. Histopathologic examination revealing diffuse alveolar damage, organizing phase (A-1); denudation of alveolar lining cells (arrow 1), with presence of reactive type II pneumocyte hyperplasia (arrow 2) (A-2); intra-alveolar fibrinous exudates (arrow 3) and interstitial loose fibrosis with chronic inflammatory infiltrates (arrow 4) (A-3); and intra-alveolar loose fibrous plugs (arrow 5) (A-4). B. Immunostaining of SARS-CoV-2 in lung sections. cache = ./cache/cord-309513-dleo9rpl.txt txt = ./txt/cord-309513-dleo9rpl.txt === reduce.pl bib === id = cord-308996-tf0v2ojk author = Maas, Angela HEM title = The Coronavirus Disease 2019 Outbreak Highlights the Importance of Sex-sensitive Medicine date = 2020-08-24 pages = extension = .txt mime = text/plain words = 2188 sentences = 138 flesch = 45 summary = The novel coronavirus disease 2019 (COVID-19) pandemic has revealed important differences between the sexes in epidemiology, risk factors, clinical course, mortality and socioeconomic dimensions of the disease in all populations worldwide. The role of the TMPRSS2 protease in SARS-CoV-2 needs to be further investigated, but information on other diseases points towards sexspecific differences. 34 Sex differences in the binding of SARS-CoV-2 to the ACE2 receptor have been identified as an important contributor to the initiation and course of the disease. 27, 35, 36 Sex differences regarding potential protective effects of renin-angiotensin-aldosterone system inhibitors in SARS-CoV-2 infections are as yet unknown. Sex-specific SARS-CoV-2 mortality: among hormone-modulated ACE2 expression, risk of venous thromboembolism and hypovitaminosis D The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Gender differences in patients with COVID-19: focus on severity and mortality cache = ./cache/cord-308996-tf0v2ojk.txt txt = ./txt/cord-308996-tf0v2ojk.txt === reduce.pl bib === id = cord-309289-vm0k7hfx author = Rothan, Hussin A. title = The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date = 2020-04-14 pages = extension = .txt mime = text/plain words = 1463 sentences = 91 flesch = 46 summary = title: The FDAapproved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, antiinflammatory and anti-ROS properties. We investigated the anti-viral activity of auranofin against SARS-CoV-2 and its effect on virus-induced inflammation in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury. cache = ./cache/cord-309289-vm0k7hfx.txt txt = ./txt/cord-309289-vm0k7hfx.txt === reduce.pl bib === id = cord-309541-2vqk7fx1 author = Sekizuka, Tsuyoshi title = Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak date = 2020-08-18 pages = extension = .txt mime = text/plain words = 3302 sentences = 161 flesch = 50 summary = Here, we have generated a haplotype network of the SARS-CoV-2 outbreak using genome-wide single nucleotide variations (SNVs), identifying the genotypes of isolates that disseminated in the DP cruise ship after quarantine on February 5, 2020. The frequencies of SNVs suggested that all 73 isolates shared a SNV: The G nucleotide at the 11,083 position on the Wuhan-Hu-1 genome sequence was mutated to T (G 11083 T transversion), leading to a nonsynonymous amino Significance On February 5, 2020, the Diamond Princess cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed to have coronavirus disease 2019. Maximum-likelihood (ML) phylogenetic analysis including other SARS-CoV-2 genome sequences that are publicly available on GISAID and haplotype networks from genomic SNVs (HN-GSNVs) were used to map the genotypes of the SARS-CoV-2 isolates that disseminated in the DP cruise ship after isolation of the passengers on February 5, 2020 (Fig. 2) . cache = ./cache/cord-309541-2vqk7fx1.txt txt = ./txt/cord-309541-2vqk7fx1.txt === reduce.pl bib === id = cord-309089-ex9nh1yi author = Coperchini, Francesca title = The Cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system date = 2020-05-11 pages = extension = .txt mime = text/plain words = 6132 sentences = 303 flesch = 43 summary = Since the first reports on COVID-19 disease, it appeared clear that Acute respiratory distress syndrome (ARDS) accounted for a significant number of deaths among infected patients and that ARDS should be regarded as the hallmark immune-mediated clinical consequence in SARS-CoV-2, similarly to what described for SARS-CoV and MERS-CoV infections [11] . As shown by previous data in the literature, increased circulating levels of pro-inflammatory cytokines (eg, Interferon γ, interleukin (IL-) 1B, IL-6, IL-12) and chemokines (CXCL10, and CCL2) are associated with pulmonary inflammation and extensive lung involvement in SARS patients, similarly to what happens in MERS-CoV infection [13] . In mice infected with SARS-CoV, the clinical features of the syndrome showed an age-dependent increase in severity (similarly to what observed in humans), which was related to an increased level of pro-inflammatory cytokines and chemokines, paralleled by a reduction in T-cell responses [78] . cache = ./cache/cord-309089-ex9nh1yi.txt txt = ./txt/cord-309089-ex9nh1yi.txt === reduce.pl bib === id = cord-309120-05bg7rfa author = Niazi, Sadegh title = The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date = 2020-11-06 pages = extension = .txt mime = text/plain words = 2717 sentences = 180 flesch = 38 summary = title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs cache = ./cache/cord-309120-05bg7rfa.txt txt = ./txt/cord-309120-05bg7rfa.txt === reduce.pl bib === id = cord-309147-c3ikb81g author = Nadeem, Muhammad Shahid title = Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19) date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4984 sentences = 315 flesch = 51 summary = According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The recent reports have suggested that SARS-CoV-2 is a modified coronavirus of bat origin [22, 32] , which came to humans as a result of zoonotic transmission [33, 34] . The receptor-binding domain (RBD) of pangolin-CoV has only a one amino acid difference with that of SARS-CoV-2; the infected pangolins exhibit pathological symptoms similar to humans suffering from COVID-19, and their blood circulating antibodies can react with the spike protein of SARS-CoV-2 [35, 36] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): The epidemic and the challenges cache = ./cache/cord-309147-c3ikb81g.txt txt = ./txt/cord-309147-c3ikb81g.txt === reduce.pl bib === id = cord-309394-vroscj3m author = Belingheri, Michael title = Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers date = 2020-04-07 pages = extension = .txt mime = text/plain words = 722 sentences = 57 flesch = 54 summary = title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers 3 As known, the risk of exposure to coronavirus is higher among healthcare workers than other workers, due to their role in assistance and care of COVID-19 patients. Some limited data are available about previous coronavirus infections, such as severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome (MERS-CoV). Unauthorized reproduction of this article is prohibited Since the structural analysis of novel coronavirus has suggested that it would use the same mechanism of SARS-CoV, it is fundamental to consider the potential role of SARS-CoV-2 during pregnancy. [9] [10] [11] Furthermore, there is no evidence for intrauterine infection due to a vertical transmission in pregnant women affected by COVID-19. Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes cache = ./cache/cord-309394-vroscj3m.txt txt = ./txt/cord-309394-vroscj3m.txt === reduce.pl bib === id = cord-309629-7jtnhn65 author = Thomas, Viju title = International society for gynecologic endoscopy (ISGE) guidelines and recommendations on gynecological endoscopy during the evolutionary phases of the SARS-CoV-2 pandemic date = 2020-08-26 pages = extension = .txt mime = text/plain words = 4633 sentences = 306 flesch = 50 summary = We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports' closure (such as using gas filters and smoke evacuation systems). We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports' closure (such as using gas filters and smoke evacuation systems). did assess the risk of open and laparoscopic surgery to be the same provided the gas/smoke was evacuated safely and water lock filters were used or if gasless laparoscopy was performed [24] . cache = ./cache/cord-309629-7jtnhn65.txt txt = ./txt/cord-309629-7jtnhn65.txt === reduce.pl bib === id = cord-309411-2dfiwo65 author = Paris, Kristina A. title = Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date = 2020-06-23 pages = extension = .txt mime = text/plain words = 4728 sentences = 256 flesch = 58 summary = On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. Work on SARS-CoV (CoV1) has already determined that the virus enters cells via receptormediated endocytosis in a pH-dependent manner (Wang et al., 2008) that is characterized by cotranslocation of the viral spike glycoprotein and its specific functional receptor, the angiotensinconverting enzyme 2 (ACE2), from the cell surface to early endosomes. This newly discovered difference in protein sequence in the receptor binding domain of the spike glycoprotein and its impact on receptor binding reveals a mechanism that allows SARS-CoV2 internalization to take advantage of the high expression of ACE2 in the nasal epithelium¾resulting in increased retention times in the upper respiratory tract and augmented infectivity. cache = ./cache/cord-309411-2dfiwo65.txt txt = ./txt/cord-309411-2dfiwo65.txt === reduce.pl bib === id = cord-309554-ctc84tfy author = Pang, Ronald TK title = Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome date = 2006-03-01 pages = extension = .txt mime = text/plain words = 5189 sentences = 273 flesch = 52 summary = To identify proteomic features associated only with disease, we used 2 criteria: (a) the normalized peak intensities had to be significantly higher/lower in SARS patients than in non-SARS individuals; and (b) the normalized peak intensities had to correlate with 2 or more clinical/ biochemical variables, indicating their biological meaningfulness. These potential biomarkers were found to be significantly associated with SARS-CoV viral load (2 correlated with SARS-CoV RNA), acute-phase reaction [ differentiation of sars by two-way hierarchical clustering analysis of serum proteomic fingerprints We successfully identified potential biomarkers reflecting various physiologic or pathologic responses of the body to SARS infection, including acute-phase reaction (7, 17 ) , lung damage (18 -20 ) , impairment of liver function (21) (22) (23) , neutrophil activation (24 -26 ) , and viral load (5, 10, 27, 28 ) . Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia cache = ./cache/cord-309554-ctc84tfy.txt txt = ./txt/cord-309554-ctc84tfy.txt === reduce.pl bib === id = cord-309650-6xz9gjq0 author = Chou, Roger title = Update Alert 4: Epidemiology of and Risk Factors for Coronavirus Infection in Health Care Workers date = 2020-09-11 pages = extension = .txt mime = text/plain words = 1472 sentences = 95 flesch = 45 summary = Specific risk factors for SARS-CoV-2 transmission among health care workers in a university hospital Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers Prevalence of SARS-CoV-2 infection among health care workers in a tertiary community hospital Asymptomatic infection by SARS-CoV-2 in healthcare workers: a study in a large teaching hospital in Wuhan, China Dynamic of SARS-CoV-2 RT-PCR positivity and seroprevalence among high-risk health care workers and hospital staff Risk factors of healthcare workers with Corona Virus Disease 2019: a retrospective cohort study in a designated hospital of Wuhan in China Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 Novel Coronavirus Disease outbreak: a cross-sectional study Analysis of the infection status of the health care workers in Wuhan during the COVID-19 outbreak: A cross-sectional study SARS-CoV-2 infection among healthcare workers in a hospital in cache = ./cache/cord-309650-6xz9gjq0.txt txt = ./txt/cord-309650-6xz9gjq0.txt === reduce.pl bib === id = cord-309582-ihrj84hr author = AlNaamani, Khalid title = Medical research during the COVID-19 pandemic date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4047 sentences = 188 flesch = 36 summary = Despite the dedication of enormous resources, the advancement in health care systems and collaboration between different investigators across the world, only a small number of patients over the last decade have in fact benefited from clinical research performed during different outbreaks of respiratory viruses such as was the case for the severe acute respiratory syndrome (SARS), the HIN1 flu virus (swine flu) or the Middle East Respiratory Syndrome. An example of unpublished results that need to be widely acknowledged because of a negative outcome leading to early termination is that of a Brazilian study (CloroCovid19 ) which was a parallel, double-blind, randomized, phase IIb clinical trial, which started on March 23, 2020, aiming to assess safety and efficacy of Chloroquine diphosphate (CQ) in the treatment of hospitalized patients with severe respiratory syndrome secondary to SARS-CoV-2 infection. cache = ./cache/cord-309582-ihrj84hr.txt txt = ./txt/cord-309582-ihrj84hr.txt === reduce.pl bib === id = cord-309577-438fotfd author = Xing, Yuhan title = Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase date = 2020-04-10 pages = extension = .txt mime = text/plain words = 965 sentences = 73 flesch = 56 summary = 1 We would like to share findings from our paediatric patients who were positive for nucleic acid testing for SARS-CoV-2 in stools up to 8-20 days after clearance of viral RNA in respiratory specimens. Surprisingly, we found SARS-CoV-2 remained detectable in faeces of paediatric patients for approximately 4 weeks, whereas negative conversion of viral RNA in respiratory specimens occurred within 2 weeks after disease onset. Two children showed negative results for faecal detection of SARS-CoV-2 20 days after clear-ance of viral RNA in the respiratory tract, while another child persistently tested positive on faecal samples even 8 days after respiratory samples turning negative. Faecal shedding of viral RNA has been constantly reported in patients infected with SARS-CoV-2. 7 -10 One study reported over half of the 17 patients had faecal samples positive for SARS-CoV-2 detection, although virus copies in stools were less than those in respiratory specimens. cache = ./cache/cord-309577-438fotfd.txt txt = ./txt/cord-309577-438fotfd.txt === reduce.pl bib === id = cord-309193-v8lphej4 author = Lemriss, Sanaâ title = Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco date = 2020-07-02 pages = extension = .txt mime = text/plain words = 544 sentences = 42 flesch = 51 summary = title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19). Phylogenetic tree of the complete nucleotide sequence of hCoV-19_Morocco_OUA677_19_2020 and 54 other global strains obtained from the GISAID database, associated with a table representing single-nucleotide polymorphisms (SNPs). Phylogenetic analysis of this virus genome compared with 54 selected sequences showed that it was grouped in SARS-CoV-2 clade G, which includes strains from Asia, Europe, North America, Australia, and Africa (Fig. 1) . We are currently sequencing and analyzing more complete genomes from different regions of Morocco to understand the virus dispersion and to associate this information with epidemiological data. cache = ./cache/cord-309193-v8lphej4.txt txt = ./txt/cord-309193-v8lphej4.txt === reduce.pl bib === id = cord-309418-dx6e0lri author = Segalés, Joaquim title = Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3135 sentences = 178 flesch = 48 summary = Several models for SARS-CoV-2 infection have been so far developed in animals, including Egyptian fruit bat, ferret, golden Syrian hamster, cat, humanized angiotensin-converting enzyme 2 (ACE2) transgenic mice (hACE2 mice), and some nonhuman primate species (3) (4) (5) (6) (7) (8) . The clinical condition was finally attributed to a feline hypertrophic cardiomyopathy, but the animal was also infected by SARS-CoV-2. The detection of SARS-CoV-2 RNA in several samples of C1, all of them with Ct values over 30 (low viral load), and presence of antibodies (neutralizing and nonneutralizing) in both C1 and C2, indicated both animals suffered from a productive viral infection, probably linked to the exposure of the cats to COVID-19−affected owners. These experimental results, together with the few reports on SARS-CoV-2 detection in domestic cats and wild felids, indicate that felines are susceptible to infection by the novel coronavirus. cache = ./cache/cord-309418-dx6e0lri.txt txt = ./txt/cord-309418-dx6e0lri.txt === reduce.pl bib === id = cord-309323-yflng8m3 author = Thomas, T. title = COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status date = 2020-05-16 pages = extension = .txt mime = text/plain words = 6928 sentences = 387 flesch = 40 summary = Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). The current study provides the first comprehensive targeted and untargeted metabolomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to inflammatory markers and renal function. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint described impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients (44), though they also described that progressive increases in disease severity, from mild to severe to critical, correlated with the levels of transcripts for JAK1, STAT1 and 2, interferon alpha 2, interferon alpha receptors 1 and 2, and interferon regulatory factors 1, 4, 5 and 7. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint Serum levels of free fatty acids and acylcarnitines were significantly different when comparing COVID-19positive patients and controls. cache = ./cache/cord-309323-yflng8m3.txt txt = ./txt/cord-309323-yflng8m3.txt === reduce.pl bib === id = cord-309182-t9ywnshj author = Premkumar, Lakshmanane title = The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date = 2020-06-11 pages = extension = .txt mime = text/plain words = 6068 sentences = 319 flesch = 52 summary = These results establish that most individuals, including people who have been recently exposed to acute common HCoV infections, do not have detectable levels of cross-reactive antibodies to the recombinant RBD of SARS-CoVs. To evaluate the sensitivity of the RBD of SARS-CoV-2 for identifying infected individuals, we obtained a total of 77 serum samples from 63 patients with laboratory-confirmed (i.e., PCR positive) SARS-CoV-2 infections collected at different times after the onset of symptoms. All the samples were tested for binding of total immunoglobulin (Ig) and IgM antibodies to recombinant RBD antigens from SARS-CoVs and common-cold HCoVs. The sensitivity of the assay was high (98% and 81% respectively for Ig and IgM) for specimens collected 9 days or more after onset of symptoms (Fig. 4A ). A total of 50 serum samples collected between 1 and 39 days after onset of symptoms from PCR-confirmed SARS-CoV-2 subjects were measured for Ig and IgM binding to spike RBD antigen and SARS-CoV-2 neutralization assay. cache = ./cache/cord-309182-t9ywnshj.txt txt = ./txt/cord-309182-t9ywnshj.txt === reduce.pl bib === id = cord-309794-scqkyr5g author = Sharif‐Askari, Fatemeh Saheb title = Are patients with chronic rhinosinusitis with nasal polyps at a decreased risk of COVID‐19 infection? date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1885 sentences = 105 flesch = 52 summary = In fact, higher SARS-CoV-2 viral load was detected in nasal compared to throat swabs obtained from COVID-19 infected patients [4] , and that was attributed to the difference in ACE2 expression between both tissues. Interestingly, a significant reduction in the expression of ACE2 and TMPRSS2 was observed in the nasal polyps of CRSwNPs patients compared to healthy controls ( Figure 1A ). This data suggest that eosinophilic inflammation and the associated type 2 cytokines downregulate the expression of ACE2 in nasal tissue of CRS patients and thus may have a protective role against COVID-19 infection. In conclusion, as presented in Figure 2 , our data suggest that the type of inflammation underlying CRS, as well as corticosteroid treatment, may modulate ACE2 and TEMPRSS2 gene expression levels in the nasal polyps of CRSwNPs patients. cache = ./cache/cord-309794-scqkyr5g.txt txt = ./txt/cord-309794-scqkyr5g.txt === reduce.pl bib === id = cord-309633-1cd74xdl author = Rogers, Julia H. title = Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study date = 2020-09-15 pages = extension = .txt mime = text/plain words = 4018 sentences = 241 flesch = 53 summary = MEASUREMENTS: The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. CONCLUSION: Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. Surge testing was initiated on 30 March 2020 (and continued through 24 April) in collaboration with Public Health-Seattle & King County's Communicable Disease Epidemiology Team to conduct contact tracing at 6 shelters where cases of SARS-CoV-2 were previously detected ( Figure 2 ). We calculated the test positivity rate of SARS-CoV-2 infection at shelters by dividing the number of positive cases by the total number of participant encounters in the study period. Overall, 2% of participant encounters involved positive SARS-CoV-2 results, with most cases detected through surge testing events. cache = ./cache/cord-309633-1cd74xdl.txt txt = ./txt/cord-309633-1cd74xdl.txt === reduce.pl bib === id = cord-309729-nd48uh8e author = Antunes, Adriane E.C. title = Potential contribution of beneficial microbes to face the COVID- 19 pandemic date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4843 sentences = 216 flesch = 36 summary = Then, dietary strategies for the promotion of the gut microbiota, and thus the strengthening of the immune system associated with the gut, include increased consumption of fiber and prebiotics (Holscher, 2017) , and incorporating fermented foods (Marco et al., 2017) , and probiotics (Zmora, Suez, & Elinav, 2019) into the diet. There is scientific evidence about the ability of probiotics to promote gut immunity (Sánchez et al., 2017) and, for the moment, a modest evidence of their role in reducing the severity of acute upper respiratory tract infections (AURTI) (Hao, Dong, & Wu, 2015) . In a context of impoverished and threatened intestinal microbiota, the consumption of home-made fermented foods (yoghurt, kefir, sauerkraut, kombucha) or the incorporation into the diet of commercial products containing probiotics and prebiotics, as food or food supplements, is part of a comprehensive nutritional strategy to enhance the function of the gut microbiota, to promote mucosal immunity and potentially upper respiratory tract immunity, to be potentially better prepared to face viral or bacterial infections caused by respiratory syndromes. cache = ./cache/cord-309729-nd48uh8e.txt txt = ./txt/cord-309729-nd48uh8e.txt === reduce.pl bib === id = cord-309540-4pk5tq5w author = Brandsma, E. title = Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4283 sentences = 268 flesch = 54 summary = Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) in combination with Cas12 detection does not need expensive specialised equipment, is highly sensitive and specific, has a short TAT and is easy to implement and therefore could be used as an alternative for qRT-PCR (5, 6) . Since DETECTR depends on both signal amplification by RT-LAMP and reporter degradation after Cas12-dependent amplicon recognition, the assay produces a binary readout and is potentially more sensitive and specific compared to qRT-PCR (5, 6) . In this manuscript we describe the development of an in-house SARS-CoV-2 DETECTR assay, compare its performance with routine diagnostic qRT-PCR on almost 400 patient samples of three Dutch hospitals, thereby providing a first field test of this novel Cas12-mediated SARS-CoV-2 detection tool. cache = ./cache/cord-309540-4pk5tq5w.txt txt = ./txt/cord-309540-4pk5tq5w.txt === reduce.pl bib === id = cord-309856-flkjl1dm author = Westblade, Lars F. title = SARS-CoV-2 Viral Load Predicts Mortality in Patients with and Without Cancer Who Are Hospitalized with COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 1971 sentences = 96 flesch = 52 summary = For data generated using the cobas assay, we used viral load cutoffs based on C T values for the 123 ORF1ab gene target that were previously shown to correlate with in-hospital mortality among 124 hospitalized patients with COVID-19: high, C T value <25; medium, C T value 25-30, low, C T value 125 >30 (Magleby et al., 2020) . In the overall cohort, using assay-specific C T value cutoffs, 38.8% of patients with a high viral 156 load died during their hospitalization, compared to 24.1% of patients with a medium viral load, active cancer that adjusted for age and need for supplemental oxygen within 3 hours of 169 presentation to the ED (Table 4) , we found that having a high viral load was independently 170 associated with increased in-hospital mortality (aOR 5.00; 95% CI: 1. In conclusion, using two different diagnostic platforms, we found that admission SARS-CoV-2 277 viral load, as assessed by C T values that are generated by routine RT-PCR diagnostic assays, 278 was highly associated with in-hospital mortality in COVID-19 patients with and without cancer. cache = ./cache/cord-309856-flkjl1dm.txt txt = ./txt/cord-309856-flkjl1dm.txt === reduce.pl bib === id = cord-309869-gk0svt2f author = Wiwanitkit, Viroj title = SARS-CoV-2 in Semen date = 2020-10-23 pages = extension = .txt mime = text/plain words = 233 sentences = 23 flesch = 64 summary = key: cord-309869-gk0svt2f cord_uid: gk0svt2f Dear Editor, I would like to discuss the publication "Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection" [1] . [1] concluded that "although all semen samples were obtained in the acute stage of the infection when the nasopharyngeal swab test was positive, we did not detect SARS-CoV-2 in semen." In fact, there are some previous reports showing no existence of pathogen in semen samples [2, 3] . Nevertheless, a recent meta-analysis still noted that there is still a requirement for caution on the possibility of COVID-19 transmission via sexual contact [4] . Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection Italian males recovering from mild COVID-19 show no evidence of SARS-CoV-2 in semen despite prolonged nasopharyngeal swab positivity Atypical modes of COVID-19 transmission: how likely are they? cache = ./cache/cord-309869-gk0svt2f.txt txt = ./txt/cord-309869-gk0svt2f.txt === reduce.pl bib === id = cord-309619-glb2y82u author = Domingo, Pere title = The four horsemen of a viral Apocalypse: The pathogenesis of SARS-CoV-2 infection (COVID-19) date = 2020-07-29 pages = extension = .txt mime = text/plain words = 9353 sentences = 508 flesch = 40 summary = Severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 lights the wick by infecting alveolar epithelial cells (AECs) and downregulating the angiotensin converting enzyme-2 (ACE2)/angiotensin (Ang-1–7)/Mas1R axis. SARS-CoV induces the signal transducer and activator of transcription 1 TACE TNF-a converting enzyme TBK1 TANK-binding kinase 1 TLR toll-like receptor TMPRSS2 type II transmembrane serine protease TNF-a tumor necrosis alpha TRAF3 TNF receptor-associated factor 3 XCR1 XCL1 (Chemokine [C motif] ligand 1) and XCL3 (Chemokine [C motif] ligand 3) receptor production of double-membrane vesicles that lack PRRs and can then replicate in these vesicles [18] . COVID-19 patients have high serum levels of inflammatory cytokines, including interleukin (IL)-2, IL-7, IL-10, granulocyte-colony stimulating factor (G-CSF), interferon gamma-induced protein (IP)-10, monocyte chemoattractant protein (MCP)-1, macrophage SARS-CoV-2 infects primarily type II pneumocytes through binding to the ACE2 receptor. ACE2 = Angiotensin-converting enzyme 2; SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2; Ang II = Angiotensin II; ROS = Reactive oxygen species; AT1R = Angiotensin 1 receptor; ADAM17 = A disintegrin and metalloproteinase domain 17; TNF-a = Tumor necrosis factor alpha; TMPRSS2 = transmembrane protease serine 2. cache = ./cache/cord-309619-glb2y82u.txt txt = ./txt/cord-309619-glb2y82u.txt === reduce.pl bib === id = cord-309737-u960ftdm author = Lolachi, Sanaz title = Macrophage activation syndrome as an unusual presentation of paucisymptomatic severe acute respiratory syndrome coronavirus 2 infection: A case report date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1553 sentences = 108 flesch = 42 summary = PATIENT CONCERNS: We describe the unique case of young man who developed MAS as the sole manifestation of an otherwise paucisymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. DIAGNOSES: Clinical and biological criteria led to the diagnosis of MAS; cytokine profile was highly suggestive reverse transcription polymerase chain reaction for SARS-CoV-2 in nasopharyngeal swabs was negative, but serum anti-SARS-CoV-2 immunoglobulin A and immunoglobulin G resulted positive leading to the diagnosis of SARS-CoV-2 infection. [2] Aims and scope of the report: to describe the unique case of a patient who developed MAS as the sole manifestation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and to highlight that even paucisymptomatic COVID-19 patients can develop life-threatening complications. Rapid clinical deterioration with high, sustained fever, cytopenias, rising transaminases and ferritin, and evolving coagulopathy prompted us to suspect a MAS (or secondary hemophagocytic lymphohistiocytosis, HLH) in the context of SARS-CoV-2 infection. cache = ./cache/cord-309737-u960ftdm.txt txt = ./txt/cord-309737-u960ftdm.txt === reduce.pl bib === id = cord-309588-kw4d32dt author = Chan, Michael H.M. title = Steroid-induced osteonecrosis in severe acute respiratory syndrome: a retrospective analysis of biochemical markers of bone metabolism and corticosteroid therapy date = 2006-06-30 pages = extension = .txt mime = text/plain words = 4614 sentences = 245 flesch = 46 summary = Summary Aim We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. Biochemical markers of bone metabolism were analysed retrospectively using serial clotted blood samples collected from each patient during the course of hospital admission to discharge and subsequent follow-up at out-patient clinic using the arbitrary time periods: (i) Day <10; (ii) Day 28-44; (iii) Day 51-84; and (iv) Day >90 after the onset of fever. Aim: We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. 9, 10 In this study, biochemical markers of bone metabolism were used retrospectively to investigate the effect of massive doses of pulse and maintenance corticosteroid therapies on patients with SARS. cache = ./cache/cord-309588-kw4d32dt.txt txt = ./txt/cord-309588-kw4d32dt.txt === reduce.pl bib === id = cord-309556-xv3413k1 author = Chow, Ryan D. title = The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date = 2020-04-15 pages = extension = .txt mime = text/plain words = 5761 sentences = 373 flesch = 53 summary = In aggregate, these analyses showed that the age-associated genes with functional roles in SARS-CoV are expressed in specific cell types of the human lung. Of note, the overlap between lung ageassociated genes and SARS-CoV-2 regulated genes was statistically significant across all 3 cell lines (Figure 6d-f) , suggesting a degree of similarity between the transcriptional changes associated with aging and with SARS-CoV-2 infection. Among the age-associated genes that were induced by SARS-CoV-2 infection, the majority of these genes increase in expression with age (Cluster 1) (Figure 6g-i) . To identify a consensus set of age-associated genes that are regulated by SARS-CoV-2 infection, we integrated the analyses from all 3 cell lines. By integrating these data with single cell transcriptomes of human lung tissue, we further pinpointed the specific cell types that normally express the age-associated genes. cache = ./cache/cord-309556-xv3413k1.txt txt = ./txt/cord-309556-xv3413k1.txt === reduce.pl bib === id = cord-309930-zlzuoeh2 author = Zhou, Zhiming title = Coronavirus disease 2019: initial chest CT findings date = 2020-03-24 pages = extension = .txt mime = text/plain words = 4232 sentences = 199 flesch = 50 summary = METHODS: We retrospectively reviewed the initial chest CT data of 62 confirmed coronavirus disease 2019 patients (34 men, 28 women; age range 20–91 years old) who did not receive any antiviral treatment between January 21 and February 4, 2020, in Chongqing, China. Since December 2019, an increasing number of pneumonia cases caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei, China, and subsequently, an outbreak of coronavirus disease 2019 (COVID-19) swept the globe [1] [2] [3] [4] . Hence, it is very necessary to systematically analyze the chest CT findings associated with this disease systematically, for the timely isolation, COVID-19 RT-PCR and respiratory care of patients, and early implementation of infection prevention and control measures. To fully understand and early discriminate the CT features of this disease in its early stages, we collected initial chest CT data from confirmed COVID-19 patients who did not receive any antiviral treatment mainly from Chongqing Three Gorges Central Hospital for analysis. cache = ./cache/cord-309930-zlzuoeh2.txt txt = ./txt/cord-309930-zlzuoeh2.txt === reduce.pl bib === id = cord-309934-kcyao9i9 author = Tan, Emily L.C. title = Inhibition of SARS Coronavirus Infection In Vitro with Clinically Approved Antiviral Drugs date = 2004-04-17 pages = extension = .txt mime = text/plain words = 3489 sentences = 180 flesch = 47 summary = Here we report that certain interferon subtypes exhibit in vitro inhibitory activity against SARS-CoV and are candidates for follow-up studies in animal models and patients to determine their efficacy in vivo. A collection of 19 antiviral drugs was tested in the SARS-CoV CPE inhibition assay ( Table 2) . Because the criteria for ascertaining anti-SARS-CoV activity in this screen were set at 100% inhibition of CPE, and as high doses of interferons may result in severe clinical side effects, we chose to conduct further evaluations only in the interferons that showed complete inhibition from initial screen, namely, Wellferon, Multiferon, Betaferon, and Alferon. Betaferon, Alferon, Multiferon, Wellferon, and ribavirin inhibited CPE in SARS-CoV-infected Vero E6 cells, in decreasing order of potency. Ribavirin, a drug widely used in initial efforts to manage SARS infections, inhibited CPE completely at 500-5,000 µg/mL at virus loads of 100-10,000 PFU per well. cache = ./cache/cord-309934-kcyao9i9.txt txt = ./txt/cord-309934-kcyao9i9.txt === reduce.pl bib === id = cord-310027-846vp7ii author = Ma, Lin-Lu title = Coronavirus Disease 2019 Related Clinical Studies: A Cross-Sectional Analysis date = 2020-09-02 pages = extension = .txt mime = text/plain words = 4246 sentences = 245 flesch = 49 summary = METHODS: We did an electronic search of COVID-19 related clinical studies registered between December 1, 2019 and February 21, 2020 (updated to May 28, 2020) from the ClinicalTrials.gov, and collected registration information, study details, recruitment status, characteristics of the subjects, and relevant information about the trial implementation process. We extracted the following information from registered studies: registration number, registration date, registration title, primary sponsor, funding source, study type, study phase, study objectives, study design, length of the study, intervention, countries of recruitment and research settings, recruiting status, allocation, sample size, participant age, gender, masking, the time and method of sharing individual participant data (IPD), data management committee. Among the 943 interventional studies, 416 studies (44.1%) explored the effectiveness and/or safety of drugs commonly used in preventing and treating COVID-19, such as hydroxychloroquine (HCQ), chloroquine (CQ), immunotherapy (including stem cell therapy, monoclonal antibody, immunoregulation), lopinavir/ritonavir, glucocorticoids, interferon, targeted therapy (Baricitinib, Ruxolitinib, Imatinib), favipiravir, and Remdesivir. cache = ./cache/cord-310027-846vp7ii.txt txt = ./txt/cord-310027-846vp7ii.txt === reduce.pl bib === id = cord-309999-izdl0f2i author = Qin, Ede title = Immunogenicity and protective efficacy in monkeys of purified inactivated Vero-cell SARS vaccine date = 2006-02-13 pages = extension = .txt mime = text/plain words = 3944 sentences = 205 flesch = 46 summary = Additionally, three groups of rhesus monkeys were immunized with different doses of the purified inactivated SARS vaccine (0.5, 1 and 2 μg/time/monkey) on days 0 and 7, and the monkeys were challenged with SARS-CoV GZ-01 strain. INTERPRETATION: The purified inactivated SARS vaccine could induce high levels of neutralizing antibody, and protect the monkeys from the challenge of SARS-CoV. The results showed that both the purified and the unpurified SARS vaccines can induce high levels of SARS-CoV specific neutralizing antibodies in monkeys, thus demonstrating high immunogenicity. Our observations of immunogenicity in monkeys showed that the unpurified inactivated SARS vaccine induced almost the same level of neutralizing antibody as the purified vaccine. The results indicated that the purified inactivated SARS vaccine we developed could induce high levels of neutralizing antibody, protect monkeys after a SARS-CoV challenge, and be administered safely in monkeys. cache = ./cache/cord-309999-izdl0f2i.txt txt = ./txt/cord-309999-izdl0f2i.txt === reduce.pl bib === id = cord-309914-1lpl26eo author = Peterson, Danielle title = The use of Janus kinase inhibitors in the time of SARS-CoV-2 date = 2020-04-09 pages = extension = .txt mime = text/plain words = 503 sentences = 40 flesch = 60 summary = During the time of the SARS-CoV-2 pandemic, questions arise regarding patients being treated with 37 immunomodulatory therapies. In particular, is there an increased risk of acquiring the infection or 38 experiencing a worse outcome from SARS-CoV-2? we can look at safety data from clinical trials to try to understand patient susceptibility to different 40 infections. In light of the 42 growing off-label use of JAKi in dermatology in addition to pharmaceutical industry sponsored clinical 43 trials of JAKi for alopecia areata, atopic dermatitis, vitiligo, etc, dermatologists need data to better 44 understand the risks of JAKi treatment in order to best manage and counsel our patients during this 45 unique time. We analyzed and collated Adverse Events data from JAKi clinical trials. We also collated pulmonary 53 toxicities of JAKi to identify potential risks of worsening severe respiratory disease from SARS-CoV-2, and 54 such toxicities are all but absent. cache = ./cache/cord-309914-1lpl26eo.txt txt = ./txt/cord-309914-1lpl26eo.txt === reduce.pl bib === id = cord-309829-3dlfcy31 author = Parupudi, Tejasvi title = Evidence-based point-of-care technology development during the COVID-19 pandemic date = 2020-11-09 pages = extension = .txt mime = text/plain words = 4774 sentences = 223 flesch = 44 summary = As learnt from previous viral epidemicsfor example, influenza (H1N1) in 2009, Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 and the SARS outbreak during 2003 -rapid and accurate diagnostic testing with point-of-care technologies (POCTs) is beneficial in early identification [2, 3] . The need for rapid screening, triage and isolation of affected populations, the ability to monitor and stratify patients at home, in the clinic and in intensive care units (ICUs), and the associated decisions caregivers must take based on the test results underline the significance of POCTs. The WHO forum responsible for identifying immediate research needs and research gaps for COVID-19 recognized mobilizing research on rapid POC diagnostics for use at the community level and ensuring access to accurate and standardized diagnostics as one of the eight immediate research actions [4] . cache = ./cache/cord-309829-3dlfcy31.txt txt = ./txt/cord-309829-3dlfcy31.txt === reduce.pl bib === id = cord-309728-7vfotgrr author = Johnson, Kristen M. title = Managing COVID‐19 in Renal Transplant Recipients: A Review of Recent Literature and Case Supporting Corticosteroid‐sparing Immunosuppression date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3202 sentences = 169 flesch = 36 summary = PHARMACOTHERAPY Volume **, Number **, 2020 We present the case and outcomes of a renal transplant recipient with SAR-CoV-2 treated in our hospital whose immunosuppressive therapy was managed with only a modest reduction in calcineurin inhibitor target trough concentration and antiproliferative dose reduction. We have described the case of a renal transplant recipient who was successfully treated for COVID-19 with supportive care along with steroid-sparing immunosuppression regimen changes that included dose-reduced antiproliferative therapy and a modest decrease in tacrolimus target trough level. [22] [23] [24] Finally, currently published cases of SARS-CoV-2 in renal transplant recipients have demonstrated variable results in progression of respiratory disease and survival when substituting higher doses of corticosteroids for complete cessation of maintenance calcineurin inhibitor and antiproliferative therapy. 8, 11 Conclusion It is difficult to compare and draw conclusions regarding optimal immunosuppressant management in renal transplant recipients treated for SARS-CoV-2 from the limited data presented in currently published cases along with significant confounding variables. cache = ./cache/cord-309728-7vfotgrr.txt txt = ./txt/cord-309728-7vfotgrr.txt === reduce.pl bib === id = cord-309931-cpzp33b3 author = Zawawi, Ayat title = The impact of COVID-19 pandemic on malaria elimination date = 2020-10-20 pages = extension = .txt mime = text/plain words = 4183 sentences = 219 flesch = 48 summary = As lowand middle-income countries shift increasingly to focus on identifying and treating COVID-19, questions are emerging about the impact this shift in focus will have on ongoing efforts to control other infectious diseases, such as malaria. This review discusses how the spread of SARS-CoV-2 in lowand middle-income countries might impact these efforts, focusing in particular on the effects of co-infection and the use of antimalarial drugs used to treat malaria as therapeutic interventions for COVID-19. This review addresses this gap in the literature by discussing how the spread of SARS-CoV-2 in low-and middle-income countries might impact efforts to control malaria. Despite the CQ and HCQ treatment potential for COVID-19, the use of these two drugs could pose many challenges in low-and middle-income countries and not just in malaria-endemic areas. cache = ./cache/cord-309931-cpzp33b3.txt txt = ./txt/cord-309931-cpzp33b3.txt === reduce.pl bib === id = cord-309898-sju15hev author = Hu, Yiwen title = Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date = 2020-11-02 pages = extension = .txt mime = text/plain words = 4295 sentences = 219 flesch = 50 summary = The key result of our work is that both, the overall flexibility of upward RBD and the mobility ratio of RBDs in different conformations, represent two significant factors that show a positive scaling with virus lethality and an inverse correlation with the infection rate. Figure 2 depicts data that shows that the lowest-frequency normal modes of MERS-CoV, SARS-CoV and SARS-CoV-2 spike proteins are all associated with a swing motion of upward receptor-binding domain (RBD) to different extents. Figure 4 provides a correlation diagram for MERS-CoV, SARS-CoV and SARS-CoV-2 spike protein, where the overall flexibility of upward RBD is evaluated by the average fluctuation of open-state RBD and the mobility ratio is quantified as the ratio of maximum fluctuations over upward and downward RBDs. The data shows that both factors have positive correlation with case fatality rate and inverse relationship with the virus infectivity. cache = ./cache/cord-309898-sju15hev.txt txt = ./txt/cord-309898-sju15hev.txt === reduce.pl bib === id = cord-309986-p7pqla6l author = Harkin, Timothy J title = Delayed diagnosis of COVID-19 in a 34-year-old man with atypical presentation date = 2020-05-18 pages = extension = .txt mime = text/plain words = 2110 sentences = 118 flesch = 52 summary = [1] [2] [3] Infection with SARS-CoV-2 is confirmed by real-time RT-PCR, typically done on naso pharyngeal (NP) swabs or, less commonly, samples from the lower respiratory tract, including broncho alveolar lavage (BAL). 5 Here, we present a man who developed rapidly progressive pulmonary disease and, following two negative NP tests, was diagnosed with COVID-19 on the basis of broncho scopic biopsy and BAL after 9 days of illness. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course. normal in the first 48 h (appendix p 1), serum and BAL galactomannan were negative, and the pathological finding of acute lung injury in the lesion was already present on day 2, which argue against this explanation. cache = ./cache/cord-309986-p7pqla6l.txt txt = ./txt/cord-309986-p7pqla6l.txt === reduce.pl bib === id = cord-309970-jkmjiika author = Liu, Qin title = From SARS to COVID-19: What lessons have we learned? date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3421 sentences = 187 flesch = 53 summary = On December 1, 2019, the first case of coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), was reported in Wuhan, China, and CoVs returned to public view. In this review, we systematically compare COVID-19 and SARS in terms of epidemiology, pathogenesis and clinical characteristics and discuss the current treatment approaches, scientific advancements and Chinese experience in fighting the epidemic to combat the novel coronavirus pandemic. As the virus continued to spread, on March 11, 2020 , the WHO declared that COVID-19 is a pandemic disease, making this the first time that a coronavirus infection has been regarded as a global pandemic, in contrast to SARS in 2002, which did not reach this level. This paper summarizes the differences in the epidemiology, clinical manifestations, and treatment of SARS and COVID-19 during the two outbreaks, summarizes the lessons learned, and provides a comprehensive reference for the global epidemic prevention and treatment of reported in China and resulted in a large number of infections. cache = ./cache/cord-309970-jkmjiika.txt txt = ./txt/cord-309970-jkmjiika.txt === reduce.pl bib === id = cord-309915-isw1arrp author = Perez-Jurado, L. A. title = Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men? date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3328 sentences = 200 flesch = 49 summary = The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has an estimated overall case fatality ratio of 1.38% in China, being 53% higher in males and increasing exponentially with age. Using comparative transcriptomic data, we have defined that XCM/LOY is associated with abnormal peripheral blood cell counts with decreased progenitor cells and multiple biomarkers of immune system dysfunction, pro-coagulation activity and increased cardiovascular risk. 8 Individuals with XCM have an increased risk for autoimmune disease, recurrent viral infections and earlier cardiovascular mortality, 9 which has been attributed to X-chromosome haploinsufficiency for multiple genes, and is associated with excessive production of proinflammatory cytokines (IL-6), decrease in anti-inflammatory cytokines (IL-10, TGF-β) and a lower CD4:CD8 ratio. 19.20071357 doi: medRxiv preprint Association analysis between LOY status and clinical data, including blood cell counts and biochemical parameters, was assessed using linear models adjusted by age. cache = ./cache/cord-309915-isw1arrp.txt txt = ./txt/cord-309915-isw1arrp.txt === reduce.pl bib === id = cord-310017-c8rd714a author = Popa, Alexandra title = Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date = 2020-07-17 pages = extension = .txt mime = text/plain words = 5572 sentences = 330 flesch = 49 summary = Moreover, we combined our deep viral genome sequencing data with epidemiologically identified chains of transmissions and family clusters together with biomathematical analyses to study genetic bottlenecks and the dynamics of genome evolution of SARS-CoV-2. We assembled SARS-CoV-2 genome sequences, constructed phylogenies and identified low 15 frequency mutations based on high-quality sequencing results with >5 million reads per sample and >80% of mapped viral reads (Fig. S2A-B) . Our pipeline was validated by experimental controls involving sample titration and technical sample replicates ( Fig. S2CTo investigate the link between local outbreaks in Austria and the global pandemic, we 20 performed phylogenetic analysis of 305 SARS-CoV-2 genomes from the Austrian cases (>96% genome coverage, >80% aligned viral reads) and 7,695 global genomes from the GISAID database (Fig. 1B, Table S1 ). 7 Dynamics of low frequency and fixed mutations in clusters Next, we sought to gain insights into the fundamental processes of SARS-CoV-2 infection by integrative analysis of viral genomes. cache = ./cache/cord-310017-c8rd714a.txt txt = ./txt/cord-310017-c8rd714a.txt === reduce.pl bib === id = cord-310051-bl8l4bgo author = Leitner, Thomas title = Where did SARS-CoV-2 come from? date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1185 sentences = 78 flesch = 55 summary = Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastro-intestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. While it is possible that a bat coronavirus jumped directly to a human, the closest known bat virus, RaTG13 found in a Rhinolophus affinis bat , shows 96% genomic similarity to SARS-CoV-2. Canine coronaviruses were not the only viruses with CpG patterns similar to those observed in SARS-CoV-2. Therefore, reduced genomic CpG content alone cannot predict the zoonotic origin of SARS-CoV-2, even though Xia (2020) (Pollock et al. Identification of the zoonotic origin of SARS-CoV-2 may be particularly challenging, as coronaviruses frequently recombine and are found in many different host species in the wild (Graham and Baric 2010) . cache = ./cache/cord-310051-bl8l4bgo.txt txt = ./txt/cord-310051-bl8l4bgo.txt === reduce.pl bib === id = cord-309876-l0xginsa author = Vena, Antonio title = Prevalence of Antibodies to SARS-CoV-2 in Italian Adults and Associated Risk Factors date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3065 sentences = 168 flesch = 45 summary = A generalized estimating equations model showed that the main risk factors associated with SARS-CoV-2 seroprevalence were the following: an occupational exposure to the virus [Odd ratio (OR) = 2.36; 95% CI 1.59–3.50, p = 0.001], being a long-term care facility resident (OR = 4.53; 95% CI 3.19–6.45, p = 0.001), and reporting previous symptoms of influenza-like illness (OR = 4.86; 95% CI 3.75–6.30, p = 0.001) or loss of sense of smell or taste (OR = 41.00; 95% CI 18.94–88.71, p = 0.001). In the present observational study performed on a large sample of subject in northern Italy, we found the following: (1) the overall seroprevalence of anti-SARS-CoV-2 antibodies (IgG and/or IgM) was 11.0%; (2) occupational exposure to the virus, long-term care facility residency, as well as previous symptoms of influenza-like illness or loss of sense of smell or taste were independently associated with anti-SARS-CoV-2 positivity. cache = ./cache/cord-309876-l0xginsa.txt txt = ./txt/cord-309876-l0xginsa.txt === reduce.pl bib === id = cord-310064-p8u424ch author = Katz, Andrew P. title = False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date = 2020-06-12 pages = extension = .txt mime = text/plain words = 4503 sentences = 242 flesch = 49 summary = [4] [5] [6] The virus responsible for COVID-19, SARS-CoV-2, poses a particular risk to providers involved in the care of otolaryngology patients due to examinations and surgeries involving the nasopharynx, oropharynx, and upper aerodigestive tract, which harbor high concentrations of viral particles. 6 In line with other institutions across the globe, these protocols call for preoperative testing of asymptomatic patients using reverse transcriptase polymerase chain reaction (RT-PCR) given reports of asymptomatic carriers of SARS-CoV-2 capable of transmission. Tahamtan and Ardebili discuss possible factors causing false negative results of SARS-CoV-2 RT-PCR, namely mismatches between the testing primers and viral genome or low viral loads in samples due to timing of disease or location of collection. In the most recent patient with positive preoperative testing without symptoms (patient #3), pathologists recommended immediate re-testing based on the borderline titers in her test results rather than delaying surgery for weeks for a potential COVID-19 infection. cache = ./cache/cord-310064-p8u424ch.txt txt = ./txt/cord-310064-p8u424ch.txt === reduce.pl bib === id = cord-310091-x31g02xw author = Zhang, Zhilan title = Pan-cancer analysis reveals that ACE2 is positively associated with immunotherapy response and is a potential protective factor for cancer progression date = 2020-09-02 pages = extension = .txt mime = text/plain words = 2941 sentences = 169 flesch = 42 summary = Using cancer genomics datasets from the Cancer Genome Atlas (TCGA) program, we performed computational analyses of associations between ACE2 expression and antitumor immunity, immunotherapy response, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in 13 cancer cohorts. A recent study [9] showed that ACE2 expression was associated with increased tumor immune infiltration and was a positive prognostic factor in uterine corpus endometrial and renal papillary cell cancers. Despite these previous studies, a systemic investigation into the association between ACE2 expression and antitumor immunity, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in pan-cancer remains lacking. We also explored associations between ACE2 expression and multiple tumor phenotypes, including cell proliferation, stemness, epithelial-mesenchymal transition (EMT), oncogenic signaling, and clinical outcomes in these cancer cohorts. We found that ACE2 expression levels inversely correlated with the activity of cell cycle, mismatch repair, TGF-β, Wnt, VEGF, and Notch signaling pathways in 10, 7, 9, 7, 5, and 7 individual cancer types, respectively (Spearman's correlation test, FDR < 0.05) ( Fig. 2A) . cache = ./cache/cord-310091-x31g02xw.txt txt = ./txt/cord-310091-x31g02xw.txt === reduce.pl bib === id = cord-310096-a242g5kg author = Yokota, I. title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1956 sentences = 131 flesch = 49 summary = Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (self-collected saliva and NPS) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. cache = ./cache/cord-310096-a242g5kg.txt txt = ./txt/cord-310096-a242g5kg.txt === reduce.pl bib === id = cord-310299-isdsestc author = Hosseini, Akram A. title = Delirium as a presenting feature in COVID-19: neuroinvasive infection or autoimmune encephalopathy? date = 2020-06-09 pages = extension = .txt mime = text/plain words = 981 sentences = 84 flesch = 46 summary = 1 We report two cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) infection with acute onset of altered mental status and delirium with normal respiration and metabolic balance in the first 48 hours. Despite normal brain CT at 48 hours, MRI on day 6 showed three hyperintense foci on diffusion-weighted images, but no overt restriction, consistent with T2-shine-through suggesting cellular infiltration/inflammation or small infarcts ( Figure 1 ). 1,2 However, there is currently no report of limbic encephalitis associated with COVID-19 that presented with delirium in the absence of respiratory, metabolic or systemic features, while patients may be hidden sources of spreading the virus in busy clinical settings. The detection of SARS-CoV2 in the CSF in a patient with meningo-encephalitis supports neurotropic and neuroinvasive potential of the virus 2 presumably through the blood vesselrich meninges once the blood brain barrier is damaged. Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) cache = ./cache/cord-310299-isdsestc.txt txt = ./txt/cord-310299-isdsestc.txt === reduce.pl bib === id = cord-310195-am3u7z76 author = Waller, J. title = Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date = 2020-05-10 pages = extension = .txt mime = text/plain words = 4813 sentences = 281 flesch = 55 summary = Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. This study was designed to test two hypotheses: describing a test indicating the presence of antibodies using the term Immunity (vs Antibody), and describing test results as Passports or Certificates (vs Test), increases the likelihood that those with this test result erroneously perceive they have no risk of becoming infected in the future with coronavirus. . https://doi.org/10.1101/2020.05.06.20093401 doi: medRxiv preprint Primary outcome Proportion of participants perceiving an antibody-positive test result to mean no risk of catching coronavirus in the future, assessed in response to a question with four response options. cache = ./cache/cord-310195-am3u7z76.txt txt = ./txt/cord-310195-am3u7z76.txt === reduce.pl bib === id = cord-310008-hwpn7ti1 author = Lyons-Weiler, James title = Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity date = 2020-04-09 pages = extension = .txt mime = text/plain words = 2090 sentences = 122 flesch = 45 summary = Failure of SARS and MERS vaccines in animal trials involved pathogenesis consistent with an immunological priming that could involve autoimmunity in lung tissues due to previous exposure to the SARS and MERS spike protein. In this study, I present the likely human epitopic targets of biomimicry-induced autoimmunological components of morbidity and mortality caused by SARS-CoV-2 infection. This is achieved via bioinformatics analysis of the homology between highly immunogenic SARS-CoV-2 epitopes and human proteins to promote comprehension of the etiologies of pathogenesis of SARS-CoV-2 in COVID-19. A list of human peptides with high local homology was compiled and their roles in the pathogenesis of COVID-19 from SARS-CoV-2 infection noted. Remarkably, over 1/3 (11/27) of the immunogenic proteins in SARS-CoV-2 have potentially problematic homology to proteins that are key to the human adaptive immune system (emboldened in Table 1 ). cache = ./cache/cord-310008-hwpn7ti1.txt txt = ./txt/cord-310008-hwpn7ti1.txt === reduce.pl bib === id = cord-310160-55yltan1 author = Pham, Jimmykim title = Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2745 sentences = 147 flesch = 48 summary = In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. The analytical sensitivity of the SARS-CoV-2 TMA assay was assessed using 2 lots of reagents to test 60 replicates each of dilution panels containing cultured SARS-CoV-2 virus strain USA-WA1/2020 (BEI Resources, Manassas, VA) and diluted in Aptima specimen transport medium (STM) matrix to a range of 0.03 to 0.0003 50% tissue culture infectious dose (TCID 50 )/ml. This analysis resulted in positive, negative, and overall agreements of 100% (95% CI, 94.3% to 100%), Clinical performance of the SARS-CoV-2 TMA assay was also assessed by testing sets of NP swab, OP swab, and nasal swab specimens co-collected from 35 symptomatic patients suspected of being infected with SARS-CoV-2. cache = ./cache/cord-310160-55yltan1.txt txt = ./txt/cord-310160-55yltan1.txt === reduce.pl bib === id = cord-310184-qth1y88o author = Alunno, Alessia title = Storm, typhoon, cyclone or hurricane in patients with COVID-19? Beware of the same storm that has a different origin date = 2020-05-18 pages = extension = .txt mime = text/plain words = 2981 sentences = 143 flesch = 38 summary = Some of the articles being published during the severe acute respiratory syndrome–coronavirus (SARS-CoV)-2 pandemic highlight a link between severe forms of coronavirus disease 2019 (COVID-19) and the so-called cytokine storm, also with increased ferritin levels. Some patients with coronavirus 2019 disease (COVID-19) develop a fully blown secondary haemophagocytic lymphohistiocytosis (sHLH), whereas others, despite a consistent release of pro-inflammatory cytokines, do not fulfil sHLH criteria but still show some features resembling the phenotype of the hyperferritinemic syndrome. Other immunomodulating agents like IL-1 or IL-6 inhibitors are only recommended in selected cases including the macrophage activation syndrome (MAS), a subtype of sHLH associated with systemic juvenile idiopathic arthritis (sJIA), adult-onset Still's disease (AOSD) and other autoimmune disorders. cache = ./cache/cord-310184-qth1y88o.txt txt = ./txt/cord-310184-qth1y88o.txt === reduce.pl bib === id = cord-310062-mmlh9i1o author = Luo, Haibin title = In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS date = 2004-12-01 pages = extension = .txt mime = text/plain words = 5161 sentences = 269 flesch = 54 summary = Both the thermal and chemical denaturant-induced denaturation analyses showed that oligomeric SARS_NP unfolds and refolds through a two-state model, and the electrostatic interactions among the charge groups of SARS_NP made a significant contribution to its conformational stability. In addition, the unfolding and refolding characterizations of SARS _ NP dimer caused by thermaland chemical denaturant-induced denaturations were also inspected by fluorescent and CD spectral investigation, it is found that SARS _ NP exhibits its most stable conformation near pH 9.0, and its oligomer dissociation and protein unfolding seem to be of coinstantaneous occurring events. The fluorescent intensity was found to decrease with increase of temperature accompanied by a shift in emission k max from 333 to 343 nm ( Fig. 4A and C) , whereas far-UV CD spectral information suggested the loss of secondary structure for SARS _ NP during its thermal-induced denaturation (Fig. 4B and D) . cache = ./cache/cord-310062-mmlh9i1o.txt txt = ./txt/cord-310062-mmlh9i1o.txt === reduce.pl bib === id = cord-310230-9wfb43gt author = Ghorbani, Mahdi title = Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date = 2020-06-27 pages = extension = .txt mime = text/plain words = 3479 sentences = 220 flesch = 56 summary = Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body. The focus of this article is to elucidate the differences between the interface of SARS-COV and nCOV-2019 with ACE2 to understand with atomic resolution the interaction mechanism and hotspot residues at the RBD/ACE2 interface using long-timescale molecular dynamics (MD) simulation. The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019 and all its mutant complexes were investigated by the MMPBSA method. Computational Simulations Reveal the Binding Dynamics between Human ACE2 and the Receptor Binding Domain of SARS-CoV-2 Spike Protein cache = ./cache/cord-310230-9wfb43gt.txt txt = ./txt/cord-310230-9wfb43gt.txt === reduce.pl bib === id = cord-310042-9z8rkzq8 author = Aysha, Al‐Ani title = Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date = 2020-07-12 pages = extension = .txt mime = text/plain words = 3471 sentences = 214 flesch = 43 summary = This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. A significant proportion of IBD patients are treated with long-term immunomodulator/immunosuppressive therapy which potentially places them at increased risk of infections and associated complications. Practitioners and patients alike are therefore concerned about the risk and implications of COVID-19 infection in the IBD patient, despite a paucity of evidence supporting an altered predisposition to disease or more severe disease course. Despite concerns regarding immunosuppression and consequent predisposition to infection, there is no evidence to suggest increased infection rates of COVID-19 in IBD patients to date. 8, 9 Hence, expert consensus currently is that patients with IBD do not appear to be at increased risk of SARS-CoV-2 infection compared with the general population. 2 • Reducing disease activitythere is evidence that moderate to severe disease activity increases the risk of infection in IBD patients. cache = ./cache/cord-310042-9z8rkzq8.txt txt = ./txt/cord-310042-9z8rkzq8.txt === reduce.pl bib === id = cord-310061-nro623aa author = Valitutto, Marc T. title = Detection of novel coronaviruses in bats in Myanmar date = 2020-04-09 pages = extension = .txt mime = text/plain words = 3678 sentences = 192 flesch = 48 summary = Historically, bats have been linked to highly pathogenic viruses that pose a serious threat to human health, including the coronaviruses responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), the hemorrhagic ebola and Marburg filoviruses, and paramyxoviruses such as Nipah virus [10, 11, [13] [14] [15] [16] [17] [18] . The 2002-2003 SARS epidemic, the emergence of MERS in people in 2012, and the ongoing COVID-19 pandemic have prompted substantial interest in detecting coronaviruses of bat origin due to public health concern and their pandemic potential [10, [13] [14] [15] [16] [17] [18] . In addition to human-associated CoVs, bats are also hosts of coronaviruses that infect production animals, and have been implicated in the emergence and origin of swine acute diarrhea syndrome (SADS), transmissible gastroenteritis virus (TGEV) in pigs, and porcine epidemic diarrhea (PED), which can cause considerable losses [23] [24] [25] [26] . cache = ./cache/cord-310061-nro623aa.txt txt = ./txt/cord-310061-nro623aa.txt === reduce.pl bib === id = cord-310291-z79x349o author = Holland, LaRinda A. title = An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1052 sentences = 67 flesch = 52 summary = title: An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) Here, we report on early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sentinel surveillance in Tempe, Arizona. Genomic characterization identified an isolate encoding a 27-amino-acid in-frame deletion in accessory protein ORF7a, the ortholog of SARS-CoV immune antagonist ORF7a/X4. In anticipation of COVID-19 spreading in Arizona, we initiated a surveillance effort for the local emergence of SARS-CoV-2 starting 24 January 2020. To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we performed next-generation sequencing (NGS; Illumina NextSeq, 2ϫ76) directly on specimen RNA, thereby avoiding cell culture passage and potentially associated mutations. We found that the SARS-CoV-2 AZ-ASU2923 genome has an 81-nucleotide (nt) deletion in the ORF7a gene, resulting in a 27-amino-acid in-frame deletion (Fig. 2B) . Severe acute respiratory syndrome coronavirus gene 7 products contribute to virus-induced apoptosis cache = ./cache/cord-310291-z79x349o.txt txt = ./txt/cord-310291-z79x349o.txt === reduce.pl bib === id = cord-310438-744r7gc3 author = Chan, Ta-Chien title = The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date = 2010-06-25 pages = extension = .txt mime = text/plain words = 5083 sentences = 226 flesch = 40 summary = This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan's influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. The aims of this study were: (1) to evaluate the effectiveness of matching or mismatching influenza vaccine strains on influenzaassociated mortality, (2) to assess whether public health improvements during the post-SARS period might have decreased elderly mortality, and (3) to investigate molecular variation among vaccine-mismatched influenza viruses that may be associated with increased excess influenza-associated mortality. Explanatory variables for the above three outcome measures include monthly meteorological parameters (monthly means of temperature and humidity), annual periodic cycle (i.e., sine/cosine function of seasonal periodicity), monthly virus isolation rates for different subtypes/types of influenza viruses [A (H3N2) or A (H1N1) or B], matching status of different vaccine strains for each subtype/type in each of the studied years, post-SARS effect, and linear temporal monthly trends. cache = ./cache/cord-310438-744r7gc3.txt txt = ./txt/cord-310438-744r7gc3.txt === reduce.pl bib === id = cord-310392-fmobf1f1 author = Sekizuka, Tsuyoshi title = SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date = 2020-06-05 pages = extension = .txt mime = text/plain words = 2410 sentences = 132 flesch = 59 summary = A field FIGURE 1 | Summary of travel history, clinical course, and PCR testing for 10 SARS-CoV-2-positive travelers who returned to Japan from Egypt, as well as the associated patients who were their close contacts. In this study, we have evaluated viral genome sequences from SARS-CoV-2-positive travelers who returned from Egypt, and characterized the haplotype networks to demonstrate possible routes of the spread. SARS-CoV-2 genome sequences with nearly fulllength information (≥ 29 kb) were retrieved from the GISAID EpiCoV database on March 30, 2020, and we generated haplotype networks by median-joining network analysis using PopART software 3 to highlight and trace a potential infectious route among COVID-19 patient populations. P2-1 and P2-2 had visited Egypt together and traveled aboard the same Nile River cruise ship, and SARS-CoV-2 genome sequences isolated from them are identical with that of P1 (Figure 3) . cache = ./cache/cord-310392-fmobf1f1.txt txt = ./txt/cord-310392-fmobf1f1.txt === reduce.pl bib === id = cord-310221-car394ou author = Chandrashekar, Abishek title = SARS-CoV-2 infection protects against rechallenge in rhesus macaques date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2540 sentences = 140 flesch = 44 summary = We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. On day 2 following challenge, both necropsied animals demonstrated multifocal regions of inflammation and evidence of viral pneumonia, including expansion of alveolar septae with mononuclear cell infiltrates, consolidation, and edema (Fig. 3, A and B) . SARS-CoV-2 infection in rhesus macaques led to humoral and cellular immune responses (Fig. 2) and provided protection against rechallenge (Fig. 5) . In summary, SARS-CoV-2 infection in rhesus macaques induced humoral and cellular immune responses and provided protective efficacy against SARS-CoV-2 rechallenge. cache = ./cache/cord-310221-car394ou.txt txt = ./txt/cord-310221-car394ou.txt === reduce.pl bib === id = cord-310124-3bc8zeww author = Ratajczak, Mariusz Z. title = SARS-CoV-2 Entry Receptor ACE2 Is Expressed on Very Small CD45(−) Precursors of Hematopoietic and Endothelial Cells and in Response to Virus Spike Protein Activates the Nlrp3 Inflammasome date = 2020-07-20 pages = extension = .txt mime = text/plain words = 5165 sentences = 281 flesch = 52 summary = We demonstrate for the first time that ACE2 and the entry-facilitating transmembrane protease TMPRSS2 are expressed on very small CD133(+)CD34(+)Lin(−)CD45(−) cells in human umbilical cord blood (UCB), which can be specified into functional HSCs and EPCs. The existence of these cells known as very small embryonic-like stem cells (VSELs) has been confirmed by several laboratories, and some of them may correspond to putative postnatal hemangioblasts. Moreover, we demonstrate for the first time that, in human VSELs and HSCs, the interaction of the ACE2 receptor with the SARS-CoV-2 spike protein activates the Nlrp3 inflammasome, which if hyperactivated may lead to cell death by pyroptosis. We sorted very small CD34 + Lin − CD45 − cells (VSELs) and CD34 + Lin − CD45 + cells (HSCs) from UCB by FACS (Fig. 1) and phenotyped them by real-time PCR for expression of mRNAs for the ACE2 entry receptor for SARS-CoV-2, the spike protein-processing enzyme TIMPRSS2, the receptors for Ang II (AT 1 R and AT 2 R), and the Ang (1-7) receptor (MasR, Fig. 2) . cache = ./cache/cord-310124-3bc8zeww.txt txt = ./txt/cord-310124-3bc8zeww.txt === reduce.pl bib === id = cord-310201-70fj4fhr author = Wei, D.-Q. title = Anti-SARS drug screening by molecular docking date = 2006-05-22 pages = extension = .txt mime = text/plain words = 3577 sentences = 202 flesch = 60 summary = (2003) and Chou (2004) found the fitting problem of AG7088 to the binding pocket of SARS CoV Mpro, and they suggested its derivative KZ7088 as a better starting point. Furthermore, the intermolecular hydrogen bonds and electrostatic interaction, whose effects have already been counted in the binding energy, were also investigated in order to find useful information for drug design. In contrast, if ranking the docking results according to the binding free energy which includes the torsional term as shown in Rank 2 of Table 1 , it was found that most of the top-20 ligands interacted quite well with the receptor in the pocket. A comparison of the results between Ranks 1 and 2 suggests that the binding free energy is more reliable as a criterion for the virtual screening via molecular docking. Hydrogen bonds between ligand 4 and the involved residues of SARS CoV Mpro. cache = ./cache/cord-310201-70fj4fhr.txt txt = ./txt/cord-310201-70fj4fhr.txt === reduce.pl bib === id = cord-310396-jitao9k0 author = Lei, Yu title = MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date = 2009-03-07 pages = extension = .txt mime = text/plain words = 6031 sentences = 325 flesch = 46 summary = The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. Currently, there are no reports of viral proteins targeting MAVS for inhibition of virus-induced cell death responses. In this report, we describe a novel function of MAVS in mediating virus-induced apoptosis, and identify viral proteins as inhibitors of this response. In addition, the involvement of proteins on IFN axis in virusinduced host cell apoptosis has been implicated in another previous report, in which MAVS has been shown to be critical for reovirus-triggered caspase-3/7 activation in HEK293T cells [46] , however, the study did not evaluate whether MAVS mediates virus-induced apoptosis and what roles type 1 IFNs play in MAVS-mediated apoptosis. cache = ./cache/cord-310396-jitao9k0.txt txt = ./txt/cord-310396-jitao9k0.txt === reduce.pl bib === id = cord-310464-lkdkdque author = Rayko, Mikhail title = Quality control of low-frequency variants in SARS-CoV-2 genomes date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1702 sentences = 109 flesch = 58 summary = During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. As a result of the collaborative efforts of the researchers worldwide, on April 14, 2020 it contained over 8,000 SARS-nCoV-2 genomes from different countries, sequenced and assembled using various technologies and approaches. GISAID database curators do a tremendous job of filtering submitted sequences, but sometimes it is difficult to distinguish real variants from errors, especially at the lack of information about coverage. Dataset 8,053 full-length (>29,000 bp) sequences of the SARS-CoV-2 were downloaded from the GISAID database ( www.epicov.org ) on April 14, 2020, including 5,556 genomes marked as "high coverage". Full table with percentage of singleton-containing genomes depending on sequencing and assembly method. cache = ./cache/cord-310464-lkdkdque.txt txt = ./txt/cord-310464-lkdkdque.txt === reduce.pl bib === id = cord-310419-s3qkscw7 author = Lephart, Paul R. title = Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2049 sentences = 110 flesch = 55 summary = title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. Within a few weeks, additional SARS-CoV-2 NAAT options emerged that were specifically designed for rapid testing of patients in the point of care setting: the Cepheid Xpert Xpress SARS-CoV-2 (Xpert) assay, which could provide results in 45 minutes, and the Abbott ID NOW COVID-19 (ID NOW) assay, ultimately approved for direct nasal, nasopharyngeal and throat swab testing only, with results in 5-15 minutes. This comparative analysis of SARS-CoV-2 NAATs utilizing the m2000, Simplexa, Xpert and ID NOW assays demonstrated that significant performance deficits were found in the ID NOW assay when tested in a mixed patient population using both NP and nasal specimens. cache = ./cache/cord-310419-s3qkscw7.txt txt = ./txt/cord-310419-s3qkscw7.txt === reduce.pl bib === id = cord-310594-i0586vfw author = Weemaes, Matthias title = Laboratory information system requirements to manage the COVID-19 pandemic: a report from the Belgian national reference testing center date = 2020-04-29 pages = extension = .txt mime = text/plain words = 2537 sentences = 136 flesch = 34 summary = OBJECTIVE: To describe the development, implementation and requirements of laboratory information system (LIS) functionality to manage test ordering, registration, sample flow, and result reporting during the COVID-19 pandemic. RESULTS: We outline the design, implementation and requirements of LIS functionality related to managing increased test demand during the COVID-19 crisis, including tools for test ordering, standardized order sets integrated into a computerized provider order entry module, notifications on shipping requirements, automated triaging based on digital metadata forms, and the establishment of databases with contact details of other laboratories and primary care physicians to enable automated reporting. DISCUSSION: Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turn-around-time of SARS-CoV-2 testing. During the early stages of the COVID-19 outbreak, our laboratory was the only SARSNotably, the large majority of our expanded work force (30 of the 38 additional FTE) was assigned to help with administrative tasks (sample reception, triaging, patient registration, result validation and reporting, and epidemiological studies), and not directly involved in expanding analytical capacity (i.e. PCR analysis) ( Figure 2 ). cache = ./cache/cord-310594-i0586vfw.txt txt = ./txt/cord-310594-i0586vfw.txt === reduce.pl bib === id = cord-310063-8nbmrjrw author = Selva, K. J. title = Distinct systems serology features in children, elderly and COVID patients date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3779 sentences = 218 flesch = 55 summary = . https://doi.org/10.1101 /2020 6 147 To interrogate Ab functionality and cross-reactivity between antigens of selected CoV signatures, we 148 conducted a correlation network analysis, focusing upon significant correlations of Ab features 149 selected by Elastic-Net. The children's network (Figure 1f ) demonstrates how SARS-CoV-2 Abs that 150 engaged FcγRIIa-H131 are associated with SARS-CoV-2 IgG, specifically of IgG1 subclass. In particular, we found that in the majority of COVID-19 190 patients, the SARS-CoV-2 antigen-specific Abs bound to FcγRIIIaV158 and FcγRIIaH131 soluble 191 dimers at high levels, even at 1:800 plasma titrations, suggesting potent ADCC and ADCP CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.05.11.20098459 doi: medRxiv preprint 8 notably being the healthy exposed SARS-CoV-2 PCR-negative individual (Figure 3d) The majority of COVID-19 moderate/severe samples were collected upon hospital presentation, 235 whereas mild samples were collected upon convalescence (Extended Data Table 3 ). cache = ./cache/cord-310063-8nbmrjrw.txt txt = ./txt/cord-310063-8nbmrjrw.txt === reduce.pl bib === id = cord-310692-8fuj9td2 author = Coste, A. T. title = Indication for SARS-CoV-2 serology: first month follow-up date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1536 sentences = 99 flesch = 51 summary = Our laboratory performed a prospective surveillance of the SARS-CoV-2 serologic test requested during the first 5 weeks, by specifically looking at rate of the different accepted indications. For the 303 serologies requested by hospital-based physicians working in tertiary hospitals or clinics, 94 were positive (31%), 205 were negative (68%), and four were undetermined (13%). They had specific directives in their hospital to systematically perform a SARS-CoV-2 RT-PCR screening and serology to any patient arriving at the hospital. The residuals symptoms with no documented or negative RT-PCR (indication N°6.4) appeared to be very important for patient care but was totally unexpected, since on 14 th April, when we started the SARS-CoV-2 serology, the occurrence of such post-infectious complications were not yet reported [5] . This work may serve as a seed for international guidelines regarding the indications of SARS-CoV-2 serology for patients care. cache = ./cache/cord-310692-8fuj9td2.txt txt = ./txt/cord-310692-8fuj9td2.txt === reduce.pl bib === id = cord-310333-70ldbw3r author = de Souza, Wanderley title = COVID-19 and parasitology date = 2020-05-30 pages = extension = .txt mime = text/plain words = 842 sentences = 43 flesch = 52 summary = Emerging and reemerging diseases are a challenge for public health worldwide and particularly for Brazil, where the existence of the Amazon region provides a constant source of new pathogens that are transmitted from wild animals to man. Infectious diseases, such as severe acute respiratory syndrome (SARS), represent a major threat to public health. At present, the available data indicate the presence of 2.6 million infected people and 178 thousand dead (April 22), demonstrating the severity of COVID-19 due to the rapid spread of the virus and its high pathogenicity, which mainly, but not exclusively, affects the pulmonary system. Therefore, members of the parasitology community, especially those working with parasite-host cell interaction processes, can and shall contribute at this time. Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease Epidemiology and cause of severe acute respiratory syndrome (SARS) in 304 Guangdong, People's Republic of China cache = ./cache/cord-310333-70ldbw3r.txt txt = ./txt/cord-310333-70ldbw3r.txt === reduce.pl bib === id = cord-310687-qw164eyl author = Chan, Ming-Chin title = Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 date = 2020-09-01 pages = extension = .txt mime = text/plain words = 290 sentences = 21 flesch = 60 summary = title: Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 Healthcare workers (HCWs) have been singled out, by mass screening supporters, as a high-risk group which are particularly in need to be mass-screened for the presence of SARS-CoV-2 virus or anti-SARS-CoV-2 antibodies, despite the fact that all Taiwanese If HCWs are indeed at high risk of contracting and carrying SARS-CoV-2 virus, then the current HCWs virological surveillance for COVID-19 should be able to detect SARS-CoV-2-positive cases among HCWs. Therefore, we reviewed the HCWs surveillance results at our hospital. 5 Since March 31, 2020, in consistent with Taiwan Central Epidemic Command Center's HCWs surveillance policy, 5 all HCWs who developed fever or any respiratory symptoms were required to be tested for SARS-CoV-2 regardless of the presence of occupational exposure history or not . Taiwan Centers for Disease Control: COVID-19 statistics Taiwan Centers for Disease Control. cache = ./cache/cord-310687-qw164eyl.txt txt = ./txt/cord-310687-qw164eyl.txt === reduce.pl bib === id = cord-310753-sv88b0dt author = Marks, M. title = Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study date = 2020-10-27 pages = extension = .txt mime = text/plain words = 3585 sentences = 210 flesch = 56 summary = By the time of performing this search, various 57 authors had reported on retrospective analyses of clusters of index cases and their corresponding contacts, 58 as well as series of patients who developed symptomatic Covid-19 disease after PCR positive result. The objective of this study was to evaluate transmission dynamics of SARS-CoV-2 in the context of a trial 109 of post-exposure prophylaxis and evaluate the influence of baseline variables-including viral load of the 110 index cases and exposed contacts-to transmission, development of symptomatic disease, and the 111 incubation period. Also, after excluding 215 contacts who were PCR positive at the first study visit, we found no association between the viral load of 216 the index case and the time to onset of incident SARS-CoV-2 infection (HR 1.01 95% CI 0.83-1.23). cache = ./cache/cord-310753-sv88b0dt.txt txt = ./txt/cord-310753-sv88b0dt.txt === reduce.pl bib === id = cord-310477-vniokol0 author = Pontes, Camila title = Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date = 2020-08-21 pages = extension = .txt mime = text/plain words = 4371 sentences = 197 flesch = 46 summary = More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). In summary, the SDPs found within these β-CoV subgenera define a specific region of the receptor binding domains: they are part of, or in direct contact with, the ACE2 interacting surface ( A second S3Det analysis was performed on the full β-CoV MSA. On the other hand, the analysis performed on individual β-CoV subgenera, i.e. Sarbecovirus, Merbecovirus and Embecovirus subgroups, allowed a fine-grained classification into subfamily clusters that clearly reflect the functional diversification of the spike protein family, that is, the specificity to different host-cell receptors (Figure 2-3) . cache = ./cache/cord-310477-vniokol0.txt txt = ./txt/cord-310477-vniokol0.txt === reduce.pl bib === id = cord-310879-b8tdug93 author = Beddingfield, Brandon J. title = In the Age of CoVID: Genomic Changes Over the Lifespan Help Explain Severe SARS-CoV-2 Disease date = 2020-10-23 pages = extension = .txt mime = text/plain words = 615 sentences = 47 flesch = 62 summary = Because additional receptor interactions have been implicated in host cell invasion by previous coronaviruses, other receptors have been investigated for their potential role in SARS-CoV-2 infection. Previous studies have also The potential entry gene BSG was found to be in higher abundance in cardiorenal tissues than in the lung, though it was well expressed in all tissues examined. This is in contrast to ACE2, which was found to be expressed at low levels in lung, but higher levels in cardiorenal tissues (kidney, heart and blood vessels) across the individuals examined. Taken together, this could explain the higher levels of viral replication in lung tissue for SARS-CoV-2, even if the receptor itself is not highly expressed. Males also had an increased expression of BSG, PPIA, PPIB in endothelial cells, and higher levels of ACE2 and TMPRSS2 in the coronary artery. Airways Expression of SARS-CoV-2 Receptor, ACE2, and TMPRSS2 Is Lower in Children Than Adults and Increases with Smoking and COPD cache = ./cache/cord-310879-b8tdug93.txt txt = ./txt/cord-310879-b8tdug93.txt === reduce.pl bib === id = cord-310605-r63sg73c author = Dorward, D. A. title = Tissue-specific tolerance in fatal Covid-19 date = 2020-07-04 pages = extension = .txt mime = text/plain words = 4482 sentences = 256 flesch = 39 summary = Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. As analysis of SARS-CoV-2 RNA confirmed presence in numerous organs, detailed histological analysis of multiple tissues was undertaken on every patient to determine the associated pathological consequences and inflammatory responses. The present study shows that fatal Covid-19 is associated with variable but widespread distribution of viral RNA and protein but with a discordant inflammatory response to local viral presence, both between and within tissues, demonstrating tissue-specific tolerance of SARS-CoV-2. cache = ./cache/cord-310605-r63sg73c.txt txt = ./txt/cord-310605-r63sg73c.txt === reduce.pl bib === id = cord-310239-mmvuij3k author = Arentz, Susan title = Clinical significance summary: Preliminary results of a rapid review of zinc for the prevention and treatment of SARS-CoV-2 and other acute viral respiratory infections date = 2020-08-01 pages = extension = .txt mime = text/plain words = 3941 sentences = 215 flesch = 47 summary = Indirect evidence from systematic reviews have found zinc supplementation is effective for the prevention of acute respiratory infections in young children and zinc lozenges may reduce the duration of the common cold in adults. As of the 9 June 2020, the preliminary findings of a rapid review of zinc for the prevention or treatment Pending any definitive evidence, clinicians might consider assessing the zinc status of people with chronic disease co-morbidities and older adults as part of a SARS-CoV-2 clinical work-up, as both groups have a higher risk of zinc deficiency/insufficiency and poorer outcomes from SARS-CoV-2. The primary objective of this rapid review was to assess the effects of zinc on the incidence, duration and severity of acute upper or lower respiratory tract infections caused by SARS-CoV-2 infection in people of any age and of any zinc status when used as a preventive supplement or as a therapy. cache = ./cache/cord-310239-mmvuij3k.txt txt = ./txt/cord-310239-mmvuij3k.txt === reduce.pl bib === id = cord-310623-zbjgr9jk author = Ellington, Sascha title = Characteristics of Women of Reproductive Age with Laboratory-Confirmed SARS-CoV-2 Infection by Pregnancy Status — United States, January 22–June 7, 2020 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2985 sentences = 160 flesch = 45 summary = These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation compared with nonpregnant women, but their risk for death is similar. These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation * https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html. In contrast, however, ICU admission and receipt of mechanical ventilation are distinct proxies for illness severity (8) , and after adjusting for age, presence of underlying conditions, and race/ethnicity, the risks for both (N = 91,412) , by pregnancy status, age group, and race/ethnicity, and relative risk for these outcomes comparing pregnant women to nonpregnant women aged 15-44 years -United States, January 22-June 7, 2020 Among reproductive-age women with SARS-CoV-2 infection, pregnancy was associated with hospitalization and increased risk for intensive care unit admission, and receipt of mechanical ventilation, but not with death. cache = ./cache/cord-310623-zbjgr9jk.txt txt = ./txt/cord-310623-zbjgr9jk.txt === reduce.pl bib === id = cord-310947-aqau2n7q author = Pan, Ji'An title = Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date = 2008-10-01 pages = extension = .txt mime = text/plain words = 6821 sentences = 302 flesch = 43 summary = In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . cache = ./cache/cord-310947-aqau2n7q.txt txt = ./txt/cord-310947-aqau2n7q.txt === reduce.pl bib === id = cord-310411-l0slp1wa author = Rusanen, J. title = Rapid homogeneous assay for detecting antibodies against SARS-CoV-2 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 2117 sentences = 162 flesch = 57 summary = 73 We have previously set up rapid homogeneous (wash-free) immunoassays utilizing time(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In this study we introduce rapid wash-free LFRET assays for detection of antibodies 114 against SARS-CoV-2 N and S antigens and compare them with ELISAs and 115 microneutralization. ; https://doi.org/10.1101/2020.11.01.20224113 doi: medRxiv preprint 119 LFRET assays for SARS-CoV-2 S and N were set up using Eu-labeled in-house antigens 120 and AF-labeled protein L. 140 In order to compare the performance of LFRET with classical serology, we tested the set (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. After overnight incubation at Protein expression and purification 299 We initially attempted producing SARS-CoV-2 S protein in Expi293F cells utilizing the (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-310411-l0slp1wa.txt txt = ./txt/cord-310411-l0slp1wa.txt === reduce.pl bib === id = cord-310920-itqwhi6a author = Haddad, Christina title = Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3698 sentences = 205 flesch = 44 summary = Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. cache = ./cache/cord-310920-itqwhi6a.txt txt = ./txt/cord-310920-itqwhi6a.txt === reduce.pl bib === id = cord-310606-msmh7d8m author = Westerhuis, B. M. title = Severe COVID-19 patients display a back boost of seasonal coronavirus-specific antibodies date = 2020-10-12 pages = extension = .txt mime = text/plain words = 4297 sentences = 306 flesch = 65 summary = . https://doi.org/10.1101/2020.10.10.20210070 doi: medRxiv preprint All patients mounted a strong SARS-CoV-2 immune response shown by rising IgG titers against 174 SARS2-SECTO, SARS2-S1 and SARS2-SRBD which peaked around 4 weeks post onset of clinical 175 symptoms ( Figure 1A and Supplementary figure 1A for individual patients). Besides the SARS-CoV-2 IgG response, serum IgG reactivity towards various, but not 183 all seasonal CoV antigens, increased in longitudinally analyzed COVID-19 patients ( Figure 1A is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint However, cross-reactivity 282 between OC43-SECTO and SARS-CoV-2 S antigens showed significant weak negative 283 correlations (range R=-0.038 --0.088, range p=4,7x10 -6 -0.014) suggesting that OC43-S ECTO 284 specific clones are unlikely to cross-react with SARS-CoV-2 S in severe COVID-19 patients 285 ( Figure 3B ). cache = ./cache/cord-310606-msmh7d8m.txt txt = ./txt/cord-310606-msmh7d8m.txt === reduce.pl bib === id = cord-310636-y7n22ykt author = Garcia-Beltran, W. F. title = COVID-19 neutralizing antibodies predict disease severity and survival date = 2020-10-20 pages = extension = .txt mime = text/plain words = 10879 sentences = 545 flesch = 47 summary = A quantitative ELISA that measures IgG, IgM, and IgA antibodies to the receptor binding domain (RBD) of SARS-CoV-2 and a high-throughput neutralization assay using lentiviral vectors pseudotyped with SARS-CoV-2 and WIV1-CoV were developed to assess neutralization potency and cross-neutralizing responses. We determined the sensitivity and specificity of this assay by assessing anti-RBD antibody levels in a cohort of SARS-CoV-2-infected patient serum samples collected between 14 to 42 days after symptom onset ( n = 85) in order to maximize seropositivity for IgG, IgM, and IgA. Anti-RBD IgG, IgM, and IgA levels were measured for each sample by interpolation on to the standard curve and a receiver operating curve (ROC) analysis was used to determined optimal cut-offs that distinguished SARS-CoV-2-infected patients from pre-pandemic controls ( Figure 2C ). However, a principle components analysis (PCA) that included demographic data, pre-existing medical conditions, laboratory data, treatments received, anti-RBD antibody levels and neutralization titers but not clinical outcomes demonstrated clustering of patients by the severity cohorts ( Figure 4A ). cache = ./cache/cord-310636-y7n22ykt.txt txt = ./txt/cord-310636-y7n22ykt.txt === reduce.pl bib === id = cord-310624-3kojrkz7 author = Flores-Alanis, Alejandro title = The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789 date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3064 sentences = 181 flesch = 56 summary = In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved. cache = ./cache/cord-310624-3kojrkz7.txt txt = ./txt/cord-310624-3kojrkz7.txt === reduce.pl bib === id = cord-310507-5h6egve4 author = van Doorn, Amarylle S. title = Systematic review with meta‐analysis: SARS‐CoV‐2 stool testing and the potential for faecal‐oral transmission date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3532 sentences = 238 flesch = 49 summary = Since December 2019, the world has been dealing with the outbreak of the novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) leading to Corona Virus Disease 2019 (COVID-19) that emerged in Wuhan, China. However, there is a growing body of studies in which SARS-CoV-2 RNA was detected in stool samples (including anal swabs) from COVID-19 patients. 11, 15, 16 This study aims to (1) critically assess the clinical relevance of testing stool samples and anal swabs and (2) provide a critical overview of the available literature regarding the faecal-oral transmission of SARS-CoV-2. We collected the following data from the eligible original articles: study design, geographic location, study period, number of patients, age, types of tested specimens, number of tested specimens, methods of the performed tests, duration and prevalence of positive test results in different specimens, disease severity, gastrointestinal symptoms, endoscopic results, specific evidence supporting faecal-oral transmission and remarkable patient/population characteristics. cache = ./cache/cord-310507-5h6egve4.txt txt = ./txt/cord-310507-5h6egve4.txt === reduce.pl bib === id = cord-310909-nc82a70n author = Qiu, Maofeng title = Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date = 2005-04-13 pages = extension = .txt mime = text/plain words = 4520 sentences = 196 flesch = 48 summary = In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. In the present study, to understand the profile of antibodies to individual proteins of the SARS-CoV, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of this virus were prepared and used to screen and monitor their specific IgG antibodies in SARS patient sera using protein microarray, and the rabbit antisera to recombi-nant proteins S3 (aa 241-591), N (full length), 3a (aa 125-274) and 9b (full length) were prepared and used to investigate their neutralizing activity to the SARS-CoV infection in Vero E6 cells. cache = ./cache/cord-310909-nc82a70n.txt txt = ./txt/cord-310909-nc82a70n.txt === reduce.pl bib === id = cord-310657-04pp0o74 author = Lu, Renfei title = A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date = 2020-04-18 pages = extension = .txt mime = text/plain words = 4064 sentences = 206 flesch = 51 summary = Using a mismatch-tolerant amplification technique, we developed a simple, rapid, sensitive and visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection based on its N gene. In this study, we applied the mismatch-tolerant technique to develop novel real-time fluorescent and visual RT-LAMP assays for the rapid and sensitive detection of SARS-CoV-2 RNA, and evaluated the novel assays using clinical samples. The novel RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies per reaction, and shows no cross-reactivity with 17 common human respiratory viruses, including four other human coronaviruses (OC43, 229E, HKU-1 and NL63). In view of a mean viral load of 1.4 × 10 6 copies/mL in nasal swabs of COVID-19 patients, the novel assay is sufficiently sensitive for the detection of SARS-CoV-2 at an early stage of infection using nasal swab specimens. The RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies of SARS-CoV-2 RNA per 25 µL reaction, and good specificity regarding common respiratory viruses. cache = ./cache/cord-310657-04pp0o74.txt txt = ./txt/cord-310657-04pp0o74.txt === reduce.pl bib === id = cord-310331-29srzbuk author = Xu, Jiuyang title = 2019 novel Coronavirus outbreak: a quiz or final exam? date = 2020-03-20 pages = extension = .txt mime = text/plain words = 2004 sentences = 107 flesch = 51 summary = Armed with experience from previous epidemics in the last two decades, clinicians, scientists, officials, and citizens in China are all contributing to the prevention of further 2019-nCoV transmission. The 2019 novel coronavirus (2019-nCoV) outbreak is currently bringing challenges to China and the whole world. Since direct human transmission and asymptomatic infection have been revealed for 2019-nCoV [3] , health authorities in China are facing an enormous challenge on disease management and control. Realizing the severity of SARS-CoV as a respiratory virus, the detection of pneumonia of unknown origin in 2019-nCoV outbreak enabled relatively early alarm from health authorities and raised awareness for medical staff to equip personal protection methods when dealing with suspected cases. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-310331-29srzbuk.txt txt = ./txt/cord-310331-29srzbuk.txt === reduce.pl bib === id = cord-310803-iig414jg author = Khazeei Tabari, Mohammad Amin title = Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic date = 2020-10-17 pages = extension = .txt mime = text/plain words = 1337 sentences = 85 flesch = 48 summary = COVID-19 is a disorder caused by SARS-CoV-2, which has CoV-2 genome sequencing demonstrated that ORF1a/b is closely similar to those from the bat, 4 civet, and other human SARS-CoVs, but the external sub-domain amino acid sequence of the 5 spike receptor-binding domain for this novel virus is only 40% similar to other SARS-related 6 coronaviruses. Nelfinavir was predicted to be a potential 5 inhibitor of 2019-nCov main protease by an integrative approach combining homology 6 modelling, molecular docking and binding free energy calculation Structural and molecular modelling studies 24 reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 25 infection Network-based drug repurposing 29 for novel coronavirus 2019-nCoV/SARS-CoV-2 Emodin blocks the SARS coronavirus 46 spike protein and angiotensin-converting enzyme 2 interaction Repurposing didanosine as a potential treatment for COVID-19 using scRNA-18 seq data Repurposing Didanosine as a Potential Treatment for COVID-19 Using Single-Cell 20 RNA Sequencing Data cache = ./cache/cord-310803-iig414jg.txt txt = ./txt/cord-310803-iig414jg.txt === reduce.pl bib === id = cord-310651-pxfwe67t author = Leung, Gabriel M. title = SARS-CoV Antibody Prevalence in All Hong Kong Patient Contacts date = 2004-09-17 pages = extension = .txt mime = text/plain words = 1927 sentences = 69 flesch = 42 summary = A total of 1,068 asymptomatic close contacts of patients with severe acute respiratory (SARS) from the 2003 epidemic in Hong Kong were serologically tested, and 2 (0.19%) were positive for SARS coronavirus immunoglobulin G antibody. Serologic surveys can be based on a random sample from the total population with appropriate stratification, on serum collected for other reasons (e.g., blood donors, all hospital admissions), or on surveys of persons who resided in sites of superspreading events or who have had close contact with a confirmed SARS patient. During the epidemic, close contacts were prospectively identified by the Hong Kong Special Administrative Region Government Department of Health through standardized telephone interviews with all 1,755 confirmed SARS patients within 1 week of hospital admission (February 15-June 22, 2003). cache = ./cache/cord-310651-pxfwe67t.txt txt = ./txt/cord-310651-pxfwe67t.txt === reduce.pl bib === id = cord-310304-f28tjmi8 author = Alcendor, Donald J. title = Racial Disparities-Associated COVID-19 Mortality among Minority Populations in the US date = 2020-07-30 pages = extension = .txt mime = text/plain words = 7719 sentences = 366 flesch = 41 summary = Maintaining glycemic control in COVID-19 patients is essential, as hyperglycemia could affect pulmonary function, the immune response to infection, and the development of the pro-inflammatory cytokine storm associated with more severe clinical disease ( Figure 1 ). Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, upon infection with SARS-CoV-2 the ACE2 protein serves as the entry receptor for the virus and is internalized in the endosome with SARS-CoV-2 during membrane fusion and uptake by Hypothetical model of uncontrolled blood pressure in patients with hypertension and increased risk for complications due to COVID-19. Longstanding health disparities such as diabetes, hypertension, CVD, and pulmonary disease among minority populations in the US may serve to predispose these communities to SARS-CoV-2 infection and increased risk for clinically severe COVID-19. cache = ./cache/cord-310304-f28tjmi8.txt txt = ./txt/cord-310304-f28tjmi8.txt === reduce.pl bib === id = cord-310631-ru5f69qg author = Joachim, Denner title = SARS-CoV-2 and enhancing antibodies date = 2020-05-07 pages = extension = .txt mime = text/plain words = 567 sentences = 40 flesch = 50 summary = In contrast, other CoV infections including the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS) and the recent COVID-19 are characterised by a higher pathogenicity in certain human populations and may be lethal. In persons infected by SARS-CoV enhancing antibodies and neutralising antibodies may partly counteract each other's function. In the case, cross-reactive enhancing antibodies exist, the infection with the new SARS-CoV-2 may be enhanced by these pre-existing antibodies against common CoV. Common CoV circulate every year in the human population [1] and it sounds logical that the amount of anti-CoV antibodies including potentially enhancing antibodies is higher in older persons. The assumption of ADE with pre-existing enhancing antibodies against common CoV may also explain why in some regions the infection rate with SARS-CoV-2 and its pathogenicity is higher compared with other regions. The possible existence of enhancing antibodies is also of importance for the development of a vaccine against SARS-CoV-2. cache = ./cache/cord-310631-ru5f69qg.txt txt = ./txt/cord-310631-ru5f69qg.txt === reduce.pl bib === id = cord-310946-rjwyirld author = Wiseman, Jessica title = False negative SARS-CoV-2 PCR - A case report and literature review date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1690 sentences = 98 flesch = 53 summary = The first case of the novel Coronavirus Diseases (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected in Wuhan, China in December 2019. A nasopharyngeal SARS-CoV-2 PCR was obtained on day 1 of his admission and was negative. This case highlights multiple negative nasopharyngeal SARS-CoV-2 PCR swabs in a patient with high clinical suspicion for SARS-CoV-2, who ultimately tested positive when deep sputum was sent for PCR nine days into his admission (10 days after respiratory symptoms started). Therefore, to improve the odds of making a definitive diagnosis, additional testing methods such as sputum for PCR and serology testing should be considered in patients with a high clinical suspicion of COVID-19 who have a negative nasopharyngeal PCR. Subsequently [7] , conducted a study on 127 patients in Beijing Ditan Hospital comparing RT-PCR versus droplet digital PCR (ddPCR) testing, which is reported as being more sensitive in virus detection, in addition to assessing viral load with disease progression. cache = ./cache/cord-310946-rjwyirld.txt txt = ./txt/cord-310946-rjwyirld.txt === reduce.pl bib === id = cord-310928-g553afo9 author = Murch, Simon H title = Common determinants of severe Covid-19 infection are explicable by SARS-CoV-2 secreted glycoprotein interaction with the CD33-related Siglecs, Siglec-3 and Siglec-5/14 date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3724 sentences = 224 flesch = 46 summary = In contrast to the SARS secreted glycoprotein (SGP), SARS-CoV-2 SGP are thus potential ligands for Sialic acid-binding Siglecs on host immune cells, known to regulate immune function. CD33 + MDSC populations release Arginase-1 to cause arginine depletion, inducing decreased T cell receptor (TCR)- chain expression and impaired adaptive immune responses 20, 21 . There is so far no clear consensus on their eventual phenotype but these new marrow derived cells are initially characterised as Early stage MDSC (eMDSC), which do not initially express lineage markers but do express CD33 and would thus be susceptible to SARS-CoV-2 SGP manipulation until the virus was cleared ( Figure 3 ). In due course, this might allow persons who fail to respond to immunisation to be pre-treated to block Siglec binding sites, allowing them to be exposed to small infecting doses of SARS-Cov-2 in clinically controlled circumstances and thus generate a broad immune response, including to the pathogenic glycan determinants cache = ./cache/cord-310928-g553afo9.txt txt = ./txt/cord-310928-g553afo9.txt === reduce.pl bib === id = cord-310774-rpc8hrrx author = Yang, Chongtu title = Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1671 sentences = 117 flesch = 52 summary = We designed this study to investigate the association between carcinoembryonic antigen (CEA) elevation and SARS-CoV-2 infection. METHODS: We retrospectively analyzed 177 patients with confirmed SARS-CoV-2 infection who received plasma CEA assays during hospitalization. CONCLUSION: SARS-CoV-2 infection might be another cause of CEA elevation, with nearly 20% of patients experienced transient and marked CEA increment during COVID-19 pneumonia. We found a portion of patients with COVID-19 pneumonia had raised serum of CEA, and we designed this study to investigate the association between CEA elevation and SARS-CoV-2 infection. However, as none of our participants had any clinical indication of malignancy, further studies are needed to investigate the role of CEA level in COVID-19 patients accompanied with colorectal cancer. In conclusion, SARS-CoV-2 infection might cause transient and marked CEA elevation especially in non-survivors, and this abnormal increment was not correlated with the severity of inflammation. cache = ./cache/cord-310774-rpc8hrrx.txt txt = ./txt/cord-310774-rpc8hrrx.txt === reduce.pl bib === id = cord-310691-6danlh8h author = Ma, Simin title = Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date = 2020-05-26 pages = extension = .txt mime = text/plain words = 2297 sentences = 149 flesch = 57 summary = title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. cache = ./cache/cord-310691-6danlh8h.txt txt = ./txt/cord-310691-6danlh8h.txt === reduce.pl bib === id = cord-311035-s3tkbh9r author = Procko, Erik title = Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4033 sentences = 210 flesch = 45 summary = A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. • The experimental mutational landscape of ACE2 for binding the RBD of SARS-CoV-2 provides a blueprint for engineering high affinity decoy receptors. Following FACS selection of the human culture to enrich a cell population with high binding activity for SARS-CoV-2 protein S, RNA transcripts were isolated and Illumina sequenced. The deep mutational scan of ACE2 revealed that mutations can indeed be found to enhance binding toward SARS-CoV-2 RBD (Figure 2) , suitable for engineering high affinity soluble decoy receptors [15] . A soluble ACE2 variant that combines three mutations, called sACE2 2 .v2.4, was found to be highly expressed, is a stable monodisperse dimer, binds SARS-CoV-2 S with picomolar affinity and potently neutralizes infection of a susceptible cell line by authentic virus. cache = ./cache/cord-311035-s3tkbh9r.txt txt = ./txt/cord-311035-s3tkbh9r.txt === reduce.pl bib === id = cord-310680-klywz85w author = Li, Qihan title = The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date = 2005-04-06 pages = extension = .txt mime = text/plain words = 4397 sentences = 210 flesch = 53 summary = The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The pathological analysis of the lung tissue from the deceased patients revealed severe Abbreviations: SARS-CoV, severe acute respiratory syndrome coronavirus; BTF3, basic transcription factor-3; ATF5, activation transcription factor-5; NADH, nicotinamide adenine dinucleotide dehydrogenase; FBS, fetal bovine serum; DMEM, double minimal essential media; QDO, quartdrop-out; NC, nitrocellulose; HE, hematoxyline and eosin method; GFP, green fluorescence protein; GST, glutathione S-transferase * Corresponding author. To further investigate the contribution of this interaction to the cytopathic effect of SARS-CoV, a detection series of mitochondrial function and the activity of the oxido-reductase system in the human embryo lung fibroblast transfected with the nsp10 gene was performed. cache = ./cache/cord-310680-klywz85w.txt txt = ./txt/cord-310680-klywz85w.txt === reduce.pl bib === id = cord-311026-mpr3xb2a author = Petersen, Eskild title = COVID-19–We urgently need to start developing an exit strategy date = 2020-04-29 pages = extension = .txt mime = text/plain words = 5624 sentences = 339 flesch = 56 summary = Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state's strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. cache = ./cache/cord-311026-mpr3xb2a.txt txt = ./txt/cord-311026-mpr3xb2a.txt === reduce.pl bib === id = cord-310857-i9v9antx author = Blaisdell, Laura L. title = Preventing and Mitigating SARS-CoV-2 Transmission — Four Overnight Camps, Maine, June–August 2020 date = 2020-09-04 pages = extension = .txt mime = text/plain words = 2583 sentences = 133 flesch = 47 summary = The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020.* Shortly thereafter, closures of 124,000 U.S. public and private schools affected at least 55.1 million students through the end of the 2019-20 school year.† During the summer of 2020, approximately 82% of 8,947 U.S. overnight camps did not operate.§ In Maine, only approximately 20% of 100 overnight camps opened.¶ An overnight camp in Georgia recently reported SARS-CoV-2, the virus that causes COVID-19, transmission among campers and staff members when nonpharmaceutical interventions (NPIs) were not strictly followed (1); however, NPIs have been successfully used to mitigate SARS-CoV-2 transmission among military basic trainees (2). During June-August 2020, four overnight camps in Maine implemented several NPIs to prevent and mitigate the transmission of SARS-CoV-2, including prearrival quarantine, preand postarrival testing and symptom screening, cohorting, use of face coverings, physical distancing, enhanced hygiene measures, cleaning and disinfecting, and maximal outdoor programming. To prevent, identify, and mitigate spread of COVID-19, four Maine overnight summer camps with similar size, session duration, and camper and staff member characteristics opened with uniform NPIs, including precamp quarantine, pre-and postarrival testing and symptom screening, cohorting, and physical distancing between cohorts. cache = ./cache/cord-310857-i9v9antx.txt txt = ./txt/cord-310857-i9v9antx.txt === reduce.pl bib === id = cord-311044-kjx0z1hc author = Rubio-Pérez, Inés title = COVID-19: key concepts for the surgeon date = 2020-05-28 pages = extension = .txt mime = text/plain words = 4652 sentences = 301 flesch = 51 summary = Abstract In view of the current pandemic by SARS-CoV-2 it deems essential to understand the key concepts about the infection: its epidemiological origin, presentation, clinical course, diagnosis and treatment (still experimental in many cases). The authors have provided a narrative review of the literature available for certain key aspects of COVID-19 epidemiology, clinical presentation, diagnosis and treatment, which are of special interest to the readers of the journal. Decisions on whether or not to proceed with elective surgery in cancer patients currently depend on the local epidemiological situation, availability of operating rooms J o u r n a l P r e -p r o o f and ICU at the corresponding hospital, disease status and the risk of progression or complications (individualized), assessment of surgical risk and potential complications of the procedure. cache = ./cache/cord-311044-kjx0z1hc.txt txt = ./txt/cord-311044-kjx0z1hc.txt === reduce.pl bib === id = cord-311207-qkkn0297 author = Pegoraro, Manuela title = Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1664 sentences = 92 flesch = 46 summary = Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. In COVID-19 confirmed cases (symptomatic patient with SARS-CoV-2 positive molecular detection), date of symptoms onset was used to timing infection at the moment of specimens' collection. Three stages were identified: early (0-7 days from symptoms onset), intermediate (8China), COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co., Ltd Huzhou, Zhejiang, China), and PRIMA Professional (PRIMA Lab SA, Balerbna, Switzerland) are lateral flow immunochromatographic assays. Sensitivities were assessed on confirmed COVID-19 cases, combining IgG and IgM/IgA positive results, while specificities were estimated on the group of healthy volunteer's. Compared with the automated immunoassays, the ability of ICTs to detect anti-SARS-CoV-2 IgG was equivalent to that of CLIA-MAGLUMI and better than ELISA-Euroimmun, whose IgG positive rates ranged between 0 and 86% at 14 days after symptoms onset. cache = ./cache/cord-311207-qkkn0297.txt txt = ./txt/cord-311207-qkkn0297.txt === reduce.pl bib === id = cord-311105-8edwb59c author = Karamese, M. title = The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey date = 2020-06-26 pages = extension = .txt mime = text/plain words = 1386 sentences = 85 flesch = 62 summary = title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world. In this study, we retrospectively analyzed RT-PCR results of 10,000 cases from April 2 to May 30, 2020 in Kars, Iğdır, and Ardahan cities that are located on the Eastern of Turkey. All the cases were suspected of SARS-CoV-2 infection because of the symptoms or close contact with a COVID-19 patient. . https://doi.org/10.1101/2020.06.25.20138131 doi: medRxiv preprint that are located on the Eastern of Turkey; however, 7853 cases were evaluated who had typical respiratory infection symptoms such as fever, cough and shortness of breath, or close contact with a COVID-19 patient. To our knowledge, this is one of the first epidemiologic study about the RT-PCR positivity of SARS-CoV-2 suspected cases in our country. cache = ./cache/cord-311105-8edwb59c.txt txt = ./txt/cord-311105-8edwb59c.txt === reduce.pl bib === id = cord-310790-3ikgmiof author = Cherrak, Sabri Ahmed title = Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3471 sentences = 226 flesch = 50 summary = title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. The three compounds with highest affinity (Fig 2) for the active site are quercetin 3-rhamonoside, myricetin 3-rutinoside and rutin with binding energies of -9.7, -9,3 and -9.2 kcal.mol -1 respectively. Thirty eight flavonoids have been tested in this study by molecular docking against the active site of the SARS-CoV-2Mpro. Glycosylated flavonoids as SARS-CoV-2 Inhibitors: A molecular docking and simulation studies Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies cache = ./cache/cord-310790-3ikgmiof.txt txt = ./txt/cord-310790-3ikgmiof.txt === reduce.pl bib === id = cord-311066-62edsbfc author = Cox, Brian J. title = Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2926 sentences = 172 flesch = 61 summary = Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5'-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. Some RNAs, especially non-coding RNAs, generally lack a poly-A tail, which could explain poor detection of TRS independent sgmRNAs. Using published sequencing data of ribosome depleted total RNA from SARS-CoV-2 infected cells and animals (Blanco-Melo et al., 2020) , I aligned these against the viral genome (Figure 2) . Using the aligned reads, I generated transcript models using stringtie, which identified multiple spliced species that aligned with the TRS-L templated events (Figure 2) . Split reads also identified TRS-independent sgmRNAs. In support of my observations on SARS-CoV-2, I also assessed SARS-CoV and MERs transcriptional data, two other human pathogenic CoV. I also identified the TIR motif, a novel sequence element (ATTGGC) flanking the spliced regions of TRS independent sgmRNAs in both SARS-CoV-2 and SARS-CoV. cache = ./cache/cord-311066-62edsbfc.txt txt = ./txt/cord-311066-62edsbfc.txt === reduce.pl bib === id = cord-311333-shvtfxog author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-05-28 pages = extension = .txt mime = text/plain words = 414 sentences = 37 flesch = 70 summary = title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. Nasopharyngeal swab, sputum and saliva samples were collected from 9 patients who 69 were admitted to our hospital after a diagnosis of COVID-19. Saliva as a 187 non-invasive specimen for detection of SARS-CoV-2 Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva Detection of noroviruses in fecal specimens by direct RT-PCR 195 without RNA purification cache = ./cache/cord-311333-shvtfxog.txt txt = ./txt/cord-311333-shvtfxog.txt === reduce.pl bib === id = cord-311114-ggcpsjk8 author = Radhakrishnan, Chandni title = Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4383 sentences = 274 flesch = 52 summary = The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. In our analysis, we mapped the SARS-CoV-2 genetic variants obtained from Kerala genomes to the 132 primer or probes sequence and calculated the melting temperature (Tm) of the mutant with the wild type sequence. cache = ./cache/cord-311114-ggcpsjk8.txt txt = ./txt/cord-311114-ggcpsjk8.txt === reduce.pl bib === id = cord-311123-swiewewq author = Zhuang, Shu-Fan title = Low-grade fever during COVID-19 convalescence: A report of 3 cases date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2484 sentences = 141 flesch = 53 summary = Reports of such cases are rare, and the mechanism and outcome of low-grade fever during COVID-19 convalescence are not completely clear. The patient's condition did not improve, and COVID-19 was confirmed on February 7 by positive SARS-CoV-2 oropharyngeal swab test at our local Center for Disease Control (CDC). From disease onset on 4 February 2020, the patient had a fever with a maximum axillary temperature of 38.1°C, accompanied by a cough (details shown in Table 1 ) and multiple lesions on CT ( Figure 1 ). The patient's condition did not improve, and COVID-19 was confirmed on February 5 by positive SARS-CoV-2 oropharyngeal swab test at our local CDC. During convalescence, the patient's cough was completely relieved, and CT lesions resolved ( Figure 1 ), but her SARS-CoV-2 test remained positive. During the course of low-grade fever, the 3 patients had no other discomfort or comorbidities, and their temperature returned to normal without any treatment. cache = ./cache/cord-311123-swiewewq.txt txt = ./txt/cord-311123-swiewewq.txt === reduce.pl bib === id = cord-311144-tumtzad8 author = Franco-Muñoz, Carlos title = Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date = 2020-09-17 pages = extension = .txt mime = text/plain words = 2822 sentences = 163 flesch = 54 summary = A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016) . The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with J o u r n a l P r e -p r o o f Journal Pre-proof 80-100% of the reported sequences ( Fig. 2A) . cache = ./cache/cord-311144-tumtzad8.txt txt = ./txt/cord-311144-tumtzad8.txt === reduce.pl bib === id = cord-311216-mfqlv3nh author = Buckley, Leo F. title = Cardiovascular Pharmacology in the Time of COVID-19: A Focus on Angiotensin-Converting Enzyme 2 date = 2020-04-13 pages = extension = .txt mime = text/plain words = 2126 sentences = 124 flesch = 38 summary = Severe acute respiratory syndrome coronavirus-2019 (SARS-CoV-2), the causative virus of COVID-19, infects host cells through angiotensin-converting enzyme 2 (ACE2). We review current knowledge of the role of ACE2 in cardiovascular physiology and SARS-CoV-2 virology, as well as clinical data to inform the management of patients with or at risk for COVID-19 who require renin–angiotensin–aldosterone system inhibitor therapy. [2] [3] [4] [5] [6] [7] [8] SARS-CoV-2 infects host cells by binding to human angiotensin-converting enzyme-2 (ACE2), [9] [10] [11] a membranebound enzyme expressed in the lungs, heart, and kidneys (among many other organs). 15 It has been proposed that renin-angiotensin-aldosterone system (RAAS) inhibitors predispose to SARS-CoV-19 infection and worsen outcomes after COVID-19 by upregulating ACE2 expression. Epidemiologic studies should be performed to estimate the association of RAAS inhibitor use to risk of COVID-19 in patients with hypertension, heart failure or chronic kidney disease. Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients cache = ./cache/cord-311216-mfqlv3nh.txt txt = ./txt/cord-311216-mfqlv3nh.txt === reduce.pl bib === id = cord-311377-ffkwis40 author = Forns, Xavier title = Inmunosupresión en el trasplante hepático en la era Covid-19 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 3930 sentences = 344 flesch = 50 summary = La presencia de linfopenia con neutrofilia, niveles elevados de IL-6, incremento de la proteína C reactiva así como el hallazgo de niveles elevados de citoquinas asociadas a la inmunidad innata como IP-10, MCP-1, MIP-1α y TNFα sugieren que ésta juega un papel muy importante en la respuesta inflamatoria asociada a la infección (que también se observó con el SARS-CoV y MERS-CoV) y por tanto, sea responsable de la evolución hacia la gravedad de Covid La respuesta efectora inmune innata contra los virus se basa mayoritariamente en el interferón (IFN-1) (23). En caso de enfermedad grave Covid 19, la substitución temporal de anticalcineurínicos y micofenolato mofetilo (MMF) por GC permite a estos pacientes evitar efectos indeseables secundarios a la interacción de dichos inmunosupresores con los múltiples medicamentos que reciben para el tratamiento de la infección por SARS-Cov 2. cache = ./cache/cord-311377-ffkwis40.txt txt = ./txt/cord-311377-ffkwis40.txt === reduce.pl bib === id = cord-311029-x0lk4110 author = Palermo, Sara title = Covid-19 Pandemic: Maximizing Future Vaccination Treatments Considering Aging and Frailty date = 2020-09-18 pages = extension = .txt mime = text/plain words = 6411 sentences = 353 flesch = 40 summary = For that reason, the Clinical Trials Regulation (EC) No. 536/2014 states that "in order to improve treatments available for vulnerable groups such as frail or older people, people suffering from multiple chronic conditions, and people affected by mental health disorders, medicinal products which are likely to be of significant clinical value should be fully and appropriately studied for their effects in these specific groups, including as regards requirements related to their specific characteristics and the protection of the health and well-being of subjects belonging to these groups." Indeed, EMA develops scientific guidelines to help medicine developers address the specific requirements of older people in their medicine development programs, including in the design and conduct of clinical trials. EMA disclosed a reflection paper on "Physical frailty: instruments for baseline characterization of older populations in clinical trials" (7), actively recognizing the importance of considering the various types of aging when experimenting and developing new pharmacological treatments. cache = ./cache/cord-311029-x0lk4110.txt txt = ./txt/cord-311029-x0lk4110.txt === reduce.pl bib === id = cord-311240-o0zyt2vb author = Motayo, Babatunde Olarenwaju title = Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date = 2020-07-27 pages = extension = .txt mime = text/plain words = 3091 sentences = 167 flesch = 50 summary = Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa. The pathogen was later identified to be a novel coronavirus closely related to the severe acute respiratory syndrome virus (SARS), with a possible bat origin (Zhou et al, 2020) . This study was designed to determine to the genetic diversity and evolutionary history of genome sequences of SARSCoV-2 isolated in Africa. Results of recombination analysis of the African SARSCoV-2 (AfrSARSCoV-2) sequences against references whole genome sequences of SARS, Recombination signals were observed between the African SARSCoV-2 sequences and reference sequence (Major recombinant hCoV-19 Pangolin/Guangu P4L/2017; Minor parent hCoV-19 B batYunan/RaTG13) between the RdRP and S gene regions (Figure 2 ). cache = ./cache/cord-311240-o0zyt2vb.txt txt = ./txt/cord-311240-o0zyt2vb.txt === reduce.pl bib === id = cord-311012-wyglrpqh author = Meyers, Craig title = Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3271 sentences = 171 flesch = 54 summary = AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. cache = ./cache/cord-311012-wyglrpqh.txt txt = ./txt/cord-311012-wyglrpqh.txt === reduce.pl bib === id = cord-311358-nrj4aysh author = Peng, Yuzhu title = Is novel coronavirus disease (COVID‐19) transmitted through conjunctiva? date = 2020-03-16 pages = extension = .txt mime = text/plain words = 346 sentences = 35 flesch = 58 summary = In theory, the premise for transmission through conjunctiva is that SARS-CoV-2 can replicate in conjunctival epithelia. 7 Currently it is unknown whether conjunctival epithelia can express ACE2. However, oral, nasal, and nasopharyngeal epithelia do not express ACE2, 8 which can explain that most of the COVID-19 patients did not have upper respiratory symptoms. It has been proposed that ''2019-nCoV transmission through the ocular surface must not be ignored'' based on the nosocomial infection of some ophthalmologists and an expert who wore an N95 mask but did not wear anything to protect his eyes was infected with SARS-CoV-2. Moreover, the inEvaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical characteristics of 50466 hospitalized patients with 2019-nCoV infection cache = ./cache/cord-311358-nrj4aysh.txt txt = ./txt/cord-311358-nrj4aysh.txt === reduce.pl bib === id = cord-311383-1aqt65cc author = Tan, Jinzhi title = The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes date = 2009-05-15 pages = extension = .txt mime = text/plain words = 7613 sentences = 391 flesch = 58 summary = However, within the large Nsp3 (1922 amino-acid residues), the structure and function of the so-called SARS-unique domain (SUD) have remained elusive. The SARS-CoV genome is devoid of G-stretches longer than 5–6 nucleotides, but more extended G-stretches are found in the 3′-nontranslated regions of mRNAs coding for certain host-cell proteins involved in apoptosis or signal transduction, and have been shown to bind to SUD in vitro. In this communication, we describe the crystal structures at 2.2 Å and 2.8 Å resolution (monoclinic and triclinic form, respectively) of the core of the SARS-unique domain (SUD core , Nsp3 residues 389-652). One potential binding site for G-quadruplexes might be in a cleft between two consecutive SUD core dimers as they occur in both the monoclinic and triclinic crystal forms ( Figure S2B ), but for confirmation, any of these models will have to await crystallographic determination of the complex. cache = ./cache/cord-311383-1aqt65cc.txt txt = ./txt/cord-311383-1aqt65cc.txt === reduce.pl bib === id = cord-311415-wwwqqvca author = Alamri, Mubarak A. title = Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) date = 2020-06-24 pages = extension = .txt mime = text/plain words = 6968 sentences = 384 flesch = 50 summary = title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) Molecular dynamics (MD) simulations were utilized to investigate the binding mode of the potential inhibitors at the active site of SARS-CoV-2 main protease. Since the active site of SARS-CoV-2 main protease contains a catalytic cysteine, it is possible to target it with covalently binding compounds. In order to investigate the binding mode of the most promising hit compounds inside the active site of SARS-CoV-2 3CL pro , molecular dynamics (MD) simulations of each complex were performed for a period of 50 ns. (C-E) Representation of the chemical reaction of the reactive thiol group of Cys145 with the reactive nucleophilic group of the hit compounds, and the corresponding covalently docked poses (green sticks) inside the substrate-binding site of SARS-CoV-2 3CL pro (white ribbon presentation, ligand-interacting amino acids are shown in sticks). In Silico discovery of novel inhibitors against main protease (Mpro) of SARS-CoV-2 using pharmacophore and molecular docking based virtual screening from ZINC database cache = ./cache/cord-311415-wwwqqvca.txt txt = ./txt/cord-311415-wwwqqvca.txt === reduce.pl bib === id = cord-311125-v9ddes3c author = Cooper, Keiland W. title = COVID-19 and the chemical senses: supporting players take center stage date = 2020-07-01 pages = extension = .txt mime = text/plain words = 9480 sentences = 510 flesch = 49 summary = Given data suggesting that ACE2 is necessary for SARS-CoV2 to infect host cells, researchers have used a variety of approaches to discern the pattern of expression of ACE2 and other viral entry proteins across the tissue landscape, with the goal of inferring possible target cells and disease mechanisms. It remains unclear whether SARS-CoV-2 (given that it likely does not directly infect OSNs, and thus cannot pass directly through the olfactory nerve, see However, scSeq and immunostaining of the mouse OB has revealed -as in the nose -that bulb neurons do not express detectable levels of ACE2 ( Figure 2 ) . This model suggests that neural function is altered indirectly due to sequelae of SARS-CoV-2 infection of peripheral support cells, including (but not limited to) local inflammation and changes in OSN gene expression and ciliary structure. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia cache = ./cache/cord-311125-v9ddes3c.txt txt = ./txt/cord-311125-v9ddes3c.txt === reduce.pl bib === id = cord-311446-afhw0450 author = Suhandynata, Raymond T title = Multi-platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19 date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3328 sentences = 194 flesch = 56 summary = Diazyme, Roche, and Abbott SARS-CoV-2 serology assays were compared by correlating the raw quantitative values from each platform for all samples from PCR positive patients ( Supplementary Figure 2A-C) . The impact of disease prevalence on the PPV and negative predictive value (NPV) for the Diazyme, Roche, and Abbott SARS-CoV-2 serology platforms were calculated using the PPA and NPA of the ≥ 15 day patient group ( Table 4 and Supplementary Table 4 ). The prevalence for COVID-19 in the ≥ 15 day patient group was 12.3%, and the observed PPV for the Diazyme IgM/IgG panel, the Roche total Ig, and the Abbott IgG assays were 89.3%, 96.0%, and 92.6%, respectively. We evaluated longitudinal samples from 16 SARS-CoV-2 PCR positive patients with the Diazyme, Roche, and Abbott serology platforms (Figure 2A -2D) . We evaluated the PPA and NPA of the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays using the same samples across all three platforms. cache = ./cache/cord-311446-afhw0450.txt txt = ./txt/cord-311446-afhw0450.txt === reduce.pl bib === id = cord-311477-gm0vg53l author = Doboszewska, Urszula title = Targeting zinc metalloenzymes in COVID‐19 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 6194 sentences = 327 flesch = 49 summary = We attempt to integrate data on the effects of agents targeting zinc fingers in viral metalloenzymes (zinc fingers targeting agents), which cause removal of zinc from the proteins, thus destabilizing the proteins and leading to increased intracellular concentration of zinc ions, and other agents which induce changes in intracellular levels of zinc (zinc ionophores), with data on consequences of altered level of intracellular zinc, with a focus on SARS-CoV-2 and related pathogens. Chloroquine, an old antimalarial drug (Blount, 1967) , was demonstrated to block virus infection at low micromolar concentration in Vero E6 cells infected with SARS-CoV-2 , thus suggesting the possible use of chloroquine in patients with COVID-19. With regard to COVID-19, a novel drug would target labile zinc fingers in SARS-CoV-2 proteins, thus destroying the proteins and producing an increase in intracellular concentration of zinc ions. cache = ./cache/cord-311477-gm0vg53l.txt txt = ./txt/cord-311477-gm0vg53l.txt === reduce.pl bib === id = cord-311429-adcmgd1i author = Salzberger, B. title = Epidemiologie von SARS-CoV-2/COVID 19: Aktueller Stand date = 2020-10-29 pages = extension = .txt mime = text/plain words = 1795 sentences = 212 flesch = 51 summary = Die Basisreproduktionszahl R0 (Mittelwert der Zahl von Personen, die von Tab. 1 Kennzahlen der Epidemiologie von SARS("severe acute respiratory syndrome")-CoV("coronavirus")-2 Die Altersverteilung kann sich über die Zeit ändern, in Deutschland ist ein deutlicher Trend zu sehen: Infektionen nach Mai treten überwiegend bei jüngeren auf, die Infektionsraten bei diesen Gruppen sind in der Periode nach der ersten Welle höher als in der ersten Periode (. Der Anteil der Infektionen bei Personen des medizinischen Personals lag in China bei 2,7 %, in Italien bei 11,1 % und in Deutschland bei 5,8 % [9, 18, 27] . Die Ausbreitung lag bei den genannten Influenzapandemien zwischen 9 und 40 % der Gesamtbevölkerung -eine starke Motivation zur effektiven Kontrolle der SARS-CoV-2-Infektion. SARS-CoV-2 hat sich nach dem ersten Ausbruch in Wuhan rasch international verbreitet, und eine Verbreitung und eine Übertragung sind auf allen Kontinenten zu verzeichnen. cache = ./cache/cord-311429-adcmgd1i.txt txt = ./txt/cord-311429-adcmgd1i.txt === reduce.pl bib === id = cord-311585-h4holhit author = Ling, R. title = Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3784 sentences = 247 flesch = 53 summary = Background The seroprevalence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. This retrospective study estimated the seroprevalence of IgM and IgG and compared the epidemiological characteristics of asymptomatic SARS-CoV-2-infected population. Hubei province including IgM and IgG tests for SARS-CoV-2 antibody, nucleic acid tests from March 26 to April 28, 2020 among people aged 16-64 years who went back to work. Clinical data were collected from March 26 to April 28, 2020, including serum IgG positivity and IgM positivity or negative results for SARS-CoV-2 antibodies, nucleic acid testing, clinical symptoms, previous medical history, and chest CT. . https://doi.org/10.1101/2020.06.16.20132423 doi: medRxiv preprint study, the IgG seroprevalence was higher in females than in males, indicating that women were more likely to have asymptomatic infections. cache = ./cache/cord-311585-h4holhit.txt txt = ./txt/cord-311585-h4holhit.txt === reduce.pl bib === id = cord-311264-zn7ydrvh author = Deurenberg-Yap, M. title = The Singaporean response to the SARS outbreak: knowledge sufficiency versus public trust date = 2005-06-17 pages = extension = .txt mime = text/plain words = 3445 sentences = 159 flesch = 50 summary = In this paper, the informing seeking and processing mindset of Singaporeans during a severe outbreak situation is assessed by testing the level of knowledge on SARS and its preventive/ control measures following the earlier communication efforts and subsequent public education campaign. More than nine out of 10 respondents thought that infection control measures undertaken at hospitals were Overall, the public trust index was high at 11.4 out of a maximum score of 14, with no significant difference between gender, age groups and educational levels. First, while knowledge about infection control measures undertaken at TTSH was low (mean per cent score of 20 ± 16%), the level of confidence was high, with 82% of the respondents expressing confidence in the hospital's ability to deal with SARS. cache = ./cache/cord-311264-zn7ydrvh.txt txt = ./txt/cord-311264-zn7ydrvh.txt === reduce.pl bib === id = cord-311445-b6bc6vwd author = Bansal, Kanika title = Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2749 sentences = 169 flesch = 60 summary = Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. In the present study, we have focused on codon usage pattern (CUP) of SARS coronavirus from different hosts under debate (bat, pangolin, and dog) as a probable origin for SARS-CoV-2. However, another study comparing the codon usage pattern of SARS-CoV-2 with other betacoronaviruses suggested that current pandemic coronavirus is subjected to different evolutionary pressures (Gu et al., 2020) . The above analysis reveals single patterns for all five genes in different lineages of SARS-CoV-2 affirms a single event of host jump of codon-optimized SARS strain from its animal reservoir. cache = ./cache/cord-311445-b6bc6vwd.txt txt = ./txt/cord-311445-b6bc6vwd.txt === reduce.pl bib === id = cord-311214-eqwxkwqa author = Kumar, Roshan title = Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date = 2020-04-16 pages = extension = .txt mime = text/plain words = 2724 sentences = 184 flesch = 60 summary = Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-β, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. A manually annotated reference database was generated using the Genbank 128 file of Severe acute respiratory syndrome coronavirus 2 isolate-SARS-CoV-129 2/SH01/human/2020/CHN (Accession number: MT121215) and open reading frames (ORFs) 130 were predicted against the formatted database using prokka (-gcode 1) [22] . All these isolates 189 were found to harbor 9 open reading frames coding for ORF1a (13218 bp) and ORF1b (7788 190 bp) polyproteins, surface glycoprotein or S-protein (3822 bp), ORF3a protein (828 bp Our analysis revealed that strains of human infecting SARS-CoV-2 are novel and highly 201 identical (>99.9%). In this study, the analysis was 358 performed on the genomes of the novel SARS-CoV-2 isolates recently reported from different 359 countries to understand viral pathogenesis. cache = ./cache/cord-311214-eqwxkwqa.txt txt = ./txt/cord-311214-eqwxkwqa.txt === reduce.pl bib === id = cord-311545-3rll9mca author = Bentley, Gillian R title = Don't blame the BAME: Ethnic and structural inequalities in susceptibilities to COVID‐19 date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2806 sentences = 137 flesch = 47 summary = However, more recently, insidious and potentially racist allusions are beginning to emerge appearing to blame African Americans as somehow responsible for the relatively large number of cases and deaths from COVID-19 in the USA, stoking age-old tropes, and attributing morbidity and mortality to the behaviors and predispositions of BAME groups (Guardian, 2020b; Strings, 2020) . In reality, structural or social inequalities that affect individual vulnerabilities to SARS-CoV-2 include exposures through types of employment, whether people are working in essential transport networks carrying large numbers of people, or in small grocery shops that place BAME communities at greater risk of contracting COVID-19 ( Figure 1 ). cache = ./cache/cord-311545-3rll9mca.txt txt = ./txt/cord-311545-3rll9mca.txt === reduce.pl bib === id = cord-311604-qsc3nks6 author = Wong, River Chun‐Wai title = Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date = 2020-09-30 pages = extension = .txt mime = text/plain words = 932 sentences = 61 flesch = 56 summary = title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens This study aims to evaluate the diagnostic performance of PF assay for detection of SARS-CoV-2 in comparison to the TIB-Molbiol LightMix® SarbecoV E-gene assay (TIB-Molbiol assay) (TIB-Molbiol, Berlin, Germany) using DTS, NP and LRT specimens. Despite the manufacturer of TIB Miobiol regarded results with Ct <36 as positive, when use as an initial screening test in our laboratory, sample with any Ct value will be tested supplementary with Xpert Xpress assay. Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens cache = ./cache/cord-311604-qsc3nks6.txt txt = ./txt/cord-311604-qsc3nks6.txt === reduce.pl bib === id = cord-311635-hf6vrbyx author = Reuken, Philipp Alexander title = Between Fear and Courage: Attitudes, Beliefs, and Behavior of Liver Transplantation Recipients and Waiting List Candidates during the COVID‐19 Pandemic date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3481 sentences = 209 flesch = 47 summary = We evaluated fears, attitudes, and opinions associated with COVID‐19 in 365 SOT recipients (95% liver, 5% pancreas/kidney), 112 SOT candidates, and 394 immediate household contacts in two German transplant centers. Thus, we assessed COVID-19 prevalence/exposure, perception, compliance and behavior of transplant recipients and candidates on the waiting list in two German liver transplant centers in April 2020 using a crosssectional anonymous survey in patients and their household members. Responding to the item "I am afraid to become infected with the Coronavirus", SOT recipients reported a significantly greater fear of being infected with SARS-CoV-2 than their household controls ( Figure 1A and Supplementary Table S1). Here we demonstrate that fears associated with the SARS-CoV-2 pandemic are frequently expressed by liver transplantation recipients and candidates as well as by their household members. While fears and concerns associated with the SARS-CoV-2 pandemic are frequently expressed by SOT recipients and candidates, measures to prevent infection were frequently followed in the vast majority of patients. cache = ./cache/cord-311635-hf6vrbyx.txt txt = ./txt/cord-311635-hf6vrbyx.txt === reduce.pl bib === id = cord-311332-n8tvglif author = Kostoff, Ronald N. title = Literature-related discovery: Potential treatments and preventatives for SARS() date = 2011-04-20 pages = extension = .txt mime = text/plain words = 7191 sentences = 380 flesch = 46 summary = The present paper presents a comprehensive approach to systematic acceleration of potential discovery and innovation, and demonstrates the generation of large amounts of potential discovery for prevention/treatment of an infectious disease: severe acute respiratory syndrome (SARS). Approximately four times as many records were retrieved from Medline when MeSH terms were included in the query compared to using only terms in the title or Abstract, due to the greater choice of potential discovery substances. To retrieve the directly related literature from which potential discovery would be extracted, this higher level functional query was applied to the search engines of three databases: SCI, Medline, and SD. This proximity form of the query (as contrasted to the Boolean form used in prior LRD studies) provided highly 'relevant' retrievals, where 'relevant' is defined as any article that contains a potential discovery or innovation candidate. cache = ./cache/cord-311332-n8tvglif.txt txt = ./txt/cord-311332-n8tvglif.txt === reduce.pl bib === id = cord-311696-ccbc1k1m author = Pelisser, Michel title = Sports balls as potential SARS-CoV-2 transmission vectors date = 2020-07-10 pages = extension = .txt mime = text/plain words = 2295 sentences = 111 flesch = 55 summary = Sports objects can only harbour inactivated SARS-CoV-2 under specific, directly transferred conditions, but wiping with a dry tissue or moist 'baby wipe' or dropping and rolling the balls removes all detectable viral traces. The transmission potential of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) includes exposure duration of the virus, the number of viral particles one is exposed to and the route of exposure such as inhalation or skin contact [1, 2] . When SARS-CoV-2 positive control materials at 1,000 and 5,000 dC/mL concentrations are applied onto the whole surface of sport balls using BD polyester swabs, there was no detectable levels of the virus when observing the variables imposed in the experiment, including very short term testing after 30 seconds. On the other hand, when positive control at 5,000 copies/mL and 10,000 copies/mL concentrations are directly applied to the surface of cricket ball there are detectable levels of the virus at 30 seconds, 5 minutes and 1 hour (experiment 3). cache = ./cache/cord-311696-ccbc1k1m.txt txt = ./txt/cord-311696-ccbc1k1m.txt === reduce.pl bib === id = cord-311599-m400cal3 author = Lehmann, Christian title = A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses date = 2008-05-31 pages = extension = .txt mime = text/plain words = 5031 sentences = 289 flesch = 50 summary = Here, we report the development of a serologic assay for detection of antibodies to human coronaviruses (HCoVs) based on recombinant nucleocapsid (N) proteins of all known pathogenic strains (229E, NL63, OC43, HKU1, SARS). Here, we describe the establishment of a line immunoassay for rapid and simultaneous detection of antibodies directed against the 5 known HCoVs (229E, NL63, OC43, HKU1, and SARS) in human sera based on recombinant viral N proteins. Table 2 Reactions of clinically defined sera with HCoV nucleocapsids In sera taken during acute phase of HCoV infection, no OC43-or 229E-specific antibodies could be detected, whereas samples collected after convalescence strongly reacted with the corresponding antigens. Consistently, all available human sera sampled from convalescent patients (tested positive for HCoVs 229E, OC43, or SARS-CoV by microneutralization experiments, Western blotting, ELISA, or IF) reacted with their respective antigens as expected, indicating an excellent sensitivity of our line immunoassay. cache = ./cache/cord-311599-m400cal3.txt txt = ./txt/cord-311599-m400cal3.txt === reduce.pl bib === id = cord-311730-189vax2m author = Becker, Richard C. title = Covid-19 treatment update: follow the scientific evidence date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4514 sentences = 222 flesch = 40 summary = The SNS exists under the authority of the United States Department of Health and Human Services (HHS) and accepted 30 million doses of hydroxychloroquine sulfate donated by Sandoz™, the Novartis™ generics and biosimilars division, and one million doses of chloroquine phosphate donated by Bayer Pharmaceuticals™ for potential use in treating patients who were hospitalized with COVID-19 or for use in clinical trials. The adverse effects associated with taking hydroxychloroquine are similar to those observed with chloroquine and include nausea, vomiting, diarrhea, AV conduction defects, a prolonged QTc interval with torsades de pointe ventricular tachycardia, hypokalemia, hypotension and circulatory collapse. Similarly, patients with Covid-19 for whom a clinician believes that either chloroquine or hydroxychloroquine is indicated must receive information, preferably in the form of a fact sheet that clearly summarized the dose, duration of treatment, potential risks, side-effects and drug-drug interactions. cache = ./cache/cord-311730-189vax2m.txt txt = ./txt/cord-311730-189vax2m.txt === reduce.pl bib === id = cord-311762-f6muhf3d author = Chen, Yu Wai title = Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates date = 2020-02-21 pages = extension = .txt mime = text/plain words = 2798 sentences = 183 flesch = 60 summary = title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates Therefore, we are confident to prepare a structural model of the SARS-CoV-2 3CL pro by molecular modelling (Extended data 7 , Figure S1 ), which will be immediately useful for in silico development of targeted treatment. After we submitted the first draft of this study, the crystal structure of SARS-CoV-2 3CL pro was solved and released (PDB ID 6LU7), which confirms that the predicted model is good within experimental errors (Extended data 7 , Figure S2 ). By analogy, these compounds were speculated to act on SARS-CoV 3CL pro specifically, but there is as yet no crystal structure to support that, although docking studies were carried out to propose various binding modes 20-23 . • Tab S2.docx (The results of virtual screening of drugs on the active site of SARS-CoV-2 3CL pro crystal structure). cache = ./cache/cord-311762-f6muhf3d.txt txt = ./txt/cord-311762-f6muhf3d.txt === reduce.pl bib === id = cord-311535-ppkwd1kp author = Korakas, Emmanouil title = Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2778 sentences = 124 flesch = 36 summary = The production of increased amounts of cytokines such as TNFα, IL-1, IL-6, and monocyte chemoattractant protein (MCP-1) lead to oxidative stress and defective function of innate and adaptive immunity, whereas the activation of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome seems to play a crucial role in the pathogenesis of the infection. Endothelial dysfunction and arterial stiffness could favor the recently discovered infection of the endothelium by SARS-CoV-2, whereas alterations in cardiac structure and function and the prothrombotic microenvironment in obesity could provide a link for the increased cardiovascular events in these patients. Chronic inflammation and oxidative stress, hypercytokinemia, immune dysregulation, endothelial dysfunction, and cardiovascular abnormalities are all possible mechanisms through which the excess in adipose tissue could lead to the acute hyperinflammatory state that characterizes severe SARS-CoV-2 infections and is responsible for its complications. cache = ./cache/cord-311535-ppkwd1kp.txt txt = ./txt/cord-311535-ppkwd1kp.txt === reduce.pl bib === id = cord-311523-erntrh3p author = Gisondi, P title = Dermatologists and SARS‐CoV‐2: The impact of the pandemic on daily practice date = 2020-04-22 pages = extension = .txt mime = text/plain words = 2757 sentences = 150 flesch = 43 summary = Since the first case of "pneumonia of unknown aetiology" was diagnosed at the Wuhan Jinyintan Hospital in China on 30 December 2019, what was recognised thereafter as "severe acute respiratory syndrome coronavirus 2" (SARS‐CoV‐2) has spread over the four continents, causing the respiratory manifestations of Coronavirus disease‐19 (COVID‐ 19) and satisfying the epidemiological criteria for a label of "pandemic." The ongoing SARS‐CoV‐2 pandemic is having a huge impact on dermatological practice including the marked reduction of face‐to‐face consultations in favour of teledermatology, the uncertainties concerning the outcome of COVID‐19 infection in patients with common inflammatory disorders such as psoriasis or atopic dermatitis receiving immunosuppressive/immunomodulating systemic therapies; the direct involvement of dermatologists in COVID‐19 care for patients assistance and new research needs to be addressed. cache = ./cache/cord-311523-erntrh3p.txt txt = ./txt/cord-311523-erntrh3p.txt === reduce.pl bib === id = cord-311610-uniz8tuc author = Wang, Shi-Yi title = The impact on neonatal mortality of shifting childbirth services among levels of hospitals: Taiwan's experience date = 2009-06-08 pages = extension = .txt mime = text/plain words = 3476 sentences = 161 flesch = 44 summary = This evidence indicates that the neonatal mortality rate in areas with large hospitals was significantly lower than predicted, despite the shift of childbirth services to local community hospitals during the SARS epidemic. Furthermore, this study's large sample size of 1,848 observations allows us to demonstrate clearly that the shifting of childbirth services among hospitals associated with the SARS epidemic did not increase the risk of neonatal deaths. Although it has not been documented conclusively whether or not advanced hospitals provide better care for normal birthweight deliveries than small maternity units [7] [8] [9] [10] [11] [12] [13] [14] [15] , this study has demonstrated that childbirth outcomes were not influenced by the shift in maternity services to local community hospitals during the SARS epidemic in Taiwan. cache = ./cache/cord-311610-uniz8tuc.txt txt = ./txt/cord-311610-uniz8tuc.txt === reduce.pl bib === id = cord-311835-dmqfij6j author = Siu, Kam-Leung title = Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 date = 2014-01-13 pages = extension = .txt mime = text/plain words = 4917 sentences = 306 flesch = 55 summary = title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 We and others have previously shown that severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis virus (MHV) spike (S) proteins induce ER stress and activate cellular unfolded protein response (UPR) in the ER [3] [4] [5] . We compared the UPR-activating activity of SARS-CoV and HCoV-HKU1 S proteins in terms of their influence on the expression of UPR effectors Grp78, Grp94, CHOP and PERK. To analyze further whether PERK activity is required for transcriptional activation of Grp78 and Grp94 promoters by SARS-CoV and HCoV-HKU1 S proteins, we made use of a dominant negative (DN) mutant of PERK which constitutively inhibits PERK kinase activity [48] . To determine whether the UPR-activating property of SARS-CoV S protein is mediated by S1 (amino acids 1-770) or S2 (amino acids 771-1255) subunit, we expressed them in 293FT cells ( Figure 6A, lanes 2 and 3) . cache = ./cache/cord-311835-dmqfij6j.txt txt = ./txt/cord-311835-dmqfij6j.txt === reduce.pl bib === id = cord-311633-i9ret7bw author = Péré, Hélène title = Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1673 sentences = 103 flesch = 52 summary = We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. To analytically and clinically validate the Abbott SARS-CoV-2 IgG assay, we tested pre-epidemic sera, sera from pauci-symptomatic health-worker with SARS-CoV-2 positive RT-PCR and sera from hospitalized patients from both the COVID-positive area and the COVID-free area. cache = ./cache/cord-311633-i9ret7bw.txt txt = ./txt/cord-311633-i9ret7bw.txt === reduce.pl bib === id = cord-311758-wof4yi39 author = Clauw, Daniel J. title = Considering the potential for an increase in chronic pain after the COVID-19 pandemic date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3182 sentences = 165 flesch = 43 summary = The experience of living within this pandemic has disrupted daily life across all sectors, including those living with chronic pain (CP), those infected with the coronavirus Severe Acute Respiratory Syndrome (SARS)-CoV2, healthcare providers and essential workers, as well as those who remained physically healthy. Specific possibilities might include: (1) CP as part of a postviral syndrome or the result of viral-associated organ damage; (2) worsening of CP due to exacerbation of preexisting pain physical or mental complaints; and (3) CP newly triggered in individuals not infected with COVID by exacerbation of risk factors (poor sleep, inactivity, fear, anxiety, and depression). In a small study of 22 subjects (21 of whom were healthcare workers) infected during the SARS epidemic, a chronic post-SARS syndrome consisting of fatigue, diffuse myalgia, depression, and nonrestorative sleep persisted for almost 2 years. cache = ./cache/cord-311758-wof4yi39.txt txt = ./txt/cord-311758-wof4yi39.txt === reduce.pl bib === id = cord-311766-m9yv4qkm author = Demey, Baptiste title = Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1754 sentences = 92 flesch = 49 summary = Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection. cache = ./cache/cord-311766-m9yv4qkm.txt txt = ./txt/cord-311766-m9yv4qkm.txt === reduce.pl bib === id = cord-311566-x8n1bbwn author = Aouidate, Adnane title = Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation date = 2020-06-18 pages = extension = .txt mime = text/plain words = 6355 sentences = 281 flesch = 54 summary = As we are running of time and the virus is spreading quickly, we have screened the CAS COVID-19 Antiviral Compound Dataset, which includes $50000 chemical compounds against 3CLpro and RNA-dependent RNA polymerase (RdRp) using computational methods and ligand and structure based screening and in this study, we report the identification of different compounds with CAS IDs (2001083-69-6, 2001083-68-5, 63248-75-9, 264621-13-8, 1025098-90-1, 1253912-09-2) as potent inhibitors of 3CLpro and (833463-10-8, 833463-11-9, 833465-33-1, 2001083-69-6, 833463-19-7, 833464-45-2) as potent inhibitors RNA-dependent RNA-polymerase (RdRp), most compounds are 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives, the analysis of SARS-CoV-2 main protease and RNAdependent RNA polymerase binding sites reveals are combinations of hydrophobic, hydrophilic and charged residues holding with hydrogen bonds in excess, therefore, the 1,3,5triazine that is aligned centrally in both proteins binding pockets could be a good choice to occupy the central part of the molecules to be substituted by different hydrophobic, hydrophilic and charged fragments. cache = ./cache/cord-311566-x8n1bbwn.txt txt = ./txt/cord-311566-x8n1bbwn.txt === reduce.pl bib === id = cord-312036-5867bc6i author = Decker, Annegrit title = Prolonged SARS‐CoV‐2 shedding and mild course of COVID‐19 in a patient after recent heart transplantation date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1943 sentences = 142 flesch = 49 summary = Here, we present a 62‐year old male COVID‐19 patient with recent heart transplantation who developed only mild symptoms, but had prolonged virus shedding, and summarize the available data on COVID‐19 in cardiac allograft recipients. [5] [6] [7] Here, we report a mild course of SARS-CoV-2 infection with prolonged virus persistence in a patient only five months after heart transplantation. In fact, in 71.8 % of patients with COVID-19 after heart transplant, immunosuppressive agents have been (partially) discontinued or reduced in dose (Table 1) , thus potentially increasing the risk of organ rejection. 19 In our case, continuation of the immunosuppressant regime was associated with a mild course of COVID-19, though we observed a transient increase in CRP and IL-6. Although the cardiovascular system seems to be a critical target site of SARS-CoV-2 infection, a mild course of COVID-19 is possible even in a high-risk patient after recent heart transplantation. cache = ./cache/cord-312036-5867bc6i.txt txt = ./txt/cord-312036-5867bc6i.txt === reduce.pl bib === id = cord-312065-nqy7m38f author = Peng, Philip W. H. title = Infection control and anesthesia: Lessons learned from the Toronto SARS outbreak date = 2003 pages = extension = .txt mime = text/plain words = 4582 sentences = 384 flesch = 66 summary = PURPOSE: To describe the outbreak of severe acute respiratory syndrome (SARS) in Toronto, its impact on anesthesia practice and the infection control guidelines adopted to manage patients in the operating room (OR) and to provide emergency intubation outside the OR. S of July 10, 2003, 438 cases (250 probable, 188 suspect) of severe acute respiratory syndrome (SARS) were reported in Canada, 375 (85.3%) of which occurred in Ontario. Because of early reports of clusters of cases in community settings such as apartment buildings and the high infection rates among health care workers in Hong Kong, Taiwan, Hanoi and Toronto, the etiological agent of SARS was thought to be highly contagious. Time should be allowed for the anesthesiologist and assistant to remove contaminated gloves, gowns, face shields or masks and head cover and renew protective precautions at the end of the case. cache = ./cache/cord-312065-nqy7m38f.txt txt = ./txt/cord-312065-nqy7m38f.txt === reduce.pl bib === id = cord-311848-8n9ee57a author = Giesen, Nicola title = Evidence-based Management of COVID-19 in Cancer Patients – Guideline by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) date = 2020-09-21 pages = extension = .txt mime = text/plain words = 7678 sentences = 516 flesch = 48 summary = It was prepared by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) by critically reviewing the currently available data on SARS-CoV-2 and COVID-19 in cancer patients applying evidence-based medicine criteria. We do not 285 recommend to delay/discontinue radiotherapy, targeted therapy, endocrine therapy or surgery in 286 cancer patients without suspected/confirmed SARS-CoV-2 infection (DII u ) as no impact on mortality 287 of such prior treatments was seen in several large cohort studies of 20, 31, 40, 94 288 In patients with COVID-19, it is strongly recommended to delay/discontinue chemotherapy, if 289 possible, as chemotherapy within two weeks of admission was a major risk factor for severe COVID-290 19 in a large Chinese cohort study (AII u ). Clinical characteristics and risk factors 38 associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, 39 retrospective, cohort study cache = ./cache/cord-311848-8n9ee57a.txt txt = ./txt/cord-311848-8n9ee57a.txt === reduce.pl bib === id = cord-311926-n7co0jtu author = Donà, Daniele title = COVID-19 Pandemic: Perspective of an Italian Tertiary Care Pediatric Center date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3176 sentences = 132 flesch = 51 summary = Predicting a rapid spread of the SARS-CoV-2 virus within our region, the Department for Women's and Children's Health promptly decided (i) to revise the distribution of the clinical areas in order to create both designated COVID-19 and COVID-19-free areas with their own access, (ii) to reinforce infection prevention control (IPC) measures for all healthcare workers and administrative staff and (iii) to adopt the new "double-gate approach": a phone call pre-triage and nasopharyngeal swab for SARS-CoV-2 detection before the admission of all patients and caregivers. • to ensure the protection of the healthcare workers, as the top priority; • to rigorously implement all the conventional rules emanated by the WHO for preventing the infection • to minimize the risk of admitting into hospital asymptomatic COVID-19 positive patients; • to adapt/transform some hospital areas in order to be able to admit and treat suspected/confirmed; COVID-19 pediatric patients Predicting a rapid spread of the SARS-CoV-2 virus within our region, in the afternoon of February 24th the Chief Executive Officer (CEO) of Padua University Hospital called for an emergency meeting with all the department chairmen and the mandates received were: cache = ./cache/cord-311926-n7co0jtu.txt txt = ./txt/cord-311926-n7co0jtu.txt === reduce.pl bib === id = cord-311782-d2t8bzio author = Fiore, Josè Ramòn title = Results from a survey in healthy blood donors in South Eastern Italy indicate that we are far away from herd immunity to SARS‐CoV‐2 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1725 sentences = 95 flesch = 53 summary = We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general population three months after the local start of the epidemic. In our study, we confirm a low rate of antibodies against SARS-CoV-2 on a group of blood donors from a geographical region with a moderate incidence (187 cases/100.000 inhabitants vs the national data of 390 infections/100.000 inhabitants); our results are at variance with those observed in other regions of Italy. cache = ./cache/cord-311782-d2t8bzio.txt txt = ./txt/cord-311782-d2t8bzio.txt === reduce.pl bib === id = cord-311847-2czqs84q author = Pennisi, Manuela title = SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms date = 2020-07-31 pages = extension = .txt mime = text/plain words = 9002 sentences = 433 flesch = 40 summary = Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). Although there are limitations in the epidemiological studies carried on COVID-19, as well as limited case records for determining the actual incidence of these complications, some patients reported neurological symptoms, but clinical findings and pathogenic features have not yet systematically addressed. The aims of this review are i) to summarize the available information on the relationship between CoVs and the nervous system, ii) to identify the potential targets and routes of entry of SARS-CoV-2 into the nervous system, and iii) to describe the range of the neurological features reported to date in patients with COVID-19 and the proposed pathogenic mechanisms. Indeed, no axonal transport of SARS-CoV-2 to the brain has been demonstrated in the hamster model during the first two weeks after infection [89] , and no viral accumulation or persistence has been reported in cerebral olfactory regions of autopsy material from patients with COVID-19 [90] . cache = ./cache/cord-311847-2czqs84q.txt txt = ./txt/cord-311847-2czqs84q.txt === reduce.pl bib === id = cord-311965-3x3tjzhi author = Alexander, Jan title = Early Nutritional Interventions with Zinc, Selenium and Vitamin D for Raising Anti-Viral Resistance Against Progressive COVID-19 date = 2020-08-07 pages = extension = .txt mime = text/plain words = 5156 sentences = 273 flesch = 39 summary = Adequate supply of zinc, selenium, and vitamin D is essential for resistance to other viral infections, immune function, and reduced inflammation. Clinical and subclinical micronutrient deficiencies common in older adults are known to contribute to decreased immune function and age-related diseases [11] , implying that nutritional management is essential to reduce the risk of severe infection [12] . In view of a lack of clinical data on preventive and/or therapeutic efficiency of the nutritive adequacy of selenium, zinc, and vitamin D in COVID-19, we, in the present narrative review, discussed recent clinical data on the role of these micronutrients in the protection against bronchopulmonary infections, as well as the existing indications of their impact on COVID-19. We did a literature search for the period 2010-2020 on PubMed, Medline, and Google Scholar with the keywords of SARS, SARS-CoV-2, COVID 19, coronavirus, micronutrients (zinc, selenium, vitamin D), immune system, inflammation, prevention, and treatment. cache = ./cache/cord-311965-3x3tjzhi.txt txt = ./txt/cord-311965-3x3tjzhi.txt === reduce.pl bib === id = cord-311673-z4hkw17g author = Uzzan, Mathieu title = Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2969 sentences = 154 flesch = 40 summary = As the visceral fat possesses an intense immune activity, is involved in metabolic syndrome and is at the crossroad between the intestines, the systemic circulation and the lung, we hypothesized that it plays a major role in severe forms of SARS-CoV-2 infection. Several factors may increase intestinal permeability including, direct enterocyte damage by SARS-CoV2, systemic inflammatory response syndrome (SIRS) and epithelial ischemia secondary to SARS-CoV2associated endothelial dysfunction. This increase permeability further leads to translocation of microbial components such as MAMPS (microbial-associated molecular pattern), triggering an inflammatory immune response by TLR-expressing cells of the mesentery fat (mostly macrophages and adipocytes). As the increased volume of mesentery fat in overweight men play a key role in the occurrence of metabolic syndrome [8] , we hypothesized that the visceral adipose tissue plays a central role in severe forms of COVID-19. cache = ./cache/cord-311673-z4hkw17g.txt txt = ./txt/cord-311673-z4hkw17g.txt === reduce.pl bib === id = cord-311843-un6urdb1 author = Baray, Juwel Chandra title = BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date = 2020-09-30 pages = extension = .txt mime = text/plain words = 3173 sentences = 230 flesch = 62 summary = title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. The reactivity of the sera from each 221 group of mice immunized with BANCOVID was measured against SARS-CoV-2 S antigen 222 (SinoBiologicals, China). Analysis revealed IgG binding against SARS-CoV-2 S protein 223 antigens in the sera of the immunized mice. Flow cytometric analysis of total T cell (CD4 + ) populations producing TFN alpha on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. cache = ./cache/cord-311843-un6urdb1.txt txt = ./txt/cord-311843-un6urdb1.txt === reduce.pl bib === id = cord-312027-5tntdjp9 author = Charlton, Carmen L. title = Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies date = 2020-09-22 pages = extension = .txt mime = text/plain words = 4210 sentences = 202 flesch = 47 summary = We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. To develop a panel of positive sera from patients with COVID-19, serum samples were collected from hospitalized patients confirmed to be positive for SARS-CoV-2 upon nasopharyngeal swab or endotracheal aspirate testing by rRT-PCR. Performance characteristics of EIAs. In total, 46 samples from 28 different patients testing positive for SARS-CoV-2 by rRT-PCR and 50 negative samples from serum samples stored prior to 1 November 2019 were run on each assay. Interestingly, despite four different samples collected from patient 6 (ranging from 18 to 29 days after symptom onset), antibodies were never detected by the Roche assay. cache = ./cache/cord-312027-5tntdjp9.txt txt = ./txt/cord-312027-5tntdjp9.txt === reduce.pl bib === id = cord-311905-4yu29b49 author = Kakoulidis, Ioannis title = SARS-CoV-2 infection and glucose homeostasis in pregnancy. What about antenatal corticosteroids? date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1084 sentences = 69 flesch = 40 summary = METHODS: We performed a literature search on PubMed, regarding the use of corticosteroids in patients with SARS-CoV-2 infection, in pregnancies complicated by SARS-CoV-2, as well as their impact on glycemia in pregnant women with or without diabetes. While the healthcare community worldwide struggles to manage the novel SARS-CoV-2 (Severe Acute Respiratory Coronavirus 2; Covid-19) pandemic, it is of great importance to ensure that optimal care continues to be given to special groups of patients such as pregnant women. Therefore, extreme caution should be given, regarding the use of antenatal corticosteroids, in case of pregnant women with SARS-CoV-2 requiring preterm delivery [1, 3, 4, 16] . Since there are few small studies in the 6 literature regarding the management of pregnant women with SARS-CoV-2 (and possibly lacking reliable conclusions), the decision about the use of antenatal corticosteroids should be carefully made in consultation with infectious disease specialists, obstetricians and neonatologists [4, 16] . Timedependent changes in insulin requirement for maternal glycemic control during antenatal corticosteroid therapy in women with gestational diabetes: a retrospective study cache = ./cache/cord-311905-4yu29b49.txt txt = ./txt/cord-311905-4yu29b49.txt === reduce.pl bib === id = cord-312170-p2yrbosz author = Chiu, Man-Chun title = Suggested management of immunocompromized kidney patients suffering from SARS date = 2003-10-24 pages = extension = .txt mime = text/plain words = 832 sentences = 57 flesch = 55 summary = The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial. The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial, and little is known worldwide about the treatment for SARS kidney transplant patients. It seems children suffered much less from the infection than adults, although some adolescents could have severe lung involvement [3, 4, 5] . In Hong Kong, 7 of 19 adult ESRD patients on haemodialysis or peritoneal dialysis infected with SARS died (C.B. Leung et al., pers. Paediatric nephrologists should be on the alert for SARS, because we have to care for a group of immunocompromised patients including those transplant children. Cumulative number of reported probable cases of severe acute respiratory syndrome (SARS) www Clinical presentations and outcome of severe acute respiratory syndrome in children Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong Treatment of severe acute respiratory syndrome with convalescent plasma cache = ./cache/cord-312170-p2yrbosz.txt txt = ./txt/cord-312170-p2yrbosz.txt === reduce.pl bib === id = cord-312005-9so3orib author = Klussmeier, Anja title = Etablierung der PCR-basierten SARS-CoV-2-Testung im Hochdurchsatz date = 2020-09-05 pages = extension = .txt mime = text/plain words = 414 sentences = 57 flesch = 57 summary = Eine entscheidende Maßnahme zur Eindämmung des SARS-CoV-2-Infektionsgeschehens ist die rechtzeitige Diagnose von Einzelfällen. Ende März 2020 war daher abzusehen, dass bei einem stark steigendem Infektionsgeschehen, wie es zu diesem Zeitpunkt in Italien oder Spanien beobachtet werden konnte, hohe Laborkapazitäten für die Diagnostik von SARS-CoV-2 in Deutschland benötigt werden würden. Das DKMS Life Science Lab ist das weltweit größte Labor für die HLA-Genotypisierung von Personen, die sich für eine Stammzellspende registrieren möchten. Pro Werktag werden hier rund 5.000 Proben im Hochdurchsatz bearbeitet: von der Annahme der Abstrichtupfer, über die DNA-Isolation, PCR und Sequenzierung bis hin zur Datenanalyse [2, 3] Der hier beschriebene Laborprozess zur Diag nostik von akuten SARS-CoV-2-Infektionen wurde in einem Zeitraum von etwa drei Monaten geplant, umgesetzt und validiert. 2016-2019 Spezialist für Labortechnik und Automation und seit 2019 Business Development Manager bei DKMS Life Science Lab GmbH in Dresden. Abteilungsleiter Labortechnik und seit 2016 Geschäftsführer (CTO) der DKMS Life Science Lab GmbH in Dresden cache = ./cache/cord-312005-9so3orib.txt txt = ./txt/cord-312005-9so3orib.txt === reduce.pl bib === id = cord-312038-g76cpjp7 author = Brunaugh, Ashlee D. title = Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date = 2020-10-07 pages = extension = .txt mime = text/plain words = 11043 sentences = 517 flesch = 47 summary = Utilizing repurposed NIC, and with the goal of developing a therapeutically effective, rapidly scalable and globally distributable antiviral therapy to reduce the spread of SARS-CoV-2, we describe an inhalable NIC formulation that can be administered using three major models or respiratory tract delivery systems: DPI, nasal spray and nebulizer. At the highest dose tested (0.125 µg/mL NIC), Vero cells with an established MERS-CoV infection exhibited an 82.2% ± 0.8% decrease in viral load compared to untreated controls after 24-hours of exposure to NIC-hLYS particles ( Fig 1D) . While brain viral titres did not exhibit further reduction from levels noted in the preliminary efficacy study, the inoculation of Vero E6 cells with viral particles obtained from lung and brain homogenates of surviving animals resulted in no observation of CPE at any of the inoculum concentrations tested, which indicates that remaining viral particles were not active. cache = ./cache/cord-312038-g76cpjp7.txt txt = ./txt/cord-312038-g76cpjp7.txt === reduce.pl bib === id = cord-312473-7i7efdp2 author = Sidhom, John-William title = Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1181 sentences = 62 flesch = 46 summary = We first examined the distribution of TCRs within the McPas database over the types of pathogens present in the database and cross-referenced the SARS-CoV-2 specific TCRs into the McPas database ( Figure 1A) , and we noted that there was a statistically significant enrichment (from 17.3% to 32.9%) of SARS-CoV-2 specific TCRs that had known specificity to the immunodominant M1 GILGFVFTL epitope We then examined the distribution of TCRs within the ImmuneCode database across the various open readings frames (orfs) and mapped the M1 specific TCRs within this database ( Figure 1B) . In conclusion, while these results are preliminary in a small cohort of individuals, we have identified a set of TCRs that is known to both recognize an immunodominant epitope derived from Influenza and SARS-CoV-2, suggesting that immune control of one infection may play a role in the control of the other. cache = ./cache/cord-312473-7i7efdp2.txt txt = ./txt/cord-312473-7i7efdp2.txt === reduce.pl bib === id = cord-312178-tojgojjf author = Segars, James title = Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known? date = 2020-04-16 pages = extension = .txt mime = text/plain words = 5355 sentences = 309 flesch = 48 summary = Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a pandemic of Coronavirus Disease 2019 (COVID-19) across the globe. The novel SARS-CoV-2 virus spreads rapidly, with 2-3 people infected from every index case, a reproduction number (R 0 ) or transmission rate of 2.24 -3.58 (2) . The aim of this review is to summarize what is currently known about the impact of prior coronaviruses and the novel SARS-CoV-2 infection on reproduction and pregnancy. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: Report of two cases & review of the literature An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes cache = ./cache/cord-312178-tojgojjf.txt txt = ./txt/cord-312178-tojgojjf.txt === reduce.pl bib === id = cord-312476-20ifwznd author = Kline, Jeffrey A. title = Crash Course in Decision Making date = 2008-01-08 pages = extension = .txt mime = text/plain words = 1089 sentences = 63 flesch = 57 summary = in this month's Academic Emergency Medicine shows how emergency physicians can use scientific method to ''get it in gear'' to produce a decision instrument, used in real time on huge numbers of patients, to render a major impact on public health. The Centers for Disease Control and Prevention (CDC) have issued specific recommendations for the diagnosis and evaluation of patients with suspected SARS. Curiously, at the time of this writing, no areas of the world are reporting ongoing SARS transmission, yet the CDC's recommendation for infection control stated above were issued in September 2003, and are current and active. 2 Regardless of whether SARS returns to the public consciousness, the CDC's recommendations for infection control of SARS have several major ramifications on the practice of emergency medicine. Numerous other contagious diseases that cause an ILI prodrome could emerge at any time and the CDC could issue similar infectious control recommendations. cache = ./cache/cord-312476-20ifwznd.txt txt = ./txt/cord-312476-20ifwznd.txt === reduce.pl bib === id = cord-312401-y1tat1bf author = Sakurai, Aki title = Natural History of Asymptomatic SARS-CoV-2 Infection date = 2020-06-12 pages = extension = .txt mime = text/plain words = 918 sentences = 56 flesch = 52 summary = On February 1, a passenger from Hong Kong, who traveled for 5 days from Yokohama and left the ship at Hong Kong on January 25, tested positive for SARS-CoV-2. Ten of 31 symptomatic passengers, crew and their cabinmates tested positive for SARS-CoV-2 on February 5, when the quarantine was implemented off the coast. Given the circumstances, a decision was made to accommodate some of the asymptomatic SARS-CoV-2 confirmed cases, both passengers and crew as well as their cabinmates who tested negative on the ship, at this hospital to continue their isolation and observation off the ship. Asymptomatic confirmed cases were cohorted on two floors, while their cabinmates who tested positive on the ship were isolated in private rooms on a separate floor to prevent further transmission. If the test was positive, they were cohorted with asymptomatic SARS-CoV-2 confirmed cases. cache = ./cache/cord-312401-y1tat1bf.txt txt = ./txt/cord-312401-y1tat1bf.txt === reduce.pl bib === id = cord-312275-plqturzi author = Nielsen, Sandra C.A. title = Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2624 sentences = 219 flesch = 65 summary = To directly test the 154 antigen specificity of these convergent clones, we expressed human IgG1 monoclonal antibodies 155 (mAbs 2A and 4A, Table S2 ) from two COVID-19 convergence groups in two patients 156 following paired immunoglobulin heavy and light chain sequencing of single B cells with the immunosorbent assay (ELISA) testing, both mAbs bound SARS-CoV-2 spike and S1 domain, 160 but not the RBD or nucleocapsid ( Figure 3C ). To evaluate whether such in silico IGH 185 sequence comparisons could predict the serological responses of patients, we tested the plasma 186 samples from COVID-19 patients in SARS-CoV RBD ELISAs and detected cross-reactivity in 187 five of the 13 patients ( Figure 3F) or RBD antigens will also stimulate B cells expressing these common antibody types in a 214 significant fraction of the human population. cache = ./cache/cord-312275-plqturzi.txt txt = ./txt/cord-312275-plqturzi.txt === reduce.pl bib === id = cord-311948-3v311fnd author = Ishiguro, Takashi title = Clinical Course and Findings of 14 Patients with COVID-19 Compared with 5 Patients with Conventional Human Coronavirus Pneumonia date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2614 sentences = 183 flesch = 56 summary = Because her symptoms, laboratory data, and radiological findings were mild with patchy GGOs detectable only by CT ( Figure 11 ), we did not administer antibiotics or antivirals, and she remained in stable condition during hospitalization. Only one of the SARS-CoV-2 pneumonia patients was in severe condition on admission (Table 3) , but 5 patients worsened during hospitalization, and one patient (Case 5) required HFNC therapy. Abnormal X-ray shadows were not detectable in 4 (36.3%) of the 11 SARS-CoV-2 pneumonia patients throughout their course, but abnormal shadows were found in the other patients on admission or during hospitalization. 10 Abnormal shadows were not detected on initial chest X-ray in 5 of our 11 patients with SARS-CoV-2 pneumonia. (11) We administered ritonavir/lopinavir to 5 of the 11 SARS-CoV-2 pneumonia patients, and chest X-ray findings gradually began to improve 3 days after the initiation of these agents in 3 patients. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-311948-3v311fnd.txt txt = ./txt/cord-311948-3v311fnd.txt === reduce.pl bib === id = cord-312278-rin733w4 author = Wang, Yung‐Chih title = Current diagnostic tools for coronaviruses–From laboratory diagnosis to POC diagnosis for COVID‐19 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2250 sentences = 171 flesch = 53 summary = 22 For detecting the presence of novel infectious diseases, the gold standard method has been the use of qRT-PCR for the detection of 29 Saliva has also been approved as a noninvasive specimen for detecting SARS-CoV-2. Another well-known test is the Vivalytic COVID-19 test (Bosch, Germany), which delivers results in less than 2.5 hr using multiplex PCR and μArray-detection to identify SARS-CoV-2. All of these tests employ PCR to detect the presence of SARS-CoV-2 RNA, and can provide results within 72 hr. Second, all of these at-home kits are designed to detect SARS-CoV-2 RNA during early-stage infection, but they are not used to determine the presence of antibodies. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using fieldeffect transistor-based biosensor Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis cache = ./cache/cord-312278-rin733w4.txt txt = ./txt/cord-312278-rin733w4.txt === reduce.pl bib === id = cord-312524-ee5xw1r8 author = Moustafa, Ahmed M. title = Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2058 sentences = 129 flesch = 61 summary = Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. Rapid sequencing of the SARS-CoV-2 pandemic virus has presented an 40 unprecedented opportunity to track the evolution of the virus and to understand the 41 emergence of a new pathogen in near-real time. Our panallelome approach to developing a whole genome (wgMLST) scheme for 58 SARS-CoV-2 uses a modified version of our recently developed tool, WhatsGNU [10], 59 to rapidly assign an allele number to each gene nucleotide sequence in the virus's 60 genome creating a sequence type (ST). We developed the GNU-based Virus IDentification (GNUVID) system as a tool 71 that automatically assigns a number to each unique allele of the 10 open reading 72 frames (ORFs) of SARS-CoV-2 ( Figure 1A) information. When the global region of origin for each genome sequence was mapped to 102 each CC there was a strong association of some CCs with certain geographical 103 locations. cache = ./cache/cord-312524-ee5xw1r8.txt txt = ./txt/cord-312524-ee5xw1r8.txt === reduce.pl bib === id = cord-312340-hpuoren5 author = Holstein, Sarah A. title = Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1964 sentences = 91 flesch = 40 summary = Given the expected duration of the pandemic, it is imperative that treatment of the patient's cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Given the expected duration of the pandemic, it is imperative that treatment of the patient's cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Despite the barriers that lead to this low rate of participation, clinical trials remain the cornerstone for improving oncology patient outcomes through the development of new therapies. To this end, there are many groups, including ASCO and the American Society of Hematology, that have created registries in order to collect data on outcomes of oncology patients infected with SARS-CoV-2. It is imperative that comprehensive immune profiling studies be performed to evaluate the immune responses in these patient populations and that oncology patients be included in COVID-19 clinical trials. cache = ./cache/cord-312340-hpuoren5.txt txt = ./txt/cord-312340-hpuoren5.txt === reduce.pl bib === id = cord-312367-24huwt3y author = Coelho, Camila title = Biochemical screening for SARS-CoV-2 main protease inhibitors date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3351 sentences = 210 flesch = 49 summary = As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). As viral proteases, following polymerases, are the most prominent targets for antiviral drug design [9] , here we describe initial biochemical screenings with recombinant purified SARS-CoV-2 M pro performed in order to define possible candidates which could serve as lead compounds for the design of future COVID-19 therapies. In order to contribute to the ongoing worldwide research and development efforts to contain COVID-19, we cloned, expressed recombinantly in E.coli BL21(DE3) and purified an important drug target of SARS-CoV-2, its main protease (M pro ). From these obtained compounds, esculetin-4-carboxylic acid ethyl ester (IC 50 = 46 μM in M pro inhibition assays), a coumarin derivative and natural product, demonstrated an EC 50 of 112 μM (median toxic concentration TC 50 >800μM) in Vero-cell SARS-CoV assays [13] and MP576 (IC 50 = 2.5 μM), a quinolinecarboxylate, demonstrated an EC 50 of 7 μM (TC 50 >50μM) [15, 17] , thus validating the M pro biochemical screening approach for the development of SARS-CoV drugs. cache = ./cache/cord-312367-24huwt3y.txt txt = ./txt/cord-312367-24huwt3y.txt === reduce.pl bib === id = cord-312559-ygh507x2 author = Fiesco-Sepulveda, K. Y. title = Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1890 sentences = 177 flesch = 60 summary = title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, meta-analyses 248 using Latin American cases would also be ideal for determining how COVID-19 could affect this 249 region, which has some differences, such as lower average age or higher exposure to respiratory 250 infections than other regions like Europe (Amariles et al., 2020a). (2020) concluded that the novel virus could come from a bat SARS-like coronavirus isolate, 168 which is in agreement with reports from the GISAID database Clinical features of patients infected 644 with 2019 novel coronavirus in Wuhan The novel coronavirus (SARS-CoV-2) emergency and the role of timely and 674 effective national health surveillance Complete genome sequence of a 2019 novel coronavirus (SARS-COV-2) strain isolated 792 in Nepal. cache = ./cache/cord-312559-ygh507x2.txt txt = ./txt/cord-312559-ygh507x2.txt === reduce.pl bib === id = cord-311918-gifwg2ho author = BENDER, Whitney R. title = Universal Testing for SARS-CoV-2 in Two Philadelphia Hospitals: Carrier Prevalence and Symptom Development Over Two Weeks date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2826 sentences = 187 flesch = 54 summary = Objectives To describe the prevalence of positive SARS-CoV-2 tests among asymptomatic pregnant women at two Philadelphia obstetric hospitals, characterize the clinical course of those testing positive, and report symptom development among all women tested in the two weeks post-hospitalization. 242 (78.1%) and 213 (68.7%) of the 310 women who were SARS-CoV-2 negative at time of initial hospitalization were reached for telephone follow-up at one and two weeks post-admission, respectively. Conclusions The asymptomatic positive SARS-CoV-2 test rate among an obstetric population in Philadelphia differed between two hospitals and was lower than described in other geographic regions. The objectives of this study are to describe the prevalence of positive SARS-Cov-2 tests 123 at time of admission for delivery among asymptomatic pregnant women in Philadelphia within 124 two large academic hospitals, characterize the in-hospital clinical course for those who tested 125 positive, and report the development of viral symptoms in all women tested for two weeks 126 after hospital discharge. cache = ./cache/cord-311918-gifwg2ho.txt txt = ./txt/cord-311918-gifwg2ho.txt === reduce.pl bib === id = cord-312434-yx24golq author = Deng, Ziqin title = Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6219 sentences = 294 flesch = 49 summary = Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. Therefore, in order to accurately, effectively and systematically reveal connections within the human coronavirus field, our study applied bibliometrics and visualization methods to analyze human coronaviruses-related publications and citations, countries and affiliations, as well as journal performance, author impact and keyword cooccurrence cluster. According to these keywords, human coronavirus diseases like "SARS, " "MERS" and COVID-19 may have something worthwhile for comparison with other "infectious diseases" like "influenza" in their epidemiological characteristics; "healthcare workers, " "transmission, " "surveillance, " "quarantine, " or "isolation" may be the focuses of these studies, which can help to promote current disease control and prevention measures. cache = ./cache/cord-312434-yx24golq.txt txt = ./txt/cord-312434-yx24golq.txt === reduce.pl bib === id = cord-312160-2820aftb author = Ibrahim, Mahmoud A.A. title = In silico Drug Discovery of Major Metabolites from Spices as SARS-CoV-2 Main Protease Inhibitors date = 2020-10-08 pages = extension = .txt mime = text/plain words = 2443 sentences = 162 flesch = 51 summary = Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). The binding energies of the investigated spices compounds with SARS-CoV-2 M pro were estimated using molecular mechanical-generalized Born surface area (MM-GBSA) approach with modified GB model (igb=2) implemented in AMBER16 software [27] . The physicochemical parameters of the most promising natural spices as SARS-CoV-2 M pro inhibitors were predicted using the online Molinspiration cheminformatics software %ABS was estimated as follows [28] : The online web-based tools of SwissTargetPredicition (http://www.swisstargetprediction.ch) were applied to predict the biological targets for the most promising natural spices as SARS-CoV-2 M pro inhibitors. Since the main protease of SARS-CoV-2 (M pro ) plays a critical role in the viral replication process, structure-based computational modeling of ligand-receptor interactions and molecular dynamics has been used to screen metabolites from common spices as potential M pro inhibitors. cache = ./cache/cord-312160-2820aftb.txt txt = ./txt/cord-312160-2820aftb.txt === reduce.pl bib === id = cord-312632-g4250q6l author = Cai, Xiaofang title = Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children date = 2020-05-12 pages = extension = .txt mime = text/plain words = 4647 sentences = 230 flesch = 48 summary = Five patients with non-respiratory symptoms as the first manifestation were hospitalized from the emergency department, and were later confirmed to have COVID-19, between 23 January and 20 February 2020, at the Wuhan Children's Hospital. Severe COVID-19 was defined when the pediatric patients Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; WHO, World Health Organization; ICTV, the International Committee on Taxonomy of Viruses; MERS-CoV, Middle East respiratory syndrome coronavirus; CT, computed tomography; PICU, pediatric intensive care unit; NK, natural killer; CRRT, continuous renal replacement therapy; CRP, C-reactive protein; PCT, procalcitonin; PT, prothrombin time; APTT, activated partial thromboplastin time; IL, interleukin; EEG, electroencephalogram; ACE2, angiotensin converting enzyme 2. This might explain why case 3, who was admitted with head trauma but with no respiratory symptoms, tested positive for SARS-CoV-2 nucleic acid and his lung CT scan showed pneumonia. cache = ./cache/cord-312632-g4250q6l.txt txt = ./txt/cord-312632-g4250q6l.txt === reduce.pl bib === id = cord-312560-onfabcfv author = Klingler, J. title = Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 5861 sentences = 353 flesch = 55 summary = The data demonstrate high prevalence of spike-and RBD-specific IgM and IgA, similar to that of IgG1, in plasma/serum from COVID-19 patients and their significant contributions to virusneutralizing activities. In Fig. 3 , comparing levels of total Ig with the different Ig isotypes showed a highly significant correlation with IgG1 for both Abs specific for spike and RBD indicating that IgG1 is the major isotype induced by SARS-CoV-2 infection. To ask directly to what extent Abs of different isotypes mediate neutralization, we evaluated the neutralization activities of IgM, IgG, and IgA fractions purified from plasma from five COVID-19-convalescent individuals (RP#1-5). Several SARS-CoV-2 vaccine candidates tested in animal models and humans were shown to induce IgG responses against spike and RBD as well as virus neutralizing activities, but in many of these studies, the induction of other Ig isotypes was not evaluated 46-49 . cache = ./cache/cord-312560-onfabcfv.txt txt = ./txt/cord-312560-onfabcfv.txt === reduce.pl bib === id = cord-312444-c1dz5o85 author = Faure‐Bardon, V title = How should we treat pregnant women infected with SARS‐CoV‐2? date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1827 sentences = 133 flesch = 50 summary = (Hydroxy) chloroquine has been used in SARS-CoV-2-infected humans with highly controversial results 14,15 but several phase 3 studies are underway to analyse its efficacy both as a cure for patients at each stage of the disease and as a preventive measure. Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with severe coronavirus disease (COVID-19) -Full Text View -ClinicalTrials Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with moderate coronavirus disease (COVID-19) compared to standard of care treatment -Full Text View -ClinicalTrials The efficacy of different anti-viral drugs in COVID 19 infected patients -Full Text View -ClinicalTrials In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine versus placebo in COVID-19 patients at risk for severe disease -Full Text View -ClinicalTrials cache = ./cache/cord-312444-c1dz5o85.txt txt = ./txt/cord-312444-c1dz5o85.txt === reduce.pl bib === id = cord-312350-klxw65qa author = Khan, Zafran title = Diagnostic approaches and potential therapeutic options for coronavirus disease (COVID-19) date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1017 sentences = 84 flesch = 47 summary = To date, more than 300 clinical trials have been conducted on various antiviral drugs, and immunomodulators are being evaluated at various stages of COVID-19. This review is aimed to collect and summarize a list of drugs used to treat COVID-19 for instance, dexamethasone, chloroquine, hydroxychloroquine, lopinavir/ritonavir, favipiravir, remdesivir, tociluzimab, nitazoxanide, and ivermectin. WHO 154 launches the "Solidarity" clinical trial for COVID-19 treatment to further evaluate remdesivir, 155 hydroxychloroquine/chloroquine, and lopinavir-ritonavir with and without interferon-beta [64] . Recently in Singapore, the five COVID-19 patients were subjected to treatment with lopinavir 258 and ritonavir within 1 to 3 days of desaturation, but evidence of clinical use is ambiguous. Clinical and 708 microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-709 19 patients with at least a six-day follow up: A pilot observational study. Effective treatment of severe COVID-749 19 patients with tocilizumab Antigen Detection Tests for Respiratory Syncytial Virus Infection: Systematic Review and Meta-779 analysis cache = ./cache/cord-312350-klxw65qa.txt txt = ./txt/cord-312350-klxw65qa.txt === reduce.pl bib === id = cord-312509-m3p9fuq0 author = Tohidinia, Maryam title = Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 2722 sentences = 174 flesch = 50 summary = title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 The main aim of the 91 current is to use of bioinformatics tool to identify potential B-and T-cell epitope(s) of S protein with high 92 antigenicity that could be used to develop promising vaccines [20] . In 161 addition, Bcepred server at http://www.imtech.res.in/raghava/bcepred/ [32] was employed to predict linear B-162 cell epitopes in a protein sequence. Therefore, the usage of several tools to predict linear B-168 cell epitopes in protein sequences are more reliable. Ellipro at http://tools.immuneepitope.org [33] was used to 169 predict linear and discontinuous antibody epitopes based on a protein antigen's 3D structure. The spike protein on the surface of the viral particle plays key roles in the binding of the cell receptor and 459 membrane fusion, by which the host range is firmly determined. cache = ./cache/cord-312509-m3p9fuq0.txt txt = ./txt/cord-312509-m3p9fuq0.txt === reduce.pl bib === id = cord-312305-ll29frwc author = Sun, Shihui title = Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date = 2020-11-11 pages = extension = .txt mime = text/plain words = 4720 sentences = 270 flesch = 52 summary = Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. We further characterized the in vivo replication dynamics of MASCp6 in both young and aged mice, and the results from qRT-PCR showed that high levels of SARS-CoV-2 subgenomic RNAs were persistent in the lung and tracheas till 4 day post infection (dpi) in aged mice (Fig. 1E) . The skewed age distribution of COVID-19 disease was reproduced in the MASCp36 infected mouse model where more severe symptoms were observed in aged mice when compared to young mice. In addition to the age-related skewed distribution of COVID-19, gender-related differences in distribution of COVID-19 disease is also recapitulated in this MASCp36 infected mouse model with increased susceptibility and enhanced pathogenicity observed in male mice when compared to their female counterparts. cache = ./cache/cord-312305-ll29frwc.txt txt = ./txt/cord-312305-ll29frwc.txt === reduce.pl bib === id = cord-312533-4u3bmb0e author = Shen, Li Wen title = TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections date = 2017-08-01 pages = extension = .txt mime = text/plain words = 4771 sentences = 251 flesch = 42 summary = Recently, a great deal of evidence has suggested that a transmembrane protease, serine 2 (TMPRSS2), a type II transmembrane serine protease (TTSP), plays a critical role in SARS and Abbreviations: ARE, androgen receptor element; AEBSF, 4-(2-Aminomethyl) benzenesulfonyl fluoride hydrochloride; BHH, Bromhexine hydrochloride; CoV, coronavirus; DESC1, serine protease DESC1; EST, (2S,3S)-trans-Epoxysuccinyl-Lleucylamido-3-methylbutane ethyl ester; FDA, Food and Drug Administration; HAT, human airway trypsin-like protease; HAI-2, hepatocyte growth factor activator inhibitor 2; HGF, hepatocyte growth factor; IFITM, Interferon-induced transmembrane protein; MMP-2, matrix metalloproteinase-2; MSPL, transmembrane protease, serine 13; PAI-1, plasminogen activator inhibitor 1; PAR-2, protease activated receptor 2; PPMO, peptide-conjugated phosphorodiamidate morpholino oligomer; RBS, receptor binding subdomain; THE, human tracheal epithelial; TMPRSS2, transmembrane protease, serine 2; TMPRSS4, transmembrane protease serine 4; TTSP, type II transmembrane serine protease; vRNPs, viral ribonucleoproteins. Although FDA-approved inhibitors that specifically inhibit TMPRSS2 are not yet available, some drugs such as camostat and nafamostat that have inhibitory activity against a variety of serine proteases have been approved for the treatment of other diseases and also suppress influenza virus and coronavirus infections. cache = ./cache/cord-312533-4u3bmb0e.txt txt = ./txt/cord-312533-4u3bmb0e.txt === reduce.pl bib === id = cord-312663-hhd5f823 author = Fiorino, Gionata title = Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date = 2020-03-24 pages = extension = .txt mime = text/plain words = 2199 sentences = 109 flesch = 52 summary = The outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. IBD patients are severely worried about the impact of their disease and medications on the risk and the prognosis of COVID-19, and many of them are forced to come to hospital because of active disease, complications and drug administration. Patients scheduled for a follow-up visit are required to stay at home and to complete a questionnaire about IBD symptoms and quality of life, together with their routine laboratory tests, to the nurse and the dedicated doctor, who give recommendations and information about therapy and follow-up procedures. Based on the assumption that the risk of coronavirus infection is not different between the general population and IBD patients, but that IBD flares are difficult to manage in this situation, we advise all patients to continue their therapies, especially if in remission. cache = ./cache/cord-312663-hhd5f823.txt txt = ./txt/cord-312663-hhd5f823.txt === reduce.pl bib === id = cord-312561-9o2fhi6e author = Hung, I.F.N. title = Viral Loads in Clinical Specimens and SARS Manifestations date = 2004-09-17 pages = extension = .txt mime = text/plain words = 3328 sentences = 171 flesch = 51 summary = A retrospective viral load study was performed on clinical specimens from 154 patients with laboratory-confirmed severe acute respiratory syndrome (SARS); the specimens were prospectively collected during patients' illness. Viral load in nasopharyngeal aspirates (n = 142) from day 10 to day 15 after onset of symptoms was associated with oxygen desaturation, mechanical ventilation, diarrhea, hepatic dysfunction, and death. We compared the viral load in these specimens with the presence or absence of diarrhea, oxygen desaturation, mechanical ventilation, lymphopenia, hepatic dysfunction, abnormal urinalysis findings, and death rate by chi-square or Fisher exact test for categorical variables and by Mann-Whitney U test for continuous variables. A high viral load in serum was also associated with oxygen desaturation, mechanical ventilation, hepatic dysfunction, and death (all p < 0.01) but not with diarrhea or abnormal urinalysis findings. The importance of SARS-CoV as a respiratory pathogen is supported by the strong association of viral load in NPA with oxygen desaturation, mechanical ventilation, and death. cache = ./cache/cord-312561-9o2fhi6e.txt txt = ./txt/cord-312561-9o2fhi6e.txt === reduce.pl bib === id = cord-312414-g5px0b65 author = Takagi, Akira title = An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 4076 sentences = 230 flesch = 61 summary = As shown in Fig. 2 , the intracellular cytokine staining (ICS) assay showed that 173 significant numbers of IFN--producing CD8+ T cells were elicited in mice immunized 174 with 18 liposomal peptides including pp1a-38, -52, -84, -103, -445, -597, -641, -1675, 175 -2785, -2884, -3083, -3403, -3467, -3583, -3662, -3710, -3732, and -3886, revealing that 176 these 18 peptides are HLA-A*02:01-restricted CTL epitopes derived from SARS-CoV-2 177 pp1a. However, any of 18 185 epitopes are not found in the amino acid sequence of either MERS-CoV or the four 186 common cold human coronaviruses involving HCoV-OC43, In the 18 positive peptides, 10 peptides including pp1a-38, -84, -641, -1675, -2884, 189 -3467, -3583, -3662, -3710, and -3732 were selected for the following analyses because 190 of the high ratios of IFN- + cells in CD8 + T cells (Fig. 2) . At first glance, the graphs of CD107a ( Taken together, 10 peptides differed significantly in their ability to induce 226 SARS-CoV-2 pp1a-specific CTLs when mice were immunized with the mixture of 10 227 peptides in liposomes. cache = ./cache/cord-312414-g5px0b65.txt txt = ./txt/cord-312414-g5px0b65.txt === reduce.pl bib === id = cord-312646-hfv7ce3f author = Pfützner, Andreas title = Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV- 2 in a community screening setting shows low sensitivity date = 2020-06-02 pages = extension = .txt mime = text/plain words = 485 sentences = 30 flesch = 58 summary = title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV2 in a community screening setting shows low sensitivity In this manuscript, a point-of-care rapid test for assessment of anti-SARS-CoV-2 virus antibodies (IgG/IgM) is evaluated for sensitivity and specificity to detect the viral infection. They found that the antibody rapid test only detects 36.4 % of the samples identified as positive by means of RT-PCR, and conclude that this POCT is not recommendable for community screenings. In case that recent reports are confirmed that people with past infections may become asymptomatic carriers of the SARS-CoV-2 virus [3] , the antibody tests may be the only way to differentiate PCR-positive subjects into two groups: i.) patients who are freshly infected and may soon develop clinical symptoms (negative IgG result) and ii.) patients who have developed antibodies and may now be asymptomatic virus spreaders (positive IgG result). Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity cache = ./cache/cord-312646-hfv7ce3f.txt txt = ./txt/cord-312646-hfv7ce3f.txt === reduce.pl bib === id = cord-312115-foy3dsq4 author = Sekine, Takuya title = Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 date = 2020-08-14 pages = extension = .txt mime = text/plain words = 4891 sentences = 272 flesch = 52 summary = In line with these data, we found that CD8 + T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) more commonly expressed CD38, but not HLA-DR, Ki-67, or PD-1, in patients with acute moderate or severe COVID-19 compared with convalescent individuals and healthy blood donors, indicating limited bystander activation and proliferation during the early phase of infection with SARS-CoV-2 ( Figure 2A , B and Figure S3C ). On the basis of these observations, we quantified functional SARS-CoV-2-specific memory T cell responses across five distinct cohorts, including healthy individuals who donated blood either before or during the pandemic, family members who shared a household with convalescent individuals and were exposed at the time of symptomatic disease, and individuals in the convalescent phase after mild or severe COVID-19. These donors exhibited robust memory T cell responses months after infection, even in the absence of detectable circulating antibodies specific for SARS-CoV-2, indicating a previously unanticipated degree of population-level immunity against COVID-19. cache = ./cache/cord-312115-foy3dsq4.txt txt = ./txt/cord-312115-foy3dsq4.txt === reduce.pl bib === id = cord-312633-cks6aij2 author = Cotten, Matthew title = Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus date = 2013-05-17 pages = extension = .txt mime = text/plain words = 4063 sentences = 229 flesch = 55 summary = Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events. We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. A map of the primer mapping positions Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus and the predicted PCR products using EMC/2012 as the target is shown in Figure 1 , panel A. A ML phylogenetic tree inferred from the whole genome alignment indicated that the 3 novel human beta-CoVs sequences (England1, England/Qatar/2012, and EMC/2012) clustered closely, forming a monophyletic lineage that falls into group 2c (Figure 3 , panel A, Appendix, wwwnc.cdc.gov/EID/article/19/5/13-0057-F3.htm). cache = ./cache/cord-312633-cks6aij2.txt txt = ./txt/cord-312633-cks6aij2.txt === reduce.pl bib === id = cord-312477-2y88gzji author = Mlcochova, P. title = Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date = 2020-06-18 pages = extension = .txt mime = text/plain words = 4920 sentences = 281 flesch = 52 summary = title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. cache = ./cache/cord-312477-2y88gzji.txt txt = ./txt/cord-312477-2y88gzji.txt === reduce.pl bib === id = cord-312619-7jpf81yz author = Ilyas, Sadia title = Disinfection technology and strategies for COVID-19 hospital and bio-medical waste management date = 2020-08-12 pages = extension = .txt mime = text/plain words = 5989 sentences = 263 flesch = 48 summary = The exposure to COVID-waste may potentially increase the virus spread by increasing the reproductive number (R 0 ) from its determined range between 2.2 to 3.58 Thus, effective management of COVID-waste including the appropriate disinfect and disposal techniques are necessary to control the pandemic spread, which has not been focused yet albeit posing a similar threat as SARS-CoV-2 itself can have to the public health. The present article reviews the disinfection technologies to control/prevent the novel coronavirus spread and the proper management of COVID-waste including the effective strategies and reprocessing possibilities of the used items. Not only the COVID-waste generated by the hospitals, health centers, and self-quarantines, but the waste generated during the disinfection of public area or, where an infected person visited have been directed to treat as medical waste and collection of those waste in double-packed designated bags are mandatory before sending to burning at the high-temperature incinerator facility. cache = ./cache/cord-312619-7jpf81yz.txt txt = ./txt/cord-312619-7jpf81yz.txt === reduce.pl bib === id = cord-312652-zhccmfgw author = Hu, Xiumei title = Impact of Heat-Inactivation on the detection of SARS-CoV-2 IgM and IgG Antibody by ELISA date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3001 sentences = 176 flesch = 50 summary = According to Chinese Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (Trial Version 7), SARS-CoV-2 specific IgM becomes detectable around 3-5 days after onset and IgG reaches a titration of at least 4-fold increase during convalescence compared with the acute [9] . In order to establish a safe and accurate method for detecting SARS-CoV-2 specific antibodies, we retrospectively assessed the impact of sera heat-inactivation at 56℃ for 30 minutes on the levels of SARS-CoV-2 IgM or IgG antibodies. Therefore, our analysis provide evidence that sera inactivated by heating at 56℃ for 30 minutes could reduce the risk of virus contamination, and would not impair the detection efficacy of SARS-CoV-2 IgM or IgG testing using this ELISA assay. In summary, sera inactivated by heating at 56℃ for 30 minutes could minimize the risk of virus contamination and did not impair the positive detection rate using SARS-CoV-2 antibody detection kit (ELISA-immunoassay) and eventually represents a valuable contribution to a safer COVID-19 serological diagnosis. cache = ./cache/cord-312652-zhccmfgw.txt txt = ./txt/cord-312652-zhccmfgw.txt === reduce.pl bib === id = cord-312486-rumqopg0 author = Jacob, Chaim Oscar title = On the genetics and immunopathogenesis of COVID-19 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 11514 sentences = 579 flesch = 44 summary = The question is whether ACE2 expression levels are pertinent to SARS-CoV-2 infection only in the tissues relevant to viral entry and the lungs as its major target, [44, 45] or, given that COVID-19 in its severe form is a systemic disease with multi-organ disfunction [46, 47] , ACE2 expression levels may be important in multiple organs and tissues other than those of the respiratory system. However, the activation of multiple complement pathways, dysregulated neutrophil responses, endothelial injury, and hypercoagulability appear to be interlinked with SARS-CoV-2 infection and instead serve to drive the severity of the disease [91] . Regarding SLE, the prototypic systemic autoimmune disease, a group of investigators suggested that inherent epigenetic dysregulation causing hypomethylation and overexpression of ACE2, the functional receptor for SARS-CoV-2, might facilitate viral J o u r n a l P r e -p r o o f entry, viremia, and increased likelihood of cytokine storm in such patients [153] . cache = ./cache/cord-312486-rumqopg0.txt txt = ./txt/cord-312486-rumqopg0.txt === reduce.pl bib === id = cord-312684-3i2r2ahr author = Iba, Toshiaki title = Coagulopathy in COVID‐19 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3630 sentences = 213 flesch = 39 summary = For example, the coronavirus that caused severe acute respiratory syndrome (SARS) in 2002 (SARS-CoV-1) were reported to be associated with thrombocytopenia (55%), thrombocytosis (49%), and prolonged activated partial thromboplastin time (aPTT) (63%), but the incidence of bleeding was not high [5, 6] . In this respect, Chinese experts noted that in severe cases, patients can develop acute respiratory distress syndrome (ARDS), with coagulation predominant-type coagulopathy [9] . The excess production of proinflammatory cytokines, increased levels of damage-associated molecular patterns (DAMPs), the stimulation of cell-death mechanisms and vascular endothelial damage are the major causes of coagulation disorder in any severe infection (Fig. 1) . The major targets of the SARS-CoV-2 are the lung epithelial cell, lymphocyte, and the vascular endothelial cell, and these findings can explain that the clinical presentation of severe COVID-19 is characterized by ARDS, shock, and coagulopathy [12, 47] . cache = ./cache/cord-312684-3i2r2ahr.txt txt = ./txt/cord-312684-3i2r2ahr.txt === reduce.pl bib === id = cord-312702-fruzsn26 author = Finch, Courtney L. title = Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2785 sentences = 167 flesch = 46 summary = title: Characteristic and quantifiable COVID-19-like abnormalities in CTand PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) Based on the rather limited X-97 ray findings in the lungs of reported NHP models of SARS-CoV-2 infection with either 98 mild or no clinical signs (11, 25, 27-29), we turned to high-resolution chest CT and 99 Increases in PCLH or PCLH/LV 169 were not seen in the mock-exposed macaques over the entire study (Figure 8a A key advantage of quantifiable CT chest imaging readout over serial euthanasia 212 studies, in addition to potentially reduced experimental animal numbers, is the ability not 213 only to evaluate between-group differences, but also to compare severity and duration of 214 disease at higher resolution in single animals and even in isolated parenchymal areas 215 sequentially. follow-up confirmation of these pilot results in this model of mild-moderate COVID-19 233 is needed to further establish quantifiable lung CT as a reliable disease readout and to 234 forge imaging-pathologic correlates in macaques euthanized at peak radiographic 235 abnormality. cache = ./cache/cord-312702-fruzsn26.txt txt = ./txt/cord-312702-fruzsn26.txt === reduce.pl bib === id = cord-312664-tgpaidhp author = Liang, Julia title = Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex date = 2020-05-28 pages = extension = .txt mime = text/plain words = 3050 sentences = 189 flesch = 52 summary = title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. Further, molecular dynamics simulations highlight the stability of the interaction of the α-ketoamide 13b ligand with the SARS-CoV-2 M(pro) (ΔG = -25.2 and -22.3 kcal/mol for protomers A and B). Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . cache = ./cache/cord-312664-tgpaidhp.txt txt = ./txt/cord-312664-tgpaidhp.txt === reduce.pl bib === id = cord-312730-4ejjmab4 author = Wong, Rebecca S. Y. title = The SARS-CoV-2 Outbreak: an Epidemiological and Clinical Perspective date = 2020-09-29 pages = extension = .txt mime = text/plain words = 6475 sentences = 301 flesch = 51 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started with the detection of an increasing number of pneumonia cases of unknown origin in Wuhan, China, since December 2019. In response to the rapidly growing number of confirmed cases and deaths, some measures taken by the Chinese authorities include the quarantine of millions of its citizens with the unprecedented lockdown of many cities, in an attempt to contain the virus and slow down the spread of the disease [3] . One study in China reported a young 22-year-old male who spread SARS-CoV-2 infection to his contacts (1 relative and 6 classmates, all of which were youngsters from 16 to 23 years) just after a few-hour contact during the incubation period, when he was totally asymptomatic [18] , suggesting that the disease is highly infectious during the incubation period. cache = ./cache/cord-312730-4ejjmab4.txt txt = ./txt/cord-312730-4ejjmab4.txt === reduce.pl bib === id = cord-312849-vgzvpwz9 author = Eckbo, Eric J. title = Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples date = 2020-11-10 pages = extension = .txt mime = text/plain words = 1421 sentences = 74 flesch = 48 summary = title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of SARS-CoV-2 in nasopharyngeal swabs. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RdRP and E genes. This report describes the results of an independent evaluation of the performance characteristics of the BioFire COVID-19 Test and the RP2.1 for detection of SARS-CoV-2. The BioFire COVID-19 Test and Respiratory Panel 2.1 are easy-to-use, highly sensitive, and rapid assays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. This evaluation demonstrates that the assays perform comparably to our laboratory developed real-time PCR assay, with 100% agreement in testing results for clinical specimens and acceptable performance at their stated limits of detection. cache = ./cache/cord-312849-vgzvpwz9.txt txt = ./txt/cord-312849-vgzvpwz9.txt === reduce.pl bib === id = cord-312697-ffxcze6c author = Dübel, Stefan title = Rekombinante, vollständig humane Antikörper zur Behandlung akuter COVID-19 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 1015 sentences = 129 flesch = 41 summary = COVID-19 (coronavirus disease 2019) ist eine akute schwere virale Erkrankung der oberen Atemwege und Lungen, die vom neuartigen SARS-CoV-2-Virus hervorgerufen wird und zum ersten Mal in Wuhan (China) Ende 2019 beschrieben wurde. Solche Antikörper sind eine komplementäre Ergänzung zu den derzeit laufenden Virus-Impfstoff-Entwicklungen, da sie mit sehr hoher Wahrscheinlichkeit auch den bereits an COVID-19 erkrankten Patienten helfen können. Dies könnte sehr schnell gehen: Aufgrund der großen Erfolge rekombinanter Antikörperwirkstoffe (fast 100 zugelassene Medikamente) stehen dafür zudem bereits heute umfangreiche Produktionskapazitäten und defi nierte Produktionsprozesse zur Verfügung, während diese bei einem neuartigen Impfstoff aus Viruskomponenten erst noch zeitaufwendig entwickelt, skaliert und zugelassen werden müssen. Auf Basis dieser Erfahrungen begannen wir im Februar dieses Jahres in Braunschweig an der TU und parallel an deren Ausgründung YUMAB GmbH mit Arbeiten zu dem Ziel, vollständig menschliche Antikörper zu entwickeln, welche die SARS-CoV-2-Infektion verhindern können. So konnte bisher ein sehr großer Satz von mehr als 750 komplett menschlichen monoklonalen Antikörpern gegen das SARS-CoV-2-Spike(S)-Protein gefunden und sequenziert werden. cache = ./cache/cord-312697-ffxcze6c.txt txt = ./txt/cord-312697-ffxcze6c.txt === reduce.pl bib === id = cord-312677-rwznqiib author = Razmi, Mahdieh title = Immunomodulatory-Based Therapy as a Potential Promising Treatment Strategy against Severe COVID-19 Patients: A Systematic Review date = 2020-08-29 pages = extension = .txt mime = text/plain words = 6545 sentences = 306 flesch = 39 summary = Sixty-six publications and 111 clinical trials were recognized as eligible, reporting the efficacy of the immunomodulatory agents, including corticosteroids, hydroxychloroquine, passive and cytokine-targeted therapies, mesenchymal stem cells, and blood-purification therapy, in COVID-19 patients. Various studies have focused on the efficacy of the immunomodulatory agents including corticosteroids, hydroxychloroquine or chloroquine, cytokine-targeted therapies (e.g., anakinra, siltuximab, or tocilizumab), passive immunotherapy (convalescent plasma and intravenous immunoglobulin), mesenchymal stem cells, and bloodpurification therapy, mostly as adjuvant therapy for treatment of the patients with severe COVID-19 and partly have reported promising outcomes. Included clinical studies with 1-63 participants have shown that both antagonists, specially TCZ, are effective in reducing the mortality rate specially in the severely ill patients, improving the symptoms including fever resolution, oxygenation and resolved CT scans, reducing the inflammation markers (ferritin, CRP, and D-dimer), weaning from the ICU hospitalization and ventilation, and dampening the risk of disease progression to ARDS by mitigating the cytokine storm in the NCP patients [60, 62] , as applied for CRS controlling in the CAR-T therapy [90] . cache = ./cache/cord-312677-rwznqiib.txt txt = ./txt/cord-312677-rwznqiib.txt === reduce.pl bib === id = cord-312670-hi3fjne4 author = Corman, V. M. title = Coronaviren als Ursache respiratorischer Infektionen date = 2019-08-27 pages = extension = .txt mime = text/plain words = 2307 sentences = 257 flesch = 49 summary = Zusätzlich zu diesen ständig im Menschen zirkulierenden Varianten wurden in den vergangenen Jahren zwei CoV im Menschen gefunden, nämlich SARS-CoV und MERS-CoV, die aus dem Tierreservoir auf den Menschen übergegangen sind und bei einem deutlich größeren Anteil der Infizierten schwere virale Pneumonien mit tödlichem Verlauf auslösen [25, 28] . Obwohl die Mehrzahl der Infektionen mit den vier endemischen CoV nur leichte Atemwegserkrankungen verursacht, können alle HCoV auch schwere Hier steht eine Anzeige. Inwiefern diese sekundären Infektionen auf die intensivmedizinische Behandlung und Beatmung zurückzuführen sind oder ein spezifisches grundsätzliches Risiko einer CoV-Infektion darstellen, ist noch nicht verstanden. Jedoch ist eine spezifische Labordiagnostik bei Verdacht auf eine Infektion mit endemi-schen CoV bei harmlosem Verlauf und Patienten ohne besonderes Risiko für die Entstehung von Komplikationen auch nicht indiziert. Bei der typischerweise unspezifischen Klinik von MERS-CoV-Infektionen sollte auch die Möglichkeit einer Infektion mit anderen Pathogenen in Betracht gezogen werden [26] . RKI (2015) Schwere respiratorische Erkrankungen in Verbindung mit Middle East Respiratory Syndrome Coronavirus (MERS-CoV). cache = ./cache/cord-312670-hi3fjne4.txt txt = ./txt/cord-312670-hi3fjne4.txt === reduce.pl bib === id = cord-312741-0au4nctt author = Lin, Panpan title = Coronavirus in human diseases: Mechanisms and advances in clinical treatment date = 2020-10-01 pages = extension = .txt mime = text/plain words = 14665 sentences = 840 flesch = 42 summary = 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein cache = ./cache/cord-312741-0au4nctt.txt txt = ./txt/cord-312741-0au4nctt.txt === reduce.pl bib === id = cord-312488-uzhj4i1q author = Petrosillo, Nicola title = SARS-CoV-2, “common cold” coronaviruses’ cross-reactivity and “herd immunity”: The razor of Ockham (1285-1347)? date = 2020-05-29 pages = extension = .txt mime = text/plain words = 1033 sentences = 69 flesch = 59 summary = After the rapid spread of coronavirus-19 infectious disease (COVID-19) worldwide between February and April 2020, with a total of 5,267,419 confirmed cases and 341,155 deaths as of May 25, 2020, 1 in the last weeks we are observing a decrease in new infections in European countries, and the confirmed cases are not as severe as in the past, so much so that the number of patients transferred to intensive care for the worsening of the systemic and pulmonary disease is dramatically decreasing. 8 Virologists are claiming that there is no evidence of SARS-CoV-2 mutations causing less virulence and change of pathogenicity, 9 therefore, bending the epidemic curve could be simply the effect of progressive exhaustion of people susceptible to infection either due to a COVID-19 infection or for previous/recent "common cold" coronaviruses' infections. cache = ./cache/cord-312488-uzhj4i1q.txt txt = ./txt/cord-312488-uzhj4i1q.txt === reduce.pl bib === id = cord-312736-bm6t2bxz author = Bach, Paxton title = Innovative strategies to support physical distancing among individuals with active addiction date = 2020-05-27 pages = extension = .txt mime = text/plain words = 998 sentences = 55 flesch = 48 summary = In response to these dual crises, health authorities have implemented policy changes to provide new tools to practitioners who treat patients with substance use disorders, circumventing previous barriers to treatment, such as inadequate access and prohibitively regimented medication management. In British Columbia, an epicentre of the overdose epidemic in Canada, unique steps are being taken to mitigate risk for people who use drugs in the context of SARS-CoV-2. Clinical guidance published by the British Columbia Centre on Substance Use in collaboration with the provincial Ministry of Health has, for the first time, proposed an approach to prescribing these medications to patients with active substance use disorders who are thought to be at high risk for SARS-CoV-2. People with substance use disorders face compounded risk in the context of SARS-CoV-2, and implementing physical distancing measures among this population presents unique challenges. cache = ./cache/cord-312736-bm6t2bxz.txt txt = ./txt/cord-312736-bm6t2bxz.txt === reduce.pl bib === id = cord-312997-wcqdksfg author = Favresse, Julien title = Clinical performance of the Elecsys electrochemiluminescent immunoassay for the detection of SARS-CoV-2 total antibodies date = 2020-06-02 pages = extension = .txt mime = text/plain words = 651 sentences = 44 flesch = 47 summary = In the context of COVID-19, a wide range of serology immunoassays with different SARS-CoV-2 antigen recognition and antibody specificity have been developed to complement RT-PCR assays [1] . This study is the first to report the external validation of a new electrochemiluminescent immunoassay (ECLIA) test, the Elecsys anti-SARS-CoV-2 from Roche Diagnostics ® . This retrospective study was conducted from May 6 to 12, 2020 at the clinical biology Analyses of serum samples obtained 28 days or more after symptom onset provided a sensitivity of 96.7% (95%CI: 82.8-99.9%) and 100% (95%CI: 88.9-100%) with the manufacturer and the optimized cut-off, respectively (Figure 1) . The optimal ROC cut-off showed excellent clinical performance 14 days or more following RT-PCR positivity or following the onset of COVID-19 symptoms. cache = ./cache/cord-312997-wcqdksfg.txt txt = ./txt/cord-312997-wcqdksfg.txt === reduce.pl bib === id = cord-312950-ggywr91e author = Fuller, Julie title = Surveillance for Febrile Respiratory Infections during Cobra Gold 2003 date = 2006-05-17 pages = extension = .txt mime = text/plain words = 1855 sentences = 99 flesch = 43 summary = The Naval Health Research Center conducted laboratory-based surveillance for febrile respiratory infections at the 2003 Cobra Gold Exercise in Thailand. To ease these concerns, the Naval Health Research Center (NHRC), with an 8-year history of surveillance and diagnosis of febrile respiratory illness (FRI) within active duty continental United States and deployed forces, was tasked with conducting laboratory-based, active surveillance for respiratory illnesses (including SARS) during the exercise, with the intent of early recognition and response. 7, 8 As concerns over SARS importation were eased with implementation of surveillance, valuable information on circulating respiratory pathogens during such an exercise was collected. Supplies, including viral transport medium, swabs (sterile Dacron), preprinted subject identification labels, FRI log sheets, and informed consent/case forms, were provided to both units. Of the 16 diagnostic specimens received, seven (44%) tested positive for influenza A, 2 (13%) for coronavirus OC43, 2 (13%) for respiratory syncytial virus, and 1 (6%) for rhinovirus. cache = ./cache/cord-312950-ggywr91e.txt txt = ./txt/cord-312950-ggywr91e.txt === reduce.pl bib === id = cord-313076-531wksez author = Rauch, J. N. title = CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population date = 2020-08-07 pages = extension = .txt mime = text/plain words = 5576 sentences = 313 flesch = 54 summary = Our results substantiate that large, population-level asymptomatic screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPRand PCR-based assays indicate expanded options for surveillance testing The objectives of our study were to: (i) establish the prevalence of asymptomatic SARS-CoV2 infection in a university population, (ii) assess for any dynamic change associated with the changing community conditions related to NPIs, and (iii) systematically compare the performance of our newly developed CRISPR-based test alongside that of the established, CDC-recommended reference testing by RT-qPCR. We used two assays to detect SARS-CoV-2 genomes in the collected OP swab samples: a CRISPR-based method we recently developed at UCSB known as CREST 23 , and the RT-qPCR test recommended by the CDC 24 (Sup. Fig. cache = ./cache/cord-313076-531wksez.txt txt = ./txt/cord-313076-531wksez.txt === reduce.pl bib === id = cord-312722-talu4geh author = Ahmed, Nausheen title = COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1179 sentences = 83 flesch = 51 summary = title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient 3, 4 As a result of the high mortality in this population, the American Society of Transplantation and Cellular Therapy (ASTCT) recently published guidelines on March 18, 2020, suggesting universal testing of patients before admission for cellular therapy or stem cell transplant to mitigate the risk of transmission and outbreaks in transplant wards. 5 Accordingly, at our institution a policy to screen all patients planned for HCT or cellular therapy the day prior to admission with a nasopharyngeal swab real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2 infection was implemented. 8 The skin rash, such as livedo reticularis and petechial rash have been reported, but our patient's positive SARS-CoV-2 test and biopsy suggest Covid-19 may also cause a more classic viral exanthem. cache = ./cache/cord-312722-talu4geh.txt txt = ./txt/cord-312722-talu4geh.txt === reduce.pl bib === id = cord-312955-gs65c3fy author = Schreiber, Gideon title = The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date = 2020-09-30 pages = extension = .txt mime = text/plain words = 8418 sentences = 467 flesch = 48 summary = Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I–receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Thereby, it inhibits the nuclear transport of phosphorylated STAT1, rendering cells refractory to IFN-Is. Another example of viral mechanisms that evolved to eliminate IFN-I functions in inducing innate immunity is given by the SARS corona virus, where both the production of IFNb and the IFN-I induced signaling are attenuated. This gene was found to preferentially cleave the ubiquitin-like modifier interferon-stimulated gene 15 (ISG15), FIGURE 4 | SARS-CoV-2 has multiple effects on the immune system, including inhibition of IFNb production, which results in ISGs not to be produced, CD4+ and CD8+ exhaustion and increased levels of pro-inflammatory proteins (TNFa, IL6, NF-kB). cache = ./cache/cord-312955-gs65c3fy.txt txt = ./txt/cord-312955-gs65c3fy.txt === reduce.pl bib === id = cord-312708-9ywu6r2t author = Sharma, Dhruv title = Cadaveric Simulation of Otologic Procedures: An Analysis of Droplet Splatter Patterns During the COVID-19 Pandemic date = 2020-05-19 pages = extension = .txt mime = text/plain words = 2222 sentences = 124 flesch = 47 summary = OBJECTIVE: The otolaryngology community has significant concerns regarding the spread of SARS-CoV-2 through droplet contamination and viral aerosolization during head and neck examinations and procedures. RESULTS: There were no fluorescein droplets or splatter contamination observed in the measured surgical field in any direction after myringotomy and insertion of ventilation tube. 7 As a result, the American Academy of Otolaryngology-Head and Neck Surgery has issued a position statement to limit elective procedures requiring interaction with upper airway mucosal surfaces or those with increased risk of aerosolization, which may include otologic procedures such as myringotomy and mastoidectomy. Since the upper respiratory tract harbors a high viral load, 3 otolaryngologists are vulnerable to SARS-CoV-2 transmission while performing head and neck procedures that utilize suction and powered instrumentation, such as the surgical drill, especially if they are doing so without appropriate protective personal equipment. cache = ./cache/cord-312708-9ywu6r2t.txt txt = ./txt/cord-312708-9ywu6r2t.txt === reduce.pl bib === id = cord-313084-l7odplqg author = Sampson, Victoria title = Could there be a link between oral hygiene and the severity of SARS-CoV-2 infections? date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3352 sentences = 203 flesch = 42 summary = The risk factors already identified for developing complications from a COVID-19 infection are age, gender and comorbidities such as diabetes, hypertension, obesity and cardiovascular disease. This paper investigates the potential link between SARS-CoV-2 and bacterial load, questioning whether bacteria may play a role in bacterial superinfections and complications such as pneumonia, acute respiratory distress syndrome and sepsis. 1 While COVID-19 has a viral origin, it is suspected that in severe cases, bacterial superinfections may contribute to causing complications such as pneumonia and acute respiratory distress syndrome (ARDS). 18 It is common for respiratory viral infections to predispose patients to bacterial superinfections, leading to increased disease severity and mortality; for example, during the influenza pandemic in 1918, where the primary cause of death was not from the virus itself but from bacterial superinfections. Bacteria present in patients with severe COVID-19 are associated with the oral cavity and improved oral hygiene may play a part in reducing the risk of complications. cache = ./cache/cord-313084-l7odplqg.txt txt = ./txt/cord-313084-l7odplqg.txt === reduce.pl bib === id = cord-313099-rpdlk1b6 author = Han, Xiaoyu title = Severe Acute Respiratory Syndrome Coronavirus 2 among Asymptomatic Workers Screened for Work Resumption, China date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1154 sentences = 77 flesch = 55 summary = After the outbreak in Wuhan, China, we assessed 29,299 workers screened for severe acute respiratory syndrome coronavirus 2 by reverse transcription PCR. We noted 18 (0.061%) cases of asymptomatic infection; 13 turned negative within 8.0 days, and 41 close contacts tested negative. A s the population of Wuhan, China, returns to work, asymptomatic cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being discovered among workers receiving health checkups for work resumption. We report on cases of asymptomatic SARS-CoV-2 infection among persons during work resumption screening in Wuhan. Among 29,299 persons screened by RT-PCR, we confirmed 18 (0.061%) cases of SARS-CoV-2 infection. Half the cases in our study showed negative IgM and IgG at the time of positive RT-PCR, suggesting recent infections (<14 days). In addition, 13 cases had negative RT-PCR assays <8 (range 3-14) days, suggesting a favorable prognosis for persons with asymptomatic infections. In addition, all 41 close contacts of the asymptomatic case-patients tested negative by RT-PCR. cache = ./cache/cord-313099-rpdlk1b6.txt txt = ./txt/cord-313099-rpdlk1b6.txt === reduce.pl bib === id = cord-312899-ot5pvtbl author = Chen, F title = In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds date = 2004-09-30 pages = extension = .txt mime = text/plain words = 3161 sentences = 164 flesch = 43 summary = Commercial antiviral agents and pure chemical compounds extracted from traditional Chinese medicinal herbs were screened against 10 clinical isolates of SARS coronavirus by neutralisation tests with confirmation by plaque reduction assays. Interferon-beta-1a, leukocytic interferon-alpha, ribavirin, lopinavir, rimantadine, baicalin and glycyrrhizin showed antiviral activity. We report in this study on the in vitro antiviral susceptibility of 10 isolates of SARS coronavirus to commercially available antiviral agents and pure chemical compounds including baicalin, glycyrrhizin, and chlorogenic acid extracted from traditional Chinese herbs. Further testing by neutralization tests Table 3 Comparison of antiviral activity of 10 compounds against 10 strains of SARS-CoV in fRhK4 cell line, against the prototype strains (39849) with the other 9 isolates of SARS coronavirus against the active compounds confirmed detectable inhibitory activities for leukocytic interferon-alpha, interferon-beta-1a, ribavirin, lopinavir, rimantadine, and baicalin. cache = ./cache/cord-312899-ot5pvtbl.txt txt = ./txt/cord-312899-ot5pvtbl.txt === reduce.pl bib === id = cord-313246-2gtiqrnj author = Hazra, Aniruddha title = Coinfections with SARS-CoV-2 and other respiratory pathogens date = 2020-07-03 pages = extension = .txt mime = text/plain words = 801 sentences = 52 flesch = 50 summary = 3 The same specimen can be tested via RT-PCR for a respiratory panel (RP) of other common pathogens, including adenovirus, coronavirus 229E/HKU1/NL63/OC43, human metapneumovirus, influenza A/B, parainfluenza 1-4, respiratory syncytial virus, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, and rhinovirus/enterovirus (BioFire FilmArray respiratory panel 2). This report examines patients with influenza-like illness symptoms who were simultaneously tested for SARS-CoV-2 and the above panel from March 12, 2020, through April 15, 2020. During the observed period, 2,535 specimens were simultaneously tested for SARS-CoV-2 and RP pathogens on 2,458 symptomatic patients. Notably, the median age of coinfected patients was nearly 20 years younger than those only infected with SARS-CoV-2. During the study period, the Illinois Department of Public Health noted a decline in influenza tests positivity from 14.9% to 1.6% between the weeks ending March 14, 2020, and April 11, 2020, respectively. Rates of coinfection between SARS-CoV-2 and other respiratory pathogens cache = ./cache/cord-313246-2gtiqrnj.txt txt = ./txt/cord-313246-2gtiqrnj.txt === reduce.pl bib === id = cord-312971-r9sggqh8 author = Mancino, Enrica title = A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1306 sentences = 83 flesch = 46 summary = title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Key words: Community Acquired Pneumonia, SARS-CoV-2, COVID-19, virus Community Acquired Pneumonia (CAP) remains the leading cause of mortality and morbidity in children worldwide [1] . Surprisingly, only a small number of cases of COVID-19 has been described in children, suggesting that SARS-CoV-2 infection in the paediatric population is unusual [6] . Our aim was to describe viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children under 14 years of age. However, the clinical severity score was higher in RSV patients and hRV was found in 9/17 cases (53%) in coinfection, consistent with the notion that hRV is very frequently detected in respiratory infections J o u r n a l P r e -p r o o f during childhood. cache = ./cache/cord-312971-r9sggqh8.txt txt = ./txt/cord-312971-r9sggqh8.txt === reduce.pl bib === id = cord-313058-nrrl4kjc author = Rivas, Magali Noval title = COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis date = 2020-10-16 pages = extension = .txt mime = text/plain words = 1054 sentences = 68 flesch = 51 summary = title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. As of mid-September, the novel severe acute respiratory syndrome coronavirus 2 26 (SARS-CoV-2) has infected more than 30 million people, resulting in approximately one 27 million deaths worldwide, including over 200,000 deaths in the USA alone. Exacerbation of the COVID-19 immune response manifested by extensive cytokines 33 release, called cytokine storm, may lead to multisystem inflammatory syndrome that is 34 fatal in 28% of cases 1 . Interestingly, SAg-induced TSS has been associated with long-term 94 neuropsychologic deficits in adults, including cognitive decline 10 , and we identified a 95 homology between the SAg motif of SARS-CoV-2 and neurotoxin-like sequences which 96 are able to bind the TCR 5 . Clinical 131 Characteristics of 58 Children With a Pediatric Inflammatory Multisystem Syndrome 132 Temporally Associated With SARS-CoV-2 cache = ./cache/cord-313058-nrrl4kjc.txt txt = ./txt/cord-313058-nrrl4kjc.txt === reduce.pl bib === id = cord-312884-anlp8lab author = Iyer, Gayatri R. title = Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants date = 2020-09-04 pages = extension = .txt mime = text/plain words = 6268 sentences = 317 flesch = 44 summary = Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. The aim of the present study was to identify variants in these five selected candidate genes from the clinical exome data available with us for more than 100 individuals and make an attempt to classify them as relevant to the present COVID-19 aetiopathology, especially for the Indian population. The selected candidate gene variants were assessed in our internal cohort of 103 individuals, who had earlier provided consent, to perform a pilot study on the susceptibility and disease severity of Indians for COVID-19. Since host genetic polymorphisms have been demonstrated to be associated with vulnerability to human infection, in this study five candidate genes-ACE2, TMPRSS2, CD209, IFITM3, and MUC5B-were selected based on their relevance to the current pandemic. cache = ./cache/cord-312884-anlp8lab.txt txt = ./txt/cord-312884-anlp8lab.txt === reduce.pl bib === id = cord-312740-2ro2p77q author = Babadaei, Mohammad Mahdi Nejadi title = Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3820 sentences = 217 flesch = 50 summary = A broad-spectrum of antiviral agents are being currently evaluated in clinical trials, and in this review, we specifically focus on the application of Remdesivir (RVD) as a potential anti-viral compound against Middle East respiratory syndrome (MERS) -CoV, SARS-CoV and SARS-CoV-2. First, we overview the general information about SARS-CoV-2, followed by application of RDV as a nucleotide analogue which can potentially inhibits RNA-dependent RNA polymerase of COVs. Afterwards, we discussed the kinetics of SARSor MERS-CoV proliferation in animal models which is significantly different compared to that in humans. With Having a considerable number of people worldwide infected with COVID-19, scientists have identified a number of cases of broad-spectrum antiviral agents (BSAAs) that could serve as potential candidates for the treatment of the viral diseases (Andersen et al., 2020; Ianevski et al., 2018) . Corona virus SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics cache = ./cache/cord-312740-2ro2p77q.txt txt = ./txt/cord-312740-2ro2p77q.txt === reduce.pl bib === id = cord-313028-0nhgxoim author = Huang, Chaolin title = Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China date = 2020-01-24 pages = extension = .txt mime = text/plain words = 4784 sentences = 248 flesch = 49 summary = INTERPRETATION: The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Following the pneumonia cases of unknown cause reported in Wuhan and considering the shared history of exposure to Huanan seafood market across the patients, an epidemiological alert was released by the local health authority on Dec 31, 2019, and the market was shut down on Jan 1, 2020. 16 Secondary infection was diagnosed if the patients had clinical symptoms or signs of nosocomial pneumonia or bacteraemia, and was combined with a positive culture of a new pathogen from a lower respiratory tract specimen (including the sputum, transtracheal aspirates, or bronchoalveolar lavage fluid, or from blood samples taken ≥48 h after admission). In view of the high amount of cytokines induced by SARS-CoV, 22, 24 MERS-CoV, 25, 26 and 2019-nCoV infections, corticosteroids were used frequently for treatment of patients with severe illness, for possible benefit by reducing inflammatory-induced lung injury. cache = ./cache/cord-313028-0nhgxoim.txt txt = ./txt/cord-313028-0nhgxoim.txt === reduce.pl bib === id = cord-313215-diqfmitr author = Luo, Lei title = Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date = 2020-07-09 pages = extension = .txt mime = text/plain words = 1593 sentences = 90 flesch = 52 summary = title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. To address this question, in this study, we sampled total of 641 surfaces 63 environmental and air specimens among 39 cases in Guangzhou, China, to explore the 64 surrounding environmental surfaces and air contamination by SARS-CoV-2 in non-65 health care settings. A total of 641 157 environmental surfaces and air specimens were collected among 39 COVID-19 cases, 158 and 20 specimens (20/641, 3.1%) were positive by RT-PCR testing from 9 COVID-19 159 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic 160 cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases 161 ( of SARS-CoV-2 (Table 2) . cache = ./cache/cord-313215-diqfmitr.txt txt = ./txt/cord-313215-diqfmitr.txt === reduce.pl bib === id = cord-312999-3erodkv9 author = Hassan, Sk. Sarif title = Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date = 2020-09-06 pages = extension = .txt mime = text/plain words = 3920 sentences = 236 flesch = 53 summary = SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Based on the mutations, conserved and non-conserved residues in ORF10 proteins are identified and marked in different colors in (Figure There are altogether 22 distinct missense mutations which were examined across 22 unique ORF10 variants of SARS-CoV-2. cache = ./cache/cord-312999-3erodkv9.txt txt = ./txt/cord-312999-3erodkv9.txt === reduce.pl bib === id = cord-312743-9e4yufo5 author = Breiman, Adrien title = Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1388 sentences = 66 flesch = 45 summary = These observations suggested that, when produced in cells that express the A or B blood group enzymes, infectious SARS virions are decorated by the corresponding glycan antigens and that the presence of anti-A and anti-B antibodies in blood group O individuals could prevent infection by blocking virus attachment and entry. We therefore hypothesize that as they are produced in cells coexpressing the ACE2 receptor and either the αGal, NeuGc, or A/B blood group antigens, both SARS-CoV and SARS-CoV2 harbor the corresponding glycan epitopes. Likewise, impairment of transmission by the anti-blood group antibodies may not work to its full potential because of their variable titers in the population and of the high affinity of the SARS-CoV2 for ACE2 [18] , rendering its neutralization more difficult. cache = ./cache/cord-312743-9e4yufo5.txt txt = ./txt/cord-312743-9e4yufo5.txt === reduce.pl bib === id = cord-312991-ypgrw78s author = Wang, Zhi-Gang title = Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV date = 2005-09-12 pages = extension = .txt mime = text/plain words = 3744 sentences = 224 flesch = 64 summary = In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. According to 5 polymorphism sites, 63 SARS-CoV genomes were divided into early, middle and late phase genotype groups [19] . Key mutation loci are shown in Table 3 (identified by using nucleotide-nucleotide BLAST program at NEBI and Clustalw 1.83), and the phylogenetic tree of 174 loci ( Fig. 1) showed that, according to the polymorphism sites of C9404T, C9479T, G17564T, G19838A, A21721G, C22222T, G22517A, G23823T, T27243C and C27827T, the SARS-CoV genomes of the first epidemic can be divided into two genotypes, genotype C and T. among the genotypes and the groups The genetic characteristics of the genotypes were further analyzed based on the sequence polymorphism of the spike protein genes ( Table 4 ). SARS-CoV GD03T0013 was from the patient with ''mild clinical symptoms'', and its genome sequence was similar to that of the sub-genotype C1. cache = ./cache/cord-312991-ypgrw78s.txt txt = ./txt/cord-312991-ypgrw78s.txt === reduce.pl bib === id = cord-313117-0qur0isb author = Gardinassi, Luiz G. title = Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3565 sentences = 177 flesch = 35 summary = To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. In addition, our approach also detected increased signals of monocytes (Figure 1B) , dendritic cells ( Figure 1C ) and of the mitochondrial respiratory electron transport chain in SARS-CoV-2 infection (Figure 1A) , suggesting a critical role of metabolic pathways for the immune response of COVID-19 patients. cache = ./cache/cord-313117-0qur0isb.txt txt = ./txt/cord-313117-0qur0isb.txt === reduce.pl bib === id = cord-313193-q5zeoqlb author = Carrat, F. title = Seroprevalence of SARS-CoV-2 among adults in three regions of France following the lockdown and associated risk factors: a multicohort study. date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4076 sentences = 265 flesch = 57 summary = Methods Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE), two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA), with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE) -two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA) -with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants with a positive ELISA-S had a higher rate of self-reported symptoms than those with negative tests except for skin lesions (table 2) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint cache = ./cache/cord-313193-q5zeoqlb.txt txt = ./txt/cord-313193-q5zeoqlb.txt === reduce.pl bib === id = cord-312996-qzu8pkyt author = Iles, R. K. title = A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date = 2020-08-22 pages = extension = .txt mime = text/plain words = 6845 sentences = 375 flesch = 51 summary = Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. cache = ./cache/cord-312996-qzu8pkyt.txt txt = ./txt/cord-312996-qzu8pkyt.txt === reduce.pl bib === id = cord-313082-n3bo9jw1 author = Tenenbein, Paul title = The case for routine screening for SARS-CoV-2 before surgery date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3816 sentences = 269 flesch = 58 summary = Herein, we focus on one specific aspect of this question, namely whether all surgical patients should, in addition to detailed clinical screening (i.e., exposure risk and symptoms) for COVID-19, undergo routine preoperative testing for SARS-CoV-2 with nasopharyngeal swabbing and nucleicacid-based testing. Dans cet éditorial, nous nous intéressons à un aspect en particulier de cette question : faudrait-il faire passer un test préopératoire systématique pour dépister le SARS-CoV-2 à l'aide d'un écouvillon nasopharyngé et d'un test d'amplification des acides nucléiques à tous les patients chirurgicaux, en plus du dépistage clinique détaillé (c.-à-d. É tant donné le risque que la COVID-19 pose aux patients chirurgicaux, il est conseillé de remettre toute intervention qui peut être retardée en toute sécurité ou d'envisager des options thérapeutiques non chirurgicales, le cas échéant, pour tout patient positif au SARS-CoV-2. cache = ./cache/cord-313082-n3bo9jw1.txt txt = ./txt/cord-313082-n3bo9jw1.txt === reduce.pl bib === id = cord-312918-iof45k1r author = Ortolani, Claudio title = Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4637 sentences = 213 flesch = 45 summary = Recently, four large Randomized Controlled Trials (RCTs) have been performed in record time delivering reliable data: (1) the National Institutes of Health (NIH) RCT included 60 hospitals participating all over the world and showed the efficacy of remdesivir in reducing the recovery time in hospitalized adults with COVID-19 pneumonia; (2) three large RCTs already completed, for hydroxychloroquine, dexamethasone and Lopinavir and Ritonavir respectively. In 2019, at the beginning of the SARS-CoV-2 pandemic, at least 4 anti-inflammatory and antiviral drugs were available and in use, with possible efficacy for COVID-19: hydroxychloroquine, corticosteroids, remdesivir and Lopinavir / Ritonavir. Remark 1 cited a number of systematic reviews, which however had selected only observational clinical studies that addressed the efficacy and side effects of the corticosteroid treatment of viral pneumonia from SARS, H1N1 influenza virus and MERS virus, but not from SARS-CoV-2 virus [31] [32] [33] [34] . cache = ./cache/cord-312918-iof45k1r.txt txt = ./txt/cord-312918-iof45k1r.txt === reduce.pl bib === id = cord-312984-rzryn3on author = Pan, Daniel title = Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity date = 2020-09-19 pages = extension = .txt mime = text/plain words = 946 sentences = 63 flesch = 59 summary = title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity 8 From this small longitudinal cohort study on serially collected samples in acute COVID-19 cases of differing severity, we conclude that for symptomatic patients, it is difficult to obtain a 'false negative' result on NPS, OPS, NS or CS samples, if sampled early (within 5 days) post-symptom onset, even if the swab was 'poorly' taken. Despite a previous meta-analysis showing that sputum testing is possibly more sensitive for SARS-CoV-2 PCR testing, 9 other studies have shown that self-sampling from various URT sites performed satisfactorily for the diagnosis of acute COVID-19. Therefore, we further confirm that early (within 5 days of symptom onset), self-swabbed NPS, OPS, NS or CS samples for SARS-CoV-2 diagnostic testing in acute COVID-19 cases is a sensitive, practical approach, which reduces patient discomfort (as self-swabbing can be controlled) and minimises virus exposure to healthcare workers. cache = ./cache/cord-312984-rzryn3on.txt txt = ./txt/cord-312984-rzryn3on.txt === reduce.pl bib === id = cord-313316-l147b7jk author = Freudenthal, Bernard title = Misuse of SARS-CoV-2 testing in symptomatic health-care staff in the UK date = 2020-10-22 pages = extension = .txt mime = text/plain words = 1110 sentences = 72 flesch = 57 summary = An initiative to screen asymptomatic health-care workers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was timely and logical, 1 and contrasted markedly with the UK Government's testing strategy stated. His opened-out presentation of a brain does not show the paired lateral ventricles and the foramen of Monro, as several authors erroneously down, and the way to do that is to get the amount of testing up". Overzealous redirection of self-isolating staff back to work before they had completed sufficient self-isolation to exclude infectivity was therefore likely to increase spread of the virus to other staff and to patients or care-receivers in a substantial number of cases, especially given the high prevalence and likelihood of SARS-CoV-2 infection among exposed health-care workers during the epidemic. 5 We believe a symptom-agnostic testing approach for SARS-CoV-2 among HCWs is an effective measure of reducing viral transmission. 1 We agree that use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing among health-care workers (HCWs) solely to reduce absenteeism is inappro priate. cache = ./cache/cord-313316-l147b7jk.txt txt = ./txt/cord-313316-l147b7jk.txt === reduce.pl bib === id = cord-313345-zwe3tmq0 author = Chou, Roger title = Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings date = 2020-07-20 pages = extension = .txt mime = text/plain words = 602 sentences = 40 flesch = 43 summary = title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings Masks for prevention of respiratory virus infections, including SARS-CoV-2, in health care and community settings: a living rapid review Facemasks and hand hygiene to prevent influenza transmission in households: a cluster randomized trial Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study A case-control study on the risk factors of severe acute respiratory syndromes among health care workers Factors associated with transmission of severe acute respiratory syndrome among health-care workers in Singapore Surgical mask vs N95 respirator for preventing influenza among health care workers: a randomized trial A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. N95 Respirators vs medical masks for preventing influenza among health care personnel: a randomized clinical trial cache = ./cache/cord-313345-zwe3tmq0.txt txt = ./txt/cord-313345-zwe3tmq0.txt === reduce.pl bib === id = cord-313174-ig0h2s6l author = Hecht, Jonathon L. title = SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers date = 2020-08-02 pages = extension = .txt mime = text/plain words = 4188 sentences = 244 flesch = 52 summary = title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers Herein, we describe 19 placentas from mothers with COVID-19 studied for gross and histopathologic findings, viral expression by in situ hybridization (ISH) and immunohistochemistry (IHC), and ACE2 and TMPRSS2 expression by IHC. Ten placentas of COVID-19 negative mothers (delivered either before the pandemic or with negative tests) with clinical histories focusing on infections by an RNA virus (one case each of Zika exposure, HIV infection, and Hepatitis C infection), two cases of intrauterine fetal demise, and with histopathologies associated with congenital infections and coagulopathies (one case each of high stage and grade acute chorioamnionitis, high grade maternal vascular malperfusion (MVM), high grade fetal vascular malperfusion (FVM), high grade villitis of unknown etiology (VUE), chronic histiocytic intervillositis, and multiple intervillous thrombi) were identified from the pathology database using this diagnostic terminology and used as this set of controls. cache = ./cache/cord-313174-ig0h2s6l.txt txt = ./txt/cord-313174-ig0h2s6l.txt === reduce.pl bib === id = cord-313275-znrvkmee author = Bwire, G. M. title = A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM date = 2020-06-12 pages = extension = .txt mime = text/plain words = 2965 sentences = 230 flesch = 56 summary = title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM The research included studies on IgG/ IgM against SARS-CoV-2 among infants born to mother with COVID-19 published in English from December 1, 2019 onwards. On the other hand, natural passive immunity and detection of specific IgG and IgM antibodies to SARS-CoV-2 in infants born to COVID 19 confirmed mothers have been indicated in some studies where the newborns tested negative for the virus (8) . In this regard, a systematic review was conducted to determine the magnitude of IgG/ IgM in infants born to mothers with COVID-19 but tested negative for SARS-CoV-2. The median antibody levels detected in COVID-19 exposed newborns who tested negative for the virus after delivery but were born to mothers with COVID-19 were 75.49AU/mL (range: 7.25AU/mL-140.32AU/mL ) and for 3.79AU/mL (range: 0.16AU/mL-45.83AU/mL) (P = 0.0041) for anti-SARS-CoV-2 IgG and IgM, respectively. cache = ./cache/cord-313275-znrvkmee.txt txt = ./txt/cord-313275-znrvkmee.txt === reduce.pl bib === id = cord-313268-j51zyodw author = Zeng, Xiangxiang title = Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning date = 2020-07-12 pages = extension = .txt mime = text/plain words = 4081 sentences = 217 flesch = 42 summary = Using Amazon's AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. 10−12 Deep learning has also recently demonstrated its better performance than classic machine learning methods to assist drug repurposing, 13 −16 yet without foreknowledge of the complex networks connecting drugs, targets, SARS-CoV-2, and diseases, the development of affordable approaches for the effective treatment of COVID-19 is challenging. Via systematic validation using transcriptomics and proteomics data generated from SARS-CoV-2-infected human cells and the ongoing clinical trial data, we successfully identified 41 drug candidates that can be further tested in large-scale randomized control trials for the potential treatment of COVID-19. Using Amazon's AWS computing resources, we identified 41 high-confidence repurposed drug candidates (including dexamethasone, indomethacin, niclosamide, and toremifene) for COVID-19, which were validated by an enrichment analysis of gene expression and proteomics data in SARS-CoV-2 infected human cells. cache = ./cache/cord-313268-j51zyodw.txt txt = ./txt/cord-313268-j51zyodw.txt === reduce.pl bib === id = cord-313247-55loucvc author = Pipes, Lenore title = Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date = 2020-10-07 pages = extension = .txt mime = text/plain words = 2546 sentences = 209 flesch = 64 summary = We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. There are many different methods for inferring the root of a phylogenetic tree, but they largely depend on three possible sources of information: outgroups, the molecular clock, and non-reversibility. To investigate the possible rootings of the SARS-CoV-2 phylogeny we used six different methods and quantified the uncertainty in the placement of the root for each method on the inferred maximum likelihood topology. We note that while interpretation of bootstrap proportions in phylogenetics can be problematic (see Efron et al., 1996) we performed 1,000 parametric simulations using pyvolve (Spielman and Wilke, 2015) using maximum likelihood estimates, from the original data set, of the model of molecular evolution and the phylogenetic tree, including branch lengths (see Table S2 ). cache = ./cache/cord-313247-55loucvc.txt txt = ./txt/cord-313247-55loucvc.txt === reduce.pl bib === id = cord-313349-ikjivfce author = Finsterer, Josef title = Causes of hypogeusia/hyposmia in SARS‐CoV2 infected patients date = 2020-04-20 pages = extension = .txt mime = text/plain words = 1132 sentences = 85 flesch = 49 summary = It is well appreciated that SARS‐CoV2 does not exclusively affect the lungs.(1,2) Virus‐RNA can be detected in most of the body compartments, including the cerebrospinal fluid (CSF).(3) Neurological manifestations have been recently investigated in a retrospective study of 214 SARS‐CoV2‐infected patients.(1) This article is protected by copyright. A further argument against hypothesis one is that SARS-CoV2-associated meningitis is rare Accepted Article but smelling/taste abnormalities are frequent. In COVID-19 patients, ACE2-expressing cells of the taste buds and/or olfactory epithelium might be targeted by SARS-Cov2 via a cytopathic effect. 15 Besides the hypothesis of a cytopathic effect on neurosensory cells, the high incidence of smell and/or taste loss in COVID-19 patients might thus reflect the impact of SARS-Cov2 on the synthesis of neurotransmitters (notably serotonin and dopamine) by ACE2-expressing cells. In summary, the most likely cause for transient hypogeusia and hyposmia in SARS-CoV2-infected patients is a direct contact and interaction of the virus with gustatory receptors or olfactory receptor cells. cache = ./cache/cord-313349-ikjivfce.txt txt = ./txt/cord-313349-ikjivfce.txt === reduce.pl bib === id = cord-313356-ninzeazy author = Fiorillo, Luca title = COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3803 sentences = 248 flesch = 53 summary = title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention cache = ./cache/cord-313356-ninzeazy.txt txt = ./txt/cord-313356-ninzeazy.txt === reduce.pl bib === id = cord-313427-6y4zvrmn author = Mani, Nandita S title = Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3433 sentences = 226 flesch = 57 summary = Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. cache = ./cache/cord-313427-6y4zvrmn.txt txt = ./txt/cord-313427-6y4zvrmn.txt === reduce.pl bib === id = cord-313379-6sa6oc6u author = Bahar, B. title = Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2674 sentences = 181 flesch = 54 summary = title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children 14 We report viral and antibody testing results from our 95 pediatric patient population in order to contribute to a better understanding of timing of viral 96 clearance and antibody production in children with In addition to the RT-PCR results, qualitative and quantitative serologic testing results, age and 107 sex were also included in the data extracts. In this study, we demonstrated that IgG class antibodies directed against S1 and S2 228 glycoproteins could be detected in blood samples of children before viral clearance. . https://doi.org/10.1101/2020.08.06.20162446 doi: medRxiv preprint A strength of our study was the inclusion of patients from multiple pediatric age groups with 262 sequential PCR testing, which allowed comparison between age groups and sex serologic assays for SARS-CoV-2 are still in early phases of development. cache = ./cache/cord-313379-6sa6oc6u.txt txt = ./txt/cord-313379-6sa6oc6u.txt === reduce.pl bib === id = cord-313282-z5cues67 author = Schaefer, Inga-Marie title = In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3975 sentences = 189 flesch = 41 summary = Among five patients with acute-phase DAD (≤7 days from onset of respiratory failure), SARS-CoV-2 was detected in pulmonary pneumocytes and ciliated airway cells (N = 5), and in upper airway epithelium (N = 2). The findings suggest that SARS-CoV-2 infection of epithelial cells in lungs and airways of patients with COVID-19 who developed respiratory failure can be detected during the acute phase of lung injury and is absent in the organizing phase. The aim of this study was to examine the gross and histologic patterns of tissue injury in correlation with viral protein expression in the conducting airways and lungs at autopsy in a series of patients with confirmed SARS-CoV-2 infection. Overall, the different stages of DAD observed histologically correspond to the estimated time interval from onset of respiratory failure to death; however, the exact timing of severe lung injury may be difficult to determine in certain cases given reports of silent hypoxemia in COVID-19 infected patients [27, 28] . cache = ./cache/cord-313282-z5cues67.txt txt = ./txt/cord-313282-z5cues67.txt === reduce.pl bib === id = cord-313371-fdyfg0kf author = Brancatella, Alessandro title = Subacute Thyroiditis After Sars-COV-2 Infection date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1612 sentences = 116 flesch = 53 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that began in Wuhan, China, has spread rapidly worldwide and Italy has been severely affected by this outbreak. OBJECTIVES: The objective of this work is to report the first case of SAT related to SARS-CoV-2 infection. METHODS: We describe the clinical, laboratory, and imaging features of an 18-year-old woman who came to our attention for fever, neck pain radiated to the jaw, and palpitations occurring 15 days after a SARS-CoV-2–positive oropharyngeal swab. S ubacute thyroiditis (SAT) is a self-limited inflammatory thyroid disease characterized by neck pain, general symptoms, and thyroid dysfunction (1, 2) . Here, we report the first case of SAT in a patient affected by SARS-CoV-2. SAT is a self-limited, inflammatory disorder characterized by neck pain and general symptoms, often associated with thyroid dysfunction (1, 2) . SAT is usually preceded by an upper respiratory infection and usually presents in association with characteristic symptoms of viral disease. cache = ./cache/cord-313371-fdyfg0kf.txt txt = ./txt/cord-313371-fdyfg0kf.txt === reduce.pl bib === id = cord-313227-6zwkfzab author = Scala, Stefania title = Fighting the Host Reaction to SARS-COv-2 in Critically Ill Patients: The Possible Contribution of Off-Label Drugs date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3872 sentences = 202 flesch = 36 summary = Interestingly, in patients infected by SARS-COv-2, there is an increase in IL1β, IFNγ, IP10, and MCP1, probably leading to activated T-helper-1 (TH1) cell responses, and increased production of T-helper-2 (TH2) immunosuppressive cytokines, such as IL4 and IL10 (18) . Peripheral blood examinations on admission in the majority of patients with COVID-19 displayed lymphopenia, elevated infection-related biomarkers (i.e., procalcitonin, erythrocyte sedimentation rate, serum ferritin, and C-reactive protein) (20) and several elevated inflammatory cytokines (i.e., tumor necrosis factor (TNF)-α, interleukin (IL)-2R and IL-6). Despite markedly reducing virus titers, anti-S-IgG caused lung injury during the early stages of infection, impairing the wound-healing macrophage response and TGF-β production, while promoting pro inflammatory cytokine IL-8, MCP1 production, and inflammatory macrophage accumulation (22) . Another proteasome inhibitor, VR23, possess powerful antiinflammatory activity reducing IL-6 in synovial cells from RA patients, and improving LPS-induced acute lung injury by decreasing neutrophil migration, TNF-α secretion, and tissue inflammation in a mice model (52) . cache = ./cache/cord-313227-6zwkfzab.txt txt = ./txt/cord-313227-6zwkfzab.txt === reduce.pl bib === id = cord-313603-y8p9bmph author = Akter, Shahina title = Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh date = 2020-09-24 pages = extension = .txt mime = text/plain words = 957 sentences = 58 flesch = 57 summary = title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. After generating a FASTA file from the FASTQ files using the DRAGEN software, it was found that the complete genome sequences of the Bangladeshi SARS-CoV-2 strains (BCSIR_ NILMRC_006, BCSIR_NILMRC_007, and BCSIR_NILMRC_008) have linear RNAs of 29,892 bp, 29,823 bp, and 29,758 bp, respectively, with an average GC content of 39%. The sequences of these SARS-CoV-2 genomes from Bangladesh were submitted to the GISAID database (accession no. We extend special thanks to Architect Yeafesh Osman, Honorable Minister of Science and Technology. Anwar Hossain, Senior Secretary, Ministry of Science and Technology. cache = ./cache/cord-313603-y8p9bmph.txt txt = ./txt/cord-313603-y8p9bmph.txt === reduce.pl bib === id = cord-313627-g1iqhsdk author = Zou, Xiaojing title = Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1804 sentences = 126 flesch = 55 summary = Conclusion Liver injury in patients with SARS-CoV-2 and chronic HBV co-infection was associated with severity and poor prognosis of disease. In this study, we aimed to describe the characteristics of liver function and its 3 relation with severity and prognosis in patients with SARS-CoV-2 and chronic HBV 4 co-infection, in order to provide evidence for the clinical treatment of these specific 5 patients and contribute to improving their prognosis. In the present study, we found that liver test abnormalities were relatively common 1 in patients with SARS-CoV-2 and chronic HBV co-infection, and the values of ALT, 2 AST, TBIL, ALP and γ-GT increased substantially during hospitalization. 6 The present study reported evidence of liver injury in patients with SARS-CoV-2 7 and chronic HBV co-infection. These findings 9 indicate that liver injury in patients with SARS-CoV-2 and chronic HBV co-infection 10 was associated with disease severity and worse prognosis. cache = ./cache/cord-313627-g1iqhsdk.txt txt = ./txt/cord-313627-g1iqhsdk.txt === reduce.pl bib === id = cord-313265-lff5cajm author = Conway, Michael J. title = Identification of coronavirus sequences in carp cDNA from Wuhan, China date = 2020-03-16 pages = extension = .txt mime = text/plain words = 918 sentences = 61 flesch = 61 summary = Severe acute respiratory syndrome (SARS)‐like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. SARS-like virus sequences that were highly homologous to SARS-CoV-2 were identified in two separate complementary DNA (cDNA) pools. Tblastn analysis using this sequence identified two cDNA clones that were highly homologous to SARS-like coronaviruses. The first cDNA pool was made from Carassius auratus (crucian carp) blastulae embryonic cell line and contained a sequence of 152 amino acids that covered 2% of the SARS-CoV-2 genome and was 93.42% The second cDNA pool was made from Ctenopharyngodon idella (grass carp) head kidney and contained a sequence of 88 amino acids that covered 1% of the SARS-CoV-2 genome and was 93.18% identical. Protein and nucleic acid alignments of each cDNA clone were performed to compare with the most related coronavirus sequences (Figures 1 and 2) . cache = ./cache/cord-313265-lff5cajm.txt txt = ./txt/cord-313265-lff5cajm.txt === reduce.pl bib === id = cord-313571-umcbulcw author = Martínez-Murcia, Antonio title = In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1189 sentences = 85 flesch = 54 summary = title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. As the number of genomes available rapidly expanded during last January, the GPS™ CoVID-19 230 dtec-RT-qPCR Test was based on a more specific target for SARS-CoV-2 detection, being this 231 company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. cache = ./cache/cord-313571-umcbulcw.txt txt = ./txt/cord-313571-umcbulcw.txt === reduce.pl bib === id = cord-313415-5qrpucr4 author = Lai, Rongtao title = Sentinel surveillance strategies for early detection of coronavirus disease in fever clinics: experience from China date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1902 sentences = 107 flesch = 50 summary = During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. It is employed for discerning patients with suspected symptoms and signs, for timely isolation, for effectively blocking disease transmission during the early outbreak period before the pathogen has been identified, and for determining effective therapeutic methods; this strategy was used during the severe acute respiratory syndrome (SARS) epidemic in 2003 [2] . In the early outbreak period, the use of the sentinel surveillance strategy in fever clinics can provide benefits in terms of identifying patients with suspected symptoms, effectively blocking disease transmission, and protecting vulnerable populations. cache = ./cache/cord-313415-5qrpucr4.txt txt = ./txt/cord-313415-5qrpucr4.txt === reduce.pl bib === id = cord-313639-qpt47sx2 author = Zheng, Yi title = Clinical characteristics of 34 COVID-19 patients admitted to intensive care unit in Hangzhou, China date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3723 sentences = 191 flesch = 49 summary = OBJECTIVE: This study summarizes and compares clinical and laboratory characteristics of 34 patients admitted to the intensive care unit (ICU) for complications from coronavirus disease 2019 (COVID-19) at the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China from Jan. 22 to Mar. 5, 2020. For this retrospective study, we analyzed data from patients admitted between Jan. 22 and Mar. 5, 2020, who had been diagnosed (according to the guidance of NHC (2020a)) with SARS-CoV-2 pneumonia in the ICU in the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. In this single-center case series of 34 ICU patients with SARS-CoV-2 infection in Hangzhou, China, 97.1% (33 cases) of patients had complications caused by ARDS, 44.1% (15) received IMV, 55.9% (19) only needed noninvasive respiratory support. cache = ./cache/cord-313639-qpt47sx2.txt txt = ./txt/cord-313639-qpt47sx2.txt === reduce.pl bib === id = cord-313305-tih33rys author = Castro, Rodolfo title = COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil date = 2020-04-18 pages = extension = .txt mime = text/plain words = 838 sentences = 55 flesch = 54 summary = We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se=82% [76-87]; Sp=97% [96-98]; DOR=168 [92-305] and SROC=0.98 [0.96-0.99]; (ii) for IgG antibodies Se=97% [90-99]; Sp=98% [97-99]; DOR=1994 [385-10334] and SROC=0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se=97% [85-99]; Sp=99% [77-100]; DOR=2649 [30-233056] and SROC=0.99 [0.98-1.00]. The aim of this study was to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. Our study reports that antigen testing and/or molecular assays using nasopharyngeal and oropharyngeal specimens had high accuracy for SARS-CoV-2 detection. cache = ./cache/cord-313305-tih33rys.txt txt = ./txt/cord-313305-tih33rys.txt === reduce.pl bib === id = cord-313984-7wvfnag1 author = Remy, Kenneth E title = Immunotherapies for COVID-19: lessons learned from sepsis date = 2020-04-28 pages = extension = .txt mime = text/plain words = 2174 sentences = 108 flesch = 39 summary = Although more recent controlled studies indicate that plasma IL-6 concentrations can be in the range seen in bacterial infections, the time course of change is very different; in some cases, concentrations in patients with coronavirus disease 2019 (COVID-19) seem to increase over time with illness severity and worsening lung function. Indeed, when measured in patients infected with SARS-CoV-2, IL-10 concentrations (the most immunosuppressant cytokine in the body) are also elevated, which might lead to a different conclusion for therapeutic approaches and in understanding the disease pathophysiology. In particular, the modest inflammatory response and the progressive and profound suppression of adaptive immunity in COVID-19 relative to sepsis argues for perhaps a different therapeutic approach. However, if SARS-CoV-2 infection is similar to other chronic inflammatory and immune suppressive diseases, such as sepsis, we argue that immune stimulants, and not anti-inflammatory agents, should be considered as the first-line treatment option. cache = ./cache/cord-313984-7wvfnag1.txt txt = ./txt/cord-313984-7wvfnag1.txt === reduce.pl bib === id = cord-313489-i969aqn9 author = Galbadage, Thushara title = Does COVID-19 Spread Through Droplets Alone? date = 2020-04-24 pages = extension = .txt mime = text/plain words = 2342 sentences = 126 flesch = 50 summary = Social or physical distancing helps reduce the transmission of respiratory droplets containing SARS-CoV-2 and slows the incidence of the disease by reducing the opportunities for potential viral exposures. Precautions to prevent the spread by droplets as recommended by both the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) are to (1) wash hands with soap, (2) avoid touching viral entry points, such as eyes, nose, and mouth, (3) cover the mouth when coughing or sneezing, (4) wear a facemask if sick and (5) practice social distancing by putting 6 feet of distance between individuals. The ability of SARS-CoV-2 to remain viable longer on surfaces taken together with its higher virulence in establishing an infection makes it very likely that this coronavirus uses other modes of transmission in addition to respiratory droplets (Figure 1) . cache = ./cache/cord-313489-i969aqn9.txt txt = ./txt/cord-313489-i969aqn9.txt === reduce.pl bib === id = cord-313756-2pqpk3v7 author = De Vriese, An S. title = In Reply to ‘Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?’ date = 2020-06-27 pages = extension = .txt mime = text/plain words = 292 sentences = 25 flesch = 54 summary = key: cord-313756-2pqpk3v7 title: In Reply to 'Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?' cord_uid: 2pqpk3v7 In a small group of hemodialysis patients with confirmed SARS-CoV-2 infection, we reported that the presence of anti-SARS-CoV-2 IgG overlaps by several weeks with detectable viral RNA in the upper airways (1) . Viral load was highest during the first week of illness, suggesting that patients are most infectious during this period. It remains unclear whether the lower viral loads during the following weeks associate with a clinically relevant transmissibility of SARS-CoV-2 requiring further quarantining. We measured anti-SARS-CoV-2 IgG with a N protein-based ELISA (NovaLisa, NovaTec). Dudreuilh and Moutzouris suggest that the combination with a S protein-based assay may provide additional information. IgG Antibody Response to SARS-CoV-2 Infection and Viral RNA Persistence in Patients on Maintenance Hemodialysis Clinical performance of different SARS-CoV-2 IgG antibody tests cache = ./cache/cord-313756-2pqpk3v7.txt txt = ./txt/cord-313756-2pqpk3v7.txt === reduce.pl bib === id = cord-313541-fpqwzf9k author = Ulloa, S. title = A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date = 2020-08-22 pages = extension = .txt mime = text/plain words = 1776 sentences = 104 flesch = 55 summary = The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Thus, the four different media used in this study (UTM, PBS 1x solution, Hanks medium and DNA/RNA Shield TM ) did not affect analytical results, because all precipitated samples were able to be detected by rRT-PCR using the whole viral panel (Orf1ab, N and S genes) and the internal control gene. Here, a simple protocol to detect SARS-CoV-2 from NPSs using rRT-PCR after a heat inactivation and a precipitation/concentration step is proposed. cache = ./cache/cord-313541-fpqwzf9k.txt txt = ./txt/cord-313541-fpqwzf9k.txt === reduce.pl bib === id = cord-313537-920tgv1j author = Carbonell, Ana Piera title = Covid-19 y tromboprofilaxis: recomendaciones para nuestra práctica clínica en atención primaria date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2640 sentences = 268 flesch = 48 summary = Teniendo en cuenta que muchos de nuestros pacientes ya reciben terapia antitrombótica o anticoagulante, el hecho de que puedan desarrollar una infección por COVID-19 tendrá implicaciones para la elección, dosificación y control en associated with SARS-CoV-2 infection, increasing its severity and conferring a worse prognosis. La enfermedad producida por coronavirus SARS-CoV-2 (COVID19) , si bien en la mayoría de los pacientes infectados cursa con síntomas leves, en casos más severos puede progresar rápidamente y desarrollar un síndrome de dificultad respiratoria aguda, shock séptico, coagulopatía y disfunción endotelial, que son los determinantes principales de la afectación microvascular, al producir una mayor vasoconstricción, isquemia orgánica, inflamación con edema tisular asociado y un estado procoagulante que predispone a la enfermedad tromboembólica venosa (ETEV) y arterial. cache = ./cache/cord-313537-920tgv1j.txt txt = ./txt/cord-313537-920tgv1j.txt === reduce.pl bib === id = cord-313684-61hkogdh author = Samaddar, Arghadip title = Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date = 2020-09-17 pages = extension = .txt mime = text/plain words = 11700 sentences = 585 flesch = 42 summary = Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. cache = ./cache/cord-313684-61hkogdh.txt txt = ./txt/cord-313684-61hkogdh.txt === reduce.pl bib === id = cord-313458-ka02rsla author = Zhou, Yitian title = Single-cell transcriptional profile of ACE2 in healthy and failing human hearts date = 2020-09-01 pages = extension = .txt mime = text/plain words = 1695 sentences = 86 flesch = 46 summary = To explore the potential mechanisms contributing to this finding, we examined the expression of ACE2 in the different cells of the heart for heart samples from healthy individuals and heart failure patients and compared the results between these two groups. We found that the expression of ACE2 in cardiomyocytes was significantly increased compared to the other cells in the heart failure patients ( Figure 1L ). These results suggest that the cardiomyocytes of heart failure patients may be directly attacked by the virus and that this may contribute to the development of myocardial injury and severe conditions. We speculate that SARS-CoV-2 mainly attacks pericytes via ACE2, which leads to coronary microvascular disorder and myocardial injury in COVID-19 patients. This finding suggests that heart failure patients infected by the SARS-CoV-2 virus may suffer viral myocarditis and severe myocardial injury by direct attack on their cardiomyocytes. cache = ./cache/cord-313458-ka02rsla.txt txt = ./txt/cord-313458-ka02rsla.txt === reduce.pl bib === id = cord-313755-y7regza1 author = Mitra, Kartik title = Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5226 sentences = 285 flesch = 50 summary = Further, docking of these candidates against SARS-CoV-2 3CLp and PLp indicated that nelfinavir, tipranavir, novobiocin and ofloxacin, possessed better binding potential when compared to lopinavir (binding energy ¼ -7.3 kcal/mol). Our study suggests that nelfinavir and tipranavir (existing anti-HIV protease inhibitors) which bears the desired pharmacophoric features could be considered as potential candidates for inhibiting SARS-CoV-2 proteases. It is heartening to note that these natural products identified in the study have also shown in vitro anti-viral activity against several viruses and hence can be considered as potential lead candidates for designing SARS-CoV-2 inhibitors. The top two candidates with best docking binding energy were selected from the final shortlisted candidates, namely nelfinavir and tipranavir from FDA-approved drugs and licochalcone-D and wedelolactone from natural product database for molecular dynamics simulations studies with both the proteases. cache = ./cache/cord-313755-y7regza1.txt txt = ./txt/cord-313755-y7regza1.txt === reduce.pl bib === id = cord-313505-2lr4xara author = Resende, Paola Cristina title = Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1145 sentences = 99 flesch = 55 summary = title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. Introduction 59 COVID-19, the disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 60 (SARS-CoV-2), is leading to high rates of acute respiratory syndrome, hospitalization, and death 61 genomes (> 10% of ambiguous positions), we obtained a final dataset of 7,674 sequences. The prevalence of the sub-clade 211 B.1.1 in our sample (92%) was much higher than that observed in other Brazilian sequences 212 available in GISAID (36%) (Fig. 1C) phylogenetic tree, consistent with the hypothesis of multiple independent introductions (Fig. 2) (Fig. 2) . Revealing COVID-19 Transmission by SARS-CoV-2 Genome 410 Sequencing and Agent Based Modelling. cache = ./cache/cord-313505-2lr4xara.txt txt = ./txt/cord-313505-2lr4xara.txt === reduce.pl bib === id = cord-313460-oao2zppd author = D’Ardes, Damiano title = Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection date = 2020-05-11 pages = extension = .txt mime = text/plain words = 878 sentences = 57 flesch = 60 summary = title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection We describe the case of a 65-year-old woman who clinically recovered from COVID-19 but showed persistent infection with SARS-CoV-2 for 51 days. Although the patient had clinically recovered and had been transferred from our acute department to a unit for clinically stable patients, the nasopharyngeal swabs for SARS-CoV-2 continued to be positive until the end of April (swabs taken in mid-April, 22 April and 30 April), an interval of around 51 days from the onset of symptoms on 10 March. In contrast to the 15-20 days usually described as the average duration of mild COVID-19 disease, in this case we demonstrated SARS-CoV-2 positivity which lasted for over 50 days even though the patient was clinically well 2 weeks after the onset of symptoms. Positive RT-PCR test results in patients recovered from COVID-19 cache = ./cache/cord-313460-oao2zppd.txt txt = ./txt/cord-313460-oao2zppd.txt === reduce.pl bib === id = cord-313957-hviv5zar author = Masucci, Maria Grazia title = Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection date = 2020-08-01 pages = extension = .txt mime = text/plain words = 11747 sentences = 541 flesch = 37 summary = UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. cache = ./cache/cord-313957-hviv5zar.txt txt = ./txt/cord-313957-hviv5zar.txt === reduce.pl bib === id = cord-314025-h9gj814e author = Lai, Mary Y. Y. title = Survival of Severe Acute Respiratory Syndrome Coronavirus date = 2005-10-01 pages = extension = .txt mime = text/plain words = 3089 sentences = 159 flesch = 58 summary = SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. cache = ./cache/cord-314025-h9gj814e.txt txt = ./txt/cord-314025-h9gj814e.txt === reduce.pl bib === id = cord-314229-9k2dd95b author = Spaccaferri, G. title = Cas groupés d’infections au nouveau coronavirus (SARS-CoV-2) aux Contamines-Montjoie, Haute-Savoie, janvier–février 2020 date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1971 sentences = 212 flesch = 69 summary = Matériels et méthodes Un cas possible était défini comme tout patient présentant des signes cliniques d'infection respiratoire aiguë et ayant un lien avec le cas index ou avec un cas confirmé lié à ce cas index ; un cas confirmé était un cas possible avec un prélèvement positif par RT-PCR à SARS-CoV-2. Cinq autres touristes anglais ayant séjourné dans le chalet après le départ du cas index ont été en contact avec les cas confirmés symptomatiques : l'un d'eux a été confirmé positif à SARS-CoV-2 le 15/02, traduisant une seconde chaîne de transmission au sein du chalet ; aucun des 6 cas confirmés en France ne présentaient alors de signe de gravité. Introduction Peu de cas de COVID-19 chez des patients infectés par le VIH ont été rapportés dans la littérature. cache = ./cache/cord-314229-9k2dd95b.txt txt = ./txt/cord-314229-9k2dd95b.txt === reduce.pl bib === id = cord-313795-jr3n3uo9 author = McAuley, Julie L. title = Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date = 2020-11-02 pages = extension = .txt mime = text/plain words = 1411 sentences = 85 flesch = 56 summary = We investigated whether liquid chalk is an antiseptic against highly pathogenic human viruses including, SARS-CoV-2, influenza virus and noroviruses. We observed that addition of chalk before or after virus contact lead to a significant reduction on recovery of infectious SARS-CoV-2 and influenza but had little impact on norovirus. To further our study, we also tested the antiviral effect of Liquid Chalk against another 155 highly infectious and pathogenic respiratory viral pathogen IAV. 157 As can be observed in Figure 2 , all four Liquid Chalk products were effective in restricting the 158 recovery of IAV compared to SARS-CoV-2. transmission of SARS-CoV-2 (the 52 causative agent of the COVID-19 pandemic), influenza A virus (H1N1) (IAV) and norovirus, 53 using the surrogate model of mouse norovirus As a comparator, we also investigated the ability of Liquid Chalk to inactivate another 178 highly infectious viral pathogen, norovirus. cache = ./cache/cord-313795-jr3n3uo9.txt txt = ./txt/cord-313795-jr3n3uo9.txt === reduce.pl bib === id = cord-314124-yk4y0kea author = Tsou, Ian Y. title = Severe acute respiratory syndrome (SARS) in a paediatric cluster in Singapore date = 2003-08-20 pages = extension = .txt mime = text/plain words = 1955 sentences = 117 flesch = 55 summary = BACKGROUND: Severe acute respiratory syndrome (SARS) is a major infectious disease pandemic that occurred in early 2003, and one of the diagnostic criteria is the presence of chest radiographic findings. Severe acute respiratory syndrome (SARS) is a new form of atypical pneumonia, and is an infectious disease which has caused a pandemic with significant public health concerns. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Chest radiographic findings of a case of severe acute respiratory syndrome (SARS) in Singapore cache = ./cache/cord-314124-yk4y0kea.txt txt = ./txt/cord-314124-yk4y0kea.txt === reduce.pl bib === id = cord-314109-wb45naw2 author = Maiese, Kenneth title = The Mechanistic Target of Rapamycin (mTOR): Novel Considerations as an Antiviral Treatment date = 2020-06-17 pages = extension = .txt mime = text/plain words = 4134 sentences = 226 flesch = 35 summary = One such avenue that may prove to be exceedingly fruitful and offer exciting potential as new antiviral therapy involves the mechanistic target of rapamycin (mTOR) and its associated pathways of mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK). Recent work has shown that mTOR pathways in conjunction with AMPK may offer valuable targets to control cell injury, oxidative stress, mitochondrial dysfunction, and the onset of hyperinflammation, a significant disability associated with COVID-19. Considering that one of the mechanisms that can lead to severe disability and death during infection with SARS-CoV-2 is an exaggerated activation of the host's immune system that results in systemic hyperinflammation with the elevation of multiple pro-inflammatory cytokines, it is interesting to note that mTOR pathways have been tied to immune system modulation [40, 54, 55] . • The mechanistic target of rapamycin (mTOR) and its associated pathways with mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK) offer new avenues of opportunity for the development of innovative antiviral treatment strategies. cache = ./cache/cord-314109-wb45naw2.txt txt = ./txt/cord-314109-wb45naw2.txt === reduce.pl bib === id = cord-314013-g091lv0s author = Belladonna, Maria Laura title = Potential Benefits of Tryptophan Metabolism to the Efficacy of Tocilizumab in COVID-19 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2388 sentences = 119 flesch = 35 summary = Here, we briefly discuss the potentially multiple, synergistic mechanisms whereby tocilizumab might exert therapeutic activity, mostly focusing on the production of tryptophan-derived catabolites that would result from blockade of IL-6 signaling, as contextualized to the cytokine storm occurring in COVID-19 patients. If a cytokine storm occurs, the ensuing cytokine release syndrome (CRS) is typically associated with severe, rather than moderate, COVID-19, with an immunopathology being characterized by high serum levels of cytokines, CD4 + and CD8 + T (but not B) cell lymphopenia, diffused alveolar damage, pulmonary hypertension, pneumonia, and acute RDS (Pedersen and Ho, 2020) . COVID-19 is associated to a CRS referred as "cytokine storm" (A), whose reduction at lung level (the main target organ of SARS-CoV2 viral infection) may be achieved by TCZ therapy inhibiting IL-6 proinflammatory effect (B). TCZ treatment might restore a proper IDO1 activity, providing immunoactive Kyn as a ligand for AhR-dependent immune regulation, including the fostering of T-regulatory cell responses. cache = ./cache/cord-314013-g091lv0s.txt txt = ./txt/cord-314013-g091lv0s.txt === reduce.pl bib === id = cord-314070-8qz23nn4 author = Gubbi, Sriram title = Catecholamine physiology and its implications in patients with COVID-19 date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5313 sentences = 296 flesch = 31 summary = The risk factors for severe COVID-19 are diverse, yet closely resemble the clinical manifestations of catecholamine excess states (eg, hypertension, cardiovascular disease, immune dysregulation, and hyperglycaemia), suggesting a potentially common basis for disease. 6 Consequently, catecholamine excess states such as PPGL can cause substantial dysregulation of physiological systems, and lead to pronounced changes in pulmonary (vasoplegia), coronary (myocardial infarction), cerebro vascular (stroke), and remaining systemic vascular tone (hypertension), as well as myocardial disease (cardio myopathies), tachyarrhythmias (benign and fatal), hyper coagulability (thromboem bolism), immune dysreg u lation (cytokine storm), and diabetogenic states; these outcomes are the same as the risk factors that lead to adverse outcomes from COVID-19. 19 Increased concentrations of these cytokines and their downstream acute phase reactants (eg, ferritin) have been associated with a higher likelihood of severe disease and mortality in patients with 20 Catecholamines augment the production of IL-6, IL-10, and other cytokines through a self-amplifying feed-forward loop within myeloid cells, an effect mediated through α1-adrenoceptors. cache = ./cache/cord-314070-8qz23nn4.txt txt = ./txt/cord-314070-8qz23nn4.txt === reduce.pl bib === id = cord-314111-bqmfmcfm author = Yazdanpanah, Yazdan title = Les antirétroviraux ont-ils une place dans le traitement du syndrome respiratoire aigu sévère ? date = 2006-01-31 pages = extension = .txt mime = text/plain words = 1902 sentences = 180 flesch = 67 summary = Dans le traitement du syndrome respiratoire aigu sévère (SRAS) liés à severe acute respiratory syndrome-Coronavirus (SARS-CoV), l'évaluation de l'efficacité des anti-VIH était essentiellement motivée par l'absence d'alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Dans le traitement du SARS-CoV, l'évaluation de l'efficacité des anti-VIH, le virus pour lequel il existe le plus grand nombre de molécules, était essentiellement motivée par l'absence d'alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Compte tenu de ces observations, 2 hypothèses ont été proposées: l'interférence de l'infection par le VIH avec la réplication du SARS-CoV pouvant empêcher le développement du SRAS, et/ou un éventuel effet prophylactique des traitements antirétroviraux. Les auteurs ont observé un nombre significativement moins important de syndromes respiratoires aigus et de décès (2,4 %) chez 41 patients atteints de SRAS recevant dès l'admission un traitement par lopinavir/ritonavir (400/100 mg x 2/j) et ribavirine que dans une cohorte historique de 111 patients ayant reçu la ribavirine seule à leur admission (28,8 %). cache = ./cache/cord-314111-bqmfmcfm.txt txt = ./txt/cord-314111-bqmfmcfm.txt === reduce.pl bib === id = cord-313910-bwe2f7xf author = Bojadzic, Damir title = Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date = 2020-10-22 pages = extension = .txt mime = text/plain words = 7049 sentences = 346 flesch = 54 summary = Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. We were able to set up a cell-free ELISA-type assay to quantify the binding of SARS-CoV-2 S protein (as well as its SARS-CoV analog) to their cognate receptors (human ACE2) and used this to screen our existing in-house compound library containing a large variety of organic dyes and a set of colorless analogs prepared as potential SMIs for costimulatory PPIs. These maintain the main molecular framework of dyes but lack the aromatic azo chromophores responsible for the color as they are replaced with amide linkers (58, 59). cache = ./cache/cord-313910-bwe2f7xf.txt txt = ./txt/cord-313910-bwe2f7xf.txt === reduce.pl bib === id = cord-314072-av3r7it7 author = Liu, Zhuoming title = Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date = 2020-11-08 pages = extension = .txt mime = text/plain words = 1105 sentences = 74 flesch = 54 summary = title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans. To select for SARS-CoV-2 S variants that escape neutralization, we used VSV-SARSas we isolated this mutation alone, and acquisition of the L517R substitution appeared to 141 increase viral fitness as judged by plaque morphology (Fig S2) . cache = ./cache/cord-314072-av3r7it7.txt txt = ./txt/cord-314072-av3r7it7.txt === reduce.pl bib === id = cord-314135-udce22id author = Geisslinger, Franz title = Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? date = 2020-07-06 pages = extension = .txt mime = text/plain words = 6414 sentences = 379 flesch = 46 summary = The responsible virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causes the coronavirus disease 2019 (COVID-19), which is mainly characterized by fever, cough and shortness of breath. We summarize the available literature on COVID-19 suggesting an increased risk for severe disease progression in cancer patients, and we discuss the possibility that SARS-CoV-2 could contribute to cancer development. The main symptoms of COVID-19, the lung disease following SARS-CoV-2 infection are fever, cough, shortness of breath and respiratory distress syndrome with risk for septic shock. Preliminary evidence suggests that such a cytokine storm in response to infection with SARS-CoV-2 is a major factor, promoting severe COVID-19 progress and subsequently disease fatality [8, 12] . Chemotherapy-and radiation therapy-induced immunosuppression is a major risk factor for cancer patients to acquire a severe and probably fatal SARS-CoV-2 infection. Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: Relation to the acute lung injury and pathogenesis of SARS † cache = ./cache/cord-314135-udce22id.txt txt = ./txt/cord-314135-udce22id.txt === reduce.pl bib === id = cord-313805-6mnclfeg author = Suzuki, Yuichiro J. title = SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2299 sentences = 128 flesch = 56 summary = Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. Our results showing that SARS-CoV-2 spike protein is capable of activating the MEK/ERK pathway in pulmonary artery smooth muscle and endothelial cells suggest that cell growth signaling may be triggered in the pulmonary vascular walls in response to SARS-CoV-2. The major finding of this study is that the SARS-CoV-2 spike protein without the rest of the virus can elicit cell signaling, specifically the activation of the MEK/ERK pathway, in human host lung vascular smooth muscle and endothelial cells. cache = ./cache/cord-313805-6mnclfeg.txt txt = ./txt/cord-313805-6mnclfeg.txt === reduce.pl bib === id = cord-314051-dr27bsvt author = Lother, Sylvain A. title = Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3121 sentences = 259 flesch = 56 summary = If viral carriage is not detected by testing, patients may proceed with elective surgery whereby signs and symptoms of coronavirus disease (COVID-19) may arise in the postoperative period, leading to adverse outcomes. 3 While screening with RT-PCR may detect some presymptomatic preoperative patients, the window of diagnostic utility is small, and careful interpretation of negative and positive test results must be considered prior to altering the course of therapy. A positive RT-PCR result identifies a group of patients who may be infected with SARS-CoV-2 and should have elective surgeries delayed. Si la présence virale n'est pas dépistée par un test, les patients peuvent aller de l'avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d'une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. cache = ./cache/cord-314051-dr27bsvt.txt txt = ./txt/cord-314051-dr27bsvt.txt === reduce.pl bib === id = cord-313829-pjscmen8 author = Caballero, A.E. title = COVID-19 in people living with diabetes: An international consensus date = 2020-07-06 pages = extension = .txt mime = text/plain words = 4355 sentences = 252 flesch = 52 summary = The current clinical management of diabetes is a work in progress, requiring a shift in patient-provider interaction beyond the walls of clinics and hospitals: the use of tele-medicine when feasible, innovative patient education programs, strategies to ensure medication and glucose testing availability and affordability, as well as numerous ideas on how to improve meal plans and physical activity. It is difficult to predict but some indicators are available from the model of Harpreet In summary, while overall mortality due to COVID-19 is lower in India than in other countries, the elderly population, where most patients with diabetes, hypertension and CVD are concentrated, remains at high risk. Although it is clear that this option of care is not available to most people around the world, exploring how to improve the communication between providers and patients and families at home, in their own communities facing day to day challenges, may prove to be a more effective approach to managing the disease well beyond the COVID pandemic. cache = ./cache/cord-313829-pjscmen8.txt txt = ./txt/cord-313829-pjscmen8.txt === reduce.pl bib === id = cord-313728-08kwkbmd author = Binda, Barbara title = Follow-up and Management of Kidney Transplant Recipients During the COVID-19 Lockdown: the experience of an Italian Transplant Center, Including Two Cases of COVID-19 Pneumonia date = 2020-06-28 pages = extension = .txt mime = text/plain words = 3208 sentences = 170 flesch = 39 summary = Conclusion In the context of a lockdown, such as that occurring in response to COVID-19, we suggest implementing remote surveillance programs in kidney transplant recipients, with the help of any available technology, and offering medical consulting and logistic support as needed. In this article, we report the strategy implemented by our KT transplant center in Central Italy to maintain follow-up of KT recipients during the lockdown response to COVID-19. Both of our COVID-19 patients had several risk factors for an unfavorable outcome of the infection: chronic immunosuppression, advanced age, cardiovascular chronic disease and, in one case, diabetes. Consistent with this, we suggest implementing remote surveillance programs in fragile populations, such as transplant recipients, with the help of any available technology (e-mail, phone calls, video calls) as soon as possible, and offering medical consulting and logistic support as needed during the COVID-19 pandemic. Case report of COVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? cache = ./cache/cord-313728-08kwkbmd.txt txt = ./txt/cord-313728-08kwkbmd.txt === reduce.pl bib === id = cord-313754-f4sq45gy author = Wong, Chi-Yan title = Practice of habitual and volitional health behaviors to prevent severe acute respiratory syndrome among Chinese adolescents in Hong Kong date = 2005-03-31 pages = extension = .txt mime = text/plain words = 4713 sentences = 228 flesch = 43 summary = Abstract Purpose To explore factors relating to the practice of habitual and volitional health behaviors against the severe acute respiratory syndrome (SARS) among Chinese adolescents in Hong Kong. Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy). Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy) ( Table 1) . For volitional health behaviors of facemask-wearing to prevent SARS, environmental cues, practice of habitual health behaviors, and perceived threat were positive correlates (r ϭ .40, .38, and .27, respectively; p Ͻ .05). This study showed that among six components of the HBM, perceived threat and cues to action were more salient correlates of SARS preventive health behaviors among Chinese adolescents. cache = ./cache/cord-313754-f4sq45gy.txt txt = ./txt/cord-313754-f4sq45gy.txt === reduce.pl bib === id = cord-314102-8jf3fnqe author = Wu, Jie title = Advances in research on ACE2 as a receptor for 2019-nCoV date = 2020-08-11 pages = extension = .txt mime = text/plain words = 8322 sentences = 389 flesch = 47 summary = Although 2019-nCoV and SARS-CoV are very similar viruses genomically and structurally, the huge number of severe cases and deaths now being caused by 2019-nCoV infections has understandably prompted intense research on the receptor used by it to enter human cells. Angiotensin converting enzyme 2 (ACE2), a functional receptor for SARS-CoV, now appears likely to mediate 2019-nCoV entry into human cells. Some recent studies have suggested Cellular and Molecular Life Sciences * Xiuhong Yang yangxiuhong@ncst.edu.cn 1 that 2019-nCoV may infect host cells through the ACE2 receptor, as has already been established for SARS-CoV [7] [8] [9] [10] . In this review, the latest advances in our understanding of the roles played by ACE2 in enzyme catalysis, CoV invasion, cellular expression changes after viral-host cell binding, and its relationships with viral transmission and population susceptibility are described in the context of the pathogenesis of COVID-19. Therefore, it is speculated that like SARS-CoV, 2019-nCoV infects host cells via the mediating effects of its S protein and ACE2 receptors on the surfaces of human cells. cache = ./cache/cord-314102-8jf3fnqe.txt txt = ./txt/cord-314102-8jf3fnqe.txt === reduce.pl bib === id = cord-314381-ltil9hwl author = Cheng, Cecilia title = The psychology behind the masks: Psychological responses to the severe acute respiratory syndrome outbreak in different regions date = 2004-03-11 pages = extension = .txt mime = text/plain words = 2253 sentences = 112 flesch = 50 summary = The present paper proposes the influence of psychological factors on people's cognitive, affective, and behavioral responses during the SARS outbreak. Because SARS affected a number of regions, including people from both Asian and Western cultures, did individuals from different cultures perceive and cope with the crisis in distinct manners? These results suggest a link between general coping strategies and specific health behavior to avoid contracting SARS, which applies to people in areas that were and were not affected by SARS. This commentary, together with the five articles, provides valuable information on the ways in which people from different regions of the world responded affectively, cognitively, and behaviorally to the SARS outbreak. In conclusion, this special issue highlights the role of psychological factors in people's cognitive and behavioral responses to the SARS outbreak. cache = ./cache/cord-314381-ltil9hwl.txt txt = ./txt/cord-314381-ltil9hwl.txt === reduce.pl bib === id = cord-314445-4cb4a9r5 author = McNamara, Ryan P. title = High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1960 sentences = 131 flesch = 53 summary = This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. The current COVID-19 pandemic is an urgent public health emergency with over 112,000 deaths in the United States (U.S.) alone. At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 227 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 228 and coverage was more variable. In sum, this study generated exhaustive SNV information representing the introduction and 325 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 326 from symptomatic cases and the majority of genomes clustered with variants that predominate the 327 outbreak in the U.S., rather than Europe or China. cache = ./cache/cord-314445-4cb4a9r5.txt txt = ./txt/cord-314445-4cb4a9r5.txt === reduce.pl bib === id = cord-314679-lmfalzni author = Sangith, Nikhil title = Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions date = 2020-06-24 pages = extension = .txt mime = text/plain words = 585 sentences = 43 flesch = 43 summary = title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. aureus)coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. The role of the fibrinogen-binding motif of N-protein in formation of blood clots and 142 mimicking functions of Efb for pathogen survival in host will be investigated. Staphylococcus aureus secretes coagulase 187 and von Willebrand factor binding protein to modify the coagulation cascade and establish 188 host infections cache = ./cache/cord-314679-lmfalzni.txt txt = ./txt/cord-314679-lmfalzni.txt === reduce.pl bib === id = cord-314333-hkyiy1gm author = Nagata, Noriyo title = Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice date = 2008-06-30 pages = extension = .txt mime = text/plain words = 6908 sentences = 334 flesch = 52 summary = title: Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice Adult mice showed early and acute excessive proinflammatory responses (ie, cytokine storm) in the lungs after SARS-CoV infection, which led to severe pulmonary edema and diffuse alveolar damage. Because advanced age is associated with higher mortality in human SARS patients and SARS-CoV replicates better in aged mice, 6 -10,29 we experimentally infected 6-month-old (adult) female BALB/c mice with F-musX-VeroE6 or the Frankfurt 1 isolate. With regard to the cytokine responses of the mice, the lung homogenates of adult mice on day 1 after inoculation had significantly higher levels of monocyterelated chemokines [ie, MCP-1, macrophage inflammatory protein 1 (MIP-1), and IFN-␥-inducible protein 10 (IP-10)] than those from young mice ( Figure 5 ). cache = ./cache/cord-314333-hkyiy1gm.txt txt = ./txt/cord-314333-hkyiy1gm.txt === reduce.pl bib === id = cord-313344-rqvi2ksc author = Farcas, Gabriella A. title = Fatal Severe Acute Respiratory Syndrome Is Associated with Multiorgan Involvement by Coronavirus date = 2005-01-15 pages = extension = .txt mime = text/plain words = 2427 sentences = 104 flesch = 46 summary = Severe acute respiratory syndrome (SARS) is characterized by pulmonary compromise; however, patients often have evidence of other organ dysfunction that may reflect extrapulmonary dissemination of SARS coronavirus (SARS-CoV). The purpose of the present study was to investigate the presence of SARS-CoV, the degree of viral dissemination, and the viral loads in multiple organ samples from all patients who died of SARS during the Toronto outbreak (March to September 2003) and underwent a postmortem examination and compare the results with those found in patients who died of other causes during the outbreak. A total of 212 discrete postmortem organ samples, including lung, liver, spleen, kidney, small bowel, large bowel, lymph nodes, heart, and skeletal muscle, were prospectively collected from the 21 patients who died of SARS and underwent autopsies. cache = ./cache/cord-313344-rqvi2ksc.txt txt = ./txt/cord-313344-rqvi2ksc.txt === reduce.pl bib === id = cord-314489-e5r5s5ee author = Katsidzira, Leolin title = The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1948 sentences = 132 flesch = 57 summary = The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . cache = ./cache/cord-314489-e5r5s5ee.txt txt = ./txt/cord-314489-e5r5s5ee.txt === reduce.pl bib === id = cord-314663-8cf0jci9 author = Ampuero, M. title = SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results. date = 2020-07-03 pages = extension = .txt mime = text/plain words = 882 sentences = 68 flesch = 56 summary = This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. The goal of this study was to detect SARS-CoV-2 in sewage samples in Santiago, Chile. cache = ./cache/cord-314663-8cf0jci9.txt txt = ./txt/cord-314663-8cf0jci9.txt === reduce.pl bib === id = cord-314669-lvibjx97 author = Shang, Guifang title = Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 date = 2007-11-26 pages = extension = .txt mime = text/plain words = 4044 sentences = 186 flesch = 53 summary = title: Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 STUDY DESIGN AND METHODS: Case onset dates from the 2003 Shenzhen SARS epidemic and investigational results from Taiwan on viremia in humans are used to estimate the number of cases that were viremic throughout the epidemic. RESULTS: Based on data from Shenzhen, Hongkong and Taiwan, the maximum and mean risk (per million) of SARS-CoV transmission from donors in Shenzhen were estimated as 23.57 (95% CI: 6.83–47.69) and 14.11 (95% CI: 11.00–17.22), respectively. Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 Then, using this information and information on the asymptomatic or subclinical SARS-CoV infection-to-clinically confirmed SARS ratio (R), the proportion of infected individuals who remain asymptomatic (A), and the population size, we estimated the risk of SARS-CoV transmission by transfusion from a unit of blood donated at time t during the epidemic. cache = ./cache/cord-314669-lvibjx97.txt txt = ./txt/cord-314669-lvibjx97.txt === reduce.pl bib === id = cord-314107-x6e1jhcd author = Walker, M. title = SARS-CoV-2 Infection and Stroke: Coincident or Causal? date = 2020-07-29 pages = extension = .txt mime = text/plain words = 656 sentences = 44 flesch = 55 summary = Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Consistent with global reports, we observed a regional reduction in overall stroke volume during the COVID-19 pandemic peak. Surprisingly, less than 0.1% of patients suffered coincident SARS-CoV-2 infection and ischemic stroke. We also found no association between SARS-CoV-2 infection and stroke in younger patients. Similarly, a retrospective review in the UK during this same period [4] failed to identify a causal relationship in six patients with large vessel strokes and coincident SARS-CoV-2 infection because competing vascular risk factors were present. Regional data from five U.S. states suggests that among patients who sought care or were hospitalized during the peak of COVID-19, acute ischemic stroke in the setting of SARS-CoV-2 infection is rare and may be coincident. Large-Vessel Stroke as a Presenting Feature of Covid-19 in the Young cache = ./cache/cord-314107-x6e1jhcd.txt txt = ./txt/cord-314107-x6e1jhcd.txt === reduce.pl bib === id = cord-314687-kyj6etnc author = Gunalan, Vithiagaran title = A putative diacidic motif in the SARS-CoV ORF6 protein influences its subcellular localization and suppression of expression of co-transfected expression constructs date = 2011-10-25 pages = extension = .txt mime = text/plain words = 4918 sentences = 222 flesch = 45 summary = Following this, a mammalian expression plasmid pXJ3'-ORF6 was transfected into Vero E6 cells and Confocal microscopy showed that the ORF6 protein localized to a similar population of intracellular vesicles. These alanine substitution mutants were cloned into the same vector as the wildtype ORF6 gene and titrated against the nsp8 gene, by co-transfection of Vero E6 cells with plasmids encoding for myc-nsp8 and either 2 g pXJ3' ORF6 Figure 3 The ORF6 protein exerts a transcriptional effect on nsp8 expression. This indicated that the reduction in the suppression of the expression of co-transfected myc-nsp8 by ORF6A53-56 was significant, and therefore that the putative diacidic motif defined by amino acids 53-56 has a role to play in this ability of the ORF6 protein. This indicated that the putative diacidic motif from amino acids 53-56, in addition to being involved in the suppression of the expression of co-transfected myc-nsp8, is also involved in the subcellular localization of the ORF6 protein and therefore these 2 phenomena may be linked. cache = ./cache/cord-314687-kyj6etnc.txt txt = ./txt/cord-314687-kyj6etnc.txt === reduce.pl bib === id = cord-314024-n6l2804j author = Gonçalves, Antonio title = Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date = 2020-04-07 pages = extension = .txt mime = text/plain words = 2091 sentences = 130 flesch = 54 summary = We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We 162 considered a simple case where the drug effectiveness is assumed to be constant after therapy 163 initiation (see methods) and we calculated the minimal efficacy that would be needed to 164 generate more than 2 logs of viral decline at peak viral load in the 13 studied patients (Fig. 1) . For a putative 167 treatment initiated at the time of infection, symptom onset, or 3 days post symptom onset, a 168 median efficacy of at least 60, 90 and 99% in reducing viral replication would be needed, 169 respectively, to generate more than 2 log of decline in the peak viral load (Fig. 1) . cache = ./cache/cord-314024-n6l2804j.txt txt = ./txt/cord-314024-n6l2804j.txt === reduce.pl bib === id = cord-314311-xbpb9nfi author = Ge, Huipeng title = The epidemiology and clinical information about COVID-19 date = 2020-04-14 pages = extension = .txt mime = text/plain words = 5263 sentences = 325 flesch = 55 summary = In November 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong, China, and resulted in more than 8000 infections and 774 deaths in 37 countries. This review makes a comprehensive introduction about this disease, including the genome structure and receptor of SARS-CoV-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of COVID-19. The clinical manifestations of SARS-CoV-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. The COVID-19 patients around the world were diagnosed based on World Health Organization interim guidance [65] , and China updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in Chinese) according to epidemic situation and improved awareness of disease. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-314311-xbpb9nfi.txt txt = ./txt/cord-314311-xbpb9nfi.txt === reduce.pl bib === id = cord-314451-mqnqjn0c author = Roberts, Anjeanette title = A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice date = 2007-01-12 pages = extension = .txt mime = text/plain words = 9794 sentences = 433 flesch = 48 summary = To generate a model that satisfies these criteria, we have serially passaged SARS-CoV in the respiratory tract of young BALB/c mice, resulting in a lethal virus that causes dosedependent weight loss and mortality associated with higher viral titers in the respiratory tract than are seen with the wildtype virus and with histopathologic findings of severe pulmonary disease. Northern blot analysis of RNA from infected Vero E6 cells indicated that genomic vRNA and viral mRNA and all eight sub-genomic mRNAs were present in similar ratios for the recombinant viruses and MA15 virus as for SARS-CoV (Urbani) ( Figure 2A ). In order to evaluate whether changes in tissue tropism or levels of viral replication could contribute to the lethal phenotype of the MA15 virus, viral titers in lungs, spleen, liver, and brain of BALB/c mice were determined at various time points following intranasal inoculation with SARS-CoV (Urbani) or MA15. cache = ./cache/cord-314451-mqnqjn0c.txt txt = ./txt/cord-314451-mqnqjn0c.txt === reduce.pl bib === id = cord-314386-cxq9v218 author = Nitsche, Andreas title = SARS Coronavirus Detection date = 2004-07-17 pages = extension = .txt mime = text/plain words = 1904 sentences = 96 flesch = 55 summary = We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. To improve the ability to detect SARS-CoV safely and reduce the risk of eliciting false-negative results caused by genome sequence variations, we established three individual real-time RT-PCR assays. Target sequences were chosen by using the following criteria: 1) the regions are distributed over the whole genome, including the nonstructural polyprotein 1a and 1ab genes and the spike glycoprotein gene (Table 1) ; 2) the regions are highly conserved among the 89, 90, and 100 respective sequences available in public sequence databases; 3) the regions are suitable for the design of a real-time RT-PCR assay; and 4) the designed primers, 5′-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from http://www.ncbi.nlm.nih.gov/BLAST/). cache = ./cache/cord-314386-cxq9v218.txt txt = ./txt/cord-314386-cxq9v218.txt === reduce.pl bib === id = cord-314369-o4nis91y author = Lopez-Lopes, G. I. S. title = Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date = 2020-08-01 pages = extension = .txt mime = text/plain words = 3684 sentences = 211 flesch = 55 summary = Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. During the initial months of the COVID-19 swabs and other collection methods were used by LHW in the institute to identify SARS-Cov-2 RNA in upper respiratory tract, but occasionally throat wash (TW) was alternatively used. We compared the CT obtained at this survey to results generated from contemporary swab collections, sent as routine testing at the institute, that provide SARS-CoV-2 rtPCR testing to clinical services. The study did not compare the rate of positivity in paired samples, and only one individual was documented that performed both a swab test (negative) and a positive throat wash collection at a same day. The study suggests that throat wash may be a valid alternative to the detection of SARS-CoV-2 RNA. cache = ./cache/cord-314369-o4nis91y.txt txt = ./txt/cord-314369-o4nis91y.txt === reduce.pl bib === id = cord-314515-p40x3cxr author = NGAI, Jenny C. title = The long‐term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status date = 2010-03-19 pages = extension = .txt mime = text/plain words = 3506 sentences = 209 flesch = 57 summary = Methods: A prospective cohort study of SARS patients at the Prince of Wales Hospital, Hong Kong was conducted, with serial assessments of lung function, 6MWD and 36 item Short Form General Health Survey at 3, 6, 12, 18 and 24 months after disease onset. 1 3 Previous studies of survivors of acute lung injury and ARDS unrelated to SARS have shown variable degrees of residual abnormalities in pulmonary function, exercise capacity and impairment in health-related quality of life. 20, 21 The objectives of the present study were to evaluate the 2-year outcome of lung function, exercise capacity, health and work status of SARS survivors based on updated normative lung function data collected in Hong Kong (HK) from 2001-2003. This prospective cohort study has shown that 52% of SARS survivors had persistent impairment in DLCO and that exercise capacity and health status were significantly lower than the normal controls of the same age groups at 24 months post-illness. cache = ./cache/cord-314515-p40x3cxr.txt txt = ./txt/cord-314515-p40x3cxr.txt === reduce.pl bib === id = cord-314321-klb8oe9q author = Chen, Serena H. title = Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date = 2020-04-18 pages = extension = .txt mime = text/plain words = 3168 sentences = 174 flesch = 52 summary = Recent experimental structures of the SARS-CoV-2 S protein receptor binding domain (RBD) in complex with ACE2 provide detailed interface information [4] , [6] ; targeting this interface represents an active area of research for therapeutic development [11] . By first comparing the S protein protomer structure of SARS-CoV-2 to those from previous human coronaviruses, we identified distinct clusters for each virus in the 3-D latent space, where representative structures from these clusters highlight their differences in domain flexibility. To further understand the molecular structures of different human coronavirus S proteins and the oligomeric state of SARS-CoV-2 S protein, we deployed a custom-built deep learning architecture, a convolutional variational autoencoder (CVAE), to encode the high dimensional protein structures from the MD simulations into lower dimensional latent spaces. The size of each resulting matrix was also 191 ⇥ 191, and we merged a total of 10,000 distance matrices of the protomer and trimer of SARS-CoV-2 S protein. cache = ./cache/cord-314321-klb8oe9q.txt txt = ./txt/cord-314321-klb8oe9q.txt === reduce.pl bib === id = cord-314171-431buxxr author = Dariya, Begum title = Understanding novel COVID-19: its impact on organ failure and risk assessment for diabetic and cancer patients date = 2020-05-06 pages = extension = .txt mime = text/plain words = 6892 sentences = 421 flesch = 51 summary = In this review article, we have presented the effect of SARS-CoV-2 infection in comorbid patients and discussed organ failure caused by this virus. The mRNA and protein ACE2 expression levels are higher in these patients with cardiac disease, creating an increased risk for severe COVID-19 complications, including heart failure. After SARS-CoV-2 binds with ACE2, the virus degrades it, and thus the free angiotensin II induces acute lung injury [58] . Thus, targeting the binding site of the ACE2 receptor and SARS-CoV-2 with antibodies or therapeutic drugs might provide a successful treatment strategy. Moreover, this also increases the level of soluble ACE2 that competitively binds with SARS-CoV-2, causing delayed entry of the virus into cells and protecting against lung injury. The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 cache = ./cache/cord-314171-431buxxr.txt txt = ./txt/cord-314171-431buxxr.txt === reduce.pl bib === id = cord-314714-ehxxvenb author = Pang, Xiaocong title = Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1219 sentences = 74 flesch = 44 summary = title: Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication However, the addition of exogenous ACE2 could be a potential treatment for SARS-CoV-2 infection, which might not only restrain the spread of SARS-CoV-2 by blocking its interaction with ACE2 on the host cell, but also modulate RAS to treat SARS-CoV-2-related underlying comorbidities and protect the lung from developing ARDS. Although Ang II receptor and ACE blockage were also effective in lung failure in animal models, this treatment could cause potential adverse effects, causing systemic hypotension in humans [22] . Currently, phase I (NCT00886353) and phase II (NCT01597635) clinical studies with a recombinant version of the catalytic ectodomain of human ACE2 (GSK2586881) have been successfully completed, providing safety and efficacy for ARDS treatment [25, 26] . Recombinant human ACE2 and the angiotensin 1-7 axis as potential new therapies for heart failure A pilot clinical trial of recombinant human angiotensin-converting enzyme 2 in acute respiratory distress syndrome cache = ./cache/cord-314714-ehxxvenb.txt txt = ./txt/cord-314714-ehxxvenb.txt === reduce.pl bib === id = cord-314676-ndke9agh author = Gollapalli, Pavan title = Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 7090 sentences = 338 flesch = 51 summary = title: Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 The top hit molecules from this screening were then docked to the SARS-CoV-2 spike glycoprotein RBD-ACE2 interface, after which molecular dynamic simulations of the top scored compound and a reference ligand were performed to compare their binding affinities. To focus on the role of amino acid residues Asn501B and Tyr41A, we performed a docking simulation of the top 5 ligands at the interface of the spike glycoprotein RBD-hACE2 complex (amino acid residues were taken from PDBSum) by setting exhaustiveness to 100 (supplementary material, Table 7 and Figure 4) . The docking calculations at the spike glycoprotein RBD-hACE2 interface showed an even better binding energy and formation of H-bond interactions, and the detailed interaction analysis for the top 5 ligands is reported in Table 2 . cache = ./cache/cord-314676-ndke9agh.txt txt = ./txt/cord-314676-ndke9agh.txt === reduce.pl bib === id = cord-314662-nem6dw34 author = Nakra, Natasha A. title = Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management date = 2020-07-01 pages = extension = .txt mime = text/plain words = 5543 sentences = 299 flesch = 40 summary = Initial reports surfaced in the UK [3] and Italy [4] , followed by New York and other parts of the U.S. Preliminary accounts of the features of this syndrome resemble those of known entities such as Kawasaki Disease (KD), toxic shock syndrome (TSS), and secondary hemophagocytic lymphohistiocytosis (SHLH)/macrophage activation syndrome (MAS). Early consultation of specialists to assist in management, such as intensive care, cardiology, rheumatology, infectious diseases, allergy/immunology, neurology Abbreviations: ALT, alanine transaminase; AST, aspartate transaminase; pro-BNP, pro-B-type natriuretic peptide; BUN, blood urea nitrogen; CRP, C-reactive protein; CT, computed tomography; ESR, erythrocyte sedimentation rate; GI, gastrointestinal; HLH, hemophagocytic lymphohistiocytosis; IL, interleukin; MIS-C, multisystem inflammatory syndrome in children; NK, natural killer; NP, nasopharyngeal; PT, prothrombin time; PTT, partial thromboplastin time; RT-PCR, reverse transcriptase polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. cache = ./cache/cord-314662-nem6dw34.txt txt = ./txt/cord-314662-nem6dw34.txt === reduce.pl bib === id = cord-314572-1pou702r author = Lin, Ya-Hui title = Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date = 2016-10-14 pages = extension = .txt mime = text/plain words = 7182 sentences = 337 flesch = 47 summary = Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. In a first step to constructing a ligand-responsive −1 PRF stimulator, we designed Switch-0 RNA with a theophylline aptamer replacing the stem 3 of SARS-PK ( Figure 1A and C). We rationalized that such an engineered switch hairpin of reasonable stability (predicted free energy of −12.7 kcal/mole (37)) would be the dominant conformation that could interfere with the formation of pseudoknot stem 2 in the absence of theophylline (Supplementary Figure S2A) . To improve the dynamic range of ligand response and to see if theophylline aptamers can be functional while existing in both positive and negative regulators of −1 PRF, we fused previously designed theophylline-dependent upstream attenuator, theoOFF2 (24) with Switch-1 ( Figure 5A ) and examined theophylline-dependent −1 PRF activity in vitro. cache = ./cache/cord-314572-1pou702r.txt txt = ./txt/cord-314572-1pou702r.txt === reduce.pl bib === id = cord-314574-3e6u4aza author = Tian, Xiaolong title = Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody date = 2020-02-17 pages = extension = .txt mime = text/plain words = 1816 sentences = 88 flesch = 49 summary = Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3] , CR3014 [4] , CR3022 [5] , as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15] , and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)) . cache = ./cache/cord-314574-3e6u4aza.txt txt = ./txt/cord-314574-3e6u4aza.txt === reduce.pl bib === id = cord-314926-4bltio08 author = Ha, Le Dang title = Lack of SARS Transmission among Public Hospital Workers, Vietnam date = 2004-02-17 pages = extension = .txt mime = text/plain words = 2096 sentences = 99 flesch = 48 summary = The severe acute respiratory syndrome (SARS) outbreak in Vietnam was amplified by nosocomial spread within hospital A, but no transmission was reported in hospital B, the second of two designated SARS hospitals. Our study documents lack of SARS-associated coronavirus transmission to hospital B workers, despite variable infection control measures and the use of personal protective equipment. In conclusion, we found no evidence of SARS-CoV transmission among hospital B workers, despite contact with laboratory-confirmed SARS case-patients and variable infection control practices and use of personal protective equipment. This finding may be explained by differences in infection control practices, use of personal protective equipment (including masks for patients as well as healthcare workers), nursing style, environmental features, and clinical factors such as severity of illness and the absence of a highly infectious SARS-CoV spreader. cache = ./cache/cord-314926-4bltio08.txt txt = ./txt/cord-314926-4bltio08.txt === reduce.pl bib === id = cord-314933-wq1xo0z0 author = Zores, Florian title = COVID and the Renin-Angiotensin System: Are Hypertension or Its Treatments Deleterious? date = 2020-04-23 pages = extension = .txt mime = text/plain words = 3161 sentences = 172 flesch = 49 summary = In this paper, we hypothesize that the reductions in Angiotensin-Converting Enzyme 2 (ACE-2) observed in hypertension and obesity can explain many abnormalities observed in SARS-CoV-2 and question the role of treatments interfering with ACE2. Like SARS-CoV, SARS-CoV-2 fuses with human cells after the receptor-binding domain of its S (Spike) protein binds with Angiotensin-Converting Enzyme 2 (ACE-2), an enzyme located on membrane of lung alveolar epithelial cells, renal tubular epithelial cells, enterocytes of the small intestine, and arterial and venous endothelial cells of the kidney (5-10). ACE2, Angiotensin Converting Enzyme 2; ACEi, Angiotensin Converting Enzyme Inhibitor; ang-(1-7), Angiotensin-(1-7); ANGII, angiotensin II; ANGIV, angiotensin IV; ARB, Angiotensin Receptor Blocker; ARDS, Acute Respiratory Distress Syndrome; AT1R, Angiotensin II Type 1 Receptor; AT4R, Angiotensin II Type 4 Receptor; SARS-CoV-2, Severe Acute Respiratory Syndrome CoronaVirus 2. Thus, decreased ACE2 expression promotes increased lung injury and ARB prevents it by limiting ANGII binding to AT1R (7, 8, 24, 25) (Figure 1C) . cache = ./cache/cord-314933-wq1xo0z0.txt txt = ./txt/cord-314933-wq1xo0z0.txt === reduce.pl bib === id = cord-314793-kb319t4c author = Borroni, Barbara title = Diaphragmatic myoclonus due to SARS-CoV-2 infection date = 2020-10-22 pages = extension = .txt mime = text/plain words = 1636 sentences = 101 flesch = 47 summary = Neurological signs in patients with SARS-CoV-2 have been widely reported, suggesting a neuroinvasive nature of virus [2, 3] . With the present observation, we report two cases of diaphragmatic myoclonus as neurological subacute manifestation of SARS-CoV-2 infection. The Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10072-020-04766-y) contains supplementary material, which is available to authorized users. Electromyographic recording confirmed rhythmic and synchronous contractions of the diaphragm at 3-Hz frequency as the cause of her abdominal movements (see Fig. 1 ), thus making the diagnosis of diaphragmatic myoclonus or van Leeuwenhoek's disease [5] . Here, we draw attention to two patients who developed focal diaphragmatic myoclonus after SARS-CoV-2 infection. Indeed, three cases of generalized myoclonus due to SARS-CoV-2 infection have been recently reported [10] . With the present report of two cases, we confirm and extend the neurotropic properties of SARS-CoV-2 virus and point out to a further neurological clinical manifestation of the infection. cache = ./cache/cord-314793-kb319t4c.txt txt = ./txt/cord-314793-kb319t4c.txt === reduce.pl bib === id = cord-314833-6fue84x6 author = Chang, Chung-ke title = The SARS coronavirus nucleocapsid protein – Forms and functions date = 2014-01-11 pages = extension = .txt mime = text/plain words = 9459 sentences = 464 flesch = 51 summary = The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. proposed a structure-based domain arrangement for SARS-CoV N protein where the NTD and CTD are sandwiched between three IDRs. Sequence alignments suggested that other coronavirus N proteins might share the same structural organization based on intrinsic disorder predictor profiles and secondary structure predictions (Fig. 2) . noticed that effective binding to RNA by MHV N protein in host cells required the presence of both the NTD and CTD (Hurst et al., 2009) , suggesting that the NTD and CTD formed a single bipartite RNA interaction site, a feature to be reiterated in the final SARS-CoV RNP model. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-314833-6fue84x6.txt txt = ./txt/cord-314833-6fue84x6.txt === reduce.pl bib === id = cord-314798-n6oofe3i author = Stall, N. M. title = Sex-specific differences in COVID-19 testing, cases and outcomes: a population-wide study in Ontario, Canada date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1020 sentences = 68 flesch = 57 summary = In this population-wide study in Ontario, Canada we report on all 194,372 unique residents who received testing for SARS-CoV-2 between January 23, 2020 and April 28, 2020. This population-wide cohort study included all residents of Ontario, Canada who received a nasopharyngeal swab for SARS-CoV-2 between January 23, 2020 (date swab was performed for first reported case of COVID-19 in Canada) and April 28, 2020. We obtained data for this study from the Ontario Ministry of Health as part of the province's emergency "modeling table", including deidentified line level data on all SARS-CoV-2 testing via the Ontario Laboratories Information System (OLIS) and from the integrated Public Health Information System (iPHIS) for all reported COVID-19 cases and related clinical outcomes. We reported sex-and age-disaggregated data on SARS-CoV-2 testing, COVID-19 cases and related rates of hospitalization, intensive care unit (ICU) admission and death. cache = ./cache/cord-314798-n6oofe3i.txt txt = ./txt/cord-314798-n6oofe3i.txt === reduce.pl bib === id = cord-314796-bek92zs9 author = Hartung, Hans-Peter title = COVID-19 and management of neuroimmunological disorders date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1313 sentences = 82 flesch = 36 summary = The pathogen was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the diseasecoronavirus disease 2019 (COVID-19) -has caused the first recorded non-influenza pandemic. On the basis of their presumed mode of action and evidence from their use in patients, β-interferons, glatiramer acetate and teriflunomide are safe in COVID-19 because they do not cause relevant immunosuppression or increase the risk of viral infections. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. The complement-blocking mAb eculizumab, which is approved for treatment of NMOSD, has not been associated with an increased risk of viral infections. However, COVID-19 affects the management of patients with neurological diseases in many ways. cache = ./cache/cord-314796-bek92zs9.txt txt = ./txt/cord-314796-bek92zs9.txt === reduce.pl bib === id = cord-314942-eym2rh8v author = El Tabaa, Manar Mohammed title = New putative insights into neprilysin (NEP)-dependent pharmacotherapeutic role of roflumilast in treating COVID-19 date = 2020-10-01 pages = extension = .txt mime = text/plain words = 7634 sentences = 473 flesch = 48 summary = Being a highly selective phosphodiesterase-4 inhibitors (PDE4i), roflumilast acts by enhancing the level of cyclic adenosine monophosphate (cAMP), that probably potentiates its anti-inflammatory action via increasing neprilysin (NEP) activity. Because activating NEP was previously reported to mitigate several airway inflammatory ailments; this review thoroughly discusses the proposed NEP-based therapeutic properties of roflumilast, which may be of great importance in curing COVID-19. Additionally, breaking ET-1 by NEP will prolong the anti-inflammatory effect of 716 roflumilast via maintaining the high cAMP level which is underscored to play an 717 important role in improving the immune system of highly risk COVID-19 groups 718 (Graf et al., 1995; Raker et al., 2016) . Degrading ET-1 can also inhibit pulmonary fibrosis via blocking the ET-1-induced transforming growth factor-β1 (TGF-β1), and at the same time, maintain the high level of cAMP which may contribute for long-term anti-inflammatory effect of roflumilast. cache = ./cache/cord-314942-eym2rh8v.txt txt = ./txt/cord-314942-eym2rh8v.txt === reduce.pl bib === id = cord-314947-fy1lqk00 author = WU, Xiao Dong title = The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells date = 2004-10-17 pages = extension = .txt mime = text/plain words = 3908 sentences = 211 flesch = 60 summary = title: The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells In order to investigate the maturation and proteolytic processing of the S protein of SARS CoV, we generated S1 and S2 subunit specific antibodies (Abs) as well as N, E and 3CL protein-specific Abs. Our results showed that the antibodies could efficiently and specifically bind to their corresponding proteins from E.coli expressed or lysate of SARS-CoV infected Vero-E6 cells by Western blot analysis. When S2 Ab was used to perform immune precipitation with lysate of SARS-CoV infected cells, a cleaved S2 fragment was detected with S2-specific mAb by Western blot analysis. Furthermore, antibodies against S1, S2, N protein could detect their corresponding proteins from the lysates of SARS-CoV infected Vero E6 cells. To First, S2-specific mAb was directly used to detect native S2 fragment or full length of S protein in the lysate of SARS-CoV infected Vero E6 cells. cache = ./cache/cord-314947-fy1lqk00.txt txt = ./txt/cord-314947-fy1lqk00.txt === reduce.pl bib === id = cord-314880-0cfq52hn author = Meireles, Pedro Antunes title = Acalculous Acute Pancreatitis in a COVID-19 Patient date = 2020-05-13 pages = extension = .txt mime = text/plain words = 803 sentences = 53 flesch = 43 summary = An increase in pancreatic enzymes has been increasingly recognized in patients with COVID-19, but little is known about the real prevalence of acute pancreatitis in this population. We report a case of acute pancreatitis in a patient with SARS-CoV-2 infection. Liu et al [1] showed an increase in amylase and lipase in a series of 121 patients admitted with COVID-19 pneumonia, suggesting some degree of pancreatic injury in these patients. Similarly, Anand et al [3] have reported the case of a 59-year-old female patient who was diagnosed with acute pancreatitis based on typical abdominal pain and imaging findings 10 days after positive PCR-confirmed SARS-CoV-2 infection. The authors report a case of acute pancreatitis in a COVID-19 patient, highlighting the importance of considering SARS-CoV-2 as a new aetiological agent of acute viral pancreatitis. We suggest that pancreatic enzymes should be evaluated in COVID-19 in-patients presenting with gastrointestinal symptoms, since it could reveal unrecognized pancreatic involvement in this population. cache = ./cache/cord-314880-0cfq52hn.txt txt = ./txt/cord-314880-0cfq52hn.txt === reduce.pl bib === id = cord-314746-1o0rf0ii author = Bergasa-Caceres, Fernando title = Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 5038 sentences = 304 flesch = 56 summary = [Image: see text] In this article, we predict the folding initiation events of the ribose phosphatase domain of protein Nsp3 and the receptor binding domain of the spike protein from the severe acute respiratory syndrome (SARS) coronavirus-2. The identification of the primary contacts along the folding pathway of viral proteins constitutes an important result for at least two reasons: (a) the sequences of the specific segments involved in the primary contacts provide a template to specify candidate peptide drugs of inhibitory effect with the maximum possible contact affinity to compete with the natural folding mechanism; and (b) it provides insight for further investigation into the subsequent folding steps leading to a fully functional viral protein, potentially providing for additional FITRs. The fact that the primary contact is defined by the interaction between two well defined amino acid sequences suggests that a strategy to develop FITR-based therapeutic drugs could be one utilizing trial peptide drugs as suggested above. cache = ./cache/cord-314746-1o0rf0ii.txt txt = ./txt/cord-314746-1o0rf0ii.txt === reduce.pl bib === id = cord-314694-g0pes5o3 author = Cortiula, F. title = Managing COVID-19 in the oncology clinic and avoiding the distraction effect date = 2020-03-19 pages = extension = .txt mime = text/plain words = 1163 sentences = 69 flesch = 49 summary = The safety and management of cancer patients in the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is urgent and most cancer clinics need to establish a contingency plan. The authors suggest that postponing adjuvant chemotherapy or elective surgery for less aggressive cancers should be considered and that the increased risk for personal protection provisions should be emphasized for patients with cancer or cancer survivors. Furthermore, more intensive surveillance or treatment should be considered for those patients with cancer who are infected with SARS-CoV-2. Re-allocating an excessive amount of health care personnel, both nurses and doctors, to the COVID-19 triage and management may stretch an already fragile system and potentially leave uncovered some vital activities, such as treatment administration, surgeries and inpatient assistance. 5 Patients with advanced disease, and no suggestive symptoms of COVID-19, should keep receiving planned chemotherapy or radiotherapy treatment, without unnecessary delays. Risk of COVID-19 for patients with cancer cache = ./cache/cord-314694-g0pes5o3.txt txt = ./txt/cord-314694-g0pes5o3.txt === reduce.pl bib === id = cord-314734-ai0hz4uq author = Hung, Ivan Fan-Ngai title = SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: a case series date = 2020-06-12 pages = extension = .txt mime = text/plain words = 4595 sentences = 248 flesch = 56 summary = Thus, the Diamond Princess cruise ship, which was quarantined because of an onboard outbreak of COVID-19 in February, 2020, provides an opportunity to define the shedding pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient antibody responses before and after the onset of symptoms. Participants were prospectively screened by quantitative RT-PCR (RT-qPCR) of nasopharyngeal and throat swabs, and serum IgG and IgM against internal nucleoprotein and the surface spike receptor-binding protein (RBD) of SARS-CoV-2 at baseline (upon entering quarantine) and on days 4, 8, and 12 of quarantine. Evidence before this study We searched PubMed on March 14, 2020, with no date restrictions, for articles in English, using the terms "Covid-19", "coronavirus", "antibody", "viral load", "cruise ship", "quarantine", "shedding", and "seroconversion". By Feb 20, 2020, 76 passengers from Hong Kong were hospitalised in Japan after testing positive for SARS-CoV-2 by throat swab RT-PCR, of whom two individuals died from complications of the infection (appendix). cache = ./cache/cord-314734-ai0hz4uq.txt txt = ./txt/cord-314734-ai0hz4uq.txt === reduce.pl bib === id = cord-314948-7tnrfk24 author = Borrás, A title = Pandemia del SARS-CoV-2 y reproducción asistida date = 2020-06-19 pages = extension = .txt mime = text/plain words = 5419 sentences = 561 flesch = 53 summary = Estas medidas fueron cruciales no sólo para permitir hospitales e instalaciones médicas tratar el aumento explosivo de pacientes con la infección por SARS-CoV-2 (denominada COVID19) , sino también para reducir la transmisión de la enfermedad, mediante estrategias de mitigación, especialmente individuales (el aislamiento). Se sugiere que la presencia de ACE2 puede ser uno de los principales determinantes de la susceptibilidad de las células a la infección por SARS-CoV-2. Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida cache = ./cache/cord-314948-7tnrfk24.txt txt = ./txt/cord-314948-7tnrfk24.txt === reduce.pl bib === id = cord-314439-ufeiv47z author = Barkan, Elad title = Comparison of SARS-CoV-2 Exit Strategies Building Blocks date = 2020-04-28 pages = extension = .txt mime = text/plain words = 8597 sentences = 489 flesch = 60 summary = For example, our simulations indicate that dividing the population into two groups completely released except for taking turns on a long weekend (Fri-Tue) self-isolation once every two weeks, while protecting the 5% most sensitive population would reduce R below 1 even if ten percent of the population does not follow it. 1. Quick and accurate measure of actual coronavirus spread -as on average symptoms onset about 5.2 days after infection 30 , and households enter immediate self-isolation, immediate testing gives an accurate and near real-time measure of virus spread in the community, and could prevent the need for population survey-testing for the virus. We compare the efficiency of several key exit strategies building blocks, comparing how much they are efficient in stopping the epidemic in terms of R, while in relation to how effective they are the amount of average released business days they allow for the population. cache = ./cache/cord-314439-ufeiv47z.txt txt = ./txt/cord-314439-ufeiv47z.txt === reduce.pl bib === id = cord-314932-edf9xjwr author = Yan, Junqiang title = Research Progress of Drug Treatment in Novel Coronavirus Pneumonia date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2940 sentences = 161 flesch = 41 summary = Studies have found that 2019-nCoV is a single-stranded RNA beta coronavirus similar to SARS and MERS (12) , so current treatment is mainly based on the treatment experience of these two diseases (13) and further development of new targeted drugs. Currently, the drugs studied for the treatment of 2019-nCoV mainly include antivirals, antimalarials, glucocorticoids, plasma therapy, biological agents, and traditional Chinese medicine, among which lopinavir/ritonavir, ribavirin, remdesivir, chloroquine phosphate, and interferon are the main drugs. Recent studies have shown that chloroquine can inhibit 2019-nCoV by increasing the endosome pH required for viral cell fusion (26) , and its antiviral and antiinflammatory activity considerations are also involved (36) . New research shows that interferon-α nebulization, injection of interferon-α2b (57) , and α-interferon combined with lopinavir/ritonavir drugs (58) may be applicable to the current treatment of 2019-nCoV infection. Current studies have shown that the drug treatment of 2019-nCoV-related pneumonia mainly includes antivirals, antimalarials, and interferon. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro cache = ./cache/cord-314932-edf9xjwr.txt txt = ./txt/cord-314932-edf9xjwr.txt === reduce.pl bib === id = cord-314546-fbddxbhd author = Ko, Meehyun title = Comparative analysis of antiviral efficacy of FDA‐approved drugs against SARS‐CoV‐2 in human lung cells date = 2020-08-16 pages = extension = .txt mime = text/plain words = 1345 sentences = 83 flesch = 47 summary = Although nafamostat mesylate and camostat mesylate were not selected as potent antiviral drug candidates in our earlier study, we compared the antiviral efficacy of these drugs at this time in between Vero and Calu-3 cells following the discovery that TMPRSS2, a host protease necessary for priming viral spike glycoprotein, could be a target for COVID-19 antiviral development. 11 The discrepancy in IC 50 was specifically remarkable with nafamostat mesylate; the IC 50 decreased by approximately 6000 folds when the drug was used in the SARS-CoV-2-infected Calu-3 cells perhaps due to the dominant role of TMPRSS2-dependent viral entry in the Calu-3 human lung epithelial cells. In summary, we compared antiviral efficacy of the potential antiviral drug candidates against SARS-CoV-2 in between Vero and Calu-3 cells and found that nafamostat mesylate is the most potent antiviral drug candidate in vitro. Comparative analysis of antiviral efficacy of FDA-approved drugs against SARS-CoV-2 in human lung cells cache = ./cache/cord-314546-fbddxbhd.txt txt = ./txt/cord-314546-fbddxbhd.txt === reduce.pl bib === id = cord-315046-ltmuw6f8 author = Li, Keying title = SARS‐CoV‐2 infection‐induced immune responses: friends or foes? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 3390 sentences = 227 flesch = 47 summary = 6-7 SARS-COV-2-infected patients were observed to have massive accumulation of inflammatory cytokines and aberrant T cell responses compared to healthy individuals, providing evidence that COVID-19 may be an immune interrelated disease. [12] [13] So, viral RNA and S protein of SARS-related coronaviruses may have evolved as major PAMPs which can mediate innate immune signaling cascades, initiating an antiviral state in infected-cells. All rights reserved SARS-CoV-2-induced respiratory distress syndrome may involve deranged innate immune effector molecule production, abnormal elevation of inflammatory immune cells and cytokine storms. Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice▿ Response of Memory CD8+ T Cells to Severe Acute Respiratory Syndrome (SARS) Coronavirus in Recovered SARS Patients and Healthy Individuals cache = ./cache/cord-315046-ltmuw6f8.txt txt = ./txt/cord-315046-ltmuw6f8.txt === reduce.pl bib === id = cord-315056-ohyb6oa0 author = Xu, Juanjuan title = Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4426 sentences = 247 flesch = 50 summary = title: Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset This retrospective study presents the clinical, laboratory, and radiological profiles, treatments, and outcomes of atypical COVID-19 patients without respiratory symptoms or fever at onset. The study examined ten atypical patients out of 909 severe or critical patients diagnosed with COVID-19 in Wuhan Union Hospital West Campus between 25 January 2020 and 10 February 2020. Chest computed tomography (CT) scan and nucleic acid detection should be performed immediately on close contacts of COVID-19 patients to screen out those with atypical infections, even if the contacts present without respiratory symptoms or fever at onset. In this study, we aimed to describe the clinical, laboratory, and radiological characteristics, treatments, and outcomes of severe or critical COVID-19 patients who presented no respiratory symptoms or fever at onset. An atypical patient was defined as a patient with laboratory-confirmed COVID-19 but without characteristic fever or respiratory symptoms before hospital admission. cache = ./cache/cord-315056-ohyb6oa0.txt txt = ./txt/cord-315056-ohyb6oa0.txt === reduce.pl bib === id = cord-315337-vgi91uzg author = Mizutani, Tetsuya title = Characterization of Persistent SARS-CoV Infection in Vero E6 Cells date = 2006 pages = extension = .txt mime = text/plain words = 912 sentences = 63 flesch = 54 summary = A human intestinal cell line, LoVo, was shown to permit SARS-CoV infection, resulting in the establishment of persistent infection. This cell line expresses the viral receptor ACE-2 4 at high levels, and SARS-CoV infection of Vero E6 causes cytopathic effects within 24 h. In the present study, we established a persistently SARS-CoV-infected cell line after passage 6. Here, we reported a possible mechanism of the establishment of persistent SARS-CoV infection in Vero E6 cells (Fig. 2) . Although the majority of cells died due to apoptosis after SARS-CoV infection, activation of JNK and PI3K/Akt signaling pathways aided a minor population of cells with the potential to support persistent infection to establish persistence. pathways are required for establishing persistent SARS-CoV-infection in Vero E6 cells cache = ./cache/cord-315337-vgi91uzg.txt txt = ./txt/cord-315337-vgi91uzg.txt === reduce.pl bib === id = cord-315193-z6v6s46n author = Adhikari, Nilanjan title = Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date = 2017-07-14 pages = extension = .txt mime = text/plain words = 9954 sentences = 585 flesch = 59 summary = In the present report, quantitative structure-activity relationships (QSARs) techniques have been explored to understand the relation between the SARS-CoV 3CL pro and HRV 3C pro enzyme inhibitory activity with the physicochemical and structural properties of these inhibitors developed till now. (2008) reported some cinanserin analogs as SARS-CoV 3CL pro inhibitors (Table 11 .18), for which the QSAR model obtained was as shown by Eq. (2013b) reported a series of dipeptide-type SARS-CoV 3CL protease inhibitors (Table 11 .27) whose activity was shown to be controlled by the molar refractivity (CMR) and the polar volume (Pol Vol) of the compounds [Eq. QSAR models exhibited that the physicochemical parameters, such as dipole moment, PSA, polar volume, hydrophobicity, molar refractivity, SA, and molecular volume of the compounds play a crucial role in controlling both SARS-CoV 3CL pro and HRV 3C pro inhibitory activities. cache = ./cache/cord-315193-z6v6s46n.txt txt = ./txt/cord-315193-z6v6s46n.txt === reduce.pl bib === id = cord-315198-v4ay9kwg author = Siddiqui, Ruqaiyyah title = SARS-CoV-2: The Increasing Importance of Water Filtration against Highly Pathogenic Microbes date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1412 sentences = 78 flesch = 46 summary = Additionally, the frequent use of contaminated water for bathing, nasal irrigation, swimming, and ablution can be a risk factor in contracting infectious agents such as the brain-eating amoebae and possibly SARS-CoV-2. For example, the observation of primary amoebic meningoencephalitis due to brain-eating amoebae (i.e., Naegleria fowleri) is mostly unnoticed, especially in rural areas and disadvantaged communities, and is known to be associated with nasal irrigation for cleansing, ritual ablution, bathing, and swimming. Thus, the contamination of human waste as well as human wastewater into drinking water supplies highlights a major risk factor in contracting infectious agents such as brain-eating amoeba and possibly COVID-19, especially for developing countries. The use of simple tap water filters in households prior to ablution or nasal irrigation ( Figure 1E ,F) can be effective in eradicating microbial contaminants. cache = ./cache/cord-315198-v4ay9kwg.txt txt = ./txt/cord-315198-v4ay9kwg.txt === reduce.pl bib === id = cord-315288-fcx4q6mp author = Hussain, Mohammed Hassan title = Tracheal swab from front of neck airway for SARS-CoV-2; a bronchial foreign body date = 2020-08-27 pages = extension = .txt mime = text/plain words = 1566 sentences = 105 flesch = 62 summary = We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. Patients with front of neck airways, either in the form of a laryngectomy or tracheostomy stoma site, present a challenge in terms of testing for SARS-CoV-2. There is a need for clear guidance on how to test patients with front of neck airways for SARS-CoV-2. cache = ./cache/cord-315288-fcx4q6mp.txt txt = ./txt/cord-315288-fcx4q6mp.txt === reduce.pl bib === id = cord-315129-p31vm79o author = Bock, Jens-Ole title = Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3553 sentences = 181 flesch = 48 summary = title: Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. Here, we use the publicly available proteomics data from this study to re-analyze the in vitro cellular consequences of SARS-CoV-2 infection by impact pathways analysis and network analysis. Cellular factors exploited by SARS-CoV-2 to gain entry into cells have recently been studied, revealing that the virus uses the angiotensin-converting enzyme 2 (ACE2) host cell receptor, together with the serine protease TMPRSS2. Host cell proteomics studies that measure changes in protein abundance following viral entry and subsequent global pathway and network analysis can shed some light on the mechanisms that are used and/or altered by the virus and may reveal novel drug targets. cache = ./cache/cord-315129-p31vm79o.txt txt = ./txt/cord-315129-p31vm79o.txt === reduce.pl bib === id = cord-314960-f4hj35dr author = Kissler, Stephen M title = Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period date = 2020-03-06 pages = extension = .txt mime = text/plain words = 6253 sentences = 375 flesch = 52 summary = To quantify the relative contribution of immunity versus seasonal forcing on the transmission dynamics of the betacoronaviruses, we adopted a regression model (22) that expressed the effective reproduction number for each strain (HKU1 and OC43) as the product of a baseline transmissibility constant (related to the basic reproduction number and the proportion of the population susceptible at the start of the season), the depletion of susceptibles due to infection with the same strain, the depletion of susceptibles due to infection with the other strain, and a spline to capture further unexplained seasonal variation in transmission strength (seasonal forcing). https://doi.org/10.1101/2020.03.04.20031112 doi: medRxiv preprint infection due to SARS-CoV-2, and autumn establishments and smaller seasonal fluctuations in transmissibility were associated with larger pandemic peak sizes. Peak simulated SARS-CoV-2 epidemic sizes, in units of percent influenza-like illness (ILI) x percent positive laboratory tests, by year for a representative set of cross immunities, immunity durations, and establishment times. cache = ./cache/cord-314960-f4hj35dr.txt txt = ./txt/cord-314960-f4hj35dr.txt === reduce.pl bib === id = cord-315064-2mgv9j6n author = Escher, Felicitas title = Detection of viral SARS‐CoV‐2 genomes and histopathological changes in endomyocardial biopsies date = 2020-06-12 pages = extension = .txt mime = text/plain words = 3813 sentences = 241 flesch = 48 summary = Accordingly, we prospectively analysed endomyocardial biopsies (EMBs) from a cohort of 104 samples of patients with suspected myocarditis or unexplained heart disease for the presence of SARS-CoV-2 RNA by RT-qPCR and hints for histopathological injury. Up to 8 EMBs each of 104 patients [mean age: 57.90 ± 16.37 years; left ventricular ejection fraction (LVEF): 33.7 ± 14.6%, sex: n = 79 male/25 female] with suspected myocarditis or unexplained heart failure were analysed between 3 February and 26 March 2020 in German clinical centres in accordance with SARS-CoV2 spread in Germany. In this study, we established for the first time the evidence of SARS-CoV-2 genome detection in 5 of 104 EMBs of patients with suspected myocarditis or unexplained heart failure. Our finding of SARS-CoV-2 genome detection in EMBs of patients suffering from myocarditis/inflammatory cardiomyopathy cannot rule out or confirm the infection of cardiac cells but revealed incremental insights into organ-specific infection of SARS-CoV-2 using possibly macrophage migration as a shuttle from the lung to the heart. cache = ./cache/cord-315064-2mgv9j6n.txt txt = ./txt/cord-315064-2mgv9j6n.txt === reduce.pl bib === id = cord-314822-lmoc0xwi author = Flegel, Willy A. title = CoVID‐19 insights from transfusion medicine date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1746 sentences = 113 flesch = 52 summary = 5 The first analyses of patients with CoVID-19 in Wuhan, China did not report a substantial need for blood transfusion. In rapid reporting succession, patients with CoVID-19 infection have been documented to develop cold agglutinin disease, 11 the relatively more common autoimmune haemolytic anaemia 12, 13 or immune thrombocytopenia 14 and their combination as Evans syndrome. 23, 24 The safety profile has to be established, particularly for patients in early stage CoVID-19, where convalescent plasma, if safe, may be most effective. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and Transfusion Medicine: reflections from Italy Blood component use in critical care in patients with COVID-19 infection: a single centre experience Improved clinical symptoms and mortality on severe/critical COVID-19 patients utilizing convalescent plasma transfusion Relationship between ABO blood group distribution and clinical characteristics in patients with COVID-19 More on 'Association between ABO blood groups and risk of SARS-CoV-2 pneumonia' More on 'Association between ABO blood groups and risk of SARS-CoV-2 pneumonia' cache = ./cache/cord-314822-lmoc0xwi.txt txt = ./txt/cord-314822-lmoc0xwi.txt === reduce.pl bib === id = cord-315058-t7bq4yqw author = Brand, Samuel P C title = Forecasting the scale of the COVID-19 epidemic in Kenya date = 2020-04-14 pages = extension = .txt mime = text/plain words = 7568 sentences = 432 flesch = 49 summary = Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. In the scenario with no transmission from asymptomatics the observed epidemic was dominated by cases among the working-age population (Figure 3 ), who we estimated as having high rates of assortative (i.e. within same age-group) mixing ( Figure 4 ) and a small but not negligible risk of developing symptoms of COVID-19 after infection. In this modelling study we have integrated existing data on the social structure, and mobility, of the Kenyan population with rapidly evolving estimates of the fundamental epidemiology of SARS-CoV-2 so as to make the best possible prediction of the scale of the epidemic risk that Kenya faces from the first coronavirus pandemic. cache = ./cache/cord-315058-t7bq4yqw.txt txt = ./txt/cord-315058-t7bq4yqw.txt === reduce.pl bib === id = cord-314901-b18vy7dc author = Ali, Elrazi title = A Case of Fulminant Liver Failure in a 24-Year-Old Man with Coinfection with Hepatitis B Virus and SARS-CoV-2 date = 2020-10-13 pages = extension = .txt mime = text/plain words = 2164 sentences = 129 flesch = 47 summary = Patient: Male, 24-year-old Final Diagnosis: Acute kidney injury • coagulopathy • liver failure • SARS-CoV-2 Symptoms: Cough • fever Medication: — Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases OBJECTIVE: Unusual clinical course BACKGROUND: Coronavirus disease 2019 (COVID-19) is a newly emerging disease that is still not fully characterized. CONCLUSIONS: It is uncommon for SARS-CoV-2 infection with mild respiratory symptoms to result in severe systemic disease and organ failure. We report an unusual case of acute hepatitis B infection with concomitant SARS-CoV-2 leading to fulminant hepatitis, multiorgan failure, and death. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been a central health concern worldwide for the last 6 months. Similarly, patients with chronic liver disease, including patients with chronic hepatitis B infection co-occurring with SARS-CoV-2 infection, had more severe illness and poor outcomes [17] . Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection cache = ./cache/cord-314901-b18vy7dc.txt txt = ./txt/cord-314901-b18vy7dc.txt === reduce.pl bib === id = cord-315152-v3l33up6 author = Figlerowicz, Magdalena title = First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1701 sentences = 114 flesch = 57 summary = title: First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia We present the case of a six-year-old girl with severe COVID-19, in whom SARS-CoV-2 was successfully eliminated after convalescent plasma transfusion. In December 2019, a novel coronavirus disease (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) arose unexpectedly in China. In pediatric patients with a severe or critical course of COVID-19, acute respiratory distress syndrome (ARDS) can occur; toxic shock is also observed. Here, we present a case of using a J o u r n a l P r e -p r o o f convalescent plasma transfusion as a therapeutic method for severe pediatric COVID-19associated aplastic anemia. We present a case of using convalescent plasma in the therapy of a child with severe COVID-19. Effectiveness of convalescent plasma therapy in severe COVID-19 patients cache = ./cache/cord-315152-v3l33up6.txt txt = ./txt/cord-315152-v3l33up6.txt === reduce.pl bib === id = cord-315424-i3nnennw author = Willer, Brittany L. title = The otolaryngologist’s and anesthesiologist’s collaborative role in a pandemic: a large quaternary pediatric center’s experience with COVID-19 preparation and simulation date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2607 sentences = 145 flesch = 36 summary = Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be intimately familiar with strategies to mitigate the high-risk periods of viral contamination that are posed to the environment and healthcare personnel during tracheal intubation and extubation procedures. Since both the pediatric otolaryngologist and anesthesiologist are directly involved in emergency airway interventions, both specialties impact the safety of caring for COVID-19 patients and are a part of overall hospital pandemic preparedness. The pediatric otolaryngologist and anesthesiologist will encounter the COVID-19 patient in a variety of clinical settings (perioperative/operative, intensive care unit, emergency department, and radiology suite) and situations (emergent airway management, urgent or emergent surgical intervention, diagnostic or interventional radiology, and critical care resuscitation). Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be welleducated in and familiar with strategies to mitigate these high risk periods of viral contamination that are posed to the environment and healthcare personnel during endotracheal intubation and extubation procedures [9] . cache = ./cache/cord-315424-i3nnennw.txt txt = ./txt/cord-315424-i3nnennw.txt === reduce.pl bib === id = cord-315181-emf4i6ir author = Ryoo, Nayoung title = Coping with Dementia in the Middle of the COVID-19 Pandemic date = 2020-10-27 pages = extension = .txt mime = text/plain words = 7135 sentences = 400 flesch = 42 summary = • Home based exercise and planned outdoor activities, avoiding densely populated areas, with caregivers are encouraged • Have more organized daily plans that include enjoyable therapeutic activities • Create a new routine which fits within the context of the current circumstances • Prevent overuse or addiction to TV/video by scheduling and restricting daily use • Counselling for behavioural management of FTD via telephone hotlines is helpful • Providing self-help guidance for reducing stress through electronic media can result in beneficial effects for FTD patients ADL = activities of daily living, PPE = personal protective equipment, COVID-19 = coronavirus disease 2019, BPSD = behavioral and psychological symptoms of dementia, VD = vascular dementia, AD = Alzheimer's disease, FTD = frontotemporal dementia, ICU = intensive care unit, DLB = diffuse Lewy body. cache = ./cache/cord-315181-emf4i6ir.txt txt = ./txt/cord-315181-emf4i6ir.txt === reduce.pl bib === id = cord-315085-rucfowvv author = Sekulic, Miroslav title = Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5025 sentences = 302 flesch = 47 summary = In this study we report postmortem findings and detection and sequencing of SARS-CoV-2 viral RNA from formalin-fixed paraffinembedded (FFPE) samples of multiple organs collected in 2 patients with antemortem detection of SARS-CoV-2. The patient's medical history was otherwise notable for dementia, radiologic evidence of a left lung mass (managed with hospice care), coronary artery disease (status post coronary artery bypass grafting), atrial fibrillation (biventricular pacemaker implanted), congestive heart failure, peripheral artery disease (status post iliac stenting), diabetes mellitus, hypertension, dyslipidemia, chronic kidney disease, gout, smoking, cerebrovascular accidents, and urinary tract infections. On day 1 after admission, ❚Image 2❚ (Case 1) Postmortem microscopic examination of the lungs showed diffuse alveolar damage characterized by hyaline membrane formation (A, ×100) and scattered squamous metaplasia of distal airways (B, ×100) on a background of emphysematous changes. cache = ./cache/cord-315085-rucfowvv.txt txt = ./txt/cord-315085-rucfowvv.txt === reduce.pl bib === id = cord-314937-jrxu65bl author = Kuwelker, K. title = High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date = 2020-11-04 pages = extension = .txt mime = text/plain words = 5868 sentences = 391 flesch = 55 summary = The secondary attack rate of SARS-CoV-2 from index cases to household contacts reflects the natural spread of infection in immunologically naive populations with limited preventive measures to control transmission. Here, we estimated the secondary household attack rate of SARS-CoV-2 and identified the determinants of household transmission by measuring SARS-CoV-2-specific antibodies in household members of RT-PCR confirmed cases during the first month of the COVID-19 pandemic in Norway. Our study was specifically designed to assess household attack rates as measured by seropositivity in household members 6-8 weeks after onset of symptoms in the index case, with low prevalence of SARS-CoV-2 virus in the community. We calculated attack rates based on SARS-CoV-2-specific antibodies in household members, whereas the majority of previous studies have ascertained transmission based on RT-PCR, with estimates of 7·6% to 38% (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . cache = ./cache/cord-314937-jrxu65bl.txt txt = ./txt/cord-314937-jrxu65bl.txt === reduce.pl bib === id = cord-315289-4x229n8n author = Foresta, C. title = Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome date = 2020-09-16 pages = extension = .txt mime = text/plain words = 3417 sentences = 166 flesch = 43 summary = Although it is assumed that older men have more comorbidities than women of similar age, a tentative hypothesis to explain these epidemiologic findings is the role of the angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 engages ACE2 in alveolar epithelial On the top of the figure, epidemiological data from the Italian Ministry of Health are reported, with respective gender distribution of cases and deaths. The lack of increased ACE2 pool in men due to low estrogens would favor the ACE pathway (red arrows) in the RAS axis, which further promotes tissue injury and disease severity in men, compared with women with the same viral load cells as the entry receptor and employs the serine protease TMPRSS2 for S protein priming [8, 9] . Altogether, available evidence points toward two not-mutually exclusive mechanisms in differential gender susceptibility to COVID-19 by sex hormonal regulation of the two main actors in SARS-CoV-2 infection: ACE2 and TMPRSS2. cache = ./cache/cord-315289-4x229n8n.txt txt = ./txt/cord-315289-4x229n8n.txt === reduce.pl bib === id = cord-315453-mbv8vb2r author = Jean, Shio-Shin title = Old and re-purposed drugs for the treatment of COVID-19 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 3462 sentences = 169 flesch = 40 summary = EXPERT OPINION: Although strong evidence of well-designed randomized controlled studies regarding COVID-19 therapy is presently lacking, remdesivir, teicoplanin, hydroxychloroquine (not in combination with azithromycin), and ivermectin might be effective antiviral drugs and are deemed promising candidates for controlling SARS-CoV-2. In future, clinical trials regarding a combination of potentially effective drugs against SARS-CoV-2 need to be conducted to establish the optimal regimen for the treatment of patients with moderate-to-severe COVID-19. Recently, US Food and Drug Administration (FDA) approved the phase 3, double-blind ODYSSEY study (ClinicalTrials.gov Identifier: NCT04326426, initiated on 12 April 2020) to investigate the efficacy and safety of tradipitant at a dosage of 85 mg orally twice daily for the treatment of inflammatory lung injury following critical COVID-19 infection [35] . Apart from remdesivir that was shown to have acceptable clinical efficacy against moderate-to-severe COVID-19 and acceptable side effects, the potential antiviral drugs that are likely useful in the treatment of patients with mild-to-moderate COVID-19 included hydroxychloroquine, teicoplanin, and ivermectin. cache = ./cache/cord-315453-mbv8vb2r.txt txt = ./txt/cord-315453-mbv8vb2r.txt === reduce.pl bib === id = cord-315328-8g40ukml author = Clementi, Nicola title = Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2275 sentences = 115 flesch = 50 summary = In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In the current study, we assessed its anti-SARS-CoV-2 activity in vitro to give a preclinical background to clinical trials evaluating the possible therapeutic role of IFN-β-1a in patients with coronavirus disease 2019 (COVID-19). Vero E6 cells were treated with concentrations ranging from 5000 to 0.01 IU/mL of IFN-β-1a 1 hour after inoculation with SARS-CoV-2 and monitored for cytopathic effect and real-time-PCR quantitative evaluation at 48, 72, and 96 hours after infection. Our in vitro observations shed light for the first time on that antiviral activity of IFN-β-1a against SARS-CoV-2 when administered after the infection of cells, highlighting its possible efficacy in an early therapeutic setting. cache = ./cache/cord-315328-8g40ukml.txt txt = ./txt/cord-315328-8g40ukml.txt === reduce.pl bib === id = cord-315415-3aotsb2g author = Dong, Jianbo title = Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2 date = 2020-10-20 pages = extension = .txt mime = text/plain words = 7194 sentences = 427 flesch = 57 summary = In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19. (c) The binding of VHH-Fcs and ACE2 to Expi293 cells expressing SARS-CoV-2 S1 wild type (WT) or mutant proteins (del1-del5) were assessed by flow cytometry following FITC-conjugated secondary antibody treatment. Based on the binding and epitope binning data, we constructed 3D docking models that predicted the interactions between SARS-CoV-2 S1 RBD, ACE2 and lead VHH-Fcs (Fig. 2e) . Next, we tested whether the combination of individual VHHs binding to different S1 RBD epitopes into bi-specific antibody molecules would yield synergistic effects in SARS-CoV-2 binding and S/ACE2 blocking. cache = ./cache/cord-315415-3aotsb2g.txt txt = ./txt/cord-315415-3aotsb2g.txt === reduce.pl bib === id = cord-315278-iv2zj67t author = Moazzam, Zorays title = Intussusception in an infant as a manifestation of COVID-19 date = 2020-06-20 pages = extension = .txt mime = text/plain words = 2166 sentences = 137 flesch = 51 summary = This is the first documented case of survival in a SARS-CoV-2 positive patient presenting with intussusception as the primary manifestation. A case series from the UK documented 8 COVID-19 patients presenting with fever, abdominal pain and diarrhea with a working diagnosis of systemic sepsis secondary to suspected appendicitis [6] . According to our literature review, this is only the second such instance of a SARS-CoV-2 positive patient presenting to a healthcare center with intussusception as the primary manifestation, and the first documented case in which the patient survived. This would be the first such reported incidence of intussusception as a manifestation of SARS-CoV-2 infection, with no respiratory symptoms. We report, to the best of our knowledge, the first documented instance of survival in a case of intussusception in a SARS-CoV-2 positive pediatric patient. Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children cache = ./cache/cord-315278-iv2zj67t.txt txt = ./txt/cord-315278-iv2zj67t.txt === reduce.pl bib === id = cord-315411-11mq8wll author = Rahman, Mohammad Azizur title = Neurobiochemical Cross-talk Between COVID-19 and Alzheimer’s Disease date = 2020-10-19 pages = extension = .txt mime = text/plain words = 4116 sentences = 224 flesch = 41 summary = COVID-19 and AD share common links with respect to angiotensin-converting enzyme 2 (ACE2) receptors and pro-inflammatory markers such as interleukin-1 (IL-1), IL-6, cytoskeleton-associated protein 4 (CKAP4), galectin-9 (GAL-9 or Gal-9), and APOE4 allele. Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that attacks predominantly the human respiratory system and has also central nervous system (CNS) targeting and neuroinvasive capabilities [1, 2] . Among inflammatory markers, interleukin 6 (IL-6), interleukin 1 (IL-1), cytoskeleton-associated protein 4 (CKAP4), and galectin-9 (GAL-9 or Gal-9) had received most attention as the common links between COVID-19 and AD manifestations [18] (Fig. 1 ). Among its three alleles (ε2, ε3, and ε4), individuals carrying the ε4 allele are at a heightened risk of developing AD as the ApoE ɛ4/ɛ4 genotype increases fibrinogenesis in the brains of Alzheimer's disease patients [41] . cache = ./cache/cord-315411-11mq8wll.txt txt = ./txt/cord-315411-11mq8wll.txt === reduce.pl bib === id = cord-315388-8sv00zqz author = Ghosh, Ritwik title = Famotidine against SARS-CoV2: A hope or hype? date = 2020-06-06 pages = extension = .txt mime = text/plain words = 1097 sentences = 65 flesch = 40 summary = In the absence of a specific anti-viral or vaccine against the novel severe acute respiratory syndrome-corona virus (SARS-CoV2), "repurposing" of old time-tested medications are being tried. Through binding with H 2 R and modulating the effector pathways mediated by protein kinase A (PKA), famotidine potentially regulates innate and adaptive immune responses. Comparison of immunomodulative effects of the histamine-2 receptor antagonists cimetidine, ranitidine, and famotidine on peripheral blood mononuclear cells in gastric cancer patients Histamine Receptor 2 is Required to Suppress Innate Immune Responses to Bacterial Ligands in Patients with Inflammatory Bowel Disease The effect of histamine type 2 receptor antagonists on human immunodeficiency virus (HIV) replication: identification of a new class of antiviral agents A placebocontrolled trial of ranitidine in patients with early human immunodeficiency virus infection Effects of the H2-receptor antagonist famotidine on the pharmacokinetics of atazanavir-ritonavir with or without tenofovir in HIV-infected patients cache = ./cache/cord-315388-8sv00zqz.txt txt = ./txt/cord-315388-8sv00zqz.txt === reduce.pl bib === id = cord-315465-u3zq9k5j author = de Jesus, Myrela Conceição Santos title = Family COVID-19 cluster analysis of an infant without respiratory symptoms date = 2020-08-26 pages = extension = .txt mime = text/plain words = 1854 sentences = 107 flesch = 55 summary = Here, we report the case of a child with COVID-19 who attended an outpatient clinic in Aracaju, Northeast-Brazil, with gastrointestinal symptoms and no respiratory problems and the subsequent screening of his close family members. A 45-year-old asymptomatic uncle, who was unable to maintain social isolation due to work commitments had a positive nasopharyngeal/oropharyngeal RT-PCR assay result on 15th May 2020, but his IgM and IgG tests performed on the same day yielded negative results. This is a case report comprising a child with a chief complaint of diarrhea and the clinical history of his six contact family members during the 20 days prior to the onset of his symptoms. We also describe the clinical findings, molecular and serological assay results of the family members with whom he had been in contact up to 20 days before symptom onset. cache = ./cache/cord-315465-u3zq9k5j.txt txt = ./txt/cord-315465-u3zq9k5j.txt === reduce.pl bib === id = cord-315585-bjij8ds7 author = Wee, Liang En title = Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore date = 2020-05-08 pages = extension = .txt mime = text/plain words = 3960 sentences = 215 flesch = 50 summary = METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. 15 Here, we report our experience with a novel concept, a respiratory surveillance ward (RSW), which was introduced as a strategy for admission, triage and disposition of patients presenting with respiratory syndromes during a SARS-CoV-2 outbreak. Respiratory surveillance wards (RSWs): Admissions criteria, layout, infection control, and transfer criteria At our institution, high-risk patients that fulfilled suspect case criteria for COVID-19 were admitted to an isolation ward with 37 negative-pressure rooms. During an outbreak of SARS-CoV-2 with local transmission, an RSW to cohort all inpatients admitted from the community with respiratory symptoms may enhance case detection and reduce the potential of nosocomial transmission. cache = ./cache/cord-315585-bjij8ds7.txt txt = ./txt/cord-315585-bjij8ds7.txt === reduce.pl bib === id = cord-315576-bgcqkz0p author = Yamamoto, Naoki title = Apparent difference in fatalities between Central Europe and East Asia due to SARS-COV-2 and COVID-19: Four hypotheses for possible explanation date = 2020-08-05 pages = extension = .txt mime = text/plain words = 6114 sentences = 280 flesch = 51 summary = The comparison of the numbers of cases and deaths due to SARS-CoV-2 / COVID-19 shows that people in Central Europe are much more affected than people in East Asia where the disease originally occurred. Trying to explain this difference, this communication presents four hypotheses that propose the following reasons for the observed findings: 1) Differences in social behaviors and cultures of people in the two regions; 2) Possible outbreak of virulent viruses in Central Europe due to multiple viral infection, and the involvement of immuno-virological factors associated with it, 3) Possibility of corona resistance gene mutation occurring among East Asians as a result of long-term co-evolution of virus and host, and 4) possible involvement of hygienic factors. For the analysis of the difference regarding the number of infected people and the death tolls due to COVID-19 between Central European and East Asian 5 countries, we have chosen Italy, Spain, France, Germany and UK from Central Europe and China, South Korea, Japan, and Taiwan from South East Asia. cache = ./cache/cord-315576-bgcqkz0p.txt txt = ./txt/cord-315576-bgcqkz0p.txt === reduce.pl bib === id = cord-315760-9g8901v6 author = Teng, Xufei title = Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date = 2020-08-30 pages = extension = .txt mime = text/plain words = 3532 sentences = 182 flesch = 59 summary = Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. We have further examined the compositional subtleties among the clades and clusters with 304 a focus on G+C and purine content variability as both contents appear drifting toward optima 305 in SARS-CoV-2 and its relatives ( Figure 5C and 5D). cache = ./cache/cord-315760-9g8901v6.txt txt = ./txt/cord-315760-9g8901v6.txt === reduce.pl bib === id = cord-315498-gpzee1f2 author = Parkinson, N. title = Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date = 2020-09-01 pages = extension = .txt mime = text/plain words = 4964 sentences = 296 flesch = 46 summary = 2, 6, 7, 8, 9, 10 In this analysis we systematically identify and combine existing data from human betacoronavirus research to generate a comprehensive ranked list of host genes as a resource to inform further work on COVID-19. To identify existing literature which could provide informative datasets for host gene prioritisation, we conducted a systematic review of published studies and preprint manuscripts pertaining to host gene involvement in human betacoronavirus infection and associated disease. Results from identified studies, in the form of lists of implicated host factor genes, were combined using meta-analysis by information content (MAIC), 3 an approach we previously developed to identify host genes necessary for Influenza A virus (IAV) replication. Table 2 Candidate-gene human genetic studies < 5 hosts in virus group or control group in patient studies Meta-analyses, in silico anayses, re-analysis of data published elsewhere Potentially relevant pre-print manuscripts were identified by screening all papers categorised as COVID-19-related in the bioRxiv and medRxiv servers. cache = ./cache/cord-315498-gpzee1f2.txt txt = ./txt/cord-315498-gpzee1f2.txt === reduce.pl bib === id = cord-315283-xwan2t1u author = Ooi, Setthasorn Zhi Yang title = Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching date = 2020-09-15 pages = extension = .txt mime = text/plain words = 797 sentences = 56 flesch = 50 summary = title: Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. The Human Tissue Authority has also released a statement that medical schools in the UK (UK) are not allowed to receive body donations due to the SARS-CoV-2 virus outbreak [3] . In the upcoming academic years, incoming students of medical schools who practice cadaveric dissection teaching will miss out on the opportunity to learn anatomy through dissections. This letter aims to explore the implications of the cancellation of cadaveric dissection in anatomy teaching as a result of the SARS-CoV-2 virus pandemic. What does this mean for medical students at schools who traditionally teach anatomy through cadaveric dissections? cache = ./cache/cord-315283-xwan2t1u.txt txt = ./txt/cord-315283-xwan2t1u.txt === reduce.pl bib === id = cord-315448-bosazmlm author = Crawford, Katharine H D title = Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection date = 2020-09-30 pages = extension = .txt mime = text/plain words = 3872 sentences = 267 flesch = 54 summary = Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post symptom onset from a prospective cohort of 32 recovered individuals with asymptomatic, mild, or moderate-severe disease. Most of these studies have reported that over the first three months, antibodies targeting spike decline several fold from a peak reached a few weeks post symptom onset [5, 7, 19] , suggesting that the early dynamics of the antibody response to SARS-CoV-2 are similar to those for other acute viral infections. A c c e p t e d M a n u s c r i p t 5 Here we build on these studies by measuring both the neutralizing and binding antibody levels in serial plasma samples from 32 SARS-CoV-2-infected individuals across a range of disease severity with follow-up as long as 152 days post symptom onset. cache = ./cache/cord-315448-bosazmlm.txt txt = ./txt/cord-315448-bosazmlm.txt === reduce.pl bib === id = cord-315440-he7sm7nj author = Wassie, Gizachew Tadesse title = Incubation period of SARS-CoV-2: A systematic review and meta-analysis date = 2020-10-11 pages = extension = .txt mime = text/plain words = 3756 sentences = 232 flesch = 51 summary = Since there is no effective COVID-19 vaccine available yet, it is increasingly important to understand the average incubation period of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to design appropriate preventive and control strategies. Therefore, this systematic review and meta-analysis was designed to estimate the pooled average incubation period of SARS-CoV-2. We included peer-reviewed research studies written in the English language on the incubation period of SARS-CoV-2 using pre-defined quality and inclusion criteria. With regard to studies published in peer-reviewed journals or found in grey literature, all observational study designs (i.e. cross-sectional, case-control, and cohort), studies involving humans, and studies reporting the incubation period of SARS-CoV-2 were eligible for inclusion in this systematic review and meta-analysis. Studies with no accessible full text after using all the PRISMA-P search strategies and studies not reporting a specific incubation period for SARS-CoV-2 were excluded from this systematic review and meta-analysis. cache = ./cache/cord-315440-he7sm7nj.txt txt = ./txt/cord-315440-he7sm7nj.txt === reduce.pl bib === id = cord-315556-84rgd2s9 author = Pilotto, A. title = Steroid-responsive severe encephalopathy in SARS-CoV-2 infection date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2335 sentences = 176 flesch = 46 summary = SARS-CoV-2 infection has the potential for targeting central nervous system and several neurological symptoms have been described in patients with severe respiratory distress. Here we described the case of an otherwise healthy 60-year old subject with SARS-CoV-2 infection but only mild respiratory abnormalities who developed severe progressive encephalopathy associated with mild pleocytosis and hyperproteinorrachia. The patient dramatically improved after high-doses steroid treatment suggesting an inflammatory-mediated brain involvement related to SARS-CoV-2 infection Recently, a study posted in medRxiv4 and still unpublished has reported neurological manifestations in COVID-19 in the outbreak in China in up to 36.4% of patients hospitalized, including alteration of consciousness, headache, dizziness and delirium 6 . The here described COVID-19 case is of particular interest, as the patients presented with severe encephalopathy with only mild respiratory alterations. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. cache = ./cache/cord-315556-84rgd2s9.txt txt = ./txt/cord-315556-84rgd2s9.txt === reduce.pl bib === id = cord-315617-mhm9wh9q author = Gottschalk, René title = Bioterrorism: is it a real threat? date = 2004-09-02 pages = extension = .txt mime = text/plain words = 3326 sentences = 142 flesch = 43 summary = However, it is the developments over the past years that are causing the greatest concern: new threats to the security of nations are emerging in the form of terrorist organizations that seem to increasingly explore novel ways of spreading terror [1] . Terrorists will know that using highly infectious agents such as the smallpox virus for biological attacks might well mean their spread also to their own followers because they do not have smallpox vaccine or other preventative measures available. tuberculosis, Nipah virus) Third highest priority agents include emerging pathogens that could be engineered for mass dissemination in the future because of: -availability -ease of production and dissemination -potential for high morbidity and mortality rates and major health impact in the aftermath of the 2001 anthrax attacks, with numerous letters allegedly containing B. cache = ./cache/cord-315617-mhm9wh9q.txt txt = ./txt/cord-315617-mhm9wh9q.txt === reduce.pl bib === id = cord-315652-hct9yh3n author = Wehbe, Zena title = Molecular Insights Into SARS COV-2 Interaction With Cardiovascular Disease: Role of RAAS and MAPK Signaling date = 2020-06-03 pages = extension = .txt mime = text/plain words = 6560 sentences = 372 flesch = 41 summary = As such, a thorough understanding of the signaling pathways common to the pathogenesis of CVD and SARS-CoV-2 infection is necessary to identify crucial sites of crosstalk and direct future investigation of potential therapeutic interventions mitigating both COVID-19 complications in CVD patients as well as short-and long-term viral-induced cardiovascular impairment. The chronic nature and gradual development timeframe of these diseases might argue that the crosstalk among increased MAPK signaling cascades and SARS-CoV-2 pathogenesis leads to increased infection severity and complications in patients with established CVD rather than being involved in viraltriggered cardiovascular involvement. This raises the possibility for a beneficial effect of eplerenone or other aldosterone receptor antagonists in reducing risk of severe COVID-19 infection in CVD patients or to mitigate the cardiovascular burden of SARS-CoV-2 infection. cache = ./cache/cord-315652-hct9yh3n.txt txt = ./txt/cord-315652-hct9yh3n.txt === reduce.pl bib === id = cord-315666-ngozukzj author = Altundag, Aytug title = Olfactory Cleft Measurements and COVID-19–Related Anosmia date = 2020-10-13 pages = extension = .txt mime = text/plain words = 4278 sentences = 231 flesch = 54 summary = OBJECTIVE: This study aimed to investigate the differences in olfactory cleft (OC) morphology in coronavirus disease 2019 (COVID-19) anosmia compared to control subjects and postviral anosmia related to infection other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RESULTS: This study showed 3 major findings: the right and left OC widths were significantly wider in anosmic patients due to SARS-CoV-2 (group 1) or OD due to non–SARS-CoV-2 viral infection (group 2) when compared to healthy controls. Exclusion criteria for groups 1 and 2 were age younger than 18 years, pregnancy, normosmia detected on Sniffin' Sticks olfactory test (a threshold discrimination identification [TDI] score of .30.5), acute and/or chronic rhinosinusitis or other acute/chronic nasal disease, nasal polyposis, allergic or idiopathic rhinitis, posttraumatic olfactory loss, severe turbinate hypertrophy or nasal septum deviation affecting the air passage, malignancy history, and a history of nasal or paranasal surgery. cache = ./cache/cord-315666-ngozukzj.txt txt = ./txt/cord-315666-ngozukzj.txt === reduce.pl bib === id = cord-315637-7td617dm author = Rothe, M. title = A systematic review of mask disinfection and reuse for SARS-CoV-2 date = 2020-11-12 pages = extension = .txt mime = text/plain words = 3849 sentences = 234 flesch = 53 summary = However, results show it is possible to achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) disinfection on N95 masks. However, results did show that it is possible to 160 achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical 161 (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) 162 disinfection. Given the wide differences in test conditions, results are 185 summarized by disinfection agent for N95s only, for agents with >5 samples or those agents identified in 186 the disinfection efficacy section as achieving >3 log reduction of SARS-CoV-2, including ethanol, 187 hydrogen peroxide, peracetic acid, PX-UV, UVGI, autoclaving, and heat. cache = ./cache/cord-315637-7td617dm.txt txt = ./txt/cord-315637-7td617dm.txt === reduce.pl bib === id = cord-315730-fzgxuak7 author = Penman, Sophie L. title = Safety perspectives on presently considered drugs for the treatment of COVID‐19 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 12067 sentences = 627 flesch = 42 summary = Owing to their efficacy against viruses (mostly demonstrated in vitro) including influenza, HIV, coronavirus OC43, and SARS-CoV, a large number of clinical trials (>230) have been registered worldwide using chloroquine/hydroxychloroquine alone, or in combination with other drugs (e.g. azithromycin) for the treatment of COVID-19. At the time of writing, the RECOVERY trial (clinical trial identifier NCT04381936) which is the largest randomised control trial so far conducted for the treatment of COVID, has stopped recruiting to the hydroxychloroquine arm (1542 patients compared with 3132 on standard care) because of no beneficial effect either in terms of mortality or hospital stay (P. Assessment of QT Intervals in a Case Series of Patients With Coronavirus Disease 2019 (COVID-19) Infection Treated With Hydroxychloroquine Alone or in Combination With Azithromycin in an Intensive Care Unit Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-315730-fzgxuak7.txt txt = ./txt/cord-315730-fzgxuak7.txt === reduce.pl bib === id = cord-315604-a6fvsd45 author = Maurya, Santosh K. title = Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 3219 sentences = 198 flesch = 55 summary = title: Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. HIGHLIGHTS: NSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs. Hydrophobic interaction successfully delineates specific functional groups that may be responsible for the hydrophobic generating effect of these compounds with strong binding affinity against target proteins and may play a highly influencing against SARS-CoV-2 infection All the compounds showed good binding free energy with their respective proteins of SARS-CoV-2. In this study, it has been shown that selected screened compounds have good docking score, high DG binding free energy as well as strong hydrophobic interactions, and follows the Lipinski rule of five. cache = ./cache/cord-315604-a6fvsd45.txt txt = ./txt/cord-315604-a6fvsd45.txt === reduce.pl bib === id = cord-315685-ute3dxwu author = Ehaideb, Salleh N. title = Evidence of a wide gap between COVID-19 in humans and animal models: a systematic review date = 2020-10-06 pages = extension = .txt mime = text/plain words = 5542 sentences = 352 flesch = 48 summary = The systematic search identified 101 studies and 326 preprints, of which 400 articles were excluded because they were reviews, non-original articles, unrelated to the COVID-19 infection, or experimental animals that do not support SARS-CoV-2 replication such as pigs, ducks, and chickens ( Fig. 1 and Additional file 2). The aims were to investigate the pathogenesis of COVID-19 (n = 15), testing drugs and vaccines (n = 14), the host Table 1 Search strategy and selection criteria We searched the MEDLINE, as well as BioRxiv and MedRxiv preprint servers for original research describing or using an animal model of SARS-CoV-2 induced COVID published in English from January 1, 2020, to May 20, 2020. We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). cache = ./cache/cord-315685-ute3dxwu.txt txt = ./txt/cord-315685-ute3dxwu.txt === reduce.pl bib === id = cord-315632-29x6l5yh author = Rali, Aniket S title = High-flow Nasal Cannula Oxygenation Revisited in COVID-19 date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1098 sentences = 60 flesch = 48 summary = A case series of 138 COVID-19 patients from Wuhan, China showed that a total of 36 (26%) patients required ICU level care, of whom 22 (61%) developed ARDS and 17 (47.2%) required invasive mechanical ventilation. 1 Other retrospective analyses have reported similarly that 20-31% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients develop ARDS and require ICU care. [2] [3] [4] Therefore, it is critical that we explore the utility and safety of other forms of respiratory support devices, including high-flow nasal cannula oxygenation (HFNCO) in the treatment of acute respiratory failure. 4 We present a case of a SARS-CoV-2-positive patient with acute respiratory failure who was successfully treated with HFNCO. On day 3, his hypoxic respiratory failure worsened, requiring high-flow nasal cannula at 40 l/min and 90% fractional inspired oxygen, (FiO 2 ) and he was transferred to the medical ICU. Beneficial effects of humidified high flow nasal oxygen in critical care patients: a prospective pilot study cache = ./cache/cord-315632-29x6l5yh.txt txt = ./txt/cord-315632-29x6l5yh.txt === reduce.pl bib === id = cord-315462-u2dj79yw author = Hewitt, Judith A. title = ACTIVating Resources for the COVID-19 Pandemic: In vivo Models for Vaccines and Therapeutics date = 2020-10-01 pages = extension = .txt mime = text/plain words = 8953 sentences = 469 flesch = 44 summary = The selection of appropriate animal models of infection, disease manifestation, and efficacy measurements is important for vaccines and therapeutics to be compared under ACTIV's umbrella using Master Protocols with standardized endpoints and assay readouts. Models of SARS-CoV-2 infection include mice (ACE2 transgenic strains, mouse adapted virus, and AAV transduced ACE2 mice), hamsters, rats, ferrets and non-human primates (NHPs). Following infection by the intranasal route, golden Syrian Hamsters demonstrate clinical features, viral kinetics, histopathological changes, and immune responses that closely mimic the mild to moderate disease described in human COVID-19 patients (Chan et al., 2020b; Imai et al., 2020; Sia et al., 2020) . In an initial study of SARS-CoV-2 infection of hACE2-hamsters, clinical signs were observed including elevated body temperatures, slow or reduced mobility, weight loss and mortality (1 out of 4 animals). Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease. cache = ./cache/cord-315462-u2dj79yw.txt txt = ./txt/cord-315462-u2dj79yw.txt === reduce.pl bib === id = cord-315931-kc8gnj6z author = Klempt, Petr title = Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4812 sentences = 224 flesch = 49 summary = During the first attempt, thirty libraries (including 4 positive and 2 negative controls) were prepared in three plexes (10 samples each, see Supplementary Table S1 ) employing NEBNext ® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) followed by capture-based workflow utilizing the Twist SARS-CoV-2 Research Panel (Twist Bioscience). Compare to NEB+TWIST the capture-based Illumina approach data showed in average a lower percentage of mapped reads (Supplementary Table S1 ), this consequence could be related to the lower specificity of Respiratory Oligo Viral Panel designed next to the SARS-CoV-2 also for other pathogens (see https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/ngsenrichment-coronavirus-app-note-1270-2020-002.pdf). Also, the viral load in a sample (corresponding to sample Ct value ≤ 23.29 or positive control value ≤ 25.84) showed to be the limiting factor in case of each workflow, samples with higher Ct value resulted in either poor genome coverage (NEB+Twist workflow and Illumina workflow) or in absence of expected library preparation product (Paragon workflow). cache = ./cache/cord-315931-kc8gnj6z.txt txt = ./txt/cord-315931-kc8gnj6z.txt === reduce.pl bib === id = cord-315866-6vcts4w3 author = Chan, KC Allen title = Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study date = 2005-04-09 pages = extension = .txt mime = text/plain words = 2555 sentences = 137 flesch = 50 summary = title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Therefore, in this study, we investigated the association of the ACE insertion/deletion (I/D) polymorphism of the 287 bp Alu repeat to the susceptibility to SARS and the development of adult respiratory distress syndrome (ARDS) with a larger population. The genotypic distributions and allelic frequencies of ACE I/D polymorphism in the SARS patients and control subjects are shown in table 2. cache = ./cache/cord-315866-6vcts4w3.txt txt = ./txt/cord-315866-6vcts4w3.txt === reduce.pl bib === id = cord-315849-e16lln3f author = Takayama, Kazuo title = In vitro and Animal Models for SARS-CoV-2 research date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1167 sentences = 94 flesch = 54 summary = An in vitro cell model for SARS-CoV-2 research is essential for understanding the viral life cycle, for amplifying and isolating the virus for further research and for preclinical evaluation of therapeutic molecules. This section lays out the cell lines used to replicate and isolate SARS-CoV-2, as well as organoids that can be used to examine the effects of SARS-CoV-2 infection on specific human tissues (Table 1A, Figure 1 ). They showed that their organoids were permissive to the SARS-CoV-2 infection and could evaluate anti-viral effects of COVID-19 candidate therapeutic compounds including camostat [17] . who conducted SARS-CoV-2 infection experiments using HeLa cells that expressed ACE2 proteins taken from multiple animal species from mice to humans [11] . The team found that such mice after SARS-CoV-2 infection, showed weight loss, virus replication in the lungs, and interstitial pneumonia [25] . Human ACE2 transgenic mice After SARS-CoV-2 infection, the mice show weight loss, virus replication in the lungs, and interstitial pneumonia. cache = ./cache/cord-315849-e16lln3f.txt txt = ./txt/cord-315849-e16lln3f.txt === reduce.pl bib === id = cord-315754-dq2empne author = Hasan, Anwarul title = A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4662 sentences = 272 flesch = 50 summary = Angiotensin-converting enzyme-2 (ACE-2) is one of the most important receptors on the cell membrane of the host cells (HCs) which its interaction with spike protein (SP) with a furin-cleavage site results in the SARS-CoV-2 invasion. Genomic analysis of the new CoV has shown that its SP differs from that of other viruses (Du et al., 2017; Li, 2016) , indicating that the protein has a site activated by a HC enzyme called furin (Millet & Whittaker, 2015) (Figure 1 ). The furin activation site (FAS) makes the new CoV much different in cell entry than SARS, and probably affects the stability of the virus and, consequently, the transmission process (Li et al., 2015; Millet & Whittaker, 2014; Yamada & Liu, 2009) . A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 cache = ./cache/cord-315754-dq2empne.txt txt = ./txt/cord-315754-dq2empne.txt === reduce.pl bib === id = cord-315641-bzfrd7xj author = Abenavoli, Fabio Massimo title = Plastic Surgery in the Age of Coronavirus date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2981 sentences = 159 flesch = 55 summary = [24] [25] [26] The ability of the Chinese authorities to build hospital facilities for infected patients within a very short time appeared to be a test of "strength." However, little attention was paid to the conclusions that should have been drawn about how to assist new patients during the emergency situation. Severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2), which results in a high percentage of infected patients, has been enormously difficult to manage. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study From SARS to COVID-19: a previously unknown SARS-related coronavirus (SARS-CoV-2) of pandemic potential infecting humans-call for a One Health approach 2019-nCoV (Wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness Isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-nCoV) outbreak cache = ./cache/cord-315641-bzfrd7xj.txt txt = ./txt/cord-315641-bzfrd7xj.txt === reduce.pl bib === id = cord-316018-zrui9i5z author = Bristow, Michael R. title = Dynamic Regulation of SARS-CoV-2 Binding and Cell Entry Mechanisms in Remodeled Human Ventricular Myocardium date = 2020-06-24 pages = extension = .txt mime = text/plain words = 3527 sentences = 172 flesch = 43 summary = SUMMARY Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling down-regulates into the normal range. Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling downregulates into the normal range. In explanted human heart preparations from patients with end stage reduced ejection fraction heart failure (HFrEF), ACE2 enzyme activity (22) as well as gene expression at the mRNA (20,23) and protein (20,22) levels are upregulated compared to organ donor controls. F/NDC baseline data for 10 integrins previously reported to bind to ACE2 (18,19), facilitate viral internalization (17) or be associated with LV remodeling (36) or cardiac myocyte injury protection (37) . cache = ./cache/cord-316018-zrui9i5z.txt txt = ./txt/cord-316018-zrui9i5z.txt === reduce.pl bib === id = cord-315972-5g2hnk1x author = Tong, Suxiang title = Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya date = 2009-03-17 pages = extension = .txt mime = text/plain words = 1691 sentences = 87 flesch = 58 summary = The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans. Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identifi ed from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species (6) (7) (8) (9) (10) (11) . To characterize the overall diversity of CoV sequences, in this study a phylogenetic tree (Figure 2 ) of the 121-bp fragment of RdRp was generated from 39 coronaviruses from bats in Kenya and 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database based on the Bayesian Monte Carlo Markov Chain method (14) . bats (location 17) were closely related to a SARS-like CoV cluster, including 1 sequence shown in Figure 2 (BtKY15) and another (BtKY16) that was 1 of the 3 low-quality sequences excluded from the tree. cache = ./cache/cord-315972-5g2hnk1x.txt txt = ./txt/cord-315972-5g2hnk1x.txt === reduce.pl bib === id = cord-315982-iuez41zj author = Achdout, Hagit title = COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date = 2020-10-30 pages = extension = .txt mime = text/plain words = 4103 sentences = 223 flesch = 54 summary = title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. The COVID Moonshot project has focused on progressing early fragment-screening results into potent compounds with activity against both the main protease and the virus. The rationales for each design include docking-based approaches, by-eye structure-based designs, machine learning approaches, crawling of the past literature on SARS and MERS compounds, and other general medicinal-chemistry insights that can be visualised at https://postera.ai/covid. At 24 h post-seeding, cell culture medium was discarded, cells were washed twice with PBS and infected with SARS-CoV-2 at an MOI of 0.01 in the presence of six concentrations of the inhibitors (25 M -0.06 M). cache = ./cache/cord-315982-iuez41zj.txt txt = ./txt/cord-315982-iuez41zj.txt === reduce.pl bib === id = cord-315656-asvf4roo author = Wu, Junjiao title = Revisiting the Immune Balance Theory: A Neurological Insight Into the Epidemic of COVID-19 and Its Alike date = 2020-10-15 pages = extension = .txt mime = text/plain words = 5937 sentences = 286 flesch = 37 summary = However, in the central nervous system (CNS), the activation of resident immune cells including microglia and astrocytes may lead to chronic immune imbalance, which underlies the potential long-term effects in synaptic changes and neuropsychiatric impairments. (II) Multiple organ failure in severe COVID-19 is caused by the systemic acute immune responses, the cytokine storm, and unsurprisingly caused the brain inflammation and led to encephalitis. Apart from the direct infection of the brain, SARS-CoV-2 may cause neurological disorders indirectly by triggering an over-activated immune responses, characterized as cytokine storm. Although with exciting benefits, the inhibition of IL-6 pathway works mostly for severe cases, the long-term treatment strategy against the SARS-CoV-2 infection requires the rapid development of effective anti-viral drugs and, more importantly, vaccines. However, in addition to protective effects, microglia may also mediate hippocampal presynaptic membrane damage through complement system, resulting in long-term memory impairment and cognitive decline in patients with encephalitis, caused by coronavirus or human immunodeficiency virus (HIV) infection (69) . cache = ./cache/cord-315656-asvf4roo.txt txt = ./txt/cord-315656-asvf4roo.txt === reduce.pl bib === id = cord-315611-xbj41ekc author = Ahmad, Mohammed title = Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5038 sentences = 301 flesch = 49 summary = Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. 20−22 In this report, using computer-aided homology modeling, docking, and molecular simulations, we have predicted the protein structure and probable small-molecule inhibitors against SARS-CoV2 RdRp (CoV2-RdRp). Taking together the aforementioned interaction and comparison of the model and experimentally determined structures, we propose the probable initiation complex of CoV2-RdRp bound to RNA and GTP molecules in Figure 2D . Molecular Dynamics simulation studies of the native and ligand-bound complexes of CoV2-RdRp. MD (Molecular dynamics) simulations were performed for the modelled structure of the RdRp protein and docked complexes for the GTP, lead optimized, and FIH compounds for a 50 ns time period. cache = ./cache/cord-315611-xbj41ekc.txt txt = ./txt/cord-315611-xbj41ekc.txt === reduce.pl bib === id = cord-315339-dcui85lw author = Broadbent, Andrew J. title = Respiratory Virus Vaccines date = 2015-03-13 pages = extension = .txt mime = text/plain words = 28246 sentences = 1270 flesch = 39 summary = Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . cache = ./cache/cord-315339-dcui85lw.txt txt = ./txt/cord-315339-dcui85lw.txt === reduce.pl bib === id = cord-316179-kmdxltie author = Fozouni, P. title = Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date = 2020-09-30 pages = extension = .txt mime = text/plain words = 8244 sentences = 507 flesch = 58 summary = Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. When the SARS-CoV-2 sequence became public in January 2020, we set out to develop a Cas13-based direct-detection assay for viral RNA that would avoid the need for amplification and enable point-of-care testing. We tested the performance of the device for detecting SARS-CoV-2 RNA using the triple-crRNA Cas13a assay and a dilution series with full viral RNA isolated from supernatants of infected Vero CCL-81 cells . (B) RNPs made with crRNA 2 and crRNA 4 individually and in combination (50 nM total RNP concentration for each reaction) were tested against 2.9 x 10 5 copies/µL (480 fM) of SARS-CoV-2 IVT N gene RNA, and compared to fluorescence from no target RNA RNP alone controls ("RNP 2," "RNP 4," and "RNP 2+4"). cache = ./cache/cord-316179-kmdxltie.txt txt = ./txt/cord-316179-kmdxltie.txt === reduce.pl bib === id = cord-315696-43wmazxa author = Marinaki, Smaragdi title = A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients’ Lives and Allografts date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6015 sentences = 368 flesch = 46 summary = title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients' Lives and Allografts Kidney transplant (KTx) recipients have been recently classified by the Center for Disease Control and Prevention (CDC) as a high-risk group for severe COVID-19 [2] . All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. A Case Report of Oligosymptomatic Kidney Transplant Patients with COVID-19: Do They Pose a Risk to Other Recipients? cache = ./cache/cord-315696-43wmazxa.txt txt = ./txt/cord-315696-43wmazxa.txt === reduce.pl bib === id = cord-316180-g3lfecp0 author = Zhang, Jingshu title = Membrane heist: Coronavirus host membrane remodeling during replication date = 2020-10-25 pages = extension = .txt mime = text/plain words = 1790 sentences = 122 flesch = 43 summary = Here we review the current knowledge of the structure, lipid composition, function, and biogenesis of coronavirus-induced DMVs, highlighting the druggable viral and cellular factors that are involved in the formation and function of DMVs. Prior to the emergence of Coronavirus Disease-2019 (COVID-19) caused by severe 2 acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the outbreak of highly approximately 50 to 250 nm of these DMVs as described in detail elsewhere 9, 10 . Severe 503 acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 504 induce double-membrane vesicles Mutation in 521 murine coronavirus replication protein nsp4 alters assembly of double 522 membrane vesicles Expression and cleavage of middle east respiratory 537 syndrome coronavirus nsp3-4 polyprotein induce the formation of double-538 membrane vesicles that mimic those associated with coronaviral RNA 539 replication The N-terminal region of severe acute respiratory syndrome 546 coronavirus protein 6 induces membrane rearrangement and enhances virus 547 replication cache = ./cache/cord-316180-g3lfecp0.txt txt = ./txt/cord-316180-g3lfecp0.txt === reduce.pl bib === id = cord-315951-5gsbtfag author = Kiemer, Lars title = Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date = 2004-06-06 pages = extension = .txt mime = text/plain words = 3766 sentences = 200 flesch = 51 summary = The general approach is still valid though, and we decided to apply this method to the problem of predicting the 3CL pro proteinase cleavage sites and identifying potential host cell target proteins. In this paper, we describe the development of a computational prediction method using artificial neural networks for predicting coronavirus 3CL pro proteinase cleavage sites. We discuss potential targets of 3CL pro proteinase, e.g. the cystic fibrosis transmembrane conductance regulator (CFTR) and translational and transcriptional factors, which may be involved in the molecular pathology of coronaviruses in general and SARS virus in particular. Another known target for viral infections is the microtubule-associated protein 4 (MAP-4) which is cleavable in HeLa cells by the poliovirus 3C pro proteinase [26, 27] . We have developed a neural network capable of identifying the cleavage site of the coronavirus proteinase 3CL pro and use this model to predict potential cleavage sites in host cell proteins. cache = ./cache/cord-315951-5gsbtfag.txt txt = ./txt/cord-315951-5gsbtfag.txt === reduce.pl bib === id = cord-315756-g6g34uvh author = Danchin, A. title = Immunity after COVID-19: protection or sensitization ? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 4278 sentences = 249 flesch = 62 summary = Then we use a compartmental epidemic model structured by immunity level (taken here as age classes) that we fit on available data; this allows to derive quantitative insights into the future number of severe cases and deaths. Note that in both cases the results depend on the total epidemic infection rate, which is between α t = 5.7% (present) and the group immunity rate 1 − 1/R 0 (i.e., 70% for R 0 = 3.3). Note first that the relatively controlled nature of the 2003 SARS epidemic did not allow us to draw conclusions on how the 2003 epidemic influenced the infected (too few cases); by contrast, if a sensitizing process in the immune response triggered by SARS-CoV-2 exists, the pandemic nature of the 2019/20 COVID-19 outbreak will likely have noticeable effects on the overall population health state. cache = ./cache/cord-315756-g6g34uvh.txt txt = ./txt/cord-315756-g6g34uvh.txt === reduce.pl bib === id = cord-316080-y6ypbdtu author = Fajnzylber, J. M. title = SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1701 sentences = 124 flesch = 53 summary = We quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. Amongst the participants hospitalized with COVID-19, higher prevalence of detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. Amongst hospitalized individuals, the majority still 92 had detectable SARS-CoV-2 RNA at the time of initial sample collection, including 50% with variable, individuals with detectable plasma, nasopharyngeal or sputum viral loads had 124 significantly lower absolute lymphocyte counts, and higher CRP and IL-6 levels compared to 125 those without detectable plasma viremia (Fig 2b-d) . . https://doi.org/10.1101/2020.07.15.20131789 doi: medRxiv preprint DISCUSSION 151 We report a comprehensive analysis of SARS-CoV-2 respiratory tract, plasma, and urine viral 152 loads of 235 participants who were either hospitalized with COVID-19, evaluated as 153 symptomatic outpatients, or had recovered from COVID-19 disease. cache = ./cache/cord-316080-y6ypbdtu.txt txt = ./txt/cord-316080-y6ypbdtu.txt === reduce.pl bib === id = cord-316117-o29773cz author = Menzella, Francesco title = Pharmacologicaltreatment of COVID-19: lights and shadows date = 2020-05-19 pages = extension = .txt mime = text/plain words = 4459 sentences = 265 flesch = 45 summary = At the end of December 2019, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China and then the entire world, forcing the World Health Organization (WHO) to make the assessment that the coronavirus disease (COVID19) can be characterized as a pandemic, the first ever caused by a coronavirus. The search strategy was based on the following keywords: coronavirus, SARS-CoV-2 pneumonia, COVID-19, severe acute respiratory syndrome, antivirals, corticosteroids, biologics, and anticoagulants. Current antiviral treatments are mainly based on previous experiences (favipiravir) or on experimental drugs (remdesivir) used for the treatment of viral infections due to different viruses, such as influenza virus (InfV), Ebolavirus (EBOV), human immunodeficiency virus (HIV), MERS, and SARS. 38 On the contrary, in a study with a small cohort of patients hospitalized for severe SARS-CoV-2 infection, no strong antiviral activity or clinical efficacy of the combination of hydroxychloroquine and azithromycin was found. cache = ./cache/cord-316117-o29773cz.txt txt = ./txt/cord-316117-o29773cz.txt === reduce.pl bib === id = cord-316083-f1h2j6jx author = Alamri, Ahmad title = nan date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1431 sentences = 77 flesch = 54 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the origin of the current pandemic of coronavirus disease 2019 (COVID-19) that was identified in hospitalized patients in Wuhan, China, in December 2019 [1] . She reported a total anosmia with an associated dysgeusia that started on the 21 st of March, with no rhinorrhea, no stuffy nose, no fever, no dyspnea, no myalgia nor fatigue, and no swollen lymph nodes on the clinical examination and no other We started olfactory training for both patients, with different aliments like vanilla, lavender, spices and coffee. Here, we have two cases of confirmed SARS-CoV-2 infection, both having isolated anosmia; with a probable context of a worker to worker transmission (with an interval of the onset of symptoms around 24 hours). The fact that both cases were physicians working in the same structure with a possible worker to worker transmission could justify systematic (or focused) screening of health care providers which could drastically minimize the health worker-patient transmission by applying the necessary measures (like home confinement). cache = ./cache/cord-316083-f1h2j6jx.txt txt = ./txt/cord-316083-f1h2j6jx.txt === reduce.pl bib === id = cord-315968-q2rxj90s author = Douglas, Jennifer E. title = Management of a Unique Sinonasal Undifferentiated Carcinoma Subtype in the Era of SARS-CoV-2 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 1379 sentences = 80 flesch = 43 summary = Sinonasal undifferentiated carcinoma (SNUC) represents a rare malignancy of the sinonasal tract, a unique subset of which has never been previously reported in the otolaryngology literature and is characterized by inactivation of the SMARCB (INI-1) tumor suppressor gene. Here we present the case of an individual who was diagnosed with a sinonasal mass during the SARS-CoV-2 pandemic, which was ultimately found to be SMARCB (INI-1)-deficient sinonasal carcinoma. While SNUC has itself a poor prognosis, a subset of sinonasal neoplasms with inactivation of the SMARCB (INI-1) tumor suppressor gene exhibits particularly treatment-recalcitrant disease. Here we present the case of an individual with a sinonasal mass who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma and the unique management required during the SARS-CoV-2 pandemic. Here we present the case of an individual initially diagnosed with nasal polyps who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma during the SARS-CoV-2 pandemic and the unique management required. cache = ./cache/cord-315968-q2rxj90s.txt txt = ./txt/cord-315968-q2rxj90s.txt === reduce.pl bib === id = cord-316066-pge0vx04 author = Zhang, Zheng title = Longitudinal alteration of circulating dendritic cell subsets and its correlation with steroid treatment in patients with severe acute respiratory syndrome date = 2005-06-16 pages = extension = .txt mime = text/plain words = 5115 sentences = 251 flesch = 52 summary = In this study, we found that 74 patients with severe acute respiratory syndrome (SARS) exhibited a rapid, dramatic decrease in numbers of circulating myeloid and plasmacytoid dendritic cells (mDCs and pDCs) during the first 2 weeks of illness (5.3and 28.4-fold reductions for mDCs and pDCs compared with 25 healthy individuals, respectively), with slow return to normal cell numbers during convalescence (weeks 5–7 of illness on average). A marked lymphocytopenia occurred in most patients during the acute phase of SARS, with CD4 and CD8 T-cell subsets particularly affected, and the degree of reduction of circulating T lymphocyte counts was found to be associated with disease severity, indicating that host immune functional changes are involved in the initiation and progression of SARS [3 -6] . In addition, our findings suggest that acute SARS-CoV infection may contribute to the rapid initial reduction of both circulating mDCs and pDCs. Subsequently, steroid administration, particularly at high doses over weeks, probably exacerbated and prolonged the decrease in numbers of DC subset as well as T-cell subsets. cache = ./cache/cord-316066-pge0vx04.txt txt = ./txt/cord-316066-pge0vx04.txt === reduce.pl bib === id = cord-316096-3fnwosst author = Jin, Huali title = Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice date = 2005-03-25 pages = extension = .txt mime = text/plain words = 4521 sentences = 222 flesch = 54 summary = After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. All DNA vaccine constructs, encoding the E protein, the M glycoprotein, and the N protein of SARS-CoV, were obtained as follows: these genes were amplified from the cDNA by PCR amplifications using each set of specific primers, respectively. In the present study, it was consistent with their work that the N protein construct could induce the highest SARS-specific IgG, T cell proliferation, and in vivo CTL response (lysis rate of 50.6%) compared with M protein gene (lysis rate of 17%) and E protein gene (lysis rate of 5.6%) (Fig. 4) . In summary, the administrations with all three SARS-CoV DNA vaccines in our study were able to induce high levels of the antigen-specific IgG antibody, the T cell proliferation, IFN-c, DTH, and in vivo CTL responses. cache = ./cache/cord-316096-3fnwosst.txt txt = ./txt/cord-316096-3fnwosst.txt === reduce.pl bib === id = cord-315970-m5o962yw author = Di Ciaula, Agostino title = COVID‐19, internists and resilience: the north‐south Italy outbreak. date = 2020-06-01 pages = extension = .txt mime = text/plain words = 3971 sentences = 220 flesch = 48 summary = The rates of infected subjects and deaths in Italy (whole country and regional level) per 100,000 residents were calculated considering the official number of residents derived from the National Institute of Statistics (ISTAT). Figure 1 summarizes the daily progression in the cumulative number of COVID-19 positive subjects and in the incidence of deaths related to COVID-19 in southern and northern Italy, since the start of the outbreak. On the national "lockdown" day (March 12), in northern Italy there was a total of 14,335 infected patients and 997 COVID-19 related deaths. Following the COVID-19 outbreak, the local Apulian government firstly increased the number of available beds in the units of intensive care, pneumology, and infectious diseases across the Region. In the most affected regions (northern Italy, mainly Lombardy) serious concerns existed about the effective capacity of the national health system to adequately face the burden of disease. cache = ./cache/cord-315970-m5o962yw.txt txt = ./txt/cord-315970-m5o962yw.txt === reduce.pl bib === id = cord-316186-254z62e4 author = Kario, Kazuomi title = COVID‐19 and hypertension—evidence and practical management: Guidance from the HOPE Asia Network date = 2020-07-09 pages = extension = .txt mime = text/plain words = 3315 sentences = 197 flesch = 43 summary = 1 Early clinical experience suggested that older age and the presence of a number of comorbidities, including hypertension, cardiovascular disease, diabetes mellitus and chronic respiratory disease increased the risk of death in patients with 3 In addition, the renin-angiotensin aldosterone (RAS) system (specifically the angiotensin-converting enzyme 2 [ACE2] protein) has been identified as playing an important role in facilitating entry of coronaviruses, including SARS-CoV-2, into target cells, especially in the lungs. Despite the theoretical possibility that use of RAS inhibitors increases the risk of infection with SARS-CoV-2 and the severity of COVID-19 illness, analyses including patients from the current pandemic indicate that this does not seem to be the case ( Table 2 ). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China cache = ./cache/cord-316186-254z62e4.txt txt = ./txt/cord-316186-254z62e4.txt === reduce.pl bib === id = cord-316126-j51dik7f author = Zhang, X. Sophie title = SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles date = 2020-10-28 pages = extension = .txt mime = text/plain words = 12434 sentences = 576 flesch = 42 summary = title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles Since the beginning of the COVID-19 pandemic, there has been intense debate over SARS-CoV-2's mode of transmission and appropriate personal protective equipment for health care workers in low-risk settings. This review attempts to summarize current cumulative data on SARS-CoV-2's modes of transmission and identify gaps in research while offering preliminary answers to the question on everyone's mind: is the airborne route significant and should we modify our COVID-19 PPE recommendations for frontline workers in low-risk settings? Given that substantial disagreement persists on the importance of natural aerosol generation by COVID-19 patients, and consequently, the necessary level of respiratory protection in non-AGP contexts, our review will focus on transmission and PPE in low-risk health care settings. cache = ./cache/cord-316126-j51dik7f.txt txt = ./txt/cord-316126-j51dik7f.txt === reduce.pl bib === id = cord-316003-xt59voyt author = Say, Daphne S. title = Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1465 sentences = 77 flesch = 40 summary = title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol Endoscopists face risk for infection with viruses like SARS-CoV-2, as the aerosol generating nature of endoscopy diffuses respiratory disease that can be spread via an airborne and droplet route. It is unclear how much of the risk was related to community transmission or to breaches in use of personal protective equipment (PPE) during the care of patients with COVID-19. Given initial limitations in the availability of testing for SARS-CoV-2 infection, however, our institution's current screening algorithm specifies testing only individuals with influenza-like illness and exposure to a patient with known COVID-19. If viral testing for SARS-CoV-2 infection is not available, patient risk stratification before endoscopy may be accomplished based on symptoms and sick contacts. At minimum, those in the pediatric endoscopy suite will require use of gloves, water-resistant gowns, surgical face masks, eye protection, and hair coverings for all endoscopic procedures. cache = ./cache/cord-316003-xt59voyt.txt txt = ./txt/cord-316003-xt59voyt.txt === reduce.pl bib === id = cord-316330-55nd3pwe author = Ramos-Lopez, Omar title = Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3499 sentences = 193 flesch = 37 summary = RESULTS: Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. CONCLUSIONS: Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments. Observational (cross-sectional, cohort, or case-control) studies exploring the role of host genetic polymorphisms in SARS-CoV disease (infection susceptibility, disease progression, and clinical outcomes) in adult subjects were included. The present systematic review revealed that 29 polymorphisms located in 21 genes were associated with SARS-CoV susceptibility/resistance, disease severity, and clinical manifestations/outcomes (Table 1) . cache = ./cache/cord-316330-55nd3pwe.txt txt = ./txt/cord-316330-55nd3pwe.txt === reduce.pl bib === id = cord-316498-f43apjul author = Karlsson, Jan Olof G title = May Mangafodipir or Other SOD Mimetics Contribute to Better Care in COVID-19 Patients? date = 2020-10-10 pages = extension = .txt mime = text/plain words = 1931 sentences = 102 flesch = 42 summary = The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate—MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate-MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. Intravenously administration of mangafodipir will, in contrast to INO [1] : "Everyone will be exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and most people will become infected; the disease is known as COVID-19. When it comes to mangafodipir, its combined MnSOD mimetic and redox metal binding activity may be of particular importance when attacking the inflammatory storm in SARS-CoV-2 patients. cache = ./cache/cord-316498-f43apjul.txt txt = ./txt/cord-316498-f43apjul.txt === reduce.pl bib === id = cord-316374-mzomj1ab author = Brufsky, Adam title = Boning up: amino-bisphophonates as immunostimulants and endosomal disruptors of dendritic cell in SARS-CoV-2 infection date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2774 sentences = 153 flesch = 41 summary = Amino-bisphosphonates such as zoledronic acid (ZA) can possibly ameliorate or prevent severe COVID-19 disease by at least three distinct mechanisms: (1) as immunostimulants which could boost γδ T cell expansion, important in the acute response in the lung; (2) as DC modulators, limiting their ability to only partially activate T cells; and (3) as prenylation inhibitors of small GTPases in the endosomal pathway of the DC to prevent expulsion of lysosomes containing SARS-CoV-2 virions. Early and central infection of tissue resident dendritic cells (DC) by the SARS-CoV-2 coronavirus explain some of the immunopathology of the COVID-19 pandemic. Agents that alter endosomal pH such as hydroxychloroquine (HCQ) could be protective in SARS-CoV-2 infected DCs in maintaining the immune response as well as the lymphocyte count, as was observed in a recently reported randomized, parallel, open label, multicenter clinical trial of hydroxychloroquine (HCQ) and usual care versus usual care alone for the treatment of COVID infection [36] . cache = ./cache/cord-316374-mzomj1ab.txt txt = ./txt/cord-316374-mzomj1ab.txt === reduce.pl bib === id = cord-316129-mjg3un0l author = Khamar, Pooja title = Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases date = 2020-07-13 pages = extension = .txt mime = text/plain words = 3672 sentences = 228 flesch = 59 summary = title: Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases METHOD: In an experimental setup, flap creation was performed on enucleated goat's eyes (n = 8) mounted on a stand using One Use-Plus SBK Moria microkeratome (Moria SA) to assess the spread of aerosols and droplets using high-speed shadowgraphy. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. 13, 14 Therefore, we quantified the aerosol and droplet generation during flap creation using the Moria One Use-Plus SBK microkeratome (Moria SA) and assessed their trajectory using high-speed shadowgraphy and fluid mechanics principles. cache = ./cache/cord-316129-mjg3un0l.txt txt = ./txt/cord-316129-mjg3un0l.txt === reduce.pl bib === id = cord-315598-qwh72inx author = Mendoza, Jose Luis Accini title = ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 69640 sentences = 6489 flesch = 54 summary = De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). cache = ./cache/cord-315598-qwh72inx.txt txt = ./txt/cord-315598-qwh72inx.txt === reduce.pl bib === id = cord-316095-jzyb4jn5 author = Falahchai, Mehran title = Dental care management during the COVID‐19 outbreak date = 2020-09-19 pages = extension = .txt mime = text/plain words = 5601 sentences = 369 flesch = 50 summary = Sixteen English papers were enrolled to answer questions about procedures that are allowed to perform during the COVID‐19 outbreak, patients who are in priority to receive dental care services, the conditions and necessities for patient admission, waiting room and operatory room, and personal protective equipment (PPE) that is necessary for dental clinicians and the office staff. Considering the generation of high amounts of droplets and aerosols during routine dental procedures, the conventional protective measures that are routinely followed by dental clinicians are no longer efficient for prevention of COVID-19 transmission. Urgent dental treatments include management of conditions that require immediate attention such as alleviation of severe pain with/without the risk of infection and balancing the patient load in the hospital emergency departments. According to the data acquired from the screening questionnaires, patients who need emergency/urgent dental treatment can be divided into three groups of apparently healthy, suspected, and confirmed cases. cache = ./cache/cord-316095-jzyb4jn5.txt txt = ./txt/cord-316095-jzyb4jn5.txt === reduce.pl bib === id = cord-316616-j82q99in author = Su, Yen-Bo title = Cardiovascular manifestation and treatment in COVID-19 date = 2020-05-19 pages = extension = .txt mime = text/plain words = 4445 sentences = 243 flesch = 36 summary = The novel coronavirus disease 2019 (COVID-19), with first presentation of atypical pneumonia, has spread rapidly from Wuhan, China, on December 12, 2019 to over 200 countries, caused 2 310 572 infected individuals and 158 691 mortalities, updated on April 19, 2020. 33, 41 In a small singlearm study of patients with confirmed COVID-19, treatment with hydroxychloroquine was associated with a significant difference in clearing of viral nasopharyngeal carriage of SARS-CoV2 within 3 to 6 days when compared with untreated controls. ACE2 levels are increased following treatment with ACE inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), which yield the concerns that using these medications might increase the severity of COVID-19, especially in patients with existing cardiovascular diseases. Patients with comorbidities including hypertension, cardiovascular diseases, and diabetes tend to have higher risk for having severe COVID-19 which leads to acute respiratory distress syndrome (ARDS) and mortality. Risk factors associated with acute respiratory distress syndrome and death in patients With coronavirus disease 2019 pneumonia in Wuhan, China cache = ./cache/cord-316616-j82q99in.txt txt = ./txt/cord-316616-j82q99in.txt === reduce.pl bib === id = cord-316646-rd3zl9qz author = Lebedin, Y. S. title = Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia date = 2020-09-25 pages = extension = .txt mime = text/plain words = 2531 sentences = 132 flesch = 49 summary = The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia In this report, we evaluate the SARS-CoV-2 nucleocapsid antigen (N-Ag) and respective antibodies as diagnostic markers and demonstrate the total prevalence of N-Ag seroconversion in SARS-CoV-2-associated pneumonia patients. The immunoassay-based detection of serum N-Ag in combination with its respective antibodies confirmed COVID-19 in 280 patients (59%) of the studied cohort. The results indicate high relevance of combined serological tests for SARS-CoV-2 N-Ag and the antibodies to SARS-CoV-2 antigens as applied to the infectious pneumonia emergency patients at the admission, since: According to the results of the study, hospitalization of the patients with SARS-CoV-2associated pneumonia at the height of pandemic most frequently occurred before the onset of seroconversion (i.e. against the background of detectable serum N-Ag concentrations). cache = ./cache/cord-316646-rd3zl9qz.txt txt = ./txt/cord-316646-rd3zl9qz.txt === reduce.pl bib === id = cord-316215-4mj7n0ax author = Haveri, Anu title = Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020 date = 2020-03-19 pages = extension = .txt mime = text/plain words = 2968 sentences = 156 flesch = 53 summary = Suspicion of COVID-19 led to her direct transfer to the Lapland Central Hospital in Rovaniemi, where she was isolated and sampled on 28 and 29 January for laboratory confirmation of SARS-CoV-2 infection ( Figure 1 ). SARS-CoV-2 infection was confirmed from nasopharyngeal samples on 29 January by the Helsinki University Hospital Laboratory (HUSLAB), and further confirmed at the Finnish Institute for Health and Welfare (THL) ( Table) . Presence of serum IgM and IgG antibodies against SARS-CoV-2 was analysed by immunofluorescence assays (IFA) based on Vero E6 cells infected with passage 4 of the patient's isolate SARS-CoV-2/ Finland/1/2020 virus and transferred onto microscope slides and fixed with acetone ( Figure 2 ). Western blot of mock-and SARS-CoV-2 infected Vero E6 cells using patient serum collected 20 days after onset of symptoms, Finland, January-February 2020 No neutralising SARS-CoV-2 antibodies were detected in the close contacts nor in the control population samples collected during 2019 in Finland. cache = ./cache/cord-316215-4mj7n0ax.txt txt = ./txt/cord-316215-4mj7n0ax.txt === reduce.pl bib === id = cord-316425-fnlgeubu author = Rahimi, Farid title = Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 date = 2020-04-15 pages = extension = .txt mime = text/plain words = 811 sentences = 51 flesch = 54 summary = title: Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 We were delighted to read the enlightening letter titled, The Global Threat of SARS-CoV-2/COVID-19 and the Need for More and Better Diagnostic Tools submitted to the Archives of Medical Research (1). The main rationale behind the recent advances in developing diagnostics for COVID-19 is achieving fast and cheap initial detection and confirmation of SARS-CoV-2 infection in different biological samples, including fecal samples, nasopharyngeal or oropharyngeal swabs, and environmental samples. Thus, providing a rapid, accurate and cheap diagnostic kit will efficiently help the health authorities in the developing countries to expedite case-finding within the population. Global threat of SARS-CoV-2/ COVID-19 and the need for more and better diagnostic tools Mesa biotech receives emergency use authorization from FDA for a 30 minute point of care molecular COVID-19 test: Mesa Biotech cache = ./cache/cord-316425-fnlgeubu.txt txt = ./txt/cord-316425-fnlgeubu.txt === reduce.pl bib === id = cord-316232-7w1vrx96 author = Radon, K. title = Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19) date = 2020-05-02 pages = extension = .txt mime = text/plain words = 6356 sentences = 392 flesch = 54 summary = For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children <14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. 28.20082743 doi: medRxiv preprint 3 a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. With the community-based household study presented in this paper, we therefore aim to study the sero-prevalence and -incidence of SARS-CoV-2 antibodies in a representative household sample of the Munich population. 28.20082743 doi: medRxiv preprint • The temporal course of SARS-CoV-2 sero-positivity in the Munich general population (point prevalence and incidence) stratified for symptomatic and asymptomatic subjects and reported cases • The daily prevalence and incidence of possible COVID-19 symptoms in the study population cache = ./cache/cord-316232-7w1vrx96.txt txt = ./txt/cord-316232-7w1vrx96.txt === reduce.pl bib === id = cord-316345-a1cirnya author = Comas, Carmina title = COVID‐19 and pregnancy: An opportunity to correct an historic gender bias date = 2020-08-02 pages = extension = .txt mime = text/plain words = 1447 sentences = 74 flesch = 40 summary = Unfortunately, this bias seems to be maintained in the COVID‐19 epidemic: most current guidelines for diagnosing SARS‐CoV‐2 infection during pregnancy apply the same standard criteria as for the general population. Unfortunately, this bias seems to be maintained in the COVID-19 epidemic: most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population. This pandemic is an opportunity to begin redressing this historic gender bias against pregnant women, and to achieve this, we recommend two actions that are easy to implement, and would have a large impact. Indeed, despite significant variation in protocols between hospitals, most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population, namely performing one of the available molecular tests, such as quantitative reverse transcription polymerase chain reaction. cache = ./cache/cord-316345-a1cirnya.txt txt = ./txt/cord-316345-a1cirnya.txt === reduce.pl bib === id = cord-316260-1t3ifsfi author = Nogueira-de-Almeida, Carlos Alberto title = COVID-19 and obesity in childhood and adolescence: A clinical review()() date = 2020-08-04 pages = extension = .txt mime = text/plain words = 7974 sentences = 450 flesch = 43 summary = In severe acute respiratory syndrome coronavirus 2 infection, these organic changes from obesity may increase the need for ventilatory assistance, risk of thromboembolism, reduced glomerular filtration rate, changes in the innate and adaptive immune response, and perpetuation of the chronic inflammatory response. 3--6 The present review aims to identify the factors that contribute to the increase in the susceptibility and severity of COVID-19 in obese children and adolescents, and its health consequences, to collaborate for better clinical care of these patients. The three main risk factors that link obesity to COVID-19 demonstrated for adults 52 are also present among children and adolescents: chronic subclinical inflammation, impaired immune response, and underlying cardiorespiratory diseases. In conclusion, obesity in childhood and adolescence can be considered a risk factor for greater susceptibility and severity of COVID-19 and is associated with nutritional, cardiac, respiratory, renal, and immunological alterations, which may potentiate the complications of SARS-CoV-2 infection. cache = ./cache/cord-316260-1t3ifsfi.txt txt = ./txt/cord-316260-1t3ifsfi.txt === reduce.pl bib === id = cord-316432-xemz7zn9 author = Talaie, Haleh title = Is there any potential management against COVID-19? A systematic review and meta-analysis date = 2020-08-18 pages = extension = .txt mime = text/plain words = 5089 sentences = 261 flesch = 38 summary = METHODS: Pubmed, Embase, Scopus, Cochrane, and Scholar databases were searched from inception to July 1, 2020, to identify studies reporting the current treatment process and medications (e.g. hydroxychloroquine, antiviral therapy, convalescent plasma, and immunomodulatory agents) for COVID-19. Zhong et al., provided a systematic review and meta-analysis including the therapies for severe acute respiratory syndrome (SARS), Middle Eastern respiratory syndrome (MERS) mainly besides COVID-19 and assessed their safety and efficacy profiles [31] . All types of studies i.e. randomized controlled trials (RCTs), prospective or retrospective cohort studies, and the case series that investigated clinical outcomes and/or viral clearance among adult patients were included to conduct this study. In agreement with previous researches, our meta-analysis results showed that the administration of immunomodulatory agents (especially tocilizumab and anakinra) significantly decreased the mortality rate and ameliorate clinical symptoms in patients with COVID-19 [113, 114] . Virological and clinical cure in COVID-19 patients treated with hydroxychloroquine: a systematic review and meta-analysis cache = ./cache/cord-316432-xemz7zn9.txt txt = ./txt/cord-316432-xemz7zn9.txt === reduce.pl bib === id = cord-316667-b1xabkzk author = Konopka, Kristine E. title = Diffuse Alveolar Damage (DAD) from Coronavirus Disease 2019 Infection is Morphologically Indistinguishable from Other Causes of DAD date = 2020-06-15 pages = extension = .txt mime = text/plain words = 2694 sentences = 157 flesch = 45 summary = Additionally, to better understand if COVID-19 represents a histologic variant of DAD we systematically compare the pathologic findings of SARS-CoV-2-positive patients to uninfected controls. 11 Our autopsy databases were then searched from January 1, 2016 through December 31, 2019 for inpatient and nonhospitalized community cases diagnosed as "diffuse alveolar damage." Since these deaths occurred prior to the first reported case of COVID-19 in the United States, 12 they are considered SARS-CoV-2negative (further referred to as "control cohort"). To our knowledge, this is the first comparison of autopsy lung findings in SARS-CoV-2-positive medically managed inpatients and untreated, non-hospitalized decedents to uninfected historical control cases of DAD. Nonetheless, we think our SARS-CoV-2 positive cases are likely representative of the broader COVID-19 patient population, since both hospitalized and non-hospitalized decedents had underlying conditions previously identified as risk factors for severe disease, including diabetes, chronic lung disease, cardiovascular disease, 13 and obesity. cache = ./cache/cord-316667-b1xabkzk.txt txt = ./txt/cord-316667-b1xabkzk.txt === reduce.pl bib === id = cord-316493-wszoi6p2 author = Zhou, Weimin title = First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood date = 2013-09-16 pages = extension = .txt mime = text/plain words = 4322 sentences = 237 flesch = 55 summary = BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. To expand the epidemiological knowledge of four non-SARS-related endemic HCoVs in China, we expressed S proteins in a eukaryotic system and established an IFA for the detection of IgG or IgM antibodies against these four viruses. Our results showed that the S-based IFA enabled specific detection of IgG or IgM to four individual HCoVs. Using IFA, we investigated the natural seroprevalence of four non-SARS-related HCoVs in blood samples from a general population that comprised a variety of age groups. cache = ./cache/cord-316493-wszoi6p2.txt txt = ./txt/cord-316493-wszoi6p2.txt === reduce.pl bib === id = cord-316623-tv5yyfak author = Zhang, Jianmin title = Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase date = 2008-03-04 pages = extension = .txt mime = text/plain words = 4944 sentences = 258 flesch = 65 summary = The product was purified by column chromatography (50:50 EtOAc/hexanes) to yield 12a as a solid (16 mg To a solution of 11a (10 mg, 0.045 mmol) in dry THF (5 mL) was added LiHMDS (0.1 mL, 1.0 M solution in THF, 0.1 mmol) over a period of 5 min. The mixture was stirred for 1 h at À78°C, and a solution of NFSi (32 mg, 0.1 mmol) in dry THF (3 mL) was added dropwise over 10 min. After 3 h of stirring at 20°C, the solvent was removed in vacuo and the product was purified by column chromatography on silica gel (25:75 EtOAc/hexanes) to yield 21 as a solid (1.35 g, 68%) Based on our previous modeling studies [10b,23], the three-ringed esters utilize a non-covalent and reversible mechanism of inhibition in a S4-S1 binding mode, by blocking entry of substrates into the active site of SARS-CoV 3CL pro . cache = ./cache/cord-316623-tv5yyfak.txt txt = ./txt/cord-316623-tv5yyfak.txt === reduce.pl bib === id = cord-316712-1ngcwdln author = Laxminarayan, Ramanan title = India’s Battle against COVID-19: Progress and Challenges date = 2020-08-24 pages = extension = .txt mime = text/plain words = 2592 sentences = 149 flesch = 56 summary = The first reported case of infection with the SARS-CoV-2, the virus that causes COVID-19, in India was reported on January 30, 2020 in an Indian student evacuated from Wuhan, and the first death was reported on March 12, 2020. Model-based estimates 8 produced in March 2020 had indicated that a national lockdown could reduce the number of infections at the peak of the pandemic-expected in early May-by 70-80%, depending on the degree of public compliance with physical distancing. Mortality rates (based on reported cases and deaths) appear to be low in India, as they are in most countries in the region, perhaps indicative of both limited testing and other unexplained factors. 12 At the current time, India has conducted approximately 18,000 tests per million population, a rate that is a third that of South Africa, about 60% that of Nepal, and among the lowest of any large country. cache = ./cache/cord-316712-1ngcwdln.txt txt = ./txt/cord-316712-1ngcwdln.txt === reduce.pl bib === id = cord-316930-0s7k9guq author = Caldas, Lucio Ayres title = Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2901 sentences = 192 flesch = 52 summary = title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2. At the same time, and with a MOI of 1, viruses that egressed from a previous cycle of infection were observed during the process of attachment to the cell plasma membrane ( Fig. 2A) . To approach SARS-CoV-2/cell interactions, we investigate several steps of virus infection in Vero cells at 2 and 48 hpi by SEM. These sites were appropriate to register the attachment of SARS-CoV-2 particles ( Fig. 2A ) similar to transmission electron microscopy images of the same early step of SARS-CoV infection of Vero cells 28 . Drastic vacuolization due to viral infection was previously described for other RNA viruses including SARS-CoV 20,32 . cache = ./cache/cord-316930-0s7k9guq.txt txt = ./txt/cord-316930-0s7k9guq.txt === reduce.pl bib === id = cord-316536-jpbfgwhl author = Raj, V. Stalin title = Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC date = 2013-03-13 pages = extension = .txt mime = text/plain words = 4501 sentences = 221 flesch = 48 summary = Moreover, transient expression of human DPP4 in the non-susceptible COS-7 cells rendered these cells susceptible to binding the hCoV-EMC S1-Fc protein to their surface ( Supplementary Fig. 4) . e, Double-stranded viral RNA (cyan) was detected in hCoV-EMC-infected primary human bronchiolar epithelial cell cultures and appeared to be localized to nonciliated cells that express DPP4 (red). In addition, hCoV-EMC infection of human bronchiolar epithelial cell cultures appeared to be localized to the non-ciliated cells that express DPP4 (Fig. 3e) . COS-7 cells transfected with the human DPP4 expression plasmid, but not with the empty plasmid, were efficiently infected by hCoV-EMC as demonstrated by the presence of viral non-structural proteins in the cells (Fig. 4c) and of viral RNA (Fig. 4d) and infectious virus in the cell supernatants (not shown). S1 receptor-binding domains of hCoV-EMC, SARS-CoV and FIPV fused to the Fc region of human IgG, and soluble versions of DPP4 and ACE2 were expressed and purified as described in the Methods. cache = ./cache/cord-316536-jpbfgwhl.txt txt = ./txt/cord-316536-jpbfgwhl.txt === reduce.pl bib === id = cord-316946-bxfdq8e1 author = Danion, François title = The Good, the Bad, and the Hoax: When Publication Instantaneously Impacts Treatment Strategies for COVID-19 date = 2020-07-22 pages = extension = .txt mime = text/plain words = 762 sentences = 50 flesch = 49 summary = In Strasbourg University Hospital, France, which was severely affected by the SARS-CoV-2 epidemic at the beginning of March 2020, we analyzed the consumption of antiviral agents according to the emergence of relevant scientific data. The treatment strategies in our center, outside clinical trials, included standard of care alone or in combination with lopinavir-ritonavir or hydroxychloroquine (HCQ) in off-label utilization and without grading of the recommendations. Despite the major limitations of this study-including no outcome data on clinical efficacy or safety, the small number of patients enrolled, and the absence of randomization-we experienced a dramatic increase in our HCQ prescriptions following this publication (Fig. 1) . Following the publication of a large observational study on 22 May showing no beneficial effect of HCQ, this treatment regimen is not authorized anymore in France outside clinical trials (6) . Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial cache = ./cache/cord-316946-bxfdq8e1.txt txt = ./txt/cord-316946-bxfdq8e1.txt === reduce.pl bib === id = cord-316255-93srx4s7 author = Cacho, Pedro Muñoz title = Can climatic factors explain the differences in COVID-19 incidence and severity across the Spanish regions?: An ecological study date = 2020-10-13 pages = extension = .txt mime = text/plain words = 3814 sentences = 194 flesch = 44 summary = Besides, temperature (February: rho = − 0.832; p < 0.001 and March: rho = − 0.904; p < 0.001), was the main climatic factor responsible for the infectivity of the coronavirus and directly contributed to a different spread of SARS-CoV-2 across the Spanish regions. To assess the possible influence on the infectivity of SARS-CoV-2 [9] [10] [11] , data on UVR (J/m 2 ), temperature (°C), and relative humidity (%) were also collected from the months with the highest infectivity (February and March 2020) to the peak of the pandemic in our country. Climatic parameters (temperature, UVR, and relative humidity) were considered as independent variables and epidemiological variables related to COVID-19 (cumulative incidence during the previous 14 days, total cases, newly diagnosed cases, hospital admissions, intensive care unit (ICU) admissions, and mortality, all referring to the period from 1 to 30 March 2020) were analyzed as dependent variables. cache = ./cache/cord-316255-93srx4s7.txt txt = ./txt/cord-316255-93srx4s7.txt === reduce.pl bib === id = cord-316670-x9x54fxw author = Flinck, Heini title = Comparison of two fully automated tests detecting antibodies against nucleocapsid N and spike S1/S2 proteins in COVID-19 date = 2020-08-29 pages = extension = .txt mime = text/plain words = 1869 sentences = 108 flesch = 52 summary = Based on our results, the SARS-CoV-2 antibodies can be quite reliable detected 2 weeks after NAAT positivity and 3 weeks after the symptom onset with both tests. In this paper, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. N protein based tests may be more sensitive to detect past COVID-19, but S protein may be a possible target for neutralizing antibodies, and SARS-CoV-2 antibodies against that antigen may better predict the protective immunity (Walls et al. In this study, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. Response of anti-SARS-CoV-2 total antibodies to nucleocapsid antigen in COVID-19 patients: a longitudinal study cache = ./cache/cord-316670-x9x54fxw.txt txt = ./txt/cord-316670-x9x54fxw.txt === reduce.pl bib === id = cord-316617-8cqxz3wi author = Ward, Michael P. title = SARS‐CoV‐2, where to now? date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1239 sentences = 69 flesch = 45 summary = (2020) present the results of a SARS-CoV-2 serological survey in 35 animal species in China, including the dog of a COVID-19 patient and an additional two in-contact dogs. Tests available for the detection of SARS-CoV-2 are comprehensively described in this issue of Transboundary and Emerging Diseases (Li & Ren, 2020) . In addition to the publication of new knowledge about SARS-CoV-2 in this issue of Transboundary and Emerging Diseases, new ideas are also presented. A key enabler of such a shift in our thinking and approach to disease emergence and spread is a One Health workforce capable of undertaking integrated monitoring, surveillance, risk assessment and response activities. The COVID-19 pandemic could be a catalyst for such a seismic shift in how we approach emerging infectious diseases and One Health. We can be sure, even when the current COVID-19 pandemic is resolved, that the need for surveillance, response and prevention of transboundary and emerging diseases will remain. cache = ./cache/cord-316617-8cqxz3wi.txt txt = ./txt/cord-316617-8cqxz3wi.txt === reduce.pl bib === id = cord-316658-zwxtbena author = Butler, S. E. title = Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3487 sentences = 225 flesch = 45 summary = SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. In contrast to 168 observations in serum, nasal samples from subjects with severe disease showed little to no viral 169 neutralization, whereas subjects with elevated mucosal neutralization activity tended to have 170 experienced mild or moderate symptoms (Fig. 5b) . In contrast, the IgA-associated feature defined by nasal RBD-specific Abs binding to FcaR 226 ( Fig. 7C ) and its correlated function neutralization (Fig. 7D) were lowest in subjects with either mild or 227 severe disease, and elevated among those who recovered from moderate illness. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding 580 domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein 581 induces strong mucosal immune responses and provides long-term protection against 582 SARS-CoV infection cache = ./cache/cord-316658-zwxtbena.txt txt = ./txt/cord-316658-zwxtbena.txt === reduce.pl bib === id = cord-316705-3wzurnfp author = Lalmuanawma, Samuel title = Applications of Machine Learning and Artificial Intelligence for Covid-19 (SARS-CoV-2) pandemic: A review date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2939 sentences = 142 flesch = 40 summary = A new novel model, that forecast and predicting 1-3 to 6 days ahead of total Covid-19 patient of 10 Brazilian states, using stacking-ensemble with support vector regression algorithm on the cumulative positive Covid-19 cases of Brazilian data was proposed, thus augmenting the short-term forecasting process to alert the healthcare expert and the government to tackle the pandemic [38] . A Canadian based forecasting model using time-series was developed employing Deep learning algorithm for the long-short-term-memory network, the studies found out a key factor intended for predicting the course with an ending point estimation of the current SARS-CoV-2 epidemic in Canada and all over the globe [40] . Since the outbreak of the novel SARS-CoV-2, scientists and medical industries around the globe ubiquitously urged to fight against the pandemic, searching alternative method of rapid screening and prediction process, contact tracing, forecasting, and development of vaccine or drugs with the more accurate and reliable operation. cache = ./cache/cord-316705-3wzurnfp.txt txt = ./txt/cord-316705-3wzurnfp.txt === reduce.pl bib === id = cord-316632-rr9f88oi author = Kimura, Yurika title = Society of swallowing and dysphagia of Japan: Position statement on dysphagia management during the COVID-19 outbreak date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3098 sentences = 188 flesch = 52 summary = On April 14, the Society of Swallowing and Dysphagia of Japan (SSDJ) proposed its position statement on dysphagia treatment considering the ongoing spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This statement is arranged into separate sections providing information and advice in consideration of the COVID-19 outbreak, including "terminology", "clinical swallowing assessment and examination", "swallowing therapy", "oral care", "surgical procedure for dysphagia", "tracheotomy care", and "nursing care". The current set of statements on dysphagia management in the COVID-19 outbreak is not an evidence-based clinical practice guideline, but a guide for all healthcare workers involved in the treatment of dysphagia during the COVID-19 epidemic to prevent SARS-CoV-2 infection. 48 This statement is arranged into separate sections provid-49 ing information and advice considering the COVID-19 out-50 break, including "clinical swallowing assessment and ex-51 amination", "dysphagia rehabilitation", "oral care", "nursing 52 care", "surgical procedure for dysphagia", and "tracheotomy 53 care". cache = ./cache/cord-316632-rr9f88oi.txt txt = ./txt/cord-316632-rr9f88oi.txt === reduce.pl bib === id = cord-316525-uadfehr6 author = Zhang, X. W. title = Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date = 2004-10-11 pages = extension = .txt mime = text/plain words = 3023 sentences = 152 flesch = 52 summary = Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). cache = ./cache/cord-316525-uadfehr6.txt txt = ./txt/cord-316525-uadfehr6.txt === reduce.pl bib === id = cord-316702-dj2fo8sn author = Vignesh, Ramachandran title = Is Herd Immunity Against SARS-CoV-2 a Silver Lining? date = 2020-09-30 pages = extension = .txt mime = text/plain words = 3250 sentences = 169 flesch = 45 summary = Since many studies from different geographical locations are documenting preexisting immunity to SARS-CoV-2, it will be important to define specificities of these T and B cell immune response carefully to assess their association with COVID-19 disease severity. This preexisting cross-reactive T and B cell immunity to SARS-CoV-2 may have wide implications as this could explain differential clinical outcomes in COVID-19 patients, disease severity, vaccine development, and important in accessing herd immunity for SARS-CoV-2 viral infection/COVID-19 disease. Several studies have provided strong evidence for the importance of SARS-CoV-2 specific CTLs, and T helper cells in mild and moderate patients compared to severe COVID-19 disease (27, 28, (31) (32) (33) . Several studies have provided strong evidence for the importance of SARS-CoV-2specific neutralizing antibodies in association with less disease severity in COVID-19 patients (38, 39) . A recent modelling study has estimated that about one in five individuals worldwide would be at increased risk of severe COVID-19, upon infection with SARS-CoV-2, owing to the underlying conditions. cache = ./cache/cord-316702-dj2fo8sn.txt txt = ./txt/cord-316702-dj2fo8sn.txt === reduce.pl bib === id = cord-317000-bfc51e0m author = Visci, G. title = Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date = 2020-10-27 pages = extension = .txt mime = text/plain words = 2663 sentences = 142 flesch = 51 summary = In the present study we aimed to analyze the prevalence of positive serology testing following positive RT-PCR or the appearance of symptoms suggestive of Covid-19 among high-risk HCWs employed in public hospitals of Bologna, Northern Italy, an area at high incidence of infection with SARS-CoV-2 and mortality from Covid-19, and to compare the sensitivity of different types of serological tests, including chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA). An additional group of healthcare workers who developed symptoms related to Covid-19, but did not have a positive RT-PCR result, was included in the surveillance program (based on clinical diagnostic criteria). Based on the results reported in Table 2 , and sensitivity of LFIA test equal to 75.2%, we estimated that 73.4% of HCWs with Covid-19 related symptoms, who were not tested with RT-PCR, were not infected with SARS-CoV-2. cache = ./cache/cord-317000-bfc51e0m.txt txt = ./txt/cord-317000-bfc51e0m.txt === reduce.pl bib === id = cord-316647-jj8anf5g author = Shang, You title = Management of critically ill patients with COVID-19 in ICU: statement from front-line intensive care experts in Wuhan, China date = 2020-06-06 pages = extension = .txt mime = text/plain words = 13583 sentences = 668 flesch = 39 summary = RESULTS: A comprehensive document with 46 statements are presented, including protection of medical personnel, etiological treatment, diagnosis and treatment of tissue and organ functional impairment, psychological interventions, immunity therapy, nutritional support, and transportation of critically ill COVID-19 patients. Statement 8 Convalescent plasma therapy should probably be used for severe and critically ill patients with COVID-19 (Grade 2+, weak recommendation). However, critically ill patients with COVID-19 have a longer mechanical ventilation time, and daily sedatives interruption is not suggested for patients receiving deep sedation in order to reduce lung damage during early stage of severe ARDS. Light sedation is suggested for severe COVID-19 patients receiving HFNC oxygen therapy and non-invasive mechanical ventilation, and also for critically ill patients in the recovering stage (expert opinion). Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial cache = ./cache/cord-316647-jj8anf5g.txt txt = ./txt/cord-316647-jj8anf5g.txt === reduce.pl bib === id = cord-317057-c2bwky6e author = Pickering, S. title = Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date = 2020-06-04 pages = extension = .txt mime = text/plain words = 5304 sentences = 269 flesch = 53 summary = A highly specific in-house ELISA was developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs) on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative 4 ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing gold standard for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the best performing configuration of the in-house ELISA (detection of anti-S IgM and IgG antibodies), which was also most likely to represent antibodies detected by the commercial tests. cache = ./cache/cord-317057-c2bwky6e.txt txt = ./txt/cord-317057-c2bwky6e.txt === reduce.pl bib === id = cord-316723-srenbxa7 author = Zhao, Jincun title = Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus date = 2004-11-23 pages = extension = .txt mime = text/plain words = 3093 sentences = 180 flesch = 64 summary = Amino acid residues 450–650 of the spike (S) glycoprotein of SARS-CoV (S450-650) contains dominant epitopes for anti-viral antibodies (Abs) in patient sera. However, so far there is no enzyme-linked immunosorbent assay (ELISA) available for easier and more sensitive detection of anti-S Abs. Our computer-assisted analysis suggested that amino acid residues 450-650 of the S glycoprotein (S450-650) of SARS-CoV is largely solvent accessible and likely to contain dominant B cell epitopes. (2004) showing that residues 441-700 of the S protein of SARS-CoV contained dominant epitope(s) for anti-S Abs in patient sera, as determined in WB assays. All patient sera were tested for anti-SARS-CoV IgG Abs using an ELISA kit produced by Huada Institute (see below). Sera from three convalescent SARS patients and two healthy individuals were serial diluted and tested in the S450-650-based ELISAs, which detected anti-S IgG Abs in a specific and sensitive manner, with the reactivity end point from 1:400 to 1:800 diluted patient sera (Fig. 2) . cache = ./cache/cord-316723-srenbxa7.txt txt = ./txt/cord-316723-srenbxa7.txt === reduce.pl bib === id = cord-317042-dll3qt4g author = Lv, Jun title = Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2710 sentences = 153 flesch = 54 summary = title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. In this study, we aimed to 1) determine the concentration of SARS-Cov-2 present on the object surfaces and personal protective equipment after the nucleic acid test, 2) identify the risk areas and operation behaviors that may cause contamination, and 3) provide reference basis for the targeted formulation of laboratory disinfection programs and personal operating specifications. The SARS-CoV-2 test results of object surface samples from nucleic acid detection laboratory were shown in Table 1 . In this study, all objects in nucleic acid detection laboratory that tested positive for SARS-CoV-2 were directly or indirectly contacted by the operator's gloved hands. cache = ./cache/cord-317042-dll3qt4g.txt txt = ./txt/cord-317042-dll3qt4g.txt === reduce.pl bib === id = cord-317037-1qydcc5e author = Kumar, Asit title = Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date = 2020-08-13 pages = extension = .txt mime = text/plain words = 9406 sentences = 511 flesch = 37 summary = Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. cache = ./cache/cord-317037-1qydcc5e.txt txt = ./txt/cord-317037-1qydcc5e.txt === reduce.pl bib === id = cord-316814-9fv9xrln author = Li, Hong-Ye title = Use of GFP to Investigate Expression of Plant-Derived Vaccines date = 2009 pages = extension = .txt mime = text/plain words = 2817 sentences = 204 flesch = 53 summary = Agroinfiltration is a more recent technique that can be applied to investigate transient expression in plant cells by which an Agrobacterium liquid culture is infiltrated into intact plant leaves (7) . By simple infiltration of Agrobacterium cells carrying appropriate gene constructs into tobacco plants leaves, transient expression assays can be performed within 3 days without using expensive instruments or complicated procedures. Two days after agroinfiltration, expression and subcellular localization of the GFP fusion proteins in tobacco leaves can be determined by simple observation under fluorescence or confocal laser scanning microscopy. 7. Generate plasmid pCV12 (Fig. 1 ) or similar nuclear transformation vector for expression of a fusion protein consisting of the SARS-CoV S1 and GFP. Production of tobacco leaves transiently expressing a protein fusion consisting of the SARS-CoV S1 protein fused with the GFP was carried out using Agrobacterium-mediated transformation with plasmid pCV12. cache = ./cache/cord-316814-9fv9xrln.txt txt = ./txt/cord-316814-9fv9xrln.txt === reduce.pl bib === id = cord-317085-qc8bfb9g author = Zhang, Nan title = Risk Factors for Poor Outcomes of Diabetes Patients With COVID-19: A Single-Center, Retrospective Study in Early Outbreak in China date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4754 sentences = 241 flesch = 53 summary = In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In the present study, the clinical characteristics of 52 diabetic patients with COVID-19 from a designated hospital in Wuhan, China are described, and the risk factors associated with severe clinical events which were defined as the patients' admission to ICU, the use of mechanical ventilation, or death are investigated. cache = ./cache/cord-317085-qc8bfb9g.txt txt = ./txt/cord-317085-qc8bfb9g.txt === reduce.pl bib === id = cord-316979-uadlclsv author = Pierri, Ciro Leonardo title = SARS-CoV-2 spike protein: flexibility as a new target for fighting infection date = 2020-10-30 pages = extension = .txt mime = text/plain words = 1456 sentences = 82 flesch = 52 summary = The recent study of Turoňová et al., is the first to combine cryoelectron tomography, subtomogram averaging, and molecular dynamics simulations for analyzing the structure of the SARS-CoV-2 spike protein in situ, 1 i.e. while the virus interacts with tissue cultured cells. Notably, in a recent analysis of conformational changes determining the post-fusion conformation observed for a similar coronavirus spike cryo-EM structure 5 and the related SARS-CoV-2 spike 3D comparative model 2 ( Fig. 1) , it was proposed that the loss of the N-terminal domain (residues 1-703, black cartoon) causes the reorientation of the 704-715 peptide, which was involved in maintaining the tight packing of the central helix (CH) and the heptad repeat 1 (HR1) domain, together with the N-terminal domain. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies cache = ./cache/cord-316979-uadlclsv.txt txt = ./txt/cord-316979-uadlclsv.txt === reduce.pl bib === id = cord-316970-n2dly3oa author = Kerbaj, Jad title = COVID-19: The New Caledonia experience date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1444 sentences = 115 flesch = 68 summary = Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island's hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. cache = ./cache/cord-316970-n2dly3oa.txt txt = ./txt/cord-316970-n2dly3oa.txt === reduce.pl bib === id = cord-316894-zhmuzv7z author = Stetzenbach, L.D. title = Airborne Infectious Microorganisms date = 2009-02-17 pages = extension = .txt mime = text/plain words = 4393 sentences = 259 flesch = 40 summary = Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. cache = ./cache/cord-316894-zhmuzv7z.txt txt = ./txt/cord-316894-zhmuzv7z.txt === reduce.pl bib === id = cord-317233-k3wuqwyu author = Lorenzo-Redondo, Ramon title = A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways date = 2020-11-11 pages = extension = .txt mime = text/plain words = 8170 sentences = 400 flesch = 52 summary = INTERPRETATION: These results show that multiple variants of SARS-CoV-2 were circulating in the Chicago area in mid-March 2020 that differed in their relative viral loads in patient upper airways. While the predominant virus genotype in Washington state was most closely related to viruses in China in the early epidemic, the predominant virus genotype in New York was more closely related to viruses from Europe [12] .The latter viruses carry a mutation in their Spike protein (D614G) that has not only become more common worldwide over time, but that has also been associated with higher viral loads in COVID-19 patients. Furthermore, this study supports a correlation between SARS-CoV-2 clade and relative viral load in the upper airways of infected patients. In this study, we report the phylogenetic and phylodynamic analyses of 88 SARS-CoV-2 genomes from COVID-19 patients in Chicago, Illinois, US, which largely fall into three major clades. cache = ./cache/cord-317233-k3wuqwyu.txt txt = ./txt/cord-317233-k3wuqwyu.txt === reduce.pl bib === id = cord-316859-h8lfmr3e author = Mu, Jingfang title = SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells date = 2020-04-10 pages = extension = .txt mime = text/plain words = 2063 sentences = 132 flesch = 59 summary = Previous study has reported that severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N) protein displayed a VSR activity in mammalian cells via a cellular reversal-of-silencing assay (Cui et al., 2015) . We first examined whether SARS-CoV-2 N possessed VSR activity via a classic reversal-of-silencing assay, in which enhanced green fluorescent protein (EGFP)-specific shRNA was transfected into EGFP-expressing 293T cells, together with a plasmid encoding SARS-CoV-2 N protein with Flag tag. Our data showed that expression of SARS-CoV-2 N markedly restored the protein level of EGFP ( Figure 1A Because RNAi directly results in the cleavage and degradation of target mRNAs, we further examined the VSR activity of SARS-CoV-2 N using the reversal-of-silencing system via Northern blotting with a digoxin (DIG)-labeled RNA probe targeting EGFP ORF 1-400 nt. Our findings showed that SARS-CoV-2 N can antagonize RNAi in both initiation (i.e., siRNA biogenesis) and effector (i.e., RISC assembly and target RNA cleavage) steps. cache = ./cache/cord-316859-h8lfmr3e.txt txt = ./txt/cord-316859-h8lfmr3e.txt === reduce.pl bib === id = cord-316880-hbw6jbz5 author = Sutton, Melissa title = Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 date = 2020-08-14 pages = extension = .txt mime = text/plain words = 517 sentences = 43 flesch = 48 summary = title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 to the Oregon State Public Health Laboratory for testing with the Abbott Architect Laboratories SARS-CoV-2 IgG immunoassay. Antibodies to SARS-CoV-2 were detected in nine of 897 specimens, yielding an unadjusted seroprevalence of 1.0% (95% confidence interval = 0.2%-1.8%). The estimated seroprevalence of SARS-CoV-2 antibodies in a convenience sample of adult Oregonians was approximately 10 times the measured cumulative COVID-19 incidence obtained by nucleic acid testing, consistent with results from seven other U.S. states and geographic areas (4). Population point prevalence of SARS-CoV-2 infection based on a statewide random sample-Indiana Estimated community seroprevalence of SARS-CoV-2 antibodies-two Georgia counties Seroprevalence of antibodies to SARS-CoV-2 in 10 sites in the United States All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. cache = ./cache/cord-316880-hbw6jbz5.txt txt = ./txt/cord-316880-hbw6jbz5.txt === reduce.pl bib === id = cord-317151-cxx5pcln author = Papa, Alfredo title = Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date = 2020-10-24 pages = extension = .txt mime = text/plain words = 5030 sentences = 254 flesch = 44 summary = 14 Since the beginning of the pandemic, the World Health Organization has provided general recommendations for the prevention of They include: to wash hands frequently and properly with soap or alcohol-based sanitizer, to maintain social distancing (at least 1 m of distance), to avoid touching eyes, nose and mouth, to cover mouth and nose when coughing or sneezing, to seek medical care early when fever, cough or difficulty in breathing are recorded, to wear personal protective equipment (PPE), in particular the facial mask when social distancing is not possible to maintain or in closed places, to stay informed and follow any advice provided by own healthcare providers. This may require further changes in the planning of healthcare activities, both by using different prioritization criteria for outpatient visits, diagnostic tests and surgical interventions and by continuing to use treatment strategies that have worked well during the pandemic such as telemedicine, psychological support to patients and the educational function of patient associations (Table 1) . cache = ./cache/cord-317151-cxx5pcln.txt txt = ./txt/cord-317151-cxx5pcln.txt === reduce.pl bib === id = cord-316845-k9zvsfvj author = Robertson, Mary M. title = Gilles de la Tourette Syndrome: advice in the times of COVID-19 date = 2020-04-28 pages = extension = .txt mime = text/plain words = 3763 sentences = 212 flesch = 53 summary = These include the coronaviruses, which have caused multiple major public health events that resulted in global pandemics such as severe acute respiratory syndrome (SARS; or "bat SARS"), Middle East respiratory syndrome (MERS) and the current coronavirus disease (COVID-19) (Kandeel et al., 2020). GTS, as a complex neuropsychiatric disorder, offers many angles of attack for the current COVID-19 pandemic and its consequences (social distancing, home schooling, confinement/quarantine, and living in a general climate of fear). The authors discuss similarities of COVID-19 and tics in GTS and outline specific problems that may result from the pandemic for this group of patients. I like this small paper and find it interesting to read, since it alerts us that the current pandemic may be much more challenging for patients with GTS compared to healthy people. Also in Table 1 : "Viral infection -Coronavirus 19" please change in "SARS-CoV-2".The authors describe the different symptoms associated with COVID-19 including neurological complications. cache = ./cache/cord-316845-k9zvsfvj.txt txt = ./txt/cord-316845-k9zvsfvj.txt === reduce.pl bib === id = cord-316788-4x5l2h4d author = Ryu, Young Bae title = Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition date = 2010-11-15 pages = extension = .txt mime = text/plain words = 3222 sentences = 173 flesch = 59 summary = Following bioactivity-guided fractionation, eight diterpenoids (1–8) and four biflavonoids (9–12) were isolated and evaluated for SARS-CoV 3CL(pro) inhibition using fluorescence resonance energy transfer analysis. As part of an ongoing investigation of potential SARS-CoV 3CL pro inhibitors from medicinal plants, we performed an initial screen of ethanol extracts of the leaves of Torreya nucifera using a fluorescence resonance energy transfer (FRET) assay. We isolated 12 phytochemicals-eight diterpenoids and four biflavonoids-with SARS-CoV 3CL pro inhibitory activity from the ethanol extracts of the leaves of T. Of the isolated compounds, biflavonoid amentoflavone (9) was identified as a potent inhibitor of SARS-CoV 3CL pro , exhibiting an IC 50 value of 8.3 lM. nucifera, is an effective inhibitor of SARS-CoV 3CL pro and is more effective than the corresponding flavones (apigenin and luteolin) and biflavonoid derivatives containing various numbers of methoxy groups. cache = ./cache/cord-316788-4x5l2h4d.txt txt = ./txt/cord-316788-4x5l2h4d.txt === reduce.pl bib === id = cord-317129-wa1j2f6b author = Zhang, Jia title = De Novo synthesis of PCR templates for the development of SARS diagnostic assay date = 2003 pages = extension = .txt mime = text/plain words = 2319 sentences = 117 flesch = 58 summary = This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. This single-step sequential primer extension was expected to yield mainly final templates with no intermediate products. As shown in Figure 1 , DNA fragments in lengths of 182 and 204 bp were obtained from primers of set A and set B, respectively, by the single-step sequential primer extension where each reaction contained four partially overlapping a The expected products were extended from reverse primers (AR or BR) to the first forward primers. De novo synthesis of the PCR template complimentary to a viral genome provides a tool for the rapid development of early diagnostic assays for any new pathogen as soon as its sequence is known. cache = ./cache/cord-317129-wa1j2f6b.txt txt = ./txt/cord-317129-wa1j2f6b.txt === reduce.pl bib === id = cord-317092-5qba9jiq author = Singh, Tulika title = Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date = 2020-05-08 pages = extension = .txt mime = text/plain words = 4971 sentences = 355 flesch = 49 summary = The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children's immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. cache = ./cache/cord-317092-5qba9jiq.txt txt = ./txt/cord-317092-5qba9jiq.txt === reduce.pl bib === id = cord-317355-z5tk3v3b author = Dunker, Susanne title = No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread date = 2020-10-13 pages = extension = .txt mime = text/plain words = 1954 sentences = 139 flesch = 62 summary = title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread Air samples collected at our measuring station in Leipzig and purified pollen were analyzed for SARS-CoV-2 typical signals or for virus-induced cytopathic effects, to test if the virus could bind to bioaerosols and if so, whether these complexes are infectious. We therefore aimed at investigating whether SARS-CoV-2 can bind to pollen or other kind of particulate matter within bioaerosols sampled at our station in Leipzig and if so, whether these complexes are infectious. In none of these samples SARS-CoV-2 typical For a detailed analysis of a possible correlation between concentrations of the most abundant pollen, particulate matter and registered Covid-19 cases, a correlation matrix was created with R (package "PerformanceAnalytics") (Fig. 2) . cache = ./cache/cord-317355-z5tk3v3b.txt txt = ./txt/cord-317355-z5tk3v3b.txt === reduce.pl bib === id = cord-317123-0tdfvlqd author = Tan, Xiaotian title = Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4154 sentences = 220 flesch = 52 summary = Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. In this work, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, and sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen -S protein, both of which are spiked in serum, as a model system. For the anti-S1 IgG detection experiments (see Figure S2 (B) for the detailed protocol), various concentrations of monoclonal antibodies were prepared by diluting the stock solutions with 50 times diluted human serum (the serum was diluted with 1× reagent diluent, which correlates to 1% BSA). cache = ./cache/cord-317123-0tdfvlqd.txt txt = ./txt/cord-317123-0tdfvlqd.txt === reduce.pl bib === id = cord-317227-zb434ve3 author = Beck, Bo Ram title = Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model date = 2020-03-30 pages = extension = .txt mime = text/plain words = 3187 sentences = 174 flesch = 49 summary = title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model In this study, we applied our pre-trained MT-DTI model to identify commercially available antiviral drugs that could potentially disrupt SARS-CoV-2's viral components, such as proteinase, RNA-dependent RNA polymerase, and/or helicase. AutoDock Vina (version 1.1.2), which is a molecular docking and virtual screening application (17) , was used to predict binding affinities (kcal/mol) between 3C-like proteinase of SARS-CoV-2 and 3,410 FDA-approved drugs. To identify potent FDA-approved drugs that may inhibit the functions of SARS-CoV-2's core proteins, we used the MT-DTI deep learning-based model, which can accurately predict binding affinities based on chemical sequences (SMILES) and amino acid sequences (FASTA) of a target protein, without their structural information (12) . Drug-target interaction (DTI) prediction results of antiviral drugs available on markets against a novel coronavirus (SARS-CoV-2, NCBI reference sequence NC_045512.2) RNA-dependent RNA polymerase (accession YP_009725307.1). cache = ./cache/cord-317227-zb434ve3.txt txt = ./txt/cord-317227-zb434ve3.txt === reduce.pl bib === id = cord-317067-u90zkjk9 author = Trottein, François title = Potential causes and consequences of gastrointestinal disorders during a SARS-CoV-2 infection date = 2020-07-03 pages = extension = .txt mime = text/plain words = 639 sentences = 48 flesch = 44 summary = Intensive research on the pathogenic mechanisms used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed – notably in order to identify potential drug targets. Here, we review gastrointestinal disorders in patients with COVID-19, suggest hypothetical mechanisms leading to gut symptoms, and discuss the potential consequences of gastrointestinal disorders on the outcome of the disease. Lastly, we discuss the role of the gut microbiota during respiratory viral infections and suggest that targeting gut dysbiosis may help to control the pathogenesis of COVID-19. In this review, Trottein & Sokol present hypothetical mechanisms leading to gut symptoms in patients with COVID-19 and discuss their potential consequences on disease severity. They also discuss the role of the gut microbiota in disease and the potential interest of targeting it to improve COVID-19 pathogenesis. Clinical characteristics of 138 hospitalized patients with 2019 novel 589 coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-317067-u90zkjk9.txt txt = ./txt/cord-317067-u90zkjk9.txt === reduce.pl bib === id = cord-317246-8c7d5ynz author = Cagetti, Maria Grazia title = Could SARS‐CoV‐2 burst the use of Non‐Invasive and Minimally Invasive treatments in paediatric dentistry? date = 2020-08-03 pages = extension = .txt mime = text/plain words = 2133 sentences = 128 flesch = 46 summary = The non-invasive treatment includes the non-restorative cavity control that manages non-cavitated and cavitated active caries lesions making them cleanable and promoting their arrest through the use fluoride vehicles only. Non-operative caries treatment is mostly recommended for decayed primary teeth, but may represent a suitable alternative also for permanent teeth of children with dental anxiety or disabilities, who offer insufficient collaboration for the traditional restorative treatment. 27 The non-invasive treatment and the minimally invasive treatment are often recommended in controlling and treating dental caries in children; however, even though dentists seem to know the advantages of these strategies, the traditional caries removal and restoration therapy are still preferred. 29 In conclusion, caries treatment using the non-invasive or the minimally invasive treatments is desirable, especially since the transmission risk of SARS-CoV-2 is potentially higher in the dental environment. cache = ./cache/cord-317246-8c7d5ynz.txt txt = ./txt/cord-317246-8c7d5ynz.txt === reduce.pl bib === id = cord-317413-w2xfdwea author = Maurya, Vimal K. title = Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection date = 2020-10-19 pages = extension = .txt mime = text/plain words = 5654 sentences = 285 flesch = 30 summary = Therefore, we have planned to investigate the active constituents present in these medicinal plants for possible antiviral activity against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor using structure-based drug design method. Besides these active constituents, molecules such as 6-gingerol, glycyrrhetic acid, piperine, sawertiamarine, magnoflorine, scopolamine, atropine, eupafolin, and hyoscyamine also have strong binding affinity towards spike glycoprotein and may be developed potential candidates against SARS-CoV-2 infection (supplementary Figures 1 and 2 ). The active constituents present in selected plants were evaluated for the prediction of potential attachment inhibitors against SARS-CoV-2 via targeting spike glycoprotein as well as its host receptor ACE2. Structure-based drug designing for potential antiviral activity of selected natural products from Ayurveda against SARS-CoV-2 spike glycoprotein and its cellular receptor cache = ./cache/cord-317413-w2xfdwea.txt txt = ./txt/cord-317413-w2xfdwea.txt === reduce.pl bib === id = cord-317333-unrd76bo author = Danesh, Ali title = Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date = 2011-01-05 pages = extension = .txt mime = text/plain words = 5467 sentences = 278 flesch = 48 summary = Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) . cache = ./cache/cord-317333-unrd76bo.txt txt = ./txt/cord-317333-unrd76bo.txt === reduce.pl bib === id = cord-317429-pp6hb4q5 author = Aslam, Saima title = COVID-19: Yet another coronavirus challenge in transplantation date = 2020-03-14 pages = extension = .txt mime = text/plain words = 1405 sentences = 78 flesch = 47 summary = A novel coronavirus, severe acute respiratory syndrome −coronavirus-2 (SARS-CoV-2), causing a severe acute respiratory syndrome with its disease designated as COVID-19, emerged from its epicenter in Wuhan, China, in December 2019 and is now a global pandemic. 7 report on the presentation and outcome of 2 microbiologically confirmed COVID-19 cases in heart transplantation detected in the Hubei Province in China. These 2 patients apparently were part of a community of at least 200 heart transplant survivors in that region and presented with variable severity of disease (one mild and another with more severe manifestations requiring a prolonged hospitalization); however, both survived the event. It is important to note that the clinical presentations were not distinct from those described in non-immunosuppressed individuals, and the patient with severe disease presented with a viral prodrome, displayed the typical findings on CT scan imaging, and progressed to clinical hypoxia. In summary, the novel coronavirus and its disease, COVID-19, require thoughtful approaches for the prevention, mitigation, timely detection, and appropriate therapeutic intervention for our vulnerable patients. cache = ./cache/cord-317429-pp6hb4q5.txt txt = ./txt/cord-317429-pp6hb4q5.txt === reduce.pl bib === id = cord-318018-ybdkp398 author = Bruni, Margherita title = Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date = 2020-10-01 pages = extension = .txt mime = text/plain words = 5481 sentences = 263 flesch = 46 summary = Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Our data show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory cytokines. Here we show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory mediators. Moreover, we showed that the vast majority of COVID-19 mildly symptomatic patients analyzed in the study halved their anti-RBD antibody titers after 4 weeks from viral negativization, thus confirming the short lifespan of humoral immune responses against SARS-CoV-2. cache = ./cache/cord-318018-ybdkp398.txt txt = ./txt/cord-318018-ybdkp398.txt === reduce.pl bib === id = cord-317591-qa6oxy4j author = Fukushima, Akiko title = Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date = 2009-05-07 pages = extension = .txt mime = text/plain words = 3605 sentences = 196 flesch = 53 summary = To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells. cache = ./cache/cord-317591-qa6oxy4j.txt txt = ./txt/cord-317591-qa6oxy4j.txt === reduce.pl bib === id = cord-317240-d7ioosi6 author = Shah, Niyati title = Review: An insight into coronaviruses: Challenges, security and scope date = 2020-08-04 pages = extension = .txt mime = text/plain words = 2285 sentences = 151 flesch = 59 summary = In principle, a molecule can act as an anti-viral drug if it inhibits some stage of the virus replication cycle, without being too toxic to the body cells. Out of these, the data of 8 patients could not be analyzed F I G U R E 2 A general mechanism of viral replication in host cells and functions of inhibitors at various stages during the process. A drug which is designed to be a fusion inhibitor will function at this stage by preventing the virus from binding with the receptor. This trial reported reduced mortality rates and also clinical improvements in 68% of the patients by the use of remdesivir. In cell culture, chloroquine shows activity against the SARS-CoV-2 virus, but the dosage requirements are usually high which may lead to serious toxicities if administered to humans. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (H1N1) 2009 virus infection cache = ./cache/cord-317240-d7ioosi6.txt txt = ./txt/cord-317240-d7ioosi6.txt === reduce.pl bib === id = cord-317435-4yuw7jo3 author = Zhou, Yadi title = Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 date = 2020-03-16 pages = extension = .txt mime = text/plain words = 7742 sentences = 388 flesch = 39 summary = Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. The high druggability of HCoV-host interactome motivates us to develop a drug repurposing strategy by specifically targeting cellular proteins associated with HCoVs for potential treatment of 2019-nCoV/SARS-CoV-2. These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). cache = ./cache/cord-317435-4yuw7jo3.txt txt = ./txt/cord-317435-4yuw7jo3.txt === reduce.pl bib === id = cord-317523-idji1l0a author = Xu, Huanzhou title = SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date = 2020-10-27 pages = extension = .txt mime = text/plain words = 1192 sentences = 59 flesch = 42 summary = With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. To assess if ORF3a also 135 mediates activation of other prominent inflammasomes including NLRP1 and NLRC4, we 136 depleted each of these molecules but were unable to block cleavage of pro-caspase 1 (Fig.2G) , 137 indicating that ORF3a predominantly activates the NLRP3 inflammasome. In summary, an essential viroporin required for release of SARS-CoV-2 from infected cells is also 178 able to prime and activate the NLRP3 inflammasome, the machinery responsible for much of the cache = ./cache/cord-317523-idji1l0a.txt txt = ./txt/cord-317523-idji1l0a.txt === reduce.pl bib === id = cord-317563-mu47vvma author = Yuan, Chunhui title = Viral loads in throat and anal swabs in children infected with SARS-CoV-2 date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2297 sentences = 108 flesch = 50 summary = Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay on anal swabs was recently reported to be persistently positive even after throat testing was negative during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Furthermore, viral loads detected on both throat and anal swabs also showed no significant difference (P = 0.9511) and correlation (Pearson r = 0.0434, P = 0.8406), and exhibited an inconsistent kinetic change through the course of SARS-CoV-2 infection. These findings revealed that RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune state in paediatric patients. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay has been widely used for clinical diagnosis and SARS-CoV-2 has been detected in specimens from multiple sites, including bronchoalveolar lavage fluid, sputum, nasal, anal, and throat swabs of patients with COVID-19 [2] . In conclusion, RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune states in paediatric patients. cache = ./cache/cord-317563-mu47vvma.txt txt = ./txt/cord-317563-mu47vvma.txt === reduce.pl bib === id = cord-317761-tkqmu1va author = Shukla, Ashutosh M title = Chloroquine and hydroxychloroquine in the context of COVID-19 date = 2020-04-28 pages = extension = .txt mime = text/plain words = 4111 sentences = 191 flesch = 42 summary = This review aims to present the available in vitro and clinical data for the role of chloroquine/hydroxychloroquine in COVID-19 and attempts to put them into perspective, especially in relation to the different risks/benefits particular to each patient who may require treatment. 1 These agents have also shown a promising role in viral infections, and with the recent declaration on March 12th, 2020, by the World Health Organization that coronavirus disease (COVID) of 2019 (COVID-19) is a pandemic, these compounds have rapidly gained worldwide attention for their ability to control the causative virus, severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2). 1 These include inhibition of ligand-based toll-like receptor stimulation, inhibition of nuclear factor kappalight-chain-enhancer of activated B cells (NFkB) pathways in macrophages with resultant reduction in the generation of pro-inflammatory cytokines, reduced processing of the endogenous and exogenous ligands through lysosomes and endosomes with resultant reduction in the availability of processed antigens for presentation to the major ISSN: 1740-4398 REVIEW -Chloroquine, hydroxychloroquine, and COVID-19 drugsincontext.com histocompatibility complex-T cell receptor interactions, and downstream activation of cellular immunity. cache = ./cache/cord-317761-tkqmu1va.txt txt = ./txt/cord-317761-tkqmu1va.txt === reduce.pl bib === id = cord-317423-3nkzp1z2 author = Turk, Can title = In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4303 sentences = 266 flesch = 53 summary = RESULTS: The whole-genome expression data of the lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were analyzed, and a total of 15 RAS family and 29 immune genes were found to be highly correlated with the exposure time to the virus in the studied groups. 13, 21 The main purpose of this present in silico genomic study was to assess how the expressions of the RAS gene family changes after cellular infection with SARS-CoV in the lung epithelial cell culture. The whole normalized gene expression data of lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were compared between different groups in order to determine significantly and differentially expressed RAS family genes. Based on our results, in this phase, as the exposure time to SARS-CoV increases, EGFR and IGF2R, two receptors with key roles in the RAS signaling pathway, were significantly down-regulated in the infected human bronchial epithelial cells. cache = ./cache/cord-317423-3nkzp1z2.txt txt = ./txt/cord-317423-3nkzp1z2.txt === reduce.pl bib === id = cord-317359-7yuygcew author = Straccia, Patrizia title = Description of a new biosafe procedure for cytological specimens from patients with COVID‐19 processed by liquid‐based preparations date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1782 sentences = 99 flesch = 43 summary = CONCLUSIONS: Despite some minor changes in the morphology of the cells, the results of this study highlight that the adoption of the new protocol for the biosafety of LBC‐processed samples in pathology laboratories is important for minimizing the risk for personnel, trainees, and cytopathologists without impairing the diagnostic efficacy of the technique. 8 The new coronavirus, Cancer Cytopathology Month 2020 originally called 2019 novel coronavirus (2019-nCoV) and officially renamed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and the disease it causes, namely coronavirus disease 2019 (COVID-19), have quickly become of tremendous concern worldwide. Because the laboratory personnel might be exposed to contamination during the preparation and handling of fresh specimens from such patients, a new procedure for the sterilization of material to be processed by liquid-based cytology (LBC) has been applied. cache = ./cache/cord-317359-7yuygcew.txt txt = ./txt/cord-317359-7yuygcew.txt === reduce.pl bib === id = cord-317379-ljdaj80d author = Faure‐Bardon, V. title = Anatomical and timely assessment of protein expression of angiotensin‐converting enzyme 2, SARS‐CoV‐2 specific receptor, in fetal and placental tissues: new insight for perinatal counseling date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2190 sentences = 157 flesch = 54 summary = Beyond theoretical assessment of risk and pathways for vertical transmission, the low incidence of perinatal infections might relate to a lower expression of ACE2 in the placenta and targeted organs. We aimed to evaluate protein expression of ACE2 both in placentas and in all fetal organs from pregnancies not infected with SARS-CoV2 at various gestational ages. Seven placentas were analyzed including 5 from the cases described above, 1 from a 7 weeks'-miscarriage, and 1 from a symptomatic infected pregnant woman with positive SARS-CoV2 RT-PCR delivered by cesarean section at 34 weeks'. These results broaden the insight on likelihood, pathways and morbidities of vertical transmission of SARS-CoV-2, providing a unique anatomical and timely validation of the protein distributions in fetal organs and placentas. The marked placental presence of the specific SARS-CoV2 receptor, ACE2, and its absence from the amnion suggests that ascending vertical transmission could mainly occur following rupture of the amniotic membranes. cache = ./cache/cord-317379-ljdaj80d.txt txt = ./txt/cord-317379-ljdaj80d.txt === reduce.pl bib === id = cord-317608-otd81rvy author = Corman, Victor M. title = SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission date = 2020-05-27 pages = extension = .txt mime = text/plain words = 1245 sentences = 75 flesch = 56 summary = Oral swabs, sputum, and blood samples from 18 asymptomatic and symptomatic patients with SARS‐CoV‐2 infection were examined using RT‐PCR testing in order to assess the risk of transfusion‐related transmission. In asymptomatic patients as well as patients with flu‐like symptoms and fever, no SARS‐CoV‐2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • In asymptomatic patients as well as patients with flulike symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • As patients with symptoms of infectious disease will not be admitted to blood donation, the risk for transfusion transmission of SARS-CoV-2 seems to be negligible. In asymptomatic patients who are eligible for blood donation as well as patients with flu-like symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. cache = ./cache/cord-317608-otd81rvy.txt txt = ./txt/cord-317608-otd81rvy.txt === reduce.pl bib === id = cord-317573-wp2wr3b5 author = Peng, Hui title = Human memory T cell responses to SARS-CoV E protein date = 2006-06-30 pages = extension = .txt mime = text/plain words = 4124 sentences = 197 flesch = 60 summary = In this study, we found that peripheral blood mononuclear cells (PBMCs) from fully recovered SARS individuals rapidly produced IFN-γ and IL-2 following stimulation with a pool of 9 peptides overlapping the entire E protein sequence. To assess memory T cell response specific for E protein after SARS-CoV infection in humans, PBMCs from individuals who had fully recovered from SARS two years after infection were stimulated with a pool of 9 peptides spanning the entire amino acid sequence of the SARS-CoV E protein, or the cells were stimulated with anti-CD3 and anti-CD28 antibodies under the same culture conditions as positive controls. Similarly, the frequency of SARS-CoV E antigen-specific IFN-g-producing cells determined by IFN-g ELISPOT assay in PBMCs from 8 fully recovered SARS individuals was significantly higher than that of the cells from the normal donor controls in response to E peptides (Fig. 1B) . cache = ./cache/cord-317573-wp2wr3b5.txt txt = ./txt/cord-317573-wp2wr3b5.txt === reduce.pl bib === id = cord-317820-od9l7p1r author = Goker Bagca, Bakiye title = Overview of the COVID-19 and JAK/STAT Pathway Inhibition: Ruxolitinib Perspective date = 2020-06-20 pages = extension = .txt mime = text/plain words = 3961 sentences = 233 flesch = 41 summary = The virus, which is the cause of the COVID-19 was named as Severe Acute Respiratory Syndromerelated Coronavirus (SARS-CoV-2) by Coronaviridae Study Group of the International Committee on Taxonomy of Viruses (Figure 1a) . As an expected result of SARS-CoV-2 infection, it was reported cytokine storm syndrome triggered by the dysregulated immunity in numerous patients. There are clinical studies including baricitinib, tofacitinib, and ruxolitinib JAK inhibitors against cytokine storm caused by COVID-19. It is reported that tocilizumab which is an approved IL6 receptor antagonist, treatment reduced cytokine release syndrome symptoms in severe patients COVID-19 [66] . It is reported that the usage of ruxolitinib suppresses cytokine levels and JAK/STAT pathway in Epstein-Barr Virus (EBV) -associated hemophagocytic lymphohistiocytosis [71] . In this context, it is clear that ruxolitinib, which is used especially in older age patients, has an important potential in overcoming complications that are caused by over activation of the immune system which is triggered through JAK/STAT signaling pathway. cache = ./cache/cord-317820-od9l7p1r.txt txt = ./txt/cord-317820-od9l7p1r.txt === reduce.pl bib === id = cord-317647-vcktnsv8 author = Wang, Yinhua title = Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1766 sentences = 152 flesch = 53 summary = title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis We plan to systematically review the use of ribavirin in patients with coronavirus-related pneumonia and meta-analyze the data with updated studies. Therefore, we aim to systematically review the use of ribavirin on coronavirus-related pneumonia (SARS, MERSS, and COVID-19) and meta-analyze the data with the results of the updated RCTs to provide advanced evidence. We aim to assess the safety and efficacy of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19). Our systematic review and meta-analysis will include these updated results and re-assess the efficacy and safety of ribavirin in patients with coronavirus-related pneumonia. Efficacy and safety of antiviral treatment for COVID-19 from evidence in studies of SARSCoV-2 and other acute viral infections: a systematic review and meta-analysis cache = ./cache/cord-317647-vcktnsv8.txt txt = ./txt/cord-317647-vcktnsv8.txt === reduce.pl bib === id = cord-317628-1inxq7t5 author = Cuccarese, Michael F. title = Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date = 2020-08-14 pages = extension = .txt mime = text/plain words = 9573 sentences = 487 flesch = 43 summary = We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. We used these capabilities to rapidly develop high-throughput-ready disease models for both SARS-CoV-2 viral infection and the resulting cytokine storm, and immediately launched large-scale drug screens that recapitulated known effective and ineffective therapies and, more importantly, identified several new potential treatments for both SARS-CoV-2 infection and COVID-19-associated cytokine storm. To define the model, we evaluated the effect of SARS-CoV-2 infection in multiple cell types, of which three resulted in robust phenoprints as compared to either mock infected or inactivated virus control populations: Calu3 (a lung adenocarcinoma line), Vero (an immortalized interferondeficient African green monkey kidney line 55 ), and primary Human Renal Cortical Epithelium (HRCE) (Fig. 5C, Fig. S6D ). cache = ./cache/cord-317628-1inxq7t5.txt txt = ./txt/cord-317628-1inxq7t5.txt === reduce.pl bib === id = cord-317952-4oa9hfb4 author = Bourgonje, Arno R. title = Angiotensin‐converting enzyme‐2 (ACE2), SARS‐CoV‐2 and pathophysiology of coronavirus disease 2019 (COVID‐19) date = 2020-05-17 pages = extension = .txt mime = text/plain words = 12082 sentences = 664 flesch = 38 summary = ACE2 was highly expressed on lung alveolar epithelial cells and small intestinal epithelial cells, consistent with potential routes of viral transmission of SARS-CoV-2, as both respiratory and gastrointestinal systems share interfaces with the external environment. ACE2 expression in the lungs and SARS-CoV-2 viral load have been suggested to increase with age, which might provide an explanation to the higher disease severity observed in older patients with COVID-19 [35] . Both SARS-CoV-2 infection, directly mediated by ACE2 expression and activity, and superimposed disease triggers may be responsible for the observed pathological findings. Additionally, another study reported purpura and livedo racemosa in several severely affected COVID-19 patients with small vessel thrombosis with co-localization of complement and SARS-CoV-2 spike proteins on histopathology [148] .This indicates direct viral infection of the small skin vessels. Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone-inhibitors: Potential implications for coronavirus SARS-CoV-2 infected patients cache = ./cache/cord-317952-4oa9hfb4.txt txt = ./txt/cord-317952-4oa9hfb4.txt === reduce.pl bib === id = cord-317468-pnxni1x5 author = Louie, Philip K. title = Early Peri-operative Outcomes Were Unchanged in Patients Undergoing Spine Surgery During the COVID-19 Pandemic in New York City date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3474 sentences = 151 flesch = 39 summary = The purpose of this study was to describe the peri-operative outcomes of patients undergoing spine surgery for spine pathology during the heights of the COVID-19 pandemic in New York City, including particular attention to the development of SARS-CoV-2 symptoms, post-operative complications, and patient monitoring following hospital discharge during the early post-operative period. The surgical dates also encompass a period of time in which the institution (1) followed state directives to suspend elective surgery and instead utilize strict criteria to define essential surgical cases (Table 1) , (2) dispensed personal protective equipment to medical personnel, (3) selectively performed post-admission SARS-CoV-2 testing (Cepheid Xpert Xpress SARS-CoV-2 RT-PCR, Sunnyvale, CA, USA) following patient assessment by a multidisciplinary team, (4) initiated a telehealth service for post-operative follow-up, and (5) began a progressively intensive patient screening process (Fig. 1) . cache = ./cache/cord-317468-pnxni1x5.txt txt = ./txt/cord-317468-pnxni1x5.txt === reduce.pl bib === id = cord-317971-kuwargnp author = Opatz, Till title = Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2881 sentences = 176 flesch = 53 summary = [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. cache = ./cache/cord-317971-kuwargnp.txt txt = ./txt/cord-317971-kuwargnp.txt === reduce.pl bib === id = cord-317622-o10ntfi8 author = Evans, Ronald M. title = Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing date = 2020-09-11 pages = extension = .txt mime = text/plain words = 4646 sentences = 230 flesch = 39 summary = In patients, severity of liver disease correlates inversely with VDR expression, levels of vitamin D, and metabolites (Oh et al., 2020) , and hepatocellular injury directly with progressive COVID-19 (Henry et al., 2020; Ji et al., 2020) . Similar effects were observed in non-lung models; e.g., vitamin D deficiency (or VDR knockout) was associated with increased renin and Ang II (and IL-6 and TGFb) levels in diabetic mice (Zhang et al., 2008) . Human intestinal organoids (ACE2 expressing), suggesting a gut enterocyte reservoir for SARS-CoV-2, fuel viral spread and cytokine response in COVID-19 pathogenesis, another potential enteric-phase inflammatory hurdle to oral vitamin D administration (Clevers, 2020) . Heightened basal RAS (e.g., reduced ACE2 expression, higher Ang II levels) activation and inflammatory states (Ajilore and Thames, 2020; Albert and Ridker, 2004; Suthanthiran et al., 2000; Vinciguerra and Greco, 2020) , reported in African Americans, are associated with severe COVID-19 outcomes and relevant risk co-morbidities (e.g., hypertension, diabetes), some linked to vitamin D deficiency (Rostand, 2010; Yancy, 2020) . cache = ./cache/cord-317622-o10ntfi8.txt txt = ./txt/cord-317622-o10ntfi8.txt === reduce.pl bib === id = cord-317593-tajy3p9e author = Xi, AIqi title = Epidemiological and clinical characteristics of discharged patients infected with SARS-CoV-2 on the Qinghai plateau date = 2020-04-29 pages = extension = .txt mime = text/plain words = 3146 sentences = 212 flesch = 56 summary = Since the outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, a series of confirmed cases of COVID-19 were found on the Qinghai-Tibet plateau. Coronavirus disease 2019 , caused by infection with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, Hubei, China in December 2019 [1] [2] [3] [4] and rapidly spread worldwide. For this retrospective study, we enrolled all 18 patients infected with SARS-CoV-2 from the hospitals designated for treatment by the Health Commission of Qinghai Province from Jan 21 to April 6, 2020. Convalescent plasma has been used to improve the survival rate of patients with severe acute respiratory syndrome (SARS) coronavirus infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China cache = ./cache/cord-317593-tajy3p9e.txt txt = ./txt/cord-317593-tajy3p9e.txt === reduce.pl bib === id = cord-317707-r0q7ipa6 author = Saracco, Margherita title = Carrying on with Liver Transplantation during the COVID-19 emergency: Report from Piedmont Region date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2843 sentences = 159 flesch = 58 summary = We aimed to analyze the number of LT performed between February 24 th , 2020 and April 17 th , 2020 with the same period of time in 2019, in our high-volume transplant Center (median 150 LT/year). Furthermore, among the 5 intensive care units of our hospital, the one dedicated to transplants was maintained COVID-free, by testing each transplant recipient in advance with SARS-CoV-2 RNA in NPS or BAL, starting from the 22 nd of March. Between February 24 th , 2020 and April 17 th , 2020, among 22 admissions in our 7-bed sub-intensive liver unit, a 40-year-old woman, who was listed during hospitalization, developed fever during hospitalization and tested positive for SARS-CoV-2 RNA in NPSs. Immediately transferred to a COVID unit, she came back to our unit after 7 days and 2 negative SARS-CoV-2 RNA in NPS and underwent LT the day after readmission to our unit. Despite all our efforts to maintain a transplant COVID-free pathway, two transplant patients, one before and one after LT were tested SARS-CoV-2 virus positive during hospitalization and both were safely discharged home. cache = ./cache/cord-317707-r0q7ipa6.txt txt = ./txt/cord-317707-r0q7ipa6.txt === reduce.pl bib === id = cord-318204-t024w7h6 author = Fang, Ferric C title = The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2976 sentences = 218 flesch = 51 summary = As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection cache = ./cache/cord-318204-t024w7h6.txt txt = ./txt/cord-318204-t024w7h6.txt === reduce.pl bib === id = cord-317906-u5z5cpfk author = Gupta, Ishita title = Atypical Neurological Manifestations of COVID-19 date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2184 sentences = 163 flesch = 58 summary = The novel coronavirus (SARS-CoV-2), belonging to a group of RNA-enveloped viruses and believed to be transmitted by aerosol route, is a worldwide pandemic. However, to our knowledge, there are minimal studies on the neurological manifestations in SARS-CoV-2 positive patients. Our review aims to identify the various neurological manifestations in SARS-CoV-2 positive patients, which could be an added advantage in the early diagnosis and prevention of further complications of the nervous system. Other non-neurological symptoms were diarrhea, anorexia, myalgia, sore throat, dyspnea, chest pain, fatigue, headache, arthralgia, nausea, and vomiting (see Figure 2 and Table 3 ) [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] . The presentation of olfactory symptoms in SARS-CoV-2-affected patients is due to the fact that the illness spreads through the cribriform plate, which is in close proximity to the olfactory region [30] . Neurological manifestations in COVID-19 caused by SARS-CoV-2 cache = ./cache/cord-317906-u5z5cpfk.txt txt = ./txt/cord-317906-u5z5cpfk.txt === reduce.pl bib === id = cord-318262-w8oixzdg author = Chevance, A title = Ensuring mental health care during the SARS-CoV-2 epidemic in France: a narrative review date = 2020-04-22 pages = extension = .txt mime = text/plain words = 6747 sentences = 303 flesch = 40 summary = Results: We identified four types of major vulnerabilities among patients with mental disorders during this pandemic: 1) medical comorbidities that are more frequently found among patients with mental disorders (cardiovascular and pulmonary pathologies, diabetes, obesity, etc.) which are risk factors for severe covid-19 infection; 2) age (the elderly form the population most vulnerable to the coronavirus); 3) cognitive and behavioural disorders, which can hamper compliance with confinement and hygiene measures and finally and 4) psychosocial vulnerability as a result of stigmatization and/or socio-economic difficulties. At the end of hospitalization, in particular for the population of patients in compulsory ambulatory care situations, specific case-management are organized with the possibility of home visits, in order to support patients when they get back home and to help them cope with the experience of confinement, which is liable to induce recurrences of mental disorders. cache = ./cache/cord-318262-w8oixzdg.txt txt = ./txt/cord-318262-w8oixzdg.txt === reduce.pl bib === id = cord-318048-6nvi63rq author = Arshad, Usman title = Prioritisation of Anti‐SARS‐Cov‐2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5663 sentences = 288 flesch = 46 summary = An indication of the degree to which candidate drugs are expected to accumulate in lung (a presumed site of primary efficacy and for prevention of SARS-CoV-2 infection) was provided by calculation of unbound Accepted Article lung to plasma tissue partition coefficient (K p U lung ) according to the methodology of Rodgers and Rowland (20-22). All rights reserved Simulated exposure relative to reported anti-SARS-CoV-2 activity in lung and other tissues Lung K p U was simulated for all molecules for which the necessary physicochemical properties and in vitro drug binding information were available. The rank order of lung Cmax/EC 90 ratio was chloroquine > atazanavir (ritonavir boosted) > tipranavir (ritonavir boosted) > hydroxychloroquine > mefloquine > ivermectin > lopinavir (ritonavir boosted) > azithromycin > nitazoxanide > ritonavir > gilteritinib > amodiaquine > imatinib > oxprenolol (data excluded due to this analysis only being possible for 33 of the 56 drugs). cache = ./cache/cord-318048-6nvi63rq.txt txt = ./txt/cord-318048-6nvi63rq.txt === reduce.pl bib === id = cord-317928-doj39520 author = Thum, Thomas title = SARS-CoV-2 receptor ACE2 expression in the human heart: cause of a post-pandemic wave of heart failure? date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1462 sentences = 85 flesch = 48 summary = A number of pre-clinical studies have shown various organ systems to express the primary SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2). Potentially, the COVID-19 outbreak will also lead to an increase of long-term complications of patients with CVD such as heart failure in both patients infected with SARS-CoV-2 and those that are not infected but that were treated suboptimally during the ongoing pandemic ( Figure 1 ). In conclusion, Nicin and co-workers report here an important observation with future implications in both research and, potentially, treatment of SARS-CoV-2-infected cardiovascular patients. These novel data at least suggest that it will be important to monitor SARS-CoV-2-infected patients for cardiovascular complications and assess the impact of ARB/ACE inhibitor therapy in more detail. Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 cache = ./cache/cord-317928-doj39520.txt txt = ./txt/cord-317928-doj39520.txt === reduce.pl bib === id = cord-318253-vp22xd8p author = Parisi, Ortensia Ilaria title = “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1858 sentences = 96 flesch = 38 summary = Our idea is focused on the development of "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. In this context, our idea is to develop "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) for the selective recognition and binding of the RBD of the novel coronavirus SARS-CoV-2 in the aim to block the function of its spike protein (Figure 1.) . cache = ./cache/cord-318253-vp22xd8p.txt txt = ./txt/cord-318253-vp22xd8p.txt === reduce.pl bib === id = cord-317693-l08q2lhp author = Jacob, Michelle Cristine Medeiros title = Animal-based food systems are unsafe: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fosters the debate on meat consumption date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3262 sentences = 173 flesch = 49 summary = CONCLUSION: To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases (5) . Uses of bushmeat vary from COMMENTARY SNAPSHOT SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases. To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. FNS, food and nutrition security; SARS, severe acute respiratory syndrome subsistence-based rural consumption and subsistencecommercial hunting to a luxury commodity in urban areas (18) . cache = ./cache/cord-317693-l08q2lhp.txt txt = ./txt/cord-317693-l08q2lhp.txt === reduce.pl bib === id = cord-318205-qxkel0ww author = Parkulo, Mark A. title = Risk of SARS-CoV-2 Transmission Among Coworkers in a Surgical Environment date = 2020-10-22 pages = extension = .txt mime = text/plain words = 1266 sentences = 75 flesch = 60 summary = This was an observational study of 394 health care workers in a surgical environment who were exposed to 2 known SARS-CoV-2–positive coworkers. Infections of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) among health care workers is a serious consequence of the coronavirus disease 2019 (COVID-19) pandemic. Of the COVID-19 cases reported to the US Centers for Disease Control and Prevention (CDC) between February 12 and April 9, 2020, that contained information about workers, 19% were identified as health care personnel. 2, 3 Here we report the outcome of a widespread surveillance program in a surgical area which was implemented as a result of health care workers testing positive for SARS-CoV-2 at Mayo Clinic, Jacksonville, Florida. Employee Health determined that 394 other employees worked in the surgical area at the same time as the index cases, and all were recommended to undergo SARS-CoV-2 PCR testing as surveillance. cache = ./cache/cord-318205-qxkel0ww.txt txt = ./txt/cord-318205-qxkel0ww.txt === reduce.pl bib === id = cord-318316-9unfl966 author = Ortega, Joseph T. title = Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies date = 2020-10-23 pages = extension = .txt mime = text/plain words = 4022 sentences = 236 flesch = 46 summary = SUMMARY: This review focused on the basic principles of virology and pharmacology to understand the importance of early stages of virus-cell interaction as therapeutic targets and other main processes vital for SARS-CoV-2 replication. Furthermore, we focused on describing the main targets associated with SARS-CoV-2 antiviral therapy and the rationale of drug combinations for efficiently suppressing viral replication. Another early target evaluated against SARS-CoV-2 is a cellular protease related to the priming of the spike protein (S), which exposes the fusion motive and allows the release of viral RNA into the cytosol. HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; ORF, open reading frame. Favipiravir, another antiviral agent with broad activity against other RNA viruses by inhibiting the RdRp, halting viral replication, was evaluated against SARS-CoV-2, showing effects in vitro and in vivo [43] [44] [45] . cache = ./cache/cord-318316-9unfl966.txt txt = ./txt/cord-318316-9unfl966.txt === reduce.pl bib === id = cord-318036-t05ummop author = Peng, Liang title = 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples date = 2020-02-25 pages = extension = .txt mime = text/plain words = 1000 sentences = 84 flesch = 60 summary = title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples We aim to detect SARS-CoV-2 nucleic acid from urine, blood, anal swab and oropharyngeal swab samples. Nine patients confirmed diagnosed with SARS-CoV-2 infection(2) were included in this prospective study. https://doi.org/10.1101/2020.02.21.20026179 doi: medRxiv preprint enrolled patients were obtained and detected SARS-CoV-2 RNA level by quantitative real-time polymerase chain reaction (qRT-PCR). Patient 7, a 31 years old female without any urinary irritation, had positive results of SARS-CoV-2 in both urine and oropharyngeal swab on the 7 th day after symptom onset. Patient 8 had three positive results in blood, anal swab and oropharyngeal swab on the 3 rd day after onset. In our study, urine, blood, anal swab and oropharyngeal swab from 9 patients were retested by qRT-PCR. Nevertheless, the relative symptoms, including diarrhea and urinary irritation did not happen to every patient with virus in anal swab and urine specimens. cache = ./cache/cord-318036-t05ummop.txt txt = ./txt/cord-318036-t05ummop.txt === reduce.pl bib === id = cord-318387-s4d442kx author = Wang, Ming title = Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses date = 2020-03-06 pages = extension = .txt mime = text/plain words = 4680 sentences = 304 flesch = 56 summary = COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. https://doi.org/10.1101/2020.03.04.20029538 doi: medRxiv preprint read numbers of the test sample to those of the negative control (with "0" in the negative control 129 calculated as "1"), we defined that a ratio of ≥10 indicates a positive result for that fragment, 130 scoring 1; ≥3 to 10 fold is inconclusive, scoring 0.4; and <3 is negative, scoring 0. The 4 h sequencing output data (Fig. 4a ) revealed that all 153 19 samples defined as positive by qPCR were recognized SARS-CoV-2-infected by NTS, 154 cache = ./cache/cord-318387-s4d442kx.txt txt = ./txt/cord-318387-s4d442kx.txt === reduce.pl bib === id = cord-318164-6rqi17oz author = Paoli, D. title = Sperm cryopreservation during the SARS-CoV-2 pandemic date = 2020-10-10 pages = extension = .txt mime = text/plain words = 3258 sentences = 177 flesch = 48 summary = This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. This study thus aimed to evaluate the safety of sperm cryopreservation of cancer patients referred to our sperm bank after the onset of the pandemic in Italy through the assessment of the risk of SARS-CoV-2 exposure and, in selected volunteers, viral RNA testing of semen samples. This was further confirmed by testing seminal fluid samples from 10 asymptomatic cancer patients for SARS-CoV-2 RNA. cache = ./cache/cord-318164-6rqi17oz.txt txt = ./txt/cord-318164-6rqi17oz.txt === reduce.pl bib === id = cord-318342-eipscagh author = Chen, Juan title = The Impact of COVID-19 on Blood Glucose: A Systematic Review and Meta-Analysis date = 2020-10-05 pages = extension = .txt mime = text/plain words = 3598 sentences = 205 flesch = 48 summary = Results: Three studies reported blood glucose and HbA1c according to the severity of COVID-19 and were included in this meta-analysis. It remains unclear regarding the effect of severity of COVID-19 infection on glycemic parameters, including blood glucose and glycated haemoglobinA1c (HbA1c). Finally, three papers were included in the meta-analysis that evaluated blood glucose and/or HbA1c levels according to the severity of COVID-19 (17) (18) (19) . The z-test result for overall effects was statistically significant (P < 0.001), indicating a significantly greater elevation in blood glucose in patients with severe COVID-19 infection than those in the mild group. In the present meta-analysis, we found that blood glucose was significantly higher in patients with severe COVID-19 than those with mild COVID-19 (WMD 2.21, 95% CI: 1.30-3.13, P < 0.001, I 2 = 0%). cache = ./cache/cord-318342-eipscagh.txt txt = ./txt/cord-318342-eipscagh.txt === reduce.pl bib === id = cord-318426-kv7aa0og author = Kritsotakis, Evangelos I. title = On the importance of population-based serological surveys of SARS-CoV-2 without overlooking their inherent uncertainties date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1652 sentences = 101 flesch = 53 summary = This brief note aims to explain the scope in conducting large-scale serological surveys of SARS-CoV-2 to define the landscape of population immunity, without overlooking the inherent uncertainty steaming from sampling design and diagnostic validity. The note completes with a succinct appendix of simple statistical methods for estimating prevalence from random population samples using imperfect diagnostic tests. They use serological tests to examine a large number of blood samples from people without a confirmed SARS-CoV-2 infection to detect signs that they were once infected with the virus. Available serological tests are not perfect but are acceptable for use in the context of surveying populations for SARS-CoV-2 antibodies, because survey estimates can be corrected for imperfect diagnostic performance. Large-scale seroprevalence surveys are an important tool in combating COVID-19 disease as they can provide much-needed estimates of the fraction of the population with antibodies against SARS-CoV-2. The quality of the antibody prevalence estimates depends on the sampling design and the diagnostic accuracy of serological tests. cache = ./cache/cord-318426-kv7aa0og.txt txt = ./txt/cord-318426-kv7aa0og.txt === reduce.pl bib === id = cord-318126-gg68o52z author = Zhou, Juan title = Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection date = 2020-04-03 pages = extension = .txt mime = text/plain words = 972 sentences = 67 flesch = 54 summary = We read with interest the article in this journal which revealed that CT scanning provides important bases for early diagnosis and treatment of COVID-19 (Corona Virus Infection Disease 2019) which is caused by SARS-COV2 (Severe Acute Respiratory Syndrome Coronavirus 2). We observed and analyzed the phenotypic characteristics of asymptomatic individuals originating from the active detection of high-risk individuals who had close contacts with COVID-19 patients during isolated observation with viral nucleic acid positive. A total of 26 cases of asymptomatic infection were detected as SARS-COV2 positive through swab specimen between January 20 to February 30. These data showed that people of different ages are generally susceptible to SARS-COV2, but the average age of asymptomatic patients is lower than the reported age of COVID-19 patients which was 40-70 years old (propinquity 73%). These cases proved that asymptomatic SARS-COV2 carriers can also spread the virus before the https://doi.org/10.1016/j.jinf.2020.03.028 0163-4453/© 2020 The British Infection Association. cache = ./cache/cord-318126-gg68o52z.txt txt = ./txt/cord-318126-gg68o52z.txt === reduce.pl bib === id = cord-318239-2sraqm6e author = Phan, Lan T. title = Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam date = 2020-05-28 pages = extension = .txt mime = text/plain words = 1591 sentences = 100 flesch = 54 summary = title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent In this report, we describe clinical features, virus isolation, and complete genome sequences from the first two SARS-CoV-2 infections in Vietnam. A suspected case was defined as a person with an acute respiratory tract illness, who reported that he/she had fever and cough (with and without difficulty in breathing) and that within 14 days before the onset of disease, he/she had returned or came from areas where SARS-CoV-2 was spreading or had exposed to a laboratory-confirmed case of Covid-19. NP and OP swab specimens of the patients were collected in a single tube containing 3mL virus transport media and tested for SARS-CoV-2 by real-time RT-PCR assays described previously. Once the CPE was observed under the microscope, cell culture supernatants were harvested, divided into aliquots, tested for the presence of SARS-CoV-2 by real-time RT-PCR assays, and stored at -70°C until virus titration and sequencing were performed. cache = ./cache/cord-318239-2sraqm6e.txt txt = ./txt/cord-318239-2sraqm6e.txt === reduce.pl bib === id = cord-317786-iv1br2oj author = Waterfield, T. title = Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study. date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3769 sentences = 271 flesch = 54 summary = Discussion In this study children demonstrated similar antibody titres in response to SARS-CoV-2 irrespective of age. The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. Participants and their parents provided information at enrollment relating to age, sex, previous health and potential predictors of SARS-CoV-2 infection including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/antibody testing. Seroprevalence of SARS-CoV-2 antibodies in children of healthcare workers-A prospective multicentre cohort study protocol -Accepted for publication cache = ./cache/cord-317786-iv1br2oj.txt txt = ./txt/cord-317786-iv1br2oj.txt === reduce.pl bib === id = cord-318339-j35w1vsw author = Stockman, Lauren J title = SARS: Systematic Review of Treatment Effects date = 2006-09-12 pages = extension = .txt mime = text/plain words = 4388 sentences = 233 flesch = 50 summary = METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients. cache = ./cache/cord-318339-j35w1vsw.txt txt = ./txt/cord-318339-j35w1vsw.txt === reduce.pl bib === id = cord-318499-uihof6k6 author = Beddingfield, Brandon title = The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1550 sentences = 100 flesch = 54 summary = Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5β1integrin-based mechanism, and indicates that inhibiting α5β1 integrin interaction with ACE2 and the spike protein using a novel molecule ATN-161 represents a promising approach to treat COVID-19. In order to assess disruption of binding of α5β1 to SARS-CoV-2 Spike protein, 96-well plates were coated as before, but incubation with ATN-161 was performed in conjunction with 1µg/mL spike (produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH: Spike Glycoprotein Receptor Binding Domain (RBD) from SARS-Related Coronavirus 2, Wuhan-Hu-1, Recombinant from HEK293 Cells, NR-52306) in the presence of 1mM MnCl2, followed by detection with an anti-spike antibody. Inhibition of SARS-CoV-2 spike protein binding to human ACE2 by ATN-161. cache = ./cache/cord-318499-uihof6k6.txt txt = ./txt/cord-318499-uihof6k6.txt === reduce.pl bib === id = cord-318069-logh6rnu author = Ordás, Carlos M. title = Concurrent tonic pupil and trochlear nerve palsy in COVID-19 date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1334 sentences = 85 flesch = 50 summary = We report a case of concurrent tonic pupil and trochlear nerve palsy in this context. A 62-year-old man reported a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. Clinical exam showed a right trochlear nerve palsy and a left mydriatic pupil. This is the first case reporting Adie's pupil as a postinfectious manifestation of COVID-19. Here, we report a case of a fourth cranial mononeuropathy coexisting with a contralateral tonic pupil developing 2 weeks after a SARS-CoV-2 infection. A 62-year-old man with an antecedent of hypertension attended our hospital reporting a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. In conclusion, we report an exceptional case of trochlear mononeuropathy and tonic pupil occurring shortly after a SARS-CoV-2 infection, with a presumable immunemediated mechanism. cache = ./cache/cord-318069-logh6rnu.txt txt = ./txt/cord-318069-logh6rnu.txt === reduce.pl bib === id = cord-318444-sgm24q1i author = Walter, Justin D. title = Sybodies targeting the SARS-CoV-2 receptor-binding domain date = 2020-05-16 pages = extension = .txt mime = text/plain words = 5902 sentences = 416 flesch = 49 summary = Two independently prepared RBD constructs were used for in vitro sybody selections, and resulting single clones that could bind the full spike ectodomain were sequenced, expressed, and purified. Six unique sybodies show favorable binding affinity to the SARS-CoV-2 spike, and five of these were also found to substantially attenuate the interaction between the viral RBD and human ACE2. While this purified pre-fusion spike (PFS) had not yet been available for binder selections and characterization by grating-coupled interferometry, it was used to conduct ELISAs in order to identify selected sybodies which recognize the RBD in the pre-fusion context (see below). Since virulence of SARS-CoV-2 is dependent on the ability of the viral RBD to bind to human ACE2 (hACE2), we sought to determine which of the 57 selected sybodies that were well-behaved upon purification could inhibit interaction between the isolated RBD and purified hACE2. cache = ./cache/cord-318444-sgm24q1i.txt txt = ./txt/cord-318444-sgm24q1i.txt === reduce.pl bib === id = cord-318920-njurbf3d author = Romana Ponziani, Francesca title = Liver involvement is not associated with mortality: results from a large cohort of SARS‐CoV‐2 positive patients date = 2020-07-06 pages = extension = .txt mime = text/plain words = 2267 sentences = 131 flesch = 50 summary = CONCLUSIONS: In SARS‐CoV‐2 positive patients without pre‐existing severe chronic liver disease, baseline liver tests abnormalities are associated with the risk of ICU admission and tend to normalize over time. To investigate the prevalence of liver damage in our cohort of patients, serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT), gamma glutamyl transferase (GGT), alkaline phosphatase (ALP), total bilirubin and albumin were collected at baseline, then on the date closest to 15 days from the admission. This study demonstrates that in patients without severe chronic liver disease liver involvement during SARS-CoV-2 infection is usually mild, is not associated with increased risk of ICU admission or mortality, and tends to resolve over time. Baseline liver tests abnormalities can be found in more than 30% of cases, especially in patients with ARDS; these alterations are associated with the risk of ICU admission but not with mortality, and tend to normalize over time. cache = ./cache/cord-318920-njurbf3d.txt txt = ./txt/cord-318920-njurbf3d.txt === reduce.pl bib === id = cord-317863-xf0bn3cv author = Pata, Ramakanth title = Probability of COVID-19 Being the Culprit in Neurocognitive Deception: A Case Series of Incidental Strokes in ICU Patients With COVID-19 date = 2020-08-18 pages = extension = .txt mime = text/plain words = 2201 sentences = 113 flesch = 48 summary = The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, originated in Wuhan, China, and spread rapidly throughout the world, infecting millions and killing thousands. Additionally, it has a high incubation period (average 6.4 and range of 0-24 days) [2] , reproductive number (R0 ranged from 1.4 to 6.49, with a mean of 3.28) [3] , and reports have shown that the majority of patients are asymptomatic or have a mild response to the SARS-CoV-2 virus but release large amounts of viruses [2] . Furthermore, a chest X-ray showed no acute pathologies (Figure 3) , and the COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCT) was performed due to the recent outbreak of the SARS-CoV-2 virus, which came back positive. Other reports suggest a higher rate of cerebrovascular disease (mainly ischemic stroke) in severe COVID-19 patients as compared to non-severe cases [5] . cache = ./cache/cord-317863-xf0bn3cv.txt txt = ./txt/cord-317863-xf0bn3cv.txt === reduce.pl bib === id = cord-317795-689at1qx author = Bielicki, Julia A title = Monitoring approaches for health-care workers during the COVID-19 pandemic date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4876 sentences = 213 flesch = 45 summary = One of the greatest risks to the health-care system is a high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health-care workers and the consequent lack of skilled staff to ensure a functioning local or regional response to the pandemic. 5 National and international recommendations for risk assessment and management of hospital health-care staff working with patients infected with SARS-CoV-2 are detailed and publicly available. Can rapidly deplete the workforce, particularly in cases of HCWs infected with SARS-CoV-2 exposing many colleagues or when there is uncontrolled community transmission, with HCWs exposed outside of the hospital; might not be relevant in settings where some level of PPE is universally recommended (eg, wearing surgical mask for all patient contacts) and there is high adherence to other IPC measures Specific recommendations for monitoring health-care workers for potential SARS-CoV-2 infection should be available for all staff who are expecting to see or currently managing patients with COVID-19. cache = ./cache/cord-317795-689at1qx.txt txt = ./txt/cord-317795-689at1qx.txt === reduce.pl bib === id = cord-318184-atlslk0e author = Germain, N. title = Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2380 sentences = 173 flesch = 60 summary = We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. First identified in Wuhan (China), in early January 2020, the new severe acute respiratory syndrome virus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID19) , rapidly spread to other countries worldwide causing an unprecedented pandemic 1 . Taking into account the information available, the French Biomedicine Agency updated the guidance on SARS-CoV-2 transmission risk via donated organs and tissues on March 5, 2020 and recommended to exclude donors with symptoms suggestive of COVID-19 (fever, cough, etc.) and donors who had stayed or traveled to high risk regions within the prior 28 days, or . Archived blood specimens collected on the day of donation for donor screening of infectious diseases were retrospectively tested for SARS-CoV-2 antibodies (Fig.2 ). cache = ./cache/cord-318184-atlslk0e.txt txt = ./txt/cord-318184-atlslk0e.txt === reduce.pl bib === id = cord-318738-7dgbc4um author = Schmidt, Marco Florian title = Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening date = 2008-03-17 pages = extension = .txt mime = text/plain words = 1957 sentences = 93 flesch = 47 summary = A potential anti‐SARS drug has been developed by dynamic ligation screening (DLS), by which nucleophilic fragments are directed to the protein's active site by reversible reaction with an aldehyde inhibitor. To establish DLS for site-directed identification of inhibitory fragments, at first a fluorescence-based assay [4] for SARS-CoV M pro activity was developed by employing the substrate Ac-TSAVLQ-AMCA (1). To obtain an entirely non-peptidic inhibitor of SARS-CoV M pro targeting both the S1' and S1 pockets, the dynamic ligation screening was conducted iteratively in a "reverted" mode ( Table 2 ). Dynamic ligation screening for the S1' site was performed for a library of 234 nucleophilic fragments using 1 mm of SARS-CoV M pro , 200 mm 1, 400 mm of one nucleophilic fragment per well, and 50 mm of the peptide aldehyde inhibitor Ac-DSFDQ-H (2) on a 384-well microtiter plate. cache = ./cache/cord-318738-7dgbc4um.txt txt = ./txt/cord-318738-7dgbc4um.txt === reduce.pl bib === id = cord-318006-9op556q2 author = Luo, Y. R. title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-08-02 pages = extension = .txt mime = text/plain words = 1063 sentences = 67 flesch = 51 summary = Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. . https://doi.org/10.1101/2020.07.30.20165522 doi: medRxiv preprint Further studies are needed to determine if the antibody response, both IgG concentration and avidity, correlate with virus neutralization and persist over time. cache = ./cache/cord-318006-9op556q2.txt txt = ./txt/cord-318006-9op556q2.txt === reduce.pl bib === id = cord-318766-vx0dnnxh author = Wendt, Ralph title = Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany date = 2020-06-03 pages = extension = .txt mime = text/plain words = 1553 sentences = 91 flesch = 50 summary = title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany We investigated potential transmissions of a symptomatic SARS-CoV-2–positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. We tested all 254 potential contacts of the symptomatic SARS-CoV-2-positive index physician, including 67 patients, and 187 nurses and doctors, technical and medical assistants, and other healthcare staff, on day 5 after the exposure by specific RT-PCR from nose and throat swabs or pharyngeal lavage, irrespective of reported symptoms. We tested a large number of possible contact persons of a symptomatic SARS-CoV-2-infected physician among HCWs and patients on day 5 after exposure; all were negative. 6 For further analysis and confirmation of our results, we investigated the serum of all high-risk contacts (n = 23) on days 15 or 16 and 22 or 23 for SARS-CoV-2-specific antibodies. cache = ./cache/cord-318766-vx0dnnxh.txt txt = ./txt/cord-318766-vx0dnnxh.txt === reduce.pl bib === id = cord-318235-2e5er0x0 author = Yanai, Hidekatsu title = Adiposity is the Crucial Enhancer of COVID-19 date = 2020-08-01 pages = extension = .txt mime = text/plain words = 884 sentences = 49 flesch = 42 summary = A very recent study showed that patients with overweight and obesity admitted in a medical ward for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related pneumonia, despite their younger age, required more frequently assisted ventilation and access to intensive care units (ICUs) or semi-ICU than normal-weight patients [1] . Increased DPP4 expression was observed in vascular endothelial cells, adipose tissue and liver in obese people [8] , which can also make it easy for SARS-CoV-2 to enter human tissues. It has been proposed that the increase of secretion of interleukin-6 and tumor necrosis factor-alpha by adipose tissue in obesity-induced insulin resistance, could underlie the associations of insulin resistance with endothelial dysfunction and coagulopathy [9] . Elevation of inflammatory cytokines, endothelial dysfunction and procoagulant state already exist in obese people even before SARS-CoV-2 infection. In conclusion, obese people have various factors including high likelihood of entry of SARS-CoV-2 into human vital tissues, elevated cytokines, endothelial dysfunction and procoagulant state, which may enhance the severity of COVID-19. cache = ./cache/cord-318235-2e5er0x0.txt txt = ./txt/cord-318235-2e5er0x0.txt === reduce.pl bib === id = cord-318492-uu1p1rgi author = Mansueto, Gelsomina title = COVID-19: Brief Check Point Through The Pathologist's Eye (autopsy archive) date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1971 sentences = 100 flesch = 41 summary = The autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (DAD), myocarditis, acute myocardial infarction (AMI), and disseminated intravascular coagulation (DIC); these aspects are not only in COVID-19 but also in other viral infections and associated sepsis. In this brief summary, I would like to induce the reader's reflection to the fact that coronavirus appears already before the pandemic in many texts of medical doctrine and that the pathological findings related to lung and multi-organ damage are described similar to those induced by other viral pathogens both from the same or different family. The autopsy pathologists can confirm that many deaths are due to complications from viral infections especially in subjects with comorbidities and they can also confirm that the aspects often observed are diffuse alveolar damage (DAD), cardiac damage from myocarditis or acute myocardial infarction (AMI), or even disseminated intra-vascular coagulation (DIC); these findings are also present in sepsis associated with various viral infections. cache = ./cache/cord-318492-uu1p1rgi.txt txt = ./txt/cord-318492-uu1p1rgi.txt === reduce.pl bib === id = cord-318934-dxipu00r author = Matsuyama, Shutoku title = Enhancement of SARS-CoV Infection by Proteases date = 2006 pages = extension = .txt mime = text/plain words = 1861 sentences = 109 flesch = 56 summary = Moreover, SARS-CoV entry from the cell surface mediated by proteases was a 100-fold more efficient infection than entry through endosomes. However, no S2 band was detected in SARS-CoV infected cells treated with proteases that failed to induce fusion. 3 stated that SARS-CoV is able to enter cells directly from their surface, if receptor-bound virus is treated with trypsin and other proteases that induce fusion. Treatment of VeroE6 cells with bafilomycin was shown to suppress SARS-CoV infection via the endosomal pathway to less than 1/100 (Fig. 2) . Pseudotype VSV bearing SARS-CoV S protein infection was also facilitated in bafilomycin-treated VeroE6 cells after treatment with proteases that induce fusion of SARS-CoV infected cells. These observations suggest that proteases that facilitate SARS-CoV entry from the cell surface support efficient SARS-CoV infection. Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry cache = ./cache/cord-318934-dxipu00r.txt txt = ./txt/cord-318934-dxipu00r.txt === reduce.pl bib === id = cord-318483-il5aq8py author = Perez Gaxiola, G. title = Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa date = 2020-07-11 pages = extension = .txt mime = text/plain words = 1758 sentences = 125 flesch = 54 summary = Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children admitted with COVID-19 to a secondary hospital. Although the prevalence of COVID-19 in childhood represents a low percentage of the totality of reported cases, varying between 0.8% and 2.7% (9) (10) (11) , the number of children that may become affected and the different clinical presentation of the disease compared to the adult population (4, 12) may be a challenge for pediatricians and general practitioners. The objectives of this study were to describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic in the region, and of a subset of those children admitted with COVID-19 to Sinaloa Pediatric Hospital (Hospital Pediátrico de Sinaloa "Dr. Rigoberto Aguilar Pico", HPS). This case series describes the clinical and epidemiological characteristics of children infected by SARS-CoV-2 during the first three months of the pandemic in the state of Sinaloa. cache = ./cache/cord-318483-il5aq8py.txt txt = ./txt/cord-318483-il5aq8py.txt === reduce.pl bib === id = cord-319100-3gdawhfn author = Kirkland, P.D. title = The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date = 2020-06-10 pages = extension = .txt mime = text/plain words = 4624 sentences = 204 flesch = 49 summary = authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). cache = ./cache/cord-319100-3gdawhfn.txt txt = ./txt/cord-319100-3gdawhfn.txt === reduce.pl bib === id = cord-318944-13zk6cco author = Bizzoca, Maria Eleonora title = Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date = 2020-05-27 pages = extension = .txt mime = text/plain words = 11691 sentences = 617 flesch = 50 summary = The authors performed a narrative review on Severe Acute Respiratory SyndromeCoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (prevs post-COVID19) for the most common dental procedures. After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The precautions for infection control require wearing gloves, aprons, as well as eye and mouth protection (goggles and mask, such as medical masks and Filtering Face Piece or FPP) for each procedure involving direct contact with the patient body fluids. cache = ./cache/cord-318944-13zk6cco.txt txt = ./txt/cord-318944-13zk6cco.txt === reduce.pl bib === id = cord-318715-p6agoqu8 author = Belser, Jessica A title = Assessment of SARS-CoV-2 replication in the context of other respiratory viruses date = 2020-05-07 pages = extension = .txt mime = text/plain words = 740 sentences = 37 flesch = 38 summary = Hui and colleagues show the susceptibility of human conjunctival explant cultures to SARS-CoV-2 infection (with higher levels of virus replication than SARS-CoV), a notable finding considering reports of ocular manifestations in some patients with confirmed COVID-19 infection, and detection of viral RNA in ocular swabs. 6 Human colorectal carcinoma epithelial cells were also found to support virus replication with SARS-CoV-2, consistent with reports of detection of viral RNA in faecal samples and other tissues from the gastrointestinal tracts of patients with confirmed COVID-19, even in the absence of gastrointestinal symptoms. Tropism of the novel coronavirus SARS-CoV-2 in human respiratory tract: an analysis in ex vivo and in vitro cultures Tropism and innate host responses of a novel avian influenza A H7N9 virus: an analysis of ex-vivo and in-vitro cultures of the human respiratory tract cache = ./cache/cord-318715-p6agoqu8.txt txt = ./txt/cord-318715-p6agoqu8.txt === reduce.pl bib === id = cord-318478-fn0gcxbb author = Ziv, Omer title = The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date = 2020-10-07 pages = extension = .txt mime = text/plain words = 5760 sentences = 343 flesch = 56 summary = Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. cache = ./cache/cord-318478-fn0gcxbb.txt txt = ./txt/cord-318478-fn0gcxbb.txt === reduce.pl bib === id = cord-318029-xd7nuahh author = Ke, Chunjin title = 2019 novel coronavirus disease (COVID-19) in hemodialysis patients: a report of two cases date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1097 sentences = 93 flesch = 47 summary = authors: Ke, Chunjin; Wang, Yufeng; Zeng, Xing; Yang, Chunguang; Hu, Zhiquan OBJECTIVE: To analyze the diagnosis and treatment of patients with chronic renal failure complicated with novel coronavirus pneumonia, and to evaluate the effect of blood purification technology on the treatment and prognosis of such patients METHODS: Two COVID-19 cases undergoing hemodialysis with chronic renal failure were retrospectively analysed in our hospital. On January 8, 2020, the Chinese Center for Disease Control and Prevention officially announced the pneumonia was caused by a new type of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2] . Hyperviremia and cytokine storm are important causes for COVID-19's evolution to severe pneumonia, even to multiple organ dysfunction in a few cases [6] . Blood purification technology seems to be helpful for preventing COVID-19 patients with chronic renal failure from severe pneumonia or even multiple organ dysfunction. Interferon and cytokine responses to SARS-coronavirus infection cache = ./cache/cord-318029-xd7nuahh.txt txt = ./txt/cord-318029-xd7nuahh.txt === reduce.pl bib === id = cord-319022-1twsxzcd author = Desai, Antonio title = The role of anti-hypertensive treatment, comorbidities and early introduction of LMWH in the setting of COVID-19: A retrospective, observational study in Northern Italy() date = 2020-09-25 pages = extension = .txt mime = text/plain words = 2874 sentences = 132 flesch = 47 summary = BACKGROUND: There is a great deal of debate about the role of cardiovascular comorbidities and the chronic use of antihypertensive agents (such as ACE-I and ARBs) on mortality on COVID-19 patients. The aim of the study was to evaluate the role of chronic treatment with ACE-I or ARBs and other clinical predictors on in-hospital mortality in a cohort of COVID-19 patients. As for today, there are discordant results regarding the use of either angiotensin converting enzyme inhibitors (ACE-I) or angiotensin II receptor blockers (ARBs) as for their possible impact on COVID-19 mortality. We found that ACE-I, which acts by inhibiting the conversion from angiotensin I to angiotensin II, showed a trend in protecting from mortality from COVID-19 and was significant in delaying mortality as shown by multivariate Cox regression analysis unlike ARBs, which antagonize the effects of angiotensin II on its receptors 2,3 . Association of Inpatient Use of Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers with Mortality Among Patients With Hypertension Hospitalized With COVID-19 cache = ./cache/cord-319022-1twsxzcd.txt txt = ./txt/cord-319022-1twsxzcd.txt === reduce.pl bib === id = cord-319236-gxcs77pl author = Chen, Qingyan title = Can we migrate COVID-19 spreading risk? date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1478 sentences = 89 flesch = 66 summary = However, we may have under-estimated the disease transmission by small droplets or aerosols that contain SARS-CoV-2 virus. This paper recommended wearing masks in airplanes and use partition screens in the middle of a table in a restaurant to reduce the infectioncausedbySARS-CoV-2virus. Experts so far cannot agree if SARS-CoV-2 transmission could be airborne (Lewis, 2020) , via small droplets or aerosols, although research has shown the risk. Figure 1 shows the droplet cloud that may contain SARS-CoV-2 virus with and without a screen in the middle of a table in a restaurant. The air with displacement ventilation does not mix so that the risk of inhaling airborne infectious disease virus from a neighboring student can be greatly reduced. for a long time, everyone should wear a mask to reduce infection risk although the SARS-CoV-2 virus concentration in indoor air may not be very high. Wearing mask would help as it can reduce the exposure to SARS-CoV-2 virus in air. cache = ./cache/cord-319236-gxcs77pl.txt txt = ./txt/cord-319236-gxcs77pl.txt === reduce.pl bib === id = cord-319241-div9rzax author = Singh, Bhuchitra title = Severe Acute Respiratory Syndrome‐Corona Virus‐2 (SARS‐CoV‐2) and its Effect on Gametogenesis and Early Pregnancy date = 2020-09-23 pages = extension = .txt mime = text/plain words = 4386 sentences = 305 flesch = 50 summary = There is also evidence of significant placental pathology in SARS‐CoV‐2 infection, but it is unclear what effects there may be for early pregnancy, though available data suggest less severe effects compared to other respiratory virus outbreaks. We searched for articles that contained information related to SARS-CoV-2 and reproductive tissues (ovaries, testes), gametes, placentation, and early pregnancy in humans. Our search phrases included: "severe acute respiratory syndrome coronavirus 2", "2019 ncov", "sarscov 2", "SARS-Cov-2", "pregnancy", "gravidity", "abortion", "germ cells", "oocytes", "gametes", "embryonic structures", "embryo", "fertility", "testes", "miscarriage"(See Appendix 1 for completed list of databases search strategy and Figure 1 for PRISMA table). Specifically, 10 women with severe COVID-19 were tested or SARS-CoV-2 in vaginal fluid, with all samples negative for virus [48] . Another study performed during the 2002-2003 SARS pandemic showed that 4 of 7 (57%) pregnant women infected with SARS-CoV had a spontaneous miscarriage in the first trimester of pregnancy [55] , though notably no viral inclusion bodies or particles were detected in the products of conception. cache = ./cache/cord-319241-div9rzax.txt txt = ./txt/cord-319241-div9rzax.txt === reduce.pl bib === id = cord-318786-qd0k8174 author = Mauriz, Elba title = Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date = 2020-08-22 pages = extension = .txt mime = text/plain words = 9868 sentences = 516 flesch = 35 summary = Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. cache = ./cache/cord-318786-qd0k8174.txt txt = ./txt/cord-318786-qd0k8174.txt === reduce.pl bib === id = cord-318789-ylxh8vi2 author = Byrne, R. L. title = Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis. date = 2020-07-11 pages = extension = .txt mime = text/plain words = 1875 sentences = 133 flesch = 62 summary = Samples were classified as RT-qPCR positive if both the internal extraction and the SARS-CoV-2 probes were detected at <40Ct. Virus copies/ml were quantified using the manufacturer's positive control (1.67 Here we report for the first time the analytical sensitivity of saliva for the detection of SARS-CoV-2 compared to NT swab samples. In spiked saliva samples, SARS-CoV-2 can be detected with greater sensitivity in saliva compared to NT swabs by 100fold copies/ml, presumably due to the dilution factor of the amies transport medium. All saliva-positive, NT swab-negative samples in D2 (n=2) and D28 (n=1) reported low viral titre (<10 1 copies/ml) and are likely due to similar limitations outlined in the analytical sensitivity, a greater dilution factor of amies. This is in agreement with Wyllie et al., (2020) who reported that saliva had a greater sensitivity and was more likely to be constantly positive throughout the course of infection on a subset of COVID-19 hospitalised participants (n=29). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 participants than nasopharyngeal swabs cache = ./cache/cord-318789-ylxh8vi2.txt txt = ./txt/cord-318789-ylxh8vi2.txt === reduce.pl bib === id = cord-319023-ucm8frol author = Nuzzo, Andrea title = Universal Shelter-in-Place vs. Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics date = 2020-06-22 pages = extension = .txt mime = text/plain words = 3141 sentences = 190 flesch = 45 summary = Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Conclusion Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated. Such Advanced Automated Contact Tracing (AACT) systems -which could infer exposure risk and propagate warnings to people at risk -may help curb disease spread by facilitating targeted self-isolation rather than universal mandates such as shelter-inplace. In AACT, an additional compartment Sq (Traced contacts that are exposed and under selfisolation) was used while for shelter-in-place, the compartment Q (Individuals isolated through universal enforcement measures) was used. The basic difference between the models is that isolation/quarantine is based solely on exposure history in AACT, while isolation orders apply to the entire population in universal shelter-in-place. Contact tracing can mitigate disease spread through a curated approach of identifying and isolating exposed individuals, as opposed to shelter-in-place orders. cache = ./cache/cord-319023-ucm8frol.txt txt = ./txt/cord-319023-ucm8frol.txt === reduce.pl bib === id = cord-318364-5bmdzgla author = Sun, Xinjuan title = Cytokine storm intervention in the early stages of COVID-19 pneumonia date = 2020-04-25 pages = extension = .txt mime = text/plain words = 3102 sentences = 158 flesch = 40 summary = In a retrospective study of 41 patients with COVID-19, most patients with SARS-CoV-2 infection developed mild symptoms, whereas some patients later developed aggravated disease symptoms, and eventually passed away because of multiple organ dysfunction syndrome (MODS), as a consequence of a severe cytokine storm. In view of the severe morbidity and mortality of COVID-19 pneumonia, we review the current understanding of treatment of human coronavirus infections from the perspective of a dysregulated cytokine and immune response. In support of the above observations, a retrospective study of 41 patients with COVID-19 2 showed that most SARS-CoV-2 infected patients present clinically with mild symptoms, while a minority of patients progressively declined from the infection and eventually died of acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MOD). Severe pneumonia caused by pathogenic human coronaviruses (HCoV) are often associated with induced hypercytokinemia, also termed cytokine storm, in immunocompetent individuals; uncontrolled overproduction of inflammatory cytokines contributes to acute lung injury and acute respiratory distress syndrome (ARDS). cache = ./cache/cord-318364-5bmdzgla.txt txt = ./txt/cord-318364-5bmdzgla.txt === reduce.pl bib === id = cord-318957-gp5drg71 author = Freedman, Matthew title = Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography date = 2004-06-30 pages = extension = .txt mime = text/plain words = 756 sentences = 52 flesch = 53 summary = title: Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography Abstract Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. A computer-aided detection system has been developed that marks locations on chest radiographs of minimal areas of pneumonia. It has been tested on a small series of chest radiographs with minimal SARS pneumonia and provided 88% sensitivity with 1.3 false-positive marks per image. Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. In this process of early detection, the chest radiograph is used as the primary screening method for people presenting with symptoms of potential SARS pneumonia. Severe Acute Respiratory Syndrome: radiographic review of 40 probable cases in Toronto Severe Acute Respiratory Syndrome: radiographic appearances and pattern of progression in 138 patients cache = ./cache/cord-318957-gp5drg71.txt txt = ./txt/cord-318957-gp5drg71.txt === reduce.pl bib === id = cord-319013-oytqcifa author = Focosi, Daniele title = Convalescent Plasma Therapy for COVID-19: State of the Art date = 2020-08-12 pages = extension = .txt mime = text/plain words = 7474 sentences = 335 flesch = 41 summary = In the first retrospective, randomized controlled trial published to date, 39 patients in New York with severe COVID-19 were transfused with 2 units of ABO-type matched CP with anti-Spike antibody titers of Ն1:320 (measured by a two-step Spike proteindirected ELISA). CP (9 to 13 ml/kg from donors with S-RBD IgG titer of Ն1:640) was associated with a negative SARS-CoV-2 PCR test at 72 h in 87.2% of the CP group versus 37.5% of the BSC group, but clinical improvement at 28 days was statistically different only in patients with severe, but not in life-threatening, disease (104) . Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol Anti-SARS-CoV-2 virus antibody levels in convalescent plasma of six donors who have recovered from COVID-19 cache = ./cache/cord-319013-oytqcifa.txt txt = ./txt/cord-319013-oytqcifa.txt === reduce.pl bib === id = cord-319248-ynoxec7k author = Matsuyama, Toshifumi title = An aberrant STAT pathway is central to COVID-19 date = 2020-10-09 pages = extension = .txt mime = text/plain words = 9962 sentences = 619 flesch = 45 summary = In SARS-CoV-2-infected cells, a positive feedback loop established between STAT3 and plasminogen activator inhibitor-1 (PAI-1) may lead to an escalating cycle of activation in common with the interdependent signaling networks affected in COVID-19. After a careful review of the scientific literature, we realized that the SARS-CoV-2-mediated inhibition of IFN and STAT1, and the subsequent shift to a STAT3dominant signaling network (see below), could result in almost all of the clinical features of COVID-19. Molecular patterns derived from SARS-CoV-2-associated molecules, such as ssRNA, dsRNA, and viral proteins, bind to host PRRs and trigger the activation of signal transducers and transcription factors that drive the production of IFN-I and proinflammatory cytokines and chemokines. Therefore, in COVID-19, EGFR signaling may become an alternative pathway that activates STAT3 specifically when the lung is damaged while the production of IFN-I is severely impaired by SARS-CoV-2 infection [12] . cache = ./cache/cord-319248-ynoxec7k.txt txt = ./txt/cord-319248-ynoxec7k.txt === reduce.pl bib === id = cord-318938-7d731q65 author = Wallentin, Lars title = Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation date = 2020-09-27 pages = extension = .txt mime = text/plain words = 4630 sentences = 229 flesch = 43 summary = In unadjusted analyses and after adjustment for clinical variables and medical treatment, male sex, diabetes, congestive heart failure, prior myocardial infarction, and age were consistently associated with higher sACE2 levels in both cohorts ( Figure 3A ; Supplementary material online, Table S2 ). The results showed that higher levels of sACE2 were associated with male sex, cardiovascular disease, diabetes, and older age, which are also the main risk factors for complications and mortality of COVID-19 infections. The indication that male sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes might be associated with a specific mechanism leading to higher risk of more severe SARS-CoV-2 infection might be useful for risk stratification concerning COVID-19. The close association between biomarkers and the sACE2 level suggests that biological ageing and cardiovascular disease and dysfunction might lead to increased ACE2 expression and a potentially higher risk for SARS-CoV-2 binding and more severe COVID-19 infection. cache = ./cache/cord-318938-7d731q65.txt txt = ./txt/cord-318938-7d731q65.txt === reduce.pl bib === id = cord-318625-hf7fgtnp author = Vashi, Yoya title = Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2923 sentences = 180 flesch = 57 summary = The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. The potential epitope regions were predicted using the sequence of the S protein of SARS-CoV-2 that showed the least variability (GenBank accession number NC_045512). We identified 18 linear epitopes, predicted by ElliPro (IEDB), which contained regions from 19 of our selected peptides (highlighted in red in Table 2 ). The study could help us to use the predicted peptide as an immunogen for the development of diagnostics and vaccines against SARS-CoV-2. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2. cache = ./cache/cord-318625-hf7fgtnp.txt txt = ./txt/cord-318625-hf7fgtnp.txt === reduce.pl bib === id = cord-319089-hxpoy4gd author = Du, Li title = Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2219 sentences = 150 flesch = 51 summary = title: Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews BACKGROUND: The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has emerged to be the biggest global health threat worldwide. METHODS: Two independent reviewers will conduct comprehensively searches in PubMed, EMBASE.com, Web of Science, the Cochrane Library, Chinese biomedical literature database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wan fang Database, Chongqing VIP (CQVIP). Prevalence of stress, anxiety, depression among the general population during the COVID-19 pandemic: a systematic review and meta-analysis The psychological and mental impact of coronavirus disease 2019 (COVID-19) on medical staff and general public: a systematic review and meta-analysis Prevalence of depression, anxiety, and insomnia among healthcare workers during the COVID-19 pandemic: a systematic review and meta-analysis Psychological effects caused by the COVID-19 pandemic in health professionals: a systematic review with meta-analysis cache = ./cache/cord-319089-hxpoy4gd.txt txt = ./txt/cord-319089-hxpoy4gd.txt === reduce.pl bib === id = cord-319194-ukuia48s author = Liò, Pietro title = Phylogenomics and bioinformatics of SARS-CoV date = 2004-02-04 pages = extension = .txt mime = text/plain words = 4488 sentences = 201 flesch = 45 summary = Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Figure 1 shows the maximum likelihood tree produced using a set of homologous replicases from five SARS-CoV strains, 12 other coronaviruses representing both groups 1 and 2 of the genus [2, 3] , one torovirus (Breda virus) and one okavirus [yellow head (YH) virus], which were determined to most closely represent the consensus coronavirus sequence by a PSI-Blast search [12] . cache = ./cache/cord-319194-ukuia48s.txt txt = ./txt/cord-319194-ukuia48s.txt === reduce.pl bib === id = cord-319337-w9zyshzb author = Yu, Jingyou title = DNA vaccine protection against SARS-CoV-2 in rhesus macaques date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2719 sentences = 156 flesch = 50 summary = Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. Following vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log(10) reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with sham controls. S3 and S4), including 1.92 and 2.16 log 10 reductions of median peak viral RNA in BAL and NS, respectively, in S vaccinated animals compared with sham controls (P = 0.02 and P = 0.04, two-sided Mann-Whitney tests) ( fig. Viral RNA assays were confirmed by PFU assays, which similarly showed lower infectious virus titers in S vaccinated animals compared with sham controls (P = 0.04, two-sided Mann-Whitney test) ( fig. In this study, we generated a series of prototype DNA vaccines expressing various S immunogens and assessed protective efficacy against intranasal and intratracheal SARS-CoV-2 challenge in rhesus macaques. cache = ./cache/cord-319337-w9zyshzb.txt txt = ./txt/cord-319337-w9zyshzb.txt === reduce.pl bib === id = cord-319164-wbrnhpgs author = Luellen, E. title = A Machine Learning Explanation of Incidence Inequalities of SARS-CoV-2 Across 88 Days in 157 Countries date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1911 sentences = 114 flesch = 49 summary = Because the SARS-CoV-2 (COVID-19) pandemic viral outbreaks will likely continue until effective vaccines are widely administered, (1) new capabilities to accurately predict incidence rates by location and time to know in advance the disease burden and specific needs for any given population are valuable to minimize morbidity and mortality. In this study, a random forest of 9,250 regression trees was applied to 6,941 observations of 13 statistically significant predictor variables targeting SARS-CoV-2 incidence rates per 100,000 across 88 days in 157 countries. One key finding is an algorithm that can predict the incidence rate per day of a SARS-CoV-2 epidemic cycle with a pseudo-R2 accuracy of 98.5% and explain 97.4% of the variances. In this study, machine learning -a robust statistical version of artificial intelligence -was applied to a data set of 6,941 observations to identify the relative importance of 13 demographic, economic, environmental, and public health factors in modulating the incidence rate per 100,000 population of SARS-CoV-2 across 88 days in 157 countries. cache = ./cache/cord-319164-wbrnhpgs.txt txt = ./txt/cord-319164-wbrnhpgs.txt === reduce.pl bib === id = cord-319447-xanewi59 author = Sun, Jiya title = Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date = 2020-05-01 pages = extension = .txt mime = text/plain words = 3250 sentences = 163 flesch = 52 summary = To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. In this study, we used the SARS-CoV-2 strain isolated from patients [11] to infect in vitro Calu-3 cells, and performed RNA sequencing to determine the time-series transcriptome profiling data of the host. Next, to gain possible explanations for the distinct patterns in host antiviral capacity and cytokine production during SARS-CoV-2 infection, dynamic expression of four types of key genes were evaluated, including virus receptors for cell entry, pathogen recognition receptors (PRRs) for an innate immune startup, regulator genes for induction of antiviral-related genes and interferon production (Figure 4) . cache = ./cache/cord-319447-xanewi59.txt txt = ./txt/cord-319447-xanewi59.txt === reduce.pl bib === id = cord-319158-n8e2n30b author = Mackenzie, John S title = COVID-19: a novel zoonotic disease caused by a coronavirus from China: what we know and what we don’t date = 2020-03-17 pages = extension = .txt mime = text/plain words = 1862 sentences = 113 flesch = 51 summary = Based on established practice, the new virus was named SARS-CoV-2 by the Coronavirus Study Group of the International Committee for the Taxonomy of Viruses 10 , and the disease it causes as COVID-19 by WHO 11 . Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven modelling analysis of the early outbreak Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China SARS-CoV-2 viral load in upper respiratory specimens of infected patients A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan (2020) The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) -China cache = ./cache/cord-319158-n8e2n30b.txt txt = ./txt/cord-319158-n8e2n30b.txt === reduce.pl bib === id = cord-319184-voc0eqb9 author = Abduljalil, Jameel M. title = Laboratory diagnosis of SARS-CoV-2: available approaches and limitations date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1115 sentences = 101 flesch = 44 summary = Clinical 397 evaluation of the cobas SARS-CoV-2 test and a diagnostic platform switch during 48 398 hours in the midst of the COVID-19 pandemic Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-406 19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro Rapid and visual detection of 2019 458 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal 459 amplification assay Transcription Loop-Mediated Isothermal Amplification Assays Targeting SARS-CoV-2 Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of 467 SARS-CoV-2 Development of a reverse 469 transcription-loop-mediated isothermal amplification as a rapid early-detection method for 470 novel SARS-CoV-2 Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Development and clinical application of a 500 rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Novel Antigen-Based Rapid Detection Test for the Diagnosis of SARS-CoV-2 in Serological immunochromatographic 525 approach in diagnosis with SARS-CoV-2 infected COVID-19 patients cache = ./cache/cord-319184-voc0eqb9.txt txt = ./txt/cord-319184-voc0eqb9.txt === reduce.pl bib === id = cord-318909-h5b7mncf author = Liguori, Claudio title = Subjective neurological symptoms frequently occur in patients with SARS-CoV2 infection date = 2020-05-19 pages = extension = .txt mime = text/plain words = 3476 sentences = 203 flesch = 45 summary = 7 A large retrospective analysis carried out in China on 214 patients affected by SARS-CoV2 infection confirmed that hospitalized patients complained of subjective neurological symptoms (sNS) in a 36 .4% of cases, including headache, disturbed consciousness, and paresthesia as the most frequent. This observational study, carried out in 103 patients affected by SARS-CoV2 infection, documented the high prevalence of sNS during the course of the disease, even immediately after admission to the Hospital. Although the involvement of nervous system during SARS-CoV2 infection has been extensively proposed, [10] [11] [12] few studies focused the investigation on neurological symptoms in patients with 7 The largest study examining the neurological manifestations of hospitalized patients with COVID-19 was a retrospective analysis achieved by reviewing patients' clinical charts. 15 In the present study, we performed a prospective observation in patients with non-severe respiratory form of SARS-CoV2 by using an anamnestic interview designed to better determinate the occurrence and type of sNS over the course of the disease. cache = ./cache/cord-318909-h5b7mncf.txt txt = ./txt/cord-318909-h5b7mncf.txt === reduce.pl bib === id = cord-319580-awtp0mpg author = McCartney, Stephen A. title = Obesity as a contributor to immunopathology in pregnant and non‐pregnant adults with COVID‐19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 3709 sentences = 221 flesch = 46 summary = The synergistic effects of obesity‐associated delays in immune control of COVID‐19 with mechanical stress of increased adipose tissue may contribute to a greater risk of pulmonary compromise in obese pregnant women. The expression of ACE2 by adipocytes and immune cells also suggests the possibility that adipose tissue may represent a potential reservoir for viral infection and may lead to increased viral burden or persistence; however, no studies to date have demonstrated that adipocytes can be directly infected with SARS-CoV-2. Maternal obesity has emerged as a key risk factor increasing susceptibility of pregnant women to severe COVID-19 disease. There is also an urgent need to focus research on how risk factors, like obesity, alter the immune response to SARS-CoV-2 and influence disease pathogenesis of COVID-19 (Box 1). What is the mechanism of increased risk for severe COVID-19 disease in obese nonpregnant and pregnant women? cache = ./cache/cord-319580-awtp0mpg.txt txt = ./txt/cord-319580-awtp0mpg.txt === reduce.pl bib === id = cord-319590-f9qcabcx author = Han, Yanxiao title = Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2768 sentences = 176 flesch = 58 summary = Molecular dynamics simulations revealed that the α-helical peptides maintain their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. 17 In this work, we design and simulate several peptide inhibitors against SARS-CoV-2, which included components from the virus-binding domains of ACE2; based on the recently released crystal structure (PDB code: 6M17 9 ). We have also designed other inhibitors that are closer to the ACE2 protein, whose parts are connected by peptide bonds, and which contain all 15 residues that initially bind to RBD in the 6M17 crystal structure. To examine how these potential inhibitors bind to RBD of SARS-CoV-2, we prepared these systems in the initial position known from the crystal structure (PDB: 6M17) and simulated them in physiological solution (Methods), as shown in Figure 2a −d. In Figure 2a , 200 ns long simulations showed that the helical structure of inhibitor 1 deforms from the left sideloose end unfolding, although it still binds to the RBD of SARS-CoV-2. cache = ./cache/cord-319590-f9qcabcx.txt txt = ./txt/cord-319590-f9qcabcx.txt === reduce.pl bib === id = cord-319333-jwbgytwd author = Radmard, Sara title = Inpatient Neurology Consultations During the Onset of the SARS-CoV-2 New York City Pandemic: A Single Center Case Series date = 2020-07-10 pages = extension = .txt mime = text/plain words = 3401 sentences = 214 flesch = 46 summary = The encountered neurological problems associated with SARS-CoV-2 infection were encephalopathy (12 patients, 36.4%), seizure (9 patients, 27.2%), stroke (5 patients, 15.2%), recrudescence of prior neurological disease symptoms (4 patients, 12.1%), and neuromuscular (3 patients, 9.1%). Adult inpatients diagnosed with COVID-19 infection by nasopharyngeal swab reverse transcription polymerase chain reaction (RT-PCR) and required neurological evaluation by consultation or admission for primary neurological care were included in this single-center retrospective case-series study at Columbia University Irving Medical Center (CUIMC)-New York Presbyterian Hospital. Most of the patients in our case series developed neurological symptoms several days after COVID-19 symptom-onset and demonstrated elevated inflammatory markers. As in prior literature reviewing neurological manifestations of COVID-19 infection, our case series included instances of both ischemic stroke and intracranial hemorrhage, although our patients also had other cardiovascular risk factors for stroke. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study cache = ./cache/cord-319333-jwbgytwd.txt txt = ./txt/cord-319333-jwbgytwd.txt === reduce.pl bib === id = cord-319519-mb9ofh12 author = Ding, J. title = A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date = 2020-07-02 pages = extension = .txt mime = text/plain words = 7247 sentences = 474 flesch = 52 summary = The algorithm establishes the shortest path between 118 the candidate genes and the known host interacting proteins with SARS-CoV-2 and calculates an 119 overall connectivity score for the network (a smaller value represents a greater connectivity) ( Fig 120 1 and Supplementary Table S1 ). The network-informed analysis presented in this paper, 262 revealed that 1) the top GO biological function associated with HLH genes is neutrophil 263 degranulation, consistent with a recent report highlighting the undervalued role of neutrophils in 264 HLH 36 ; 2) HLH genes are significantly enriched with the SARS-CoV-2 human interactome; 3) the 265 top-ranked HLH gene, AP3B1, has roles in cargo loading of type II pneumocytes, where it may 266 interact with SARS-CoV-2 to disturb surfactant physiological functions to promote 267 inflammation/pro-coagulation activities; 4) diseases/syndromes-associated with increased release 268 of Neutrophil Extracellular Traps (NETs) may predict vulnerable populations, including those 269 affecting children. cache = ./cache/cord-319519-mb9ofh12.txt txt = ./txt/cord-319519-mb9ofh12.txt === reduce.pl bib === id = cord-319571-fspmgg4s author = Sehailia, Moussa title = Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 date = 2020-07-22 pages = extension = .txt mime = text/plain words = 4894 sentences = 232 flesch = 49 summary = Although, functional importance of different targets has been linked to the viral replication and maturation of coronaviruses' family such as Chymotrypsin-like protease(3CLpro) or known as Mpro (Khan et al., 2020; Muralidharan et al., 2020) or Envelope protein (E) (Gupta et al., 2020; Boopathi et al., 2020) but it has been confirmed that the binding of the viral trimeric surface spike glycoprotein (SProtein) of SARS-CoV-2 to the human receptor angiotensin-converting enzyme 2 (hACE2) is the first step in host infection . Therefore, it is very likely that selective interaction of HCQ with the surface of SARS-CoV-2 SProtein through the formation of an inclined tape over the hydrophobic pocket responsible for hosting the Lys353 hotspot (the OH group in this case is acting like a hook by forming a hydrogen bond with Asn501), can be responsible for the prevention of tighter binding with hACE2 protein via restricting penetration of Lys353 into its finally assigned destination on the SProtein RBD (Figure 2 ). cache = ./cache/cord-319571-fspmgg4s.txt txt = ./txt/cord-319571-fspmgg4s.txt === reduce.pl bib === id = cord-319273-ok2p1h9f author = Lai, Yu-Ju title = Severe acute respiratory syndrome coronavirus-2 and the deduction effect of angiotensin-converting enzyme 2 in pregnancy date = 2020-08-17 pages = extension = .txt mime = text/plain words = 2688 sentences = 214 flesch = 53 summary = Angiotensin-converting enzyme 2 (ACE2) has transient overexpression and increased activity during pregnancy, which is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. The management strategy includes monitoring fetal heart rate and uterine contractions; early oxygenation if O(2) saturation is less than 95%; empiric antibiotics for prevention of secondary infection; corticosteroid to treat maternal SARS-CoV-2 disease routinely is not suggested, only for fetal lung maturation in selected cases; and consideration of delivery is according to the obstetric indication, gestational age, and severity of the disease. 40 But a study indicated that angiotensin-converting enzyme 2 (ACE2), which is the receptor of SARS-CoV-2, was highly expressed in maternal-fetal interface cells, suggesting the possibility of vertical transmission. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-319273-ok2p1h9f.txt txt = ./txt/cord-319273-ok2p1h9f.txt === reduce.pl bib === id = cord-319540-kivk3h1k author = Uhe, Tobias title = Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy date = 2020-07-13 pages = extension = .txt mime = text/plain words = 849 sentences = 61 flesch = 48 summary = title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy An 84-year-old male patient with known ischemic cardiomyopathy was admitted to the emergency department of Leipzig University Hospital with typical signs and symptoms of an acute coronary syndrome in the midst of the SARS-Cov2 pandemic on April 22, 2020. Echocardiography (Fig. 2) showed wall motion abnormalities with apical septal dyskinesis, mid ubiquitous akinesia and basal septal and anterior hypokinesis. Due to media reports, she was highly afraid of SARS-CoV2 infections for her husband and herself, because age and hypertension were communicated as high risk for a severe course of COVID-19. Her condition acutely and severely exacerbated when her husband was admitted to the hospital, which she felt would place him at a high risk of death, and because she was not allowed to visit him due to the SARS-CoV2-specific regulations. The patient was provided with psychological support and the SARS-CoV2-negative couple was allowed to meet. cache = ./cache/cord-319540-kivk3h1k.txt txt = ./txt/cord-319540-kivk3h1k.txt === reduce.pl bib === id = cord-319555-pccqo36g author = Beggs, Clive B. title = Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study date = 2020-10-13 pages = extension = .txt mime = text/plain words = 6202 sentences = 260 flesch = 52 summary = Given that COVID-19 can be transmitted by the inhalation of aerosolised respiratory droplets containing the SARS-CoV-2 virus (Beggs, 2020; Miller et al., 2020; Morawska et al., 2020; Stadnytskyi et al., 2020) , and that several studies have recovered viral RNA from hospital air samples (Chia et al., 2020; Guo et al., 2020; Jiang et al., 2020; Santarpia et al., 2020) , there is reason to believe that upper-room UVGI might be effective at "killingx201D; (inactivating) SARS-CoV-2 virions in the air, thus reducing the transmission of COVID-19 in buildings and other enclosed spaces. Because no UV irradiation experiments have to date been performed on aerosols containing the SARS-CoV-2 virus, it was necessary when undertaking the feasibility study to make assumptions regarding an appropriate value of Z ur to use in the upper-room UVGI analysis. The results for the expected and worst-case scenarios in Table 7 , strongly suggest that upper-room UVGI, if applied correctly, should be effective at disinfecting SARS-CoV-2 virions suspended in respiratory droplets in the air. cache = ./cache/cord-319555-pccqo36g.txt txt = ./txt/cord-319555-pccqo36g.txt === reduce.pl bib === id = cord-319706-2e9jrv0s author = Ebinger, Joseph E. title = Pre-existing traits associated with Covid-19 illness severity date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4904 sentences = 219 flesch = 40 summary = For all patients considered to have Covid-19, based on direct or documented laboratory test result and suggestive signs and/or symptoms, we obtained information from the electronic health record (EHR) and verified data for the following demographic and clinical characteristics: age at the time of diagnosis; sex; race; ethnicity; smoking status defined as current versus prior, never, or unknown; comorbidities, including obesity, as clinically assessed and documented by a provider with ICD-10 coding; and, chronic use of angiotensin converting enzyme (ACE) inhibitor or angiotensin II receptor blocker (ARB) medications. For the primary outcome of illness severity, categorized by escalating levels of care (i.e., hospitalization, intensive care, intubation), the pre-existing characteristics that demonstrated statistical significance in age-and sex-adjusted models included older age, male sex, African American race, obesity, hypertension, diabetes mellitus, and the Elixhauser comorbidity score ( Table 2 ; Fig 3) . cache = ./cache/cord-319706-2e9jrv0s.txt txt = ./txt/cord-319706-2e9jrv0s.txt === reduce.pl bib === id = cord-319469-fkuqs3ie author = Ray, A. title = Seroprevalence of anti-SARS-CoV-2 IgG antibody in hospitalized patients in a tertiary referral center in North India date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2937 sentences = 171 flesch = 54 summary = While there was no significant difference in the different age groups and socio-economic classes; residence in Delhi was associated with increased risk (relative risk of 3.62, 95% CI 1.59-8.21) Key Words: SARS-CoV-2 IgG Antibody, Seroprevalence, Hospitalized patient, COVID-19 Seroprevalence studies for SARS-CoV-2 have been conducted in different settings, including community(4)(5)(6)(7), special populations like parturients (8) , liver disease patients (9) , hemodialysis patients (10) , blood donors (11) , health care workers (12) (13) as well in hospitals (14) . In this study, the seroprevalence of SARS-CoV-2 IgG antibody in patients admitted to a major tertiary hospital in Delhi was estimated as well as characteristics of the seropositive patients vis-à-vis the seronegative patients were determined. . https://doi.org/10.1101/2020.08.22.20179937 doi: medRxiv preprint statistically significant difference in seroprevalence of anti-SARS-CoV-2 IgG antibodies were observed between patients admitted with or without comorbidities. cache = ./cache/cord-319469-fkuqs3ie.txt txt = ./txt/cord-319469-fkuqs3ie.txt === reduce.pl bib === id = cord-319749-je0l22l5 author = Lippi, Alice title = SARS‐CoV‐2: At the Crossroad Between Aging and Neurodegeneration date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3090 sentences = 190 flesch = 43 summary = Here, we posit that severe acute respiratory distress syndrome coronavirus 2 infection may, in the long-term, lead to accelerated aging phenotypes in survivors, not only in affected tissues but also in other organs, including the brain. 1, 2 As the causative agent of coronavirus disease 2019 (COVID19) , the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) is now responsible for the third coronavirus-associated pandemic in recent human history. SARS-CoV-2 proteins with human proteins from several aging-related pathways, like vesicle trafficking (Nsp6, Nsp7, Nsp10, Nsp13, Nsp15, Orf3a, E, and Orf8), lipid modifications (Spike), RNA processing and regulation (Nsp8, N), ubiquitin ligases (Orf10), and mitochondrial activity (Nsp4, Nsp8, and Orf9c). Moreover, Hsp40-NP interaction plays a role at the late stages of infection by inhibiting protein kinase R (PKR) activation, essential in the antiviral response of the host. 25 The infection with SARS-CoV induces the unfolded protein response (UPR) in the host cell. cache = ./cache/cord-319749-je0l22l5.txt txt = ./txt/cord-319749-je0l22l5.txt === reduce.pl bib === id = cord-319707-j8y9gt2o author = Kato, Verstrepen title = Neurological manifestations of COVID-19, SARS and MERS date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3552 sentences = 188 flesch = 43 summary = The novel coronavirus, SARS-CoV-2, is likewise a causative pathogen for severe viral pneumonia with the risk of progression to respiratory failure and systemic manifestations. Articles related to the topic were identified by following terms: "Severe Acute Respiratory Syndrome", "Middle East Respiratory Syndrome", Coronavirus disease 2019", "Neurology", "MERS", "SARS", "COVID-19", "Stroke", "Epilepsy", "Guillain-Barré Syndrome", "Encephalitis", "Myelitis", "Meningitis", "Neurological Sequels", "Polyneuropathy" and "Carotid Dissection". Several recent articles report associated cases of encephalitis, acute flaccid paralysis and other neurological symptoms, such as Guillain-Barré syndrome or ADEM, as possible complications of a HCoV infection [6] . Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Neurological complications of middle east respiratory syndrome coronavirus: a report of two cases and review of the literature cache = ./cache/cord-319707-j8y9gt2o.txt txt = ./txt/cord-319707-j8y9gt2o.txt === reduce.pl bib === id = cord-319704-xzhoa03d author = Zuercher, S. J. title = Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence date = 2020-05-22 pages = extension = .txt mime = text/plain words = 6873 sentences = 370 flesch = 47 summary = Results: Most original studies on MHP were conducted in China in the context of SARS-CoV-1, and reported on anxiety, depression, post-traumatic stress symptoms/disorder, general psychiatric morbidity, and psychological symptoms. While considerable efforts rely on protective and treatment measures such as virus transmission pathways, clinical presentations, and the development of vaccinations, attention is only recently given to short or long-term mental health problems (MHP, hereafter defined as psychiatric/psychological symptoms and mental illness/disorders) (Rajkumar, 2020) that may arise due to the different surrounding consequences of an epidemic in the general public, health care workers (HCW), and survivors of infectious diseases (survivors). In this rapid review of 74 original articles we found a wide range of MHP including anxiety, depression, PTSD and stress related symptoms or disorders, psychiatric morbidity, and many further MHP like paranoid ideation, hallucinations, and insomnia that may occur in the general public, HCW or survivors during and after epidemic outbreaks. cache = ./cache/cord-319704-xzhoa03d.txt txt = ./txt/cord-319704-xzhoa03d.txt === reduce.pl bib === id = cord-319797-455ldhiy author = Kumar, Deepali title = COVID‐19: A global transplant perspective on successfully navigating a pandemic date = 2020-04-12 pages = extension = .txt mime = text/plain words = 2058 sentences = 112 flesch = 48 summary = The impact has not been just restricted to issues pertaining to donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. Here we provide a personal viewpoint representing different jurisdictions from around the world in order to outline the impact of the current COVID-19 pandemic on organ transplantation. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. The impact has not been just restricted to issues around donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. cache = ./cache/cord-319797-455ldhiy.txt txt = ./txt/cord-319797-455ldhiy.txt === reduce.pl bib === id = cord-319501-a2x1hvkk author = Wong, Lok-Yin Roy title = A molecular arms race between host innate antiviral response and emerging human coronaviruses date = 2016-01-15 pages = extension = .txt mime = text/plain words = 7759 sentences = 460 flesch = 51 summary = Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. This suggests SARS-CoV N may interfere with RNA recognition by host immune sensors such as RIG-I and MDA5 thus achieving suppressive role in IFN production. Our group demonstrated that MERS-CoV ORF4a interacts with PACT, a cellular dsRNA-binding protein that optimally activates RIG-Iand MDA5-induced type I IFN production, in an RNAdependent manner (Siu et al., 2014c) . Infection with SARS-CoV and MERS-CoV has been accompanied with suppression of innate immune response, most notably with the suppression of type I IFN production and signaling pathways. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses pact-induced activation of RIG-I and MDA5 in the innate antiviral response cache = ./cache/cord-319501-a2x1hvkk.txt txt = ./txt/cord-319501-a2x1hvkk.txt === reduce.pl bib === id = cord-319408-841c0g1c author = Salvatore, Christine M title = Neonatal management and outcomes during the COVID-19 pandemic: an observation cohort study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4636 sentences = 232 flesch = 55 summary = [8] [9] [10] [11] [12] [13] [14] We aimed to follow up neonates born to mothers positive for SARS-CoV-2 at time of delivery, to elucidate best practices regarding infection control and identify potential risk factors associated with transmission. For this observational cohort study, we identified all neonates born between March 22 and May 17, 2020, at New York Presbyterian-Komansky Children's Hospital, Weill Cornell Medicine, New York Presbyterian-Lower Manhattan Hospital, and New York Presbyterian-Queens in New York City to mothers who tested positive for SARS-CoV-2 from a nasopharyngeal swab sample at the time of delivery. Data collected included demographics, neonatal and maternal clinical presentation at time of delivery, during hospit alisation, and once discharged, microbiology results (SARS-CoV-2 rtPCR testing), and infection control practices in the hospital and at home. cache = ./cache/cord-319408-841c0g1c.txt txt = ./txt/cord-319408-841c0g1c.txt === reduce.pl bib === id = cord-319718-blqzi69t author = Zhang, L. title = Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route date = 2020-05-03 pages = extension = .txt mime = text/plain words = 1689 sentences = 110 flesch = 62 summary = Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. . https://doi.org/10.1101 /2020 Based on the position and nucleotide variation of the phylogenetic tree, 104 we compared the evolutionary variation between SARS-CoV-2 representative 105 strains. cache = ./cache/cord-319718-blqzi69t.txt txt = ./txt/cord-319718-blqzi69t.txt === reduce.pl bib === id = cord-319781-6thdg2up author = Payne, Kelly title = Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date = 2020-07-24 pages = extension = .txt mime = text/plain words = 8233 sentences = 454 flesch = 51 summary = To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). Then, we present the state of current research regarding presence in semen, sexual transmission, and fertility effects for the Zika virus (ZIKV), Ebola virus (EBOV), West Nile virus (WNV), pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-coronavirus-2 (SARS-CoV-2) ( Table 1) . In this article, we have reviewed the presence in semen, possibility of sexual transmission, and fertility implications of each of the major recent viral pandemics: Zika, Ebola, West Nile, pandemic influenza, SARS, and SARS-CoV-2. cache = ./cache/cord-319781-6thdg2up.txt txt = ./txt/cord-319781-6thdg2up.txt === reduce.pl bib === id = cord-319831-e07vt846 author = Popescu, Saskia title = Roadblocks to Infection Prevention Efforts in Health Care: SARS-CoV-2/COVID-19 Response date = 2020-03-30 pages = extension = .txt mime = text/plain words = 1827 sentences = 86 flesch = 44 summary = T he emergence of a novel coronavirus (SARS-CoV-2) causing the disease, COVID-19, in Wuhan, China, in late 2019 is currently testing international public health and preparedness efforts. 1 These IPC outbreak efforts include education, reinforcement of infection prevention standards like isolation and proper usage of personal protective equipment (PPE), and established processes to ensure that the i3 strategy (identify, isolate, and inform) is used and that the health care facilities meet the guidance of the Centers for Disease Control and Prevention and World Health Organization. Unfortunately, to truly use IPC programs for COVID-19 response, it is important to understand why health-care-associated outbreaks and infection prevention failures occur all too often. A 2018 Report by the Office Inspector General of the US Department of Health and Human Services assessed hospital readiness to emerging infectious disease threats following the 2013-2016 Ebola outbreak. cache = ./cache/cord-319831-e07vt846.txt txt = ./txt/cord-319831-e07vt846.txt === reduce.pl bib === id = cord-319664-gyktrd36 author = Mancini, Fabiola title = Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2082 sentences = 112 flesch = 54 summary = Finally, to evaluate the performance of molecular assays a standard curve was generated by 10-fold dilutions of SARS-CoV-2 RNA, isolated and extracted at Istituto Superiore di Sanità in Rome, Italy, and quantified by a well-established copy number of RNA synthetic E gene (Wuhan coronavirus, EVAg, www. All specimens were also manually extracted and tested for the presence of SARS-CoV-2 by in-house rt-Realtime PCR and the 2019-nCoV TaqMan RT-PCR Kit. In particular, we investigated the RNA availability and virus detection using both the purified and thermal/non-extractive procedures also with this commercial kit because it is based on the same primers, probes and assays developed by the CDC and used in the inhouse molecular method. This study corroborates our results for in-house rt-Real Time PCR, showing a lower sensitivity of the heat treatment (range ΔCT value of 0.5-1.0) when compared with purified samples, but, dissimilar to our findings, a total inhibition was found by the commercial kit RealStar SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), where all positive samples failed in the detection of Sars-CoV-2 [14] . cache = ./cache/cord-319664-gyktrd36.txt txt = ./txt/cord-319664-gyktrd36.txt === reduce.pl bib === id = cord-319351-hcxbkvgd author = Benrahma, H. title = Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1547 sentences = 110 flesch = 61 summary = title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp gene, N gene, and E gene in patients from diagnosis until the recovery. To date, no studies exploring the variation of RdRp, N and E genes expression of SARS-CoV-94 2 in the patient's specimen. In this study, in first time, we analyses the epidemiological profile The LNR provide a RT-PCR to clinically suspected COVID-19 patients when they were (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-319351-hcxbkvgd.txt txt = ./txt/cord-319351-hcxbkvgd.txt === reduce.pl bib === id = cord-319799-h9kot3og author = Schäfer, Alexandra title = Epigenetic Landscape during Coronavirus Infection date = 2017-02-15 pages = extension = .txt mime = text/plain words = 10080 sentences = 465 flesch = 33 summary = By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host's innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. By utilizing Calu3 cells, we have developed a robust human model platform to study innate immune regulatory control and epigenetics following emerging coronavirus and influenza virus infections as well as other highly pathogenic viruses ( Figure 6 ). Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. cache = ./cache/cord-319799-h9kot3og.txt txt = ./txt/cord-319799-h9kot3og.txt === reduce.pl bib === id = cord-319728-d0kf9gme author = Lucchini, Matteo title = Is serological response to SARS-CoV-2 preserved in MS patients on ocrelizumab treatment? A case report date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1382 sentences = 85 flesch = 50 summary = We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. Few case reports of multiple sclerosis (MS) patients receiving ocrelizumab who contracted COVID-19 with a benign course have recently been published (Novi et al., 2020; Suwanwongse and Shabarek, 2020) . Forty days before COVID-19 onset, the patient performed routine blood tests including cell blood count (CBC), lymphocyte subtypes, immunoglobulin dosage and liver and kidney function showing CD19+ complete depletion (normal CD4+ and CD8+) and IgG at lower limit (700 mg/dl, normal range 700-1600). Despite an optimal recovery from COVID-19, our patient did not develop a full serological response against SARS-CoV-2 as demonstrated by the absence of specific IgG production. cache = ./cache/cord-319728-d0kf9gme.txt txt = ./txt/cord-319728-d0kf9gme.txt === reduce.pl bib === id = cord-319833-u9uuuu38 author = Rodriguez-Martinez, Carlos E. title = Decontamination and reuse of N95 filtering facemask respirators: a systematic review of the literature date = 2020-07-08 pages = extension = .txt mime = text/plain words = 7259 sentences = 380 flesch = 47 summary = METHODS: We performed a systematic review of the literature in order to identify studies reporting outcomes of at least one decontamination method for inactivating or removing any potentially infectious material from the surface of N95 FFRs, specifically addressing issues related to reduction of the microbial threat (including SARS-CoV-2 when available), maintaining the function of N95 FFRs and a lack of residual toxicity. 10 Although various decontamination methods have been used, there are concerns over certain characteristics of the N95 FFRs with respect to their utilization, such as alterations in their physical appearance/odor, structural integrity, filtration efficiency, fit and seal and filter airflow resistance, degradation of their material, and chemical residues that are potentially toxic or irritate the skin (due to the chemical disinfectants required for rinsing and drying). cache = ./cache/cord-319833-u9uuuu38.txt txt = ./txt/cord-319833-u9uuuu38.txt === reduce.pl bib === id = cord-319920-vn5si7xm author = Sampogna, Gianluca title = Spinal cord dysfunction after COVID-19 infection date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2524 sentences = 164 flesch = 47 summary = INTRODUCTION: We observed individuals affected by spinal cord dysfunction (SCD) after coronavirus disease 2019 (COVID-19). Case 1, aged 69 years, experienced T10 AIS B paraplegia upon awakening due to spinal cord ischemia from T8 to conus medullaris, besides diffuse thromboses, 27 days after the onset of COVID-19 symptoms. Prior to SCD, all three individuals suffered from respiratory failure due to COVID-19, required mechanical ventilation, had cardiovascular risk factors, experienced lymphopenia, and received tocilizumab (TCZ). The aim of our report is to provide our initial experience with people experiencing SCD after COVID-19 in a referral USU in the Northern Italian region most affected by the SARS-CoV-2 infection. As a consequence of the neurotropic and neuro-invasive potential of this virus, it has been reported that 36.4% of patients with COVID-19 suffer from neurological complications, and up to 45.5% patients in case of severe SARS-CoV-2 infection [14] . cache = ./cache/cord-319920-vn5si7xm.txt txt = ./txt/cord-319920-vn5si7xm.txt === reduce.pl bib === id = cord-319877-izn315hb author = de Wit, Emmie title = SARS and MERS: recent insights into emerging coronaviruses date = 2016-06-27 pages = extension = .txt mime = text/plain words = 9387 sentences = 424 flesch = 43 summary = Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters). cache = ./cache/cord-319877-izn315hb.txt txt = ./txt/cord-319877-izn315hb.txt === reduce.pl bib === id = cord-319754-5isw53wl author = Balgoma, David title = Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date = 2020-08-31 pages = extension = .txt mime = text/plain words = 12092 sentences = 541 flesch = 41 summary = Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . cache = ./cache/cord-319754-5isw53wl.txt txt = ./txt/cord-319754-5isw53wl.txt === reduce.pl bib === id = cord-319876-psilbis0 author = Zhu, Jian title = COVID-19 Epidemic: Clinical Characteristics of Patients in Pediatric Isolation Ward date = 2020-07-09 pages = extension = .txt mime = text/plain words = 2424 sentences = 145 flesch = 59 summary = It was found that 55 cases (83.3%) had fever and 48 cases (72.7%) coughed in the isolated area, 31 cases (47%) had a history of exposure, 26 cases (39.4%) had a decrease in lymphocytes (LYM), more than half had an increase in lactate dehydrogenase and creatine kinase isoenzyme, 14 cases (21.2%) had positive SARS-CoV-2 nucleic acid, 58 cases (87.9%) had abnormal chest computed tomography (CT), and 11 cases (16.7%) had sinus arrhythmia. Therefore, for some suspected children with COVID-19, we can make a comprehensive judgment through clinical symptoms, epidemiological history, LYM number, myocardial enzyme spectrum, chest CT, and electrocardiogram; put these children in an isolation ward for treatment; and then transfer them to a general ward for treatment after excluding COVID-19. At present, some of COVID-19 are asymptomatic infection, 10, 11 which suggests that it is not only from the clinical symptoms to judge whether the children should be admitted to the isolation ward. cache = ./cache/cord-319876-psilbis0.txt txt = ./txt/cord-319876-psilbis0.txt === reduce.pl bib === id = cord-319930-ymqnb54a author = Kremer, Stéphane title = Brain MRI Findings in Severe COVID-19: A Retrospective Observational Study date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3185 sentences = 188 flesch = 40 summary = Eight distinctive neuroradiologic patterns (excluding ischemic infarcts) were identified in patients with severe COVID-19 infection with abnormal brain MRIs. In patients with COVID-19, the most frequent neuroimaging features were: involvement of the medial temporal lobe, non-confluent multifocal white matter hyperintense lesions on FLAIR with variable enhancement and hemorrhagic lesions, and extensive and isolated white matter microhemorrhages. Inclusion criteria were: (i) diagnosis of COVID-19 based on possible exposure history or symptoms clinically compatible, validated with a detection of SARS-CoV-2 by reverse transcriptase-polymerase chain reaction (RT-PCR) assays on the nasopharyngeal, throat or lower respiratory tract swabs; (ii) severe COVID-19 infection defined as requirement for hospitalization and oxygen therapy; (iii) neurologic manifestations; (iv) abnormal brain MRI with acute/subacute abnormalities. Among the eight groups of brain MRI features classification, three main neuroradiological patterns appeared more frequently in patient with severe COVID-19: signal abnormalities located in the medial temporal lobe, non-confluent multifocal WM hyperintense lesions on FLAIR and diffusion with variable enhancement, associated with hemorrhagic lesions, and extensive and isolated WM microhemorrhages. cache = ./cache/cord-319930-ymqnb54a.txt txt = ./txt/cord-319930-ymqnb54a.txt === reduce.pl bib === id = cord-319780-rfj9t99r author = Alexander, S.P.H. title = A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date = 2020-05-01 pages = extension = .txt mime = text/plain words = 15196 sentences = 814 flesch = 47 summary = Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-319780-rfj9t99r.txt txt = ./txt/cord-319780-rfj9t99r.txt === reduce.pl bib === id = cord-319864-t6ql9hz2 author = Lima, Amorce title = Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens date = 2020-11-11 pages = extension = .txt mime = text/plain words = 3048 sentences = 190 flesch = 65 summary = In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. In this study, we sought to describe a modified CDC SARS-CoV-2 assay validation and compare its performance and workflow to that of the NeuMoDx SARS-CoV-2 and DiaSorin Simplexa Covid-19 Direct assays using respiratory specimens. The primer/probe sets used in this validation were selected from regions of the SARS-CoV-2 virus nucleocapsid (N) gene and were described in the CDC EUA protocol for COVID-19 diagnostic testing (7) . Of the 43 samples used for comparison between modified CDC SARS-CoV-2 assay and Simplexa Covid 19 Direct assay, 37 samples were run within 2 days and 6 were run within 5 days of first testing. The clinical performance comparison between NeuMoDx SARS-CoV-2 assay, Simplexa Covid-19 Direct assay, and the modified CDC SARS-CoV-2 assay showed an overall agreement of 100%. cache = ./cache/cord-319864-t6ql9hz2.txt txt = ./txt/cord-319864-t6ql9hz2.txt === reduce.pl bib === id = cord-319900-16osnnga author = Arcadepani, Felipe B. title = The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1046 sentences = 63 flesch = 52 summary = title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil All these issues make these individuals a high-risk group for infected by SARS-Cov-2 as they present several clinical (including pulmonary) comorbidities and social conditions that, besides posing difficulties for disease prevention, may play a role in hampering their immunological responses and general health. The population living or frequenting outdoor scenes lack adequate support from the Brazilian Public Health System, and the current pandemic adds more urgency to specific policies to address their susceptibility to this and other diseases. A pandemic that requires social isolation, especially for high-risk populations, turns this existing necessity into an emergency measure, taking into account basic public health principles and human rights. Health care facilities must provide treatment for their clinical comorbidities, focusing particularly on primary conditions such as hypertension and diabetes, which may be highly underdiagnosed among people who frequently use crackcocaine and are highly vulnerable to severe cases of COVID-19. cache = ./cache/cord-319900-16osnnga.txt txt = ./txt/cord-319900-16osnnga.txt === reduce.pl bib === id = cord-319855-78xmxymu author = BR, Bharath title = In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19 date = 2020-07-01 pages = extension = .txt mime = text/plain words = 4752 sentences = 251 flesch = 53 summary = The three molecules streptomycin, ciprofloxacin, and GA had low interaction penalties and displayed better interactions with the ACE2 binding site on the RBD of SARS-CoV-2-S, as shown in Figure 8A -C, respectively. Further, in the RMSF plot for the RBD domain of the GA/SARS-CoV-2-S complex, shown in Figure 11C , the RMSF at loop region was 6.3Å with a high number of ligand contacts (green-coloured vertical bars), justifying the interactions seen in molecular docking. In the protein-ligand contact plot for the streptomycin/ SARS-CoV-2-S complex, shown in Figure 12A , residues Glu493 and Lys544 showed maximum interactions fractions, i.e. 0.20 facilitated by hydrogen bonds and water bridges. In the protein-ligand contact plot for the ciprofloxacin/ SARS-CoV-2-S complex shown in Figure 12B , residues Phe465, Tyr482, Tyr498, and Phe499 were seen to have the interactions fractions 0.75, 0.6, 0.35 and 0.39 respectively facilitated by hydrophobic, hydrogen bonds and water bridges. cache = ./cache/cord-319855-78xmxymu.txt txt = ./txt/cord-319855-78xmxymu.txt === reduce.pl bib === id = cord-320087-iu4ulxtu author = Lampe, Anne title = Guillain-Barré syndrome and SARS-CoV-2 date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1748 sentences = 109 flesch = 50 summary = Since January 2020, after Chinese health authorities identified a new type of coronavirus (SARS-CoV-2), the virus has spread throughout China and consecutively throughout the whole world. This article presents the case of a 65-years old man who was presumptively infected with SARS-CoV-2 during his ski vacation in Austria in March 2020 and acutely presented with typical symptoms of Guillain-Barré syndrome. We herein report about a COVID-19 patient who was admitted to the emergency department of our hospital with typical symptoms of Guillain-Barré syndrome (GBS). The interval between the onset of symptoms of SARS-CoV-2 infection and first symptoms of GBS was only 1 day in the case presented here. A case study of 5 patients with SARS-CoV-2 infection and GBS was published a few weeks ago [14] . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Guillain-Barre syndrome associated with SARS-CoV-2 infection: Causality or coincidence? cache = ./cache/cord-320087-iu4ulxtu.txt txt = ./txt/cord-320087-iu4ulxtu.txt === reduce.pl bib === id = cord-320085-n9i54wzh author = Pfefferle, Susanne title = Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date = 2020-03-05 pages = extension = .txt mime = text/plain words = 2032 sentences = 116 flesch = 52 summary = We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the 'open channel' for integration of a laboratory-developed assay. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the 'open channel' for integration of a laboratory-developed assay. The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus. In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. cache = ./cache/cord-320085-n9i54wzh.txt txt = ./txt/cord-320085-n9i54wzh.txt === reduce.pl bib === id = cord-319964-ju9japd8 author = Lu, Jing title = Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China date = 2020-04-04 pages = extension = .txt mime = text/plain words = 4100 sentences = 250 flesch = 53 summary = Highlights: 1) 1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020; 2) Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint To understand the genetic diversity of the SARS-CoV-2 epidemic in Guangdong we performed phylogenetic analyses using maximum likelihood and Bayesian molecular clock approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint Our analyses of the genomic epidemiology of SARS-CoV-2 in Guangdong province indicate that, following the first COVID-19 case detected in early January, most infections were the result of virus importation from elsewhere, and that chains of local transmission were limited in size and duration. cache = ./cache/cord-319964-ju9japd8.txt txt = ./txt/cord-319964-ju9japd8.txt === reduce.pl bib === id = cord-319935-ni6a8vje author = Somsen, G. A. title = Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters date = 2020-10-14 pages = extension = .txt mime = text/plain words = 1846 sentences = 114 flesch = 56 summary = To demonstrate the usefulness of our novel method, we perform measurements in typical public spaces that can play a role in aerosol transmission of SARS-CoV-2, each differing in volume, number of people and ventilation rate. Using this easily applicable method, aerosol concentrations can be measured in any public space which is important to determine the risk is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Using the half-times as measured by us, we calculate that the decrease in the number of aerosol particles after these 6 minutes will vary between 50 and 100%, depending on the ventilation method and the size of the public space. Small droplet aerosols in poorly ventilated spaces; the need for specific measures to prevent SARS-CoV-2 transmission cache = ./cache/cord-319935-ni6a8vje.txt txt = ./txt/cord-319935-ni6a8vje.txt === reduce.pl bib === id = cord-319955-spnykv96 author = Arafah, Azher title = S1 Subunit and Host Proteases as Potential Therapeutic Avenues for the Treatment of COVID-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 909 sentences = 47 flesch = 49 summary = Abstract The novel corona virus (SARS-CoV-2) that causes severe acute respiratory syndrome, now called COVID-19 initially originated in Wuhan city of China and later spread across borders and infected more than two million people and killed over 2.9 lakh people all over the globe. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. cache = ./cache/cord-319955-spnykv96.txt txt = ./txt/cord-319955-spnykv96.txt === reduce.pl bib === id = cord-319983-e4f2sfl4 author = Tripathi, Shweta title = The COVID-19: Current understanding date = 2020-09-26 pages = extension = .txt mime = text/plain words = 4293 sentences = 261 flesch = 53 summary = Till the date of writing this article (August 15, 2020), a total number of 2526192+65002 laboratory-confirmed cases of COVID-19 from 35 states and Union Territories, out of which 1,915,580 (71.91%) recovered, while 50,924 (1.93%) deaths are reported in India [8, 10] . According to the Ministry of Family and Health Welfare of India; a suspected case is defined as a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, and shortness of breath) and a history of travel to or residence in a location reporting community transmission of COVID-19, 14 days prior of the beginning of symptoms. However, more clinical trials are needed to prove the safety and effectiveness of convalescent plasma transfusion in SARS-CoV-2 infected patients [48] . Epidemiological and clinical characteristics of 99 cases of 2019 novel Coronavirus pneumonia in Wuhan, China: A descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel Coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-319983-e4f2sfl4.txt txt = ./txt/cord-319983-e4f2sfl4.txt === reduce.pl bib === id = cord-320063-n9qzbnup author = Calender, Alain title = Modeling Potential Autophagy Pathways in COVID-19 and Sarcoidosis date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1595 sentences = 75 flesch = 34 summary = Of note, SARS-CoV2 protein has a high affinity for human ACE2, a membrane-bound peptidase highly expressed in the heart, lungs, digestive and renal tracts; this molecular interaction leads to a membrane fusion process and further formation of syncytia with multinucleated alveolar epithelial cells ( Figure 1 ) [7] . Different cellular receptors such as TLR3 (Toll Like Receptor 3) and RIG-1 (Retinoic Acid Inducible Gene 1) -closely related to autophagy activation in mammalian granulocyte and macrophage models -have been implicated in innate immunity response to RNA virus infections -e.g. Coronavirus, Measles, Hepatitis viruses, and Influenza virus [10] . These clinical observations raise the question of what the sensitivity of patients with sarcoidosis to respiratory viral disease is, such as that induced from SARS-CoV2 infection (COVID-19)presently being explored in several international projects [6] . cache = ./cache/cord-320063-n9qzbnup.txt txt = ./txt/cord-320063-n9qzbnup.txt === reduce.pl bib === id = cord-320158-6dh9e5rg author = Hansen, Richard title = Adaptations to the current ECCO/ESPGHAN guidelines on the management of paediatric acute severe colitis in the context of the COVID-19 pandemic: a RAND appropriateness panel date = 2020-09-01 pages = extension = .txt mime = text/plain words = 5593 sentences = 284 flesch = 37 summary = CONCLUSION: Our COVID-19-specific adaptations to paediatric ASC guidelines using a RAND panel generally support existing recommendations, particularly the use of corticosteroids and escalation to infliximab, irrespective of SARS-CoV-2 status. [10] [11] [12] Panellists rated the appropriateness of specific interventions at various time points during a patient's admission with ASC (admission, first-line therapy, rescue therapy, continued medical therapy on discharge and surgery) in the context of their SARS-CoV-2 swab status and the presence or absence of symptoms or signs of COVID-19 infection. After the second round of voting, agreement was present for all scenarios (DI<1) except two, both relating to SARS-CoV-2positive patients with symptoms or signs of infection; the use of ciclosporin with corticosteroids as rescue therapy and the use of prophylactic anticoagulation after discharge A detailed list of all scenarios, complete with median score, appropriateness rating and DI is shown in online supplementary table 2. cache = ./cache/cord-320158-6dh9e5rg.txt txt = ./txt/cord-320158-6dh9e5rg.txt === reduce.pl bib === id = cord-320149-3q4q98a6 author = Di Carlo, Davide Tiziano title = Exploring the clinical association between neurological symptoms and COVID-19 pandemic outbreak: a systematic review of current literature date = 2020-08-01 pages = extension = .txt mime = text/plain words = 3482 sentences = 196 flesch = 39 summary = An increasing body of evidence suggests that patients with the coronavirus disease (COVID-19) might have a heterogeneous spectrum of neurological symptoms METHODS: A systematic search of two databases was performed for studies published up to May 29th, 2020. The pathophysiology of this association is under investigation and warrants additional studies, Physicians should be aware of this possible association because during the epidemic period of COVID-19, early recognition of neurologic manifestations otherwise not explained would raise the suspect of acute respiratory syndrome coronavirus 2 infection. Our systematic review of 2499 patients reported the occurrence of a wide spectrum of neurologic complications in hospitalized patients with laboratory-confirmed COVID-19 infection, supporting the possible neuroinvasive potential of SARS-CoV-2. Recently, several case reports described the occurrence of ischemic and hemorrhagic stroke (see supplementary material 1), confirming the association of cerebrovascular complications with severe COVID-19 infection, older age, and the presence of multiple comorbidity [46, 47] . cache = ./cache/cord-320149-3q4q98a6.txt txt = ./txt/cord-320149-3q4q98a6.txt === reduce.pl bib === id = cord-320127-55h4hhm3 author = Mazingi, Dennis title = Mitigating the impact of COVID-19 on children's surgery in Africa date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2671 sentences = 159 flesch = 46 summary = 13 The COVID-19 pandemic has placed unprecedented strain on health services around the world, and paediatric surgical services are no exception. During the 2003 severe acute respiratory syndrome-related coronavirus (SARS-CoV)-1 outbreak in Toronto, stringent restrictions on non-essential surgical services were thought to have aggravated precipitous declines in surgical volume, with only small increases in surge capacity for the outbreak. 42 Paediatric care in Africa is typically characterised by significant involvement by guardians and other family members who support the child during hospital admission, assist the overburdened healthcare workforce and act as care advocates. A recent global review of paediatric surgical workforce density showed that a minimum of four paediatric surgeons per million children under 15 years of age would be required to achieve a survival of >80% for a group of four bellwether paediatric surgical conditions. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review cache = ./cache/cord-320127-55h4hhm3.txt txt = ./txt/cord-320127-55h4hhm3.txt === reduce.pl bib === id = cord-320428-sg3srt8r author = Ling, Zhoukun title = Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings date = 2020-03-12 pages = extension = .txt mime = text/plain words = 513 sentences = 39 flesch = 52 summary = title: Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings In this family, a 10-year-old child had no clinical symptoms, but showed ground glass lung opacification on CT, subsequently, the patient presented positive for the SARS-CoV-2 nucleic acid by real time polymerase chain reaction (RT-PCR). Therefore, these findings indicated the clinical symptoms were not essential components of SARS-CoV-2 infection. In our observation, we found that four patients with SARS-CoV-2 infection, showed no clinical symptoms or abnormal chest CT images. It is worth noting that, the clinical symptoms and radiological abnormalities are not the essential components of SARS-CoV-2 infection. If some people have a history of exposure to infected areas or contact with patients, regardless of radiological manifestations or clinical symptoms, medical observation and home isolation or SARS-CoV-2 nucleic acid tests are quite important to rule out infection. SARS-CoV-2 viral load in upper respiratory specimens of infected patients cache = ./cache/cord-320428-sg3srt8r.txt txt = ./txt/cord-320428-sg3srt8r.txt === reduce.pl bib === id = cord-319933-yp9ofhi8 author = Ruiz, Sara I. title = Chapter 38 Animal Models of Human Viral Diseases date = 2013-12-31 pages = extension = .txt mime = text/plain words = 28834 sentences = 1797 flesch = 46 summary = An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. cache = ./cache/cord-319933-yp9ofhi8.txt txt = ./txt/cord-319933-yp9ofhi8.txt === reduce.pl bib === id = cord-320169-dtv7to3l author = Liu, Yen-Chin title = COVID-19: the First Documented Coronavirus Pandemic in History date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1935 sentences = 127 flesch = 51 summary = The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. The spike glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) in human and Chinese horseshoe bats, civet for cell entry, that is also dependent on S protein priming by the serine protease TMPRSS2. Domestic animals can suffer from disease as intermediate hosts that cause virus transmission from natural hosts to humans; for example, SARS-CoV and MERS-CoV crossed the species barriers into masked palm civets and camels, respectively [30, 31] [ Table 1 ]. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. cache = ./cache/cord-320169-dtv7to3l.txt txt = ./txt/cord-320169-dtv7to3l.txt === reduce.pl bib === id = cord-320054-wqpr8v3p author = Yuan, Xianlin title = The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date = 2020-08-24 pages = extension = .txt mime = text/plain words = 2588 sentences = 156 flesch = 58 summary = In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. To explore these questions, here we report 94 to used these immuno-bioinformatic tools from the IEDB and related resources to 95 predict the B cell epitopes of S protein from the prototype and mutated strains of 96 SARS-CoV-2 and compare the changes of the likely epitope sites from dominant and 97 rare mutations of S protein. The major variation sequences were available 409 from The Global Initiative for Sharing All Influenza Data (GISAID) [26] and GenBank 446 We used the sequence from early onset SARS-CoV-2 as the wildtype or prototype and 447 the recent variant virus as mutation strains to predict the B-cell epitopes of S protein. cache = ./cache/cord-320054-wqpr8v3p.txt txt = ./txt/cord-320054-wqpr8v3p.txt === reduce.pl bib === id = cord-320092-0qnvydux author = Ehsani, Sepehr title = COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date = 2020-10-16 pages = extension = .txt mime = text/plain words = 7536 sentences = 406 flesch = 45 summary = An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. c The position of the disulfide bonds in the sequence of the mature human hepcidin is illustrated along with the potential palmitoylation residues (ten cysteines) of the cytoplasmic tail of the SARS-CoV-2 spike protein. If the sequence similarity reported here is actually playing a significant role at the cellular level, could it be that, although the cellular localizations appear to be different based on current knowledge, the SARS-CoV-2 spike protein cytoplasmic tail can partly mimic the structure of hepcidin and interact with ferroportin? In addition, a notyet-fully-established link of relevance here is the observations of a Kawasaki-disease-like systemic vasculitis syndrome in children infected with the novel Fig. 3 Summary of salient facets of coronavirus spike protein and human hepcidin biology. cache = ./cache/cord-320092-0qnvydux.txt txt = ./txt/cord-320092-0qnvydux.txt === reduce.pl bib === id = cord-320165-1b6sycgv author = Guo, Qirui title = Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date = 2020-09-09 pages = extension = .txt mime = text/plain words = 6762 sentences = 425 flesch = 54 summary = S100A8/A9 specific inhibitor, Paquinimod, significantly reduced the number of neutrophils activated by the coronavirus, inhibited viral replication and rescued lung damage a result of SARS-CoV-2 infection. The whole genome wide RNA-seq analysis of the lungs from infected rhesus macaques showed that a number of transcripts were induced or inhibited at day 3 and day 5 after SARS-CoV-2 infection (Supplementary Figure 1A) . Similar to the data from rhesus macaque experiments, compared to other alarmins, S100A8 was robustly induced by SARS-CoV-2 but not by IAV infection in mice ( Figure 2E ). The expression of these B cell related genes was rescued or induced by Paquinimod during MHV infection, which was confirmed by qRT-PCR analysis ( Figure 3M ). Moreover, both Paquinimod and Resatorvid suppressed the activation of coronavirus related neutrophils in lung during SARS-CoV-2 infection ( Figure 4D ). cache = ./cache/cord-320165-1b6sycgv.txt txt = ./txt/cord-320165-1b6sycgv.txt === reduce.pl bib === id = cord-320455-doup2bqq author = Werion, Alexis title = SARS-CoV-2 Causes a Specific Dysfunction of the Kidney Proximal Tubule date = 2020-08-10 pages = extension = .txt mime = text/plain words = 2871 sentences = 182 flesch = 44 summary = Coronavirus disease 2019 (COVID-19) is commonly associated with kidney damage, and the angiotensin converting enzyme 2 (ACE2) receptor for SARS-CoV-2 is highly expressed in the proximal tubule cells. At the structural level, kidneys from patients with COVID-19 showed prominent tubular injury, including in the initial part of the proximal tubule, with brush border loss, acute tubular necrosis, intraluminal debris, and a marked decrease in the expression of megalin in the brush border. Thus, our data establish that SARS-CoV-2 causes specific manifestations of proximal tubule dysfunction and provide novel insights into COVID-19 severity and outcome. The angiotensin converting enzyme 2 (ACE2), the receptor mediating the entry of SARS-CoV-2 in human cells, is expressed in the lung, heart, intestine and kidney, providing a rationale for the systemic manifestations of the disease [4] [5] [6] [7] . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection cache = ./cache/cord-320455-doup2bqq.txt txt = ./txt/cord-320455-doup2bqq.txt === reduce.pl bib === id = cord-320207-cwt7dswz author = Zeng, Yingchun title = The nucleocapsid protein of SARS-associated coronavirus inhibits B23 phosphorylation date = 2008-05-02 pages = extension = .txt mime = text/plain words = 3129 sentences = 173 flesch = 53 summary = B23 protein is also identified as one of the substrates of CDK2/cyclin E and plays a critical role in centrosome duplication during cell cycle progression, which is regulated by the phosphorylation of B23 at Thr199 [26, 27] . The overlayed result indicated that the SARS-CoV N protein co-localized with B23 protein in the perinuclear region of HeLa cells (Fig. 1f) . In our previous research, we found that SARS-CoV N protein contained three NLS motifs and a nuclear export signal, acting as a shuttle protein between nucleus and cytoplasm, and it could arrest the cell cycle progression [10] . B23 protein can bind NLS, facilitate protein nuclear import and play a role in centrosome duplication during cell cycle progression [20, 21, 26] . In our previous research, we have shown that the N protein of SARS-CoV can arrest cell cycle progression [10] , which is in accordance with the result of Surjit et al. cache = ./cache/cord-320207-cwt7dswz.txt txt = ./txt/cord-320207-cwt7dswz.txt === reduce.pl bib === id = cord-320333-audnwp8t author = Chen, Qi-Lin title = Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis date = 2020-05-19 pages = extension = .txt mime = text/plain words = 5260 sentences = 293 flesch = 58 summary = BACKGROUND: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. METHODS: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. The GSE121862 database is a combination of data from different experiments and institutions, and studies have suggested that single-nuclear transcriptome sequencing technology is more suitable in the kidney than other methods of gene expression analysis [25] . To compare cell receptor-related genes of SARS-CoV-2 in different tissues, high-quality single-cell transcriptome databases of the lung and small intestine were used for further analysis. For the first time from the single-cell level analysis, our results demonstrate that cell receptor-related genes of SARS-CoV-2 are differentially expressed in cell subgroups of different tissues. cache = ./cache/cord-320333-audnwp8t.txt txt = ./txt/cord-320333-audnwp8t.txt === reduce.pl bib === id = cord-320350-zeeozmm9 author = Nisoli, Enzo title = COVID-19 and Hartnup disease: an affair of intestinal amino acid malabsorption date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2496 sentences = 140 flesch = 44 summary = We hypothesize that SARS-CoV-2 spike protein, binding to intestinal angiotensin-converting enzyme 2, negatively regulates the absorption of neutral amino acids, and this could explain not only the GI, but also systemic disturbances in COVID-19. Altered composition of the gut microbiota (as a consequence of impaired amino acid transport and reduced secretion of antimicrobial peptides by Paneth cells in the small intestine) and changes in innate immunity contribute to the colitis phenotype observed in ACE2 knockout mice [17] . Based on clinical observations and basic research, we hypothesise that, in response to the SARS-CoV-2 binding to intestinal ACE2, the absorption of neutral amino acids is negatively regulated in COVID-19 patients. In malnourished patients or conditions of intestinal amino acid malabsorption, as in the COVID-19 or Hartnup patients, the adaptive immune response cannot be effectively initiated because the absorption of essential energy substrates is impaired by SARS-CoV-2 binding to ACE2. cache = ./cache/cord-320350-zeeozmm9.txt txt = ./txt/cord-320350-zeeozmm9.txt === reduce.pl bib === id = cord-320535-fo4lzcav author = Geyer, Howard L. title = Movement Disorders in COVID-19: Whither Art Thou? date = 2020-08-12 pages = extension = .txt mime = text/plain words = 1662 sentences = 86 flesch = 37 summary = The paucity of movement disorders associated with COVID-19 is particularly striking when contrasted with the neurologic syndrome which affected over a million people worldwide in the aftermath of the 1918 "Spanish" influenza, termed by Constanin von Economo encephalitis lethargica. That encephalitis was associated with a wide range of movement disorders, of which post-encephalitic parkinsonism is the best known, although other manifestations in the acute phase included dystonia, tremor, chorea, myoclonus, and oculomasticatory myorhythmia [6, 7] . Although encephalitis has been described as a cardinal neurological manifestation of COVID-19 during the acute phase of illness [8, 9] , we have yet to encounter any of these associated movement disorder presentations. (In the time since this write-up was first prepared, patients with acute movement disorders and COVID-19 have been reported exiguously; we know of four such reports, which describe myoclonus [10, 11] , a hypokinetic-rigid syndrome [12] , and tremor/ataxia [13] . cache = ./cache/cord-320535-fo4lzcav.txt txt = ./txt/cord-320535-fo4lzcav.txt === reduce.pl bib === id = cord-320266-7gzx6ljt author = Vigneshwar, Navin G. title = Positive tracheal SARS-CoV-2 RNA test after three negative SARS-CoV-2 RNA tests in a patient with COVID-19 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 939 sentences = 70 flesch = 52 summary = Perioperative guidelines for patients with suspected coronavirus disease (COVID-19) often rely on nasopharyngeal swab testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Herein, we report the case of a patient with three consecutive negative nasopharyngeal swab tests followed by a positive tracheal aspirate test for SARS-CoV-2 RNA (Figure 1 ). On admission, a viral respiratory panel and two nasopharyngeal swab SARS-CoV-2 RT-PCR tests separated by four hours were negative. On hospital day 1, the patient's hypoxia improved, and results from a repeat SARS-CoV-2 RT-PCR test from a nasopharyngeal swab were negative. During the novel influenza A (H1N1) pandemic, approximately 10% of patients showed positive RT-PCR test results in respiratory secretions after intubation when prior tests on nasopharyngeal swab gave negative results. Following further deterioration of the patient's respiratory status and endotracheal intubation, a tracheal sample was positive for SARS-CoV-2 RNA. cache = ./cache/cord-320266-7gzx6ljt.txt txt = ./txt/cord-320266-7gzx6ljt.txt === reduce.pl bib === id = cord-320270-lduhhdld author = Obek, Can title = Management of prostate cancer patients during COVID-19 pandemic date = 2020-07-20 pages = extension = .txt mime = text/plain words = 5550 sentences = 322 flesch = 43 summary = National Comprehensive Cancer Network (NCCN), European Association of Urology (EAU), and the Canadian Framework advise against routine PC screening, including prostate specific antigen (PSA) testing and digital rectal examination (DRE), for all asymptomatic individuals until the pandemic subsides [11, 14, 17] . Although authors recognize that neoadjuvant ADT prior to surgery is normally not recommended outside of clinical trials, they state that upfront ADT may be an option in patients with UIR, HR, and VHR disease during COVID-19 crisis, if prolonged surgical delays are expected [11] . Likewise, Royal College of Surgeons' Updated Intercollegiate General Surgery Guidance on COVID-19 initial statement of "laparoscopy should generally not be used during the pandemic" was later changed to "consider laparoscopy only in selected individual cases, where clinical benefit to the patient substantially exceeds the risk of viral transmission to surgical and theater teams" [27, 28] . cache = ./cache/cord-320270-lduhhdld.txt txt = ./txt/cord-320270-lduhhdld.txt === reduce.pl bib === id = cord-320308-pzex799x author = Erol, Adnan title = Role of oxidized LDL-induced “trained macrophages” in the pathogenesis of COVID-19 and benefits of pioglitazone: A hypothesis date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1916 sentences = 129 flesch = 43 summary = CONCLUSIONS: When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. CARD9 is critical adaptor protein and a central integrator in innate immune cell activation that triggers the inflammatory signaling pathway in response to viral infection. Consequently, while SARS-CoV-infection in oxLDL-trained macrophages cannot produce protective type I interferons, they readily potentiates existing low-grade inflammation through ASC-mediated caspase-1 activation [10, 11] . All COVID-19 patients who develop severe respiratory failure display hyper-inflammatory responses with features of either immune dysregulation or macrophage activation syndrome. The information provided here must match the contributors' statement in the manuscript.Importance of oxidized lipid-trained macrophages in the severity of COVID-19Adnan Erol Comment Role of the funding source Please disclose any funding sources and their role, if any, in the writing of the manuscript or the decision to submit it for publication. cache = ./cache/cord-320308-pzex799x.txt txt = ./txt/cord-320308-pzex799x.txt === reduce.pl bib === id = cord-320331-wtxja5i9 author = Cabbab, Iris Louise N. title = Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection date = 2020-10-08 pages = extension = .txt mime = text/plain words = 10061 sentences = 433 flesch = 41 summary = It is important to note that since the approach of this paper is to provide current knowledge on the anatomic, physiologic and molecular bases of anti-inflammatory drug and corticosteroid action on the RAAS, this paper will not demonstrate a systematic review or meta-analysis of current clinical evidence, but will only provide insight on the probable influences of the discussed pathways on early SARS-CoV-2 infection. A correspondence by Fang et al published at The Lancet this March discussed that hypertensives and diabetics taking ACE2 inhibitor (ACEi) and angiotensin receptor blocking (ARB) drugs may be at an increased risk of infection and severity by SARS-CoV-2 and COVID-19, respectively, citing three studies wherein diabetes and hypertension were major comorbidities of patients with severe COVID-19 and of non-survivors [20] . cache = ./cache/cord-320331-wtxja5i9.txt txt = ./txt/cord-320331-wtxja5i9.txt === reduce.pl bib === id = cord-320627-7vi6skvh author = Horejsh, Douglas title = A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry date = 2005-01-19 pages = extension = .txt mime = text/plain words = 3725 sentences = 172 flesch = 48 summary = We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. In this report, we describe the construction of molecular beacon-conjugated beads that we have called 'BeadCons', whose specific hybridization with complementary target sequences can be resolved by flow cytometry (see Figure 1 ). In the multiplex detection experiment, the test sample contained 0.5 ml of the positive oligo DNA (100 mM stock) diluted in 9.5 ml of a complex mixture of oligonucleotides (equimolar levels of 10 mM each, equalling a 100 mM total concentration; sequences listed in Supplementary Table 1 ). cache = ./cache/cord-320627-7vi6skvh.txt txt = ./txt/cord-320627-7vi6skvh.txt === reduce.pl bib === id = cord-320175-w00rcvd8 author = Shi, Jiahai title = The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain date = 2006-02-08 pages = extension = .txt mime = text/plain words = 5485 sentences = 261 flesch = 51 summary = Based on this, a super‐active triple‐mutant STI/A with a 3.7‐fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild‐type (WT) and STI/A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Based on this, a super-active triple-mutant STI ⁄ A with a 3.7-fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild-type (WT) and STI ⁄ A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Dynamic light scattering (DLS) was used to measure the apparent molecular mass resulting from monomer-dimer equilibrium of the wild-type and mutated proteases at three different NaCl concentrations. cache = ./cache/cord-320175-w00rcvd8.txt txt = ./txt/cord-320175-w00rcvd8.txt === reduce.pl bib === id = cord-320417-01l27d99 author = Wang, Hai-Long title = The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5013 sentences = 257 flesch = 52 summary = I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intraand inter-viral clades. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination. SARS-CoV-2 is an RNA virus with limited genome length, but its high mutation rate and homologous genetic recombination nonetheless gave rise to exponentially increased variants. This is why all previously reported recombination events of SARS-Cov-2 have relied on clade-defining SNPs. The 2D co-occurring variant mapping is a simple way to display inter-clade hybrid lineages, and it can be used to directly compare distributions of populations for intra-and inter-clade from different geographic locations or the same location but at a different time point. I downloaded ~18,000 SARS-CoV-2 genome sequences from NCBI (on September 2 nd ) and used the same criterion as before to search for inter-clade co-occurring SNP pairs (see method for details). cache = ./cache/cord-320417-01l27d99.txt txt = ./txt/cord-320417-01l27d99.txt === reduce.pl bib === id = cord-320466-l7017jis author = Akgun, Emel title = Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3722 sentences = 226 flesch = 42 summary = Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified up-regulated proteins Myeloperoxidase, Myeloblastin, Neutrophil Elastase, Cathepsin G, and Azurocidin (MPO, PRTN3, ELANE, CTSG, and AZU1) in nasooropharyngeal swab samples are discussed to highlight the molecular mechanism changes in the site of infection. Pathway analysis of the significantly altered protein levels between COVID-19 positive and negative patients' naso-oropharyngeal swab samples were analyzed using the STRING online database. In SARS-CoV-2 patients' naso-oropharyngeal samples, we have identified azurophilic granule (AG) proteins like Myeloperoxidase (MPO), elastase (ELANE), cathepsin G (CTSG), azurocidin 1 (AZU1) and proteinase 3 (PRTN3) to be highly overexpressed. The alterations of various proteins in SARS-CoV-2 infected patients' naso-oropharyngeal samples depict the molecular changes that govern the host antiviral defense system. cache = ./cache/cord-320466-l7017jis.txt txt = ./txt/cord-320466-l7017jis.txt === reduce.pl bib === id = cord-320729-imyfo83x author = Spiga, Ottavia title = Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein date = 2003-10-10 pages = extension = .txt mime = text/plain words = 2919 sentences = 122 flesch = 50 summary = The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. After sequence alignment of SARS S protein (SwissProt Accession Number P59594) with the corresponding ones from human and canine coronaviruses, model building of S1 and S2 subunits was obtained by using the latter two pdb files and shuffled PsiPred runs [13] , with subsequent manual optimisation to enhance the overlapping between the predicted and observed secondary structure elements. As a final remark, it should be underlined that the consistent series of structural features, exhibited by the proposed models for the S1 and S2 subunits of the SARS_CoV spike protein, supports their reliability as a possible rational starting point for anti-viral drug design. cache = ./cache/cord-320729-imyfo83x.txt txt = ./txt/cord-320729-imyfo83x.txt === reduce.pl bib === id = cord-320567-7je1i8qd author = Muenchhoff, Maximilian title = Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1759 sentences = 91 flesch = 52 summary = The aim of this study was to compare the inter-laboratory and inter-method sensitivity of different RT-PCR assays by providing a blinded, frozen dilution series of a nucleic acid extract of a highly positive biosample to seven different diagnostic laboratories in Germany in March 2020. Digital droplet PCR quantification of the distributed dilution series of nucleic acid eluate of SARS-CoV-2-positive clinical material, Germany, March 2020 The undiluted sample showed between 4,325 and 5,015 SARS-CoV-2 RNA copies per reaction using 5 µL of eluate for the CDC N1, N2, N3 and Charité E protocols, but only 850 and 1,951 RNA copies for the Charité N and P primer/probe combinations ( Figure 1A) , respectively, indicating a lower sensitivity of the latter. Driven by false-negative results for samples with low PCR-positivity using the original Charité RdRp reaction (see below and others [8, 9] ), we compared the primer/ probe sequences with currently available SARS-CoV-2 genomes. cache = ./cache/cord-320567-7je1i8qd.txt txt = ./txt/cord-320567-7je1i8qd.txt === reduce.pl bib === id = cord-320646-xk77u4g0 author = Zumla, Alimuddin title = The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security date = 2020-04-09 pages = extension = .txt mime = text/plain words = 2396 sentences = 132 flesch = 48 summary = The emergence of new pathogens that cause lethal human respiratory illnesses with pandemic potential [2, 3] pose major challenges and rapidly focus the attention of global public health authorities and HCWs. Two zoonotic coronaviruses which cause lethal respiratory tract infections in humans feature on the WHO Blueprint list of priority pathogens for research and development [4] because of their pandemic potential. The World Health Organization International Health Regulations Emergency Committee declared COVID-19 outbreak a Global emergency [11] because SARS-CoV has spread rapidly within and outside China at an alarming pace and has caused considerable consternation and panic among the national, regional, and international public and political communities compounded by news media and social media hype [12] . Although the world awaits the development and evaluation of new vaccines, anti-SARS-CoV-2 specific drugs, antibody, and/or other host-directed interventions [32, 33] , public health infection control measures remain of prime importance in limiting human-to-human transmission, especially among close contacts and HCWs, and minimizing risk of international spread by identifying and isolating patients early. cache = ./cache/cord-320646-xk77u4g0.txt txt = ./txt/cord-320646-xk77u4g0.txt === reduce.pl bib === id = cord-320612-vam0bli3 author = Höring, Steffen title = Management of a Hospital-Wide COVID-19 Outbreak Affecting Patients and Healthcare Workers date = 2020-10-26 pages = extension = .txt mime = text/plain words = 3403 sentences = 190 flesch = 48 summary = Here, we report a large nosocomial outbreak of SARS-CoV-2 that occurred at a satellite hospital of the University Hospital Aachen, Germany, with 26 patients and 21 healthcare workers infected. Considering the numerous COVID-19 cases among patients and HCW, a hospital-wide screening was initiated on April 8 for all remaining SARS-CoV-2-negative patients and entire hospital staff. On the other hand, we analyzed the first cases among hospital staff, starting with the potential index nurse tested positive for SARS-CoV-2 on the 6th of April. By the time the outbreak emerged, the hospital policy already comprised preemptive infection control measures in order to prevent intrahospital spread of SARS-CoV-2. The second route of transmission addressed by our measures was infected HCW, who potentially spread SARS-CoV-2 to patients as well as to their co-workers. In the post-outbreak period, we have continued to screen all patients on their day of admission and all geriatric inpatients once weekly for SARS-CoV-2 in order to detect new cases timely. cache = ./cache/cord-320612-vam0bli3.txt txt = ./txt/cord-320612-vam0bli3.txt === reduce.pl bib === id = cord-320619-r466dc5t author = Chand Dakal, Tikam title = SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 date = 2020-11-05 pages = extension = .txt mime = text/plain words = 3843 sentences = 210 flesch = 46 summary = title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 The higher expression of integrins in lungs along with their previously known high binding affinity (∼K(D) = 4.0nM) for virus RGD motif could serve as a possible explanation for high infectivity of SARS-CoV-2. This study is the first study to present striking evidence (substantiated by existing facts in literature) favoring the role of calcium and other divalent ions (magnesium, manganese etc.) in RGD-integrins mediated virus attachment with the host cells for and that lowering the concentration of calcium and other divalent ions in lungs could be a possible mechanism to avert SARs-CoV-2 infection and invasion. A number of motifs were predicted in the spike protein sequence such as RGD (from 403-405 aa in receptor binding domain of SARS-CoV-2) ( Table 2 ). cache = ./cache/cord-320619-r466dc5t.txt txt = ./txt/cord-320619-r466dc5t.txt === reduce.pl bib === id = cord-320587-936cavob author = Ruscio, M. title = Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay date = 2020-11-07 pages = extension = .txt mime = text/plain words = 4092 sentences = 221 flesch = 46 summary = This analytical assessment encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, and comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using DiaSorin Liaison SARS-CoV-2 S1/S2 IgG and Roche Elecsys Anti-SARS-CoV-2 total antibodies. The assessment of this novel Beckman Coulter Access SARS-CoV-2 IgG immunoassay on UniCel DxI800 has originally encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, as well as comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using two other commercial anti-SARS-CoV-2 immunoassays, as comprehensively described below. As for the diagnostic performance calculated using manufacturers' cut-off, the AUCs of Beckman Coulter Access SARS-CoV-2 IgG (p<0.001) and Roche Elecsys Anti-SARS-CoV-2 (p=0.01) antibodies titers were found to be both significantly higher than that of DiaSorin Liaison SARS-CoV-2 S1/S2 IgG, whilst they were not significantly different between them (p=0.785). cache = ./cache/cord-320587-936cavob.txt txt = ./txt/cord-320587-936cavob.txt === reduce.pl bib === id = cord-320717-wk4zxmz9 author = Li, Yang title = Lack of Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2, China date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1073 sentences = 71 flesch = 56 summary = We report a pregnant woman with confirmed SARS-CoV-2 infection who underwent cesarean section delivery of a SARS-CoV-2-negative infant in Zhejiang Province, China. On days 4 and 5 of hospitalization, the woman's sputum tests were negative for SARS-CoV-2, and she remained afebrile. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. In conclusion, we report a pregnant woman with SARS-CoV-2 infection who delivered a healthy infant, suggesting that mother-to-child transmission is unlikely for this virus. Because our conclusions are limited by our sample size of 1, we cannot definitively state whether cesarean section is better than vaginal delivery for preventing transmission from a pregnant mother with SARS-CoV-2 infection. cache = ./cache/cord-320717-wk4zxmz9.txt txt = ./txt/cord-320717-wk4zxmz9.txt === reduce.pl bib === id = cord-320673-4guarm0k author = Lopera, E. title = Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes date = 2020-04-25 pages = extension = .txt mime = text/plain words = 4180 sentences = 215 flesch = 47 summary = title: Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes While large-scale genetic studies of COVID-19 patients are being assembled, such as those coordinated by the COVID host genetics consortium (https://www.covid19hg.com/), it is worthwhile to evaluate the effects of genetic variants in genes involved in SARS-CoV-2 infection on human phenotypes, including quantitative traits, taking advantage of already existing cohorts. Therefore, understanding the role of genetic variants at genes essential for SARS-CoV-2 infection in human quantitative phenotypes is important to explain the observed variability in infection susceptibility and severity of COVID-19 and this understanding may suggest potential treatments. In conclusion we carried out an extensive screening of potential genetic associations at common and low frequency variants in the ACE2 and TMPRSS2 genes, and found a lack of substantial effect in human quantitative phenotype variation in the general population. cache = ./cache/cord-320673-4guarm0k.txt txt = ./txt/cord-320673-4guarm0k.txt === reduce.pl bib === id = cord-320401-itltvh3f author = Clementi, Nicola title = NARINGENIN IS A POWERFUL INHIBITOR OF SARS-CoV-2 INFECTION IN VITRO date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1495 sentences = 85 flesch = 51 summary = In the present insight, we highlight novel experimental evidence that the flavanone Naringenin, targeting the endo-lysosomal Two-Pore Channels (TPCs), could be added to the list of potential weapons against SARS-CoV-2 infection and COVID-19 disease. Noteworthy, our recent evidence has shown that the activity of human TPC channels can be inhibited by the natural flavonoid compound Naringenin (Nar) [4] , one of the main flavonoids present in the human diet. Images showed that Nar treatment did not cause toxicity on uninfected cells at any of the tested concentrations and DMSO (vehicle) did not significantly affect SARS-CoV-2 replication (Fig.1D-E) . Of note, results indicated a strong decrease of CPE (>90%) at 48hpi when Vero E6 cells were treated with 250 and 62.5 μM Nar (Fig.1E) . Differences between treated samples (n=4, n=3 at 72hpi) and controls (untreated infected cells, n=4, not shown) were significant Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? cache = ./cache/cord-320401-itltvh3f.txt txt = ./txt/cord-320401-itltvh3f.txt === reduce.pl bib === id = cord-320490-3jmo35jc author = Ismail, Saba title = Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date = 2020-04-12 pages = extension = .txt mime = text/plain words = 6688 sentences = 412 flesch = 52 summary = In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . cache = ./cache/cord-320490-3jmo35jc.txt txt = ./txt/cord-320490-3jmo35jc.txt === reduce.pl bib === id = cord-320560-yn3bbkdh author = Kohanski, Michael A. title = Review of indoor aerosol generation, transport, and control in the context of COVID‐19 date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4514 sentences = 220 flesch = 41 summary = [5] [6] [7] [8] [9] The lack of studies within the otorhinolaryngology field assessing the aerosol-generating potential of procedures involving mucosal surfaces pre-COVID-19 made it challenging to understand in an evidence-based fashion the potential risks of SARS-CoV-2 transmission associated with instrumentation of the upper airway; that is, whether these procedures may be infectious AGPs. At the early stages of the pandemic, based on the risks of exposure to high viral load mucosal surfaces, 10, 11 as well as on the lack of any immunity to SARS-CoV-2 and of any vaccines or effective treatments, an array of practice changes to protect health-care workers and patients were recommended and instituted for otorhinolaryngology procedures involving upper airway mucosal surfaces. cache = ./cache/cord-320560-yn3bbkdh.txt txt = ./txt/cord-320560-yn3bbkdh.txt === reduce.pl bib === id = cord-320912-jfeu4tho author = Fukui, M. title = Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models date = 2020-06-12 pages = extension = .txt mime = text/plain words = 11777 sentences = 786 flesch = 59 summary = This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection dynamics, even with large populations. . https://doi.org/10.1101/2020.06.11.20128058 doi: medRxiv preprint Figure 3 plots the predicted ranking of infection cases given the estimated negative binomial (NB) distribution, in addition to the log-log plots and estimated power law (PL) distributions. The mean is set to the same value as power law case, R 0 = 2.5, Figure 4a shows 10 sample paths of infected population generated through the simulation of the model with α = 1.1. cache = ./cache/cord-320912-jfeu4tho.txt txt = ./txt/cord-320912-jfeu4tho.txt === reduce.pl bib === id = cord-320511-qnxj7d9l author = Hueston, Linda title = The antibody response to SARS-CoV-2 infection date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3106 sentences = 180 flesch = 47 summary = METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for IgG, IgA and IgM was developed, and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Diagnosis is primarily by detecting SARS-CoV-2-specific RNA by nucleic acid testing (NAT), but this has limitations, including the possibility of false-negative results due to low virus load in patients with minimal disease, inadequate respiratory tract sampling or mutations in the target sequence, and false-positive results due to contamination or nonspecific amplification. The objective of this study was to develop and evaluate an immunofluorescent antibody (IFA) test for SARS-CoV-2-specific IgG, IgM and IgA, and apply it to document the serological response in individuals with confirmed COVID-19. Since the start of the epidemic in Australia, the Public Health Laboratory Network recommended collecting acute and convalescent sera for serological assays on individuals being tested for SARS-CoV-2 infection, in addition to respiratory tract samples for NAT, though this has not been universally adopted [5] . cache = ./cache/cord-320511-qnxj7d9l.txt txt = ./txt/cord-320511-qnxj7d9l.txt === reduce.pl bib === id = cord-320864-k9zksbyt author = Remes-Troche, J. M. title = Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date = 2020-11-01 pages = extension = .txt mime = text/plain words = 4669 sentences = 256 flesch = 46 summary = When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. Positions have already been established on how to work and/or resume activities at those units (e.g., those issued by the American Neurogastroenterology and Motility Society [ANMS] 4 and the Grupo Español de Motilidad Digestiva [GEMD]) 5 but due to the fact that the epidemiologic behavior, protective equipment avail-ability, serologic diagnostic test performance capacity for corroborating immunity, and socioeconomic context are different throughout Latin America, a group of experts that are members of the Sociedad Latinoamericana de Neurogastroenterología (SLNG) had a virtual meeting to formulate a consensus document with recommendations for the performance of gastrointestinal motility tests. cache = ./cache/cord-320864-k9zksbyt.txt txt = ./txt/cord-320864-k9zksbyt.txt === reduce.pl bib === id = cord-320848-bz9pf2p6 author = Sepehrinezhad, Ali title = COVID-19 virus may have neuroinvasive potential and cause neurological complications: a perspective review date = 2020-05-16 pages = extension = .txt mime = text/plain words = 2758 sentences = 186 flesch = 52 summary = Here, we reviewed the evidence of the neuroinvasive potential of coronaviruses and discussed the possible pathogenic processes in CNS infection by COVID-19 to provide a precise insight for future studies. Therefore, the aim of the present study was to review neuroinvasive potential and neurotropism effects of human coronaviruses (HCoVs) and discuss the probable neurological complication followed by COVID-19 to give an insight for future studies. We used the terms "coronavirus," "SARS," "SARS-CoV-2," "MERS," "229E-CoV," and "COVID-19," w i t h c o m bi n a t i o n th e t e r m s " n er vo us sy s t e m , " "neuroinvasion," and "neurological manifestation." In vitro studies on neurotropism potentials of CoVs on neural or glial cells cultures were considered. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 cache = ./cache/cord-320848-bz9pf2p6.txt txt = ./txt/cord-320848-bz9pf2p6.txt === reduce.pl bib === id = cord-320704-rrq6x25k author = Sharma, Shruti title = COVID-19: A Concern for Cardiovascular Disease Patients date = 2020-07-29 pages = extension = .txt mime = text/plain words = 3068 sentences = 189 flesch = 46 summary = The organism responsible for the cause of disease is Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Coronavirus Disease (COVID-19) is a recently emerged disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2), a novel coronavirus that leads to adverse pulmonary pathological features [1] . Therefore, in the present review, the role of ACE2 receptors in the viral entry into the host cell, the effect of COVID-19 on the symptoms and prognosis of CVDs, impact of ACE inhibitors (ACEI), and angiotensin receptor blockers (ARBs) on patients of CVDs suffering from COVID-19 have been discussed. Various cardiac complications like cardiovascular disease, arrhythmia (ventricular tachyarrhythmia, atrial fibrillation and ventricular fibrillation), hypertension, cardiac injury, heart failure, and fulminant myocarditis have been found to influence the mortality of the COVID -19 patients [27] . There is a possibility that polymorphism in ACE2 gene, linked to hypertension, particularly, in Asian populations, affects the susceptibility of SARS-CoV-2 infection and COVID-19 disease outcome. ACE2 receptor polymorphism: Susceptibility to SARS-CoV-2, hypertension, multi-organ failure, and COVID-19 disease outcome cache = ./cache/cord-320704-rrq6x25k.txt txt = ./txt/cord-320704-rrq6x25k.txt === reduce.pl bib === id = cord-320826-o6ih2f23 author = Blairon, Laurent title = Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak date = 2020-07-31 pages = extension = .txt mime = text/plain words = 862 sentences = 56 flesch = 53 summary = title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak We read with great interest the study of Chen Y et al., who analyzed, during the Chinese epidemic peak, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 105 healthcare workers (HCWs) exposed to COVID-19 patients [1] . Our purpose was to document at the end of the Belgium epidemic the seroprevalence of SARS-CoV-2 in HCWs exposed to COVID-19 at varying degrees and to compare these rates with those observed by other teams worldwide. On the same day, all asymptomatic HCWs who agreed to participate benefited from both serological and RT-qPCR SARS-CoV-2 tests. High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients COVID-19 study: 8,4% of Belgian health workers have antibodies to SARS-COV-2 n cache = ./cache/cord-320826-o6ih2f23.txt txt = ./txt/cord-320826-o6ih2f23.txt === reduce.pl bib === id = cord-320740-npoje09j author = Musa, Arif title = Remdesivir for the Treatment of COVID-19: A Systematic Review of the Literature date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2292 sentences = 153 flesch = 54 summary = To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Given the worldwide urgency for an effective and safe treatment for COVID-19 and the therapeutic potential of remdesivir, this systematic review was performed to determine the outcomes and adverse events associated with this investigational, anti-viral medication. cache = ./cache/cord-320740-npoje09j.txt txt = ./txt/cord-320740-npoje09j.txt === reduce.pl bib === id = cord-320681-b3ui95vx author = Zhang, Rui title = COVID-19: Melatonin as a potential adjuvant treatment date = 2020-06-01 pages = extension = .txt mime = text/plain words = 4138 sentences = 219 flesch = 39 summary = Based on clinical features, pathology, the pathogenesis of acute respiratory disorder induced by either highly homogenous coronaviruses or other pathogens, the evidence suggests that excessive inflammation, oxidation, and an exaggerated immune response very likely contribute to COVID-19 pathology. Herein, we review the evidence indicating that melatonin will have supportive adjuvant utility in treating COVID-19 induced pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In SARS-CoV and MERS-CoV infected animal model, marked inflammatory and immune responses may activate a "cytokine storm", and apoptosis of epithelial cells and endothelial cells; subsequently, vascular leakage, abnormal T cell and macrophages responses ensue and induce ALI/ARDS or even death [13] . The amplification of the inflammatory response would promote cellular apoptosis or We postulated that lungs infected by SARS-CoV-2, and a suppressed immune response, elevated inflammation and excessive oxidation stress proceed unabated, this results in the activation of the cytokine storm. cache = ./cache/cord-320681-b3ui95vx.txt txt = ./txt/cord-320681-b3ui95vx.txt === reduce.pl bib === id = cord-320970-ru2iw0py author = Peeling, Rosanna W title = Serology testing in the COVID-19 pandemic response date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3669 sentences = 186 flesch = 49 summary = On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. Point-of-care molecular assays for SARS-CoV-2 detection are now available to enable community-based testing for COVID-19 in LMICs. Unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving LMICs struggling for access. On the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. cache = ./cache/cord-320970-ru2iw0py.txt txt = ./txt/cord-320970-ru2iw0py.txt === reduce.pl bib === id = cord-321013-8pkrg0mx author = McBride, Ruth title = The Coronavirus Nucleocapsid Is a Multifunctional Protein date = 2014-08-07 pages = extension = .txt mime = text/plain words = 10761 sentences = 476 flesch = 44 summary = The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-321013-8pkrg0mx.txt txt = ./txt/cord-321013-8pkrg0mx.txt === reduce.pl bib === id = cord-320829-uepneyug author = He, Zhongping title = Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date = 2005-08-10 pages = extension = .txt mime = text/plain words = 2631 sentences = 138 flesch = 59 summary = title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS cache = ./cache/cord-320829-uepneyug.txt txt = ./txt/cord-320829-uepneyug.txt === reduce.pl bib === id = cord-321155-dty18esg author = Zhang, Rongxin title = Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4927 sentences = 331 flesch = 57 summary = We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. cache = ./cache/cord-321155-dty18esg.txt txt = ./txt/cord-321155-dty18esg.txt === reduce.pl bib === id = cord-320788-ln8ddyuj author = Wang, Chun-Hua title = Persistence of lung inflammation and lung cytokines with high-resolution CT abnormalities during recovery from SARS date = 2005-05-11 pages = extension = .txt mime = text/plain words = 4399 sentences = 229 flesch = 49 summary = BACKGROUND: During the acute phase of severe acute respiratory syndrome (SARS), mononuclear cells infiltration, alveolar cell desquamation and hyaline membrane formation have been described, together with dysregulation of plasma cytokine levels. In the current study, we conducted a study to examine HRCT changes in patients who recovered from the acute phase of SARS at days 60 and 90, and measured the associated inflammatory profiles directly by examining bronchoalveolar lavage fluid (BALF). At 60 days, compared to normal subjects, there was a significant increase in total cell counts in BAL fluid from SARS patients (Table 3 ) with a significant increase in alveolar macrophages (AM) and lymphocytes., The proportion of CD8+ T cells was increased to a greater extent than CD4+ T cells, leading to a significant decrease in CD4/CD8 ratio (Table 4 ). Coronavirus infected cells were not detected in any of SARS patients with low HRCT score or in normal subjects (Table 1) . cache = ./cache/cord-320788-ln8ddyuj.txt txt = ./txt/cord-320788-ln8ddyuj.txt === reduce.pl bib === id = cord-320909-p93gxjm2 author = Natoli, S. title = Does SARS‐Cov‐2 invade the brain? Translational lessons from animal models date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4718 sentences = 246 flesch = 39 summary = Animal models of SARS and Middle East respiratory syndrome, caused by structurally similar CoVs during the 2002 and 2012 epidemics, have provided valuable data on nervous system involvement by CoVs and the potential for central nervous system spread of SARS‐CoV‐2. The expression of this receptor in neurons and endothelial cells hints that SARS‐CoV‐2 may have higher neuroinvasive potential compared with previous CoVs. However, it remains to be determined how such invasiveness might contribute to respiratory failure or cause direct neurological damage. Highly pathogenic coronavirus (CoV) infections are well-established sources of previous epidemics in humans, i.e. severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice cache = ./cache/cord-320909-p93gxjm2.txt txt = ./txt/cord-320909-p93gxjm2.txt === reduce.pl bib === id = cord-320902-1hfxju5f author = Filocamo, Giovanni title = Use of anakinra in severe COVID-19: a case report date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1440 sentences = 88 flesch = 46 summary = As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still's disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient's critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). cache = ./cache/cord-320902-1hfxju5f.txt txt = ./txt/cord-320902-1hfxju5f.txt === reduce.pl bib === id = cord-320882-cr0ccsnp author = Li Volti, Giovanni title = Smoking and SARS-CoV-2 Disease (COVID-19): Dangerous Liaisons or Confusing Relationships? date = 2020-05-02 pages = extension = .txt mime = text/plain words = 1235 sentences = 69 flesch = 47 summary = Keywords: COVID-19; SARS-Cov-2; smoking; angiotensin-converting enzyme-2 We read with great interest the article by Brake SJ and colleagues [1] investigating the relationship between smoking and angiotensin-converting enzyme-2 (ACE-2) and the potential implication for COVID-19. The authors present findings linking ACE-2 expression to smoking in a variety of experimental models together with observations of their own; immunohistochemistry data showing an increased expression of ACE-2 in a series of biopsies from a group of current smokers with chronic obstructive pulmonary disease when compared to a control group. The authors then venture into reporting existing Chinese case reports to support their hypothesis that smoking could increase the risk of COVID-19 via upregulation of ACE-2 expression, a known cellular entry gateway for SARS-CoV-2 [2] . Smoking upregulates angiotensin-converting enzyme-2 receptor: A potential adhesion site for novel coronavirus SARS-CoV-2 (Covid-19) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target cache = ./cache/cord-320882-cr0ccsnp.txt txt = ./txt/cord-320882-cr0ccsnp.txt === reduce.pl bib === id = cord-321027-64y43o0y author = Andreano, Emanuele title = Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date = 2020-05-09 pages = extension = .txt mime = text/plain words = 2287 sentences = 114 flesch = 51 summary = The SARS-CoV-2 spike glycoprotein (S-protein) has a pivotal role in viral pathogenesis and it is 63 considered the main target to elicit potent neutralizing antibodies and the focus for the development 64 of therapeutic and prophylactic tools against this virus (3, 4) . Results shown in Table 1 and Figure 1 show that, among the seven donors 97 included in this study, six were able to produce high titers of SARS-CoV-2 S-protein specific 98 antibodies and in particular donors R-042, R-122 and R-188 showed the highest virus neutralizing 99 titers. In the case of SARS-CoV-2, where so far we do not have any effective therapeutic nor prophylactic 154 interventions, mAbs have the possibility to become one of the first drugs that can be used for 155 immediate therapy of any patient testing positive for the virus, and even to provide immediate 156 protection from infection in high risk populations. cache = ./cache/cord-321027-64y43o0y.txt txt = ./txt/cord-321027-64y43o0y.txt === reduce.pl bib === id = cord-320787-dwyyjq6o author = La Rosa, Giuseppina title = First detection of SARS-CoV-2 in untreated wastewaters in Italy date = 2020-05-23 pages = extension = .txt mime = text/plain words = 2747 sentences = 141 flesch = 54 summary = Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Herein we report the results of the screening for SARS-CoV-2 presence in sewage samples collected between the end of February and the beginning of April 2020 from WWTPs in Milan (Northern Italy) and Rome (Central Italy). In the absence of a standardized method for SARS-CoV-2 detection in environmental samples, RNAs were tested for the presence of SARS-CoV-2 using three different nested RT-PCR assays and one real-time qPCR assay (Table 1 and Figure 1 b) a newly designed primer set specific for SARS-CoV-2. cache = ./cache/cord-320787-dwyyjq6o.txt txt = ./txt/cord-320787-dwyyjq6o.txt === reduce.pl bib === id = cord-320964-1gg33gdn author = Sampieri, Clara Luz title = Revisión de nuevas evidencias acerca de la posible transmisión vertical de la COVID-19 date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4036 sentences = 363 flesch = 60 summary = En el contexto de la pandemia por COVID-19 se ha generado nueva evidencia tras la publicación de la guía de la Organización Mundial de la Salud, el 13 de marzo de 2020 14 , por lo que efectuamos una revisión sistemática de la literatura en PubMed de estudios revisados por pares publicados entre el 27 de marzo y el 21 de mayo de 2020, enfocándonos en aquellos trabajos que incluyeran análisis de muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical y Se identificaron 107 registros, de los cuales dos condujeron a la misma referencia y uno indicó una ruta de acceso no válida. En los estudios incluidos se identificó la etapa en que la madre tuvo la confirmación de la infección por SARS-CoV-2 o el diagnóstico clínico de COVID-19, el pronóstico del binomio madre-hijo/a, los resultados del análisis de SARS-CoV-2 del bebé, y las muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical o leche humana. cache = ./cache/cord-320964-1gg33gdn.txt txt = ./txt/cord-320964-1gg33gdn.txt === reduce.pl bib === id = cord-320935-3n157yl4 author = Kumar, Manish title = Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date = 2020-09-12 pages = extension = .txt mime = text/plain words = 6613 sentences = 346 flesch = 44 summary = This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. cache = ./cache/cord-320935-3n157yl4.txt txt = ./txt/cord-320935-3n157yl4.txt === reduce.pl bib === id = cord-320815-p9oh54nt author = Gentile, Pietro title = Research progress on Mesenchymal Stem Cells (MSCs), Adipose-Derived Mesenchymal Stem Cells (AD-MSCs), Drugs, and Vaccines in Inhibiting COVID-19 Disease date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4718 sentences = 234 flesch = 46 summary = Additionally, recent studies reported improved respiratory activity after intravenous administration of MSCs into patients affected by coronavirus disease 2019 (COVID-19) caused by the Coronavirus 2 (SARS-CoV-2) suggesting their role as anti-viral therapy. In this literature review, the role of regenerative strategies through MSCs, AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. In this current review, the role of regenerative strategies through MSCs, focusing on AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. Two clinical trials (EUCTR2020-001364-29-ES and EUCTR2020-001266-11-ES) were registered in April 2020, after the pandemic situation produced by COVID-19 but the last one (EUCTR2019-002688-89-ES) based on the possibility "To assess the feasibility, safety, and tolerability of the administration of HCR040, a drug whose active substance is HC016, allogeneic adiposederived adult mesenchymal stem cells expanded and pulsed with H2O2, in patients with acute respiratory distress syndrome. cache = ./cache/cord-320815-p9oh54nt.txt txt = ./txt/cord-320815-p9oh54nt.txt === reduce.pl bib === id = cord-321315-bzmokdzk author = Tanacan, Atakan title = The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2136 sentences = 136 flesch = 54 summary = title: The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey OBJECTIVE: To investigate the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. CONCLUSION: Healthcare professionals should be cautious in the labor and delivery of high-risk pregnant women during the pandemic period and universal testing for COVID-19 may be considered in selected populations. The aim of this study is to investigate the rate of SARS-CoV-2 positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. Maternal age, gravidity, parity, number of previous miscarriages, body mass index (BMI) (kg/m2), gestational age at birth, birth weight, 1st-5th minute Apgar scores, route of delivery (spontaneous vaginal deliver yor cesarean section) and SARS-CoV-2 positivity rates were compared between the healthy and high-risk pregnant women. cache = ./cache/cord-321315-bzmokdzk.txt txt = ./txt/cord-321315-bzmokdzk.txt === reduce.pl bib === id = cord-321166-nvphu1fm author = Thomson, Emma C. title = The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date = 2020-11-05 pages = extension = .txt mime = text/plain words = 9813 sentences = 514 flesch = 55 summary = We find that the N439K mutation is associated with a similar clinical spectrum of disease and slightly higher viral loads in vivo compared with isolates with the wild-type N439 residue, and that it results in immune escape from polyclonal sera from a proportion of recovered individuals and a panel of neutralizing mAbs. N439K provides a sentinel example of immune escape, indicating that RBM variants must be evaluated when considering vaccines and the therapeutic or prophylactic use of mAbs. Long term control of the pandemic will require systematic monitoring of immune escape variants and selection of strategies that address the variants circulating in targeted populations. Fitness of this variant, N439K, was demonstrated by repeated emergence by convergent evolution, spread to multiple countries and significant representation in the SARS-CoV-2 sequence databases, the fact that the N439K RBD retains a high affinity interaction with the hACE2 receptor, efficient viral replication in cultured cells, and no disease attenuation in a large cohort of infected individuals. cache = ./cache/cord-321166-nvphu1fm.txt txt = ./txt/cord-321166-nvphu1fm.txt === reduce.pl bib === id = cord-321208-zemex8bf author = Reina, Jordi title = Evaluación de diferentes genes en la detección por RT-PCR del SARS-CoV-2 en muestras respiratorias y su evolución en la infección date = 2020-05-27 pages = extension = .txt mime = text/plain words = 999 sentences = 135 flesch = 70 summary = En nuestro estudio el 96,5% de las primeras muestras positivas presentaron positividad en este gen y el 94% con el gen E, a pesar que su capacidad de detección es de unas 100 genomas-copias/reacción. Sin embargo, al analizar las segundas muestras se observa como la detección del gen E ha mostrado una disminución significativa, a pesar de que todavía el 42% de todos los pacientes seguían siendo positivos a los tres genes, frente al 84% de la primoinfección. Por ello podría afirmarse que para el primer diagnóstico de infección por SARS-CoV-2 debería utilizarse de forma preferentemente el gen E o el gen RpRd. Este mismo dato lo confirma el estudio comparativo de Nalla et al. Por ello se presenta un estudio prospectivo que evalúa la capacidad de amplificación de los tres genes del SARS-CoV-2 (E, RpRd y N) en el diagnóstico de infección por este virus. cache = ./cache/cord-321208-zemex8bf.txt txt = ./txt/cord-321208-zemex8bf.txt === reduce.pl bib === id = cord-321131-f8qeytxc author = Zhou, Yanchen title = Protease inhibitors targeting coronavirus and filovirus entry date = 2015-04-30 pages = extension = .txt mime = text/plain words = 5517 sentences = 254 flesch = 45 summary = Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. Cell culture studies demonstrated that endosomal cysteine proteases, in particular cathepsin B (CTSB) and/or L (CTSL), can activate the glycoproteins of filoviruses, SARS-CoV, other coronaviruses, and NiV and Hendra (HeV) viruses to facilitate entry into certain cell lines. The notion that coronaviruses, including SARS-CoV, use both a cathepsin-dependent endosomal pathway and a direct cell-surface serine protease-mediated pathway for entry (Simmons et al., 2013) is supported by our finding that the combination of K11777 and camostat was superior to either compound alone. cache = ./cache/cord-321131-f8qeytxc.txt txt = ./txt/cord-321131-f8qeytxc.txt === reduce.pl bib === id = cord-320845-imxby1b1 author = Morley, G. L. title = Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1711 sentences = 106 flesch = 52 summary = title: Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples Objective: To validate the use of dried blood spot sampling for the detection of SARS-CoV-2-specific antibodies. Results: Specific anti-SARS-Cov-2 spike glycoprotein antibodies were detectable in both serum and DBS eluate and there was a significant correlation between the antibody levels detected in matched samples (r = 0.96, p<0.0001). Using serum as the gold standard in the assay, matched DBS samples achieved a Cohens kappa coefficient of 0.975 (near-perfect agreement), a sensitivity of 98.1% and specificity of 100%, for detecting anti-spike glycoprotein antibodies. . https://doi.org/10.1101/2020.07.01.20144295 doi: medRxiv preprint against matched serum in a highly sensitive and specific SARS-CoV-2 Enzyme Linked Immunosorbent Assay (ELISA). To detect antibodies to SARS-CoV-2-anti-spike (S) glycoprotein, matched serum and DBS titration curves were generated. We show that DBS samples can be used for the detection of SARS-CoV-2-specific antibodies with high levels of sensitivity and specificity and compared well with matched serum samples. cache = ./cache/cord-320845-imxby1b1.txt txt = ./txt/cord-320845-imxby1b1.txt === reduce.pl bib === id = cord-321049-9ozn6il7 author = de Almeida, Paula Rodrigues title = SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date = 2020-05-01 pages = extension = .txt mime = text/plain words = 1308 sentences = 73 flesch = 49 summary = title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. Here, we present a fast, accurate and simple method of viral titration using QuantStudio 3D® microchip based RT-dPCR to titrate SARS-CoV2 genomic copies from controls to be used in RT-qPCR assays for diagnosis and research purposes. A dilution that results in approximately 200 to 2000 target copies in the final reaction usually presents better precision values. Results with precision values below 5% were selected to estimate quantity of SARS-CoV2 genomic copies based on RT-dPCR. RT-dPCR results of 10-fold serial dilution of SARS-CoV2 control using assays for three targets in the Nucleocapsid gene. These results indicate that these primer-probe assays are suitable for SARS-CoV2 quantification through RT-dPCR. cache = ./cache/cord-321049-9ozn6il7.txt txt = ./txt/cord-321049-9ozn6il7.txt === reduce.pl bib === id = cord-321455-ooouqna7 author = Li, Tao title = Characteristics of laboratory indexes in COVID-19 patients with non-severe symptoms in Hefei City, China: diagnostic value in organ injuries date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2117 sentences = 119 flesch = 52 summary = In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. In the process of continuous monitoring, the expression of CRE in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, and 7th days of admission, and showed an overall downward trend (Fig. 3a) . The expression of Ca 2+ in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, 7th and 10th days of admission, and showed an overall upward trend (Fig. 3d ). cache = ./cache/cord-321455-ooouqna7.txt txt = ./txt/cord-321455-ooouqna7.txt === reduce.pl bib === id = cord-321308-rwxhdg8r author = Grubaugh, Nathan D. title = Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1505 sentences = 87 flesch = 60 summary = While clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown. Following the emergence of SARS-CoV-2 in China in late 2019, and the rapid expansion of the COVID-19 pandemic in 2020, questions about viral evolution have come tumbling after. They present compelling data that an amino acid change in the virus' spike protein, D614G, emerged early during the pandemic, and viruses containing G614 are now dominant in many places around the world. In support of their hypothesis, the authors provided evidence that clinical samples from G614 infections have a higher levels of viral RNA, and produced higher titers in pseudoviruses from in vitro experiments; results that now seem to be corroborated by others [e.g. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry cache = ./cache/cord-321308-rwxhdg8r.txt txt = ./txt/cord-321308-rwxhdg8r.txt === reduce.pl bib === id = cord-321146-dd8z5c6d author = Mishra, Rakesh title = SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem date = 2020-07-30 pages = extension = .txt mime = text/plain words = 530 sentences = 43 flesch = 50 summary = title: SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem It is prudent to identify if SARS CoV-2 affects the respiratory control mechanisms at the brainstem and lead to complications in addition to primary respiratory damage. 5 There are reports which suggest that involvement of pontine and medullary centres by SARS-CoV-2 is a mechanism implicated in potential central respiratory failure complicating primary pulmonary injury. Recently a case report published illustrated brainstem dysfunction due to rhombencephalitis in a patient with acute COVID-19. 7 Therefore, patients with SARS-CoV-2 with neurological symptoms must be followed up closely as they can have further deterioration in their respiratory function. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Does SARS-Cov-2 invade the brain? Neurologic features in severe SARS-CoV-2 infection Neurological manifestations of patients with COVID-19: potential routes of SARS-CoV-2 neuroinvasion from the periphery to the brain cache = ./cache/cord-321146-dd8z5c6d.txt txt = ./txt/cord-321146-dd8z5c6d.txt === reduce.pl bib === id = cord-320663-xypg6evo author = Market, Marisa title = Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies date = 2020-06-23 pages = extension = .txt mime = text/plain words = 14038 sentences = 659 flesch = 42 summary = A common feature of coronavirus infections is that significant morbidity and mortality is associated with lung injury and acute respiratory distress syndrome resulting from an exaggerated immune response, of which NK cells are an important component. Natural Killer (NK) cells are a key component of the innate immune system and are critical in the response to many viral infections in humans and animal models (1) (2) (3) . Altogether these studies show that during acute CoV infection, inflammatory monocyte-macrophages and neutrophils accumulate in the lungs and produce cytokines and chemokines that induce the activation and migration of lymphocytes, including NK cells, to the lungs, where they could be one of the main producers of IFN-γ (148). Studies have reported that patients infected with SARS-CoV-2 have lower levels of circulating NK cells and these express a greater level of inhibitory receptors (e.g., NKG2A) while producing less IFN-γ (127, 129, 130) . cache = ./cache/cord-320663-xypg6evo.txt txt = ./txt/cord-320663-xypg6evo.txt === reduce.pl bib === id = cord-321259-wio2b49i author = Carmona-Gutierrez, Didac title = Digesting the crisis: autophagy and coronaviruses date = 2020-05-04 pages = extension = .txt mime = text/plain words = 4350 sentences = 243 flesch = 35 summary = Of note, cellular manipulation of autophagic levels during infection may also reflect desperate attempts of the cell to reestablish homeostasis, either through restriction of viral entry by actively shunting endocytosis/endosomal trafficking (possibly resulting in autophagy reduction as a sideeffect) [39] or to counteract virally induced cell death by increasing cytoprotective autophagy. Thus, the group-specific accessory proteins, which by definition are not essential for viral replication but are involved in the modulation of host cells and immune evasion [66, 67] , may represent targets for reducing the autophagy-inhibitory effects of CoVs. The FDA-approved anti-malarial drugs chloroquine and hydroxychloroquine have been suggested to be repurposed for the treatment of COVID-19 [68] [69] [70] , but this remains widely controversial [71] [72] [73] . Intriguingly, another recent preprint presents in vitro data showing that SARS-CoV-2 infection restricts autophagy and that, in turn, pro-autophagic compounds -including spermidine -may inhibit viral propagation [85] . cache = ./cache/cord-321259-wio2b49i.txt txt = ./txt/cord-321259-wio2b49i.txt === reduce.pl bib === id = cord-320860-qt84oicg author = Zhang, Aining title = Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2359 sentences = 131 flesch = 47 summary = title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis cache = ./cache/cord-320860-qt84oicg.txt txt = ./txt/cord-320860-qt84oicg.txt === reduce.pl bib === id = cord-321231-zlpa3x2x author = Anand, Pratima title = Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India date = 2020-09-10 pages = extension = .txt mime = text/plain words = 6895 sentences = 348 flesch = 53 summary = title: Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India The study was conducted to describe the clinical profile of neonates born to mothers who tested positive for COVID 19 infection and to determine the association of neonatal COVID 19 status and viral load with maternal clinical status and viral load. • In this study on a limited number of neonates, maternal viral load of COVID 19 (E and RdRp cycle thresholds) was not associated with severity of illness or COVID 19 positivity in neonates. Neonates born to COVID 19 positive mothers and requiring NICU care for any reason (comorbidity like prematurity, low birth weight, or transient tachypnoea of neonate) were nursed in separate designated NICU in COVID block. cache = ./cache/cord-321231-zlpa3x2x.txt txt = ./txt/cord-321231-zlpa3x2x.txt === reduce.pl bib === id = cord-321380-e5zq15hz author = del Campo, P. Lázaro title = No transmission of SARS-CoV-2 in a patient undergoing allogeneic Hematopoietic Cell Transplantation from a matched-related donor with unknown COVID-19 date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1883 sentences = 122 flesch = 53 summary = In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. Lastly, applied to our case, the low concentration of viral RNA in plasma of asymptomatic patients with COVID-19 [5] , and a theoretical inefficacy of SARS-CoV-2 J o u r n a l P r e -p r o o f to replicate inside lymphocytes could support the safety of blood products, including peripheral blood hematopoietic cells. cache = ./cache/cord-321380-e5zq15hz.txt txt = ./txt/cord-321380-e5zq15hz.txt === reduce.pl bib === id = cord-321369-xzu2faol author = Andreano, Emanuele title = Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date = 2020-10-07 pages = extension = .txt mime = text/plain words = 3685 sentences = 192 flesch = 52 summary = By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. As for the authentic virus neutralization assay, supernatants containing naturally produced IgG or IgA were tested for their ability to protect the layer of Vero E6 cells from the cytopathic effect triggered by SARS-CoV-2 infection (Fig. S2) . This work describes a systematic screening of memory B cells from convalescent people to identify extremely potent human monoclonal antibodies against the spike protein of the SARS-CoV-2 virus, to be used for prevention and therapy of Covid-19. cache = ./cache/cord-321369-xzu2faol.txt txt = ./txt/cord-321369-xzu2faol.txt === reduce.pl bib === id = cord-321235-h3w8827o author = Cabrera Alvargonzalez, Jorge Julio title = Pooling for SARS-CoV-2 control in care institutions date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2839 sentences = 195 flesch = 58 summary = The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. The rationale in this study is to develop a new strategy based on initial individual identification of positive coronavirus cases in order to organize low prevalence clusters, followed by a serial pooling strategy testing of these clusters, in order to control areas free of virus circulation, allowing them to be fully operative. During the Coronavirus pandemic, SARS-CoV-2 prevalence was obtained by individually testing of 25, 386 people from 306 Galician Care Homes: 16,477 residents, 8599 workers and 310 not specified. A global SARS-CoV-2 seroprevalence of 5% in Spain [12] and a global viral prevalence around 3% at Care Homes reported in the present study, suggest that the number of people at risk of acquiring the infection continue to be very high. cache = ./cache/cord-321235-h3w8827o.txt txt = ./txt/cord-321235-h3w8827o.txt === reduce.pl bib === id = cord-321267-ihd30qi0 author = Daughton, Christian G. title = Natural experiment concept to accelerate the Re-purposing of existing therapeutics for Covid-19 date = 2020-05-15 pages = extension = .txt mime = text/plain words = 5350 sentences = 263 flesch = 45 summary = Proposed here is a new but simple concept that would capitalize on the opportunity presented by the on-going natural experiment involving the collection of data from epidemiological surveillance screening and diagnostic testing for clinical treatment. These drug usage data would be collected for several major test groups those who test positive for active SARS-CoV-2 infection (using molecular methods) and those who test negative for current infection but also test positive for past infection (using serologic antibody tests). (1) As Covid-19 epidemiological surveillance screening and diagnostic testing proceeds, a national database would be continually populated with drug usage data collected from each case among three different combinations of sub-groups based upon whether they tested positive or negative for active SARS-CoV-2 infection or tested positive for past SARS-CoV-2 infection (see Table 1 ). cache = ./cache/cord-321267-ihd30qi0.txt txt = ./txt/cord-321267-ihd30qi0.txt === reduce.pl bib === id = cord-321358-plxz5mkg author = Zheng, Jun title = SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat date = 2020-03-15 pages = extension = .txt mime = text/plain words = 4759 sentences = 251 flesch = 53 summary = An ongoing outbreak of pneumonia caused by a novel coronavirus, currently designated as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was reported recently. In this review, we summarize the key events occurred during the early stage of SARS-CoV-2 outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients as well as the possible transmission pathways of the virus. CoVs have been identified in both avian hosts and various mammals, including bat, camels, dogs and masked palm civets, and are previously regarded as pathogens that only cause mild diseases in the immunocompetent people until the emergence of the coronavirus causing severe acute respiratory syndrome (SARS-CoV) in late of 2002 [3] [4] [5] [6] . cache = ./cache/cord-321358-plxz5mkg.txt txt = ./txt/cord-321358-plxz5mkg.txt === reduce.pl bib === id = cord-321549-r7bmtloy author = Jendrny, Paula title = Scent dog identification of samples from COVID-19 patients – a pilot study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3459 sentences = 184 flesch = 52 summary = METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. As dogs can be trained quickly, the aim of the present study was to test the concept of using dogs reliably and in real-time to discriminate between samples of SARS-CoV-2 infected patients and non-infected controls. The individuals were only tested for SARS-CoV-2 virus and therefore one cannot exclude that a former infection, especially with another human coronavirus like HCoV-OC43 resulted in false positive indications of the dogs and that cross detection occurred. Detection dogs were able to discriminate respiratory secretions of infected SARS-CoV-2 individuals from those of healthy controls with high rates of sensitivity and specificity. cache = ./cache/cord-321549-r7bmtloy.txt txt = ./txt/cord-321549-r7bmtloy.txt === reduce.pl bib === id = cord-321552-lsz1onrj author = Membrilla, Javier A. title = Headache as a Cardinal Symptom of Coronavirus Disease 2019: A Cross‐Sectional Study date = 2020-09-28 pages = extension = .txt mime = text/plain words = 4335 sentences = 256 flesch = 46 summary = OBJECTIVE: To describe the semiology of pain and its associated features in patients with coronavirus disease 2019 (COVID‐19) and headache presenting to the emergency department who do not require urgent services. 27 We hypothesized that COVID-19-related headache might be one of the most frequent symptoms of the infection and can have a more severe presentation in patients with migraine. We aimed to describe the semiology of pain and associated symptoms in patients with COVID-19-related headache in a clinical setting who visit the emergency department but do not require urgent services. Study Population and Eligibility.-Patients attending the emergency department of our hospital were included if they met all of the following inclusion criteria: (1) patients classified by the Manchester Triage System 29 as priority levels 5 (non-urgent) and 4 (standard); (2) fulfilled the criteria for a "probable COVID-19 case" or "confirmed COVID-19 case" according to the WHO guidance on global surveillance for COVID-19; 30 (3) and presented with headache alongside other COVID-19-related symptoms. cache = ./cache/cord-321552-lsz1onrj.txt txt = ./txt/cord-321552-lsz1onrj.txt === reduce.pl bib === id = cord-320632-369kax2m author = Song, Yang title = COVID-19 Treatment: Close to a Cure? – A Rapid Review of Pharmacotherapies for the Novel Coronavirus date = 2020-07-04 pages = extension = .txt mime = text/plain words = 5659 sentences = 335 flesch = 45 summary = The selection of medications in this review is based the 7 th edition of COVID-19 diagnosis and treatment guideline issued by the National Health Commission (NHC) of the People's Republic of China ( Table 2) and relevant clinical studies. In a phase 2 open-label COVID-19 trial, which enrolled 127 patients from 6 Hong Kong hospitals, Hung and his colleagues compared triple therapy (lopinavir/ritonavir 400/100 mg PO every 12 hours, ribavirin 400 mg PO every 12 hours, and interferon β-1b 8 million IU SQ on alternative days) with a control group of LPV/r [33] . During the 2013 SARS epidemic, observational studies and case reports described IVIG for the treatment of critically ill patients in combination with antiviral therapies. In a COVID-19 case series study, the combination of umifenovir, lopinavir/ritonavir and traditional Chinese medicine alleviated pneumonia symptoms in all four patients and decreased viral load to undetectable in two [68] . cache = ./cache/cord-320632-369kax2m.txt txt = ./txt/cord-320632-369kax2m.txt === reduce.pl bib === id = cord-320831-owfnttqr author = Klimek, Ludger title = Allergen immunotherapy in the current COVID-19 pandemic: A position paper of AeDA, ARIA, EAACI, DGAKI and GPA: Position paper of the German ARIA Group(A) in cooperation with the Austrian ARIA Group(B), the Swiss ARIA Group(C), German Society for Applied Allergology (AEDA)(D), German Society for Allergology and Clinical Immunology (DGAKI)(E), Society for Pediatric Allergology (GPA)(F) in cooperation with AG Clinical Immunology, Allergology and Environmental Medicine of the DGHNO-KHC(G) and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date = 2020-05-28 pages = extension = .txt mime = text/plain words = 3683 sentences = 195 flesch = 41 summary = The highest risk of transmission for medical staff is present when standard precautions are missing, when primary infection prevention and control measures for respiratory infections are not undertaken, and when infected, potentially asymptomatic patients who are not yet tested positive for COVID-19 are treated without protective measures. The staff, including doctors, medical assistants, nutritional scientists, nursing and administrative staff, and all other staff at the facility with patient contact, should be made aware of: a) the current epidemiological situation of COVID-19 in Germany/Austria/ Switzerland and worldwide; b) known risk factors for infection; c) clinical signs and symptoms of COVID-19; d) recommended measures to prevent and contain infections in their region or country, including those mentioned in this document; e) procedures for reporting and transferring examined patients and probable/confirmed cases taking into account the appropriate regional regulations and specifications [36, 40] . cache = ./cache/cord-320831-owfnttqr.txt txt = ./txt/cord-320831-owfnttqr.txt === reduce.pl bib === id = cord-321468-nkl2mls8 author = Yang, Mo title = Thrombopoietin levels increased in patients with severe acute respiratory syndrome date = 2008-03-07 pages = extension = .txt mime = text/plain words = 2433 sentences = 118 flesch = 53 summary = Using a ELISA method, we found an increase in thrombopoietin (TPO) levels in the plasma of convalesced SARS patients (290 ± 53 pg/ml) and active SARS patients (251 ± 23 pg/ml) comparing to that from normal control patients (228 ± 17 pg/ml). Severe Acute Respiratory Syndrome (SARS) is a recently emerged human disease caused by the infection of a novel coronavirus (SARS-CoV) [1] . In this study, TPO levels in plasmas from SARS patients, the effect of these plasmas on in vitro megakaryocytopoiesis, and whether SARS-CoV can directly infect hematopoietic stem cells and megakaryocytic cells are investigated. To study the correlation of platelet counts and the plasma TPO levels, linear regression analyses were carried out for the normal, convalesced SARS and active SARS patient groups respectively. The present study showed that there was an increase of TPO levels in the plasma of convalescence SARS patients comparing to those from normal control and active SARS patients. cache = ./cache/cord-321468-nkl2mls8.txt txt = ./txt/cord-321468-nkl2mls8.txt === reduce.pl bib === id = cord-321564-6950p8i9 author = Wang, Shiu‐Mei title = Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date = 2019-07-10 pages = extension = .txt mime = text/plain words = 2794 sentences = 148 flesch = 42 summary = BST2 is a component of innate immune response in the form of restricted enveloped virion release, and many viruses have evolved specific antagonists to counteract BST2 antiviral activity: HIV-1 Vpu, HIV-2 Env, simian immunodeficiency virus (SIV) Nef and Env, Ebola and Sendai virus GP, Kaposi's sarcoma-associated herpesvirus K5, and influenza virus neuraminidase are all capable of antagonizing BST2. 23 We also found that the SARS-CoV spike (S) protein is capable of downmodulating BST2, thus mitigating the BST2-mediated restriction of virus-like particle (VLP) release, and suggesting that SARS-CoV and other enveloped viruses are capable of evolving additional anti-BST2 factors. BST2, bone marrow stromal antigen 2; SARS-CoV, severe acute respiratory syndrome coronavirus SARS-CoV virion release is mitigated by SARS-CoV S, it is possible that a number of enveloped viruses have developed supplementary anti-BST2 factors over time-note that in addition to Vpu, HIV-1 Nef is capable of overcoming BST2 restrictions on virus release under certain conditions. cache = ./cache/cord-321564-6950p8i9.txt txt = ./txt/cord-321564-6950p8i9.txt === reduce.pl bib === id = cord-321624-z2mntwef author = Kowitdamrong, Ekasit title = Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date = 2020-10-09 pages = extension = .txt mime = text/plain words = 3382 sentences = 184 flesch = 57 summary = AIM: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19. The objective of this study was to investigate the response of IgA and IgG antibodies to SARS--CoV-2 in serial blood samples collected from a population of Thai patients with confirmed COVID-19, and the association of these responses with the severity of the illness. The second subgroup included 49 plasma samples collected from May 1 to May 31, 2020, from patients under investigation (PUI) for COVID-19 with RT-PCR results that were negative for SARS-CoV-2. In the present study, 30% of COVID-19 patients developed positive IgA antibodies very early, within 3 days after the onset of symptoms. In the present study, 20% of the patients with mild symptoms did not develop any IgG antibodies specific to COVID-19, even after 2 weeks after the onset of symptoms. cache = ./cache/cord-321624-z2mntwef.txt txt = ./txt/cord-321624-z2mntwef.txt === reduce.pl bib === id = cord-321603-lbbsnriv author = Rao, Mohan title = Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 2186 sentences = 172 flesch = 59 summary = The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. cache = ./cache/cord-321603-lbbsnriv.txt txt = ./txt/cord-321603-lbbsnriv.txt === reduce.pl bib === id = cord-321670-f2d4bykp author = Longardt, Ann Carolin title = Perinatale Aspekte der SARS-CoV-2 Infektion date = 2020-08-24 pages = extension = .txt mime = text/plain words = 2927 sentences = 409 flesch = 55 summary = In einer Studie aus den 50 Kliniken in Wuhan wurden 118 Frauen mit COVID-19 zwischen Dezember 2019 und März 2020 erfasst; 109 zeigten einen milden Verlauf und 9 (8 %) einen schweren Verlauf mit Hypoxämie, eine hiervon wurde beatmet. Abgesehen davon, dass das Virus selten im Blut detektiert wurde, stellt sich auch die Frage nach der Expres sion des SARS-CoV-2-Rezeptors ACE2 im Bereich der maternofetalen Grenzfläche beziehungsweise in der Plazenta. Gesichert ist der Infektionsweg durch eine SARS-CoV-2-Übertragung über die Muttermilch damit jedoch nicht. Anzunehmen ist aber auch die Weitergabe von SARSCoV2Antikörpern über die Muttermilch an das Kind, was den klinischen Verlauf einer kindlichen Infektion positiv beeinflussen könnte, ähnlich wie es bei der SARS-Epidemie 2002/2003 berichtet wurde [42] . Vertical Transmission of Coronavirus Disease 19 (COVID-19) from Infected Pregnant Mothers to Neonates: A Review An Analysis of 38 Pregnant Women with COVID19, Their Newborn Infants, and MaternalFetal Transmission of SARS CoV2: Maternal Coronavirus Infections and Pregnancy Outcomes cache = ./cache/cord-321670-f2d4bykp.txt txt = ./txt/cord-321670-f2d4bykp.txt === reduce.pl bib === id = cord-321580-3ru92tra author = Hadler, James L title = Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1134 sentences = 71 flesch = 51 summary = The initial country-level responses to SARS-CoV-2 have provided substantial evidence of their collective impact on the COVID-19 pandemic and, incidentally, on seasonal influenza epidemics. As a country, it has perhaps the largest influenza sentinel surveillance system in the world, including active testing for influenza, and it was the first country to implement highly successful NPIs against SARS-CoV-2, giving it the best opportunity to see a possible change in influenza before the expected seasonal decline. To know what might happen with influenza this coming fall and winter, we need to know what has happened prospectively in southern hemisphere countries, especially those that like the US have used fewer NPI's and used them with less rigor and, correspondingly, been less successful in controlling SARS-CoV-2 transmission. Nonpharmaceutical interventions used to control COVID-19 reduced seasonal influenza transmission in China cache = ./cache/cord-321580-3ru92tra.txt txt = ./txt/cord-321580-3ru92tra.txt === reduce.pl bib === id = cord-321568-okvt1fg3 author = Alberca, Ricardo Wesley title = Perspective: The Potential Effects of Naringenin in COVID-19 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4111 sentences = 225 flesch = 40 summary = Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Among many compounds, naringenin (NAR) a flavonoid present in citrus fruits has been investigated for antiviral and anti-inflammatory properties like reducing viral replication and cytokine production. In this perspective, we summarize NAR potential anti-inflammatory role in COVID-19 associated risk factors and SARS-CoV-2 infection. Naringenin (NAR) is an important natural flavonoid present in citrus fruits, like grapefruit (43.5 mg/100 mL) and oranges (2.13 mg/100 mL) (19), with a high analgesic, anti-oxidant, anti-inflammatory, anti-tumoral, and anti-viral effect (20-23) (Figure 1) . Further investigations and clinical trials are needed to help understand the role of NAR consumption in humans during a viral infection, especially in SARS-CoV-2 infection and COVID-19. cache = ./cache/cord-321568-okvt1fg3.txt txt = ./txt/cord-321568-okvt1fg3.txt === reduce.pl bib === id = cord-321784-nubu5fuz author = Salazar, E. title = Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3560 sentences = 224 flesch = 58 summary = Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. 22 We performed the present study to provide additional data on these initial clinical observations of patients' clinical course and subsequent improvement after receiving convalescent plasma therapy for COVID-19. Although our study has limitations, the data indicate that transfusion of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Our study was performed to evaluate the safety and potential benefit of transfusing convalescent plasma to patients with severe COVID-19 disease. Outcomes from this case series of 25 patients indicates that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. cache = ./cache/cord-321784-nubu5fuz.txt txt = ./txt/cord-321784-nubu5fuz.txt === reduce.pl bib === id = cord-321664-3qlfsei6 author = Somsen, G Aernout title = Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission date = 2020-05-27 pages = extension = .txt mime = text/plain words = 1244 sentences = 59 flesch = 55 summary = title: Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission Globally, health-care authorities are searching for effective measures to prevent community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, aerosols containing a small concentration of virus in poorly ventilated spaces, combined with low humidity and high temperature, 6 might result in an infectious dose over time. To better understand the spreading of respiratory droplets and possible preventive measures, we analysed droplet production due to coughs and speech by measuring the droplet size distribution, travel distance and velocity, and the airborne time in relation to the level of air ventilation. Although we only studied healthy volunteers and did not study patients with COVID-19 or virus-laden aerosol droplets directly, our data on droplet size distribution and persistence does have implications on requirements to use face masks to prevent virus transmission. The persistence of small respiratory droplets in such poorly ventilated spaces could contribute to the spread of SARS-CoV-2. cache = ./cache/cord-321664-3qlfsei6.txt txt = ./txt/cord-321664-3qlfsei6.txt === reduce.pl bib === id = cord-321797-2xhusfth author = Lee‐Baggley, Dayna title = Coping with the threat of severe acute respiratory syndrome: Role of threat appraisals and coping responses in health behaviors date = 2004-03-11 pages = extension = .txt mime = text/plain words = 6358 sentences = 278 flesch = 49 summary = Hierarchical linear regression indicated that the use of wishful thinking in response to the threat of SARS was related to both avoiding public places and avoiding people perceived to be possible carriers of the SARS virus, but was not associated with the use of more adaptive health behaviors, such as using disinfectants and hand washing. Perception of SARS threat was significantly related to reports of both coping (wishful thinking and support seeking) and health behaviors (avoidant behavior, avoiding people perceived to be at risk for SARS and taking precautions). In sum, multivariate analyses controlling for differences in perceived threat of SARS, state anxiety and other ways of coping indicated that both wishful thinking and empathic responding were significantly associated with specific SARS-related health behaviors. 4 Controlling for differences in perceived threat of SARS, state anxiety and other ways of coping, support seeking was not significantly related to the SARS-related health behaviors examined in the present study. cache = ./cache/cord-321797-2xhusfth.txt txt = ./txt/cord-321797-2xhusfth.txt === reduce.pl bib === id = cord-321598-ae241pmd author = de Vries, A.P.J. title = Immediate impact of COVID-19 on transplant activity in the Netherlands date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2280 sentences = 132 flesch = 49 summary = Worldwide, the delivery of transplant care is severely challenged by matters concerning but not limited to organ procurement, risk of SARS-CoV-2 transmission, screening strategies of donors and recipients, decisions to postpone or proceed with transplantation, the attributable risk of immunosuppression for COVID-19 and entrenched health care resources and capacity. In less than 60 days, despite increasingly stringent measures of the Dutch government to halt the spread of the infection, 28, 153 individuals have tested positive for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), 9,127 patients have been admitted to hospitals across the country (of which 2,508 in the Intensive Care Units (ICU) [4] ) and 3,134 have died, according to RIVM (National Institute for Public health and the Environment, April 15, 2020). To facilitate extra time needed for recipient test results to become available, allocation for liver, heart and lung transplantation is initiated before donor SARS-CoV-2 screening is known (Table 1A) . cache = ./cache/cord-321598-ae241pmd.txt txt = ./txt/cord-321598-ae241pmd.txt === reduce.pl bib === id = cord-321800-0h28pg3b author = Klingelhöfer, Doris title = Coronavirus: An insight into global research until outbreak of COVID-19 and its implications for the future date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6119 sentences = 337 flesch = 55 summary = RESULTS: The trend in publication and citation numbers shows the strong influence of the past pandemics SARS and MERS with an untypical decline afterward. The current extremely rapid global spread of SARS-CoV-2 has led to the highly dangerous outbreak of the pandemic CoVID-19 with daily increasing numbers of new infections and deaths around the world. Additionally, socio-economic, scientific and epidemiological parameters were related to the publication numbers to obtain an even more meaningful picture of the global landscape of CoV research. The resulting scientific interest and the possible in-si-VIEWPOINTS RESEARCH THEME 1: COVID-19 PANDEMIC tu investigation of the cases caused the publication figures to rise at the beginning of the SARS disease and to fall rapidly thereafter. Here, the USA and China are the highest-ranking countries, demonstrating their overall interest in CoV research and also focusing on the MERS pandemic, despite the relatively low case numbers. cache = ./cache/cord-321800-0h28pg3b.txt txt = ./txt/cord-321800-0h28pg3b.txt === reduce.pl bib === id = cord-321770-g5xcfhnh author = de Farias, Emmerson Carlos Franco title = MULTISYSTEM INFLAMMATORY SYNDROME IN A CHILD ASSOCIATED WITH CORONAVIRUS DISEASE 19 IN THE BRAZILIAN AMAZON: FATAL OUTCOME IN AN INFANT date = 2020-08-26 pages = extension = .txt mime = text/plain words = 2337 sentences = 117 flesch = 42 summary = CASE DESCRIPTION: A seven-month-old infant, with SARS-CoV-2 infection and a history of extreme preterm birth and very low weight at birth, with an initial course of mild respiratory symptoms and abrupt progression to vasoplegic shock, myocarditis and hyperinflammation syndrome, shown by high levels of troponin I, ferritin, CRP, D-dimer and hypoalbuminemia. The diagnosis of MIS-C should be considered among children and adolescents aged from zero to 19 years, with characteristics of typical or atypical Kawasaki disease or shock syndrome, according to the case definition proposed by the World Health Organization (WHO) 8 , described in Chart 1. In this study, we describe a case of MIS-C in an infant infected with SARS-CoV-2, after parental authorization, which had a fatal outcome despite the support received in pediatric intensive care. This case report emphasizes the fatal clinical course of an infant admitted with infection by SARS-CoV-2, associated with significant comorbidity, presenting with hyperinflammatory and multiple organ dysfunction syndromes. cache = ./cache/cord-321770-g5xcfhnh.txt txt = ./txt/cord-321770-g5xcfhnh.txt === reduce.pl bib === id = cord-321819-lqyo9px1 author = Chaw, Liling title = Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei date = 2020-11-17 pages = extension = .txt mime = text/plain words = 4170 sentences = 215 flesch = 47 summary = We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. Brunei's thorough contact tracing provides a rare opportunity to study the epidemiologic and transmission characteristics of SARS-CoV-2 in different community settings. Among 1,755 close contacts of the COVID-19 cluster among Tablighi members in Brunei, 52 local transmissions were detected, giving an overall nonprimary attack rate of 2.9% (95% CI 2.2%-3.8%). We could not calculate the attack rate for attendees of the local religious gathering because the 3 primary cases at the event had different symptom statuses and we could not ascertain how transmission occurred. In the household setting, symptomatic casepatients had 2.7 times the risk of transmitting SARS-CoV-2 to their close contacts, compared with asymptomatic and presymptomatic case-patients (crude risk ratio 2.66 [95% CI 1.12-6.34]; Table 3 ). cache = ./cache/cord-321819-lqyo9px1.txt txt = ./txt/cord-321819-lqyo9px1.txt === reduce.pl bib === id = cord-321691-46la29tm author = Hsueh, Po-Ren title = SARS Antibody Test for Serosurveillance date = 2004-09-17 pages = extension = .txt mime = text/plain words = 2800 sentences = 133 flesch = 44 summary = A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. Such surveillance may be key to tracking the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) because mild and asymptomatic cases of SARS-CoV infection that do not meet the World Health Organization's case definition (1) have been identified by immunoassays (2) (3) (4) , and SARS-CoV-like viruses have been isolated from wild mammals (5) . The diagnostic sensitivity of the peptide ELISA was 100% on a panel of 69 convalescent-phase serum samples from SARS patients provided as a reference panel by the Center for Disease Control, Department of Health, Taiwan. The peptide ELISA was evaluated for specificity on serum samples drawn from patients associated with typical and atypical respiratory pathogens other than SARS-CoV (National Taiwan University Hospital). cache = ./cache/cord-321691-46la29tm.txt txt = ./txt/cord-321691-46la29tm.txt === reduce.pl bib === id = cord-321867-7n88rl6p author = Jee, J. title = Oncologic Immunomodulatory Agents in Patients with Cancer and COVID-19 date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3944 sentences = 259 flesch = 49 summary = A recent retrospective study found a possible trend toward worse outcomes associated with corticosteroid use in cancer patients, although no analysis was performed to correct for possible selection bias in which sicker patients received those medications [11] . For all analyses we considered the number of patients who developed a primary composite endpoint of respiratory failure (use of nonrebreather, high-flow nasal oxygen, or mechanical ventilation) or death within 28 days of SARS-CoV-2 diagnosis. When patients were stratified by level of respiratory support, corticosteroid use was associated with worse outcomes in the pre-2L oxygen cohort (HR 2.3, 95% CI 1.1-4.9), a trend not observed in the post-2L oxygen (HR 0.9, 95% CI 0.4-1.9) and post-critical cohorts (HR 0.8, 95% CI 0.5-1.4), though these additional analyses were limited by All rights reserved. . https://doi.org/10.1101/2020.08.11.20145458 doi: medRxiv preprint from neutropenia 60 to 180 days prior to SARS-CoV-2 diagnosis did not have worse outcomes. cache = ./cache/cord-321867-7n88rl6p.txt txt = ./txt/cord-321867-7n88rl6p.txt === reduce.pl bib === id = cord-321742-cstub5zz author = Tovar, Isabel title = Rationale for the Use of Radiation-Activated Mesenchymal Stromal/Stem Cells in Acute Respiratory Distress Syndrome date = 2020-09-02 pages = extension = .txt mime = text/plain words = 6896 sentences = 292 flesch = 36 summary = We have previously shown that the combination of radiotherapy with human umbilical-cord-derived mesenchymal stromal/stem cells (MSCs) cell therapy significantly reduces the size of the xenotumors in mice, both in the directly irradiated tumor and in the distant nonirradiated tumor or its metastasis. Knowing the role of annexin A1 in the control of hypoxia and inflammation that is characteristic of acute respiratory-distress syndrome (ARDS), we designed a hypothetical therapeutic strategy, based on the transplantation of mesenchymal stromal/stem cells stimulated with radiation, to alleviate the symptoms of patients who, due to pneumonia caused by SARS-CoV-2, require to be admitted to an intensive care unit for patients with life-threatening conditions. Supposedly a vectorized signaling system, we now believe that the exosomes released from radiation-activated-MSCs cells can reach other organs different from the lungs, where they will be up-taken after intravenous injection and thus extend the anti-inflammatory and antimicrobiological effects of the treatment, to cover systemic problems such as the treatment of patients with septic shock in general and for COVID-19 at this particular time. cache = ./cache/cord-321742-cstub5zz.txt txt = ./txt/cord-321742-cstub5zz.txt === reduce.pl bib === id = cord-321673-v5o49ees author = Nieto-Torres, Jose L. title = Relevance of Viroporin Ion Channel Activity on Viral Replication and Pathogenesis date = 2015-07-03 pages = extension = .txt mime = text/plain words = 8398 sentences = 451 flesch = 38 summary = Modification of host-cell ionic content is a significant issue for viruses, as several viral proteins displaying ion channel activity, named viroporins, have been identified. Noticeably, these proteins oligomerize in cell membranes to form ion conductive pores, which generally display mild ion selectivity, indicating that viroporins do not show preference for particular ionic species. Influenza viruses lacking M2 ion conductivity, presented either a 15-fold reduction of viral titer in tissue culture [74] , or showed a standard production in cell culture but a restricted growth in the nasal turbinates of infected mice [75] . Several compounds inhibit viroporin ion conductivity in artificial lipid membranes, and some of them efficiently reduce viral growth when administered to infected cells. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells cache = ./cache/cord-321673-v5o49ees.txt txt = ./txt/cord-321673-v5o49ees.txt === reduce.pl bib === id = cord-321918-9jwma2y6 author = Xiu, Siyu title = Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities date = 2020-06-15 pages = extension = .txt mime = text/plain words = 10526 sentences = 621 flesch = 52 summary = The spike protein can be divided into two domains; S1 is responsible for angiotensin-converting enzyme II(ACE2) recognition, the recently identified host cell receptor, and S2 mediates membrane fusion (Figure 2 ). 98 99 On the basis of this approach, they identified two small molecules, TGG (12, Table 4 ) and luteolin (13) , that can bind avidly to the SARS-CoV S2 protein and inhibit viral entry of SARS-CoV into Vero E6 cells with IC 50 values of 4.5 and 10.6 μM, respectively. 113 A high-throughput screen (HTS) of a 1000-compound library that resulted in the identification of MDL28170 (17 , Table 4 ) by Bates et al., and in an antiviral activity assay, 17 specifically inhibited cathepsin L-mediated substrate cleavage and blocked SARS-CoV viral entry, with an IC 50 value of 2.5 nM and EC 50 value in the range of 100 nM. cache = ./cache/cord-321918-9jwma2y6.txt txt = ./txt/cord-321918-9jwma2y6.txt === reduce.pl bib === id = cord-321855-7b1c2xdh author = Alshami, Alanoud title = Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3380 sentences = 190 flesch = 56 summary = title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. cache = ./cache/cord-321855-7b1c2xdh.txt txt = ./txt/cord-321855-7b1c2xdh.txt === reduce.pl bib === id = cord-321714-yhruzu7f author = Ryu, Young Bae title = SARS-CoV 3CL(pro) inhibitory effects of quinone-methide triterpenes from Tripterygium regelii date = 2010-03-15 pages = extension = .txt mime = text/plain words = 1933 sentences = 114 flesch = 59 summary = Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). We then further characterized the inhibitory mechanism of the isolated quinone-methide triterpenes against SARS-CoV 3CL pro activity. Although all isolated quinone-methide triterpenes has previously been known compounds, this is the first time it has been shown to possess SARS-CoV 3CL pro inhibitory activity. cache = ./cache/cord-321714-yhruzu7f.txt txt = ./txt/cord-321714-yhruzu7f.txt === reduce.pl bib === id = cord-321858-c5m4dj9m author = Yoshizawa, Shin-ichiro title = Evaluation of an octahydroisochromene scaffold used as a novel SARS 3CL protease inhibitor date = 2020-02-15 pages = extension = .txt mime = text/plain words = 6519 sentences = 337 flesch = 56 summary = The inhibitory activities of the diastereoisomerically-pure inhibitors (3a–d) strongly suggest that a specific stereo-isomer of the octahydroisochromene scaffold, (1S, 3S) 3b, directs the P1 site imidazole, the warhead aldehyde, and substituent at the 1-position of the fused ring to their appropriate pockets in the protease. To access whether the octahydroisochromene derivatives containing substituents at the 1-position of the ring system function as a novel inhibitor scaffold, the inhibitory activity of compounds 16a-d toward SARS 3CL pro was preliminary evaluated by the IC 50 values obtained using the procedure described below. To determine the configuration of each diastereomer (13a and 13b), the major product obtained after the asymmetric dihydroxylation reaction using (DHQ) 2 Pyr as the chiral ligand (Table 2, entry 3) was isolated and purified using preparative thin layer chromatography (PTLC). cache = ./cache/cord-321858-c5m4dj9m.txt txt = ./txt/cord-321858-c5m4dj9m.txt === reduce.pl bib === id = cord-321854-cy8vyb6j author = Ripperger, Tyler J. title = Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3289 sentences = 193 flesch = 51 summary = Relative to mild COVID-19 cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against nucleocapsid (N) and the receptor binding domain (RBD) of spike protein. However, 6.5% of the expanded negative control 149 group displayed RBD reactivity that overlapped with PCR+ individuals (Figure 1B, blue shade) , 150 some of whom may have been early into disease and had not yet generated high levels of 151 antibodies. To quantify the sensitivity of the assay relative to time of diagnosis, we measured 152 antibody levels to RBD and plotted these values against time following SARS-CoV-2 PCR+ 153 confirmation. For 308 both memory and plasma cells, there appears to be a 'sweet spot' of antigen avidity that Taken together, we have reported a highly specific serological assay for SARS-CoV-2 323 exposure that is usable in very low seroprevalence communities, and that returns positive 324 results that are highly co-incident with virus neutralization. cache = ./cache/cord-321854-cy8vyb6j.txt txt = ./txt/cord-321854-cy8vyb6j.txt === reduce.pl bib === id = cord-321933-cq0fa3hs author = Koff, Alan G. title = Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy date = 2020-10-07 pages = extension = .txt mime = text/plain words = 1223 sentences = 77 flesch = 50 summary = title: Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy The incubation period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rarely >14 days. We report a patient with hypogammaglobulinemia who developed coronavirus disease 2019 (COVID-19) with a confirmed incubation period of at least 21 days. [2] [3] [4] 6, 7 In the vast majority of cases, the incubation period is far less than 14 days, which has helped to inform the Centers for Disease Control and Prevention (CDC) recommendations for a 14-day quarantine period after a known coronavirus disease 2019 (COVID-19) exposure. This case demonstrates an objectively confirmed asymptomatic SARS-CoV-2 infection with symptom onset 21 days after her positive test. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application The difference in the incubation period of 2019 novel coronavirus (SARS-CoV-2) infection between travelers to Hubei and nontravelers: the need for a longer quarantine period cache = ./cache/cord-321933-cq0fa3hs.txt txt = ./txt/cord-321933-cq0fa3hs.txt === reduce.pl bib === id = cord-322044-4eejzpmn author = Frediansyah, Andri title = Remdesivir and its antiviral activity against COVID-19: A systematic review date = 2020-08-07 pages = extension = .txt mime = text/plain words = 613 sentences = 55 flesch = 47 summary = title: Remdesivir and its antiviral activity against COVID-19: A systematic review BACKGROUND: To summarize the antiviral activities of remdesivir against SARS-CoV-2, the causative agent of COVID-19. Although remdesivir has been used as a compassionate drug for treating COVID-19 patients, it has only moderate efficacy. CONCLUSION: Although remdesivir has shown potent antiviral activities, more efficacy assessments are urgently warranted in clinical trials. The first randomized, double-blind, placebo-controlled, multicenter clinical trial was 175 reported on April 29, 2020 [48] . Prophylactic 341 and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of 342 MERS-CoV infection Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2 Compassionate use 355 of remdesivir for patients with severe Covid-19 The authors whose names are listed immediately below report the following details of affiliation or involvement in an organization or entity with a financial or non-financial interest in the subject matter or materials discussed in this manuscript. cache = ./cache/cord-322044-4eejzpmn.txt txt = ./txt/cord-322044-4eejzpmn.txt === reduce.pl bib === id = cord-322005-70snojec author = Yao, Pingping title = Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell date = 2020-06-19 pages = extension = .txt mime = text/plain words = 890 sentences = 71 flesch = 65 summary = title: Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell In a recent report, 149 mutations were found among 103 sequenced isolates of SARS-CoV-2 . To investigate whether our viruses show mutations different from other reported SARS-CoV-2, all the seven isolates were sequenced at the 3rd passage and the sequences were aligned with coding sequence (CDS) of SARS-CoV-2 Wuhan-Hu-1 (NC_045512). It is interesting to note that these seven patients infected with SARS-CoV-2 have high viral load in the early stage of clinical sign, which is consistent with previous reports (Kim et al. A The cytopathic effect was observed in Vero cells infected with the isolated viruses at 5 dpi. In conclusion, seven SARS-CoV-2 strains were isolated, sequenced and characterized in Vero cells, and a deletion mutation was identified after short passage in Vero cells. Viral load kinetics of SARS-CoV-2 infection in first two patients in Korea SARS-CoV-2 viral load in upper respiratory specimens of infected patients cache = ./cache/cord-322005-70snojec.txt txt = ./txt/cord-322005-70snojec.txt === reduce.pl bib === id = cord-322129-uyswj4ow author = Melin, Amanda D. title = Comparative ACE2 variation and primate COVID-19 risk date = 2020-10-27 pages = extension = .txt mime = text/plain words = 6310 sentences = 305 flesch = 47 summary = Infection studies of rhesus monkeys, long-tailed macaques, and vervets as biomedical models have made it clear that at least some nonhuman primate species are permissive to SARS-CoV-2 infection and develop symptoms in response to infection that resemble those of humans following the development of COVID-19, including similar age-related effects [11] [12] [13] [14] [15] [16] . We assessed the variation at amino acid residues identified as critical for ACE2 recognition by the SARS-CoV-2 RBD and undertook an analysis of positive selection and protein modeling to gauge the potential for adaptive differences and the likely effects of protein variation. In particular, the twelve sites in the ACE2 protein that are critical for binding of the SARS-CoV-2 virus are invariant across the Catarrhini, which includes great apes, gibbons, and monkeys of Africa and Asia (Fig. 1) . cache = ./cache/cord-322129-uyswj4ow.txt txt = ./txt/cord-322129-uyswj4ow.txt === reduce.pl bib === id = cord-321901-zpi7uis1 author = Roberts, Anjeanette title = Animal models and antibody assays for evaluating candidate SARS vaccines: Summary of a technical meeting 25–26 August 2005, London, UK date = 2006-11-30 pages = extension = .txt mime = text/plain words = 6600 sentences = 311 flesch = 40 summary = Scientists at the WHO Technical Meeting on Animal Models and Antibody Assays for Evaluating Candidate SARS Vaccines held on 25-26 August 2005 in South Mimms, UK, discussed many aspects of research pertaining to the use of animal models in vaccine development including available animal models, suitability of the various models, correlates of protection, critical components of potential vaccines, and the potential for disease enhancement in vaccinated animals following exposure to SARS-CoV. It may actually be worthwhile to enhance the virulence of a SARS-CoV isolate by serial passages in an animal model to produce a challenge virus stock for vaccine studies that would elicit more reproducible disease in the animals. Although none of the studies to date have shown enhanced respiratory disease following SARS-CoV challenge in previously immunized animals, further studies in this area are warranted in view of some of the available in vitro data. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice cache = ./cache/cord-321901-zpi7uis1.txt txt = ./txt/cord-321901-zpi7uis1.txt === reduce.pl bib === id = cord-322204-kc7dy2za author = Khalil, Asma title = SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date = 2020-08-08 pages = extension = .txt mime = text/plain words = 448 sentences = 50 flesch = 60 summary = title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of cache = ./cache/cord-322204-kc7dy2za.txt txt = ./txt/cord-322204-kc7dy2za.txt === reduce.pl bib === id = cord-321938-pda4a5n7 author = Weisshoff, Hardy title = Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5076 sentences = 266 flesch = 57 summary = We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). In the Spike protein of SARS-CoV-2, several sequences which are highly susceptible to interaction with DNA (multiple amino acids with positive charged side chains) were identified, in particular at the angiotensin I-converting enzyme 2 (ACE2)-receptor binding domain (RBD): YRLFRK (SARS-CoV-2 specific from protein data bank (PDB) data base entry PBD ID: 6VXX, source: [23] ), as well as NRKRISN (PBD ID: 6VXX) and KIKRMK (PDB ID: 5X5B source: [24] ). This enabled us to exploit NMR-spectroscopy to investigate whether the selected peptide-sequences from SARS-CoV-2 proteins bind to this clinically advanced aptamer (BC 007), forcing it into its well described quadruple structure just by molecular interaction. cache = ./cache/cord-321938-pda4a5n7.txt txt = ./txt/cord-321938-pda4a5n7.txt === reduce.pl bib === id = cord-322148-sfr9twfa author = Verbeek, P. Richard title = Loss of Paramedic Availability in an Urban Emergency Medical Services System during a Severe Acute Respiratory Syndrome Outbreak date = 2008-06-28 pages = extension = .txt mime = text/plain words = 2481 sentences = 142 flesch = 55 summary = Objectives: To describe the loss of paramedic availability to Toronto Emergency Medical Services during a biphasic (SARS‐1 and SARS‐2) outbreak of severe acute respiratory syndrome (SARS). [3] [4] [5] Ontario 8, 9 In response to the SARS outbreak, a program of contact tracing, quarantine, and medical surveillance of paramedics was implemented by Toronto Emergency Medical Services (EMS) and base hospital of Sunnybrook and Women's College Health Sciences Centre. Paramedics were advised to wear gloves, mask, and gown for patients with ''an acute Home quarantine (HQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital or to a patient with suspect/probable SARS under home observation for ten days from the last known exposure date. Work quarantine (WQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital during the SARS-2 outbreak on duty while wearing PPE at all times. cache = ./cache/cord-322148-sfr9twfa.txt txt = ./txt/cord-322148-sfr9twfa.txt === reduce.pl bib === id = cord-322141-4a81mapc author = Rizzo, Emanuele title = A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government date = 2020-09-09 pages = extension = .txt mime = text/plain words = 722 sentences = 41 flesch = 44 summary = title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government For these reasons, the territorial medicine and the operators of the Apulian prevention services have decided to propose to the regional government the possibility of adopting a specific exemption code for COVID-19, taking on the economic burden deriving from treatments and diagnostic investigations once the acute phase of the disease has been overcome. Moreover, a similar procedure would also have the comfort of numbers: the sum of confirmed cases remains limited to date (as reported by the latest epidemiological bulletin -01/08/2020 h :14:00 CEST -, there are 4631 total cases of COVID-19 syndrome in Apulia, including 112 currently positive, 3967 healed subjects and 552 deaths [6] ), which makes the operation sustainable and not expensive for the regional finances. cache = ./cache/cord-322141-4a81mapc.txt txt = ./txt/cord-322141-4a81mapc.txt === reduce.pl bib === id = cord-322087-gj5mfzxz author = de Sanctis, Vincenzo title = Coronavirus Disease 2019 (COVID-19) in adolescents: An update on current clinical and diagnostic characteristics date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4581 sentences = 244 flesch = 48 summary = This paper summarises the current findings (April 3,2020) from a systematic literature review on the current knowledge of COVID-19 in adolescents (10-19 years according to the WHO definition) and reports the preliminary epidemiological data stated by the Italian National Institute of Health. SARS-CoV-2 RNA was also detected in stool specimens but according to WHO-China report, fecal-oral transmission did not appear to be a significant factor in the spread of infection (Report of the WHO-China Joint Mission on Coronavirus Disease 2019,COVID-2019. Detailed epidemiological information based on a larger sample of COVID-19 patients is needed to determine the infectious period of SARS-CoV-2, as well as whether transmission can occur from asymptomatic individuals during the incubation period ("pre-symptomatic" period). In a small number of case reports and studies, a familial cluster of infection associated with SARS-CoV-2 has been reported, indicating possible personto-person transmission during the incubation period (18, 19) . cache = ./cache/cord-322087-gj5mfzxz.txt txt = ./txt/cord-322087-gj5mfzxz.txt === reduce.pl bib === id = cord-322388-c2nymio9 author = Manopo, Ivanus title = Evaluation of a safe and sensitive Spike protein-based immunofluorescence assay for the detection of antibody responses to SARS-CoV date = 2005-01-31 pages = extension = .txt mime = text/plain words = 3546 sentences = 185 flesch = 52 summary = To study the diagnostic potential of our Spike protein-based immunoassay based on protein C expressed by recombinant baculovirus in Sf-9 cell, a panel of sera containing 21 SARS-positive samples collected 7-76 days after the onset of SARS symptom, 42 non-SARS serum samples, and 100 normal serum samples were subjected to our Spike protein-based IFA test. The immunoblot showed a 32-kDa band, indicating that protein C expressed in a baculovirus system is antigenic for antibody detection of SARS-CoV infection (represented by Fig. 1a) . Fig. 2 shows representative IFA results in the detection of positive serum samples using our Spike protein-based IFA, compared to the conventional IFA performed by SGH and the commercial SARS IFA kit (EUROIMMUN). In this study, we are the first to show that the immunogenic protein C-based IFA is a sensitive and specific method for detecting SARS-CoV infection. cache = ./cache/cord-322388-c2nymio9.txt txt = ./txt/cord-322388-c2nymio9.txt === reduce.pl bib === id = cord-322184-kgv9f58a author = Sohn, Yujin title = Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3476 sentences = 182 flesch = 55 summary = Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In this study, we attempted to confirm the presence of viable virus by performing RT-PCR assay and culture using salivary and nasopharyngeal swabs of asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease and admitted to a CTC at least two weeks previously. Therefore, based on the evidence that the virus is rarely detected in respiratory specimens after 10 days following the onset of symptoms, especially in mild or asymptomatic cases of SARS-CoV-2 infection, even if viral shedding is sustained in the later phase of COVID-19, it can be expected that the transmission risk of the virus is low. cache = ./cache/cord-322184-kgv9f58a.txt txt = ./txt/cord-322184-kgv9f58a.txt === reduce.pl bib === id = cord-322102-4fi0y96f author = Zimmermann, Matthias title = Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic date = 2020-04-04 pages = extension = .txt mime = text/plain words = 4690 sentences = 252 flesch = 47 summary = During the SARS-CoV-2 pandemic, the specialty must organize patient treatment in such a way that infection transmission is reduced to a minimum, while all relevant treatment options are at hand to provide adequate patient care. The search items used were "coronavirus disease 19, COVID-19, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, transmission, pandemic, oral surgical procedures, oral and maxillofacial surgery, dental, personal protective equipment, infection prevention and control." The last search was run on 29 March 2020. Healthcare workers who have been infected with SARS-CoV-2 and have recovered from COVID-19 should continue to follow infection control precautions, including use of the recommended personal protective equipment. Depending on the number of infected patients, there might come a time of risk of a scarcity of medical staff, ventilators, negative pressure rooms, and personal protective equipment. cache = ./cache/cord-322102-4fi0y96f.txt txt = ./txt/cord-322102-4fi0y96f.txt === reduce.pl bib === id = cord-322329-zqjiiy4l author = Liu, Chunyu title = Establishment of a reference panel for the detection of anti-SARS-CoV antibodies date = 2007-06-30 pages = extension = .txt mime = text/plain words = 4227 sentences = 200 flesch = 56 summary = In this study, we have expressed and purified severe acute respiratory syndrome (SARS) structural proteins and their fragments and developed indirect enzyme-linked immunosorbent assays (ELISAs) that detect antibodies against the SARS N, N1, N2, S1, SC, S2, and M proteins as well as the human coronavirus OC43 and 229E N proteins. In this study, SARS N and S proteins and their fragments were expressed and purified, and samples from convalescent SARS patients and blood donors were screened with enzyme-linked immunosorbent assays (ELISAs) that were developed with these proteins. IgG and IgM immunoglobulin were detected in the 58 SARS convalescent plasma specimens using an indirect ELISA developed with entire virus antigens. In this study, the indirect ELISAs were developed with different fragments of SARS structure proteins and used to detect antibodies in 58 SARS plasma specimens donated by convalescent patients 3 months after onset of SARS. cache = ./cache/cord-322329-zqjiiy4l.txt txt = ./txt/cord-322329-zqjiiy4l.txt === reduce.pl bib === id = cord-322212-8xrehbd1 author = Wang, Hanyin title = Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1467 sentences = 112 flesch = 51 summary = title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock We report the case of an 88-year-old man with coronavirus disease 2019 (COVID-19) who presented with ARDS and septic shock. 1 An estimated 5.0% of patients with coronavirus disease 2019 (COVID-19) required ICU admission, 2.3% underwent mechanical ventilation, and 1.1% had septic shock. 2 Angiotensin II (Ang-2) is a synthetic vasopressor that received US Food and Drug Administration approval in 2017 for treatment of refractory vasodilatory shock. We report our experience with Ang-2 for septic shock in a critically ill patient with COVID-19. He became hypotensive and required ABBREVIATIONS: ACE = angiotensin-converting enzyme; ACE2 = angiotensin-converting enzyme 2; Ang-2 = angiotensin II; COVID-19 = coronavirus disease 2019; SARS-CoV = severe acute respiratory syndrome-related coronavirus; SARS-CoV-2 = 2019 novel coronavirus On ICU day 2, the SARS-CoV-2 polymerase chain reaction result was positive. cache = ./cache/cord-322212-8xrehbd1.txt txt = ./txt/cord-322212-8xrehbd1.txt === reduce.pl bib === id = cord-322051-89wgv100 author = Tanasa, Ingrid Andrada title = Anosmia and ageusia associated with coronavirus infection (COVID-19) - what is known? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 2260 sentences = 132 flesch = 44 summary = This study summarizes the existing data regarding the association of anosmia and ageusia with the SARS-CoV-2 infection. In a retrospective observational study, Klopfenstein et al (20) reported that 54 patients (47%) with confirmed SARS-CoV-2 infection developed anosmia, 4.4 (±1.9) days after infection onset, and that was the third symptom to manifest in 38% (22/52) of the cases. Some authors reported three mechanisms for anosmia in COVID-19 patients: i) local infection of support cells and vascular pericytes in the nose and olfactory bulb that may affect the function of bipolar neurons or mitral cells; ii) damage to support cells in the sensory epithelium that may indirectly influence the signaling pathway from sensory neurons to the brain; and iii) damage to sustentacular cells and Bowman's gland cells that could lead to diffuse morphological damage to the olfactory sensory epithelium and altering of smell perception (28, 29) . Further research is needed to demonstrate the association between anosmia and ageusia with SARS-CoV-2 infection, the clinical manifestations determined by variants of ACE2 receptor, and recovery rates of olfactory and gustative dysfunction, and specific treatment protocols of these manifestations. cache = ./cache/cord-322051-89wgv100.txt txt = ./txt/cord-322051-89wgv100.txt === reduce.pl bib === id = cord-322503-fynprt6f author = Thakur, Aarzoo title = Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3527 sentences = 210 flesch = 48 summary = Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. To address this possibility, we utilized physiologically-based pharmacokinetic (PBPK) modeling to simulate the unbound lung concentration of lopinavir achieved by 400/100 mg twice daily dose of lopinavir/ritonavir in both Caucasians and Chinese populations. 14, 15 Therefore, we derived unbound EC 50 (EC 50,unbound ) values against SARS-CoV-2 from various literature reports and compared it against the predicted C u,lung values to determine if clinically used doses of 400/100 mg twice a day would reach efficacious lung concentrations in Caucasian and Chinese populations. The impact of protein binding on PK/PD assessments were then assessed by comparing the predicted total and unbound lung concentrations of 400/100 mg twice daily lopinavir/ritonavir with EC 50 and EC 50,unbound values of lopinavir against SARS-CoV-2 respectively. cache = ./cache/cord-322503-fynprt6f.txt txt = ./txt/cord-322503-fynprt6f.txt === reduce.pl bib === id = cord-322417-9e95m4kz author = Segovia-Juarez, Jose title = High altitude reduces infection rate of COVID-19 but not case-fatality rate date = 2020-07-15 pages = extension = .txt mime = text/plain words = 1256 sentences = 88 flesch = 59 summary = authors: Segovia-Juarez, Jose; Castagnetto, Jesús M.; Gonzales, Gustavo F. title: High altitude reduces infection rate of COVID-19 but not case-fatality rate It is suggested that life at high altitude may reduce COVID infections and case-fatality rates (cases/deaths). A recent paper with data as of April 7th from the Tibet, Bolivia and Ecuador suggests that high-altitude (HA) may provide protection from pathogenesis of SAR-CoV-2 infection (Arias-Reyes et al, 2020). The current study has been designed to determine COVID-19 cases, deaths by COVID-19 and case-fatality rates in Peru in an altitude range from 3 to 4,342 meters above sea level. The sex ratio (male/female) for positive cases of COVID-19 is maintained at any altitude of residence ( Figure 1D ). Another important finding from our study is that the cumulative case-fatality rate (cumulative deaths/cumulative positive cases) by COVID-19 does not appear to change with altitude of residence ( Figure 3 ). cache = ./cache/cord-322417-9e95m4kz.txt txt = ./txt/cord-322417-9e95m4kz.txt === reduce.pl bib === id = cord-322473-fmob6k0q author = Charpiat, Bruno title = Proton Pump Inhibitors are Risk Factors for Viral Infections: Even for COVID-19? date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1573 sentences = 76 flesch = 42 summary = During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more attention should be paid to the balance of risks and benefits associated with proton pump inhibitors for the following reasons. Studies have documented that proton pump inhibitors are a risk factor for rotavirus, influenza virus, norovirus, and Middle East respiratory syndrome coronavirus infections, and are associated with an increased risk of acute gastroenteritis during periods of highest circulation of enteric viruses. Given the magnitude of the SARS-CoV-2/COVID-19 pandemic, associated with the widespread misuse of PPIs, this suggests that we cannot/should not rule out the hypothesis that patients treated with PPIs may be more at risk of being infected by COVID-19. They, therefore, hypothesized that PPI treatment may also be a potential risk factor for the development of secondary infections and of acute respiratory distress syndrome in hospitalized patients with COVID-19 [12] . cache = ./cache/cord-322473-fmob6k0q.txt txt = ./txt/cord-322473-fmob6k0q.txt === reduce.pl bib === id = cord-322007-xy66t0ls author = Humbert, S title = COVID-19 as a cause of immune thrombocytopenia date = 2020-05-20 pages = extension = .txt mime = text/plain words = 946 sentences = 71 flesch = 49 summary = ITP has been described during the course of several viral infections: HIV, EBV, CMV, HCV but only once during severe acute respiratory distress coronavirus 2 (SARS-CoV-2) [2] . As immune thrombocytopenia was the most relevant diagnosis and due to severe bleeding, we started prednisone (1 mg/kg/day) and one course of intravenous immunoglobulins 1 g/kg. We describe here the second case of SARS-CoV-2-induced ITP. COVID-19 is caused by SARS-CoV-2, responsible for severe pneumonia in less than 20% of cases. COVID-19 thrombocytopenia could be secondary to direct platelet-virus interaction via pathogen recognition receptors (PRR). In our case, thrombocytopenia is lower than what is usually observed during COVID-19 and may be secondary to an immune-related mechanism. The suddenness and severity of thrombocytopenia could be explained by the patient's advanced age as coronavirus induced higher antibodies production in older people [10] . Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 cache = ./cache/cord-322007-xy66t0ls.txt txt = ./txt/cord-322007-xy66t0ls.txt === reduce.pl bib === id = cord-322345-rq5gh710 author = Zheng, Fang title = A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 3617 sentences = 205 flesch = 54 summary = We aimed to determine the anti-SARS-CoV-2 effects of Novaferon in vitro, and conducted a randomized, open-label, parallel group study to explore the antiviral effects of Novaferon for COVID-19. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to the SARS-CoV-2 clearance in COVID-19 patients Results Novaferon inhibited the viral replication in infected cells (EC50=1.02 ng/ml), and protected healthy cells from SARS-CoV-2 infection (EC50=0.1 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher SARS-CoV-2 clearance rates on day 6 than the Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). We first determined whether Novaferon was able to inhibit SARS-CoV-2 at cellular level, and then conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in patients with COVID-19 by observing the SARS-CoV-2 clearance rates at different times during the treatment period. cache = ./cache/cord-322345-rq5gh710.txt txt = ./txt/cord-322345-rq5gh710.txt === reduce.pl bib === id = cord-322451-cwpz4akv author = Hsin, Dena Hsin-Chen title = Heroes of SARS: professional roles and ethics of health care workers date = 2004-07-27 pages = extension = .txt mime = text/plain words = 3598 sentences = 200 flesch = 66 summary = To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. In a number of countries in order to encourage HCW, the government and the public started to give the title of 'hero' to nurses and doctors who are working in the frontline of SARS outbreak. While the ethical ideal of self-less sacrifice of life for curing disease is promoted in the public image and media, discussions with HCW in several countries suggests that being a hero is not what modern medical practice is for some HCWs. Most HCWs in Taiwan are working in the commercial hospital, where the hirer pushes them to focus their effort of work on business competition rather than the basic role of helpers to human's health. Nurses' professional care obligation and their attitudes towards SARS infection control measures in Taiwan during and after the 2003 epidemic cache = ./cache/cord-322451-cwpz4akv.txt txt = ./txt/cord-322451-cwpz4akv.txt === reduce.pl bib === id = cord-322446-ddv86eoy author = Sharma, Kulbhushan title = SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date = 2011-05-27 pages = extension = .txt mime = text/plain words = 8437 sentences = 512 flesch = 56 summary = We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. Analysis of 9b-YFP localization showed that in addition to the extranuclear region, some amount of 9b was also present within the nucleus similar to the SARS-CoV infected cells (Fig. S1 , panel (i), (ii) and (iii)). Panel (ii) shows that even in in-vitro transport assay, SARS-CoV 9b protein localizes in both cytoplasm as well as nucleus. As shown in panel (v), the SARS-CoV 9b protein was able to enter the nucleus even in the presence of WGA showing that its entry is independent of active transport pathway. The SARS-CoV 9b protein triggers caspase 3 mediated apoptosis when retained in the nucleus of mammalian cells While performing pulse-chase assays, we found that a significant number of Vero E6 cells, in which nuclear export of 9b has been inhibited (either by treating with LMB or using NES deficient 9b), were showing caspase 3 dependent apoptosis. cache = ./cache/cord-322446-ddv86eoy.txt txt = ./txt/cord-322446-ddv86eoy.txt === reduce.pl bib === id = cord-322009-0cwljo0c author = Ma, Ling title = Coinfection of SARS-CoV-2 and Other Respiratory Pathogens date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3793 sentences = 170 flesch = 42 summary = Although the number of confirmed global cases of COVID-19 now exceeds 16 million, as of July 29, and several retrospective observational studies have noted that coinfection with other respiratory pathogens is relatively common, [1] [2] [3] [4] the clinical features of coinfection and its impact on patient outcomes, is yet to be clarified. All these patients were tested for SARS-CoV-2, respiratory syncytial virus, influenza A virus, influenza B virus, adenovirus, Chlamydia pneumoniae, and Mycoplasma pneumoniae, using sputum or nasopharyngeal swab specimens collected in the interval between the onset of symptoms, and up to seven days after their hospital admission. Routine laboratory tests, including tests for SARS-CoV-2 and other common respiratory viral and atypical bacterial pathogens, routine blood investigations, coagulation studies, organ function tests and inflammatory biomarkers, such as c-reactive protein (CRP) and procalcitonin (PCT), were taken at the time of patient presentation, while the serum interleukin (IL)-2, IL-4, IL-6, IL-10, TNF-α and IFN-γ levels were obtained on the 2nd day of admission. cache = ./cache/cord-322009-0cwljo0c.txt txt = ./txt/cord-322009-0cwljo0c.txt === reduce.pl bib === id = cord-322456-5at1euqm author = Rokohl, Alexander C. title = Die Rolle der Augenheilkunde in der COVID-19-Pandemie date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1837 sentences = 210 flesch = 47 summary = Im Dezember 2019 wurde Dr. Li Wenliang, ein Augenarzt aus der Volksrepublik China, in seinem Krankenhaus auf 7 Patienten, die alle unter einem schweren akuten Atemnotsyndrom litten und vorher einen Großmarkt in Wuhan besuchten, aufmerksam. Das COVID-19 auslösende Severe-Acute-Respiratory-Syndrome-related Coronavirus-2 (SARS-CoV-2) wurde durch die Coronavirus-Studiengruppe des Internationalen Komitees zur Taxonomie von Viren (International Committee on Taxonomy of Viruses) aufgrund der sehr engen Verwandtschaft zum Sars-Virus (Sars-CoV), an dem 2002/2003 Hunderte Menschen gestorben waren, benannt. Auch Dr. Li Wenliang, der Augenarzt, der die COVID-19 als einer der Ersten entdeckte und später auch an der Krankheit verstarb, könnte von einem asymptomatischen Patienten infiziert worden sein [23] . Zudem konnte in mehreren Studien mit hospitalisierten COVID-19-Patienten SARS-CoV-2-RNA in der Tränenflüssigkeit nachgewiesen werden [2, 28, 30, 32] . Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV-2. cache = ./cache/cord-322456-5at1euqm.txt txt = ./txt/cord-322456-5at1euqm.txt === reduce.pl bib === id = cord-322596-vfmzk2el author = Ming, Yi title = Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications date = 2020-07-11 pages = extension = .txt mime = text/plain words = 3595 sentences = 193 flesch = 43 summary = Current clinical reports indicate that SARS-CoV-2 is associated with significant morbidity of cardiovascular diseases and complications, such as hypertension (HTN), myocarditis, acute myocardial infarction, and increased heart failure [5, 6] . Based on these theoretical assumptions, it can be concluded that the S protein/host furin/ACE2 signal axis exists in the pathological process of SARS-Cov-S2 infection and mediates the occurrence of adverse cardiovascular prognosis events. Furthermore, a unique furin-like cleavage site exists in the S protein of SARS-Cov-S2 [16] ; thus, the theoretical advantage inferred from this cleavage site in disease infection models can be deduced to prevent and combat COVID-19 caused by SARS-CoV-2. However, in the process of infection, the S protein plays a direct damaging role by recognizing and binding to the ACE2 receptor and invading the host cell [10] . Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein cache = ./cache/cord-322596-vfmzk2el.txt txt = ./txt/cord-322596-vfmzk2el.txt === reduce.pl bib === id = cord-322348-8opy5z9h author = Morelli, Mara title = Parents and Children During the COVID-19 Lockdown: The Influence of Parenting Distress and Parenting Self-Efficacy on Children’s Emotional Well-Being date = 2020-10-06 pages = extension = .txt mime = text/plain words = 7098 sentences = 309 flesch = 46 summary = Within the Social Cognitive Theory framework, a path model in which parenting self-efficacy and parental regulatory emotional self-efficacy mediated the relationship between parents' psychological distress and both children's emotional regulation, and children's lability/negativity, was investigated. (2020) in Italy showed that it was the parenting stress related to the health emergency, the pandemic, and the lockdown that increased children's psychological, emotional, and behavioral problems. For this reason, this study focused on identifying which parental psychological variables can mediate the relationship between parents' psychological distress during the pandemic and the lockdown and their children's emotional regulation, in order to understand which possible intervention should be implemented to ameliorate families' well-being. A SEM was employed to test the hypothesized mediation model in which parenting self-efficacy and parents' regulatory emotional self-efficacy (related to the COVID-19 lockdown) mediated the relationship between parents' psychological distress and both children's emotional regulation and children's lability/negativity. cache = ./cache/cord-322348-8opy5z9h.txt txt = ./txt/cord-322348-8opy5z9h.txt === reduce.pl bib === id = cord-322311-cg5xwx5a author = Broder, Kari title = Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges date = 2020-07-23 pages = extension = .txt mime = text/plain words = 773 sentences = 51 flesch = 60 summary = title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges Our institution utilizes the Roche Cobas 6800 SARS-CoV-2 assay, the Cepheid GeneXpert Xpress SARS-CoV-2 assay, and a laboratory-developed test (LDT) based on a modified CDC protocol, but there is no gold standard for the diagnostic accuracy of these assays. We collected 35 positive (positivity determined per assay instructions) nasopharyngeal samples with an E target C T value of Ն30 on the Roche Cobas 6800 assay; those samples then underwent secondary testing on the Cepheid GeneXpert assay within 3 days of initial testing. One sample tested positive on the Cobas 6800 assay (C T ϭ 37.9) and negative by the GeneXpert assay and was confirmed to be negative on the LDT. Overall, the Cepheid GeneXpert Xpress SARS-CoV-2 assay and the Roche Cobas 6800 SARS-CoV-2 assay showed a high level of agreement among patients with high C T values. cache = ./cache/cord-322311-cg5xwx5a.txt txt = ./txt/cord-322311-cg5xwx5a.txt === reduce.pl bib === id = cord-322562-3gvsn9vf author = Hatada, Ryo title = Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) date = 2020-06-15 pages = extension = .txt mime = text/plain words = 4813 sentences = 295 flesch = 55 summary = Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). As illustrated in a recent book of in silico drug design, 8 the fragment molecular orbital (FMO) method 9−12 provides an efficient tool for performing ab initio quantum-chemical calculations for biomolecular systems and accurately analyzing their intermolecular interactions in terms of the interfragment interaction energies (IFIEs). Table 1 compiles the results of IFIE and decomposed contributions (PIEDA) interacting with Fragment 1 of the ligand, where the listing threshold is set as 2.0 kcal/mol The distance between the main chain >CO of Thr190 and the N−H part of Fragment 1 is as close as 1.99 Å as illustrated in Figure 6 , suggesting that they are forming a typical hydrogen bond. cache = ./cache/cord-322562-3gvsn9vf.txt txt = ./txt/cord-322562-3gvsn9vf.txt === reduce.pl bib === id = cord-322385-sc2vxxnn author = Ebinger, J. title = SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3672 sentences = 205 flesch = 38 summary = Main Outcomes: Using Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection. Recognizing the range of factors that might influence antibody status in a given individual, we focused our study on not only estimating seroprevalence but also on identifying factors associated with seropositivity and relative antibody levels within the following three categories: (1) pre-existing demographic and clinical characteristics; (2) potential Covid-19 illness related exposures; and, (3) Covid-19 illness related response variables (i.e. different types of self-reported symptoms). In adjusted analyses, we compared differences between serology status (i.e. antibody positive versus negative) in each variable of interest, grouped into one of three categories: (1) preexisting demographic and clinical characteristics (e.g. age, gender, ethnicity, race, and selfreported medical comorbidities); (2) Covid-19 related exposures (e.g. self-reported medical diagnosis of Covid-19 illness, household member with Covid-19 illness, number of people living in the home including children, type of home dwelling, etc); and, (3) Covid-19 related response variables (e.g. self-reported fever, chills, dry cough, anosmia, nausea, myalgias, etc.). cache = ./cache/cord-322385-sc2vxxnn.txt txt = ./txt/cord-322385-sc2vxxnn.txt === reduce.pl bib === id = cord-322789-9elfpx0e author = Abbaspour Kasgari, Hamideh title = Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2711 sentences = 155 flesch = 49 summary = title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial 29 We therefore conducted a randomized controlled trial in adult patients hospitalized with COVID-19 in Ghaem Shahr Razi Hospital to evaluate the efficacy and safety of sofosbuvir and daclatasvir in combination with ribavirin compared with standard care. This study was a single-centre, randomized clinical trial to evaluate the effectiveness of sofosbuvir/daclatasvir with ribavirin against controls who received standard of care for COVID-19 at the time of the study. This randomized trial found that the combination of sofosbuvir/ daclatasvir/ribavirin compared with standard care showed limited clinical improvement in moderate COVID-19 patients. To our knowledge, this is the first clinical trial of sofosbuvir/ daclatasvir/ribavirin in COVID-19 patients; however, there are limitations to our study. cache = ./cache/cord-322789-9elfpx0e.txt txt = ./txt/cord-322789-9elfpx0e.txt === reduce.pl bib === id = cord-322672-gjph61cq author = Ashok, Vishnu title = Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1816 sentences = 123 flesch = 52 summary = title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis A few cases of concurrent myocarditis have been reported, but the extent of cardiac complications with the SARS-CoV-2 strain of coronavirus is still largely unknown. Myocarditis and non-specific cardiac arrhythmias have been reported in a few cases of COVID-19, but this is the first reported case of a high-grade atrioventricular conduction block with SARS-CoV-2 infection. 7 In the European Study of the Epidemiology and Treatment of Inflammatory Heart Disease, 18% of the 3055 patients in the study had high-grade arrhythmias including complete heart block. Since the onset of the current pandemic, cases of myocarditis in patients with COVID-19 have been reported. In a case series of 150 patients with COVID-19 conducted in Wuhan City, China, 7% of the reported 68 deaths (5 deaths) were attributed to myocarditis with circulatory failure; however, their pre-morbid cardiac status was unclear. cache = ./cache/cord-322672-gjph61cq.txt txt = ./txt/cord-322672-gjph61cq.txt === reduce.pl bib === id = cord-322603-8ajckhzc author = Wongsawat, Jurai title = Risk of novel coronavirus 2019 transmission from children to caregivers: A case series date = 2020-06-22 pages = extension = .txt mime = text/plain words = 923 sentences = 86 flesch = 62 summary = World Health Organization (WHO) characterised coronavirus disease 2019 (COVID-19) as a pandemic on 11 March 2020. [4] [5] [6] The potential risk of transmission from infected children to adults is of concern due to prolonged detection of the SARS-CoV-2 RNA in respiratory specimens and faeces. Children were allowed to be discharged when their swabs turned negative for SARS-CoV-2 RNA on 2 consecutive days; this happened on days 15, 23 and 27 of illness for cases 1, 2 and 3, respectively. 8, 9 While our study revealed no evidence of transmission from mildly ill, afebrile children to their caregivers despite prolonged positivity of the SARS-CoV-2 RNA in their respiratory specimens, our findings are consistent with WHO's recommendations for alternatively managing patients with mild COVID-19 disease at home. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: An observational cohort study SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics cache = ./cache/cord-322603-8ajckhzc.txt txt = ./txt/cord-322603-8ajckhzc.txt === reduce.pl bib === id = cord-322807-b24ujorz author = Koyama, Takahiko title = Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment date = 2020-04-26 pages = extension = .txt mime = text/plain words = 1869 sentences = 95 flesch = 50 summary = The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. Typically, surface proteins outside of the viral virion are selected for antigens so that antibodies generated from a vaccine-trained B-cell can bind to the virus for neutralization. This study's objective is to interrogate currently identified sub-strains of SARS-CoV-2 and identify genetic drifts and potential immune recognition escape sites that would be integral for the development of a successful vaccine. In these countries, the majority of infected patients possess the variant; therefore, vaccine design and convalescent plasma antibody treatment might require further considerations to accommodate the drift. A spike glycoprotein peptide encompassing residues 604-625 derived from a convalescent SARS-CoV-1 patient was successfully able to elicit humoral immune response and prevent infection in non-human primates, underscoring the immunogenic importance of this region [10] . cache = ./cache/cord-322807-b24ujorz.txt txt = ./txt/cord-322807-b24ujorz.txt === reduce.pl bib === id = cord-322812-9u3ptqjs author = Wells, Philippa M. title = Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3730 sentences = 197 flesch = 51 summary = METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. cache = ./cache/cord-322812-9u3ptqjs.txt txt = ./txt/cord-322812-9u3ptqjs.txt === reduce.pl bib === id = cord-322885-ob5euspo author = Durdagi, Serdar title = Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date = 2020-09-09 pages = extension = .txt mime = text/plain words = 10818 sentences = 656 flesch = 54 summary = One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. Radiation-damage-free SFX method which enables obtaining the novel high-resolution ambient-temperature structures of the binding pocket of Mpro provides an unprecedented opportunity for identification of highly effective inhibitors for drug repurposing by using a hybrid approach that combines structural and in silico methods. We determined two radiation-damage-free SFX crystal structures of SARS-CoV-2 Mpro in two crystal forms at 1.9 Å and 2.1 Å resolutions with the following PDB IDs: 7CWB and 7CWC, respectively (Fig. 1A, B) (Supplementary Table 1&2 The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al., They reveal novel active site residue conformations and dynamics at atomic level, revealing several differences compared to the prior ambient-temperature structure of SARS-CoV-2 Mpro that was obtained at a home X-ray source (Fig. 1A, B ). cache = ./cache/cord-322885-ob5euspo.txt txt = ./txt/cord-322885-ob5euspo.txt === reduce.pl bib === id = cord-322585-5gio6ruj author = Lanari, Marcello title = Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date = 2020-06-25 pages = extension = .txt mime = text/plain words = 441 sentences = 33 flesch = 55 summary = The possible role of children in the COVID-19 viral disease pandemic is also commented. However, the current available data on severe acute respiratory syndrome 31 coronavirus 2 (SARS-CoV-2) show that, from the beginning of the outbreak until now, there is a 32 low attack rate in paediatrics worldwide. Particularly, in Madrid region (Spain), individuals <18 33 years-old accounted for 0.8% of the laboratory-confirmed cases during the first 2 weeks of the Finally, the lockdown imposed until recently by some governments, along with the growing fear of 103 going to hospitals, has led to a significant reduction in the circulation of the other respiratory pathogens and in the number of Paediatric ER visits. Screening 158 and severity of Coronavirus Disease 2019 (COVID-19) in children in Paediatric inflammatory multisystem 163 syndrome and SARS-CoV-2 infection in children -15 A Case Series of children with 2019 novel 180 coronavirus infection: clinical and epidemiological features cache = ./cache/cord-322585-5gio6ruj.txt txt = ./txt/cord-322585-5gio6ruj.txt === reduce.pl bib === id = cord-322834-rl6yum7n author = Wallinga, Jacco title = Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures date = 2004-09-15 pages = extension = .txt mime = text/plain words = 4139 sentences = 185 flesch = 46 summary = The available epidemic curves for SARS show marked differences between the affected regions with respect to the total number of cases and epidemic duration, even for those regions in which outbreaks started almost simultaneously and similar control measures were implemented at the same time. In this paper, we interpret the observed epidemic curves with regard to disease transmission potential and effectiveness of control measures, and we compare the epidemiologic profiles of SARS outbreaks in Hong Kong, Vietnam, Singapore, and Canada. The model uses values of k t = 0.18 for cases with a symptom onset date before March 12, 2003 , and k t = 0.08 for cases with a symptom onset date on or after March 12, 2003 ; these values correspond to the distribution of the number of secondary infections per case as observed during the severe acute respiratory syndrome (SARS) outbreak in Singapore (4). cache = ./cache/cord-322834-rl6yum7n.txt txt = ./txt/cord-322834-rl6yum7n.txt === reduce.pl bib === id = cord-322724-7l1668bf author = Challener, Douglas title = In Reply - Repeated testing in SARS-CoV-2 infection date = 2020-08-10 pages = extension = .txt mime = text/plain words = 472 sentences = 35 flesch = 56 summary = In general, we agree that repeat testing may be helpful in certain situations of ongoing high suspicion for active infection where alternative approaches are not feasible; however, we believe that testing should not be applied indiscriminately in a resource-constrained situation. Several studies have suggested that the number of unique patient specimens tested for SARS-CoV-2 is directly related to the positive identification of the virus and that there may be a high false-negative rate of molecular testing. 2, 3 The study by Zhang et al reported 41 hospitalized patients with an initial negative PCR test who had at least one positive result on subsequent testing. 4 We agree that there may be a role for repeat testing in patients with high clinical suspicion of Low Utility of Repeat Real-Time PCR Testing for SARS-CoV-2 in Clinical Specimens Distinct characteristics of COVID-19 patients with initial rRT-PCRpositive and rRT-PCR-negative results for SARS-CoV-2 cache = ./cache/cord-322724-7l1668bf.txt txt = ./txt/cord-322724-7l1668bf.txt === reduce.pl bib === id = cord-322811-6lebh7ca author = Baig, Mirza S. title = Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4119 sentences = 245 flesch = 53 summary = METHODS: Docking and Molecular Dynamics (MD) simulation studies revealed that designed peptide maintains their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. RESULTS: We have designed a novel peptide that could inhibit SARS-CoV-2 spike protein interaction with ACE2, thereby blocking the cellular entry of the virus. Currently, the computational analysis of structural differences in human ACE2 impact its binding to the SARS-CoV-2 spike protein, which thereby lays a foundation for the design and development of ACE2-based peptide inhibitors of SARS-CoV-2 [47] [48] [49] . After a detailed analysis of interface residues, a small stretch of the ACE2 PD N-terminal region (23-amino acids: Glu23 to Leu45) was found to be interacting majorly with the SARS-CoV-2 spike protein ( Fig. 2 and Table 1 ). Computational alanine (A) scanning was performed to identify the critically important amino acids of the 23aa peptide inhibitor involved in binding to the SARS-CoV-2 spike protein. cache = ./cache/cord-322811-6lebh7ca.txt txt = ./txt/cord-322811-6lebh7ca.txt === reduce.pl bib === id = cord-322908-e3gok0ot author = Huang, Fangfang title = A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19) date = 2020-05-20 pages = extension = .txt mime = text/plain words = 5056 sentences = 275 flesch = 42 summary = In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19. In this review, we summarized potential Chinese herbal medicines ( Table 2 ) that may treat COVID-19 by targeting proteins such as Spike protein, ACE2, 3CLpro, PLpro and RdRp. We also predicted the binding affinities between these compounds and COVID-19 related targets by molecular docking, with a focus on six compounds: quercetin, andrographolide, glycyrrhizic acid, baicalin, patchouli alcohol, and luteolin. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-322908-e3gok0ot.txt txt = ./txt/cord-322908-e3gok0ot.txt === reduce.pl bib === id = cord-323185-n0rubc72 author = Varshney, Bhavna title = SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date = 2012-01-12 pages = extension = .txt mime = text/plain words = 5667 sentences = 345 flesch = 51 summary = Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. In this study, we confirmed the putative interaction of 3b and RUNX1b and observed in vivo recruitment of 3b on the RUNX1 binding element on the IL2 promoter in transiently transfected human T, jurkat cells. We next determined the positive effect of 3b-RUNX1b interaction on the expression of RUNX1b regulated chemokine MIP-1a, reported to be upregulated in SARS-CoV infected monocyte derived dendritic cells. To investigate whether 3b-RUNX1b interaction leads to the recruitment of 3b on RUNX1 binding elements on the endogenous IL2 promoter, ChIP assays were performed in RUNX1b/CBFb endogenously expressing jurkat cells that are abortively infected by SARS-CoV. To investigate the effect of SARS-CoV 3b protein on the RUNX1b transcriptional activity, reporter gene assays were performed using the mouse IL2 promoter. cache = ./cache/cord-323185-n0rubc72.txt txt = ./txt/cord-323185-n0rubc72.txt === reduce.pl bib === id = cord-322650-q8inhgtr author = Fung, Yin-Wan Wendy title = Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date = 2004-08-15 pages = extension = .txt mime = text/plain words = 1132 sentences = 64 flesch = 50 summary = title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests cache = ./cache/cord-322650-q8inhgtr.txt txt = ./txt/cord-322650-q8inhgtr.txt === reduce.pl bib === id = cord-322641-mz0b91xr author = Farnsworth, Christopher W title = SARS-CoV-2 Serology: Much Hype, Little Data date = 2020-04-28 pages = extension = .txt mime = text/plain words = 1566 sentences = 96 flesch = 48 summary = In response to a lack of COVID-19 testing the FDA issued guidance regarding serologic assays, stating that although manufacturers could use the Emergency Use Authorization (EUA) pathway for approval, serologic assays could also be marketed in the US bypassing this approval process (2) . Serology has been suggested to play three roles in the COVID-19 pandemic; 1) diagnosis, 2) identification of convalescent plasma donors, 3) screening populations with the purpose of determining exposure and immunity. If the prevalence of COVID-19 in the population is 20% a test with a sensitivity and specificity of 98% will make the value of a positive result (PPV) 92.5% (Figure 1 ). The importance of specificity of serologic tests for screening low prevalence populations was recently demonstrated in a non-peer reviewed publication (11) . The authors found that 1.5% of those screened were positive for SARS-CoV-2 antibodies and, after analysis, found the estimated prevalence to be 2.4%. cache = ./cache/cord-322641-mz0b91xr.txt txt = ./txt/cord-322641-mz0b91xr.txt === reduce.pl bib === id = cord-322957-clf8f90t author = Crespo, Javier title = Resumption of activity in gastroenterology departments. Recommendations by SEPD, AEEH, GETECCU and AEG date = 2020-04-28 pages = extension = .txt mime = text/plain words = 5297 sentences = 364 flesch = 51 summary = The general objectives of these recommendations include: • To protect our patients against the risks of infection with SARS-CoV-2 and to provide them with high-quality care. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. cache = ./cache/cord-322957-clf8f90t.txt txt = ./txt/cord-322957-clf8f90t.txt === reduce.pl bib === id = cord-322980-rembksdr author = Talwar, Shivangi title = Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020 date = 2020-10-22 pages = extension = .txt mime = text/plain words = 4536 sentences = 233 flesch = 48 summary = The severe acute respiratory syndrome coronavirus (SARS-CoV-2019) emerged in 2019 in the month of December in Wuhan city of China, which again made the life of humans miserable with numerous fatal health issues and slowly and gradually this virus entrapped the whole world [2, 3] . Before the doctors, scientists, and researchers could study and come up with a cure for treatment, this virus had already infected more than lakhs of people across the world with the human coronavirus pathogens, i.e., HCoV-22E and HCoV-OC43, which affects the upper respiratory tract. Because of broad reach, presently, remdesivir and its in vitro studies against coronavirus help in treating SARS-CoV-2 with EC50 and EC90 estimations of 0.77 μM and 1.76 μM, respectively, and are proved to be a fruitful expected treatment for COVID-19 [ cache = ./cache/cord-322980-rembksdr.txt txt = ./txt/cord-322980-rembksdr.txt === reduce.pl bib === id = cord-322660-bis2arbu author = Alexander, Regi title = Guidance for the Treatment and Management of COVID‐19 Among People with Intellectual Disabilities date = 2020-06-10 pages = extension = .txt mime = text/plain words = 10807 sentences = 487 flesch = 44 summary = The guidelines cover specific issues associated with hospital passports, individual COVID‐19 care plans, the important role of families and carers, capacity to make decisions, issues associated with social distancing, ceiling of care/treatment escalation plans, mental health and challenging behavior, and caring for someone suspected of contracting or who has contracted SARS‐CoV‐2 within community or inpatient psychiatric settings. These teams provide a range of care and support to people with IDs, while during the current pandemic there will be an increased focus upon providing TABLE 1 Group at risk because they are clinically vulnerable due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection who need particularly stringent social distancing measures Issues associated with diagnostic overshadowing, the views of parents, family members and carers, the required reasonable adjustments, communication needs, specialist mental health support, anticipatory care plans, any end-of-life or do not attempt cardiopulmonary resuscitation (DNACPR) discussions should be reported. cache = ./cache/cord-322660-bis2arbu.txt txt = ./txt/cord-322660-bis2arbu.txt === reduce.pl bib === id = cord-323072-4rsgeag7 author = Han, Xueqing title = The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date = 2004-12-01 pages = extension = .txt mime = text/plain words = 3741 sentences = 185 flesch = 54 summary = Since the outbreak of SARS in 2003, several laboratory diagnostic methods have been established, including real-time RT-PCR assay, whole-virus-based immunofluorescence assay (IFA), recombinant protein-based enzyme-linked immunosorbent assay (ELISA) and immunochromatographic tests, antigencapturing enzyme-linked immunosorbent assay, and Western blot (WB) assay. To test whether the recombinant M protein is effective as an ELISA antigen for detecting SARS-CoV patient serum, the sera from four healthy people and four SARS patients were used. Detection results of eight human sera by ELISA using purified recombinant M protein as antigen.# 1-4: sera from four healthy people, respectively, # 5-8: sera from four SARS patients, respectively. The results were in complete accordance with those of other assays, thus indicating that the recombinant M protein may be useful as an ELISA antigen for detecting specific antibodies to SARS-CoV in human sera. Recombinant protein-based enzyme-linked imunosorbent assay and immunochromatographic tests for detection of immunoglobulin G antibodies to severe acute respiratory syndrome (SARS) coronavirus in SARS patients cache = ./cache/cord-323072-4rsgeag7.txt txt = ./txt/cord-323072-4rsgeag7.txt === reduce.pl bib === id = cord-323093-u3ozc9ry author = Rathnayake, Athri D. title = 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice date = 2020-08-19 pages = extension = .txt mime = text/plain words = 7158 sentences = 362 flesch = 56 summary = After we observed that treatment with compound 6j resulted in the survival of MERS MA -CoV-infected hDPP4-KI mice, we conducted another study by delaying treatment initiation until 3 dpi. This nucleoside analog was originally developed as an antiviral drug against Ebola virus and has been shown to be effective against both MERS-CoV and SARS-CoV in cell culture assays and in animal models of coronavirus infection (23) (24) (25) (26) . Prophylactic treatment or early therapeutic treatment of infected mice with remdesivir reduced MERS-CoV-or SARS-CoV-mediated weight loss and decreased lung virus titers and lung injury scores compared to those of vehicle-treated animals (23, 26) . The goal of this study was to evaluate the efficacy of 3CLpro inhibitors against human coronaviruses, including SARS-CoV-2, in a FRET enzyme assay and cell culture assays, as well as in a mouse model of MERS-CoV infection. cache = ./cache/cord-323093-u3ozc9ry.txt txt = ./txt/cord-323093-u3ozc9ry.txt === reduce.pl bib === id = cord-323038-hmi061vn author = Lai, Christopher K C title = Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy date = 2020-06-30 pages = extension = .txt mime = text/plain words = 4264 sentences = 257 flesch = 53 summary = title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy METHODS: We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (R(t)), incubation period and time to containment. [8] [9] [10] The key measures included: (i) emergency arrangements according to a Preparedness and Response Plan that stipulated the Government's actions against novel infectious diseases, (ii) mandatory quarantine for people at risk of carrying the infection, (iii) promoting 'social distancing' including a work-from-home policy and school closure, (iv) implementing border control, (v) increasing the supply of surgical masks, and (vi) transparent communication with the public. We controlled for age (in four age strata: 0-24, 25-44, 45-64 and !65 years), gender, source of infection (local vs imported), case identification (self vs by others) and whether the patient had attended any healthcare services before admission to hospital. cache = ./cache/cord-323038-hmi061vn.txt txt = ./txt/cord-323038-hmi061vn.txt === reduce.pl bib === id = cord-322837-tqgwgvo0 author = Gable, Lance title = Legal and Ethical Implications of Wastewater SARS-CoV-2 Monitoring for COVID-19 Surveillance date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1909 sentences = 104 flesch = 47 summary = Even if reliability and efficacy are established, limits on sample and data collection, use, and sharing, must also be considered to prevent undermining privacy and autonomy in order to implement these public health strategies consistent with legal and ethical considerations. The proposed use of wastewater screening to detect SARS-CoV-2 viral RNA has the potential to greatly enhance our technical capabilities to identify, track, pinpoint, and quantify 32 Second, public health authorities could use this information to justify increased testing among people living in homes or working at sites close to where the virus has been found in wastewater, or to implement neighborhood-wide screening programs in these areas. Wastewater screening for SARS-CoV-2 could provide an important tool to detect new outbreaks of COVID-19 and to target resources to intervene to stop the spread of the disease; however, scientific research must establish the efficacy of such testing in identifying communitybased COVID-19 infections before its use can be considered as the basis for public policy. cache = ./cache/cord-322837-tqgwgvo0.txt txt = ./txt/cord-322837-tqgwgvo0.txt === reduce.pl bib === id = cord-323061-0i5w7vm9 author = Kharel Sitaula, Ranju title = Unfolding COVID-19: Lessons-in-Learning in Ophthalmology date = 2020-09-28 pages = extension = .txt mime = text/plain words = 4845 sentences = 266 flesch = 51 summary = 10 Epiphora and Conjunctival redness had been the first manifestation of SARS-CoV-2 infection in 3 reported cases till date which includes a member of National expert on pneumonia during his visit to endemic areas of Wuhan and an anesthesiologist contracting the virus from a known patient of novel coronavirus pneumonia during intubation in Italy; similarly, it was reported in a nurse working in the emergency department of ophthalmology who presented with viral conjunctivitis and watering as a first sign. Hence, our knowledge and understanding about the SARS-CoV-2 virus, modes of entry to the eye, hypothesis on the interaction with the Renin-Angiotensin System (RAS) system and ACE2 receptor and ocular pathogenesis and RT PCR analysis from the ocular secretions have been summarized below using text, tables, diagrams, and flowcharts. cache = ./cache/cord-323061-0i5w7vm9.txt txt = ./txt/cord-323061-0i5w7vm9.txt === reduce.pl bib === id = cord-323216-rgj8vs9z author = Plotkin, Stanley A title = Vaccination Against Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-08-03 pages = extension = .txt mime = text/plain words = 970 sentences = 63 flesch = 51 summary = There is a universal and widely acknowledged need for a vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because of its widespread circulation and high mortality and morbidity. Although some vaccine efforts use the whole inactivated or attenuated virus, the great majority concentrate on the Spike protein, which contains 2 parts: S1 and S2. Table 1 summarizes the current approaches to development of vaccines against SARS-CoV-2. Vaccine developers have experimented with many different ways to present the S protein or, in some cases, the RBD domain to the immune system. There are many important issues that must be answered in these trials, including: Can vaccination prevent infection as well as disease? Will evolution of the SARS-CoV-2 virus require changes in vaccine antigens? Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry The challenges of vaccine development against a new virus during a pandemic cache = ./cache/cord-323216-rgj8vs9z.txt txt = ./txt/cord-323216-rgj8vs9z.txt === reduce.pl bib === id = cord-322877-jy1uvwre author = Yuen, Kenneth S.C. title = Ocular screening in severe acute respiratory syndrome date = 2004-03-30 pages = extension = .txt mime = text/plain words = 1260 sentences = 86 flesch = 56 summary = To investigate the ocular manifestations of patients with severe acute respiratory syndrome (SARS) and to monitor the possible ocular complications arising from the treatment regimen with high-dose systemic corticosteroid drugs. In March 2003, Hong Kong was seriously affected by a massive outbreak of SARS, and we took that opportunity to conduct a prospective observational study to investigate the probable ocular manifestations arising from SARS and the possible short-term complications resulting from the pulse or high-dose corticosteroid therapy. Patients were assessed with a comprehensive ocular examination including best-corrected visual acuity, intraocular pressure (IOP) by noncontact tonometer ([NCT] Xpert Noncontact Tonometer Plus; Reichert Ophthalmic Instruments, New York, New York, USA), slit-lamp, and binocular indirect ophthalmoscopy at baseline and at 2 months and 3 months. 2 With the unremarkable ophthalmologic findings of this study, routine ocular screening in patients with SARS for diagnosis or for complications may not be worthwhile. cache = ./cache/cord-322877-jy1uvwre.txt txt = ./txt/cord-322877-jy1uvwre.txt === reduce.pl bib === id = cord-322955-7dw32xby author = Kathwate, Gunderao H title = In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date = 2020-06-12 pages = extension = .txt mime = text/plain words = 5729 sentences = 392 flesch = 47 summary = title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Those properties are calculated by different methods at IEDB server (http://tools.iedb.org/bcell/ )like Kolaskar-Tongaonkar antigenicity scale provide physiology of the amino acid residues(45), Emini Surface accessible score for accessible surface of the epitope(46), Secondary structure of epitopes also has role in antigenicity. High scored and common peptides predicted by various tools were selected for deriving sequence of potential vaccine candidate. We designed a multi-epitopes vaccine construct from S-protein of SARS-CoV2. From various epitopes predicted by the online server based on common sequence and high score three TCR and two BCR epitopes were selected as part of COVID19 vaccine. This vaccine codes epitopes form S protein of SARS-CoV2 virus for T and B cell receptors. cache = ./cache/cord-322955-7dw32xby.txt txt = ./txt/cord-322955-7dw32xby.txt === reduce.pl bib === id = cord-323131-l726qv1g author = Atogebania, Julius Wedam title = An Invited Commentary on ‘ Evidence Based Management Guideline for the COVID-19 Pandemic- Review article’ date = 2020-04-23 pages = extension = .txt mime = text/plain words = 943 sentences = 65 flesch = 51 summary = COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. AUTHOR SUMMARY: To date over one(1) million persons have been affected indicating exponential spread of the disease and more rigorous implementation and adherence to more strengthen restrictions of social distancing would mitigate the spread of the pandemic disease and may prove to be even tedious. Abstract COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. COVID-19 has recently been declared a pandemic by WHO • Increased cases globally have highlighted the need for updated management guidelines • Currently, supportive management is the first-line treatment • New medical therapies are currently in phase 1 and 2 trials • Invited Commentary' Evidence cache = ./cache/cord-323131-l726qv1g.txt txt = ./txt/cord-323131-l726qv1g.txt === reduce.pl bib === id = cord-322913-sq9mq6f1 author = Ciabattini, Annalisa title = Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date = 2020-11-06 pages = extension = .txt mime = text/plain words = 8068 sentences = 363 flesch = 33 summary = The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of innate and adaptive immune responses, and the lack of a clear correlate of protection, make the design of vaccination strategies for older people extremely challenging (Fig. 3 ). cache = ./cache/cord-322913-sq9mq6f1.txt txt = ./txt/cord-322913-sq9mq6f1.txt === reduce.pl bib === id = cord-323241-1twnqr4k author = Patrì, Angela title = Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? date = 2020-04-09 pages = extension = .txt mime = text/plain words = 633 sentences = 50 flesch = 51 summary = title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? 2, 3 In addition, SARS-CoV-2 RNA identification and intracellular staining of viral nucleocapsid protein in rectal epithelia demonstrated that the virus infects such epithelial cells. [2] [3] [4] Moreover, SARS-CoV-2 can also be transmitted through the saliva, and ACE2 has been detected on the mucosa of oral cavity, which is rich in epithelial cells. 4 Therefore, if saliva and feces are both capable of carrying the virus and ACE2 is expressed both in the glandular cells of rectal epithelia and oral mucosa, how can we be sure that sexual intercourse does not represent another way of contagion? 5 This means that the gastrointestinal tract may continue shedding the virus and that fecal-oral, or eventually sexual, transmission may be possible despite the apparent recovery. cache = ./cache/cord-323241-1twnqr4k.txt txt = ./txt/cord-323241-1twnqr4k.txt === reduce.pl bib === id = cord-323148-rsjocuh3 author = Assaad, Souad title = Risk of death of cancer patients presenting with severe symptoms of infection, with or without documented COVID-19 date = 2020-09-06 pages = extension = .txt mime = text/plain words = 1035 sentences = 54 flesch = 57 summary = The striking observation of our series is the high risk of death (actuarial survival close to 20% at day 28) of cancer patients who did not demonstrate detectable SARS-COV-2 using the standard Cobas test. The high death rates of RT-PCR negative cancer patients observed in our series may result from a sensitivity of SARS-COV-2 diagnostic assays (false negativity), and also other undocumented infections in the context of patients with a progressive cancer. From these different series and works, it can be concluded that cancer patients under active treatment are at high risk of lethal complications when presenting with symptoms resembling those of COVID -19 and requiring hospitalisation even in the absence of documented SARS-COV-2 infection. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR The impact of the COVID-19 pandemic on cancer deaths due to delays in diagnosis in England, UK: a national, population-based, modelling study cache = ./cache/cord-323148-rsjocuh3.txt txt = ./txt/cord-323148-rsjocuh3.txt === reduce.pl bib === id = cord-323327-08p122lw author = van de Veerdonk, Frank L. title = Blocking IL-1 to prevent respiratory failure in COVID-19 date = 2020-07-18 pages = extension = .txt mime = text/plain words = 3019 sentences = 145 flesch = 41 summary = These findings open new avenues for host-directed therapies in patients with symptomatic SARS-CoV-2 infection and might in addition to antiviral treatment be enough to curb the currently unacceptably high morbidity and mortality associated with COVID-19. Although ICU patients have been treated with glucocorticoids, some experts have even argued, based on studies in Middle-Eastern respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome (SARS), influenza, and respiratory syncytial virus (RSV), that they are likely to do more harm than good [1, 2] . The autoinflammatory loop can exacerbate from increase innate immune response into uncontrolled MAS a spectrum that associates with increasing ferritin levels van de Veerdonk and Netea Critical Care (2020) 24:445 patients in the early phase and reports that high dose intravenous anakinra started in patients outside of the ICU was safe and resulted in clinical benefit in 72% of patients [56] . cache = ./cache/cord-323327-08p122lw.txt txt = ./txt/cord-323327-08p122lw.txt === reduce.pl bib === id = cord-323397-5yop6clu author = Albalate, M. title = Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date = 2020-04-30 pages = extension = .txt mime = text/plain words = 5233 sentences = 540 flesch = 63 summary = El objetivo de este trabajo es describir la experiencia del primer mes de pandemia por SARS-Cov2 en una unidad hospitalaria de hemodiálisis (HD) que atiende al 2º distrito madrileño con más en incidencia de COVID19 (casi 1000 pacientes en 100000 h). Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. cache = ./cache/cord-323397-5yop6clu.txt txt = ./txt/cord-323397-5yop6clu.txt === reduce.pl bib === id = cord-322942-y4zd2oui author = Olagnier, David title = Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3756 sentences = 203 flesch = 50 summary = Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. Here we demonstrate that expression of NRF2-dependent genes is suppressed in biopsies from 104 COVID-19 patients and that treatment of cells with NRF2 agonists 4-OI and DMF induces a 105 strong anti-viral program that limits SARS-CoV2 replication. Interestingly, when 176 treating Calu3 cells with DMF, another known NRF2 inducer and a clinically approved drug in 177 the first-line-of treatment of multiple sclerosis, we could also observe an anti-viral effect toward 178 SARS-CoV2 replication similar in magnitude as what we had observed with 4-OI (Fig 2p-q) as 179 well as a reduced but significant effect when using Vero cells (Fig. 2r) . cache = ./cache/cord-322942-y4zd2oui.txt txt = ./txt/cord-322942-y4zd2oui.txt === reduce.pl bib === id = cord-323394-osx7llte author = Lanser, Lukas title = Evaluating the clinical utility and sensitivity of SARS-CoV-2 antigen testing in relation to RT-PCR Ct values date = 2020-11-13 pages = extension = .txt mime = text/plain words = 1214 sentences = 63 flesch = 53 summary = We compared the SARS-CoV-2 antigen detection in nasopharyngeal swab samples by the Panbio™ COVID-19 Ag Rapid test (Abbott, Chicago, Illionis) with the simultaneous routinely conducted RT-PCR analysis of SARS-CoV-2 orf1 RNA detection with the cobas ® analyzer (Roche Diagnostics GmbH, Mannheim, Germany). Among 51 RT-PCR SARS-CoV-2 positive patients, the Pan-bio™ COVID-19 Ag Rapid test was positive in 31 subjects depicting a poor sensitivity of 60.8% (95% CI 46.1-74.2%), compared to 93.3% in the manufacturer's information. In the 14 patients with a Ct-value ≤ 25, being indicative for higher viral loads, the sensitivity for the Panbio™ COVID-19 Ag Rapid test was at a level of 85.7% (95% CI 57.2-98.2%, Table 1 ). Although our results are quite encouraging regarding the use of antigen test as point-of-care diagnostic which may contribute to a better control of the pandemic, we need longitudinal studied which larger patient cohorts to corroborate our results and to develop algorithms or to identify those subjects who are contagious but not detected by that test. cache = ./cache/cord-323394-osx7llte.txt txt = ./txt/cord-323394-osx7llte.txt === reduce.pl bib === id = cord-323095-q8tj826i author = Sokolowska, Milena title = Outsmarting SARS-CoV-2 by empowering a decoy ACE2 date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1473 sentences = 85 flesch = 50 summary = Along with the current efforts to develop high-affinity neutralizing antibodies, Chan and colleagues engineered the soluble variant of human ACE2 with enhanced binding to the spike protein, outranking the soluble wild-type protein in blocking SARS-CoV-2 infection in vitro. There are currently a few therapeutic approaches focused on blocking SARS-CoV-2 binding to its key receptor, an angiotensin-converting enzyme 2 (ACE2), or on inhibition of virus spike cleavage (Fig. 1a) . 2 Therefore, other approaches are also intensively studied including soluble recombinant human ACE2 (rhACE2) or peptide-based binders, developed to block SARS-CoV-2-RBD-ACE2 binding interface or small molecule inhibitors blocking the host cell proteases, such as TMPRSS2 or furin, block virus fusion with the host cell. Therefore, in designing the soluble ACE2 (sACE2) variant the authors introduced the combinations of 3-7 mutations, which gave the large increases in S binding. Engineered soluble construct of ACE2 with enhanced affinity to SARS-CoV-2 spike RBD opens up several possibilities of its usage in the current pandemics. cache = ./cache/cord-323095-q8tj826i.txt txt = ./txt/cord-323095-q8tj826i.txt === reduce.pl bib === id = cord-323449-r1gyjxei author = Kim, Uh Jin title = Air and Environmental Contamination Caused by COVID-19 Patients: a Multi-Center Study date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2012 sentences = 141 flesch = 51 summary = BACKGROUND: The purpose of this study was to determine the extent of air and surface contamination of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in four health care facilities with hospitalized coronavirus disease 2019 (COVID-19) patients. CONCLUSION: Our data suggest that remote (> 2 m) airborne transmission of SARS-CoV-2 from hospitalized COVID-19 patients is uncommon when aerosol-generating procedures have not been performed. 10, 11 The objectives of the present study were 1) to investigate air and environmental contamination caused by COVID-19 patients in a variety of hospital settings; 2) to evaluate the effectiveness of environmental cleaning; and 3) to examine the potential for remote airborne transmission in the absence of aerosol-generating procedures. Despite extensive surface sampling, SARS-CoV-2 RNA was not detected in the room in Hospital B (AIIR with routine surface cleansing using disinfectant wipes the patient's respiratory samples (Ct value 22.4-28.9) (Fig. 1B) . cache = ./cache/cord-323449-r1gyjxei.txt txt = ./txt/cord-323449-r1gyjxei.txt === reduce.pl bib === id = cord-323024-blc3mnbj author = Bernard-Valnet, R. title = CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology date = 2020-11-04 pages = extension = .txt mime = text/plain words = 3478 sentences = 226 flesch = 49 summary = Methods: We checked for SARS-CoV-2 RNA by RT-qPCR, SARS-CoV-2-specific antibodies and for 48 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluids (CSF) +/sera of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological control patients (inflammatory [IND], non inflammatory [NIND], multiple sclerosis [MS]). Methods: We checked for SARS-CoV-2 mRNA by qPCR, SARS-CoV-2-specific antibodies and for 49 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluid (CSF) +/serum of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological controls (inflammatory, non inflammatory, multiple sclerosis). Thus, the main hypotheses to explain neurological complications in COVID patients point at mechanisms either related to low grade presence of the virus in the CNS, to cytokine storm or to the presence of an auto-immune response, such as anti-neuronal antibodies by analogy to what occurs in autoimmune encephalitis. We found that SARS-CoV-2 patients tend to have signs of blood brain barrier opening and possible astrocytes activation, but no strong immune response in the CSF or obvious CNS infection by the virus. cache = ./cache/cord-323024-blc3mnbj.txt txt = ./txt/cord-323024-blc3mnbj.txt === reduce.pl bib === id = cord-323324-h2a25xym author = Armijos‐Jaramillo, Vinicio title = SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-05-07 pages = extension = .txt mime = text/plain words = 3340 sentences = 192 flesch = 55 summary = With this analysis, we determine a region inside the receptor‐binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor ACE2. In the case of SARS-CoV, ACE2 binding was found to be a critical determinant for the range of hosts the virus can infect, and key amino acid residues in the RBD were identified to be essential for ACE2-mediated SARS-CoV infection and adaptation to humans (Li et al., 2005 (Li et al., , 2006 . We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. Additionally, important hACE2-binding residues in the RBD from SARS-COV-2 obtained from the crystallography and structure determination performed by Shang et al. cache = ./cache/cord-323324-h2a25xym.txt txt = ./txt/cord-323324-h2a25xym.txt === reduce.pl bib === id = cord-323514-jaom3p6s author = He, Yuxian title = A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date = 2006-05-26 pages = extension = .txt mime = text/plain words = 4007 sentences = 182 flesch = 48 summary = Abstract The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has two major functions: interacting with the receptor to mediate virus entry and inducing protective immunity. Coincidently, the receptor-binding domain (RBD, residues 318–510) of SAR-CoV S protein is a major antigenic site to induce neutralizing antibodies. We also demonstrated that the RBD-Fc bearing R441A mutation could not bind to soluble and cell-associated angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV and failed to block S protein-mediated pseudovirus entry, indicating that this point mutation also disrupted the receptor-binding motif (RBM) in the RBD. In this study, we used the RBD-Fc as a model to study how a single residue mutation in the RBD can abolish the major function of full-length S protein, since this molecule can efficiently bind to the receptor ACE2 and contains multiple conformation-dependent epitopes (Conf I-VI) capable of inducing highly potent neutralizing antibodies [29] . cache = ./cache/cord-323514-jaom3p6s.txt txt = ./txt/cord-323514-jaom3p6s.txt === reduce.pl bib === id = cord-321768-oevswvvd author = Duan, Ya-qi title = Deficiency of Tfh Cells and Germinal Center in Deceased COVID-19 Patients date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2307 sentences = 125 flesch = 51 summary = In this study, we examined the immune cell compositions in the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients and 4 focal organizing pneumonia (FOP) patients who underwent lung surgery and served as controls. In contrast to the FOP patients, Tfh cells and germinal center formation were largely absent in the draining hilar lymph nodes in the deceased COVID-19 patients. Characterization of compositions of the immune cells within the lung tissues and draining hilar lymph nodes from the postmortem specimens might provide valuable insights on how the immune responses in the deceased patients were dysregulated and offer new strategies for treatment. To gain insight into the human immune responses during a fatal SARS-CoV2 infection, we performed postmortem autopsy studies of the immune cell compositions within the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients, and 4 FOP patients who underwent lung surgery served as controls. cache = ./cache/cord-321768-oevswvvd.txt txt = ./txt/cord-321768-oevswvvd.txt === reduce.pl bib === id = cord-323094-zugrtvyo author = Rose, R. title = Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1774 sentences = 119 flesch = 58 summary = Here, we quantify and characterize intra-host variation in SARS-CoV-2 raw sequence data uploaded to SRA as of 14 April 2020, and compare results between two sequencing methods (amplicon and RNA-Seq). While mutations resulting from amplification and/or sequencing errors cannot be excluded, the observation of shared polymorphic sites with high MAF across multiple samples and sequencing methods is consistent with true underlying variation. Our goal in this study was to quantify and characterize intra-host variation in all SARS-CoV-2 raw sequence data available in SRA as of 14 April 2020, and compare results between two All rights reserved. . https://doi.org/10.1101/2020.04.24.20078691 doi: medRxiv preprint 5 percent of the genome covered at 10x and 25x remained high with the amplicon data (10x IQR: 0.987 -0.997; 25x IQR: 0.980 -0.997), the range was much broader for the RNA-Seq data (10x IQR: 0.240 -0.997; 25x IQR: 0.024 -0.993). cache = ./cache/cord-323094-zugrtvyo.txt txt = ./txt/cord-323094-zugrtvyo.txt === reduce.pl bib === id = cord-323092-j2u0ny2u author = Crosby, James C. title = COVID‐19: A review of therapeutics under investigation date = 2020-04-19 pages = extension = .txt mime = text/plain words = 3896 sentences = 270 flesch = 51 summary = The World Health Organization (WHO) has released general guidelines for managing the illness caused by the virus (COVID-19), which includes supportive care similar to other viral pneumonias: airway and respiratory support, empiric antibiotics for secondary bacterial infection, and acute respiratory distress syndrome (ARDS) management. 2 While these treatments are thought to offer the best chance of survival for the approximately 20% of COVID-19 cases that progress to severe disease, limited health care resources and the speed at which the pandemic has developed are pressuring clinicians and scientists to provide therapeutics that specifically target SARS-CoV-2 and improve mortality. 32, 33 There are a number of promising studies that have demonstrated shorter hospital stays, lower mortality rates, and reduced viral loads in SARS-CoV-1 and H1N1 influenza infected patients treated with convalescent plasma. There is another single ongoing observational trial examining the efficacy of anti-SARS-CoV-2 inactivated convalescent plasma in COVID-19 patients, the results of which remain to be seen. cache = ./cache/cord-323092-j2u0ny2u.txt txt = ./txt/cord-323092-j2u0ny2u.txt === reduce.pl bib === id = cord-323603-99d0wv1h author = Nunez Garcia, B. title = Real-world data: Cancer and SARS-CoV-2 infection date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1537 sentences = 106 flesch = 56 summary = Methods: EGFR, KRAS, BRAF, BRCA1/2 mutation testing of advanced lung adenocarcinoma, metastatic colorectal, metastatic melanoma and ovarian cancer patients were performed by qPCR and NGS. Methods: During the period 11 th March to 15 th May 2020, patients diagnosed with COVID-19 infection who were attending Beaumont Hospital for systemic anti-cancer therapy were included. Those with an ECOG performance status (PS) 3 were more likely to die than those with PS 2 (p<0.001).Compared to those who recovered, patients who died from COVID-19 had higher mean number of organs affected by cancer (3.7 vs. Conclusions: Patients with cancer who contracted COVID-19 and died had more sites of metastatic disease, a poorer performance status, and a higher Palliative Prognostic Score. Results: Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. cache = ./cache/cord-323603-99d0wv1h.txt txt = ./txt/cord-323603-99d0wv1h.txt === reduce.pl bib === id = cord-323440-u3iz79kk author = de Niet, Annikki title = The role of children in the transmission of mild SARS‐CoV‐2 infection date = 2020-05-04 pages = extension = .txt mime = text/plain words = 506 sentences = 36 flesch = 54 summary = We thank Dr Ludvigsson 1 on his effort to improve knowledge on SARS-CoV-2 infection in children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. 4 Furthermore, SARS-CoV-2 infection in children differs from adults in that they have a lower prevalence of increased C-reactive protein, signifying a milder immunological response and less immune damage. 1 The viral load in patients with mild disease showed to be lower compared with those having severe SARS-CoV-2 infection. 2 Reports from severe disease in infected healthcare workers further hint towards an association between higher viral load in critically ill patients and transmission of more severe SARS-CoV-2 infection. cache = ./cache/cord-323440-u3iz79kk.txt txt = ./txt/cord-323440-u3iz79kk.txt === reduce.pl bib === id = cord-323389-8vp57c1o author = Wei, S. title = Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2. date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1563 sentences = 105 flesch = 62 summary = We developed an assay that detects single copies of SARS-CoV-2 virus directly from saliva and swab samples in 30 min using a simple, one-step protocol that utilizes only a heat block and microcentrifuge tube prefilled with a mixture containing the necessary reagents and has a sensitivity and specificity of 97% and 100%, respectively. To determine which primer set was most sensitive and specific to SARS-CoV-2, we tested the eight primer sets that we designed, along with previously published primer sets 9, 10 , using serial dilutions of 500 to 0.5 copies of SARS-CoV-2 RNA standard spiked into a 25 μ L RT-LAMP reaction ( Figure 1C ). . https://doi.org/10.1101/2020.06.13.20129841 doi: medRxiv preprint necessary for testing clinical samples ( Figure 1D ). In summary, we developed HP-LAMP, which enables rapid detection of SARS-CoV-2 directly from saliva in 30 min using a simple one-step protocol with a LoD of 2 viral copies per μ L of saliva and a sensitivity and specificity of 97% and 100%, respectively. cache = ./cache/cord-323389-8vp57c1o.txt txt = ./txt/cord-323389-8vp57c1o.txt === reduce.pl bib === id = cord-323424-86wh4u6l author = Santos, M. M. title = Survival and predictors of deaths of patients hospitalised due to COVID-19 from a retrospective and multicentre cohort study in Brazil date = 2020-09-07 pages = extension = .txt mime = text/plain words = 3746 sentences = 163 flesch = 47 summary = The co-variables used to compare survival curves were socioeconomic factors (age, sex, race, education and area of residence), clinical signs and symptoms (fever, cough, sore throat, diarrhoea and vomiting), hospital variables (influenza-like outbreak, hospital-acquired infection, dyspnoea, respiratory distress, O 2 saturation <95%, intensive care unit (ICU) admission, ICU length of stay and X-ray result), chronic disease (heart disease, haematology, Down's syndrome, liver disease, asthma, diabetes mellitus, neurological disease, pneumopathy, immunodepression, kidney disease and body mass index (BMI)), if the patient has had a flu vaccine, use of antiviral against influenza and what is the type of such antiviral. This multicentre retrospective cohort study of patients hospitalised with COVID-19 found important differences in survival times, as well as risk factors or protection for the death of patients in Brazilian hospitals. cache = ./cache/cord-323424-86wh4u6l.txt txt = ./txt/cord-323424-86wh4u6l.txt === reduce.pl bib === id = cord-323383-dmzhywb9 author = Lundon, DJ title = Early Mortality Risk Stratification after SARS-CoV-2 Infection date = 2020-07-04 pages = extension = .txt mime = text/plain words = 899 sentences = 50 flesch = 50 summary = While the majority of those who test positive for SARS-CoV-2 will not require hospital admission, intensive care or mechanical ventilation, some will (data from our institution suggest ~13% of those hospitalized due to COVID-19 underwent mechanical ventilation). Using the Mount Sinai Health Systems' database of all SARS-Co-V-2 positive patients with an encounter in New York City, we developed a prediction model to identify those patients most likely to succumb to the disease thin 7 days (the median time to death of those who died) from the onset of COVID-19 symptoms. The risk probability of death within 7 days for patients was calculated from a model developed in 80% of this cohort, using the 3 demographic and 4 clinical variables listed above. This model demonstrates the significant role that both clinical and social determinants play in predicting the clinical outcome for patients infected with SARS-CoV-2 and tested positive for COVID-19. cache = ./cache/cord-323383-dmzhywb9.txt txt = ./txt/cord-323383-dmzhywb9.txt === reduce.pl bib === id = cord-323618-d09b65gd author = Vabret, A. title = Coronavirus humains (HCoV) date = 2008-05-05 pages = extension = .txt mime = text/plain words = 6301 sentences = 541 flesch = 63 summary = La survenue récente, en 2002 à 2003, de l'épidémie de SRAS (ou syndrome respiratoire aigu sévère), et l'identification de l'agent pathogène responsable, un coronavirus émergent dans la population humaine, ont conduit à un vif regain d'intérêt et une intensification importante des recherches sur ces virus. Certaines données expérimentales sont inattendues : malgré des séquences en aminoacides conservées au niveau de la protéine S1 des HCoV 229E et NL63, ces deux coronavirus humains utilisent des récepteurs différents (APN et ACE2, respectivement) ; par ailleurs, le SARS-CoV utilise le même récepteur cellulaire que NL63 alors que les séquences S1 sont éloignées, cependant le RBD des deux virus semble proche et il est absent chez les SL-CoV. Une des conséquences biologiques de cette grande délétion est le changement de tropisme du virus qui, d'entérique pour le TGEV, est devenu respiratoire pour le PRCV [36] De nombreuses études ont été menées à la recherche du réservoir animal du SARS-CoV. cache = ./cache/cord-323618-d09b65gd.txt txt = ./txt/cord-323618-d09b65gd.txt === reduce.pl bib === id = cord-323105-gqqzekfk author = Lin, Chen-Si title = Enhancement of anti-murine colon cancer immunity by fusion of a SARS fragment to a low-immunogenic carcinoembryonic antigen date = 2012-02-03 pages = extension = .txt mime = text/plain words = 3208 sentences = 153 flesch = 46 summary = Oral vaccination of an attenuated Salmonella typhimurium strain transformed with plasmids encoding CEA-SARS-CoV fusion gene into BALB/c mice elicited significant increases in TNF-α and IL-10 in the serum. For achieving simple administration of drugs and enhancement of host immunity, an oral DNA vaccine vector, Salmonella typhimurium (SL3261) [7] , was used as a carrier to deliver the SARS-CoV-CEA fusion genes. By combining SARS-CoV epitope, a tumor unrelated antigenic fragment, with CEA, we finally demonstrated this could be a promising anti-cancer strategy through effectively increasing both Th1 and Th2 cytokines and decreasing tumor volume. In comparison with the negative control group, no significant differences in tumor volume were observed in mice immunized with CEA alone, while the tumor volume was found to be smaller in the pCEA-SARS-CoV group in the protection and therapy assays (Figure 3 &4) . cache = ./cache/cord-323105-gqqzekfk.txt txt = ./txt/cord-323105-gqqzekfk.txt === reduce.pl bib === id = cord-323468-xn7anxj6 author = Olloquequi, Jordi title = COVID‐19 Susceptibility in chronic obstructive pulmonary disease date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4155 sentences = 220 flesch = 45 summary = Chronic obstructive pulmonary disease (COPD) is a leading cause of death and disability globally, characterized by persistent respiratory symptoms and airflow limitation due to airway inflammation and/or alveolar abnormalities 10 . All rights reserved are associated to impaired lung function and risk of developing COPD 42-44 , it has also been demonstrated that people born with a diminished airway function are more likely to suffer COPD symptoms and subsequent viral infections [45] [46] [47] . In any case, there is no doubt that subjects who develop COPD are at an increased risk of suffering respiratory infections, a matter of importance in the context of COVID-19 pandemics. Increased cytokine response of rhinovirus-infected airway epithelial cells in chronic obstructive pulmonary disease DPP4, the Middle East Respiratory Syndrome Coronavirus Receptor, is Upregulated in Lungs of Smokers and Chronic Obstructive Pulmonary Disease Patients cache = ./cache/cord-323468-xn7anxj6.txt txt = ./txt/cord-323468-xn7anxj6.txt === reduce.pl bib === id = cord-323489-ro7kbnu3 author = Arenas, María Dolores title = Protection of nephrology health professionals during the COVID-19 pandemic date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4137 sentences = 194 flesch = 50 summary = There are a number of reasons why the protection of healthcare professionals has to be one of the main objectives in the SARS-CoV-2 pandemic: 1) They are necessary to guarantee the continuity of care; 2) They have a high risk of contagion due to their front-line exposure to infected patients; and 3) They may act as transmission vehicles in their day-to-day work to patients, other colleagues, and members of their families and the community. a Special care or protective measures for medical, nursing and auxiliary staff who work daily with haemodialysis patients As has previously been described in other publications 3,10 , the main protection measures for healthcare professionals and patients in haemodialysis units are: 1) adequate information for patients attending the centre in terms of maintaining a safe distance from fellow patients in waiting rooms and ambulances, and in the use of surgical masks and frequent hand washing; 2) early detection of patients suspected to be infected on arrival at the unit (questionnaires about symptoms or close contacts, taking temperature), and if highly suspect, taking a nasopharyngeal swab for PCR testing. cache = ./cache/cord-323489-ro7kbnu3.txt txt = ./txt/cord-323489-ro7kbnu3.txt === reduce.pl bib === id = cord-323481-uz6usokd author = Wang, Yixuan title = Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures date = 2020-03-29 pages = extension = .txt mime = text/plain words = 2943 sentences = 210 flesch = 50 summary = title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures By 27 February 2020, the outbreak of coronavirus disease 2019 (COVID‐19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (SARS) (8273 cases, 775 deaths) and Middle East respiratory syndrome (MERS) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China The guidelines for diagnosis and treatment of novel coronavirus (2019-nCoV) infected pneumonia (the sixth edition draft) issued by the National Health Commission of China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection cache = ./cache/cord-323481-uz6usokd.txt txt = ./txt/cord-323481-uz6usokd.txt === reduce.pl bib === id = cord-323737-6ajqy0ch author = Jiang, Yuanyuan title = Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date = 2020-10-04 pages = extension = .txt mime = text/plain words = 6799 sentences = 399 flesch = 51 summary = title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify potential inhibitors targeting 2 0 -O-MTase of SARS-CoV-2. To identify inhibitors targeting nsp16, we first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs. Supplementary Table 1 lists the detailed genome and protein information that were employed in this study. As seen from MM-PBSA results and docking studies, drugs including Hesperidin, Osi-027, Rimegepant, Sonedenoson, and Gs-9667 had higher binding affinities than SAM with the 2 0 -O-MTase of SARS-CoV-2. cache = ./cache/cord-323737-6ajqy0ch.txt txt = ./txt/cord-323737-6ajqy0ch.txt === reduce.pl bib === id = cord-323596-dh7oh54z author = Advani, Sonali D. title = Assessing severe acute respiratory coronavirus virus 2 (SARS-CoV-2) preparedness in US community hospitals: A forgotten entity date = 2020-10-07 pages = extension = .txt mime = text/plain words = 1550 sentences = 88 flesch = 46 summary = Several differences in hospital preparedness for SARS-CoV-2 emerged with respect to personal protective equipment conservation strategies, protocols related to testing, universal masking, and restarting elective procedures. Hence, we conducted a cross-sectional survey of SARS-CoV-2 preparedness among community hospitals in southeastern United States. The survey included 13 questions related to PPE availability, crisis capacity strategies to extend and reuse PPE, policies related to restarting surgeries, testing prior to elective surgery and prior to transfer to extended care facilities, universal masking, and daily screening of hospital staff. In addition, 80% of hospitals reported an adequate supply of N95 respirators, face shields, and googles, likely due to use of crisis capacity strategies to extend, reuse, and reprocess these PPE. We found several differences in community hospital preparedness for SARS-CoV-2 with respect to type of conservation strategies used to preserve PPE, protocols related to testing, masking, and restarting elective procedures. cache = ./cache/cord-323596-dh7oh54z.txt txt = ./txt/cord-323596-dh7oh54z.txt === reduce.pl bib === id = cord-323666-t7cshj05 author = Cegolon, L. title = Nasal Disinfection for the Prevention and Control of COVID-19: A Scoping Review on Potential Chemo-preventive Agents. date = 2020-08-18 pages = extension = .txt mime = text/plain words = 6187 sentences = 339 flesch = 46 summary = Figure 1 reports the corresponding changes as percentage or odds; the latter detects the improvement of the index score better than the former because it is able to overcome the ceiling effects J o u r n a l P r e -p r o o f Therefore, in addition to an effective treatment for symptomatic patients, there is an urgent need to abate the carriage of SARS-CoV-2 in the human nasal cavity of asymptomatic/pre-symptomatic individuals, in order to contain the transmission of the novel coronavirus within the community. The abstracts of the original articles were explored for the following terms: mechanism(s) of action, tolerability and any evidence of toxic effects or selection of resistant strains, whether the treatment was tested in vitro (in particular against SARS-CoV-2), or reached the clinical trials stage, or is currently marketed/promoted/sold. cache = ./cache/cord-323666-t7cshj05.txt txt = ./txt/cord-323666-t7cshj05.txt === reduce.pl bib === id = cord-323831-1qadv7r1 author = Coleman, H title = Severe acute respiratory syndrome coronavirus-2 in post-laryngectomy patients: case series of four patients date = 2020-06-23 pages = extension = .txt mime = text/plain words = 1999 sentences = 125 flesch = 53 summary = OBJECTIVE: To report our experience of diagnosis, investigation and management in patients who had undergone laryngectomy secondary to previous squamous cell carcinoma, who were subsequently infected with severe acute respiratory syndrome coronavirus-2 during the coronavirus disease 2019 pandemic. CASE REPORTS: Four post-laryngectomy patients with laboratory-proven severe acute respiratory syndrome coronavirus-2 infection were admitted to our institution from 1 March to 1 May 2020. 2 There is no published evidence to date on the post-operative and ward management of this group of patients with laboratory-proven SARS-CoV-2 infection. 3 Here, we present our experience of the diagnosis, investigation and management of SARS-CoV-2 positive, post-laryngectomy patients, who attended our institution between 1 March and 1 May 2020, during the Covid-19 pandemic. Patient one, a 50-year-old female, was an in-patient on the ENT ward, who was progressing well 2 weeks following total laryngectomy, bilateral neck dissection and pectoralis major flap reconstruction for a tumour-node staged T 3 N 2c moderately differentiated supraglottic SCC. cache = ./cache/cord-323831-1qadv7r1.txt txt = ./txt/cord-323831-1qadv7r1.txt === reduce.pl bib === id = cord-323839-a4oejky0 author = Sasaki, Michihito title = SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2100 sentences = 128 flesch = 63 summary = These results indicated that S gene mutants are resistant to the 1 5 9 treatment with TMPRRSS2 inhibitors, but are sensitive to antivirals that target post entry In an effort to understand the selection mechanisms underlying the generation of these 1 6 4 mutant variants, we estimated the frequency of S gene mutants in virus population of 1 6 5 SARS-CoV-2 that had undergone serial passage in cultured cells. In contrast, nucleotide sequence 1 7 2 deletions around the S1/S2 cleavage site corresponding to del1 and del2 mutants were 1 7 3 observed in all three biological replicates of SARS-CoV-2 populations passaged in Vero 1 7 4 cells (Fig. 5a) . Moreover, we must be very objective when interpreting the results 2 3 0 from studies using Vero-passaged virus, especially those focused on S protein cleavage, Cells were infected with either WT or S mutants of SARS-CoV-2 at an MOI of 1. cache = ./cache/cord-323839-a4oejky0.txt txt = ./txt/cord-323839-a4oejky0.txt === reduce.pl bib === id = cord-323908-8dgngwmw author = He, Zhesheng title = Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date = 2020-05-31 pages = extension = .txt mime = text/plain words = 881 sentences = 61 flesch = 59 summary = title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity. These compounds could serve as potential anti-SARS-CoV-2 lead molecules for further drug studies to combat COVID-19. The interactions between the gold atom with the binding pockets of proteins were studied by density functional theory (DFT) calculations. cache = ./cache/cord-323908-8dgngwmw.txt txt = ./txt/cord-323908-8dgngwmw.txt === reduce.pl bib === id = cord-323828-ug2duzw1 author = Ni, Dongchun title = Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date = 2020-10-12 pages = extension = .txt mime = text/plain words = 3408 sentences = 234 flesch = 65 summary = Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. The clinical-grade soluble form of hACE2 has been reported to be a 74 potential novel therapeutic approach for reducing the infection of SARS-CoV-2 (Monteil et al., 2020) by preventing the viral Spike from interacting with other hACE2 present on human cells. The final 3D 115 reconstruction from 72'446 particles at 5.1Å overall resolution showed a density map corresponding to a single, 116 monomeric Spike protein in complex with hACE2 (Fig. 1a) . Figure 1 Cryo-EM maps of SARS-CoV-2 Spike-hACE2 complexes and fitted models. Cryo-EM structure of the SARS coronavirus spike glycoprotein in 352 complex with its host cell receptor ACE2 cache = ./cache/cord-323828-ug2duzw1.txt txt = ./txt/cord-323828-ug2duzw1.txt === reduce.pl bib === id = cord-323695-jkik03lb author = Paolo, Gisondi title = Incidence rates of hospitalization and death from COVID-19 in patients with psoriasis receiving biological treatment: a Northern Italy experience date = 2020-11-05 pages = extension = .txt mime = text/plain words = 1745 sentences = 88 flesch = 46 summary = Objective investigating the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. Materials and methods This is a retrospective multicenter cohort study including patients with chronic plaque psoriasis (n=6,501) being treated with biologic therapy and regularly followed up at the Divisions of Dermatology of several main hospitals in the Northern Italian cities of Verona, Padua, Vicenza, Modena, Bologna, Piacenza, Turin, and Milan. Incidence rates (IR) of hospitalization and death per 10,000 person-months with exact mid-p 95% confidence intervals (CI) and standardized incidence ratios (SIR) were estimated in the psoriasis patients and compared with the general population in the same geographic areas. We would not advise biologic discontinuation in patients on treatment since more than 6 months and not infected with SARS-CoV-2 to prevent hospitalization and death from COVID-19. In this study, we evaluated the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. cache = ./cache/cord-323695-jkik03lb.txt txt = ./txt/cord-323695-jkik03lb.txt === reduce.pl bib === id = cord-323882-127c5bve author = Yu, Wen-Bin title = Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data date = 2020-05-17 pages = extension = .txt mime = text/plain words = 5560 sentences = 282 flesch = 57 summary = Of the 93 genomes of SARS-CoV-2, 39 (41.93%) were from infected patients in 11 countries outside China and encoded 31 haplotypes (H d =0.987±0.009 (SD), P i =0.16×10 -3 ± 0.01×10 -3 ), with 27 nationally/regionally private haplotypes. Three different datasets were used to infer evolutionary networks, which consistently supported H13 and H38 as the potentially ancestral haplotypes, i.e., the outgroup bat-RaTG13-CoV could connect to both H13 and H38, or H38 alone, or through a medium vector mv1 (an intermediate host or the first infected humans) connected to both H13 and H38 by single mutations at positions 18067 (S, synonymous substitution) and/or 29102 (S), referring to the numbering of the alignment length 29 910 bp ( Figure 5 ). To clarify the exact origins of these haplotypes outside China, we need more epidemiological investigative efforts and more SARS-CoV-2 genomic data from patients at the early stage of transmissions. cache = ./cache/cord-323882-127c5bve.txt txt = ./txt/cord-323882-127c5bve.txt === reduce.pl bib === id = cord-323871-2hx4fuk2 author = Ho, Sheau Ling title = Structural bioinformatics analysis of free cysteines in protein environments date = 2009-03-14 pages = extension = .txt mime = text/plain words = 3244 sentences = 198 flesch = 59 summary = For non-membrane proteins: the hydrophobic residues such as leucine, valine, isoleucine and alanine were more frequently seen in the spatial neighborhood around free cysteines; the same was observed for the aromatic phenylalanine residue. Thus, we applied a structure-base sequence alignment of these nine coronavirus main proteinases to identify any spatial correspondences involving cysteine among them. It can be observed that this multiple sequences alignment figure shows a strong conservation of hydrophobic residues (valine, leucine, isoleucine, alanine phenylalanine and proline) and small residues (serine and glycine) in proximity to cysteine residues. A superimposition (stereo image) of the structures of SARS 3CLpro demonstrates that cysteine residues not only favor positioning in a hydrophobic environment but also develop hunched posture in the surroundings of aromatic residues, see Fig. 3 . cache = ./cache/cord-323871-2hx4fuk2.txt txt = ./txt/cord-323871-2hx4fuk2.txt === reduce.pl bib === id = cord-323622-229kub7c author = Ou, Xueting title = A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens date = 2020-04-16 pages = extension = .txt mime = text/plain words = 663 sentences = 50 flesch = 62 summary = title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens To the Editor Since December, 2019, corona virus disease 2019 (COVID-19) caused by SARS-CoV-2, has spread to the majority of countries worldwide [1, 2] . Here, we reported the clinical characteristics of a severe case with co-infection of SARS-CoV-2 and common respiratory pathogens. However, sputum samples collected on the same day were positive for SARS-CoV-2 by NGS. The patient was diagnosed as severe COVID-19, and was transferred to the First Affiliated Hospital of Guangzhou Medical University for isolation and treatment where are designed to treat severe COVID-19 cases by local health authorities. In the present study, the cause that resulted in severe condition of the patient could be the co-infection of SARS-CoV-2, Haemophilus parainfluenzae and Moraxella catarrhalis. Older patients, having diabetes, hypertension are causes of severe COVID-19 cases [3, 4] . cache = ./cache/cord-323622-229kub7c.txt txt = ./txt/cord-323622-229kub7c.txt === reduce.pl bib === id = cord-323905-ayufx3wv author = Kort, N. P. title = Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members date = 2020-08-18 pages = extension = .txt mime = text/plain words = 3708 sentences = 225 flesch = 53 summary = title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members The April 2020 SARS-CoV-2 survey completed by EHS and EKA members in Europe has confirmed the impact of SARS-CoV-2: this pandemic has resulted in a tremendous reduction in primary hip and knee arthroplasty procedures as shown in the survey. The benefits of hip and knee arthroplasty should be carefully weighed against the risks of viral transmission and infection, complications and mortality in the mostly elderly population requiring joint arthroplasty Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: pre-operative phase 1. Is there a need for -Modification or reorganization of hospital wards (patient density, bed density, medical and nursing stuff density, etc.)?417 (81) 70 (14) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase 1. cache = ./cache/cord-323905-ayufx3wv.txt txt = ./txt/cord-323905-ayufx3wv.txt === reduce.pl bib === id = cord-323824-74xvvwrw author = de Oliveira, Osmair Vital title = Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening date = 2020-06-02 pages = extension = .txt mime = text/plain words = 5373 sentences = 295 flesch = 57 summary = Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below –8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. Our approach adopted here differs from those studies in the following way: the isolated S-protein receptor for docking calculations will be obtained from molecular dynamics (MD) simulation, and not directly from crystal structure or S-protein@ACE2 complex. (Muralidharan et al., 2020) obtained from docking calculations a binding energy of -4.1 kcal/mol using the SARS-CoV-2 protease and lopinavir drug, respectively, as receptor and ligand. In this way, our calculations indicate that the ivermectin drug may bind in the RBD region, inhibiting the coupling of the SARS-CoV-2 S-protein with the human ACE2 receptor. Therefore, herein we used molecular dynamics (MD) simulation and docking calculations to study the SARS-CoV-2 S-protein with the main goal to obtain possible drugs candidates for repurposing them against to COVID-19. cache = ./cache/cord-323824-74xvvwrw.txt txt = ./txt/cord-323824-74xvvwrw.txt === reduce.pl bib === id = cord-323822-jtbfpx88 author = Barnett, Brad P. title = Potential of Ocular Transmission of SARS-CoV-2: A Review date = 2020-09-01 pages = extension = .txt mime = text/plain words = 4031 sentences = 227 flesch = 47 summary = Analysis of gene expression profiles from available datasets, published immunohistochemistry, as well as current literature was reviewed, to assess the likelihood that ocular inoculation of SARS-CoV-2 results in systemic infection. Recent findings: The ocular surface and retina have the necessary proteins, Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL) necessary to be infected with SARS-CoV-2. Summary: There is evidence that SARS-CoV-2 may either directly infect cells on the ocular surface, or virus can be carried by tears through the nasolacrimal duct to infect the nasal or gastrointestinal epithelium. From this literature search, four key proteins implicated in SARS-CoV-2 infection were identified: Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL), and datasets were utilized to analyze the expression of these proteins in ocular and non-ocular tissue. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection cache = ./cache/cord-323822-jtbfpx88.txt txt = ./txt/cord-323822-jtbfpx88.txt === reduce.pl bib === id = cord-323807-e220ut9u author = Bassetti, Matteo title = The novel Chinese coronavirus (2019‐nCoV) infections: Challenges for fighting the storm date = 2020-02-05 pages = extension = .txt mime = text/plain words = 2236 sentences = 112 flesch = 50 summary = Four (229E, NL63, OC43 and HKU1) are responsible for mild upper respiratory tract infections (common cold), whereas the severe acute respiratory syndrome coronavirus (SARS-CoV, which has been contained 4 ) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are able to cause atypical pneumonia. Worth noting is also that the case fatality rate of 2019-nCoV reported in the press news is lower than those previously described for SARS-CoV and MERS-CoV infections (9.5% and 40%, respectively 11 ). Lopinavir/ritonavir is available in several hospitals and has shown promising results in pre-clinical models and case series of SARS-CoV and MERS-CoV infections, 14, 15 although no high-level evidence of efficacy and safety is currently available for its use either as monotherapy or in combination with interferons or other drugs (a randomized controlled trial has been initiated in patients with 2019-nCoV pneumonia in China). cache = ./cache/cord-323807-e220ut9u.txt txt = ./txt/cord-323807-e220ut9u.txt === reduce.pl bib === id = cord-323643-lu3ngt6r author = Chow, C.B. title = Post-SARS infection control in the hospital and clinic date = 2004-11-05 pages = extension = .txt mime = text/plain words = 4449 sentences = 252 flesch = 53 summary = The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. PAEDIATRIC Summary The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. 17 Despite great concerns, compliance to infection control precautions by community general practitioners in Hong Kong lagged behind their hospital counterparts -97.7% had not worn masks at all times, a third did not wash their hands after seeing/examining a patient and half did not wear gowns. In a study looking into factors affecting nosocomial infection in Hong Kong, it was found that all HCWs consistently used N95s or surgical masks and perceived that the inadequacy of personal protective equipment (PPE) supply, infection control training <2 h and inconsistent use of goggles, gowns, gloves and caps were significant independent risk factors for SARS infection. cache = ./cache/cord-323643-lu3ngt6r.txt txt = ./txt/cord-323643-lu3ngt6r.txt === reduce.pl bib === id = cord-323943-9916y6x0 author = Platt, Daniel E title = Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails date = 2020-04-21 pages = extension = .txt mime = text/plain words = 4149 sentences = 230 flesch = 46 summary = Therefore, we sought to understand whether the parameters of epidemic models could be determined from the trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the quality and comparability of data between jurisdictions reporting their statistics necessary for the analysis of model parameters across populations. Beside host and viral genetic impacts, other aspects driving SARS-COV-2 rates are population specific and demic, such as the impact of age on both asymptomatic and mild cases, as well as the proportion of severe and critical cases. In this paper, we seek to identify the limitations of using compartmental models to estimate or test hypotheses concerning parameters governing the growth of SARS-COV-2 epidemics. Therefore, infected population growth may be more closely reflected in the fraction of positive results normalized by total number of tests applied, in spite of very highly biased sampling selection. The rate of growth and doubling time may reflect availability and levels of testing more than the actual disease in the population. cache = ./cache/cord-323943-9916y6x0.txt txt = ./txt/cord-323943-9916y6x0.txt === reduce.pl bib === id = cord-323930-pl3qlcpo author = Sohail, Ayesha title = Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1497 sentences = 95 flesch = 53 summary = The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. cache = ./cache/cord-323930-pl3qlcpo.txt txt = ./txt/cord-323930-pl3qlcpo.txt === reduce.pl bib === id = cord-324128-css42bsb author = Boukli, Narjis title = High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies date = 2020-10-21 pages = extension = .txt mime = text/plain words = 949 sentences = 56 flesch = 53 summary = title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies The median day of IgG seroconversion is around 14 days after symptom onset (2), but a high interindividual variation has been reported, as well as contrasting performances between commercial assays (3) (4) (5) (6) . Furthermore, the 100 samples in our specificity panel were negative with the Alinity I SARS-CoV-2 IgG assay, except for one serum sample from a patient with coronavirus 229E infection, which was weakly reactive (signal-to-cutoff index ϭ 1.93; cutoff is 1.4 index), which leads to a specificity of 99%. While the clinical significance of SARS-Cov-2 antibody detection remains to be determined, our results confirm that careful evaluation of the tests on appropriate samples is required before implementing assays for routine use. cache = ./cache/cord-324128-css42bsb.txt txt = ./txt/cord-324128-css42bsb.txt === reduce.pl bib === id = cord-324255-ize21we2 author = Fouchier, Ron A. M. title = Koch's postulates fulfilled for SARS virus date = 2003 pages = extension = .txt mime = text/plain words = 769 sentences = 44 flesch = 47 summary = Severe acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003). S evere acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003) . We inoculated two macaques with Vero-cellcultured SCV isolated from a fatal SARS case, and monitored their clinical signs, virus excretion and antibody response. The macaques excreted virus from the nose and throat at 2-6 d.p.i., as shown by polymerase chain reaction with reverse transcription (RT-PCR) and by virus isolation (see supplementary information). At gross necropsy, one macaque had severe multifocal pulmonary consolidation, and SCV infection was detected in lung tissue by RT-PCR and virus isolation. However, these were not present in SCV-inoculated macaques (results not shown), were not found consistently in SARS patients, and do not usually cause the lesions associated with SARS. cache = ./cache/cord-324255-ize21we2.txt txt = ./txt/cord-324255-ize21we2.txt === reduce.pl bib === id = cord-324344-dxuabscn author = Zhao, Xuesen title = LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date = 2020-04-05 pages = extension = .txt mime = text/plain words = 3152 sentences = 186 flesch = 48 summary = In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. Finally, the findings that LY6E inhibits human CoV entry cannot be evaded by ectopic 284 expression of membrane-associated serine protease TMPRSS2 and compromised by AmphoB 285 treatment strongly indicate that LY6E modulates virus entry via a distinct mechanism from that 286 IFITM proteins do (Figs. cache = ./cache/cord-324344-dxuabscn.txt txt = ./txt/cord-324344-dxuabscn.txt === reduce.pl bib === id = cord-323967-2mo915u1 author = Miersch, Shane title = Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date = 2020-11-01 pages = extension = .txt mime = text/plain words = 3231 sentences = 173 flesch = 57 summary = Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Moreover, the use of a highly stable framework 77 enabled facile and modular design of ultra-high affinity nAbs in tetravalent formats that retained 78 favorable drug-like properties and exhibited neutralization potencies that greatly exceeded those 79 of the bivalent IgG format. Fab-phage were screened by ELISA and those that exhibited >50% loss in binding 92 to RBD in the presence of 200 nM ACE2 were sequenced, revealing 34 unique clones (Fig. 1A) , 93 deemed to be potential nAbs and converted into the full-length human IgG1 format for 94 purification and functional characterization. cache = ./cache/cord-323967-2mo915u1.txt txt = ./txt/cord-323967-2mo915u1.txt === reduce.pl bib === id = cord-324102-75v4ebag author = Garcia Rodriguez, Alejandro title = SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? Case report date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1728 sentences = 110 flesch = 49 summary = title: SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? BACKGROUND: There are no published cases of tonic-clonic seizures and posterior bilateral blindness during pregnancy and Severe Acute Respiratory Syndrome (SARS) Coronavirus (COV) 2 (SARS-COV-2) infection. CONCLUSION: The authors conclude that SARS COV-2 infection could promote brain endothelial damage and facilitate neurological complications during pregnancy. That is the reason why we present a case report of a pregnant woman infected with SARS-COV-2 who showed seizures and sudden blindness. Therefore, we consider that SARS-COV-2 infection during pregnancy could increase the risk of suffering posterior reversible leukoencephalopathy or preeclampsia/eclampsia syndrome. To our knowledge, this is the first report of a patient with COVID-19 presenting preeclampsia associated with eclampsia versus posterior reversible leukoencephalopathy without alarm signs or symptoms. We consider further studies are needed to confirm that SARS-COV-2 infection is a risk factor to develop neurological complications of pregnant woman during pregnancy. cache = ./cache/cord-324102-75v4ebag.txt txt = ./txt/cord-324102-75v4ebag.txt === reduce.pl bib === id = cord-323940-ubazgvov author = Cafiero, Concetta title = Pharmacogenomics and Pharmacogenetics: In Silico Prediction of Drug Effects in Treatments for Novel Coronavirus SARS-CoV2 Disease date = 2020-10-13 pages = extension = .txt mime = text/plain words = 7359 sentences = 408 flesch = 34 summary = Recently, pharmacogenomics (the effects of a single genetic marker) and pharmacogenetics (the collective influence of variability across the genome to modulate an individual's drug response) have received great attention for their abilities to provide a new way to select drugs for personalized therapy (optimal dosing for maximizing drug efficacy or minimizing the risk of toxicity). 35 Search terms were "Covid-19", "novel coronavirus", "SARS-CoV2", "pharmacogenetics", "treatment/s", "adverse side effects", "therapy", "lung", "ocular", "pulmonary infection", "drugs", "drug response", "virus", "candidate drugs", "potential inhibitors", "protease inhibitors", "personalized medicine", "individual therapy", "pneumonia", "ACE", "heparin", "vasculitis", "conjunctivitis", "rhinitis", "hematological complication" and "main metabolic routes", either alone or in combination. Drugs in use as routine therapy or in clinical trials for Covid-19 include steroids and antiviral and biological humanized neutralizing antibodies against some proinflammatory cytokines, such as IL1, IL6, IFN, and TNFα, in addition to supportive measures and symptomatic treatment, according to the severity of the disease. cache = ./cache/cord-323940-ubazgvov.txt txt = ./txt/cord-323940-ubazgvov.txt === reduce.pl bib === id = cord-323685-gjocoa60 author = Tsai, Shang-Jui title = Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date = 2020-11-06 pages = extension = .txt mime = text/plain words = 5332 sentences = 289 flesch = 49 summary = The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Conclusion Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins. These antigen-responsive CD4+ and CD8+ populations were present nearly two months after the final boost injection, indicating that LSNME/S W1 vaccination had elicited a sustained cellular immune response to both of these SARS-CoV-2 structural proteins. As for the future development of the LSNME/S W1 vaccine, we anticipate that follow-on studies in larger animal models at doses comparable to other mRNA vaccines will demonstrate a desirable combination of safety, balanced immune responses, and when challenged, protection against SARS-CoV-2 infection and/or disease. cache = ./cache/cord-323685-gjocoa60.txt txt = ./txt/cord-323685-gjocoa60.txt === reduce.pl bib === id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3770 sentences = 212 flesch = 51 summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . cache = ./cache/cord-324295-9c1zxjng.txt txt = ./txt/cord-324295-9c1zxjng.txt === reduce.pl bib === id = cord-324246-liyk6mna author = Shakoor, Hira title = Be well: A potential role for vitamin B in COVID-19 date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2240 sentences = 132 flesch = 40 summary = Vitamin B assists in proper activation of both the innate and adaptive immune responses, reduces pro-inflammatory cytokine levels, improves respiratory function, maintains endothelial integrity, prevents hypercoagulability and can reduce the length of stay in hospital [7, 8] . In a recent preprint it is suggested that PLP supplementation mitigates COVID-19 symptoms by regulating immune responses, decreasing pro-inflammatory cytokines, maintaining endothelial integrity and preventing hypercoagulability [22] . J o u r n a l P r e -p r o o f Vitamin B not only helps to build and maintain a healthy immune system but it could potentially prevent or reduce COVID-19 symptoms or treat SARS-CoV-2 infection. In particular, vitamin B modulates immune response by downregulating pro-inflammatory cytokines and inflammation, reducing breathing difficulty and gastrointestinal problems, preventing hypercoagulability, potentially improving outcomes and reducing the length of stay in the hospital for COVID-19 patients. cache = ./cache/cord-324246-liyk6mna.txt txt = ./txt/cord-324246-liyk6mna.txt === reduce.pl bib === id = cord-324166-6ydn2bvy author = Kumar, Neeraj title = Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis date = 2020-08-20 pages = extension = .txt mime = text/plain words = 5482 sentences = 284 flesch = 45 summary = We found that Noscapine-Hydroxychloroquine (Nos-Hcq) conjugate has strong binding affinity for the main protease (Mpro) of SARS-CoV-2, which performs key biological function in virus infection and progression. Also, dynamical residue cross-correlation map with principal component analysis depicted the stable binding of Nos-Hcq conjugate to Mpro domains with optimal secondary structure statistics of complex dynamics. Similar binding sites were employed for performing the molecular docking of the noscapine conjugations with the target Mpro of coronavirus using the Hex 8.0 and SwissDock servers. With these significant results, it can be attributed that Nos-Hcq conjugate has a high potential to bind the target Mpro enzyme and further can be used as effective therapeutics for SARS-CoV-2. We report the efficient combinatorial therapy by conjugating the noscapine (antitussive drug) with potential hydroxychloroquine (Nos-Hcq) against the SARS-CoV-2, through the computational assays with insights into the experimental results. cache = ./cache/cord-324166-6ydn2bvy.txt txt = ./txt/cord-324166-6ydn2bvy.txt === reduce.pl bib === id = cord-323832-w19ump0o author = Mishra, Vijaya Nath title = Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection date = 2020-09-19 pages = extension = .txt mime = text/plain words = 2881 sentences = 183 flesch = 52 summary = It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. Since currently available antiviral drugs attack influenza and coronavirus after they have already infected the lung cells, it is important to target the virus and prevent infection in the first stage of viral infection. Phages in the body compete with the other highly infective eukaryotic viruses for cellular receptors and thereby restrict their harmful actions on the host cell [23] . A study of staphylococcal phages on the expression of genes which are involved in antimicrobial immunity in the A549 cell line showed that there is an increased translation of interleukin-2 (IL-2) [25] . e in vitro studies on bacteriophage influence on the ability of human viruses to infect epithelial cells cache = ./cache/cord-323832-w19ump0o.txt txt = ./txt/cord-323832-w19ump0o.txt === reduce.pl bib === id = cord-324345-j43rpvwk author = Leong, Hoe Nam title = SARS – My personal battle date = 2010-11-19 pages = extension = .txt mime = text/plain words = 3111 sentences = 219 flesch = 70 summary = I vividly remember the time when I first saw the index patient with Severe Acute Respiratory Syndrome (SARS) in Singapore. The index patient was admitted to Tan Tock Seng Hospital (TTSH) on Saturday, (1st March 2003), and an infectious disease consult was sought on the following Monday. It was an exceedingly busy day for me as I had to attend to new referrals, run an outpatient clinic, and subsequently draft a clinical summary of these two patients by the early evening. Eventually, the patient's fever defervesced on day 14 of illness. I wasn't scheduled to perform the ward round that day, but I returned to visit the patient that Sunday morning. My wife and I telephoned a colleague in Singapore and we concurred to have a full blood count test done at the clinic the next day. My wife eventually joined me when she developed fever at the end of the second day of arrival. With that news, my days as a patient in isolation continued. cache = ./cache/cord-324345-j43rpvwk.txt txt = ./txt/cord-324345-j43rpvwk.txt === reduce.pl bib === id = cord-324405-6uanhe2p author = Burke, Rachel M. title = Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date = 2020-09-02 pages = extension = .txt mime = text/plain words = 6616 sentences = 242 flesch = 41 summary = To interrupt transmission and facilitate early identification of secondary cases (i.e., transmissions of SARS-CoV-2 from the original travel-related case patient to a close contact), public health authorities at the state, county, and local levels, in consultation with subject-matter experts from the U.S. Centers for Disease Control and Prevention (CDC), mobilized rapidly to place the patients under appropriate isolation and identify contacts exposed to these patients. To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with � 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members and some healthcare personnel. cache = ./cache/cord-324405-6uanhe2p.txt txt = ./txt/cord-324405-6uanhe2p.txt === reduce.pl bib === id = cord-324328-olnwynfu author = Nakamichi, K. title = Outcomes associated with SARS-CoV-2 viral clades in COVID-19 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4633 sentences = 305 flesch = 49 summary = This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Even though we found several baseline clinical factors to be significantly associated with clade 2 in univariate analyses and history of malignancy in the multivariate model, rates of hospitalization were not significantly different between patients infected with the two major clades of virus in our study (p=0.063), nor were mortality rates (p=0.58). Patient demographics and clinical history were strongly predictive of hospitalization, and viral clade information did not substantially improve predictions, suggesting that it contributes minimally to determination of outcome. cache = ./cache/cord-324328-olnwynfu.txt txt = ./txt/cord-324328-olnwynfu.txt === reduce.pl bib === id = cord-324165-afdmsbw2 author = Joo, Heesoo title = The effects of past SARS experience and proximity on declines in numbers of travelers to the Republic of Korea during the 2015 MERS outbreak: A retrospective study date = 2019-08-31 pages = extension = .txt mime = text/plain words = 5124 sentences = 236 flesch = 56 summary = The results from regression models and sensitivity analyses demonstrated that areas with ≥100 SARS cases and closer proximity to the ROK had significantly larger percentage decreases in traveler volumes during the outbreak. This evaluation estimates the changes in numbers of non-citizen short-term visitor arrivals from selected areas to the ROK during the 2015 MERS outbreak and examines the correlation between travel volume declines and previous experience of the most similar sizable outbreak, the 2003 severe acute respiratory syndrome (SARS) outbreak. Although WHO did not recommend any travel restrictions to the ROK during the 2015 MERS outbreak [17] , WHO noted that raising awareness about Table 4 Monthly marginal percentage change between actual (2015) and baseline projected (average of 2013 and 2014) non-citizen arrivals to the Republic of Korea (ROK) associated with areas that experienced ≥100 probable severe acute respiratory syndrome (SARS) cases and distance to the Republic of Korea. cache = ./cache/cord-324165-afdmsbw2.txt txt = ./txt/cord-324165-afdmsbw2.txt === reduce.pl bib === id = cord-324325-rmlrhyf2 author = Chan, Wai S title = Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date = 2005-05-13 pages = extension = .txt mime = text/plain words = 3733 sentences = 225 flesch = 43 summary = Immunohistochemical studies on different human tissues, including a cohort of nine autopsies, two liver biopsies and intestinal biopsies of SARS patients, further confirmed the existence of coronaviral hypothetical and structural proteins in the cytoplasm of pneumocytes and small intestinal surface enterocytes in SARS patients. In those tissue sections showing positive signals for immunohistochemical staining, we further performed immunohistochemical studies using all other antibodies tested positive in SARS-CoV-infected Vero E6 cells. The cellular distribution of SARS-CoV protein and viral genome in immunohistochemical-positive lung and small intestine sections was further evaluated by immunofluorescence-fluorescence in situ hybridization analysis (Figure 4) . 3 In Vero E6 cells, positive cytoplasmic immunohistochemical signals were detected by Figure 3 Immunohistochemical studies of antipeptide antibody SARS-AbS13a against the nucleocapsid protein on small intestine sections. In addition, in the study of tissue sections, only those cells with viral genome detected by fluorescence in situ hybridization were positive for immunohistochemical stainings for the antipeptide antibodies. cache = ./cache/cord-324325-rmlrhyf2.txt txt = ./txt/cord-324325-rmlrhyf2.txt === reduce.pl bib === id = cord-324270-8rgkop42 author = Renaud-Picard, Benjamin title = Delayed pulmonary abscess following COVID-19 pneumonia: a case report date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1184 sentences = 80 flesch = 43 summary = The chest radiography showed bilateral diffuse ground-glass opacities that were consistent with a COVID-19 infection ( Figure 1A) . A nasopharyngeal swab, using RT-PCR, tested positive for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between Days 8 and 25 of hospitalization, three specific serologies for SARS-CoV-2 were performed, all of which strongly demonstrated positive IgM and IgG levels (BIOSYNEX COVID-19 BSS rapid test, Strasbourg, France). We believe that patients that present with a severe form of COVID-19 pneumonia would benefit from a well-defined and specific followup after hospital discharge, including early clinical examination, chest CT, and pulmonary-function tests. Figure 1 : A: Chest radiography showing bilateral diffuse ground-glass opacities, which are consistent with a COVID-19 infection, four days after symptom onset. B: Axial chest CT, one month after symptom onset, revealing one pulmonary abscess in the right lower lobe, which is associated with sub-pleural bilateral ground-glass opacities that are consistent with partially resolved moderate-to-severe COVID-19 pneumonia. cache = ./cache/cord-324270-8rgkop42.txt txt = ./txt/cord-324270-8rgkop42.txt === reduce.pl bib === id = cord-324518-a346cjx4 author = Zhang, Zhibin title = The outbreak pattern of the SARS cases in Asia date = 2004 pages = extension = .txt mime = text/plain words = 1935 sentences = 118 flesch = 54 summary = The increase rate of SARS cases is expected to decrease with the cumulative SARS cases, as described by the traditional logistical model, which is widely used in population dynamic studies. The maximum instantaneous rate of increase, basic reproductive number, and maximum cumulative SARS cases were also calculated by using the logistic model. The outbreak pattern of cumulative SARS cases is likely of a logistic type because at the initial stage, it grows exponentially, later due to the increasing control effort by people and/or due to depletion of susceptible individuals, the infection will be slowed down. significant and negative linear "density dependency" of the instantaneous rate of increase on the cumulative cases of SARS indicates that the outbreak pattern of SARS can be well described by the logistic model( Fig. 1(a) and (b) ). cache = ./cache/cord-324518-a346cjx4.txt txt = ./txt/cord-324518-a346cjx4.txt === reduce.pl bib === id = cord-324480-7u5lh4jx author = Sharma, A. title = Structural stability of SARS-CoV-2 degrades with temperature date = 2020-10-14 pages = extension = .txt mime = text/plain words = 1541 sentences = 88 flesch = 51 summary = Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter. However an understanding of how SARS-CoV-2 survives different environmental conditions is still incomplete and mechanisms of virus particle degradation are poorly mapped out. A key challenge in studying SARS-CoV-2 is the extreme level of threat associated with the live virus and the resultant need for high safety standards for such work. Here we used this technology to study the stability of the viral envelope and associated proteins (M, E, and S) under different environmental conditions. Environmental stability of SARS-CoV-2 on different types of surfaces under indoor and seasonal climate conditions cache = ./cache/cord-324480-7u5lh4jx.txt txt = ./txt/cord-324480-7u5lh4jx.txt === reduce.pl bib === id = cord-324307-2zbm4iwn author = Kam, Kai-qian title = A Well Infant With Coronavirus Disease 2019 With High Viral Load date = 2020-02-28 pages = extension = .txt mime = text/plain words = 1914 sentences = 123 flesch = 62 summary = A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. cache = ./cache/cord-324307-2zbm4iwn.txt txt = ./txt/cord-324307-2zbm4iwn.txt === reduce.pl bib === id = cord-323980-rcyjthze author = Willems, Laurent M. title = SARS-CoV-2-related rapid reorganization of an epilepsy outpatient clinic from personal appointments to telemedicine services: A German single-center experience date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4373 sentences = 186 flesch = 40 summary = METHODS: Documentations of telephone contacts and telemedicine consultations at the Epilepsy Center Frankfurt Rhine-Main were recorded in detail between March and May 2020 and analyzed for acceptance, feasibility, and satisfaction of the conversion from personal to telemedicine appointments from both patients' and medical professionals' perspectives. The aim of this study was to analyze the acceptance, feasibility, and satisfaction of the SARS-CoV-2-related conversion from face-to-face to telemedicine appointments from the perspectives of both patients and medical professionals. General understanding and acceptance of cancelations of elective face-to-face ambulatory visits and of the option to have telemedicine consultations during the SARS-CoV-2 pandemic in Germany was high, especially in patients with very urgent or urgent appointment priority. cache = ./cache/cord-323980-rcyjthze.txt txt = ./txt/cord-323980-rcyjthze.txt === reduce.pl bib === id = cord-324265-j3v3i8vm author = Marietta, Marco title = COVID-19, coagulopathy and venous thromboembolism: more questions than answers date = 2020-07-11 pages = extension = .txt mime = text/plain words = 5031 sentences = 242 flesch = 37 summary = The severity of the derangement of coagulation parameters in COVID-19 patients has been associated with a poor prognosis, and the use of low molecular weight heparin (LMWH) at doses registered for prevention of venous thromboembolism (VTE) has been endorsed by the World Health Organization and by Several Scientific societies. In these patients, low molecular weight heparin (LMWH) or unfractionated heparin (UFH) at doses registered for prevention of venous thromboembolism (VTE) seemed to be associated with a lower risk of death [10] and is currently recommended by the World Health Organization [11] and by several scientific societies [12] [13] [14] [15] [16] [17] [18] (Table 1) . cache = ./cache/cord-324265-j3v3i8vm.txt txt = ./txt/cord-324265-j3v3i8vm.txt === reduce.pl bib === id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 pages = extension = .txt mime = text/plain words = 14927 sentences = 720 flesch = 49 summary = In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. cache = ./cache/cord-324324-8ybfiz8f.txt txt = ./txt/cord-324324-8ybfiz8f.txt === reduce.pl bib === id = cord-324623-x6eom6kh author = Zhang, Jingyi title = Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4246 sentences = 286 flesch = 56 summary = This rapid review aims to explore the clinical effectiveness and safety of IVIG in the treatment of children with severe COVID-19. Methods: We systematically searched the literature on the use of IVIG in patients with COVID-19, Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS), including both adults and children. Results: A total of 1519 articles were identified by initial literature search, and finally six studies, included one randomized controlled trial (RCT), four case series and one case report involving 198 patients. The risk of death was not associated with the use of IVIG in the patients with ARDS (31) .A case report of three adults with COVID-19 reported that a high dose IVIG (25 g/d for 5 days) administered at the appropriate point could successfully block the progression of disease cascade (result of the clinical symptoms, laboratory inspection indicators and chest CT scan), and finally improve the outcome of COVID 19 (32) . cache = ./cache/cord-324623-x6eom6kh.txt txt = ./txt/cord-324623-x6eom6kh.txt === reduce.pl bib === id = cord-324557-4u8dja0n author = Leblanc, Jean‐François title = Risk of Transmission of Severe Acute Respiratory Syndrome Coronavirus‐2 by Transfusion: A Literature Review date = 2020-08-15 pages = extension = .txt mime = text/plain words = 3044 sentences = 195 flesch = 50 summary = Complementary searches have identified reports demonstrating that the correlation between the presence of viral RNA in a biological sample and infectivity requires a minimal RNA load, which is rarely, if at all observed, in blood components. More specifically, PubMed was interrogated with a series of queries aimed at identifying references that relate to COVID-19/SARS-CoV-2 and the detection of viral genomic material in blood, plasma, or serum. From this screen, 23 references reporting any data or stating any information on the detection of SARS-CoV-2 genomic material in human blood, plasma, or serum, were selected ( Table 2) . An exhaustive search strategy led to the identification of 23 references reporting data on the detection of SARS-CoV-2 genomic material in blood components (Table 2) . cache = ./cache/cord-324557-4u8dja0n.txt txt = ./txt/cord-324557-4u8dja0n.txt === reduce.pl bib === id = cord-324288-qgxswltx author = Padhi, Sunali title = Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study date = 2020-09-14 pages = extension = .txt mime = text/plain words = 3332 sentences = 179 flesch = 37 summary = title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study In the present study, we hypothesized that vitamin D deficiency would be associated with the SARS-CoV-2 infection rate and mortality in the Indian population. Further, a recent report highlighted a higher chance of SARS-CoV-2 infected patients being admitted to an intensive care unit compared to those with insufficient or sufficient levels of vitamin D in the UK population [9] . Low plasma 25(OH) vitamin D level is associated with increased risk of COVID-19 infection: an Israeli population-based study Current Scenario of Prevalence of Vitamin D Deficiency in Ostensibly Healthy Indian Population: A Hospital Based Retrospective Study Serum Vitamin D Levels and Alopecia Areata-A Hospital Based Case-Control Study from North-India Low levels of serum Vitamin D in chronic periodontitis patients with type 2 diabetes mellitus: A hospital-based crosssectional clinical study cache = ./cache/cord-324288-qgxswltx.txt txt = ./txt/cord-324288-qgxswltx.txt === reduce.pl bib === id = cord-324251-wgtatr8v author = Joshi, Madhvi title = Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology date = 2020-07-13 pages = extension = .txt mime = text/plain words = 608 sentences = 46 flesch = 57 summary = title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID. Positive selection of ORF3a and 477 ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic Full-genome sequences of the first two SARS-CoV-2 485 viruses from India cache = ./cache/cord-324251-wgtatr8v.txt txt = ./txt/cord-324251-wgtatr8v.txt === reduce.pl bib === id = cord-324357-ys4tqy5x author = nan title = Hygiene at home: A bulwark against COVID-19 to be protect from SARS-CoV-2 date = 2020-05-15 pages = extension = .txt mime = text/plain words = 681 sentences = 51 flesch = 67 summary = • by droplets emitted from the nose and mouth (splutering) when coughing, sneezing, but also when speaking, singing and screaming, • by direct contact between people: shaking hands, hugging, kissing, • secondarily through indirect contact: objects contaminated by an infected person. The National Academy of Medicine wishes to recall the fundamental rules of hygiene at home which it is essential to observe in the current epidemic context, especially in families with children. The respiratory hygiene rules are: • cover your mouth and nose if you cough or sneeze, preferably with a disposable tissue, throw away the tissue immediately and wash your hands immediately before touching anything. • avoid touching your face, nose, eyes and mouth, which can spread respiratory viruses through contaminated hands; • ventilate the housing by opening the windows for at least 20 min in the morning and evening and during houseworking. Hydro-alcoholic solutions disinfect but do not clean: so they cannot replace washing with soap and water when hands are dirty. cache = ./cache/cord-324357-ys4tqy5x.txt txt = ./txt/cord-324357-ys4tqy5x.txt === reduce.pl bib === id = cord-324800-l8xl4g2a author = Eisenberg, Michael L. title = Coronavirus Disease 2019 (COVID-19) and men’s reproductive health date = 2020-04-22 pages = extension = .txt mime = text/plain words = 682 sentences = 45 flesch = 54 summary = As the COVID-19 pandemic rages across the world, the scientific community continues to study the pathophysiology of SARS-Cov-2 virus to guide transmission, susceptibility, and treatment. While cardiac, ocular, and neurologic symptoms of the COVID-19 have been reported, the reproductive implications of coronavirus infection remain unknown. Indeed, the current report was not able to assess any changes in semen quality among the participants thus it remains unknown how and if the fecundability of infected men is impaired. In addition, as more than 80% of those who are infected by the coronavirus are asymptomatic, the reproductive implications for these men would likely be favorable but also remains unknown. But given the current impact of the pandemic on the world, the likelihood the virus will remain for some time, and that over 100 million babies are born every year, the reproductive implications of SARS-Cov-2 should be further studied. cache = ./cache/cord-324800-l8xl4g2a.txt txt = ./txt/cord-324800-l8xl4g2a.txt === reduce.pl bib === id = cord-324531-lpoelp91 author = Artesi, Maria title = A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2882 sentences = 185 flesch = 61 summary = title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. The cobas system (Roche) implements a dual-target assay to detect SARS-CoV-2, with qRT-PCRs targeting both the ORF1ab region and the E gene (see Fig. S1 in the supplemental material). We speculated that these samples carried a common variant that interfered with the E gene qRT-PCR and carried out whole-genome sequencing of the viruses using the Artic Network protocol (17) . cache = ./cache/cord-324531-lpoelp91.txt txt = ./txt/cord-324531-lpoelp91.txt === reduce.pl bib === id = cord-324856-hf969tav author = Abir, Tanvir title = Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4144 sentences = 221 flesch = 53 summary = title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys Since the sheer illness of the whole country is sufficient to destroy the health care system, this current study is to examine changes of individual perception of risk for contracting SARS-Cov-2, and the awareness level in Bangladesh during the early and late lockdowns implemented by the government of Bangladesh. In this study, males who were worried about contracting SARS-Cov-2 were more likely to perceive themselves as being at high risk of contracting the infection, as well as those who did not quarantine themselves or only did so at the request of the public health officers. Moreover, in India, it was found that a higher level of knowledge on COVID-19 was associated with the high-risk perception of contracting the infection during the consistent lockdown period [28] . cache = ./cache/cord-324856-hf969tav.txt txt = ./txt/cord-324856-hf969tav.txt === reduce.pl bib === id = cord-324707-9ld73wv1 author = Mitjà, Oriol title = Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date = 2020-07-16 pages = extension = .txt mime = text/plain words = 4268 sentences = 263 flesch = 54 summary = Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . cache = ./cache/cord-324707-9ld73wv1.txt txt = ./txt/cord-324707-9ld73wv1.txt === reduce.pl bib === id = cord-324619-y7gilopu author = Alam, S.B. title = Severe acute respiratory syndrome coronavirus‐2 may be an underappreciated pathogen of the central nervous system date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5244 sentences = 254 flesch = 42 summary = In this review, we examine some of the most recent data of COVID-19-associated neurological disease and the possibility that SARS-CoV-2 may be infecting the CNS. suggested that since SARS-CoV-2 shared significant similarities to severe acute respiratory syndrome coronavirus (SARS-CoV), it was entirely possible that SARS-CoV-2 could similarly penetrate the brain and CNS of infected patients through synapses in the medullary cardiorespiratory center and thereby cause respiratory failure (5) . Similar to these neurotropic HCoVs, SARS-CoV-2 infection in the lungs of some COVID-19 patients may also lead to entry into the CNS and this could occur via two main pathways: i) infection of peripheral nerves and retrograde axonal transport; and/or ii) hematogenous spread and infection of the cells of the blood-brain barrier. In this review, we have extrapolated information from other neurotropic viruses to make some predictions and it is clear that SARS-CoV-2 has the potential to infect the CNS and cause long-term neurologic damage in COVID-19 patients. cache = ./cache/cord-324619-y7gilopu.txt txt = ./txt/cord-324619-y7gilopu.txt === reduce.pl bib === id = cord-324644-sz5n7a5z author = Rehman, Mahin title = Atypical Manifestation of COVID-19-Induced Myocarditis date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1906 sentences = 91 flesch = 45 summary = There was a case report that described a patient with COVID-19 with regional wall motion abnormalities who had a biopsy consistent with lymphocytic myocarditis but histopathological and viral genomic polymerase chain reaction (PCR) analysis of the biopsy did not reveal the SARS-CoV-2 viral genome to be present within the myocytes [3] . With this report, we aim to highlight an atypical presentation of COVID-19 (SARS-CoV-2)induced myocarditis as this patient was completely afebrile and had no respiratory symptoms, both of which are typical characteristics. Current consensus around COVID-19-induced myocardial injury is to maintain conservative management especially in those without suspected acute coronary syndrome (ACS) who have mild troponin elevation, as in our young patient. COVID-19-induced myocardial injury can present as a STEMI or non-STEMI (given the evidence of troponin leak) and without concurrent febrile illness or respiratory symptoms of the disease. cache = ./cache/cord-324644-sz5n7a5z.txt txt = ./txt/cord-324644-sz5n7a5z.txt === reduce.pl bib === id = cord-324727-bj8oei0v author = Zhang, Xiaomei title = Management of Digestive Disorders and Procedures Associated With COVID-19 date = 2020-06-03 pages = extension = .txt mime = text/plain words = 1864 sentences = 129 flesch = 42 summary = The Chinese Gastroenterology Expert Group, comprising experts from the gastroenterology units and national medical aid teams of the epidemic region of Wuhan, along with the Chinese Society of Gastroenterology introduce and recommend this management consensus for digestive disorders in patients with COVID-19. Liver injury in patients with COVID-19 may be caused by either systemic inflammation or direct effects of SARS-CoV-2 on the angiotensin-converting enzyme 22 of cholangiocytes (13) . To prevent or control the transmission of SARS-CoV-2 in epidemic communities, gastroenterological procedures such as esophageal pH test, gastrointestinal motility, hydrogen breath test, fecal microbiota transplantation, Helicobacter pylori breath test, and stool antigen detection are recommended for suspension or postponement until the epidemic is under control. Don't overlook digestive symptoms in patients with 2019 novel coronavirus disease (COVID-19) Digestive symptoms in COVID-19 patients with mild disease severity: Clinical presentation, stool viral RNA testing, and outcomes cache = ./cache/cord-324727-bj8oei0v.txt txt = ./txt/cord-324727-bj8oei0v.txt === reduce.pl bib === id = cord-324638-gwd8qin6 author = Chiu, Rossa WK title = Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date = 2006-02-09 pages = extension = .txt mime = text/plain words = 3360 sentences = 152 flesch = 49 summary = We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. cache = ./cache/cord-324638-gwd8qin6.txt txt = ./txt/cord-324638-gwd8qin6.txt === reduce.pl bib === id = cord-324888-oak27okj author = Leng, Ling title = Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2814 sentences = 155 flesch = 46 summary = title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. Therefore, we wonder whether there are some key local microenvironment proteins specifically expressed on the surface of airway EpC that makes the virus prefer airway EpCs. In some cases, additional cell surface molecules or co-receptors are required for sufficient viral entry into host cells. We used the human protein atlas (HPA) database [16] to extract the protein expression level of 65 receptors involved in "virus receptor activity" (GO:0001618) of EpCs and epithelial or epithelial-derived cells from 14 organs (16 cell types) ( Figure 1A and Supplementary Materials and Methods). cache = ./cache/cord-324888-oak27okj.txt txt = ./txt/cord-324888-oak27okj.txt === reduce.pl bib === id = cord-324919-ciamusjs author = Scialo, Filippo title = ACE2: The Major Cell Entry Receptor for SARS-CoV-2 date = 2020-11-10 pages = extension = .txt mime = text/plain words = 5356 sentences = 257 flesch = 42 summary = Since the beginning of the COVID-19 pandemic, hypertension and diabetes have been correlated with higher risk of mortality, and initial reports speculated that angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs), which are commonly used therapeutic agents for these conditions, would up-regulate ACE2 expression, thus increasing the risk of severe illness [37] . Binding of S1 subunit of the Spike protein of SARS-CoV-2 to the ACE2 receptor triggers the cleavage of ACE2 by ADAM17/tumor necrosis factorconverting enzyme (TACE) at the ectodomain sites [41] and a soluble form that retains its catalytic activity (sACE2) is produced [42] . ACE2 shedding can be stimulated by proinflammatory cytokines such as IL-1β and tumor necrosis factor (TNF)-α, and endotoxin [47] that could result in a positive effect reducing SARS-CoV-2 entry, but at the same time, may cause an increase in AngII and further activation of the AngII/AT1R axis worsening inflammation (discussed below) (Fig. 1) . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-324919-ciamusjs.txt txt = ./txt/cord-324919-ciamusjs.txt === reduce.pl bib === id = cord-324938-2lu9z5b2 author = Wu, Li-Ping title = Duration of Antibody Responses after Severe Acute Respiratory Syndrome date = 2007-10-17 pages = extension = .txt mime = text/plain words = 1478 sentences = 84 flesch = 60 summary = Among 176 patients who had had severe acute respiratory syndrome (SARS), SARS-specific antibodies were maintained for an average of 2 years, and significant reduction of immunoglobulin G–positive percentage and titers occurred in the third year. Both the OD readings (0.93) and positive percentages peaked at 90-120 days; however, the rate of reduction of the average OD readings was much faster, dropping by 22% (0.73) and 40% (0.54) at 1 and 2 years, respectively, after symptom onset (Figure 1) . Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Longitudinal profi le of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus Longitudinal analysis of severe acute respiratory syndrome (SARS) coronavirus-specifi c antibody in SARS patients cache = ./cache/cord-324938-2lu9z5b2.txt txt = ./txt/cord-324938-2lu9z5b2.txt === reduce.pl bib === id = cord-324752-t50bg7pq author = Lavery, Michael Joseph title = Cutaneous manifestations of COVID-19 in children (and adults): A virus that does not discriminate date = 2020-11-01 pages = extension = .txt mime = text/plain words = 2649 sentences = 185 flesch = 49 summary = COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a beta coronavirus with a characteristic S-glycoprotein 'spike' on the cell surface.(1) Initial reports did not include cutaneous manifestations as a feature of COVID-19; however, there is a growing repertoire of reports demonstrating an array of dermatologic manifestations on the skin in children and adults. Dermatologic afflictions have been summarized into different categories several times, with the most recent analysis identifying six clinical patterns: urticaria, maculopapular-morbilliform eruption, papulovesicular exanthem, chilblain-like acral pattern, livedo reticularis-livedo racemose pattern, and purpuric 'vasculitic' pattern.(2) In children, the dermatologic features appear to occur before or concomitantly with other COVID-19 manifestations. 24 Recently, nail changes have been identified in patients with COVID-19 manifesting as a convex half-moon shaped erythematous band at the distal margin of the lunula and coined 'the red half-moon nail sign.' 25, 26 In the United Kingdom (UK), researchers analyzed data from users of the COVID Symptom Study application and noted 8.8% of 336,847 users, with a positive SARS-CoV-2 viral swab, reported a skin eruption. cache = ./cache/cord-324752-t50bg7pq.txt txt = ./txt/cord-324752-t50bg7pq.txt === reduce.pl bib === id = cord-324963-zg3ghl2m author = Salzberger, B. title = COVID-19 – eine neue und vielseitige Herausforderung date = 2020-08-03 pages = extension = .txt mime = text/plain words = 877 sentences = 127 flesch = 46 summary = Affinität zum ACE2-Rezeptor kann die Infektion in den oberen Atemwegen stattfinden Das Virus ist ein neues β-Coronavirus, das vermutlich von Fledermäusen auf eine noch unbekannte Säugerspezies übergesprungen ist. Es bindet wie SARS-CoV an den Angiotensinconverting-enzyme-2(ACE2)-Rezeptor, aber mit einer sehr viel höheren Affinität, sodass die Infektion in den oberen Atemwegen stattfinden kann. In einer ersten großen genomweiten Studie konnten einige genetische Faktoren als Risiken identifiziert werden, für eine individuelle Risikoabschätzung sind alle diese Daten jedoch noch nicht geeignet [5] . Die schweren Krankheitsverläufe einer Infektionskrankheit mit der realen Gefahr nosokomialer Infektionen konnten spezialisierte Infektions-oder Intensivmediziner nicht allein behandeln, es waren breit interdisziplinäre Teams im Einsatz, die von der Diagnostik über die Therapie bis zu Isolations-und Quarantänestrategien ein breites Portfolio von klinischen und organisatorischen Aufgaben lösten. Immunmodulatorische Therapien sind bisher kaum systematisch evaluiert worden, in einer randomisierten Studie aus Großbritannien konnte gerade erstmals gezeigt werden, dass Dexamethason bei schwer verlaufender COVID-19-Erkrankung die Prognose verbessert [9] . Epidemiologie von SARS-CoV-2-Infektion und COVID-19 cache = ./cache/cord-324963-zg3ghl2m.txt txt = ./txt/cord-324963-zg3ghl2m.txt === reduce.pl bib === id = cord-324651-8teb5jrn author = Filippini, Antonio title = Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2052 sentences = 97 flesch = 43 summary = title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? In the present opinion article we highlight evidence from different laboratories to drive the attention of the scientific community on the role played by endo-lysosomal Two-Pore Channels (TPCs) in viral infection. In particular, cross linking our recent data and existing literature, we focus on evidence indicating that virus intracellular pathway could be targeted by a novel occurring TPCs inhibitor, the flavonoid Naringenin. Intriguingly, our recent evidence has shown that the activity of human TPC channels can be inhibited by a natural flavonoid compound, in fact present in citruses and tomatoes, Naringenin (Pafumi et al., 2017) . In conclusion, these considerations offer a perspective on specific molecular targets, TPCs, and underpin a role for Naringenin as pharmacological blockade of SARS-CoV-2 infectivity providing further support for exploration of TPCs inhibition as novel antiviral therapy. cache = ./cache/cord-324651-8teb5jrn.txt txt = ./txt/cord-324651-8teb5jrn.txt === reduce.pl bib === id = cord-324902-18h0maxi author = Liu, Xuemei title = Patterns of IgG and IgM antibody response in COVID-19 patients date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1117 sentences = 66 flesch = 54 summary = As shown in Figure 1 , anti-SARS-CoV-2 S-specific IgG and IgM antibodies were not detectable in the very early days of infection (from day 0 to day 3). Anti-SARS-CoV-2 S-specific IgG antibodies were identifiable from day 7 onwards, peaking at approximately day 25, as shown in Figure 1(A) . Figure 1(B) shows a typical IgG and IgM antibody response in a 65-year-old woman with COVID-19 (supplementary materials, Table 1 ). As shown in Figure 1 (C), serum IgG antibody levels were not significantly correlated with clinical severity in the early stage of infection. Severe cases of COVID-19 tended to have a more vigorous IgG response against SARS-CoV-2 compared with mild cases. Our results also showed that mild cases tended to develop faster peak anti-SARS-CoV-2 S-specific IgM responses (approximately 17 days after symptom onset) compared with severe cases (approximately 21 days after symptom onset). cache = ./cache/cord-324902-18h0maxi.txt txt = ./txt/cord-324902-18h0maxi.txt === reduce.pl bib === id = cord-325113-sou8xyld author = Kuiper, Johannes W. P. title = Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date = 2020-11-02 pages = extension = .txt mime = text/plain words = 4973 sentences = 241 flesch = 51 summary = The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. cache = ./cache/cord-325113-sou8xyld.txt txt = ./txt/cord-325113-sou8xyld.txt === reduce.pl bib === id = cord-324926-3c5ab73l author = Xia, Shuai title = A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike date = 2019-04-10 pages = extension = .txt mime = text/plain words = 10849 sentences = 515 flesch = 55 summary = Therefore, it is reasonable to speculate that HR1 could also be a good target for the development of fusion inhibitors against highly pathogenic HCoVs. We and others have reported that peptides derived from the HR2 regions of SARS-CoV and MERS-CoV S proteins can competitively inhibit viral 6-HB formation, thereby preventing viral fusion and entry into host cells (18, 27) . Moreover, structural studies of EK1 in complex with HR1s from different HCoVs explain the conserved basis for the HR1-EK1 interaction, further indicating that HR1 region could serve as a promising target site for the development of broad-spectrum pan-CoV fusion inhibitors. On the other hand, HR2P peptides derived from the two -HCoVs, i.e., 229E and NL63, showed potent and broad inhibitory activity against -HCoV S-mediated cell-cell fusion with IC 50 values ranging from 0.13 to 0.51 M or from 0.21 to 0.56 M, respectively, but no effective inhibitory activity against -HCoVs (including MERS-CoV, SARS-CoV, and OC43) S-mediated fusion ( Fig. 1D and table S1 ). cache = ./cache/cord-324926-3c5ab73l.txt txt = ./txt/cord-324926-3c5ab73l.txt === reduce.pl bib === id = cord-325197-j1uo8qmf author = Crimi, Ettore title = Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date = 2020-08-20 pages = extension = .txt mime = text/plain words = 6066 sentences = 342 flesch = 34 summary = Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. The goal of the review was to provide an appropriate pathogenic scenario in which epigenetic-sensitive mechanisms and epidrugs may be clinically useful to stratify risk and treatment of patients in ICU affected by severe viral respiratory infections. Here, we give an update on clinical evidence about the usefulness of novel and FDA-approved drugs interfering with epigenetic pathways, which were applied to ICU patients affected by highly pathogenic strains of influenza virus and CoV, with a particular interest about the novel SARS-CoV-2 (Table 4 ). cache = ./cache/cord-325197-j1uo8qmf.txt txt = ./txt/cord-325197-j1uo8qmf.txt === reduce.pl bib === id = cord-324892-mg2dziuw author = Carneiro, João title = CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 901 sentences = 76 flesch = 48 summary = The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens cache = ./cache/cord-324892-mg2dziuw.txt txt = ./txt/cord-324892-mg2dziuw.txt === reduce.pl bib === id = cord-325261-bdumhy5b author = Clemente, Valentino title = Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19 date = 2020-05-15 pages = extension = .txt mime = text/plain words = 7815 sentences = 380 flesch = 44 summary = Since viral PLPs are used by coronaviruses to both replicate and to antagonize the innate immune response, they are considered important therapeutic targets for coronavirus infections and thus may be of interest for future COVID-19 treatment strategies. The multifunctional activities of PLPs, namely as cysteine proteases, DUBs and deISGylating enzymes, play two important roles in coronavirus pathogenesis: the first involves the production of non-structural proteins (nsp) required for the replication process and the second consists of blocking the innate immune system of the infected host cell. Since it is known that cellular antiviral pathways include (de)ubiquitination within their regulatory mechanisms [14, 15] , PLPs are believed to contribute to infection pathogenesis by using their intrinsic DUB and deISGylating activities to antagonize the activation of the host cell innate immune response [5] . Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression cache = ./cache/cord-325261-bdumhy5b.txt txt = ./txt/cord-325261-bdumhy5b.txt === reduce.pl bib === id = cord-325014-n7mnhk2v author = Gujski, Mariusz title = Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date = 2020-10-11 pages = extension = .txt mime = text/plain words = 4892 sentences = 254 flesch = 49 summary = As the time window for a positive RT-PCR result is short, serological testing, which provides information about whether a person has been exposed to SARS-CoV-2, may be useful for epidemiological purposes to detect the overall burden of previous infection in a given community. The aim of this study was to determine the prevalence of current and past SARS-CoV-2 infections among police employees, a high-risk population due to their professional duties, during the COVID-19 epidemic. Neither sex (p =0.155) nor other variables listed in Figure 2 were significantly associated with the IgG results ( Figure 2 A logistic regression model predicting a positive anti-SARS-CoV-2 IgM+IgA index was developed (Cox and Snell R Square at 0.015 andNagelkerke R Square at 0.033). After including all variables listed in Figures 1 and 2 along with the number of registered cases and deaths due to COVID-19 (per 10,000 inhabitants), only 4 variables showed a correlation with a positive anti-SARS-CoV-2 IgM+IgA index. cache = ./cache/cord-325014-n7mnhk2v.txt txt = ./txt/cord-325014-n7mnhk2v.txt === reduce.pl bib === id = cord-325055-todb1d4x author = Rychter, Anna Maria title = Should patients with obesity be more afraid of COVID‐19? date = 2020-06-24 pages = extension = .txt mime = text/plain words = 3270 sentences = 217 flesch = 49 summary = Furthermore, obesity is increasingly considered as a yet another risk factor, particularly, because it has been observed that people suffering from excessive body weight may experience a more severe course of COVID‐19 infection. Although the data regarding the impact of SARS-CoV-2 in individuals with obesity are limited and their association has not been fully defined yet, it has been observed that people suffering from excessive body weight may experience a more serious COVID-19 infection. 68 Whether the obesity paradox will be present among COVID-19 patients remains to be seen, nevertheless, the phenomenon was reported among other respiratory diseases, such as COPD or ARDS. 53, 69 Its pathophysiological basis remains unknown; however, an increased BMI seems to be associated with a better survival and a slower decline in the lung function in patients with a mild course of chronic obstructive pulmonary disease. Obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Association of obesity with disease severity among patients with COVID-19. cache = ./cache/cord-325055-todb1d4x.txt txt = ./txt/cord-325055-todb1d4x.txt === reduce.pl bib === id = cord-325134-z9n17z72 author = Nolan, Brodie title = Recommendations for emergency departments receiving patients with vital signs absent from paramedics during COVID-19 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1693 sentences = 86 flesch = 49 summary = Due to their small size and potential to be suspended in the air for prolonged periods, additional precautions are required for health care workers who are exposed to AGMPs. Obtaining an accurate history and COVID-19 risk factors for patients in cardiac arrest is difficult; therefore, we suggest presuming all patients presenting vital signs absent (VSA) to be infectious with COVID-19. The purpose of this study is to provide recommendations to enhance staff and patient safety during COVID-19 by reducing unnecessary exposure to AGMPs for ED staff, paramedics, and other ED patients when receiving patients with VSA. 3 To aid in justification of our recommendations, we present a brief summary of available evidence regarding common AGMPs that occur during cardiopulmonary resuscitation (CPR) and the risks of transmission to health care workers ( Figure 1 ). cache = ./cache/cord-325134-z9n17z72.txt txt = ./txt/cord-325134-z9n17z72.txt === reduce.pl bib === id = cord-324949-sqy03dks author = Poe, Francis L. title = N-Acetylcysteine: a potential therapeutic agent for SARS-CoV-2 date = 2020-05-30 pages = extension = .txt mime = text/plain words = 3485 sentences = 208 flesch = 47 summary = In vivo, in vitro, and human clinical trials have demonstrated N-acetylcysteine (NAC) as an effective method of improving redox status, especially when under oxidative stress. Mediation of the viral load could occur through NAC's ability to increase cellular redox status via maximizing the rate limiting step of glutathione synthesis, and thereby potentially decreasing the effects of virally induced oxidative stress and cell death. The pathogenic factors of SARS-CoV-2 that could possibly be mediated by NAC are (1) T cell exhaustion, which manifests as lower counts and decreased functional capacity of CD4+ and CD8+ cells; (2) pro-inflammatory state via increase in TNF-ɑ, IL1β, IL18; and (3) modulation of viral activity through increased glutathione. Mediation of the viral load could occur through the ability of NAC to increase cellular redox status by maximizing the rate limiting step of glutathione synthesis, and thereby decreasing the effects of virally induced oxidative stress and cell death. cache = ./cache/cord-324949-sqy03dks.txt txt = ./txt/cord-324949-sqy03dks.txt === reduce.pl bib === id = cord-325070-583innd7 author = Lee, Lennard Y.W. title = Utility of COVID-19 Screening in Cancer Patients date = 2020-07-24 pages = extension = .txt mime = text/plain words = 1121 sentences = 61 flesch = 41 summary = We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care in the era of COVID-19. Patients with cancer are at increased risk of contracting SARS-CoV-2 and have a high mortality rate from COVID-19 (Lee et al., 2020) . A number of national and international cancer guidelines now advise the screening of every patient undergoing chemotherapy to enable early identification and isolation of patients with asymptomatic SARS-CoV-2 infections to prevent hospital transmission (https://www.idsociety.org/practice-guideline/covid-19-guidelinediagnostics/; https://www.rcr.ac.uk/sites/default/files/guidance-covid19-testing-asymptomatic-hcw-patientsoncology.pdf; https://www.asco.org/sites/new-www.asco.org/files/content-files/2020-ASCO-Guide-Cancer-COVID19.pdf). Our cohort demonstrates that uptake for screening of SARS-CoV-2 through nasopharyngeal testing is high in cancer patients. We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care; this will be monitored as the pandemic evolves. Screening for COVID-19 in asymptomatic patients with cancer in a hospital in the United Arab Emirates cache = ./cache/cord-325070-583innd7.txt txt = ./txt/cord-325070-583innd7.txt === reduce.pl bib === id = cord-325038-q7gxw1go author = Joyce, Andrew A title = Changes in Interventional Pain Physician Decision-Making, Practice Patterns, and Mental Health During the Early Phase of the SARS-CoV-2 Global Pandemic date = 2020-08-31 pages = extension = .txt mime = text/plain words = 4519 sentences = 224 flesch = 43 summary = The survey consisted of a series of questions assessing prepandemic physician demographics and practice patterns, as well as new beliefs and behaviors following government-based medical policy changes resulting from the SARS-CoV-2 global pandemic (Supplementary Data). Multiple linear and logistic regression models were fit to continuous and dichotomous dependent variables, respectively, with independent variables consisting of the following: age, sex, training background (primary residency), number of years since completion of training, geographic region (Northeast, Midwest, South, Northwest, and international), regional density (rural, suburban, or urban) of practice location, practice setting (private practice, academic/university, hospital system employee, or other), prepandemic clinic/ procedure volumes, and personal relationship with someone who had tested positive for SARS-CoV-2 infection (defined as a positive test for the respondent, someone they live with, a personal patient, staff member they work with, or colleague in the group). cache = ./cache/cord-325038-q7gxw1go.txt txt = ./txt/cord-325038-q7gxw1go.txt === reduce.pl bib === id = cord-325172-a8ntxnmm author = Yip, Ming Shum title = Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus date = 2014-05-06 pages = extension = .txt mime = text/plain words = 5791 sentences = 253 flesch = 44 summary = More recently, we demonstrated that anti-Spike antibody potentiates infection of both monocytic and lymphoid immune cell lines, not only by SARS-CoVpp but also by replication-competent SARS-coronavirus [16] , thus providing evidence for a novel and versatile mechanism by which SARS-CoV can enter into target cells that do not express the conventional ACE2 virus receptor and are otherwise refractory to the virus. Finally, we have provided evidence that the intracellular signaling motifbut not the IgG binding motifof the FcγR is the key molecular determinant for triggering ADE of SARS-CoVpp. Our findings conclusively demonstrate that anti-spike serum promotes internalization of SARS-CoV by human macrophages. All the endodomain-truncated constructs (FcγRIIA-H.ΔIC, FcγRIIA-R.ΔIC and FcγRIIB.ΔIC, corresponding to constructs 2, 6, 11 respectively) were not susceptible to ADE of infection, indicating that binding of anti-Spike IgG-SARS-CoVpp immune complexes was not sufficient to mediate entry and that the signaling-competent endodomain was required. cache = ./cache/cord-325172-a8ntxnmm.txt txt = ./txt/cord-325172-a8ntxnmm.txt === reduce.pl bib === id = cord-325213-e6i6buow author = Mak, Ivan Wing Chit title = Risk factors for chronic post-traumatic stress disorder (PTSD) in SARS survivors date = 2010-09-15 pages = extension = .txt mime = text/plain words = 4871 sentences = 254 flesch = 46 summary = BACKGROUND: Post-traumatic stress disorder (PTSD) is one of the most prevalent long-term psychiatric diagnoses among survivors of severe acute respiratory syndrome (SARS). Previous reported predictors of acute psychiatric complications include sociodemographic variables [e.g., being a health care worker (HCW)] [11] [12] [13] ; illness-related variables [e.g., the severity of disease and the administration of high-dose corticosteroids [11] , lowest level of arterial oxygen saturation (SaO 2 ) during hospitalisation] [14] ; and psychosocial variables including social support, cognitive appraisal and coping style [13, 15] . In the univariate analysis, variables significantly associated with current PTSD in the predictor block included female gender (P=.019), being a HCW(P=.031), pre-SARS chronic medical illness (P=.044) and having AVN as a complication (P=.035) ( Table 1) . Logistic regression of predictor and association factor block Multivariate logistic regression analysis showed that being of the female gender (P=.003), the presence of chronic medical illness before SARS (P=.014) and having AVN as a physical complication (P=.01) were predictors of PTSD at 30 months post-SARS (Table 3) . cache = ./cache/cord-325213-e6i6buow.txt txt = ./txt/cord-325213-e6i6buow.txt === reduce.pl bib === id = cord-325045-ak7rouhb author = Sotgiu, Giovanni title = Advanced forecasting of SARS‐CoV‐2‐related deaths in Italy, Germany, Spain, and New York State date = 2020-05-11 pages = extension = .txt mime = text/plain words = 718 sentences = 37 flesch = 52 summary = Based on this model, we aimed at predicting SARS-Cov-2-related mortality in Italy, 7 Germany, 8 Spain, 9 and New York State. 10 To validate the model, we calculated R 2 correlations for Italy (0.995), Germany (0.996), Spain (0.988), and New York State (0.998) after 30, 18, 11, and 10 days of prediction, respectively, thus confirming the reliability of our modeling approach during the first month of this outbreak in each of these countries ( Figure 1A) . Instead, the expected SARS-Cov-2related mortality is more closely related to early events within the first days of the outbreak and to timing to regional/national interventions (eg, social distancing, confinement), which suggests that superspreading events (eg Lombardia region, Italy) deeply impact on the magnitude of the curve and, in turn, on the number of deaths. Figure 1B illustrates the curves of the expected deaths based on daily peak after 28 and 21 days in Italy, Germany, Spain, and New York State. cache = ./cache/cord-325045-ak7rouhb.txt txt = ./txt/cord-325045-ak7rouhb.txt === reduce.pl bib === id = cord-325019-hznnoxw6 author = Benavides-Cordoba, Vicente title = Drug Repositioning for COVID-19 date = 2020-06-30 pages = extension = .txt mime = text/plain words = 2897 sentences = 165 flesch = 45 summary = In this review, we present a selection of drugs, of different classes and with potential activity against COVID-19, whose trials are ongoing; and as proofs of concept, double blind, add-on event-driven, would allow proposing research that generates results in less time and preserving quality criteria for drug development and approval by regulatory agencies. Likewise, when researching new molecules in humans, it is necessary to ask several questions that could improve the designs, and avoid some failures, such as, for example, did the drug hit the target?, did the medication change the target?, what was the dose response?, and what are the characteristics of the study patients?. Hydroxychloroquine, a chloroquine analog, is a medicine widely used in the treatment of systemic autoimmune diseases 35 , being currently the most studied drug for treating COVID-19. In COVID 19, 133 clinical trials are registered, taking different degrees of severity, ranging from prophylactic use in the general population and in health workers 38 to patients with severe acute respiratory syndrome (SARS). cache = ./cache/cord-325019-hznnoxw6.txt txt = ./txt/cord-325019-hznnoxw6.txt === reduce.pl bib === id = cord-324953-3sacf4wu author = Childs, James E. title = Introduction: Conceptualizing and Partitioning the Emergence Process of Zoonotic Viruses from Wildlife to Humans date = 2007 pages = extension = .txt mime = text/plain words = 9017 sentences = 379 flesch = 40 summary = The process of zoonotic disease emergence can be understood by coupling knowledge of how zoonotic viruses have evolved and are maintained among their wildlife hosts, transmitted across a species barrier to cause productive infection in a taxonomically distinct secondary host, initiate a pathologic process causing disease, and, by repetitive infection within the secondary host species, result in incident morbidity or mortality of sufficient magnitude to be detected and characterized as a novel health concern of local, regional, or global significance (see the chapter by Childs, this volume). The ecologic process of zoonotic disease emergence can be schematized by four transition stages (Fig. 1 ) , of which only the first two are prerequisites for emergence: (1) contact between infectious propagules originating from the wildlife H R with individuals of a susceptible H S and (2) cross-species transmission, a transition subsuming the complex interactions of the virus infectious cycle within the H S (Nayak 2000; Childs 2004 ). cache = ./cache/cord-324953-3sacf4wu.txt txt = ./txt/cord-324953-3sacf4wu.txt === reduce.pl bib === id = cord-325320-v9e2axf4 author = Vigil‐De Gracia, P. title = Pregnancies recovered from SARS‐CoV‐2 infection in the second and third trimesters: obstetric evolution date = 2020-09-30 pages = extension = .txt mime = text/plain words = 811 sentences = 46 flesch = 54 summary = However we do not know the maternal and perinatal results of pregnant women recovered from SARS-CoV-2 infection continuing the pregnancy. This first report of pregnant women infected with COVID-19 and recovered allows us to know that the patient continues to be at high obstetric risk, especially due to the PROM and labor before 39 weeks. A study of 16 placentas from SARS-CoV-2 patients reports an increase in the rates of maternal and fetal vascular malperfusion features; two cases were more than 30 days after the appearance of symptoms and these placentas showed fetal vascular malperfusion (clustered avascular villi, hipercoiled umbilical cord, chorangiosis) 3 . In our opinion, in pregnant patients infected and recovered with SARS-CoV-2, there is a "placental inflammatory syndrome" characterized by spontaneous onset of labor, premature births, premature rupture of membranes, alteration in the cardiotocograph trace, fetal distress, death and placental alterations. Fetal deaths in pregnancies with SARS-CoV-2 infection in Brazil: A case series. cache = ./cache/cord-325320-v9e2axf4.txt txt = ./txt/cord-325320-v9e2axf4.txt === reduce.pl bib === id = cord-325293-nwxtyrpl author = Akhtar, Hubba title = COVID-19 (SARS-CoV-2) Infection in Pregnancy: A Systematic Review date = 2020-07-30 pages = extension = .txt mime = text/plain words = 3502 sentences = 279 flesch = 56 summary = INTRODUCTION: To review published studies related to the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with pregnancy, foetal, and neonatal outcomes during coronavirus disease 2019 (COVID-19) pandemic in a systematic manner. This study was done according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method identifying published literature on COVID-19 and its potential impact on pregnancy and neonates. The comprehensive literature search was carried out with PubMed, Medline, Scopus, Cochrane database, and Google Scholar, using key MeSH words, which include "COVID-19," "Pregnancy," "Coronavirus 2019," "Newborn," "Foetus," "Neonate," "vertical transmission," and "outcomes." All published articles have been reviewed, and the findings have been included in this study. [6] Clinical analysis of 10 neonates born to mothers with 2019-nCoV pneumonia 9 10 (2 twins) Fever (8) Intrauterine distress (6) Shortness of breath (6) Infections (4) (3) PROM (3) Fever (2) NRDS (2) Sore throat (1) (3) Dyspnoea (1) Sore throat (1) NVD (1) Diarrhoea (1) Unknown as still pregnant (4) Yu et al. cache = ./cache/cord-325293-nwxtyrpl.txt txt = ./txt/cord-325293-nwxtyrpl.txt === reduce.pl bib === id = cord-325324-kh2aal5n author = Teng, Shaolei title = ACE2 Enhance Viral Infection or Viral Infection Aggravate the Underlying Diseases date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4403 sentences = 274 flesch = 53 summary = SARS-CoV-2 spike protein (S) is cleaved by the human furin enzyme to generate S1, which binds to the host receptor, ACE-2. It is possible that the released free spike or the cleaved S1 protein in the blood might bind to cellular membrane ACE2 of heart, artery and alveolar lung cells to block the conversion of Angiotensin II to Ang-(1-7) and/or Angiotensin I to Ang-(1-9), which is consistent with a previous experimental result on SARS-CoV-1 (59) . Therefore, our hypothesis, as shown in the right side of Fig. 1 as "Viral aggravating existing diseases", is that comorbidities in COVID-19 patients are aggravated by the infection of SARS-CoV-2 to causes higher fatalities because the viral S protein interacts with ACE2 to inhibit ACE2 function. The claims that COVID-19 disproportionately affects the individuals of minority groups and aged people are not only supported by reported data but also by our hypothesis that SARS-CoV-2 infection generates spike protein that interacts with ACE2 to either exhaust ACE2 or inhibit ACE2 function or both so that the comorbidities are aggravated (Figure 1 ). cache = ./cache/cord-325324-kh2aal5n.txt txt = ./txt/cord-325324-kh2aal5n.txt === reduce.pl bib === id = cord-325377-g68onkjt author = Dey, Anusree title = COVID-19: Scientific Overview of the global Pandemic date = 2020-10-28 pages = extension = .txt mime = text/plain words = 1515 sentences = 108 flesch = 60 summary = COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics. According to the global data as well as the early estimates from China, both old 69 J o u r n a l P r e -p r o o f age and comorbidities may render the patients at higher risk of developing severe disease or 70 death due to COVID-19 infection, perhaps due to a weaker immune functioning [8, 10] . Interestingly, in an independent study, researchers have found 124 three blood based biomarkers which can predict disease severity at least ten days in advance 125 with more than 90% accuracy, based on a database of 485 infected patients from Wuhan, 126 cache = ./cache/cord-325377-g68onkjt.txt txt = ./txt/cord-325377-g68onkjt.txt === reduce.pl bib === id = cord-325124-0hxan9rw author = Li, Chenyu title = Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date = 2020-05-18 pages = extension = .txt mime = text/plain words = 6119 sentences = 364 flesch = 53 summary = However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. cache = ./cache/cord-325124-0hxan9rw.txt txt = ./txt/cord-325124-0hxan9rw.txt === reduce.pl bib === id = cord-325348-yi6yu5l1 author = Zhang, G. title = Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date = 2020-06-17 pages = extension = .txt mime = text/plain words = 2664 sentences = 160 flesch = 54 summary = Recent cryo-electron microscopy (cryo-EM) structural studies of the SARS-CoV-2 spike protein 68 receptor binding domain (RBD) in complex with full-length human ACE2 receptor revealed key 69 amino acid residues at the contact interface between the two proteins and estimated the binding 70 affinity at ~15 nM [7, 8] . The results of this MD simulation suggest 108 that SBP1 and SBP2 peptides derived from the ACE-PD α1 helix may alone potentially bind the 109 SARS-CoV-2 spike RBD protein with sufficient affinity to disrupt the associated PPI. However, competition was not observed when using non-biotinylated SBP1 pre-140 mixed in solution with Sino Biological insect-derived SARS-CoV-2-RBD, even with a 1000-fold 141 excess of the peptide (Fig. 3C, 3E ). In conclusion, a biotinylated peptide sequence derived from human ACE2 was found to 205 bind Sino Biological insect-derived SARS-CoV-2 spike protein RBD with micromolar affinity, but 206 did not associate with SARS-CoV-2-RBD variants obtained from other commercial sources. cache = ./cache/cord-325348-yi6yu5l1.txt txt = ./txt/cord-325348-yi6yu5l1.txt === reduce.pl bib === id = cord-325282-20l9xcmg author = Helal, Mohamed A. title = Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6739 sentences = 365 flesch = 53 summary = title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The entry of the virus into host cells is facilitated by binding of its transmembrane spike (S) protein with angiotensin-converting enzyme 2 (ACE-2) receptor (Hoffmann et al., 2020) . To understand the mechanism of interaction of the SARS-CoV-2 spike protein with the CD147 receptor, we have performed a four-stage in-silico study. The recently reported crystal structure of SARS-Cov-2 spike protein complex with ACE2 (PDB ID: 6LZG) reveals that the virus utilizes the external subdomain of the spike Receptor Binding Domain (RBD) to recognize the human ACE2 receptor . cache = ./cache/cord-325282-20l9xcmg.txt txt = ./txt/cord-325282-20l9xcmg.txt === reduce.pl bib === id = cord-325449-fl6ob5ja author = Wang, Jing title = COVID-19 and diabetes: the contributions of hyperglycemia date = 2020-10-01 pages = extension = .txt mime = text/plain words = 3424 sentences = 164 flesch = 42 summary = Thus, following SARS-CoV-2 infection, poor-controlled blood glucose in diabetes patients may promote macrophage inflammation and antigen presentation impairment in DCs, resulting in a great increase in the secretion of inflammatory cytokines and chemokines from immune cells and ultimately cytokine storm and increased mortality (Figure 1) . The exact mechanisms linking diabetes and COVID-19 remain to be further elucidated, but available clinical/laboratory observations suggest that hyperglycemia-induced immune dysfunction, cytokines storm, and elevated lactate levels may play critical roles in the severity of COVID-19 in patients with pre-existing diabetes. A large body of evidence shows that hyperglycemia or diabetes may impair immune response mediated by macrophages, monocytes, and DCs, weaken T-cell function, and promote cytokine storm, ultimately resulting in increased susceptibility of SARS-CoV-2 infection and COVID-19-associated mortality. Hyperglycemia may also increase lactate production via HIF-1α, which suppresses the innate immune RLR signaling by targeting MAVS, leading to delayed clearance of SARS-CoV-2 and thus severe outcomes in diabetes patients with COVID-19, including ARDS, septic shock, and MODS. cache = ./cache/cord-325449-fl6ob5ja.txt txt = ./txt/cord-325449-fl6ob5ja.txt === reduce.pl bib === id = cord-324970-yty7aajj author = Ma, Di title = Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea date = 2020-05-07 pages = extension = .txt mime = text/plain words = 3734 sentences = 194 flesch = 51 summary = title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea PURPOSE: To determine the expressions of SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS2) genes in human and mouse ocular cells and comparison to other tissue cells. The expression of ACE2 and TMPRSS2 genes was determined in human primary conjunctival and pterygium cells, human ocular and other tissue cell lines, mesenchymal stem cells as well as mouse ocular and other tissues by reverse transcription-polymerase chain reaction (RT-PCR) and SYBR green PCR. Herein, this study aimed to determine the expressions of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human and mouse ocular cells and tissues. In summary, this study revealed the expression of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human conjunctival and pterygium cells as well as mouse cornea tissue. cache = ./cache/cord-324970-yty7aajj.txt txt = ./txt/cord-324970-yty7aajj.txt === reduce.pl bib === id = cord-325136-oyizfh2z author = Pham, Quang Thai title = The first 100 days of SARS-CoV-2 control in Vietnam date = 2020-08-01 pages = extension = .txt mime = text/plain words = 2655 sentences = 164 flesch = 53 summary = METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). cache = ./cache/cord-325136-oyizfh2z.txt txt = ./txt/cord-325136-oyizfh2z.txt === reduce.pl bib === id = cord-325419-15vm22d8 author = Dai, C. L. title = Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity date = 2020-10-15 pages = extension = .txt mime = text/plain words = 4227 sentences = 238 flesch = 46 summary = All multivariate models included race/ethnicity as an independent variable, with demographic factors (age; age-squared; sex), socioeconomic factors (insurance; neighborhood rates of poverty, crowded housing, limited English proficiency, and minority), and comorbidities (Charlson Comorbidity Index score; hypertension; and obesity) as covariates. Minority populations including Hispanic, Black, Asian, NH/PI and AI/AN had increased odds of SARS-CoV-2 infection compared to Whites in unadjusted and adjusted analysis ( race/ethnicity with White patients as the reference category. Minority races/ethnicities were not consistently associated with increased odds for COVID-19 hospitalization, until adjusting for demographics, comorbidities, insurance status and neighborhood characteristics. Race/ethnicity was associated with SARS-CoV-2 infection and COVID-19 hospitalization, with adjusted odds of both outcomes highest among Hispanics and NH/PI patients. The significant associations of minority races/ethnicities with SARS-CoV-2 infection and COVID-19-related hospitalization builds on previous analyses of Black and Hispanic patients(24-27). cache = ./cache/cord-325419-15vm22d8.txt txt = ./txt/cord-325419-15vm22d8.txt === reduce.pl bib === id = cord-325420-e9fjo7tl author = Xiao, Xia title = Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1282 sentences = 78 flesch = 58 summary = Here we performed a high throughput screen of approximately 1700 US FDA approved compounds to identify novel therapeutic agents that can effectively inhibit replication of coronaviruses including SARS-CoV-2. These screens have identified 24 anti-SARS-CoV-2 drugs including previously reported compounds such as hydroxychloroquine, amlodipine, arbidol hydrochloride, tilorone 2HCl, dronedarone hydrochloride, and merfloquine hydrochloride. Positive compounds from the initial screen were tested for their antiviral 120 efficacy against SARS-CoV-2 in Vero cells. Our data show that 24 of these compounds show significant 124 efficacy in inhibiting SARS-CoV-2 replication with sub micromolar IC50 for many of these 125 drugs such as nilotinib, clofazimine and raloxifene. This screen identified five new compounds that 187 are highly efficacious in inhibiting the viral replication of SARS-CoV-2 with SI >600. The positively identified drugs from this screen were used to perform dose response curves 220 against OC43 on LLC-MK2 and against SARS-CoV-2 using Vero cells as described below. cache = ./cache/cord-325420-e9fjo7tl.txt txt = ./txt/cord-325420-e9fjo7tl.txt === reduce.pl bib === id = cord-325473-hrdanbn1 author = Ghahremanpour, Mohammad M. title = Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2915 sentences = 205 flesch = 56 summary = 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 5 Thus, M pro is viewed as a promising target for anti SARS-CoV-2 drug design; it has been the focus of several studies since the pandemic has emerged. For instance, a molecular docking study suggested remdesivir as a potential therapeutic that could be used against SARS-CoV-2, 10 which was supported experimentally by an EC50 value of 23 μM in an infected-cell assay. Structural Basis for the Inhibition of SARS-CoV-2 Main Protease by Antineoplastic Drug Carmofur Crystal Structure of SARS-CoV-2 Main Protease Provides a Basis for Design of Improved α-Ketoamide Inhibitors Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition Structure-based Design of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease Targeting the SARS-CoV-2 Main Protease to Repurpose Drugs for cache = ./cache/cord-325473-hrdanbn1.txt txt = ./txt/cord-325473-hrdanbn1.txt === reduce.pl bib === id = cord-325421-1ysn0kyr author = Christensen, Johanna title = Covid-19 Viremia, Serologies and Clinical Course in a Case Series of Transplant Recipients date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2551 sentences = 169 flesch = 56 summary = In this preliminary report, we find that immunocompromised transplant patients had higher rates of RNAemia (67%) than reported in the general population (15%), seeming absence of allo-immune injury despite systemic inflammation and formation of IgG overtime after recovery from infection. 8, 9 J o u r n a l P r e -p r o o f In this first case series, we report the characteristics, inflammatory immune response, biomarkers of graft injury along with SARS-CoV-2 RNAemia and serological response in a small cohort of kidney/liver transplant patients. Between, March 2020 and May 2020, six symptomatic kidney transplant recipients presented to the Virginia Commonwealth University hospital and tested positive for SARS-CoV-2. While it is not yet established if J o u r n a l P r e -p r o o f seroconversion confers immunity in the general population, 8, 9 the low re-infection rates and early reports of favorable efficacy of convalescent plasma in patients with severe COVID-19 manifestations [15] [16] [17] [18] suggest that this may be true. cache = ./cache/cord-325421-1ysn0kyr.txt txt = ./txt/cord-325421-1ysn0kyr.txt === reduce.pl bib === id = cord-325460-4fhegc0z author = Jacobs, Werner title = Fatal lymphocytic cardiac damage in coronavirus disease 2019 (COVID‐19): autopsy reveals a ferroptosis signature date = 2020-09-22 pages = extension = .txt mime = text/plain words = 3977 sentences = 241 flesch = 39 summary = Immunohistochemical staining with E06, a monoclonal antibody binding to oxidized phosphatidylcholine (reflecting lipid peroxidation during ferroptosis), was positive in morphologically degenerating and necrotic cardiomyocytes adjacent to the infiltrate of lymphocytes, near arteries, in the epicardium and myocardium. We examined the patient's myocardial tissue for markers of ferroptosis, an iron-catalysed form of regulated cell death that occurs through excessive peroxidation of polyunsaturated fatty acids and is also proposed to detrimentally contribute to some forms of ischaemia-reperfusion injury, stroke, and degenerative diseases. Renal tissue from the COVID-19 patient with myocarditis and multiple organ dysfunction syndrome showed morphological signs of acute tubular necrosis, intratubular oxalate crystals, as well as E06 positivity in proximal tubuli (A). By comparison, in the case of sudden death due to myocarditis of other aetiology, immunohistochemical staining with E06 (B) and anti-4-HNE antibody (D) in the renal tissue showed no presence of these ferroptosis markers (non-specific staining in the corticomedullary junction is also present on control stains). cache = ./cache/cord-325460-4fhegc0z.txt txt = ./txt/cord-325460-4fhegc0z.txt === reduce.pl bib === id = cord-325234-skshcrh1 author = Jin, Tingxu title = SARS-CoV-2 presented in the air of an intensive care unit (ICU) date = 2020-08-15 pages = extension = .txt mime = text/plain words = 4276 sentences = 205 flesch = 54 summary = Therefore, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, it is necessary to 1) determine whether SARS-CoV-2 particles are present in the indoor air and 2) determine whether recovered patients are still shedding virus, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. To date, some studies have reported the presence of SARS-CoV-2 particles in the air in isolation rooms from hospitals treating COVID-19 patients (Yuanfang J,2020; Guo, Wang, Zhang, Li, & Chen,2020; Joshua L. Therefore, our study aims to 1) determine whether SARS-CoV-2 particles are present in the indoor air, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, and 2) determine whether recovered patients are still shedding SARS-CoV-2 particles, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. Our findings revealed the presence of SARS-CoV-2 in the indoor air of the ICU and indicate that the virus may be shed via aerosol for days, even after a patient has tested negative. cache = ./cache/cord-325234-skshcrh1.txt txt = ./txt/cord-325234-skshcrh1.txt === reduce.pl bib === id = cord-325452-2sywbgje author = Sun, Pengfei title = Understanding of COVID‐19 based on current evidence date = 2020-03-05 pages = extension = .txt mime = text/plain words = 963 sentences = 68 flesch = 57 summary = A study by Wang et al 12 In the absence of effective treatments, the best way to deal with the SARS-CoV-2 epidemic is to control the sources of infection. 9 According to the official Chinese data, the case fatality rate among the SARS-CoV-2-infected patients was much lower than that of SARS and MERS. These studies will help further reduce the case fatality and transmission rates among SARS-CoV-2-infected patients. Moreover, super-spreaders were reported during the SARS and MERS epidemics. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in Wuhan, China Updated understanding of the outbreak of 2019 novel coronavirus (2019-nCoV) in Wuhan Clinical features of patients infected with 2019 novel coronavirus in Wuhan Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 Clinical characteristics of 2019 novel coronavirus infection in China cache = ./cache/cord-325452-2sywbgje.txt txt = ./txt/cord-325452-2sywbgje.txt === reduce.pl bib === id = cord-325479-2r4oomdp author = Torii, Shotaro title = Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date = 2020-10-17 pages = extension = .txt mime = text/plain words = 5881 sentences = 363 flesch = 58 summary = This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. This study aims (1) to compare the combination of primary concentration (UF, EMV, and PEG) and RNA extraction (QIAamp Viral RNA Mini Kit and TRIzol) for the whole process recovery of nonenveloped and enveloped virus surrogates and (2) to test the applicability of the method providing the highest φ6 recovery to detect SARS-CoV-2 cache = ./cache/cord-325479-2r4oomdp.txt txt = ./txt/cord-325479-2r4oomdp.txt === reduce.pl bib === id = cord-325112-7ie23c7f author = Heimer, Carol A. title = The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date = 2018-10-04 pages = extension = .txt mime = text/plain words = 10440 sentences = 448 flesch = 43 summary = Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Thus although the long silence of the Chinese government was not technically a violation of the IHR, it nevertheless appeared dishonest and inappropriate to the international community, undermining rather than supporting emerging cooperative norms and in fact harming global public health by allowing the new disease to spread beyond China's borders. cache = ./cache/cord-325112-7ie23c7f.txt txt = ./txt/cord-325112-7ie23c7f.txt === reduce.pl bib === id = cord-325498-4yciuh1n author = Del Brutto, Oscar H. title = Incident SARS-CoV-2 Infection and a Shared Latrine date = 2020-07-22 pages = extension = .txt mime = text/plain words = 649 sentences = 38 flesch = 55 summary = title: Incident SARS-CoV-2 Infection and a Shared Latrine Incident SARS-CoV-2 Infection and a Shared Latrine. In a recent serosurvey, we found that the use of open latrines (instead of flushing toilet systems) was significantly associated with seropositivity to SARS-CoV-2 on lateral flowbased antibody testing (BIOHIT Health Care Ltd., Cheshire, United Kingdom), suggesting a contributory role for fecal-oral transmission of the disease, as previously proposed by others. Here, we present a cluster of incident cases of SARS-CoV-2 involving a woman who lived alone (house A), and a five-member family (house B) who were seronegative during the first survey. Two weeks after our baseline serosurvey, a 22-year-old grandson of the old woman moved into Atahualpa from Guayaquil (a heavily infected urban center), staying at her house and using the shared latrine. There were no other incident cases in the entire block, where only one person in a distant house had tested positive at baseline, and several other inhabitants of other houses remained seronegative (Figure 2, left) . cache = ./cache/cord-325498-4yciuh1n.txt txt = ./txt/cord-325498-4yciuh1n.txt === reduce.pl bib === id = cord-325529-pid58g2r author = Ben-Ami, Roni title = Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2822 sentences = 158 flesch = 50 summary = METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. cache = ./cache/cord-325529-pid58g2r.txt txt = ./txt/cord-325529-pid58g2r.txt === reduce.pl bib === id = cord-325744-i3r3ff3t author = Chan, Angelina O. M. title = Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore date = 2004-05-17 pages = extension = .txt mime = text/plain words = 3255 sentences = 179 flesch = 57 summary = title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore Aims To describe the psychological impact of severe acute respiratory syndrome (SARS) on health care workers in a regional general hospital 2 months post-outbreak. The questionnaires consisted of demographics, the General Health Questionnaire (GHQ) 28, the Impact of Events Scale (IES) and a set of questions enquiring about changes in life's priorities and circumstances that helped them to cope with the SARS situation better. This questionnaire was developed specifically for this study, as there were no suitable scales available for measuring changes in life's priorities and coping among health care workers as a result of SARS. From this survey, although it was perceived that the SARS situation had greatly impacted on the emotional state of health care workers, there was no significant change in the prevalence of psychiatric disorders among health care workers (35% of doctors and 25% of nurses) in this hospital who responded. cache = ./cache/cord-325744-i3r3ff3t.txt txt = ./txt/cord-325744-i3r3ff3t.txt === reduce.pl bib === id = cord-325783-pqonn0as author = Nicholls, John M title = Lung pathology of fatal severe acute respiratory syndrome date = 2003-05-24 pages = extension = .txt mime = text/plain words = 4022 sentences = 250 flesch = 49 summary = Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines). cache = ./cache/cord-325783-pqonn0as.txt txt = ./txt/cord-325783-pqonn0as.txt === reduce.pl bib === id = cord-325657-s2vdazq0 author = Huang, Yan-Jang S. title = SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1589 sentences = 105 flesch = 46 summary = Three widely distributed species of mosquito; Aedes aegypti, Ae. albopictus and Culex quinquefasciatus, representing the two most significant genera of arbovirus vectors that infect people, were tested. In this study, the susceptibility of three mosquito species, Ae. aegypti, Ae. albopictus and Cx. quinquefasciatus, were determined through the intrathoracic inoculation with SARS-CoV-2. No virus was detected in the 277 inoculated mosquitoes collected and titrated at time points beyond 24 h, suggesting a rapid loss of infectivity and the lack of replication after injection. Based upon the lack of detectable infectious virus in any of the 277 samples collected at all time points beyond 24 h post-inoculation, we conclude that SARS-CoV-2 is unable to replicate in mosquitoes and that even if a mosquito fed on a person with virus in the blood, that the mosquito would not be a vector if feeding on a naïve host. cache = ./cache/cord-325657-s2vdazq0.txt txt = ./txt/cord-325657-s2vdazq0.txt === reduce.pl bib === id = cord-325559-di8lljoi author = Cappello, Francesco title = Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date = 2020-06-29 pages = extension = .txt mime = text/plain words = 5204 sentences = 298 flesch = 44 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced disease (COVID-19) is a planetary emergency that is urging many research groups to redirect their efforts and to channel their experience towards understanding its pathogenesis. These human epitopes, in turn, can be recognized by circulating antibodies made against crossreactive microbial antigens; these antibodies behave like autoantibodies, causing the destruction of the stressed cells, representing a typical example of pathology caused by molecular mimicry and manifested as autoimmunity [30] . We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. cache = ./cache/cord-325559-di8lljoi.txt txt = ./txt/cord-325559-di8lljoi.txt === reduce.pl bib === id = cord-325593-ww2vq3n4 author = Hendren, Nicholas S. title = Unique Patterns of Cardiovascular Involvement in COVID-19 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1298 sentences = 71 flesch = 35 summary = However, to our knowledge, a framework describing the variable presentations of cardiac involvement in COVID-19 within the broader spectrum of symptomatic SARS-CoV-2 infection has not been previously proposed. First, the prevalence of mixed cardiopulmonary disease as assessed by elevated cardiac troponin levels, is variable, but occurs in 10-25% of patients hospitalized with COVID-19 3, 4 . ACovCS with cardiac predominate disease may be more apparent at hospital presentation relative to mixed cardiopulmonary disease because the predominate cardiac manifestations (e.g. chest pain due to a myocardial infarction) often results in symptoms which lead patients to seek emergent care. Just as there is variability in cardiac presentations of COVID-19, SARS-CoV-2 infection overall has a wide spectrum of disease penetrance with many patients displaying few to no symptoms, while an unfortunate minority develop severe life limiting disease. Other factors which may influence the variable presentation of COVID-19 include mutations in the circulating SARS-CoV-2 virus though it remains uncertain whether such observations explain the regional differences in the outcomes of COVID-19. cache = ./cache/cord-325593-ww2vq3n4.txt txt = ./txt/cord-325593-ww2vq3n4.txt === reduce.pl bib === id = cord-325598-gy809ee0 author = Lyne, Cloutier title = Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1483 sentences = 102 flesch = 53 summary = title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study In our cross-sectional study, 1.82% of 330 asymptomatic confined individuals living in the community carried SARS-CoV-2 despite no contact with declared cases, raising concerns about unnoticed transmission. Cloutier, Lyne 1 ; Merindol, Natacha 2,3 ; Pépin, Geneviève 4 ; Marcoux-Huard, Caroline 5 ; Vasil, Pier-Alexandre 5 ; Houle, Claudia 6, 7 ; Todkar, Shweta 1 ; Lehoux, Marie-Claude 3 ; Houle, Nathalie 1 ; Germain, Hugo 2,3 ; Danylo, Alexis 6  SARS-CoV-2 may spread asymptomatically in a population under social distancing restrictions. Studies conducted on individuals from the same households have convincingly shown that pre-symptomatic or asymptomatic SARS-CoV-2 carriers might transmit to their family members [8] [9] [10] . Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China. cache = ./cache/cord-325598-gy809ee0.txt txt = ./txt/cord-325598-gy809ee0.txt === reduce.pl bib === id = cord-325959-uqg2xkie author = Bundschuh, Christian title = Evaluation of the EDI enzyme linked immunosorbent assays for the detection of SARS-CoV-2 IgM and IgG antibodies in human plasma date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2208 sentences = 125 flesch = 57 summary = METHODS: Using EDI(TM) Novel Coronavirus COVID-19 Enzyme Linked Immunosorbent Assays (ELISAs), we measured SARS-CoV-2 IgM and IgG antibodies in 64 SARS-CoV-2 RT-PCR confirmed COVID-19 patients with serial blood samples (n=104) collected at different time points from symptom onset. low "false" positivity rates for the EDI(TM) SARS-CoV-2 IgM and IgG ELISAs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus that causes Coronavirus Disease 2019 (COVID-19), has recently emerged to cause a human pandemic. For the clinical evaluation we measured SARS-CoV-2 IgM and IgG antibodies in three different cohorts: First in a "positive cohort" of patients with SARS-CoV-2 RT-PCR confirmed 5 COVID-19 with serial blood samples at different time points from symptom onset. Furthermore, the clinical evaluation study demonstrated high "true" positivity rates in the SARS-CoV-2 RT-PCR confirmed COVID-19 patients with symptom onset after 15 days with 94.4% for IgM and 100% for IgG SARS-CoV-2 cache = ./cache/cord-325959-uqg2xkie.txt txt = ./txt/cord-325959-uqg2xkie.txt === reduce.pl bib === id = cord-325481-uzch2hwd author = Simmons, Graham title = Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date = 2011-05-01 pages = extension = .txt mime = text/plain words = 7139 sentences = 315 flesch = 49 summary = For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) . cache = ./cache/cord-325481-uzch2hwd.txt txt = ./txt/cord-325481-uzch2hwd.txt === reduce.pl bib === id = cord-325614-e9hnhzfg author = Todorov, German title = A Possible Path towards Rapid Development of Live-Attenuated SARS-CoV-2 Vaccines: Plunging into the Natural Pool date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3122 sentences = 145 flesch = 41 summary = Our proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, which may lead to a shorter cycle of vaccine development, as well as higher vaccine effectiveness. The proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, potentially leading to a more rapid cycle of vaccine development, as well as higher vaccine effectiveness. If the candidate attenuated SARS-CoV-2 strain is easily transmissible, we would need to evaluate whether a live-attenuated virus that causes a very mild form of infection but is easy to transmit can be considered sufficiently safe for use as a vaccine, or whether it needs to be further attenuated in the lab, which could slow down the development of the vaccine. All in all, at present there are too many unknowns to predict how much screening of suitable individuals in high-risk subpopulations will be required to find naturally-evolved candidate strains for the development of live-attenuated vaccines. cache = ./cache/cord-325614-e9hnhzfg.txt txt = ./txt/cord-325614-e9hnhzfg.txt === reduce.pl bib === id = cord-325595-y9ae6zbr author = Montopoli, M. title = Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality date = 2020-10-23 pages = extension = .txt mime = text/plain words = 1251 sentences = 72 flesch = 46 summary = title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality in the Annals of Oncology reported findings congruent with the prevailing notion that high SARS-CoV-2 infection rates and disease severity in men may be the result of high androgen-driven TMPRSS2 expression in the lungs. The authors posit that since TMPRSS2 is under positive transcriptional control by the androgen receptor (AR), reduction of TMPRSS2 expression following androgen deprivation therapy (ADT) in prostate cancer patients would be expected to correlate with reduced SARS-CoV-2 incidence, and in case of infection, with lesser disease severity. In particular, disease stage and the type of treatment that may affect AR or TMPRSS2 expression and/or patients' The current thinking posits that under ADT, expression of TMPRSS2 (a co-factor for SARS-CoV-2 activation and virulence) would be reduced in the lungs, leading to less severe disease, hospitalizations, ICU admissions, and deaths. cache = ./cache/cord-325595-y9ae6zbr.txt txt = ./txt/cord-325595-y9ae6zbr.txt === reduce.pl bib === id = cord-325910-qiay8n43 author = Green, D. A. title = Clinical Performance of SARS-CoV-2 Molecular Testing date = 2020-05-08 pages = extension = .txt mime = text/plain words = 3945 sentences = 201 flesch = 56 summary = In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19. For the time-dependent analysis of conversion rates, we considered "initially positive" 216 patients with any "Detected" or "Indeterminate" SARS-CoV-2 result obtained during the 217 first calendar day of testing rather than the first positive test, to reduce bias due to 218 nasopharyngeal sampling inadequacy (Table 1) . Considering 'Detected' and "Indeterminate" as 239 positive, 1,471 repeat-tested patients had one or more SARS-CoV-2 positive results over 240 time; only 61.9% were positive on the initial test and only 69.3% had a positive result on 241 the first day (Table 1) . cache = ./cache/cord-325910-qiay8n43.txt txt = ./txt/cord-325910-qiay8n43.txt === reduce.pl bib === id = cord-326198-6okk3u49 author = Walker, A. title = Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1943 sentences = 94 flesch = 46 summary = An analysis (Supplementary Text) of other publicly available SARS-CoV-2 sequences did not reveal an obvious origin of the Heinsberg outbreak (Supplementary Table S4 ); the Heinsberg isolates are not related to early sequences from other German outbreak areas (Bavaria, Baden Wuerttemberg), and, despite intense Dutch viral sampling efforts (585 available viral genomes from the Netherlands at the time of analysis), our analysis identified only 2 closely related isolates from the Netherlands (one collected on 21 st March, the other with undefined collection date). A minimum spanning tree analysis of unambiguously resolved viral sequences ( Figure 1 ) showed that there were at least 5 clusters of viral haplotypes circulating in the Düsseldorf area; the number of variant positions relative to the SARS-CoV-2 reference genome in the Düsseldorf samples varied between 2 and 13 (Supplementary Table 2 ). cache = ./cache/cord-326198-6okk3u49.txt txt = ./txt/cord-326198-6okk3u49.txt === reduce.pl bib === id = cord-325863-3t73v4ng author = Foss, Francine M. title = Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1989 sentences = 113 flesch = 45 summary = title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib We report a mild and attenuated SARS CoV-2 infection in a patient who is 17 months post stem cell transplantation and maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia. Due to the signal transduction role that the JAK-STAT pathway plays in mediating Immune-effector cell activation, there has been interest in pursuing inhibitors of this pathway as potential therapeutic agents in mitigating COVID19-associated lung inflammation 9, 10 . We recently diagnosed COVID19 infection in a patient who was on oral ruxolitinib for management of graft-vs-host disease after allogeneic stem cell transplant and report on his presentation and the evolution of his clinical course. Our patient was 17 months post stem cell transplantation and was maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia, throughout his clinical course with successful attenuation of symptoms. cache = ./cache/cord-325863-3t73v4ng.txt txt = ./txt/cord-325863-3t73v4ng.txt === reduce.pl bib === id = cord-325830-mrtpihc7 author = Nelson, Philipp P. title = Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4974 sentences = 273 flesch = 46 summary = In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. cache = ./cache/cord-325830-mrtpihc7.txt txt = ./txt/cord-325830-mrtpihc7.txt === reduce.pl bib === id = cord-325991-dktffiaa author = Gross, Oliver title = COVID-19-associated nephritis: early warning for disease severity and complications? date = 2020-05-06 pages = extension = .txt mime = text/plain words = 593 sentences = 41 flesch = 45 summary = title: COVID-19-associated nephritis: early warning for disease severity and complications? COVID-19-associated nephritis: early warning for disease severity and complications? Here we report that analysis of a urine sample on admission to hospital can be used to detect systemic capillary leak syndrome, which can be a predictor of fluid overload, respiratory failure, need for ICU admission, and death. Three of these patients had coincidentally submitted urine samples in the few weeks before their infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On the basis of these findings, we generated an algorithm for early detection of COVID-19-associated nephritis and to assess the risk of respiratory decompensation by capillary leak syndrome (figure). In summary, the respiratory tract is the gateway for SARS-CoV-2 infection, but we postulate that COVID-19associated nephritis, which can be easily screened for through a simple and inexpensive urine sample analysis, might help predict complications. cache = ./cache/cord-325991-dktffiaa.txt txt = ./txt/cord-325991-dktffiaa.txt === reduce.pl bib === id = cord-326150-cf4rlqe5 author = Carrascosa, J M title = Manifestaciones cutáneas en el contexto de la infección por SARS-CoV-2 (COVID-19) date = 2020-08-31 pages = extension = .txt mime = text/plain words = 2443 sentences = 233 flesch = 51 summary = Desde el punto de vista patogénico, la respuesta inmune desencadenada frente a la infección por SARS-CoV-2 puede resultar en efectos deletéreos, como la disfunción de las células endoteliales y la activación de las vías de la coagulación, que podrían explicar las complicaciones cardiovasculares y trombóticas que afectan a un subgrupo de pacientes. Desde el punto de vista histológico, en el conjunto de exantemas J o u r n a l P r e -p r o o f En el estudio histológico de lesiones purpúricas cutáneas se ha encontrado la presencia de una vasculopatía trombogénica pauciinflamatoria, con depósito de C5b-9 y C4d , con localización de partículas virales, lo que ha permitido proponer la existencia de un síndrome de lesión microvascular catastrófica mediada por la activación del complemento 6 . De este modo, no puede descartarse que las lesiones acrales, descritas como características por su coincidencia epidemiológica más que por pruebas microbiológicas en la mayoría de los casos, puedan no tener que ver directamente con la COVID-19. cache = ./cache/cord-326150-cf4rlqe5.txt txt = ./txt/cord-326150-cf4rlqe5.txt === reduce.pl bib === id = cord-325966-0g7a9s5z author = Shih, Hsin-I. title = Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date = 2020-05-30 pages = extension = .txt mime = text/plain words = 7324 sentences = 365 flesch = 39 summary = Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. However, these clinical, laboratory, and imaging findings are nonspecific and cannot differentiate COVID-19 from other viral respiratory infections; viral diagnostic methods specific for SARS-CoV-2 should be applied for disease confirmation. An open-label study published in 2004 suggested, by comparison with a control group that received only ribavirin, that the addition of lopinavir-ritonavir (400 mg and 100 mg, respectively) to ribavirin reduced the risk of adverse clinical outcomes (acute respiratory distress syndrome or death) and viral load among patients with SARS [29] . Some available candidate drugs targeting different levels of human responses to COVID-19, such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, IL-6 blocker and convalescent plasma, may improve the clinical outcomes of critical COVID-19 patients. cache = ./cache/cord-325966-0g7a9s5z.txt txt = ./txt/cord-325966-0g7a9s5z.txt === reduce.pl bib === id = cord-326169-delehk6x author = CJ Jorgensen, Sarah title = Baricitinib: A review of pharmacology, safety and emerging clinical experience in COVID‐19 date = 2020-06-15 pages = extension = .txt mime = text/plain words = 2704 sentences = 180 flesch = 44 summary = The lack of reliable biomarkers to monitor patients' immune status as illness evolves complicates deployment of immunosuppressive drugs like baricitinib. In this article we review available data on baricitinib with an emphasis on immunosuppressive and antiviral pharmacology, pharmacokinetics, safety and current progress in COVID‐19 clinical trials. In population PK analyses, body weight did not have a clinically meaningful 250 impact on baricitinib clearance, however obese RA patients have been reported to have lower 251 response rates. Thrombocytosis Accepted Article 499 treatment strategies aimed at attenuating both pathogen virulence and the pro-inflammatory 500 phenotype seen in the many critically ill patients with COVID-19. 5, 9, 12, 13, 20, 56 As detailed in this 501 review, baricitinib pairs immunosuppressive properties with antiviral activity making it a logical 502 candidate for further evaluation in COVID-19 clinical trials . Baricitinib therapy in 626 COVID-19: A pilot study on safety and clinical impact Impaired type I interferon activity and exacerbated 662 inflammatory responses in severe Covid-19 patients cache = ./cache/cord-326169-delehk6x.txt txt = ./txt/cord-326169-delehk6x.txt === reduce.pl bib === id = cord-326017-qw4qynqv author = Laskar, Partha title = “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date = 2020-08-06 pages = extension = .txt mime = text/plain words = 14797 sentences = 760 flesch = 42 summary = Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Overall, real-time RT-PCR based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against COVID-19 in clinical settings [39] . Another newly developed method, SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), was found to perform simultaneous reverse transcription and isothermal amplification by (i) RT-LAMP for RNA extracted (for nasopharyngeal or oropharyngeal swabs), (ii) Cas12 detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [56] . cache = ./cache/cord-326017-qw4qynqv.txt txt = ./txt/cord-326017-qw4qynqv.txt === reduce.pl bib === id = cord-325936-rwxg187r author = Eyal, Nir title = AIDS Activism and Coronavirus Vaccine Challenge Trials date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2220 sentences = 115 flesch = 51 summary = To minimize risk to participants, live SARS-CoV-2 vaccine challenge trials would need to recruit participants who, in the-likely-event of infection, would remain at relatively low fatality risk. Shortly after HIV sterilizing cure trials transplanted allogenic stem cell in participants, with well over a thousand times the fatal risk of SARS-Cov-2 infection in healthy young participants [17, 18] , AIDS activist David Evans interviewed the participants of these risky trials and concluded, "We should recognize their great capacity to understand the risks they may confront as research participants and, after a careful ethical and scientific review, respect the motivations of those who decide that the benefits of knowing that their contributions may help others outweighs the risks" [19] . That is not the case for COVID-19, which means that adequately communicating about and assessing potential risks and benefits of participating in a challenge study and ensuring appropriate informed consent may be impossible. cache = ./cache/cord-325936-rwxg187r.txt txt = ./txt/cord-325936-rwxg187r.txt === reduce.pl bib === id = cord-325669-6kjlcakt author = Fogacci, Silvia title = Management of pregnancy-related hypertensive disorders in patients infected with SARS CoV-2: pharmacological and clinical issues date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3373 sentences = 186 flesch = 38 summary = The purpose of the current review is to highlight the safety of drug treatment for COVID -19 in pregnant women treated with anti-hypertensive medications. In accordance with the European Society of Cardiology (ESC) guidelines for the management of CV diseases during pregnancy, 100-150 mg/day acetylsalicylic acid (aspirin) should be recommended to pregnant women with a high or moderate risk to develop pre-eclampsia (class I; level of evidence A) [17] . In accordance with the American Heart Association (AHA) recommendations [25] , methyldopa should only be prescribed in cases of severe hypertension during pregnancy, considering potential maternal and fetal side effects (class I; level of evidence A). In accordance with the latest ESC guidelines for the management of CV disease during the COVID-19 pandemic, drug-drug interactions should be considered before administering azithromycin in patients treated with LMWH [37] , despite possible beneficial effects by azithromycin in patients infected with SARS-CoV-2 [48] . cache = ./cache/cord-325669-6kjlcakt.txt txt = ./txt/cord-325669-6kjlcakt.txt === reduce.pl bib === id = cord-326273-6rp12py3 author = Chow, Kuan-Chih title = Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date = 2004-04-01 pages = extension = .txt mime = text/plain words = 3202 sentences = 190 flesch = 45 summary = Previous reports have indicated that patients with severe acute respiratory syndrome (SARS)–associated coronavirus infection could develop atypical pneumonia with fulminant pulmonary edema. Severe acute respiratory syndrome (SARS) is an acute infectious disease that affects primarily the lower respiratory tract, with clinical manifestations of atypical pneumonia with dry cough, persistent fever, progressive dyspnea, and, sometimes, the abrupt deterioration of lung function [1] [2] [3] [4] [5] and the ensuing oxygen deprivation-associated systemic organ failures. Nevertheless, when antisense oligonucleotide probes specific to the replicase-encoding (REP) region of the SARS viral genome were used to determine the presence of virus, the intensity of the in situ hybridization signal decreased substantially compared with that detected by probes to the N and M regions ❚Image 2D❚ ❚Table 3❚. B, By using in situ hybridization and antisense oligonucleotide probes specific to the nucleic acid binding protein-encoding (N) and membrane protein-encoding (M) regions of the severe acute respiratory syndrome (SARS) viral genome, the SARS viral signal was detected in the enlarged and multinucleated cell (arrow, purple blue precipitates). cache = ./cache/cord-326273-6rp12py3.txt txt = ./txt/cord-326273-6rp12py3.txt === reduce.pl bib === id = cord-326305-mjd5agvf author = Ashraf, Mohammad Ali title = The application of direct viral cytopathic hypothesis to design drug trials in the battle against COVID-19 date = 2020-08-15 pages = extension = .txt mime = text/plain words = 1109 sentences = 68 flesch = 44 summary = As previously shown, clathrin-mediated endocytosis is the main pathway for virus entry, while doublemembrane vesicles formation and autophagy in the host cell is the mechanism for viral replication [14] . Imatinib, a protein-tyrosine kinase inhibitor that inhibits the BCR-ABL tyrosine kinase which is approved to treat chronic myeloid leukemia by inhibiting ABL oncogenetic pathway has previously shown success in disrupting the viral entry mechanism of both SARS-CoVand MERS-CoV into the cell; hence, it can also be considered as a potentially useful drug to treat patients with severe forms of COVID-19. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor cache = ./cache/cord-326305-mjd5agvf.txt txt = ./txt/cord-326305-mjd5agvf.txt === reduce.pl bib === id = cord-326254-8dlxsf57 author = Glasbey, T. title = Flawed disinfectant recommendations during a pandemic date = 2020-06-15 pages = extension = .txt mime = text/plain words = 907 sentences = 53 flesch = 46 summary = We are deeply concerned over the recommendations in the paper by Kampf [1] recently published in this journal as to what disinfectants are appropriate for use with respect to surface disinfection in the setting of the current Coronavirus pandemic. In that recent paper [1] , the author also suggests that the use of disinfectants containing benzalkonium chloride may be problematic as 'data obtained with benzalkonium chloride at reasonable contact times were conflicting. of Kampf are also diametrically opposed to the United States EPA recommendations for suitable disinfectant products given on their List N: 'Products with Emerging Viral Pathogens and Human Coronavirus claims for use against SARS-CoV-2' [5] . Here, any disinfectant recommended for use against SARS-CoV-2 is required to be included the Australian Register of Therapeutic Goods (ARTG), and the manufacturer or product sponsor is required to hold suitable efficacy data against either the SARS-CoV-2 virus or recognised surrogate [8] . cache = ./cache/cord-326254-8dlxsf57.txt txt = ./txt/cord-326254-8dlxsf57.txt === reduce.pl bib === id = cord-325609-n6dpac6i author = Dawson, Kathryn L. title = Acute increase in deaths among adult congenital heart disease patients during COVID-19 - single center experience. date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1512 sentences = 79 flesch = 49 summary = title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 single center experience. Over the 12-month period preceding the SARS-CoV-2 related stay-at-home order, a total of 4 patients followed by the ACHD service at the University of Washington Medical Center with defects of various severities died in an acute setting. We believe that this change in emergency department volume, combined with the acute increase in mortality reported in this case series, emphasizes the potential adverse outcomes of delayed presentations in medically complex patients. These cases highlight the need for public education regarding the imperative to present for medical care when symptoms would have merited emergency treatment prior to the pandemic, particularly amongst our most vulnerable populations. It also highlights the need for routine follow-up care for patients with congenital heart disease, even in the presence of clinical stability, to assess for subclinical symptom burdens that may herald future acute presentations. cache = ./cache/cord-325609-n6dpac6i.txt txt = ./txt/cord-325609-n6dpac6i.txt === reduce.pl bib === id = cord-326282-uxn64olw author = Lu, Maolin title = Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date = 2020-09-13 pages = extension = .txt mime = text/plain words = 3264 sentences = 207 flesch = 55 summary = To measure conformational dynamics of the SARS-CoV-2 S trimer on the surface of virus particles, we established two types of particles, lentiviral pseudoparticles carrying S, as well as coronaviruslike particles generated by expression of S, membrane (M), envelope (E) and nucleocapsid (N) 15 protein (S-MEN)(24, 25) (Fig. 1, A and B ). Analyses of smFRET data from ligand-free S protein on lentiviral particles revealed that the SARS-CoV-2 S protein is dynamic, sampling at least four distinct conformational states To identify the receptor-bound conformation of the SARS-CoV-2 S protein by smFRET, we measured the conformational consequences of soluble, monomeric hACE2 binding. Addition of 5 the monomeric hACE2 receptor to surface-immobilized virus particles lead to increased occupancy of the low-(~0.1) FRET S protein conformation (Fig. 2E) , which was observed at both the single-molecule and population level (Fig. 2F ). Relative state-occupancy and fitting parameters in each of four FRET-defined conformational states of SARS-CoV-2 spike protein on the surface of virus particles. cache = ./cache/cord-326282-uxn64olw.txt txt = ./txt/cord-326282-uxn64olw.txt === reduce.pl bib === id = cord-326013-5i35zdmv author = Carpinteiro, Alexander title = Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells date = 2020-10-29 pages = extension = .txt mime = text/plain words = 3113 sentences = 175 flesch = 47 summary = The data justify clinical studies investigating whether amitriptyline, a safe drug used clinically for almost 60 years, or other antidepressants that functionally block acid sphingomyelinase prevent SARS-CoV-2 infection. Pretreatment of the cells with 5, 10, 20, or 25 µM amitriptyline prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike for 30 min (Fig. 3B, Fig. 4A ). Treating Vero cells with neutralizing antibodies to spike or with recombinant ACE2 protein prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike (Fig. 3B, Fig. 4A Amitriptyline and other drugs with similar structure and properties have been clinically used for many years (since 1962) to treat patients with depressive disorder. Best results were obtained with venlafaxin, fluoxetine, escitalopram and mirtazipine, drugs that were also shown in the present study to inhibit acid sphingomyelinase and ceramide release upon pp-VSV-SARS-CoV-2 spike infection. cache = ./cache/cord-326013-5i35zdmv.txt txt = ./txt/cord-326013-5i35zdmv.txt === reduce.pl bib === id = cord-326375-8m4110k3 author = Seitzman, Gerami D. title = No Time for Tears date = 2020-03-26 pages = extension = .txt mime = text/plain words = 968 sentences = 77 flesch = 52 summary = In this issue, Jun et al, 1 (https:// www.aaojournal.org/article/S0161-6420(20)30311-0/fulltext) from the National Health Care Group Eye Institute in Singapore, report that they were unable to detect SARS-CoV-2 in the tears of 17 patients diagnosed with COVID-19. 2, 3 In a separate study that evaluated conjunctival swabs of 30 patients with COVID-19 pneumonia in China, only 1 patient demonstrated conjunctivitis, and those swabs showed positive results for SARS-CoV-2 by reverse-transcriptase polymerase chain reaction analysis. Patients who seek treatment from an ophthalmologist and screen positive for signs, symptoms, or both of COVID-19 should forgo an eye examination for prompt SARS-CoV-2 screening. Patients with conjunctivitis seeking treatment from ophthalmology departments should be considered contagious, and SARS-CoV-2 precautions should be taken. Assessing viral shedding and infectivity of tears in coronavirus disease 2019 (COVID-19) patients SARS-CoV-2 viral load in upper respiratory specimens of infected patients Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection cache = ./cache/cord-326375-8m4110k3.txt txt = ./txt/cord-326375-8m4110k3.txt === reduce.pl bib === id = cord-326503-ljle4vq3 author = Morioka, Shinichiro title = Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study date = 2020-07-30 pages = extension = .txt mime = text/plain words = 447 sentences = 39 flesch = 61 summary = key: cord-326503-ljle4vq3 authors: Morioka, Shinichiro; Nakamura, Keiji; Iida, Shun; Kutsuna, Satoshi; Kinoshita, Noriko; Suzuki, Tetsuya; Suzuki, Tadaki; Yamamoto, Kei; Hayakawa, Kayoko; Saito, Sho; Ohmagari, Norio title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study Summary This report aimed to investigate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a hospital setting. A 63-year-old man with pneumonia and an asymptomatic 70-year-old man were admitted to a tertiary hospital with SARS-CoV-2 infection. He was admitted to a general ward of our hospital due to SARS-CoV-2 63 pneumonia on Day 7, and was intubated on Day 10 from diagnosis. of Novel Coronavirus-Infected Pneumonia Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient Evidence of airborne 226 transmission of the severe acute respiratory syndrome virus cache = ./cache/cord-326503-ljle4vq3.txt txt = ./txt/cord-326503-ljle4vq3.txt === reduce.pl bib === id = cord-326148-9wpxm5of author = Van Walle, I. title = Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3790 sentences = 218 flesch = 49 summary = title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Studies containing potentially usable data on clinical performance of SARS-CoV-2 nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. cache = ./cache/cord-326148-9wpxm5of.txt txt = ./txt/cord-326148-9wpxm5of.txt === reduce.pl bib === id = cord-326498-8oa5gkrp author = Gemmati, Donato title = COVID-19 and Individual Genetic Susceptibility/Receptivity: Role of ACE1/ACE2 Genes, Immunity, Inflammation and Coagulation. Might the Double X-Chromosome in Females Be Protective against SARS-CoV-2 Compared to the Single X-Chromosome in Males? date = 2020-05-14 pages = extension = .txt mime = text/plain words = 9876 sentences = 474 flesch = 40 summary = Firstly, SARS-CoV-2 has a strong interaction with the human ACE2 receptor, which plays an essential role in cell entry together with transmembrane serine protease 2 (TMPRSS2); it is interesting to note that the ACE2 gene lays on the X-chromosome, thus allowing females to be potentially heterozygous and differently assorted compared to men who are definitely hemizygous. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. cache = ./cache/cord-326498-8oa5gkrp.txt txt = ./txt/cord-326498-8oa5gkrp.txt === reduce.pl bib === id = cord-326337-s0fp5z1q author = Chan, Kui K. title = An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date = 2020-10-19 pages = extension = .txt mime = text/plain words = 4573 sentences = 256 flesch = 54 summary = Deep mutagenesis of the isolated receptor-binding domain (RBD) by yeast surface display 44 has easily identified mutations in S that retain high expression and ACE2 affinity, yet are no longer bound 45 by monoclonal antibodies and confer resistance (19) . An alternative protein-based antiviral to monoclonal antibodies is to use soluble ACE2 (sACE2) as a 56 decoy to compete for receptor-binding sites on the viral spike (6, (22) (23) (24) (25) of diverse SARS-associated betacoronaviruses that use ACE2 for entry. The sequence 162 diversity observed among natural betacoronaviruses, which display high diversity at the ACE2 binding 163 site, is therefore replicated in the deep mutational scan, which predicts the SARS-CoV-2 spike tolerates 164 substantial genetic diversity at the receptor-binding site for function. From this accessible sequence 165 diversity SARS-CoV-2 might feasibly mutate to acquire resistance to monoclonal antibodies or 166 engineered decoy receptors targeting the ACE2-binding site. cache = ./cache/cord-326337-s0fp5z1q.txt txt = ./txt/cord-326337-s0fp5z1q.txt === reduce.pl bib === id = cord-326045-x8xntne7 author = Chng, Shu-Sin title = Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate date = 2004-12-20 pages = extension = .txt mime = text/plain words = 1254 sentences = 78 flesch = 60 summary = title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate Synthesis of intermediate 1 and analogues proceeded via a highly diastereoselective indium-mediated allylation of α-aminoaldehydes. Based on these findings, it was suggested that the HRV 3C pro inhibitor, AG7088, could serve as a good starting point for modifications leading to an efficient and bio-available inhibitor for the SARS-CoV M pro and other coronavirus main proteinases. The synthesis of 1 in our group has proceeded via the highly stereoselective indium-mediated allylation reaction of N-protected valinal as illustrated in Scheme 2. 8 In addition, when we performed the same indium-mediated allylation reaction on N-t-butyloxycarbonyl-L L-valinal, we obtained the homoallylic alcohol as an 87:13 mixture of syn/anti isomers (Scheme 4). The critical step in the synthesis involved a highly diastereoselective indium-mediated allylation reaction. cache = ./cache/cord-326045-x8xntne7.txt txt = ./txt/cord-326045-x8xntne7.txt === reduce.pl bib === id = cord-326257-rcv8sh22 author = Simmonds, P. title = Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date = 2020-05-01 pages = extension = .txt mime = text/plain words = 3499 sentences = 172 flesch = 47 summary = C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5'U/A and 3'U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). cache = ./cache/cord-326257-rcv8sh22.txt txt = ./txt/cord-326257-rcv8sh22.txt === reduce.pl bib === id = cord-326730-aprb819p author = Perkmann, T. title = Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity date = 2020-06-05 pages = extension = .txt mime = text/plain words = 3232 sentences = 236 flesch = 53 summary = Methods: We included a total of 1,154 specimens from pre-COVID-19 times and 65 samples from COVID-19 patients ([≥]14 days after symptom onset) to evaluate the test performance of SARS-CoV-2 serological assays by Abbott, Roche, and DiaSorin. Conclusion: We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. The present evaluation aims to compare three of these test systems manufactured by Abbott (11), DiaSorin (12), and Roche (13) , with particular emphasis on specificity, which is crucial for an adequate positive predictive value given the current low seroprevalence worldwide. We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. cache = ./cache/cord-326730-aprb819p.txt txt = ./txt/cord-326730-aprb819p.txt === reduce.pl bib === id = cord-326393-gxy1w0qk author = Martino, Marcello Di title = CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4243 sentences = 399 flesch = 52 summary = title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD Desde que se produjeron los primeros casos de infección por SARS-CoV-2 (COVID-19) a finales de diciembre de 2019 en Wuhan (China), el crecimiento exponencial de esta enfermedad ha llevado a una pandemia, declarada como tal por la Organización Mundial de la Sanidad (OMS) el 11 de marzo J o u r n a l P r e -p r o o f 2020 (1, 2) . Se analizaron la edad, sexo, estado funcional definido según la escala ECOG (21), antecedentes personales, diagnóstico, tipo de intervención quirúrgica, momento en que se confirmó la infección por SARS-CoV-2, el tratamiento requerido para la misma (Tabla 1), la gravedad de la infección respiratoria según la BRCSS (20) y las complicaciones postoperatorias según la clasificación de Dindo-Clavien (19) . cache = ./cache/cord-326393-gxy1w0qk.txt txt = ./txt/cord-326393-gxy1w0qk.txt === reduce.pl bib === id = cord-326532-2ehuuvnx author = Götzinger, Florian title = COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study date = 2020-06-25 pages = extension = .txt mime = text/plain words = 5321 sentences = 282 flesch = 46 summary = This study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across Europe to inform physicians and health-care service planning during the ongoing pandemic. Significant risk factors for requiring ICU admission in multivariable analyses were being younger than 1 month (odds ratio 5·06, 95% CI 1·72–14·87; p=0·0035), male sex (2·12, 1·06–4·21; p=0·033), pre-existing medical conditions (3·27, 1·67–6·42; p=0·0015), and presence of lower respiratory tract infection signs or symptoms at presentation (10·46, 5·16–21·23; p<0·0001). For this cohort study, European members of the Paediatric Tuberculosis Network European Trials Group (ptbnet)-which currently includes 304 clinicians and researchers, most of whom are based at tertiary or quaternary paediatric infectious diseases or paediatric pulmonology units, across 128 paediatric health-care institutions in 31 European countries [15] [16] [17] [18] [19] [20] -were invited to contribute cases of confirmed SARS-CoV-2 infection that had been managed at or managed remotely by their health-care institution (including individuals admitted to other hospitals or identified during community screening) before or during the study period. cache = ./cache/cord-326532-2ehuuvnx.txt txt = ./txt/cord-326532-2ehuuvnx.txt === reduce.pl bib === id = cord-326706-75mjs6vm author = Waterfield, Thomas title = Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study date = 2020-11-10 pages = extension = .txt mime = text/plain words = 3573 sentences = 242 flesch = 49 summary = Following multivariable analysis four independent variables were identified as significantly associated with SARS-CoV-2 seropositivity: known infected household contact OR=10.9 (95% CI 6.1 to 19.6); fatigue OR=16.8 (95% CI 5.5 to 51.9); gastrointestinal symptoms OR=6.6 (95% CI 3.0 to 13.8); and changes in sense of smell or taste OR=10.0 (95% CI 2.4 to 11.4). The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. 26 Participants and their parents provided information at enrolment relating to age, sex, previous health and potential predictors of SARS-CoV-2 seropositivity including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/ antibody testing. cache = ./cache/cord-326706-75mjs6vm.txt txt = ./txt/cord-326706-75mjs6vm.txt === reduce.pl bib === id = cord-325958-1v1pg2z0 author = Lange, Clemens title = Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2672 sentences = 149 flesch = 45 summary = In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. Since the outbreak, many studies described ACE2 expression across human tissues, including lung, stomach, ileum, colon, liver and kidney 8, 9 , supporting the clinical observation that SARS-CoV-2 can infect multiple organs. To obtain information on transcription of ACE2 and associated molecules required for cell entry by SARS-CoV-2, existing datasets of 38 conjunctival samples from 38 patients were included in this study. This study shows that ACE2, which is the main receptor for SARS-CoV-2 6 , is not significantly expressed in healthy and diseased human conjunctival samples. cache = ./cache/cord-325958-1v1pg2z0.txt txt = ./txt/cord-325958-1v1pg2z0.txt === reduce.pl bib === id = cord-326514-7plamtl8 author = Veerus, Piret title = Seroprevalence of SARS‐CoV‐2 antibodies among pregnant women in Estonia: a call for epidemiological studies date = 2020-09-24 pages = extension = .txt mime = text/plain words = 662 sentences = 37 flesch = 51 summary = On April 7, 2020 Mehreen Zaigham and Ola Andersson published a systematic review of maternal and perinatal outcomes in 108 pregnancies with Covid‐19 concluding that careful monitoring of such pregnancies and is warranted.(1) We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS‐CoV‐2) causing Covid‐19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. 1 We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS-CoV-2) causing Covid-19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. In comparison with available data from Spain, 9 seroprevalence of SARS-CoV-2 antibodies among pregnant women in Estonia was 10 times lower than among the general population in Spain indicating the possibility of regional differences in the incidence of COVID-19 across Europe. cache = ./cache/cord-326514-7plamtl8.txt txt = ./txt/cord-326514-7plamtl8.txt === reduce.pl bib === id = cord-326718-jboiufoq author = Deming, Meagan E. title = COVID-19 and Lessons to Be Learned from Prior Coronavirus Outbreaks date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2539 sentences = 121 flesch = 41 summary = In addition, three novel CoVs have emerged as zoonotic human infections in the past 17 years; SARS-CoV, Middle East respiratory syndrome CoV (MERS-CoV), and the 2019 novel CoV (SARS-CoV-2) (2) have each been associated with lower respiratory symptoms, progressing in a subset of individuals to acute respiratory distress syndrome (ARDS) and death. Interestingly NL63, an hCoV that also uses angiotensin converting enzyme 2 as the host receptor, but typically causes mild upper respiratory disease, was the cause of a cluster of severe pediatric pneumonias in China in 2018, during which half of the patients were identified with viruses containing a specific substitution in the spike glycoprotein that enhanced binding to and entry via angiotensin converting enzyme 2 (4). It can be hypothesized that the spike glycoprotein of SARS-CoV-2, with its PERSPECTIVE structural similarity and higher affinity binding to angiotensin converting enzyme 2, provokes a similar mechanism of lung pathology leading to ARDS with severe COVID-19. cache = ./cache/cord-326718-jboiufoq.txt txt = ./txt/cord-326718-jboiufoq.txt === reduce.pl bib === id = cord-326643-obfvi3ms author = Lo Giudice, Roberto title = The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in Dentistry. Management of Biological Risk in Dental Practice date = 2020-04-28 pages = extension = .txt mime = text/plain words = 4574 sentences = 293 flesch = 54 summary = Considering the virus' route of transmission, a specific protocol should be applied to reduce the risk of infection in addition to measures that prevent the spread of infection from a patient to another person or medical tools and equipment (cross-infection). Due to the transmission route, in addition to measures that prevent diffusion of the infection from a patient to another person or medical tools and equipment (cross-infection), it is advisable to add further airborne and contact precautions to the routine standard hygienic procedures in order to reduce the risk of SARS-CoV-2 transmission. The use of personal protective equipment (PPE) such as gloves, masks, visors, goggles, dental uniform, and surgical gown and shoes (see section on PPEs below). To reduce the risk of SARS-CoV-2 infection, given how the disease spreads and the current health crisis, the following prevention measures are suggested in addition to what is already generally performed: cache = ./cache/cord-326643-obfvi3ms.txt txt = ./txt/cord-326643-obfvi3ms.txt === reduce.pl bib === id = cord-326721-2v5wkjrq author = Xiao, Wenlei title = A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks date = 2020-03-17 pages = extension = .txt mime = text/plain words = 4478 sentences = 282 flesch = 57 summary = Distinguished with other epidemiological models, such as SIR, SEIR, etc., that compute the theoretical number of infected people in a closed population, CDIM considers the immigration and emigration population as system inputs, and administrative and medical resources as dynamic control variables. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint : Effective infectious increment (can be negative); : Total non-isolated cases (asymptomatic carriers); : Patient increment (symptom onset); : Total isolated cases (confirmed patients after symptom onset); Figure 4 : Basic principle of the cybernetics-based dynamic infection model be made. In the view of this, we used the data from Shanghai, a relatively well controlled city, to identify and calibrate the key parameters of the incubation period and the basic reproductive number. In Shanghai Model, there is no worry about the shortage of medical supplies, so a negative summation channel performs a direct control effect on the positive feedback infection loop, which is thus of paramount importance in reducing the number of total infectious cases. cache = ./cache/cord-326721-2v5wkjrq.txt txt = ./txt/cord-326721-2v5wkjrq.txt === reduce.pl bib === id = cord-326341-egtnqlov author = Liotti, Flora Marzia title = Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date = 2020-09-23 pages = extension = .txt mime = text/plain words = 514 sentences = 35 flesch = 60 summary = title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus cache = ./cache/cord-326341-egtnqlov.txt txt = ./txt/cord-326341-egtnqlov.txt === reduce.pl bib === id = cord-326427-06djb0sd author = Cao, Dongmei title = Vaginal delivery in women with COVID-19: report of two cases date = 2020-10-02 pages = extension = .txt mime = text/plain words = 2582 sentences = 148 flesch = 52 summary = Because of the positive result of the maternal swabs for SARS-CoV-2 obtained on the 2nd day after sampling, we transferred the mother to the designated hospital and followed up with her by telephone interviews. Although the nucleic acid test for SARS-CoV-2 of the second patient was negative on February 29, the result was positive Delayed cord clamping and skin-to-skin contact between the mother and infant were not permitted in either case. The pregnant woman in case 2 had the typical manifestations of COVID-19, including cough, lymphopenia, and abnormal chest CT images, and her infant's nasopharyngeal swab tested negative for SARS-CoV-2. The two cases in our study showed that there is still insufficient evidence supporting maternal-fetal vertical transmission of COVID-19 in late pregnancy, and there is no evidence that vaginal delivery would increase the possibility of neonatal infection. In conclusion, there is still insufficient evidence supporting maternal-fetus vertical transmission of COVID-19 for pregnant women in late pregnancy, and vaginal delivery may not increase the possibility of neonatal infection. cache = ./cache/cord-326427-06djb0sd.txt txt = ./txt/cord-326427-06djb0sd.txt === reduce.pl bib === id = cord-326568-twv2i3fb author = Bruminhent, Jackrapong title = Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date = 2020-09-15 pages = extension = .txt mime = text/plain words = 4402 sentences = 245 flesch = 48 summary = To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians' diagnoses. Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. Apart from close contact with an infected case and visiting high-risk places, we found that having no medical coverage and presenting with productive cough were predictors of being diagnosed with COVID-19 among PUIs. SARS-CoV-2 is an emerging respiratory virus that commonly causes no or mild respiratory tract infection and is occasionally complicated by severe pneumonia [1] . cache = ./cache/cord-326568-twv2i3fb.txt txt = ./txt/cord-326568-twv2i3fb.txt === reduce.pl bib === id = cord-326320-flfrdrbi author = Choudhary, Shalki title = Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date = 2020-08-29 pages = extension = .txt mime = text/plain words = 4675 sentences = 280 flesch = 56 summary = title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 The multi-targeting potential of generated analogues was explored against various targets involved in the pathogenesis of COVID-19 including SARS-CoV-2 SP, ACE2, furin, TMPRSS2 (in viral attachment) and 3CLPro (in viral replication). A cutoff value of 3 was used for the screening of compounds based on synthetic possibility and topranked molecules were submitted to structure-guided drug binding analysis such as molecular docking studies. All these molecules were docked against SARS-CoV-2 SP-ACE2 complex, furin, TMPRSS2 and main protease (3CLPro) and the binding affinity of their docked complexes was also calculated in terms of MM-GBSA score. J o u r n a l P r e -p r o o f 44 A combination of scaffold morphing and a structure-based drug designing approach was successfully utilized to identify putative multi-targeting analogues of arbidol against COVID-19. cache = ./cache/cord-326320-flfrdrbi.txt txt = ./txt/cord-326320-flfrdrbi.txt === reduce.pl bib === id = cord-326581-31trqhi1 author = Ihling, Christian title = Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients date = 2020-06-22 pages = extension = .txt mime = text/plain words = 1147 sentences = 81 flesch = 54 summary = title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. 2 On the basis of the prospective goals of this coalition, the aim of this "proof-of-principle" study is to highlight the potential of MS in identifying SARS-CoV-2 proteins, even from highly diluted samples, such as gargle solutions of COVID-19 patients. All samples had been classified as SARS-CoV-2-positive by three reverse-transcription and quantitative polymerase chain reaction (RT-qPCR) analyses identifying E-, S-, and N-gene RNAs. For protein precipitation, 1 mL of acetone (−20°C) was added to 750 μL of gargle solution and stored overnight at −20°C. We present a protein MS-based method to specifically detect SARS-CoV-2 virus proteins from highly diluted gargle solutions of COVID-19 patients. Using this approach, we were able to identify peptides originating from SARS-CoV-2 nucleoprotein in gargle solution samples. cache = ./cache/cord-326581-31trqhi1.txt txt = ./txt/cord-326581-31trqhi1.txt === reduce.pl bib === id = cord-326911-va3x6au2 author = Ramos-Mandujano, G. title = A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4424 sentences = 288 flesch = 55 summary = We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. To date, molecular diagnosis of COVID-19 predominantly relies on detection of SARS-CoV-2 RNA using real-time reverse transcription polymerase chain reaction (rRT-PCR) assays, such as those approved by the US Centers for Disease Control and Prevention (US CDC) 1 . MAVRICS performed on par or better than commercial RNA extraction kits in rRT-PCR detection of SARS-CoV-2, influenza viruses and respiratory syncytial virus in various clinical and environmental samples. . https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint Next, we aimed to develop an efficient SiMNP-based RNA extraction protocol using the contrived SARS-CoV-2 samples and US CDC 2019-nCoV_N1 and N3 rRT-PCR assays. cache = ./cache/cord-326911-va3x6au2.txt txt = ./txt/cord-326911-va3x6au2.txt === reduce.pl bib === id = cord-326916-bakwk4tm author = Fauver, Joseph R. title = Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States date = 2020-05-07 pages = extension = .txt mime = text/plain words = 5556 sentences = 323 flesch = 53 summary = To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. To delineate the roles of domestic and international virus spread in the emergence of new United States COVID-19 outbreaks, we sequenced SARS-CoV-2 viruses collected from cases identified in Connecticut. We sequenced SARS-CoV-2 genomes from nine of the first COVID-19 cases reported in Connecticut, with sample collection dating from March 6-14, 2020 (Data S1). By combining daily passenger volumes ( Figure 2B ) with COVID-19 prevalence at the travel route origin (Figures 2C and 2D) and accounting for differences in reporting rates, we found that the domestic and international SARS-CoV-2 importation risk started to increase dramatically at the beginning of March 2020 ( Figure 2E ). cache = ./cache/cord-326916-bakwk4tm.txt txt = ./txt/cord-326916-bakwk4tm.txt === reduce.pl bib === id = cord-326736-jd6fvaop author = Bosco-Lauth, Angela M. title = Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date = 2020-05-29 pages = extension = .txt mime = text/plain words = 922 sentences = 68 flesch = 50 summary = title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. The first report of reverse zoonosis, or transmission from human to animal, was reported 46 from Hong Kong, where a COVID patient's dog tested PCR positive for SARS2 multiple times 47 (Sit et al. Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of 414 COVID-19 patients in a veterinary campus Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Transmission of 422 SARS-CoV-2 in Domestic Cats cache = ./cache/cord-326736-jd6fvaop.txt txt = ./txt/cord-326736-jd6fvaop.txt === reduce.pl bib === id = cord-326864-i1r3bv4p author = Hon, Kam Lun title = Coronavirus disease 2019 (COVID-19): latest developments in potential treatments date = 2020-06-29 pages = extension = .txt mime = text/plain words = 6265 sentences = 370 flesch = 46 summary = 4 COVID-19 is a respiratory tract infection that causes mild symptoms in the majority of cases, but can also lead to ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 : latest developments in potential treatments drugsincontext.com mortality and morbidity. SARS-CoV is closely related to civet and bat CoVs, but it is phylogenetically divergent from other coronaviruses associated with human infections, including ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com OC43, NL63, 229E, and HKU1. In a clinical trial involving 199 patients with laboratory-confirmed SARS-CoV-2 infection, lopinavir-ritonavir treatment was not associated with any clinical improvements compared with standard care. 25 Long and colleagues reported that corticosteroid therapy using methylprednisolone, dexamethasone, and hydrocortisone was beneficial in treating ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com SARS-CoV patients, 78 and significantly prolonged survival time in clinical cases. cache = ./cache/cord-326864-i1r3bv4p.txt txt = ./txt/cord-326864-i1r3bv4p.txt === reduce.pl bib === id = cord-326406-n0qi6gs8 author = Creed, Marina title = Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1801 sentences = 111 flesch = 48 summary = title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. Here, we report a 59-year-old woman with aquaporin-4-positive (AQPR4+) neuromyelitis Optica treated with rituximab who developed mild respiratory symptoms with COVID-19, despite B cell depletion at the time of infection. To infect the host, SARS-CoV-2 uses the viral receptors ACE2 and TMPRSS2, which are membrane associated proteins expressed in many cells throughout the body, particularly the respiratory system 2 . Most cases are mild, but in a number of patients, the disease evolves into an acute respiratory distress syndrome (ARDS) 3 or a dysregulated immune system state leading to cytokine storm, most often in older adults, requiring intensive care and resulting in increased mortality 4 . Here, we describe an AQPR4+ NMOSD patient treated with rituximab who developed mild COVID-19 infection despite B cell depletion. cache = ./cache/cord-326406-n0qi6gs8.txt txt = ./txt/cord-326406-n0qi6gs8.txt === reduce.pl bib === id = cord-326929-ytix4l1o author = Samillan, V. J. title = Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4344 sentences = 214 flesch = 48 summary = In this study, we explored the relationship between the cumulative number of infections and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection and mortality of SARS-CoV-2 in Peru. Although more studies are necessary, the rate of infection and the severity of the diseases seems different for people living in cities at high altitudes, where not only hipoxia is a major factor, but other factors such as air quality, solar radiation, and population density, could play a role in SARS-CoV-2 person-to-person transmission. The main objectives of this study was to explore the relationship between SARS-CoV-2 infection and mortality cases, case-fatality rates with a set of climate (temperature, precipitation, solar radiation, water vapor pressure, and wind), environmental data (elevation, NDVI, PM 2.5 and NO 2 concentration), and population density in Peru. cache = ./cache/cord-326929-ytix4l1o.txt txt = ./txt/cord-326929-ytix4l1o.txt === reduce.pl bib === id = cord-326882-bbn1tfq5 author = Li, Quan title = Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date = 2020-04-14 pages = extension = .txt mime = text/plain words = 1675 sentences = 104 flesch = 55 summary = We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARSCoV-2. To explore the variability in genetic polymorphisms and expression in human ACE2 (hACE2), we set out to determine if there were any differences between the Asian and Caucasian populations for ACE2 polymorphisms and compare the variability of hACE2 expression in peripheral blood among eight different populations. In order to investigate whether differences in genetic variations exist between Caucasians and Asians and if these variants can influence the efficiency of cell entry of SARS-CoV-2, we retrieved the variants in the hACE2 from gnomAD v2.1 exomes13. Asians and Other Races Express Similar Levels of and Share the Same Genetic Polymorphisms of the SARS-CoV-2 Cell-Entry Receptor cache = ./cache/cord-326882-bbn1tfq5.txt txt = ./txt/cord-326882-bbn1tfq5.txt === reduce.pl bib === id = cord-326888-0p8nctpy author = Gercina, Anne Caroline title = What is the best mouthrinse against Coronaviruses? date = 2020-08-13 pages = extension = .txt mime = text/plain words = 548 sentences = 49 flesch = 42 summary = (1) Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post‐surgical infectious complications. The person-to-person transmission of SARS-CoV-2 may occur directly or indirectly through saliva, and a preoperational use of antimicrobial mouthwash is considered to reduce the number of oral microbes. 1 Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post-surgical infectious complications. All rights reserved Even assuming that 1% of hydrogen peroxide is the best alternative to prevent transmission during oral procedures, its use on postoperative does not seem to be necessary. The purpose of rinsing 1% hydrogen peroxide is to protect the professional from avoiding transmission during the procedure from patients already infected by SARS-CoV-2. Comparison of In Vitro Inactivation of SARS CoV-2 with Hydrogen Peroxide and Povidone-Iodine Oral Antiseptic Rinses cache = ./cache/cord-326888-0p8nctpy.txt txt = ./txt/cord-326888-0p8nctpy.txt === reduce.pl bib === id = cord-326965-xrnhkcsv author = Lacout, Carole title = A new diagnosis of systemic capillary leak syndrome in a patient with COVID-19 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 968 sentences = 64 flesch = 49 summary = SIR, With the coronavirus disease 2019 (COVID-19) pandemic, we are discovering that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has properties to induce a dysregulated immune response that exceed the simple respiratory infection [1] . Systemic capillary leak syndrome is a rare immune disorder that evolves with repeated episodes of pseudoshock that can occur spontaneously or can be triggered by viral infections. Systemic capillary leak syndrome is a rare disorder that can be secondary to blood malignancies, immune disorders, toxics, medication, infections or idiopathic (Clarkson's disease) [4] . In conclusion, we think that it is not a coincidence that a first episode of systemic capillary leak syndrome, which is a very rare disease, occurred simultaneously with a respiratory infection caused by SARS-CoV-2. Idiopathic systemic capillary leak syndrome (Clarkson disease) SARS-CoV-2 induces acute and refractory relapse of systemic capillary leak syndrome (Clarkson's disease) cache = ./cache/cord-326965-xrnhkcsv.txt txt = ./txt/cord-326965-xrnhkcsv.txt === reduce.pl bib === id = cord-327028-dbvucvy3 author = Zhang, Cantong title = Controversial treatments: An updated understanding of the coronavirus disease 2019 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 1898 sentences = 123 flesch = 40 summary = To reduce the case‐fatality rate among coronavirus disease 2019 patients, we should not ignore the complications, such as RNAaemia, acute respiratory distress syndrome, and multiple organ dysfunction. To help understand the advantages and limitations of differential treatments, we provide a timely review and discuss the complications and corresponding major treatments, especially controversial ones such as antiviral therapy (remdesivir, ribavirin, and chloroquine), glucocorticoid therapy, extracorporeal support including an artificial liver system, and extracorporeal membrane oxygenation based on available evidence. Furthermore, we list a table to conclude the mechanism, advantages, and limitations for different treatments mentioned in this review (Table 2) The mechanism of remdesivir against the virus showed that the drug effectively inhibited the Ebola virus RNA-dependent RNA polymerase (RdRp) complex. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-327028-dbvucvy3.txt txt = ./txt/cord-327028-dbvucvy3.txt === reduce.pl bib === id = cord-327169-sz4ildnd author = Mondoni, Michele title = Utility and safety of bronchoscopy during SARS-CoV-2 outbreak in Italy: a retrospective, multicenter study date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1346 sentences = 86 flesch = 42 summary = The primary aim of the present study was to describe the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swab(s) and a clinical and radiological suspicion of COVID-19 pneumonia. The indications of bronchoscopy were: -diagnosis of SARS-CoV-2 pneumonia in patients with previously negative nasopharyngeal swab (clinical and radiological suspicion of pneumonia); -need for undelayable procedures in COVID-19 patients (e.g., massive hemoptysis, post-obstructive atelectasis). The diagnostic yield of bronchoscopy was calculated dividing the number of patients with a molecular diagnosis of SARS-CoV-2 infection following the collection of bronchoscopic specimens by the number of patients with a suspected diagnosis of COVID-19 pneumonia. This is to our knowledge the largest study on the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swabs and a clinical/radiological suspicion of SARS-CoV-2 infection. Urgent/life-saving bronchoscopies were performed in 31 patients with a confirmed COVID-19 diagnosis for obstructive atelectasis, suspected concomitant lower respiratory tract infections, severe hemoptysis, suspected tracheal lacerations in patients mechanically ventilated, tracheostomy complications, and suspected concomitant pulmonary tuberculosis. cache = ./cache/cord-327169-sz4ildnd.txt txt = ./txt/cord-327169-sz4ildnd.txt === reduce.pl bib === id = cord-326883-j7pbe50g author = Stöbe, Stephan title = Echocardiographic characteristics of patients with SARS-CoV-2 infection date = 2020-08-14 pages = extension = .txt mime = text/plain words = 4812 sentences = 265 flesch = 39 summary = RESULTS AND METHODS: An extended echocardiographic image acquisition protocol was performed in 18 patients with SARS-CoV-2 infection assessing LV longitudinal, radial, and circumferential deformation including rotation, twist, and untwisting. The present paper describes the experience at the Leipzig University Hospital in detecting myocardial involvement in SARS-CoV-2-infected patients by echocardiography using a specialized extended imaging and analysis protocol to analyze different components of myocardial deformation [19] . In contrast to conventional echocardiography, deformation imaging (n = 14) revealed several interesting findings potentially documenting myocardial involvement in SARS-CoV-2-infected patients with mild/moderate and severe symptoms ( Table 2 ; Figs. The finding of a "reverse basal tako-tsubo-like syndrome" of basal LV segments might also be explained by the edema, which leads to abnormal basal rRS curves without any alterations Fig. 2 Rotational deformation pattern of the same SARS-CoV-2-infected patient with COVID-19 pulmonary disease as in Fig. 1 : normal radial strain patterns are documented in apical (a) and basal (b) left-ventricular (LV) segments. cache = ./cache/cord-326883-j7pbe50g.txt txt = ./txt/cord-326883-j7pbe50g.txt === reduce.pl bib === id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 pages = extension = .txt mime = text/plain words = 11098 sentences = 688 flesch = 48 summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. cache = ./cache/cord-327000-oyg3oyx1.txt txt = ./txt/cord-327000-oyg3oyx1.txt === reduce.pl bib === id = cord-327086-u3l8nr73 author = Mauvais-Jarvis, Franck title = Estradiol, Progesterone, Immunomodulation, and COVID-19 Outcomes date = 2020-07-30 pages = extension = .txt mime = text/plain words = 4712 sentences = 214 flesch = 34 summary = Abbreviations: COVID-19, coronavirus disease-2019; E2, 17β-estradiol; ER, estrogen receptor; HCC, hepatocellular carcinoma; IL-1β, interleukin-1β; IL-6, interleukin-6; ISARIC, International Severe Acute Respiratory and Emerging Infections Consortium; MERS-CoV, Middle East respiratory syndrome coronavirus; MHT, menopausal hormone therapy; P4, progesterone; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SERM, selective estrogen receptor modulator; TNF-α, tumor necrosis factor α; Tregs, regulatory T cells. In most experimental human or rodent models, the anti-inflammatory actions of E2 on innate immunity includes the suppression of the production of proinflammatory cytokines, for example, IL-6, IL-1β, and TNF-α, by monocytes and macrophages (a major factor in the COVID-19 cytokine storm) and a strong inhibition of CCL2, thus preventing innate immune cells migration into inflamed areas, particularly neutrophils and monocytes. Taken together, these findings suggest that E2 and related SERMs have 2 potential protective mechanisms of action against SARS-CoV-mediated pneumonias in mice: 1) an estrogen-dependent decrease in the deadly innate immune response and cytokine storm in the lungs, thus preventing respiratory failure, and 2) specific to SERMs, an off-target direct inhibition of SARS-CoV replication and cytopathic effects. cache = ./cache/cord-327086-u3l8nr73.txt txt = ./txt/cord-327086-u3l8nr73.txt === reduce.pl bib === id = cord-326983-h6gdck2u author = Ferretti, Andrew P. title = Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date = 2020-10-20 pages = extension = .txt mime = text/plain words = 5634 sentences = 274 flesch = 56 summary = We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). cache = ./cache/cord-326983-h6gdck2u.txt txt = ./txt/cord-326983-h6gdck2u.txt === reduce.pl bib === id = cord-326956-oz047qmf author = Lu, Yiping title = Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study date = 2020-08-03 pages = extension = .txt mime = text/plain words = 5822 sentences = 287 flesch = 48 summary = COVID-19 patients had statistically significantly higher bilateral gray matter volumes (GMV) in olfactory cortices, hippocampi, insulas, left Rolandic operculum, left Heschl's gyrus and right cingulate gyrus and a general decline of MD, AD, RD accompanied with an increase of FA in white matter, especially AD in the right CR, EC and SFF, and MD in SFF compared with non-COVID-19 volunteers (corrected p value <0.05). We found that these recovered COVID-19 patients were more likely to have enlarged olfactory cortices, hippocampi, insulas, Heschl's gyrus, Rolandic operculum and cingulate gyrus, and a general decline of Mean Diffusivity (MD), Axial Diffusivity (AD), Radial Diffusivity (RD) accompanied with an increase of Fractional Anisotropy (FA) in white matter, especially AD in the right Coronal Radiata (CR), External Capsule (EC) and Superior Frontal-occipital Fasciculus (SFF), and MD in SFF compared with non-COVID-19 volunteers. cache = ./cache/cord-326956-oz047qmf.txt txt = ./txt/cord-326956-oz047qmf.txt === reduce.pl bib === id = cord-326833-boxgt4kb author = Marimuthu, Janakiram title = HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date = 2020-07-07 pages = extension = .txt mime = text/plain words = 1364 sentences = 103 flesch = 65 summary = We conducted a retrospective, record based case series including three males, 2 females and 1 transgender PLHA co‐infected with SARS CoV‐2 in the Indian state of Tamil Nadu. Through literature search in PubMed and World Health organization' (WHO) database on COVID-19, we obtained 5 case reports, and 5 case series on PLHA infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). Hence, we conducted a retrospective, record based case series on the PLHA who were infected with SARS CoV-2, in the Indian state of Tamil Nadu. 5 Our study reports that the clinical features of COVID-19 co-infection among PLHA in South India is mild, and the clinical outcomes are favorable. Further studies including greater number of patients should be done, to better understand the epidemiology, clinical outcomes and appropriate treatment modalities in the HIV-COVID 19 co-infection. COVID-19 in patients with HIV: clinical case series cache = ./cache/cord-326833-boxgt4kb.txt txt = ./txt/cord-326833-boxgt4kb.txt === reduce.pl bib === id = cord-327240-nohxk3y6 author = Muller, Matthew P. title = Adverse Events Associated with High‐Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome date = 2012-01-06 pages = extension = .txt mime = text/plain words = 4551 sentences = 254 flesch = 48 summary = Logistic regression was used to evaluate the association between ribavirin use and each adverse event (progressive anemia, hypomagnesemia, hypocalcemia, bradycardia, transaminitis, and hyperamylasemia) after adjusting for SARS‐related prognostic factors and corticosteroid use. 11, 12 In Toronto, Ontario, Canada, most patients seen during the initial phase of the outbreak were treated with high-dose intravenous ribavirin, based on a protocol recommended for the treatment of hemorrhagic fever. [13] [14] [15] [16] Studies of the clinical efficacy of ribavirin in patients with SARS were inconclusive, 11, [17] [18] [19] [20] and significant adverse events were reported, including severe hemolysis. 27, 28 We report the frequency of adverse events in 183 patients treated with high-dose ribavirin during the Toronto SARS outbreak. Our finding that 57% of patients developed progressive anemia (largely associated with hemolysis) is substantially higher than the 9-19% rate seen in ribavirin-treated patients with hepatitis C but is consistent with the 49-73% reported in previous noncontrolled studies of ribavirin-related adverse events in patients with SARS. cache = ./cache/cord-327240-nohxk3y6.txt txt = ./txt/cord-327240-nohxk3y6.txt === reduce.pl bib === id = cord-326984-o27rp468 author = CHIEN, Jung‐Yien title = Temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome date = 2006-10-16 pages = extension = .txt mime = text/plain words = 3569 sentences = 202 flesch = 53 summary = To improve understanding of the immuno‐pathological processes involved in lung injury associated with SARS, the temporal changes in cytokine/chemokine profiles in the sera of SARS patients were compared with those of patients with community‐acquired pneumonia (CAP), according to the degree of lung involvement. 5 In order to improve the understanding of the immuno-pathogenesis of SARS, an analysis of the dynamic changes in cytokine/chemokine profiles was undertaken in SARS patients who initially had a normal CXR, but who later progressed to typical manifestations of lung involvement. In this study, we investigated 14 SARS patients with initially normal CXR and 24 patients with non-SARS CAP, to clarify the association between temporal changes in cytokine/chemokine profiles and the severity of lung involvement during SARS. 15, 17, 18 Similar to the current study, many of the 'classic' cytokines mediating inflammation in acute lung injury, 18 such as TNF-α and IFN-γ, were not reported to be significantly increased during SARS. cache = ./cache/cord-326984-o27rp468.txt txt = ./txt/cord-326984-o27rp468.txt === reduce.pl bib === id = cord-326666-melz5fq4 author = Sun, Weitao title = The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date = 2020-09-03 pages = extension = .txt mime = text/plain words = 1723 sentences = 138 flesch = 62 summary = title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. 578 shown with special markers at the top of colored blocks representing ORFs. Mutation 623 10818G>T in ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which 624 results in amino acid M37F mutation in transmembrane protein nsp6. ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which results in amino 631 acid M37F mutation in transmembrane protein nsp6. cache = ./cache/cord-326666-melz5fq4.txt txt = ./txt/cord-326666-melz5fq4.txt === reduce.pl bib === id = cord-327124-kzavc4ez author = Wang, Ming title = SARS-CoV Infection in a Restaurant from Palm Civet date = 2005-12-17 pages = extension = .txt mime = text/plain words = 3408 sentences = 172 flesch = 60 summary = Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003–2004 were a waitress at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant a short distance from animal cages. Only 5 signature nt variations (SNVs) were observed in the 5 complete S gene sequences from palm civets determined in this study, indicating that SARS-CoV sequences from civets at the restaurant were not different from those of the original animal SARS source. These most recent SARS patients were therefore infected by SARS-CoV that is most closely related to virus isolates from palm civets at the restaurant (Figure) (6) . When the complete genomes of SARS-CoV from palm civets at the restaurant were compared with sequences of human isolates, 62 SNVs were identified. However, when the complete genome was compared with sequences of virus isolated from palm civets from animal markets in the 2003 epidemic, only 37 SNVs were identified. cache = ./cache/cord-327124-kzavc4ez.txt txt = ./txt/cord-327124-kzavc4ez.txt === reduce.pl bib === id = cord-327005-7zgolyqf author = Zhang, Lan title = Clinical Features of 33 Cases in Children Infected With SARS-CoV-2 in Anhui Province, China–A Multi-Center Retrospective Cohort Study date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3747 sentences = 213 flesch = 57 summary = Here, we report 33 patients under the age of 19 years with confirmed COVID-19 infection from Anhui province, China, and describe the clinical features, laboratory, and radiological characteristics of a chest CT, treatment, and clinical outcome. Information recorded included demographic data, medical history, familial clustering, details of the confirmed patients, if any, in the family, whether they were residents of Wuhan, or traveled to Wuhan, whether they came in contact with confirmed patients, signs, and symptoms, including pharyngodynia, fever, cough, vomiting and diarrhea, fatigue, tightness in the chest, total WBC and lymphocyte percentages, levels of C-reactive protein (CRP), IL-6, liver function, CKMB, a marker of myocardial injury, chest CT, administration of INF a, lopinavir and ritonavir, ribavirin, or arbidol, and titers of Mp-IgM, anti-parainfluenza virus IgM, anti-influenza virus IgM, and anti-adenovirus IgM. A retrospective cohort study was used to analyze the epidemiological data, clinical symptoms, and signs, changes in WBC and total lymphocyte counts, chest CT, and the different treatments in children infected with SARS-COV-2. cache = ./cache/cord-327005-7zgolyqf.txt txt = ./txt/cord-327005-7zgolyqf.txt === reduce.pl bib === id = cord-327095-y2zsm8sc author = Boretti, Alberto title = Favipiravir use for SARS CoV-2 infection date = 2020-10-27 pages = extension = .txt mime = text/plain words = 2310 sentences = 158 flesch = 55 summary = For the specific use against SARS CoV-2, [22] evaluated the in vitro efficacy of different drugs, from Remdesivir to Chloroquine, also including Favipiravir. Li and De Clercq [23] include Favipiravir together with Remdesivir, Galidesivir, and Ribavirin in between the existing antiviral agents' RNA-dependent RNA polymerase inhibitors to repurpose to treat SARS CoV-2 infection. [24] also include Favipiravir, together with Chloroquine, Arbidol, and Remdesivir, all under clinical studies in China to test their efficacy and safety for SARS CoV-2 infection. Up to date, there is not enough information from specific trials to infer any conclusion on the use of Favipiravir for SARS CoV-2 infection. SARS-CoV-2: recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus Dose rationale for favipiravir use in patients infected with SARS-CoV-2 cache = ./cache/cord-327095-y2zsm8sc.txt txt = ./txt/cord-327095-y2zsm8sc.txt === reduce.pl bib === id = cord-327134-egp4t82x author = Mukherjee, Prasenjit title = Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits date = 2008-04-01 pages = extension = .txt mime = text/plain words = 6100 sentences = 286 flesch = 54 summary = A series of phthalhydrazide based peptidic analogues 45 (Supplementary information, Fig. S1 ) with inhibitory activity against the SARS-3CL pro had been reported and was utilized in a validation study using Gold 2.2 to select the binding site definition and scoring function utilized for binding pose calculation. The group of top-ranking structurally diverse molecules obtained through the clustering analysis were visually inspected based on their (1) ability to occupy the key substrate specificity sites S1 0 , S1, S2, and S4, (2) geometric quality of the ligand binding pose, (3) hydrophilic/ lipophilic mismatches, and (4) complementarity of the key interacting features. The final docking parameters (binding site definition, scoring function for pose generation) selected through this study were identical to those used in the first phase of screening except for the addition of a constraint set. cache = ./cache/cord-327134-egp4t82x.txt txt = ./txt/cord-327134-egp4t82x.txt === reduce.pl bib === id = cord-327063-ea7a1xfl author = Dhama, Kuldeep title = SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus date = 2020-08-02 pages = extension = .txt mime = text/plain words = 11048 sentences = 600 flesch = 48 summary = The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARSand MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease. Further research exploring the SARS-CoV-2 associated zoonosis and mechanisms accounting for its initial transmission from animals to humans, will lead to sort out the spread of this virus as well as design and develop appropriate prevention and control strategies to counter COVID-19. The present comprehensive manuscript presents an overview on COVID-19, an emerging SARS-CoV-2 infectious disease while focusing mainly on the events and circumstantial evidences with regards to this virus jumping the species barriers, sharing a few lessons learned from SARS-and MERS-CoVs, zoonotic spillover events (zoonosis), acquiring transmission ability to infect humans, and adopting appropriate preventive and control measures [42] . cache = ./cache/cord-327063-ea7a1xfl.txt txt = ./txt/cord-327063-ea7a1xfl.txt === reduce.pl bib === id = cord-327084-r12copka author = Zhang, Chenxi title = Survey of Insomnia and Related Social Psychological Factors Among Medical Staff Involved in the 2019 Novel Coronavirus Disease Outbreak date = 2020-04-14 pages = extension = .txt mime = text/plain words = 4087 sentences = 198 flesch = 49 summary = A multiple binary logistic regression model revealed that insomnia symptoms were associated with an education level of high school or below (OR = 2.69, p = 0.042, 95% CI = 1.0–7.0), being a doctor (OR = 0.44, p = 0.007, 95% CI = 0.2–0.8), currently working in an isolation unit (OR = 1.71, p = 0.038, 95% CI = 1.0–2.8), is worried about being infected (OR = 2.30, p < 0.001, 95% CI = 1.6–3.4), perceived lack of helpfulness in terms of psychological support from news or social media with regard to COVID-19 (OR = 2.10, p = 0.001, 95% CI = 1.3–3.3), and having very strong uncertainty regarding effective disease control (OR = 3.30, p = 0.013, 95% CI = 1.3–8.5). cache = ./cache/cord-327084-r12copka.txt txt = ./txt/cord-327084-r12copka.txt === reduce.pl bib === id = cord-327272-fspxett8 author = Buonaguro, Luigi title = Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1432 sentences = 83 flesch = 46 summary = The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. The only positive-sense RNA virus, for which a very effective drug targeting specifically the RdRp is available and approved world-wide for clinical use, is hepatitis C virus (HCV). All these sequence and structural modelling evidences strongly support the concept that the SARS-CoV-2 RdRp is much more similar to the one from HCV than the one from negative-sense Influenza and Ebola RNA viruses. Therefore, repositioning of Sofosbuvir (Sovaldi®; Epclusa® by Gilead), the inhibitor of the HCV NS5B RdRp protein, as antiviral in the treatment of the SARS-CoV-2 infection has an extremely high potentiality of success, as recently postulated by others [17] , and is suggested as a potential drug for the treatment of COVID-19 in the very recent EASL-ESCMID position paper [18] . cache = ./cache/cord-327272-fspxett8.txt txt = ./txt/cord-327272-fspxett8.txt === reduce.pl bib === id = cord-327273-7ntp7x8d author = Street, Renée title = COVID-19 wastewater surveillance: An African perspective date = 2020-07-03 pages = extension = .txt mime = text/plain words = 842 sentences = 61 flesch = 54 summary = Abstract The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water, and sanitation in public health. In the current COVID-19 pandemic, tracking of wastewater has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease [11, 12] . Thus SARS-CoV-2 surveillance through water-based epidemiology (WBE) is a potential complimentary and cost-effective approach to enable wide scale screening which would reduce labor intensive and costly personal COVID-19 testing and tracings [11, 17, 18] . Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges cache = ./cache/cord-327273-7ntp7x8d.txt txt = ./txt/cord-327273-7ntp7x8d.txt === reduce.pl bib === id = cord-327214-kcbxyhhh author = Eketunde, Adenike O title = A Review of Postmortem Findings in Patients With COVID-19 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2725 sentences = 139 flesch = 43 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus originated in Wuhan, China, and has spread rapidly across the world. According to Merad and Martin's study, the hyper inflammation in severe COVID-19 patients shared similarities with cytokine release syndromes, including macrophages activation syndrome. Minimally invasive autopsies of three COVID-19 patients in Chongqing, China revealed damage to the alveolar structure with minor serous and fibrin exudation and hyaline membrane formation [8] . The hypercoagulable state has been linked to a poor prognosis in patients with severe COVID-19, which leads to a microthrombi formation in the lungs, lower limbs, hands, brain, heart, liver, and kidneys, as a result of the activation of the coagulation pathway. There is a strong association with the hyperinflammatory state, which can be explained by most of the signs and symptoms that are exhibited by COVID-19 patients, including most of the pathological findings. Fatal eosinophilic myocarditis in a healthy 17-year-old male with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2c) cache = ./cache/cord-327214-kcbxyhhh.txt txt = ./txt/cord-327214-kcbxyhhh.txt === reduce.pl bib === id = cord-327247-dbcacphq author = Grace, Sherry L. title = The Occupational and Psychosocial Impact of SARS on Academic Physicians in Three Affected Hospitals date = 2011-04-12 pages = extension = .txt mime = text/plain words = 3019 sentences = 154 flesch = 46 summary = The survey that was developed was based on a literature review and input from key health care professionals and included items on sociodemographic variables (sex, age, specialty, number and ages of children, number of years in practice, and ethnocultural background); health status; attitudes and perceptions toward SARS; SARSrelated coping methods, concerns, and symptoms; and effects on personal relationships and changes to work resulting from the SARS outbreak. On a scale from 1 (a lot) to 5 (not at all), physicians perceived that their work had been seriously affected by the SARS outbreaks (mean‫,97.1ס‬ SD‫.)98.0ס‬ Ways in which their work had been affected included: interruptions to teaching and education (84.5%, N‫,)361ס‬ unwillingness of patients to attend outpatient clinics (79.8%, N‫,)451ס‬ infection control precautions (77.2%, N‫,)941ס‬ inability to see outpatients (71.0%, N‫,)731ס‬ inability to perform regular activities (51.8%, N‫,)001ס‬ interruptions to research (51.8%, N‫,)001ס‬ new involvement in SARS-related work (8.8%, N‫,)71ס‬ and inability to enter work due to symptoms (4.1%, N‫.)8ס‬ cache = ./cache/cord-327247-dbcacphq.txt txt = ./txt/cord-327247-dbcacphq.txt === reduce.pl bib === id = cord-327454-o1mrpgvj author = Hemmati-Dinarvand, Farshad title = Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV date = 2020-05-06 pages = extension = .txt mime = text/plain words = 3200 sentences = 168 flesch = 47 summary = Instead, the extremely pathogenic CoVs, containing Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), mostly contaminate lower airways and lead to pneumonia (5) . Based on the genomic structure and phylogenetic analysis, the family Coronaviridae is currently classified into two subfamilies, Sarbecovirus containing SARS-CoV are two major zoonotic pathogenic coronaviruses (Table 1) . Accordingly, the International Committee on Taxonomy of Viruses named it severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently reported that between the SARS-CoV genome sequence and the novel coronavirus exist 82% similarity, thus, named 2019-nCoV by WHO (18) . This theory may be indicating that 2019-nCoV uses the same SARS-CoV mechanism i.e. through angiotensin-converting enzyme2 (ACE2) receptor and the TMPRSS2 protease to infect the human cells. Sequence analysis has shown that some of the 2019-nCoV clusters and bat-associated SARS76 CoV viruses (SARSr-CoV) can use the ACE2 receptor to enter the host cell. cache = ./cache/cord-327454-o1mrpgvj.txt txt = ./txt/cord-327454-o1mrpgvj.txt === reduce.pl bib === id = cord-327259-7o7fs4yb author = Correa, I. A. title = Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date = 2020-08-19 pages = extension = .txt mime = text/plain words = 4584 sentences = 265 flesch = 56 summary = We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . cache = ./cache/cord-327259-7o7fs4yb.txt txt = ./txt/cord-327259-7o7fs4yb.txt === reduce.pl bib === id = cord-327499-4aps0kvp author = Zhang, Wei title = Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes date = 2020-02-17 pages = extension = .txt mime = text/plain words = 1962 sentences = 131 flesch = 62 summary = It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Human samples, including oral swabs, anal swabs and blood samples were collected by Wuhan pulmonary hospital with the consent from all patients and approved by the ethics committee of the designated hospital for emerging infectious diseases. We conducted a molecular investigation to patients in Wuhan pulmonary hospital, who were detected as oral swabs positive for 2019-nCoV upon admission. We collected blood, oral swabs and anal swabs for 2019-nCoV qPCR test using previously established method [5] . We detected the virus in oral swabs, anal swabs and blood, thus infected patients can potentially shed this pathogen through respiratory, fecal-oral or body fluid routes. Above all, we strongly suggest using viral IgM and IgG serological test to confirm an infection, considering the unreliable results from oral swabs detection. cache = ./cache/cord-327499-4aps0kvp.txt txt = ./txt/cord-327499-4aps0kvp.txt === reduce.pl bib === id = cord-327349-rxb6zfoc author = Au, Lewis title = Cancer, COVID-19, and antiviral immunity: the CAPTURE study date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4531 sentences = 183 flesch = 32 summary = Inherent perturbations on cell subsets (e.g. lymphoid and myeloid malignancies), or therapy-induced impact on immune states (e.g. immune checkpoint blockade) may provide opportunities to understand contributions of distinct immune compartments and key regulators of the anti-SARS-CoV-2 response. Herein, we aim to provide an overview of knowledge to-date of the clinical features of COVID-19 observed in cancer patients, as well as potential impact of cancer and anti-cancer interventions on the immune response to SARS-CoV-2. However, what has been critically missing in cohort and registry reports to date are data on 1) the true prevalence of SARS-CoV-2 infection in the cancer population, given population screening has not been widely implemented; and 2) the experience of those who remain well (uninfected, asymptomatic or subclinically affected), to determine the drivers of mortality and the absolute risks of severe adverse events within the cancer community as a whole. A longitudinal understanding of the degree to which the immunocompromised states of cancer patients impact infection, viral clearance, clinical course of COVID-19, and subsequent generation of long-term immunity is needed. cache = ./cache/cord-327349-rxb6zfoc.txt txt = ./txt/cord-327349-rxb6zfoc.txt === reduce.pl bib === id = cord-327431-dnppshnv author = Hognon, Cécilia title = Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2460 sentences = 133 flesch = 48 summary = In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. 28, 37 In this letter, we report an extended all-atom molecular dynamics (MD) study of the interactions produced between a dimeric SUD domain and a short RNA G4 sequence. To further examine the conformational space spanned by the G4/SUD complex, and in particular the role of the RNA in favoring the dimerization and the structure of the interface, we resorted to enhanced sampling MD simulations to obtain the 2D free energy profile along two relevant collective variables: first, the distance between G4 and SUD, and second, the separation between the two SUD subdomains. cache = ./cache/cord-327431-dnppshnv.txt txt = ./txt/cord-327431-dnppshnv.txt === reduce.pl bib === id = cord-327263-d5mmeu96 author = Christoff, A. P. title = Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 4134 sentences = 258 flesch = 49 summary = Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint detect clear differences due to dilution alone, with point estimates from 0.43 to 0.61 Cq. In practice, observational data from 246 positive patients generated point estimates of mean Cq differences between individual tests and their corresponding pools ranging from 0.1 to 2.09 Cq. While such values are hardly significant in terms of analytical sensitivity, the expected counterparts for traditional pooling would range from 3.3 to 5 Cq under optimal amplification conditions. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint of diagnostic samples for SARS-CoV-2 can also perform swab pool analysis using the same detection methods and infrastructure already in use. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint CONCLUSION Pool testing is a major alternative for large-scale screening of SARS-CoV-2 in low prevalence populations. cache = ./cache/cord-327263-d5mmeu96.txt txt = ./txt/cord-327263-d5mmeu96.txt === reduce.pl bib === id = cord-327138-l2m2g0v8 author = Ren, Chao title = Comparison of clinical laboratory tests between bacterial sepsis and SARS-CoV-2-associated viral sepsis date = 2020-08-04 pages = extension = .txt mime = text/plain words = 870 sentences = 59 flesch = 54 summary = Twenty-one patients with SARS-CoV-2-induced sepsis and 46 patients with bacterial sepsis were finally recruited (Additional file 2). The median age was 64.0 years (IQR, 60.5-68.0) and 65.5 years (IQR, 49.3-77.3) for patients of SARS-CoV-2-induced sepsis and bacterial sepsis, respectively (Additional file 1). 8.0 (IQR, 6.5-9.5), P < 0.001] were consistently higher among patients with bacterial sepsis than those with SARS-CoV-2-induced sepsis. In this study, ICU patients with SARS-CoV-2-induced sepsis and those with bacterial sepsis revealed comparable demographic characteristics, like age, gender distribution, and comorbidities, after rigorous screening processes. However, patients with bacterial sepsis were found with more severe organ dysfunction and poor outcomes when compared with those caused by SARS-CoV-2-induced sepsis, including higher values in SOFA and APACHE II, as well as more ICU deaths. This is the first report that compared clinical features and host responses between bacterial and SARS-CoV-2-induced viral sepsis. Baseline characteristics of critically ill patients with SARS-CoV-2-and bacteria-induced sepsis. cache = ./cache/cord-327138-l2m2g0v8.txt txt = ./txt/cord-327138-l2m2g0v8.txt === reduce.pl bib === id = cord-326710-vc9wkcro author = Stevens, Bryan title = Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA date = 2020-08-06 pages = extension = .txt mime = text/plain words = 1796 sentences = 107 flesch = 50 summary = BACKGROUND: Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). METHODS: A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. CONCLUSIONS: The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. In this study, we demonstrated comparable test performance between the Cepheid Xpert Xpress SARS-CoV-2 assay and the Panther Fusion SARS-CoV-2 assay, with an overall agreement of 99%. cache = ./cache/cord-326710-vc9wkcro.txt txt = ./txt/cord-326710-vc9wkcro.txt === reduce.pl bib === id = cord-327318-qhrsli0b author = Shen, Qian title = Consensus recommendations for the care of children receiving chronic dialysis in association with the COVID-19 epidemic date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3149 sentences = 160 flesch = 46 summary = In turn, a set of recommendations for the prevention and control of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 in pediatric hemodialysis (HD) centers and in home peritoneal dialysis (PD) settings have been proposed. The recommendations are based on the epidemiological features of the SARS-CoV-2 virus and COVID-19 disease, susceptibility factors, and preventive and control strategies. In turn, the factors associated with an increased risk for contracting SARS-CoV-2 infection among pediatric chronic dialysis patients, especially those who receive in-center HD, include the following: (a) compromised immune system (the result of long-term malnutrition, uremia, and/or immunosuppressants); (b) close proximity to other Preventive and control strategies for in-center HD Staff management (Table 2 ) In order to effectively prevent and control the transmission of SARS-CoV-2 among children who receive maintenance dialysis, we formulated this set of recommendations based on infectious disease guidelines and our experience with the COVID-19 epidemic, which healthcare staff in pediatric dialysis centers can refer to. cache = ./cache/cord-327318-qhrsli0b.txt txt = ./txt/cord-327318-qhrsli0b.txt === reduce.pl bib === id = cord-327392-9psblokc author = Srivastava, A.K. title = Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4055 sentences = 218 flesch = 52 summary = Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. cache = ./cache/cord-327392-9psblokc.txt txt = ./txt/cord-327392-9psblokc.txt === reduce.pl bib === id = cord-327459-tyhy784d author = Gómez-Rial, J. title = A strategy targeting monocyte-macrophage differentiation to avoid pulmonary complications in SARS-Cov2 infection date = 2020-04-23 pages = extension = .txt mime = text/plain words = 785 sentences = 51 flesch = 35 summary = Gómez-Rial J, MD 1,2 , Martinón-Torres F, MD, Phd, Assoc Prof 1 The immune dysregulation and cytokine storm observed in severe COVID-19 cases has led to the trial of licensed RA drugs such as Chloroquine, IL-1/IL-6 blockers, TNF or Janus kinase inhibitors in COVID-19 patients [1] In addition we propose that blockade of granulocyte macrophage-colony stimulating factor (GM-CSF) may be an effective strategy to prevent pulmonary complications and fatality in SARS-Cov2 infection. and inflammation-related phenotypic changes in peripheral blood monocytes, and correlation with acute respiratory distress syndrome (ARDS) in severe patients [5] Furthermore, single-cell RNA sequencing of lung bronchoalveolar immune cells infection [6] If these findings are confirmed, they would indicate that in SARS-Cov2, similarly to SARS-Cov1, acute lethal disease is produced by delayed and dysregulated type I interferon response and pulmonary accumulation of inflammatory monocytemacrophages, which are mainly responsible for immunopathology [6, 7] . cache = ./cache/cord-327459-tyhy784d.txt txt = ./txt/cord-327459-tyhy784d.txt === reduce.pl bib === id = cord-325971-volbaipv author = Neupane, Karun title = Potential Treatment Options for COVID-19: A Comprehensive Review of Global Pharmacological Development Efforts date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3017 sentences = 141 flesch = 45 summary = Several drugs are being tested in the trials, and the United States Food and Drugs Administration (FDA) has given Emergency Use Authorization (EUA) for remdesivir to treat COVID-19 patients on May 1, 2020 [5] . Therapeutic remdesivir treatment in MERS-CoV inoculated rhesus macaques resulted in the reduction in clinical signs, virus replication, and the absence of lung lesions in 2/6 remdesivirtreated animals along with the reduction in lesion severity in three additional animals. In a randomized controlled clinical trial of 1063 patients conducted by the National Institute of Allergy and Infectious Disease (NIAID), remdesivir has shown the efficacy in the early results against advanced COVID-19 (NCT04280705). In a retrospective observational study involving twenty patients with severe or critical COVID-19, treatment with tocilizumab in addition to lopinavir, methylprednisolone, other symptom relievers, and oxygen therapy, resulted in body temperature of all the patients returning to normal on the first day of receiving tocilizumab and significant relief of clinical symptoms synchronously in the following days. cache = ./cache/cord-325971-volbaipv.txt txt = ./txt/cord-325971-volbaipv.txt === reduce.pl bib === id = cord-327575-5pcnuqgy author = Morrisette, Taylor title = The Pharmacokinetic and Pharmacodynamic Properties of Hydroxychloroquine and Dose Selection for COVID-19: Putting the Cart Before the Horse date = 2020-08-01 pages = extension = .txt mime = text/plain words = 5447 sentences = 233 flesch = 45 summary = The objective of this review was to describe the current understanding of the PK/PD and dose selection of HCQ against SARS-CoV-2, discuss knowledge gaps, and identify future studies that are needed to optimize the efficacy and safety of treatments against COVID-19. Although studies completed thus far show variable results, Arshad and colleagues performed a large multicenter, retrospective, observational analysis that evaluated patients hospitalized because of a COVID-19-related admission receiving HCQ 400 mg twice daily on day 1, followed by HCQ 200 mg twice daily on days 2 to 5 [14] [15] [16] [17] . Furthermore, the World Health Organization discontinued the HCQ arm in the Solidarity trial because it showed ''little or no reduction in the mortality of hospitalized COVID-19 patients when compared to standard of care'' (HCQ dosed 800 mg twice daily on day 1, followed by HCQ 400 mg twice daily for a total of 10 days), and the Food and Drug Administration revoked the emergency use authorization to utilize HCQ for the treatment of COVID-19 [16] [17] [18] . cache = ./cache/cord-327575-5pcnuqgy.txt txt = ./txt/cord-327575-5pcnuqgy.txt === reduce.pl bib === id = cord-327622-ezgufe24 author = Kaur, Ramandeep title = Practical strategies to reduce nosocomial transmission to healthcare professionals providing respiratory care to patients with COVID-19 date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6333 sentences = 355 flesch = 43 summary = • When removing the endotracheal tube, simultaneously turn off the ventilator • Avoid disconnecting ETT from the ventilator circuit before extubation to reduce spray of contaminated aerosols 9 Transport • Place a filter between the artificial airway and the transport ventilator circuit • Use HME that has filter function (HME-F) • Consider clamping the ETT before disconnection from ventilator circuit 10 Bronchoscopy assist* 2 in vivo [44, 45] • For spontaneously breathing patients, place a surgical mask on patient's face (Fig. 7a, b) • Use NIV mask with examination port for patients on NIV (Fig. 7d) • Use swivel adapter to insert bronchoscope for intubated patient (Fig. 7c) Abbreviations: HFNC high-flow nasal cannula, IPPB intermittent positive pressure breathing, HME heat moisture exchanger, ETT endotracheal tube, NIV non-invasive ventilation *Based on CDC guidelines, these procedures should ideally be performed in airborne infection isolation rooms entrainment or nonrebreather mask [53] . cache = ./cache/cord-327622-ezgufe24.txt txt = ./txt/cord-327622-ezgufe24.txt === reduce.pl bib === id = cord-327501-8s6dvanf author = Schwaiger, Julia title = No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date = 2020-09-17 pages = extension = .txt mime = text/plain words = 2367 sentences = 124 flesch = 52 summary = Testing 54 intravenous immunoglobulin preparations, produced from plasma collected in Europe and the United States, confirmed highly potent neutralization of a seasonal coronavirus; however, no cross-neutralization of the new SARS-CoV-2 was seen. The question is of significant clinical relevance, as SARS-CoV-2 cross-neutralizing antibodies in IVIGs, if they were present, might afford some protection to people with immune deficiencies and may even represent a treatment option for coronavirus disease 2019 (COVID-19) patients. The current study tested a representative number of IVIG lots for nAbs against SARS-CoV-2 and the longer-circulating HCoV-229E, to establish clarity about cross-neutralization of the pandemic virus by antibodies induced by earlier circulating seasonal coronaviruses. SARS-CoV-2 nAb titers were below the limit of detection for all 54 IVIG lots tested, irrespective of geographic origin of the plasma (Europe vs United States) and plasma collection modality (recovered vs source) ( Figure 1A) . cache = ./cache/cord-327501-8s6dvanf.txt txt = ./txt/cord-327501-8s6dvanf.txt === reduce.pl bib === id = cord-327681-c2kmog0g author = Feng, Zhilan title = Timely identification of optimal control strategies for emerging infectious diseases() date = 2009-07-07 pages = extension = .txt mime = text/plain words = 4608 sentences = 282 flesch = 51 summary = RESULTS: Stage-specific infection rate estimates from cases hospitalized before quarantine began exceed those from the entire outbreak, but are qualitatively similar: infectiousness was negligible until symptom onset, and increased 10-fold from prodrome to acute illness. Our model resembles theirs (Fig. 1 ), but we distinguish the prodrome and acute respiratory phase and allow infected people to become infectious before or after becoming ill, at rates-products of contact rates and probabilities of transmission on contact-that may differ among stages. A Mathematica TM notebook that evaluates these expressions for user-supplied parameter values, comparing the impact of non-pharmaceutical interventions on any disease transmitted by close contact, is available from the Table 1 Parameter estimates (b represents infection, r isolation efficiency, f hospitalization; subscripts E, P and R refer to pre-symptomatic, prodrome, and acute respiratory stage) from fitting predicted to observed cumulative admissions to TTSH during the first 30 days of the outbreak (cf. cache = ./cache/cord-327681-c2kmog0g.txt txt = ./txt/cord-327681-c2kmog0g.txt === reduce.pl bib === id = cord-327405-xgtqfwyn author = Liu, Bing title = Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3725 sentences = 199 flesch = 52 summary = 37 non-severe patients with persistent SARS-CoV-2 presence that were transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to the PP (persistently positive) group, which was further allocated to PPP group (n = 19) and PPN group (n = 18), according to their testing results after 7 days (N = negative). Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. These results indicated that non-severe COVID-19 patients (PA group) have already dysregulated immune system at disease onset, and those with persistent SARS-CoV-2 shedding could restore this abnormality to certain level. Together, these results indicated that the abnormalities in adaptive immune cells, but not symptoms and laboratory indicators, were associated with SARS-CoV-2 viral RNA detection in non-severe COVID-19 patients. cache = ./cache/cord-327405-xgtqfwyn.txt txt = ./txt/cord-327405-xgtqfwyn.txt === reduce.pl bib === id = cord-327685-fymfqvp3 author = Channappanavar, Rudragouda title = Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date = 2017-05-02 pages = extension = .txt mime = text/plain words = 5834 sentences = 288 flesch = 33 summary = In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice cache = ./cache/cord-327685-fymfqvp3.txt txt = ./txt/cord-327685-fymfqvp3.txt === reduce.pl bib === id = cord-327511-e3idvknz author = Trifan, G. title = Characteristics of a Diverse Cohort of Stroke Patients with SARS-CoV-2 and Outcome by Sex date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3482 sentences = 233 flesch = 52 summary = CONCLUSION: In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this multicenter study of patients with stroke and SARS-CoV-2 infection admitted to comprehensive stroke centers in the Chicagoland area, males were more likely than females to have severe COVID-19 manifestations and worse ischemic stroke outcome at hospital discharge. cache = ./cache/cord-327511-e3idvknz.txt txt = ./txt/cord-327511-e3idvknz.txt === reduce.pl bib === id = cord-327601-4uqgwlnx author = Bangash, Mansoor N. title = SARS-CoV-2: is the liver merely a bystander to severe disease? date = 2020-06-02 pages = extension = .txt mime = text/plain words = 979 sentences = 61 flesch = 43 summary = 1 Their study shows SARS-CoV-2 positive patients with ≥1 week history of increased aminotransferases have worse acute pulmonary disease (radiological and physiological) than those without. Considering that Interleukin (IL)-6 and C-reactive protein (CRP) are similar between patients with normal and prolonged abnormal liver aminotransferases, the authors speculate that liver injury is a direct effect of SARS-CoV-2 viral hepatitis rather than an indirect immune mediated injury. The fact that increases in liver aminotransferases occur and tend to parallel the severity of pulmonary disease remains unquestioned 2 , however, whether the liver injury is a true viral hepatitis rather than a bystander to the multi-organ pathophysiology of critical illness requires further discussion. Based on the above perspectives, we feel that raised liver aminotransferases associated with SARS-CoV-2 positivity are more likely attributable to illness severity, in which host response and iatrogenic harm (i.e. drugs, ventilation) drive bystander liver injury, thus explaining its association with mortality and in an analogous fashion to patterns seen in sepsis. cache = ./cache/cord-327601-4uqgwlnx.txt txt = ./txt/cord-327601-4uqgwlnx.txt === reduce.pl bib === id = cord-327661-osx42wdh author = Schaefer, E. J. title = Coronavirus Disease-2019 Case, Death, and Testing Rates in the United States and Worldwide: Primary Data and Review date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3995 sentences = 232 flesch = 60 summary = ABSTRACT Coronavirus disease-2019 (COVID-19), due to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been associated with a world-wide pandemic, with the United States (US) having the largest total number of cases and deaths (>7 million and >200,000, respectively) at this time. We assessed data as of September 1, 2020 from our combined laboratories and as reported for selected states and countries for case, death, and testing rates per 1 million in the population. Our positive rates per state agreed reasonably well with reported Centers for Disease Control and Prevention (CDC) data (r=0.609, P<0.0001) based on 19,898 cases, 593 deaths, and 271,637 tests, all per 1 million in the US population. 7 Our goals were to assess our own data as well as available US and worldwide data in terms of cases, deaths, and testing per 1 million in the population, in order to examine potential causes for the large rate differences observed between states and countries. cache = ./cache/cord-327661-osx42wdh.txt txt = ./txt/cord-327661-osx42wdh.txt === reduce.pl bib === id = cord-327520-qj7coqfr author = Wei, Yulong title = Coronavirus genomes carry the signatures of their habitats date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1395 sentences = 93 flesch = 54 summary = Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Here we compared the CpG and U content 327 of these coronaviruses and found that viruses that regularly infect AVP-rich tissues tend to Based on global sequence comparison, figure 4a shows that most SNPs are C->U substitutions. cache = ./cache/cord-327520-qj7coqfr.txt txt = ./txt/cord-327520-qj7coqfr.txt === reduce.pl bib === id = cord-327933-u0fcs3yg author = Doná, Daniele title = Pediatric transplantation in Europe during the COVID‐19 pandemic: early impact on activity and healthcare date = 2020-08-12 pages = extension = .txt mime = text/plain words = 2634 sentences = 142 flesch = 41 summary = Indeed, although severe outcomes (including deaths) have been reported in the pediatric population 6 , relatively fewer children with COVID-19 require hospitalization or admission to the intensive care unit (ICU) 7 . The survey included relevant questions to: i) assess pediatric transplantation activity, including living-donation issues; ii) identify the protocols adopted to prevent and manage SARS-CoV-2 infection at the hospital level; iii) evaluate the impact of these practices on the healthcare of transplanted children; and iv), describe the management of confirmed COVID-19 cases among the special population of pediatric transplant recipients and candidates. In eight centers (44%) outpatient visits were performed only after a telephone pretriage excluding epidemiological (e.g., close contact with a known COVID-19 case) and clinical risk factors (e.g., ongoing fever or respiratory symptoms in the patient or in the caregiver) for SARS-CoV-2 infection. Due to lack of experience in treating affected pediatric transplant patients, hospital admission criteria for suspected and confirmed COVID-19 cases varied between ERN-TransplantChild centers. cache = ./cache/cord-327933-u0fcs3yg.txt txt = ./txt/cord-327933-u0fcs3yg.txt === reduce.pl bib === id = cord-327654-9g8zcxaa author = Chi, Xiaojing title = Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4993 sentences = 302 flesch = 51 summary = Here, using SARS-CoV-2 spike receptor-binding domain (RBD) as a bait, we generate a panel of humanized single domain antibodies (sdAbs) from a synthetic library. Competitive ligand-binding experiments suggest that the sdAbs either completely block or significantly inhibit the association between SARS-CoV-2 RBD and viral entry receptor ACE2. To determine whether sdAbs targeted different antigenic regions on the SARS-CoV-2 RBD surface, we performed a competition-binding assay using a real-time biosensor (Fig. 3) . Fc fusion sdAbs in culture supernatants were affinity purified with HiTrap Protein A HP antibody purification columns ( Supplementary Fig. 2 ) and analyzed in both reducing and non-reducing conditions in Western blot using an anti-human IgG to detect Fc. As shown in Fig. 4c , the size of the constructed intact sdAb-Fc is around 80 KDa in the non-reducing condition, but a 40 KDa monomer was observed by prior treatment in reducing condition to break disulfide bonds. cache = ./cache/cord-327654-9g8zcxaa.txt txt = ./txt/cord-327654-9g8zcxaa.txt === reduce.pl bib === id = cord-327616-uu9uygic author = Wazny, Vanessa title = Vascular underpinning of COVID-19 date = 2020-08-27 pages = extension = .txt mime = text/plain words = 6970 sentences = 359 flesch = 33 summary = Coronavirus disease 2019 (COVID-19) case study reports have called attention to the overrepresentation of cardiovascular diseases, in addition to respiratory diseases, among patients at risk of critical illness and mortality following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection [1] [2] [3] [4] [5] [6] [7] [8] . Initial concerns were also raised regarding the medical treatment of hypertension with adverse COVID-19 outcomes, as studies in animals have shown that the use of renin-angiotensin system blockers-angiotensin-converting enzyme inhibitors and angiotensin receptor blockers result in the upregulation of angiotensin-converting enzyme 2 (ACE2) expression, which is an entry factor for SARS-CoV-2 [13] . Collectively, these case reports of confirmed COVID-19 hospitalized patients strongly indicate a strong association between underlying cardiovascular diseases and diabetes with severe health outcomes and fatality following SARS-CoV-2 infection. In COVID-19 research, nasal and alveolar epithelial cells are generally believed to be the primary sites of viral infection due to the high expressions of SARS-CoV-2 entry factors [51] . cache = ./cache/cord-327616-uu9uygic.txt txt = ./txt/cord-327616-uu9uygic.txt === reduce.pl bib === id = cord-327653-2gn9h4i2 author = Vallinoto, Antonio Carlos Rosário title = The challenges of COVID-19 in the Brazilian Amazonian communities and the importance of seroepidemiological surveillance studies date = 2020-08-15 pages = extension = .txt mime = text/plain words = 1721 sentences = 74 flesch = 36 summary = Since the elimination of beta-coronavirus circulation requires a minimum herd immunity (indications 50-66%) [7] , the information for which is still unknown at the local, national or global levels, conducting seroepidemiological and surveillance studies on SARS-CoV-2 in geographic areas such as the Amazon is extremely important, as it will allow for the assessment of the prevalence and titre of antibodies anti-SARS-CoV-2, mortality and case fatality rates and the epidemiological aspects of risk of exposure in communities from different population strata, such as riberinhos (riverain communities), quilombola (Afro-descendant communities) and indigenous peoples, providing an improvement in the decisionmaking of future epidemics. cache = ./cache/cord-327653-2gn9h4i2.txt txt = ./txt/cord-327653-2gn9h4i2.txt === reduce.pl bib === id = cord-327690-di7hfghi author = Yang, Xiaobo title = Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study date = 2020-02-24 pages = extension = .txt mime = text/plain words = 3848 sentences = 241 flesch = 53 summary = title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study METHODS: In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. In this study, we investigated critically ill patients with confirmed SARS-CoV-2 pneumonia who were admitted to Wuhan Jin Yin-tan hospital. The baseline SARS-CoV-2-associated morbidity and mortality data from this study will be of considerable value for the early identification of individuals who are at risk of becoming critically ill and who are most likely to benefit from intensive care treatment. During the outbreak of SARS-CoV-2 infection, the number of critically ill patients exceeded the capacity of ICUs. Therefore, two provisional ICUs were urgently established in Jin Yin-tan hospital and hence most mechanical ventilator settings and recordings were not recorded, except records of positive end-expiratory pressure in some cases. cache = ./cache/cord-327690-di7hfghi.txt txt = ./txt/cord-327690-di7hfghi.txt === reduce.pl bib === id = cord-327862-zcg3baym author = Luo, Yiqi Ruben title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1141 sentences = 93 flesch = 59 summary = The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity cache = ./cache/cord-327862-zcg3baym.txt txt = ./txt/cord-327862-zcg3baym.txt === reduce.pl bib === id = cord-327711-welf0eb1 author = Zhou, Daming title = Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date = 2020-06-13 pages = extension = .txt mime = text/plain words = 4847 sentences = 290 flesch = 59 summary = Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. A neutralisation test for EY6A based on quantitative PCR detection of virus in the supernatant bathing infected Vero E6 cells after 5 days of culture, showed a ~1000-fold reduction in virus signal (Methods, Extended Data Fig. 3 ) indicating that it is highly neutralising. To elucidate the epitope of EY6A, we determined the crystal structures of the deglycosylated SARS-CoV-2 RBD in complex with EY6A Fab alone and in a ternary complex incorporating a nanobody (Nb) which has been shown to compete with ACE2 (for data on a closely related Nb see Huo 2020, submitted), as a crystallisation chaperone. cache = ./cache/cord-327711-welf0eb1.txt txt = ./txt/cord-327711-welf0eb1.txt === reduce.pl bib === id = cord-327799-ngzvdd8c author = Chaumont, Claire title = The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date = 2020-09-21 pages = extension = .txt mime = text/plain words = 1796 sentences = 90 flesch = 45 summary = The current global priority is to protect people from attaining the COVID-19 infection and to attend to those infected, resulting in the disruption of other activities of the health sector, such as neglected tropical disease (NTD) control and elimination programs, which, across the globe, have postponed mass drug administration (MDA) campaigns. The most obvious impact of the crisis on NTD programs relates to its effect on infection prevalence due to delayed mass drug administration campaigns. Shifts in human capital availability and transmission dynamics of SARS-CoV-2 will require national NTD programs to adopt different implementation approaches to ensure availability and use of appropriate personnel, as well as preventive measures, including social distancing, safe hygiene practices, and face masks and/or coverings. This approach could better mitigate the risk of SARS-CoV-2 transmission, but community acceptance and costs would need to be carefully considered, as well as its potential impact on coverage. cache = ./cache/cord-327799-ngzvdd8c.txt txt = ./txt/cord-327799-ngzvdd8c.txt === reduce.pl bib === id = cord-327808-k3jec87p author = Zhu, Yunkai title = The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2754 sentences = 155 flesch = 61 summary = We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. The sequence at the S1/S2 boundary contains a cleavage site for the furin protease, 61 which could preactivate the S protein for membrane fusion and potentially reduce the 62 dependence of SARS-CoV-2 on plasma membrane proteases, such as transmembrane 63 serine protease 2 (TMPRSS2), to enable efficient cell entry (Shang et al., 2020) . Intriguingly, 188 these genes edited also significantly inhibited the infection by pseudovirus bearing the 189 spike protein of MERS-CoV in A549-ACE2-DPP4 cells ( Figure 3D ). Although no infectious virus was detected by focus-forming 299 assay (data not shown), viral RNA levels were higher in fecal samples for Sfull (20 and 300 40-fold) than Sdel at days 2 and 4, respectively ( Figure 5B ). cache = ./cache/cord-327808-k3jec87p.txt txt = ./txt/cord-327808-k3jec87p.txt === reduce.pl bib === id = cord-327890-ocisq7e4 author = Pallett, Scott J C title = Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study date = 2020-07-24 pages = extension = .txt mime = text/plain words = 5947 sentences = 271 flesch = 42 summary = In phase 1, two point-of-care lateral flow serological assays, the Onsite CTK Biotech COVID-19 split IgG/IgM Rapid Test (CTK Bitotech, Poway, CA, USA) and the Encode SARS-CoV-2 split IgM/IgG One Step Rapid Test Device (Zhuhai Encode Medical Engineering, Zhuhai, China), were evaluated for performance against a laboratory immunoassay (EDI Novel Coronavirus COVID-19 IgG ELISA kit [Epitope Diagnostics, San Diego, CA, USA]) in 300 samples from health-care workers and 100 pre-COVID-19 negative control samples. These include point-of-care molecular platforms for acute phase testing, and laboratory ELISA or lateral flow serological assays for antibodies specific to SARS-CoV-2 for delayed case identification. To derive a measure of sensitivity, the results of lateral flow serological assays and ELISA were compared in 300 health-care workers who had previously received PCR testing (AusDiagnostics, Sydney, Australia) at initial presentation with COVID-19 symptoms. cache = ./cache/cord-327890-ocisq7e4.txt txt = ./txt/cord-327890-ocisq7e4.txt === reduce.pl bib === id = cord-327912-wfjdxgxh author = Swann, Heather title = Minimal system for assembly of SARS-CoV-2 virus like particles date = 2020-08-24 pages = extension = .txt mime = text/plain words = 1695 sentences = 98 flesch = 59 summary = Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. Non-infectious virus like particles (VLPs) displaying essential viral proteins can be used to study the structural properties of the SARS-CoV-2 virions and due to their maximum immunogenicity are also vaccine candidates 2, 3 . Similarly, expression of M, E and S proteins are shown to result in release of morphologically identical particles to wild type SARS-CoV virus 9, 10 . We then tested the structural integrity of the SARS-CoV-2 VLPs attached to dry glass using Atomic Force Microscopy (AFM), since SARS-CoV-2 virions have been reported to survive on solid surfaces in dry conditions for many hours 13 . SARS-CoV-2 M, S and E protein genes were identified from the full genome sequence of the virus 1 , these genes were then humanized and inserted in CMV driven mammalian expression vectors (see supplement for complete plasmid sequences). cache = ./cache/cord-327912-wfjdxgxh.txt txt = ./txt/cord-327912-wfjdxgxh.txt === reduce.pl bib === id = cord-327721-y39751g4 author = Zhang, Yan title = Emotional “inflection point” in public health emergencies with the 2019 New Coronavirus Pneumonia (NCP) in China date = 2020-07-19 pages = extension = .txt mime = text/plain words = 5385 sentences = 276 flesch = 55 summary = BACKGROUND: The outbreak of the new coronavirus pneumonia (NCP) in Wuhan, Hubei, has caused very serious consequences and severely affected people's lives and mental health. METHODS: This study used self-designed questionnaires and artificial intelligence (AI) to assess and analyze the emotional state of over 30,000 college students during the outbreak period in January (T1) and home quarantine in February (T2). From these data, it indicated that during the period of home isolation, college students in Hubei Province showed more negative emotions due to their long-term exposure to the epidemic. There is also the stress symptom of "seeming as being infected" caused by too much browsing of the relevant news every day, which directly affects the emotions of students, they became more sensible and anxious to disease, this is a mental tension (Peng et al., 2019) . This survey found that there is an emotional "infection point" in February among college students, especially in the Hubei area. cache = ./cache/cord-327721-y39751g4.txt txt = ./txt/cord-327721-y39751g4.txt === reduce.pl bib === id = cord-328040-5qd05e4r author = Zhao, Xin-Ying title = Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date = 2020-04-29 pages = extension = .txt mime = text/plain words = 3416 sentences = 191 flesch = 54 summary = title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study Since December 2019, several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were first reported the virus has caused an outbreak in a short time by human-to-human transmission throughout China, especially in Hubei Province. A considerable proportion of COVID-19 patients develop severe pneumonia, pulmonary edema, acute respiratory distress syndrome, and even multiple organ failure within a short time. Patients suspected of having COVID-19 were admitted and quarantined, and throat swab samples were collected and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative polymerase chain reaction assay (qPCR). Clinical data [age, previous chronic disease, epidemiological history, symptoms, vital signs, computed tomography (CT) images, virus load, laboratory tests, complications, and treatment process] of the 91 patients involved in this study were collected. cache = ./cache/cord-328040-5qd05e4r.txt txt = ./txt/cord-328040-5qd05e4r.txt === reduce.pl bib === id = cord-327920-51s4figy author = Kohler, Philipp P. title = Prevalence of SARS-CoV-2 antibodies among Swiss hospital workers: Results of a prospective cohort study date = 2020-10-08 pages = extension = .txt mime = text/plain words = 1539 sentences = 92 flesch = 50 summary = 5 The aims of this prospective cohort study were to assess seropositivity for SARS-CoV-2, to identify risk exposures, and to describe the spectrum of COVID-19 symptoms among hospital workers. Participants' sera were analyzed for SARS-CoV-2 antibodies using 3 different tests: a lateral flow immunochromatographic assay (LFIA, Sugentech, Yuseong-gu, Daejeon, Republic of Korea), a chemiluminescence microparticle immunoassay (CMIA, Abbott Diagnostics, Lake Bluff, IL), and an electro-chemiluminescence immunoassay (ECLIA, Roche Diagnostics, Basel, Switzerland). At followup, 2 participants showed a positive LFIA (IgG) and ECLIA/ CMIA result in addition to the 8 samples confirmed at baseline, resulting in 10 of 1,012 true seropositives (1.0%) and 48 of 1,012 false seropositives (4.7%) (Fig. 1) . This finding is in line with data from the Infectious Diseases Society of America (IDSA) guideline on SARS-CoV serology testing showing a lower sensitivity of CMIA IgG compared to LFIA IgM early after infection. cache = ./cache/cord-327920-51s4figy.txt txt = ./txt/cord-327920-51s4figy.txt === reduce.pl bib === id = cord-327894-b0bsseui author = Pecellín, Lidia Gestoso title = Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date = 2020-10-14 pages = extension = .txt mime = text/plain words = 4897 sentences = 446 flesch = 56 summary = En respuesta a la COVID-19, el gobierno español inicialmente instó a limitar el contacto social como medida general, sin embargo, otros países, además, implementaron pruebas generalizadas para la infección por SARS-COV-2 desde el principio de la pandemia. Son test sencillos de hacer, pero deben ser interpretados con prudencia, en relación con el curso de la infección, sobre todo por la tasa de falsos negativos en la detección de IgM ya que la respuesta de IgM en un enfermo COVID-19 puede tardar en aparecer desde varios días a dos semanas 21 Algunos estudios han mostrado que durante los primeros 7 días desde el inicio de síntomas, menos de un 40% de pacientes presentan anticuerpos IgM detectables. cache = ./cache/cord-327894-b0bsseui.txt txt = ./txt/cord-327894-b0bsseui.txt === reduce.pl bib === id = cord-328011-6lf3no6u author = Zayed, Hatem title = Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1449 sentences = 84 flesch = 49 summary = title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics Since coronaviruses are increasing alarmingly, there is an urgent need for a safe and effective vaccine to prevent the spread of the virus during pandemic outbreaks, and stop deaths associated with the virulent COVID-19. We now know that SARS-CoV-2 shares 88% identity with two SARS-like coronaviruses (bat-SL-CoVZXC21 and bat-SL-CoVZC45) that both originated in China, and use the same human angiotensin-converting enzyme 2 receptor for cell entry during the process of infection (3). In response to such forewarnings from scientists, a predictive vaccine could have been designed and developed for the potential virus pandemic. Thereafter, during the time of pandemic, suitable stored transgenic cell lines could be used, based on the Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; VLP, virus-like particle; WHO, World Health Organization. cache = ./cache/cord-328011-6lf3no6u.txt txt = ./txt/cord-328011-6lf3no6u.txt === reduce.pl bib === id = cord-328073-bqeffvzl author = Limonta, Daniel title = Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date = 2020-11-06 pages = extension = .txt mime = text/plain words = 1878 sentences = 113 flesch = 55 summary = The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Next, we demonstrated that the NOD2 inhibitor GSK717 blocks infection by and 205 spread of ZIKV in human fetal brain and cell lines. Similarly, the work here which demonstrated the antiviral activity of NOD2 and RIPK2 inhibitors using tissue explants, 216 primary cells and cell lines, support the potential clinical use of these compounds in mono or co-217 infections by arboviruses as well as coronavirus infections at early and/or advanced stages. Calu-3 and Huh7 cells infected with SARS-CoV-2 (MOI=0.1) were also treated with GSK583 for 24 hours before collecting the cell supernatants for viral titer determination. cache = ./cache/cord-328073-bqeffvzl.txt txt = ./txt/cord-328073-bqeffvzl.txt === reduce.pl bib === id = cord-328122-nfvbog77 author = Tresoldi, Ilaria title = SARS‐COV‐2 and infectivity: Possible increase in infectivity associated to integrin motif expression date = 2020-04-10 pages = extension = .txt mime = text/plain words = 698 sentences = 48 flesch = 48 summary = It has been proposed that SARS-COV-2 has acquired the spike glycoprotein RGD (KGD in SARS-CoV) 1 integrin-binding site which is considered significant for the virus transmission efficiency. The most common of these motifs is the minimal peptide sequence for binding integrins, RGD, which is known for its role in virus infection via its ability to interact with over half of the more than 20 known integrins. 4 Besides the fibronectin binding motif RGD, other integrinbinding sites are specifically expressed in SARS-COV-2, and, particularly, a change from a LDV to a LDI motif is likely significant. 5 We investigated the protein sequence of the human coronavirus and compared it to SARS and bat coronavirus to identify any eventual overexpression of other integrin-binding sites. Orf1ab polyprotein has many integrin-binding motifs implicated in cell adhesion with binding sites on Fibronectin, Tenascin_C, and VCAM. cache = ./cache/cord-328122-nfvbog77.txt txt = ./txt/cord-328122-nfvbog77.txt === reduce.pl bib === id = cord-328209-uc37poce author = Javid, Babak title = Impact of population mask wearing on Covid-19 post lockdown date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1251 sentences = 67 flesch = 44 summary = Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high, the reduction on deaths was dramatic as the effective R approached 1, as might be expected after aggressive social-distancing measures such as wide-spread lockdowns. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high (Fig. 1a) , the reduction on deaths was dramatic as the effective R approached 1 (Fig. 1b) , as might be expected after aggressive socialdistancing measures such as wide-spread lockdowns 5 . cache = ./cache/cord-328209-uc37poce.txt txt = ./txt/cord-328209-uc37poce.txt === reduce.pl bib === id = cord-328042-e1is656g author = Klein, Steffen title = SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date = 2020-08-07 pages = extension = .txt mime = text/plain words = 6328 sentences = 329 flesch = 56 summary = The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] . cache = ./cache/cord-328042-e1is656g.txt txt = ./txt/cord-328042-e1is656g.txt === reduce.pl bib === id = cord-328069-a9fi9ssg author = Pathan, Refat Khan title = Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model date = 2020-06-13 pages = extension = .txt mime = text/plain words = 3402 sentences = 202 flesch = 64 summary = title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, The United States, and the rest of the World. Using this train and testing process, the nucleotide mutation rate of 400(th) patient in future time has been predicted. The complete genomic sequence (Wuhan-HU1) of this large RNA virus (SARS-CoV-2) was first discovered in the laboratory of China on 10th January [10] and placed in the NCBI GenBank. al have performed Phylogenetic analysis of SARS-CoV-2 virus based on the spike gene of the genomic sequence [17] . An adequate amount of gene dataset is currently available in the NCBI GenBank which has the complete genome sequence of SARS-CoV-2. cache = ./cache/cord-328069-a9fi9ssg.txt txt = ./txt/cord-328069-a9fi9ssg.txt === reduce.pl bib === id = cord-328000-i9tzr13z author = Cockrell, Adam S. title = Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date = 2018-07-24 pages = extension = .txt mime = text/plain words = 11004 sentences = 519 flesch = 44 summary = Three different strategies were employed for development of SARS-CoV mouse models: (i) different mouse species (or subspecies) were challenged with wildtype human SARS-CoV isolates in order to find a model that allows for replication and reflects severe respiratory disease symptoms observed in infected human patients; (ii) mice were genetically engineered to modify the host receptor, which facilitated productive SARS-CoV replication and pathogenesis; and (iii) adaptive evolution of wild-type SARS-CoV to a chosen mouse species was done to enhance pathogenesis, and associated clinical phenotypes in vivo. To adapt SARS-CoV to cause severe acute respiratory disease in mouse lungs, 6-week-old female BALB/c mice were intra-nasally infected with the clinical Urbani isolate (Roberts et al. Virus infection studies in CC mouse lines, including SARS-CoV, have led to mapping of high and low host response alleles as they relate to development of clinical signs of disease following viral pathogenesis (Bottomly et al. cache = ./cache/cord-328000-i9tzr13z.txt txt = ./txt/cord-328000-i9tzr13z.txt === reduce.pl bib === id = cord-328242-afof417h author = Nuñez, M. A. title = Invasion Science and the Global Spread of SARS-CoV-2 date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1363 sentences = 67 flesch = 28 summary = Invasion science inherently examines the connectedness between natural and anthropogenic systems by integrating perspectives of, inter alia, ecology, biogeography, population dynamics, evolutionary biology, risk analysis, human history, and environmental management to understand the spread and impact of introduced organisms in non-native contexts. Biomedical research on emergent infectious diseases would benefit from what invasion science can offer in terms of, for example, 1) a consolidated array of frameworks for studying the consequences of eco-evolutionary novelty, and specifically the release of organisms lacking ecological analogues in their recipient environments [4] ; 2) expanding knowledge of the eco-evolutionary factors that determine the success of transitions between stages of invasion (Figure 1 ), which are influenced by a combination of human activities, environmental conditions, and their feedbacks [4, 11, 12] ; and 3) a rich literature on the context-dependent dynamics and predictive modeling of organismal spread and their effects. cache = ./cache/cord-328242-afof417h.txt txt = ./txt/cord-328242-afof417h.txt === reduce.pl bib === id = cord-328246-boxsf2sz author = Hadi-Alijanvand, Hamid title = Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes date = 2020-07-27 pages = extension = .txt mime = text/plain words = 10124 sentences = 563 flesch = 55 summary = 48 In the current study, the input structures for PISA to predict the dissociation free energy of the complex are FoldX-generated mutant 3D structures of ACE2 in association with the RBD of the S1 protein. Free energy of ACE2 binding to RBD of SARS-CoV-2 spike protein 1 is also estimated in the current work by using MM-GBSA approach for mutations in ACE2 that are reported for Iranian ethnic groups by NAMD 2.13. In the current study, we predict the effect of 240 widespread missense mutations in the ACE2 gene reported for different human populations and especially eight ones specific for Iranian ethnic populations on the binding affinity between ACE2 and S1 RBD of SARS-CoV-2 with different computational approaches from bioinformatic methods to a thermodynamic integration procedure. We report the predicted affinities of 240 mutated versions of ACE2 to S1 of SARS-CoV-2 using the mentioned fast structure-based computational methods in Figure 1 . cache = ./cache/cord-328246-boxsf2sz.txt txt = ./txt/cord-328246-boxsf2sz.txt === reduce.pl bib === id = cord-328064-7owd28rr author = Callahan, Cody J. title = Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4879 sentences = 258 flesch = 51 summary = We tested PCR compatibility by placing the swab head-downward after breaking it off at the break point, when present (as in a typical NP swab collection), in 3 ml of modified CDC VTM (Hanks' balanced salt solution containing 2% heat-inactivated fetal bovine serum [FBS], 100 g/ml gentamicin, 0.5 g/ml amphotericin B [Fungizone], and 10 mg/liter phenol red [15] ) overnight to allow any PCR-inhibitory material to leach into the medium, spiking 1.5 ml with 200 copies/ml of control SARS-CoV-2 amplicon target (representing 2 times the limit of detection on our system), vortexing, and testing using the Abbott RealTime SARS-CoV-2 assay on an Abbott m2000 RealTime system platform (16) , following the same protocol as for clinical testing (37 cycles, with a cycle threshold [C T ] of Յ31.50 being reported as positive). Control and prototype swabs were placed in separate vials of VTM and transported to the BIDMC Clinical Microbiology Laboratories, where each sample was tested on the Abbott m2000 SARS-CoV-2 RT-PCR platform per the standard clinical protocol. cache = ./cache/cord-328064-7owd28rr.txt txt = ./txt/cord-328064-7owd28rr.txt === reduce.pl bib === id = cord-328003-yovp8squ author = Duan, Liangwei title = The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date = 2020-10-07 pages = extension = .txt mime = text/plain words = 7346 sentences = 386 flesch = 46 summary = Here, we provide a comprehensive overview of the wealth of research related to the SARS-CoV-2 S glycoprotein biosynthesis, structure, function, and antigenicity, aiming to provide useful insights into the design and development of the S protein-based vaccines as well as therapeutics to prevent or treat the ongoing global spread of SARS-CoV-2/COVID-19. Prefusion structures of human coronavirus HKU1 (HCoV-HKU1) and mouse hepatitis virus S protein ectodomains without two consecutive proline mutations reveal only fully closed conformation (37, 42) , similar to that observed for a full-length, wild-type prefusion form of the SARS-CoV-2 S glycoprotein (41) . Therefore, SARS-CoV-2 evades immune surveillance also through conformational masking, which is well-documented for HIV-1 (43, 44) ; while at the same time, the S protein could transiently sample the functional state to engage ACE2, consistent with the notion that the fusion glycoprotein of highly pathogenic viruses have evolved to perform its functions while evading host neutralizing antibody responses. cache = ./cache/cord-328003-yovp8squ.txt txt = ./txt/cord-328003-yovp8squ.txt === reduce.pl bib === id = cord-328074-pcvdr052 author = Fuereder, Thorsten title = Circumnavigating the challenges of COVID-19 in oncology date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1842 sentences = 83 flesch = 40 summary = authors: Fuereder, Thorsten; Gunsilius, Eberhard; Bartsch, Rupert; Hilbe, Wolfgang At this time, patients with haematological malignancies may well be the most threatened patient population as many are heavily immunosuppressed due to the underlying disease, their treatment, or both, and thus are highly susceptible to severe complications if infected with SARS CoV-2. The European Society of Medical Oncology (ESMO) has meanwhile provided comprehensive guidelines for the management and treatment of lung cancer patients in the SARS CoV-2 era [6] : High priority in stage IV lung cancer remains the initiation of firstor second-line chemotherapy, immunotherapy or TKI therapy. Based on these findings the interleukin-6 inhibitor tocilizumab, which is used for the treatment of severe CPI (and CAR-T cells) induced adverse events, is currently being evaluated in clinical trials in patients with COVID-19. Therefore, no recommendations can be given to delay CPI therapy for cancer patients during the SARS CoV-2 pandemic [7] . cache = ./cache/cord-328074-pcvdr052.txt txt = ./txt/cord-328074-pcvdr052.txt === reduce.pl bib === id = cord-327997-noqbcxua author = Wu, Kevin E. title = RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date = 2020-06-20 pages = extension = .txt mime = text/plain words = 7201 sentences = 377 flesch = 42 summary = We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5' and 3' viral untranslated regions contain the strongest, most distinct localization signals. As previously discussed, since much of the APEX-seq mitochondrial data used to train RNA-GPS actually consists of nuclear-encoded transcripts likely picked up as the APEX-COX4 fusion protein is transported to the mitochondria, we hypothesize that our predicted mitochondrial residency is alluding to similarity in localization pathways, rather than localization destination. To further validate the robustness of these results, we also trained a different predictive algorithm (a recurrent neural network, see STAR Methods for additional details) on the APEX-seq data and performed a similar set of experiments, comparing SARS-CoV-2 dominant subcellular residency predictions to human and coronavirus baselines ( Figure S3A /B). cache = ./cache/cord-327997-noqbcxua.txt txt = ./txt/cord-327997-noqbcxua.txt === reduce.pl bib === id = cord-328187-9zd79gai author = Zhang, Yali title = Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3018 sentences = 165 flesch = 55 summary = The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. 22 On 293T-ACE2iRb3 cells, both the SARS-CoV2-RBG and SARS-CoV2-STG 23 probes showed effective-binding to the cells, as membrane-bound and hACE2-24 mRuby3-colocalized mGam signals were observed after a 6-min incubation with the 25 cells ( Figure 2C ). Compared with 3 samples from healthy donors (n=40), all COVID-19-convalescent plasmas showed 4 significant cMFI inhibition on CSBT assay, whereas only 12 samples (37.5%) had 5 detectable CRBT activity ( Figure 3A ). Among the antibody titers derived from various assays, the 10 CSBT titer showed the best correlation with LVppNAT ( Figure 3D and Table S2, 11 r=0.832, p<0.001), and it also well correlated (r=0.959, p<0.001, Figure 3D ) with the 12 neutralization activity against authentic SARS-CoV-2 virus in 12 representative 13 samples (Table S3) . cache = ./cache/cord-328187-9zd79gai.txt txt = ./txt/cord-328187-9zd79gai.txt === reduce.pl bib === id = cord-328113-eczjjc2v author = D’Alessandro, Angelo title = Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level date = 2020-07-30 pages = extension = .txt mime = text/plain words = 4662 sentences = 237 flesch = 40 summary = Subjects seen at Columbia University Irving Medical Center/New York−Presbyterian Hospital included 33 COVID-19-positive patients, as determined by SARS-CoV-2 nucleic acid testing of nasopharyngeal swabs; in this group, the severity of the disease was inferred from serum levels of IL-6, which were determined by CLIAcertified ELISA-based measurements. Sera of COVID-19 patients, especially those with IL-6 levels >10 pg/mL, contained increased levels of multiple proteins in the acute phase response that is initiated by IL-6specifically components of the coagulation and complement cascades (top enriched pathway, p-value: 1.6 × 10 −31 ; Figure 2 ). Other RBC-derived proteins (i.e., band 3, anion exchanger 1 (AE1; the most abundant RBC membrane protein), peroxiredoxins 2 and 6, catalase, and Journal of Proteome Research pubs.acs.org/jpr Article biliverdin reductase B) correlated significantly with HBA and HBB levels, despite not reaching significance when compared to COVID-19-negative subjects, suggesting that minimal hemolysis was present in a subset of the most severely ill patients in our study ( Figure 4A ), perhaps due to mechanical ventilation or other iatrogenic interventions−including the sample collection protocol adopted in this study. cache = ./cache/cord-328113-eczjjc2v.txt txt = ./txt/cord-328113-eczjjc2v.txt === reduce.pl bib === id = cord-328396-p2gvpe8i author = Kaur, Savneet title = The Enigma of Endothelium in COVID-19 date = 2020-08-04 pages = extension = .txt mime = text/plain words = 4427 sentences = 246 flesch = 39 summary = In the current perspective, we envisage a key role of mEC in the pathogenesis of coronavirus disease 2019 caused by the novel coronavirus, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV2). These studies along with the fact that the pulmonary epithelium is more resistant to injury than the endothelium signify that SARS-CoV-2-induced ARDS and associated coagulopathy may be caused by a direct endothelial infection by the virus in the lungs (Matthay et al., 2019) . A summary of such recent reviews and short reports is provided in Table 1 (Alvarado-Moreno and Majluf-Cruz, 2020; Amraei and Rahimi, 2020; Cure and Cure, 2020; Froldi and Dorigo, 2020; Guler et al., 2020; Gupta et al., 2020; Gustafson et al., 2020; Mangalmurti et al., 2020; Marchetti, 2020; Mondal et al., 2020; Panfoli, 2020; Pons et al., 2020; Sardu et al., 2020b; Teuwen et al., 2020) . cache = ./cache/cord-328396-p2gvpe8i.txt txt = ./txt/cord-328396-p2gvpe8i.txt === reduce.pl bib === id = cord-328373-cubp1cc1 author = Jiang, Yanfang title = Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date = 2020-11-04 pages = extension = .txt mime = text/plain words = 3564 sentences = 217 flesch = 50 summary = In the current study the use of a novel digital PCR assay to detect SARS-CoV-2 in both clinical patient-derived samples and environmentally derived samples was investigated, with the ultimate aim of reducing the rate of false negative results. Thirty-two patient samples including nasopharyngeal swabs, throat swabs, oropharyngeal swabs, phlegm, plasma/blood, and eye conjunctiva were collected at multiple timepoints during the disease course, and tested for the presence of SARS-CoV-2 via RT-PCR. SARS-CoV-2 nucleic acid sequences were detected in all clinical patient samples (respiratory tract samples including nasopharyngeal and oropharyngeal swabs). To prevent false-negative SARS-CoV-2 nucleic acid-based test results, and develop a new sensitive detection assay, we evaluated the performance of real-time RT-PCR and digital PCR for detecting SARS-CoV-2 nucleic acid in clinical patient-derived samples and environmentally derived samples. Strikingly, digital PCR detected SARS-CoV-2 nucleic acids in several samples that had previously tested negative via real-time RT-PCR, including 3 patient-derived samples and 5 environmentally derived samples. cache = ./cache/cord-328373-cubp1cc1.txt txt = ./txt/cord-328373-cubp1cc1.txt === reduce.pl bib === id = cord-328325-yonbkrwe author = Nielsen, Sandra C. A. title = B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date = 2020-05-06 pages = extension = .txt mime = text/plain words = 3377 sentences = 180 flesch = 57 summary = Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of V genes, and extensive activation of IgG and IgA subclasses without significant somatic mutation. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Sequences convergent to known SARS-CoV-speci c antibody IGH sequences13 were identi ed in one COVID-19 patient (7453-D2) but were not detected in the HHC samples (Fig. 4c) . cache = ./cache/cord-328325-yonbkrwe.txt txt = ./txt/cord-328325-yonbkrwe.txt === reduce.pl bib === id = cord-328289-3h3kmjlz author = Iadecola, Costantino title = Effects of COVID-19 on the nervous system date = 2020-08-19 pages = extension = .txt mime = text/plain words = 6524 sentences = 349 flesch = 40 summary = Another Parkinson's disease patient with obesity, hypertension and diabetes, exhibited at autopsy, in addition to hypoxic-ischemic neuronal damage, microhemorrhages, white matter lesions and enlarged perivascular spaces, but no evidence of SARS-CoV-2 in the brain (Kantonen et al., 2020) . The encephalopathy is most likely a consequence of systemic factors, such as cytokine sickness, hypoxia and metabolic dysfunction due to peripheral organ failure, while the strokes seem to be related more to hypercoagulability and endothelial injury than to SARS-CoV-2 vasculitis affecting brain vessels. In some cases, the possibility of a SARS-CoV-2 encephalitis could not be ruled out based on the potential for the virus to infect neurons (Song et al., 2020) , but definitive clinical and pathological evidence of neurotropism is lacking. cache = ./cache/cord-328289-3h3kmjlz.txt txt = ./txt/cord-328289-3h3kmjlz.txt === reduce.pl bib === id = cord-328587-vctvcyim author = Jun, Sun title = The hypothesis that SARS-CoV-2 affects male reproductive ability by regulating autophagy date = 2020-07-10 pages = extension = .txt mime = text/plain words = 2990 sentences = 143 flesch = 47 summary = According to the existing clinical data, some patients not only suffer from respiratory diseases, but also have complications such as acute renal injury and even renal necrosis [2] [3] [4] , in addition, SARS-CoV-2 was also found in recent semen analysis of male patients [5] . Previous clinical data have shown that in addition to respiratory diseases, some male patients with COVID-19 are accompanied by kidney damage and even renal failure [2] [4], which suggest that SARS-CoV-2 may affect male fertility. Furthermore, clinical data also show that the receptor protein ACE2 that mediates the entry of SARS-CoV-2 into host cells is not only expressed in alveolar cells, but also highly expressed in male renal tubular cells [4] [21] [30] .All these suggest that SARS-CoV-2 not only causes damage to the respiratory system of patients, but also has a certain impact on the reproductive system of male patients. cache = ./cache/cord-328587-vctvcyim.txt txt = ./txt/cord-328587-vctvcyim.txt === reduce.pl bib === id = cord-328585-1rkrrx8a author = Lu, Shuai title = The immunodominant and neutralization linear epitopes for SARS-CoV-2 date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2954 sentences = 254 flesch = 69 summary = To investigate the spectrum of antibodies in COVID-19 patients, we detected the binding of the 155 early convalescent sera of 8 imported (Europe) cases which infected SARS-CoV-2 in early April, 156 2020 and 12 domestic (China) cases in early February, 2020 to various epitopes ( Table 1) K203R204/G189R203G204/R203G204/R203G204S344 in N protein, respectively (Table 1) , 172 resulting in different immunodominant epitopes of different virus sub-strains which provide the 173 bases for the differential diagnosis. The predicted epitopes induce neutralization antibody production 175 SARS-CoV-2 pseudo-virus neutralization assay is a well-accepted method to detect the ability of 176 vaccine to inhibit SARS-CoV-2 infection . To assess 8 neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with 178 D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT 179 cells which stably expressed ACE2. cache = ./cache/cord-328585-1rkrrx8a.txt txt = ./txt/cord-328585-1rkrrx8a.txt === reduce.pl bib === id = cord-328505-5fkpnbdb author = Thornton, Jeanine Rempe title = Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab date = 2020-06-26 pages = extension = .txt mime = text/plain words = 997 sentences = 75 flesch = 48 summary = title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab We report a series of two MS patients who developed COVID-19 while on Ocrelizumab therapy and subsequently exhibited negative SARS-CoV-2 serology. The sensitivity may be diminished by inadequate timing of testing following an infection, but the most recent literature suggests that the vast majority of patients with symptomatic COVID-19 produce antibodies within the first two to three weeks after symptom onset (Long et al., 2020) . In MS, a possible concern is the impact of certain DMTs, such as CD-20 monoclonal antibodies In this article, we report serology results from the first two patients at our center to have undergone SARS-CoV-2 antibody testing after developing COVID-19 while on Ocrelizumab therapy. In this case series, we present negative results from the first two MS patients at our site who underwent SARS-CoV-2 antibody testing after developing PCR-confirmed COVID-19 while on Ocrelizumab. cache = ./cache/cord-328505-5fkpnbdb.txt txt = ./txt/cord-328505-5fkpnbdb.txt === reduce.pl bib === id = cord-328287-3qgzulgj author = Moni, Mohammad Ali title = Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date = 2014-10-24 pages = extension = .txt mime = text/plain words = 10643 sentences = 547 flesch = 43 summary = Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . cache = ./cache/cord-328287-3qgzulgj.txt txt = ./txt/cord-328287-3qgzulgj.txt === reduce.pl bib === id = cord-328381-bfvdhai8 author = Hattermann, K. title = Susceptibility of different eukaryotic cell lines to SARS-coronavirus date = 2005-01-13 pages = extension = .txt mime = text/plain words = 1829 sentences = 103 flesch = 60 summary = In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown). cache = ./cache/cord-328381-bfvdhai8.txt txt = ./txt/cord-328381-bfvdhai8.txt === reduce.pl bib === id = cord-328499-d6cvaxm9 author = Matzkies, Lucie-Marie title = Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date = 2020-07-08 pages = extension = .txt mime = text/plain words = 569 sentences = 50 flesch = 62 summary = RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. Clinical Evaluation of 179 the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the VIASURE SARS-CoV-2 S-gene Real Time PCR Detection Kit cache = ./cache/cord-328499-d6cvaxm9.txt txt = ./txt/cord-328499-d6cvaxm9.txt === reduce.pl bib === id = cord-328395-2cakgmsj author = Oxford, Alexandra E. title = Endothelial Cell Contributions to COVID-19 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 6707 sentences = 353 flesch = 39 summary = Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. This review will focus on the concept of endothelial cell infection and dysfunction as an active driver of COVID-19, which begins as a respiratory illness, with vascular pathology contributing significantly to the most negative patient outcomes. Endothelial cell infection that proceeds via ACE2 shows how SARS-CoV-2 can replicate into a wide range of cells, which may explain some of the clinical symptoms found in COVID-19 patients. Thus far, we have discussed the viral mechanisms of SARS-CoV-2 and resultant COVID-19 sequelae as they relate to endotheliitis and endothelial cell infection mediated by viral spike protein-ACE2 interaction. The successful use of anti-interleukin drugs to treat the inflammatory symptoms seen in severe COVID-19 would have marked effects on endothelial pathology as these cells are highly responsive to cytokine signaling [59] . cache = ./cache/cord-328395-2cakgmsj.txt txt = ./txt/cord-328395-2cakgmsj.txt === reduce.pl bib === id = cord-328659-miujzgtd author = Mishra, Akhilesh title = Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date = 2020-07-27 pages = extension = .txt mime = text/plain words = 6064 sentences = 361 flesch = 55 summary = title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. cache = ./cache/cord-328659-miujzgtd.txt txt = ./txt/cord-328659-miujzgtd.txt === reduce.pl bib === id = cord-328704-m2seavg6 author = Malfertheiner, Peter title = COVID-19: Don't Neglect the Gastrointestinal Tract! date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1206 sentences = 63 flesch = 45 summary = There are 2 main aspects of concern: one being related to gastrointestinal symptoms (GIS) and their influence on the course of disease; the other being related to excretion of the virus (or its RNA fragments) in the patient's faeces and a possible role for faecal-oral transmission. To prevent faecal SARS-CoV-2 transmission, a group of experts proposed assessing potential donors for the presence of typical COVID-19 symptoms within 30 days prior to donation. It certainly demands for studies on (a) the pathogenesis and impact of direct viral damage of the whole digestive system; and (b) factors contributing to COVID-19-associated diarrhoea with special emphasis on the gut microbiome and anti-diarrhoea management.A special focus should be directed on the role of the digestive system in transmitting the infection, on how to reduce the length of infectiousness, and on which precautions to be taken with regard to this matter. Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-328704-m2seavg6.txt txt = ./txt/cord-328704-m2seavg6.txt === reduce.pl bib === id = cord-328262-hw8swbt5 author = O’Neill, Luke A. J. title = BCG-induced trained immunity: can it offer protection against COVID-19? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2177 sentences = 102 flesch = 42 summary = Bacillus Calmette–Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. This effect was mediated by peritoneal macrophages 10 Bacillus Calmette-Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity cache = ./cache/cord-328262-hw8swbt5.txt txt = ./txt/cord-328262-hw8swbt5.txt === reduce.pl bib === id = cord-328705-024y5k72 author = Rahman, Md. Mahbubur title = Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4487 sentences = 246 flesch = 51 summary = In this study, computational screening is performed by molecular docking of 1615 Food and Drug Administration (FDA) approved drugs against the main protease (Mpro) of SARS-CoV-2. Several promising approved drugs, including Simeprevir, Ergotamine, Bromocriptine and Tadalafil, stand out as the best candidates based on their binding energy, fitting score and noncovalent interactions at the binding sites of the receptor. The MD simulations for the main protease were conducted (6LU7) in apo-form (protein without ligand) and in holo-form (protein-drug complex) to assess any probable conformational changes to and interactions with their structures over the 100 nanoseconds (ns). The selected four drug-main protease complexes may have dissimilarities with the apo-Mpro during MD simulation regarding the energy profile. Identification of potential binders of the SARS-Cov-2 spike protein via molecular docking, dynamics simulation and binding free energy calculation cache = ./cache/cord-328705-024y5k72.txt txt = ./txt/cord-328705-024y5k72.txt === reduce.pl bib === id = cord-328471-oz99upzz author = Ahmad, Jamshaid title = SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 5089 sentences = 282 flesch = 55 summary = In this global health emergency, drug repurposing (or repositioning) is one of the fast track option that involves screening of existing FDA approved drugs for the identification of potential molecules that can disrupt the function of key proteins of the SARS-CoV-2 and can be used for treatment against COVID-19. Whereas, Demoxytocin showed ten H-bonds with both active site Asp760 and Asp761 and other key residues e.g. Trp617, Tyr619, Lys621, Ser682, Glu811, Lys621, Tyr619, Trp617, Ser682 and Glu811 with dock score -9.68kcal/mol and ligand efficiency of -0.142 (Supplementary Figure S3) . Colistin (polymyxin E, polypeptide antibiotics) showed most of the H-bonding with Lys551, Trp617, Tyr619, Asp618, Ser682, Asp684, Asn691, and both catalytic residues i.e. Asp760, Asp761, with a docking score of -9.24kcal/mol and ligand efficiency of -0.113 (Supplementary Figure S5) . Examorelin, Lypressin, Ornipressin, and Colistin are also common drugs in both form of RdRp. Only one H-bond with His810 and other non-covalent interactions were observed for Examorelin showed a docking score of -12.139 kcal/mol and ligand efficiency of -0.187. cache = ./cache/cord-328471-oz99upzz.txt txt = ./txt/cord-328471-oz99upzz.txt === reduce.pl bib === id = cord-328680-zdwep5b2 author = Burr, Tyler title = NMDA-receptor encephalitis associated with COVID-19 infection in a toddler date = 2020-10-09 pages = extension = .txt mime = text/plain words = 897 sentences = 63 flesch = 40 summary = Anti-NMDA receptor (NMDAR) encephalitis is characterized by mood and behavior changes, seizures, abnormal movements, autonomic instability, and encephalopathy. More recently, cases of anti-NMDAR encephalitis following viral infections have been reported, including herpes simplex virus (HSV), Japanese encephalitis virus (JEV), and now the 2019 novel coronavirus (SARS-CoV-2) 2-5 . We present the first pediatric case of SARS-CoV-2-associated anti-NMDAR Encephalitis. A post-infectious inflammatory condition following acute SARS-CoV-2, termed multisystem inflammatory syndrome in children (MIS-C), has been described. There have been two cases of anti-NMDAR encephalitis associated with SARS-CoV-2 in adults reported 5, 9 . At the time of publication, the authors are unaware of other cases of anti-NMDAR encephalitis with recent SARS-CoV-2 infection in pediatric populations. Herpes simplex virus-induced anti-N-methyl-d-aspartate receptor encephalitis: a systematic literature review with analysis of 43 cases Anti-N-methyl-D-aspartate receptor encephalitis associated with reactivated Epstein-Barr virus infection in pediatric patients: Three case reports Anti-NMDA receptor encephalitis in a psychiatric Covid-19 patient: A case report cache = ./cache/cord-328680-zdwep5b2.txt txt = ./txt/cord-328680-zdwep5b2.txt === reduce.pl bib === id = cord-328687-clr1e9p6 author = Zhou, Fuling title = Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3719 sentences = 189 flesch = 45 summary = BACKGROUND: Asymptomatic carriers were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without developing symptoms, which might be a potential source of infection outbreak. Recently, in order to avoid further nosocomial infection, all staff without clinical symptoms in our hospital participated in the physical examination before resumption of ordinary job, including chest CT, throat swab RT-PCR test and plasma COVID-19 IgM/IgG antibodies test. This study aims to analyze the examination results, understand the infection status of staff, track the infection related risk factors, as well as tracing of asymptomatic infection individual, so as to provide effective suggestions for other hospitals and non-medical institution in Wuhan, ensuring scientific and safe return to work. In our study, asymptomatic carrier refers to patients who have mild or non-symptoms but with positive test for viral nucleic acid of SARS-CoV-2 or with positive test for serum specific IgM antibody. cache = ./cache/cord-328687-clr1e9p6.txt txt = ./txt/cord-328687-clr1e9p6.txt === reduce.pl bib === id = cord-328712-7q9mg2tu author = Moore, Nicholas title = Chloroquine for COVID-19 Infection date = 2020-04-07 pages = extension = .txt mime = text/plain words = 794 sentences = 55 flesch = 60 summary = Caused by a new virus, SARS-CoV2, COVID-19 is related to the common cold and the SARS-CoV1 virus that was responsible for the 2003 Severe Acute Respiratory Syndrome (SARS) infection in Asia, causing about 8000 cases and 774 deaths (https ://www. Raoult was based on theory [5] , on the effects of the drug on coronavirus replication in vitro [1, 4, [6] [7] [8] , and on experimental data [2] showing SARS-CoV inhibition [3] , concluding to a hypothetical effect of hydroxychloroquine on COVID-19 [9] without clinical proof other than a non-randomized open study of 20 patients, purported to show extraordinary results on virus washout (notwithstanding a slew of typical biases) [10] . In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) cache = ./cache/cord-328712-7q9mg2tu.txt txt = ./txt/cord-328712-7q9mg2tu.txt === reduce.pl bib === id = cord-328644-odtue60a author = Comandatore, Francesco title = Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date = 2020-05-28 pages = extension = .txt mime = text/plain words = 6535 sentences = 301 flesch = 50 summary = These variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded RNA viruses -as in the case of SARS-CoV-2 (Sanjuán and Domingo-Calap 2016) , which has a single, positive-strand RNA genome. To have a better insight on the history and spread of the COVID-19 pandemic in Italy and thanks to the sequences deposited in the Gisaid database, we identified 7 non synonymous mutations that are differentially frequent in Italian SARS-CoV-2 strains respect to strains circulating globally. Our analysis allowed us to identify 7 positions in four proteins that present drastic changes in amino acid frequencies when comparing Italian sequences with worldwide sequences available on Gisaid.org on April, 10, 2020 ( Figure 1 ). cache = ./cache/cord-328644-odtue60a.txt txt = ./txt/cord-328644-odtue60a.txt === reduce.pl bib === id = cord-329069-ejdunj41 author = Yang, He S title = Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date = 2020-08-21 pages = extension = .txt mime = text/plain words = 2361 sentences = 134 flesch = 50 summary = METHOD: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. CONCLUSION: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. In this study, we hypothesized that the results of routine laboratory tests performed within a short time frame as the RT-PCR testing, in conjunction with a limited number of previously identified predictive demographic factors (age, gender, race) (17), can predict SARS-CoV-2 infection status. Laboratory tests were selected to construct the input feature vectors of the prediction model based on the following criteria: 1) a result available for at least 30% of the patients two days before a specific SARS-CoV-2 RT-PCR test, and 2) showing a significant difference (P-value, P-value after Bonferroni correction, P-value after demographics adjustment all less than 0.05) between patients with positive and negative RT-PCR results. cache = ./cache/cord-329069-ejdunj41.txt txt = ./txt/cord-329069-ejdunj41.txt === reduce.pl bib === id = cord-328686-5ik5em5a author = Zhao, L. title = First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1606 sentences = 110 flesch = 61 summary = In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint From the findings of this study, during the middle risk period, positive samples were detected both in 83 municipal and hospital wastewater systems. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Although SARS-CoV-2 RNA surveillance in wastewaters is a useful WBE drive, the public health risk associated 109 with water cycle is unclear since viral particles infectivity in sewage and faeces is yet to be determined in 110 addition to its probable fecal-oral transmission. cache = ./cache/cord-328686-5ik5em5a.txt txt = ./txt/cord-328686-5ik5em5a.txt === reduce.pl bib === id = cord-328856-1l7x72j7 author = Ucciferri, Claudio title = Pidotimod in Paucisymptomatic SARS-CoV2 Infected Patients date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1207 sentences = 83 flesch = 45 summary = Several studies on COVID-19 are focusing on severe forms; however, the most frequent SARS-CoV-2 clinical presentation is a mild disease with or without pneumonia in about 80% of patients. Notwithstanding immune response appeared fundamental for SARS infection resolution, SARS-Cov-2 disease present increased levels of plasma pro-inflammatory mediators, as a consequence of an induced dysregulated cytokine storm. We enrolled SARS-CoV2 positive patients (Brescia-COVID Respiratory Severity Scale 0), with fever and cough without acute respiratory failure or sign of pneumonia from March to April 2020 at the Infectious Diseases Clinic, University 'G. 9 In our study, in the outpatient population affected by SARS-CoV2 infection, pidotimod appears as a valid option to reduce the duration of symptoms in patients, as an earlier defervescence of fever and it could prevent the cytokine cascade activation. In conclusion, in ambulatorial adult patients with SARS-Cov2 infection without pneumonia, pidotimod could be considered an option, well tolerated and associated with a rapid reduction of systemic symptoms of disease. cache = ./cache/cord-328856-1l7x72j7.txt txt = ./txt/cord-328856-1l7x72j7.txt === reduce.pl bib === id = cord-328479-1tzysg7u author = Chen, Jianjun title = Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China date = 2020-06-21 pages = extension = .txt mime = text/plain words = 722 sentences = 44 flesch = 56 summary = In this study, we collected swab and blood samples from pet cats and dogs in Wuhan whose owners were confirmed to have COVID-19. Swab and whole blood samples were collected from 10 cats (four female, six male) and 9 dogs (four female, five male) (Supplementary Table 1 We then conducted telephone questionnaires with the owners of the three pets. In this study, we conducted a survey for SARS-CoV-2 in pets whose owners were diagnosed with COVID-19, in 15 communities in Wuhan. Prior to our study, a preprint of a research article posted online at bioRxiv indicated that SARS-CoV-2-specific antibodies were detected in cats in Wuhan at the time of the COVID-19 epidemic (7) . In addition, pet dogs and cats in Hong Kong (8), whose owners had been diagnosed with COVID-19, tested positive for SARS-CoV-2 RNA. Collectively, these results indicate the SARS-CoV-2 can be transmitted to companion animals, possible through contact with owners carrying COVID-19. cache = ./cache/cord-328479-1tzysg7u.txt txt = ./txt/cord-328479-1tzysg7u.txt === reduce.pl bib === id = cord-328484-4iptwc3n author = Li, Tao title = Clinical Characteristics of 312 Hospitalized Older Patients with COVID-19 in Wuhan, China date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3077 sentences = 195 flesch = 51 summary = Although some case series have been published, no previous studies focused on older patients exclusively (Novel Coronavirus Pneumonia Emergency Response Epidemiology Team, 2020; Fu et al., 2020; . Further regression analysis suggested that age(OR 1.59, 95%CI 1.13-2.08), SOFA score(OR 5.89, 95%CI 3.48-7.96), APACHEⅡ score(OR 3.13, 95%CI 1.85-5.62), platelet count＜125×10 9 /L(OR 2.36, 95%CI 1.03-4.14), d-dimer(OR 4.37, 95%CI 2.58-7.16), creatinine＞133μmol/L(OR 1.85, 95%CI 1.12-3.04), interleukin-6(OR 4.32, 95%CI 2.07-7.13), and lung consolidation(OR 1.94, 95%CI 1.45-4.27) on admission were independent risk factors for severe COVID-19 (Table 3) . This study compared clinical characteristics between non-severe and severe COVID-19 cases among older patients, and identified several risk factors for severe cases. This study identified several risk factors for severe COVID-19 cases among older patients. Age, SOFA score, APACHEⅡ score, platelet count＜125×109/L, d-dimer, creatinine＞ 133μmol/L, interleukin-6, and lung consolidation on admission were independent risk factors for severe cases among older patients with COVID-19. cache = ./cache/cord-328484-4iptwc3n.txt txt = ./txt/cord-328484-4iptwc3n.txt === reduce.pl bib === id = cord-328695-nptfd6c2 author = Tengs, Torstein title = A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1969 sentences = 102 flesch = 51 summary = title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. The presence of s2m in the SARS-CoV-2 genome (GenBank accession MN908947, position 29727-29768) and other members of this group is probably the result of a single horizontal transfer event, predating the divergence of the SARS-related viruses (Tengs, et al. The insect species that contain s2m (and the associated protein) are distantly related, indicating either a deep evolutionary origin with multiple losses or that this genetic construct is also a mobile element, perhaps using viruses as a vector . cache = ./cache/cord-328695-nptfd6c2.txt txt = ./txt/cord-328695-nptfd6c2.txt === reduce.pl bib === id = cord-328865-ekgqdjlk author = Anand, Shuchi title = Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study date = 2020-09-25 pages = extension = .txt mime = text/plain words = 5647 sentences = 279 flesch = 45 summary = METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). 12 Testing remainder plasma from monthly samples obtained for routine care of patients on dialysis for SARS-CoV-2 antibodies therefore represents a practical approach to a population-representative surveillance strat egy, 13 informing risks faced by a susceptible population while ensuring representation from racial and ethnic minorities. In our analysis of seroprevalence of SARS-CoV-2 spike protein receptor binding antibodies from a nationwide representative sample of patients receiving dialysis, we find that despite the USA contemporaneously leading the world in the numbers of diagnosed cases, overall, fewer than 10% of US adults had evidence of seroconversion in July, 2020. cache = ./cache/cord-328865-ekgqdjlk.txt txt = ./txt/cord-328865-ekgqdjlk.txt === reduce.pl bib === id = cord-328683-zvabpty9 author = Fontanet, A. title = SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4046 sentences = 224 flesch = 56 summary = Methods: Between 28-30 April 2020, a retrospective cohort study was conducted among pupils, their parents and relatives, and staff of primary schools exposed to SARS-CoV-2 in February and March 2020 in a city north of Paris, France. Seroepidemiological studies are thus needed to determine the extent of infection in children and to decipher the role they may play in transmission To our knowledge, the number of SARS-CoV-2 secondary transmissions in school setting documented in scientific literature is limited, with very few or no secondary cases in investigations in . The epidemic curve, based on symptoms experienced by participants with SARS-CoV-2 antibodies, had no specific pattern, and transmission does not appear to have been impacted by the closure of schools for holidays on February 14 (end of week 7) ( Figure 2A ). They differ however from the results of the study performed in the high school of the same city in France, in which 38% of pupils, 43% of teaching staff and 59% of nonteaching staff who participated in the investigation had anti-SARS-CoV-2 antibodies 27 . cache = ./cache/cord-328683-zvabpty9.txt txt = ./txt/cord-328683-zvabpty9.txt === reduce.pl bib === id = cord-328762-2b1pl8jr author = Fuest, Matthias title = Postmortem conjunctival and nasopharyngeal swabs in SARS‐CoV‐2 infected and uninfected patients date = 2020-08-06 pages = extension = .txt mime = text/plain words = 888 sentences = 60 flesch = 64 summary = The specifity of ocular tissue/fluid in detecting SARS-CoV-2 was very low in comparison with standard sample collection from nasopharyngeal swabs (NPS) (Ulhaq & Soraya 2020) . To date, no data are available on the postmortem prevalence of virus RNA in ocular and pharyngeal tissue in SARS-CoV-2 patients. Accordingly, in a prospective cohort study, potential corneal donors (uninfected with negative premortem NPS) in our institution had postmortem conjunctival (COS) and NPS taken starting March 17, 2020. SARS-CoV-2 RNA was not detected in any postmortem NPS or COS in the uninfected group. The absence of virus RNA in our postmortem swabs agrees with the literature on premortem samples, where only 3/315 COS = 0.95% (compared to NPS 604/849 = 71.1%) were positive even in symptomatic eyes, indicating that the human conjunctiva is not a typical site of SARS-CoV-2 replication (Lu et al. All these SARS-CoV-2 patients were diagnosed by premortem positive NPS. cache = ./cache/cord-328762-2b1pl8jr.txt txt = ./txt/cord-328762-2b1pl8jr.txt === reduce.pl bib === id = cord-328853-0iqdqcp6 author = Neidleman, Jason title = SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2431 sentences = 133 flesch = 52 summary = title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential SUMMARY Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19. Furthermore, the clonality of T cell receptor (TCR) sequences 54 5 is higher in patients with mild rather than severe COVID-19, suggesting a role for antigen-55 specific T cell responses in symptom resolution. We report here that SARS-CoV-2-specific CD4+ and CD8+ T cells from convalescent 86 individuals are diverse, exhibit features different from antigen-specific T cells against CMV, 87 include cells with both lymphoid and tissue homing potential, harbor phenotypic features of 88 functional effector cells, and are long-lived and capable of homeostatic proliferation. cache = ./cache/cord-328853-0iqdqcp6.txt txt = ./txt/cord-328853-0iqdqcp6.txt === reduce.pl bib === id = cord-329186-0eoz4npg author = Xia, Shuai title = The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin date = 2020-06-12 pages = extension = .txt mime = text/plain words = 1742 sentences = 112 flesch = 64 summary = title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin It has been speculated that RRAR, a unique furin-like cleavage site (FCS) in the spike protein (S), which is absent in other lineage B βCoVs, such as SARS-CoV, is responsible for its high infectivity and transmissibility. Then, by calculating the ratio of the fused cells, we can assess the fusogenic capacity of the S protein in the presence or absence of exogenous trypsin or human airway trypsin-like protease (HAT). Next, we compared the fusogenic capacity of SARS-CoV-2-S, SARS-CoV-S and their mutants via an S-mediated cell-cell fusion assay in the absence of exogenous trypsin or human airway trypsin-like protease (HAT). © The Author(s) 2020 Fig. 1 The function of furin cleavage site in SARS-CoV-2-S mediated fusion. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion cache = ./cache/cord-329186-0eoz4npg.txt txt = ./txt/cord-329186-0eoz4npg.txt === reduce.pl bib === id = cord-328557-f6o1aynz author = Samad, Abdus title = Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach date = 2020-07-17 pages = extension = .txt mime = text/plain words = 7593 sentences = 423 flesch = 50 summary = So, targeting S-protein can provide an immunogenic response in the human host, and has been chosen for designing a multi-epitopes vaccine candidate against the SARS-CoV-2. For the prediction of CTLs epitope, the sequence of the selected protein was submitted into the NetCTL v1.2 server available at http://www.cbs.dtu. For this purpose, we submitted the refined vaccine model as ligand and TLR4 protein as immunological receptor into the ClusPro v2.0 server, available at https://cluspro.bu.edu/, for molecular docking (Kozakov et al., 2017) . Due to the high number of potential epitopes, we selected the top four CTL epitopes for the final vaccine construction based on the antigenicity score (Table 1) . Likewise, we considered the top four HTL epitopes for incorporating into the final vaccine construct based on the antigenic score (Table 2) . In this study, we designed an epitope-based vaccine that could provide a strong immune response against SARS-CoV-2, thereby, preventing the COVID-19 pandemic. cache = ./cache/cord-328557-f6o1aynz.txt txt = ./txt/cord-328557-f6o1aynz.txt === reduce.pl bib === id = cord-328409-px92ff89 author = Hornuss, Daniel title = COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1575 sentences = 172 flesch = 42 summary = After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Als Diagnostik der Wahl zur schnellen Identifikation von COVID-19-Fällen hat sich dabei die PCR-Analyse auf SARS-CoV-2 aus tiefen nasopharyngealen oder oropharyngealen Abstrichen etabliert [3] . cache = ./cache/cord-328409-px92ff89.txt txt = ./txt/cord-328409-px92ff89.txt === reduce.pl bib === id = cord-329129-t84pu00z author = Zuo, J title = Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3486 sentences = 175 flesch = 50 summary = We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection. In this study we characterised SARS-CoV-2-specific T cell immune responses in a cohort of 100 donors at 6-months post-infection. Peptide pools from a range of viral proteins, including spike, nucleoprotein and membrane protein, were used to stimulate fresh PBMC and the magnitude of the global SARS-CoV-2-specific T-cell response was determined. Here we undertook, to our knowledge, the first assessment of the SARS-CoV-2-specific T cell immune response at six months following primary infection in a unique cohort of healthy adults with asymptomatic or mild-to-moderate COVID-19. cache = ./cache/cord-329129-t84pu00z.txt txt = ./txt/cord-329129-t84pu00z.txt === reduce.pl bib === id = cord-329221-miztel9l author = rudolf, f. title = Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3683 sentences = 249 flesch = 54 summary = Conclusions and Relevance: This study emphasizes the need for large and diverse negative cohorts when determining specificities, and for diverse and representative positive samples when determining sensitivities of lateral flow assays for SARS-CoV-2 infections. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint On the other hand, the sensitivity needs to be assayed using a sufficiently large and representative sample of the antibody response in a population for time post infection, (but especially also in disease severity) i don't know what you mean. To accurately calculate the specificity, we used the plasma of a blood donor cohort comWe characterised eleven different commercially available lateral flow assays (LFA) for detection of SARS-CoV-2 specific IgM and IgG with serum samples from the three cohorts (Table 1 ). cache = ./cache/cord-329221-miztel9l.txt txt = ./txt/cord-329221-miztel9l.txt === reduce.pl bib === id = cord-329011-spiuqngp author = Huang, Yuan title = Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date = 2020-08-03 pages = extension = .txt mime = text/plain words = 6045 sentences = 340 flesch = 53 summary = The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. A large number of glycosylated S proteins cover the surface of SARS-CoV-2 and bind to the host cell receptor angiotensinconverting enzyme 2 (ACE2), mediating viral cell entry [8] . The SARS-CoV-2 S protein is highly conserved among all human coronaviruses (HCoVs) and is involved in receptor recognition, viral attachment, and entry into host cells. Structure of the S1 subunit The binding of virus particles to cell receptors on the surface of the host cell is the initiation of virus infection; therefore, receptor recognition is an important determinant of viral entry and a drug design target. Therefore, the development of antibodies targeting this functional motif may cross-bind and neutralize these two viruses and related CoVs. Antiviral peptides prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infection. cache = ./cache/cord-329011-spiuqngp.txt txt = ./txt/cord-329011-spiuqngp.txt === reduce.pl bib === id = cord-328778-mjzsz7rz author = Steinchen, N. title = Biologikatherapie nach COVID-19-Infektion: Keine Reaktivierung einer COVID-19-Infektion bei positivem Antikörperstatus SARS-CoV-2 unter Biologikatherapie date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1126 sentences = 180 flesch = 40 summary = In der kurzen Beobachtungszeit zeigten sich bis heute erfreulicherweise keine klinischen Hinweise auf eine Reaktivierung der COVID-19-Infektion, die bDMARD-Therapie wurde nebenwirkungsfrei vertragen. Die Fragen, ob bei Vorliegen einer entzündlich rheumatischen Erkrankung eine besondere Gefahr besteht, sich mit SARS-CoV-2 zu infizieren, und im Fall einer Infektion diese auch schwerer verläuft, sind bis heute aufgrund begrenzter Daten nicht sicher zu beantworten. Die Patienten*innen standen alle unter einer Zytokinhemmertherapie und wiesen im Vergleich zu den 2 Kontrollen (ohne Anti-Zytokin-Therapie) keine Antikörper gegen SARS-CoV-2 auf, während bei 2 % des nichtmedizinisch tätigen und 4 % des medizinisch tätigen Kontrollpersonals Antikörper gegen Corona-Virus detektierbar waren. Ursache des geringen Antikörpernachweises gegen SARS-CoV-2 in der Gruppe der Patienten*innen mit entzündlich rheumatischen Erkrankungen unter Anti-Zytokin-Therapie könnte sein, dass im Vergleich zu den anderen beiden Gruppen die RKI-Abstands-und Hygieneempfehlungen konsequenter aus Furcht vor einer Ansteckung unter immunsuppressiver Therapie umgesetzt wurden. Andererseits kann die Schlussfolgerung, dass eine Biologikatherapie vor einer SARS-CoV-2-Infektion mit einem schweren Verlauf möglicherweise schützt, aus den Daten nicht abgeleitet werden. cache = ./cache/cord-328778-mjzsz7rz.txt txt = ./txt/cord-328778-mjzsz7rz.txt === reduce.pl bib === id = cord-329010-n0mz098o author = McKee, Dwight L. title = Candidate drugs against SARS-CoV-2 and COVID-19 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 5193 sentences = 260 flesch = 41 summary = Further, chloroquine and hydroxychloroquine, and off-label antiviral drugs, such as the nucleotide analogue remdesivir, HIV protease inhibitors lopinavir and ritonavir, broad-spectrum antiviral drugs arbidol and favipiravir as well as antiviral phytochemicals available to date may prevent spread of SARS-CoV-2 and morbidity and mortality of COVID-19 pandemic. Drugs that have recently been shown to target MERS-CoV in mice [15] , and to inhibit Ebola virus RdRP and SARS-CoV-2 proteases in humans, such as remdesivir and ritonavir/lopinavir, also constitute candidate drugs against SARS-CoV-2 and are now investigated for their therapeutic efficacy in COVID-19 patients in 2 international clinical trials (SOLIDARITY Trial and DisCoVeRy Trial). The emergence of the novel beta coronavirus SARS-CoV-2 from Wuhan, Hubei province, China in December 2019 rapidly led to a pandemic involving more than 2,500,000 infected persons and more proven drugs such as camostat mesilate which prevents virus host cell entry by inhibiting TMPRSS2 [8] , and chloroquine phosphate which inhibits terminal phosphorylation of ACE2, or hydroxychloroquine which is metabolized in vivo to chloroquine [44] . cache = ./cache/cord-329010-n0mz098o.txt txt = ./txt/cord-329010-n0mz098o.txt === reduce.pl bib === id = cord-329262-ybr1auo2 author = Moriel‐Carretero, María title = The hypothetical role of Phosphatidic Acid in subverting ER membranes during SARS‐CoV infection date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3957 sentences = 203 flesch = 44 summary = Subsequently, a major path for viral internalization relies on the endocytic pathway and culminates with the release of the viral RNA genome into the cytoplasm of the infected cell (reviewed in 3 After this, +RNA viruses need to establish a complex capable of amplifying and further expressing their genome, the "replication/transcription complex", as well as additional (termed "non-structural") proteins capable of coordinating accessory functions. A relevant point when analyzing the morphological particularities of DMVs induced during SARS-CoV infection is that, in contrast to those triggered by other +RNA viruses, the inner layer indeed constitutes a closed circle, but the outer one is continuous all along with that of the other DMVs, giving the impression that the whole is disconnected from the cytoplasm ( Figure 1A , right panel) 11 . cache = ./cache/cord-329262-ybr1auo2.txt txt = ./txt/cord-329262-ybr1auo2.txt === reduce.pl bib === id = cord-329041-coryaz2s author = Brown, Ariane J. title = Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date = 2019-09-30 pages = extension = .txt mime = text/plain words = 5934 sentences = 325 flesch = 54 summary = These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. We previously reported the antiviral activity of RDV against a genetically diverse panel of human endemic, emerging and zoonotic CoV including HCoV-NL63 (alpha 1b), mouse hepatitis virus (MHV, beta 2a), SARS-CoV and related Bat CoVs WIV1 and SHC014 (beta 2b), as well as MERS-CoV and related Bat CoV HKU5 (beta 2c) (Agostini et al., 2018; Sheahan et al., 2017) . Inhibition of viral protease has also been evaluated with lopinavir, a protease inhibitor designed for human immunodeficiency virus, which like chloroquine exerts a moderate antiviral effect on CoV replication (EC 50 values: MERS-CoV 8 μM, SARS-CoV 17.1 μM, HCoV-229E 6.6 μM) (de Wilde et al., 2014) . cache = ./cache/cord-329041-coryaz2s.txt txt = ./txt/cord-329041-coryaz2s.txt === reduce.pl bib === id = cord-328962-1c4vqaqr author = Benítez-Cardoza, Claudia Guadalupe title = Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug date = 2020-06-15 pages = extension = .txt mime = text/plain words = 3344 sentences = 184 flesch = 54 summary = KEY FINDINGS: 20 best compounds directed to interact in ACE2 with a high probability to be safe in humans, validated by web servers of prediction of ADME and toxicity (ProTox-II and PreADMET), to difficult the interaction between ACE2 and region binding domain (RBD) of SARS-CoV-2. We use the amino acids reported in the crystallographic structure of the interaction between the S-protein-RBD of SARS-CoV-2 and ACE2 (Gln24, Asp30, His34, Tyr41, Gln42, Met82, Lys353 and Arg357 in ACE2) [10] [22] , therefore, using the crystallographic structure of ACE2 (PDB 1R42), we carried out a Docking directed to these mentioned residues using a library of compounds (EXPRESS-pick Collection from Chembridge Corp.) to select the best compounds, and that these can affect the interaction between ACE2 and SARS-CoV-2, making these results an important contribution to establishing the foundations that allow the development of a drug that optimizes the resolution of this pandemic. cache = ./cache/cord-328962-1c4vqaqr.txt txt = ./txt/cord-328962-1c4vqaqr.txt === reduce.pl bib === id = cord-329102-2y49kcwu author = Lan, Tammy C. T. title = Structure of the full SARS-CoV-2 RNA genome in infected cells date = 2020-06-30 pages = extension = .txt mime = text/plain words = 9315 sentences = 507 flesch = 61 summary = We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. cache = ./cache/cord-329102-2y49kcwu.txt txt = ./txt/cord-329102-2y49kcwu.txt === reduce.pl bib === id = cord-328960-46zui1sl author = Hillen, Hauke S. title = Structure of replicating SARS-CoV-2 polymerase date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4541 sentences = 285 flesch = 62 summary = Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). cache = ./cache/cord-328960-46zui1sl.txt txt = ./txt/cord-328960-46zui1sl.txt === reduce.pl bib === id = cord-329395-4k8js9v2 author = Ratcliff, Jeremy title = Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1662 sentences = 124 flesch = 55 summary = Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 cache = ./cache/cord-329395-4k8js9v2.txt txt = ./txt/cord-329395-4k8js9v2.txt === reduce.pl bib === id = cord-329363-kaw3h5xm author = Vardeny, Orly title = Applying the Lessons of Influenza to COVID-19 During a Time of Uncertainty date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1030 sentences = 42 flesch = 30 summary = For patients with underlying cardiovascular disease, other opportunities for minimizing complications from infection include remaining up to date on other immunizations, including influenza vaccine, which is available and effective, and pneumococcal vaccine, as secondary bacterial infections often lead to hospitalizations among those with primary viral infections. Because viral illness has been shown to exacerbate underlying cardiac illness and can lead to acute events such as acute myocardial infarction or decompensated heart failure, efforts should be made to optimize guideline-directed treatment strategies that have been shown to improve clinical status in high-risk patients, and thus reduce the risk of worsening symptoms or acute events in case of infection. In patients without known or suspected COVID-19, this includes all evidence-based therapies in cardiovascular disease, such as aspirin, statins, and β-blockers for secondary prevention in patients with coronary disease, and guideline-directed medical therapy in those with heart failure. cache = ./cache/cord-329363-kaw3h5xm.txt txt = ./txt/cord-329363-kaw3h5xm.txt === reduce.pl bib === id = cord-329710-vqorb6j7 author = Kumar, Krishna title = Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2477 sentences = 147 flesch = 49 summary = We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. cache = ./cache/cord-329710-vqorb6j7.txt txt = ./txt/cord-329710-vqorb6j7.txt === reduce.pl bib === id = cord-329290-vqvujry3 author = Kempker, Russell R title = Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1907 sentences = 90 flesch = 55 summary = HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. cache = ./cache/cord-329290-vqvujry3.txt txt = ./txt/cord-329290-vqvujry3.txt === reduce.pl bib === id = cord-329308-ipui7lo6 author = Lim, Soo title = Proper Management of People with Obesity during the COVID-19 Pandemic date = 2020-06-30 pages = extension = .txt mime = text/plain words = 4611 sentences = 281 flesch = 43 summary = During the COVID-19 pandemic, people have tended to gain weight because of environmental factors imposed by quarantine policies, such as decreased physical activity and increased consumption of unhealthy food. The common medications used to treat people with obesity, such as glucagon-like peptide-1 analogues, statins, and antiplatelets agents, should be continued because these agents have anti-inflammatory properties and play protective roles against cardiovascular and all-cause mortality. 54 A cumulative effect of chronic inflammation and hypercytokinemia seems to bring about a hyperinflammatory response through macrophage active syndrome, especially in patients with severe COVID-19 (Fig. 2) . Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease cache = ./cache/cord-329308-ipui7lo6.txt txt = ./txt/cord-329308-ipui7lo6.txt === reduce.pl bib === id = cord-329454-69z28yli author = Humar, Atul title = Severe acute respiratory syndrome and the liver date = 2004-01-30 pages = extension = .txt mime = text/plain words = 1889 sentences = 117 flesch = 45 summary = Liver enzyme abnormalities are common in SARS patients, although hepatic impair-ment has not been reported to be a prominent feature of this illness. However, this is the first report to associate hepatic SCoV infection and liver pathologic features. Defining the basis for susceptibility to severe inflammatory outcomes after coronavirus infection has obvious implications for the study and treatment of clinical SARS. Although the exact mechanisms for resistance and susceptibility to MHV3 coronavirus infection have not be determined, studies have shown that in resistant mice, infection leads to a T helper type 1 (TH1)-dominant response that, through the production of interferon, neutralizing antibodies, and cytotoxic T cells, results in viral clearance. A novel coronaviruses associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases cache = ./cache/cord-329454-69z28yli.txt txt = ./txt/cord-329454-69z28yli.txt === reduce.pl bib === id = cord-329193-xuxbqbsf author = Park, Soo-kyung title = Detection of SARS-CoV-2 in Fecal Samples from Patients with Asymptomatic and Mild COVID-19 in Korea date = 2020-06-10 pages = extension = .txt mime = text/plain words = 3532 sentences = 184 flesch = 53 summary = Methods We collected data from 46 patients (median age, 26 years; 46% men) with asymptomatic or mild COVID-19 (without fever and pneumonia) and prolonged respiratory shedding of SARS-CoV-2, quarantined from April 4, 2020 through April 24, 2020 in Korea. Conclusions In an analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea, we found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. cache = ./cache/cord-329193-xuxbqbsf.txt txt = ./txt/cord-329193-xuxbqbsf.txt === reduce.pl bib === id = cord-329311-p68kr4ga author = Prebensen, Christian title = SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 1454 sentences = 111 flesch = 61 summary = title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . cache = ./cache/cord-329311-p68kr4ga.txt txt = ./txt/cord-329311-p68kr4ga.txt === reduce.pl bib === id = cord-329190-kv9n2qj3 author = Rabaan, Ali A. title = A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective date = 2017-09-01 pages = extension = .txt mime = text/plain words = 8886 sentences = 433 flesch = 44 summary = The current therapies have mainly been adapted from severe acute respiratory syndrome (SARS-CoV) treatments, including broad-spectrum antibiotics, corticosteroids, interferons, ribavirin, lopinavir–ritonavir or mycophenolate mofetil, and have not been subject to well-organized clinical trials. The Medline database was searched using combinations and variations of terms, including 'Middle East respiratory syndrome coronavirus', 'MERS-CoV', 'SARS', 'therapy', 'molecular', 'vaccine', 'prophylactic', 'S protein', 'DPP4', 'heptad repeat', 'protease', 'inhibitor', 'anti-viral', 'broad-spectrum', 'interferon', 'convalescent plasma', 'lopinavir ritonavir', 'antibodies', 'antiviral peptides' and 'live attenuated viruses'. A position paper on the evidence base for specific MERS-CoV therapies, published by Public Health England (PHE) and the World Health Organization-International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC-WHO), suggested that benefit was likely to exceed risk for convalescent plasma, lopinavir-ritonavir, IFNs and monoclonal/polyclonal antibodies, while, by contrast, for ribavirin monotherapy and corticosteroids it was considered that the risks would outweigh the benefits [42] . cache = ./cache/cord-329190-kv9n2qj3.txt txt = ./txt/cord-329190-kv9n2qj3.txt === reduce.pl bib === id = cord-329392-fufattj8 author = den Hartog, Gerco title = SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date = 2020-08-08 pages = extension = .txt mime = text/plain words = 4326 sentences = 218 flesch = 41 summary = Serum samples were obtained from the following cohorts: (1) a random selection of individuals (n = 224) from a national (Dutch) cohort representing all age groups and obtained 3 years prior to SARS-CoV-2 emergence (Pienter3 study, Netherlands trial register number NL5467); (2) individuals (Supplementary Table 2 ) with proven non-SARS-CoV-2 ILI caused by human coronaviruses (n = 110, HCoV ILI) or other viruses (n = 74, non-HCoV ILI) obtained from the National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands (trial register number NL4666) [18] , and from Erasmus Medical Center, Rotterdam, collected prior to the SARS-CoV-2 outbreak and at least 2 weeks after polymerase chain reaction (PCR) detection of the virus; and (3) The steps in assay validation were similar to recently developed bead-based multiplex immunoassays for CMV, EBV, and RSV, with minor modifications as described below [16, 17] . cache = ./cache/cord-329392-fufattj8.txt txt = ./txt/cord-329392-fufattj8.txt === reduce.pl bib === id = cord-329840-f3dsu36p author = Hati, Sanchita title = Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2497 sentences = 173 flesch = 51 summary = In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. In the backdrop of significant mortality rate for SARS-CoV-2 (hereinafter referred to as CoV-2) infection, it is important to know if the thiol-disulfide balance plays any role on the binding of the spike glycoprotein on to the host cell receptor protein ACE2. Using these reported structures, molecular dynamics simulations and electrostatic field calculations were performed to explore the impact of thioldisulfide balance on CoV/CoV-2 and ACE2 binding affinities. The structural and dynamical changes due to the change in the redox states of cysteines in the interacting proteins were analyzed and their effects on binding free energies were studied. cache = ./cache/cord-329840-f3dsu36p.txt txt = ./txt/cord-329840-f3dsu36p.txt === reduce.pl bib === id = cord-329504-91te3nu8 author = Croll, Tristan title = Making the invisible enemy visible date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4826 sentences = 219 flesch = 52 summary = A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. cache = ./cache/cord-329504-91te3nu8.txt txt = ./txt/cord-329504-91te3nu8.txt === reduce.pl bib === id = cord-329473-dtlwjndn author = Guo, Ao-Xiang title = The clinical characteristics and mortal causes analysis of COVID-19 death patients date = 2020-04-15 pages = extension = .txt mime = text/plain words = 3279 sentences = 240 flesch = 63 summary = Therefore, we supposed that the expression of ACE2 and TMPRSS2 in human tissues could be used to explain the clinical characteristics of COVID-19 patients, including coexisting disorders, direct causes of death and initial symptoms. Our results also proved that coexisting disorders of hypertension and heart disease and initial symptoms of dyspnea were significantly higher in death patients, which was consistent with the one previous study [7] . While that ACE2 was highly expressed in heart may be related with the attack of SARS-CoV-2 in heart, which may lead to the initial symptoms of palpitate and chest tightness in some patients, and the direct causes of death including circulatory failure, heart disease and cardiac arrest. The expression of the SARS-CoV-2 targets in these important organs such as lung, heart, liver and kidney may help to explain the clinical characteristics of death patients. cache = ./cache/cord-329473-dtlwjndn.txt txt = ./txt/cord-329473-dtlwjndn.txt === reduce.pl bib === id = cord-329890-wg23sa1u author = Quah, Stella R. title = Public image and governance of epidemics: Comparing HIV/AIDS and SARS date = 2007-02-28 pages = extension = .txt mime = text/plain words = 9734 sentences = 423 flesch = 49 summary = Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people's lifestyles and approaches to the control and prevention of epidemics. The second assumption is that in contrast to SARS, the overall negative public 'image' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people's perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. The second assumption to be explored here is that in contrast to SARS, the overall negative social 'image' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people's perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. cache = ./cache/cord-329890-wg23sa1u.txt txt = ./txt/cord-329890-wg23sa1u.txt === reduce.pl bib === id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 pages = extension = .txt mime = text/plain words = 5146 sentences = 248 flesch = 51 summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-329493-ueqlhgn0.txt txt = ./txt/cord-329493-ueqlhgn0.txt === reduce.pl bib === id = cord-329328-c6svx4qa author = Reydon, Thomas A. C. title = How can science be well-ordered in times of crisis? Learning from the SARS-CoV-2 pandemic date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1740 sentences = 67 flesch = 49 summary = Kitcher's ideal should play a role in assessing the allocation of research resources in future crisis situations, as it provides a way to balance highly divergent interests and incorporate the common good into decision-making processes on research. I want to suggest that one way of doing better is to explicitly pose the question what the common good in a crisis such as the SARS-CoV-2 pandemic encompasses, and how during such a crisis and its aftermath research can be directed toward accommodating the needs of all. While this cannot and should not replace an ongoing global dialogue about how research can serve the common good in times of crisis, making Kitcher's ideal more concrete and familiarizing researchers, policy makers and other stakeholders with it (which both are tasks for philosophers of science) will be a first step in the right direction. cache = ./cache/cord-329328-c6svx4qa.txt txt = ./txt/cord-329328-c6svx4qa.txt === reduce.pl bib === id = cord-329877-vish6v8e author = Lapinsky, Stephen E. title = ICU management of severe acute respiratory syndrome date = 2003-05-09 pages = extension = .txt mime = text/plain words = 2639 sentences = 149 flesch = 45 summary = BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ). cache = ./cache/cord-329877-vish6v8e.txt txt = ./txt/cord-329877-vish6v8e.txt === reduce.pl bib === id = cord-329959-4yecwdlo author = Lin, Min-Han title = Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes date = 2017-12-28 pages = extension = .txt mime = text/plain words = 5576 sentences = 319 flesch = 58 summary = Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL(pro)s) of MERS-CoV and SARS-CoV. The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL(pro) by disulfiram, while synergistic inhibition of MERS-CoV PL(pro) by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. For the inactivation studies, SARS-CoV PL pro (0.05 μM in 20 mM phosphate buffer, pH 6.5) was incubated with different concentrations of disulfiram and peptide substrate, and enzymatic activity was traced for 5 min. On the other hand, the results of kinetic assays, continued inactivation after the removal of disulfiram, reactivation by reductant, and the phenomenon of slow-binding inhibition suggest that disulfiram may act at the active site of SARS-CoV PL pro , forming a covalent adduct with residue Cys112. cache = ./cache/cord-329959-4yecwdlo.txt txt = ./txt/cord-329959-4yecwdlo.txt === reduce.pl bib === id = cord-329240-atisrhas author = Fedorenko, Aliza title = Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date = 2020-06-16 pages = extension = .txt mime = text/plain words = 4493 sentences = 233 flesch = 50 summary = Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic. To study virus survival in microdroplets deposited on a smooth inanimate surface, we sprayed Phi6, MS2, and PhiX174 viruses suspended in three media -human saliva, water, and SM bufferon glass-bottom 12-well plates (Fig. 1, Methods) . The observation that at a given RH, the microscopic hydration conditions of deposited droplets of various media can differ so widely (see along the rows of Fig. 3 ) suggests that RH does not directly affect virus stability and infectivity in drying microdroplets deposited on surfaces, but rather RH indirectly affects survival through its effect on physicochemical conditions at the scale that matters for viruses (~ µm). cache = ./cache/cord-329240-atisrhas.txt txt = ./txt/cord-329240-atisrhas.txt === reduce.pl bib === id = cord-329318-eo8auo1f author = Gusarov, Sergey title = COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2 date = 2020-10-26 pages = extension = .txt mime = text/plain words = 3971 sentences = 217 flesch = 46 summary = [Image: see text] Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. In this study, we propose a novel set of drug screening descriptors based on COSMO-RS σ-profiles, augmented by dipole moment and induced charge of the phosphorus atom, to evaluate the chemical similarity of the drugs with nucleotides, as RNA replication transcription initiation activators. A novel set of descriptors based on COSMO-RS σ-profiles and chemical thermodynamics is proposed and evaluated using PCA for the initial screening of a series of nucleotides and nucleotide-analog RdRp replication inhibitor drugs to help accelerate the discovery of COVID-19 treatments. The PCA results show that the novel σ-profile-based descriptor set I clearly correlates the leading COVID-19 drugs remdesivir and EIDD-2801 in monophosphate forms and highlights weaker correlations with drugs that have been reported to exhibit anti-SARS-CoV-2 activity. cache = ./cache/cord-329318-eo8auo1f.txt txt = ./txt/cord-329318-eo8auo1f.txt === reduce.pl bib === id = cord-329794-msxrdhb3 author = Lu, Aili title = Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date = 2004-06-20 pages = extension = .txt mime = text/plain words = 2679 sentences = 172 flesch = 61 summary = Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. cache = ./cache/cord-329794-msxrdhb3.txt txt = ./txt/cord-329794-msxrdhb3.txt === reduce.pl bib === id = cord-330074-5iqqgy65 author = Patel, Smit D. title = Malignant Cerebral Ischemia in A COVID-19 Infected Patient: Case Review and Histopathological Findings date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1451 sentences = 89 flesch = 38 summary = However, this data is limited and comes from recent small case series and observational studies on stroke types, mechanisms, and outcomes.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Furthermore, evidence on the role of therapeutic anticoagulation in SARS-CoV-2 infected patients with elevated inflammatory markers, such as D-dimer, is also limited. We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection (COVID-19). We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection . Ischemic stroke, Inflammatory conditions, COVID-19, Corona virus, SARS-CoV-2 RNA, cerebrovascular disease, hemorrhagic stroke, cerebral sinus thrombosis, vasculitis, anticoagulation, thrombotic conditions, thromboembolic conditions Introduction: cache = ./cache/cord-330074-5iqqgy65.txt txt = ./txt/cord-330074-5iqqgy65.txt === reduce.pl bib === id = cord-329944-ywusapij author = Harbourt, D. title = Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing date = 2020-07-03 pages = extension = .txt mime = text/plain words = 2103 sentences = 150 flesch = 62 summary = title: Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing Skin, currency, and clothing samples were exposed to SARS-CoV-2 under laboratory conditions and incubated at three different temperatures (4C, 22C, and 37C). Herein, we model the stability of SARS-CoV-2 77 across animal skin, paper currency, and clothing. . https://doi.org/10.1101/2020.07.01.20144253 doi: medRxiv preprint 9 190 SARS-CoV-2 remained viable at 37°C on skin samples for up to 8 h (Fig 1 and Fig 2) . Significant differences 200 were observed in virus stability between the skin samples and all other tested surfaces (Fig S2) . The results in this study demonstrate the continued inverse relationship between virus stability 259 and temperature which is seen both in the laboratory and in the field when evaluating different was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-329944-ywusapij.txt txt = ./txt/cord-329944-ywusapij.txt === reduce.pl bib === id = cord-329904-e05ywn5e author = Jose, Merin title = Fatal Superimposed Bacterial Sepsis in a Healthy Coronavirus (COVID-19) Patient date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2256 sentences = 118 flesch = 46 summary = We present a case of a healthy COVID positive individual, with no underlying comorbidities, who rapidly deteriorated overnight on readmission to the hospital after initial discharge and succumbed to this disease due to a superimposed bacterial infection with COVID pneumonia. This case report highlights the importance of educating COVID-19 positive patients about the precautions, as well as signs and symptoms of a superimposed bacterial infection, when their plan of care is in a home setting. It also emphasizes the potential role of checking procalcitonin levels as a part of routine laboratory investigation at initial presentation in all suspected as well as confirmed COVID-19 cases to rule out an on-going bacterial infection that can prove fatal in the course of the disease. Our emphasis from this case report is to highlight the risk of superimposed bacterial infection in COVID-19 patients. cache = ./cache/cord-329904-e05ywn5e.txt txt = ./txt/cord-329904-e05ywn5e.txt === reduce.pl bib === id = cord-329643-hhk900c1 author = Skalina, K. A. title = Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date = 2020-05-20 pages = extension = .txt mime = text/plain words = 1869 sentences = 114 flesch = 49 summary = Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. determined that short delays (up to 4 days) in processing influenza nasal and throat swabs did not significantly affect the ability to detect viral particles by real-time RT-PCR.(5) More recently the stability of SARS-CoV-2 detection in different types of storage media over a 14-day period was evaluated. This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. cache = ./cache/cord-329643-hhk900c1.txt txt = ./txt/cord-329643-hhk900c1.txt === reduce.pl bib === id = cord-329707-89zyu8bl author = Zhang, Xue title = Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date = 2006-11-30 pages = extension = .txt mime = text/plain words = 3212 sentences = 210 flesch = 54 summary = We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. cache = ./cache/cord-329707-89zyu8bl.txt txt = ./txt/cord-329707-89zyu8bl.txt === reduce.pl bib === id = cord-329876-4cgrjnjo author = Lei, Jian title = Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin date = 2016-05-30 pages = extension = .txt mime = text/plain words = 6809 sentences = 421 flesch = 69 summary = title: Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. The substrate-binding site of MERS-CoV PL pro features significant differences from those of the corresponding SARS-CoV enzyme and human ubiquitin-specific proteases (USPs, such as, USP14) (Hu et al., 2005; Chou et al., 2014; Ratia et al., 2014) . Hence, we crystallized the ubiquitin (Ub) complex of a MERS-CoV PL pro variant that had the active-site Cys111 replaced by serine (C111S) and determined the structure at 3.16 Å ( Figure 1A ). Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression cache = ./cache/cord-329876-4cgrjnjo.txt txt = ./txt/cord-329876-4cgrjnjo.txt === reduce.pl bib === id = cord-330131-yfhrmbvx author = Danchin, Antoine title = Cytosine drives evolution of SARS‐CoV‐2 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 5318 sentences = 244 flesch = 42 summary = In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. cache = ./cache/cord-330131-yfhrmbvx.txt txt = ./txt/cord-330131-yfhrmbvx.txt === reduce.pl bib === id = cord-330067-ujhgb3b0 author = Huang, Yi title = CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes date = 2007-10-02 pages = extension = .txt mime = text/plain words = 3007 sentences = 168 flesch = 55 summary = To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. In CoVDB, with the aim of facilitating gene retrieval, we tried to unify the naming of these non-structural proteins from different groups of coronaviruses. When we compared their putative amino acid sequences to the corresponding ones in other group 1 coronavirus genomes using BLAST, as well as searching for conserved domains using motifscan, results showed that the putative proteins encoded by these ORFs belonged to a protein family in Pfam originally assigned as 'Corona_NS3b' (accession number PF03053). database, CoVDB, of annotated coronavirus genes and genomes, which offers efficient batch sequence retrieval and analysis. cache = ./cache/cord-330067-ujhgb3b0.txt txt = ./txt/cord-330067-ujhgb3b0.txt === reduce.pl bib === id = cord-330045-4gj9d181 author = Sun, Jiufeng title = Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1541 sentences = 93 flesch = 57 summary = We recruited hospitalized patients with COVID-19 from 2 designated provincial emergency hospitals for e merging infectious diseases in Guangdong, China, and tested specimens by real-time reverse transcription PCR (rRT-PCR) to estimate the duration of the detection of SARS-CoV-2 RNA in various body fluids, using an accelerated failure time (AFT)-based modeling study. We used parametric Weibull regression models (AFT) to estimate the time until the loss of SARS-CoV-2 RNA detection in each body fluid and reported findings in medians and 95th percentiles using R software version 3.6.1 with flexsurv, survival, and survminer packages (9) . We used Weibull models to estimate the median and the 95th percentile for the time until the loss of SARS-CoV-2 RNA detection in swab, sputum, and fecal samples (Table; Figures 1, 2) . In this study, we estimated the time for COVID-19 case-patients to clear SARS-CoV-2 RNA in the acute phase of infection through an AFT-based modeling study. cache = ./cache/cord-330045-4gj9d181.txt txt = ./txt/cord-330045-4gj9d181.txt === reduce.pl bib === id = cord-329825-e9mepqvn author = Giamarellos-Bourboulis, Evangelos J. title = Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date = 2020-04-21 pages = extension = .txt mime = text/plain words = 3756 sentences = 177 flesch = 47 summary = Immune responses of critically ill patients with sepsis can be classified into three patterns: macrophage-activation syndrome (MAS) (Kyriazopoulou et al., 2017) , sepsis-induced immunoparalysis characterized by low expression of the human leukocyte antigen D related (HLA-DR) on CD14 monocytes (Lukaszewicz et al., 2009) , and an intermediate functional state of the immune system lacking obvious dysregulation. Abbreviations are as follows: ALT, alanine aminotransferase; aPTT, activated partial thromboplastin time; AST, aspartate aminotransferase; APACHE, acute physiology and chronic health evaluation; CCI, Charlson's comorbidity index; INR, international normalized ratio; PSI, pneumonia severity index; SD, standard deviation; SOFA, sequential organ failure assessment Immune classification of patients with SARS-CoV-2 was performed by using the tools suggested for bacterial sepsis, i.e., ferritin more than 4,420 ng/mL for MAS (Kyriazopoulou et al., 2017) , and HLA-DR molecules on CD14 monocytes lower than 5,000, in the absence of elevated ferritin, for the immune dysregulation phenotype (Lukaszewicz et al., 2009) . cache = ./cache/cord-329825-e9mepqvn.txt txt = ./txt/cord-329825-e9mepqvn.txt === reduce.pl bib === id = cord-330022-n3d130t8 author = Pan, Daniel title = The impact of ethnicity on clinical outcomes in COVID-19: A systematic review date = 2020-06-03 pages = extension = .txt mime = text/plain words = 5069 sentences = 254 flesch = 44 summary = However, emerging data from the grey literature and preprint articles suggest BAME individuals are at an increased risk of acquiring SARS-CoV-2 infection compared to White individuals and also worse clinical outcomes from COVID-19. We found 17 published studies of patients with COVID-19 which reported data on ethnicity; 1 reported an increased risk of acquiring SARS-CoV-2 in Black compared to White patients and 5 reported no association between ethnicity and clinical outcomes. 34 preprint articles on MedRxiv reported ethnicity; 13 reported an increased risk of acquiring infection with SARS-CoV-2 and 12 reported adverse clinical outcomes with COVID-19 in BAME compared to White patients. Increasing numbers of articles from the UK and USA in the grey literature and in preprint suggest that individuals from BAME communities are at increased risk of infection from SARS-CoV-2 and worse clinical outcomes including hospitalization, ITU admission and mortality, compared to White patients. cache = ./cache/cord-330022-n3d130t8.txt txt = ./txt/cord-330022-n3d130t8.txt === reduce.pl bib === id = cord-329914-3b233vxl author = Plantier, L. title = Pratique des explorations fonctionnelles respiratoires pendant l’épidémie COVID-19 date = 2020-06-05 pages = extension = .txt mime = text/plain words = 2169 sentences = 239 flesch = 61 summary = Préambule et mise en garde L'objectif de ces propositions est de prévenir la transmission du virus SARS-Cov2 lors de la pratique des explorations fonctionnelles respiratoires au repos et à l'exercice, dans le contexte général de l'assouplissement progressif des mesures de distanciation sociale débuté le 11 mai 2020. On peut rappeler que la persistance dans le poumon profond de l'ARN viral au-delà du 50 e jour avait été observée chez des patients infectés par SARS-Cov1 [7] . Proposition 3 : Bien que la structure d'EFR réponde à la définition d'un secteur à faible densité virale, nous considérons que des précautions complémentaires visant à protéger les personnels et les patients sont indispensables du fait 1) de la contagiosité des sujets asymptomatiques et 2) des particularités de l'EFR et notamment de la génération de gouttelettes et/ou d'aérosols potentiellement infectants lors des manoeuvres expiratoires [12] et la toux [13, 14] , du risque de déconnexion accidentelle du filtre antimicrobien et de la possibilité d'une toux induite par l'examen. cache = ./cache/cord-329914-3b233vxl.txt txt = ./txt/cord-329914-3b233vxl.txt === reduce.pl bib === id = cord-329200-o5hxpl8f author = Houlihan, Catherine F title = The complexities of SARS-CoV-2 serology date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1010 sentences = 60 flesch = 40 summary = Our understanding of individual and population-level immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains incomplete and developing reliable serological assays to detect previous infection has been an intense focus of the global scientific effort. For public health planning we need scalable assays validated against large banks of samples from individuals who had proven seasonal (non-severe acute respiratory syndrome) coronaviruses and those who had well characterised symptomatic and asymptomatic confirmed SARS-CoV-2 infection. In The Lancet Infectious Diseases, the National SARS-CoV-2 Serology Assay Evaluation Group 1 provide the first large comparative investigation of the performance of four widely available commercial assays and a single in-house assay. Antibody responses to SARS-CoV-2 are predominantly directed at the spike glycoprotein, which the virus requires for entry, and the nucleocapsid protein, which binds the viral RNA genome. 2,3 The DiaSorin, Siemens, and in-house assays measured these potentially protective antibodies, with the inhouse ELISA using trimerised spike protein, which shows a high correlation with neutralisation. cache = ./cache/cord-329200-o5hxpl8f.txt txt = ./txt/cord-329200-o5hxpl8f.txt === reduce.pl bib === id = cord-330031-c1n994j6 author = Kratzel, Annika title = Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date = 2020-03-17 pages = extension = .txt mime = text/plain words = 752 sentences = 51 flesch = 50 summary = title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. We therefore determined the virucidal activity of two 5 alcohol-based hand rub solutions for hand disinfection recommended by the World 6 Hand Hygiene in Health Care' suggests two alcohol-based formulations for hand 9 sanitization to reduce pathogen infectivity and spreading. cache = ./cache/cord-330031-c1n994j6.txt txt = ./txt/cord-330031-c1n994j6.txt === reduce.pl bib === id = cord-330061-q4xi260z author = Ferreira, João Guimarães title = Pneumothorax as a late complication of COVID-19 date = 2020-08-31 pages = extension = .txt mime = text/plain words = 2421 sentences = 151 flesch = 48 summary = We present a typical laboratory confirmed case of COVID-19 pneumonia, that was hospitalized due to hypoxemia but did not require mechanical ventilation. On the other hand, patients with more severe disease comprise 14% of the cases, with progressive tachypnea and dyspnea after five to eight days from the beginning of the symptoms, low blood oxygen saturation, and/or lung infiltrates in > 50% of the lungs. Regarding laboratory abnormalities in patients with COVID-2019 infections, the most frequent findings for those who need admission to the intensive care unit are leukocytosis, higher neutrophil count, lymphopenia, increased values of CRP, LDH, aminotransferases, total bilirubin, creatinine, cardiac troponin, procalcitonin and D-dimer. Herein, we present a typical and laboratory confirmed case of COVID-19 pneumonia, with clinical course deterioration during the third week of the disease due to a massive hypertensive pneumothorax with no known previous risk factor. Spontaneous pneumothorax and subcutaneous emphysema in COVID-19 patient: case report cache = ./cache/cord-330061-q4xi260z.txt txt = ./txt/cord-330061-q4xi260z.txt === reduce.pl bib === id = cord-329971-09ubsq2k author = Tranoulis, Anastasios title = Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic date = 2020-06-30 pages = extension = .txt mime = text/plain words = 665 sentences = 38 flesch = 43 summary = title: Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic To date, there is no clear evidence concerning the impact of SARS-CoV-2 on tubo-ovarian cancer care. Generally, cancer patients are seemingly at increased risk of SARS-CoV-2 infection owing to the underlying immunosuppression. According to the cases treated using the 'do no harm' principle, we believe that the following situations should be considered for surgery: (1) To conclude, the effects of SARS-CoV-2 pandemic can be mitigated to a certain degree for patients with ovarian cancer, by adopting a careful and individualised triage and treatment management. A rigorous counseling concerning the risk of undergoing surgery during SARS-CoV-2 pandemic should be done, whilst the national and international health bodies recommendations will supportively guide clinicians prioritise ovarian cancer care. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan cache = ./cache/cord-329971-09ubsq2k.txt txt = ./txt/cord-329971-09ubsq2k.txt === reduce.pl bib === id = cord-329844-w969lczb author = Robson, B. title = Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date = 2020-06-08 pages = extension = .txt mime = text/plain words = 15903 sentences = 664 flesch = 49 summary = The location of any sialic acid glycan binding region of SARS-CoV-2 is, a priori unclear, although intuitively (a) it would likely be associated with the cap or knob at the outer end of the spike protein, or (b) at least not involve exactly the same domain as is required for other important functions. An algorithm for predicting the domains and proteins involved in sialic acid glycan binding is developed in the course of the project described in Results Section 4, but this is primarily of a highly empirical nature. This, plus a sequence rather than three dimensional structure perspective, and a specific focus on binding sialic acid glycans rather than sugars in general, resulted in a substantial difference in scores from another major method of predicting sugar binding regions of proteins also discussed later below. cache = ./cache/cord-329844-w969lczb.txt txt = ./txt/cord-329844-w969lczb.txt === reduce.pl bib === id = cord-329853-kf3kh26y author = Trimarchi, Hernán title = Eculizumab, SARS-CoV-2 and atypical hemolytic uremic syndrome date = 2020-09-27 pages = extension = .txt mime = text/plain words = 1097 sentences = 64 flesch = 39 summary = Complement activation is thought to contribute to endothelial injury and there are at least seven ongoing clinical trials testing six different anti-complement strategies for coronavirus disease 2019 (COVID-19), including eculizumab. We herein report on a kidney transplant patient with aHUS on chronic eculizumab therapy that developed severe COVID-19 despite eculizumab administration early in the course of the disease. Although eculizumab was unable to prevent the development of severe endothelial cell injury, as assessed by increasing D-dimer levels from 292 to 10 586 ng/mL, the patient eventually recovered following dexamethasone and convalescent plasma administration. To our knowledge, this is the first report of a kidney transplant recipient with aHUS on eculizumab therapy who developed SARS-CoV-2 infection. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: a report of five cases cache = ./cache/cord-329853-kf3kh26y.txt txt = ./txt/cord-329853-kf3kh26y.txt === reduce.pl bib === id = cord-330338-i6ozygkp author = Babacic, H. title = Global between-countries variance in SARS-CoV-2 mortality is driven by reported prevalence, age distribution, and case detection rate date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3604 sentences = 216 flesch = 59 summary = Objective: To explain the global between-countries variance in number of deaths per million citizens (nDpm) and case fatality rate (CFR) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The derived explanators age-adjusted infection fatality rate (IFRadj) and case detection rate (CDR) were estimated for each country based on a SARS-CoV-2 model of China. (9) Studies suggest that the reported number of cases per million citizens (nCpm) is probably lower than the true number of infected individuals, and that this contributes to the varying CFR between countries.(5,6) CFR appears higher than the true infection fatality rate (IFR), i.e. the true proportion of individuals with a SARS-CoV-2 infection who will die in the population regardless of whether they are confirmed or not. The aim of this study was to test two mathematical hypotheses that explain the global between-countries variance in SARS-CoV-2 mortality expressed as nDpm and CFR on real data. cache = ./cache/cord-330338-i6ozygkp.txt txt = ./txt/cord-330338-i6ozygkp.txt === reduce.pl bib === id = cord-330337-d41imvo7 author = Basu, Souradip title = Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date = 2020-10-20 pages = extension = .txt mime = text/plain words = 6428 sentences = 311 flesch = 52 summary = Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. The secondary structure of the wild type and the mutant proteins along with their degree of disordered residues and accessible surface area was predicted using the primary sequence of the protein. Each of the seven proteins were assigned a score of either '-1' or '0', for each of the four computational tools used for epitope prediction, where '-1' corresponds to any change in number or binding efficacy of antigenic determinants, that may have surfaced because of mutation and '0' corresponds to no changes between wild type and mutant forms. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure cache = ./cache/cord-330337-d41imvo7.txt txt = ./txt/cord-330337-d41imvo7.txt === reduce.pl bib === id = cord-330093-asba80bi author = Leung, Janice M. title = Smoking, ACE-2 and COVID-19: ongoing controversies date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2777 sentences = 145 flesch = 48 summary = Both research teams are reporting increased angiotensin-converting enzyme 2 (ACE-2) expression in airways of current smokers and those with COPD, with important implications for coronavirus disease 2019 (COVID-19) patients. Since ACE-2 has been shown to be the main receptor utilised by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to enter the host cells [2] , the authors conclude that nicotine is a risk factor for COVID-19. Here, we bring to the discussion whether the increased susceptibility and virulence of SARS-CoV-2 via α7-nAChR and the upregulation of small airway ACE-2 expression may also be relevant for those who vape using nicotine-based e-cigarettes. While smoking may not necessarily increase one's risk for contracting COVID-19, the biological and inflammatory cascade that occurs upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may be particularly devastating for a smoker. cache = ./cache/cord-330093-asba80bi.txt txt = ./txt/cord-330093-asba80bi.txt === reduce.pl bib === id = cord-330121-eadu2ba3 author = Gudmundsdottir, Ágústa title = Inactivation of SARS‐CoV‐2 and HCoV‐229E in vitro by ColdZyme® a medical device mouth spray against common cold date = 2020-09-25 pages = extension = .txt mime = text/plain words = 1628 sentences = 114 flesch = 58 summary = It contains glycerol and minor amounts of purified cold-adapted trypsin 5 The entry of coronaviruses into host cells is mediated by the spike (S) glycoprotein that forms homo-trimers protruding from the virus surface 11 . Based on the results presented in this study, CZ-MD was found to inactivate SARS-CoV-2 (98.3%) and HCoV-229E (99.9%) in vitro (Table I) Coronaviruses cause about one-third of the common cold cases 4 Entry of coronaviruses into susceptible cells requires receptor-binding of the S protein and it's proteolytic processing by host cell proteases that occurs in a concerted action to promote virus-cell fusion 3 . However, the in vitro study presented here clearly demonstrates that the CZ-MD (containing cod trypsin) inactivates SARS-CoV-2 and HCoV-229E. Although the in vitro results presented cannot be directly translated into clinical efficacy, the study indicates that CZ-MD might offer a protective barrier against coronaviruses such as SARS-CoV-2 and a decreased risk of COVID-19 transmission. cache = ./cache/cord-330121-eadu2ba3.txt txt = ./txt/cord-330121-eadu2ba3.txt === reduce.pl bib === id = cord-330266-uypjqif7 author = Firpo, Mason R. title = Targeting Polyamines Inhibits Coronavirus Infection by Reducing Cellular Attachment and Entry date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5471 sentences = 330 flesch = 51 summary = To determine if coronaviruses are susceptible to polyamine depletion, we treated Vero-E6 cells with doses of DFMO ranging from 750 μM to 5 mM for 4 days prior to infection with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.1 plaque forming units (pfu) per cell. To determine if DFMO-mediated virus restriction was a result of polyamine depletion, we treated BHK-R cells with DFMO and, at the time of infection, supplemented with the individual polyamines putrescine, spermidine, and spermine at 1 μM, a level that did not affect cellular viability ( Figure 2A ). We observed that DFMO reduced viral titers and that supplementation with any of the individual polyamines rescued virus replication to untreated levels ( Figure 2C ). 19 We observed no changes in plaque size ( Figure 3A ) or morphology ( Figure 3B ) with DFMO supplementation to the media, suggesting that DFMO was not sufficiently antiviral when applied to cells after infection and highlighting that DFMO must be applied prophylactically to reduce coronavirus replication. cache = ./cache/cord-330266-uypjqif7.txt txt = ./txt/cord-330266-uypjqif7.txt === reduce.pl bib === id = cord-330315-upcf15q5 author = Oudshoorn, Diede title = Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication date = 2017-11-21 pages = extension = .txt mime = text/plain words = 7718 sentences = 349 flesch = 50 summary = Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. To study whether the transmembrane nsp's of MERS-CoV are able to induce DMV formation, we expressed nsp3 and nsp4 from a CAG promoter (43) either by cotransfection of cells with plasmids encoding individual proteins or by transfection with a single plasmid encoding a self-cleaving nsp3-4 polyprotein fragment ( Fig. 1A ; Table S1 ). The observation of maze-like bodies and circular double-membrane profiles, which were interpreted to represent tubular structures, led these authors to conclude that coexpression of SARS-CoV nsp3 and nsp4 was not sufficient for DMV formation. cache = ./cache/cord-330315-upcf15q5.txt txt = ./txt/cord-330315-upcf15q5.txt === reduce.pl bib === id = cord-330287-bkqjkhwu author = Miller, Danielle title = Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel date = 2020-11-02 pages = extension = .txt mime = text/plain words = 6758 sentences = 329 flesch = 49 summary = So-called genomic epidemiology allows for effective reconstruction of viral geographical spread as well as estimation of key epidemiological quantities such as the basic reproduction number of a virus, its growth rate and doubling time, and patterns of disease incidence and prevalence. Here, we set out to sequence SARS-CoV-2 from samples across the state of Israel, with the aim of gaining a better understanding of introductions of the virus into Israel, spread of the virus inside the country, and the epidemiology of the disease, including (a) the basic reproduction number of the virus before and after social distancing measures were implemented, and (b) the extent of viral superspreading within Israel. To estimate the basic reproduction number of SARS-CoV-2 in Israel initially and then following the implementation of social distancing measures, we performed coalescent-based phylodynamic inference using the PhyDyn program implemented in BEAST2 (Methods). Our phylodynamic analysis assumes an underlying susceptibleexposed-infected-recovered (SEIR)-type epidemiological model for SARS-CoV-2 transmission dynamics and explicitly incorporates transmission heterogeneity ( Supplementary Fig. 4 , Methods). cache = ./cache/cord-330287-bkqjkhwu.txt txt = ./txt/cord-330287-bkqjkhwu.txt === reduce.pl bib === id = cord-330200-l6bnxi40 author = Huang, Jianping title = Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4472 sentences = 306 flesch = 59 summary = title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. cache = ./cache/cord-330200-l6bnxi40.txt txt = ./txt/cord-330200-l6bnxi40.txt === reduce.pl bib === id = cord-330473-f03ka7bd author = Yuan, Meng title = A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date = 2020-03-14 pages = extension = .txt mime = text/plain words = 1563 sentences = 107 flesch = 65 summary = In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. ONE SENTENCE SUMMARY Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain. A recent study has shown that CR3022, which is a human 49 neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4), Nonetheless, despite having a 70 high conservation in the epitope residues, CR3022 Fab binds to SARS-CoV RBD (K d = 1 71 nM) with a much higher affinity than to SARS-CoV-2 RBD (K d = 115 nM) (Table 1 Previous cryo-EM studies have also shown that the recombinant SARS-CoV S 121 protein is mostly found in the none-"up", single-"up", or double-"up" conformations (19, 122 21), but rarely in the triple-"up" conformation, even with ACE2 receptor bound (21, 22) . cache = ./cache/cord-330473-f03ka7bd.txt txt = ./txt/cord-330473-f03ka7bd.txt === reduce.pl bib === id = cord-330198-pwkxgbxk author = Cai, Xiaofang title = Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19 date = 2020-10-27 pages = extension = .txt mime = text/plain words = 4287 sentences = 223 flesch = 50 summary = All febrile or suspected COVID-19 cases were referred to the fever clinic, and the others-including critically ill children-were received by the emergency department after pediatric 5-level triage. We retrospectively analyzed the clinical data of these children admitted from the emergency department to characterize thoroughly the features of COVID-19 that can be evaluated to distinguish this novel disease from pneumonia caused by other pathogens in pediatric patients. Owing to the parents' fear that their children were infected with SARS-CoV-2, the median time from symptom onset to hospital admission was shorter for confirmed COVID-19 cases (2.0 days) than that for suspected COVID-19 cases (3.0 days) and non-COVID-19 cases (4.0 days) (P < 0.05). Moreover, serologic testing can serve as an important adjunctive method for COVID-19 diagnosis, especially when the patient is highly suspected of SARS-CoV-2 infection but is found to be negative by nucleic acid testing. cache = ./cache/cord-330198-pwkxgbxk.txt txt = ./txt/cord-330198-pwkxgbxk.txt === reduce.pl bib === id = cord-330583-ltkpt80u author = Lee, Kyu-Myoung title = Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date = 2019-04-22 pages = extension = .txt mime = text/plain words = 9200 sentences = 414 flesch = 37 summary = Following the 2003 the severe acute respiratory syndrome (SARS) and the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to explore and examine the factors influencing the response to infectious diseases, which encompasses both communicable and non-communicable diseases. As the results conducted meta-analyses to comprehensively analyze the correlations of factors influencing disaster response from a Korean context, the findings show that the legislative factor had direct and indirect influence on the overall process of infectious disease response and that Leadership of the central government, establishment of an intergovernmental response system, the need for communication, information sharing and disclosure and onsite response were identified as key factors influencing effective infectious disease response. However, there is also need for comprehensive discussions that include the establishment of laws; regulations; resources; information on infectious disease response from administrative and policy perspectives; information sharing system; and the establishment of an international cooperation system and national response system involving the central government, the regional government, private organizations and the public for effective response when an actual infectious disease outbreak occurs. cache = ./cache/cord-330583-ltkpt80u.txt txt = ./txt/cord-330583-ltkpt80u.txt === reduce.pl bib === id = cord-330129-izr62c68 author = Omer, Sumaira title = Preventive measures and management of COVID-19 in pregnancy date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1950 sentences = 124 flesch = 51 summary = As of 17 March 2020, there are 153 countries who have reported cases of infection caused by this virus [i.e., coronavirus disease-2019 (COVID19) ], with Italy becoming the new epicentre [1] . Importantly, viral respiratory illnesses, such as influenza, can easily develop during pregnancy, which means pregnant women may be more vulnerable to COVID-19 and require prioritized medical care. Interim COVID-19 guidelines for the effective counselling and education of pregnant women are currently available from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) [5, 6] . For effective management, pregnant women with suspected COVID-19 should be isolated and then transferred to a hospital equipped with sufficient health facilities and fully trained clinicians to take proper care of critically ill obstetric patients. Interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease 2019 (COVID-19) in healthcare settings cache = ./cache/cord-330129-izr62c68.txt txt = ./txt/cord-330129-izr62c68.txt === reduce.pl bib === id = cord-330384-yujbcwg5 author = Al-Mulla, Fahd title = A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date = 2020-05-16 pages = extension = .txt mime = text/plain words = 4684 sentences = 249 flesch = 52 summary = The increased cleavage activity of this protease was suggested to diminish viral recognition by neutralizing antibodies and by activating SARS spike (S) protein for virus-cell fusion 11 and facilitates the active binding of SARS-CoV-2 through ACE2 receptor, which is a risk factor for a more serious COVID-19 presentation [8] [9] [10] . Recent studies, assessed the genetic variations and eQTL (expression quantitative trait locus) expression profiles in the candidate genes ACE2, TMPRSS2, and FURIN to demonstrate the sex and population-wise differences that may influence the pathogenicity of SARS-CoV-2 9, [15] [16] [17] [18] [19] . Therefore, we screened the genetic variations and eQTL expression of the SARS-CoV-2 candidate genes, ACE2, TMPRSS2 and FURIN in three Middle Eastern populations: Kuwaiti, Iranian, and Qatari and compared them to available MAF data in the gnomAD database 41 . cache = ./cache/cord-330384-yujbcwg5.txt txt = ./txt/cord-330384-yujbcwg5.txt === reduce.pl bib === id = cord-330369-75cotmn2 author = López, Verónica title = Recommendations on management of the SARS-CoV-2 coronavirus pandemic (Covid-19) in kidney transplant patients date = 2020-04-06 pages = extension = .txt mime = text/plain words = 3483 sentences = 219 flesch = 49 summary = In kidney transplant recipients, due to their status of immunosuppression, the clinical manifestations, treatment, and prognosis of COVID-19 pneumonia may differ from the general population, hence the importance of early diagnosis by SARS-CoV-2 screening, in those cases where the infection is suspected. Currently there is no evidence from controlled clinical trials to recommend a specific treatment for the SARS-CoV-2 coronavirus in the general population in patients with suspected or confirmed COVID19. 7 Therefore, given the limited experience accumulated and the high probability of torpid evolution in a short period of time, with the development of multi-organ failure and the need for respiratory support, the immunosuppressive strategy recommended a priori, at least in the most severe cases of kidney transplant patients with COVID-19 pneumonia, should involve the temporary interruption of immunosuppressants and the start of methylprednisolone at low doses between 20 and 40 mg/day, to confer the rapid acquisition of the necessary cellular immunity to control the infection and thus prevent vital complications. cache = ./cache/cord-330369-75cotmn2.txt txt = ./txt/cord-330369-75cotmn2.txt === reduce.pl bib === id = cord-330213-reb9vo7x author = Miladi, Milad title = The landscape of SARS-CoV-2 RNA modifications date = 2020-07-18 pages = extension = .txt mime = text/plain words = 3213 sentences = 210 flesch = 55 summary = From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). cache = ./cache/cord-330213-reb9vo7x.txt txt = ./txt/cord-330213-reb9vo7x.txt === reduce.pl bib === id = cord-330433-y5dvlcda author = Olivieri, Emily R. title = Analysis of SARS-CoV Receptor Activity of ACE2 Orthologs date = 2006 pages = extension = .txt mime = text/plain words = 1730 sentences = 102 flesch = 60 summary = 2 Coronavirus spike-receptor interactions are major determinants of species specificity, and transfection of viral genomic RNA or expression of receptors in nonpermissive cell lines usually results in productive infection. The goals of this study were to determine whether ACE2 transcript is produced by permissive and nonpermissive cells derived from diverse species and to use speciesspecific differences in ACE2 to identify amino acids or other post-translational modifications critical for SARS-CoV binding and/or fusion. Cell lines derived from monkey (VeroE6, pRhMk, and pCMK), human (HRT-18, HEK293T, and Huh-7), mink (Mv1Lu), dog (MDCK), cat (CRFK), hamster (BHK-21), and chicken (CEF) were analyzed for susceptibility to SARS-CoV. This data suggests that dog ACE2 and chicken ACE2 may have amino acid or other differences, which inhibit their function as SARS-CoV receptors. 13 We used multiple sequence alignment of efficient and poor receptors, combined with difference mapping on the hACE2 structure, to identify specific residues or post-translational modifications within ACE2 that may be critical for SARS-CoV entry. cache = ./cache/cord-330433-y5dvlcda.txt txt = ./txt/cord-330433-y5dvlcda.txt === reduce.pl bib === id = cord-330597-nftwj0d5 author = Hopfer, Helmut title = Hunting coronavirus by transmission electron microscopy – a guide to SARS‐CoV‐2‐associated ultrastructural pathology in COVID‐19 tissues date = 2020-09-27 pages = extension = .txt mime = text/plain words = 4636 sentences = 328 flesch = 48 summary = Using micrographs from infected cell cultures and autopsy tissues, we show how coronavirus replication affects ultrastructure and put the morphological findings in the context of viral replication, which induces extensive remodelling of the intracellular membrane systems. To better understand the ultrastructural morphology of SARS-CoV-2 infection and COVID-19, we will first briefly discuss the pathogenesis of COVID-19 and coronavirus replication in general and then examine the TEM findings in more detail. All rights reserved Coronaviruses including SARS-CoV-2 and the morphological changes associated with replication can be visualised by TEM in infected cell lines (figure 3A-G) [81] [82] [83] [84] [85] 87, 88] or organoids [96, 97] . Based on the cell culture findings outlined above, we expect to find the same SARS-CoV-2 morphology and distribution in vesicles of autopsy and biopsy tissues of COVID-19 patients. cache = ./cache/cord-330597-nftwj0d5.txt txt = ./txt/cord-330597-nftwj0d5.txt === reduce.pl bib === id = cord-330465-16j5vm7h author = Marciniec, Krzysztof title = Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date = 2020-08-05 pages = extension = .txt mime = text/plain words = 6908 sentences = 396 flesch = 48 summary = The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. In order to check the potential toxic properties of the compounds 3-5, docking study of phosphate betulin derivatives to cellular proteins was carried out. According to the results of docking (Table S1 ) obtained from AutoDock Vina, four potential SARS-CoV-2 inhibitors (BVM, betulinic acid, and compounds 4 and 6) were selected based on a lower negative dock energy value. cache = ./cache/cord-330465-16j5vm7h.txt txt = ./txt/cord-330465-16j5vm7h.txt === reduce.pl bib === id = cord-330692-rqwkkfp0 author = He, Daihai title = Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date = 2020-06-26 pages = extension = .txt mime = text/plain words = 727 sentences = 50 flesch = 56 summary = title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom We found that the on-going COVID-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. The fast spread and high fatality of the coronavirus disease 2019 (COVID-19) remind us of the first pandemic in last century, the 1918-19 influenza pandemic. A comparison between the YLLs for COVID-19 and 1918-19 influenza should be conducted, because YLL is the other important indicator of the severity of a pandemic. If we assume a 0.5% IFR for COVID-19 in 2020 and a 2% infection fatality rate in 1918, we may calculate and compare the infections based on reported deaths which should be more reliable than reported cases. cache = ./cache/cord-330692-rqwkkfp0.txt txt = ./txt/cord-330692-rqwkkfp0.txt === reduce.pl bib === id = cord-330701-k68b0wqe author = Gerc, Vjekoslav title = Cardiovascular Diseases (CVDs) in COVID-19 Pandemic Era date = 2020-06-17 pages = extension = .txt mime = text/plain words = 5521 sentences = 282 flesch = 48 summary = AIM: The aim of this study is to retreive published papers about COVID-19 infection deposited in PubMed data base and analyzed current results of investigations regarding morbidity and mortality rates as consequences of COVID-19 infection and opinions of experts about treatment of afected patients with COVID-19 who have Cardiovascular diseases (CVDs). COVID-19 infection is caused by a new beta-coronavirus, which the WHO has called (SARS-CoV-2) -Severe Acute Respiratory Syndrome. Initially, the main complications of COVID-19 were thought to be lung-related, then it was quickly observed that COVID-19 is attacking many organs, including the heart muscle, vascular endothelium and the cardiovascular system in general, increasing morbidity and mortality, especially in patients with other cardiovascular risk factors presented (hypertension, diabetes, obesity, cerebrovascular and renal disease). In Wuhan, according to reports of Chinese physicians, in patients infected with COVID-19 and with acute coronary syndrome, the complete clinical picture was very severe and associated with high mortality (9) . cache = ./cache/cord-330701-k68b0wqe.txt txt = ./txt/cord-330701-k68b0wqe.txt === reduce.pl bib === id = cord-330324-4hqhty5o author = Yu, Meng title = Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date = 2008-02-29 pages = extension = .txt mime = text/plain words = 5799 sentences = 284 flesch = 50 summary = title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. In this study we identified and characterized the major immunodominant domains of the SARS-CoV N and S proteins recognized by different animal species, and then developed competition ELISAs based on these findings. The specificity of the antibody was further confirmed using Western blot against viral antigen (data not shown) and IFAT using SARS-CoV infected Vero cells. One of the main aims of this study was to assess the feasibility of developing a competition ELISA for detection of SARS-CoV antibodies from different animal species. Inhibition of binding of mono-specific chicken antibodies to SARS-CoV by sera from different species. cache = ./cache/cord-330324-4hqhty5o.txt txt = ./txt/cord-330324-4hqhty5o.txt === reduce.pl bib === id = cord-330478-g9n2mfni author = Hattenbach, Lars-Olof title = Krisenstrategien der Kliniken während der Pandemie date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1540 sentences = 184 flesch = 41 summary = authors: Hattenbach, Lars-Olof; Reinhard, Thomas; Walter, Peter; Roider, Johannes; Feltgen, Nicolas; Hesse, Lutz; Schrecker, Jens; Eter, Nicole Hintergrund Die SARS-CoV-2(Severe Acute Respiratory Syndrome Coronavirus 2)-Pandemie hat während der ersten Monate des Jahres 2020 weltweit zu tiefgreifenden Veränderungen der medizinischen Versorgung mit massiven Einschränkungen bei chirurgischen Eingriffen und nichtdringlichen ambulanten wie stationären Behandlungen geführt [1] [2] [3] [4] . Jüngere Publikationen zeigen jedoch, dass das Risiko einer Ansteckung durch Tränenflüssigkeit selbst bei COVID-19-Patienten eher gering ist und auch die Häufigkeit des Auftretens einer Konjunktivitis nur bei etwa 1 % liegt [12] [13] [14] . Despite the challenge of a significant shift of medical resources during the SARS-CoV-2 pandemic, medically urgently necessary ophthalmological treatments are continuously provided by maximum care clinics; however, based on currently available data, it cannot be ruled out whether treatment of emergency patients was delayed during the pandemic. cache = ./cache/cord-330478-g9n2mfni.txt txt = ./txt/cord-330478-g9n2mfni.txt === reduce.pl bib === id = cord-330887-q5i8lpan author = Li, K. title = The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 4021 sentences = 214 flesch = 54 summary = By comprehensively analyzing the laboratory findings of 1,850 patients, we describe the dynamic changes of the total antibody, spike protein (S)-, receptor-binding domain (RBD)-, and nucleoprotein (N)specific IgM and IgG levels during SARS-CoV-2 infection and recovery. Our results indicate that the S-, RBD-, and Nspecific IgG generation of severe/critical COVID-19 patients is one week later than mild/moderate cases, while the levels of these antibodies are 1.5-fold higher in severe/critical patients during hospitalization (P<0.01). To explore the temporal dynamics of immune response after SARS-Cov-2 infection, we analyzed the antibody levels at different time points after symptoms onset, and the timing and level were compared between mild/moderate and severe/critical COVID-19 Results showed that total IgG, S-, RBD-, and N-specific IgG levels of the severe/critical COVID-19 patients were lower than that of the mild/moderate patients on admission, but these levels sharply increased during hospitalization and on discharge ( Figure 1 , Table 1 ). cache = ./cache/cord-330887-q5i8lpan.txt txt = ./txt/cord-330887-q5i8lpan.txt === reduce.pl bib === id = cord-330779-mso2zfom author = Sunkari, Emmanuel Daanoba title = Sources and routes of SARS-CoV-2 transmission in water systems in Africa: Are there any sustainable remedies? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4162 sentences = 200 flesch = 50 summary = Hence, it is proposed that governments in Africa must put measures like improved WASH facilities and public awareness campaigns, suburbanization of wastewater treatment facilities, utilizing low-cost point-of-use water treatment systems, legally backed policy interventions, and Community-Led Total Sanitation (CLTS). Overall, since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water is very high and thus, the sources and routes of community spread of the virus, which is currently being reported must be critically re-examined. Since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water from wastewater systems is very high. cache = ./cache/cord-330779-mso2zfom.txt txt = ./txt/cord-330779-mso2zfom.txt === reduce.pl bib === id = cord-330387-7lci44w5 author = Bird, Paul title = High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1294 sentences = 82 flesch = 59 summary = title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads Similarly, another study from Leicester, UK compared hospitalised and community patient SARS-CoV-2 PCR (polymerase chain reaction) positivity rates with that of staff, 2 but again, did not assess which staff groups or clinical specialties were at most risk of acquiring COVID-19. In addition, we compared the SARS-CoV-2 PCR positivity rate against ethnicity for both the HCW and household contacts combined (Fig. 1C) . 8 We then compared the SARS-CoV-2 PCR positivity rates against various demographic parameters, ethnicity and symptom patterns in both the HCWs and household contacts (n=47, Table 1 ). In summary, we have compared the SARS-CoV-2 PCR positivity rates in this HCW and household contact cohort, across different clinical roles and specialties, ethnic groups, and explored the correlation between their symptom patterns and swab viral loads. cache = ./cache/cord-330387-7lci44w5.txt txt = ./txt/cord-330387-7lci44w5.txt === reduce.pl bib === id = cord-330743-o11d0aa1 author = Yu, Xi title = Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date = 2020-05-25 pages = extension = .txt mime = text/plain words = 4470 sentences = 245 flesch = 54 summary = Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). Incubation of the culture supernatant but not the bacterial lysates resulted in significant suppression of DENV ( Figure 1B ) and ZIKV ( Figure 1C ) infectivity in Vero cells, indicating that an extracellular effector(s) secreted by Csp_BJ was responsible for viral inhibition. DENV, ZIKV, HSV-1 and SARS-CoV-2 virus stocks were diluted to 50 plaque-forming units (pfu) per ml and incubated untreated or with a serial dilution of the CbAEs in five-fold steps at 37°C for 1 hr before being added onto Vero cell monolayers for 2 hr of infection. cache = ./cache/cord-330743-o11d0aa1.txt txt = ./txt/cord-330743-o11d0aa1.txt === reduce.pl bib === id = cord-330690-cupy89gl author = Vierucci, Francesco title = How COVID-19 Pandemic Changed Children and Adolescents Use of the Emergency Department: the Experience of a Secondary Care Pediatric Unit in Central Italy date = 2020-09-23 pages = extension = .txt mime = text/plain words = 4321 sentences = 211 flesch = 43 summary = During phase 1 (national lockdown period, March 9th-May 3rd, 2020) the Italian Ministry of Health recommended to avoid direct access to the emergency department (ED) in case of fever and/or cough or other respiratory symptoms, favoring home care or phone consultation for ill patients without compromised general conditions [10] . The aims of this study were to (1) evaluate the impact of COVID-19 pandemic on the activity of a secondary care Italian Pediatric Unit assessing, in particular, the characteristics of pediatric ED consultations performed in 2020 before and after the beginning of lockdown; (2) evaluate the prevalence of SARS-CoV-2 infection in children and adolescents referred to ED; and (3) compare pediatric ED activity during the same period of 2019 and 2020. cache = ./cache/cord-330690-cupy89gl.txt txt = ./txt/cord-330690-cupy89gl.txt === reduce.pl bib === id = cord-330807-abi8pra7 author = Garcia-Pachon, Eduardo title = Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization date = 2020-07-04 pages = extension = .txt mime = text/plain words = 1471 sentences = 96 flesch = 52 summary = title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization INTRODUCTION: The prevalence of asthma in patients hospitalized with SARS-CoV-2 has been studied and varies widely in the different series. METHODS AND RESULTS: A total of 218 patients (58% of those who tested positive) did not require hospitalization; they had a median age of 45 years (IQR 34–57) and 57% were female. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. For this reason we have analyzed the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay [12] for SARS-CoV-2 and did not require hospital admission. cache = ./cache/cord-330807-abi8pra7.txt txt = ./txt/cord-330807-abi8pra7.txt === reduce.pl bib === id = cord-330536-q8zr0mkl author = Lopinto, Julien title = Severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1239 sentences = 82 flesch = 45 summary = We report here a case of severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and managed in a referral center. CASE PRESENTATION: A 58-year-old man was admitted to our intensive care unit for severe hemoptysis with history of post-tuberculosis bronchiectasis. CONCLUSIONS: To our knowledge, this is the first case of acute exacerbation of bronchiectasis related to SARS-CoV-2 infection and complicated by severe hemoptysis. Since the beginning of SARS-CoV-2 outbreak in China, severe acute respiratory syndrome has been widely descripted [1] [2] [3] and hemoptysis has rarely been observed in this condition [1, 2, 4, 5] . We report here a case of acute exacerbation of posttuberculosis bronchiectasis precipitated by SARS-CoV-2 infection complicated by severe hemoptysis and managed in a referral center. To our knowledge, this is the first case reported of acute exacerbation of post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and complicated by severe hemoptysis. cache = ./cache/cord-330536-q8zr0mkl.txt txt = ./txt/cord-330536-q8zr0mkl.txt === reduce.pl bib === id = cord-330607-zn4urrxc author = Chi, Qiong title = Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3215 sentences = 165 flesch = 47 summary = METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. cache = ./cache/cord-330607-zn4urrxc.txt txt = ./txt/cord-330607-zn4urrxc.txt === reduce.pl bib === id = cord-330715-olypwdoq author = Sun, Zeyu title = Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date = 2020-08-30 pages = extension = .txt mime = text/plain words = 5567 sentences = 275 flesch = 50 summary = title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications In this study, we report a comprehensive N-glycosylation profile-as well as other PTMs-of the HCoV-19 S protein and hACE2, elucidated by high-resolution mass spectrometry (MS) analyses. To resolve glycan camouflage on the surface of the HCoV-19 S protein and hACE2, intact glycopeptides derived from protease digestion and fractionated by HILIC were directly subjected to LC-MSMS analysis specifically designed to detect peptides with extra molecular weight due to N-glycan attachment. Fig. 2 (c) provides a summary of the most dominant N-glycan composition and predicted structure for each site of the HCoV-19 spike protein and hACE2. When the spike proteins from HCoV-19 and SARS-CoV were compared, it was noticeable that the majority of differences in the glycosylation sites occurred in the distal S1 subunit, resulting in a significant difference in the glycan profile in the outermost canopy of the virus formed by spike trimer clusters. cache = ./cache/cord-330715-olypwdoq.txt txt = ./txt/cord-330715-olypwdoq.txt === reduce.pl bib === id = cord-331010-4phhz79k author = Knight, M. title = Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) date = 2020-05-12 pages = extension = .txt mime = text/plain words = 4582 sentences = 274 flesch = 52 summary = title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) Objective: To describe a national cohort of pregnant women hospitalised with SARS-CoV-2 infection in the UK, identify factors associated with infection and describe outcomes, including transmission of infection, for mother and infant. Rates of maternal death, level 3 critical care unit admission, preterm birth, stillbirth, early neonatal death, perinatal death; odds ratios for infected versus comparison women. The incidence of hospitalisation with confirmed SARS-CoV-2 infection in pregnancy was calculated using denominator estimates based on the most recently available (2018) national maternity data for the constituent countries of the United Kingdom. The clinical data from this national surveillance study show black and minority ethnicity is significantly associated with admission with SARS-CoV-2 infection in pregnancy, along with preexisting co-morbidities, overweight and obesity and older maternal age. cache = ./cache/cord-331010-4phhz79k.txt txt = ./txt/cord-331010-4phhz79k.txt === reduce.pl bib === id = cord-330717-uzrxtgrg author = Gupta, Madhu title = The need for COVID-19 research in low- and middle-income countries date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1840 sentences = 96 flesch = 40 summary = We therefore propose research in three broad areas as urgently needed to inform responses in lowand middle-income countries: transmission patterns of SARS-CoV-2, the clinical characteristics of the disease, and the impact of pandemic prevention and response measures. Targeted research activities should be done to help mitigate the potential burden of COVID-19 in lowand middle-income countries without diverting the limited human resources, funding, or medical supplies from response activities. We propose three broad research questions to inform public health and policy responses to COVID-19 in LMICs: (1) how do the patterns of SARS-CoV-2 transmission differ in resource-poor settings? A more thorough understanding of the relationship between climate, seasonality, and virus transmissibility could provide insights into the potential course of the pandemic in LMICs that tend to be warmer and more humid, supporting preparedness and response efforts in these settings. cache = ./cache/cord-330717-uzrxtgrg.txt txt = ./txt/cord-330717-uzrxtgrg.txt === reduce.pl bib === id = cord-331066-ediowz4s author = Chechetkin, Vladimir R. title = Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date = 2020-09-09 pages = extension = .txt mime = text/plain words = 7040 sentences = 416 flesch = 57 summary = Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Therefore, the putative weakly specific assembly/packaging signals in the genomic RNA of coronaviruses should be coordinated with the parameters of the helical nucleocapsid (such as the helix pitch, inner and outer diameters) which are established by cryoelectron microscopy (cryo-EM) and other structural methods. In this article, we provide methods for the detection and comparative analysis of assembly/packaging signals in the genomic RNA of the coronaviruses SARS-CoV and SARS-CoV-2 and describe main results of our study. The abundance of quasi-periodic patterns in the genomic DNA/RNA sequences can be assessed by the spectral entropy (Balakirev et al., 2003 (Balakirev et al., , 2005 (Balakirev et al., , 2014 Chechetkin, 2011; Chechetkin & Lobzin, 1996; Chechetkin & Turygin, 1994) . cache = ./cache/cord-331066-ediowz4s.txt txt = ./txt/cord-331066-ediowz4s.txt === reduce.pl bib === id = cord-330626-0aidit63 author = Sepulveda, Jorge title = Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2695 sentences = 125 flesch = 47 summary = A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase in blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity. Frequent ordering of blood cultures for patients with COVID-19 may overwhelm a laboratory's capacity to perform and process these tests, which may negatively impact the overall benefit of testing for the entire medical center. cache = ./cache/cord-330626-0aidit63.txt txt = ./txt/cord-330626-0aidit63.txt === reduce.pl bib === id = cord-330827-gu2mt6zp author = Shanmugaraj, Balamurugan title = Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date = 2020-02-22 pages = extension = .txt mime = text/plain words = 3730 sentences = 175 flesch = 40 summary = The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. cache = ./cache/cord-330827-gu2mt6zp.txt txt = ./txt/cord-330827-gu2mt6zp.txt === reduce.pl bib === id = cord-330994-6nu7utu1 author = Abdelrheem, Doaa A. title = The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation date = 2020-10-01 pages = extension = .txt mime = text/plain words = 5306 sentences = 323 flesch = 48 summary = title: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. [6] So, we study the inhibitory effect of some bioactive compounds obtained from natural sources against SARS-CoV-2-3CLpro and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT). The crystal structures of SARS-CoV-2-3CLpro (PDB code: 6LU7) and main proteases of SARS-Coronavirus (Mpro) with (PDB IDs: 2GTB and 3TNT) were downloaded from the Protein Data Bank (www.pdb.org), and any heteroatoms and water molecules were removed before molecular docking studies. Based on our molecular docking analysis we found that among all studied compounds, caulerpin has the highest binding affinity against all studied receptors 6LU7, 3TNT, and 2GTB with compared to some proposed antiviral drug currently used in COVID-19 treatment. cache = ./cache/cord-330994-6nu7utu1.txt txt = ./txt/cord-330994-6nu7utu1.txt === reduce.pl bib === id = cord-330814-7incf20e author = Parikh, Priyanka A title = COVID-19 Pandemic: Knowledge and Perceptions of the Public and Healthcare Professionals date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3804 sentences = 184 flesch = 51 summary = Background and objective The recent pandemic due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major concern for the people and governments across the world due to its impact on individuals as well as on public health. Conclusion Most healthcare professionals and the general public that we surveyed were well informed about SARS-CoV-2 and have been taking adequate measures in preventing the spread of the same. Social media platforms arguably support the conditions necessary for attitude change by exposing individuals to correct, accurate, health-promoting messages from healthcare professionals In order to investigate community responses to SARS-CoV-2, we conducted this online survey among the general public and healthcare professionals to identify awareness of SARS-CoV-2 (perceived burden and risk), trusted sources of information, awareness of preventative measures and support for governmental policies and trust in authority to handle SARS-CoV-2 outbreak and put forward policy recommendations in case of similar future conditions. cache = ./cache/cord-330814-7incf20e.txt txt = ./txt/cord-330814-7incf20e.txt === reduce.pl bib === id = cord-330849-yt44k88m author = Han, Rachel H. title = Planning for Mental Health Needs During COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5521 sentences = 262 flesch = 39 summary = The purpose of this article, written from the perspective of military medical planners, is to present available data on the prevalence of specific mental health concerns and conditions from previous recent pandemics and COVID-19, as well as to provide data-informed recommendations for meeting the psychological needs of affected individuals. A combination of the following keywords in the title and/or abstract was used in searches of literature on the Southeast Asian Respiratory Syndrome (SARS), H1N1 influenza (H1N1), Middle Eastern Respiratory Syndrome (MERS), Ebola, and COVID-19 pandemics: mental health OR mental illness OR psychiatry OR psychology OR therapist OR PTSD OR posttraumatic OR post-traumatic stress disorder OR behavioral health OR anxiety [disorder] OR GAD OR depression/depressed OR complex grief AND data analysis OR statistic* OR prevalence OR percentage OR increase OR decrease. cache = ./cache/cord-330849-yt44k88m.txt txt = ./txt/cord-330849-yt44k88m.txt === reduce.pl bib === id = cord-330800-s91zfzfi author = Reta, Daniel Hussien title = Molecular and Immunological Diagnostic Techniques of Medical Viruses date = 2020-09-04 pages = extension = .txt mime = text/plain words = 10548 sentences = 574 flesch = 43 summary = e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. cache = ./cache/cord-330800-s91zfzfi.txt txt = ./txt/cord-330800-s91zfzfi.txt === reduce.pl bib === id = cord-330868-7ocseuz3 author = Donnelly, Christl A title = Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong date = 2003-05-24 pages = extension = .txt mime = text/plain words = 3812 sentences = 167 flesch = 47 summary = Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Key epidemiological determinants of the magnitude and timescale of the epidemic (figure 1) include the interval between infection and onset of symptoms and between onset and hospital admission, the degree and duration of the infectiousness of the agent, and the extent of contact and mixing between infectious and susceptible people enabling transmission of the virus. If ␥ distribution is assumed, the estimated distributions and case fatality rate varied as a function of patients' age, but not the time from onset to admission (figure 2). cache = ./cache/cord-330868-7ocseuz3.txt txt = ./txt/cord-330868-7ocseuz3.txt === reduce.pl bib === id = cord-330944-54xmnum8 author = Hsu, You-Ren title = Investigation of C-terminal domain of SARS nucleocapsid protein–Duplex DNA interaction using transistors and binding-site models date = 2014-03-31 pages = extension = .txt mime = text/plain words = 3927 sentences = 248 flesch = 58 summary = AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. With a quantitative analysis of the signals from the sensors through binding-site models, we are able to reveal how many binding sites are on the receptor (dsDNA) for certain ligands (SARS-N protein) and what the dissociation constants are for ligand-receptor complexes. The chemical reaction for the surface-immobilized receptor (dsDNA) and the free ligand (SARS-N protein-CTD) in bulk solution can be expressed as the following equations: Therefore, we conclude that for a one-binding-site model, the most significant change of the surface coverage ratio is within the range of the ligand concentration between one order higher and one order lower than the value of the dissociation constant. cache = ./cache/cord-330944-54xmnum8.txt txt = ./txt/cord-330944-54xmnum8.txt === reduce.pl bib === id = cord-330873-hwbdreul author = Yang, Wan title = The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal date = 2020-07-07 pages = extension = .txt mime = text/plain words = 810 sentences = 47 flesch = 47 summary = title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal After infectious SARS-CoV-2 was isolated from COVID-19 patients' feces and urines, the corresponding RNA in the wastewater and sewage sludge was also observed (Randazzo et al., 2020) , implying the possibility of transmission of SARS-CoV-2 through the wastewater treatment plants (WWTP). Therefore, it is imperative to understand the potential exposure and transmission risk of this virus in sludge for the sake of public health. While limited evidence was found that sludge would play an essential role in SARS-CoV-2 transmission, there is still a need to understand the fate of coronaviruses outside the human host, including their persistence and inactivation mechanisms in 5 sludge, which would help to reveal their potential risks during sludge treatment and disposal. Aerosol Transmission Figure 1 The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal cache = ./cache/cord-330873-hwbdreul.txt txt = ./txt/cord-330873-hwbdreul.txt === reduce.pl bib === id = cord-331039-qgom2e3n author = Kavitha, Kuppuswamy title = 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates date = 2020-09-22 pages = extension = .txt mime = text/plain words = 4929 sentences = 326 flesch = 57 summary = A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 M(pro) and the top 2 lead compounds based on binding affinity were found to be 1,2,4 triazolo[1,5-a] pyrimidin-7-one compounds. The objectives of this study were i) to identify evolutionarily important active site amino acids by structure-based sequence alignment of SARS-CoV-2 and SARS-CoV M pro enzymes ii) to identify potential non-covalent M pro inhibitors by screening protease-inhibitor-like compounds available in the ZINC database by molecular docking studies iii) prediction of absorption, distribution metabolism, excretion and toxicity properties of the top-scoring inhibitors using in silico methods iv) to validate the stable binding of the lead compounds with SARS-CoV-2 M pro by molecular dynamics (MD) simulations and v) to calculate thermodynamic binding energies for each lead compound -SARS-CoV-2 M pro complex using Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) calculations. cache = ./cache/cord-331039-qgom2e3n.txt txt = ./txt/cord-331039-qgom2e3n.txt === reduce.pl bib === id = cord-330908-402eb8wg author = Tsuji, Motonori title = Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2619 sentences = 148 flesch = 48 summary = title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease Additional docking simulations for predicted compounds with high binding affinity with M(pro) suggested that 28 bioactive compounds may have potential as effective anti‐SARS‐CoV‐2 drug candidates. Additional docking simulations for predicted compounds with high binding affinity with M pro suggested that 28 bioactive compounds may have potential as effective anti-SARS-CoV-2 drug candidates. In this study, I performed stepwise structure-based virtual screenings using two different docking simulations in order to discover potential drugs that target M pro using the ChEMBL database [4] , which mainly lists drugs and known bioactive compounds. Structure-based virtual screenings were performed using RDOCK (2013) [11] and AUTODOCK VINA version 1.1.2 [12] ; both interfaces are available in Docking Study with HYPER-CHEM (DSHC) software [5, 13] , and the resulting docking modes filtered by the RDOCK score threshold were more precisely simulated using AUTODOCK VINA. cache = ./cache/cord-330908-402eb8wg.txt txt = ./txt/cord-330908-402eb8wg.txt === reduce.pl bib === id = cord-331060-b3z1zb4t author = Cruickshank, Marilyn title = COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2291 sentences = 107 flesch = 53 summary = Some of this includes the extent to which humans develop a protective immune response to COVID-19 via antibodies (The World Health Organization, 2020), the extent to which asymptomatic people can spread the infection (Bai et al., 2020; Kimball et al., 2020) , whether the use of face masks by asymptomatic members of the community can affect transmission (Feng et al., 2020) , the significance of the loss of smell as an early predictive or differential symptom of disease, the role of herd immunity and whether infection confers immunity, and if so, for how long. Once the number of new cases have stabilised, there can be a move to mitigation strategies which might not necessarily stop the spread, but can help to protect those most at risk of severe disease by isolating suspected cases and their households, while continuing to implement social distancing measures for older people and others at high risk. cache = ./cache/cord-331060-b3z1zb4t.txt txt = ./txt/cord-331060-b3z1zb4t.txt === reduce.pl bib === id = cord-331076-ak481qew author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-10-12 pages = extension = .txt mime = text/plain words = 3858 sentences = 192 flesch = 52 summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are under less selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020a) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors (Fig. 1) . Three of the five most common nsp14 mutations, namely 18060C>T, 18736T>C and 18877C>T are associated with increases in both genome-wide mutational load, as well as MoE status, an alternative indicator of mutational rate and virus evolution. cache = ./cache/cord-331076-ak481qew.txt txt = ./txt/cord-331076-ak481qew.txt === reduce.pl bib === id = cord-331109-a8e7r80d author = Ibrahim, Yassmin S. title = Case Report: Paralytic Ileus: A Potential Extrapulmonary Manifestation of Severe COVID-19 date = 2020-08-31 pages = extension = .txt mime = text/plain words = 2354 sentences = 160 flesch = 48 summary = We report two cases of SARS-CoV-2 infection complicated by paralytic ileus. Several authors have postulated that the angiotensin-converting enzyme 2 receptors, the host receptors for COVID-19, that are present on enterocytes in both the small and large bowel might mediate viral entry and resultant inflammation. We describe two cases of severe COVID-19 pneumonia who developed paralytic ileus during their disease course, which may represent one of the luminal manifestations of severe SARS-CoV-2 infection. 7 A review of 29 studies noted that 12% of patients with SARS-CoV-2 infection had gastrointestinal symptoms, including diarrhea, nausea, and vomiting. In conclusion, we report paralytic small and large bowel ileus as a complication of COVID-19. The added value of the present case report is the detailed histopathological evidence supporting a role for COVID-19-induced micro-thrombosis, thereby compromising microcirculatory function and resultant colonic bowel dilatation and perforation in the first patient. cache = ./cache/cord-331109-a8e7r80d.txt txt = ./txt/cord-331109-a8e7r80d.txt === reduce.pl bib === id = cord-331022-tek4u751 author = Sinderewicz, Emilia title = Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 8464 sentences = 427 flesch = 46 summary = The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. The current study reviewed the role of interleukins (ILs) with tumor necrosis factors (TNFs), chemokines and interferons (IFNs) in the immune response to HCoVs. A comparison of the content of proinflammatory Th1 and Th2 cytokines in the serum of SARS patients with healthy controls documented a significantly greater concentration of TNF-α, IL-6, IL-8, IL-10, and IL-12 in the early stage of the SARS-CoV infection [32, 40] . cache = ./cache/cord-331022-tek4u751.txt txt = ./txt/cord-331022-tek4u751.txt === reduce.pl bib === id = cord-331283-bfyoavon author = Meca-Lallana, Dra. Virginia title = COVID-19 IN 7 MULTIPLE SCLEROSIS PATIENTS IN TREATMENT WITH ANTI-CD20 THERAPIES date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1223 sentences = 85 flesch = 53 summary = We describe our experience in seven cases of patients with multiple sclerosis who have been affected by SARS-COV-2 (with a clinical/serological diagnosis or PCR diagnosis) and who were being treated with anti-CD20+ monoclonal antibodies. CONCLUSIONS: Patients treated with anti-CD20+ have adequate resolution of COVID-19 despite the fact that the presence of antibodies against SARS-CoV-2 was not detected in all cases. Ocrelizumab is associated with decreased levels of IgM (and to a lesser degree for IgA and IgG), and serious infections occurred, but their incidence was low in clinical trials and extended phases 4 In this work, we report our experience in MS patients with anti-CD20+ antibodies who have 2. We have found antibodies against SARS-CoV-2 in patients treated with ocrelizumab, but in patients who previously used rituximab this immunity is not achieved or we are not able to detect it. cache = ./cache/cord-331283-bfyoavon.txt txt = ./txt/cord-331283-bfyoavon.txt === reduce.pl bib === id = cord-331002-7uojryqz author = Valent, Francesca title = Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date = 2020-09-06 pages = extension = .txt mime = text/plain words = 784 sentences = 64 flesch = 59 summary = METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. The main finding of our study is the long duration of SARS-CoV-2 positivity in a population 133 including patients ranging from asymptomatic to acute respiratory distress syndrome requiring ICU 134 care. SARS-CoV-2 Viral Load in Upper 236 Respiratory Specimens of Infected Patients cache = ./cache/cord-331002-7uojryqz.txt txt = ./txt/cord-331002-7uojryqz.txt === reduce.pl bib === id = cord-331428-6pvr2vew author = Heffernan, Kevin S. title = Exercise as medicine for COVID-19: on PPAR with emerging pharmacotherapy date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1835 sentences = 107 flesch = 34 summary = Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating peroxisome proliferator-activated receptor alpha (PPARα), possibly contributing to lipotoxicity, inflammation and untoward respiratory effects. While we all eagerly await the development of a vaccine, scientists and clinicians have begun exploring "off-label" use of various drugs with that hope that strategic repurposing may help manage and treat COVID-19.(1) Fenofibrate (a peroxisome proliferator-activated receptor alpha agonist) is one such medication that holds promise given its favorable effects on inflammation and endothelial function. This paper will explore the hypothesis that exercise may be a useful adjuvant in a setting of COVID-19 management/rehabilitation due to its effects on PPAR and vascular endothelial function. (3) Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating PPAR, possibly contributing to lipotoxicity and untoward respiratory effects. Peroxisome Proliferator-Activated Receptor α Agonists Increase Nitric Oxide Synthase Expression in Vascular Endothelial Cells cache = ./cache/cord-331428-6pvr2vew.txt txt = ./txt/cord-331428-6pvr2vew.txt === reduce.pl bib === id = cord-331147-numz9onx author = Al‐Kofahi, Mahmoud title = Finding the Dose for Hydroxychloroquine Prophylaxis for COVID‐19: The Desperate Search for Effectiveness date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2301 sentences = 109 flesch = 48 summary = Our aim was to identify possible hydroxychloroquine dosing regimens through simulation in those at high risk of infections by optimizing exposures above the in vitro generated half maximal effective concentration (EC(50)) and to help guide researchers in dose‐selection for COVID‐19 prophylactic studies. 8 We simulated the current FDA approved dosing for malaria treatment (800 mg followed by 400 mg at 6, 24, and 48 hours after the initial dose, a total of 3 days) and prophylaxis (400 mg weekly) and other regimens, such as those tested in recent COVID-19 trials (i.e., 400 mg/day for 5 days or 200 mg 3 times daily for 6 days). For the FDA recommended treatment dose of malaria (800 mg loading dose followed by 400 mg daily for a total of 3 days), simulations predicted 89% of subjects would have troughs above the target on day 1, however, this number dropped to 7% by day 14 post-exposure after the start of prophylaxis ( Table 1) . cache = ./cache/cord-331147-numz9onx.txt txt = ./txt/cord-331147-numz9onx.txt === reduce.pl bib === id = cord-331429-mh2hd5fe author = Srikantiah, Padmini title = SARS Clinical Features, United States, 2003 date = 2005-01-17 pages = extension = .txt mime = text/plain words = 1948 sentences = 100 flesch = 48 summary = We compared the clinical features of 8 U.S. case-patients with laboratory-confirmed severe acute respiratory syndrome (SARS) to 65 controls who tested negative for SARS coronavirus (SARS-CoV) infection. Shortness of breath, vomiting, diarrhea, progressive bilateral infiltrates on chest radiograph, and need for supplemental oxygen were significantly associated with confirmed SARS-CoV infection. Case-patients with laboratory-confirmed SARS were compared to a convenience sample of persons who met the clinical and epidemiologic criteria for suspected or probable SARS but subsequently tested negative for SARS-CoV infection. Controls had negative findings on all testing performed for SARS-CoV, including the absence of antibody against the virus in convalescent-phase serum samples obtained >21 days after onset of symptoms. Over the course of their illness, findings suggestive of a lower respiratory tract infection developed in all 8 patients with laboratory-confirmed SARS; these findings included dyspnea (n = 8), rales (n = 5), and hypoxia (n = 5) (Table 1) . cache = ./cache/cord-331429-mh2hd5fe.txt txt = ./txt/cord-331429-mh2hd5fe.txt === reduce.pl bib === id = cord-331087-kpze9xux author = Siddiqui, S. title = SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3245 sentences = 179 flesch = 49 summary = To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW. We conducted a prospective longitudinal observational study to estimate the prevalence of anti SARS-CoV-2 antibodies among workers of a private hospital in Delhi with different levels of exposure to COVID-19 cases. The present study was conducted to estimate the seroprevalence of SARS-CoV-2 infection in Delhi and to observe how long the antibodies persist in the body. In a recently published brief report from Mumbai, India, conducted among the HCWs of three hospitals, highlighted that SARS-CoV-2 antibodies are not detected after 50 days, in RT-PCR positive individuals contrasting our observations 24 . cache = ./cache/cord-331087-kpze9xux.txt txt = ./txt/cord-331087-kpze9xux.txt === reduce.pl bib === id = cord-331300-u5fltc10 author = Patel, Jay title = Viability of SARS‐CoV‐2 in faecal bio‐aerosols date = 2020-06-09 pages = extension = .txt mime = text/plain words = 469 sentences = 33 flesch = 53 summary = I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) positive faecal samples in patients with coronavirus disease 2019 (COVID‐19). The authors acknowledge insufficient evidence in support of transmission via faeco‐oral route and identify the need for further research regarding the viability of SARS‐CoV‐2 in the context of human faeces. Dear Editor, I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive faecal samples in patients with coronavirus disease 2019 (COVID-19). The authors acknowledge insufficient evidence in support of transmission via faeco-oral route and identify the need for further Accepted Article research regarding the viability of SARS-CoV-2 in the context of human faeces. Put a lid on it: Are faecal bio-aerosols a route of transmission for SARS-CoV-2? cache = ./cache/cord-331300-u5fltc10.txt txt = ./txt/cord-331300-u5fltc10.txt === reduce.pl bib === id = cord-331094-22366b81 author = Ianevski, Aleksandr title = Potential Antiviral Options against SARS-CoV-2 Infection date = 2020-06-13 pages = extension = .txt mime = text/plain words = 6822 sentences = 424 flesch = 49 summary = We also screened 136 safe-in-man broad-spectrum antivirals against the SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. After the initial screening, we identified apilimod, emetine, amodiaquine, obatoclax, homoharringtonine, salinomycin, arbidol, posaconazole and nelfinavir as compounds that rescued virus-infected cells from death (AUC from 285 to 585; Table S1 ). We next profiled transcriptional responses to nelfinavir, amodiaquine or both drugs in virus-or mock-infected Vero-E6 cells at 24 h. Anti-SARS-CoV-2 activity of safe-in man broad-spectrum antivirals in Vero-E6 cells. Here, we found that combinations of nelfinavir with salinomycin, amodiaquine, obatoclax, emetine or homoharringtonine were synergistic against SARS-CoV-2 in Vero-E6 cells. Thus, the amodiaquine and nelfinavir combination could result in better efficacy and decreased toxicity for the treatment of SARS-CoV-2 and perhaps other viral infections. Transcriptomic analysis of mock-and SARS-CoV-2-infected Vero-E6 cells treated with nelfinavir, amodiaquine or both drugs. cache = ./cache/cord-331094-22366b81.txt txt = ./txt/cord-331094-22366b81.txt === reduce.pl bib === id = cord-331055-5ni0jxij author = Bouche, Pierre-Alban title = Were protective procedures against SARS-CoV-2 effective in an orthopaedic and trauma centre during the lockdown period? A retrospective study date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2361 sentences = 151 flesch = 51 summary = To take care of COVID-19 positive and negative patients, various procedures have been set up: reverse transcriptase polymerase chain reaction (RT-PCR) tests for all hospitalized patients, a specific unit for COVID-positive patients, a specific surgical room, and use of protective personal equipment. To allow the effectiveness of the procedures implemented, we evaluated the number of complications attributed to SARS-CoV-2 and the number of patients who became COVID positive during hospitalization. All elective surgery had to be stopped in order to decrease the influx of patients into hospitals and to redeploy medical and paramedical staff in different units to provide assistance in emergency departments, COVID-19 units, and intensive care units [6] . The purpose of this retrospective study was to assess the effectiveness of the guidelines implemented in our orthopaedic and trauma centre, Cochin Hospital, during the lockdown imposed in France period between March 15 and May 11, 2020. cache = ./cache/cord-331055-5ni0jxij.txt txt = ./txt/cord-331055-5ni0jxij.txt === reduce.pl bib === id = cord-331517-o5ejfq86 author = Hirayama, Takehisa title = Guillain-Barré syndrome after COVID-19 in Japan date = 2020-10-29 pages = extension = .txt mime = text/plain words = 2135 sentences = 148 flesch = 47 summary = We report the first case of Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection in Japan. In previous reports, most patients with SARS-CoV-2-infection-related GBS had lower limb predominant symptoms, and antiganglioside antibody tests were negative. Our findings support the notion that non-immune abnormalities such as hyperinflammation following cytokine storms and microvascular disorders due to vascular endothelial damage may lead to neurological symptoms in patients with SARS-CoV-2 infection. 4 In the present report, we discuss a case of axonal-type GBS associated with SARS-CoV-2 infection, where the patient was tested for various antiganglioside antibodies. Furthermore, we review the cases of SARS-CoV-2-infection-related GBS reported to date, in order to provide insight into the clinical characteristics and pathological mechanisms underlying the disease. In conclusion, our report supports the notion that patients with GBS associated with SARS-CoV-2 infection tend to test negative for antiganglioside antibodies. ► Patients with Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection may test negative for many known antiganglioside antibodies. cache = ./cache/cord-331517-o5ejfq86.txt txt = ./txt/cord-331517-o5ejfq86.txt === reduce.pl bib === id = cord-331155-jkm4fuw4 author = Nakashima, Akiko title = Virus database annotations assist in tracing information on patients infected with emerging pathogens date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3868 sentences = 238 flesch = 48 summary = Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. COVID-19 presents varied symptomatic features [2] , [3] , [4] , [5] , [6] , [7] with a wide range of incubation periods and epidemic curves J o u r n a l P r e -p r o o f 4 are occurring [21] , [22] , the pathogenicity and origins of the mutated substrains of SARS-CoV-2 should be available in real time to adopt early measures by authorities at the onset of emergence. We examined the nucleotide mutations and visualized the transmission trajectories of SARS-CoV-2 by consulting the world specimens registered in the virus data bank of the National Center for Biotechnology Information (NCBI) [32] . Collectively, the annotations in the virus genome database are of fundamental use to hypothesize the pathogenicity and to trace the transmission route at the early phase of emergence of the new substrains. cache = ./cache/cord-331155-jkm4fuw4.txt txt = ./txt/cord-331155-jkm4fuw4.txt === reduce.pl bib === id = cord-331465-humpwwk2 author = Canaday, David H title = On setting expectations for a SARS-CoV-2 Vaccine date = 2020-06-04 pages = extension = .txt mime = text/plain words = 997 sentences = 67 flesch = 45 summary = Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials cache = ./cache/cord-331465-humpwwk2.txt txt = ./txt/cord-331465-humpwwk2.txt === reduce.pl bib === id = cord-331611-pwj226j0 author = Shrimp, Jonathan H. title = An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3894 sentences = 216 flesch = 45 summary = We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan for pancreatitis due to their inhibition of trypsin-like proteases. The structurally related trypsin-like serine protease inhibitor nafamostat was shown to similarly inhibit spike protein-mediated cell fusion of MERS-CoV 7 . Herein we report the development of a TMPRSS2 fluorogenic biochemical assay and testing of clinical repurposing candidates for COVID19. To identify inhibitors of TMPRSS2 that may be used to validate its role in SARS-CoV-2 entry and potentially expedite to clinical trials, we developed a biochemical assay using active TMPRSS2 protease and a fluorogenic peptide substrate ( Figure 1B) . We developed a fluorogenic biochemical assay for measuring recombinant human TMPRSS2 activity for high-throughput screening that can be readily replicated and used to demonstrate that nafamostat is a more potent inhibitor than camostat and gabexate. cache = ./cache/cord-331611-pwj226j0.txt txt = ./txt/cord-331611-pwj226j0.txt === reduce.pl bib === id = cord-331193-33cyvidx author = Mawhinney, Jamie A title = Neurotropism of SARS-CoV-2: COVID-19 presenting with an acute manic episode date = 2020-06-14 pages = extension = .txt mime = text/plain words = 2512 sentences = 161 flesch = 50 summary = Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. [9] [10] [11] [12] This article outlines a case of COVID-19 presenting with an acute manic episode necessitating emergency intubation and discusses potential mechanisms for the development of neuropsychiatric disease. ► The neuroinvasive potential of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (neurotropism) has been reported, but the pathophysiology remains unclear with uncertainty over its long-term consequences. cache = ./cache/cord-331193-33cyvidx.txt txt = ./txt/cord-331193-33cyvidx.txt === reduce.pl bib === id = cord-331423-5wpx0bd0 author = Pelea, Teodor title = SARS-CoV-2 associated Guillain–Barré syndrome date = 2020-08-08 pages = extension = .txt mime = text/plain words = 2174 sentences = 126 flesch = 50 summary = Presented herein is a severe case of SARS-CoV-2 associated Guillain–Barré syndrome (GBS), showing only slight improvement despite adequate therapy. Therefore patients with SARS-CoV-2 infection are at risk of being affected by coincident immune-mediated neurological diseases such as GBS. Severe course of GBS-associated SARS-CoV-2 infections occur also in patients with mild respiratory symptoms, but must be taken into account with seriously ill cases. To date, the previously described courses of the SARS-CoV-2 infection-associated GBS do not describe a special clinical pattern. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. cache = ./cache/cord-331423-5wpx0bd0.txt txt = ./txt/cord-331423-5wpx0bd0.txt === reduce.pl bib === id = cord-331666-iwkuwnun author = Schweitzer, Wolf title = Implications for forensic death investigations from first Swiss post-mortem CT in a case of non-hospital treatment with COVID-19 date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3810 sentences = 191 flesch = 49 summary = Comment: With the pandemic impact of SARS-COV-2, a range of issues unfolds, also for medicolegal investigations into deaths, as we report the first Swiss case with post-mortem CT where death had occurred due to a SARS-COV-2 infection, with features of a severe acute respiratory distress syndrome, as an outpatient. Control: Case of a 24 year old woman who had no acute respiratory distress syndrome related findings at all; there was post-mortem hypostasis dorsally at the right lung. While this man's subjective report apparently did not include dyspnea, even less than a day prior to his death, the pulmonary pathology of this outpatient, as evidenced by PMCT, appears to extend beyond the severity shown in descriptions of currently published SARS-CoV-2-related fatalities, all of which apparently had obtained prior hospital and intensive-care treatment [39] [40] [41] . As post-mortem RT-PCR testing for SARS-CoV-2 in a forensic setting may not be available or too slow, PMCT may identify lung changes possibly related to COVID-19. cache = ./cache/cord-331666-iwkuwnun.txt txt = ./txt/cord-331666-iwkuwnun.txt === reduce.pl bib === id = cord-331140-5b0y1xzb author = Cardona Maya, Walter D. title = SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health date = 2020-06-01 pages = extension = .txt mime = text/plain words = 326 sentences = 30 flesch = 58 summary = key: cord-331140-5b0y1xzb title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health cord_uid: 5b0y1xzb . Recently, SARS-CoV-2 was detected in semen samples (5) . Therefore, it is not unreasonable to believe that the latest coronavirus could potentially be transmitted via semen (6) . It was also reported that angiotensin converting enzyme 2 (ACE2) is a functional receptor that mediates the entry of SARS-CoV-1 (7) and 2 (8) , and this receptor is expressed in the prostate. Perhaps in the coming years, the real effect of SARS-CoV-2 on prostatitis cases will be evaluated and scope for researching factors that cause the clinical syndrome will be expanded. Male infertility: a public health issue caused by sexually transmitted pathogens Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease SARS-CoV-2 and the Testis: similarity to other viruses and routes of infection Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus cache = ./cache/cord-331140-5b0y1xzb.txt txt = ./txt/cord-331140-5b0y1xzb.txt === reduce.pl bib === id = cord-331786-wgt7kg6f author = Diego-Martin, Borja title = Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date = 2020-10-13 pages = extension = .txt mime = text/plain words = 7034 sentences = 326 flesch = 45 summary = For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. cache = ./cache/cord-331786-wgt7kg6f.txt txt = ./txt/cord-331786-wgt7kg6f.txt === reduce.pl bib === id = cord-331496-5xak7z6b author = Garnett, Emily title = Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3450 sentences = 187 flesch = 43 summary = We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. In this study, we describe validation of one of the first assays to receive EUA on an automated platform, the Vitros Anti-SARS-CoV-2 Total (CoV2T; Ortho Clinical Diagnostics) antibody assay, for screening of previous exposure to SARS-CoV-2 in our patient population. Seroconversion in our patient population was assessed by correlation of chart review of 55 patients known to be positive for SARS-CoV-2 by RT-PCR and known date of symptom onset with sample reactivity by the CoV2T assay. Specimens from 14 patients with acute infections, previously tested to be negative for SARS-CoV-2 by RT-PCR but positive for another respiratory viral infection by molecular analysis, were nonreactive by the CoV2T assay. cache = ./cache/cord-331496-5xak7z6b.txt txt = ./txt/cord-331496-5xak7z6b.txt === reduce.pl bib === id = cord-331520-o9e4qqn4 author = Kistler, Christine E. title = The Winter Respiratory Viral Season During the COVID-19 Pandemic date = 2020-10-26 pages = extension = .txt mime = text/plain words = 2724 sentences = 168 flesch = 44 summary = The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research. cache = ./cache/cord-331520-o9e4qqn4.txt txt = ./txt/cord-331520-o9e4qqn4.txt === reduce.pl bib === id = cord-331375-tbuijeje author = Villalobos, Carlos title = SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives date = 2020-09-25 pages = extension = .txt mime = text/plain words = 7205 sentences = 354 flesch = 48 summary = This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). By weighting the age-stratified IFRs by the country population agegroups shares in each country, it is possible to obtain countryspecific IFRs. The relevance of this study is 3-fold: Firstly, the estimation of the true number of infections includes not only confirmed cases but COVID-19 undetected cases, as well as SARS-CoV-2infected individuals without the disease, or in a pre-symptomatic stage. In order to provide reliable estimates of the number of SARS-CoV-2 infections and of the cumulative detection rates, it is necessary that governments provide real-time information about the number of COVID-19 deaths. cache = ./cache/cord-331375-tbuijeje.txt txt = ./txt/cord-331375-tbuijeje.txt === reduce.pl bib === id = cord-331472-kd4uxcve author = Shahid, Zainab title = COVID‐19 and Older Adults: What We Know date = 2020-04-20 pages = extension = .txt mime = text/plain words = 2314 sentences = 153 flesch = 53 summary = Studies have shown that this virus causes worse outcomes and a higher mortality rate in older adults and those with comorbidities such as hypertension, cardiovascular disease, diabetes, chronic respiratory disease, and chronic kidney disease (CKD). 5 The Centers for Disease Control and Prevention (CDC) reported that although individuals older than age 65 comprise 17% of the total population in the United States, they make up 31% of COVID-19 infections, 45% of hospitalizations, 53% of intensive care unit admissions, and 80% of deaths caused by this infection. 15, 16 These symptoms are also common in older adults; one study on 21 critically ill patients with SARS-CoV-2 infection, with a mean age of 70 years, found that the most common presenting symptoms were shortness of breath (76%), fever (52%), and cough (48%). 19 One study on 46 fatal cases of SARS-CoV-2, in which 84% of patients were older than age 60, found that diabetes is likely associated with increased mortality. cache = ./cache/cord-331472-kd4uxcve.txt txt = ./txt/cord-331472-kd4uxcve.txt === reduce.pl bib === id = cord-331558-6rqd3fmj author = Sun, Chuan-bin title = Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5459 sentences = 234 flesch = 48 summary = Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. cache = ./cache/cord-331558-6rqd3fmj.txt txt = ./txt/cord-331558-6rqd3fmj.txt === reduce.pl bib === id = cord-331571-v01kstbr author = Rossoff, Jenna title = Benign course of SARS‐CoV‐2 infection in a series of pediatric oncology patients date = 2020-06-23 pages = extension = .txt mime = text/plain words = 722 sentences = 49 flesch = 51 summary = Repeat SARS-CoV-2 testing the next day was again negative, and blood cultures grew both Acinetobacter junii and Pseudomonas aeruginosa. He had an uncomplicated hospital course, but still tested positive for SARS-CoV-2 on the day of discharge and again 5 days later. Repeat testing after another 10 days, 6 weeks after symptom onset, was negative. Our series of pediatric oncology patients with relatively benign courses of SARS-CoV-2 infection is consistent with reports from both Italy and New York city, where five and 20 pediatric cancer patients, respectively, were identified as having mild or asymptomatic SARS-CoV-2 infection, 8, 9 and mirror the experience in some patients on biologics for immune-mediated inflammatory disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China Patients with cancer appear more vulnerable to SARS-COV-2: a multi-center study during the COVID-19 outbreak cache = ./cache/cord-331571-v01kstbr.txt txt = ./txt/cord-331571-v01kstbr.txt === reduce.pl bib === id = cord-331277-fjsuo3yy author = Hoste, Alexis C.R. title = Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: A screening tool and a point-of-care test date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2407 sentences = 136 flesch = 52 summary = Two serological tools based on a Double Recognition assay (Enzyme-Linked Immunosorbent Assay, DR-ELISA and Lateral Flow Assay, DR-LFA) to detect total antibodies to SARS-CoV-2, have been developed based on the recombinant nucleocapsid protein. Therefore, the aim of the present work was the development of serological tools to determine the presence of antibodies against SARS-CoV-2 in the population, as an indicator of an ongoing or previous infection. In the current study, a Double Recognition Enzyme-Linked Immunosorbent Assay (DR-ELISA) was developed to determine the presence of immunoglobulins of different classes (IgG, IgM and IgA) to SARS-CoV-2 in human serum, to support the diagnosis of COVID-19. In the present study, we developed two serological assays using the recombinant N protein Table 1, a group of 14 serum samples from early days post infection, positive to COVID-19 by respiratory-PCR yet still negative in the commercial serological assay (with seroconversion a few days later) were also tested in our assays. cache = ./cache/cord-331277-fjsuo3yy.txt txt = ./txt/cord-331277-fjsuo3yy.txt === reduce.pl bib === id = cord-331701-izkz1hz4 author = Eden, John-Sebastian title = An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date = 2020-03-17 pages = extension = .txt mime = text/plain words = 1271 sentences = 70 flesch = 50 summary = Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is linked to the Iranian epidemic, from where genomic data is currently lacking. cache = ./cache/cord-331701-izkz1hz4.txt txt = ./txt/cord-331701-izkz1hz4.txt === reduce.pl bib === id = cord-331243-0u65qguq author = Ucciferri, Claudio title = Role of monoclonal antibody drugs in the treatment of COVID-19 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1695 sentences = 94 flesch = 39 summary = Evidence suggests that elevated cytokine levels, reflecting a hyperinflammatory response secondary to SARS-CoV-2 infection, are responsible for multi-organ damage in patients with COVID-19. These studies suggest that tocilizumab may be a candidate to improve the outcome of patients with severe COVID-19 infections. Recent data on anakinra showed that, in a cohort of patients with COVID-19 and Acute respiratory distress syndrome managed with non-invasive mechanical ventilation, treatment with highdose anakinra was safe and associated with clinical improvement [16, 17] . Currently available data on SARS-CoV-2 infection show that the extent of the inflammatory response correlates with disease progression and subsequent organ damage. Tocilizumab for the treatment of severe COVID-19 pneumonia with hyperinflammatory syndrome and acute respiratory failure: A single center study of 100 patients in Interleukin-1 blockade with high-dose anakinra in patients with COVID-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study cache = ./cache/cord-331243-0u65qguq.txt txt = ./txt/cord-331243-0u65qguq.txt === reduce.pl bib === id = cord-331790-0w0pjjg1 author = Abu Jawdeh, Bassam G. title = COVID-19 in Kidney Transplantation: Outcomes, Immunosuppression Management and Operational Challenges date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3057 sentences = 204 flesch = 47 summary = This review summarizes the published COVID-19 literature as it relates to outcomes and immunosuppression management in kidney transplant recipients. These multiple studies have elucidated that COVID-19 is a systemic disease that often manifests with gastrointestinal (GI) symptoms, liver injury, cardiac involvement, encephalitis, atypical stroke, acute kidney injury (AKI) in addition to endothelial cell injury and coagulopathy -the likely mediators of multi-organ involvement (3) (4) (5) (6) (7) (8) . In a 36-patient study, the median age was 60 years, 72% were male, 39% were African American and 75% received deceased-donor kidney transplants (DDKT)(9). Notably, the Columbia transplant program adopts an early steroid withdrawal strategy, however their sample was enriched with patients on prednisone maintenance (67%) which confirms the plausible role of enhanced immunosuppression as a susceptibility factor. cache = ./cache/cord-331790-0w0pjjg1.txt txt = ./txt/cord-331790-0w0pjjg1.txt === reduce.pl bib === id = cord-331547-uqmjhhna author = Bonalumi, Giorgia title = A call to action becomes practice: cardiac and vascular surgery during the COVID-19 pandemic based on the Lombardy emergency guidelines date = 2020-06-25 pages = extension = .txt mime = text/plain words = 4218 sentences = 226 flesch = 50 summary = In Lombardy, the hub-and-spoke system was introduced to guarantee emergency and urgent cardiovascular surgery, whereas most hospitals were dedicated to patients with coronavirus disease 2019 (COVID-19). Daily morning briefings were held internally at the Monzino hospital to monitor every aspect of all in-patients (COVID-19 status, number of available beds) and to share news from the Health Care Lombardy Regional System and the national government. If the test results were positive (chest CT scan indicative of interstitial pneumonia and/or positive results from the nasal swab), the patient was transferred to a dedicated zone called the 'red area', a separate zone with physical barriers and heavy use of personal protective equipment to protect working personnel, where only patients with COVID-19 were hospitalized. In cases of emergency surgery, the patient was considered and treated as positive for SARS-CoV-2 by the health care staff, who wore personal protective equipment, until screening results were available. cache = ./cache/cord-331547-uqmjhhna.txt txt = ./txt/cord-331547-uqmjhhna.txt === reduce.pl bib === id = cord-331617-1ytcd0ax author = Horvath, Karl title = Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2635 sentences = 331 flesch = 55 summary = Da weitgehend alle zur Diagnose eingesetzten Tests nicht vollständig fehlerfrei funktionieren, ist auch bei der Testung auf Vorliegen von SARS-CoV-2 spezifischen AK damit zu rechnen, dass es einen Anteil von Personen gibt, der vom Test falsch klassifiziert wird. Wie groß dieser jeweilig falsch klassifizierte Anteil an allen getesteten Personen ist, d.h. wie sicher ein positives oder negatives Testresultat ist, ist abhängig von der Sensitivität und Spezifität des jeweiligen Tests sowie von der gegebenen Vortestwahrscheinlichkeit. Mit anderen Worten beschreibt die Vortestwahrscheinlichkeit das Risiko, dass bei einer bisher ungetesteten Person eine SARS-CoV-2 Infektion vorliegt bzw. Zu bedenken ist auch, dass sich die Prävalenz einer SARS-CoV-2 Infektion und damit die Vortestwahrscheinlichkeit mit Fortschreiten der Pandemie ändern wird. Auch bei nahezu idealen Testeigenschaften sind bei geringer Vortestwahrscheinlichkeit (wie sie bei der Testung von Personen ohne Symptome und Risikofaktoren für eine SARS-CoV-2 Infektion besteht) positive Testresultate häufig falsch. cache = ./cache/cord-331617-1ytcd0ax.txt txt = ./txt/cord-331617-1ytcd0ax.txt === reduce.pl bib === id = cord-331673-xv1tcugl author = Reina, Giacomo title = Hard Nanomaterials in Time of Viral Pandemics date = 2020-07-15 pages = extension = .txt mime = text/plain words = 15712 sentences = 976 flesch = 44 summary = For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). cache = ./cache/cord-331673-xv1tcugl.txt txt = ./txt/cord-331673-xv1tcugl.txt === reduce.pl bib === id = cord-331825-dwi350c0 author = Teherani, Mehgan F title = Burden of illness in households with SARS-CoV-2 infected children date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1629 sentences = 117 flesch = 63 summary = We investigated the dynamics of illness among household members of SARS-CoV-2 infected children that received medical care (n=32). To address this knowledge gap, we utilized a prospective registry of laboratory-confirmed pediatric COVID-19 cases and conducted contact tracing of household members to characterize the presumed transmission before and after the child's diagnosis. We defined the suspected index case as the first person (child or adult) to report symptoms or test positive for SARS-CoV-2 in the household, documented 14 days prior to, during, or after symptoms of other family members. Because pediatric patients are more likely to be asymptomatic or show mild symptoms, it has been challenging to define their role in SARS-CoV-2 household transmission, which this study aimed to address. In our study of child-to-adult transmission cases, children were symptomatic for at least 4 days prior to seeking care, the time period when they were most likely to be infectious to other household members 5,9 . cache = ./cache/cord-331825-dwi350c0.txt txt = ./txt/cord-331825-dwi350c0.txt === reduce.pl bib === id = cord-331831-gw42e6ce author = Moore, Luke S P title = Near-patient SARS-CoV-2 molecular platforms: new-old tools for new-old problems date = 2020-10-08 pages = extension = .txt mime = text/plain words = 1101 sentences = 53 flesch = 48 summary = In their prospective, interventional, non-randomised, controlled trial published in The Lancet Respiratory Medicine, Nathan Brendish and colleagues 1 move COVID-19 diagnostics forward, both by expanding the repertoire of in-situ evaluated molecular platforms, and also methodologically, with a diagnostic controlled trial using clinical impact as a primary outcome measure, analogous to their previous work on other respiratory viruses. 1 Nevertheless, this level of accuracy is attractive in the context of the recently published (yet perhaps already outdated) Cochrane review 3 of early-tomarket, rapid, point-of-care molecular tests for SARS-CoV-2, which looked at 13 evaluations of four platforms, finding a mean sensitivity of 95·2% (86·7-98·3) with a specificity of 98·9% (97·3-99·5). Brendish and colleagues also showed that the fast turnaround time of the QIAstat-Dx Respiratory SARS-CoV-2 Panel decreased the time taken for patients to be placed in an appropriate care area, and led to fewer bed moves and faster time to enrolment into other COVID-19 clinical trials-all significant advantages. Clinical impact of molecular point-ofcare testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study cache = ./cache/cord-331831-gw42e6ce.txt txt = ./txt/cord-331831-gw42e6ce.txt === reduce.pl bib === id = cord-331835-nuhrd92z author = Hung, Kevin K. C. title = The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date = 2018-11-27 pages = extension = .txt mime = text/plain words = 4011 sentences = 201 flesch = 51 summary = title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. This case study will use the example of the Metropole Hotel in Hong Kong in the international spread of Severe Acute Respiratory Syndrome (SARS) in 2003, and the effect of the government mandated quarantine of the Metropark Hotel during the swine flu 2009 in Hong Kong. After the SARS outbreak in Hong Kong the health authority established the Guidelines for Hotels in Preventing Severe Acute Respiratory Syndrome (SARS) [24] cache = ./cache/cord-331835-nuhrd92z.txt txt = ./txt/cord-331835-nuhrd92z.txt === reduce.pl bib === id = cord-331856-j0gedx43 author = Basile, K. title = Accuracy amidst ambiguity: false positive SARS-CoV-2 nucleic acid tests when COVID-19 prevalence is low date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1238 sentences = 69 flesch = 45 summary = In countries with a low prevalence of COVID-19 and a low pre-test probability, confirmation of positive nucleic acid test (NAT) results for SARS-CoV-2 is recommended given the potential for false positive results. [2] [3] [4] Initially, the Public Health Laboratory Network (PHLN) Australia recommended that confirmatory testing be performed on samples where SARS-CoV-2 RNA had been detected to ensure that the result was a true positive. In the context of Australia's low prevalence of COVID-19 and thus low pre-test probability for infection, we recommend that all positive SARS-CoV-2 NAT results be confirmed by supplementary testing on the original nucleic acid extract and/or re-extraction of nucleic acid from the original sample (if available) and tested using another assay(s) with different gene targets and/or lower limits of detection 10 (Fig. 1) . cache = ./cache/cord-331856-j0gedx43.txt txt = ./txt/cord-331856-j0gedx43.txt === reduce.pl bib === id = cord-331563-4yvfdqbq author = Chughtai, Abrar Ahmad title = Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis date = 2013-05-31 pages = extension = .txt mime = text/plain words = 5634 sentences = 312 flesch = 51 summary = title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis BACKGROUND: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). RESULTS: Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). This study aimed to examine available policies and guidelines around the use of masks and respirator for HCWs, for the prevention of influenza, SARS and TB; and to describe areas of consistency and inconsistency between guidelines, as well as gaps, with reference to the WHO and the CDC guidelines. Health care organizations and countries have different policies and guidelines around mask and respirator use for influenza, SARS and TB. cache = ./cache/cord-331563-4yvfdqbq.txt txt = ./txt/cord-331563-4yvfdqbq.txt === reduce.pl bib === id = cord-331807-ooym5eh3 author = Wu, Tao title = A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date = 2020-07-29 pages = extension = .txt mime = text/plain words = 556 sentences = 48 flesch = 51 summary = title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA cache = ./cache/cord-331807-ooym5eh3.txt txt = ./txt/cord-331807-ooym5eh3.txt === reduce.pl bib === id = cord-331930-w2055c42 author = Tso, Eugene Y. K. title = Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date = 2004-05-01 pages = extension = .txt mime = text/plain words = 529 sentences = 34 flesch = 61 summary = title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. cache = ./cache/cord-331930-w2055c42.txt txt = ./txt/cord-331930-w2055c42.txt === reduce.pl bib === id = cord-331680-qlzhtxs0 author = Goryachev, A.N. title = Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date = 2020-11-03 pages = extension = .txt mime = text/plain words = 4106 sentences = 200 flesch = 51 summary = In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. cache = ./cache/cord-331680-qlzhtxs0.txt txt = ./txt/cord-331680-qlzhtxs0.txt === reduce.pl bib === id = cord-331910-s474ecvk author = Thota, Sai Manohar title = Natural products as home‐based prophylactic and symptom management agents in the setting of COVID‐19 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 8669 sentences = 457 flesch = 37 summary = Natural products like ginger, turmeric, garlic, onion, cinnamon, lemon, neem, basil, and black pepper have been scientifically proven to have therapeutic benefits against acute respiratory tract infections including pulmonary fibrosis, diffuse alveolar damage, pneumonia, and acute respiratory distress syndrome, as well as associated septic shock, lung and kidney injury, all of which are symptoms associated with COVID‐19 infection. In this context, this review highlights the potential beneficial effects of natural products that are actively used in alternative/ traditional medicines to treat many of the acute pulmonary infections, routinely seen in COVID-19 patients. Importantly, these pre-clinical studies highlight the efficacy of garlic in mitigating pulmonary fibrosis, lung injury, and sepsis-associated organ failure, all of which are symptoms observed in patients with advanced COVID-19 infection. Taken together, preclinical and clinical studies suggest that vitamin-C could have promising therapeutic benefits in individuals with pulmonary fibrosis, pneumonia, ARDS, sepsis, acute lung injury, and multiple organ dysfunction all of which are observed in advanced COVID-19 patients. cache = ./cache/cord-331910-s474ecvk.txt txt = ./txt/cord-331910-s474ecvk.txt === reduce.pl bib === id = cord-331541-u0xm9a89 author = Lankes, Heather A title = Biospecimen Collection During the COVID-19 Pandemic: Considerations for Biobanking date = 2020-09-25 pages = extension = .txt mime = text/plain words = 3580 sentences = 250 flesch = 40 summary = METHODS: Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Additional CDC SARS guidance recommended that laboratory personnel have a baseline serum sample collected prior to working with SARS-CoV biospecimens and stored for future reference. Testing of banked biospecimens collected in late 2019 may help define asymptomatic (or mildly symptomatic) circulation of SARS-CoV-2 prior to the presentation of severe cases in December; however, until a more accurate date is defined, use of October 1, 2019, as the start of the pandemic window is reasonable. Per CDC and WHO SARS-CoV-2 interim biosafety guidance 48, 49 and reported COVID-19 experience, 57 biobanks handling pandemic window biospecimens must: SARS-CoV-2 is the highly transmittable respiratory virus that causes COVID-19, a disease hallmarked by asymptomatic infection in some, and severe symptoms, including death, in others. cache = ./cache/cord-331541-u0xm9a89.txt txt = ./txt/cord-331541-u0xm9a89.txt === reduce.pl bib === id = cord-331897-4wnoa4l7 author = Cai, Yi title = Temporal event searches based on event maps and relationships() date = 2019-09-25 pages = extension = .txt mime = text/plain words = 10502 sentences = 595 flesch = 61 summary = Experiments conducted on a real data set show that our method outperforms the baseline method Event Evolution Graph (EEG), and it can help discover certain new relationships missed by previous methods and even by human annotators. Although some work has been done to find and link incidents in news stories [4, 5] or discover event evolution graphs [6, 7] , this scholarship has only focused on time sequences and content similarity between two component events to identify the dependence relationships. To the best of our knowledge, this is the first piece of work that (1) formalizes and handles the event search problem by analyzing all temporal, content dependence and event reference relationships between events to construct an overall picture of the event's evolution; and (2) measures the importance of events based on the interrelationships of events. cache = ./cache/cord-331897-4wnoa4l7.txt txt = ./txt/cord-331897-4wnoa4l7.txt === reduce.pl bib === id = cord-332076-b0qtzzac author = Zhen, Wei title = Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4082 sentences = 216 flesch = 50 summary = In the present study, we evaluated the analytical sensitivity and clinical performance of the following four SARS-CoV-2 molecular diagnostic assays granted emergency use authorization by the FDA using nasopharyngeal swabs from symptomatic patients: the New York SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel (modified CDC) assay, the Simplexa COVID-19 Direct (Diasorin Molecular) assay, GenMark ePlex SARS-CoV-2 (GenMark) assay, and the Hologic Panther Fusion SARS-CoV-2 (Hologic) assay. In this study, we evaluated the analytical and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted EUA by the FDA, including the modified CDC, DiaSorin Molecular, GenMark, and Hologic assays. For workflow, TAT, and ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, and GenMark) outperformed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, and separate areas for processing and performing the test. cache = ./cache/cord-332076-b0qtzzac.txt txt = ./txt/cord-332076-b0qtzzac.txt === reduce.pl bib === id = cord-332071-bqvn3ceq author = Lee, Jeong Seok title = Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 date = 2020-07-10 pages = extension = .txt mime = text/plain words = 7099 sentences = 412 flesch = 53 summary = In a murine model of SARS-CoV infection, a delayed, but considerable type I IFN (IFN-I) response CORONAVIRUS Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 (Page numbers not final at time of first release) 2 promotes the accumulation of monocytes-macrophages and the production of pro-inflammatory cytokines, resulting in lethal pneumonia with vascular leakage and impaired virusspecific T-cell responses (10) . To examine the host immune responses in a cell type-specific manner, we subjected 59,572 cells to t-distributed stochastic neighbor embedding (tSNE) based on highly variable genes using the Seurat package (17) and identified 22 different clusters unbiased by patients or experimental batches of scRNA-seq (Fig. 1A, Fig. S1D ). First, we combined both mild and severe COVID-19 as a COVID-19 group and identified disease-specific changes in genes for each cell type compared to the healthy donor group using model-based analysis of single cell transcriptomics (MAST) (18) . cache = ./cache/cord-332071-bqvn3ceq.txt txt = ./txt/cord-332071-bqvn3ceq.txt === reduce.pl bib === id = cord-332013-bl5d4xkc author = Sánchez-Álvarez, J. Emilio title = Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) date = 2020-04-27 pages = extension = .txt mime = text/plain words = 3619 sentences = 214 flesch = 54 summary = title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) Conclusions SARS-CoV-2 infection already affects a significant number of Spanish patients on RRT, mainly those on ICH, hospitalization rates are very high and mortality is high; age and the development of pneumonia are factors associated with mortality. As of April 11, data from 868 patients on RRT with documented SARS-CoV-2 coronavirus infection had been entered into the Registry. The analysis of data collected during the first three weeks of the Covid-19 Registry of SEN shows that the SARS-CoV-2 infection affects a significant number of Spanish patients on RRT, mainly those that are in HDC . Nevertheless our registry show that , hydroxychloroquine and other commonly used drugs in the SARS-CoV infection-2 are used more frequently in transplant than in dialysis patients. cache = ./cache/cord-332013-bl5d4xkc.txt txt = ./txt/cord-332013-bl5d4xkc.txt === reduce.pl bib === id = cord-332268-x30svp5y author = Bearden, Donna M. title = COVID-19: a primer for healthcare providers date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3692 sentences = 226 flesch = 49 summary = A viral genome sequence of a novel coronavirus, currently termed SARS-CoV‑2, with a disease process called COVID-19 was released 1 week later via online resources to obtain public health support in control of spread. Perhaps the most detailed study to date, shedding light on how patients may present and progress, is an analysis of the first 99 cases of confirmed novel corona pneumonia in Wuhan [12] . Nowak and Walkowiak, in a recently released review of five in vitro studies reporting on the effect of lithium in coronavirus infections, concluded that the drug does have antiviral activity and should be explored as a potential treatment or prophylaxis for COVID-19 [24] . The authors concluded "our work suggests that remdesivir may improve disease outcomes in coronavirus patients, serve to protect health care workers in area with endemic MERS-CoV and prove valuable in preventing future epidemics " [3] . cache = ./cache/cord-332268-x30svp5y.txt txt = ./txt/cord-332268-x30svp5y.txt === reduce.pl bib === id = cord-331878-ww9fu8ey author = Gao, Xiaopan title = Crystal structure of SARS-CoV-2 papain-like protease date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3510 sentences = 222 flesch = 58 summary = The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. We then determined the structure of SARS-CoV-2 PLpro complex by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The initial hydrolysis rate was plotted as the function of inhibitor concentration and the plot was fitted by the equation Y=Bottom+(Top-Bottom)/(1+(X/IC 50 )) using software GraphPad. To gain structural and biochemical insight into SARS-CoV-2 PLpro domain (nsp3 746-1063aa, Supporting Information Fig. S1 ), we expressed two PLpro variants. For example, several crystal structures of SARS-CoV-2 PLpro C111S mutant complexed by various non-covalent inhibitors have been recently deposited in Protein Data Bank (PDB ID: 7JIT, 7JIR and 7JIV), which support our assertion. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors cache = ./cache/cord-331878-ww9fu8ey.txt txt = ./txt/cord-331878-ww9fu8ey.txt === reduce.pl bib === id = cord-331871-colmj7uk author = Feehan, A. K. title = Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1227 sentences = 88 flesch = 60 summary = Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. This study was designed to estimate SARS-CoV-2 infections in Orleans and Jefferson Parishes (O/JP) and the COVID-19 related IFR by race. . https://doi.org/10.1101/2020.06.23.20138321 doi: medRxiv preprint was used to calculate "presumed recovered." IFR was calculated by dividing cumulative deaths by race, reported by the Louisiana Department of Health, by "presumed recovered" individuals. 2018 population estimates are indicated in Table 1 and multiplied by weighted seroprevalence (percent IgG+) to generate the number of "presumed recovered." Reported deaths are divided by "presumed recovered" to calculate the IFR, which was 1.63% overall. cache = ./cache/cord-331871-colmj7uk.txt txt = ./txt/cord-331871-colmj7uk.txt === reduce.pl bib === id = cord-331927-b7pfm3i0 author = Winn, Soe P title = Diabetic Ketoacidosis in Coronavirus Disease Patients With Type 2 Diabetes Mellitus date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1772 sentences = 97 flesch = 53 summary = Since the emergence of the coronavirus disease (COVID-19) pandemic, we have seen many cases and studies on the underlying pathophysiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia with or without respiratory failure. We have also learned that the angiotensin-converting enzyme receptor is one of the major entry sites of SARS-CoV-2 infection, and it might be one of the causes that predispose patients to DKA. also stated that the human pancreas also expresses ACE2, and therefore, patients with diabetes are more vulnerable to SARS-CoV-2 infection than the general population [9] . In our cases, the transient damage of pancreatic beta-cell function leading to reduced levels of serum C peptide may be the reason for our patients experiencing acute insulin-dependent DKA for a brief period during the course of COVID-19. COVID-19 may cause DKA by increasing insulin requirement induced by ACE2-mediated destruction of pancreatic beta cells, as evidenced by reversible decreased serum C peptide levels or other unexplored mechanisms. cache = ./cache/cord-331927-b7pfm3i0.txt txt = ./txt/cord-331927-b7pfm3i0.txt === reduce.pl bib === id = cord-332080-923jpec0 author = Lai, Chih-Cheng title = In vitro diagnostics of coronavirus disease 2019: technologies and application date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1189 sentences = 92 flesch = 58 summary = Abstract Laboratory-based diagnostic measures including virological and serological tests are essential for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, serological tests cannot confirm SARS-CoV-2, and results will be false-negative when antibody concentrations fall below detection limits. (Hangzhou Bigfish Bio-tech Co., Ltd., Zhejiang, China) was recently registered 127 as a CE-IVD for detecting SARS-CoV-2 ORF-1ab and N genes in 128 nasopharyngeal swabs, sputum, and BAL fluids. The 145 performance of the Xpress SARS-CoV-2 test was clinically evaluated in 146 patients with respiratory illnesses from whom contrived nasopharyngeal swab 147 samples were collected into viral transport media. Serological tests that can detect SARS-CoV-2 IgG-IgM antibodies are simpler 248 than rRT-PCR, and do not require complicated equipment and protocols 249 (Table 3) . During the previous SARS 251 epidemic, the IgM antibody was the first line of defense during viral infections 252 and was detectable in blood samples from patients after 3 -6 days. Dynamics of 617 anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients cache = ./cache/cord-332080-923jpec0.txt txt = ./txt/cord-332080-923jpec0.txt === reduce.pl bib === id = cord-332134-88wfcc3y author = Li, Tingting title = A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date = 2020-09-24 pages = extension = .txt mime = text/plain words = 2051 sentences = 158 flesch = 57 summary = title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection Molecular mechanism for neutralization 157 Structure alignment of SR4-, MR17-and ACE2-RBD 4 showed that both sybodies 158 engage with RBD at the receptor-binding motif (RBM) ( Fig. 2A, 2B) . Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. As LR5 showed 209 higher affinity and neutralization activity than LR1 (Fig. 1A) , we fused this non-210 competing sybody to the N-terminal of MR3 with various length of GS linkers ranging 211 from 13 to 34 amino acids (Extended Data Table S1 ). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with 803 cache = ./cache/cord-332134-88wfcc3y.txt txt = ./txt/cord-332134-88wfcc3y.txt === reduce.pl bib === id = cord-332109-ont0tqpn author = Wei, Yufeng title = Substance Use Disorder in the COVID-19 Pandemic: A Systematic Review of Vulnerabilities and Complications date = 2020-07-18 pages = extension = .txt mime = text/plain words = 11728 sentences = 668 flesch = 39 summary = The immunosuppression reduces antibody production, cytotoxicity, and T cell-mediated immune responses, and is linked to higher incidences of pathogen infections, slowed recovery, and severe disease progression in COVID-19. Due to compromised immune responses, cocaine abusers have considerably high incidences of viral infections, including human immunodeficiency virus (HIV), influenza, and potentially SARS-CoV-2. Cardiac arrhythmias and acute MI; oxygen imbalance; microvascular diseases and thrombosis [122] [123] [124] [125] [126] [127] [129] [130] [131] [132] Increased severity and mortality [12, 37, 38] Immune system Stimulating HPA axis; immunosuppression; defects in antibody formation, lymphocyte proliferation, macrophage and NK activation [141, 142] High incidence of viral infection [142] CNS Increased BBB permeability due to loss of tight junction proteins; rearrangement of cytoskeleton structure [143] [144] [145] [146] Endotheliitis and CNS infection [53, [55] [56] [57] Amphetamine, METH, MDMA cache = ./cache/cord-332109-ont0tqpn.txt txt = ./txt/cord-332109-ont0tqpn.txt === reduce.pl bib === id = cord-332245-yfj1kkj7 author = nan title = SARS-CoV-2 Infektion bei Kindern und Jugendlichen: Ein Literaturüberblick der AG Infektiologie der ÖGKJ1 date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2336 sentences = 334 flesch = 55 summary = aktuell Infektiologie SARS-CoV-2 Infektion bei Kindern und Jugendlichen Ein Literaturüberblick der AG Infektiologie der ÖGKJ 1 F Im Dezember 2019 kam es in der chinesischen Region Hubei zum gehäuften Auftreten von Pneumoniefällen unbekannter Ätiologie [1] . Allerdings waren in dieser Altersgruppe knapp 80 % der Fälle lediglich Verdachtsfälle (ohne SARS-CoV-2-Laborbestätigung), sodass die Autoren davon ausgehen, dass ein nicht unbeträchtlicher Teil dieser schweren Verläufe durch andere Viren (v. Jedoch zeigten sich in einer diesen Kohorten vermehrte fetale Komplikationen wie Frühgeburtlichkeit oder respiratorischer Stress, wobei der direkte Zusammenhang mit SARS-CoV-2 nicht geklärt ist. So muss natürlich auf neonatalen Intensivstationen damit gerechnet werden, dass aufgrund einer SARS-CoV-2-Erkrankung der Mutter eine prämature Entbindung indiziert wird und die Frühgeborenen behandelt werden müssen. Bei den wenigen detaillierten Berichten über spezifische Symptome bei Kindern mit COVID-19 wird Fieber in 40-100 % und Husten in 40-100 % der symptomatischen Fälle beschrieben [7, 8, [15] [16] [17] [18] [19] . Bisher gibt es keine zugelassenen Medikamente zur Therapie von COVID-19 bei Erwachsenen und Kindern [32] . cache = ./cache/cord-332245-yfj1kkj7.txt txt = ./txt/cord-332245-yfj1kkj7.txt === reduce.pl bib === id = cord-332150-j76726no author = De Stefano, Ludovico title = A “Window of Therapeutic Opportunity” for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3616 sentences = 166 flesch = 28 summary = The main challenge for effective administration of anti-cytokine therapy in COVID-19 will be therefore to better define a precise "window of therapeutic opportunity." Only considering a more specific set of criteria able to integrate information on direct viral damage, the cytokine burden, and the patient's immune vulnerability, it will be possible to decide, carefully balancing both benefits and risks, the appropriateness of using immunosuppressive drugs even in patients affected primarily by an infectious disease. Discovery of virus and host genomic factors will undoubtedly support risk stratification and targeted treatment; however, as genomic studies require long times before entering clinical practice, it is urgent to integrate easily accessible information on the dynamics and pathogenicity of the immune response during the different phases of SARS-CoV-2 infection. Accordingly, longitudinal immune profiling of hospitalized COVID-19 cases with different outcomes has recently shown that, despite similar levels of inflammatory cytokines in the first 10 days from symptom onset, patients with less severe disease evolution also express mediators of wound healing and tissue repair (41) . cache = ./cache/cord-332150-j76726no.txt txt = ./txt/cord-332150-j76726no.txt === reduce.pl bib === id = cord-332178-0xyrmk5a author = Chadchan, Sangappa B. title = The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2449 sentences = 163 flesch = 50 summary = title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization STUDY QUESTION Is SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization? The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. WIDER IMPLICATIONS OF THE FINDINGS Expression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. Given the important function of the uterine stroma and the possibility that SARS-CoV-2 could infect the uterus, our goal here was to 101 determine whether ACE2 is expressed in endometrial stromal cells, is regulated by progesterone, 102 and is required for decidualization. Given the high ACE2 expression in the human 143 endometrium, SARS-CoV-2 may be able to enter endometrial stromal cells and elicit pathological 144 manifestations in women with COVID-19. cache = ./cache/cord-332178-0xyrmk5a.txt txt = ./txt/cord-332178-0xyrmk5a.txt === reduce.pl bib === id = cord-332065-afq26621 author = Ghanchi, Hammad title = Racial Disparity Amongst Stroke Patients During the Coronavirus Disease 2019 Pandemic date = 2020-09-10 pages = extension = .txt mime = text/plain words = 2855 sentences = 151 flesch = 46 summary = The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting with stroke during the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A statistically significant increase in the number of Black and Hispanic patients presenting with strokes was noted in California, Pacific hospitals, Western hospitals, and all hospitals in the United States during various months studied comparing 2020 to 2019. Given the recent pandemic and racial disparity among patients afflicted with SARS-CoV-2 and the possible link of this virus and cerebrovascular accidents (CVA), we sought to analyze whether there was a disparity for stroke patients presenting to hospitals during this time using the Get with the Guidelines (GWTG) National Stroke Database. The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting to our institution with stroke during the COVID-19 pandemic caused by SARS-CoV-2. cache = ./cache/cord-332065-afq26621.txt txt = ./txt/cord-332065-afq26621.txt === reduce.pl bib === id = cord-332271-slouuryl author = Baker, Jeremy D. title = A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2683 sentences = 172 flesch = 52 summary = title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing 27 as selective and potent inhibitors of SARS-CoV-2 Mpro. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Before screening the Broad library, 100 we piloted our assay conditions against the NIH Clinical collections library (~650 compounds) and 101 calculated our Z'-factor for each plate at 0.780 and 0.784 (Fig 1C and D) . cache = ./cache/cord-332271-slouuryl.txt txt = ./txt/cord-332271-slouuryl.txt === reduce.pl bib === id = cord-332196-03cklmm3 author = Kennedy, Amy J. title = Retesting for severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Patterns of testing from a large US healthcare system date = 2020-08-10 pages = extension = .txt mime = text/plain words = 1056 sentences = 61 flesch = 52 summary = Often decisions on who to test are left to individual clinicians, which leads to questions about when and who to retest for COVID-19, how often false positives or negatives might occur, and the duration of positivity. This report describes patterns of SARS-CoV-2 nucleic acid polymerase chain reaction (PCR) retesting in inpatients and outpatients within a large US healthcare system. We performed a retrospective chart review of all inpatients and outpatients aged ≥18 years receiving care within the University of Pittsburgh Medical Center (UPMC) with ≥2 SARS-CoV-2 PCR tests with an initial test between March 3 and May 3, 2020, and a subsequent test before May 21, 2020. In this retrospective study of a large US healthcare system, we found that retesting for SARS-CoV-2 was uncommon and often resulted in multiple negative tests. Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: impact of the interval between tests cache = ./cache/cord-332196-03cklmm3.txt txt = ./txt/cord-332196-03cklmm3.txt === reduce.pl bib === id = cord-332292-n7k4va9k author = Yen, Yung-Feng title = Olfactory disorder in patients infected with SARS-CoV-2 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1239 sentences = 86 flesch = 57 summary = Therefore, we conducted this cohort study to characterize the clinical course of olfactory disorder in COVID-19 patients in Taiwan. Two patients exhibited anosmia as the main symptom at the onset of SARS-CoV-2 infection, while one patient had hyposmia 4 days after the onset of COVID-19. 7 All patients with olfactory disorder in our study fully recovered their olfactory function before the RT-PCR results for SARS-CoV-2 turned negative. This cohort study was the first to characterize the clinical course of olfactory disorder in COVID-19 patients. 2 Limited COVID-19 cases in this study may preclude this J o u r n a l P r e -p r o o f analysis from estimating the precise prevalence of olfactory disorder in patients infected with SARS-CoV-2. However, consistent with a current report, 7 the findings of our study suggest that olfactory disorder is not an uncommon symptom in COVID-19 patients. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study cache = ./cache/cord-332292-n7k4va9k.txt txt = ./txt/cord-332292-n7k4va9k.txt === reduce.pl bib === id = cord-332469-zegawla5 author = Li, Wei title = The characteristics of household transmission of COVID-19 date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2513 sentences = 164 flesch = 64 summary = Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. cache = ./cache/cord-332469-zegawla5.txt txt = ./txt/cord-332469-zegawla5.txt === reduce.pl bib === id = cord-332278-2p64ab2z author = Vivas, David title = Recomendaciones sobre el tratamiento antitrombótico durante la pandemia COVID-19. Posicionamiento del Grupo de Trabajo de Trombosis Cardiovascular de la Sociedad Española de Cardiología date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3074 sentences = 166 flesch = 46 summary = Thus, even patients who are not infected with SARS-CoV-2 are being affected by the pandemic, which is having a strong influence on the optimization of antithrombotic therapy due to the current health care situation. Its aim is to summarize the available information and provide simple guidelines for the use of antithrombotic drugs in order to guarantee optimal care for patients infected by the SARS-CoV-2 virus. Patients with SARS-CoV-2 infection are at increased risk of thromboembolic events, especially VTE, which is associated with the critical situation and immobilization entailed by this disease. Figure 2 shows an algorithm for the treatment approach to patients with prior oral anticoagulation therapy admitted for COVID-19 infection, in which a change to parenteral anticoagulation is proposed (mainly due to the severe situation or to interactions with COVID-19 drugs). cache = ./cache/cord-332278-2p64ab2z.txt txt = ./txt/cord-332278-2p64ab2z.txt === reduce.pl bib === id = cord-332153-fczf3lzc author = Azkur, Ahmet Kursat title = Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19 date = 2020-05-12 pages = extension = .txt mime = text/plain words = 6181 sentences = 439 flesch = 50 summary = In this review, we aim to improve our understanding on the immune response and immunopathological changes in patients linked to detoriating clinical conditions such as, cytokine storm, acute respiratory distress syndrome, autopsy findings and changes in acute phase reactants and serum biochemistry in COVID‐19. The IgM, IgA and IgG type virus‐specific antibodies levels are important measurements to predict population immunity against this disease and whether cross‐reactivity with other coronaviruses is taking place.High viral‐load during the first infection and repeated exposure to virus especially in healthcare workers can be an important factor for severity of disease. It should be noted that many aspects of severe patients are unique to COVID‐19 and are rarely observed in other respiratory viral infections, such as severe lymphopenia and eosinopenia, extensive pneumonia and lung tissue damage, a cytokine storm leading to acute respiratory distress syndrome and multiorgan failure. cache = ./cache/cord-332153-fczf3lzc.txt txt = ./txt/cord-332153-fczf3lzc.txt === reduce.pl bib === id = cord-332276-gs80celr author = Tan, Yee‐Joo title = Regulation of cell death during infection by the severe acute respiratory syndrome coronavirus and other coronaviruses date = 2007-08-20 pages = extension = .txt mime = text/plain words = 5790 sentences = 272 flesch = 48 summary = In two independent studies, it was demonstrated that the inhibition of apoptosis, either by caspase inhibitors or by overexpression of the Bcl-2 protein, did not affect SARS-CoV replication in Vero cells (Ren et al., 2005; Bordi et al., 2006) , suggesting that apoptosis does not play a role in facilitating viral release. The mechanisms for induction of apoptosis by these SARS-CoV proteins are unclear, although in some cases, it could be related to their abilities to interfere with cellular functions, such as blocking cell cycle progression, altering membrane permeability, activating signal transduction pathways, upregulating transcription factors and other regulatory genes (Table 1 ). (2007) The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) gene 7 products contribute to virus-induced apoptosis. Over-expression of 7a, a protein specifically encoded by the severe acute respiratory syndrome (SARS) -coronavirus, induces apoptosis via a caspase-dependent pathway cache = ./cache/cord-332276-gs80celr.txt txt = ./txt/cord-332276-gs80celr.txt === reduce.pl bib === id = cord-332185-a96r1k7a author = Zhang, Shuyuan title = Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date = 2020-09-22 pages = extension = .txt mime = text/plain words = 1228 sentences = 103 flesch = 63 summary = title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. Cryo-electron microscopy structures of the SARS-CoV spike 464 glycoprotein reveal a prerequisite conformational state for receptor binding Cryo-EM structure of the SARS 467 coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Cryo-EM structures of MERS-CoV and SARS-CoV spike 495 glycoproteins reveal the dynamic receptor binding domains cache = ./cache/cord-332185-a96r1k7a.txt txt = ./txt/cord-332185-a96r1k7a.txt === reduce.pl bib === id = cord-332480-3uodkrkp author = Bonam, Srinivasa Reddy title = Adjunct immunotherapies for the management of severely ill COVID-19 patients date = 2020-04-30 pages = extension = .txt mime = text/plain words = 5440 sentences = 334 flesch = 43 summary = Current COVID-19 data clearly highlight that cytokine storm and activated immune cell migration to the lungs characterize the early immune response to COVID-19 that causes severe lung damage and development of acute respiratory distress syndrome. 13, 14, 16, 17 Of note, similar to severely ill COVID-19 cases, elevated serum levels of IL-6, TNF-α and IFN-γ have been consistently observed in cytokine release syndrome (CRS) that is common in the patients receiving T cell-engaging immunotherapies (bispecific antibody constructs or chimeric antigen receptor (CAR) T cell therapies). A randomized Phase 1b/2, double-blind, placebo-controlled clinical trial is currently recruiting patients to investigate the therapeutic efficacy of a humanized anti-GM-CSF IgG1 monoclonal antibody TJ003234 in severely ill COVID-19 patients (NCT04341116). 68 Similarly, treatment of ten severely ill COVID-19 patients with 200 mL of convalescent plasma containing viral neutralizing antibody titers more than 1:640 (A dilution of plasma that neutralized 100 TCID 50 (50% tissue-culture-infective dose) of SARS-CoV-2) led to reduced CRP levels, undetectable viremia and improved clinical symptoms. cache = ./cache/cord-332480-3uodkrkp.txt txt = ./txt/cord-332480-3uodkrkp.txt === reduce.pl bib === id = cord-332348-yi85sfks author = Liang, Yujie title = Neurosensory dysfunction: a diagnostic marker of early COVID-19 date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2748 sentences = 172 flesch = 56 summary = Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. cache = ./cache/cord-332348-yi85sfks.txt txt = ./txt/cord-332348-yi85sfks.txt === reduce.pl bib === id = cord-332448-5fz8ef4f author = Mutnal, M. B. title = Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2583 sentences = 159 flesch = 55 summary = Testing for SARS-CoV-2 was performed by real-time RT-PCR assay and results were shared with State public health officials for immediate interventions. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint of this study is to encourage other laboratories to consider an early start to testing during pandemics, share 74 initial trends in this part of the world and possible impact of SARS-CoV-2 on other seasonal respiratory 75 This report describes the early trends of SARS-CoV-2 infections in the central and north Texas, 76 USA and impact of epidemiological interventions that may have led to the decrease in the incidence of was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. BSWH laboratory provided test results data on both ambulatory and inpatient 275 population, and shared patient demographics with local public health officials. cache = ./cache/cord-332448-5fz8ef4f.txt txt = ./txt/cord-332448-5fz8ef4f.txt === reduce.pl bib === id = cord-332312-od3vjuw5 author = Pagani, G. title = Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA). date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1030 sentences = 73 flesch = 59 summary = In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. Results were reported in terms of 54 estimated probabilities of being positive to IgG test as a function of age, with respective 95% 55 confidence intervals. Estimates of probabilities of 64 being positive to IgG test, from a model including only age as independent variable, are reported in 65 susceptibility to the infection. In conclusion, our findings suggest that IgG seroprevalence for SARS-CoV-2 increases with 83 increasing age and these data suggest a lower susceptibility to infection in the lower age groups. cache = ./cache/cord-332312-od3vjuw5.txt txt = ./txt/cord-332312-od3vjuw5.txt === reduce.pl bib === id = cord-332303-0bbw64p5 author = Schuit, Michael title = Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date = 2020-06-11 pages = extension = .txt mime = text/plain words = 3598 sentences = 241 flesch = 54 summary = This study examined the effect of simulated sunlight, relative humidity, and suspension matrix on the stability of SARS-CoV-2 in aerosols. Therefore, the present study examined the influence of both simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in different liquid matrices. Two different environmentally controlled rotating drum aerosol chambers, with volumes of 16-L and 208-L, were used in the present study to expose aerosols containing SARS-CoV-2 to controlled levels of temperature, relative humidity, and simulated sunlight. The present study examined the influence of simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in either simulated saliva or culture medium at 20°C. The half-lives estimated from the mean decay constants across all relative humidity levels without simulated sunlight present were 55 and 86 minutes for aerosols generated from virus suspended in culture medium and simulated saliva, respectively. cache = ./cache/cord-332303-0bbw64p5.txt txt = ./txt/cord-332303-0bbw64p5.txt === reduce.pl bib === id = cord-332179-du1zjupf author = Sayed, Shomoita title = COVID-19 and Diabetes; possible role of polymorphism and rise of telemedicine date = 2020-08-31 pages = extension = .txt mime = text/plain words = 4009 sentences = 234 flesch = 48 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is facilitated by interaction with Angiotensin Converting Enzyme-2 (ACE2) and possible polymorphisms in ACE2 can be a determining factor in host-viral protein interaction. Another population study in England showed a 31.4% mortality rate for type 2 diabetes (T2D) patients suffering from COVID-19 infection [17] . So, increased viral entry via increased ACE2 expression and circulating proteases, lymphocytopenia and concurrent increase of inflammatory cytokines can exacerbate SARS-CoV-2 infection in patients with diabetes [23] . Diabetic patients on medication with abovementioned drugs with their elevated ACE2 expression can be susceptible to facilitated SARS-CoV-2 entry, leading to increased chances of disease severity. Whether the polymorphisms have more pronounced effects among diabetic patients with COVID-19 infection should be taken into consideration while exploring the possible role of viral entry in hosts. cache = ./cache/cord-332179-du1zjupf.txt txt = ./txt/cord-332179-du1zjupf.txt === reduce.pl bib === id = cord-332207-dmxbk7ad author = Sastry, Sangeeta R. title = Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1202 sentences = 78 flesch = 41 summary = title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence In 2 New York City (NYC) hospitals, 13.7% of asymptomatic pregnant women admitted for delivery tested positive for SARS-CoV-2 virus. 3 Universal screening of healthcare populations may prevent in-hospital transmission of SARS-CoV-2 virus. Upon developing real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) tests in-house with >98% sensitivity, as well as increasing the availability of PPE at our institution, we initiated universal screening of patients on hospital admission using nasopharyngeal swabs to identify and isolate asymptomatic positive patients to prevent in-hospital transmission of SARS-CoV-2. On April 27, 2020, our 1,000-bed academic center instituted universal SARS-CoV-2 testing of patients on hospital admission. Universal screening for the detection of SARS-CoV-2 at our institution revealed that during the study period, the number of asymptomatic persons admitted to the hospital was relatively small. cache = ./cache/cord-332207-dmxbk7ad.txt txt = ./txt/cord-332207-dmxbk7ad.txt === reduce.pl bib === id = cord-332300-5osg046o author = Yu, Luo title = Catching and killing of airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system date = 2020-07-07 pages = extension = .txt mime = text/plain words = 2756 sentences = 125 flesch = 55 summary = Traditional air-conditioner filters based on fiberglass or aluminum (Al) mesh are difficult to heat or have large pores (about 1 centimeter in size), so they cannot effectively catch and kill the virus contained in aerosols (generally smaller than 5 µm in size) [23] or other airborne highly infectious agents, such as anthrax spores. In order to realize a filter for preventing the spread of SARS-CoV-2 and anthrax spores, here we designed and fabricated a filter device consisting of folded pieces of Ni foam in multiple compartments connected electrically in series to efficiently increase the resistance to a manageable level so that a temperature up to 250 was able to be achieved, and found that the filter device exhibits almost 100% ability to catch and kill aerosolized SARS-CoV-2 and anthrax spores in air passed once through the Ni foam heated up to 200 (temperature optimization will be addressed in a future study). cache = ./cache/cord-332300-5osg046o.txt txt = ./txt/cord-332300-5osg046o.txt === reduce.pl bib === id = cord-332537-rtdu4jae author = Tong, Tommy R. title = Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date = 2005-05-01 pages = extension = .txt mime = text/plain words = 1162 sentences = 68 flesch = 48 summary = Airborne transmission of the severe acute respiratory syndrome (SARS) coronavirus (CoV) has been the favored explanation for its transmission on an aircraft [1] and appeared to explain a large community outbreak of SARS in the Amoy Gardens in Hong Kong [2] . in this issue of the Journal of Infectious Diseases [3] suggests that airborne dissemination of SARS-CoV may also occur in the health-care setting. However, if SARS-CoV is naturally airborne (produced by breathing and coughing), as was shown by Booth et al., then there is sufficient concern that it can be transmitted successfully by air. Acknowledgment of the fact that SARS-CoV can be aerosolized justifies the actions of those who have already committed resources for providing a safer environment in terms of preventing airborne transmission of infectious diseases and might provide the needed pressure for others to follow suit. Evidence of airborne transmission of the severe acute respiratory syndrome virus cache = ./cache/cord-332537-rtdu4jae.txt txt = ./txt/cord-332537-rtdu4jae.txt === reduce.pl bib === id = cord-332610-t99l3zii author = Mayer, J.D. title = Emerging Diseases: Overview date = 2008-08-26 pages = extension = .txt mime = text/plain words = 9596 sentences = 469 flesch = 52 summary = The potential for new diseases to emerge in the United States was there, and it took just a few years until this happened, catching the medical and public health communities by surprise. The issue at the time was whether legionnaires disease and toxic shock syndrome were anomalies, whether the assumption of the conquest of infectious diseases had clearly been erroneous, or whether these two outbreaks were harbingers of a new stage in 'epidemiologic history'a historical period during which emerging infections would become common and would catch the attention of the public, the public health community, the medical community, and government agencies. Severe acute respiratory syndrome (SARS) proved to be of great import in both the public awareness of emerging infectious diseases and in the testing and real-time construction of both domestic and international systems of public health surveillance and response. cache = ./cache/cord-332610-t99l3zii.txt txt = ./txt/cord-332610-t99l3zii.txt === reduce.pl bib === id = cord-332404-va3rxy5p author = Landeros, A. title = An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic date = 2020-08-06 pages = extension = .txt mime = text/plain words = 6144 sentences = 360 flesch = 54 summary = Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence. Given transmission of SARS-CoV-2 occurs through respiratory droplets, any reopening policy must adequately reduce crowded environments at school to protect children, teachers, staff, and ultimately communities. A recent study on the effects of school closure in March in the U.S. suggests that it reduced COVID-19 cases in states with low cumulative incidence [2] , yet education researchers worry that teachers will face lagging educational development of children once schools reopen due to the extended period of remote learning [11] . Our simulations with a single cohort indicate that a 5% percent threshold policy can shift infections in children from 80% to 55% over a 6 month period when child-to-child transmission rates in school are high ( Figure 3C ). cache = ./cache/cord-332404-va3rxy5p.txt txt = ./txt/cord-332404-va3rxy5p.txt === reduce.pl bib === id = cord-332458-2kwfcgz9 author = Ji, Henry title = Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus date = 2020-03-25 pages = extension = .txt mime = text/plain words = 1101 sentences = 58 flesch = 34 summary = title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. cache = ./cache/cord-332458-2kwfcgz9.txt txt = ./txt/cord-332458-2kwfcgz9.txt === reduce.pl bib === id = cord-332510-x3znuwc0 author = Freire-Álvarez, Eric title = COVID-19-associated encephalitis successfully treated with combination therapy date = 2020-11-01 pages = extension = .txt mime = text/plain words = 1901 sentences = 117 flesch = 38 summary = We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. Conclusion: This case report indicates that COVID-19 may present as an encephalitis syndrome mimicking acute demyelinating encephalomyelitis that could be amenable to therapeutic modulation. Despite most of the patients with altered mental in this cohort had a brain MRI performed, they did not observe any case of acute disseminated encephalomyelitis, an immune mediated disease that often occurs following viral infections [12] . The negative RT-PCR CSF results for SARS-CoV-2 along with the hyperinflammatory systemic response observed and the impressive findings in the MRI after therapy with immunoglobulins and tocilizumab suggest an acute disseminated encephalomyelitis. cache = ./cache/cord-332510-x3znuwc0.txt txt = ./txt/cord-332510-x3znuwc0.txt === reduce.pl bib === id = cord-332654-nav15g8k author = Paniri, Alireza title = Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations date = 2020-08-04 pages = extension = .txt mime = text/plain words = 5712 sentences = 341 flesch = 47 summary = The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy. Furthermore, growing body of evidence demonstrated that several factors including CYP450 single nucleotide polymorphisms (SNPs), and epigenetic molecules such as non-coding RNAs (ncRNAs), DNA methylation and histone acetylation influenced the expression levels of CYP450, and consequently might influence HCQ metabolism. The major purpose of this review is to discuss the pharmacokinetic and pharmacodynamic characteristics of CQ and HCQ that may be influenced by epigenetic mechanisms including ncRNAs and CYP2D6 SNPs, and thereby cause several side effects such as cardiotoxicity, prolonged QT interval, gastrointestinal problems (like dyspepsia and abdominal cramps), central nervous system or skin disorders, and especially retinopathy. cache = ./cache/cord-332654-nav15g8k.txt txt = ./txt/cord-332654-nav15g8k.txt === reduce.pl bib === id = cord-332457-gan10za0 author = de Ángel Solá, David E. title = Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 2867 sentences = 168 flesch = 39 summary = On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . cache = ./cache/cord-332457-gan10za0.txt txt = ./txt/cord-332457-gan10za0.txt === reduce.pl bib === id = cord-332592-bfqsyiyf author = Goette, Andreas title = COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation date = 2020-09-26 pages = extension = .txt mime = text/plain words = 3539 sentences = 261 flesch = 41 summary = title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation Coronavirus disease 2019 (COVID-19) is a viral disease induced by severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2), which may cause an acute respiratory distress syndrome (ARDS). Here, we can present a case of cytokine release syndrome induced by SARS-CoV-2 causing multiorgan failure and death. In summary, the present case shows that severe COVID-19 induces CRS associated with ARDS, acute kidney failure, liver pathologies, vascular intimal inflammation, pulmonary arterial, and venous thromboses and an inflammatory atrial cardiomyopathy. In the present case, we can show that COVID-19 can induce the occurrences of ARDS, which was associated with pulmonary embolism, as well as thrombogenesis, in pulmonary veins and the right atrial appendage. In addition to COVID-19-induced ARDS, CRS might be associated with pulmonary artery, as well as vein thromboses, atrial fibrillation, sinus node dysfunction, right atrial clot formation, and inflammatory invasion of autonomic atrial nerve ganglia. cache = ./cache/cord-332592-bfqsyiyf.txt txt = ./txt/cord-332592-bfqsyiyf.txt === reduce.pl bib === id = cord-332374-cbiw6yvb author = Israeli, Ofir title = Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1051 sentences = 77 flesch = 55 summary = Very recently, two studies [6] [7] used a direct no-buffer RT-qPCR approach which identified > 90% of the tested clinical samples. In this study, we tested the diagnostic efficiency following thermal inactivation (65°C for 30min and 95°C for 10min) without addition of lysis buffers ("no buffer") or following lysis by three buffers (Virotype, QuickExtract and 2% Triton-X-100) and compared it to diagnosis after standard RNA extraction. Samples included buffers spiked with SARS-CoV-2, at concentrations 0.1-100,000 PFU/ml and 30 clinical samples, previously diagnosed as positive (20) and negative (10). The limit of detection was 1 PFU/ml: In this concentration samples in the no buffer mode and Virotype at 95°C were not detected, while the RNA extraction mode averaged the lowest critical threshold ( Ct=29.8) followed by QuickExtract and Triton. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step cache = ./cache/cord-332374-cbiw6yvb.txt txt = ./txt/cord-332374-cbiw6yvb.txt === reduce.pl bib === id = cord-332723-rz1iilsv author = Creager, Hannah M. title = Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1474 sentences = 114 flesch = 60 summary = Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10-7 dilution. Ten-fold serial dilutions of a natural nasopharyngeal swab specimen with known high positivity for SARS-CoV-2 RNA (E gene detected at a cycle threshold (Ct) of 16.6 by the cobas SARS-CoV-2 assay) were prepared with a diluent of pooled NPS. Comparison of SARS-CoV-2 Detection from Nasopharyngeal Swab Samples by the Roche cobas(R) 6800 SARS-CoV-2 Test and a Laboratory-Developed Real-Time RT-PCR test cache = ./cache/cord-332723-rz1iilsv.txt txt = ./txt/cord-332723-rz1iilsv.txt === reduce.pl bib === id = cord-332820-6qx6svs5 author = Buck, M. D. title = Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay date = 2020-07-01 pages = extension = .txt mime = text/plain words = 4095 sentences = 252 flesch = 52 summary = The pipeline utilises a series of in-house buffers to first inactivate patient samples received from care homes and hospitals, and to then extract RNA before using a CE marked commercial kit to detect SARS-CoV-2 by RT-qPCR. Herein, we describe the use of loop mediated isothermal amplification PCR coupled with reverse transcription (RT-LAMP) as a robust method for SARS-CoV-2 detection in clinical specimens 6 . Our results demonstrate that within the CCC pipeline, RT-LAMP can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nosethroat swabs and endotracheal secretions/bronchoalveolar lavage fluid. The RT-LAMP assay reproducibility and precision were determined by extracting RNA 5 times from a confirmed COVID-19 positive patient sample through the CCC pipeline and assessing by N gene and 18S RT-LAMP in 5 independent experiments, performed by two different operators ( Figure 4D ). cache = ./cache/cord-332820-6qx6svs5.txt txt = ./txt/cord-332820-6qx6svs5.txt === reduce.pl bib === id = cord-332992-8rmqg4rf author = de Vries, A. A. F. title = SARS-CoV-2/COVID-19: a primer for cardiologists date = 2020-07-15 pages = extension = .txt mime = text/plain words = 9182 sentences = 433 flesch = 39 summary = Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . cache = ./cache/cord-332992-8rmqg4rf.txt txt = ./txt/cord-332992-8rmqg4rf.txt === reduce.pl bib === id = cord-332555-jfqlkd72 author = Du, Hengzhi title = The potential effects of DPP‐4 inhibitors on cardiovascular system in COVID‐19 patients date = 2020-07-26 pages = extension = .txt mime = text/plain words = 1411 sentences = 96 flesch = 41 summary = similar outer membrane spike glycoproteins among the coronavirus, it is possible that DPP-4 might also be a functional receptor of SARS-CoV-2. It has been reported that membrane-associated human DPP-4, as a functional MERS-CoV receptor, interacted with MERS-CoV through the spike glycoprotein S1b domain to facilitate the entry of MERS-CoV. Evidence from severely ill patients with COVID-19 suggested that the release of cytokines and chemokines was delayed in respiratory epithelial cells, dendritic cells (DCs) and macrophages at the early stage of SARS-CoV-2 infection. 17 Similar findings were also observed in SARS-CoV and MERS-CoV infected human airway epithelial cells, THP-1 cells, human peripheral blood monocyte-derived macrophages and DCs. 18 Although inflammation initially only damages limited organs, such as the lungs, an over-activated inflammatory response will spread all over the body rapidly, including the heart. Meanwhile, DPP-4 inhibitors could inhibit the over-activated inflammatory caused by SARS-CoV-2 and thus improve cardiovascular function. The potential effects of DPP-4 inhibitors on cardiovascular system in COVID-19 patients cache = ./cache/cord-332555-jfqlkd72.txt txt = ./txt/cord-332555-jfqlkd72.txt === reduce.pl bib === id = cord-332962-8y3t0r2d author = Xu, Xi title = Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 date = 2020-02-28 pages = extension = .txt mime = text/plain words = 2439 sentences = 145 flesch = 50 summary = We aimed to report the imaging and clinical characteristics of these patients infected with SARS-CoV-2 in Guangzhou, China. CONCLUSION: SARS-CoV-2 infection can be confirmed based on the patient's history, clinical manifestations, imaging characteristics, and laboratory tests. Image analysis, focused on the lesion features of each patient, included (a) distribution characteristics, (b) number of lobes involved, (c) lobe of lesion distribution, (d) Fig. 1 A 49-year-old man with history of recent travel to Wuhan presented with fever and cough for 6 days. Our study showed some common CT imaging features in patients affected by SARS-CoV-2 pneumonia: bilateral, multifocal ground glass opacities, with peripheral distribution. In our study, few patients initially negative for SARS-CoV-2 nucleic acid test had bilateral ground glass opacities in chest CT scans. In a patient with a history of close contact with a SARS-CoV-2-infected patient, early manifestation of bilateral, multifocal, and peripheral ground glass opacities on a chest CT scan might be a sign of a 2019 novel coronavirus infection. cache = ./cache/cord-332962-8y3t0r2d.txt txt = ./txt/cord-332962-8y3t0r2d.txt === reduce.pl bib === id = cord-332522-adul9nzf author = Wu, Qingfa title = Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date = 2004-04-02 pages = extension = .txt mime = text/plain words = 2810 sentences = 143 flesch = 62 summary = In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. To compare the sensitivities of these 12 sets of nested primers, serial 10-fold di-lution genome cDNA of BJ01 that reverse transcribed with random primer was used as the template to carry out the nested PCR. cache = ./cache/cord-332522-adul9nzf.txt txt = ./txt/cord-332522-adul9nzf.txt === reduce.pl bib === id = cord-332778-rf47ptj6 author = Vivarelli, Silvia title = Cancer Management during COVID-19 Pandemic: Is Immune Checkpoint Inhibitors-Based Immunotherapy Harmful or Beneficial? date = 2020-08-10 pages = extension = .txt mime = text/plain words = 7447 sentences = 374 flesch = 44 summary = It was demonstrated that cancer patients have an increased risk of developing a worse symptomatology upon severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV-2) infection, often leading to hospitalization and intensive care. Given their immune-compromised status, cancer patients infected by SARS-CoV-2 might be at a higher risk of developing severe and critical consequences upon COVID-19, including ARDS, septic shock and acute myocardial infarction [29] [30] [31] . Nevertheless, cancer patients, when infected by SARS-CoV-2 might develop more severe outcomes, if anti-cancer treatments induce a weakening of the host immune health [38] . Since the beginning of this pandemic, nine independent clinical studies have been published about the risks possibly related to SARS-CoV-2 infection in patients with cancer. In line with this concept, three additional independent clinical studies are currently enrolling non-cancer COVID-19 patients to test the efficacy of administering ICIs to reshape the impaired immune system of SARS-CoV-2 infected individuals (i.e., NCT04268537; NCT04356508 and NCT04413838). cache = ./cache/cord-332778-rf47ptj6.txt txt = ./txt/cord-332778-rf47ptj6.txt === reduce.pl bib === id = cord-332970-atwz3rgf author = Gentile, Pietro title = Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease date = 2020-05-09 pages = extension = .txt mime = text/plain words = 2635 sentences = 133 flesch = 52 summary = title: Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease A recent and interesting study reported improved respiratory activity after intravenous administration of mesenchymal stem cells (MSCs) into patients affected by coronavirus disease 2019 (COVID-19). The MSCs could represent an effective, autologous and safe therapy, and therefore, sharing these published results, here is reported the potential use possibilities in COVID-19 of the most common MSCs represented by Adipose Stem Cells (ASCs). Robert Chunhua Zhao's group [1] reported in a recent study, published in March 2020, an interesting improvement in pulmonary functional activity, into 7 patients affected by Coronavirus Disease 2019 (COVID-19) after a intravenous administration of clinical-grade mesenchymal stem cells (MSCs). In the preliminary study of Robert Chunhua Zhao's group [1] , 7 patients affected by SARS-CoV-2, with COVID-19 pneumonia displayed a sensible improvement pulmonary function after several intravenous infusion of clinicalgrade MSCs [1] . cache = ./cache/cord-332970-atwz3rgf.txt txt = ./txt/cord-332970-atwz3rgf.txt === reduce.pl bib === id = cord-333041-69n2wwn3 author = Pal, Anandita title = Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4394 sentences = 227 flesch = 43 summary = Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Obesity is an independent risk factor for increased morbidity and mortality upon infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic. The SPM precursor 17-hydroxydocosahexaenoic acid (17-HDHA) increased antibody levels and improved survival upon pH1N1 influenza vaccination and infection in lean mice by promoting B cell differentiation toward the formation of CD138 + long-lived antibody secreting cells (18) . Taken together, these data suggest that the susceptibility of obese individuals to environmental lung diseases may drive an altered pulmonary immune response and a state of SPM deficiency that increases the morbidity and mortality to respiratory infections, including COVID-19. cache = ./cache/cord-333041-69n2wwn3.txt txt = ./txt/cord-333041-69n2wwn3.txt === reduce.pl bib === id = cord-332557-qm3qfvry author = Lau, Susanna K.P. title = SARS Coronavirus Detection Methods date = 2005-07-17 pages = extension = .txt mime = text/plain words = 1388 sentences = 67 flesch = 54 summary = Using clinical samples from patients with severe acute respiratory syndrome, we showed that the sensitivities of a quantitative reverse transcription–polymerase chain reaction (80% for fecal samples and 25% for urine samples) were higher than those of the polyclonal (50% and 5%) and monoclonal (35% and 8%) antibody-based nucleocapsid antigen capture enzyme-linked immunosorbent assays. Specimens were tested with polyclonal and monoclonal antibody-based capture ELISAs for SARS-CoV nucleocapsid protein and realtime qRT-PCR. Among the 40 fecal samples from SARS patients, 32 (80%) were positive by qRT-PCR, which was significantly higher than that of the polyclonal (50%) and monoclonal (35%) antibody-based ELISAs (McNemar test, p<0.005 and p<0.001, respectively). Of the 133 urine samples from SARS patients, 33 (25%) were positive by qRT-PCR, which was also significantly higher than that of the polyclonal (5%) and monoclonal (8%) antibody-based ELISAs (McNemar test, p<0.001 for both comparisons). cache = ./cache/cord-332557-qm3qfvry.txt txt = ./txt/cord-332557-qm3qfvry.txt === reduce.pl bib === id = cord-332595-874tpi09 author = Salehi, Najmeh title = Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients date = 2020-09-08 pages = extension = .txt mime = text/plain words = 1800 sentences = 111 flesch = 61 summary = To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). On the other hand, nineteen sequences of the full genome sequence of SARS-CoV-2 on the GISAID database from patients in different countries that had a travel history to Iran or contacts with Iranian cases were retrieved from the database. In this study, the full genome sequences of SARS-CoV-2 from the 20 Iranian related COVID-19 patients were profiled in detail. B. The nucleotide and protein mutations, the number of mutation events in data from the 20 Iranian related patients, the entropy values of these mutations in all 3927 SARS-CoV-2 sequences, and the corresponded proteins are depicted. cache = ./cache/cord-332595-874tpi09.txt txt = ./txt/cord-332595-874tpi09.txt === reduce.pl bib === id = cord-332539-v1bfm57x author = Gohl, Daryl M. title = A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 5048 sentences = 246 flesch = 55 summary = Several variants of the ARTIC protocol exist in which the pooled SARS-CoV-2 amplicons from a sample are taken through a NGS library preparation protocol (using either ligation or tagmentation-based approaches) in which sample-specific barcodes are added, and are then sequenced using either short-read (Illumina) or long-read (Oxford Nanopore, PacBio) technologies. We sequenced these samples using Illumina's Nextera DNA Flex Enrichment protocol using a respiratory virus oligo panel containing probes for SARS-CoV-2, the ARTIC v3 tiled primers, and a novel tailed amplicon method designed to reduce cost and streamline the preparation of SARS-CoV-2 sequencing libraries. For the Illumina DNA Flex Enrichment protocol, SARS-CoV-2 genome coverage was more complete for samples with lower N1 and N2 Cts (ranging from ~20-30) at comparable read depths and coverage thresholds than with amplicon approaches, similar to the BEI WA isolate data ( Figure 3C , Supplemental Figure S2 -S3). cache = ./cache/cord-332539-v1bfm57x.txt txt = ./txt/cord-332539-v1bfm57x.txt === reduce.pl bib === id = cord-332948-h297ukuu author = Olotu, Fisayo A. title = Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date = 2020-10-16 pages = extension = .txt mime = text/plain words = 5176 sentences = 315 flesch = 51 summary = authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. 30 Identification of other functional (allosteric) sites on the prefusion S protein could present another dynamic and effective approach of preventing SARS-CoV-2 infectivity relative to its interaction with the host cell ACE2 and proteases. 53 Relatively, this study was implemented to (i) identify potential druggable sites across the S1 and S2 domains of the SARS-CoV-2 S protein other than the RBD-hACE2 interface (ii) perform high-throughput (virtual) screening of ~1500 FDA approved drugs against the most druggable site(s) (iii) investigate the binding dynamics and interaction mechanisms of the compounds and their consequential effects on the S-protein RBD-ACE2 complex. We believe this systematic study will be able to provide structural and molecular insights into possible allosteric sites on SARS-CoV-2 S protein suitable for selective targeting and structureComputational methodologies cache = ./cache/cord-332948-h297ukuu.txt txt = ./txt/cord-332948-h297ukuu.txt === reduce.pl bib === id = cord-332672-fbwz8oxp author = Wang, Manli title = Bats as animal reservoirs for the SARS coronavirus: Hypothesis proved after 10 years of virus hunting date = 2013-10-30 pages = extension = .txt mime = text/plain words = 1114 sentences = 51 flesch = 61 summary = It was suggested that the previously known bat SL-CoV stains cannot jump from bats to civets or humans owing to the significant differences between their RBDs (Li F, 2013); 2) although SL-CoVs have been identified from different bat species, isolation of a live SL-CoVs from bats never succeed; 3) no native SL-CoV from bats could use ACE2 as receptors and infect human cells, only when its RBD is replaced with the counterpart from a human SARS-CoV strain (Li W, et al, 2003; Becker M M, et al, 2008; Ren W, et al, 2008) . The residue 479 is known to be an asparagine only in human SAR-CoVs, but not in the previously identified bat SL-CoVs or civet SAR-CoVs. It is proposed that an asparagine at position 479 has a higher binding affinity with human ACE2 and is likely to determine whether the virus can infect humans (Li F, 2013) . cache = ./cache/cord-332672-fbwz8oxp.txt txt = ./txt/cord-332672-fbwz8oxp.txt === reduce.pl bib === id = cord-333121-kt6t41ff author = Kwenandar, Felix title = Coronavirus Disease 2019 and Cardiovascular System: A Narrative Review date = 2020-06-03 pages = extension = .txt mime = text/plain words = 1923 sentences = 123 flesch = 39 summary = At the end of 2019, a viral pneumonia disease called coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2), emerged in Wuhan, China. Although this infective disease is mostly characterized by respiratory tract symptoms, increasing numbers of evidence had shown considerable amounts of patients with cardiovascular involvements and these were associated with higher mortality among COVID-19 patients. Cardiovascular manifestation in COVID-19 patients include myocardial injury (MI), arrhythmias, cardiac arrests, heart failure and coagulation abnormality, ranging from 7.2% up to 33%. [2] With the increasing number of confirmed cases and the accumulating clinical data, in addition to the common clinical presentation of respiratory failure caused by COVID-19, the cardiovascular manifestations induced by this viral infection has generated considerable concern. Although the exact pathophysiological mechanism underlying myocardial injury caused by COVID-19 is not fully understood, a previous report showed that in 35% of the patients infected, the SARS-CoV genome was positively detected in the heart. cache = ./cache/cord-333121-kt6t41ff.txt txt = ./txt/cord-333121-kt6t41ff.txt === reduce.pl bib === id = cord-332716-1d89j7jh author = Choi, Marcelo title = El SRAA y el SARS-CoV-2: el acertijo a resolver date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3334 sentences = 366 flesch = 59 summary = Uno de los temas que ha generado debate se vincula con la asociación entre la terapia antihipertensiva con inhibidores del sistema renina-angiotensina-aldosterona (SRAA) y la infección por el virus SARS-CoV-2. Para ingresar a las células el coronavirus interactúa, utilizando como receptor, con la ECA2 y serina-proteasas transmembrana de tipo II (TMPRSS2) ubicadas en la superficie celular del huésped (7) . Los estudios clínicos llevados a cabo hasta el día de hoy no han demostrado que existen diferencias entre ambos tratamientos en términos de aumento del riesgo de infección por SARS-CoV-2 o de desarrollo de resultados graves en pacientes con COVID-19 (27) (28) (29) (30) (31) . Si bien existe evidencia in vitro de que el SARS-CoV-2 se une a los receptores ECA2 y que éstos se encuentran aumentados en presencia de IECA o ARA-II, no hay evidencia al momento de que la exposición a estos fármacos facilite la entrada del coronavirus ni que produzcan un mayor riesgo de COVID-19. cache = ./cache/cord-332716-1d89j7jh.txt txt = ./txt/cord-332716-1d89j7jh.txt === reduce.pl bib === id = cord-332827-gll4nqdd author = Peixe, Paula title = Hepatology in the COVID Era: Another C Virus, again Challenging the Liver date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3989 sentences = 221 flesch = 52 summary = In published series, liver disease was not identified as a risk factor for SARS-Cov2 infection [11] [12] [13] [14] [15] . The authors state that NAFLD patients also had a higher risk of progression to severe COVID-19 and present an increased viral clearance time. Immune-mediated liver diseases, particularly autoimmune hepatitis, have not been mentioned as risk factors for COVID-19, but the immunosuppressive treatment required has triggered fears about the risk of infection in patients. Extensive records and targeted studies are needed to explore multiple open-ended questions such as the severity and mortality of COVID-19 and episodes of acute-on-chronic or decompensation associated with the presence of this disease (ascites, hepatic encephalopathy, digestive bleeding, kidney dysfunction, and the risk of infection) or the response to treatment [25, 26] . However, it is not yet possible to say whether transplantation-associated immunosuppression can alter the predisposition for the acquisition of SARS-Cov2 infection or how COVID-19 evolves in these patients. cache = ./cache/cord-332827-gll4nqdd.txt txt = ./txt/cord-332827-gll4nqdd.txt === reduce.pl bib === id = cord-333176-6v7ficfk author = Snell, Jonathan title = SARS-CoV-2 infection and its association with thrombosis and ischemic stroke: A review COVID-19, thrombosis, and ischemic stroke date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2059 sentences = 122 flesch = 45 summary = SARS-CoV-2 infection is well-documented to cause severe pneumonia, however, thrombosis and thrombotic complications, such as ischemic stroke, have also been documented in a variety of patient demographics. 5,6 This is likely due to the presence of asymptomatic or mildly symptomatic transmission of SARS-CoV-2, and its current prevalence in the human population supports the infective potential of this novel coronavirus. 37 Imbalance of the interactions between ACE2 and the RAS axis may also contribute to the thromboembolic events seen in SARS-CoV-2 infection. 44, 45 Ischemic stroke due to occlusion of large arteries has been a documented complication of SARS-CoV infection in patients with minimal to no risk factors. 46 SARS-CoV-2 infection seems to also increase risk of developing ischemic stroke, among other neurological consequences. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: A report of five cases Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Ischemic Stroke cache = ./cache/cord-333176-6v7ficfk.txt txt = ./txt/cord-333176-6v7ficfk.txt === reduce.pl bib === id = cord-333174-g10kvc0c author = Ahmed, Sinthyia title = Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 6773 sentences = 394 flesch = 54 summary = title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro. In this study, we employ drug repurposing approach to identify potential candidates which can bind and interact with RdRp and Mpro proteins of SARS-CoV-2. cache = ./cache/cord-333174-g10kvc0c.txt txt = ./txt/cord-333174-g10kvc0c.txt === reduce.pl bib === id = cord-333018-2h8y118z author = Sun, Xingxing title = Safety Considerations for Neuraxial Anaesthesia in Parturients with COVID-19 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 649 sentences = 43 flesch = 42 summary = To decide the mode of anaesthesia for parturients with COVID-19, one should evaluate neurological symptoms in addition to respiratory symptoms. Angiotensin-converting enzyme 2 (ACE2) is the functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); 7 it is expressed in the cell membrane of various tissues and organs including lung, small intestine, and brain. When deciding on anaesthetic strategy for patients with COVID-19, we think that one should consider the possible deleterious effects on the nervous system by neuraxial anaesthesia. For patients with apparent central or peripheral nervous system symptoms, although direct evidence is still lacking, general anaesthesia might be an acceptable alternative. However, general anaesthesia can impair the blood-brain barrier 10 , which might facilitate the invasion of SARS-CoV-2 into the central nervous system. Emergency Caesarean delivery in a patient with confirmed coronavirus disease 2019 under spinal anaesthesia cache = ./cache/cord-333018-2h8y118z.txt txt = ./txt/cord-333018-2h8y118z.txt === reduce.pl bib === id = cord-333144-gyuh2fvl author = Siddiqui, Arif Jamal title = Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 7806 sentences = 436 flesch = 50 summary = Therefore, this review focuses on the current use of various drugs as single agents (hydroxychloroquine, ivermectin, azithromycin, favipiravir, remdesivir, umifenovir, teicoplanin, nitazoxanide, doxycycline, and dexamethasone) or in combinations with immunomodulators additionally. While some drugs have shown therapeutic effect against COVID-19 infection such as hydroxychloroquine (Al-Kofahi et al., 2020; Choudhary & Sharma 2020; Liu et al., 2020; Sinha & Balayla 2020) , azithromycin, (Andreani et al., 2020a; Choudhary & Sharma 2020) ivermectin (Caly et al., 2020; Chaccour et al., 2020; Choudhary & Sharma 2020) and some other antivirals (Asai et al., 2020; Boopathi et al., 2020; Lian et al., 2020) . Consequently, this review will provide an insight and comprehensive view on different therapeutic approaches including combining of different known anti-parasitic drugs, as well as proposing novel suggestions of chemoprophylaxis drug therapy, which can be used in the current treatment and vaccine development strategies against COVID-19 disease. cache = ./cache/cord-333144-gyuh2fvl.txt txt = ./txt/cord-333144-gyuh2fvl.txt === reduce.pl bib === id = cord-333042-icgsbelo author = Fisher, Kiva A. title = Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities — United States, July 2020 date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3405 sentences = 186 flesch = 49 summary = Restricting the analysis to participants without known close contact with a person with confirmed COVID-19, case-patients were more likely to report dining at a restaurant (aOR = 2.8, 95% CI = 1.9-4.3) or going to a bar/coffee shop (aOR = 3.9, 95% CI = 1.5-10.1) than were control-participants. For each reported activity, participants were asked to quantify degree of adherence to recommendations such as wearing a face mask of any kind or social distancing among other persons at that location, with response options ranging from "none" to "almost all." Descriptive and statistical analyses were performed to compare case-patients with control-participants, assessing differences in demographic characteristics, community exposures, and close contact. In addition to dining at a restaurant, case-patients were more likely to report going to a bar/coffee shop, but only when the analysis was restricted to participants without close contact with persons with known COVID-19 before illness onset. cache = ./cache/cord-333042-icgsbelo.txt txt = ./txt/cord-333042-icgsbelo.txt === reduce.pl bib === id = cord-333092-78vo7i6v author = Taksande, Amar title = Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age date = 2020-08-11 pages = extension = .txt mime = text/plain words = 475 sentences = 35 flesch = 56 summary = title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age The authors studied the SARS-CoV-2 infection in infants under 1 year of age in Wuhan City, China. [2] reported that the prevalence of malnutrition in elderly patients with coronavirus disease 2019 (COVID-19) was high, and nutritional support should be strengthened during treatment. Have the authors used any cardiac biomarkers, such as troponin-T or echocardiography (tissue Doppler imaging), to assess myocardial function in the infants? The authors found that 61.11% of infants have bilateral pneumonia and that 41.67% have received antibiotics treatment. This means that procalcitonin is a better indicator of inflammation than CRP in infants with SARS-CoV-2 infection. To my knowledge, this is the best study of the SARS-CoV-2 infection in infants under 1 year of age carried out by the author. SARS-CoV-2 infection in infants under 1 year of age in Wuhan City cache = ./cache/cord-333092-78vo7i6v.txt txt = ./txt/cord-333092-78vo7i6v.txt === reduce.pl bib === id = cord-332832-kjppd6uz author = Ward, B. J. title = Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants date = 2020-11-06 pages = extension = .txt mime = text/plain words = 7024 sentences = 466 flesch = 58 summary = (ClinicalTrials.gov number NCT04450004) Methods: The study was a randomized, partially-blinded, prime-boost 21 days apart, dose-escalation Phase 1 study intended to assess the safety, tolerability, and immunogenicity of CoVLP at three dose levels (3.75 microgram, 7.5 microgram, and 15 microgram) unadjuvanted or adjuvanted with either CpG 1018 or AS03 in 180 SARS-CoV-2 seronegative healthy adults 18 to 55 years of age. We report here the results of a Phase 1 study initiated in July 2020 evaluating the safety, 203 tolerability and immunogenicity of two doses, 21-days apart of 3.75, 7.5 or 15 µg of a virus-204 like-particle vaccine candidate for Covid-19 produced in plants (hereafter called CoVLP). ; https://doi.org/10.1101/2020.11.04.20226282 doi: medRxiv preprint Like any early-phase clinical trial, this study has several limitations beyond the obvious 459 concern regarding small group size when testing multiple dose levels and formulations 460 (n=20/group). cache = ./cache/cord-332832-kjppd6uz.txt txt = ./txt/cord-332832-kjppd6uz.txt === reduce.pl bib === id = cord-333140-cdikbi1l author = Zhao, Helong title = Imatinib is not a potent anti-SARS-CoV-2 drug date = 2020-09-30 pages = extension = .txt mime = text/plain words = 913 sentences = 52 flesch = 43 summary = We tested the effects of imatinib and asciminib, a highly specific and potent ABL inhibitor binding to the myristate pocket of the kinase domain [7] , on SARS-CoV-2 infection and replication in the naturally susceptible ACE2 + human Caco-2 cells [5] . We then performed the standard viral replication assay using the USA-WA1/2020 strain of SARS-CoV-2 to test imatinib and asciminib in a blinded fashion, including remdesivir as a positive control. Therefore, our data indicate that, within clinically achievable dose ranges, imatinib and asciminib have no significant effect on SARS-CoV-2 infection and replication. These data support additional prospective investigations into the potential beneficial effect of imatinib and possibly other ABL inhibitors on COVID-19, but provide insufficient evidence for the off-label use of imatinib in patients with COVID-19. Prevalence of COVID-19 diagnosis in Dutch CML patients during the 2020 SARS-CoV2 pandemic. Imatinib is not a potent anti-SARS-CoV-2 drug cache = ./cache/cord-333140-cdikbi1l.txt txt = ./txt/cord-333140-cdikbi1l.txt === reduce.pl bib === id = cord-333465-cha7ndv5 author = Horspool, A. M. title = Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date = 2020-08-31 pages = extension = .txt mime = text/plain words = 4309 sentences = 286 flesch = 52 summary = Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations. We evaluated anti-193 SARS-CoV-2 antibody production to 3 antigens (RBD, N, and S1) in 82 in-patients 194 Table 1 ) by developing a novel rapid-ELISA technique. Our survey of SARS-CoV-2 positive patients demonstrated that antibody (IgG) 198 production to RBD, N, and S1 proteins developed over the first 10 to 20 days post-199 symptom onset (Figure 1a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. To accurately assess 223 differences in antibody production independently of disease outcome, we quantified anti-224 SARS-CoV-2 IgG production in patients who survived infection grouped by biological sex, 225 . . https://doi.org/10.1101/2020.08.24.20180877 doi: medRxiv preprint significantly increased in patients that did not survive SARS-CoV-2 infection compared to 272 those that did (Figure 4d ). cache = ./cache/cord-333465-cha7ndv5.txt txt = ./txt/cord-333465-cha7ndv5.txt === reduce.pl bib === id = cord-333264-jdvb8px4 author = Hanke, Leo title = An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date = 2020-09-04 pages = extension = .txt mime = text/plain words = 6380 sentences = 380 flesch = 51 summary = Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. The S ectodomain was purified from filtered supernatant on Streptactin XT resin (IBA Lifesciences), followed by size-exclusion chromatography on a Superdex 200 in 5 mM Tris pH 8, 200 mM NaCl. The RBD domain (RVQ-VNF) of SARS-CoV-2 was cloned upstream of an enterokinase cleavage site and a human IgG1 Fc. This plasmid was used to transiently transfect FreeStyle 293F cells using the FreeStyle MAX reagent. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 cache = ./cache/cord-333264-jdvb8px4.txt txt = ./txt/cord-333264-jdvb8px4.txt === reduce.pl bib === id = cord-333089-ufyzqgqk author = Aguilar-Pineda, Jorge Alberto title = Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date = 2020-07-29 pages = extension = .txt mime = text/plain words = 6957 sentences = 359 flesch = 51 summary = Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. cache = ./cache/cord-333089-ufyzqgqk.txt txt = ./txt/cord-333089-ufyzqgqk.txt === reduce.pl bib === id = cord-333453-v3gap8kj author = Dima, Mirabela title = First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3020 sentences = 173 flesch = 52 summary = The novel coronavirus officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Virus generated a pandemic, which erupted in Hubei, Wuhan, China and quickly spread throughout the world, [1, 2] has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. The clinic where the patient was born discharged her and the mother on April 6, 2020 both being negative for SARS-CoV-2 (RT-PCR test). On April 15, after 3 days of observing cough, lethargy, loss of appetite, jaundice, and constant fever, the mother presented in emergency room with the newborn, both being tested positive for SARS-CoV-2. [10] We believe it is important in the current epidemiologic context to mention that all 3 patients were discharged from the clinic where they were born with SARS-CoV-2 negative tests (RT-PCR), which were taken in conformity with our national protocol regarding COVID-19. cache = ./cache/cord-333453-v3gap8kj.txt txt = ./txt/cord-333453-v3gap8kj.txt === reduce.pl bib === id = cord-333320-ndmmbckb author = Samore, M. title = SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample date = 2020-10-27 pages = extension = .txt mime = text/plain words = 7433 sentences = 403 flesch = 53 summary = Probability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah. Although seroprevalence has been touted as a more standardized way to estimate the incidence of SaRS-COV-2 infection across different populations, it also presents challenges because of inconsistencies in test performance and sampling methods. Using a statistical sampling frame and adjusting for test performance and non-response, we estimated the prevalence of IgG antibody to SARS-CoV-2 in four urban counties in Utah between May and June to be only 0.8%. We used a serological test that is reported by the manufacturer to have a specificity at 99.6%; however, even at this level of accuracy, statistically accounting for false positives is necessary given the low population prevalence of IgG antibody to SARS-CoV-2. cache = ./cache/cord-333320-ndmmbckb.txt txt = ./txt/cord-333320-ndmmbckb.txt === reduce.pl bib === id = cord-333195-m4gvpsf8 author = Lu, Renfei title = Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date = 2020-04-01 pages = extension = .txt mime = text/plain words = 1894 sentences = 102 flesch = 54 summary = title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Here, we present a novel visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid and sensitive detection of SARS-CoV-2 using mismatch-tolerant technique. The RdRp primers showed higher amplification efficiency, and were selected to establish the SARS-CoV-2 detection assay using the mismatch-tolerant RT-LAMP method Zhou et al. For the POCT diagnosis of SARS-CoV-2 infection in the resource-poor settings, we developed the assay into a visual detection using WarmStart Colorimetric LAMP 2 9 Master Mix (New England Biolabs, Beverly, MA, United States). The sensitivity of the colorimetric RT-LAMP assay for SARS-CoV-2 was 30 copies per reaction, slightly lower than the real-time monitoring (Fig. 1E) . The evaluation with 24 clinical samples showed that all 17 COVID-19 patients in Nantong city were positive for SARS-CoV-2 by both the RT-LAMP and the RT-qPCR assays, showing a full consistence. cache = ./cache/cord-333195-m4gvpsf8.txt txt = ./txt/cord-333195-m4gvpsf8.txt === reduce.pl bib === id = cord-333239-nj5dma98 author = Ducrest, P. J. title = Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2 date = 2020-10-13 pages = extension = .txt mime = text/plain words = 1771 sentences = 121 flesch = 63 summary = Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). The aim of this study is to develop and evaluate the performance of a new IgM/IgG rapid diagnostic test (RDT) based on lateral flow assay (LFA) technology, in a high COVID-19 prevalence setting using gold standard RT-PCR as well as an Electro-chemiluminescence immunoassay (ECLIA) Elecsys® Anti-SARS-CoV-2 total Ig (Roche, Switzerland). The key finding of the present evaluation study, using an unmatched case-control design including 73.5% of negative control samples, is that the diagnostic accuracy of IgG/IgM RDT on plasma samples when compared to RT-PCR or ECLIA is the same and displayed a SE of 100%, a SP of 93% and a NPV of 100%. cache = ./cache/cord-333239-nj5dma98.txt txt = ./txt/cord-333239-nj5dma98.txt === reduce.pl bib === id = cord-333080-qytwbsne author = Alahari, Suresh K. title = SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2244 sentences = 123 flesch = 49 summary = Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. Developing functional computational models and networks to predict potential SARS-CoV -miRNA/lncRNA association may benefit not only the understanding of COVID-19 mechanism at the noncoding RNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis, and prevention. Since multiple ways of interaction between miRNAs, lncRNAs, and mRNA have been reported to play key roles in determining the cellular functions during viral infection, it is essential to discover these interactions in an integrated fashion to comprehensively decipher the networks and key regulatory noncoding-RNA hubs underpinning the pathology of SARS-CoV. Our in-silico analysis has built a network of protein-protein interaction between the Human SARS coronavirus (SARS-CoV) and host proteome (Figure 1) , as well as strong miRNA-mRNA-lncRNA crosstalk ( Figure 4 and Table 2 ) possibly modulating the human response to the viral infection. cache = ./cache/cord-333080-qytwbsne.txt txt = ./txt/cord-333080-qytwbsne.txt === reduce.pl bib === id = cord-333234-yvixy77x author = Triposkiadis, Filippos title = Renin-angiotensin-system inhibition in the context of corona virus disease-19: experimental evidence, observational studies, and clinical implications date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3226 sentences = 153 flesch = 46 summary = While the potential for benefit with the use of renin-angiotensin-aldosterone system inhibitors (RAASi) and the risks from stopping them is more evident, potential harm by RAΑSi may also be caused by the increase in the activity of the ACE2 receptor, the inefficient counter regulatory axis in the lungs in which the proinflammatory prolyloligopeptidase (POP) is the main enzyme responsible for the conversion of deleterious angiotensin (ANG) II to protective ANG [1–7] and the proinflammatory properties of ACE2(+) cells infected with SARS-CoV-2. In a recent statement of the European Medicinal Agencies (EMA), it is emphasized (10 June 2020 EMA/284513/2020): "Recent observational studies of angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs, also called sartans) have not shown an effect of these medicines on the risk of becoming infected with severe acute respiratory syndrome coronavirus 2 (the virus causing COVID-19) and do not indicate a negative impact on the outcome for patients with COVID-19 disease. cache = ./cache/cord-333234-yvixy77x.txt txt = ./txt/cord-333234-yvixy77x.txt === reduce.pl bib === id = cord-333200-yka7wfbi author = Dhampalwar, Swapnil title = Treatment armamentarium of COVID-19: Evolving strategies & evidence so far date = 2020-07-16 pages = extension = .txt mime = text/plain words = 1253 sentences = 82 flesch = 48 summary = Keeping up with this current pace of information, we review the clinical studies of different therapeutic options available to treat SARS-CoV-2. (20) Since, these studies with CQ & HCQ have different therapeutic regimens, heterogenous study population, unequal arms to compare, ill-defined outcomes, and non-reproducible results; further randomized trials are needed before recommending the routine use of HCQ in mild COVID-19. Since Favipiravir and Lopinavir-ritonavir did not provide significant benefits in viral clearance or clinical improvement in severe disease, further randomized trials are necessary before recommending these drugs in clinical practice. A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an openlabel non-randomized clinical trial No Evidence of Rapid Antiviral Clearance or Clinical Benefit with the Combination of Hydroxychloroquine and Azithromycin in Patients with Severe COVID-19 Infection cache = ./cache/cord-333200-yka7wfbi.txt txt = ./txt/cord-333200-yka7wfbi.txt === reduce.pl bib === id = cord-333429-bq7kfpby author = Shi, Ding title = Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3513 sentences = 251 flesch = 57 summary = title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. cache = ./cache/cord-333429-bq7kfpby.txt txt = ./txt/cord-333429-bq7kfpby.txt === reduce.pl bib === id = cord-332680-zfn81hew author = Chan, Chieh-Kai title = Renin-Angiotensin-Aldosterone System Inhibitors and Risks of Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Systematic Review and Meta-Analysis date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4301 sentences = 204 flesch = 45 summary = The following variables were extracted: author, journal, publication year, study design, geographic location, participants' details (number, study population, age, sex, and comorbidities, including hypertension, diabetes mellitus, heart failure, and chronic kidney disease), use of antihypertensive drugs, such as ACE inhibitors, ARBs, calcium-channel blockers, beta-blockers, diuretics, outcomes (including positive SARS-CoV-2 test results and disease prognosis/severity, if available). The systematic review findings of the 7 high-quality studies (with comparative data on the controls) on SARS-COV-2 infection provide the best available evidence proving that therapy with ACE inhibitors or ARBs is not associated with an increase of positive SARS-CoV-2 test result and the severity of COVID-19 disease or overall population mortality as a whole in case-population and cohort studies. ACE indicates angiotensin-converting enzyme; ARBs, angiotensin receptor blockers; BMI, body mass index; CKD, chronic kidney disease; DM, diabetes mellitus; HTN, hypertension; ICU, intensive care unit; N/A, not applicable; OHA, oral hypoglycemic agents; RAASi, renin-angiotensin-aldosterone system inhibitors; and SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. cache = ./cache/cord-332680-zfn81hew.txt txt = ./txt/cord-332680-zfn81hew.txt === reduce.pl bib === id = cord-333381-wz70o9tt author = Liu, Shao title = Providing pharmacy services during the coronavirus pandemic date = 2020-03-28 pages = extension = .txt mime = text/plain words = 3195 sentences = 154 flesch = 40 summary = Chinese pharmacists have acted swiftly in the public health response in China, such as drafting professional service guidance to pharmacists and pharmacies, establishing emergency drug formularies, monitoring and resolving drug shortages, establishing remote pharmacy services to prevent human-to-human infections, providing event-driven pharmaceutical care, educating the public on infection prevention and disease management, and participating in clinical trials and drug evaluation. Specifically, pharmacy needs to work with other healthcare organizations, professionals, and government agencies to address the following seven service needs: (1) drafting professional service guidances to pharmacists and pharmacies, (2) establishing emergency drug formularies based on treatment guidelines, (3) coordinating with drug companies and distributors to ensure adequate supply, storage and transport of identified formulary drugs, (4) providing event-driven pharmaceutical care, (5) establishing remote pharmacy services to reduce the incidence of human-to-human infections, (6) educating the public with a focus on infection prevention and disease management, and (7) involving in clinical trial research to screen, evaluate and develop antiviral medications in line with national and international guidelines [4] . cache = ./cache/cord-333381-wz70o9tt.txt txt = ./txt/cord-333381-wz70o9tt.txt === reduce.pl bib === id = cord-333487-zem2d4y6 author = Thomaz Ugliara Barone, Mark title = The Impact of COVID-19 on People with Diabetes in Brazil date = 2020-07-03 pages = extension = .txt mime = text/plain words = 4658 sentences = 216 flesch = 47 summary = Methods In a convenience sampling study, data were collected from 1701 individuals, aged 18 or above; 75.54% female participants; 60.73% T1D and 30.75% T2D, between April 22nd and May 4th, using an anonymous and untraceable survey containing 20 multiple choice questions (socio-demographic; health status and habits of life during COVID-19 pandemic). Conclusions This study provides a firsthand revelation of the severity of COVID-19 on individuals with diabetes in Brazil, altering their habits, which impacted their glycemia, potentially increasing their risk of poor outcomes if infected by SARS-CoV-2. This also harmed adjustments to continue the proper follow-up and management of other diseases, including both communicable and NCDs. For these reasons, the present study aims to investigate challenges encountered by people living with diabetes in Brazil during the COVID-19 pandemic. cache = ./cache/cord-333487-zem2d4y6.txt txt = ./txt/cord-333487-zem2d4y6.txt === reduce.pl bib === id = cord-333099-hy4nmy7l author = Thoms, Matthias title = Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3441 sentences = 219 flesch = 53 summary = Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. To elucidate the molecular interaction of SARS-CoV-2 Nsp1 with human ribosomes, we reconstituted a complex from purified, recombinant Nsp1 and purified human 40S ribosomal subunits and determined its structure by cryo-EM at an average resolution of 2.6 Å (Fig. 2, A and B , and figs. To characterize the ribosomal targets and the mode of interaction of Nsp1 in human cells, we expressed N-terminally 3xFLAG tagged Nsp1 in HEK293T cells and affinity purified associated native complexes for analysis by cryo-EM and mass spectrometry (Fig. 2E , figs. The second major population of Nsp1-bound 80S ribosomes (Fig. 2 , M and N) lacked CCDC124, but contained the cell growth regulating nucleolar protein LYAR, which has been implicated in processing of pre-rRNA and in negative regulation of antiviral innate immune responses (34, 35) . cache = ./cache/cord-333099-hy4nmy7l.txt txt = ./txt/cord-333099-hy4nmy7l.txt === reduce.pl bib === id = cord-333368-kjrk8nn9 author = Huizinga, Gabrielle P title = The Collision of Meta-Inflammation and SARS-CoV-2 Pandemic Infection date = 2020-09-03 pages = extension = .txt mime = text/plain words = 5490 sentences = 347 flesch = 47 summary = While obesity and diabetes may complicate the delivery of supportive care in critical illness regardless of the underlying disease, lessons learned from the interaction of obesity with other systemic inflammatory syndromes suggest that obesity modifies biologic factors related to SARS-CoV-2 infection and the COVID-19 syndrome. In seasonal and pandemic influenza, however, obese individuals may be more susceptible to severe viral respiratory disease even if they mount a serologic response to vaccination 25 A c c e p t e d M a n u s c r i p t 11 Along with possible impairments in pathogen clearance, obese hosts are more likely to experience the breakdown of respiratory epithelium during a pulmonary infection, which leads to increased fluid in the airway space. cache = ./cache/cord-333368-kjrk8nn9.txt txt = ./txt/cord-333368-kjrk8nn9.txt === reduce.pl bib === id = cord-333524-a6p6ma8r author = Khan, Pavana title = Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date = 2020-09-23 pages = extension = .txt mime = text/plain words = 8841 sentences = 603 flesch = 50 summary = 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). cache = ./cache/cord-333524-a6p6ma8r.txt txt = ./txt/cord-333524-a6p6ma8r.txt === reduce.pl bib === id = cord-333326-n9ifhw5s author = Wardell, Hanna title = Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Febrile Neonates date = 2020-07-09 pages = extension = .txt mime = text/plain words = 2919 sentences = 173 flesch = 44 summary = Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in pediatric patients are mild or asymptomatic. We report a case series of 4 full-term neonates hospitalized with fever and found to have SARS-CoV-2 infection with a spectrum of illness severities. Herein we present a case series of 4 full-term neonates who were hospitalized with fever and found to be infected with SARS-CoV-2. Due to the concern for end-organ involvement with possibly evolving acute myocardial injury as well as a supplemental oxygen requirement, the patient was initiated on therapy with remdesivir on inpatient day 4 via an expanded-access program from the manufacturer after approval from the US Food and Drug Administration and local institutional review board, with informed consent. In this report, we present 4 febrile neonates hospitalized with SARS-CoV-2 infection with favorable outcomes. SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress cache = ./cache/cord-333326-n9ifhw5s.txt txt = ./txt/cord-333326-n9ifhw5s.txt === reduce.pl bib === id = cord-333515-llqpfhwg author = Zhao, Juanjuan title = Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date = 2020-03-03 pages = extension = .txt mime = text/plain words = 3575 sentences = 230 flesch = 56 summary = Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. To mitigate this knowledge gap, and to provide scientific analysis on the benefit of antibody testing when used in combination with the current RNA testing, this study investigates the dynamics of total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 in serial blood samples collected from 173 confirmed COVID-19 patients and provides discussion on the clinical value of antibody testing. A total of 535 plasma samples collected during the hospitalization period of the 173 patients were tested for antibodies against SARS-CoV-2. In addition to the diagnosis value of Ab test, our study revealed a strong positive correlation between clinical severity and antibody titer since 2-week after illness onset, for the first time in COVID-19 patients. cache = ./cache/cord-333515-llqpfhwg.txt txt = ./txt/cord-333515-llqpfhwg.txt === reduce.pl bib === id = cord-333520-v2sb90rc author = Gardin, Chiara title = Could Mesenchymal Stem Cell-Derived Exosomes Be a Therapeutic Option for Critically Ill COVID-19 Patients? date = 2020-08-26 pages = extension = .txt mime = text/plain words = 10154 sentences = 466 flesch = 36 summary = Exosomes derived from mesenchymal stem cells (MSCs) are being explored for the management of a number of diseases that currently have limited or no therapeutic options, thanks to their anti-inflammatory, immunomodulatory, and pro-angiogenic properties. Next, we describe some of the most significant clinical evidence of the successful use of MSC-derived exosomes in animal models of lung and heart injuries, which might strengthen our hypothesis in terms of their utility for also treating critically ill COVID-19 patients. Recently, MSC-derived exosomes have been demonstrated to have comparable and even greater effects than cells themselves in improving inflammation and injury in a variety of pre-clinical lung disease models, including ALI/ARDS (Table 1) . From the studies discussed above, it emerged that the rationale for using MSC-derived exosomes, MVs, or EVs in ALI/ARDS is based on several processes, many of which are shared with those identified in the parent MSCs. These include immunomodulation and anti-inflammatory properties on host tissue, reduction of the permeability of alveolar epithelium and endothelium, improvement of alveolar fluid clearance, enhancement of macrophage phagocytosis, and tissue repair through direct mitochondrial transfer with host cells (Figure 2 ). cache = ./cache/cord-333520-v2sb90rc.txt txt = ./txt/cord-333520-v2sb90rc.txt === reduce.pl bib === id = cord-333606-5z3kumu9 author = Lee, SangJoon title = Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1178 sentences = 69 flesch = 44 summary = title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. Despite these limitations, significant work has been done to molecularly characterize the innate immune pathways involved in detecting and controlling CoV infections. patients with severe or critical COVID-19 also found that reduced amounts of type I IFNs in the blood during SARS-CoV-2 infection were associated with increased viral load in the blood, and exacerbation of the inflammatory response [38] . Pyroptosis and necroptosis are similar in that they are lytic forms of cell death driven by the GSDMD pore and MLKL channel, respectively, that release proinflammatory cytokines and other cellular factors to alert the surrounding cells of danger and to recruit innate and adaptive inflammatory cells [54, 55].  Specific CoV infections can activate inflammatory cell death (PANoptosis), thereby inducing cytokine release. cache = ./cache/cord-333606-5z3kumu9.txt txt = ./txt/cord-333606-5z3kumu9.txt === reduce.pl bib === id = cord-333262-xvfl7ycj author = Robson, B. title = COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date = 2020-04-11 pages = extension = .txt mime = text/plain words = 21671 sentences = 953 flesch = 50 summary = The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). cache = ./cache/cord-333262-xvfl7ycj.txt txt = ./txt/cord-333262-xvfl7ycj.txt === reduce.pl bib === id = cord-333391-6l0cpvgr author = Bortolotti, Daria title = SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5689 sentences = 309 flesch = 57 summary = title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. cache = ./cache/cord-333391-6l0cpvgr.txt txt = ./txt/cord-333391-6l0cpvgr.txt === reduce.pl bib === id = cord-333670-qv1orlv5 author = Mutti, Luciano title = Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 2500 sentences = 123 flesch = 40 summary = In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . cache = ./cache/cord-333670-qv1orlv5.txt txt = ./txt/cord-333670-qv1orlv5.txt === reduce.pl bib === id = cord-333498-d25qfq0f author = Chitranshi, Nitin title = Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL(pro) targeting repurposed drug candidates date = 2020-07-09 pages = extension = .txt mime = text/plain words = 5999 sentences = 378 flesch = 51 summary = Recent release of the high-resolution crystal structure for the main proteinase 3CL pro (Protein Data Bank, PDB ID: 6Y2G), describing an additional amide bond with the α-ketoamide inhibitor pyridone ring to enhance the half-life of the compound in plasma [16] is suggested to accelerate the targeted drug discovery efforts. Since the initial stages of the SARS-CoV-2 outbreak, laboratories and hospitals around the world have sequenced viral genome data with unprecedented speed, enabling real-time understanding of this novel disease process, which will hopefully contribute to the development of novel candidate drugs. In contrast, our docking studies revealed that bilobetin, predicted almost comparable binding energy with that of amentaflavone (− 8.29 kcal/mol) suggesting that mutation in SARS-CoV-2 3CL pro could potentially disrupt hydrogen bonding or induce some conformational change that could result in alterations in the binding site thus affecting inhibitor interactions with the enzyme active site residues. cache = ./cache/cord-333498-d25qfq0f.txt txt = ./txt/cord-333498-d25qfq0f.txt === reduce.pl bib === id = cord-333420-qqyg9um9 author = Zhu, Xun title = idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date = 2020-10-09 pages = extension = .txt mime = text/plain words = 460 sentences = 35 flesch = 58 summary = title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. The on-going Coronavirus disease 2019 (Covid-19) pandemic has resulted in over 734,000 deaths, affect-20 ing more than 188 countries and territories (CSSE, 2020; Dong, et al., 2020) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV) 23 is the pathogenic cause of Covid-19 (Lescure, et al., 2020) . In order to quickly identify the clade of an isolate of SARS-Cov-2 given its sequencing FastQ files, 30 we have developed a bioinformatics pipeline and a user-friendly web interface. cache = ./cache/cord-333420-qqyg9um9.txt txt = ./txt/cord-333420-qqyg9um9.txt === reduce.pl bib === id = cord-333713-nz36i2oa author = Andonegui-Elguera, Sergio title = Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1729 sentences = 88 flesch = 37 summary = Results Alterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, NK cells, T CD4+ cell and macrophages. Conclusions In summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. Therefore, in the present work we carried out comprehensive and stringent transcriptomic metanalysis of SARS-CoV-2 infected bronchoalveolar cells and peripheral blood mononuclear cells to unveil the molecular alterations caused by viral infection as well as deconvolution analysis to identify the immune cell profiles in COVID-19 patients. Using molecular deconvolution analysis, we identified the presence of neutrophils, NK cells, T CD4+ lymphocytes and macrophages infiltrating the lungs of COVID-19 patients, consistently our findings with the previously reported (14) . cache = ./cache/cord-333713-nz36i2oa.txt txt = ./txt/cord-333713-nz36i2oa.txt === reduce.pl bib === id = cord-333703-1ku3jc9s author = Kraus, Aurora title = A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date = 2020-11-08 pages = extension = .txt mime = text/plain words = 8452 sentences = 605 flesch = 57 summary = Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. In mice and humans, ace2 expression is detected in 121 sustentacular cells, olfactory stem cells known as horizontal and globose basal cells in the 122 olfactory epithelium, and vascular cells (pericytes) in the olfactory bulb (Brann et al., 2020 The present study reports for the first time that zebrafish larvae exposed to SARS-CoV-2 appear 134 to mount innate immune responses that resemble cytokine responses of mild COVID-19 patients. There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 cache = ./cache/cord-333703-1ku3jc9s.txt txt = ./txt/cord-333703-1ku3jc9s.txt === reduce.pl bib === id = cord-333929-oprpgcyr author = Lee, Justin title = Impact of Severe Acute Respiratory Syndrome on Patient Access to Palliative Radiation Therapy date = 2005-01-31 pages = extension = .txt mime = text/plain words = 2326 sentences = 130 flesch = 56 summary = Abstract This study evaluated the impact of the severe acute respiratory syndrome (SARS) epidemic on access and utilization of palliative radiation therapy (RT) at a single institution using a retrospective chart review. 2, 3 Recent studies have demonstrated the negative impact of the SARS epidemic on access to health care services such as emergency room visits, cardiac surgery, lumpectomy/mastectomy, and chemotherapy procedures. The primary objective of the study was to identify any significant change in the number of patients seen and/or treated by the Rapid Response Radiotherapy Program (RRRP) at our center. A retrospective chart review was used to evaluate all patients who attended the RRRP at the Toronto Sunnybrook Regional Cancer Centre between January 1 and May 31, 2002, and the same time period in 2003. There was a significant decrease in the waiting times of patients seen during the SARS epidemic compared with the previous year ( Table 3 ). cache = ./cache/cord-333929-oprpgcyr.txt txt = ./txt/cord-333929-oprpgcyr.txt === reduce.pl bib === id = cord-333532-vrfduv5a author = Patel, Kishan Pravin title = COVID-19 Patients: Are Current Isolation Guidelines Effective Enough? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 862 sentences = 49 flesch = 48 summary = We believe the current isolation guidelines need to be revisited and clinicians should counsel COVID-19 patients to practice contact precautions for longer durations given new evidence suggesting the possibility of a fecaloral route of transmission. Furthermore, a recent case reported an asymptomatic COVID-19 patient who retested positive for SARS-CoV-2 despite being discharged after two negative consecutive respiratory nucleic acid tests at least 24 hours apart, raising concern for inadequate discharge protocol. With consideration of its high virulence, high infectivity, and the concern for a fecal-oral route of transmission, we suggest modifying guidelines to extend isolation and/or contact precautions in the best interest of patients, healthcare workers, and the global community as a whole. Key words: COVID 19; SARS CoV-2; Gastrointestinal; Isolation; Fecal-oral; transmission; precautions cache = ./cache/cord-333532-vrfduv5a.txt txt = ./txt/cord-333532-vrfduv5a.txt === reduce.pl bib === id = cord-333696-3ci9re9a author = Alomari, Safwan O. title = COVID-19 and the Central Nervous System date = 2020-08-04 pages = extension = .txt mime = text/plain words = 4407 sentences = 266 flesch = 46 summary = Li and colleagues (2020) have suggested that SARS-CoV-2 can enter the brain, and it might be the cause of the respiratory failure in patients with COVID-19 [25] . Recently, Olds & Kabbani (2020) raised the question of nicotine associated neurological comorbidity in COVID19 patients depending on published evidence that the viral target receptor J o u r n a l P r e -p r o o f ACE2 is expressed in the brain and functionally interacts with nAChRs [29, 30] . This was the first reported case of MERS associated with coronavirus infection, which adds to the expanding list of differential diagnoses to be considered in a COVID-19 patient with neurological signs, most notably; cerebellar ataxia and disturbance in consciousness [49, 52, 53] . Laboratory work-up was negative for influenza, with the diagnosis of COVID-19 made by detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) PCR. cache = ./cache/cord-333696-3ci9re9a.txt txt = ./txt/cord-333696-3ci9re9a.txt === reduce.pl bib === id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4920 sentences = 297 flesch = 35 summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial cache = ./cache/cord-333730-qsx0m68e.txt txt = ./txt/cord-333730-qsx0m68e.txt === reduce.pl bib === id = cord-333712-sdtxi8xw author = Yu, Ping title = Geographical structure of bat SARS-related coronaviruses date = 2019-02-06 pages = extension = .txt mime = text/plain words = 3662 sentences = 163 flesch = 53 summary = In 2005, the discovery of novel CoVs related to human SARS-CoVs in Chinese horseshoe bats (genus Rhinolophus), named SARS-related coronaviruses (SARSr-CoVs), provided new clue that bats may be the natural host for SARS-CoV (Lau et al., 2005; Li et al., 2005) . SARS-CoV and SARSr-CoVs belong to lineage B of genus Betacoronavirus in the family Coronaviridae and share the same genomic organization with other coronaviruses, including genes coding for 16 nonstructural proteins (nsp, in ORF1ab domain), the structural proteins like spike protein (S), envelope (E), membrane (M), nucleocapsid (N) and other several genes (Perlman and Netland, 2009; Woo et al., 2009) . Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China cache = ./cache/cord-333712-sdtxi8xw.txt txt = ./txt/cord-333712-sdtxi8xw.txt === reduce.pl bib === id = cord-333654-8rg99di5 author = Pillai, Presaad title = COVID-19 AND MAJOR ORGAN THROMBOEMBOLISM: MANIFESTATIONS IN NEUROVASCULAR AND CARDIOVASCULAR SYSTEMS. date = 2020-10-24 pages = extension = .txt mime = text/plain words = 4128 sentences = 210 flesch = 39 summary = The disease, caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2), has to date been responsible for more than 800,000 deaths globally, economic upheaval and significant lifestyle changes. 5, 6, 7 However, more recently immune mediated thrombosis has been a consistent finding in a significant number of patients with of Covid-19 and understanding its pathophysiological mechanisms and impact on morbidity and mortality in COVID-19 may open new avenues in disease prognostication and management. Thus, D-dimer level could potentially be an early and helpful marker to improve the management of COVID-19 and point clinicians to the possibility of silent thrombosis occurring in the pre-symptomatic stage which might dictate the natural history, progression and severity of the disease in a manner that has not been seen in previous coronavirus infections. Other significant risk factors, excluding raised D-dimer and CRP, that were associated with a high mortality rate for these patients with NVD, were comorbidities, age and increased severity of COVID-19 infection. cache = ./cache/cord-333654-8rg99di5.txt txt = ./txt/cord-333654-8rg99di5.txt === reduce.pl bib === id = cord-333682-ktbnrkwh author = Dong, Yunzhu title = Antibodies in the breast milk of a maternal woman with COVID-19 date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1332 sentences = 82 flesch = 58 summary = A maternal woman was positive for SARS-CoV-2 tested in throat swabs but negative tested in other body fluids, and she had IgG and IgA detected in breast milk. Although clinical and laboratory characteristics, and outcomes of pregnant women with COVID-19 have been reported [4], there are no continuously monitored data about the viral loads in several body fluids of the maternal women that would bring potential risks of SARS-CoV-2 infection to neonates [8] . The titers of IgG antibody in breast milk were 2.34, 3.02, 2.84, 2.79, and 3.35, respectively, when three SARS-CoV-2 negative maternal woman's breast milk were tested as control (mean titer 0.98) (Figure 1, panel D) . (D) Titers of IgG antibody to SARS-CoV-2 in maternal woman's breast milk determined using ELISA. cache = ./cache/cord-333682-ktbnrkwh.txt txt = ./txt/cord-333682-ktbnrkwh.txt === reduce.pl bib === id = cord-333763-45dzsn2j author = Bestle, Dorothea title = TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells date = 2020-07-23 pages = extension = .txt mime = text/plain words = 8969 sentences = 441 flesch = 49 summary = The data demonstrate that efficient inhibition of S cleavage by a combination of TMPRSS2 and furin inhibitors can dramatically block SARS-CoV-2 replication in human airway epithelial cells. In conclusion, our data demonstrate that both TMPRSS2 and furin cleave the SARS-CoV-2 S protein and are essential for efficient virus multicycle replication in Calu-3 human airway cells. Virus titers in supernatants were determined by TCID 50 multicycle replication of SARS-CoV-2 in Calu-3 human airway cells is strongly suppressed by inhibiting TMPRSS2 and furin activity, demonstrating that both proteases are crucial for S activation in these cells. Together, our data indicate that furin and TMPRSS2 cleave S at different sites and that cleavage by both proteases is crucial to render the S protein active for mediating virus entry and membrane fusion (Fig 6) . cache = ./cache/cord-333763-45dzsn2j.txt txt = ./txt/cord-333763-45dzsn2j.txt === reduce.pl bib === id = cord-333632-i2bjap7m author = Senthil Kumar, K. J. title = Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3864 sentences = 227 flesch = 49 summary = title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells The results suggest that geranium and lemon essential oils and their derivative compounds are valuable natural anti-viral agents that may contribute to the prevention of the invasion of SARS-CoV-2/COVID-19 into the human body. To the best of our knowledge, this is the first report indicating that geranium and lemon essential oils and their major components citronellol, geraniol, limonene, linalool, and neryl acetate downregulate ACE2 receptor activity in virus-host epithelial cells. In this study, we presented the first piece of evidence that geranium and lemon essential oils and their major compounds, citronellol, geraniol, limonene, linalool, and neryl acetate, could downregulate ACE2 expression in epithelial cells, thereby blocking virus entry into host cells, and eventually preventing viral infection. cache = ./cache/cord-333632-i2bjap7m.txt txt = ./txt/cord-333632-i2bjap7m.txt === reduce.pl bib === id = cord-333909-uco4c946 author = Murray, Meghan T. title = Mitigating a COVID-19 Outbreak Among Major League Baseball Players — United States, 2020 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 2988 sentences = 149 flesch = 52 summary = Certain MLB health and safety protocols, which include frequent diagnostic testing for rapid case identification, isolation of persons with positive test results, quarantine for close contacts, mask wearing, and social distancing, might have limited COVID-19 transmission between teams. The health and safety protocols established tiered, risk-based testing for MLB teams, which called for persons who received a positive SARS-CoV-2 test result to be placed in isolation and for close contacts to be quarantined separately. Before game play on day 4, the index team A player (an asymptomatic tier 1 risk group member who received every other day testing, per protocol) received a positive SARS-CoV-2 real-time reverse transcription-polymerase chain reaction (RT-PCR) test result from collection on day 2. Investigators received from MLB a deidentified line list of team members with diagnosed COVID-19, a timeline of the outbreak response, the duration of on-field play by potentially infectious persons (within 24 hours before the date of collection of the test-positive specimen), contact tracing procedures, and the MLB health and safety protocols. cache = ./cache/cord-333909-uco4c946.txt txt = ./txt/cord-333909-uco4c946.txt === reduce.pl bib === id = cord-333688-bykbyojs author = Wang, Junxue title = Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report date = 2020-08-21 pages = extension = .txt mime = text/plain words = 2618 sentences = 146 flesch = 49 summary = RATIONALE: Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. We report the case of a patient with mild symptoms of coronavirus disease (COVID-19), who achieved clinical recovery but showed persistently positive SARS-CoV-2 nucleic acid test results until Day 92 after disease onset. The third scenario is that the COVID-19-related symptoms have disappeared and the patient has entered the convalescent phase, but SARS-CoV-2 nucleic acid test results are positive for a long period of time. [4] In this study, we report the case of a patient with COVID-19 who achieved clinical recovery but showed persistently positive results on the SARS-CoV-2 nucleic acid test for up to 92 days after disease onset. Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. cache = ./cache/cord-333688-bykbyojs.txt txt = ./txt/cord-333688-bykbyojs.txt === reduce.pl bib === id = cord-333547-88dkh6xd author = Hasan, Shadi W. title = Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3980 sentences = 220 flesch = 54 summary = Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. A limited number of studies have shown that the shedding period of SARS-CoV-2 in stool samples varies considerably, and can still be detected up to 27.9 ± 10.7 days after infection in some cases [9, 11] . Consequently, the main objectives of this study were: (i) to detect the presence of SARS-CoV-2 virus in municipal (untreated) wastewater and treated effluents of wastewater treatment plants (WWTPs) in the UAE; (ii) to quantify the viral concentration in viral gene copies per liter; and (iii) to explore whether these measurements mirror infections in the population in order to comment on the utility of this method to track the epidemiology of the disease. cache = ./cache/cord-333547-88dkh6xd.txt txt = ./txt/cord-333547-88dkh6xd.txt === reduce.pl bib === id = cord-333863-mtljy3s6 author = Hong, Nan title = Evaluation of ocular symptoms and tropism of SARS‐CoV‐2 in patients confirmed with COVID‐19 date = 2020-04-26 pages = extension = .txt mime = text/plain words = 4033 sentences = 232 flesch = 53 summary = Patients with COVID-19 may show prodromal symptom of conjunctivitis in cases where eye goggles were not worn while in close proximity with COVID-19 positive patients, leading to suggestions that ocular exposure might be a potential route of SARS-CoV-2 infection (Lu et al. Previously hospitalized patients (admission date from 19 January to 29 February 2020) in the isolation ward of the First Affiliated Hospital of Zhejiang University, diagnosed as COVID-19 positive based on their clinical symptoms and positive SARS-CoV-2 test results of their sputum swab specimens, were the target subject population. After the onset of COVID-19, the mean scores of the SEEQ and OSDI questionnaires were significantly raised, suggesting a degraded ocular surface condition (Table 2) . In our study, fifteen subjects (27%) reported new onset ocular irritation symptoms or aggravated pre-existing ocular surface irritation symptoms after infection of SARS-CoV-2. cache = ./cache/cord-333863-mtljy3s6.txt txt = ./txt/cord-333863-mtljy3s6.txt === reduce.pl bib === id = cord-334049-r3rlykli author = Lobo-Galo, Naún title = FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication date = 2020-05-14 pages = extension = .txt mime = text/plain words = 4132 sentences = 199 flesch = 48 summary = Our inclusion criteria for the selection of drugs for potential COVID-19 therapy were: (1) The drug is a FDA-approved that can potentially be repurposed as an ready-to-use therapeutic antiviral; (2) Its use has been extensively studied, and there is sufficient literature on its pharmacology; (3) The drug has few side effects in long-term administration, with not known direct fatalities associated to it, and not additional extensive toxicological studies are needed; (4) Drug can interact with active site of SARS-CoV-2 main protease and reacts with thiol group of its catalytic cysteine, producing an irreversible covalent-inhibition; (5) Administered drug shows efficient distribution through multiple organs, as recent publications suggest the possibility that SARS-CoV-2 has tropism for multiple tissues, beyond the pneumocytes, including heart and blood vessels, liver, intestine, neural cortex and brain stem (Wadman et al., 2020); (6) Drug penetrates the cell membrane, as its antiviral target, the protease acts early during replication in the host cytoplasm; and (7) When administered, drug is metabolized and excreted slowly; and possible metabolites have also potential inhibitory activity. cache = ./cache/cord-334049-r3rlykli.txt txt = ./txt/cord-334049-r3rlykli.txt === reduce.pl bib === id = cord-333738-3xtb8gye author = Rabets, A. title = Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients date = 2020-08-22 pages = extension = .txt mime = text/plain words = 2486 sentences = 146 flesch = 49 summary = Investigating patient serum samples after SARS-CoV-2 infection in cross-reactivity studies of immunogenic peptides from Middle East respiratory syndrome coronavirus (MERS-CoV), we were able to detect the production of antibodies also recognizing MERS virus antigens. Indeed, the peptide of the HR2 domain of the MERS spike protein, previously proven to induce antibodies against MERS-CoV is sharing 74% homology with the corresponding sequence of SARS-CoV-19 virus. If used as an antigen, the peptide of the HR2 domain of the MERS spike protein allows discrimination between post-Covid populations from non-infected ones by the presence of antibodies in blood samples. The high homology of the spike protein domain suggests in addition that the opposite effect can also be true: coronaviral infections producing cross-reactive antibodies affective against SARS-CoV-19. SARS-CoV-2 infections results in the generation of antibodies with significantly strong cross-reactive towards a MERS specific peptide with 76% homology. Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein cache = ./cache/cord-333738-3xtb8gye.txt txt = ./txt/cord-333738-3xtb8gye.txt === reduce.pl bib === id = cord-333754-copxoyqu author = Ma, Hsin-Chieh title = Expression and membrane integration of SARS-CoV M protein date = 2008-04-09 pages = extension = .txt mime = text/plain words = 3930 sentences = 191 flesch = 60 summary = Full-length SARS-CoV M gene fragment was cloned and expressed as a recombinant protein (221 a.a.) with a C-terminal V5-His tag (29 a.a.) in Vero E6 cells (Fig. 1a) . In addition to the glycosylated and un-glycosylated SARS-CoV M proteins, two smaller protein products (marked by thick line and thin line, respectively) were also detected when M gene was expressed in Vero E6 cells ( Fig. 1a and b) . The protein translated in-frame from the third Met (amino acid 83) could still be detected when the authentic 5 0 -untranslated region of SARS-CoV M gene was included in the expression vector (lane 3 in supplement Fig. 2 ). In this study, SARS-CoV M gene fragment was cloned and expressed as a recombinant protein fused with a C-terminal V5 tag in Vero E6 cells (Fig. 1) . Two other expressed SARS-CoV M protein products with smaller size than the full-length one were also detected in Vero E6 cells (Figs. cache = ./cache/cord-333754-copxoyqu.txt txt = ./txt/cord-333754-copxoyqu.txt === reduce.pl bib === id = cord-333805-xmqs2ax7 author = Romoli, Michele title = A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4025 sentences = 257 flesch = 44 summary = BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. This study therefore aimed to identify clinical cases of confirmed nervous system invasion or postinfectious neurological disease in the available COVID-19 literature on the basis of a systematic review. A systematic review was carried out to study all cases reporting nervous system involvement in patients with proven SARS-CoV2 infection. There were just 2 cases with positive SARS-CoV-2 PCR in CSF among 27 patients with potential neurologic symptoms and proven COVID-19. In this regard, we see a clear need for the use of precise case definitions and focused diagnostic work-up to distinguish nonspecific complications of severe disease and focused reporting of neurological involvement in association with SARS-CoV-2 infection. cache = ./cache/cord-333805-xmqs2ax7.txt txt = ./txt/cord-333805-xmqs2ax7.txt === reduce.pl bib === id = cord-333868-qrnsmhws author = Rothman, Richard E. title = Respiratory Hygiene in the Emergency Department date = 2006-08-23 pages = extension = .txt mime = text/plain words = 7437 sentences = 362 flesch = 35 summary = These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection. cache = ./cache/cord-333868-qrnsmhws.txt txt = ./txt/cord-333868-qrnsmhws.txt === reduce.pl bib === id = cord-333999-k92fmnq7 author = Yang, Chih-Jen title = Remdesivir Use in the Coronavirus Disease 2019 Pandemic: A Mini-Review date = 2020-10-05 pages = extension = .txt mime = text/plain words = 2581 sentences = 158 flesch = 47 summary = In this mini-review, we summarize the current evidence on the efficacy and challenges of remdesivir for the treatment of coronavirus disease 2019 (COVID-19). J o u r n a l P r e -p r o o f Based on several clinical trials and reports on its compassionate use, remdesivir is considered by many to be the most promising drug for the treatment of COVID-19 [44] [45] [46] . First, to evaluate the efficacy and safety of remdesivir in patients with COVID-19, a randomized, placebo-controlled, double-blind, multicenter, phase 3 clinical trial was launched on February 5, 2020, in China 30, 60 . Clinically, common adverse drug reactions (ADRs) noted during the compassionate use of remdesivir in patients with COVID-19 reported by Grein et al. cache = ./cache/cord-333999-k92fmnq7.txt txt = ./txt/cord-333999-k92fmnq7.txt === reduce.pl bib === id = cord-334268-n2hon61o author = Ren, Yanfang title = Risk for dental healthcare professionals during the COVID-19 global pandemic: an evidence-based assessment date = 2020-07-18 pages = extension = .txt mime = text/plain words = 6861 sentences = 300 flesch = 48 summary = Considering that the primary route of transmission for COVID-19 is from respiratory droplets, and potentially from spatters or aerosols generated during dental treatments, risks of COVID-19 J o u r n a l P r e -p r o o f transmission from asymptomatic patients to DHPs are dependent on several factors: effectiveness of PPE, specifically the N95 masks in preventing virus transmission, prevalence of asymptomatic cases in the local community, rate of transmission from asymptomatic patients to healthcare providers in close contact, probability for an infection acquired from an asymptomatic patient become symptomatic, and age-adjusted infection fatality rate of symptomatic COVID-19 patients. To understand the potential impact of COVID-19 on dental care and oral health and assess the risks to DHPs from the disease while providing essential services to the community, we periodically searched and reviewed published literature in PubMed and Google Scholar using various combinations of keywords, including SARS CoV-2, COVID-19, Dental, Dentist, Dentistry, Droplets, Aerosols, Healthcare Workers, Symptomatic, Asymptomatic, Saliva, PPE, N95 Masks, Face Shields, and Infection Fatality Rate. cache = ./cache/cord-334268-n2hon61o.txt txt = ./txt/cord-334268-n2hon61o.txt === reduce.pl bib === id = cord-334194-28ygsbo1 author = Qiu, Tianyi title = Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus date = 2020-02-20 pages = extension = .txt mime = text/plain words = 1727 sentences = 98 flesch = 53 summary = title: Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Letter to the editor Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Recently, a new type of unknown virus causing severe acute respiratory infection was reported in Wuhan city, Hubei province, China (WHO, 2020b) . Recently, the binding sites of S protein to human ACE2 were identified as residues 455, 486, 493, 501, and 505 (numbered according to the 2019-nCoV S protein sequence), which are located near the potential CRE positions (Fig. 1E) . Possibility of an additional CRE may also exist in other regions of S protein or other antigens between 2019-nCoV and SARS-CoV. In summary, a highly similar epitope was identified computationally between the 2019-nCoV and SARS virus, in the region of the binding site of the S proteins to the human ACE2 receptor. cache = ./cache/cord-334194-28ygsbo1.txt txt = ./txt/cord-334194-28ygsbo1.txt === reduce.pl bib === id = cord-334220-sqvfr31q author = Messina, Francesco title = Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date = 2020-11-03 pages = extension = .txt mime = text/plain words = 4218 sentences = 237 flesch = 44 summary = The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. In SFigure For KEGG database the gene enrichment analysis on interactomes of NS7b, ORF1a, ORF3a and ORF8 showed pathway clusters highly significant and consistent with possible pathogenic mechanisms, such as the activation of the complement and of the coagulative cascade, (29) and the TGF-β-dominated immune response (30) . We identified different host response induced by specific proteins of SARS-CoV-2, underlining the important role of ORF3a and ORF8 in phenotypes of severe COVID-19 patients. cache = ./cache/cord-334220-sqvfr31q.txt txt = ./txt/cord-334220-sqvfr31q.txt === reduce.pl bib === id = cord-334278-ajdjfzd2 author = Gilis, M. title = Caractéristiques de la COVID-19 chez les patients âgés de 75 ans et plus, hospitalisés date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2156 sentences = 222 flesch = 75 summary = Matériels et méthodes Il s'agit d'une étude prospective observationnelle descriptive monocentrique incluant tous les patients hospitalisés, initialement hors réanimation, avec une COVID-19 confirmée par RT-PCR et/ou par imagerie scanographique entre le 3 mars et le 24 avril 2020. Conclusion Sur la période de mars 2020 alors que l'épidémie de SARS-CoV-2 a touché la France de plein fouet, les virus respiratoires classiques ont rapidement disparu tandis que la COVID-19 touchait plus du tiers des personnes consultant pour un syndrome grippal dans un centre de dépistage hospitalier francilien. Matériels et méthodes Dans notre hôpital, les soignants symptomatiques étaient systématiquement testés par une RT-PCR SARS-CoV2 sur frottis rhinopharyngé. Les soignants COVID avaient été plus souvent en contact avec un cas confirmé d'infection à SARS-CoV-2 (75 % vs 63 %, p < 0,001) mais n'étaient pas plus souvent affectés dans les unités COVID (16 % vs 12 %, p = 0,17). cache = ./cache/cord-334278-ajdjfzd2.txt txt = ./txt/cord-334278-ajdjfzd2.txt === reduce.pl bib === id = cord-334099-rtv6xm90 author = Farrow, Robert title = Early Multi-organ Point-of-Care Ultrasound Evaluation of Respiratory Distress During SARS-CoV-2 Outbreak: Case Report date = 2020-04-15 pages = extension = .txt mime = text/plain words = 2039 sentences = 121 flesch = 44 summary = 1, 2 In our early experience during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, with multiple patients presenting with acute dyspnea of suspected parenchymal Highland Hospital / Alameda Health System, Department of Emergency Medicine, Oakland, California pulmonary pathology, we found that the prompt differentiation between an underlying cardiac versus pulmonary source can be instrumental in both triage and early resuscitation. Herein we present a case of SARS-CoV-2 related multifocal pneumonia diagnosed by POCUS in the ED during the initial triage of a return ED visit, which highlights its clinical utility and our proposed imaging pathway for evaluating patients with acute dyspnea during the current SARS-CoV-2 outbreak. While the majority of patients infected with SARS-CoV-2 will experience only mild illness, a subset will progress to multifocal pneumonia, acute respiratory distress syndrome, and cardiomyopathy [10] [11] [12] pathologies that can be identified rapidly with POCUS. cache = ./cache/cord-334099-rtv6xm90.txt txt = ./txt/cord-334099-rtv6xm90.txt === reduce.pl bib === id = cord-333897-isodrtly author = Shenoy, Niraj title = Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting? date = 2020-08-19 pages = extension = .txt mime = text/plain words = 2833 sentences = 150 flesch = 39 summary = Finally, it discusses potential implications of specific clinical observations and considerations in COVID-19 patients on target oxygen saturation, such as diffuse systemic endothelitis and microthrombi playing an important pathogenic role in the wide range of systemic manifestations, exacerbation of hypoxic pulmonary vasoconstriction in the setting of pulmonary vascular endothelitis/microthrombi, the phenomenon of "silent hypoxemia" with some patients presenting to the hospital with severe hypoxemia disproportional to symptoms, and overburdened health systems and public health resources in many parts of the world with adverse implications on outpatient monitoring and early institution of oxygen supplementation. -The LOCO-2 trial [2] where ARDS (acute respiratory distress syndrome) patients were randomized to conservative (target partial pressure of arterial oxyHere, we examine the above two studies guiding current target oxygen saturation recommendations for COVID-19; discuss, with supporting transcriptomic analyses, the influence of hypoxia on ACE2 (angiotensin converting enzyme-2, target receptor for SARS-CoV-2 entry) expression; reflect on relevant clinical observations and considerations in COVID-19 patients; and propose a reevaluation of target oxygen saturation in these patients-both in the inpatient and outpatient settings. cache = ./cache/cord-333897-isodrtly.txt txt = ./txt/cord-333897-isodrtly.txt === reduce.pl bib === id = cord-334162-j8m2zqbr author = Hoechter, D. J. title = Besonderheiten der kardiopulmonalen Reanimation zu Zeiten von SARS-CoV-2 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 1385 sentences = 181 flesch = 42 summary = Als Beispiel seien hier die Empfehlungen der Deutscher Gesellschaft für Anaesthesiologie und Intensivmedizin (DGAI) und des Berufsverbands Deutscher Anästhesisten (BDA) zu den Besonderheiten des Atemwegsmanagements bei Patienten mit vermuteter oder gesicherter COVID-19-Erkrankung und bei Patienten ohne Infektion während der Coronapandemie genannt [13] . Besteht bei dem Patienten ein begründeter oder bestätigter Verdacht auf COVID-19 sollen Laienhelfer, die über keine Schutzausrüstung verfügen, auf die Thoraxkompressionen verzichten und ggf. Dabei wird angenommen, dass es bei der Defibrillation wahrscheinlich zu keiner oder allenfalls zu einer kurzzeitigen und geringen Aerosolbildung kommt und die mittlerweile flächendeckende Nutzung von Klebepads den Anwender Distanz zum Patienten halten lässt. Bei innerklinischen Reanimationen von Patienten mit vermuteter oder bestätigter Infektion mit SARS-CoV-2 sollen folgende Besonderheiten hervorgehoben werden: Die Verwendung von Frühwarnsystemen (wie beispielsweise dem "early warning score") wird verstärkt empfohlen, um kritisch kranke Patienten frühzeitig zu erkennen und die Notwendigkeit zur Durchführung einer Reanimation möglichst zu vermeiden [5, 10] . cache = ./cache/cord-334162-j8m2zqbr.txt txt = ./txt/cord-334162-j8m2zqbr.txt === reduce.pl bib === id = cord-334012-b2akycst author = Liguori, Claudio title = Sleep and wake impairment in patients with SARS-CoV2 infection date = 2020-07-17 pages = extension = .txt mime = text/plain words = 474 sentences = 29 flesch = 43 summary = Coronavirus Disease 2019 (COVID-19) is unquestionably a worldwide life-threatening condition causing severe acute respiratory distress; 1 however, pauci-symptomatic or non-severe forms of pneumonia currently represent the more frequent manifestations of the infection. [3] [4] Our NeuroCOVID-19 group performed a prospective observational study focused on the occurrence of subjective neurological symptoms in hospitalized patients with a non-severe respiratory form of COVID-19. 4 Here, we present data deriving from a secondary analysis of the previous study with the aims to emphasize and deepen the characteristics of sleep and wake impairment in patients with SARS-CoV2 infection and their relationships with the other neurological symptoms, white blood cells (WBC), C-reactive protein (CRP), and days of hospitalization. Considering patients with sleep impairment, they had higher CRP serum levels, more frequent dysgeusia, headache, and dizziness, and more concomitant neurological symptoms than patients without sleep alteration ( Table 1) . Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection cache = ./cache/cord-334012-b2akycst.txt txt = ./txt/cord-334012-b2akycst.txt === reduce.pl bib === id = cord-334210-lhadzo7o author = Lepak, Alexander J title = Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date = 2020-08-27 pages = extension = .txt mime = text/plain words = 3673 sentences = 227 flesch = 55 summary = Key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible COVID-19 or for asymptomatic screening. CONCLUSIONS: In a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. In this paper we report the findings of a retrospective observational study to examine results of repeat SARS-CoV-2 RT-PCR testing for patients who were suspected of having COVID-19 (persons under investigation, or PUI) and asymptomatic patients and how the results may inform diagnostic stewardship within our academic medical center in Wisconsin. We believe the biggest lesson learned for our institution is that we found no cases of conversion from a negative to a positive result for inpatients undergoing a repeat PUI test or a repeat asymptomatic screen test. cache = ./cache/cord-334210-lhadzo7o.txt txt = ./txt/cord-334210-lhadzo7o.txt === reduce.pl bib === id = cord-334175-x10bbv7y author = Okur, Hacer Kuzu title = Preliminary report of In vitro and In vivo Effectiveness of Dornase alfa on SARS-CoV-2 infection date = 2020-09-07 pages = extension = .txt mime = text/plain words = 4026 sentences = 251 flesch = 55 summary = Dornase alfa, the recombinant form of the human DNase I enzyme, breaks down neutrophil extracellular traps (NET) that include a vast amount of DNA fragments, histones, microbicidal proteins and oxidant enzymes released from necrotic neutrophils in the highly viscous mucus of cystic fibrosis patients. We followed clinical improvement in the radiological analysis (2-of-3 cases), oxygen saturation (SpO2), respiratory rate, disappearing of dyspnea, coughing and a decrease in NET formation and SARS-CoV-2 viral load after the treatment. Also here, we share our preliminary results suggesting that Dornase alfa has an anti-viral effect against SARS-CoV-2 infection in a green monkey kidney cell line, Vero, and a bovine kidney cell line, MDBK without determined cytotoxicity on healthy peripheral blood mononuclear cells. In this study, preliminary data is presented about in-vitro and in-vivo anti-viral and nuclease activity of Dornase alfa for the clearance of SARS-CoV-2 viral load and NETs in the lungs of COVID-19 patients. cache = ./cache/cord-334175-x10bbv7y.txt txt = ./txt/cord-334175-x10bbv7y.txt === reduce.pl bib === id = cord-334300-hnrmaytm author = Ventura Fernandes, Bianca H title = Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1799 sentences = 126 flesch = 50 summary = Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus. 169 In the global task to develop the vaccine and possible therapeutic approaches for 170 COVID-19, several animal models have been proposed, such as mice 10 , hACE2 171 transgenic mice 11 , alpaca 12 , golden Syrian hamsters, ferrets, dogs, pigs, chickens, and 172 cats 9 , and species of non-human primates 10 . cache = ./cache/cord-334300-hnrmaytm.txt txt = ./txt/cord-334300-hnrmaytm.txt === reduce.pl bib === id = cord-334188-bggt1i2e author = Solari, Domenico title = The nose lid for the endoscopic endonasal procedures during COVID-19 era: technical note date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2604 sentences = 122 flesch = 44 summary = We describe peculiar surgical technique modifications and the use of an endonasal face mask, i.e., the nose lid, to be applied to the patient during transnasal procedures for skull base pathologies as a further possible COVID-19 mitigation strategy. CONCLUSIONS: Transnasal surgery, transgressing respiratory mucosa, can definitely increase the risk of virus transmission: we find that adopting further precautions, above all limiting high-speed drill can help preventing or at least reducing aerosol/droplets. After usual nasal pyramid sterile draping, an endonasal surgery facial mask, namely a nose lid, is assembled: a sterile non-latex glove layer is used to cover nostril and fixed with adhesive protection film over the nasal bridge; initially, two and then three narrow slit cut are placed over the nares to let instruments enter the nostrils (Figs. cache = ./cache/cord-334188-bggt1i2e.txt txt = ./txt/cord-334188-bggt1i2e.txt === reduce.pl bib === id = cord-334425-6zrmavps author = SanJuan-Reyes, Sindy title = COVID-19 in the environment date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2084 sentences = 139 flesch = 50 summary = The WHO has named it COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV2). New studies provide information of the role of the environment in COVID-19 transmission process, mortality related to this infectious disease and the impact on human health. The following review aims to analyze information on the implications of COVID-19 infection on human health and the impact of its presence on the environment, from its transmission capacity and the role of air pollutants and climatological factors to reducing the air pollution during confinement. Until now, there are no specific pharmacological treatment or vaccines against COVID-19 infection 104 for potential therapy in humans, so extensive isolation measures and the use of disinfection products 105 have been implemented to reduce their transmission from person to person. First known person-to-person transmission of severe acute 593 respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA cache = ./cache/cord-334425-6zrmavps.txt txt = ./txt/cord-334425-6zrmavps.txt === reduce.pl bib === id = cord-334299-0zn1z7rc author = Ahmed, Warish title = Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1373 sentences = 73 flesch = 47 summary = title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In view of this need, we recommend methodological and quality assurance approaches for SARS-CoV-2 RNA detection in 158 wastewater using molecular methods. cache = ./cache/cord-334299-0zn1z7rc.txt txt = ./txt/cord-334299-0zn1z7rc.txt === reduce.pl bib === id = cord-334228-n69iewmx author = Li, Chunmei title = Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity date = 2016-02-16 pages = extension = .txt mime = text/plain words = 4643 sentences = 251 flesch = 59 summary = Like other known CoV-3CLpro structures, such as TGEV, hCoV-229E, hCoV-HKU1, and IBV 2-5 , SARS-3CLpro has a highly conserved three-dimensional structure, dimer interface, catalysis dyad, and substrate binding site, but an extremely low homology with cellular proteases. Ser139 and Phe140 are two key residues that not only contribute to interactions between the two protomers in the parent dimer but also maintain the correct conformation of the S1 subsite in the substrate-binding pocket. Other residue mutations, which are neither on the dimer interface nor key to catalysis, can also influence enzyme activity and dimer association-dissociation of SARS-3CLpro via long-range interactions 15, 16 . Our molecular dynamics simulations showed that Ser139-Leu141 maintains a stable 3 10 -helix conformation in the inactive monomer structure and a well-defined loop conformation in the active protomer of the dimer structure. Although SARS-3CLpro uses the dimer structure to maintain its enzyme activity, our study shows that the monomer can also be evolved into an active enzyme via mutations. cache = ./cache/cord-334228-n69iewmx.txt txt = ./txt/cord-334228-n69iewmx.txt === reduce.pl bib === id = cord-334313-v2syspu6 author = Long, S. Wesley title = Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date = 2020-05-03 pages = extension = .txt mime = text/plain words = 4525 sentences = 251 flesch = 48 summary = We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. Because in vitro resistance of SARS-CoV to remdesivir has been reported to be caused by either of two amino acid replacements in RdRp (Phe476Leu and Val553Leu), we interrogated our data for polymorphisms in the nsp12 gene. cache = ./cache/cord-334313-v2syspu6.txt txt = ./txt/cord-334313-v2syspu6.txt === reduce.pl bib === id = cord-334518-mjr6u7ak author = Hu, X. title = Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection date = 2020-05-23 pages = extension = .txt mime = text/plain words = 5158 sentences = 294 flesch = 51 summary = To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on the serial upper respiratory samples from an asymptomatic carrier, and the insistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. . https://doi.org/10.1101/2020.05.20.20108530 doi: medRxiv preprint As described in the Materials and Methods, we developed a rapid and simple RT-LAMP assay to detect SARS-CoV-2 RNA, and positive reactions resulted in a color change from purple to blue due to decreased magnesium concentration in the presence of extensive Bst DNA polymerase activity, while negative reactions retained the purple color. cache = ./cache/cord-334518-mjr6u7ak.txt txt = ./txt/cord-334518-mjr6u7ak.txt === reduce.pl bib === id = cord-334378-dqtnj3y3 author = Zhang, Yi title = Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2 date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1452 sentences = 86 flesch = 55 summary = How does RBD of the SARS-CoV-2 spike protein binds to the human receptor ACE2? The precise binding interface of the SARS-CoV-2 spike RBD and ACE2 can be dissected from the crystal structures of the complex determined by Shang et al. Analysis of the crystal structures of RBD from the SARS-CoV spike protein in complex with established SARS-CoV neutralizing human m396 and 80R antibodies reveals that the antibodies are bound in the same binding site as ACE2 9,10 , implying that their neutralizing mechanism is a direct blockage of receptor binding. Proteolytic cleavage of the SARS-CoV-2 spike protein by the human serine protease TMPRSS2 is a critical step in the virus entry through the plasma membrane fusion mechanism (Fig. 2) , as shown by Hoffmann et al. In addition to targeting components of the viral attachment and the membrane fusion machinery, other strategies to eliminate SARS-CoV-2 include impeding virus entry into the host cell through the endosomal pathway and disrupting activities of viral proteins. cache = ./cache/cord-334378-dqtnj3y3.txt txt = ./txt/cord-334378-dqtnj3y3.txt === reduce.pl bib === id = cord-334430-1udn20wo author = Qin, Li title = The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice date = 2007 pages = extension = .txt mime = text/plain words = 1890 sentences = 107 flesch = 58 summary = title: The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice The immune effect of two recombinant protein fragments of spike protein in severe acute respiratory syndrome coronavirus (SARS CoV) was investigated in Balb/c mice. Two partial spike gene fragments S1 (322 1464 bp) and S2 (2170 2814 bp) of SARS coronavirus were amplified by RT-PCR, and cloned into pET-23a prokaryotic expression vector, then transformed into competent Escherichia E. The results showed that recombinant proteins of SARS coronavirus spike protein induced hormonal and cellular immune response in Balb/c mice. Spike protein is also the main protective antigen inducing the generation of neutralizing antibodies, and it can be detected in infected cell culture supernatants with antisera from SARS patients [7, 8] . An exposed domain in the severe acute respiratory syndrome coronavirus spike protein induces neutralizing antibodies cache = ./cache/cord-334430-1udn20wo.txt txt = ./txt/cord-334430-1udn20wo.txt === reduce.pl bib === id = cord-334321-3c10ecgd author = Arora, S. title = Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1306 sentences = 82 flesch = 62 summary = Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks. cache = ./cache/cord-334321-3c10ecgd.txt txt = ./txt/cord-334321-3c10ecgd.txt === reduce.pl bib === id = cord-334550-xb0alubj author = Samaddar, Arghadip title = The Enigma of Low COVID-19 Fatality Rate in India date = 2020-07-28 pages = extension = .txt mime = text/plain words = 6405 sentences = 367 flesch = 48 summary = These include some ongoing mutations that can alter the virulence of the circulating SARS-CoV-2 strains, host factors like innate immunity, genetic diversity in immune responses, epigenetic factors, genetic polymorphisms of ACE2 receptors, micro RNAs and universal BCG vaccination, and environmental factors like high temperature and humidity which may alter the viability and transmissibility of the strain. Researchers from Translational Bioinformatics Group at International Center for Genetic Engineering and Biotechnology (ICGEB) in collaboration with the Department of Biochemistry, Jamia Hamdard, New Delhi, India, performed an integrated mutational analysis of SARS-CoV-2 genomes from different geographical locations, including India, Italy, United States, Nepal and Wuhan, and observed a novel mutation in S protein (A930V, 24351C>T) of the Indian strain, which was absent in other strains (Sardar et al., 2020) . While this apparent protection among Indians is largely attributed to non-heritable influences as discussed earlier, a safe and effective vaccine against SARS-CoV-2 can reduce disease severity, control transmission, and prevent future infections across all populations. cache = ./cache/cord-334550-xb0alubj.txt txt = ./txt/cord-334550-xb0alubj.txt === reduce.pl bib === id = cord-334495-7y1la856 author = Agricola, Eustachio title = Heart and Lung Multimodality Imaging in COVID-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 6791 sentences = 325 flesch = 33 summary = From a clinical point of view, cardiac involvement during COVID-19 may present a wide spectrum of severity ranging from subclinical myocardial injury to well-defined clinical entities (myocarditis, myocardial infarction, pulmonary embolism and heart failure), whose incidence and prognostic implications are currently largely unknown due to a significant lack of imaging data. The use of integrated heart and lung multimodality imaging plays a central role in different clinical settings and is essential in diagnosis, risk stratification and management of COVID-19 patients. In this context, the use of multiple diagnostic imaging techniques may apply to both heart and lung to provide an integrated assessment of cardiac and pulmonary function and to refine diagnosis, risk stratification and management of COVID-19 patients. patients not requiring ICU, when clinical presentation and biomarker alterations suggest acute-onset myocardial inflammation, if the diagnosis is likely to impact on management, CMR may be considered to confirm acute myocarditis, after exclusion of alternative relevant clinical conditions, including ACS and HF, by means of other rapidly available imaging modalities (i.e. cardiac CT scan or TTE). cache = ./cache/cord-334495-7y1la856.txt txt = ./txt/cord-334495-7y1la856.txt === reduce.pl bib === id = cord-334443-3pyu8ucs author = He, Yu title = Public health might be endangered by possible prolonged discharge of SARS-CoV-2 in stool date = 2020-03-05 pages = extension = .txt mime = text/plain words = 1015 sentences = 61 flesch = 55 summary = According to a recent report, since December 8 2019, a novel identified coronavirus, SARS-CoV-2(previously named as 2019-nCOV) is causing outbreak of pneumonia in Wuhan, China and become the major concern throughout the world [1] . Those early reports may not represent actual rate of gastrointestinal symptoms caused by SARS-CoV-2, because in early stages of the outbreak, the limited resources for detection were only provided to those patients with severe symptoms like respiratory distress syndrome. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Detection and monitoring of SARS coronavirus in the plasma and peripheral blood lymphocytes of patients with severe acute respiratory syndrome cache = ./cache/cord-334443-3pyu8ucs.txt txt = ./txt/cord-334443-3pyu8ucs.txt === reduce.pl bib === id = cord-334584-xh41koro author = Dilucca, Maddalena title = Temporal evolution and adaptation of SARS-COV 2 codon usage date = 2020-05-29 pages = extension = .txt mime = text/plain words = 3955 sentences = 210 flesch = 56 summary = Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), non-structural 3C-like proteinase (3CLpro), ssRNA-binding protein (RBP), 2'-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase, RNA-dependent RNA polymerase (RdRp), Nsp7, Nsp8, and exonuclease ExoN. An EN C plot analysis was performed to estimate the relative contributions of mutational bias and natural selection in shaping CUB of 13 genes encoding proteins that are crucial for SARS-CoV-2. For the funtionally important genes in each genome, we calculated the average values of CAI and ENC over time, as compared to the reference SARS-CoV-2 sequence (WSM). Based on the SiD combined with the CAI results ( Figure 5 ), we suggest that SARS-CoV-2, over time, has preferentially accumulated mutations in its genome which correspond to codons that adapt better to the human host. cache = ./cache/cord-334584-xh41koro.txt txt = ./txt/cord-334584-xh41koro.txt === reduce.pl bib === id = cord-334277-g3go3u02 author = Kovac, Marc title = EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA) date = 2020-08-14 pages = extension = .txt mime = text/plain words = 4725 sentences = 237 flesch = 53 summary = While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). It can thus be concluded that the anti-SARS-CoV-2 antibody results in whole blood corrected for hematocrit with weakly and moderately positive findings are comparable to those obtained from serum. cache = ./cache/cord-334277-g3go3u02.txt txt = ./txt/cord-334277-g3go3u02.txt === reduce.pl bib === id = cord-334309-rddznfax author = Craver, Randall title = Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1672 sentences = 118 flesch = 46 summary = title: Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) Postmortem nasopharyngeal swabs detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) known to cause coronavirus disease 2019 (COVID-19). Myocardial damage, myocarditis, and cardiomyopathy is often referred to in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] [2] [3] [4] [5] [6] . There is little information regarding cardiac complications in children [11] [12] [13] We present a previously healthy 17 year male old dying suddenly with an eosinophilic myocarditis (EM) in which a nasopharyngeal swab detected SARS-CoV-2 at autopsy (Figs. The question of whether this is a direct complication of SARS-CoV-2 infection, or if this is an idiopathic eosinophilic myocarditis in which the stress of the COVID-19 contributed to the cardiac decompensation cannot be answered definitively at this time. cache = ./cache/cord-334309-rddznfax.txt txt = ./txt/cord-334309-rddznfax.txt === reduce.pl bib === id = cord-333122-xw8o189s author = Blasiak, A. title = IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-05-08 pages = extension = .txt mime = text/plain words = 5116 sentences = 351 flesch = 43 summary = IDentif.AI harnesses a quadratic relationship between therapeutic inputs (e.g. drug and dose) and biological outputs (e.g. quantifiable measurements of efficacy, safety) to experimentally pinpoint optimal combinations from large parameter spaces with a marked reduction in the number of required experiments (Fig. 1 ). The 12drug set included a broad spectrum of repurposed agents that are currently being evaluated in clinical studies for treatment of COVID-19 or being administered in conjunction with these therapies, including remdesivir (RDV), favipiravir (FPV), ritonavir (RTV), lopinavir (LPV), oseltamivir (OSV-P), dexamethasone (DEX), ribavirin (RBV), teicoplanin (TEC), losartan (LST), azithromycin (AZT), chloroquine (CQ), and hydroxychloroquine (HCQ). With a 3-order of magnitude reduction in required tests, we identified a clinically actionable list of 2-,3-, and 4-drug combinations ranked based on viral inhibition efficacy with accompanying safety data against kidney epithelial cells (Vero E6), liver epithelial cells (THLE-2) and cardiomyocytes (AC16). This study harnessed the IDentif.AI platform to interrogate a 12 drug-dose parameter space against the SARS-CoV-2 live virus to develop actionable and optimized combination therapy regimens. cache = ./cache/cord-333122-xw8o189s.txt txt = ./txt/cord-333122-xw8o189s.txt === reduce.pl bib === id = cord-334564-bqh9jkds author = Raony, Ícaro title = Psycho-Neuroendocrine-Immune Interactions in COVID-19: Potential Impacts on Mental Health date = 2020-05-27 pages = extension = .txt mime = text/plain words = 9893 sentences = 464 flesch = 41 summary = Since COVID-19 is associated with increased levels of pro-inflammatory cytokines (8) , an immune signature shared with several psychiatric disorders, we propose how the relationship between SARS-CoV-2/host can possibly impair interactions between the immune, nervous and endocrine systems, leading to psychiatric symptoms. Several studies have demonstrated psychiatric manifestations in patients with MERS or SARS during the acute phase, such as increased stress levels, impaired memory, symptoms of depression, anxiety, PTSD, psychoses, and suicidal behavior (28) (29) (30) (31) (32) (33) . If the increase in cytokine levels and the manifestation of psychiatric symptoms are related to the severity of the symptoms of SARS-CoV infection, the "cytokine storm" might also be related to the "mental health thunderstorms" seen in patients with COVID-19? Similar to possible mechanisms involved in the impacts of SARS-CoV-2 infection on mental health, social isolation may also be associated with dysfunctional psycho-neuroendocrine-immune interactions, which in turn can contribute to the development or the worsening of psychiatric disturbances (Figure 2) . cache = ./cache/cord-334564-bqh9jkds.txt txt = ./txt/cord-334564-bqh9jkds.txt === reduce.pl bib === id = cord-334582-ccg27nmf author = Bonora, Benedetta Maria title = Glycaemic Control Among People with Type 1 Diabetes During Lockdown for the SARS-CoV-2 Outbreak in Italy date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3846 sentences = 184 flesch = 50 summary = CONCLUSION: Despite the limited possibility to exercise and the incumbent psychologic stress, glycaemic control improved in patients with T1D who stopped working during the lockdown, suggesting that slowing down routine daily activities can have beneficial effects on T1D management, at least in the short term. Using data collected by remote monitoring of glucose sensors, we investigated whether glycaemic control in people with type 1 diabetes (T1D) during lockdown improved or worsened. None of the patients who continued to work showed improvement in any of the measures of glucose control during the lockdown period (period 2) compared to the 3 months or the week before the SARS-CoV-2 outbreak: average glucose, standard deviation, CV%, time in hypoglycaemia, time in range and time in hyperglycaemia remained unchanged (Table 2) , as did the number of scans per day. cache = ./cache/cord-334582-ccg27nmf.txt txt = ./txt/cord-334582-ccg27nmf.txt === reduce.pl bib === id = cord-334612-lxqcvqca author = Rao, Nirmala title = Sars, preschool routines and children’s behaviour: Observations from preschools in Hong Kong date = 2006 pages = extension = .txt mime = text/plain words = 4265 sentences = 239 flesch = 62 summary = This paper considers the influence of the SARS epidemic on children's routines and behaviour when preschools re-opened, after a six-week closure. Items on the survey fell into 6 categories including: Information about the preschool and children (21 questions); Routines before the SARS outbreak (4 questions); Learning during School Closure (2 questions); Preparing the kindergarten for re-opening (2 questions); Students return to kindergartens (18 questions); Lessons from SARS (4 questions); and Demographic information about the observers. The 18 items on Students' return to kindergartens included questions on Daily routines (3 questions); Health issues (2 questions); Social Interaction among children (6 questions); Preschool Management (3 questions); and School Holidays (4 questions). During the SARS outbreak, the Education and Manpower Bureau of the Hong Kong Government issued a curriculum for children ranging in age from 3-6 years. As mentioned earlier the Education and Manpower Bureau of the Hong Kong Government developed a programme for preschool children on SARS. cache = ./cache/cord-334612-lxqcvqca.txt txt = ./txt/cord-334612-lxqcvqca.txt === reduce.pl bib === id = cord-334688-0i1pu8wc author = Martos Pérez, F. title = Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date = 2020-08-19 pages = extension = .txt mime = text/plain words = 3445 sentences = 208 flesch = 57 summary = Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. In this study, we describe the first cases of COVID-19 in patients hospitalized in a general hospital and analyze the characteristics upon admission associated with in-hospital death. Our model shows that a medical history of cardiopathy, LDH levels ≥345 IU/L upon admission, and age ≥65 years are associated with greater in-hospital mortality due to COVID-19. Predictors of Mortality for Patients with COVID-19 Pneumonia Caused by SARS-CoV-2: A Prospective Cohort Study Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. cache = ./cache/cord-334688-0i1pu8wc.txt txt = ./txt/cord-334688-0i1pu8wc.txt === reduce.pl bib === id = cord-334945-lxowaacg author = Luo, Yi title = Asymptomatic SARS-CoV-2 Infection in Household Contacts of a Healthcare Provider, Wuhan, China date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1796 sentences = 95 flesch = 48 summary = We describe the case of a physician in Wuhan, China, who had mildly symptomatic COVID-19 and the subsequent asymptomatic SARS-CoV-2 infection in all 5 of his household contacts. All 5 household contacts of patient 1 had laboratory evidence of SARS-CoV-2 infection but remained asymptomatic throughout the period of observation (February 11-March 1) (Figure, panel A) . An early report from China on 72,314 COVID-19 cases found that only 1% of SARS-CoV-2 infections were asymptomatic; however, asymptomatic close contacts were not routinely tested in that study (7) . In summary, this single-household study found a high attack rate for asymptomatic SARS-CoV-2 infection among the immediate family members of a symptomatic COVID-19 case-patient. Moreover, our experience indicates that screening symptomatic contacts with a single throat swab test for SARS-CoV-2 might lead to an underestimate of the rate of infection and that asymptomatic persons can repeatedly revert between positive and negative PCR results on throat specimens. cache = ./cache/cord-334945-lxowaacg.txt txt = ./txt/cord-334945-lxowaacg.txt === reduce.pl bib === id = cord-334540-ggnkdnky author = Singh, Pankaj title = Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1593 sentences = 203 flesch = 45 summary = title: Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie Bei infizierten Patienten lässt sich regelhaft (auch schon in der Anfangsphase der Erkrankung) eine hohe Viruslast in den oberen und unteren Atemwegen nachweisen. Im Eingangsbereich zum Haupthaus des Klinikums werden alle Patienten nach dem MTS "triagiert" [4, 5] und bezüglich einer möglichen COVID-Erkrankung befragt. Ergibt sich der Verdacht auf eine CO-VID-19-Erkrankung, wird der Patient abgestrichen und bei möglicher ambulanter Behandlung mit Medikation nach Hause geschickt. B. einer pp-Vitrektomie bei Amotio retinae, die in Intubationsnarkose stattfinden sollen, erfolgt unmittelbar vor stationärer Aufnahme des Patienten ein Rachen-/Nasenabstrich zum Nachweis/Ausschluss von SARS-CoV-2. Auch im Op.-Bereich sind die Patienten so terminiert worden, dass zwischen den Op.s ein ausreichender Zeitabstand eingehalten werden kann, entsteht und der genügend Zeit für die Einhaltung und Umsetzung aller Hygienestandards lässt. Implementierung eines Betriebskonzeptes in einer HNO-Klinik im Rahmen der SARS-CoV-2-Pandemie. cache = ./cache/cord-334540-ggnkdnky.txt txt = ./txt/cord-334540-ggnkdnky.txt === reduce.pl bib === id = cord-334628-axon4jdc author = Lee, Saemi title = Genetic Characteristics of Coronaviruses from Korean Bats in 2016 date = 2017-07-19 pages = extension = .txt mime = text/plain words = 3227 sentences = 205 flesch = 66 summary = In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. Given the import of MERS into South Korea [14] and the presence of SARS in the relatively close geographic location of China [9] (Fig. 3) , together with the fact that bats are a reservoir for coronaviruses, the prevalence of coronavirus infection in Korean bat species should provide valuable information. Oral swabs and other samples (n = 60) were obtained from three species of bats, Rhinolophus ferrumequinum, Miniopterus schreibersii, and Myotis macrodactylus, but coronaviruses were only detected in samples from R. Thirteen sequences from oral swabs were clustered with Bat-CoV B15-21, which was detected in fecal bat samples collected from an abandoned mine in Gangwon province. cache = ./cache/cord-334628-axon4jdc.txt txt = ./txt/cord-334628-axon4jdc.txt === reduce.pl bib === id = cord-334695-cjxlw1tu author = Kam, Yiu-Wing title = Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date = 2009-11-17 pages = extension = .txt mime = text/plain words = 6404 sentences = 315 flesch = 43 summary = title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro We observed that SARS-CoV spike glycoprotein can be efficiently cleaved by several airway proteases and that this processing enhances entry of SARS-CoVpp. Furthermore, we have identified the putative cleavage sites of airway proteases and, by site-directed mutagenesis, have determined the role of specific amino acid residue for proteolytic processing of the envelope glycoprotein, and for SARS-CoVpp entry into human airway epithelial cells (16HBE) in vitro. In an effort to directly demonstrate that airway protease mediated virus entry enhancement is due to the presence of cleavage site on the SARS spike glycoprotein, 16HBE cells were pre-incubated with wild-type (SARS-CoVpp) or mutant (R667App) pseudotypes on ice, which allowed virus attachment but not entry. cache = ./cache/cord-334695-cjxlw1tu.txt txt = ./txt/cord-334695-cjxlw1tu.txt === reduce.pl bib === id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 pages = extension = .txt mime = text/plain words = 1791 sentences = 101 flesch = 41 summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave's disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. cache = ./cache/cord-334603-yt2pmxi3.txt txt = ./txt/cord-334603-yt2pmxi3.txt === reduce.pl bib === id = cord-334735-up81jotp author = Gillissen, Adrian title = Das schwere akute Atemwegssyndrom (SARS) date = 2003 pages = extension = .txt mime = text/plain words = 1298 sentences = 139 flesch = 58 summary = Severe acute respiratory syndrome (SARS) is a viral disease, observed primarily in Southern China in November 2002, with variable flu-like symptoms and pneumonia, in approx. Weitere Fälle wurden aus Vietnam, Singapur und den USA (hier mation about a new syndrome by the end of February 2003, after the first cases outside the Republic of China had been observed. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong Identification of a novel coronavirus in patients with severe acute respiratory syndrome Guideline on management of severe acute respiratory syndrome (SARS) A novel coronavirus associated with severe acute respiratory syndrome SARS: imaging of severe acute respiratory syndrome Coronavirus as possible cause of severe acute respiratory syndrome A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS): infection control Dieses Prinzip ist bei den Neuraminidaseinhibitoren zur Therapie der Influenza bekannt und klinisch umgesetzt [7, 9, 21] . cache = ./cache/cord-334735-up81jotp.txt txt = ./txt/cord-334735-up81jotp.txt === reduce.pl bib === id = cord-334624-chnibsa1 author = Hayn, Manuel title = Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date = 2020-10-30 pages = extension = .txt mime = text/plain words = 5355 sentences = 432 flesch = 57 summary = Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation. SARS-CoV-1 ORF6 is about 4-fold less potent in antagonizing type I IFN signaling (Fig. 243 4b) but induces higher levels of autophagy (Fig. 4c) . Examination of the functional conservation showed that SARS-CoV-2 Nsp15 was less 319 efficient in blocking innate immune activation, both type I IFN induction and signaling, than SARS-320 Hepatitis C virus viruses to block anti-viral autophagic turnover 50 and thus may represent a common studies will see more mechanistic data to explain the molecular details of the impact of SARS-CoV-2 343 proteins on innate immune activation. cache = ./cache/cord-334624-chnibsa1.txt txt = ./txt/cord-334624-chnibsa1.txt === reduce.pl bib === id = cord-334773-yw2qgv13 author = Lisco, Giuseppe title = Hypothesized mechanisms explaining poor prognosis in type 2 diabetes patients with COVID-19: a review date = 2020-08-10 pages = extension = .txt mime = text/plain words = 7901 sentences = 359 flesch = 32 summary = This concern has been further confirmed by the results of a cohort study among 85 fatal cases of COVID-19 in Wuhan, hence defining DM as a potentially harmful comorbidity predisposing to worse clinical course or death once SARS-CoV-2 infection occurred [49] . Different hypothesis should be considered for explaining this clinical phenomenon, including glucose control at baseline and during the infection course, pathophysiology and immune system response in SARS-CoV-2 infected patients with T2D, diabetes-related comorbidities and concomitant medications. In conclusion, diabetic patients especially elderly individuals and those with worse baseline glucose control may exhibit immune system dysregulation that predispose them to a less effective response against SARS-CoV-2 and to a dysfunctional inflammation that requires to be carefully monitored in confirmed cases of COVID-19, for preventing or avoiding a harmful progression of the disease. Immune response and systemic inflammation play a crucial role in SARS-CoV-2 infection, particularly in case of severe clinical course of the disease. cache = ./cache/cord-334773-yw2qgv13.txt txt = ./txt/cord-334773-yw2qgv13.txt === reduce.pl bib === id = cord-334790-lav794w0 author = Jin, Huijuan title = Consensus for prevention and management of coronavirus disease 2019 (COVID-19) for neurologists date = 2020-04-01 pages = extension = .txt mime = text/plain words = 3557 sentences = 225 flesch = 50 summary = 1 Clinical symptoms of 2019-nCoV have mostly resembled that of severe acute respiratory syndrome coronavirus (SARS-CoV) of 2003. The nervous system manifestations were significantly more common in patients with severe infection, manifested as ischaemic stroke and cerebral haemorrhage diagnosed by clinical symptoms and head CT, impaired consciousness and skeletal muscle injury. Symptoms related to the development of acute cerebrovascular diseases Among patients with SARS-CoV-2 infection, middle-aged and elderly people accounted for the majority of strokes, especially in critically ill patients. According to the 'Technical guidelines for prevention and control of new coronavirus infection in medical institutions (First Edition)' 16 developed by General Office of the National Health Commission of the People's Republic of China and clinical characteristics of these patients, we propose the following precautions for neurologists, especially for those who are working in high-risk areas. cache = ./cache/cord-334790-lav794w0.txt txt = ./txt/cord-334790-lav794w0.txt === reduce.pl bib === id = cord-334833-7gv1c7we author = Ding, Yanqing title = The clinical pathology of severe acute respiratory syndrome (SARS): a report from China date = 2003-07-01 pages = extension = .txt mime = text/plain words = 2615 sentences = 138 flesch = 48 summary = The pulmonary lesions included bilateral extensive consolidation, localized haemorrhage and necrosis, desquamative pulmonary alveolitis and bronchitis, proliferation and desquamation of alveolar epithelial cells, exudation of protein and monocytes, lymphocytes and plasma cells in alveoli, hyaline membrane formation, and viral inclusion bodies in alveolar epithelial cells. Systemic vasculitis included oedema, localized fibrinoid necrosis, and infiltration of monocytes, lymphocytes, and plasma cells into vessel walls in the heart, lung, liver, kidney, adrenal gland, and the stroma of striated muscles. With regard to the aetiology and pathogenesis of SARS, this study has demonstrated extensive pulmonary consolidation; significant pulmonary oedema; localized haemorrhage and necrosis; widespread hyaline membrane formation; a local inflammatory reaction consisting mostly of monocytes, lymphocytes, and plasma cells; desquamation of bronchial and alveolar epithelial cells; numerous multinucleate and mononuclear giant cells in pulmonary alveoli in two cases; and typical viral inclusion bodies in epithelial cells in alveoli in all the three cases. cache = ./cache/cord-334833-7gv1c7we.txt txt = ./txt/cord-334833-7gv1c7we.txt === reduce.pl bib === id = cord-334976-53cd16w5 author = Jo, Seri title = Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3659 sentences = 222 flesch = 55 summary = An in silico docking study showed that the binding modes of herbacetin and pectolinarin are similar to those obtained from the catalytic domain of SARS-CoV 3CLpro. Baicalin showed an effective inhibitory activity against SARS-CoV-2 3CLpro and its docking mode is different from those of herbacetin and pectolinarin. The proteolytic assay using SARS-CoV-2 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The compound showed the severely reduced fluorescent intensity and thus represented their SARS-CoV-2 3CLpro inhibitory activity. Among them, baicalin, herbacetin and pectolinarin revealed the prominent inhibitory activity against SARS-CoV-2 3CLpro. The binding modes of herbacetin and pectolinarin were similar to those obtained from the docking study of the catalytic domain of SARS-CoV 3CLpro 21 . In the previous results of SARS-CoV 3CLpro 21 , only the three effect flavonoids (herbacetin, pectolinarin, and rhoifolin) were mentioned. cache = ./cache/cord-334976-53cd16w5.txt txt = ./txt/cord-334976-53cd16w5.txt === reduce.pl bib === id = cord-334717-zg9f19p8 author = Chung, Mina K. title = SARS-CoV-2 and ACE2: The biology and clinical data settling the ARB and ACEI controversy date = 2020-08-06 pages = extension = .txt mime = text/plain words = 6048 sentences = 311 flesch = 45 summary = Angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) have been reported to increase ACE2 expression in animal models, and worse outcomes are reported in patients with co-morbidities commonly treated with these agents, leading to controversy during the COVID-19 pandemic over whether these drugs might be helpful or harmful. Recently there has been controversy over whether use of angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) might be harmful in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with cardiovascular disease, hypertension, or diabetes mellitus under treatment with these agents. SARS-CoV-2, the coronavirus causing COVID-19, enters host cells via binding of the virus spike protein to angiotensin-converting enzyme 2 (ACE2). In a study of 2877 hospitalized patients with COVID-19, 850 had hypertension of which 183 were treated with renin-angiotensin-aldosterone system inhibitors (RAASi) and 527 were not; RAASi use was not associated with severity of disease or mortality [66] . cache = ./cache/cord-334717-zg9f19p8.txt txt = ./txt/cord-334717-zg9f19p8.txt === reduce.pl bib === id = cord-334858-wxexl0qy author = Lozada-Nur, Francina title = Dysgeusia in COVID-19: possible mechanisms and implications date = 2020-06-27 pages = extension = .txt mime = text/plain words = 1839 sentences = 113 flesch = 50 summary = A European multi-center epidemiological study 6 analyzing the prevalence of olfactory and gustatory dysfunctions as a clinical presentation in a cohort of 417 laboratory-confirmed cases of COVID-19 with mild-to-moderate disease presentation reported that 88.8% of patients population had gustatory disorders. 18, 19 It may be quite plausible that SARS-Cov-2 binds to ACE2 receptors present in oral mucosa, triggering an inflammatory response that leads to cellular and genetic changes which could alter taste. It is possible that zinc chelation through immune mechanisms and molecules known to increase in concentration with inflammatory processes may result in acute hypozincemia 27 or a more localized change in cellular zinc homeostasis of oral gustatory cells due to infection with SARS-Cov-2. We hypothesize that changes in localized cellular zinc homeostasis in oral gustatory cells due to immune responses to SARS-Cov-2 viral replication, may result in dysgeusia which may or may not be accompanied by hypozincemia. cache = ./cache/cord-334858-wxexl0qy.txt txt = ./txt/cord-334858-wxexl0qy.txt === reduce.pl bib === id = cord-334715-902pfxyz author = Sirico, Domenico title = Cardiac imaging in congenital heart disease during the coronavirus disease-2019 pandemic: recommendations from the Working Group on Congenital Heart Disease of the Italian Society of Cardiology date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2547 sentences = 130 flesch = 41 summary = The aim of this position paper is to provide clinical recommendation regarding the execution of imaging investigations for the cardiac diagnostic work-up of paediatric patients with suspected or confirmed infection. In particular, the Echo-Lab leading team along with referring physicians should identify all those investigations that have an urgent/emergent indication and reschedule all the elective ones, especially for patients at higher risk of infection and low priority for echocardiogram. Echocardiogram execution Echocardiographic studies performed on paediatric patients with suspected or confirmed COVID-19 should be as focused as necessary to be of any diagnostic value. In the case of an echocardiogram in a suspected or confirmed COVID-19 hospital inpatient, a bedside investigation with a portable machine in the isolated room should be preferred, avoiding moving patients within the clinic or hospital. In this setting (suspected/confirmed COVID-19 and signs of myocarditis), CMR can be performed, considering the risk/benefit ratio according to the patient's hemodynamic status and exam's therapeutic impact. cache = ./cache/cord-334715-902pfxyz.txt txt = ./txt/cord-334715-902pfxyz.txt === reduce.pl bib === id = cord-334849-8rblgq9b author = LoPresti, Marissa title = The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature date = 2020-08-12 pages = extension = .txt mime = text/plain words = 7290 sentences = 456 flesch = 45 summary = 1 As with many complex diseases, the reality for most individuals likely involves a combination of genetic -including viral and host genetics -and non-genetic Relative to other coronaviruses, SARS-CoV-2 has unique biological properties and related clinical impact, but data regarding other coronaviruses may be relevant. This can help populate lists of genes that -along with data from related biological studies -may bear scrutiny in the developing and important large-scale host genetic 6 and porcine epidemic diarrhea virus (PEDV)in pigs. In various species, efforts have focused on genes encoding the relevant coronavirus receptor, including effects of viral and host genetic changes and how these may impact the disease process. 30 In humans (see Tables 1 and S2 and Figures 3 and 4 for details on human studies of these genes, including specific references), studies of specific ACE2 polymorphisms have not shown significant associations with SARS-CoV-1 susceptibility or outcome. cache = ./cache/cord-334849-8rblgq9b.txt txt = ./txt/cord-334849-8rblgq9b.txt === reduce.pl bib === id = cord-334891-4jgtxg07 author = Choudhury, Abhigyan title = In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date = 2020-11-11 pages = extension = .txt mime = text/plain words = 2926 sentences = 169 flesch = 54 summary = This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. cache = ./cache/cord-334891-4jgtxg07.txt txt = ./txt/cord-334891-4jgtxg07.txt === reduce.pl bib === id = cord-335118-oa9jfots author = Taka, E. title = Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date = 2020-09-21 pages = extension = .txt mime = text/plain words = 5264 sentences = 344 flesch = 61 summary = By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Initial studies have constructed a homology model of SARS-CoV-2 RBD in complex with ACE2, based on the SARS-CoV crystal structure (8, 14) and performed conventional MD (cMD) simulations totaling 10 ns (15, 16) and 100 ns (17, 18) in length to estimate binding free energies (15, 16) and interaction scores (18) . In this study, we performed a comprehensive set of all-atom MD simulations totaling 16.5 µs in length using the recently-solved structure of the RBD of the SARS-CoV-2 S protein in complex with the PD of ACE2 (7) . In 20 SMD simulations (each 15 ns, totaling 300 ns in length, table S1), the average work applied to unbind RBD from PD was 71.1 ± 12.7 kcal/mol (mean ± s.d.), demonstrating that the S protein binds stably to ACE2 (Fig. 3B) . cache = ./cache/cord-335118-oa9jfots.txt txt = ./txt/cord-335118-oa9jfots.txt === reduce.pl bib === id = cord-335172-5ig907on author = Busse, Laurence W. title = COVID-19 and the RAAS—a potential role for angiotensin II? date = 2020-04-07 pages = extension = .txt mime = text/plain words = 1668 sentences = 106 flesch = 52 summary = Likewise, patients on angiotensin-converting enzyme (ACE) inhibitors or angiotensin receptor blockers (ARB) could be at a greater risk due to the mechanism by which SARS-CoV-2 enters the cell. First, because it normally binds to ACE2 during its degradation and hydrolysis into angiotensin-(1-7) [11] , it may compete with the SARS-CoV-2 for the ACE2 receptor (Fig. 1) . Second, the binding of AngII to the AT1 receptor has been shown to cause internalization and downregulation of ACE2 through an ERK1/2 and p38 MAP kinase pathway in both in vitro animal and in vivo human models [12, 13] . However, to date, the link between ACE inhibitors and ARBs and severity of illness of SARS-CoV-2 infection is purely speculative. Ang-2, angiotensin II; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; ACE1, angiotensinconverting-enzyme 1; ACE2, angiotensin-converting-enzyme 2; H 2 O, water; Na + , sodium Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus cache = ./cache/cord-335172-5ig907on.txt txt = ./txt/cord-335172-5ig907on.txt === reduce.pl bib === id = cord-334960-l5q5wc06 author = Park, Su Eun title = Epidemiology, virology, and clinical features of severe acute respiratory syndrome -coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19) date = 2020-04-02 pages = extension = .txt mime = text/plain words = 3757 sentences = 258 flesch = 58 summary = 9) Two novel strains of coronavirus have jumped species from animal to human, spread by human-to-human transmission, and caused severe acute respiratory syndrome leading to high fatality rate in the past 2 decades. 10) Severe acute respiratory syndrome-associated virus (SARS-CoV), previously unknown coronavirus traced to horseshoe bats in southern China, caused 8,096 confirmed cases and 774 deaths (9.6% fatality rate) in 29 countries from November 2002 to July 2003. 19, 20) The virus was initially called 2019-novel coronavirus (2019-nCoV) upon its emergence, until the Coronaviridae Study Group of International Committee on Taxonomy of Viruses named the virus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the phylogenetic analysis, on February 11, 2020. 10) Conclusion Within 3 months since the discovery of a novel coronavirus in patients with pneumonia of unknown origin in Wuhan City, China, COVID-19 has spread rapidly throughout the world and is beating SARS-CoV and MERS-CoV in the number of confirmed cases and deaths. cache = ./cache/cord-334960-l5q5wc06.txt txt = ./txt/cord-334960-l5q5wc06.txt === reduce.pl bib === id = cord-334988-brumg6jh author = Traugott, Marianna title = Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in Different Stages of Infection: Comparison of Commercial Enzyme-Linked Immunosorbent Assays and Rapid Tests date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2236 sentences = 103 flesch = 51 summary = We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction–confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. In the current study, we compared the diagnostic ability of 4 enzyme-linked immunosorbent assays (ELISAs), which assess SARS-CoV-2-specific antibodies of different immunoglobulin (Ig) classes (Euroimmun SARS-CoV-2 IgA and IgG and Wantai SARS-CoV-2 IgM and total antibody), and 2 rapid tests (Wantai SARS-CoV-2 Ab Rapid Test and Hangzhou AllTest Biotech 2019-nCoV IgG/IgM Rapid Test) in 77 patients with symptomatic SARS-CoV-2 infection. Of the 77 patients with PCR-confirmed SARS-CoV-2 infection, 30 individuals (12 female, 18 male; median age, 58 years; age range, 15-83 years) provided serum/plasma samples that were obtained at symptom onset or 1-5 days after the onset of disease (group 1). cache = ./cache/cord-334988-brumg6jh.txt txt = ./txt/cord-334988-brumg6jh.txt === reduce.pl bib === id = cord-335156-l4jie8g6 author = Andreozzi, Fabio title = Eosinopenia and COVID-19 patients: So specific ? date = 2020-06-27 pages = extension = .txt mime = text/plain words = 308 sentences = 31 flesch = 66 summary = key: cord-335156-l4jie8g6 title: Eosinopenia and COVID-19 patients: So specific ? cord_uid: l4jie8g6 For the prediction of positive SARS-CoV-2 cases (diagnosis based on RT-PCR), eosinopenia has a sensitivity of 74.7% and specificity of 68.7% with the area under the curve AUC of 0.717. Up until end of March 20, Seasonal Influenza and COVID-19 were simultaneously present in Europe. We reviewed the laboratory results of two cohorts of SARS-CoV-2 (N = 50) and Influenza A (N = 41) patients (diagnosis confirmed by RT PCR). As such from the above, we can reach to the conclusion that complete eosinopenia is a common finding in both COVID-19 and Seasonal Influenza infections. Thus result could imply that eosinopenia could be considered as a potential biological indicator of either Influenza or SARS-COV-2 infections. Eosinopenia and elevated C-reactive protein facilitate triage of COVID-19 patients in fever clinic: a retrospective casecontrol study Co-infection with SARS-CoV-2 and influenza a virus in patient with pneumonia cache = ./cache/cord-335156-l4jie8g6.txt txt = ./txt/cord-335156-l4jie8g6.txt === reduce.pl bib === id = cord-335077-ievtvhge author = Hogan, Catherine A. title = Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2217 sentences = 115 flesch = 52 summary = The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. The aim of this study was to evaluate the test performance characteristics of the Accula SARS-CoV-2 test in a clinical setting against a high-complexity reference standard. The manufacturer's instructions comprise the following steps: collection of NP swab, lysis of viral particles in SARS-CoV-2 buffer, transfer of nucleic acid solution to a test cassette that contains internal process positive and negative controls, reverse transcription of viral RNA to cDNA, nucleic acid amplification, and detection by lateral flow. We included 100 samples (50 positive, 50 negative) previously tested by the SHC-LDT and subsequently tested with the Accula SARS-CoV-2 POCT. In individuals with moderate to high pretest probability of SARS-CoV-2, reflex testing of negative samples on a separate EUA assay should be performed. cache = ./cache/cord-335077-ievtvhge.txt txt = ./txt/cord-335077-ievtvhge.txt === reduce.pl bib === id = cord-335446-8l1vfsbc author = Liao, M. title = The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing date = 2020-02-26 pages = extension = .txt mime = text/plain words = 4710 sentences = 311 flesch = 55 summary = Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. To characterize the immune microenvironment of the SARS-CoV-2-infected lung, we performed scRNA-seq analysis of single cells in the lung BALF (37, 820 cells) using the 10X Genomics platform, from 3 of recovered mild cases and 3 of severe cases ( Figure 1A , Table 1 ). Our data indicated that the monocytes are recruited from circulation (FCN1 + ) to the lung to fuel the inflammation during severe diseases, and some monocytes may further go through the differentiation process into the SPP1 + populations and eventually the FABP4 + AMs. robust and early T cell response played crucial roles in viral clearance during acute respiratory infections [14] . cache = ./cache/cord-335446-8l1vfsbc.txt txt = ./txt/cord-335446-8l1vfsbc.txt === reduce.pl bib === id = cord-335155-x9az3twa author = Qi, Zhen title = Phylogeny of SARS-CoV as inferred from complete genome comparison date = 2003 pages = extension = .txt mime = text/plain words = 1616 sentences = 97 flesch = 59 summary = SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. To date, genomes from 12 SARS-CoV isolates and 12 previously identified coronaviruses have been completely sequenced. The unrooted phylogenetic tree was constructed for genomes from 12 SARS-CoV isolates and that from 12 previously identified coronviruses (Fig. 1) . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJOI) cache = ./cache/cord-335155-x9az3twa.txt txt = ./txt/cord-335155-x9az3twa.txt === reduce.pl bib === id = cord-335270-edga753o author = Lopez-Alvarez, Diana title = Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing date = 2020-06-25 pages = extension = .txt mime = text/plain words = 974 sentences = 70 flesch = 50 summary = title: Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing We report the genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a patient with symptoms of coronavirus disease 2019 (COVID-19) who was infected in Cali, Colombia. We report the coding-complete genome sequence of SARS-CoV-2 isolate Cali-01, obtained from a Colombian patient with no recent record of international travel. First, for quality control and filtering of reads (fragments of 400 to 700 bp), we used the gupplyplex script of the ARTIC Network bioinformatics protocol (https://artic.network/ncov-2019/ncov2019-bioinformatics -sop.html), followed by a reference assembly with minimap2 (6) and Pilon (7), using the sequence of the Wuhan-Hu-1 isolate (GenBank accession number MN908947.3). The genome sequence of SARS-CoV-2 isolate Cali-01 was deposited in GISAID and GenBank under accession numbers EPI_ISL_445219 and MT470219, respectively. The sequencing work was carried out at the Virology Laboratory, Department of Microbiology, of the Universidad del Valle, in Cali. cache = ./cache/cord-335270-edga753o.txt txt = ./txt/cord-335270-edga753o.txt === reduce.pl bib === id = cord-334884-ig6n9cet author = Jiménez-Alberto, Alicia title = Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors date = 2020-06-25 pages = extension = .txt mime = text/plain words = 4071 sentences = 257 flesch = 52 summary = The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. Taking this into consideration, we performed in silico evaluation of a set of approved drugs as potential inhibitors of Mpro from SARS-CoV-2; our findings show that several molecules warrant further analysis as treatment options against COVID-19. The SARS-CoV-2 Mpro structure and two of its main conformers, extracted from the molecular dynamics simulation trajectory file, were processed with AutoDockTools (Morris et al., 2009 ). Next, solvent-explicit molecular dynamics simulations were performed on Mpro; the resulting trajectory showed that the protein has a highly flexible active site as the amino acids surrounding the binding site had high RMSF (Root-Mean-Square Fluctuation) values. cache = ./cache/cord-334884-ig6n9cet.txt txt = ./txt/cord-334884-ig6n9cet.txt === reduce.pl bib === id = cord-335338-wzxjn5ip author = Wei, Lan title = Pathology of the thyroid in severe acute respiratory syndrome() date = 2006-09-25 pages = extension = .txt mime = text/plain words = 3536 sentences = 169 flesch = 44 summary = To further investigate the effects of SARS associated coronavirus (CoV) on the thyroid, we have undertaken a detailed study of the thyroid gland with special attention to the pattern of cellular and architectural alterations on parafollicular and follicular cells. In contrast to normal thyroid, the thyroid glands from patients with SARS consistently showed destruction of the follicular epithelium and exfoliation of epithelial cells into the follicle. Our study has demonstrated that thyroid glands in patients with SARS were significantly affected by the disease with extensive injury to the follicular epithelial cells and the parafollicular cells. The extent of morphological injury and the large quantity of cells undergoing apoptosis that we observed in the thyroid follicular epithelium provide an explanation for the diminished serum T3 and T4 levels in patients with SARS. Evaluation and observation of serum thyroid hormone and parathyroid hormone in patients with severe acute respiratory syndrome The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells cache = ./cache/cord-335338-wzxjn5ip.txt txt = ./txt/cord-335338-wzxjn5ip.txt === reduce.pl bib === id = cord-335292-x2vjzp18 author = Nagashima, S. title = The Endothelial Dysfunction and Pyroptosis Driving the SARS-CoV-2 Immune-Thrombosis date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3502 sentences = 221 flesch = 43 summary = Approach and Results: Post-mortem lung (6 cases of COVID-19 group; 10 cases of H1N1 group and 11 cases of Control group) and myocardial samples (2 cases of COVID-19 and one control) were analyzed by conventional immunohistochemistry by using antibodies to identify molecules involving with endothelial activation (CD163, Interleukin-6 (IL-6), Tumor Necrosis Factor alpha (TNF-alpha), Intercellular Adhesion Molecule 1 (ICAM-1)) and pyroptosis (Caspase-1). In addition to COVID-19 endothelial activation, the probable higher significant involvement of pyroptosis, in this pandemic disease, but not in H1N1pdm09, may drive the massive endothelial cell death contributing to thrombogenic mechanism. The presence of the same pattern of tissue expression (COVID-19 patients with higher CD163, IL-6, ICAM-1, TNF-alpha, and Caspase-1 tissue expression than control patient) in the myocardial samples might suggest that endothelial dysfunction and pyroptosis mechanism could be more than a local lung process, but a systemic event. cache = ./cache/cord-335292-x2vjzp18.txt txt = ./txt/cord-335292-x2vjzp18.txt === reduce.pl bib === id = cord-335364-qwjuzebd author = Fernandez-Rivas, G. title = Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4200 sentences = 233 flesch = 51 summary = title: Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave Methods: IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22nd, 2020) by chemiluminescence assays. IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22 nd , 2020) by chemiluminescence assays. Hence, in this study we analyzed the SARS-CoV-2 IgG seroprevalence in Healthcare workers of the Northern Metropolitan Area of Barcelona, Spain. From May 4th to May 22 nd , 2020, all Healthcare workers of the ICS-Northern Metropolitan Area of Barcelona (n=9315) were offered to have serum testing performed for SARS-CoV-2 IgG antibodies. cache = ./cache/cord-335364-qwjuzebd.txt txt = ./txt/cord-335364-qwjuzebd.txt === reduce.pl bib === id = cord-335040-1qa6pe4v author = Rogstam, Annika title = Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 7408 sentences = 385 flesch = 59 summary = The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. observed SARS nsp10 in the same space group as reported here, I213, reporting a monomer in the asymmetric unit but a dimer in solution, as was determined by size exclusion Residues shaded in red are fully conserved, while residues with text in red indicate a change to a similar residue. We determined the crystal structure and behaviour in solution of SARS-CoV-2 nsp10 in its unbound form. cache = ./cache/cord-335040-1qa6pe4v.txt txt = ./txt/cord-335040-1qa6pe4v.txt === reduce.pl bib === id = cord-335122-8s3bcyo8 author = Marshall, Steve title = COVID-19: What do we know? date = 2020-09-21 pages = extension = .txt mime = text/plain words = 5249 sentences = 375 flesch = 41 summary = 44, 45, [47] [48] [49] The amount of viable SARS-CoV-2 in droplet nuclei remains unclear, but in subjects infected with other respiratory viruses, such as influenza, experiments comparing coughing and breathing suggest an equivalent production of viral RNA and replication-competent virus, detected at close range (< 12 inches). 78 In situations where healthcare workers wearing personal protective equipment (PPE) attend to patients with COVID-19 and do not perform medical AGPs, direct airborne transmission of replicationcompetent SARS-CoV-2 has not been confirmed. 79 The results of hospital studies evaluating aerosolization of body fluids and respiratory droplets of SARS-CoV-1 infected patients generated during certain medical AGPs (tracheal intubation, non-invasive ventilation, bronchoscopy, etc.), suggest that airborne transmission of SARS-CoV-2 may be possible during these procedures. Currently there are no studies reporting airborne viable (replication-competent) SARS-CoV-2 virus J o u r n a l P r e -p r o o f in hospital settings where infected patients are cared for, but not subjected to medical AGPs, by healthcare workers wearing surgical masks. cache = ./cache/cord-335122-8s3bcyo8.txt txt = ./txt/cord-335122-8s3bcyo8.txt === reduce.pl bib === id = cord-334973-jemeyudi author = Wu, Dingye title = Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center date = 2020-07-22 pages = extension = .txt mime = text/plain words = 2429 sentences = 151 flesch = 54 summary = title: Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center Hospitalization days, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid positive days, minimal lymphocyte count, and occurrence time were collected and comparatively analyzed. In addition, a multiple linear regression model was used to analyze the effect of diabetes on minimal lymphocyte count and its emergence time, patient's hospitalization days, and SARS-CoV-2 nucleic acid positive days by adjusting for potential confounding factors including age; gender; BMI; SBP; DBP; and ALT, AST, and Cr levels. This single center, observational, retrospective study of patients with COVID-19 showed that, patients with T2DM have higher CRP, lower level and more rapid decline in lymphocyte count, and longer hospitalization time than those without T2DM. Our study found a decrease in lymphocyte count in patients with COVID-19, and the lower the lymphocyte count, the longer SARS-CoV-2 nucleic acid positive days and hospitalization days. cache = ./cache/cord-334973-jemeyudi.txt txt = ./txt/cord-334973-jemeyudi.txt === reduce.pl bib === id = cord-335075-6wo2o5pp author = Bangaru, Sandhya title = Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4715 sentences = 240 flesch = 51 summary = Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Site-specific glycosylation of the SARS-CoV-2 prefusion spike protein produced in SF9 insect cells was analyzed using our recently described mass spectrometry proteomics-based method, involving treatment with proteases followed by sequential treatment with the endoglycosidases (Endo H and PNGase F) to introduce mass signatures in peptides with N-linked sequons (Asn-X-Thr/Ser) to assess the extent of glycosylation and the degree of glycan processing from high mannose/hybrid type to complex type (24) . In this study, we performed structural analysis of the Novavax SARS-CoV We also observed two non-spike densities within the spike trimer that corresponded with linoleic acid and polysorbate 80 detergent. cache = ./cache/cord-335075-6wo2o5pp.txt txt = ./txt/cord-335075-6wo2o5pp.txt === reduce.pl bib === id = cord-335347-vxl2flbn author = Diercks, Gillian R. title = Asymptomatic COVID-19 Infection in a Child with Nasal Foreign Body date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1914 sentences = 104 flesch = 40 summary = Aerosolized SARS-CoV-2 viral particles have been shown to remain viable for up to 3 hours 10 , raising concern about risk of exposure for healthcare workers during aerosol generating procedures (APGs), including endoscopy, in the nasal cavity, nasopharynx and upper airway. Prior to bringing the patient to the operating room, COVID-19 testing was pursued given concerns about the potential for asymptomatic infection in the pediatric population, and generation of aerosolized respiratory secretions during nasal endoscopy, suctioning and foreign body removal, in order to optimize protection of the perioperative care team and surgical staff. Preoperative planning and SARS-CoV2 testing is of particular importance for the pediatric population given the high proportion of SARS-CoV-2 infected children who are asymptomatic or exhibit minimal symptoms of COVID-19, but who may harbor significant viral loads in the nasopharynx and upper airway, placing healthcare workers at particular risk. cache = ./cache/cord-335347-vxl2flbn.txt txt = ./txt/cord-335347-vxl2flbn.txt === reduce.pl bib === id = cord-335386-eflyypev author = Steinman, Jonathan Baruch title = Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics date = 2020-10-06 pages = extension = .txt mime = text/plain words = 5373 sentences = 287 flesch = 48 summary = Exploring why the pediatric population is generally far less likely to develop COVID-19, even though their rate of infection is similar to adults (10), may offer productive clues, enabling strategies for (1) Coronavirus associated with common colds in children may offer some protection due to cross-reactive T cell immunity and crossreactive antibody immunity between common coronaviruses and SARS-CoV-2, and due to reduced ACE2 in nasal mucosa of children. A reasonable conjecture might be that, if ACE2 and/or TMPRSS2 expression is diminished in children, then viral infection of respiratory cells by SARS-CoV-2 might be less likely at any given viral load, and, additionally, there might be reduced expression of associated inflammatory modules. T[h]2 inflammation may predispose individuals to experience better COVID-19 outcomes through a decrease in airway levels of ACE2 that override any countervailing effect from increased expression of TMPRSS2." It is indeed surprising that the Th2 immune type associated with allergic diseases including asthma, and with eosinophilia, provides some protection to COVID-19 in children. cache = ./cache/cord-335386-eflyypev.txt txt = ./txt/cord-335386-eflyypev.txt === reduce.pl bib === id = cord-335302-6wsx0jby author = Mahy, Brian W.J. title = The diversity of viruses infecting humans date = 2011-12-12 pages = extension = .txt mime = text/plain words = 2865 sentences = 123 flesch = 48 summary = Other new viruses have been recognized because of a new disease they caused in humans, such as the severe acute respiratory syndrome (SARS) coronavirus . Studies on the origin of the SARS coronavirus are still ongoing: there is recent evidence of a zoonotic origin of the human disease, perhaps from palm civets, but the true natural reservoir of the virus seems most likely to be in a bat species, probably Chinese horseshoe bats (Lau et al. This was the only known human parvovirus until very recently, when a new parvovirus was discovered to be the cause of lower respiratory tract infections in children. 2006 ) and elsewhere (unpublished) have revealed a significant number of children whose lower respiratory tract disease appears to be caused by human bocavirus infection. New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children cache = ./cache/cord-335302-6wsx0jby.txt txt = ./txt/cord-335302-6wsx0jby.txt === reduce.pl bib === id = cord-335599-98ovzui5 author = Raony, Ícaro title = Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1198 sentences = 54 flesch = 42 summary = title: Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus Notwithstanding this, it was not discussed whether the patients already presenting changes in the retina before infection with COVID-19, or even if there was any systemic disease (e.g. type 2 diabetes mellitus) that could also be associated with retinal lesions. Thus, it is possible that CD147, by mediating the breakdown of the blood-retinal barrier in a hyperglycemic context, may facilitate the invasion of retinal cells by SARS-CoV-2 in people with DM, which deserves to be investigated by future studies with animal models and humans. The reverse is also possible, with COVID-19 being able to precipitate or worsen retinal lesions present in patients with DM in the short or long term, either by direct effects of retinal SARS-CoV-2 infection, or by the indirect effects of the cytokine storm associated with COVID-19. cache = ./cache/cord-335599-98ovzui5.txt txt = ./txt/cord-335599-98ovzui5.txt === reduce.pl bib === id = cord-335443-iv2gs3kg author = Kim, Youngchang title = Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date = 2020-06-28 pages = extension = .txt mime = text/plain words = 5464 sentences = 333 flesch = 57 summary = Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme's active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5'GAACU¯CAU¯GGACCU¯U¯GGCAG3' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5'UMP, 3'UMP, 5'GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5'GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5'UMP complex. cache = ./cache/cord-335443-iv2gs3kg.txt txt = ./txt/cord-335443-iv2gs3kg.txt === reduce.pl bib === id = cord-335137-5qt286kc author = Chatterjee, Swapan K. title = Molecular Pathogenesis, Immunopathogenesis and Novel Therapeutic Strategy Against COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 7124 sentences = 369 flesch = 47 summary = It is believed that interaction between angiotensin converting enzyme 2 (ACE2) cell receptor and viral Spike protein mediates the coronavirus entry into human respiratory epithelial cells and establishes the host tropism. The most significant surface protein is spike glycoprotein which interferes in establishing the association between the human respiratory epithelial cells to the virus via cell surface membrane receptor angiotensin-converting enzyme 2 (ACE2) and finally establishes the host tropism (Li et al., 2003) . A recent study suggests that prediction of SARS-CoV-2 spike glycoprotein structure, glycan shield pattern and pattern of glycosylation has great inference on understanding the viral camouflage as well as the outline of cell entry, and also facilitate the development of new small-molecule drugs, vaccines, antibodies, and screening of the human host targets (Song et al., 2018) . Various studies have proved that SARS-CoV-2 infection initiation and spread of disease into the host cells mainly depends upon S protein priming by TMPRSS2 (Transmembrane protease serine type 2), the serine protease. cache = ./cache/cord-335137-5qt286kc.txt txt = ./txt/cord-335137-5qt286kc.txt === reduce.pl bib === id = cord-335610-3v8140b6 author = Prasanth, D. S. N. B. K. title = In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2 date = 2020-06-22 pages = extension = .txt mime = text/plain words = 5031 sentences = 310 flesch = 49 summary = Our research study is intended to recognize the phyto-derived antiviral substances from Cinnamon against COVID-19 main protease enzyme and to understand the in silico molecular basis of its activity. Based on the above properties of Cinnamon, this research aimed to show a variety of active compounds across all Cinnamon varities and decide whether and how they interact with proteins i.e. main protease (Joshi et al., 2020) and spike protein, that are essential in the management of SARS-CoV-2. The crystal structure of Main protease (6LU7) and Spike receptor-binding domain complexed with its receptor ACE2 (6LZG) with selected top ligands identified from docking analysis such as Tenufolin (TEN) and Pavetannin C1 (PAV) were subjected to molecular dynamics using gromacs GPU enabled package. The main protease with tenufolin Spike protein (6LZG), associated with SARS was found to exhibit the best possible interaction with Pavetannin C1 (À11.1 kcal/mol) among the phytochemicals ( Table 2) . cache = ./cache/cord-335610-3v8140b6.txt txt = ./txt/cord-335610-3v8140b6.txt === reduce.pl bib === id = cord-335538-thd5oaef author = Ji, Xiaoyang title = TWIRLS, a knowledge‐mining technology, suggests a possible mechanism for the pathological changes in the human host after coronavirus infection via ACE2 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5274 sentences = 252 flesch = 46 summary = First, TWIRLS can process and summarize the massive biomedical literature on coronaviruses, and then collect, classify, and analyze reported coronavirus studies to reveal host-related entities based on the distribution of specific genes in the text of the articles. We obtained text data (referred to as the local samples) from all related peer reviewed articles published by human researchers that contained the keyword "coronavirus" including the title, abstracts, and author and affiliation information (total 3,182,687 words). TWIRLS first calculates the specific co-distribution between CSHGs in local samples, then determines the distance between each pair of CSSEs and performs dichotomy clustering according to the linkage relationship between CSSEs and CSHGs. This step classified the 623 entities into 32 categories represented as C0-C31 (see category number in Table S1 , Sheet 1 second column). Interestingly, CSHGs in the 2 connections of ACE2 and DPP4 associated with category C5 were also enriched in category C3, inferring that the information summarized in category C3 probably describes the underlying mechanisms of the pathological changes after coronavirus infection. cache = ./cache/cord-335538-thd5oaef.txt txt = ./txt/cord-335538-thd5oaef.txt === reduce.pl bib === id = cord-335648-lbmhprjn author = Estrich, Cameron G. title = Estimating COVID-19 prevalence and infection control practices among US dentists date = 2020-10-15 pages = extension = .txt mime = text/plain words = 4197 sentences = 207 flesch = 49 summary = Dentists from every US state (n = 2,195) answered questions about COVID-19–associated symptoms, SARS-CoV-2 infection, mental and physical health conditions, and infection control procedures used in their primary dental practices. As early as March 2020, Journal of Dental Research published the infection control guidelines that dentists at Wuhan University used, 7 and, in April and May 2020, the American Dental Association (ADA) and the Centers for Disease Control and Prevention (CDC), respectively, released interim guidance on infection control protocols and changes to the practice and office environments. In this article, we used the first month of study data to estimate the prevalence of COVID-19 among US dentists and to determine the rate of compliance with CDC and ADA infection prevention and control procedures. 14, 15 Respondents who reported providing oral health care in the past month were asked about infection prevention or control procedures in their primary dental practice. cache = ./cache/cord-335648-lbmhprjn.txt txt = ./txt/cord-335648-lbmhprjn.txt === reduce.pl bib === id = cord-335308-5kh7wgvx author = Ponnusamy, Rajesh title = Variable Oligomerization Modes in Coronavirus Non-structural Protein 9 date = 2008-11-28 pages = extension = .txt mime = text/plain words = 10725 sentences = 580 flesch = 62 summary = In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Although the residue responsible for disulfide formation in HCoV-229E Nsp9, Cys69, is conserved in SARS-CoV Nsp9, and the sequence identity is as high as 45% between the two proteins (see Supplementary Data Fig. S3 ), the mode of dimerization in the latter is very different from what we observe in our structure. Wild-type SARS-CoV Nsp9 and the HCoV-229E Nsp9 Cys69Ala mutant form higher oligomers at a protein concentration of 100 μM, presumably involving interactions similar to those seen in the crystal structure. On the other hand, the HCoV-229E Cys69Ala mutant has a dimerization mode similar to that of the wild-type SARS-CoV Nsp9 but it does not show binding with the nucleic acid in the gel mobility-shift experiment (except for the small shift seen for the 55-mer, the longest oligonucleotide tested). cache = ./cache/cord-335308-5kh7wgvx.txt txt = ./txt/cord-335308-5kh7wgvx.txt === reduce.pl bib === id = cord-335492-od3c25qg author = UGUREL, Osman Mutluhan title = An updated analysis of variations in SARS-CoV-2 genome date = 2020-06-21 pages = extension = .txt mime = text/plain words = 4971 sentences = 273 flesch = 57 summary = In this study; we have used these data to analyse the mutations on SARS-CoV-2 genome using a software based on multiple sequence alignment (Strategy Based Local Alignment Tool: ODOTool) that have been originally developed for bacterial SNP determination in our studies. Now, we targeted to analyse the mutations that have emerged in at least 10% of SARS-CoV-2 genomes in all 30366 sequences submitted in GISAID by May 20th, 2020 using the ODOTool in terms of date and location they occurred, the relationship with each other and their effect on the primary protein structure. Despite the Strategy Based Local Alignment Tool (ODOTool) used in this study was originally developed by our group for bacterial single nucleotide polymorphism (SNP) determination, it was reasonable to test the abilities of the tool using a different dataset with the emergence of SARS-CoV-2 causing COVID-19 pandemic and this is applied in the present study to analyse variations in viral genome. cache = ./cache/cord-335492-od3c25qg.txt txt = ./txt/cord-335492-od3c25qg.txt === reduce.pl bib === id = cord-335597-anrzcsrt author = nan title = 44. Jahrestagung der Österreichischen Gesellschaft für Pneumologie date = 2020-10-26 pages = extension = .txt mime = text/plain words = 14629 sentences = 921 flesch = 49 summary = Conclusions: In this study assessing the prognostic relevance of pulmonary exercise hemodynamics in patients with systemic sclerosis, PVR and TPR at peak exercise as well as mPAP/CO-slope and TPG/CO-slope turned out as age-independent predictors of all-cause mortality. Later-line treatment with lorlatinib in ALKand ROS1-rearrangement-positive NSCLC: a retrospective, multicenter analysis Background: Anti-fibrotic medication is effective in progressive fibrosing interstitial lung diseases (ILD), but a subgroup of fibrotic ILD patients also benefits from immunomodulatory therapies. Methods: HRCT of 127 subsequent single-center ILDboard patients (mean age 65 (standard deviation 14) years, 65 % male), were evaluated for radiological findings considered noninflammatory (reticulation including honeycombing (RET), traction bronchiectasis (TBR), emphysema (EMP)) or active inflammatory (consolidations (CON), ground glass opacities (GGO), noduli (NDL), mosaic attenuation (MOS)) in 6 distinct lung regions. cache = ./cache/cord-335597-anrzcsrt.txt txt = ./txt/cord-335597-anrzcsrt.txt === reduce.pl bib === id = cord-335652-v98gv5uf author = Salazar, Cecilia title = Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date = 2020-05-10 pages = extension = .txt mime = text/plain words = 2063 sentences = 131 flesch = 48 summary = Methods We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region. This global health emergency has deployed international efforts to apply genomic epidemiology to track the spread of SARS-CoV-2 in real time. The recent development of targeted sequencing protocols by the ARTIC Network [3] , open sharing of genomic data through the GISAID (www.gisaid.org) database and straightforward bioinformatic tools for viral phylogenomics [4] , provides the opportunity to reconstruct global spatio-temporal dynamics of the COVID-19 pandemic with unprecedented comprehensiveness and resolution. We therefore aimed to characterize the spatio-temporal dynamics of SARS-CoV-2 by sequencing around 10% of cases occurred during the first week of outbreak in Montevideo, allowing us to identify transmission patterns, geographic origins and genetic variation among local strains. cache = ./cache/cord-335652-v98gv5uf.txt txt = ./txt/cord-335652-v98gv5uf.txt === reduce.pl bib === id = cord-335768-ry5boej6 author = Chauhan, Shaylika title = Comprehensive review of coronavirus disease 2019 (COVID-19) date = 2020-06-01 pages = extension = .txt mime = text/plain words = 4382 sentences = 242 flesch = 55 summary = Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, the capital of China's Hubei province and has rapidly spread all over the world. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 12, 2020, as shown in Fig. 1 , this has evolved into a pandemic affecting 187 countries/regions with 1, 484, 811 cases in the world with maximum being in USA(1, 347,936) followed by 227,436 in Spain and 224, 422 in United Kingdom at the time of writing .6 It is an un-precedented global health crisis with 286,355 deaths since the virus was first reported. Severe outcomes among patients with coronavirus disease 2019 (COVID-19) d United States cache = ./cache/cord-335768-ry5boej6.txt txt = ./txt/cord-335768-ry5boej6.txt === reduce.pl bib === id = cord-335567-ssnvr6nj author = Berry, Michael title = Identification of New Respiratory Viruses in the New Millennium date = 2015-03-06 pages = extension = .txt mime = text/plain words = 7477 sentences = 379 flesch = 40 summary = In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients cache = ./cache/cord-335567-ssnvr6nj.txt txt = ./txt/cord-335567-ssnvr6nj.txt === reduce.pl bib === id = cord-335591-r0x8yaqj author = Ohnishi, Kazuo title = Establishment and Characterization of Monoclonal Antibodies Against SARS Coronavirus date = 2007-11-28 pages = extension = .txt mime = text/plain words = 3126 sentences = 242 flesch = 67 summary = The hybridomas produce monoclonal antibodies that recognize viral component molecules, including the spike protein (S) and the nucleocapsid protein (N), enabling the immunological detection of SARS-CoV by immunofluorescence staining, immunoblot, or an antigen-capture ELISA system. Based on clinical experience, several options have been considered in the quest to develop the capacity to accurately diagnose SARS-CoV infection, including molecular biology techniques and serological tests such as antigen-capture ELISA assay and immunofluorescence assay to detect virus-infected cells in respiratory swabs (3-7) . These mAbs enable the general immunological detection of SARS-CoV by methods such as immunofluorescent staining, immunoblotting, and immunohistology, in addition to the construction of a highly sensitive antigen-capture sandwich ELISA (6). The UV-inactivated purified SARS-CoV samples (see Note 1), which are serially diluted with 1% OVA/PBS-Tween, are added to the wells and incubated for 1 h at room temperature cache = ./cache/cord-335591-r0x8yaqj.txt txt = ./txt/cord-335591-r0x8yaqj.txt === reduce.pl bib === id = cord-335375-n6q70o35 author = Chan, Paul K. S. title = Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date = 2005-07-01 pages = extension = .txt mime = text/plain words = 2186 sentences = 109 flesch = 55 summary = Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. cache = ./cache/cord-335375-n6q70o35.txt txt = ./txt/cord-335375-n6q70o35.txt === reduce.pl bib === id = cord-335859-k37jivp6 author = Wu, Daphne C. title = Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date = 2020-10-21 pages = extension = .txt mime = text/plain words = 3112 sentences = 160 flesch = 52 summary = To understand the socio-demographic predictors of COVID symptoms, we conducted a logistic regression analysis where the outcome was self-reported symptoms suggestive of COVID infection which we defined in this study as the respondent reporting himself/herself and/or at least one member of the household having had a combination of fever (with or without hallucinations) and any of i) difficulty breathing/shortness of breath or ii) dry cough so severe that it disrupts sleep or iii) a loss of a sense of smell in the past month; and the explanatory variables were gender (male, female, or other), education level (high school and under, or some college/ university and higher), province, age, ethnicity (Indigenous, English and other European, or others), visible minority (defined as persons, other than Aboriginal peoples, who are nonwhite in race or colour) [6] , and number of household members. cache = ./cache/cord-335859-k37jivp6.txt txt = ./txt/cord-335859-k37jivp6.txt === reduce.pl bib === id = cord-335377-zrbn637z author = Ishimaru, Daniella title = RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date = 2012-12-26 pages = extension = .txt mime = text/plain words = 7699 sentences = 376 flesch = 52 summary = Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. We further show that kissing dimer formation plays a role in frameshift-stimulation and modulates the relative abundance of full-length and subgenomic viral RNAs. Plasmids containing wild-type pseudoknot as well as the ÁS3 pk mutant were described in Plant et al (1) . Our previous NMR analysis of exchangeable imino protons of the SARS-CoV pseudoknot ( Figure 1A , wild-type pk) provided unequivocal evidence for the existence of Stem 3 (1). Surprisingly, in the context of the SARS-CoV Stem 3 sequence, 5 0 -cuug-3 0 tetraloop-capped mutants readily formed extended duplex structures as revealed by native gel and NMR analysis. cache = ./cache/cord-335377-zrbn637z.txt txt = ./txt/cord-335377-zrbn637z.txt === reduce.pl bib === id = cord-335467-0b0m8v5r author = Saha, Asit title = Novel coronavirus SARS‐CoV‐2 (Covid‐19) dynamics inside the human body date = 2020-07-19 pages = extension = .txt mime = text/plain words = 2617 sentences = 162 flesch = 51 summary = A time‐dependent nonlinear system of ordinary differential equations model was constructed involving type‐I cells, type‐II cells, SARS‐CoV‐2 virus, inflammatory mediators, interleukins along with host pulmonary gas exchange rate, thermostat control, and mean pressure difference. The cybernetic model can simulate a dynamic response to the reduced pulmonary alveolar gas exchange rate, thermostat control, and mean pressure difference under a very critical condition based on equilibrium (steady state) values of the inflammatory mediators and system parameters. 13, 14 In the present study, we aim to understand the chain of events after the SARS-CoV-2 virus invaded the human body, creating chaos in the respiratory system, thermostat control, and multiple organ failure systematic networks using the knowledge-based cybernetic model. cache = ./cache/cord-335467-0b0m8v5r.txt txt = ./txt/cord-335467-0b0m8v5r.txt === reduce.pl bib === id = cord-335844-dybozins author = Berkowitz, Kathleen M. title = IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY date = 2020-07-11 pages = extension = .txt mime = text/plain words = 255 sentences = 33 flesch = 64 summary = key: cord-335844-dybozins title: IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY cord_uid: dybozins Cleveland Clinic Foundation recently implemented a policy OF SARS-CoV-2 testing for all 9 pregnant patients with planned delivery or admitted for labor at obstetric units in Ohio. In contrast to a recent report (1) on universal screening of pregnant women residing in an 12 area of high disease prevalence, our experience derives from a population experiencing a low 13 prevalence of active disease. 14 Patients with planned delivery were tested 3-5 days prior to admission using a CDC approved 15 RT-PCR testing platform. Patients presenting 16 in spontaneous labor were tested using a rapid platform (Xpert Xpress SARS-CoV-2 (Cepheid, Screening all pregnant women admitted to 40 labor and delivery for the virus responsible for coronavirus disease 2019 Universal Screening for SARS-CoV-2 in 46 Women Admitted for Delivery Women Admitted for Delivery cache = ./cache/cord-335844-dybozins.txt txt = ./txt/cord-335844-dybozins.txt === reduce.pl bib === id = cord-336000-v88bq4bx author = Barco, Stefano title = Enoxaparin for primary thromboprophylaxis in ambulatory patients with coronavirus disease-2019 (the OVID study): a structured summary of a study protocol for a randomized controlled trial date = 2020-09-09 pages = extension = .txt mime = text/plain words = 20392 sentences = 1064 flesch = 44 summary = OBJECTIVES: The OVID study will demonstrate whether prophylactic-dose enoxaparin improves survival and reduces hospitalizations in symptomatic ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. The OVID study will show whether prophylactic-dose enoxaparin improves survival and reduces any hospitalizations in ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. <30% of the expected number of patients six months after the enrolment of the first patient, also based on the course of SARS-CoV2 infections in Switzerland;  when the safety of the participants is doubtful or at risk, respectively, based on recommendations received from DSMB committee;  changes in accepted clinical practice that make the continuation of a clinical trial unwise, including the results of similar studies or the publication of international guidances. cache = ./cache/cord-336000-v88bq4bx.txt txt = ./txt/cord-336000-v88bq4bx.txt === reduce.pl bib === id = cord-335293-pac6wbgz author = Nijman, Ruud G. title = Pediatric Inflammatory Multisystem Syndrome: Statement by the Pediatric Section of the European Society for Emergency Medicine and European Academy of Pediatrics date = 2020-08-28 pages = extension = .txt mime = text/plain words = 3516 sentences = 175 flesch = 45 summary = A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome—temporally associated with SARS-CoV-2 (PIMS-TS). A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS). This statement aims to -provide information about the Pediatric Inflammatory Multisystem Syndrome temporally associated with SARS-CoV-2 (PIMS-TS); -give initial guidance on the clinical assessment and management of children suspected of this new condition for health care professionals dealing with acutely unwell children; -point out useful resources on the recognition and management of these children. The initial guidance from the Royal College of Pediatrics and Child Health in the United Kingdom provided a case definition and called this emerging disease entity the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS) (28) . cache = ./cache/cord-335293-pac6wbgz.txt txt = ./txt/cord-335293-pac6wbgz.txt === reduce.pl bib === id = cord-335784-v7nbck0n author = Barak, N. title = Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3136 sentences = 202 flesch = 57 summary = Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Major diagnostic challenges have emerged, mainly, the need for high throughput SARS-CoV-2 RT-PCR tests, aimed to detect not only symptomatic but also asymptomatic infectious viral carriers and to screen special or at-risk populations (such as health care personnel or nursing home tenants), in order to contain viral spread and guide control measures. To our knowledge, this is the most extensive analysis, addressing key considerations of efficiency, sensitivity and feasibility in the actual reality of routine, large-scale implementation of sample pooling for SARS-CoV-2 detection. cache = ./cache/cord-335784-v7nbck0n.txt txt = ./txt/cord-335784-v7nbck0n.txt === reduce.pl bib === id = cord-336022-b2fwktld author = Addetia, Amin title = Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3979 sentences = 263 flesch = 56 summary = Only three 34 crewmembers tested seropositive prior to the boat's departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Only three 34 crewmembers tested seropositive prior to the boat's departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Prior to the ship's departure, crewmembers were screened for active SARS-CoV-2 182 infection by RT-PCR, or for serological evidence of prior or ongoing infection using the 183 Abbott Architect assay which detects antibodies against the viral nucleoprotein (N). . https://doi.org/10.1101/2020.08.13.20173161 doi: medRxiv preprint observed in humans who have been infected with SARS-CoV-2 within the previous few 198 months (29, 34, 35) . . https://doi.org/10.1101 pre-departure Abbot Architect anti-N serological screening, since only individuals 335 positive in that screening were subjected to additional serological assays for anti-spike 336 and neutralizing antibodies. cache = ./cache/cord-336022-b2fwktld.txt txt = ./txt/cord-336022-b2fwktld.txt === reduce.pl bib === id = cord-335932-0phqok4g author = Vanhems, Philippe title = Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit date = 2020-03-30 pages = extension = .txt mime = text/plain words = 579 sentences = 46 flesch = 60 summary = title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit Lyon Study Group on Covid19 infection (Geriatric sectionAlphabetic order): Adrait, A, Benoist F, Castel-Kremer E, Chuzeville M, Dupin AC, Doh S, Kim B, Favrelle L, Hilliquin D, Kanafer N, Marion E, Martin-Gaujard G, Moyenin Y, Paulet-Lafuma H, Ricanet A, Saadatian-Elahi M, Vanhems P. To the Editor-SARS-CoV2 nosocomial transmission has been reported among healthcare professionals and patients. The nasal swab previously collected was retested on March 6 and confirmed positive for SARS-CoV2 by RT-PCR. Strict infection control measures and close monitoring of suspected cases of patients and healthcare professionals were subsequently performed to contain the intraunit transmission of the SARS-Cov-2 virus. The rapid spread of nosocomial COVID-19 in this ward confirms the contagiousness of SARS-CoV-2 in healthcare settings and the high mortality rates in this population. Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit cache = ./cache/cord-335932-0phqok4g.txt txt = ./txt/cord-335932-0phqok4g.txt === reduce.pl bib === id = cord-336012-8klkojpo author = Harilal, Divinlal title = SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3040 sentences = 144 flesch = 45 summary = Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. cache = ./cache/cord-336012-8klkojpo.txt txt = ./txt/cord-336012-8klkojpo.txt === reduce.pl bib === id = cord-336094-ssr5y4u3 author = Blumberg, Dean A. title = Vertical Transmission of SARS-CoV-2: What is the Optimal Definition? date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1423 sentences = 82 flesch = 47 summary = 11 We start with several underlying assumptions (►Fig. 1) as follows: (1) the incubation period is 1 to 14 days 12,13 ; (2) intrauterine infection may potentially occur transplacentally via blood, or via transmission through swallowed or aspirated amniotic fluid; (3) maternal viremia is unlikely during the incubation period >48 hours before symptom onset and the likelihood of positive SARS-CoV-2 through RT-PCR in blood samples is low (< 1%) in COVID-19 patients 9 ; (4) intrapartum transmission may potentially occur due to exposure to maternal blood, vaginal secretions, or feces; (5) early postnatal infection may occur via the respiratory route or due to direct contact with the infected mother or other caretakers, or potential transmission through breast milk (however, to date we are not aware of any reports of viral presence in breast milk); and (6) SARS-CoV-2 virus may be transiently detected for up to 24 hours after birth due to superficial contamination or transient viremia (similar to HIV). cache = ./cache/cord-336094-ssr5y4u3.txt txt = ./txt/cord-336094-ssr5y4u3.txt === reduce.pl bib === id = cord-335938-hscgmis5 author = Gralinski, Lisa E. title = Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury date = 2013-08-06 pages = extension = .txt mime = text/plain words = 7816 sentences = 370 flesch = 42 summary = The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. To model system-wide behaviors following SARS-CoV infection, we performed a dose-response study that included biological sampling at multiple time points, transcriptional and proteomic systems biology data, and mathematical modeling algorithms to identify signaling networks associated with progression from severe to lethal disease outcomes. These data demonstrate the successful use of highly refined modeling algorithms to identify and validate novel genes and pathways that play critical roles in SARS-CoV pathogenesis and the development of ALI following virus infection in the lung. Similar changes in the urokinase, coagulation, and fibrinolysin pathway expression signatures are noted following highly pathogenic SARS-CoV and influenza virus infections (see Fig. S5B and S6 in the supplemental material), arguing for a con-served role for these pathways in virus-induced end-stage lung diseases, like ALI and ARDS. cache = ./cache/cord-335938-hscgmis5.txt txt = ./txt/cord-335938-hscgmis5.txt === reduce.pl bib === id = cord-335619-t3yv5y7h author = Wang, Song-mi title = Screening of SARS-CoV-2 in 299 Hospitalized Children with Hemato-oncological Diseases: A Multicenter Survey in Hubei, China date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2426 sentences = 131 flesch = 48 summary = A cross-sectional study was performed to investigate the clinical characteristics, lung CT scan, SARS-CoV-2 nucleic acid test and serum antibodies of hospitalized children with hemato-oncological diseases from January 23 to April 24, 2020. A cross-sectional study was performed to inves-tigate the SARS-CoV-2 infection status of children with hemato-oncological diseases hospitalized in three medical institutions from January 23 to April 24, 2020. The findings of this study showed that the SARS-CoV-2 infection rate in enrolled children with hematological malignancies was 0.33%. Zhang [3] reported that 53.6% of COVID-19infected cancer patients had serious clinical events, with a mortality rate of 28.6%. Therefore, for patients with hematological malignancies, the possibility of COVID-19 cannot be ruled out by negative antibody detection, which needs to be combined with multiple nucleic acid test, epidemiological history, and lung imaging to assist in the diagnosis. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-335619-t3yv5y7h.txt txt = ./txt/cord-335619-t3yv5y7h.txt === reduce.pl bib === id = cord-335958-dtvlo0kz author = Satyam, Rohit title = Deciphering the SSR incidences across viral members of Coronaviridae family date = 2020-09-21 pages = extension = .txt mime = text/plain words = 4611 sentences = 274 flesch = 55 summary = Thus, the aims of the current study were 1) to analyze various facets of the distribution and dynamics of SSRs in the genomes of Coronaviridae members, 2) to identify patterns of SSR incidences across genomes, if any i.e the underrepresentation/overrepresentation of specific repeat motif classes, 3) the preferential genomic localization of SSRs & 4) to investigate if SSRs serves as mutation hotspots in SARS-CoV-2, a novel SARS strain causing COVID-19 outbreak. Additionally, the attributes of SSRs across genomes under study were quite similar in terms of length (preferentially found to be 12-13 nucleotides long with polyA repeats of varying lengths), GC composition, abundance (SSR frequency didn't exceed 2 irrespective of genome size) and localization. The BED files (eg.sequence_perf_default.tsv) so produced by PERF comprise of SSRs genomic coordinates (Column 1-3) followed by repeat class, repeat Length, repeat Strand, motif Number & actual repeat (more details: https://github.com/RKMlab/perf) and were used for the downstream analysis. cache = ./cache/cord-335958-dtvlo0kz.txt txt = ./txt/cord-335958-dtvlo0kz.txt === reduce.pl bib === id = cord-336103-ufvq0ngl author = Sharma, R. title = Optimal sample pooling: an efficient tool against SARS-CoV-2 date = 2020-07-04 pages = extension = .txt mime = text/plain words = 1563 sentences = 125 flesch = 64 summary = 2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2 cache = ./cache/cord-336103-ufvq0ngl.txt txt = ./txt/cord-336103-ufvq0ngl.txt === reduce.pl bib === id = cord-336026-x02f7byo author = Lommatzsch, Marek title = COVID‐19 in a patient with severe asthma treated with Omalizumab date = 2020-06-27 pages = extension = .txt mime = text/plain words = 650 sentences = 52 flesch = 56 summary = 1, 3, 4 This is supwith asthma following Omalizumab treatment is primarily mediated by a downregulation of the high-affinity IgE receptor on pDCs. 8, 9 Thus, we hypothesize that the patient described in this case report might have been protected from an asthma exacerbation or pneumonia during COVID-19, either because of the underlying disease (allergic asthma) or because of the antibody used for treatment (Omalizumab), or both. Therefore, studies are needed to characterize the precise interaction of chronic airway diseases (such as asthma) and of biologics (such as Omalizumab) with SARS-CoV-2 infections in humans. We report a case of a 52-year-old man with severe allergic asthma treated with Omalizumab with no evidence of an asthma exacerbation, loss of asthma control or pneumonia during symptomatic COVID-19 disease. We hypothesize that the underlying disease (allergic asthma) or the antibody used for treatment (Omalizumab), or both, might have exerted protective effects. cache = ./cache/cord-336026-x02f7byo.txt txt = ./txt/cord-336026-x02f7byo.txt === reduce.pl bib === id = cord-336066-n9yq8enz author = Lai, Chien‐Chen title = Proteomic analysis of up‐regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C‐like protease date = 2007-04-04 pages = extension = .txt mime = text/plain words = 4014 sentences = 213 flesch = 45 summary = Functional classification of identified up-regulated proteins indicated that protein metabolism and modification, particularly in the ubiquitin proteasome pathway, was the main biological process occurring in SARS CoV 3CLpro-expressing cells. Interestingly, analysis of apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Table 3 ). Confocal imaging of the stained cells revealed that the release of apoptosis-inducing factor from mitochondria was found in the SARS CoV 3CLpro-expressing cells (Fig. 7A, right) , but not in mock cells (Fig. 7A, left) . Interestingly, analysis of the apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Figs. cache = ./cache/cord-336066-n9yq8enz.txt txt = ./txt/cord-336066-n9yq8enz.txt === reduce.pl bib === id = cord-336053-cjq7szcn author = Mottola, Filiberto Fausto title = Cardiovascular System in COVID-19: Simply a Viewer or a Leading Actor? date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5639 sentences = 268 flesch = 41 summary = Several studies have observed a relationship between coronavirus disease (COVID-19) infection and the cardiovascular system with the appearance of myocardial damage, myocarditis, pericarditis, heart failure and various arrhythmic manifestations, as well as an increase in thromboembolic risk. Compared to those without an increase in TnT, these patients were more likely to require invasive or non-invasive ventilation (22% versus 4%, and 46% versus 4%, respectively) and to develop acute respiratory distress syndrome (59% versus 15%) or acute kidney injury (9% versus 0%; p < 0.001 for all); in addition, the mortality rate was higher (51.2% vs. A recent meta-analysis showed that cardiac troponin I (cTnI) values were significantly higher in patients with severe SARS-CoV-2 infection compared to those observed with mild forms [14] . However, myocardial damage alone is not enough and there are other factors involved in enhancing the arrhythmic risk in COVID-19: in fact, in these patients, only half showed acute cardiac injury despite the high frequency of arrhythmias [32] . cache = ./cache/cord-336053-cjq7szcn.txt txt = ./txt/cord-336053-cjq7szcn.txt === reduce.pl bib === id = cord-336049-n3swuykg author = Ahmed, Mubbasheer title = Multisystem inflammatory syndrome in children: A systematic review date = 2020-09-04 pages = extension = .txt mime = text/plain words = 5676 sentences = 343 flesch = 47 summary = INTERPRETATION: Multisystem inflammatory syndrome is a new pediatric disease associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is dangerous and potentially lethal. However, in early May 2020, investigators from South Thames Retrieval Service in London, UK published a report describing eight severely ill pediatric patients presenting in hyperinflammatory shock with multiorgan involvement [6] Specifically, the children manifested with high fever, rash, conjunctivitis, peripheral edema, and gastrointestinal symptoms. We included patients with COVID-19 to reinforce to the healthcare community and public the differences in the clinical presentation, to highlight the degree of systemic inflammation in MIS-C, and to iterate the differences in treatment and outcome between the two diseases. Data collected from the studies included demographics, number of patients, signs and symptoms, laboratory markers, imaging results, medications, and outcomes. Cardiac MRI of children with multisystem inflammatory syndrome (MIS-C) associated with COVID-19: case series cache = ./cache/cord-336049-n3swuykg.txt txt = ./txt/cord-336049-n3swuykg.txt === reduce.pl bib === id = cord-335955-2bw2sly8 author = Shi, Yuejun title = A Dimerization-Dependent Mechanism Drives the Endoribonuclease Function of Porcine Reproductive and Respiratory Syndrome Virus nsp11 date = 2016-04-14 pages = extension = .txt mime = text/plain words = 7045 sentences = 383 flesch = 53 summary = The crystal structures of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp15 and murine hepatitis virus (MHV) nsp15 show that the biological unit of nsp15 is a hexamer (19, 21) and that the N-terminal domain (NTD) is important for oligomerization (23) . We report the crystal structure of PRRSV endoribonuclease nsp11 and demonstrate that the folding of NendoU active site residues is widely conserved among members of the order Nidovirales (families Arteriviridae and Coronaviridae). Additionally, the structural comparison demonstrated that residues His129, His144, Lys173, Thr177, Asp180, Asp204, and Tyr219 from nsp11 superimpose well onto the corresponding residues of coronavirus nsp15 (Fig. 5 and 6 ), indicating the relative conservation of key active site residues and similar endoribonuclease cleavage mechanisms shared among nidoviruses (families Arteriviridae and Coronaviridae). In this study, endoribonuclease activity of the wild-type and mutant nsp11 protein was measured, and the results are shown in Fig. 7C . cache = ./cache/cord-335955-2bw2sly8.txt txt = ./txt/cord-335955-2bw2sly8.txt === reduce.pl bib === id = cord-336057-tj9qcuf8 author = Lv, Yantian title = No intrauterine vertical transmission in pregnancy with COVID-19: a case report date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1338 sentences = 88 flesch = 59 summary = The data of status of pregnant women and neonates after infection of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is limited. We report a case of pregnant woman in her third trimester with critical COVID-19, and amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were retained during cesarean section. Amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were collected during the operation and tested for the SARS-COV-2 nucleic acid, and the mother and infant were separated after the operation. In addition, not only SARS-COV-2 nucleic acid test results were negative in 4 times pharyngeal swabs, but also the anal swab, amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were negative. Li 9 also reported a 35-week pregnant woman with COVID-19, whose amniotic fluid, cord blood and placenta, breast milk samples as well as neonates swab SARS-COV-2 nucleic acid were all negative. cache = ./cache/cord-336057-tj9qcuf8.txt txt = ./txt/cord-336057-tj9qcuf8.txt === reduce.pl bib === id = cord-335802-1kiqfy68 author = Azoulay, Elie title = Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset date = 2020-08-11 pages = extension = .txt mime = text/plain words = 3515 sentences = 194 flesch = 48 summary = METHODS: In a multicentre retrospective study, we included 379 COVID-19 patients admitted to four ICUs between 20 February and 24 April 2020 and categorised according to time from disease onset to ICU admission. To test the hypothesis that COVID-19-related critical illness differs according to time from viral symptom onset to ICU admission, we assessed patient characteristics and outcomes in a cohort of 379 critically ill patients admitted to four university-affiliated hospitals in Paris. This study collecting data from 379 COVID-19 patients showed that mortality decreased with increasing time from viral symptom onset to ICU admission. Mortality was significantly higher in patients admitted to the ICU within a week after viral symptom onset, independently from acute illness severity at ICU admission. Second, the excess mortality in patients admitted to the ICU within 7 days after viral symptom onset was associated with an increased prevalence of non-respiratory injury and, more specifically, of acute kidney and myocardial injury. cache = ./cache/cord-335802-1kiqfy68.txt txt = ./txt/cord-335802-1kiqfy68.txt === reduce.pl bib === id = cord-336488-opjjowcq author = Kenanidis, Eustathios title = Organizing an Orthopaedic Department During COVID-19 Pandemic to Mitigate In-Hospital Transmission: Experience From Greece date = 2020-06-17 pages = extension = .txt mime = text/plain words = 3384 sentences = 160 flesch = 42 summary = The aim of this paper is to review the existing orthopaedic literature and to present the principles of management and care implemented in the orthopaedic departments of a tertiary academic hospital in Greece to operate during COVID-19 pandemic in order to mitigate the risk of in-hospital transmission of SARS-CoV-2 to the medical, nursing and administrative orthopaedic personnel. In addition, we presented the clinical indications to delineate orthopaedic patients who deserve emergency or urgent in-hospital care from those that can be treated in the outpatient setting, as well as from the day surgery clinics or could not be admitted in the hospital, in order to decrease the SARS-CoV-2 transmission load. The proposed principles of management and care are deployed below as (1) general management of the orthopaedic departments, (2) recommendations for the management of traumatic orthopaedic injuries, (3) hospital pathways for the admitted orthopaedic patients (4) workflow of the isolated and negative pressure COVID-19 operating theatre (COT) and (5) postoperative care of the COVID-19 infected patients. cache = ./cache/cord-336488-opjjowcq.txt txt = ./txt/cord-336488-opjjowcq.txt === reduce.pl bib === id = cord-336093-ic6q6ke8 author = Sun, Ying title = Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date = 2014-02-11 pages = extension = .txt mime = text/plain words = 6321 sentences = 361 flesch = 57 summary = Abbreviations: SARS, severe acute respiratory syndrome; SARS-CoV, SARS coronavirus; nsp, nonstructural protein; N7-MTase, guanine-N7-methyltransferase; 2 0 -O-MTase, 2 0 -O-methyltransferase; AdoMet, S-adenosyl-L-methionine; AdoHcy, S-adenosyl-L-homocysteine; ATA, aurintricarboxylic acid; IC 50 , inhibitory concentration at 50% activity. A single transformed colony of the YBS40 strain containing plasmids expressing human N7-MTase (MT-Human), SARS-CoV N7-MTase (MT-SARS), N7-MTases of other coronaviruses (MT-MHV, MT-TGEV, and MT-IBV), and the pMceK294A vector as control (representing the yeast N7-MTase [MT-Yeast]), were inoculated separately into 5 ml of a basic medium (Min SD Base) lacking tryptophan and incubated at 30°C for 21-24 h until reaching a similar final cell density in the stationary phase (0.5-1.0  10 8 cells/ml) (Chrebet et al., 2005) . Although AdoHcy, ATA and sinefungin, were previously reported to be inhibitors of coronavirus RNA MTases in vitro , only sinefungin significantly suppressed the growth of the MT-yeast, MT-human, and MT-SARS yeast cells (Fig. 3 ). cache = ./cache/cord-336093-ic6q6ke8.txt txt = ./txt/cord-336093-ic6q6ke8.txt === reduce.pl bib === id = cord-336119-8g37xsys author = Nimgampalle, Mallikarjuna title = Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date = 2020-06-24 pages = extension = .txt mime = text/plain words = 5464 sentences = 283 flesch = 50 summary = Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . cache = ./cache/cord-336119-8g37xsys.txt txt = ./txt/cord-336119-8g37xsys.txt === reduce.pl bib === id = cord-336150-l8w7xk0b author = Rathore, Jitendra Singh title = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview date = 2020-08-25 pages = extension = .txt mime = text/plain words = 7362 sentences = 399 flesch = 54 summary = The essential surface glycoprotein of SARS-CoV-2 known as spike (S) protein, essential for host cell receptor binding, showed only 72% similarity with SARS-CoV at the nucleotide level. Comparative genome analysis of RaTG13, a virus from a Rhinolophusaffinis (i.e. horseshoe) bat sampled from Yunnan province in China in 2013, with SARS-CoV-2, showed that SARS-CoV-2 has 96% similarity at the nucleotide sequence level . Later, it was found that the disease was caused by a virus designated as a novel human coronavirus, MERS-CoV, phylogenetic data showed that it belonged to lineage C of the Betacoronavirusgenus and was highly similar to bat coronaviruses HKU4 (Tylonycterispachypus) and HKU5 (Pipistrelluspipistrellus; Lau et al. When cell lines over-expressed the transmembrane protein 'angiotensin-converting enzyme 2' (ACE2) from humans, bats, pig or civet cats and were infected with SARS-CoV-2, results showed that they became hypersensitized to infection, thus indicating that ACE2 is a SARS-CoV-2 receptor . Recently, neutralizing monoclonal antibodies and nanobodies against the RBD domain of S protein showed protection against SARS-CoV and MERS-CoV (Du et al. cache = ./cache/cord-336150-l8w7xk0b.txt txt = ./txt/cord-336150-l8w7xk0b.txt === reduce.pl bib === id = cord-335916-fh28qrt7 author = Liu, Cuiwei title = COVID-19 in cancer patients: risk, clinical features, and management date = 2020-08-15 pages = extension = .txt mime = text/plain words = 3937 sentences = 189 flesch = 40 summary = Cancer patients are regarded as a highly vulnerable population to SARS-CoV-2 infection and development of more severe COVID-19 symptoms, which is possibly due to the systemic immunosuppressive state caused directly by tumor growth and indirectly by effects of anticancer treatment. Another cohort study of 28 COVID-19 cancer patients reported that patients with Stage IV disease accounted for a higher percentage of infected patients (35.7%), suggesting that later stage cancer patients may be more susceptible to SARS-CoV-2 5 . Notably, a retrospective study of 28 COVID-19 cancer patients found that anti-cancer treatment within 14 days before COVID-19 diagnosis was more frequently associated with severe clinical events due to SARS-CoV-2 infection 5 . The higher proportion of COVID-19 patients with cancer requiring oxygen therapy and mechanical ventilation may be related to more severe disease and an immunosuppressive state in cancer patients, who are more susceptible to secondary lung infection with other pathogens. cache = ./cache/cord-335916-fh28qrt7.txt txt = ./txt/cord-335916-fh28qrt7.txt === reduce.pl bib === id = cord-336535-r3a57m57 author = Kohmer, Niko title = Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays date = 2020-06-01 pages = extension = .txt mime = text/plain words = 1479 sentences = 91 flesch = 52 summary = So far, there is limited data on how recently commercially available, high-throughput immunoassays, using different recombinant SARS-CoV-2 antigens, perform with clinical samples. Five follow-up samples of three individuals were only detected in either an S and/or N protein-based assay, indicating an individual different immune response to SARS-CoV-2 and the influence of the used assay in the detection of IgG antibodies. This study aims to provide a quick overview on some of these assays (two commercially available ELISA assays, four automated immunoassays and a plaque reduction neutralization test (PRNT)) focusing on the detection and neutralization capacity of IgG antibodies in follow up serum or plasma samples of individuals with PCR-diagnosed infections with SARS-CoV-2. The commercially available assays examined in our study, generated consistent results regarding the detection of SARS-CoV-2-IgG antibodies. Interestingly, in samples of three individuals with mild clinical course of COVID-19, examined in our study (1, 2, 3 in The automated immunoassays demonstrated a higher overall sensitivity than the ELISA based assays. cache = ./cache/cord-336535-r3a57m57.txt txt = ./txt/cord-336535-r3a57m57.txt === reduce.pl bib === id = cord-336227-0j0nbm9k author = Aranda‐Abreu, Gonzalo Emiliano title = Use of amantadine in a patient with SARS‐CoV‐2 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 688 sentences = 38 flesch = 62 summary = Due to a persistent cough, 500 mg of azithromycin was added for three days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time PCR test for SARS-Cov-2 which was positive. Due to a persistent cough, 500 mg of azithromycin was added for 3 days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was positive. Asymptomatic family members (wife and daughter 54 and 33 years old, respectively) positive for SARS-CoV-2 were prescribed amantadine 100 mg twice daily for 14 days as a preventive measure. Family members (wife and daughter) who were in contact with the patient and also tested positive for SARS-CoV-2 took amantadine 1 100 mg twice a day for 14 days and did not develop symptoms. cache = ./cache/cord-336227-0j0nbm9k.txt txt = ./txt/cord-336227-0j0nbm9k.txt === reduce.pl bib === id = cord-336373-xb3jrg75 author = Vivas, Esther X. title = COVID19 and Otology/Neurotology date = 2020-08-22 pages = extension = .txt mime = text/plain words = 1981 sentences = 105 flesch = 49 summary = The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. In the following text I will review some of the changes to the practice of otology and neurotology in the US, in the context of the COVID-19 pandemic. In general, it is safe to say that while N95s have been used extensively, the role of CAPR and PAPR is limited for routine otologic and neurotologic procedures, but may be necessary on COVID-19 positive patients. Another change to standard operating procedures has been the implementation of pre-operative COVID-19 testing for all patients undergoing surgery. The COVID-19 pandemic has required otologists and neurotologists to implement several changes into our practice. cache = ./cache/cord-336373-xb3jrg75.txt txt = ./txt/cord-336373-xb3jrg75.txt === reduce.pl bib === id = cord-336142-jmetfa6x author = MacDougall, Heather title = Toronto’s Health Department in Action: Influenza in 1918 and SARS in 2003 date = 2006-10-11 pages = extension = .txt mime = text/plain words = 10366 sentences = 520 flesch = 55 summary = This article compares the Toronto Health Department's role in controlling the 1918 influenza epidemic with its activities during the SARS outbreak in 2003 and concludes that local health departments are the foundation for successful disease containment, provided that there is effective coordination, communication, and capacity. 3 By comparing and contrasting the way in which public health authorities in Toronto managed the 1918 influenza pandemic and SARS in 2003, we can see how a century of medical advances had conditioned the public and health care professionals to expect prompt control of communicable diseases, speedy development of a prophylactic vaccine, and effective exchange of information at the provincial, national, and international levels. For Toronto's medical officer and its Local Board of Health (LBH), this presented a challenge, because influenza was not a reportable disease under the 1912 Ontario Public Health Act, and most doctors were hoping that the outbreak would be similar to the one in 1889-90 that had attacked primarily the elderly and apparently provided some immunity to those who survived. cache = ./cache/cord-336142-jmetfa6x.txt txt = ./txt/cord-336142-jmetfa6x.txt === reduce.pl bib === id = cord-336543-ydrmlujj author = Cavalli, Eugenio title = Entangling COVID-19 associated thrombosis into a secondary antiphospholipid antibody syndrome: Diagnostic and therapeutic perspectives (Review) date = 2020-06-25 pages = extension = .txt mime = text/plain words = 5813 sentences = 260 flesch = 39 summary = We propose here that the thromboembolic events and eventually the development of DIC provoked by SARS-CoV-2 infection may represent a secondary anti-phospholipid antibody syndrome (APS). On the basis of empirical observations and emerging laboratoristic findings, we will elaborate the hypothesis that several cases of thrombotic events during cOVId-19 infection represent the clinical epiphenomenon of a viral-induced secondary anti-phospholipid antibody syndrome (APS) that, in the most severe cases, may develop as catastrophic anti-phospholipid antibody syndrome (cAPS). clinical evidence and emerging data from pathological examinations indicate that a thrombotic diathesis, potentially leading to venous thromboembolism (VTE), and to dIc in some of the most severe cases, may occur in a substantial proportion of patients with cOVId-19 infection, also in a manner independent of long-term bed rest and eventual hormonal treatment. cache = ./cache/cord-336543-ydrmlujj.txt txt = ./txt/cord-336543-ydrmlujj.txt === reduce.pl bib === id = cord-336177-p7b7yw28 author = Selvi, Valeria title = Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5461 sentences = 265 flesch = 45 summary = Regarding the pandemic 2009 influenza A H1N1, the results from the prospective cohort study by Hung and colleagues showed that plasma treatment reduced mortality (the patients involved in the study were seriously ill and required intensive care); no adverse events were observed [4, 8, 20] . A meta-analysis by Mair-Jenkins and colleagues, including 32 studies of SARS coronavirus and severe influenza, reported that convalescent plasma reduced mortality and it was safe (no relevant adverse events or complications after treatment were reported). Based on the evidence from past experience in passive immunization, the BRN explained that there was a considerable possibility that the application of whole blood (as well as plasma, serum, or immunoglobulin concentrates) from convalescent persons could be effective in the treatment/prevention of infectious disease. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection cache = ./cache/cord-336177-p7b7yw28.txt txt = ./txt/cord-336177-p7b7yw28.txt === reduce.pl bib === id = cord-336364-2ust3qoq author = Artigas, Laura title = In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date = 2020-10-02 pages = extension = .txt mime = text/plain words = 5858 sentences = 295 flesch = 45 summary = title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). cache = ./cache/cord-336364-2ust3qoq.txt txt = ./txt/cord-336364-2ust3qoq.txt === reduce.pl bib === id = cord-336517-v7z62tld author = Chu, Hsu-Feng title = Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine date = 2018-08-20 pages = extension = .txt mime = text/plain words = 5193 sentences = 324 flesch = 59 summary = Further studies suggest that PEDV PL2 pro exhibits much higher DUB activity than that of SARS-and MERS-CoV PL pro s and can be inhibited by the anti-leukemia drug 6-thioguanine (6TG). Previous studies suggested that the Ubl domain was not involved in the catalytic activity of SARS-and MERS-CoV PL pro s (Chou et al., 2012; Clasman et al., 2017) . Overall, the secondary, tertiary and quaternary structures of the PEDV PL2 pro catalytic core are similar to those of SARS-and MERS-CoV PL pro s, even though their sequence identity is only 22-25% (Fig. S1 ). In contrast, previous studies suggested that the binding site of 6TG for SARS-and MERS-CoV PL pro s may be near the catalytic triad's cysteine residue due to its competitive pattern of inhibition Chou et al., 2008) . Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin cache = ./cache/cord-336517-v7z62tld.txt txt = ./txt/cord-336517-v7z62tld.txt === reduce.pl bib === id = cord-336585-19vwpjkt author = Adem, Şevki title = Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19 date = 2020-08-22 pages = extension = .txt mime = text/plain words = 3578 sentences = 210 flesch = 46 summary = Based upon these results, we have screened a library of caffeic acid derivatives (CAFDs) (Figure 1 ) for the identification of novel natural anti-COVID-19 compounds against various SARS-CoV-2 drug targets including COVID-19 M pro (6LU7), SARS-CoV-2 S2 subunit (6LXT), Nsp15 endoribonuclease (6VWW), SARS-CoV-2 spike ectodomain open state structure (6VYB), and SARS-CoV-2 spike closed state glycoprotein structure (6VXX). Our results present in silico-based identification of khainaoside C, 6-O-Caffeoylarbutin, khainaoside B, khainaoside C and vitexfolin A as potent modulators of COVID-19 M pro , Nsp15, coronavirus fusion protein, spike open state and closed state structure respectively. Based on these in-silico results, khainaoside C, calceolarioside B, vitexfolin A, calceolarioside C and scrophuloside B exhibited best binding potential with COVID-19 virus Figure 2B represents residual wise van der Waals interactions, piNelfinavir which possess MolDock score of -148.413 The interactions of these compounds with amino acid residues of target protein are shown in Figure 3A . cache = ./cache/cord-336585-19vwpjkt.txt txt = ./txt/cord-336585-19vwpjkt.txt === reduce.pl bib === id = cord-336117-hit4kza8 author = Heymann, D.L. title = Emerging Infections, the International Health Regulations, and Macro-Economy date = 2014-02-27 pages = extension = .txt mime = text/plain words = 3357 sentences = 130 flesch = 46 summary = Under the IHR, countries are able to work transparently with WHO and its scientific experts and collaborating laboratories to conduct joint risk assessments of public health events such as outbreaks of infectious diseases; to make evidence-based recommendations to help prevent or control their international spread; and, by providing valid and transparent information to national focal points, to help prevent unnecessary panic and misunderstanding about risk. Precautionary measures to prevent international spread of the infection were immediately recommended by the WHO -it was first recommended that persons who were ill with similar symptoms and contact with geographic areas where outbreaks were occurring defer their travel until they were well. The IHR 1969 were revised in 2005, incorporating many of the lessons learned during the SARS outbreak, and now ensure broader disease coverage, and in addition require countries to develop core capacities in public health laboratory and epidemiology in order to detect and respond to diseases where and when it occurs, and before it spreads internationally (Box 1). cache = ./cache/cord-336117-hit4kza8.txt txt = ./txt/cord-336117-hit4kza8.txt === reduce.pl bib === id = cord-336522-y9nzsv95 author = Rosenke, Kyle title = Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1723 sentences = 121 flesch = 54 summary = title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers Cell viability was 33 evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR 34 and TCID50 infectivity assays. Results: PPMO designed to base-pair with sequence in the 5'-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. Results: PPMO designed to base-pair with sequence in the 5'-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. In this study, five PPMO were designed to target the 5' UTR 107 and first translation start site-region of SARS-CoV-2 positive sense genomic RNA ( Table 1) . cache = ./cache/cord-336522-y9nzsv95.txt txt = ./txt/cord-336522-y9nzsv95.txt === reduce.pl bib === id = cord-336447-hpnkou41 author = Pitlik, Silvio Daniel title = COVID-19 Compared to Other Pandemic Diseases date = 2020-07-31 pages = extension = .txt mime = text/plain words = 6148 sentences = 396 flesch = 49 summary = Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. cache = ./cache/cord-336447-hpnkou41.txt txt = ./txt/cord-336447-hpnkou41.txt === reduce.pl bib === id = cord-336366-2y68n8s0 author = Liguori, Claudio title = Depressive and anxiety symptoms in patients with SARS-CoV2 infection date = 2020-09-14 pages = extension = .txt mime = text/plain words = 871 sentences = 52 flesch = 40 summary = 5 Based on the study protocol, all patients underwent an anamnestic interview requiring a dichotomized answer (YES/NO) about 13 neurological symptoms (hyposmia, dysgeusia, auditory dysfunction, headache, confusion, dizziness, numbness/paresthesia, fatigue, daytime sleepiness, sleep impairment, muscle ache, depression, and anxiety). In this secondary analysis derived from this previous investigation, 5 we aimed at primarily focusing on the occurrence of depressive and anxiety symptoms in patients with COVID-19, also considering the possible correlation of these symptoms with the other neurological symptoms investigated and the demographic, clinical, and laboratory data achieved. 6 Depression, anxiety, and post-traumatic stress symptoms were more frequent in patients with COVID-19 compared to volunteers not affected by SARS-CoV2 infection. This result can be explained by a higher psychological burden in patients with several neurological symptoms, or by a more severe nervous system involvement also producing depression and anxiety. Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection cache = ./cache/cord-336366-2y68n8s0.txt txt = ./txt/cord-336366-2y68n8s0.txt === reduce.pl bib === id = cord-336561-llwjsds8 author = Ghosh, Sanhita title = siRNA could be a potential therapy for COVID-19 date = 2020-04-22 pages = extension = .txt mime = text/plain words = 743 sentences = 51 flesch = 60 summary = Thus, the sequence coding for nsp5 can be treated as a potential target for RNAi using siRNA based therapeutics. Further, Alnylam Pharmaceuticals (USA) has designed and synthesized over 350 siRNA targeting highly conserved regions of the available SARS-CoV-2 genome (Hodgson, 2020) . In this context, Conti and co-researchers have demonstrated an in vitro testing of poly (amidoamine) dendrimer nanocarriers for the potential aerosol-based delivery system of siRNA onto lung epithelial cells (Conti et al., 2014) . Thus, for the treatment of COVID-19 siRNA based therapy can be developed against the novel coronavirus SARS-CoV-2, where siRNAs can hit the highly conserved region of SARS-CoV-2 RNA and also can act as an inhibitor to suppress the genetic disorders of the lungs. The cytopathic effect (CPE) was observed in Vero cells when it was infected with SARS and reduced the CPE after siRNA treatment. Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases cache = ./cache/cord-336561-llwjsds8.txt txt = ./txt/cord-336561-llwjsds8.txt === reduce.pl bib === id = cord-336628-0evl3wnd author = Neufeldt, Christopher J. title = SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date = 2020-07-21 pages = extension = .txt mime = text/plain words = 5880 sentences = 362 flesch = 49 summary = Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. cache = ./cache/cord-336628-0evl3wnd.txt txt = ./txt/cord-336628-0evl3wnd.txt === reduce.pl bib === id = cord-336722-41eqt97y author = Sehmi, P. title = Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1688 sentences = 131 flesch = 59 summary = title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review Recent studies have confirmed the presence of SARS-CoV-2 nucleic acids in feces of Coronavirus disease 2019 (COVID-19) patients using RT-PCR tests. Larger studies are needed to corroborate these findings, as well as to determine its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. . https://doi.org/10.1101/2020.06.27.20105429 doi: medRxiv preprint A total of 4 studies describing isolation of live SARS-CoV-2 virus in fecal samples of COVID-19 patients were included. The findings from these four studies, though limited by the small sample sizes, confirm that live SARS-CoV-2 virus is present in fecal samples of COVID-19 patients, and therefore supports the hypothesis that COVID-19 could potentially be transmitted via the feco-oral route. Larger high-quality studies are urgently needed to better characterize the magnitude of live SARS-CoV-2 viral shedding in feces, as well as its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. cache = ./cache/cord-336722-41eqt97y.txt txt = ./txt/cord-336722-41eqt97y.txt === reduce.pl bib === id = cord-336481-vrnxu217 author = Bonifácio, Lívia Pimenta title = Are SARS-CoV-2 reinfection and Covid-19 recurrence possible? a case report from Brazil date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1521 sentences = 93 flesch = 54 summary = Case reports have identified persistent or recurrent elimination of viral RNA in nasopharyngeal samples, raising the possibility of reinfection by SARS-CoV-2 [4] [5] [6] [7] . She also reported that the doctor who provided medical care for her on the second episode developed flu-like symptoms about a week after the contact, and Covid-19 was lately confirmed on him by means of nasopharyngeal RT-PCR. DISCUSSION Since the beginning of the Covid-19 pandemic, due to several reports of persistent detection of viral RNA by RT-PCR in a nasopharyngeal or oropharyngeal swab, but without recurrence of symptoms, the possibility of SARS-CoV-2 reinfection has been suggested and investigated by different researchers around the world 5,6,10,11 . In conclusion, this case report presents strong evidence that SARS-CoV-2 reinfection and Covid-19 recurrence, although rare, are possible. This possibility should be further investigated in patients presenting with recurrence of Covid-19 symptoms. cache = ./cache/cord-336481-vrnxu217.txt txt = ./txt/cord-336481-vrnxu217.txt === reduce.pl bib === id = cord-336782-0zkb39v1 author = Fraile Gutiérrez, V. title = Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine date = 2020-11-02 pages = extension = .txt mime = text/plain words = 6658 sentences = 394 flesch = 47 summary = title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine The disease caused by SARS-CoV-2 (COVID-19) is characterized by pneumonia clinical presentation with fever and cough accompanied by multifocal nodular (round or oval) ground-glass opacities in the lungs that can progress to acute respiratory distress syndrome (ARDS) and requires admission to an Intensive Care Medicine Service (ICMS) in a high percentage of patients. Ultrasound can be a very useful tool during the management of the COVID-19 pandemic because it provides real-time non-invasive bedside images of patients admitted to intensive care units (ICU). • It is superior to the simple x-ray for the detection of pneumothorax, pleural effusion, pneumonia, interstitial syndrome, and for the differential diagnosis of acute dyspnea • In the thoracic ultrasound, the clinical signs are the determinant factor regarding the interpretation of the data obtained. cache = ./cache/cord-336782-0zkb39v1.txt txt = ./txt/cord-336782-0zkb39v1.txt === reduce.pl bib === id = cord-336560-m5u6ryy9 author = Boudewijns, Robbert title = STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date = 2020-07-02 pages = extension = .txt mime = text/plain words = 5019 sentences = 308 flesch = 51 summary = Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . cache = ./cache/cord-336560-m5u6ryy9.txt txt = ./txt/cord-336560-m5u6ryy9.txt === reduce.pl bib === id = cord-336696-c3rbmysh author = Oberfeld, Blake title = SnapShot: COVID-19 date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1228 sentences = 75 flesch = 44 summary = authors: Oberfeld, Blake; Achanta, Aditya; Carpenter, Kendall; Chen, Pamela; Gilette, Nicole M.; Langat, Pinky; Said, Jordan Taylor; Schiff, Abigail E.; Zhou, Allen S.; Barczak, Amy K.; Pillai, Shiv Abstract Coronavirus disease 2019 (COVID-19) is a novel respiratory illness caused by SARS-CoV-2. The causative agent was characterized as a novel coronavirus, initially referred to as 2019-nCoV and renamed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (Zhou et al., 2020b) . This respiratory illness, coronavirus disease 2019 (COVID-19), has spread rapidly by human-to-human transmission, caused major outbreaks worldwide, and resulted in considerable morbidity and mortality. Based on our understanding of SARS and MERS, and their similarity to COVID-19, the human immune response in mild cases is likely characterized by a robust type I interferon antiviral response and CD4+ Th1 and CD8+ T cell response, resulting in viral clearance. cache = ./cache/cord-336696-c3rbmysh.txt txt = ./txt/cord-336696-c3rbmysh.txt === reduce.pl bib === id = cord-336720-2bf3xzni author = Zhen, Wei title = Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3045 sentences = 205 flesch = 60 summary = In the present study, we have evaluated the analytical sensitivity and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted Emergency Use Authorization by the FDA using nasopharyngeal swabs from symptomatic patients. The LoD established by percent positive rate ranged from 1,000 copies/mL by both the GenMark and the 172 modified CDC assays to 50 copies/mL by the DiaSorin Molecular assay ( Table 2) . Overall turn-around time assessment, from sample to results, showed DiaSorin Molecular with the least 224 overall turn-around time to results, followed by GenMark, modified CDC assay and Hologic with the 225 greatest overall time ( Table 5) . DiaSorin 268 Molecular and GenMark showed 100% specificity, while Hologic and the CDC assay initially had two and 269 one discordant results, respectively. For workflow, TAT, and 298 ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, GenMark) out-299 performed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, 300 cache = ./cache/cord-336720-2bf3xzni.txt txt = ./txt/cord-336720-2bf3xzni.txt === reduce.pl bib === id = cord-336394-1xf2sxtv author = Li, Yu title = The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1175 sentences = 76 flesch = 57 summary = Here, bioinformatics approaches combining human-virus protein interaction prediction and protein docking based on crystal structures have revealed the high affinity between human dipeptidyl peptidase 4 (DPP4) and the spike (S) receptor-binding domain of SARS-CoV-2. The atomic interaction details of the 145 binding interface showed that almost all of the contacting residues of DPP4 with 146 SARS-CoV-2-S RBD were consistent with those for binding with MERS-CoV-S 147 RBD (Table S1 ) (Song et al., 2014) . In addition, the models evaluated the 228 binding potential, interface residues and structures that were consistent with those 229 Comparison of the key residues between human and pangolin DPP4 protein 471 Identification of residues on human receptor DPP4 critical for MERS-CoV binding 401 and entry Structure of MERS-CoV spike receptor-binding domain 417 complexed with human receptor DPP4 SARS-CoV-2 spike receptor-binding domain has a potentially high affinity with DPP4 cache = ./cache/cord-336394-1xf2sxtv.txt txt = ./txt/cord-336394-1xf2sxtv.txt === reduce.pl bib === id = cord-336752-cpxnof1b author = Zeng, Qi‐Qiang title = Radiomics‐based model for accurately distinguishing between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) and influenza A infected pneumonia date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3366 sentences = 186 flesch = 39 summary = Patients were excluded if they met any of the following criteria: (a) history of American Society of Anesthesiologists (ASA) score of more than 2; (b) history of existing respiratory disease prior to outbreak of SARS-CoV-2; (c) pneumonia of etiology other than SARS-CoV-2 or influenza A virus by measuring nucleic acid by fluorogenic quantitative PCR of serum samples and/or oropharyngeal swab samples in conjunction to radiographic evidence and clinically established diagnosis; or (d) absent of obvious pulmonary lesions on radiographic imaging. Abbreviation: ASA score, American society of anesthesiologists score F I G U R E 2 Radiomics-based machine learning workflow, including computed tomography (CT) images acquisition and region-of-interest (ROI) segmentation of inflammatory lesions; radiomic feature extraction by LIFEx; features selection by least absolute shrinkage and selection operator (LASSO) with 10-fold cross-validation; radiomics prediction score and calibration; and nomogram development for a more clinicianfriendly application, and support vector machine (SVM) were used to distinguish these two kinds of diseases effectively drawn to compare the predicted outcome versus observed outcome of each patient in order to illustrate the probability of NCP. cache = ./cache/cord-336752-cpxnof1b.txt txt = ./txt/cord-336752-cpxnof1b.txt === reduce.pl bib === id = cord-336677-h62angfw author = Rousseau, Antoine title = Sars-Cov-2, Covid-19 Et Œil: Le Point Sur Les Données Publiées date = 2020-05-30 pages = extension = .txt mime = text/plain words = 3187 sentences = 298 flesch = 60 summary = Par ailleurs, la protéine Spike de SARS-CoV-2 comprend aussi un site de clivage compatible avec l'action de la furine, une autre protéase membranaire déjà connue pour être impliquée dans la pénétration d'autres coronavirus [14, 20] , et là encore, des inhibiteurs spécifiques de la furine sont à l'étude pour connaître leur propriété antivirale sur SARS-CoVUn second récepteur cellulaire semble jouer un rôle important dans la sensibilité au virus, il s'agit du récepteur CD147, aussi nommé basigine ou encore EMMPRIN (extracellular matrix metalloproteinase inducer). Les propriétés antivirales de l'hydroxychloroquine ont d'ailleurs été suspectées pour un grand nombre d'autres virus que SARS-CoV-2, mais jusqu'à présent, aucun des essais thérapeutiques chez l'homme n'a montré son efficacité dans ces autres infections [25] . Les essais thérapeutiques visant à réguler cette réaction immunitaire exacerbée représentent une part importante de l'effort de recherche clinique sur les formes sévères de COVID-19, et c'est d'ailleurs dans ce domaine que l'un des premiers essais randomisés contrôlé a montré des résultats préliminaires encourageants, (mais qui restent encore à confirmer) à propos d'un inhibiteur de l'interleukine 6 (le tocilizumab) [38] . cache = ./cache/cord-336677-h62angfw.txt txt = ./txt/cord-336677-h62angfw.txt === reduce.pl bib === id = cord-336775-d4hi9myk author = Kirtipal, Nikhil title = From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date = 2020-08-13 pages = extension = .txt mime = text/plain words = 8606 sentences = 442 flesch = 46 summary = Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Hence, acute respiratory distress syndrome (ARDS) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of SARS-CoV-2 outbreak; similar observations were noted in case of SARS-CoV infection (Kumar et al., 2020) . When developing novel therapeutic strategies to check the immunoregulatory cytokines such as TNFβ and IL6, investigation should be considered on the viral strain and targeted organ specificity; for example, SARS-CoV-2 has more affinity to ACE2 which are scattering on different organs like lung and kidney while MERS-like CoV can even infect T-cells. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-336775-d4hi9myk.txt txt = ./txt/cord-336775-d4hi9myk.txt === reduce.pl bib === id = cord-336605-d4loia11 author = Zhang, Xue Wu title = Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs date = 2004-05-15 pages = extension = .txt mime = text/plain words = 1566 sentences = 87 flesch = 58 summary = To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Except four drugs (lopinavir, ritonavir, niclosamide and promazine), we also conducted the docking studies of two other molecules, PNU and UC2, for their molecular formulas are close to those of niclosamide and promazine, respectively (Fig. 2) , and they both are the inhibitors of HIV-1 reverse transcriptase. Figure 3 displays the overall structures of docking for four drugs (lopinavir, ritonavir, niclosamide and promazine) and two inhibitors (PNU and UC2) to SARS-CoV main proteinase. Thus, the four drugs and two inhibitors studied here can basically bind to the active site of SARS-CoV main proteinase, a cleft between domains I and II. cache = ./cache/cord-336605-d4loia11.txt txt = ./txt/cord-336605-d4loia11.txt === reduce.pl bib === id = cord-336870-nirg3269 author = Abebe, Endeshaw Chekol title = The newly emerged COVID-19 disease: a systemic review date = 2020-07-08 pages = extension = .txt mime = text/plain words = 4157 sentences = 209 flesch = 54 summary = The novel COVID-19 infection, caused by a beta coronavirus called SARS-CoV-2, is a new outbreak that has been emerged in Wuhan, China in December 2019. i. If a patient with a severe acute respiratory infection (fever, cough, and requiring admission to hospital), and with no other etiology that fully explains the clinical presentation and a history of travel to or residence in a country/area or territory reporting local transmission during the 14 days prior to symptom onset, OR ii. It is caused by a novel beta-coronavirus, resulting from genetic recombination, called SARS-CoV-2, The most common symptoms of COVID-19 are fever, cough, and dyspnea. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-336870-nirg3269.txt txt = ./txt/cord-336870-nirg3269.txt === reduce.pl bib === id = cord-336702-2qa4u8gv author = Agarwal, Sangya title = Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19 date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2364 sentences = 124 flesch = 44 summary = Consistent with HLH, accumulations of macrophages are found in the lungs of patients with COVID-19 ( 9 ) , and HLH has previously been reported in patients with SARS, MERS, and other severe systemic viral infections. Drug treatments used for HLH/MAS and ARDS may also be effective in treating patients with COVID-19. Thus, an urgent need emerges to uncover therapies that may be effective for patients with SARS-CoV-2 infection. Thus, if properly timed in patients after exposure to virus, CSA could serve as a broad-spectrum inhibitor to control SARS-CoV-2 infection and decrease the magnitude of cytokine release. This shows not only the coincidence of treatments that modulate dysfunctional host immune responses, but also the potential complications with overlapping SARS-CoV-2 infections and cancer immunotherapies. This is important because comorbidities from CRS due to CAR T-cell therapy and HLH-like symptoms due to SARS-CoV 2 infection could be fatal. cache = ./cache/cord-336702-2qa4u8gv.txt txt = ./txt/cord-336702-2qa4u8gv.txt === reduce.pl bib === id = cord-336563-hwemigk7 author = Bhimraj, Adarsh title = Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 8308 sentences = 448 flesch = 42 summary = Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . cache = ./cache/cord-336563-hwemigk7.txt txt = ./txt/cord-336563-hwemigk7.txt === reduce.pl bib === id = cord-337198-4sors3bg author = Clementi, Nicola title = Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4259 sentences = 224 flesch = 54 summary = In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . cache = ./cache/cord-337198-4sors3bg.txt txt = ./txt/cord-337198-4sors3bg.txt === reduce.pl bib === id = cord-336554-n8n5ii5k author = Singh, Thakur Uttam title = Drug repurposing approach to fight COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 13032 sentences = 690 flesch = 44 summary = Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . cache = ./cache/cord-336554-n8n5ii5k.txt txt = ./txt/cord-336554-n8n5ii5k.txt === reduce.pl bib === id = cord-337089-ksh62ni0 author = Salajegheh Tazerji, Sina title = Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review date = 2020-09-21 pages = extension = .txt mime = text/plain words = 4901 sentences = 293 flesch = 53 summary = In addition to the considerable COVID-19 cases, hospitalizations, and deaths in humans, several cases of SARS-CoV-2 infections in animal hosts (dog, cat, tiger, lion, and mink) have been reported. Therefore, this study aimed to gather information about the reported cases of COVID-19 transmission in animals through a literary review of works published in scientific journals and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. However, based on recently published findings, other authors hypothesized that an immunological cross-protection between SARS-CoV-2 and canine respiratory coronavirus (CRCoV) exists due to the high homology between the spike protein epitopes of the two taxonomicallyrelated coronaviruses [21] . The objective of the present study was to gather, present, and discuss information on the reported cases of COVID-19 in animals focusing on the virus transmission cases in pets and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. cache = ./cache/cord-337089-ksh62ni0.txt txt = ./txt/cord-337089-ksh62ni0.txt === reduce.pl bib === id = cord-336671-vfq5ft08 author = Ai, Jing-Wen title = Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date = 2020-03-16 pages = extension = .txt mime = text/plain words = 1883 sentences = 108 flesch = 50 summary = Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19. cache = ./cache/cord-336671-vfq5ft08.txt txt = ./txt/cord-336671-vfq5ft08.txt === reduce.pl bib === id = cord-336711-bnb62wa6 author = Wang, Xiaoyang title = CT findings of patients infected with SARS-CoV-2 date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2043 sentences = 143 flesch = 61 summary = BACKGROUND: We aimed to describe the chest CT findings in sixty-seven patients infected by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The typical CT findings in hospitalized patients with SARS-CoV-2 infection were ground glass opacities (42/54), lesions located in the peripheral area (50/54), multiple lesions (46/54), and lesions located in the lower lobes (42/54). There were less typical CT findings, including air bronchogram (18/54), pleural thickening or pleural effusion (14/54), consolidation (12/54), lesions in the upper lobes (12/54), interlobular septal thickening (11/54), reversed halo sign (9/54), single lesion (8/54), air cavities (4/54), bronchial wall thickening (3/54), and intrathoracic lymph node enlargement (2/54). The chest CT image shows ground glass opacities occupying the left lower lobe (blue arrow) Fig. 4 A female patient infected with SARS-CoV-2. Chest CT images showed the enlargement of ground glass opacity (red arrows) and intrathoracic lymph node (blue arrows) after 10-day treatment found in the patients infected with SARS-CoV-2 ( Table 2 ). cache = ./cache/cord-336711-bnb62wa6.txt txt = ./txt/cord-336711-bnb62wa6.txt === reduce.pl bib === id = cord-336837-rerp1g1w author = Jones, Nick K title = Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3082 sentences = 156 flesch = 46 summary = These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent 'hubs' of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely. Testing for SARS-CoV-2 RNA was performed with real-time RT-PCR using throat and nose swab samples of HCWs from Cambridge University Hospitals NHS Foundation Trust (CUHNFT) and their symptomatic household contacts. In the HCW symptomatic and HCW symptomatic household contact screening arms combined (reflecting all individuals with self-reported symptoms at the time of testing), 13/771 (1.7%) tests were positive, which was significantly lower than 30/221 (13%) in the original study period (Fisher's exact test p<0.0001). In particular, during the last 2 weeks of the study period (11th to 24th May 2020), we identified only four positive SARS-CoV-2 samples from 2016 tests performed, two from the HCW asymptomatic and two from the HCW symptomatic/symptomatic household contact arms. cache = ./cache/cord-336837-rerp1g1w.txt txt = ./txt/cord-336837-rerp1g1w.txt === reduce.pl bib === id = cord-337220-yv7qdvzi author = Demeke, Addis title = Biosensor and molecular-based methods for the detection of human coronaviruses: A review date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2215 sentences = 128 flesch = 39 summary = This assay involves simultaneous 130 reverse transcription and isothermal amplification using loop-mediated amplification (RT-131 LAMP) for RNA, followed by Cas12 detection of predefined coronavirus sequences, after which 132 cleavage of a reporter molecule confirms detection of the E and N genes of SARS-CoV-2. Rapid lateral flow-based assays for anti-COVID-19 antibodies (IgM and IgG) are under 147 development which will play an important role in the epidemiological investigation of the 148 disease [9] . Therefore, the convalescent plasma has been used as 155 therapy for the treatment of critically ill COVID-19 patients [26, 27] The biosensor was developed by using a spike protein of SARS-CoV-2 immobilized onto the 237 FET graphene sheet (a two-dimensional sheet of hexagonal oriented carbon atom) with 1-pyrene 238 butyric acid N-hydroxy succinimide ester (PBASE) (Figure 1) . Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription 473 loop-mediated isothermal amplification assay cache = ./cache/cord-337220-yv7qdvzi.txt txt = ./txt/cord-337220-yv7qdvzi.txt === reduce.pl bib === id = cord-337297-fkw8780t author = Fan, Siyuan title = Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4698 sentences = 267 flesch = 41 summary = Methods: This retrospective single-center case series analyzed critically ill patients with COVID-19 at the intensive care unit of Tongji Hospital, Wuhan, China from February 5 to April 2, 2020. Herein, we conducted a retrospective study to analyze the neurological manifestations of critically ill patients with COVID-19 in intensive care units (ICU) to explore various pathophysiological mechanisms that could contribute to neurological complications in these patients. COVID-19, corona virus disease 2019; AIS, acute ischemic stroke; WBC, white blood cell; ALT, alanine transaminase, cTnI, High-sensitive cardiac troponin I; NT-proBNP, N-terminal prohormone of brain natriuretic peptide; LDL-C, low-density-lipoprotein cholesterol; aPTT, activated partial thromboplastin time; hsCRP, high sensitivity C-reactive protein; LDH, lactate dehydrogenase; IQR, interquartile range. The clinical spectrum of neurological complications in critically ill patients with COVID-19 was broad, including delirium, acute ischemic stroke, intracerebral hemorrhage, hypoxic-ischemic brain injury, flaccid paralysis and rhabdomyolysis. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-337297-fkw8780t.txt txt = ./txt/cord-337297-fkw8780t.txt === reduce.pl bib === id = cord-336742-42ebj3gi author = Demmler, Gail J title = Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future date = 2003-07-31 pages = extension = .txt mime = text/plain words = 3156 sentences = 177 flesch = 55 summary = The disease, severe acute respiratory syndrome (SARS), spread quickly and caused numerous deaths, as well as public panic. The first report of the new disease, given the name "severe acute respiratory syndrome" (SARS), was received by WHO on February 11 from the Chinese Ministry of Health, which documented that 305 cases and 5 deaths had occurred in the Guangdon Province. 2, 5 By March 5, secondary probable SARS cases were identified among healthcare workers in Hanoi, and at the urging of Dr. Urbani and his colleagues, Vietnam closed the hospital to new patients and visitors on March 11. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: Clinical features of index patient and initial contacts Identification of a novel coronavirus in patients with severe acute respiratory syndrome cache = ./cache/cord-336742-42ebj3gi.txt txt = ./txt/cord-336742-42ebj3gi.txt === reduce.pl bib === id = cord-337093-7pxfzuq0 author = Hess, David C. title = COVID-19-Related Stroke date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1846 sentences = 118 flesch = 49 summary = The SARS-CoV-2 virus binds to angiotensin-converting enzyme 2 (ACE2) present on brain endothelial and smooth muscle cells. Depletion of ACE2 by SARS-CoV-2 may tip the balance in favor of the "harmful" ACE1/angiotensin II axis and promote tissue injury including stroke. There is a rationale to continue to treat with tissue plasminogen activator for COVID-19-related stroke and low molecular weight heparinoids may reduce thrombosis and mortality in sepsis-induced coagulopathy. The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) via its spike (S) protein [9] . The depletion of ACE2 by the SARS-CoV-2 virus coupled with the age-related decline in ACE2 and increase of ACE-1-Ang II tips the balance in favor of ACE-1/ angiotensin II with proinflammatory and organ damaging effects. Binding to and depletion of ACE2 may tip the RAS balance in favor of the ACE-1-angiotensin II-AT1 axis and contribute to endothelial dysfunction, organ damage, and stroke. cache = ./cache/cord-337093-7pxfzuq0.txt txt = ./txt/cord-337093-7pxfzuq0.txt === reduce.pl bib === id = cord-336836-54o9vjdl author = Zhen, Wei title = Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3410 sentences = 165 flesch = 54 summary = Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. In this study, our objective was to evaluate the analytical and clinical performance as well as the workflow of these three sample-to-answer platforms for SARS-CoV-2 detection in 108 nasopharyngeal (NP) swab specimens from symptomatic patients. We evaluated three sample-to-answer platforms currently in use in our health system for the detection of SARS-CoV-2, including Xpert Xpress and ID NOW, which are designed to be used in near-patient testing environments and outside the clinical laboratory environment. In summary, we evaluated three sample-to-answer platforms for the detection of SARS-CoV-2 using NP specimens, including two platforms that are designed to be used in the near-patient testing environment, Xpert Xpress and ID NOW. cache = ./cache/cord-336836-54o9vjdl.txt txt = ./txt/cord-336836-54o9vjdl.txt === reduce.pl bib === id = cord-336793-9bbyu1qx author = Matsuyama, Shutoku title = The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date = 2020-08-24 pages = extension = .txt mime = text/plain words = 709 sentences = 48 flesch = 62 summary = title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells We screened steroid compounds to obtain a drug expected to block host inflammatory responses and MERS-CoV replication. Ciclesonide, an inhaled corticosteroid, suppressed replication of MERS-CoV and other coronaviruses, including SARS-CoV-2, the cause of COVID-19, in cultured cells. Eight consecutive passages of 43 SARS-CoV-2 isolates in the presence of ciclesonide generated 15 resistant mutants harboring single amino acid substitutions in non-structural protein 3 (nsp3) or nsp4. These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. In the present study, we found that an inhaled corticosteroid, ciclesonide suppresses replication of coronaviruses, including beta-coronaviruses (MHV-2, MERS-CoV, SARS-CoV, and SARS-CoV-2) and an alpha-coronavirus (HCoV-229E) in cultured cells. The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral cache = ./cache/cord-336793-9bbyu1qx.txt txt = ./txt/cord-336793-9bbyu1qx.txt === reduce.pl bib === id = cord-336769-5x6xjuew author = Payne, Daniel C. title = SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 2567 sentences = 112 flesch = 42 summary = In April, the U.S. Navy and CDC investigated this outbreak, and the demographic, epidemiologic, and laboratory findings among a convenience sample of 382 service members serving aboard the aircraft carrier are reported in this study. At the time of specimen collection, participants completed a questionnaire eliciting information on demographic characteristics, exposure, COVID-19 protective behaviors, health history, and symptoms; participants also reported whether they had had a previous positive COVID-19 test since deployment but before this investigation. Among a convenience sample of 382 young adult U.S. service members aboard an aircraft carrier experiencing a COVID-19 outbreak, 60% had reactive antibodies, and 59% of those also had neutralizing antibodies at the time of specimen collection. In this convenience sample of young, healthy U.S. service members experiencing close contact aboard an aircraft carrier, those with previous or current SARS-CoV-2 infection experienced mild illness overall, and nearly 20% were asymptomatic. cache = ./cache/cord-336769-5x6xjuew.txt txt = ./txt/cord-336769-5x6xjuew.txt === reduce.pl bib === id = cord-337026-osgi06o4 author = Panoutsopoulos, Alexios A. title = Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3174 sentences = 171 flesch = 48 summary = Given the uprising number of publications and case reports of COVID-19 patients showing conjunctivitis [61, 62] and the history of other coronaviruses that are found in tears, we have to consider the possibility of a separate, alternative viral mechanism through which the virus can enter the patient's organism through epithelial cells of the eye [63] . The growing evidence on COVID-19 and its ocular implications and manifestations, in both animals and humans, is covered by many interesting reviews, all published 5 to 6 months after the novel coronavirus' outbreak [64] [65] [66] [67] [68] , something that reveals the need to understand the virus from different perspectiveswhich at first may have seemed secondary in priority-in order to be able to reach a treatment. cache = ./cache/cord-337026-osgi06o4.txt txt = ./txt/cord-337026-osgi06o4.txt === reduce.pl bib === id = cord-336604-2auhkxce author = Kumar, Pramod title = Integrated genomic view of SARS-CoV-2 in India date = 2020-08-03 pages = extension = .txt mime = text/plain words = 4927 sentences = 324 flesch = 58 summary = Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). A total of 127 laboratory-confirmed cases of COVID-19 from targeted testing and available samples at NCDC which represent different geographic locations or states and travel history from different countries during the early phase of the outbreak (Table 1 and Extended data, Supplementary figure S1 [Kumar et al., 2020b] ). We also compared SARS-CoV-2 mutation sites with other six coronavirus sequences (Extended data, Supplementary figure S5b [Kumar et al., 2020b] ). cache = ./cache/cord-336604-2auhkxce.txt txt = ./txt/cord-336604-2auhkxce.txt === reduce.pl bib === id = cord-337324-jxtch47t author = Qian, Guo-Qing title = Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series date = 2020-02-25 pages = extension = .txt mime = text/plain words = 3331 sentences = 207 flesch = 59 summary = title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series 8 Three further cases were reported in Ningbo cohort as clinical-diagnosed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to National Health Commission of the People's Republic of China guidance, though they tested negative for the SARS-CoV-2. This report, to our knowledge, is the largest case study to date of hospitalized patients with COVID-19 in Zhejiang province, which is outwith of Wuhan and Hubei. Our study provided three cases as clinical-confirmed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to guidance, though they tested negative for the SARS-CoV-2. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-337324-jxtch47t.txt txt = ./txt/cord-337324-jxtch47t.txt === reduce.pl bib === id = cord-337105-jlmh79qv author = Jacob, Fadi title = Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date = 2020-09-21 pages = extension = .txt mime = text/plain words = 9954 sentences = 567 flesch = 53 summary = We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. QPCR analysis also showed higher levels of ACE2 and TMPRSS2 expression in CPOs at 50 DIV and 100 DIV than in hippocampal organoids ( Figure S2D ) Together, these results show that our CPOs exhibit a similar transcriptome as adult human choroid plexus tissue and express markers for choroid plexus epithelial cells and SARS-CoV-2 receptors, representing a suitable experimental model to study SARS-CoV-2 infection. Our finding that dysregulated gene expression varies widely among hepatocyte, intestinal, and choroid plexus organoids infected with SARS-CoV-2 suggests unique responses in different cell types and highlights the need for diverse human cellular model systems when studying the disease. cache = ./cache/cord-337105-jlmh79qv.txt txt = ./txt/cord-337105-jlmh79qv.txt === reduce.pl bib === id = cord-337200-2qwty2jp author = Kempfle, J. S. title = Management von Patienten mit Tracheostoma während der COVID-19-Pandemie: Literaturüberblick und Demonstration date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3529 sentences = 479 flesch = 52 summary = Die durch das neue Coronavirus, auch Severe-Acute-Respiratory-Syndrome-Coronavirus 2, kurz SARS-CoV-2 genannt, ausgelöste Erkrankung (COVID19) , zeichnet sich durch eine hohe Variabilität an Symptomen aus. Während eine große Anzahl an SARS-CoV-2-positiven Patienten keine oder nur leichte Symptome einer oberen Atemwegsinfektion hat, gibt es eine Gruppe von Patienten, die eine deutliche Einschränkung ihrer Lungenfunktion mit Pneumonie bis hin zur lebensbedrohlichen Variante mit akutem Lungenversagen ("acute respiratory distress syndrome", ARDS) entwickelt [18, 37, 40] . Eine kürzlich in Nature Medicine erschienene Studie, welche sich mit den Erkältungs-Coronaviren beschäftigte, konnte diese sowohl in der ausgeatmeten Luft über einen Zeitraum von 30 min als auch in erhöhter Konzentration in Aerosolen und Tröpfchen von wiederholt hustenden Patienten nachweisen [19] . Während erste Leitlinien sowohl in Deutschland als auch international vorläufige Empfehlungen zu Vorsichtsmaßnahmen bei In-und Extubationen oder Tracheotomien von beatmungspflichtigen COVID-19-Patienten aussprechen [1, 4, 12, 20, 22, 30, 35] , ist vergleichsweise wenig Information zum weiteren Umgang mit einem tracheotomierten SARS-CoV-2-positiven Patienten auf Station, ambulant oder während der Rehabilitation zu finden [10] . cache = ./cache/cord-337200-2qwty2jp.txt txt = ./txt/cord-337200-2qwty2jp.txt === reduce.pl bib === id = cord-337339-0vkigjv2 author = Osterrieder, Nikolaus title = Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date = 2020-07-20 pages = extension = .txt mime = text/plain words = 4327 sentences = 220 flesch = 47 summary = We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Moreover, transgenic mice expressing human ACE2 represent a lethal SARS-CoV-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . In contrast to SARS-CoV-2 titers, histopathological changes differed markedly between young and aged Syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. Based on the data presented here, we propose that comparative preclinical assessments of SARS-CoV-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. cache = ./cache/cord-337339-0vkigjv2.txt txt = ./txt/cord-337339-0vkigjv2.txt === reduce.pl bib === id = cord-337032-s4g4g80w author = Gupta, Manoj Kumar title = In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date = 2020-04-15 pages = extension = .txt mime = text/plain words = 3964 sentences = 191 flesch = 52 summary = Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human 'SARS-CoV2 E' protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. By considering the above information, in the present study, authors employed computational approach for identifying the best possible structure of the 'SARS-CoV2 E' protein present in the PDB database to understand its structure and function as well as its behaviour towards various phytochemicals. Subsequently, molecular docking of the 'SARS-CoV2 E' protein with ligands having 250 conformations using the AutoDock tool revealed that the best ten phytochemicals with minimal binding energy are TIP006452 (Belachinal), TIP005365 (Macaflavanone E), TIP003272 (Vibsanol B), TIP003258 (14 R à ,15-Epoxyvibsanin C), TIP005363 (Macaflavanone C), TIP000749 (Luzonoid D), TIP008605 (Grossamide K), TIP009461 ((-)-Blestriarene C), TIP005366 (Macaflavanone F) and TIP005783 (Dolichosterone). cache = ./cache/cord-337032-s4g4g80w.txt txt = ./txt/cord-337032-s4g4g80w.txt === reduce.pl bib === id = cord-337302-fpz2jfuj author = Abdihamid, Omar title = The Landscape of COVID-19 in Cancer Patients: Prevalence, Impacts, and Recommendations date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5958 sentences = 357 flesch = 48 summary = 21 Similar to cases seen during the MERS-outbreak where having cancer was identified as a risk factor for MERS-CoV mortality, the COVID-19 pandemic also poses threats to cancer patients. 23 In one of the early data by Yu et al published in JAMA Oncology, the infection rate of SARS-CoV-2 in cancer patients from Wuhan, China, was at 0.79% (12 of 1524 patients; 95% CI, 0.31.2%). 15 In a retrospective cohort study of 28 COVID-19infected cancer patients with laboratory-confirmed COVID-19 from three hospitals in China, a total of 15 (53.6%) patients had severe outcomes with a mortality rate of 28.6%. Patients' age, tumor type, underlying comorbidities, stage of the disease, and treatment type all affect the risk and outcomes of contracting SARS-CoV-2 in cancer patients. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-337302-fpz2jfuj.txt txt = ./txt/cord-337302-fpz2jfuj.txt === reduce.pl bib === id = cord-337511-20yaol5r author = Ryan, Paul MacDaragh title = COVID-19 and relative angiotensin-converting enzyme 2 deficiency: role in disease severity and therapeutic response date = 2020-06-11 pages = extension = .txt mime = text/plain words = 3244 sentences = 182 flesch = 37 summary = Interestingly, comparative analysis of two successive SARS epidemics in early 2000s showed that increased affinity of the SARS virus for human ACE2 receptor strongly predicted severity of clinical disease suggesting that spike protein conformation is potentially a key determinant of virulence. 15 Interestingly, in several Wuhan cohorts cardiac injury and arrythmia were prominent in high-risk Figure 3 Homeostasis of RAS-ACE2 under normal healthy conditions 10 19 ; perturbation of RAS-ACE2 homeostasis in cardiovascular disease, hypertension and diabetes mellitus 22 27 ; COVID-19 may potentially further upregulate RAS in CVD patients and deplete ACE2 33 ; proposition that rhACE2 replacement therapy improves RAS-ACE2 balance by augmenting ACE2 and decreasing RAS activation. 35 If the same holds true for SARS-CoV-2, then soluble rhACE2 may reduce ongoing SARS-CoV-2 access to membrane-bound ACE2 receptor, alter favourably local AngII/Ang1-7 levels and inhibit deleterious RAS effects on remaining at risk tissues in COVID-19 patients. cache = ./cache/cord-337511-20yaol5r.txt txt = ./txt/cord-337511-20yaol5r.txt === reduce.pl bib === id = cord-337396-g69bb60d author = Ogawa, Yoshihiko title = Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date = 2020-11-07 pages = extension = .txt mime = text/plain words = 1785 sentences = 121 flesch = 56 summary = A follow-up survey was conducted with healthcare personnel (HCP) who were exposed to a patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative PCR results. No apparent infection was found in any of the HCP who had contact exposure with and/or aerosol exposure to the patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative results of PCR tests for SARS-CoV-2. Thus, we created a policy that for patients whose sputum and/or nasopharyngeal PCR test results for SARS-CoV-2 were negative when measured twice separately over 24 h, we stopped the precautions against aerosol transmission. We did not perform PCR tests for SARS-CoV-2 until the 63rd day of illness, and the result of this test was re-negative. In conclusion, no HCP were infected by contact with and aerosol exposures to SARS-CoV-2 re-positive patients in our hospital. cache = ./cache/cord-337396-g69bb60d.txt txt = ./txt/cord-337396-g69bb60d.txt === reduce.pl bib === id = cord-337599-dyxfsojh author = Ahamad, Shakir title = Primed for Global Coronavirus Pandemic: Emerging Research and Clinical Outcome date = 2020-09-19 pages = extension = .txt mime = text/plain words = 1978 sentences = 163 flesch = 48 summary = Under such circumstances, drug repurposing has emerged as a realistic and effective strategy to counter the virus menace in the short run, and several antiviral and antimalarial medicines are currently in different stages of clinical trials. Researchers are also experimenting with nutrients, vitamins, monoclonal antibodies, and convalescent plasma as immunity boosters against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This report presents a critical analysis of the global clinical trial landscape for COVID-19 with an emphasis on the therapeutic agents and vaccines currently being tested at pandemic speed. 166 The Institute of Biotechnology, AMMS, China, registered a randomized, double-blind, 167 placebo-controlled Phase-II clinical trial of recombinant novel coronavirus (2019-nCOV) 168 vaccine (adenovirus vector) in healthy adults aged 18 and above on April 10, 2020, (Table1, 169 Entry 6). Clinical study for safety and efficacy of Favipiravir in the treatment of novel 924 coronavirus pneumonia (COVID-19) Genentech Announces FDA Approval of Clinical Trial for Actemra to Treat 1093 Hospitalized Patients with Severe COVID-19 Pneumonia cache = ./cache/cord-337599-dyxfsojh.txt txt = ./txt/cord-337599-dyxfsojh.txt === reduce.pl bib === id = cord-337208-6rs1sgx1 author = Wang, Jingbo title = Enlightenments of Asymptomatic Cases of SARS-CoV-2 Infection date = 2020-06-30 pages = extension = .txt mime = text/plain words = 1529 sentences = 83 flesch = 61 summary = They both had normal lymphocyte counts and CT scans, without clinical symptoms; however, their qRT-PCR results of throat swabs and sputum samples both showed positive for SARS-CoV-2. The wife, daughter, and son-in-law of Case 1 were successively diagnosed with novel coronavirus-infected pneumonia, all of which were common types, and all had clinical symptoms such as fever, cough, sore throat, decreased lymphocyte count, and the CT examination of both lungs showed typical ground-glass and patchy shadows, and qRT-PCR results of pharyngeal brush and sputum specimens were positive for SARS-CoV-2. Among them, infected patients 1, 2 and 3 had clinical symptoms (fever, cough, sore throat, etc.), lymphocyte count decreased, lung CT scan showed typical ground-glass and patch shadows, and qRT-PCR tests of pharyngeal swabs and sputum specimens revealed positive for SARS-CoV-2. On February 2, Case 2 had tested positive for SARS-CoV-2 by qRT-PCR of pharyngeal swabs, and was hospitalized in isolation. cache = ./cache/cord-337208-6rs1sgx1.txt txt = ./txt/cord-337208-6rs1sgx1.txt === reduce.pl bib === id = cord-337127-pc9hez28 author = García-Salido, Alberto title = Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a date = 2020-09-30 pages = extension = .txt mime = text/plain words = 989 sentences = 68 flesch = 52 summary = title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a The immune response to SARS-CoV-2 infection appears to be a critical factor in the development and prognosis of COVID-19 patients 2 . In children, severe forms of the disease like the pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 appears to be related with some immune dysregulation 3 . We study in this report three children with severe SARS-CoV-2 infection. As can be seen in Figure 1 children with SARS-CoV-2 show levels of CD64 expression that are higher than in previous published reports of bacterial or viral infections or autoinflammatory diseases 5 . In summary, we describe the immunophenotype of three children with severe SARS-CoV-2 infection. Neutrophil CD64 expression as a longitudinal biomarker for severe disease and acute infection in critically ill patients cache = ./cache/cord-337127-pc9hez28.txt txt = ./txt/cord-337127-pc9hez28.txt === reduce.pl bib === id = cord-337444-pqoq8aew author = Doi, Kent title = Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series date = 2020-07-03 pages = extension = .txt mime = text/plain words = 988 sentences = 55 flesch = 43 summary = title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series Through high-throughput screening of 1017 existing drugs, a clinically available serine protease inhibitor nafamostat mesylate was identified as a potent inhibitor of Middle East respiratory syndrome coronavirus entry into human epithelial cells [2] . Eleven adults with reverse transcriptase polymerase chain reaction-confirmed SARS-CoV-2 infection were admitted to the intensive care unit (ICU) at The University of Tokyo Hospital between April 6 and April 21, 2020, and treated with nafamostat mesylate in combination with favipiravir. Although the number of patients in this case series was very small, this low mortality rate suggests that combination treatment of favipiravir and nafamostat mesylate may be effective for critically ill Covid-19 patients. A clinical trial for the combination treatment of nafamostat mesylate and favipiravir against Covid-19 will be initiated in Japan (jRCTs031200026). Nafamostat mesylate blocks activation of SARS-CoV-2: new treatment option for COVID-19 cache = ./cache/cord-337444-pqoq8aew.txt txt = ./txt/cord-337444-pqoq8aew.txt === reduce.pl bib === id = cord-337436-3xzgv370 author = Khider, Lina title = Curative anticoagulation prevents endothelial lesion in COVID‐19 patients date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1774 sentences = 110 flesch = 44 summary = METHODS: Study analyzed clinical and biological profiles of patients with suspected COVID‐19 infection at admission, including hemostasis tests and quantification of circulating endothelial cells (CECs). Circulating endothelial cells (CECs) are considered as relevant markers of Accepted Article 1 endothelial lesion or dysfunction (12) and were used to explore the potential vascular dysfunction 2 in COVID-19 patients. Among COVID-19 positive patients, 64% were above this threshold, suggesting a SARSThe originality of this study was to evidence an endothelial lesion during SARS-CoV-2 infection, 3 as witnessed by increased levels of CECs. Second, we show that this endothelial damage is 4 thwarted by curative anticoagulation. Interestingly, patients enrolled while they were treated with 6 curative anticoagulation had a significantly lower level of CECs, especially in the hypertensive 7 population treated with ACEi or ARBs. Increased mortality and/or morbidity of COVID-19 in 8 patients with hypertension has been described in China (3). cache = ./cache/cord-337436-3xzgv370.txt txt = ./txt/cord-337436-3xzgv370.txt === reduce.pl bib === id = cord-337421-4v48kkus author = Ribeiro, Servio Pontes title = Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil date = 2020-03-27 pages = extension = .txt mime = text/plain words = 3488 sentences = 178 flesch = 56 summary = After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. We developed a SIR (Susceptible-Infected-Recovered) model divided in 9 a metapopulation structure, where cities with airports were demes connected by the 10 number of flights. 142 143 Results 144 The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to 145 the airport closeness centrality within the Brazilian air transportation network. cache = ./cache/cord-337421-4v48kkus.txt txt = ./txt/cord-337421-4v48kkus.txt === reduce.pl bib === id = cord-337491-ztco6guw author = Kucharski, Adam J title = Using serological data to understand unobserved SARS-CoV-2 risk in health-care settings date = 2020-08-03 pages = extension = .txt mime = text/plain words = 929 sentences = 51 flesch = 42 summary = 1 Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), growing evidence of nosocomial transmission has been observed, but tracking such outbreaks is challenging because a substantial proportion of infected individuals might exhibit mild or no symptoms. Staff working in dedicated COVID-19 wards showed substantially higher rates of seropositivity (1·65 [1·34-2·03]; p<0·001) than other frontline health-care workers working in hospitals, reflecting increased risk for this group, a pattern that has also been reported in neighbouring Sweden. The results highlight the risk that SARS-CoV-2 can pose to health-care workers, particularly those in regular contact with patients with COVID-19, and the importance of understanding possible routes of exposure in hospitals. However, the prevalence of asymptomatic SARS-CoV-2 infections and COVID-19-like symptoms among seronegative staff illustrates the limitations of relying on symptom-based surveillance alone. Risk of COVID-19 in health-care workers in Denmark: an observational cohort study SARS-CoV-2 exposure, symptoms and seroprevalence in health care workers cache = ./cache/cord-337491-ztco6guw.txt txt = ./txt/cord-337491-ztco6guw.txt === reduce.pl bib === id = cord-337430-c2vdnml7 author = Timpka, Toomas title = Sports Health During the SARS-Cov-2 Pandemic date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2261 sentences = 122 flesch = 47 summary = In December 2019, the Chinese city of Wuhan reported an outbreak of SARS-Cov-2 (severe acute respiratory syndrome coronavirus-2) infection that causes the Covid-19 disease, an atypical pneumonia [1] . The national public health agencies choose social distancing regulations based on an overall assessment of how critical certain activities are for society as a whole and whether motivation to comply with the rules can be assumed. During the SARS-Cov-2 pandemic, effectively all population-level interventions include the recommendation that social contacts with the elderly, and especially the senior elderly, are to be reduced to an absolute minimum. Sports organisations should develop a pandemic response strategy that addresses the needs of its athletes and coaches, while complying with the regulations and recommendations issued by the government and national public health agency. The temporary frameworks for organised sports practice and competitions must be developed based on the social distancing and quarantine protocols activated during the pandemic. cache = ./cache/cord-337430-c2vdnml7.txt txt = ./txt/cord-337430-c2vdnml7.txt === reduce.pl bib === id = cord-337137-0ey40gzw author = Lo, Anthony WI title = How the SARS coronavirus causes disease: host or organism? date = 2005-12-17 pages = extension = .txt mime = text/plain words = 5201 sentences = 289 flesch = 45 summary = Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection cache = ./cache/cord-337137-0ey40gzw.txt txt = ./txt/cord-337137-0ey40gzw.txt === reduce.pl bib === id = cord-336810-77wq9laa author = Klocperk, Adam title = Complex Immunometabolic Profiling Reveals the Activation of Cellular Immunity and Biliary Lesions in Patients with Severe COVID-19 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4679 sentences = 207 flesch = 43 summary = Therefore, we observed a gradual increase of CRP, procalcitonin, ferritin, and serum IL-6 corresponding to the severity of the disease; however, these markers displayed a relative failure to upregulate in patients with a fatal course, who instead displayed high sIL2R and D-dimers ( Figure 1C ). Most markers of inflammation, the immune response, and liver damage presented in patients with a fatal course of COVID-19 so far seem mostly on par with those seen in patients with a moderate form of the disease, suggesting a weaker response to the infection compared to severely ill patients, which resulted in the patients' deaths. In contrast, patients with fatal COVID-19 ( Figure 5B ) displayed a negative correlation between leukocytes and lymphocytes, and their inflammatory markers increased with markers of organ failure (liver enzymes, amylase, GGT, urea, and creatinine) and cytotoxic cellular immunity (activated CD38+ HLA-DR+ CD8 T cells) instead. cache = ./cache/cord-336810-77wq9laa.txt txt = ./txt/cord-336810-77wq9laa.txt === reduce.pl bib === id = cord-337602-5evfkk70 author = Focosi, Daniele title = Anti‐A Isohemagglutinin titers and SARS‐CoV2 neutralization: implications for children and convalescent plasma selection date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1163 sentences = 55 flesch = 44 summary = . Most importantly, the Italian-Spanish genome-wide association study identified the rs657152 polymorphism in the ABO locus on chromosome 9q34 (and only another polymorphism in chromosome 3p21.31) as the only susceptibility locus for respiratory failure in COVID-19 (6) , suggesting that, in addition to disease acquisition, ABO blood group could also affect disease severity. If confirmed, this hypothesis will have implications for convalescent plasma therapy, since anti-A1 IgG could confer additional benefit over anti-SARS-CoV2 neutralizing antibodies: in fact, while preserving ABO match compatibility, it could be wiser to prefer blood group O donors for CP in COVID-19. All rights reserved Accepted Article considered that hyperimmune serum, arising from pooled diverse ABO groups, contains far lower anti-A isoagglutinin titer than an average O-group convalescent donation. The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis cache = ./cache/cord-337602-5evfkk70.txt txt = ./txt/cord-337602-5evfkk70.txt === reduce.pl bib === id = cord-337179-qytruuif author = Guazzi, Marco title = The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1887 sentences = 109 flesch = 43 summary = title: The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients The main clinical manifestation of SARS-CoV-2 is severe acute respiratory syndrome which yields to inflammatory reaction and alveolar fluid floading ultimately impairing gas exchange. We gained previous experience on the effects of renin-angiotensin system inhibition on the pulmonary function of HF patients showing a protective effect on the perturbed gas exchange and lung fluid handling, i.e. alveolar capillary stress-failure, an effect especially observed with enalapril treatment, with a positive but statistically not signfiicnat trend for losartan 11, 12 . Based on this, we outline how renin angiotensin blockers may interact with the lung fluid handling and gas diffusion process in patients with HF infected by SARS-CoV-2, and propose areas for further research. cache = ./cache/cord-337179-qytruuif.txt txt = ./txt/cord-337179-qytruuif.txt === reduce.pl bib === id = cord-337304-2ad2m317 author = Chang, Le title = Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1295 sentences = 85 flesch = 62 summary = Because of high rates of 2019 novel coronavirus disease in Wuhan, China, Wuhan Blood Center began screening for severe acute respiratory syndrome coronavirus 2 RNA on January 25, 2020. We screened donations in real-time and retrospectively and found plasma samples positive for viral RNA from 4 asymptomatic donors. Lei Zhao, 1 1) and detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in plasma (2, 3) , the safety of China's blood supply became a major concern (4). By March 4, we identified 4 blood donors in Wuhan whose plasma samples tested positive for SARS-CoV-2 RNA (Figure; Appendix Table) . We tested the 4 donors multiple times, using different sample sources, including sample tubes, retained nucleic acid templates, or blood products, indicating the accuracy and validity of our results (Appendix Table) . We extracted total nucleic acids from samples on an Most reverse transcription PCR protocols for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include 2-3 targets for detection. cache = ./cache/cord-337304-2ad2m317.txt txt = ./txt/cord-337304-2ad2m317.txt === reduce.pl bib === id = cord-337646-gkcm6ds0 author = nan title = The Federation’s Pages: WFPHA: World Federation of Public Health Associations www.wfpha.org Bettina Borisch and Marta Lomazzi, Federation’s Pages Editors date = 2020-09-17 pages = extension = .txt mime = text/plain words = 2529 sentences = 140 flesch = 45 summary = The next coronavirus to generate a global public health crisis was the Middle East Respiratory Syndrome (MERS-CoV) that emerged in Saudi Arabia in 2012 among people working closely with camels. During the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV), held on 30 January 2020, the COVID-19 pandemic was underway. The association between Emerging Infectious Diseases (EIDs) and environmental destruction is widely recognized: deforestation destroys natural habitats, increases the density of remaining wild animal populations, increases their movements to look for food accompanied by the probability of human contact-all induce stress that impairs immune systems and increases viral shedding [16] . Environment preservation is urgent for many reasons: conservation of biodiversity, the fight against climate change, reduction of air, water and food pollution, and improvement of human health and quality of life [18] . cache = ./cache/cord-337646-gkcm6ds0.txt txt = ./txt/cord-337646-gkcm6ds0.txt === reduce.pl bib === id = cord-337681-579cz2tc author = Sk, Md Fulbabu title = Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations date = 2020-06-01 pages = extension = .txt mime = text/plain words = 5882 sentences = 340 flesch = 53 summary = title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations In the present work, we have elucidated the mechanism of binding of two inhibitors, namely α-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. The initial coordinates for our molecular dynamics simulations were obtained from the X-ray crystallographic structure of the SARS-CoV-2 3CL pro complexed with the inhibitors a-ketoamide (PDB: 6Y2G) and Z31792168 (PDB: 5R84) (Berman et al., 2002; Zhang et al., 2020) . Next, in our study, the binding affinity of a-ketoamide was further evaluated and compared with the FDA approved anti-HIV protease inhibitors, such as lopinavir and darunavir, which has been reported as potent drugs against 3CL pro of SARS-CoV-2. cache = ./cache/cord-337681-579cz2tc.txt txt = ./txt/cord-337681-579cz2tc.txt === reduce.pl bib === id = cord-337673-1nau263l author = Wu, Chang-Jer title = Antiviral applications of RNAi for coronavirus date = 2006-01-24 pages = extension = .txt mime = text/plain words = 4329 sentences = 253 flesch = 52 summary = Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . cache = ./cache/cord-337673-1nau263l.txt txt = ./txt/cord-337673-1nau263l.txt === reduce.pl bib === id = cord-336938-03366q9t author = Thacker, Vivek V title = Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date = 2020-08-10 pages = extension = .txt mime = text/plain words = 2818 sentences = 169 flesch = 49 summary = title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model A combination of qRT-PCR, RNAscope, immunofluorescence, and ELISA measurements are used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 delivered to the apical surface of the epithelial face maintained at an air-liquid interface. We therefore establish a human lung-on-chip model for SARS-CoV-2 infections, and probe the viral growth kinetics, cellular localization and responses to a low dose infection using qRT-PCR, ELISA, RNAscope, immunofluorescence and confocal imaging (Fig. 1J) . Nevertheless, total RNA extracted from the apical and vascular channels of an infected LoC without macrophages at 1 dpi revealed >10 4 genomes in both epithelial and endothelial cells (Fig. 2C ) and genome copy numbers exceeded those for cellular housekeeping gene RNAseP (Fig. 2D ). Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors cache = ./cache/cord-336938-03366q9t.txt txt = ./txt/cord-336938-03366q9t.txt === reduce.pl bib === id = cord-336909-nnxa5ant author = Guedez-López, Gladys Virginia title = Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3246 sentences = 159 flesch = 52 summary = The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. RT-qPCR tests presented a high specificity with a low probability of false positive; however, sensitivity relies on different factors as specimen site, method of collection, viral load and time from the onset of symptoms [3, 7] . Detection rate of IgM, IgG and IgM/IgG antibodies against SARS-CoV-2 with the three ICT strip assays in positive and negative RT-PCR patients along three periods of time since the onset of symptoms is shown in Table 3 . Detection rates of total antibodies (IgM/IgG) obtained with Sienna® and Wondfo® by the two groups of patients along the three stages since the symptoms onset are collected in Table 4 . In this study, we have investigated the diagnostic value of detection of SARS-CoV-2 IgM and IgG antibodies in different stages of the disease, using three ICT strip assays, in comparison with RT-qPCR. cache = ./cache/cord-336909-nnxa5ant.txt txt = ./txt/cord-336909-nnxa5ant.txt === reduce.pl bib === id = cord-337557-ct43uoir author = Guetl, Katharina title = SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia date = 2020-10-27 pages = extension = .txt mime = text/plain words = 855 sentences = 58 flesch = 46 summary = title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia (4, 5) Here, we report SARS-CoV-2 positive viral culture 7 weeks after onset of COVID-19 in a patient with an underlying immunosuppressive disorder, so-called X chromosome-linked agammaglobulinemia (XLA), demonstrating the potential of prolonged SARS-CoV-2 spreading beyond widely accepted isolation precautions. On April 15, five days after tocilizumab and convalescent plasma administration and five weeks after the initial diagnosis of COVID-19, SARS-CoV-2 RNA was not detectable for the first time. The patient showed progressive clinical recovery, but an alternating course of three negative followed by three positive SARS-CoV-2 RT-PCR results was subsequently observed. In summary, we have to assume that in our patient shedding of infectious SARS-CoV-2 stopped between week 7 and 10 of disease. cache = ./cache/cord-337557-ct43uoir.txt txt = ./txt/cord-337557-ct43uoir.txt === reduce.pl bib === id = cord-337700-2n9tswr8 author = Chilimuri, Sridhar title = Predictors of Mortality in Adults Admitted with COVID-19: Retrospective Cohort Study from New York City date = 2020-07-08 pages = extension = .txt mime = text/plain words = 2355 sentences = 146 flesch = 51 summary = On multiple regression analysis, increasing odds of mortality during hospitalization was associated with older age (odds ratio [OR] 1.04; 95% confidence interval [CI], 1.01–1.06 per year increase; p < 0.0001), admission D-dimer more than 1000 nanograms per milliliter (ng/mL) (OR 3.16; 95% CI, 1.75–5.73; p<0.0001), admission C-reactive protein (CRP) levels of more than 200 milligrams per liter (mg/L) (OR 2.43; 95% CI, 1.36–4.34; p = 0.0028), and admission lymphopenia (OR 2.63; CI, 1.47–4.69; p 0.0010). CONCLUSION: In this retrospective cohort study originating in NYC, older age, admission levels of D-dimer of more than 1000 ng/mL, CRP of more than 200 mg/L and lymphopenia were associated with mortality in individuals hospitalized for COVID-19. In the final analysis, we excluded the following patients: those whose SARS-Cov-2 results were pending or whose definitive outcomes were not available at the time of the study as they were still hospitalized; and those with incomplete information. cache = ./cache/cord-337700-2n9tswr8.txt txt = ./txt/cord-337700-2n9tswr8.txt === reduce.pl bib === id = cord-337674-mb6ue2hl author = Voulgaris, Athanasios title = Sleep medicine and COVID-19. Has a new era begun? date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4544 sentences = 207 flesch = 47 summary = This is especially important for the treatment of patients with sleep disordered breathing (SDB) since the application of positive airway pressure (PAP) can induce spread of aerosol and increase substantially the risk of infection [6] . A group of experts in SDB from the Chinese Thoracic Society provided feedback on the management of patients with OSA and suggested that sleep studies and initiation of PAP application should be continued only in regions with low incidence of COVID-19, preferably with the use of home sleep apnea tests (HSAT) [19] . In case where in-laboratory sleep studies are necessary, especially for PAP titration or insurance demands, these could be performed only after patients' negative screening for COVID-19, according to local recommendations and hospital guidelines, with the personnel using all necessary personal protective equipment (PPE) and keeping safe distances, as previously mentioned and according to WHO infection prevention and control guidance [34] . cache = ./cache/cord-337674-mb6ue2hl.txt txt = ./txt/cord-337674-mb6ue2hl.txt === reduce.pl bib === id = cord-337799-mc1oqhf4 author = Mak, Gannon CK title = Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus date = 2020-10-29 pages = extension = .txt mime = text/plain words = 2329 sentences = 153 flesch = 60 summary = STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using PCR as a reference method. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. Besides RT-PCR, rapid antigen detection (RAD) kits for qualitative determination of SARS-CoV-2 antigen are available. The purpose of this evaluation is to assess analytical sensitivity of the three SARS-CoV-2 RAD kits by means of limit of detection (LOD) using a set of serial tenfold dilution samples; and It means that if we set a cut off by means of ≤day X after symptom onset for performing RAD kits, we will miss another group of specimens having a similar high viral load. cache = ./cache/cord-337799-mc1oqhf4.txt txt = ./txt/cord-337799-mc1oqhf4.txt === reduce.pl bib === id = cord-337372-y43prnko author = bin‐Reza, Faisal title = The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence date = 2011-12-21 pages = extension = .txt mime = text/plain words = 4040 sentences = 226 flesch = 45 summary = A limited effort was made to identify additional studies: reference lists of review articles were examined; the European Centre for Disease Prevention and Control's (ECDC) Antimicrobial Resistance and Health Care Associated Infection Programme was consulted; and MEC's and AN's hardcopy literature files were hand-searched. [7] [8] [9] [10] [11] Two of these studies compared N95 respirators (designed to seal tightly to the wearer's face and filter out very small particles or aerosols that may contain viruses) and surgical masks (used to block large droplets from coming into contact with the wearer's mouth or nose) amongst healthcare workers; one trial found a lower rate of clinical respiratory illness associated with the use of non-fit-tested N95 respirators compared with medical masks, 6 whilst a non-inferiority trial found that masks and respirators offered similar protection to nurses against laboratory-confirmed influenza infection. cache = ./cache/cord-337372-y43prnko.txt txt = ./txt/cord-337372-y43prnko.txt === reduce.pl bib === id = cord-337485-nqcnd9py author = Buetti, Niccolò title = SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients date = 2020-10-16 pages = extension = .txt mime = text/plain words = 2144 sentences = 133 flesch = 49 summary = Our objectives were to describe the viral shedding and the viral load in LRT and to determine their association with mortality in critically ill COVID-19 patients. Third, we assessed the association between viral presence in LRT and mortality using mixed-effect logistic models for clustered data adjusting for the time between symptoms' onset and date of sampling. Our objectives were (1) to describe the viral shedding and the viral load in LRT and (2) to determine THE ASSOCIATION BETWEEN VIRAL PRESENCE AND MORTALITY in critically ill COVID-19 patients. The viral shedding in LRT lasted almost 30 days in median in critically ill patients, and the SARS-CoV-2 viral presence in the LRT was associated with the 6week mortality. Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients cache = ./cache/cord-337485-nqcnd9py.txt txt = ./txt/cord-337485-nqcnd9py.txt === reduce.pl bib === id = cord-337462-9mvk86q6 author = nan title = Humanity tested date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1263 sentences = 59 flesch = 50 summary = The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus' RNA in selected populations. Singapore, Hong Kong and Taiwan have shown the world that, to contain the propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments need to quickly implement aggressive testing (by detecting the viral RNA through polymerase chain reaction (PCR)), the isolation of those infected and the tracing and quarantining of their contacts, while educating their citizens about the need for physical distancing and basic public health measures (in particular, frequent hand-washing and staying at home if feeling unwell). Medical-device companies and government and research laboratories around the world have rushed to adapt and scale up nucleic acid tests (mostly employing PCR, but also CRISPR-based detection and loop-mediated isothermal amplification) to detect the virus' RNA, and government agencies are scrambling to assess them via emergency routes (such as the Emergency Use Authorization program 3 by the United States Food and Drug Administration (FDA)). cache = ./cache/cord-337462-9mvk86q6.txt txt = ./txt/cord-337462-9mvk86q6.txt === reduce.pl bib === id = cord-337663-ow1l18li author = Qu, Liang G. title = Scoping review: hotspots for COVID-19 urological research: what is being published and from where? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4694 sentences = 306 flesch = 45 summary = This comprehensive review aimed to: identify all up-to-date original publications relating to urology and COVID-19, characterise where publications were from, and outline what topics were investigated. Topics of the study included pathophysiological, administrative, and clinical fields: translational (n = 14), COVID-19-related outcomes (n = 5), urology training (n = 4), telemedicine (n = 7), equipment and safety (n = 2), urology in general (n = 4), uro-oncology (n = 3), urolithiasis (n = 1), and kidney transplantation (n = 8). A registered study in France (NCT04341714) is similarly assessing the efficiency and satisfaction of telemedicine consults, aiming to recruit 400 patients from a neuro-urology clinic. 48 studies were included, investigating pathophysiological, administrative, and clinical outcomes relating to COVID-19 and urology. Clinical fields of COVID-19-related urological research seem to focus on uro-oncology, urolithiasis, and kidney transplant recipients. Nevertheless, our review is the first to provide a comprehensive country-level analysis of current original urological research related to COVID-19. cache = ./cache/cord-337663-ow1l18li.txt txt = ./txt/cord-337663-ow1l18li.txt === reduce.pl bib === id = cord-337636-3yc0ribg author = Morehouse, Zachary P. title = A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2980 sentences = 169 flesch = 52 summary = Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. Using human coronavirus 229E (HCoV-229E) as our model organism, we developed a novel two-step methodology of optimized shaker-mill homogenization parameters that allowed for direct-to-PCR viral detection. cache = ./cache/cord-337636-3yc0ribg.txt txt = ./txt/cord-337636-3yc0ribg.txt === reduce.pl bib === id = cord-337854-5ogip9tz author = Huang, Wanqiu title = The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1020 sentences = 67 flesch = 53 summary = In our study, we developed an improved strategy, termed as nestRPA (nest recombinase polymerase amplification), which could greatly improve the sensitivity of nucleic acid detection for SARS-CoV-2 than RPA or qPCR. Using nestRPA technology, we found that positive plasmid containing SARS-CoV-2 with the concentration of 1 copy/ul could also be stably detected by Fragment 5 and nucleic acid detection results were negative using qPCR. Our results suggested that the ultra-sensitive nucleic acid detection technique has important implications for early identification of those asymptomatic carriers infected with SARS-CoV-2. In addition, many experts of COVID-19 prevention and treatment clearly pointed out that the inaccurate sample collection were also one of the important reasons for the false negative result of SARS-CoV-2 nucleic acid [6] [7] [8] . If all the links in the detection of SARS-CoV-2 nucleic acid could be strictly administrated, false negative could be completely eliminated, and the discontinuation of isolation will no longer be a dilemma for us. cache = ./cache/cord-337854-5ogip9tz.txt txt = ./txt/cord-337854-5ogip9tz.txt === reduce.pl bib === id = cord-337753-olc00glo author = Franco, D. title = Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. date = 2020-08-04 pages = extension = .txt mime = text/plain words = 2737 sentences = 160 flesch = 52 summary = The protocol EC-CNBI-202-04-46 was approved by the National Committee on Bioethics of Research of Panama to use de-identified epidemiological data to analyze SARS-CoV-2 transmission and spread, as well as to sequence the complete genome of SARS-CoV-2 from Gorgas Memorial Institute of Health Studies (GMI)'s confirmed cases. . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama detected the first SARS-CoV-2 infection one month after Brazil 15 , being the 11 th country with confirmed cases in Latin America (Supplementary Figure 2) . To characterize the distribution of genetic lineages in Panama, we generated 313 SARS-CoV-2 sequences, which represents 7.4 % of the total confirmed cases by April 15 th (Supplementary Figure 4A Figure 4A ). . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama has the most confirmed SARS-CoV-2 infections and associated fatalities in Central America, although control strategies were rapidly implemented at the beginning of the outbreak. cache = ./cache/cord-337753-olc00glo.txt txt = ./txt/cord-337753-olc00glo.txt === reduce.pl bib === id = cord-337572-kx5hihnr author = Ludwig, Stephan title = Coronaviruses and SARS-CoV-2: A Brief Overview date = 2020-04-20 pages = extension = .txt mime = text/plain words = 2668 sentences = 167 flesch = 54 summary = The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 . Here we provide a short background on coronaviruses and their origin, and we describe in more detail the novel SARS-CoV-2 and the efforts thus far to identify effective therapies against COVID-19. The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). 19 SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 At the end of December 2019, China reported the increasing occurrence of pneumonia in the city of Wuhan, Hubei province. Identification of a novel coronavirus in patients with severe acute respiratory syndrome cache = ./cache/cord-337572-kx5hihnr.txt txt = ./txt/cord-337572-kx5hihnr.txt === reduce.pl bib === id = cord-337712-ylqgraos author = Heinz, Franz X. title = Profile of SARS-CoV-2 date = 2020-10-30 pages = extension = .txt mime = text/plain words = 6028 sentences = 301 flesch = 44 summary = Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . cache = ./cache/cord-337712-ylqgraos.txt txt = ./txt/cord-337712-ylqgraos.txt === reduce.pl bib === id = cord-337692-b89ow1mf author = Petti, S. title = Ecologic association between influenza and COVID-19 mortality rates in European countries date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5103 sentences = 251 flesch = 41 summary = Ecologic studies investigating COVID-19 mortality determinants, used to make predictions and design public health control measures, generally focused on population-based variable counterparts of individual-based risk factors. We considered the 3-year average influenza (2014–2016) and COVID-19 (31 May 2020) crude mortality rates in 34 countries using EUROSTAT and ECDC databases and performed correlation and regression analyses. An apparently perplexing characteristic of the reported association between the two mortality rates was that while influenza virus circulation during the seasons considered in the present analysis was uncontrolled, SARS-CoV-2 circulation was probably limited by the widespread exceptional public health measures implemented in Europe [32] . This study reported an inverse association between number of hospital beds and mortality rates (Table 2) , thus showing that high influenza and COVID-19 mortality was also due to inefficiencies of the healthcare systems, and corroborated by data from several European countries [45] . cache = ./cache/cord-337692-b89ow1mf.txt txt = ./txt/cord-337692-b89ow1mf.txt === reduce.pl bib === id = cord-337809-bxvgr6qg author = Xiong, Yong title = Family cluster of three recovered cases of pneumonia due to severe acute respiratory syndrome coronavirus 2 infection date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1738 sentences = 122 flesch = 53 summary = Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. [2] [3] [4] [5] [6] [7] [8] This report describes the epidemiological and clinical features of coronavirus disease (COVID-19) among three members of a family following SARS-CoV-2 infection. On 10 and 11 January 2020, a family of three, comprising the father (65 years), the mother (61 years) and the son (38 years), were admitted to the Department of Infectious Disease at the Zhongnan Hospital of Wuhan University with symptoms of cough and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China cache = ./cache/cord-337809-bxvgr6qg.txt txt = ./txt/cord-337809-bxvgr6qg.txt === reduce.pl bib === id = cord-337595-0p5f5o5v author = Tagliamento, Marco title = Call for ensuring cancer care continuity during COVID-19 pandemic date = 2020-05-07 pages = extension = .txt mime = text/plain words = 874 sentences = 48 flesch = 50 summary = On 11 March 2020, WHO declared the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to be a pandemic, and the related syndrome was then named coronavirus disease 2019 (COVID-19). At a median follow-up of 15 days since the confirmed diagnosis of SARS-CoV-2 infection, the case fatality rate was 24%: four patients out of 17 died due to severe COVID-19, two of whom were on oncological follow-up (ie, off therapy). Widespread testing for SARS-CoV-2 among patients with cancer and their healthcare providers could also help to control the potential negative consequences of this outbreak on cancer care. With the current uncertainty, the important aim behind this decision is to ensure continuity of care to those selected patients who can reasonably receive oncological treatments in spite of SARS-CoV-2 positivity, balancing the risks associated with the infection and the disruption of proper antineoplastic strategies. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan cache = ./cache/cord-337595-0p5f5o5v.txt txt = ./txt/cord-337595-0p5f5o5v.txt === reduce.pl bib === id = cord-337812-arivkkj0 author = Chu, Ling-Hon Matthew title = Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry date = 2006-03-07 pages = extension = .txt mime = text/plain words = 6860 sentences = 286 flesch = 52 summary = To screen the substrate specificity of SARS-CoV 3CL pro in a rapid and highthroughput manner in contrast to the traditional tedious procedures, we applied the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis in combination with the novel "cartridge replacement" solid-phase peptide synthesis approach to investigate the biological significance of amino acid residues in the P2, P3, P4, P1¢, P2¢, and P3¢ positions that are flanking the conserved Gln residue in the P1 position at the SARS-CoV 3CL pro cleavage site (Schechter and Berger 1967; Fan et al. In this study, we used MALDI-TOF MS analysis in combination with the solid-phase peptide synthesis approach to examine the biological significance of amino acid residues in a total of six target positions at the SARS-CoV 3CL pro cleavage sites, including the P2, P3, and P4 positions at the amino side of the P1 position; and the P1¢, P2¢, and P3¢ positions at the carboxyl side of the P1 position (Table 1) . cache = ./cache/cord-337812-arivkkj0.txt txt = ./txt/cord-337812-arivkkj0.txt === reduce.pl bib === id = cord-337896-mct29erg author = Kornbluth, Asher title = Management of Inflammatory Bowel Disease and COVID-19 in New York City 2020: The Epicenter of IBD in the First Epicenter of the Global Pandemic date = 2020-09-03 pages = extension = .txt mime = text/plain words = 5111 sentences = 212 flesch = 55 summary = A number of the major GI societies, the Crohn's & Colitis Foundation, 3 British Society of Gastroenterology, 4 European Crohn's and Colitis Organization, 5 The American Gastroenterology Association, 6 and the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) 7 have published guidelines regarding treating the IBD patient with SARS-CoV-2 and COVID-19. 8 The key features are that the patient without proven or suspected SARS-CoV-2 should continue on their current medications with aggressive attempts to reduce steroid usage because this is the only single agent that has been associated with increased poor outcomes with COVID-19, defined in the SECURE registry as a composite score of hospitalization, intubation, or death. 14 We are now participating in the development of a database that will follow patients after clearance of the SARS-CoV-2 virus to determine the courses and outcomes of the IBD and of any sequelae or recurrence of COVID-19 after any drug therapy has been suspended. cache = ./cache/cord-337896-mct29erg.txt txt = ./txt/cord-337896-mct29erg.txt === reduce.pl bib === id = cord-338001-jig46hsk author = Ong, Jacqueline S. M. title = Coronavirus Disease 2019 in Critically Ill Children: A Narrative Review of the Literature date = 2020-04-21 pages = extension = .txt mime = text/plain words = 3418 sentences = 178 flesch = 50 summary = In the small cohort from Tongji Hospital (6), Wuhan, one out of the six children with COVID-19 was admitted to intensive care. Given that children appear to have mild disease and may have a clinical picture similar to that of viral bronchiolitis, the use of noninvasive ventilation (NIV), and/or high-flow nasal cannula (HFNC) for respiratory support would likely be preferred amongst PICU clinicians. Caregivers are close contacts of the infected patient, although they may be asymptomatic at the time-in the Wuhan Children's Hospital series with active case finding of close contacts, 90% of confirmed cases had family members who were either confirmed or suspect disease (5) . Given the low rates of critical illness due to COVID-19, this process will likely exert more impact on day-to-day processes in PICUs than sick patients with confirmed infection. Paediatric Intensive Care Society UK: PICS Guidance on Management of Critically Ill Children With COVID-19 Infection cache = ./cache/cord-338001-jig46hsk.txt txt = ./txt/cord-338001-jig46hsk.txt === reduce.pl bib === id = cord-338023-gb5jgqcg author = Obara, Shinju title = Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2820 sentences = 123 flesch = 39 summary = title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission Because SARS-CoV-2 can be transmitted via aerosols and surface contaminations of the environment, appropriate use of anesthesia machines and appropriate behavior in the operation room (OR) are required specifically in relation to this disease. For patients with confirmed or suspected COVID-19 infection, recommendations are use of (1) a high-performance hydrophobic filter (artificial nose) with a high rate of virus rejection (viral filtration efficiency > 99.99% [12] ), and (2) use of a viral filter at the expiratory gas inlet of the anesthesia machine from the expiratory circuit to protect the machine from viruses passing through the artificial nose [12, 13] . Recommendations for anesthesia in patients suspected of COVID-19 Coronavirus infection cache = ./cache/cord-338023-gb5jgqcg.txt txt = ./txt/cord-338023-gb5jgqcg.txt === reduce.pl bib === id = cord-337789-pabaoiqs author = Oprinca, George-Călin title = Postmortem examination of three SARS-CoV-2-positive autopsies including histopathologic and immunohistochemical analysis date = 2020-08-27 pages = extension = .txt mime = text/plain words = 4995 sentences = 282 flesch = 47 summary = This paper describes three autopsy cases with postmortem diagnosis of SARS-CoV-2 infection, with detailed macroscopic examination as well as advanced microscopic studies of organ tissues collected using hematoxylin-eosin stains and immunohistochemical markers. Microscopic evaluation revealed viral cytopathic effect of type II pneumocytes with a couple of cells that presented cytoplasmic and nuclear inclusions and who tend to form clusters mimicking multinucleated giant cells. This paper describes three autopsy cases with unknown cause of death, with full macroscopic examination as well as histopathologic and immunohistochemical analysis of collected organ tissues, including the lung from which reverse transcription polymerase chain reaction (rt-PCR) tests were made to determine SARS-CoV-2 infection. Microscopic examination of the pulmonary tissue revealed large areas of alveolar damage with destruction of the alveolar wall lining and intra-alveolar septa, marked vascular congestion, accompanied by intra-alveolar hemorrhage. cache = ./cache/cord-337789-pabaoiqs.txt txt = ./txt/cord-337789-pabaoiqs.txt === reduce.pl bib === id = cord-337825-ujq9mxk7 author = Chen, Bin title = Overview of lethal human coronaviruses date = 2020-06-10 pages = extension = .txt mime = text/plain words = 13423 sentences = 761 flesch = 51 summary = Coronaviruses are the largest +ssRNA viruses and contain at least 14 ORFs, 16 protein combines with viral RNA to form a nucleocapsid, which is involved in the replication of SARS-CoV and is the most abundant protein in virus-infected cells. MERS-CoV can infect T-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, Nanopore Targeted Sequencing, also has the potential for efficiently detecting viruses in a reasonable time. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine cache = ./cache/cord-337825-ujq9mxk7.txt txt = ./txt/cord-337825-ujq9mxk7.txt === reduce.pl bib === id = cord-337973-djqzgc1k author = Hao, Siyuan title = Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2624 sentences = 166 flesch = 54 summary = title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Our observation that SARS-CoV-2 was unable to infect epithelial cells from the 299 basolateral side supports that the viral entry receptor ACE2 is polarly expressed at the apical 300 side 30, 31 . We 332 determined that 1 pfu of SARS-CoV-2 in Vero-E6 cells has a particle (viral genome copy) 333 number of 820, suggesting that a load of 2.46 x 10 5 particles is required to productively infect 1 334 cm 2 of the airway epithelium, which is much higher than the small DNA virus parvovirus human 335 bocavirus 1 (HBoV1) we studied 55 . cache = ./cache/cord-337973-djqzgc1k.txt txt = ./txt/cord-337973-djqzgc1k.txt === reduce.pl bib === id = cord-338054-n2r4pzan author = Lau, Joseph TF title = Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date = 2007-03-15 pages = extension = .txt mime = text/plain words = 3846 sentences = 202 flesch = 48 summary = Respondents were asked how likely they would be to adopt the following preventive behaviors if a local human-to-human H5N1 outbreak (defined as "if 2-3 new human-to-human transmission of H5N1 cases were to be reported in Hong Kong") were to occur: face mask use in public venues, increased frequency of handwashing, avoidance of eating poultry, declaration of influenzalike illness (ILI) symptoms at border health checkpoints, the seeking of medical consultation immediately with the onset of a fever, face mask use in public venues when having ILI symptoms and compliance with any quarantine policies. Respondents were asked about perceptions related to human-to-human H5N1 transmission, including perceived modes of transmission (whether human-to-human transmission of the H5N1 virus could occur via respiratory droplets, bodily contact, contaminated objects, eating well-cooked poultry), perceived susceptibility to H5N1 in different groups of people (self, family members, children, adults, older people, health care workers, food handlers, food vendors and the general public), perceived chance of having a major outbreak in Hong Kong in the next 12 months and perceived efficacy of various prevention measures (quarantine of infected people, face mask use in public venues, frequent handwashing, home disinfection, mass extermination of poultry). cache = ./cache/cord-338054-n2r4pzan.txt txt = ./txt/cord-338054-n2r4pzan.txt === reduce.pl bib === id = cord-337962-9le56say author = Duan, Fuyu title = Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 5337 sentences = 262 flesch = 51 summary = Here, we used directed differentiation of human pluripotent stem cells (hPSCs) to establish a lung and macrophage co-culture system and model the host-pathogen interaction and immune response caused by SARS-CoV-2 infection. Recent studies (Liao et al., 2020; Xu et al., 2020) on immunity of COVID-19 patients indicate that the cells damaged by SARS-CoV-2 infection induced innate in ammation in the lungs that is largely mediated by pro-in ammatory macrophages and granulocytes. To further characterize at the transcriptomic level the response of iLung and iMφ following viral infection, scRNA-seq was performed on the co-cultures with SARS-CoV-2 pseudo virus infection and the analysis revealed that a set of anti-in ammatory factors and anti-viral activity related genes, such as CCL26, CCL13, ISG15, IFITM2 and IFITM3, were clearly upregulated when cultures contained M2-iMφ ( Figure 4A and C, Figures S8A) . cache = ./cache/cord-337962-9le56say.txt txt = ./txt/cord-337962-9le56say.txt === reduce.pl bib === id = cord-337867-hqmf6r7t author = Shim, Byoung-Shik title = Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses date = 2010-12-31 pages = extension = .txt mime = text/plain words = 3762 sentences = 221 flesch = 54 summary = title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses RESULTS: In the present study, the immune responses of BALB/c mice immunized via intranasal (i.n.) route with SARS DNA vaccine (pci-S) in a PEI/pci-S complex form have been examined. The result showed that SARS S-specific IgA antibody response was significantly (P < 0.01) increased in lung wash from mice immunized with PEI/pci-S complexes ( Figure 2B ). B220 + cells from mice immunized with PEI/pci-S complexes were highly proliferated after in vitro re-stimulation with SARS-CoV S protein ( Figure 2C ). The surface expression of CD80 and CD86 co-stimulatory molecules were significantly (P < 0.05) higher on DCs from mice treated with PEI/pci-S complexes than those from SARS-CoV DNA S vaccine alone ( Figure 3 ). DNA vaccine encoding full-length S protein has shown to induce humoral, cellular and protective immune responses against SARS-CoV [6] . cache = ./cache/cord-337867-hqmf6r7t.txt txt = ./txt/cord-337867-hqmf6r7t.txt === reduce.pl bib === id = cord-338152-e8e3lv79 author = Zhang, Peilin title = Detection of SARS-CoV-2 in placentas with pathology and vertical transmission date = 2020-08-03 pages = extension = .txt mime = text/plain words = 610 sentences = 50 flesch = 55 summary = We examined 364 consecutive placentas from the mothers tested in our facilities since the universal testing policy was adopted in March 2020 including 74 positive and 290 negative for SARS-CoV2 by nasopharyngeal swab PCR method as previously described [1] . One positive placenta for SARS-CoV2 by ISH was delivered by C-section at 35 weeks 6 days due to placental previa 4 associated with placental infarcts, and the newborn baby was tested positive by swab PCR at 24 hours, 48 hours and 7 days. The other positive placenta was from a mother with 40 week gestation associated with no significant clinical and pathological features, and the baby was tested negative for SARS-CoV2 by swab PCR method within the first 24 hours. The current study showed that SARS-COV2 viral particles are uncommon in placentas from PCR-positive mothers at late gestation. Neonatal testing for SARS-CoV2 by swab PCR also showed rare positive cases from positive mothers. cache = ./cache/cord-338152-e8e3lv79.txt txt = ./txt/cord-338152-e8e3lv79.txt === reduce.pl bib === id = cord-338203-le5lbw5y author = O’Reilly, GM title = Epidemiology and clinical features of emergency department patients with suspected COVID‐19: Results from the first month of the COVED Quality Improvement Project (COVED‐2). date = 2020-06-13 pages = extension = .txt mime = text/plain words = 2848 sentences = 151 flesch = 50 summary = METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study that includes all adult patients presenting to The Alfred Hospital ED who undergo testing for SARS‐CoV‐2. As cases accumulate, the COVED Project aims to determine and report the clinical and epidemiological predictors of a positive SARS-CoV-2 test result and the requirement for intensive respiratory support among patients presenting to the ED with suspected COVID-19. In the first full month of the COVED Project, the daily number and proportion of patients with a positive SARS-CoV-2 test remained relatively low, but the rate of patients presenting to the ED with suspected COVID-19 increased significantly. The low incidence of SARS-CoV-2 positive results over the first full month of the COVED Project has precluded valid inferential analyses regarding how COVID-19 patients differ in terms of their demographic features, clinical presentation, severity risk factors, need for intensive respiratory support and key outcomes. cache = ./cache/cord-338203-le5lbw5y.txt txt = ./txt/cord-338203-le5lbw5y.txt === reduce.pl bib === id = cord-338055-2d6n4cve author = Hassan, Sk. Sarif title = A unique view of SARS-CoV-2 through the lens of ORF8 protein date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5942 sentences = 322 flesch = 55 summary = In this present study, we identified the distinct mutations present across unique variants of the SARS-CoV-2 ORF8 and classified them according to their predicted effect on the host, i.e disease or neutral and the consequences on protein structural stability. The ORF8 sequences of SARS-CoV-2, Bat-CoV RaTG13 and Pangolin-CoV have almost the same positive and negative charged amino acids, therefore we can say that probably they have similar kind of electrostatic and hydrophobic interactions, 135 which also contribute to the functionality of the proteins. • QKV07730.1: The T11A mutation occurred as the second mutation in this sequence, which was predicted to be of disease-increasing type and the polarity was changed from hydrophilic to hydrophobic, hence the structure and 305 function of the protein are expected to differ. cache = ./cache/cord-338055-2d6n4cve.txt txt = ./txt/cord-338055-2d6n4cve.txt === reduce.pl bib === id = cord-338097-kdrq81w5 author = Brescia, Marilia D'Elboux Guimarães title = “Green July” 2020 and Another Good Reason to Quit Smoking: Help to Stop Spreading SARS-COV-2 and Save Lives! date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1205 sentences = 83 flesch = 64 summary = In Brazil, the initiative has been a great success coordinated by the Brazilian Society of Head and Neck Surgery (BSHNS), and it was expanded to one entire month, named "Green July." All around the country, besides press and television interviews and social media posts, members of the BSHNS and its accredited training centers run talks, shows and physical activities with the population to encourage healthy habits and to avoid exposure to the major risk factors associated with head and neck cancer. 2 Fortunately, for the time being, we are unaware of any Brazilian head and neck surgeons dying of SARS-Cov-2, even though the risk of severe infection to this medical specialty is quite real. Besides their individual risk for head and neck cancer, smoking is now a major risk factor for transmitting SARS-Cov 2. Tobacco Smoking a Potential Risk Factor in Transmission of COVID-19 Infection cache = ./cache/cord-338097-kdrq81w5.txt txt = ./txt/cord-338097-kdrq81w5.txt === reduce.pl bib === id = cord-338123-4pshh5ov author = nan title = SARS Alert Applicability date = 2004-08-17 pages = extension = .txt mime = text/plain words = 1461 sentences = 67 flesch = 41 summary = If the illness is included in the list of notifiable infectious diseases, the case must be reported to the local public health authority so infection control measures can be implemented. To determine how the sickness certification system in other European Union countries operates and assesses the feasibility of the WHO alert surveillance, we interviewed specialists in infectious diseases or public health in France (seven imported cases of SARS, two in healthcare workers), Spain (one case), and Denmark (no cases) (2) by electronic mail. All hospitals that treated patients with suspected SARS either had their own committee to classify patients according to World Health Organization guidelines or followed the protocol for classification or reclassification of reported cases by the team members (3). From the first day that suspected cases were reported to the Taiwan Center for Disease Control, the patients were placed in negative-pressure isolation rooms when available. cache = ./cache/cord-338123-4pshh5ov.txt txt = ./txt/cord-338123-4pshh5ov.txt === reduce.pl bib === id = cord-338225-8dlxnpcn author = De Meyer, Sandra title = Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date = 2020-05-29 pages = extension = .txt mime = text/plain words = 329 sentences = 27 flesch = 60 summary = Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. cache = ./cache/cord-338225-8dlxnpcn.txt txt = ./txt/cord-338225-8dlxnpcn.txt === reduce.pl bib === id = cord-338359-pd4bfjet author = Yu, J. title = Risk assessment of admission procedures for cancer patients during the convalescence of COVID-19 date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1094 sentences = 74 flesch = 49 summary = Conclusions: Unbiased proteomic profiling of COVID-19 patient serum identified a panel of candidate protein biomarkers that associate with tocilizumab treatment response as well as the ensuing course of the disease. Background: There are limited data on cancer patients (pts) and the novel coronavirus (SARS-CoV2) respiratory disease (COVID-19). We aim to evaluate the frequency of ILI in cancer pts during the pandemic, and to identify high-risk subjects to test for COVID-19. Results: Overall, 562 pts were enrolled: 13 (2%) pts had a positive SARS-CoV2 swab, none of which performed on the basis of triage procedures or questionnaires, rather detected through telephone communications and triage; 52 (9%) pts reported suspect symptoms and/or laboratory tests. The incidence of both COVID-19 diagnosis (2%), and SARS-CoV2 Ab positivity in pts tested on the basis of suspect symptoms (<1%), were similar to those observed in the general population. cache = ./cache/cord-338359-pd4bfjet.txt txt = ./txt/cord-338359-pd4bfjet.txt === reduce.pl bib === id = cord-338140-p88fgojk author = Cervantes-Pérez, Enrique title = Medical Nutrition Therapy in Hospitalized Patients With SARS-CoV-2 (COVID-19) Infection in a Non-critical Care Setting: Knowledge in Progress date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3964 sentences = 214 flesch = 42 summary = The purpose of this review is to provide concise guidance for the nutritional management of individuals with COVID-19 based on the current literature and focused on those in the non-ICU setting or with an older age and polymorbidity, which are independently associated with malnutrition and its negative impact on mortality. Numerous cases of pneumonia caused by a new virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were initially reported in Wuhan, China, at the end of December 2019. The purpose of this review is to summarize what is known about SARS-CoV-2 infection and provide possible and potential nutritional interventions on novel coronaviruses for clinicians. Older adults and polymorbid individuals suffering from chronic and acute disease conditions are at increased risk for poor outcomes and higher mortality following infection with the COVID-19-causing virus. cache = ./cache/cord-338140-p88fgojk.txt txt = ./txt/cord-338140-p88fgojk.txt === reduce.pl bib === id = cord-338041-gl65i3s0 author = Tang, Qin title = Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date = 2015-11-26 pages = extension = .txt mime = text/plain words = 4455 sentences = 230 flesch = 53 summary = Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Based on the data matrix of nucleotide composition, the MD and SVM were applied to predict hosts of coronaviruses. The data matrix with 19 factors as columns and 730 samples as rows was fitted to SVM and MD models, all predictions in leave-one-out cross-validations were listed in Supplementary Table S2 and summarized in Table 1 according to host species. Cross-host evolution research of SARS-CoV in palm civet and humans indicated that the variations in spike genes seemed to be essential for the transition of coronavirus from animal-to-human transmission to human-to-human transmission 25 . The MD correctly predicts bats as the natural hosts of the three viruses, and the SVM indicates that Rs3367 and SL-CoV-WIV1 are harmful to humans. cache = ./cache/cord-338041-gl65i3s0.txt txt = ./txt/cord-338041-gl65i3s0.txt === reduce.pl bib === id = cord-338333-yvm3d6xy author = Tu, Danna title = Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 date = 2020-07-25 pages = extension = .txt mime = text/plain words = 1067 sentences = 67 flesch = 47 summary = title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. Here we would like to share our finding about the serum antibodies analyzed in a special group of pediatric medical workers exposed to varying levels of SARS-CoV-2 after Wuhan severe epidemic of COVID-19. The overall positive rate for SARS-CoV-2 IgG and IgM antibodies in the pediatric medical workers was 43.08 and 5.85%, respectively. This research revealed that pediatric medical workers are a high-risk group for infection by SARS-CoV-2, and the higher the exposure levels to COVID-19 patients and aerosol production, the greater chance of being infected. Table 1 Test results of serum antibodies in pediatric medical workers exposed to different levels of SARS-CoV-2 High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients cache = ./cache/cord-338333-yvm3d6xy.txt txt = ./txt/cord-338333-yvm3d6xy.txt === reduce.pl bib === id = cord-338517-1mxcssjj author = Ishay, Yuval title = Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date = 2020-08-26 pages = extension = .txt mime = text/plain words = 7387 sentences = 399 flesch = 40 summary = The phage display method, allowing rapid and wide display of proteins directly correlated to their associated genes, can detect NAbs against SARS-CoV from both naïve and immune antibody libraries, capable of blocking the binding of S1 domain, thereby showing virus neutralization and prophylaxis capability either in vitro or in the animal models (31, 33, 36) . Another method, possibly allowing the production and utilization of existing NAbs, may include the use of Epstein-Barr virus (EBV) transformation of human B cells to improve the isolation of NAbs from the memory B cells harvested from the SARS-CoV infected patients (11) . Experimental and clinical data on the use of convalescent plasma products and humanized monoclonal antibodies for H5N1 influenza infection have also shown positive outcomes, and this treatment was proposed as a mean for overcoming anti-viral drug resistance (62, 79, 80) . In a study involving 20 patients with severe pandemic influenza A (H1N1) 2009 virus infection, administration of convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality (81) . cache = ./cache/cord-338517-1mxcssjj.txt txt = ./txt/cord-338517-1mxcssjj.txt === reduce.pl bib === id = cord-338243-njkhwkwk author = Zhang, Dayi title = Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2831 sentences = 158 flesch = 51 summary = title: Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital In this study, we evaluated the presence of SARS-CoV-2 viral RNA in septic tanks of Wuchang Cabin Hospital and found a striking high level of (0.5–18.7) × 103 copies/L after disinfection with sodium hypochlorite. In septic tanks, disinfection achieved free chlorine > 6.5 mg/L for 1.5 hours when the dosage of sodium hypochlorite was 800 g/m 3 , meeting well with the guideline for emergency treatment of medical sewage containing SARS-CoV-2 suggested by China CDC. Septic tanks can behave as a long-term source J o u r n a l P r e -p r o o f to release SARS-CoV-2 viral RNA into waters when disinfection is not sufficient and challenges public health via potentially spreading viruses in drainage pipelines. cache = ./cache/cord-338243-njkhwkwk.txt txt = ./txt/cord-338243-njkhwkwk.txt === reduce.pl bib === id = cord-338317-ro041w5l author = Lockhart, Sam M. title = When two pandemics meet: Why is obesity associated with increased COVID-19 mortality? date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4664 sentences = 247 flesch = 47 summary = Thus, the association of obesity with worse 105 outcomes in acute lung infection or widespread alveolar damage of other types, appears to be 106 strongest and most consistent with COVID-19 and pandemic H1N1 influenza. In addition to being lower in obesity and most insulin 168 resistant states it is worth noting that adiponectin levels have been reported to be significantly 169 lower in many of the COVID-19 "at risk" groups e.g. Male < Females 20 and South Asians < White 170 is secreted from adipose tissue, associated with insulin resistance and likely contributes to 197 thrombotic risk in obesity by impairing fibrinolysis 23 . In summary, we have applied insights into the pathophysiology of the adverse consequences of 279 obesity and emerging evidence regarding the pathological mechanisms in COVID-19 to suggest 280 possible routes whereby obesity can exacerbate the tissue damage associated with infection by the 281 SARS-CoV-2 virus. cache = ./cache/cord-338317-ro041w5l.txt txt = ./txt/cord-338317-ro041w5l.txt === reduce.pl bib === id = cord-338205-sy91rnse author = Li, Chenxi title = Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date = 2020-07-02 pages = extension = .txt mime = text/plain words = 7515 sentences = 436 flesch = 51 summary = With limited understanding of COVID-19, it is difficult to exclude SARS-CoV-2 infection based on a single negative PCR result, especially when testing was used for upper respiratory tract specimens. The study found that SARS-CoV-2 could be detected in all primer-probe sets applied in the qRT-PCR tests, but significant discrepancy was observed in the detection limit and the ability to identify negatives and positives with a lower viral load. Compared with the qRT-PCR kit, nested RT-PCR analysis showed higher sensitivity and specificity, indicating that it is more suitable for clinical application to detect SARS-CoV-2 in cases with low viral load. In cases where RT-PCR assays are negative and there is a strong epidemiological link to SARS-CoV-2 infection, paired serum samples (in the acute and convalescent-phase) could support diagnosis once validated serology tests are available with the initial samples collected in the first week of COVID-19 and the second collected after 2-4 weeks [28] . cache = ./cache/cord-338205-sy91rnse.txt txt = ./txt/cord-338205-sy91rnse.txt === reduce.pl bib === id = cord-338351-y1t9emu1 author = Ora, Josuel title = Does bronchoscopy help the diagnosis in Covid-19 infection? date = 2020-06-11 pages = extension = .txt mime = text/plain words = 968 sentences = 59 flesch = 46 summary = The diagnosis of COVID-19 is mainly based on typical symptoms, history of exposure to an infected person and bilateral involvement on chest radiographs, and it is confirmed by a positive nucleic acid test for SARS-CoV-2 from numerous types of specimens including Oropharyngeal (OP) and nasopharyngeal (NP) swabs, anal swabs, stool, urine and bronchoalveoalr lavage fluid (BALF) 1,2 . Here we report our experience from a COVID-19 hospital in Rome, Italy, where patients with typical symptoms of the disease, suggestive CT scans and three NP/OP negative swabs performed on consecutive days and IgG and IgM serology negative for SARS-CoV-2 underwent bronchoscopy with BAL to define the diagnostic issue. In conclusion, our findings demonstrate that three negative swabs along with negative antibodies, despite a suggestive CT scan, can safely rule out the SARS-CoV-2 infection in suspected patients, hence to proceed in alternative diagnosis process. cache = ./cache/cord-338351-y1t9emu1.txt txt = ./txt/cord-338351-y1t9emu1.txt === reduce.pl bib === id = cord-338498-3238fz73 author = Kleen, Thomas-Oliver title = Mitigating Coronavirus Induced Dysfunctional Immunity for At-Risk Populations in COVID-19: Trained Immunity, BCG and “New Old Friends” date = 2020-09-04 pages = extension = .txt mime = text/plain words = 12523 sentences = 559 flesch = 39 summary = Bacterial "new old friends" such as Bacille Calmette-Guérin (BCG) or Mycobacterium obuense have the ability to elevate basal systemic levels of type 1 cytokines and immune cells, correlating with increased protection against diverse and unrelated infectious agents, called "trained immunity." Here we describe dysfunctional immune responses induced by coronaviruses, representing potentially difficult to overcome obstacles to safe, effective vaccine development for COVID-19, and outline how trained immunity could help protect high risk populations through immunomodulation with BCG and other "new old friends." One recent example of the need for continued vigilance is a study using Chinese macaques indicating cause for concern by showing that vaccine-induced, S-specific immunity in the form of anti-spike IgG resulted in severe ALI by skewing macrophage responses during subsequent, acute infection with closely related SARS-CoV (139) . cache = ./cache/cord-338498-3238fz73.txt txt = ./txt/cord-338498-3238fz73.txt === reduce.pl bib === id = cord-338417-7kw9lws0 author = Singh, Awadhesh Kumar title = Comorbidities in COVID-19: Outcomes in hypertensive cohort and controversies with renin angiotensin system blockers date = 2020-04-09 pages = extension = .txt mime = text/plain words = 3212 sentences = 172 flesch = 48 summary = RESULTS: From the pooled data of all ten available Chinese studies (n = 2209) that have reported the characteristics of comorbidities in patients with COVID-19, hypertension was present in nearly 21%, followed by diabetes in nearly 11%, and established cardiovascular disease (CVD) in approximately 7% of patients. Emerging data suggests that older COVID-19 patients with other comorbid conditions such as diabetes, hypertension, cardiac and pulmonary disease are in particular more susceptible, compared to general populations and have higher mortality. We have systematically searched the PubMed medical database up till March 27, 2020 using MeSH key words that include Covid-19, coronavirus, hypertension, diabetes, cardiovascular disease, angiotensin receptor blockers, angiotensin converting enzyme inhibitors. Interestingly, in the pooled data from the ten Chinese studies (n ¼ 2209) that have reported the characteristics of comorbidities in patients with COVID-19; associations of hypertension, diabetes and presence of established cardiovascular disease (CVD) are larger, varying from 15 to 30% (average 21%), 5e20% (average 11%) and 2e40% (average 7%) respectively (Table 1) . cache = ./cache/cord-338417-7kw9lws0.txt txt = ./txt/cord-338417-7kw9lws0.txt === reduce.pl bib === id = cord-338544-eph89g47 author = Spuntarelli, Valerio title = COVID-19: is it just a lung disease? A case-based review date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2279 sentences = 142 flesch = 44 summary = COVID-19 pandemic reached 3.78 million confirmed reported cases worldwide, and it is generally associated to the acronym that precedes its name: severe acute respiratory syndrome (SARS). A prospective study investigating left ventricular performance in 46 patients with severe acute respiratory syndrome showed subclinical diastolic impairment without systolic involvement [3] . Pathological findings of COVID-19 associated with acute respiratory distress syndrome showed few interstitial mononuclear inflammatory infiltrates, but no other substantial damage in the heart tissue [7] . A case report highlights myocarditis as a complication associated with COVID-19, even without symptoms and signs of interstitial pneumonia in an otherwise healthy 53-year-old white woman [8] . The authors concluded that the presence of the characteristic features of symmetric, multifocal lesions with thalamic involvement suggests that this is a case of acute necrotizing hemorrhagic encephalopathy associated with COVID-19. Guillain Barre syndrome associated with COVID-19 infection: a case report cache = ./cache/cord-338544-eph89g47.txt txt = ./txt/cord-338544-eph89g47.txt === reduce.pl bib === id = cord-338647-dtuohsf5 author = Başcı, Semih title = Outcome of COVID-19 in patients with chronic myeloid leukemia receiving tyrosine kinase inhibitors date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2709 sentences = 169 flesch = 55 summary = INTRODUCTION: In this study, we aim to report the outcome of COVID-19 in chronic myeloid leukemia (CML) patients receiving tyrosine kinase inhibitor (TKI). METHOD: The data of 16 laboratory-confirmed COVID-19 patients with CML receiving TKI and age, gender, and comorbid disease matched COVID-19 patients without cancer at a 3/1 ratio (n = 48), diagnosed between March 11, 2020 and May 22, 2020 and included in the Republic of Turkey, Ministry of Health database, were analyzed retrospectively. RESULTS: The rates of intensive care unit (ICU) admission, and mechanical ventilation (MV) support were lower in CML patients compared to the control group, however, these differences did not achieve statistical significance (p = 0.1, and p = 0.2, respectively). Moreover, the rates of ICU admission and MV support, CFR were lower and length of hospital stay was shorter in CML patients receiving TKI compared to the age, gender and comorbidity matched control group but these differences were not statistically significant. cache = ./cache/cord-338647-dtuohsf5.txt txt = ./txt/cord-338647-dtuohsf5.txt === reduce.pl bib === id = cord-338723-3vm23fgy author = Lee, In-Hee title = A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date = 2020-08-26 pages = extension = .txt mime = text/plain words = 2784 sentences = 183 flesch = 57 summary = title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. SARS-CoV-2 is an enveloped and positive single-stranded RNA (ssRNA) virus and initiates human cell entry by binding of spike (S) protein present on the viral envelope to angiotensin converting enzyme 2 (ACE2) receptor on the host cells (Zhou et al., 2020b) . Here we surveyed the genetic variants in functional residues of ACE2, TMPRSS2, CTSB/L (CatB/L), and TLR3/7/8 to investigate the difference in the genetic predisposition to the susceptibly of SARS-CoV-2 infection and the initiation of innate immune response. The list of reported genetic variants in the genes and their allele frequencies (AFs) were ACE2 is highly conserved with few nonsynonymous variants in the interacting domain with the SARS-CoV-2 RBM (Lan et al., 2020) . cache = ./cache/cord-338723-3vm23fgy.txt txt = ./txt/cord-338723-3vm23fgy.txt === reduce.pl bib === id = cord-338578-e0aiknb6 author = Patel, Kajal title = Applying the WHO ICF Framework to the Outcome Measures Used in the Evaluation of Long-Term Clinical Outcomes in Coronavirus Outbreaks date = 2020-09-05 pages = extension = .txt mime = text/plain words = 3937 sentences = 201 flesch = 46 summary = (2) Methods: EMBASE, MEDLINE, CINAHL and PsycINFO were systematically searched for original studies assessing clinical outcomes in adult survivors of severe acute respiratory distress syndrome (SARS), middle east respiratory syndrome (MERS) and coronavirus disease-19 (COVID-19) after hospital discharge. (4) Conclusions: We recommend future COVID-19 follow-up studies to use the ICF framework to select a combination of outcome measures that capture all the components for a better understanding of the impact on survivors and planning interventions to maximize functional return. The aim of this systematic review is to identify outcome measures which have been used in follow-up studies in the coronavirus outbreaks, including SARS in 2002 and MERS in 2012 [21] , and to classify them using the ICF model. In conclusion, we are proposing an ICF-based framework to assist researchers in selecting outcome measures for future follow-up studies of COVID-19 survivors. cache = ./cache/cord-338578-e0aiknb6.txt txt = ./txt/cord-338578-e0aiknb6.txt === reduce.pl bib === id = cord-338320-jc00ulx5 author = Siu, Kam-Leung title = Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain date = 2014-02-10 pages = extension = .txt mime = text/plain words = 3684 sentences = 238 flesch = 53 summary = title: Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain We have previously shown that severe acute respiratory syndrome (SARS) coronavirus M protein suppresses type I interferon (IFN) production by impeding the formation of functional TRAF3-containing complex. 12 , 13 We have previously reported that SARS coronavirus M protein suppresses type I IFN production potently by preventing the formation of functional TRAF3-TANK-TBK1/IKKe complex. IFN antagonism of SARS coronavirus M protein was mediated by N-terminal TM1 (amino acids 1-38), which targets M protein to the Golgi complex and associates with TRAF3 to prevent it from interacting with TANK, TBK1 and IKKe. Our findings provide additional molecular details for suppression of type I IFN production by SARS coronavirus M protein. Notably, human coronavirus HKU1 M protein also targets the Golgi complex, interacts with TRAF3, but does not suppress IFN production. cache = ./cache/cord-338320-jc00ulx5.txt txt = ./txt/cord-338320-jc00ulx5.txt === reduce.pl bib === id = cord-338403-mfde6juv author = Li, Bo title = Prevalence and impact of cardiovascular metabolic diseases on COVID-19 in China date = 2020-03-11 pages = extension = .txt mime = text/plain words = 3419 sentences = 181 flesch = 50 summary = METHODS: A meta-analysis of eligible studies that summarized the prevalence of cardiovascular metabolic diseases in COVID-19 and compared the incidences of the comorbidities in ICU/severe and non-ICU/severe patients was performed. Inclusion criteria are as follows: (1) comparative studies: randomised controlled trials RCTs or non-RCTs published in English; (2) study population: more than ten participants were included in the study; (3) study intervention: patients in the studies should be confirmed to have been infected by 2019 novel coronavirus; (4) parameters: the comorbidities of cardiovascular metabolic diseases and the outcome of cardiac injury should be given. Systematic analysis of studies that described the epidemiological and clinical features of COVID-19 cases and reported the prevalence of cardiovascular metabolic diseases as well as the impact on cardiac injury in the infectious disease, has identified six reports with 1527 patients ( Table 1 ). cache = ./cache/cord-338403-mfde6juv.txt txt = ./txt/cord-338403-mfde6juv.txt === reduce.pl bib === id = cord-338543-q6cl5kjp author = Salguero, Francisco J. title = Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1093 sentences = 59 flesch = 56 summary = Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Throat swabs from cynomolgus macaques contained 147 higher levels of viral RNA early in infection (one to three dpc) and remained ≥4.5 x 148 10 4 copies/ml for all animals between four and nine dpc. However viral RNA 159 levels above the LLOQ were detected at both three dpc and five dpc in cynomolgus 160 macaques in comparison to two dpc and three dpc in rhesus macaques ( Figure 2D ). cache = ./cache/cord-338543-q6cl5kjp.txt txt = ./txt/cord-338543-q6cl5kjp.txt === reduce.pl bib === id = cord-338365-9sd62a2w author = Patrício Silva, Ana L. title = Increased plastic pollution due to Covid-19 pandemic: challenges and recommendations date = 2020-08-17 pages = extension = .txt mime = text/plain words = 7418 sentences = 354 flesch = 42 summary = This paper provides a comprehensive review on the potential impact of COVID-19 pandemic precautionary measures in the environment while considering the shift on public behaviour and policies towards single-use items and waste management. At first glance COVID-19 pandemic seems to be indirectly contributing towards the UN 2030 Sustainable Development Goals (namely 11, 12, 13, 15 SGDs) by increasing overall health and safety of cities by reducing the greenhouse gas emissions (GHG), outdoor air pollution, environmental noise level (including underwater noise due to reduced marine transportation activities), land and wildlife pressure. While the positive impacts of COVID-19 in the environment are resulting from a "postponed" anthropogenic activity that soon will entail after the pandemic scenario; the negative short-term effects (that are mostly related with plastic use, consumption and waste mismanagement as discussed below) will shortly add-up to the current environmental issues, aggravating their impact in the natural ecosystems and compromising potential mitigation/remediation measures. cache = ./cache/cord-338365-9sd62a2w.txt txt = ./txt/cord-338365-9sd62a2w.txt === reduce.pl bib === id = cord-338790-rvdoq616 author = Wang, Xiaowen title = Be aware of acute kidney injury in critically ill children with COVID-19 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 2904 sentences = 155 flesch = 47 summary = BACKGROUND: Acute kidney injury (AKI) is a common complication of critically ill adult patients with COVID-19. METHODS: By extracting data from electronic medical records, we conducted a retrospective observational study of kidney involvement in confirmed pediatric COVID-19 cases in Wuhan Children's Hospital during the coronavirus outbreak, from January 24 to March 20, 2020. The AWARE (Assessment of Worldwide Acute Kidney Injury, Renal Angina, and Epidemiology) study, which enrolled ICUs in 32 hospitals in Asia, Australia, Europe, and North America, showed that the overall incidence of AKI in 4683 critically ill children was 26.9%, and the incidence of severe AKI (KDIGO stage 2 or 3) was 11.6% [8, 14] . The correlation between IL-6 titer and serum creatinine level in our patients suggests that cytokine storm might play a more important role in critically ill COVID-19 children with AKI, in addition to the prerenal and intrarenal injuries. cache = ./cache/cord-338790-rvdoq616.txt txt = ./txt/cord-338790-rvdoq616.txt === reduce.pl bib === id = cord-338468-c0jv3i1t author = Kanduc, Darja title = From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date = 2020-07-16 pages = extension = .txt mime = text/plain words = 4143 sentences = 234 flesch = 41 summary = Results: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. In the wake of such results, in order to validate (or, as well, invalidate) the cross-reactivity hypothesis, investigation was expanded here by analyzing the peptide sharing between the human host and immunoreactive epitopes that are also present in SARS-CoV-2. Table 2 documents that numerous immunoreactive SARS-CoV-2 epitopes are composed mostly or, in many instances, uniquely of peptide sequences shared with human proteins. This study shows that hexapeptides from immunoreactive epitopes present in SARS-CoV-2 are widespread among a high number of human proteins. Table S2 : Hexapeptide sharing between 233 epitopes present in SARS-CoV-2 and human proteins. Table S3 : List and short description of 460 human proteins that share hexapeptides with the 233 SARS-CoV-2 epitopes. cache = ./cache/cord-338468-c0jv3i1t.txt txt = ./txt/cord-338468-c0jv3i1t.txt === reduce.pl bib === id = cord-338648-5evr2v3r author = Shental, Noam title = Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5352 sentences = 274 flesch = 56 summary = We developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, which identifies all positive subjects within a set of samples using a single round of testing. Here, we developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, using a single-stage nonadaptive group-testing approach, which significantly reduces the number of tests required to identify all positive subjects within a large set of samples. PCR results for each of the pools are provided to the detection algorithm (see Methods), which identifies all positive carriers without the need for an additional testing stage (Fig. 1 , A to C). RNA was extracted from each single sample and pools and was then tested for SARS-CoV-2 using the Seegene COVID-19 diagnostic kit. Using a pooling scheme designed for a carrier rate of ~1%, we showed that our method correctly identified all positive carriers in sets of 384 samples pooled into 48 pools, thereby providing an eightfold reduction in the number of required tests. cache = ./cache/cord-338648-5evr2v3r.txt txt = ./txt/cord-338648-5evr2v3r.txt === reduce.pl bib === id = cord-338436-0z828org author = Tzou, Philip L. title = Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds date = 2020-09-09 pages = extension = .txt mime = text/plain words = 8193 sentences = 522 flesch = 46 summary = Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. Figure 4 displays EC 50 values for many of the directly acting antiviral compounds currently in clinical trials for the treatment of COVID-19 including six polymerase inhibitors (remdesivir, EIDD-2801, favipiravir, ribavirin, galidesivir, and sofosbuvir), three HIV-1 protease inhibitors (lopinavir, atazanavir, and darunavir), and three entry inhibitors (receptor binding monoclonal antibodies, soluble recombinant human ACE2, and umifenovir). Viruses 2020, 12, x FOR PEER REVIEW 11 of 22 Table 4 describes a set of the most promising compounds for the treatment of SARS-CoV-2 based on the following criteria: (i) act by a validated direct or indirect antiviral mechanism, (ii) display submicromolar activity in vitro and/or inhibitory activity in an animal model, and (iii) have a record of safety and favorable pharmacokinetics in human subjects. cache = ./cache/cord-338436-0z828org.txt txt = ./txt/cord-338436-0z828org.txt === reduce.pl bib === id = cord-338684-po3hfibp author = Cheong, Kai Xiong title = Systematic Review of Ocular Involvement of SARS-CoV-2 in Coronavirus Disease 2019 date = 2020-09-26 pages = extension = .txt mime = text/plain words = 5033 sentences = 330 flesch = 58 summary = PURPOSE OF REVIEW: Studies have reported ocular involvement in the coronavirus disease 2019 (COVID-19), with SARS-CoV-2 having been detected in ocular swab samples. Observational studies which both described ocular involvement among patients with COVID-19 and attempted to detect SARS-CoV-2 in ocular samples via RT-PCR and/or viral cultures were included. In contrast, other studies have reported the detection of SARS-CoV-2 in ocular samples from patients who did not experience ocular symptoms and signs [5, 9, 10] . reported in a retrospective case series that SARS-CoV-2 was detected in conjunctival swab samples from both eyes of two patients (6.06%) in a population of 33 patients. Seah et al., in a prospective case series of 17 patients, reported that SARS-CoV-2 could not be detected in RT-PCR of tear samples. In the studies that took serial samples, SARS-CoV-2 was reported to remain detectable up to 27 days after the onset of ocular and respiratory symptoms [16, 18] . cache = ./cache/cord-338684-po3hfibp.txt txt = ./txt/cord-338684-po3hfibp.txt === reduce.pl bib === id = cord-338680-wwlttymp author = Khonyongwa, K. title = Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date = 2020-07-30 pages = extension = .txt mime = text/plain words = 4839 sentences = 288 flesch = 53 summary = Due to the high prevalence of infection during the peak of the outbreak, one of the suggested strategies to prevent healthcare transmission was to screen all patients on admission by a single combined nose and throat swab assessed for SARS-CoV-2 RNA to allow segregation into COVID-19 positive and non COVID-19 cohort wards. The latter included assessment of the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity, COVID-19 patients as sources of infection, self-reported COVID-19 sickness absence among hospital staff hospital bed occupancy, community incidence, and the incidence of other significant hospital-acquired infections. NHS England released its reporting criteria in May 2020 (written communication described in supplementary data) following which cases were also classified as per date of the SARS-CoV-2 RNA detection. Correlation between weekly incidence of HA-COVID-19 (including late indeterminate cases) and staff self-reported sickness absence, delayed RNA positive cases, community incidence and Trust COVID-19 bed occupancy is displayed in figure 3. cache = ./cache/cord-338680-wwlttymp.txt txt = ./txt/cord-338680-wwlttymp.txt === reduce.pl bib === id = cord-338755-f5g2r4n9 author = Alam, Nawsad title = A spike with which to beat COVID-19? date = 2020-05-15 pages = extension = .txt mime = text/plain words = 760 sentences = 53 flesch = 64 summary = This month's Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine. Coronavirus spikes have been structurally characterized before, in particular for SARS-CoV and MERS-CoV, two related viruses that have caused epidemics of respiratory disease. Shortly after this, the first structure of a neutralizing antibody bound to the RBD of the spike glycoprotein showed that SARS-CoV-reactive antibodies could neutralize the new virus 3 , and polyclonal antibody sera against SARS-CoV also proved effective 1 . Two spike-based vaccine-design strategies, developed for SARS-CoV, should be applicable. To generate the most effective neutralizing antibody responses, vaccinated individuals should generate antibodies to the pre-fusion spike, thus preventing ACE2 binding and cell entry. For this reason, structure-guided mutations have been designed that fix the SARS-CoV spike into this pre-fusion state 4 . Stabilized SARS-CoV-2 spikes, designed using this method, are therefore promising for a vaccine. cache = ./cache/cord-338755-f5g2r4n9.txt txt = ./txt/cord-338755-f5g2r4n9.txt === reduce.pl bib === id = cord-338741-gy3ovkrt author = Sethi, Atin title = Evaluation of Current Therapies for COVID-19 Treatment date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5580 sentences = 333 flesch = 47 summary = No survival benefit for those not requiring respiratory support [22] Convalescent plasma n = 10 severely ill patients Treatment: 200 mL IV In all 10 patients, fever, cough, shortness of breath, and chest pain disappeared or largely improved within 1-3 days of therapy initiation [23] In vitro study determining the activity of convalescent plasma from a recovered SARS-1 patient against SARS-CoV-2 Although the focus of this study was not to explore the efficacy of hydroxychloroquine/azithromycin, it outlines the importance of appropriate risk-benefit analysis while treating patients with COVID-19. This randomized control trial [10] of 199 patients explored the efficacy of lopinavir-ritonavir in hospitalized COVID-19 patients with relatively mild respiratory illness. Efficacy of hydroxychloroquine in patients with COVID-19: Results of a randomized clinical trial Clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-19 patients with at least a six-day follow up: A pilot observational study cache = ./cache/cord-338741-gy3ovkrt.txt txt = ./txt/cord-338741-gy3ovkrt.txt === reduce.pl bib === id = cord-338589-1ent68fx author = Stoddard, Shana V. title = Optimization Rules for SARS-CoV-2 M(pro) Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site date = 2020-08-26 pages = extension = .txt mime = text/plain words = 11437 sentences = 606 flesch = 55 summary = The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 M(pro) active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 −log(10)(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M(pro) [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The use of multiple conformations when using docking will assist in the prediction of new antivirals agents targeting SARS-CoV-2 M pro as the diversity of accessible variations can produce distinct binding poses for an inhibitor compound. cache = ./cache/cord-338589-1ent68fx.txt txt = ./txt/cord-338589-1ent68fx.txt === reduce.pl bib === id = cord-338889-7hd3iibk author = Solbakk, Jan Helge title = Back to WHAT? The role of research ethics in pandemic times date = 2020-11-03 pages = extension = .txt mime = text/plain words = 11689 sentences = 709 flesch = 53 summary = 10 Of the 10 standards laid down in this Code, and with which physician-researchers must comply when carrying out experiments on human subjects, standard 5, in particular, has become highly relevant these days due to pressure from influential medical stakeholders, agencies and bioethicists to permit the conduct of controlled human infection studies (CHIs), also labeled human challenge trials (HCTs), or challenge studies (CSs) to possibly shorten the development time of vaccines to protect against Covid-19 caused by the SARS-CoV-2 virus. cache = ./cache/cord-338889-7hd3iibk.txt txt = ./txt/cord-338889-7hd3iibk.txt === reduce.pl bib === id = cord-339012-4juhmjaj author = Hou, Wei title = Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date = 2020-07-28 pages = extension = .txt mime = text/plain words = 6756 sentences = 344 flesch = 48 summary = Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and "synaptic clefts" between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The detected sets of differential expressed genes (DEGs) for PEDV and MRV were analyzed by gene set enrichment analysis (GSEA) using functional bioinformatic programs to retrieve biological processes (pathways and Gene Ontology terms [GO-term]) and associations with chemical compounds, including drugs. cache = ./cache/cord-339012-4juhmjaj.txt txt = ./txt/cord-339012-4juhmjaj.txt === reduce.pl bib === id = cord-338798-xsun927w author = Ciorba, Andrea title = Ototoxicity prevention during the SARS-CoV-2 (Covid-19) emergency date = 2020-10-17 pages = extension = .txt mime = text/plain words = 499 sentences = 37 flesch = 42 summary = • To remind the risk of ototoxicity when using chloroquine and hydroxychloroquine, in particular as prophylactic agents against SARS-CoV-2, during the pandemic. • Healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. eventually adequate treatment is established (3) (4) (5) . Pure tone audiometry represents the main instrument for the identification and classification of hearing impairment; however, Otoacoustic Emissions (OAEs) are reported to be very sensitive in evaluating early manifestations of cochlear damages (6), as ototoxic drugs typically affect primarily outer hair cells (1, (3) (4) (5) . Therefore, healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. Clearly, even without a fatal condition, it is important to avoid the onset of ototoxic manifestations, especially when chloroquine and hydroxychloroquine are administered with a prophylaxis intent. cache = ./cache/cord-338798-xsun927w.txt txt = ./txt/cord-338798-xsun927w.txt === reduce.pl bib === id = cord-338901-1kzy7rts author = Li, Heng title = Overview of therapeutic drug research for COVID-19 in China date = 2020-06-17 pages = extension = .txt mime = text/plain words = 5098 sentences = 253 flesch = 48 summary = According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. In these 155 pooled clinical trials, a number of approved chemical and biomacromolecule drugs have been used in COVID-19 treatment clinical trials for drug repurposing, most of which are nucleotide analogs and protease inhibitors against other viral pathogens, including influenza virus, HIV and HCV. In vitro studies have shown that lopinavir/ritonavir can inhibit the replication of MERS-CoV and SARS-CoV and exert antiviral effects [22] [23] [24] [25] . In the latest "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia", it is recommended to use ribavirin at a dose of 500 mg each time for adults and in combination with interferon or lopinavir/ritonavir, with 2-3 intravenous infusions daily. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-338901-1kzy7rts.txt txt = ./txt/cord-338901-1kzy7rts.txt === reduce.pl bib === id = cord-338751-2eo7ityc author = Anzalone, Nicoletta title = Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients date = 2020-06-06 pages = extension = .txt mime = text/plain words = 1084 sentences = 68 flesch = 42 summary = title: Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients They are part of a series of 21 patients presenting with neurological symptoms studied with brain MRI with otherwise no significant imaging findings. Although the predominantly parieto-occipital distribution of the lesions recalls posterior reversible encephalopathy syndrome (PRES) [5] , the prevalent cortical involvement and diffusion MRI pattern are not typical of PRES. More recently, evidence of direct viral infection of the endothelial cell and diffuse endothelial inflammation has been reported, resulting Fig. 1 Forty-seven-year-old man diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. Multiple, cortical areas of punctiform and gyriform FLAIR and DWI hyperintensity (arrows) in both parietal lobes, with no ADC changes Fig. 2 Fifty-four-year-old woman diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. cache = ./cache/cord-338751-2eo7ityc.txt txt = ./txt/cord-338751-2eo7ityc.txt === reduce.pl bib === id = cord-338775-gh3a0wuf author = Gulersen, Moti title = Histopathological evaluation of placentas after diagnosis of maternal SARS-CoV-2 infection date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2512 sentences = 152 flesch = 44 summary = Study Design Retrospective cohort study of women diagnosed with SARS-CoV-2 infection who delivered at a single center from April 9th to April 27th, 2020, and had placental specimens reviewed by pathology. Histopathological characteristics were evaluated in each placenta and the incidence of these findings were compared between placentas after diagnosis of maternal SARS-CoV-2 infection and historical controls, as well as between placentas from patients with or without typical symptoms related to infection. Conclusions Based on our data, there are no significant placental histopathological changes that occur after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared to a gestational age-matched historical control group. The results of our study did not demonstrate significant placental histopathological changes 229 occurring after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared 230 to a gestational-age-matched historical control group with a similar incidence of antepartum or Pathology for examination or due to history of melanoma. cache = ./cache/cord-338775-gh3a0wuf.txt txt = ./txt/cord-338775-gh3a0wuf.txt === reduce.pl bib === id = cord-338689-4u1ezk64 author = Ata, Fateen title = COVID-19 presenting with diarrhoea and hyponatraemia date = 2020-06-07 pages = extension = .txt mime = text/plain words = 1405 sentences = 124 flesch = 52 summary = We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. COVID-19 is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ► We recommend studies to evaluate the effectiveness of stool PCR for severe acute respiratory syndrome coronavirus 2 if initial nasopharyngeal PCR is negative and suspicion remains high. 4 Gastrointestinal symptoms such as diarrhoea, abdominal pain and vomiting have been previously seen with acute viral respiratory infections and reported recently as rare manifestations of COVID-19. 15 Our patient had acute hyponatraemia, abdominal pain and diarrhoea with minimal Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical and virological factors associated with gastrointestinal symptoms in patients with acute respiratory infection: a two-year prospective study in general practice medicine cache = ./cache/cord-338689-4u1ezk64.txt txt = ./txt/cord-338689-4u1ezk64.txt === reduce.pl bib === id = cord-339009-wcoch07b author = File, Thomas M. title = Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date = 2012-08-23 pages = extension = .txt mime = text/plain words = 6023 sentences = 324 flesch = 50 summary = Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world. cache = ./cache/cord-339009-wcoch07b.txt txt = ./txt/cord-339009-wcoch07b.txt === reduce.pl bib === id = cord-339019-vgnxhksv author = Lee, Ting-Wai title = Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase date = 2007-02-23 pages = extension = .txt mime = text/plain words = 8447 sentences = 450 flesch = 62 summary = We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M+A(-1) pro), both at a resolution of 2.00 Å, in space group P43212: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). 25 We have now grown crystals of M pro in the same space group (P2 1 with the same unit-cell constants) at pH 6.0 under slightly different conditions; the active sites and the S1 specificity pockets of both protomers are in the catalytically competent conformation (Figures 2(a) and (b), 3(a) and (b), 4(a) and (b)). Active sites and substrate-binding regions of the unbound SARS-CoV M +A(-1) pro We have reported the crystal structure of the SARS-CoV M +A (-1) pro :APE complex in space group P2 1 2 1 2 1 , whose asymmetric unit contains both protomers of the M +A(-1) pro dimer. cache = ./cache/cord-339019-vgnxhksv.txt txt = ./txt/cord-339019-vgnxhksv.txt === reduce.pl bib === id = cord-338683-nzgnpi6f author = Karligkiotis, Apostolos title = Changing paradigms in sinus and skull base surgery as the COVID‐19 pandemic evolves: Preliminary experience from a single Italian tertiary care center date = 2020-06-08 pages = extension = .txt mime = text/plain words = 4301 sentences = 206 flesch = 43 summary = The aim of the present paper is to report our preliminary experience with the management of urgent and nondeferrable endoscopic surgeries for sinus and skull base diseases, during the COVID-19 period, describing the evolving recommendations which have been implemented day by day, as new evidences emerged, until reaching the actual protocol of precautions. At the beginning, no specific protection was recommended during surgery and all health care workers in the operating room (OR) continued to wear standard surgical masks and gowns, leaving viral-filtering-PPE available to be used only in case of confirmed COVID-19 patients. 10 In order to investigate the health of the patients belonging to the PANDEMIC-group after their last postoperative medication, a telephone interview was carried out retrospectively, examining the following factors: fever, cough, dyspnoea, anosmia, dysgeusia, gastrointestinal signs/symptoms, myalgias, fatigue, headache, pharyngodynia, rhinorrhea, active pneumonia, need for hospitalization for any reason, potential swab or serological tests performed, and if they had been in contact with COVID-19 positive individuals. cache = ./cache/cord-338683-nzgnpi6f.txt txt = ./txt/cord-338683-nzgnpi6f.txt === reduce.pl bib === id = cord-338923-hc7gagnq author = Jääskeläinen, AJ title = Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation date = 2020-06-15 pages = extension = .txt mime = text/plain words = 2101 sentences = 131 flesch = 53 summary = We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). In this study, we assessed the specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 antibodies, including two rapid lateral flow tests, in comparison with a neutralisation test. cache = ./cache/cord-338923-hc7gagnq.txt txt = ./txt/cord-338923-hc7gagnq.txt === reduce.pl bib === id = cord-338541-0yiuh017 author = Hannan, Md. Abdul title = Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4302 sentences = 244 flesch = 42 summary = title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response As a healthy practice, calorie restriction in the form of intermittent fasting (IF) in several clinical settings has been reported to promote several health benefits, including priming of the immune response. A comprehensive review has therefore been planned to highlight the beneficial role of fasting in immunity and autophagy, that underlie the possible defense against SARS-CoV-2 infection. In this review, we revisit the current knowledge of fasting as a possible important mediator that is involved in the diverse pathophysiological phenomena, including host immune response, autophagy, and the pathogenesis of SARS-CoV-2 infection. During adaptive immunity, autophagy plays an important role in major histocompatibility complex (MHC)-antigen presentation, lymphocyte development, thymic selection, inflammatory signaling, and cytokine regulation [10] . cache = ./cache/cord-338541-0yiuh017.txt txt = ./txt/cord-338541-0yiuh017.txt === reduce.pl bib === id = cord-338734-laeocs3j author = Lima, Amorce title = Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date = 2020-06-30 pages = extension = .txt mime = text/plain words = 2533 sentences = 141 flesch = 61 summary = In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. A 149 series of two-fold dilutions of SARS-CoV-2 strain USA_WA1/2020 RNA were spiked in pooled 150 sputum at concentrations of 800 copies/ml to 0.05 copy/ml in order to determine the limit of 151 detection (LoD) of the assay. On the other hand, the average Ct values difference between 235 samples run within 2 days between DiaSorin Simplexa Covid 19 Direct assay and the modified 236 CDC SARS-CoV-2 assay was -2.42, and -6.0 between samples run within 5 days. In this study, we validated a modified CDC SARS-CoV-2 assay and compared its 263 performance to two commercial automated sample-to-answer assays for the detection of SARS-264 The difference is even greater 286 in samples that were run 5 days after the routine testing on the modified CDC SARS-CoV-2 287 assay. cache = ./cache/cord-338734-laeocs3j.txt txt = ./txt/cord-338734-laeocs3j.txt === reduce.pl bib === id = cord-339241-e2nl766y author = Turriziani, Ombretta title = SARS‐CoV‐2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period date = 2020-08-02 pages = extension = .txt mime = text/plain words = 1290 sentences = 93 flesch = 53 summary = The study retrospectively included 6565 subjects tested for SARS‐CoV‐2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. This analysis allowed to gather comprehensive information on SARS‐CoV‐2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown. In this scenario this paper aims to take a snapshot of the epidemiological characteristics of the population resulted positive for SARS-CoV-2 at Sapienza University Hospital "Policlinico Umberto I" in Rome starting from 6 March until 4 May. This study includes all individuals (n = 6565) who have been tested 2.1 | Statistical analysis χ 2 Test was used to analyze the differences in positivity between groups. cache = ./cache/cord-339241-e2nl766y.txt txt = ./txt/cord-339241-e2nl766y.txt === reduce.pl bib === id = cord-339303-feiy6xed author = Tan, Xiaodong title = Severe Acute Respiratory Syndrome epidemic and change of people's health behavior in China date = 2004-10-17 pages = extension = .txt mime = text/plain words = 1733 sentences = 100 flesch = 58 summary = title: Severe Acute Respiratory Syndrome epidemic and change of people's health behavior in China Severe Acute Respiratory Syndrome (SARS) has become a new worldwide epidemic whose origin was until recently unknown. This study presents an inquiry into people's knowledge and self-reported changes in behavior in response to the epidemic. Most respondents took action to avoid being infected by SARS, including, most commonly, efforts to improve indoor ventilation, to disinfect the indoor environment and to increase hand-washing frequency. Severe Acute Respiratory Syndrome (SARS) is a new flu-like disease that made its appearance in late 2002 and spread to over 30 countries by mid-2003. The adoption of these measures, due to the initially unclear nature of SARS transmission, actually increased panic among the Chinese people who began wearing masks, reducing the chances of outdoor activities, disinfecting the environment and washing their hands. Seven questions about health behavior change in the previous 2 weeks addressed recent preventive measures generally and hand-washing specifically. cache = ./cache/cord-339303-feiy6xed.txt txt = ./txt/cord-339303-feiy6xed.txt === reduce.pl bib === id = cord-339128-npfoircv author = Blair, Robert V. title = Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques date = 2020-11-07 pages = extension = .txt mime = text/plain words = 3097 sentences = 166 flesch = 50 summary = Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. This study demonstrates that following exposure to SARS-CoV-2 aged AGMs develop a spectrum of disease, from mild to severe COVID-19, which in some cases progress to ARDS. cache = ./cache/cord-339128-npfoircv.txt txt = ./txt/cord-339128-npfoircv.txt === reduce.pl bib === id = cord-339077-pxf2u68u author = Zerwes, Sebastian title = Erhöhtes Risiko für tiefe Beinvenenthrombosen bei Intensivpatienten mit CoViD-19-Infektion? – Erste Daten date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1558 sentences = 195 flesch = 44 summary = BACKGROUND: The incidence of deep vein thrombosis (DVT) in CoViD-19 patients in intensive care units (ICU) has so far been investigated in only a few studies. MATERIAL AND METHODS: In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. Es ist bekannt, dass intensivpflichtige Patienten per se ein erhöhtes Risiko für thrombembolische Ereignisse aufweisen: So treten bei Intensivpatienten Thrombosen je nach Grunderkrankung mit einer Wahrscheinlichkeit von 10-80 % auf; 10-15 % der Patienten entwickeln trotz Thromboseprophylaxe eine tiefe Beinvenenthrombosen (TVT; [8, 9] ). In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. cache = ./cache/cord-339077-pxf2u68u.txt txt = ./txt/cord-339077-pxf2u68u.txt === reduce.pl bib === id = cord-338980-pygykil7 author = Rahaman, Jordon title = Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date = 2016-11-09 pages = extension = .txt mime = text/plain words = 5801 sentences = 308 flesch = 52 summary = Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. For the DISOPRED2 predictions that were inferred using the nr database, the continuous disorder propensities for every site in a protein were mapped onto their corresponding position in the multiple sequence alignment as raw disorder propensities and as binary states, order or disorder, using a cutoff of 5. For regions with five or more consecutive sites that were 100% conserved in sequence across 1) all CoV or 2) across the MERS and SARS clades, the information of structural disorder prediction from IUPred and DISOPRED2 was used to identify all ungapped sites that were consistently predicted to have 100% conserved order. cache = ./cache/cord-338980-pygykil7.txt txt = ./txt/cord-338980-pygykil7.txt === reduce.pl bib === id = cord-339271-t7cxqkp1 author = Pan, Yanfeng title = Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3277 sentences = 230 flesch = 55 summary = The median period from diagnosis to negative nucleic acid test was significantly different between patients with normal or atypical chest computed tomography (CT) findings (n=16, 61.5%; 7.5 days [2–20 days]) and patients with typical ground-glass or patchy opacities on CT(n=10, 38.5%; 12.5 days[8–22 days]; P<0.01). Here, we identified a total of 26 persistently asymptomatic patients with positive test results for SARS-CoV-2 nucleic acid to determine the clinical characteristics and asymptomatic carrier transmission of COVID-19 infection. A total of 26 hospitalized patients with a SARS-CoV-2 epidemiological history and positive SARS-CoV-2 nucleic acid test results were identified to analyze the epidemiological and clinical characteristics of COVID-19infected asymptomatic carriers. Discharge criteria for COVID-19 were as follows: 1) normal body temperature for more than 3 days; 2) significantly improved respiratory symptoms; 3) significantly improved chest radiography; and 4) two consecutive negative SARS-CoV-2 nucleic acid test results (sampling interval at least 1 day). cache = ./cache/cord-339271-t7cxqkp1.txt txt = ./txt/cord-339271-t7cxqkp1.txt === reduce.pl bib === id = cord-338973-73a7uvyz author = Xu, Jiabao title = Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV date = 2020-02-22 pages = extension = .txt mime = text/plain words = 7110 sentences = 426 flesch = 57 summary = After the outbreak of the severe acute respiratory syndrome (SARS) in the world in 2003, human coronaviruses (HCoVs) have been reported as pathogens that cause severe symptoms in respiratory tract infections. Recently, a new emerged HCoV isolated from the respiratory epithelium of unexplained pneumonia patients in the Wuhan seafood market caused a major disease outbreak and has been named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The source of unexplained pneumonia was first discovered in Wuhan in Dec, 2019, and SARS-CoV-2, a new coronavirus, was isolated from the respiratory epithelium of patients. Hong Kong scholars found that, compared with ribavirin alone, patients treated with lopinavir/ritonavir and ribavirin had lower risk of acute respiratory distress syndrome (ARDS) or death caused by SARS-CoV [76, 77] . A high-resolution crystal structure of SARS-CoV-2 coronavirus 3CL hydrolase (Mpro) was announced after the outbreak of COVID-19 in the world [80] , and human coronaviruses (HCoVs) have been treated as severe pathogens in respiratory tract infections. cache = ./cache/cord-338973-73a7uvyz.txt txt = ./txt/cord-338973-73a7uvyz.txt === reduce.pl bib === id = cord-339172-210dwhgj author = Knoops, Kèvin title = SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date = 2008-09-16 pages = extension = .txt mime = text/plain words = 9930 sentences = 411 flesch = 43 summary = Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''inner vesicles,'' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. cache = ./cache/cord-339172-210dwhgj.txt txt = ./txt/cord-339172-210dwhgj.txt === reduce.pl bib === id = cord-339352-c9uh8vjx author = Islam, Muhammad Torequl title = Environmental Integrants Affecting the Spreadability of SARS-CoV-12 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 772 sentences = 61 flesch = 54 summary = The SARS-CoVs can survive in water and remain infectious for long periods (days to weeks), therefore, these may affect people and other animals if aerosols are generated (Casanova et al. It has been demonstrated that SARS-CoVs have low stability in the environment, very sensitive to oxidants (e.g., chlorine) and are inactivated significantly faster in water. However, SARS-CoV-2 has been found in the fecal samples and anal swabs of some patients, therefore, there is a possibility of fecal-oral (including waterborne) transmission of this virus (Rosa et al. Additionally, it is also necessary to study all the environmental components that affecting the survival, replication, spreadability or transmission and pathogenicity of SARS-CoV-2 in human and other animals. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Selenium and RNA virus interactions: Potential implications for SARS-CoV-2 infection (COVID-19) TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes cache = ./cache/cord-339352-c9uh8vjx.txt txt = ./txt/cord-339352-c9uh8vjx.txt === reduce.pl bib === id = cord-338744-2kizbzns author = González-Castro, A. title = Síndrome post-cuidados intensivos después de la pandemia por SARS-CoV-2 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 465 sentences = 48 flesch = 57 summary = El mundo está inmerso en una pandemia por SARS-CoV-2 que Q2 está llevando a los sistemas sanitarios al borde del colapso y a las unidades de cuidados intensivos a trabajar por encima de su capacidad. Dentro de este panorama general, los servicios de cuidados intensivos deben de estar alertados para identificar «la cola de la primera oleada», que englobará un síndrome post-cuidados intensivos (SPCI) de una gran magnitud y con características especiales. En circunstancias normales el SPCI afecta al 30-50% de nuestros pacientes 3 y sus secuelas pueden persistir incluso más allá de los 5 años tras el alta hospitalaria, especialmente en la recuperación del síndrome respiratorio agudo 4 . Si otras condiciones nos mostraron que hasta el 16% de los familiares no habían reducido el nivel de depresión al año del alta 5 ¿estaremos preparados para el SPCI-post Working experiences of nurses during the Middle East respiratory syndrome outbreak Functional disability 5 years after acute respiratory distress syndrome cache = ./cache/cord-338744-2kizbzns.txt txt = ./txt/cord-338744-2kizbzns.txt === reduce.pl bib === id = cord-339093-mwxkvwaz author = Li, Wei title = High potency of a bivalent human VH domain in SARS-CoV-2 animal models date = 2020-09-04 pages = extension = .txt mime = text/plain words = 11419 sentences = 687 flesch = 59 summary = It potently neutralized mouse adapted SARS-CoV-2 in wild type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. To identify potent neutralizing V H s against SARS-CoV-2, we panned our large (10 11 clones) and diverse phage-displayed human V H antibody library against recombinant RBD. One of those V H s, ab8, in an Fc (human IgG1, crystallizable fragment) fusion format, showed potent neutralization activity and specificity against SARS-CoV-2 both in vitro and in two animal models. They also suggest that the double mutations Q498T/P499Y on RBD did not influence V H -Fc ab8 binding and contribute to the validation of the mouse adapted SARS-CoV-2 model for evaluation of neutralizing antibody efficacy. In conclusion, we identified a fully human antibody V H domain that shows strong competition with ACE2 for binding to RBD and potent neutralization of SARS-CoV-2 in vitro and in two animal models. cache = ./cache/cord-339093-mwxkvwaz.txt txt = ./txt/cord-339093-mwxkvwaz.txt === reduce.pl bib === id = cord-339506-pkusvf82 author = Zaki, N. title = The estimations of the COVID-19 incubation period: a systematic review of the literature date = 2020-05-23 pages = extension = .txt mime = text/plain words = 5969 sentences = 280 flesch = 50 summary = One reason for this is that generally we can only discover the times when the patient was in contact with persons carrying the virus, and then assume that the incubation period runs from the earliest date of exposure to the appearance of clinical symptoms or medical diagnosis. et al [15] researched the early data regarding transmission dynamics for the virus in Wuhan, estimating the mean incubation period at 5.2 days (95% CI: 4.1-7.0), with the distribution's 95 th percentile being 12.5 days. They took individual patient histories from COVID-19 subjects in China (not from Hubei Province) for estimating the distribution of the time for generation, incubation, and the time span between onset of symptoms and isolation/diagnosis. The researchers undertook analysis of clinical data for 34 subjects submitting to elective surgery during the COVID-19 incubation period at four Chinese hospitals (Renmin, Tongji, Zhongnan, and Central) in Wuhan between January 1 and February 5, 2020. cache = ./cache/cord-339506-pkusvf82.txt txt = ./txt/cord-339506-pkusvf82.txt === reduce.pl bib === id = cord-339570-vf79fefg author = Jain, Vidhi title = Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists date = 2020-06-22 pages = extension = .txt mime = text/plain words = 352 sentences = 27 flesch = 50 summary = title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists While the former highlighted the importance of human secretions like tears as a potential source of transmission of the virus, the latter explored the possibility of SARS-CoV-2 in amniotic membrane grafts. The amniotic membrane, while having great potential for healing ophthalmologic wounds, was recently shown to be RT-PCR positive for viral RNA in two critically ill pregnant females with COVID-19 [3] . While there is no confirmed data on the survival of SARS CoV-2 in cryopreserved amniotic membranes, it is clear that temperature strongly influences viral persistence (>2 weeks survival at 4°C vs only 2 days at 20°C) [5] . In light of these findings, we strongly suggest ophthalmologists to observe extreme caution while handling body fluids and placental membranes during the current COVID-19 pandemic. Amniotic membrane harvesting during COVID-19 pandemic Detection of SARS-COV-2 in placental and fetal membrane samples cache = ./cache/cord-339570-vf79fefg.txt txt = ./txt/cord-339570-vf79fefg.txt === reduce.pl bib === id = cord-339329-8yvre7qc author = Kumar, Prashant title = Could fighting airborne transmission be the next line of defence against COVID-19 spread? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 1011 sentences = 49 flesch = 53 summary = Abstract The World Health Organization declared the infectious spread of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) an epidemic during its initial outbreak in Wuhan (China) and has since declared it a pandemic and, more recently, an endemic infection that may remain in our communities. While these measures have worked well under lockdowns, the potential of airborne transmission of COVID-19 under the eased restrictions has not been considered important enough. Social distancing, self-isolation, handwashing, provision of hand sanitisers in public buildings, frequent disinfection of high-touch surfaces and the use of face masks have been recommended as effective mitigation measures against the spread of COVID-19 by the SARS-CoV-2 virus. Another study has reported a high concentration of viral RNA peaks in sub-and super-micrometre particle ranges and highlighted the potential transmission of SARS-CoV-2 via aerosols inside two Wuhan hospitals [3] . This work highlighted the probability of a much higher COVID-19 infection rate in closed environments with re-circulated air, and substantiates our below point regarding airborne transmission. cache = ./cache/cord-339329-8yvre7qc.txt txt = ./txt/cord-339329-8yvre7qc.txt === reduce.pl bib === id = cord-339431-kyr5lv15 author = Saçar Demirci, Müşerref Duygu title = Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date = 2020-03-17 pages = extension = .txt mime = text/plain words = 2323 sentences = 163 flesch = 52 summary = In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. cache = ./cache/cord-339431-kyr5lv15.txt txt = ./txt/cord-339431-kyr5lv15.txt === reduce.pl bib === id = cord-338979-ew046wcr author = Jasti, Madhu title = A review of pathophysiology and neuropsychiatric manifestations of COVID-19 date = 2020-06-03 pages = extension = .txt mime = text/plain words = 2972 sentences = 167 flesch = 44 summary = This novel coronavirus reportedly had symptoms resembling that of Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV) seen in the year 2003 [3] . A recently published study that looked at 214 cases of severe coronavirus illness treated in Wuhan during the early phase of the global pandemic reported that about 36% of patients displayed neurological symptoms [11] . There have been a fair number of reports suggesting SARS-CoV-2 infecting the neurons, raising questions about the direct effects of the virus on the brain that play a role in patients' deaths. By contrast, there have been a few case reports which mention no penetrance of virus into the central nervous system as evidenced by the absence of SARS-CoV-2 in CSF and that the CNS effects are secondary to elevated inflammatory markers as CSF analyses during the acute stage showed pleocytosis with increased IL-8 and TNF-α concentrations [17] . cache = ./cache/cord-338979-ew046wcr.txt txt = ./txt/cord-338979-ew046wcr.txt === reduce.pl bib === id = cord-339459-z22a5yzo author = Mackey, Katherine title = Risks and Impact of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers on SARS-CoV-2 Infection in Adults: A Living Systematic Review date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4132 sentences = 202 flesch = 44 summary = PURPOSE: To evaluate, on an ongoing basis, whether use of ACEIs or ARBs either increases risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or is associated with worse COVID-19 disease outcomes, and to assess the efficacy of these medications for COVID-19 treatment. STUDY SELECTION: Observational studies and trials in adults that examined associations and effects of ACEIs or ARBs on risk for SARS-CoV-2 infection and COVID-19 disease severity and mortality. Three studies (33, 36, 37) , which included a total of 8766 patients with COVID-19 and presented analyses adjusted for important confounding factors, had consistent results and provide moderate-certainty evidence that ACEIs or ARBs are not associated with a higher likelihood of positive SARS-CoV-2 test results among symptomatic patients ( Table 1) . Risks and Impact of ACEIs or ARBs in Adults With SARS-CoV-2 Infection REVIEW Annals.org Annals of Internal Medicine other U.S. study included patients with COVID-19 in the New York University health system and examined ICU admission, assisted ventilation, and death as outcomes (37) . cache = ./cache/cord-339459-z22a5yzo.txt txt = ./txt/cord-339459-z22a5yzo.txt === reduce.pl bib === id = cord-338972-uq2ha8xs author = Olson, Michael T. title = Resumption of elective surgery during the COVID-19 pandemic: what lessons can we apply? date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1688 sentences = 84 flesch = 37 summary = authors: Olson, Michael T.; Triantafyllou, Tania; Singhal, Saurabh Ensure quality and quantity assessment of local PPE availability, and closely follow PPE recommendations for COVID-19+ patients, patients under investigations, and non-COVID-19 patients Re-evaluate health care facility capacity, including resources (e.g., beds, ICUs, ventilators), and expansion strategies Operating rooms should take inventory of existing surgical and cleaning supplies before re-activating elective surgeries Ensure coordination among surgery, anesthesia, nursing, engineering, housekeeping, and other hospital staff or specialties involved in multidisciplinary care; assure adequate staff volume Assign a governance committee to clarify, interpret, and iterate policies, make real-time decisions, and initiate and communicate messaging Although leading surgical societies have guided surgeons in terms of appropriate surgical practice amid the ongoing viral pandemic, certain questions remain, particularly pertaining to the safety of performing minimally invasive surgery in the setting of COVID-19. It remains to be determined how these infection-control measures, albeit contributing to the safety of the patient and staff, impact surgical care when elective surgeries are again performed. cache = ./cache/cord-338972-uq2ha8xs.txt txt = ./txt/cord-338972-uq2ha8xs.txt === reduce.pl bib === id = cord-339381-vvh06d2c author = Han, Deheng title = SARS‐CoV‐2 was found in the bile juice from a patient with severe COVID‐19 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 967 sentences = 60 flesch = 57 summary = In the case report, the novel coronavirus was found in the bile specimen from a patient with severe COVID‐19 by real‐time fluorescent RT‐PCR. SARS-CoV-2 was found in the bile juice from a patient with severe COVID-19 Coronavirus disease 2019 (Covid-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to 163 countries/areas since December 2019. Previous studies have reported that the SARS-CoV-2 could be detected in sputum, faeces, tears, urine and other specimens of infected patients [3, 4] . In the case report, the novel coronavirus was found in the bile specimen from a patient with severe Covid-19. In view of the patient's medical history, the attending doctor considered bile duct obstruction as one of the reasons for liver function failure. To our knowledge, this is the first case in which bile juice SARS-CoV-2 was detected. cache = ./cache/cord-339381-vvh06d2c.txt txt = ./txt/cord-339381-vvh06d2c.txt === reduce.pl bib === id = cord-339516-xfwxtjry author = Nakashima, Tsutomu title = Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses date = 2020-05-05 pages = extension = .txt mime = text/plain words = 692 sentences = 52 flesch = 47 summary = title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses Two nurses working in the National Cancer Center Hospital underwent the viral PCR test because they had similar symptoms, and they were both SARS-CoV-2 positive, although they had neither fever nor cough (Asahi Shimbun newspaper [digital], March 28, 2020). [2] [3] [4] The influenza and parainfluenza type 3 viruses were reported to be causative of olfactory loss most frequently. However, the adverse effect of olfactory dysfunction due to influenza vaccination was also reported. Suzuki et al 8 confirmed the presence of various viruses in the nasal discharge of patients with postviral infection olfactory dysfunction, such as rhinovirus, parainfluenza virus, Epstein-Barr virus, and coronavirus. However, only short-term follow-up investigation has been conducted regarding the effect of SARS-CoV-2 infection on the chemosensory function. We believe that epidemiological investigation is required regarding the effect of SARS-CoV-2 on the olfactory and gustatory functions in terms of the frequency, time course, and relationship with other symptoms. cache = ./cache/cord-339516-xfwxtjry.txt txt = ./txt/cord-339516-xfwxtjry.txt === reduce.pl bib === id = cord-338928-y5l7cf31 author = Leonardi, Matilde title = Neurological manifestations associated with COVID-19: a review and a call for action date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2109 sentences = 110 flesch = 36 summary = While the epidemic of Coronavirus disease 2019 (COVID-19) continues to spread globally, more and more evidences are collected about the presence of neurological manifestations and symptoms associated with it. The review shows that although more and more papers are reporting neurological manifestations associated with COVID-19; however, many items remain unclear and this uncertainty calls for a global action that requires close coordination and open-data sharing between hospitals, academic institutions and the fast establishment of harmonised research priorities and research consortia to face the NeuroCOVID-19 complications. Reports are emerging from China and Italy and increasingly from several countries of neurological symptoms associated with SARS-CoV-2, which may be worsening clinical pictures, respiratory outcomes and mortality rates in patients with COVID-19. Observations from Italy have confirmed Chinese data noting a high number of patients with hyposmia, anosmia and varying patterns of possibly centrally mediated symptoms including respiratory manifestations. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice cache = ./cache/cord-338928-y5l7cf31.txt txt = ./txt/cord-338928-y5l7cf31.txt === reduce.pl bib === id = cord-339344-qd73h1ie author = Simon, David title = Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4094 sentences = 202 flesch = 43 summary = To test whether differences in social exposure between the groups account for the low prevalence of SARS-CoV-2 IgG responses in IMID patients treated with cytokine inhibitors, we assessed exposure risk variables (contact with persons with a respiratory infection, presence at workplace outside home, travel to risk areas) of IMID patient groups and control groups. The low seroprevalence of SARS-CoV-2 in anti-cytokine treated IMIDs could have two principle explanations: While (i) the four groups were recruited in the same region, (ii) the HC control group having the highest prevalence for SARS-CoV-2 IgG was in direct contact with the IMID patients and (iii) all participants were exposed to similar detailed information regarding social behavior during the outbreak of the COVID-19 pandemic in Germany, IMID patients may have followed an even more stringent exposure prophylaxis than healthy individuals. cache = ./cache/cord-339344-qd73h1ie.txt txt = ./txt/cord-339344-qd73h1ie.txt === reduce.pl bib === id = cord-339670-lq46nj8j author = Takahashi, Nozomi title = Clinical course of a critically ill patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1746 sentences = 98 flesch = 43 summary = Although several studies have reported on the clinical and epidemiological characteristics of the patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinical course of the most severe cases requiring treatment in ICU have been insufficiently reported. A 73-year-old man traveling on a cruise ship with history of hypertension and dyslipidemia developed high fever, dyspnea and cough after 7 days of steroid treatment for sudden sensorineural hearing loss, and tested positive for SARS-CoV-2 in sputa polymerase chain reaction (PCR) examination. The sustained excessive inflammatory cytokines in the present case might have led to the exacerbation of the disease, requiring vigorous organ support therapies to allow for survival and recovery from the rapid progression of multiple organ dysfunctions and severe respiratory failure. (SARS-CoV-2), who developed multiple organ dysfunctions, treated with artificial organ supports including mechanical ventilation, extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT). cache = ./cache/cord-339670-lq46nj8j.txt txt = ./txt/cord-339670-lq46nj8j.txt === reduce.pl bib === id = cord-339859-anatn295 author = Paret, Michal title = SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date = 2020-04-17 pages = extension = .txt mime = text/plain words = 1286 sentences = 105 flesch = 59 summary = title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient's NP sample. cache = ./cache/cord-339859-anatn295.txt txt = ./txt/cord-339859-anatn295.txt === reduce.pl bib === id = cord-339152-wfakzb6w author = Trovato, Maria title = Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date = 2020-09-03 pages = extension = .txt mime = text/plain words = 12000 sentences = 540 flesch = 38 summary = Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. cache = ./cache/cord-339152-wfakzb6w.txt txt = ./txt/cord-339152-wfakzb6w.txt === reduce.pl bib === id = cord-339521-qfnu319w author = Lin, Shiming title = Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy date = 2005-08-08 pages = extension = .txt mime = text/plain words = 3647 sentences = 220 flesch = 58 summary = Here, we used AFM to determine the surface ultra structure of each single SARS-CoV virion and observe the surface characteristics and their topography and phase changes after treatments with hydroxyoctanoic acid or protease. The higher-resolution image shows that many individual spherical protrusions exist on the surface and the corresponding cursor profile (Fig. 1 a ) clearly reveals the presence of SARS-CoV particles and each single particle is readily distinguishable. The corresponding cursor profile provides quantitative measurements of the heights for the SARS-CoV particles on the surface. It was found that from the contour map (Fig. 5C ) 15 spike proteins (arrowheads) surround the envelope of a single SARS-CoV virion. The phase image provides a measure of sample heterogeneity and also indicates that the small spherical particles (arrowheads) come from the SARS-CoV virion itself (Fig. 6B) . cache = ./cache/cord-339521-qfnu319w.txt txt = ./txt/cord-339521-qfnu319w.txt === reduce.pl bib === id = cord-339625-ucfjo73c author = Qiu, Xiang title = Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus date = 2012-07-26 pages = extension = .txt mime = text/plain words = 3586 sentences = 178 flesch = 55 summary = Given that rCRT/39–272 can drive the maturation of bone‐marrow‐derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39–272 of CRT is an effective molecular adjuvant capable of enhancing target Ag‐specific humoral responses in both a T cell‐dependent and independent manner. By using DNA vaccines encoding fusion proteins between CRT and target antigens such as tumor antigen E7, N protein of SARS-CoV and Bacillus anthracis protective antigen domain IV, previous investigators have also observed that CRT can function as a molecular adjuvant (13) (14) (15) (16) . Cheng and colleagues found that intradermal immunization with a DNA vaccine encoding a fusion protein between CRT, or CRT fragments, and the E7 tumor antigen was more efficient at eliciting E7-specific CD8 + T cells and protecting against E7-expressing tumors in C57BL/6 mice (13, 14) . cache = ./cache/cord-339625-ucfjo73c.txt txt = ./txt/cord-339625-ucfjo73c.txt === reduce.pl bib === id = cord-339558-li65qvq9 author = Rana, Rashmi title = A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5934 sentences = 334 flesch = 44 summary = Structural proteome analysis of earlier SARS epidemic in 2003 revealed a large array of proteins that could be targeted for this pandemic too. They used affinity purification followed by mass spectrometry analysis and statistical modeling of the MS1level quantitative data which allowed the identification of 1484 interactions between 1086 cellular proteins and 24 SARS-CoV bait proteins. 2013 ) A recently published study involves the development of an Opto-microfluidic sensing platform to rapidly detect antibodies against SARS-CoV2 spike protein in diluted human plasma with high sensitivity. It is the first study to detect the SARS-CoV-2 antigens in the blood plasma of COVID-19-positive patients. Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry cache = ./cache/cord-339558-li65qvq9.txt txt = ./txt/cord-339558-li65qvq9.txt === reduce.pl bib === id = cord-339669-p61j2caf author = Monzani, Alice title = QTc evaluation in COVID‐19 patients treated with chloroquine/hydroxychloroquine date = 2020-05-18 pages = extension = .txt mime = text/plain words = 1244 sentences = 63 flesch = 44 summary = In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China and has spread rapidly initially throughout Europe and later USA (1). In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China, and has spread rapidly initially throughout Europe and later in the United States. Despite poor real clinical evidence of unequivocal beneficial effect of chloroquine/hydroxychloroquine (CQ/HCQ), the absence of an effective COVID-19 treatment and the social pressure raised the demand of these drugs for its compassionate use, both in hospital and outpatient settings. 10 High-dosed HCQ showed promising potential effect in reducing SARS-CoV-2 viral load in COVID-19 patients with enhanced effects in combination with azithromycin or several antiviral drugs. In so forth, we believe that is probably time to have prospective clinical trials that will evaluate the safety and efficacy of HCQ during treatment of COVID-infected patients. cache = ./cache/cord-339669-p61j2caf.txt txt = ./txt/cord-339669-p61j2caf.txt === reduce.pl bib === id = cord-339386-sxyeuiw1 author = McIntosh, Kenneth title = 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date = 2015-12-31 pages = extension = .txt mime = text/plain words = 8499 sentences = 482 flesch = 49 summary = The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. cache = ./cache/cord-339386-sxyeuiw1.txt txt = ./txt/cord-339386-sxyeuiw1.txt === reduce.pl bib === id = cord-339514-0aa58pi6 author = Ho, Yu title = Assembly of human severe acute respiratory syndrome coronavirus-like particles date = 2004-06-11 pages = extension = .txt mime = text/plain words = 2662 sentences = 140 flesch = 53 summary = Viral particles of human severe acute respiratory syndrome coronavirus (SARS CoV) consist of three virion structural proteins, including spike protein, membrane protein, and envelope protein. In this report, virus-like particles were assembled in insect cells by the co-infection with recombinant baculoviruses, which separately express one of these three virion proteins. Sucrose gradient purification followed by Western blot analysis and immunogold labeling showed that the spike protein could be incorporated into the virus like particle also. Recombinant baculoviruses encoding E, M, and S protein genes were used to infect Sf21 insect cell, and the expression of each protein was checked by Western blot at 4 dpi (data not shown). The packaging signal of coronavirus RNA was previously identified by using defective interfering viral particles [26] , since the SARS-CoV is a highly infectious virus, it would be much more feasible to identify this signal by using VLPs. Moreover, S protein-containing VLPs should be able to specifically target to the host cell of the SARS CoV and serve as a safe and efficient tool to deliver Western analysis confirmed the presence of S and E proteins mainly in fractions 16-18. cache = ./cache/cord-339514-0aa58pi6.txt txt = ./txt/cord-339514-0aa58pi6.txt === reduce.pl bib === id = cord-339709-49q2xxkw author = sermet, i. title = Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children date = 2020-06-30 pages = extension = .txt mime = text/plain words = 4753 sentences = 317 flesch = 58 summary = Despite a low frequency of respiratory symptoms, cases of Multisystem Inflammatory 108 Syndrome (MIS) have been reported in children that were infected by SARS-CoV-2 or were in contact 109 with COVID-19 patients 14, 15 . We also analysed SARS-CoV-2 and seasonal HCoVs humoral responses of patients with MIS 122 regarding antibody targets and functional neutralizing activity. Our study is the first to analyse in depth 123 the typology of humoral responses to SARS-CoV-2 in children, and provides evidence that prior 124 infections by seasonal coronaviruses has no significant impact on SARS-CoV-2 infection or related MIS 125 disease in children. We compared the prevalence of anti-N and -S antibodies against the four seasonal HCoVs in a 220 subpopulation of children among the HOS-P (n=54), MIS-P (n=15) and CTL (n=118) groups (Figure 1) . cache = ./cache/cord-339709-49q2xxkw.txt txt = ./txt/cord-339709-49q2xxkw.txt === reduce.pl bib === id = cord-339508-nf6ov39g author = Weil, Ana A. title = Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3734 sentences = 207 flesch = 48 summary = In this study, we describe the results of cross-sectional resident and employee SARS-CoV-2 testing, and infection control and personnel policies associated with 16 Seattle area SNFs. Through two testing strategies, a total of 16 SNFs offered testing to either residents, employees, or both. For employees tested through the Seattle Flu Study, data included participant date of birth, date of testing, race and ethnicity, location and nature of work, new symptoms experienced during the last 7 days, and history of SARS-CoV-2 testing (Appendix 1 in the Supplementary Material). For employees, positive or inconclusive SARS-CoV-2 test results were reported directly to participants by phone within 48 h and to the Washington State Department of Health. We report the results of a large cross-sectional study evaluating SARS-CoV-2 prevalence in skilled nursing facilities (SNFs) in the Seattle area during the spring 2020 peak of the COVID-19 pandemic. cache = ./cache/cord-339508-nf6ov39g.txt txt = ./txt/cord-339508-nf6ov39g.txt === reduce.pl bib === id = cord-339568-th2xmhb6 author = Yan, Meitian title = Analysis of the diagnostic value of serum specific antibody testing for coronavirus disease 2019 date = 2020-06-27 pages = extension = .txt mime = text/plain words = 1869 sentences = 114 flesch = 53 summary = The detection of antibodies produced during the immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has become an important laboratory method for the diagnosis of COVID‐19. In this study, retrospective analysis was used to explore the dynamic changes of serum IgM and IgG antibody and factors affecting diagnostic efficacy, so as to provide a theoretical basis for clinical diagnosis and treatment. Serum IgM antibodies against SARS-CoV can be detected 3-6 days after infection, but levels rapidly decrease thereafter. The positive rates of IgM and IgG antibodies in the non-severe group (71.62% and 71.14%, respectively) were higher than that in the severe group (28.38% and 28.86%, respectively), but these differences were not statistically significant (p > 0.05). Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-339568-th2xmhb6.txt txt = ./txt/cord-339568-th2xmhb6.txt === reduce.pl bib === id = cord-339701-j0sr3ifq author = Mikami, Takahisa title = Risk Factors for Mortality in Patients with COVID-19 in New York City date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3406 sentences = 183 flesch = 44 summary = PARTICIPANTS: 6493 patients who had laboratory-confirmed COVID-19 with clinical outcomes between March 13 and April 17, 2020, who were seen in one of the 8 hospitals and/or over 400 ambulatory practices in the New York City metropolitan area MAIN MEASURES: Clinical characteristics and risk factors associated with in-hospital mortality. Cox proportional hazard regression modeling showed an increased risk of in-hospital mortality associated with age older than 50 years (hazard ratio [HR] 2.34, CI 1.47–3.71), systolic blood pressure less than 90 mmHg (HR 1.38, CI 1.06–1.80), a respiratory rate greater than 24 per min (HR 1.43, CI 1.13–1.83), peripheral oxygen saturation less than 92% (HR 2.12, CI 1.56–2.88), estimated glomerular filtration rate less than 60 mL/min/1.73m(2) (HR 1.80, CI 1.60–2.02), IL-6 greater than 100 pg/mL (HR 1.50, CI 1.12–2.03), D-dimer greater than 2 mcg/mL (HR 1.19, CI 1.02–1.39), and troponin greater than 0.03 ng/mL (HR 1.40, CI 1.23–1.62). In this study, we describe the clinical characteristics of COVID-19 in ambulatory and inpatient settings and identify risk factors associated with mortality in hospitalized patients. cache = ./cache/cord-339701-j0sr3ifq.txt txt = ./txt/cord-339701-j0sr3ifq.txt === reduce.pl bib === id = cord-339436-0k73tlna author = Giagulli, Vito Angelo title = Worse progression of COVID‐19 in men: Is Testosterone a key factor? date = 2020-06-11 pages = extension = .txt mime = text/plain words = 7894 sentences = 520 flesch = 40 summary = Considering that low serum T levels induce detrimental effects on cardiovascular system and predispose to impaired immune response, endothelial dysfunction and systemic inflammation, respectively 28 , herein, we will overview on possible putative mechanisms by which circulating T might affect the prognosis in men with COVID-19 (Table 1) . All rights reserved adipose tissue dysfunction and male hypogonadism, even if subclinical, are associated with higher circulating levels of cytokine (IL-6, IL-1 and TNF-alpha), endothelial dysfunction 163 , and amplified thrombosis risk, possibly prompting to detrimental clinical consequences in case of SARS-CoV-2 infection. It may affect baseline respiratory function, thus increasing the risk of mechanical ventilation requirement once the infection occurred; increase the number of baseline comorbidities, consequently predisposing to poor prognosis or death as certificated by epidemiological studies; fosters hormonal imbalance (decline in circulating serum T and increase in serum estrogen concentration) which are involved in the fine regulation of immune system and coagulative homeostasis in case of infection, and predispose men to poor effective immune response, cytokine dysregulation; endothelial dysfunction and thrombosis. cache = ./cache/cord-339436-0k73tlna.txt txt = ./txt/cord-339436-0k73tlna.txt === reduce.pl bib === id = cord-339576-0d6sa9pe author = Guallar, María Pilar title = Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1380 sentences = 79 flesch = 56 summary = Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure cache = ./cache/cord-339576-0d6sa9pe.txt txt = ./txt/cord-339576-0d6sa9pe.txt === reduce.pl bib === id = cord-339772-q814d6l7 author = Pach, Szymon title = ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3735 sentences = 229 flesch = 60 summary = To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Moreover, we compared ACE2 sequences from rodents (mouse, rat, hamster, and red squirrel) to sample additional binding pockets in the ACE2-RBD interface and predict susceptibility to SARS-CoV-2 of the red squirrel (Sciurus vulgaris). To compare three-dimensional binding interfaces of animal ACE2-RBD complexes, we developed homology models of dog, cat, ferret, hamster, mouse, rat, and red squirrel proteins. Both outlier residues are located on flexible loops of ACE2 distal to the S binding site and represent polymorphic mutations from glycine in human crystal structure to serine in homology models. Based on known susceptibility of animal species to SARS-CoV-2 and the comparison of MD trajectories, we were able to develop models for prediction of RBD binding to ACE2. cache = ./cache/cord-339772-q814d6l7.txt txt = ./txt/cord-339772-q814d6l7.txt === reduce.pl bib === id = cord-339524-r0a6a1jw author = Islam, M. T. title = A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades date = 2020-10-13 pages = extension = .txt mime = text/plain words = 2518 sentences = 157 flesch = 60 summary = title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2. 137 A set of 15 primers ( Table 1) was designed based on the ARMS for differentiating six major 138 clades of SARS-CoV-2: S, L, V, G, GH, and GR. Hence, the single-variant specific PCRs were able to identify the 228 SARS-CoV-2 positive sample containing GR-clade of the virus. This study proposes a simple and exclusive ARMS-based SNP-discriminating method using 257 conventional PCR to establish multiplex-assays in detecting SARS-CoV-2 mutation clades. cache = ./cache/cord-339524-r0a6a1jw.txt txt = ./txt/cord-339524-r0a6a1jw.txt === reduce.pl bib === id = cord-340010-t1m7dxzc author = Schaefer, Esperance A. K. title = Interrelationship Between Coronavirus Infection and Liver Disease date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1416 sentences = 97 flesch = 43 summary = Several published studies have characterized the frequency and severity of liver biochemistry abnormalities on presentation, and a few have determined whether these abnormalities are associated with increased disease-related morbidity or death, as summarized in Table 1 . 9, 10, [12] [13] [14] [16] [17] [18] [19] [20] [21] [22] [23] [24] The largest published study to date encompassed 5700 hospitalized patients in New York and examined admission serologies: aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were both frequently elevated (58.4% and 39.0% of subjects, respectively), and a separate large cohort found elevations to be more common in severe disease. 28 Thus, the liver injury observed in COVID-19 may reflect a direct viral effect, but other potential contributors must be considered, both at the time of initial presentation and during disease progression and management. Hepatic injury from SARS-CoV2 infection is observed from the time of initial contact with the medical system, suggesting that the primary insult is unrelated to medical management but rather due to either direct effect of the virus or a consequence of the systemic disease. cache = ./cache/cord-340010-t1m7dxzc.txt txt = ./txt/cord-340010-t1m7dxzc.txt === reduce.pl bib === id = cord-339762-lh8czr0a author = Ng, Dianna L. title = Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 date = 2016-03-31 pages = extension = .txt mime = text/plain words = 3207 sentences = 162 flesch = 38 summary = title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) was initially isolated from a sputum specimen of a patient who died of respiratory and renal failure in Saudi Arabia in 2012. Although the pathogenesis of severe and fatal MERS-CoV infection is unknown, these postmortem findings provide critical insights, including evidence that pneumocytes are important targets, suggesting that direct cytopathic effects contribute to MERS-CoV respiratory symptoms. cache = ./cache/cord-339762-lh8czr0a.txt txt = ./txt/cord-339762-lh8czr0a.txt === reduce.pl bib === id = cord-339665-nwwutduy author = Patel, Ami title = Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date = 2020-07-29 pages = extension = .txt mime = text/plain words = 5258 sentences = 286 flesch = 52 summary = Prior work with the related coronaviruses, SARS-CoV and MERS-CoV, delineated that the Spike protein of these viruses was an important target for development of neutralizing antibodies, and in animal viral challenges vaccine targeted immunity (reviewed in (Du et al., 2009; Roper and Rehm, 2009; Thanh Le et al., 2020) (Liu et al., 2018; Muthumani et al., 2015; van Doremalen et al., 2020a) . These memory titers were comparable to those observed in other reported protection studies in macaques performed at the acute phase of the vaccine-induced immune response (Gao et al., 2020; van Doremalen et al., 2020b; Yu et al., 2020) and those reported in the sera of convalescent patients (Ni et al., 2020; Robbiani et al., 2020) . Our study and other published reports show that DNA vaccination with candidates targeting the full-length SARS-CoV-2 spike protein likely increase the availability of T cell immunodominant epitopes leading to a broader and more potent immune response, compared to partial domains and truncated immunogens. cache = ./cache/cord-339665-nwwutduy.txt txt = ./txt/cord-339665-nwwutduy.txt === reduce.pl bib === id = cord-339752-o6atz33c author = Xiao, Li title = ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel? date = 2020-04-28 pages = extension = .txt mime = text/plain words = 3937 sentences = 257 flesch = 49 summary = According to a report based on 72,314 cases (test confirmed cases: 44,672 (62%) from the Chinese Center for Disease Control and Prevention, 81% of COVID-19 patients have cold-like symptoms and mild pneumonia, 14% have severe respiratory inflammation, and 5% have critical conditions including respiratory failure, septic shock, and/or multiple organ dysfunction or failure. Similar to SARS (severe acute respiratory syndrome, [2002] [2003] coronavirus (SARS-CoV) [3] , SARS-CoV-2 primarily uses the S protein to invade host cells through ACE2, an enzyme which is known to be important in the renin-angiotensin-aldosterone system (RAAS) [4, 5] . Since TMPRSS2 plays a very important role in SARS-CoV-2 cell entry and ACE2 dysfunction, blocking the activity of TMPRSS2 should be the primary strategy for preventing severe and critical conditions of COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-339752-o6atz33c.txt txt = ./txt/cord-339752-o6atz33c.txt === reduce.pl bib === id = cord-340015-x9frt0jh author = de Carvalho, Werther Brunow title = Expert recommendations for the care of newborns of mothers with COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2822 sentences = 153 flesch = 50 summary = Despite the lack of scientific evidence regarding the potential for viral transmission to their fetus in pregnant mothers diagnosed with or suspected of COVID-19, it is important to elaborate the lines of care by specialists from hospitals caring for suspected and confirmed COVID-19 cases to guide multidisciplinary teams and families diagnosed with the disease or involved in the care of pregnant women and newborns in this context. (10) proposed the presence of at least one of following clinical signs or symptoms as criteria for the neonatal diagnosis of COVID-2: thermal instability, hypoactivity, feeding difficulty, respiratory distress, chest X-ray with changes (including single or bilateral ground-glass patterns), COVID-19 diagnosis in family or caregiver of the newborn, intimate contact with people with suspected or confirmed COVID-19, or patients with unclear pneumonia. Despite the lack of scientific evidence regarding the potential viral transmission to their fetus by pregnant women with suspected or positive for COVID-19, multidisciplinary teams must be attentive to the disease signs and symptoms for guided and assertive decision making in the management of both mothers and newborns in the hospital environment and discharge. cache = ./cache/cord-340015-x9frt0jh.txt txt = ./txt/cord-340015-x9frt0jh.txt === reduce.pl bib === id = cord-340103-dc3wye9s author = Pallanti, Stefano title = Importance of SARs-Cov-2 anosmia: From phenomenology to neurobiology date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2348 sentences = 99 flesch = 42 summary = All clinicians should be aware that the presentation of SARS-CoV-2's symptoms goes far beyond respiratory and sensorial dimensions and involves psychosensorial and neurological dimensions; these clinical observations could shed light on the neurobiological substrates involved in COVID-19 disease. In the long list of clinical symptoms of COVID-19, ENT-UK (The British Association of Otorhinolaryngology) has recently identified anosmia-hyposmia and hypogeusia, respectively, the sudden loss of sense of smell and taste, as "significant symptoms" which were found even in the absence of other symptoms, so that they could identify otherwise hidden carriers of this highly contagious disease. In the present report, anticipation of anosmia and hypogeusia to respiratory symptoms seems consistent with the ENT UK hypothesis that loss of sense of smell (and taste) could be considered as a symptom of COVID-19 infection; and, if confirmed, these symptoms may represent markers or early signs of SARS-CoV-2 sufficient to trigger quarantine. cache = ./cache/cord-340103-dc3wye9s.txt txt = ./txt/cord-340103-dc3wye9s.txt === reduce.pl bib === id = cord-339720-d1stzy8w author = Zhao, Yuan title = Susceptibility of tree shrew to SARS-CoV-2 infection date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2572 sentences = 180 flesch = 58 summary = No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. In three young tree shrews (TS26, TS27 and TS28), we could detect viral RNA from only lungs in TS26 and TS27, but not in any tissue from TS28, although these animal had higher number of viral genomic copy numbers at the earlier stage of SARS-CoV-2 infection. Although SARS-CoV-2 infection didn't cause severe disease in all three ages of tree shrews, viral replication and mild histopathological changes were still observed in this study. In conclusion, tree shrew is not as susceptible to SARS-CoV-2 infection as the reported animal models of COVID-19, though limited replication of SARS-CoV-2 and mild histopathology was detected and observed in some tissues. Young Old Adult 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Histopathological examination of affected tissues from SARS-CoV-2 infected tree shrews. cache = ./cache/cord-339720-d1stzy8w.txt txt = ./txt/cord-339720-d1stzy8w.txt === reduce.pl bib === id = cord-339968-s1kmipir author = Osier, Faith title = The global response to the COVID-19 pandemic: how have immunology societies contributed? date = 2020-09-10 pages = extension = .txt mime = text/plain words = 6123 sentences = 290 flesch = 36 summary = Y.; Fraser, John; Lambrecht, Bart N.; Romano, Marta; Gazzinelli, Ricardo T.; Bortoluci, Karina R.; Zamboni, Dario S.; Akbar, Arne N.; Evans, Jennie; Brown, Doug E.; Patel, Kamala D.; Wu, Yuzhang; Perez, Ana B.; Pérez, Oliver; Kamradt, Thomas; Falk, Christine; Barda-Saad, Mira; Ariel, Amiram; Santoni, Angela; Annunziato, Francesco; Cassatella, Marco A.; Kiyono, Hiroshi; Chereshnev, Valeriy; Dieye, Alioune; Mbow, Moustapha; Mbengue, Babacar; Niang, Maguette D. Efforts included writing to President Donald Trump and Congressional leaders urging that they heed the advice of scientific/public health leaders, including AAI member Anthony Fauci 3 ; writing to National Institutes of Health (NIH) Director Francis Collins requesting justification for terminating an NIH-funded grant focusing on understanding the risk of bat coronavirus emergence 4 ; advocating supplemental funding for federal science agencies, including the NIH, for pandemic-related research losses and additional trainee support; and issuing a statement opposing actions taken by the Trump administration that will damage international scientific collaboration 5 . cache = ./cache/cord-339968-s1kmipir.txt txt = ./txt/cord-339968-s1kmipir.txt === reduce.pl bib === id = cord-340070-de7sfccy author = Pérez-Martinez, Antonio title = Clinical outcome of SARS-CoV-2 infection in immunosuppressed children in Spain date = 2020-08-29 pages = extension = .txt mime = text/plain words = 2306 sentences = 119 flesch = 45 summary = In this series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. A retrospective study (1st to 31st of March, 2020) of children less than 15 years old with primary or secondary immunosuppression infected with SARS-CoV-2 and treated at the University Hospital La Paz, Madrid, Spain, was performed. Hydroxychloroquine was initiated upon diagnosis (positive PCR for SARS-CoV-2) when there were signs/ symptoms of moderate-severe disease (respiratory signs, pneumonia on chest X ray, blood parameters of severity such as lymphopenia or elevated CRP, D-dimer or Il-6). In this small series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. Based on our experience, monitoring of children with immunosuppression and COVID-19 disease can be performed as outpatients, if close monitoring is possible with radiological and blood test controls if necessary, and carefully selecting the patients depending on their individual risk. cache = ./cache/cord-340070-de7sfccy.txt txt = ./txt/cord-340070-de7sfccy.txt === reduce.pl bib === id = cord-340114-ycgc6yyc author = Rajagopal, Kalirajan title = Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3640 sentences = 225 flesch = 52 summary = title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies In this article, some oxazine substituted 9-anilinoacridines (A1–A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1–A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Using different modules (Glide, QikProp, Prime and Desmond) of Schr€ odinger suite LLC, various computational methods such as molecular docking, ADMET screening, binding free energy calculations and molecular dynamics (MD) simulations were performed to find the interactions responsible for COVID-19 inhibition. cache = ./cache/cord-340114-ycgc6yyc.txt txt = ./txt/cord-340114-ycgc6yyc.txt === reduce.pl bib === id = cord-339934-g6ufz29l author = Yu, Hai-qiong title = Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients date = 2020-05-13 pages = extension = .txt mime = text/plain words = 993 sentences = 55 flesch = 45 summary = In the case of respiratory infection, while IgM and IgG isotypes have been the primary emphasis in characterizing immunity, mucosal and systemic IgA responses that may play a critical role in the disease pathogenesis, have received much less attention. This pattern of humoral immune response is different in case of SARS-CoV infection, in which IgM and IgA showed similar chronological profiles in terms of both seroconversion time and antibody titres [5] , in line with the knowledge that viremia is common in SARS. Upregulated IgA production may be the result of increased levels of TGF-β and IL-10 that promote antibody switching in SARS-CoV-2 infection. Considering the roles of mucosal and systemic IgA in COVID-19, inducing IgA production, e.g. using Lactoferrin to activate canonical TGF-β signaling [13] , or retinoic acid to enhance lactoferrin-induced IgA responses [14] , has been proposed as novel therapies for severe COVID-19. cache = ./cache/cord-339934-g6ufz29l.txt txt = ./txt/cord-339934-g6ufz29l.txt === reduce.pl bib === id = cord-339711-f7xifne8 author = Bal, A. title = Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2743 sentences = 166 flesch = 52 summary = title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test The first study exploring the association of 75 commercial serological assays and VNT claimed that the Wantai Total Ab assay detecting 76 total antibodies directed against the SARS-CoV-2 receptor binding domain (RBD) had the 77 best characteristics to detect functional antibodies at different stages and severity of disease 78 [12] . In the first study comparing VNT with commercialized 215 tests, the authors found that the Wantai Total Ab assay had the best characteristics to detect 216 functional antibodies in different stages and severity of disease [12] . For evaluating protective immunity, the Wantai Total Ab assay 247 with an optimized cut-off or other tests targeting the S protein as Euroimmun, DiaSorin or 248 bioMérieux IgG could be more useful, notably to screen serum specimens candidate for the 249 presence of neutralizing antibodies. cache = ./cache/cord-339711-f7xifne8.txt txt = ./txt/cord-339711-f7xifne8.txt === reduce.pl bib === id = cord-339782-rybjc58j author = Carmo, Anália title = Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1844 sentences = 106 flesch = 52 summary = The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. In men, the first negative test took 24 ± 9 days (range: 7 -46) and in women it took 25 ± 9 days (range: 9 -44), P>0.05, In an attempt to understand why some patients maintained positive tests for longer, we correlated the detection of SARS-CoV-2 RNA with the host immune response to virus infection. The lack of information regarding persistence of virus RNA and infectivity, disease severity and immune response, supports the current guidance of viral clearance confirmation prior to patient transference out of dedicated COVID-19 wards and of ending isolation in mild illness patients. cache = ./cache/cord-339782-rybjc58j.txt txt = ./txt/cord-339782-rybjc58j.txt === reduce.pl bib === id = cord-340049-6rqmc89u author = Salvatori, Giovanni title = SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines date = 2020-06-03 pages = extension = .txt mime = text/plain words = 1411 sentences = 86 flesch = 44 summary = Evidence of the key role played by the S protein in counteracting coronavirus infection came from studies on human-neutralizing antibodies from rare memory B cells of individuals infected with SARS-CoV [2] or MERS-CoV [3] . Journal of Translational Medicine antibody responses, and vigorously neutralized SARS-CoV-2 S-mediated entry into cells, thus further encouraging the use of this molecular target for vaccination and immunotherapies [4] . Given the above and that the coronavirus S glycoprotein is surface-exposed and mediates entry into host cells by interacting with angiotensin-converting enzyme 2 (ACE2), it rapidly became the main target of neutralizing antibodies and the focus of therapeutic and vaccine design. Several companies and research institutes have started developing a vaccine that has the SARS-CoV-2 protein S as its target (see Table 1 ), although the various vaccination strategies show a differing ability to induce in the host both an antibody-mediated humoral response and a cell response mediated by CD4 or CD8 T lymphocytes in preclinical models. cache = ./cache/cord-340049-6rqmc89u.txt txt = ./txt/cord-340049-6rqmc89u.txt === reduce.pl bib === id = cord-339976-tg2jkss7 author = Wang, Haibin title = Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date = 2004-07-01 pages = extension = .txt mime = text/plain words = 2579 sentences = 120 flesch = 50 summary = title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient's clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome cache = ./cache/cord-339976-tg2jkss7.txt txt = ./txt/cord-339976-tg2jkss7.txt === reduce.pl bib === id = cord-340042-intxyu46 author = Chaudhry, Sundas Nasir title = New insight on possible vaccine development against SARS-CoV-2 date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5457 sentences = 260 flesch = 43 summary = In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . cache = ./cache/cord-340042-intxyu46.txt txt = ./txt/cord-340042-intxyu46.txt === reduce.pl bib === id = cord-340028-6oicmeam author = Zhavoronkov, Alex title = Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date = 2020-03-31 pages = extension = .txt mime = text/plain words = 7228 sentences = 366 flesch = 36 summary = Here we compare the expected benefit of treatments for elderly populations (60 years and older) that are currently in development, including standard preventative strategies such as vaccines and antivirals targeting SARS-CoV-2, and the potential added benefit of speculative geroprotective strategies such as rapalogs, NAD+ boosters, senolytics, and stem cell treatment. People >60 years of age with chronic medical conditions, such as type 2 diabetes or cardiovascular disease, direct immunosuppression from HIV, posttransplant or biologic treatment, pregnant individuals, or those with BMI>40, are believed to be at higher risk for influenza infection due to a weakened immune response [31] . As discussed in this paper, small clinical studies have shown that several geroprotective and senoremediative interventions, such as treatment with AGING sirolimus and rapalogs, can induce immunopotentiation, increase resistance to infection, and reduce disease severity in the elderly, without severe side effects. cache = ./cache/cord-340028-6oicmeam.txt txt = ./txt/cord-340028-6oicmeam.txt === reduce.pl bib === id = cord-340138-u8hxyfml author = Seneviratne, Chaminda Jayampath title = The Role of Dentists in COVID-19 Is Beyond Dentistry: Voluntary Medical Engagements and Future Preparedness date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3861 sentences = 217 flesch = 46 summary = Keywords: COVID-19, dentistry, voluntary work, preparedness, infection control BACKGROUND The emergence of the highly infectious novel coronavirus has led to a global pandemic in a span of just 3 months. Thus, the robust training of clinical medicine in dentistry strengthens the candidature of dentists to volunteer services for COVID-19 control and spread. Many dentists have therefore discontinued the provision of elective dental treatment, in accordance with guidelines released by national-level government healthcare authorities such as the Centers for Disease Control and Prevention (CDC) in the US and National Health Service (NHS) in the UK. In this context, dental clinics that are well equipped with facilities to control aerosol spread of infections, such as negative pressure rooms and high-volume excavators, can offer help to augment the capacity for COVID-19 screening. Precautions when providing dental care during Coronavirus Disease 2019 (COVID-19) pandemic cache = ./cache/cord-340138-u8hxyfml.txt txt = ./txt/cord-340138-u8hxyfml.txt === reduce.pl bib === id = cord-339786-elrzlbsg author = Gurala, Dhineshreddy title = Acute Liver Failure in a COVID-19 Patient Without any Preexisting Liver Disease date = 2020-08-26 pages = extension = .txt mime = text/plain words = 2058 sentences = 117 flesch = 51 summary = Studies and data so far on coronavirus infections from China, Singapore, and other countries showed that liver enzymes elevation could be seen in 20-50% of cases. In another study published in the Lancet in February 2020 by Huang et al., an increase in aspartate aminotransferase (AST) was observed in 62% in intensive care unit (ICU) patients compared to 25% in non-ICU patients, indicating that more severe disease correlates with worsening of liver enzymes [10] . Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. In summary, we describe the first case of acute liver failure caused by the COVID-19 infection. cache = ./cache/cord-339786-elrzlbsg.txt txt = ./txt/cord-339786-elrzlbsg.txt === reduce.pl bib === id = cord-339686-oybnk1j8 author = Suassuna, José Hermógenes Rocco title = Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5770 sentences = 281 flesch = 41 summary = title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine We produced this document to bring pertinent information to the practice of nephrology, as regards to the renal involvement with COVID-19, the management of acute kidney injury cases, and practical guidance on the provision of dialysis support.As information on COVID-19 evolves at a pace never before seen in medical science, these recommendations, although based on recent scientific evidence, refer to the present moment. Every professional involved in nephrological care must provide the best possible assistance to the patients under their responsibility, adopt practices that minimize their personal risk of contamination, that of their patients and the whole range of other professionals who participate in hospital kidney support, including nurses and technicians, dialysis staff, healthcare professionals from all areas (for example, doctors and nurses in intensive care medicine), laboratory and radiology technicians, cleaning and transport staff, etc. cache = ./cache/cord-339686-oybnk1j8.txt txt = ./txt/cord-339686-oybnk1j8.txt === reduce.pl bib === id = cord-340063-nmx91h0a author = Müller, Olaf title = Epidemiologie und Kontrollmaßnahmen bei COVID-19 date = 2020-04-28 pages = extension = .txt mime = text/plain words = 3011 sentences = 349 flesch = 53 summary = The Coronavirus Disease Pandemic 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), started in December 2019 in China. Es gibt bisher weder wirksame Medikamente noch eine Impfung, somit stehen nur Public-Health-Interventionen wie einerseits physisches Abstandhalten und Hygienemaßnahmen sowie andererseits gezieltes Testen gefolgt von Isolations-und Quarantänemaßnahmen zur Verfügung. Der Erreger des Coronavirus Disease 2019 (COVID19) , das Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), gehört zu einer RNA-Virusfamilie, die sowohl bei Tieren als auch beim Menschen Erkrankungen hervorrufen kann. Der Verlauf nationaler Epidemien sowie der Pandemie wird von Faktoren bestimmt, die bisher für COVID-19 noch nicht vollständig verstanden sind. Prinzipiell unterscheidet man hierbei Isolationsmaßnahmen (SARS-CoV-2-Infizierte und COVID-19-Patienten) und Quarantänemaßnahmen (Kontaktpersonen von Infizierten und Erkrankten, stark betroffene Gemeinden); diese Maßnahmen sind besonders wirksam zum Beginn einer Epidemie, wenn Infektionsketten noch nachvollziehbar sind [35] . Es ist momentan auch noch offen, welche Ausmaße die Pandemie in den Industrieländern erlangen wird; dies hängt primär von der Intensität und Dauer der durchgeführten Public-Health-Maßnahmen ab. cache = ./cache/cord-340063-nmx91h0a.txt txt = ./txt/cord-340063-nmx91h0a.txt === reduce.pl bib === id = cord-339951-how9cmw8 author = Zhou, Yaqing title = Clinical and Autoimmune Characteristics of Severe and Critical Cases of COVID‐19 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2580 sentences = 157 flesch = 50 summary = The clinical, autoimmune, and laboratory characteristics of 21 patients who had laboratory‐confirmed severe and critical cases of coronavirus disease 2019 (COVID‐19) from the intensive care unit of the Huangshi Central Hospital, Hubei Province, China, were investigated. According to the sixth edition of Guidance for Corona Virus Disease 2019: Prevention, Control, Diagnosis and Management, issued by China's National Health Commission, the diagnostic criteria for the clinical classification of COVID-19 are as follows: (i) mild-clinical symptoms are mild and no pneumonia manifestation can be found on imaging; (ii) ordinary-symptoms such as fever and respiratory tract symptoms and pneumonia manifestations can be seen on imaging; (iii) severe-any of the following: respiratory distress, respiratory rate (RR) ≥30 breaths/min, oxygen saturation <93% at rest, arterial partial pressure of oxygen (PaO 2 )/oxygen concentration (FIO 2 ) ≤300 mmHg (1 mmHg = 0.133 kPa), or >50% lesion progression within 24-48 hours on pulmonary imaging; and (iv) critical-any of the following: respiratory failure in which mechanical ventilation is required, shock occurs, or complications with another organ failure that require monitoring and treatment in the ICU. In this single-center and retrospective study, we have reported on the clinical and laboratory characteristics of 8 severe and 13 critical cases of SARS-CoV-2 in Huangshi, Hubei Province, China. cache = ./cache/cord-339951-how9cmw8.txt txt = ./txt/cord-339951-how9cmw8.txt === reduce.pl bib === id = cord-340240-dk48pdqa author = Kuo, Tsun-Yung title = Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1240 sentences = 91 flesch = 53 summary = title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 S-2P was combined with various adjuvants, including CpG 1018, and administered to mice to test its effectiveness in eliciting anti-SARS-CoV-2 neutralizing antibodies. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of spike-specific antibodies in sera of immunized mice. In this study, we present data from preclinical studies aimed at developing a COVID-19 candidate subunit 84 vaccine using CHO cell-expressed SARS-CoV-2 S-2P antigen combined with various adjuvants. We have 85 shown that S-2P, when mixed with CpG 1018 and aluminum hydroxide adjuvants, was most effective in 86 inducing antibodies that neutralized pseudovirus and wild-type live virus while minimizing Th2-biased 87 responses with no vaccine-related adverse effects. Previous studies showed that the lung-infiltrating eosinophils were a common 308 indication of Th2-biased immune responses seen in animal models testing SARS-CoV vaccine candidates [22] . cache = ./cache/cord-340240-dk48pdqa.txt txt = ./txt/cord-340240-dk48pdqa.txt === reduce.pl bib === id = cord-339727-q8pjwl3s author = Sahu, Kamal Kant title = Mesenchymal Stem Cells in COVID-19: A Journey from Bench to Bedside date = 2020-07-30 pages = extension = .txt mime = text/plain words = 3325 sentences = 214 flesch = 48 summary = Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. [6] [7] [8] [9] [10] Recently, a few studies have examined the role of mesenchymal stem cells (MSCs) in critically ill patients with COVID-19. Because H7N9 and SARS-CoV-2 share similar complications-ARDS, hypoxic respiratory failure, severe inflammation, overt immune response, and multiorgan dysfunction syndrome-MSCs therapy may be beneficial for patients with COVID-19 pneumonia as well. Rationale for the clinical use of adipose-derived mesenchymal stem cells for COVID-19 patients Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use cache = ./cache/cord-339727-q8pjwl3s.txt txt = ./txt/cord-339727-q8pjwl3s.txt === reduce.pl bib === id = cord-340008-2efzyki4 author = Haddadi, Kaveh title = Coronavirus Disease 2019: Latest Data on Neuroinvasive Potential date = 2020-09-17 pages = extension = .txt mime = text/plain words = 3581 sentences = 209 flesch = 42 summary = Similar to other respiratory viruses, severe acute respiratory syndrome coronavirus (SARS-COV-2) may enter the brain via the hematogenous or neuronal route; however, only a few reports are available on the neurological complications of COVID-19. Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel coronavirus, originated in China in December 2019 and rapidly progressed into an epidemic infection, such that the World Health Organization (WHO) termed this calamitous virus "coronavirus disease 2019 (COVID-19)". Indeed, while the bulk of research conducted and published thus far has focused on the mechanisms whereby SARS-CoV-2 targets the respiratory system, more recent investigations have reported disconcerting evidence of the entrance of this new coronavirus into the CNS via different ways, resulting in significant damage to this system or even death due to its infection. Some investigators in China reported that more than 30% of their 214 patients with COVID-19 presented with neurological signs and symptoms; they, therefore, concluded that SARS-CoV-2 might attack the CNS through blood or retrograde neuronal routes, causing the destruction of the CNS. cache = ./cache/cord-340008-2efzyki4.txt txt = ./txt/cord-340008-2efzyki4.txt === reduce.pl bib === id = cord-340260-z13aa1wk author = Farewell, V. T. title = SARS incubation and quarantine times: when is an exposed individual known to be disease free? date = 2005-10-19 pages = extension = .txt mime = text/plain words = 4727 sentences = 232 flesch = 55 summary = For the data set of averaged times, Figure 1 presents the proÿle likelihoods, L * P (M ), based on the gamma, log-normal and log-gamma models discussed in Section 2. For the truncated gamma model, the proÿle likelihood never drops below 60 per cent suggesting that any value of M greater than the maximum time observed, 14, is plausible. For public health purposes, it could therefore be argued that, based only on such data and an assumed log-normal model, that a quarantine time of 20 days might be necessary to ensure that SARS cases were not released 'too early'. Finally, to show the e ect of more extreme interval-censoring, we consider extending the set of data in Table II by including additional SARS cases from Hong Kong whose period of possible exposure, which deÿnes the width of the interval within which their incubation time lies, is thought to be less than 10 days rather than 5 days. cache = ./cache/cord-340260-z13aa1wk.txt txt = ./txt/cord-340260-z13aa1wk.txt === reduce.pl bib === id = cord-339726-eg0hajzl author = Jamrozik, Euzebiusz title = Coronavirus Human Infection Challenge Studies: Assessing Potential Benefits and Risks date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3643 sentences = 154 flesch = 40 summary = Novel research designs, particularly where such studies might be controversial as in the case of SARS-CoV-2 HCS, require especially careful ethical evaluation including rigorous risk-benefit assessments as well as timely, thorough, public engagement ( WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020; Bambery et al. To be ethically acceptable, SARS-CoV-2 HCS would need to have multiple risk minimization strategies in place, including (i) selection of low risk participants (e.g., healthy young adults 1 ), (ii) careful strain selection and development, (iii) careful titration of viral dose, (iv) early diagnosis and availability of all necessary medical care, (v) long-term follow-up of participants, (vi) compensation for any lasting harms, and (vii) stringent infection control including measures to protect and screen research staff for infection (WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020). Tensions between public health and vaccine research priorities: A comparative modelling assessment of the risks and benefits of SARS-CoV-2 vaccine field trials versus human challenge studies cache = ./cache/cord-339726-eg0hajzl.txt txt = ./txt/cord-339726-eg0hajzl.txt === reduce.pl bib === id = cord-339817-qqitdrz6 author = Sousa Gonçalves, Catarina title = Erythematous Papular Rash: A Dermatological Feature of COVID-19 date = 2020-06-10 pages = extension = .txt mime = text/plain words = 871 sentences = 56 flesch = 44 summary = COVID-19 is the clinical expression of the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection. The cutaneous clinical spectrum is wide and includes maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, and pityriasis rosea-like, violaceous and pustular lesions. Clinicians should be aware of patients presenting only with cutaneous symptoms, which in some cases are the initial clinical feature of COVID-19. The clinical presentation of SARS-CoV-2 infection is called COVID-19 and has a wide spectrum of clinical manifestations. As with other viral infections, SARS-CoV-2 may also have cutaneous manifestations. In the absence of other possible syndromes and diseases, the skin rash was very likely due to SARS-CoV-2 infection. The cutaneous manifestations include maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, pityriasis rosea-like and violaceous lesions, and vesicular and maculopapular pustular lesions (as in other viral infections). cache = ./cache/cord-339817-qqitdrz6.txt txt = ./txt/cord-339817-qqitdrz6.txt === reduce.pl bib === id = cord-340305-jtvn9tlm author = Cimolai, Nevio title = A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 5105 sentences = 294 flesch = 40 summary = At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Others have found strong correlations between neutralizing antibodies and EIA-detected antibodies to various SARS-CoV-2 antigens [41, 42] .Some have found diversity in immune responses contingent on the nature of presenting disease [38, 43] . With the availability of viral antigen, most scientists in the know-how would be able to fashion a test for antibody determination in short order and most would likely choose an enzyme immunoassay (EIA) (or nearly equivalent non-enzymebased assay) for its potential of automation and widespread use. Sensitive and specific detection of low-level antibody responses in mild Middle East Respiratory Syndrome coronavirus infections A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients cache = ./cache/cord-340305-jtvn9tlm.txt txt = ./txt/cord-340305-jtvn9tlm.txt === reduce.pl bib === id = cord-340336-u59l0taa author = Perchetti, Garrett A. title = Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1390 sentences = 99 flesch = 50 summary =  -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control. cache = ./cache/cord-340336-u59l0taa.txt txt = ./txt/cord-340336-u59l0taa.txt === reduce.pl bib === id = cord-340201-ai4apr4w author = List, Wolfgang title = Occurrence of SARS-CoV-2 in the intraocular milieu date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1439 sentences = 112 flesch = 65 summary = All individuals were previously positive in nasopharyngeal swabbing and cause of death was respiratory failure due to SARS-CoV-2 infection. (Chen et al., 2020; Siedlecki et al., 2020; Wu et al., 2020; Xia et al., 2020; Zhang et al., 2020) In this study, we tested for SARS-CoV-2 in the aqueous humor and the vitreous representing the intraocular milieu. In sixteen individuals with confirmed SARS-CoV-2 infection samples from the vitreous and aqueous humor were taken during postmortem examinations. PCR was negative for all aqueous humor and vitreous samples for SARS-CoV-2. (Table 1) In this case series, SARS-CoV-2 could not be found in the aqueous humor and in the vitreous. In these patients, SARS-CoV-2 might be found in the aqueous humor and/or vitreous. In conclusion, this case series did not find SARS-CoV-2 in aqueous humor and vitreous samples during postmortem examinations of 16 patients with cause of death by SARS-CoV-2 infections. cache = ./cache/cord-340201-ai4apr4w.txt txt = ./txt/cord-340201-ai4apr4w.txt === reduce.pl bib === id = cord-340323-xz6v95yy author = Urbach, Horst title = Notfällige Neurointerventionen, Covid-19 und Thorax-CT: SOP und Literaturübersicht date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1427 sentences = 154 flesch = 51 summary = Bei Schlaganfall-und anderen Notfallpatienten kann das Ergebnis einer RT-PCR zum Nachweis von SARS-CoV-2, dem Erreger der COVID-19, aus einem Abstrich in der Mehrzahl der Fälle nicht abgewartet werden. Ein solcher Patient wird also wie ein COVID-19-Verdacht betrachtet, auch wenn die Wahrscheinlichkeit, dass er mit SARS-CoV-2 infiziert ist, eher gering erscheint. Das wünschenswerte Szenario ist nun, dass der Patient die Bereiche Computertomographie (CT), Angiographie und Intensivstation wie ein COVID-19-Patient durchläuft sowie Isolierung und Verdacht nach negativem RT-PCR-Ergebnis aufgehoben werden [1] [2] [3] . V. eine Umfrage darüber gestartet, welche diagnostischen und Schutzmaßnahmen in den einzelnen Kliniken bei Patienten mit möglicher SARS-CoV-2-Infektion getroffen werden. Das unterschiedliche Vorgehen neuroradiologischer Abteilungen in Deutschland spiegelt die Unsicherheit im Umgang mit Schlaganfallpatienten und möglicher "coronavirus disease 2019" (COVID-19) wider. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 cache = ./cache/cord-340323-xz6v95yy.txt txt = ./txt/cord-340323-xz6v95yy.txt === reduce.pl bib === id = cord-340291-bah2ege0 author = Kohmer, Niko title = Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date = 2020-05-10 pages = extension = .txt mime = text/plain words = 1001 sentences = 63 flesch = 55 summary = With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. With exception of one sample, all positive tested samples in the analysed cohort, using the 37 commercially available assays examined (including the in-house developed IFA), demonstrated 38 neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-39 there is an increasing demand in the detection of antibodies -especially of IgG antibodies. Currently there are many S 57 protein based commercially or in-house developed assays available, but there is limited data on how 58 these tests perform with clinical samples and if the detected IgG antibodies provide protective 59 cache = ./cache/cord-340291-bah2ege0.txt txt = ./txt/cord-340291-bah2ege0.txt === reduce.pl bib === id = cord-340205-cwn0gx7h author = Chen, Yih-Ting title = Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis date = 2020-07-16 pages = extension = .txt mime = text/plain words = 950 sentences = 57 flesch = 43 summary = title: Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis There was no evidence of statistical heterogeneity among studies reporting AKI mortality in SARS (I2: 0.0%, p = 0.589) and MERS (I2: 0.0%, p =v0.758), but there was for COVID-19 infection (I2: 97.0%, p < 0.001) (Fig. 1 ). Possible mechanisms of higher AKI mortality following coronavirus infections are multifactorial (e.g., severe sepsis-related multiorgan failure, direct kidney involvement, and acute respiratory distress syndrome) [26] [27] [28] , although comparative pathogenesis of kidney involvement among the three infections remains unclear. A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-340205-cwn0gx7h.txt txt = ./txt/cord-340205-cwn0gx7h.txt === reduce.pl bib === id = cord-340415-6fte7krp author = Thevarajan, Irani title = Clinical presentation and management of COVID‐19 date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4287 sentences = 244 flesch = 43 summary = In the face of high health care demand during the peak of a pandemic, safe management of low risk patients in the community will likely be essential to preserve hospital capacity for the more severely ill. This position is endorsed by the Australasian Society for Infectious Diseases interim guidelines for the clinical management of COVID-19 in adults, 20 guidelines for the clinical care of people with COVID-19, 19 which state that even where conditional recommendations for use of disease modifying agents are made, whenever possible these should be administered in the context of randomised trials with appropriate ethical approval. 37, 38 However, given the current lack of evidence of clinical benefit and reports of significant limitations of supply of hydroxychloroquine for patients with rheumatological conditions, in March 2020, the Pharmaceutical Society of Australia and the Australasian Society for Infectious Diseases called for immediate cessation of prescribing and dispensing of hydroxychloroquine for indications relating to COVID-19, outside use in approved clinical trials. Specific antiviral therapy in the clinical management of acute respiratory infection with SARS-CoV-2 (COVID-19). cache = ./cache/cord-340415-6fte7krp.txt txt = ./txt/cord-340415-6fte7krp.txt === reduce.pl bib === id = cord-340357-gyvvcnuf author = Fallahi, Hamid Reza title = Being a front-line dentist during the Covid-19 pandemic: a literature review date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3777 sentences = 212 flesch = 46 summary = This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. The purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the CDC and the ADA guidelines. Due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for 2019-nCoV infection. 2019-nCoV transmission in dental settings occurs through four major routes: (1) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials; cache = ./cache/cord-340357-gyvvcnuf.txt txt = ./txt/cord-340357-gyvvcnuf.txt === reduce.pl bib === id = cord-340163-ex03l0pc author = Hu, Tingting title = A comparison of COVID-19, SARS and MERS date = 2020-08-19 pages = extension = .txt mime = text/plain words = 7908 sentences = 459 flesch = 53 summary = In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The latest diagnostic criteria of COVID-19, SARS and MERS including clinical presentations, labora tory diagnosis and radiological feature Latest treatment and prevention methods of Published in a peer-reviewed article Availability of the full text publication Availability of the paper in English According to a study among 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China, the male-to-female ratio was 1.06:1, and the median age was 56 years (interquartile range, 42-68; range, 22-92 years) (Wu & McGoogan, 2020; Wang et al., 2020) . CXR findings In the early phase, CXR of COVID-19 patients is not highly recommended for clinical diagnosis because of its low sensitivity in detecting SARS-CoV-2 pneumonia. cache = ./cache/cord-340163-ex03l0pc.txt txt = ./txt/cord-340163-ex03l0pc.txt === reduce.pl bib === id = cord-340535-78bpvtuf author = Elbay, Rümeysa Yeni title = Depression, Anxiety, Stress Levels of Physicians and Associated Factors In Covid-19 Pandemics date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2429 sentences = 131 flesch = 50 summary = AIM: To investigate anxiety, stress, and depression levels of physicians during the Covid-19 outbreak and explored associated factors in both clinical and general site. Factors found to be associated with higher DAS-21 total scores in frontline workers were as follows: increased weekly working hours, increased number of Covid-19 patients cared for, lower level of support from peers and supervisors, lower logistic support, and lower feelings of competence during Covid-19 related tasks. In an early study investigating immediate psychological response during Covid-19 epidemic among general population in China, 53.8% of participants rated the psychological impact of the outbreak as moderate or severe (1) . In another study investigating long term psychological effects of SARS outbreak on healthcare workers, 23% of staff were found to have moderate or severe depressive symptoms in a 3year follow-up (4) . Based on this perspective, here, we aimed to investigate anxiety, stress and depression levels of physicians during Covid-19 outbreak and explored associated factors in both clinical and general site. cache = ./cache/cord-340535-78bpvtuf.txt txt = ./txt/cord-340535-78bpvtuf.txt === reduce.pl bib === id = cord-340432-vm6m0kb4 author = Srivastava, Sukrit title = Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date = 2020-09-06 pages = extension = .txt mime = text/plain words = 2661 sentences = 199 flesch = 54 summary = title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide Methodology A novel reverse epitomics approach, "overlapping-epitope-clusters-to-patches" method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. Multi-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, "Overlapping-epitope-clusters-to-patches" method. In the present study, we have reported a novel method to design a 1170 vaccine against SARS-CoV-2 by utilizing multiple antigenic patches from the viral 1171 proteins. The designed MPVs from the antigenic patches of SARS-CoV-2 proteins 1182 have several advantages over to the subunit and multi-epitope based vaccines. Design of multi epitope-based peptide vaccine against E 1409 protein of human 2019-nCoV: An immunoinformatics approach Multi-epitope based peptide 1549 vaccine design against SARS-CoV-2 using its spike protein In silico approach for designing of a multi-epitope based 1587 vaccine against novel Coronavirus (SARS-COV-2) cache = ./cache/cord-340432-vm6m0kb4.txt txt = ./txt/cord-340432-vm6m0kb4.txt === reduce.pl bib === id = cord-340410-s9haq8y1 author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-06-26 pages = extension = .txt mime = text/plain words = 1072 sentences = 81 flesch = 68 summary = The virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct PCR and nCoV-DK, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. The nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. The 2019 Novel Coronavirus Detection Kit (nCoV-DK, Shimadzu Corporation, Kyoto, Japan) eliminates the steps of RNA extraction and purification by using the Ampdirect TM technology (Nishimura et al., 2010) , thus significantly reducing the time required for sample preparation and PCR detection from more than 2 hours to about 1 hour. We herein compared efficacy of the nCoV-DK with the direct PCR method requiring RNA extraction and purification. Particularly, it should be noted saliva is a reliable tool to detect the virus by the nCoV-KD even without process of RNA extraction and purification. cache = ./cache/cord-340410-s9haq8y1.txt txt = ./txt/cord-340410-s9haq8y1.txt === reduce.pl bib === id = cord-340252-9gr2iw15 author = Olalla, J. title = Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2398 sentences = 140 flesch = 54 summary = Conclusions: the prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This identification, together with the appropriate measures, could result in less spread of the virus from the healthcare center and, therefore, in fewer healthcare providers and patients affected by In this article, we present the results of an active search study of asymptomatic and seroprevalence carriers of SARS-CoV-2 among high-risk healthcare workers in a hospital in southern Spain. The main objective was to determine the prevalence of asymptomatic carriers of SARS-CoV-2 in healthcare professionals, defined as those individuals with PCR of a positive respiratory sample without presenting symptoms suggestive of CoVID-19 on the day of sampling. . https://doi.org/10.1101/2020.05.18.20103283 doi: medRxiv preprint workers in the total workforce presented positive PCR, although in this study it was performed testing only symptomatic workers (6) . cache = ./cache/cord-340252-9gr2iw15.txt txt = ./txt/cord-340252-9gr2iw15.txt === reduce.pl bib === id = cord-340472-9ijlj4so author = Li, Wenhui title = Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 date = 2005-03-24 pages = extension = .txt mime = text/plain words = 6610 sentences = 297 flesch = 53 summary = Figure 3B -D shows three views of the crystal structure of human ACE2, in which residues that convert rat ACE2 to an efficient SARS-CoV receptor are shown in red, and additional residues whose alteration interferes with S1-Ig association are shown in yellow. (C) Murine leukemia viruses (MLV) expressing green fluorescent protein (GFP), lacking its endogenous envelope glycoprotein (MLV-GFP), and pseudotyped with the S protein of SARS-CoV (TOR2 isolate) were incubated with HEK293T cells transfected with plasmids encoding the indicated human or rat ACE2 variants. We have shown that entry is the primary barrier to SARS-CoV infection of murine Surface plasmon resonance experiments in which the indicated RBD-Ig TOR2 variants shown in Figure 6B bound to immobilized anti-human antibody were assayed for association with soluble human ACE2. S-protein alterations at residues 479 and 487 are important for high-affinity association with human ACE2, and for efficient infection of cells expressing this receptor. cache = ./cache/cord-340472-9ijlj4so.txt txt = ./txt/cord-340472-9ijlj4so.txt === reduce.pl bib === id = cord-340351-ee8wjp5u author = Jiang, Fa-Chun title = Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1090 sentences = 83 flesch = 57 summary = We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. Approximately 3 hours after the 2 patients were identified as positive for SARS-CoV-2 RNA, we sampled the environmental surfaces of the 2 rooms in the centralized quarantine hotel in which they had stayed. One surface sample from the faucet in patient B's room was positive for SARS-CoV-2 RNA; the C t was 28.75 for the ORF1ab gene. We also detected SARS-CoV-2 RNA in the surface swab samples of the pillow cover, duvet cover, and sheet. SARS-CoV-2 RNA has been detected on environmental surfaces in isolation rooms where the symptomatic or paucisymptomatic patients stayed for several days (3) (4) (5) . cache = ./cache/cord-340351-ee8wjp5u.txt txt = ./txt/cord-340351-ee8wjp5u.txt === reduce.pl bib === id = cord-340523-wujzihbn author = Ravelli, Angelo title = Kawasaki disease or Kawasaki syndrome? date = 2020-06-22 pages = extension = .txt mime = text/plain words = 2158 sentences = 115 flesch = 43 summary = 3 4 However, between April and May 2020, a rise in the number of children and adolescents with an acute multisystem hyperinflammatory state fulfilling full or partial criteria for Kawasaki disease (KD), 5 although frequently accompanied by unusual or less common symptoms, such as abdominal pain, diarrhoea and myocardial failure, was noticed in European and North American countries or regions mostly hit by the COVID-19 pandemic. One month later, Riphagen et al 6 described the features of eight children with the aforementioned hyperinflammatory syndrome, which presented with clinical manifestations similar to atypical KD, together with prominent gastrointestinal symptoms, and progressed towards multiorgan involvement and severe shock, requiring admission to the Intensive Care Unit (ICU) and haemodynamic support. Interim guidance on Kawasaki disease and acute multisystem inflammatory syndrome in children and adolescents in the current emergency scenario of SARS-CoV-2 infection Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort cache = ./cache/cord-340523-wujzihbn.txt txt = ./txt/cord-340523-wujzihbn.txt === reduce.pl bib === id = cord-340189-jo38hjqa author = Bar-On, Yinon M title = SARS-CoV-2 (COVID-19) by the numbers date = 2020-04-02 pages = extension = .txt mime = text/plain words = 7246 sentences = 458 flesch = 58 summary = If you are infectious for 4 days, then you will infect four others on average, which is on the high end of the R 0 values for SARS-CoV-2 in the absence of physical distancing. Assuming entry of the virus to the cells is rapid (we estimate 10 min for SARS-CoV-2), the time it takes to produce progeny can be estimated by quantifying the lag between inoculation and the appearance of new intracellular virions, also known as the 'eclipse period'. While both the time to complete a replication cycle and the burst size may vary significantly in an animal host due to factors including the type of cell infected or the action of the immune system, these numbers provide us with an approximate quantitative view of the viral life-cycle at the cellular level. (Hirano et al., 1976) : "The average per-cell yield of active virus was estimated to be about 6-7  10 2 plaque-forming units." This data is for MHV, so more research is needed to verify these values for SARS-CoV-2. cache = ./cache/cord-340189-jo38hjqa.txt txt = ./txt/cord-340189-jo38hjqa.txt === reduce.pl bib === id = cord-340581-ngwgb3y0 author = Abassi, Zaid title = ACE2, COVID-19 Infection, Inflammation, and Coagulopathy: Missing Pieces in the Puzzle date = 2020-10-06 pages = extension = .txt mime = text/plain words = 4644 sentences = 247 flesch = 42 summary = Angiotensin-converting enzyme is expressed on the plasma membranes of various cell types, including alveolar and intestinal epithelia, vascular endothelial cells in the heart, kidney, and testis, and on macrophages, where it catalyzes the production of Ang 1-7 and its likely paracrine activity (Crackower et al., 2002; Hamming et al., 2007; Santos et al., 2008; Clarke and Turner, 2012; Abassi et al., 2020c) . In this context, testosterone has been described to induce ACE2 expression, the receptor entry of the SARS-CoV-2 infection, but also exerts protective effect against lung injury (Kuba et al., 2005) . FIGURE 2 | Physiology of coronavirus disease 2019 (COVID 19) homing to target host cells expressing ACE2: viral spike-domains enable attachment to cellmembrane-bound ACE2. Thus, viral cellular invasion and replication, initially facilitated by ACE2 and in particular under conditions characterized by enhanced ACE2 expression, later lead to diminution of cell membrane-attached ACE2, and likely increase circulating sACE2 (Figures 2, 3) . cache = ./cache/cord-340581-ngwgb3y0.txt txt = ./txt/cord-340581-ngwgb3y0.txt === reduce.pl bib === id = cord-340279-bq5owwot author = Espíndola, Otávio de Melo title = Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date = 2020-06-04 pages = extension = .txt mime = text/plain words = 285 sentences = 37 flesch = 52 summary = key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection cache = ./cache/cord-340279-bq5owwot.txt txt = ./txt/cord-340279-bq5owwot.txt === reduce.pl bib === id = cord-340537-pdvpmydk author = Bañon-Gonzalez, Rafael title = Autopsies of suspected SARS-CoV-2 cases date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3682 sentences = 244 flesch = 54 summary = Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body's tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. cache = ./cache/cord-340537-pdvpmydk.txt txt = ./txt/cord-340537-pdvpmydk.txt === reduce.pl bib === id = cord-340516-9dfaqsv7 author = Moore, Anne C. title = Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date = 2020-09-06 pages = extension = .txt mime = text/plain words = 6679 sentences = 335 flesch = 48 summary = We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Here, we report the induction of neutralizing antibody (Nab), IgG and IgA antibody responses, and T cell responses in mice following immunization of rAd vectors expressing one or more SARS-CoV-2 antigens. We have previously demonstrated that an oral, tableted rAd-based vaccine can induce protection against respiratory infection and shedding following influenza virus challenge 15 as well as intestinal immunity to norovirus antigens in humans 12 . In summary, these studies in mice represent our first step in creating a vaccine candidate, demonstrating the immunogenicity of the construct at even low vaccine doses and the elucidation of the full-length spike protein as a leading candidate antigen to induce T cell responses and superior systemic and mucosal neutralizing antibody. cache = ./cache/cord-340516-9dfaqsv7.txt txt = ./txt/cord-340516-9dfaqsv7.txt === reduce.pl bib === id = cord-340619-3tjquzx8 author = Menghua, Wu title = Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1601 sentences = 119 flesch = 63 summary = title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. Here we reported a case of HIV and SARS-CoV-2 coinfection who had a prolonged viral shedding duration about 28 days. [11] reported a patient with kidney transplantation who had a prolonged viral shedding duration for 63 days. This is the first report of a patient co-infected with HIV and SARS-CoV-2 who showed a prolonged viral shedding duration. The lymphocyte count of our case was also less than 2.0 × 10 9 /L, which might be a co-factor for the prolonged viral shedding duration. Viral shedding prolongation in a kidney transplant patient with COVID-19 pneumonia cache = ./cache/cord-340619-3tjquzx8.txt txt = ./txt/cord-340619-3tjquzx8.txt === reduce.pl bib === id = cord-340085-ywg4rhnn author = Maras, J. S. title = Multi-Omics integration analysis of respiratory specimen characterizes baseline molecular determinants associated with COVID-19 diagnosis. date = 2020-07-07 pages = extension = .txt mime = text/plain words = 7383 sentences = 476 flesch = 42 summary = Quantitative proteomics identified significant increase in 6 SARS-CoV-2 proteins along with ACE2 in the respiratory specimen of COVID-19 positive patients compared to negative patients (p<0.05, Figure 1C , H1N1 samples did not enrich any or associated proteins). /2020 Diagnostic accuracy: Amongst the identified DEP's, mean decrease in the accuracy (calculated by random forest; 1000 trees) was highest for MX1 (MX Dynamin like GTPase 1) and WARS (Tryptophan--tRNA ligase) making them the most important proteins for segregating COVID-19 positive patients from negative or H1N1 patients ( Figure Together these findings showed that COVID-19 positive patients have virus mediated hyper immune activation involving monocytes and neutrophils, deregulated oxygen transport, increased fluid shear stress, bacterial invasion of the epithelial cells and glucose metabolism. Viral infection are also known for metabolic reprograming of host (Thaker et al., 2019) and proteome analysis of the respiratory specimen showed that there is significant increase in proteins associated to glucose metabolism suggesting that SARS-CoV-2 induces energy metabolism (Supplementary Figure 18 ). cache = ./cache/cord-340085-ywg4rhnn.txt txt = ./txt/cord-340085-ywg4rhnn.txt === reduce.pl bib === id = cord-340627-xyvzgkxl author = Ornaghi, Sara title = Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3804 sentences = 228 flesch = 51 summary = title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening cache = ./cache/cord-340627-xyvzgkxl.txt txt = ./txt/cord-340627-xyvzgkxl.txt === reduce.pl bib === id = cord-340590-7jql1ftj author = Massullo, Domenico title = Mountain Rescue During the COVID-19 Outbreak: Considerations and Practical Implications date = 2020-09-23 pages = extension = .txt mime = text/plain words = 889 sentences = 62 flesch = 52 summary = The COVID-19 pandemic causes several issues during rescue 48 operations in the wilderness environment due to concern for viral contagiousness during prolonged 49 close interaction between rescuers and victims. The key points during rescues are the protection of operators and patients from 59 infection and disinfection of materials and vehicles used during outdoor operations. In addition, each rescuer, before giving their availability to participate in 65 rescue operations, should perform a self-check through a COVID-19 screening questionnaire 66 ( Figure 1 ). In conclusion, during the COVID-19 pandemic, protocols for mountain rescue services should be 85 reassessed in order to protect both rescuers and victims from possible contagion. Characteristics of and important lessons from the coronavirus disease 144 2019 (COVID-19) outbreak in China: summary of a report of 72 SARS-CoV-2 in patients with COVID-19 Protection 155 and disinfection policies against SARS-CoV-2 (COVID-19) cache = ./cache/cord-340590-7jql1ftj.txt txt = ./txt/cord-340590-7jql1ftj.txt === reduce.pl bib === id = cord-340486-wydlqq2z author = Grandbastien, Manon title = SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2102 sentences = 132 flesch = 50 summary = title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation Conclusion Our results demonstrate that asthmatic patients appeared not to be at risk for severe SARS-CoV-2 pneumonia. Moreover, SARS-CoV-2 pneumonia did not induce severe asthma exacerbation. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. The propensity score allows analyzing 245 an observational nonrandomized study so that it mimics some of the particular 246 characteristics of a randomized controlled trial as it accounts for systematic differences in 247 baseline characteristics between asthmatic and non-asthmatic subjects when estimating the 248 effect of asthma on severe COVID-19 outcomes. This suggests that the risk factors for hospitalization in our patients were 390 related more to the risk factors of SARS-CoV-2 pneumonia than to asthma. cache = ./cache/cord-340486-wydlqq2z.txt txt = ./txt/cord-340486-wydlqq2z.txt === reduce.pl bib === id = cord-340687-99ad1rwq author = Abourida, Yassamine title = Management of Severe COVID-19 in Pregnancy date = 2020-07-27 pages = extension = .txt mime = text/plain words = 2527 sentences = 143 flesch = 46 summary = The scarcity of data concerning pregnant patients gravely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) makes their management difficult, as most of the reported cases in the literature present mild pneumonia symptoms. Herein, we outline a case of severe COVID-19 infection in a pregnant woman abruptly rupturing her membranes and undergoing cesarean delivery. Herein, we report the case of a healthy parturient infected with SARS-CoV-2 in her third trimester, whose condition deteriorated leading to premature rupture of membranes, a premature birth via a caesarian delivery, and neonatal death. It is noteworthy that recent reports highlighted elevated SARS-CoV-2 antibody levels (IgM and IgG) and abnormal cytokine test results 2 hours after birth in a neonate born to a mother with COVID-19 via a caesarian delivery, whereas RT-PCR tests on nasopharyngeal swabs taken were negative [20] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn cache = ./cache/cord-340687-99ad1rwq.txt txt = ./txt/cord-340687-99ad1rwq.txt === reduce.pl bib === id = cord-340883-zf8jbhdl author = He, Zhongping title = Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date = 2007-03-27 pages = extension = .txt mime = text/plain words = 2892 sentences = 119 flesch = 56 summary = title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR. cache = ./cache/cord-340883-zf8jbhdl.txt txt = ./txt/cord-340883-zf8jbhdl.txt === reduce.pl bib === id = cord-340908-8q7i5ds3 author = D’Ambrosi, Riccardo title = Guidelines for Resuming Elective Hip and Knee Surgical Activity Following the COVID-19 Pandemic: An Italian Perspective date = 2020-10-13 pages = extension = .txt mime = text/plain words = 1838 sentences = 116 flesch = 46 summary = 1. Facility requirement: All diagnosis and treatment activities related to surgery for patients not infected with SARS-CoV-2 must be performed in a COVID-19-free environment. 3. Patient selection: Patient selection must take into account age, urgency of treatment, risk of exposure to SARS-CoV-2, American Society of Anesthesiologists (ASA) classification, comorbidity, socio-professional situation, and the possibility of performing post-operative physiotherapy [7, 13] . (However, if these patients did have surgery, the procedure must take place in a separate environment within the hospital and with adequate assessment of the risk to healthcare staff and planning to optimize their ability to avoid infection.) Also, patients classified as ASA I or ASA II had priority for intervention regardless of the urgency of the treatment. The complete program including surgical treatment, post-operative physiotherapy management, and follow-up must be discussed and planned with the patient before surgery. cache = ./cache/cord-340908-8q7i5ds3.txt txt = ./txt/cord-340908-8q7i5ds3.txt === reduce.pl bib === id = cord-340563-hsj53inh author = Baud, David title = Using Probiotics to Flatten the Curve of Coronavirus Disease COVID-2019 Pandemic date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2592 sentences = 137 flesch = 31 summary = Clinical evidence shows that certain probiotic strains help to prevent bacterial and viral infections, including gastroenteritis, sepsis, and respiratory tract infections (RTIs). In one analysis of more than 8,000 preterm infants included in randomized control trials (RCTs), patients receiving enteral supplementation with probiotics showed a reduction in necrotizing enterocolitis, nosocomial sepsis, and all-cause mortality (14) . But low quality of evidence and conflicting results among different studies calls for additional well-conducted RCTs. It should be noted that not all probiotics, even those with gastrointestinal benefits, necessarily contribute in every way to reducing the risk of respiratory infection. Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial Lactobacillus plantarum DR7 improved upper respiratory tract infections via enhancing immune and inflammatory parameters: a randomized, double-blind, placebo-controlled study cache = ./cache/cord-340563-hsj53inh.txt txt = ./txt/cord-340563-hsj53inh.txt === reduce.pl bib === id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 pages = extension = .txt mime = text/plain words = 9409 sentences = 500 flesch = 46 summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. cache = ./cache/cord-340629-1fle5fpz.txt txt = ./txt/cord-340629-1fle5fpz.txt === reduce.pl bib === id = cord-341000-9xs8aukq author = Ghiasvand, Fereshteh title = Symmetrical polyneuropathy in Coronavirus Disease 2019 (COVID-19) date = 2020-05-15 pages = extension = .txt mime = text/plain words = 1425 sentences = 96 flesch = 42 summary = The knowledge around the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still evolving with the cases increasing globally. A case series presented data of four Severe Acute Respiratory Syndrome (SARS) patients who developed polyneuropathy, myopathy, or both approximately three weeks after the onset of SARS with a probable diagnosis of critical-illness polyneuropathy (CIP) and/or critical-illness myopathy (CIM) [9] . A case of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported with developing weakness and numbness in lower limbs and inability to walk with a likely diagnosis of critical illness polyneuropathy (CIP) [10] . Since no symptoms were present before the development of COVID-19 and toxic neuropathy was excluded after a review of all her medications, critical illness polyneuropathy (CIP) and Guillain-Barré syndrome (GBS) were considered to be the J o u r n a l P r e -p r o o f most likely diagnosis. cache = ./cache/cord-341000-9xs8aukq.txt txt = ./txt/cord-341000-9xs8aukq.txt === reduce.pl bib === id = cord-340970-389t032s author = Choy, Wai-Yan title = Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development date = 2004-06-01 pages = extension = .txt mime = text/plain words = 3526 sentences = 172 flesch = 51 summary = Background: The S (spike) protein of the etiologic coronavirus (CoV) agent of severe acute respiratory syndrome (SARS) plays a central role in mediating viral infection via receptor binding and membrane fusion between the virion and the host cell. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. The rabbit and monkey antisera against the synthetic peptides were diluted to 1:40-fold with PBS, and 10 L of each diluted serum was added to a well of the slide that was coated with SARS-CoV-infected African green monkey kidney Vero cells and incubated at 37°C for 1 h. The first batch of the rabbit and monkey antisera against the six synthetic peptides was collected 1 week after the second immunization and was tested for antibody specificity against the corresponding antigen (either conjugatefree or KLH-conjugated peptide) by ELISA analysis. cache = ./cache/cord-340970-389t032s.txt txt = ./txt/cord-340970-389t032s.txt === reduce.pl bib === id = cord-340579-cvze15cj author = Dudley, Joseph P title = Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1430 sentences = 74 flesch = 46 summary = There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 cache = ./cache/cord-340579-cvze15cj.txt txt = ./txt/cord-340579-cvze15cj.txt === reduce.pl bib === id = cord-340635-8wki7noy author = Yu, Bin title = Innate and adaptive immunity of murine neural stem cell-derived piRNA exosomes/microvesicles against pseudotyped SARS-CoV-2 and HIV-based lentivirus date = 2020-11-13 pages = extension = .txt mime = text/plain words = 6017 sentences = 300 flesch = 56 summary = Through testing pseudotyped SARS-CoV-2 and HIV-based lentivirus, this study reports that exosomes/microvesicles (Ex/Mv) isolated from murine hypothalamic neural stem/progenitor cells (htNSC) or subtype htNSCPGHM as well as hippocampal NSC have innate immunity-like actions against these RNA viruses. We then measured some of these piRNAs in NSC Ex/Mv (using htNSC PGHM and J o u r n a l P r e -p r o o f hpNSC as the representative) compared to the levels in MSC Ex/Mv. As shown in Fig. S2B and S3, most of these piRNAs were present in these NSC Ex/Mv but were much less detectable in MSC Ex/Mv. Our additional assays showed that htNSC PGHM were comparable or slightly stronger than htNSC in producing these piRNAs. Thus, based on the information from wildtype and pseudotyped SARS-CoV-2, NSC Ex/Mv contain piRNAs against the genomic sequences of both viruses, although these NSC were not previously exposed to either virus, suggesting that mouse species has evolved to establish large antiviral piRNA libraries in NSC Ex/Mv. We asked if an initial pre-exposure of a specific virus to NSC could lead to an enhancement or enrichment of specific antiviral piRNAs in NSC Ex/Mv. Thus, we treated these NSCs with pseudotyped SARS-CoV-2 virus for 2 generations, and then maintained them under normal culture for about 5 generations. cache = ./cache/cord-340635-8wki7noy.txt txt = ./txt/cord-340635-8wki7noy.txt === reduce.pl bib === id = cord-340746-icuzy3vp author = Liang, Yunfei title = Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date = 2005-08-01 pages = extension = .txt mime = text/plain words = 8408 sentences = 374 flesch = 47 summary = We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display. The full-length SARS-CoV N protein (amino acids 1-422) was expressed on the yeast cell surface, as indicated by reactivity of the Xpress epitope tag with the anti-Xpress antibody (Fig. 2) . We used heat denaturation of the fusion proteins tethered to the EBY100 yeast cell surface to categorize the specific linear and conformational SARS-CoV N protein mAb epitopes (35, 36 ) . Our subsequent determination of the antigenic structures of the N protein responsible for antibodies in polyclonal antisera from immunized mice and sera from convalescent SARS patients demonstrated the immunogenic specificity of 3 conformational (amino acids 1-69, 68 -213, and 337-422) and 3 linear (amino acids 1-69, 121-213, and 337-422) epitopes (Fig. 1C) . cache = ./cache/cord-340746-icuzy3vp.txt txt = ./txt/cord-340746-icuzy3vp.txt === reduce.pl bib === id = cord-340651-g3518bq2 author = Hsu, Chung-Hua title = An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study date = 2007-05-29 pages = extension = .txt mime = text/plain words = 3363 sentences = 210 flesch = 62 summary = title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study The cases were too few to be conclusive, the initial observations seem to indicate NHM appears to be safe in non-criticallly ill patients and clinical trials are feasible in the setting of pandemic outbreaks. In view of the possible beneficial effect of NHM on SARS or SARS-like infectious diseases, we conducted this randomized, double-blind clinical trial with placebo-control to examine its effectiveness. To our knowledge, this is the first double-blind and placebo-controlled clinical pilot study on supplementary treatment of SARS or SAR-like diseases. cache = ./cache/cord-340651-g3518bq2.txt txt = ./txt/cord-340651-g3518bq2.txt === reduce.pl bib === id = cord-341069-kngf6qpe author = Chan, Kwok-Hung title = Factors affecting stability and infectivity of SARS-CoV-2 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 749 sentences = 54 flesch = 67 summary = AIM: The aim of this study was to investigate the infectivity of SARS-CoV-2 under various environmental factors, disinfectants and different pH conditions. The viability of virus was determined after treatment with different disinfectants and pH solutions at room temperature (20∼25(o)C). SARS-CoV-2 could be detected under a wide range of pH conditions from pH4 to pH11 for several days and 1 to 2 days in stool at room temperature but lost 5 logs of infectivity. One hundred microliters of SARS-CoV-2 with 114 10 6.5 TCID 50 /ml was added into each bottles of 0.9 ml VTM and incubated at room temperature 115 (20-25 o C). When SARS-CoV-2 was added in VTM with pH ranging from 2 to 13, the virus remained 163 viable up to 6 days but lost between 2.9 and 5.33 logs of infectivity from pH5 to pH9 and up 164 to 1~2 days in pH4 and pH11 ( Table 2) . cache = ./cache/cord-341069-kngf6qpe.txt txt = ./txt/cord-341069-kngf6qpe.txt === reduce.pl bib === id = cord-341234-2zgfcrwc author = Hallak, Jorge title = Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3614 sentences = 178 flesch = 41 summary = title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil Recently, a group of 27 experts from 15 countries and five continents has argued that postponing andrological services and male infertility care during the COVID-19 pandemic could permanently compromise the prospects of biological parenthood for 'time-sensitive' patients, thus resulting in a devastating psychological impact on men undergoing fertility-related treatment (1) . A recent probabilistic pilot study conducted in seven districts of the city of São Paulo to estimate the prevalence of herd immunity showed that about 5.2% individuals had SARS-CoV-2 IgG antibodies, corresponding to an overall infection rate We reiterate that andrological services and male infertility care cannot be considered low priority during the current SARS-CoV-2 pandemic, particularly for the most vulnerable patients, like those with cancer, patients using immunosuppressive therapy, and the azoospermic/cryptozoospermic men under medical or post-surgical treatment to improve spermatogenesis. cache = ./cache/cord-341234-2zgfcrwc.txt txt = ./txt/cord-341234-2zgfcrwc.txt === reduce.pl bib === id = cord-340666-zl9pp2h3 author = Reifer, Josh title = SARS-CoV-2 IgG antibody responses in New York City date = 2020-07-21 pages = extension = .txt mime = text/plain words = 764 sentences = 56 flesch = 60 summary = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a strain of coronavirus that causes coronavirus disease 2019 (Covid-19) and has been declared a global pandemic by the World Health Organization. Additionally, for a subset of patients, we report on the correlation between SARS-CoV-2 patient symptom severity and level of SARS-CoV-2 IgG antibody found in the patient sample. We next sought to evaluate whether semi-quantitative SARS-CoV-2 IgG antibody levels were correlated to severity of symptoms as measured by the SSI. Levels of SARS-CoV-2 IgG antibody are plotted against SSI in Figure 2A . A linear regression analysis of the data indicates that SARS-CoV-2 IgG antibody levels are positively correlated with SSI (p-value < 0.01). In addition, we tested 28,523 patient specimens for SARS-CoV-2 IgG antibody levels for whom we did not obtain a SSI. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease Antibody responses to SARS-CoV-2 in patients with COVID-19 cache = ./cache/cord-340666-zl9pp2h3.txt txt = ./txt/cord-340666-zl9pp2h3.txt === reduce.pl bib === id = cord-340583-kjrxrk50 author = Castro‐Rodriguez, Jose A. title = Asthma and COVID‐19 in children – a systematic review and call for data date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3081 sentences = 172 flesch = 45 summary = Importantly, none of the largest epidemiological studies including children with COVID-19 reported clinical findings or underlying characteristics to help assess whether asthma -or other chronic lung diseases-constitutes a risk factor for SARS-CoV-2 infection or COVID-19 severity. Rather than a risk factor, a recent review of data in adults reported that both asthma and COPD appear to be under-represented in the comorbidities reported for patients with COVID-19, compared with global estimates of prevalence for these conditions in the general population (63) . After an extensive review of the current literature, only two reports included information on asthma as a potential risk factor for COVID-19 infection -but not severity or mortality-in children. However, the largest studies to date have been limited to a description of the number of cases by age group, and so it remains unclear whether childhood asthma -or other pediatric respiratory diseases-are associated with COVID-19 risk or severity. cache = ./cache/cord-340583-kjrxrk50.txt txt = ./txt/cord-340583-kjrxrk50.txt === reduce.pl bib === id = cord-340960-abanr641 author = Brigger, D. title = Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date = 2020-09-30 pages = extension = .txt mime = text/plain words = 4479 sentences = 289 flesch = 50 summary = In a mixed‐design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS‐CoV‐2 proteins and assessed the neutralizing activity of antibodies in patient sera. A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay (all collected in April 2020). Recombinantly expressed RBD has been used to establish an in-house ELISA for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in human serum samples (supplementary Fig. 1a,b) . A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay using ACE2-expressing Vero-E6 cells (34 inpatient samples, and 26 samples of medical personnel). cache = ./cache/cord-340960-abanr641.txt txt = ./txt/cord-340960-abanr641.txt === reduce.pl bib === id = cord-340992-88t1c0zs author = Nikolai, Lea A title = Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3092 sentences = 193 flesch = 44 summary = Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection cache = ./cache/cord-340992-88t1c0zs.txt txt = ./txt/cord-340992-88t1c0zs.txt === reduce.pl bib === id = cord-341045-75of9ys6 author = Shah, Abdullah title = Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1041 sentences = 64 flesch = 56 summary = By multiple sequence alignment of amino acids, we observed substitutions and deletion in S protein at 13 different sites in the isolates of five countries (China, USA, Finland, India and Australia) as compared to the reference sequence. Interestingly, in ORF8 substitution of Leucine, a nonpolar to Serine a polar amino acid at same position (aa84 L to S) in 23 isolates of five countries i.e. China, USA, Spain, Taiwan and India were observed, which may affect the conformation of peptides. Thus, we observed several mutations in the isolates thereafter the first sequencing of SARS-CoV-2 isolate, NC_045512.2, which suggested that this virus might be a threat to the whole world and therefore further studies are needed to characterize how these mutations in different proteins affect the functionality and pathogenesis of SARS-CoV-2. Thus, further studies are required to characterize how these amino acids substitutions in different proteins affect the functionality and pathogenesis of SARS-CoV-2. cache = ./cache/cord-341045-75of9ys6.txt txt = ./txt/cord-341045-75of9ys6.txt === reduce.pl bib === id = cord-341287-i1hyk962 author = Smith, Trevor R. F. title = Immunogenicity of a DNA vaccine candidate for COVID-19 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 7803 sentences = 446 flesch = 54 summary = Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. In subjects immunized with INO-4700 (MERS-CoV S protein DNA vaccine) durable neutralizing antibodies (nAbs) and T cell immune responses were measured, and a seroconversion rate of 96% was observed and immunity was followed for 60 weeks in most study volunteers 9 . We followed the induction of immunity by the selected immunogen in mice and guinea pigs, measuring SARS-CoV-2 S protein-specific antibody levels in serum and in the lung fluid, and antibody functionality through competitive inhibition of ACE2 binding, pseudovirus and live virus neutralization. In summary, humoral immunogenicity testing in both mice and guinea pigs revealed the COVID-19 vaccine candidate, INO-4800, was capable of eliciting functional blocking antibody responses to SARS-CoV-2 spike protein. cache = ./cache/cord-341287-i1hyk962.txt txt = ./txt/cord-341287-i1hyk962.txt === reduce.pl bib === id = cord-340799-1awmtj52 author = Krajewska, Joanna title = Review of practical recommendations for otolaryngologists and head and neck surgeons during the COVID-19 pandemic: Recommendations for otolaryngologists during the COVID-19 pandemic date = 2020-06-06 pages = extension = .txt mime = text/plain words = 7941 sentences = 395 flesch = 42 summary = Laryngectomy patients and individuals after tracheotomy with COVID-19 carry a particularly high risk of infecting ENT specialists and other members of medical staff as the way of breathing is these individuals is modified and enables the easy spread of SARS-CoV-2 containing aerosolized tracheal secretions [11] . In accordance with such high risk of infection, only emergency consultations and procedures should be performed by ENT specialists in times of COVID-19 pandemic in areas with confirmed SARS-CoV-2 cases [23, 28] . American Head and Neck Society, AAO-HNS, and the American Colleges of Surgeons, recommended that preoperative testing for SARS-CoV-2 presence should be performed in all individuals undergoing high-risk procedures [22, 30] . Patients with acute airway obstruction requiring tracheotomy should be considered as COVID-19 positive, as there is no time for SARS-CoV-2 testing in case of such urgent surgery [29] . cache = ./cache/cord-340799-1awmtj52.txt txt = ./txt/cord-340799-1awmtj52.txt === reduce.pl bib === id = cord-341254-xnj6slby author = Li, Hua title = A new and rapid approach for detecting COVID‐19 based on S1 protein fragments date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1945 sentences = 120 flesch = 46 summary = Based on it, the detection of IgM/IgG in blood became an optional approach to improve the diagnosis, especially for the COVID-19 patient with negative nucleic acid test result. 2. Colloidal gold-labeled mouse-antihuman lgM/lgG antibody was manufactured by SAIYA Hebei Biotechnology Co., Ltd. To obtain the well-performance antibody, the antibody was selected for functional test including the positive and negative coincidence rates, minimum test threshold, and accelerated stability. Due to only around 50% positive rate of SARS-CoV-2 nucleic acid test 8, 12 under various condition of sample collection and storage, viral infection regions, RNA extraction methods, the quality of nucleic acid detection kit, and so on, 13 detection of IgM/IgG became a powerful approach for the early diagnosis of COVID-19 and could help identify the patients with negative nucleic acid but with obvious clinical symptoms. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis cache = ./cache/cord-341254-xnj6slby.txt txt = ./txt/cord-341254-xnj6slby.txt === reduce.pl bib === id = cord-340821-kelq45dw author = Misrahi, James J. title = HHS/CDC Legal Response to SARS Outbreak date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1856 sentences = 65 flesch = 35 summary = Before the severe acute respiratory syndrome (SARS) outbreak, the Centers for Disease Control and Prevention's (CDC) legal authority to apprehend, detain, or conditionally release persons was limited to seven listed diseases, not including SARS, and could only be changed using a two-step process: 1) executive order of the President of the United States on recommendation by the Secretary, U.S. Department of Health and Human Services (HHS), and 2) amendment to CDC quarantine regulations (42 CFR Parts 70 and 71). Recognizing the cross border nature of some communicable diseases and in light of this nation's constitutional structure, section 361 of the Public Health Service Act (42 United States Code section 264) authorizes the Health and Human Services (HHS) Secretary to make and enforce regulations necessary to prevent the introduction, transmission, and spread of communicable diseases from foreign countries into the United States and from one state or possession into another. cache = ./cache/cord-340821-kelq45dw.txt txt = ./txt/cord-340821-kelq45dw.txt === reduce.pl bib === id = cord-341176-83khavoh author = Lotfi, Melika title = CRISPR/Cas13: A potential therapeutic option of COVID-19 date = 2020-09-17 pages = extension = .txt mime = text/plain words = 5287 sentences = 274 flesch = 49 summary = In contrast to traditional vaccines and therapies, which rely on priming the human immune system to identify viral proteins and components and reduce viral entrance into cells (12) , the CRISPR-based system has focused on identifying and degrading the intracellular viral genome and its resulting viral mRNAs. Thus, for using CRISPR as a therapeutic option, it is critical to identify the SARS-CoV-2 molecular characteristics. They found that the two highly-conserved regions in SARS-CoV-2 genome, which can be appropriate to be targeted by PAC-MAN as a potential pan-coronavirus inhibition strategy are respectively the RNA-dependent RNA polymerase (RdRP) gene in the open reading frame1a/b or ORF1a/b region, which maintains the proliferation of all coronaviruses, and the Nucleocapsid (N) gene at the 3' end of the genome, which encodes the capsid protein for viral packaging (13) . cache = ./cache/cord-341176-83khavoh.txt txt = ./txt/cord-341176-83khavoh.txt === reduce.pl bib === id = cord-340656-ltd6ueoi author = Grant, Michael C. title = The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3435 sentences = 199 flesch = 48 summary = title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries Furthermore, with few included studies (30 in the largest and most recent [12] ), the range of symptoms were limited and the estimates of prevalence are likely to be upwardly biased because only unwell patients (largely those admitted to hospital) were tested in the early phase of the outbreak. We excluded case reports, articles which failed to disaggregate symptoms in adult and paediatric cohorts, studies of patients with prior respiratory infections (e.g. tuberculosis) or co-infections with other viruses (e.g. similar viruses SARS-CoV-1 or HCoV-EMC/2012, etc) and articles which we are unable to translate to English in a timely fashion. Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: A retrospective single center analysis Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-340656-ltd6ueoi.txt txt = ./txt/cord-340656-ltd6ueoi.txt === reduce.pl bib === id = cord-340857-teq5txm9 author = Galloro, Giuseppe title = SAFETY IN DIGESTIVE ENDOSCOPY PROCEDURES IN THE COVID ERA RECOMMENDATIONS IN PROGRES OF THE ITALIAN SOCIETY OF DIGESTIVE ENDOSCOPY date = 2020-05-13 pages = extension = .txt mime = text/plain words = 3414 sentences = 177 flesch = 49 summary = Based on the most recent scientific literature and strong statements by the most prestigious international health institutions, the Italian Society of Digestive Endoscopy has drawn up some recommendations about the use of personal protective equipment, the correct way of dressing and undressing of endoscopists and nurses, before and after digestive endoscopy procedures. In addition the CDC and some other Authors detected the virus in the feces of CoViD-19 positive patients (in up to 54% of the cases), suggesting a potential fecal-oral transmission (31, 32) . A recent ad-interim guidance, about the preventive measures of infection control (shown in table 3 ) and about the right use of appropriate PPE for healthcare workers performing endoscopy on subjects with CoViD-19, has been published by the WHO (45) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus infected pneumonia in Wuhan, China. cache = ./cache/cord-340857-teq5txm9.txt txt = ./txt/cord-340857-teq5txm9.txt === reduce.pl bib === id = cord-340811-w4x4falm author = Frizzelli, Annalisa title = What happens to people’s lungs when they get coronavirus disease 2019? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1779 sentences = 106 flesch = 46 summary = Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-340811-w4x4falm.txt txt = ./txt/cord-340811-w4x4falm.txt === reduce.pl bib === id = cord-341246-fz66z2p2 author = Bhattacharyya, Pranab J title = Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1298 sentences = 84 flesch = 48 summary = title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection A 32-year-old primigravida at a 38-week gestation was initially admitted in cardiology isolation ward on referral by her local obstetrician for inferolateral ST-segment elevation on ECG (figure 1A) which was obtained for complaints of New York Heart Association functional class II symptoms with palpitations of a 3-day duration. As typified by this index case, TTC can mimic acute ST-segment elevation myocardial infarction and is considered to be a reversible form of cardiomyopathy characterised by a complete recovery of RWMA and LV function within weeks of presentation. 2 This is the first reported case of TTC in pregnancy as a manifestation of SARS-CoV-2 infection during this ongoing pandemic. ► The presentation of takotsubo cardiomyopathy can mimic STsegment elevation myocardial infarction but in the absence of angiographic evidence of significant obstructive coronary artery disease. cache = ./cache/cord-341246-fz66z2p2.txt txt = ./txt/cord-341246-fz66z2p2.txt === reduce.pl bib === id = cord-341284-jmqdnart author = Panagopoulos, Periklis title = Lopinavir/ritonavir as a third agent in the antiviral regimen for SARS-CoV-2 infection date = 2020-06-12 pages = extension = .txt mime = text/plain words = 1548 sentences = 106 flesch = 53 summary = Further studies are needed in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection. 9 The aim of the present study was to assess the impact of lopinavir/ritonavir as a third agent for the treatment of SARS COV 2 infection especially for patients with severe pneumonia emphasizing in the number of days needed for reduction of viral load. However, the number of days needed for the first negative result of RT-PCR for SARS-CoV-2 was significantly lower for patients of group A. The present study suggests that lopinavir/ritonavir could be a potential effective choice in treatment of patients with CoVID-19. 12 However, a retrospective study conducted in China including 134 patients with CoVID-19 showed no effect on accelerating the clearance of SARS-CoV-2. Further studies are needed with larger patient series in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection and confirm the findings of the present study. cache = ./cache/cord-341284-jmqdnart.txt txt = ./txt/cord-341284-jmqdnart.txt === reduce.pl bib === id = cord-340984-blkhfhe2 author = Gklinos, Panagiotis title = Neurological manifestations of COVID-19: a review of what we know so far date = 2020-05-26 pages = extension = .txt mime = text/plain words = 2665 sentences = 139 flesch = 45 summary = Prompt diagnosis and immediate management of the neurological manifestations of the novel coronavirus will not only improve the prognosis of COVID-19 patients but will also prevent the dissemination of the disease due to misdiagnosed cases. COVID-19 is confirmed to be caused by a novel coronavirus (2019 novel coronavirus, 2019-nCoV) and presents with symptoms similar to those of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. However, neurological manifestations of the novel coronavirus are not precepted by all clinicians, thus, leading to inappropriate management of COVID-19 patients presenting with non-specific neurological symptoms initially. This article aims to review the cases, which reported neurological symptoms at presentation or during the course of the disease and discuss the potential mechanisms of Central Nervous System (CNS) involvement in COVID-19. The other study is a retrospective case series in Wuhan, China, which reported the neurological symptoms of COVID-19 patients [13] . cache = ./cache/cord-340984-blkhfhe2.txt txt = ./txt/cord-340984-blkhfhe2.txt === reduce.pl bib === id = cord-340942-oatf59k0 author = Magalhães, Jurandy Júnior Ferraz de title = Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil date = 2020-09-21 pages = extension = .txt mime = text/plain words = 3949 sentences = 225 flesch = 59 summary = METHODS: In this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for SARS-CoV-2 living in Pernambuco state, Northeast Brazil. Here, we describe for the first time the clinical, epidemiological and demographic features of the first 557 laboratory-confirmed COVID-19 cases in Pernambuco state, Northeast Brazil, who were diagnosed between March 12 and April 22, 2020. Patient epidemiological information, demographic and clinical characteristics, including medical history, signs and symptoms, laboratory findings, underlying co-morbidities, and date of disease onset were obtained from electronic medical records of the Pernambuco Central Public Health Laboratory (LACEN) and analyzed. Regarding the distribution of COVID-19 cases in the different household income ranges (Fig. 1B) , we found that SARS-CoV-2 infections occurred in neighborhoods with greater purchasing power. Here, we described for the first time the epidemiological and clinical characteristics of the first 557 consecutive patients diagnosed with SARS-CoV-2 in the state of Pernambuco between 12 March and April 22, 2020. cache = ./cache/cord-340942-oatf59k0.txt txt = ./txt/cord-340942-oatf59k0.txt === reduce.pl bib === id = cord-341396-0tn06al2 author = Ni, Ling title = Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals date = 2020-05-03 pages = extension = .txt mime = text/plain words = 2100 sentences = 128 flesch = 64 summary = In this study, we collected blood from COVID-19 patients who have recently become 5 virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody 6 and T cell responses. NP-and S-RBD-specific 9 IgM and IgG antibodies were both detected in the sera of newly discharged patients, 10 compared with healthy donor groups. Anti-SARS-CoV-2 IgG antibodies were also more 11 obviously observed than IgM in the follow-up patients (#9-14), when compared with healthy 12 donors ( Figure 1B ). As shown in Figure 3C , compared with healthy donors, 25 the numbers of IFN-γ-secreting NP-specific T cells in patients #1, 2, 4, 5 and 8 were much 26 higher than other patients, suggesting that they had developed SARS-CoV-2-specific T cell responses. More interestingly, when combining all 14 patients in our analysis, there 9 was a significant correlation between the neutralizing antibody titers and the numbers of NPIn this study, we characterized SARS-CoV-2-specific humoral and cellular immunity in 2 recovered patients. cache = ./cache/cord-341396-0tn06al2.txt txt = ./txt/cord-341396-0tn06al2.txt === reduce.pl bib === id = cord-341416-6bh08901 author = Smithgall, Marie C. title = Laboratory Testing of SARS CoV-2: A New York Institutional Experience date = 2020-07-19 pages = extension = .txt mime = text/plain words = 2923 sentences = 161 flesch = 47 summary = The World Health Organization developed the first quantitative RT-PCR test for detecting SARS-CoV-2 and subsequently the U.S. Centers for Disease Control and Prevention (CDC) began shipping its own RT-PCR test kits after receiving Emergency Use Authorization (EUA) by the U.S. Food and Drug Administration (FDA) on February 4, 2020. To date there are more than 80 commercial laboratories and/or test kit manufacturers that have received approval for emergency use by the Federal Drug Administration (FDA) for SARS-CoV-2 testing with molecular assays accounting for the vast majority [6] . In addition, the FDA recently granted EUA for an RT-PCR lab developed test for qualitative detection of SARS-CoV-2 in saliva specimens and a test that uses a home collection kit with nasal swabs [6] for details see https://www.fda.gov/emergency-preparednessand-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization]. During this time, termed the "window period," a patient who is infected with SARS-CoV-2, but has not yet produced antibodies, would test negative on such an assay. cache = ./cache/cord-341416-6bh08901.txt txt = ./txt/cord-341416-6bh08901.txt === reduce.pl bib === id = cord-341543-gcnph9gf author = Kuryntseva, P. title = A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1831 sentences = 123 flesch = 55 summary = The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of wastewater samples and their serial dilutions but the approach excludes usage of concentration techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. In the modelling experiment with the excreta of ten COVID-19 235 patients, it was demonstrated that the minimal rate of infected people in the community that can 236 be detected by this method is 10-2%. cache = ./cache/cord-341543-gcnph9gf.txt txt = ./txt/cord-341543-gcnph9gf.txt === reduce.pl bib === id = cord-341502-jlzufa28 author = Lee, Sungyul title = The SARS-CoV-2 RNA interactome date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5845 sentences = 362 flesch = 51 summary = The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). cache = ./cache/cord-341502-jlzufa28.txt txt = ./txt/cord-341502-jlzufa28.txt === reduce.pl bib === id = cord-341101-5yvjbr5q author = Hashem, Anwar M. title = Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4823 sentences = 275 flesch = 43 summary = While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro cache = ./cache/cord-341101-5yvjbr5q.txt txt = ./txt/cord-341101-5yvjbr5q.txt === reduce.pl bib === id = cord-341453-9yrvjlpx author = Clay, Candice C title = Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses date = 2014-03-19 pages = extension = .txt mime = text/plain words = 8130 sentences = 395 flesch = 48 summary = The aim of this study was to determine how the peripheral and mucosal immune responses to SARS-CoV infection compare in the aged and juvenile nonhuman primate host and to determine how this may impact viral replication levels. No virus was detected in any sample collected from either age group at 10 d.p.i. To determine if advanced age correlated with increased severity of lung pathology, a comprehensive histological analysis of the respiratory tract following SARS-CoV infection was conducted in aged and juvenile animals. To determine how mucosal cytokines in SARS-CoV infection compared to systemic responses and how age may impact mucosal cytokine expression; the inflammatory protein profile was evaluated by bead-based arrays in standardized-collected lung tissue from the proximal portion of the right caudal lobe. Although no age-dependent differences were observed in the frequency of naïve (CD45RA + CCR7+) CD8 T cells in peripheral blood, there were significantly lower levels of these cells in the lung and lymph node of aged animals during SARS-CoV infection ( Figure 6A -C; unpaired student T-tests). cache = ./cache/cord-341453-9yrvjlpx.txt txt = ./txt/cord-341453-9yrvjlpx.txt === reduce.pl bib === id = cord-341524-zvic4xc9 author = KARAKURT, Hamza Umut title = Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks date = 2020-06-21 pages = extension = .txt mime = text/plain words = 3611 sentences = 192 flesch = 45 summary = We analysed transcriptome of SARS-CoV-2 infected human lung epithelial cells, compared it with mock-infected cells, used network-based reporter metabolite approach and integrated the transcriptome data with protein-protein interaction network to elucidate the early cellular response. The response in signalling pathways, gene expression, protein levels and metabolic profiles are regulated as a result of interactions in multilayer biological networks, hence a holistic view of the cellular response can be elucidated by an integrated approach. Here, we provide an analysis of transcriptional response after 24 h of infection, further, we integrated transcriptome profile with metabolic and protein-protein interaction networks to reveal multilayer mechanistic details of the SARS-CoV-2 infection in NHBE cells. Significant upregulation in expression of matrix metalloproteinase 9 (MMP9) in NHBE cells indicates that drugs which target MMP9 have potential uses in SARS-CoV-2 infection. This complex network structure between signalling pathways indicated that RAGE receptor targeting drugs have the potential to be used in SARS-CoV-2 patients to suppress symptoms. cache = ./cache/cord-341524-zvic4xc9.txt txt = ./txt/cord-341524-zvic4xc9.txt === reduce.pl bib === id = cord-341648-z4lflkmo author = Isaacs, David title = To what extent do children transmit SARS‐CoV‐2 virus? date = 2020-06-16 pages = extension = .txt mime = text/plain words = 576 sentences = 50 flesch = 63 summary = A current child care outbreak in Sydney was initiated and spread by infected adults. 6 An unreviewed study of 15 New South Wales schools found nine staff and nine students who had tested positive for SARS-CoV-2. 7 It is possible that asymptomatic and mildly infected children are important transmitters of SARS-CoV-2, but the evidence to date suggests children rarely spread the virus. 8 Studies suggest school closures in China, Hong Kong and Singapore had little or no effect on control of the 2003 outbreak with the related SARS virus, which like infection with SARS-CoV-2 was much milder in children than adults. 9 In conclusion, the available evidence to date suggests children are unlikely to be major transmitters of SARSEpidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China School closure and management practices during coronavirus outbreaks including COVID-19: A systematic review cache = ./cache/cord-341648-z4lflkmo.txt txt = ./txt/cord-341648-z4lflkmo.txt === reduce.pl bib === id = cord-341415-g781zhu6 author = Jhaveri, Kenar D. title = Thrombotic microangiopathy in a patient with COVID-19 date = 2020-06-07 pages = extension = .txt mime = text/plain words = 1002 sentences = 86 flesch = 51 summary = We describe a patient with coronavirus disease 2019 (COVID-19) and clinically significant kidney biopsy proven thrombotic microangiopathy(TMA). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was confirmed in the patient by reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay or serologic testing at our center. On day 20, the patient underwent a kidney biopsy that revealed severe acute thrombotic microangiopathy with cortical necrosis (Figure 1 ). While beta 2 glycoprotein-1 IgM levels were elevated, other laboratory and clinical features of anti-phospholipid antibody were absent( Table 2) . We report the first case of TMA associated with SARS-CoV-2 with presence of diffuse cortical necrosis and widespread microthrombi in the kidney biopsy. Physicians treating patients with COVID-19 should keep microangiopathic disease in the differential diagnosis when systemic findings of hemolysis are present along with thrombocytopenia and AKI. Coagulopathy and Antiphospholipid Antibodies in Patients with Covid-19 Acute Kidney injury in patients hospitalized with COVID cache = ./cache/cord-341415-g781zhu6.txt txt = ./txt/cord-341415-g781zhu6.txt === reduce.pl bib === id = cord-341474-06113cn0 author = Huynh, Tien title = In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease date = 2020-05-14 pages = extension = .txt mime = text/plain words = 5393 sentences = 259 flesch = 56 summary = Besides the identification of several high-potency drugs and/or molecules, we unveiled the consensus binding mechanism that a ligand prefers to bind the "anchor" site of the Mpro pocket, which might facilitate the future design and optimization of an inhibitor for the SARS-CoV-2's Mpro. To verify the docking results, as an example, we further performed the MD simulation to investigate the stability of entecavir's pose with the best affinity score inside the Mpro pocket (Figure 5a ). As shown in Figure 3c , our docking result verifies that the Boc group indeed occupies the "anchor" site, further validating the binding mechanisms discovered in this work for stabilizing the ligand inside the Mpro's pocket. We found that the docking affinity scores of several molecules (such as nelfinavir and entecavir) are very close to those of the ligands found experimentally (N3 and O6K), and their binding stabilities with the Mpro were verified in MD simulations. cache = ./cache/cord-341474-06113cn0.txt txt = ./txt/cord-341474-06113cn0.txt === reduce.pl bib === id = cord-341331-l24oe2pd author = Zheng, Baojia title = An increasing public health burden arising from children infected with SARS‐CoV2: a systematic review and meta‐analysis date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3322 sentences = 214 flesch = 52 summary = Therefore, it is valuable to perform a comprehensive analysis of the different published SARS-CoV2 pediatric cases recording clinical and epidemiological features, merging and This article is protected by copyright. The included studies were required to meet the following eligibility criteria: (1) studies focused on pediatric patients infected with SARS-CoV2 whose nucleic acid test or CT scan were positive; (2) retrospective observational studies, case reports or research articles describing the epidemiological, demographic, and clinical features of confirmed cases, which allowed stratification; and (3) a minimum size of patients (n>3) to conduct a meta-analysis. analysis, aiming to evaluate the features and situation of the children infected with SARS-CoV2 and their possibly increasing health burden on the public. In our study, we found that the proportion of asymptomatic infections in children was high; both males and females were susceptible to SARS-CoV2. cache = ./cache/cord-341331-l24oe2pd.txt txt = ./txt/cord-341331-l24oe2pd.txt === reduce.pl bib === id = cord-341670-o1v63zg8 author = Estevez-Ordonez, Dagoberto title = Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage date = 2020-05-20 pages = extension = .txt mime = text/plain words = 887 sentences = 59 flesch = 54 summary = title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage Postoperative cerebrospinal fluid (CSF) samples were also tested for SARS-CoV-2 viral ribonucleic acid (RNA), which was not detected. CSF sample was obtained on hospital day 6, 5 d after testing positive for SARS-CoV-2 and evaluated by RT-qPCR. At 20 d, no one involved in her care has reported symptoms of infection with COVID-19 or has tested positive for SARS-CoV-2. Testing of CSF in a SARS-CoV-2-infected patient is also reported here, which to our knowledge has not been documented in the peered-reviewed literature. The present approach to the management of this patient with aSAH may provide some insight when caring for patients with urgent/emergent surgical pathologies in the setting of SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges cache = ./cache/cord-341670-o1v63zg8.txt txt = ./txt/cord-341670-o1v63zg8.txt === reduce.pl bib === id = cord-341804-rnj3wtg4 author = Jin, Zhe title = Drug treatment of coronavirus disease 2019 (COVID-19) in China. date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2048 sentences = 136 flesch = 43 summary = This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. However, more evidence is needed either for 4 supporting or opposing the systemic therapeutic administration of glucocorticoids in 5 patients with SARS-CoV-2 infection (Qin et al., 2020 a variety of immune cells 20 and improves the immunity, while IFN-β takes effect by inhibiting the adsorption of certain 1 viruses, enhancing phagocytosis of natural killer cells and mononuclear macrophages Tocilizumab is a recombinant humanized anti-IL-6 receptor (IL-6R) monoclonal antibody, 21 13 which can specifically bind to soluble and membrane-bound IL-6 receptors and inhibit 1 signal transduction mediated by IL-6, thereby reducing inflammation and blocking cytokine 2 storm caused by COVID-19 (Scheinecker et al., 2009) . cache = ./cache/cord-341804-rnj3wtg4.txt txt = ./txt/cord-341804-rnj3wtg4.txt === reduce.pl bib === id = cord-341838-lkz8ro90 author = Gervasoni, Cristina title = Clinical features and outcomes of HIV patients with coronavirus disease 2019 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1794 sentences = 117 flesch = 59 summary = The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. cache = ./cache/cord-341838-lkz8ro90.txt txt = ./txt/cord-341838-lkz8ro90.txt === reduce.pl bib === id = cord-341531-w788qwya author = Montero Feijoo, A. title = Practical recommendations for the perioperative management of patients with suspicion or serious infection by coronavirus SARS-CoV date = 2020-05-04 pages = extension = .txt mime = text/plain words = 3716 sentences = 202 flesch = 44 summary = Protective measures should be maximised when caring for patients with confirmed infection, in critically ill patients with a high viral load, and in patients that require invasive aerosol-generating procedures and manoeuvres such as aerosol therapy and nebulisation, aspiration of respiratory secretions, bag-mask ventilation, non-invasive ventilation, intubation, respiratory sampling, bronchoalveolar lavage, tracheostomy or cardiopulmonary resuscitation. If postoperative surveillance is necessary, it will be carried out in adequately monitored isolation units, preferably with negative pressure Avoid using aerosols, high-flow nasal oxygen or non-invasive ventilation as far as possible in patients requiring postoperative oxygen therapy Healthcare personnel who care for patients during postoperative surveillance must wear appropriate personal protective equipment at all times and must be taught donning and doffing techniques The same recommendations for transferring patients to the operating room apply to postoperative transfer cache = ./cache/cord-341531-w788qwya.txt txt = ./txt/cord-341531-w788qwya.txt === reduce.pl bib === id = cord-341783-e7xz4utr author = Vistisen, Simon T. title = Risk and prognosis of COVID-19 in patients treated with renin–angiotensin–aldosterone inhibitors date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1907 sentences = 99 flesch = 47 summary = 2 Because ACE2 plays an important role in the renin-angiotensin system and also acts as a receptor for SARS-CoV-2 cell entry, hypotheses about an association between ACEi/ARBs and COVID-19 outcomes were rapidly generated. Nevertheless, based on these initial observational findings, there seems to be no increased risk of SARS-CoV-2 infection for ACEi/ARB users. Four studies examined the prognosis of COVID-19 patients and uniformly found that risk of severe outcomes was not higher for the collapsed group of ACEi and ARB 740 Vistisen et al. The transmembrane angiotensin-converting enzyme 2 receptor allows SARS-CoV-2 entry and leads to virus replication, activation of innate immune system/complement, cytokine formation followed by neutrophils/lymphocytes in the lung and development of acute respiratory distress syndrome (ARDS). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China cache = ./cache/cord-341783-e7xz4utr.txt txt = ./txt/cord-341783-e7xz4utr.txt === reduce.pl bib === id = cord-341819-emjg3dsw author = Kouznetsova, Valentina L. title = Potential COVID-19 papain-like protease PL(pro) inhibitors: repurposing FDA-approved drugs date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3312 sentences = 178 flesch = 54 summary = Using the crystal structure of SARS-CoV-2 papain-like protease (PL(pro)) as a template, we developed a pharmacophore model of functional centers of the PL(pro) inhibitor-binding pocket. In a previous report, we (Kouznetsova, Huang & Tsigelny, 2020 ) and others (Kandeel & Al-Nazawi, 2020; Arya et al., 2020; Plewczynski et al., 2007; Ton et al., 2020) have used molecular modeling studies to identify FDA-approved drugs and other compounds (Arya et al., 2020; Ton et al., 2020; Alamri, Tahir ul Qamar & Alqahtani, 2020) that are predicted to bind to 3CL pro . Based on the crystal structure of SARS-CoV-2 PL pro (PDB ID: 6W9C), we developed two pharmacophore models of the binding pocket of this protein. We developed a pharmacophore model of the binding pocket site S3/S4 of COVID-19 PL pro then conducted multi-conformational docking of these drug compounds to this site for ranging the potential inhibitors selected by pharmacophore-based search. Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs cache = ./cache/cord-341819-emjg3dsw.txt txt = ./txt/cord-341819-emjg3dsw.txt === reduce.pl bib === id = cord-341776-y7kpp10x author = Hamm, C. title = Zusammenhang zwischen Angiotensinblockade und Influenza-A-Inzidenz date = 2020-06-05 pages = extension = .txt mime = text/plain words = 286 sentences = 45 flesch = 51 summary = key: cord-341776-y7kpp10x cord_uid: y7kpp10x So wird unter anderem diskutiert, ob Medikamente, die auf das Renin-Angiotensin-Aldosteron-System (RAAS) wirken, für eine Infektion mit Coronaviren sensibilisieren. Bekannt ist, dass ACE2-Rezeptoren bei Influenza-A-induzierten Lungenschäden, insbesondere beim schweren akuten respiratorischen Syndrom (SARS), eine wichtige Rolle spielen. Ziel der im Folgenden vorgestellten epidemiologischen Studie war es daher, den Zusammenhang zwischen der Häufigkeit einer Influenzainfektion und der Therapie mit ACE-Hemmern bzw. Obwohl nicht sicher ist, ob diese Beobachtung auch auf SARS-CoV-2 übertragbar ist, ist sie in der derzeitigen Pandemieunsicherheit ein Beitrag, der bei eingeschränkten Therapieoptionen hohe Aufmerksamkeit hervorrufen muss. Wenn das Risiko zu erkranken geringer ist, verläuft dann die Erkrankung auch anders? Insgesamt stützt diese Beobachtung derzeit sicherlich die Empfehlung aller kardiologischen und Hypertoniefachgesellschaften [5] , die Therapie mit ACE-Hemmern oder ARB auch in Zeiten der COVID-19-Pandemie uneingeschränkt fortzuführen. Renin-angiotensin-aldosterone system blockers and the risk of Covid-19 Renin-angiotensin-aldosteronesysteminhibitors and risk of Covid-19 cache = ./cache/cord-341776-y7kpp10x.txt txt = ./txt/cord-341776-y7kpp10x.txt === reduce.pl bib === id = cord-341701-zropd3mo author = Adhikari, Subash title = A high-stringency blueprint of the human proteome date = 2020-10-16 pages = extension = .txt mime = text/plain words = 10138 sentences = 533 flesch = 33 summary = During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. • Be a focal point for life sciences researchers, pathologists, clinicians and industry communities seeking to translate and leverage proteomic and proteogenomic data to improve human health through: (i) greater understanding of the molecular mechanisms of common and rare diseases, (ii) identification of pathophysiological changes to generate disease and wellness diagnostic biomarkers, and (iii) development of new effective and safe personalized therapeutics. The HPP Ab Resource Pillar, ostensibly led by the Human Protein Atlas (HPA; www.proteinatlas.org), was initiated in 2003 and uses Ab-based strategies to analyse spatio-temporal aspects of the proteome 39 . Community encouragement to identify biological data that complement high-stringency MS strategies to accelerate discovery and understanding of human proteome PE2,3,4 missing proteins. cache = ./cache/cord-341701-zropd3mo.txt txt = ./txt/cord-341701-zropd3mo.txt === reduce.pl bib === id = cord-341620-nmrkhx5t author = Chirico, Francesco title = Can Air-Conditioning Systems Contribute to the Spread of SARS/MERS/COVID-19 Infection? Insights from a Rapid Review of the Literature date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4577 sentences = 241 flesch = 44 summary = Therefore, to evaluate the COVID-19 risk associated with the presence of air-conditioning systems, we conducted a rapid review of the literature concerning outbreaks of coronaviruses (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) in indoor environments. We utilized the participants-exposure-comparisons-outcome (PECOS) criteria, and we defined them according to evidence-based practice [32] -P (participants) is human subjects residing in indoor environments, E (exposure) is exposed to air-conditioning systems (HVAC), C (comparisons) is any comparison between the pathogens under study, and O (outcome) is respiratory infection outbreaks caused by SARS-CoV-1, MERS-CoV, or SARS CoV-2. A retrospective study of on outbreak involving 74 patients in the same hospital indicated that the rapid evaporation of the droplets produced by coughing in a relatively dry, air-conditioned environment, could also induce virus-laden aerosol, which was probably responsible for spreading the infection to patients who were not in the same room [35] . cache = ./cache/cord-341620-nmrkhx5t.txt txt = ./txt/cord-341620-nmrkhx5t.txt === reduce.pl bib === id = cord-342091-xus5kxs0 author = YAVARIAN, Jila title = First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1241 sentences = 80 flesch = 59 summary = In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. Here we report the first cases of SARS-CoV-2 infections in Qom, central Iran in Feb 2020. Collectively seven patients' residents of Qom City were positive for SARS-CoV-2 on Feb 19 in Iran. We identified the first cases of SARS-CoV-2 in Qom city, Iran with unclear transmission route. Futureresearch should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. cache = ./cache/cord-342091-xus5kxs0.txt txt = ./txt/cord-342091-xus5kxs0.txt === reduce.pl bib === id = cord-342139-t2tukk0z author = Livingston, Gill title = Prevalence, management, and outcomes of SARS-CoV-2 infections in older people and those with dementia in mental health wards in London, UK: a retrospective observational study date = 2020-10-05 pages = extension = .txt mime = text/plain words = 6631 sentences = 318 flesch = 54 summary = For individuals, the following data were collected: demographic data (age, sex, ethnicity); mental health clinical details (ie, dementia or other diagnosis); Mental Health Act 1983 or Mental Capacity Act 2005 status 31 (these are legislative frameworks for those with mental illness, including an absence of decisional capacity, which in defined circumstances allow people to be detained in a hospital without giving consent); physical comorbidities; and COVID-19-related details, which were COVID-19 clinical diagnosis (date of clinical suspicion of COVID-19 and SARS-CoV-2 RT-PCR test result or results, if retested), possible COVID-19 symptoms (first symptom noted, presence of new persistent cough, shortness of breath [respiratory rate >20 breaths per min], temperature ≥37·8°C, new loss of smell or taste, sore throat, gastrointestinal symptoms, fatigue, loss of appetite, asymptomatic, duration of symptoms [days]), change to mental state related to COVID-19 (increased cognitive impairment or delirium, increased or new mood disturbance or psychosis); and manage ment (do not attempt resuscitation status; whether the patient was receiving vitamin D treatment; isolation of patients and duration [days] if applicable; whether venous thromboembolism [VTE] prophylaxis was given before the patient became symptomatic; whether VTE prophylaxis was given after symptoms developed; whether antipsychotic medication had been stopped, started, or increased during SARS-CoV-2 infection and treatment, and new antipsychotic sideeffects; whether prophylactic antibiotics were prescribed for community-acquired pneumonia or hospital-acquired pneumonia; whether oxygen therapy was administered on the ward; and whether the patient was transferred to a medical ward in a general hospital). cache = ./cache/cord-342139-t2tukk0z.txt txt = ./txt/cord-342139-t2tukk0z.txt === reduce.pl bib === id = cord-342013-k54u2q0d author = Martenot, Antoine title = Favorable outcomes among neonates not separated from their symptomatic SARS-CoV-2-infected mothers date = 2020-11-03 pages = extension = .txt mime = text/plain words = 1944 sentences = 124 flesch = 55 summary = 1, 2 Although neonates born of mothers infected with SARS-CoV-2 during pregnancy are seemingly vulnerable to infection, studies have found that they were not at a high risk for severe infection and were very rarely affected by COVID-19. This strategy involved preservation of continuous mother-infant proximity with specific hygienic measures, breast milk as the main source of feeding, early discharge with home isolation, and a structured follow-up with hospital-assisted home care. Breastfeeding may protect against the horizontal transmission of SARS-CoV-2, as specific antibodies against this virus have been found in the breast milk of a COVID-19-infected mother. 19 Our results support early postnatal proximity, despite many mothers worldwide being separated from their newborn infants during the COVID-19 pandemic. Even during the COVID-19 pandemic, safely maintaining familycentered perinatal care and continuing the promotion of bonding between neonates and their SARS-CoV-2-positive mothers appear possible, as these newborns are very rarely infected and, if infected, show only mild symptoms. cache = ./cache/cord-342013-k54u2q0d.txt txt = ./txt/cord-342013-k54u2q0d.txt === reduce.pl bib === id = cord-342024-kaku49xd author = Espejo, Andrea P title = Review of Current Advances in Serologic Testing for COVID-19 date = 2020-06-25 pages = extension = .txt mime = text/plain words = 6480 sentences = 373 flesch = 50 summary = • The use of total antibody or simultaneous IgG/IgM measurements (regardless of method) significantly adds sensitivity to reverse transcription polymerase chain reaction testing protocols early post onset of symptoms and becomes the most accurate diagnostic test at later time points. The SP, RBD, and NP proteins appear to be the main targets of the humoral immune response in coronavirus infections including SARS-CoV-2 and were the antigens used in the majority of the serologic assays examined in this literature review. Overall, while these results are similar to that reported in a review of serologic testing for MERS-CoV and SARS-CoV, they may have been affected by choice of target antigens, the various immunoassay kits, and the level of detail of case history used to categorize the time of sample acquisition post onset of symptoms. cache = ./cache/cord-342024-kaku49xd.txt txt = ./txt/cord-342024-kaku49xd.txt === reduce.pl bib === id = cord-341970-pho6dksc author = Huang, Jun title = Immunization with SARS-CoV S DNA vaccine generates memory CD4(+) and CD8(+) T cell immune responses date = 2006-06-05 pages = extension = .txt mime = text/plain words = 4417 sentences = 259 flesch = 64 summary = In the present study, mice were immunized i.m. with SARS-CoV S DNA vaccine, and three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses when the cells were stimulated in vitro with a pool of peptides overlapping entire SARS spike protein. Moreover, mice boosted with SARS S DNA vaccine exhibited a 3-30-fold increase in the frequency of IFN-␥-producing cells in spleens (P < 0.01) and lymph nodes (P < 0.05), respectively (Fig. 1) , compared with the prime immunization. To further ascertain whether the frequency of SARS-CoV S specific CD4 + and CD8 + T cell responses was increased after boost vaccination, mice were boosted i.m. with SARS-CoV S DNA vaccine, seven days after injection, IFN-␥-and IL-2-producing CD4 + and CD8 + T cells were determined in lymph nodes, spleen and lungs. cache = ./cache/cord-341970-pho6dksc.txt txt = ./txt/cord-341970-pho6dksc.txt === reduce.pl bib === id = cord-342204-9tgxijvn author = Nuzzo, Domenico title = Potential neurological effects of severe COVID-19 infection date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3227 sentences = 183 flesch = 44 summary = In this axis, virus-induced inflammation and oxidative stress could be the common mechanisms responsible for CoV neurological symptoms. People with COVID-19 generally develop respiratory symptoms but the increasing evidence shows that some patients with a severe infection also develop neurological ailments like confusion, stroke, seizure, or loss of smell and taste. Recent studies discussed the neuroinvasive potential of SARS-CoV-2; in fact, some infected subjects did show neurological effects. In fact, detection of some RNA of human-coronavirus in human brain samples clearly demonstrates that these respiratory pathogens are naturally neuroinvasive in J o u r n a l P r e -p r o o f humans and suggests that they establish a persistent infection in human CNS (Arbour et al., 2000) . Therefore, inflammation and oxidative stress systemic, induced by SARS-CoV-2 lung injury, could has effect in CNS causing neuronal dysfunction. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-342204-9tgxijvn.txt txt = ./txt/cord-342204-9tgxijvn.txt === reduce.pl bib === id = cord-342254-vdovpfu1 author = Mugheddu, C. title = CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management date = 2020-06-04 pages = extension = .txt mime = text/plain words = 766 sentences = 54 flesch = 45 summary = title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management Novel coronavirus 2019 (SARS-CoV2) pandemic has particularly affected Italy, with a profound impact on the therapeutic strategy for complex disorder such as psoriasis, whose extensive skin damage might expose to an increased infective risk compared to the general population. Psoriasis treatment relies on immunosuppression, and although most experts agree that the benefit-to risk-ratio is in favor of maintaining selective biologic therapies, and small molecules such as apremilast, they recommend dismission if severe COVID-19 symptoms occur. The fact that patient with a severe form of psoriasis contracted the COVID-19 pneumonia, while on treatment with apremilast is worth of some considerations. 11 Recently, another Italian psoriasis patient contracting COVID-19 under IL-23 inhibitor treatment (guselkumab) has been reported, and completely recovered from the infection. 12 From our experience, apremilast confirms its safety in very critical patients with severe infections, including COVID-19. cache = ./cache/cord-342254-vdovpfu1.txt txt = ./txt/cord-342254-vdovpfu1.txt === reduce.pl bib === id = cord-341919-8gnthufw author = Basi, Saajan title = Clinical course of a 66-year-old man with an acute ischaemic stroke in the setting of a COVID-19 infection date = 2020-08-23 pages = extension = .txt mime = text/plain words = 4192 sentences = 221 flesch = 50 summary = 3 There appears to be a growing correlation between COVID-19 positive patients presenting to hospital with ischaemic stroke; however, studies investigating this are in progress, with new data emerging daily. 10 The patient, in this case, illustrates the clinical relevance of understanding COVID-19, as he presented with an ischaemic stroke underlined by minimal respiratory symptoms, which progressed expeditiously, resulting in acute respiratory distress syndrome and subsequent death. Our case is an example of a new and ever-evolving clinical correlation, between patients who present with a radiological confirmed ischaemic stroke and severe COVID-19 pneumonia. As of April 2020, no comprehensive data of the relationship between ischaemic stroke and COVID-19 has been published, however early retrospective case series from three hospitals in Wuhan, China have indicated that up to 36% of COVID-19 patients had neurological manifestations, including stroke. cache = ./cache/cord-341919-8gnthufw.txt txt = ./txt/cord-341919-8gnthufw.txt === reduce.pl bib === id = cord-342177-iqt3ghc0 author = Laine, Roger A title = The case for re-examining glycosylation inhibitors, mimetics, primers and glycosylation decoys as antivirals and anti-inflammatories in COVID19 date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3060 sentences = 198 flesch = 39 summary = 1974) and in 1976 showed that tunicamycin, which inhibits the formation of N-acetylglucosamine-lipid intermediates in N-linked glycan synthesis (Lennarz 1975) , suppressed glycoprotein synthesis in Semliki Forest, influenza and avian sarcoma virus (Schwarz et al. The "peplomeric glycoprotein E2 was not detectable upon tunicamycin treatment," indicating its synthesis was interdicted or its degradation was facilitated by lack of N-linked glycosylation and was improperly processed (Holmes et al. (1982) showed swainsonine, an α-mannosidase inhibitor, to inhibit processing of oligosaccharides on influenza viral hemagglutinin, and in 1983 showed its effect on vesicular stomatitis virus (Kang and Elbein 1983) . It seems a reasonable approach that interfering with host glycosylation systems hijacked by SARS COV2, plus interfering with the ACE2 receptor glycosylation may combine to 1) interdict infectivity and 2) glycosylation interference with Sialyl LeX can inhibit E-selectin-based inflammatory responses, mitigating the Covid19 ARDS pathology. Antiviral effect of alpha-glucosidase inhibitors on viral morphogenesis and binding properties of hepatitis C virus-like particles cache = ./cache/cord-342177-iqt3ghc0.txt txt = ./txt/cord-342177-iqt3ghc0.txt === reduce.pl bib === id = cord-341883-eh0aw3re author = Bellanger, Anne-Pauline title = Studying smoking benefit in farmer’s lung to understand Covid-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1291 sentences = 73 flesch = 50 summary = It was observed, first in China, and then in France, that the proportion of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients was significantly lower in active smokers compared to the proportion of active smokers in the general population. The protection conferred by smoking for a respiratory disease has so far only been described for hypersensitivity pneumonitis (HP), especially for farmer's lung, and to a lesser degree, for bird fancier's lung. The under-representation of active smokers in SARS-CoV-2 patients suggests a protective effect of smoking, similar to that in the farmer's lung. We chose to highlight the most obvious similarities between SARS-CoV-2 and farmer's lung but there are probably others, especially concerning the hyperactive immune response described as 'cytokine storm'. The lack of knowledge about the mode of action of smoking in farmer's lung disease limits comparisons with SARS-CoV-2 and more research is required. cache = ./cache/cord-341883-eh0aw3re.txt txt = ./txt/cord-341883-eh0aw3re.txt === reduce.pl bib === id = cord-342221-xvrpx9p8 author = Duan, Qing title = Reovirus, isolated from SARS patients date = 2003 pages = extension = .txt mime = text/plain words = 1783 sentences = 103 flesch = 55 summary = In this report, reovirus was isolated from throat swabs of SARS patients, including the first case in Beijing and her mother. SCV was isolated in lung tissue collected at autopsy from her father, and the first isolate in Beijing was named the BJO 1 strain of SARS-associated coronavirus, whose genome sequence has been determined [4] . Isolation of reovirus: To isolate viruses associated with SARS, we inoculated the clinical specimen (material from throat swabs) obtained from the first patient with SARS admitted to hospital in Beijing onto Hep-2 cells. We isolated the virus in throat swab specimen from the first case in Beijing and her mother, and initially considered it as a possible variant of SCv, but the PCR test failed to amplify DNA from it. Electron microscopy (EM) examination of Hep-2 cells and Vero-E6 cells infected with the virus isolated from throat swab specimens of the first case in Beijing revealed characteristic reovirus particles with a size of about 60-80 urn in diameter. cache = ./cache/cord-342221-xvrpx9p8.txt txt = ./txt/cord-342221-xvrpx9p8.txt === reduce.pl bib === id = cord-342084-fbtx7rwi author = Ceccarelli, Giancarlo title = IS TEICOPLANIN A COMPLEMENTARY TREATMENT OPTION FOR COVID-19? THE QUESTION REMAINS date = 2020-05-23 pages = extension = .txt mime = text/plain words = 643 sentences = 41 flesch = 47 summary = We read with great interest the editorial by Baron Coronavirus (MERS-CoV), but also Ebola virus, influenza A and B viruses, and feline infectious peritonitis virus (FIPV), were reported as potential targets of teicoplanin and its chemical derivatives. Based on the aforementioned, teicoplanin has been used either as a potential antiviral agent and treatment of possible Staphylococcus aureus superinfection in our critical patients with severe SARS-CoV-2 pneumonia, since this latter may represent a major complication of respiratory viral infections. Moreover, a recent study showed that teicoplanin potently prevents the entrance of SARS-CoV2 into the cytoplasm with an IC50 of only 1.66 μM which is much lower than the routine trough serum drug concentration (approximately 7-8 μM/L). Therefore, the routinely-used teicoplanin doses adopted in our series might be considered as potentially adequate for treatment of patients with SARS-CoV2 infection. Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) cache = ./cache/cord-342084-fbtx7rwi.txt txt = ./txt/cord-342084-fbtx7rwi.txt === reduce.pl bib === id = cord-342144-awtiqxx5 author = Hufert, F. title = Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie date = 2020-04-01 pages = extension = .txt mime = text/plain words = 3305 sentences = 352 flesch = 48 summary = Ein klinischer Nutzen konnte beim Einsatz der eigentlich für die Behandlung von Humane-Immundefizienz(HIV)-Infektionen verwendeten Proteaseinhibitoren Lopinavir und Ritonavir (Kaletra ® ) zur Therapie des SARS-CoV nachgewiesen werden [6] . Im Dezember 2019 trat in China erstmalig ein neues Coronavirus auf, das zunächst als 2019-nCoV bezeichnet wurde und nach aktueller Nomenklatur des International Committee on Taxonomy of Viruses (ICTV) nun als SARS-CoV-2 bezeichnet wird [7] . So ist der kombinierte Einsatz der Proteaseinhibitoren Lopinavir und Ritonavir bei SARS-CoV-Patienten von klinischem Nutzen [6] . Eine weitere Studie mit MERS-CoV-Infizierten wird in Saudi-Arabien durchgeführt, bei der mit Lopinavir/Ritonavir plus Interferon-β behandelt wird [30] ; Daten zu den Ergebnissen liegen noch nicht vor. konnte gezeigt werden, dass die zelluläre Protease TMPRSS2 für die Infektiosität von SARS-CoV-2 essenziell ist und eine Hemmung dieser Protease mithilfe von Camostat-Mesilat die Vermehrung des Virus u. cache = ./cache/cord-342144-awtiqxx5.txt txt = ./txt/cord-342144-awtiqxx5.txt === reduce.pl bib === id = cord-342391-arp07mck author = Magiorkinis, G. title = Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions date = 2004-09-14 pages = extension = .txt mime = text/plain words = 1901 sentences = 81 flesch = 49 summary = Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. Bayesian scanning and subsequent phylogenetic analysis revealed that the SARS-CoV sequence was related more closely to Group II than the other two groups in most of its genome (e.g., at the region spanning amino acid positions 4309-5612 in reference to the murine hepatitis virus ORF1ab gene) (Fig. 1) . This clustering was supported by high quartet puzzling support values and high posterior probabilities under various substitution models, thus suggesting that 80% of the SARS-CoV genomic sequence is related more closely to coronaviruses Group II than any other members of this family. cache = ./cache/cord-342391-arp07mck.txt txt = ./txt/cord-342391-arp07mck.txt === reduce.pl bib === id = cord-342344-jjnf4yje author = Mello, C. J. title = Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3122 sentences = 190 flesch = 55 summary = Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. cache = ./cache/cord-342344-jjnf4yje.txt txt = ./txt/cord-342344-jjnf4yje.txt === reduce.pl bib === id = cord-342145-cq6xe5r7 author = Dao Thi, Viet Loan title = A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date = 2020-08-12 pages = extension = .txt mime = text/plain words = 9311 sentences = 507 flesch = 58 summary = The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital's diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ). cache = ./cache/cord-342145-cq6xe5r7.txt txt = ./txt/cord-342145-cq6xe5r7.txt === reduce.pl bib === id = cord-342383-ckswlo9o author = Pawlowski, C. title = Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5479 sentences = 273 flesch = 51 summary = Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). Given this study population, we assess the rates of SARS-CoV-2 infection among individuals who did and did not receive one of 18 vaccines in the past 1, 2, and 5 years relative to the date of PCR testing. In Figure 6 , we present the results from the tipping point analysis on the statistically significant associations between vaccination and reduced rates of SARS-CoV-2 infection in the overall study population. For example, for the polio vaccine at the 1 year time horizon, an unobserved confounder with a relative risk of 2.78 which is prevalent in 17.8% of the vaccinated cohort and 0% of the unvaccinated cohort could explain the differences in SARS-CoV-2 infection rates that we observe in the data. cache = ./cache/cord-342383-ckswlo9o.txt txt = ./txt/cord-342383-ckswlo9o.txt === reduce.pl bib === id = cord-341976-yts6pzn3 author = Liu, Xintian title = Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China date = 2020-07-06 pages = extension = .txt mime = text/plain words = 3062 sentences = 213 flesch = 57 summary = title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China We conducted a single-center, retrospective, cohort study to investigate the relationship between serum immunoglobulin G (IgG) and IgM and clinical outcomes in severe/critical patients with COVID-19. Specific serum immunoglobulin G (IgG) and IgM against SARS-CoV or Middle East Respiratory Syndrome-coronavirus (MERS-CoV) became detectable in patients as early as 11-15 days post illness onset [11, 12] . AGING Additionally, the titers of IgM and IgG were significantly correlated with viral load in patients infected by SARS-CoV-2 in a recent finding [14] , which promoted the hypothesis that specific antibody against virus might be associated with disease progression in COVID-19. In this retrospective cohort study, IgG and IgM against SARS-CoV-2 in severe/critical patients with COVID-19 were profiled, and relationship between antibody titers AGING and outcomes was also assessed. cache = ./cache/cord-341976-yts6pzn3.txt txt = ./txt/cord-341976-yts6pzn3.txt === reduce.pl bib === id = cord-342396-n3txsvf7 author = Ciaglia, Elena title = COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1701 sentences = 83 flesch = 47 summary = title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children In another case control study conducted in the north eastern Chinese Han population, the serum ACE2 activity negatively correlated with body mass index (BMI), pulse pressure, and estrogen levels in female EH (essential hypertension) patients (14) . Cases of coronavirus disease 2019 (COVID-19) among children in China have been less severe than those in adults, according to a new study. Now, circulating level of ACE2 may have prognostic effect in monitoring COVID-infection, and the genetic analysis of ACE2 polymorphisms might be a key element of individualized care for its prevention, diagnosis, and treatment. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury cache = ./cache/cord-342396-n3txsvf7.txt txt = ./txt/cord-342396-n3txsvf7.txt === reduce.pl bib === id = cord-342220-lrqt2gcw author = Dearlove, Bethany title = A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants date = 2020-09-22 pages = extension = .txt mime = text/plain words = 7874 sentences = 415 flesch = 49 summary = Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute While the evolutionary rate is likely to decrease over time (18) , it is important to monitor the introduction of any mutation that may compromise the potential efficacy of vaccine candidates derived from the first available SARS-CoV-2 sequences. In S, only site 614 was estimated to be under diversifying selection in a majority of subsampled alignments (58%); evidence of diversifying selection indicates that genetic diversity increases in the viral population (i.e., there was a higher proportion of mutations causing an amino acid change than not at site 614, or, the nonsynonymous/synonymous substitution rates ratio, dN/dS, was over 1, P < 0.1) (SI Appendix, Fig. S4 ). cache = ./cache/cord-342220-lrqt2gcw.txt txt = ./txt/cord-342220-lrqt2gcw.txt === reduce.pl bib === id = cord-342639-vf9n2vf9 author = Chang, Chung-ke title = Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date = 2013-05-23 pages = extension = .txt mime = text/plain words = 5386 sentences = 243 flesch = 42 summary = For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-342639-vf9n2vf9.txt txt = ./txt/cord-342639-vf9n2vf9.txt === reduce.pl bib === id = cord-342362-j7vuoer6 author = Gegúndez-Fernández, José A title = Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19 date = 2020-04-25 pages = extension = .txt mime = text/plain words = 3525 sentences = 354 flesch = 53 summary = Conclusiones: Durante la pandemia COVID-19, la atención a los potenciales riesgos de salud para la población ocasionados por el coronavirus deberá prevalecer sobre la posible progresión de enfermedades oculares comunes. Recoge recomendaciones de máximos para la atención a pacientes oftalmológicos, tanto COVID positivos como negativos, durante la pandemia por coronavirus SARS-CoV-2. Durante este periodo la atención a los potenciales riesgos de salud para la población general ocasionados por la pandemia COVID-19 debe primar sobre la posible progresión de enfermedades tales como el glaucoma crónico, la retinopatía diabética, la degeneración macular asociada a la edad (DMAE), enfermedades corneales e inflamatorias, entre otras. Las precauciones tomadas para la elaboración de los derivados hemáticos serán las propias establecidas según el informe de la AEMPS 20 de 23/mayo/2013 sobre el uso de Plasma Rico en Plaquetas (PRP) y teniendo en cuenta los criterios de exclusión del Anexo II del Real Decreto 21 1088/2005, el cual especifica que pacientes con infecciones se excluirán durante y como mínimo las dos semanas posteriores al restablecimiento clínico completo de una enfermedad infecciosa y tras la desaparición de síntomas, incluyendo fiebre superior a 38ºC y afección pseudogripal, donde podríamos clasificar la infección por SARS-CoV-2. cache = ./cache/cord-342362-j7vuoer6.txt txt = ./txt/cord-342362-j7vuoer6.txt === reduce.pl bib === id = cord-342340-q6j7vy8u author = Jefferies, Sarah title = COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5717 sentences = 281 flesch = 43 summary = METHODS: We did a descriptive epidemiological study of all laboratory-confirmed and probable cases of COVID-19 and all patients tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New Zealand from Feb 2 to May 13, 2020, after which time community transmission ceased. Demographic features and disease outcomes, transmission patterns (source of infection, outbreaks, household transmission), time-to-event intervals, and testing coverage were described over five phases of the response, capturing different levels of non-pharmaceutical interventions. This descriptive epidemiological study examined a cohort of all confirmed and probable COVID-19 cases and all people tested for SARS-CoV-2 infection in New Zealand up to May 13, 2020 , which marked the easing of the most restrictive non-pharmaceutical interventions, after which community transmission ceased. cache = ./cache/cord-342340-q6j7vy8u.txt txt = ./txt/cord-342340-q6j7vy8u.txt === reduce.pl bib === id = cord-342599-558yn6pu author = Rinchai, Darawan title = A modular framework for the development of targeted Covid-19 blood transcript profiling panels date = 2020-05-22 pages = extension = .txt mime = text/plain words = 5230 sentences = 298 flesch = 42 summary = Here we aimed to develop an approach to support the design of focused blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: therapeutic development relevance, SARS biology relevance and immunological relevance. In this proof of principle study, we used the available transcript profiling data from two separate studies to select Covid-19 relevant sets of modules (8, 9) . One of these applications provides access to module-level transcript abundance profiles for available Covid-19 blood transcriptome profiling datasets. Despite large differences between the two studies in terms of design, range of clinical severity, technology platforms and module coverage, the combined overall changes (detected at a high-level perspective) are consistent with those observed in known acute infections, such as those caused by influenza, respiratory syncytial virus (RSV) or S. cache = ./cache/cord-342599-558yn6pu.txt txt = ./txt/cord-342599-558yn6pu.txt === reduce.pl bib === id = cord-342189-ya05m58o author = Banerjee, Abhik K. title = SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date = 2020-10-08 pages = extension = .txt mime = text/plain words = 11469 sentences = 647 flesch = 55 summary = Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. cache = ./cache/cord-342189-ya05m58o.txt txt = ./txt/cord-342189-ya05m58o.txt === reduce.pl bib === id = cord-342453-1vj9p7vm author = Ip, A. title = Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study date = 2020-08-25 pages = extension = .txt mime = text/plain words = 4165 sentences = 325 flesch = 48 summary = Methods: We examined the association between outpatient hydroxychloroquine exposure and the subsequent progression of disease among mildly symptomatic non-hospitalized patients with documented SARS-CoV-2 infection. [15] [16] [17] [18] In this multi-center observational cohort study we report progression from mildly symptomatic SARS-CoV-2 infection diagnosed as an outpatient progressing to subsequent need for in-patient hospitalization according to outpatient exposure to hydroxychloroquine. This retrospective, observational, multicenter cohort study within the Hackensack Meridian Health network (HMH) utilized EHR-derived data of patients with documented SARS-CoV-2 infection who received care initially within an outpatient setting. Our primary objective was to evaluate the association between hydroxychloroquine exposure and subsequent need for hospitalization in a population of patients with documented SARS-CoV-2 infection diagnosed in the outpatient setting. In this multicenter retrospective observational cohort study of mildly symptomatic outpatients with polymerase chain reaction documented SARS-CoV-2 infection, we noted an association (OR 0.53; 95% CI, 0.29, 0.95) between outpatient exposure to hydroxychloroquine and a reduction in subsequent need for hospitalization. cache = ./cache/cord-342453-1vj9p7vm.txt txt = ./txt/cord-342453-1vj9p7vm.txt === reduce.pl bib === id = cord-342681-pqzcy9wu author = Pongpirul, Wannarat A. title = Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1740 sentences = 117 flesch = 41 summary = Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. During the study period, Thailand's discharge criteria for hospitalized COV-ID-19 patients required resolution of clinical signs and symptoms and 2 respiratory specimens without detectable SARS-CoV-2 RNA collected >24 hours apart. Clinical resolution occurred a median of 12 (9-13.5 ) days after illness onset, and these patients had detectable SARS-CoV-2 RNA in upper respiratory tract specimens for a median of 14 (9-26) days after illness onset (Table 2) . However, patients became afebrile 6 days after illness onset, with a median of 9 (3-19.75 ) additional days of detectable SARS-CoV-2 RNA in respiratory specimens after resolution of fever ( Table 2 ). Other studies have described asymptomatic patients with upper respiratory specimens positive for SARS-CoV-2 (9), and evidence suggests such cases pose a risk for transmission (10) (11) (12) . cache = ./cache/cord-342681-pqzcy9wu.txt txt = ./txt/cord-342681-pqzcy9wu.txt === reduce.pl bib === id = cord-342361-eu3rry7p author = Lu, Jiatao title = ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China date = 2020-02-23 pages = extension = .txt mime = text/plain words = 3782 sentences = 232 flesch = 55 summary = title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China Our current study was conducted aiming to characterize the clinical features of either confirmed or suspected COVID-19 patients who were hospitalized in a COVID-19-designated hospital in Wuhan, and to develop a mortality risk index, as an evaluation tool used for establishing a COVID-19 hierarchical management system in highly endemic areas. To our knowledge, this is the first-ever study to compare the clinical characteristics of pneumonia patients who were either positive or negative for SARS-CoV-2 by RT-PCR assay, and to develop a first-ever COVID-19 mortality risk index derived from patients in highly endemic areas during early stage of outbreak. cache = ./cache/cord-342361-eu3rry7p.txt txt = ./txt/cord-342361-eu3rry7p.txt === reduce.pl bib === id = cord-342294-x18xmrji author = Yan, Nao title = Medium Term Follow-Up of 337 Patients With Coronavirus Disease 2019 (COVID-19) in a Fangcang Shelter Hospital in Wuhan, China date = 2020-07-03 pages = extension = .txt mime = text/plain words = 2707 sentences = 147 flesch = 48 summary = Risk factors of nucleic acid re-positivity including the number of lobes infiltration (odds ratio[OR], 1.14; 95% CI, 1.09–1.19), distribution (OR, 0.16; 95% CI, 0.13–0.19), CT imaging feature of patchy shadowing accompanying with consolidation (OR, 9.36; 95% CI, 7.84–11.17), respiratory symptoms of cough accompanying with expectoration (OR, 1.39; 95% CI, 1.28–1.52), and chest congestion accompanying by dyspnea (OR, 1.42; 95% CI, 1.28–1.57). Considering the high infectious characteristics of the SARS-CoV-2 virus, all recovered patients continue to undergo 14 days postdischarge quarantine at designated locations, which is required by the diagnosis and treatment program for novel coronavirus pneumonia (Trial Version 6). All patients were detected to be SARS-CoV-2 nucleic acid positive by a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and classified as mild to moderate cases on admission based on the criteria issued by the National Health Commission (NHC) of the People's Republic of China. cache = ./cache/cord-342294-x18xmrji.txt txt = ./txt/cord-342294-x18xmrji.txt === reduce.pl bib === id = cord-342380-lihz7h1k author = Meguid Kassem, Abdel title = SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date = 2020-07-21 pages = extension = .txt mime = text/plain words = 3044 sentences = 164 flesch = 51 summary = BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). This work has been conducted to determine the extent of infection by realtime reverse transcription polymerase chain reaction (RT-PCR) and rapid serological test (RST) for SARS-CoV-2 among frontline HCWs providing gastrointestinal services. Previous studies in developed countries reported variable infection rates in HCWs. In a study on 957 employees in a German university hospital, 52 of them (5.4%) tested positive for SARS-CoV-2 by PCR [13] . cache = ./cache/cord-342380-lihz7h1k.txt txt = ./txt/cord-342380-lihz7h1k.txt === reduce.pl bib === id = cord-342539-o004ggon author = Lam, Tommy Tsan-Yuk title = Tracking the genomic footprints of SARS-CoV-2 transmission date = 2020-05-28 pages = extension = .txt mime = text/plain words = 906 sentences = 47 flesch = 43 summary = [1], conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains. Several studies using mathematical modelling of the COVID-19 incidence and other coronavirus infections have suggested the effectiveness of disease control such as social distancing and city lockdown [6, 7] , but these methods seldom assess individual transmission It is evident in literature that genomic information of pathogens provide valuable empirical information about their transmission histories [2] , such as the identification of transmission chains through phylogenetic analysis of the genome sequences as illustrated in the work done by Lu et al. In addition to revealing the evolutionary process of the pathogen and acting as a proxy of disease transmission history, phylogenetic trees also serve as versatile frameworks for comparative analysis of virus genetics and phenotypes, disease epidemiology and clinical manifestations, and population demography and environment, thus facilitating identification of a possible interplay between these various aspects in disease dynamics ( Figure 1 ). cache = ./cache/cord-342539-o004ggon.txt txt = ./txt/cord-342539-o004ggon.txt === reduce.pl bib === id = cord-342456-5gp3cry0 author = Hoagland, Daisy A. title = Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date = 2020-07-13 pages = extension = .txt mime = text/plain words = 4511 sentences = 240 flesch = 48 summary = Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. cache = ./cache/cord-342456-5gp3cry0.txt txt = ./txt/cord-342456-5gp3cry0.txt === reduce.pl bib === id = cord-342938-rzhsnkn4 author = Huang, Bo-Ruei title = Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan date = 2020-06-30 pages = extension = .txt mime = text/plain words = 977 sentences = 68 flesch = 52 summary = title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan 1, 2 Here, we report a unique case of influenza B virus co-infection with SARS-CoV-2 in Taiwan. The co-infection of influenza virus and SARS-CoV-2 is unusual, and to date, most reported cases are from China. Beside co-infection of influenza virus, increased co-infection of other virus or bacteria had also been reported among In our case, the newly developed dry cough and fever during hospitalization was the warning sign and the subsequent chest image confirmed clinical deterioration, which prompted the initiation of hydroxychloroquine. Single dose baloxavir marboxil was also superior to oseltamivir in reducing the viral load one day after the initiation of the trial regimen in patients with uncomplicated influenza. The clinical characteristics of pneumonia patients co-infected with 2019 novel coronavirus and influenza virus in Wuhan Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia cache = ./cache/cord-342938-rzhsnkn4.txt txt = ./txt/cord-342938-rzhsnkn4.txt === reduce.pl bib === id = cord-342739-iy9vjpuh author = Schwartz, David A. title = Potential Maternal and Infant Outcomes from Coronavirus 2019-nCoV (SARS-CoV-2) Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections date = 2020-02-10 pages = extension = .txt mime = text/plain words = 8414 sentences = 406 flesch = 49 summary = In order to assess the potential of the Wuhan 2019-nCoV to cause maternal, fetal and neonatal morbidity and other poor obstetrical outcomes, this communication reviews the published data addressing the epidemiological and clinical effects of SARS, MERS, and other coronavirus infections on pregnant women and their infants. The most common adverse obstetrical outcomes associated with maternal pneumonias from all causes include This newly recognized coronavirus, producing a disease that has been termed COVID-19, is rapidly spreading throughout China, has crossed international borders to infect persons in neighboring countries, and humans infected by the virus are travelling via commercial airlines to other continents. Pregnant women may develop severe disease and fatal maternal and/or fetal outcomes as a result of MERS-CoV infection; however, little is known of the pathophysiology of this infection during pregnancy. cache = ./cache/cord-342739-iy9vjpuh.txt txt = ./txt/cord-342739-iy9vjpuh.txt === reduce.pl bib === id = cord-342951-nirue1x4 author = Theophanous, Christos title = Bell’s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-09-04 pages = extension = .txt mime = text/plain words = 1454 sentences = 92 flesch = 52 summary = title: Bell's palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) This is the first reported pediatric case of Bell's palsy in the setting of SARS-CoV-2 infection. [5, 6] There are limited reports of an association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and Bell's palsy in adults but this seems to be rare with only two cases reports at the time of this report. Herein, we report the first case of a pediatric patient presenting with acute onset Bell's Palsy in the setting of SARS-CoV-2 infection. To our knowledge, this is the first report of an association between Bell's palsy and SARS-CoV-2 in a pediatric patient. Few cases of Bell's palsy in the setting of SARS-CoV2 infection have been reported in adults and appear to be very infrequent [9, 10] . Our patient's history of hyper-IgM syndrome may complicate his response to a SARS-CoV-2 infection. cache = ./cache/cord-342951-nirue1x4.txt txt = ./txt/cord-342951-nirue1x4.txt === reduce.pl bib === id = cord-342942-1s32o9m8 author = Stamatakis, George title = Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date = 2020-06-22 pages = extension = .txt mime = text/plain words = 4074 sentences = 209 flesch = 47 summary = Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. cache = ./cache/cord-342942-1s32o9m8.txt txt = ./txt/cord-342942-1s32o9m8.txt === reduce.pl bib === id = cord-342765-rw8valjp author = Wacharapluesadee, Supaporn title = Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19 date = 2020-05-13 pages = extension = .txt mime = text/plain words = 2125 sentences = 123 flesch = 52 summary = Additionally, NT specimens with PCR cycle threshold (Ct) greater than 35 were pooled to determine the limit of detection and sensitivity of pooling samples to test for SARS-CoV-2. Previously positive specimens with high and low-concentrations of RNA, as determined by PCR Ct values at the time of detection, were selected to determine the effect of viral load on pooling to ensure that the sensitivity and accuracy of the assay was maintained (Table 1) The fifteen 1X (L>35) pools were tested by performing duplicate (replicates I and II) qPCR assays to determine the limit of detection of specimen pooling when compared to individual testing. This study demonstrates that specimen pooling (either 1X or 2X pooling ratios) does not compromise the sensitivity of detecting SARS-CoV-2 provided the Ct value of the individually tested sample is lower than 35. cache = ./cache/cord-342765-rw8valjp.txt txt = ./txt/cord-342765-rw8valjp.txt === reduce.pl bib === id = cord-342557-a7q8vp8m author = Chowdhury, Surid Mohammad title = Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 3554 sentences = 232 flesch = 54 summary = [Image: see text] Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Peptides that showed higher S protein-binding affinity compared to the α-helix (AH) of the ACE2 peptidase were further analyzed with molecular dynamics (MD) simulation and the structure− activity relationship (SAR) in order to achieve a high-affinity binder for the S protein. 30 Initially, stepwise multiple linear regression (MLR) was performed considering these properties as variables to predict the calculated binding affinity of the test peptides with the RBD of the SARS CoV-2 spike protein. All 51 peptides were docked to the RBD of the SARS CoV-2 spike protein using PatchDock. Various residues including Glu484, Tyr449, and Tyr505 present in the ACE2 binding site of the RBD were involved in noncovalent interaction with the antiviral peptides ( Figure 1a) . cache = ./cache/cord-342557-a7q8vp8m.txt txt = ./txt/cord-342557-a7q8vp8m.txt === reduce.pl bib === id = cord-342947-dhe31r3a author = Li, Xin title = Preliminary recommendations for lung surgery during COVID‐19 epidemic period date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2107 sentences = 103 flesch = 51 summary = After SARS-CoV-2 infection has been excluded and space-occupying lesions in the lungs confirmed by computed tomography (CT) scan, they could be transferred to thoracic surgery for further diagnosis and treatment. • For peripheral solid nodules with a diameter of less than 3 cm considered as malignant lesions by PET-CT or percutaneous pulmonary puncture biopsy, short-term regular follow-up (once a month) can be recommended during the outbreak prevention and control period. 3 Therefore, we suggest that during the epidemic prevention and control period, whether the patient has pure GGNs, mixed GGNs or multiple GGNs (SARS-CoV-2 infection should be excluded for multiple GGNs), follow-up re-examination should be the main recommendation, and surgery should not be carried out. For patients undergoing emergency thoracic surgery, if the symptoms mentioned above occur, isolation measures should be taken during the operation, and the possibility of SARS-CoV-2 latent infection should be eliminated without delay. Preliminary recommendations for lung surgery during 2019 novel coronavirus disease (COVID-19) epidemic period cache = ./cache/cord-342947-dhe31r3a.txt txt = ./txt/cord-342947-dhe31r3a.txt === reduce.pl bib === id = cord-342569-ja96xfns author = Azer, Samy A. title = COVID-19: Pathophysiology, diagnosis, complications and Investigational therapeutics date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2669 sentences = 186 flesch = 46 summary = On 31 December 2019, the Chinese authorities reported to the World Health Organisation (WHO) an emerging of a novice coronavirus, currently the virus is known as SARS-CoV-2 and the disease name is coronavirus-19 disease (COVID19) , that has emerged in patients from Wuhan city, Hubel Province [1] . Recently it was debated that targeting the Notch signalling to prevent SARS-CoV-2 infection and interfering with the progression of COVID-19associated heart and lungs disease pathogenesis [13] . It is not clear whether the observed SARS-CoV-2-associated liver injury is cause by direct viral injury or related to hepatoxic drugs, coexisting systemic inflammatory changes, sepsis, respiratory distress syndrome-induced hypoxia, and multiple organ failure [18] . In patients with type 2 diabetes mellitus who are infected with COVID-19, it is important to remember that two receptor proteins ACE-2 and dipeptidyl peptidase-4 (DPP-4) are test can detect IgM, and IgG antibodies against SARS-CoV-2 in the serum, plasma, and whole blood [23] . cache = ./cache/cord-342569-ja96xfns.txt txt = ./txt/cord-342569-ja96xfns.txt === reduce.pl bib === id = cord-342796-f7n8sxbu author = Stowe, J. title = Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3923 sentences = 218 flesch = 48 summary = Findings: The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible pathogenic competition between the two viruses. The odds of ventilator use or death and ICU admission or death was greatest among coinfection patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Severity and risk of death among individuals with a coinfection: The mortality rate among individuals with a SARS-CoV-2 and influenza coinfection and those with SARS-CoV-2 infection who tested negative for influenza was calculated by dividing the number of deaths by the total number of individuals tested by age group. We also found strong evidence that coinfection with influenza and SARS-CoV-2 was associated with an increased risk of death or severe disease and that this appears to be beyond the additive effect of the two viruses acting independently. cache = ./cache/cord-342796-f7n8sxbu.txt txt = ./txt/cord-342796-f7n8sxbu.txt === reduce.pl bib === id = cord-342625-31fe1neb author = Baba, Hiroaki title = Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1457 sentences = 76 flesch = 48 summary = The patient who continued iguratimod therapy without dose reduction was treated with ciclesonide had an uneventful clinical course, but prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed after resolution of symptoms. The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly across the world, yet investigations of in patients with rheumatologic disease taking disease-modifying antirheumatic drugs (DMARDs) with immunomodulatory or immunosuppressive effects remain scarce [1] . Here we report a case of COVID-19 in a patient with rheumatoid arthritis taking iguratimod, who had prolonged viral RNA presence. A woman in her 40s with rheumatoid arthritis treated with iguratimod 25 mg twice a day was admitted to Tohoku University Hospital, Sendai, Japan, with a diagnosis of COVID-19 based on real-time reverse transcription polymerase chain reaction (real-time RT-PCR) with primers that target the N2 gene of SARS-CoV-2 as described previously [2] from nasopharyngeal swabs and sputum. cache = ./cache/cord-342625-31fe1neb.txt txt = ./txt/cord-342625-31fe1neb.txt === reduce.pl bib === id = cord-343029-85ga6r7d author = Haghpanah, Abdolreza title = Potential mechanisms of SARS‐CoV‐2 action on male gonadal function and fertility: Current status and future prospects date = 2020-10-27 pages = extension = .txt mime = text/plain words = 4375 sentences = 218 flesch = 43 summary = The aim of this review was to provide new insights into different possible mechanisms of involvement of male gonads with SARS‐CoV‐2 including investigating the ACE2 axis in testis, hormonal alterations in patients with COVID‐19, possible formation of anti‐sperm antibodies (ASA) and subsequently immunological infertility as a complication of SARS‐CoV‐2 infection. Considering the fact that the testis is highly enriched in ACE2 receptors and its vulnerability to SARS-CoV-2 invasion, detectable changes in semen analysis, alteration in sex hormones balance and, most importantly, anti-sperm antibodies (ASA) formation and sperm DNA fragmentation are considered to play a major role in male infertility. Search phrases used for different databases strategy included the following: "severe acute respiratory syndrome coronavirus 2", "2019 nCoV", "SARS-CoV-2", "coronavirus", "COVID-19", "reproductive system", "fertility", "infertility", "germ cells", "gamete", "spermatogonia", "spermatogenesis" "spermatozoa", "spermatozoan", "testis", "Sertoli cells", "Leydig cells", "Androgen", "steroidogenesis", "spermiogenesis", "spermiation", "development", "fertilization", "gonadal function", "sex hormones", "angiotensin-converting enzyme 2 receptor", "ACE2", "anti-sperm antibodies", "ASA", "sperm DNA fragmentation index", "DFI", and "semen analysis". cache = ./cache/cord-343029-85ga6r7d.txt txt = ./txt/cord-343029-85ga6r7d.txt === reduce.pl bib === id = cord-342915-r9kv67we author = Hayden, Frederick G. title = Advances in antivirals for non‐influenza respiratory virus infections date = 2013-11-01 pages = extension = .txt mime = text/plain words = 5748 sentences = 281 flesch = 33 summary = Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. cache = ./cache/cord-342915-r9kv67we.txt txt = ./txt/cord-342915-r9kv67we.txt === reduce.pl bib === id = cord-343034-dzvo9v01 author = Chen, Chun-Fan title = Role of dipeptidyl peptidase-4 inhibitors in patients with diabetes infected with coronavirus-19 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1294 sentences = 77 flesch = 52 summary = The pandemic infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is widely increasing the patients affiliated with coronavirus disease 2019 (COVID-19) from last December of 2019. Notably, whether the ACE-related inhibitors or drugs modulated ACE2 activity in affecting the viral activity and disease severity of SARS-CoV-2 is still an open question. In this article, we are focusing on the impact of ACE inhibitors (ACEI) and DPP4 inhibitors used on SARS-CoV-2 activity and discussions about those drugs that may be related to infectious condition of COVID-19 diseases. Severe acute respiratory syndrome coronavirus (SARS-CoV-1) was the first epidemic coronavirus threat infected more than 8000 people with case-fatality rate (CFR) about 11%. Previous experiments had confirmed that angiotensin-converting enzyme 2 (ACE2) is the entry receptor in SARS-CoV-1 and dipeptidyl peptidase-4 (DPP4, also known as CD26) is the entry receptor in MERS-CoV. Among numerous anti-diabetic drugs, DPP4 inhibitors might play an important role during coronavirus infection, including pandemic COVID-19. cache = ./cache/cord-343034-dzvo9v01.txt txt = ./txt/cord-343034-dzvo9v01.txt === reduce.pl bib === id = cord-342902-y1v8wzxq author = Yuan, Shuofeng title = Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date = 2020-10-07 pages = extension = .txt mime = text/plain words = 5692 sentences = 291 flesch = 45 summary = Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. We found that co-application of clofazimine and remdesivir impacts SARS-CoV-2 replication in a manner that extends beyond the additive combinatorial activity predicted by the Bliss independence model (maximal Bliss Synergy Score of 44.28; Figure 5a , Extended Data Figure 2) , and indicates these two drugs harbor a synergistic antiviral relationship. cache = ./cache/cord-342902-y1v8wzxq.txt txt = ./txt/cord-342902-y1v8wzxq.txt === reduce.pl bib === id = cord-342783-85b4lwh3 author = Prazuck, T. title = Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2640 sentences = 174 flesch = 61 summary = In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. Methods RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orleans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated. The SARS-CoV-2 IgG/IgM antibody test kits, COVID-PRESTO ® and COVID-DUO ® , are 137 RDT test, the IgM were the first antibodies to be detected and were systematically present in 209 the few positive patients with an onset of symptoms from 0 to 5 days ago (n=2 in COVID-210 PRESTO ® population; n=5 in COVID-DUO ® ). Development and Clinical Application of A 371 Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-342783-85b4lwh3.txt txt = ./txt/cord-342783-85b4lwh3.txt === reduce.pl bib === id = cord-343127-n3fs8ph8 author = Pousa, Pedro A. title = Extrapulmonary manifestations of COVID-19 in children: a comprehensive review and pathophysiological considerations date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5503 sentences = 318 flesch = 46 summary = OBJECTIVE: The aim of this review was to summarize the most common extrapulmonary manifestations in pediatric patients with COVID-19, as well as to discuss clinical, epidemiological, and pathophysiological aspects of these clinical presentations in children. In addition, epithelial cells of the small intestine is another tissue that highly express ACE2 in cell membrane, [42] creating another potential region for SARS-CoV-2 infection and enteric manifestations of COVID-19. Hence, the present authors speculate that, although children and adults have similar rates of GI symptoms, children GI symptoms are usually associated as a primary response of SARS-CoV-2 infection, due to this minor expression of ACE2, and represent milder symptoms. Children are susceptible to liver injury, as shown by a meta-analysis of 551 laboratory-confirmed pediatric COVID-19 patients reporting that 9% (35/290) presented increased ALT and 18% (58/280), high levels of AST. Therefore, children might present less severe cases of kidney injury associated with COVID-19 due to this greater expression of AT2R than adults. cache = ./cache/cord-343127-n3fs8ph8.txt txt = ./txt/cord-343127-n3fs8ph8.txt === reduce.pl bib === id = cord-342660-xigv4u3f author = Benotmane, I. title = In-depth virological assessment of kidney transplant recipients with COVID-19 date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2499 sentences = 171 flesch = 55 summary = We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. We thus conducted a retrospective cohort study in kidney transplant recipients (KTR) in Alsace, Grand-Est France, to determine the dynamics of nasopharyngeal and plasma viral loads and SARS-CoV-2 serology and to study their association with mortality and severe forms of COVID-19. . https://doi.org/10.1101/2020.06.17.20132076 doi: medRxiv preprint positive viral load greater than 3 log10 copies/reaction after D10, and ten patients (24.4 %) In this retrospective study conducted in a sample of 40 immunocompromised KTR hospitalized for COVID-19, we precisely determined the temporal evolution of nasopharyngeal and plasma SARS-CoV-2 loads, as well as the serological response to the virus. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China cache = ./cache/cord-342660-xigv4u3f.txt txt = ./txt/cord-342660-xigv4u3f.txt === reduce.pl bib === id = cord-342996-honeavwj author = Mair-Jenkins, John title = The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date = 2015-01-01 pages = extension = .txt mime = text/plain words = 5306 sentences = 284 flesch = 45 summary = title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . cache = ./cache/cord-342996-honeavwj.txt txt = ./txt/cord-342996-honeavwj.txt === reduce.pl bib === id = cord-342983-7o0slu0z author = Killeen, G. F. title = A simple arithmetic rationale for crushing the epidemic curve of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) instead of flattening it date = 2020-05-10 pages = extension = .txt mime = text/plain words = 2328 sentences = 103 flesch = 43 summary = Here is presented a simple set of arithmetic modelling analyses that explain why preferable crush the "curve strategies", to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to "flatten the curve" strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. Here is presented a simple arithmetic rationale for why preferable crush the curve strategies, to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to flatten the curve strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. 2 From this assumed starting point, a country that contains its epidemic sufficiently to flatten the curve to a plateau, so that the rate of incidence of new infections remains constant, would have achieved a controlled reproductive number (Rc) of exactly 1.0 ( Figure 1A ). cache = ./cache/cord-342983-7o0slu0z.txt txt = ./txt/cord-342983-7o0slu0z.txt === reduce.pl bib === id = cord-343136-kftffes0 author = Mohon, Abu Naser title = Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2591 sentences = 164 flesch = 54 summary = A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. Limit of detection of the LAMP assay was evaluated by using a nasopharyngeal (NP) swab sample infected with SARS-CoV-2 for which the viral load was quantified using digital droplet PCR (see Supplementary Methods). Twenty four replicates from a serial dilution containing 25-50 copies of SARS-CoV-2 which equates to 1X LOD (patient sample NP swab in VTM viral load confirmed by digital droplet PCR) per reaction were tested using dual-target RT-LAMP (Table 3) . The dual-target RT-LAMP test for SARS-CoV-2 developed in this study has comparable analytical sensitivity and specificity, limit of detection, precision, and achieved excellent agreement compared to the reference RT-PCR methods used internationally. cache = ./cache/cord-343136-kftffes0.txt txt = ./txt/cord-343136-kftffes0.txt === reduce.pl bib === id = cord-342857-vj6sw2ne author = McCullough, Peter A. title = Pathophysiological Basis and Rationale for Early Outpatient Treatment of SARS-CoV-2 (COVID-19) Infection date = 2020-08-07 pages = extension = .txt mime = text/plain words = 2215 sentences = 120 flesch = 39 summary = In the absence of clinical trial results, physicians must use what has been learned about the pathophysiology of SARS-CoV-2 infection in determining early outpatient treatment of the illness with the aim of preventing hospitalization or death. Thus, in the context of present knowledge, given the severity of the outcomes and the relative availability, cost, and toxicity of the therapy, each physician and patient must make a choice: watchful waiting in self-quarantine or empiric treatment with the aim of reducing hospitalization and death. (10) For the ambulatory patient with recognized early signs and symptoms of COVID-19, often with nasal real-time reverse transcription or oral antigen testing pending, the following four principles could be deployed in a layered and escalating manner depending on clinical manifestations of COVID-19 like illness(11) and confirmed infection: 1) reduction of reinoculation, 2) combination antiviral therapy, 3) immunomodulation, 4) antiplatelet/antithrombotic therapy. cache = ./cache/cord-342857-vj6sw2ne.txt txt = ./txt/cord-342857-vj6sw2ne.txt === reduce.pl bib === id = cord-343192-fkc7af9y author = Chen, Siyang title = Comment on “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ‐2 (SARS‐CoV‐2)” date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1197 sentences = 69 flesch = 45 summary = We read the article "Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)" with great interest. Although there have been several reports previously suggesting that the similar SARS-CoV-2 virus could infect neuronal cells and cause central and peripheral neurological morbidities in COVID-19 patients (3) (4) (5) , few direct detection of virus by RT-PCR in cerebrospinal fluid (CSF) has casted earlier doubt whether there is indeed a direct infection of central nervous system (CNS). It is not clear whether SARS-CoV-2 viruses can be similarly detected in endothelial cells from other severe COVID-19 patients with central neurological involvement (3). It is worthy to point out that one very recent report from a Chinese case demonstrating the presence of SARS-CoV-2 virus sequence in the CSF fluid of a COVID-19 patient presenting viral encephalitis (7) . Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) cache = ./cache/cord-343192-fkc7af9y.txt txt = ./txt/cord-343192-fkc7af9y.txt === reduce.pl bib === id = cord-342756-rgm9ffpk author = Senger, Mario Roberto title = COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date = 2020-10-02 pages = extension = .txt mime = text/plain words = 16108 sentences = 1024 flesch = 51 summary = Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. cache = ./cache/cord-342756-rgm9ffpk.txt txt = ./txt/cord-342756-rgm9ffpk.txt === reduce.pl bib === id = cord-342538-5bwsm290 author = Izquierdo Lara, R. W. title = Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5031 sentences = 281 flesch = 56 summary = Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina). cache = ./cache/cord-342538-5bwsm290.txt txt = ./txt/cord-342538-5bwsm290.txt === reduce.pl bib === id = cord-343330-wuzts3mt author = Ramos da Silva, S. title = Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19 date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3447 sentences = 229 flesch = 56 summary = Background Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection in patients with Coronavirus Disease 2019 (COVID-19) prominently manifests with pulmonary symptoms histologically reflected by diffuse alveolar damage (DAD), excess inflammation, pneumocyte hyperplasia and proliferation, and formation of platelet aggregates or thromboemboli. Methods We performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections. Single cell RNA sequencing (scRNA-seq) analysis of lung tissues from healthy 120 subjects have revealed that many cell types express SARS-CoV-2 entry receptor and 121 cofactors including angiotensin-converting enzyme-2 (ACE2), transmembrane serine 122 protease 2 (TMPRSS2), and furin, that are involved in viral entry, suggesting 123 susceptibility of these cells to infection. 7-10 Furthermore, scRNA-seq analysis of 124 bronchoalveolar lavage fluid (BALF), blood, oropharyngeal or lung tissues from COVID-125 19 patients has identified different types of SARS-CoV-2-infected cells, including 126 macrophages, neutrophils, type II pneumocytes (AT2), and ciliated and endothelial 127 cells. cache = ./cache/cord-343330-wuzts3mt.txt txt = ./txt/cord-343330-wuzts3mt.txt === reduce.pl bib === id = cord-343043-piyt3i0h author = Baker, S. A. title = Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation. date = 2020-07-07 pages = extension = .txt mime = text/plain words = 4608 sentences = 268 flesch = 47 summary = In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly. Given that the mechanism of death in Covid-19 typically involves severe lower respiratory tract infection, a disease feature strongly correlated with age, previous studies have sought to connect lung ACE2 expression with aging 28, 29 . If lung ACE2 expression is triggered by mechanical ventilation itself via inflammatory cytokine production, then these factors may predispose older individuals to severe SARS-CoV-2 infection. In this small series of cases, we identified increased ACE2 RNA and ACE2 protein expression within the human lung associated with age, when controlling for ventilator status. cache = ./cache/cord-343043-piyt3i0h.txt txt = ./txt/cord-343043-piyt3i0h.txt === reduce.pl bib === id = cord-343317-97n1j0jj author = Duan, Xiaohua title = Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date = 2020-05-02 pages = extension = .txt mime = text/plain words = 3776 sentences = 222 flesch = 56 summary = Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. The organoids infected with SARS-CoV-2 pseudo-entry virus at MOI=0.01 showed a strong signal at 24 hpi (Fig. 2a) . The mRNAs of SARS-CoV-2 pseudo-entry virus, including VSV-NS, VSV-N, and VSV-M, were detected in all five cell populations (Fig. 2f) , but not in the uninfected COs (Extended Data Fig. 2f) . Immunohistochemistry detected luciferase in ACE2 + and Villin + cells, suggesting these are permissive to SARS-CoV-2 pseudo-entry virus infection in vivo (Fig. 2k) . Next, we adapted hPSC-COs to a high throughput screening platform and probed the Prestwick FDA-approved drug library to identify drug candidates capable of blocking SARS-CoV-2 pseudo-virus infection. cache = ./cache/cord-343317-97n1j0jj.txt txt = ./txt/cord-343317-97n1j0jj.txt === reduce.pl bib === id = cord-342776-hkjhqgie author = Jewett, Anahid title = The Potential Effect of Novel Coronavirus SARS-CoV-2 on NK Cells; A Perspective on Potential Therapeutic Interventions date = 2020-07-10 pages = extension = .txt mime = text/plain words = 3612 sentences = 159 flesch = 41 summary = While studies on SARS-CoV-2 effects on immune cell function continue to progress, we know very little about the significance of depletion of key immune effectors by the virus in the mortality and morbidity of the disease. It also underscores the necessity for the future comprehensive studies of NK cells in SARS-CoV-2 infected individuals and animal models to better understand the role and significance of reported NK cell depletion and functional inactivation in disease morbidity and mortality, in hope to design effective therapeutic interventions for the disease. In particular, in the peripheral blood of patients that were infected with SARS, it was noted that there were significantly lower numbers of natural killer (NK) cells compared to healthy subjects (14) . As mentioned above the infectious agent of COVID-19 disease depletes NK cells in the peripheral blood, and potentially even in the lung tissues of patients, thereby, disabling and depleting the core immune effectors necessary to remove the virus and regulate uncontrolled immune activation. cache = ./cache/cord-342776-hkjhqgie.txt txt = ./txt/cord-342776-hkjhqgie.txt === reduce.pl bib === id = cord-343273-zaaraiy7 author = Hensley, Lisa E. title = Interferon-β 1a and SARS Coronavirus Replication date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1009 sentences = 58 flesch = 49 summary = Here, we report that recombinant human interferon (IFN)-β 1a potently inhibits SARS coronavirus replication in vitro. The IFN-β 1a preparation employed in this study was selected because it is currently used as part of the most effective treatment regimen for relapsing forms of multiple sclerosis (8) , and more importantly, because it was shown to have antiviral activity (as measured in a vesicular stomatitis virus cytopathic assay system) 14 times greater than the currently available treatment using IFN-β 1b (9) . In the current study, Vero E6 cells were treated with concentrations (5,000 to 500,000 IU/mL) of IFN-β 1a either 24 h before or 1 h after inoculation with the SARS-CoV (multiplicity of infection 0.1 PFU/cell), and monitored for cytopathic effect and production of infectious SARS-CoV at 24, 48, and 72 h postinfection. Production of infectious SARS-CoV was potently inhibited (>99.5% or 2.00 log 10 PFU/mL) at 24 h postinfection by pretreatment of Vero E6 cells with IFN-β 1a at all concentrations tested (Figure 1 ). cache = ./cache/cord-343273-zaaraiy7.txt txt = ./txt/cord-343273-zaaraiy7.txt === reduce.pl bib === id = cord-343362-4u2re1cu author = Liu, Jianjun title = SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis date = 2005-02-22 pages = extension = .txt mime = text/plain words = 5408 sentences = 234 flesch = 49 summary = METHODS AND FINDINGS: The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. We present here a novel application of mass spectrometry (MS)-based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore. The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. A further application of MS-based viral sequence variation analysis in tracking the virus strain and thus the transmission of SARS-CoV was demonstrated by our confirmation of the Singapore origin of a SARS-CoV isolate from a German patient. cache = ./cache/cord-343362-4u2re1cu.txt txt = ./txt/cord-343362-4u2re1cu.txt === reduce.pl bib === id = cord-343712-gn7fw891 author = Taglauer, Elizabeth title = Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads date = 2020-08-25 pages = extension = .txt mime = text/plain words = 1497 sentences = 86 flesch = 41 summary = title: Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads Parenchymal changes of placentas from COVID-19 infected mothers have been reported by several groups, but the localization and relative abundance of SARS-CoV-2 viral proteins and cellular entry machinery has not been fully characterized within larger placental tissue cohorts. Overall this study provides an important basis for the ongoing evaluation of SARS-CoV-2 physiology in pregnancy and highlights the importance of the placenta as a key source of primary human tissue for ongoing diagnostic and therapeutic research efforts to reduce the global burden of COVID-19. While ACE2 was consistently found in the sTB layer of all tissues 148 surveyed (COVID-19 Maternal and controls), TMPRSS2 expression was absent in both groups of 149 placentas (Fig. 3 A,B) . Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of 301 the placenta in pregnancies with COVID-19 positive mothers and neonates at birth cache = ./cache/cord-343712-gn7fw891.txt txt = ./txt/cord-343712-gn7fw891.txt === reduce.pl bib === id = cord-342731-rilr45yb author = Donia, Ahmed title = RNA interference as a promising treatment against SARS-CoV-2 date = 2020-09-01 pages = extension = .txt mime = text/plain words = 844 sentences = 58 flesch = 55 summary = Previous study also reported the production of plasmid-mediated small interfering RNAs (siRNAs) to target the viral RNA polymerase, which successfully inhibited the cytopathic effects of SARS-CoV on Vero cells (Wang et al. The genomic and the subgenomic mRNAs of coronaviruses have an identical 5′ leader sequence (via a unique mechanism called discontinuous transcription) and common 3′-ends, a unique feature in coronavirus replication. The siRNA targeting the leader sequence reduced the abundance of mRNA and protein expression levels of the reporter genes in 293 T cell line. They also found that the siRNA targeting the leader sequence could inhibit the replication of SARS-CoV via silencing gene expression in Vero E6 cells. Additionally, siRNA targeting the leader sequence exhibited a much potent inhibitory effect on the replication of SARS-CoV than the siRNAs targeting the spike gene made (Enjuanes et al. ) siRNA targeting the leader sequence of SARS-CoV inhibits virus replication cache = ./cache/cord-342731-rilr45yb.txt txt = ./txt/cord-342731-rilr45yb.txt === reduce.pl bib === id = cord-343455-v1648kng author = Zhu, Na title = Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4132 sentences = 237 flesch = 49 summary = Here, we characterize the replication dynamics, cell tropism and morphogenesis of SARS-CoV-2 in organotypic human airway epithelial (HAE) cultures. SARS-CoV-2 replicates efficiently and infects both ciliated and secretory cells in HAE cultures. In this study, we compared the characteristics of the replication dynamics, cell tropism, and morphogenesis of SARS-CoV-2 and HCoV-NL63 in HAE cells, which express the shared receptor, to better understand the pathogenesis and transmission of SARS-CoV-2. As shown in Fig. 1a , HAE cells were highly susceptible to SARS-CoV-2 infection with peak virus production from apical wash at 48-72 h post infection (h pi) and remained at a high level from 3 to 6 days. As shown in Fig. 1c , virus particles were found on the apical surface of both ciliated cells and secretory cells; inclusion bodies formed by viral components were observed in the cytoplasm, which confirmed the infection of both cell types. cache = ./cache/cord-343455-v1648kng.txt txt = ./txt/cord-343455-v1648kng.txt === reduce.pl bib === id = cord-343128-sh77c0af author = Bwire, G. M. title = Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis date = 2020-06-12 pages = extension = .txt mime = text/plain words = 3327 sentences = 221 flesch = 51 summary = title: Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted. Recent study by Wang et al (6) using 1070 clinical specimens such as bronchoalveolar lavage fluid (BLF), fibrobronchoscope brush biopsy (FBB), sputum, nasal and pharyngeal swabs, urine, feces and blood collected from 205 patients revealed a dynamic profile with high detection rate of virus from lower respiratory tract (LRT) specimens, i.e., BLF and zero detection from urogenital tract specimen, i.e., urine. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2 from different types clinical specimens using a standard diagnostic test (qRT-PCR). A systematic review protocol was developed based on the question "What is the positivity rate for SARS-CoV-2 using qRT-PCR in different types of clinical specimens". cache = ./cache/cord-343128-sh77c0af.txt txt = ./txt/cord-343128-sh77c0af.txt === reduce.pl bib === id = cord-343090-dsjq98ks author = Fragkou, Paraskevi C. title = Review of trials currently testing treatment and prevention of COVID-19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 2027 sentences = 153 flesch = 46 summary = OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. property to achieve at least 10-fold higher concentrations in epithelial lung fluid than in 202 serum, have led researchers to repurpose them against SARS-CoV-2 (Table 1, Table S1 observations the antifibrotic agent pirfenidone is being evaluated in at least three randomised 215 clinical trials for its efficacy in the prevention of post-COVID-19 pneumonia fibrosis (Table 216 1, Table S1 ). Among the eligible treatment studies, 310 children recruitment (i.e.< 14 years old) was reported in 7 clinical trials in total: 1 testing 311 darunavir with cobicistat (NCT04252274); 2 on human stem cells transfusion 312 (ChiCTR2000029606, ChiCTR2000030944); 1 testing hydroxycholoroquine (EudraCT 313 Phase IV and phase III treatment trials were the most commonly reported interventional study 319 types (n=40, 20% and n=35, 18% respectively) as demonstrated in Table 3 . cache = ./cache/cord-343090-dsjq98ks.txt txt = ./txt/cord-343090-dsjq98ks.txt === reduce.pl bib === id = cord-343143-tzuhig3f author = Chen, Rong-chang title = Treatment of Severe Acute Respiratory Syndrome With Glucosteroids The Guangzhou Experience date = 2006-06-30 pages = extension = .txt mime = text/plain words = 4649 sentences = 222 flesch = 44 summary = Conclusion This Guangzhou retrospective study revealed that proper use of corticosteroid in confirmed critical SARS resulted in lowered mortality and shorter hospitalization stay, and was not associated with significant secondary lower respiratory infection and other complications. However, the result of a logistic regression based on the data of 152 critical SARS cases showed that steroid therapy significantly reduced the case fatality among critical SARS patients after the death-related variables were adjusted, such as age, rigor at onset, secondary lower respiratory infection, pulmonary rales, and OI grading (1, Ͻ 100; 2, Ն 100 and Ͻ 200; 3, Ն 200 and Ͻ 300; and 4, Ն 300). cache = ./cache/cord-343143-tzuhig3f.txt txt = ./txt/cord-343143-tzuhig3f.txt === reduce.pl bib === id = cord-343185-lbmbp9ca author = Hansen, C. B. title = SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals date = 2020-07-29 pages = extension = .txt mime = text/plain words = 5349 sentences = 332 flesch = 51 summary = Here we have developed novel flexible ELISA-based assays for specific detection of SARS-CoV-2 antibodies against the receptor-binding domain (RBD): An antigen sandwich-ELISA relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Detection of IgM, IgA and IgG antibodies against SARS-CoV-2 protein N was evaluated by analyzing 136 positive samples and 174 negative controls and ROC curve analyses were assessed to estimate the assay performance . To provide a better insight into antibody seroconversion during SARS-CoV-2 infection and reactivity against different locations on protein S and protein N, we conducted IgM, IgA and IgG detection in 90 positive samples against 14 protein fragments and short peptides located on the protein S and protein N structures, full-length RBD, protein S and protein N (Figure 2A ). We have developed an ELISA-based platform for detection SARS-CoV-2 antibodies comprising an indirect RBD S-ELISA for pan Ig detection and direct ELISAs for in-depth analyses of the IgM, IgA and IgG isotype responses towards RBD and protein N. cache = ./cache/cord-343185-lbmbp9ca.txt txt = ./txt/cord-343185-lbmbp9ca.txt === reduce.pl bib === id = cord-343365-4y9fedcr author = Chang, Christopher title = Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date = 2013-11-30 pages = extension = .txt mime = text/plain words = 7295 sentences = 407 flesch = 50 summary = The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] . cache = ./cache/cord-343365-4y9fedcr.txt txt = ./txt/cord-343365-4y9fedcr.txt === reduce.pl bib === id = cord-343333-4krrmjio author = Salazar, Martín title = COVID-19, Hipertensión y Enfermedad cardiovascular date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2412 sentences = 249 flesch = 52 summary = Las comunicaciones provenientes de China en el inicio de la pandemia de COVID-19 mostraron una marcada asociación de los casos severos y la mortalidad con la edad avanzada, la hipertensión arterial, las enfermedades cardiovasculares y la diabetes. Las estimaciones de China coinciden con estos datos: que mientras la mortalidad sin comorbilidades fue de 0,9%, se incrementó a 10,5% con enfermedad Page 4 of 13 J o u r n a l P r e -p r o o f 4 cardiovascular, 6,3% con enfermedad pulmonar obstructiva crónica, 6% con hipertensión arterial y 5,6% con cáncer. En el reporte Morbidity and Mortality Weekly Report (MMWR), con datos al 28 de marzo, 78% de los pacientes internados en terapia intensiva por COVID-19 tenían comorbilidades, las más frecuentes eran la enfermedad cardiovascular (29%) y la enfermedad pulmonar crónica (21%). peor evolución del COVID-19, encontrando que la prevalencia de esta patología entre quienes fallecen o requieren cuidados críticos debido a la infección por SARS-CoV-2 es elevada, rondando entre un 7,5 y 39,5%, según los distintos reportes. cache = ./cache/cord-343333-4krrmjio.txt txt = ./txt/cord-343333-4krrmjio.txt === reduce.pl bib === id = cord-343148-rp3kmd80 author = Ayatollahi, Parisa title = Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection date = 2020-09-17 pages = extension = .txt mime = text/plain words = 1029 sentences = 68 flesch = 40 summary = title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection On the third day of admission, new behavioral changes appeared including elated mood, inappropriate laughing, anxiety, and insomnia, leading to treatment with clonazepam, risperidone, and sertraline, in addition to sodium divalproex. Repeat brain MRI showed signal hyperintensities on fluidattenuated inversion recovery (FLAIR) and T2-weighted sequences in the claustrum bilaterally, which were not present on the initial scan 2 weeks earlier. Follow-up MRI 1 month after the abnormal scan showed near-complete resolution of the claustrum hyperintensities ( Figure 2 ). [1] [2] [3] The MRI abnormality ("the claustrum sign") may extend to external/extreme capsules and insular cortices 3 and typically resolves in weeks or months. The finding of the claustrum sign on brain MRI, not previously reported in a COVID-19 patient, [4] [5] [6] [7] [8] provides further support for the idea that acute SARS-CoV-2 infection may present as an autoimmune encephalitis. cache = ./cache/cord-343148-rp3kmd80.txt txt = ./txt/cord-343148-rp3kmd80.txt === reduce.pl bib === id = cord-343523-xb4ee5r5 author = Azouz, Haya title = COVID-19 in an Infant with Congenital Adrenal Hyperplasia: A Case Report date = 2020-10-05 pages = extension = .txt mime = text/plain words = 1192 sentences = 85 flesch = 54 summary = Herein, we present a case of a 5-week-old infant with congenital adrenal hyperplasia who acquired SARS-CoV-2 and recovered with minimal medical support. Unlike 10% to 33% of the adult population, only 5.7% to 20% of known pediatric patients with SARS-CoV-2 infection required hospitalizations. We present a case report of an infant with a prior diagnosis of congenital adrenal hyperplasia (CAH) who was found to have SARS-CoV-2 infection. Since the start of the SARS-CoV-2 pandemic, several studies have been published pertaining to clinical presentation in various age groups, possible management options and its implications in patients with other comorbidities. To our knowledge, this is the first case report of SARS-CoV-2 infection in an infant with underlying adrenal insufficiency secondary to CAH. Our patient presented with fever and irritability that was worrisome given his age, the current pandemic and his underlying adrenal insufficiency. Interestingly, a prior case report of a 2-week-old infant with SARS-CoV-2 noted skin and soft tissue infection. cache = ./cache/cord-343523-xb4ee5r5.txt txt = ./txt/cord-343523-xb4ee5r5.txt === reduce.pl bib === id = cord-343800-nbydaoac author = Cerutti, Francesco title = Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2 date = 2020-09-29 pages = extension = .txt mime = text/plain words = 1209 sentences = 65 flesch = 56 summary = We evaluated the recently CE-approved rapid POCT SD-Biosensor for SARS-CoV-2 nucleoprotein detection in nasopharyngeal secretions from 330 patients admitted to the Emergency Room for a suspect of COVID-19 and travelers returning home from high risk countries. Point-of-care diagnostic tests (POCTs) for detecting viral antigens in clinical samples would be very helpful for the diagnosis of COVID-19 [2] either as mass-screening or first aid tests at the emergency room. To evaluate a recently CE-approved POCT, the STANDARD Q COVID-19 Ag (SD-Biosensor, RELAB, I), for the detection of SARS CoV-2 nucleoprotein in NP swabs in comparison with the gold standard RT-PCR. POCTs for the detection of SARS-CoV-2 J o u r n a l P r e -p r o o f antigens are quite promising; however, the principal concerns are the false-negative rate due to low viral loads [3] [4] [5] [6] [7] [8] . Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples cache = ./cache/cord-343800-nbydaoac.txt txt = ./txt/cord-343800-nbydaoac.txt === reduce.pl bib === id = cord-343586-28ezisog author = Rocca, María Florencia title = A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1498 sentences = 78 flesch = 47 summary = title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied. These preliminary results suggest that MALDI-TOF MS coupled with ClinProTools software represents an interesting alternative as a screening tool for diagnosis of SARS-CoV-2, especially because of the good performance and accuracy obtained with samples in which viral presence was not detected. cache = ./cache/cord-343586-28ezisog.txt txt = ./txt/cord-343586-28ezisog.txt === reduce.pl bib === id = cord-343502-1n0o4akm author = Chen, Zhang-Ren title = Pharmacotherapics Advice in Guidelines for COVID-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 4051 sentences = 216 flesch = 48 summary = SARS-CoV-2 (previously termed 2019 novel coronavirus, 2019-nCoV), a virus that causes COVID-19, likely initially transmitted from bat to human (Gorbalenya et al., 2020) , infected over 6 million people worldwide from its outbreak in December 2019 to May 2020 (China CDC, 2020; WHO, 2020a) . China, Italy, Germany, the ATS (American Thoracic Society), the SSC (Surviving Sepsis Campaign), the NIH (National Institutes of Health), the IDSA (Infectious Diseases Society of America), and the FDA (Food and Drug Administration) released guidelines and recommended several medicines for the treatment of COVID-19 (Table 1) . The majority of anti-SARS-CoV-2 virus drugs are adopted from the treatment of severe acute respiratory syndrome (SARS) or Middle East respiratory syndrome (MERS): alpha-interferon, lopinavir/ritonavir, and ribavirin. The guideline from Italy recommended remdesivir (Italian Society of Infectious and Tropical Diseases SECTION, 2020), and the FDA approved emergency use authorization (EUA) of remdesivir for the treatment of COVID-19 (FDA, 2020). cache = ./cache/cord-343502-1n0o4akm.txt txt = ./txt/cord-343502-1n0o4akm.txt === reduce.pl bib === id = cord-343515-fad1yyqx author = Felgenhauer, Ulrike title = Inhibition of SARS–CoV-2 by type I and type III interferons date = 2020-10-09 pages = extension = .txt mime = text/plain words = 2934 sentences = 157 flesch = 53 summary = For SARS-CoV-2 (dark gray bars), statistically significant negative correlation coefficients (CC) were obtained for both cell lines, indicating that viral replication is increasingly inhibited by IFN-a. Observations were similar when the input MOI was reduced to 0.001 (Fig. S1 ), except that titers of SARS-CoV-1 in Calu-3 cells were already very low in the absence of any IFN-a, resulting in a nonsignificant effect of additional IFN. Our data thus indicate that (i) if anything, ruxolitinib is an enhancer rather than an inhibitor of SARS-CoV-2 multiplication, and (ii) the boosting effect is most likely due to inhibition of the antiviral JAK/ STAT signaling pathway, because it is not present in the IFN induction-deficient Vero E6 cells. For the statistical testing of the dose-response effect of IFN (type I and III) against SARS-coronaviruses, the typical regression procedures were not applicable because of several values below the detection limit and some ties in the data. cache = ./cache/cord-343515-fad1yyqx.txt txt = ./txt/cord-343515-fad1yyqx.txt === reduce.pl bib === id = cord-343415-lj2trn85 author = Del Barba, Paolo title = COVID‐19 cardiac involvement in a 38‐day old infant date = 2020-06-18 pages = extension = .txt mime = text/plain words = 996 sentences = 61 flesch = 47 summary = We report the case of an infant who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and developed mild cardiovascular inflammation, a novelty for patients of very young age, that contributes to defining the puzzling nature of this disease in pediatric patients. 1 COVID-19 may indeed have cardiac complications, including myocarditis, 2 and up to 31% of children have myocardial enzyme elevation, mainly creatine kinase MB, despite no specific sign or symptom of clinical cardiac disease. For the first time, we report the case of an infant affected by COVID-19 with documented mild cardiac involvement. The chest computed tomograpghy scan was not performed, thus avoiding the exposure to Abbreviations: ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. We suggest that SARS-CoV-2 cardiac involvement should always be taken into account also in children; while our case was mild, it might be of concern especially in patients with other underlying conditions. cache = ./cache/cord-343415-lj2trn85.txt txt = ./txt/cord-343415-lj2trn85.txt === reduce.pl bib === id = cord-343569-9th5bcv0 author = Fu, Yu-Zhi title = SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response date = 2020-10-27 pages = extension = .txt mime = text/plain words = 3403 sentences = 239 flesch = 51 summary = [28] [29] [30] To identify SARS-CoV-2 proteins that may inhibit the RLR-mediated induction of downstream antiviral genes, we constructed 17 SARS-CoV-2 protein expression clones and screened for candidates that inhibit the Sendai virus (SeV, an RNA virus)-induced activation of the IFNβ promoter in HEK293 cells by reporter assays (Fig. 1A) . In reporter assays, ectopic expression of the M protein dose-dependently inhibited the SeV-induced activation of We next performed ELISA experiments and found that the secretion of IFN-β and TNF-α following SeV infection or poly (I:C) transfection was also impaired in HEK293-M cells (Fig. 1G ). These results suggest that the M protein impairs the recruitment of TRAF3, TBK1 and IRF3 to the MAVS complex, leading to the inhibition of the innate antiviral response. In this study, we identified the SARS-CoV-2 M protein as a factor underlying the inhibition of host antiviral innate immunity by directly targeting the central adaptor MAVS in the RLR-mediated induction of type I IFNs. Several lines of evidence suggest that M directly targets MAVS to inhibit the innate immune response. cache = ./cache/cord-343569-9th5bcv0.txt txt = ./txt/cord-343569-9th5bcv0.txt === reduce.pl bib === id = cord-343082-46lo7xtx author = Awasthi, Ankit title = OUTBREAK of novel corona virus disease (COVID-19): Antecedence and aftermath date = 2020-07-25 pages = extension = .txt mime = text/plain words = 3945 sentences = 225 flesch = 46 summary = Studies also confirm that flu shots are not efficient in the fight against COVID-19 as the patients continue to suffer despite the treatment (https://www.wsj.com/articles/gilead-sciences-offers-experimental-drug-for-coronavirustreatments-testing-11580511519).In the meantime, Thai health officials claimed to have successfully handled the infection with acocktail of antiviral drugs that include lopinavir and ritonavir under the name "Kaetra" along with flu medication oseltamivir. In 2016, this drug was used as an emergency aid for the Ebola virus outbreak.A clinical trial involving 80 participants (in Shenzhen city) demonstrated chest symptoms improvement in patients of COVID-19 treated with favipiravir. Favipiravirhas been reported to be effective, without any obvious side-effects, in helping coronavirus patients recover.In another study carried out in China, two mild and two severe COVID-19 associated pneumonia patients were treated with combined Western and Chinese medicine treatment (Lopinavir/ritonavir/arbidol/ShufengJiedu Capsule). In recent clinical studies the use of steroidal drug Dexamethasone has been very effective to treat patients suffering from COVID-19. cache = ./cache/cord-343082-46lo7xtx.txt txt = ./txt/cord-343082-46lo7xtx.txt === reduce.pl bib === id = cord-341987-lsvifqyo author = Kalyanasundaram, Sridhar title = Novel Corona Virus Pandemic and Neonatal Care: It’s Too Early to Speculate on Impact! date = 2020-08-03 pages = extension = .txt mime = text/plain words = 3967 sentences = 206 flesch = 50 summary = We discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 (COVID-19) in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. In this article, we discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. Another recent case study published in Nature Communication reported transplacental transmission of COVID-19 from a positive pregnant mother during the last trimester to her offspring which occurred due to maternal viremia, placental infection, and neonatal viremia following placental infection [34] . cache = ./cache/cord-341987-lsvifqyo.txt txt = ./txt/cord-341987-lsvifqyo.txt === reduce.pl bib === id = cord-343357-5nhyumxl author = Heegaard, Peter M. H. title = Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date = 2020-09-25 pages = extension = .txt mime = text/plain words = 3446 sentences = 180 flesch = 46 summary = We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. cache = ./cache/cord-343357-5nhyumxl.txt txt = ./txt/cord-343357-5nhyumxl.txt === reduce.pl bib === id = cord-343618-jjb8da4a author = Nie, Kai title = Gastrointestinal insights during the COVID-19 epidemic date = 2020-09-26 pages = extension = .txt mime = text/plain words = 2046 sentences = 129 flesch = 40 summary = Thus, cancer and inflammatory bowel disease (IBD) management, stool viral tests, and virus exposure are major concerns in the context of COVID-19 epidemic. Patients with digestive disease bear a relatively high risk of SARS-CoV-2 infection. This finding suggests that gastrointestinal cancer patients may be more susceptible to SARS-CoV-2 infection [47] . To date, several cases of SARS-CoV-2 infection in IBD patients have been reported. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China cache = ./cache/cord-343618-jjb8da4a.txt txt = ./txt/cord-343618-jjb8da4a.txt === reduce.pl bib === id = cord-343715-y594iewi author = Gavriatopoulou, Maria title = Organ-specific manifestations of COVID-19 infection date = 2020-07-27 pages = extension = .txt mime = text/plain words = 8765 sentences = 447 flesch = 38 summary = Patients infected with this new coronavirus present with a variety of symptoms, which range from asymptomatic disease to mild and moderate symptoms (mild pneumonia), severe symptoms (dyspnoea, hypoxia, or > 50% lung involvement on imaging) and symptoms of critical illness (acute respiratory distress syndrome, respiratory failure, shock or multiorgan system dysfunction). A large retrospective observational study from China showed that among 214 hospitalized patients with confirmed SARS-CoV-2 infection, 36.4% had neurological manifestations [114] . The correlation of disease severity with neurological symptoms was confirmed by another retrospective study from France, reporting a prevalence of 84% of neurological manifestations in 58 hospitalized patients with acute respiratory distress syndrome (ARDS) due to COVID-19 [115] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-343715-y594iewi.txt txt = ./txt/cord-343715-y594iewi.txt === reduce.pl bib === id = cord-343766-hlg7t5i5 author = Vinken, Mathieu title = A putative AOP for pneumonia related to COVID-19 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 994 sentences = 59 flesch = 47 summary = In order to further encourage research in this direction, an updated version of the putative AOP for pneumonia linked to COVID-19 is proposed, which encompasses new knowledge that is rapidly accumulating (Fig. 1) . One of the major MIEs in this AOP is the binding of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor at the plasma membrane surface of type II pneumocytes lining the alveoli in lung. Such AOP network should comprise the mechanisms driving the multi-organ failure frequently observed in severe COVID-19 patients, for which the causes (i.e. MIEs) are as yet not entirely clear or delineated. Thus, liver failure may be caused by the direct binding and actions of SARS-CoV-2 in hepatocytes or cholangiocytes, but could also be an indirect consequence of the systemic inflammatory response syndrome associated with COVID-19. A putative AOP for pneumonia linked to COVID-19 cache = ./cache/cord-343766-hlg7t5i5.txt txt = ./txt/cord-343766-hlg7t5i5.txt === reduce.pl bib === id = cord-343566-epvswt7f author = Wang, Zhao-Hua title = Critically Ill Patients with Coronavirus Disease 2019 in a Designated ICU: Clinical Features and Predictors for Mortality date = 2020-07-20 pages = extension = .txt mime = text/plain words = 3291 sentences = 198 flesch = 50 summary = CONCLUSION: Critically ill COVID-19 patients aged higher than 70, arrhythmia, or a SOFA score above 4 have a high risk of mortality, and need prior medical intervention. In the present study, we present details of 59 critically ill patients with SARS-CoV-2 infection, admitted to the intensive care unit (ICU) of Caidian Branch of Tongji Hospital, and then identified prognostic factors for mortality of these critically ill patients. 3, 4 According to the WHO interim guidance and Diagnostic and Treatment Program of COVID-19 (Version 7.0) published by the National Health Commission of the People's Republic of China, all patients were diagnosed with severe pneumonia induced by SARS-CoV-2 infection who required mechanical ventilation, had inspiratory oxygen fraction (FiO₂) ≥60%, or had the shock or organ failure. cache = ./cache/cord-343566-epvswt7f.txt txt = ./txt/cord-343566-epvswt7f.txt === reduce.pl bib === id = cord-343836-daqrym0b author = Lange, Clemens title = Welche Bedeutung hat die Bindehaut als möglicher Übertragungsweg für eine SARS-CoV-2-Infektion? date = 2020-06-22 pages = extension = .txt mime = text/plain words = 985 sentences = 87 flesch = 48 summary = Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV‑2 via these mediators unlikely. Es ist derzeit nicht eindeutig geklärt, ob Zellen der Augenoberfläche ACE2 oder TMPRSS2 exprimieren und damit für eine SARS-CoV-2-Infektion anfällig sind. The current body of evidence indicates that SARS-CoV-2 requires the membrane-bound angiotensinconverting enzyme 2 (ACE2) and the membrane-bound serine protease TMPRSS2 to enter cells. Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV-2 via these mediators unlikely. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection cache = ./cache/cord-343836-daqrym0b.txt txt = ./txt/cord-343836-daqrym0b.txt === reduce.pl bib === id = cord-344017-qldawc8m author = Edouard, S. title = Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France date = 2020-11-11 pages = extension = .txt mime = text/plain words = 4013 sentences = 191 flesch = 48 summary = Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. In this study, we are reporting our experience to develop an indirect immunofluorescent assay (IFA) for the detection of anti-SARS-CoV-2 antibodies that we implemented before any other serological test was available in France. ELISA To compare our IFA with commercial ELISA IgG, we randomly selected 70 sera with possible cross-reactivity (including 45 sera with possible nonspecific serological interference and 25 sera from patients diagnosed with common others human coronavirus), 30 sera collected before the pandemic and 100 sera from our cohort of SARS-CoV-2-infected patients among all the sera that we tested by IFA. Some other studies also reported an earlier serological response in severe compared to mild SARS-CoV-2 infection [5, 20, 25] that is consistent with the earlier seroconversion that we found in patients with poor clinical outcome (PClinO). cache = ./cache/cord-344017-qldawc8m.txt txt = ./txt/cord-344017-qldawc8m.txt === reduce.pl bib === id = cord-343870-g2v7ihud author = Liu, Wei title = Virus-, host-, immune-based targets for COVID-19 therapy date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1716 sentences = 102 flesch = 46 summary = Anti-viral agents against different targets had exhibited profound therapeutic effect on SARS-CoV-2 through which the clinicians were able to control the COVID-19 outbreak. Clinicians worldwide have been voraciously seeking for a potential anti-COVID-19 drug of all modules such as vaccines; targetspecific monoclonal antibodies; viral oligonucleotide-based peptide drugs; interferons and other small bio-actives [2] . S protein being the crucial protein facilitating the SARS-CoV-2 entry into the host has been preferred as a potential therapeutic target of interests as it could be spliced into two individual peptides by the furin-like proteases [5] . The other novel drug-like K22 that inhibits the viral-dependent RNA synthesis exhibited strong anti-replicative activity against the coronaviruses in an in-vitro set-up. Stimulation of innate immune response is crucial for controlling the SARS-CoV-2 replication and its virulence on the infected hosts [8] . cache = ./cache/cord-343870-g2v7ihud.txt txt = ./txt/cord-343870-g2v7ihud.txt === reduce.pl bib === id = cord-342786-dl8vjwfn author = Sattar, Yasar title = COVID-19 Cardiovascular Epidemiology, Cellular Pathogenesis, Clinical Manifestations and Management date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5268 sentences = 349 flesch = 37 summary = Abstract Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. The infected patients may also present with cardiovascular disease (CVD) like acute coronary syndrome(ACS) and congestive cardiac failure(CHF) [6] . The systemic inflammation in COVID-19 may also dysregulate the post-translational modification of cardiac ion channels resulting in arrhythmia [25, 26] It is also noteworthy that viral proteins of SARS-CoV-2, ORF3 and ORF8, activate NLRP3 inflammasomes which inturn promotes atrial fibrillation [27, 28] . cache = ./cache/cord-342786-dl8vjwfn.txt txt = ./txt/cord-342786-dl8vjwfn.txt === reduce.pl bib === id = cord-343604-v986m9jd author = Vijayakumar, Balaji Gowrivel title = In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 1258 sentences = 90 flesch = 47 summary = title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. Coronavirus main 403 proteinase (3CLpro) structure: basis for design of anti-SARS drugs Structural basis for inhibition 675 of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir cache = ./cache/cord-343604-v986m9jd.txt txt = ./txt/cord-343604-v986m9jd.txt === reduce.pl bib === id = cord-343691-sjz5og78 author = Nakajima, Kei title = Serious Conditions in COVID-19 Accompanied With a Feature of Metabolic Syndrome date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1224 sentences = 75 flesch = 47 summary = Retrospective research has shown that COVID-19 is frequently observed in people with obesity, diabetes, and hypertension [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] , which are pivotal components of metabolic syndrome (MetS), a cluster of cardiometabolic risks based on excess visceral fat. In recent decades, many investigators have convincingly shown that people with obesity, prediabetes, diabetes and MetS are at increased risk for impaired lung function, and especially impaired restrictive lung pattern [16] [17] [18] [19] [20] [21] [22] , which is primarily determined by reduced predicted forced vital capacity. In patients with any of the specific metabolic abnormalities of MetS, pre-existing impaired lung function can predispose them to SARS-CoV-2 infection and even accelerate it, potentially worsening the condition. cache = ./cache/cord-343691-sjz5og78.txt txt = ./txt/cord-343691-sjz5og78.txt === reduce.pl bib === id = cord-343827-jo61t3m0 author = Qian, Qun title = Direct evidence of active SARS-CoV-2 replication in the intestine date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1314 sentences = 98 flesch = 53 summary = We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. cache = ./cache/cord-343827-jo61t3m0.txt txt = ./txt/cord-343827-jo61t3m0.txt === reduce.pl bib === id = cord-343876-2inr4mcy author = Xie, Qin title = COVID-19 patients managed in psychiatric inpatient settings due to first-episode mental disorders in Wuhan, China: clinical characteristics, treatments, outcomes, and our experiences date = 2020-10-02 pages = extension = .txt mime = text/plain words = 4834 sentences = 215 flesch = 40 summary = During the outbreak of COVID-19, the selection of an appropriate treatment setting for COVID-19 patients with mental disorders is a dilemma: in respiratory treatment settings these patients are more likely to not adhere with The main findings of this comparative study are 1) adjustment disorder and acute and transient psychotic disorders, with associated acute stress were the main clinical diagnoses in the COVID-19 group and some other disorders had their organic basis such as delirium due to infection and chloroquine-induced psychosis, while serious mental illnesses (SMIs) and alcohol use disorders were overrepresented in the control group, a common feature of inpatients of most Chinese psychiatric hospitals; 2) a wide range of psychiatric symptoms were found in COVID-19 patients with mental disorders on admission, including psychotic symptoms, aggressive behaviors, and anxiety symptoms; 3) the most common respiratory symptom of COVID-19 patients was cough, followed by fever, chills, and fatigue; and 4) mental disorders and COVID-19 of most patients were successfully treated after symptomatic and supportive treatments, including conventional psychotropic treatment and antiviral treatment, and, COVID-19 patients left the hospital earlier than psychiatric patients without COVID-19, on average by 16 days after admission. cache = ./cache/cord-343876-2inr4mcy.txt txt = ./txt/cord-343876-2inr4mcy.txt === reduce.pl bib === id = cord-343845-suoy3ojr author = Martín, Vicente title = Prevalencia de la Infección por SARS-CoV-2 en médicos y enfermeras de Atención Primaria y Residencias de Ancianos del Área de Salud de León y Factores asociados date = 2020-06-06 pages = extension = .txt mime = text/plain words = 2712 sentences = 194 flesch = 56 summary = ABSTRACT Objective: To evaluate the prevalence and associated factors with SARS-CoV-2 infection in general practitioners and nurses of primary care centers and nursing homes in the health area of León (Spain). The aim of this study is to evaluate the prevalence and factors associated with SARS-CoV-2 infection in General Practitioners and Nurses of primary care centers and nursing homes in the health area of León. The most relevant results of this study indicate that the observed prevalence of SARS-CoV-2 infection in the health workers analyzed is 5.9% (CI95% 4.4%-8.0%), being higher in nursing home workers compared to primary care centers (9.5% vs. Our results indicate that a high number of professionals remain susceptible to SARS-CoV-2 infection and therefore protective measures should be taken, not only in primary care, as the main contact with the health system, but also in nursing homes. cache = ./cache/cord-343845-suoy3ojr.txt txt = ./txt/cord-343845-suoy3ojr.txt === reduce.pl bib === id = cord-343476-0chuwvg6 author = MacLean, Oscar A. title = Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date = 2020-05-29 pages = extension = .txt mime = text/plain words = 1386 sentences = 73 flesch = 51 summary = Here we contrast the role of positive selection and recombination in the Sarbecoviruses in horseshoe bats to SARS-CoV-2 evolution in humans. While methods can detect some evidence for positive selection in SARS-CoV-2, we demonstrate these are mostly due to recombination and sequencing artefacts. For all but two of the ten positive selected codons, this signal was being driven by apparent convergent evolution (or homoplasy) in the tree, with the same mutation occurring in parallel across the phylogeny. To investigate whether this observation was truly due to independent events or because of recombination signatures in the SARS-CoV-2 outbreak tree, we firstly determined if the samples with these convergent mutations were geographically correlated. The Spike V367F signal was driven by apparent convergent evolution between four french samples sequenced in January and a Hong Kong sample 412028, which shows shared variation either side of the homoplasy suggesting it is not a recombinant (Supplementary figure 3C) . cache = ./cache/cord-343476-0chuwvg6.txt txt = ./txt/cord-343476-0chuwvg6.txt === reduce.pl bib === id = cord-344006-0iq9s94n author = Atzrodt, Cassandra L. title = A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7283 sentences = 428 flesch = 54 summary = All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . cache = ./cache/cord-344006-0iq9s94n.txt txt = ./txt/cord-344006-0iq9s94n.txt === reduce.pl bib === id = cord-343340-zi0rfidc author = Aragón‐Caqueo, Diego title = Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date = 2020-05-03 pages = extension = .txt mime = text/plain words = 3319 sentences = 155 flesch = 51 summary = The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. Therefore, the aim of this study is to provide a mathematical model to estimate the optimum number of pooled samples according to the specific prevalences of positive tests in a particular country context, in order to save as many tests as possible and cover as many people as possible, knowing that if a group tests out positive, all the individuals of the sample would have to be individually tested. This article proposed a simple and landed model to estimate the most optimum group number to implement pool testing strategy for SARS-CoV-2, according to the specific historical positive tests prevalence for a determined healthcare context. cache = ./cache/cord-343340-zi0rfidc.txt txt = ./txt/cord-343340-zi0rfidc.txt === reduce.pl bib === id = cord-343850-p4bbb6vm author = Lin, Meng-Hsuan title = Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain date = 2020-09-18 pages = extension = .txt mime = text/plain words = 5149 sentences = 313 flesch = 59 summary = SARS-CoV-2 encodes the conserved macro domain within nonstructural protein 3, which may reverse cellular ADP-ribosylation and potentially cut the signal of a viral infection in the cell. Herein, we report that the SARS-CoV-2 macro domain was examined as a poly-ADP-ribose (ADPR) binding module and possessed mono-ADPR cleavage enzyme activity. After confirming the ADPR binding ability via a biophysical approach, the X-ray crystal structure of the SARS-CoV-2 macro domain was determined and structurally compared with those of other viruses. This study provides structural, biophysical, and biochemical bases to further evaluate the role of the SARS-CoV-2 macro domain in the host response via ADP-ribose binding but also as a potential target for drug design against COVID-19. Virus macro domains were reported to have multiple functions, including a ADP-ribose (ADPR) 8−10 or poly-ADPR 9 interaction, adenine-rich RNA 11 binding, enzyme activities of ADPR-1″ phosphohydrolase, 7, 9 and the removal of mono(ADP-ribose) from protein. cache = ./cache/cord-343850-p4bbb6vm.txt txt = ./txt/cord-343850-p4bbb6vm.txt === reduce.pl bib === id = cord-343966-bfon094h author = Djaparidze, L. title = SARS-CoV-2 waves in Europe: A 2-stratum SEIRS model solution date = 2020-10-13 pages = extension = .txt mime = text/plain words = 9878 sentences = 605 flesch = 61 summary = Almost every other finding in this paper also came from this tool: Immune level estimation sensitivity analysis (e.g. change Ro and fit); Estimating the spreading day if only one non-communitarian spreader is assumed (i.e. change initial spreading day until fitted initial spreaders is 1); Finding that Do=2 coupled with Eo=5 can explain the multiple valleys after lockdowns observed in the 1-day moving average daily death curves (i.e. fitting a dozen of different pairs of Do and Eo); Include lack of IgG in asymptomatic when predicting reported serology ratio (i.e. add TAK variable and equation); Estimate the proportion of asymptomatic for <60 and >60 (i.e. change proportions and fit until predicted asymptomatic to symptomatic ratio in Spain matches the reported = 1); Estimate that the proportion of SARS-CoV-2 positive reported deaths that are "with" the virus is 15% (i.e. add testing positive period parameter and yearly probability of dying for other causes to the predicted sars-cov2 positive deaths and lower IFR_vul until predicted serology ratio matches again); Estimate the minimum value of IFR_vul to have another wave in Brussels or the maximum that avoids the low one in Stockholm (i.e. change IFR_vul and fit until the second wave appears or disappears); Hypothesize that an early wave of a D614 like variant can be the cause of low mortality in most locations in Asia (i.e. fit with an hypothetical lower IFR_vul competing strain and then simulate setting the dominant spreading event 60 days earlier). cache = ./cache/cord-343966-bfon094h.txt txt = ./txt/cord-343966-bfon094h.txt === reduce.pl bib === id = cord-343517-vf32wxkx author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date = 2020-04-11 pages = extension = .txt mime = text/plain words = 2745 sentences = 163 flesch = 53 summary = However, SARS-CoV-2 has emerged with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. The evolutionary distances showed that all the SARS-CoV-2 spike proteins cluster in the same node of the phylogenetic tree confirming the sequences are similar to Refseq YP_009724390 (Fig. 2) . cache = ./cache/cord-343517-vf32wxkx.txt txt = ./txt/cord-343517-vf32wxkx.txt === reduce.pl bib === id = cord-344120-7t5ce2hb author = Baroutjian, Amanda title = SARS-CoV-2 pharmacologic therapies and their safety/effectiveness according to level of evidence date = 2020-09-01 pages = extension = .txt mime = text/plain words = 5264 sentences = 336 flesch = 53 summary = CONCLUSION: According to level 1 evidence reviewed here, the most effective SARS-Co-V-2 pharmacologic treatments include remdesivir for mild to severe disease, and a triple regimen therapy consisting of lopinavir-ritonavir, ribavirin and interferon beta-1b for mild to moderate disease. 20 Another randomized controlled open-label trial in 199 hospitalized patients with confirmed SARS-CoV-2 with severe COVID-19 was done to compare the clinical effectiveness of lopinavir-ritonavir to standard care alone. According to the level 1 evidence reviewed here, the most effective treatments against SARS-CoV-2, measured by time to negative RT-PCR and time to clinical improvement, are remdesivir therapy and a triple medication regimen (lopinavir-ritonavir, ribavirin, and interferon beta-1b). First, in patients with severe COVID-19, treatment with lopinavir-ritonavir showed no significant difference in time to clinical improvement, mortality at day 28, or detectable viral load compared to standard care alone. cache = ./cache/cord-344120-7t5ce2hb.txt txt = ./txt/cord-344120-7t5ce2hb.txt === reduce.pl bib === id = cord-343757-e4hmo4yc author = Velavan, Thirumalaisamy P. title = The COVID‐19 epidemic date = 2020-02-16 pages = extension = .txt mime = text/plain words = 1307 sentences = 74 flesch = 45 summary = The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People's Republic of China, has spread to many other countries. The initial clinical sign of the SARS-CoV-2-related disease COVID-19 which allowed case detection was pneumonia. A combination of the antiretroviral drugs lopinavir and ritonavir significantly improved the clinical condition of SARS-CoV patients [17] and might be an option in COVID-19 infections. Repurposing these available drugs for immediate use in treatment in SARS-CoV-2 infections could improve the currently available clinical management. Given the fragile health systems in most sub-Saharan African countries, new and re-emerging disease outbreaks such as the current COVID-19 epidemic can potentially paralyse health systems at the expense of primary healthcare requirements. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Clinical characteristics of 2019 novel coronavirus infection in China. cache = ./cache/cord-343757-e4hmo4yc.txt txt = ./txt/cord-343757-e4hmo4yc.txt === reduce.pl bib === id = cord-343919-n8884bli author = Salvio, Gianmaria title = Bone Metabolism in SARS-CoV-2 Disease: Possible Osteoimmunology and Gender Implications date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3908 sentences = 183 flesch = 39 summary = We present a brief review of the molecular mechanisms linking inflammatory diseases to increased fracture risk/osteoporosis and of the therapeutic strategies that can prevent bone resorption in patients with inflammatory disease, focusing on the RANK-RANKL system. A subsequent in vitro study showed that a specific SARS-CoV protein, 3a/X1, directly promotes osteoclastogenesis, accelerating osteoclast differentiation from monocyte/macrophage precursors, enhancing the expression of receptor activator of NF-kB ligand (RANKL) and inflammatory cytokines such as TNF-α, which indirectly promote osteoclastogenesis [20] . As will be explained later in the text, IL-6 represents an important cofactor for bone resorption in inflammatory diseases; therefore, during SARS-CoV-2 infection, men, though less affected by osteoporosis, may experience more bone metabolism alterations than women for higher levels of IL-6 resulting from the lack of suppression by estrogen. cache = ./cache/cord-343919-n8884bli.txt txt = ./txt/cord-343919-n8884bli.txt === reduce.pl bib === id = cord-344012-npob20n0 author = Gheblawi, Mahmoud title = Angiotensin-Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System: Celebrating the 20th Anniversary of the Discovery of ACE2 date = 2020-05-08 pages = extension = .txt mime = text/plain words = 10479 sentences = 569 flesch = 39 summary = ACE2 (angiotensin-converting enzyme 2) has a multiplicity of physiological roles that revolve around its trivalent function: a negative regulator of the renin-angiotensin system, facilitator of amino acid transport, and the severe acute respiratory syndrome-coronavirus (SARS-CoV) and SARS-CoV-2 receptor. Our review summarizes the progress over the past 20 years, highlighting the critical role of ACE2 as the novel SARS-CoV-2 receptor and as the negative regulator of the renin-angiotensin system, together with implications for the coronavirus disease 2019 pandemic and associated cardiovascular diseases. 21, 22 Ongoing global efforts are focused on manipulating the ACE2/Ang 1-7 axis to curtail SARS-CoV-2 infection while affording maximal protective effects against lung and cardiovascular damage in patients with In this review, we summarize the diverse roles of ACE2, highlighting its role as the SARS-CoV-2 receptor and negative regulator of the RAS, and the implications for the COVID-19 pandemic. cache = ./cache/cord-344012-npob20n0.txt txt = ./txt/cord-344012-npob20n0.txt === reduce.pl bib === id = cord-344170-qrupbtem author = Biswas, Subrata K title = Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 date = 2020-05-24 pages = extension = .txt mime = text/plain words = 910 sentences = 57 flesch = 56 summary = Variations in the genomic sequences were also observed when sequencing data from viral isolates of patients from other European and North American countries were compared with each other and with reference sequence [1] . However, this recent study [2] did not explore the association between genetic variation in SARS-CoV-2 and the severity of COVID-19. Therefore, it is an urgent need to explore the association of the mutation pattern of SARS-CoV-2 genome with the severity and fatality of COVID-19. Based on the above discussion, we hypothesize that the genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 in the population. Analysis of sequencing data of SARS-CoV-2 genome showed evidence of mutation at the beginning of the worldwide spread of COVID-19 [1] . This hypothesis can be tested by obtaining genetic sequences of SARS-CoV-2 from two groups of COVID-19 patients. cache = ./cache/cord-344170-qrupbtem.txt txt = ./txt/cord-344170-qrupbtem.txt === reduce.pl bib === id = cord-344003-oul2hdyq author = Maleki Dana, Parisa title = An Insight into the Sex Differences in COVID-19 Patients: What are the Possible Causes? date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2761 sentences = 168 flesch = 51 summary = Moreover, it is observed that men have a higher risk of developing a severe form of the disease compared to women, highlighting the importance of disaggregated data of male and female COVID-19 patients. ACE2: angiotensin converting enzyme-2 ADAM-17: ADAM metallopeptidase domain-17 AR: androgen receptor CCL: chemokine (C-C motif) ligand cFT: calculated free testosterone CRP: C-reactive protein CXCL: chemokine (C-X-C motif) ligand E2: estradiol ESR: estrogen receptor ICU: intensive care unit IL: interleukin mACE2: myocardial angiotensin converting enzyme-2 NHBE: normal human bronchial epithelial RICU: respiratory intensive care unit sACE2: soluble angiotensin converting enzyme-2 SARS: Severe Acute Respiratory Syndrome SARS-CoV: Severe Acute Respiratory Syndrome Coronavirus TMPRSS2: transmembrane serine protease-2 TT: total testosterone with the virus will die in comparison with men (1.7%/2.8%). Studies of COVID-19 patients have shown that men have a higher risk of developing to the severe form of the disease compared to women. cache = ./cache/cord-344003-oul2hdyq.txt txt = ./txt/cord-344003-oul2hdyq.txt === reduce.pl bib === id = cord-344356-up53a0k4 author = Feaster, Matt title = High Proportion of Asymptomatic SARS-CoV-2 Infections in 9 Long-Term Care Facilities, Pasadena, California, USA, April 2020 date = 2020-10-17 pages = extension = .txt mime = text/plain words = 956 sentences = 62 flesch = 53 summary = Our analysis of coronavirus disease prevalence in 9 long-term care facilities demonstrated a high proportion (40.7%) of asymptomatic infections among residents and staff members. Infection control measures in congregate settings should include mass testing–based strategies in concert with symptom screening for greater effectiveness in preventing the spread of severe acute respiratory syndrome coronavirus 2. Early in the COVID-19 pandemic, the supply of both nasopharyngeal swabs and test kits for SARS-CoV-2 rRT-PCR testing in the United States was extremely limited and made available only for symptomatic persons meeting certain criteria determined by the Centers for Disease Control and Prevention (CDC) (12). Our findings demonstrate a high prevalence of both symptomatic and asymptomatic COVID-19 infection among residents and staff in 9 LTCFs. Because the potential for asymptomatic transmission of SARS-CoV-2 is concerning, for greater effectiveness, infection control efforts in LTCFs should include both mass testing-based strategies and symptom screening. cache = ./cache/cord-344356-up53a0k4.txt txt = ./txt/cord-344356-up53a0k4.txt === reduce.pl bib === id = cord-343970-anocx4y1 author = Bansal, Rashika title = Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course date = 2020-06-30 pages = extension = .txt mime = text/plain words = 6526 sentences = 409 flesch = 45 summary = ACE2 is expressed in pancreatic islets, vascular endothelium, and adipose tissue, and the SARS-CoV-2 -ACE2 interaction in these tissues, along with other factors, govern the spectrum and the severity of clinical manifestations among COVID-19 patients with metabolic syndrome. Moreover, the pro-inflammatory milieu observed in patients with metabolic syndrome may contribute towards COVID-19-mediated host immune dysregulation, including sub-optimal immune responses, hyper-inflammation, microvascular dysfunction, and thrombosis. SARS-CoV-2 virus attaches to the host cell membrane-bound angiotensin-converting enzyme 2 (ACE2) that is expressed in many cells, including the respiratory epithelial cells (type II alveolar A c c e p t e d M a n u s c r i p t epithelial cells), myocardium, Leydig cells and cells in seminiferous ducts in the testes, vascular endothelial cells, proximal renal tubular cells, gastrointestinal epithelial cells, urothelial cells lining the bladder, alveolar monocytes, macrophages, and in both exocrine pancreas and pancreatic islets (43, (46) (47) (48) . cache = ./cache/cord-343970-anocx4y1.txt txt = ./txt/cord-343970-anocx4y1.txt === reduce.pl bib === id = cord-344213-j3yextjl author = Sze, Shirley title = The need for improved discharge criteria for hospitalised patients with COVID-19—implications for patients in long term care facilities date = 2020-09-19 pages = extension = .txt mime = text/plain words = 1195 sentences = 76 flesch = 52 summary = In the COVID-19 pandemic, patients who are older and residents of long term care facilities (LTCF) are at greatest risk of worse clinical outcomes. We reviewed discharge criteria for hospitalised COVID-19 patients from ten countries with the highest incidence of COVID-19 cases as of 26th July 2020. We recommend a unified, simpler discharge criteria, based on current studies which suggest that most SARS-CoV-2 loses its infectivity by 10 days post-symptom onset. This represents a practical compromise between unnecessarily prolonged admissions and returning highly infectious patients back to their care facilities, and is of particular importance in older patients discharged to LTCFs, residents of which may be at greatest risk of transmission and worse clinical outcomes.  Current evidence suggests that most patients are non-infective 10 days post symptom onset or after first positive PCR result COVID-19 is a global pandemic. cache = ./cache/cord-344213-j3yextjl.txt txt = ./txt/cord-344213-j3yextjl.txt === reduce.pl bib === id = cord-344270-874i31h8 author = Radke, Robert M title = Adult congenital heart disease and the COVID-19 pandemic date = 2020-06-10 pages = extension = .txt mime = text/plain words = 4677 sentences = 273 flesch = 39 summary = Based on anatomy and additional physiological factors including symptoms, exercise capacity, heart failure, pulmonary hypertension and cyanosis, we propose a pragmatic approach to categorising patients into low-risk, intermediate-risk and high-risk groups. Patients with right heart dilatation or dysfunction are potentially at increased risk of right heart failure as mechanical ventilation and acute respiratory distress syndrome can lead to increase in pulmonary arterial pressures. While this may have ample indirect implications for the regular care of adults with congenital heart disease (ACHD) due to postponement of diagnostic and therapeutic procedures, the focus of the current review is on the direct impact of SARS-CoV-2 on congenital patients. 31 Infection with SARS-CoV-2 should be suspected in ACHD patients presenting with fever, onset or worsening of dyspnoea, lower than usual peripheral oxygen saturation but also in case of unexplained worsening of ventricular function or new arrhythmia. Patients with Down syndrome (commonly associated with congenital heart disease and immune defects) are at higher risk for pulmonary infections and ARDS. cache = ./cache/cord-344270-874i31h8.txt txt = ./txt/cord-344270-874i31h8.txt === reduce.pl bib === id = cord-344236-qp3ianzf author = Ali, Fedaa title = ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2465 sentences = 163 flesch = 54 summary = Classical electrostatic calculations based on solving Poisson-Boltzmann (PB) equation is used to investigate the interaction energies between SARS-CoV-2 and ACE2 for different mutated ACE2 structures. In an attempt to better understand the susceptibility of different populations to infection by SARS-CoV-2, we gathered data on ACE2 missense variants from different projects and databases that aggregate allele frequencies (AF). These projects and databases included Single Nucleotide Polymorphism Database (dbSNP) 12, 13 , 1000 genomes project phase 3 (1KGP3) 14 , Allele Frequency Aggregator (ALFA project) a , Exome Aggregation Consortium (ExAC) 15 SARS-CoV-2 was reported to bind to human ACE2 via different ACE2 residues; Q24, D30, H34, Y41, Q42, M82, K353 and R357 5 . The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-2/ACE2 were compared between single mutated and WT protein at pH =7 (Table 1 ). cache = ./cache/cord-344236-qp3ianzf.txt txt = ./txt/cord-344236-qp3ianzf.txt === reduce.pl bib === id = cord-344364-vu389d88 author = Wang, Wei title = Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1754 sentences = 115 flesch = 61 summary = Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. cache = ./cache/cord-344364-vu389d88.txt txt = ./txt/cord-344364-vu389d88.txt === reduce.pl bib === id = cord-344204-qq2vqzc2 author = Hariharan, Apurva title = The Role and Therapeutic Potential of NF-kappa-B Pathway in Severe COVID-19 Patients date = 2020-11-07 pages = extension = .txt mime = text/plain words = 5647 sentences = 307 flesch = 47 summary = Severe presentations of COVID-19 such as severe pneumonia and acute respiratory distress syndrome (ARDS) have been associated with the post-viral activation and release of cytokine/chemokines which leads to a "cytokine storm" causing inflammatory response and destruction, mainly affecting the lungs. Immunomodulation at the level of NF-κB activation and inhibitors of NF-κB (IκB) degradation along with TNF-α inhibition will potentially result in a reduction in the cytokine storm and alleviate the severity of COVID-19. During previous coronavirus outbreaks, such as SARS-CoV and the Middle East Respiratory syndrome coronavirus (MERS-CoV) , it was reported that viral proteins such as nsp1, nsp3a, nsp7a, spike, and nucleocapsid protein all caused excessive NF-κB activation, possibly contributing to severe disease and high case-fatality rate (DeDiego et al. Herein, we review current literature on the effect of SARS-nCoV-2 infection on NF-κB activation and discuss the potential therapeutic role of inhibitors of this pathway in the treatment of COVID-19. cache = ./cache/cord-344204-qq2vqzc2.txt txt = ./txt/cord-344204-qq2vqzc2.txt === reduce.pl bib === id = cord-343808-uqhiyj56 author = Kuo, Hsiao-I. title = Assessing impacts of SARS and Avian Flu on international tourism demand to Asia date = 2008-01-07 pages = extension = .txt mime = text/plain words = 7254 sentences = 328 flesch = 53 summary = In order to estimate the impacts of epidemic diseases including SARS and Avian Flu on tourism demand in most Asian affected countries, the methodology of the ARMAX model is adopted in our study. The monthly data for international tourist arrivals are collected from statistical datasets for each country, and the probable numbers of SARS-infected patients and the confirmed human cases of Avian Flu are obtained from the World Health Organization (WHO, 2006 Furthermore, the ARMA and ARMAX models are estimated by using nonlinear least squares estimators, while dynamic panel models are implemented by using the panel GMM technique. Table 3 presents the results of the ADF tests for the three series, including tourism demand, namely, international tourist arrivals, the probable SARS-infected patients and the number of confirmed cases of Avian Flu. The ADF test statistics are compared with the critical values from the nonstandard Dickey-Fuller distribution at the 5% significance level. cache = ./cache/cord-343808-uqhiyj56.txt txt = ./txt/cord-343808-uqhiyj56.txt === reduce.pl bib === id = cord-344180-v8xs5ej8 author = Vadlamani, Bhaskar S. title = Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date = 2020-10-17 pages = extension = .txt mime = text/plain words = 5150 sentences = 280 flesch = 52 summary = In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO(2) nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. In this study, we developed a Co-metal functionalized TNT as a sensing material for electrochemical detection of SARS-CoV-2 infection through the detection of the receptor binding domain (RBD) of spike glycoprotein. cache = ./cache/cord-344180-v8xs5ej8.txt txt = ./txt/cord-344180-v8xs5ej8.txt === reduce.pl bib === id = cord-344316-mwnnmwnw author = Herst, C.V. title = An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design date = 2020-04-28 pages = extension = .txt mime = text/plain words = 3495 sentences = 194 flesch = 49 summary = title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors' CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. Wilson We set out to see if we could drive CTL expansion directed against NP43-53 to occur after vaccinating C57BL/6 mice with Ebola Zaire NP43-53 (VYQVNNLEEIC), 50 and to subsequently conduct an in-vivo EBOV challenge study to see if this peptide was protective. We show here that the H2-D b restricted epitopes VSV (RGYVYQGL) and OVA (SIINFEKL), when administered to C57BL/6 mice, each produce a CD8+ We used this adjuvanted microsphere peptide vaccine platform to immunize C57BL/6 mice with NP43-53, the CTL+ class I peptide antigen from the Ebola Ziare NP protein identified as protective by Wilson et al. cache = ./cache/cord-344316-mwnnmwnw.txt txt = ./txt/cord-344316-mwnnmwnw.txt === reduce.pl bib === id = cord-344038-20n74z3o author = Han, Mi Seon title = Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1548 sentences = 110 flesch = 67 summary = In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate's clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother's respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . cache = ./cache/cord-344038-20n74z3o.txt txt = ./txt/cord-344038-20n74z3o.txt === reduce.pl bib === id = cord-344419-3wcfpw2z author = Niedzwiedz, C. L. title = Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study date = 2020-04-27 pages = extension = .txt mime = text/plain words = 5025 sentences = 271 flesch = 48 summary = Interpretation Some minority ethnic groups have a higher risk of confirmed SARS-CoV-2 infection in the UK Biobank study which was not accounted for by differences in socioeconomic conditions, measured baseline health or behavioural risk factors. In a large population-based cohort study in the UK, we found an increased risk of developing confirmed SARS-CoV-2 infection in Black, South Asian and White Irish ethnic groups. The ideal approach to estimating infection risk across different social groups is to analyse data from a cohort study, but most existing cohort studies which include detailed information about ethnicity and socioeconomic position are subject to long delays in data being available for analysis and are too small to provide useful estimates of infection risk. We therefore aimed to investigate the relationship between ethnicity, socioeconomic position and the risk of having confirmed SARS-CoV-2 infection in the population-based UK Biobank study. Several ethnic minority groups had a higher risk of both being diagnosed and testing positive as an inpatient with laboratory-confirmed SARS-CoV-2 infection in the UK Biobank study. cache = ./cache/cord-344419-3wcfpw2z.txt txt = ./txt/cord-344419-3wcfpw2z.txt === reduce.pl bib === id = cord-344454-hs3tthzi author = nan title = Les animaux contaminés par le SARS-CoV-2 représentent-ils un risque pour l’Homme ? date = 2020-09-15 pages = extension = .txt mime = text/plain words = 740 sentences = 76 flesch = 70 summary = Bien que l'origine zoonotique de la COVID-19 soit bien établie (chauves-souris du genre Rhinolophus, hôtes intermédiaires possibles, dont le Pangolin asiatique), un seul cas de contamination animal-Homme par le SARS-CoV-2 ayant été documenté avec des visons d'élevage aux Pays-Bas, rien ne prouve à l'heure actuelle que les animaux participent à la propagation de la pandémie dans la population humaine. Bien que ces infections animales ne jouent pas de rôle dans l'évolution de la pandémie de COVID-19, l'Académie nationale de médecine et l'Académie vétérinaire de France recommandent, dans le cadre d'une stratégie globale « une seule santé » : • de mettre en oeuvre les mesures de biosécurité les plus strictes dans les élevages de visons encore indemnes afin d'éviter les contaminations humaines et tout risque de propagation ultérieure, voire la constitution d'un réservoir animal ; • d'éviter tout contact entre les personnes infectées par le SARS-CoV-2 ou suspectes de l'être, avec leurs animaux de compagnie, notamment s'il s'agit de furet ou de chat, et d'observer les mêmes mesures barrière que pour prévenir la contamination de leur entourage (lavage des mains, masques. cache = ./cache/cord-344454-hs3tthzi.txt txt = ./txt/cord-344454-hs3tthzi.txt === reduce.pl bib === id = cord-344064-l3u4l3se author = Ghosh, Rajesh title = Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves date = 2020-11-03 pages = extension = .txt mime = text/plain words = 8644 sentences = 453 flesch = 51 summary = Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. The leaves of the traditional medicinal plant Torreya nucifera contains eight well-known diterpenoids (18-hydroxyferruginol, hinokiol, ferruginol, 18-oxoferruginol, O-acetyl-18hydroxyferruginol, methyl dehydroabietate, isopimaric acid, kayadiol) and four biflavonoids (amentoflavone, bilobetin, ginkgetin, sciadopitysin) ( Figure 1 ) (Ryu et al., 2010) . Overall, molecular docking studies clearly revealed that selected three biflavonoids (amentoflavone, bilobetin and ginkgetin) interacted with two key residues (His41 and Cys145) of Mpro via alkyl bond(s) interactions ( Figure 2 ). Overall, this study showed that three important biflavonoids of Torreya nucifera leaves (amentoflavone, bilobetin and ginkgetin) can act as SARS CoV-2 Mpro inhibitors. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study cache = ./cache/cord-344064-l3u4l3se.txt txt = ./txt/cord-344064-l3u4l3se.txt === reduce.pl bib === id = cord-343864-0258nh92 author = Straughn, Alex R. title = Withaferin A: a potential therapeutic agent against COVID-19 infection date = 2020-07-19 pages = extension = .txt mime = text/plain words = 2916 sentences = 141 flesch = 45 summary = Therefore, WFA demonstrates real potential as a therapeutic agent to treat or prevent the spread of COVID-19 due to the reported interference in viral S-protein to host receptor binding and its lack of effect on ACE2 expression in the lungs. Data from four SARS-CoV-2 hot spots (the United States, Italy, Spain and China) has shown that cancer patients infected with the novel coronavirus have a significantly increased risk of admission to an intensive care unit (ICU) and/or requiring mechanical ventilation, as well as an increase in patient mortality [15, [17] [18] [19] . Withaferin A alone or in combination with drugs, such as: hydroxychloroquine, dexamethasone or other treatments (under clinical trials), could be developed into an attractive therapeutic agent for both the general population and cancer patients due to its anti-tumorigenic properties and the preliminary studies showing that it is capable of binding to the Sprotein of SARS-CoV-2, thereby potentially inhibiting infection and/or spread of the disease. cache = ./cache/cord-343864-0258nh92.txt txt = ./txt/cord-343864-0258nh92.txt === reduce.pl bib === id = cord-344266-ug2uew71 author = Crema, E. title = The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3951 sentences = 215 flesch = 54 summary = Currently, this phenomenon has gained tragic relevance due to the uncontrolled dispersion of the Covid-19 throughout the planet, since airborne transmission is one of the forms of viral contamination, as well as the direct reception of drops exhaled by a contaminated person and the contact with infected surfaces. A relevant study issued in the journal Nature revealed the existence of the RNA of the SARS-COV-2 in aerosols collected from the air of several closed environments and open places of two hospitals in Wuhan dedicated only to patients infected with Covid-19 (12) . This indication is based only on old studies about the direct transmission by larger drops, dangerously ignoring the contamination by the virus airborne in droplets that remain suspended in the air for several hours, and even days after the environment has been visited by an infected person. cache = ./cache/cord-344266-ug2uew71.txt txt = ./txt/cord-344266-ug2uew71.txt === reduce.pl bib === id = cord-344330-zsx7wfyj author = Su, Shuo title = Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses date = 2016-03-21 pages = extension = .txt mime = text/plain words = 4537 sentences = 227 flesch = 49 summary = Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans. In humans, CoV infections primarily involve the upper respiratory tract and the gastrointestinal tract, and vary from mild, self-limiting disease, such as the common cold, to more severe manifestations, such as bronchitis and pneumonia with renal involvement [15] . A recent investigation discovered that multiple HCoV species, including MERS-CoV, beta-CoV group A, and a 229E-like virus, circulate amongst dromedary camels in Saudi Arabia [62] . Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection cache = ./cache/cord-344330-zsx7wfyj.txt txt = ./txt/cord-344330-zsx7wfyj.txt === reduce.pl bib === id = cord-344714-0cam9ipf author = Russo, Maria title = Roles of flavonoids against coronavirus infection date = 2020-07-28 pages = extension = .txt mime = text/plain words = 8395 sentences = 394 flesch = 46 summary = Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Inhibition of TMPRSS2 and Furin protease activities can be considered an interesting therapeutic option against coronavirus infection, especially COVID-19, allowing the block and/or prevention of SARS-CoV-2 infection, as recently reported [28] . Based on these observations, it is not surprising that molecular docking approach, summarized in Fig. 3 , supports the role of flavonoids in the inhibition of SARS-CoV 3CL pro by binding His41 and Cys145 of the catalytic site and other active site residues (e.g., Met49, Gly143, His163, His164, Glu166, Pro168, and Gln89), stimulating their validation by in vitro and in vivo studies. cache = ./cache/cord-344714-0cam9ipf.txt txt = ./txt/cord-344714-0cam9ipf.txt === reduce.pl bib === id = cord-343818-pj1oludh author = Liu, Chan title = Children with COVID-19 behaving milder may challenge the public policies: a systematic review and meta-analysis date = 2020-09-01 pages = extension = .txt mime = text/plain words = 4850 sentences = 256 flesch = 50 summary = We searched PubMed, Google Scholar, Web of Science, and several Chinese databases for studies presenting characteristics of children confirmed with Coronavirus Disease 2019 (COVID-19) from December 12, 2019 to May 10, 2020. The studies included in this meta-analysis should meet the following criteria: (1) all types of studies either retrospective or prospective (e.g. cohort, cross-sectional study, case report, case series); (2) studies reporting information regarding COVID-19; (3) studies describing clinical characteristics of pediatric patients (0-19 years) diagnosed by RT-PCR; (4) clinical data of more than five cases can be drawn from the articles. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha Clinical features of coronavirus disease 2019 in children aged <18 years in Jiangxi, China: an analysis of 23 cases cache = ./cache/cord-343818-pj1oludh.txt txt = ./txt/cord-343818-pj1oludh.txt === reduce.pl bib === id = cord-344217-kci4uw7u author = Majid, Sabhiya title = Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5645 sentences = 316 flesch = 46 summary = Coronavirus disease 2019 (COVID-19), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses (CoVs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-CoV (SARS-CoV) in 2002–2003, Middle East respiratory syndrome-CoV (MERS-CoV) in 2012, and currently this devastating COVID-19. Beta coronaviruses are a subgroup of the coronavirus family, large enveloped positive-sense singlestranded RNA (+ssRNA) viruses able to infect a wide variety of mammals and avian species, causing mainly respiratory or enteric diseases [2] . The disease caused by SARS-CoV-2 has been named COVID-19, a highly transmittable and pathogenic respiratory infection, which has become a public health emergency of international concern as no clinically approved antiviral drug or vaccine is available-though few broad spectrum antiviral drugs and drug combinations in clinical trials have resulted in clinical recovery [23] [24] [25] [26] [27] . cache = ./cache/cord-344217-kci4uw7u.txt txt = ./txt/cord-344217-kci4uw7u.txt === reduce.pl bib === id = cord-344901-mgnaprgt author = Holz, Frank G. title = SARS-CoV-2: Herausforderung für alle date = 2020-03-30 pages = extension = .txt mime = text/plain words = 112 sentences = 18 flesch = 67 summary = key: cord-344901-mgnaprgt authors: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 journal: Ophthalmologe DOI: 10.1007/s00347-020-01097-3 sha: doc_id: 344901 cord_uid: mgnaprgt nan Der Augenarzt, Dr. Li Wenliang, war in China einer der ersten, der auf eine "SARS-ähnliche" Epidemie hinwies. Er selbst hat sich an einem asymptomatischen Glaukom-Patienten infiziert und ist an Komplikationen der Erkrankung verstorben [3] . Insbesondere Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection The China Medical Treatment Expert Group for Covid-19, Guan W et al (2020) Clinical characteristics of Coronavirus disease 2019 in China Chinese doctor, silenced after warning of outbreak, dies from Coronavirus cache = ./cache/cord-344901-mgnaprgt.txt txt = ./txt/cord-344901-mgnaprgt.txt === reduce.pl bib === id = cord-344227-rdlinzrn author = Gralinski, Lisa E. title = Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date = 2018-10-09 pages = extension = .txt mime = text/plain words = 6557 sentences = 309 flesch = 43 summary = As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. cache = ./cache/cord-344227-rdlinzrn.txt txt = ./txt/cord-344227-rdlinzrn.txt === reduce.pl bib === id = cord-344614-5zcylf6k author = Moriconi, Diego title = Obesity prolongs the hospital stay in patients affected by COVID-19, and may impact on SARS-COV-2 shedding date = 2020-06-04 pages = extension = .txt mime = text/plain words = 3225 sentences = 168 flesch = 49 summary = Partial least square regression analysis showed that BMI, age and CRP at admission were related to longer length of hospital stay, and time for negative swab. Our study shows that obesity is associated with a severer respiratory presentation of COVID-19 and severer elevation of inflammatory markers, likely leading to higher oxygen demands at admission, prolonged oxygen requirement during hospitalization, delayed viral clearance and extended hospital stay. For this reason, beyond the potential impact on the lung mechanics, obesity might influence the clinical presentation and evolution of SARS-COV-2 infection through J o u r n a l P r e -p r o o f exacerbation of the immune-inflammatory response related to the disease, as confirmed by the increased levels of several inflammatory markers detected in the peripheral blood of patients with obesity in our population. cache = ./cache/cord-344614-5zcylf6k.txt txt = ./txt/cord-344614-5zcylf6k.txt === reduce.pl bib === id = cord-344909-0o55l4iy author = Cross, Robert W. title = Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5711 sentences = 291 flesch = 49 summary = However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Differences in clinical parameters of the LD-treated group with untreated control animals from this study or historical control animals were minimal; however, the lack of infectious SARS-CoV-2 in the BAL samples from all of the LD-treated animals and reduced lung pathology suggest that an antiviral effect was present despite the lower concentration of neutralizing antibodies in the dose of convalescent sera administered. PRNT50 assays were performed on pooled convalescent sera from AGMs challenged with the homologous isolate of SARS-CoV-2 in previous studies (Cross et al., 2020; Woolsey et al., 2020) compared with control animals on day 2 post infection (d) and cache = ./cache/cord-344909-0o55l4iy.txt txt = ./txt/cord-344909-0o55l4iy.txt === reduce.pl bib === id = cord-344070-17oac3bg author = Silverman, Justin D title = Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date = 2020-04-03 pages = extension = .txt mime = text/plain words = 5095 sentences = 284 flesch = 59 summary = ILI correlates with known patterns of SARS-CoV-2 spread across states within the US, suggesting the surge is unlikely to be due to other endemic respiratory pathogens, yet is orders of magnitude larger than the number of confirmed COVID cases reported. We find that as the seasonal surge of endemic non-influenza respiratory pathogens declines, this excess ILI correlates more strongly with state-level patterns of newly confirmed COVID cases suggesting that 75 this surge is a reflection of ILI due to SARS-CoV-2 (Pearson ρ = 0.8 and p < 10 −10 for the last two weeks; Figure S1 ). However, if we assume the excess non-influenza ILI is almost entirely due to SARS-CoV-2, an assumption that becomes more valid as the virus becomes more prevalent, we can use the excess non-influenza ILI to understand the constraints and mutual dependence of exponential growth rates, the rate of subclinical infections, and the time 95 between the onset of infectiousness and a patient reporting as ILI Figure 3 . cache = ./cache/cord-344070-17oac3bg.txt txt = ./txt/cord-344070-17oac3bg.txt === reduce.pl bib === id = cord-344829-adlp2rjy author = de Rivero Vaccari, Juan Carlos title = The Inflammasome in Times of COVID-19 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 8722 sentences = 423 flesch = 37 summary = Here we review the literature regarding the mechanism of inflammasome activation by CoV infection, the role of the inflammasome in ARDS, ventilator-induced lung injury (VILI), and Disseminated Intravascular Coagulation (DIC) as well as the potential mechanism by which the inflammasome may contribute to the damaging effects of inflammation in the cardiac, renal, digestive, and nervous systems in COVID-19 patients. Here we review the literature on the role of the inflammasome in CoV infections, which includes how CoVs activate inflammasomes upon infection, the role of the inflammasome in acute respiratory distress syndrome (ARDS), how ventilator-induced lung injury (VILI) activates the inflammasome, how the inflammasome plays a role in the systemic complications associated with COVID-19, and how the inflammasome is involved in the process of Disseminated Intravascular Coagulation (DIC). cache = ./cache/cord-344829-adlp2rjy.txt txt = ./txt/cord-344829-adlp2rjy.txt === reduce.pl bib === id = cord-344778-2p1mm3vg author = Gasparri, Maria Luisa title = Changes in breast cancer management during the Corona Virus Disease 19 pandemic: an international survey of the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) date = 2020-05-29 pages = extension = .txt mime = text/plain words = 2685 sentences = 165 flesch = 47 summary = The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. Two-hundred and fifty-two/377 (67%) responders considered chemotherapy as being riskier for developing severe COVID-19-related complications compared to surgery and radiation therapy. The reported cases of patients diagnosed with SARS-CoV-2 during BC treatment or within 14 days following treatment are 10%, 7% and 4% for chemotherapy, surgery and radiation therapy, respectively. This large international survey among breast cancer centres showed that the COVID-19 pandemic affected management of BC patients, including treatment modifications, longer waiting times and increased use of genomic profile analysis. Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic cache = ./cache/cord-344778-2p1mm3vg.txt txt = ./txt/cord-344778-2p1mm3vg.txt === reduce.pl bib === id = cord-344853-s2p2csrx author = Hendren, Nicholas S. title = Description and Proposed Management of the Acute COVID-19 Cardiovascular Syndrome date = 2020-04-16 pages = extension = .txt mime = text/plain words = 6688 sentences = 357 flesch = 34 summary = A substantial minority of patients hospitalized develop an acute COVID-19 cardiovascular syndrome, which can manifest with a variety of clinical presentations but often presents as an acute cardiac injury with cardiomyopathy, ventricular arrhythmias, and hemodynamic instability in the absence of obstructive coronary artery disease. S ince the index cases were first reported in Wuhan, China, in December 2019, coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic infecting >1 million individuals by early April 2020. In this document, we focus on a prominent myocarditis-like syndrome involving acute myocardial injury often associated with reduced left ventricular ejection fraction in the absence of obstructive coronary artery disease. Additional studies, including collection of endomyocardial tissue by biopsy and autopsy studies, are required to delineate the pattern and proportion of ACovCS related to acute myocarditis versus general myocardial injury caused by systemic cytokine dysregulation. cache = ./cache/cord-344853-s2p2csrx.txt txt = ./txt/cord-344853-s2p2csrx.txt === reduce.pl bib === id = cord-344647-jr85915d author = Joseph, Adrien title = Acute kidney injury in patients with SARS-CoV-2 infection date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3537 sentences = 193 flesch = 51 summary = Acute Kidney Injury (AKI) is a frequent complication of severe SARS-CoV-2 infection but data are scarce in ICUs. AKI has been previously reported with an average incidence of 11% (8-17%) overall, with highest ranges in the critically ill (23%; 14-35%) [2] [3] [4] . Different applications of the Kidney Disease Improving Global Outcomes (KDIGO) criteria for AKI, in particular different methods to estimate missing baseline creatinine and handling urinary output, can cause important variations of estimated incidence [5, 6] and may contribute to the discrepancies among these studies. High levels of IL-6 have been associated with the development of severe disease [24, 25] and acute respiratory distress syndrome [8] during COVID-19 infection, but the role of inflammation markers in COVID-19-induced-AKI remains speculative [7] . Our study suggests a tremendously high incidence of AKI in our cohort of critically ill COVID-19 patients, along with an independent association between AKI and outcome. cache = ./cache/cord-344647-jr85915d.txt txt = ./txt/cord-344647-jr85915d.txt === reduce.pl bib === id = cord-344246-sf9cymhc author = Diriba, Kuma title = The effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and the possibility of vertical maternal–fetal transmission: a systematic review and meta-analysis date = 2020-09-04 pages = extension = .txt mime = text/plain words = 5141 sentences = 253 flesch = 46 summary = Previous outbreaks of coronaviruses include the severe acute respiratory syndrome (SARS)-CoV epidemic in 2003 [2] and the Middle East respiratory syndrome (MERS)-CoV in 2012 [3] , while the newly emergent coronavirus, initially referred to as 2019-nCoV and subsequently termed SARS-CoV-2, the disease it produces has been termed COVID-19, which causes respiratory infection and can progress to severe pneumonia and, in a small number of cases, death [4] . A systematic review and meta-analysis was aimed to assess the effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and its possibility of vertical maternal-fetal transmission following the methodological framework suggested by Arksey and O'Malley [15] . The primary outcome variable of this study was the pregnancy outcomes observed, listed as follows: preterm birth (PTB; either before 37 or 34 weeks of gestation), preeclampsia, preterm prelabor rupture of membranes, (pPROM), fetal growth restriction (FGR), miscarriage, maternal death, mode of delivery and other clinical feature, laboratory findings and coexisting disease. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-344246-sf9cymhc.txt txt = ./txt/cord-344246-sf9cymhc.txt === reduce.pl bib === id = cord-344751-i4qnrtjq author = Van Praet, Jens T. title = Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date = 2020-09-10 pages = extension = .txt mime = text/plain words = 2399 sentences = 119 flesch = 49 summary = Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. To evaluate the specificity of the immuno-assays, we used a set of serum samples from control patients with recent respiratory viral or atypical bacterial infections. To this end, we tested for cross-reactivity with sera of patients with other respiratory viral or atypical bacterial infections, including common coronavirus infections, since these may present with clinical and radiological findings similar to Covid-19. Our study focused on the clinical sensitivity and specificity of four commercial immuno-assays for anti-SARS-COV-2 IgG in the subset of patients presenting with negative RT-PCR and suspect CT findings. In summary, we found good clinical sensitivity of anti-SARS-Cov-2 IgG immunoassays for Covid-19 in the subset of patients with negative RT-PCR 14 days after onset of symptoms. cache = ./cache/cord-344751-i4qnrtjq.txt txt = ./txt/cord-344751-i4qnrtjq.txt === reduce.pl bib === id = cord-344949-9zyz4hll author = Luban, Jeremy title = The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date = 2020-08-05 pages = extension = .txt mime = text/plain words = 5552 sentences = 277 flesch = 47 summary = a Selectivity index is the ratio of CC50 to EC50 b values are mean ± standard deviation (SD) Abbreviations: CC50, compound concentration at which cell number is reduced by 50%; EC50, compound concentration at which viral replication on a linear scale is inhibited by 50%; GFP, green fluorescent protein; HCV, hepatitis C virus replicon genotype 1b; PIV-3, Parainfluenza type 3; RSV, respiratory syncytial virus; RT-qPCR, quantitative reverse transcription PCR; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TCID50, tissue culture infectious dose 50%. In the BT co-cell culture system, which models chronic inflammatory conditions driven by B cell activation and antibody production, incubation of cells with 10 nM PTC299 resulted in a significant reduction in the levels of soluble (s)IgG, sIL-17A, sIL-17F, sIL-6, and sTNFα released from the cells after 72 hours of stimulation (range, 49% to 68%) (all p values <0.01) ( Figure 4 and Table 2 ). cache = ./cache/cord-344949-9zyz4hll.txt txt = ./txt/cord-344949-9zyz4hll.txt === reduce.pl bib === id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 pages = extension = .txt mime = text/plain words = 5433 sentences = 276 flesch = 43 summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). cache = ./cache/cord-344970-ud1lhkyi.txt txt = ./txt/cord-344970-ud1lhkyi.txt === reduce.pl bib === id = cord-344446-5d7yuoz1 author = Naughton, Sean X. title = The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection date = 2020-05-12 pages = extension = .txt mime = text/plain words = 754 sentences = 45 flesch = 46 summary = One of the more perplexing aspects of the recent SARS-CoV-2 pandemic is the high level of variability among patients in terms of disease severity. Exposure to environmental toxins as well as lifestyle choices can affect ACE2 expression, and may possibly increase the severity of infection. For example, exposure to ultrafine particulate matter from air pollution (PM 2.5) has previously been shown to increase the expression of ACE2 [4] . In line with these findings, a recent report indicates that higher levels of air pollution may be a contributing factor to the increased fatality rate among COVID-19 patients in northern Italy [5] . Dietary/lifestyle factors may also play a role in determining resilience or susceptibility to severe outcomes after SARS-CoV-2 infection. Thus, it is possible that multiple independent variables may affect ACE2 expression and thereby confer resilience or susceptibility towards severe life-threatening conditions after SARS-Cov-2 infection. cache = ./cache/cord-344446-5d7yuoz1.txt txt = ./txt/cord-344446-5d7yuoz1.txt === reduce.pl bib === id = cord-344383-7s4gnxs4 author = Tee, Augustine K.H. title = Atypical SARS in Geriatric Patient date = 2004-02-17 pages = extension = .txt mime = text/plain words = 2056 sentences = 125 flesch = 52 summary = We describe an atypical presentation of severe acute respiratory syndrome (SARS) in a geriatric patient with multiple coexisting conditions. On the basis of epidemiologic data (contact tracing linking her to one of the three original index cases in Singapore) (12) , the index patient's cause of death was determined to be SARS (Figure 3 ). Since the issue of a global alert on atypical pneumonia by the World Health Organization on March 12, reported cases of SARS increased daily and appeared in other countries, including Canada, the United States, Europe, and Africa. Our case serves to highlight atypical signs and symptoms of SARS, especially the resolving fever, delay in establishing a positive contact history, and the nonspecific chest radiographic appearance that could be affected by concurrent coexisting conditions, such as cardiac failure. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-344383-7s4gnxs4.txt txt = ./txt/cord-344383-7s4gnxs4.txt === reduce.pl bib === id = cord-344658-4z2697q6 author = Hutasoit, Novana title = Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology date = 2020-08-29 pages = extension = .txt mime = text/plain words = 2469 sentences = 132 flesch = 54 summary = title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology The primary intention was to alleviate the tendency of SARS-CoV-2 (COVID-19) virus to linger longer on touch surfaces that attract high-to-medium volume human contact, such as the push plates used in publicly accessed buildings and hospitals. This work showcases the capability of cold-spray as a potential copper-coating solution for different in-use parts and components that can act as sources for the spread of the virus. In this work the authors have deposited copper coatings onto the stainless steel push-plates in a matter of 7 mins only, which is a marvellous demonstration of the application of the cold spray coating process for ongoing and future challenges arising from the pandemic. Table 1 and Fig. 2 presents the viricidal activity results of SARS-CoV-2 virus when exposed to three different metallic surfaces and compared with COVID-19 only and positive control solutions. cache = ./cache/cord-344658-4z2697q6.txt txt = ./txt/cord-344658-4z2697q6.txt === reduce.pl bib === id = cord-344486-iu5flbcl author = Chiotos, Kathleen title = Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2 date = 2020-09-12 pages = extension = .txt mime = text/plain words = 8595 sentences = 416 flesch = 37 summary = In the few months since this initial publication, new evidence has emerged demonstrating the efficacy of the antiviral medication remdesivir in shortening time to clinical recovery in adults with COVID-19, while several other studies have shown ineffectiveness of hydroxychloroquine and lopinavir-ritonavir (4) (5) (6) (7) (8) . Further, additional observational studies have provided insight into the clinical epidemiology of COVID-19 in children, demonstrating that while most young patients experience mild illness, a small proportion develop severe illness associated with adverse clinical outcomes, including need for pediatric intensive care unit (PICU) admission and mortality (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) . Nevertheless, the panel recognizes that pediatric clinicians are likely to consider comorbidities when weighing the risks and benefits of antiviral therapy on a case-bycase basis, and in making these decisions may consider: 1) the available, albeit limited, pediatric COVID-19 literature; 2) risk factors associated with severe COVID-19 in adults; and 3) pre-existing medical conditions in children associated with worse clinical outcomes for other viral infections. cache = ./cache/cord-344486-iu5flbcl.txt txt = ./txt/cord-344486-iu5flbcl.txt === reduce.pl bib === id = cord-344884-dcoq9srf author = El Otmani, H. title = Neuro-COVID-19: What are we talking about? date = 2020-06-06 pages = extension = .txt mime = text/plain words = 879 sentences = 60 flesch = 51 summary = Q2 In a very short time after the onset of the COVID-19 infection, a ''flood'' of reports regarding SARS-Cov-2 related neurological manifestations were published. While more than three and a half million individuals are affected worldwide to date, most arguments of COVID-19related neurological manifestations are supported by case reports or small series [1] [2] [3] . On the other hand, a review of the available data shows that the implication of the SARS-Cov-2 virus as a direct cause of neurological complications is not established yet. In support to this, to date, only 2 cases of meningitis or encephalitis with evidence of viral SARS-Cov-2 detection in CSF are reported [6, 7] . So far, a dozen of COVID-19-related Guillain-Barré syndromes (GBS) have been reported, which seems to be marginal compared to the high prevalence of infected individuals [10] . Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Neurologic Features in Severe SARS-CoV-2 Infection cache = ./cache/cord-344884-dcoq9srf.txt txt = ./txt/cord-344884-dcoq9srf.txt === reduce.pl bib === id = cord-344382-vge4ho2v author = De Flora, Silvio title = Rationale for the use of N‐acetylcysteine in both prevention and adjuvant therapy of COVID‐19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4995 sentences = 271 flesch = 41 summary = 5 Elderly individuals maintain a chronic low level of inflammation that is associated with oxidative stress and inflammatory cytokine production, a condition that increases the severity of viral infections in this population and that could be attenuated by administration of antioxidants. 36 A randomized, double-blind, placebo-controlled, prospective clinical trial in 5 ICUs in the USA and Canada showed that the intravenous administration of NAC (70 mg/ kg body weight), every 8 hours for 10 days, effectively repleted GSH in red blood cells, decreased the number of days of acute lung injury, and significantly increased the cardiac index. 50 NAC inhibited the pulmonary inflammation and edema as well as myeloperoxidase (MPO) activity, total cells, neutrophils, macrophages, TNF-α, IL-6, IL-1β, and chemokine (C-X-C motif) ligand-10 (CXCL-10) in the bronchoalveolar lavage fluid and reduced the levels of toll-like receptor 4 (TLR4) protein and mRNA in the lungs of BALB/c mice inoculated intranasally with A/swine/HeBei/012/2008/ H9N2 influenza virus. cache = ./cache/cord-344382-vge4ho2v.txt txt = ./txt/cord-344382-vge4ho2v.txt === reduce.pl bib === id = cord-345033-guisyj11 author = Massarotti, Claudia title = SARS‐CoV‐2 in the semen: where does it come from? date = 2020-06-13 pages = extension = .txt mime = text/plain words = 694 sentences = 49 flesch = 55 summary = This finding re‐opened the discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and safety of fertility treatments during the pandemic period [1]. 2 A recent report by Li et al., described the presence of SARS-CoV-2 in semen samples of six patients, 3 including two subjects who were recovering from the clinical disease. This finding re-opened the 4 discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and 5 safety of fertility treatments during the pandemic period [1] . Regarding Coronaviruses, there is evidence that 35 MERS-CoV binds to the host cell receptor dipeptidyl peptidase 4 (DPP4), which is broadly expressed 36 on prostate cells [12] . The ACE2 Expression in Sertoli cells and Germ cells may cause male reproductive disorder after SARS-CoV-2 Infection. Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues cache = ./cache/cord-345033-guisyj11.txt txt = ./txt/cord-345033-guisyj11.txt === reduce.pl bib === id = cord-345183-80rflm7u author = Moore, Nicholas M. title = Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3635 sentences = 228 flesch = 58 summary = We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. In this study, we compared the performance of the ACOV and IDNOW assays and a laboratory developed test that is a modification of the CDC 2019-nCoV assay (CDC COV) for the detection of SARS-CoV-2 RNA from upper respiratory tract specimens. cache = ./cache/cord-345183-80rflm7u.txt txt = ./txt/cord-345183-80rflm7u.txt === reduce.pl bib === id = cord-345019-i7zm9bt1 author = Al-Waleedi, Ali Ahmed title = The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4496 sentences = 236 flesch = 55 summary = A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. For early detection of SARS-CoV-2 in Yemen, as in other countries, a case definition, active surveillance, and contact tracing were required [10, 11] . The first 2 months after confirmation of the SARS-CoV-2 epidemic in Yemen was characterized by a 57% hospitalization rate in the southern and eastern parts of the country included in The First 2 Months of the SARS-CoV-2 Epidemic in Yemen our study, 63% of deaths occurring in individuals aged <60 years, confirmatory testing of <50% of the suspected cases, and majority of cases were not related to a defined chain of transmission. cache = ./cache/cord-345019-i7zm9bt1.txt txt = ./txt/cord-345019-i7zm9bt1.txt === reduce.pl bib === id = cord-345103-b2wkm03g author = Yao, Hangping title = Molecular architecture of the SARS-CoV-2 virus date = 2020-09-06 pages = extension = .txt mime = text/plain words = 5755 sentences = 313 flesch = 54 summary = Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). The postfusion S observed on the SARS-CoV-2 virus may come from 1) products of occasional, spontaneous dissociation of S1 (Cai et al., 2020) , which was cleaved by host proteinases; 2) syncytium naturally formed on infected cells , when budding progeny virions carried a few residual postfusion S from the cell surface; 3) sample preparation procedure, as cryo-EM images of ßpropiolactone fixed viruses showed most spikes present on the virus are postfusion-like Gao et al., 2020) . Three representative SARS-CoV-2 virus (Figures 1B and 4D ) and a bundle of postfusion S ( Figure 3B ) were reconstructed by projecting all spikes and RNPs onto their refined coordinates and merging the structures using Jsubtomo (Huiskonen et al., 2014) . Structures and distributions of SARS-CoV-2 spike proteins on intact virions cache = ./cache/cord-345103-b2wkm03g.txt txt = ./txt/cord-345103-b2wkm03g.txt === reduce.pl bib === id = cord-344979-ngujhhp6 author = Lübke, Nadine title = Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3242 sentences = 217 flesch = 59 summary = OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. Ct values of 91 SARS-CoV-2 positive samples analyzed in direct comparison by RT-qPCR using different primary materials and extracted RNA showed a significant correlation. cache = ./cache/cord-344979-ngujhhp6.txt txt = ./txt/cord-344979-ngujhhp6.txt === reduce.pl bib === id = cord-344967-t88pedeb author = Tang, Hon Lok title = Severe acute respiratory syndrome in haemodialysis patients: a report of two cases date = 2003-10-17 pages = extension = .txt mime = text/plain words = 1666 sentences = 107 flesch = 64 summary = A 49-year-old male, who had end-stage renal failure and was receiving chronic haemodialysis twice weekly, was admitted to the Princess Margaret Hospital on April 6, 2003, because of fever, chills, rigors and cough for 1 day. In view of his contact history with SARS patients, he was put on anti-viral therapy with i.v. ribavirin on day 5. Despite ribavirin treatment, the patient ran a persistently low-grade fever and a chest radiograph on day 21 revealed new shadows over the right lower zone. We report two cases of SARS occurring in end-stage renal failure patients. The diagnosis of SARS was based on his strong contact history, chest radiograph shadows and the second RT-PCR assay for coronavirus of his throat and nasal swabs on day 24. The optimal ribavirin dose for treating SARS in patients with end-stage renal failure and in those receiving haemodialysis is unknown. cache = ./cache/cord-344967-t88pedeb.txt txt = ./txt/cord-344967-t88pedeb.txt === reduce.pl bib === id = cord-344636-go5cw92q author = Huang, Wei E. title = RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date = 2020-04-25 pages = extension = .txt mime = text/plain words = 4771 sentences = 253 flesch = 61 summary = In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample. cache = ./cache/cord-344636-go5cw92q.txt txt = ./txt/cord-344636-go5cw92q.txt === reduce.pl bib === id = cord-344934-m0q7rm6z author = Mahapatra, Sovesh title = Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking date = 2020-04-07 pages = extension = .txt mime = text/plain words = 3876 sentences = 228 flesch = 56 summary = Here, we report the ML model based on the Naive Bayes algorithm, which has an accuracy of around 73% to predict the drugs that could be used for the treatment of COVID-19. Bioactivity datasets which are available from the numerous high throughput screens deliver useful means for machine learning classifiers as they contain binary information (active/inactive) as well as numerical values to classify different compounds under consideration 22, 23 . These drugs were downloaded in the form of SDFs and after processing, the descriptions generated were taken as the test model for developing the train model which was made on the basis of a database containing the inhibitors of the SARS coronavirus. Around 178 drugs were predicted by our ML model which can be effective for the treatment of diseases caused by SARS-Cov-2. cache = ./cache/cord-344934-m0q7rm6z.txt txt = ./txt/cord-344934-m0q7rm6z.txt === reduce.pl bib === id = cord-345092-1ztfcpsb author = Iwasaki, Masae title = Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications date = 2020-10-08 pages = extension = .txt mime = text/plain words = 11428 sentences = 550 flesch = 44 summary = Severe patients of COVID-19 often develop acute respiratory distress syndrome and multiple organ dysfunction/failure with high mortality that may be closely related to the hyper-proinflammatory status called the "cytokine storm." Massive cytokines including interleukin-6, nuclear factor kappa B (NFκB), and tumor necrosis factor alpha (TNFα) released from SARS-CoV-2-infected macrophages and monocytes lead inflammation-derived injurious cascades causing multi-organ injury/failure. ARB/ACE-I, angiotensin receptor blocker/ACE2 inhibitor; AT1aR, angiotensin receptor subtype 1a; C3, complement component 3; E-cadherin, epithelial cadherin; gp130, glycoprotein 130; IL, interleukin; JAK, Janus kinase; MAPK, mitogenactivated protein kinase; MCP-1, monocyte chemoattractant protein 1; mIL-6R, membrane interleukin 6 receptor; MMP9, matrix metallopeptidase 9; MyD88, myeloid differentiation primary response 88; NFκB, nuclear factor kappa-light-chain-enhancer of activated B cells; NFκB, nuclear factor kappa B; PI3K/Akt, phosphoinositide-3-kinase/protein Kinase B; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; sIL-6R, soluble interleukin 6 receptor; SOCS3, the suppressor of cytokine signaling-3; STAT3, signal transducers and activators of transcription; sTNFα, soluble tumor necrosis factor alpha; Tfh, follicular helper T cell; Th0, naive T cell; Th17, T helper 17 cell; TMPRSS2, transmembrane protease serine 2; TNFα, tumor necrosis factor alpha; TPO, thrombopoietin; VEGF, vascular endothelial growth factor. cache = ./cache/cord-345092-1ztfcpsb.txt txt = ./txt/cord-345092-1ztfcpsb.txt === reduce.pl bib === id = cord-344798-q34j4zxu author = Villalba, María Caridad Montalvo title = Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients date = 2020-08-29 pages = extension = .txt mime = text/plain words = 4141 sentences = 232 flesch = 44 summary = title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients The aim of this study was evaluate inflammatory response using the expression of immune mediators with antiviral, immunosuppression and chemotactic functions in the primary site of SARS-CoV-2 replication, at early stage of infection. J o u r n a l P r e -p r o o f Taking into account that Ct value has a correlation with the amount of RNA present in the samples, it was found that medians and IQR of SARS-CoV-2 viral titer was similar in asymptomatic (33.00, 29.00-37.00) and symptomatic (30, 27 .00-37.00) cases; and comparison between groups did not show difference (p=0.4373). As show our results, SARS-CoV-2 infection induced high IFN-γ expression in swabbed cells from upper airway; its expression was higher in symptomatic patients in comparison with asymptomatic individuals. Also, positive correlation between IFN-γ and TGF-β1 provided evidence of immune response control could determinate the asymptomatic presentation of SARS-CoV-2 infection. cache = ./cache/cord-344798-q34j4zxu.txt txt = ./txt/cord-344798-q34j4zxu.txt === reduce.pl bib === id = cord-345275-h0hvaxgx author = Sun, Mengyao title = Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date = 2020-07-04 pages = extension = .txt mime = text/plain words = 5308 sentences = 286 flesch = 56 summary = title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection cache = ./cache/cord-345275-h0hvaxgx.txt txt = ./txt/cord-345275-h0hvaxgx.txt === reduce.pl bib === id = cord-345405-ngpsgn63 author = Tremiliosi, Guilherme C. title = Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 6259 sentences = 339 flesch = 46 summary = An adaptation of ISO 18184 Determination of antiviral activity of textile products Standard Method [23] was used as a reference for a quantitative method to evaluate the treated polycotton's ability to inactivate the SARS-CoV-2 virus particles (SARS-CoV-2/human/BRA/SP02cc/2020 -MT350282), under the tested conditions, at two different time intervals (2 and 5 minutes of contact time). The antiviral activity test was designed to determine the inactivation of viral particles upon short exposure to the products, which in this case were the Ag-based treated polycotton samples incubated in liquid media. Table 6 shows the number of copies of the control media without any fabric sample, non-treated polycotton, and the two Ag-based treated polycotton samples at the two different tested time periods. Application of silver nanoparticles to cotton fabric as an antibacterial textile finish Fibers Polym Antibacterial properties of cotton fabric treated with silver nanoparticles cache = ./cache/cord-345405-ngpsgn63.txt txt = ./txt/cord-345405-ngpsgn63.txt === reduce.pl bib === id = cord-345296-4z7yfj5s author = Ho, Mei-Shang title = Neutralizing Antibody Response and SARS Severity date = 2005-11-17 pages = extension = .txt mime = text/plain words = 4600 sentences = 190 flesch = 42 summary = Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. To adjust the time effects and other covariates of interest, the relationship between antibody titer, based on logarithmic transformation of base 2 (serum dilution) and other potential factors, i.e., age, sex, infection source, and duration of illness, was quantified by linear mixed models (18) , which took into account the correlation between repeated measurements of each study participants. In the model, patients with a more severe clinical course had earlier and higher antibody responses; we then examined the death rate of the early responders (Table 6 ). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways cache = ./cache/cord-345296-4z7yfj5s.txt txt = ./txt/cord-345296-4z7yfj5s.txt === reduce.pl bib === id = cord-345288-qyz83xx2 author = Pata, Francesco title = Enteral stoma care during COVID‐19 pandemic: practical advice date = 2020-07-21 pages = extension = .txt mime = text/plain words = 2700 sentences = 158 flesch = 48 summary = To face the COVID-19 pandemic, metamorphosis of surgical services is required to prevent in-hospital transmission, optimize allocation of scarce resources, establish new intensive care units (ICUs) and redeploy healthcare workers to emergency departments or COVID-19 dedicated wards [8] [9] [10] . Furthermore, although many recommendations suggest to consider performing stoma surgery instead of primary anastomosis in high-risk emergency surgery 14,20-23 none of those consider the potential problems related to reduced availability of stoma care services and reduced access in the hospital to caregivers for stoma training which may represent a problem for elderly and frail patients after discharge. Second, in-hospital stoma training pathways should be implemented to allow patients to confidently manage their own stomas independently prior to discharge and reduce the need for home nursing care 37 . In addition to standard precautions for infection prevention and control (i.e. correct use of PPE, keeping appropriate interpersonal distance, proper hand washing) indoor air quality should be preserved to limit the SARS-CoV-2 spread, and to protect patients and healthcare workers. cache = ./cache/cord-345288-qyz83xx2.txt txt = ./txt/cord-345288-qyz83xx2.txt === reduce.pl bib === id = cord-344842-9cfbb7p6 author = Coppola, Maurizio title = Potential Unconventional Medicines for the Treatment of SARS-CoV-2 date = 2020-05-19 pages = extension = .txt mime = text/plain words = 723 sentences = 43 flesch = 45 summary = Adem and colleagues in their virtual screening based molecular docking study reported a potential binding affinity exerted by various bioflavonoids at the active site of the MPro, the main protease of the SARS-CoV-2 [1] . Potential inhibition properties were studied using the Molegro Virtual Docker Program and some flavonoids, in particular hesperidin, rutin, and diosmin showed a better affinity for the MPro than nelfinavir [1] . Rutin showed the second strongest binding energy at the active site of the MPro with a MoLDock score of −176.2740 and a HBond of −21.2402. Recently, Caly and colleagues reported a potential antiretroviral activity of the anti-parasitic agent ivermectin against SARS-CoV-2 virus. Despite the absence of clinical evidences regarding some potential anti-SARS-CoV-2 drugs, preliminar information reported by researchers suggest anyhow further studies in order to evaluate the clinical effects as well as the possibility to synthesize derivatives with stronger antiretroviral properties. cache = ./cache/cord-344842-9cfbb7p6.txt txt = ./txt/cord-344842-9cfbb7p6.txt === reduce.pl bib === id = cord-345603-mirsz6m8 author = Wehrhahn, Michael C. title = Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2345 sentences = 125 flesch = 57 summary = Self-collected swabs in the community for SARS-CoV-2, the agent of COVID-19, and for other respiratory viruses offers potential significant benefit in the current pandemic by J o u r n a l P r e -p r o o f reducing requirement for PPE, limiting exposure of patients and staff to infection, increased convenience and access for patients and timeliness of a sample receipt. 9 Recent reports on SARS-CoV-2 in respiratory specimens indicate early high viral loads in symptomatic and asymptomatic patients in a variety of clinical specimens including nasal and throat swabs, sputum and saliva samples. The aim of this study was to compare prospectively the performance of HC with separate SC nasal (SCN) and throat swabs (SCT) and the combination of the two (SCNT) for respiratory viruses including SARS-CoV-2. cache = ./cache/cord-345603-mirsz6m8.txt txt = ./txt/cord-345603-mirsz6m8.txt === reduce.pl bib === id = cord-345139-gyvlikye author = Izquierdo-Domínguez, Adriana title = Pérdida del sentido del olfato durante la pandemia COVID-19 date = 2020-06-12 pages = extension = .txt mime = text/plain words = 2888 sentences = 290 flesch = 54 summary = Mientras que la función olfatoria normal se define como normosmia, los trastornos cuantitativos se clasifican en pérdida parcial (hiposmia) o total (anosmia) del olfato 4 . Se habla de estudio cuantitativo al referirse a la cantidad de olor necesitado para ser detectado (umbral olfativo) y tiene por objeto el estudio de las variaciones olfativas en función de la concentración de la sustancia olorosa y de la cantidad de los olores detectados, dando un resultado de anosmia (pérdida total), hiposmia (pérdida parcial) o normosmia (olfato normal). Durante la pandemia COVID-19, se aconseja a aquellos pacientes con pérdida repentina y grave del sentido del olfato, iniciar medidas de distanciamiento social, aislamiento domiciliario preventivo y realizar pruebas de diagnóstico para el SARS-CoV-2 cuando sea posible. cache = ./cache/cord-345139-gyvlikye.txt txt = ./txt/cord-345139-gyvlikye.txt === reduce.pl bib === id = cord-345381-9cckppk2 author = Klimek, Ludger title = Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date = 2020-09-07 pages = extension = .txt mime = text/plain words = 6146 sentences = 332 flesch = 43 summary = title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontaneous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontane-ous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. cache = ./cache/cord-345381-9cckppk2.txt txt = ./txt/cord-345381-9cckppk2.txt === reduce.pl bib === id = cord-345827-yo3uq03v author = Antiochia, Riccarda title = Developments in biosensors for CoV detection and future trends date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5968 sentences = 278 flesch = 44 summary = Since MERS and COVID-19 are highly contagious diseases with the potential to cause a pandemic, in absence of a specific vaccine or effective therapeutic drugs, it is of extreme importance to find rapid and accurate detection methods for control and prevention of virus spread. Current methods used for screening and diagnosis of novel COVID-19 are based on three different approaches: SARS-CoV-2 antigen detection in nasopharyngeal secretions through molecular biology techniques, computed tomography, and SARS-CoV-2 antibody analysis in serum using immunoassay methods (Carter et al., 2020) . According to the Food and Drug Administration (FDA) Emergency Use Authorizations (EUAs) for COVID-19 diagnostics, in addition to the most common ELISA method, there are two serological assays used for the detection of antibodies generated against SARS-CoV-2, the chemiluminescence immunoassays (CLIA) and the lateral flow immunoassays (LFIA). Biosensors based on specific biomolecular interactions offer an alternative and reliable solution to current methods for clinical diagnosis of COVID-19, due to their high sensitivity, low-cost, easy to use and possibility of POC utilization. cache = ./cache/cord-345827-yo3uq03v.txt txt = ./txt/cord-345827-yo3uq03v.txt === reduce.pl bib === id = cord-345356-gn1iwis0 author = Glebov, Oleg O. title = Understanding SARS‐CoV‐2 endocytosis for COVID‐19 drug repurposing date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3502 sentences = 175 flesch = 35 summary = Given that most viruses use endocytosis to enter the host cell, mechanistic investigation of SARS‐CoV‐2 infection needs to consider the diversity of endocytic pathways available for SARS‐CoV‐2 entry in the human lung epithelium. Taken together, the above evidence suggests that SARS-CoV-2 may employ distinct endocytic pathways for cell entry in the upper and lower respiratory tract (Fig. 1) . This approach would allow tracking of the virus in relation to other endocytic pathways and also to investigate the effect of viral infection on the general membrane trafficking network of the host cell. Taken together, the combination of adequate cell models with the newly developed SARS-CoV-2 toolkit and established tools of membrane trafficking research is well-poised to deliver a key insight into the mechanisms underlying COVID-19 infection. Furthermore, considering that various viruses may use the same endocytic pathways of the host cell [15] , targeting viral entry at the point of endocytosis holds a more general promise for the development of broad-spectrum antiviral drugs [51] . cache = ./cache/cord-345356-gn1iwis0.txt txt = ./txt/cord-345356-gn1iwis0.txt === reduce.pl bib === id = cord-345304-n74m5ucs author = Safadi, Marco Aurelio Palazzi title = THE CHALLENGING AND UNPREDICTABLE SPECTRUM OF COVID-19 IN CHILDREN AND ADOLESCENTS date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1855 sentences = 95 flesch = 39 summary = 6 Based on current evidence, older adults and people of all ages with underlying medical conditions, including severe obesity, chronic lung disease, cardiovascular disease, diabetes mellitus, chronic kidney disease, liver disease, active cancer, transplantation and immunocompromised have been associated with poor clinical outcomes and higher fatality rates from COVID-19. One of the largest pediatric cancer programs in the USA, in New York city, reported that 20/178 (11%) children and adolescents with cancer had positive test for SARS-CoV-2. 11 The overwhelmed public health systems by the COVID-19 pandemic represents a serious risk for pediatric general health, limiting access of children and adolescents to basic health care, compromising immunization coverages and postponing consultations for patients with underlying conditions. Clinical characteristics of 58 children with a pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 Clinical characteristics and outcomes of hospitalized and critically Ill children and adolescents with coronavirus disease 2019 (COVID-19) at a tertiary care medical center in New York City cache = ./cache/cord-345304-n74m5ucs.txt txt = ./txt/cord-345304-n74m5ucs.txt === reduce.pl bib === id = cord-345371-pjbviagq author = Lisi, Lucia title = Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 10648 sentences = 512 flesch = 37 summary = The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. Here, we review the recently published literature on the pharmacological treatments used so far and/or undergoing evaluation in clinical trials, with focus on the biochemical mechanisms of action of repurposed or investigational drugs, classified as agents directly targeting the virus ( Figure 1 and Table 1 ) and those used to treat the respiratory distress and inflammation associated with the cytokine release syndrome ( Figure 2 and Table 2 ). cache = ./cache/cord-345371-pjbviagq.txt txt = ./txt/cord-345371-pjbviagq.txt === reduce.pl bib === id = cord-345841-pq5f82gf author = PATBERG, Elizabeth T. title = COVID-19 Infection and Placental Histopathology in Women Delivering at Term date = 2020-10-19 pages = extension = .txt mime = text/plain words = 5903 sentences = 282 flesch = 46 summary = Conclusions – Despite the fact that all neonates born to mothers with COVID-19 were negative for SARS-CoV-2 by PCR, we found that COVID-19 in term patients admitted to Labor and Delivery is associated with increased rates of placental histopathologic abnormalities, particularly fetal vascular malperfusion and villitis of unknown etiology. In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . cache = ./cache/cord-345841-pq5f82gf.txt txt = ./txt/cord-345841-pq5f82gf.txt === reduce.pl bib === id = cord-345679-ydwcp75s author = Younas, Amber title = SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN date = 2020-08-24 pages = extension = .txt mime = text/plain words = 2370 sentences = 148 flesch = 59 summary = title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN Despite the prevailing pandemic, there are no recommendations available as yet for testing SARS-CoV-2 antibodies as part of blood screening. In our study, we conducted specific serological testing (total antibodies) to identify prevalence of SARS-2-CoV antibodies among the healthy blood donors who visited Blood Bank at our Institute.Their results were compared with specific serologic results of blood donors that came before the onset of pandemic(October, 2019). In July 2020, we tested 300 healthy blood donors, 113 donors (37.7%) were found to be reactive for anti-SARS-CoV-2antibodies. Another study in Northern France reported 25.8% of population positive for COVID-19 antibody(19)but they also did not exclude previously symptomatic cases. To conclude, seroprevalence of SARS-COV-2 antibodies has increased in Pakistan over a period of time and could help in recognizing the actual number of COVID-19 cases. The prevalence of antibodies to SARS-CoV-2 among blood donors in China.medRxiv cache = ./cache/cord-345679-ydwcp75s.txt txt = ./txt/cord-345679-ydwcp75s.txt === reduce.pl bib === id = cord-345101-h0i5o0do author = Koo, Bon-Sang title = Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date = 2020-08-03 pages = extension = .txt mime = text/plain words = 1808 sentences = 123 flesch = 55 summary = Using a reliable primate model is critical for developing therapeutic advances to treat humans infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The absence of a reliable preclinical animal model that recapitulates patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection poses a major limitation to the development of improved diagnostics and therapeutics. Studies reported that SARS-CoV-2 developed no severe clinical signs, but pulmonary pneumonia in 50% of cynomolgus macaques, recapitulating mild symptoms in humans [6] . The viral RNA was highest in the upper respiratory swab samples and lung tissues at the earliest phase of infection, and the viral antigen was present in the lungs ( Figure 1C and D) , suggesting the predominant site of the virus. Using a high viral titre administered through combined routes, virus assays, and histopathological changes suggests that both cynomolgus and rhesus macaques are permissive to infection of SARS-CoV-2 and recapitulate COVID-19-like disease in human. cache = ./cache/cord-345101-h0i5o0do.txt txt = ./txt/cord-345101-h0i5o0do.txt === reduce.pl bib === id = cord-345299-4k7qymqd author = Xiong, Hua-Long title = Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date = 2020-06-05 pages = extension = .txt mime = text/plain words = 1471 sentences = 88 flesch = 47 summary = To identify drugs that are potentially used for the treatment of COVID-19, the potency of 1403 FDA-approved drugs were evaluated using a robust pseudovirus assay and the candidates were further confirmed by authentic SARS-CoV-2 assay. Four compounds, Clomiphene (citrate), Vortioxetine, Vortioxetine (hydrobromide) and Asenapine (hydrochloride), showed potent inhibitory effects in both pseudovirus and authentic virus assay. In this study, the anti-SARS-Cov-2 potentiality of 1403 FDA approved drugs were quantitatively evaluated by the pseudovirus-based assay. In the second round of screening, inhibition of VSV-SARS-CoV-2-Sdel18 virus infection and cell cytotoxicity were both detected (Supplementary Figure 1) . The robust assay based on VSV-SARS-CoV-2-Sdel18 pseudovirus screened out the potential drugs with high efficiency, then the inhibitory effect was confirmed by authentic SARS-CoV-2 assay. The relative value or inhibition rate of candidate drugs were calculated according to the decrease of GFP positive cell number (for pseudovirus-based assay) or cytopathic effect (for authentic SARS-CoV-2-based assay). cache = ./cache/cord-345299-4k7qymqd.txt txt = ./txt/cord-345299-4k7qymqd.txt === reduce.pl bib === id = cord-345014-qp13h0un author = Stein, Richard Albert title = The 2019 coronavirus: Learning curves, lessons, and the weakest link date = 2020-03-13 pages = extension = .txt mime = text/plain words = 2268 sentences = 155 flesch = 57 summary = 14 In the most recent of the three coronavirus outbreaks, several clusters of patients with pneumonia started to be reported on December 8, 2019 from Wuhan, China, and most of them were epidemiologically linked to the Huanan Seafood Wholesale Market. 24, 25 The virus shares >70% genetic similarity with the 2002-2003 SARS-CoV strain, 5 is most closely related to coronaviruses of bat origin, 17 its spike glycoprotein gene appears to have emerged by recombination between a bat coronavirus and a coronavirus of unknown origins, and relative synonymous codon usage bias analyses indicate that snakes may be a potential reservoir. 26 The SARS-CoV spike protein receptor binds the angiotensin-converting enzyme 2 (ACE2) on host cells, an interaction that shapes cross-species and human-to-human transmission. 10,58-60 Every outbreak brings something new, provides opportunities to reap the benefits gained from past epidemics and pandemics, and provides novel lessons that will shape the framework to manage emerging infectious diseases. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in Wuhan, China cache = ./cache/cord-345014-qp13h0un.txt txt = ./txt/cord-345014-qp13h0un.txt === reduce.pl bib === id = cord-345106-5szz1et3 author = Bhattacharya, D. D. title = Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2 date = 2020-09-11 pages = extension = .txt mime = text/plain words = 2348 sentences = 176 flesch = 63 summary = Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Total RNA was isolated from the SARS-CoV-2-infected saliva samples using QIAamp Viral preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.09.11.20192591 doi: medRxiv preprint A total number of 53 subjects were tested positive both in NPS and saliva assay, whereas 5 samples were found only as NPS positive (Table 1) Statistically, we detected lower C T value for ORF1 gene in the saliva specimens (mean C T = 27.07; 95% confidence interval [CI], 25.62 to 28.52) than in the NPS specimens (mean C T = 28.24; 95% CI, 26.62 to 29.85) (Figure 2A) . cache = ./cache/cord-345106-5szz1et3.txt txt = ./txt/cord-345106-5szz1et3.txt === reduce.pl bib === id = cord-345864-87b5qdjx author = Rudolph, James L. title = Temperature in Nursing Home Residents Systematically Tested for SARS-CoV-2 date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1482 sentences = 121 flesch = 57 summary = Abstract Objectives Many nursing home residents infected with SARS-CoV-2 fail to be identified with standard screening for the associated COVID-19 syndrome. The objective of this study is to describe the temperature changes before and after universal testing for SARS-CoV-2 in nursing home residents. We report the temperature in window of the 14 days before and after universal SARS-CoV-2 testing among CLC residents. Administration Community Life Centers (CLCs) infected with SARS-CoV-2 do have 57 temperature elevations well ahead of a confirmatory test, but also that peak temperatures will not 58 typically meet the current screening criterion threshold of 38°C that follows the Centers for 59 Disease Control's (CDC) guidance. The purpose of this analysis is to compare temperature 73 trends and identify maximum temperatures in nursing home residents fourteen days prior to and 74 following systematic testing for SARS-CoV-2 throughout VHA CLCs. 75 cache = ./cache/cord-345864-87b5qdjx.txt txt = ./txt/cord-345864-87b5qdjx.txt === reduce.pl bib === id = cord-345929-z7yfegr5 author = Thakur, Suman S. title = Proteomics and Its Application in Pandemic Diseases date = 2020-11-06 pages = extension = .txt mime = text/plain words = 1355 sentences = 94 flesch = 39 summary = found that the antimalarial drug metaquine and anti-HIV antiretroviral saquinavir interact with four SARS-CoV-2 receptors, including Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S protein), interacting with human ACE2; therefore, they may be repurposed for COVID-19 treatment. Furthermore, Maffucci and Contini used an in silico approach to find drug candidates against the main proteinase and spike protein of SARS-CoV-2. suggested that the antigenic peptides generated from the S1 spike glycoprotein of SARS-CoV-2 using aminopeptidases ERAP1, ERAP2, and IRAP might be helpful in selecting better epitopes for immunogenic studies and the design of a vaccine for COVID-19. Interestingly, a computational method was used to find an allosteric site on the SARS-CoV-2 spike protein by Di Paola et al., as its detection would weaken the spike−ACE2 interaction and thereby reduce the viral infection. cache = ./cache/cord-345929-z7yfegr5.txt txt = ./txt/cord-345929-z7yfegr5.txt === reduce.pl bib === id = cord-345854-f0dq94j1 author = Chong, Wai Po title = The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date = 2006-05-04 pages = extension = .txt mime = text/plain words = 1770 sentences = 116 flesch = 54 summary = We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). In this study, we hypothesized that the polymorphisms of the cytokine genes, i.e. IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C, might be associated with SARS. We tested our hypotheses in 476 SARS patients and 449 healthy controls and found that polymorphism of IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner. The frequencies of genotypes and alleles of the 4 single nucleotide polymorphisms (SNPs) were compared between the SARS patients and healthy controls by 3 × 2 and 2 × 2 chi square test respectively. Our case-control study genotyped the 4 SNPs IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C in 476 Chinese patients with SARS and 449 healthy controls. Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection cache = ./cache/cord-345854-f0dq94j1.txt txt = ./txt/cord-345854-f0dq94j1.txt === reduce.pl bib === id = cord-345529-f12v6bp0 author = Pan, Q. title = Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1588 sentences = 109 flesch = 57 summary = In order to better treat these patients and provide basis for further control measures, we analyze the epidemiological outcomes and clinical features of patients with residual Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) in Linyi city. Gender, age, exposure history to Hubei Province or contact with confirmed patients, onsets of symptoms, data of diagnosis, date of testing first negative, date of re-positive testing , severity of disease and other information were included for further analysis. The reason maybe that serious illness resulted from more virus infections, and more residual SARS-Cov-2 remained in the body of these patients, which makes the positive testing appear easier and more likely. The analysis also indicates that even discharge from hospital with negative testing at least two times, some patients still carry residual SARS-Cov-2 and show repeatedly positive testing outcome for 22.44±13.61 days. cache = ./cache/cord-345529-f12v6bp0.txt txt = ./txt/cord-345529-f12v6bp0.txt === reduce.pl bib === id = cord-345499-hq5um68k author = Xiong, Rui title = Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date = 2020-03-12 pages = extension = .txt mime = text/plain words = 5275 sentences = 317 flesch = 53 summary = title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. We identified that targeting DHODH offers broad-spectrum antiviral efficacies against various RNA viruses, including the DAA-resistant influenza virus and the newly emerged coronavirus SARS-CoV-2. cache = ./cache/cord-345499-hq5um68k.txt txt = ./txt/cord-345499-hq5um68k.txt === reduce.pl bib === id = cord-345628-a4c46m2w author = Unudurthi, Sathya D. title = Cardiac inflammation in COVID-19: Lessons from heart failure date = 2020-09-21 pages = extension = .txt mime = text/plain words = 7725 sentences = 413 flesch = 41 summary = Autopsies of COVID-19 patients reveal an infiltration of inflammatory mononuclear cells in the myocardium, confirming the role of the immune system in mediating cardiovascular damage in response to COVID-19 infection and also suggesting potential causal mechanisms for the development of new cardiac pathologies and/or exacerbation of underlying CVDs in infected patients. Myocyte damage and lymphocytic myocarditis have also been independently confirmed by recent autopsies carried out on multiple COVID-19 patients from Seattle and Germany (Bradley et al., 2020; Wichmann et al., 2020) Recently, SARS-CoV-2 viral particles have been identified in cardiac macrophages, suggesting that these cells can be directly infected by the virus, potentially transmitting the disease systemically to multiple tissues (Tavazzi et al., 2020) . cache = ./cache/cord-345628-a4c46m2w.txt txt = ./txt/cord-345628-a4c46m2w.txt === reduce.pl bib === id = cord-345754-mgixsfcc author = Arena, Patrick J. title = Race, COVID-19 and deaths of despair date = 2020-07-31 pages = extension = .txt mime = text/plain words = 927 sentences = 57 flesch = 49 summary = 1 The higher burden of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection and COVID-19 mortality among ethnic and racial minorities does not appear to be explained by biological factors, but instead by longstanding discriminatory societal and historical factors whereby the simple fact of belonging to a specific race/ethnicity limits access to education and wealth and precipitates exposure to the criminal justice system and poor health outcomes. COVID-19 morbidity and mortality is influenced by specific pre-existing health conditions, such as diabetes, hypertension, heart disease, food insecurity and lack of health insurance, all of which are highly prevalent among ethnic and racial minority groups, such as Black, Latinx and Native American populations in the United States (US). Similarly, a recent systematic review suggested that Black, Asian, and minority ethnic (BAME) individuals had a higher risk of SARS-CoV-2 infection and also experienced worse clinical outcomes than White individuals. Although some public health officials are taking concrete steps to address COVID-19 disparities among impacted ethnic groups, 8 data on the effectiveness of lockdowns on BAME communities is lacking. cache = ./cache/cord-345754-mgixsfcc.txt txt = ./txt/cord-345754-mgixsfcc.txt === reduce.pl bib === id = cord-345225-2s5xd1oc author = Soares, F. title = A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence date = 2020-04-14 pages = extension = .txt mime = text/plain words = 4558 sentences = 236 flesch = 51 summary = We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). Based on this data, we built an artificial intelligence classification framework, ER-CoV, aiming at determining which patients were more likely to be negative for SARS-CoV-2 when visiting an ER and that were categorized as a suspect case by medical professionals. Considering the aforementioned successes in integrating AI and medicine, we propose ER-CoV, an artificial intelligence-based screening method that uses blood exams to triage patients suspect of COVID-19 arriving at emergency rooms. cache = ./cache/cord-345225-2s5xd1oc.txt txt = ./txt/cord-345225-2s5xd1oc.txt === reduce.pl bib === id = cord-345992-3ij1vbqp author = Drosten, Christian title = SARS Molecular Detection External Quality Assurance date = 2004-12-17 pages = extension = .txt mime = text/plain words = 1746 sentences = 98 flesch = 42 summary = Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Inactivated severe acute respiratory syndrome-associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Highly sensitive methods for virus detection, such as reverse transcription-polymerase chain reaction (RT-PCR) are required to confirm SARS in the acute phase and prevent transmission. First, laboratories had to correctly detect the four samples containing >9,400 copies of viral RNA per milliliter, a concentration well above the detection limit of published and commercial nucleic acid amplification tests (NAT) for SARS-CoV, (6, 7, (10) (11) (12) . Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-345992-3ij1vbqp.txt txt = ./txt/cord-345992-3ij1vbqp.txt === reduce.pl bib === id = cord-345887-ymo4mxx7 author = Pinky title = Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5713 sentences = 306 flesch = 42 summary = title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 With an urgent need for the development of potential strategies, two recent studies from China using Mesenchymal Stem Cells (MSCs) to treat COVID-19 pneumonia have shed some light on a potential cure for the COVID-19 infected patients. Also, attractive features like cell targeting, low-immunogenicity, safety, and high biocompatibility distinguish these exosomes from other synthetic nano-vesicles and thus potentiate their role as a drug delivery nano-platform. However, this study is first of its kind evaluating MSCs derived exosomes therapeutic potential for COVID-19 [45] . Some of the pre-clinical studies evaluating the effect of MSC derived exosomes on lung macrophages in various lung injury models have provided insights into the exosome derived approach as a new strategy for treating nCOV associated pathogenicity. Exosomes derived from bone marrow mesenchymal stem cells as treatment for severe COVID-19 cache = ./cache/cord-345887-ymo4mxx7.txt txt = ./txt/cord-345887-ymo4mxx7.txt === reduce.pl bib === id = cord-345730-bxwsup70 author = Kočar, Eva title = Cholesterol, lipoproteins, and COVID-19: basic concepts and clinical applications date = 2020-11-04 pages = extension = .txt mime = text/plain words = 4028 sentences = 221 flesch = 40 summary = In vitro depletion of membrane-bound cholesterol from Angiotensin-Converting Enzyme 2 (ACE2)-expressing cells led to a reduced infectivity of CoVs, since the binding of the spike protein was reduced by half [44] . By participating in cholesterol outflow from the cell membrane to HDL particles, PON1 contributes to lowering the cholesterol levels within lipid rafts, thus modulating viral infection (Fig. 1c) . Therefore, it is intriguing to contemplate whether NAFLD patients without treatment are more J o u r n a l P r e -p r o o f susceptible for SARS-CoV-2 infection, or whether statin application may directly affect the entry of SARS-CoV-2 into the host cell by regulating cholesterol cell levels. As lipid lowering drugs, statins might thus significantly reduce the attachment and internalization of SARS-CoV-2 by lowering membrane cholesterol levels (Fig. 1c ) [37] . cache = ./cache/cord-345730-bxwsup70.txt txt = ./txt/cord-345730-bxwsup70.txt === reduce.pl bib === id = cord-346032-188gnf8j author = Cheung, Ying-Kit title = Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date = 2007-08-10 pages = extension = .txt mime = text/plain words = 4754 sentences = 228 flesch = 53 summary = title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. cache = ./cache/cord-346032-188gnf8j.txt txt = ./txt/cord-346032-188gnf8j.txt === reduce.pl bib === id = cord-346138-ip42zcld author = Zhurakivska, Khrystyna title = An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3947 sentences = 211 flesch = 56 summary = The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. Several authors therefore suppose an infection of the gastrointestinal tract by the virus (11, 24) , with its continuous elimination with the feces which has been reported to last from 1 to 12 days (24) and in some cases, viral RNA were detected in feces or anal swabs even after the respiratory tests became negative (11, 22, 24) . The reference method for testing positivity to SARS-CoV-2 infection is represented by the pharyngeal swab that is taken from the patient's nasopharynx or oropharynx and, through an RT-PCR analyzed for the presence of viral RNA (8) . cache = ./cache/cord-346138-ip42zcld.txt txt = ./txt/cord-346138-ip42zcld.txt === reduce.pl bib === id = cord-345879-nbfg47x5 author = Bonaz, Bruno title = Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4072 sentences = 213 flesch = 44 summary = title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? We hypothesize that this cytokine storm and the worsening of patients' health status can be dampened or even prevented by specifically targeting the vagal-driven cholinergic anti-inflammatory pathway (CAP). Hence, targeting the α7nAChRs through vagus nerve stimulation (VNS) could be of interest in the management of patients with SARS-CoV-2 infection. Indeed, through the wide innervation of the organism by the vagus nerve, especially the lungs and gastrointestinal tract, VNS appears as a serious candidate for a few side effect treatment that could dampen or prevent the cytokine storm observed in COVID-19 patients with severe symptoms. Indeed, a septic shock-induced increase of TNF in the liver and the blood in mice was dampened by stimulation of the distal end cut of the vagus nerve thus arguing for an anti-inflammatory effect of vagal efferents which release acetylcholine (ACh) (Borovikova et al. cache = ./cache/cord-345879-nbfg47x5.txt txt = ./txt/cord-345879-nbfg47x5.txt === reduce.pl bib === id = cord-345493-3bb1zuqp author = Itoyama, Satoru title = Identification of an alternative 5′‐untranslated exon and new polymorphisms of angiotensin‐converting enzyme 2 gene: Lack of association with SARS in the Vietnamese population date = 2005-06-03 pages = extension = .txt mime = text/plain words = 3331 sentences = 172 flesch = 54 summary = We analyzed genetic variations of angiotensin‐converting enzyme 2 (ACE2), considering that it might influence patients' susceptibility to severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) or development of SARS as a functional receptor. © 2005 Wiley‐Liss, Inc. We analyzed genetic variations of angiotensinconverting enzyme 2 (ACE2), considering that it might influence patients' susceptibility to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) or development of SARS as a functional receptor. A case control study involving 44 SARS cases, 16 anti-SARS-CoV antibodypositive contacts, 87 antibody-negative contacts, and 50 non-contacts in Vietnam, failed to obtain any evidence that the ACE2 gene polymorphisms are involved in the disease process in the population. Using the PCR-based cloning procedure, we identified for the first time an alternative exon upstream of the original exon 1 of ACE2 that is expressed in various organs, including the lung and trachea, primary-cultured bronchial epithelial cells, and the small intestine. cache = ./cache/cord-345493-3bb1zuqp.txt txt = ./txt/cord-345493-3bb1zuqp.txt === reduce.pl bib === id = cord-346222-rzbzlnr4 author = Kim, Dae-Kyum title = A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions date = 2020-08-06 pages = extension = .txt mime = text/plain words = 1749 sentences = 110 flesch = 48 summary = Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. SARS-CoV-2 coding sequence collection Gatewaycompatible TEV (tobacco etch virus) sequence A global pandemic of the coronavirus disease COVID-19, a severe respiratory illness caused by a novel virus from the family Coronaviridae (SARS-CoV-2), has infected millions and caused hundreds of thousands of deaths (World Health Organization 2020a). Broad availability of a collection of SARS-CoV-2 CDSs has the potential to enable many downstream biochemical and structural studies and thus a better understanding of processes within the viral life cycle, including scalable assays for screening drug candidates that could potentially disrupt these processes. However, to enable the subsequent removal of such N-terminal fusion tags, we generated an additional set of clones containing, at the N-terminus of the ORF, a recognition sequence for nuclear inclusion protease from tobacco etch virus (TEV). cache = ./cache/cord-346222-rzbzlnr4.txt txt = ./txt/cord-346222-rzbzlnr4.txt === reduce.pl bib === id = cord-345999-iiw4cs8p author = Khare, Prashant title = Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3283 sentences = 320 flesch = 62 summary = Since it is a newly emerging viral disease and obviously there is a lack of anti-SARS-CoV-2 therapeutic agents, it is urgently required to develop an effective anti-SARS-CoV-2-agent.Through recent advancements in computational biology and biological assays, several natural compounds and their derivatives have been reported to confirm their target specific antiviral potential against Middle East respiratory syndrome coronavirus (MERS-CoV) or Severe Acute Respiratory Syndrome(SARS-CoV).These targets including an important host cell receptor, i.e., angiotensin-converting enzyme ACE2 and several viral proteins e.g. spike glycoprotein (S) containing S1 and S2 domains, SARS CoV Chymotrypsin-like cysteine protease (3CL(pro)), papain-like cysteine protease (PL(pro)), helicases and RNA-dependent RNA polymerase (RdRp). For the management J o u r n a l P r e -p r o o f of COVID-19 infection, various molecular targets playing important role in the SARS-CoV-2 life cycle including host cell receptor-Angiotensin-converting enzyme ACE2 (PDB ID 3D0G) and viral proteins such as S protein (containing S1 and S2 domains) (PDB ID 6XM0); various cysteine proteases such as papain-like cysteine protease (PL pro ) (PDB ID 6WX4) or Chymotrypsin like nprotease (3CL pro ) (PDB ID 1P9U), helicases and RNA-dependent RNA polymerase (RdRp) (PDB ID 6M71) could be evaluated . cache = ./cache/cord-345999-iiw4cs8p.txt txt = ./txt/cord-345999-iiw4cs8p.txt === reduce.pl bib === === reduce.pl bib === id = cord-345717-ktajrf7d author = Monagin, Corina title = Serologic and behavioral risk survey of workers with wildlife contact in China date = 2018-04-03 pages = extension = .txt mime = text/plain words = 4585 sentences = 241 flesch = 45 summary = We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. The present study focuses on the potential for zoonotic viral transfer through contact with wildlife in Guangdong prefectures in China, and seeks to augment our understanding and identification of risky populations, occupations, and behaviors, as well as the perceptions of risk at these interfaces. We performed a serological survey and concurrent behavioral questionnaire of individuals with wildlife contact in Guangdong Province, China, in order to better characterize occupations and community-level behavioral risks that contribute to zoonotic transmission of various wildlife pathogens with pandemic potential. We targeted high-risk individuals, defined as individuals with high levels of exposure to wildlife (wild animal blood or bodily fluids)-primarily hunters, persons working in wet markets and restaurants that butcher wild game, who could be followed over a period of time. cache = ./cache/cord-345717-ktajrf7d.txt txt = ./txt/cord-345717-ktajrf7d.txt === reduce.pl bib === === reduce.pl bib === id = cord-346008-6v2gdz4a author = Jeong, Areum title = Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1152 sentences = 84 flesch = 52 summary = title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea Due to close contact during examination, frequent exposure to tears and ocular discharge, and the inevitable sharing of equipment, ophthalmologists and patients are at a higher risk of SARS-CoV-2 infection. To prevent the transmission of COVID-19 in clinics, we follow steps based on three levels of control measures: administrative control, environmental control, and the use of personal protective equipment (PPE). If any of the aforementioned conditions are met, the patient is masked, isolated, and instructed to visit the COVID-19 screening center for reverse transcription polymerase chain reaction. Patients who have fever but negative test results postpone the appointment or attend the clinic. To reduce the exposure time, all patients should wear a mask in the waiting room. Characteristics of ocular findings of patients with coronavirus disease 2019 (COVID-19 cache = ./cache/cord-346008-6v2gdz4a.txt txt = ./txt/cord-346008-6v2gdz4a.txt === reduce.pl bib === id = cord-346092-fo83f99f author = Fang, Li‐Qun title = Geographical spread of SARS in mainland China date = 2009-06-05 pages = extension = .txt mime = text/plain words = 2763 sentences = 126 flesch = 50 summary = Objectives To describe the spatiotemporal diffusion of the severe acute respiratory syndrome (SARS) epidemic in mainland China, and to analyse the spatial pattern of SARS transmission from the Beijing epicentre to its neighbouring areas. SARS cases that got infected in Beijing but were reported in three provinces surrounding Beijing were mapped, and logistic regression using a 'case–control' design at the county level was performed to analyse the impact of travel‐related risk factors in the diffusion pattern. Results The SARS epidemic in mainland China spanned a large geographical extent but clustered in two areas: first in Guangdong Province, and about 3 months later in Beijing with its surrounding areas in Shanxi Province, Inner Mongolia Autonomic Region, Hebei Province and Tianjin. Using the tracking analysis, we identified geographic features associated with SARS outbreaks in mainland We found that 34 SARS cases became infected in Beijing and travelled to the Inner Mongolia Autonomic Region, Shanxi Province or Hebei Province after onset, and were reported by hospitals outside Beijing. cache = ./cache/cord-346092-fo83f99f.txt txt = ./txt/cord-346092-fo83f99f.txt === reduce.pl bib === id = cord-346146-yal0ctpq author = Peyronnet, Violaine title = Infection par le SARS-CoV-2 chez les femmes enceintes. Actualisation de l’état des connaissances et de la proposition de prise en charge. CNGOF date = 2020-10-05 pages = extension = .txt mime = text/plain words = 9027 sentences = 922 flesch = 67 summary = L'objectif de la rédaction de ce document est d'actualiser les connaissances des professionnels de santé sur le SARS-Covid-2, ses symptômes, la connaissance actuelle sur la transmission inter individuelle et pendant la grossesse et de proposer un protocole de prise en charge pour les femmes enceintes en France modifiant celui proposé précédemment (1) . Cependant, des symptômes plus graves ont également été décrits dans ce contexte (16 à 32%) comme la pneumonie ou le syndrome de détresse respiratoire aiguë (SDRA) qui sont présents majoritairement chez les personnes âgées, les patients présentant une immunodépression ou des comorbidités telles que le diabète, un cancer ou une maladie respiratoire chronique et les femmes enceintes (4; 8; 12-17) Les caractéristiques épidémiologiques, cliniques, biologiques et radiologiques ont été décrites dans la population générale en premier par Huang et al. Enfin une autre série française multicentrique portant sur 100 femmes enceintes avec une infection certaine rapporte 5 cas de césariennes avant 32 SA pour cause de COVID chez des patientes hospitalisées en réanimation. cache = ./cache/cord-346146-yal0ctpq.txt txt = ./txt/cord-346146-yal0ctpq.txt === reduce.pl bib === === reduce.pl bib === id = cord-346089-u31n0qxa author = McDade, Thomas W. title = High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2232 sentences = 140 flesch = 52 summary = title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. In addition, we demonstrate the feasibility and utility of quantifying SARS-CoV-2 antibodies in self-collected DBS with results from a community-based sample enriched with health care workers. We have validated a DBS assay to facilitate large-scale serological testing of SARS-CoV-2 IgG antibodies, and results from our feasibility study document a high rate of household transmission. cache = ./cache/cord-346089-u31n0qxa.txt txt = ./txt/cord-346089-u31n0qxa.txt === reduce.pl bib === id = cord-346176-w6uaet7l author = Nayeri, Shadi title = Conducting Translational Gastrointestinal Research in the Era of COVID-19 date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3097 sentences = 213 flesch = 49 summary = In this document we provide a suggested roadmap for resuming gastrointestinal translational research activities, emphasising physical distancing and use of personal protective equipment. We discuss modes of virus transmission in enclosed environments [including clinical workplaces and laboratories] and potential risks of exposure in the endoscopy environment for research staff. Efforts focus primarily on physical distancing, use of PHASE personal protective equipment [PPE] , and addressing capacity needs of health care systems to deal with the outbreak. Local and institutional guidance is required to resume translational research activities, including patient interactions. • Invitation of persons currently infected with SARS-CoV-2 from the community into the research environment would cause unnecessary and inappropriate risk of viral transmission. These guidelines address safety precautions in relevant workspaces [including laboratory and endoscopy environments] as well as in specific research activities such as sample collection, handling, and transportation. cache = ./cache/cord-346176-w6uaet7l.txt txt = ./txt/cord-346176-w6uaet7l.txt === reduce.pl bib === id = cord-346015-bzeqs5oh author = Wang, Yeming title = Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial date = 2020-04-29 pages = extension = .txt mime = text/plain words = 5233 sentences = 246 flesch = 46 summary = Although several approved drugs and investigational agents have shown antiviral activity against SARS-CoV-2 in vitro, 6, 7 at present there are no antiviral therapies of proven effectiveness in treating severely ill patients with A multicentre, open-label, randomised controlled trial (RCT) of hydroxychloroquine involving 150 adults admitted to hospital for COVID-19 reported no significant effect of the drug on accelerating viral clearance. This was an investigator-initiated, individually randomised, placebo-controlled, double-blind trial to assess the effectiveness and safety of intravenous remdesivir in adults (aged ≥18 years) admitted to hospital with severe COVID-19. Our study is the first randomised, double-blind, placebocontrolled clinical trial assessing the effect of intravenous remdesivir in adults admitted to hospital with severe COVID-19. Future studies of remdesivir, including earlier treatment in patients with COVID-19 and higher-dose regimens or in combination with other antivirals or SARS-CoV-2 neutralising antibodies in those with severe COVID-19 are needed to better understand its potential effectiveness. cache = ./cache/cord-346015-bzeqs5oh.txt txt = ./txt/cord-346015-bzeqs5oh.txt === reduce.pl bib === id = cord-346197-7g5d9x57 author = Capecchi, E. title = Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? date = 2020-07-05 pages = extension = .txt mime = text/plain words = 859 sentences = 76 flesch = 61 summary = title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? Since the use of nasopharyngeal aspirate (NPA) seemed to be better than nasopharyngeal swab (NS) to identify respiratory virus in paediatrics 4,5 we decided to compare these methods in detecting SARS-CoV-2 in children. . https://doi.org/10.1101/2020.07.02.20142521 doi: medRxiv preprint Considering NPA as the gold standard for detection of SARS-CoV-2, we calculated sensitivities and specificities of NS. The NS has in any case a low sensitivity in detecting SARS-CoV-2 in children when referred to NPA. Our results, the first we know are available, suggest to prefer the collection of NPA whenever possible for the detection of SARS-CoV-2 in children. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 5, 2020. cache = ./cache/cord-346197-7g5d9x57.txt txt = ./txt/cord-346197-7g5d9x57.txt === reduce.pl bib === id = cord-346055-7fa57pmf author = Visani, Giuseppe title = SARS-CoV-2 impact in a community-based hematological ward in an Italian Red Zone date = 2020-06-13 pages = extension = .txt mime = text/plain words = 741 sentences = 48 flesch = 49 summary = Initial reports from China suggested that patients with cancer had an estimated two-fold increased risk of contracting SARS-CoV-2 than the general population and, if infected, also had a higher risk of either ICU admission, invasive ventilation, or death, compared to patients without cancer [2] . Up to now, 5924 cases resulted SARS-CoV-2 positive in Marche Region (out of 30,543 test done), with a rhythm of infection and death toll five times superior those of China [4] ; 845 patients died (452 in Pesaro Area) due to Covid-19, with high case-fatality rate (14%). Finally, we implemented testing with nasopharyngeal swabs and a quantitative polymerase-chain-reaction test to detect SARS-CoV-2 infection in patients admitted for chemotherapy/stem cell transplantation. Thirty-five HCPs, working exclusively at our Center, were tested: none of them resulted SARS-CoV-2 positive by nasopharyngeal swab. Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China cache = ./cache/cord-346055-7fa57pmf.txt txt = ./txt/cord-346055-7fa57pmf.txt === reduce.pl bib === id = cord-346263-8znpqcth author = Ding, Huiling title = Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu date = 2014-04-13 pages = extension = .txt mime = text/plain words = 9976 sentences = 415 flesch = 44 summary = This essay examines how Chinese governments, local communities, and overseas Chinese in North America responded to the perceived health risks of Severe Acute Respiratory Syndrome (SARS) and H1N1 flu through the use of public and participatory rhetoric about risk and quarantines. One instance of mandatory quarantine is the widespread use of community entry surveillance tools such as temperature monitoring and health registration forms to identify floating people returning from severely SARS affected regions such as Guangdong or Beijing. As a sharp contrast to Asian American and Asian Canadian's use of coerced quarantines as responses to racial targeting in SARS, overseas Chinese from H1N1 epicenters implemented voluntary quarantines when travelling back to China to reduce potential health risks they might have posed to local communities and the nation. cache = ./cache/cord-346263-8znpqcth.txt txt = ./txt/cord-346263-8znpqcth.txt === reduce.pl bib === id = cord-346281-sma6e891 author = Maldonado, Valente title = Repositioning of pentoxifylline as an immunomodulator and regulator of the renin-angiotensin system in the treatment of COVID-19 date = 2020-06-09 pages = extension = .txt mime = text/plain words = 5711 sentences = 260 flesch = 35 summary = Pentoxifylline (PTX) is a phosphodiesterase inhibitor that increases cyclic adenosine monophosphate levels, which in turn activate protein kinase, leading to a reduction in the synthesis of proinflammatory cytokines to ultimately influence the renin-angiotensin system (RAS) in vitro by inhibiting angiotensin 1 receptor (AT1R) expression. The rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19 by helping reduce the production of the inflammatory cytokines without deleterious effects on the immune system to delay viral clearance. 5 Overall, the rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19, which can help reduce the production of the inflammatory cytokines TNF-α, IL-6, IFN-γ, and IL-17 and increase the anti-inflammatory cytokine IL-10. cache = ./cache/cord-346281-sma6e891.txt txt = ./txt/cord-346281-sma6e891.txt === reduce.pl bib === id = cord-346291-qqy9ld94 author = Noroozi, Rezvan title = Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1464 sentences = 88 flesch = 42 summary = In the current review, we summarize the results of studies which reported alterations in cytokine levels and immune cell functions in patients affected with SARS-CoV-2 and related viruses. Alternatively named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus has been shown to induce various clinical manifestation in hosts ranging from asymptomatic conditions to severe symptoms including respiratory failure, shock, or multiorgan system dysfunction (1) Notably, this condition has been accompanied by a significant increase in the proportion of naïve helper T cells while reduction in memory helper T cells and regulatory T cells (5) . Notably, author reported significant over-production of IL-2, IL-7, IL-10, GCSF, IP-10, MCP1, MIP1A, and TNF-α in ICU patients compared with other group of SARS-CoV-2 infected persons (6) . Notably, T cell counts and cytokine concentrations in severe SARS-CoV-2 infected patients who stayed alive gradually returned to their levels in the mild cases. cache = ./cache/cord-346291-qqy9ld94.txt txt = ./txt/cord-346291-qqy9ld94.txt === reduce.pl bib === id = cord-346345-jc9bq0zu author = Smith, Colin M title = COVID-19-associated brief psychotic disorder date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2601 sentences = 144 flesch = 43 summary = This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. Here, we report a case of symptomatic COVID-19-related psychosis in a patient with no personal or family history of mental illness and briefly discuss the relevant literature on coronavirus-associated psychosis. 8 However, all patients were incidentally found to have positive SARS-CoV-2 test and did not present with other symptoms to suggest infection, calling into question whether the diagnosis of COVID-19 was related to the psychosis. cache = ./cache/cord-346345-jc9bq0zu.txt txt = ./txt/cord-346345-jc9bq0zu.txt === reduce.pl bib === id = cord-346145-hnfeauow author = Pillay, Sureshnee title = Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic date = 2020-08-17 pages = extension = .txt mime = text/plain words = 7281 sentences = 371 flesch = 56 summary = title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic In our SARS-CoV-2 assembly workflow, the initial assembly obtained from Genome Detective was polished by aligning mapped reads to the reference (NC_045512) and filtering out mutations with low genotype likelihoods, using bcftools 1.7-2 mpileup method. Furthermore, reagents for only 24 samples were available, as the order of Illumina TruSeq DNA Library preparation kit (x 96 sample libraries), which was placed in February and was enough to produce 480 genomes, had not arrived, due to the restrictions on international flights. The Nextera Flex library preparation kit was suggested by their technical team as a potentially better and quicker solution to produce SARS-CoV-2 genomes, which we found to be true. The Nextera Flex DNA library preparation kit was also evaluated, and we found it saved up to nine hours of hands-on time, when compared with the original ARTIC protocol that uses TruSeq. All three library preparation methods produced high-quality genomes. cache = ./cache/cord-346145-hnfeauow.txt txt = ./txt/cord-346145-hnfeauow.txt === reduce.pl bib === id = cord-346445-hgqohdct author = Toyoshima, Yujiro title = SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3553 sentences = 187 flesch = 53 summary = Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. cache = ./cache/cord-346445-hgqohdct.txt txt = ./txt/cord-346445-hgqohdct.txt === reduce.pl bib === id = cord-346325-grt67p73 author = Reilev, M. title = Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4655 sentences = 258 flesch = 48 summary = Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. In this population-based study of a Danish COVID-19 cohort capturing all individuals with a positive PCR test for SARS-CoV-2 in Denmark, we provide nationwide data on clinical characteristics and predictors of hospitalization and death for all SARS-CoV-2 PCR-positive cases identified from February 27 th , 2020 to April 30 th , 2020. In this nationwide cohort of SARS-CoV-2 PCR positive cases and test-negative individuals from the general population in Denmark, we found that older age (e.g., >70 years), male sex, and number of comorbidities were risk factors for hospitalization and death. In this first nationwide population-based study, increasing age, sex, and number and type of comorbidities were closely associated with hospitalization requirement and death in SARS-CoV-2 PCR positive cases. cache = ./cache/cord-346325-grt67p73.txt txt = ./txt/cord-346325-grt67p73.txt === reduce.pl bib === id = cord-346335-el45v0a5 author = Tan, H.S. title = Fourier spectral density of the coronavirus genome date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4646 sentences = 224 flesch = 56 summary = We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density. An example of a seminal paper in this subject is that of Voss in [2] where the author found that the spectral density of the genome of many different species follows a power law of the form 1/k β in the low-frequency domain, with the exponent β potentially related to the organism's evolutionary category. We develop a few models to characterize the typical spectrum, and in the process stumble upon a linear scaling law between a measure of the complexity of each genome and the power-law exponent that describes the enveloping curve of the low-frequency domain. cache = ./cache/cord-346335-el45v0a5.txt txt = ./txt/cord-346335-el45v0a5.txt === reduce.pl bib === id = cord-346331-d0s028wl author = Lackey, Kimberly A. title = SARS‐CoV‐2 and human milk: What is the evidence? date = 2020-05-30 pages = extension = .txt mime = text/plain words = 5628 sentences = 300 flesch = 53 summary = Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. • Limited, weak evidence suggests that some coronaviruses (including SARS-CoV-2) may be present in human milk, but these studies do not report methods of sample collection and validation of reverse transcription polymerase chain reaction (RT-PCR) assays for human milk. Of particular interest in this context are (1) the potential role that breastfeeding could play in vertical transmission of SARS-CoV-2 from women to infants via human milk and (2) the potential protective effects of targeted antibodies and other immunoprotective components in human milk against COVID-19. Milk was submitted to the CDC, where it was analysed using reverse transcription polymerase chain reaction (RTSearch terms, databases and preprint servers used to identify existing literature reporting the possibility of vertical transmission of coronaviruses from mother to infant during breastfeeding as of 17 April 2020 The infant in this study was never tested for SARS-CoV infection. cache = ./cache/cord-346331-d0s028wl.txt txt = ./txt/cord-346331-d0s028wl.txt === reduce.pl bib === id = cord-346441-b1r6i0wq author = Polverino, Francesca title = Cigarette Smoking and COVID-19: A Complex Interaction date = 2020-08-01 pages = extension = .txt mime = text/plain words = 895 sentences = 53 flesch = 48 summary = These findings have putatively important implications for patients with COVID-19 because ACE2 has been shown to be the receptor used by SARS-CoV-2 to enter the host cells (3) and yet seem in contrast with the consolidated epidemiological data worldwide indicating a low prevalence of active smokers among patients with COVID-19. Last, though it is possible that cigarette smoke increases the ACE2 expression by the bronchial epithelium, thus facilitating the entry of SARS-CoV-2, this does not necessarily translate into a higher risk for developing COVID-19 pneumonia. To conclude, what is unchallengeable is that cigarette smoke is detrimental for the lungs in several ways, and further studies are needed to clarify the reasons behind the reported low prevalence of current smokers among hospitalized patients with COVID-19. Tobacco smoking increases the lung gene expression of ACE2, the receptor of SARS-CoV-2 cache = ./cache/cord-346441-b1r6i0wq.txt txt = ./txt/cord-346441-b1r6i0wq.txt === reduce.pl bib === id = cord-346153-9162w7il author = Openshaw, P J title = Crossing barriers: infections of the lung and the gut date = 2008-12-24 pages = extension = .txt mime = text/plain words = 1716 sentences = 90 flesch = 43 summary = Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. However, the coronavirus copy number in some studies showed an increase between day 5 and day 10, so that maximal infectivity followed the fever, 7 leading perhaps to a false sense of security amongst those caring for SARS patients. e reason for these interactions are incompletely understood, but intriguing recent study show that in uenza and respiratory syndrome virus are both capable of causing a persistent inhibition of the innate response to bacterial superinfection, and therefore to increased bacterial replication and disease. Highly pathogenic strains of in uenza also cause intense systemic symptoms, sometimes associated with gastrointestinal disease. Microbial translocation is a cause of systemic immune activation in chronic HIV infection cache = ./cache/cord-346153-9162w7il.txt txt = ./txt/cord-346153-9162w7il.txt === reduce.pl bib === id = cord-346389-gbmnoo84 author = Callender, Lauren A. title = The Impact of Pre-existing Comorbidities and Therapeutic Interventions on COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 10042 sentences = 514 flesch = 40 summary = Here, we review immune dysfunction in response to SARS-CoV-2 infection and the impact of pre-existing comorbidities on the development of COVID-19. Furthermore, cardiovascular complications such as thromboembolic events, myocarditis, acute coronary syndrome, arrythmia, cardiogenic shock and heat failure, have been documented in COVID-19 patients without prior cardiovascular disease (71), demonstrating a significant impact of SARS-CoV-2 infection on the heart. As infection with SARS-CoV-2 results in an acute respiratory disease that can progress to ARDS, respiratory failure and potentially even death, it is reasonable to speculate that patients with pre-existing respiratory disease would be at increased risk of severe COVID-19. Consequently, it has been proposed that liver damage associated with severe COVID-19 patients is due to dysregulated innate immunity against SARS-CoV-2, or hepatoxicity in response to treatments, rather than pre-existing liver disease. Therefore, the underlying pathogenesis of chronic kidney disease may increase vulnerability to hyperinflammation and cytokine storm upon SARS-CoV-2 infection, resulting in severe COVID-19. cache = ./cache/cord-346389-gbmnoo84.txt txt = ./txt/cord-346389-gbmnoo84.txt === reduce.pl bib === id = cord-346248-6wkyar57 author = de Moura, Diogo Turiani Hourneaux title = Diagnostic Characteristics of Serological-Based COVID-19 Testing: A Systematic Review and Meta-Analysis date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3892 sentences = 214 flesch = 42 summary = The aim of this study was to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based COVID-19 testing. This meta-analysis demonstrates suboptimal sensitivity and specificity of serologic-based diagnostic testing for SARS-CoV-2 and suggests that antibody testing alone, in its current form, is unlikely to be an adequate solution to the difficulties posed by COVID-19 and in guiding future policy decisions regarding social distancing and reopening of the economy worldwide. While this test is still the most effective method to date for the diagnosis of active COVID-19, serologic-based antibody testing to assist with known exposure to SARS-CoV-2 remains pivotal to accurately assessing the burden of disease. Therefore, we aim to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based testing (IgG and IgM) for COVID-19. cache = ./cache/cord-346248-6wkyar57.txt txt = ./txt/cord-346248-6wkyar57.txt === reduce.pl bib === id = cord-346544-kk7qyn4w author = Andersson, M. title = SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4992 sentences = 305 flesch = 53 summary = Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. . https://doi.org/10.1101/2020.05.21.20105486 doi: medRxiv preprint prevalence of vRNA detection in blood, serum or plasma, noting whether this attribute was correlated with clinical or laboratory phenotypes of disease, and recording Ct values when these were reported. We collected 212 serum samples through the microbiology department at Oxford University Hospitals NHS Foundation Trust, OUH NHSFT, comprising adults with a diagnosis of COVID-19, confirmed by SARS-CoV-2 detection by a clinical diagnostic microbiology laboratory using RT-PCR on a respiratory swab, classified in three groups as follows: Based on a systematic review of the literature, together with our own data, we estimate that SARS-CoV-2 RNA may be present at low copy numbers in ~10% of blood samples obtained from individuals with COVID-19 prior to day 28, most of which arise at earlier timepoints and in the setting of more severe disease. cache = ./cache/cord-346544-kk7qyn4w.txt txt = ./txt/cord-346544-kk7qyn4w.txt === reduce.pl bib === id = cord-346512-y5d8q5b9 author = Pellicciaro, Marco title = Breast cancer patients with hormone neoadjuvant bridging therapy due to asymptomatic Corona virus infection. Case report, clinical and histopathologic findings date = 2020-10-08 pages = extension = .txt mime = text/plain words = 2050 sentences = 145 flesch = 45 summary = INTRODUCTION: Breast cancer management during COVID-19 pandemic has changed and in case of COVID-19 patients with simultaneous neoplasia, it has been strongly recommended to treat Sars-CoV-2 infection firstly. According to COVID-19 breast cancer recommendations she underwent hormone neoadjuvant treatment as a bridging therapy for surgery. We report a case of woman with COVID-19 and simultaneous early breast cancer treated with neoadjuvant endocrine therapy in lieu of upfront surgery and with lymph node micrometastases at pathological examination. Immunohistochemical staining revealed strongly and diffusely ER and PR positive in tumor cells: <95% and 40% respectively ( Figure 1B Before COVID-19 pandemic, patient such as this, with clinical stage T1N0, hormone receptors positive HER2-negative breast cancer, would have been a candidate for upfront surgery [11] . Therefore, the use of bridging therapy in patients with early breast cancer, during pandemic, that could benefit from upfront surgery should be evaluated in large sample studies. cache = ./cache/cord-346512-y5d8q5b9.txt txt = ./txt/cord-346512-y5d8q5b9.txt === reduce.pl bib === id = cord-346403-fuxs1axy author = Davanzo, G. G. title = SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3490 sentences = 214 flesch = 59 summary = We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARSCoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Since CD4 + T lymphocytes orchestrate innate and adaptive immune responses 19, 20 , infection of CD4 + T cells by SARS-CoV-2 might explain lymphocytopenia and dysregulated inflammatory response in severe COVID-19 patients. cache = ./cache/cord-346403-fuxs1axy.txt txt = ./txt/cord-346403-fuxs1axy.txt === reduce.pl bib === id = cord-346413-2njl0fd3 author = Nakazawa, Daigo title = Immunothrombosis in severe COVID-19 date = 2020-08-15 pages = extension = .txt mime = text/plain words = 836 sentences = 52 flesch = 39 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread all over the world immediately after the first patient infected with this virus was discovered in Wuhan, China, in December 2019. It has been demonstrated that SARS-CoV-2 infection induces vascular endothelial injury, resulting from coagulation [3] . Because these are degradation products of fibrin or neutrophil extracellular traps (NETs), an enhanced turnover of coagulation and NET formation appears to characterize severe COVID-19. Based on the loss of CD31 + cells in the endothelium that were close to the aggregated NETs, Leppkes and coworkers suggested that the injury of vascular endothelial cells infected with SARS-CoV-2 could trigger neutrophil attraction and NET formation (Fig. 1) . Leppkes and coworkers suggested that the prevention of excessive NET formation and aggregation could provide an approach to inhibit vascular occlusion and the development of severe COVID-19. When SARS-CoV-2 injures vascular endothelial cells, coagulation is invoked, and simultaneously, DAMPs are secreted from the damaged cells. cache = ./cache/cord-346413-2njl0fd3.txt txt = ./txt/cord-346413-2njl0fd3.txt === reduce.pl bib === id = cord-346658-ij5sr88p author = Hilgenfeld, Rolf title = Sometimes Intermediates Do the Job! date = 2006-04-07 pages = extension = .txt mime = text/plain words = 1196 sentences = 73 flesch = 60 summary = The mode of binding of this inhibitor to the target enzyme was found to be related (although not identical) to what had been seen earlier in a complex between the rhinovirus (HRV-2) 3C proteinase and compound AG7088 (Figure 1A) , a vinylogous ethyl ester developed by Agouron Inc. The structural insight along with information on the flexibility of the enzyme [9] enabled researchers world-wide to use structure-based design [5] and virtual screening methods [10] to prepare new inhibitors of the SARS-CoV M pro . Several lopinavir derivatives showed somewhat improved binding affinities, but it came as a big surprise that some of the intermediate benzotriazole esters resulting from the activation of the acid components by HBTU were nanomolar inhibitors of the M pro ! The discovery of compounds binding noncovalently to the M pro may, in the end, constitute a more important milestone on the way to clinically useful inhibitors of the coronavirus main proteinase than identification of the acylating agents. cache = ./cache/cord-346658-ij5sr88p.txt txt = ./txt/cord-346658-ij5sr88p.txt === reduce.pl bib === id = cord-346530-o65m0whe author = Chaumont, H. title = Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection date = 2020-06-12 pages = extension = .txt mime = text/plain words = 770 sentences = 49 flesch = 36 summary = title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection We report four cases of severe COVID-19 in male patients aged 50-70 with the combination of central and peripheral nervous system disorders occurring unexpectedly late after the first symptoms. Several acute neurological syndromes have been associated with SARS-CoV-2 infection, including anosmia and ageusia [1, 2] , meningoencephalitis [3, 4] , acute hemorrhagic necrotizing encephalopathy [5] , axonal or demyelinating polyradiculoneuropathy [6] [7] [8] , polyneuritis cranialis [8] . They consisted of miscellaneous symptoms such as confusion, cognitive dysfunction (memory deficit, frontal syndrome), psychiatric disorders (paranoid delusion, hallucinations), weakness, pyramidal signs, dysautonomia, swallowing dysfunction, vertical supranuclear eye palsy, upper limbs myoclonus, fasciculation and focal muscle atrophy (Table 1) . COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection cache = ./cache/cord-346530-o65m0whe.txt txt = ./txt/cord-346530-o65m0whe.txt === reduce.pl bib === id = cord-346532-4xpnd93d author = Strömich, Léonie title = Allosteric Hotspots in the Main Protease of SARS-CoV-2 date = 2020-11-06 pages = extension = .txt mime = text/plain words = 2370 sentences = 145 flesch = 60 summary = Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Bond-to-bond propensities have been shown to successfully detect allosteric sites on proteins [43] and we here present 141 the results in the SARS-CoV-2 M pro to that effect. After a full Bond-to-bond propensity analysis and quantile regression to rank all residues, we are able to score the active 156 site to obtain a measure for the connectivity towards the catalytic center (Tab. S8). A complementary, node-based method, Markov Transient analysis (MTA) 276 identifies areas of the protein that are significantly connected to a site of interest, the source, such as the active site, and 277 obtains the signal propagation that connects the two sites at the atomistic level. cache = ./cache/cord-346532-4xpnd93d.txt txt = ./txt/cord-346532-4xpnd93d.txt === reduce.pl bib === id = cord-346711-2k736hvr author = Shetty, Rohit title = Stem cell therapy in COVID-19 – current evidence and future potential date = 2020-11-09 pages = extension = .txt mime = text/plain words = 3231 sentences = 225 flesch = 45 summary = Acute respiratory distress syndrome (ARDS) caused by an unregulated host inflammatory response towards the viral infection, followed by multi-organ dysfunction or failure, is one of the primary causes of deaths in severe cases of COVID-19 infection. Expanded Umbilical Cord Mesenchymal Stem Cells (UC-MSCs) as a Therapeutic Strategy in Managing Critically Ill COVID-19 Patients: The Case for Compassionate Use Clinical remission of a critically ill COVID-19 patient treated by human umbilical cord mesenchymal stem cells FDA approved mesenchymal stem cell (MSC) treatments as compassionate use in the very sickest COVID-19 patients Adipose-derived mesenchymal stromal cells for the treatment of patients with severe SARS-CoV-2 pneumonia requiring mechanical ventilation. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial, The Lancet Therapeutic Effects of Human Umbilical Cord-Derived Mesenchymal Stem Cells in Acute Lung Injury Mice cache = ./cache/cord-346711-2k736hvr.txt txt = ./txt/cord-346711-2k736hvr.txt === reduce.pl bib === id = cord-346299-2s9j01q7 author = Salim Khan, S Muhammad title = Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date = 2020-09-04 pages = extension = .txt mime = text/plain words = 1407 sentences = 102 flesch = 55 summary = title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. 65 Besides, assuming that antibodies provide partial or total immunity, seroprevalence surveys give Here, we present the results of a cross-sectional seroprevalence study in District Srinagar, 70 conducted between 1 st and 15 th July 2020, to estimate the prevalence of IgG antibodies against 71 SARS-CoV-2 among adults using a sensitive and specific chemiluminescent microparticle 72 immunoassay (CMIA)-based test. 156 We estimated the number of infections till two weeks before the study period, i.e., 15 th June 2020 157 to 30 th June 2020, by applying the age-and gender-specific seroprevalence rates found in the Table) . cache = ./cache/cord-346299-2s9j01q7.txt txt = ./txt/cord-346299-2s9j01q7.txt === reduce.pl bib === id = cord-346546-yffwd0dc author = Douangamath, Alice title = Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4059 sentences = 259 flesch = 56 summary = To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. For 113 another series of hit compounds, containing a N-chloroacetyl piperidinyl-4-carboxamide 114 motif (Table S2 ) which displays lower reactivity and were not frequent hitters in previous 115 screens, we attempted crystallization despite their absence of labelling in the stringent 116 The bound fragments comprehensively sample all subsites of the active 287 site revealing diverse expansion vectors, and the electrophiles provide extensive, systematic 288 as well as serendipitous, data for designing covalent compounds. Crystal structure of SARS-CoV-2 main protease 763 provides a basis for design of improved alpha-ketoamide inhibitors cache = ./cache/cord-346546-yffwd0dc.txt txt = ./txt/cord-346546-yffwd0dc.txt === reduce.pl bib === id = cord-346670-34wfy52f author = Gobeil, Sophie M-C. title = D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date = 2020-10-12 pages = extension = .txt mime = text/plain words = 7065 sentences = 359 flesch = 57 summary = Most structures of the SARS-CoV-2 S ectodomain currently available include two mutations, one to disrupt the furin cleavage site (RRAR to GSAS = S-GSAS), and a double proline mutation (PP) of residues 986-987, designed to prevent conformational change to the post-fusion state (Wrapp et al., 2020) . While the SARS-CoV-2 S ectodomain construct that includes mutations of residues K986 and V987, between the HR1 and CH subdomains (S2 domain), to prolines (PP) (named S-GSAS/PP in this study) (Figure 1 ) is widely used in the field, the origin of this PP construct was based upon the stabilization of the pre-fusion conformation of other coronavirus spikes (Pallesen et al., 2017; Walls et al., 2020; Wrapp et al., 2020) . Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 b sheet ( Figure 7C, S8B) . cache = ./cache/cord-346670-34wfy52f.txt txt = ./txt/cord-346670-34wfy52f.txt === reduce.pl bib === id = cord-346370-jdfsacds author = Sergi, Consolato M. title = The Facemask in Public and Healthcare Workers– A Need not a Belief date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1186 sentences = 63 flesch = 51 summary = Strict isolation and social distancing measures can flatten the coronavirus infectious curve, and the use of facemask needs to be encouraged and facilitated in crowded places, particularly in hospitals where the 6-feet social distancing cannot be adopted because of physical barriers. I If most people wear a mask in public at any time the transmission rate can easily decrease beneath 1.0, thus stopping the spread of the disease and limit the long-standing Lockdown measures 13 . It is important to emphasize that while a protective mask may reduce the likelihood of infection, it will not eliminate the risk, particularly when a disease has more than one route of transmission, as identified in SARS-Cov-2. While strict isolation and social distancing measures can flatten the infectious curve, the use of facemask needs to be encouraged and facilitated where the 6-feet social distancing cannot be implemented because of physical barriers. cache = ./cache/cord-346370-jdfsacds.txt txt = ./txt/cord-346370-jdfsacds.txt === reduce.pl bib === id = cord-346555-3hrbea6d author = Hu, Xiumei title = Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS‐CoV‐2 date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1187 sentences = 80 flesch = 50 summary = Since many coronaviruses are sensitive to heat, heating inactivation of samples at 56°C prior to testing is considered a possible method to reduce the risk of transmission, but the effect of heating on the measurement of SARS‐CoV‐2 antibodies is still unclear. CONCLUSION: Our results indicate that heat inactivation of serum at 56°C for 30 minutes interferes with the immunoanalysis of antibodies to SARS‐CoV‐2. The current outbreak of coronavirus disease 2019 (COVID19) caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is posing a serious threat to public health. The signal intensity of the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before and after heat inactivation The changes in the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before (blue dot) and after heat inactivation (red dot) Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS-CoV-2 cache = ./cache/cord-346555-3hrbea6d.txt txt = ./txt/cord-346555-3hrbea6d.txt === reduce.pl bib === id = cord-346763-xdfl659q author = Herman, A. title = Drug reaction with eosinophilia and systemic symptoms syndrome in a patient with COVID‐19 date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1319 sentences = 68 flesch = 50 summary = We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. According to the scoring system for classifying DRESS cases (RegiSCAR) reported by Kardaun et al., 1 a drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome was diagnosed as follows: fever ≥38.5°C (0), enlarged lymph nodes (0), eosinophilia (1), atypical lymphocytes (1), skin rash extent >50% body surface area (1), skin rash suggesting DRESS (1), biopsy suggesting DRESS (0), organ involvement (liver, kidney, lung) (2), resolution ≥15 days (0), viral titers (HBV/HCV) negative (1) . Drug reaction with eosinophilia and systemic symptoms syndrome (DRESS) syndrome associated with azithromycin presenting like septic shock: a case report Drug reaction with eosinophilia and systemic symptoms (DRESS) associated with azithromycin in acute Epstein-Barr virus infection cache = ./cache/cord-346763-xdfl659q.txt txt = ./txt/cord-346763-xdfl659q.txt === reduce.pl bib === id = cord-346669-7n75m669 author = Wang, Shixin title = Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date = 2008-02-29 pages = extension = .txt mime = text/plain words = 3814 sentences = 200 flesch = 53 summary = This study was to investigate the relationship between tumor necrosis factor (TNF)-α gene polymorphisms with the occurrence of SARS-CoV infection and its role in prognosis of patients with lung interstitial fibrosis and femoral head osteonecrosis. METHODS: The association between genetic polymorphisms of TNF-α gene and susceptibility to severe acute respiratory syndromes (SARS) was conducted in a hospital-based case-control study including 75 SARS patients, 41 health care workers and 92 healthy controls. Relationships of TNF-α gene polymorphisms with interstitial lung fibrosis and femoral head osteonecrosis were carried out in two case-case studies in discharged SARS patients. In this paper, we aimed to study whether polymorphisms in TNF-α promoter region were associated with SARS-CoV infection, development, and progression of interstitial lung fibrosis and femoral head necrosis in cure SARS patients. Considered that the progression of interstitial lung fibrosis or femoral head necrosis may be affected by hormone therapy, hormone using dosage, method and lasting period were considered in this study when analyzing the associations between gene polymorphisms with disease. cache = ./cache/cord-346669-7n75m669.txt txt = ./txt/cord-346669-7n75m669.txt === reduce.pl bib === id = cord-346539-kxnrf5g5 author = Riggioni, Carmen title = A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date = 2020-06-14 pages = extension = .txt mime = text/plain words = 15760 sentences = 1112 flesch = 48 summary = This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-346539-kxnrf5g5.txt txt = ./txt/cord-346539-kxnrf5g5.txt === reduce.pl bib === id = cord-346758-pi1hf6xg author = Egerup, P. title = Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3802 sentences = 304 flesch = 54 summary = Two smaller case reports from China documented SARS-CoV-2 antibodies in newborns with COVID-19 positive mothers indicating possible vertical transmission. This study aimed to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns. We here report the results of a prospective cohort study with unselected serological testing in 1,313 parturient women, 1,189 partners and 1,206 newborns to identify if SARS-CoV-2 infection is associated with obstetric and neonatal complications. The serum from the blood samples from women, partners and newborns were analyzed for SARS-CoV-2 antibodies (IgM and IgG). There was no significant difference between pre-pregnancy characteristics in relation to SARS-CoV-2 antibodies, except blood type and that women with antibodies reported more COVID-19-like symptoms (p=0.025). In this prospective cohort study with serological testing of parturient women, partners and newborns we found no association between COVID-19 and obstetric-or neonatal complications. cache = ./cache/cord-346758-pi1hf6xg.txt txt = ./txt/cord-346758-pi1hf6xg.txt === reduce.pl bib === id = cord-347090-sqw7n1v2 author = Rodriguez-Gonzalez, Moises title = New onset severe right ventricular failure associated with COVID-19 in a young infant without previous heart disease date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1816 sentences = 110 flesch = 44 summary = We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. cache = ./cache/cord-347090-sqw7n1v2.txt txt = ./txt/cord-347090-sqw7n1v2.txt === reduce.pl bib === id = cord-346930-gl573ip9 author = Hussain, Azhar title = Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date = 2020-05-24 pages = extension = .txt mime = text/plain words = 4177 sentences = 207 flesch = 45 summary = Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. Since the emergence of the virus in China in December of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the globe resulting in the current global pandemic. Arbidol (also known as Umifenovir) is a promising repurposed antiviral agent with a unique mechanism of action targeting the S protein/ACE2 interaction and inhibiting membrane fusion of the viral envelope to the host cell [7] . cache = ./cache/cord-346930-gl573ip9.txt txt = ./txt/cord-346930-gl573ip9.txt === reduce.pl bib === id = cord-346677-20ky3t6y author = Sun, Pengfei title = Clinical characteristics of hospitalized patients with SARS‐CoV‐2 infection: A single arm meta‐analysis date = 2020-03-11 pages = extension = .txt mime = text/plain words = 1647 sentences = 112 flesch = 52 summary = OBJECTIVE: We aim to summarize reliable evidence of evidence‐based medicine for the treatment and prevention of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) by analyzing all the published studies on the clinical characteristics of patients with SARS‐CoV‐2. Since December 2019, the epidemic of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infectious pneumonia in Wuhan, China. To acquire more accurate conclusions on the clinical characteristics and mortality of patients with SARS-CoV-2 infection, we searched the relevant literatures and carried out single-arm metaanalysis. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 17 hospitalized patients with 2019 novel coronavirus infections outside Wuhan, China. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: A single arm meta-analysis cache = ./cache/cord-346677-20ky3t6y.txt txt = ./txt/cord-346677-20ky3t6y.txt === reduce.pl bib === id = cord-346957-bmajkabp author = Lv, Yanbo title = Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date = 2009-12-03 pages = extension = .txt mime = text/plain words = 4933 sentences = 261 flesch = 57 summary = RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. cache = ./cache/cord-346957-bmajkabp.txt txt = ./txt/cord-346957-bmajkabp.txt === reduce.pl bib === id = cord-346859-r1v6ir8u author = Mallett, Sue title = At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date = 2020-11-04 pages = extension = .txt mime = text/plain words = 5020 sentences = 277 flesch = 52 summary = BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. Because testing is pivotal to management and containment of COVID-19, we performed an individual participant data (IPD) systematic review of emerging evidence about test accuracy by anatomical sampling site to inform optimal sampling strategies for SARS-CoV-2. Previous studies have established that in COVID-19 infection, viral loads typically peak just before symptoms and at symptom onset [4] and estimated false negative test results over time since exposure from upper respiratory tract samples [2] . • Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). cache = ./cache/cord-346859-r1v6ir8u.txt txt = ./txt/cord-346859-r1v6ir8u.txt === reduce.pl bib === id = cord-347079-1zbsbcdd author = Silverman, Justin D. title = Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date = 2020-06-22 pages = extension = .txt mime = text/plain words = 6234 sentences = 266 flesch = 49 summary = To estimate the proportion and magnitude of the March 2020 US ILI surge attributable to SARS-CoV-2 infections, we made the following three assumptions: (1) that the patient population reported by sentinel providers is representative of their state each week; (2) that changes in care-seeking behavior of ILI patients is occurring at a similar rate as that of other non-ILI patients; and (3) that the total number of patients in the US who require medical care over the course of a year has not substantially changed since 2018. The goal of our study was to use publicly available data to estimate the number of patients seeking care for non-influenza ILI in excess of seasonal trends during the three weeks spanning March 8 to March 28, 2020 and then use this ILI surge to estimate COVID-19 incidence in March and parameterize epidemiological model growth rates and clinical rates. cache = ./cache/cord-347079-1zbsbcdd.txt txt = ./txt/cord-347079-1zbsbcdd.txt === reduce.pl bib === id = cord-347104-h168kqjn author = Ghosh, Ritwik title = A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection date = 2020-11-11 pages = extension = .txt mime = text/plain words = 2596 sentences = 184 flesch = 38 summary = title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection J o u r n a l P r e -p r o o f It has recently reported a case of a young man presenting with bilateral severe optic neuritis and myelitis, determined to be simultaneously SARS-CoV-2 and MOG IgG antibody positive, i.e. a variant of NMOSD. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. cache = ./cache/cord-347104-h168kqjn.txt txt = ./txt/cord-347104-h168kqjn.txt === reduce.pl bib === id = cord-346816-xys0g8b8 author = Shichijo, S. title = Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity date = 2004-10-20 pages = extension = .txt mime = text/plain words = 1141 sentences = 61 flesch = 54 summary = title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity Abstract: In order to determine highly immunogenic severe acute respiratory syndrome coronavirus (SARS‐CoV) epitope peptides capable of inducing long‐lasting immunity, we first screened immunoglobulin‐G (IgG) antibodies reactive to 197 different overlapping 15‐mers from the SARS‐CoV proteins in the sera of three infected patients. The significantly higher levels of IgG antibodies specific to three (S791, M207 and N161) of 42 peptides were detectable in the post‐infection sera from 23 (51%), 27 (60%) and 19 (42%) of 45 patients, respectively. In contrast to these four peptides, significant levels of IgG reactive to the remaining 36 peptides were either scarcely or not detected in the patients (Table 1) Fig. 5 . Dynamic observation IgG and IgM antibodies in patients with severe acute respiratory syndrome cache = ./cache/cord-346816-xys0g8b8.txt txt = ./txt/cord-346816-xys0g8b8.txt === reduce.pl bib === id = cord-346787-uo8k6qic author = Jorgensen, Sarah CJ title = Remdesivir: Review of pharmacology, pre‐clinical data and emerging clinical experience for COVID‐19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 5476 sentences = 367 flesch = 51 summary = 3 The remdesivir dosing regimen being evaluated in clinical trials (200 mg IV on day 1, then 100 mg IV on days 2 through 5 or 10) was substantiated by in vitro data and bridging the PK with the rhesus monkey experience to humans. Prophylactic and therapeutic remdesivir treatment significantly reduced MERS-CoV-induced clinical signs, viral titers in respiratory specimens and the severity of lung lesions compared to control animals. 14 In the SARS-CoV-2 study, remdesivir was again initiated shortly before viral titers are expected to peak at 12 hours post-inoculation and a dosing regimen equivalent to the regimen being tested in human COVID-19 clinical trials was used (10 mg/kg load ~ 200 mg in humans, then 5 mg/kg daily ~ 100mg daily in humans x 6 days). In a summary of safety data reported by the FDA from the a remdesivir clinical trial comparing 5 and 10day treatment courses in patients with COVID-19, Grade 3 and 4 ALT and/or AST elevations occurred in 7% patients. cache = ./cache/cord-346787-uo8k6qic.txt txt = ./txt/cord-346787-uo8k6qic.txt === reduce.pl bib === id = cord-346998-01i6zxv8 author = Kulkarni, Spoorthy title = COVID-19 and hypertension date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2584 sentences = 163 flesch = 48 summary = COVID-19 seems to follow a pattern seen with influenza and previous severe acute respiratory syndrome coronavirus (SARS-CoV) outbreaks: that the severity and mortality of the infection is higher in the elderly age group. The controversy regarding continuing or discontinuing angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) in COVID-19 patients arose after it became apparent that SARS-CoV uses angiotensin-converting enzyme 2 (ACE2) to gain entry in host cells. 12 Consequently, the increased expression of ACE2 would facilitate an increased rate or susceptibility to infection with SARS-CoV-2 and further hypothesis that this may increase the risk of developing severe and fatal COVID-19. The study tested the hypothesis of an increased risk of severe illness in COVID-19 with hypertension with ACEi use (on ACEi n=37; not on ACEi n=168) in admitted patients. Effect of angiotensin converting enzyme gene I/D polymorphism and its expression on clinical outcome in acute respiratory distress syndrome cache = ./cache/cord-346998-01i6zxv8.txt txt = ./txt/cord-346998-01i6zxv8.txt === reduce.pl bib === id = cord-347121-5drl3xas author = Farah, I. title = A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform. date = 2020-09-29 pages = extension = .txt mime = text/plain words = 16886 sentences = 784 flesch = 48 summary = The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The platform is a proven research ecosystem used by universities, biotech, and bioinformatics organizations to share and analyze omics data and can be used for a variety of use cases; from precision medicine, drug discovery, translational science to building data repositories, and tackling a disease outbreak. Our approach is designed to provide healthcare professionals with an urgently needed platform to find and analyze genetic data, and securely and anonymously share sensitive patient data to fight the disease outbreak. Among other use-cases, the provided platform can be used to rapidly study SARS-CoV-2, including analyses of the host response to COVID-19 disease, establish a multi-institutional collaborative datahub for rapid response for current and future pandemics, characterizing potential co-infections, and identifying potential therapeutic targets for preclinical and clinical development. cache = ./cache/cord-347121-5drl3xas.txt txt = ./txt/cord-347121-5drl3xas.txt === reduce.pl bib === id = cord-346819-11fkgzaa author = Khan, Mohd Imran title = Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4405 sentences = 291 flesch = 57 summary = title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. The genome analysis of the SARS-CoV-2 strains from 13 different countries showed a large number of mutations within the major structural proteins. This study provides a deeper insight into the emergence of these mutations within the major structural as well as nsp encoded by the SARS-CoV-2 genome from different countries. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations backbone RMSD was also noticed (Fig 4A) . cache = ./cache/cord-346819-11fkgzaa.txt txt = ./txt/cord-346819-11fkgzaa.txt === reduce.pl bib === id = cord-346960-3empldlo author = Plebani, M. title = Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity date = 2020-08-04 pages = extension = .txt mime = text/plain words = 2282 sentences = 134 flesch = 46 summary = In 184 serum samples from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). On limiting the analysis to samples collected 12 days after onset of symptoms, the sensitivity of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. 54 SARS-CoV-2 negative subjects (33 healthcare workers, 21 autoimmune patients, 8 pregnant women) were included in the study ( Moreover, Liaison SARS-CoV-2 S1/S2 IgG (Diasorin, Sallugia-VC, Italy), ENZY-Well SARS-CoV-2 IgA and IgM were evaluated for the correlation with the neutralization results. . To provide insight on neutralization activity compared with immunoassays results, PRNT assay was performed on 52 samples from SARS-CoV-2 positive subjects. cache = ./cache/cord-346960-3empldlo.txt txt = ./txt/cord-346960-3empldlo.txt === reduce.pl bib === id = cord-347119-w780f0om author = Blitz, Matthew J. title = Race/ethnicity and spatiotemporal trends in SARS-CoV-2 prevalence on obstetrical units in New York date = 2020-08-17 pages = extension = .txt mime = text/plain words = 923 sentences = 65 flesch = 58 summary = We evaluated 7 temporal trends, regional geographic variation, and racial/ethnic disparity in SARS-CoV-8 2 prevalence among gravid women presenting to obstetrical units within a large health 9 system in New York during the COVID-19 outbreak. This retrospective study included all pregnant women who had SARS-CoV-2 testing 13 (both symptomatic and asymptomatic) at 7 hospitals within a 30-mile radius from April 14 1, 2020, before the peak of the outbreak in New York State, 4 to June 9, 2020. Of 4,811 pregnant women presenting to the 7 hospital sites after implementation of 38 universal SARS-CoV-2 testing, PCR results were obtained for 4,674 patients: 500 39 (11%) were positive. Non-Hispanic black women 50 constituted 12% (n=567) of the study population, had a test positivity rate of 14% 51 Considerable heterogeneity in SARS-CoV-2 prevalence was observed across hospitals 64 in the region (p<0.0001; Table 1 ). cache = ./cache/cord-347119-w780f0om.txt txt = ./txt/cord-347119-w780f0om.txt === reduce.pl bib === id = cord-347048-qqft4yc9 author = Araten, David J. title = Mild Clinical Course of COVID-19 in 3 Patients Receiving Therapeutic Monoclonal Antibodies Targeting C5 Complement for Hematologic Disorders date = 2020-09-12 pages = extension = .txt mime = text/plain words = 2161 sentences = 125 flesch = 55 summary = CASE REPORTS: Case 1 is a 39-year-old woman with an approximately 20-year history of paroxysmal nocturnal hemoglobinuria (PNH), who had recently been switched from treatment with eculizumab to ravulizumab prior to SARS-CoV-2 infection. Case 2 is a 54-year-old woman with a cadaveric renal transplant for lupus nephritis, complicated by thrombotic microangiopathy, who was maintained on eculizumab, which she started several months before she developed the SARS-CoV-2 infection. CONCLUSIONS: We see no evidence of increased susceptibility to SARS-CoV-2 in these patients on anti-complement therapy, which might actually have accounted for the mild course of infection. We now have the opportunity to report on 3 patients who were on therapeutic anti-complement therapy at the time they became infected with the SARS-CoV-2 virus. The mild cases of SARS-CoV-2 infection in these 3 patients may have been related to anti-complement therapy, as suggested by preclinical models and reports of other patients who have received anti-complement therapy for COVID-19. cache = ./cache/cord-347048-qqft4yc9.txt txt = ./txt/cord-347048-qqft4yc9.txt === reduce.pl bib === id = cord-347030-yx3j6373 author = Cao, Xuetao title = COVID-19: immunopathology and its implications for therapy date = 2020-04-09 pages = extension = .txt mime = text/plain words = 1519 sentences = 74 flesch = 35 summary = Most patients with COVID-19 exhibit mild to moderate symptoms, but approximately 15% progress to severe pneumonia and about 5% eventually develop acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure 1, 2 . Convalescent plasma containing neutralizing antibodies has been used to treat a small number of patients with severe disease, and preliminary results show clinical improvement in 5 of 5 critically ill patients with COVID-19 who developed ARDS 8 . High levels of pro-inflammatory cytokines may lead to shock and tissue damage in the heart, liver and kidney, as well as respiratory failure COVID-19: immunopathology and its implications for therapy Xuetao Cao 1, 2 Severe coronavirus disease 2019 (COVID-19) is characterized by pneumonia, lymphopenia, exhausted lymphocytes and a cytokine storm. In addition to the cytokine-based pathology in patients with severe COVID-19, complement activation has also been observed, indicating that complement inhibitors, if used at an early stage of the infection, may attenuate the inflammatory damage. cache = ./cache/cord-347030-yx3j6373.txt txt = ./txt/cord-347030-yx3j6373.txt === reduce.pl bib === id = cord-347351-emdj66vj author = Kampf, Günter title = Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 10283 sentences = 592 flesch = 50 summary = Originating from a single travel-associated primary case from China, the first documented chain of multiple human-to-human transmissions of SARS-CoV-2 outside of Asia allowed a detailed study of transmission events and identified several factors (e.g. cumulative face-toface contact, direct contact with secretions or body fluids of a patient, personal protective equipment) to classify contacts as low or high risk [32] . In the close surrounding of COVID-19 patients in hospitals SARS-CoV-2 RNA is detected more frequently compared to surfaces outside the patient rooms but samples were so far consistently negative for infectious virus. General disinfection of frequently touched surfaces in the public such as shopping carts or door handles is, however, unlikely to add any protective value because even in COVID-19 wards inanimate surfaces were mainly contaminated in the permanent and immediate surrounding of symptomatic patients (detection of viral RNA, not of infectious virus) and only rarely one room away [138] suggesting that the risk to find SARS-CoV-2 on frequently touched surfaces in the public is low. cache = ./cache/cord-347351-emdj66vj.txt txt = ./txt/cord-347351-emdj66vj.txt === reduce.pl bib === id = cord-347441-8ow952d8 author = Parvez, Md Sorwer Alam title = Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date = 2020-06-07 pages = extension = .txt mime = text/plain words = 1027 sentences = 75 flesch = 62 summary = title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh. As many of the Bangladeshi people return during the COVID-19 39 outbreak mainly from China, India, Saudi Arabia, Spain, Italy, Japan, Qatar, Canada, Kuwait, USA, 40 France, Sweden, and Switzerland, the first deposited genome sequence of those countries were also 41 retrieved. In total, three models were generated using the template PDB ID: 6VSB; one model for the spike protein 118 of reference strain, and the two others were for two different mutant isolates from Bangladesh (Fig 3) . cache = ./cache/cord-347441-8ow952d8.txt txt = ./txt/cord-347441-8ow952d8.txt === reduce.pl bib === id = cord-346978-ubkqny8j author = Ranoa, Diana Rose E. title = Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date = 2020-06-18 pages = extension = .txt mime = text/plain words = 6476 sentences = 325 flesch = 54 summary = 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) . Similar results were observed with heat-inactivated SARS-CoV-2, whereby the LOD was measured to be 5000 viral copies/mL for both RNA extraction of saliva samples and direct saliva-to-RT-qPCR, with greater detection if the virus was directly analyzed in water (Supporting Limit of Detection (LOD) for assessment of SARS-CoV-2 from saliva, comparing a process utilizing RNA isolation/purification to one that bypasses RNA isolation/purification. Altogether, these findings indicate that the optimized protocol (heat treatment of saliva samples at 95°C for 30 min / addition of TBE buffer and Tween 20) yields a LOD that is comparable to reported clinical viral shedding concentrations in oral fluid, thus emphasizing the translatability of the protocol to detecting SARS-CoV-2 in patient samples. cache = ./cache/cord-346978-ubkqny8j.txt txt = ./txt/cord-346978-ubkqny8j.txt === reduce.pl bib === id = cord-347428-2isuaiyx author = Schulz-Stübner, Sebastian title = Hygiene in der Anästhesie in Zeiten der SARS-CoV-2-Pandemie date = 2020-07-31 pages = extension = .txt mime = text/plain words = 1435 sentences = 177 flesch = 50 summary = Im Verlauf kann es bei etwa 20 % der Patienten zu einer klinischen Verschlechterung kommen, mit Entwicklung von Dyspnoe und/oder Hypoxämien, typischerweise ca. In einer systematischen Übersicht aus dem Jahr 2016 wurde gezeigt, dass N95-Atemschutzmasken (entspricht FFP2) zwar im Laborversuch einen größeren Schutz gegen die Erreger akuter Atemwegsinfektionen einschließlich pandemischer Influenza zu bieten scheinen als chirurgische Masken, dass sich mittels Metaanalyse aber kein höherer Schutzeffekt für medizinisches Personal bei klinischer Anwendung nachweisen lässt [8] . Sie berichtet retrospektiv, in einer Gondelbahn neben einer Person mit Symptomen einer viralen Atemwegsinfektion gesessen zu haben, sie entwickelt 4 Tage nach Arbeitsbeginn selbst Symptome und wird positiv auf SARS-CoV-2 getestet. Effectiveness of N95 respirators versus surgical masks in protecting health care workers from acute respiratory infection: a systematic review and meta-analysis Medical masks vs N95 respirators for preventing COVID-19 in healthcare workers: A systematic review and meta-analysis of randomized trials. cache = ./cache/cord-347428-2isuaiyx.txt txt = ./txt/cord-347428-2isuaiyx.txt === reduce.pl bib === id = cord-347225-gh51ag2x author = Fu, Weihui title = A clinical pilot study on the safety and efficacy of aerosol inhalation treatment of IFN-κ plus TFF2 in patients with moderate COVID-19 date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4921 sentences = 233 flesch = 46 summary = INTERPRETATION: Aerosol inhalation of IFN-κ plus TFF2 is a safe treatment and is likely to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby achieves an early release from hospitalization. Therefore, to evaluate the efficacy and safety of intranasal inhalation of TFF2 and IFN-k protein for SARS-CoV-2 infection, we conducted an open-label, nonrandomized, clinical trial in adult patients hospitalized with moderate COVID-19 disease in China. In this trial, any AE from the beginning of aerosol inhalation to 5 days after the end of the last aerosol inhalation were taken as an adverse event during treatment (TEAE); The secondary objective of the pilot study was to evaluate the clinical efficacy of IFN-k plus TFF2 as compared to the control group as assessed by days of hospitalization staying, CT imaging improvement and cough relief time and negative reversion of viral RNA after 10 days of treatment. cache = ./cache/cord-347225-gh51ag2x.txt txt = ./txt/cord-347225-gh51ag2x.txt === reduce.pl bib === id = cord-346987-fbqqf00i author = Guo, Yongwen title = Controls of SARS-CoV-2 transmission in orthodontic practice date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4660 sentences = 244 flesch = 47 summary = ABSTRACT The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted worldwide concerns because of its high person-to-person infectivity and lethality, and it was labeled as a pandemic as the rapid increase of confirmed cases in most areas around the world became evident. Although the spread of COVID-19 has been effectively controlled in China and many areas have gradually resumed work and classes, orthodontic participants are still under high risks of SARS-CoV-2 infection. What's more, the close contact between dental staffs and patients as well as the droplets and aerosols generated during treatment containing saliva and blood further increase the risk of SARS-CoV-2 transmission in dental practice 5 . We must constantly bear in mind that the threat of infection is not visible which poses a challenge on the orthodontic practice thus effective control measures should be taken to prevent the transmission of SARS-CoV-2 and protect both practitioners and patients from the COVID-19. cache = ./cache/cord-346987-fbqqf00i.txt txt = ./txt/cord-346987-fbqqf00i.txt === reduce.pl bib === id = cord-347374-mryazbnq author = Okba, Nisreen M.A. title = Severe Acute Respiratory Syndrome Coronavirus 2−Specific Antibody Responses in Coronavirus Disease Patients date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3565 sentences = 186 flesch = 51 summary = Using serum samples from patients with PCR-confirmed SARS-CoV-2 infections, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrated that most PCR-confirmed SARS-CoV-2–infected persons seroconverted by 2 weeks after disease onset. Using a well-characterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house, as well as a commercial platform. We evaluated SARS-CoV-2-specific antibody responses in severe and mild cases by using serum samples collected at different times postonset of disease from 3 PCR-confirmed COVID-19 patients from France. We tested serum samples for SARS-CoV-2specific antibodies by using different ELISAs. After infection, all 3 patients seroconverted between days 13 and 21 after onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S, S1 subunit, and RBD, but only 2/3 patients had detectable antibodies to the N-terminal (S1 A ) domain. cache = ./cache/cord-347374-mryazbnq.txt txt = ./txt/cord-347374-mryazbnq.txt === reduce.pl bib === id = cord-347128-6lyoz8nn author = Kim, Cheorl-Ho title = SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date = 2020-06-26 pages = extension = .txt mime = text/plain words = 15413 sentences = 988 flesch = 53 summary = O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. In RNA viruses, the S glycoprotein (PDB: 6VSB) is the biggest protein, heavily glycosylated and its N-terminal domain (NTD) sequence binds to the host receptor to enter the ER of host cells. However, MERS-CoV does not have a similar enzyme and thus MER-CoV binding to SA receptors is mediated by energetically reversible interactions of the lipid rafts with increased SA receptors [75] , thus enhancing dipeptidyl peptidase 4 (DPP4) or carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) recognition power and viral entry [76] and membrane-associated 78-kDa glucose-regulated protein (GRP78) [77] . Entry of host cells needs binding of S glycoproteins to the CEACAM receptor, forming S-protein-mediated membrane fusion. For example, impairment of ACE2 receptor glycosylation does not influence S-glycoprotein-ACE2 interaction, however, SARS-CoV-2 virus entry into respiratory epithelial host cells was downregulated [133] . cache = ./cache/cord-347128-6lyoz8nn.txt txt = ./txt/cord-347128-6lyoz8nn.txt === reduce.pl bib === id = cord-347221-g98q9cga author = Piyush, Ravikant title = Nucleic acid-based therapy for coronavirus disease 2019 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 4217 sentences = 246 flesch = 50 summary = This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen. cache = ./cache/cord-347221-g98q9cga.txt txt = ./txt/cord-347221-g98q9cga.txt === reduce.pl bib === id = cord-347458-za7cot2n author = Ruan, Qiurong title = Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China date = 2020-03-03 pages = extension = .txt mime = text/plain words = 915 sentences = 53 flesch = 59 summary = title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China Using the database of Jin Yin-tan Hospital and Tongji Hospital, we conducted a retrospective multicenter study of 68 death cases (68/150, 45%) and 82 discharged cases (82/150, 55%) with laboratory-confirmed infection of SARS-CoV-2. Patients met the discharge criteria if they had no fever for at least 3 days, significantly improved respiratory function, and had negative SARS-CoV-2 laboratory test results twice in succession. It should be noted that patients with cardiovascular diseases have a significantly increased risk of death when they are infected with SARS-CoV-2 (p < 0.001). Based on the analysis of the clinical data, we confirmed that some patients died of fulminant myocarditis. KY, WXW, LYJ and JXS contributed to the analysis and interpretation of the data. cache = ./cache/cord-347458-za7cot2n.txt txt = ./txt/cord-347458-za7cot2n.txt === reduce.pl bib === id = cord-346894-iy35298o author = Miranda-Schaeubinger, Monica title = A primer for pediatric radiologists on infection control in an era of COVID-19 date = 2020-07-07 pages = extension = .txt mime = text/plain words = 7262 sentences = 372 flesch = 42 summary = In pediatric radiology departments, the risk involved ranges from low (e.g., office workers, remote workers, telemedicine) to very high (e.g., workers performing aerosol-generating procedures on known or suspected COVID-19 patients), depending on the job task assigned [28, 29] . Standard precautions to minimize the spread of infection within health care facilities from direct contact with contaminations include hand hygiene, use of PPE based on anticipated contact with contaminated material, respiratory hygiene/ cough etiquette, cleaning and disinfection of the environment, and proper handling of patient care equipment and waste [10] . Appropriate personal protective equipment usage stratified by COVID-19 status (Table 3) Because of the possibility of airborne transmission of the virus, the CDC recommends respirators for care of all patients with COVID-19 if adequate supplies are available. For all aerosol-generating procedures in children who have either unknown or confirmed positive COVID-19 status, radiologists should adhere to the highest level of respiratory protection available: a respirator, an eye shield, a disposable gown and gloves. cache = ./cache/cord-346894-iy35298o.txt txt = ./txt/cord-346894-iy35298o.txt === reduce.pl bib === id = cord-347460-9vechh4x author = Chang, Feng-Yee title = Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date = 2020-06-04 pages = extension = .txt mime = text/plain words = 8050 sentences = 384 flesch = 43 summary = Three components are crucial for SARS-CoV induced diseases: 1) the role of CD8+ T cells in defense against the virus, which causes apoptosis in the infected cells, 2) interactions of the virus with macrophages and dendritic cells, which initiate the early innate and subsequent adaptive immune responses, and 3) type I interferon (IFN) system, an innate response against viral infections, which can inhibit virus replication in the early phase. Existing information suggests that the SARS-CoV-infected airways and alveolar epithelial cells secrete abundant chemokines to attract immune cell infiltrations to the lungs, including macrophages and neutrophils, thereby causing damage due to high levels of proinflammatory cytokines and other mediators secreted by these cell types. After a decade of research on coronavirus, unfortunately, still there are no licensed vaccines, effective specific antivirals, nor drug combinations supported by high-level evidence to treat the infection, especially for newly emerging strains such as SARS-COV-2 [59] . cache = ./cache/cord-347460-9vechh4x.txt txt = ./txt/cord-347460-9vechh4x.txt === reduce.pl bib === id = cord-347262-q88g1561 author = Schutzer‐Weissmann, J. title = Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date = 2020-07-11 pages = extension = .txt mime = text/plain words = 4753 sentences = 279 flesch = 39 summary = Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review cache = ./cache/cord-347262-q88g1561.txt txt = ./txt/cord-347262-q88g1561.txt === reduce.pl bib === id = cord-347462-yz67t10x author = Chan, Tak Yeung title = A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date = 2004-07-19 pages = extension = .txt mime = text/plain words = 3590 sentences = 214 flesch = 54 summary = title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). A retrospective study was undertaken in the department of medicine and geriatrics of the hospital to evaluate the clinical course of young and elderly SARS patients. Single or paired serum samples were tested for SARS-CoV antibody in 96% (50/52) of young and 76% (19/25) of older patients. Because the proportion of patients with positive RT-PCR in stool samples was similar in two groups, fewer older patients with diarrhea probably represents a generalized paucity of symptoms rather than a different site of involvement by SARS-CoV. In the current study, similar proportions of young and older patients with SARS had RT-PCR performed, and comparable positivity rates were achieved. cache = ./cache/cord-347462-yz67t10x.txt txt = ./txt/cord-347462-yz67t10x.txt === reduce.pl bib === id = cord-347484-7vn93t58 author = Zamoto, Aya title = Identification of Ferret ACE2 and its Receptor Function for Sars-Coronavirus date = 2006 pages = extension = .txt mime = text/plain words = 773 sentences = 50 flesch = 61 summary = Severe acute respiratory syndrome associated coronavirus (SARS-CoV) was the causative agent of SARS, which occurred as an emerging pneumonic disease in 2002. Amplification of partial ACE2 gene by RT-PCR: RNAs were extracted from heart, lung, kidney, and small intestine of a ferret. Determination of nucleotide sequence of ferret ACE2 (feACE2): Two overlapping regions of feACE2 genes were amplified by RT-PCR from kidney RNA. The partial feACE2 gene was amplified from RNAs isolated from the lung, heart, kidney, and small intestine by RT-PCR. HeLa cells expressing feACE2 supported SARS-CoV replication to the same extent as those expressing human ACE2 (Fig. 3) . From these observations, it is postulated that animal species whose ACE2 functions as an efficient SARS-CoV receptor would be a susceptible in feACE2 expressing HeLa cells was over 10 times more efficient than that in mouse efficiently. Furthermore, transgenic mouse expressing ferret or human ACE2 may serve a useful animal model for SARS-CoV infection. cache = ./cache/cord-347484-7vn93t58.txt txt = ./txt/cord-347484-7vn93t58.txt === reduce.pl bib === id = cord-347289-3yi5tz04 author = Poon, L. . C. title = ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update date = 2020-06-01 pages = extension = .txt mime = text/plain words = 8036 sentences = 413 flesch = 42 summary = American College of Obstetricians and Gynecologists (ACOG): https://www.acog.org/clinical-information/phys ician-faqs/covid-19-faqs-for-ob-gyns-obstetrics Centers for Disease Control , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health emergency. A case series of 12 pregnant women with SARS-CoV in Hong Kong, China, reported three maternal deaths, that four of seven patients who presented in the first trimester had spontaneous miscarriage, four of five patients who presented after 24 weeks had preterm birth and two mothers recovered without delivery but their ongoing pregnancies were complicated by FGR 8 . In two studies, with a combined total of 10 pregnant women with COVID-19 in the third trimester, amniotic fluid, cord blood and neonatal throat swab samples tested negative for SARS-CoV-2, suggesting there was no evidence of vertical transmission in women who developed COVID-19 pneumonia in late pregnancy 26, 76 . An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes cache = ./cache/cord-347289-3yi5tz04.txt txt = ./txt/cord-347289-3yi5tz04.txt === reduce.pl bib === id = cord-347263-ci6mv72z author = Berekashvili, k. title = Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2971 sentences = 223 flesch = 56 summary = Methods: Over the last 6 weeks, data from four centers in New York City were collected to review the possible ischemic stroke types seen in COVID-19 positive patients. We also wanted to better describe the different ischemic stroke subtypes seen in patients with SARS-COV2 infection especially with the view to assess its unique features seen in the context of COVID-19. Two patients who presented with LVO had no prior complaints of viral illness but went on to develop a severe course of the disease. Only three patients had a severe course of the pulmonary disease prior to the neurological event requiring them to be hospitalized. The LVO cases were typically younger, had a worse neurological presentation, more severe form of viral disease and higher levels of hypercoagulability markers than the non-LVO patients. Ischemic stroke can be a presenting symptom of COVID-19 and may not always be associated with severe disease markers including in the young, minorities and healthcare workers. cache = ./cache/cord-347263-ci6mv72z.txt txt = ./txt/cord-347263-ci6mv72z.txt === reduce.pl bib === id = cord-347208-leo0x10l author = Zhou, Y. title = Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study date = 2020-06-10 pages = extension = .txt mime = text/plain words = 3429 sentences = 217 flesch = 55 summary = title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study . https://doi.org/10.1101/2020.06.09.20076646 doi: medRxiv preprint 9 time from illness onset to arbidol or interferon treatment, elevated C-reactive protein (CRP), elevated interleukin-4 (IL-4) and interleukin-6 (IL-6), elevated D-dimer and more lobes lesion in lung CT images were significantly associated with the prolonged viral shedding of COVID-19. The results of univariable regression analysis demonstrated that age older than 65 years, illness onset before January 31, the time from illness onset to first medical visitation, hypertension, arbidol combination with interferon, lobe lesions in lung computed tomography (CT) images, and the time from illness onset to arbidol or interferon initiation were significantly associated with the duration of SARS-CoV-2 RNA shedding by univariable regression analysis. cache = ./cache/cord-347208-leo0x10l.txt txt = ./txt/cord-347208-leo0x10l.txt === reduce.pl bib === id = cord-347706-r0rs3ls1 author = Roberts, Anjeanette title = Animal Models for Sars date = 2006 pages = extension = .txt mime = text/plain words = 3013 sentences = 139 flesch = 43 summary = Mice that recover from infection develop a neutralizing antibody response and are protected from subsequent challenge; antibody alone is sufficient to protect mice from replication of SARS-CoV in the lower respiratory tract and NK, NK-T, T, and B cells are not required for viral clearance. 13, 13b CoV disease, with weight loss and pneumonitis that begins with acute bronchiolitis and In summary, SARS-CoV replicates efficiently in the respiratory tract of young viremia occurs 1 to 2 days following infection and virus is detected in the liver and spleen in hamsters. As seen with the other animal models, the course of infection in experimentally infected nonhuman primates is short, with a rapid peak in viral replication and clearance of virus from the lungs by days 4 to 7 in different species. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice cache = ./cache/cord-347706-r0rs3ls1.txt txt = ./txt/cord-347706-r0rs3ls1.txt === reduce.pl bib === id = cord-347516-linjv64o author = Abdelaziz, Osama S. title = Neuropathogenic human coronaviruses: A review date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2338 sentences = 144 flesch = 39 summary = authors: Abdelaziz, Osama S.; Waffa, Zuraiha However, there are reports of neurological findings in HCoV infections, particularly in patients infected with the novel severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) amid Coronavirus disease 2019 (COVID‐19) pandemic. 26, 29 Reports of neuromusculoskeletal disorders, complicating HCoV infections and COVID-19, postulate that myopathies and neuropathies are a result of the significantly elevated inflammatory cytokines in patients' sera leading to virus-induced immune damage. 20, 24, 32, 33 This primary neurotropism could be further supported by the recent reports of the occurrence of olfactory and/or taste disorders, as early atypical manifestations of SARS-CoV-2, which may precede the onset of full-blown clinical COVID-19 in more than onethird of patients. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome cache = ./cache/cord-347516-linjv64o.txt txt = ./txt/cord-347516-linjv64o.txt === reduce.pl bib === id = cord-347308-l19snjyf author = García-Howard, Marcos title = Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3095 sentences = 170 flesch = 47 summary = Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. Additionally, during hospitalization, the patient and her mother were included in a collaborative study of genomic medicine for identifying genetic variants causing hyperimmunity due to SARS-CoV-2 infection. cache = ./cache/cord-347308-l19snjyf.txt txt = ./txt/cord-347308-l19snjyf.txt === reduce.pl bib === id = cord-347553-d7q6u7vj author = Criado, Paulo Ricardo title = Lessons from dermatology about inflammatory responses in Covid‐19 date = 2020-07-12 pages = extension = .txt mime = text/plain words = 5067 sentences = 326 flesch = 40 summary = The antithrombotic effect of chloroquine analogues has been attributed to a range of mechanisms, including reduction in red blood cell aggregation, inhibition of platelet aggregation and adhesion, reduction in blood viscosity and enhancement of antiplatelet activity 86 Hydroxychloroquine and chloroquine were indicated for treat patients with COVID-19, under in vitro effects due to capacity as 87 : (a) an inhibitor of endocytic pathways through an elevation of endosomal pH, and (b) these drugs shown to interfere with the terminal glycosylation of angiotensin-converting enzyme-2 (ACE2), which acts as a plasma membrane receptor for both SARS-CoV and SARS-CoV-2. 61 99 Procoagulant factors, such F I G U R E 5 Clinical outcomes in SARS-CoV-2 infected patients/Covid-19, immune system responses, systemic and possible cutaneous manifestations.① The outcome spectrum is probably related to intrinsic host factors. ③ In a selected group of patients, with moderate and severe Covid-19, some authors proposed that a genetic background in these subjects might determinate one new immune response as ④ 'second wave' of cytokines production, the 'CSS' in response to the SARS-CoV-2 infection, similar to Macrophage Activation Syndrome (MAS-like/sHLH). cache = ./cache/cord-347553-d7q6u7vj.txt txt = ./txt/cord-347553-d7q6u7vj.txt === reduce.pl bib === id = cord-347366-0gier0lu author = Gurwitz, David title = Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1917 sentences = 105 flesch = 45 summary = A tentative suggestion based on existing therapeutics, which would likely be resistant to new coronavirus mutations, is to use available angiotensin receptor 1 (AT1R) blockers, such as losartan, as therapeutics for reducing the aggressiveness and mortality from SARS‐CoV‐2 virus infections. These tentative suggestions were based on the observation that SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor binding domain for its spike protein (Lu et al., 2020; Wan, Shang, Graham, Baric, & Li, 2020) , similarly to the coronavirus strain implicated in the 2002-2003 SARS epidemic (Dimitrov, 2003; Ge et al., 2013; Li et al., 2003; Prabakaran et al 2004; Turner, Hiscox, & Hooper, 2004) . The tentative suggestion to apply AT1R antagonists such as losartan and telmisartan as SARS-CoV-2 therapeutics for treating patients prior to the development of acute respiratory syndrome remains unproven until tried. cache = ./cache/cord-347366-0gier0lu.txt txt = ./txt/cord-347366-0gier0lu.txt === reduce.pl bib === id = cord-347356-uc9dqhyq author = Cooper, TJ title = Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3949 sentences = 228 flesch = 54 summary = OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The aim of this systematic review was to identify studies that discuss PLHIV who have been infected with SARS-CoV-2 and that report whether coinfection results in a greater risk of adverse outcomes and, furthermore, whether controlled HIV infection vs. A comprehensive literature search was carried out in Global Health, SCOPUS, Medline and EMBASE to identify articles that discussed HIV-positive patients and the clinical implications of HIV infection in COVID-19 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines [13] . [21] , also highlighted a case study of a HIV patient with SARS-CoV2 co-infection, diagnosis of viral pneumonia was made on clinical examination and chest CT findings. cache = ./cache/cord-347356-uc9dqhyq.txt txt = ./txt/cord-347356-uc9dqhyq.txt === reduce.pl bib === id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3707 sentences = 191 flesch = 44 summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach cache = ./cache/cord-347714-vxxhglx7.txt txt = ./txt/cord-347714-vxxhglx7.txt === reduce.pl bib === id = cord-347613-tjeo62dv author = da Silva, Priscilla Gomes title = Corrigendum to “Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2”[Sci. Total Environ. 750 (2021) 141483] date = 2020-09-10 pages = extension = .txt mime = text/plain words = 445 sentences = 36 flesch = 71 summary = In this study, HeLa cells that expressed or did not express ACE2 proteins from humans, Chinese horseshoe bats, civets, pigs and mice were used, and it was found that SARS-CoV-2 is able to use all ACE2 proteins (except for mouse ACE2) as an entry receptor to enter ACE2-expressing cells, but it could not enter cells that did not express ACE2, indicating that ACE2 is probably the cell receptor through which SARS-CoV-2 enters cells (Zhou et al., 2020) . This and other bat-coronaviruses share 88-92% nucleotide sequence homology with SARS-CoV-1 (Ye et al., 2020) , leading scientists to believe that SARS-CoV was transmitted directly to humans from wet market civets, with bats as the main reservoir hosts (Cui et al., 2019; Hu et al., 2017) ". Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus cache = ./cache/cord-347613-tjeo62dv.txt txt = ./txt/cord-347613-tjeo62dv.txt === reduce.pl bib === id = cord-347499-7q47jh14 author = Burrel, Sonia title = Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date = 2020-10-25 pages = extension = .txt mime = text/plain words = 1353 sentences = 75 flesch = 51 summary = METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. In line with previous studies, different types of other respiratory viruses were detected together with SARS-CoV-2 among co-infected patients, including non-SARS-CoV-2 coronavirus, influenzavirus, adenovirus, rhinovirus/enterovirus, and parainfluenzavirus (Kim et al., 2020; Leuzinger et al., 2020; Lin et al., 2020a; Wee et al., 2020) . We evidenced the higher efficiency of LRT than URT samples for COVID-19 diagnosis, with a significantly higher rate of detection of SARS-CoV-2 and a 1 log-higher SARS-CoV-2 load for the majority of infected patients. In conclusion, the detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection, and LRT samples increases the accuracy of diagnosis of viral respiratory infections, including COVID-19. cache = ./cache/cord-347499-7q47jh14.txt txt = ./txt/cord-347499-7q47jh14.txt === reduce.pl bib === id = cord-347731-eqxn6auk author = Garcia‐Cremades, Maria title = Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date = 2020-05-12 pages = extension = .txt mime = text/plain words = 5430 sentences = 333 flesch = 50 summary = The data sources included were (i) longitudinal clinical, pharmacokinetic (PK), and virologic data from patients with severe acute respiratory syndrome‐2 (SARS‐CoV‐2) infection who received HCQ with or without azithromycin (n = 116), (ii) in vitro viral replication data and SARS‐CoV‐2 viral load inhibition by HCQ, (iii) a population PK model of HCQ, and (iv) a model relating chloroquine PKs to corrected QT (QTc) prolongation. 12 The drug effect over time on viral replication rate was established by simulating unbound plasma concentrations or unbound lung tissue concentrations using a previously defined partition coefficient (10 2.45 ; HCQ unbound fraction assumed to be ~ 50%) and using the established in vitro sigmoidal efficacy parameters. 3, 9, 10 Viral kinetics were estimated from in vitro replication rate of severe acute respiratory syndrome-coronavirus (SARS-CoV)-1 and unbound drug concentration in plasma and lungs were simulated with HCQ PK model. cache = ./cache/cord-347731-eqxn6auk.txt txt = ./txt/cord-347731-eqxn6auk.txt === reduce.pl bib === id = cord-347767-aq9niccc author = Zhao, Jie title = Yidu-toxicity blocking lung decoction ameliorates inflammation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome by eliminating IL-6 and TNF-a date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3538 sentences = 198 flesch = 49 summary = The present study investigates the differences in inflammatory agents alterations, immune function, and leukocyte differential count evaluation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome after the recommended Chinese medicine prescription of Yidu-toxicity blocking lung decoction. A total of 40 patients with yidu-toxicity blocking lung syndrome, diagnosed as severe pneumonia of SARS-COV-2 following the latest Chinese national recommendations for the diagnosis and treatment of pneumonia caused by SARS-COV-2 (the 5th edition), were recruited. To characterize the effect of herbal medicine, immune function, and inflammatory agents, levels of white blood cells were detected for all patients according to the manufacturer's instructions at the beginning and at the end of the two weeks. In conclusion, our study suggests that the 5th edition recommendation's CM prescription, can be safely used in the treatment of severe pneumonia of SARS-COV-2 with yidu-toxicity blocking lung syndrome. cache = ./cache/cord-347767-aq9niccc.txt txt = ./txt/cord-347767-aq9niccc.txt === reduce.pl bib === id = cord-347548-h5fk64p8 author = Zarza, José title = Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1843 sentences = 122 flesch = 51 summary = title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection Coronavirus disease 2019 (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which has sparked growing interest and concern in the international community. 1 We present a case of COVID-19 associated with Evans syndrome (hemolytic anemia plus thrombocytopenia, both with autoimmune causes) and antiphospholipid antibodies. With these findings, her diagnoses upon admission were SARS-COV-2 infection, SLE with associated antiphospholipid antibodies, and Evans syndrome. We present the case of a young patient who was apparently in good health but had a history of venous thrombosis of unknown cause in her childhood, which started with Evans syndrome and a high titer of antiphospholipid antibodies, in coincidence with a SARS-COV-2 infection. 4 Although the decreased platelet count is usually mild in COVID-19, some cases of severe thrombocytopenia have been reported in the context of disseminated intravascular coagulation in these patients. cache = ./cache/cord-347548-h5fk64p8.txt txt = ./txt/cord-347548-h5fk64p8.txt === reduce.pl bib === id = cord-347472-n6811ens author = Rosebrock, Adam P. title = Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date = 2020-05-15 pages = extension = .txt mime = text/plain words = 6252 sentences = 344 flesch = 51 summary = The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. cache = ./cache/cord-347472-n6811ens.txt txt = ./txt/cord-347472-n6811ens.txt === reduce.pl bib === id = cord-347813-9vfwl7c0 author = Jackson, M. L. title = Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2 date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3783 sentences = 224 flesch = 47 summary = Interventions considered were (a) encouraging telecommuting; (b) reducing contacts to seniors and nursing home residents; (c) modest reductions to contacts outside of the home; (d) encouraging self-isolation of persons with COVID-19 symptoms; (e) rapid testing and household quarantining. This report presents findings from an agent-based model of SARS-CoV-2 transmission that can help guide decisions about mitigating the impact of COVID-19 during this re-opening. 6 The per-contact probability of transmitting SARS-CoV-2 in homes and in non-home settings was estimated by fitting simulated daily COVID-19 hospitalizations to hospitalizations in King County from 28 February -27 May 2020, in the presence of social distancing interventions as actually implemented in King County. Rather than estimating the impact of generic reductions in Reff, this report uses an agent-based model to estimate the impact of specific policies on SARS-CoV-2 transmission and COVID-19 hospitalizations. 15 used also agent-based models to explore the impact of combinations of social distancing measures on SARS-CoV-2 transmission. cache = ./cache/cord-347813-9vfwl7c0.txt txt = ./txt/cord-347813-9vfwl7c0.txt === reduce.pl bib === id = cord-348071-0zlzblwi author = Tseng, Jen-Yu title = Potential implications of SARS-CoV-2 on pregnancy date = 2020-05-13 pages = extension = .txt mime = text/plain words = 509 sentences = 33 flesch = 62 summary = The Wuhan Coronavirus (recently named SARS-CoV-2) has been making headline news around the world as there are over 60,000 confirmed cases and a total of over 1300 deaths in China alone since the start of the outbreak [1]. In a review of previous coronavirus infections in pregnancy, there were 13 cases of SARS-CoV and 11 cases of MERS-CoV reported in the literature [3, 4] . Maternal outcome of the 13 cases: 4 cases had miscarriage, 2 opted for termination of pregnancy, 2 succumbed to SARS, 2 required mechanical ventilation, and 3 were treated conservatively. Maternal outcome of the 11 MERS-CoV cases: 2 were asymptomatic, 3 succumbed to MERS, 2 required mechanical ventilation, 3 were treated conservatively, and 1 refused treatment. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature cache = ./cache/cord-348071-0zlzblwi.txt txt = ./txt/cord-348071-0zlzblwi.txt === reduce.pl bib === id = cord-348192-ibohbjfb author = Odih, Erkison E. title = Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks? date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2676 sentences = 163 flesch = 49 summary = Endemic and epidemic transmission of multiple feco-oral pathogens via this route continues to be documented in areas without safely managed sanitation, and, therefore, the risk of SARS-CoV-2 transmission needs to be evaluated, tracked, and forestalled in such settings. Furthermore, environmental surveillance of SARS-CoV-2 in wastewater and accumulated human waste, as well as efforts to mitigate the virus' entry into unprotected household water sources, should be a priority part of the COVID-19 response in settings without safely managed sanitation for the duration of the pandemic. 3, 5, 6 Considerable concern has been expressed in the literature that the feco-oral transmission potential for SARS-CoV-2 places endoscopists, caregivers of diapered children who shed the virus, 7 and fecal transplant recipients 8 at high risk of contracting the infection. 20, 21 Although there are as yet no reports of transmission of SARS-CoV-2 via sewage or fecal matter in settings without safely managed sanitation, or recovery from household water, these examples demonstrate that feco-oral transmission by endemic pathogenic organisms is commonplace in these settings. cache = ./cache/cord-348192-ibohbjfb.txt txt = ./txt/cord-348192-ibohbjfb.txt === reduce.pl bib === id = cord-347734-0z2kin6r author = Armann, J. P. title = Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates date = 2020-07-17 pages = extension = .txt mime = text/plain words = 2294 sentences = 138 flesch = 51 summary = title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates However, there is reason to believe that children play a less significant role in SARS-CoV-2 transmission compared to influenza, making control measures focused on this age group less effective: Most countries-including Germany-report a much lower proportion of cases in children compared to their population size 4-6 . The findings from this unique study in older students and their teachers indicate that the prevalence of IgG antibodies against SARS-CoV-2 remains extremely low after the first wave of the corona pandemic in Germany. In fact, 5 of the 12 participants with antibodies against SARS-CoV-2 had a personal or household history of COVID-19, yielding a ratio of unidentified to identified cases of 2.4, which is much smaller than that previously assumed by some authors 9 . cache = ./cache/cord-347734-0z2kin6r.txt txt = ./txt/cord-347734-0z2kin6r.txt === reduce.pl bib === id = cord-348384-8cvt1fo6 author = Butsashvili, M. title = Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1988 sentences = 120 flesch = 54 summary = This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus among Georgian population, including health care workers (HCWs). 20% of HCWs as well as other study subjects believe that SARS-COV-2 vaccine and medications do exist but are simply not available in Georgia. This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus and perceptions of preventive measures among the Georgian population, including health care workers (HCWs). We collected information on demographic data (age, gender, marital status, education, employment status), knowledge of symptoms and transmission modes of coronavirus, perceived differences between coronavirus and influenza, availability of antiviral medication and vaccination. In response to the question "Are you afraid of getting infected with SARS-COV-2?" almost half of study participants (46.3%) said "no." The majority of survey respondents correctly identified the transmission route and symptoms of the new coronavirus (96.9% and 98.0%, respectively). cache = ./cache/cord-348384-8cvt1fo6.txt txt = ./txt/cord-348384-8cvt1fo6.txt === reduce.pl bib === id = cord-348283-7xorq5ce author = Naz, Anam title = Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date = 2020-07-10 pages = extension = .txt mime = text/plain words = 8183 sentences = 482 flesch = 56 summary = The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. cache = ./cache/cord-348283-7xorq5ce.txt txt = ./txt/cord-348283-7xorq5ce.txt === reduce.pl bib === id = cord-348392-e35cd9sg author = Moraleda, Cinta title = Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date = 2020-07-25 pages = extension = .txt mime = text/plain words = 1759 sentences = 165 flesch = 66 summary = Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. cache = ./cache/cord-348392-e35cd9sg.txt txt = ./txt/cord-348392-e35cd9sg.txt === reduce.pl bib === id = cord-348178-6bjimde4 author = Li, Ling title = Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date = 2005-09-15 pages = extension = .txt mime = text/plain words = 3684 sentences = 205 flesch = 52 summary = title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) cache = ./cache/cord-348178-6bjimde4.txt txt = ./txt/cord-348178-6bjimde4.txt === reduce.pl bib === id = cord-347804-kxhasabe author = Luo, Ruibang title = Tracking cytosine depletion in SARS-CoV-2 date = 2020-10-26 pages = extension = .txt mime = text/plain words = 1084 sentences = 69 flesch = 63 summary = Results We built a website to track the composition change of mono-, di-, and tri-nucleotide of SARS-CoV-2 over time. Using 137,315 SARS-CoV-2 strains collected in ten months, we observed cytosine depletion at a rate of about one cytosine loss per month from the whole genome. We built an interactive website at http://www.bio8.cs.hku.hk/sarscov2 to show the mono-, di-, and tri-nucleotide composition trends of the whole genome and single genes. In Table 1 , we first compared the composition of nucleotides in multiple coronaviruses, including SARS-CoV-2 (an average of 76 strands collected from Dec 20, 2019 to Feb 15, 2020), SARS, MERS, and four that causes a common cold. Compared to SARS-CoV-2, which we assumed a relative mortality level of 3, the percentage of cytosine is lower in almost all of the eleven genes in the four common cold coronaviruses with a lower mortality level 1. The results are available on an interactive website at http://www.bio8.cs.hku.hk/sarscov2. cache = ./cache/cord-347804-kxhasabe.txt txt = ./txt/cord-347804-kxhasabe.txt === reduce.pl bib === id = cord-348342-iqq8kmn0 author = Uyoga, S. title = Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors date = 2020-07-29 pages = extension = .txt mime = text/plain words = 3103 sentences = 198 flesch = 58 summary = Methods We measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance. Based on these data, we defined anti-SARS-CoV-2 IgG seropositivity as an OD ratio >2 and selected the spike ELISA for this study; the sensitivity and specificity of this threshold was 83% (95% CI: 59-96%) and 99.0% (95% CI 98.1-99.5%), respectively (Table 1, Figure S3 panels A & B). The Bayesian population-weighted and test-adjusted seroprevalence for Kenya was 5.2% (95% CI 3.7-7.1%, Table 3 ) and the posterior sensitivity and specificity estimates were 82.5% (95% CI 69.6-91.2%) and 99.2 (95% CI 98.7-99.6%), respectively. In this anti-SARS-CoV-2 IgG seroprevalence study of blood donors in Kenya, the crude prevalence was 5.6% and the population-weighted test-adjusted seroprevalence was 5.2%. cache = ./cache/cord-348342-iqq8kmn0.txt txt = ./txt/cord-348342-iqq8kmn0.txt === reduce.pl bib === id = cord-348360-20eq5meh author = Esposito, Dominic title = Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date = 2020-06-04 pages = extension = .txt mime = text/plain words = 3438 sentences = 158 flesch = 49 summary = To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Thus, the work presented here is intended to provide a robust method for those wishing to reliably produce SARS CoV-2 spike protein in quantities sufficient for serology assays, structural biology, or simply to better understand some of the production variables affecting the yield. Nevertheless, the approaches outlined here allowed us to improve the production yield of spike protein significantly by modifying cell culture temperature and harvest time, as well as improving the purification process. To produce SARS-CoV-2 antigens for the development of serology assays, we initially followed standard procedures for secreted protein production: transfection using the manufacturer's protocols, expression at 37°C, harvest at three days post-transfection, tangential flow filtration of the culture supernatant, immobilized metal ion chromatography with linear gradient elution, and size exclusion chromatography. cache = ./cache/cord-348360-20eq5meh.txt txt = ./txt/cord-348360-20eq5meh.txt === reduce.pl bib === id = cord-348202-6we8e60b author = Drake, Daniel H. title = Echo in Pandemic: Front Line Perspective, Expanding Role of Ultrasound and Ethics of Resource Allocation date = 2020-04-10 pages = extension = .txt mime = text/plain words = 4115 sentences = 308 flesch = 40 summary = During a declared health care crisis, providers must be familiar with the ethical principles, organizational structure, practical application, and gravity of limited resource allocation. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Echocardiography has been most useful for 1) initial assessment of patients with respiratory complaints who are seen in the COVID-19 evaluation pathway but may have another etiology for their symptoms, 2) assessment of cardiac function in critical care patients, where SARS-CoV-2 associated cardiomyopathy is prevalent and 3) volume assessment of patients with acute respiratory distress syndrome (ARDS), where sparing unnecessary fluids is mandatory. Ethical Considerations for Decision Making Regarding Allocation of Mechanical Ventilators During a Severe Influenza Pandemic or Other Public Health Emergency cache = ./cache/cord-348202-6we8e60b.txt txt = ./txt/cord-348202-6we8e60b.txt === reduce.pl bib === id = cord-347965-zluu0i41 author = Essahib, Wafaa title = SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts date = 2020-09-21 pages = extension = .txt mime = text/plain words = 1684 sentences = 114 flesch = 58 summary = title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts PURPOSE: To visualize SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. RESULTS: SARS-CoV-2 host receptors ACE2 and CD147 are present on the membrane of trophectoderm, epiblast and hypoblast cells in human blastocysts. The aim of our study was to visualize SARS-CoV-2 receptors ACE2 and CD147 on human oocytes and blastocysts. In pre (5 days post fertilization (dpf5) and (dpf6))-and peri (dpf7)-implantation blastocysts, CD147 and ACE2 are present on the membrane of trophectoderm and hypoblast cells, which will both contribute to the embryonic part of the placenta (chorion). The presence of the receptors ACE2 and CD147, especially on the membrane, implicates that SARS-CoV-2 is theoretically able to bind and infect human oocytes and pre-and periimplantation embryos. Samples were washed in 2% BSA/PBS before Fig. 1 Immunofluorescent staining and confocal microscopy for SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. cache = ./cache/cord-347965-zluu0i41.txt txt = ./txt/cord-347965-zluu0i41.txt === reduce.pl bib === id = cord-347968-jhnr8k3j author = Herrera, David title = Is the oral cavity relevant in SARS-CoV-2 pandemic? date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3388 sentences = 140 flesch = 36 summary = CONCLUSIONS: Antiseptic mouth rinses, such as those containing cetylpyridinium chloride or povidone-iodine, may be able to decrease the severity of COVID-19 by reducing oral viral load in infected subjects and decreasing the risk of transmission by limiting viral load in droplets, generated in normal life, or in aerosols, produced during dental procedures. The information presented in this narrative review supports the use of antiseptic mouth rinses, both as a single preprocedural use and as daily use during a limited period of time, to impact the transmission and/or pathogenicity of SARS-CoV-2, since they have shown to reduce the oral viral load and, therefore, they may reduce the severity of the disease in an infected subject and may reduce the risk of transmission, by reducing the viral load in aerosols, expelled during dental procedures, or in droplets generated when breathing, talking, sneezing, coughing, etc. cache = ./cache/cord-347968-jhnr8k3j.txt txt = ./txt/cord-347968-jhnr8k3j.txt === reduce.pl bib === id = cord-348526-g3asp1ps author = Wang, Wenjun title = WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019 date = 2020-02-26 pages = extension = .txt mime = text/plain words = 2341 sentences = 149 flesch = 63 summary = We plotted daily data on the frequencies of keywords related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from WeChat, a Chinese social media. Using WeChat Index, we obtained daily data from Nov 17, 2019 to Feb 14, 2020 for the keywords related to the SARS-Cov-2 disease such as "SARS", "Feidian (Chinese abbreviation for severe acute respiratory syndrome)", "pneumonia", "fever", "cough", "shortness of breath", "dyspnea", "fatigue", "stuffy nose", "runny nose", "diarrhea", "coronavirus", "novel coronavirus", and "infection" (see the raw data in Appendix A). By exploring daily data from WeChat, a Chinese social media, we found that the frequencies of several keywords related to the SARS-Cov-2 disease behaved abnormally during a period ahead of the outbreak in China, 2019. Gathering and analyzing data from social media, Internet search queries, news wires and web sites represents a novel approach to early warning and detection of disease outbreaks and is a supplementary to traditional surveillance systems [6] . cache = ./cache/cord-348526-g3asp1ps.txt txt = ./txt/cord-348526-g3asp1ps.txt === reduce.pl bib === id = cord-348010-m3a3utvz author = Wolff, Michael title = On build‐up of epidemiologic models—Development of a SEI(3)RSD model for the spread of SARS‐CoV‐2 date = 2020-10-13 pages = extension = .txt mime = text/plain words = 13018 sentences = 991 flesch = 61 summary = (Adequate contacts, reproduction and contact numbers) (i) A contact is called adequate (also effective), if it leads to a transmission of the pathogen from an infectious person to another one, and, if the affected individual is susceptible, then an infection is provoked. In the case of concrete models one uses generally contact and replacement numbers, and , which reflect the current infection behaviour. (i) (Closed-population model) An assumed constant number of community members (see Remark 2.2) seems to be justified, if the infection spreads quickly, approximately within a year, and/or, if there is a balance between births, migration and non-disease-related deaths. (Using , there arise difficulties with the dot indicating the time derivation.) If the model is to be to take a latent period into account, the class of infected is divided into subclasses in the following way. cache = ./cache/cord-348010-m3a3utvz.txt txt = ./txt/cord-348010-m3a3utvz.txt === reduce.pl bib === id = cord-348748-rxyh58eu author = Gorospe, Luis title = COVID-19: Thoracic Diagnostic Interventional Procedures in Troubled Times() date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1272 sentences = 64 flesch = 49 summary = Some publications have addressed the clinical management of cancer patients in the current SARS-CoV-2 pandemic, but there are no specific guidelines for performing thoracic diagnostic interventional procedures in patients with tumors who are also infected with SARS-CoV-2. Because of this situation, most of the hospital's clinical activity (like many other centers throughout the country) was focused on the treatment of Covid-19 patients, and large numbers of medical personnel (including pulmonologists, medical oncologists and radiation therapists, thoracic surgeons, pathologists, and radiologists) had been recruited from different departments of the center for the care and management of these patients. 15 Recent articles have reminded us how important it is for radiology departments to be prepared for COVID-19 (from the indication of chest X-rays or CT to the protection of their staff), 16 but there are no specific guidelines for performing diagnostic thoracic interventional procedures in patients with tumor lesions who are also infected with SARS-CoV-2. cache = ./cache/cord-348748-rxyh58eu.txt txt = ./txt/cord-348748-rxyh58eu.txt === reduce.pl bib === id = cord-348301-bk80pps9 author = Wahl, Angela title = Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801 date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4279 sentences = 238 flesch = 47 summary = Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Human lung tissues of LoM were inoculated with SARS-CoV-2 and titers of replication competent virus determined 2, 6, and 14 days post-exposure (Fig. 1c , Extended Data Table 2 ). Collectively, our results indicate that LoM re ect the pathogenic effects in icted by SARS-CoV-2 on the human lung and demonstrate their utility as a single in vivo platform to evaluate and compare the replication and pathogenesis of past, present, and future pre-emergent, epidemic, and pandemic coronaviruses accelerating the development and testing of pre-exposure prophylaxis agents such as EIDD-2801. cache = ./cache/cord-348301-bk80pps9.txt txt = ./txt/cord-348301-bk80pps9.txt === reduce.pl bib === id = cord-348478-ho89o8mj author = Pawlotsky, Jean-Michel title = SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2100 sentences = 138 flesch = 48 summary = This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) cache = ./cache/cord-348478-ho89o8mj.txt txt = ./txt/cord-348478-ho89o8mj.txt === reduce.pl bib === id = cord-348723-sf073cmj author = Chen, Liang title = The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 date = 2020-03-30 pages = extension = .txt mime = text/plain words = 2015 sentences = 104 flesch = 51 summary = title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Angiotensin-converting enzyme 2 (ACE2), the key host cellular receptor of SARS-CoV-2, has been identified in multiple organs, but its cellular distribution in human heart is not illuminated clearly. This study performed the first state-of-art single cell atlas of adult human heart, and revealed that pericytes with high expression of ACE2 might act as the target cardiac cell of SARS-CoV-2. The finding of this study explains the high rate of severe cases among COVID-19 patients with basic cardiovascular disease; and these results also perhaps provide important reference to clinical treatment of cardiac injury among severe patients infected by SARS-CoV-2. In the present study, we investigated ACE2 expression in the adult human hearts from healthy and diseased individuals, to illuminate the potential capacity of heart infection by SARS-CoV-2. This result suggested that pericyte was a potential SARS-CoV-2 virus targeted host cell type in the human heart. cache = ./cache/cord-348723-sf073cmj.txt txt = ./txt/cord-348723-sf073cmj.txt === reduce.pl bib === id = cord-348209-rkkhv4mw author = Noerz, Dominik title = Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date = 2020-04-11 pages = extension = .txt mime = text/plain words = 1643 sentences = 125 flesch = 61 summary = title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 30 system, a fully automated device performing extraction and real-time PCR. Due to its random-access workflow concept and rapid time-to-39 result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 40 diagnostics for urgent clinical samples in the hospital setting. For the assay presented in this study, we used a fully automated random-access platform for molecular 56 diagnostics, handling everything from extraction, amplification, signal detection to reporting of results 57 (10). Evaluation of a quantitative RT-PCR assay for 180 the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system cache = ./cache/cord-348209-rkkhv4mw.txt txt = ./txt/cord-348209-rkkhv4mw.txt === reduce.pl bib === id = cord-348752-bbghqy1a author = Li, Yuguo title = Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4052 sentences = 252 flesch = 60 summary = We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions. Methods: We collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Results: Three families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Year's Eve (January 24, 2020) at three neighboring tables. healthy) of each person at non-A tables as the dependent variable and applied a binary logistic regression model to investigate the association between the measured concentrations of trace gas and infection probability. cache = ./cache/cord-348752-bbghqy1a.txt txt = ./txt/cord-348752-bbghqy1a.txt === reduce.pl bib === id = cord-347818-93ixqyfp author = Hojyo, Shintaro title = How COVID-19 induces cytokine storm with high mortality date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4508 sentences = 214 flesch = 39 summary = Thus, IL-6 serves as a possible mechanism of treatment for severe COVID-19 patients, raising the possibility that one therapeutic option for the disease may be targeting excessive inflammation caused by IL-6 receptor (IL-6R) signaling with monoclonal antibody therapy or treatment with chemical modulators to block the signaling cascade while maintaining a sufficient antiviral primary immune response. IL-6-STAT3 signaling as a potential cause of the ARDS via cytokine storms in COVID-19 patients IL-6 amplifier, machinery for excessive inflammation SARS-CoV-2 infection induces the endocytosis of ACE2 together with SARS-CoV in target cells including epithelial cells and endothelial cells, resulting in an increase of serum angiotensin II (Ang II) levels due to the reduction of ACE2 surface expression (Fig. 1) [17, 48] . cache = ./cache/cord-347818-93ixqyfp.txt txt = ./txt/cord-347818-93ixqyfp.txt === reduce.pl bib === id = cord-348635-1pb2ag9j author = Anand, Praveen title = SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1658 sentences = 94 flesch = 51 summary = We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). We extrapolate that the evolution of SARS-CoV-2 into a global coronavirus pandemic may be in part due to its targeted mimicry of human ENaC and hijack of the associated host proteolytic network. The overlap of the cell-types expressing ACE2 and ENaC-ɑ, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. In order to extrapolate the tissue tropism of SARS-CoV-2 from the lens of the host proteolytic network, we assessed the co-expression of these proteases concomitant with the viral receptor ACE2 and ENaC-ɑ (Figure 2) . cache = ./cache/cord-348635-1pb2ag9j.txt txt = ./txt/cord-348635-1pb2ag9j.txt === reduce.pl bib === id = cord-348065-0tkx7aas author = Liu, Bing title = Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients date = 2020-03-30 pages = extension = .txt mime = text/plain words = 2285 sentences = 124 flesch = 54 summary = Methods 37 non-severe patients with persistent SARS-CoV-2 presence transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to PP (persistently positive) group, which was further allocated to PPP group (n=19) and PPN group (n=18), according to their testing results after 7 days (N=negative). Conclusion Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Next, we determined the abnormalities for each parameters Lymphopenia was observed at illness onset in 72.8% of non-severe COVID-19 patients (the PA group) in our study, which is similar to those reported by Zhang et al [15] (75.4%), Mo et al [17] (73.5%), Wang et al [27] (70.3%), and Guan et al [2] (83.2%), suggesting the involvement of lymphocytes in the early phase of SARS-CoV-2 infection. Together, these results suggest that measurement of these lymphocyte subpopulations could be used to distinguish non-severe patients with persistent viral presence from healthy subjects and those turned negative, and thus have clinical relevance for discharge management. cache = ./cache/cord-348065-0tkx7aas.txt txt = ./txt/cord-348065-0tkx7aas.txt === reduce.pl bib === id = cord-348243-e5tdb08v author = Schermer, Bernhard title = Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3958 sentences = 236 flesch = 56 summary = METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. cache = ./cache/cord-348243-e5tdb08v.txt txt = ./txt/cord-348243-e5tdb08v.txt === reduce.pl bib === id = cord-348823-u2gm3kyh author = Baksh, Mizba title = A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic date = 2020-05-18 pages = extension = .txt mime = text/plain words = 2249 sentences = 116 flesch = 45 summary = About 80% of COVID-19 infections are mild or asymptomatic and never require hospitalization but about 5% of patients become critically ill and develop acute respiratory distress syndrome (ARDS). The widely used management for ARDS in COVID-19 has been in line with the standard approach, but the need to adjust the treatment protocols has been questioned based on the reports of higher mortality risk among those requiring mechanical ventilation. Although some antimalarial and antiviral drugs may prove effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), their safety and efficacy are still under clinical trials. We conducted a systematic review of case reports on ARDS in SARS-CoV-2 infection to summarize the clinical presentation, laboratory and chest imaging findings, management protocols, and outcome of ARDS in COVID-19-positive patients. Tissue plasminogen activator (tPA) treatment for COVID-19 associated acute respiratory distress syndrome (ARDS): a case series cache = ./cache/cord-348823-u2gm3kyh.txt txt = ./txt/cord-348823-u2gm3kyh.txt === reduce.pl bib === id = cord-348727-o38uplxe author = Beaudoin-Bussières, Guillaume title = Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date = 2020-07-09 pages = extension = .txt mime = text/plain words = 920 sentences = 63 flesch = 54 summary = Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. Neutralizing activity against pseudoparticles bearing the SARS-CoV S 120 glycoprotein was detected in only 25% of convalescent plasma and exhibited low potency, as 121 previously reported (Figure 2) (14) . Of note, while we observed enhanced infectivity for the 122 D614G variant compared to its WT SARS-CoV-2 S counterpart ( Figure S3A ), no major 123 differences in neutralization with convalescent plasma were detected at both time-points ( Figure 124 S3B), thus suggesting that the D614G change does not affect the overall conformation of the 125 Spike, in agreement with recent findings (18) . 126 127 The capacity to neutralize SARS-CoV-2 S WT or D614G-pseudotyped particles 128 significantly correlated with the presence of RBD-specific IgG, IgM and anti-S antibodies 129 ( Figure S4 ). Interestingly, we observed a pronounced decrease (20-30%) in the percentage of 130 patients able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 131 10 weeks after symptoms onset. cache = ./cache/cord-348727-o38uplxe.txt txt = ./txt/cord-348727-o38uplxe.txt === reduce.pl bib === id = cord-348455-vcxalkeo author = Graham, N. R. title = Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date = 2020-07-22 pages = extension = .txt mime = text/plain words = 4105 sentences = 283 flesch = 62 summary = title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. We first piloted our antigen preps for the RBD-S IgG screening assay using serum 81 samples from a PCR-confirmed severe COVID-19 patient (defined as admission to the Intensive 82 Care Unit, ICU) who was admitted to the hospital 10 days following symptom onset and based 83 on an early report suggesting that SARS-CoV-2 could trigger antibody responses in this 84 timeframe (24). Anti-S titers in patients with a negative RBD-S test were 138 generally low and in RBD-positive samples, followed the same trends as RBD-reactivity, 139 providing further confirmation of robust serological responses to SARS-CoV-2 during acute 140 COVID-19. cache = ./cache/cord-348455-vcxalkeo.txt txt = ./txt/cord-348455-vcxalkeo.txt === reduce.pl bib === id = cord-348567-rvwxysvc author = Panfili, F. M. title = Possible role of vitamin D in Covid-19 infection in pediatric population date = 2020-06-15 pages = extension = .txt mime = text/plain words = 5375 sentences = 229 flesch = 36 summary = CONCLUSIONS: In this review, we suggest that vitamin D supplementation might play a role in the prevention and/or treatment to SARS-CoV-2 infection disease, by modulating the immune response to the virus both in the adult and pediatric population. Although the effect of normal to high levels of vitamin D on increasing CD4+ count is still unclear, a recent review proved that vitamin D plays an important role in reducing the immune activation of HIV-infected patients. In this autoimmune disease using calcitriol supplementation reduces serum levels of antibodies and slows the progression of β cell destruction down in the early stages of the disease [38] , Interestingly, it has also been demonstrated that in Systemic Sclerosis (SSc) [39] the VDR could act as a negative regulator of TGF-β/ Hydroxyproline, col1a1, col3a1 and alfa-SMA mRNAs ↓ Prevention of bleomycin-induced lung fibrosis in a murine model [48] Smad signaling, thus making vitamin D a putative antifibrotic treatment in the early stages of the disease. cache = ./cache/cord-348567-rvwxysvc.txt txt = ./txt/cord-348567-rvwxysvc.txt === reduce.pl bib === id = cord-349070-bqv03u2e author = Jiang, Shih Sheng title = Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date = 2004-01-15 pages = extension = .txt mime = text/plain words = 2465 sentences = 110 flesch = 51 summary = title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. cache = ./cache/cord-349070-bqv03u2e.txt txt = ./txt/cord-349070-bqv03u2e.txt === reduce.pl bib === id = cord-348391-xytmq2f2 author = Wyganowska-Swiatkowska, Marzena title = Influence of Herbal Medicines on HMGB1 Release, SARS-CoV-2 Viral Attachment, Acute Respiratory Failure, and Sepsis. A Literature Review date = 2020-06-30 pages = extension = .txt mime = text/plain words = 8077 sentences = 461 flesch = 41 summary = While long term proteinase and ACE-2 inhibition could be detrimental to cellular function and bodily homeostasis, targeted treatment partially reducing the effectiveness of coronavirus S protein attachment to the ACE2 or to the priming proteinase could have the potential to drop the SARS-CoV-2 viral load before a state of septic shock is reached at the peak of infection. Aspalathin and nothofagin extracted from Rooibos have been shown to effectively inhibit LPS-induced release of HMGB1, and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules [124] . The effect and mechanism of salidroside on sepsis-induced acute lung injury is mediated by the inhibition of inflammatory responses and HMGB1 production in bacterial LPS-treated macrophages and mice. Study has shown that pelargonidin (PEL) had effectively inhibited LPS-induced release of HMGB1 and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules. cache = ./cache/cord-348391-xytmq2f2.txt txt = ./txt/cord-348391-xytmq2f2.txt === reduce.pl bib === id = cord-348729-kejlm425 author = Liu, Xiaoyu title = Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date = 2020-05-04 pages = extension = .txt mime = text/plain words = 3457 sentences = 178 flesch = 50 summary = SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. These determined infection mechanisms indicated that blocking the interaction of SARS-CoV-2-RBD and ACE2 would cause a direct neutralizing effect against virus. This information suggests that the ACE2 interface of SARS-CoV-2-RBD might have high immunogenicity, which would be a suitable targeting epitope to develop SARS-CoV-2-specific antibodies with potent neutralizing function by in vitro screening. We performed site-directed antibody screening by phage display and finally obtained one IgG antibody and three single domain antibodies with potent neutralizing activities for SARS-CoV-2. Notably, the eluted phage exhibited a stronger binding signal on SARS-CoV-2-RBD compared to that on SARS-CoV-2-RBD mut, especially those from the domain antibody library ( Figure 2C ), indicating an expected precleaning effect during selection. cache = ./cache/cord-348729-kejlm425.txt txt = ./txt/cord-348729-kejlm425.txt === reduce.pl bib === id = cord-348636-qqcb85uk author = Lekone, Phenyo E. title = Bayesian Analysis of Severe Acute Respiratory Syndrome: The 2003 Hong Kong Epidemic date = 2008-07-09 pages = extension = .txt mime = text/plain words = 4878 sentences = 286 flesch = 62 summary = This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. These parameters were obtained using maximum likelihood estimation methods assuming a gamma distribution for each period with allowance for censoring due to incomplete observation. A simple model that captures the form of distributions of epidemiological determinants has been introduced to estimate the basic reproduction number and to assess the effect of control interventions introduced during the course of the epidemic. cache = ./cache/cord-348636-qqcb85uk.txt txt = ./txt/cord-348636-qqcb85uk.txt === reduce.pl bib === id = cord-348777-pk9y6vfp author = Ding, Cheng title = Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3609 sentences = 190 flesch = 46 summary = title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Our observational results revealed that corticosteroid therapy had no positive effect on the durations of SARS-CoV-2 RNA clearance among patients with mild COVID-19. Results from this study suggested that patients with mild COVID-19 may not benefit from corticosteroid therapy in terms of the duration of SARS-CoV-2 clearance. cache = ./cache/cord-348777-pk9y6vfp.txt txt = ./txt/cord-348777-pk9y6vfp.txt === reduce.pl bib === id = cord-348855-lnltoj1n author = Iannaccone, Giulia title = Weathering the Cytokine Storm in COVID-19: Therapeutic Implications date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4669 sentences = 207 flesch = 37 summary = The exaggerated cytokine release in response to viral infection, a condition known as cytokine release syndrome (CRS) or cytokine storm, is emerging as the mechanism leading to ARDS and MOF in COVID-19, thus endorsing the hypothesis that properly timed anti-inflammatory therapeutic strategies could improve patients' clinical outcomes and prognosis. CS are the cornerstone of treatments for cytokine storms and macrophage activation syndrome in autoimmune/autoinflammatory diseases [18] ; in the COVID-19 scenario they may be useful in the more severe forms of CRS to curb the systemic inflammatory response and prevent the occurrence of ARDS, if appropriately timed [10, 19] , 20]. Tocilizumab is now already included in many practice guidelines for COVID-19 management, especially for the treatment of critically ill patients with severe refractory hypoxemia in a later stage after the high-viral-load initial phase all over the world, while we wait for more definite data from multiple ongoing clinical trials [42] . cache = ./cache/cord-348855-lnltoj1n.txt txt = ./txt/cord-348855-lnltoj1n.txt === reduce.pl bib === id = cord-348713-tucolje2 author = Cao, Yanan title = Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations date = 2020-02-24 pages = extension = .txt mime = text/plain words = 1570 sentences = 79 flesch = 48 summary = Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations Yanan Cao 1 , Lin Li 1 , Zhimin Feng 1 , Shengqing Wan 1 , Peide Huang 1 , Xiaohui Sun 1 , Fang Wen 1 , Xuanlin Huang 1 , Guang Ning 1 and Weiqing Wang 1 Therefore, genetic analysis of expression quantitative trait loci (eQTLs) 8 and potential functional coding variants in ACE2 among populations are required for further epidemiological investigations of 2019-nCoV/SARS-CoV-2 spreading in East Asian (EAS) and other populations. To systematically investigate the candidate functional coding variants in ACE2 and the allele frequency (AF) differences between populations, we analyzed all the 1700 variants (Supplementary Table S1) in ACE2 gene region from the ChinaMAP (China Metabolic Analytics Project, under reviewing) and 1KGP (1000 Genomes Project) 9 databases. cache = ./cache/cord-348713-tucolje2.txt txt = ./txt/cord-348713-tucolje2.txt === reduce.pl bib === id = cord-349015-5oisrm5s author = Liu, Zhe title = Identification of a common deletion in the spike protein of SARS-CoV-2 date = 2020-04-02 pages = extension = .txt mime = text/plain words = 1182 sentences = 63 flesch = 57 summary = In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. By sequencing the whole genome of SARS-CoV-2, we identified two variants having deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. To investigate whether these deletions described above are random mutations occasionally identified in a strain or would commonly occur after cell passages, we performed whole genome sequencing on the other 21 SARS-CoV-2 viral strains collected after 2 rounds of cell passage in Vero-E6 or Vero cells (Supplemental Table) . cache = ./cache/cord-349015-5oisrm5s.txt txt = ./txt/cord-349015-5oisrm5s.txt === reduce.pl bib === id = cord-349210-8t4a5qqo author = Ji, Ping title = Immunomodulatory Therapeutic Proteins in COVID‐19: Current Clinical Development and Clinical Pharmacology Considerations date = 2020-08-10 pages = extension = .txt mime = text/plain words = 7698 sentences = 436 flesch = 40 summary = Immunomodulatory biological therapies are being evaluated in clinical trials for the management of the systemic inflammatory response and pulmonary complications in patients with advanced stages of COVID‐19. A randomized, open-label, controlled trial for the efficacy and safety of adalimumab in patients with elevated TNF-α levels in the critical stages of severe COVID-19 is ongoing in Shanghai, China, with the main outcome of time to clinical improvement. A Phase 2 trial of the efficacy and safety of infliximab was initiated to evaluate whether early institution of TNF-α inhibitor therapy in patients with severe COVID-19 infections could prevent further clinical deterioration and reduce the need for advanced cardiorespiratory support and early mortality at a 5 mg/kg IV single dose. extrinsic factors ( Route of administration: As described before, the immunomodulatory therapeutic proteins currently in clinical trials for the treatment of COVID-19 mostly are directed towards patients with moderate and severe stages of the disease. cache = ./cache/cord-349210-8t4a5qqo.txt txt = ./txt/cord-349210-8t4a5qqo.txt === reduce.pl bib === id = cord-349392-r71g2e9y author = Wang, L. -F. title = Bats, Civets and the Emergence of SARS date = 2007 pages = extension = .txt mime = text/plain words = 7011 sentences = 301 flesch = 52 summary = Virological and serological studies indicated that masked palm civets ( Paguma larvata ), together with two other wildlife animals, sampled from a live animal market were infected with SARS-CoV or a closely related virus. Here, we review studies by different groups demonstrating that SARS-CoV succeeded in spillover from a wildlife reservoir (probably bats) to human population via an intermediate host(s) and that rapid virus evolution played a key role in the adaptation of SARS-CoVs in at least two nonreservoir species within a short period. Recently, two groups independently demonstrated that bats in the genus Rhinolophus are natural reservoirs of SARS-like viruses , providing strong evidence that SARS-CoV is indeed a new zoonotic virus with a wildlife origin. (2003) , SARS-CoV-like viruses were isolated from palm civets and a raccoon dog in a live animal market in southern China and serologic evidence indicted that a third species, the Chinese ferret-badger, was also infected by a similar virus. cache = ./cache/cord-349392-r71g2e9y.txt txt = ./txt/cord-349392-r71g2e9y.txt === reduce.pl bib === id = cord-349031-tbof9yqi author = Chen, Shiu-Jau title = Novel Antiviral Strategies in the Treatment of COVID-19: A Review date = 2020-08-20 pages = extension = .txt mime = text/plain words = 5464 sentences = 303 flesch = 43 summary = Fortunately, some novel antiviral strategies, such as convalescent plasma, clustered regularly interspaced short palindromic repeats (CRISPR), and mesenchymal stem cell (MSC) therapy, potentially offer an additional or alternative option or compassionate use for the people suffering from COVID-19, especially for critically ill patients, although their safety and efficacy are also under study. In this review, we explore the applications, possible mechanisms, and efficacy in successful cases using convalescent plasma, CRISPR, and MSC therapy for COVID-19 treatment, respectively. In this case series study of five critically ill patients with COVID-19 and ARDS, the administration of convalescent plasma containing neutralizing antibodies significantly improved their clinical status [53] . Under the condition that traditional drugs cannot assure their safety and efficacy for COVID-19 treatment, novel antiviral strategies, including convalescent plasma, CRISPR, and cell therapy, may be able to provide an additional or alternative option or compassionate use for the treatment of COVID-19, particular for critically ill patients. cache = ./cache/cord-349031-tbof9yqi.txt txt = ./txt/cord-349031-tbof9yqi.txt === reduce.pl bib === id = cord-349029-zyfop43z author = Dobrovolny, Hana M. title = Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4596 sentences = 233 flesch = 48 summary = In order to estimate how effective these strategies will be, we will need a better understanding of the role of asymptomatic individuals in SARS-CoV-2 spread and the effect the proportion and relative infectiousness of asymptomatics have on the time course of the epidemic. In this paper, we study a compartmental epidemic model that includes asymptomatic infections to determine the role that asymptomatic individuals might play in the spread of SARS-CoV-2. We apply our model to data from SARS-CoV-2 epidemics in California, Florida, New York, and Texas, finding that a large number of infections in these states are unreported and that relaxing social distancing measures too early will cause a rapid spike in infections driven in part by these hidden infections. For the SARS-CoV epidemics examined here, the model predicts that there are far more asymptomatic or unreported cases at the peak of the infection, suggesting that there might be widespread community transmission if stay-at-home orders are relaxed too early. cache = ./cache/cord-349029-zyfop43z.txt txt = ./txt/cord-349029-zyfop43z.txt === reduce.pl bib === id = cord-348773-ulnc9gdv author = Hammoud, H. title = Post mortem pathological findings in COVID-19 cases: A Systematic Review date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5075 sentences = 341 flesch = 54 summary = Methods: A systematic search of electronic databases (PubMed, ScienceDirect, Google scholar, Medrxiv & Biorxiv) was carried out from December 2019 to August, 15th 2020, for journal articles of different study designs reporting postmortem pathological findings in COVID-19 cases. Articles were included if they met the following eligibility criteria: (1) addressed pathological reports of COVID-19 autopsies or postmortem cases, (2) involved human subjects (at least one case), (3) all study designs were involved (case report, case series, cross-sectional, case-control, randomized and non-randomized studies), (4) no language restrictions were applied. (13, 19, 20, 22-32, 34, 38-41, 44-65, 67) Regarding the included organs, this review described the histopathology of different organs as follows; Lung and pulmonary system was the most common described organ in 42 articles, ( is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Regarding the postmortem pulmonary pathology, our review showed that different histopathological findings had been identified among COVID-19 cases. cache = ./cache/cord-348773-ulnc9gdv.txt txt = ./txt/cord-348773-ulnc9gdv.txt === reduce.pl bib === id = cord-349124-nhnl7zgi author = de Sandes‐Freitas, Tainá Veras title = Lessons from SARS‐CoV‐2 screening in a Brazilian organ transplant unit date = 2020-07-13 pages = extension = .txt mime = text/plain words = 1193 sentences = 85 flesch = 47 summary = Evidence suggests that asymptomatic carriers might transmit the SARS‐CoV‐2, challenging the implementation of transmission preventive strategies. We report a single‐center experience using universal SARS‐CoV‐2 screening for all inpatients and newly admitted patients to an Organ Transplant Unit located in a region with significantly high community‐based transmission. We will describe the experience of a single center of screening all inpatients and newly admitted patients to the Organ Transplant Unit. On March 31, 2020, a 43-year-old man with alcoholic liver cirrhosis, hospitalized since March 23rd presented acute dyspnea and fever and was tested positive for SARS-CoV-2 (patient 1). We reported the COVID-19 screening strategy adopted by our center in a attempt to prevent nosocomial transmission and keep "clean" the Transplant Unit. Alert for non-respiratory symptoms of coronavirus disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Lessons from SARS-CoV-2 screening in a Brazilian organ transplant unit cache = ./cache/cord-349124-nhnl7zgi.txt txt = ./txt/cord-349124-nhnl7zgi.txt === reduce.pl bib === id = cord-348696-86nbwon2 author = Güemes-Villahoz, Noemi title = Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4199 sentences = 216 flesch = 43 summary = title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review A multicenter study which documented potential risk factors for SARS-CoV-2 transmission in patients requiring intubation [7] reported that unprotected eye contact with secretions from infected patients was the most predictive variable for transmission to healthcare workers. A recent study evaluated the ocular tropism of SARS-CoV-2 in patients with confirmed COVID-19. Of the 56 subjects investigated there was only one patient who gave a history of prior pterygium surgery, with conjunctivitis and a positive PCR result from the conjunctival swab highlighting the importance of an intact ocular surface in resisting virus invasion [25] . Despite ocular complications not being a common clinically detectable manifestation of SARS-CoV-2 infection, recent evidence suggests that ocular exposure may represent a major transmission route for the virus. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection SARS-CoV-2 RNA detection in tears and conjunctival secretions of COVID-19 patients with conjunctivitis cache = ./cache/cord-348696-86nbwon2.txt txt = ./txt/cord-348696-86nbwon2.txt === reduce.pl bib === id = cord-349311-yo4up42r author = De Maria, Andrea title = High prevalence of olfactory and taste disorder during SARS‐CoV‐2 infection in outpatients date = 2020-05-17 pages = extension = .txt mime = text/plain words = 741 sentences = 47 flesch = 46 summary = Here we comment on Sun and coll Metaanlysis with particular nuance to olfactory and taste disorders that very often herald SARS-CoV-2 in our country, particularly in outpatients, and are not reported so far in the medical literature from China. Limited or no information has been so far gathered on the majority of milder cases of SARS-CoV-2-disease that are cared for at home since they are not progressing to respiratory insufficiency and hospitalization/ventilation. In addition, profound olfactory and taste disorder (OTD), that has been reported to be frequent in hospitalized patients in Italy, 7 is not reported in China or other areas, 2,3,5 and correspondingly fails to be reported in the meta-analysis. Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: a single arm metaanalysis Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study cache = ./cache/cord-349311-yo4up42r.txt txt = ./txt/cord-349311-yo4up42r.txt === reduce.pl bib === id = cord-349159-rndtf508 author = Brosseau, Lisa M title = Selecting Controls for Minimizing SARS-CoV-2 Aerosol Transmission in Workplaces and Conserving Respiratory Protective Equipment Supplies date = 2020-08-21 pages = extension = .txt mime = text/plain words = 5946 sentences = 272 flesch = 45 summary = Built on the recognition that aerosol-transmissible organisms are likely to exhibit a dose–response function, such that higher exposures result from longer contact times or higher air concentrations, this control banding model offers a systematic method for identifying a set of source and pathway controls that could eliminate or reduce the need for receptor controls. From that perspective, occupational hygienists have an obligation Annals of Work Exposures and Health, 2020, 1-10 doi: 10.1093/annweh/wxaa083 Original Article to consider hazardous SARS-CoV-2 aerosols in workplace risk assessments and to encourage employers to utilize well-studied and proven source and pathway control strategies for minimizing aerosol exposures. (2019) proposed a control banding method for aerosol-transmissible diseases, such as COVID-19, for two reasons: (i) to identify those jobs at highest risk and (ii) encourage the use of source and pathway controls before resorting to personal protective equipment (PPE), for the ultimate goal of conserving PPE for those in the highest risk categories. cache = ./cache/cord-349159-rndtf508.txt txt = ./txt/cord-349159-rndtf508.txt === reduce.pl bib === id = cord-349117-xfir3m5p author = Hyseni, Inesa title = Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays date = 2020-09-10 pages = extension = .txt mime = text/plain words = 8298 sentences = 403 flesch = 52 summary = After fully characterising lentiviral pseudotypes bearing the SARS-CoV-2 spike protein, we employed them in pseudotype-based neutralisation assays in order to profile the neutralising activity of human serum samples from an Italian sero-epidemiological study. SARS CoV-2 strain 2019-nCov/Italy wild-type virus (LV), which was handled in a level 3 bio-containment facility (BSL 3), was used as positive control in order to evaluate the spike glycoprotein expression, while a ∆-envelope pseudotype, prepared with the same procedure, was used as a negative control. To verify the expression of the spike protein in the SARS-CoV-2 pseudotypes, the spike was detected by Western blot; sera from convalescent SARS-CoV-2 patients, which have been shown to have a high neutralising titre in microneutralisation with a live virus, were used as the primary antibody, and goat anti-Human IgG as the secondary antibody. cache = ./cache/cord-349117-xfir3m5p.txt txt = ./txt/cord-349117-xfir3m5p.txt === reduce.pl bib === id = cord-349365-2ot1kf2k author = Shi, Yi title = Antisense downregulation of SARS‐CoV gene expression in Vero E6 cells date = 2004-11-15 pages = extension = .txt mime = text/plain words = 3217 sentences = 175 flesch = 52 summary = Cells were then treated with the antisense oligonucleotides used by adding them to the culture medium, which then reached the nuclei and resulted in sequence-specific antisense downregulation of SARS-CoV gene expression. We conclude that the antisense PS-ODNs could effectively and sequence-specifically downregulate SARS-CoV gene expression in a dose-dependent manner. In this work, we have evaluated the down-regulation effects of 26 antisense PS-ODNs targeting different sites along the open reading frames (ORFs) of E, M, and N proteins and obtained 12 antisense oligos which could reduce target gene expression by over 50% in Vero E6 cells at the concentration of 50 µM in the culture medium. Our present results indicate a sequencespecific down-regulation effect of antisense PS-ODN (20mer) in Vero E6 cells, and we found an effective range of concentrations, where the antisense oligo inhibited expression of the E, M, and N genes of SARS-CoV in a concentration-dependent manner. cache = ./cache/cord-349365-2ot1kf2k.txt txt = ./txt/cord-349365-2ot1kf2k.txt === reduce.pl bib === id = cord-349226-xzlc1pni author = Khatiwada, Saroj title = Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date = 2020-08-05 pages = extension = .txt mime = text/plain words = 4312 sentences = 231 flesch = 35 summary = To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease. cache = ./cache/cord-349226-xzlc1pni.txt txt = ./txt/cord-349226-xzlc1pni.txt === reduce.pl bib === id = cord-349541-7g50vg14 author = Poulikakos, Dimitrios title = SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date = 2020-07-07 pages = extension = .txt mime = text/plain words = 427 sentences = 39 flesch = 66 summary = key: cord-349541-7g50vg14 title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England cord_uid: 7g50vg14 Please cite this article as: Poulikakos D, Sinha S, Kalra PA, SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104545 Amongst the 22 (7·8%) HCW with previous SARS-Cov-2 PCR nasopharyngeal swabs, 2 were positive, 12 were negative, and 7 did not disclose the result. Positive SARS-Cov-2 IgG was detected in 17 (6%) HCW and 6 (35·3%) had been asymptomatic. All IgG positive cases were in DIPC HCW (17 out of 195; 8·7%). One IgG positive HCW did not disclose ethnicity. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients Hospital-Wide SARS-CoV-2 Antibody Screening Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics First experience of COVID-19 screening of health-care workers in England cache = ./cache/cord-349541-7g50vg14.txt txt = ./txt/cord-349541-7g50vg14.txt === reduce.pl bib === id = cord-349500-603v8lfb author = Neurath, Markus F title = Covid-19 and immunomodulation in IBD date = 2020-04-16 pages = extension = .txt mime = text/plain words = 6548 sentences = 386 flesch = 45 summary = Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infects ACE2 expressing epithelial cells in the lung and/or the intestine. The covid-19 receptor ACE2 is particularly highly expressed in intestinal epithelial cells from the terminal ileum and to a lesser extent in the colon, where mucosal inflammation in patients with IBD (Crohn's disease (CD); UC) is frequently detected. cache = ./cache/cord-349500-603v8lfb.txt txt = ./txt/cord-349500-603v8lfb.txt === reduce.pl bib === id = cord-349417-vn7q8wc4 author = Ziebuhr, John title = The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date = 2006 pages = extension = .txt mime = text/plain words = 3379 sentences = 179 flesch = 45 summary = Activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce 16 (in IBV: 15) mature products called nonstructural proteins (nsp) 1 to 16 (reviewed in Refs. The N-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups I, II, and III, are cleaved at two (in IBV) or three sites (in all other coronaviruses) by one (IBV and SARS-CoV) or two zinc-finger-containing papain-like cysteine proteases called PL1 pro and PL2 pro . The observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified RNA-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, NendoU, playing a central role. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication cache = ./cache/cord-349417-vn7q8wc4.txt txt = ./txt/cord-349417-vn7q8wc4.txt === reduce.pl bib === id = cord-349485-iomk99lv author = Eis-Hübinger, Anna M. title = Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples date = 2020-04-22 pages = extension = .txt mime = text/plain words = 1633 sentences = 103 flesch = 56 summary = title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples To rapidly identify unrecognized cases in hospitals in an efficient, resource-saving and cost effective manner we propose an ad hoc laboratory-based surveillance approach for SARS-CoV-2. It is based upon minipool (MP) testing of nucleic acid preparations of respiratory samples submitted to laboratories for routine diagnostics. The workflow comprises individual nucleic acid (NA) extraction of respiratory samples, pooling of extracted NA samples in batches of 10 and SARS-CoV-2 specific real-time RT-PCR. We report a diagnostic workflow for the laboratory-based surveillance of SARS-CoV-2 in a rapid and cost effective manner. From a public health perspective an easy to establish and cost effective laboratory-based screening strategy may assist in rapid case detection, surveillance and ultimately in a better understanding of this epidemic (7) . cache = ./cache/cord-349485-iomk99lv.txt txt = ./txt/cord-349485-iomk99lv.txt === reduce.pl bib === id = cord-349313-2gupfqnl author = Martinez-Perez, Clara title = Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19) date = 2020-10-21 pages = extension = .txt mime = text/plain words = 7148 sentences = 437 flesch = 53 summary = This study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. Methods: The search for publications was carried out through the Web of Science database using terms such as "COVID-19" and "SARS-CoV-2" for the period between January and July 2020. The search of publications was carried out using the Web of Science (WOS) database with the following search terms: "COVID-19", "SARS-CoV-2", "The Coronavirus Disease 2019" and "Corona Virus Disease 2019". Moreover, the most common keywords used in Chinese journals were "COVID-19", "SARS-CoV-2", "Prevention and control", "Traditional Chinese Medicine", "Computed tomography", "Epidemic", "Public health", "MERS", "Pneumonia" and "Male". In this group, the different articles analyze the viral transmission of SARS-CoV-2, the most frequent symptoms (fever, cough, diarrhea, etc.) and experimental treatment methods such as chloroquine phosphate (Figure 7 ). cache = ./cache/cord-349313-2gupfqnl.txt txt = ./txt/cord-349313-2gupfqnl.txt === reduce.pl bib === id = cord-349445-yh6ndtgm author = Mohammed El Tabaa, Manar title = Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost date = 2020-05-27 pages = extension = .txt mime = text/plain words = 11840 sentences = 618 flesch = 39 summary = Therefore, researchers suggested that the use of angiotensin converting enzyme inhibitors (ACEIs) and/or angiotensin receptor blockers (ARBs), may show a positive trend towards the severe inflammatory reactions and endothelial dysfunction caused by stimulating the function of ACE/Ang II/AT-1 axis and thereby, towards the bad pulmonary effects associated with the COVID-19 infection [29, 30] . Since IL-6 would inactivate endothelial nitric oxide synthase (eNOS), it could disrupt NO production [90] , decreasing its level and inducing a state of oxidative stress that may lead to Ang II-induced impairment in endothelial responses [91] Postulating impaired endothelium functions as a principal factor in the pathogenesis of heart failure, hypertension and diabetes, it will be expected to classify the patients of such diseases as high risk groups for COVID-19 development [92] [93] [94] . Taken into consideration the numerous harmful effects possibly induced by Ang II during COVID-19 pathogenesis, we found that most novel studies aim to use the anti-hypertensive drugs which act either by inhibiting the ACE activity or by blocking AT1 receptor, suggesting that action may mitigate the disease severity in COVID-19 patients. cache = ./cache/cord-349445-yh6ndtgm.txt txt = ./txt/cord-349445-yh6ndtgm.txt === reduce.pl bib === id = cord-349428-i2s41kl7 author = Griffin, Ian title = The Impact of COVID-19 Infection on Labor and Delivery, Newborn Nursery, and Neonatal Intensive Care Unit: Prospective Observational Data from a Single Hospital System date = 2020-06-13 pages = extension = .txt mime = text/plain words = 4416 sentences = 228 flesch = 53 summary = The study population consisted of maternal-infant dyads whose mothers were identified to be either COVID-19 positive or persons under investigation (PUI) before their admission to labor and delivery (L&D) or at any time before their discharge. Obstetric patients who were COVID-19 positive or PUIs were cared for in a designated suite of single-person airborne infection isolation (AIIRs) negative pressure rooms separate from the main L&D unit through delivery and the postpartum period, while awaiting testing for COVID-19 or if they had tested positive for COVID-19. If a mother tested positive for COVID-19 and newborn infants had been immediately separated at birth from their mother, neonatal isolation precautions were suspended after two negative polymerase chain reaction (PCR)-based nasopharyngeal swab tests, performed at 48 hours and at 5 days of life, respectively. cache = ./cache/cord-349428-i2s41kl7.txt txt = ./txt/cord-349428-i2s41kl7.txt === reduce.pl bib === id = cord-349556-k312qkvh author = Roldán-Santiago, Ernesto title = SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1831 sentences = 148 flesch = 64 summary = title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient's cervical LN. cache = ./cache/cord-349556-k312qkvh.txt txt = ./txt/cord-349556-k312qkvh.txt === reduce.pl bib === id = cord-349690-hgdjbeht author = Alonso, Fábio de O. Martinez title = Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report date = 2020-08-14 pages = extension = .txt mime = text/plain words = 723 sentences = 49 flesch = 52 summary = title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report Although cases vary in terms of serological data, timing of reactivation and clinics, patients who retested positive to SARS-CoV-2 generally have a mild or asymptomatic course 5, 6 , which is perhaps the result of some level of immunity, while symptomatic reactivation is rare but may happen 7 . Our patient, on the other hand, presented a more potent form of COVID-19 after more than 40 days from the first mild infection, and with a detectable antibody response only after the second infectious episode. In this paper, we describe a COVID-19 recurrence from a mild to a moderate form after convalescence, with RT-qPCR turning positive and antibody detection after more severe symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report cache = ./cache/cord-349690-hgdjbeht.txt txt = ./txt/cord-349690-hgdjbeht.txt === reduce.pl bib === id = cord-349645-6o8773c5 author = Li, He title = Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3018 sentences = 177 flesch = 50 summary = METHODS: A retrospective study is conducted to study whether air quality index (AQI), four ambient air pollutants (PM(2.5), PM(10), NO(2) and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26(th) to Feb 29(th) in 2020. In this retrospective study, we attempted to conduct an exploratory analysis looking at the association between environment conditions (including ambient pollutants and meteoroidal parameter) and COVID-19 incidence/mortality in Wuhan, given a city-wide lockdown and varying pollution/meteorological data throughout the entire study period. In the current study, although the NO 2 level was constantly lower than the US EPA standards (United States Environmental Protection Agency, 2016), our data revealed that COVID-19 incidence were highly correlated with the ambient NO 2 concentration. The correlation between the COVID-19 incidence and three ambient air pollution along with five meteorological parameters Jan 26 th to Feb 29 th in 2020 in Wuhan and XiaoGan, China. cache = ./cache/cord-349645-6o8773c5.txt txt = ./txt/cord-349645-6o8773c5.txt === reduce.pl bib === id = cord-349504-oqpjqgv4 author = Escudero, Dolores title = Análisis de SARS-CoV-2 en el aire de una UCI dedicada a pacientes Covid-19 date = 2020-10-10 pages = extension = .txt mime = text/plain words = 1627 sentences = 140 flesch = 66 summary = Algunos estudios han documentado que el SARS-CoV-2 puede permanecer en el aire generado por aerosoles hasta 3 horas (7) demostrándose la presencia de genoma viral en el aire y filtros de los hospitales. El estudio se realizó a finales de mayo del 2020 en 5 boxes diferentes de la UCI (Tabla 1), colocando los equipos de extracción en el suelo, cerca de la cabeza del paciente y lo más alejado posible de la salida de aire, recogiéndo las muestras de aire durante un tiempo de 2-4 horas. El análisis mediante RT-PCR cuantitativa no mostró en ningún caso detección del genoma de SARS-CoV-2 en las muestras recogidas por los dos métodos descritos, por lo que en nuestro estudio no hemos podido demostrar la presencia de SARS-CoV-2 en el aire de la UCI ni en la planta de hospitalización. En nuestra UCI todos los boxes estaban equipados con presión negativa de -10 pascales y un intercambio de 15-20 ciclos/h de aire lo cual puede justificar la ausencia de RNA del SARS-CoV-2 en nuestra investigación. cache = ./cache/cord-349504-oqpjqgv4.txt txt = ./txt/cord-349504-oqpjqgv4.txt === reduce.pl bib === id = cord-349501-p1fttfpr author = Ratia, Kiira title = Chapter 494 Coronavirus Papain-like Peptidases date = 2013-12-31 pages = extension = .txt mime = text/plain words = 1322 sentences = 77 flesch = 45 summary = Keywords: Coronavirus, Severe acute respiratory syndrome, SARS-CoV, polyprotein processing, ubiquitin-like domain, noncovalent protease inhibitors, de-ubiquitination, DUB, ISG-15, de-ISGylation. For coronaviruses, a family of positive-stranded RNA viruses with large genomes (28À32 kb), the gene encoding the viral non-structural proteins (nsp's), including the RNA-dependent RNA-polymerase, is translated into a large precursor polyprotein, which must be proteolytically processed to mediate viral transcription and replication [1] . Cloning and expression of the N-terminal region of the murine coronavirus replicase polyprotein revealed that a predicted papain-family protease (papain-like protease, PLP) domain was responsible for processing the aminoterminal non-structural protein (nsp) from the replicase polyprotein [2À3] . Analysis of the N-terminal region of the replicase polyprotein of SARS-CoV revealed only one PLP domain, termed PLpro, which was shown to process the nsp1/2, nsp2/3 and nsp3/4 cleavage sites using the LXGG recognition motif [18] . Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme cache = ./cache/cord-349501-p1fttfpr.txt txt = ./txt/cord-349501-p1fttfpr.txt === reduce.pl bib === id = cord-349659-6drnriun author = Grant, Benjamin D. title = SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents date = 2020-07-01 pages = extension = .txt mime = text/plain words = 3203 sentences = 207 flesch = 57 summary = title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents In this work, we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. 10 Antigen detecting ELISAs were previously developed in 2004 for SARS-CoV-1, with limits of detection of approximately 50 pg/mL and clinical sensitivity as a function of days since onset that was significantly better than the useful time window for the current generation of SARS-CoV-2 serology assays. A dose response curve was generated for the half-strip LFA using two commercially available SARS-CoV-2 nucleocapsid (N) proteins, from Genemedi and Genscript. Analytical Chemistry pubs.acs.org/ac Article and determination of realistic limits of detection for a full strip LFA in multiple sample matrices will help point the way toward the best approach for an antigen detecting LFA for SARS-CoV-2. In this paper, we present a half-strip LFA for the detection of nucleocapsid protein of SARS-CoV-2. cache = ./cache/cord-349659-6drnriun.txt txt = ./txt/cord-349659-6drnriun.txt === reduce.pl bib === id = cord-349744-8cg5yj20 author = Lassaunière, Ria title = Evaluation of nine commercial SARS-CoV-2 immunoassays date = 2020-04-10 pages = extension = .txt mime = text/plain words = 2649 sentences = 145 flesch = 53 summary = The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. While the four POC tests evaluated according to illness duration were often weakly positive or detected only IgG or IgM during the early phase (data not shown), their sensitivities were comparable to the Wantai Total Ab ELISA and Euroimmun IgA ELISA in all three phases. In the present study, three SARS-CoV-2-specific commercial ELISA assays and six POC rapid tests were evaluated using sera from hospitalized adult patients with PCR-confirmed diagnoses for SARS-CoV-2 and a collection of control serum samples taken before the emergence of the virus in China in December 2019. Overall, the Wantai Total Ab ELISA had superior sensitivity and specificity compared to both Euroimmun IgA and IgG ELISAs. The POC tests varied notably, with the best performance observed for the test produced by AutoBio Diagnostics, followed by the tests produced by Dynamiker Biotechnology and CTK Biotech. cache = ./cache/cord-349744-8cg5yj20.txt txt = ./txt/cord-349744-8cg5yj20.txt === reduce.pl bib === id = cord-348899-vynk8q8c author = Jo, Seri title = Inhibition of SARS-CoV 3CL protease by flavonoids date = 2019-11-14 pages = extension = .txt mime = text/plain words = 3989 sentences = 236 flesch = 54 summary = A synthetic peptide labelled with an Edans-Dabcyl FRET (Fluorescence resonance energy transfer) pair 12 was used to search SARS-CoV 3CLpro inhibitory compounds against a flavonoid library. The proteolytic assay using the SARS-CoV 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The three compounds showed the severely reduced fluorescent intensity and thus represented their SARS-CoV 3CLpro inhibitory activity. The interactions between SARS-CoV 3CLpro and three inhibitory flavonoids were analysed to predict their binding affinities. We have created a library of flavonoids to systematically investigate SARS-CoV 3CLpro inhibitory compound by a FRET method. Herbacetin, rhoifolin and pectolinarin were the best inhibitory compounds against SARS-CoV 3CLpro in the flavonoid library. In order to predict the flavonoid scaffolds needed to interact with the catalytic site of SARS-CoV 3CLpro, an induced-fit docking study was performed and analysed. cache = ./cache/cord-348899-vynk8q8c.txt txt = ./txt/cord-348899-vynk8q8c.txt === reduce.pl bib === id = cord-349794-mhviub6e author = Le, Brian L. title = Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 3810 sentences = 216 flesch = 43 summary = We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. By infecting human adenocarcinomic alveolar basal epithelial cells with SARS-CoV-2 and comparing to controls, the authors generated a list of 120 differentially expressed genes. Here, we applied our existing computational drug repositioning pipeline to identify drug profiles with significantly reversed differential gene expression compared to predicted inhibitors (including one tested in Calu-3) were incubated with SARS-CoV-2 infected human embryonic kidney 293T cells overexpressing ACE2 (293T-ACE2) with viral replication determined using an immunofluorescence-based assay. In this study, we applied our drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available RNA-seq data ( Figure 1 ). Here, we used a transcriptomics-based drug repositioning pipeline to predict therapeutic drug hits for three different input SARS-CoV-2 signatures, each of which came from distinct human cell or tissue origins. cache = ./cache/cord-349794-mhviub6e.txt txt = ./txt/cord-349794-mhviub6e.txt === reduce.pl bib === id = cord-349545-w7c2tu5a author = Wang, Mengmeng title = Analytical performance evaluation of five RT‐PCR kits for severe acute respiratory syndrome coronavirus 2 date = 2020-10-27 pages = extension = .txt mime = text/plain words = 1838 sentences = 126 flesch = 55 summary = BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT‐PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS‐CoV‐2 infection. 8 Pan et al found that thermal inactivation adversely affected the efficiency of RT-PCR for SARS-CoV-2 detection samples with low viral loads. In the work, we presented the analytical performance evaluations of five RT-PCR kits using nasopharyngeal swabs samples from patients with confirmed SARS-CoV-2 infection, and negative nasopharyngeal swabs samples ( Figure 1 ). To further confirm the detection ability of the five kits, a positive clinical specimen (Ct: ORF1ab 26.99, N: 28.19) was diluted with 5-fold using RNase-free water, and the resulting dilution is considered as Level 1. No positive result was obtained in testing of 30 negative clinical samples by using five kits for ORF1ab and N gene. cache = ./cache/cord-349545-w7c2tu5a.txt txt = ./txt/cord-349545-w7c2tu5a.txt === reduce.pl bib === id = cord-349684-2tioh80m author = Pezzotti, Giuseppe title = Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date = 2020-06-20 pages = extension = .txt mime = text/plain words = 5388 sentences = 338 flesch = 51 summary = The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. cache = ./cache/cord-349684-2tioh80m.txt txt = ./txt/cord-349684-2tioh80m.txt === reduce.pl bib === id = cord-349089-ta07bho2 author = Antushevich, Hanna title = Interplays between inflammasomes and viruses, bacteria (pathogenic and probiotic), yeasts and parasites date = 2020-09-22 pages = extension = .txt mime = text/plain words = 8174 sentences = 467 flesch = 34 summary = For example, in in vitro experiments on human primary neurons (HPNs) and microglial cells (HFMG) collected from healthy patients, it was discovered that treatment of the cells with HIV ssRNA40 (specific GU-rich single-stranded RNA from the HIV long terminal repeat region) activates the NLRP3 inflammasome and increases the expression and extracellular secretion of pro-inflammatory cytokines (IL-1β, IL-18) and neurotoxic cytokines (TNF-α, IL-1α, C1q). Another report has shown that HIV-1 induces the expression of NLRP3 inflammasome and IL-1β secretion in dendritic cells from healthy individuals but not HIV-1-infected patients, suggesting that inflammasome activation contributes to disease progression [23] . Based on the strong inflammatory potential of the NLRP3 inflammasome during infections caused by MERS-and SARS-CoVs, inhibition of the NLRP3 inflammasome activity may attenuate the cytokine storm and be a therapeutic target in the treatment of tissue inflammation in SARS patients [33, 41] . cache = ./cache/cord-349089-ta07bho2.txt txt = ./txt/cord-349089-ta07bho2.txt === reduce.pl bib === id = cord-349682-kpg0vley author = Ojha, Probir Kumar title = Therapeutics for COVID-19: from computation to practices—where we are, where we are heading to date = 2020-09-02 pages = extension = .txt mime = text/plain words = 7923 sentences = 416 flesch = 49 summary = For example, the broad-spectrum antiviral drug Arbidol recently entered the clinical trial for the treatment of SARS-CoV-2 which may act by inhibiting virus-host cell fusion, thus preventing the viral entry into host cells against influenza virus [37] [38] [39] . Smith and Smith [22] analyzed 8000 small drug molecules and natural products (SWEETLEAD library database) employing restrained temperature replica-exchange MD simulations combining virtual screening through the ensemble docking to identify the effective drug for COVID-19 which might stop the virus by two ways: (a) disrupting S protein and ACE2 receptor interface stability; or (b) by troubling the capability of the S protein to recognize Table 2 Pharmacological safety data of selected potential drug candidates [11, 12, 14, 34, 38, 39, 43-45, 57-59, 64, 69, 70, 89] Drug Dose Drug-drug interaction Toxicity Chloroquine phosphate (Aralen) [11, 12, 14, 43, 89] This is a genetically engineered vaccine candidate with the replicationdefective adenovirus type 5 as the vector to express SARS-CoV-2 spike protein. cache = ./cache/cord-349682-kpg0vley.txt txt = ./txt/cord-349682-kpg0vley.txt === reduce.pl bib === id = cord-349774-898tmq14 author = Zhang, Haiyang title = Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3172 sentences = 188 flesch = 52 summary = title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein Here, we report for the first time that the 11S proteasomal activator PA28γ regulates the intracellular abundance of the SARS-CoV-2 N protein (nCoV N). These results suggest that PA28γ binding is important in regulating 20S proteasome activity, which in turn regulates levels of the critical nCoV N nucleocapsid protein of SARS-CoV-2, furthering our understanding of the pathogenesis of COVID-19. The SARS-CoV-2 nucleocapsid protein (hereafter, referred to as nCoV N) accounts for the largest proportion of viral structure proteins and is the most abundant protein in virus-infected cells. PA28γ could be critical for degrading the SARS-CoV-19 nCoV N protein in the nucleus as part of the 20S proteasome, which acts to degrade proteins in a ubiquitin-independent manner, such as seen in the hepatitis C virus (HCV) core protein [11] . Interactions of SARS Coronavirus Nucleocapsid Protein with the host cell proteasome subunit p42 cache = ./cache/cord-349774-898tmq14.txt txt = ./txt/cord-349774-898tmq14.txt === reduce.pl bib === id = cord-349838-p6vfzbla author = Algwaiz, Ghada title = Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4060 sentences = 229 flesch = 44 summary = Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. While acknowledging all aforementioned challenges and taking into account current recommendations or guidelines issued by the American Society for Transplantation and Cellular Therapy (ASTCT) and the European Society for Blood and Marrow Transplantation (EBMT) (which are WBMT members), herein, we aim at providing a consensus among the authors from WBMT and CIBMTR's HSIS committee and other HCT experts who represent multiple continents and allude to the current worldwide threat to HCT patient from the COVID-19 pandemic (7, 8) . cache = ./cache/cord-349838-p6vfzbla.txt txt = ./txt/cord-349838-p6vfzbla.txt === reduce.pl bib === id = cord-349827-0trvostt author = Tse, Alan C.B. title = Crisis management and recovery: how restaurants in Hong Kong responded to SARS date = 2005-01-29 pages = extension = .txt mime = text/plain words = 2934 sentences = 154 flesch = 55 summary = This article reviews a typology of crises, examines the crisis response of restaurants in Hong Kong, illustrates how local restaurants deal with this unprecedented situation and develop strategies for management and recovery. Restaurants in Hong Kong have already been put under great pressure to survive in the harsh market environment resulting from the Asian financial crisis of 1997, but the Severe Acute Respiratory Syndrome (SARS) outbreak in March 2003 was a death sentence to the industry. The SARS instance in Hong Kong had indirectly generated crises of the social environment because many restaurants experienced liquidity problems after the outbreak, and had to lay off thousands of staff or force them to take no-pay leave. In the SARS outbreak, for example, restaurant managers' attempt to lay off staff without proper compensation to improve their cash flow position may lead to confrontation with the labour, which may subsequently cause a crisis of the social environment type. cache = ./cache/cord-349827-0trvostt.txt txt = ./txt/cord-349827-0trvostt.txt === reduce.pl bib === id = cord-349721-wdjlr4z4 author = Szpiro, L. title = Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3991 sentences = 190 flesch = 42 summary = To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. In an attempt to better understand and thus better control the transmission of SARS-CoV-2 behind the recent and ongoing pandemic, the impact of body fluid secretions, from coughing or sneezing corresponding to an artificial mixture containing nasal mucus and saliva, on the surface stability of SARS-CoV-2 and the virucidal efficiency of disinfectant were tested. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers (according to the EN14476 standard suspension test) and 1 surface chemical disinfectant (according to the virucidal surface quantitative EN16777 test) against SARS-CoV-2, HCoV-229E and FCoV was then measured. The virucidal activity of three commercial hand rub products against SARS-CoV-2, HCoV-229E and FCoV was determined using the quantitative suspension test according to EN 14476, comparing standardized interfering substance (clean condition, 0.3 g/l BSA) and our artificial mucus/saliva mixture. cache = ./cache/cord-349721-wdjlr4z4.txt txt = ./txt/cord-349721-wdjlr4z4.txt === reduce.pl bib === id = cord-349912-em1abdrg author = Meng, Xiangming title = COVID-19 and anosmia: A review based on up-to-date knowledge date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1517 sentences = 111 flesch = 57 summary = Multiple cross-sectional studies have demonstrated that the incidence rate of Olfactory dysfunction in COVID-19 patients varies from 33.9–68% with female dominance. Clinical evidence has shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted by person-to-person [1] . Furthermore, SARS-CoV-2 was detected in the tears of COVID-19 patient and can cause nasal infection via the nasolacrimal duct [17, 18] . performed the olfactory function test (OFT)of 60 SARS-CoV-2 positive patients and took 60 subjects from previous studies as a control group matching the age and gender of the patient's group [35] . Another investigation, using a self-reported questionnaire, analyzed the prevalence of smell and/or taste disorders in J o u r n a l P r e -p r o o f 8 OFT has been the mainstay for diagnosis of OD; however, the patients in most studies were untested by OFT. cache = ./cache/cord-349912-em1abdrg.txt txt = ./txt/cord-349912-em1abdrg.txt === reduce.pl bib === id = cord-350094-nkzbtcfw author = Barrett, Lisa F. title = Self-Limited Gastrointestinal Bleeding in COVID-19 date = 2020-07-15 pages = extension = .txt mime = text/plain words = 649 sentences = 52 flesch = 53 summary = Clinicians should be aware of a possible increased risk of GI bleeding and its complications when managing critically ill COVID-19 patients. SARS-CoV-2, a single-stranded RNA virus of the beta coronavirus genus, enters the body via the angiotensin converting enzyme 2 (ACE2) receptor [2] [3] . ACE2 is expressed in gastrointestinal (GI) epithelial cells suggesting that SARS-CoV-2 can infect and replicate in the GI tract [4] . We present a case series of six patients, most without a known source of GI bleeding, who tested positive for SARS-CoV-2 and concurrently suffered from hematochezia or melena. We recorded cases of SARS-CoV-2 infection and concurrent GI bleeding from March 1, 2020 to April 24, 2020. Coagulopathy is associated with SARS-CoV-2 infection. Given the possible increased risk of bleeding in COVID-19, therapeutic anticoagulation in infected patients should be used cautiously. This case series shows a possible increased risk of bleeding among patients with COVID-19. cache = ./cache/cord-350094-nkzbtcfw.txt txt = ./txt/cord-350094-nkzbtcfw.txt === reduce.pl bib === id = cord-349907-dwhyx97y author = Noh, Ji Yeong title = Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date = 2017-02-20 pages = extension = .txt mime = text/plain words = 3274 sentences = 138 flesch = 62 summary = Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] . cache = ./cache/cord-349907-dwhyx97y.txt txt = ./txt/cord-349907-dwhyx97y.txt === reduce.pl bib === id = cord-349821-5ykwwq75 author = Ippolito, G. title = Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date = 2006-09-09 pages = extension = .txt mime = text/plain words = 6497 sentences = 257 flesch = 35 summary = The term 'highly infectious diseases' describes infections caused by pathogens that are transmissible from person to person, cause severe or life-threatening illness; present a serious hazard in healthcare settings and in the community; and require specific control measures, which may include management of cases in a highly secure isolation unit. In Canada, where SARS 'paralysed the Greater Toronto Area healthcare system for weeks' [27] , and the Toronto public health department investigated 2132 potential cases of SARS, identified over 23,000 contacts as requiring quarantine and logged more than 316,000 calls on its SARS hotline [28] , a national review commission identified systemic deficiencies in response capacity, including 'inadequacies in institutional outbreak management protocols, infection control and infectious disease surveillance', and found that these deficiencies resulted at least in part from failure to implement lessons learned from earlier public health emergencies [22] . cache = ./cache/cord-349821-5ykwwq75.txt txt = ./txt/cord-349821-5ykwwq75.txt === reduce.pl bib === id = cord-349954-bozgrzvf author = Quintaliani, Giuseppe title = Exposure to novel coronavirus in patients on renal replacement therapy during the exponential phase of COVID-19 pandemic: survey of the Italian Society of Nephrology date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3454 sentences = 206 flesch = 50 summary = During the COVID-19 pandemic, among SARS-Cov-2 positive RRT patients the fatality rate was 32.8%, as compared to 13.3% observed in the Italian population as of April 23rd. CONCLUSIONS: A substantial proportion of the 60,441 surveyed RRT patients in Italy were SARS-Cov-2 positive and subsequently died during the exponential phase of COVID-19 pandemic. The urgent need for a better understanding of the epidemic in RRT patients was immediately evident, and therefore we designed a survey of the Nephrology centers in Italy, aimed to capture the main features, impact and geographical distribution of SARS-CoV-2 spread in over 60,000 prevalent RRT patients during the exponential phase of the COVID-19 pandemic in Italy. The Italian Society of Nephrology COVID-19 survey confirms and extends previous preliminary observations suggesting that RRT patients, especially those on HD, are at increased risk of developing severe SARS-Cov-2 infections. cache = ./cache/cord-349954-bozgrzvf.txt txt = ./txt/cord-349954-bozgrzvf.txt === reduce.pl bib === id = cord-349745-zlhu1jit author = Konrad, Regina title = Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date = 2020-03-05 pages = extension = .txt mime = text/plain words = 2417 sentences = 137 flesch = 55 summary = The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2 ), which complicated the evaluation of the qPCR result. The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. cache = ./cache/cord-349745-zlhu1jit.txt txt = ./txt/cord-349745-zlhu1jit.txt === reduce.pl bib === id = cord-350045-85jug39x author = Pruc, Michal title = Risk of coronavirus infections among medical personnel date = 2020-05-08 pages = extension = .txt mime = text/plain words = 632 sentences = 40 flesch = 65 summary = Due to the current situation of the COVID-19 pandemic, we can predict how the morbidity of health care workers will develop based on data on other viruses from the coronavirus group. In global research on SARS-CoV-1, MERS-CoV and SARS-CoV-2, it can be seen that a very large percentage of the number of infected people are health professionals struggling with them in various medical facilities. In the Netherlands a survey was conducted from 6-8 March 2020 on 1097 health care workers, among whom the percentage of infected was 4.1%. 4 Currently, the total number of infected healthcare workers on SARS-CoV-2 is unknown due to the steadily increasing number of infections and the lack of global data on the problem. The data on SARS-CoV-1 and MERS-CoV can predict how much health care workers may be infected despite the lack of up-to-date data on SARS-CoV-2. Risks to healthcare workers with emerging diseases: lessons from MERS-CoV, Ebola, SARS, and avian flu cache = ./cache/cord-350045-85jug39x.txt txt = ./txt/cord-350045-85jug39x.txt === reduce.pl bib === id = cord-350015-mg5wiihj author = Chen, Yiyin title = Aging in COVID-19: Vulnerability, immunity and intervention date = 2020-10-31 pages = extension = .txt mime = text/plain words = 7489 sentences = 407 flesch = 47 summary = The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic was first reported in Wuhan, China in December 2019, moved across the globe at an unprecedented speed, and has caused a profound and yet still unfolding health and socioeconomic impacts. We hypothesize that age-related decline and dysregulation of immune function, i.e., immunosenescence and inflammaging play a major role in contributing to heightened vulnerability to severe COVID-19 outcomes in older adults. Therefore, age-associated reduction in type 1 IFN response coupled with direct viral suppression could serve as a critical innate immune mechanism that leads to poor cell mediated immunity and increased vulnerability of older adults against SARS-CoV-2 infection with therapeutic implication (Sallard et al., 2020) . On the other hand, children with COVID-19 manifested lower levels of T cell activation than adult COVID-19 patients (Moratto et al., 2020) , suggesting better immune system control and regulation in response to SARS-CoV-2 infection in children. cache = ./cache/cord-350015-mg5wiihj.txt txt = ./txt/cord-350015-mg5wiihj.txt === reduce.pl bib === id = cord-350352-wgppovfx author = Temmam, Sarah title = Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus date = 2020-08-29 pages = extension = .txt mime = text/plain words = 2470 sentences = 125 flesch = 54 summary = In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others (n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc.) compatible with COVID-19 infection. We investigated the presence of SARS-CoV-2 infection of domestic cats (n = 9) and dogs (n = 12) living in close contact with a cluster of French veterinary students, their owners (n = 18), whose median age was 23 years (21-28 years). Although based on a small cluster of 21 domestic pets, our cross-sectional study based on the antibody response one month after exposure to the index case points to J o u r n a l P r e -p r o o f Journal Pre-proof undetectable interspecific transmission of the SARS-CoV-2 virus between COVID-19 patients and domestic dogs or cats under natural exposure conditions. cache = ./cache/cord-350352-wgppovfx.txt txt = ./txt/cord-350352-wgppovfx.txt === reduce.pl bib === id = cord-350103-liwvhuzj author = Brooks, Nathan A. title = The role of the urologist, BCG vaccine administration, and SARS‐CoV‐2: An overview date = 2020-06-22 pages = extension = .txt mime = text/plain words = 2850 sentences = 144 flesch = 39 summary = OBJECTIVES: To summarize the available literature regarding bacillus Calmette‐Guerin (BCG) administration, severe acute respiratory syndrome conoravirus‐2 (SARS‐CoV‐2), and the resulting clinical condition coronavirus disease (COVID‐19) in light of recent epidemiologic work suggesting decreased infection severity in BCG immunized populations while highlighting the potential role of the urologist in clinical trials and ongoing research efforts. Specifically, the epidemiologic evidence for decreased COVID‐19 morbidity in countries with BCG vaccination programs, current clinical trials for BCG vaccination to protect against COVID‐19, potential mechanisms and rationale for this protection, and the role of the urologist and urology clinic in providing support and/or leading ongoing efforts. 18 In both animal and human studies, BCG vaccination provides a non-specific benefit to the immune system, relative protection against, and reduced mortality from infections by other microbes (bacteria and viruses) which may occur by epigenetic reprogramming and induction of trained immunity. cache = ./cache/cord-350103-liwvhuzj.txt txt = ./txt/cord-350103-liwvhuzj.txt === reduce.pl bib === id = cord-350235-yoy3hj3j author = Sansonetti, Philippe J title = COVID‐19, chronicle of an expected pandemic date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2988 sentences = 152 flesch = 56 summary = Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. cache = ./cache/cord-350235-yoy3hj3j.txt txt = ./txt/cord-350235-yoy3hj3j.txt === reduce.pl bib === id = cord-350130-c4u0gxp5 author = Wu, Yi-Chi title = The outbreak of COVID-19: An overview date = 2020-02-12 pages = extension = .txt mime = text/plain words = 3325 sentences = 228 flesch = 57 summary = In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus#, emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The 2019-nCoV, SARS-CoV, and bat SARS-like CoV belong to Abstract: In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus # , emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The virus has a preferential tropism to human airway epithelial cells and the cellular receptor, The first confirmed nCoV case in Wuhan (no Huanan seafood market exposure) December 10 cache = ./cache/cord-350130-c4u0gxp5.txt txt = ./txt/cord-350130-c4u0gxp5.txt === reduce.pl bib === id = cord-350212-448mv4lt author = Chiuppesi, Flavia title = Development of a Multi-Antigenic SARS-CoV-2 Vaccine Using a Synthetic Poxvirus Platform date = 2020-07-17 pages = extension = .txt mime = text/plain words = 7728 sentences = 446 flesch = 52 summary = We demonstrate that these sMVA vectors stimulate robust SARS-CoV-2 antigen-speci c humoral and cellular immunity in mice, including potent NAb. These results emphasize the value of a novel vaccine platform based on synthetic DNA to e ciently produce recombinant poxvirus vectors and warrant further pre-clinical and clinical testing of a multiantigenic sMVA vaccine candidate to control the ongoing SARS-CoV-2 pandemic and its devastating consequences. In response to the ongoing global SARS-CoV-2 pandemic, we used this novel vaccine platform to rapidly produce sMVA vectors co-expressing SARS-CoV-2 S and N antigens and show that these vectors can induce potent SARS-CoV-2 antigen-speci c humoral and cellular immune responses in mice, including potent NAb. These results highlight the feasibility to e ciently produce recombinant MVA vectors from chemically synthesized DNA and to rapidly develop a synthetic poxvirusbased vaccine candidate to prevent SARS-CoV-2 infection. cache = ./cache/cord-350212-448mv4lt.txt txt = ./txt/cord-350212-448mv4lt.txt === reduce.pl bib === id = cord-349656-baoqgu8v author = Wang, Chen title = Intrauterine vertical transmission of SARS‐CoV‐2: what we know so far date = 2020-04-07 pages = extension = .txt mime = text/plain words = 735 sentences = 62 flesch = 68 summary = [2] In a study by Chen et al., [3] paired neonatal pharyngeal swab samples and placental tissues of three pregnant women with COVID-19 were used as samples to evaluate the potential risk of intrauterine vertical transmission, and all samples tested negative for SARS-CoV-2 RNA. Notably, a neonate born to a pregnant woman with COVID-19 tested positive for SARS-CoV-2 RNA in the pharyngeal swab sample at 36 hours after birth was subsequently confirmed that the qRT-PCR testing of the placenta and cord blood was negative for SARS-CoV-2, suggesting that intrauterine vertical transmission might not have occurred. Furthermore, in a cohort study by Zeng et al., [13] 3 of 33 (9%) infants were diagnosed with neonatal early-onset infection with SARS-CoV-2 based on positive qRT-PCR results of the nasopharyngeal and anal swabs in two consecutive tests at day 2 and 4 of age. Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn. cache = ./cache/cord-349656-baoqgu8v.txt txt = ./txt/cord-349656-baoqgu8v.txt === reduce.pl bib === id = cord-350393-j80k2v21 author = Chen, Liping title = Clinical characteristics in patients with SARS‐CoV‐2/HBV co‐infection date = 2020-07-15 pages = extension = .txt mime = text/plain words = 1502 sentences = 78 flesch = 47 summary = In our previous study 7 (138 cases), there were only 9 (6.1%) cases (too small) with underlying liver diseases, so no further analysis was made Accepted Article over the clinical features of COVID-19 patients with HBV infection. In this retrospective study, we expanded the sample size and aimed to evaluate the influence of SARS-CoV-2/HBV co-infection on the clinical characteristics including liver function and disease outcome. Taken into consideration that viral co-infection can exacerbate liver injury thus have a big impact on disease progression and outcome 11, 12 , we investigated the prevalence of HBV infection in COVID-19 patients and found that there was a comparable rate of SARS-CoV-2/HBV co-infection to that of general population (6.1% vs 6%). Taken together, our study is the first to elaborate on the clinical characteristics of SARS-CoV-2/HBV co-infection patients and demonstrate that the coinfection with HBV slightly affect liver function, showing no impact on the COVID-19 outcome. cache = ./cache/cord-350393-j80k2v21.txt txt = ./txt/cord-350393-j80k2v21.txt === reduce.pl bib === id = cord-350211-vuxs5wtt author = Johanna, Barón‐Sánchez title = Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date = 2020-07-28 pages = extension = .txt mime = text/plain words = 4028 sentences = 355 flesch = 58 summary = Sin embargo, algunos autores sugieren que el virus puede infectar el sistema nervioso central (SNC), 17 donde el nivel de expresión de ECA2 es muy bajo, [18] [19] [20] [21] así, aunque la etiopatogenia de la anosmia por el virus SARS-CoV-2 no está todavía clara, esta podría estar medida por una infección directa la mucosa olfatoria, provocando destrucción de las neuronas sensoriales olfativas, por lo que la recuperación sería mas lenta y habría mayor probabilidad de que la perdida olfatoria permaneciera por mas tiempo, pudiendo incluso quedar un déficit permanente residual, 15 o por una afectación directa del lóbulo frontal como se ha reportado recientemente. cache = ./cache/cord-350211-vuxs5wtt.txt txt = ./txt/cord-350211-vuxs5wtt.txt === reduce.pl bib === id = cord-349623-dw5o9i59 author = Miranda, José P. title = Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3813 sentences = 174 flesch = 48 summary = Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise's buffer pH 7.2. For the standard protocol, routinely used in the laboratory for the detection of SARS-CoV-2, an aliquot of 180 ul of the sample from the nasopharyngeal swab, including 10 ul of extraction control, was used to extract RNA with the MagNA Pure 96 DNA and Viral NA LV Kit (Roche Diagnostics, Cat. No. For the standardization of the direct SARS-CoV-2 detection protocol without RNA extraction steps, 50 ul aliquots from the primary sample (nasopharyngeal swabs) of 5 anonymized patients were subjected to heat shock (65, 70, or 95 • C) during different incubation times (5, 10, or 30 min), and then were quickly placed at 4 • C until the moment of amplification. cache = ./cache/cord-349623-dw5o9i59.txt txt = ./txt/cord-349623-dw5o9i59.txt === reduce.pl bib === id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 pages = extension = .txt mime = text/plain words = 15827 sentences = 874 flesch = 56 summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . cache = ./cache/cord-350286-n7ylgqfu.txt txt = ./txt/cord-350286-n7ylgqfu.txt === reduce.pl bib === id = cord-350104-b99y6n43 author = de Zwart, Onno title = Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey date = 2009-01-06 pages = extension = .txt mime = text/plain words = 5379 sentences = 255 flesch = 52 summary = title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey PURPOSE: To study the levels of perceived threat, perceived severity, perceived vulnerability, response efficacy, and self-efficacy for severe acute respiratory syndrome (SARS) and eight other diseases in five European and three Asian countries. To explore if country differences were specific for SARS, perceived threat, risk perception, and efficacy beliefs related to avian influenza and other (infectious) diseases were also investigated. -To study levels of perceived threat, vulnerability (or risk perception), severity and comparative vulnerability for SARS in Denmark, The Netherlands, Poland, Spain, the UK, China, Hong Kong, and Singapore; -To compare perceived severity, vulnerability, and threat of SARS with other diseases and conditions, i.e., avian influenza, common cold, diabetes, HIV, high blood pressure, tuberculosis, food poisoning, and a heart attack; -To study differences and associations between these factors across the eight countries and between Europe and Asia. cache = ./cache/cord-350104-b99y6n43.txt txt = ./txt/cord-350104-b99y6n43.txt === reduce.pl bib === id = cord-350182-s10nong7 author = Milionis, Charalampos title = A brief analysis and hypotheses about the risk of COVID-19 for people with type 1 and type 2 diabetes mellitus date = 2020-07-20 pages = extension = .txt mime = text/plain words = 2733 sentences = 164 flesch = 42 summary = Coronavirus disease 2019 (COVID-19) is a respiratory infection which is caused by a novel virus belonging to the Coronaviridae family [1] and is officially named SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The existence of diabetes is strongly associated with an increased risk of developing severe COVID-19 in case of infection with SARS-CoV-2 [24, 25] . The present article supports that heightened inflammatory processes constitute the main pathophysiologic factor for the severity of COVID-19 among patients with diabetes mellitus, whilst impairments in immune response and diabetic comorbidities contribute to the aggravated pathogenesis. Yet it remains unclear whether the innate immune response is vitally impaired in both types of diabetes mellitus and whether hyperglycaemia favours the initial virulence of SARS-CoV-2. Furthermore, patients with diabetes mellitus may present dysfunctional type IV (delayed) hypersensitivity reaction and abnormal complement activation [35] which may hinder the immune response. Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? cache = ./cache/cord-350182-s10nong7.txt txt = ./txt/cord-350182-s10nong7.txt === reduce.pl bib === id = cord-350172-w3yoxhsg author = Mertens, Pascal title = Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date = 2020-05-08 pages = extension = .txt mime = text/plain words = 7563 sentences = 336 flesch = 47 summary = Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. Regarding the COVID-19 pandemic and the urgency of sharing relevant data, in this original research article we describe the analytical performance of the COVID-19 Ag Respi-Strip according to the requirements of the current European Directive 98/79/EC (9) , the future European Regulation 2017/746 on in vitro diagnostic (IVD) medical devices (10) , the Scandinavian SKUP-protocol (11) used for the validation of qualitative tests and the clinical performance obtained with a multi-centric retrospective study. Overall, 328 nasopharyngeal samples from symptomatic patients suspected of SARS-CoV-2 infections attending from 19th to 30th March 2020 in three university laboratories located in Belgium were tested following the manufacturer's instructions to assess the clinical sensitivity, clinical specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy in order to propose a diagnostic algorithm adapted to the current situation. cache = ./cache/cord-350172-w3yoxhsg.txt txt = ./txt/cord-350172-w3yoxhsg.txt === reduce.pl bib === id = cord-349762-f5no10eq author = Nagura-Ikeda, Mayu title = Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date = 2020-08-24 pages = extension = .txt mime = text/plain words = 4270 sentences = 233 flesch = 54 summary = The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). Here, we describe the clinical performance of various molecular diagnostic methods, including the RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, 3 direct RT-qPCR kits, and RT-LAMP, and a commercial SARS-CoV-2 RAT used on self-collected saliva specimens in diagnosing COVID-19. The RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed different sensitivities for detecting viral RNA in saliva specimens, but each can be selectively used according to the clinical setting and facilities if close attention is paid to any false-negative results. cache = ./cache/cord-349762-f5no10eq.txt txt = ./txt/cord-349762-f5no10eq.txt === reduce.pl bib === id = cord-350134-gl3qtoug author = Brun, Gilles title = COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1006 sentences = 76 flesch = 44 summary = title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? Since December 2019, a novel coronavirus, also called severe acute respiratory syndrome CoV-2 (SARS-CoV-2), emerged in Wuhan, China, and caused a pandemic disease . Herein, we report a case of SARS-CoV-2 brain lesions suggesting an acute demyelination. At day 7, a brain MRI revealed lesions with restricted diffusion without any hemorrhage or enhancement after gadolinium injection (figure). 4 In our case, the distribution of bilateral but asymmetrical lesions with periventricular and deep white matter involvement is rather suggestive of an acute demyelination. Although mechanisms remain obscure, our case shows the importance of the MRI in the exploration of neurologic symptoms in COVID-19. Demyelination or small-vessel CNS vasculitis might be a rare but silent complication of sedated patients with COVID-19. COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection cache = ./cache/cord-350134-gl3qtoug.txt txt = ./txt/cord-350134-gl3qtoug.txt === reduce.pl bib === id = cord-350513-ho32ajsx author = Chen, Paul Chih‐Hsueh title = Re: To KF, Tong JH, Chan PK, et al. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. J Pathol 2004; 202: 157–163 date = 2004-05-07 pages = extension = .txt mime = text/plain words = 1099 sentences = 63 flesch = 49 summary = Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. Using in situ hybridization (ISH), To et al demonstrated the presence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in pneumocytes and in the surface enterocytes of the small intestine. Supplementing their findings, we report here our recent study, which suggests that the SARS-CoV may not be exclusively located in pneumocytes, but also in pulmonary macrophages. Under low magnification, scattered cells containing dark bluish signals, which represented the SARS-CoV, were visualized ( Figure 1A , nuclear fast red counterstain) within the damaged alveolar spaces, small bronchioles, and even the vascular lumina. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Chen and Hsiao make an interesting observation on the pathology of severe acute respiratory syndrome (SARS). cache = ./cache/cord-350513-ho32ajsx.txt txt = ./txt/cord-350513-ho32ajsx.txt === reduce.pl bib === id = cord-350189-2su7oqbz author = Elmén, Joacim title = Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date = 2005-01-14 pages = extension = .txt mime = text/plain words = 5415 sentences = 322 flesch = 55 summary = A priori, this suggests that LNA may be used to increase the functional half-life of siRNA in vivo by two different mechanisms, e.g. by enhancing the resistance of the constituent RNA strands against degradation by single-stranded RNases and by stabilizing the siRNA duplex structure that is critical for activity. Next, we examined the effect of making single RNA to LNA exchanges at base-paired positions in the antisense strand of the firefly luciferase siLNA1. Although we cannot exclude that these modifications somehow prevent loading of the antisense strand into RISC, we believe this to be unlikely given the functionality of many significantly more modified siLNAs. Rather, as these positions are all close to the site where RNA target cleavage occurs [between pos. The SARS siRNA (Table 1) has identical closing base-pairs at both ends (A:U) making it likely that enough of both the antisense and sense strand would be incorporated into RISC to observe activity on the respective targets. cache = ./cache/cord-350189-2su7oqbz.txt txt = ./txt/cord-350189-2su7oqbz.txt === reduce.pl bib === id = cord-349477-3qhpu7v0 author = Jarynowski, A. title = An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland date = 2020-10-15 pages = extension = .txt mime = text/plain words = 7012 sentences = 438 flesch = 51 summary = Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. Demographic (like age, mobility, migration etc.), social ("income","PiS_support") and COVID-related factors (population size,forest_density,population_density,arrival_SARS) are the ground for our proposal of proper sanitary staff allocation. The aim of this paper is an exploratory and preliminary quantitative evaluation of the geographical spread on the level of county/poviat (NUTS-4) of SARS-CoV-2 virus (and COVID-19 disease caused by it) in Poland during the Spring wave of infections. The main statistical approach is calculating multiple regressions with Akaike selection criteria on the SARS-CoV-2 arrival time to each poviat and the number of COVID-19 cases based on socio-economic variables. cache = ./cache/cord-349477-3qhpu7v0.txt txt = ./txt/cord-349477-3qhpu7v0.txt === reduce.pl bib === id = cord-350328-wu1ygt6w author = Tambyah, P. A. title = SARS: responding to an unknown virus date = 2004-07-14 pages = extension = .txt mime = text/plain words = 4855 sentences = 221 flesch = 53 summary = The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. The severe acute respiratory syndrome (SARS) is a newly recognized coronavirus infection that emerged in southern China [1] with subsequent global spread to 29 countries [2] [3] [4] [5] . The newly infected individuals traveled onward to their homes or next destinations in the USA, Canada, Singapore, Hong Kong and Ireland sparking off epidemics of varying degrees of severity in each of those countries, mainly in hospitals but also in their respective communities. A directive had gone out from the Hong Kong Department of Health on 21 February 2003 to maintain strict infection control with droplet precautions for all cases of "atypical" community-acquired pneumonia because of concerns that highly pathogenic avian influenza might be easily transmissible from person to person. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-350328-wu1ygt6w.txt txt = ./txt/cord-350328-wu1ygt6w.txt === reduce.pl bib === id = cord-350242-4u1iyf0p author = Yaniv, K. title = City-level SARS-CoV-2 sewage surveillance date = 2020-10-21 pages = extension = .txt mime = text/plain words = 2017 sentences = 140 flesch = 61 summary = In this study we sampled an urban wastewater infrastructure in the city of Ashkelon, Israel, during the end of the first COVID-19 wave in May 2020 when the number of infections seemed to be waning. Using the linear equation, we calculated copy number of N1 gene in sewage samples reported in this study. If the sampling is extended to 24 hours, then the NVL can be expressed as number of SARS-CoV-2 RNA copies per 1,000 people per day. Ashkelon was chosen for surveillance of SARS-CoV-2 in sewage due to a relatively low COVID-19 prevalence during the time of study following a national lockdown period during Table S1 ). In conclusion, we present a proof-of-concept study demonstrating the feasibility of SARS-CoV-2 RNA detection in raw sewage originating from the city sewer system that reflects virus circulation in the assessed area. cache = ./cache/cord-350242-4u1iyf0p.txt txt = ./txt/cord-350242-4u1iyf0p.txt === reduce.pl bib === id = cord-350342-j4p8235a author = Brocato, Rebecca L. title = Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date = 2020-10-27 pages = extension = .txt mime = text/plain words = 5265 sentences = 283 flesch = 49 summary = All of the SARS-CoV-2-challenged hamsters had detectable viral RNA in pharyngeal swabs at the first time point assayed, 3 dpi, and remained consistent (10 3 to 10 5 molecules of nucleocapsid using a second primer set [N2] per 100 ng RNA) throughout the duration of CyP treatment (Fig. 1C) . Viral RNA and infectious virus were detected in lung tissue from a subset of hamsters collected 13 dpi, on the day of euthanasia of moribund animals (14 to 34 dpi), or after euthanasia at 35 dpi (end of study) ( Fig. 1E and F). Electron microscopy studies were performed on lung sections of SARS-CoV-2infected, CyP-treated hamsters with various lung viral loads (Fig. 1) . Similarly, lung tissue collected at 13 dpi (end of study) indicate comparable levels of viral RNA detected (Fig. 6D ) but significantly reduced infectious virus in Centi-F1 MAb-treated animals (P ϭ 0.0002; unpaired t test) (Fig. 6E) . cache = ./cache/cord-350342-j4p8235a.txt txt = ./txt/cord-350342-j4p8235a.txt === reduce.pl bib === id = cord-350557-7i7122zi author = Rawlings, Stephen A title = No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1750 sentences = 115 flesch = 57 summary = We evaluated the presence and level of SARS-CoV-2 RNA in semen, nasal secretion, and saliva collected after confirmed infection. SARS-CoV-2 RNA was not detected in semen 6–17 days after the onset of symptoms despite concomitant shedding in oral secretions. Here, we evaluated the presence and level of SARS-CoV-2 in paired semen, nasal secretion, and saliva samples collected in the short and medium term after confirmed SARS-CoV-2 symptomatic infections. Before enrollment, 5/6 participants tested positive for SARS-CoV-2 RNA on NP swab samples collected within 1-3 days following the onset of symptoms. Upon enrollment in the study, the diagnosis of active SARS-CoV-2 infection was confirmed by positive PCR on NP swab on day 6 post-symptom onset. We found no evidence of SARS-CoV-2 in semen collected 6-17 days after the onset of symptoms despite all men having concomitant shedding of virus in oral secretions up to 792 copies/µL. cache = ./cache/cord-350557-7i7122zi.txt txt = ./txt/cord-350557-7i7122zi.txt === reduce.pl bib === id = cord-350095-hsl1hfds author = Shiu, Stephen Y. W. title = Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? date = 2003-06-16 pages = extension = .txt mime = text/plain words = 1326 sentences = 66 flesch = 40 summary = title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? Since the end of February of this year, global health is being threatened by the emergence of a new infectious disease, severe acute respiratory syndrome (SARS), caused by a novel coronavirus [1] [2] [3] . However, the most immediate concerns to the health authorities of Hong Kong and mainland China are to contain the spread of the disease and to reduce the mortality of those SARS patients who succumb to acute respiratory failure. While health officials are working hard to contain the spread of the disease in the hard-hit places such as China, Hong Kong [4] , Singapore and Canada [5] , clinicians are racing against time to find effective drugs to rescue SARS patients from serious illness and death. cache = ./cache/cord-350095-hsl1hfds.txt txt = ./txt/cord-350095-hsl1hfds.txt === reduce.pl bib === id = cord-350627-4pgish5x author = Zhao, Yu title = Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date = 2020-01-26 pages = extension = .txt mime = text/plain words = 1865 sentences = 129 flesch = 56 summary = Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. These studies showed that in normal human lung, ACE2 is mainly expressed by type II and type I alveolar epithelial cells. In total, we analyzed 43,134 cells derived from normal lung tissue of To further understand the special population of ACE2-expressing AT2, we performed gene ontology enrichment analysis to study which biological processes are involved with this cell population by comparing them with the AT2 cells not expressing ACE2. Of note, the 2 male donors have a higher ACE2-expressing cell ratio than all other 6 female author/funder. We also noticed that the only Asian donor (male) has a much higher ACE2Altogether, in the current study, we report the RNA expression profile of ACE2 in the human lung at single-cell resolution. https://doi.org/10.1101/2020.01.26.919985 doi: bioRxiv preprint author/funder. cache = ./cache/cord-350627-4pgish5x.txt txt = ./txt/cord-350627-4pgish5x.txt === reduce.pl bib === id = cord-350029-1y5ex4d5 author = McDade, Thomas W. title = Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date = 2020-08-09 pages = extension = .txt mime = text/plain words = 2690 sentences = 129 flesch = 43 summary = Serological testing is a complementary approach that detects the presence of antibodies against SARS-CoV-2 in blood samples from exposed individuals (World Health Organization, 2020). If sufficient time has passed since the initial infection, the presence of IgM antibodies against SARS-CoV-2 antigens can be used to confirm a clinical case of COVID-19. In developing a low-cost ELISA for SARS-CoV-2 antibodies, our hope is that others can draw on the longstanding tradition of methodological innovation in human biology to promote community-based research on COVID-19. Human biologists are also well-positioned to consider a life course perspective on variation in outcomes in response to SARS-CoV-2 infection. Human biologists are uniquely positioned to make important contributions to our understanding of COVID-19, and methods that facilitate research in community-based settings globally will be central to that effort. Enzyme immunoassay for SARS-CoV-2 antibodies in dried blood spot samples: A minimally-invasive approach to facilitate community-and population-based screening cache = ./cache/cord-350029-1y5ex4d5.txt txt = ./txt/cord-350029-1y5ex4d5.txt === reduce.pl bib === id = cord-350451-lf27iuwk author = Benedetti, Francesca title = SARS‐CoV‐2: March toward adaptation date = 2020-07-11 pages = extension = .txt mime = text/plain words = 1212 sentences = 79 flesch = 44 summary = A third factor still subject of debate is how and how much the mutations observed in SARS-CoV-2 provide an indication of viral fitness and adaptation, and their role first into the initial phases of transmission and now during the reduction of viral spreading. The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel human pathogen, first detected in China quickly became a global health emergency, culminating with the World Health Organization publicly proclaiming the SARS-CoV-2 outbreak as a pandemic (11 March 2020) . Several reports result show that SARS-CoV-2 is rapidly moving across countries, and new mutation hotspots are emerging in different parts of the genome. Although SARS-CoV-2 is less lethal than MERS-CoV, up to 20% of the infected people develop rapidly a severe disease characterized by interstitial pneumonia and acute respiratory distress syndrome that can ultimately lead to death. Davide Zella http://orcid.org/0000-0001-5576-5770 Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant cache = ./cache/cord-350451-lf27iuwk.txt txt = ./txt/cord-350451-lf27iuwk.txt === reduce.pl bib === id = cord-350437-dq1il88y author = Reale, Maria Lucia title = SARS-CoV-2 Infection in Cancer Patients: A Picture of an Italian Onco-Covid Unit date = 2020-08-19 pages = extension = .txt mime = text/plain words = 4177 sentences = 216 flesch = 47 summary = This retrospective study aims to collect epidemiological, clinical, laboratory, and therapeutic data from SARS-CoV-2 positive cancer patients hospitalized at the Onco-Covid unit in San Luigi Gonzaga Hospital, Italy, one of the few oncological wards for cancer patients with SARS-Cov-2 infection, in order to provide a deeper insight into the clinical evolution of infection in cancer patients, particularly in lung cancer patients. This retrospective study included all SARS-CoV-2 oncological patients accepted at the Onco-Covid Unit at San Luigi Gonzaga Hospital, Orbassano, between March 27th and April 19th 2020. The mean length of hospitalization at data cut-off was 30 days ±14 (0-53), while it resulted 16 ± 9 days (0-37) when calculated from COVID 19 positivity (characteristics and outcomes of individual patients included in the analysis are reported in Supplementary Table 2) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China cache = ./cache/cord-350437-dq1il88y.txt txt = ./txt/cord-350437-dq1il88y.txt === reduce.pl bib === id = cord-350401-suefuurq author = Lima-Setta, Fernanda title = Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() date = 2020-11-09 pages = extension = .txt mime = text/plain words = 3943 sentences = 215 flesch = 52 summary = title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() From March 25 to August 23, 2020, pediatric patients (age range: 1 month -19 years) were consecutively included if they met the CDC case definition[8] for MIS-C: 1) fever > 38.0°C for ≥ 24 hours (objective or subjective); 2) laboratory evidence of inflammation, including, but not limited to, one or more of the following: high values of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), fibrinogen, procalcitonin, d-dimer, ferritin, lactic acid dehydrogenase (LDH), or interleukin 6 (IL-6); elevated neutrophils, reduced lymphocytes, and low albumin; 3) no alternative plausible diagnosis; 4) current or recent SARS-CoV-2 infection diagnosed by a positive reverse transcription polymerase chain reaction (RT-PCR) or positive serological tests (IgM, IgG or IgA), or exposure to a suspected or confirmed COVID-19 case within the four weeks prior to the onset of symptoms. cache = ./cache/cord-350401-suefuurq.txt txt = ./txt/cord-350401-suefuurq.txt === reduce.pl bib === id = cord-350817-tmszrtju author = Hoepel, Willianne title = Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date = 2020-07-13 pages = extension = .txt mime = text/plain words = 5626 sentences = 296 flesch = 47 summary = Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. Taken together, these data demonstrate that anti-Spike IgG immune complexes generated from serum of severely ill COVID-19 patients induce a strong pro-inflammatory response by (otherwise immunosuppressive) human M2 macrophages, which is characterized by high production of classical cytokine storm mediators such as IL-1β, IL-6, IL-8, and TNF. As shown in Figure 4A , the used human macrophage model highly expressed all FcγRs. To determine whether FcγRs are involved in activation by anti-Spike immune complexes, we blocked the different FcγRs with specific antibodies during stimulation, and analyzed cytokine production. In conclusion, our data show that anti-Spike IgG from serum of severely ill COVID-19 patients strongly amplifies pro-inflammatory responses by human macrophages, and can contribute to subsequent endothelial barrier disruption and thrombosis. cache = ./cache/cord-350817-tmszrtju.txt txt = ./txt/cord-350817-tmszrtju.txt === reduce.pl bib === id = cord-350101-t34myl7l author = Henrique Braz‐Silva, Paulo title = SARS‐CoV‐2: What can saliva tell us? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 887 sentences = 47 flesch = 46 summary = The World Health Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. In addition to the diagnosis itself, the study of saliva in cases of COVID-19 will help understanding its pathogenesis, since it has been recently reported that epithelial cells of the oral cavity showed abundant expression of the angiotensin-converting enzyme II (ACE2), a receptor playing a key role in the entry of SARS-CoV-2 into the cells (Xu et al., 2020) . Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: A diagnostic validity study cache = ./cache/cord-350101-t34myl7l.txt txt = ./txt/cord-350101-t34myl7l.txt === reduce.pl bib === id = cord-350733-0zghspb8 author = Aronson, Jeffrey K. title = The use of mechanistic reasoning in assessing coronavirus interventions date = 2020-07-15 pages = extension = .txt mime = text/plain words = 4461 sentences = 265 flesch = 42 summary = RATIONALE: Evidence‐based medicine (EBM), the dominant approach to assessing the effectiveness of clinical and public health interventions, focuses on the results of association studies. That treatment for hypertension is a risk factor for severe disease in the case of SARS-CoV-2 suggests that altering hypertension treatment might alleviate disease, but the mechanisms are complex, and it is essential to consider and evaluate more than one mechanistic hypothesis (Section 3). This strategy makes much use of evidence from mechanistic studies: evidence that the drug has some action against the novel virus in the laboratory, both in vitro and in vivo in experimental animals, is used to justify the decision to use the treatment clinically. Some evidence, for instance, supports a behavioural mechanism known as the "intention-behaviour gap," 53 In sum, the explicit and systematic assessment of mechanistic studies is essential for the development of effective vaccination programs in a given context. cache = ./cache/cord-350733-0zghspb8.txt txt = ./txt/cord-350733-0zghspb8.txt === reduce.pl bib === id = cord-349923-cja8i0hw author = Habibzadeh, Parham title = The Novel Coronavirus: A Bird's Eye View date = 2020-02-05 pages = extension = .txt mime = text/plain words = 2444 sentences = 143 flesch = 50 summary = C oronaviruses typically result in respiratory and enteric infections affecting both animals and humans, and were considered relatively benign to humans before the severe acute respiratory syndrome (SARS-CoV) outbreak in 2002 and 2003 in China. [1] [2] [3] [4] A decade later, Middle East respiratory syndrome coronavirus (MERS-CoV), another pathogenic coronavirus with a clinical picture reminiscent of SARS, was isolated in patients presenting with pneumonia in the Middle Eastern countries. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. cache = ./cache/cord-349923-cja8i0hw.txt txt = ./txt/cord-349923-cja8i0hw.txt === reduce.pl bib === id = cord-350679-69lv4wbz author = Shinde, Rajesh S. title = To Do or Not to Do?—A Review of Cancer Surgery Triage Guidelines in COVID-19 Pandemic date = 2020-05-11 pages = extension = .txt mime = text/plain words = 3474 sentences = 176 flesch = 44 summary = In the absence of actual data on cancer surgery care during this pandemic, clinical decisions should be based on careful consideration of disease-related and patient-related factors. As cancer surgeries involve significant healthcare resources in terms of infrastructure, intensive care unit beds, blood products and manpower, surgical oncologists face a dilemma regarding the triage of surgical patients during this period of uncertainty. A particular concern for a cancer surgeon is to weigh the risk of deferring cancer surgery versus the risk of COVID-19 exposure and infection to patients as well as health care providers. Smoking, one of the commonest risk factors in lung cancer, has not been independently shown to affect the mortality in SARS-CoV-2 patient; however, pre-existing chronic obstructive lung disease is associated with increased mortality [4] . Clinical management of lung cancer patients during the outbreak of 2019 novel coronavirus disease (COVID-19) cache = ./cache/cord-350679-69lv4wbz.txt txt = ./txt/cord-350679-69lv4wbz.txt === reduce.pl bib === id = cord-350686-q2bu7o4i author = Bilder, Christopher R title = Pool size selection when testing for SARS-CoV-2 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 539 sentences = 55 flesch = 71 summary = title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people cache = ./cache/cord-350686-q2bu7o4i.txt txt = ./txt/cord-350686-q2bu7o4i.txt === reduce.pl bib === id = cord-350737-nrtrhq1f author = Chen, Xinchun title = Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date = 2004-04-01 pages = extension = .txt mime = text/plain words = 3474 sentences = 133 flesch = 50 summary = A virus from the family Coronaviridae, termed "SARS coronavirus" (SARS CoV), has been identified as the cause [2] [3] [4] [5] [6] [7] , and criteria for laboratory confirmation of SARS CoV infection have been provided by WHO, on the basis of the following methods: (1) detection of SARS CoV RNA by reversetranscription polymerase chain reaction (RT-PCR); (2) serological detection of SARS CoV-related antibody; and (3) isolation of SARS CoV by cell culture [4] . Using an indirect immunofluorescence assay and parallel acute and convalescent serum samples obtained from patients with SARS, tested for IgG antibody to SARS CoV, Peiris et al. In addition, our results indicated that 9 (25.0%) of 36 patients with probable SARS CoV infection had not produced detectable anti-SARS CoV antibody by day 21 after the onset of fever; this implies that 25.0% of patients with SARS might be misdiagnosed by the laboratory confirmation guidelines that WHO currently recommends [5] . cache = ./cache/cord-350737-nrtrhq1f.txt txt = ./txt/cord-350737-nrtrhq1f.txt === reduce.pl bib === id = cord-350309-j4oh1z8m author = Liu, D. X. title = Coronavirus envelope protein: A small membrane protein with multiple functions date = 2007-05-29 pages = extension = .txt mime = text/plain words = 3403 sentences = 167 flesch = 48 summary = The E proteins from infectious bronchitis virus (IBV) and mouse hepatitis virus (MHV) are translated from the third and second ORFs of mRNA 3 and 5 of the respective viruses by a cap-independent, internal ribosomal entry mechanism [6] [7] [8] [9] [10] [11] [12] . This modification is unique to SARS-CoV E protein, and it is still unknown whether the modification can also be detected in virus-infected cells and in virions. However, the membrane topologies of SARS-CoV E protein in virions and in virusinfected cells are still unknown. Similar to other viroporins [46] , expression of SARS-CoV and MHV E protein enhanced the membrane permeability of bacterial and mammalian cells [47, 48] . These results indicate that the ion channel activity of coronavirus E protein is important for virus replication, especially in the case of some coronaviruses, such as MHV. Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells cache = ./cache/cord-350309-j4oh1z8m.txt txt = ./txt/cord-350309-j4oh1z8m.txt === reduce.pl bib === id = cord-350317-a9qd3xdr author = Xu, Qiannan title = If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 date = 2020-11-05 pages = extension = .txt mime = text/plain words = 700 sentences = 49 flesch = 58 summary = title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 The expression of ACE2 is associated with the potential risk of making the target tissue susceptible to infection by SARS-CoV-2. Elevated ACE2 expression and detection of SARS-CoV-2 in the skin 4 of COVID-19 patients implied skin was a potential host of SARS-CoV-2. After IL-17 antibody treatment, the skin ACE2 expression was downregulated which meant IL-17 antibody could lower the risk of COVID-19 through lessening the cells which could interact with SARS-CoV-2. Additionally, IL-17 antibody could reverse the deteriorated barrier and inflammatory status in the skin of psoriasis patient which meant less microbe infection.Herein, the specific microbe could be SARS-CoV-2. Thus, whether IL-17 antibody could reduce the COVID-19 risk through reversing the inflammatory skin status with deteriorated barrier and preventing SARS-CoV-2 transmitting should be further discussed. Skin is a potential host of SARS-CoV-2: a clinical, single-cell transcriptome-profiling and histological study cache = ./cache/cord-350317-a9qd3xdr.txt txt = ./txt/cord-350317-a9qd3xdr.txt === reduce.pl bib === id = cord-350505-uh8r2vyz author = Kalantar-Zadeh, Kourosh title = Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles date = 2020-05-01 pages = extension = .txt mime = text/plain words = 2343 sentences = 145 flesch = 38 summary = [Image: see text] The impact of dietary patterns and the commensal microbiome on susceptibility to and severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has been largely ignored to date. 2 Therefore, the elucidation of host cytokine molecular pathways and microbiota components 17 as well as bacterial reactions in association with cytokine responses may provide novel microbiome-based therapeutic approaches to SARS-CoV-2 infection. Considering the presented discussion, nutritional and dietary strategies directed at restoring the well-known beneficial microbiota, which can possibly suppress viral infection in the elderly and those with underlying health problems, may be an effective strategy to mitigate the harmful effects of this virus. One approach, as a whole and to be undertaken prior to any viral infection, could include strengthening the intestinal barrier against pathogens, increasing intestinal motility, and reducing an underlying pro-inflammatory state by adopting a Many different direct or indirect microbiome pathways could contribute to SARS-CoV-2-gut interactions. cache = ./cache/cord-350505-uh8r2vyz.txt txt = ./txt/cord-350505-uh8r2vyz.txt === reduce.pl bib === id = cord-350925-1h6pbfwp author = da Silva, Priscilla Gomes title = Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5221 sentences = 279 flesch = 49 summary = Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . cache = ./cache/cord-350925-1h6pbfwp.txt txt = ./txt/cord-350925-1h6pbfwp.txt === reduce.pl bib === id = cord-350753-qbm145tr author = Krüttgen, Alexander title = Determination of SARS-CoV-2 antibodies with assays from Diasorin, Roche and IDvet date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1826 sentences = 108 flesch = 49 summary = Using 75 sera from patients tested positive or negative by SARS-CoV-2 PCR, we investigated the sensitivity and specificity of the Liaison SARS-CoV-2 S1/S2 IgG assay (DiaSorin), the Elecsys Anti-SARS-CoV-2 assay (Roche), and the ID Screen SARS-CoV-2-N IgG indirect kit (IDVet). We and others have published results of the assessment of the first commercially available serological assays, such as the Anti SARS-CoV-2 ELISA (IgG) from Euroimmun (Krüttgen et al., 2020; Okba et al., 2020) . We therefore compared these three new assays with respect to their sensitivity and specificity to detect SARS-CoV-2 specific antibodies using a collection of serum samples employed previously for the analysis of four other assays. Our comparative approach to test in total seven different SARS-CoV-2 antibody assays with an identical collection of serum samples allowed for the first time the direct comparison of performance indicators of such a large number of automated assays. cache = ./cache/cord-350753-qbm145tr.txt txt = ./txt/cord-350753-qbm145tr.txt === reduce.pl bib === id = cord-350821-0qfoc553 author = Jahromi, Reza title = Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 1941 sentences = 113 flesch = 46 summary = title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 In this study, we present the effect of surfactants on coronavirus (SARS-CoV-2) virucidal efficiency in sanitizing fluids. Sodium dodecylbenzenesulfonate (SDBS), sodium laureth sulfate (SLS), and two commercial dish soap and liquid hand soap were studied with the goal of evaporation rate reduction in sanitizing liquids to maximize surface contact time. Twelve fluids with different recipes composed of ethanol, isopropanol, SDBS, SLS, glycerin, and water of standardized hardness (WSH) were tested for their evaporation time and virucidal efficiency. Twelve sanitizing fluids with different recipes, as shown in Table 1 , were prepared to examine the effect of individual components and mixtures on evaporation rate and SARS-CoV-2 virucidal efficiency of the solutions. Furthermore, the addition of 3% dish soap to the ethanol solution (S1) increased the evaporation time by about 63% from 24 to 39 s (of fluid S9), as shown in Figure 2 . cache = ./cache/cord-350821-0qfoc553.txt txt = ./txt/cord-350821-0qfoc553.txt === reduce.pl bib === id = cord-350959-bsbz3a1l author = Dovey, Zachary title = Impact of COVID-19 on Prostate Cancer Management: Guidelines for Urologists date = 2020-06-16 pages = extension = .txt mime = text/plain words = 5079 sentences = 241 flesch = 47 summary = There is also epidemiological evidence that PCa patients have increased incidence and mortality from SARS-CoV-2 infection due to gender differences, age, and higher propensity for risk factors (eg, respiratory disease, obesity, hypertension, and smoking status). Patient summary Prostate cancer patients can be followed up remotely until the severe acute respiratory syndrome coronavirus 2 pandemic resolves, but higher-risk cases may have treatment expedited to limit any negative impact on prostate cancer outcomes. As shown in Table 2 , PCa patients with either diabetes or hypertension should seek advice from their physicians to optimize their treatment, especially if this includes ACE inhibitors or ARBs [32] , to reduce their risk of SARS-CoV-2 infection and morbidity. Tewari Prostate cancer (PCa) patients may have an increased risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. cache = ./cache/cord-350959-bsbz3a1l.txt txt = ./txt/cord-350959-bsbz3a1l.txt === reduce.pl bib === id = cord-351169-y91fdf66 author = Phillips, Lia title = Successful management of SARS-CoV-2 acute respiratory distress syndrome and newly diagnosed acute lymphoblastic leukemia date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1732 sentences = 105 flesch = 37 summary = Corticosteroid can be given safely to patients with SARS-CoV-2 presenting with acute respiratory distress syndrome and ALL. Although recommendations are emerging for the general management of oncology patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 1,2 there is little experience in patients with newly diagnosed acute lymphoblastic leukemia (ALL). Providers may have concern about initiating multiagent chemotherapy in patients with SARS-CoV-2, particularly corticosteroids, which are an essential part of induction regimens, but raise the theoretical possibility of delayed viral clearance. We describe our experience of successfully initiating therapy for an adolescent diagnosed with ALL, while managing severe SARS-CoV-2 infection marked by respiratory failure, systemic inflammation, and autoimmune hemolytic anemia (AIHA). 1, 2 In this case, intensive remission induction chemotherapy was initially delayed due to concern for potential worsening of SARS-CoV-2 disease by exacerbating the patient's already immunocompromised state in the setting of ALL. cache = ./cache/cord-351169-y91fdf66.txt txt = ./txt/cord-351169-y91fdf66.txt === reduce.pl bib === id = cord-350618-rtilfnzi author = Lambelet, Valentine title = Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date = 2020-05-26 pages = extension = .txt mime = text/plain words = 7287 sentences = 452 flesch = 50 summary = College of Obstetricians and Gynaecologists (RCOG), pregnant women with moderate symptoms should self-isolate, unless they attend a maternity unit where patients in the 2 nd or 3 rd trimester meeting PHE criteria ( ≥ 1 of: (1) Clinical/radiological evidence of pneumonia, (2) Acute Respiratory Distress Syndrome (ARDS), (3) Fever ≥37.8 and at least one of acute persistent cough, hoarseness, nasal discharge/congestion, shortness of breath, sore throat, wheezing or sneezing) should be tested for COVID-19 and treated as infected until results are available. Past coronavirus epidemics were associated with adverse outcomes for the fetus and/or newborns including miscarriages (57%), preterm birth, fetal distress and FGR with SARS-CoV-1 infection during the 2 nd and 3 rd trimesters. In this review, we found that of 142 cases of SARS-CoV-2 infections in pregnancy, 28% experienced preterm birth and 14% had adverse fetal/neonata l outcomes (FGR, fetal/neonatal demise, severe symptoms at birth). cache = ./cache/cord-350618-rtilfnzi.txt txt = ./txt/cord-350618-rtilfnzi.txt === reduce.pl bib === id = cord-350972-0n4dumgg author = Sing, Chor-Wing title = Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date = 2020-07-16 pages = extension = .txt mime = text/plain words = 1789 sentences = 143 flesch = 59 summary = title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. cache = ./cache/cord-350972-0n4dumgg.txt txt = ./txt/cord-350972-0n4dumgg.txt === reduce.pl bib === id = cord-350903-nwagvvc5 author = Softic, Laurent title = Inhibition of SARS-CoV-2 Infection by the Cyclophilin Inhibitor Alisporivir (Debio 025) date = 2020-06-23 pages = extension = .txt mime = text/plain words = 1398 sentences = 80 flesch = 47 summary = Alisporivir reduced SARS-CoV-2 RNA production in a dose-dependent manner in Vero E6 cells, with a 50% effective concentration (EC(50)) of 0.46 ± 0.04 μM. For instance, chloroquine has been shown to bear potent antiviral properties against SARS-CoV-2 in vitro, and several clinical trials are under way to assess its efficacy in patients with COVID-19. Cyclosporine A (CsA), a potent cyclophilin inhibitor, blocks the replication of various coronaviruses in vitro, including HCoV-229E, HCoV-NL63, FPIV, mouse hepatitis virus (MHV), avian infectious bronchitis virus, and SARS-CoV (5, (8) (9) (10) . The antiviral effectiveness of increasing concentrations of alisporivir was measured in Vero E6 cells infected with a clinical isolate of SARS-CoV-2 at a multiplicity of infection (MOI) of 0.02 (Fig. 1A) . These results justify rapidly conducting a proof-of-concept phase 2 trial to assess the antiviral properties and the effect of alisporivir on COVID-19 clinical outcomes in infected patients. cache = ./cache/cord-350903-nwagvvc5.txt txt = ./txt/cord-350903-nwagvvc5.txt === reduce.pl bib === id = cord-350990-tywbe4o2 author = Checchi, Vittorio title = COVID‐19 dentistry‐related aspects: a literature overview date = 2020-07-05 pages = extension = .txt mime = text/plain words = 3715 sentences = 168 flesch = 43 summary = The terms used for the identification of keywords were: COVID-19, 2019-nCov, Sars-CoV-2, COVID-19 transmission, Coronavirus pneumonia, Coronavirus infection, Severe acute respiratory syndrome, Atmospheric contamination, Droplets, Aerosol, PPE/DPI, COVID-19 guidelines, Airborne contamination, Masks and respirators, and COVID-19 dental-related aspects. Therefore, dental procedures can be considered as one of the most probable causes of Sars-CoV-2 infection because such procedures require close proximity to the patient's mouth, possess a risk of contact with saliva, blood and other biological fluids and involve the use of instrumentation that creates large aerosols 4, 19, 20 . Moreover Sars-CoV-2 demonstrates persistent adherence, for a maximum of 9 days, to various surfaces 1, 21 ; therefore, all surfaces and instruments in a dental clinic should be considered as potential sources of virus transmission because infected droplets from saliva or aerosols could land on any exposed surface 16, 19, 22 . cache = ./cache/cord-350990-tywbe4o2.txt txt = ./txt/cord-350990-tywbe4o2.txt === reduce.pl bib === id = cord-350957-10wcqgaq author = Shen, Zu T. title = SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice date = 2016-06-28 pages = extension = .txt mime = text/plain words = 5609 sentences = 265 flesch = 48 summary = Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). Previously, we reported that incorporation of another immunomodulatory peptide, GF9, that employs the SCHOOL mechanisms of action and targets triggering receptor expressed on myeloid cells 1 (TREM-1), into synthetic HDL-like nanoparticles of spherical shape (sHDL) significantly reduces the effective therapeutic dosage of GF9 in animal models of sepsis, lung cancer, and RA 33, 34 . As expected from the anti-arthritic activities demonstrated in animal models of autoimmune arthritis for TCR CP 20,21,23 and HIV gp41 FP 18 , the SARS-CoV FP-derived peptide sequence MG11 significantly suppresses CIA in mice: the peptide at 25 mg/kg/day inhibits inflammation in CIA as assessed by clinical evaluation and scoring of the disease (Fig. 2) . cache = ./cache/cord-350957-10wcqgaq.txt txt = ./txt/cord-350957-10wcqgaq.txt === reduce.pl bib === id = cord-350622-8tgxdbyi author = Palit, Partha title = Phytopharmaceuticals mediated Furin and TMPRSS2 receptor blocking: can it be a potential therapeutic option for Covid-19? date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5083 sentences = 206 flesch = 37 summary = Hence, this strategy may limit life-threatening Covid-19 infection and its mortality rate through nano-suspension based intra-nasal or oral nebulizer spray, to treat mild to moderate SARS-COV-2 infection, when Furin and TMPRSS2 receptor may initiate to express and activate for processing the virus to cause cellular infection by replication within the host cell. Drug particle formulated as a harmonious combination of cocktail receptor inhibitors at optimal and pharmacologically relevant dose could block the host cell receptor Furin, and TMPRSS2 receptor located in the target organs like esophagus, lungs, as well as in colon, liver, heart, kidneys, intestine and pancreas to prevent the entry of the SARS-CoV-2. Hence, some selected lead phytopharmaceuticals can primarily be focused on anti-COVID-19 drug discovery and development as mentioned in Table 1 and Table 2 based on their anti-viral activity reported against influenza, HIV, and other RNA viruses through host cell surface receptors ACE2, Furin and TMPRSS2 blocking action. cache = ./cache/cord-350622-8tgxdbyi.txt txt = ./txt/cord-350622-8tgxdbyi.txt === reduce.pl bib === id = cord-351031-e8suoeim author = Liang En Ian, Wee title = Containing COVID-19 outside the isolation ward: the impact of an infection control bundle on environmental contamination and transmission in a cohorted general ward date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4123 sentences = 206 flesch = 45 summary = In these general wards, termed as respiratory surveillance wards (RSWs), an infection control bundle was implemented comprising infrastructural enhancements, improved personal-protective-equipment (PPE), and social distancing between patients, in order to mitigate the risk of a potential COVID-19 case initially admitted outside of an AIIR. The main finding of our study was that an infection control bundle comprising infrastructural enhancements, improved PPE and social distancing mitigated the risk of environmental contamination and transmission in a cohorted general ward setting. In conclusion, over a 3-month period, our institution implemented a bundle of interventions to reduce risk of intra-hospital transmission of COVID-19 in a multi-bedded cohorted general ward setting, through the implementation of an infection control bundle comprising infrastructural enhancements, improved PPE, and social distancing between patients. cache = ./cache/cord-351031-e8suoeim.txt txt = ./txt/cord-351031-e8suoeim.txt === reduce.pl bib === id = cord-350935-p6euuop3 author = Doğan, Tunca title = CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date = 2020-09-15 pages = extension = .txt mime = text/plain words = 7066 sentences = 298 flesch = 45 summary = We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. In this project, we aimed to address the current shortcomings by developing a comprehensive open access biomedical system entitled CROssBAR via integrating various biological databases to each other, inferring the missing relations between existing data points, and constructing informative knowledge graphs based on specific biomedical components/terms such as a disease/phenotype, biological process, gene/protein and drug/compound, or specific combinations of them. cache = ./cache/cord-350935-p6euuop3.txt txt = ./txt/cord-350935-p6euuop3.txt === reduce.pl bib === id = cord-350992-l6l24pco author = Roldan, Eugenia Quiros title = The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against Sars-Cov-2 infection (COVID-19): A role for iron homeostasis? date = 2020-05-13 pages = extension = .txt mime = text/plain words = 8037 sentences = 393 flesch = 40 summary = Here we review what is currently known on the mechanisms of action of CQ and HCQ as anti-viral, anti-inflammatory and anti-thrombotic drugs and discuss the up-to-date experimental evidence on the potential mechanisms of action of CQ/HCQ in Sars-Cov2 infection and the current clinical knowledge on their efficacy in the treatment of COVID-19 patients. We also propose a different insight into some of CQ and HCQ effects, suggesting a potential role of iron homeostasis in Sars-Cov-2 disease (COVID-19), similarly to several other human viral infections [2] [3] [4] . The search strategy was to use different search terms alone and in any combination, such as "Sars-Cov-2 disease", "COVID-19", "Sars-Cov-2", "coronavirus", "clinical trial", "treatment", "drug", "chloroquine", "hydroxychloroquine", "iron", "virus", "viral entry", "viral spread", "anti-viral activity", "infection", "inflammation", "immunity", "innate immunity", "cytokine", "IL-6", "TNF-", "IL-1", "adaptive immunity", "thrombosis", "in vitro". cache = ./cache/cord-350992-l6l24pco.txt txt = ./txt/cord-350992-l6l24pco.txt === reduce.pl bib === id = cord-351002-msjurww1 author = Ouanes, Y. title = Does BCG protect against SARS-CoV-2 infection ?: elements of proof. date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2997 sentences = 185 flesch = 53 summary = Results : Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). Based on these observations, we hypothesized that countries which have an early start of universal BCG vaccination policy would have a reduced morbidity and mortality attributed to SARS-CoV-2 infection. Or results revealed that countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection. cache = ./cache/cord-351002-msjurww1.txt txt = ./txt/cord-351002-msjurww1.txt === reduce.pl bib === id = cord-351100-llyl97ry author = Cariani, Lisa title = Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3248 sentences = 171 flesch = 53 summary = We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. We collected cycle threshold values of the first SARS-CoV-2-positive nasopharyngeal swabs (T0) for all 182 HCWs and CT values at one week before the two negative RT-PCR tests (T1) for the 58 subjects who healed by 30 April 2020 (Figure 2 ). In the present study, we analyzed 2443 nasopharyngeal swabs from 1683 HCWs by molecular laboratory testing for suspected SARS-CoV-2 infection in a large university hospital in Milan, showing 10.8% positive HCWs. Overall, the majority of HCWs with COVID-19 were physicians, and the main reported symptoms were fever, cough, and headache. cache = ./cache/cord-351100-llyl97ry.txt txt = ./txt/cord-351100-llyl97ry.txt === reduce.pl bib === id = cord-350904-wyg8ikph author = Gubernatorova, E.O. title = IL-6: relevance for immunopathology of SARS-CoV-2 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 8298 sentences = 410 flesch = 35 summary = In turn, SARS-CoV-2 infection of recruited immune cells may increase their apoptosis and exacerbate lymphocytosis [32, 33] , and, finally, may lead in some patients to life-threatening conditions, such as respiratory distress syndrome, cytokine storm, and secondary hemophagocytic lymphohistiocytosis. Interestingly, patients requiring intensive care and invasive lung ventilation display negative correlation between IL-6, TNF and IL-1b concentrations and CD4 + and CD8 + T cell counts [75] , confirming previous studies in animal models, which suggested that cytokine storm actually dampens adaptive immunity against SARS-CoV infection [76] . Taking together, Angiotensin II accumulation due to SARS-CoV-2-mediated ACE2 downregulation may cause Angiotensin 1 receptor downstream activation of NADPH oxidase, which, in turn, leads to elevated ROS production and to induction of transcriptional mechanisms that directly promote IL-6 expression, implicated in inflammation-induced injury and immunopathology. cache = ./cache/cord-350904-wyg8ikph.txt txt = ./txt/cord-350904-wyg8ikph.txt === reduce.pl bib === id = cord-351028-p5cq2is5 author = Yang, Jia-Wei title = Corticosteroid administration for viral pneumonia: COVID-19 and beyond date = 2020-06-27 pages = extension = .txt mime = text/plain words = 1058 sentences = 85 flesch = 40 summary = IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Corticosteroid therapy for 386 critically ill patients with the Middle East respiratory syndrome: a multicenter 387 retrospective cohort study Epidemiological and clinical characteristics of 432 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive 433 study Clinical course and outcomes of critically ill patients 449 with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, 450 observational study cache = ./cache/cord-351028-p5cq2is5.txt txt = ./txt/cord-351028-p5cq2is5.txt === reduce.pl bib === id = cord-351218-ei8dyxfg author = Charles Bronson, Stephen title = Letter to the Editor in response to the article “Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? date = 2020-07-03 pages = extension = .txt mime = text/plain words = 549 sentences = 43 flesch = 62 summary = title: Letter to the Editor in response to the article "Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? Dear Sir, I read with great interest the article by Pitocco et al titled "Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence?". The authors have pointed towards an apparent lack of involvement of type 1 diabetes patients in the COVID-19 patients' population in the data from three studies. Also, I have come across another COVID-19 patient who was detected to have increased blood glucose levels along with ketosis for the very first-time during his admission for COVID-19. This is in line with reports where newly detected diabetes presented with ketoacidosis in COVID-19 patients. Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence? Association of Blood Glucose Control and Outcomes in Patients with COVID-19 and Pre-existing Type 2 Diabetes cache = ./cache/cord-351218-ei8dyxfg.txt txt = ./txt/cord-351218-ei8dyxfg.txt === reduce.pl bib === id = cord-351115-dy81dtnk author = Wang, Chen title = Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date = 2020-10-20 pages = extension = .txt mime = text/plain words = 6133 sentences = 310 flesch = 50 summary = This study addresses both by utilizing evolutionary information from SARS-CoV-2 sequence and structural data to search for actionable functional sites for each protein in the SARS-CoV-2 genome. Here we systematically suggest potential drug target sites for most SARS-CoV-2 proteins based on evolutionary information. This relative ranking re ects the variation entropy of each sequence position within and across the branches of an associated phylogenetic tree, revealing evolutionary pressure points that correspond to functional and structural determinants, and the protein sites at which they often cluster (30) . As in our approach to discover ET drug sites, we combined ET residue ranking information with sequencing data from SARS-CoV-2 isolates to arrive at linear peptides along the proteome that are evolutionarily important and also show little variation in the current outbreak ( Figure S6 , Dataset S5). The data include, for example, multiple sequence alignments, precalculated ET ranks, and predicted epitopes (both linear and structural) for all SARS-CoV-2 proteins. cache = ./cache/cord-351115-dy81dtnk.txt txt = ./txt/cord-351115-dy81dtnk.txt === reduce.pl bib === id = cord-351038-k2m6woow author = Arun Krishnan, R. title = COVID-19: Current Trends in Invitro Diagnostics date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2895 sentences = 172 flesch = 50 summary = Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. The limitation of rRT-PCR to detect COVID-19 past infection and the progress of the disease, increases the importance of serological assays. Currently COVID-19 antigen LFIA test is under development which will offer more sensitive and specific result for COVID-19 diagnosis and will detect the viral antigen in 3 days of infection [22] . have developed an enzyme linked immunosorbent assay for the detection of COVID-19 IgM and IgG antibody from serum sample. The complexity, cost effectiveness and limitations of nucleic acid based diagnostic tools, impetus the innovative development of well standardized, high sensitive, specific and low cost serological assays for COVID-19 diagnosis. Evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). cache = ./cache/cord-351038-k2m6woow.txt txt = ./txt/cord-351038-k2m6woow.txt === reduce.pl bib === id = cord-351116-jwy6k0ih author = O'Reilly, GM title = Epidemiology and clinical features of emergency department patients with suspected and confirmed COVID‐19: A multisite report from the COVED Quality Improvement Project for July 2020 (COVED‐3) date = 2020-09-21 pages = extension = .txt mime = text/plain words = 3598 sentences = 222 flesch = 49 summary = METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study in Australian EDs. This analysis presents data from eight sites across Victoria and Tasmania for July 2020 (during Australia's 'second wave'). 3 The objectives of this analysis (COVED-3), undertaken during the ‗second wave', were to explore the association between SARS-CoV-2 test result and mechanical ventilation and death in hospital and to identify clinical and epidemiological variables predictive of SARS-CoV-2 positivity. 12 These include history (age, sex, symptoms and duration of presenting complaint, epidemiological features, co-morbidities), findings on clinical examination, radiological and blood investigations, care provided in the ED and hospital (including commencement of invasive mechanical ventilation and ED disposition destination) and patient outcomes (including survival to discharge). In terms of clinical and epidemiological risk factors, SARS-CoV-2 positive patients were more likely to report close contact with a confirmed case of COVID-19 or a positive SARS-CoV-2 PCR swab result in the 14 days prior to their ED presentation. cache = ./cache/cord-351116-jwy6k0ih.txt txt = ./txt/cord-351116-jwy6k0ih.txt === reduce.pl bib === id = cord-351278-nm2bq717 author = Thompson, Craig title = Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2995 sentences = 204 flesch = 55 summary = title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors a pilot study of the value of serology to determine population exposure We performed a serological study of recent blood donors in Scotland to detect antibodies to SARS-CoV-2 as a marker of past infection. Serial follow up studies are needed to track infection and seroconversion in this and other similar populations However, these data indicate that sero-surveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic like the current SARS-CoV-2 outbreak. Since the first reports in December, 2019, infections with SARS-CoV-2 have been reported from an increasing number of countries worldwide, with particularly high incidence of diagnosed infections and associated deaths from respiratory disease initially in China but more recently in Italy, Iran, Spain, France and the USA (https://www.who.int/emergencies/diseases/novel-coronavirus-2019). cache = ./cache/cord-351278-nm2bq717.txt txt = ./txt/cord-351278-nm2bq717.txt === reduce.pl bib === id = cord-351189-56am76lb author = Rosen, Melissa H title = Management of Acute Severe Ulcerative Colitis in a Pregnant Woman With COVID-19 Infection: A Case Report and Review of the Literature date = 2020-05-12 pages = extension = .txt mime = text/plain words = 2373 sentences = 136 flesch = 47 summary = As the patient was improving on steroids and given the rapidly increasing rate of COVID-19 infected patients at our institution, the decision was made to discharge the patient home on an oral prednisone taper on hospital day 5 with plans to start infliximab as an outpatient. Although intravenous steroids are the mainstay of treatment for acute severe UC in the hospitalized patient, the use of steroids in the first trimester of pregnancy may be associated with a risk of cleft lip or cleft palate. The necessity for guidance was addressed by the International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) in their publication, "Management of Patients with Crohn's Disease and Ulcerative Colitis During the COVID-19 Pandemic: Results of an International Meeting." 9 The recommendation is to continue biologic therapy in the absence of SARS-CoV-2 infection. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes cache = ./cache/cord-351189-56am76lb.txt txt = ./txt/cord-351189-56am76lb.txt === reduce.pl bib === id = cord-351314-atsuh8e2 author = Bryson-Cahn, Chloe title = A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date = 2020-03-12 pages = extension = .txt mime = text/plain words = 1255 sentences = 67 flesch = 45 summary = Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. cache = ./cache/cord-351314-atsuh8e2.txt txt = ./txt/cord-351314-atsuh8e2.txt === reduce.pl bib === id = cord-351092-b01o6f69 author = De Francesco, Maria A. title = Pneumocystis jirevocii and SARS-CoV-2 Co-Infection: A Common Feature in Transplant Recipients? date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2229 sentences = 126 flesch = 39 summary = Here we describe, for the first time in Europe, a fatal case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii in a kidney transplant recipient. Pneumocystis jirevocii pneumonia is an opportunistic infection affecting patients with cellular immunity defects due to human immunodeficiency virus (HIV) infections or iatrogenic immunosuppression [15, 16] . Here, we report the fatal case of a SARS-CoV-2 and Pneumocystis jirevocii co-infection in a kidney transplant recipient. This is, to the best of our knowledge, the first case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii reported in Europe in a kidney transplant recipient. Pneumocystis jirevocii pneumonia in immunocompromised patients: Delayed diagnosis and poor outcomes in non-HIV infected individuals Acute respiratory failure due to Pneumocystis pneumonia in patients without human immunodeficiency virus infection: Outcome and associated features Critical care management and outcome of severe Pneumocystis pneumonia in patients with and without HIV infection cache = ./cache/cord-351092-b01o6f69.txt txt = ./txt/cord-351092-b01o6f69.txt === reduce.pl bib === id = cord-350949-ystkjdwk author = Gao, Yi-jie title = Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date = 2020-08-03 pages = extension = .txt mime = text/plain words = 4518 sentences = 274 flesch = 55 summary = The meta-analysis showed the following results: the incidence of severe case or death was 12, 95% CI: 0.03-0.20, I 2 = 0%, P = 0.006; the incidence of fever was 51, 95% CI: 0.35-0.67, I 2 = 89%, P < 0.00001; the incidence of cough was 31, 95% CI: 0.23-0.39, I 2 = 38%, P < 0.00001; the incidence of lymphopenia was 49, 95% CI: 0.29-0.70, I 2 = 83%, P < 0.00001; the incidence of positive CT findings was 71, 95% CI: 0.49-0.93, I 2 = 90%, P < 0.00001; the incidence of coexisting disorders was 33, 95% CI: 0.21-0.44, I 2 = 70%, P < 0.00001; the incidence of preterm labor was 23, 95% CI: 0.14-0.32, I 2 = 21%, P < 0.00001; the incidence of caesarean section was 65, 95% CI: 0.42-0.87, I 2 = 90%, P < 0.00001; the incidence of fetal distress was 29, 95% CI: 0.08-0.49, I 2 = 68%, P = 0.007; the incidence of neonatal asphyxia or neonatal death or stillbirth was 9, 95% CI: − 0.03-0.21, I 2 = 0%, P = 0.14; the incidence of neonatal infection was 12, 95% CI: − 0.01-0.26, I 2 = 0%, P = 0.06; and SARS-CoV-2 testing of breast milk was only mentioned in the study by Chen H (2020.2.12), and the incidence was 0, which cannot be calculated by metaanalysis. cache = ./cache/cord-350949-ystkjdwk.txt txt = ./txt/cord-350949-ystkjdwk.txt === reduce.pl bib === id = cord-351011-v4zmksio author = Golden, Joseph W. title = Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date = 2020-07-09 pages = extension = .txt mime = text/plain words = 4650 sentences = 268 flesch = 52 summary = In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. In comparison with the normal lung architecture in uninfected control animals, infected mice necropsied on day 3, and those succumbing to disease on days 5-11, had varying levels of lung injury including area of lung consolidation characterized by inflammation/expansion of 145 alveolar septa with fibrin, edema and mononuclear leukocytes and infiltration of vessel walls by numerous mononuclear leukocytes (Fig 3A, Fig S4, and Table S1 ). Importantly, in our study some animals at the lower dose survived infection despite significant Infection of K18-hACE2 mice by SARS-CoV-2 produces a disease similar to that observed in acute human cases, with development of an acute lung injury associated with edema, production 285 of inflammatory cytokines and the accumulation of mononuclear cells in the lung. cache = ./cache/cord-351011-v4zmksio.txt txt = ./txt/cord-351011-v4zmksio.txt === reduce.pl bib === id = cord-350855-gofzhff7 author = Hou, Yixuan J. title = SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3416 sentences = 222 flesch = 50 summary = High-sensitivity RNA in situ mapping revealed the highest ACE2 expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) vs distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. We measured the relative infectivity of the SARS-CoV-2 GFP virus in primary 283 cells based on the average peak titers and observed that infectivity exhibited the same 284 pattern as the ACE2 expression levels from the upper to lower respiratory tract ( Figure 285 6Bi-6Biv). Gene 1230 expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human 1231 airway epithelial cells and lung tissue cache = ./cache/cord-350855-gofzhff7.txt txt = ./txt/cord-350855-gofzhff7.txt === reduce.pl bib === id = cord-351224-jeedo5mc author = GeurtsvanKessel, Corine H. title = An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment date = 2020-07-06 pages = extension = .txt mime = text/plain words = 3046 sentences = 153 flesch = 46 summary = The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. Despite the differences in sensitivity, all laboratory assays had sufficient positive predictive value (PPV) in COVID-19 hospitalized patients when assuming an expected seroprevalence in this population of ≥50% (Table 1) , or when using serology as an adjunct to RT-PCR testing to monitor the clinical course of illness. To determine specificity of the assays, we used a well-defined panel of 147 serum and plasma samples from 147 individuals exposed to human coronaviruses (HCoV-229E, NL63 or OC43), SARS, MERS), or with a range of other respiratory viruses ( Sensitivity was calculated by using a total of 187 sera from 107 individuals in the Netherlands, in whom COVID-19 was confirmed by RT-PCR and antibodies were detected by PRNT50. cache = ./cache/cord-351224-jeedo5mc.txt txt = ./txt/cord-351224-jeedo5mc.txt === reduce.pl bib === id = cord-351283-1y9dfobn author = Tan, Bai‐Hong title = The possible impairment of respiratory‐related neural loops may be associated with the silent pneumonia induced by SARS‐CoV‐2 date = 2020-06-11 pages = extension = .txt mime = text/plain words = 1364 sentences = 66 flesch = 38 summary = As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID‐19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit stay for those requiring invasive mechanical ventilation. In view of the findings for H5N1 influenza virus, the silence of pneumonia induced by SARS-CoV-2 may be due to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID-19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit (ICU) stay for those requiring invasive mechanical ventilation. Therefore, we propose that the peculiar manifestations in COVID-19 patients may be attributed to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. cache = ./cache/cord-351283-1y9dfobn.txt txt = ./txt/cord-351283-1y9dfobn.txt === reduce.pl bib === id = cord-351305-6vtv2xuh author = Schramm, Markus A. title = COVID-19 in a Severely Immunosuppressed Patient With Life-Threatening Eosinophilic Granulomatosis With Polyangiitis date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1260 sentences = 64 flesch = 38 summary = The current pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compels clinicians to develop recommendations for successful clinical management and surveillance of immunocompromised patients at high risk for severe disease progression. With only few case studies published on SARS-CoV-2 infection in patients with rheumatic diseases, we report a 25-year-old male who developed moderate coronavirus disease 2019 (COVID-19) with fever, mild dyspnea, and no major complications despite having received high-dose prednisolone, cyclophosphamide, and rituximab for the treatment of highly active, life-threatening eosinophilic granulomatosis with polyangiitis (EGPA). Thus, due to severity and refractory disease the previously healthy patient was continuously hospitalized from January to March 2020, receiving intravenous cyclophosphamide (CYCLOPS-protocol, cumulative dose 4.76 g), rituximab (4 × 375 mg/m 2 ), and a long-term, slowly tapered high-dose prednisolone treatment (up to 1 g/day). Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients cache = ./cache/cord-351305-6vtv2xuh.txt txt = ./txt/cord-351305-6vtv2xuh.txt === reduce.pl bib === id = cord-351107-a5bx74ao author = Phua, Ghee-Chee title = Mechanical Ventilation in an Airborne Epidemic date = 2008-06-30 pages = extension = .txt mime = text/plain words = 2981 sentences = 145 flesch = 40 summary = The severe acute respiratory syndrome outbreak exposed the vulnerability of health care workers and highlighted the importance of establishing stringent infection control and crisis management protocols. Approximately 20% to 30% of SARS patients required intensive care and mechanical ventilation for acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) [9] . Adjuvant strategies shown to decrease morbidity and mortality in critically ill patients on mechanical ventilation include deep venous thrombosis prophylaxis, stress ulcer prophylaxis, sedation protocols, and avoidance of neuromuscular blockage, if possible; semirecumbent position should also be employed during airborne epidemics causing hypoxemic respiratory failure [18] . With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. cache = ./cache/cord-351107-a5bx74ao.txt txt = ./txt/cord-351107-a5bx74ao.txt === reduce.pl bib === id = cord-351225-dq0xu85c author = Poutanen, Susan M. title = Transmission and control of SARS date = 2004 pages = extension = .txt mime = text/plain words = 5584 sentences = 229 flesch = 45 summary = During the outbreak, it was evident that SARS was readily transmissible from person to person, especially in health Severe acute respiratory syndrome (SARS) was first recognized in China in November 2002 and was subsequently associated with a worldwide outbreak involving 8098 people, 774 of whom died. Evidence for this includes studies in Hong Kong and Toronto, Canada that show an increased risk for SARS in health care workers who entered the room of a patient with SARS, with increasing risk in those with closer proximity to the patient and those remaining in the room for a longer duration, suggesting that transmission is enhanced by close, prolonged contact [19•,20 •] In addition, an increased risk in household members of patients with SARS has been shown in those who had close, prolonged contact with the index person, and in particular, in those who shared a bed, reported being within 1 meter of the index person, and dined together [21•] . cache = ./cache/cord-351225-dq0xu85c.txt txt = ./txt/cord-351225-dq0xu85c.txt === reduce.pl bib === id = cord-351430-bpv7p7zo author = Pequeno, Pedro title = Air transportation, population density and temperature predict the spread of COVID-19 in Brazil date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4780 sentences = 222 flesch = 47 summary = Further, we considered the following predictors: (1) time in days, to account for the exponential growth in case numbers during this period (Fig. 2) ; (2) number of arriving flights in the city's metropolitan area in 2020, as airline connections can facilitate the spread of the virus (Ribeiro et al., 2020) ; (3) city population density, to account for facilitation of transmission under higher densities (Poole, 2020) ; (4) proportion of elderly people (≥60 years old) in the population, assuming that the elderly may be more likely to show severe symptoms of SARS-CoV-2 and, thus, to be diagnosed with COVID-19; (5) citizen mean income, which may affect the likelihood of people being infected by the virus, for example, due to limited access to basic sanitation or limited social isolation capabilities; (6) and the following meteorological variables: mean daily temperature ( C), mean daily solar radiation (kJ/m 2 ), mean daily relative humidity (%) and mean daily precipitation (mm). cache = ./cache/cord-351430-bpv7p7zo.txt txt = ./txt/cord-351430-bpv7p7zo.txt === reduce.pl bib === id = cord-351321-6d2mn5ok author = Gouveia, Duarte title = Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date = 2020-06-19 pages = extension = .txt mime = text/plain words = 6241 sentences = 294 flesch = 52 summary = Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. To assess the performance of shotgun MS-based proteomics in detecting SARS-CoV-2 peptides in a background matrix consisting of nasopharyngeal swab protein material, we experimentally created tryptic peptidomes from i) a purified virus solution obtained from Vero E6 cells infected with a SARS-CoV-2 reference strain, and ii) nasopharyngeal swabs obtained from two healthy volunteers (Figure 1) . Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analysed by MS/MS with a short gradient. cache = ./cache/cord-351321-6d2mn5ok.txt txt = ./txt/cord-351321-6d2mn5ok.txt === reduce.pl bib === id = cord-351269-xjy6chia author = Wu, Y title = Coronavirus disease 2019 among pregnant Chinese women: case series data on the safety of vaginal birth and breastfeeding date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3516 sentences = 208 flesch = 50 summary = METHODS: We collected clinical data, vaginal secretions, stool specimens and breast milk from SARS‐CoV‐2‐infected women during different stages of pregnancy and collected neonatal throat and anal swabs. 2 Previous studies have suggested that SARS-CoV infection during pregnancy may carry severe complications including maternal death, spontaneous miscarriage, preterm delivery and intrauterine growth restriction; 3 and MERS has been associated with intrauterine fetal demise and stillbirth. All pregnant women with SARS-CoV-2 admitted to Renmin Hospital of Wuhan University in China between 31 We extracted demographic information, clinical course, laboratory indices and imaging results of infected pregnant women from the medical records, maternal throat swabs were collected upon admission. None of the newborns delivered in our study was infected, a result consistent with previous reports (e.g. negative tests for the novel coronavirus nucleic acid in pharyngeal swab samples from 19 neonates born to mothers with COVID-19 pneumonia, and for three placental samples 13, 14 ) . cache = ./cache/cord-351269-xjy6chia.txt txt = ./txt/cord-351269-xjy6chia.txt === reduce.pl bib === id = cord-351367-ral9sbfy author = Scarlattei, Maura title = Unknown SARS-CoV-2 pneumonia detected by PET/CT in patients with cancer date = 2020-06-22 pages = extension = .txt mime = text/plain words = 3010 sentences = 153 flesch = 45 summary = METHODS: We report 5 patients with unknown SARS-CoV-2 infection undergoing positron emission tomography (PET)/computed tomography (CT) with radiopharmaceuticals targeting different tumor processes: (18)F-FDG, (18)F-choline (FCH), and (68)Ga-PSMA. Correct management of a PET session presents many difficulties because of the coexistence of asymptomatic SARS-CoV-2 infection and patients with mild symptoms before the PET scan (https://www.sirm.org/2020/03/30/ covid-19-caso-69/), mostly not tested on RT-PCR, but variably presenting with chest CT findings compatible with pulmonary interstitial infiltrates, potentially associated with infection or drug-related reactions. In this study, we report 5 patients (Table 1) with unknown SARS-CoV-2 infection undergoing PET/CT scan for restaging breast and prostate cancer (patients 1, 3, 4), characterization of lung nodule (patient 2), and focal splenic lesions (patient 5). Recent case series about PET in patients with SARS-CoV-2 pneumonia showed high 18 F-FDG uptake in lung lesions accompanied by nodal involvement detectable on PET/CT images. cache = ./cache/cord-351367-ral9sbfy.txt txt = ./txt/cord-351367-ral9sbfy.txt === reduce.pl bib === id = cord-351512-h4vigeuy author = Zhang, Lin title = How scientific research reacts to international public health emergencies: a global analysis of response patterns date = 2020-06-09 pages = extension = .txt mime = text/plain words = 7123 sentences = 347 flesch = 49 summary = In the present paper, we attempt to characterise, quantify and measure the response of academia to international public health emergencies in a comparative bibliometric study of multiple outbreaks. From our analysis of six infectious disease outbreaks since 2000, including COVID-19, we find that academia always responded quickly to public health emergencies with a sharp increase in the number of publications immediately following the declaration of an outbreak by the WHO. Researches in the fields of virology, infectious diseases and immunology are the most active, and we identified two characteristic patterns in global science distinguishing research in Europe and America that is more focused on public health from that conducted in China and Japan with more emphasis on biomedical research and clinical pharmacy, respectively. From the perspective of countries and world regions, funding agencies in the USA, China, and the UK contributed most to supporting research in response to public health emergencies, as shown in Fig. 11 . cache = ./cache/cord-351512-h4vigeuy.txt txt = ./txt/cord-351512-h4vigeuy.txt === reduce.pl bib === id = cord-351340-7y19ystp author = Rao, Gundu H. R. title = Coronavirus Disease and Acute Vascular Events date = 2020-07-31 pages = extension = .txt mime = text/plain words = 2557 sentences = 140 flesch = 43 summary = 3 On the other hand, in a study performed in COVID-19 patients in New York, with observed ST-segment elevated myocardial infraction, 64% had normal D-dimer levels according to Dr Bangalore and associates from the New York University Grossman School of Medicine. At the time of admission, COVID-19 patients reported as having at least 1 acute comorbidity: diabetes (10%-20%), hypertension (10%-15%), or other CVD and cerebrovascular diseases (7%-40%). 12 In a seminal article by Bikdeli et al, endorsed by multiple specialty societies, the authors summarize their findings in the following way: "Coronavirus disease 2019 (COVID-19) , a viral respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), may predispose patients to thrombotic disease, both in the venous and arterial circulations, due to excessive inflammation, platelet activation, endothelial dysfunction, and stasis. Elevated plasmin(ogen) seems to be a common biomarker in people with hypertension, diabetes, CVD, and cerebrovascular diseases, who are susceptible to SARS-CoV-2 infection. cache = ./cache/cord-351340-7y19ystp.txt txt = ./txt/cord-351340-7y19ystp.txt === reduce.pl bib === id = cord-351503-2f0sk24j author = Pua, Uei title = What Is Needed to Make Interventional Radiology Ready for COVID-19? Lessons from SARS-CoV Epidemic date = 2020-03-13 pages = extension = .txt mime = text/plain words = 1276 sentences = 76 flesch = 53 summary = During the initial stage, Singapore recorded one of the highest number of infections outside of China (3), reminiscence of the SARS-CoV epidemic 17 years ago (4). In 2003, the authors were deployed to perform IR as well as critical care procedures in critically ill SARS-CoV patients, and today, providing IR support to the COVID-19 patients. Save for the critically ill, the vast majority of patients with viral pneumonia will not require any IR procedure (28 IR procedures in 27 patients out of the cohort of 206 during SARS-CoV epidemic) (4) . Similarly during the SARS-CoV epidemic in Singapore, among the 206 cases, there were 84 healthcare workers infection resulting in 5 deaths. To assume that the COVID-19 outbreak would be the same as the SARS-CoV epidemic, would be overly simplistic and to ignore our prior experience. cache = ./cache/cord-351503-2f0sk24j.txt txt = ./txt/cord-351503-2f0sk24j.txt === reduce.pl bib === id = cord-351489-tzmev77c author = Yuan, Shuofeng title = Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date = 2020-06-10 pages = extension = .txt mime = text/plain words = 5002 sentences = 238 flesch = 40 summary = They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. In this primary screening, chloroquine, lopinavir, and remdesivir which were recently reported to have anti-SARS-CoV-2 activity, exhibited about 1.3-2.0 log10 copies/mL reduction in viral RNA load ( Figure 1 ). In comparison, recombinant IFN-β demonstrated the most potent anti-SARS-CoV-2 activity, with Avonex (IFN-β1a), Rebif (IFN-β1a), and Betaferon (IFN-β1b) each achieving about 3 log10 copies/mL reduction in viral load. In our primary screening using a fixed antiviral agent concentration and virus inoculum, we identified recombinant IFNs and lipogenesis modulators to be the most potent anti-SARS-CoV-2 agents among 22 broad-spectrum antivirals. cache = ./cache/cord-351489-tzmev77c.txt txt = ./txt/cord-351489-tzmev77c.txt === reduce.pl bib === id = cord-351354-10rusr6j author = Chan, Louis Y. title = Diagnostic Criteria during SARS Outbreak in Hong Kong date = 2004-06-17 pages = extension = .txt mime = text/plain words = 1947 sentences = 104 flesch = 54 summary = Before the etiologic agent was identified, the diagnosis of SARS was made according to a set of clinical-epidemiologic criteria as suggested by the Centers for Disease Control and Prevention (CDC) (1-3). These criteria remained important in the initial diagnosis and prompt isolation of patients because the overall sensitivity of initial reverse transcriptase-polymerase chain reaction (RT-PCR) testing for SARSassociated coronavirus (SARS CoV) RNA on upper respiratory specimens ranged from approximately 60% to 70% (though sensitivity improved with a second test) (4, 5) . By using paired serologic testing to determine SARS-CoV infection (3), we evaluated the relative importance of the clinical-epidemiologic diagnostic criteria during an outbreak. Probable SARS case-patients were those who met the CDC clinical criteria for severe respiratory illness of unknown etiology (3), and met the epidemiologic criterion for exposure in either a close or a possible contact. Our findings showed that 5.9% of cases defined as probable SARS on the basis of clinical-epidemiologic criteria had no serologic evidence of coronavirus infection. cache = ./cache/cord-351354-10rusr6j.txt txt = ./txt/cord-351354-10rusr6j.txt === reduce.pl bib === id = cord-351532-2yd4wg9v author = Huang, Yin-Qiu title = No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5739 sentences = 260 flesch = 48 summary = title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study The proportion of patients with SARS-CoV-2 nucleic acid negativity in the LPV/r+IFN-α-treated group (61.1%) was higher than the RBV+ IFN-α-treated group (51.5%) and the RBV+LPV/r+IFN-α-treated group (46.9%) at day 14; however, the difference between these groups was calculated to be statistically insignificant. The office of National Health Commission of the People's Republic of China, and the National Administration Bureau of Traditional Chinese Medicine have jointly issued different versions of the "Guidelines for diagnosis and treatment of novel coronavirus pneumonia", in which LPV/r, IFNa, and RBV are recommended for on-trial use in patients with COVID-19. cache = ./cache/cord-351532-2yd4wg9v.txt txt = ./txt/cord-351532-2yd4wg9v.txt === reduce.pl bib === id = cord-351559-az4pgi9k author = Turjya, Rafeed Rahman title = Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2438 sentences = 173 flesch = 48 summary = Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. cache = ./cache/cord-351559-az4pgi9k.txt txt = ./txt/cord-351559-az4pgi9k.txt === reduce.pl bib === id = cord-351691-3egwvb59 author = Elzupir, Amin O. title = Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 2948 sentences = 181 flesch = 52 summary = This study investigates the inhibitory effect of SARS-CoV-2 3-chymotrypsin-like protease (3CL(pro)) using caffeine and caffeine-containing pharmaceuticals (3CPs) based on molecular dynamics simulations and free energy calculations by means of molecular mechanics-Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics-generalized-Born surface area (MMGBSA). Of these 3CPs, seven drugs approved by the US-Food and Drug Administration have shown a good binding affinity to the catalytic residues of 3CL(pro) of His(41) and Cys(145): caffeine, theophylline, dyphylline, pentoxifylline, linagliptin, bromotheophylline and istradefylline. This study demonstrates the inhibitory effect of 3CL pro by means of approved caffeine and caffeine-containing pharmaceuticals (3CPs) using the molecular docking approach. An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations cache = ./cache/cord-351691-3egwvb59.txt txt = ./txt/cord-351691-3egwvb59.txt === reduce.pl bib === id = cord-351644-pl7xpivx author = Gao, Yelei title = Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis date = 2020-04-17 pages = extension = .txt mime = text/plain words = 4712 sentences = 336 flesch = 55 summary = We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. Data extracted included: 1) Basic information: title, first author, publication year and study design; 2) participants: baseline characteristics and sample size; and 3) results: proportions of individuals using telemedicine for different contents of consultation (e.g. symptoms, therapy and prevention, policy, public service), details of screening of suspected cases, the provision of advice given to people who had symptoms or contact history, and the limitations of telemedicine. https://doi.org/10.1101/2020.04.14.20065664 doi: medRxiv preprint proportion of consultation on public issues (including disease knowledge, epidemic situation and public issues of COVID-19/SARS). cache = ./cache/cord-351644-pl7xpivx.txt txt = ./txt/cord-351644-pl7xpivx.txt === reduce.pl bib === id = cord-351662-rmkcb6o3 author = Huang, Zhifeng title = Characteristics and roles of SARS‐CoV‐2 specific antibodies in patients with different severities of COVID‐19 date = 2020-07-24 pages = extension = .txt mime = text/plain words = 2855 sentences = 179 flesch = 54 summary = We aimed to quantify the levels of SARS‐CoV‐2‐specific IgM, IgA, and IgG antibodies, identify changes in them based on COVID‐19 severity, and establish the significance of combined antibody detection. The rise times for specific IgM and IgG levels are different, and combined detection could be more advantageous in the diagnosis of COVID-19 [5] . In this study, SARS-CoV-2-specific IgM, IgA, and IgG levels were measured in patients with varying severities of COVID-19, the relationship between specific antibody levels and disease severity was classified, and the significance of combined antibody detection was clarified, providing a reference for the clinical diagnosis of COVID-19. We also found that while IgA and IgG levels were significantly higher in the severe & critical patients than in moderate patients, there was no difference in IgM between the two groups. Levels of IgA and IgG were higher in severe & critical COVID-19 patients than in moderate COVID-19 patients, while IgM levels were no different between the two groups. cache = ./cache/cord-351662-rmkcb6o3.txt txt = ./txt/cord-351662-rmkcb6o3.txt === reduce.pl bib === id = cord-351446-j4ambec5 author = Sinonquel, P. title = COVID‐19 and gastrointestinal endoscopy: what should be taken into account? date = 2020-04-26 pages = extension = .txt mime = text/plain words = 2673 sentences = 178 flesch = 51 summary = With this report we aim to provide recommendations and practical relevant information for gastroenterologists based on the limited amount of available data and local experience, to guarantee a high‐quality patient care and adequate infection prevention in the gastroenterology clinic. [6] SARS-CoV-2 virus spreads via droplets and aerosols, and indirectly by contact with contaminated surfaces which implies the absolute need of personal protective equipment (PPE) for both patients and health care workers/professionals, especially those operating in the aero-digestive tract. The aim of this report is to provide a practical guide for the protective management when performing endoscopic/endoluminal procedures of the GI tract in emergency, ambulatory or hospitalized patients, based upon the current available information worldwide and local experience in our tertiary university hospital. Before any procedure can be performed, the patient should wear a surgical mask and should be questioned about contact with COVID-19 positive individuals and recent or present symptoms like fever, cough and dyspnea, rhinitis, sudden loss of smell and/or taste. cache = ./cache/cord-351446-j4ambec5.txt txt = ./txt/cord-351446-j4ambec5.txt === reduce.pl bib === id = cord-351555-hsgsuor2 author = Constantinou, Constantina title = Developing a holistic contingency plan: Challenges and dilemmas for cancer patients during the COVID‐19 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 7593 sentences = 406 flesch = 48 summary = Zhang et al, 21 reported that patients who had their last anti-tumor treatment (including chemotherapy, immunotherapy, and radiation) within 14 days prior to infection with SARS-CoV-2 had a significantly increased risk of developing severe events (HR = 4.079, 95% CI 1.086-15.322, P = .037). 37, 38 In order to achieve this, in the most affected areas medical specialists, including oncologists, were asked to provide their assistance in managing patients suffering from COVID-19 requiring hospitalization in ICUs or in the departments of infectious or respiratory diseases or general internal medicine. 40 Currently, there are no official reports of how the treatment of cancer patients has been affected by the lack of resources and limited access to healthcare due to the COVID-19 pandemic in most afflicted countries. The decision should be based on the cancer type and stage, the clinical condition of the patient, the treatment indicated for the condition, the patient's response to anticancer therapy, and the potential risks for an infection with SARS-CoV-2. cache = ./cache/cord-351555-hsgsuor2.txt txt = ./txt/cord-351555-hsgsuor2.txt === reduce.pl bib === id = cord-351567-ifoe8x28 author = Rabi, Firas A. title = SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far date = 2020-03-20 pages = extension = .txt mime = text/plain words = 5745 sentences = 315 flesch = 54 summary = However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. To assess the magnitude of the risk posed by the SARS-CoV-2, we review four parameters that we believe important: the transmission rate, the incubation period, the case fatality rate (CFR), and the determination of whether asymptomatic transmission can occur. A small study of 17 patients showed that nasal viral load peaks within days of symptom onset, suggesting that transmission of disease is more likely to occur early in the course of infection [40] . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19)-China 2020 Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia cache = ./cache/cord-351567-ifoe8x28.txt txt = ./txt/cord-351567-ifoe8x28.txt === reduce.pl bib === id = cord-351482-hzh5tyoo author = Peng, Xinxia title = Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date = 2011-11-15 pages = extension = .txt mime = text/plain words = 7697 sentences = 348 flesch = 49 summary = The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). cache = ./cache/cord-351482-hzh5tyoo.txt txt = ./txt/cord-351482-hzh5tyoo.txt === reduce.pl bib === id = cord-351651-6dbt99h0 author = Sun, Zhong title = Potential Factors Influencing Repeated SARS Outbreaks in China date = 2020-03-03 pages = extension = .txt mime = text/plain words = 4985 sentences = 260 flesch = 55 summary = Thus, if bats were the natural hosts of SARS-CoVs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. A study on the genome sequence of diseased pangolins smuggled from Malaysia to China found that pangolins carry coronavirus, suggesting that pangolins may be intermediate hosts for SARS-COV-2 [35] . However, the only source of bats that have been publicly identified as carrying virus phylogenetically close to SARS-CoV-2 is far away from Wuhan in Zhoushan, Zhejiang. However, to confirm this scenario, it is necessary to find wild bats in Wuhan and its neighboring areas that carry CoVs identical to those isolated from various SARS-2 patients. This mini-review evaluated the common epidemiological patterns of both SARS epidemics in China and identified cold, dry winter as a common environmental condition conducive for SARS virus infection to human beings. cache = ./cache/cord-351651-6dbt99h0.txt txt = ./txt/cord-351651-6dbt99h0.txt === reduce.pl bib === id = cord-351492-8jv7ip67 author = Urwin, S. G. title = FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date = 2020-10-20 pages = extension = .txt mime = text/plain words = 7241 sentences = 397 flesch = 53 summary = Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. In this systematic review and pooled analysis of IPD, we found that the FebriDx LFD had a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) for COVID-19 across two studies performed within acute hospitals in the UK when compared to RT-PCR on nose and throat swabs during the first wave of the SARS-CoV-2 pandemic. cache = ./cache/cord-351492-8jv7ip67.txt txt = ./txt/cord-351492-8jv7ip67.txt === reduce.pl bib === id = cord-351649-87g7g5au author = Haagmans, Bart L. title = SARS date = 2009-01-30 pages = extension = .txt mime = text/plain words = 6736 sentences = 298 flesch = 40 summary = Because the disease in macaques caused by SARS-CoV infection was pathologically similar to that seen in human patients with SARS, and since the virus should induce highly cross-reactive neutralizing antibodies to protect against newly emerging viruses related to SARS-CoV and protect both the gastrointestinal and respiratory tract in the absence of significant side effects. African green monkeys immunized via the respiratory tract with two doses of a recombinant Newcastle disease virus encoding the S protein developed a relatively high titer of SARS-CoV neutralizing antibodies and upon challenge demonstrated a 1000-fold zoonotic coronaviruses. Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies cache = ./cache/cord-351649-87g7g5au.txt txt = ./txt/cord-351649-87g7g5au.txt === reduce.pl bib === id = cord-351625-1we9wi1g author = Han, Huan title = Descriptive, Retrospective Study of the Clinical Characteristics of Asymptomatic COVID-19 Patients date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4062 sentences = 245 flesch = 48 summary = Since asymptomatic patients may be a greater risk of virus transmission than symptomatic patients, public health interventions and a broader range of testing may be necessary for the control of COVID-19. IMPORTANCE Asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a potential problem for pandemic control through public health strategies. Since asymptomatic patients have no clinical symptoms which can easily prevent timely diagnosis and treatment, they may cause a greater risk of virus transmission than symptomatic patients, which poses a major challenge to infection control. Thus far, many studies have analyzed the clinical characteristics of SARS-CoV-2-infected patients presenting levels of illness ranging from mild to severely critical (10, 11) . In this study, we enrolled 25 asymptomatic and 27 symptomatic COVID-19 patients and performed systematic analysis of different clinical characteristics. In this study, we systematically compared different complete blood counts, serum biochemistries, and immunologic responses from SARS-CoV-2-infected asymptomatic and symptomatic individuals. cache = ./cache/cord-351625-1we9wi1g.txt txt = ./txt/cord-351625-1we9wi1g.txt === reduce.pl bib === id = cord-351718-sf5zp5wg author = Kohli, Utkarsh title = COVID-19 pneumonia in an infant with a hemodynamically significant ventricular septal defect date = 2020-10-12 pages = extension = .txt mime = text/plain words = 1371 sentences = 77 flesch = 42 summary = Reports thus far suggest a mild course for acute COVID-19 infection in children; however, its effects in vulnerable paediatric populations, including children with haemodynamically significant congenital heart disease, have rarely been reported. We therefore report on a 4-month-old Hispanic male with a moderate sized conoventricular ventricular septal defect and pulmonary overcirculation who presented with COVID-19-associated pneumonia. 6 Children with haemodynamically significant congenital heart disease are at an increased risk of decompensation and hospitalisation when concomitantly infected with other respiratory viruses such as respiratory syncytial virus and influenza, [12] [13] [14] lending credence to the notion that COVID-19 could run a more severe course in these children. Given the probable paucity of these patients at any single paediatric centre, there is a dire need for collaborative research efforts on a global scale to characterise the clinical features and outcomes of COVID-19 in children with haemodynamically significant congenital heart disease as well as other vulnerable paediatric populations. cache = ./cache/cord-351718-sf5zp5wg.txt txt = ./txt/cord-351718-sf5zp5wg.txt === reduce.pl bib === id = cord-351694-nb7230s1 author = Jatt, Lauren P. title = Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1522 sentences = 79 flesch = 44 summary = title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings We describe a widespread laboratory surveillance program for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) at an integrated medical campus that includes a tertiary-care center, a skilled nursing facility, a rehabilitation treatment center, and temporary shelter units. As part of its coronavirus disease 2019 (COVID-19) response, VAGLAHS implemented a widespread laboratory surveillance program for SARS-CoV-2 in both hospital and residential facilities. Finally, on March 31, the laboratory at VALBHS initiated SARS-CoV-2 testing using the cobas system and began accepting specimens from other VA facilities, substantially increasing testing capacity and further decreasing turnaround time to a median of 1 day (IQR, 1-1). On April 3 and April 6, 57 residents who originally tested negative but lived in the same SNF unit as the SARS-CoV-2 positive individuals were retested, and 2 additional asymptomatic cases were identified. cache = ./cache/cord-351694-nb7230s1.txt txt = ./txt/cord-351694-nb7230s1.txt === reduce.pl bib === id = cord-351845-bli3qm8w author = Prasad, Kartikay title = Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4626 sentences = 293 flesch = 46 summary = Towards this goal, in this study, we have generated a human-SARS-CoV-2 interactome based on recently published RNA-Seq analysis of human adenocarcinomic alveolar basal epithelial (A549) cells infected with SARS-CoV-2, and identified disease-related functional genes that will provide the insights into the patho-J o u r n a l P r e -p r o o f 4 mechanisms of COVID-19. Overall, the analysis demonstrated that the upregulated genes are mainly linked to the host response to SARS-CoV-2 infection, type I interferon signaling and the cytokine-mediated signaling pathway. The PPI network analysis indicates that the pathways are enriched in host response to virus infection, type I interferons signaling, and cytokine activation. [74] reported high SARS-CoV-2 loads very early during infection, suggesting that the virus may have developed arsenals that is able to delay the IFN response by inhibiting innate immune signaling. cache = ./cache/cord-351845-bli3qm8w.txt txt = ./txt/cord-351845-bli3qm8w.txt === reduce.pl bib === id = cord-351952-lhhjax3s author = Pickering, Suzanne title = Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5310 sentences = 247 flesch = 48 summary = Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays—a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)—on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing standardised diagnostic test for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the configuration of the in-house ELISA most likely to represent antibodies detected by the commercial tests (detection of anti-S IgM and IgG antibodies), and that had high specificity and sensitivity (S1 Table) . cache = ./cache/cord-351952-lhhjax3s.txt txt = ./txt/cord-351952-lhhjax3s.txt === reduce.pl bib === id = cord-352073-rdhjj72g author = Taniwaki, S.A title = Resource optimization in COVID-19 diagnosis date = 2020-06-26 pages = extension = .txt mime = text/plain words = 1910 sentences = 98 flesch = 57 summary = The emergence and rapid dissemination worldwide of a novel Coronavirus (SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This manuscript reports on the optimization of the Charité and the CDC RT-qPCR protocols for SARS-CoV-2 detection regarding concentration and volumes of reagents for both probe and intercalant agent-based platforms, as well as on the substitution of rayon swabs for cotton swabs for sample collection. Performance of E and RdRp genes of SARS-CoV-2 RT-qPCRs, based on final reaction volume of 10 µL with 2 µL of RNA (Table 1) , were verified with a relative standard curve built with 10 -2 to 10 -8 dilutions of positive RNA control. Tabela 4 -Probe-based RT-qPCR to the E gene of serial dilutions of SARS-CoV-2 sampled with cotton and rayon swabs. cache = ./cache/cord-352073-rdhjj72g.txt txt = ./txt/cord-352073-rdhjj72g.txt === reduce.pl bib === id = cord-351930-puhm3w42 author = Juan, J. title = Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4503 sentences = 285 flesch = 53 summary = . https://doi.org/10.1101/2020.05.02.20088484 doi: medRxiv preprint are fever, cough, dyspnea/shortness of breath and fatigue; third, on admission, most cases have patchy shadowing or ground-glass opacity on CT of the chest, and that normal or low leukocyte, lymphocytopenia and raised CRP are the most common laboratory findings observed in COVID-19-infected pregnant patients; fourth, the rate of severe COVID-19 pneumonia is relatively low but there are two reported maternal deaths, as of April 23, 2020; fifth, COVID-19 does not appear to increase the risk of adverse pregnancy outcomes such as preeclampsia; sixth, only a few pregnancies have resulted in a spontaneous miscarriage or abortion; seventh, of those who have delivered, the gestational age at delivery ranged from 28 to 41 weeks and the majority of cases have had Cesarean delivery; and eighth, in the case-series there have been no reported cases of neonates tested positive for SARS-CoV-2, however, in the case-reports there has been one case each with positive SARS-CoV-2 in amniotic fluid and neonatal throat swab. cache = ./cache/cord-351930-puhm3w42.txt txt = ./txt/cord-351930-puhm3w42.txt === reduce.pl bib === id = cord-351687-6otr8zl3 author = Yesilkaya, Umit Haluk title = Neuroimmune correlates of the nervous system involvement of COVID-19: A commentary date = 2020-05-27 pages = extension = .txt mime = text/plain words = 934 sentences = 62 flesch = 40 summary = • Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Strikingly, they postulated that enhanced inflammatory signalling and immune-mediated processes which are activated by SARS-CoV-2 might imitate the molecular architecture of self-directed immunity in the peripheral nervous system and might lead to Guillain Barre syndrome (GBS), an autoimmune disorder. It should be considered that neuropsychiatric manifestations related to human coronaviruses including SARS-CoV-2 might be associated with the involvement of both neuroimmune response and direct viral transmission.  Pathophysiological underpinnings of nervous system involvement of SARS-CoV-2 are yet to be elucidated  Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Severe Acute Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the Absence of Encephalitis in Mice Transgenic for Human ACE2 The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients cache = ./cache/cord-351687-6otr8zl3.txt txt = ./txt/cord-351687-6otr8zl3.txt === reduce.pl bib === id = cord-351837-vasuu70k author = Shannon, Ashleigh title = Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date = 2020-09-17 pages = extension = .txt mime = text/plain words = 6507 sentences = 349 flesch = 50 summary = title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 . cache = ./cache/cord-351837-vasuu70k.txt txt = ./txt/cord-351837-vasuu70k.txt === reduce.pl bib === id = cord-351854-5s03f0pp author = Ben-Ami, Roni title = Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3316 sentences = 197 flesch = 54 summary = title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. cache = ./cache/cord-351854-5s03f0pp.txt txt = ./txt/cord-351854-5s03f0pp.txt === reduce.pl bib === id = cord-352030-hnm54k4r author = Liu, Jie title = Epidemiological, Clinical Characteristics and Outcome of Medical Staff Infected with COVID-19 in Wuhan, China: A Retrospective Case Series Analysis date = 2020-03-13 pages = extension = .txt mime = text/plain words = 5263 sentences = 281 flesch = 51 summary = These included age, sex, occupation (doctor, or nurse), body mass index (BMI ≥ 24, or <24 kg/m 2 ), current smoking status (yes, or no), disease severity (non-severe, or severe), date of symptom onset, symptoms before hospital admission (fever, cough, fatigue, sore throat, myalgia, sputum production, difficulty breathing or chest tightness, chill, loss of appetite, diarrhea, and chest pain), coexisting conditions (e.g. hypertension, diabetes, etc.), laboratory testing indicators on admission (leucocyte count, lymphocyte count, platelet count, D-dimer, creatinine, creatine kinase, lactose dehydrogenase, alanine aminotransferase, aspartate aminotransferase, hemoglobin, ferritin, C-reactive protein, Amyloid A, total bilirubin, procalcitonin, erythrocyte sedimentation rate, interleukin-6 (IL-6) and lymphocyte subsets, etc.), radiologic assessments of chest CT (lung involvement, lung lobe involvement, predominant CT changes, predominant distribution of opacities, etc.), treatment measures (antibiotics agents, antiviral agents, traditional Chinese medicine, immune globulin, thymosin, corticosteroids and oxygen therapy), and complications (e.g. pneumonia, acute respiratory distress syndrome, acute cardiac injury, acute kidney injury, shock, etc.). cache = ./cache/cord-352030-hnm54k4r.txt txt = ./txt/cord-352030-hnm54k4r.txt === reduce.pl bib === id = cord-351835-1s2zsqoq author = Liu, Zhixin title = Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 date = 2020-03-11 pages = extension = .txt mime = text/plain words = 1514 sentences = 101 flesch = 54 summary = title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 In this study, we used systematic comparison and analysis to predict the interaction between the receptor‐binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin‐converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor-binding domain, contains core binding motif in the external subdomain; SP, signal peptide Phylogenetic reconstruction determines the evolutionary relationship and host selection between spike glycoproteins in the human-close beta coronaviruses. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2 cache = ./cache/cord-351835-1s2zsqoq.txt txt = ./txt/cord-351835-1s2zsqoq.txt === reduce.pl bib === id = cord-351770-cirq6pfx author = Chen, Wei title = SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3771 sentences = 226 flesch = 54 summary = In this study, we analyzed the SARS-CoV-2 NAb titers in patients recently recovered from COVID-19 using a novel SARS-CoV-2 surrogate virus neutralization test (sVNT) [12] . The distribution of NAb titers in patients with COVID-19 were then plotted based on the variables of age, sex, symptom, laboratory parameters and chest CT findings at the time of admission, treatment during hospitalization and the time of blood collection for antibody analysis (Figure 1 ). Independent variables included in the OLS model included age, sex, CT score, comorbidity, laboratory parameters that associated with disease severity (CRP level and lymphocyte counts), treatment that may influence immune response to pathogen (corticosteroids and intravenous immunoglobulin) and time of blood collection for NAb analysis. In multivariate analyses, after adjustment for age, sex, comorbidity, corticosteroid treatment, CRP level, lymphocyte count and time of NAb analysis, baseline chest CT scores still strongly correlated with NAb titers in patients recovered from COVID-19 (Table 2 , p=0.02). cache = ./cache/cord-351770-cirq6pfx.txt txt = ./txt/cord-351770-cirq6pfx.txt === reduce.pl bib === id = cord-351864-zozrj7w5 author = Chappleboim, A. title = ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date = 2020-08-13 pages = extension = .txt mime = text/plain words = 5782 sentences = 321 flesch = 57 summary = Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Briefly, we show ( Figure 1 ) that we can introduce barcoded and target-specific reverse transcription primers to the samples, allowing them to hybridize to target RNA molecules already in the lysis buffer, or after a brief RNA cleanup step. Observing the target sequence directly allowed us to identify viral sequence variations in some cases ( Figure 2D ).Cross-Sample Contamination is minimal When pooling samples early on in the protocol, the main concern is that RNA molecules will be erroneously tagged due to residual free primers, or due to other artifacts during RT, PCR, or sequencing. cache = ./cache/cord-351864-zozrj7w5.txt txt = ./txt/cord-351864-zozrj7w5.txt === reduce.pl bib === id = cord-352123-0bflqj1c author = Csiszar, Anna title = Companion animals likely do not spread COVID-19 but may get infected themselves date = 2020-08-07 pages = extension = .txt mime = text/plain words = 4752 sentences = 225 flesch = 51 summary = Recent evidence suggests that SARS-CoV-2, similar to other coronaviruses, can infect several species of animals, including companion animals such as dogs, cats, and ferrets although their viral loads remain low. In late March 2020, the Federal Agency for the Safety of the Food Chain (FASFC) in Belgium reported that a pet cat was diagnosed to be infected with SARS-CoV-2 [21, 22] , showing that felines living in the household of people with COVID-19 are at risk of contracting the disease and may potentially spread the virus. On April 23, it was reported that two pet cats in New York state have tested positive for the SARS-CoV-2, which are the first confirmed COVID-19 cases in companion animals in the USA [22] . In the current SARS-CoV-2 pandemic, the situation is rapidly evolving and in the light of the recent evidence, we should be aware of the possibility that humans can be potentially infected with COVID-19 by animals, including by pet cats, dogs, or other domesticated species. cache = ./cache/cord-352123-0bflqj1c.txt txt = ./txt/cord-352123-0bflqj1c.txt === reduce.pl bib === id = cord-352304-tt2q5mgs author = Sun, Dan title = Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center’s observational study date = 2020-03-19 pages = extension = .txt mime = text/plain words = 3229 sentences = 194 flesch = 52 summary = METHODS: We included eight severe or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children's Hospital from January 24 to February 24. The outbreak of coronavirus disease 2019 (COVID-19, previously known as 2019-nCoV) caused by SARS-CoV-2 infection in Wuhan City, China, has spread around the world [1] . We included eight severely or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children's Hospital from January 24 to February 24. Critically ill COVID-19 was defined when the pediatric patients met any of the following criteria: (1) respiratory failure which requires mechanical ventilation; (2) septic shock, and (3) accompanied by other organ failure that needs ICU monitoring and treatment. Demographic information and clinical characteristics including exposure history, anamnesis, signs and symptoms, chest computed tomographic (CT) scan or X-ray results, complications, treatments, clinical outcomes, and laboratory findings of each patient were obtained from the Electronic Medical Record System of Wuhan Children's Hospital. cache = ./cache/cord-352304-tt2q5mgs.txt txt = ./txt/cord-352304-tt2q5mgs.txt === reduce.pl bib === id = cord-351719-xqmir1ca author = Olaimat, Amin N. title = Food Safety During and After the Era of COVID-19 Pandemic date = 2020-08-04 pages = extension = .txt mime = text/plain words = 3906 sentences = 208 flesch = 51 summary = The coronavirus disease 2019 (COVID-19) is a clinical syndrome caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). COVID-19 is the clinical syndrome caused by SARS-CoV-2 infection which is characterized by a respiratory disease with symptoms ranging from mild influenza (flu-like) to severe pneumonia and acute respiratory distress syndrome (Petrosillo et al., 2020) . A previous study reported that food products were a plausible transmission route for respiratory viruses including SARS-CoV-1 and influenza (Klein, 2004) . The proper use of gloves, sanitizers, and disinfectants can minimize the risk of virus spread and disease transmission (Food and Agriculture Organization of the United Nations [FAO] and World Health Organization [WHO], 2020; Food and Drug Administration [FDA], 2020a). The current guidelines issued by public health authorities are based on the disease patterns of previously encountered coronaviruses and they need to be updated according to the novel coronavirus SARS-CoV-2 as this virus is likely to persist and people will have to modify their "normal behavior" to a "new normal." cache = ./cache/cord-351719-xqmir1ca.txt txt = ./txt/cord-351719-xqmir1ca.txt === reduce.pl bib === id = cord-351896-j6h02ab5 author = Ghannam, Malik title = Neurological involvement of coronavirus disease 2019: a systematic review date = 2020-06-19 pages = extension = .txt mime = text/plain words = 5060 sentences = 271 flesch = 40 summary = The following search strategy was implemented and these keywords and their synonyms (in the all fields) were combined in each database as follows: ("COVID 19" OR "coronavirus") AND ("brain" OR "CNS" OR "spinal cord" OR "nerve" OR "neurologic" OR "stroke" OR "cerebrovascular" OR "cerebral vein thrombosis" OR "sinus thrombosis" OR "Intracerebral hemorrhage" OR "hemorrhage" OR "myelitis" OR "GBS" OR "Guillain Barre syndrome" OR "neuropathy" OR "radiculopathy" OR "cranial neuropathy" OR "myopathy" OR "myositis" OR "rhabdomyolysis" OR "encephalitis" OR "encephalopathy" OR "meningitis" OR "meningoencephalitis" OR "seizure" OR "convulsion" OR "epilepsy") [ Fig. 1 ]. [11] For each study, the following descriptive, microbiological, and clinical information was extracted: patient demographic data, SARS-CoV-2 testing from nasal swab and CSF, neurological symptoms and signs and their onset in relation to respiratory or gastrointestinal (GI) symptoms or anosmia or dysgeusia, any neurological investigations and CSF or any other relevant laboratory testing (such as CK, LDH, CRP, D-dimer, lupus anticoagulant, fibrinogen, ganglioside antibodies), neurological diagnosis, occurrence of respiratory failure (defined as need for intubation, abnormal PO2 in blood gas, or Glasgow Coma Scale score less than or equal 8), treatments administered for the neurological diagnosis, and final outcome. cache = ./cache/cord-351896-j6h02ab5.txt txt = ./txt/cord-351896-j6h02ab5.txt === reduce.pl bib === id = cord-352080-3rcqbgl7 author = Shidham, Vinod B. title = Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date = 2020-04-10 pages = extension = .txt mime = text/plain words = 3486 sentences = 227 flesch = 50 summary = It is therefore mandatory to practice all the universal/standard precautions with basic protective measures while handling any biological specimen irrespective of SARS-CoV-2 status [Tables 1 -3] . [16] Although, appropriate disinfectants and precautions related to cytopathological/histological fixation and processing of samples during the current COVID 19 pandemic are not known, information can likely be extrapolated from other recent coronaviruses (e.g., SARS and MERS). 5. If the diagnostic testing specimens are processed outside of a BSL-2 laboratory, [33] such as preparation of cytology direct smears, rinsing of FNAB aspirates for cell block, the Standard Precautions (similar to those mentioned under Table 1 ) should be practiced as a barrier between the specimen and personnel. [14, 15] In cases suspected or positive for SARS-CoV-2 virus-perform the processing in certified Class II [35] Biological Safety Cabinet FNAB procedure [22] Based on the aforementioned, SARS-CoV-2 in any specimen processed with routine fixatives in cytopathology should be inactivated [ Table 5 ]. cache = ./cache/cord-352080-3rcqbgl7.txt txt = ./txt/cord-352080-3rcqbgl7.txt === reduce.pl bib === id = cord-351736-4x5u4qsy author = Fernandez-Garcia, Cristina title = Severe COVID-19 During Pregnancy and the Subsequent Premature Delivery date = 2020-09-19 pages = extension = .txt mime = text/plain words = 556 sentences = 44 flesch = 62 summary = Only a few case of SARS-CoV-2 infection in preterm neonates delivered by mothers with COVID-19 have been reported till date. We report the cases of three premature babies delivered by two mothers with severe COVID-19 pneumonia, whose condition deteriorated to the point that necessitated the use of mechanical ventilation on the mothers as well as accelerated child delivery of the mothers. There have been very few reports of preterm delivery in mothers with COVID-19 and most babies have tested negative to SARS-CoV-2. 3, 4 In the few reported neonates who tested positive to SARS-CoV-2 via PCR, there is no evidence of in utero transmission, since infection in the immediate neonatal period could not be completely excluded. 5, 6 Preterm delivery was required in the three cases described in this report, since the mothers developed severe COVID-19 pneumonia. There was no evidence of in utero transmission, such that all the babies (3) tested negative to SARS-CoV-2 immediately after birth and at 24 hours, 5, and 14 days of life. cache = ./cache/cord-351736-4x5u4qsy.txt txt = ./txt/cord-351736-4x5u4qsy.txt === reduce.pl bib === id = cord-352096-cc3dzycl author = Richman, Douglas D. title = Antiviral Drug Discovery To Address the COVID-19 Pandemic date = 2020-09-25 pages = extension = .txt mime = text/plain words = 1520 sentences = 70 flesch = 35 summary = Regardless of whether or when a vaccine becomes available, antivirals for SARS-CoV-2 will still be needed for several reasons: the unlikelihood that a vaccine will be 100% effective, the incompleteness of vaccine coverage because of both vaccine hesitancy and the numerous logistical challenges to accomplishing prompt large-scale immunization of the majority of the population, the possibility of limited durability of vaccine protection, the need for additional prophylaxis for high-risk subjects and poor vaccine responders, and the future value of effective antiviral treatment for Middle East respiratory syndrome (MERS) and new coronaviruses that will likely emerge from zoonoses. suggest that the purported activity against SARS-CoV-2 of the two HIV protease inhibitors, lopinavir and nelfinavir, is probably attributable to cellular toxicity. Structurebased design of antiviral drug candidates targeting the SARS-CoV-2 main protease AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic cache = ./cache/cord-352096-cc3dzycl.txt txt = ./txt/cord-352096-cc3dzycl.txt === reduce.pl bib === id = cord-352059-1bjskqyg author = Gupta, Nivedita title = Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories date = 2020-04-28 pages = extension = .txt mime = text/plain words = 4174 sentences = 224 flesch = 53 summary = The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, which is the apex laboratory for viral diagnosis and research in India, optimized the conventional and real-time PCR assays targeting different genomic regions of SARS-CoV-2 and initiated testing of suspected cases. Before initiating testing of clinical specimens from suspected cases of SARS-CoV-2, each VRDL shared results from the rRT-PCR runs performed with positive and negative controls with the apex laboratory (NIV, Pune). Expansion of testing capabilities and selection of testing laboratories for SARS-CoV-2: Following the increase in the load of screening samples from suspected cases with symptoms and travel history to China or asymptomatic persons with travel history to Wuhan after January 15, 2020, it was decided that strategically located VRDLs needed to start testing for SARS-CoV-2 in addition to Thereafter, NCDC, Delhi, initiated independent testing; however, results were shared with ICMR on a daily basis. cache = ./cache/cord-352059-1bjskqyg.txt txt = ./txt/cord-352059-1bjskqyg.txt === reduce.pl bib === id = cord-351974-1najtyui author = Smith, E. title = Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2661 sentences = 181 flesch = 60 summary = 1 2 Transmission of SARS-CoV-2 may be possible up to two-days prior to the appearance of typical symptoms yet older patients frequently have atypical presentation, 3-5 making recognition and control of infection in care homes difficult. SARS-CoV-2 has highlighted serious gaps in data intelligence surrounding care homes, 13 with regional test results typically not available to local authorities until 2 July 2020. In addition, for SARS-CoV-2-positive residents who were asymptomatic at the point of test, data on any symptoms recorded in the 14-day post-test period were extracted. Data for residents and staff tests comprised unique ID, care home ID, date of SARS-CoV-2 test(s) and test outcome(s). Early screening of residents and staff after ingress into care homes identified prevalence of truly asymptomatic infections and symptom presentation in residents relatively early in the UK COVID-19 outbreak. Early testing and screening of staff and residents in care homes can accurately identify outbreaks, prevalence of infection and death, and cause of death. cache = ./cache/cord-351974-1najtyui.txt txt = ./txt/cord-351974-1najtyui.txt === reduce.pl bib === id = cord-352296-rpjehijd author = Azzi, Lorenzo title = Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern date = 2020-05-11 pages = extension = .txt mime = text/plain words = 639 sentences = 44 flesch = 62 summary = title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern During our research, we found two patients out of 25 subjects (i.e., 8%) affected by COVID-19 with different degrees of severity, who showed positive salivary results on the same days when their pharyngeal or bronchoalveolar swabs proved to be negative . These findings, together with those reported by the F I G U R E 1 The temporal line of the clinical course in the two patients shows how their salivary samples tested positive, while the pharyngeal or bronchoalveolar swabs were negative on the same day (Patient 1 on March 19) or during the interval between two consecutive salivary swabs (Patient 2, March 23-28) Chinese colleagues on sputum, rise the concern about how to manage these patients before hospital discharging. Two cases of COVID-19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern cache = ./cache/cord-352296-rpjehijd.txt txt = ./txt/cord-352296-rpjehijd.txt === reduce.pl bib === id = cord-352196-rpyoeg9n author = Alberici, Federico title = A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2630 sentences = 136 flesch = 51 summary = title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. The main clinical characteristics of the overall MHD population with SARS-CoV2 infection and the subgroups managed as outpatient or in hospital are shown in Table 2 . In our cohort including four centers of the "Brescia Renal COVID task force", we have identified 94 patients with SARS-CoV-2 infection. The finding of worse outcome of hemodialysis patients with SARS-CoV-2 infection may be explained by high prevalence of comorbidities as well as other risk factors related to end stage renal disease per se (2). Management of Patients on Dialysis and With Kidney Transplantation During the SARS-CoV-2 (COVID-19) Pandemic in Brescia A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia cache = ./cache/cord-352196-rpyoeg9n.txt txt = ./txt/cord-352196-rpyoeg9n.txt === reduce.pl bib === id = cord-352146-i4ezsclf author = Cimolai, Nevio title = Efficacy of povidone‐iodine to reduce viral load date = 2020-07-31 pages = extension = .txt mime = text/plain words = 580 sentences = 43 flesch = 52 summary = (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. While povidone-iodine may be the main ingredient in the specific mouthwash preparation, there are often a number of unlisted ingredients (e.g., alcohol) which can potentially provide both antisepsis and RT-PCR inhibition. As another form of control, however, it would be of relevance to see what the lavage properties of gargling in itself have for reducing viral load in those samples assessed. COVID-19, povidone-iodine, quantitation, respiratory, SARS-CoV-2 Is povidone-iodine mouthwash effective against SARS-CoV-2? cache = ./cache/cord-352146-i4ezsclf.txt txt = ./txt/cord-352146-i4ezsclf.txt === reduce.pl bib === id = cord-352228-dzkf7c7l author = Fontanet, Arnaud title = Cluster of COVID-19 in northern France: A retrospective closed cohort study date = 2020-04-23 pages = extension = .txt mime = text/plain words = 4248 sentences = 225 flesch = 54 summary = Methods: Between 30 March and 4 April 2020, we conducted a retrospective closed cohort study among pupils, their parents and siblings, as well as teachers and non-teaching staff of a high-school located in Oise. Participants completed a questionnaire that covered history of fever and/or respiratory symptoms since 13 January 2020 and had blood tested for the presence of anti-SARS-CoV-2 antibodies. Interpretation: The relatively low IAR observed in an area where SARS-CoV-2 actively circulated weeks before confinement measures indicates that establishing herd immunity will take time, and that lifting these measures in France will be long and complex. Using a combination of serologic assays with high sensitivity and specificity for anti-SARS-CoV-2 antibodies, we conducted a retrospective closed cohort study. This is, to our knowledge, the first study estimating by antibody detection the IAR of SARS-CoV-2 infection in a community affected by COVID-19, and the fist description of a COVID-19 outbreak in a school. cache = ./cache/cord-352228-dzkf7c7l.txt txt = ./txt/cord-352228-dzkf7c7l.txt === reduce.pl bib === id = cord-352379-q5inrxcm author = Lai, Michael M. C. title = SARS virus: The beginning of the unraveling of a new coronavirus date = 2003-10-17 pages = extension = .txt mime = text/plain words = 7004 sentences = 376 flesch = 49 summary = Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public's interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-352379-q5inrxcm.txt txt = ./txt/cord-352379-q5inrxcm.txt === reduce.pl bib === id = cord-352509-qrzt4zva author = Chen, Haohui title = Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak date = 2020-03-16 pages = extension = .txt mime = text/plain words = 3903 sentences = 223 flesch = 63 summary = This study examines publicly available online search data in China to investigate the spread of public awareness of the 2019 novel coronavirus (COVID-19) outbreak. We use the continuing Wuhan coronavirus outbreak as our case study to estimate the effects of social distance and SARS memory on the spread of public awareness. The effects of social distance and SARS memory on the lead-time advantage are estimated according to Eq. 4, controlled by Euclidean distances, GDP per capita and the city's administrative level (Table 1) . That means cities of strong SARS memory and which are closer to Wuhan in terms of Social distances develop early awareness. Through controlling for development, administrative levels, and Euclidean distances, we observe cities that were struck by SARS and have more migration to the epicentre, Wuhan, showed earlier, stronger and more durable public awareness of the outbreak. cache = ./cache/cord-352509-qrzt4zva.txt txt = ./txt/cord-352509-qrzt4zva.txt === reduce.pl bib === id = cord-352526-t8odetzw author = Pinto, Bruna G G title = ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date = 2020-06-11 pages = extension = .txt mime = text/plain words = 3032 sentences = 199 flesch = 50 summary = Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. The molecular mechanism responsible for the increased disease severity in patients with these comorbidities is not fully understood, but previous studies suggest a role for angiotensin-converting enzyme 2 (ACE2) (5) . Here, we showed that the expression of the gene encoding the ACE2 receptor in lung tissue is upregulated by diseases representing comorbidities along with COVID-19. cache = ./cache/cord-352526-t8odetzw.txt txt = ./txt/cord-352526-t8odetzw.txt === reduce.pl bib === id = cord-352341-dhc748pn author = Miranda-Zazueta, G. title = Manejo farmacológico de pacientes con enfermedades hepáticas y pancreáticas que involucran terapias inmunosupresoras. Posicionamiento en el marco de la pandemia de SARS-COV-2 (COVID-19) date = 2020-06-17 pages = extension = .txt mime = text/plain words = 4118 sentences = 422 flesch = 54 summary = 5 Hasta este momento se han emitido las siguientes recomendaciones en pacientes infectados por COVID-19 que tienen una enfermedad hepática autoinmune de base y usan inmunosupresores: [5] [6] [7] [8]  El presentar alteraciones en las pruebas de función hepática no limita iniciar el tratamiento para COVID-19. Las recomendaciones generales para el manejo de pacientes con trasplante hepático y diagnóstico de COVID-19 se realizan de acuerdo con los diferentes escenarios posibles que nos podemos enfrentar en la práctica clínica. No existe hasta el momento de esta publicación información sobre el riesgo de infecciones en pacientes con inmunosupresión y Pancreatitis Autoinmune (PAI), muchos menos en el contexto del nuevo coronavirus SARS-CoV-2, Sin embargo, teóricamente este riesgo no debería ser mayor al observado para otro tipo de infecciones. cache = ./cache/cord-352341-dhc748pn.txt txt = ./txt/cord-352341-dhc748pn.txt === reduce.pl bib === id = cord-352365-b9cmviny author = Marchetti, Monia title = COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure date = 2020-06-24 pages = extension = .txt mime = text/plain words = 3887 sentences = 176 flesch = 29 summary = This review also highlights potential targets for prevention and therapy of COVID-19-related organ damage and discusses the role of marketed drugs, such as eculizumab and imatinib, as suitable candidates for clinical trials. Also, C3a complement fraction plays a relevant role in the pathogenesis of infection-related lung injury: high serum C3a predicts evolution to ARDS [9, 10] , while both C3a and C5a increase endothelial permeability and activate endothelial cells, thereby increasing the expression of adhesion molecules and cytokines [11, 12] , and the distal complement activation product C5 b-9 triggers intracellular fluxes of calcium in epithelial and endothelial cells. Apoptosis of human pulmonary microvascular endothelial cell may be chronically triggered by inflammation, such as in COPD, or acutely induced by ARDS; the latter is mediated by Bruton kinase (BTK), IL-17, and macrophage stimulating-1, while IL-35 seems protective [41] [42] [43] [44] . cache = ./cache/cord-352365-b9cmviny.txt txt = ./txt/cord-352365-b9cmviny.txt === reduce.pl bib === id = cord-352230-8mazd3eu author = Beeraka, Narasimha M. title = Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date = 2020-09-18 pages = extension = .txt mime = text/plain words = 9394 sentences = 543 flesch = 40 summary = Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. COVID-19 is a devastating disease caused by a coronavirus related to the one that caused outbreaks of Severe Acute Respiratory Syndrome (SARS) in the year 2002 (1, 2) . cache = ./cache/cord-352230-8mazd3eu.txt txt = ./txt/cord-352230-8mazd3eu.txt === reduce.pl bib === id = cord-352281-9huyb4cs author = Ayoub, Houssein H. title = Age could be driving variable SARS-CoV-2 epidemic trajectories worldwide date = 2020-04-17 pages = extension = .txt mime = text/plain words = 5128 sentences = 361 flesch = 53 summary = We aimed here to answer this question and to estimate for each country (with a population ≥1 million), region, and globally, 0 R , and the rate per 100 persons (out of the total population by the end of the epidemic cycle) of each of the cumulative number of incident infections, mild infections, severe and/or critical disease cases, and deaths, in addition to the number of days needed for the national epidemic to reach its incidence peak (a measure of how fast the epidemic will grow). 13.20059253 doi: medRxiv preprint Figure S11 : Sensitivity analysis assessing the impact of a 50% increase in the susceptibility to SARS-CoV-2 infection among those aged <30 years on our estimates for the basic reproduction number, R0, for the select countries presented in the main text. cache = ./cache/cord-352281-9huyb4cs.txt txt = ./txt/cord-352281-9huyb4cs.txt === reduce.pl bib === id = cord-352557-l7sahv5t author = Takla, Michael title = Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety date = 2020-11-13 pages = extension = .txt mime = text/plain words = 7587 sentences = 347 flesch = 43 summary = In contrast, only 58% of observational studies employing an endpoint specific to efficacy recorded no significant difference in the attainment of outcomes, such as duration of hospital stay, need for mechanical ventilation, and probability of transfer to an intensive care unit (ICU), between COVID-19 patients given a range of CQ and/or HCQ doses, and the control groups. Indeed, of the remaining papers, 60% found evidence of a higher probability of discharge rate (Sbidian et al., 2020) , viral clearance and shorter symptom duration (Huang et al., 2020a) in a therapeutic context, and a lower incidence of SARS-CoV-2 infection in a prophylactic context (Bhattacharya et al., 2020 Although 60% of clinical trials found evidence of higher mild adverse drug-related events in the treatment group, none of those specifically focusing on cardiac-side effects discovered any significant difference relative to the control. cache = ./cache/cord-352557-l7sahv5t.txt txt = ./txt/cord-352557-l7sahv5t.txt === reduce.pl bib === id = cord-352156-sa8cvyuw author = Lindeman, Robbert-Jan title = Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1834 sentences = 96 flesch = 44 summary = title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries In both countries, the first weeks of preparation has seen a strong reduction in elective surgery, with several implemented principles to mitigate SARS-CoV-2 spread and prepare for surgical care for COVID-19 diseases as needed. Norway, that initially started with aggressive testing of subjects with symptoms or returning from high-endemic areas in order to get control over the spread pattern and asymptomatic COVID-19 patients, needed to restrict its activity later in March. An early effect of the initially suboptimal test routines for healthcare workers (HCW) was experienced in Norway, when one HCW returning from central Europe, was confirmed positive to SARS-CoV-2 only after having spent several days at work on the advice from the hospital. The acute threat of the COVID-19 epidemic to global healthcare has led to forced reorganization of surgical care in Norway and Sweden. cache = ./cache/cord-352156-sa8cvyuw.txt txt = ./txt/cord-352156-sa8cvyuw.txt === reduce.pl bib === id = cord-352562-qfb478sf author = Yamamoto, Lidia title = SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date = 2020-09-04 pages = extension = .txt mime = text/plain words = 7315 sentences = 341 flesch = 45 summary = In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. They identified 191 cases in hospitalized patients younger than 21 years of age, reported by hospitals in the New York State with the diagnosis of Kawasaki disease, toxic shock syndrome, myocarditis, and suspected multisystem inflammatory syndrome associated with COVID-19 in children (MIS-C). The laboratory diagnosis of COVID-19 are based on the detection of viral RNA by real time amplifications (RT-PCR) 40 or the detection of antibodies (immunoglobulins) anti-SARS-CoV-2 from the classes IgM, IgA and IgG, produced by the host's immune system. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review cache = ./cache/cord-352562-qfb478sf.txt txt = ./txt/cord-352562-qfb478sf.txt === reduce.pl bib === id = cord-352433-sts48u9i author = Galanti, Marta title = Direct Observation of Repeated Infections With Endemic Coronaviruses date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3824 sentences = 170 flesch = 41 summary = BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. However, in Korea, as reported by the Korean Centers for Disease Control and Prevention, viable SARS-CoV-2 was not isolated in cell culture of respiratory samples from potentially reinfected individuals [5] ; thus, these subsequent positive results may have been due to inactive genetic material detected by molecular testing. cache = ./cache/cord-352433-sts48u9i.txt txt = ./txt/cord-352433-sts48u9i.txt === reduce.pl bib === id = cord-352020-9wxwktck author = Zhang, Baoshan title = A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone date = 2020-10-23 pages = extension = .txt mime = text/plain words = 4914 sentences = 266 flesch = 46 summary = To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses. To improve protein solubility and expression, we added glycans to the surface of the nanoparticles, designing a panel of LuS and ferritin constructs with SpyTag and SpyCatcher (Table 1 and Supplementary Table S1 ). To demonstrate the versatility of our SpyTag-displaying nanoparticles in immunogen development, we conjugated them to three viral antigens of vaccine interest, the DS2-preF stabilized RSV F 33 , a DS2-stabilized version of PIV3 F 34 , and the 2P-stabilized version of SARS-CoV-2 spike 24 . cache = ./cache/cord-352020-9wxwktck.txt txt = ./txt/cord-352020-9wxwktck.txt === reduce.pl bib === id = cord-352256-qxdakdk0 author = Yousefi, Bahman title = A global treatments for coronaviruses including COVID‐19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4017 sentences = 213 flesch = 48 summary = Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Chloroquine inhibits SARS-CoV entry, which exerts its inhibitory effect by altering glycosylation of the ACE2 receptor and spike protein. | 5 in a MERS-CoV rhesus macaque model were promising, with the results of the trial and the effect of ribavirin and IFN (either α2a or β1) on MERS-CoV infected patients it was different, however, ribavirin lowers hemoglobin concentrations in respiratory patients and therefore reduces its potential as an antiviral against SARS-CoV-2 (Arabi et al., 2017; Falzarano et al., 2013) . cache = ./cache/cord-352256-qxdakdk0.txt txt = ./txt/cord-352256-qxdakdk0.txt === reduce.pl bib === id = cord-352580-l6vkzja0 author = Iltaf, Samar title = Frequency of Neurological Presentations of Coronavirus Disease in Patients Presenting to a Tertiary Care Hospital During the 2019 Coronavirus Disease Pandemic date = 2020-08-18 pages = extension = .txt mime = text/plain words = 2266 sentences = 130 flesch = 42 summary = Background Coronavirus disease 2019 (COVID-19), caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), usually presents clinically with cough, fever, shortness of breath, and loss of taste and/or smell. COVID-19 can also present with neurologic signs and symptoms, including headache, hyposmia/anosmia, encephalopathy, meningoencephalitis, Guillain-Barré syndrome, stroke, and seizure. This subjective survey addressed 10 neurological manifestations of COVID-19: headache, altered sensation, nausea and vomiting, sudden hemiparesis (stroke), numbness and paresthesia, vertigo, ataxia, seizure, encephalitis/meningitis, Guillain-Barré Syndrome (GBS), and myelitis. Our study confirmed that headache (6%), altered level of consciousness and encephalopathy (2%), hemiparesis (stroke; 0.6%), GBS (0.3%) and seizure (0.3%) were the most frequently reported neurological presentations [5, 6, 7, 8] . A case study reported that a patient positive for SARS-CoV-2 presented with isolated sudden onset anosmia but no other symptoms of COVID-19 [11] . cache = ./cache/cord-352580-l6vkzja0.txt txt = ./txt/cord-352580-l6vkzja0.txt === reduce.pl bib === id = cord-352720-z1cvjc2y author = Díaz-Corvillón, Pilar title = Routine screening for SARS CoV-2 in unselected pregnant women at delivery date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4061 sentences = 244 flesch = 49 summary = While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. cache = ./cache/cord-352720-z1cvjc2y.txt txt = ./txt/cord-352720-z1cvjc2y.txt === reduce.pl bib === id = cord-352737-3ttrx3lf author = Cunha, Lucas Leite title = Remodeling of the Immune Response With Aging: Immunosenescence and Its Potential Impact on COVID-19 Immune Response date = 2020-08-07 pages = extension = .txt mime = text/plain words = 6824 sentences = 337 flesch = 37 summary = Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Interestingly, polymorphonuclear leucocytes from the elderly are less capable of modulating the triggering receptor expressed on myeloid cell-1 (TREM-1)-induced oxidative bursts, suggesting that TREM-1 signal transduction altered with aging may be one of the mediators of the decrease in microbicidal potential of innate immune cells in older adults (41) . cache = ./cache/cord-352737-3ttrx3lf.txt txt = ./txt/cord-352737-3ttrx3lf.txt === reduce.pl bib === id = cord-352065-960xqft4 author = Rello, Jordi title = Update in COVID-19 in the Intensive Care Unit from the 2020 HELLENIC Athens International Symposium date = 2020-10-22 pages = extension = .txt mime = text/plain words = 4976 sentences = 264 flesch = 41 summary = Experts reviewed the latest literature relating to the COVID-19 pandemic in critically ill patients, such as epidemiology, pathophysiology, phenotypes of infection, COVID-19 as a systematic infection, molecular diagnosis, mechanical ventilation, thromboprophylaxis, COVID-19 associated co-infections, immunotherapy, plasma treatment, Catheter-Related bloodstream infections, artificial intelligence for COVID-19, and vaccination. A major problem of the coronavirus pandemic is the considerable burden imposed on National Health Systems worldwide due to the hyperacute outbreak and the proportional increase of patients requiring intensive care unit (ICU) support in an extremely limited period of time, while outcomes vary according to the burden of the disease in each country. Acute respiratory distress syndrome (ARDS) is the primary cause of death in COVID-19 [7] and a recent scope review found that for COVID-19, < 5% of patients were reported as experiencing bacterial/fungal coinfection at admission, but development of secondary infections during ICU admission is common [8, 9] . cache = ./cache/cord-352065-960xqft4.txt txt = ./txt/cord-352065-960xqft4.txt === reduce.pl bib === id = cord-352871-0xgjpd80 author = Pérez Bartolomé, Francisco title = Manifestaciones oftalmológicas del SARS-Cov-2: Revisión de la literatura date = 2020-08-08 pages = extension = .txt mime = text/plain words = 4221 sentences = 371 flesch = 54 summary = En Diciembre de 2019 se identificaron a los primeros pacientes diagnosticados con la enfermedad causada por el nuevo coronavirus (SARS-CoV2), denominada COVID-19, en Wuhan, China 1,2 . Se procedió a la combinación de diferentes palabras clave, tales como "SARS-Cov-2", "COVID 19", "2019-nCoV", "Coronavirus 2019", y (término "AND" en el proceso de búsqueda avanzada) "Ophthalmology", "Eye disease", "Conjunctivitis", "Ocular Surface", "Glaucoma", "Orbit", "Tears", "Uveitis", "Retina", "Vasculitis", "ophthalmoparesis", "palsy", "optic nerve", "anterior ischemic optic neuropathy" (AION), "retinal venous occlusion" (RVO), "retinal artery occlusion" (RAO). La primera referencia de conjuntivitis por SARS-CoV-2 figura en una carta al editor, publicada en la revista "The Lancet" 28 , en la que describe el cuadro de enrojecimiento ocular unilateral en un experto neumólogo (ataviado con su equipo de protección y una mascarilla N95, pero sin gafas protectoras), días después de haber visitado un hospital de Wuhan. cache = ./cache/cord-352871-0xgjpd80.txt txt = ./txt/cord-352871-0xgjpd80.txt === reduce.pl bib === id = cord-352642-u513wnu1 author = Patrocínio de Jesus, Rita title = Reactivation of SARS-CoV-2 after Asymptomatic Infection while on High-Dose Corticosteroids. Case Report date = 2020-10-02 pages = extension = .txt mime = text/plain words = 2211 sentences = 113 flesch = 46 summary = After reviewing this case in light of current evidence and debates surrounding SARS-CoV-2 RT-PCR results, we hypothesize that patients on corticosteroids may have particular viral shedding dynamics and should prompt a more conservative approach in regard to isolation discontinuation and monitoring. Since the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the cause of the disease which was later named COVID-19, and as it progressed to the current worldwide pandemic, much investigation has been made regarding its clinical presentation, transmission route, and immunity. This could point either to a reactivation of the disease in a patient who first presented as asymptomatic or to a long incubation period (18 days from risk contact until developing symptoms, with a CT performed 3 days prior to the onset of symptoms showing an evolving disease, which is consistent with previous studies reporting typical radiological findings of COVID-19 in asymptomatic or presymptomatic patients [2] ). cache = ./cache/cord-352642-u513wnu1.txt txt = ./txt/cord-352642-u513wnu1.txt === reduce.pl bib === id = cord-352322-tsjwnvkk author = Khamassi Khbou, Médiha title = Coronaviruses in farm animals: Epidemiology and public health implications date = 2020-09-25 pages = extension = .txt mime = text/plain words = 8114 sentences = 453 flesch = 49 summary = As consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (TGEV) of swine and the bovine CoV (BCoV) likely originated from the closely related canine coronavirus (CCoV) (Pratelli, 2011) . Coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean CoVs were also considered, as marine mammals are a food source in many countries around the world. Since the first case of human infected by the MERS-CoV was identified in September 2012 in Saudi Arabia (World Health Organization, 2019), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (Omrani, Al-Tawfiq, & Memish, 2015) . Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Infection with a new porcine respiratory coronavirus in Denmark: Serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies cache = ./cache/cord-352322-tsjwnvkk.txt txt = ./txt/cord-352322-tsjwnvkk.txt === reduce.pl bib === id = cord-352943-ztonp62x author = Nagpal, Sunil title = What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date = 2020-08-20 pages = extension = .txt mime = text/plain words = 2776 sentences = 174 flesch = 47 summary = Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a 'Bag of Words' to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes). In fact, Latent Dirichlet Allocation (LDA), an unsupervised machine learning approach, is particularly known for identifying latent topics in large document collections and deciphering the words that define the inferred topics using a generative statistical model. Classical LDA was employed to generate topic models leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through rigorous hyper-parameter tuning for coherence optimization (Figure 2) . cache = ./cache/cord-352943-ztonp62x.txt txt = ./txt/cord-352943-ztonp62x.txt === reduce.pl bib === id = cord-352668-qjlqsb2k author = Cabello, Francisco title = Consensus on Recommendations for Safe Sexual Activity during the COVID-19 Coronavirus Pandemic date = 2020-07-20 pages = extension = .txt mime = text/plain words = 4834 sentences = 232 flesch = 43 summary = Sexual activity offers numerous advantages for physical and mental health but maintains inherent risks in a pandemic situation, such as the current one caused by SARS-CoV-2. A group of experts from the Spanish Association of Sexuality and Mental Health (AESexSAME) has reached a consensus on recommendations to maintain lower-risk sexual activity, depending on one's clinical and partner situations, based on the current knowledge of SARS-CoV-2. In all other cases (for those under quarantine, those with some clinical symptoms, health professionals in contact with COVID-19 patients, and during pregnancy), abstaining from coital/oral/anal sex, substituting it with masturbatory or virtual sexual activity to provide maximum protection from the contagion, and increasing the benefits inherent to sexual activity are recommended. Due to the ease of contagion and the lack of information about the possible transmission of SARS-CoV-2, a group of experts from the Spanish Association for Sexuality and Mental Health, covering the fields of sexology, psychiatry, psychology and medicine reached a consensus. cache = ./cache/cord-352668-qjlqsb2k.txt txt = ./txt/cord-352668-qjlqsb2k.txt === reduce.pl bib === id = cord-352891-ljmkqdzx author = Parang, Keykavous title = Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3165 sentences = 182 flesch = 52 summary = title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells. cache = ./cache/cord-352891-ljmkqdzx.txt txt = ./txt/cord-352891-ljmkqdzx.txt === reduce.pl bib === id = cord-352768-16vgnq14 author = Tang, Qingquan title = Application of siRNA Against SARS in the Rhesus Macaque Model date = 2008 pages = extension = .txt mime = text/plain words = 4389 sentences = 274 flesch = 48 summary = Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen's genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. A pair of siRNAs showing prominent prophylactic and therapeutic activities in the cell culture study (29), referred to as siSC2 and siSC5, were further evaluated in vivo, first in mice using a reporter gene assay and subsequently using a clinically acceptable intranasal administration in the recently established rhesus macaque SARS model (23-26). cache = ./cache/cord-352768-16vgnq14.txt txt = ./txt/cord-352768-16vgnq14.txt === reduce.pl bib === id = cord-352909-s11tpfoq author = Sun, Zhiping title = Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1747 sentences = 106 flesch = 66 summary = Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions Zhiping Sun 1 , Xia Cai 1 , Chenjian Gu 2 , Rong Zhang 2 , Wendong Han 1 , Yun Qian 1 , Yuyan Wang 2 , Wei Xu 2 , Yang Wu 2 , Xunjia Cheng 2 , Zhenghong Yuan 2 , Youhua Xie 2 and Di Qu 1, 2 Dear Editor, The pneumonia caused by a novel coronavirus was first reported in December 2019 in Wuhan of China, and since then has become a pandemic 1, 2 . Here, we first investigated the infectivity of SARS-COV-2 using a plaque-purified strain nCoV-SH01 isolated from a patient in Shanghai (GenBank MT121215) 6 , studied subsequently its stability in liquid medium, on dry filter paper, and under acidic condition (pH2.2) at RT. cache = ./cache/cord-352909-s11tpfoq.txt txt = ./txt/cord-352909-s11tpfoq.txt === reduce.pl bib === id = cord-352779-zdtpnip0 author = Patti, Ravi Karan title = Subacute Aspergillosis “Fungal Balls” Complicating COVID-19 date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1548 sentences = 108 flesch = 39 summary = Severe acute respiratory syndrome coronavirus-2 infection (SARS-CoV-2), commonly known as COVID-19 (coronavirus disease-2019), began in the Wuhan District of Hubei Province, China. We report the case of a 73-year-old male who presented with progressive dyspnea; diagnosed with SARS-CoV-2–related severe acute respiratory distress syndrome and complicated with lung cavitations growing Aspergillus sp. Due to persistence of the SARS-CoV-2 and severe acute respiratory distress syndrome complicated by pulmonary aspergillosis, the patient further underwent tracheostomy and was discharged to a subacute rehabilitation facility. 11 We report this case of subacute invasive pulmonary aspergillosis in a patient with SARS-CoV-2 infection, who did not have any history of pulmonary tuberculosis, sarcoidosis, or preformed cavities to predispose for aspergillus infection. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. cache = ./cache/cord-352779-zdtpnip0.txt txt = ./txt/cord-352779-zdtpnip0.txt === reduce.pl bib === id = cord-352799-qmzh976f author = Paquin, Leo J. title = Was WHO SARS-related Travel Advisory for Toronto Ethical? date = 2007-05-01 pages = extension = .txt mime = text/plain words = 2302 sentences = 183 flesch = 68 summary = Guénaël R.M. Rodier thinks WHO's decision to impose a SARS-related travel advisory was justifiable, even reasonable, though it caused a loss of over $1.1 billion in the Greater Toronto Area. However, as suggested in the Naylor report, issuing a travel advisory does not keep infected individuals from leaving Toronto and such individuals account for 5 of 6 cases where SARS was spread from Canada. "…a decision to lift the travel advisory, effective April 30, was made based on consideration of 3 criteria: a decrease to below 5 new SARS cases per day, a period of 20 days since the last case of community transmission occurred, and no new confirmed cases of exportation." 4 There are some data that suggest that Rodier is justified in his views. Why was Toronto included in the World Health Organization's SARS-related travel advisory cache = ./cache/cord-352799-qmzh976f.txt txt = ./txt/cord-352799-qmzh976f.txt === reduce.pl bib === id = cord-352886-6lzlt6ur author = Bai, Qifeng title = MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm date = 2020-08-11 pages = extension = .txt mime = text/plain words = 6655 sentences = 377 flesch = 51 summary = Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. To use the merit of deep learning, our designed soft tool employs the sequencebased generative model and graph neural networks (GNNs) generative model for producing the ligand set and small molecular fragments (see Figure 1 ). Figure 7B shows the drug virtual screening results of SARS-CoV-2 M pro from 2 million druglike ligands by deep learning generative model and molecular docking. cache = ./cache/cord-352886-6lzlt6ur.txt txt = ./txt/cord-352886-6lzlt6ur.txt === reduce.pl bib === id = cord-352905-ge3u32hm author = Galimberti, Sara title = Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2 date = 2020-09-02 pages = extension = .txt mime = text/plain words = 5383 sentences = 231 flesch = 45 summary = Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Translated in the COVID-19 context, if TKIs would sustain the coronavirus infection or replication, we might expect to observe a significant increase of TTV load during treatment of our patients with nilotinib. In the second phase of our study, we employed the NanoString technology for analyzing the expression of 770 inflammationand immunity-related genes in five CML patients before and after 6 months of treatment with imatinib, with the aim of testing the impact of this TKI on the possible immunological control of viral infection. Considering that it has been proven that at diagnosis, the immunity of these patients is severely impaired (63) , the low infection rate observed during the 2020 pandemic could prove that TKIs play an antiviral role or, at least, could not impair the host response against the new coronavirus. cache = ./cache/cord-352905-ge3u32hm.txt txt = ./txt/cord-352905-ge3u32hm.txt === reduce.pl bib === id = cord-352741-0pdeehai author = Geramizadeh, Bita title = Histopathologic Findings of Coronavirus in Lung: A Mini-Review date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2158 sentences = 143 flesch = 44 summary = In this report, we will review the published reports about the histopathologic findings of lung tissue in the patients infected with SARS-CoV-2 in comparison with 2 other coronaviruses that have caused outbreaks, ie, SARS-CoV-1 and MERS-CoV. The keywords for searching were "lung," " pulmonary," and CoVs, ie, "severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2])," "coronavirus disease (COVID-19)," "pathology," "biopsy," "autopsy," "histopathology," "severe acute respiratory syndrome (SARS)," and "Middle East Respiratory syndrome (MERS)." Histological examination of lung in rare cases reported from SARS-CoV-2 showed "edema, bilateral diffuse alveolar damage with cellular fibromyxoid exudates, desquamation of pneumocytes and hyaline membrane formation," indicating acute respiratory distress syndrome. 19 One histopathologic finding in the new SARS-CoV-2infected lung disease that has not been reported in the previous epidemics of coronaviruses is the presence of pulmonary fibrosis that can be indicative of future pulmonary dysfunction if the patient recovers. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore cache = ./cache/cord-352741-0pdeehai.txt txt = ./txt/cord-352741-0pdeehai.txt === reduce.pl bib === id = cord-352863-6cttilm8 author = Hennighausen, Lothar title = Activation of the SARS-CoV-2 receptor Ace2 through JAK/STAT-dependent enhancers during pregnancy date = 2020-09-06 pages = extension = .txt mime = text/plain words = 3450 sentences = 197 flesch = 55 summary = Expression of the ACE2 gene in type II pneumocytes is activated by interferons (Ziegler et al., 2020) , opening the possibility that the cytokine storm in COVID-19 patients, and peptide hormones in general, might lead to increased levels of ACE2 in a range of putative SARS-CoV-2 target tissues. Next, we mined RNA-seq data from our lab and demonstrated increased Ace2 expression throughout pregnancy and lactation ( Figure 1B ) with a pattern similar to that of other prolactin-regulation genes (Lee et al., 2018; Yamaji et al., 2013) . Our study directly demonstrates that the Ace2 gene is expressed in mammary tissue and activated during pregnancy and lactation through intronic enhancers built on the transcription factor STAT5. While SARS-CoV-2 has been detected in breast milk in at least seven studies and our research has demonstrated that its receptor ACE2 is present in mammary tissue and highly induced during lactation, the impact of these findings on COVID-19 requires further investigations. cache = ./cache/cord-352863-6cttilm8.txt txt = ./txt/cord-352863-6cttilm8.txt === reduce.pl bib === id = cord-352814-fcl2g5wr author = Balboni, Andrea title = A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date = 2011-11-22 pages = extension = .txt mime = text/plain words = 3998 sentences = 177 flesch = 49 summary = In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The aim of this work was to develop a real-time PCR assay for diagnosing infection with SARS-related coronaviruses from bat guano in order to use it as a screening tool in epidemiological surveys for the detection of the viruses. The developed SYBR Green real-time PCR techniques were applied to an SARS-like coronavirus survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) which were sampled in Italy in 2009, resulting in a prevalence of coronavirus infection of 42%. After optimisation of the SYBR Green real-time PCR assay, for each run, duplicates of six 10-fold dilutions of the standard plasmid, triplicates of the viral reverse-transcribed RNA of the bat samples, and a no template control were simultaneously subjected to analysis. cache = ./cache/cord-352814-fcl2g5wr.txt txt = ./txt/cord-352814-fcl2g5wr.txt === reduce.pl bib === id = cord-352925-abry6oz3 author = Lim, Jia Yin title = Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic date = 2020-05-21 pages = extension = .txt mime = text/plain words = 716 sentences = 43 flesch = 45 summary = title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic Months into the coronavirus disease (COVID-19) pandemic, healthcare workers continue the fight against an increasing disease burden worldwide. This requires mental resilience and perseverance to function under challenging working conditions, sometimes with limited resources and risking personal safety. [1] What often gets overlooked is the "heartware", such as addressing burnout, anxiety of perceived risks, moral injury [2] and the resultant long-term psychological impact that may impair performance and compromise staff and patient safety. [4] In this current pandemic, a considerable proportion of healthcare workers in China reported symptoms of depression, anxiety, insomnia, and distress, signifying the need for psychological support or interventions. [5] With these in mind, we recognized the need to prepare our anesthesia department staff for the threat and associated challenges when managing COVID-19 patients. Managing mental health challenges faced by healthcare workers during covid-19 pandemic cache = ./cache/cord-352925-abry6oz3.txt txt = ./txt/cord-352925-abry6oz3.txt === reduce.pl bib === id = cord-352577-h3652seb author = Kopić, Jasminka title = Expanding the Use of Noninvasive Ventilation During an Epidemic date = 2014-08-27 pages = extension = .txt mime = text/plain words = 3340 sentences = 183 flesch = 39 summary = 4 When appropriately indicated and promptly administered, NIV offers an alternative to tracheal intubation, sedation, risk of infection, and myriad complications associated with invasive ventilation, and it can promote rapid respiratory recovery, and reduce a patient's dependence on critical care facilities. Rello et al described NIV use at ICU admission in 1 of 3 patients with H1N1 virus and respiratory failure, but 75% of them had an unfavorable clinical course and required tracheal intubation and invasive mechanical ventilation. In a position statement, the Australian Society for Infectious Diseases recommends "reserving negative-pressure ventilation rooms (if available) for intensive care patients, especially those receiving non-invasive ventilation." 31 The UK Department of Health, in "Guidance for infection control in critical care for pandemic influenza," approved the use of NIV under strict infection control measures. cache = ./cache/cord-352577-h3652seb.txt txt = ./txt/cord-352577-h3652seb.txt === reduce.pl bib === id = cord-352849-vd62r8qu author = Artesi, M. title = Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome date = 2020-05-03 pages = extension = .txt mime = text/plain words = 2825 sentences = 177 flesch = 61 summary = Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals, while also clearing essential staff to continue work. At the current time a number of RT-PCR tests have been developed to identify SARS-CoV-2, targeting multiple regions in the viral genome. Out of the 186 SARS-CoV-2 genomes we have sequenced, only these four samples carry a SNP at position 26340. Vogels et al [17] also identified this 3 base change as well as other SNPs in primer/probe binding sites from a number of RT-PCR assays for SARS-CoV-2. The cobas® E-gene assay may use an alternate primer probe combination that is more sensitive to the presence of the SNP, alternatively it may target the same positions as the Corman et al. . https://doi.org/10.1101/2020.04.28.20083337 doi: medRxiv preprint However, our ability to show that each individual carries a genetically identical virus demonstrates the potential whole genome sequencing has for tracking chains of transmission. cache = ./cache/cord-352849-vd62r8qu.txt txt = ./txt/cord-352849-vd62r8qu.txt === reduce.pl bib === id = cord-353099-38bz0acw author = Tang, Mei San title = Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1034 sentences = 70 flesch = 51 summary = Methods 67 specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Results The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46 respectively. Conclusion COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. The correlation of the SARS-CoV-2 neutralizing titer with the ratio reported by the 162 Roche, Abbott, and EI assays was 0.29, 0.47, and 0.46 respectively (Figure 2A-C) . Increased neutralizing antibody titers were also higher in patients that were intubated, 201 had cardiac injury, or AKI relative to those with milder COVID-19 symptoms ( Figure 202 4B-D). cache = ./cache/cord-353099-38bz0acw.txt txt = ./txt/cord-353099-38bz0acw.txt === reduce.pl bib === id = cord-353200-5csewb1k author = Jehi, Lara title = Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4344 sentences = 226 flesch = 40 summary = OBJECTIVE: To characterize a large cohort of patients hospitalized with COVID-19, their outcomes, develop and validate a statistical model that allows individualized prediction of future hospitalization risk for a patient newly diagnosed with COVID-19. DESIGN: Retrospective cohort study of patients with COVID-19 applying a least absolute shrinkage and selection operator (LASSO) logistic regression algorithm to retain the most predictive features for hospitalization risk, followed by validation in a temporally distinct patient cohort. MEASUREMENTS: Demographic, clinical, social influencers of health, exposure risk, medical co-morbidities, vaccination history, presenting symptoms, medications, and laboratory values were collected on all patients, and considered in our model development. Hospitalization risk prediction and outcomes in COVID-19 PLOS ONE | https://doi.org/10.1371/journal.pone.0237419 August 11, 2020 2 / 15 ethical restrictions by the Cleveland clinic regulatory bodies including the institutional review Board and legal counsel. We also develop and validate a statistical model that can assist with individualized prediction of hospitalization risk for a patient with COVID-19. cache = ./cache/cord-353200-5csewb1k.txt txt = ./txt/cord-353200-5csewb1k.txt === reduce.pl bib === id = cord-353103-sdij1d90 author = Yao, Xueting title = In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-09 pages = extension = .txt mime = text/plain words = 3449 sentences = 191 flesch = 52 summary = title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug's safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. cache = ./cache/cord-353103-sdij1d90.txt txt = ./txt/cord-353103-sdij1d90.txt === reduce.pl bib === id = cord-352935-kb0i58z1 author = Aguila, Enrik John T. title = Repurposed GI Drugs in the Treatment of COVID-19 date = 2020-06-29 pages = extension = .txt mime = text/plain words = 990 sentences = 63 flesch = 49 summary = A recent drug research in Germany has shown that omeprazole interfered viral formation of SARS-CoV-2 beyond therapeutic plasma concentrations at 8 µM [6] . To date, there is still little knowledge on the potential of famotidine and omeprazole as repurposed drugs to treat COVID-19. In their letter, Aguila and colleagues provide an insight into commonly used acid suppressants such as famotidine and omeprazole as the potential agents for drug repurposing against COVID-19. The role of famotidine in interfering maturation of SARS-CoV-2 by inhibiting 2-chymotrypsin-like protein and reduction in inflammation needs to be studied. The authors also note that omeprazole at therapeutic concentration increased the anti-SARS-CoV-2 effects of remdesivir and aprotinin. Therefore, there is a theoretical concern that the use of H2-blockers and PPIs could diminish or abolish the neutralizing effects of gastric acid on SARS-CoV-2, which could potentially increase the risk of GI manifestations and severity in COVID-19. cache = ./cache/cord-352935-kb0i58z1.txt txt = ./txt/cord-352935-kb0i58z1.txt === reduce.pl bib === id = cord-353274-wozwpvpq author = Borremans, B. title = Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date = 2020-05-20 pages = extension = .txt mime = text/plain words = 6160 sentences = 362 flesch = 50 summary = In this study we quantified IgG and IgM antibody kinetics and RNA shedding probability during SARS-CoV-2 infection (up to 60 days post symptom onset) by drawing on published data. This formal integration approach enabled us to leverage 3,214 data points from 516 individuals with symptoms ranging from asymptomatic to critical, published in 22 studies, resulting in a quantitative synthesis of diverse data on anti-SARS-CoV-2 antibody patterns and RNA shedding during the early phase of infection. One of the goals of this study is to estimate the means and variation of IgG and IgM seroconversion times (time between symptom onset and first antibody detection) for different assays, antigens, and disease severity. . https://doi.org/10.1101/2020.05.15.20103275 doi: medRxiv preprint weighted bootstrapping procedure integrates all types of data that contain useful information about the timing of seroconversion of different antibodies in day(s) post symptom onset (dpo). The probability of detecting SARS-CoV-2 specific IgG or IgM in plasma or serum samples was estimated by integrating data on whether an individual tested positive or negative on a given dpo. cache = ./cache/cord-353274-wozwpvpq.txt txt = ./txt/cord-353274-wozwpvpq.txt === reduce.pl bib === id = cord-353012-rxhi8wd2 author = Zhou, Nan title = Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date = 2016-03-07 pages = extension = .txt mime = text/plain words = 6412 sentences = 334 flesch = 53 summary = Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Considering that the inhibitory dose of teicoplanin on the activity of cathepsin L is higher than that required for Ebola virus infection inhibition, a cell viability assay was performed to confirm that the inhibitory effect is not due to cytotoxicity (Fig. 6C) . Ebola trVLP system (28) , which can simulate the life cycle of wild-type Ebola viruses to a large extent, was applied to investigate whether teicoplanin and its glycopeptide antibiotic homologs dalbavancin, oritavancin, telavancin, and vancomycin can also inhibit the entry of Ebola trVLPs. Accordingly, the p4cis plasmid encoding Renilla luciferase, VP40, GP, and VP24 was transfected into HEK293T cells along with plasmids expressing T7 RNA polymerase, NP, VP35, VP30, and L viral proteins to produce Ebola trVLPs (Fig. 7A) . cache = ./cache/cord-353012-rxhi8wd2.txt txt = ./txt/cord-353012-rxhi8wd2.txt === reduce.pl bib === id = cord-352796-6einbent author = Theodore Coroneo, Minas title = The eye as the discrete but defensible portal of coronavirus infection date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5340 sentences = 259 flesch = 44 summary = The virus may bind to corneal and conjunctival angiotensin converting enzyme 2 (ACE2) receptors and potentially to the lipophilic periocular skin and superficial tear film with downstream carriage into the nasopharynx and subsequent access to the lungs and gut. A combination such as hydroxychloroquine, azithromycin and zinc, all of which have previously been used topically in the eye and which work at least in part by blocking ACE2 receptors, may offer a safe, cost-effective and resource-sparing intervention. At the height of the 1918 world influenza epidemic, a landmark paper appeared, proposing transmission of acute respiratory infections via the eye and lacrimal-nasal pathway (5) (Figure 1) . Table 2 summarises the drugs that have been identified as potential treatments for coronavirus infection, their efficacy (in vitro and in vivo) and for which there is data (for that agent or a related compound) for previous topical ocular surface usage. cache = ./cache/cord-352796-6einbent.txt txt = ./txt/cord-352796-6einbent.txt === reduce.pl bib === id = cord-352678-8f2ygul2 author = Prasad, Ashish title = Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading? date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3488 sentences = 191 flesch = 48 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causal agent of Coronavirus disease 2019 (COVID19) , is a single-stranded RNA virus with a non-segmented genome. In another study with COVID-19 patients in China, an early response of IgA instead of IgG was observed in the humoral immune response against SARS-CoV-2 (11) . It has been observed that 5% of COVID-19 patients become critically ill with severe pneumonia and multiple-organ damage and cytokine storm might be a possible explanation for such an observation. A case study on 214 COVID-19 patients from three special care centers of Union Hospital, Wuhan, revealed that 36.4% of the infected people had neurologic symptoms (46) . The adverse effects of antiviral drugs like hydroxychloroquine, which is reported to cause acute toxic hepatitis (54) and cytokine burst, might be responsible for such high percentage of hepatic damage cases in severely ill patients. cache = ./cache/cord-352678-8f2ygul2.txt txt = ./txt/cord-352678-8f2ygul2.txt === reduce.pl bib === id = cord-353072-n92atcrx author = Kadkhoda, Kamran title = COVID-19: an Immunopathological View date = 2020-04-22 pages = extension = .txt mime = text/plain words = 2045 sentences = 107 flesch = 45 summary = Unravelling these mechanisms can assist basic scientists, laboratory medicine practitioners, clinicians, public health practitioners, funding agencies, and health care policymakers in responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This is consistent with high-level surface expression of angiotensin-converting enzyme 2 (ACE2), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, on pneumocytes (2) . In the context of COVID-19, since ACE2 is highly expressed in the gastrointestinal (GI) tract (9), shedding the virus in the stool is prolonged (10); however, diarrhea is uncommon likely because virus-specific effector memory T cells typically home to the mucosal surfaces they had previously encountered with an infection with a common CoV, i.e., upper and lower respiratory tract. It has recently been shown that SARS-CoV and the Middle East respiratory syndrome (MERS)-CoV take advantage of non-or subneutralizing antibodies and enter cells via surface CD32a receptors (Trojan horse mechanism) (11, 12) . cache = ./cache/cord-353072-n92atcrx.txt txt = ./txt/cord-353072-n92atcrx.txt === reduce.pl bib === id = cord-352911-9wbq9qo2 author = de Oliveira, Pedro Gonçalves title = Diacerein: a potential multi-target therapeutic drug for COVID-19 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2539 sentences = 135 flesch = 45 summary = The mortality related to severe acute respiratory distress syndrome (ARDS) and multi-organ failure in COVID-19 patients has been suggested to be connected with cytokine storm syndrome (CSS), an excessive immune response that severely damages healthy lung tissue. Total extracts from monolayer cell cultures infected with SARS-CoV-2 and treated with rhein under the conditions described above will be analysed using commercially available protein arrays to determine the levels and activation state of proteins involved in the TLR-, Akt-, MAPK-, and NF-B-regulated signalling pathways. The mechanisms of action involved include the control of hyperinflammatory conditions by multi-faceted cytokine inhibition of IL-1, IL-2, IL-6, IL-8, IL-12, IL-18 and TNF-α; anti-platelet aggregation activity; and potential effects on viral infection and replication. Rhein suppresses lung inflammatory injury induced by human respiratory syncytial virus through inhibiting NLRP3 inflammasome activation via NF-κB pathway in mice cache = ./cache/cord-352911-9wbq9qo2.txt txt = ./txt/cord-352911-9wbq9qo2.txt === reduce.pl bib === id = cord-353229-k3zerr83 author = Akca, Ummusen Kaya title = Kawasaki-like disease in children with COVID-19 date = 2020-09-16 pages = extension = .txt mime = text/plain words = 4365 sentences = 281 flesch = 42 summary = Herein, we report the characteristics of four patients with Kawasaki-like phenotype associated with COVID-19 from Turkey and analyze the features of similar published cases through a systematic literature review. Diagnosis of complete KD was based on the criteria of the American Heart Association (AHA): the presence of fever for at least 5 days accompanied by the presence of at least four of the following five findings: bilateral non-exudative conjunctival injection, unilateral cervical lymphadenopathy, changes in the lips and oral cavity, skin rash, and changes in extremities, including indurative angioedema and desquamation [18] . Children with persistent fever, inflammation (neutrophilia, high CRP, and lymphopenia), and single or multi-organ dysfunction have been identified in the UK as "Pediatric Multisystem Inflammatory Syndrome in relation to SARSCoV-2 (PMIS-TS)" regardless of the SARS-CoV-2 RT-PCR test results [73] . Pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort cache = ./cache/cord-353229-k3zerr83.txt txt = ./txt/cord-353229-k3zerr83.txt === reduce.pl bib === id = cord-353329-ju3vwlow author = Haroon, Khawaja Hassan title = COVID-19 Related Cerebrovascular Thromboembolic Complications in Three Young Patients date = 2020-09-28 pages = extension = .txt mime = text/plain words = 2006 sentences = 128 flesch = 56 summary = We describe clinical, radiological and laboratory findings of three young patients who presented with ischemic stroke and cerebral venous sinus thrombosis to our hospital within the first few weeks of COVID-19 outbreak. His CT of the brain, CT angiogram and CT perfusion ( Fig. 1a -e) showed acute established infarct in the right frontal lobe and basal ganglia, large matched defect in the right MCA territory and occlusion of right CCA and right terminal ICA with no evidence of dissection as well as lung findings suggestive of COVID-19 pneumonia. He was transferred to medical ICU for close monitoring and his follow-up non-contrast CT of the head (Fig. 1f ) revealed large right MCA territory infarct. Our first and second patient showed significant arterial lesions, while the third patient showed a high burden of cerebral venous sinus thrombosis with raised D-dimers and inflammatory markers, leading to stroke. cache = ./cache/cord-353329-ju3vwlow.txt txt = ./txt/cord-353329-ju3vwlow.txt === reduce.pl bib === id = cord-353092-4hz2yyl5 author = Sama, Iziah E title = Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin–angiotensin–aldosterone inhibitors date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3472 sentences = 182 flesch = 49 summary = CONCLUSION: In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. We therefore investigated plasma concentrations of ACE2 in two large and independent cohorts of men and women with heart failure according to the use of RAAS inhibitors. In two large independent cohorts of patients with heart failure, we found that plasma ACE2 concentrations were higher in men than in women. In two large cohorts of patients with heart failure, plasma ACE2 concentrations were higher in men than in women, possibly reflecting higher tissue expression of this receptor for SARS coronavirus infections. cache = ./cache/cord-353092-4hz2yyl5.txt txt = ./txt/cord-353092-4hz2yyl5.txt === reduce.pl bib === id = cord-353217-gmc3qrci author = de Miranda Santos, Isabel Kinney Ferreira title = Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus date = 2020-08-04 pages = extension = .txt mime = text/plain words = 551 sentences = 34 flesch = 36 summary = Recent large observational studies indicate that hydroxychloroquine (HY) does not affect outcomes of patients hospitalized with COVID-19 (1, 2) and may even be harmful (3) . In view of this situation and of the importance of correct interpretation of antibody profiles for planning preventive measures for COVID-19, we would like to bring the attention of readers to studies that raise concerns about the possible impact of HY upon antibody responses to SARS-CoV-2. To the best of our knowledge, there are no new facts in the scientific and medical literature that indicate that the same mechanism could not operate in HY-treated patients suffering from COVID-19 and negatively impact their SARS-CoV-2-specific antibody responses. As more needs to be learned about the role of antibodies in recovery from and protection against infection with SARS-CoV-2, the impact of HY and other treatment regimens on antibody responses requires systematic evaluation. cache = ./cache/cord-353217-gmc3qrci.txt txt = ./txt/cord-353217-gmc3qrci.txt === reduce.pl bib === id = cord-353392-rqeultbq author = Kumar, Govindarajan Venkat title = A short review on antibody therapy for COVID-19 date = 2020-04-20 pages = extension = .txt mime = text/plain words = 1944 sentences = 105 flesch = 48 summary = Abstract The beginning of the novel SARS-CoV-2 human coronavirus in Wuhan, China, has triggered a worldwide respiratory disease outbreak (COVID-19). The third outbreak of severe illness caused by the novel SARS-CoV-2 coronavirus (COVID-19) that emerged in the Wuhan city, China, is pandemic and spread to more than 200 countries [5, 6, 7] . Based on the previous studies and reports in treating other coronaviruses such as SARS and MERS, the early administration of convalescent plasma from patients that contains raised antibodies can possibly reduce the spreading of infection and mortality [19, 20, 21, 22] . reported that the convalescent plasma transfusion may be beneficial in the treatment of critically ill patients with SARS-CoV-2 infections. After getting approval from the ethical committee, Shenzhen, Third People's Hospital, they administrated convalescent plasma containing neutralizing antibodies to 5 critically ill patients with SARS-CoV-2. cache = ./cache/cord-353392-rqeultbq.txt txt = ./txt/cord-353392-rqeultbq.txt === reduce.pl bib === id = cord-353209-qkhfp66l author = Steiner, Daniel J. title = Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2517 sentences = 129 flesch = 45 summary = We report a multiplex label-free antigen microarray on the Arrayed Imaging Reflectometry (AIR) platform for detection of antibodies to SARS-CoV-2, SARS-CoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43) and three strains of influenza. Aminereactive substrates for fabrication of AIR arrays were provided by Adarza BioSystems, Inc. For ELISA assays, SARS-CoV-2 full-length spike and RBD were produced in-house using a mammalian expression system, 20,21 as was influenza A/H1N1/California 2009 hemagglutinin. To that end, we have presented preliminary data on a 15-plex array on the AIR platform, developed in response to the need to study SARS-CoV-2 but incorporating antigens for other coronaviruses and influenza. Responses to SARS-CoV-2 antigens on the array effectively discriminated between serum samples from uninfected and COVID-19 convalescent subjects, with generally good correlation to ELISA data. cache = ./cache/cord-353209-qkhfp66l.txt txt = ./txt/cord-353209-qkhfp66l.txt === reduce.pl bib === id = cord-352934-ypls4zau author = Wan, Jinkai title = Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date = 2020-07-03 pages = extension = .txt mime = text/plain words = 2406 sentences = 151 flesch = 59 summary = title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection We screened sera samples from 11 patients recently recovered from COVID-19, and 119 found all individuals showed certain levels of serological responses, with #507 and 120 #501 being the weakest, to SARS-CoV-2 Spike RBD and S1 proteins ( Figure 1A ). We 121 also found that 10 sera, except for 507, showed neutralization abilities against 122 SARS-CoV-2 pseudoviral infection of HEK293T cells stably expressing human ACE2 123 ( Figure 1B ). In order to screen for SARS-CoV-2 spike antigen specific monoclonal antibodies, we 143 used two primary assays based on ELISA (enzyme linked immunosorbent assay) and 144 FCA (flow cytometry assay), respectively. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin 561 converting enzyme 2 receptor A potent neutralizing human antibody reveals the N-terminal domain of the 564 Spike protein of SARS-CoV-2 as a site of vulnerability Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific 612 human monoclonal antibody cache = ./cache/cord-352934-ypls4zau.txt txt = ./txt/cord-352934-ypls4zau.txt === reduce.pl bib === id = cord-352969-rpt7xja6 author = Kataria, Ashish title = COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5975 sentences = 367 flesch = 45 summary = 1, 4 Solid organ transplant (SOT) patients including kidney transplant recipients (KTRs) are at a uniquely increased risk of serious complications from COVID-19 because of immunosuppressive (IS) medication use, elderly age (>65 y), and preexisting comorbidities like diabetes, hypertension, and cardiovascular diseases. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. 71, 72 At this time, there is no evidence to suggest that kidney transplant patients are at an increased risk of thrombotic events compared with the general population for disease of similar severity. cache = ./cache/cord-352969-rpt7xja6.txt txt = ./txt/cord-352969-rpt7xja6.txt === reduce.pl bib === id = cord-353235-jiqhgf56 author = Bigliardi, Guido title = Middle cerebral artery ischemic stroke and COVID-19: a case report date = 2020-09-08 pages = extension = .txt mime = text/plain words = 1062 sentences = 82 flesch = 49 summary = We present a clinical case of a patient with SARS-CoV-2 infection and respiratory symptoms, complicated with a pro-thrombotic state involving multiple vascular territories and concomitant interleukin-6 increase. Here, we report a case of a patient with SARS-CoV-2 infection that developed severe coagulopathy affecting both pulmonary and cerebral vessels. In the following days, the patient respiratory symptoms worsened with increasing need for oxygen therapy. Arterial and venous thrombotic events are recognized complications of SARS-CoV-2 infection (Klok et al. Of note, severe respiratory failure was heralded by a marked D-dimer increase 5 days earlier (Fig. 1) . This case underlines the importance of constant neurological monitoring in COVID-19 patients during ICU staying, especially in those with suspected thrombotic events, to detect possible neurological complications. High risk of thrombosis in patients with severe SARS-CoV-2 infection: a multicenter prospective cohort study Incidence of thrombotic complications in critically ill ICU patients with COVID-19 cache = ./cache/cord-353235-jiqhgf56.txt txt = ./txt/cord-353235-jiqhgf56.txt === reduce.pl bib === id = cord-353365-ujz5nkk3 author = Pirnay, Jean-Paul title = Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger date = 2020-08-27 pages = extension = .txt mime = text/plain words = 4773 sentences = 246 flesch = 53 summary = The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. cache = ./cache/cord-353365-ujz5nkk3.txt txt = ./txt/cord-353365-ujz5nkk3.txt === reduce.pl bib === id = cord-353479-kwi8zxo6 author = Chuang, H.-L. title = Impact of enhanced infection control procedures on clinical outcome following resuscitation attempts date = 2007-11-30 pages = extension = .txt mime = text/plain words = 2902 sentences = 144 flesch = 39 summary = Other strict hospital ICMs in period 2 included the following: (i) all new admissions were required to be examined by our emergency department's SARS screening team; (ii) all febrile patients were required to be admitted to the fever screening ward regardless of their diagnoses; (iii) unnecessary contact between HCWs was restricted and regular meetings and conferences were cancelled; (iv) each step of the standard operating procedure was strictly audited during resuscitation. There were also more emergency resuscitations performed without intubation and a higher number of 'do not resuscitate' orders signed during resuscitation in the period of strict implementation of ICMs. These changes resulted in an abnormal situation in which the hospital's facilities were adversely affected and the ability of the hospital to provide patients with medical care during the SARS outbreak was reduced. cache = ./cache/cord-353479-kwi8zxo6.txt txt = ./txt/cord-353479-kwi8zxo6.txt === reduce.pl bib === id = cord-353391-o0s2h0y0 author = Haj Bloukh, Samir title = A Look Behind the Scenes at COVID-19: National Strategies of Infection Control and Their Impact on Mortality date = 2020-08-04 pages = extension = .txt mime = text/plain words = 9925 sentences = 539 flesch = 54 summary = To investigate the importance of serum vitamin D levels, median age, temperature, and humidity we compare infection control measures and their impact on COVID-19-related fatalities in Portugal, Sweden, and Switzerland ( Figure 1 ). A study compared community-wide mask compliance in relation to the number of confirmed SARS-CoV-2 cases/fatalities in Hong Kong, Singapore, and other countries [29] . This mask-wearing strategy combined with social distancing, personal hygiene, cancellation of social gatherings, use of the home office, and school closures resulted in the effective control of the SARS-CoV-2 transmission compared to other neighboring countries [29] . We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. cache = ./cache/cord-353391-o0s2h0y0.txt txt = ./txt/cord-353391-o0s2h0y0.txt === reduce.pl bib === id = cord-353133-tsqb6pa8 author = Long, Dustin R. title = Considerations for Assessing Risk of Provider Exposure to SARS-CoV-2 after a Negative Test date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1189 sentences = 66 flesch = 39 summary = Recent publication of data suggesting imperfect clinical sensitivity of reverse transcription polymerase chain reaction assays for SARS-CoV-2 3 could lead healthcare providers to intuitively question the wisdom of a strategy that relies on a negative SARS-CoV-2 test, particularly when planning high-risk procedures such as endotracheal intubation. To help providers and clinical leaders grapple with this dynamic uncertainty, we have developed an online tool (https://covid-airway-npv.info) that enables the user to examine the impact of different assumptions regarding SARS-CoV-2 reverse transcription polymerase chain reaction test characteristics and disease prevalence on the potential risk of provider exposure during airway management. Uncertainty is modeled by asking the user to provide the most likely, minimum, and maximum value of the parameter (here, SARS-CoV-2 testing characteristics and COVID-19 community prevalence), using a Project Evaluation and Review Techniques distribution. cache = ./cache/cord-353133-tsqb6pa8.txt txt = ./txt/cord-353133-tsqb6pa8.txt === reduce.pl bib === id = cord-353293-vjdwh19x author = nan title = Post-COVID-19 global health strategies: the need for an interdisciplinary approach date = 2020-06-11 pages = extension = .txt mime = text/plain words = 3856 sentences = 175 flesch = 36 summary = Gemelli IRCSS (Rome, Italy) has set up a multidisciplinary healthcare service called "Post-COVID-19 Day Hospital." The specialist assessments offered to patients are outlined in the following sections. Furthermore, the important role of geriatrician acting as a care manager of patients who suffered COVID-19 disease is described. A respiratory follow-up is of pivotal importance to evaluate lung function, alveolar-arterial gas exchange, and exercise tolerance in recovered non-infective COVID-19 patients [5] . In this Post-COVID-19 Day Hospital, internal medicine and geriatric specialists are integrated with infectious disease physicians, pneumologists, immuno-rheumatologists, and other specialists into the management of the SARS-CoV-2 infection. As a whole, the post-acute care service at the Fondazione Policlinico Gemelli aims at expanding the knowledge of COVID-19 and its impact on health status and care needs as well as at promoting healthcare strategies to treat and prevent the clinical consequence of SARS-CoV-2 infection across different organs and systems. cache = ./cache/cord-353293-vjdwh19x.txt txt = ./txt/cord-353293-vjdwh19x.txt === reduce.pl bib === id = cord-353523-gwud4bb7 author = Abobaker, Anis title = The Eye: A Possible New Route of Infection in COVID-19 date = 2020-07-27 pages = extension = .txt mime = text/plain words = 928 sentences = 63 flesch = 53 summary = 1 This might indicate that the eye is not a potential target for coronaviruses; however, this does not rule out the possibility that the conjunctiva and the ocular mucous membrane could act as a port of entry to CoVs to the upper respiratory tract given the close anatomical proximity and the similar epithelial receptors. There is evidence that lack of eye protection in clinical settings increased the risk of infection of the severe acute respiratory disease (SARS) caused by SARS-CoV. The low frequency of conjunctivitis and corneal involvement in COVID-19 patients could be explained with the fact that the level of ACE2 expression in ocular tissues is much less compared with other organs, such as the lungs and kidneys. SARS-CoV-2 has been detected by PCR in conjunctival swabs taken from COVID-19 patients with conjunctivitis as well as patients without ocular LETTER TO THE EDITOR manifestations. SARS-CoV-2 in the ocular surface of COVID-19 patients cache = ./cache/cord-353523-gwud4bb7.txt txt = ./txt/cord-353523-gwud4bb7.txt === reduce.pl bib === id = cord-353116-7t1prfkr author = Bhargava, Ashish title = Predictors for Severe COVID-19 Infection date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2635 sentences = 188 flesch = 55 summary = BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. cache = ./cache/cord-353116-7t1prfkr.txt txt = ./txt/cord-353116-7t1prfkr.txt === reduce.pl bib === id = cord-353484-q7d0ysbo author = Liu, Xue title = COVID-19: Progress in diagnostics, therapy and vaccination date = 2020-06-19 pages = extension = .txt mime = text/plain words = 8557 sentences = 465 flesch = 41 summary = Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] . cache = ./cache/cord-353484-q7d0ysbo.txt txt = ./txt/cord-353484-q7d0ysbo.txt === reduce.pl bib === id = cord-353576-f29kmtot author = Maricic, T. title = A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3499 sentences = 200 flesch = 60 summary = We then tested 1 l of mouthwash from each of the 20 individuals using two RT-qPCR kits advertised to allow direct detection of SARS-CoV-2 from nasopharyngeal swabs: Luna Universal Probe (NEB, Ipswich, USA) and PrimeDirect (Takara, Kyoto, Japan) as well as another kit, SuperScript III with Platinum Taq (Invitrogen, Waltham, USA). To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations. In the first scheme, the samples were tested individually using the direct RT-qPCR protocol and the results were evaluated and reported back to the facility by 7 p.m. To detect any inhibition that the mouthwash samples may introduce into the RT-qPCR reactions, we added a synthesized control RNA that was quantified in parallel with SARS-CoV-2 by a probe . cache = ./cache/cord-353576-f29kmtot.txt txt = ./txt/cord-353576-f29kmtot.txt === reduce.pl bib === id = cord-353237-rob4ems7 author = De Maio, Antonio title = COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? date = 2020-05-18 pages = extension = .txt mime = text/plain words = 2861 sentences = 148 flesch = 43 summary = title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? The virus has been detected in the lungs and immune cells of patients who have succumbed to the infection, consistent with direct injury to the pulmonary tissue and activation of the immune response. Experimental animal studies about the response to sepsis have suggested that early interventions are critical to ameliorate the condition, such as source control of the infection or injury (Cauvi et al. In this regard, hyperbaric oxygen therapy (HBOT) that consists of exposure to 100% oxygen under increased atmospheric pressure up to 2.4 atm could be a great resource to improve the outcome from the infection when it is administered at early stages as soon as a reduction of arterial oxygen concentration is detected. Indeed, experimental animal studies have shown that an initial HBOT improved dramatically the outcome from sepsis, which was correlated with a reduction of the inflammatory response triggered by the initial insult (Halbach et al. cache = ./cache/cord-353237-rob4ems7.txt txt = ./txt/cord-353237-rob4ems7.txt === reduce.pl bib === id = cord-353615-9aj5yxkd author = Colaneri, Marta title = Running out of bullets: the challenging management of acute hepatitis and SARS‐COV‐2 from the SMatteo COvid19 Registry (SMACORE) date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1604 sentences = 89 flesch = 45 summary = Since several of the currently administered drugs against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are possibly hepatotoxic, the management of patients with COVID‐19 and liver failure is still an almost unexplored field. Beyond the well-known catastrophic pulmonary effects of coronavirus disease 2019 , the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has also been associated with a significant damage to other organ systems, including kidney, heart, vessels and liver (1) (2) (3) (4) (5) . et al (12) , patients with SARS-CoV-2 and chronic HBV co-infection with liver injury and coagulation dysfunction were more likely to develop severe illness and had higher mortality. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: A retrospective study Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection cache = ./cache/cord-353615-9aj5yxkd.txt txt = ./txt/cord-353615-9aj5yxkd.txt === reduce.pl bib === id = cord-353599-cw29edwr author = Kelleni, Mina T. title = Early use of Non-steroidal anti-inflammatory drugs in COVID-19 might reverse pathogenesis, prevent complications and improve clinical outcomes date = 2020-11-04 pages = extension = .txt mime = text/plain words = 2610 sentences = 116 flesch = 39 summary = In this manuscript, we present a novel theory to explain the pathogenesis of COVID-19; lymphocyte distraction theory upon which the author has used, in a preprinted protocol, non-steroidal anti-inflammatory drugs (NSAIDs); diclofenac potassium, ibuprofen and ketoprofen, successfully to treat COVID-19 patients. It was previously suggested that SARS CoV induced lymphopenia is likely to be caused by indirect mechanisms such as an increase in cortisol levels that occurred as part of the body stress response to this severe respiratory viral infection or by an iatrogenic effect of glucocorticoids used to manage those patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-353599-cw29edwr.txt txt = ./txt/cord-353599-cw29edwr.txt === reduce.pl bib === id = cord-353628-f6ew980g author = Zayet, Souheil title = Encephalopathy in patients with COVID‐19: ‘Causality or coincidence?’ date = 2020-05-19 pages = extension = .txt mime = text/plain words = 1521 sentences = 102 flesch = 51 summary = Since its discovery in December 2019, the novel coronavirus disease 2019 (COVID-19) has caused several clinical presentations: mainly respiratory, rarely gastrointestinal, and exceptionally neurological. In addition to the usual symptoms (general, respiratory and otorhinolaryngological) of the infection with SARS-CoV-2, several authors have described neurological manifestations as headache, nausea, and vomiting. These viruses can invade brainstem via a synapse-connected route from the lungs and airways 9 .Considering the high similarity between SARS-CoV-2 and others CoVs 10 , it is still not clearly known whether the potential neuro-invasion of SARS-CoV2 is partially responsible for respiratory failure in patients with COVID-19 9,11,12 . Therefore, in the context of COVID pandemic, it would be reasonable to perform a thoracic CT and a RT-PCR for SARS-CoV-2 in case of encephalopathy with normal lumbar puncture and brain imaging. The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-353628-f6ew980g.txt txt = ./txt/cord-353628-f6ew980g.txt === reduce.pl bib === id = cord-353475-dtn7h1gj author = Haddad, Hazem title = miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1462 sentences = 103 flesch = 64 summary = In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. To understand the early steps of COVID-19 infection, we predicted miRNAs sequences targeting the submitted 29903bp of viral ss-RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 complete genomic RNA sequence) from the isolate of Wuhan-Hu-J o u r n a l P r e -p r o o f 1. cache = ./cache/cord-353475-dtn7h1gj.txt txt = ./txt/cord-353475-dtn7h1gj.txt === reduce.pl bib === id = cord-353742-k4gxww2c author = Arévalo, AP title = Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date = 2020-11-02 pages = extension = .txt mime = text/plain words = 721 sentences = 66 flesch = 48 summary = SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases. cache = ./cache/cord-353742-k4gxww2c.txt txt = ./txt/cord-353742-k4gxww2c.txt === reduce.pl bib === id = cord-353373-zhkqnu0w author = Seidu, Samuel title = The impact of obesity on severe disease and mortality in people with SARS‐CoV‐2: A systematic review and meta‐analysis date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2872 sentences = 159 flesch = 50 summary = BACKGROUND: Obesity accompanied by excess ectopic fat storage has been postulated as a risk factor for severe disease in people with SARS‐CoV‐2 through the stimulation of inflammation, functional immunologic deficit and a pro‐thrombotic disseminated intravascular coagulation with associated high rates of venous thromboembolism. METHODS: Observational studies in COVID‐19 patients reporting data on raised body mass index at admission and associated clinical outcomes were identified from MEDLINE, Embase, Web of Science and the Cochrane Library up to 16 May 2020. 2 Recent studies have increasingly described obesity as an associating factor for people at an increased risk of severe disease. 15 In order to attempt to quantify the relationship between raised body weight and severe outcomes from COVID-19, we conducted a systematic review and meta-analysis to determine whether people with overweight or obesity and with SARS-CoV-2 have different outcomes compared to those within normal weight thresholds. cache = ./cache/cord-353373-zhkqnu0w.txt txt = ./txt/cord-353373-zhkqnu0w.txt === reduce.pl bib === id = cord-353551-un4jw7aw author = Margoni, Monica title = Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic date = 2020-10-12 pages = extension = .txt mime = text/plain words = 836 sentences = 49 flesch = 56 summary = title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic The authors, considering the impact of MS on brain atrophy and the high risk POMS have to develop cognitive impairment and evolve in the secondary progressive disease phase, recommend to keep in mind that MS in children/teens is a severe, highly active form of disease, and suggest the early use of highly effective second-line disease modifying drugs rather than the first-line injectable ones. May these drugs expose POMS to a greater risk of SARS-Cov-2 infection as well as to a symptomatic and potentially more severe COVID-19 or to longterm autoimmune severe adverse events? NTZ treatment does not seem not to expose POMS to a higher risk of SARS-Cov-2 infection. No evidence of disease activity including cognition (NEDA-3 plus) in naive pediatric multiple sclerosis patients treated with natalizumab Disease Modifying Therapies and COVID-19 Severity in Multiple Sclerosis cache = ./cache/cord-353551-un4jw7aw.txt txt = ./txt/cord-353551-un4jw7aw.txt === reduce.pl bib === id = cord-353524-3w970ycx author = Dömling, Alexander title = Chemistry and Biology of SARS-CoV-2 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3942 sentences = 237 flesch = 52 summary = Given that SARS-CoV-2 and SARS-CoV share very high identical sequence in their 3CLpro, these HIV protease inhibitors are currently again repurposed for the treatment of COVID-19 (Chinese Clinical Trial Registry: ChiCTR2000029539). 30, 31 The interplay of the ACE receptor in cardiovascular diseases (with the well-known drug class of ACE inhibitors) and as the docking point for SARS-CoV-2 cellular infection is a current point of intense debate and research. For example, the crystal structure of SARS-CoV-2 N protein RNA-binding domain was just published and will give structural insight as a potential drug target. Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure-based drug design study Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites cache = ./cache/cord-353524-3w970ycx.txt txt = ./txt/cord-353524-3w970ycx.txt === reduce.pl bib === id = cord-353548-kf4om6iu author = Ruiz-Manriquez, J. title = Knowledge of Latin American gastroenterologists and endoscopists regarding SARS-CoV-2 infection date = 2020-05-31 pages = extension = .txt mime = text/plain words = 2749 sentences = 180 flesch = 53 summary = An electronic questionnaire was applied that was designed to evaluate the knowledge of symptoms, risk groups for severe disease, prevention measures, and the reprocessing of endoscopes utilized in patients with COVID-19. [10] [11] The aim of the present study was to evaluate the knowledge of Latin American gastroenterology and endoscopy professionals in relation to the characteristics of SARS-CoV-2 infection and the prevention measures recommended during patient care and the performance of endoscopic procedures, including the reprocessing of equipment utilized on patients with the disease. We conducted a cross-sectional study on gastroenterologists and endoscopists (residents and specialists) working in public hospitals from nine Latin American countries (Mexico, Costa Rica, Ecuador, Paraguay, Peru, Guatemala, Uruguay, Honduras, and the Dominican Republic). The present study described the current knowledge of 133 Latin American residents and specialists in gastroenterology and endoscopy about symptoms, risk groups, transmission, and endoscopic equipment reprocessing in relation to COVID-19. cache = ./cache/cord-353548-kf4om6iu.txt txt = ./txt/cord-353548-kf4om6iu.txt === reduce.pl bib === id = cord-353308-e4s8el0s author = Parashar, Umesh D title = Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date = 2004-05-20 pages = extension = .txt mime = text/plain words = 4499 sentences = 224 flesch = 45 summary = This dramatic chain of transmission brought to the world's attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV) cache = ./cache/cord-353308-e4s8el0s.txt txt = ./txt/cord-353308-e4s8el0s.txt === reduce.pl bib === id = cord-353862-7xe3fvd5 author = Li, Na title = Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date = 2020-03-30 pages = extension = .txt mime = text/plain words = 3515 sentences = 199 flesch = 52 summary = METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. cache = ./cache/cord-353862-7xe3fvd5.txt txt = ./txt/cord-353862-7xe3fvd5.txt === reduce.pl bib === id = cord-353342-2n6kqyeo author = Corman, Victor M. title = Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date = 2016-02-15 pages = extension = .txt mime = text/plain words = 4046 sentences = 223 flesch = 52 summary = title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-353342-2n6kqyeo.txt txt = ./txt/cord-353342-2n6kqyeo.txt === reduce.pl bib === id = cord-353509-yfkiaq80 author = Nugraha, Rhea Veda title = Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date = 2020-10-10 pages = extension = .txt mime = text/plain words = 7433 sentences = 413 flesch = 48 summary = This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. cache = ./cache/cord-353509-yfkiaq80.txt txt = ./txt/cord-353509-yfkiaq80.txt === reduce.pl bib === id = cord-353748-y1a52z8e author = Bhattacharya, Rajarshi title = A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date = 2021-01-02 pages = extension = .txt mime = text/plain words = 3308 sentences = 211 flesch = 61 summary = title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. cache = ./cache/cord-353748-y1a52z8e.txt txt = ./txt/cord-353748-y1a52z8e.txt === reduce.pl bib === id = cord-353594-z1vxamvp author = Gagiannis, Daniel title = Clinical, Serological, and Histopathological Similarities Between Severe COVID-19 and Acute Exacerbation of Connective Tissue Disease-Associated Interstitial Lung Disease (CTD-ILD) date = 2020-10-02 pages = extension = .txt mime = text/plain words = 4997 sentences = 246 flesch = 40 summary = Since we observed similarities between COVID-19 and interstitial lung disease in connective tissue disease (CTD-ILD), we investigated features of autoimmunity in SARS-CoV-2-associated respiratory failure. Patients or their relatives had given written informed consent to routine diagnostic procedures (serology, bronchoscopy, radiology) as well as (partial) autopsy in the case of death, respectively, as well as to the scientific use of data and tissue samples in the present study. Our finding that significant ANA titers and/or detection of specific autoantibodies are found in most patients who develop ARDS raises the question if there is a comparable mechanism of lung damage between SARS-CoV-2 infection and exacerbating autoimmune disease. Our observation of CTD-associated autoantibodies together with the CTD-like radiologic and histopathologic lung findings in severe cases of COVID-19 point towards a possible dysregulation of the immune response upon SARS-CoV-2 infection that might fuel organizing pneumonia and trigger interstitial fibrosis, with deleterious effects on the functional outcome in long-term survivors. cache = ./cache/cord-353594-z1vxamvp.txt txt = ./txt/cord-353594-z1vxamvp.txt === reduce.pl bib === id = cord-353812-4oxbczqe author = Zoghi, Anahita title = A case of possible atypical demyelinating event of the central nervous system following COVID-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1543 sentences = 99 flesch = 47 summary = Some COVID-19 patients, especially those suffering from a severe disease, are highly likely to have central nervous system (CNS) manifestations. It has been shown that severe infection with SARS-CoV-2 is associated with neurological manifestations such as headache, epilepsy, cerebrovascular events, and encephalitis (Bohmwald et al. Studies on SARS-CoV-1 revealed a delayed self-reactive T-cell suppression due to viral replication, which leads to neuroinflammation, demyelination or axonal damage of the CNS (Savarin et al., 2017 . Recent studies have shown that the novel coronavirus appears to cross the blood-brain barrier and cause acute or delayed CNS demyelination or axonal damage (Desforges et al., 2020) . Moreover, a recent report revealed that CNS delayed demyelinating events following COVID-19 . Severe COVID-19 may affect the CNS and have various acute or delayed neurological complications. During the COVID-19 pandemic, it is important to consider SARS-CoV-2 infection when seeing patients with neurological manifestations, especially those needing immune-modulator therapy, since the established recommendations are insufficient at this time. cache = ./cache/cord-353812-4oxbczqe.txt txt = ./txt/cord-353812-4oxbczqe.txt === reduce.pl bib === id = cord-353731-7xn7m662 author = Heaton, Brook E. title = SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date = 2020-08-18 pages = extension = .txt mime = text/plain words = 2233 sentences = 139 flesch = 51 summary = sgRNA sequencing data indicated that the host gene with the highest probability of being 125 required for SARS-CoV-2 infection was the serine/arginine-rich protein kinase, SRPK1 126 ( Figure 1B) . We next wanted to define the degree to which inhibition of SRPK1 mediated N 141 phosphorylation would affect viral replication, especially since other non-SRPK1 kinases 142 have been predicted to be responsible for SARS-CoV-2 protein phosphorylation 12,13 . SRPIN340 treatment of cells infected with the 183 alphacoronavirus 229E (which is only distantly related to betacoronavirus SARS-CoV-2) 184 inhibited the virus by more than 1,000-fold at non-toxic concentrations of the drug ( Figure 185 2G-H). Human papillomavirus type 1 E1^E4 protein is a potent 533 inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits 534 phosphorylation of host SR proteins and of the viral transcription and replication 535 regulator E2 cache = ./cache/cord-353731-7xn7m662.txt txt = ./txt/cord-353731-7xn7m662.txt === reduce.pl bib === id = cord-353161-mtq6yh25 author = Rodrigues, João PGLM title = Insights on cross-species transmission of SARS-CoV-2 from structural modeling date = 2020-06-05 pages = extension = .txt mime = text/plain words = 6169 sentences = 369 flesch = 56 summary = We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Collectively, our results provide a structural framework that explains why certain animal species are not susceptible to SARS-CoV-2 infection, and also suggests potential mutations that can enhance binding to the viral RBD. Although it is well-known that docking scores do not quantitatively correlate with experimental binding affinities [19] , these scores suggest that SARS-CoV-2 neg species lack one or more key ACE2 residues that contribute significantly to the interaction with RBD. Models of SARS-CoV-2 neg species -chicken, duck, guinea pig, mouse, and rat -generally have higher (worse) HADDOCK scores than average (Figure 2 ), suggesting that these species' non-susceptibility to infection could stem from deficient RBD binding to ACE2. cache = ./cache/cord-353161-mtq6yh25.txt txt = ./txt/cord-353161-mtq6yh25.txt === reduce.pl bib === id = cord-353963-d3gk3519 author = Karampela, Irene title = Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19? date = 2020-06-06 pages = extension = .txt mime = text/plain words = 807 sentences = 48 flesch = 29 summary = A recent in silico study has shown that the fluoroquinolones, ciprofloxacin and moxifloxacin, may inhibit SARS-CoV-2 replication by exhibiting stronger capacity for binding to its main protease than chloroquine and nelfinavir, a protease inhibitor antiretroviral drug. Based on their potential antiviral activity and immunomodulatory properties, the favorable pharmacokinetics and safety profile, we propose the use of respiratory fluoroquinolones as adjuncts in the treatment of SARS-CoV-2 associated pneumonia. However, preliminary clinical trials reported conflicting results regarding the use of the anti-malarial and anti-inflammatory chloroquine and the macrolide azithromycin, while the antiviral remdesivir has not been shown to significantly decrease COVID-19 mortality (1, 2) . Considering the potential antiviral activity of respiratory fluoroquinolones against SARS-CoV-2, along with their immunomodulatory properties, their favorable pharmacokinetics and the excellent safety profile, we propose their use as adjuncts in treating patients presenting COVID-19. Therefore, randomized clinical trials of respiratory fluoroquinolones are necessary to explore their potential Arch Med Res E20_832 3 therapeutic effect as an adjunct in the treatment of SARS-CoV-2 associated pneumonia. cache = ./cache/cord-353963-d3gk3519.txt txt = ./txt/cord-353963-d3gk3519.txt === reduce.pl bib === id = cord-353923-ou7w3zkv author = Ren, Shi-Yan title = Stability and infectivity of coronaviruses in inanimate environments date = 2020-04-26 pages = extension = .txt mime = text/plain words = 4946 sentences = 267 flesch = 58 summary = Most viruses from the respiratory tract, such as coronaviruses, influenza, SARS-CoV, or rhinovirus, can persist on surfaces for a few days. The SARS-CoV-2 is presumed to be transmitted by respiratory droplets, viral aerosols, close contacts, and self-inoculation to nose, mouth, or eyes after touching a contaminated surface [16] . We therefore reviewed the persistence and infectivity of viruses on inanimate surfaces to provide clear information for containing the epidemic of SARS-CoV-2. One COVID-19 patient had upper respiratory tract infection with no pneumonia or diarrhea, and his two stool samples were positive for SARS-CoV-2 on RT-PCR. Persistence of most bacteria, fungi, and viruses (e.g., SARS-CoV) on surfaces depends on environmental conditions [37] , such as air temperature and RH [39] , inoculums, and the materials that they stayed on. Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient cache = ./cache/cord-353923-ou7w3zkv.txt txt = ./txt/cord-353923-ou7w3zkv.txt === reduce.pl bib === id = cord-353826-owoec2ud author = Graham, Simon P. title = Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date = 2020-07-27 pages = extension = .txt mime = text/plain words = 5496 sentences = 269 flesch = 53 summary = Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Analysis of SARS-CoV-2 S proteinspecific murine splenocyte responses by IFN-γ ELISpot assay showed no statistically significant difference between the primeonly and prime-boost vaccination regimens, in either strain of mouse (Fig. 1a) . SARS-CoV-2 S protein-specific antibody responses following ChAdOx1 nCoV-19 prime-only and prime-boost vaccination regimens in mice and pigs SARS-CoV-2 S protein-specific antibody titres in serum were determined by ELISA using recombinant soluble trimeric S (FL-S) and receptor binding domain (RBD) proteins. Small animal models have variable success in predicting vaccine efficacy in larger animals but are an important To analyse SARS-CoV-2 S-specific T cell responses, all mice were sacrificed on day 49 for isolation of splenocytes and pigs were blood sampled longitudinally to isolate PBMC. cache = ./cache/cord-353826-owoec2ud.txt txt = ./txt/cord-353826-owoec2ud.txt === reduce.pl bib === id = cord-353612-9ux181xg author = Josset, Laurence title = Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus date = 2013-04-30 pages = extension = .txt mime = text/plain words = 6299 sentences = 303 flesch = 49 summary = Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. In addition, several kinase inhibitors (including SB203580, LY294002, and U0126) and a glucocorticoid (dexamethasone) were also predicted to be negative regulators of genes changed similarly after SARS-CoV and HCoV-EMC infection at late times postinfection (see Table S2 in the supplemental material). Importantly, this kinase inhibitor was predicted to regulate genes that were DE similarly by SARS-CoV and HCoV-EMC at late times postinfection (see Table S2 in the supplemental material) and could therefore inhibit both viruses' replication. cache = ./cache/cord-353612-9ux181xg.txt txt = ./txt/cord-353612-9ux181xg.txt === reduce.pl bib === id = cord-353537-skeajydw author = Zhang, Xian title = Asymptomatic Subclinical Cases of Coronavirus Disease 2019 without Viral Transmission in Three Independent Families date = 2020-09-24 pages = extension = .txt mime = text/plain words = 2098 sentences = 119 flesch = 49 summary = Their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected by SARS-CoV-2. Three medical staff diagnosed with asymptomatic SARS-CoV-2 infection by serological tests after returning to work and their family members were recruited for this study. The patients and their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected with SARS-CoV-2. All their family members-including four old people, three young persons, and three children-showed no symptoms of COVID-19, and their nucleic acid and antibody tests were negative, indicating that they were not infected. During the following 2 months more, almost covering the whole disease process, from the incubation period to the recovery period, the indexes lived together with their family members, including a nasopharyngeal carcinoma patient who is theoretically vulnerable to SARS-CoV-2 infection due to impaired immune function as a result of radiotherapy or chemotherapy, without taking any protective measures. cache = ./cache/cord-353537-skeajydw.txt txt = ./txt/cord-353537-skeajydw.txt === reduce.pl bib === id = cord-354353-hyz0gmpz author = Farhangrazi, Z. Shadi title = Airborne Particulate Matter and SARS-CoV-2 Partnership: Virus Hitchhiking, Stabilization and Immune Cell Targeting — A Hypothesis date = 2020-09-24 pages = extension = .txt mime = text/plain words = 2465 sentences = 108 flesch = 38 summary = While long-term exposure to air pollutants such as PM 2.5 and nitrous dioxide contributes to persistent inflammatory responses and cardiopulmonary diseases (7) , which might increase vulnerability to COVID-19, it is also plausible that depending on the environment SARS-CoV-2 "hitchhiking" on airborne PM pollutants might be an additional mechanism for spreading the infection. In summary, although long-term exposure to polluted air might increase vulnerability to COVID-19 through prior adverse cellular effects of settled PM (24), our proposed "hitchhiking" hypothesis offers an additional multi-mechanistic pathogenic process through delivery of low viral titres with diverse PM-virus composites and is applicable to both indoor and outdoor situations, where the pathogenic severity is dependent on PM concentration, composition, shape and size as well as the infectious viral load. Contrary to the suggestions that long-term exposure to PM might increase vulnerability to SAR-CoV-2 infection, inhaled PM might promote some forms of immunity to the virus in some individuals. cache = ./cache/cord-354353-hyz0gmpz.txt txt = ./txt/cord-354353-hyz0gmpz.txt === reduce.pl bib === id = cord-354103-4dldgqzf author = Grubic, Andrew D title = COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date = 2020-06-27 pages = extension = .txt mime = text/plain words = 4869 sentences = 266 flesch = 47 summary = While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a "stress test" to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. On the same day, the United States Surgeon General echoed the recommendation from the American College of Surgeons and urged hospitals and healthcare systems to consider suspending elective surgical procedures during the outbreak of COVID-19. This pandemic started with identification of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent from a cluster of pneumonias in the Hubei providence of China in December 2019. On March 25, 2000, American College of Surgeons released the guidelines for emergency general surgery in COVID-19 positive patients or those at high clinical suspicion for COVID infection. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases cache = ./cache/cord-354103-4dldgqzf.txt txt = ./txt/cord-354103-4dldgqzf.txt === reduce.pl bib === id = cord-353659-wtacr6qj author = Almutairi, Nawaf title = Coronavirus Disease‐2019 with Dermatologic Manifestations and Implications: An Unfolding Conundrum date = 2020-05-09 pages = extension = .txt mime = text/plain words = 1026 sentences = 62 flesch = 45 summary = As a nosocomial infection for hospital and nursing home patients and health care workers, it represents an extraordinary challenge. Lungs are the most severely affected organ by COVID-19 because the virus enters the host cells via the integral membrane protein angiotensin-converting enzyme 2 (ACE2), which is attached to cellular membranes in the lungs, arteries, heart, kidney, and intestines. A study of 663 COVID-19 patients from Wuhan, China stressed that patients more than 60 years old and those with chronic diseases were at enhanced risk of severe COVID-19, and more likely to die (43). Clinical Characteristics of Coronavirus Disease 2019 in China Prevalence of venous thromboembolism in patients with severe novel coronavirus pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-353659-wtacr6qj.txt txt = ./txt/cord-353659-wtacr6qj.txt === reduce.pl bib === id = cord-353887-f4yd7guj author = Tang, Yujun title = Cytokine Storm in COVID-19: The Current Evidence and Treatment Strategies date = 2020-07-10 pages = extension = .txt mime = text/plain words = 8532 sentences = 461 flesch = 44 summary = Besides, corticosteroids, programmed cell death protein (PD)-1/PD-L1 checkpoint inhibition, cytokine-adsorption devices, intravenous immunoglobulin, and antimalarial agents could be potentially useful and reliable approaches to counteract cytokine storm in COVID-19 patients. In this review, we referred COVID-19 associated cytokine storm as the patients who are severely ill along with a high concentration of pro-inflammatory cytokines. The innate and adaptive immune responses activated by SARS-CoV-2 infection lead to uncontrolled inflammatory responses and ultimately cause the cytokine storm (14) . MERS-CoV infects the cells mentioned above to induce delayed (but increased) levels of pro-inflammatory cytokines (e.g., IL-2) and chemokines (e.g., CCL2, CCL3) (27, 30) . Although SARS-CoV is abortive in macrophages and DCs, the virus induces an increase in levels of pro-inflammatory cytokines and chemokines (31, 32) . A comment and a meta-analysis, which mainly bases on the evidence of SARS and MERS (64, 65) , stated that corticosteroid would increase mortality and delayed clearance of viral in coronavirus infection diseases. cache = ./cache/cord-353887-f4yd7guj.txt txt = ./txt/cord-353887-f4yd7guj.txt === reduce.pl bib === id = cord-353494-72fvkx7f author = Singh, Rajveer title = Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study date = 2020-10-10 pages = extension = .txt mime = text/plain words = 4677 sentences = 267 flesch = 54 summary = The RMSD plots of all the three ligand-protein complexes showed very stable conformation throughout the simulation study, which demonstrates that it has a huge impact on the Mpro target ( Figure S2A ) as the reference compound N3. RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). The molecular dynamic simulation showed that the selected natural compounds bind and stabilized the active site of both the proteins such as Mpro and TMPRSS2. cache = ./cache/cord-353494-72fvkx7f.txt txt = ./txt/cord-353494-72fvkx7f.txt === reduce.pl bib === id = cord-354051-ro3o27pv author = Peccia, J. title = SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1244 sentences = 101 flesch = 57 summary = title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant. SARS-CoV-2 viral RNA concentrations were quantitatively compared with local hospital admission data and community COVID-19 compiled testing data. SARS-CoV-2 RNA sludge concentrations were quantitatively compared with data that are commonly used to track the community progression of COVID-19 including hospital admissions (Figure 2A This study uniquely utilized primary sewage sludge instead of raw wastewater for virus RNA measurements. cache = ./cache/cord-354051-ro3o27pv.txt txt = ./txt/cord-354051-ro3o27pv.txt === reduce.pl bib === id = cord-353704-lfndq85x author = Ye, Zi-Wei title = Zoonotic origins of human coronaviruses date = 2020-03-15 pages = extension = .txt mime = text/plain words = 8096 sentences = 434 flesch = 54 summary = In contrast, SARS-CoV, MERS-CoV and the newly-identified SARS-CoV-2 are highly pathogenic, causing severe lower respiratory tract infection in relatively more patients with a higher chance to develop acute respiratory distress syndrome (ARDS) and extrapulmonary manifestations. The 2019 novel HCoV (2019-nCoV), which has subsequently been renamed SARS-CoV-2, is the causative agent of the ongoing epidemic of coronavirus disease 2019 (COVID19) , which has claimed more than 3,120 lives and infected more than 91,000 people as of March 3, 2020 [19] . All these four communityacquired HCoVs have been well adapted to humans and are generally less likely to mutate to cause highly pathogenic diseases, though accidents did occur for unknown reasons as in the rare case of a more virulent subtype of HCoV-NL63, which has recently been reported to cause severe lower respiratory tract infection in China [38] . Alternatively, whereas bat alpha-CoVs serve as the gene pool of HCoV-229E, alpacas and dromedary camels might serve as intermediate hosts that transmit viruses to humans, exactly as in the case of MERS-CoV [69] . cache = ./cache/cord-353704-lfndq85x.txt txt = ./txt/cord-353704-lfndq85x.txt === reduce.pl bib === id = cord-353716-gxgvhhv1 author = Kumar, Ashutosh title = SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients date = 2020-09-30 pages = extension = .txt mime = text/plain words = 2300 sentences = 136 flesch = 40 summary = title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients Based on the circumstantial evidence present in the literature, we propose a SARS-CoV-2 cell entry receptor ACE2 based mechanism for vascular thrombosis in COVID-19 patients. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). SARS-CoV-2 binding to the cell entry receptor ACE2 downregulates receptor expression that in turn induces vascular endothelial dysfunction, which activates prothrombotic cascade and eventually leads to vascular thrombosis observed in COVID-19 patients. cache = ./cache/cord-353716-gxgvhhv1.txt txt = ./txt/cord-353716-gxgvhhv1.txt === reduce.pl bib === id = cord-353777-t8q99tlq author = Jia, Yong title = Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date = 2020-04-11 pages = extension = .txt mime = text/plain words = 3217 sentences = 180 flesch = 58 summary = The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020. The discrepant phylogenies for the spike protein and its 23 receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARSDespite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that 25 leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27 th January 2020 from 26 cache = ./cache/cord-353777-t8q99tlq.txt txt = ./txt/cord-353777-t8q99tlq.txt === reduce.pl bib === id = cord-353572-b4mdiont author = Zhou, Yadi title = Network-based Drug Repurposing for Human Coronavirus date = 2020-02-05 pages = extension = .txt mime = text/plain words = 6871 sentences = 390 flesch = 42 summary = Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs. Coronaviruses (CoVs) typically affect the respiratory tract of mammals, including humans, and lead to mild to severe respiratory tract infections [1] . These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). cache = ./cache/cord-353572-b4mdiont.txt txt = ./txt/cord-353572-b4mdiont.txt === reduce.pl bib === id = cord-354458-o2kcd085 author = Caffo, Orazio title = On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 630 sentences = 27 flesch = 49 summary = title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 prostate cancer (PC) and risk of infection by SARSCoV-2 through a population-based study of patients with laboratory-confirmed SARS-CoV-2 infection from 68 hospitals in Veneto (1) . To further investigate this potential relationship, we identified all of the cases of COVID-19 that have occurred in metastatic castration-resistant PC (mCRPC) and metastatic castration-sensitive PC (mCSPC) patients treated in most of the high-volume referral medical oncology departments in northern Italy. The 19 high-volume medical oncology departments contributing to this study were treating a median of 80 metastatic PC patients each (range 48-230) for a total of 1,949. On the contrary, we identified a homogenous population of consecutive mCSPC/mCRPC patients treated in most of the high-volume referral medical oncology departments in northern Italy. Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (n=4532) cache = ./cache/cord-354458-o2kcd085.txt txt = ./txt/cord-354458-o2kcd085.txt === reduce.pl bib === id = cord-354315-yfn9vaan author = Meirson, Tomer title = Structural basis of SARS-CoV-2 spike protein induced by ACE2 date = 2020-05-24 pages = extension = .txt mime = text/plain words = 5190 sentences = 253 flesch = 49 summary = This conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The critical step in SARS-CoV-2 infection which involves the transition between a metastable prefusion state to a stable post-fusion state is triggered by binding to ACE2 which induces conformational changes in the RBD and the hinge region (Gui, et al., 2017; Pallesen, et al., 2017; Song, et al., 2018; Walls, et al., 2020) . To gain insights into the effects of ACE2 interaction on the S protein of SARS-COV-2, we analyzed the intramolecular structural variations in the bound versus the unbound-closed Numerous structures of the prefusion human CoV S proteins were determined at different states, and the key regions responsible for the interaction with the receptor were previously reported (Lan, et al., 2020; Shang, et al., 2020; Walls, et al., 2020; Wan, et al., 2020; Wrapp, et al., 2020; Yan, et al., 2020) . cache = ./cache/cord-354315-yfn9vaan.txt txt = ./txt/cord-354315-yfn9vaan.txt === reduce.pl bib === id = cord-354261-gdvawnp6 author = Gale, Chris title = National active surveillance to understand and inform neonatal care in COVID-19 date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1626 sentences = 92 flesch = 46 summary = Vertical transmission of SARS-CoV-2 has yet to be definitively established; neonatal infection with the virus has been detected in the first days after birth to mothers with COVID-19 1 ; however, this could represent early horizontal transmission. For more complete case ascertainment, this BPSU surveillance will link with other related data sources, including ongoing UKOSS surveillance of COVID-19 in pregnancy for maternal cases, Mothers and Babies: Reducing Risk through Audits and Confidential Enquiries across the UK (MBRRACE-UK), for neonatal deaths and stillbirths, and Public Health England (PHE), Health Protection Scotland, Public Health Wales and the Health and Social Care Public Health Agency in Northern Ireland. Active surveillance through established national systems such as the BPSU and UKOSS with very high population-based case ascertainment is among the simplest, quickest and most efficient way to obtain the accurate population level incidence data and to determine true infection rates, clinical characteristics and outcomes, which are needed to inform optimal perinatal and neonatal care. cache = ./cache/cord-354261-gdvawnp6.txt txt = ./txt/cord-354261-gdvawnp6.txt === reduce.pl bib === id = cord-354510-jlg5je0s author = de Carvalho, A. F. title = THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4112 sentences = 234 flesch = 58 summary = Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. 13 Here we describe the use of a simple, virus-inactivating and denaturing solution as part of a swab collection kit, aiming to decrease the infectious potential of the clinical sample and, at the same time, to preserve highly frail RNA molecules during transportation and short-term storage before testing. In order to increase personnel safety, to avoid losing collaborators due to infections by SARS-CoV-2, and at the same time to increase preservation of the RNA contained in clinical samples, we introduced the use of the guanidinecontaining solution as collection and transport media instead of commonly used viral transport media (VTM). cache = ./cache/cord-354510-jlg5je0s.txt txt = ./txt/cord-354510-jlg5je0s.txt === reduce.pl bib === id = cord-354101-8a7tohcx author = Silva de Oliveira, Daniela title = Immune response in COVID-19: What do we currently know? date = 2020-09-09 pages = extension = .txt mime = text/plain words = 553 sentences = 53 flesch = 53 summary = In 2002/2003 there was a pandemic denominate SARS (severe acute respiratory syndrome), caused by the SARS-CoV virus that belongs to the genera Betacoranavirus and the family Coronaviridae, generally responsible for influenza infections. In mid of 2019, a new disease by the coronavirus named by COVID-19 (SARS-CoV-2) emerged, both infections have flu symptoms, however they are infections that variable intensity, being medium to severe. The acute respiratory syndrome is a disease caused by the SARS-CoV-2 virus (COVID-37 19), where symptoms include difficulty breathing, high fever, and cough (WHO, 2020). Clinicopathologic, immunohistochemical, and ultrastructural findings of 673 a fatal case of Middle East respiratory syndrome coronavirus infection in the United 674 Immune responses in COVID-19 700 and potential vaccines: Lessons learned from SARS and MERS epidemic Middle East respiratory syndrome coronavirus Middle East respiratory syndrome coronavirus 766 (MERS-CoV) sheets/detail/middle-east-respiratory-syndrome-coronavirus-(mers-cov)> Access Pathological findings of COVID-19 associated with acute respiratory 786 distress syndrome. cache = ./cache/cord-354101-8a7tohcx.txt txt = ./txt/cord-354101-8a7tohcx.txt === reduce.pl bib === id = cord-353953-83d0g8ix author = Mendoza, Emelissa J. title = Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2 date = 2020-05-31 pages = extension = .txt mime = text/plain words = 4265 sentences = 281 flesch = 57 summary = Plaque assays are a quantitative method of measuring infectious SARS‐CoV‐2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen. Plaque assays are a quantitative method of measuring infectious SARS-CoV-2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen (Harcourt et al., 2020) . The first plaque assay method that we describe (Basic Protocol) uses Noble agar as the matrix in a solid overlay and neutral red as the stain to enhance plaque visualization. This protocol outlines a plaque assay method that can be used for the quantification of SARS-CoV-2 plaque-forming units (PFUs) in virus specimens, including viral stocks prepared from infected cell culture supernatants, and with further optimization, bodily fluids from animals infected with SARS-CoV-2. Use Formula 8 (see Basic Protocol) to calculate the titer of SARS-CoV-2 in the specimen using the identified dilution factor and the inoculum volume of 0.1 ml. cache = ./cache/cord-353953-83d0g8ix.txt txt = ./txt/cord-353953-83d0g8ix.txt === reduce.pl bib === id = cord-353914-zzla4frm author = Hu, Bo title = Cardiac involvement of COVID-19: Looking forward to novel discoveries and clinically valuable evidence() date = 2020-09-01 pages = extension = .txt mime = text/plain words = 423 sentences = 36 flesch = 42 summary = Since the Coronavirus Disease-2019 (COVID-19) outbreak, several clinical studies [1] [2] [3] have discovered the evidence of myocardial injury as significant elevation of cardiac troponin among the infected patients, especially those required intensive care. From our experiences, myocardial injury is almost in COVID-19 patients of severe and critical types and/or with underlying cardiovascular diseases [1] [2] [3] . Currently, the number of infected people has reached 3.6 million, while cases with myocarditis were extremely rare in the published clinical studies and case reports. In line with our study [1] , although SARS-CoV-2 infection can be detected in myocardial tissue, cardiac involvement of COVID-19 is possibly more integrated with systemic disorders. Clinical investigation of SARS-CoV-2 myocarditis should focus on young patients without any underlying cardiovascular diseases. We look forward to novel discoveries and clinically valuable evidence regarding to cardiac involvement of COVID-19. Suspected myocardial injury in patients with COVID-19: evidence from front-line clinical observation in Wuhan, China cache = ./cache/cord-353914-zzla4frm.txt txt = ./txt/cord-353914-zzla4frm.txt === reduce.pl bib === id = cord-354407-zzxjv666 author = Campanacci, Valérie title = Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date = 2004-06-07 pages = extension = .txt mime = text/plain words = 2338 sentences = 137 flesch = 60 summary = title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. The crystal structure of the main (or 3CL) protease of transmissible gastroenteritis virus, a related coronavirus, has been determined and was used to construct a model of the SARS-CoV 3CL protease, facilitating future drug design against this important target (Anand et al., 2003) . In the related mouse hepatitis virus, which is a group 2 coronavirus, the SARS-CoV Nsp9 corresponds to a 12 kDa cleavage product (P1a-12) that is found preferentially in the perinuclear region of infected cells, where it co-localizes with other components of the viral replication complex (Bost et al., 2000) . cache = ./cache/cord-354407-zzxjv666.txt txt = ./txt/cord-354407-zzxjv666.txt === reduce.pl bib === id = cord-354534-0b7zwzjv author = Fuccillo, E title = Olfactory disorders in coronavirus disease 2019 patients: a systematic literature review date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2847 sentences = 161 flesch = 43 summary = The patients, intervention, comparison and outcomes ('PICO') criteria for the review were considered as follows: (1) patientspatients with SARS-CoV-2 infection certified on laboratory tests who underwent a clinical evaluation of smell impairment using anamnestic data, a smell questionnaire and/or olfactory tests; (2) interventionclinical evaluation of olfactory disorders; (3) comparisondifferent methods of evaluating olfactory function (subjective and objective); and (4) outcomeprevalence and characteristics of olfactory dysfunction in Covid-19 patients. The reported data show that smell dysfunction was, overall, more prevalent in patients investigated with validated questionnaires and/or tests with odorants (Table 3 ), compared to PubMed (("COVID" OR "COVID-19" OR "SARS-COV-2" OR "coronavirus")) AND ("smell" or "anosmia" or "dysosmia" or "hyposmia" or "parosmia" or "olfaction" or "olfactory") The Journal of Laryngology & Otology individuals evaluated using anamnestic data, simple surveys and/or non-validated questionnaires. cache = ./cache/cord-354534-0b7zwzjv.txt txt = ./txt/cord-354534-0b7zwzjv.txt === reduce.pl bib === id = cord-354394-zojhdnlu author = Wang, Wei-Kung title = Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date = 2004-07-17 pages = extension = .txt mime = text/plain words = 3972 sentences = 175 flesch = 56 summary = We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. Using a quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay and fractionation experiment, we investigated the load of SARS-CoV in these samples and different components of the throat wash. As shown in Table 1 , SARS-CoV RNA was detected in the cell-associated component of the throat wash from all 16 specimens examined. cache = ./cache/cord-354394-zojhdnlu.txt txt = ./txt/cord-354394-zojhdnlu.txt === reduce.pl bib === id = cord-354080-glcq4qp9 author = Bodro, Marta title = Increased CSF levels of IL-1β, IL-6, and ACE in SARS-CoV-2–associated encephalitis date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1176 sentences = 79 flesch = 47 summary = For the latest articles, invited commentaries, and blogs from physicians around the world NPub.org/COVID19 Clinical features, serum, and CSF characteristics including cytokines and angiotensin-converting enzyme (ACE) profile from both cases are shown in the table. Three previous case reports of CNS involvement in COVID-19 suggest different pathogenic mechanisms: direct CNS infection demonstrated by detection of SARS-CoV-2 RNA in CSF, 2 recrudescence of symptoms related to previous lesions (e.g., brain infarction) in the context of systemic infection, 3 and inflammatory-mediated mechanisms resulting in acute hemorrhagic necrotizing encephalopathy. Hence, in a study of children with acute encephalitis-like syndrome, serum anti-human coronavirus-OC43 immunoglobulin M antibodies were present in 12% of patients and levels of IL-6, IL-8, monocyte chemotactic protein-1, and Granulocyte Macrophage Colony-Stimulating Factor were increased in their CSF. The main implication of these 2 patients is that physicians should be aware of COVID-19 infections presenting or predominantly manifesting as encephalitis, likely resulting from activation of inflammatory pathways with increased ILs and ACE in CSF. cache = ./cache/cord-354080-glcq4qp9.txt txt = ./txt/cord-354080-glcq4qp9.txt === reduce.pl bib === id = cord-354030-8tfg881h author = Dong, Rong title = Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date = 2020-07-28 pages = extension = .txt mime = text/plain words = 7983 sentences = 442 flesch = 52 summary = The realm of immunoinformatics tools considers the mechanism of the host immune response to yield additional methodologies in the design of vaccine against diseases are cost-effective and convenient, as in silico predictions can reduce the number of experiments needed (13, 14) . In this present, we employed immunoinformatics to predict multiple immunogenic proteins from the SARS-CoV-2 proteome and thereby design a multi-epitope vaccine. developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . A vaccine based on the spike protein could induce antibodies to block SARS-COV-2 binding and fusion or neutralize virus infection (18) , as well as induce harmful immune responses that cause liver damage (19) . To design an effective vaccine, we selected the SARS-CoV-2 protein through the above-mentioned methods for epitope prediction. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach cache = ./cache/cord-354030-8tfg881h.txt txt = ./txt/cord-354030-8tfg881h.txt === reduce.pl bib === id = cord-354453-uze6ze8o author = McCloskey, Brian title = SARS to novel coronavirus – old lessons and new lessons date = 2020-02-05 pages = extension = .txt mime = text/plain words = 3153 sentences = 116 flesch = 47 summary = By 26 January also, almost 50 million people in Wuhan and neighbouring cities had effectively been placed in quarantine while the WHO had determined that the event should not yet be declared as a Public Health Emergency of International Concern (PHEIC) [2] and had recommended no specific travel restrictions. There was extensive criticism of China for its perceived failure to share information about the emerging SARS infection early enough in the outbreak to allow countries to prepare and respond. The rapid sharing of information in this outbreak and the speed of the coordinated response both in the country and internationally suggest that lessons have been learned from SARS that improve global capacity. The global media response to the unfolding events has been relatively balanced and informed but the nuances of the evolving situation have not been critically examined in partnership with the media and as a result the public perception of the risk may be exaggeratedalthough it of course remains possible that the outbreak will develop in a way that matches up to the perceived risk. cache = ./cache/cord-354453-uze6ze8o.txt txt = ./txt/cord-354453-uze6ze8o.txt === reduce.pl bib === id = cord-353749-2vlc11rx author = Stricker, Raphael B title = Flattening the Risk: Pre-Exposure Prophylaxis for COVID-19 date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3090 sentences = 200 flesch = 50 summary = 24 In one uncontrolled study, HCQ prophylaxis in a hospital setting with a known SARS-CoV-2 exposure prevented dissemination of viral infection. 40 The second case-control study of HCWs found that four or more weekly doses of HCQ resulted in significantly less infection with SARS-CoV-2 (adjusted odds ratio 0.44, p<0.001). 45 In a retrospective cohort study of 32,109 rheumatic disease patients from the US Veterans Health Administration, the incidence of SARS-CoV-2 infection was equivalent regardless of chronic HCQ use (0.3% in users versus 0.4% in non-users), but mortality was significantly decreased in patients taking HCQ (odds ratio 0.70, p=0.0031). SARS-CoV-2 infection in a patient on chronic hydroxychloroquine therapy: implications for prophylaxis Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study Hydroxychloroquine in the COVID-19 pandemic era: in pursuit of a rational use for prophylaxis of SARS-CoV-2 infection cache = ./cache/cord-353749-2vlc11rx.txt txt = ./txt/cord-353749-2vlc11rx.txt === reduce.pl bib === id = cord-353996-slnyun4l author = Baumgartner, M. T. title = Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil date = 2020-05-08 pages = extension = .txt mime = text/plain words = 6874 sentences = 350 flesch = 52 summary = In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the cityand country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. We studied the exponential growth of time series data for over 460 cities with reported cases of infections by the new coronavirus, considering the effect of the environment, socioeconomic indicators, movement of people across the country, and social distancing. Our results show that the early spread of the new coronavirus in Brazil was mitigated by social distancing in some regions, but was also positively related to the size of the population of cities and how people moved across them. . https://doi.org/10.1101 In Great China, the ongoing COVID-19 outbreak expanded fast throughout the country and the majority of early cases reported outside of its origin had admitted recent travels to Wuhan, the core of the disease spread (Chinazzi et al., 2020) . cache = ./cache/cord-353996-slnyun4l.txt txt = ./txt/cord-353996-slnyun4l.txt === reduce.pl bib === id = cord-354372-vfvnjmv1 author = Carpenito, L. title = The autopsy at the time of SARS-CoV-2: Protocol and lessons date = 2020-07-04 pages = extension = .txt mime = text/plain words = 5696 sentences = 256 flesch = 51 summary = In the current pandemic scenario of SARS-CoV-2, the autopsy appears to be a crucial tool to clarify the virus target cells in human, the frameworks of organ damage and the biological mechanisms that lead to death or allow the patient to heal. To minimize the dispersion of blood and biological fluids, it is essential to always operate in the area of the autopsy table: the viscera removed from the body must be placed either on the iron section table, placed above the patient's thighs, or in a large tray with high steel edges resting on the patient's legs, during weighing, macroscopic examination and sampling of the viscera. Given the multiple clinical findings of neurological symptoms in patients infected with SARS-CoV-2 [22, 23] , it appears indispensable to perform the evisceration and examination of the brain and brainstem, for the completeness of the autopsy and for the very few morphological data available today on the central nervous system. cache = ./cache/cord-354372-vfvnjmv1.txt txt = ./txt/cord-354372-vfvnjmv1.txt === reduce.pl bib === id = cord-354209-g1zynbul author = Person, Bobbie title = Fear and Stigma: The Epidemic within the SARS Outbreak date = 2004-02-17 pages = extension = .txt mime = text/plain words = 3913 sentences = 160 flesch = 35 summary = While other NCID/CDC response teams dealt with laboratory investigations, surveillance, communica-tion, and clinical infection control practices, the Community Outreach Team worked to implement rapid public health strategies to document, monitor, and assist in ameliorating specific problems associated with fear, stigmatization, and discrimination attributed to the SARS outbreak in the United States. The team carried out the following activities: 1) facilitated group discussions with key opinion leaders within the Asian community in the United States; 2) collected and monitored the CDC Public Response Service data; 3) collected and monitored Asian-language newspapers, Internet sites, and other information sources; 4) reviewed polling data and other communication information; 5) conducted community visits, panel discussions, and media interviews; 6) solicited information from state and regional minority health liaisons nationwide; 7) developed ongoing relationships with the Asian-American communities; particularly in major metropolitan areas throughout the United States; and 8) determined new datagathering strategies as needed. cache = ./cache/cord-354209-g1zynbul.txt txt = ./txt/cord-354209-g1zynbul.txt === reduce.pl bib === id = cord-354349-hbk2p6ej author = Sardar, Sundus title = COVID-19 and Plasmodium vivax malaria co-infection date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1722 sentences = 118 flesch = 49 summary = With its variety of clinical manifestations including, but not limited to, fever, cough, diarrhea, vomiting, headache, myalgia and fatigue, it may be challenging to distinguish COVID-19 from a spectrum of diseases with similar presentations, such as malaria, especially in endemic areas. The coronavirus infection 2019 (COVID-19), which is caused by SARS-CoV-2, emerged in Wuhan, China in December 2019 and has since reached pandemic proportions affecting more than 8 million cases worldwide with total deaths exceeding 400,000 [1] . SARS-CoV-2, COVID-19, malaria, Plasmodium vivax, co-infection, artesunate In this case, artesunate and artemether were initiated as the treatment regimen; whether these agents offered protective effects from respiratory deterioration or multi-organ involvement despite SARS-CoV-2 infection is unclear and should be further explored. Our case highlights the importance of identifying possible underlying secondary infections in concurrence with SARS-CoV-2, which may be otherwise overlooked amidst the challenges of the current unprecedented COVID-19 pandemic. cache = ./cache/cord-354349-hbk2p6ej.txt txt = ./txt/cord-354349-hbk2p6ej.txt === reduce.pl bib === id = cord-353873-88ud20oq author = Hoyler, Marguerite M. title = The importance of challenges in COVID-19 screening and testing in the obstetric patient population date = 2020-05-28 pages = extension = .txt mime = text/plain words = 539 sentences = 37 flesch = 49 summary = We reviewed with interest the recent article and accompanying infographic published by Herman and colleagues regarding anesthesia management of the obstetric patient in the era of COVID-19. [1] We commend the authors for a compelling visual summary of strategies to help care for patients as well as protect obstetric anesthesia providers from possible SARS-CoV-2 transmission. These observations support a low threshold for testing parturients for COVID-19, even if they present with symptoms that occur in normal pregnancy; this is particularly important in communities with high rates of SARS-CoV-2 infection. As part of obstetric anesthesia care considerations, and particularly in communities and institutions with high burdens of SARS-CoV-2 infection, it may be prudent to routinely manage parturients as high risk for COVID-19 infection and to encourage conservative measures that J o u r n a l P r e -p r o o f cache = ./cache/cord-353873-88ud20oq.txt txt = ./txt/cord-353873-88ud20oq.txt === reduce.pl bib === id = cord-354538-vqi67h6a author = Sydney, Elana R. title = Antibody evidence of SARS-CoV-2 infection in healthcare workers in the Bronx date = 2020-08-26 pages = extension = .txt mime = text/plain words = 793 sentences = 68 flesch = 50 summary = 5. What is the prevalence of antibodies in those healthcare workers with self-reported positive and negative SARS-CoV-2 PCR tests? In total, 1,700 healthcare workers were tested for SARS-CoV-2 IgG antibody between April 28 and May 4, 2020. We analyzed the data by looking at those healthcare workers that had positive antibodies and stratified it based on department, presence or absence of symptoms, and previously reported positive PCR. Notably, 12% of those who tested positive for the presence of IgG reported a negative SARS-CoV-2 PCR result. As expected, 92% of individuals that reported a positive PCR test developed IgG antibodies. A small number of individuals, representing 1% of those reporting a positive SARS-CoV-2 PCR test prior to being tested, had a negative antibody test. 6 Our results reflect a higher overall rate of SARS-CoV-2 antibody development among healthcare workers in the Bronx compared to reported rates in NYC healthcare workers. cache = ./cache/cord-354538-vqi67h6a.txt txt = ./txt/cord-354538-vqi67h6a.txt === reduce.pl bib === id = cord-354582-fniymnmf author = Ma, Zhiqian title = Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date = 2020-06-30 pages = extension = .txt mime = text/plain words = 8373 sentences = 423 flesch = 44 summary = In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . cache = ./cache/cord-354582-fniymnmf.txt txt = ./txt/cord-354582-fniymnmf.txt === reduce.pl bib === id = cord-354134-gb2pf5kb author = Güemes-Villahoz, Noemi title = Conjunctivitis in COVID-19 patients: frequency and clinical presentation date = 2020-08-29 pages = extension = .txt mime = text/plain words = 3461 sentences = 170 flesch = 41 summary = Given the current situation of the SARS-CoV-2 pandemic, describing the clinical characteristics of conjunctivitis associated with the novel coronavirus has relevant implications in the future identification of suspected COVID-19 patients and the differential diagnosis from other forms viral conjunctivitis. A study analyzing a sample of 1099 patients hospitalized for COVID-19 disease in China found a prevalence of conjunctivitis symptoms of only 0.8% and other small series have reported a prevalence around 3% [4, 6, 7] . Despite our study showed no difference in the clinical presentation of conjunctivitis in male and female, we found that conjunctivitis was more frequent in males with moderate COVID-19 and women with mild disease. A better understanding of the ocular manifestations of the virus will assist in early identification of SARS-CoV-2infected cases, prioritizing diagnostic testing in patients with clinical findings compatible with conjunctivitis associated with COVID-19. cache = ./cache/cord-354134-gb2pf5kb.txt txt = ./txt/cord-354134-gb2pf5kb.txt === reduce.pl bib === id = cord-354113-j8odxs1h author = Miao, Congliang title = A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19 date = 2020-03-24 pages = extension = .txt mime = text/plain words = 3129 sentences = 200 flesch = 52 summary = Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group. Methods We retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in We retrospectively collected demographic data, medical history, epidemiological, clinical, laboratory, and CT imaging characteristics of all suspected patients on admission from medical records. 22.20040782 doi: medRxiv preprint This report demonstrated that the incidence of dry cough in confirmed group was significantly higher than that in unconfirmed group, but the clinical symptoms of patients with COVID-19 were nonspecific. cache = ./cache/cord-354113-j8odxs1h.txt txt = ./txt/cord-354113-j8odxs1h.txt === reduce.pl bib === id = cord-353911-hp6s6ebh author = Petráš, Marek title = Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date = 2020-11-03 pages = extension = .txt mime = text/plain words = 2119 sentences = 134 flesch = 54 summary = title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. The above laboratory procedure generated a semi-split inactivated vaccine, i.e., a vaccine with 307 the S protein separated from the viral particle exhibiting an early, both humoral and cellular, 308 immune response. Safety and immunogenicity of the ChAdOx1 nCoV-386 19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, 387 randomised controlled trial An in-depth investigation of the safety and immunogenicity of an 468 inactivated SARS-CoV-2 vaccine A double-inactivated 499 whole virus candidate SARS coronavirus vaccine stimulates neutralising and 500 protective antibody responses. Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity 526 cache = ./cache/cord-353911-hp6s6ebh.txt txt = ./txt/cord-353911-hp6s6ebh.txt === reduce.pl bib === id = cord-354612-7f91l0n9 author = Villar, Livia Melo title = USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS date = 2020-07-23 pages = extension = .txt mime = text/plain words = 572 sentences = 51 flesch = 65 summary = title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS A total of four individuals (two hepatitis cases and two without liver disease) were negative to SARS CoV-2 in NPS and saliva (100% of specificity). Positive concordant results in NPS and saliva were observed in seven individuals (two hepatitis cases and 5 without liver disease) until 7 days after onset of symptoms (100% of sensitivity). This is the first report of SARS CoV-2 detection in saliva samples among liver disease patients showing best results until 7 days of beginning of symptoms. In addition, there is no information regarding the usefulness of saliva for detecting SARS CoV-2 RNA in individuals presenting comorbidities, such as liver disease. Since saliva can be collected easily, SARS CoV-2 RNA detection in saliva can be useful strategy to increase the access of sample collection for the diagnosis of COVID-19 in patients with liver disease. cache = ./cache/cord-354612-7f91l0n9.txt txt = ./txt/cord-354612-7f91l0n9.txt === reduce.pl bib === id = cord-354685-oggtmum4 author = Kurup, Drishya title = Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2 date = 2020-10-16 pages = extension = .txt mime = text/plain words = 6509 sentences = 355 flesch = 55 summary = This study reports that both a live and an inactivated rabies virus containing the SARS-CoV-2 spike S1 protein induces potent virus-neutralizing antibodies at much higher levels than seen in the sera of convalescent patients. To assess the correct confirmation of the chimeric S1 incorporated into CORAVAX, we first analyzed the binding of the recombinant human ACE-2 receptor-Fc chimera (human IgG) protein (Fig. 2a) and a SARS-COV-2 receptor binding domain (RBD) directed mouse monoclonal antibody (Fig. 2b) . After blocking, the membrane was incubated overnight with a human monoclonal 4C12 specific for the RABV glycoprotein (hybridoma kindly provided by Dr. Scott Dessain) or rabbit serum against the S1 subunit of SARS-CoV-2 Spike protein (Invitrogen, ThermoFisher Scientific, Cat# PA5-81798) at a dilution of 1:1000 in PBS containing 5% BSA. The cells were then stained for 2 h at RT with mouse polyclonal antiserum against the S1 subunit of SARS-CoV-2 Spike protein and a human monoclonal antibody 4C12 against RABV glycoprotein (2 µg/ ml). cache = ./cache/cord-354685-oggtmum4.txt txt = ./txt/cord-354685-oggtmum4.txt === reduce.pl bib === id = cord-354148-87tpjvs6 author = Bidra, Avinash S. title = Rapid In‐Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Using Povidone‐Iodine Oral Antiseptic Rinse date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3069 sentences = 177 flesch = 49 summary = PURPOSE: To investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone‐iodine (PVP‐I) against SARS‐CoV‐2 ('corona virus') to mitigate the risk and transmission of the virus in the dental practice. MATERIALS AND METHODS: The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) USA‐WA1/2020 strain, virus stock was tested against oral antiseptic solutions consisting of aqueous povidone‐iodine (PVP‐I) as the sole active ingredient. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 ('corona virus') to mitigate the risk and transmission of the virus in the dental practice. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 ('corona virus') to mitigate the risk and transmission of the virus in the dental practice. cache = ./cache/cord-354148-87tpjvs6.txt txt = ./txt/cord-354148-87tpjvs6.txt === reduce.pl bib === id = cord-354373-lldfoptb author = Chi, Jeffrey title = COVID-19 Clinical Research date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2491 sentences = 153 flesch = 49 summary = They can be categorized into four groups: drugs that combat SARS-CoV-2, immunomodulatory agents to counteract cytokine storm, convalescence plasma therapies and vaccines trials. They can be categorized into 1) drugs that combat SARS-CoV-2, 2) immunomodulatory agents to counteract cytokine storm, 3) convalescent plasma therapies and 4) vaccines trials (Table 1) . In vitro studies of these agents showed antiviral activities against SARS-VoV-2 and they are now repurposed for treating COVID-19 in clinical trials (Table 1) . Currently there are many ongoing clinical trials (e.g. NCT04292899, NCT04292730) to evaluate the efficacy of remdesivir in patients with mild to moderate or severe COVID-19. Sarilumab, another IL-6 receptor antagonist approved for RA, is also being studied in clinical trials (e.g. NCT04288713) in hospitalized patients with severe COVID-19 (Table 1) . As of April 19, 2020, there were 5 registered convalescent plasma therapy clinical trials in the United States for the treatment of severe and critically ill COVID-19 patients (Table 1) . cache = ./cache/cord-354373-lldfoptb.txt txt = ./txt/cord-354373-lldfoptb.txt === reduce.pl bib === id = cord-354619-pftjhtpo author = Farronato, Marco title = A Call for Action to Safely Deliver Oral Health Care during and Post COVID-19 Pandemic date = 2020-09-15 pages = extension = .txt mime = text/plain words = 5041 sentences = 258 flesch = 49 summary = The oral cavity is purported to be one of the main host sites, both for entry and transmission, implicated in SARS-CoV-2 spread either through contact, droplet, aerosols, or saliva. Evidence suggests that the classic mechanism of transmission, contact and droplet spread, can be contained mostly by isolating symptomatic patients and by the use of facial masks/facial coverings, which de facto provides a physical barrier to the oral cavity and nose, the primary source of infection for droplets and larger aerosol particles. Following the above proposed guidelines, no cases COVID-19 disease transmission after single or multiple dental consultations was registered among the DHCW or patients. Classified as operative and non-operative, depending on their ability to work in the oral cavity or/and provide an essential outside support, the DHCW and the patients visiting the dental practice are undeniably at higher risk of SARS-CoV-2 infection and further transmission [41] . cache = ./cache/cord-354619-pftjhtpo.txt txt = ./txt/cord-354619-pftjhtpo.txt === reduce.pl bib === id = cord-354608-1me3nopu author = Rabinowicz, Shira title = COVID-19 in the Pediatric Population—Review and Current Evidence date = 2020-09-19 pages = extension = .txt mime = text/plain words = 5426 sentences = 298 flesch = 42 summary = By mid-August 2020, the World Health Organization reported over 23 million confirmed cases of infection with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), resulting in more than 710,000 death worldwide [1] . We review the current evidence of epidemiology, clinical presentation, treatment, and indirect health consequences of SARS-CoV-2 on children. In reports from countries that were severely affected early in course of the pandemic, children comprise 1-2% the diagnosed COVID-19 cases, underrepresented compared with other age groups [3, [13] [14] [15] . In summary, children at any age may be infected with SARS-CoV-2, with reduced frequency and severity compared with adults, although clear epidemiologic data is still missing. Characteristics and outcomes of children with coronavirus disease 2019 (COVID-19) infection admitted to US and Canadian Pediatric Intensive Care Units American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS-C) associated with SARS-CoV-2 and hyperinflammation in COVID-19. cache = ./cache/cord-354608-1me3nopu.txt txt = ./txt/cord-354608-1me3nopu.txt === reduce.pl bib === id = cord-354531-7klivhut author = Feng, Liqiang title = An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques date = 2020-08-21 pages = extension = .txt mime = text/plain words = 8295 sentences = 482 flesch = 58 summary = title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques In an attempt to develop a prophylactic vaccine against SARS-CoV-2, we constructed a replication-incompetent recombinant adenovirus, Ad5-S-nb2, that can efficiently express SARS-CoV-2 S protein in infected cells (Fig. 1a) . All non-vaccinated macaques showed no serum neutralizing activities (<1:50) against SARS-CoV-2 either before or 7 days after challenge (Fig. 4f) (Fig. 4g) . This study demonstrated that candidate vaccine Ad5-S-nb2 can elicit S-specific antibody and CMI responses in rodents and in NHPs. A single IM injection with a low-dose of 1 × 10 10 vp Ad5-S-nb2 can confer effective protection against SAR-CoV-2 challenge in aged Chinese rhesus macaques. Consistently, other studies in rhesus macaques also showed that the immune responses elicited by a primary SARS-CoV-2 infection or inactivated whole virus effectively protected against SARS-CoV-2 challenge without observing ADE 18, 19, 29, 30 . cache = ./cache/cord-354531-7klivhut.txt txt = ./txt/cord-354531-7klivhut.txt === reduce.pl bib === id = cord-354398-f3cg8gi1 author = Al-Saud, Haya title = Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date = 2020-09-20 pages = extension = .txt mime = text/plain words = 4018 sentences = 199 flesch = 55 summary = The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. We validated the modified Invitrogen Forensic DNA Purification kit in extracting in-laboratory propagated SARS-COV-2 RNA by conducting manual and automated extractions on titrations from 15 000 copies to 60 copies of SARS-COV-2 followed by RT-qPCR methods: the commercially available TaqPath One-Step qRT-QP-CR kit (using the N, S, and ORF1b genes) and primers and probes from Metabion, Germany to establish an inhouse RT-qPCR assay based on E, RdRp2 and RdRp4 gene detection as per recommended SARS-COV-2 testing from CDC and WHO. cache = ./cache/cord-354398-f3cg8gi1.txt txt = ./txt/cord-354398-f3cg8gi1.txt === reduce.pl bib === id = cord-354529-k8p2u7iq author = Wu, Yongran title = Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3753 sentences = 223 flesch = 57 summary = Clinical information of patients was collected from the electronic medical information system of Jinyintan Hospital, including the following factors: demographic data; date of symptom onset, admission, first CP infusion and discharge; laboratory data before and after infusion of CP, including white blood cell count, neutrophil count, lymphocyte count, liver and kidney function test, and inflammatory factors such as high sensitive C-reaction protein (HsCRP); results of SARS-CoV-2 test and cycle threshold value (Ct value) of quantitative reverse transcription-polymerase chain reaction; patients' status and treatments before or after the CP therapy, including the vital signs, anti-virus therapy, oxygen therapy, and other treatments; total volume dose of CP; pulmonary imaging examination data; information on complications such as transfusion-related adverse reactions. Clinical Benefit and Outcome of Patients with Prolonged Positivity of SARS-CoV-2 RNA after CP Therapy As shown in Table 3 , the median and interquartile ranged total volume of CP transfusion was 400 (200-400) mL in EN group and 400 (400-800) mL in LN group. cache = ./cache/cord-354529-k8p2u7iq.txt txt = ./txt/cord-354529-k8p2u7iq.txt === reduce.pl bib === id = cord-354720-fu19u2b0 author = White-Dzuro, Gabrielle title = Multisystem effects of COVID-19: a concise review for practitioners date = 2020-11-04 pages = extension = .txt mime = text/plain words = 5088 sentences = 285 flesch = 35 summary = It is important that clinicians managing critically ill COVID-19 patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. It is important that clinicians managing these critically ill patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. The indirect effects of the virus result from the host's response to the viral infection, and are associated with a cytokine storm characterized by very high circulating levels of pro-inflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukins, granulocyte-colony stimulating factor, and chemokines [9] . include direct viral damage of nervous tissue, injury resulting from the excessive inflammatory response, unintended host immune response effects after the acute infection (e.g., Guillain-Barré syndrome as reported in a case series of four patients [24] ), and injury resulting from the effects of systemic illness. cache = ./cache/cord-354720-fu19u2b0.txt txt = ./txt/cord-354720-fu19u2b0.txt === reduce.pl bib === id = cord-354773-u86bdmvf author = Suo, Tao title = ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date = 2020-06-07 pages = extension = .txt mime = text/plain words = 4490 sentences = 242 flesch = 57 summary = To improve the diagnostic accuracy of nucleic acid detection of SARS-Cov-2 in low viral load samples using droplet digital PCR, we compared the dynamic range and the limit of detection (LoD) with a 95% repeatable probability between ddPCR and RT-PCR in laboratory, and tested the clinical samples from 77 patients by both ddPCR and RT-PCR for head to head comparison. Throat swab samples of each patient were firstly collected for official approved RT-PCR diagnosis in hospitals and blinding laboratory RT-PCR and ddPCR tests simultaneously with the same primers/probe sets approved by Chinese CDC. As shown in Figure 3 , throat swab samples of each suspected outpatient were firstly collected for laboratory RT-PCR, ddPCR tests and official approved RT-PCR diagnosis in hospitals simultaneously with the same primers/probe sets approved by Chinese CDC (Table 1) . In this study, two throat swab samples of each supposed convalescent were collected for laboratory RT-PCR, ddPCR and official approved RT-PCR tests simultaneously with the same primers/probe sets (Table 2) . cache = ./cache/cord-354773-u86bdmvf.txt txt = ./txt/cord-354773-u86bdmvf.txt === reduce.pl bib === id = cord-354536-c9v9kbw8 author = Han, Yan-Jie title = Advances and challenges in the prevention and treatment of COVID-19 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 5268 sentences = 330 flesch = 48 summary = This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. cache = ./cache/cord-354536-c9v9kbw8.txt txt = ./txt/cord-354536-c9v9kbw8.txt === reduce.pl bib === id = cord-354868-pqn59ojj author = Yao, Hebang title = A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 3231 sentences = 236 flesch = 58 summary = title: A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2 Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. A high-affinity RBD binder without neutralizing activity 85 Previously, we generated 99 sybodies from three highly diverse synthetic libraries by ribosome and phage display with in vitro selections against the SARS-CoV-2 RBD. Consistent with its inability to neutralize SARS-CoV-2 pseudovirus, SR31 did not affect RBD-ACE2 binding (Fig. 1C) . Most RBD-targeting neutralizing antibodies, including neutralizing nanobodies characterized so far (8, 13-15, 19, 20, 22-24, 26-28, 34, 35, 37) , engage the RBD at the receptor-binding motif (RBM) (Fig. 3A) , thus competing off ACE2 and preventing viral entry. Taken together, the structural data rationalize the high-affinity binding between SR31 and RBD, and its inability to neutralize SARS-CoV-2. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 cache = ./cache/cord-354868-pqn59ojj.txt txt = ./txt/cord-354868-pqn59ojj.txt === reduce.pl bib === id = cord-354893-tku1dr32 author = Shi, Zhengli title = Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology date = 2010-12-24 pages = extension = .txt mime = text/plain words = 5894 sentences = 259 flesch = 52 summary = Comparative genome sequence analysis indicated that SARS-CoVs civets experience rapid ongoing mutation, suggesting that the viruses were still adapting to the host rather than persisting in equilibrium expected for viruses in their natural reservoir species Song et al., 2005) . Analysis of all the viral sequences available from human patients and animals revealed two major hallmarks of rapid virus evolution during the initial stages of the 2002À2003 outbreaks: (1) All isolates from early patients and market animals contained a 29-nt sequence in ORF8 that is absent in most of the publicly available human SARS-CoV sequences derived from later phases of the outbreaks; (2) a characteristic motif of single-nucleotide variations (SNVs) were identified in SARS-CoV of different phases, and all these SNVs were located in the S gene that codes for the spike protein responsible for attachment to host cellular receptor . Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections cache = ./cache/cord-354893-tku1dr32.txt txt = ./txt/cord-354893-tku1dr32.txt === reduce.pl bib === id = cord-354658-v451z3jq author = Rajagopal, Keshava title = Advanced Pulmonary and Cardiac Support of COVID-19 Patients: Emerging Recommendations From ASAIO—A “Living Working Document” date = 2020-05-11 pages = extension = .txt mime = text/plain words = 8876 sentences = 483 flesch = 41 summary = The severe acute respiratory syndrome (SARS)-CoV-2 is an emerging viral pathogen responsible for the global coronavirus disease 2019 (COVID)-19 pandemic resulting in significant human morbidity and mortality. We review the rapidly changing epidemiology, pathophysiology, emerging therapy, and clinical outcomes of COVID-19; and based on these data and previous experience with artificial cardiopulmonary support strategies, particularly in the setting of infectious diseases, provide consensus recommendations from ASAIO. It is the specific goal of the present paper to provide a resource document to the clinical community regarding evolving best practice strategies for advanced pulmonary and cardiac support in patients with severe progressive COVID-19. Although central cannulation is hemodynamically advantageous (with respect to higher flow rates; hemodynamic support is not relevant in pure V-V ECMO), in light of its invasiveness, bleeding risks, and specialized training required, it is more reasonable to propose peripheral cannulation as the initial approach of choice for COVID-19-related respiratory failure. cache = ./cache/cord-354658-v451z3jq.txt txt = ./txt/cord-354658-v451z3jq.txt === reduce.pl bib === id = cord-354948-q5eouyi2 author = Tsao, Kuo‐Chien title = False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome date = 2005-09-19 pages = extension = .txt mime = text/plain words = 2812 sentences = 161 flesch = 63 summary = title: False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome An earlier serum collected from the same patient on the 3rd day after disease onset was retested, and it was found that the results were negative for both SARS-CoV and HTLV antibodies. It was speculated that some SARS-CoV peptides common to HTLV might be responsible for the false positive results observed in HTLV antibody detection. These four common peptides were synthesized and tested the cross-reactivity of antibodies in the sera of SARS versus HTLV-infected patients. These four common peptides were synthesized further and tested for crossreactivity of antibodies in the sera of SARS versus HTLV infected-patients. This finding suggests that among the antibodies in the sera of SARS patients, those with cross-reactivity with HTLV peptides might disappear Six SARS coronavirus genomes are TW1/ay291451, CUHK-W1/ay278554, TOR2/nc_004718, CUHK-Su10/ay282752, BJ01/ay278488, and Urbani /ay278741. cache = ./cache/cord-354948-q5eouyi2.txt txt = ./txt/cord-354948-q5eouyi2.txt === reduce.pl bib === id = cord-354763-odzrco6q author = Drake, John M. title = Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date = 2006-12-20 pages = extension = .txt mime = text/plain words = 5739 sentences = 283 flesch = 46 summary = We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. We also retrospectively explore the effect of societal learning during the 2003 outbreak of SARS in Singapore, using weekly data on the time between onset of symptoms and removal of infectious individuals. Finally, we discuss societal and epidemiological factors that might affect societal learning, we observe that a difficult task during the early stages of an outbreak is to estimate the learning rate and suggest that the rate estimated here might be used as prior information in future outbreaks, and we conclude by recommending rapid investment in research at the time of initial detection when actions taken to reduce disease spread can be most efficient and cost effective. cache = ./cache/cord-354763-odzrco6q.txt txt = ./txt/cord-354763-odzrco6q.txt === reduce.pl bib === id = cord-354762-3a3a3ku9 author = Afsar, Cigdem Usul title = SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES date = 2020-06-02 pages = extension = .txt mime = text/plain words = 987 sentences = 70 flesch = 54 summary = title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES IFN is particularly expressed in epithelial cells and it is essential in skin and mucosal immunity (lung, intestines and reproductive tissues) of all African and Asian pangolin species (Choo and others, 2016) . IFN, like the other type I IFNs, might be responsible of decreased mortality in females because of its antiviral effects. The JAK/STAT pathway responds to type I IFN secreted from neighboring cells and SARS-CoV proteins have been shown to affect this pathway before (Frieman and Baric, 2008) . JAK-STAT signal blocking by baricitinib (a selective JAK1 and JAK2 inhibitor) produces an impairment of IFN-mediated antiviral response, with a potential facilitating effect on the evolution of SARS-CoV-2 infection. Interferon-epsilon protects the female reproductive tract from viral and bacterial infection cache = ./cache/cord-354762-3a3a3ku9.txt txt = ./txt/cord-354762-3a3a3ku9.txt === reduce.pl bib === id = cord-354900-bzv4yhqi author = Jawhara, Samir title = How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections date = 2020-10-12 pages = extension = .txt mime = text/plain words = 3691 sentences = 162 flesch = 34 summary = During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. This short review focuses on the role of baker's yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available. Of note, the SARS-CoV-2 particles first invade the respiratory mucosa and infect other cell types, causing a series of immune responses and the overproduction of cytokines 'cytokine storm' , which may be related to the critical condition of COVID-19 patients [21] . cache = ./cache/cord-354900-bzv4yhqi.txt txt = ./txt/cord-354900-bzv4yhqi.txt === reduce.pl bib === id = cord-354943-wxhbwcfr author = Guo, Li title = Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date = 2020-03-21 pages = extension = .txt mime = text/plain words = 3486 sentences = 181 flesch = 55 summary = METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. cache = ./cache/cord-354943-wxhbwcfr.txt txt = ./txt/cord-354943-wxhbwcfr.txt === reduce.pl bib === id = cord-354881-7o20cn1x author = Brown, Rebecca C H title = The scientific and ethical feasibility of immunity passports date = 2020-10-16 pages = extension = .txt mime = text/plain words = 4134 sentences = 239 flesch = 48 summary = Immunity passports could be implemented on the basis of either a laboratory test of immune response (a correlate of protection) or an immunising event (infection or vaccination), which would identify individuals less likely to get disease or transmit virus when exposed to SARS-CoV-2. 33, 34 Given the scale of the pandemic and the research into COVID-19, there is likely to be rapid progress in understanding the nature of infection and immunity such that clinical infection, with or without a measure ment of antibody response, might form the basis of a time-limited immunity passport. Evidence from previous work with seasonal coronaviruses and studies of SARS-CoV-2 vaccines in macaques suggests that previous infection or vaccination might protect from severe disease but an individual might nevertheless carry the virus at similar levels, and for a similar duration, to those previously uninfected, with an unchanged potential for transmission. cache = ./cache/cord-354881-7o20cn1x.txt txt = ./txt/cord-354881-7o20cn1x.txt === reduce.pl bib === id = cord-354597-xubsodnk author = Carvalho, Alexandre title = SARS-CoV-2 Gastrointestinal Infection Causing Hemorrhagic Colitis: Implications for Detection and Transmission of COVID-19 Disease date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2779 sentences = 159 flesch = 47 summary = Recent reports from China have described concomitant digestive symptoms, such as nausea, vomiting, diarrhea, and abdominal pain, in patients with confirmed SARS-CoV-2 pulmonary infection (5) (6) (7) (8) and the presence of SARS-CoV-2 RNA in fecal samples (8, 9) . We present a case of SARS-CoV-2 gastrointestinal infection causing acute hemorrhagic colitis and signaling COVID-19 disease which endoscopy confirmed colonic injury and helped exclude other etiologies of disease. On hospital day 4, 9 days after the onset of her digestive symptoms, the patient developed a cough; nasopharyngeal swabs were sent for comprehensive viral detection, including SARS-CoV-2 RNA (Quest Diagnostics). Given the patient's elevated C-reactive protein and persistent abdominal pain and bloody diarrhea, a flexible sigmoidoscopy was performed on hospital day 4 to evaluate for evidence of inflammatory bowel disease or ischemic colitis. cache = ./cache/cord-354597-xubsodnk.txt txt = ./txt/cord-354597-xubsodnk.txt === reduce.pl bib === id = cord-354950-kmpbdvof author = Demurtas, Olivia C. title = Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date = 2016-02-05 pages = extension = .txt mime = text/plain words = 8651 sentences = 406 flesch = 51 summary = Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. In addition, the WHO guidelines for SARS diagnosis, developed during the outbreak in 2003, suggested the use of N-based ELISA for specific IgG detection as confirmatory test of SARS-CoV infection (World Health Organization [WHO] , 2003 SARS: Laboratory diagnostic tests) due to the ability of the host to mount an early antibody response against the N protein (Che et al., 2004) . As the plant-derived recombinant M protein, the M RLV was also specifically recognized by the mouse anti-M pAb ( Figure 6C ) that had previously validated by Immunofluorescence Antibody Assay (IFA) in SARS CoV infected Vero cells (Carattoli et al., 2005) . cache = ./cache/cord-354950-kmpbdvof.txt txt = ./txt/cord-354950-kmpbdvof.txt === reduce.pl bib === id = cord-354733-qxivrhj8 author = Gniazdowski, V. title = Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3924 sentences = 251 flesch = 56 summary = Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. cache = ./cache/cord-354733-qxivrhj8.txt txt = ./txt/cord-354733-qxivrhj8.txt === reduce.pl bib === id = cord-354780-yzyixucr author = Lin, Chih-Yen title = Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1757 sentences = 120 flesch = 60 summary = title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan Conclusion This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This novel coronavirus was initially named 2019-novel coronavirus (2019-nCoV), however, currently the name has been established as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); with the disease being named as coronavirus disease 2019 (COVID-19) (Coronaviridae Study Group of the International Committee on Taxonomy of, 2020) Since the first reported case, there has been a rapid increase in the number of cases, with outbreaks being reported in countries all over the world. Accordingly, we suggest that the constant importation of SARS-CoV-2 infection is the major risk factor leading the COVID-19 epidemic in Taiwan. cache = ./cache/cord-354780-yzyixucr.txt txt = ./txt/cord-354780-yzyixucr.txt === reduce.pl bib === id = cord-355283-ny1ju7vc author = Colombo, L. title = How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism date = 2020-08-12 pages = extension = .txt mime = text/plain words = 1953 sentences = 95 flesch = 40 summary = title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism Although the most known feature of SARS-CoV-2 associated infection is a mild to severe pneumonia, increasing evidence suggests the existence of an infection-associated risk of both arterial and venous thromboembolism (VTE), but the exact magnitude of this phenomenon is still unknown. Only a few months have passed since the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19) , have spread all over the world, resulting in more than 17 million cases, more than 670,000 infection-related deaths [1] and a global health threat that has no comparison in the last decades. High incidence of venous thromboembolic events in anticoagulated severe COVID-19 patients cache = ./cache/cord-355283-ny1ju7vc.txt txt = ./txt/cord-355283-ny1ju7vc.txt === reduce.pl bib === id = cord-354972-nc496v6s author = Margolin, Emmanuel title = Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date = 2020-09-10 pages = extension = .txt mime = text/plain words = 10919 sentences = 464 flesch = 37 summary = As of 8 August 2020, there have been over 1.2 million confirmed cases of COVID-19 in Africa, with 29,833 deaths reported (Africa CDC) There is concern that the pandemic may pose an even greater risk to countries in Africa owing to their weak health-care infrastructure, large burden of co-infections, including HIV-1 and tuberculosis, and ongoing outbreaks of emerging and re-emerging infections such as Ebola virus (Democratic Republic of Congo) and Lassa haemorrhagic fever (Nigeria) that will divert much-needed resources away from the fight against COVID-19 (ref. Given the optimistic development timeline of 12-18 months before any vaccines could be available for widespread use, it is clear that these efforts will not Box 1 | Potential impact of climate on SArS-coV-2 dissemination the comparatively low incidence of coronavirus disease-2019 (COviD19) in africa has raised the possibility that climate could influence the spread of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2). cache = ./cache/cord-354972-nc496v6s.txt txt = ./txt/cord-354972-nc496v6s.txt === reduce.pl bib === id = cord-355039-qi4fwqbc author = Azar, William S. title = COVID-19 and diabetes mellitus: how one pandemic worsens the other date = 2020-08-02 pages = extension = .txt mime = text/plain words = 7350 sentences = 392 flesch = 44 summary = In this review, we elucidate suggested mechanisms underlying the increased susceptibility of patients with diabetes to infection with SARS-CoV-2 with a more severe COVID-19 disease. The different studies presented suggest that patients with diabetes may not only be prone to a more severe COVID-19 disease, but also to an increased risk of infection with SARS-CoV-2. Although plausible hypotheses for the increased risk of COVID-19 infection in patients with diabetes and other chronic diseases like hypertension are still under investigation, ACE2 seems to play a key role in the association between COVID-19 and DM [60] (Table 1 ). suggested that higher ACE2 expression in the lungs increased susceptibility to SARS-CoV-2 infection with more severe complications and was causally correlated with diabetes [68] . In this review, we describe three potential mechanisms underlying the increased susceptibility of patients with diabetes to a more severe COVID-19 disease, leading to higher morbidity and mortality. cache = ./cache/cord-355039-qi4fwqbc.txt txt = ./txt/cord-355039-qi4fwqbc.txt === reduce.pl bib === id = cord-355181-affuyn8z author = Poggio, Claudio title = Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5793 sentences = 304 flesch = 43 summary = SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . cache = ./cache/cord-355181-affuyn8z.txt txt = ./txt/cord-355181-affuyn8z.txt === reduce.pl bib === id = cord-355477-7xd93aqv author = SATIJA, NAMITA title = The Molecular Biology of SARS Coronavirus date = 2007-04-23 pages = extension = .txt mime = text/plain words = 4946 sentences = 279 flesch = 52 summary = abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells cache = ./cache/cord-355477-7xd93aqv.txt txt = ./txt/cord-355477-7xd93aqv.txt === reduce.pl bib === id = cord-354824-7fdcu2f0 author = Wu, Renyi title = An Update on Current Therapeutic Drugs Treating COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 9652 sentences = 504 flesch = 42 summary = Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. This estimated 20% of patients developing more severe disease with SARS-CoV-2 infection are most likely due to genetics, epigenetics, and or other factors, with dampened innate immune response to fight the virus coupled with enhanced viral load leading to cytokine storm, severe inflammatory/oxidative stress response, and severe lung injury secondary to ARDS. Chloroquine can inhibit the entry of SARS-CoV-2 and prevent virus-cell fusion by interfering with glycosylation of ACE2 receptor and its binding with spike protein, suggesting that chloroquine treatment might be more effective in the early stage of infection, before COVID-19 reduces ACE2 expression and activity [30, 38, 39] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, doubleblinded, phase IIb clinical trial (CloroCovid-19 Study) cache = ./cache/cord-354824-7fdcu2f0.txt txt = ./txt/cord-354824-7fdcu2f0.txt === reduce.pl bib === id = cord-355306-fj8utkfe author = Xia Chao, Yin title = The role of IgA in COVID-19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 832 sentences = 52 flesch = 51 summary = Secretory IgA plays a crucial role in the immune defense of mucosal surfaces, the first point of entry of SARS-CoV-2. Reported serology tests focus on IgM, IgG and total immunoglobulins although IgA is playing an important role in mucosal immunity. As an immune barrier, secretory IgA can neutralize SARS-CoV-2 before they reach and bind the epithelial cells (Figure1) . Mucosal vaccine targeting SARS-CoV-2 RBD given via oral or nasal targets to induce secretion of IgA within the mucosa may be a therapeutic strategy for preventing COVID-19 development. Plasma cells, which can be the target of mucosal vaccine, produce IgA and secreted into the mucus where they meet and neutralize the invaded virus through binding to the Spike protein on the surface of SARS-Cov-2. Other neutralization antibodies can also bind to SARS-Cov-2 to prevent it from infecting other cells. cache = ./cache/cord-355306-fj8utkfe.txt txt = ./txt/cord-355306-fj8utkfe.txt === reduce.pl bib === id = cord-355422-c4odhdql author = Vaira, Luigi Angelo title = Potential pathogenesis of ageusia and anosmia in COVID‐19 patients date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1008 sentences = 67 flesch = 49 summary = From the first reports, ageusia and anosmia appear to be frequent clinical features in coronavirus disease 19 (COVID‐19) patients. 3 We report our survey of the literature up to April 14, 2020 , analyzing the possible causes of these chemosensory alterations, which may be useful as a starting point for specific future studies. Moreover, the Middle East Respiratory Syndrome (MERS) coronavirus may bind to the sialic acid receptors 9 , an ability which has also recently been described for SARS-CoV-2 10 . In such a way, SARS-CoV-2 could therefore occupy the binding sites of sialic acid on the taste buds, accelerating the degradation of the gustatory particles. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia cache = ./cache/cord-355422-c4odhdql.txt txt = ./txt/cord-355422-c4odhdql.txt === reduce.pl bib === id = cord-355175-uo9fx6jy author = Ferrazzi, E title = Vaginal delivery in SARS‐CoV‐2‐infected pregnant women in Northern Italy: a retrospective analysis date = 2020-05-28 pages = extension = .txt mime = text/plain words = 3176 sentences = 195 flesch = 51 summary = Data were collected from the clinical records using a standardised questionnaire on maternal general characteristics, any medical or obstetric co‐morbidity, course of pregnancy, clinical signs and symptoms, treatment of COVID 19 infection, mode of delivery, neonatal data and breastfeeding. Conclusions Although postpartum infection cannot be excluded with 100% certainty, these findings suggest that vaginal delivery is associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. Another clinical series of 11 women with COVID 19 infection who had successful deliveries (10 caesarean and 1 vaginal) has been reported: in all the newborns, the 2019-nCoV nucleic acid test was negative. This paper reports the obstetric outcome of a cohort of COVID-19-affected pregnant women and the rate of SARS-CoV-2 positivity in newborns according to mode of delivery and breastfeeding status. Although postpartum infection cannot be excluded, our study also suggests that vaginal delivery may be associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. cache = ./cache/cord-355175-uo9fx6jy.txt txt = ./txt/cord-355175-uo9fx6jy.txt === reduce.pl bib === id = cord-355294-gifsqph6 author = García-Suárez, Julio title = Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study date = 2020-10-08 pages = extension = .txt mime = text/plain words = 4736 sentences = 300 flesch = 46 summary = title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study METHODS: In this population-based registry study, we collected de-identified data on clinical characteristics, treatment and outcomes in adult patients with hematologic malignancies and confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection within the Madrid region of Spain. This case series included consecutive patients with hematologic malignancies aged ≥ 18 years who received a confirmed diagnosis of COVID-19 in the emergency departments, hospital wards (patients infected while hospitalized) or outpatient clinics of these Madrid hospitals up to May 25, 2020. Potential prognostic factors were collected including pre-infection patient characteristics (age, sex, comorbidities, type of hematologic malignancy and therapy), COVID-19 clinical severity, treatments and care setting. Clinical severity of COVID-19 was worse, and mortality rates were higher among older patients and those with a greater number of comorbidities and varied by type of hematologic malignancy and active antineoplastic treatment. cache = ./cache/cord-355294-gifsqph6.txt txt = ./txt/cord-355294-gifsqph6.txt === reduce.pl bib === id = cord-355528-y4a1g6km author = Balla, Mamtha title = COVID-19, Modern Pandemic: A Systematic Review From Front-Line Health Care Providers’ Perspective date = 2020-03-30 pages = extension = .txt mime = text/plain words = 7504 sentences = 398 flesch = 53 summary = The main aim of this systematic review is to provide a comprehensive clinical summary of all the available data from high-quality research articles relevant to the epidemiology, demographics, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic methods and treatment methods of COVID-19, thus increasing awareness in health care providers. Coronavirus disease 2019 (COVID19) infection, which is a global pandemic declared on March 11, 2020, by World Health Organization (WHO), was reported to have infected 168,000 cases worldwide in about 148 countries and territories and killed more than 6,610 people around the world as of March 16, 2020 [1]. According to the study by Xu et al, 60% of people diagnosed with COVID-19 had traveled to Wuhan or nearby regions (60%), 36% had close contact with novel coronavirus pneumonia (NCP) patients and 4% had no definite exposure [12] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-355528-y4a1g6km.txt txt = ./txt/cord-355528-y4a1g6km.txt === reduce.pl bib === id = cord-355122-x3v80bdp author = Desterke, Christophe title = PPARγ cistrome repression during activation of lung monocyte-macrophages in severe COVID-19 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 7873 sentences = 368 flesch = 43 summary = Overall, these results demonstrate for the first time, the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte / macrophage-mediated inflammatory storm. A differentially expressed gene (DEG) analysis was performed on lung biopsies from COVID-19 patients and healthy donors; this revealed widespread repression of many gene pathways in COVID-19 lungs (Supplemental Figures 4A-4B) , which could affect major functionalities of the cells in this organ. Specifically, the gene-set enrichment analysis (performed using the 'hallmarks' gene set of the MsigDB database) highlighted repression of the mitosis spindle and p53 pathway (cell cycle gatekeeper) in samples of COVID-19 lungs compared to those of healthy donors (NES = -3.45 and -2.77, respectively, with p-value<0.001, Supplemental Figure 5A ). Mononuclear cells, monocytes, and macrophages were found in positions similar to the COVID-19 lung samples, suggesting major infiltrations in this tissue (Supplemental Figure 4E ) and confirming the results of the 'xcell' immune score analysis (Supplemental Figure 4C ). cache = ./cache/cord-355122-x3v80bdp.txt txt = ./txt/cord-355122-x3v80bdp.txt === reduce.pl bib === id = cord-355356-g7lvb8b4 author = Lamb, Yvette N. title = Remdesivir: First Approval date = 2020-09-01 pages = extension = .txt mime = text/plain words = 5025 sentences = 235 flesch = 44 summary = Having demonstrated potent antiviral activity against coronaviruses in preclinical studies, remdesivir emerged as a candidate drug for the treatment of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, during the current global pandemic. Based on preliminary results from the randomized, double-blind, placebo-controlled, multinational phase III ACTT-1 trial (NCT04280705) in patients with COVID-19, remdesivir significantly reduced time to recovery relative to placebo (median 11 days vs 15 days; rate ratio for recovery 1.32; 95% CI 1.12-1.55; p < 0.001) [primary endpoint] [41] . Among pregnant women (n = 67) and postpartum women (n = 19) who received compassionate use remdesivir for severe COVID-19, rates of clinical improvement were 96% and 89%, respectively, at day 28 [45] . In paediatric patients (aged 0-17 years) with severe COVID-19 treated with compassionate use remdesivir (n = 77), the clinical improvement rate was 88% at day 28 [46] . cache = ./cache/cord-355356-g7lvb8b4.txt txt = ./txt/cord-355356-g7lvb8b4.txt === reduce.pl bib === id = cord-355475-kdubhh73 author = Patton, Lauren L. title = Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date = 2020-11-05 pages = extension = .txt mime = text/plain words = 2161 sentences = 104 flesch = 45 summary = An early survey in May and June 2020 of practicing dentists in private practice and public health settings in the United States (U.S.), a short 2 months after the first COVID-19 wave and national shortages of personal protective equipment caused offices to move to emergency only dental care, showed that 99.7% of offices had implemented enhanced infection control procedures. While hope for a COVID-19 vaccine to quell transmission is widespread, we must not lose sight of the fact that diverse vaccine development technologies and novel drug discovery efforts made today will benefit our response to the next pandemic. 14 When the diversity of oral mucosal and salivary gland disorders were observed in HIV/AIDS patients, international collaborative groups such as the European Community We learned from HIV disease management that the antiretroviral drugs can have acute and long-term toxicities including ulcers, xerostomia/parotid lipomatosis, taste disturbances, perioral paresthesia, erythema multiforme and facial fat wasting. cache = ./cache/cord-355475-kdubhh73.txt txt = ./txt/cord-355475-kdubhh73.txt === reduce.pl bib === id = cord-355439-eqtk51q3 author = Lesko, Catherine R title = HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3288 sentences = 154 flesch = 46 summary = Surveillance data, such as those available from South Africa or Wuhan, will provide the most complete picture of COVID-19 risk among PLWH (e.g., by not restricting to PLWH who are in care and who are more likely to have wellcontrolled HIV disease); however clinical data, such as those from Madrid, may provide the most depth (e.g., by allowing examination of the role of comorbidities, medications, and COVID-19 treatments) as long as potential selection bias is considered. Despite some good telehealth outcomes for some PLWH, telehealth has the potential to exacerbate disparities in care for people with lower socio-economic status: lack of necessary technology and services, technology literacy, and safe, confidential surroundings to participate fully in telehealth may be barriers to engagement in care (32 distancing restrictions if they need to go outside their homes to access alcohol or other drugs, or critically, medication assisted treatments (such as methadone or buprenorphine). cache = ./cache/cord-355439-eqtk51q3.txt txt = ./txt/cord-355439-eqtk51q3.txt === reduce.pl bib === id = cord-355567-60sfv60p author = Azuma, Kenichi title = Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control date = 2020-11-03 pages = extension = .txt mime = text/plain words = 9229 sentences = 436 flesch = 42 summary = Recently, 36 researchers insisted on the potential risk of indoor airborne transmission of SARS-CoV-2 and the importance of sufficient and effective ventilation, particle filtration, and air sterilization as infection control measures inside buildings [43] . Therefore, the MHLW published a document titled "Prevention of the COVID-19 Clusters" Abbreviation: SARS-CoV severe acute respiratory syndrome coronavirus Fig. 1 Traditional Japanese office building HVAC systems: a a centralized HVAC system; and b a centralized ventilation system with an individual air-conditioning system on March 1, 2020 [94] , showing the need for adequate ventilation in buildings because a ventilation standard for infection control has not been established in general buildings in Japan and the characteristics of indoor spaces where the clusters occurred might include poor ventilation and crowding. cache = ./cache/cord-355567-60sfv60p.txt txt = ./txt/cord-355567-60sfv60p.txt === reduce.pl bib === id = cord-355318-qm79gz8w author = Smit, Albertus J. title = Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 15419 sentences = 706 flesch = 41 summary = Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Thus, if climate factors do play a role in COVID-19 infection rates, the concurrence of transition of southern hemisphere countries to their winter season with the mid-stages of the disease transmission trajectory is of concern, especially with respect to containment policy and health system resource allocation. Environmental variables considered in preprint and peer-reviewed publications as modulators of SARS-CoV-2 transmission rates include mean, minimum and/or maximum daily temperature, and diurnal temperature range; an undefined 'humidity' variable, relative humidity, specific humidity and absolute humidity; dew point temperature; rainfall; wind speed or wind power; air pressure; some metric of solar or UV radiation; and 'air quality' (Supplementary Tables S1 and S2 ). The general prevalence of climatologically-coupled seasonal signals and environmental variable modulation seen in the majority of other viral respiratory diseases creates the expectation for a similar effect on SARS-CoV-2 and in COVID-19 epidemiology. cache = ./cache/cord-355318-qm79gz8w.txt txt = ./txt/cord-355318-qm79gz8w.txt === reduce.pl bib === id = cord-355560-vsxe97xs author = Alves, Amanda Mandarino title = SARS-CoV-2 leading to Acute Pancreatitis: an unusual presentation date = 2020-09-15 pages = extension = .txt mime = text/plain words = 1659 sentences = 98 flesch = 43 summary = During SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) pandemic, the etiologic agent of COVID-19, several studies described the involvement of other tissues besides the respiratory tract, such as the gastrointestinal tract. Diagnosing acute pancreatitis secondary to SARS-CoV-2 infection is challenging due to the need to rule out other etiologies as well the notable heterogeneous presentations. The mechanisms of pancreatic injury in SARS-CoV-2 infection include direct cytopathic effects or indirect systemic inflammatory and immune-mediated cellular responses, resulting in organ damage or secondary enzyme abnormalities [1] . This case report describes a patient with COVID-19 that developed severe acute pancreatitis. ACE2 receptor is highly expressed in pancreatic islet cells [16] , therefore SARS-CoV-2 infection can theoretically cause islet damage resulting in acute diabetes [7] . ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection cache = ./cache/cord-355560-vsxe97xs.txt txt = ./txt/cord-355560-vsxe97xs.txt === reduce.pl bib === id = cord-355718-7dafsxp9 author = Leong, Hoe‐Nam title = Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 date = 2004-08-10 pages = extension = .txt mime = text/plain words = 2714 sentences = 172 flesch = 60 summary = title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 We performed a retrospective cohort study assessing the effectiveness of ribavirin use in our patients with SARS. We compared the results of clinical and laboratory investigations at the start of ribavirin treatment with correspondent parameters of patients who did not receive ribavirin on day 6 of illness. * Parameters taken on start of treatment for those on ribavirin, and day 6 for the control group. Most patients received this combination therapy but no comparative efficacy data from treatment and control groups were available. After correcting for steroid use, the hazard ratio of death for patients treated with ribavirin was 1.03 (95% CI: 0.44-2.41, P ¼ 0.939). Our study was a retrospective analysis with two groups of patients being treated at different times of the epidemic. cache = ./cache/cord-355718-7dafsxp9.txt txt = ./txt/cord-355718-7dafsxp9.txt === reduce.pl bib === id = cord-355728-wivk0bm0 author = Schoof, Michael title = An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3613 sentences = 377 flesch = 68 summary = Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Class I nanobodies emerged with highly 144 variable activity in this assay with Nb6 and Nb11 as two of the most potent clones with IC50 145 values of 370 and 540 nM, respectively (Table 1) To define the binding sites of Nb6 and Nb11, we determined their cryogenic electron 156 microscopy (cryo-EM) structures bound to Spike* ( Fig. 2A state RBDs only contacts a single RBD (Fig. 2D) . 277 278 mNb6-tri displays further gains in potency in both pseudovirus and live SARS-CoV-2 infection 279 assays with IC50 values of 120 pM (5.0 ng/mL) and 54 pM (2.3 ng/mL), respectively (Fig. 4H-I, 280 Table 1). cache = ./cache/cord-355728-wivk0bm0.txt txt = ./txt/cord-355728-wivk0bm0.txt === reduce.pl bib === id = cord-355514-2qjbc3bd author = Shibata, Shun title = High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection date = 2020-07-25 pages = extension = .txt mime = text/plain words = 2044 sentences = 117 flesch = 48 summary = title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 1 High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 2 Because of high incidence of false positive RIAT results, cross antigenicity between human common cold coronaviruses and SARS-CoV-2 can be considered. We experienced a patient suffering human coronavirus HKU1 pneumonia who showed false-positive results for IgG against SARS-CoV-2 using an RIAT. We performed RIAT using a commercially available kit for IgM and IgG against SARS-CoV-2 in serum samples of 24 patients with laboratory-confirmed COVID-19 (admitted from February to April 2020), 7 patients with human common cold coronavirus pneumonia (Table 1) and IgM with median 12 days from illness onset was compatible with previous reports [3, 4] . cache = ./cache/cord-355514-2qjbc3bd.txt txt = ./txt/cord-355514-2qjbc3bd.txt === reduce.pl bib === id = cord-355655-l684uy4h author = Ning, Ling title = Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1426 sentences = 99 flesch = 49 summary = title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report This case states the importance of close monitoring of the concentration of cyclosporine in patients treated with lopinavir/ritonavir; the routine treatment of corticosteroid can be continued. Further data are needed to achieve better understanding of the impact of immunosuppressive therapy on the clinical presentation, severity, and outcome of SARS‐CoV‐2 infections in solid organ transplant recipients. Laboratory results on day 6 of hospitalization showed improved creatinine level and hyponatremia; again, the sputum and oropharyngeal swab specimens tested negative on RT-PCR for SARS-CoV-2. Methylprednisolone was routinely used as baseline immunosuppression in this case, although its use for the treatment of SARS-CoV-2 infection remains controversial. 15 No clinical data exist to indicate that net benefit is derived from corticosteroids in the treatment of respiratory infection due to coronavirus included SARS-CoV and MERS-CoV. Novel coronavirus (SARS-CoV-2) infection in a renal transplant recipient: Case report cache = ./cache/cord-355655-l684uy4h.txt txt = ./txt/cord-355655-l684uy4h.txt === reduce.pl bib === id = cord-355577-w1yhtbz8 author = Kowalski, Luiz Paulo title = Effect of the COVID-19 Pandemic on the Activity of Physicians Working in the Areas of Head and Neck Surgery and Otorhinolaryngology date = 2020-05-22 pages = extension = .txt mime = text/plain words = 4750 sentences = 253 flesch = 50 summary = Conclusion The study demonstrated a direct impact of the COVID-19 pandemic on the clinical practice of specialties related to the treatment of patients with diseases of the head and neck region already in the beginning of the illness management in Brazil. Specifically, we collected data regarding the impact of de COVID-19 pandemic on: 1) the amount and type of outpatient appointments, surgeries and exams with the risk of generating aerosols; 2) availability of adequate PPE in different settings and practices; 3) the preparedness of the responder's health institution in orienting their HCPs and developing strategies to manage COVID-19 suspected and confirmed patients. Although the pandemic is already in its 7 th week in Brazil, since the identification of the 1 st case, 45.3% and 48.8% of physicians in the private and public sectors, respectively, reported that they had not received face-to-face or distance training in the management of confirmed or suspected patients with COVID-19. cache = ./cache/cord-355577-w1yhtbz8.txt txt = ./txt/cord-355577-w1yhtbz8.txt === reduce.pl bib === id = cord-355589-3zdv9zim author = Simons, David title = The association of smoking status with SARS‐CoV‐2 infection, hospitalisation and mortality from COVID‐19: A living rapid evidence review with Bayesian meta‐analyses (version 7) date = 2020-10-02 pages = extension = .txt mime = text/plain words = 5236 sentences = 322 flesch = 46 summary = However, early data from the COVID-19 pandemic have not provided clear evidence for a negative impact of current or former smoking on SARS-CoV-2 infection or COVID-19 disease outcomes, such as hospitalisation or mortality 11 . We aimed to produce a rapid synthesis of available evidence pertaining to the rates of infection, hospitalisation, disease severity and mortality from SARS-CoV-2/COVID-19 stratified by smoking status. Sixty studies reported disease severity in hospitalised patients stratified by smoking status (see Table 4 ). Current smokers were at reduced risk of testing positive for SARS-CoV-2 and former smokers were at increased risk of hospitalisation, disease severity and mortality compared with never smokers. Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: a Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study cache = ./cache/cord-355589-3zdv9zim.txt txt = ./txt/cord-355589-3zdv9zim.txt === reduce.pl bib === id = cord-355674-mhi85px5 author = Siddiqi, Hasan K. title = Increased prevalence of myocardial injury in patients with SARS-CoV-2 viremia. date = 2020-11-10 pages = extension = .txt mime = text/plain words = 1731 sentences = 134 flesch = 48 summary = The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. Conclusions: Hospitalized COVID-19 patients with SARS-CoV-2 viremia have a significantly higher prevalence of detectable troponin and myocardial injury during their hospitalization, compared to non-viremic patients. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. cache = ./cache/cord-355674-mhi85px5.txt txt = ./txt/cord-355674-mhi85px5.txt === reduce.pl bib === id = cord-355395-rckzi8vz author = Tian, Dandan title = Hepatic complications of COVID‐19 and its treatment date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2896 sentences = 137 flesch = 40 summary = SARS‐CoV‐2 can cause liver injury through systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia‐reperfusion injury, side effects of treatment drugs, and underlying liver disease and can attack liver cells directly via ACE2. Considering limited number of autopsy cases in patients with COVID-19 studied and the relatively low expression of ACE2 in liver, liver damage directly caused by SARS-CoV-2 infection of hepatocytes deserves further investigation. It was speculated that in addition to the virus itself causing liver injury, immune injury, systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia and hypoxia reperfusion injury, and drug-induced injury may be the main mechanisms that cause secondary liver injury in patients with COVID-19 [11] [12] 14, 27 . Patients with COVID-19 have varying degrees of hypoxemia, with more than 40% requiring oxygen therapy 5 Drug hepatotoxicity( Figure 2) In China, the incidence of drug-induced liver injury is second only to viral hepatitis and fatty liver disease (including alcoholic and non-alcoholic). cache = ./cache/cord-355395-rckzi8vz.txt txt = ./txt/cord-355395-rckzi8vz.txt === reduce.pl bib === id = cord-355734-pz64534w author = Antonio-Villa, Neftali Eduardo title = Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3261 sentences = 215 flesch = 49 summary = Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. cache = ./cache/cord-355734-pz64534w.txt txt = ./txt/cord-355734-pz64534w.txt === reduce.pl bib === id = cord-355672-egjdy7o0 author = Castillo, Edward M. title = Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1106 sentences = 67 flesch = 49 summary = Initial testing protocols from the US Centers for Disease Control and Prevention (CDC) for COVID-19 for detection in patients with possible infection recommend that samples also should be first sent for influenza viruses along with respiratory panels for detection of parainfluenza virus, adenovirus, human rhinovirus, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae. 1 The problem with testing for coinfections in suspected patients is that the presence of a positive upper respiratory pathogen nucleic acid detection (RPNA) test for viruses other than SARS-CoV-2 may suggest to the clinicians alternate explanations for the patients' symptoms. This study is a retrospective analysis of data from an academic medical center with 2 hospitals and 2 urgent care centers in San Diego, California, during the initial 2 weeks of SARS-CoV-2 testing, March 10, 2020 Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID-19) cache = ./cache/cord-355672-egjdy7o0.txt txt = ./txt/cord-355672-egjdy7o0.txt === reduce.pl bib === id = cord-355758-tk7eturq author = Berrio, Alejandro title = Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2175 sentences = 156 flesch = 49 summary = Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. cache = ./cache/cord-355758-tk7eturq.txt txt = ./txt/cord-355758-tk7eturq.txt === reduce.pl bib === id = cord-355811-aq7p1uxo author = Węglarz-Tomczak, Ewelina title = Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2008 sentences = 151 flesch = 57 summary = A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). In recent studies, peptide analogues [11] and ebselen [12] have been identified as highly active inhibitors for PL pro . We show that some of them indeed possess higher activity than ebselen, that has been recently reported as PL pro CoV2 inhibitor [12] , and, thus, could be considered as novel potential drugs against COVID-19. In this work, we used the ebselen derivatives/analogues library and performed a comprehensive inhibition study of PL pro CoV2. In the case of PL pro SARS, none of the presented ebselen derivatives was able to block the enzyme. Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design Ebselen as a highly active inhibitor of PL pro CoV2 cache = ./cache/cord-355811-aq7p1uxo.txt txt = ./txt/cord-355811-aq7p1uxo.txt === reduce.pl bib === id = cord-355807-q3bngari author = Yepes-Pérez, Andres F. title = Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling date = 2020-10-29 pages = extension = .txt mime = text/plain words = 8807 sentences = 453 flesch = 48 summary = Molecular modeling was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (cat's claw) focusing on the binding interface of the RBD–ACE-2 and the viral spike protein. tomentosa against focusing both on the binding interface of the RBD-ACE-2 and inside SARS-CoV-2 RBD spike protein, (2) simulations of ligand pathway of the best predicted compounds from step 1 to evaluate convenient entrance mechanism of the compounds to the binding site, (3) MD simulation to assess the stability of the best protein-ligand complexes from 1, (4) calculation of pharmacokinetics parameters for the most qualified compounds resulting from the previous parts of the docking protocol. Next, we used the cryo-EM structure of SARS-CoV-2 spike protein (PDB code: 6VYB) in their open state (Lipinski et al., 2012) to explore the potential inhibition of components of the cat's claw, selecting ACE-2-binding pocket to this study. cache = ./cache/cord-355807-q3bngari.txt txt = ./txt/cord-355807-q3bngari.txt === reduce.pl bib === id = cord-355788-6hteott0 author = Shirvani, Edris title = Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2 date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4090 sentences = 220 flesch = 50 summary = In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Currently, a number of DNA and RNA virus vector platforms are under evaluation for a SARS-CoV-2 vaccine, including attenuated vaccinia virus, replication-defective adenovirus, vesicular stomatitis virus, human parainfluenza viruses, and alphavirus replicons. Keeping these limitations in mind, we think Newcastle disease virus (NDV), as avian virus, has a number of characteristics that make it suitable for use as a vaccine vector for SARS-CoV-2. The effectiveness of NDV-vectored vaccines has already been evaluated against SARS-CoV in monkeys [8] , against MERS-CoV in camels [9] , and against avian infectious bronchitis virus (IBV) in chickens, a natural host challenge model [10] . Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus cache = ./cache/cord-355788-6hteott0.txt txt = ./txt/cord-355788-6hteott0.txt === reduce.pl bib === id = cord-355841-m6dl8a0w author = Munz, Maike title = Acute transverse myelitis after COVID-19 pneumonia date = 2020-05-26 pages = extension = .txt mime = text/plain words = 858 sentences = 72 flesch = 47 summary = A repeated throat swab showed a negative SARS-CoV2 PCR. Magnetic resonance imaging (MRI) of the spine revealed T2 signal hyperintensity of the thoracic spinal cord at Th9 level suggestive of acute transverse myelitis rather than multiple sclerosis [3] (Fig. 1a) . SARS-CoV2-PCR in the CSF and oligoclonal bands were negative. Follow-up MRI on day 6 further showed a patchy hyperintensity of the thoracic myelon at Th9-10 and at Th3-5 level (Fig. 1d) , suggestive of transverse myelitis. Follow-up CSF on day 12 showed normalization of cell count (3/µl) and regressing protein levels (734 mg/l), no Maike Munz and Swen Weßendorf authors contributed equally. Cases of Guillain-Barré Syndrome in association with severe COVID-19 infections were reported [6] . In a series of 58 severely affected COVID-19 patients, 67% showed clinical corticospinal tract signs but received no spinal MRI [7] . Preprint) Acute myelitis after SARS-CoV-2 infection: A case report https cache = ./cache/cord-355841-m6dl8a0w.txt txt = ./txt/cord-355841-m6dl8a0w.txt === reduce.pl bib === id = cord-355760-2a12nsnl author = Shields, A. M. title = SARS-CoV-2 seroconversion in health care workers date = 2020-05-19 pages = extension = .txt mime = text/plain words = 3159 sentences = 178 flesch = 44 summary = Conclusions In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. Evidence before the study To date, no study has examined the cross-sectional seroprevalence of anti-SARS-CoV-2 antibodies in health care workers during the COVID-19 pandemic. We conducted a cross-sectional study of 554 staff at UHBFT to determine the incidence of infection and seroconversion in health care workers and their relationship to prior symptoms of COVID-19. In light of further evidence of asymptomatic infection and seroconversion, the impact of mandatory screening of health care workers should be thoroughly investigated [12] The seroprevalence of SARS-CoV-2 antibodies amongst the UK general population remains unknown and few studies have considered seroprevalence in other populations. In conclusion, we provide evidence of SARS-CoV-2 seroconversion in health care workers with and without prior symptomatic illness. cache = ./cache/cord-355760-2a12nsnl.txt txt = ./txt/cord-355760-2a12nsnl.txt === reduce.pl bib === id = cord-355935-psnqrdo2 author = Paez, Antonio title = A Spatio‐Temporal Analysis of the Environmental Correlates of COVID‐19 Incidence in Spain date = 2020-06-08 pages = extension = .txt mime = text/plain words = 8984 sentences = 487 flesch = 54 summary = Use of spatial Seemingly Unrelated Regressions (SUR) allows us to model the incidence of reported cases of the disease per 100,000 population as an interregional contagion process, in addition to a function of temperature, humidity, and sunshine. We adopt a population health approach, and report results from a spatio-temporal model of the incidence of COVID-19 in the coterminous provinces in Spain, one of the countries hardest hit by the pandemic. Higher incidence is associated with higher GDP per capita and presence of mass transit systems in the province; in contrast, population density and percentage of older adults display negative associations with incidence of COVID-19. The coefficients of the spatially lagged variable are estimated for each time period ρ t and identify the intensity and the sign of the contagion effect. Fig. 3 includes three maps that display the spatial variation of our control variables, namely GDP per capita, percentage of older adults in province, population density, and presence of mass transit systems. cache = ./cache/cord-355935-psnqrdo2.txt txt = ./txt/cord-355935-psnqrdo2.txt === reduce.pl bib === id = cord-355854-hksq8gy4 author = Pagliaro, Pasquale title = ACE/ACE2 Ratio: A Key Also in 2019 Coronavirus Disease (Covid-19)? date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3027 sentences = 171 flesch = 46 summary = Therefore, we wonder whether the invasion by SARS-CoV-2 and the downregulation of ACE2 are jointly responsible for a high incidence of dramatic acute respiratory distress syndrome (ARDS), cardiovascular complications, and high lethality of Covid-19. Moreover, estrogen shifts the system toward the ACE2/Ang 1-7 formation and ACE2 activity is higher in female than that in the male serum (18) ; however, the worst and most lethal Covid-19 infections occur predominantly in males [the Italian ISS (https://www.epicentro.iss.it/coronavirus/ sars-cov-2-decessi-italia, accessed on April 26th 2020) reports that among 23,188 SARS-CoV-2 patients dying in Italy, women are 8,500 (36.7%)]. It has also been suggested that the increased concentration of ACE2 receptors in in the lungs of children may have a protective effect on severe clinical manifestations due to SARS-CoV-2 invasion (36) . ACE/ACE2 ratio is increased in many pathologies (especially dis-metabolisms and cardiovascular diseases) and conditions (obesity and aging) that exacerbate Covid-19 symptomatology and worsen outcomes. cache = ./cache/cord-355854-hksq8gy4.txt txt = ./txt/cord-355854-hksq8gy4.txt === reduce.pl bib === id = cord-356021-lr3wj8we author = Choudhury, Chinmayee title = Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6858 sentences = 346 flesch = 53 summary = With the arrival of the very first structure (6LU7) of this protein in PDB (Jin et al., 2020) , several groups have come up with interesting strategies such as artificial intelligence based de novo design (Bung et al., 2020) , repurposing existing drugs that can bind this protein or virtually screening large chemical databases to identify peptide like small molecules (Pant et al., 2020) , natural products such as Moroccan medicinal plants products (Aanouz et al., 2020) , against this protein (Islam et al., 2020; Sarma et al., 2020) , identification of Andrographolide as a potential inhibitor of SARS-CoV-2 main protease through in silico screening (Enmozhi et al., 2020) using molecular docking, molecular dynamics simulations and PCA based quantitative structureactivity relationship (QSAR) for pattern recognition of the best ligands (Islam et al., 2020) , to mention a few. cache = ./cache/cord-356021-lr3wj8we.txt txt = ./txt/cord-356021-lr3wj8we.txt === reduce.pl bib === id = cord-355924-8sk9al0n author = Allam, Loubna title = Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4753 sentences = 288 flesch = 52 summary = Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. For this purpose, a targeted analysis of the expression of candidate genes involved in SARS-CoV-2 infection confirmed the presence of the GRP78 protein in vitro in epithelial cells of the human respiratory tract and lung tissue. In this direction, our study focused on the repositioning of approved drugs as well as the investigation of other bioactive compounds that may prevent the penetration of SARS-CoV-2 into host cells by targeting the region of GRP78 that is required for the interaction with the Spike protein of the virus. Inhibition of the interaction between the spike protein SARS-CoV-2 and the receptor by blocking the GRP78 is a strategy interesting to identify drugs that decrease the rate of viral infection. cache = ./cache/cord-355924-8sk9al0n.txt txt = ./txt/cord-355924-8sk9al0n.txt === reduce.pl bib === id = cord-356005-zhwtlik6 author = Yazhini, Arangasamy title = D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date = 2020-11-02 pages = extension = .txt mime = text/plain words = 2626 sentences = 142 flesch = 47 summary = Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in 'closed' and 'partially open' conformations. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant. To study the effect of D614G variation on the thermodynamic stability of the spike protein trimer, we calculated free energy changes upon aspartate to glycine substitution using buildmodel function in FoldX (Schymkowitz et al., 2005) . The table contains details of frustration index of inter-residue contacts present at 614th position of spike protein trimer in closed and partially open conformations. cache = ./cache/cord-356005-zhwtlik6.txt txt = ./txt/cord-356005-zhwtlik6.txt === reduce.pl bib === id = cord-355899-wd00f8cw author = Dawson, E. D. title = Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses date = 2020-09-04 pages = extension = .txt mime = text/plain words = 5841 sentences = 294 flesch = 48 summary = This study reports on the VaxArray CoV SeroAssay linear dynamic range, limit of detection, specificity, reproducibility, accuracy, and investigates assay performance on a retrospective set of 263 blinded, de-identified human serum and plasma specimens to demonstrate positive and negative percent agreement to a mixed reference method of RT-PCR on a patient-matched specimen and collection date prior to the COVID-19 outbreak. A total of 132 serum samples known to be negative for the presence of antibodies to SARS-CoV-2 based on date of collection prior to December 2019, including 33 specimens from pediatric donors age 2-16, were analyzed via the standard VaxArray CoV SeroAssay procedure at a 1:100 dilution in PBB. To assess reproducibility and accuracy, a pooled human serum sample positive for antibodies to SARS-CoV-2, and also known to be reactive to the SARS antigen and the 4 endemic Table 3 shows the % CV in the back-calculated concentration value obtained on each relevant capture antigen for all 216 replicate measurements over all 3 days and all three lots of slides, with values ranging from 7 to 19 %CV for the 9 antigens. cache = ./cache/cord-355899-wd00f8cw.txt txt = ./txt/cord-355899-wd00f8cw.txt === reduce.pl bib === id = cord-355943-bezpprrk author = Li, Y. title = Urine Proteome of COVID-19 Patients date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4439 sentences = 278 flesch = 50 summary = In this study, we performed proteomic profiling of urine samples from 32 healthy control individuals and 6 COVID-19 positive patients (3 mild and 3 severe). We found that urine proteome samples from the mild and severe COVID-19 patients with comorbidities can be clearly differentiated from healthy proteome samples based on the clustering analysis. We identified and quantified 1380 and 1641 proteins in urine samples from COVID-19 and two recovery person in total, which was significantly lower than that of healthy controls ( Figure 2B and 2C , Tables S2 and S3 ). The molecular features used to distinguish the patient type (M and S) in our classifier ( Figure 5B and 5D, Tables S4-5) contain several potential biomarkers which were highly associated with the clinical characteristics of mild and severe COVID-19. . https://doi.org/10.1101/2020.05.02.20088666 doi: medRxiv preprint dysregulated proteins in the COVID-19 patients. cache = ./cache/cord-355943-bezpprrk.txt txt = ./txt/cord-355943-bezpprrk.txt === reduce.pl bib === id = cord-356030-bbj4r81i author = Haehner, Antje title = Predictive Value of Sudden Olfactory Loss in the Diagnosis of COVID-19 date = 2020-06-11 pages = extension = .txt mime = text/plain words = 2041 sentences = 105 flesch = 53 summary = The aim of this study was to investigate the frequency of olfactory loss in an outpatient population who presented to a coronavirus testing center during a 2-week period and to evaluate the diagnostic value of the symptom "sudden smell loss" for screening procedures. METHODS: In this cross-sectional controlled cohort study, 500 patients who presented with symptoms of a common cold to a corona testing center and fulfilled corona testing criteria completed a standardized diagnostic questionnaire which included the patients' main symptoms, time course, and an additional self-assessment of the patients' current smell, taste function, and nasal breathing compared to the level before the onset of symptoms. CONCLUSION: Considering the high frequency of smell loss in non-hospitalized COVID-19 patients, acute olfactory impairment should be recognized as an early symptom of the disease and should be tested for on a regular basis. cache = ./cache/cord-356030-bbj4r81i.txt txt = ./txt/cord-356030-bbj4r81i.txt === reduce.pl bib === id = cord-356084-621qzpqd author = Qu, Jiuxin title = Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1578 sentences = 98 flesch = 61 summary = title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus cache = ./cache/cord-356084-621qzpqd.txt txt = ./txt/cord-356084-621qzpqd.txt === reduce.pl bib === id = cord-356009-emn2w8if author = Roshandel, M. R. title = What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date = 2020-10-13 pages = extension = .txt mime = text/plain words = 4687 sentences = 292 flesch = 49 summary = Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. The searches included medical subject headings (MeSH) and keywords for SARS-CoV-2, COVID, Corona, together with shedding, persistence, urine, urinary, specimen, viral load, or RNA body fluids. We completed the data abstraction process using created forms to record study characteristics, clinical data, and laboratory data including study year and design, country of study origin, total initial population size, test type for disease diagnosis, test type for samples (urine/stool/rectal swab/blood), patients age (including mean and range), number of positive and total patients and/or (wherever applicable) number of positive and total specimens collected for each test category, disease severity, ICU admission, and fatality rate. cache = ./cache/cord-356009-emn2w8if.txt txt = ./txt/cord-356009-emn2w8if.txt === reduce.pl bib === id = cord-356154-ifb3qiz7 author = Zhang, Rong title = A Study of Two Cases Co-Infected with SARS-CoV-2 and Human Immunodeficiency Virus date = 2020-09-07 pages = extension = .txt mime = text/plain words = 1066 sentences = 73 flesch = 56 summary = CT scan results in early February indicated lesions in bilateral lungs (Supplementary Table S1 ), but the result of the SARS-CoV-2 nucleic acid test was negative. However, the patient's condition deteriorated again on February 20, and the nucleic acid test results were single positive for COVID-19 SARS-CoV-2. Notes: ND, no data; ?, positive; -, negative We assumed that HIV infection had damaged their immune systems; this could also explain why the patient tested negative for SARS-CoV-2 antibodies in the late stages of treatment when the disease became worse. In general, the blocking of the IL-6 receptor with tocilizumab has a particular effect on the treatment of COVID-19 patients with severe disease, but it may have little effect on patients with Fig. 1 The clinical courses of two cases co-infected with SARS-CoV-2 and HIV. COVID-19 patients with immunodeficiency disease may cause more severe illness and poor treatment response due to the destruction of the immune system. cache = ./cache/cord-356154-ifb3qiz7.txt txt = ./txt/cord-356154-ifb3qiz7.txt === reduce.pl bib === id = cord-355912-ioihqf0r author = Shomuradova, A. S. title = SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors date = 2020-05-25 pages = extension = .txt mime = text/plain words = 8632 sentences = 494 flesch = 57 summary = Here we assayed both antibody and T-cell reactivity to SARS-CoV-2 antigens in COVID-19 convalescent patients and healthy donors sampled before and during the pandemic. 20.20107813 doi: medRxiv preprint Analysis of the humoral immune response to SARS-CoV-2 demonstrated that the IgG antibodies of the majority of COVID-19 -CPs were specific to one or more viral antigens. To describe the structure and clonality of SARS-CoV-2 directed T-cell immune response we performed analysis of T-cell receptor (TCR) repertoires of FACS-sorted IFNγ-secreting CD8+/CD4+ cells and MHC-tetramer-positive populations as well as the total fraction of PBMC by high throughput sequencing using the Illumina platform. Two patients (p1472 and p1473) had no detectable antibody levels in the serum to any of the tested SARS-CoV-2 antigens and no T-cellular response to any of the peptide pools, albeit they had T-cells reactive to the recombinant S-protein. cache = ./cache/cord-355912-ioihqf0r.txt txt = ./txt/cord-355912-ioihqf0r.txt === reduce.pl bib === id = cord-356174-40k6m7l0 author = Ducloyer, Mathilde title = Complete post-mortem data in a fatal case of COVID-19: clinical, radiological and pathological correlations date = 2020-08-06 pages = extension = .txt mime = text/plain words = 2874 sentences = 176 flesch = 46 summary = A reverse-transcription polymerase chain reaction test was positive for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using a nasopharyngeal swab sample. Post-mortem virology studies detected the presence of SARS-CoV-2 (B.1 lineage) in the nasopharynx, plasma, lung biopsies, pleural effusion and faeces confirming the persistence of viral ribonucleic acid 48 h after death. This case is one of the first to describe complete post-mortem data for a COVID-19 death and highlights the ability of PMCT to detect severe involvement of the lungs before autopsy in an apparently natural death. The present pathology results are concordant with previously reported findings and reinforce the disease pathogenesis hypothesis of combined viral replication with an inappropriate immune response. Concerning the post-mortem virology data, this case demonstrated that RNA from SARS-CoV-2 was still detectable in blood, faeces, the lungs and the upper airways more than 48 h after death. cache = ./cache/cord-356174-40k6m7l0.txt txt = ./txt/cord-356174-40k6m7l0.txt === reduce.pl bib === id = cord-356090-oj3d9ail author = Gorgun, D. title = Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date = 2020-10-27 pages = extension = .txt mime = text/plain words = 6065 sentences = 277 flesch = 51 summary = Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. In this study, using a large set of simulations, we describe how the SARS-CoV2 FP binds mammalian cellular membranes and characterize, at atomic details, lipid-protein interactions important for the stability of the bound state. cache = ./cache/cord-356090-oj3d9ail.txt txt = ./txt/cord-356090-oj3d9ail.txt === reduce.pl bib === id = cord-356150-ivso91ln author = Torretta, Sara title = Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3497 sentences = 195 flesch = 48 summary = 2 Despite suboptimal detection rates, 3 collection of secretions from the upper airway by means of NPS/OPS still represents the first-line diagnostic modality to test patients and otherwise asymptomatic population for COVID-19, provided that it is early and adequately performed after onset of symptoms. 2 As a fact, reduced detection rates reflect analytical sensitivity of RT-PCR test and the epidemiologic characteristics of COVID-19, given that a false negative RT-PCR result could be possibly obtained both in the initial phase of the disease (ie, a few days before symptom onset) and at the ''tail end'' of SARS-CoV-2 infection (ie, from 20 days after symptom onset) due to a low viral load and a viral shedding below analytical RT-PCR sensitivity threshold. 3 On the basis of the reported detection rates, 4 the US Center for Disease Control and Prevention (US-CDC) has recommended the collection of sole upper respiratory NPS, 2 but the US Food and Drug Administration pointed out that a negative RT-PCR test result does not completely rule out SARS-CoV-2 infection and it shall not be used as a single element for patient management decisions. cache = ./cache/cord-356150-ivso91ln.txt txt = ./txt/cord-356150-ivso91ln.txt === reduce.pl bib === id = cord-356166-fpno9zg5 author = Miyakawa, Kei title = Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles date = 2020-09-15 pages = extension = .txt mime = text/plain words = 1548 sentences = 94 flesch = 52 summary = title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles However, a simple, convenient, rapid, and high-throughput test capable of directly detecting nAbs with high specificity, which could act as an ideal alternative to the neutralization assay, is yet to be developed (Ozcurumez et al., 2020) . In this report, we have developed a HiBiT-VLP-based neutralization test (hiVNT) that can readily detect SARS-CoV-2 nAbs ( Figure 1A ). We noticed a robust increase in NanoLuc activity when the LgBiT-expressing We next tested whether our newly developed hiVLP-SARS2 system could detect nAbs in the serum of COVID-19 patients. In this study, we established the hiVNT, a simple, high-throughput assay system for the quantitative and rapid determination of SARS-CoV-2 nAbs in the sera of individuals after recovery from symptomatic or subclinical COVID-19. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells cache = ./cache/cord-356166-fpno9zg5.txt txt = ./txt/cord-356166-fpno9zg5.txt === reduce.pl bib === id = cord-356370-jjl1hbeb author = Sahajpal, Nikhil Shri title = Role of clinical laboratories in response to the COVID-19 pandemic date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1602 sentences = 77 flesch = 41 summary = In response to the outbreak, several state authorities and commercial companies have developed diagnostic assays to test individuals for the SARS-CoV-2 infection. In the US, clinical laboratories are required to perform 'bridging studies' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. Although, the reverse transcription-polymerase chain reaction (RT-PCR) based assays for the detection of SARS-CoV-2 nucleic acid regions might be the most practical approach at present, qualitative assays are far from providing insights into the evolution of the virus and the varied immune response in different populations. In addition, the RT-PCR based assays provide a unique opportunity to implement pooling sample strategy for wide-scale population screening for SARS-CoV-2. Several studies, including from our laboratory (under review) have demonstrated that pooling sample strategy is a practical and feasible method for screening populations for SARS-CoV-2 [2] . Laboratories should therefore prime for serologic testing by validating assays using RT-PCR confirmed COVID-19 samples. cache = ./cache/cord-356370-jjl1hbeb.txt txt = ./txt/cord-356370-jjl1hbeb.txt === reduce.pl bib === id = cord-356264-q0yqnlyl author = Armijos-Jaramillo, Vinicio title = SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-03-23 pages = extension = .txt mime = text/plain words = 4974 sentences = 253 flesch = 53 summary = With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene, and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. All these experiments were performed again using the S-protein genes of a shorter list of accessions and more distantly related (broad dataset) to SARS-COV-2 (AY304488, AY395003, DQ412043, FJ882957, KY417144, MG772933, MG772934, MN908947, NC_004718) to test the reproducibility of the predicted branches and sites under positive selection. Modeling results suggest that interference with the hot spot 353 could be and effective strategy for inhibiting the recognition of the RBD of the SARS-COV-2 spike protein by its human host receptor ACE2 and hence prevent infections. cache = ./cache/cord-356264-q0yqnlyl.txt txt = ./txt/cord-356264-q0yqnlyl.txt === reduce.pl bib === id = cord-356195-5pcaxpp9 author = Jothimani, Dinesh title = COVID-19 and Liver. date = 2020-06-15 pages = extension = .txt mime = text/plain words = 3969 sentences = 267 flesch = 47 summary = Similar to SARS Co-V, Angiotensin Converting Enzyme2 (ACE2) appears to be the susceptible receptor for COVID-19 and is expressed in more than 80% of alveolar cells in the lungs. Interestingly, the level of ACE2 expression in cholangiocytes was similar to type 2 alveolar cells of the lungs, indicating that the liver could be a potential target for SARS-CoV-2. Summary of recently published studies are in described in Table 2 With the knowledge of current evidence, it is clear that elevated liver enzymes are observed predominantly severe and critical cases of COVID-19 compared to mild infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection cache = ./cache/cord-356195-5pcaxpp9.txt txt = ./txt/cord-356195-5pcaxpp9.txt === reduce.pl bib === id = cord-356217-igm2t7md author = Noda, Sakura title = Severe COVID-19 initially presenting as mesenteric adenopathy date = 2020-10-10 pages = extension = .txt mime = text/plain words = 1597 sentences = 87 flesch = 40 summary = We report a case of COVID-19 in a healthy teenager who initially presented with isolated mesenteric adenopathy, typically a self-limited illness, which progressed to severe illness requiring intensive care before complete recovery. A generally healthy, immunized, non-obese White 17-yearold boy presented to an outside emergency department (ED) with 3 days of initially moderate progressing to severe abdominal pain focused in the right lower quadrant, fever as high as 103°F, and vomiting without diarrhea. Although we did not obtain tissue sampling to prove that the mesenteric adenopathy was secondary to COVID-19, the boy eventually developed chest CT findings and severe hyperinflammatory response consistent with COVID-19, tested positive for SARS-CoV-2 by PCR from sputum, and recovered with primarily supportive care. This case report describes a severe case of COVID-19 in a previously healthy teenage patient who initially presented with gastrointestinal symptoms and isolated acute mesenteric adenopathy on imaging. cache = ./cache/cord-356217-igm2t7md.txt txt = ./txt/cord-356217-igm2t7md.txt === reduce.pl bib === id = cord-356364-ipi81ce3 author = Ho, Bo-Lin title = Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date = 2015-12-14 pages = extension = .txt mime = text/plain words = 5038 sentences = 277 flesch = 62 summary = In the present study, MERS-CoV main protease (M(pro)) is expressed; the dimerization of the protein and its relationship to catalysis are investigated. The colorimetry-based peptide substrate, TSAVLQ-para-nitroanilide (TQ6-pNA) (purity 95-99% by HPLC; GL Biochem Ltd, Shanghai, China), was used to measure the proteolytic activity of MERS-CoV M pro and its mutants throughout the course of the study as described previously [25, 28] . In addition, although the K d values of wild-type SARS-CoV M pro without or with substrates show no significant difference (Table 2) , it was possible to detect substrate-induced dimerization at a protein concentration of 1 μM by AEC [33] . Biochemical and AUC studies indicated that MERS-CoV M pro shows almost the same proteolytic activity as SARS-CoV M pro ; although it is a monomer in aqueous buffer and displays substrate-induced dimerization (Fig 6) . cache = ./cache/cord-356364-ipi81ce3.txt txt = ./txt/cord-356364-ipi81ce3.txt === reduce.pl bib === id = cord-356325-gk5jve0i author = Beaudoin-Bussières, Guillaume title = Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals date = 2020-10-16 pages = extension = .txt mime = text/plain words = 2143 sentences = 120 flesch = 50 summary = Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. Of note, while we observed enhanced infectivity for the D614G variant compared to its WT SARS-CoV-2 S counterpart (see Fig. S2A in the supplemental material), no major differences in neutralization with convalescent plasma were detected at either time point (Fig. S2B) , thus suggesting that the D614G change does not affect the overall conformation of the Spike, in agreement with recent findings (17, 22) . The capacity to neutralize SARS-CoV-2 S WT-or D614G-pseudotyped particles significantly correlated with the presence of RBD-specific IgG, IgM, IgA, and anti-S antibodies (Fig. S3) . Interestingly, we observed a pronounced (20% to 30%) decrease in the proportion of convalescent individuals able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 10 weeks after the onset of symptoms. cache = ./cache/cord-356325-gk5jve0i.txt txt = ./txt/cord-356325-gk5jve0i.txt ===== Reducing email addresses cord-008841-r17qhfsj cord-009153-zxx4m1kz cord-015183-1eytelxn cord-015181-875gf11z cord-009891-gqrhbhbn cord-026111-pb3r74uq cord-035067-ic843wr9 cord-029332-yn603pvb cord-102807-cxtzf5oe cord-103837-iuvigqdx cord-122092-gdyt02er cord-196608-k4f79dr4 cord-196265-mvnkkcow cord-220618-segffkbn cord-252922-cdhnlvxv cord-253502-v2hh3w3r cord-253606-o8a0jhx2 cord-254505-mjj8xrer cord-254957-jqp1gto6 cord-255229-w2xtxo9a cord-256156-mywhe6w9 cord-256872-jekx1czw cord-256808-lxlerb13 cord-257533-i85dyg8n cord-257802-vgizgq2y cord-257487-xanqvdhn cord-259593-shrd1s7r cord-261634-vfe1lawl cord-262020-ygl8xlhk cord-263450-v6vdg8os cord-263739-xoum5e0k 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temporarily unavailable cord-315598-qwh72inx cord-346539-kxnrf5g5 cord-279255-v861kk0i cord-312741-0au4nctt cord-319877-izn315hb cord-329190-kv9n2qj3 number of items: 5,187 sum of words: 19,413,726 average size in words: 3,765 average readability score: 49 nouns: patients; infection; coronavirus; virus; disease; protein; cells; study; cell; cases; syndrome; data; treatment; studies; analysis; risk; transmission; time; results; symptoms; health; receptor; response; case; samples; proteins; pandemic; days; outbreak; viruses; infections; expression; patient; pneumonia; number; care; use; lung; host; system; spike; antibodies; antibody; control; activity; detection; levels; role; vaccine; review verbs: used; showed; including; report; associated; based; binds; increasing; infects; found; suggests; identified; cause; provide; compared; followed; performed; developed; induced; tested; confirmed; reduces; require; detected; observed; considering; indicating; related; make; led; known; described; contain; treated; result; presented; given; demonstrated; inhibits; needed; determine; expressed; occurred; remain; involved; revealing; obtained; emerging; targeted; took adjectives: respiratory; viral; severe; clinical; acute; human; covid-19; high; positive; novel; immune; different; specific; potential; new; higher; available; first; non; anti; inflammatory; negative; antiviral; important; several; infectious; possible; low; significant; early; similar; many; molecular; effective; lower; asymptomatic; large; recent; infected; multiple; current; single; medical; common; therapeutic; like; public; key; structural; present adverbs: also; however; well; therefore; respectively; highly; even; significantly; previously; currently; still; recently; especially; moreover; furthermore; first; rapidly; potentially; less; particularly; directly; now; critically; often; mainly; finally; together; already; relatively; approximately; yet; worldwide; far; clinically; interestingly; prior; additionally; much; later; specifically; rather; likely; subsequently; least; indeed; generally; similarly; hence; usually; widely pronouns: we; it; their; our; its; they; i; them; his; he; us; her; she; itself; you; one; themselves; your; my; him; me; ourselves; mg; nsp10; ha3; himself; ours; mcr-9; oneself; em; yourself; herself; nsp15; myself; covid-19; s; mrnas; nsp7; rad5; 's; mine; ≥100; il-1β; igg1; p3ile; imagej; iga1; https://doi.org/10.1101/2020.08; https://doi.org/10.1101/2020.06.02.20120345; ya proper nouns: SARS; CoV-2; COVID-19; CoV; ACE2; RNA; China; PCR; MERS; Coronavirus; S; Fig; Wuhan; RT; Health; •; T; M; C; Table; RBD; Disease; IFN; CT; March; East; N; S1; II; IL-6; Middle; IgG; sha; TMPRSS2; World; IgM; J; HIV; ARDS; Hong; el; DOI; Kong; Syndrome; ICU; United; April; Figure; A; Organization keywords: sars; covid-19; patient; cov-2; ace2; rna; mers; china; pcr; cell; protein; virus; rbd; coronavirus; health; cov; infection; ifn; disease; wuhan; respiratory; drug; vaccine; il-6; tmprss2; human; hcq; elisa; case; clinical; dna; hiv; hong; kong; child; hla; spike; severe; ppe; icu; ards; 3cl; study; cd8; care; acute; viral; test; preprint; vero one topic; one dimension: sars file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095033/ titles(s): How and who does SARS kill? three topics; one dimension: sars; covid; sars file(s): https://doi.org/10.1007/s10912-014-9282-8, https://api.elsevier.com/content/article/pii/S0006295220302914, https://api.elsevier.com/content/article/pii/S0065352716300471 titles(s): Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu | Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost | The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing five topics; three dimensions: sars covid patients; covid sars patients; sars cov protein; cov sars samples; sars cov en file(s): https://www.ncbi.nlm.nih.gov/pubmed/32837529/, https://www.ncbi.nlm.nih.gov/pubmed/33029758/, https://api.elsevier.com/content/article/pii/S0065352716300471, https://www.ncbi.nlm.nih.gov/pubmed/32690074/, https://doi.org/10.1016/j.gastrohep.2020.05.004 titles(s): Guidance for the Treatment and Management of COVID‐19 Among People with Intellectual Disabilities | Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications | The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing | Efficacy of local budesonide therapy in the management of persistent hyposmia in COVID-19 patients without signs of severity: A structured summary of a study protocol for a randomised controlled trial | Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 Type: cord title: keyword-sars-cord date: 2021-05-25 time: 16:24 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:sars ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-298989-qk0k2lmz author: , Umesh title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target date: 2020-05-13 words: 3226.0 sentences: 179.0 pages: flesch: 52.0 cache: ./cache/cord-298989-qk0k2lmz.txt txt: ./txt/cord-298989-qk0k2lmz.txt summary: title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. SARS-CoV-2 main protease, a potential drug target, crystal structure (PDB-ID: 6Y84) was available and used for docking simulation and identification of potential drug molecule form Indian spices. Details of various kinds of interaction shown between the amino acids near the active site of SARS-CoV-2 main protease along with their respective inhibitor constant (Ki) and biological source and binding energy. Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study abstract: The 2019-novel coronavirus (nCoV) has caused a global health crisis by causing coronavirus disease-19 (COVID-19) pandemic in the human population. The unavailability of specific vaccines and anti-viral drug for nCoV, science demands sincere efforts in the field of drug design and discovery for COVID-19. The novel coronavirus main protease (SARS-CoV-2 Mpro) play a crucial role during the disease propagation, and hence SARS-CoV-2 Mpro represents as a drug target for the drug discovery. Herein, we have applied bioinformatics approach for screening of chemical compounds from Indian spices as potent inhibitors of SARS-CoV-2 main protease (PDBID: 6Y84). The structure files of Indian spices chemical compounds were taken from PubChem database or Zinc database and screened by molecular docking, by using AutoDock-4.2, MGLTools-1.5.6, Raccoon virtual screening tools. Top 04 hits based on their highest binding affinity were analyzed. Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Arjunglucoside-I (-7.88 Kcal/mol) and Rosmanol (-7.99 Kcal/mol) also showed a strong and stable binding affinity with favourable ADME properties. These compounds on MD simulations for 50 ns shows strong hydrogen-bonding interactions with the protein active site and remains stable inside the active site. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. However, further validation and investigation of these inhibitors against SARS-CoV-2 main protease are needed to claim their candidacy for clinical trials. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32362243/ doi: 10.1080/07391102.2020.1763202 id: cord-282449-7mxp3sdy author: A, Amouroux title: Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-05-04 words: 1511.0 sentences: 95.0 pages: flesch: 55.0 cache: ./cache/cord-282449-7mxp3sdy.txt txt: ./txt/cord-282449-7mxp3sdy.txt summary: Abstract COVID-19 can severely affect pregnant women and the issue of vertical transmission of sars-cov-2 has also emerged. Sars-cov-2 could be recovered by real-time (RT) PCR from nasal and throat swabs, sputum and feces of symptomatic patients including neonates but not from vaginal swabs, amniotic fluid, placenta, cord blood, neonatal blood or breast milk. Detection rates of real-time PCR and the interpretation of IgM and IgG antibodies levels in cord and neonatal blood are discussed in relation with the immaturity of the fetal and neonatal immune system. Based upon RT-PCR identification of SARS-CoV-2 virus, early reports from China suggested that intrauterine vertical transmission was unlikely 1 . Total (Ab) and IgG antibodies seem to be acquired over 2 weeks'' in infected individuals from the onset of symptoms and the introduction of SARS-CoV-2 serology is a rapidly evolving field of research and much-needed aid in the management of the pandemic. abstract: Abstract COVID-19 can severely affect pregnant women and the issue of vertical transmission of sars-cov-2 has also emerged. Sars-cov-2 could be recovered by real-time (RT) PCR from nasal and throat swabs, sputum and feces of symptomatic patients including neonates but not from vaginal swabs, amniotic fluid, placenta, cord blood, neonatal blood or breast milk. Viremia was present in 1% of symptomatic adults. We identified 12 articles published between February 10th and April 4th 2020 reporting on 68 deliveries and 71 neonates with maternal infection in the third trimester of pregnancy. Perinatal exposure, including mode of delivery and time interval from delivery to the diagnosis of neonatal infection are crucial in differentiating congenital from perinatal infection. Neonatal infection is usually asymptomatic. Neonatal infection was diagnosed within 48 hours of life in 4 cases. Detection rates of real-time PCR and the interpretation of IgM and IgG antibodies levels in cord and neonatal blood are discussed in relation with the immaturity of the fetal and neonatal immune system. url: https://www.sciencedirect.com/science/article/pii/S000293782030524X?v=s5 doi: 10.1016/j.ajog.2020.04.039 id: cord-308615-4fobikeh author: AKTAS, Busra title: Gut-lung axis and dysbiosis in COVID-19 date: 2020-06-21 words: 4221.0 sentences: 216.0 pages: flesch: 45.0 cache: ./cache/cord-308615-4fobikeh.txt txt: ./txt/cord-308615-4fobikeh.txt summary: Although SARS-CoV-2 mainly causes lung infection, gastrointestinal symptoms described in COVID-19 patients and detection of the viral RNA in feces of infected patients drove attentions to a possible fecal-oral transmission route of SARS-CoV-2. This review points out the role of dysbiosis of the gut microbiota involving in sepsis, on the severity of SARS-CoV-2 infection. Due to the common symptoms, indicating respiratory tract disease, of patients infected with SARS-CoV-2, the main organ effected by the COVID-19 seems to be lung. In addition to the data detecting viral RNA in feces previously, these results suggest that SARS-CoV-2 infection does not remain with the respiratory tract only and the gastrointestinal system contribute to the course of the disease as well. However, with the limited data until today, it is hard to propose a fecal-oral transmission route to explain the enteric symptoms in COVID-19 patients and claim that SARS-CoV-2 pass through stomach and reach intestine to infect the intestinal cells as enteric viruses accomplish. abstract: COVID-19, a novel infectious disease, caused by SARS-CoV-2, affected millions of people around the world with a high mortality rate. Although SARS-CoV-2 mainly causes lung infection, gastrointestinal symptoms described in COVID-19 patients and detection of the viral RNA in feces of infected patients drove attentions to a possible fecal-oral transmission route of SARS-CoV-2. However, not only the viral RNA but also the infectious viral particles are required for the viral infection and no proof has been demonstrated the transmission of the infectious virus particles via the fecal-oral route yet. Growing evidence indicates the crosstalk between gut microbiota and lung, that maintains host homeostasis and disease development with the association of immune system. This gut-lung interaction may influence the COVID-19 severity in patients with extrapulmonary conditions. Severity of COVID-19 has mostly associated with old ages and underlying medical conditions. Since the diversity in the gut microbiota decreases during aging, dysbiosis could be the reason for older adults being at high risk for severe illness from COVID-19. We believe that gut microbiota contributes to the course of COVID-19 due to its bidirectional relationship with immune system and lung. Dysbiosis in gut microbiota results in gut permeability leading to secondary infection and multiple organ failure. Conversely, disruption of the gut barrier integrity due to dysbiosis may lead to translocation of SARS-CoV-2 from the lung into the intestinal lumen via circulatory and lymphatic system. This review points out the role of dysbiosis of the gut microbiota involving in sepsis, on the severity of SARS-CoV-2 infection. Additionally, this review aims to clarify the ambiguity in fecal-oral transmission of SARS- CoV-2. url: https://doi.org/10.3906/biy-2005-102 doi: 10.3906/biy-2005-102 id: cord-279435-ffgd2ets author: ALBalawi, Hani B title: COVID-19: Precautionary Guidelines for Ophthalmologists date: 2020-06-25 words: 3183.0 sentences: 148.0 pages: flesch: 49.0 cache: ./cache/cord-279435-ffgd2ets.txt txt: ./txt/cord-279435-ffgd2ets.txt summary: Healthcare providers, particularly ophthalmologists, are at high risk of a COVID-19 infection through unprotected contact with eye secretions during routine ophthalmic examinations that involve the use of direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that allows for close doctor-patient contact. In fact, ophthalmologists are at high risk of contracting the COVID-19 virus through unprotected eye contact with secretions during routine ophthalmic examinations with direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that has close doctor-patient contact. A three-stage control measure to reduce the transmission of the virus in the ophthalmology department in Hong Kong was based on text messaging to reschedule refill visits [6] ; a triage to identify patients with fever, conjunctivitis, and respiratory symptoms; asking those who recently traveled to areas infected with the virus to postpone their ophthalmology visits for 14 days; and the avoidance of micro-aerosol generating procedures, nasal endoscopy, and operations under general anesthesia. abstract: Several coronaviruses can infect humans, and the globally endemic human coronaviruses, HCoV-229E (human coronavirus 229E), HCoV-NL63 (human coronavirus NL63), and others, tend to cause mild respiratory diseases. The zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus type1 (SARS-CoV-1) have high fatality rates. In December 2019, the World Health Organization (WHO) was notified by Chinese authorities about an outbreak of pneumonia before the causative organism was identified in January 2020 as a novel coronavirus family. The WHO refers to the virus as coronavirus disease 2019 (COVID-19). Within several weeks, the outbreak has become an emergency, and many countries have since been affected. The method of transmission is not yet fully known but is thought to be mainly respiratory. Healthcare providers, particularly ophthalmologists, are at high risk of a COVID-19 infection through unprotected contact with eye secretions during routine ophthalmic examinations that involve the use of direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that allows for close doctor-patient contact. In light of these, specific measures are needed from an ophthalmic point of view to control the COVID-19 outbreak and to protect health care providers. url: https://doi.org/10.7759/cureus.8815 doi: 10.7759/cureus.8815 id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 words: 19181.0 sentences: 1041.0 pages: flesch: 43.0 cache: ./cache/cord-022084-hap7flng.txt txt: ./txt/cord-022084-hap7flng.txt summary: The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152450/ doi: 10.1016/b978-0-443-06668-9.50064-8 id: cord-273726-24mi50rv author: Aaroe, Ashley title: Potential Neurologic and Oncologic Implications of the Novel Coronavirus date: 2020-04-16 words: 1091.0 sentences: 79.0 pages: flesch: 54.0 cache: ./cache/cord-273726-24mi50rv.txt txt: ./txt/cord-273726-24mi50rv.txt summary: It is one of seven coronaviruses that are known to infect humans, along with SARS-CoV1, MERS-CoV, and four endemic species that cause cold-like symptoms (229E, OC43, NL63 and HKU1). Human coronavirus species have been detected in CNS samples of patients with MS as early as the 1980s in autopsy studies [3] , and also in the CSF of children with acute disseminated encephalomyelitis. A similar phenomenon may be evident in SARS-CoV2, as an estimated 63% of COVID-19 patients develop lymphopenia, and recent data shows a trend to worsened lymphopenia in patients with CNS symptoms compared with those without [5] . A preliminary report describes a case of acute myelitis following SARS-CoV2 infection [9] . Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. Acute myelitis after SARS-CoV-2 infection: a case report. The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients abstract: nan url: https://doi.org/10.1093/neuonc/noaa096 doi: 10.1093/neuonc/noaa096 id: cord-340581-ngwgb3y0 author: Abassi, Zaid title: ACE2, COVID-19 Infection, Inflammation, and Coagulopathy: Missing Pieces in the Puzzle date: 2020-10-06 words: 4644.0 sentences: 247.0 pages: flesch: 42.0 cache: ./cache/cord-340581-ngwgb3y0.txt txt: ./txt/cord-340581-ngwgb3y0.txt summary: Angiotensin-converting enzyme is expressed on the plasma membranes of various cell types, including alveolar and intestinal epithelia, vascular endothelial cells in the heart, kidney, and testis, and on macrophages, where it catalyzes the production of Ang 1-7 and its likely paracrine activity (Crackower et al., 2002; Hamming et al., 2007; Santos et al., 2008; Clarke and Turner, 2012; Abassi et al., 2020c) . In this context, testosterone has been described to induce ACE2 expression, the receptor entry of the SARS-CoV-2 infection, but also exerts protective effect against lung injury (Kuba et al., 2005) . FIGURE 2 | Physiology of coronavirus disease 2019 (COVID 19) homing to target host cells expressing ACE2: viral spike-domains enable attachment to cellmembrane-bound ACE2. Thus, viral cellular invasion and replication, initially facilitated by ACE2 and in particular under conditions characterized by enhanced ACE2 expression, later lead to diminution of cell membrane-attached ACE2, and likely increase circulating sACE2 (Figures 2, 3) . abstract: Engulfed by the grave consequences of the coronavirus disease 2019 (COVID-19) pandemic, a better understanding of the unique pattern of viral invasion and virulence is of utmost importance. Angiotensin (Ang)-converting enzyme (ACE) 2 is a key component in COVID-19 infection. Expressed on cell membranes in target pulmonary and intestinal host cells, ACE2 serves as an anchor for initial viral homing, binding to COVID-19 spike-protein domains to enable viral entry into cells and subsequent replication. Viral attachment is facilitated by a multiplicity of membranal and circulating proteases that further uncover attachment loci. Inherent or acquired enhancement of membrane ACE2 expression, likely leads to a higher degree of infection and may explain the predisposition to severe disease among males, diabetics, or patients with respiratory or cardiac diseases. Additionally, once attached, viral intracellular translocation and replication leads to depletion of membranal ACE2 through degradation and shedding. ACE2 generates Ang 1-7, which serves a critical role in counterbalancing the vasoconstrictive, pro-inflammatory, and pro-coagulant effects of ACE-induced Ang II. Therefore, Ang 1-7 may decline in tissues infected by COVID-19, leading to unopposed deleterious outcomes of Ang II. This likely leads to microcirculatory derangement with endothelial damage, profound inflammation, and coagulopathy that characterize the more severe clinical manifestations of COVID-19 infection. Our understanding of COVID-ACE2 associations is incomplete, and some conceptual formulations are currently speculative, leading to controversies over issues such as the usage of ACE inhibitors or Ang-receptor blockers (ARBs). This highlights the importance of focusing on ACE2 physiology in the evaluation and management of COVID-19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33123031/ doi: 10.3389/fphys.2020.574753 id: cord-257820-4qmajxtb author: Abate, Giulia title: Impact of COVID-19 on Alzheimer’s Disease Risk: Viewpoint for Research Action date: 2020-08-21 words: 4086.0 sentences: 241.0 pages: flesch: 45.0 cache: ./cache/cord-257820-4qmajxtb.txt txt: ./txt/cord-257820-4qmajxtb.txt summary: On the other hand, we cannot exclude that, in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) positive subjects, the virus infection could have long-term consequences, leading to chronic medical conditions such as dementia and neurodegenerative disease. Based on the belief that the tissue distribution of host receptors are generally consistent with the tropism of the virus [35] , ACE2 expression and its modulation in CNS might aid in dissecting the invasion rate and distribution of SARS-CoV-2 in the brain area. Recently, in the UK Biobank Community Cohort (n = 451,367), the ApoE e4e4 (homozygous) genotype was also found associated with an increased risk of severe COVID-19 infection, independent of preexisting dementia, cardiovascular disease, and type-2 diabetes [81] . All of these hypotheses about the theoretical impact of SARS-CoV-2 brain infection on Alzheimer''s disease risk are summarized Table 1 . Theoretical impact of SARS-CoV-2 brain infection on Alzheimer''s disease risk. AD, Alzheimer''s disease; Aβ, Beta-amyloid; ACE2, Angiotensin-Converting Enzyme 2; NO, nitric oxide. abstract: In the middle of the coronavirus disease 19 (COVID-19) outbreak, the main efforts of the scientific community are rightly all focused on identifying efficient pharmacological treatments to cure the acute severe symptoms and developing a reliable vaccine. On the other hand, we cannot exclude that, in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) positive subjects, the virus infection could have long-term consequences, leading to chronic medical conditions such as dementia and neurodegenerative disease. Considering the age of SARS-CoV-2 infected subjects, the neuroinvasive potential might lead/contribute to the development of neurodegenerative diseases. Here, we analyzed a possible link between SARS-CoV-2 infection and Alzheimer’s disease risk, hypothesizing possible mechanisms at the base of disease development. This reflection raises the need to start to experimentally investigating today the mechanistic link between Alzheimer’s disease (AD) and COVID-19 to be ready tomorrow. url: https://www.ncbi.nlm.nih.gov/pubmed/32839380/ doi: 10.3390/healthcare8030286 id: cord-288403-m6qe57he author: Abbas, K. M. title: Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa date: 2020-05-26 words: 7098.0 sentences: 317.0 pages: flesch: 45.0 cache: ./cache/cord-288403-m6qe57he.txt txt: ./txt/cord-288403-m6qe57he.txt summary: First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month Covid-19 risk period without catch-up campaigns. Specifically, we conducted a benefit-risk analysis of vaccine-preventable deaths averted by sustaining routine childhood immunisation in comparison to excess Covid-19 deaths from SARS-CoV-2 infections acquired by visiting routine vaccination service delivery points. The central estimates for benefit-risk ratio at the household level show the child deaths averted by continuing the routine childhood immunisation programmes (1-dose MCV1, RCV1, MenA, YFV for 9-month-old children) per excess Covid-19 death caused by SARS-CoV2 infections acquired in the vaccination service delivery points. abstract: Background: National immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 pandemic. Our aim is to compare the health benefits of sustaining routine childhood immunisation in Africa against the risk of acquiring SARS-CoV-2 infections through visiting routine vaccination service delivery points. Methods: We used two scenarios to approximate the child deaths that may be caused by immunisation coverage reductions during COVID-19 outbreaks. First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month Covid-19 risk period without catch-up campaigns. Second, we analysed an alternative scenario that approximates the health benefits of sustaining routine childhood immunisation to only the child deaths averted from measles outbreaks during the Covid-19 risk period. The excess number of infections due to additional SARS-CoV-2 exposure during immunisation visits assumes that contact reducing interventions flatten the outbreak curve during the Covid-19 risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport and that upon child infection the whole household would be infected. Country specific household age structure estimates and age dependent infection fatality rates are then applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit-risk ratios for routine childhood immunisation alongside 95% uncertainty range estimates from probabilistic sensitivity analysis. Findings: For every one excess Covid-19 death attributable to SARS-CoV-2 infections acquired during routine vaccination clinic visits, there could be 143 (38 - 576) deaths in children prevented by sustaining routine childhood immunisation in Africa. The benefit-risk ratio for the vaccinated children, siblings, parents or adult care-givers, and older adults in the households of vaccinated children are 58,000 (3,200 - 21,350,000), 52,000 (2,800 - 18,884,000), 2,000 (393 - 12,000), and 157 (41 - 652) respectively. In the alternative scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit-risk ratio to the households of vaccinated children is 5 (1 - 21) under these highly conservative assumptions and if the risk to only the vaccinated children is considered, the benefit-risk ratio is 2,000 (131 - 839,000). Interpretation: Our analysis suggests that the health benefits of deaths prevented by sustaining routine childhood immunisation in Africa far outweighs the excess risk of Covid-19 deaths associated with vaccination clinic visits. However, there are other factors that must be considered for strategic decision making to sustain routine childhood immunisation in African countries during the Covid-19 pandemic. These include logistical constraints of vaccine supply chain problems caused by the Covid-19 pandemic, reallocation of immunisation providers to other prioritised health services, healthcare staff shortages caused by SARS-CoV-2 infections among the staff, decreased demand for vaccination arising from community reluctance to visit vaccination clinics for fear of contracting SARS-CoV-2 infections, and infection risk to healthcare staff providing immunisation services as well as to their households and onward SARS-CoV-2 transmission into the wider community. url: http://medrxiv.org/cgi/content/short/2020.05.19.20106278v1?rss=1 doi: 10.1101/2020.05.19.20106278 id: cord-322789-9elfpx0e author: Abbaspour Kasgari, Hamideh title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial date: 2020-08-19 words: 2711.0 sentences: 155.0 pages: flesch: 49.0 cache: ./cache/cord-322789-9elfpx0e.txt txt: ./txt/cord-322789-9elfpx0e.txt summary: title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial 29 We therefore conducted a randomized controlled trial in adult patients hospitalized with COVID-19 in Ghaem Shahr Razi Hospital to evaluate the efficacy and safety of sofosbuvir and daclatasvir in combination with ribavirin compared with standard care. This study was a single-centre, randomized clinical trial to evaluate the effectiveness of sofosbuvir/daclatasvir with ribavirin against controls who received standard of care for COVID-19 at the time of the study. This randomized trial found that the combination of sofosbuvir/ daclatasvir/ribavirin compared with standard care showed limited clinical improvement in moderate COVID-19 patients. To our knowledge, this is the first clinical trial of sofosbuvir/ daclatasvir/ribavirin in COVID-19 patients; however, there are limitations to our study. abstract: BACKGROUND: New therapeutic options are urgently needed to tackle the novel coronavirus disease 2019 (COVID-19). Repurposing existing pharmaceuticals provides an immediate treatment opportunity. We assessed the efficacy of sofosbuvir and daclatasvir with ribavirin for treating patients with COVID-19. METHODS: This was a single-centre, randomized controlled trial in adults with moderate COVID-19 admitted to the Ghaem Shahr Razi Hospital in Mazandaran Province, Iran. Patients were randomly assigned to 400 mg sofosbuvir, 60 mg daclatasvir and 1200 mg ribavirin (intervention group) or to standard care (control group). The primary endpoint of this study was length of hospital stay. This study is registered by IRCT.ir under the ID: IRCT20200328046886N1. RESULTS: Between 20 March 2020 and 8 April 2020, 48 patients were recruited; 24 patients were randomly assigned to the intervention group and 24 to the control group. The median duration of hospital stay was 6 days in both groups (P = 0.398). The number of ICU admissions in the sofosbuvir/daclatasvir/ribavirin group was not significantly lower than the control group (0 versus 4, P = 0.109). There was no difference in the number of deaths between the groups (0 versus 3, P = 0.234). The cumulative incidence of recovery was higher in the sofosbuvir/daclatasvir/ribavirin arm (Gray’s P = 0.033). CONCLUSIONS: This randomized trial was too small to make definitive conclusions. There were trends in favour of the sofosbuvir/daclatasvir/ribavirin arm for recovery and lower death rates. However, there was an imbalance in the baseline characteristics between the arms. Larger randomized trials should be conducted to investigate this treatment further. url: https://www.ncbi.nlm.nih.gov/pubmed/32812025/ doi: 10.1093/jac/dkaa332 id: cord-285486-99trkti1 author: Abd-Elsalam, Sherief title: Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study date: 2020-08-14 words: 2928.0 sentences: 166.0 pages: flesch: 53.0 cache: ./cache/cord-285486-99trkti1.txt txt: ./txt/cord-285486-99trkti1.txt summary: Univariate logistic regression analysis showed that HCQ treatment was not significantly associated with decreased mortality in COVID-19 patients. So, adding HCQ to standard care did not add significant benefit, did not decrease the need for ventilation, and did not reduce mortality rates in COVID-19 patients. 1. Hydroxychloroquine group: This group included 97 patients who received HCQ 400 mg twice daily (in day 1) followed by 200 mg tablets twice daily added to the standard of care treatment adopted by the Egyptian MOH for 15 days. 18 Although cardiac toxicity is a known adverse event requiring monitoring during treatment, HCQ showed promise in treating SARS-CoV-2-infected patients with multiple comorbidities including coronary artery disease. 12 studied the change in symptom severity over 14 days in nonhospitalized patients between HCQ and control groups and did not find any significant difference (P = 0.12). abstract: The COVID-19 pandemic is showing an exponential growth, mandating an urgent need to develop an effective treatment. Indeed, to date, a well-established therapy is still lacking. We aimed to evaluate the safety and efficacy of hydroxychloroquine (HCQ) added to standard care in patients with COVID-19. This was a multicenter, randomized controlled trial conducted at three major university hospitals in Egypt. One hundred ninety-four patients with confirmed diagnosis of COVID-19 were included in the study after signing informed consent. They were equally randomized into two arms: 97 patients administrated HCQ plus standard care (HCQ group) and 97 patients administered only standard care as a control arm (control group). The primary endpoints were recovery within 28 days, need for mechanical ventilation, or death. The two groups were matched for age and gender. There was no significant difference between them regarding any of the baseline characteristics or laboratory parameters. Four patients (4.1%) in the HCQ group and 5 (5.2%) patients in the control group needed mechanical ventilation (P = 0.75). The overall mortality did not differ between the two groups, as six patients (6.2%) died in the HCQ group and 5 (5.2%) died in the control group (P = 0.77). Univariate logistic regression analysis showed that HCQ treatment was not significantly associated with decreased mortality in COVID-19 patients. So, adding HCQ to standard care did not add significant benefit, did not decrease the need for ventilation, and did not reduce mortality rates in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32828135/ doi: 10.4269/ajtmh.20-0873 id: cord-298722-rmibv5z7 author: Abdel-latif, Rania G title: Statin therapy and SAR-COV-2: an available and potential therapy? date: 2020-05-07 words: 712.0 sentences: 49.0 pages: flesch: 39.0 cache: ./cache/cord-298722-rmibv5z7.txt txt: ./txt/cord-298722-rmibv5z7.txt summary: 4 In fact, some observational data suggest that moderate dose statin therapy was associated with lower mortality among patients with influenza pneumonia. 9 Host ACE2 receptors utilized by SARS-CoV-2 might be potential targets for viral therapeutic intervention. 10 Clinical studies are encouraged to investigate the effect of ACE2 expression in protection against respiratory distress and the role of statin therapy for this postulated hypothesis. Further clinical studies are warranted to evaluate the efficacy of statin therapy against COVID-19 and determine the effective therapeutic dose. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region, Italy Cardiovascular implications of fatal outcomes of patients with coronavirus disease 2019 (COVID-19) Statins reduce the expression of proinflammatory cytokines in influenza A virus infected CrFK cells A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury abstract: nan url: https://doi.org/10.1093/ehjcvp/pvaa050 doi: 10.1093/ehjcvp/pvaa050 id: cord-347516-linjv64o author: Abdelaziz, Osama S. title: Neuropathogenic human coronaviruses: A review date: 2020-07-20 words: 2338.0 sentences: 144.0 pages: flesch: 39.0 cache: ./cache/cord-347516-linjv64o.txt txt: ./txt/cord-347516-linjv64o.txt summary: authors: Abdelaziz, Osama S.; Waffa, Zuraiha However, there are reports of neurological findings in HCoV infections, particularly in patients infected with the novel severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) amid Coronavirus disease 2019 (COVID‐19) pandemic. 26, 29 Reports of neuromusculoskeletal disorders, complicating HCoV infections and COVID-19, postulate that myopathies and neuropathies are a result of the significantly elevated inflammatory cytokines in patients'' sera leading to virus-induced immune damage. 20, 24, 32, 33 This primary neurotropism could be further supported by the recent reports of the occurrence of olfactory and/or taste disorders, as early atypical manifestations of SARS-CoV-2, which may precede the onset of full-blown clinical COVID-19 in more than onethird of patients. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome abstract: Human Coronaviruses (HCoVs) have long been known as respiratory viruses. However, there are reports of neurological findings in HCoV infections, particularly in patients infected with the novel severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) amid Coronavirus disease 2019 (COVID‐19) pandemic. Therefore, it is essential to interpret the interaction of HCoVs and the nervous system and apply this understanding to the COVID‐19 pandemic. This review of the literature analyses how HCoVs, in general, and SARS‐CoV‐2, in particular, affect the nervous system, highlights the various underlying mechanisms, addresses the associated neurological and psychiatric manifestations, and identifies the neurological risk factors involved. This review of literature shows the magnitude of neurological conditions associated with HCoV infections, including SARS‐CoV‐2. This review emphasises, that, during HCoV outbreaks, such as COVID‐19, a focus on early detection of neurotropism, alertness for the resulting neurological complications, and the recognition of neurological risk factors are crucial to reduce the workload on hospitals, particularly intensive‐care units and neurological departments. url: https://www.ncbi.nlm.nih.gov/pubmed/32687681/ doi: 10.1002/rmv.2118 id: cord-330994-6nu7utu1 author: Abdelrheem, Doaa A. title: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation date: 2020-10-01 words: 5306.0 sentences: 323.0 pages: flesch: 48.0 cache: ./cache/cord-330994-6nu7utu1.txt txt: ./txt/cord-330994-6nu7utu1.txt summary: title: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. [6] So, we study the inhibitory effect of some bioactive compounds obtained from natural sources against SARS-CoV-2-3CLpro and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT). The crystal structures of SARS-CoV-2-3CLpro (PDB code: 6LU7) and main proteases of SARS-Coronavirus (Mpro) with (PDB IDs: 2GTB and 3TNT) were downloaded from the Protein Data Bank (www.pdb.org), and any heteroatoms and water molecules were removed before molecular docking studies. Based on our molecular docking analysis we found that among all studied compounds, caulerpin has the highest binding affinity against all studied receptors 6LU7, 3TNT, and 2GTB with compared to some proposed antiviral drug currently used in COVID-19 treatment. abstract: This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The inhibitory effect of all studied compounds was studied with compared to some proposed antiviral drugs which currently used in COVID-19 treatment such as chloroquine, hydroxychloroquine, azithromycin, remdesivir, baloxvir, lopinavir, and favipiravir. Homology modeling and sequence alignment was computed to evaluate the similarity between the SARS-CoV-2-3CL main protease and other SARS-CoV receptors. ADMET properties of all studied compounds were computed and reported. Also, molecular dynamic (MD) simulation was performed on the compound which has the highest binding affinity inside 6LU7 obtained from molecular docking analysis to study it is stability inside receptor in explicit water solvent. Based on molecular docking analysis, we found that caulerpin has the highest binding affinity inside all studied receptors compared to other bioactive compounds and studied drugs. Our homology modeling and sequence alignment showed that SARS-CoV main protease (PDB ID: 3TNT) shares high similarity with 3CLpro (96.00%). Also, ADMET properties confirmed that caulerpin obeys Lipinski’s rule and passes ADMET property, which make it a promising compound to act as a new safe natural drug against SARS-CoV-2-3CL main protease. Finally, MD simulation confirmed that the complex formed between caulerpin and 3CLpro is stable in water explicit and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. Also, binding free energy between caulerpin and 6LU7 confirmed the efficacy of the caulerpin molecule against SARS-CoV-2 main protease. So, this study suggested that caulerpin could be used as a potential candidate in COVID-19 treatment. url: https://doi.org/10.1080/10934529.2020.1826192 doi: 10.1080/10934529.2020.1826192 id: cord-337302-fpz2jfuj author: Abdihamid, Omar title: The Landscape of COVID-19 in Cancer Patients: Prevalence, Impacts, and Recommendations date: 2020-09-23 words: 5958.0 sentences: 357.0 pages: flesch: 48.0 cache: ./cache/cord-337302-fpz2jfuj.txt txt: ./txt/cord-337302-fpz2jfuj.txt summary: 21 Similar to cases seen during the MERS-outbreak where having cancer was identified as a risk factor for MERS-CoV mortality, the COVID-19 pandemic also poses threats to cancer patients. 23 In one of the early data by Yu et al published in JAMA Oncology, the infection rate of SARS-CoV-2 in cancer patients from Wuhan, China, was at 0.79% (12 of 1524 patients; 95% CI, 0.31.2%). 15 In a retrospective cohort study of 28 COVID-19infected cancer patients with laboratory-confirmed COVID-19 from three hospitals in China, a total of 15 (53.6%) patients had severe outcomes with a mortality rate of 28.6%. Patients'' age, tumor type, underlying comorbidities, stage of the disease, and treatment type all affect the risk and outcomes of contracting SARS-CoV-2 in cancer patients. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: Cancer patients are susceptible groups to COVID-19, and risk-adjusted models show that most cancer patients have a 25–39% mortality risk if infected with COVID-19. The infection rate of SARS-CoV-2 in cancer patients in China was 0.79% (12 of 1524 patients; 95% CI, 0.31.2%). The case fatality rate of COVID-19 in the overall population ranges from 2.3 to 8.0%; among these, the case fatality rate for cancer patients is at 5.6%. In a retrospective cohort study of 28 COVID-19-infected cancer patients, a total of 15 (53.6%) patients had severe outcomes with a mortality rate of 28.6%. In a pooled analysis by Aakash et al, a 2% cancer prevalence was found among admitted patients with COVID-19. In Italy, a report shows that among the 3200 patients who died of SARS-CoV-2, 19.4% were patients with cancer. In New York, 61 (28%) cancer patients succumbed to COVID-19 with a case fatality rate of 37% (20/54) and 25% (41/164) for hematologic and solid malignancies, respectively. Impacts of COVID-19 in cancer care include interruptions of life-saving therapies, distraction effects, and diagnostic overshadowing that involve diverting attention to the pandemic rather than to cancer patients and disruptions of primary palliative care to patients due to forced quarantine. Herein, we review the landscape of COVID-19 in cancer care. We also briefly share our experience and the measures in place to protect cancer patients against COVID-19 in our center. url: https://doi.org/10.2147/cmar.s272008 doi: 10.2147/cmar.s272008 id: cord-299422-s5evsj96 author: Abdollahi, Alireza title: The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types date: 2020-05-23 words: 2909.0 sentences: 139.0 pages: flesch: 50.0 cache: ./cache/cord-299422-s5evsj96.txt txt: ./txt/cord-299422-s5evsj96.txt summary: CONCLUSION: Similar to several previous studies about other viral diseases'' association with ABO histo-blood groups, we have concluded that an individual''s ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. Previous researches have proved the potential role of ABO blood groups on a host''s genetic susceptibility to various viral diseases such as influenza, Ebola, enteric viruses, and SARS-CoV infections (8) (9) (10) (11) (12) . In the present study, 397 COVID-19 patients and 500 normal controls were analyzed to evaluate the association of the ABO histo-blood group phenotypes with COVID-19 disease in the Iranian population. Further studies are required to determine the exact mechanism through which ABO blood group influences COVID-19 susceptibility, which could be helpful in patient management and disease control. However, our results were discordant regarding the ABO histo-blood antigens which make people susceptible to COVID-19 (AB versus A histo-blood group phenotype in Iran and China, respectively). abstract: BACKGROUND & OBJECTIVE: Coronavirus disease 2019 (COVID-19) is the most recent emerging viral disease. Defining the epidemiological aspects and factors influencing the susceptibility of the patients to COVID-19 has been an ongoing struggle. In the present study, we have investigated the connection between ABO histo-blood group phenotypes and the COVID-19. METHODS: This study was conducted on 397 patients with confirmed diagnoses of COVID-19 admitted to our center. Also, 500 individuals were selected to form the controls, all of whom had been disclosed to the same medical center in June 2019, before the onset of the outbreak. RESULTS: Our results demonstrated ABO histo-blood phenotypes are correlated with patients’ susceptibility to the infection. A higher rate of infection was observed among patients with the AB histo-blood group, while patients with the O histo-blood group have shown a lower rate of infection. The Rh blood group phenotype was not statistically significant in determining a patient’s vulnerability. CONCLUSION: Similar to several previous studies about other viral diseases’ association with ABO histo-blood groups, we have concluded that an individual’s ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. So far, only one research has been conducted about this association. Interestingly, while we observed a decreased vulnerability to the disease among patients with an O histo-blood group, we have reached discordant results regarding the increased susceptibility among individuals with an AB histo-blood group, unlike A histo-blood group in the previous study. url: https://www.ncbi.nlm.nih.gov/pubmed/32754209/ doi: 10.30699/ijp.2020.125135.2367 id: cord-319184-voc0eqb9 author: Abduljalil, Jameel M. title: Laboratory diagnosis of SARS-CoV-2: available approaches and limitations date: 2020-06-14 words: 1115.0 sentences: 101.0 pages: flesch: 44.0 cache: ./cache/cord-319184-voc0eqb9.txt txt: ./txt/cord-319184-voc0eqb9.txt summary: Clinical 397 evaluation of the cobas SARS-CoV-2 test and a diagnostic platform switch during 48 398 hours in the midst of the COVID-19 pandemic Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-406 19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro Rapid and visual detection of 2019 458 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal 459 amplification assay Transcription Loop-Mediated Isothermal Amplification Assays Targeting SARS-CoV-2 Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of 467 SARS-CoV-2 Development of a reverse 469 transcription-loop-mediated isothermal amplification as a rapid early-detection method for 470 novel SARS-CoV-2 Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Development and clinical application of a 500 rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Novel Antigen-Based Rapid Detection Test for the Diagnosis of SARS-CoV-2 in Serological immunochromatographic 525 approach in diagnosis with SARS-CoV-2 infected COVID-19 patients abstract: Abstract The ongoing pandemic of SARS-CoV-2 is a one of the most devastating outbreaks witnessed in the last 100 years. The outbreak started in China's hinterland and spread rapidly to almost every country culminating in woefully overwhelmed healthcare systems in most countries. The only approved diagnostic test to accompany radiographic evaluation is the reverse-transcriptase PCR. However, the applicability of this test in diagnosis and surveillance is challenged by global shortage in reagents and unavailability of well-equipped laboratories with specialized staff in several low- and middle-income countries. The need for development of accurate and rapid diagnostic assays became apparent. Handful of immunodiagnostic tests and other molecular approaches were developed and tested. Other recently developed point-of-care molecular tests are expected to be helpful in pandemic management since no particular skills are required from the operator. Fortunately, handful of serological tests have granted authorization to be used under emergency situation by FDA in diagnosis of SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S2052297520300652 doi: 10.1016/j.nmni.2020.100713 id: cord-031061-48xwfr9i author: Abdullah, Abdullah title: Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 date: 2020-08-16 words: 2530.0 sentences: 153.0 pages: flesch: 43.0 cache: ./cache/cord-031061-48xwfr9i.txt txt: ./txt/cord-031061-48xwfr9i.txt summary: title: Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 The convalescent sera of the recovered COVID-19 patients are containing antiviral neutralizing antibodies and is used therapeutically for infected individuals by SARS-CoV-2 and for the purpose of prophylaxis in exposed individuals. Three SARS-CoV-1 infected patients were treated with 500ml of convalescent sera, the reduction in viral titer and mortality were recorded (39) . Three MERS infected patients were also treated with Convalescent or Passive antibody therapy, two of them produce nAbs and remaining one not (40) , this study highlights the limitation in using of convalescent sera it means that the recovered individual may not have enough titer of nAbs (41) . The available information on the use of convalescent sera or passive immunization for the treatment of SARS-CoV-2 suggests that early administration of convalescent serum reduces viral abundance and was found safe. abstract: The whole world is confronting the pandemic of SARS-CoV-2. Unfortunately there is no vaccine to prevent from novel coronavirus infection. Beside several experimental drugs, the strong immune responses and convalescent sera are the current two potential options to tackle COVID-19 infection. Innate immune-mediated antiviral responses is initiated by the recognition of viral invasion through PAMPs. In coronavirus the pathogen associated molecular patterns are recognized by toll like receptors (TLR-3 & 7), endosomal ribonucleic acid receptors, RNA in cytosol and by pattern recognition receptor (PRR RIG-1) in the alveolar cells and site of invasion. Nuclear factor (NF-κB) and interferon regulatory transcription factor (IRF3) are activated in response to above recognition episode and translocate to nucleus. These transcription factors in the nucleus initiate the expression of interferon type 1 and pro-inflammatory cytokine storm, which leads to first line of defense at the site of viral entrance. The effectiveness of innate immune system is greatly relies on type 1 interferons and its cascade, because of their role in inhibition of viral replication and initiation of adaptive immune responses. The successful interferon type 1 response put down the viral replication and transmission at prompt point. Passive immunization is the administering of antibodies into infected patients which is taken from recovered individuals. The convalescent sera of the recovered COVID-19 patients are containing antiviral neutralizing antibodies and is used therapeutically for infected individuals by SARS-CoV-2 and for the purpose of prophylaxis in exposed individuals. The convalescent sera is found effective when administered early at the onset of symptoms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454257/ doi: 10.1093/abt/tbaa019 id: cord-280939-d478p8u6 author: Abe, Kento T. title: A simple protein-based surrogate neutralization assay for SARS-CoV-2 date: 2020-10-02 words: 7576.0 sentences: 380.0 pages: flesch: 53.0 cache: ./cache/cord-280939-d478p8u6.txt txt: ./txt/cord-280939-d478p8u6.txt summary: Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). SARS-CoV-2 ELISAs are performed by immobilizing a recombinantly produced viral antigen (such as the spike trimer or RBD) ( Figure 1B and Supplemental Figures 1 and 2; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.142362DS1) (see Methods) onto multiwell plastic plates that are then incubated with diluted patient serum or plasma samples. abstract: Most of the patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mount a humoral immune response to the virus within a few weeks of infection, but the duration of this response and how it correlates with clinical outcomes has not been completely characterized. Of particular importance is the identification of immune correlates of infection that would support public health decision-making on treatment approaches, vaccination strategies, and convalescent plasma therapy. While ELISA-based assays to detect and quantitate antibodies to SARS-CoV-2 in patient samples have been developed, the detection of neutralizing antibodies typically requires more demanding cell-based viral assays. Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). The assay serves as a surrogate neutralization assay and is performed on the same platform and in parallel with an ELISA for the detection of antibodies against the RBD, enabling a direct comparison. The results obtained with our assay correlate with those of 2 viral-based assays, a plaque reduction neutralization test (PRNT) that uses live SARS-CoV-2 virus and a spike pseudotyped viral vector–based assay. url: https://www.ncbi.nlm.nih.gov/pubmed/32870820/ doi: 10.1172/jci.insight.142362 id: cord-336870-nirg3269 author: Abebe, Endeshaw Chekol title: The newly emerged COVID-19 disease: a systemic review date: 2020-07-08 words: 4157.0 sentences: 209.0 pages: flesch: 54.0 cache: ./cache/cord-336870-nirg3269.txt txt: ./txt/cord-336870-nirg3269.txt summary: The novel COVID-19 infection, caused by a beta coronavirus called SARS-CoV-2, is a new outbreak that has been emerged in Wuhan, China in December 2019. i. If a patient with a severe acute respiratory infection (fever, cough, and requiring admission to hospital), and with no other etiology that fully explains the clinical presentation and a history of travel to or residence in a country/area or territory reporting local transmission during the 14 days prior to symptom onset, OR ii. It is caused by a novel beta-coronavirus, resulting from genetic recombination, called SARS-CoV-2, The most common symptoms of COVID-19 are fever, cough, and dyspnea. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Coronaviruses are large family-RNA viruses that belong to the order Nidovirales, family Coronaviridae, subfamily Coronavirinae. The novel COVID-19 infection, caused by a beta coronavirus called SARS-CoV-2, is a new outbreak that has been emerged in Wuhan, China in December 2019. The most common symptoms of COVID-19 are fever, cough, and dyspnea. As per the March 12, 2020, WHO report, more than 125,048 confirmed COVID-19 cases and over 4613 deaths have been identified in more than 117 countries. It is now regarded as a pandemic that seriously spread and attack the world. The primary means of transmission is person to person through droplets that occurred during coughing or sneezing, through personal contact (shaking hands), or by touching contaminated objects. So far, there is no effective therapy and vaccine available against this novel virus and therefore, only supportive care is used as the mainstay of management of patients with COVID-19. The mortality rate of COVID-19 is considerable. This work aimed to provide insight on the newly emerged COVID-19, in the hope to gain a better understanding on the general overview, epidemiology, transmission, clinical features, diagnosis, treatment, and clinical outcomes as well as the prevention and control of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32641059/ doi: 10.1186/s12985-020-01363-5 id: cord-315641-bzfrd7xj author: Abenavoli, Fabio Massimo title: Plastic Surgery in the Age of Coronavirus date: 2020-06-16 words: 2981.0 sentences: 159.0 pages: flesch: 55.0 cache: ./cache/cord-315641-bzfrd7xj.txt txt: ./txt/cord-315641-bzfrd7xj.txt summary: [24] [25] [26] The ability of the Chinese authorities to build hospital facilities for infected patients within a very short time appeared to be a test of "strength." However, little attention was paid to the conclusions that should have been drawn about how to assist new patients during the emergency situation. Severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2), which results in a high percentage of infected patients, has been enormously difficult to manage. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study From SARS to COVID-19: a previously unknown SARS-related coronavirus (SARS-CoV-2) of pandemic potential infecting humans-call for a One Health approach 2019-nCoV (Wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness Isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-nCoV) outbreak abstract: nan url: https://doi.org/10.1097/gox.0000000000002957 doi: 10.1097/gox.0000000000002957 id: cord-033311-e5axxrm1 author: Abenza Abildúa, M.J. title: Myopathy associated with serious SARS-CoV-2 infection() date: 2020-10-07 words: 831.0 sentences: 63.0 pages: flesch: 49.0 cache: ./cache/cord-033311-e5axxrm1.txt txt: ./txt/cord-033311-e5axxrm1.txt summary: 1,2 Reports of neurological symptoms associated with the infection are increasingly frequent, and include cases of Guillain-Barré syndrome, stroke, intraparenchymal haemorrhage, and cerebral thrombosis. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] We present the case of a 45-year-old woman with no relevant history who was admitted to the ICU due to severe respiratory insufficiency secondary to bilateral pneumonia, with positive nasal swab PCR results for SARS-CoV-2; therefore, the patient met the World Health Organization criteria for COVID-19. The muscle study showed positive sharp waves at rest, reduced motor unit potential amplitude and duration, and no polyphasia, especially in the abductor digiti minimi and the tibialis anterior (Fig. 2) . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS-CoV2 infection: causality or coincidence? Guillain-Barré syndrome associated with SARS-CoV2 Patients with COVID-19 and neurological manifestations show indetectable SARS-CoV2 abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540193/ doi: 10.1016/j.nrleng.2020.07.004 id: cord-324856-hf969tav author: Abir, Tanvir title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys date: 2020-07-21 words: 4144.0 sentences: 221.0 pages: flesch: 53.0 cache: ./cache/cord-324856-hf969tav.txt txt: ./txt/cord-324856-hf969tav.txt summary: title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys Since the sheer illness of the whole country is sufficient to destroy the health care system, this current study is to examine changes of individual perception of risk for contracting SARS-Cov-2, and the awareness level in Bangladesh during the early and late lockdowns implemented by the government of Bangladesh. In this study, males who were worried about contracting SARS-Cov-2 were more likely to perceive themselves as being at high risk of contracting the infection, as well as those who did not quarantine themselves or only did so at the request of the public health officers. Moreover, in India, it was found that a higher level of knowledge on COVID-19 was associated with the high-risk perception of contracting the infection during the consistent lockdown period [28] . abstract: This study investigated the perception and awareness of risk among adult participants in Bangladesh about Coronavirus Disease 2019 (COVID-19). During the lockdown era in Bangladesh at two different time points, from 26−31 March 2020 (early lockdown) and 11−16 May 2020 (late lockdown), two self-administered online surveys were conducted on 1005 respondents (322 and 683 participants, respectively) via social media. To examine risk perception and knowledge-related factors towards COVID-19, univariate and multiple linear regression models were employed. Scores of mean knowledge (8.4 vs. 8.1, p = 0.022) and perception of risk (11.2 vs. 10.6, p < 0.001) differed significantly between early and late lockdown. There was a significant decrease in perceived risk scores for contracting SARS-Cov-2 [β = −0.85, 95%CI: −1.31, −0.39], while knowledge about SARS-Cov-2 decreased insignificantly [β = −0.22, 95%CI: −0.46, 0.03] in late lockdown compared with early lockdown period. Self-quarantine was a common factor linked to increased perceived risks and knowledge of SARS-Cov-2 during the lockdown period. Any effort to increase public awareness and comprehension of SARS-Cov-2 in Bangladesh will then offer preference to males, who did not practice self-quarantine and are less worried about the propagation of this kind of virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32708161/ doi: 10.3390/ijerph17145252 id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 words: 3707.0 sentences: 191.0 pages: flesch: 44.0 cache: ./cache/cord-347714-vxxhglx7.txt txt: ./txt/cord-347714-vxxhglx7.txt summary: (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach abstract: The COVID19 pandemic has resulted in 1,092,342 deaths as of 14th October 2020, indicating the urgent need for a vaccine. This study highlights novel protein sequences generated by shot gun sequencing protocols that could serve as potential antigens in the development of novel subunit vaccines and through a stringent inclusion criterion, we characterized these protein sequences and predicted their 3D structures. We found distinctly antigenic sequences from the SARS-CoV-2 that have led to identification of 4 proteins that demonstrate an advantageous binding with Human leukocyte antigen-1 molecules. Results show how previously unexplored proteins may serve as better candidates for subunit vaccine development due to their high stability and immunogenicity, reinforce by their HLA-1 binding propensities and low global binding energies. This study thus takes a unique approach towards furthering the development of vaccines by employing multiple consensus strategies involved in immuno-informatics technique. url: https://doi.org/10.1101/2020.10.14.339689 doi: 10.1101/2020.10.14.339689 id: cord-353523-gwud4bb7 author: Abobaker, Anis title: The Eye: A Possible New Route of Infection in COVID-19 date: 2020-07-27 words: 928.0 sentences: 63.0 pages: flesch: 53.0 cache: ./cache/cord-353523-gwud4bb7.txt txt: ./txt/cord-353523-gwud4bb7.txt summary: 1 This might indicate that the eye is not a potential target for coronaviruses; however, this does not rule out the possibility that the conjunctiva and the ocular mucous membrane could act as a port of entry to CoVs to the upper respiratory tract given the close anatomical proximity and the similar epithelial receptors. There is evidence that lack of eye protection in clinical settings increased the risk of infection of the severe acute respiratory disease (SARS) caused by SARS-CoV. The low frequency of conjunctivitis and corneal involvement in COVID-19 patients could be explained with the fact that the level of ACE2 expression in ocular tissues is much less compared with other organs, such as the lungs and kidneys. SARS-CoV-2 has been detected by PCR in conjunctival swabs taken from COVID-19 patients with conjunctivitis as well as patients without ocular LETTER TO THE EDITOR manifestations. SARS-CoV-2 in the ocular surface of COVID-19 patients abstract: nan url: https://doi.org/10.1017/dmp.2020.270 doi: 10.1017/dmp.2020.270 id: cord-284398-rhfwbyav author: Aboubakr, Hamada A. title: Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date: 2020-07-14 words: 6425.0 sentences: 341.0 pages: flesch: 54.0 cache: ./cache/cord-284398-rhfwbyav.txt txt: ./txt/cord-284398-rhfwbyav.txt summary: In another study, aerosolized SARS-CoV-2 retained its infectivity for a period of 16h at room temperature and the authors concluded that the virus can be considered as an airborne pathogen (Fears et al., 2020 and was infectious after 72 hr of aerosolization (Ijaz, Brunner, Sattar, Nair, & Johnson-Lussenburg, 1985) . In the first study, SARS-CoV-2 retained its infectivity for 4 days but was completely decayed after 7 days on plastic surface at room temperature and 65% RH (Chin et al., 2020) . Although this study reported longer virus survival, it has been shown that the survivability of SARS-CoV-1 on plastic surface is drastically affected by increases in temperature and RH as described below. In another study, a this virus with a higher initial load (5.5 log TCID 50 ) retained its infectivity for 4 days and was completely inactivated after 7 days on stainless steel at room temperature and RH of 65% (Chin et al., 2020) . abstract: Although the unprecedented efforts the world has been taking to control the spread of the human coronavirus disease (COVID‐19) and its causative aetiology [severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)], the number of confirmed cases has been increasing drastically. Therefore, there is an urgent need for devising more efficient preventive measures, to limit the spread of the infection until an effective treatment or vaccine is available. The preventive measures depend mainly on the understanding of the transmission routes of this virus, its environmental stability, and its persistence on common touch surfaces. Due to the very limited knowledge about SARS‐CoV‐2, we can speculate its stability in the light of previous studies conducted on other human and animal coronaviruses. In this review, we present the available data on the stability of coronaviruses (CoVs), including SARS‐CoV‐2, from previous reports to help understand its environmental survival. According to available data, possible airborne transmission of SARS‐CoV‐2 has been suggested. SARS‐CoV‐2 and other human and animal CoVs have remarkably short persistence on copper, latex and surfaces with low porosity as compared to other surfaces like stainless steel, plastics, glass and highly porous fabrics. It has also been reported that SARS‐CoV‐2 is associated with diarrhoea and that it is shed in the faeces of COVID‐19 patients. Some CoVs show persistence in human excrement, sewage and waters for a few days. These findings suggest a possible risk of faecal–oral, foodborne and waterborne transmission of SARS‐CoV‐2 in developing countries that often use sewage‐polluted waters in irrigation and have poor water treatment systems. CoVs survive longer in the environment at lower temperatures and lower relative humidity. It has been suggested that large numbers of COVID‐19 cases are associated with cold and dry climates in temperate regions of the world and that seasonality of the virus spread is suspected. url: https://doi.org/10.1111/tbed.13707 doi: 10.1111/tbed.13707 id: cord-340687-99ad1rwq author: Abourida, Yassamine title: Management of Severe COVID-19 in Pregnancy date: 2020-07-27 words: 2527.0 sentences: 143.0 pages: flesch: 46.0 cache: ./cache/cord-340687-99ad1rwq.txt txt: ./txt/cord-340687-99ad1rwq.txt summary: The scarcity of data concerning pregnant patients gravely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) makes their management difficult, as most of the reported cases in the literature present mild pneumonia symptoms. Herein, we outline a case of severe COVID-19 infection in a pregnant woman abruptly rupturing her membranes and undergoing cesarean delivery. Herein, we report the case of a healthy parturient infected with SARS-CoV-2 in her third trimester, whose condition deteriorated leading to premature rupture of membranes, a premature birth via a caesarian delivery, and neonatal death. It is noteworthy that recent reports highlighted elevated SARS-CoV-2 antibody levels (IgM and IgG) and abnormal cytokine test results 2 hours after birth in a neonate born to a mother with COVID-19 via a caesarian delivery, whereas RT-PCR tests on nasopharyngeal swabs taken were negative [20] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn abstract: The scarcity of data concerning pregnant patients gravely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) makes their management difficult, as most of the reported cases in the literature present mild pneumonia symptoms. The core problem is laying out evidence on coronavirus's implications on pregnancy and delivery, as well as vertical transmission and neonatal mortality. A healthy 30-year-old pregnant woman, gravida 6, para 4, at 31 weeks of gestation, presented severe pneumonia symptoms promptly complicated with premature rupture of membranes (PROM). A nasopharyngeal swab returned positive for SARS-CoV-2 using reverse transcription polymerase chain reactions (RT-PCR). The parturient underwent a cesarean delivery. This paper is an attempt to outline management of the critical condition of COVID-19 during pregnancy. url: https://doi.org/10.1155/2020/8852816 doi: 10.1155/2020/8852816 id: cord-264915-g5ar0pwb author: Abrams, Rory M.C. title: Severe rapidly progressive Guillain-Barré syndrome in the setting of acute COVID-19 disease date: 2020-07-27 words: 1596.0 sentences: 88.0 pages: flesch: 41.0 cache: ./cache/cord-264915-g5ar0pwb.txt txt: ./txt/cord-264915-g5ar0pwb.txt summary: There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS). We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss diagnostic and management issues and complications that may warrant special consideration in similar patients. There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS) (Guidon and Amato 2020) . We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss management dilemmas that may warrant special attention in similar patients. abstract: There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS). It is currently unknown whether concomitant SARS-CoV-2 infection and GBS are pathophysiologically related, what biomarkers are useful for diagnosis, and what is the optimal treatment given the medical comorbidities, complications, and simultaneous infection. We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss diagnostic and management issues and complications that may warrant special consideration in similar patients. url: https://doi.org/10.1007/s13365-020-00884-7 doi: 10.1007/s13365-020-00884-7 id: cord-331790-0w0pjjg1 author: Abu Jawdeh, Bassam G. title: COVID-19 in Kidney Transplantation: Outcomes, Immunosuppression Management and Operational Challenges date: 2020-07-17 words: 3057.0 sentences: 204.0 pages: flesch: 47.0 cache: ./cache/cord-331790-0w0pjjg1.txt txt: ./txt/cord-331790-0w0pjjg1.txt summary: This review summarizes the published COVID-19 literature as it relates to outcomes and immunosuppression management in kidney transplant recipients. These multiple studies have elucidated that COVID-19 is a systemic disease that often manifests with gastrointestinal (GI) symptoms, liver injury, cardiac involvement, encephalitis, atypical stroke, acute kidney injury (AKI) in addition to endothelial cell injury and coagulopathy -the likely mediators of multi-organ involvement (3) (4) (5) (6) (7) (8) . In a 36-patient study, the median age was 60 years, 72% were male, 39% were African American and 75% received deceased-donor kidney transplants (DDKT)(9). Notably, the Columbia transplant program adopts an early steroid withdrawal strategy, however their sample was enriched with patients on prednisone maintenance (67%) which confirms the plausible role of enhanced immunosuppression as a susceptibility factor. abstract: Abstract The Coronavirus disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2, has led to the death of hundreds of thousands of people worldwide. If infected, older individuals and those with diabetes, hypertension, cardiovascular disease and compromised immune systems are at higher risk for unfavorable outcomes. These comorbidities are prevalent in patients with kidney disease, hence the significant burden of COVID-19 on kidney transplant programs. Multiple case series of kidney transplant recipients with COVID-19 have shown increased mortality compared to non-transplant patients. To-date, we do not have high-level evidence to inform immunosuppression minimization strategies in infected transplant recipients. Most centers however have adopted early anti-metabolite withdrawal in addition to other interventions. This review summarizes the published COVID-19 literature as it relates to outcomes and immunosuppression management in kidney transplant recipients. It also discusses challenges pertaining to pre-transplant evaluation and wait-listed patients. url: https://api.elsevier.com/content/article/pii/S1548559520301130 doi: 10.1053/j.ackd.2020.07.004 id: cord-287459-k9x3z2h1 author: Abu-Farha, Mohamed title: The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date: 2020-05-17 words: 4822.0 sentences: 253.0 pages: flesch: 41.0 cache: ./cache/cord-287459-k9x3z2h1.txt txt: ./txt/cord-287459-k9x3z2h1.txt summary: Since lipids play a crucial function in the viral life cycle, we asked whether drugs targeting lipid metabolism, such as statins, can be utilized against SARS-CoV-2 and other viruses. Similarly, increased expression of age-dependent phospholipase A2 group IID (PLA2G2D), an enzyme that usually contributes to anti-inflammatory/pro-resolving lipid mediator expression, resulted in worsened outcomes in aged mice infected with SARS-CoV, suggesting that inhibition of such factor could represent a potential therapeutic option [36] . Of high relevance to this review and the ongoing COVID-19 pandemic is the role of lipid rafts in viral entry into the host cells. Taken together, these studies suggest a beneficial impact for statins and potentially other lipid-lowering drugs such as PCSK9 inhibitors for treatment of COVID-19, especially that of the most severely infected people which are suffering from cardiovascular disease and diabetes [55] . abstract: The current Coronavirus disease 2019 or COVID-19 pandemic has infected over two million people and resulted in the death of over one hundred thousand people at the time of writing this review. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Even though multiple vaccines and treatments are under development so far, the disease is only slowing down under extreme social distancing measures that are difficult to maintain. SARS-COV-2 is an enveloped virus that is surrounded by a lipid bilayer. Lipids are fundamental cell components that play various biological roles ranging from being a structural building block to a signaling molecule as well as a central energy store. The role lipids play in viral infection involves the fusion of the viral membrane to the host cell, viral replication, and viral endocytosis and exocytosis. Since lipids play a crucial function in the viral life cycle, we asked whether drugs targeting lipid metabolism, such as statins, can be utilized against SARS-CoV-2 and other viruses. In this review, we discuss the role of lipid metabolism in viral infection as well as the possibility of targeting lipid metabolism to interfere with the viral life cycle. url: https://doi.org/10.3390/ijms21103544 doi: 10.3390/ijms21103544 id: cord-262090-nbxzyjvf author: Acharya, Arpan title: SARS-CoV-2 Infection Leads to Neurological Dysfunction date: 2020-05-23 words: 3434.0 sentences: 213.0 pages: flesch: 50.0 cache: ./cache/cord-262090-nbxzyjvf.txt txt: ./txt/cord-262090-nbxzyjvf.txt summary: A number of neurological disease complications have been seen following infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Such central nervous system (CNS) signs and symptoms linked to laboratory-confirmed SARS-CoV-2 infection is often life threatening. As cardio-respiratory impairments could reflect brainstem dysfunction it may, in part, be responsible for ARDS as frequently occurs as a cause of COVID-19 mortality among SARS-CoV-2 infected patients (Netland et al. As the impaired ability to smell and test are a common manifestation of respiratory neurotropic viral invasion of the olfactory system, we suspect there is a possibility that SARS-CoV-2 can infect the olfactory system and may enter the CNS using the olfactory pathway. A retrospective study substantiates this, wherein, 36.4% of patients out of 214 confirmed cases of SARS-CoV-2 have been documented to present with varying degree of neurological manifestations that include skeletal muscle injury, delirium and acute cerebrovascular disease (Fig. 2) . abstract: A number of neurological disease complications have been seen following infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While most person with COVID-19 respiratory disease demonstrate headache, nausea and vomiting, up to 40% present also experience dizziness, confusion, cerebrovascular disease, muscle pain, ataxia and seizures. Loss of taste and smell, defects in visual acuity and pain occur in parallel. Such central nervous system (CNS) signs and symptoms linked to laboratory-confirmed SARS-CoV-2 infection is often life threatening. Health care providers currently evaluating patients with neurologic symptoms need consider COVID-19 in any differential diagnosis. These considerations will facilitate prompt testing, isolation and prevention of viral transmission speeding best clinical outcomes. [Figure: see text] url: https://doi.org/10.1007/s11481-020-09924-9 doi: 10.1007/s11481-020-09924-9 id: cord-276350-lcl9jn35 author: Acharya, Dhiraj title: Dysregulation of type I interferon responses in COVID-19 date: 2020-05-26 words: 1608.0 sentences: 83.0 pages: flesch: 40.0 cache: ./cache/cord-276350-lcl9jn35.txt txt: ./txt/cord-276350-lcl9jn35.txt summary: In a mouse model of SARS-CoV infection, local IFN responses in the lungs were delayed relative to peak viral replication, which impeded virus clearance and was associated with the development of CRS 5 . By contrast, IFNAR inhibition enhanced the recruitment of neutrophils to the lungs in MERS-CoV-infected mice, leading to elevated production of pro-inflammatory cytokines 6 . While patients with severe COVID-19 showed profound depletion and functional exhaustion of NK cells 8 , it is unclear whether this NK cell dysfunction is due to dysregulation of IFN responses. It is thus tempting to speculate that the deficient or dysregulated IFN responses elicited by SARS-CoV-2 infection may influence the generation of T reg cells during the recovery phase of COVID-19. Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice abstract: Infection with SARS-CoV-2 can lead to excessive production of pro-inflammatory cytokines, but the production of type I interferons, which are key antiviral mediators, is reportedly blunted. Here, we discuss how imbalanced interferon responses may contribute to the pathology of COVID-19. url: https://doi.org/10.1038/s41577-020-0346-x doi: 10.1038/s41577-020-0346-x id: cord-315982-iuez41zj author: Achdout, Hagit title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date: 2020-10-30 words: 4103.0 sentences: 223.0 pages: flesch: 54.0 cache: ./cache/cord-315982-iuez41zj.txt txt: ./txt/cord-315982-iuez41zj.txt summary: title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. The COVID Moonshot project has focused on progressing early fragment-screening results into potent compounds with activity against both the main protease and the virus. The rationales for each design include docking-based approaches, by-eye structure-based designs, machine learning approaches, crawling of the past literature on SARS and MERS compounds, and other general medicinal-chemistry insights that can be visualised at https://postera.ai/covid. At 24 h post-seeding, cell culture medium was discarded, cells were washed twice with PBS and infected with SARS-CoV-2 at an MOI of 0.01 in the presence of six concentrations of the inhibitors (25 M -0.06 M). abstract: Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. Our approach uniquely combines crowdsourced medicinal chemistry insights with high throughput crystallography, exascale computational chemistry infrastructure for simulations, and machine learning in triaging designs and predicting synthetic routes. This manuscript describes our methodologies leading to both covalent and non-covalent inhibitors displaying protease IC50 values under 150 nM and viral inhibition under 5 uM in multiple different viral replication assays. Furthermore, we provide over 200 crystal structures of fragment-like and lead-like molecules in complex with the main protease. Over 1000 synthesized and ordered compounds are also reported with the corresponding activity in Mpro enzymatic assays using two different experimental setups. The data referenced in this document will be continually updated to reflect the current experimental progress of the COVID Moonshot project, and serves as a citable reference for ensuing publications. All of the generated data is open to other researchers who may find it of use. url: https://doi.org/10.1101/2020.10.29.339317 doi: 10.1101/2020.10.29.339317 id: cord-266307-w56rii2p author: Acheampong, Desmond Omane title: Male Predisposition to Severe COVID-19: Review of Evidence and Potential Therapeutic Prospects date: 2020-09-09 words: 8837.0 sentences: 467.0 pages: flesch: 46.0 cache: ./cache/cord-266307-w56rii2p.txt txt: ./txt/cord-266307-w56rii2p.txt summary: The sex hormones, estrogens and androgens which exist in varying functional levels respectively in females and males are cited as the underlying cause for the differential immune response to COVID-19. In this review efforts are made to expand understanding and explain the possible roles of the immune system, the sex hormones and the angiotensin-converting enzyme (ACE) systems in male bias to severe COVID-19. Hence, females known for producing high-level estrogen will be better protected against infections including COVID-19 compared to their male counterparts. Hence, women are better protected against viral infections and for that matter the severe COVID-19 due to the over-expression of TLR7 in females compared to their male counterparts. This explains J o u r n a l P r e -p r o o f why prolong inflammation is very common in males infected with SARS-CoV-2 virus compared to females, and could be one of the factors that promote severe COVID-19 in men. abstract: The severe form of COVID-19 has significant sex disparities, with high fatalities commonly reported among males than females. The incidence of COVID-19 has also been higher in males compared with their female counterparts. This trend could be attributed to a better responsive and robust immune system in females. Cytokine storm is one of the pathophysiological features of severe COVID-19, and it occurs as a result of over-activation of immune cells leading to severe inflammation and tissue damage. However, it is well modulated in females compared to their male counterparts. Severe inflammation in males is reported to facilitate progression of mild to severe COVID-19. The sex hormones, estrogens and androgens which exist in varying functional levels respectively in females and males are cited as the underlying cause for the differential immune response to COVID-19. Evidence abounds that immune system modulation by estrogen protect females from severe inflammation and for that matter severe COVID-19. On the contrary, androgen has been implicated in over-activation of immune cells, cytokine storm and the attendant severe inflammation, which perhaps predispose males to severe COVID-19. In this review efforts are made to expand understanding and explain the possible roles of the immune system, the sex hormones and the angiotensin-converting enzyme (ACE) systems in male bias to severe COVID-19. Also, this review explores possible therapeutic avenues including androgen deprivation therapy (ADT), estrogen-based therapy, and ACE inhibitors for consideration in the fight against COVID-19. url: https://api.elsevier.com/content/article/pii/S0753332220309410 doi: 10.1016/j.biopha.2020.110748 id: cord-280819-z6ucnwk0 author: Achilonu, Ikechukwu title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach date: 2020-09-02 words: 5411.0 sentences: 301.0 pages: flesch: 52.0 cache: ./cache/cord-280819-z6ucnwk0.txt txt: ./txt/cord-280819-z6ucnwk0.txt summary: title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach The SARS-CoV-2 main protease (M(pro)) is an attractive target towards discovery of drugs to treat COVID-19 because of its key role in virus replication. Using 6Y2G and the prior knowledge that protease inhibitors could eradicate COVID-19, we designed a computational study aimed at identifying FDA-approved drugs that could interact with M(pro). We used HTVS, induced-fit ligand docking and molecular dynamics simulation studies to identify additional classes of plausible FDA-approved drugs as possible drug candidate to treat COVID-19. In conclusion, we have used a computational approach which includes HTVS, IFD, MM/GBSA free binding energy calculations and MD simulation to study potential drug candidates for COVID-19. Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach Ikechukwu Achilonu 1 * abstract: The SARS-CoV-2 main protease (M(pro)) is an attractive target towards discovery of drugs to treat COVID-19 because of its key role in virus replication. The atomic structure of M(pro) in complex with an α-ketoamide inhibitor (Lig13b) is available (PDB ID:6Y2G). Using 6Y2G and the prior knowledge that protease inhibitors could eradicate COVID-19, we designed a computational study aimed at identifying FDA-approved drugs that could interact with M(pro). We searched the DrugBank and PubChem for analogs and built a virtual library containing ∼33000 conformers. Using high-throughput virtual screening and ligand docking, we identified Isavuconazonium, a ketoamide inhibitor (α-KI) and Pentagastrin as the top three molecules (Lig13b as the benchmark) based on docking energy. The ΔG(bind) of Lig13b, Isavuconazonium, α-KI, Pentagastrin was -28.1, -45.7, -44.7, -34.8 kcal/mol, respectively. Molecular dynamics simulation revealed that these ligands are stable within the M(pro) active site. Binding of these ligands is driven by a variety of non-bonded interaction, including polar bonds, H-bonds, van der Waals and salt bridges. The overall conformational dynamics of the complexed-M(pro) was slightly altered relative to apo-M(pro). This study demonstrates that three distinct classes molecules, Isavuconazonium (triazole), α-KI (ketoamide) and Pentagastrin (peptide) could serve as potential drugs to treat patients with COVID-19. url: https://doi.org/10.1016/j.jmgm.2020.107730 doi: 10.1016/j.jmgm.2020.107730 id: cord-293304-kakxmc14 author: Achutha, A. S. title: Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors date: 2020-09-22 words: 5877.0 sentences: 369.0 pages: flesch: 58.0 cache: ./cache/cord-293304-kakxmc14.txt txt: ./txt/cord-293304-kakxmc14.txt summary: The interactions with the active site residues especially with Cys145 and His41, which are involved in catalytic diad for proteolysis, make these compounds potent main protease inhibitors. Molecular docking studies with the 3CL pro protein were performed to analyze the drug likeness as well as to correlate the binding energy of the docked complex with various physicochemical properties of the active molecules, which will aid in the design of new anti-COVID-19 medicatives. By using the formulated regression Model 2, we predicted the binding energy of some primaquine analogs obtained from the literature and PubChem database and then carried out their molecular docking studies on 3CL pro target to check the inhibitory potency of the ligands, given in Table 4 . Thirty molecules that showed lower binding energies were subjected to molecular docking analysis to identify the potent 3CL pro inhibitors (Supplementary Figure S5) . abstract: [Image: see text] Corona virus disease (COVID-19) is a dangerous disease rapidly spreading all over the world today. Currently there are no treatment options for it. Drug repurposing studies explored the potency of antimalarial drugs, chloroquine and hydroxychloroquine, against SARS-CoV-2 virus. These drugs can inhibit the viral protease, called chymotrypsin-like cysteine protease, also known as Main protease (3CL(pro)); hence, we studied the binding efficiencies of 4-aminoquinoline and 8-aminoquinoline analogs of chloroquine. Six compounds furnished better binding energies than chloroquine and hydroxychloroquine. The interactions with the active site residues especially with Cys145 and His41, which are involved in catalytic diad for proteolysis, make these compounds potent main protease inhibitors. A regression model correlating binding energy and the molecular descriptors for chloroquine analogs was generated with R(2) = 0.9039 and Q(2) = 0.8848. This model was used to screen new analogs of primaquine and molecules from the Asinex compound library. The docking and regression analysis showed these analogs to be more potent inhibitors of 3CL(pro) than hydroxychloroquine and primaquine. The molecular dynamic simulations of the hits were carried out to determine the binding stabilities. Finally, we propose four compounds that show drug likeness toward SARS-CoV-2 that can be further validated through in vitro and in vivo studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32960061/ doi: 10.1021/acs.jproteome.0c00683 id: cord-292050-x3isowrt author: Ackerman, Emily E. title: Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning date: 2020-09-26 words: 6948.0 sentences: 384.0 pages: flesch: 44.0 cache: ./cache/cord-292050-x3isowrt.txt txt: ./txt/cord-292050-x3isowrt.txt summary: Based on network topology and controllability, 16 proteins involved in translation, cellular transport, cellular stress, and host immune response are predicted as regulators of the SARS-CoV-2 infected cell. Screenings of experimentally verified SARS-CoV-2 interacting host proteins [7] have elucidated key infection mechanisms which, when compared to drug databases, have predicted a range of possible targets for repurposing. To assess whether the robust controllability classifications of the driver and virus interacting proteins are a result of the network''s connectivity structure, a randomization analysis was performed as developed in previous work [11] . The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. abstract: In a short time, the COVID-19 pandemic has left the world with over 25 million cases and staggering death tolls that are still rising. Treatments for SARS-CoV-2 infection are desperately needed as there are currently no approved drug therapies. With limited knowledge of viral mechanisms, a network controllability method of prioritizing existing drugs for repurposing efforts is optimal for quickly moving through the drug approval pipeline using limited, available, virus-specific data. Based on network topology and controllability, 16 proteins involved in translation, cellular transport, cellular stress, and host immune response are predicted as regulators of the SARS-CoV-2 infected cell. Of the 16, eight are prioritized as possible drug targets where two, PVR and SCARB1, are previously unexplored. Known compounds targeting these genes are suggested for viral inhibition study. Prioritized proteins in agreement with previous analysis and viral inhibition studies verify the ability of network controllability to predict biologically relevant candidates. url: https://www.ncbi.nlm.nih.gov/pubmed/32993136/ doi: 10.3390/v12101087 id: cord-271915-nvilxnzl author: Adachi, D. title: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date: 2004-12-01 words: 3591.0 sentences: 152.0 pages: flesch: 54.0 cache: ./cache/cord-271915-nvilxnzl.txt txt: ./txt/cord-271915-nvilxnzl.txt summary: The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada. This single-tube RT-PCR is based on consensus primers targeting conserved regions of coronavirus genome sequences and allows for the detection and species identification of several coronaviruses including SARS-HCoV, with high analytical sensitivity. Aliquots of a 10-fold serial RNA dilution prepared from a lung biopsy sample of a patient with SARS (see Section 2) were used to compare our assay with the RealArt HPA coronavirus RT-PCR (Artus GmbH). abstract: The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada. url: https://www.sciencedirect.com/science/article/pii/S0166093404002162 doi: 10.1016/j.jviromet.2004.07.008 id: cord-271419-v6dfel3l author: Adachi, Shun title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 words: 1211.0 sentences: 77.0 pages: flesch: 51.0 cache: ./cache/cord-271419-v6dfel3l.txt txt: ./txt/cord-271419-v6dfel3l.txt summary: Among viruses, some coronaviruses (CoVs) are notorious for causing the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The said article has successfully predicted today''s COVID-19 outbreak by pointing out that novel pathogenic variants will readily emerge from very diversified severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) of the bat origin through their close coexistence and high genetic recombination ability (Figure 1) . Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. Thus, to consider the origin of new pathogens and the prevention of their transmission to humans, and control of the viruses, not only studies on SARS-CoV, MERS-CoV, and SARS-CoV-2, but also those on their relatives SARSr-CoVs and MERSr-CoVs are recommendable for bats tracked for the ecology and evolution. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32373134/ doi: 10.3389/fimmu.2020.00811 id: cord-296331-i4hyzqcv author: Adapa, Sreedhar title: COVID-19 Pandemic Causing Acute Kidney Injury and Impact on Patients With Chronic Kidney Disease and Renal Transplantation date: 2020-06-04 words: 5086.0 sentences: 289.0 pages: flesch: 49.0 cache: ./cache/cord-296331-i4hyzqcv.txt txt: ./txt/cord-296331-i4hyzqcv.txt summary: COVID-19 infection causes acute kidney injury (AKI) and is an independent risk factor for mortality. The impact of COVID-19 infection on chronic kidney disease (CKD) and renal transplant patients is also discussed in the manuscript. Acute kidney injury (AKI) was seen in 5-15% of the cases infected with SARS-CoV and MERS-CoV, and had a higher mortality rate of 60-90% as per the literature [12] . We summarized the finding from multiple studies including patient characteristics, co-morbidities, incidence of AKI in general as well as ICU/severely ill patients, number of patients requiring continuous renal replacement therapy (CRRT), extracorporeal membrane oxygenation (ECMO) and mortality in Table 2 [9-11, 13, 19, 22-24, 26-32] . Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Coronavirus disease 2019 (COVID-19) caused by 2019 novel coronavirus (2019-nCoV) has caused significant mortality and has been declared as a global pandemic by the World Health Organization. The infection mainly presents as fever, cough, and breathing difficulty, and few patients develop very severe symptoms. The purpose of this review is to analyze the impact of the virus on the kidney. COVID-19 infection causes acute kidney injury (AKI) and is an independent risk factor for mortality. Angiotensin-converting enzyme 2 (ACE2) receptors, direct viral damage, and immune-mediated damage play important roles in the pathogenesis. AKI in COVID-19 infection could be from the synergistic effect of virus-induced direct cytotropic effect and cytokine-induced systemic inflammatory response. AKI caused in the viral infection has been analyzed from the available epidemiological studies. The proportion of patients developing AKI is significantly higher when they develop severe disease. Continuous renal replacement therapy (CRRT) is the most used blood purification technique when needed. The impact of COVID-19 infection on chronic kidney disease (CKD) and renal transplant patients is also discussed in the manuscript. No vaccine has been developed against the 2019-nCoV virus to date. The critical aspect of management is supportive care. Several investigative drugs have been studied, drugs approved for other indications have been used, and several clinical trials are underway across the globe. Recently remdesivir has received emergency use authorization by the Food and Drug Administration (FDA) in the USA for use in patients hospitalized with COVID-19. Prevention of the infection holds the key to management. The patients with underlying kidney problems and renal transplant patients are vulnerable to developing COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32587651/ doi: 10.14740/jocmr4200 id: cord-027649-6xn9swsq author: Addetia, Amin title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates date: 2020-06-23 words: 449.0 sentences: 47.0 pages: flesch: 52.0 cache: ./cache/cord-027649-6xn9swsq.txt txt: ./txt/cord-027649-6xn9swsq.txt summary: title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates Sequence reads were trimmed using Trimommatic v0.38 (5) , aligned to the SARS-CoV-2 reference genome (NC_045512.2) using BBMap (https://sourceforge.net/projects/bbmap/), trimmed of synthetic PCR primers using Primerclip (https://github.com/swiftbiosciences/primerclip) if appropriate, and visualized in Geneious v11.1.4 (6) . Interestingly, ORF6 of SARS-CoV-2 interacts with the mRNA export proteins NUP98 and RAE1, and may inhibit cellular translation (10) . We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization An 81 nucleotide deletion in SARS-CoV Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein A SARS-CoV-2 protein interaction map reveals targets for drug repurposing A 227-nucleotide deletion beginning at nt 27,524 was identified in b) WA-UW-5812 and resulted in the fusion of ORF7a and ORF7b. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309833/ doi: 10.1016/j.jcv.2020.104523 id: cord-336022-b2fwktld author: Addetia, Amin title: Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate date: 2020-08-14 words: 3979.0 sentences: 263.0 pages: flesch: 56.0 cache: ./cache/cord-336022-b2fwktld.txt txt: ./txt/cord-336022-b2fwktld.txt summary: Only three 34 crewmembers tested seropositive prior to the boat''s departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Only three 34 crewmembers tested seropositive prior to the boat''s departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Prior to the ship''s departure, crewmembers were screened for active SARS-CoV-2 182 infection by RT-PCR, or for serological evidence of prior or ongoing infection using the 183 Abbott Architect assay which detects antibodies against the viral nucleoprotein (N). . https://doi.org/10.1101/2020.08.13.20173161 doi: medRxiv preprint observed in humans who have been infected with SARS-CoV-2 within the previous few 198 months (29, 34, 35) . . https://doi.org/10.1101 pre-departure Abbot Architect anti-N serological screening, since only individuals 335 positive in that screening were subjected to additional serological assays for anti-spike 336 and neutralizing antibodies. abstract: The development of vaccines against SARS-CoV-2 would be greatly facilitated by the identification of immunological correlates of protection in humans. However, to date, studies on protective immunity have only been performed in animal models and correlates of protection have not been established in humans. Here, we describe an outbreak of SARS-CoV-2 on a fishing vessel associated with a high attack rate. Predeparture serological and viral RT-PCR testing along with repeat testing after return to shore was available for 120 of the 122 persons on board over a median follow-up of 32.5 days (range 18.8 to 50.5 days). A total of 104 individuals had an RT-PCR positive viral test with Ct <35 or seroconverted during the follow-up period, yielding an attack rate on board of 85.2% (104/122 individuals). Metagenomic sequencing of 39 viral genomes suggested the outbreak originated largely from a single viral clade. Only three crewmembers tested seropositive prior to the boat’s departure in initial serological screening and also had neutralizing and spike-reactive antibodies in follow-up assays. None of these crewmembers with neutralizing antibody titers showed evidence of bona fide viral infection or experienced any symptoms during the viral outbreak. Therefore, the presence of neutralizing antibodies from prior infection was significantly associated with protection against re-infection (Fisher’s exact test, p=0.002). url: https://doi.org/10.1101/2020.08.13.20173161 doi: 10.1101/2020.08.13.20173161 id: cord-336585-19vwpjkt author: Adem, Şevki title: Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19 date: 2020-08-22 words: 3578.0 sentences: 210.0 pages: flesch: 46.0 cache: ./cache/cord-336585-19vwpjkt.txt txt: ./txt/cord-336585-19vwpjkt.txt summary: Based upon these results, we have screened a library of caffeic acid derivatives (CAFDs) (Figure 1 ) for the identification of novel natural anti-COVID-19 compounds against various SARS-CoV-2 drug targets including COVID-19 M pro (6LU7), SARS-CoV-2 S2 subunit (6LXT), Nsp15 endoribonuclease (6VWW), SARS-CoV-2 spike ectodomain open state structure (6VYB), and SARS-CoV-2 spike closed state glycoprotein structure (6VXX). Our results present in silico-based identification of khainaoside C, 6-O-Caffeoylarbutin, khainaoside B, khainaoside C and vitexfolin A as potent modulators of COVID-19 M pro , Nsp15, coronavirus fusion protein, spike open state and closed state structure respectively. Based on these in-silico results, khainaoside C, calceolarioside B, vitexfolin A, calceolarioside C and scrophuloside B exhibited best binding potential with COVID-19 virus Figure 2B represents residual wise van der Waals interactions, piNelfinavir which possess MolDock score of -148.413 The interactions of these compounds with amino acid residues of target protein are shown in Figure 3A . abstract: BACKGROUND: : SARS-CoV-2, an emerging strain of coronavirus, has affected millions of people from all the continents of world and received worldwide attention. This emerging health crisis calls for the urgent development of specific therapeutics against COVID-19 to potentially reduce the burden of this emerging pandemic. PURPOSE: : This study aims to evaluate the anti-viral efficacy of natural bioactive entities against COVID-19 via molecular docking and molecular dynamics simulation. METHODS: : A library of 27 caffeic-acid derivatives was screened against 5 proteins of SARS-CoV-2 by using Molegro Virtual Docker 7 to obtain the binding energies and interactions between compounds and SARS-CoV-2 proteins. ADME properties and toxicity profiles were investigated via www.swissadme.ch web tools and Toxtree respectively. Molecular dynamics simulation was performed to determine the stability of the lead-protein interactions. RESULTS: : Our obtained results has uncovered khainaoside C, 6-O-Caffeoylarbutin, khainaoside B, khainaoside C and vitexfolin A as potent modulators of COVID-19 possessing more binding energies than nelfinavir against COVID-19 M(pro), Nsp15, SARS-CoV-2 spike S2 subunit, spike open state and closed state structure respectively. While Calceolarioside B was identified as pan inhibitor, showing strong molecular interactions with all proteins except SARS-CoV-2 spike glycoprotein closed state. The results are supported by 20 ns molecular dynamics simulations of the best complexes. CONCLUSION: : This study will hopefully pave a way for development of phytonutrients-based antiviral therapeutic for treatment or prevention of COVID-19 and further studies are recommended to evaluate the antiviral effects of these phytochemicals against SARS-CoV-2 in in vitro and in vivo models. url: https://api.elsevier.com/content/article/pii/S0944711320301422 doi: 10.1016/j.phymed.2020.153310 id: cord-315193-z6v6s46n author: Adhikari, Nilanjan title: Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date: 2017-07-14 words: 9954.0 sentences: 585.0 pages: flesch: 59.0 cache: ./cache/cord-315193-z6v6s46n.txt txt: ./txt/cord-315193-z6v6s46n.txt summary: In the present report, quantitative structure-activity relationships (QSARs) techniques have been explored to understand the relation between the SARS-CoV 3CL pro and HRV 3C pro enzyme inhibitory activity with the physicochemical and structural properties of these inhibitors developed till now. (2008) reported some cinanserin analogs as SARS-CoV 3CL pro inhibitors (Table 11 .18), for which the QSAR model obtained was as shown by Eq. (2013b) reported a series of dipeptide-type SARS-CoV 3CL protease inhibitors (Table 11 .27) whose activity was shown to be controlled by the molar refractivity (CMR) and the polar volume (Pol Vol) of the compounds [Eq. QSAR models exhibited that the physicochemical parameters, such as dipole moment, PSA, polar volume, hydrophobicity, molar refractivity, SA, and molecular volume of the compounds play a crucial role in controlling both SARS-CoV 3CL pro and HRV 3C pro inhibitory activities. abstract: Severe acute respiratory syndrome (SARS), caused by SARS-coronavirus (SARS-CoV), is a dreadful infection worldwide having economic and medical importance and a global threat for health. It was turned into an epidemic in South China followed by a chain of infections across three generations. A number of pathogeneses in human may occur due to the virus. This infection has not been taken into account before the SARS outbreak, and still it is a neglected one. Therefore, there is an urgent need to develop small molecule antivirals to combat the SARS-CoV. No vaccines are available till date though a number of SARS-CoV 3C-like and 3C protease inhibitors were reported. In this chapter, quantitative structure–activity relationship technique is used for development of anti-SARS and anti-HRV drugs and outcome discussed in details. This approach may be a useful strategy to design novel and potential anti-SARS drugs to combat these dreadful viral diseases. url: https://api.elsevier.com/content/article/pii/B9780128097120000113 doi: 10.1016/b978-0-12-809712-0.00011-3 id: cord-341701-zropd3mo author: Adhikari, Subash title: A high-stringency blueprint of the human proteome date: 2020-10-16 words: 10138.0 sentences: 533.0 pages: flesch: 33.0 cache: ./cache/cord-341701-zropd3mo.txt txt: ./txt/cord-341701-zropd3mo.txt summary: During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. • Be a focal point for life sciences researchers, pathologists, clinicians and industry communities seeking to translate and leverage proteomic and proteogenomic data to improve human health through: (i) greater understanding of the molecular mechanisms of common and rare diseases, (ii) identification of pathophysiological changes to generate disease and wellness diagnostic biomarkers, and (iii) development of new effective and safe personalized therapeutics. The HPP Ab Resource Pillar, ostensibly led by the Human Protein Atlas (HPA; www.proteinatlas.org), was initiated in 2003 and uses Ab-based strategies to analyse spatio-temporal aspects of the proteome 39 . Community encouragement to identify biological data that complement high-stringency MS strategies to accelerate discovery and understanding of human proteome PE2,3,4 missing proteins. abstract: The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP’s tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases. url: https://doi.org/10.1038/s41467-020-19045-9 doi: 10.1038/s41467-020-19045-9 id: cord-298693-x25r0gtt author: Advani, Sonali D. title: Are we forgetting the “universal” in universal masking? Current challenges and future solutions date: 2020-07-16 words: 844.0 sentences: 53.0 pages: flesch: 49.0 cache: ./cache/cord-298693-x25r0gtt.txt txt: ./txt/cord-298693-x25r0gtt.txt summary: Overall, HCP compliance with protective measures such as universal masking often correlates with the level of risk they perceive. Earlier this year, public health authorities pointed out a lack of evidence related to the use of universal masking by the general public to prevent acquisition of SARS-CoV-2. Inconsistent, contradictory and unclear advice from public health authorities has contributed to widespread confusion about the utility of universal masking in preventing the spread of SARS-COV-2 (response efficacy). COVID-19 fatigue, a term that describes drift in following preventative measures as this pandemic goes on, is an important cause of poor compliance with policies related to universal masking. Finally, we need clear, simple, and consistent messaging from public health authorities for successful implementation of universal masking policies. Our goal should be to focus on the simple message of universal masking to prevent the transmission of SARS-CoV-2. abstract: nan url: https://doi.org/10.1017/ice.2020.333 doi: 10.1017/ice.2020.333 id: cord-323596-dh7oh54z author: Advani, Sonali D. title: Assessing severe acute respiratory coronavirus virus 2 (SARS-CoV-2) preparedness in US community hospitals: A forgotten entity date: 2020-10-07 words: 1550.0 sentences: 88.0 pages: flesch: 46.0 cache: ./cache/cord-323596-dh7oh54z.txt txt: ./txt/cord-323596-dh7oh54z.txt summary: Several differences in hospital preparedness for SARS-CoV-2 emerged with respect to personal protective equipment conservation strategies, protocols related to testing, universal masking, and restarting elective procedures. Hence, we conducted a cross-sectional survey of SARS-CoV-2 preparedness among community hospitals in southeastern United States. The survey included 13 questions related to PPE availability, crisis capacity strategies to extend and reuse PPE, policies related to restarting surgeries, testing prior to elective surgery and prior to transfer to extended care facilities, universal masking, and daily screening of hospital staff. In addition, 80% of hospitals reported an adequate supply of N95 respirators, face shields, and googles, likely due to use of crisis capacity strategies to extend, reuse, and reprocess these PPE. We found several differences in community hospital preparedness for SARS-CoV-2 with respect to type of conservation strategies used to preserve PPE, protocols related to testing, masking, and restarting elective procedures. abstract: We performed a cross-sectional survey of infection preventionists in 60 US community hospitals between April 22 and May 8, 2020. Several differences in hospital preparedness for SARS-CoV-2 emerged with respect to personal protective equipment conservation strategies, protocols related to testing, universal masking, and restarting elective procedures. url: https://doi.org/10.1017/ice.2020.1238 doi: 10.1017/ice.2020.1238 id: cord-354762-3a3a3ku9 author: Afsar, Cigdem Usul title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES date: 2020-06-02 words: 987.0 sentences: 70.0 pages: flesch: 54.0 cache: ./cache/cord-354762-3a3a3ku9.txt txt: ./txt/cord-354762-3a3a3ku9.txt summary: title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES IFN is particularly expressed in epithelial cells and it is essential in skin and mucosal immunity (lung, intestines and reproductive tissues) of all African and Asian pangolin species (Choo and others, 2016) . IFN, like the other type I IFNs, might be responsible of decreased mortality in females because of its antiviral effects. The JAK/STAT pathway responds to type I IFN secreted from neighboring cells and SARS-CoV proteins have been shown to affect this pathway before (Frieman and Baric, 2008) . JAK-STAT signal blocking by baricitinib (a selective JAK1 and JAK2 inhibitor) produces an impairment of IFN-mediated antiviral response, with a potential facilitating effect on the evolution of SARS-CoV-2 infection. Interferon-epsilon protects the female reproductive tract from viral and bacterial infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32521376/ doi: 10.1016/j.jri.2020.103154 id: cord-253777-h8wy0coq author: Afshar, Hale title: Evolution and resolution of brain involvement associated with SARS- CoV2 infection: A close Clinical – Paraclinical follow up study of a case date: 2020-05-21 words: 1560.0 sentences: 85.0 pages: flesch: 46.0 cache: ./cache/cord-253777-h8wy0coq.txt txt: ./txt/cord-253777-h8wy0coq.txt summary: We report a para-infectious encephalitis patient with clinical, laboratory, and imaging findings during evolution and convalescence phase of coronavirus infection. Herein we report a case with clinical (including respiratory and neurological), laboratory, chest Computed Tomography and Brain Magnetic Resonance Imaging (B-MRI) findings during evolution and convalescence phase which can illuminate the natural history of similar cases. These results led to the diagnosis of para-infectious encephalitis associated with COVID-19 and treatment with IVIg continued to a total dosage of 3g/kg of body weight (250g total) which resulted in considerable improvement in consciousness, but discontinued because of headaches (day 28). Our patient before diagnosis of neurologic involvement had received IVIg (25 g/day for three days) as a part of treatment for COVID-19 severe pulmonary involvement; and after the CNS lesions were established, it was reinstituted and due to very good clinical and radiological response, we decided to continue IVIg therapy until complete recovery, unless there is a complication. abstract: The new severe acute respiratory syndrome- coronavirus 2 is reported to affect the nervous system. Among the reports of the various neurological manifestations, there are a few documented specific processes to explain the neurological signs. We report a para-infectious encephalitis patient with clinical, laboratory, and imaging findings during evolution and convalescence phase of coronavirus infection. This comprehensive overview can illuminate the natural history of similar cases. As the two previously reported cases of encephalitis associated with this virus were not widely discussed regarding the treatment, we share our successful approach and add some recommendations about this new and scarce entity. url: https://www.sciencedirect.com/science/article/pii/S2211034820302923?v=s5 doi: 10.1016/j.msard.2020.102216 id: cord-253970-sbj869yy author: Agarwal, Amit title: Neurological emergencies associated with COVID-19: stroke and beyond date: 2020-08-11 words: 2417.0 sentences: 149.0 pages: flesch: 40.0 cache: ./cache/cord-253970-sbj869yy.txt txt: ./txt/cord-253970-sbj869yy.txt summary: There is limited knowledge on the neurologic manifestations of COVID-19 at present, with a wide array of neurological complications reported, ranging from ischemic stroke to acute demyelination and encephalitis. The second subset of neurological presentation involves a response to the cytokine storm and multi-system inflammation including acute demyelination, vasculitis, necrotizing encephalopathy, and posterior reversible encephalopathy syndrome. Table 1 provides a summary of the most common (1) vascular complications with stroke secondary to arterial or venous thrombosis, related to the known hypercoagulable state seen in COVID [4, 5, 14] , and (2) much broader gamut including diffuse leukoencephalopathy, acute demyelination, posterior reversible encephalopathy syndrome (PRES), necrotizing encephalopathy, and focal cytotoxic edema, primarily seen as a consequence of systemic inflammation and cytokine storm seen with COVID-19 [6] [7] [8] [9] [10] [11] [12] [13] . The most common neurological presentation reported has been ischemic stroke, secondary to arterial or venous thrombosis, because of the hypercoagulable state associated with COVID-19. abstract: Novel coronavirus disease (COVID-19) was declared a global pandemic on March 1, 2020. Neurological manifestations are now being reported worldwide, including emergent presentation with acute neurological changes as well as a comorbidity in hospitalized patients. There is limited knowledge on the neurologic manifestations of COVID-19 at present, with a wide array of neurological complications reported, ranging from ischemic stroke to acute demyelination and encephalitis. We report five cases of COVID-19 presenting to the ER with acute neurological symptoms, over the course of 1 month. This includes two cases of ischemic stroke, one with large-vessel occlusion and one with embolic infarcts. The remainders of the cases include acute tumefactive demyelination, isolated cytotoxic edema of the corpus callosum with subarachnoid hemorrhage, and posterior reversible encephalopathy syndrome (PRES). url: https://www.ncbi.nlm.nih.gov/pubmed/32778985/ doi: 10.1007/s10140-020-01837-7 id: cord-280996-anq680a1 author: Agarwal, Arnav title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission date: 2020-06-15 words: 7117.0 sentences: 383.0 pages: flesch: 42.0 cache: ./cache/cord-280996-anq680a1.txt txt: ./txt/cord-280996-anq680a1.txt summary: title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission Review 1: we synthesized results from randomized-controlled trials (RCTs) comparing HFNC to conventional oxygen therapy (COT) in critically ill patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. We conducted two rapid systematic reviews commissioned by the WHO to summarize the evidence for the efficacy, safety, and risk of aerosol generation and infection transmission during HFNC use among patients with acute hypoxemic respiratory failure due to COVID-19. abstract: PURPOSE: We conducted two World Health Organization-commissioned reviews to inform use of high-flow nasal cannula (HFNC) in patients with coronavirus disease (COVID-19). We synthesized the evidence regarding efficacy and safety (review 1), as well as risks of droplet dispersion, aerosol generation, and associated transmission (review 2) of viral products. SOURCE: Literature searches were performed in Ovid MEDLINE, Embase, Web of Science, Chinese databases, and medRxiv. Review 1: we synthesized results from randomized-controlled trials (RCTs) comparing HFNC to conventional oxygen therapy (COT) in critically ill patients with acute hypoxemic respiratory failure. Review 2: we narratively summarized findings from studies evaluating droplet dispersion, aerosol generation, or infection transmission associated with HFNC. For both reviews, paired reviewers independently conducted screening, data extraction, and risk of bias assessment. We evaluated certainty of evidence using GRADE methodology. PRINCIPAL FINDINGS: No eligible studies included COVID-19 patients. Review 1: 12 RCTs (n = 1,989 patients) provided low-certainty evidence that HFNC may reduce invasive ventilation (relative risk [RR], 0.85; 95% confidence interval [CI], 0.74 to 0.99) and escalation of oxygen therapy (RR, 0.71; 95% CI, 0.51 to 0.98) in patients with respiratory failure. Results provided no support for differences in mortality (moderate certainty), or in-hospital or intensive care length of stay (moderate and low certainty, respectively). Review 2: four studies evaluating droplet dispersion and three evaluating aerosol generation and dispersion provided very low certainty evidence. Two simulation studies and a crossover study showed mixed findings regarding the effect of HFNC on droplet dispersion. Although two simulation studies reported no associated increase in aerosol dispersion, one reported that higher flow rates were associated with increased regions of aerosol density. CONCLUSIONS: High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. This benefit must be balanced against the unknown risk of airborne transmission. url: https://doi.org/10.1007/s12630-020-01740-2 doi: 10.1007/s12630-020-01740-2 id: cord-306465-7kevsl1z author: Agarwal, Krishna Mohan title: Study and Overview of the Novel Corona Virus Disease (COVID-19) date: 2020-09-06 words: 2645.0 sentences: 170.0 pages: flesch: 59.0 cache: ./cache/cord-306465-7kevsl1z.txt txt: ./txt/cord-306465-7kevsl1z.txt summary: In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. The current global pandemic is caused by the "novel coronavirus disease (2019-nCoV) or severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) popularly known as COVID19 Hunan seafood market was sealed, on 7 th January roughly a week after China''s notification of a possible outbreak the disease was confirmed to be the novel coronavirus disease or COVID-19 which has more than 95% homology with bat coronavirus and almost 70% similarity to the SARS CoV-1 Flatten the curve is a statement used during healthcare emergencies, its basic concept is to limit the spread of the virus such that at any given time during a pandemic the total number of patients required to be hospitalized is less than the maximum capacity of the state''s health infrastructure. abstract: In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. Within a span of a few days, this disease became a global threat and was termed as a pandemic by the World Health Organization (WHO) on 11th March 2020, since then the disease has affected more than 1.5 crore people worldwide and around 6.9 lakh people in India as of 5th July 2020. The origin of the COVID-19 disease has been traced back to the bats, but the intermediary contact is unknown. The disease spreads by respiratory droplets and contaminated surfaces. In most cases, the virus shows mild symptoms like fever, fatigue, dyspnea, cough, etc. which may become severe if appropriate precautions are not adhered to. For people with comorbidities (usually elderly) the disease may turn deadly and cause pneumonia, Acute Respiratory Disease Syndrome (ARDS), and multi-organ failure, thereby affecting a person's ability to breathe leading to being put on the ventilator support. The reproduction number (Rℴ) of COVID-19 is much higher than its predecessors and genetically similar diseases like SARS-CoV and MERS-CoV. This paper discusses the epidemiological characteristics of the SARS-CoV-2 virus, its phylogenetic relationship with the previous pandemic causing viruses such as SARS-CoV-1 and MERS-CoV and analyzes the various responses to this global pandemic worldwide, focusing on the actions taken by India and their outcomes. url: https://www.sciencedirect.com/science/article/pii/S2666351120300371?v=s5 doi: 10.1016/j.sintl.2020.100037 id: cord-336702-2qa4u8gv author: Agarwal, Sangya title: Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19 date: 2020-04-17 words: 2364.0 sentences: 124.0 pages: flesch: 44.0 cache: ./cache/cord-336702-2qa4u8gv.txt txt: ./txt/cord-336702-2qa4u8gv.txt summary: Consistent with HLH, accumulations of macrophages are found in the lungs of patients with COVID-19 ( 9 ) , and HLH has previously been reported in patients with SARS, MERS, and other severe systemic viral infections. Drug treatments used for HLH/MAS and ARDS may also be effective in treating patients with COVID-19. Thus, an urgent need emerges to uncover therapies that may be effective for patients with SARS-CoV-2 infection. Thus, if properly timed in patients after exposure to virus, CSA could serve as a broad-spectrum inhibitor to control SARS-CoV-2 infection and decrease the magnitude of cytokine release. This shows not only the coincidence of treatments that modulate dysfunctional host immune responses, but also the potential complications with overlapping SARS-CoV-2 infections and cancer immunotherapies. This is important because comorbidities from CRS due to CAR T-cell therapy and HLH-like symptoms due to SARS-CoV 2 infection could be fatal. abstract: Cytokine release and macrophage activation contribute to immunopathology after SARS-CoV-2 infection. We discuss approaches to decrease the morbidity and mortality in patients with COVID-19 by repurposing existing drugs previously developed for cancer therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/32303509/ doi: 10.1158/2159-8290.cd-20-0473 id: cord-262361-3f09z5pf author: Agbelele, Penance title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case date: 2020-07-30 words: 1759.0 sentences: 100.0 pages: flesch: 48.0 cache: ./cache/cord-262361-3f09z5pf.txt txt: ./txt/cord-262361-3f09z5pf.txt summary: title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case The authors present the case of a young man victim of a traffic accident during the SARS-CoV-2 confinement, having presented a fracture of the femoral shaft that was soon complicated by respiratory failure with oxygen desaturation. This case demonstrates the difficulty of differential interpretation of CT images between fatty embolism and SARS-CoV-2 infection. However, no study has investigated the specific features of CT scans to differentiate fat embolism syndrome from SARS-Cov-2 infection. His condition was further complicated by acute respiratory failure with CT images that may suggest either SARS-Cov-2 infection or a fatty embolism or both. Upon our patient''s arrival during the pandemic, he presented with fever (38°C) and oxygen desaturation (88%) strongly suggestive of a SARS-CoV-2 infection, especially since the signs of fat embolism occur on average at H39 [11, 12] . abstract: The authors present the case of a young man victim of a traffic accident during the SARS-CoV-2 confinement, having presented a fracture of the femoral shaft that was soon complicated by respiratory failure with oxygen desaturation. In this pandemic context, Covid-19 RT-PCR tests were carried out but returned negative. The CT images could suggest either a fatty embolism, a SARS-CoV-2 infection or both. The patient's condition improved significantly after going into intensive care and only symptomatic treatment. This case demonstrates the difficulty of differential interpretation of CT images between fatty embolism and SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S1930043320303812 doi: 10.1016/j.radcr.2020.07.071 id: cord-275506-3t5gf66c author: Agbuduwe, Charles title: Hematolological Manifestations of COVID‐19: From Cytopenia to Coagulopathy date: 2020-07-14 words: 4280.0 sentences: 265.0 pages: flesch: 39.0 cache: ./cache/cord-275506-3t5gf66c.txt txt: ./txt/cord-275506-3t5gf66c.txt summary: [45] A retrospective study of COVID-19 patients admitted to ICU identified DVT in 25% with advanced age, lower lymphocyte counts and elevated D-dimers being significant risk factors. [63] Currently, the evidence base for the clinical management of COVID-19 is mostly limited to case series and other relatively small observational studies of hospitalised patients. Similar to findings in SARS patients, [64] lymphopenia is the most commonly reported hematological abnormality in COVID-19 and recent data shows that it can be predictive of disease severity. The use of convalescent plasma may, in addition, provide neutralising antibodies against SARS-CoV-2 and a small-scale clinical trial has reported modest but encouraging results in severely-ill but not in critical COVID-19 patients. In view of the increased thrombotic risk associated with COVID-19, prophylactic anticoagulation with low Accepted Article molecular weight heparin is recommended for all hospitalised patients with the disease and clinical trials are needed to investigate the role of more intensive anticoagulation and other experimental therapies. abstract: s Emerging data from the management of patients with Coronavirus Disease 2019 (COVID‐19) suggests multisystemic involvement, including the hemopoietic system. The hematological manifestations of COVID‐19 include blood count anomalies notably lymphopenia and neutrophilia which are of prognostic significance. Hyperferritinemia and elevated lactate dehydrogenase have also been associated with increased mortality. Furthermore, there is considerable evidence of a distinct coagulopathy associated with COVID‐19 characterised by elevated D‐dimers and an increased risk of thrombotic events. This comprehensive review summarises the latest evidence from published studies and discusses the implications of the various hematological manifestations of COVID‐19 with a view to guiding clinical management and risk stratification in this rapidly evolving pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32663356/ doi: 10.1111/ejh.13491 id: cord-305788-z75yv88e author: Agergaard, Charlotte Nielsen title: Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date: 2020-09-28 words: 727.0 sentences: 64.0 pages: flesch: 61.0 cache: ./cache/cord-305788-z75yv88e.txt txt: ./txt/cord-305788-z75yv88e.txt summary: Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220321585?v=s5 doi: 10.1016/j.ijid.2020.09.1442 id: cord-269871-w41o1krr author: Aggarwal, Shyam title: High Viral Load and Poor Ventilation: Cause of High Mortality From COVID-19 date: 2020-07-25 words: 835.0 sentences: 50.0 pages: flesch: 57.0 cache: ./cache/cord-269871-w41o1krr.txt txt: ./txt/cord-269871-w41o1krr.txt summary: Low viral load in the nasal cavity due to open air ventilation is a plausible reason for this difference. As a result, people living in developed countries tend to build up high viral load in their nasal cavity and nasopharynx. These factors indicate a strong association between high viral load and poor ventilation, which, in turn, leads to high mortality from COVID-19 in developed Western nations. In this article, we have tried to explain that poor ventilation and subsequent buildup of high viral load could be a reason for such a drastic difference in mortality rates among these two groups of countries. 2 These studies suggest an association of high viral load in nasal cavity and nasopharynx with the severity of the disease. For this reason, the viral load in the nasal cavity and the nasopharynx could be lower and result in a less severe disease. abstract: There is a huge disparity between the mortality from COVID-19 in developed Western countries and developing Asian countries. Low viral load in the nasal cavity due to open air ventilation is a plausible reason for this difference. The transmission of SARS-CoV-2 occurs through respiratory droplets and fomites. There is ample evidence that the virus is airborne as well. The biggest factor in the transmission of SARS-C-V-2 are asymptomatic or paucisymptomatic carriers. Lack of open air ventilation is a major compounding factor as the virus remains in the environment, especially on fomites, leading to regular and repeated exposure to the virus. As a result, people living in developed countries tend to build up high viral load in their nasal cavity and nasopharynx. Studies have clearly shown that the severity of COVID-19 is directly proportional to the viral load harbored in the upper respiratory tract. These factors indicate a strong association between high viral load and poor ventilation, which, in turn, leads to high mortality from COVID-19 in developed Western nations. url: https://www.ncbi.nlm.nih.gov/pubmed/32715729/ doi: 10.1177/1010539520944725 id: cord-297132-lhfa9fl5 author: Aghagoli, Ghazal title: Neurological Involvement in COVID-19 and Potential Mechanisms: A Review date: 2020-07-13 words: 5940.0 sentences: 280.0 pages: flesch: 36.0 cache: ./cache/cord-297132-lhfa9fl5.txt txt: ./txt/cord-297132-lhfa9fl5.txt summary: In this review, we synthesize a range of clinical observations and initial case series describing potential neurologic manifestations of COVID-19 and place these observations in the context of coronavirus neuro-pathophysiology as it may relate to SARS-CoV-2 infection. The novel 2019 coronavirus disease (COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) results in a variety of symptoms including fever, cough, and fatigue [1] . The Kawasaki-like syndrome that is now described in young patients following COVID-19 infection and associated with a hyper-inflammatory state is further suggestive of a vascular inflammatory potential of SARS-CoV-2 [48, 49] . Once established in the CNS, SARS-CoV, the virus responsible for Severe Acute Respiratory Syndrome (SARS), has been shown to be capable of inducing rapid transneuronal spread and death of infected neurons in transgenic mice models expressing human ACE2 receptors [63] . abstract: As the current understanding of COVID-19 continues to evolve, a synthesis of the literature on the neurological impact of this novel virus may help inform clinical management and highlight potentially important avenues of investigation. Additionally, understanding the potential mechanisms of neurologic injury may guide efforts to better detect and ameliorate these complications. In this review, we synthesize a range of clinical observations and initial case series describing potential neurologic manifestations of COVID-19 and place these observations in the context of coronavirus neuro-pathophysiology as it may relate to SARS-CoV-2 infection. Reported nervous system manifestations range from anosmia and ageusia, to cerebral hemorrhage and infarction. While the volume of COVID-19-related case studies continues to grow, previous work examining related viruses suggests potential mechanisms through which the novel coronavirus may impact the CNS and result in neurological complications. Namely, animal studies examining the SARS-CoV have implicated the angiotensin-converting-enzyme-2 receptor as a mediator of coronavirus-related neuronal damage and have shown that SARS-CoV can infect cerebrovascular endothelium and brain parenchyma, the latter predominantly in the medial temporal lobe, resulting in apoptosis and necrosis. Human postmortem brain studies indicate that human coronavirus variants and SARS-CoV can infect neurons and glia, implying SARS-CoV-2 may have similar neurovirulence. Additionally, studies have demonstrated an increase in cytokine serum levels as a result of SARS-CoV infection, consistent with the notion that cytokine overproduction and toxicity may be a relevant potential mechanism of neurologic injury, paralleling a known pathway of pulmonary injury. We also discuss evidence that suggests that SARS-CoV-2 may be a vasculotropic and neurotropic virus. Early reports suggest COVID-19 may be associated with severe neurologic complications, and several plausible mechanisms exist to account for these observations. A heightened awareness of the potential for neurologic involvement and further investigation into the relevant pathophysiology will be necessary to understand and ultimately mitigate SARS-CoV-2-associated neurologic injury. url: https://www.ncbi.nlm.nih.gov/pubmed/32661794/ doi: 10.1007/s12028-020-01049-4 id: cord-298535-wmxlu3l1 author: Agnihothram, Sudhakar title: Evaluation of Serologic and Antigenic Relationships Between Middle Eastern Respiratory Syndrome Coronavirus and Other Coronaviruses to Develop Vaccine Platforms for the Rapid Response to Emerging Coronaviruses date: 2013-11-18 words: 5036.0 sentences: 235.0 pages: flesch: 43.0 cache: ./cache/cord-298535-wmxlu3l1.txt txt: ./txt/cord-298535-wmxlu3l1.txt summary: In this article, we use alphavirus replicon vaccine vectors to express a panel of recombinant S and N proteins from distantly related alphacoronaviruses and betacoronaviruses, including MERS-CoV and other subgroup 2c CoVs. Using mouse polyclonal antisera and recombinant proteins, we compare the cross-reactivity and neutralization titers of these antisera between distantly related human and bat CoVs. Our results indicate that the S glycoprotein but not the N protein is the major determinant of the neutralizing antibody response to MERS-CoV; that the N proteins of CoVs only cross-react within but not between subgroups; that little if any cross-neutralization or cross-reactivity exists between the S proteins of CoVs within subgroup 2c or any other subgroup; and that cross-neutralization and cross-reactive patterns were validated with the convalescent-phase serum sample from a patient infected with MERS-CoV Hu/England-N1/2012 and a donor panel of human antisera against 3 different HCoVs. Our approach provides critical reagents, antisera, and recombinant virus vaccines that allow for rapid diagnosis of and intervention against MERS-CoV and other zoonotic CoVs that emerge in the future. abstract: Background. Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012, causing severe acute respiratory disease and pneumonia, with 44% mortality among 136 cases to date. Design of vaccines to limit the virus spread or diagnostic tests to track newly emerging strains requires knowledge of antigenic and serologic relationships between MERS-CoV and other CoVs. Methods. Using synthetic genomics and Venezuelan equine encephalitis virus replicons (VRPs) expressing spike and nucleocapsid proteins from MERS-CoV and other human and bat CoVs, we characterize the antigenic responses (using Western blot and enzyme-linked immunosorbent assay) and serologic responses (using neutralization assays) against 2 MERS-CoV isolates in comparison with those of other human and bat CoVs. Results. Serologic and neutralization responses against the spike glycoprotein were primarily strain specific, with a very low level of cross-reactivity within or across subgroups. CoV N proteins within but not across subgroups share cross-reactive epitopes with MERS-CoV isolates. Our findings were validated using a convalescent-phase serum specimen from a patient infected with MERS-CoV (NA 01) and human antiserum against SARS-CoV, human CoV NL63, and human CoV OC43. Conclusions. Vaccine design for emerging CoVs should involve chimeric spike protein containing neutralizing epitopes from multiple virus strains across subgroups to reduce immune pathology, and a diagnostic platform should include a panel of nucleocapsid and spike proteins from phylogenetically distinct CoVs. url: https://doi.org/10.1093/infdis/jit609 doi: 10.1093/infdis/jit609 id: cord-334495-7y1la856 author: Agricola, Eustachio title: Heart and Lung Multimodality Imaging in COVID-19 date: 2020-06-24 words: 6791.0 sentences: 325.0 pages: flesch: 33.0 cache: ./cache/cord-334495-7y1la856.txt txt: ./txt/cord-334495-7y1la856.txt summary: From a clinical point of view, cardiac involvement during COVID-19 may present a wide spectrum of severity ranging from subclinical myocardial injury to well-defined clinical entities (myocarditis, myocardial infarction, pulmonary embolism and heart failure), whose incidence and prognostic implications are currently largely unknown due to a significant lack of imaging data. The use of integrated heart and lung multimodality imaging plays a central role in different clinical settings and is essential in diagnosis, risk stratification and management of COVID-19 patients. In this context, the use of multiple diagnostic imaging techniques may apply to both heart and lung to provide an integrated assessment of cardiac and pulmonary function and to refine diagnosis, risk stratification and management of COVID-19 patients. patients not requiring ICU, when clinical presentation and biomarker alterations suggest acute-onset myocardial inflammation, if the diagnosis is likely to impact on management, CMR may be considered to confirm acute myocarditis, after exclusion of alternative relevant clinical conditions, including ACS and HF, by means of other rapidly available imaging modalities (i.e. cardiac CT scan or TTE). abstract: Abstract SARS-CoV-2 outbreak has rapidly reached a pandemic proportion and has become a major threaten to global health. Although the predominant clinical feature of COVID-19 is an acute respiratory syndrome of varying severity, ranging from mild symptomatic interstitial pneumonia to acute respiratory distress syndrome, the cardiovascular system can be involved with several facets. As many as 40% hospitalized patients presenting with COVID-19 have pre-existing history of cardiovascular disease and current estimates report a proportion of myocardial injury in COVID-19 patients ranging up to 12%. Multiple pathways have been advocated to explain this finding and the related clinical scenarios, encompassing local and systemic inflammatory response and oxygen supply-demand imbalance. From a clinical point of view, cardiac involvement during COVID-19 may present a wide spectrum of severity ranging from subclinical myocardial injury to well-defined clinical entities (myocarditis, myocardial infarction, pulmonary embolism and heart failure), whose incidence and prognostic implications are currently largely unknown due to a significant lack of imaging data. The use of integrated heart and lung multimodality imaging plays a central role in different clinical settings and is essential in diagnosis, risk stratification and management of COVID-19 patients. Aim of this review is to summarize imaging-oriented pathophysiological mechanisms of lung and cardiac involvement in COVID-19 and to provide a guide for an integrated imaging assessment in these patients. url: https://api.elsevier.com/content/article/pii/S1936878X20304770 doi: 10.1016/j.jcmg.2020.05.017 id: cord-352935-kb0i58z1 author: Aguila, Enrik John T. title: Repurposed GI Drugs in the Treatment of COVID-19 date: 2020-06-29 words: 990.0 sentences: 63.0 pages: flesch: 49.0 cache: ./cache/cord-352935-kb0i58z1.txt txt: ./txt/cord-352935-kb0i58z1.txt summary: A recent drug research in Germany has shown that omeprazole interfered viral formation of SARS-CoV-2 beyond therapeutic plasma concentrations at 8 µM [6] . To date, there is still little knowledge on the potential of famotidine and omeprazole as repurposed drugs to treat COVID-19. In their letter, Aguila and colleagues provide an insight into commonly used acid suppressants such as famotidine and omeprazole as the potential agents for drug repurposing against COVID-19. The role of famotidine in interfering maturation of SARS-CoV-2 by inhibiting 2-chymotrypsin-like protein and reduction in inflammation needs to be studied. The authors also note that omeprazole at therapeutic concentration increased the anti-SARS-CoV-2 effects of remdesivir and aprotinin. Therefore, there is a theoretical concern that the use of H2-blockers and PPIs could diminish or abolish the neutralizing effects of gastric acid on SARS-CoV-2, which could potentially increase the risk of GI manifestations and severity in COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32601778/ doi: 10.1007/s10620-020-06430-z id: cord-333089-ufyzqgqk author: Aguilar-Pineda, Jorge Alberto title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date: 2020-07-29 words: 6957.0 sentences: 359.0 pages: flesch: 51.0 cache: ./cache/cord-333089-ufyzqgqk.txt txt: ./txt/cord-333089-ufyzqgqk.txt summary: Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. abstract: Emerging evidence suggests that males are more susceptible to severe infection by the SARS-CoV-2 virus than females. A variety of mechanisms may underlie the observed gender-related disparities including differences in sex hormones. However, the precise mechanisms by which female sex hormones may provide protection against SARS-CoV-2 infectivity remains unknown. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further observed that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV2 thereby blocking its entry into cells. In a mouse model, estrogens reduced ACE2 glycosylation and thereby alveolar uptake of the SARS-CoV-2 spike protein. These results shed light on a putative mechanism whereby female sex hormones may provide protection from developing severe infection and could inform the development of future therapies against COVID-19. url: https://doi.org/10.1101/2020.07.29.227249 doi: 10.1101/2020.07.29.227249 id: cord-281512-79g22dk6 author: Aguirre, A. Alonso title: Illicit Wildlife Trade, Wet Markets, and COVID‐19: Preventing Future Pandemics date: 2020-07-05 words: 3829.0 sentences: 188.0 pages: flesch: 54.0 cache: ./cache/cord-281512-79g22dk6.txt txt: ./txt/cord-281512-79g22dk6.txt summary: This article will explore the connections among the current pandemic, live-animal markets, the spread of animal-related diseases, and the illicit wildlife trade and will include a set of policy recommendations prescribed to prevent future outbreaks stemming from these issues. It further explains "the identification of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in civet cats and other wild animals in live animal markets suggests that this novel human pathogen emerged as a result of an interspecies transmission" (Poon et al., 2005 (Poon et al., , p. The devastation resulting from the spread of COVID-19 could potentially serve as a future warning for what is to come, if practices such as illicit wildlife trade and wet markets are allowed to continue on a global scale. Research must focus on the central causes of the spread of zoonotic diseases such as illicit wildlife trade and wet markets. abstract: Although the exact origin of SARS‐CoV‐2, the etiologic agent of COVID‐19, is currently unknown, there is substantial evidence to suggest the source of transmission of the virus occurred within the Wuhan wet market. In these markets, bats and wild animals are frequently sold and stored in close contact. During several of the world's past pandemics, bats were essential to the spread of zoonotic diseases from bat to another animal or to humans directly. Live animal markets create the perfect conditions for novel viruses such as COVID‐19 to emerge. This paper suggests that to prevent future pandemics, the sale of exotic animals be banned at wet markets. It also advocates for the integration of the analysis of illicit trade with the study of zoonotic disease transmission and pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32837772/ doi: 10.1002/wmh3.348 id: cord-337599-dyxfsojh author: Ahamad, Shakir title: Primed for Global Coronavirus Pandemic: Emerging Research and Clinical Outcome date: 2020-09-19 words: 1978.0 sentences: 163.0 pages: flesch: 48.0 cache: ./cache/cord-337599-dyxfsojh.txt txt: ./txt/cord-337599-dyxfsojh.txt summary: Under such circumstances, drug repurposing has emerged as a realistic and effective strategy to counter the virus menace in the short run, and several antiviral and antimalarial medicines are currently in different stages of clinical trials. Researchers are also experimenting with nutrients, vitamins, monoclonal antibodies, and convalescent plasma as immunity boosters against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This report presents a critical analysis of the global clinical trial landscape for COVID-19 with an emphasis on the therapeutic agents and vaccines currently being tested at pandemic speed. 166 The Institute of Biotechnology, AMMS, China, registered a randomized, double-blind, 167 placebo-controlled Phase-II clinical trial of recombinant novel coronavirus (2019-nCOV) 168 vaccine (adenovirus vector) in healthy adults aged 18 and above on April 10, 2020, (Table1, 169 Entry 6). Clinical study for safety and efficacy of Favipiravir in the treatment of novel 924 coronavirus pneumonia (COVID-19) Genentech Announces FDA Approval of Clinical Trial for Actemra to Treat 1093 Hospitalized Patients with Severe COVID-19 Pneumonia abstract: The global effort to combat and contain the coronavirus disease 2019 (COVID-19) pandemic is now proceeding on a war footing. The world was slow to react to the developing crisis, but once the contours of the impending calamity became evident, the different state and non-state actors have raced to put their act together. The COVID-19 outbreak has blatantly exposed the shortcomings of our healthcare system and the limitations of medical science, despite considerable advances in recent years. To effectively tackle the current epidemic, almost unprecedented in the modern era, there is an urgent need for a concerted, sustained, and coordinated effort towards the development of new diagnostics, therapeutic and vaccines, and the ramping up of the healthcare infrastructure, especially in the poorer, underprivileged nations. Towards this end, researchers around the world are working tirelessly to develop new diagnostics, vaccines, and therapeutics. Efforts to develop a vaccine against COVID-19 are presently underway in several countries around the world, but a new vaccine is expected only by the end of the year-at the earliest. New drug development against COVID-19 and its approval may take even longer. Under such circumstances, drug repurposing has emerged as a realistic and effective strategy to counter the virus menace in the short run, and several antiviral and antimalarial medicines are currently in different stages of clinical trials. Researchers are also experimenting with nutrients, vitamins, monoclonal antibodies, and convalescent plasma as immunity boosters against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This report presents a critical analysis of the global clinical trial landscape for COVID-19 with an emphasis on the therapeutic agents and vaccines currently being tested at pandemic speed. url: https://www.ncbi.nlm.nih.gov/pubmed/33070079/ doi: 10.1016/j.ejmech.2020.112862 id: cord-266948-n7sltd1b author: Ahamed, Jasimuddin title: Severe aortic stenosis patient risk during the COVID-19 pandemic date: 2020-09-14 words: 1314.0 sentences: 85.0 pages: flesch: 46.0 cache: ./cache/cord-266948-n7sltd1b.txt txt: ./txt/cord-266948-n7sltd1b.txt summary: The patient risk assessment typically includes patient age and surgical risk; however, given the increased general risk of the procedure and that SARS-CoV-2 infection can be an additional and very dangerous comorbidity, suggesting the less invasive TAVR should be considered. 5 AS patients therefore may have increased risk for developing thromboembolic complications during the valve replacement procedure or during subsequent hospitalisation and recovery if they are infected with SARS-CoV-2. In fact, a recent study showed that a prosthetic aortic graft thrombosis patient died from COVID-19 and that anticoagulant and thrombectomy procedure were unsuccessful. 5 Therefore, direct thrombin inhibitors should be considered for AS patients who test positive for SARS-CoV-2, since both COVID-19 and AS procedure can increase the risk of thrombosis. Studies in animals have suggested that inhibitors of this system can upregulate ACE2 expression, which led some investigators to postulate that patients receiving those inhibitors may be at high risk of contracting a SARS-CoV-2 infection, which needs to be validated experimentally. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32928913/ doi: 10.1136/openhrt-2020-001355 id: cord-328471-oz99upzz author: Ahmad, Jamshaid title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 words: 5089.0 sentences: 282.0 pages: flesch: 55.0 cache: ./cache/cord-328471-oz99upzz.txt txt: ./txt/cord-328471-oz99upzz.txt summary: In this global health emergency, drug repurposing (or repositioning) is one of the fast track option that involves screening of existing FDA approved drugs for the identification of potential molecules that can disrupt the function of key proteins of the SARS-CoV-2 and can be used for treatment against COVID-19. Whereas, Demoxytocin showed ten H-bonds with both active site Asp760 and Asp761 and other key residues e.g. Trp617, Tyr619, Lys621, Ser682, Glu811, Lys621, Tyr619, Trp617, Ser682 and Glu811 with dock score -9.68kcal/mol and ligand efficiency of -0.142 (Supplementary Figure S3) . Colistin (polymyxin E, polypeptide antibiotics) showed most of the H-bonding with Lys551, Trp617, Tyr619, Asp618, Ser682, Asp684, Asn691, and both catalytic residues i.e. Asp760, Asp761, with a docking score of -9.24kcal/mol and ligand efficiency of -0.113 (Supplementary Figure S5) . Examorelin, Lypressin, Ornipressin, and Colistin are also common drugs in both form of RdRp. Only one H-bond with His810 and other non-covalent interactions were observed for Examorelin showed a docking score of -12.139 kcal/mol and ligand efficiency of -0.187. abstract: The outbreak of SARS-CoV-2 in December 2019 in China subsequently lead to a pandemic. Lack of vaccine and specific anti-viral drugs started a global health disaster. For a sustained control and protection, development of potential anti-viral drugs is one of the targeted approach. Although, designing and developing a panel of new drugs molecules are always encouraged. However, in the current emergency, drug repurposing study is one of the most effective and fast track option. The crystal structure of a SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) RNA Dependent RNA Polymerase (RdRp) has recently been deciphered through X-ray crystallography. The single-chain of core RNA Dependent RNA Polymerase relies on virus-encoded cofactors nsp7 and two units of nsp8 for its optimum function. This study explored the FDA approved database of 7922 molecules and screened against the core polymerase along with cofactors. Here we report a panel of FDA approved drugs that show substantial interactions with key amino acid residues of the active site. Interestingly, some of the identified drugs (Ornipressin, Lypressin, Examorelin, Polymyxin B1) bind strongly within the binding pockets of both forms of RdRp. Besides, we found strong candidates for the complex form as well which include Nacortocin, Cistinexine, Cisatracurium (among others). These drugs have the potential to be considered while contriving therapeutic options. url: https://doi.org/10.1016/j.heliyon.2020.e04502 doi: 10.1016/j.heliyon.2020.e04502 id: cord-315611-xbj41ekc author: Ahmad, Mohammed title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date: 2020-07-14 words: 5038.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-315611-xbj41ekc.txt txt: ./txt/cord-315611-xbj41ekc.txt summary: Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. 20−22 In this report, using computer-aided homology modeling, docking, and molecular simulations, we have predicted the protein structure and probable small-molecule inhibitors against SARS-CoV2 RdRp (CoV2-RdRp). Taking together the aforementioned interaction and comparison of the model and experimentally determined structures, we propose the probable initiation complex of CoV2-RdRp bound to RNA and GTP molecules in Figure 2D . Molecular Dynamics simulation studies of the native and ligand-bound complexes of CoV2-RdRp. MD (Molecular dynamics) simulations were performed for the modelled structure of the RdRp protein and docked complexes for the GTP, lead optimized, and FIH compounds for a 50 ns time period. abstract: [Image: see text] The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2. url: https://www.ncbi.nlm.nih.gov/pubmed/32743211/ doi: 10.1021/acsomega.0c02096 id: cord-258624-041cf99j author: Ahmad, Sajjad title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date: 2020-05-23 words: 8187.0 sentences: 434.0 pages: flesch: 48.0 cache: ./cache/cord-258624-041cf99j.txt txt: ./txt/cord-258624-041cf99j.txt summary: title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. In order to estimate the MMPBSA binding free energies for the receptors and multi-epitope peptide vaccine construct, the MMPBSA.py module [56] of AMBER16 was castoff. The B-cell epitopes predicted for the vaccine candidates were in the following order: nine for Nsp8 and 3C-like proteinase, five for Nsp9, eight for Nsp10, 34 for spike glycoprotein and surface glycoprotein, and four for ORF1ab polyprotein| partial. Molecular interactions and binding conformation of the designed MEPVC with TLR3 and TLR4 innate immune receptors were deciphered via a protein-peptide docking approach. The dynamic simulations of the human immune system in response to the designed vaccine construct were deciphered through C-immsim server [40] . abstract: The emergence and rapid expansion of the coronavirus disease (COVID-19) require the development of effective countermeasures especially a vaccine to provide active acquired immunity against the virus. This study presented a comprehensive vaccinomics approach applied to the complete protein data published so far in the National Center for Biotechnological Information (NCBI) coronavirus data hub. We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. Epitopes prediction illustrated both B-cell and T-cell epitopes associated with the mentioned proteins. The shared B and T-cell epitopes: DRDAAMQRK and QARSEDKRA of Nsp8, EDMLNPNYEDL and EFTPFDVVR of 3C-like proteinase, and VNNSYECDIPI of the spike glycoprotein are regions of high potential interest and have a high likelihood of being recognized by the human immune system. The vaccine construct of the epitopes shows stimulation of robust primary immune responses and high level of interferon gamma. Also, the construct has the best conformation with respect to the tested innate immune receptors involving vigorous molecular mechanics and solvation energy. Designing of vaccination strategies that target immune response focusing on these conserved epitopes could generate immunity that not only provide cross protection across Betacoronaviruses but additionally resistant to virus evolution. url: https://doi.org/10.1016/j.ejps.2020.105387 doi: 10.1016/j.ejps.2020.105387 id: cord-295051-upyar7en author: Ahmadian, Elham title: Covid‐19 and kidney injury: Pathophysiology and molecular mechanisms date: 2020-10-06 words: 4859.0 sentences: 321.0 pages: flesch: 45.0 cache: ./cache/cord-295051-upyar7en.txt txt: ./txt/cord-295051-upyar7en.txt summary: The SARS‐CoV‐2‐induced kidney damage is expected to be multifactorial; directly it can infect the kidney podocytes and proximal tubular cells and based on an angiotensin‐converting enzyme 2 (ACE2) pathway it can lead to acute tubular necrosis, protein leakage in Bowman''s capsule, collapsing glomerulopathy and mitochondrial impairment. 6, 7 The initial impact might be the direct role of the virus on the renal parenchyma mediated by activating the angiotensin-converting enzyme 2 (ACE2), which functions as a SARS-CoV-2 receptor. 22 Altogether, these reports clarify that kidney cells are targeted by SARS-CoV-2 and new strategies are needed to treat Covid-19 to prevent organ infection and dysfunction. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Coronavirus disease 19 infection does not result in acute kidney injury: an analysis of 116 hospitalized patients from Wuhan, China Acute kidney injury in SARS-CoV-2 infection: direct effect of virus on kidney proximal tubule cells abstract: The novel coronavirus (SARS‐CoV‐2) has turned into a life‐threatening pandemic disease (Covid‐19). About 5% of patients with Covid‐19 have severe symptoms including septic shock, acute respiratory distress syndrome, and the failure of several organs, while most of them have mild symptoms. Frequently, the kidneys are involved through direct or indirect mechanisms. Kidney involvement mainly manifests itself as proteinuria and acute kidney injury (AKI). The SARS‐CoV‐2‐induced kidney damage is expected to be multifactorial; directly it can infect the kidney podocytes and proximal tubular cells and based on an angiotensin‐converting enzyme 2 (ACE2) pathway it can lead to acute tubular necrosis, protein leakage in Bowman's capsule, collapsing glomerulopathy and mitochondrial impairment. The SARS‐CoV‐2‐driven dysregulation of the immune responses including cytokine storm, macrophage activation syndrome, and lymphopenia can be other causes of the AKI. Organ interactions, endothelial dysfunction, hypercoagulability, rhabdomyolysis, and sepsis are other potential mechanisms of AKI. Moreover, lower oxygen delivery to kidney may cause an ischaemic injury. Understanding the fundamental molecular pathways and pathophysiology of kidney injury and AKI in Covid‐19 is necessary to develop management strategies and design effective therapies. url: https://doi.org/10.1002/rmv.2176 doi: 10.1002/rmv.2176 id: cord-336049-n3swuykg author: Ahmed, Mubbasheer title: Multisystem inflammatory syndrome in children: A systematic review date: 2020-09-04 words: 5676.0 sentences: 343.0 pages: flesch: 47.0 cache: ./cache/cord-336049-n3swuykg.txt txt: ./txt/cord-336049-n3swuykg.txt summary: INTERPRETATION: Multisystem inflammatory syndrome is a new pediatric disease associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is dangerous and potentially lethal. However, in early May 2020, investigators from South Thames Retrieval Service in London, UK published a report describing eight severely ill pediatric patients presenting in hyperinflammatory shock with multiorgan involvement [6] Specifically, the children manifested with high fever, rash, conjunctivitis, peripheral edema, and gastrointestinal symptoms. We included patients with COVID-19 to reinforce to the healthcare community and public the differences in the clinical presentation, to highlight the degree of systemic inflammation in MIS-C, and to iterate the differences in treatment and outcome between the two diseases. Data collected from the studies included demographics, number of patients, signs and symptoms, laboratory markers, imaging results, medications, and outcomes. Cardiac MRI of children with multisystem inflammatory syndrome (MIS-C) associated with COVID-19: case series abstract: BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C), also known as pediatric inflammatory multisystem syndrome, is a new dangerous childhood disease that is temporally associated with coronavirus disease 2019 (COVID-19). We aimed to describe the typical presentation and outcomes of children diagnosed with this hyperinflammatory condition. METHODS: We conducted a systematic review to communicate the clinical signs and symptoms, laboratory findings, imaging results, and outcomes of individuals with MIS-C. We searched four medical databases to encompass studies characterizing MIS-C from January 1st, 2020 to July 25th, 2020. Two independent authors screened articles, extracted data, and assessed risk of bias. This review was registered with PROSPERO CRD42020191515. FINDINGS: Our search yielded 39 observational studies (n = 662 patients). While 71·0% of children (n = 470) were admitted to the intensive care unit, only 11 deaths (1·7%) were reported. Average length of hospital stay was 7·9 ± 0·6 days. Fever (100%, n = 662), abdominal pain or diarrhea (73·7%, n = 488), and vomiting (68·3%, n = 452) were the most common clinical presentation. Serum inflammatory, coagulative, and cardiac markers were considerably abnormal. Mechanical ventilation and extracorporeal membrane oxygenation were necessary in 22·2% (n = 147) and 4·4% (n = 29) of patients, respectively. An abnormal echocardiograph was observed in 314 of 581 individuals (54·0%) with depressed ejection fraction (45·1%, n = 262 of 581) comprising the most common aberrancy. INTERPRETATION: Multisystem inflammatory syndrome is a new pediatric disease associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is dangerous and potentially lethal. With prompt recognition and medical attention, most children will survive but the long-term outcomes from this condition are presently unknown. FUNDING: Parker B. Francis and pilot grant from 2R25-HL126140. Funding agencies had no involvement in the study url: https://www.ncbi.nlm.nih.gov/pubmed/32923992/ doi: 10.1016/j.eclinm.2020.100527 id: cord-312722-talu4geh author: Ahmed, Nausheen title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient date: 2020-06-13 words: 1179.0 sentences: 83.0 pages: flesch: 51.0 cache: ./cache/cord-312722-talu4geh.txt txt: ./txt/cord-312722-talu4geh.txt summary: title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient 3, 4 As a result of the high mortality in this population, the American Society of Transplantation and Cellular Therapy (ASTCT) recently published guidelines on March 18, 2020, suggesting universal testing of patients before admission for cellular therapy or stem cell transplant to mitigate the risk of transmission and outbreaks in transplant wards. 5 Accordingly, at our institution a policy to screen all patients planned for HCT or cellular therapy the day prior to admission with a nasopharyngeal swab real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2 infection was implemented. 8 The skin rash, such as livedo reticularis and petechial rash have been reported, but our patient''s positive SARS-CoV-2 test and biopsy suggest Covid-19 may also cause a more classic viral exanthem. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2531137920300717?v=s5 doi: 10.1016/j.htct.2020.06.002 id: cord-308499-xqmguqyi author: Ahmed, Sakir title: Reply to Rheumatologists’ perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? date: 2020-05-09 words: 678.0 sentences: 47.0 pages: flesch: 43.0 cache: ./cache/cord-308499-xqmguqyi.txt txt: ./txt/cord-308499-xqmguqyi.txt summary: title: Reply to Rheumatologists'' perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? Heparin has multiple possible mechanisms of action which may support its use for COVID-19. SARS coronavirus strain HSR1 multiplication can be directly inhibited by heparin as evidenced by reduction of viral plaques by 50% on addition of heparin to Vero cell cultures [3] . One of the mechanisms of inhibition of cellular entry of SARS coronavirus is via lactoferrin binding [4] . SARS-CoV-2 entry into a cell via the ACE2 receptor leads to shedding of this receptor [6] . Furthermore, RAAS (renin-angiotensin-aldosterone system) activation is linked to thrombosis by multiple mechanisms [9] . Therefore, ACE2 downregulation by SARS-CoV-2 may lead to enhanced thrombosis. To summarize, SARS-CoV-2 can possibly activate the RAAS axis via ACE2 shedding and promote thrombosis. The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 receptor binding domain undergoes conformational change upon heparin binding. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32388748/ doi: 10.1007/s10067-020-05145-w id: cord-290445-vb53bih9 author: Ahmed, Shiek SSJ title: Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date: 2020-04-23 words: 3793.0 sentences: 208.0 pages: flesch: 42.0 cache: ./cache/cord-290445-vb53bih9.txt txt: ./txt/cord-290445-vb53bih9.txt summary: Secondly, the viral replication machinery network from SET-B with 332 seed proteins extended to 1486 neighboring proteins with 11438 interacting edges which representing the mechanism attributed to evasion of the SARS-CoV2 genome into the host. Similarly, the viral replication machinery network was acquired with 1522 proteins with 9747 interacting edges showing the complex SARS-CoV-2 mechanism in the human lungs. These common molecules represent the inter-connecting mechanism involved in the transcription machinery, immune response, cell growth and/or maintenance, transport, metabolism, protein metabolism, cell communication and signal transduction that activated upon virus binding and has been subsequently utilized for viral replication process (S5 Table) Also mapping with other viral infection dataset, 50 hub proteins of the replication machinery network have noticed in influenza virus infection (S4 Table) , which suggests SARS-CoV2 and influenza may have a similar mode of host infection machinery [17] . The molecular pathways of interconnecting protein hubs could be the intermediate phase that connects the receptor activation mechanism and viral replication process (Fig 10) . abstract: We dissect the mechanism of SARS-CoV-2 in human lung host from the initial phase of receptor binding to viral replication machinery. We constructed two independent lung protein interactome to reveal the signaling process on receptor activation and host protein hijacking machinery in the pathogenesis of virus. Further, we test the functional role of the hubs derived from both interactome. Most hubs proteins were differentially regulated on SARS-CoV-2 infection. Also, the proteins of viral replication hubs were related with cardiovascular disease, diabetes and hypertension confirming the vulnerability and severity of infection in the risk individual. Additionally, the hub proteins were closely linked with other viral infection, including MERS and HCoVs which suggest similar infection pattern in SARS-CoV-2. We identified five interconnecting cascades between hubs of both networks that show the preparation of optimal environment in the host for viral replication process upon receptor attachment. Interestingly, we propose that seven potential miRNAs, targeting the intermediate phase that connects receptor and viral replication process a better choice as a drug for SARS-CoV-2. url: https://doi.org/10.1101/2020.04.20.050138 doi: 10.1101/2020.04.20.050138 id: cord-333174-g10kvc0c author: Ahmed, Sinthyia title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 date: 2020-07-28 words: 6773.0 sentences: 394.0 pages: flesch: 54.0 cache: ./cache/cord-333174-g10kvc0c.txt txt: ./txt/cord-333174-g10kvc0c.txt summary: title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro. In this study, we employ drug repurposing approach to identify potential candidates which can bind and interact with RdRp and Mpro proteins of SARS-CoV-2. abstract: SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility. url: https://doi.org/10.1080/07391102.2020.1796804 doi: 10.1080/07391102.2020.1796804 id: cord-334299-0zn1z7rc author: Ahmed, Warish title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date: 2020-09-30 words: 1373.0 sentences: 73.0 pages: flesch: 47.0 cache: ./cache/cord-334299-0zn1z7rc.txt txt: ./txt/cord-334299-0zn1z7rc.txt summary: title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In view of this need, we recommend methodological and quality assurance approaches for SARS-CoV-2 RNA detection in 158 wastewater using molecular methods. abstract: Monitoring for SARS-CoV-2 RNA in wastewater through the process of wastewater-based epidemiology (WBE) provides an additional surveillance tool, contributing to community-based screening and prevention efforts as these measurements have preceded disease cases in some instances. Numerous detections of SARS-CoV-2 RNA have been reported globally using various methods, demonstrating the technical feasibility of routine monitoring. However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. This review summarizes published studies of SARS-CoV-2 RNA detection in wastewater as well as available information regarding concentration, extraction, and detection methods. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. Researchers are recommended to follow the Minimum Information for Publication of Quantitative Real-Time PCR (MIQE) guidelines. Adhering to these recommendations will enable robust interpretation of wastewater monitoring results and improved inferences regarding the relationship between monitoring results and disease cases. url: https://www.ncbi.nlm.nih.gov/pubmed/33052320/ doi: 10.1016/j.coesh.2020.09.003 id: cord-262673-j2ot35lt author: Ahmed-Hassan, Hanaa title: Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date: 2020-08-18 words: 8591.0 sentences: 472.0 pages: flesch: 41.0 cache: ./cache/cord-262673-j2ot35lt.txt txt: ./txt/cord-262673-j2ot35lt.txt summary: Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells abstract: The new pandemic virus SARS-CoV-2 emerged in China and spread around the world in <3 months, infecting millions of people, and causing countries to shut down public life and businesses. Nearly all nations were unprepared for this pandemic with healthcare systems stretched to their limits due to the lack of an effective vaccine and treatment. Infection with SARS-CoV-2 can lead to Coronavirus disease 2019 (COVID-19). COVID-19 is respiratory disease that can result in a cytokine storm with stark differences in morbidity and mortality between younger and older patient populations. Details regarding mechanisms of viral entry via the respiratory system and immune system correlates of protection or pathogenesis have not been fully elucidated. Here, we provide an overview of the innate immune responses in the lung to the coronaviruses MERS-CoV, SARS-CoV, and SARS-CoV-2. This review provides insight into key innate immune mechanisms that will aid in the development of therapeutics and preventive vaccines for SARS-CoV-2 infection. url: https://doi.org/10.3389/fimmu.2020.01979 doi: 10.3389/fimmu.2020.01979 id: cord-336671-vfq5ft08 author: Ai, Jing-Wen title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 words: 1883.0 sentences: 108.0 pages: flesch: 50.0 cache: ./cache/cord-336671-vfq5ft08.txt txt: ./txt/cord-336671-vfq5ft08.txt summary: Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19. abstract: Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT–PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP. url: https://doi.org/10.1080/22221751.2020.1738905 doi: 10.1080/22221751.2020.1738905 id: cord-298991-5qae0ege author: Aiello, Francesco title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 words: 3143.0 sentences: 183.0 pages: flesch: 50.0 cache: ./cache/cord-298991-5qae0ege.txt txt: ./txt/cord-298991-5qae0ege.txt summary: SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients'' conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. This systematic review will firstly attempt to analyse the current knowledge on SARS-CoV-2 colonization of ocular and periocular tissues and secretions (i.e., cornea, conjunctiva, lacrimal sac, and tears), in order elucidate if conjunctival transmission occurs, and secondarily aims to propose a potential diagnostic tool in the evaluation of suspected, infected patients. Due to the scant evidence, both original articles, editorials, letters, and reviews providing evidence (i.e., prevalence, anecdotal report) about SARS-CoV-2 colonization of ocular and periocular tissues and secretions were all included in the study. This systematic review analysed 252 SARS-CoV-2infected patients globally who underwent conjunctival swab, and demonstrates the prevalence of ocular conjunctivitis complicating the course of COVID-19 to be as high as 32% (12 patients out 38) , differently as what Lu et al. abstract: Coronavirus disease 19 (COVID-19) has been described to potentially be complicated by ocular involvement. However, scant information is available regarding severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and ocular structures tropism. We conducted a systematic review of articles referenced in PubMed, Cochrane Library, Web of Science and Chinese Clinical Trial Register (ChiCTR) from December 20, 2019 to April 6, 2020, providing information on the presence of SARS-CoV-2 in cornea, conjunctiva, lacrimal sac, and tears. We excluded ongoing clinical studies as for unobtainable conclusive results. Of 2422 articles, 11 met the inclusion criteria for analysis and were included in the study. None of the studies were multinational. Among the 11 selected papers there were three original articles, one review, four letters, two editorials, and one correspondence letter. Globally, 252 SARS-CoV-2 infected patients were included in our review. The prevalence of ocular conjunctivitis complicating the course of COVID-19 was demonstrated to be as high as 32% in one study only. Globally, three patients had conjunctivitis with a positive tear-PCR, 8 patients had positive tear-PCR in the absence of conjunctivitis, and 14 had conjunctivitis with negative tear-PCR. The majority of the available data regarding SARS-CoV-2 colonization of ocular and periocular tissues and secretions have to be considered controversial. However, it cannot be excluded that SARS-CoV-2 could both infect the eye and the surrounding structures. SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients’ conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. url: https://doi.org/10.1038/s41433-020-0926-9 doi: 10.1038/s41433-020-0926-9 id: cord-272113-j82z4q8x author: Akaji, Kenichi title: Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease date: 2020-08-27 words: 6459.0 sentences: 281.0 pages: flesch: 45.0 cache: ./cache/cord-272113-j82z4q8x.txt txt: ./txt/cord-272113-j82z4q8x.txt summary: Instead of an exhaustive survey of the inhibitors [21] , we provide an overview of several typical inhibitors, and our recent efforts for the rational design of new scaffolds are discussed based on the inhibitory mechanism and structural interactions with SARS-CoV 3CL pro . Following the interaction with the active center of the SARS-CoV 3CL pro , the nucleophilic Cys145 thiolate generated by a proton-withdrawing effect caused by His41 at the catalytic dyad promotes a typical 1,4-addition to the α,β-unsaturated structure of the Michael acceptor ( Figure 3 ). These data also indicate that the corresponding S1 pocket of the SARS-CoV 3CL pro might accept a simple ring structure containing heteroatoms at this specific interaction site, which provides a clue to our design of a potent substrate-based inhibitor described later in this review. abstract: Three types of new coronaviruses (CoVs) have been identified recently as the causative viruses for the severe pneumonia-like respiratory illnesses, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and corona-virus disease 2019 (COVID-19). Neither therapeutic agents nor vaccines have been developed to date, which is a major drawback in controlling the present global pandemic of COVID-19 caused by SARS coronavirus 2 (SARS-CoV-2) and has resulted in more than 20,439,814 cases and 744,385 deaths. Each of the 3C-like (3CL) proteases of the three CoVs is essential for the proliferation of the CoVs, and an inhibitor of the 3CL protease (3CL(pro)) is thought to be an ideal therapeutic agent against SARS, MERS, or COVID-19. Among these, SARS-CoV is the first corona-virus isolated and has been studied in detail since the first pandemic in 2003. This article briefly reviews a series of studies on SARS-CoV, focusing on the development of inhibitors for the SARS-CoV 3CL(pro) based on molecular interactions with the 3CL protease. Our recent approach, based on the structure-based rational design of a novel scaffold for SARS-CoV 3CL(pro) inhibitor, is also included. The achievements summarized in this short review would be useful for the design of a variety of novel inhibitors for corona-viruses, including SARS-CoV-2. url: https://doi.org/10.3390/molecules25173920 doi: 10.3390/molecules25173920 id: cord-353229-k3zerr83 author: Akca, Ummusen Kaya title: Kawasaki-like disease in children with COVID-19 date: 2020-09-16 words: 4365.0 sentences: 281.0 pages: flesch: 42.0 cache: ./cache/cord-353229-k3zerr83.txt txt: ./txt/cord-353229-k3zerr83.txt summary: Herein, we report the characteristics of four patients with Kawasaki-like phenotype associated with COVID-19 from Turkey and analyze the features of similar published cases through a systematic literature review. Diagnosis of complete KD was based on the criteria of the American Heart Association (AHA): the presence of fever for at least 5 days accompanied by the presence of at least four of the following five findings: bilateral non-exudative conjunctival injection, unilateral cervical lymphadenopathy, changes in the lips and oral cavity, skin rash, and changes in extremities, including indurative angioedema and desquamation [18] . Children with persistent fever, inflammation (neutrophilia, high CRP, and lymphopenia), and single or multi-organ dysfunction have been identified in the UK as "Pediatric Multisystem Inflammatory Syndrome in relation to SARSCoV-2 (PMIS-TS)" regardless of the SARS-CoV-2 RT-PCR test results [73] . Pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort abstract: Children with Coronavirus disease 2019 (COVID-19) are being reported to have manifestations of hyperinflammatory states and/or Kawasaki-like disease. In this study, we investigated children with typical and atypical Kawasaki disease (KD) likely to be associated with COVID-19. We have reported four children with Kawasaki-like disease probably associated with COVID-19. The clinical features were consistent with incomplete KD in three patients. SARS-CoV-2 RT-PCR was positive in one and the serology was positive in one patient with negative RT-PCR. Corticosteroids, anakinra, intravenous immunoglobulin (IVIG), and acetylsalicylic acid were used in the treatment. Three patients recovered after the treatment while one patient died. The literature review revealed 36 articles describing 320 children with Kawasaki-like disease associated with COVID-19. SARS-CoV-2 RT-PCR was negative in 120 (65.5%) of 183 patients while the serology was positive in 130 (83.8%) of 155 patients. The therapeutic options have included IVIG, acetylsalicylic acid, tocilizumab, anakinra, enoxaparin, and methylprednisolone. Pediatric COVID-19 cases may present with atypical/incomplete Kawasaki-like disease. Thus, pediatricians need to be aware of such atypical presentations resembling KD for early diagnosis of COVID-19. url: https://doi.org/10.1007/s00296-020-04701-6 doi: 10.1007/s00296-020-04701-6 id: cord-320466-l7017jis author: Akgun, Emel title: Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date: 2020-10-20 words: 3722.0 sentences: 226.0 pages: flesch: 42.0 cache: ./cache/cord-320466-l7017jis.txt txt: ./txt/cord-320466-l7017jis.txt summary: Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified up-regulated proteins Myeloperoxidase, Myeloblastin, Neutrophil Elastase, Cathepsin G, and Azurocidin (MPO, PRTN3, ELANE, CTSG, and AZU1) in nasooropharyngeal swab samples are discussed to highlight the molecular mechanism changes in the site of infection. Pathway analysis of the significantly altered protein levels between COVID-19 positive and negative patients'' naso-oropharyngeal swab samples were analyzed using the STRING online database. In SARS-CoV-2 patients'' naso-oropharyngeal samples, we have identified azurophilic granule (AG) proteins like Myeloperoxidase (MPO), elastase (ELANE), cathepsin G (CTSG), azurocidin 1 (AZU1) and proteinase 3 (PRTN3) to be highly overexpressed. The alterations of various proteins in SARS-CoV-2 infected patients'' naso-oropharyngeal samples depict the molecular changes that govern the host antiviral defense system. abstract: COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 9 million people and caused the death of around 470,000 patients. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rate of severe hospitalization even more so for the elderly population. Naso-oro-pharyngeal swab samples as the first step towards detecting suspected infection of SARS-CoV-2 provides a non-invasive method for PCR testing at a high confidence rate. Furthermore, proteomics analysis of PCR positive and negative naso-oropharyngeal samples provides information on the molecular level which highlights disease pathology. Samples from 15 PCR positive cases and 15 PCR negative cases were analyzed with nanoLC-MS/MS to identify the differentially expressed proteins. Proteomic analyses identified 207 proteins across the sample set and 17 of them were statistically significant. Protein-protein interaction analyses emphasized pathways like Neutrophil degranulation, Innate Immune System, Antimicrobial Peptides. Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified proteins are linked to alteration in the innate immune system specifically via neutrophil degranulation and NETosis. url: https://doi.org/10.1371/journal.pone.0240012 doi: 10.1371/journal.pone.0240012 id: cord-325293-nwxtyrpl author: Akhtar, Hubba title: COVID-19 (SARS-CoV-2) Infection in Pregnancy: A Systematic Review date: 2020-07-30 words: 3502.0 sentences: 279.0 pages: flesch: 56.0 cache: ./cache/cord-325293-nwxtyrpl.txt txt: ./txt/cord-325293-nwxtyrpl.txt summary: INTRODUCTION: To review published studies related to the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with pregnancy, foetal, and neonatal outcomes during coronavirus disease 2019 (COVID-19) pandemic in a systematic manner. This study was done according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method identifying published literature on COVID-19 and its potential impact on pregnancy and neonates. The comprehensive literature search was carried out with PubMed, Medline, Scopus, Cochrane database, and Google Scholar, using key MeSH words, which include "COVID-19," "Pregnancy," "Coronavirus 2019," "Newborn," "Foetus," "Neonate," "vertical transmission," and "outcomes." All published articles have been reviewed, and the findings have been included in this study. [6] Clinical analysis of 10 neonates born to mothers with 2019-nCoV pneumonia 9 10 (2 twins) Fever (8) Intrauterine distress (6) Shortness of breath (6) Infections (4) (3) PROM (3) Fever (2) NRDS (2) Sore throat (1) (3) Dyspnoea (1) Sore throat (1) NVD (1) Diarrhoea (1) Unknown as still pregnant (4) Yu et al. abstract: INTRODUCTION: To review published studies related to the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with pregnancy, foetal, and neonatal outcomes during coronavirus disease 2019 (COVID-19) pandemic in a systematic manner. METHODS: A comprehensive electronic search was done through PubMed, Scopus, Medline, Cochrane database, and Google Scholar from December 01, 2019, to May 22, 2020, along with the reference list of all included studies. All cohort studies that reported on outcomes of COVID-19 during pregnancy were included. Qualitative assessment of included studies was performed using the Newcastle-Ottawa scale. RESULTS: Upon admission, most pregnant women underwent a low-dose radiation CT scan; the reports of which included unilateral/bilateral pneumonia in most patients. A marked lymphopenia was also noted in many patients with COVID-19. 513 titles were screened, and 22 studies were included, which identified 156 pregnant women with COVID-19 and 108 neonatal outcomes. The most common maternal/foetal complications included intrauterine/foetal distress (14%) and premature rupture of membranes (8%). The neonatal clinical manifestations of COVID-19 commonly included shortness of breath (6%), gastrointestinal symptoms (4%), and fever (3%). CONCLUSION: COVID-19 infection in pregnancy leads to increased risk in pregnancy complications such as preterm birth, PPROM, and may possibly lead to maternal death in rare cases. There is no evidence to support vertical transmission of SARS-CoV-2 infection to the unborn child. Due to a paucity of inconsistent data regarding the impact of COVID-19 on the newborn, caution should be undertaken to further investigate and monitor possible infection in the neonates born to COVID-19-infected mothers. url: https://www.ncbi.nlm.nih.gov/pubmed/32728006/ doi: 10.1159/000509290 id: cord-291644-5y0ioety author: Akiyama, Tomohiro title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond date: 2020-08-29 words: 5835.0 sentences: 306.0 pages: flesch: 45.0 cache: ./cache/cord-291644-5y0ioety.txt txt: ./txt/cord-291644-5y0ioety.txt summary: title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond Since the long-term continuous measurement of intravascular NO was impossible, complementary tests were conducted to determine whether IFMC could increase the surface temperature, blood flow rate, velocity and vessel diameter in the human body. The present study confirmed that the natural-mineral-based novel nanomaterial IFMC, with a size of tens of nanometres (Figure 1 ), could induce an increase of intravascular NO (Figure 3) , vasodilation (vessel diameter) and blood flow rate in a living body (Figure 4) , as well as an increase of the surface temperature of a hand including fingers ( Figure 5 ). To summarise, our inter-and trans-disciplinary approach revealed that the natural-mineral-based novel nanomaterial IFMC can induce an increase of intravascular NO, vasodilation and blood flow rate, as well as an increase of hand surface temperature in a living body. abstract: There are currently no promising therapy strategies for either the treatment or prevention of novel coronavirus disease 2019 (COVID-19), despite the urgent need. In addition to respiratory diseases, vascular complications are rapidly emerging as a key threat of COVID-19. Existing nitric oxide (NO) therapies have been shown to improve the vascular system; however, they have different limitations in terms of safety, usability and availability. In light of this, we hypothesise that a natural-mineral-based novel nanomaterial, which was developed based on NO therapy, might be a viable strategy for the treatment and prevention of COVID-19. The present study examined if it could induce an increase of intravascular NO, vasodilation and the consequent increase of blood flow rate and temperature in a living body. The intravascular NO concentration in the hepatic portal of rats was increased by 0.17 nM over 35.2 s on average after its application. An ultrasonic Doppler flow meter showed significant increases in the blood flow rate and vessel diameter, but no difference in the blood flow velocity. These were corroborated by measurements of human hand surface temperature. To our knowledge, this result is the first evidence where an increase of intravascular NO and vasodilation were induced by bringing a natural-mineral-based nanomaterial into contact with or close to a living body. The precise mechanisms remain a matter for further investigation; however, we may assume that endothelial NO synthase, haemoglobin and endothelium-derived hyperpolarising factor are deeply involved in the increase of intravascular NO. url: https://www.ncbi.nlm.nih.gov/pubmed/32872395/ doi: 10.3390/nano10091699 id: cord-313603-y8p9bmph author: Akter, Shahina title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh date: 2020-09-24 words: 957.0 sentences: 58.0 pages: flesch: 57.0 cache: ./cache/cord-313603-y8p9bmph.txt txt: ./txt/cord-313603-y8p9bmph.txt summary: title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. After generating a FASTA file from the FASTQ files using the DRAGEN software, it was found that the complete genome sequences of the Bangladeshi SARS-CoV-2 strains (BCSIR_ NILMRC_006, BCSIR_NILMRC_007, and BCSIR_NILMRC_008) have linear RNAs of 29,892 bp, 29,823 bp, and 29,758 bp, respectively, with an average GC content of 39%. The sequences of these SARS-CoV-2 genomes from Bangladesh were submitted to the GISAID database (accession no. We extend special thanks to Architect Yeafesh Osman, Honorable Minister of Science and Technology. Anwar Hossain, Senior Secretary, Ministry of Science and Technology. abstract: We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. The data from this analysis will contribute to advancing our understanding of the epidemiology of SARS-CoV-2 in Bangladesh as well as worldwide at the molecular level and will identify potential new targets for interventions. url: https://www.ncbi.nlm.nih.gov/pubmed/32972934/ doi: 10.1128/mra.00764-20 id: cord-302195-25gjbyi1 author: Al Huraimel, Khalid title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 words: 7089.0 sentences: 386.0 pages: flesch: 50.0 cache: ./cache/cord-302195-25gjbyi1.txt txt: ./txt/cord-302195-25gjbyi1.txt summary: This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. There is no conclusive evidence for aerosol or faecal-oral transmission of SARS-CoV-2 despite several researchers considering them as plausible routes that may explain the high infectivity and global spread of COVID-19 (Chen et al., 2020; van Doremalen et al., 2020; Wang et al., 2020a) . From the literature studied, concerns of COVID-19 infection through environmental contact pertain mainly to areas that lack proper sanitation and wastewater treatment, lack adequate solid waste management infrastructure, in areas where raw sewage is discharged directly into natural water bodies, and in cities where air pollution is problematic.  Robust evidence is needed to assess impact of air pollution, solid waste management, and sewage contamination of water bodies on COVID-19 spread and infectivity. abstract: Abstract The coronavirus disease 2019 (COVID-19) is spreading globally having a profound effect on lives of millions of people, causing worldwide economic disruption. Curbing the spread of COVID-19 and future pandemics may be accomplished through understanding the environmental context of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and adoption of effective detection tools and mitigation policies. This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. Transmission of SARS-CoV-2 via faecal-oral or bio-aerosols lacks robust evidence and remains debatable. However, improper disinfection and defected plumbing systems in indoor environments such as hospitals and high-rise towers may facilitate the transport of virus-laden droplets of wastewater causing infection. Clinical and epidemiological studies are needed to present robust evidence that SARS-CoV-2 is transmissible via aerosols, though quantification of virus-laden aerosols at low concentrations presents a challenge. Wastewater surveillance of SARS-CoV-2 can be an effective tool in early detection of outbreak and determination of COVID-19 prevalence within a population, complementing clinical testing and providing decision makers guidance on restricting or relaxing movement. While poor air quality increases susceptibility to diseases, evidence for air pollution impact on COVID-19 infectivity is not available as infections are dynamically changing worldwide. Solid waste generated by households with infected individuals during the lockdown period may facilitate the spread of COVID-19 via fomite transmission route but has received little attention from the scientific community. Water bodies receiving raw sewage may pose risk of infection but this has not been investigated to date. Overall, our understanding of the environmental perspective of SARS-CoV-2 is imperative to detecting outbreak and predicting pandemic severity, allowing us to be equipped with the right tools to curb any future pandemic. url: https://www.sciencedirect.com/science/article/pii/S0048969720344752?v=s5 doi: 10.1016/j.scitotenv.2020.140946 id: cord-304617-5ozf18lg author: Al-Khafaji, Khattab title: Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 date: 2020-05-15 words: 4367.0 sentences: 227.0 pages: flesch: 51.0 cache: ./cache/cord-304617-5ozf18lg.txt txt: ./txt/cord-304617-5ozf18lg.txt summary: The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. The got protein-drug complex structures from covalent docking were submitted to MD simulations (saquinavir, ritonavir, and remdesivir with SARS-CoV-2 Mpro). The effect of drug-protein interactions upon dynamics of biological system is a fundamental in drug discovery thereby we used RMSD to investigate the influence of saquinavir, ritonavir, and remdesivir upon the stability of SARS-CoV-2 Mpro. One of the more noteworthy findings in this study is that MD simulation analysis that saquinavir, ritonavir, and remdesivir can form stable interaction inside the binding site of SARS-CoV-2 Mpro. abstract: SARS-CoV-2 is a new generation of coronavirus, which was first determined in Wuhan, China, in December 2019. So far, however, there no effective treatment has been found to stop this new generation of coronavirus but discovering of the crystal structure of SARS-CoV-2 main protease (SARS-CoV-2 Mpro) may facilitate searching for new therapies for SARS-COV-2. The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. We conducted the covdock module MMGBSA module in the Schrodinger suite 2020-1, to examine the covalent bonding utilizing. Besides, we submitted the top three drugs to molecular dynamics simulations via Gromacs 2018.1. The covalent docking showed that saquinavir, ritonavir, remdesivir, delavirdine, cefuroxime axetil, oseltamivir and prevacid have the highest binding energies MMGBSA of –72.17, −72.02, −65.19, −57.65, −54.25, −51.8, and −51.14 kcal/mol, respectively. The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. The current study provides a powerful in silico results, means for rapid screening of drugs as anti-protease medications and recommend that the above-mentioned drugs can be used in the treatment of SARS-CoV-2 in combined or sole therapy. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1764392 doi: 10.1080/07391102.2020.1764392 id: cord-330384-yujbcwg5 author: Al-Mulla, Fahd title: A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date: 2020-05-16 words: 4684.0 sentences: 249.0 pages: flesch: 52.0 cache: ./cache/cord-330384-yujbcwg5.txt txt: ./txt/cord-330384-yujbcwg5.txt summary: The increased cleavage activity of this protease was suggested to diminish viral recognition by neutralizing antibodies and by activating SARS spike (S) protein for virus-cell fusion 11 and facilitates the active binding of SARS-CoV-2 through ACE2 receptor, which is a risk factor for a more serious COVID-19 presentation [8] [9] [10] . Recent studies, assessed the genetic variations and eQTL (expression quantitative trait locus) expression profiles in the candidate genes ACE2, TMPRSS2, and FURIN to demonstrate the sex and population-wise differences that may influence the pathogenicity of SARS-CoV-2 9, [15] [16] [17] [18] [19] . Therefore, we screened the genetic variations and eQTL expression of the SARS-CoV-2 candidate genes, ACE2, TMPRSS2 and FURIN in three Middle Eastern populations: Kuwaiti, Iranian, and Qatari and compared them to available MAF data in the gnomAD database 41 . abstract: The severity of the new COVID-19 pandemic caused by the SARS-CoV-2 virus is strikingly variable in different global populations. SARS-CoV-2 uses ACE2 as a cell receptor, TMPRSS2 protease, and FURIN peptidase to invade human cells. Here, we investigated 1,378 whole-exome sequences of individuals from the Middle Eastern populations (Kuwait, Qatar, and Iran) to explore natural variations in the ACE2, TMPRSS2, and FURIN genes. We identified two activating variants (K26R and N720D) in the ACE2 gene that are more common in Europeans than in the Middle Eastern, East Asian, and African populations. We postulate that K26R can activate ACE2 and facilitate binding to S-protein RBD while N720D enhances TMPRSS2 cutting and, ultimately, viral entry. We also detected deleterious variants in FURIN that are frequent in the Middle Eastern but not in the European populations. This study highlights specific genetic variations in the ACE2 and FURIN genes that may explain SARS-CoV-2 clinical disparity. We showed structural evidence of the functionality of these activating variants that increase the SARS-CoV-2 aggressiveness. Finally, our data illustrate a significant correlation between ACE2 variants identified in people from Middle Eastern origins that can be further explored to explain the variation in COVID-19 infection and mortality rates globally. url: https://doi.org/10.1101/2020.05.16.099176 doi: 10.1101/2020.05.16.099176 id: cord-275191-lgze4zex author: Al-Sadeq, Duaa W. title: The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date: 2020-07-02 words: 3287.0 sentences: 221.0 pages: flesch: 48.0 cache: ./cache/cord-275191-lgze4zex.txt txt: ./txt/cord-275191-lgze4zex.txt summary: AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. abstract: BACKGROUND: the recent outbreak of the coronavirus disease 2019 (COVID‐19) has quickly spread globally since its discovery in Wuhan, China, in December 2019. A comprehensive strategy, including surveillance, diagnostics, research, and clinical treatment is urgently needed to win the battle against COVID-19. Recently, numerous studies reported the incidence of SARS-CoV-2 in asymptomatic patients. Yet, the incidence and viral transmission from the asymptomatic cases are not apparent yet. AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. METHOD: the literature was searched through four scientific databases: PubMed, Web of Science, Scopus, and Science Direct. RESULTS: a total of 63 studies satisfied the inclusion criteria where the majority of the reported studies were from China. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. Studies with a large sample size (n>1000) estimated that percentage of people contracting SARS-CoV-2 and are likely to be asymptomatic ranges from 1.2-12.9%. However, the other studies with a smaller sample size reported a much higher incidence and indicated that up to 87.9% of COVID-19 infected individuals could be asymptomatic. Most of these studies indicated that asymptopatics are a potential source of infection to the community. CONCLUSION: this review highlighted the need for more robust and well-designed studies to better estimate COVID-19 incidence among asymptomatic patients worldwide. The early identification of the asymptomatic cases, as well as monitoring and tracing close contact, could help in mitigating the spread of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305336?v=s5 doi: 10.1016/j.ijid.2020.06.098 id: cord-354398-f3cg8gi1 author: Al-Saud, Haya title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 words: 4018.0 sentences: 199.0 pages: flesch: 55.0 cache: ./cache/cord-354398-f3cg8gi1.txt txt: ./txt/cord-354398-f3cg8gi1.txt summary: The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. We validated the modified Invitrogen Forensic DNA Purification kit in extracting in-laboratory propagated SARS-COV-2 RNA by conducting manual and automated extractions on titrations from 15 000 copies to 60 copies of SARS-COV-2 followed by RT-qPCR methods: the commercially available TaqPath One-Step qRT-QP-CR kit (using the N, S, and ORF1b genes) and primers and probes from Metabion, Germany to establish an inhouse RT-qPCR assay based on E, RdRp2 and RdRp4 gene detection as per recommended SARS-COV-2 testing from CDC and WHO. abstract: BACKGROUND: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has prompted a need for mass testing to identify patients with viral infection. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. OBJECTIVES: Report on the use of a DNA extraction kit, after modifications, to extract viral RNA that could then be detected using an FDA-approved SARS-COV-2 RT-qPCR assay. MATERIALS AND METHODS: Initially, automated RNA extraction was performed using a modified DNA kit on samples from control subjects, a bacteriophage, and an RNA virus. We then verified the automated extraction using the modified kit to detect in-lab propagated SARSCOV-2 titrations using an FDA approved commercial kit (S, N, and ORF1b genes) and an in-house primer-probe based assay (E, RdRp2 and RdRp4 genes). RESULTS: Automated RNA extraction on serial dilutions SARS-COV-2 achieved successful one-step RT-qPCR detection down to 60 copies using the commercial kit assay and less than 30 copies using the in-house primer-probe assay. Moreover, RT-qPCR detection was successful after automated RNA extraction using this modified protocol on 12 patient samples of SARS-COV-2 collected by nasopharyngeal swabs and stored in viral transport media. CONCLUSIONS: We demonstrated the capacity of a modified DNA extraction kit for automated viral RNA extraction and detection using a platform that is suitable for mass testing. LIMITATIONS: Small patient sample size. CONFLICT OF INTEREST: None. url: https://doi.org/10.5144/0256-4947.2020.373 doi: 10.5144/0256-4947.2020.373 id: cord-291248-0kuc9jv9 author: Al-Sehemi, Abdullah G. title: Potential of NO donor furoxan as SARS-CoV-2 main protease (M(pro)) inhibitors: in silico analysis date: 2020-07-08 words: 4973.0 sentences: 293.0 pages: flesch: 49.0 cache: ./cache/cord-291248-0kuc9jv9.txt txt: ./txt/cord-291248-0kuc9jv9.txt summary: Herein, we evaluated the phenyl furoxan, a well-known exogenous NO donor to identify the possible potent inhibitors through in silico studies such as molecular docking as per target analysis for candidates bound to substrate binding pocket of SARS-COV-2 M(pro). In the present study to validate the molecular docking, MD simulation and MM-PBSA results, crystal structure of M(pro) bound to experimentally known inhibitor X77 was used as control and the obtained results are presented herein. Docking analysis of the studied furoxan derivatives were found to have similar binding ability to SARS-CoV-2 M pro as compared to reported inhibitors. Residue wise decomposition results confirms that the interacting residues from binding pocket of SARS-CoV-2 M pro as obtained from docking analysis (Table 1 ) also shows significantly higher energetic contribution in binding with potent furoxan derivatives 22, 26 in comparison to control ( Figure 10A -C). abstract: The sharp spurt in positive cases of novel coronavirus-19 (SARS-CoV-2) worldwide has created a big threat to human. In view to expedite new drug leads for COVID-19, Main Proteases (M(pro)) of novel Coronavirus (SARS‐CoV‐2) has emerged as a crucial target for this virus. Nitric oxide (NO) inhibits the replication cycle of SARS-CoV. Inhalation of nitric oxide is used in the treatment of severe acute respiratory syndrome. Herein, we evaluated the phenyl furoxan, a well-known exogenous NO donor to identify the possible potent inhibitors through in silico studies such as molecular docking as per target analysis for candidates bound to substrate binding pocket of SARS-COV-2 M(pro). Molecular dynamics (MD) simulations of most stable docked complexes (M(pro)-22 and M(pro)-26) helped to confirm the notable conformational stability of these docked complexes under dynamic state. Furthermore, Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations revealed energetic contributions of key residues of M(pro) in binding with potent furoxan derivatives 22, 26. In the present study to validate the molecular docking, MD simulation and MM-PBSA results, crystal structure of M(pro) bound to experimentally known inhibitor X77 was used as control and the obtained results are presented herein. We envisaged that spiro-isoquinolino-piperidine-furoxan moieties can be used as effective ligand for SARS-CoV-2 M(pro) inhibition due to the presence of key isoquinolino-piperidine skeleton with additional NO effect. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32643550/ doi: 10.1080/07391102.2020.1790038 id: cord-294349-ps3qlho2 author: Al-Sharif, Eman title: Ocular tropism of coronavirus (CoVs): a comparison of the interaction between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye date: 2020-09-03 words: 7053.0 sentences: 340.0 pages: flesch: 43.0 cache: ./cache/cord-294349-ps3qlho2.txt txt: ./txt/cord-294349-ps3qlho2.txt summary: PURPOSE: Several studies have reported conflicting results on ocular manifestations and transmission of coronavirus disease 2019 (COVID-19) whose causative virus, SARS-CoV-2, belongs to the coronavirus family, the seventh recognized as a human pathogen and the third causing a severe clinical syndrome. Coronavirus disease 2019, known as COVID-19, is an emerging infection which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first reported in Wuhan city, China, late in December 2019 [4] . Clinical ocular manifestations were absent in all SARS-CoV-1 patients, and viral RNA was detected in the conjunctival secretions and tears in three cases out of 120 (2.5%) with a range of 0-8% [6] [7] [8] [9] . Similarly, a small study testing the conjunctival secretions and tears (collected twice over 2-3 days) of 30 confirmed COVID-19 patients demonstrated the presence of viral RNA (in both samples) in one patient only who also showed clinical signs of conjunctivitis [12] . abstract: PURPOSE: Several studies have reported conflicting results on ocular manifestations and transmission of coronavirus disease 2019 (COVID-19) whose causative virus, SARS-CoV-2, belongs to the coronavirus family, the seventh recognized as a human pathogen and the third causing a severe clinical syndrome. COVID-19 primarily affects the lungs, similar to the other human coronaviruses. Comparing the relation between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-Cov-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye may contribute to determining their actual eye-tissue tropism and risk of ocular transmission. METHODS: Literature review was conducted via Pubmed.gov, Google Scholar and medRixv using the following keywords: COVID-19, SARS-CoV-2, SARS-CoV-1, MERS-CoV, CoV-229E, NL63, OC43, HKU1, conjunctivitis, tear swab, ocular expression, ocular symptoms and human angiotensin converting enzyme-2 expression. Studies with lack in methodology were excluded. RESULTS: Sixteen observational studies were selected. The range for detection of viral RNA in tears was 0–8% for SARS-CoV-1 and 0–5.3% for SARS-CoV-2, while no reports were found for other coronaviruses. Ocular manifestations have been reported for NL63 and SARS-CoV-2. Ocular symptoms in the form of conjunctivitis/conjunctival congestion predominantly were detected in 65 (3.17%) out of 2048 reported patients with COVID-19 (range of 0.8–32%). Eye symptoms were not reported for the other coronaviruses. CONCLUSIONS: Data aggregation for coronaviruses shows a relatively low eye-tissue tropism. Conjunctival congestion is an uncommon manifestation of COVID-19 similar to all human coronaviruses’ infections. In a low percentage of patients, the virus can be excreted in ocular fluids at different stages of the infection, regardless of positive SARS-Cov-2 throat swab. Albeit high viral loads in ocular tissue seem to have relatively low prevalence, the eye should be regarded as a potential source of infection dissemination for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32880786/ doi: 10.1007/s10792-020-01575-2 id: cord-345019-i7zm9bt1 author: Al-Waleedi, Ali Ahmed title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 words: 4496.0 sentences: 236.0 pages: flesch: 55.0 cache: ./cache/cord-345019-i7zm9bt1.txt txt: ./txt/cord-345019-i7zm9bt1.txt summary: A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. For early detection of SARS-CoV-2 in Yemen, as in other countries, a case definition, active surveillance, and contact tracing were required [10, 11] . The first 2 months after confirmation of the SARS-CoV-2 epidemic in Yemen was characterized by a 57% hospitalization rate in the southern and eastern parts of the country included in The First 2 Months of the SARS-CoV-2 Epidemic in Yemen our study, 63% of deaths occurring in individuals aged <60 years, confirmatory testing of <50% of the suspected cases, and majority of cases were not related to a defined chain of transmission. abstract: INTRODUCTION: Yemen was one of the last countries in the world to declare the first case of the pandemic, on 10 April 2020. Fear and concerns of catastrophic outcomes of the epidemic in Yemen were immediately raised, as the country is facing a complex humanitarian crisis. The purpose of this report is to describe the epidemiological situation in Yemen during the first 2 months of the SARS-CoV-2 epidemic. METHODS: We analyzed the epidemiological data from 18 February to 05 June 2020, including the 2 months before the confirmation of the first case. We included in our analysis the data from 10 out of 23 governorates of Yemen, located in southern and eastern part of the country. RESULTS: A total of 469 laboratory confirmed, 552 probable and 55 suspected cases with onset of symptoms between 18 February and 5 June 2020 were reported through the surveillance system. The median age among confirmed cases was 46 years (range: 1–90 years), and 75% of the confirmed cases were male. A total of 111 deaths were reported among those with confirmed infection. The mean age among those who died was 53 years (range: 14–88 years), with 63% of deaths (n = 70) occurring in individuals under the age 60 years. A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. The mild and moderate cases were not self-reported to the health facilities and surveillance system due to limited resources, stigma, and other barriers. The mortality appeared to be higher in individuals aged under 60 years, and most fatalities occurred in individuals who were in critical condition when they reached the health facilities. It is unclear whether the presence of other acute comorbidities contributed to the high death rate among SARS-CoV-2 cases. The findings only include the southern and eastern part of the country, which is home to 31% of the total population of Yemen, as the data from the northern part of the country was inaccessible for analysis. This makes our results not generalizable to the rest of the country. url: https://www.ncbi.nlm.nih.gov/pubmed/33119720/ doi: 10.1371/journal.pone.0241260 id: cord-289364-p31gt533 author: AlFehaidi, Alanoud title: A case of SARS-CoV-2 re-infection date: 2020-10-25 words: 965.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-289364-p31gt533.txt txt: ./txt/cord-289364-p31gt533.txt summary: Different reports have proposed the reactivation of SARS-CoV-2 infection, with 2 RT-PCR positive results following resolving symptoms and interim RT-PCR negative results [4] [5] [6] [7] [8] [9] [10] [11] . Early studies reported that re-detectable positive virus nucleic acid among patients with SARS-CoV-2 with an average duration of 15 days from discharge to a re-positive results 13 . Patients in those early reports did not show signs of infection with the second positive results and had negative swab results within one week later. The COCOREC (Collaborative study COvid RECurrences) study suggested that recurrence of infection is likely if the patient has two confirmed SARS-CoV-2 RT-PCR positive results over 15 days apart with one major clinical sign and no other cause to explain the symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report abstract: nan url: https://doi.org/10.1016/j.jinf.2020.10.019 doi: 10.1016/j.jinf.2020.10.019 id: cord-309582-ihrj84hr author: AlNaamani, Khalid title: Medical research during the COVID-19 pandemic date: 2020-08-06 words: 4047.0 sentences: 188.0 pages: flesch: 36.0 cache: ./cache/cord-309582-ihrj84hr.txt txt: ./txt/cord-309582-ihrj84hr.txt summary: Despite the dedication of enormous resources, the advancement in health care systems and collaboration between different investigators across the world, only a small number of patients over the last decade have in fact benefited from clinical research performed during different outbreaks of respiratory viruses such as was the case for the severe acute respiratory syndrome (SARS), the HIN1 flu virus (swine flu) or the Middle East Respiratory Syndrome. An example of unpublished results that need to be widely acknowledged because of a negative outcome leading to early termination is that of a Brazilian study (CloroCovid19 ) which was a parallel, double-blind, randomized, phase IIb clinical trial, which started on March 23, 2020, aiming to assess safety and efficacy of Chloroquine diphosphate (CQ) in the treatment of hospitalized patients with severe respiratory syndrome secondary to SARS-CoV-2 infection. abstract: The current pandemic of coronavirus disease 2019 (COVID-19) which was first detected in Wuhan, China in December 2019 is caused by the novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The virus has quickly spread to a large number of countries leading to a great number of deaths. Unfortunately, till today there is no specific treatment or vaccination for SARS-CoV-2. Most of the suggested treatment medications are based on in vitro laboratory investigations, experimental animal models, or previous clinical experience in treating similar viruses such as SARS-CoV-1 or other retroviral infections. The running of any clinical trial during a pandemic is affected at multiple levels. Reasons for this include patient hesitancy or inability to continue investigative treatments due to self-isolation/quarantine, or limited access to public places (including hospitals). Additional barriers relate to health care professionals being committed to other critical tasks or quarantining themselves due to contact with COVID-19 positive patients. The best research approaches are those that adapt to such external unplanned obstacles. Ongoing clinical trials before COVID-19 pandemic have the potential for identifying important therapies in the long-term if they can be completed as planned. However, these clinical trials may require modifications due a pandemic such as this one to ensure the rights, safety, and wellbeing of participants as well as medical staff involved in the conduction of clinical trials. Clinical trials initiated during the pandemic must be time-efficient and flexible due to high contagiousness of severe acute respiratory syndrome coronavirus 2, the significant number of reported deaths, and time constraints needed to perform high quality clinical trials, enrolling adequate sample sizes. Collaboration between different countries as well as implementation of innovative clinical trial designs are essential to successfully complete such initiatives during the current pandemic. Studies looking at the long term sequalae of COVID-19 are also of importance as recent publications describe multi-organ involvement. Long term follow-up of COVID-19 survivors is thus also important to identify possible physical and mental health sequellae. url: https://www.ncbi.nlm.nih.gov/pubmed/32874970/ doi: 10.12998/wjcc.v8.i15.3156 id: cord-104435-y7mxyein author: Alabdulmonem, Waleed title: COVID-19: A global public health disaster date: 2020 words: 596.0 sentences: 40.0 pages: flesch: 58.0 cache: ./cache/cord-104435-y7mxyein.txt txt: ./txt/cord-104435-y7mxyein.txt summary: [4] As compared to the previous CoVs, the infectivity rate of SARS-CoV-2 is comparatively much higher, and the mode of transmission of this deadly virus is primarily by respiratory droplets from an infected individual to others through coughing, sneezing within a distance up to 6 feet, or touching of infected surfaces, where the viral particles are present. [9] The transmission of virus can be decreased to a large extent by adopting strict infection control policies, which are basically a team base efforts and everyone has to play their roles. [8, 9] Being an enveloped virus, SARs-CoV-2 is comparatively easy to disinfect; therefore, hands hygiene plays a vital preventive tool from getting infected, washing hands frequently with soap and water or using alcohol-based hand sanitizers to disinfect hands have strongly been recommended by the WHO. Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica) abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269619/ doi: nan id: cord-333080-qytwbsne author: Alahari, Suresh K. title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 words: 2244.0 sentences: 123.0 pages: flesch: 49.0 cache: ./cache/cord-333080-qytwbsne.txt txt: ./txt/cord-333080-qytwbsne.txt summary: Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. Developing functional computational models and networks to predict potential SARS-CoV -miRNA/lncRNA association may benefit not only the understanding of COVID-19 mechanism at the noncoding RNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis, and prevention. Since multiple ways of interaction between miRNAs, lncRNAs, and mRNA have been reported to play key roles in determining the cellular functions during viral infection, it is essential to discover these interactions in an integrated fashion to comprehensively decipher the networks and key regulatory noncoding-RNA hubs underpinning the pathology of SARS-CoV. Our in-silico analysis has built a network of protein-protein interaction between the Human SARS coronavirus (SARS-CoV) and host proteome (Figure 1) , as well as strong miRNA-mRNA-lncRNA crosstalk ( Figure 4 and Table 2 ) possibly modulating the human response to the viral infection. abstract: Although 70% of the genome is transcribed to RNA in humans, only ∼2% of these transcripts are translated into proteins. The rest of the transcripts are defined as noncoding RNAs, including Long noncoding RNAs (LncRNAs) and MicroRNAs (miRNAs) that mostly function post-transcriptionally to regulate the gene expression. The outbreak of a novel coronavirus (SARS-CoV) has caused a major public health concern across the globe. The SARS-CoV is the seventh coronavirus that is known to cause human disease. There are currently no promising antiviral drugs with proven efficacy nor are there vaccines for its prevention. As of July 13, 2020, SARS-CoV has been infected more than 13 million cases in more than 213 countries, with an estimated mortality rate of ∼3%. Thus, it is of utmost important priority to develop novel therapies for COVID-19. It is not fully investigated whether noncoding RNAs regulate signaling pathways that SARS-CoV involved in. Hence, computational analysis of the noncoding RNA interactions and determining importance of key regulatory noncoding RNAs in antiviral defense mechanisms will likely be helpful in developing new drugs to attack SARS-CoV infection.. To elucidate this, we utilized bioinformatic approaches to find the interaction network of SARS-CoV/human proteins, miRNAs, and lncRNAs. We found TGF-beta signaling pathway as one of the potential interactive pathways. Furthermore, potential miRNAs/lncRNAs networks that the virus might engage during infection in human host cells have been shown. Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. url: https://www.sciencedirect.com/science/article/pii/S0753332220307411?v=s5 doi: 10.1016/j.biopha.2020.110548 id: cord-338755-f5g2r4n9 author: Alam, Nawsad title: A spike with which to beat COVID-19? date: 2020-05-15 words: 760.0 sentences: 53.0 pages: flesch: 64.0 cache: ./cache/cord-338755-f5g2r4n9.txt txt: ./txt/cord-338755-f5g2r4n9.txt summary: This month''s Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine. Coronavirus spikes have been structurally characterized before, in particular for SARS-CoV and MERS-CoV, two related viruses that have caused epidemics of respiratory disease. Shortly after this, the first structure of a neutralizing antibody bound to the RBD of the spike glycoprotein showed that SARS-CoV-reactive antibodies could neutralize the new virus 3 , and polyclonal antibody sera against SARS-CoV also proved effective 1 . Two spike-based vaccine-design strategies, developed for SARS-CoV, should be applicable. To generate the most effective neutralizing antibody responses, vaccinated individuals should generate antibodies to the pre-fusion spike, thus preventing ACE2 binding and cell entry. For this reason, structure-guided mutations have been designed that fix the SARS-CoV spike into this pre-fusion state 4 . Stabilized SARS-CoV-2 spikes, designed using this method, are therefore promising for a vaccine. abstract: This month’s Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/32415242/ doi: 10.1038/s41579-020-0383-2 id: cord-324619-y7gilopu author: Alam, S.B. title: Severe acute respiratory syndrome coronavirus‐2 may be an underappreciated pathogen of the central nervous system date: 2020-07-15 words: 5244.0 sentences: 254.0 pages: flesch: 42.0 cache: ./cache/cord-324619-y7gilopu.txt txt: ./txt/cord-324619-y7gilopu.txt summary: In this review, we examine some of the most recent data of COVID-19-associated neurological disease and the possibility that SARS-CoV-2 may be infecting the CNS. suggested that since SARS-CoV-2 shared significant similarities to severe acute respiratory syndrome coronavirus (SARS-CoV), it was entirely possible that SARS-CoV-2 could similarly penetrate the brain and CNS of infected patients through synapses in the medullary cardiorespiratory center and thereby cause respiratory failure (5) . Similar to these neurotropic HCoVs, SARS-CoV-2 infection in the lungs of some COVID-19 patients may also lead to entry into the CNS and this could occur via two main pathways: i) infection of peripheral nerves and retrograde axonal transport; and/or ii) hematogenous spread and infection of the cells of the blood-brain barrier. In this review, we have extrapolated information from other neurotropic viruses to make some predictions and it is clear that SARS-CoV-2 has the potential to infect the CNS and cause long-term neurologic damage in COVID-19 patients. abstract: Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) causes a highly contagious respiratory disease referred to as COVID‐19. However, emerging evidence indicates that a small, but a growing number of COVID‐19 patients also manifest neurological symptoms, suggesting that SARS‐CoV‐2 may infect the nervous system under some circumstances. SARS‐CoV‐2 primarily enters the body through the epithelial lining of the respiratory and gastrointestinal tracts, but under certain conditions this pleiotropic virus may also infect peripheral nerves and gain entry into the central nervous system (CNS). The brain is shielded by various anatomical and physiological barriers, most notably the blood‐brain barrier (BBB) which functions to prevent harmful substances, including pathogens and pro‐inflammatory mediators, from entering the brain. The BBB is composed of highly specialized endothelial cells, pericytes, mast cells and astrocytes that form the neurovascular unit, which regulates BBB permeability and maintains the integrity of the CNS. In this review, we briefly discuss potential routes of viral entry and the possible mechanisms utilized by SARS‐CoV‐2 to penetrate the CNS, either by disrupting the BBB or infecting the peripheral nerves and using the neuronal network to initiate neuroinflammation. Furthermore, we speculate on the long‐term effects of SARS‐CoV‐2 infection on the brain and in the progression of neurodegenerative diseases known to be associated with other human coronaviruses. Although the mechanisms of SARS‐CoV‐2 entry into the CNS and neurovirulence are currently unknown, the potential pathways described here might pave the way for future research in this area and enable the development of better therapeutic strategies. url: https://doi.org/10.1111/ene.14442 doi: 10.1111/ene.14442 id: cord-316083-f1h2j6jx author: Alamri, Ahmad title: nan date: 2020-05-21 words: 1431.0 sentences: 77.0 pages: flesch: 54.0 cache: ./cache/cord-316083-f1h2j6jx.txt txt: ./txt/cord-316083-f1h2j6jx.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the origin of the current pandemic of coronavirus disease 2019 (COVID-19) that was identified in hospitalized patients in Wuhan, China, in December 2019 [1] . She reported a total anosmia with an associated dysgeusia that started on the 21 st of March, with no rhinorrhea, no stuffy nose, no fever, no dyspnea, no myalgia nor fatigue, and no swollen lymph nodes on the clinical examination and no other We started olfactory training for both patients, with different aliments like vanilla, lavender, spices and coffee. Here, we have two cases of confirmed SARS-CoV-2 infection, both having isolated anosmia; with a probable context of a worker to worker transmission (with an interval of the onset of symptoms around 24 hours). The fact that both cases were physicians working in the same structure with a possible worker to worker transmission could justify systematic (or focused) screening of health care providers which could drastically minimize the health worker-patient transmission by applying the necessary measures (like home confinement). abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0755498220300154?v=s5 doi: 10.1016/j.lpm.2020.104027 id: cord-308786-e6rv5csl author: Alamri, Mubarak A. title: Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date: 2020-08-28 words: 1483.0 sentences: 94.0 pages: flesch: 47.0 cache: ./cache/cord-308786-e6rv5csl.txt txt: ./txt/cord-308786-e6rv5csl.txt summary: In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL(pro), that can be further developed as potential pan-PL(pro) based broad-spectrum antiviral drugs. Conclusively, the reported SARS-CoV-2 PL(pro) specific compounds could serve as seeds for developing potent pan-PL(pro) based broad-spectrum antiviral drugs against deadly human coronaviruses. Interestingly, the functionally 176 well-conserved catalytic triad residues within the catalytic pockets of PL pro among SARS183 Integrated computational methods comprising virtual high throughput screening, molecular 184 docking, and MD simulation are a significant approach for the exploration of potential 185 inhibitors against a target protein [22, 28, 78, 86] . Pharmacoinformatics and 655 molecular dynamics simulation studies reveal potential covalent and FDA-approved 656 inhibitors of SARS-CoV-2 main protease 3CLpro An integrated structure-based computational approach identified potential inhibitors of SARS-CoV-2 PL pro abstract: The papain-like protease (PL(pro)) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL(pro), that can be further developed as potential pan-PL(pro) based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PL(pro) were exploited, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PL(pro) and showed consistent interaction profile with SARS-CoV PL(pro) and MERS-CoV PL(pro) as well. Conclusively, the reported SARS-CoV-2 PL(pro) specific compounds could serve as seeds for developing potent pan-PL(pro) based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds. url: https://doi.org/10.1016/j.jpha.2020.08.012 doi: 10.1016/j.jpha.2020.08.012 id: cord-311415-wwwqqvca author: Alamri, Mubarak A. title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) date: 2020-06-24 words: 6968.0 sentences: 384.0 pages: flesch: 50.0 cache: ./cache/cord-311415-wwwqqvca.txt txt: ./txt/cord-311415-wwwqqvca.txt summary: title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) Molecular dynamics (MD) simulations were utilized to investigate the binding mode of the potential inhibitors at the active site of SARS-CoV-2 main protease. Since the active site of SARS-CoV-2 main protease contains a catalytic cysteine, it is possible to target it with covalently binding compounds. In order to investigate the binding mode of the most promising hit compounds inside the active site of SARS-CoV-2 3CL pro , molecular dynamics (MD) simulations of each complex were performed for a period of 50 ns. (C-E) Representation of the chemical reaction of the reactive thiol group of Cys145 with the reactive nucleophilic group of the hit compounds, and the corresponding covalently docked poses (green sticks) inside the substrate-binding site of SARS-CoV-2 3CL pro (white ribbon presentation, ligand-interacting amino acids are shown in sticks). In Silico discovery of novel inhibitors against main protease (Mpro) of SARS-CoV-2 using pharmacophore and molecular docking based virtual screening from ZINC database abstract: The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C–S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1782768 doi: 10.1080/07391102.2020.1782768 id: cord-323397-5yop6clu author: Albalate, M. title: Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date: 2020-04-30 words: 5233.0 sentences: 540.0 pages: flesch: 63.0 cache: ./cache/cord-323397-5yop6clu.txt txt: ./txt/cord-323397-5yop6clu.txt summary: El objetivo de este trabajo es describir la experiencia del primer mes de pandemia por SARS-Cov2 en una unidad hospitalaria de hemodiálisis (HD) que atiende al 2º distrito madrileño con más en incidencia de COVID19 (casi 1000 pacientes en 100000 h). Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. abstract: Resumen Los pacientes en diálisis son un grupo de riesgo de sufrir la infección por el SARS-CoV2 y posiblemente de tener más complicaciones, pero la información con la que contamos es escasa. El objetivo de este trabajo es describir la experiencia del primer mes de pandemia por SARS-Cov2 en una unidad hospitalaria de hemodiálisis (HD) que atiende al 2º distrito madrileño con más en incidencia de COVID19 (casi 1000 pacientes en 100000 h). Se presenta mediante un diario las acciones llevadas a cabo, la incidencia de COVID19 en pacientes y en el personal sanitario, algunas características clínicas y el resultado de un cribado entre todos los pacientes de la unidad. Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19, de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. El síntoma más frecuente fue la fiebre, el 50% presentó linfopenia y el 18,4% saturación de O2 <95%. Precisaron ingreso hospitalario 16(43,2%) y 6 fallecieron (16,2%). Encontramos un agrupamiento de contagio por turnos y también en aquellos que usaban transporte colectivo. En cuanto al personal, de las 44 personas involucradas, 15 (34%) presentaron sintomatología compatible y 4 (9%) tuvieron PCR SARS-Cov-2 positiva determinada por Salud Laboral y 9 (20%) precisaron algún periodo de Incapacidad Laboral Transitoria (ILT), y 5 fueron considerados casos probables. Conclusiones: Detectamos una elevada prevalencia de COVID19 con un elevado porcentaje detectado por cribado y por tanto la necesidad de ser proactivos en el diagnóstico para detener la pandemia. La mayoría están siendo manejados de forma ambulatoria, aunque también aparecen cuadros graves y la mortalidad hasta ahora es del 16,2%. En cuanto al personal un 20% ha precisado ILT en relación con COVID19. Abstract Dialysis patients are a risk group for SARS-CoV2 infection and possibly further complications, but we have little information. The aim of this paper is to describe the experience of the first month of the SARS-Cov2 pandemic in a hospital haemodialysis (HD) unit serving the district of Madrid with the second highest incidence of COVID19 (almost 1000 patients in 100000 h). In the form of a diary, we present the actions undertaken, the incidence of COVID19 in patients and health staff, some clinical characteristics and the results of screening all the patients in the unit. We started with 90 patients on HD: 37 (41.1%) had COVID19, of whom 17 (45.9%) were diagnosed through symptoms detected in triage or during the session, and 15 (40.5%) through subsequent screening of those who, until that time, had not undergone SARS-CoV2 PCR testing. Fever was the most frequent symptom, 50% had lymphopenia and 18.4% <95% O2 saturation. Sixteen (43.2%) patients required hospital admission and 6 (16.2%) died. We found a cluster of infection per shift and also among those using public transport. In terms of staff, of the 44 people involved, 15 (34%) had compatible symptoms, 4 (9%) were confirmed as SARS-Cov2 PCR cases by occupational health, 9 (20%) required some period of sick leave, temporary disability to work (ILT), and 5 were considered likely cases. Conclusions: We detected a high prevalence of COVID19 with a high percentage detected by screening; hence the need for proactive diagnosis to stop the pandemic. Most cases are managed as outpatients, however severe symptoms are also appearing and mortality to date is 16.2%. In terms of staff, 20% have required sick leave in relation to COVID19. url: https://api.elsevier.com/content/article/pii/S0211699520300436 doi: 10.1016/j.nefro.2020.04.005 id: cord-278839-uu2wlpmp author: Alberca, Ricardo Wesley title: Pregnancy, Viral Infection, and COVID-19 date: 2020-07-07 words: 7237.0 sentences: 368.0 pages: flesch: 43.0 cache: ./cache/cord-278839-uu2wlpmp.txt txt: ./txt/cord-278839-uu2wlpmp.txt summary: In 2009, during the H1N1 flu pandemic, an increased ratio of female to male cases was verified, in which pregnant women developed more complications, as severe acute respiratory syndrome, and higher mortality compared to the general population (30, 31) . Additionally, infection by the Lassa virus in pregnant women shows high levels of placental replication, and the risk of maternal-fetal mortality increases with the duration of pregnancy (38, 39) . At first, contagion occurred through contact with some infected animals but, soon there were the first reports of human-to-human transmission (93), The virus was identified as belonging to the coronaviridae family and was designated SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) (94). Chen and collaborators, verified alteration in calcium and albumin levels in the blood of pregnant women with SARS-CoV-2 infection (124) , which could potentially increase the severity in COVID-19 (125) . abstract: Pregnancy comprises a unique immunological condition, to allow fetal development and to protect the host from pathogenic infections. Viral infections during pregnancy can disrupt immunological tolerance and may generate deleterious effects on the fetus. Despite these possible links between pregnancy and infection-induced morbidity, it is unclear how pregnancy interferes with maternal response to some viral pathogens. In this context, the novel coronavirus (SARS-CoV-2) can induce the coronavirus diseases-2019 (COVID-19) in pregnant women. The potential risk of vertical transmission is unclear, babies born from COVID-19-positive mothers seems to have no serious clinical symptoms, the possible mechanisms are discussed, which highlights that checking the children's outcome and more research is warranted. In this review, we investigate the reports concerning viral infections and COVID-19 during pregnancy, to establish a correlation and possible implications of COVID-19 during pregnancy and neonatal's health. url: https://www.ncbi.nlm.nih.gov/pubmed/32733490/ doi: 10.3389/fimmu.2020.01672 id: cord-321568-okvt1fg3 author: Alberca, Ricardo Wesley title: Perspective: The Potential Effects of Naringenin in COVID-19 date: 2020-09-25 words: 4111.0 sentences: 225.0 pages: flesch: 40.0 cache: ./cache/cord-321568-okvt1fg3.txt txt: ./txt/cord-321568-okvt1fg3.txt summary: Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Among many compounds, naringenin (NAR) a flavonoid present in citrus fruits has been investigated for antiviral and anti-inflammatory properties like reducing viral replication and cytokine production. In this perspective, we summarize NAR potential anti-inflammatory role in COVID-19 associated risk factors and SARS-CoV-2 infection. Naringenin (NAR) is an important natural flavonoid present in citrus fruits, like grapefruit (43.5 mg/100 mL) and oranges (2.13 mg/100 mL) (19), with a high analgesic, anti-oxidant, anti-inflammatory, anti-tumoral, and anti-viral effect (20-23) (Figure 1) . Further investigations and clinical trials are needed to help understand the role of NAR consumption in humans during a viral infection, especially in SARS-CoV-2 infection and COVID-19. abstract: Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Severe COVID-19 cases develop severe acute respiratory syndrome, which can result in multiple organ failure, sepsis, and death. The higher risk group includes the elderly and subjects with pre-existing chronic illnesses such as obesity, hypertension, and diabetes. To date, no specific treatment or vaccine is available for COVID-19. Among many compounds, naringenin (NAR) a flavonoid present in citrus fruits has been investigated for antiviral and anti-inflammatory properties like reducing viral replication and cytokine production. In this perspective, we summarize NAR potential anti-inflammatory role in COVID-19 associated risk factors and SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33101291/ doi: 10.3389/fimmu.2020.570919 id: cord-268492-0rbmqarx author: Alberer, Martin title: Cats and kids: how a feline disease may help us unravel COVID-19 associated paediatric hyperinflammatory syndrome date: 2020-09-02 words: 1533.0 sentences: 79.0 pages: flesch: 44.0 cache: ./cache/cord-268492-0rbmqarx.txt txt: ./txt/cord-268492-0rbmqarx.txt summary: The RCPCH and CDC have published a case definition and scientists refer to this novel but still very rare severe clinical condition in children as "paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2" (PIMS-TS). While reflecting on this syndrome and its characteristic features, some interesting similarities come to mind when comparing the clinical course of PIMS-TS cases and the specific features of a disease in cats called feline infectious peritonitis (FIP) caused by the feline coronavirus (FCoV), an alphacoronavirus [2] . On this note, it would be of great interest to see whether mutations in the viral genome, particularly in regions affecting the S-protein of SARS-CoV-2, could lead to a change in cell tropism enabling the virus to more effectively infect and replicate within human monocytes/macrophages subsequently leading to the clinical picture of PIMS-TS. abstract: nan url: https://doi.org/10.1007/s15010-020-01515-3 doi: 10.1007/s15010-020-01515-3 id: cord-352196-rpyoeg9n author: Alberici, Federico title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. date: 2020-05-08 words: 2630.0 sentences: 136.0 pages: flesch: 51.0 cache: ./cache/cord-352196-rpyoeg9n.txt txt: ./txt/cord-352196-rpyoeg9n.txt summary: title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. The main clinical characteristics of the overall MHD population with SARS-CoV2 infection and the subgroups managed as outpatient or in hospital are shown in Table 2 . In our cohort including four centers of the "Brescia Renal COVID task force", we have identified 94 patients with SARS-CoV-2 infection. The finding of worse outcome of hemodialysis patients with SARS-CoV-2 infection may be explained by high prevalence of comorbidities as well as other risk factors related to end stage renal disease per se (2). Management of Patients on Dialysis and With Kidney Transplantation During the SARS-CoV-2 (COVID-19) Pandemic in Brescia A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia abstract: The SARS-CoV-2 epidemic is pressuring health care systems worldwide. Disease outcomes in certain subgroups of patients are still scarce, and data are needed. Therefore, we describe here the experience of four dialysis centers of the Brescia Renal COVID task force. During March 2020, within an overall population of 643 hemodialysis patients, SARS-CoV-2 RNA positivity was detected in 94 (15%). At disease diagnosis, 37 of the 94 (39%) patients (group 1) were managed on an outpatient basis whereas the remaining 57 (61%) (group 2) required hospitalization. Choices regarding management strategy were made based on disease severity. In group 1, 41% received antivirals and 76% hydroxychloroquine. Eight percent died and 5% developed acute respiratory distress syndrome (ARDS). In group 2, 79% received antivirals and 77% hydroxychloroquine. Forty two percent died and 79% developed ARDS. Overall mortality rate for the entire cohort was 29%. History of ischemic cardiac disease, fever, older age (over age 70) and dyspnea at presentation were associated with the risk of developing ARDS whereas fever, cough and a C-reactive protein higher than 50 mg/l at disease presentation were associated with the risk of death. Thus, in our population of hemodialysis patients with SARS-CoV-2 infection, we documented a wide range of disease severity. The risk of ARDS and death is significant for patients requiring hospital admission at disease diagnosis. url: https://doi.org/10.1016/j.kint.2020.04.030 doi: 10.1016/j.kint.2020.04.030 id: cord-264828-6w13xo2a author: Albini, Adriana title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies date: 2020-05-19 words: 3662.0 sentences: 172.0 pages: flesch: 40.0 cache: ./cache/cord-264828-6w13xo2a.txt txt: ./txt/cord-264828-6w13xo2a.txt summary: Older COVID-19-affected patients with cardiovascular comorbidities exhibit a more severe clinical course and a worse prognosis, with many of them being also treated with ARBs or ACE-Is. Another confounding factor is cigarette smoking, which has been reported to increase ACE-2 expression in both experimental models and humans. 4. Renin-angiotensin-aldosterone system (RAAS)-interfering drugs are likely to affect ACE-2 receptor-SARS-CoV-2 interaction dynamics within lung, heart, vascular, kidney and gut tissues [5, 19] , while it is still not completely elucidated how such interactions are relevant to the clinical course of cardiovascular comorbidities in patients with COVID-19 [29] . Consequently, the up-regulation of human ACE-2 induced by RAAS-antagonists in SARS-CoV-2-infected patients could be clinically useful, due to the cardiovascular protection elicited by the increased activity of angiotensin(1-7), thereby attenuating angiotensin II effects on vasoconstriction and sodium retention [31, 34] . abstract: SARS-CoV-2 is characterized by a spike protein allowing viral binding to the angiotensin-converting enzyme (ACE)-2, which acts as a viral receptor and is expressed on the surface of several pulmonary and extra-pulmonary cell types, including cardiac, renal, intestinal and endothelial cells. There is evidence that also endothelial cells are infected by SARS-COV-2, with subsequent occurrence of systemic vasculitis, thromboembolism and disseminated intravascular coagulation. Those effects, together with the “cytokine storm” are involved in a worse prognosis. In clinical practice, angiotensin-converting enzyme inhibitors (ACE-Is) and angiotensin II receptor blockers (ARBs) are extensively used for the treatment of hypertension and other cardiovascular diseases. In in vivo studies, ACE-Is and ARBs seem to paradoxically increase ACE-2 expression, which could favour SARS-CoV-2 infection of host’s cells and tissues. By contrast, in patients treated with ACE-Is and ARBs, ACE-2 shows a downregulation at the mRNA and protein levels in kidney and cardiac tissues. Yet, it has been claimed that both ARBs and ACE-Is could result potentially useful in the clinical course of SARS-CoV-2-infected patients. As detected in China and as the Italian epidemiological situation confirms, the most prevalent comorbidities in deceased patients with COVID-19 are hypertension, diabetes and cardiovascular diseases. Older COVID-19-affected patients with cardiovascular comorbidities exhibit a more severe clinical course and a worse prognosis, with many of them being also treated with ARBs or ACE-Is. Another confounding factor is cigarette smoking, which has been reported to increase ACE-2 expression in both experimental models and humans. Sex also plays a role, with chromosome X harbouring the gene coding for ACE-2, which is one of the possible explanations of why mortality in female patients is lower. Viral entry also depends on TMPRSS2 protease activity, an androgen dependent enzyme. Despite the relevance of experimental animal studies, to comprehensively address the question of the potential hazards or benefits of ACE-Is and ARBs on the clinical course of COVID-19-affected patients treated by these anti-hypertensive drugs, we will need randomized human studies. We claim the need of adequately powered, prospective studies aimed at answering the following questions of paramount importance for cardiovascular, internal and emergency medicine: Do ACE-Is and ARBs exert similar or different effects on infection or disease course? Are such effects dangerous, neutral or even useful in older, COVID-19-affected patients? Do they act on multiple cell types? Since ACE-Is and ARBs have different molecular targets, the clinical course of SARS-CoV-2 infection could be also different in patients treated by one or the other of these two drug classes. At present, insufficient detailed data from trials have been made available. url: https://doi.org/10.1007/s11739-020-02364-6 doi: 10.1007/s11739-020-02364-6 id: cord-304742-ytf2ilw4 author: Albini, Adriana title: The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based antihypertensive therapies—reply date: 2020-07-14 words: 1187.0 sentences: 52.0 pages: flesch: 41.0 cache: ./cache/cord-304742-ytf2ilw4.txt txt: ./txt/cord-304742-ytf2ilw4.txt summary: The transmembrane protease serine 2 TMPRSS2, an androgendependent enzyme, acts in reinforcing the ACE-2 receptor activity in allowing cell entry to a number of viral pathogens as well as to SARS-CoV-2 as reported in our Point of View [2] . Yet in trisomy 21 individuals a TMPRSS2 protease overexpression has been documented, as mentioned in the comment of Dr De Cauwer [1] , with this leading to an increased viral infection''s rate of susceptible host''s cells and tissues. In conclusion, the interesting comment by Dr De Cauwer points out the complex interactions between ACE-2 and TMPRSS2 with reference to the clinical course of CoViD-19 as well as to SARS-CoV-2 infection''s pathogenic evolution and severity degree in given population segments of infected individuals, like male individuals and Down syndromeaffected patients [1] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACEinhibitor-and angiotensin II receptor blocker-based cardiovascular therapies: comment The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32666177/ doi: 10.1007/s11739-020-02436-7 id: cord-310304-f28tjmi8 author: Alcendor, Donald J. title: Racial Disparities-Associated COVID-19 Mortality among Minority Populations in the US date: 2020-07-30 words: 7719.0 sentences: 366.0 pages: flesch: 41.0 cache: ./cache/cord-310304-f28tjmi8.txt txt: ./txt/cord-310304-f28tjmi8.txt summary: Maintaining glycemic control in COVID-19 patients is essential, as hyperglycemia could affect pulmonary function, the immune response to infection, and the development of the pro-inflammatory cytokine storm associated with more severe clinical disease ( Figure 1 ). Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, upon infection with SARS-CoV-2 the ACE2 protein serves as the entry receptor for the virus and is internalized in the endosome with SARS-CoV-2 during membrane fusion and uptake by Hypothetical model of uncontrolled blood pressure in patients with hypertension and increased risk for complications due to COVID-19. Longstanding health disparities such as diabetes, hypertension, CVD, and pulmonary disease among minority populations in the US may serve to predispose these communities to SARS-CoV-2 infection and increased risk for clinically severe COVID-19. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus that causes the novel coronavirus disease 2019 (COVID-19), is highly transmissible and pathogenic for humans and may cause life-threatening disease and mortality, especially in individuals with underlying comorbidities. First identified in an outbreak in Wuhan, China, COVID-19 is affecting more than 185 countries and territories around the world, with more than 15,754,651 confirmed cases and more than 640,029 deaths. Since December 2019, SARS-CoV-2 transmission has become a global threat, which includes confirmed cases in all 50 states within the United States (US). As of 25 July 2020, the Johns Hopkins Whiting School of Engineering Center for Systems Science and Engineering reports more than 4,112,651 cases and 145,546 deaths. To date, health disparities are associated with COVID-19 mortality among underserved populations. Here, the author explores potential underlying reasons for reported disproportionate, increased risks of mortality among African Americans and Hispanics/Latinos with COVID-19 compared with non-Hispanic Whites. The author examines the underlying clinical implications that may predispose minority populations and the adverse clinical outcomes that may contribute to increased risk of mortality. Government and community-based strategies to safeguard minority populations at risk for increased morbidity and mortality are essential. Underserved populations living in poverty with limited access to social services across the US are more likely to have underlying medical conditions and are among the most vulnerable. Societal and cultural barriers for ethnic minorities to achieve health equity are systemic issues that may be addressed only through shifts in governmental policies, producing long-overdue, substantive changes to end health care inequities. url: https://www.ncbi.nlm.nih.gov/pubmed/32751633/ doi: 10.3390/jcm9082442 id: cord-282421-yialyuav author: Alcoba-Florez, Julia title: Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date: 2020-08-01 words: 1049.0 sentences: 69.0 pages: flesch: 55.0 cache: ./cache/cord-282421-yialyuav.txt txt: ./txt/cord-282421-yialyuav.txt summary: In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. abstract: Abstract Objectives The ongoing COVID-19 pandemic continues imposing a demand for diagnostic screening. In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. That of best sensitivity was also assessed with direct nasopharyngeal swab viral transmission medium (VTM) heating, overcoming the RNA extraction step. Results We found a wide variability in the sensitivity of RT-qPCR solutions that associated with a range of false negatives from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Direct preheating of VTM combined with the best solution provided a sensitivity of 72.5% (62.5-81.0), in the range of some of the solutions based on standard RNA extractions. Conclusions We evidenced sensitivity limitations of currently used RT-qPCR solutions. Our results will help to calibrate the impact of false negative diagnoses of COVID-19, and to detect and control new SARS-CoV-2 outbreaks and community transmissions. url: https://doi.org/10.1016/j.ijid.2020.07.058 doi: 10.1016/j.ijid.2020.07.058 id: cord-297708-uocs65sl author: Alders, N. title: COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected date: 2020-08-22 words: 3415.0 sentences: 216.0 pages: flesch: 48.0 cache: ./cache/cord-297708-uocs65sl.txt txt: ./txt/cord-297708-uocs65sl.txt summary: Four distinct groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile illnesses with or without extra-pulmonary organ dysfunction (21%). The relative paucity of data describing SARS-CoV-2 in the paediatric population mandates a broad-arching approach to pandemic planning with preparations put in place to manage a heterogeneous population of patients presenting with a range of single and multi-organ pathology of varying severity. . https://doi.org/10.1101/2020.08.20.20178541 doi: medRxiv preprint Methods All patients aged ≤ 18 years with positive respiratory or nasal SARS-CoV-2 RT-PCR and/or serum IgG (Epitope Diagnostics Inc. TM ) up to 19 th May 2020. Four distinct clinical groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile/viral illness with or without single organ dysfunction (21%). abstract: Background: The paucity of data describing SARS-CoV-2 in the paediatric population necessitated a broad-arching approach to pandemic planning, with preparations put in place to manage a heterogeneous cohort. We describe a diverse group of SARS-CoV-2 positive paediatric patients treated at a large tertiary/quaternary children`s hospital in the United Kingdom and the adaptive coping strategies required. Methods: All paediatric patients with positive RT-PCR on a respiratory sample and/or serology for SARS-CoV-2 up to 19th May 2020 were included. Results: 57 children met the inclusion criteria. 70% were of non-Caucasian ethnicity with a median age of 9.3 years (IQR 5.16-13.48). Four distinct groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile illnesses with or without extra-pulmonary organ dysfunction (21%). These groups presented in distinct chronological blocks as the pandemic unfolded. Discussion: The diverse range of presentations of SARS-CoV-2 infection in this population exemplified the importance of preparedness for the unknown in the midst of a novel infectious pandemic. Descriptions of paediatric patients during the initial phase of the pandemic from other parts of the globe and extrapolation from adult data did not serve as an accurate representation of paediatric COVID-19 in our centre. An adaptive, multidisciplinary approach was paramount. Expanded laboratory testing and incorporation of technology platforms to facilitate remote collaboration in response to strict infection control precautions were both indispensable. Lessons learned during the preparation process will be essential in planning for a potential second wave of SARS-CoV-2. url: https://doi.org/10.1101/2020.08.20.20178541 doi: 10.1101/2020.08.20.20178541 id: cord-311965-3x3tjzhi author: Alexander, Jan title: Early Nutritional Interventions with Zinc, Selenium and Vitamin D for Raising Anti-Viral Resistance Against Progressive COVID-19 date: 2020-08-07 words: 5156.0 sentences: 273.0 pages: flesch: 39.0 cache: ./cache/cord-311965-3x3tjzhi.txt txt: ./txt/cord-311965-3x3tjzhi.txt summary: Adequate supply of zinc, selenium, and vitamin D is essential for resistance to other viral infections, immune function, and reduced inflammation. Clinical and subclinical micronutrient deficiencies common in older adults are known to contribute to decreased immune function and age-related diseases [11] , implying that nutritional management is essential to reduce the risk of severe infection [12] . In view of a lack of clinical data on preventive and/or therapeutic efficiency of the nutritive adequacy of selenium, zinc, and vitamin D in COVID-19, we, in the present narrative review, discussed recent clinical data on the role of these micronutrients in the protection against bronchopulmonary infections, as well as the existing indications of their impact on COVID-19. We did a literature search for the period 2010-2020 on PubMed, Medline, and Google Scholar with the keywords of SARS, SARS-CoV-2, COVID 19, coronavirus, micronutrients (zinc, selenium, vitamin D), immune system, inflammation, prevention, and treatment. abstract: Objectives: The novel coronavirus infection (COVID-19) conveys a serious threat globally to health and economy because of a lack of vaccines and specific treatments. A common factor for conditions that predispose for serious progress is a low-grade inflammation, e.g., as seen in metabolic syndrome, diabetes, and heart failure, to which micronutrient deficiencies may contribute. The aim of the present article was to explore the usefulness of early micronutrient intervention, with focus on zinc, selenium, and vitamin D, to relieve escalation of COVID-19. Methods: We conducted an online search for articles published in the period 2010–2020 on zinc, selenium, and vitamin D, and corona and related virus infections. Results: There were a few studies providing direct evidence on associations between zinc, selenium, and vitamin D, and COVID-19. Adequate supply of zinc, selenium, and vitamin D is essential for resistance to other viral infections, immune function, and reduced inflammation. Hence, it is suggested that nutrition intervention securing an adequate status might protect against the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome - coronavirus-2) and mitigate the course of COVID-19. Conclusion: We recommended initiation of adequate supplementation in high-risk areas and/or soon after the time of suspected infection with SARS-CoV-2. Subjects in high-risk groups should have high priority as regards this nutritive adjuvant therapy, which should be started prior to administration of specific and supportive medical measures. url: https://doi.org/10.3390/nu12082358 doi: 10.3390/nu12082358 id: cord-322660-bis2arbu author: Alexander, Regi title: Guidance for the Treatment and Management of COVID‐19 Among People with Intellectual Disabilities date: 2020-06-10 words: 10807.0 sentences: 487.0 pages: flesch: 44.0 cache: ./cache/cord-322660-bis2arbu.txt txt: ./txt/cord-322660-bis2arbu.txt summary: The guidelines cover specific issues associated with hospital passports, individual COVID‐19 care plans, the important role of families and carers, capacity to make decisions, issues associated with social distancing, ceiling of care/treatment escalation plans, mental health and challenging behavior, and caring for someone suspected of contracting or who has contracted SARS‐CoV‐2 within community or inpatient psychiatric settings. These teams provide a range of care and support to people with IDs, while during the current pandemic there will be an increased focus upon providing TABLE 1 Group at risk because they are clinically vulnerable due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection who need particularly stringent social distancing measures Issues associated with diagnostic overshadowing, the views of parents, family members and carers, the required reasonable adjustments, communication needs, specialist mental health support, anticipatory care plans, any end-of-life or do not attempt cardiopulmonary resuscitation (DNACPR) discussions should be reported. abstract: The current COVID‐19 pandemic is a pressing world crisis and people with intellectual disabilities (IDs) are vulnerable due to disparity in healthcare provision and physical and mental health multimorbidity. While most people will develop mild symptoms upon contracting severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2), some will develop serious complications. The aim of this study is to present guidelines for the care and treatment of people with IDs during the COVID‐19 pandemic for both community teams providing care to people with IDs and inpatient psychiatric settings. The guidelines cover specific issues associated with hospital passports, individual COVID‐19 care plans, the important role of families and carers, capacity to make decisions, issues associated with social distancing, ceiling of care/treatment escalation plans, mental health and challenging behavior, and caring for someone suspected of contracting or who has contracted SARS‐CoV‐2 within community or inpatient psychiatric settings. We have proposed that the included conditions recommended by Public Health England to categorize someone as high risk of severe illness due to COVID‐19 should also include mental health and challenging behavior. There are specific issues associated with providing care to people with IDs and appropriate action must be taken by care providers to ensure that disparity of healthcare is addressed during the COVID‐19 pandemic. We recognize that our guidance is focused upon healthcare delivery in England and invite others to augment our guidance for use in other jurisdictions. url: https://www.ncbi.nlm.nih.gov/pubmed/32837529/ doi: 10.1111/jppi.12352 id: cord-319780-rfj9t99r author: Alexander, S.P.H. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 words: 15196.0 sentences: 814.0 pages: flesch: 47.0 cache: ./cache/cord-319780-rfj9t99r.txt txt: ./txt/cord-319780-rfj9t99r.txt summary: Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: In this review, we identify opportunities for drug discovery in the treatment of COVID‐19 and in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic. We assess the scope for targetting key host and viral targets in the mid‐term, by first screening these targets against drugs already licensed; an agenda for drug re‐purposing, which should allow rapid translation to clinical trials. A simultaneous, multi‐pronged approach using conventional drug discovery methodologies aimed at discovering novel chemical and biological means targetting a short‐list of host and viral entities should extend the arsenal of anti‐SARS‐CoV‐2 agents. This longer‐term strategy would provide a deeper pool of drug choices for future‐proofing against acquired drug resistance. Second, there will be further viral threats, which will inevitably evade existing vaccines. This will require a coherent therapeutic strategy which pharmacology and pharmacologists are best placed to provide. url: https://www.ncbi.nlm.nih.gov/pubmed/32358833/ doi: 10.1111/bph.15094 id: cord-270588-c9rxmo44 author: Algarroba, Gabriela N. title: Visualization of SARS-CoV-2 virus invading the human placenta using electron microscopy date: 2020-05-13 words: 825.0 sentences: 61.0 pages: flesch: 50.0 cache: ./cache/cord-270588-c9rxmo44.txt txt: ./txt/cord-270588-c9rxmo44.txt summary: We present a case of rapid clinical deterioration in a woman at 28 weeks'' gestation due to 36 severe COVID-19 infection. Using electron microscopy to evaluate for potential viral transmission in the 37 placenta, we visualized and identified coronavirus virions invading into syncytiotrophoblasts in placental 38 All placentas from COVID-19 positive mothers are submitted for gross and histologic 70 evaluation in our institution. In this case, the placenta was submitted to the pathology laboratory 71 without fixative; fresh tissue was taken, using appropriate personal protective gear, under the Fisher 72 Ten representative, 3 mm thick tissue sections were 76 submitted from the placental parenchyma, membranes and umbilical cord for histologic evaluation. Preterm delivery 125 in pregnant woman with critical COVID-19 pneumonia and vertical transmission Clinical characteristics and intrauterine 130 vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective 131 review of medical records Evidence for and against 133 vertical transmission for SARS-CoV-2 (COVID-19) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32405074/ doi: 10.1016/j.ajog.2020.05.023 id: cord-349838-p6vfzbla author: Algwaiz, Ghada title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR''s Health Services and International Studies Committee date: 2020-07-24 words: 4060.0 sentences: 229.0 pages: flesch: 44.0 cache: ./cache/cord-349838-p6vfzbla.txt txt: ./txt/cord-349838-p6vfzbla.txt summary: Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. While acknowledging all aforementioned challenges and taking into account current recommendations or guidelines issued by the American Society for Transplantation and Cellular Therapy (ASTCT) and the European Society for Blood and Marrow Transplantation (EBMT) (which are WBMT members), herein, we aim at providing a consensus among the authors from WBMT and CIBMTR''s HSIS committee and other HCT experts who represent multiple continents and allude to the current worldwide threat to HCT patient from the COVID-19 pandemic (7, 8) . abstract: The current COVID-19 pandemic, caused by SARS-CoV-2, has impacted many facets of hematopoietic cell transplantation (HCT) in both developed and developing countries. Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. During these crucial times, which may last for months or years, the HCT community must reorganize to proceed with transplant activity in those patients who urgently require it, albeit with extreme caution.This shared knowledge may be of value to the HCT community in the absence of highquality evidence-based medicine. url: https://api.elsevier.com/content/article/pii/S1083879120304547 doi: 10.1016/j.bbmt.2020.07.021 id: cord-314901-b18vy7dc author: Ali, Elrazi title: A Case of Fulminant Liver Failure in a 24-Year-Old Man with Coinfection with Hepatitis B Virus and SARS-CoV-2 date: 2020-10-13 words: 2164.0 sentences: 129.0 pages: flesch: 47.0 cache: ./cache/cord-314901-b18vy7dc.txt txt: ./txt/cord-314901-b18vy7dc.txt summary: Patient: Male, 24-year-old Final Diagnosis: Acute kidney injury • coagulopathy • liver failure • SARS-CoV-2 Symptoms: Cough • fever Medication: — Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases OBJECTIVE: Unusual clinical course BACKGROUND: Coronavirus disease 2019 (COVID-19) is a newly emerging disease that is still not fully characterized. CONCLUSIONS: It is uncommon for SARS-CoV-2 infection with mild respiratory symptoms to result in severe systemic disease and organ failure. We report an unusual case of acute hepatitis B infection with concomitant SARS-CoV-2 leading to fulminant hepatitis, multiorgan failure, and death. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been a central health concern worldwide for the last 6 months. Similarly, patients with chronic liver disease, including patients with chronic hepatitis B infection co-occurring with SARS-CoV-2 infection, had more severe illness and poor outcomes [17] . Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection abstract: Patient: Male, 24-year-old Final Diagnosis: Acute kidney injury • coagulopathy • liver failure • SARS-CoV-2 Symptoms: Cough • fever Medication: — Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases OBJECTIVE: Unusual clinical course BACKGROUND: Coronavirus disease 2019 (COVID-19) is a newly emerging disease that is still not fully characterized. It is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that can be transmitted easily from human to human mainly by the respiratory route. Currently, there is no specific treatment for COVID-19 or a vaccine for prevention. The disease has various degrees of severity. It often presents with non-specific symptoms such as fever, headache, and fatigue, accompanied by respiratory symptoms (e.g., cough and dyspnea) and other systemic involvement. Severe disease is associated with hemophagocytic syndrome and cytokine storm due to altered immune response. Patients with severe disease are more likely to have increased liver enzymes. The disease can affect the liver through various mechanisms. CASE REPORT: We report an unusual case of SARS-CoV-2 infection in a 24-year-old man with no previous medical illness, who presented with mild respiratory involvement. He had no serious lung injury during the disease course. However, he experienced acute fulminant hepatitis B infection and cytokine release syndrome that led to multiorgan failure and death. CONCLUSIONS: It is uncommon for SARS-CoV-2 infection with mild respiratory symptoms to result in severe systemic disease and organ failure. We report an unusual case of acute hepatitis B infection with concomitant SARS-CoV-2 leading to fulminant hepatitis, multiorgan failure, and death. url: https://www.ncbi.nlm.nih.gov/pubmed/33046686/ doi: 10.12659/ajcr.925932 id: cord-296762-sc6crkkw author: Ali, Fedaa title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-08-20 words: 808.0 sentences: 59.0 pages: flesch: 60.0 cache: ./cache/cord-296762-sc6crkkw.txt txt: ./txt/cord-296762-sc6crkkw.txt summary: title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity Here, we combined ACE2 coding variants analysis in different populations and computational chemistry calculations to probe the effects on SARS-CoV-2/ACE2 interaction. Furthermore, the structure of ACE2 was trimmed by removing residues from P733 to the end of The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-108 2/ACE2 were compared between single mutated and WT protein at pH =7 ( Fig. 2A) . Based on our calculations, G211R mutant is shown to induce the largest increase 112 in the binding energy between SARS-CoV-2 and ACE2, where the binding is more favorable by 113 ~ 7.6 Kcal/mol than the WT. SARS-CoV-2/ACE2 interface in the 123 WT protein and corresponding mutants is showed to be a dominated by van der Waals 124 interactions, which accounts for more than 60% of the interaction energy. abstract: The susceptibility of different populations to SARS-CoV-2 infection is not yet understood. Here, we combined ACE2 coding variants analysis in different populations and computational chemistry calculations to probe the effects on SARS-CoV-2/ACE2 interaction. ACE2-K26R; which is most frequent in Ashkenazi Jewish population decreased the SARS-CoV-2/ACE2 electrostatic attraction. On the contrary, ACE2-I468V, R219C, K341R, D206G, G211R increased the electrostatic attraction; ordered by binding strength from weakest to strongest. The aforementioned variants are most frequent in East Asian, South Asian, African and African American, European, European and South Asian populations, respectively. url: https://www.ncbi.nlm.nih.gov/pubmed/32844124/ doi: 10.1016/j.bbrep.2020.100798 id: cord-344236-qp3ianzf author: Ali, Fedaa title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-05-08 words: 2465.0 sentences: 163.0 pages: flesch: 54.0 cache: ./cache/cord-344236-qp3ianzf.txt txt: ./txt/cord-344236-qp3ianzf.txt summary: Classical electrostatic calculations based on solving Poisson-Boltzmann (PB) equation is used to investigate the interaction energies between SARS-CoV-2 and ACE2 for different mutated ACE2 structures. In an attempt to better understand the susceptibility of different populations to infection by SARS-CoV-2, we gathered data on ACE2 missense variants from different projects and databases that aggregate allele frequencies (AF). These projects and databases included Single Nucleotide Polymorphism Database (dbSNP) 12, 13 , 1000 genomes project phase 3 (1KGP3) 14 , Allele Frequency Aggregator (ALFA project) a , Exome Aggregation Consortium (ExAC) 15 SARS-CoV-2 was reported to bind to human ACE2 via different ACE2 residues; Q24, D30, H34, Y41, Q42, M82, K353 and R357 5 . The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-2/ACE2 were compared between single mutated and WT protein at pH =7 (Table 1 ). abstract: The susceptibility of different populations to the SARS-CoV-2 infection is not yet understood. A deeper analysis of the genomes of individuals from different populations might explain their risk for infection. In this study, a combined analysis of ACE2 coding variants in different populations and computational chemistry calculations are conducted in order to probe the potential effects of ACE2 coding variants on SARS-CoV-2/ACE2 binding affinity. Our study reveals novel interaction data on the variants and SARS-CoV-2. We could show that ACE2-K26R; which is more frequent in the Ashkenazi Jewish population decrease the electrostatic attraction between SARS-CoV-2 and ACE2. On the contrary, ACE2-I468V, R219C, K341R, D206G, G211R were found to increase the electrostatic attraction and increase the binding to SARS-CoV-2; ordered by the strength of binding from weakest to strongest. I468V, R219C, K341R, D206G and G211R were more frequent in East Asian, South Asian, African and African American, European and European and South Asian populations, respectively. SARS-CoV-2/ACE2 interface in the WT protein and corresponding variants is showed to be a dominated by van der Waals (vdW) interactions. All the mutations except K341R induce an increase in the vdW attractions between the ACE2 and the SARS-CoV-2. The largest increase of is observed for the R219C mutant. url: https://doi.org/10.1101/2020.05.08.084384 doi: 10.1101/2020.05.08.084384 id: cord-297878-c4cq92x8 author: Ali, Mohammed title: ST-Elevation Myocardial Infarction in a 27-Year-Old Male With COVID-19 date: 2020-09-11 words: 2098.0 sentences: 128.0 pages: flesch: 53.0 cache: ./cache/cord-297878-c4cq92x8.txt txt: ./txt/cord-297878-c4cq92x8.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that led to a global public health emergency causing coronavirus disease 2019 (COVID-19). Here we present a case of a very young 27-year-old patient without any past history of hypertension, coronary artery disease, or any risk factors for coronary artery disease except obesity, who developed STEMI while in the hospital. Here we present a case of ST-elevation myocardial infarction (STEMI) in a very young 27-year-old African American patient who was admitted for respiratory 1 2 1 3, 4 failure secondary to COVID-19. revealed that STEMI was the presenting clinical manifestation in 24 out of 28 COVID-19 patients who were diagnosed with an STEMI. COVID-19 has now been associated with increased cardiovascular injury and even more so in patients with severe disease. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Cardiac involvement in a patient with coronavirus disease 2019 (COVID-19) abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that led to a global public health emergency causing coronavirus disease 2019 (COVID-19). It was initially identified in Wuhan, China after causing significant respiratory illness. Although respiratory symptoms are the most common presenting symptoms, it is now recognized that COVID-19 encompasses multiple organ systems including the cardiovascular system. Acute myocardial injury and ST-elevation myocardial infarction (STEMI) have now been associated with COVID-19. COVID-19 patients with cardiovascular manifestations are at risk for increased severity of illness. Here we present a case of a very young 27-year-old patient without any past history of hypertension, coronary artery disease, or any risk factors for coronary artery disease except obesity, who developed STEMI while in the hospital. url: https://www.ncbi.nlm.nih.gov/pubmed/33062505/ doi: 10.7759/cureus.10384 id: cord-255474-7fq9culd author: Alifano, Marco title: Renin-angiotensin system at the heart of COVID-19 pandemic date: 2020-04-16 words: 2599.0 sentences: 124.0 pages: flesch: 38.0 cache: ./cache/cord-255474-7fq9culd.txt txt: ./txt/cord-255474-7fq9culd.txt summary: We decided to use the analogy of a play and speculate about the possible impact in this tragedy of 1) air pollution via the interference of nitrogen dioxide on ACE2 expression; 2) the dual role of nicotine; 3) the hypothetical involvement of ACE2 polymorphisms, the relationships of which with ethnic factors and susceptibility to cardiovascular disease seems intriguing; 4) the impact on the severity of infection of hypertension and related medications acting on the renin/angiotensin system, and, finally, 5) the possible helpful role of chloroquine, thanks to its capacity of modifying ACE2 affinity to the viral spike protein by altering glycosylation. 6 Although concurrent cardiovascular disease might explain increased mortality in a severe infection responsible for respiratory failure and deterioration of cardiac function, the observations on hypertension warrant urgent speculation and reflection, while waiting for results of large-scale studies evaluating the independent value of each risk factor. abstract: Significant aspects of COVID-19 pandemic remain obscure. Angiotensin converting enzyme 2 (ACE2), a component of the renin-angiotensin system, whose expression dominates on lung alveolar epithelial cells, is the human cell receptor of SARS-CoV-2, the causative agent of COVID-19. We strongly encourage the concept that thorough considerations of receptor-ligand interactions should be kept at the heart of scientific debate on infection. In this idea, the whole renin-angiotensin system has to be evaluated. We hypothesize that factors related to ethnicity, environment, behaviors, associated illness, and medications involving this complex system are probably responsible for situations regarded as anomalous from both an epidemiological and a clinical point of view, but, taken together, such factors may explain most of the aspects of current outbreak. We decided to use the analogy of a play and speculate about the possible impact in this tragedy of 1) air pollution via the interference of nitrogen dioxide on ACE2 expression; 2) the dual role of nicotine; 3) the hypothetical involvement of ACE2 polymorphisms, the relationships of which with ethnic factors and susceptibility to cardiovascular disease seems intriguing; 4) the impact on the severity of infection of hypertension and related medications acting on the renin/angiotensin system, and, finally, 5) the possible helpful role of chloroquine, thanks to its capacity of modifying ACE2 affinity to the viral spike protein by altering glycosylation. This hypothesis paper is an urgent call for the development of research programs that aim at questioning whether the putative protagonists of this tragedy are real-life actors in COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32305506/ doi: 10.1016/j.biochi.2020.04.008 id: cord-355924-8sk9al0n author: Allam, Loubna title: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date: 2020-10-21 words: 4753.0 sentences: 288.0 pages: flesch: 52.0 cache: ./cache/cord-355924-8sk9al0n.txt txt: ./txt/cord-355924-8sk9al0n.txt summary: Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. For this purpose, a targeted analysis of the expression of candidate genes involved in SARS-CoV-2 infection confirmed the presence of the GRP78 protein in vitro in epithelial cells of the human respiratory tract and lung tissue. In this direction, our study focused on the repositioning of approved drugs as well as the investigation of other bioactive compounds that may prevent the penetration of SARS-CoV-2 into host cells by targeting the region of GRP78 that is required for the interaction with the Spike protein of the virus. Inhibition of the interaction between the spike protein SARS-CoV-2 and the receptor by blocking the GRP78 is a strategy interesting to identify drugs that decrease the rate of viral infection. abstract: The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78. url: https://doi.org/10.1177/1177932220965505 doi: 10.1177/1177932220965505 id: cord-272602-rywg9mek author: Allison, James R title: Evaluating aerosol and splatter following dental procedures: addressing new challenges for oral healthcare and rehabilitation date: 2020-09-23 words: 4942.0 sentences: 266.0 pages: flesch: 49.0 cache: ./cache/cord-272602-rywg9mek.txt txt: ./txt/cord-272602-rywg9mek.txt summary: A number of authors have used microbiological methods to study bacterial contamination from aerosol and splatter following dental procedures, either by air sampling 21, 32, 33 , swabbing of contaminated surfaces 34, 35 , or most commonly, by collection directly onto culture media [36] [37] [38] [39] . Many studies are small and report only one repetition of a single procedure, and some have only examined contamination of the operator and assistant; a number of studies which have measured spatial distribution of aerosol and splatter have only done so to a limited distance from the source. We present initial data on three dental procedures (high-speed air-turbine, ultrasonic scaler, and 3-in-1 spray use) and examine the effect of dental suction and the presence of an assistant on aerosol and splatter distribution. abstract: BACKGROUND: Dental procedures often produce aerosol and splatter which have the potential to transmit pathogens such as SARS‐CoV‐2. The existing literature is limited. OBJECTIVE(S): To develop a robust, reliable and valid methodology to evaluate distribution and persistence of dental aerosol and splatter, including the evaluation of clinical procedures. METHODS: Fluorescein was introduced into the irrigation reservoirs of a high‐speed air‐turbine, ultrasonic scaler and 3‐in‐1 spray, and procedures were performed on a mannequin in triplicate. Filter papers were placed in the immediate environment. The impact of dental suction and assistant presence were also evaluated. Samples were analysed using photographic image analysis, and spectrofluorometric analysis. Descriptive statistics were calculated and Pearson’s correlation for comparison of analytic methods. RESULTS: All procedures were aerosol and splatter generating. Contamination was highest closest to the source, remaining high to 1–1.5 m. Contamination was detectable at the maximum distance measured (4 m) for high‐speed air‐turbine with maximum relative fluorescence units (RFU) being: 46,091 at 0.5 m, 3,541 at 1.0 m, and 1,695 at 4 m. There was uneven spatial distribution with highest levels of contamination opposite the operator. Very low levels of contamination (≤0.1% of original) were detected at 30 and 60 minutes post procedure. Suction reduced contamination by 67–75% at 0.5–1.5 m. Mannequin and operator were heavily contaminated. The two analytic methods showed good correlation (r=0.930, n=244, p<0.001). CONCLUSION: Dental procedures have potential to deposit aerosol and splatter at some distance from the source, being effectively cleared by 30 minutes in our setting. url: https://www.ncbi.nlm.nih.gov/pubmed/32966633/ doi: 10.1111/joor.13098 id: cord-291047-mpahl77t author: Alm, Erik title: Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 date: 2020-08-13 words: 3698.0 sentences: 124.0 pages: flesch: 42.0 cache: ./cache/cord-291047-mpahl77t.txt txt: ./txt/cord-291047-mpahl77t.txt summary: We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. In this report, we applied the available nomenclatures to the European subset of the GISAID dataset to describe broad geographical and temporal trends in the distribution of SARS-CoV-2 genetic clades during the first half of 2020 and we discuss potential genomic surveillance objectives at the European level. abstract: We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32794443/ doi: 10.2807/1560-7917.es.2020.25.32.2001410 id: cord-303111-iv4lzpev author: Almazán, Fernando title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 words: 7071.0 sentences: 314.0 pages: flesch: 42.0 cache: ./cache/cord-303111-iv4lzpev.txt txt: ./txt/cord-303111-iv4lzpev.txt summary: Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. abstract: Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV). url: https://www.sciencedirect.com/science/article/pii/S0168170214003827 doi: 10.1016/j.virusres.2014.09.006 id: cord-103659-wpwfqhp2 author: Almqvist, J. title: Neurological manifestations of coronavirus infections: a systematic review date: 2020-09-01 words: 6075.0 sentences: 463.0 pages: flesch: 46.0 cache: ./cache/cord-103659-wpwfqhp2.txt txt: ./txt/cord-103659-wpwfqhp2.txt summary: In order to optimize diagnostic workup of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we systematically reviewed neurological and neuroradiological manifestations of SARS-CoV-2 and all other known human coronavirus species (HCoV). . https://doi.org/10.1101/2020.08.26.20182196 doi: medRxiv preprint symptoms/complications, neuropathological findings and/or neuroimaging findings associated to acute or prior coronavirus infection. Several case reports, comprising a total of 11 patients, described neurological complications in SARS-CoV-1, among them critical illness neuro-/myopathy, seizures, persistent sleeping difficulties, persistent anosmia, delirium and generalized pain (Table e-6). Several common neurological symptoms among SARS-CoV-2 patients have been described in these studies, such as fatigue (44 -64% of patients), 42 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Retrospective Observational Study of Brain Magnetic Resonance Imaging Findings in Patients with Acute SARS-CoV-2 Infection and Neurological Manifestations abstract: In order to optimize diagnostic workup of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we systematically reviewed neurological and neuroradiological manifestations of SARS-CoV-2 and all other known human coronavirus species (HCoV). Which lessons can we learn? We identified relevant publications (until July 26h 2020) using systematic searches in PubMed, Web of Science and Ovid EMBASE with predefined search strings. A total of 4571 unique publications were retrieved, out of which 378 publications were selected for in-depth analysis by two raters, including a total of 17549 (out of which were 14418 SARS-CoV-2) patients. Neurological complications and associated neuroradiological manifestations are prevalent for all HCoVs (HCoV-229E, HKU1, NL63, OC43, Middle East respiratory syndrome (MERS)-CoV, SARS-CoV-1 and SARS-CoV-2). Moreover, there are similarities in symptomatology across different HCoVs, particularly between SARS-CoV-1 and SARS-CoV-2. Common neurological manifestations include fatigue, headache and smell/taste disorders. Additionally, clinicians need to be attentive for at least five classes of neurological complications: (1) Cerebrovascular disorders including ischemic stroke and macro/micro-hemorrhages, (2) encephalopathies, (3) para-/postinfectious immune-mediated complications such as Guillain-Barre syndrome and acute disseminated encephalomyelitis, (4) (meningo-)encephalitis, potentially with concomitant seizures and (5) neuropsychiatric complications such as psychosis and mood disorders. Our systematic review highlights the need for vigilance regarding neurological complications in patients infected by SARS-CoV-2 and other HCoVs, especially since some complications may result in chronic disability. Neuroimaging protocols should be designed to specifically screen for these complications. Therefore, we propose practical imaging guidelines to facilitate the diagnostic workup and monitoring of patients infected with HCoVs. url: http://medrxiv.org/cgi/content/short/2020.08.26.20182196v1?rss=1 doi: 10.1101/2020.08.26.20182196 id: cord-305704-grzrkff9 author: Almutairi, Abdulelah title: Dermatological Manifestations in Patients With SARS-CoV-2: A Systematic Review date: 2020-07-28 words: 2289.0 sentences: 134.0 pages: flesch: 46.0 cache: ./cache/cord-305704-grzrkff9.txt txt: ./txt/cord-305704-grzrkff9.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been initially defined as a disease of the respiratory tract; however, with the increasing number of patients and announcing that the virus became a pandemic, new systemic clinical manifestations are observed, including dermatological manifestations. The following step was filtering the results to include only original research studies investigating the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. The results were then filtered to include only original research studies examining the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. After searching the abstracts and reviewing the eligibility criteria in identified potential abstracts, a total of seven studies [14] [15] [16] [17] [18] [19] [20] were considered as eligible to be included in the present systematic review, covering a total of 555 patients with SARS-CoV-2 who had dermatological symptoms in the form of skin lesions. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been initially defined as a disease of the respiratory tract; however, with the increasing number of patients and announcing that the virus became a pandemic, new systemic clinical manifestations are observed, including dermatological manifestations. However, the identification and characteristics of these manifestations are still controversial. This review article aims to evaluate the medical literature and explore the dermatological clinical manifestations in patients with SARS-CoV-2. The literature was reviewed through MEDLINE®, Ovid, PubMed®, and Embase®. Searching terms included were a combination of "dermatological" OR "skin" AND "symptoms" OR "manifestations" AND "SARS-CoV-2". The following step was filtering the results to include only original research studies investigating the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. A total of 879 studies were retrieved. Following the exclusion of studies on animals and including only studies on humans, 32 studies emerged. Altogether, seven studies were identified as eligible, covering 555 patients with SARS-CoV-2 who had dermatological symptoms. Three studies were retrospective, two studies were prospective, and two studies were case series. Different types of dermatological lesions can occur in patients with SARS-CoV-2, most commonly erythema, urticaria, and varicella-like rash. Dermatological manifestations with SARS-CoV-2 can be misdiagnosed with other conditions. Further studies with robust design are needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32775112/ doi: 10.7759/cureus.9446 id: cord-353659-wtacr6qj author: Almutairi, Nawaf title: Coronavirus Disease‐2019 with Dermatologic Manifestations and Implications: An Unfolding Conundrum date: 2020-05-09 words: 1026.0 sentences: 62.0 pages: flesch: 45.0 cache: ./cache/cord-353659-wtacr6qj.txt txt: ./txt/cord-353659-wtacr6qj.txt summary: As a nosocomial infection for hospital and nursing home patients and health care workers, it represents an extraordinary challenge. Lungs are the most severely affected organ by COVID-19 because the virus enters the host cells via the integral membrane protein angiotensin-converting enzyme 2 (ACE2), which is attached to cellular membranes in the lungs, arteries, heart, kidney, and intestines. A study of 663 COVID-19 patients from Wuhan, China stressed that patients more than 60 years old and those with chronic diseases were at enhanced risk of severe COVID-19, and more likely to die (43). Clinical Characteristics of Coronavirus Disease 2019 in China Prevalence of venous thromboembolism in patients with severe novel coronavirus pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: The novel coronavirus SARS‐CoV‐2 has caused Coronavirus Disease‐2019, widely known as COVID‐19, now a pandemic with extraordinary infectivity, mortality, and fomite adhesiveness. As a nosocomial infection for hospital and nursing home patients and health care workers, it represents an extraordinary challenge. The cutaneous markers of this pandemic are being elucidated with preliminary experiences being shared and rapidly communicated. We will review COVID‐19 from both a dermatologic and public health perspective. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/dth.13544 doi: 10.1111/dth.13544 id: cord-333696-3ci9re9a author: Alomari, Safwan O. title: COVID-19 and the Central Nervous System date: 2020-08-04 words: 4407.0 sentences: 266.0 pages: flesch: 46.0 cache: ./cache/cord-333696-3ci9re9a.txt txt: ./txt/cord-333696-3ci9re9a.txt summary: Li and colleagues (2020) have suggested that SARS-CoV-2 can enter the brain, and it might be the cause of the respiratory failure in patients with COVID-19 [25] . Recently, Olds & Kabbani (2020) raised the question of nicotine associated neurological comorbidity in COVID19 patients depending on published evidence that the viral target receptor J o u r n a l P r e -p r o o f ACE2 is expressed in the brain and functionally interacts with nAChRs [29, 30] . This was the first reported case of MERS associated with coronavirus infection, which adds to the expanding list of differential diagnoses to be considered in a COVID-19 patient with neurological signs, most notably; cerebellar ataxia and disturbance in consciousness [49, 52, 53] . Laboratory work-up was negative for influenza, with the diagnosis of COVID-19 made by detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) PCR. abstract: • As the number of patients with COVID-19 is increasing worldwide, it is necessary to stress on the importance of the atypical clinical presentations (including those related to the nervous system) of COVID-19 infection, since they might be the initial manifestations. • Literature on this regard should be sent by the international and local health committees to all health-care providers during this COVID -19 pandemic, to make sure that all providers are well informed and aware of these cases. • More studies are deeply needed to enable the concerned committees to make evidence-based guidelines for prevention, early detection and appropriate management of these cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32828027/ doi: 10.1016/j.clineuro.2020.106116 id: cord-349690-hgdjbeht author: Alonso, Fábio de O. Martinez title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report date: 2020-08-14 words: 723.0 sentences: 49.0 pages: flesch: 52.0 cache: ./cache/cord-349690-hgdjbeht.txt txt: ./txt/cord-349690-hgdjbeht.txt summary: title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report Although cases vary in terms of serological data, timing of reactivation and clinics, patients who retested positive to SARS-CoV-2 generally have a mild or asymptomatic course 5, 6 , which is perhaps the result of some level of immunity, while symptomatic reactivation is rare but may happen 7 . Our patient, on the other hand, presented a more potent form of COVID-19 after more than 40 days from the first mild infection, and with a detectable antibody response only after the second infectious episode. In this paper, we describe a COVID-19 recurrence from a mild to a moderate form after convalescence, with RT-qPCR turning positive and antibody detection after more severe symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report abstract: In general, SARS‐CoV‐2 replication in the host reaches its peak in the first week of infection, decreasing rapidly afterwards, while some level of immunity is build up. Yet, the infection seems to follow a distinctive course in some individuals, reactivating after the apparent resolution of symptoms(1‐3). We report here the first case to be disclosed of a more vigorous COVID‐19 recurrence with SARS‐CoV‐2 RNA redetection and late antibody response, and also the first to address COVID‐19 recurrence in Brazil. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32797634/ doi: 10.1002/jmv.26432 id: cord-280914-6k8gpp4y author: Alpaslan Kocamemi, B. title: First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey date: 2020-05-06 words: 2156.0 sentences: 147.0 pages: flesch: 62.0 cache: ./cache/cord-280914-6k8gpp4y.txt txt: ./txt/cord-280914-6k8gpp4y.txt summary: SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2, Covid-19, sewage, wastewater, RT-qPCR, virus concentration, PEG SARS-CoV-2 virus titers of manhole were higher than inlet of WWTPs. Terkos wastewater sample has the highest Case number (person)/WWTP flow (m3/d), but SARS-CoV-2 virus was not detected. So far, ultracentrifugation [6] , Polyethylene glycol 8000 (PEG 8000) adsorption [5] , electronegative membrane [3] and ultrafiltration [3, 4, 8] methods were used for SARS-CoV-2 concentration from wastewater samples. Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in Wuhan, China, in December 2019 and became a global pandemic [1]. By 26 April 2020, more than 2.9 million people were infected by SARS-CoV-2 and over 203 thousand people lost their life globally. By 26 April 2020, 107773 confirmed cases were reported in Turkey with 2706 deaths. Majority of the cases in Turkey has been observed in Istanbul. In the world, the duration of availability of SARS-CoV-2 was found to be significantly longer in stool samples than in respiratory and serum samples [2]. SARS-CoV-2 was detected in wastewaters in Australia [3], Netherlands [4], USA [5], France [6], Spain [7] and USA [8] by using different virus concentration techniques. In this work, Istanbul metropole with 65 % of Covid-19 cases was chosen as the pilot city. On the 21st of April 2020, 24-hr composite samples were collected from the Ambarli, Pasakoy and Kadikoy wastewater treatment plants (WWTP). On the 25th of April 2020, more wastewater samples were taken from Terkos, Buyukcekmece, Baltalimani and Tuzla WWTPs. These wastewater treatment plants were selected among 81 plants in Istanbul in order to take representative samples from 4 different districts of Istanbul according to the severity of Covid-19 cases, like very serious, serious, moderate and mild. Grab samples were also collected from Bagcilar and Kartal manholes located nearby the pandemic hospitals on April 21st, 2020. Polyethylene glycol 8000 (PEG 8000) adsorption [5] SARS-Cov-2 concentration method was used for SARS-CoV-2 concentration after optimization. Real time RT-PCR diagnostic panel validated by US was used to quantify SARS-CoV-2 RNA in raw sewage taken from the inlets of treatment plants and manholes. Five samples out of seven from wastewater and all samples from manholes were tested positive. SARS-CoV-2 in raw sewage from Ambarli, Pasakoy, Kadikoy, Terkos, Buyukcekmece, Baltalimani and Tuzla WWTPs were found as 8.26x103, 1.80x104, ND, ND, 3.73x103, 4.95x103, 2.89x103, respectively. The Bagcilar and Kartal manholes nearby pandemic hospitals exhibited 4.49x104 and 9.33x104, respectively. SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. Quantitative measurements of SARS-CoV-2 in wastewater can be used as a tool in wastewater-based epidemiology (WBE) and it can provide information about SARS-CoV-2 distribution in wastewater of various districts of Istanbul which exhibit different scores of Covid-19 cases. The distribution of epidemy was followed not only with blood test but with wastewater monitoring. This may allow us to identify the districts not exhibiting many Covid-19 cases, but under high risk. Continuous monitoring of wastewater for SARS-Cov-2 may provide an early warning signs before an epidemy starts in case of infection resurge. url: https://doi.org/10.1101/2020.05.03.20089417 doi: 10.1101/2020.05.03.20089417 id: cord-287321-1ro10ujr author: Alpaydin, Aylin Ozgen title: Clinical and Radiological Diagnosis of Non‐SARS‐CoV‐2 Viruses in the Era of Covid‐19 Pandemic date: 2020-08-08 words: 3288.0 sentences: 197.0 pages: flesch: 48.0 cache: ./cache/cord-287321-1ro10ujr.txt txt: ./txt/cord-287321-1ro10ujr.txt summary: INTRODUCTION: Following the announcement of first coronavirus disease 2019 (COVID‐19) case on March 11, 2020, in Turkey we aimed to report the co‐infection rates, and the clinical, laboratory, radiological distinctive features of viral pneumonia caused by viruses other than severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The spectrum of SARS-CoV-2 originated human disease named as coronavirus disease 2019 (COVID19) changes from little to no symptoms to severe pneumonia and acute respiratory distress syndrome 4 . Under these conditions; it was aimed to report the co-infection rates, the prevalence, clinical, laboratory and radiological characteristics of non-SARS-CoV-2 respiratory pathogens in a teaching hospital organized as a pandemic hospital immediately at the beginning of the pandemic in Turkey. Radiological assessments for the more frequently identified Non-SARS-CoV-2 pathogens (both metapneumovirus and rhinovirus) were compatible with indeterminate or atypical for COVID-19 disease. Some clinical, laboratory and especially radiological findings may aid in the differential diagnosis of non-SARS-CoV-2 pathogens from COVID-19. abstract: INTRODUCTION: Following the announcement of first coronavirus disease 2019 (COVID‐19) case on March 11, 2020, in Turkey we aimed to report the co‐infection rates, and the clinical, laboratory, radiological distinctive features of viral pneumonia caused by viruses other than severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). METHODS: A cross‐sectional study was conducted between 18 and 31 March 2020. COVID‐19 suspected cases admitted to pandemic policlinic who had nasopharyngeal swab specimens tested for both SARS‐CoV‐2 and other respiratory viral pathogens were included. RESULTS: Within 112 patients SARS‐CoV‐2 was detected in 34 (30%). Among the non‐SARS‐CoV‐2 viruses (n=25, 22%), metapneumovirus (n=10), was the most frequent agent. There were two co‐infections with SARS‐CoV‐2. Sputum was less in the SARS‐CoV‐2 group (p=0.003). The leukocyte, lymphocyte, and thrombocyte count and C‐reactive protein levels were lowest in the SARS‐CoV‐2 group (p<0.001, p=0.04, p<0.001, p=0.007 respectively). Peripheral involvement (80% vs. 20%, p=<0.001), pure ground‐glass opacity (65% vs. 33%, p=0.04), apicobasal gradient (60% vs. 40%, p=0.08), involvement of ≥3 lobes (80% vs. 40%, OR:6.0, 95%CI,1.33‐27.05, p=0.02) and consolidation with accompanying ground‐glass opacity (4% vs. 33%, p=0.031) were more common in SARS‐CoV‐2 group. CONCLUSION: Some clinical, laboratory and radiological findings may help in the differential diagnosis of non‐SARS‐CoV‐2 viruses from COVID‐19. However, co‐infections may occur, and a non‐SARS‐CoV‐2 pathogen positivity does not exclude accompanying COVID‐19. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32770738/ doi: 10.1002/jmv.26410 id: cord-305956-l02xdq87 author: Alqahtani, Saleh A title: Liver injury in COVID-19: The current evidence date: 2020-05-26 words: 3062.0 sentences: 198.0 pages: flesch: 44.0 cache: ./cache/cord-305956-l02xdq87.txt txt: ./txt/cord-305956-l02xdq87.txt summary: These reports highlighted that beyond severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a complicated course of the disease or even viral infection itself can lead to involvement of other organs and multiorgan failure. The current review summarizes the pathophysiology and potentially specific role of COVID-19 in liver disease based on the available data and case series published, ahead of print and non-peer-reviewed preprints as of 2 April. In this study, 47.3% of the discharged patients showed elevated LFTs at baseline, and 23.7% developed abnormalities during hospitalization, suggesting emerging liver injury from drugs or during the course of the infection. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: A single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series abstract: Patients with novel coronavirus disease 2019 (COVID-19) experience various degrees of liver function abnormalities. Liver injury requires extensive work-up and continuous surveillance and can be multifactorial and heterogeneous in nature. In the context of COVID-19, clinicians will have to determine whether liver injury is related to an underlying liver disease, drugs used for the treatment of COVID-19, direct effect of the virus, or a complicated disease course. Recent studies proposed several theories on potential mechanisms of liver injury in these patients. This review summarizes current evidence related to hepatobiliary complications in COVID-19, provides an overview of the available case series and critically elucidates the proposed mechanisms and provides recommendations for clinicians. url: https://doi.org/10.1177/2050640620924157 doi: 10.1177/2050640620924157 id: cord-281552-zfjy3m3i author: Alsaadi, Entedar A. J. title: Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date: 2020-09-22 words: 4781.0 sentences: 205.0 pages: flesch: 49.0 cache: ./cache/cord-281552-zfjy3m3i.txt txt: ./txt/cord-281552-zfjy3m3i.txt summary: Here, we test E-derived peptides for membrane binding activity in vitro and confirm those identified as positive in the context of the full length protein expressed in two different cell types. Relative densitometry of the HSP and LSP bands revealed significant differences among the mutants with regard to their localisation to the different membrane fractions of E expressing insect cells ( Figure 5B ) and confirmed a role for the amphipathic MHV CoV E 50-64 peptide in membrane interaction. An amphipathic helix, EPTM, detected in the post-TM region of E, was suggested by bioinformatics analysis and assessed for direct membrane interaction in vitro by binding to GUVs. For comparison, the predicted E protein TM domain, ETM, and an established membrane active peptide from the influenza M2 protein were also included. Following expression of the complete E protein with mutations in the same identified peptide, altered membrane binding in two distinct cell types, mammalian and insect, was apparent. abstract: Coronaviruses (CoVs) are enveloped, positive sense, single strand RNA viruses that cause respiratory, intestinal and neurological diseases in mammals and birds. Following replication, CoVs assemble on intracellular membranes including the endoplasmic reticulum Golgi intermediate compartment (ERGIC) where the envelope protein (E) functions in virus assembly and release. In consequence, E potentially contains membrane-modifying peptides. To search for such peptides, the E coding sequence of Mouse Hepatitis Virus (MHV) was inspected for its amino acid conservation, proximity to the membrane and/or predicted amphipathic helices. Peptides identified in silico were synthesized and tested for membrane-modifying activity in the presence of giant unilamellar vesicles (GUVs) consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), sphingomyelin and cholesterol. To confirm the presence of membrane binding peptides identified in the context of a full-length E protein, the wild type and a number of mutants in the putative membrane binding peptide were expressed in Lenti-X-293T mammalian and insect cells, and the distribution of E antigen within the expressing cell was assessed. Our data identify a role for the post-transmembrane region of MHV E in membrane binding. url: https://www.ncbi.nlm.nih.gov/pubmed/32971895/ doi: 10.3390/v12091054 id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 words: 3380.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-321855-7b1c2xdh.txt txt: ./txt/cord-321855-7b1c2xdh.txt summary: title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. abstract: OBJECTIVES: In this study, we aimed to study the clinical presentations, and viral clearance of SARS-COV-2 positive quarantined individuals. DESIGN: Cross-sectional study. SETTING: Governmental- designated facility in the eastern province, Saudi Arabia. PARTICIPANTS: 128 laboratory-confirmed COVID-19 quarantined individuals who had a history of travel abroad in the last 14 days before the quarantine or were in direct contact with laboratory-confirmed cases. The study was from March 18th-till April 16th. PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. RESULTS: Sixty-nine of the 128 residents (54%) were completely asymptomatic until the end of the study. The remaining 59 residents (46%) had only mild symptoms. The most common symptom was a sudden loss of smell and taste, accounting for 47.5%. The median time to virus clearance was significantly different between the two groups. Symptomatic residents cleared the virus at a median of 17 days (95% CI, 12.4–21.6) from the first positive PCR vs. 11days (95% CI, 8.7–13.3) in the asymptomatic group (P = 0.011). False-negative test results occurred in 18.8% of the total residents and false-positive results in 3%. CONCLUSION: The prevalence of asymptomatic carriers among quarantined travelers and those identified by contact tracing is high in our study. Therefore, testing, tracing, and isolating travelers and contacts of laboratory-confirmed cases, regardless of symptoms, were very effective measures for early disease identification and containment. Loss of taste and smell were the most common presentations in our mild symptomatic residents and should be used as a screening tool for COVID-19. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. url: https://doi.org/10.1371/journal.pone.0241258 doi: 10.1371/journal.pone.0241258 id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 words: 7353.0 sentences: 387.0 pages: flesch: 48.0 cache: ./cache/cord-289612-4x5t4c5u.txt txt: ./txt/cord-289612-4x5t4c5u.txt summary: Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases abstract: MOTIVATION: COVID-19 is one of the most widely affecting pandemics. As for many respiratory viruses-caused diseases, diagnosis of COVID-19 relies on two main compartments: clinical and paraclinical diagnostic criteria. Rapid and accurate diagnosis is vital in such a pandemic. On one side, rapidity may enhance management effectiveness, while on the other, coupling efficiency and less costly procedures may permit more effective community-scale management. METHODOLOGY AND MAIN STRUCTURE: In this review, we shed light on the most used and the most validated diagnostic tools. Furthermore, we intend to include few under-development techniques that may be potentially useful in this context. The practical intent of our work is to provide clinicians with a realistic summarized review of the essential elements in the applied paraclinical diagnosis of COVID-19. url: https://doi.org/10.1016/j.retram.2020.06.001 doi: 10.1016/j.retram.2020.06.001 id: cord-306351-ka6asw3m author: Alsuliman, Tamim title: A review of potential treatments to date in COVID-19 patients according to the stage of the disease date: 2020-05-30 words: 6057.0 sentences: 374.0 pages: flesch: 48.0 cache: ./cache/cord-306351-ka6asw3m.txt txt: ./txt/cord-306351-ka6asw3m.txt summary: Several trials of Remdesivir treatment on few patients in the United States have shown early promising benefits in cases with severe pneumonia [33, 34] . On the other hand, data emerging from other ongoing Chinese trials have demonstrated that CQ phosphate is superior to a control treatment in the following areas: pneumonia exacerbation inhibition, imaging findings improvement, virus negative conversion promoting, and disease course shortening [62] . For example, clinical data from reliable randomized controlled studies are still missing, and data published to date lacks homogeneity in terms of recommended dose concentration, treatment duration, and severity of patient illness [58] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The experience of clinical immunologists from China abstract: Abstract Introduction and motivation: Since the end of 2019, the COVID-19 pandemic has affected millions of people worldwide. With the rapid spread of this virus, an immense burden has fallen upon both healthcare and economic systems. As a consequence, there is an unprecedented urgency for researchers and scientific committees from all over the world to find an effective treatment and vaccine. Review Structure: Many potential therapies are currently under investigation, with some, like Hydroxychloroquine, being authorized for emergency use in some countries. The crucial issue is now clearly to find the suitable treatment strategy for patients given comorbidities and the timeline of the illness.Vaccines are also under development and phase 1 clinical trials are rolling. Despite all efforts, no single drug or vaccine has yet been approved. In this review, we aim at presenting the proposed pathophysiological mechanisms of SARS-CoV-2 and to provide clinicians with a brief and solid overview of the current potential treatments classified according to their use at the three different currently proposed disease stages. In light of pathogenesis and proposed clinical classification, this review’s purpose is to summarize and simplify the most important updates on the management and the potential treatment of this emergent disease. url: https://doi.org/10.1016/j.retram.2020.05.004 doi: 10.1016/j.retram.2020.05.004 id: cord-263840-1t4ykc01 author: Altay, Ozlem title: Current status of COVID-19 therapies and drug repositioning applications date: 2020-06-20 words: 2099.0 sentences: 140.0 pages: flesch: 44.0 cache: ./cache/cord-263840-1t4ykc01.txt txt: ./txt/cord-263840-1t4ykc01.txt summary: Summary The rapid and global spread of a new human coronavirus (SARS-CoV-2) has produced an immediate urgency to discover promising targets for treatment of COVID-19. Here, we review current information concerning the global health issue of COVID-19 including promising approved drugs and ongoing clinical trials for prospective treatment options. At the genome 60 level, SARS-CoV-2 has 79·5% homology to SARS CoVCoV-2 and other coronaviruses, and its relative ease of sample acquisition and study, it has been widely 75 accepted that drug repositioning is a promising approach to make available an effective, safety-assured 76 treatment in a timely manner. In this review, we summarize diagnosis approaches, risk groups, available 77 treatment options, and drug repositioning studies related to COVID-19. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 525 2019 (COVID-19): The experience of clinical immunologists from China abstract: Summary The rapid and global spread of a new human coronavirus (SARS-CoV-2) has produced an immediate urgency to discover promising targets for treatment of COVID-19. Drug repositioning is an attractive approach that can facilitate the drug discovery process by repurposing existing pharmaceuticals to treat illnesses other than their primary indications. Here, we review current information concerning the global health issue of COVID-19 including promising approved drugs and ongoing clinical trials for prospective treatment options. In addition, we describe computational approaches to be used in drug repurposing and highlight examples of in-silico studies of drug development efforts against SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S2589004220304909 doi: 10.1016/j.isci.2020.101303 id: cord-294912-xl0wzi16 author: Alteri, Claudia title: Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date: 2020-09-08 words: 3630.0 sentences: 216.0 pages: flesch: 49.0 cache: ./cache/cord-294912-xl0wzi16.txt txt: ./txt/cord-294912-xl0wzi16.txt summary: Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72–345). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients. In this study, the presence of SARS-CoV-2 genome was evaluated in 55 SARS-CoV-2 rtPCR negative nasopharyngeal swabs from COVID-19 suspected patients thanks to a quantitative ad hoc designed assay based on ddPCR. This proof-of-concept study shows that an in-house ddPCR-based assay can allow an efficient detection of SARS-CoV-2 at low copy number in symptomatic cases resulted negative by standard rtPCR. abstract: Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. Here we evaluated the performance of a ddPCR-based assay to quantify SARS-CoV-2 titer in 55 suspected COVID-19 cases with negative rtPCR results thanks to in-house ddPCR assay (targeting RdRp and host RNaseP). Samples were collected at ASST-GOM Niguarda between February and May 2020 at hospital admission. Clinical and imaging data were obtained for clinical staging and definition of disease severity. Patients were mainly female (45.5%) with a median age of 73 (57–84) years. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72–345). In 15 of them (78.9%), chest CT showed a classical COVID-19 bilateral interstitial pneumonia; 14 patients (73.7%) showed severe COVID-19 manifestations. ddPCR did not identify any trace of SARS-CoV-2 genome in the respiratory samples of the remaining 36 patients. The serological assay performed in a subgroup of 34 patients at the later stage of illness (from 3 days to 90 days after) confirmed the presence of SARS-CoV-2 antibodies in all patients tested positive for SARS-CoV-2 in ddPCR (100%). Contrariwise, negative tests were observed in 95.0% ddPCR negative patients (P<0.001). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32898153/ doi: 10.1371/journal.pone.0236311 id: cord-235691-en6fgilb author: Althouse, Benjamin M. title: Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 date: 2020-05-27 words: 4811.0 sentences: 212.0 pages: flesch: 47.0 cache: ./cache/cord-235691-en6fgilb.txt txt: ./txt/cord-235691-en6fgilb.txt summary: In Figure 2 we show an example by utilizing a stochastic branching process model with both Poisson and SARS-CoV-1 like NB distribution (k = 0.16) under the same mean R 0 = 2.6 26 , with different population sizes ranging from small clusters of 10 like households to large ones of 10 6 like city-wide. Because they play an important role in the spread of infection, hotspots pose an opportunity for surveillance and control: focusing on facilities and activities known to sustain hotspots, such as healthcare facilities, nursing homes, prisons, meat-packing plants, homeless shelters, schools, mass gatherings, as well as those places with closed, poorly circulated environments, can provide efficient ways to identify potential SSEs before they happen, therefore, potentially reducing a substantial amount of transmission in the population. Multiple lines of evidence at the individual-and population-level strongly indicate the role of SSEs in the transmission dynamics of SARS-CoV-2 and that we should not overlook the heterogeneity in numbers of secondary infections 57 . abstract: SARS-CoV-2 causing COVID-19 disease has moved rapidly around the globe, infecting millions and killing hundreds of thousands. The basic reproduction number, which has been widely used and misused to characterize the transmissibility of the virus, hides the fact that transmission is stochastic, is dominated by a small number of individuals, and is driven by super-spreading events (SSEs). The distinct transmission features, such as high stochasticity under low prevalence, and the central role played by SSEs on transmission dynamics, should not be overlooked. Many explosive SSEs have occurred in indoor settings stoking the pandemic and shaping its spread, such as long-term care facilities, prisons, meat-packing plants, fish factories, cruise ships, family gatherings, parties and night clubs. These SSEs demonstrate the urgent need to understand routes of transmission, while posing an opportunity that outbreak can be effectively contained with targeted interventions to eliminate SSEs. Here, we describe the potential types of SSEs, how they influence transmission, and give recommendations for control of SARS-CoV-2. url: https://arxiv.org/pdf/2005.13689v1.pdf doi: nan id: cord-030999-27wennun author: Altmann, Daniel M title: Adaptive immunity to SARS-CoV-2 date: 2020-07-09 words: 4374.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-030999-27wennun.txt txt: ./txt/cord-030999-27wennun.txt summary: The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. Since many key questions about durability of the antibody response and about correlates of protection have been hard to address in this short timeframe, there has been value in recourse to the coronavirus immunology literature, especially in relation to SARS and MERS [16] [17] [18] [19] . Experience to date with SARS-CoV-2 suggests that this may not prove to be an infection that throws up insurmountable confounders to vaccine design-approaches that can safely and durably elicit neutralizing antibody look likely to work. Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals abstract: The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. A minority makes little detectable antibody, generally those with either very mild/asymptomatic disease or those with severe/lethal infection. However, in general, antibody titre correlates with viral load and duration of exposure. There is evidence for cross-reactivity with the other human coronaviruses, though the functional impact of this is as yet unclear. Therapeutic use of neutralizing monoclonal antibodies offers potential for clinical use. While there is evidence for neutralizing antibody as a correlate of protection, some cases indicate the potential for full recovery in the absence of antibody. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. However, in severe cases, there is evidence for T-cell lymphopaenia as well as expression of exhaustion markers. Analysis of serum biomarkers of disease severity implicates a hyperinflammatory contribution to pathogenesis, though this has not been mechanistically delineated beyond a likely role of raised IL-6, considered a therapeutic target. Despite rapid progress, there remain pressing unknowns. It seems likely that immune memory to SARS-CoV-2 may be relatively short lived, but this will need longitudinal investigation. Also, this is a disease of highly variable presentation and time course, with some progressing to protracted, chronic symptoms, which are not understood. The contribution of immunopathological mechanisms to tissue damage, whether in the lung, kidney, heart or blood vessels, is unclear. The immunology underlying the differential susceptibility between the very young and the very old is unresolved, a question with ramifications for vaccine roll-out. The greatest challenge relates to rapid generation, testing and manufacture of vaccines that are immunogenic, protective (at least from symptomatic disease) and safe—a challenge that looks achievable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454881/ doi: 10.1093/oxfimm/iqaa003 id: cord-270858-ozvdz9ew author: Altmann, Daniel M title: What policy makers need to know about COVID-19 protective immunity date: 2020-04-27 words: 1563.0 sentences: 90.0 pages: flesch: 49.0 cache: ./cache/cord-270858-ozvdz9ew.txt txt: ./txt/cord-270858-ozvdz9ew.txt summary: Strategies in various countries that aim to stagger return to work on the basis of disease severity risk and age do not take account of how exposing even lower-risk individuals, such as young people with no comorbidities, to the virus so as to increase herd immunity can still result in pandemic spread. A caveat is that most studies, either of SARS survivors or of COVID-19 patients, have focused on people who were hospitalised and had severe, symptomatic disease. Anecdotal reports of reinfection from China and South Korea should be regarded with caution because some individuals who seemed to have cleared SARS-CoV-2 infection and tested negative on PCR might nevertheless have harboured persistent virus. 16 On the basis of this estimated R 0 , the herd immunity calculation suggests that at least 60% of the population would need to have protective immunity, either from natural infection or vaccination. abstract: nan url: https://api.elsevier.com/content/article/pii/S0140673620309855 doi: 10.1016/s0140-6736(20)30985-5 id: cord-315666-ngozukzj author: Altundag, Aytug title: Olfactory Cleft Measurements and COVID-19–Related Anosmia date: 2020-10-13 words: 4278.0 sentences: 231.0 pages: flesch: 54.0 cache: ./cache/cord-315666-ngozukzj.txt txt: ./txt/cord-315666-ngozukzj.txt summary: OBJECTIVE: This study aimed to investigate the differences in olfactory cleft (OC) morphology in coronavirus disease 2019 (COVID-19) anosmia compared to control subjects and postviral anosmia related to infection other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RESULTS: This study showed 3 major findings: the right and left OC widths were significantly wider in anosmic patients due to SARS-CoV-2 (group 1) or OD due to non–SARS-CoV-2 viral infection (group 2) when compared to healthy controls. Exclusion criteria for groups 1 and 2 were age younger than 18 years, pregnancy, normosmia detected on Sniffin'' Sticks olfactory test (a threshold discrimination identification [TDI] score of .30.5), acute and/or chronic rhinosinusitis or other acute/chronic nasal disease, nasal polyposis, allergic or idiopathic rhinitis, posttraumatic olfactory loss, severe turbinate hypertrophy or nasal septum deviation affecting the air passage, malignancy history, and a history of nasal or paranasal surgery. abstract: OBJECTIVE: This study aimed to investigate the differences in olfactory cleft (OC) morphology in coronavirus disease 2019 (COVID-19) anosmia compared to control subjects and postviral anosmia related to infection other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). STUDY DESIGN: Prospective. SETTING: This study comprises 91 cases, including 24 cases with anosmia due to SARS-CoV-2, 38 patients with olfactory dysfunction (OD) due to viral infection other than SARS-CoV-2, and a control group of 29 normosmic cases. METHODS: All cases had paranasal sinus computed tomography (CT), and cases with OD had magnetic resonance imaging (MRI) dedicated to the olfactory nerve. The OC width and volumes were measured on CT, and T2-weighted signal intensity (SI), olfactory bulb volumes, and olfactory sulcus depths were assessed on MRI. RESULTS: This study showed 3 major findings: the right and left OC widths were significantly wider in anosmic patients due to SARS-CoV-2 (group 1) or OD due to non–SARS-CoV-2 viral infection (group 2) when compared to healthy controls. OC volumes were significantly higher in group 1 or 2 than in healthy controls, and T2 SI of OC area was higher in groups 1 and 2 than in healthy controls. There was no significant difference in olfactory bulb volumes and olfactory sulcus depths on MRI among groups 1 and 2. CONCLUSION: In this study, patients with COVID-19 anosmia had higher OC widths and volumes compared to control subjects. In addition, there was higher T2 SI of the olfactory bulb in COVID-19 anosmia compared to control subjects, suggesting underlying inflammatory changes. There was a significant negative correlation between these morphological findings and threshold discrimination identification scores. LEVEL OF EVIDENCE: Level 4. url: https://www.ncbi.nlm.nih.gov/pubmed/33045908/ doi: 10.1177/0194599820965920 id: cord-310184-qth1y88o author: Alunno, Alessia title: Storm, typhoon, cyclone or hurricane in patients with COVID-19? Beware of the same storm that has a different origin date: 2020-05-18 words: 2981.0 sentences: 143.0 pages: flesch: 38.0 cache: ./cache/cord-310184-qth1y88o.txt txt: ./txt/cord-310184-qth1y88o.txt summary: Some of the articles being published during the severe acute respiratory syndrome–coronavirus (SARS-CoV)-2 pandemic highlight a link between severe forms of coronavirus disease 2019 (COVID-19) and the so-called cytokine storm, also with increased ferritin levels. Some patients with coronavirus 2019 disease (COVID-19) develop a fully blown secondary haemophagocytic lymphohistiocytosis (sHLH), whereas others, despite a consistent release of pro-inflammatory cytokines, do not fulfil sHLH criteria but still show some features resembling the phenotype of the hyperferritinemic syndrome. Other immunomodulating agents like IL-1 or IL-6 inhibitors are only recommended in selected cases including the macrophage activation syndrome (MAS), a subtype of sHLH associated with systemic juvenile idiopathic arthritis (sJIA), adult-onset Still''s disease (AOSD) and other autoimmune disorders. abstract: Some of the articles being published during the severe acute respiratory syndrome–coronavirus (SARS-CoV)-2 pandemic highlight a link between severe forms of coronavirus disease 2019 (COVID-19) and the so-called cytokine storm, also with increased ferritin levels. However, this scenario is more complex than initially thought due to the heterogeneity of hyperinflammation. Some patients with coronavirus 2019 disease (COVID-19) develop a fully blown secondary haemophagocytic lymphohistiocytosis (sHLH), whereas others, despite a consistent release of pro-inflammatory cytokines, do not fulfil sHLH criteria but still show some features resembling the phenotype of the hyperferritinemic syndrome. Despite the final event (the cytokine storm) is shared by various conditions leading to sHLH, the aetiology, either infectious, autoimmune or neoplastic, accounts for the differences in the various phases of this process. Moreover, the evidence of a hyperinflammatory microenvironment provided the rationale to employ immunomodulating agents for therapeutic purposes in severe COVID-19. This viewpoint aims at discussing the pitfalls and issues to be considered with regard to the use of immunomodulating agents in COVID-19, such as timing of treatment based on the viral load and the extent of cytokine/ferritin overexpression. Furthermore, it encompasses recent findings in the paediatric field about a novel multisystem inflammatory disease resembling toxic shock syndrome and atypical Kawasaki disease observed in children with proven SARS-CoV2 infection. Finally, it includes arguments in favour of adding COVID-19 to the spectrum of the recently defined ‘hyperferritinemic syndrome’, which already includes adult-onset Still’s disease, macrophage activation syndrome, septic shock and catastrophic anti-phospholipid syndrome. url: https://www.ncbi.nlm.nih.gov/pubmed/32423970/ doi: 10.1136/rmdopen-2020-001295 id: cord-033592-j1c2brb4 author: Alvarez Bravo, G. title: Encefalitis anti-NMDA-R secundaria a infección por SARS-CoV-2 Anti–NMDA receptor encephalitis secondary to SARS-CoV-2 infection date: 2020-10-09 words: 1073.0 sentences: 73.0 pages: flesch: 42.0 cache: ./cache/cord-033592-j1c2brb4.txt txt: ./txt/cord-033592-j1c2brb4.txt summary: Coronavirus disease 2019 (COVID-19), which is caused by infection with the SARS-CoV-2 coronavirus and has caused a global pandemic, presents a wide spectrum of manifestations ranging from asymptomaticity to severe infection causing systemic failure and death. We present the case of a patient with anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis secondary to SARS-CoV-2 infection. 3 In this case, we suspect that SARS-CoV-2 infection acted as a trigger for the onset of anti-NMDAR encephalitis. 4, 5 Identifying autoimmune phenomena in patients with COVID-19 has enabled us to detect some immune-mediated neurological conditions, such as Guillain-Barré syndrome, acute necrotising encephalitis, myelitis, limbic encephalitis, and multiple cranial neuropathy associated with SARS-CoV-2 infection. [6] [7] [8] This case illustrates the slow clinical progression of a patient with anti-NMDAR encephalitis and COVID-19. To our knowledge, this is the first case of anti-NMDAR encephalitis associated with COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7546184/ doi: 10.1016/j.nrleng.2020.07.011 id: cord-355560-vsxe97xs author: Alves, Amanda Mandarino title: SARS-CoV-2 leading to Acute Pancreatitis: an unusual presentation date: 2020-09-15 words: 1659.0 sentences: 98.0 pages: flesch: 43.0 cache: ./cache/cord-355560-vsxe97xs.txt txt: ./txt/cord-355560-vsxe97xs.txt summary: During SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) pandemic, the etiologic agent of COVID-19, several studies described the involvement of other tissues besides the respiratory tract, such as the gastrointestinal tract. Diagnosing acute pancreatitis secondary to SARS-CoV-2 infection is challenging due to the need to rule out other etiologies as well the notable heterogeneous presentations. The mechanisms of pancreatic injury in SARS-CoV-2 infection include direct cytopathic effects or indirect systemic inflammatory and immune-mediated cellular responses, resulting in organ damage or secondary enzyme abnormalities [1] . This case report describes a patient with COVID-19 that developed severe acute pancreatitis. ACE2 receptor is highly expressed in pancreatic islet cells [16] , therefore SARS-CoV-2 infection can theoretically cause islet damage resulting in acute diabetes [7] . ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection abstract: During SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) pandemic, the etiologic agent of COVID-19, several studies described the involvement of other tissues besides the respiratory tract, such as the gastrointestinal tract. Angiotensin-converting enzyme-2, the functional virus host cell receptor expressed by organs and tissues, seems to have an important role in the pathophysiology and presentation of this disease. In pancreas, this receptor is expressed in both exocrine glands and islets, being a potential target for the virus and subsequent pancreatic injury. There are few articles reporting pancreatic injury in COVID-19 patients but most of them do not report acute pancreatitis. Diagnosing acute pancreatitis secondary to SARS-CoV-2 infection is challenging due to the need to rule out other etiologies as well the notable heterogeneous presentations. Herein we report the case of a patient with COVID-19 who developed severe acute pancreatitis. url: https://www.ncbi.nlm.nih.gov/pubmed/32961108/ doi: 10.1016/j.bjid.2020.08.011 id: cord-276267-77903fld author: Al‐Ani, Aysha H. title: Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient date: 2020-05-26 words: 5481.0 sentences: 355.0 pages: flesch: 42.0 cache: ./cache/cord-276267-77903fld.txt txt: ./txt/cord-276267-77903fld.txt summary: 6 Consequently, there is a concern that IBD patients are at greater risk of developing COVID-19 and at increased risk of progressing to a more severe clinical course or even death compared to the general population. 18 Furthermore, there is a recent case report of a possible SARS-CoV-2 gastrointestinal infection causing acute haemorrhagic colitis and signalling COVID-19 disease. Clinical assessment of risk factors for infection in inflammatory bowel disease patients Protection of 318 inflammatory bowel disease patients from the outbreak and rapid spread of COVID-19 infection in Wuhan Risk of infection with methotrexate therapy in inflammatory diseases: a systematic review and meta-analysis Comparative risk of serious infections with biologic and/or immunosuppressive therapy in patients with inflammatory bowel diseases: a systematic review and meta-analysis Infection-related hospitalizations are associated with increased mortality in patients with inflammatory bowel diseases Respiratory tract infections in patients with inflammatory bowel disease: safety analyses from vedolizumab clinical trials abstract: BACKGROUND: The current COVID‐19 pandemic, caused by SARS‐CoV‐2, has emerged as a public health emergency. All nations are seriously challenged as the virus spreads rapidly across the globe with no regard for borders. The primary management of IBD involves treating uncontrolled inflammation with most patients requiring immune‐based therapies. However, these therapies may weaken the immune system and potentially place IBD patients at increased risk of infections and infectious complications including those from COVID‐19. AIM: To summarise the scale of the COVID‐19 pandemic, review unique concerns regarding IBD management and infection risk during the pandemic and assess COVID‐19 management options and drug interactions in the IBD population. METHODS: A literature review on IBD, SARS‐CoV‐2 and COVID‐19 was undertaken and relevant literature was summarised and critically examined. RESULTS: IBD patients do not appear to be more susceptible to SARS‐CoV‐2 infection and there is no evidence of an association between IBD therapies and increased risk of COVID‐19. IBD medication adherence should be encouraged to prevent disease flare but where possible high‐dose systemic corticosteroids should be avoided. Patients should exercise social distancing, optimise co‐morbidities and be up to date with influenza and pneumococcal vaccines. If a patient develops COVID‐19, immune suppressing medications should be withheld until infection resolution and if trial medications for COVID‐19 are being considered, potential drug interactions should be checked. CONCLUSION: IBD patient management presents a challenge in the current COVID‐19 pandemic. The primary focus should remain on keeping bowel inflammation controlled and encouraging medication adherence. url: https://www.ncbi.nlm.nih.gov/pubmed/32348598/ doi: 10.1111/apt.15779 id: cord-331147-numz9onx author: Al‐Kofahi, Mahmoud title: Finding the Dose for Hydroxychloroquine Prophylaxis for COVID‐19: The Desperate Search for Effectiveness date: 2020-06-01 words: 2301.0 sentences: 109.0 pages: flesch: 48.0 cache: ./cache/cord-331147-numz9onx.txt txt: ./txt/cord-331147-numz9onx.txt summary: Our aim was to identify possible hydroxychloroquine dosing regimens through simulation in those at high risk of infections by optimizing exposures above the in vitro generated half maximal effective concentration (EC(50)) and to help guide researchers in dose‐selection for COVID‐19 prophylactic studies. 8 We simulated the current FDA approved dosing for malaria treatment (800 mg followed by 400 mg at 6, 24, and 48 hours after the initial dose, a total of 3 days) and prophylaxis (400 mg weekly) and other regimens, such as those tested in recent COVID-19 trials (i.e., 400 mg/day for 5 days or 200 mg 3 times daily for 6 days). For the FDA recommended treatment dose of malaria (800 mg loading dose followed by 400 mg daily for a total of 3 days), simulations predicted 89% of subjects would have troughs above the target on day 1, however, this number dropped to 7% by day 14 post-exposure after the start of prophylaxis ( Table 1) . abstract: Hydroxychloroquine is an antimalarial drug being tested as a potential treatment for the novel coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2. Although the efficacy of hydroxychloroquine for COVID‐19 remains uncertain, it may serve as a potential prophylactic agent especially in those at high risk, such as healthcare workers, household contacts of infected patients, and the immunocompromised. Our aim was to identify possible hydroxychloroquine dosing regimens through simulation in those at high risk of infections by optimizing exposures above the in vitro generated half maximal effective concentration (EC(50)) and to help guide researchers in dose‐selection for COVID‐19 prophylactic studies. To maintain weekly troughs above EC(50) in > 50% of subjects at steady‐state in a pre‐exposure prophylaxis setting, an 800 mg loading dose followed by 400 mg twice or 3 times weekly is required. In an exposure driven, post‐exposure prophylaxis setting, 800 mg loading dose followed in 6 hours by 600 mg, then 600 mg daily for 4 more days achieved daily troughs above EC(50) in > 50% subjects. These doses are higher than recommended for malaria chemoprophylaxis, and clinical trials are needed to establish safety and efficacy. url: https://doi.org/10.1002/cpt.1874 doi: 10.1002/cpt.1874 id: cord-283716-tleh9323 author: Amatore, F. title: SARS‐CoV‐2 infection presenting as a febrile rash date: 2020-05-27 words: 828.0 sentences: 53.0 pages: flesch: 48.0 cache: ./cache/cord-283716-tleh9323.txt txt: ./txt/cord-283716-tleh9323.txt summary: The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide.1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide. 1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. [3] [4] [5] [6] [7] [8] [9] Herein, we describe a febrile rash as the only clinical manifestation of SARS-CoV-2 infection in a patient free from pulmonary symptoms. Firstly, Covid-19 disease can present with a distinctive rash, which is histologically similar but clinically different to classic viral exanthemata. abstract: The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide.1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. url: https://doi.org/10.1111/jdv.16528 doi: 10.1111/jdv.16528 id: cord-269909-1cso5cl4 author: Amatya, Shaili title: Management of newborns exposed to mothers with confirmed or suspected COVID-19 date: 2020-05-21 words: 5552.0 sentences: 278.0 pages: flesch: 44.0 cache: ./cache/cord-269909-1cso5cl4.txt txt: ./txt/cord-269909-1cso5cl4.txt summary: The unexpectedly high asymptomatic carrier rates reported from other institutions as well as prolonged face-to-face patient care required during labor and delivery drove this decision, allowing for judicious personal protective equipment (PPE) use and decreased potential exposure for both healthcare workers and newborns. Several reports, based on expert opinion, have recommended that DCC not be performed in neonates born to mothers with confirmed or suspected COVID-19 in order to reduce the risk of secondary transmission [15, 47, 49] . For resuscitation of premature, high-risk, and newborns with anomalies born to mothers with cinfirmed or suspected COVID-19, a fully donned neonatal resuscitation team enters the room upon delivery. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Neonatal resuscitation and postresuscitation care of infants born to mothers with suspected or confirmed SARS-CoV-2 infection abstract: There is limited information about newborns with confirmed or suspected COVID-19. Particularly in the hospital after delivery, clinicians have refined practices in order to prevent secondary infection. While guidance from international associations is continuously being updated, all facets of care of neonates born to women with confirmed or suspected COVID-19 are center-specific, given local customs, building infrastructure constraints, and availability of protective equipment. Based on anecdotal reports from institutions in the epicenter of the COVID-19 pandemic close to our hospital, together with our limited experience, in anticipation of increasing numbers of exposed newborns, we have developed a triage algorithm at the Penn State Hospital at Milton S. Hershey Medical Center that may be useful for other centers anticipating a similar surge. We discuss several care practices that have changed in the COVID-19 era including the use of antenatal steroids, delayed cord clamping (DCC), mother–newborn separation, and breastfeeding. Moreover, this paper provides comprehensive guidance on the most suitable respiratory support for newborns during the COVID-19 pandemic. We also present detailed recommendations about the discharge process and beyond, including providing scales and home phototherapy to families, parental teaching via telehealth and in-person education at the doors of the hospital, and telehealth newborn follow-up. url: https://doi.org/10.1038/s41372-020-0695-0 doi: 10.1038/s41372-020-0695-0 id: cord-275452-ymimvoq9 author: Ameen, Fuad title: Covid-19 pandemic outburst in Saudi Arabia: A Glimpse date: 2020-07-30 words: 2456.0 sentences: 142.0 pages: flesch: 47.0 cache: ./cache/cord-275452-ymimvoq9.txt txt: ./txt/cord-275452-ymimvoq9.txt summary: This short review report very briefly highlights covid-19 syndromes; propagation; Middle East outburst, natural products as cure for viral diseases, probable psychosomatic effects, protective measures and Islamic wisdom. Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. -q (2020) Traditional Chinese medicine is a resource for drug discovery against 2019 novel coronavirus (SARS-CoV-2) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: Abstract Synopsis Severe Acute Respiratory Syndrome Coronavirus2(SARS-CoV2) provoked alertness globally. Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019(covid-19). Worldwide pneumonia outburst attributable to new SARS-CoV2 alleged to be originated in Wuhan city of China and has affectation of enormous danger regarding civic wellbeing. As of 11 March 2020, international death toll owing to outburst of new coronavirus was approximately 3,800, and about 110,000 have been declared as confirmed cases. The novel SARS-CoV2 demonstrated competence with respect to human to human communication; therefore depicted exponential intensification of cases. As of March 23, there are 374,513 collective cases of global infections; more than 16,350 deaths and number of recovered cases is 101,554. Now Europe has turn out into new epicenter of lethal coronavirus. More than one third of the covid 19 cases are currently outside China. Presently Italy is one of worst hit countries followed by Spain. The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. Given to seriousness of present scenario an accurate and rapid classification of noxious pathogenic virus is important which will lend a hand in opting for best fitting drugs. The screening program will aid saving people’s lives and help to put off the pandemic situation. The scientists and researchers should collaborate nationally and internationally to win the battle against novel covid-19. We aimed to represent covid 19 outburst scenario in general and Saudi Arabia in particular. This short review report very briefly highlights covid-19 syndromes; propagation; Middle East outburst, natural products as cure for viral diseases, probable psychosomatic effects, protective measures and Islamic wisdom. SARS-CoV2 is subsequent coronavirus outburst that perturbs Middle East, after SARS-CoV and MERS-CoV which has been originated in kingdom of Saudi Arabia in year 2002 and 2012 respectively. The report covers information and developments till 23rd of March 2020 on basis of current published data and studies published on different scientific web-pages. url: https://www.sciencedirect.com/science/article/pii/S1319562X20303260?v=s5 doi: 10.1016/j.sjbs.2020.07.026 id: cord-293415-u9onutny author: Amendola, A. title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression date: 2020-11-10 words: 3522.0 sentences: 214.0 pages: flesch: 50.0 cache: ./cache/cord-293415-u9onutny.txt txt: ./txt/cord-293415-u9onutny.txt summary: title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression Our findings indicate that human cardiac stromal cells have a susceptibility to SARS-CoV-2 infection and produce variable viral yields depending on the extent of cellular ACE2 receptor expression. The susceptibility of the myocardial tissue to SARS-CoV-2 infection Tavazzi et al., 2020) has been inferred based on the expression of the Angiotensin-Converting Enzyme-2 (ACE2) receptor in various cardiac cell types (Zou et al., 2020) , and the evidence that the virus interacts with this receptor via the Spike (S) protein, as a main cellular docking/internalization site . Together, these results highlight an additional cardiac pathogenesis mechanism by SARS-CoV-2 independent of ACE2 expression, consisting of substantial upregulation of genes involved in response to viral infection, intercellular virus transmission and related to innate immunity signaling and fibrotic activation. abstract: Patients with severe respiratory syndrome caused by SARS-CoV-2 undergo cardiac complications due to hyper-inflammatory conditions. Although the presence of the virus has been detected in the myocardium of infected patients, and infection of cardiac cells may involve ACE2 receptor, the underlying molecular/cellular mechanisms are still uncharacterized. We analyzed expression of ACE2 receptor in primary human cardiac stromal cells using proteomic and transcriptomic methods before exposing them to SARS-CoV-2 in vitro. Using conventional and high sensitivity PCR methods, we measured virus production in the cellular supernatants and monitored the intracellular viral bioprocessing. We performed high-resolution imaging to show the sites of intracellular viral production. We finally used Q-RT-PCR assays to detect genes linked to innate immunity and fibrotic pathways coherently regulated in cells exposed to virus. Our findings indicate that human cardiac stromal cells have a susceptibility to SARS-CoV-2 infection and produce variable viral yields depending on the extent of cellular ACE2 receptor expression. Interestingly, these cells also evolved toward hyper-inflammatory/pro-fibrotic phenotypes independently of ACE2 levels, suggesting a dual cardiac damage mechanism that could account for the elevated numbers of cardiac complications in severe COVID-19 cases. url: http://medrxiv.org/cgi/content/short/2020.11.06.20226423v1?rss=1 doi: 10.1101/2020.11.06.20226423 id: cord-270951-6nq3jwgr author: Amerio, Paolo title: COVID‐19 and psoriasis: Should we fear for patients treated with biologics? date: 2020-05-05 words: 2258.0 sentences: 154.0 pages: flesch: 53.0 cache: ./cache/cord-270951-6nq3jwgr.txt txt: ./txt/cord-270951-6nq3jwgr.txt summary: One of question is if psoriasis patients treated with immunomodulating and immunosuppressive drugs have to discontinue their treatment in the midst of fears for the infection and its consequences. Previous coronaviruses outbreaks reports, current published evidences on pathogenesis and on clinical reports of COVID infection in immunosuppressed patients are used to make a scientifically based decision. 3 Recently some concern over the possibility that cytokine directed immunosuppressive treatment may be a risk factor for SARS-CoV-2 infection in psoriasis patients has been expressed. Given the potential role of proinflammatory cytokines in the pathogenesis of SARS and MERS severe disease, also ant inflammatory drugs have been suggested as novel treatments in these diseases. High levels of IL-2, IL-7, GM-CSF, MIP1-α, and TNF-α have also been correlated with disease severity in SARS-CoV-2 infected patients. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): the perspectives of clinical immunologists from China abstract: The new coronavirus pandemic poses question and challenges for dermatologists. One of question is if psoriasis patients treated with immunomodulating and immunosuppressive drugs have to discontinue their treatment in the midst of fears for the infection and its consequences. One of the challenges is how can we support our patients in this critical time. Previous coronaviruses outbreaks reports, current published evidences on pathogenesis and on clinical reports of COVID infection in immunosuppressed patients are used to make a scientifically based decision. url: https://www.ncbi.nlm.nih.gov/pubmed/32314483/ doi: 10.1111/dth.13434 id: cord-306365-7cydmgn2 author: Ami, Yasushi title: Co‐infection of respiratory bacterium with severe acute respiratory syndrome coronavirus induces an exacerbated pneumonia in mice date: 2008-04-01 words: 5090.0 sentences: 250.0 pages: flesch: 55.0 cache: ./cache/cord-306365-7cydmgn2.txt txt: ./txt/cord-306365-7cydmgn2.txt summary: Our results show that both low-virulent Pp infection, and administration of LPS derived from Escherichia coli, induced elastase in the lungs and enhanced the replication of SARS-CoV, resulting in exacerbation of the respiratory disease caused by SARS-CoV infection and a high mortality rate. Thus, mice co-infected with Pp + Fr-mo developed severe respiratory disease, suggesting the possibility that elastase produced by Pp infection exacerbated infection by SARS-CoV adapted to mice. An important condition for sustaining high titers beyond four days p.i. would be that of high replication in the lungs in an early phase of infection, which could be facilitated by elastase induced by Pp. These data suggest that severe respiratory disease caused by co-infection of Pp and mouse-adapted SARS-CoV is attributable to the high replication of virus in the lungs, for which the elastase produced by Pp infection is probably responsible. abstract: SARS‐CoV grows in a variety of tissues that express its receptor, although the mechanism for high replication in the lungs and severe respiratory illness is not well understood. We recently showed that elastase enhances SARS‐CoV infection in cultured cells, which suggests that SARS development may be due to elastase‐mediated, enhanced SARS‐CoV infection in the lungs. To explore this possibility, we examined whether co‐infection of mice with SARS‐CoV and Pp, a low‐pathogenic bacterium which elicits elastase production in the lungs, induces exacerbation of pneumonia. Mice co‐infected with SARS‐CoV and Pp developed severe respiratory disease with extensive weight loss, resulting in a 33∼90% mortality rate. Mice with exacerbated pneumonia showed enhanced virus infection in the lungs and histopathological lesions similar to those found in human SARS cases. Intranasal administration of LPS, another elastase inducer, showed an effect similar to that of Pp infection. Thus, this study shows that exacerbated pneumonia in mice results from co‐infection with SARS‐CoV and a respiratory bacterium that induces elastase production in the lungs, suggesting a possible role for elastase in the exacerbation of pneumonia. url: https://doi.org/10.1111/j.1348-0421.2008.00011.x doi: 10.1111/j.1348-0421.2008.00011.x id: cord-283956-zgrtux7i author: Amin, Sk. Abdul title: Fight against novel coronavirus: A perspective of medicinal chemists date: 2020-06-12 words: 5095.0 sentences: 356.0 pages: flesch: 52.0 cache: ./cache/cord-283956-zgrtux7i.txt txt: ./txt/cord-283956-zgrtux7i.txt summary: Like other RNA viruses, the functional significance of this Mpro or chymotrypsin-like protease (3CLpro) of SARS-CoV-2 emerges as an attractive drug target for the development of anti-viral agents. A group of scientists from the Cairo University, Egypt predicted COVID-19 spike binding site to a cell-surface receptor namely Glucose Regulated Protein 78 (GRP78) by employing structural bioinformatics in combination with protein-protein docking [55] . An early virtual screening (VS) study of FDA approved drugs (retrieved from Selleckchem Inc.) against the first resolved SARS-CoV-2 Mpro crystal structure (PDB: 6LU7) was performed. In another study, Elfiky [67] reported SARS-CoV-2 RdRp targeted molecular docking study of some anti-polymerase drugs which have been approved for use against various viruses. This study deals with the information currently available on potential targets for therapeutic invention and screening of new compounds or drug repurposing against SARS-CoV-2 (Figure 8 ). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 abstract: The ongoing novel coronavirus disease (COVID-19) pandemic makes us painfully perceive that our bullet shells are blank so far for fighting against severe human coronavirus (HCoV). In spite of vast research work, it is crystal clear that the evident does not warrant the commercial blossoming of anti-HCoV drugs. In this circumstance, drug repurposing and/or screening of databases are the only fastest option. This study is an initiative to recapitulate the medicinal chemistry of severe acute respiratory syndrome (SARS)-CoV-2 (SARS-CoV-2). The aim is to present an exquisite delineation of the current research from the perspective of a medicinal chemist to allow the rapid development of anti-SARS-CoV-2 agents. url: https://www.ncbi.nlm.nih.gov/pubmed/32563814/ doi: 10.1016/j.ejmech.2020.112559 id: cord-297323-l3f12hg4 author: Amor, Sandra title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 words: 4982.0 sentences: 304.0 pages: flesch: 43.0 cache: ./cache/cord-297323-l3f12hg4.txt txt: ./txt/cord-297323-l3f12hg4.txt summary: Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. These subsequently induce expression of type I IFNs (IFNα/β) and interferon stimulated genes (ISGs) [figure 2] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. Likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to SARS-CoV-2 infection, [ Table 4 ; (101) (102) (103) (104) (105) (106) (107) (108) (109) (110) (111) (112) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection abstract: Innate immune sensing of viral molecular patterns is essential for development of antiviral responses. Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. Together these strategies allow widespread infection and increased viral load. Despite the efforts of immune subversion, SARS‐CoV‐2 infection activates innate immune pathways inducing a robust type I/III interferon response, production of proinflammatory cytokines, and recruitment of neutrophils and myeloid cells. This may induce hyperinflammation or alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. The dysregulation of the renin‐angiotensin system due to downregulation of angiotensin converting enzyme 2, the receptor for SARS‐CoV‐2, together with the activation of type I/III interferon response, and inflammasome response converge to promote free radical production and oxidative stress. This exacerbates tissue damage in the respiratory system but also leads to widespread activation of coagulation pathways leading to thrombosis. Here, we review the current knowledge of the role of the innate immune response following SARS‐CoV‐2 infection, much of which is based on the knowledge from SARS‐CoV and other coronaviruses. Understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in COVID‐19 may help explain factors that contribute to the variety of clinical manifestations and outcome of SARS‐CoV‐2 infection. url: https://doi.org/10.1111/cei.13523 doi: 10.1111/cei.13523 id: cord-314663-8cf0jci9 author: Ampuero, M. title: SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results. date: 2020-07-03 words: 882.0 sentences: 68.0 pages: flesch: 56.0 cache: ./cache/cord-314663-8cf0jci9.txt txt: ./txt/cord-314663-8cf0jci9.txt summary: This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. The goal of this study was to detect SARS-CoV-2 in sewage samples in Santiago, Chile. abstract: The detection of viruses in sewage is a method of environmental surveillance, which allows evaluating the circulation of different viruses in a community. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. Using ultracentrifugation associated with RT-qPCR, we detected SARS-CoV-2 in untreated and treated wastewater samples obtained two treatment plants, which together process around 85% of the wastewater from the city. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. url: https://doi.org/10.1101/2020.07.02.20145177 doi: 10.1101/2020.07.02.20145177 id: cord-289574-engwi8h3 author: An, Peng-jiao title: Biochemical indicators of coronavirus disease 2019 exacerbation and the clinical implications date: 2020-05-23 words: 3188.0 sentences: 220.0 pages: flesch: 39.0 cache: ./cache/cord-289574-engwi8h3.txt txt: ./txt/cord-289574-engwi8h3.txt summary: Accumulating evidence suggested that the progression of COVID-19 is associated with lymphopenia and excessive inflammation, and a subset of severe cases might exhibit cytokine storm triggered by secondary hemophagocytic lymphohistiocytosis (sHLH). Previously, it has been found that the serum levels of pro-inflammatory cytokines [IFN-γ, IL-1, IL-6, IL-12, and transforming growth factor-β (TGF-β)], and chemokines (CCL2, CXCL9, CXCL10, and IL-8) in SARS-CoV infected patients were higher than those in healthy individuals. Procalcitonin (PCT), released by bacterial infectious tissues under the irritation of pro-inflammatory cytokines, is a more specific marker of serious bacterial infection compared to C-reactive protein (CRP) and IL-6 [111] PCT-based strategy has been applied to guide antibiotic use in ICU or emergency wards, since the serum PCT levels in patients with severe bacterial infections are much higher than those with simple viral infections or non-specific inflammatory diseases [111] [112] [113] . The definition and risks of Cytokine Release Syndrome-Like in 11 COVID-19-Infected Pneumonia critically ill patients: Disease Characteristics and Retrospective Analysis abstract: Coronavirus Disease 2019 (COVID-19) has sparked a global pandemic, affecting more than 4 million people worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause acute lung injury (ALI) and even acute respiratory distress syndrome (ARDS); with a fatality of 7.0 %. Accumulating evidence suggested that the progression of COVID-19 is associated with lymphopenia and excessive inflammation, and a subset of severe cases might exhibit cytokine storm triggered by secondary hemophagocytic lymphohistiocytosis (sHLH). Furthermore, secondary bacterial infection may contribute to the exacerbation of COVID-19. We recommend using both IL-10 and IL-6 as the indicators of cytokine storm, and monitoring the elevation of procalcitonin (PCT) as an alert for initiating antibacterial agents. Understanding the dynamic progression of SARS-CoV-2 infection is crucial to determine an effective treatment strategy to reduce the rising mortality of this global pandemic. url: https://api.elsevier.com/content/article/pii/S1043661820312548 doi: 10.1016/j.phrs.2020.104946 id: cord-321231-zlpa3x2x author: Anand, Pratima title: Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India date: 2020-09-10 words: 6895.0 sentences: 348.0 pages: flesch: 53.0 cache: ./cache/cord-321231-zlpa3x2x.txt txt: ./txt/cord-321231-zlpa3x2x.txt summary: title: Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India The study was conducted to describe the clinical profile of neonates born to mothers who tested positive for COVID 19 infection and to determine the association of neonatal COVID 19 status and viral load with maternal clinical status and viral load. • In this study on a limited number of neonates, maternal viral load of COVID 19 (E and RdRp cycle thresholds) was not associated with severity of illness or COVID 19 positivity in neonates. Neonates born to COVID 19 positive mothers and requiring NICU care for any reason (comorbidity like prematurity, low birth weight, or transient tachypnoea of neonate) were nursed in separate designated NICU in COVID block. abstract: Despite rapidly evolving knowledge about COVID 19 infection, routes of perinatal COVID 19 transmission and viral load in mother neonate dyad remain uncertain. Data were analysed to describe the clinicodemographic profile and viral load in neonates born to COVID 19 positive mothers. Of 2947 deliveries, 69 mothers were COVID 19 positive (2.3%), with 1 abortion, 2 macerated stillbirths and 2 fresh stillbirths as pregnancy outcomes. Of 65 tested neonates, 10.7% (7) were confirmed COVID 19 positive by RTPCR (reverse transcriptase-polymerase chain reaction). Viral load (cycle threshold, Ct of E, RDRp) in neonates was comparable with the Ct reported from adults; however, neonates had milder clinical manifestations. All 7 neonates who tested positive for COVID 19 were subsequently discharged. Six of the 7 neonates were asymptomatic and 1 neonate needed respiratory support (indication being prematurity) which resolved after 48 h. Maternal and neonatal comparison of Ct of E and RdRp gene was statistically non-significant (25.97 vs 19.68, p = 0.34 and 26.5 vs 25.0, p = 0.84). Viral loads of mothers with COVID 19 positive neonates compared with mothers with COVID 19 negative neonates for E and RdRp gene were also statistically non-significant (25 vs 27.19, p = 0.63 and 19.6 vs 27.6, p = 0.08). The majority (93%) of neonates tested later than 48 h (roomed in with mother and breastfed) tested negative. Conclusion: The study supports milder manifestation in COVID 19 positive neonates. Risk of transmission from COVID 19 positive mother to neonate by rooming-in and breastfeeding is low. In this study on a limited number of neonates, maternal viral load was not found to be associated with the positivity status or severity of the illness of neonate. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00431-020-03800-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00431-020-03800-7 doi: 10.1007/s00431-020-03800-7 id: cord-277137-k3jj5vom author: Anand, Praveen title: SARS-CoV-2 strategically mimics proteolytic activation of human ENaC date: 2020-05-26 words: 2707.0 sentences: 144.0 pages: flesch: 53.0 cache: ./cache/cord-277137-k3jj5vom.txt txt: ./txt/cord-277137-k3jj5vom.txt summary: We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site, absent in any previous coronavirus sequenced, resulting in the striking mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). Although the furin-like cleavage motifs can be found in other viruses (Coutard et al., 2020) , the exact mimicry of human ENaC-a cleavage site raises the specter that SARS-CoV-2 may be hijacking the protease network of ENaC-a for viral activation. The overlap of the cell-types expressing ACE2 and ENaC-a, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. SARS-CoV-2 then exploits enzymes called proteases to cut, or cleave, its spikes at a specific site which allows the virus to infiltrate the host cell. show that the spike proteins on SARS-CoV-2 may have the same sequence of amino acids at its cut site as a human epithelial channel protein called ENaC-a. abstract: Molecular mimicry is an evolutionary strategy adopted by viruses to exploit the host cellular machinery. We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site, absent in any previous coronavirus sequenced, resulting in the striking mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). Genetic alteration of ENaC-α causes aldosterone dysregulation in patients, highlighting that the FURIN site is critical for activation of ENaC. Single cell RNA-seq from 66 studies shows significant overlap between expression of ENaC-α and the viral receptor ACE2 in cell types linked to the cardiovascular-renal-pulmonary pathophysiology of COVID-19. Triangulating this cellular characterization with cleavage signatures of 178 proteases highlights proteolytic degeneracy wired into the SARS-CoV-2 lifecycle. Evolution of SARS-CoV-2 into a global pandemic may be driven in part by its targeted mimicry of ENaC-α, a protein critical for the homeostasis of airway surface liquid, whose misregulation is associated with respiratory conditions. url: https://doi.org/10.7554/elife.58603 doi: 10.7554/elife.58603 id: cord-348635-1pb2ag9j author: Anand, Praveen title: SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date: 2020-04-30 words: 1658.0 sentences: 94.0 pages: flesch: 51.0 cache: ./cache/cord-348635-1pb2ag9j.txt txt: ./txt/cord-348635-1pb2ag9j.txt summary: We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). We extrapolate that the evolution of SARS-CoV-2 into a global coronavirus pandemic may be in part due to its targeted mimicry of human ENaC and hijack of the associated host proteolytic network. The overlap of the cell-types expressing ACE2 and ENaC-ɑ, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. In order to extrapolate the tissue tropism of SARS-CoV-2 from the lens of the host proteolytic network, we assessed the co-expression of these proteases concomitant with the viral receptor ACE2 and ENaC-ɑ (Figure 2) . abstract: Molecular mimicry of host proteins is an evolutionary strategy adopted by viruses to evade immune surveillance and exploit host cell systems. We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). Genetic truncation at this ENaC-α cleavage site causes aldosterone dysregulation in patients, highlighting the functional importance of the mimicked SARS-CoV-2 peptide. Single cell RNA-seq from 65 studies shows significant overlap between the expression of ENaC-α and ACE2, the putative receptor for the virus, in cell types linked to the cardiovascular-renal-pulmonary pathophysiology of COVID-19. Triangulating this cellular fingerprint with amino acid cleavage signatures of 178 human proteases shows the potential for tissue-specific proteolytic degeneracy wired into the SARS-CoV-2 lifecycle. We extrapolate that the evolution of SARS-CoV-2 into a global coronavirus pandemic may be in part due to its targeted mimicry of human ENaC and hijack of the associated host proteolytic network. url: https://doi.org/10.1101/2020.04.29.069476 doi: 10.1101/2020.04.29.069476 id: cord-272010-kc0gi3cj author: Anand, Sai Priya title: Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins date: 2020-09-29 words: 3661.0 sentences: 216.0 pages: flesch: 56.0 cache: ./cache/cord-272010-kc0gi3cj.txt txt: ./txt/cord-272010-kc0gi3cj.txt summary: The viral entry of SARS-CoV-2 depends on an interaction between the receptor-binding domain of its trimeric spike glycoprotein and the human angiotensin-converting enzyme 2 (ACE2) receptor. One potential therapeutic target receiving significant attention is the interaction between the SARS-CoV-2 spike (S) glycoprotein and its receptor, human angiotensin-converting enzyme 2 (ACE2). To better understand the interactions between membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins with their receptor, human ACE2, we sought to determine the cooperativity of ACE2 within the respective trimers. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 abstract: Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The viral entry of SARS-CoV-2 depends on an interaction between the receptor-binding domain of its trimeric spike glycoprotein and the human angiotensin-converting enzyme 2 (ACE2) receptor. A better understanding of the spike/ACE2 interaction is still required to design anti-SARS-CoV-2 therapeutics. Here, we investigated the degree of cooperativity of ACE2 within both the SARS-CoV-2 and the closely related SARS-CoV-1 membrane-bound S glycoproteins. We show that there exist differential inter-protomer conformational transitions between both spike trimers. Interestingly, the SARS-CoV-2 spike exhibits a positive cooperativity for monomeric soluble ACE2 binding when compared to the SARS-CoV-1 spike, which might have more structural restraints. Our findings can be of importance in the development of therapeutics that block the spike/ACE2 interaction. url: https://doi.org/10.3390/v12101104 doi: 10.3390/v12101104 id: cord-328865-ekgqdjlk author: Anand, Shuchi title: Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study date: 2020-09-25 words: 5647.0 sentences: 279.0 pages: flesch: 45.0 cache: ./cache/cord-328865-ekgqdjlk.txt txt: ./txt/cord-328865-ekgqdjlk.txt summary: METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). 12 Testing remainder plasma from monthly samples obtained for routine care of patients on dialysis for SARS-CoV-2 antibodies therefore represents a practical approach to a population-representative surveillance strat egy, 13 informing risks faced by a susceptible population while ensuring representation from racial and ethnic minorities. In our analysis of seroprevalence of SARS-CoV-2 spike protein receptor binding antibodies from a nationwide representative sample of patients receiving dialysis, we find that despite the USA contemporaneously leading the world in the numbers of diagnosed cases, overall, fewer than 10% of US adults had evidence of seroconversion in July, 2020. abstract: BACKGROUND: Many patients receiving dialysis in the USA share the socioeconomic characteristics of underserved communities, and undergo routine monthly laboratory testing, facilitating a practical, unbiased, and repeatable assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence. METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). We extracted data on age, sex, race and ethnicity, and residence and facility ZIP codes from the anonymised electronic health records, linking patient-level residence data with cumulative and daily cases and deaths per 100 000 population and with nasal swab test positivity rates. We standardised prevalence estimates according to the overall US dialysis and adult population, and present estimates for four prespecified strata (age, sex, region, and race and ethnicity). FINDINGS: The sampled population had similar age, sex, and race and ethnicity distribution to the US dialysis population, with a higher proportion of older people, men, and people living in majority Black and Hispanic neighbourhoods than in the US adult population. Seroprevalence of SARS-CoV-2 was 8·0% (95% CI 7·7–8·4) in the sample, 8·3% (8·0–8·6) when standardised to the US dialysis population, and 9·3% (8·8–9·9) when standardised to the US adult population. When standardised to the US dialysis population, seroprevalence ranged from 3·5% (3·1–3·9) in the west to 27·2% (25·9–28·5) in the northeast. Comparing seroprevalent and case counts per 100 000 population, we found that 9·2% (8·7–9·8) of seropositive patients were diagnosed. When compared with other measures of SARS-CoV-2 spread, seroprevalence correlated best with deaths per 100 000 population (Spearman's ρ=0·77). Residents of non-Hispanic Black and Hispanic neighbourhoods experienced higher odds of seropositivity (odds ratio 3·9 [95% CI 3·4–4·6] and 2·3 [1·9–2·6], respectively) compared with residents of predominantly non-Hispanic white neighbourhoods. Residents of neighbourhoods in the highest population density quintile experienced increased odds of seropositivity (10·3 [8·7–12·2]) compared with residents of the lowest density quintile. County mobility restrictions that reduced workplace visits by at least 5% in early March, 2020, were associated with lower odds of seropositivity in July, 2020 (0·4 [0·3–0·5]) when compared with a reduction of less than 5%. INTERPRETATION: During the first wave of the COVID-19 pandemic, fewer than 10% of the US adult population formed antibodies against SARS-CoV-2, and fewer than 10% of those with antibodies were diagnosed. Public health efforts to limit SARS-CoV-2 spread need to especially target racial and ethnic minority and densely populated communities. FUNDING: Ascend Clinical Laboratories. url: https://api.elsevier.com/content/article/pii/S0140673620320092 doi: 10.1016/s0140-6736(20)32009-2 id: cord-267610-bzbr9ios author: Anastassopoulou, Cleo title: SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall date: 2020-09-03 words: 2472.0 sentences: 107.0 pages: flesch: 43.0 cache: ./cache/cord-267610-bzbr9ios.txt txt: ./txt/cord-267610-bzbr9ios.txt summary: In agreement with this reasoning, data suggest that SARS-CoV-2 infections in children involve the upper rather than the lower respiratory tract, the typical site of severe COVID-19 disease where ACE2 receptors are more abundant [29] . In this respect, a large prospective NIH-funded study of 6000 people from 2000 US families in 11 cities, called human epidemiology and response to SARS-CoV-2, will help determine the incidence of novel coronavirus infection in children in the USA and whether rates differ between children who have asthma or other allergic conditions and children who do not [45] . School children are nonetheless anticipated to contribute to the community transmission of SARS-CoV-2 through their large numbers of daily social contacts, some of which are intergenerational, with older age groups where the risk for more severe illness is increased. abstract: nan url: https://doi.org/10.2217/fmb-2020-0195 doi: 10.2217/fmb-2020-0195 id: cord-302163-0jav84zw author: Anastassopoulou, Cleo title: Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity date: 2020-10-22 words: 4823.0 sentences: 212.0 pages: flesch: 41.0 cache: ./cache/cord-302163-0jav84zw.txt txt: ./txt/cord-302163-0jav84zw.txt summary: We searched PubMed/MEDLINE for all Englishlanguage original articles or reviews reporting on potential associations between human genetic factors and susceptibility to SARS-CoV-2 infection or COVID-19 severity, up to August 12, 2020 (with updating as of September 11, 2020, during the revision of the manuscript). The search was performed using all combinations of terms related to the novel coronavirus and the disease (e.g., "SARS-CoV-2," "2019-nCoV," and "COVID-19") on the one hand, and terms concerning susceptibility to infection or disease severity (e.g., "polymorphisms," "allelic variation," "genetic predisposition," "genotype," "clinical outcome") as well as the names of individual genes in which relevant polymorphisms were found (e.g., "TLR7," "ACE2"), on the other. A recently published comparative genetic analysis of approximately 81,000 human genomes across different populations suggested possible associations of coding region variants of ACE2 and TMPRSS2 with COVID-19 susceptibility, severity, and clinical outcomes [49] . abstract: ABSTRACT: BACKGROUND: The emergence of the novel coronavirus in Wuhan, Hubei Province, China, in December 2019 marked the synchronization of the world to a peculiar clock that is counting infected cases and deaths instead of hours and minutes. The pandemic, highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has indeed caused considerable morbidity and mortality and drastically changed our everyday lives. As we continue to become acquainted with the seventh coronavirus known to infect our species, a number of its characteristics keep surprising us. Among those is the wide spectrum of clinical manifestations of the resulting coronavirus disease 2019 (COVID-19), which ranges from asymptomatic or mildly symptomatic infections to severe pneumonia, respiratory failure, and death. MAIN BODY: Data, now from patient populations, are beginning to accumulate on human genetic factors that may contribute to the observed diversified disease severity. Therefore, we deemed it prudent to review the associations between specific human genetic variants and clinical disease severity or susceptibility to infection that have been reported in the literature to date (at the time of writing this article in early August 2020 with updates in mid-September). With this work, we hope (i) to assist the fast-paced biomedical research efforts to combat the virus by critically summarizing current knowledge on the potential role of host genetics, and (ii) to help guide current genetics and genomics research towards candidate gene variants that warrant further investigation in larger studies. We found that determinants of differing severity of COVID-19 predominantly include components of the immune response to the virus, while determinants of differing susceptibility to SARS-CoV-2 mostly entail genes related to the initial stages of infection (i.e., binding of the cell surface receptor and entry). CONCLUSION: Elucidating the genetic determinants of COVID-19 severity and susceptibility to SARS-CoV-2 infection would allow for the stratification of individuals according to risk so that those at high risk would be prioritized for immunization, for example, if or when safe and effective vaccines are developed. Our enhanced understanding of the underlying biological mechanisms could also guide personalized therapeutics. Such knowledge is already beginning to provide clues that help explain, at least in part, current epidemiologic observations regarding the typically more severe or benign disease course in older males and children, respectively. url: https://doi.org/10.1186/s40246-020-00290-4 doi: 10.1186/s40246-020-00290-4 id: cord-259084-lwh3rww4 author: Anderson, Cole title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date: 2020-05-22 words: 1002.0 sentences: 66.0 pages: flesch: 52.0 cache: ./cache/cord-259084-lwh3rww4.txt txt: ./txt/cord-259084-lwh3rww4.txt summary: title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations. This protocol allows for 35 the rapid detection of SARS-CoV-2 RNA from clinical specimens such as, nasopharyngeal and 36 oropharyngeal swabs, sputum, bronchoalveolar lavage, and tracheal aspirates. 43 In this study, we examined the feasibility of pooling nasopharyngeal swab specimens submitted 44 for COVID-19 testing using the CDC 2019-nCoV RT-PCR diagnostic panel without compromising 45 Specimens were submitted to 54 the Virology laboratory at Landstuhl Regional Medical Center for routine SARS-CoV-2 testing 55 using the CDC 2019-nCoV RT-PCR assay. Pooling nasopharyngeal/throat swab specimens to increase testing 176 capacity for influenza viruses by PCR abstract: The recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations. url: https://doi.org/10.1101/2020.05.22.110932 doi: 10.1101/2020.05.22.110932 id: cord-279584-9x1d1kp1 author: Anderson, E. M. title: Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection date: 2020-11-10 words: 2949.0 sentences: 206.0 pages: flesch: 54.0 cache: ./cache/cord-279584-9x1d1kp1.txt txt: ./txt/cord-279584-9x1d1kp1.txt summary: Finally, we completed a series of studies using 36 serum collected from COVID-19 patients to determine if antibodies reactive to hCoVs are 37 boosted upon SARS-CoV-2 infections. We completed ELISAs to quantify levels of pre-pandemic SARS-CoV-2-reactive IgG 42 antibodies in 204 human serum samples collected in 2017. We completed ELISAs to quantify levels of pre-pandemic hCoV-reactive IgG antibodies 69 in all 204 human serum samples collected in 2017. We 74 completed full antibody titrations to directly compared levels of hCoV antibodies in a subset of 75 pre-pandemic samples from individuals who either did (n=12) or did not (n=51) possess cross-76 reactive SARS-CoV-2 antibodies (Figure 1f-h) . Our study demonstrates that ~23% of individuals possessed SARS-CoV-2 cross-reactive 137 serum antibodies prior to the COVID-19 pandemic. We compared antibody titers in 296 pre-pandemic serum samples from individuals who did and did not have a subsequent PCR-297 confirmed SARS-CoV-2 infection. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread within the human population. Although SARS-CoV-2 is a novel coronavirus, most humans had been previously exposed to other antigenically distinct common seasonal human coronaviruses (hCoVs) before the COVID-19 pandemic. Here, we quantified levels of SARS-CoV-2-reactive antibodies and hCoV-reactive antibodies in serum samples collected from 204 humans before the COVID-19 pandemic. We then quantified pre-pandemic antibody levels in serum from a separate cohort of 252 individuals who became PCR-confirmed infected with SARS-CoV-2. Finally, we longitudinally measured hCoV and SARS-CoV-2 antibodies in the serum of hospitalized COVID-19 patients. Our studies indicate that most individuals possessed hCoV-reactive antibodies before the COVID-19 pandemic. We determined that ~23% of these individuals possessed non-neutralizing antibodies that cross-reacted with SARS-CoV-2 spike and nucleocapsid proteins. These antibodies were not associated with protection against SARS-CoV-2 infections or hospitalizations, but paradoxically these hCoV cross-reactive antibodies were boosted upon SARS-CoV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.11.06.20227215v1?rss=1 doi: 10.1101/2020.11.06.20227215 id: cord-346544-kk7qyn4w author: Andersson, M. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 words: 4992.0 sentences: 305.0 pages: flesch: 53.0 cache: ./cache/cord-346544-kk7qyn4w.txt txt: ./txt/cord-346544-kk7qyn4w.txt summary: Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. . https://doi.org/10.1101/2020.05.21.20105486 doi: medRxiv preprint prevalence of vRNA detection in blood, serum or plasma, noting whether this attribute was correlated with clinical or laboratory phenotypes of disease, and recording Ct values when these were reported. We collected 212 serum samples through the microbiology department at Oxford University Hospitals NHS Foundation Trust, OUH NHSFT, comprising adults with a diagnosis of COVID-19, confirmed by SARS-CoV-2 detection by a clinical diagnostic microbiology laboratory using RT-PCR on a respiratory swab, classified in three groups as follows: Based on a systematic review of the literature, together with our own data, we estimate that SARS-CoV-2 RNA may be present at low copy numbers in ~10% of blood samples obtained from individuals with COVID-19 prior to day 28, most of which arise at earlier timepoints and in the setting of more severe disease. abstract: Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=212 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across clinical and convalescent samples collected [≥]28 days post symptom onset, 0/244 (0%, 95%CI 0.0-1.5%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19. url: http://medrxiv.org/cgi/content/short/2020.05.21.20105486v1?rss=1 doi: 10.1101/2020.05.21.20105486 id: cord-333713-nz36i2oa author: Andonegui-Elguera, Sergio title: Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism date: 2020-06-18 words: 1729.0 sentences: 88.0 pages: flesch: 37.0 cache: ./cache/cord-333713-nz36i2oa.txt txt: ./txt/cord-333713-nz36i2oa.txt summary: Results Alterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, NK cells, T CD4+ cell and macrophages. Conclusions In summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. Therefore, in the present work we carried out comprehensive and stringent transcriptomic metanalysis of SARS-CoV-2 infected bronchoalveolar cells and peripheral blood mononuclear cells to unveil the molecular alterations caused by viral infection as well as deconvolution analysis to identify the immune cell profiles in COVID-19 patients. Using molecular deconvolution analysis, we identified the presence of neutrophils, NK cells, T CD4+ lymphocytes and macrophages infiltrating the lungs of COVID-19 patients, consistently our findings with the previously reported (14) . abstract: Abstract Background The SARS-CoV-2 is the etiological agent causing COVID-19 which has infected more than 2 million people with more than 200000 deaths since its emergence in December 2019. In the majority of cases patients are either asymptomatic or show mild to moderate symptoms and signs of a common cold. A subset of patients, however, develop a severe atypical pneumonia, with the characteristic ground-glass appearance on chest x-ray and computerized tomography, which evolves into an acute respiratory distress syndrome, that requires mechanical ventilation and eventually results in multiple organ failure and death. The Molecular pathogenesis of COVID-19 is still unknown. Aim of the study In the present work we performed a stringent metanalysis from the publicly available RNAseq data from bronchoalveolar cells and peripheral blood mononuclear cells to elucidate molecular alterations and cellular deconvolution to identify immune cell profiles. Results Alterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, NK cells, T CD4+ cell and macrophages. The blood mononuclear cells presented a proliferative state. Dramatic reduction of neutrophils, NK and T lymphocytes, whereas an exacerbated increase in monocytes. Conclusions In summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. And the potential immune response profile in COVID-19. url: https://api.elsevier.com/content/article/pii/S0188440920307050 doi: 10.1016/j.arcmed.2020.06.011 id: cord-321027-64y43o0y author: Andreano, Emanuele title: Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date: 2020-05-09 words: 2287.0 sentences: 114.0 pages: flesch: 51.0 cache: ./cache/cord-321027-64y43o0y.txt txt: ./txt/cord-321027-64y43o0y.txt summary: The SARS-CoV-2 spike glycoprotein (S-protein) has a pivotal role in viral pathogenesis and it is 63 considered the main target to elicit potent neutralizing antibodies and the focus for the development 64 of therapeutic and prophylactic tools against this virus (3, 4) . Results shown in Table 1 and Figure 1 show that, among the seven donors 97 included in this study, six were able to produce high titers of SARS-CoV-2 S-protein specific 98 antibodies and in particular donors R-042, R-122 and R-188 showed the highest virus neutralizing 99 titers. In the case of SARS-CoV-2, where so far we do not have any effective therapeutic nor prophylactic 154 interventions, mAbs have the possibility to become one of the first drugs that can be used for 155 immediate therapy of any patient testing positive for the virus, and even to provide immediate 156 protection from infection in high risk populations. abstract: In the absence of approved drugs or vaccines, there is a pressing need to develop tools for therapy and prevention of Covid-19. Human monoclonal antibodies have very good probability of being safe and effective tools for therapy and prevention of SARS-CoV-2 infection and disease. Here we describe the screening of PBMCs from seven people who survived Covid-19 infection to isolate human monoclonal antibodies against SARS-CoV-2. Over 1,100 memory B cells were single-cell sorted using the stabilized prefusion form of the spike protein and incubated for two weeks to allow natural production of antibodies. Supernatants from each cell were tested by ELISA for spike protein binding, and positive antibodies were further tested for neutralization of spike binding to receptor(s) on Vero E6 cells and for virus neutralization in vitro. From the 1,167 memory B specific for SARS-CoV-2, we recovered 318 B lymphocytes expressing human monoclonals recognizing the spike protein and 74 of these were able to inhibit the binding of the spike protein to the receptor. Finally, 17 mAbs were able to neutralize the virus when assessed for neutralization in vitro. Lead candidates to progress into the drug development pipeline will be selected from the panel of neutralizing antibodies identified with the procedure described in this study. One Sentence Summary Neutralizing human monoclonal antibodies isolated from Covid-19 convalescent patients for therapeutic and prophylactic interventions. url: https://doi.org/10.1101/2020.05.05.078154 doi: 10.1101/2020.05.05.078154 id: cord-321369-xzu2faol author: Andreano, Emanuele title: Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date: 2020-10-07 words: 3685.0 sentences: 192.0 pages: flesch: 52.0 cache: ./cache/cord-321369-xzu2faol.txt txt: ./txt/cord-321369-xzu2faol.txt summary: By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. As for the authentic virus neutralization assay, supernatants containing naturally produced IgG or IgA were tested for their ability to protect the layer of Vero E6 cells from the cytopathic effect triggered by SARS-CoV-2 infection (Fig. S2) . This work describes a systematic screening of memory B cells from convalescent people to identify extremely potent human monoclonal antibodies against the spike protein of the SARS-CoV-2 virus, to be used for prevention and therapy of Covid-19. abstract: Human monoclonal antibodies are safe, preventive and therapeutic tools, that can be rapidly developed to help restore the massive health and economic disruption caused by the Covid-19 pandemic. By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. Up to 65,9% of monoclonals neutralized the wild type virus at a concentration of >500 ng/mL, 23,6% neutralized the virus in the range of 100 - 500 ng/mL and 9,1% had a neutralization potency in the range of 10 - 100 ng/mL. Only 1,4% neutralized the authentic virus with a potency of 1-10 ng/mL. We found that the most potent neutralizing antibodies are extremely rare and recognize the RBD, followed in potency by antibodies that recognize the S1 domain, the S-protein trimeric structure and the S2 subunit. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. One Sentence Summary Extremely potent neutralizing human monoclonal antibodies isolated from Covid-19 convalescent patients for prophylactic and therapeutic interventions. url: https://doi.org/10.1101/2020.10.07.328302 doi: 10.1101/2020.10.07.328302 id: cord-335156-l4jie8g6 author: Andreozzi, Fabio title: Eosinopenia and COVID-19 patients: So specific ? date: 2020-06-27 words: 308.0 sentences: 31.0 pages: flesch: 66.0 cache: ./cache/cord-335156-l4jie8g6.txt txt: ./txt/cord-335156-l4jie8g6.txt summary: key: cord-335156-l4jie8g6 title: Eosinopenia and COVID-19 patients: So specific ? cord_uid: l4jie8g6 For the prediction of positive SARS-CoV-2 cases (diagnosis based on RT-PCR), eosinopenia has a sensitivity of 74.7% and specificity of 68.7% with the area under the curve AUC of 0.717. Up until end of March 20, Seasonal Influenza and COVID-19 were simultaneously present in Europe. We reviewed the laboratory results of two cohorts of SARS-CoV-2 (N = 50) and Influenza A (N = 41) patients (diagnosis confirmed by RT PCR). As such from the above, we can reach to the conclusion that complete eosinopenia is a common finding in both COVID-19 and Seasonal Influenza infections. Thus result could imply that eosinopenia could be considered as a potential biological indicator of either Influenza or SARS-COV-2 infections. Eosinopenia and elevated C-reactive protein facilitate triage of COVID-19 patients in fever clinic: a retrospective casecontrol study Co-infection with SARS-CoV-2 and influenza a virus in patient with pneumonia abstract: nan url: https://api.elsevier.com/content/article/pii/S2589537020301838 doi: 10.1016/j.eclinm.2020.100439 id: cord-261662-d0tg9i90 author: Andres, Cristina title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date: 2020-06-08 words: 4673.0 sentences: 214.0 pages: flesch: 52.0 cache: ./cache/cord-261662-d0tg9i90.txt txt: ./txt/cord-261662-d0tg9i90.txt summary: title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. Because of the importance of the S protein, we carried out a deep-sequencing study of the S gene in upper respiratory tract samples from 18 patients with mild or severe SARS-CoV-2 disease. The fact that the truncated S protein was present in only a low percentage of the entire viral quasispecies suggests that natural selection may have designed a favorable equilibrium in which a limited number of deleted virions are generated to balance virus production with infection of new cells during disease progression. abstract: The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We propose that natural selection has favored a “Don’t burn down the house” strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability. url: https://doi.org/10.1101/2020.06.03.129585 doi: 10.1101/2020.06.03.129585 id: cord-259808-82drb14x author: Andrews, Paul L R title: COVID‐19, nausea, and vomiting date: 2020-10-05 words: 7911.0 sentences: 404.0 pages: flesch: 46.0 cache: ./cache/cord-259808-82drb14x.txt txt: ./txt/cord-259808-82drb14x.txt summary: Considering the likely effects of SARS-CoV-2 on the digestive tract (discussed further), a relationship between symptoms such as nausea/vomiting and diarrhea would not be unexpected but identifying the time of onset of each postinfection is essential to assessing their relative relevance for diagnosis. There are no formal studies at present so we have reviewed the effects of SARS-CoV-2 (and other coronaviruses) on the digestive tract in the light of knowledge of the established mechanisms of nausea and vomiting; this is the same approach that has been used to understand the pathogenesis of other symptoms (e.g. diarrhoea 10 ). We hypothesize that SARS-CoV-2 would induce acute (first few days postinfection) nausea and vomiting by causing the release of key hormones from the enteroendocrine cells (EECs) in the mucosa of the upper GI tract or after gaining direct entry into the blood, by acting directly within the brainstem. abstract: Exclusion of nausea (N) and vomiting (V) from detailed consideration as symptoms of COVID‐19 is surprising as N can be an early presenting symptom. We examined the incidence of NV during infection before defining potential mechanisms. We estimate that the overall incidence of nausea (median 10.5%), although variable, is comparable with diarrhea. Poor definition of N, confusion with appetite loss, and reporting of N and/or V as a single entity may contribute to reporting variability and likely underestimation. We propose that emetic mechanisms are activated by mediators released from the intestinal epithelium by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) modulate vagal afferents projecting to the brainstem and after entry into the blood, activate the area postrema (AP) also implicated in anorexia. The receptor for spike protein of SARS‐CoV‐2, angiotensin 2 converting enzyme (ACE2), and transmembrane protease serine (for viral entry) is expressed in upper gastrointestinal (GI) enterocytes, ACE2 is expressed on enteroendocrine cells (EECs), and SARS‐CoV‐2 infects enterocytes but not EECs (studies needed with native EECs). The resultant virus‐induced release of epithelial mediators due to exocytosis, inflammation, and apoptosis provides the peripheral and central emetic drives. Additionally, data from SARS‐CoV‐2 show an increase in plasma angiotensin II (consequent on SARS‐CoV‐2/ACE2 interaction), a centrally (AP) acting emetic, providing a further potential mechanism in COVID‐19. Viral invasion of the dorsal brainstem is also a possibility but more likely in delayed onset symptoms. Overall, greater attention must be given to nausea as an early symptom of COVID‐19 and for the insights provided into the GI effects of SARS‐CoV‐2. url: https://www.ncbi.nlm.nih.gov/pubmed/32955126/ doi: 10.1111/jgh.15261 id: cord-202687-z17knvts author: Angelina, Emilio title: Drug Repurposing to find Inhibitors of SARS-CoV-2 Main Protease date: 2020-06-26 words: 4110.0 sentences: 214.0 pages: flesch: 53.0 cache: ./cache/cord-202687-z17knvts.txt txt: ./txt/cord-202687-z17knvts.txt summary: [11] In another study, Jin and colleagues identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of SARS-CoV-2 M pro in complex with this compound. Moreover, another recent crystallographic fragment screening against SARS-CoV-2 M pro that has been deposited in the Protein Data Bank (DOI: 10.2210/pdb5rgj/pdb ) also might help to find structural determinants for ligand anchoring within the enzyme binding cleft. Up to date, more than 100 structures of SARS-CoV-2 M pro with ligands bound at the enzyme binding cleft, have been released. While different fragments bind to different regions of SARS-CoV-2 M pro binding cleft, there are two interaction sites at the enzyme S1 sub-pocket that are targeted by most fragments. In this work we have performed a virtual screening of FDA approved drugs for repurposing as potential inhibitors of SARS-CoV-2 main protease M pro . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. Currently there is no known vaccine or specific antiviral treatment for COVID-19 and so, there is an urgent need for expedite discovery of new therapeutics to combat the disease until a vaccine will be available worldwide. Drug repurposing is a strategy for identifying new uses for approved drugs that has the advantage (over conventional approaches that attempt to develop a drug from scratch) that time frame of the overall process can be significantly reduced because of the few number of clinical trial required. In this work, a virtual screening of FDA-approved drugs was performed for repositioning as potential inhibitors of the main protease Mpro of SARS-CoV-2. As a result of this study, 12 drugs are proposed as candidates for inhibitors of the Mpro enzyme. Some of the selected compounds are antiviral drugs that are already being tested in COVID-19 clinical trials (i.e. ribavirin) or are used to alleviate symptoms of the disease (i.e. codeine). Surprisingly, the most promising candidate is the naturally occurring broad spectrum antibiotic oxytetracycline. This compound has largely outperformed the remaining selected candidates along all filtering steps of our virtual screening protocol. If the activity of any of these drugs is experimentally corroborated, they could be used directly in clinical trials without the need for pre-clinical testing or safety evaluation since they are already used as drugs for other diseases. url: https://arxiv.org/pdf/2006.14790v1.pdf doi: nan id: cord-270348-5804ffwx author: Angelino, Andrew F. title: Design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 positive patients. date: 2020-07-02 words: 5818.0 sentences: 334.0 pages: flesch: 59.0 cache: ./cache/cord-270348-5804ffwx.txt txt: ./txt/cord-270348-5804ffwx.txt summary: To prevent COVID-19 outbreaks in our units, we next decided to require universal nasal swab testing for SARS-CoV-2 for all medically asymptomatic patients being admitted to psychiatric units 3 . Second, we realized that we needed to decide where to care for SARS-CoV-2 positive, medically asymptomatic patients with mental illnesses who required hospitalization-those without symptoms of COVID-19. In light of the above, we concluded it would best serve our patients if we developed an inpatient psychiatric unit capable of accepting SARS-CoV-2 infected patients without COVID-19 symptoms, or with mild enough symptoms that they would not require medical hospitalization. Further, it is highly beneficial for continuity of care if the patient requires transfer to a medical COVID-19 unit that the psychiatrist be able to follow them there and maintain the psychiatric treatments as indicated. abstract: Patients with psychiatric illnesses are particularly vulnerable to highly contagious, droplet spread organisms like SARS-CoV-2. Patients with mental illnesses may not be able to consistently follow behavioral prescriptions to avoid contagion, and they are frequently found in settings with close contact and inadequate infection control, such as group homes, homeless shelters, residential rehabilitation centers, and correctional facilities. Further, inpatient psychiatry settings are generally designed as communal spaces, with heavy emphasis on group and milieu therapies. As such, inpatient psychiatry services are vulnerable to rampant spread of contagion. With this in mind, the authors outline the decision process and ultimate design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 infected patients, and share key points for consideration in implementing future units elsewhere. A major take-away point of the analysis is the particular expertise of trained experts in psychosomatic medicine for treating SARS-CoV-2 infected patients. url: https://api.elsevier.com/content/article/pii/S0033318220302048 doi: 10.1016/j.psym.2020.06.018 id: cord-024130-kgzegwon author: Ankita title: COVID-19: An Ophthalmological Update date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Ever since the newscast of the novel coronavirus outbreak in Wuhan and its subsequent spread to several countries worldwide, the possible modes of spread are being anticipated by various health care professionals. Tear and other conjunctival secretions, being one of the body fluids, can potentially help transmit the disease inadvertently. Conjunctival secretions from patients and asymptomatic contacts of COVID-19 cases may also spread the disease further into the community. Direct inoculation of body fluids into the conjunctiva of healthy individual is also postulated to be another mode of spread. The risk to heath care providers thus becomes strikingly high. A vigilant ophthalmologist can play a critical role in breaking the chain of transmission. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189394/ doi: 10.1007/978-981-15-4814-7_8 id: cord-267373-nzxbogga author: Antinori, Spinello title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status date: 2020-05-11 words: 3468.0 sentences: 149.0 pages: flesch: 49.0 cache: ./cache/cord-267373-nzxbogga.txt txt: ./txt/cord-267373-nzxbogga.txt summary: title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status This prospective (compassionate), open-label study of remdesivir, which was conducted at Luigi Sacco Hospital, Milan, Italy, between February 23 and March 20, 2020, involved patients with SARS-CoV-2 pneumonia aged ≥18 years undergoing mechanical ventilation or with an oxygen saturation level of ≤94% in air or a National Early Warning Score 2 of ≥4. Patients were eligible to receive remdesivir for compassionate use if they were a male or non-pregnant female aged >18 years, had SARS-CoV-2 infection confirmed by a positive reverse-transcriptase polymerase chain reaction (RT-PCR) test of a respiratory tract sample and pneumonia confirmed by a chest X-ray or computed tomography (CT) scan, and were mechanically ventilated or had an oxygen saturation (SaO2) level of <94% in room air or a National Early Warning Score (NEWS)2 of  4 [19] . abstract: SARS-CoV-2 is causing an increasing number of deaths worldwide because no effective treatment is currently available. Remdesivir has shown in vitro activity against coronaviruses and is a possible antiviral treatment for SARS-CoV-2 infection. This prospective (compassionate), open-label study of remdesivir, which was conducted at Luigi Sacco Hospital, Milan, Italy, between February 23 and March 20, 2020, involved patients with SARS-CoV-2 pneumonia aged ≥18 years undergoing mechanical ventilation or with an oxygen saturation level of ≤94% in air or a National Early Warning Score 2 of ≥4. The primary outcome was the change in clinical status based on a 7-category ordinal scale (1 = not hospitalised, resuming normal daily activities; 7 = deceased). The 35 patients enrolled from February 23 to March 20, 2020, included 18 in intensive care unit (ICU), and 17 in our infectious diseases ward (IDW). The 10-day course of remdesivir was completed by 22 patients (63%) and discontinued by 13, of whom eight (22.8%) discontinued because of adverse events. The median follow-up was 39 days (IQR 25-44). At day 28, 14 (82.3%) patients from IDW were discharged, two were still hospitalized and one died (5.9%), whereas in ICU 6 (33.3%) were discharged, 8 (44.4%) patients died, three (16.7%) were still mechanically ventilated and one (5.6%) was improved but still hospitalized. Hypertransaminasemia and acute kidney injury were the most frequent severe adverse events observed (42.8% and 22.8% of the cases, respectively). Our data suggest that remdesivir can benefit patients with SARS-CoV-2 pneumonia hospitalised outside ICU where clinical outcome was better and adverse events are less frequently observed. Ongoing randomised controlled trials will clarify its real efficacy and safety, who to treat, and when. url: https://api.elsevier.com/content/article/pii/S104366182031207X doi: 10.1016/j.phrs.2020.104899 id: cord-345827-yo3uq03v author: Antiochia, Riccarda title: Developments in biosensors for CoV detection and future trends date: 2020-10-28 words: 5968.0 sentences: 278.0 pages: flesch: 44.0 cache: ./cache/cord-345827-yo3uq03v.txt txt: ./txt/cord-345827-yo3uq03v.txt summary: Since MERS and COVID-19 are highly contagious diseases with the potential to cause a pandemic, in absence of a specific vaccine or effective therapeutic drugs, it is of extreme importance to find rapid and accurate detection methods for control and prevention of virus spread. Current methods used for screening and diagnosis of novel COVID-19 are based on three different approaches: SARS-CoV-2 antigen detection in nasopharyngeal secretions through molecular biology techniques, computed tomography, and SARS-CoV-2 antibody analysis in serum using immunoassay methods (Carter et al., 2020) . According to the Food and Drug Administration (FDA) Emergency Use Authorizations (EUAs) for COVID-19 diagnostics, in addition to the most common ELISA method, there are two serological assays used for the detection of antibodies generated against SARS-CoV-2, the chemiluminescence immunoassays (CLIA) and the lateral flow immunoassays (LFIA). Biosensors based on specific biomolecular interactions offer an alternative and reliable solution to current methods for clinical diagnosis of COVID-19, due to their high sensitivity, low-cost, easy to use and possibility of POC utilization. abstract: This review summarizes the state of art of biosensor technology for Coronavirus (CoV) detection, the current challenges and the future perspectives. Three categories of affinity-based biosensors (ABBs) have been developed, depending on their transduction mechanism, namely electrochemical, optical and piezoelectric biosensors. The biorecognition elements include antibodies and DNA, which undergo important non-covalent binding interactions, with the formation of antigen-antibody and ssDNA/oligonucleotide-complementary strand complexes in immuno- and DNA-sensors, respectively. The analytical performances, the advantages and drawbacks of each type of biosensor are highlighted, discussed, and compared to traditional methods. It is hoped that this review will encourage scientists and academics to design and develop new biosensing platforms for point-of-care (POC) diagnostics to manage the coronavirus disease 2019 (COVID-19) pandemic, providing interesting reference for future studies. url: https://api.elsevier.com/content/article/pii/S0956566320307648 doi: 10.1016/j.bios.2020.112777 id: cord-295548-o877eog6 author: Antonio, G.E title: Imaging in Severe Acute Respiratory Syndrome (SARS) date: 2003-10-21 words: 2481.0 sentences: 136.0 pages: flesch: 48.0 cache: ./cache/cord-295548-o877eog6.txt txt: ./txt/cord-295548-o877eog6.txt summary: HRCT is an important tool for early diagnosis in patients with a high clinical suspicion and a negative initial chest radiograph [8] . (1) the majority (108/138, 78%) of patients had air-space opacification of various extent on the chest radiograph at presentation, (2) the right lung was more affected than the left (82/108, 76% versus 67/108, 62%), (3) the lower zone (70/108, 65%) and peripheral lung fields (81/108, 75%) were commonly involved, (4) unifocal involvement (59/108, 55%) was more common at presentation, high fever (.388C), AND cough or breathing difficulty, AND one or more of the following exposures during the 10 days prior to onset of symptoms: close contact with a person who is a suspect or probable case of SARS; history of travel, to an area with recent local transmission of SARS; residing in an area with recent local transmission of SARS. abstract: Severe acute respiratory syndrome (SARS) is a highly infectious disease caused by a novel coronavirus, and has become pandemic within a short period of time. Imaging plays an important role in the diagnosis, management and follow-up of patients with SARS. The current status of imaging in SARS is presented in this review. url: https://www.ncbi.nlm.nih.gov/pubmed/14581005/ doi: 10.1016/s0009-9260(03)00308-8 id: cord-355734-pz64534w author: Antonio-Villa, Neftali Eduardo title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 words: 3261.0 sentences: 215.0 pages: flesch: 49.0 cache: ./cache/cord-355734-pz64534w.txt txt: ./txt/cord-355734-pz64534w.txt summary: Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. abstract: BACKGROUND: Health-care workers (HCWs) could be at increased occupational risk for SARS-CoV-2 infection. Information regarding prevalence and risk factors for adverse outcomes in HCWs is scarce in Mexico. Here, we aimed to explore prevalence of SARS-CoV-2, symptoms, and risk factors associated with adverse outcomes in HCWs in Mexico City. METHODS: We explored data collected by the National Epidemiological Surveillance System in Mexico City. All cases underwent real-time RT-PCR test. We explored outcomes related to severe COVID-19 in HCWs and the diagnostic performance of symptoms to detect SARS-CoV-2 infection in HCWs. RESULTS: As of July 5 (th), 2020, 35,095 HCWs were tested for SARS-CoV-2 and 11,226 were confirmed (31.9%). Overall, 4,322 were nurses (38.5%), 3,324 physicians (29.6%), 131 dentists (1.16%) and 3,449 laboratory personnel and other HCWs (30.8%). After follow-up, 1,009 HCWs required hospitalization (9.00%), 203 developed severe outcomes (1.81%), and 93 required mechanical-ventilatory support (0.82%). Lethality was recorded in 226 (2.01%) cases. Symptoms associated with SARS-CoV-2 positivity were fever, cough, malaise, shivering, myalgias at evaluation but neither had significant predictive value. We also identified 341 asymptomatic SARS-CoV-2 infections (3.04%). Older HCWs with chronic non-communicable diseases, pregnancy, and severe respiratory symptoms were associated with higher risk for adverse outcomes. Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. No symptomatology can accurately discern HCWs with SARS-CoV-2 infection. Particular attention should focus on HCWs with risk factors to prevent adverse outcomes and reduce infection risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32986819/ doi: 10.1093/cid/ciaa1487 id: cord-309729-nd48uh8e author: Antunes, Adriane E.C. title: Potential contribution of beneficial microbes to face the COVID- 19 pandemic date: 2020-07-24 words: 4843.0 sentences: 216.0 pages: flesch: 36.0 cache: ./cache/cord-309729-nd48uh8e.txt txt: ./txt/cord-309729-nd48uh8e.txt summary: Then, dietary strategies for the promotion of the gut microbiota, and thus the strengthening of the immune system associated with the gut, include increased consumption of fiber and prebiotics (Holscher, 2017) , and incorporating fermented foods (Marco et al., 2017) , and probiotics (Zmora, Suez, & Elinav, 2019) into the diet. There is scientific evidence about the ability of probiotics to promote gut immunity (Sánchez et al., 2017) and, for the moment, a modest evidence of their role in reducing the severity of acute upper respiratory tract infections (AURTI) (Hao, Dong, & Wu, 2015) . In a context of impoverished and threatened intestinal microbiota, the consumption of home-made fermented foods (yoghurt, kefir, sauerkraut, kombucha) or the incorporation into the diet of commercial products containing probiotics and prebiotics, as food or food supplements, is part of a comprehensive nutritional strategy to enhance the function of the gut microbiota, to promote mucosal immunity and potentially upper respiratory tract immunity, to be potentially better prepared to face viral or bacterial infections caused by respiratory syndromes. abstract: The year 2020 will be remembered by a never before seen, at least by our generation, global pandemic of COVID-19. While a desperate search for effective vaccines or drug therapies is on the run, nutritional strategies to promote immunity against SARS-CoV-2, are being discussed. Certain fermented foods and probiotics may deliver viable microbes with the potential to promote gut immunity. Prebiotics, on their side, may enhance gut immunity by selectively stimulating certain resident microbes in the gut. Different levels of evidence support the use of fermented foods, probiotics and prebiotics to promote gut and lungs immunity. Without being a promise of efficacy against COVID-19, incorporating them into the diet may help to low down gut inflammation and to enhance mucosal immunity, to possibly better face the infection by contributing to diminishing the severity or the duration of infection episodes. url: https://doi.org/10.1016/j.foodres.2020.109577 doi: 10.1016/j.foodres.2020.109577 id: cord-268329-apl6n6jl author: Antunes, Douglas Eulálio title: Will cases of leprosy reaction increase with COVID-19 infection? date: 2020-07-17 words: 1508.0 sentences: 79.0 pages: flesch: 45.0 cache: ./cache/cord-268329-apl6n6jl.txt txt: ./txt/cord-268329-apl6n6jl.txt summary: The coronavirus disease 2019 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus (betaCoV)-emerged for the first time as an outbreak of pneumonia in Wuhan, China, and it is now spreading to several countries around the world [1] . Some studies of SARS-CoV-2 infection have reported the presence of a cytokine storm syndrome and a subgroup of patients who progressed to severe forms of the disease, expressing a pro-inflammatory profile in plasma with IL-2, IL-7, TNF-α, and others as significant complications, such as occurs in T1R [10, 11] . In both reactions, we warn of the possible effect that COVID-19 infection may have on the number of cases of these immunological events because the presence of infection is an important risk factor for triggering leprosy reactions [8] . Another disturbing factor, which may contribute to the susceptibility of those affected by leprosy reactions, are the treatments implemented during these events that interfere with the inflammatory response of these patients. abstract: nan url: https://doi.org/10.1371/journal.pntd.0008460 doi: 10.1371/journal.pntd.0008460 id: cord-349089-ta07bho2 author: Antushevich, Hanna title: Interplays between inflammasomes and viruses, bacteria (pathogenic and probiotic), yeasts and parasites date: 2020-09-22 words: 8174.0 sentences: 467.0 pages: flesch: 34.0 cache: ./cache/cord-349089-ta07bho2.txt txt: ./txt/cord-349089-ta07bho2.txt summary: For example, in in vitro experiments on human primary neurons (HPNs) and microglial cells (HFMG) collected from healthy patients, it was discovered that treatment of the cells with HIV ssRNA40 (specific GU-rich single-stranded RNA from the HIV long terminal repeat region) activates the NLRP3 inflammasome and increases the expression and extracellular secretion of pro-inflammatory cytokines (IL-1β, IL-18) and neurotoxic cytokines (TNF-α, IL-1α, C1q). Another report has shown that HIV-1 induces the expression of NLRP3 inflammasome and IL-1β secretion in dendritic cells from healthy individuals but not HIV-1-infected patients, suggesting that inflammasome activation contributes to disease progression [23] . Based on the strong inflammatory potential of the NLRP3 inflammasome during infections caused by MERS-and SARS-CoVs, inhibition of the NLRP3 inflammasome activity may attenuate the cytokine storm and be a therapeutic target in the treatment of tissue inflammation in SARS patients [33, 41] . abstract: In recent years, scientists studying the molecular mechanisms of inflammation have discovered an amazing phenomenon – the inflammasome – a component of the innate immune system that can regulate the functional activity of effector cells during inflammation. At present, it is known that inflammasomes are multimolecular complexes (cytosolic multiprotein oligomers of the innate immune system) that contain many copies of receptors recognizing the molecular structures of cell-damaging factors and pathogenic agents. Inflammasomes are mainly formed in myeloid cells, and their main function is participation in the cleavage of the pro-IL-1β and pro-IL-18 cytokines into their biologically active forms (IL-1β, IL-18). Each type of microorganism influences particular inflammasome activation, and long-term exposure of the organism to viruses, bacteria, yeasts or parasites, among others, can induce uncontrolled inflammation and autoinflammatory diseases. Therefore, this review aims to present the most current scientific data on the molecular interplay between inflammasomes and particular microorganisms. Knowledge about the mechanisms responsible for the interaction between the host and certain types of microorganisms could contribute to the individuation of innovative strategies for the treatment of uncontrolled inflammation targeting a specific type of inflammasome activated by a specific type of pathogen. url: https://api.elsevier.com/content/article/pii/S0165247820303837 doi: 10.1016/j.imlet.2020.09.004 id: cord-338751-2eo7ityc author: Anzalone, Nicoletta title: Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients date: 2020-06-06 words: 1084.0 sentences: 68.0 pages: flesch: 42.0 cache: ./cache/cord-338751-2eo7ityc.txt txt: ./txt/cord-338751-2eo7ityc.txt summary: title: Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients They are part of a series of 21 patients presenting with neurological symptoms studied with brain MRI with otherwise no significant imaging findings. Although the predominantly parieto-occipital distribution of the lesions recalls posterior reversible encephalopathy syndrome (PRES) [5] , the prevalent cortical involvement and diffusion MRI pattern are not typical of PRES. More recently, evidence of direct viral infection of the endothelial cell and diffuse endothelial inflammation has been reported, resulting Fig. 1 Forty-seven-year-old man diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. Multiple, cortical areas of punctiform and gyriform FLAIR and DWI hyperintensity (arrows) in both parietal lobes, with no ADC changes Fig. 2 Fifty-four-year-old woman diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. abstract: nan url: https://doi.org/10.1007/s00415-020-09966-2 doi: 10.1007/s00415-020-09966-2 id: cord-311566-x8n1bbwn author: Aouidate, Adnane title: Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation date: 2020-06-18 words: 6355.0 sentences: 281.0 pages: flesch: 54.0 cache: ./cache/cord-311566-x8n1bbwn.txt txt: ./txt/cord-311566-x8n1bbwn.txt summary: As we are running of time and the virus is spreading quickly, we have screened the CAS COVID-19 Antiviral Compound Dataset, which includes $50000 chemical compounds against 3CLpro and RNA-dependent RNA polymerase (RdRp) using computational methods and ligand and structure based screening and in this study, we report the identification of different compounds with CAS IDs (2001083-69-6, 2001083-68-5, 63248-75-9, 264621-13-8, 1025098-90-1, 1253912-09-2) as potent inhibitors of 3CLpro and (833463-10-8, 833463-11-9, 833465-33-1, 2001083-69-6, 833463-19-7, 833464-45-2) as potent inhibitors RNA-dependent RNA-polymerase (RdRp), most compounds are 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives, the analysis of SARS-CoV-2 main protease and RNAdependent RNA polymerase binding sites reveals are combinations of hydrophobic, hydrophilic and charged residues holding with hydrogen bonds in excess, therefore, the 1,3,5triazine that is aligned centrally in both proteins binding pockets could be a good choice to occupy the central part of the molecules to be substituted by different hydrophobic, hydrophilic and charged fragments. abstract: The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected whole the world with more than 6 million confirmed cases and over 370,000 deaths. At present, there are no effective treatments or vaccine for this disease, which constitutes a serious global health crisis. As the pandemic still spreading around the globe, it is of interest to use computational methods to identify potential inhibitors for the virus. The crystallographic structures of 3CLpro (PDB: 6LU7) and RdRp (PDB 6ML7) were used in virtual screening of 50000 chemical compounds obtained from the CAS Antiviral COVID19 database using 3D-similarity search and standard molecular docking followed by ranking and selection of compounds based on their binding affinity, computational techniques for the sake of details on the binding interactions, absorption, distribution, metabolism, excretion, and toxicity prediction; we report three 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives; two compounds (2001083-68-5 and 2001083-69-6) with optimal binding features to the active site of the main protease and one compound (833463-19-7) with optimal binding features to the active site of the polymerase for further consideration to fight COVID-19. The structural stability and dynamics of lead compounds at the active site of 3CLpro and RdRp were examined using molecular dynamics (MD) simulation. Essential dynamics demonstrated that the three complexes remain stable during simulation of 20 ns, which may be suitable candidates for further experimental analysis. As the identified leads share the same scaffold, they may serve as promising leads in the development of dual 3CLpro and RdRp inhibitors against SARS-CoV-2. Communicated by Ramaswamy H. Sarma. url: https://doi.org/10.1080/07391102.2020.1779130 doi: 10.1080/07391102.2020.1779130 id: cord-274439-y9jrdg5n author: Aoyama, Kazuyoshi title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model date: 2020-07-27 words: 593.0 sentences: 38.0 pages: flesch: 45.0 cache: ./cache/cord-274439-y9jrdg5n.txt txt: ./txt/cord-274439-y9jrdg5n.txt summary: title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model A Through the interface, users can define inputs such as surgical statistics, including percent change of surgical caseload, and constraint on the number of available N95 respirators to model expected resource utilization at the individual hospital level, community level, or provincial level. Beginning on 16 March 2020, our quaternary-care children''s hospital performed only emergent and urgent surgeries (e.g., cancer surgery), including 236 cases during the first three weeks after the pandemic was declared. We estimated that cancelling elective surgeries during those three weeks reduced the cumulative incidence of SARS-CoV-2 transmission to an anesthesiologist by more than six times (2.1% with cancellation compared with 13.5% without cancellation) (Figure) . 5 Although we considered aerosol transmission and environmental contamination of SARS-CoV-2 in the model, we did not account for transmission risks among HCWs in operating rooms, which is our future work. The user can tune the transmission risk in the model when new data emerge. SARS-CoV-2 Infection in children abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32720258/ doi: 10.1007/s12630-020-01771-9 id: cord-300978-busx8w6s author: Apetrii, Mugurel title: A brand-new cardiorenal syndrome in the Coronavirus Disease- 2019 (COVID-19) setting date: 2020-06-04 words: 2999.0 sentences: 151.0 pages: flesch: 40.0 cache: ./cache/cord-300978-busx8w6s.txt txt: ./txt/cord-300978-busx8w6s.txt summary: Although the pandemic outbreak of coronavirus disease-2019 (COVID-19) targets preferentially patient''s lungs, recent data have documented that COVID-19 causes myocarditis, acute myocardial infarction, exacerbation of heart failure and acute kidney injury. Studies show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similar to its predecessor SARS-CoV, engages angiotensin-converting enzyme 2 (ACE2) as the entry receptor. In patients with SARS-CoV-2 infection, the most important features that suggest myocardial injury are electrocardiogram changes and troponin elevation coupled with echocardiography showing signs of subclinical left ventricular diastolic impairment or even reduced ejection fraction (EF) in severe cases [11] , with a higher likelihood of the need for mechanical ventilation in those with reduced EF, as was seen during previous coronavirus outbreaks [9] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection abstract: Coronaviruses are a major pathogen for adults, causing up to one-third of community-acquired respiratory tract infections in adults during epidemics. Although the pandemic outbreak of coronavirus disease-2019 (COVID-19) targets preferentially patient’s lungs, recent data have documented that COVID-19 causes myocarditis, acute myocardial infarction, exacerbation of heart failure and acute kidney injury. Studies show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similar to its predecessor SARS-CoV, engages angiotensin-converting enzyme 2 (ACE2) as the entry receptor. ACE2 is also expressed in the heart, providing a link between coronaviruses and the cardiovascular system. url: https://www.ncbi.nlm.nih.gov/pubmed/32695320/ doi: 10.1093/ckj/sfaa082 id: cord-319955-spnykv96 author: Arafah, Azher title: S1 Subunit and Host Proteases as Potential Therapeutic Avenues for the Treatment of COVID-19 date: 2020-05-21 words: 909.0 sentences: 47.0 pages: flesch: 49.0 cache: ./cache/cord-319955-spnykv96.txt txt: ./txt/cord-319955-spnykv96.txt summary: Abstract The novel corona virus (SARS-CoV-2) that causes severe acute respiratory syndrome, now called COVID-19 initially originated in Wuhan city of China and later spread across borders and infected more than two million people and killed over 2.9 lakh people all over the globe. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. abstract: Abstract The novel corona virus (SARS-CoV-2) that causes severe acute respiratory syndrome, now called COVID-19 initially originated in Wuhan city of China and later spread across borders and infected more than two million people and killed over 2.9 lakh people all over the globe. This disease has been announced as pandemic by WHO. So far, there has been not much progress in terms of drug development for fighting against this deadliest virus, also no existing drugs has been reported completely effective for COVID-19 treatment owing to lack of effective therapeutic targets and a broad understanding of the viral behavior in target cell. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. Thus, simultaneous blocking of S1 subunit and inactivation of proteases seem to be promising therapeutic targets for the development of effective novel drugs. In current write up we hypothesize that S1 subunit and host proteases as potential therapeutic avenues for the treatment of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0188440920307700?v=s5 doi: 10.1016/j.arcmed.2020.05.013 id: cord-343340-zi0rfidc author: Aragón‐Caqueo, Diego title: Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date: 2020-05-03 words: 3319.0 sentences: 155.0 pages: flesch: 51.0 cache: ./cache/cord-343340-zi0rfidc.txt txt: ./txt/cord-343340-zi0rfidc.txt summary: The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. Therefore, the aim of this study is to provide a mathematical model to estimate the optimum number of pooled samples according to the specific prevalences of positive tests in a particular country context, in order to save as many tests as possible and cover as many people as possible, knowing that if a group tests out positive, all the individuals of the sample would have to be individually tested. This article proposed a simple and landed model to estimate the most optimum group number to implement pool testing strategy for SARS-CoV-2, according to the specific historical positive tests prevalence for a determined healthcare context. abstract: Coronavirus disease (Covid‐19) has reached unprecedented pandemic levels and is affecting almost every country in the world. Ramping up the testing capacity of a country supposes an essential public health response to this new outbreak. A pool testing strategy where multiple samples are tested in a single reverse transcriptase‐polymerase chain reaction (RT‐PCR) kit could potentially increase a country's testing capacity. The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. The model predicts group sizes that range from 11 to 3 subjects. For a prevalence of 10% of positive tests, 40.6% of tests can be saved using testing groups of four subjects. For a 20% prevalence, 17.9% of tests can be saved using groups of three subjects. For higher prevalences, the strategy flattens and loses effectiveness. Pool testing individuals for severe acute respiratory syndrome coronavirus 2 is a valuable strategy that could considerably boost a country's testing capacity. However, further studies are needed to address how large these groups can be, without losing sensitivity on the RT‐PCR. The strategy best works in settings with a low prevalence of positive tests. It is best implemented in subgroups with low clinical suspicion. The model can be adapted to specific prevalences, generating a tailored to the context implementation of the pool testing strategy. url: https://doi.org/10.1002/jmv.25929 doi: 10.1002/jmv.25929 id: cord-336227-0j0nbm9k author: Aranda‐Abreu, Gonzalo Emiliano title: Use of amantadine in a patient with SARS‐CoV‐2 date: 2020-06-24 words: 688.0 sentences: 38.0 pages: flesch: 62.0 cache: ./cache/cord-336227-0j0nbm9k.txt txt: ./txt/cord-336227-0j0nbm9k.txt summary: Due to a persistent cough, 500 mg of azithromycin was added for three days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time PCR test for SARS-Cov-2 which was positive. Due to a persistent cough, 500 mg of azithromycin was added for 3 days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was positive. Asymptomatic family members (wife and daughter 54 and 33 years old, respectively) positive for SARS-CoV-2 were prescribed amantadine 100 mg twice daily for 14 days as a preventive measure. Family members (wife and daughter) who were in contact with the patient and also tested positive for SARS-CoV-2 took amantadine 1 100 mg twice a day for 14 days and did not develop symptoms. abstract: A 57-year old man with cold symptoms and muscle pain, with elevated blood glucose of 200mg/dL, was prescribed paracetamol (500mg every 6 hours) and naproxen (550mg daily for 5 days) and continued to take 850mg of metformin twice a day for the treatment of 10-year-old type 2 diabetes. Due to a persistent cough, 500 mg of azithromycin was added for three days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time PCR test for SARS-Cov-2 which was positive. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26179 doi: 10.1002/jmv.26179 id: cord-347048-qqft4yc9 author: Araten, David J. title: Mild Clinical Course of COVID-19 in 3 Patients Receiving Therapeutic Monoclonal Antibodies Targeting C5 Complement for Hematologic Disorders date: 2020-09-12 words: 2161.0 sentences: 125.0 pages: flesch: 55.0 cache: ./cache/cord-347048-qqft4yc9.txt txt: ./txt/cord-347048-qqft4yc9.txt summary: CASE REPORTS: Case 1 is a 39-year-old woman with an approximately 20-year history of paroxysmal nocturnal hemoglobinuria (PNH), who had recently been switched from treatment with eculizumab to ravulizumab prior to SARS-CoV-2 infection. Case 2 is a 54-year-old woman with a cadaveric renal transplant for lupus nephritis, complicated by thrombotic microangiopathy, who was maintained on eculizumab, which she started several months before she developed the SARS-CoV-2 infection. CONCLUSIONS: We see no evidence of increased susceptibility to SARS-CoV-2 in these patients on anti-complement therapy, which might actually have accounted for the mild course of infection. We now have the opportunity to report on 3 patients who were on therapeutic anti-complement therapy at the time they became infected with the SARS-CoV-2 virus. The mild cases of SARS-CoV-2 infection in these 3 patients may have been related to anti-complement therapy, as suggested by preclinical models and reports of other patients who have received anti-complement therapy for COVID-19. abstract: Case series Patients: Female, 39-year-old • Female, 54-year-old • Female, 60-year-old Final Diagnosis: COVID-19 Symptoms: Fever Medication: — Clinical Procedure: — Specialty: Hematology • Nephrology • Rheumatology OBJECTIVE: Rare co-existance of disease or pathology BACKGROUND: Patients receiving immunosuppressive therapies might be more susceptible to COVID-19. Conversely, an exaggerated inflammatory response to the SARS-CoV-2 infection might be blunted by certain forms of immunosuppression, which could be protective. Indeed, there are data from animal models demonstrating that complement may be a part of the pathophysiology of coronavirus infections. There is also evidence from an autopsy series demonstrating complement deposition in the lungs of patients with COVID-19. This raises the question of whether patients on anti-complement therapy could be protected from COVID-19. CASE REPORTS: Case 1 is a 39-year-old woman with an approximately 20-year history of paroxysmal nocturnal hemoglobinuria (PNH), who had recently been switched from treatment with eculizumab to ravulizumab prior to SARS-CoV-2 infection. Case 2 is a 54-year-old woman with a cadaveric renal transplant for lupus nephritis, complicated by thrombotic microangiopathy, who was maintained on eculizumab, which she started several months before she developed the SARS-CoV-2 infection. Case 3 is a 60-year-old woman with a 14-year history of PNH, who had been treated with eculizumab since 2012, and was diagnosed with COVID-19 at the time of her scheduled infusion. All 3 patients had a relatively mild course of COVID-19. CONCLUSIONS: We see no evidence of increased susceptibility to SARS-CoV-2 in these patients on anti-complement therapy, which might actually have accounted for the mild course of infection. The effect of anti-complement therapy on COVID-19 disease needs to be determined in clinical trials. url: https://doi.org/10.12659/ajcr.927418 doi: 10.12659/ajcr.927418 id: cord-287488-h102xn29 author: Araujo, Danielle Bastos title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 words: 3927.0 sentences: 223.0 pages: flesch: 53.0 cache: ./cache/cord-287488-h102xn29.txt txt: ./txt/cord-287488-h102xn29.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. OBJECTIVES: The objective of this work is to describe the isolation and propagation properties of SARS-CoV-2 isolates from the first confirmed cases of coronavirus disease 2019 (COVID-19) in Brazil. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks - viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. MAIN CONCLUSION: We believe that the protocols for virus growth and studies here described and the distribution initiative may constitute a viable model for other developing countries, not only to help a rapid effective pandemic response, but also to facilitate and support basic scientific research. url: https://www.ncbi.nlm.nih.gov/pubmed/33111751/ doi: 10.1590/0074-02760200342 id: cord-254886-fl5ar971 author: Arav, Y. title: Understanding the indoor pre-symptomatic transmission mechanism of COVID-19 date: 2020-05-17 words: 2228.0 sentences: 121.0 pages: flesch: 54.0 cache: ./cache/cord-254886-fl5ar971.txt txt: ./txt/cord-254886-fl5ar971.txt summary: The model explicitly tracks the dynamics of contact and airborne transmission between individuals indoors, and was validated against the observed fundamental attributes of the epidemic, the secondary attack rate (SAR) and serial interval distribution. We provide evidence that a combination of rather easy to implement measures of frequent hand washing, cleaning fomites and avoiding physical contact decreases the risk of infection by an order of magnitude, similarly to wearing masks and gloves. In fact, pre-symptomatic transmission was recently referred to as the Achilles'' heel of COVID-19 pandemic control, as symptom-based detection of infection is less effective in comparison to the control of the SARS epidemic in 2003 (7) . We decided to examine five HBMs: Washing hands, cleaning fomites, maintaining social distancing (i.e avoiding physical contact), wearing a mask and 6 All rights reserved. Frequent hand washing and fomite cleaning coupled with avoiding physical contact result in a similar risk for infection as wearing gloves and a mask. abstract: Discovering the mechanism that enables pre-symptomatic individuals to transmit the SARS-CoV-2 virus has a significant impact on the possibility of controlling COVID-19 pandemic. To this end, we have developed an evidence based quantitative mechanistic mathematical model. The model explicitly tracks the dynamics of contact and airborne transmission between individuals indoors, and was validated against the observed fundamental attributes of the epidemic, the secondary attack rate (SAR) and serial interval distribution. Using the model we identified the dominant driver of pre-symptomatic transmission, which was found to be contact route, while the contribution of the airborne route is negligible. We provide evidence that a combination of rather easy to implement measures of frequent hand washing, cleaning fomites and avoiding physical contact decreases the risk of infection by an order of magnitude, similarly to wearing masks and gloves. url: http://medrxiv.org/cgi/content/short/2020.05.12.20099085v1?rss=1 doi: 10.1101/2020.05.12.20099085 id: cord-319900-16osnnga author: Arcadepani, Felipe B. title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil date: 2020-07-02 words: 1046.0 sentences: 63.0 pages: flesch: 52.0 cache: ./cache/cord-319900-16osnnga.txt txt: ./txt/cord-319900-16osnnga.txt summary: title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil All these issues make these individuals a high-risk group for infected by SARS-Cov-2 as they present several clinical (including pulmonary) comorbidities and social conditions that, besides posing difficulties for disease prevention, may play a role in hampering their immunological responses and general health. The population living or frequenting outdoor scenes lack adequate support from the Brazilian Public Health System, and the current pandemic adds more urgency to specific policies to address their susceptibility to this and other diseases. A pandemic that requires social isolation, especially for high-risk populations, turns this existing necessity into an emergency measure, taking into account basic public health principles and human rights. Health care facilities must provide treatment for their clinical comorbidities, focusing particularly on primary conditions such as hypertension and diabetes, which may be highly underdiagnosed among people who frequently use crackcocaine and are highly vulnerable to severe cases of COVID-19. abstract: nan url: https://api.elsevier.com/content/article/pii/S0955395920301766 doi: 10.1016/j.drugpo.2020.102835 id: cord-345754-mgixsfcc author: Arena, Patrick J. title: Race, COVID-19 and deaths of despair date: 2020-07-31 words: 927.0 sentences: 57.0 pages: flesch: 49.0 cache: ./cache/cord-345754-mgixsfcc.txt txt: ./txt/cord-345754-mgixsfcc.txt summary: 1 The higher burden of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection and COVID-19 mortality among ethnic and racial minorities does not appear to be explained by biological factors, but instead by longstanding discriminatory societal and historical factors whereby the simple fact of belonging to a specific race/ethnicity limits access to education and wealth and precipitates exposure to the criminal justice system and poor health outcomes. COVID-19 morbidity and mortality is influenced by specific pre-existing health conditions, such as diabetes, hypertension, heart disease, food insecurity and lack of health insurance, all of which are highly prevalent among ethnic and racial minority groups, such as Black, Latinx and Native American populations in the United States (US). Similarly, a recent systematic review suggested that Black, Asian, and minority ethnic (BAME) individuals had a higher risk of SARS-CoV-2 infection and also experienced worse clinical outcomes than White individuals. Although some public health officials are taking concrete steps to address COVID-19 disparities among impacted ethnic groups, 8 data on the effectiveness of lockdowns on BAME communities is lacking. abstract: nan url: https://doi.org/10.1016/j.eclinm.2020.100485 doi: 10.1016/j.eclinm.2020.100485 id: cord-323489-ro7kbnu3 author: Arenas, María Dolores title: Protection of nephrology health professionals during the COVID-19 pandemic date: 2020-10-06 words: 4137.0 sentences: 194.0 pages: flesch: 50.0 cache: ./cache/cord-323489-ro7kbnu3.txt txt: ./txt/cord-323489-ro7kbnu3.txt summary: There are a number of reasons why the protection of healthcare professionals has to be one of the main objectives in the SARS-CoV-2 pandemic: 1) They are necessary to guarantee the continuity of care; 2) They have a high risk of contagion due to their front-line exposure to infected patients; and 3) They may act as transmission vehicles in their day-to-day work to patients, other colleagues, and members of their families and the community. a Special care or protective measures for medical, nursing and auxiliary staff who work daily with haemodialysis patients As has previously been described in other publications 3,10 , the main protection measures for healthcare professionals and patients in haemodialysis units are: 1) adequate information for patients attending the centre in terms of maintaining a safe distance from fellow patients in waiting rooms and ambulances, and in the use of surgical masks and frequent hand washing; 2) early detection of patients suspected to be infected on arrival at the unit (questionnaires about symptoms or close contacts, taking temperature), and if highly suspect, taking a nasopharyngeal swab for PCR testing. abstract: The COVID-19 epidemic represents a special risk for kidney patients due to their comorbidities and advanced age, and the need for hemodialysis treatment in group rooms. It also represents a risk for professionals responsible for their attention. This manuscript contains a proposal for action to prevent infection of professionals in the Nephrology Services, one of the most valuable assets at the present time. url: https://api.elsevier.com/content/article/pii/S2013251420301061 doi: 10.1016/j.nefroe.2020.06.018 id: cord-310239-mmvuij3k author: Arentz, Susan title: Clinical significance summary: Preliminary results of a rapid review of zinc for the prevention and treatment of SARS-CoV-2 and other acute viral respiratory infections date: 2020-08-01 words: 3941.0 sentences: 215.0 pages: flesch: 47.0 cache: ./cache/cord-310239-mmvuij3k.txt txt: ./txt/cord-310239-mmvuij3k.txt summary: Indirect evidence from systematic reviews have found zinc supplementation is effective for the prevention of acute respiratory infections in young children and zinc lozenges may reduce the duration of the common cold in adults. As of the 9 June 2020, the preliminary findings of a rapid review of zinc for the prevention or treatment Pending any definitive evidence, clinicians might consider assessing the zinc status of people with chronic disease co-morbidities and older adults as part of a SARS-CoV-2 clinical work-up, as both groups have a higher risk of zinc deficiency/insufficiency and poorer outcomes from SARS-CoV-2. The primary objective of this rapid review was to assess the effects of zinc on the incidence, duration and severity of acute upper or lower respiratory tract infections caused by SARS-CoV-2 infection in people of any age and of any zinc status when used as a preventive supplement or as a therapy. abstract: nan url: https://doi.org/10.1016/j.aimed.2020.07.009 doi: 10.1016/j.aimed.2020.07.009 id: cord-294666-xlyuhzo9 author: Arguin, Paul M. title: Health Communication during SARS date: 2004-02-17 words: 1493.0 sentences: 67.0 pages: flesch: 44.0 cache: ./cache/cord-294666-xlyuhzo9.txt txt: ./txt/cord-294666-xlyuhzo9.txt summary: Timely health communication, along with surveillance, quarantine, isolation, and travel restrictions, figured prominently among the tools the Centers for Disease Control and Prevention (CDC) used to help contain the outbreak. By the end of September 1994, CDC had produced six documents to distribute to public health officials: an outbreak notice; a plague advisory for travelers to India; a plague alert notice handed to passengers arriving from India, which described the symptoms of plague and urged them to seek medical attention if they developed a febrile illness within 7 days; recommendations for treatment and prophylaxis; guidelines for diagnosis and biosafety; and a review article in the Morbidity and Mortality Weekly Report. Kennedy International Airport on flights from India), the departments of health in New York City and New York State supplemented CDC''s surveillance plan by using two approaches to disseminate information to heighten awareness of plague, focusing on emergency department physicians. abstract: During the severe acute respiratory syndrome (SARS) outbreak, electronic media made it possible to disseminate prevention messages rapidly. The Centers for Disease Control and Prevention’s Travelers’ Health Web site was frequently visited in the first half of 2003; more than 2.6 million visits were made to travel alerts, advisories, and other SARS-related documents. url: https://www.ncbi.nlm.nih.gov/pubmed/15030717/ doi: 10.3201/eid1002.030812 id: cord-347734-0z2kin6r author: Armann, J. P. title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates date: 2020-07-17 words: 2294.0 sentences: 138.0 pages: flesch: 51.0 cache: ./cache/cord-347734-0z2kin6r.txt txt: ./txt/cord-347734-0z2kin6r.txt summary: title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates However, there is reason to believe that children play a less significant role in SARS-CoV-2 transmission compared to influenza, making control measures focused on this age group less effective: Most countries-including Germany-report a much lower proportion of cases in children compared to their population size 4-6 . The findings from this unique study in older students and their teachers indicate that the prevalence of IgG antibodies against SARS-CoV-2 remains extremely low after the first wave of the corona pandemic in Germany. In fact, 5 of the 12 participants with antibodies against SARS-CoV-2 had a personal or household history of COVID-19, yielding a ratio of unidentified to identified cases of 2.4, which is much smaller than that previously assumed by some authors 9 . abstract: Background: School closures are part of the SARS-CoV-2 pandemic control measures in many countries, based on the assumption that children play a similar role in transmitting SARS-CoV-2 as they do in transmitting influenza. We therefore performed a SARS-CoV-2 seropraevalence-study in students and teachers to assess their role in the SARS-CoV-2 transmission. Methods: Students grade 8-11 and their teachers in 13 secondary schools in eastern Saxony, Germany, were invited to participate in the SchoolCoviDD19 study. Blood samples were collected between May 25th and June 30th, 2020. Anti-SARS-CoV-2 IgG were assed using chemiluminescence immunoassay technology and all samples with a positive or equivocal test result were re-tested with two additional serological tests. Findings: 1538 students and 507 teachers participated in this study. The seropraevalence for SARS-CoV-2 was 0.6%. Even in schools with reported Covid-19 cases before the Lockdown of March 13th no clusters could be identified. 23/24 participants with a household history of COVID-91 were seronegative. By using a combination of three different immunoassays we could exclude 16 participants with a positive or equivocal results after initial testing. Interpretation: Students and teachers do not play a crucial role in driving the SARS-CoV-2 pandemic in a low prevalence setting. Transmission in families occurs very infrequently, and the number of unreported cases is low in this age group, making school closures not appear appropriate as a strategy in this low prevalence settings. Funding: This study was supported by a grant from the state of Saxony url: https://doi.org/10.1101/2020.07.16.20155143 doi: 10.1101/2020.07.16.20155143 id: cord-356264-q0yqnlyl author: Armijos-Jaramillo, Vinicio title: SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-03-23 words: 4974.0 sentences: 253.0 pages: flesch: 53.0 cache: ./cache/cord-356264-q0yqnlyl.txt txt: ./txt/cord-356264-q0yqnlyl.txt summary: With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene, and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. All these experiments were performed again using the S-protein genes of a shorter list of accessions and more distantly related (broad dataset) to SARS-COV-2 (AY304488, AY395003, DQ412043, FJ882957, KY417144, MG772933, MG772934, MN908947, NC_004718) to test the reproducibility of the predicted branches and sites under positive selection. Modeling results suggest that interference with the hot spot 353 could be and effective strategy for inhibiting the recognition of the RBD of the SARS-COV-2 spike protein by its human host receptor ACE2 and hence prevent infections. abstract: The emergence of SARS-CoV-2 has resulted in more than 200,000 infections and nearly 9,000 deaths globally so far. This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2. In the wake of a global pandemic it is essential to improve our understanding of the evolutionary dynamics surrounding the origin and spread of a novel infectious disease. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict where these genomic regions are under directional or purifying selection between divergent viral lineages at various scales of relatedness. With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. Next, to gain further insights into factors associated with coronaviruses recognition of the human host receptor, we performed modeling studies of five different coronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of coronavirus infections. We also propose that a glycine residue at the receptor binding domain of the spike glycoprotein can have a critical role in permitting bat variants of the coronaviruses to infect human cells. url: https://doi.org/10.1101/2020.03.21.001933 doi: 10.1101/2020.03.21.001933 id: cord-323324-h2a25xym author: Armijos‐Jaramillo, Vinicio title: SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-05-07 words: 3340.0 sentences: 192.0 pages: flesch: 55.0 cache: ./cache/cord-323324-h2a25xym.txt txt: ./txt/cord-323324-h2a25xym.txt summary: With this analysis, we determine a region inside the receptor‐binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor ACE2. In the case of SARS-CoV, ACE2 binding was found to be a critical determinant for the range of hosts the virus can infect, and key amino acid residues in the RBD were identified to be essential for ACE2-mediated SARS-CoV infection and adaptation to humans (Li et al., 2005 (Li et al., , 2006 . We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. Additionally, important hACE2-binding residues in the RBD from SARS-COV-2 obtained from the crystallography and structure determination performed by Shang et al. abstract: The emergence of SARS‐CoV‐2 has resulted in nearly 1,280,000 infections and 73,000 deaths globally so far. This novel virus acquired the ability to infect human cells using the SARS‐CoV cell receptor hACE2. Because of this, it is essential to improve our understanding of the evolutionary dynamics surrounding the SARS‐CoV‐2 hACE2 interaction. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict whether these genomic regions are under directional or purifying selection between divergent viral lineages, at various scales of relatedness. With this analysis, we determine a region inside the receptor‐binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor ACE2. Next, to gain further insights into factors associated with recognition of the human host receptor, we performed modeling studies of five different betacoronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of SARS‐CoV‐2 infections. We also propose that a glycine residue at the receptor‐binding domain of the spike glycoprotein can have a critical role in permitting bat SARS‐related coronaviruses to infect human cells. url: https://www.ncbi.nlm.nih.gov/pubmed/32837536/ doi: 10.1111/eva.12980 id: cord-289813-kq3ayyip author: Arnaez, Juan title: The Impact of the Current SARS-CoV-2 Pandemic on Neonatal Care date: 2020-04-30 words: 1965.0 sentences: 90.0 pages: flesch: 41.0 cache: ./cache/cord-289813-kq3ayyip.txt txt: ./txt/cord-289813-kq3ayyip.txt summary: These changes mainly impact several key points: (1) the organization and workflow of the neonatal unit, (2) parent-infant bonding and family-centered care, and (3) stress-related consequences in health professionals (Figure 1) . The contingency plans required by the circumstances in the current SARS-CoV-2 outbreak scenario must not let us forget that restrictions on parental contact and interventions in the care of infants may entail costs to the families in addition to the loss of opportunities for the newborn to adapt to the extrauterine environment and advance in neurodevelopment. Importantly, health-workers should rely positively on the contingency plans and help parents to reduce their fear and encourage them to participate in their children''s care. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes A contingency plan for the management of the 2019 novel coronavirus outbreak in neonatal intensive care units abstract: nan url: https://doi.org/10.3389/fped.2020.00247 doi: 10.3389/fped.2020.00247 id: cord-265155-jbvrcjx8 author: Aroniadis, Olga C. title: Current Knowledge and Research Priorities in the Digestive Manifestations of COVID-19 date: 2020-04-22 words: 1606.0 sentences: 85.0 pages: flesch: 39.0 cache: ./cache/cord-265155-jbvrcjx8.txt txt: ./txt/cord-265155-jbvrcjx8.txt summary: Herein we discuss the known digestive manifestations of COVID-19 and their potential implications, important questions that remain unanswered, and what gastroenterologists should know to care for affected patients and contribute to extinguishing the pandemic. This is based on: 1) a high incidence (in some reports) of digestive symptoms among infected patients, 1-4 2) expression of Angiotensin Converting Enzyme 2 (ACE2) receptors -the viral target for cellular entry -throughout the digestive system, 1,2 3) presence of viral RNA in the stool of infected patients [1] [2] [3] 5 , and 4) prior experience with the 2003 SARS-coronavirus and the 2012 Middle Eastern Respiratory Syndrome (MERS)-coronavirus, both of which are known to infect and injure the GI tract. Multiple studies have confirmed the presence of SARS-nCoV-2 RNA in the stool of COVID-19 patients, including some who never tested positive in the upper respiratory tract. Digestive Symptoms in COVID-19 Patients with Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes abstract: nan url: https://www.sciencedirect.com/science/article/pii/S154235652030536X?v=s5 doi: 10.1016/j.cgh.2020.04.039 id: cord-350733-0zghspb8 author: Aronson, Jeffrey K. title: The use of mechanistic reasoning in assessing coronavirus interventions date: 2020-07-15 words: 4461.0 sentences: 265.0 pages: flesch: 42.0 cache: ./cache/cord-350733-0zghspb8.txt txt: ./txt/cord-350733-0zghspb8.txt summary: RATIONALE: Evidence‐based medicine (EBM), the dominant approach to assessing the effectiveness of clinical and public health interventions, focuses on the results of association studies. That treatment for hypertension is a risk factor for severe disease in the case of SARS-CoV-2 suggests that altering hypertension treatment might alleviate disease, but the mechanisms are complex, and it is essential to consider and evaluate more than one mechanistic hypothesis (Section 3). This strategy makes much use of evidence from mechanistic studies: evidence that the drug has some action against the novel virus in the laboratory, both in vitro and in vivo in experimental animals, is used to justify the decision to use the treatment clinically. Some evidence, for instance, supports a behavioural mechanism known as the "intention-behaviour gap," 53 In sum, the explicit and systematic assessment of mechanistic studies is essential for the development of effective vaccination programs in a given context. abstract: RATIONALE: Evidence‐based medicine (EBM), the dominant approach to assessing the effectiveness of clinical and public health interventions, focuses on the results of association studies. EBM+ is a development of EBM that systematically considers mechanistic studies alongside association studies. AIMS AND OBJECTIVES: To explore examples of the importance of mechanistic evidence to coronavirus research. METHODS: We have reviewed the mechanistic evidence in four major areas that are relevant to the management of COVID‐19. RESULTS AND CONCLUSIONS: (a) Assessment of combination therapy for MERS highlights the need for systematic assessment of mechanistic evidence. (b) That hypertension is a risk factor for severe disease in the case of SARS‐CoV‐2 suggests that altering hypertension treatment might alleviate disease, but the mechanisms are complex, and it is essential to consider and evaluate multiple mechanistic hypotheses. (c) Confidence that public health interventions will be effective requires a detailed assessment of social and psychological components of the mechanisms of their action, in addition to mechanisms of disease. (d) In particular, if vaccination programmes are to be effective, they must be carefully tailored to the social context; again, mechanistic evidence is crucial. We conclude that coronavirus research is best situated within the EBM+ evaluation framework. url: https://doi.org/10.1111/jep.13438 doi: 10.1111/jep.13438 id: cord-334321-3c10ecgd author: Arora, S. title: Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India date: 2020-06-20 words: 1306.0 sentences: 82.0 pages: flesch: 62.0 cache: ./cache/cord-334321-3c10ecgd.txt txt: ./txt/cord-334321-3c10ecgd.txt summary: Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks. abstract: The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected patients. Earlier reports have suggested that COVID-19 agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 target genes namely S gene, E gene, ORF1ab gene, RdRp gene and N gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks. url: https://doi.org/10.1101/2020.06.18.20135277 doi: 10.1101/2020.06.18.20135277 id: cord-318048-6nvi63rq author: Arshad, Usman title: Prioritisation of Anti‐SARS‐Cov‐2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics date: 2020-05-21 words: 5663.0 sentences: 288.0 pages: flesch: 46.0 cache: ./cache/cord-318048-6nvi63rq.txt txt: ./txt/cord-318048-6nvi63rq.txt summary: An indication of the degree to which candidate drugs are expected to accumulate in lung (a presumed site of primary efficacy and for prevention of SARS-CoV-2 infection) was provided by calculation of unbound Accepted Article lung to plasma tissue partition coefficient (K p U lung ) according to the methodology of Rodgers and Rowland (20-22). All rights reserved Simulated exposure relative to reported anti-SARS-CoV-2 activity in lung and other tissues Lung K p U was simulated for all molecules for which the necessary physicochemical properties and in vitro drug binding information were available. The rank order of lung Cmax/EC 90 ratio was chloroquine > atazanavir (ritonavir boosted) > tipranavir (ritonavir boosted) > hydroxychloroquine > mefloquine > ivermectin > lopinavir (ritonavir boosted) > azithromycin > nitazoxanide > ritonavir > gilteritinib > amodiaquine > imatinib > oxprenolol (data excluded due to this analysis only being possible for 33 of the 56 drugs). abstract: There is a rapidly expanding literature on the in vitro antiviral activity of drugs that may be repurposed for therapy or chemoprophylaxis against SARS‐CoV‐2. However, this has not been accompanied by a comprehensive evaluation of the target plasma and lung concentrations of these drugs following approved dosing in humans. Accordingly, EC(90) values recalculated from in vitro anti‐SARS‐CoV‐2 activity data was expressed as a ratio to the achievable maximum plasma concentrations (Cmax) at an approved dose in humans (Cmax/EC(90) ratio). Only 14 of the 56 analysed drugs achieved a Cmax/EC(90) ratio above 1. A more in‐depth assessment demonstrated that only nitazoxanide, nelfinavir, tipranavir (ritonavir‐boosted) and sulfadoxine achieved plasma concentrations above their reported anti‐SARS‐CoV‐2 activity across their entire approved dosing interval. An unbound lung to plasma tissue partition coefficient (K(p)U(lung)) was also simulated to derive a lung Cmax/EC(50) as a better indicator of potential human efficacy. Hydroxychloroquine, chloroquine, mefloquine, atazanavir (ritonavir‐boosted), tipranavir (ritonavir‐boosted), ivermectin, azithromycin and lopinavir (ritonavir‐boosted) were all predicted to achieve lung concentrations over 10‐fold higher than their reported EC(50). Nitazoxanide and sulfadoxine also exceeded their reported EC(50) by 7.8‐ and 1.5‐fold in lung, respectively. This analysis may be used to select potential candidates for further clinical testing, while deprioritising compounds unlikely to attain target concentrations for antiviral activity. Future studies should focus on EC(90) values and discuss findings in the context of achievable exposures in humans, especially within target compartments such as the lung, in order to maximise the potential for success of proposed human clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32438446/ doi: 10.1002/cpt.1909 id: cord-276345-xsjh3766 author: Arshad, Yasir title: Detection of SARS-CoV-2 in ophthalmic secretions in Pakistan: A preliminary report date: 2020-08-25 words: 667.0 sentences: 54.0 pages: flesch: 62.0 cache: ./cache/cord-276345-xsjh3766.txt txt: ./txt/cord-276345-xsjh3766.txt summary: All 35 oropharyngeal swab samples were detected positive for SARS CoV-2, however out of total 35 conjunctival swab samples, 3(8.5%) were detected positive by using real-time RT-PCR. There was no ocular manifestation observed among patients with positive conjunctival specimens and similar information has already been reported by the previous study [4] . Results of the present study support the evidence that ophthalmic secretions may not be the main source of transmission for the novel SARS-CoV-2, but the role of eye in the transmission of this highly contagious virus must not be ignored. In 2004, SARScoronavirus was detected from tear samples in 37.5% positive cases and in another study, positivity of SARS-CoV-2 from conjunctival swabs was 16.6% which contributed to the evidence of eye as a carrier [6, 7] . SARS-CoV-2 in the ocular surface of COVID-19 patients. New evidence of SARS-CoV-2 transmission through the ocular surface. Evaluation of ocular symptoms and tropism of SARS-CoV-2 in patients confirmed with COVID-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32853603/ doi: 10.1016/j.jinf.2020.08.035 id: cord-352849-vd62r8qu author: Artesi, M. title: Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome date: 2020-05-03 words: 2825.0 sentences: 177.0 pages: flesch: 61.0 cache: ./cache/cord-352849-vd62r8qu.txt txt: ./txt/cord-352849-vd62r8qu.txt summary: Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals, while also clearing essential staff to continue work. At the current time a number of RT-PCR tests have been developed to identify SARS-CoV-2, targeting multiple regions in the viral genome. Out of the 186 SARS-CoV-2 genomes we have sequenced, only these four samples carry a SNP at position 26340. Vogels et al [17] also identified this 3 base change as well as other SNPs in primer/probe binding sites from a number of RT-PCR assays for SARS-CoV-2. The cobas® E-gene assay may use an alternate primer probe combination that is more sensitive to the presence of the SNP, alternatively it may target the same positions as the Corman et al. . https://doi.org/10.1101/2020.04.28.20083337 doi: medRxiv preprint However, our ability to show that each individual carries a genetically identical virus demonstrates the potential whole genome sequencing has for tracking chains of transmission. abstract: Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals, while also clearing essential staff to continue work. At the current time a number of RT-PCR tests have been developed to identify SARS-CoV-2, targeting multiple regions in the viral genome. In comparison to other RNA viruses the mutation rate of SARS-CoV-2 is moderate, however given the large number of transmission chains it is prudent to monitor circulating viruses for mutations that might compromise these tests. Here we report the identification of a C-to-T transition at position 26340 of the SARS-CoV-2 genome which is associated with failure of the cobas(R) SARS-CoV-2 E-gene assay. This variant was detected in four health care workers from the same team. Whole genome sequencing of SARS-CoV-2 showed all four to carry genetically identical viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently on three occasions. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of SNPs which might adversely affect the RT-PCRs used in diagnostics. Additionally, it argues that two regions in the SARS-CoV-2 should be targeted in RT-PCRs to avoid false negatives. url: https://doi.org/10.1101/2020.04.28.20083337 doi: 10.1101/2020.04.28.20083337 id: cord-324531-lpoelp91 author: Artesi, Maria title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date: 2020-09-22 words: 2882.0 sentences: 185.0 pages: flesch: 61.0 cache: ./cache/cord-324531-lpoelp91.txt txt: ./txt/cord-324531-lpoelp91.txt summary: title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. The cobas system (Roche) implements a dual-target assay to detect SARS-CoV-2, with qRT-PCRs targeting both the ORF1ab region and the E gene (see Fig. S1 in the supplemental material). We speculated that these samples carried a common variant that interfered with the E gene qRT-PCR and carried out whole-genome sequencing of the viruses using the Artic Network protocol (17) . abstract: Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. As the cobas SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called SARS-CoV-2 positive. Whole-genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of single-nucleotide polymorphisms that might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives. url: https://www.ncbi.nlm.nih.gov/pubmed/32690547/ doi: 10.1128/jcm.01598-20 id: cord-336364-2ust3qoq author: Artigas, Laura title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 words: 5858.0 sentences: 295.0 pages: flesch: 45.0 cache: ./cache/cord-336364-2ust3qoq.txt txt: ./txt/cord-336364-2ust3qoq.txt summary: title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). abstract: From January 2020, COVID-19 is spreading around the world producing serious respiratory symptoms in infected patients that in some cases can be complicated by the severe acute respiratory syndrome, sepsis and septic shock, multiorgan failure, including acute kidney injury and cardiac injury. Cost and time efficient approaches to reduce the burthen of the disease are needed. To find potential COVID-19 treatments among the whole arsenal of existing drugs, we combined system biology and artificial intelligence-based approaches. The drug combination of pirfenidone and melatonin has been identified as a candidate treatment that may contribute to reduce the virus infection. Starting from different drug targets the effect of the drugs converges on human proteins with a known role in SARS-CoV-2 infection cycle. Simultaneously, GUILDify v2.0 web server has been used as an alternative method to corroborate the effect of pirfenidone and melatonin against the infection of SARS-CoV-2. We have also predicted a potential therapeutic effect of the drug combination over the respiratory associated pathology, thus tackling at the same time two important issues in COVID-19. These evidences, together with the fact that from a medical point of view both drugs are considered safe and can be combined with the current standard of care treatments for COVID-19 makes this combination very attractive for treating patients at stage II, non-severe symptomatic patients with the presence of virus and those patients who are at risk of developing severe pulmonary complications. url: https://doi.org/10.1371/journal.pone.0240149 doi: 10.1371/journal.pone.0240149 id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 words: 5286.0 sentences: 294.0 pages: flesch: 59.0 cache: ./cache/cord-257456-15bm9psj.txt txt: ./txt/cord-257456-15bm9psj.txt summary: Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. To further improve the speed of a diagnostic assay, we and others tested using untreated or heat-inactivated samples added directly to one-step RT-PCR master mixes without an RNA extraction step [6, [13] [14] [15] [16] [17] [18] [19] . Prior to COVID-19 emerged as a global pandemic, we have tested the feasibility of circumventing the sample preparation steps by adding a few microliters of the unprocessed sample (in VTM) directly into the RT-qPCR assay master mix targeting InfA, InfB, and RSV. abstract: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe. url: https://www.ncbi.nlm.nih.gov/pubmed/32987722/ doi: 10.3390/diagnostics10100739 id: cord-283109-ka3n9pft author: Arumugam, Arunkumar title: The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date: 2020-04-08 words: 1725.0 sentences: 103.0 pages: flesch: 58.0 cache: ./cache/cord-283109-ka3n9pft.txt txt: ./txt/cord-283109-ka3n9pft.txt summary: Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. Using Inf and RSV clinical specimens, we successfully performed RT-qPCR reactions by simply adding a few microliters of the unprocessed sample in viral transport medium (VTM) directly into the RT-qPCR assay master mix. We next tested whether the RNA from SARS-CoV-2 can be detected by directly spiking samples of the non-replicative recombinant virus particles (SeraCare AccuPlex SARS-CoV-2 reference material) in VTM to master mix without an extraction step. As shown in Fig. 3 , the SARS-CoV-2 RNA from directly spiked samples was successfully detected by the RT-qPCR reaction without a nucleic acid extraction step (N1 target shown). abstract: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection.1–4 It has been used by the Centers for Disease Control and Prevention (CDC) and several other companies in their Emergency Use Authorization (EUA) assays. With many PCR-based molecular assays, an extraction step is routinely used as part of the protocol. This step can take up a significant amount of time and labor, especially if the extraction is performed manually. Long assay time, partly caused by slow sample preparation steps, has created a large backlog when testing patient samples suspected of COVID-19. Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. We have also used this approach to test for the direct detection of SARS-CoV-2 reference materials spiked in VTM. Our data, while preliminary, suggest that using a few microliters of these untreated samples still can lead to sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests and the backlog we currently experience can be reduced drastically. Next, we will confirm our findings using patient samples. url: https://doi.org/10.1101/2020.04.06.028811 doi: 10.1101/2020.04.06.028811 id: cord-351038-k2m6woow author: Arun Krishnan, R. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 words: 2895.0 sentences: 172.0 pages: flesch: 50.0 cache: ./cache/cord-351038-k2m6woow.txt txt: ./txt/cord-351038-k2m6woow.txt summary: Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. The limitation of rRT-PCR to detect COVID-19 past infection and the progress of the disease, increases the importance of serological assays. Currently COVID-19 antigen LFIA test is under development which will offer more sensitive and specific result for COVID-19 diagnosis and will detect the viral antigen in 3 days of infection [22] . have developed an enzyme linked immunosorbent assay for the detection of COVID-19 IgM and IgG antibody from serum sample. The complexity, cost effectiveness and limitations of nucleic acid based diagnostic tools, impetus the innovative development of well standardized, high sensitive, specific and low cost serological assays for COVID-19 diagnosis. Evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). abstract: The novel coronavirus SARS-CoV-2 is the seventh known species of coronavirus, infectious to human beings. The pandemic COVID-19 spread all over the world with an unprecedented spreading rate after its first appearance in Wuhan, China. As a novel viral disease there in no antiviral treatment or vaccine for the COVID-19. At present, the early detection and the quarantine of infected patients are the ways to stop the spreading of the disease. This review will discuss about the current invitro diagnostic methods used worldwide for the early and accurate diagnosis of COVID-19. Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. url: https://doi.org/10.1007/s12291-020-00906-5 doi: 10.1007/s12291-020-00906-5 id: cord-353742-k4gxww2c author: Arévalo, AP title: Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date: 2020-11-02 words: 721.0 sentences: 66.0 pages: flesch: 48.0 cache: ./cache/cord-353742-k4gxww2c.txt txt: ./txt/cord-353742-k4gxww2c.txt summary: SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases. abstract: SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). BALB/cJ female mice were infected with 6,000 PFU of MHV-A59 (Group Infected; n=20) and immediately treated with one single dose of 500 μg/kg of ivermectin (Group Infected + IVM; n=20), or were not infected and treated with PBS (Control group; n=16). Five days after infection/treatment, mice were euthanized to obtain different tissues to check general health status and infection levels. Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). Furthermore, serum transaminase levels (aspartate aminotransferase and alanine aminotransferase) were significantly lower in treated mice compared to infected animals. In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases. url: https://doi.org/10.1101/2020.11.02.363242 doi: 10.1101/2020.11.02.363242 id: cord-309200-t2xugb8l author: Asadi, Sima title: The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? date: 2020-04-03 words: 2077.0 sentences: 108.0 pages: flesch: 45.0 cache: ./cache/cord-309200-t2xugb8l.txt txt: ./txt/cord-309200-t2xugb8l.txt summary: (2005) established that hospitalized patients infected with SARS during the 2003 epidemic emitted viable aerosolized virus into the air. Recent work on influenza (another viral respiratory disease) has established that viable virus can indeed be emitted from an infected individual by breathing or speaking, without coughing or sneezing (Yan et al. In regard to virology, information is required about the average viral titer in the respiratory fluid and the emitted aerosol particles, as well as the minimum infectious dose for COVID-19 in susceptible individuals. But given the large numbers of expiratory particles known to be emitted during breathing and speech, and given the clearly high transmissibility of COVID-19, a plausible and important hypothesis is that a face-to-face conversation with an asymptomatic infected individual, even if both individuals take care not to touch, might be adequate to transmit Note that the key word in the last sentence was "might." Many urgent questions about aerosol transmission and COVID-19 must be answered. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32308568/ doi: 10.1080/02786826.2020.1749229 id: cord-306819-otabtxin author: Asensio-Samper, JM title: Recomendaciones Prácticas Para El Manejo Del Paciente Con Dolor Crónico Durante La Pandemia De COVID-19 date: 2020-09-02 words: 5168.0 sentences: 491.0 pages: flesch: 52.0 cache: ./cache/cord-306819-otabtxin.txt txt: ./txt/cord-306819-otabtxin.txt summary: Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. En las Unidades de Tratamiento del Dolor, los casos en los que se establece la necesidad de manejo preferente de pacientes en situación de crisis sanitaria, incluyendo pandemia COVID-19, son aquellos casos no subsidiarios de atención mediante telemedicina, es decir, aquellos casos refractarios a tratamiento médico convencional que requieran evaluación clínica especializada y alta probabilidad de realización de procedimiento invasivo para control del dolor, el cual podrá ser realizado en formato de "acto único". abstract: La infección por SARS-CoV-2 ha evolucionado hasta convertirse progresivamente en una pandemia y en una Emergencia de Salud Pública de Importancia Internacional que ha obligado a las organizaciones de salud a nivel mundial, regional y local a adoptar una serie de medidas para hacer frente al COVID-19 e intentar disminuir su impacto, no sólo en el ámbito social sino también en el ámbito sanitario, modificándose las pautas de actuación en los servicios de salud. Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. Se recogen en este manuscrito una serie de pautas encaminadas a disminuir el riesgo de infección del personal de salud, otros pacientes y la comunidad. SARS-CoV-2 infection has evolved into a pandemic and a Public Health Emergency of International Importance that has forced health organizations at the global, regional and local levels to adopt a series of measures to address to COVID-19 and try to reduce its impact, not only in the social sphere but also in the health sphere, modifying the guidelines for action in the health services. Within these recommendations that include the Pain Treatment Units, patients with suspected or confirmed SARS-CoV-2 infection may be waiting for medical consult or interventional procedures for the management of chronic pain refractory to other therapies. A series of guidelines aimed at reducing the risk of infection of health personnel, other patients and the community are included in this manuscript. url: https://api.elsevier.com/content/article/pii/S003493562030205X doi: 10.1016/j.redar.2020.08.005 id: cord-218886-lqme2j8n author: Asghari, Aref title: Fast Accurate Point of Care COVID-19 Pandemic Diagnosis Enabled Through Advanced Lab-on-a-Chip Optical Biosensors: Opportunities and Challenges date: 2020-08-01 words: 6422.0 sentences: 287.0 pages: flesch: 46.0 cache: ./cache/cord-218886-lqme2j8n.txt txt: ./txt/cord-218886-lqme2j8n.txt summary: Primarily, an optical biosensor translates the capture of the target analyte in a measurable alteration of a light property, such as refractive index (RI), intensity or resonance shift, through different methods such as resonators and interferometers ( Fig. 2 ). The sensing transduction signals in Optical label-free biosensing platform functions based on miniscule changes in refractive index resulting from the attachment of biomolecules to the immobilized bioreceptors. On the other hand, by simply depositing a gold layer, the device concept can be used for a surface plasmon resonance, which can improve the LOD even further 71 In order to maximize the sensitivity of the waveguide-based biosensor, the speed of light can be reduced even further. Graphene unique electrical properties has also been exploited effectively to develop different transistor based label-free biosensors including COVID-19 detection system 39 (fig 18.a) . abstract: The sudden rise of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic early 2020 throughout the world has called into drastic action measures to do instant detection and reduce the spread rate. The common diagnostics testing methods has been only partially effective in satisfying the booming demand for fast detection methods to contain the further spread. However, the point-of-risk accurate diagnosis of this new emerging viral infection is paramount as simultaneous normal working operation and dealing with symptoms of SARS-CoV-2 can become the norm for years to come. Sensitive cost-effective biosensor with mass production capability is crucial throughout the world until a universal vaccination become available. Optical label-free biosensors can provide a non-invasive, extremely sensitive rapid detection technique up to ~1 fM concentration along with few minutes sensing. These biosensors can be manufactured on a mass-scale (billions) to detect the COVID-19 viral load in nasal, saliva, urinal, and serological samples even if the infected person is asymptotic. Methods investigated here are the most advanced available platforms for biosensing optical devices resulted from the integration of state-of-the-art designs and materials. These approaches are including but not limited to integrated optical devices, plasmonic resonance and also emerging nanomaterial biosensors. The lab-on-a-chip platforms examined here are suitable not only for SARS-CoV-2 spike protein detection but also other contagious virions such as influenza, and middle east respiratory syndrome (MERS). url: https://arxiv.org/pdf/2008.08572v1.pdf doi: nan id: cord-322672-gjph61cq author: Ashok, Vishnu title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis date: 2020-08-25 words: 1816.0 sentences: 123.0 pages: flesch: 52.0 cache: ./cache/cord-322672-gjph61cq.txt txt: ./txt/cord-322672-gjph61cq.txt summary: title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis A few cases of concurrent myocarditis have been reported, but the extent of cardiac complications with the SARS-CoV-2 strain of coronavirus is still largely unknown. Myocarditis and non-specific cardiac arrhythmias have been reported in a few cases of COVID-19, but this is the first reported case of a high-grade atrioventricular conduction block with SARS-CoV-2 infection. 7 In the European Study of the Epidemiology and Treatment of Inflammatory Heart Disease, 18% of the 3055 patients in the study had high-grade arrhythmias including complete heart block. Since the onset of the current pandemic, cases of myocarditis in patients with COVID-19 have been reported. In a case series of 150 patients with COVID-19 conducted in Wuhan City, China, 7% of the reported 68 deaths (5 deaths) were attributed to myocarditis with circulatory failure; however, their pre-morbid cardiac status was unclear. abstract: BACKGROUND: In the ongoing pandemic of COVID-19, respiratory failure has been reported as the main cause of death in those who develop critical illness. A few cases of concurrent myocarditis have been reported, but the extent of cardiac complications with the SARS-CoV-2 strain of coronavirus is still largely unknown. CASE SUMMARY: A 53-year-old man, suspected to have COVID-19 due to a new-onset cough, shortness of breath, and hypoxia, was referred to Cardiology with sudden symptomatic bradycardia. Initial rhythm analysis revealed Type 2 atrioventricular block (Mobitz II). On arrival at the coronary care unit, he was found to be in complete heart block (Type 3). Routine blood tests showed normal electrolytes and renal function, and no elevation in troponin-I levels. Echocardiography showed mild impairment in left ventricular systolic function, with no regional wall motion abnormalities or valvular lesions. He then developed high-degree AV block lasting 6.2 s, prompting the need for an urgent permanent pacemaker implantation. DISCUSSION: Just over a third of patients with myocarditis reportedly develop a rise in cardiac troponin. Clinically suspected myocarditis can occur in the absence of a troponin rise and rarely can cause high-grade bradyarrhythmias. Myocarditis and non-specific cardiac arrhythmias have been reported in a few cases of COVID-19, but this is the first reported case of a high-grade atrioventricular conduction block with SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33089060/ doi: 10.1093/ehjcr/ytaa248 id: cord-271648-m2c5bvuj author: Ashour, Hossam M. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 words: 7536.0 sentences: 401.0 pages: flesch: 56.0 cache: ./cache/cord-271648-m2c5bvuj.txt txt: ./txt/cord-271648-m2c5bvuj.txt summary: Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model abstract: Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. The continuous evolution of coronaviruses was further highlighted with the emergence of the Middle East Respiratory Syndrome-CoV (MERS-CoV) outbreak in 2012. Currently, the world is concerned about the 2019 novel CoV (SARS-CoV-2) that was initially identified in the city of Wuhan, China in December 2019. Patients presented with severe viral pneumonia and respiratory illness. The number of cases has been mounting since then. As of late February 2020, tens of thousands of cases and several thousand deaths have been reported in China alone, in addition to thousands of cases in other countries. Although the fatality rate of SARS-CoV-2 is currently lower than SARS-CoV, the virus seems to be highly contagious based on the number of infected cases to date. In this review, we discuss structure, genome organization, entry of CoVs into target cells, and provide insights into past and present outbreaks. The future of human CoV outbreaks will not only depend on how the viruses will evolve, but will also depend on how we develop efficient prevention and treatment strategies to deal with this continuous threat. url: https://doi.org/10.3390/pathogens9030186 doi: 10.3390/pathogens9030186 id: cord-326305-mjd5agvf author: Ashraf, Mohammad Ali title: The application of direct viral cytopathic hypothesis to design drug trials in the battle against COVID-19 date: 2020-08-15 words: 1109.0 sentences: 68.0 pages: flesch: 44.0 cache: ./cache/cord-326305-mjd5agvf.txt txt: ./txt/cord-326305-mjd5agvf.txt summary: As previously shown, clathrin-mediated endocytosis is the main pathway for virus entry, while doublemembrane vesicles formation and autophagy in the host cell is the mechanism for viral replication [14] . Imatinib, a protein-tyrosine kinase inhibitor that inhibits the BCR-ABL tyrosine kinase which is approved to treat chronic myeloid leukemia by inhibiting ABL oncogenetic pathway has previously shown success in disrupting the viral entry mechanism of both SARS-CoVand MERS-CoV into the cell; hence, it can also be considered as a potentially useful drug to treat patients with severe forms of COVID-19. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor abstract: COVID-19 has caused many deaths worldwide. Systemic complications alongside coagulopathy, and ARDS account for the majority of COVID-19 mortalities. The pathogenesis of the disease can be explained by two theories of direct viral cytopathy and systemic inflammatory cascade of events. ACE-2 is shown to be the cellular host receptor for SARS-CoV-2. It might be the key to explain the pathogenesis of systemic complications with a focus on the direct viral cytopathic hypothesis. Different medications tend to show up in many in vitro drug screens. However, more trials are needed to translate their application into in vivo efficacy. url: https://www.ncbi.nlm.nih.gov/pubmed/32803688/ doi: 10.1007/s40199-020-00368-3 id: cord-255883-mz6nyisw author: Asif, Muhammad title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date: 2020-08-14 words: 5273.0 sentences: 283.0 pages: flesch: 44.0 cache: ./cache/cord-255883-mz6nyisw.txt txt: ./txt/cord-255883-mz6nyisw.txt summary: Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. An in vitro study conducted by Hoffmann and colleagues revealed that SARC-CoV-2 depends on cellular serine protease (TMPRSS2) for S proteins priming which are known to interact with human ACE2 receptors in the lungs and facilitate entry into the cells. The authors opted the following keywords to find relevant studies: "essential oils", "antiviral", "COVID-19", "SARC-CoV-2", "bronchodilation", "immunomodulatory'''', "anti-inflammatory'''', "corona virus''''. Thus, on the basis of these docking and in vitro studies, it is proposed that garlic essential oils and their isolated constituents, especially DAS, have potential to prevent the entry of virus into host cells as well as to activate molecular antioxidant pathways that decrease the secretions of culprit pro-inflammatory cytokines. Essential oils have long been known to have anti-inflammatory, antioxidant, immunomodulatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2. abstract: Coronavirus disease of 2019 (COVID-19) has emerged as a global health threat. Unfortunately, there are very limited approved drugs available with established efficacy against the SARs-CoV-2 virus and its inflammatory complications. Vaccine development is actively being researched, but it may take over a year to become available to general public. Certain medications, for example, dexamethasone, antimalarials (chloroquine/hydroxychloroquine), antiviral (remdesivir), and IL-6 receptor blocking monoclonal antibodies (tocilizumab), are used in various combinations as off-label medications to treat COVID-19. Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. Owing to their lipophilic nature, EOs are advocated to penetrate viral membranes easily leading to membrane disruption. Moreover, EOs contain multiple active phytochemicals that can act synergistically on multiple stages of viral replication and also induce positive effects on host respiratory system including bronchodilation and mucus lysis. At present, only computer-aided docking and few in vitro studies are available which show anti-SARC-CoV-2 activities of EOs. In this review, role of EOs in the prevention and treatment of COVID-19 is discussed. A discussion on possible side effects associated with EOs as well as anti-corona virus claims made by EOs manufacturers are also highlighted. Based on the current knowledge a chemo-herbal (EOs) combination of the drugs could be a more feasible and effective approach to combat this viral pandemic. [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32803479/ doi: 10.1007/s10787-020-00744-0 id: cord-268468-036i1082 author: Asif, Muhammad title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 words: 3204.0 sentences: 189.0 pages: flesch: 43.0 cache: ./cache/cord-268468-036i1082.txt txt: ./txt/cord-268468-036i1082.txt summary: In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. In this outbreak, three different types of diagnosis tests are being used including (i) chest CT scan along with clinical indications, (ii) RNA detection using RT-PCR assay and (iii) lateral flow assays, full automatic chemiluminescence method, enzyme-linked immunosorbent assay (ELISA) for the determination of antibodies [5] . In this review, we have summarized the biosensor based technologies which are able to detect SARS-CoV-2 effectively. The peptide monolayer was successfully coated on SPR biosensor and further functionalized with virus nucleocapsid protein which was finally able to detect SARS-CoV-2 antibodies at nanomolar level. The sensing aptitude of the biosensor was evaluated employing antigen protein, self-cultured virus, and nasopharyngeal swab samples taken from people infected with COVID-19 pneumonia. abstract: Herein, we have summarized and argued about biomarkers and indicators used for the detection of SARS-CoV-2. Antibody detection methods are not considered suitable to screen individuals at early stages and asymptomatic cases. The diagnosis of COVID-19 using biomarkers and indicators at point of care level is much crucial. Therefore, it is urgently needed to develop rapid and sensitive detection methods which can target antigens. We have critically elaborated key role of biosensors to cope the outbreak situation. In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. Finally, we have outlined pros and cons of diagnostic approaches as-well-as future directions. url: https://www.ncbi.nlm.nih.gov/pubmed/32984642/ doi: 10.1016/j.coelec.2020.08.011 id: cord-317429-pp6hb4q5 author: Aslam, Saima title: COVID-19: Yet another coronavirus challenge in transplantation date: 2020-03-14 words: 1405.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-317429-pp6hb4q5.txt txt: ./txt/cord-317429-pp6hb4q5.txt summary: A novel coronavirus, severe acute respiratory syndrome −coronavirus-2 (SARS-CoV-2), causing a severe acute respiratory syndrome with its disease designated as COVID-19, emerged from its epicenter in Wuhan, China, in December 2019 and is now a global pandemic. 7 report on the presentation and outcome of 2 microbiologically confirmed COVID-19 cases in heart transplantation detected in the Hubei Province in China. These 2 patients apparently were part of a community of at least 200 heart transplant survivors in that region and presented with variable severity of disease (one mild and another with more severe manifestations requiring a prolonged hospitalization); however, both survived the event. It is important to note that the clinical presentations were not distinct from those described in non-immunosuppressed individuals, and the patient with severe disease presented with a viral prodrome, displayed the typical findings on CT scan imaging, and progressed to clinical hypoxia. In summary, the novel coronavirus and its disease, COVID-19, require thoughtful approaches for the prevention, mitigation, timely detection, and appropriate therapeutic intervention for our vulnerable patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32253113/ doi: 10.1016/j.healun.2020.03.007 id: cord-323148-rsjocuh3 author: Assaad, Souad title: Risk of death of cancer patients presenting with severe symptoms of infection, with or without documented COVID-19 date: 2020-09-06 words: 1035.0 sentences: 54.0 pages: flesch: 57.0 cache: ./cache/cord-323148-rsjocuh3.txt txt: ./txt/cord-323148-rsjocuh3.txt summary: The striking observation of our series is the high risk of death (actuarial survival close to 20% at day 28) of cancer patients who did not demonstrate detectable SARS-COV-2 using the standard Cobas test. The high death rates of RT-PCR negative cancer patients observed in our series may result from a sensitivity of SARS-COV-2 diagnostic assays (false negativity), and also other undocumented infections in the context of patients with a progressive cancer. From these different series and works, it can be concluded that cancer patients under active treatment are at high risk of lethal complications when presenting with symptoms resembling those of COVID -19 and requiring hospitalisation even in the absence of documented SARS-COV-2 infection. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR The impact of the COVID-19 pandemic on cancer deaths due to delays in diagnosis in England, UK: a national, population-based, modelling study abstract: nan url: https://doi.org/10.1016/j.ejca.2020.08.018 doi: 10.1016/j.ejca.2020.08.018 id: cord-256508-ce59ovan author: Asselah, Tarik title: COVID-19: discovery, diagnostics and drug development date: 2020-10-08 words: 9214.0 sentences: 556.0 pages: flesch: 46.0 cache: ./cache/cord-256508-ce59ovan.txt txt: ./txt/cord-256508-ce59ovan.txt summary: To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals abstract: An epidemic of acute respiratory syndrome (Covid-19) started in humans in Wuhan in 2019, and became a pandemic. Groups from China Identified and sequenced the virus responsible for COVID-19, named SARS-CoV-2, and determined that it was a novel coronavirus (CoV) that shared high sequence identity with bat- and pangolin-derived SARS-like CoVs, suggesting a zoonotic origin. SARS-CoV-2 is a member of Coronaviridae, a family of enveloped, positive-sense, single-stranded RNA viruses that infect a broad range of vertebrates. The rapid release of the sequence of the virus has allowed the development of diagnostic tools (e.g., RT-PCR). Additionally, serological tests can allow identification of persons who have been infected. In humans, CoVs tend to cause mild to moderate upper respiratory tract infections. The fatality rate is around 1-3% for infected persons. An acute respiratory distress syndrome (ARDS) likely due to an uncontrolled immune activation (“cytokine storm”) occurs in patients with severe disease and poor prognosis. Risk factors for mortality include: advanced age, obesity, diabetes, hypertension and other comorbidities. Drug repurposing has been used to rapidly identify potential treatment for COVID-19, which could move quickly to phase-3. Better knowledge of the virus, its enzymes, will be mandatory to develop more potent and specific direct-acting antiviral agents (DAA). In the long term, a vaccine to prevent infection would be crucial; however even if successful it might not be available before 2021-22. To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The aim of this review is to provide insights on the discovery of SARS-CoV-2, its virology, the diagnostic tools, and the ongoing drug discovery effort. url: https://www.sciencedirect.com/science/article/pii/S0168827820336758?v=s5 doi: 10.1016/j.jhep.2020.09.031 id: cord-338689-4u1ezk64 author: Ata, Fateen title: COVID-19 presenting with diarrhoea and hyponatraemia date: 2020-06-07 words: 1405.0 sentences: 124.0 pages: flesch: 52.0 cache: ./cache/cord-338689-4u1ezk64.txt txt: ./txt/cord-338689-4u1ezk64.txt summary: We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. COVID-19 is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ► We recommend studies to evaluate the effectiveness of stool PCR for severe acute respiratory syndrome coronavirus 2 if initial nasopharyngeal PCR is negative and suspicion remains high. 4 Gastrointestinal symptoms such as diarrhoea, abdominal pain and vomiting have been previously seen with acute viral respiratory infections and reported recently as rare manifestations of COVID-19. 15 Our patient had acute hyponatraemia, abdominal pain and diarrhoea with minimal Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical and virological factors associated with gastrointestinal symptoms in patients with acute respiratory infection: a two-year prospective study in general practice medicine abstract: COVID-19 is a viral disease with a high infectivity rate. The full spectrum of the disease is not yet understood. This understanding may help in limiting potential exposure. We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32513768/ doi: 10.1136/bcr-2020-235456 id: cord-268140-s5lailkp author: Atal, Shubham title: IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising Therapy? date: 2020-06-13 words: 5174.0 sentences: 258.0 pages: flesch: 41.0 cache: ./cache/cord-268140-s5lailkp.txt txt: ./txt/cord-268140-s5lailkp.txt summary: Considering the proven role of cytokine dysregulation in causing this hyperinflammation in the lungs with IL-6 being a key driver, particularly in seriously ill COVID-19 patients, it is crucial to further explore selective cytokine blockade with drugs like the IL-6 inhibitors tocilizumab, sarilumab, and siltuximab. Considering the proven role of cytokine dysregulation in serious COVID-19 and interleukin (IL)-6 being the key driver of this hyperinflammation, which can cause multi-organ failure, a series of clinical trials with IL-6 inhibitors like tocilizumab, sarilumab and siltuximab are underway. Another Italian Phase II open-label trial (NCT04315480) with tocilizumab 8 mg/kg single dose is being conducted in patients with severe multifocal interstitial pneumonia due to COVID-19 to evaluate its role in the virus-induced cytokine storm, in blocking deterioration of lung function or even promoting a rapid improvement of clinical conditions, preventing naso-tracheal intubation and/or death [51] . abstract: At present, there are no proven agents for treatment of coronavirus disease (COVID-19). The available evidence has not allowed guidelines to clearly recommend any drugs outside the context of clinical trials. The novel coronavirus SARS-CoV-2 that causes COVID-19 invokes a hyperinflammatory state driven by multiple cells and mediators like interleukin (IL)-1, IL-6, IL-12, and IL-18, tumor necrosis factor alpha (TNFα), etc. Considering the proven role of cytokine dysregulation in causing this hyperinflammation in the lungs with IL-6 being a key driver, particularly in seriously ill COVID-19 patients, it is crucial to further explore selective cytokine blockade with drugs like the IL-6 inhibitors tocilizumab, sarilumab, and siltuximab. These targeted monoclonal antibodies can dampen the downstream IL-6 signaling pathways, which can lead to decreased cell proliferation, differentiation, oxidative stress, exudation, and improve clinical outcomes in patients with evident features of cytokine-driven inflammation like persistent fever, dyspnea and elevated markers. Preliminary evidence has come for tocilizumab from some small studies, and interim analysis of a randomized controlled trial; the latter also being available for sarilumab. International guidelines do include IL-6 inhibitors as one of the options available for severe or critically ill patients. There has been increased interest in evaluating these drugs with a series of clinical trials being registered and conducted in different countries. The level of investigation though perhaps needs to be further intensified as there is a need to focus on therapeutic options that can prove to be ‘life-saving’ as the number of COVID-19 fatalities worldwide keeps increasing alarmingly. IL-6 inhibitors could be one such treatment option, with generation of more evidence and completion of a larger number of systematic studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32535732/ doi: 10.1007/s40290-020-00342-z id: cord-295431-p9iy7uaf author: Atangana, Ernestine title: Facemasks simple but powerful weapons to protect against COVID-19 spread: Can they have sides effects? date: 2020-09-30 words: 9778.0 sentences: 441.0 pages: flesch: 53.0 cache: ./cache/cord-295431-p9iy7uaf.txt txt: ./txt/cord-295431-p9iy7uaf.txt summary: Climatic factors including climate temperature, humidity, wind speed have played some crucial role in respect to the transition of the ongoing pandemic COVID-19, caused by the severe acute respiratory syndrome coronavirus2 (SARS-COV-2) and patient''s recovery and the death rate across the globe. With all these results in hand, there is a clear evidence that the wind could be a carrier of droplets containing concentration of COVID-19, while some case studied have been done for indoor and outdoor exposure with a wind speed of 2km/h, no mathematical model has been suggested to see in general how far such droplets could be transported. It was also observed that the transport followed a crossover behaviour, where during the first period, the transport followed a fading memory process but later a power law behaviour, with no steady state, this was very interesting as this shows that, when the COVID-19 infected person sneezed there were no wind effect, thus concentration released in the air with initial speed was able to spread like in the results described in [66] see Figure 8 below. abstract: In the last few months, the spread of COVID-19 among humans has caused serious damages around the globe letting many countries economically unstable. Results obtained from conducted research by epidemiologists and virologists showed that, COVID-19 is mainly spread from symptomatic individuals to others who are in close contact via respiratory droplets, mouth and nose, which are the primary mode of transmission. World health organization regulations to help stop the spread of this deadly virus, indicated that, it is compulsory to utilize respiratory protective devices such as facemasks in the public. Indeed, the use of these facemasks around the globe has helped reduce the spread of COVID-19. The primary aim of facemasks, is to avoid inhaling air that could contain droplets with COVID-19. We should note that, respiration process is the movement of oxygen from external atmosphere to the cells within tissue and the transport of carbon dioxide outside. However, the rebreathing of carbon dioxide using a facemask has not been taken into consideration. The hypercapnia (excess inhaled content of CO(2)) has been recognized to be related to symptoms of fatigue, discomfort, muscular weakness, headaches as well as drowsiness. Rebreathing of CO(2) has been a key to concern regarding the use of a facemask. Rebreathing usually occur when an expired air that is rich in CO(2) stays long than normal in the breathing space of the respirator after a breath. The increase of the arterial CO(2) concentration leads to symptoms that are aforementioned. Studies have been conducted on facemask shortages and on the appropriate facemask required to reduce the spread of COVID-19; however no study has been conducted to assess the possible relationship between CO(2) inhalation due to facemask, to determine and recommend which mask is appropriate in the reduction of the spread of the coronavirus while simultaneously avoid CO(2) inhalation by the facemask users. In the current paper, we provided a literature review on the use of facemasks with the aim to determine which facemasks could be used to avoid re-inhaling rejected CO(2). Additionally, we presented mathematical models depicting the transport of COVID-19 spread through wind with high speed. We considered first mathematical models for which the effect air-heterogeneity is neglected, such that air flow follows Markovian process with a retardation factor, these models considered two different scenarios, the speed of wind is constant and time-space dependent. Secondly, we assumed that the wind movement could follow different processes, including the power law process, fading memory process and a two-stage processes, these lead us to use differential operators with power law, exponential decay and the generalized Mittag-Leffler function with the aim to capture these processes. A numerical technique based on the Lagrange polynomial interpolation was used to solve some of these models numerically. The numerical solutions were coded in MATLAB software for simulations. The results obtained from the mathematical simulation showed that a wind with speed of 100km/h could transport droplets as far as 300 meters. The results obtained from these simulations together with those presented by other researchers lead us to conclude that, the wind could have helped spread COVID-19 in some places around the world, especially in coastal areas. Therefore, appropriate facemasks that could help avoid re-inhaling enough CO(2) should be used every time one is in open air even when alone especially in windy environment. url: https://doi.org/10.1016/j.rinp.2020.103425 doi: 10.1016/j.rinp.2020.103425 id: cord-323131-l726qv1g author: Atogebania, Julius Wedam title: An Invited Commentary on ‘ Evidence Based Management Guideline for the COVID-19 Pandemic- Review article’ date: 2020-04-23 words: 943.0 sentences: 65.0 pages: flesch: 51.0 cache: ./cache/cord-323131-l726qv1g.txt txt: ./txt/cord-323131-l726qv1g.txt summary: COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. AUTHOR SUMMARY: To date over one(1) million persons have been affected indicating exponential spread of the disease and more rigorous implementation and adherence to more strengthen restrictions of social distancing would mitigate the spread of the pandemic disease and may prove to be even tedious. Abstract COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. COVID-19 has recently been declared a pandemic by WHO • Increased cases globally have highlighted the need for updated management guidelines • Currently, supportive management is the first-line treatment • New medical therapies are currently in phase 1 and 2 trials • Invited Commentary'' Evidence abstract: COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. In this paper, the prime motive is to enlighten the key variables to the public on the pandemic and essential key points to note and practice in accordance to standard regulation to curb the aggressive COVID-19 pandemic. AUTHOR SUMMARY: To date over one(1) million persons have been affected indicating exponential spread of the disease and more rigorous implementation and adherence to more strengthen restrictions of social distancing would mitigate the spread of the pandemic disease and may prove to be even tedious. url: https://api.elsevier.com/content/article/pii/S1743919120303496 doi: 10.1016/j.ijsu.2020.04.050 id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 words: 7283.0 sentences: 428.0 pages: flesch: 54.0 cache: ./cache/cord-344006-0iq9s94n.txt txt: ./txt/cord-344006-0iq9s94n.txt summary: All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . abstract: The emergence of the SARS‐CoV‐2 strain of the human coronavirus has thrown the world into the midst of a new pandemic. In the human body, the virus causes COVID‐19, a disease characterized by shortness of breath, fever, and pneumonia, which can be fatal in vulnerable individuals. SARS‐CoV‐2 has characteristics of past human coronaviruses, with close genomic similarities to SARS‐CoV, the virus that causes the disease SARS. Like these related coronaviruses, SARS‐CoV‐2 is transmitted through the inhalation of droplets and interaction with contaminated surfaces. Across the world, laboratories are developing candidate vaccines for the virus – with vaccine trials underway in the US and the United Kingdom ‐ and considering various drugs for possible treatments and prophylaxis. Here, we provide an overview of SARS‐CoV‐2 by analyzing its virology, epidemiology, and modes of transmission while examining the current progress of testing procedures and possible treatments through drugs and vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/32446285/ doi: 10.1111/febs.15375 id: cord-327349-rxb6zfoc author: Au, Lewis title: Cancer, COVID-19, and antiviral immunity: the CAPTURE study date: 2020-09-03 words: 4531.0 sentences: 183.0 pages: flesch: 32.0 cache: ./cache/cord-327349-rxb6zfoc.txt txt: ./txt/cord-327349-rxb6zfoc.txt summary: Inherent perturbations on cell subsets (e.g. lymphoid and myeloid malignancies), or therapy-induced impact on immune states (e.g. immune checkpoint blockade) may provide opportunities to understand contributions of distinct immune compartments and key regulators of the anti-SARS-CoV-2 response. Herein, we aim to provide an overview of knowledge to-date of the clinical features of COVID-19 observed in cancer patients, as well as potential impact of cancer and anti-cancer interventions on the immune response to SARS-CoV-2. However, what has been critically missing in cohort and registry reports to date are data on 1) the true prevalence of SARS-CoV-2 infection in the cancer population, given population screening has not been widely implemented; and 2) the experience of those who remain well (uninfected, asymptomatic or subclinically affected), to determine the drivers of mortality and the absolute risks of severe adverse events within the cancer community as a whole. A longitudinal understanding of the degree to which the immunocompromised states of cancer patients impact infection, viral clearance, clinical course of COVID-19, and subsequent generation of long-term immunity is needed. abstract: The SARS-CoV-2 pandemic has posed a significant challenge for risk evaluation and mitigation amongst cancer patients. Susceptibility to and severity of COVID-19 in cancer patients has not been studied in a prospective and broadly applicable manner. CAPTURE is a pan-cancer, longitudinal immune profiling study designed to address this knowledge gap. url: https://api.elsevier.com/content/article/pii/S0092867420311466 doi: 10.1016/j.cell.2020.09.005 id: cord-256075-fudeaq7y author: Audo, Andrea title: Acute Pulmonary Embolism in SARS-CoV-2 Infection Treated with Surgical Embolectomy date: 2020-04-28 words: 752.0 sentences: 40.0 pages: flesch: 37.0 cache: ./cache/cord-256075-fudeaq7y.txt txt: ./txt/cord-256075-fudeaq7y.txt summary: We report the first case of SARS-CoV-2 complicated by massive pulmonary embolism underwent successfully surgical embolectomy. We believe that maintaining the same pro-active attitude suggested by current Guidelines might help in reducing morality and improving survival in SARS-COV-2/patients. SARS-CoV-2 infected patients usually experience fever, dry cough, fatigue and worsening dyspnoea with interstitial pneumonia that in up to 3-5% might unfortunately evolve in a severe acute respiratory distress syndrome (ARDS) requiring endotracheal intubation (ETI) and mechanical ventilation. Due to the severe ARDS unresponsive to assisted non-invasive ventilation the patient underwent ETI and was transferred to an isolation ward of the intensive care unit (ICU); the infection of SARS-CoV-2 virus was confirmed thereafter by an RT-PCR assay of a nasal swab. We are now facing this unexpected severe SARS-CoV-2 pandemic, but maintaining the same proactive attitude suggested by current Guidelines or routine standard of care might help in reducing morality rate and improving survival also in SARS-CoV-2 infected patients. abstract: Abstract A cluster of pneumonia cases caused by the novel SARS-CoV-2 has spread rapidly throughout China, Europe and USA. The pneumonia might evolve in ARDS requiring assisted mechanical-ventilation. The prolonged immobilization combined with respiratory failure, sepsis and dehydration might expose SARS-CoV-2/patients to increased risk of complication including pulmonary embolism. We report the first case of SARS-CoV-2 complicated by massive pulmonary embolism underwent successfully surgical embolectomy. We believe that maintaining the same pro-active attitude suggested by current Guidelines might help in reducing morality and improving survival in SARS-COV-2/patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32360384/ doi: 10.1016/j.athoracsur.2020.04.013 id: cord-268034-7id7sfsu author: Auerswald, Heidi title: Assessment of Inactivation Procedures for SARS-CoV-2 date: 2020-05-28 words: 1620.0 sentences: 100.0 pages: flesch: 47.0 cache: ./cache/cord-268034-7id7sfsu.txt txt: ./txt/cord-268034-7id7sfsu.txt summary: This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10. The buffers used in this lysis step yield varying results [11, 13, 15, 16] ; however, unlike 224 previous studies [11] , this study found that AVL buffer alone was successfully able to fully 225 inactivate up to 5 log10 of virus from three different primary isolates of SARS-CoV-2. Previous 234 studies have shown that GITC-lysis buffers are able to inactivate SARS-CoV-2 samples [11, 12] ; 235 however, the addition of Triton-X may be necessary for complete inactivation [11] . Therefore, formaldehyde treatment does not appear to be a 247 solution for increased molecular SARS-CoV-2 testing; however, it does remain a viable alternative 248 for sample inactivation or disinfection. abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease 2019 (COVID-19), presents a challenge to laboratorians and healthcare workers around the world. Handling of biological samples from individuals infected with the SARS-CoV-2 virus requires strict biosafety and biosecurity measures. Within the laboratory, non-propagative work with samples containing the virus requires, at minimum, Biosafety Level-2 (BSL-2) techniques and facilities. Therefore, handling of SARS-CoV-2 samples remains a major concern in areas and conditions where biosafety and biosecurity for specimen handling is difficult to maintain, such as in rural laboratories or austere field testing sites. Inactivation through physical or chemical means can reduce the risk of handling live virus and increase testing ability worldwide. Herein we assess several chemical and physical inactivation techniques employed against SARS-CoV-2 isolates from Cambodian COVID-19 patients. This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10. url: https://doi.org/10.1101/2020.05.28.120444 doi: 10.1101/2020.05.28.120444 id: cord-300791-417tzufc author: Austin, Zubin title: Pharmacy practice in times of civil crisis: The experience of SARS and “the blackout” in Ontario, Canada date: 2007-10-16 words: 6544.0 sentences: 398.0 pages: flesch: 65.0 cache: ./cache/cord-300791-417tzufc.txt txt: ./txt/cord-300791-417tzufc.txt summary: OBJECTIVES: The objectives were to describe and analyze the impact of 2 major crises (the severe acute respiratory syndrome [SARS] outbreak, and the electrical system failure ["blackout"]) on pharmacy practice and pharmacists in Toronto, Canada. RESULTS: Five key themes emerged from this research: (1) during times of crisis, pharmacies become frontline health care facilities, (2) a vacuity of leadership/lack of utility of emergency preparedness guidelines and policies, (3) role of and reliance on experience and professional judgment, (4) importance of documentation, and (5) the importance of "teamness" in enabling successful adaptation during times of crisis. In order to participate in this study, pharmacists were required to have been practicing as a pharmacist in a direct patient-care setting in Toronto for at least 25 h/wk during March 2003 to June 2003 (SARS) and August 2004 (blackout). abstract: BACKGROUND: Crises affecting civilian infrastructure (including electricity supply, clean water, and access to institutional health services) may have an effect on the delivery of pharmacy services in the community. OBJECTIVES: The objectives were to describe and analyze the impact of 2 major crises (the severe acute respiratory syndrome [SARS] outbreak, and the electrical system failure [“blackout”]) on pharmacy practice and pharmacists in Toronto, Canada. METHODS: An exploratory, qualitative study was undertaken. Pharmacists were recruited, provided informed consent, and were interviewed. Data from transcripts were coded and categorized to identify themes related to adaptive strategies undertaken by pharmacists during times of civil crisis. RESULTS: Five key themes emerged from this research: (1) during times of crisis, pharmacies become frontline health care facilities, (2) a vacuity of leadership/lack of utility of emergency preparedness guidelines and policies, (3) role of and reliance on experience and professional judgment, (4) importance of documentation, and (5) the importance of “teamness” in enabling successful adaptation during times of crisis. CONCLUSIONS: Emergencies and civil crises will continue to occur. Findings of this study include the importance of effective documentation systems and teamwork practices, as well as confident reliance on professional judgment and experience, as determinants of successful adaptation to civil crises. url: https://api.elsevier.com/content/article/pii/S1551741106000970 doi: 10.1016/j.sapharm.2006.09.001 id: cord-276147-30buoweg author: Avancini, Joao title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil date: 2020-09-15 words: 278.0 sentences: 25.0 pages: flesch: 61.0 cache: ./cache/cord-276147-30buoweg.txt txt: ./txt/cord-276147-30buoweg.txt summary: authors: Avancini, Joao; Miyamoto, Denise; Arnone, Marcelo; Villas-Boas Gabbi, Tatiana; Ferreira, Paula Silva; Neta, Cyro Festa; Sanches, Jose Antonio title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil cord_uid: 30buoweg Contents of the manuscript have not been previously published and are not currently submitted elsewhere. All listed authors have seen and approved of the manuscript and will sign off on any subsequent manuscript revisions. To the editor: We read with interest the letters from the New York City report regarding the absence of COVID toes lesions on their patients and the recommendation of caution when concluding that cutaneous findings are specifically due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cutaneous manifestations in patients with COVID-19: a preliminary review of an emerging issue Classification of the cutaneous manifestations of COVID-19: a rapid prospective nationwide consensus study in Spain with 375 cases abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32946969/ doi: 10.1016/j.jaad.2020.09.030 id: cord-299346-f13xly6q author: Awad, Mohamed E. title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic date: 2020-04-10 words: 4216.0 sentences: 254.0 pages: flesch: 42.0 cache: ./cache/cord-299346-f13xly6q.txt txt: ./txt/cord-299346-f13xly6q.txt summary: title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic To reduce the occupational risk in treating suspected or confirmed COVID-19 urgent orthopaedic patients, recommended precautions and preventive actions (triage area, ED consultation room, induction room, operating room, and recovery room) are reviewed. HCPs in high-risk areas should adhere to infection prevention and control practices, which includes the appropriate use of engineering controls (negative pressure rooms), administrative controls, and personal protective equipment (PPE) ( 6 Per CDC recommendations, a clinically suspected/ confirmed COVID-19 patient should wear a cloth face covering, over nose, and mouth and a surgical mask should be reserved for HCP and first responders. It is recommended for an environmental services worker to increase the Flowchart demonstrating the the recommended use of personal protective equipment for different activities at various settings managing suspected/clinically Coronavirus disease 2019 patients. abstract: By April 7, 2020, severe acute respiratory syndrome coronavirus 2 was responsible for 1,383,436 confirmed cases of Coronavirus disease 2019 (COVID-19), involving 209 countries around the world; 378,881 cases have been confirmed in the United States. During this pandemic, the urgent surgical requirements will not stop. As an example, the most recent Centers of Disease Control and Prevention reports estimate that there are 2.8 million trauma patients hospitalized in the United States. These data illustrate an increase in the likelihood of encountering urgent surgical patients with either clinically suspected or confirmed COVID-19 in the near future. Preparation for a pandemic involves considering the different levels in the hierarchy of controls and the different phases of the pandemic. Apart from the fact that this pandemic certainly involves many important health, economic, and community ramifications, it also requires several initiatives to mandate what measures are most appropriate to prepare for mitigating the occupational risks. This article provides evidence-based recommendations and measures for the appropriate personal protective equipment for different clinical and surgical activities in various settings. To reduce the occupational risk in treating suspected or confirmed COVID-19 urgent orthopaedic patients, recommended precautions and preventive actions (triage area, ED consultation room, induction room, operating room, and recovery room) are reviewed. url: https://www.ncbi.nlm.nih.gov/pubmed/32282441/ doi: 10.5435/jaaos-d-20-00227 id: cord-343082-46lo7xtx author: Awasthi, Ankit title: OUTBREAK of novel corona virus disease (COVID-19): Antecedence and aftermath date: 2020-07-25 words: 3945.0 sentences: 225.0 pages: flesch: 46.0 cache: ./cache/cord-343082-46lo7xtx.txt txt: ./txt/cord-343082-46lo7xtx.txt summary: Studies also confirm that flu shots are not efficient in the fight against COVID-19 as the patients continue to suffer despite the treatment (https://www.wsj.com/articles/gilead-sciences-offers-experimental-drug-for-coronavirustreatments-testing-11580511519).In the meantime, Thai health officials claimed to have successfully handled the infection with acocktail of antiviral drugs that include lopinavir and ritonavir under the name "Kaetra" along with flu medication oseltamivir. In 2016, this drug was used as an emergency aid for the Ebola virus outbreak.A clinical trial involving 80 participants (in Shenzhen city) demonstrated chest symptoms improvement in patients of COVID-19 treated with favipiravir. Favipiravirhas been reported to be effective, without any obvious side-effects, in helping coronavirus patients recover.In another study carried out in China, two mild and two severe COVID-19 associated pneumonia patients were treated with combined Western and Chinese medicine treatment (Lopinavir/ritonavir/arbidol/ShufengJiedu Capsule). In recent clinical studies the use of steroidal drug Dexamethasone has been very effective to treat patients suffering from COVID-19. abstract: Outbreak of Coronavirus disease 2019 (COVID-19) started in mid of December 2019 and spread very rapidly across the globe within a month of its outbreak. Researchers all across the globe started working to find out its possible treatments. However, most of initiatives taken were based on various hypotheses and till date no successful treatments have been achieved. Some strategies adopted by China where existing antiviral therapy was initially used to treat COVID-19 have not given very successful results. Researchers from Thailand explored the use of combination of anti-influenza drugs such as Oseltamivir, Lopinavir and Ritonavir to treat it. In some cases, combination therapy of antiviral drugs with chloroquine showed better action against COVID-19. Some of the clinical studies showed very good effect of chloroquine and hydroxychloroquine against COVID-19, however, they were not recommended due to serious clinical toxicity. In some cases, use of rho kinase inhibitor, fasudil was found very effective.In some of the countries, antibody-based therapies have proved fairly successful. The use of BCG vaccines came in light; however, they were not found successful due to lack of full-proof mechanistic studies. In Israel as well as in other developed countries, pluristems allogeneic placental expanded cell therapy has been found successful. Some phytochemicals and nutraceuticals have also been explored to treat it. In a recent report, the use of dexamethasone was found very effective in patients suffering from COVID-19. Its effect was most striking among patients on ventilator. The research for vaccines that can prevent the diseaseis still going on. In light of the dynamic trends, present review focuses on etiopathogenesis, factors associated with spreading of the virus, and possible strategies to treat this deadly infection. In addition, it attempts to compile the recent updates on development of drugs and vaccines for the dreaded disease. url: https://doi.org/10.1016/j.ejphar.2020.173381 doi: 10.1016/j.ejphar.2020.173381 id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 words: 5760.0 sentences: 318.0 pages: flesch: 47.0 cache: ./cache/cord-266036-qhlo99l7.txt txt: ./txt/cord-266036-qhlo99l7.txt summary: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. abstract: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. METHODS: We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. RESULTS: We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. CONCLUSIONS: Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19. url: https://doi.org/10.1016/j.jinf.2020.08.043 doi: 10.1016/j.jinf.2020.08.043 id: cord-343148-rp3kmd80 author: Ayatollahi, Parisa title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection date: 2020-09-17 words: 1029.0 sentences: 68.0 pages: flesch: 40.0 cache: ./cache/cord-343148-rp3kmd80.txt txt: ./txt/cord-343148-rp3kmd80.txt summary: title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection On the third day of admission, new behavioral changes appeared including elated mood, inappropriate laughing, anxiety, and insomnia, leading to treatment with clonazepam, risperidone, and sertraline, in addition to sodium divalproex. Repeat brain MRI showed signal hyperintensities on fluidattenuated inversion recovery (FLAIR) and T2-weighted sequences in the claustrum bilaterally, which were not present on the initial scan 2 weeks earlier. Follow-up MRI 1 month after the abnormal scan showed near-complete resolution of the claustrum hyperintensities ( Figure 2 ). [1] [2] [3] The MRI abnormality ("the claustrum sign") may extend to external/extreme capsules and insular cortices 3 and typically resolves in weeks or months. The finding of the claustrum sign on brain MRI, not previously reported in a COVID-19 patient, [4] [5] [6] [7] [8] provides further support for the idea that acute SARS-CoV-2 infection may present as an autoimmune encephalitis. abstract: nan url: https://doi.org/10.1017/cjn.2020.209 doi: 10.1017/cjn.2020.209 id: cord-352281-9huyb4cs author: Ayoub, Houssein H. title: Age could be driving variable SARS-CoV-2 epidemic trajectories worldwide date: 2020-04-17 words: 5128.0 sentences: 361.0 pages: flesch: 53.0 cache: ./cache/cord-352281-9huyb4cs.txt txt: ./txt/cord-352281-9huyb4cs.txt summary: We aimed here to answer this question and to estimate for each country (with a population ≥1 million), region, and globally, 0 R , and the rate per 100 persons (out of the total population by the end of the epidemic cycle) of each of the cumulative number of incident infections, mild infections, severe and/or critical disease cases, and deaths, in addition to the number of days needed for the national epidemic to reach its incidence peak (a measure of how fast the epidemic will grow). 13.20059253 doi: medRxiv preprint Figure S11 : Sensitivity analysis assessing the impact of a 50% increase in the susceptibility to SARS-CoV-2 infection among those aged <30 years on our estimates for the basic reproduction number, R0, for the select countries presented in the main text. abstract: Background Current geographic spread of documented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections shows heterogeneity. This study explores the role of age in potentially driving differentials in infection spread, epidemic potential, and rates of disease severity and mortality across countries. Methods An age-stratified deterministic mathematical model that describes SARS-CoV-2 transmission dynamics was applied to 159 countries and territories with a population ≥1 million. Results Assuming worst-case scenario for the pandemic, the results indicate that there could be stark regional differences in epidemic trajectories driven by differences in the distribution of the population by age. In the African Region (median age: 18.9 years), the median R0 was 1.05 versus 2.05 in the European Region (median age: 41.7 years), and the median (per 100 persons) for the infections rate was 22.5 (versus 69.0), for severe and/or critical disease cases rate was 3.3 (versus 13.0), and for death rate was 0.5 (versus 3.9). Conclusions Age could be a driver of variable SARS-CoV-2 epidemic trajectories worldwide. Countries with sizable adult and/or elderly populations and smaller children populations may experience large and rapid epidemics in absence of interventions. Meanwhile, countries with predominantly younger age cohorts may experience smaller and slower epidemics. These predictions, however, should not lead to complacency, as the pandemic could still have a heavy toll nearly everywhere. url: https://doi.org/10.1101/2020.04.13.20059253 doi: 10.1101/2020.04.13.20059253 id: cord-310042-9z8rkzq8 author: Aysha, Al‐Ani title: Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date: 2020-07-12 words: 3471.0 sentences: 214.0 pages: flesch: 43.0 cache: ./cache/cord-310042-9z8rkzq8.txt txt: ./txt/cord-310042-9z8rkzq8.txt summary: This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. A significant proportion of IBD patients are treated with long-term immunomodulator/immunosuppressive therapy which potentially places them at increased risk of infections and associated complications. Practitioners and patients alike are therefore concerned about the risk and implications of COVID-19 infection in the IBD patient, despite a paucity of evidence supporting an altered predisposition to disease or more severe disease course. Despite concerns regarding immunosuppression and consequent predisposition to infection, there is no evidence to suggest increased infection rates of COVID-19 in IBD patients to date. 8, 9 Hence, expert consensus currently is that patients with IBD do not appear to be at increased risk of SARS-CoV-2 infection compared with the general population. 2 • Reducing disease activitythere is evidence that moderate to severe disease activity increases the risk of infection in IBD patients. abstract: The COVID‐19 pandemic, caused by the novel coronavirus SARS‐CoV‐2, has emerged as a public health emergency and challenged healthcare systems globally. In a minority of patients, SARS‐CoV‐2 manifests with a severe acute respiratory illness and currently there are insufficient data regarding the virulence of COVID‐19 in inflammatory bowel disease patients taking immunosuppressive therapy. This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. url: https://doi.org/10.1111/imj.14889 doi: 10.1111/imj.14889 id: cord-274839-r4jg6wac author: Azam, Faizul title: An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α date: 2020-11-02 words: 5156.0 sentences: 254.0 pages: flesch: 46.0 cache: ./cache/cord-274839-r4jg6wac.txt txt: ./txt/cord-274839-r4jg6wac.txt summary: Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing −5.30 kcal/mol and −84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. Therefore, in this study, molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) and molecular dynamics protocols have been exploited to investigate the binding interactions between IVM and 15 potential drug targets associated with COVID-19 as well as IMPa co-crystallized with NS5 fragment. abstract: Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IMP)α directly and averts interaction with IMPβ1, leading to the prevention of nuclear localization signal (NLS) recognition. Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing −5.30 kcal/mol and −84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. However, moderate affinity was accounted for IMPα amounting −6.9 kcal/mol and −66.04 kcal/mol. Stability of the protein-ligand complexes of Nsp9-IVM and IMPα-IVM was ascertained by 100 ns trajectory of all-atom molecular dynamics simulation. Structural conformation of protein in complex with docked IVM exhibited stable root mean square deviation while root mean square fluctuations were also found to be consistent. In silico exploration of the potential targets and their interaction profile with IVM can assist experimental studies as well as designing of COVID-19 drugs. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1841028 doi: 10.1080/07391102.2020.1841028 id: cord-355039-qi4fwqbc author: Azar, William S. title: COVID-19 and diabetes mellitus: how one pandemic worsens the other date: 2020-08-02 words: 7350.0 sentences: 392.0 pages: flesch: 44.0 cache: ./cache/cord-355039-qi4fwqbc.txt txt: ./txt/cord-355039-qi4fwqbc.txt summary: In this review, we elucidate suggested mechanisms underlying the increased susceptibility of patients with diabetes to infection with SARS-CoV-2 with a more severe COVID-19 disease. The different studies presented suggest that patients with diabetes may not only be prone to a more severe COVID-19 disease, but also to an increased risk of infection with SARS-CoV-2. Although plausible hypotheses for the increased risk of COVID-19 infection in patients with diabetes and other chronic diseases like hypertension are still under investigation, ACE2 seems to play a key role in the association between COVID-19 and DM [60] (Table 1 ). suggested that higher ACE2 expression in the lungs increased susceptibility to SARS-CoV-2 infection with more severe complications and was causally correlated with diabetes [68] . In this review, we describe three potential mechanisms underlying the increased susceptibility of patients with diabetes to a more severe COVID-19 disease, leading to higher morbidity and mortality. abstract: In light of the most challenging public health crisis of modern history, COVID-19 mortality continues to rise at an alarming rate. Patients with co-morbidities such as hypertension, cardiovascular disease, and diabetes mellitus (DM) seem to be more prone to severe symptoms and appear to have a higher mortality rate. In this review, we elucidate suggested mechanisms underlying the increased susceptibility of patients with diabetes to infection with SARS-CoV-2 with a more severe COVID-19 disease. The worsened prognosis of COVID-19 patients with DM can be attributed to a facilitated viral uptake assisted by the host’s receptor angiotensin-converting enzyme 2 (ACE2). It can also be associated with a higher basal level of pro-inflammatory cytokines present in patients with diabetes, which enables a hyperinflammatory “cytokine storm” in response to the virus. This review also suggests a link between elevated levels of IL-6 and AMPK/mTOR signaling pathway and their role in exacerbating diabetes-induced complications and insulin resistance. If further studied, these findings could help identify novel therapeutic intervention strategies for patients with diabetes comorbid with COVID-19. url: https://doi.org/10.1007/s11154-020-09573-6 doi: 10.1007/s11154-020-09573-6 id: cord-342569-ja96xfns author: Azer, Samy A. title: COVID-19: Pathophysiology, diagnosis, complications and Investigational therapeutics date: 2020-08-05 words: 2669.0 sentences: 186.0 pages: flesch: 46.0 cache: ./cache/cord-342569-ja96xfns.txt txt: ./txt/cord-342569-ja96xfns.txt summary: On 31 December 2019, the Chinese authorities reported to the World Health Organisation (WHO) an emerging of a novice coronavirus, currently the virus is known as SARS-CoV-2 and the disease name is coronavirus-19 disease (COVID19) , that has emerged in patients from Wuhan city, Hubel Province [1] . Recently it was debated that targeting the Notch signalling to prevent SARS-CoV-2 infection and interfering with the progression of COVID-19associated heart and lungs disease pathogenesis [13] . It is not clear whether the observed SARS-CoV-2-associated liver injury is cause by direct viral injury or related to hepatoxic drugs, coexisting systemic inflammatory changes, sepsis, respiratory distress syndrome-induced hypoxia, and multiple organ failure [18] . In patients with type 2 diabetes mellitus who are infected with COVID-19, it is important to remember that two receptor proteins ACE-2 and dipeptidyl peptidase-4 (DPP-4) are test can detect IgM, and IgG antibodies against SARS-CoV-2 in the serum, plasma, and whole blood [23] . abstract: Abstract The novel coronavirus (COVID-19) outbreak started early in December 2019 in the Hubei province and its capital Wuhan of the People’s Republic of China and caused a global pandemic. The number of patients confined to this disease has exceeded nine million in more than 215 countries, and the number who died is over 480,600 (up to 25 June 2020). Coronaviruses were identified in the 1960s and recently identified to cause the Middle East Respiratory Syndrome (MERS-CoV) in 2012 and severe acute respiratory syndrome (SARS) in 2003. The current severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the most recently identified. Patients with COVID-19 may be asymptomatic. Typical symptoms including fever, dry cough, and shortness of breath. Gastrointestinal symptoms such as nausea, vomiting, abdominal pain and diarrhea, have been reported—neurologically related symptoms, particularly anosmia, hyposmia, and dysgeusia, have also been reported. Physical examination may reveal a fever in over 44% of patients (and could be documented in over 88% of patients after admission), increased respiratory rate, acute respiratory disease, and maybe decreased consciousness, agitation, and confusion. This article aims at presenting an up-to-date review on the pathogenesis, diagnosis and complications of COVID-19 infection. Currently, no therapeutics have been found to be effective. Investigational therapeutics are briefly discussed. url: https://api.elsevier.com/content/article/pii/S2052297520300901 doi: 10.1016/j.nmni.2020.100738 id: cord-297870-m7n43k4p author: Azevedo, Rafael Bellotti title: Covid-19 and the cardiovascular system: a comprehensive review date: 2020-07-27 words: 5108.0 sentences: 211.0 pages: flesch: 30.0 cache: ./cache/cord-297870-m7n43k4p.txt txt: ./txt/cord-297870-m7n43k4p.txt summary: Moreover, as in other respiratory infections, preexisting CV diseases and risk factors can increase the severity of COVID-19, leading to the aggravation and decompensation of chronic underlying cardiac pathologies as well as acute-onset of new cardiac complications [3] , highlighting that myocardial injury can be present in approximately 12% of hospitalized patients with SARS-CoV-2 infection [1] . Within the CV manifestations of COVID-19, we can highlight four different aspects: (a) CV risk factors and established CV disease is associated with a worse prognosis, (b) appearance of acute CV complications in previously healthy individuals, (c) promising therapies with antimalarials and antivirals present important CV side effects, and (d) questioning the safety of the use of renin-angiotensin-aldosterone system (RAAS) inhibitors regarding an increased risk of COVID-19 [1] . abstract: Cardiac injury in patients infected with the novel Coronavirus (COVID-19) seems to be associated with higher morbimortality. We provide a broad review of the clinical evolution of COVID-19, emphasizing its impact and implications on the cardiovascular system. The pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by overproduction of inflammatory cytokines (IL-6 and TNF-α) leading to systemic inflammation and multiple organ dysfunction syndrome, acutely affecting the cardiovascular system. Hypertension (56.6%) and diabetes (33.8%) are the most prevalent comorbidities among individuals with COVID-19, who require hospitalization. Furthermore, cardiac injury, defined as elevated us-troponin I, significantly relates to inflammation biomarkers (IL-6 and C-reactive protein (CRP), hyperferritinemia, and leukocytosis), portraying an important correlation between myocardial injury and inflammatory hyperactivity triggered by viral infection. Increased risk for myocardial infarction, fulminant myocarditis rapidly evolving with depressed systolic left ventricle function, arrhythmias, venous thromboembolism, and cardiomyopathies mimicking STEMI presentations are the most prevalent cardiovascular complications described in patients with COVID-19. Moreover, SARS-CoV-2 tropism and interaction with the RAAS system, through ACE2 receptor, possibly enhances inflammation response and cardiac aggression, leading to imperative concerns about the use of ACEi and ARBs in infected patients. Cardiovascular implications result in a worse prognosis in patients with COVID-19, emphasizing the importance of precocious detection and implementation of optimal therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32719447/ doi: 10.1038/s41371-020-0387-4 id: cord-332153-fczf3lzc author: Azkur, Ahmet Kursat title: Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19 date: 2020-05-12 words: 6181.0 sentences: 439.0 pages: flesch: 50.0 cache: ./cache/cord-332153-fczf3lzc.txt txt: ./txt/cord-332153-fczf3lzc.txt summary: In this review, we aim to improve our understanding on the immune response and immunopathological changes in patients linked to detoriating clinical conditions such as, cytokine storm, acute respiratory distress syndrome, autopsy findings and changes in acute phase reactants and serum biochemistry in COVID‐19. The IgM, IgA and IgG type virus‐specific antibodies levels are important measurements to predict population immunity against this disease and whether cross‐reactivity with other coronaviruses is taking place.High viral‐load during the first infection and repeated exposure to virus especially in healthcare workers can be an important factor for severity of disease. It should be noted that many aspects of severe patients are unique to COVID‐19 and are rarely observed in other respiratory viral infections, such as severe lymphopenia and eosinopenia, extensive pneumonia and lung tissue damage, a cytokine storm leading to acute respiratory distress syndrome and multiorgan failure. abstract: As a zoonotic disease that has already spread globally to several million human beings and possibly to domestic and wild animals, eradication of coronavirus disease 2019 (COVID‐19) appears practically impossible. There is a pressing need to improve our understanding of the immunology of this disease to contain the pandemic by developing vaccines and medicines for the prevention and treatment of patients. In this review, we aim to improve our understanding on the immune response and immunopathological changes in patients linked to detoriating clinical conditions such as, cytokine storm, acute respiratory distress syndrome, autopsy findings and changes in acute phase reactants and serum biochemistry in COVID‐19. Similar to many other viral infections, asymptomatic disease is present in a significant but currently unknown fraction of the affected individuals.In the majority of the patients, a one‐week, self‐limiting viral respiratory disease typically occurs, which ends with the development of neutralizing anti‐viral T cell and antibody immunity. The IgM, IgA and IgG type virus‐specific antibodies levels are important measurements to predict population immunity against this disease and whether cross‐reactivity with other coronaviruses is taking place.High viral‐load during the first infection and repeated exposure to virus especially in healthcare workers can be an important factor for severity of disease. It should be noted that many aspects of severe patients are unique to COVID‐19 and are rarely observed in other respiratory viral infections, such as severe lymphopenia and eosinopenia, extensive pneumonia and lung tissue damage, a cytokine storm leading to acute respiratory distress syndrome and multiorgan failure. Lymphopenia causes a defect in antiviral and immune regulatory immunity. At the same time, a cytokine storm starts with extensive activation of cytokine‐secreting cells with innate and adaptive immune mechanisms both of with contribute to a poor prognosis. Elevated levels of acute phase reactants and lymphopenia are early predictors of high disease severity. Prevention of development to severe disease, cytokine storm, acute respiratory distress syndrome and novel approachs to prevent their development will be main routes for future research areas. As we learn to live amidst the virus, understanding the immunology of the disease can assist in containing the pandemic and in developing vaccines and medicines to prevent and treat individual patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32396996/ doi: 10.1111/all.14364 id: cord-335802-1kiqfy68 author: Azoulay, Elie title: Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset date: 2020-08-11 words: 3515.0 sentences: 194.0 pages: flesch: 48.0 cache: ./cache/cord-335802-1kiqfy68.txt txt: ./txt/cord-335802-1kiqfy68.txt summary: METHODS: In a multicentre retrospective study, we included 379 COVID-19 patients admitted to four ICUs between 20 February and 24 April 2020 and categorised according to time from disease onset to ICU admission. To test the hypothesis that COVID-19-related critical illness differs according to time from viral symptom onset to ICU admission, we assessed patient characteristics and outcomes in a cohort of 379 critically ill patients admitted to four university-affiliated hospitals in Paris. This study collecting data from 379 COVID-19 patients showed that mortality decreased with increasing time from viral symptom onset to ICU admission. Mortality was significantly higher in patients admitted to the ICU within a week after viral symptom onset, independently from acute illness severity at ICU admission. Second, the excess mortality in patients admitted to the ICU within 7 days after viral symptom onset was associated with an increased prevalence of non-respiratory injury and, more specifically, of acute kidney and myocardial injury. abstract: PURPOSE: Coronavirus disease 2019 (COVID-19) is creating an unprecedented healthcare crisis. Understanding the determinants of mortality is crucial to optimise intensive care unit (ICU) resource use and to identify targets for improving survival. METHODS: In a multicentre retrospective study, we included 379 COVID-19 patients admitted to four ICUs between 20 February and 24 April 2020 and categorised according to time from disease onset to ICU admission. A Cox proportional-hazards model identified factors associated with 28-day mortality. RESULTS: Median age was 66 years (53–68) and 292 (77%) were men. The main comorbidities included obesity and overweight (67%), hypertension (49.6%) and diabetes (30.1%). Median time from disease onset (i.e., viral symptoms) to ICU admission was 8 (6–11) days (missing for three); 161 (42.5%) patients were admitted within a week of disease onset, 173 (45.6%) between 8 and 14 days, and 42 (11.1%) > 14 days after disease onset; day 28 mortality was 26.4% (22–31) and decreased as time from disease onset to ICU admission increased, from 37 to 21% and 12%, respectively. Patients admitted within the first week had higher SOFA scores, more often had thrombocytopenia or acute kidney injury, had more limited radiographic involvement, and had significantly higher blood IL-6 levels. Age, COPD, immunocompromised status, time from disease onset, troponin concentration, and acute kidney injury were independently associated with mortality. CONCLUSION: The excess mortality in patients admitted within a week of disease onset reflected greater non-respiratory severity. Therapeutic interventions against SARS-CoV-2 might impact different clinical endpoints according to time since disease onset. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00134-020-06202-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32780165/ doi: 10.1007/s00134-020-06202-3 id: cord-343523-xb4ee5r5 author: Azouz, Haya title: COVID-19 in an Infant with Congenital Adrenal Hyperplasia: A Case Report date: 2020-10-05 words: 1192.0 sentences: 85.0 pages: flesch: 54.0 cache: ./cache/cord-343523-xb4ee5r5.txt txt: ./txt/cord-343523-xb4ee5r5.txt summary: Herein, we present a case of a 5-week-old infant with congenital adrenal hyperplasia who acquired SARS-CoV-2 and recovered with minimal medical support. Unlike 10% to 33% of the adult population, only 5.7% to 20% of known pediatric patients with SARS-CoV-2 infection required hospitalizations. We present a case report of an infant with a prior diagnosis of congenital adrenal hyperplasia (CAH) who was found to have SARS-CoV-2 infection. Since the start of the SARS-CoV-2 pandemic, several studies have been published pertaining to clinical presentation in various age groups, possible management options and its implications in patients with other comorbidities. To our knowledge, this is the first case report of SARS-CoV-2 infection in an infant with underlying adrenal insufficiency secondary to CAH. Our patient presented with fever and irritability that was worrisome given his age, the current pandemic and his underlying adrenal insufficiency. Interestingly, a prior case report of a 2-week-old infant with SARS-CoV-2 noted skin and soft tissue infection. abstract: In the midst of current SARS-CoV-2 pandemic, little is known about the implications of this new virus on patients with underlying chronic comorbidities. Herein, we present a case of a 5-week-old infant with congenital adrenal hyperplasia who acquired SARS-CoV-2 and recovered with minimal medical support. url: https://doi.org/10.1177/2333794x20958933 doi: 10.1177/2333794x20958933 id: cord-355567-60sfv60p author: Azuma, Kenichi title: Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control date: 2020-11-03 words: 9229.0 sentences: 436.0 pages: flesch: 42.0 cache: ./cache/cord-355567-60sfv60p.txt txt: ./txt/cord-355567-60sfv60p.txt summary: Recently, 36 researchers insisted on the potential risk of indoor airborne transmission of SARS-CoV-2 and the importance of sufficient and effective ventilation, particle filtration, and air sterilization as infection control measures inside buildings [43] . Therefore, the MHLW published a document titled "Prevention of the COVID-19 Clusters" Abbreviation: SARS-CoV severe acute respiratory syndrome coronavirus Fig. 1 Traditional Japanese office building HVAC systems: a a centralized HVAC system; and b a centralized ventilation system with an individual air-conditioning system on March 1, 2020 [94] , showing the need for adequate ventilation in buildings because a ventilation standard for infection control has not been established in general buildings in Japan and the characteristics of indoor spaces where the clusters occurred might include poor ventilation and crowding. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new zoonotic agent that emerged in December 2019, causes coronavirus disease 2019 (COVID-19). This infection can be spread by asymptomatic, presymptomatic, and symptomatic carriers. SARS-CoV-2 spreads primarily via respiratory droplets during close person-to-person contact in a closed space, especially a building. This article summarizes the environmental factors involved in SARS-CoV-2 transmission, including a strategy to prevent SARS-CoV-2 transmission in a building environment. SARS-CoV-2 can persist on surfaces of fomites for at least 3 days depending on the conditions. If SARS-CoV-2 is aerosolized intentionally, it is stable for at least several hours. SARS-CoV-2 is inactivated rapidly on surfaces with sunlight. Close-contact aerosol transmission through smaller aerosolized particles is likely to be combined with respiratory droplets and contact transmission in a confined, crowded, and poorly ventilated indoor environment, as suggested by some cluster cases. Although evidence of the effect of aerosol transmission is limited and uncertainty remains, adequate preventive measures to control indoor environmental quality are required, based on a precautionary approach, because COVID-19 has caused serious global damages to public health, community, and the social economy. The expert panel for COVID-19 in Japan has focused on the “3 Cs,” namely, “closed spaces with poor ventilation,” “crowded spaces with many people,” and “close contact.” In addition, the Ministry of Health, Labour and Welfare of Japan has been recommending adequate ventilation in all closed spaces in accordance with the existing standards of the Law for Maintenance of Sanitation in Buildings as one of the initial political actions to prevent the spread of COVID-19. However, specific standards for indoor environmental quality control have not been recommended and many scientific uncertainties remain regarding the infection dynamics and mode of SARS-CoV-2 transmission in closed indoor spaces. Further research and evaluation are required regarding the effect and role of indoor environmental quality control, especially ventilation. url: https://doi.org/10.1186/s12199-020-00904-2 doi: 10.1186/s12199-020-00904-2 id: cord-257732-3xuy6tbn author: Azzi, Lorenzo title: Saliva is a reliable tool to detect SARS-CoV-2 date: 2020-04-14 words: 3510.0 sentences: 201.0 pages: flesch: 56.0 cache: ./cache/cord-257732-3xuy6tbn.txt txt: ./txt/cord-257732-3xuy6tbn.txt summary: OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. At present, Real Time reverse transcription Polymerase Chain Reaction (rRT-PCR) on respiratory specimens represents the gold standard test for detection of SARS-CoV-2 infection. 10 , 11 Sputum and oropharyngeal secretions have recently been suggested as a possible target for the molecular diagnosis of COVID-19, 12 and salivary droplets represent the main source of the human-to-human transmission of the SARS-CoV-2 infection when social distance is less than 2 m. There were not significant differences regarding the clinical and anamnestic history between males and females, with the only exception of the values of serum LDH, which were higher in the female patients'' haematochemical analyses carried out on the day of saliva collection ( p = 0.025). abstract: OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. METHODS: Salivary samples of 25 COVID-19 patients were analyzed by rRT-PCR. The following data were collected: age, sex, comorbidities, drugs. Lactate dehydrogenase (LDH) and ultrasensitive reactive C protein (usRCP) values were registered on the same day when a salivary swab was collected. Prevalence of positivity in saliva and association between clinical data and the cycle threshold as a semiquantitative indicator of viral load were considered. RESULTS: Twenty-five subjects were recruited into this study, 17 males and 8 females. The mean age was 61.5 +/− 11.2 years. Cardiovascular and/or dysmetabolic disorders were observed in 65.22% of cases. All the samples tested positive for the presence of SARS-CoV-2, while there was an inverse association between LDH and Ct values. Two patients showed positive salivary results on the same days when their pharyngeal or respiratory swabs showed conversion. CONCLUSIONS: Saliva is a reliable tool to detect SARS-CoV-2. The role of saliva in COVID-19 diagnosis could not be limited to a qualitative detection of the virus, but it may also provide information about the clinical evolution of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32298676/ doi: 10.1016/j.jinf.2020.04.005 id: cord-352296-rpjehijd author: Azzi, Lorenzo title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern date: 2020-05-11 words: 639.0 sentences: 44.0 pages: flesch: 62.0 cache: ./cache/cord-352296-rpjehijd.txt txt: ./txt/cord-352296-rpjehijd.txt summary: title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern During our research, we found two patients out of 25 subjects (i.e., 8%) affected by COVID-19 with different degrees of severity, who showed positive salivary results on the same days when their pharyngeal or bronchoalveolar swabs proved to be negative . These findings, together with those reported by the F I G U R E 1 The temporal line of the clinical course in the two patients shows how their salivary samples tested positive, while the pharyngeal or bronchoalveolar swabs were negative on the same day (Patient 1 on March 19) or during the interval between two consecutive salivary swabs (Patient 2, March 23-28) Chinese colleagues on sputum, rise the concern about how to manage these patients before hospital discharging. Two cases of COVID-19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern abstract: We report two cases of COVID‐19 showing negative respiratory swabs but positive salivary samples at the same time. These findings rise the concern about how to manage these patients before hospital discharging, thus avoiding contagion among their family members or a second coronavirus wave once the lockdown is over. url: https://doi.org/10.1111/odi.13368 doi: 10.1111/odi.13368 id: cord-306108-ja0wyr5w author: B K, Anupama title: A Review of Acute Myocardial Injury in Coronavirus Disease 2019 date: 2020-06-03 words: 4754.0 sentences: 219.0 pages: flesch: 34.0 cache: ./cache/cord-306108-ja0wyr5w.txt txt: ./txt/cord-306108-ja0wyr5w.txt summary: Although SARS-CoV-2 infection predominantly causes pulmonary complications, such as pneumonia and ARDS, the disease has also been associated with a variety of cardiovascular complications, including acute myocardial injury, myocarditis, arrhythmia, heart failure, and venous thromboembolism [6] . Hence, one potential explanation for the higher likelihood of acquiring infection, and the increased risk of severe disease and adverse outcomes in patients with COVID-19 with pre-existing CVD, maybe the elevated secretion of ACE2 in these patients, thus making them more susceptible to direct viral damage to cardiac myocytes [33] ; but, this has not yet been demonstrated in pathology studies. In a single-center, retrospective cohort study including 188 patients with COVID-19 in Wuhan, China, conducted to explore whether heart injury occurred during COVID-19 on admission and later increased mortality, approximately 11.2% of patients had high-sensitivity cardiac troponin I (hs-TnI) exceeding the clinical upper normal limit on admission. abstract: In December 2019, an outbreak of pneumonia caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred in Wuhan, Hubei province, China, and it has spread rapidly across the world, causing the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 infection predominantly results in pulmonary issues, accumulating evidence suggests the increased frequency of a variety of cardiovascular complications in patients with COVID-19. Acute cardiac injury, defined as elevated cardiac troponin levels, is the most reported cardiac abnormality in COVID-19 and strongly associated with mortality. In this article, we summarize the currently available data on the association of SARS-CoV-2 and COVID-19 with acute myocardial injury. url: https://www.ncbi.nlm.nih.gov/pubmed/32642342/ doi: 10.7759/cureus.8426 id: cord-311918-gifwg2ho author: BENDER, Whitney R. title: Universal Testing for SARS-CoV-2 in Two Philadelphia Hospitals: Carrier Prevalence and Symptom Development Over Two Weeks date: 2020-09-11 words: 2826.0 sentences: 187.0 pages: flesch: 54.0 cache: ./cache/cord-311918-gifwg2ho.txt txt: ./txt/cord-311918-gifwg2ho.txt summary: Objectives To describe the prevalence of positive SARS-CoV-2 tests among asymptomatic pregnant women at two Philadelphia obstetric hospitals, characterize the clinical course of those testing positive, and report symptom development among all women tested in the two weeks post-hospitalization. 242 (78.1%) and 213 (68.7%) of the 310 women who were SARS-CoV-2 negative at time of initial hospitalization were reached for telephone follow-up at one and two weeks post-admission, respectively. Conclusions The asymptomatic positive SARS-CoV-2 test rate among an obstetric population in Philadelphia differed between two hospitals and was lower than described in other geographic regions. The objectives of this study are to describe the prevalence of positive SARS-Cov-2 tests 123 at time of admission for delivery among asymptomatic pregnant women in Philadelphia within 124 two large academic hospitals, characterize the in-hospital clinical course for those who tested 125 positive, and report the development of viral symptoms in all women tested for two weeks 126 after hospital discharge. abstract: Background The COVID-19 pandemic caused by the SARS-CoV-2 virus has challenged obstetric care providers. Universal testing on labor and delivery units has been implemented by many hospitals to ensure patient and staff safety. Asymptomatic carrier rates are expected to vary based on geographic differences in disease prevalence, although differences within the same city have not previously been reported. Additionally, clinical follow-up of women testing negative for SARS-CoV-2 during obstetric hospitalization have not been included in any prior reports. Objectives To describe the prevalence of positive SARS-CoV-2 tests among asymptomatic pregnant women at two Philadelphia obstetric hospitals, characterize the clinical course of those testing positive, and report symptom development among all women tested in the two weeks post-hospitalization. Study Design This is an observational study of asymptomatic pregnant women who underwent SARS-CoV-2 testing at two academic health centers (HUP and PAH) in Philadelphia, PA between April 13, 2020 and April 26, 2020. All women tested were contacted via telephone for symptom follow-up at one and two weeks post-discharge. Asymptomatic positive test rates are reported for the overall population and by hospital. The hospital and two-week post-hospital course are described for women testing positive for SARS-CoV-2. Post-hospital symptom development among women testing negative for SARS-CoV-2 is also described. Results Three hundred and eighteen asymptomatic women underwent SARS-CoV-2 testing during this two-week period. Eight women tested positive. The overall asymptomatic test positive rate was 2.5%. The rate at HUP was 3.8% compared to 1.3% at PAH (p = 0.283). Three women (37.5%) who were initially asymptomatic developed mild symptoms in the two weeks after positive test. Repeat SARS-CoV-2 testing was performed in 14 of the 310 women (4.5%) who initially tested negative; two women (0.6%) were positive on repeat testing. 242 (78.1%) and 213 (68.7%) of the 310 women who were SARS-CoV-2 negative at time of initial hospitalization were reached for telephone follow-up at one and two weeks post-admission, respectively. Viral symptoms, including fevers, chills, shortness of breath, or cough, were self-reported in 4.5% and 4.2% of these women at one and two weeks post-discharge, respectively. Conclusions The asymptomatic positive SARS-CoV-2 test rate among an obstetric population in Philadelphia differed between two hospitals and was lower than described in other geographic regions. This supports the importance of institution-specific testing protocols. The development of symptomatic SARS-CoV-2 infection post-hospitalization among women with initial negative testing is uncommon. url: https://doi.org/10.1016/j.ajogmf.2020.100226 doi: 10.1016/j.ajogmf.2020.100226 id: cord-319855-78xmxymu author: BR, Bharath title: In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19 date: 2020-07-01 words: 4752.0 sentences: 251.0 pages: flesch: 53.0 cache: ./cache/cord-319855-78xmxymu.txt txt: ./txt/cord-319855-78xmxymu.txt summary: The three molecules streptomycin, ciprofloxacin, and GA had low interaction penalties and displayed better interactions with the ACE2 binding site on the RBD of SARS-CoV-2-S, as shown in Figure 8A -C, respectively. Further, in the RMSF plot for the RBD domain of the GA/SARS-CoV-2-S complex, shown in Figure 11C , the RMSF at loop region was 6.3Å with a high number of ligand contacts (green-coloured vertical bars), justifying the interactions seen in molecular docking. In the protein-ligand contact plot for the streptomycin/ SARS-CoV-2-S complex, shown in Figure 12A , residues Glu493 and Lys544 showed maximum interactions fractions, i.e. 0.20 facilitated by hydrogen bonds and water bridges. In the protein-ligand contact plot for the ciprofloxacin/ SARS-CoV-2-S complex shown in Figure 12B , residues Phe465, Tyr482, Tyr498, and Phe499 were seen to have the interactions fractions 0.75, 0.6, 0.35 and 0.39 respectively facilitated by hydrophobic, hydrogen bonds and water bridges. abstract: Background: Human coronavirus (SARS-CoV-2) is causing a pandemic with significant morbidity and mortality. As no effective novel drugs are available currently, drug repurposing is an alternative intervention strategy. Here we present an in silico drug repurposing study that implements successful concepts of computer-aided drug design (CADD) technology for repurposing known drugs to interfere with viral cellular entry via the spike glycoprotein (SARS-CoV-2-S), which mediates host cell entry via the hACE2 receptor. Methods: A total of 4015 known and approved small molecules were screened for interaction with SARS-CoV-2-S through docking studies and 15 lead molecules were shortlisted. Additionally, streptomycin, ciprofloxacin, and glycyrrhizic acid (GA) were selected based on their reported anti-viral activity, safety, availability and affordability. The 18 molecules were subjected to molecular dynamics (MD) simulation. Results: The MD simulation results indicate that GA of plant origin may be repurposed for SARS-CoV-2 intervention, pending further studies. Conclusions: Repurposing is a beneficial strategy for treating COVID-19 with existing drugs. It is aimed at using docking studies to screen molecules for clinical application and investigating their efficacy in inhibiting SARS-CoV-2-S. SARS-CoV-2-S is a key pathogenic protein that mediates pathogen-host interaction. Hence, the molecules screened for inhibitory properties against SARS-CoV-2-S can be clinically used to treat COVID-19 since the safety profile is already known. url: https://doi.org/10.12688/f1000research.24143.1 doi: 10.12688/f1000research.24143.1 id: cord-342625-31fe1neb author: Baba, Hiroaki title: Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide date: 2020-07-01 words: 1457.0 sentences: 76.0 pages: flesch: 48.0 cache: ./cache/cord-342625-31fe1neb.txt txt: ./txt/cord-342625-31fe1neb.txt summary: The patient who continued iguratimod therapy without dose reduction was treated with ciclesonide had an uneventful clinical course, but prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed after resolution of symptoms. The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly across the world, yet investigations of in patients with rheumatologic disease taking disease-modifying antirheumatic drugs (DMARDs) with immunomodulatory or immunosuppressive effects remain scarce [1] . Here we report a case of COVID-19 in a patient with rheumatoid arthritis taking iguratimod, who had prolonged viral RNA presence. A woman in her 40s with rheumatoid arthritis treated with iguratimod 25 mg twice a day was admitted to Tohoku University Hospital, Sendai, Japan, with a diagnosis of COVID-19 based on real-time reverse transcription polymerase chain reaction (real-time RT-PCR) with primers that target the N2 gene of SARS-CoV-2 as described previously [2] from nasopharyngeal swabs and sputum. abstract: Abstract We report a coronavirus disease 2019 (COVID-19) case with rheumatoid arthritis taking iguratimod. The patient who continued iguratimod therapy without dose reduction was treated with ciclesonide had an uneventful clinical course, but prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed after resolution of symptoms. The effects of disease-modifying antirheumatic drugs (DMARDs) and ciclesonide on clinical course and viral shedding remain unknown and warrant further investigation. url: https://doi.org/10.1016/j.jiac.2020.06.022 doi: 10.1016/j.jiac.2020.06.022 id: cord-330338-i6ozygkp author: Babacic, H. title: Global between-countries variance in SARS-CoV-2 mortality is driven by reported prevalence, age distribution, and case detection rate date: 2020-06-02 words: 3604.0 sentences: 216.0 pages: flesch: 59.0 cache: ./cache/cord-330338-i6ozygkp.txt txt: ./txt/cord-330338-i6ozygkp.txt summary: Objective: To explain the global between-countries variance in number of deaths per million citizens (nDpm) and case fatality rate (CFR) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The derived explanators age-adjusted infection fatality rate (IFRadj) and case detection rate (CDR) were estimated for each country based on a SARS-CoV-2 model of China. (9) Studies suggest that the reported number of cases per million citizens (nCpm) is probably lower than the true number of infected individuals, and that this contributes to the varying CFR between countries.(5,6) CFR appears higher than the true infection fatality rate (IFR), i.e. the true proportion of individuals with a SARS-CoV-2 infection who will die in the population regardless of whether they are confirmed or not. The aim of this study was to test two mathematical hypotheses that explain the global between-countries variance in SARS-CoV-2 mortality expressed as nDpm and CFR on real data. abstract: Objective: To explain the global between-countries variance in number of deaths per million citizens (nDpm) and case fatality rate (CFR) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Design: Systematic analysis. Data sources: Worldometer, European Centre for Disease Prevention and Control, United Nations Main outcome measures: The explanators of nDpm and CFR were mathematically hypothesised and tested on publicly-available data from 88 countries with linear regression models on May 1st 2020. The derived explanators - age-adjusted infection fatality rate (IFRadj) and case detection rate (CDR) - were estimated for each country based on a SARS-CoV-2 model of China. The accuracy and agreement of the models with observed data was assessed with R2 and Bland-Altman plots, respectively. Sensitivity analyses involved removal of outliers and testing the models at five retrospective and two prospective time points. Results: Globally, IFRadj estimates varied between countries, ranging from below 0.2% in the youngest nations, to above 1.3% in Portugal, Greece, Italy, and Japan. The median estimated global CDR of SARS-CoV-2 infections on April 16th 2020 was 12.9%, suggesting that most of the countries have a much higher number of cases than reported. At least 93% and up to 99% of the variance in nDpm was explained by reported prevalence expressed as cases per million citizens (nCpm), IFRadj, and CDR. IFRadj and CDR accounted for up to 97% of the variance in CFR, but this model was less reliable than the nDpm model, being sensitive to outliers (R2 as low as 67.5%). Conclusions: The current differences in SARS-CoV-2 mortality between countries are driven mainly by reported prevalence of infections, age distribution, and CDR. The nDpm might be a more stable estimate than CFR in comparing mortality burden between countries. url: http://medrxiv.org/cgi/content/short/2020.05.28.20114934v1?rss=1 doi: 10.1101/2020.05.28.20114934 id: cord-268622-3jireyep author: Babadaei, Mohammad Mahdi Nejadi title: The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets date: 2020-06-01 words: 4071.0 sentences: 247.0 pages: flesch: 53.0 cache: ./cache/cord-268622-3jireyep.txt txt: ./txt/cord-268622-3jireyep.txt summary: Researchers have reported some useful information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leading to CoV disease 2019 (COVID-19). Indeed, these outcomes have elucidated the principal mechanism that the oral cavity is basically in higher risk to SARS-CoV-2 infection and showed a piece of conformation for the ongoing inhibition approach in clinical implementation It has been also revealed that in addition to causing fever and respiratory symptoms, COVID-19 resulted in gastrointestinal disorders including diarrhoea, vomiting and some pains in abdominal part . Figure 2C also shows the SARS-CoV-2 infection-related sensitive organs which can explain about the non-respiratory symptoms identified in COVID-19 patients . According to a report from China, the fatality is observed in older people as well as patients with hypertension, chronic lung disease, diabetes, and CVDs. One of the most likely mechanisms by which COVID-19 can causes lung and cardiac damage is through the SARS-CoV-2 binding to ACE2 receptors. abstract: Researchers have reported some useful information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leading to CoV disease 2019 (COVID-19). Several studies have been performed in order to develop antiviral drugs, from which a few have been prescribed to patients. Also, several diagnostic tests have been designed to accelerate the process of identifying and treating COVID-19. It has been well-documented that the surface of host cells is covered by some receptors, known as angiotensin-converting enzyme 2 (ACE2), which mediates the binding and entry of CoV. After entering, the viral RNA interrupts the cell proliferation system to activate self-proliferation. However, having all the information about the outbreakof the SARS-COV-2, it is not still clear which factors determine the severity of lung and heart function impairment induced by COVID-19. A major step in exploring SARS-COV-2 pathogenesis is to determine the distribution of ACE2 in different tissues . In this review, the structure and origin of CoV, the role of ACE2 as a receptor of SARS-COV-2 on the surface of host cells, and the ACE2 distribution in different tissues with a focus on lung and cardiovascular system have been discussed. It was also revealed that acute and chronic cardiovascular diseases (CVDs) may result in the clinical severity of COVID-19. In conclusion, this review may provide useful information in developing some promising strategies to end up with a worldwide COVID-19 pandemic. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1767211 doi: 10.1080/07391102.2020.1767211 id: cord-312740-2ro2p77q author: Babadaei, Mohammad Mahdi Nejadi title: Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase date: 2020-05-20 words: 3820.0 sentences: 217.0 pages: flesch: 50.0 cache: ./cache/cord-312740-2ro2p77q.txt txt: ./txt/cord-312740-2ro2p77q.txt summary: A broad-spectrum of antiviral agents are being currently evaluated in clinical trials, and in this review, we specifically focus on the application of Remdesivir (RVD) as a potential anti-viral compound against Middle East respiratory syndrome (MERS) -CoV, SARS-CoV and SARS-CoV-2. First, we overview the general information about SARS-CoV-2, followed by application of RDV as a nucleotide analogue which can potentially inhibits RNA-dependent RNA polymerase of COVs. Afterwards, we discussed the kinetics of SARSor MERS-CoV proliferation in animal models which is significantly different compared to that in humans. With Having a considerable number of people worldwide infected with COVID-19, scientists have identified a number of cases of broad-spectrum antiviral agents (BSAAs) that could serve as potential candidates for the treatment of the viral diseases (Andersen et al., 2020; Ianevski et al., 2018) . Corona virus SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative representative of a severe respiratory illness resulted in widespread human infections and deaths in nearly all of the countries since late 2019. There is no therapeutic FDA-approved drug against SARS-CoV-2 infection, although a combination of anti-viral drugs is directly being practiced in some countries. A broad-spectrum of antiviral agents are being currently evaluated in clinical trials, and in this review, we specifically focus on the application of Remdesivir (RVD) as a potential anti-viral compound against Middle East respiratory syndrome (MERS) -CoV, SARS-CoV and SARS-CoV-2. First, we overview the general information about SARS-CoV-2, followed by application of RDV as a nucleotide analogue which can potentially inhibits RNA-dependent RNA polymerase of COVs. Afterwards, we discussed the kinetics of SARS- or MERS-CoV proliferation in animal models which is significantly different compared to that in humans. Finally, some ongoing challenges and future perspective on the application of RDV either alone or in combination with other anti-viral agents against CoVs infection were surveyed to determine the efficiency of RDV in preclinical trials. As a result, this paper provides crucial evidence of the potency of RDV to prevent SARS-CoV-2 infections. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32397906/ doi: 10.1080/07391102.2020.1767210 id: cord-306835-juitltpi author: Babaei, Fatemeh title: Curcumin (a constituent of turmeric): New treatment option against COVID‐19 date: 2020-09-06 words: 6226.0 sentences: 363.0 pages: flesch: 45.0 cache: ./cache/cord-306835-juitltpi.txt txt: ./txt/cord-306835-juitltpi.txt summary: The keywords used for the search were as follows: coronavirus-19, COVID-19, SARS-CoV-2, curcumin, Curcuma longa, turmeric, curcumin and antiviral, curcumin and anti-inflammatory, curcumin and antipyretic, curcumin and lung, curcumin and acute lung injury, curcumin and fatigue, curcumin and antioxidant, curcumin and ARDS, curcumin and bradykinin, curcumin and fibrosis, curcumin and Interleukin-6 (IL-6), curcumin and tumor necrosis factor-alpha (TNF-α), curcumin and NF-κB, curcumin and Toll-like receptors (TLRs), curcumin and antiapoptotic. AA: arachidonic acid, ALI: acute lung injury, AP-1: activator protein 1, BK: bradykinin, ACE2: angiotensin-converting enzyme 2, Ang II: angiotensin II, ARDS: acute respiratory distress syndrome, Cas-3: caspase 3, COX: cyclooxygenase, CXCL: chemokine (C-X-C motif) ligand, 12-HPETE: 12-hydroperoxyeicosatetraenoic acid, JNK: c-Jun N-terminal kinase, 12 LOX: 12-lipoxygenase, MMP: matrix metalloproteinase NF-κB: nuclear factor kappa-light-chain-enhancer of activated B cells, MAPK: mitogen-activated protein kinase, PAI-1: plasminogen activator inhibitor-1, PLA2: phospholipase A2, PG: prostaglandin, SMAD3: mothers against decapentaplegic homolog 3, TGF-β1: transforming growth factor-beta 1, TNF-α: tumor necrosis factor-α, TLR: Toll-like receptor, TRPA1: transient receptor potential channel subfamily vanilloid member 1, TRPV1: transient receptor potential channel subfamily A member 1 mechanisms that curcumin may be useful to prevent or treat the ARDS. abstract: In late December 2019, the outbreak of respiratory illness emerged in Wuhan, China, and spreads worldwide. World Health Organization (WHO) named this disease severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) caused by a new member of beta coronaviruses. Several medications are prescribed to patients, and some clinical trials are underway. Scientists are trying to find a specific drug against this virus. In this review, we summarize the pathogenesis, clinical features, and current treatments of coronavirus disease 2019 (COVID‐19). Then, we describe the possible therapeutic effects of curcumin and its molecular mechanism against coronavirus‐19. Curcumin, as an active constituent of Curcuma longa (turmeric), has been studied in several experimental and clinical trial studies. Curcumin has some useful clinical effects such as antiviral, antinociceptive, anti‐inflammatory, antipyretic, and antifatigue effects that could be effective to manage the symptoms of the infected patient with COVID‐19. It has several molecular mechanisms including antioxidant, antiapoptotic, and antifibrotic properties with inhibitory effects on Toll‐like receptors, NF‐κB, inflammatory cytokines and chemokines, and bradykinin. Scientific evidence suggests that curcumin could have a potential role to treat COVID‐19. Thus, the use of curcumin in the clinical trial, as a new treatment option, should be considered. url: https://www.ncbi.nlm.nih.gov/pubmed/33133525/ doi: 10.1002/fsn3.1858 id: cord-229246-qgp7ksq8 author: Babino, Andres title: Masks and COVID-19: a causal framework for imputing value to public-health interventions date: 2020-06-09 words: 3605.0 sentences: 219.0 pages: flesch: 69.0 cache: ./cache/cord-229246-qgp7ksq8.txt txt: ./txt/cord-229246-qgp7ksq8.txt summary: In this paper, we aim to fill this gap by testing the hypothesis that the policy change regarding masks by the CDC (and local governments) decreased the number of positive cases in the states of Connecticut (CT), Massachusetts (MA), New York (NY), Rhode Island (RI), and Virginia (VA). The data from RI is harder to interpret because stay-at-home orders and masks guidelines happened close in time, and data from before April are unreliable (with less than 500 tests a day). The framework that we presented is data-driven, and therefore it relies on only a handful of hypotheses as compared to other methods For example, the counterfactual analysis relies on one hypothesis: the log-odds are piecewise linear (see Eq. 6 in the supplementary material)without the need to assume any of the hypotheses of the SIR model. abstract: During the COVID-19 pandemic, the scientific community developed predictive models to evaluate potential governmental interventions. However, the analysis of the effects these interventions had is less advanced. Here, we propose a data-driven framework to assess these effects retrospectively. We use a regularized regression to find a parsimonious model that fits the data with the least changes in the Rt parameter. Then, we postulate each jump in Rt as the effect of an intervention. Following the do-operator prescriptions, we simulate the counterfactual case by forcing Rt to stay at the pre-jump value. We then attribute a value to the intervention from the difference between true evolution and simulated counterfactual. We show that the recommendation to use facemasks for all activities would reduce the number of cases by 170000 (95% CI 160000 to 180000) in Connecticut, Massachusetts, and New York State. The framework presented here might be used in any case where cause and effects are sparse in time. url: https://arxiv.org/pdf/2006.05532v2.pdf doi: nan id: cord-127741-h23w89h2 author: Babuji, Yadu title: Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release date: 2020-05-28 words: 2439.0 sentences: 149.0 pages: flesch: 49.0 cache: ./cache/cord-127741-h23w89h2.txt txt: ./txt/cord-127741-h23w89h2.txt summary: In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. For example, these data now include the 2D and 3D molecular descriptors, computed molecular fingerprints, 2D images representing the molecule, and canonical simplified molecular-input line-entry system (SMILES) [6] structural representations to speed development of machine learning models. We expect forthcoming data releases to extend to molecular conformers; incorporate the results of natural language processing extractions of drugs from COVID-related literature; provide the results of molecular docking simulations against SARS-CoV-2 viral and host proteins; and include the trained machine learning models that the team is building to identify top candidates for running various, more expensive calculations. abstract: Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new drugs to counter the the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One promising approach is to train machine learning (ML) and artificial intelligence (AI) tools to screen large numbers of small molecules. As a contribution to that effort, we are aggregating numerous small molecules from a variety of sources, using high-performance computing (HPC) to computer diverse properties of those molecules, using the computed properties to train ML/AI models, and then using the resulting models for screening. In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. This data release encompasses structural information on the 4.2 B molecules and 60 TB of pre-computed data. Future releases will expand the data to include more detailed molecular simulations, computed models, and other products. url: https://arxiv.org/pdf/2006.02431v1.pdf doi: nan id: cord-275708-17cz3agx author: Babyn, Paul S. title: Severe acute respiratory syndrome (SARS): chest radiographic features in children date: 2003-11-18 words: 5761.0 sentences: 296.0 pages: flesch: 47.0 cache: ./cache/cord-275708-17cz3agx.txt txt: ./txt/cord-275708-17cz3agx.txt summary: CONCLUSION: In pediatric cases, SARS manifests with nonspecific radiographic features making radiological differentiation difficult, especially from other commonly encountered childhood respiratory viral illnesses causing airspace disease. This article presents the initial chest radiographic findings collated from 62 children diagnosed as probable or suspect SARS cases during the recent SARS outbreak in Toronto, Singapore, and Hong Kong. Keywords Chest AE Severe acute respiratory syndrome (SARS) AE Radiography AE CT AE Children the following signs and symptoms: fever, chills, body ache, cough, sore throat, rhinorrhea, dyspnea, tachypnea, crackles, headache, dizziness, hypoxemia, malaise, myalgia, rigor, lethargy, and gastrointestinal symptoms including vomiting and diarrhea. In general, fever and cough were the most common clinical presentation amongst younger pediatric SARS cases (age<10 years), whereas, in addition to these symptoms, headache, myalgia, sore throat, chills, and/or rigor were reported in older patients (age ‡10 years). abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a recently recognized condition of viral origin associated with substantial morbidity and mortality rates in adults. Little information is available on its radiologic manifestations in children. OBJECTIVE: The goal of this study was to characterize the radiographic presentation of children with SARS. MATERIALS AND METHODS: We abstracted data (n=62) on the radiologic appearance and course of SARS in pediatric patients with suspect (n=25) or probable (n=37) SARS, diagnosed in five hospital sites located in three cities: Toronto, Singapore, and Hong Kong. Available chest radiographs and thoracic CTs were reviewed for the presence of the following radiographic findings: airspace disease, air bronchograms, airways inflammation and peribronchial thickening, interstitial disease, pleural effusion, and hilar adenopathy. RESULTS: A total of 62 patients (suspect=25, probable=37) were evaluated for SARS. Patient ages ranged from 5.5 months to 17 years and 11.5 months (average, 6 years and 10 months) with a female-to-male ratio of 32:30. Forty-one patients (66.1%) were in close contact with other probable, suspect, or quarantined cases; 10 patients (16.1%) had recently traveled to WHO-designated affected areas within 10 days; and 7 patients (11.2%) were transferred from other hospitals that had SARS patients. Three patients, who did not have close/hospital contact or travel history to affected areas, were classified as SARS cases based on their clinical signs and symptoms and on the fact that they were living in an endemic area. The most prominent clinical presentations were fever, with a temperature over 38 °C (100%), cough (62.9%), rhinorrhea (22.6%), myalgia (17.7%), chills (14.5%), and headache (11.3%). Other findings included sore throat (9.7%), gastrointestinal symptoms (9.7%), rigor (8.1%), and lethargy (6.5%). In general, fever and cough were the most common clinical presentations amongst younger pediatric SARS cases (age<10 years), whereas, in addition to these symptoms, headache, myalgia, sore throat, chills, and/or rigor were common in older patients (age≥10 years). The chest radiographs of 35.5% of patients were normal. The most prominent radiological findings that were observed in the remaining patients were areas of consolidation (45.2%), often peripheral with multifocal lesions in 22.6%. Peribronchial thickening was noted on chest radiographs of 14.5% of patients. Pleural effusion was observed only in one patient (age 17 years and 11.5 months), whereas interstitial disease was not observed in any patient. CONCLUSION: In pediatric cases, SARS manifests with nonspecific radiographic features making radiological differentiation difficult, especially from other commonly encountered childhood respiratory viral illnesses causing airspace disease. The radiographic presentation of suspected SARS cases ranged from normal to mild perihilar peribronchial thickening. The radiographic presentations, as expected, were relatively more pronounced in the SARS probable cases. url: https://www.ncbi.nlm.nih.gov/pubmed/14624321/ doi: 10.1007/s00247-003-1081-8 id: cord-312736-bm6t2bxz author: Bach, Paxton title: Innovative strategies to support physical distancing among individuals with active addiction date: 2020-05-27 words: 998.0 sentences: 55.0 pages: flesch: 48.0 cache: ./cache/cord-312736-bm6t2bxz.txt txt: ./txt/cord-312736-bm6t2bxz.txt summary: In response to these dual crises, health authorities have implemented policy changes to provide new tools to practitioners who treat patients with substance use disorders, circumventing previous barriers to treatment, such as inadequate access and prohibitively regimented medication management. In British Columbia, an epicentre of the overdose epidemic in Canada, unique steps are being taken to mitigate risk for people who use drugs in the context of SARS-CoV-2. Clinical guidance published by the British Columbia Centre on Substance Use in collaboration with the provincial Ministry of Health has, for the first time, proposed an approach to prescribing these medications to patients with active substance use disorders who are thought to be at high risk for SARS-CoV-2. People with substance use disorders face compounded risk in the context of SARS-CoV-2, and implementing physical distancing measures among this population presents unique challenges. abstract: nan url: https://doi.org/10.1016/s2215-0366(20)30231-5 doi: 10.1016/s2215-0366(20)30231-5 id: cord-292462-zbjig3pt author: Backhaus, Andreas title: Common Pitfalls in the Interpretation of COVID-19 Data and Statistics date: 2020-06-07 words: 3163.0 sentences: 158.0 pages: flesch: 58.0 cache: ./cache/cord-292462-zbjig3pt.txt txt: ./txt/cord-292462-zbjig3pt.txt summary: Daily data releases on confi rmed COVID-19 cases and deaths provide information on the course of the pandemic. In its simplest form, the case fatality rate divides the total number of confi rmed deaths by COVID-19 by the to-Forum hence be lower than the IFR (and the CFR). Recall that the computation of the CFR only requires the total number of confi rmed deaths by COVID-19 and the total number of confi rmed cases of infections with SARS-CoV-2. Italy and South Korea are among those countries that have published demographic characteristics of their confi rmed cases comparatively early and consistently over the course of the pandemic. Consequently, the IFR divides the total number of confi rmed deaths by COVID-19 by the total number of infections with SARS-CoV-2. abstract: Policymakers, experts and the general public heavily rely on the data that are being reported in the context of the coronavirus pandemic. Daily data releases on confirmed COVID-19 cases and deaths provide information on the course of the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32536714/ doi: 10.1007/s10272-020-0893-1 id: cord-256385-g1wcfrfi author: Badraoui, Riadh title: Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 date: 2020-08-05 words: 6071.0 sentences: 332.0 pages: flesch: 48.0 cache: ./cache/cord-256385-g1wcfrfi.txt txt: ./txt/cord-256385-g1wcfrfi.txt summary: title: Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 A better understood of ARDS key features and the pathophysiological injuries of the pulmonary parenchyma are linked to lessons learned from previous severe diseases associated previous coronaviruses outbreaks (especially SARS-CoV and MERS-CoV) and more the ongoing SARS-CoV-2. The novel coronavirus, finally named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and it''s inducing Coronavirus Disease 2019 (COVID-19) (Gorbalenya et al., 2020; Khailany et al., 2020) . While SARS-CoV-2 induces mild symptoms in several infected patients (low pathogenic), it can also be associated with a fast onset of widespread infection in the lungs worsened in an acute respiratory distress syndrome (ARDS) . Lessons learned from previous severe diseases caused by coronaviruses outbreaks (SARS-CoV and MERS-CoV) and more recently SARS-CoV-2 lead to a better understood of ARDS key features associated COVID-19. abstract: Acute Respiratory Distress Syndrome (ARDS) is a form of respiratory failure in human. The number of deaths caused by SARS-CoV-2 infection inducing this severe pneumonia (ARDS) is relatively high. In fact, COVID-19 might get worsen in ARDS and provoke respiratory failure. A better understood of ARDS key features and the pathophysiological injuries of the pulmonary parenchyma are linked to lessons learned from previous severe diseases associated previous coronaviruses outbreaks (especially SARS-CoV and MERS-CoV) and more the ongoing SARS-CoV-2. The ARDS mechanism includes a diffuse alveolar damage associated disruption of alveolar capillary membrane, pulmonary edema, damaged endothelium and increased permeability. A diffuse inflammation, with acute onset, on the lung tissue accompanied by release of biochemical signal and inflammatory mediators (TNFα, IL-1 and IL-6) leading to hypoxemia, low PaO(2)/FiO(2) ratio and the chest radiological expression of bilateral infiltrates in ARDS. The ongoing outbreak could lead to a better understood of ARDS pathophysiology and prognostic. An overview is also highlighted about the seven coronaviruses proved to infect human especially those having ability to cause severe disease SARS-CoV, MERS-CoV and SARS-CoV-2. In this review, we focused on the major pathological mechanisms leading to the ARDS development as a result of viral infection, severe COVID-19 worsening. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32752936/ doi: 10.1080/07391102.2020.1803139 id: cord-294295-sd5893ii author: Badua, Christian Luke D.C. title: Genomic and Proteomic Mutation Landscapes of SARS‐CoV‐2 date: 2020-09-24 words: 3432.0 sentences: 193.0 pages: flesch: 57.0 cache: ./cache/cord-294295-sd5893ii.txt txt: ./txt/cord-294295-sd5893ii.txt summary: The overall frequency and densities of mutations in the genes and proteins of SARS‐CoV‐2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. Altogether, approximately similar proportions of nucleotide change types were observed between genomes among the geographical areas collected from December-March 2020 versus December-May 2020 ( Figure 3B , 3C). All in all, the ORF7b gene/protein was observed to have no mutations in all geographical region and between the study timepoints, therefore this gene may be potentially conserved in SARS-CoV-2. In conclusion, this study highlights the importance of the characterization of both nucleotide and amino acid mutation landscape in SAR-CoV-2 to identify hotspots and coldspots that may be significant in the effectivity of diagnostic tools and treatment options for COVID-19, over the different areas worldwide as the pandemic continues. abstract: The ongoing pandemic caused by a novel coronavirus, SARS‐CoV‐2, affects thousands of people every day worldwide. Hence, drugs and vaccines effective against all variants of SARS‐CoV‐2 are crucial today. Viral genome mutations are commonly existent which may impact the encoded proteins, possibly resulting to varied effectivity of detection tools and disease treatment. Thus, this study surveyed the SARS‐CoV‐2 genome and proteome and evaluated its mutation characteristics. Phylogenetic analyses of SARS‐CoV‐2 genes and proteins show three major clades and one minor clade (P6810S; ORF1ab). The overall frequency and densities of mutations in the genes and proteins of SARS‐CoV‐2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. ORF8 protein had the highest mutation density across all geographical areas. Moreover, mutation hotspots neighboring and at the catalytic site of RNA‐dependent‐RNA‐polymerase were found that might challenge the binding and effectivity of remdesivir. Mutation coldspots may present as conserved diagnostic and therapeutic targets were found in ORF7b, ORF9b and ORF14. These findings suggest that the virion's genotype and phenotype in a specific population should be considered in developing diagnostic tools, and treatment options. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26548 doi: 10.1002/jmv.26548 id: cord-274788-oyk8js16 author: Bae, Sanghyuk title: Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea date: 2020-08-05 words: 3249.0 sentences: 184.0 pages: flesch: 58.0 cache: ./cache/cord-274788-oyk8js16.txt txt: ./txt/cord-274788-oyk8js16.txt summary: BACKGROUND: In February 2020, a coronavirus disease 2019 (COVID-19) outbreak was reported in fitness centers in Cheonan, Korea. We determined the epidemiological characteristics of confirmed cases of SARS-CoV-2 infection, and estimated the time-dependent reproduction number to assess the transmission dynamics of the infection. In this report, we describe the epidemiological characteristics of the COVID-19 outbreak at fitness centers in Cheonan, Korea, based on the official epidemiological investigation, and document the effectiveness of contact tracing and isolation at containing the outbreaks. In the present study, we described epidemiological characteristics of a COVID-19 outbreak in fitness centers in Cheonan, Korea from February 24 to March 13, 2020. A previous epidemiological investigation of an outbreak in a single call center in Seoul, Korea reported that 99.8% of traced contacts had been tested. abstract: BACKGROUND: In February 2020, a coronavirus disease 2019 (COVID-19) outbreak was reported in fitness centers in Cheonan, Korea. METHODS: From February 24 to March 13, an epidemiological investigation was conducted on the fitness center outbreak. All those who were screened were tested for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using real-time reverse transcriptase polymerase chain reaction. Contacts were traced and self-isolated for 14 days. We determined the epidemiological characteristics of confirmed cases of SARS-CoV-2 infection, and estimated the time-dependent reproduction number to assess the transmission dynamics of the infection. RESULTS: A total of 116 cases were confirmed, and 1,687 contacts were traced. The source cases were 8 Zumba instructors who led aerobics classes in 10 fitness centers, and had the largest average number of contacts. A total of 57 Zumba class participants, 37 of their family members, and 14 other contacts were confirmed as cases. The attack rate was 7.3%. The contacts at Zumba classes and homes had a higher attack rate than other contacts. The mean serial interval (± standard deviation) were estimated to be 5.2 (± 3.8) days. The time-dependent reproduction number was estimated to be 6.1 at the beginning of the outbreak, but it dropped to less than 1, 2 days after the epidemiological investigation was launched. CONCLUSION: The results suggest that the COVID-19 outbreak was effectively contained with rigorous contact tracing, isolating, and testing in combination with social distancing without a lock-down. url: https://doi.org/10.3346/jkms.2020.35.e288 doi: 10.3346/jkms.2020.35.e288 id: cord-294788-9usyb1nn author: Baek, Woong Kee title: A Comprehensive Review of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-05-03 words: 4459.0 sentences: 231.0 pages: flesch: 46.0 cache: ./cache/cord-294788-9usyb1nn.txt txt: ./txt/cord-294788-9usyb1nn.txt summary: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus strain that causes coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China in December 2019. It is suspected that the acute respiratory distress syndrome (ARDS)-like picture in SARS-CoV-2-infected patients is precipitated and worsened by the excess monocytes in response to GM-CSF, which is released by rapidly activated CD4+T-cell lineage [17] . have reported that the cytokine profile and the trend of the inflammatory markers of SARS-CoV-2-infected patients present similarly to the secondary hemophagocytic lymphohistiocytosis (sHLH), whose severe clinical presentation is related to the cytokine storm [23] . There is no consensus yet on how to treat SARS-CoV-2-infected patients who present with a wide spectrum of clinical symptoms and severity. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Epub ahead of print) abstract: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus strain that causes coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China in December 2019. It spread to several countries across continents and infected more than one million people within three months. While there is no consensus on the treatment of the disease yet, understanding the virus and its transmission is a cardinal priority. SARS-CoV-2 can be transmitted through bodily fluid. Upon inoculation, the surface enzyme angiotensin-converting enzyme 2 (ACE2) acts as a receptor protein for viral entry. The mean incubation period is 5.1 days, and infected individuals can exhibit a variety of symptoms from fever, cough, dyspnea, and respiratory failure to even multiorgan failure. Given the current situation, it is of paramount importance to understand the virus as thoroughly as possible. In this review, we discuss the background, epidemiology, possible pathophysiology, clinical presentation, and diagnostic studies related to SARS-CoV-2 infection. We also elaborate on the current research and evidence on treatment options and vaccine development based on the literature. url: https://doi.org/10.7759/cureus.7943 doi: 10.7759/cureus.7943 id: cord-260886-v1ei9im8 author: Baggett, Travis P. title: COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing date: 2020-04-15 words: 1103.0 sentences: 78.0 pages: flesch: 56.0 cache: ./cache/cord-260886-v1ei9im8.txt txt: ./txt/cord-260886-v1ei9im8.txt summary: Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. In mid-March, 2020, Boston Health Care for the Homeless Program (BHCHP), in partnership with city and state public health agencies and community partners, created a COVID-19 response strategy that included front-door symptom screening at area shelters, expedited referrals for SARS-CoV-2 testing and isolation for those with respiratory symptoms, dedicated treatment settings for COVID-positive individuals, and detailed contact tracing of confirmed cases. With support from the Massachusetts Department of Public Health (MDPH), BHCHP rapidly conducted polymerase chain reaction (PCR) testing for SARS-CoV-2 along with focused symptom assessments among all guests residing at the shelter over a 2-day period. abstract: The circumstances of homelessness create the potential for rapid transmission of SARS-CoV-2 in this vulnerable population. Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. Of 408 participants, 147 (36.0%) were PCR-positive for SARS-CoV-2. COVID-positive individuals were more likely to be male (p<0.001) but did not differ significantly from COVID-negative individuals with respect to other demographic and clinical characteristics. Cough (7.5%), shortness of breath (1.4%), and fever (0.7%) were all uncommon among COVID-positive individuals. Our findings illustrate the rapidity with which COVID-19 can be widely transmitted in a homeless shelter setting and suggest that universal PCR testing, rather than a symptom triggered approach, may be a better strategy for identifying and mitigating COVID-19 among people experiencing homelessness. url: https://doi.org/10.1101/2020.04.12.20059618 doi: 10.1101/2020.04.12.20059618 id: cord-259869-kwzsdhrr author: Baghizadeh Fini, Maryam title: Oral saliva and CVID-19 date: 2020-05-27 words: 2440.0 sentences: 134.0 pages: flesch: 49.0 cache: ./cache/cord-259869-kwzsdhrr.txt txt: ./txt/cord-259869-kwzsdhrr.txt summary: Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable. Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable in a dental office. The analysis of saliva in COVID-19 cases can help to explain the pathogenesis because epithelial oral cavity cells demonstrated ample expression of the Angiotensin-Converting Enzyme 2 (ACE2) receptor that plays a critical role in allowing SARS-CoV-2 to enter the cells [4] . SARS-CoV-2 in the lower and upper respiratory tract reaches the oral cavity along with the liquid droplets; SARS-CoV-2 in the blood may enter the mouth through the gingival crevicular fluid; and major and minor infection of the salivary gland, with the ensuing release of particles into the saliva through salivary ducts [7] . Detection of SARS-CoV-2 in Saliva and Characterization of Oral Symptoms in COVID-19 Patients. abstract: Outbreak pneumonia announced in Wuhan, China, in December 2019, had its causative factor classified as a new coronavirus (SARS-CoV-2). Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable. COVID-19 can be detected through salivary diagnostic testing which has lots of advantages for medical care professionals and patients. It should be noted that not only does saliva offer an ecological niche for the colonization and development of oral microorganisms, but it also prevents the overgrowth of particular pathogens such as viral factors. The aim of this study is to gather all the information about saliva and its association with COVID-19 for the whole health care professionals across the world. url: https://doi.org/10.1016/j.oraloncology.2020.104821 doi: 10.1016/j.oraloncology.2020.104821 id: cord-276414-kicu0tv5 author: Bahadur Gurung, Arun title: In silico screening of FDA approved drugs reveals ergotamine and dihydroergotamine as potential coronavirus main protease enzyme inhibitors date: 2020-06-10 words: 2423.0 sentences: 138.0 pages: flesch: 58.0 cache: ./cache/cord-276414-kicu0tv5.txt txt: ./txt/cord-276414-kicu0tv5.txt summary: Interestingly, the anti-migraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. In the present study, we have explored the possibilities of FDA approved drugs as potential inhibitors of the coronavirus main protease, a therapeutically important drug target playing a salient role in the maturation and processing of the viral polyproteins and are vital for viral replication and transcription. Interestingly, the antimigraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. abstract: Abstract Coronaviruses with the largest viral genomes are positive-sense RNA viruses associated with a history of global epidemics such as the severe respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS) and recently the coronavirus disease 2019 (COVID-19). There has been no vaccines or drugs available for the treatment of human coronavirus infections to date. In the present study, we have explored the possibilities of FDA approved drugs as potential inhibitors of the coronavirus main protease, a therapeutically important drug target playing a salient role in the maturation and processing of the viral polyproteins and are vital for viral replication and transcription. We have used molecular docking approach and have successfully identified the best lead molecules for each enzyme target. Interestingly, the anti-migraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. Hence both these lead molecules can be further taken for wet-lab experimentation studies before repurposing them as anti-coronaviral drug candidates. url: https://www.ncbi.nlm.nih.gov/pubmed/32837219/ doi: 10.1016/j.sjbs.2020.06.005 id: cord-265221-qtkwciym author: Bahadur, Gulam title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 words: 3261.0 sentences: 182.0 pages: flesch: 49.0 cache: ./cache/cord-265221-qtkwciym.txt txt: ./txt/cord-265221-qtkwciym.txt summary: It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. raising equal concerns for embryo and fetal development (Colaco et al., 2020) .In males, ACE2 receptor sites have been reported in testicular tissue which then have the capability to harbour SARS-CoV-2 virus and eventual shedding into the semen and hence its implication in sexual transmission, early pregnancy or early in utero embryonic development. Studies analysing SARS-CoV-2 in seminal fluid or testicular biopsies have so far lacked appropriate controls and patients suffered from predominantly mild infections and tested several weeks after the infection, thereby increasing the complexity of result interpretation. Also no SARS-CoV-2 was detected in expressed prostatic secretion (EPS) of 18 confirmed Covid-19 infected patients and 5 strongly suspected cases but absent semen analyses. abstract: The question on whether SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus (SARS-CoV or SARS-CoV-2, Covid-19) can be harboured in testes and/or the semen is currently unanswered. It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. Here we critically analyse the evidence so far and the possible implications. The diagnostic test limitations posed in both sampling and testing methodologies, their validation, and relevancy in interpreting data are also highlighted. url: https://doi.org/10.1016/j.rbmo.2020.05.014 doi: 10.1016/j.rbmo.2020.05.014 id: cord-313379-6sa6oc6u author: Bahar, B. title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children date: 2020-08-07 words: 2674.0 sentences: 181.0 pages: flesch: 54.0 cache: ./cache/cord-313379-6sa6oc6u.txt txt: ./txt/cord-313379-6sa6oc6u.txt summary: title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children 14 We report viral and antibody testing results from our 95 pediatric patient population in order to contribute to a better understanding of timing of viral 96 clearance and antibody production in children with In addition to the RT-PCR results, qualitative and quantitative serologic testing results, age and 107 sex were also included in the data extracts. In this study, we demonstrated that IgG class antibodies directed against S1 and S2 228 glycoproteins could be detected in blood samples of children before viral clearance. . https://doi.org/10.1101/2020.08.06.20162446 doi: medRxiv preprint A strength of our study was the inclusion of patients from multiple pediatric age groups with 262 sequential PCR testing, which allowed comparison between age groups and sex serologic assays for SARS-CoV-2 are still in early phases of development. abstract: Objectives: To improve understanding of transition from viral infection to viral clearance, and antibody response in pediatric patients with SARS-CoV-2 infection. Study design: This retrospective analysis of children tested for SARS-CoV-2 by RT-PCR and IgG antibody at a quaternary-care, free-standing pediatric hospital between March 13th, 2020 to June 21st, 2020 included 6369 patients who underwent PCR testing and 215 patients who underwent antibody testing. During the initial study period, testing focused primarily on symptomatic children; the later study period included asymptomatic patients who underwent testing as preadmission or preprocedural screening. We report the proportion of positive and negative tests, time to viral clearance, and time to seropositivity. Results: The rate of positivity varied over time due to viral circulation in the community and transition from targeted testing of symptomatic patients to more universal screening of hospitalized patients. Median duration of viral shedding (RT-PCR positivity) was 19.5 days and RT-PCR negativity from positivity was 25 days. Of note, patients aged 6 to 15 years demonstrated a longer period of RT-PCR negativity from positivity, compared to patients aged 16 to 22 years (median=32 versus 18 days, p=0.015). Median time to seropositivity from RT-PCR positivity was 18 days while median time to reach adequate levels of neutralizing antibodies (defined as equivalent to 160 titer) was 36 days. Conclusions: The majority of patients demonstrated a prolonged period of viral shedding after infection with SARS CoV-2. Whether this correlates with persistent infectivity is unknown. Only 17 of 33 patients demonstrated neutralizing antibodies, suggesting that some patients may not mount significant immune responses to infection. It remains unknown if IgG antibody production correlates with immunity and how long measurable antibodies persist and protect against future infection. url: https://doi.org/10.1101/2020.08.06.20162446 doi: 10.1101/2020.08.06.20162446 id: cord-290277-ndfoppoq author: Bahl, Prateek title: Airborne or droplet precautions for health workers treating COVID-19? date: 2020-04-16 words: 3496.0 sentences: 207.0 pages: flesch: 58.0 cache: ./cache/cord-290277-ndfoppoq.txt txt: ./txt/cord-290277-ndfoppoq.txt summary: World Health Organization (WHO) has issued guidelines for contact and droplet precautions for Healthcare Workers (HCWs) caring for suspected COVID-19 patients, whilst the US Centre for Disease Control (CDC) has recommended airborne precautions. We aimed to review the evidence for horizontal distance travelled by droplets and the guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) on respiratory protection for COVID-19. We aimed to review the evidence supporting the rule of 1 m (≈3 ft) spatial separation for droplet precautions in the context of guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) for HCWs on respiratory protection for COVID-19. Interim Infection Prevention and Control Recommendations for Hospitalized Patients with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) abstract: Cases of COVID-19 have been reported in over 200 countries. Thousands of health workers have been infected and outbreaks have occurred in hospitals, aged care facilities and prisons. World Health Organization (WHO) has issued guidelines for contact and droplet precautions for Healthcare Workers (HCWs) caring for suspected COVID-19 patients, whilst the US Centre for Disease Control (CDC) has recommended airborne precautions. The 1 – 2 m (≈3 – 6 ft) rule of spatial separation is central to droplet precautions and assumes large droplets do not travel further than 2 m (≈6 ft). We aimed to review the evidence for horizontal distance travelled by droplets and the guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) on respiratory protection for COVID-19. We found that the evidence base for current guidelines is sparse, and the available data do not support the 1 – 2 m (≈3 – 6 ft) rule of spatial separation. Of ten studies on horizontal droplet distance, eight showed droplets travel more than 2 m (≈6 ft), in some cases more than 8 meters (≈26 ft). Several studies of SARS-CoV-2 support aerosol transmission and one study documented virus at a distance of 4 meters (≈13 ft) from the patient. Moreover, evidence suggests infections cannot neatly be separated into the dichotomy of droplet versus airborne transmission routes. Available studies also show that SARS-CoV-2 can be detected in the air, 3 hours after aeroslisation. The weight of combined evidence supports airborne precautions for the occupational health and safety of health workers treating patients with COVID-19. url: https://doi.org/10.1093/infdis/jiaa189 doi: 10.1093/infdis/jiaa189 id: cord-030934-t7akdu6x author: Bahrami, Afsane title: Genetic and pathogenic characterization of SARS-CoV-2: a review date: 2020-08-26 words: 6472.0 sentences: 356.0 pages: flesch: 45.0 cache: ./cache/cord-030934-t7akdu6x.txt txt: ./txt/cord-030934-t7akdu6x.txt summary: The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. Bioinformatics analysis of the viral genome from one COVID-19 patient shared 89 and 82% sequence similarity with bat SARS-like-CoVZXC21 and human SARS-CoV, respectively [41] . In a recent report it was shown that SARS-CoV-2''s S-protein entry into 293/human ACE2 receptor cells is primarily mediated via endocytosis, and that PIKfyve, a TPC2 and cathepsin L are crucial for virus entry. Findings of an open-label nonrandomized clinical trial among 22 infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in COVID-19 cases and its effectiveness is promoted by azithromycin [99] . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response abstract: The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. This virus belongs to the beta-coronavirus group that contains a single stranded RNA with a nucleoprotein within a capsid. SARS-CoV-2 shares 80% nucleotide identity to SARS-CoV. The virus is disseminated by its binding to the ACE2 receptors on bronchial epithelial cells. The diagnosis of COVID-19 is based on a laboratory-based reverse transcription polymerase chain reaction (RT-PCR) test together with chest computed tomography imaging. To date, no antiviral therapy has been approved, and many aspects of the COVID-19 are unknown. In this review, we will focus on the recent information on genetics and pathogenesis of COVID-19 as well as its clinical presentation and potential treatments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451412/ doi: 10.2217/fvl-2020-0129 id: cord-289892-yh1lioyz author: Bai, Bingke title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 words: 5451.0 sentences: 300.0 pages: flesch: 55.0 cache: ./cache/cord-289892-yh1lioyz.txt txt: ./txt/cord-289892-yh1lioyz.txt summary: Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. In addition, because in vitro infection model of bat SL-CoV has not so far been established, we intended to use VLPs as an alternative to study the immune responses induced in DCs. Therefore, we compared the phenotypic and functional changes of immature DCs inoculated with BVLPs or with SARS CoV VLPs. The S-specific immune activation was further confirmed in mice using S DNA vaccines. Combining the flow cytometry results in Fig. 2 , it is reasonable to draw a conclusion that the structure of BVLPs, not LPS contamination, contributed to cytokine production in BVLPs-treated DCs. We previously constructed SARS CoV VLPs and investigated the humoral and cellular immune responses induced by SARS CoV VLPs in mice [29] . abstract: The pathogenesis of SARS coronavirus (CoV) remains poorly understood. In the current study, two recombinant baculovirus were generated to express the spike (S) protein of SARS-like coronavirus (SL-CoV) isolated from bats (vAcBS) and the envelope (E) and membrane (M) proteins of SARS-CoV, respectively. Co-infection of insect cells with these two recombinant baculoviruses led to self-assembly of virus-like particles (BVLPs) as demonstrated by electron microscopy. Incorporation of S protein of vAcBS (BS) into VLPs was confirmed by western blot and immunogold labeling. Such BVLPs up-regulated the level of CD40, CD80, CD86, CD83, and enhanced the secretion of IL-6, IL-10 and TNF-α in immature dendritic cells (DCs). Immune responses were compared in immature DCs inoculated with BVLPs or with VLPs formed by S, E and M proteins of human SARS-CoV. BVLPs showed a stronger ability to stimulate DCs in terms of cytokine induction as evidenced by 2 to 6 fold higher production of IL-6 and TNF-α. Further study indicated that IFN-γ+ and IL-4+ populations in CD4+ T cells increased upon co-cultivation with DCs pre-exposed with BVLPs or SARS-CoV VLPs. The observed difference in DC-stimulating activity between BVLPs and SARS CoV VLPs was very likely due to the S protein. In agreement, SL-CoV S DNA vaccine evoked a more vigorous antibody response and a stronger T cell response than SARS-CoV S DNA in mice. Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. Finding in this study may provide important information for vaccine development as well as for understanding the pathogenesis of SARS-like CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/18628832/ doi: 10.1371/journal.pone.0002685 id: cord-300423-q2i328sz author: Bai, Lei title: Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date: 2020-10-14 words: 1470.0 sentences: 106.0 pages: flesch: 64.0 cache: ./cache/cord-300423-q2i328sz.txt txt: ./txt/cord-300423-q2i328sz.txt summary: Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. The results demonstrate that the pre-infection of 57 IAV strongly enhances the infectivity of SARS-CoV-2 by boosting viral entry in the cells 58 and by elevating viral load plus more severe lung damage in infected mice. We 75 further tested more cell lines to show that the enhancement of the pSARS-CoV-2 infectivity 76 by IAV was a general effect although the increased folds were different (lower basal level 77 of infectivity, higher enhancement fold) (Fig.1D ). We found that the pre-infection of IAV 80 strongly increased the copy numbers of the SARS-CoV-2 genome (E and N genes) in both 81 cell lysates and supernatants of A549 (~15 folds) (Fig.1F) . The histological data in Fig. 2D further illustrated that IAV and 98 SARS-CoV-2 co-infection induced more severe lung pathologic changes with massive 99 infiltrating cells and obvious alveolar necrosis as compared to SARS-CoV-2 single 100 infection or mock infection. abstract: The upcoming flu season in the northern hemisphere merging with the current COVID-19 pandemic raises a potentially severe threat to public health. Through experimental co-infection of IAV with either pseudotyped or SARS-CoV-2 live virus, we found that IAV pre-infection significantly promoted the infectivity of SARS-CoV-2 in a broad range of cell types. Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. Moreover, such enhancement of SARS-CoV-2 infectivity was not seen with several other viruses probably due to a unique IAV segment as an inducer to elevate ACE2 expression. This study illustrates that IAV has a special nature to aggravate SARS-CoV-2 infection, and prevention of IAV is of great significance during the COVID-19 pandemic. url: https://doi.org/10.1101/2020.10.14.335893 doi: 10.1101/2020.10.14.335893 id: cord-352886-6lzlt6ur author: Bai, Qifeng title: MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm date: 2020-08-11 words: 6655.0 sentences: 377.0 pages: flesch: 51.0 cache: ./cache/cord-352886-6lzlt6ur.txt txt: ./txt/cord-352886-6lzlt6ur.txt summary: Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. To use the merit of deep learning, our designed soft tool employs the sequencebased generative model and graph neural networks (GNNs) generative model for producing the ligand set and small molecular fragments (see Figure 1 ). Figure 7B shows the drug virtual screening results of SARS-CoV-2 M pro from 2 million druglike ligands by deep learning generative model and molecular docking. abstract: Deep learning is an important branch of artificial intelligence that has been successfully applied into medicine and two-dimensional ligand design. The three-dimensional (3D) ligand generation in the 3D pocket of protein target is an interesting and challenging issue for drug design by deep learning. Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. The MolAICal software mainly contains two modules for 3D drug design. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. Besides, the Lipinski’s rule of five, Pan-assay interference compounds (PAINS), synthetic accessibility (SA) and other user-defined rules are introduced for filtering out unwanted ligands in MolAICal. To show the drug design modules of MolAICal, the membrane protein glucagon receptor and non-membrane protein SARS-CoV-2 main protease are chosen as the investigative drug targets. The results show MolAICal can generate the various and novel ligands with good binding scores and appropriate XLOGP values. We believe that MolAICal can use the advantages of deep learning model and classical programming for designing 3D drugs in protein pocket. MolAICal is freely for any nonprofit purpose and accessible at https://molaical.github.io. url: https://doi.org/10.1093/bib/bbaa161 doi: 10.1093/bib/bbaa161 id: cord-254162-tu81j66h author: Bai, Xiyuan title: Hypothesis: alpha-1-antitrypsin is a promising treatment option for COVID-19 date: 2020-11-12 words: 5512.0 sentences: 286.0 pages: flesch: 39.0 cache: ./cache/cord-254162-tu81j66h.txt txt: ./txt/cord-254162-tu81j66h.txt summary: Sixth, AAT inhibition of elastase can antagonize the formation of neutrophil extracellular traps (NETs), a complex extracellular structure comprised of neutrophil-derived DNA, histones, and proteases, and implicated in the immunothrombosis of COVID-19; indeed, AAT has been shown to change the shape and adherence of non-COVID-19-related NETs. Seventh, AAT inhibition of endothelial cell apoptosis may limit the endothelial injury linked to severe COVID-19-associated acute lung injury, multi-organ dysfunction, and pre-eclampsia-like syndrome seen in gravid women. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. abstract: No definitive treatment for COVID-19 exists although promising results have been reported with remdesivir and glucocorticoids. Short of a truly effective preventive or curative vaccine against SARS-CoV-2, it is becoming increasingly clear that multiple pathophysiologic processes seen with COVID-19 as well as SARS-CoV-2 itself should be targeted. Because alpha-1-antitrypsin (AAT) embraces a panoply of biologic activities that may antagonize several pathophysiologic mechanisms induced by SARS-CoV-2, we hypothesize that this naturally occurring molecule is a promising agent to ameliorate COVID-19. We posit at least seven different mechanisms by which AAT may alleviate COVID-19. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. Second, AAT has anti-viral activity against other RNA viruses HIV and influenza as well as induces autophagy, a known host effector mechanism against MERS-CoV, a related coronavirus that causes the Middle East Respiratory Syndrome. Third, AAT has potent anti-inflammatory properties, in part through inhibiting both nuclear factor-kappa B (NFκB) activation and ADAM17 (also known as tumor necrosis factor-alpha converting enzyme), and thus may dampen the hyper-inflammatory response of COVID-19. Fourth, AAT inhibits neutrophil elastase, a serine protease that helps recruit potentially injurious neutrophils and implicated in acute lung injury. AAT inhibition of ADAM17 also prevents shedding of ACE2 and hence may preserve ACE2 inhibition of bradykinin, reducing the ability of bradykinin to cause a capillary leak in COVID-19. Fifth, AAT inhibits thrombin, and venous thromboembolism and in situ microthrombi and macrothrombi are increasingly implicated in COVID-19. Sixth, AAT inhibition of elastase can antagonize the formation of neutrophil extracellular traps (NETs), a complex extracellular structure comprised of neutrophil-derived DNA, histones, and proteases, and implicated in the immunothrombosis of COVID-19; indeed, AAT has been shown to change the shape and adherence of non-COVID-19-related NETs. Seventh, AAT inhibition of endothelial cell apoptosis may limit the endothelial injury linked to severe COVID-19-associated acute lung injury, multi-organ dysfunction, and pre-eclampsia-like syndrome seen in gravid women. Furthermore, because both NETs formation and the presence of anti-phospholipid antibodies are increased in both COVID-19 and non-COVID pre-eclampsia, it suggests a similar vascular pathogenesis in both disorders. As a final point, AAT has an excellent safety profile when administered to patients with AAT deficiency and is dosed intravenously once weekly but also comes in an inhaled preparation. Thus, AAT is an appealing drug candidate to treat COVID-19 and should be studied. url: https://www.sciencedirect.com/science/article/pii/S0306987720332850?v=s5 doi: 10.1016/j.mehy.2020.110394 id: cord-269021-juh2qkm0 author: Bai, Zhihua title: The Rapid Assessment and Early Warning Models for COVID-19 date: 2020-04-01 words: 4599.0 sentences: 226.0 pages: flesch: 48.0 cache: ./cache/cord-269021-juh2qkm0.txt txt: ./txt/cord-269021-juh2qkm0.txt summary: Human beings have experienced a serious public health event as the new pneumonia (COVID-19), caused by the severe acute respiratory syndrome coronavirus has killed more than 3000 people in China, most of them elderly or people with underlying chronic diseases or immunosuppressed states. In the case of a gradually improved infectious disease surveillance system, the research on forecasting and early warning of epidemics based on models has become the focus of the public health system. In response to the current epidemic of SARS-CoV-2, many researchers have developed mathematical models with varying degrees of complexity, aiming to assess the capacity of pathogen transmission and which interventions are most likely to be effective (Fig. 2) . Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven Modelling analysis of the early outbreak abstract: Human beings have experienced a serious public health event as the new pneumonia (COVID-19), caused by the severe acute respiratory syndrome coronavirus has killed more than 3000 people in China, most of them elderly or people with underlying chronic diseases or immunosuppressed states. Rapid assessment and early warning are essential for outbreak analysis in response to serious public health events. This paper reviews the current model analysis methods and conclusions from both micro and macro perspectives. The establishment of a comprehensive assessment model, and the use of model analysis prediction, is very efficient for the early warning of infectious diseases. This would significantly improve global surveillance capacity, particularly in developing regions, and improve basic training in infectious diseases and molecular epidemiology. url: https://doi.org/10.1007/s12250-020-00219-0 doi: 10.1007/s12250-020-00219-0 id: cord-322811-6lebh7ca author: Baig, Mirza S. title: Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells date: 2020-06-26 words: 4119.0 sentences: 245.0 pages: flesch: 53.0 cache: ./cache/cord-322811-6lebh7ca.txt txt: ./txt/cord-322811-6lebh7ca.txt summary: METHODS: Docking and Molecular Dynamics (MD) simulation studies revealed that designed peptide maintains their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. RESULTS: We have designed a novel peptide that could inhibit SARS-CoV-2 spike protein interaction with ACE2, thereby blocking the cellular entry of the virus. Currently, the computational analysis of structural differences in human ACE2 impact its binding to the SARS-CoV-2 spike protein, which thereby lays a foundation for the design and development of ACE2-based peptide inhibitors of SARS-CoV-2 [47] [48] [49] . After a detailed analysis of interface residues, a small stretch of the ACE2 PD N-terminal region (23-amino acids: Glu23 to Leu45) was found to be interacting majorly with the SARS-CoV-2 spike protein ( Fig. 2 and Table 1 ). Computational alanine (A) scanning was performed to identify the critically important amino acids of the 23aa peptide inhibitor involved in binding to the SARS-CoV-2 spike protein. abstract: BACKGROUND AND OBJECTIVE: Coronavirus disease (COVID-19) is an ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the incessant spread of the disease with substantial morbidity and mortality rates, there is an urgent demand for effective therapeutics and vaccines to control and diminish this pandemic. A critical step in the crosstalk between the virus and the host cell is the binding of SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor present on the surface of the host cells. Hence, inhibition of this interaction could be a promising strategy to combat the SARS-CoV-2 infection. METHODS: Docking and Molecular Dynamics (MD) simulation studies revealed that designed peptide maintains their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. RESULTS: We have designed a novel peptide that could inhibit SARS-CoV-2 spike protein interaction with ACE2, thereby blocking the cellular entry of the virus. CONCLUSION: Our findings suggest that computationally developed inhibitory peptide may be developed as an anti-SARS-CoV-2 agent for the treatment of SARS-CoV-2 infection. We further plan to pursue the peptide in cell-based assays and eventually for clinical trials. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40268-020-00312-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s40268-020-00312-5 doi: 10.1007/s40268-020-00312-5 id: cord-270550-if748w2n author: Bailey, Adam L. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 words: 5808.0 sentences: 440.0 pages: flesch: 49.0 cache: ./cache/cord-270550-if748w2n.txt txt: ./txt/cord-270550-if748w2n.txt summary: To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. abstract: Epidemiological studies of the COVID-19 pandemic have revealed evidence of cardiac involvement and documented that myocardial injury and myocarditis are predictors of poor outcomes. Nonetheless, little is understood regarding SARS-CoV-2 tropism within the heart and whether cardiac complications result directly from myocardial infection. Here, we develop a human engineered heart tissue model and demonstrate that SARS-CoV-2 selectively infects cardiomyocytes. Viral infection is dependent on expression of angiotensin-I converting enzyme 2 (ACE2) and endosomal cysteine proteases, suggesting an endosomal mechanism of cell entry. After infection with SARS-CoV-2, engineered tissues display typical features of myocarditis, including cardiomyocyte cell death, impaired cardiac contractility, and innate immune cell activation. Consistent with these findings, autopsy tissue obtained from individuals with COVID-19 myocarditis demonstrated cardiomyocyte infection, cell death, and macrophage-predominate immune cell infiltrate. These findings establish human cardiomyocyte tropism for SARS-CoV-2 and provide an experimental platform for interrogating and mitigating cardiac complications of COVID-19. url: https://doi.org/10.1101/2020.11.04.364315 doi: 10.1101/2020.11.04.364315 id: cord-258873-l9oxmqdp author: Baker, D. title: COVID‐19 vaccine‐readiness for anti‐CD20‐depleting therapy in autoimmune diseases date: 2020-08-01 words: 6017.0 sentences: 323.0 pages: flesch: 44.0 cache: ./cache/cord-258873-l9oxmqdp.txt txt: ./txt/cord-258873-l9oxmqdp.txt summary: It appears that the innate immune response, and perhaps later anti-viral CD8 T cell responses, could eliminate the SARS-CoV2 before significant antibody responses have developed [20, 28, 33] (Fig. 1) , suggesting that most MS treatments that largely exhibit limited persistent effects on the innate immune and CD8 T cell responses would have limited influence on COVID-19. The suggestion that rituximab treatment may increase risk of infection should be considered in the context of possible sampling biases, although this Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells in the lung and the gut via the angiotensin-converting enzyme 2 (ACE2). If COVID-19-related vaccine responses become a key concern among people with MS or other autoimmune diseases choosing treatment options, the selection of B cell-depleting agents that allow quick repopulation of B cells may be relevant for optimum vaccine readiness. abstract: Although most autoimmune diseases are considered to be CD4 T cell‐ or antibody‐mediated, many respond to CD20‐depleting antibodies that have limited influence on CD4 and plasma cells. This includes rituximab, oblinutuzumab and ofatumumab that are used in cancer, rheumatoid arthritis and off‐label in a large number of other autoimmunities and ocrelizumab in multiple sclerosis. Recently, the COVID‐19 pandemic created concerns about immunosuppression in autoimmunity, leading to cessation or a delay in immunotherapy treatments. However, based on the known and emerging biology of autoimmunity and COVID‐19, it was hypothesised that while B cell depletion should not necessarily expose people to severe SARS‐CoV‐2‐related issues, it may inhibit protective immunity following infection and vaccination. As such, drug‐induced B cell subset inhibition, that controls at least some autoimmunities, would not influence innate and CD8 T cell responses, which are central to SARS‐CoV‐2 elimination, nor the hypercoagulation and innate inflammation causing severe morbidity. This is supported clinically, as the majority of SARS‐CoV‐2‐infected, CD20‐depleted people with autoimmunity have recovered. However, protective neutralizing antibody and vaccination responses are predicted to be blunted until naive B cells repopulate, based on B cell repopulation kinetics and vaccination responses, from published rituximab and unpublished ocrelizumab (NCT00676715, NCT02545868) trial data, shown here. This suggests that it may be possible to undertake dose interruption to maintain inflammatory disease control, while allowing effective vaccination against SARS‐CoV‐29, if and when an effective vaccine is available. url: https://doi.org/10.1111/cei.13495 doi: 10.1111/cei.13495 id: cord-332271-slouuryl author: Baker, Jeremy D. title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date: 2020-08-27 words: 2683.0 sentences: 172.0 pages: flesch: 52.0 cache: ./cache/cord-332271-slouuryl.txt txt: ./txt/cord-332271-slouuryl.txt summary: title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing 27 as selective and potent inhibitors of SARS-CoV-2 Mpro. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Before screening the Broad library, 100 we piloted our assay conditions against the NIH Clinical collections library (~650 compounds) and 101 calculated our Z''-factor for each plate at 0.780 and 0.784 (Fig 1C and D) . abstract: The SARS coronavirus type 2 (SARS-CoV-2) emerged in late 2019 as a zoonotic virus highly transmissible between humans that has caused the COVID-19 pandemic 1,2. This pandemic has the potential to disrupt healthcare globally and has already caused high levels of mortality, especially amongst the elderly. The overall case fatality rate for COVID-19 is estimated to be ∼2.3% overall 3 and 32.3% in hospitalized patients age 70-79 years 4. Therapeutic options for treating the underlying viremia in COVID-19 are presently limited by a lack of effective SARS-CoV-2 antiviral drugs, although steroidal anti-inflammatory treatment can be helpful. A variety of potential antiviral targets for SARS-CoV-2 have been considered including the spike protein and replicase. Based upon previous successful antiviral drug development for HIV-1 and hepatitis C, the SARS-CoV-2 main protease (Mpro) appears an attractive target for drug development. Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing as selective and potent inhibitors of SARS-CoV-2 Mpro. We screened a collection of ∼6,070 drugs with a previous history of use in humans for compounds that inhibit the activity of Mpro in vitro. In our primary screen we found ∼50 compounds with activity against Mpro (overall hit rate <0.75%). Subsequent dose validation studies demonstrated 8 dose responsive hits with an IC50 ≤ 50 μM. Hits from our screen are enriched with hepatitis C NS3/4A protease targeting drugs including Boceprevir (IC50=0.95 μM), Ciluprevir (20.77μM). Narlaprevir (IC50=1.10μM), and Telaprevir (15.25μM). These results demonstrate that some existing approved drugs can inhibit SARS-CoV-2 Mpro and that screen saturation of all approved drugs is both feasible and warranted. Taken together this work suggests previous large-scale commercial drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for rapid repurposing. url: https://doi.org/10.1101/2020.07.10.197889 doi: 10.1101/2020.07.10.197889 id: cord-343043-piyt3i0h author: Baker, S. A. title: Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation. date: 2020-07-07 words: 4608.0 sentences: 268.0 pages: flesch: 47.0 cache: ./cache/cord-343043-piyt3i0h.txt txt: ./txt/cord-343043-piyt3i0h.txt summary: In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly. Given that the mechanism of death in Covid-19 typically involves severe lower respiratory tract infection, a disease feature strongly correlated with age, previous studies have sought to connect lung ACE2 expression with aging 28, 29 . If lung ACE2 expression is triggered by mechanical ventilation itself via inflammatory cytokine production, then these factors may predispose older individuals to severe SARS-CoV-2 infection. In this small series of cases, we identified increased ACE2 RNA and ACE2 protein expression within the human lung associated with age, when controlling for ventilator status. abstract: Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). Additionally, we observed prominent pulmonary endothelial ACE2 expression in 2 patients on either an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly. url: https://doi.org/10.1101/2020.07.05.20140467 doi: 10.1101/2020.07.05.20140467 id: cord-348823-u2gm3kyh author: Baksh, Mizba title: A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic date: 2020-05-18 words: 2249.0 sentences: 116.0 pages: flesch: 45.0 cache: ./cache/cord-348823-u2gm3kyh.txt txt: ./txt/cord-348823-u2gm3kyh.txt summary: About 80% of COVID-19 infections are mild or asymptomatic and never require hospitalization but about 5% of patients become critically ill and develop acute respiratory distress syndrome (ARDS). The widely used management for ARDS in COVID-19 has been in line with the standard approach, but the need to adjust the treatment protocols has been questioned based on the reports of higher mortality risk among those requiring mechanical ventilation. Although some antimalarial and antiviral drugs may prove effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), their safety and efficacy are still under clinical trials. We conducted a systematic review of case reports on ARDS in SARS-CoV-2 infection to summarize the clinical presentation, laboratory and chest imaging findings, management protocols, and outcome of ARDS in COVID-19-positive patients. Tissue plasminogen activator (tPA) treatment for COVID-19 associated acute respiratory distress syndrome (ARDS): a case series abstract: The outbreak of coronavirus disease 2019 (COVID-19) was declared a global pandemic after it spread to 213 countries and has the highest total number of cases worldwide. About 80% of COVID-19 infections are mild or asymptomatic and never require hospitalization but about 5% of patients become critically ill and develop acute respiratory distress syndrome (ARDS). The widely used management for ARDS in COVID-19 has been in line with the standard approach, but the need to adjust the treatment protocols has been questioned based on the reports of higher mortality risk among those requiring mechanical ventilation. Treatment options for this widespread disease are limited and there are no definitive therapies or vaccines until now. Although some antimalarial and antiviral drugs may prove effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), their safety and efficacy are still under clinical trials. We conducted a systematic review of case reports on ARDS in SARS-CoV-2 infection to summarize the clinical presentation, laboratory and chest imaging findings, management protocols, and outcome of ARDS in COVID-19-positive patients. We need more data and established studies for the effective management of the novel SARS-CoV-2 and to reduce mortality in high-risk patients. url: https://doi.org/10.7759/cureus.8188 doi: 10.7759/cureus.8188 id: cord-009295-4c0zwhdh author: Bal, A. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 words: 1253.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-009295-4c0zwhdh.txt txt: ./txt/cord-009295-4c0zwhdh.txt summary: title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) The phylogenetic analysis using the 571 WGS of SARS-CoV-2 publicly available (as of March 17th 2020) found that this sequence clustered with a sequence (EPI_-ISL_408488) collected in Jiangsu, China, on January 19th, suggesting a separate introduction from Asia (Fig. 1) . Compared to the reference SARS-CoV-2 sequence, a three-nucleotide deletion in open reading frame 1a (ORF1a) at positions 1607e1609 was identified. Letter to the Editor / Clinical Microbiology and Infection xxx (xxxx) xxx SARS-CoV-2 sequences were not further compared between the two patients due to largely incomplete coverage of the SARS-CoV-2 genome in sample #1. Despite low viral loads, the mNGS workflow used herein allowed us to characterize the wholegenome sequences of SARS-CoV-2 isolated from an asymptomatic patient in two clinical samples collected 1 day apart. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142683/ doi: 10.1016/j.cmi.2020.03.020 id: cord-339711-f7xifne8 author: Bal, A. title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test date: 2020-09-30 words: 2743.0 sentences: 166.0 pages: flesch: 52.0 cache: ./cache/cord-339711-f7xifne8.txt txt: ./txt/cord-339711-f7xifne8.txt summary: title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test The first study exploring the association of 75 commercial serological assays and VNT claimed that the Wantai Total Ab assay detecting 76 total antibodies directed against the SARS-CoV-2 receptor binding domain (RBD) had the 77 best characteristics to detect functional antibodies at different stages and severity of disease 78 [12] . In the first study comparing VNT with commercialized 215 tests, the authors found that the Wantai Total Ab assay had the best characteristics to detect 216 functional antibodies in different stages and severity of disease [12] . For evaluating protective immunity, the Wantai Total Ab assay 247 with an optimized cut-off or other tests targeting the S protein as Euroimmun, DiaSorin or 248 bioMérieux IgG could be more useful, notably to screen serum specimens candidate for the 249 presence of neutralizing antibodies. abstract: Objectives: We evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients. Methods: A total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMerieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohen Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined. Results: The Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMerieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%). Conclusions: Although some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response. url: https://doi.org/10.1101/2020.09.30.20194290 doi: 10.1101/2020.09.30.20194290 id: cord-283138-18q23z8l author: Balasubramanian, S. title: Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date: 2020-04-09 words: 3464.0 sentences: 205.0 pages: flesch: 44.0 cache: ./cache/cord-283138-18q23z8l.txt txt: ./txt/cord-283138-18q23z8l.txt summary: Pediatric coronavirus disease-19 (COVID-19) infection is relatively mild when compared to adults, and children are reported to have a better prognosis. Clinical features of COVID-19 in children include fever and cough, but a large proportion of infected children appears to be asymptomatic and may contribute to transmission. It remains unclear why children and young adults are less severely affected than older individuals, but this might involve differences in immune system function in the elderly and/or differences in the expression/function of the cellular receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)Angiotensin converting enzyme 2 (ACE2). This review additionally considers COVID-19 in immunosuppressed children, and also suggests a management algorithm for the few children who appear to present with life threatening infection, including the potential use of antiviral and immunomodulatory treatment. Asymptomatic, mild and moderate infections comprise over 90% of all children who have tested positive for COVID-19 with fewer severe and critical cases (5.9%) compared to adults (18.5%) [13] . abstract: Pediatric coronavirus disease-19 (COVID-19) infection is relatively mild when compared to adults, and children are reported to have a better prognosis. Mortality in children appears rare. Clinical features of COVID-19 in children include fever and cough, but a large proportion of infected children appears to be asymptomatic and may contribute to transmission. It remains unclear why children and young adults are less severely affected than older individuals, but this might involve differences in immune system function in the elderly and/or differences in the expression/function of the cellular receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)- Angiotensin converting enzyme 2 (ACE2). Laboratory findings and chest imaging may not be specific in children with COVID-19. Diagnosis is by Reverse transcriptase-Polymerase chain reaction (RT-PCR) testing of upper or lower respiratory tract secretions. This review additionally considers COVID-19 in immunosuppressed children, and also suggests a management algorithm for the few children who appear to present with life threatening infection, including the potential use of antiviral and immunomodulatory treatment. The most significant threat to global child health from SARS-CoV-2 is unlikely to be related to COVID 19 in children, but rather the socio-economic consequences of a prolonged pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32273490/ doi: 10.1007/s13312-020-1819-5 id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 words: 3998.0 sentences: 177.0 pages: flesch: 49.0 cache: ./cache/cord-352814-fcl2g5wr.txt txt: ./txt/cord-352814-fcl2g5wr.txt summary: In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The aim of this work was to develop a real-time PCR assay for diagnosing infection with SARS-related coronaviruses from bat guano in order to use it as a screening tool in epidemiological surveys for the detection of the viruses. The developed SYBR Green real-time PCR techniques were applied to an SARS-like coronavirus survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) which were sampled in Italy in 2009, resulting in a prevalence of coronavirus infection of 42%. After optimisation of the SYBR Green real-time PCR assay, for each run, duplicates of six 10-fold dilutions of the standard plasmid, triplicates of the viral reverse-transcribed RNA of the bat samples, and a no template control were simultaneously subjected to analysis. abstract: Bats are source of coronaviruses closely related to the severe acute respiratory syndrome (SARS) virus. Numerous studies have been carried out to identify new bat viruses related to SARS-coronavirus (bat-SARS-like CoVs) using a reverse-transcribed-polymerase chain reaction assay. However, a qualitative PCR could underestimate the prevalence of infection, affecting the epidemiological evaluation of bats in viral ecology. In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The assay showed high sensitivity and reproducibility. Its application on bats screening resulted in a prevalence of 42%. This method could be suitable as screening tool in epidemiological surveys about the presence of bat-SARS-like CoVs, consequently to obtain a more realistic scenario of the viral prevalence in the population. url: https://www.ncbi.nlm.nih.gov/pubmed/22654650/ doi: 10.1100/2012/989514 id: cord-296128-kjoi54ea author: Balestri, Riccardo title: Do we have serological evidences that chilblain‐like lesions are related to SARS‐CoV‐2? A review of the literature date: 2020-08-26 words: 1631.0 sentences: 105.0 pages: flesch: 51.0 cache: ./cache/cord-296128-kjoi54ea.txt txt: ./txt/cord-296128-kjoi54ea.txt summary: Our review demonstrated a high prevalence of negative serological results in CLL: antibodies were observed only in a few patients, that are even less excluding those with positive IgA, not clearly involved in the pathogenesis of the disease. The outbreak of chilblain-like lesions (CLL) coincidentally to the COVID-19 pandemic is a topic of great concern 1 SARS-CoV-2 was hypothesized as the etiologic agent of CLL, initially on the basis of the temporal correlation between the "burst" of skin manifestations and the viral pandemic. However, it has been shown that CLL are not related to an acute infection, since real-time reverse transcription polymerase chain reaction (rt-PCR) tests from nasopharyngeal swabs seldom resulted positive 1-9Therefore, dermatologists'' attention shifted to the search for specific SARS-CoV-2 antibodies. The search was limited to articles published in English We included only case series, clearly declaring that a search for SARS-CoV-2 specific antibodies had been performed. Chilblain-like lesions during COVID-19 pandemic: a serological study on a case series abstract: The outbreak of chilblain‐like lesions (CLL) coincidentally to the COVID‐19 pandemic is a topic of great concern. SARS‐CoV‐2 was initially hypothesized as the etiologic agent of CLL, but, since nasopharyngeal swabs seldom resulted positive, dermatologists’ attention focused on the search for specific SARS‐CoV‐2 antibodies. Many papers were published contemporarily on this topic, reporting limited case series. We reviewed the English literature up to the 1(st) July 2020 and, excluding single case reports, we considered 13 studies that serologically investigated 220 patients. The presence of specific antibodies was detected in 18 subjects (8,2%): isolated IgA were found in 6 patients, IgA and IgG in 1, isolated IgG in 5, and IgM in 2. In 4 patients, isotypes were not specified. Our review demonstrated a high prevalence of negative serological results in CLL: antibodies were observed only in a few patients, that are even less excluding those with positive IgA, not clearly involved in the pathogenesis of the disease. In conclusion, although it is still uncertain whether CLL are related to SARS‐CoV‐2 infection, patients affected by CLL seem not to be prone to shedding the virus, hence, if they are asymptomatic, we can reassure them, thus avoiding hospital referral This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32844512/ doi: 10.1111/dth.14229 id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 words: 12092.0 sentences: 541.0 pages: flesch: 41.0 cache: ./cache/cord-319754-5isw53wl.txt txt: ./txt/cord-319754-5isw53wl.txt summary: Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . abstract: The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32878290/ doi: 10.3390/metabo10090356 id: cord-262192-w86qc3fq author: Balkhair, Abdullah A. title: COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases date: 2020-04-21 words: 1103.0 sentences: 85.0 pages: flesch: 54.0 cache: ./cache/cord-262192-w86qc3fq.txt txt: ./txt/cord-262192-w86qc3fq.txt summary: According to the World Health Organization (WHO), the world has witnessed the emergence of several disease outbreaks and epidemics caused by more than 20 infectious agents over the past decade. 3 Over the past two decades, the emergence of coronavirus-associated diseases (SARS and MERS) inflicted global challenges to public health systems. This is exemplified by the current COVID-19 pandemic where the appearance of a seemingly limited cluster of cases of pneumonia linked to a sea food market in Wuhan, China 7 has become one of the worst pandemics in human history with a staggering number of more than 1.4 million infections in 177 countries and more than 85 000 deaths globally as of 9 April 2020. The quest for a vaccine against SARS-CoV-2 is an urgent priority, and its development and global availability is a prerequisite for ending the COVID-19 pandemic. The current COVID-19 pandemic and its dreadful global impact is a reminder of the potential detriment of emerging infectious diseases. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32328297/ doi: 10.5001/omj.2020.41 id: cord-355528-y4a1g6km author: Balla, Mamtha title: COVID-19, Modern Pandemic: A Systematic Review From Front-Line Health Care Providers’ Perspective date: 2020-03-30 words: 7504.0 sentences: 398.0 pages: flesch: 53.0 cache: ./cache/cord-355528-y4a1g6km.txt txt: ./txt/cord-355528-y4a1g6km.txt summary: The main aim of this systematic review is to provide a comprehensive clinical summary of all the available data from high-quality research articles relevant to the epidemiology, demographics, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic methods and treatment methods of COVID-19, thus increasing awareness in health care providers. Coronavirus disease 2019 (COVID19) infection, which is a global pandemic declared on March 11, 2020, by World Health Organization (WHO), was reported to have infected 168,000 cases worldwide in about 148 countries and territories and killed more than 6,610 people around the world as of March 16, 2020 [1]. According to the study by Xu et al, 60% of people diagnosed with COVID-19 had traveled to Wuhan or nearby regions (60%), 36% had close contact with novel coronavirus pneumonia (NCP) patients and 4% had no definite exposure [12] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Coronavirus disease 2019 (COVID-19) caused infection in 168,000 cases worldwide in about 148 countries and killed more than 6,610 people around the world as of March 16, 2020, as per the World Health Organization (WHO). Compared to severe acute respiratory syndrome and Middle East respiratory syndrome, there is the rapid transmission, long incubation period, and disease containment is becoming extremely difficult. The main aim of this systematic review is to provide a comprehensive clinical summary of all the available data from high-quality research articles relevant to the epidemiology, demographics, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic methods and treatment methods of COVID-19, thus increasing awareness in health care providers. We also discussed various preventive measures to combat COVID-19 effectively. A systematic and protocol-driven approach is needed to contain this disease, which was declared as a global pandemic on March 11, 2020, by the WHO. url: https://doi.org/10.14740/jocmr4142 doi: 10.14740/jocmr4142 id: cord-265473-ju81kiyw author: Balmeh, Negar title: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date: 2020-08-07 words: 2854.0 sentences: 160.0 pages: flesch: 49.0 cache: ./cache/cord-265473-ju81kiyw.txt txt: ./txt/cord-265473-ju81kiyw.txt summary: Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Approximately 377 predicted and valid targets of hsa-miR-1307 which were predicted The best herbal compounds for ACE2, TMPRSS2, GRP78, and AT1R receptors were identified based on their binding energy. The molecular docking results of the ACE2, TMPRSS2, GRP78, and AT1R receptors with medicinal herbal compounds are presented in Supplementary Table 2 . Increased expression of hsa-miR-1307-3p may lead to a reduction in SARS-CoV-2 replication through binding to the 3''UTR site of the virus genome. It has been confirmed that endocytosis and exocytosis are associated with virus entry and spread, therefore, controlling these pathways by hsa-miR-1307-3p could be an effective strategy for SARS-CoV-2 infection. abstract: The SARS-CoV-2 causes severe pulmonary infectious disease with an exponential spread-ability. In the present research, we have tried to look into the molecular cause of disease, dealing with the development and spread of the coronavirus disease 2019 (COVID-19). Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Second, the findings presented that this miRNA had a considerable role in PI3K/Act, endocytosis, and type 2 diabetes, moreover, it may play a critical role in the prevention of GRP78 production and the virus entering, proliferation and development. Third, nearly 1033 medicinal herbal compounds were collected and docked with ACE2, TMPRSS2, GRP78, and AT1R receptors, which were the most noticeable receptors in causing the COVID-19. Among them, there were three common compounds including berbamine, hypericin, and hesperidin, which were more effective and appropriate to prevent the COVID-19 infection. Also, it was revealed some of these chemical compounds which had a greater affinity for AT1R receptor inhibitors can be suitable therapeutic targets for inhibiting AT1R and preventing the adverse side effects of this receptor. According to the result, clinical assessment of these three herbal compounds and hsa-miR-1307-3p may have significant outcomes for the prevention, control, and treatment of COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32835083/ doi: 10.1016/j.imu.2020.100407 id: cord-291577-nf80kih2 author: Baluku, Joseph Baruch title: HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date: 2020-05-21 words: 1727.0 sentences: 129.0 pages: flesch: 59.0 cache: ./cache/cord-291577-nf80kih2.txt txt: ./txt/cord-291577-nf80kih2.txt summary: From Wuhan, China, Zhu et al., reported a severe case of a newly diagnosed HIV/SARS-CoV-2 co-infected male with diabetes who presented with fever, hypoxemia, lymphopenia and chest computed tomography (CT) abnormalities, who was managed on oxygen therapy, the HIV antiviral agent lopinavir/ritonavir, moxifloxacin, gamma-globulin and methyl prednisone (5) . also reported 5 cases of HIV/SARS-CoV-2 co-infection -of whom 4 were virologically suppressed on antiretroviral therapy (ART) -from Spain, who invariably presented with cough and fever (6) . In a case series from Spain, all HIV/SARS-CoV-2 co-infected patients had cough and fever (6) . Also, similar to this patient, the HIV co-infected patient who had good adherence to ART and a suppressed viral load, presented with weakness and non-bloody diarrhoea with no significant clinical signs and laboratory abnormalities in a case series from Turkey (11) The presentation with chest pain, tachypnea, normal auscultation findings and tachycardia raises the possibility of alternative diagnoses that could mimic COVID -19. abstract: There are no reports of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and HIV co‐infection from sub‐Saharan Africa where 70% of people living with HIV are found. We report a case of HIV/SARS‐CoV‐2 co‐infection from Uganda. A 34 year old HIV‐positive female on antiretroviral therapy (tenofovir disoproxil fumarate, lamivudine and efavirenz) for 5 years, tested positive for SARS‐CoV‐2, the causative agent for coronavirus disease 19 (COVID‐19). She was asymptomatic at presentation but subsequently developed headache, chest pain, diarrhoea, anorexia and fatigue on day 3 of isolation without cough, fever or shortness of breath. Her CD4 count was 965 cells/mm(3), the HIV viral load was undetectable (<1,000 cells/mm(3)) and other laboratory work up was normal. She was successfully managed with hydroxychloroquine and broad spectrum antibiotics, and was discharged after 24 days. This case demonstrates an atypical clinical presentation of COVID – 19 in an HIV infected patient without other co‐morbidity. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26044 doi: 10.1002/jmv.26044 id: cord-342189-ya05m58o author: Banerjee, Abhik K. title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 words: 11469.0 sentences: 647.0 pages: flesch: 55.0 cache: ./cache/cord-342189-ya05m58o.txt txt: ./txt/cord-342189-ya05m58o.txt summary: Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. abstract: SARS-CoV-2 is a recently identified coronavirus that causes the respiratory disease known as COVID-19. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the Signal Recognition Particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses. url: https://api.elsevier.com/content/article/pii/S0092867420313106 doi: 10.1016/j.cell.2020.10.004 id: cord-269537-h3lzl1un author: Banerjee, Aditi title: Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19 date: 2020-05-23 words: 2937.0 sentences: 189.0 pages: flesch: 39.0 cache: ./cache/cord-269537-h3lzl1un.txt txt: ./txt/cord-269537-h3lzl1un.txt summary: Viral infections including SARS-CoV are associated with increased levels of reactive oxygen species, disturbances of Ca(++) caused by unfolded protein response (UPR) mediated by endoplasmic reticulum (ER) stress and is due to the exploitation of virus''s own protein i.e., viroporins into the host cells. Considering the properties of both compounds in terms of anti-inflammatory, antioxidant, anti-pyrogenic, anti-viral and ER stress modulation and computational approaches revealing andrographolide docks with the SARS-CoV2 binding site, we predict that this combination therapy may have potential utility against COVID-19. Accumulating evidence suggests that ER stress and sustained UPR signaling are major contributors to the pathogenesis of several diseases, including inflammatory disorders and viral infections [15] and can increase the severity of these events [16] . Endoplasmic reticulum stress and IRE-1 signaling cause apoptosis in colon cancer cells in response to andrographolide treatment abstract: The outbreak of COVID-19 caused by 2019–nCov/SARS-CoV-2 has become a pandemic with an urgent need for understanding the mechanisms and identifying a treatment. Viral infections including SARS-CoV are associated with increased levels of reactive oxygen species, disturbances of Ca(++) caused by unfolded protein response (UPR) mediated by endoplasmic reticulum (ER) stress and is due to the exploitation of virus's own protein i.e., viroporins into the host cells. Several clinical trials are on-going including testing Remdesivir (anti-viral), Chloroquine and Hydroxychloroquine derivatives (anti-malarial drugs) etc. Unfortunately, each drug has specific limitations. Herein, we review the viral protein involvement to activate ER stress transducers (IRE-1, PERK, ATF-6) and their downstream signals; and evaluate combination therapies for COVID-19 mediated ER stress alterations. Melatonin is an immunoregulator, anti-pyretic, antioxidant, anti-inflammatory and ER stress modulator during viral infections. It enhances protective mechanisms for respiratory tract disorders. Andrographolide, isolated from Andrographis paniculata, has versatile biological activities including immunomodulation and determining SARS-CoV-2 binding site. Considering the properties of both compounds in terms of anti-inflammatory, antioxidant, anti-pyrogenic, anti-viral and ER stress modulation and computational approaches revealing andrographolide docks with the SARS-CoV2 binding site, we predict that this combination therapy may have potential utility against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32454157/ doi: 10.1016/j.lfs.2020.117842 id: cord-295433-olmein3q author: Banerjee, Arinjay title: Bats and Coronaviruses date: 2019-01-09 words: 5655.0 sentences: 298.0 pages: flesch: 52.0 cache: ./cache/cord-295433-olmein3q.txt txt: ./txt/cord-295433-olmein3q.txt summary: Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . abstract: Bats are speculated to be reservoirs of several emerging viruses including coronaviruses (CoVs) that cause serious disease in humans and agricultural animals. These include CoVs that cause severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), porcine epidemic diarrhea (PED) and severe acute diarrhea syndrome (SADS). Bats that are naturally infected or experimentally infected do not demonstrate clinical signs of disease. These observations have allowed researchers to speculate that bats are the likely reservoirs or ancestral hosts for several CoVs. In this review, we follow the CoV outbreaks that are speculated to have originated in bats. We review studies that have allowed researchers to identify unique adaptation in bats that may allow them to harbor CoVs without severe disease. We speculate about future studies that are critical to identify how bats can harbor multiple strains of CoVs and factors that enable these viruses to “jump” from bats to other mammals. We hope that this review will enable readers to identify gaps in knowledge that currently exist and initiate a dialogue amongst bat researchers to share resources to overcome present limitations. url: https://www.ncbi.nlm.nih.gov/pubmed/30634396/ doi: 10.3390/v11010041 id: cord-284627-qvz63m93 author: Banerjee, Shuvam title: Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date: 2020-04-09 words: 3691.0 sentences: 336.0 pages: flesch: 67.0 cache: ./cache/cord-284627-qvz63m93.txt txt: ./txt/cord-284627-qvz63m93.txt summary: The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. 12, 14 In this study, we comprehensively analyzed the whole genome sequence homology from the available patient data uploaded by affected countries in NCBI Virus database, identified the mutations developed by different strains from the ancestor strain and studied the impact of those mutations at functional level. In summary, the present study reveals that the fatality rate increases with not only the number of mutations but also depending on its allelic rarity as well as functional alteration of protein. abstract: Background COVID-19 is a disease with global public health emergency that have shook the world since its’ first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known. Methods Available data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. Findings All the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. The molecular divergence, evolved from the ancestral strain (S) lead to extremely lethal (E), lethal(L) and non lethal (N) strains with the involvement of an Intermediate strain(I). url: https://doi.org/10.1101/2020.04.06.027854 doi: 10.1101/2020.04.06.027854 id: cord-335075-6wo2o5pp author: Bangaru, Sandhya title: Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date: 2020-08-06 words: 4715.0 sentences: 240.0 pages: flesch: 51.0 cache: ./cache/cord-335075-6wo2o5pp.txt txt: ./txt/cord-335075-6wo2o5pp.txt summary: Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Site-specific glycosylation of the SARS-CoV-2 prefusion spike protein produced in SF9 insect cells was analyzed using our recently described mass spectrometry proteomics-based method, involving treatment with proteases followed by sequential treatment with the endoglycosidases (Endo H and PNGase F) to introduce mass signatures in peptides with N-linked sequons (Asn-X-Thr/Ser) to assess the extent of glycosylation and the degree of glycan processing from high mannose/hybrid type to complex type (24) . In this study, we performed structural analysis of the Novavax SARS-CoV We also observed two non-spike densities within the spike trimer that corresponded with linoleic acid and polysorbate 80 detergent. abstract: Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared to published spike ectodomain structures. Interestingly, we also observed novel interactions between the spike trimers allowing formation of higher order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen. url: https://www.biorxiv.org/content/biorxiv/early/2020/08/06/2020.08.06.234674.full.pdf doi: 10.1101/2020.08.06.234674 id: cord-327601-4uqgwlnx author: Bangash, Mansoor N. title: SARS-CoV-2: is the liver merely a bystander to severe disease? date: 2020-06-02 words: 979.0 sentences: 61.0 pages: flesch: 43.0 cache: ./cache/cord-327601-4uqgwlnx.txt txt: ./txt/cord-327601-4uqgwlnx.txt summary: 1 Their study shows SARS-CoV-2 positive patients with ≥1 week history of increased aminotransferases have worse acute pulmonary disease (radiological and physiological) than those without. Considering that Interleukin (IL)-6 and C-reactive protein (CRP) are similar between patients with normal and prolonged abnormal liver aminotransferases, the authors speculate that liver injury is a direct effect of SARS-CoV-2 viral hepatitis rather than an indirect immune mediated injury. The fact that increases in liver aminotransferases occur and tend to parallel the severity of pulmonary disease remains unquestioned 2 , however, whether the liver injury is a true viral hepatitis rather than a bystander to the multi-organ pathophysiology of critical illness requires further discussion. Based on the above perspectives, we feel that raised liver aminotransferases associated with SARS-CoV-2 positivity are more likely attributable to illness severity, in which host response and iatrogenic harm (i.e. drugs, ventilation) drive bystander liver injury, thus explaining its association with mortality and in an analogous fashion to patterns seen in sepsis. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S016882782030355X?v=s5 doi: 10.1016/j.jhep.2020.05.035 id: cord-311445-b6bc6vwd author: Bansal, Kanika title: Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date: 2020-10-12 words: 2749.0 sentences: 169.0 pages: flesch: 60.0 cache: ./cache/cord-311445-b6bc6vwd.txt txt: ./txt/cord-311445-b6bc6vwd.txt summary: Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. In the present study, we have focused on codon usage pattern (CUP) of SARS coronavirus from different hosts under debate (bat, pangolin, and dog) as a probable origin for SARS-CoV-2. However, another study comparing the codon usage pattern of SARS-CoV-2 with other betacoronaviruses suggested that current pandemic coronavirus is subjected to different evolutionary pressures (Gu et al., 2020) . The above analysis reveals single patterns for all five genes in different lineages of SARS-CoV-2 affirms a single event of host jump of codon-optimized SARS strain from its animal reservoir. abstract: Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is a driving force in its evolution. Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. At the same time, our analysis suggests that dogs are not a source of SARS-CoV-2. Interestingly, CUP of rdrp displays conservation with two bat SARS isolates RaTG13 and RmYN02. CUP of the SARS-CoV-2 E gene is also conserved with bat and pangolin isolates with variations for a few amino acids. This suggests role allele replacement in these two genes involving SARS strains of least two hosts. At the same time, a relatively conserved CUP pattern in replicase and envelope across hosts suggests them it to be an ideal target in antiviral development for SARS-CoV-2. url: https://doi.org/10.1101/2020.10.12.335521 doi: 10.1101/2020.10.12.335521 id: cord-012424-z3mkp9y9 author: Bansal, Poonam title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) date: 2020-08-13 words: 498.0 sentences: 45.0 pages: flesch: 46.0 cache: ./cache/cord-012424-z3mkp9y9.txt txt: ./txt/cord-012424-z3mkp9y9.txt summary: title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) We write in reference to a previously reported case of acute necrotizing encephalopathy (ANE) associated with acute SARS-COV-2 infection (1) . Repeat MRI brain without contrast showed residual T2 hyperintensities and hemosiderin deposition in the medial thalami; the former were significantly improved from previous. Several cases of COVID-19 associated ANE have now been reported (Table) . Immunotherapy has some role in the treatment of COVID-19 associated ANE, as described in the literature (1, 4, 5 COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia Acute necrotizing encephalopathy and myocarditis in a young patient with COVID-19 Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid COVID-19-associated acute necrotising encephalopathy successfully treated with steroids and polyvalent immunoglobulin with unusual IgG targeting the cerebral fibre network Does SARS-Cov-2 invade the brain? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427117/ doi: 10.1148/radiol.2020203132 id: cord-343970-anocx4y1 author: Bansal, Rashika title: Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course date: 2020-06-30 words: 6526.0 sentences: 409.0 pages: flesch: 45.0 cache: ./cache/cord-343970-anocx4y1.txt txt: ./txt/cord-343970-anocx4y1.txt summary: ACE2 is expressed in pancreatic islets, vascular endothelium, and adipose tissue, and the SARS-CoV-2 -ACE2 interaction in these tissues, along with other factors, govern the spectrum and the severity of clinical manifestations among COVID-19 patients with metabolic syndrome. Moreover, the pro-inflammatory milieu observed in patients with metabolic syndrome may contribute towards COVID-19-mediated host immune dysregulation, including sub-optimal immune responses, hyper-inflammation, microvascular dysfunction, and thrombosis. SARS-CoV-2 virus attaches to the host cell membrane-bound angiotensin-converting enzyme 2 (ACE2) that is expressed in many cells, including the respiratory epithelial cells (type II alveolar A c c e p t e d M a n u s c r i p t epithelial cells), myocardium, Leydig cells and cells in seminiferous ducts in the testes, vascular endothelial cells, proximal renal tubular cells, gastrointestinal epithelial cells, urothelial cells lining the bladder, alveolar monocytes, macrophages, and in both exocrine pancreas and pancreatic islets (43, (46) (47) (48) . abstract: The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Individuals with metabolic syndrome are at increased risk for poor disease outcomes and mortality from COVID-19. The pathophysiologic mechanisms for these observations have not been fully elucidated. A critical interaction between SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) facilitates viral entry into the host cell. ACE2 is expressed in pancreatic islets, vascular endothelium, and adipose tissue, and the SARS-CoV-2 -ACE2 interaction in these tissues, along with other factors, govern the spectrum and the severity of clinical manifestations among COVID-19 patients with metabolic syndrome. Moreover, the pro-inflammatory milieu observed in patients with metabolic syndrome may contribute towards COVID-19-mediated host immune dysregulation, including sub-optimal immune responses, hyper-inflammation, microvascular dysfunction, and thrombosis. This review describes the spectrum of clinical features, the likely pathophysiologic mechanisms and potential implications for the management of metabolic syndrome in COVID-19 patients. url: https://doi.org/10.1210/endocr/bqaa112 doi: 10.1210/endocr/bqaa112 id: cord-300866-cso6l6ze author: Bao, Yi title: Clinical Features of COVID-19 in a Young Man with Massive Cerebral Hemorrhage—Case Report date: 2020-05-23 words: 4252.0 sentences: 217.0 pages: flesch: 50.0 cache: ./cache/cord-300866-cso6l6ze.txt txt: ./txt/cord-300866-cso6l6ze.txt summary: Both SARS-CoV-2 nucleic acid tests were negative (24 h interval), Fig. 2 The treatment of COVID-19 patients with intracerebral hemorrhage suggesting that antiviral treatment was effective. On February 29, the patient did not have high fever again, the results of the cerebrospinal fluid review showed that it was light red, no clot, protein decreased to 0.8 g/L, sugar increased to 4.45 mmol/L, and white blood cells decreased to 37 × 10 6 G/L, of which monocytes accounted for 74%. The patient''s cerebrospinal fluid showed improvement, and since the two re-examinations of SARS-CoV-2 nucleic acid test was negative, and the antiviral treatment with Abidol, Ribavirin, and Oseltamivir had reached the course of treatment, so it was discontinued. However, in combination with the patient''s high fever, lymphocytopenia, increased neutrophils, and poor antibacterial treatment effect, the clinical manifestations conform to the COVID-19 characteristics, and nucleic acid detection is required. abstract: COVID-19 is currently a pandemic in the world, can invade multiple systems, and has a high morbidity and mortality. So far, no cases of acute cerebrovascular disease have been reported. This article reports the clinical features of a COVID-19 patient whose first symptom was cerebral hemorrhage. More importantly, after the craniotomy, the patient had high fever and it was difficult to retreat. After cerebrospinal fluid testing, it was determined that an intracranial infection had occurred. After anti-infection and plasma infusion of the recovered person, the patient’s symptoms gradually improved. This case suggests that COVID-19 may infringe on cerebral blood vessels and cause cerebral hemorrhage. Transfusion of plasma from rehabilitation patients is effective for critically ill patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32838132/ doi: 10.1007/s42399-020-00315-y id: cord-340189-jo38hjqa author: Bar-On, Yinon M title: SARS-CoV-2 (COVID-19) by the numbers date: 2020-04-02 words: 7246.0 sentences: 458.0 pages: flesch: 58.0 cache: ./cache/cord-340189-jo38hjqa.txt txt: ./txt/cord-340189-jo38hjqa.txt summary: If you are infectious for 4 days, then you will infect four others on average, which is on the high end of the R 0 values for SARS-CoV-2 in the absence of physical distancing. Assuming entry of the virus to the cells is rapid (we estimate 10 min for SARS-CoV-2), the time it takes to produce progeny can be estimated by quantifying the lag between inoculation and the appearance of new intracellular virions, also known as the ''eclipse period''. While both the time to complete a replication cycle and the burst size may vary significantly in an animal host due to factors including the type of cell infected or the action of the immune system, these numbers provide us with an approximate quantitative view of the viral life-cycle at the cellular level. (Hirano et al., 1976) : "The average per-cell yield of active virus was estimated to be about 6-7  10 2 plaque-forming units." This data is for MHV, so more research is needed to verify these values for SARS-CoV-2. abstract: The COVID-19 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this article we provide a one-stop, curated graphical source for the key numbers (based mostly on the peer-reviewed literature) about the SARS-CoV-2 virus that is responsible for the pandemic. The discussion is framed around two broad themes: i) the biology of the virus itself; ii) the characteristics of the infection of a single human host. url: https://www.ncbi.nlm.nih.gov/pubmed/32228860/ doi: 10.7554/elife.57309 id: cord-335784-v7nbck0n author: Barak, N. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 words: 3136.0 sentences: 202.0 pages: flesch: 57.0 cache: ./cache/cord-335784-v7nbck0n.txt txt: ./txt/cord-335784-v7nbck0n.txt summary: Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Major diagnostic challenges have emerged, mainly, the need for high throughput SARS-CoV-2 RT-PCR tests, aimed to detect not only symptomatic but also asymptomatic infectious viral carriers and to screen special or at-risk populations (such as health care personnel or nursing home tenants), in order to contain viral spread and guide control measures. To our knowledge, this is the most extensive analysis, addressing key considerations of efficiency, sensitivity and feasibility in the actual reality of routine, large-scale implementation of sample pooling for SARS-CoV-2 detection. abstract: Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Here we report analysis of 133,816 samples collected at April-September 2020, tested by pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the reality of frequently changing prevalence rate (0.5%-6%). Surprisingly, we observed pooling efficiency and sensitivity that exceed theoretical predictions, which resulted from non-random distribution of positive samples in pools. Overall, the findings strongly support the use of pooling for efficient large high throughput SARS-CoV-2 testing. url: http://medrxiv.org/cgi/content/short/2020.10.16.20213405v1?rss=1 doi: 10.1101/2020.10.16.20213405 id: cord-311843-un6urdb1 author: Baray, Juwel Chandra title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date: 2020-09-30 words: 3173.0 sentences: 230.0 pages: flesch: 62.0 cache: ./cache/cord-311843-un6urdb1.txt txt: ./txt/cord-311843-un6urdb1.txt summary: title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. The reactivity of the sera from each 221 group of mice immunized with BANCOVID was measured against SARS-CoV-2 S antigen 222 (SinoBiologicals, China). Analysis revealed IgG binding against SARS-CoV-2 S protein 223 antigens in the sera of the immunized mice. Flow cytometric analysis of total T cell (CD4 + ) populations producing TFN alpha on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. abstract: Effective vaccine against SARS-CoV-2 is the utmost importance in the current world. More than 1 million deaths are accounted for relevant pandemic disease COVID-19. Recent data showed that D614G genotype of the virus is highly infectious and responsible for almost all infection for 2nd wave. Despite of multiple vaccine development initiatives, there are currently no report that has addressed this critical variant D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine considering the D614G variant and characterization of the vaccine in preclinical trial. The surface plasmon resonance (SPR) data with spike protein as probe and competitive neutralization with RBD and S2 domain revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, immunization protected mice lungs from pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+ cells with a Th1 bias. The IgG2a to IgG1 and (IgG2a+IgG2b) to (IgG1+IgG3) ratios were found 1±0.2 and 1.24±0.1, respectively. These values are comparatively higher than relevant values for other published SARS-CoV-2 vaccine in development,1, 2 and suggesting higher viral clearance capacity for our vaccine. The data suggested great promise for immediate translation of the technology to the clinic. url: https://doi.org/10.1101/2020.09.29.319061 doi: 10.1101/2020.09.29.319061 id: cord-303017-4zx94rm6 author: Barbieri, Antonio title: Can Beta-2-Adrenergic Pathway Be a New Target to Combat SARS-CoV-2 Hyperinflammatory Syndrome?—Lessons Learned From Cancer date: 2020-09-30 words: 3539.0 sentences: 191.0 pages: flesch: 41.0 cache: ./cache/cord-303017-4zx94rm6.txt txt: ./txt/cord-303017-4zx94rm6.txt summary: This hypothesis relies on different pieces of evidence: IL-6, TNFa, and IL-1b promote Th17 response and are associated with inflammatory symptoms including fever, and the two latter are also associated with vascular permeability and leakage; IL-17 has a broad inflammatory effect and together with GM-CSF is involved in inflammatory and autoimmune disease; Covid-19 patients have a significantly increased number of CCR6+ Th17 cells (4) ; elevated TH17 and IL-17 related pathways are increased in SARS-CoV, MERS-CoV, and H1N1 influenza virus patients (14) (15) (16) ; In MERS-CoV patients, IL-17 and low IFNg are associated with worse prognosis (14) . Targeting beta-2adrenergic pathway was shown to reduce inflammatory cytokine and Th17 response in different settings such as cancer and autoimmune diseases. Two different reports on cancer patients show that propranolol treatment reduces inflammatory cytokines including IL-6 and TNFa, inflammation-related transcription factors such as NFkB and STAT3 and reduces the activation of Treg lymphocytes (36, 37) . abstract: SARS-CoV-2 infection is a new threat to global public health in the 21(st) century (2020), which has now rapidly spread around the globe causing severe pneumonia often linked to Acute Respiratory Distress Syndrome (ARDS) and hyperinflammatory syndrome. SARS-CoV-2 is highly contagious through saliva droplets. The structural analysis suggests that the virus enters human cells through the ligation of the spike protein to angiotensin-converting enzyme 2 (ACE(2)). The progression of Covid-19 has been divided into three main stages: stage I—viral response, stage II—pulmonary phase, and stage III—hyperinflammation phase. Once the patients enter stage III, it will likely need ventilation and it becomes difficult to manage. Thus, it will be of paramount importance to find therapies to prevent or slow down the progression of the disease toward stage III. The key event leading to hyperinflammation seems to be the activation of Th-17 immunity response and Cytokine storm. B(2)-adrenergic receptors (B(2)ARs) are expressed on airways and on all the immune cells such as macrophages, dendritic cells, B and T lymphocytes. Blocking (B(2)AR) has been proven, also in clinical settings, to reduce Th-17 response and negatively modulate inflammatory cytokines including IL-6 while increasing IFNγ. Non-selective beta-blockers are currently used to treat several diseases and have been proven to reduce stress-induced inflammation and reduce anxiety. For these reasons, we speculate that targeting B(2)AR in the early phase of Covid-19 might be beneficial to prevent hyperinflammation. url: https://doi.org/10.3389/fimmu.2020.588724 doi: 10.3389/fimmu.2020.588724 id: cord-260866-bzdd4f5h author: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 words: 4676.0 sentences: 249.0 pages: flesch: 50.0 cache: ./cache/cord-260866-bzdd4f5h.txt txt: ./txt/cord-260866-bzdd4f5h.txt summary: Paper-based devices would be certainly one of the best measurement solutions for the rapid and onsite detection of COVID-19 in sewage waters and humans as well [2, 16] and also the use of other biomarkers of exposure [1] . Detection of SARS-CoV-2 in sewage has been employed as a complementary method to clinical test .It is an early warning indicator of virus spreading in communities, covering both symptomatic and asymptomatic cases. Hopefully at certain moment applications to detect SARS-CoV-2 and other viruses in wastewater will be developed based on these LOC/POCT systems that will enable simple, fast and sensitive virus detection. PCR platforms like RT-qPCR are still the most widely used methods for SARS-Cov-2 detection in waste waters. Sewage sensors, such as paper-based and smartphones for SARS-CoV2 detection at the population level have as well a clear potential for early warning of COVID-19 pandemic. abstract: The WHO has declared the COVID-19 epidemic on January 31, 2020. This virus has infected millions of people worldwide in just a few months. Shortly afterwards, the National Medical Products Administration (NMPA) announced nucleic acid testing as the gold standard for virus detection. Antibody testing is used as well as a supplementary test for suspected cases where nucleic acid detection was negative. In short, nucleic acid–based polymerase chain reaction (PCR) is the mainstream detection method for clinical samples as well as for the detection of SARS-CoV-2 in wastewaters. First data collected around the globe were reported in the last few months being part of the so-called Wastewater-Based Epidemiology (WBE) approach. Selection of concentration methods and primers, laboratory inter-comparison and various modalities of PCR detection of the virus in complex wastewater matrices were flagged up as main bullets that require urgent improvement. Novel approaches to enhance sensitivity, speed and automate streamlined virus detection will be discussed here as well. This list comprises devices mainly used for clinical purposes like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), Digital PCR, Lab-on-a-chip (LOC) and related platforms as well as Biosensors. The last part will be devoted to the identification of biomolecules to target Covid-19 outbreak based on inflammatory response biomarkers among others. To this end this opinion paper brings for discussion the issue of PCR detection and its limitations as well as new diagnostic methods in WBE. url: https://api.elsevier.com/content/article/pii/S2666016420300402 doi: 10.1016/j.cscee.2020.100042 id: cord-336000-v88bq4bx author: Barco, Stefano title: Enoxaparin for primary thromboprophylaxis in ambulatory patients with coronavirus disease-2019 (the OVID study): a structured summary of a study protocol for a randomized controlled trial date: 2020-09-09 words: 20392.0 sentences: 1064.0 pages: flesch: 44.0 cache: ./cache/cord-336000-v88bq4bx.txt txt: ./txt/cord-336000-v88bq4bx.txt summary: OBJECTIVES: The OVID study will demonstrate whether prophylactic-dose enoxaparin improves survival and reduces hospitalizations in symptomatic ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. The OVID study will show whether prophylactic-dose enoxaparin improves survival and reduces any hospitalizations in ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. <30% of the expected number of patients six months after the enrolment of the first patient, also based on the course of SARS-CoV2 infections in Switzerland;  when the safety of the participants is doubtful or at risk, respectively, based on recommendations received from DSMB committee;  changes in accepted clinical practice that make the continuation of a clinical trial unwise, including the results of similar studies or the publication of international guidances. abstract: OBJECTIVES: The OVID study will demonstrate whether prophylactic-dose enoxaparin improves survival and reduces hospitalizations in symptomatic ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. TRIAL DESIGN: The OVID study is conducted as a multicentre open-label superiority randomised controlled trial. PARTICIPANTS: Inclusion Criteria 1. Signed patient informed consent after being fully informed about the study’s background. 2. Patients aged 50 years or older with a positive test for SARS-CoV2 in the past 5 days and eligible for ambulatory treatment. 3. Presence of respiratory symptoms (i.e. cough, sore throat, or shortness of breath) or body temperature >37.5° C. 4. Ability of the patient to travel to the study centre by private transportation, performed either by an accompanying person from the same household or by the patient themselves 5. Ability to comply with standard hygiene requirements at the time of in-hospital visit, including a face mask and hand disinfectant. 6. Ability to walk from car to study centre or reach it by wheelchair transport with the help of an accompanying person from the same household also complying with standard hygiene requirements. 7. Ability to self-administer prefilled enoxaparin injections after instructions received at the study centre or availability of a person living with the patient to administer enoxaparin. Exclusion Criteria 1. Any acute or chronic condition posing an indication for anticoagulant treatment, e.g. atrial fibrillation, prior venous thromboembolism (VTE), acute confirmed symptomatic VTE, acute coronary syndrome. 2. Anticoagulant thromboprophylaxis deemed necessary in view of the patient's history, comorbidity or predisposing strong risk factors for thrombosis: a. Any of the following events occurring in the prior 30 days: fracture of lower limb, hospitalization for heart failure, hip/knee replacement, major trauma, spinal cord injury, stroke, b. previous VTE, c. histologically confirmed malignancy, which was diagnosed or treated (surgery, chemotherapy, radiotherapy) in the past 6 months, or recurrent, or metastatic, or inoperable. 3. Any clinically relevant bleeding (defined as bleeding requiring hospitalization, transfusion, surgical intervention, invasive procedures, occurring in a critical anatomical site, or causing disability) within 30 days prior to randomization or sign of acute bleeding. 4. Intracerebral bleeding at any time in the past or signs/symptoms consistent with acute intracranial haemorrhage. 5. Haemoglobin <8 g/dL and platelet count <50 x 10(9) cells/L confirmed by recent laboratory test (<90 days). 6. Subjects with any known coagulopathy or bleeding diathesis, including known significant liver disease associated with coagulopathy. 7. Severe renal insufficiency (baseline creatinine clearance <30 mL/min calculated using the Cockcroft-Gault formula) confirmed by recent laboratory test (<90 days). 8. Contraindications to enoxaparin therapy, including prior heparin-induced thrombocytopenia and known hypersensitivity. 9. Current use of dual antiplatelet therapy. 10. Participation in other interventional studies over the past 30 days. 11. Non-compliance or inability to adhere to treatment or lack of a family environment or support system for home treatment. 12. Cognitive impairment and/or inability to understand information provided in the study information. Patient enrolment will take place at seven Swiss centres, including five university hospitals and two large cantonal hospitals. INTERVENTION AND COMPARATOR: Patients randomized to the intervention group will receive subcutaneous enoxaparin at the recommended dose of 4,000 IU anti-Xa activity (40 mg/0.4 ml) once daily for 14 days. Patients randomized to the comparator group will receive no anticoagulation. MAIN OUTCOMES: Primary outcome: a composite of any hospitalization or all-cause death occurring within 30 days of randomization. Secondary outcomes: (i) a composite of cardiovascular events, including deep vein thrombosis (including catheter-associated), pulmonary embolism, myocardial infarction/myocarditis, arterial ischemia including mesenteric and extremities, acute splanchnic vein thrombosis, or ischemic stroke within 14 days, 30 days, and 90 days of randomization; (ii) each component of the primary efficacy outcome, within 14 days, 30 days, and 90 days of randomization; (iii) net clinical benefit (accounting for the primary efficacy outcome, composite cardiovascular events, and major bleeding), within 14 days, 30 days, and 90 days of enrolment; (iv) primary efficacy outcome, within 14 days, and 90 days of enrolment; (v) disseminated intravascular coagulation (ISTH criteria, in-hospital diagnosis) within 14 days, 30 days, and 90 days of enrolment. RANDOMISATION: Patients will undergo block stratified randomization (by age: 50-70 vs. >70 years; and by study centre) with a randomization ratio of 1:1 with block sizes varying between 4 and 8. Randomization will be performed after the signature of the informed consent for participation and the verification of the eligibility criteria using the electronic data capture software (REDCAP, Vanderbilt University, v9.1.24). BLINDING (MASKING): In this open-label study, no blinding procedures will be used. NUMBERS TO BE RANDOMISED (SAMPLE SIZE): The sample size calculation is based on the parameters α = 0.05 (2-sided), power: 1−β = 0.8, event rate in experimental group, pexp = 0.09 and event rate in control group, pcon = 0.15. The resulting total sample size is 920. To account for potential dropouts, the total sample size was fixed to 1000 with 500 patients in the intervention group and 500 in the control group. TRIAL STATUS: Protocol version 1.0, 14 April 2020. Protocol version 3.0, 18 May 2020 Recruiting start date: June 2020. Last Patient Last Visit: March 2021. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04400799 First Posted: May 26, 2020 Last Update Posted: July 16, 2020 FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. url: https://doi.org/10.1186/s13063-020-04678-4 doi: 10.1186/s13063-020-04678-4 id: cord-257958-yehnlabq author: Barh, Debmalya title: Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date: 2020-10-10 words: 5431.0 sentences: 364.0 pages: flesch: 43.0 cache: ./cache/cord-257958-yehnlabq.txt txt: ./txt/cord-257958-yehnlabq.txt summary: In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). abstract: SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management. url: https://www.sciencedirect.com/science/article/pii/S0010482520303826?v=s5 doi: 10.1016/j.compbiomed.2020.104051 id: cord-302576-fv2ib5vc author: Barisione, Emanuela title: Fibrotic progression and radiologic correlation in matched lung samples from COVID-19 post-mortems date: 2020-09-28 words: 5448.0 sentences: 238.0 pages: flesch: 37.0 cache: ./cache/cord-302576-fv2ib5vc.txt txt: ./txt/cord-302576-fv2ib5vc.txt summary: This study uses an innovative cryobiopsy approach for the post-mortem sampling of lung tissues from COVID-19 patients demonstrating the progression of fibrosis in time and correlation with computed tomography features. The main findings of this study include the following: (1) the identification of a chronological evolution of lesions from an early exudative phase with hyaline membranes to a mid-phase characterized by intra-alveolar fibrinous exudate and early fibroblastic interstitial fibrosis to a late phase with alveolar obliteration by fibrosis and possible micro-honeycombing; (2) mild degree of inflammatory infiltrates; and (3) correlation of histologic patterns with lung CT alterations. Immunohistochemistry for SARS-CoV-2 nucleocapsid protein also showed modification during disease progression as intense immunostaining was seen in early exudative phase Fig. 4 Histology and radiology of late/organizing phase of DAD pattern: aspects of progressive derangement/obliteration of alveolar structure by interstitial fibroblast proliferation. abstract: Data on the pathology of COVID-19 are scarce; available studies show diffuse alveolar damage; however, there is scarce information on the chronologic evolution of COVID-19 lung lesions. The primary aim of the study is to describe the chronology of lung pathologic changes in COVID-19 by using a post-mortem transbronchial lung cryobiopsy approach. Our secondary aim is to correlate the histologic findings with computed tomography patterns. SARS-CoV-2-positive patients, who died while intubated and mechanically ventilated, were enrolled. The procedure was performed 30 min after death, and all lung lobes sampled. Histopathologic analysis was performed on thirty-nine adequate samples from eight patients: two patients (illness duration < 14 days) showed early/exudative phase diffuse alveolar damage, while the remaining 6 patients (median illness duration—32 days) showed progressive histologic patterns (3 with mid/proliferative phase; 3 with late/fibrotic phase diffuse alveolar damage, one of which with honeycombing). Immunohistochemistry for SARS-CoV-2 nucleocapsid protein was positive predominantly in early-phase lesions. Histologic patterns and tomography categories were correlated: early/exudative phase was associated with ground-glass opacity, mid/proliferative lesions with crazy paving, while late/fibrous phase correlated with the consolidation pattern, more frequently seen in the lower/middle lobes. This study uses an innovative cryobiopsy approach for the post-mortem sampling of lung tissues from COVID-19 patients demonstrating the progression of fibrosis in time and correlation with computed tomography features. These findings may prove to be useful in the correct staging of disease, and this could have implications for treatment and patient follow-up. url: https://doi.org/10.1007/s00428-020-02934-1 doi: 10.1007/s00428-020-02934-1 id: cord-314439-ufeiv47z author: Barkan, Elad title: Comparison of SARS-CoV-2 Exit Strategies Building Blocks date: 2020-04-28 words: 8597.0 sentences: 489.0 pages: flesch: 60.0 cache: ./cache/cord-314439-ufeiv47z.txt txt: ./txt/cord-314439-ufeiv47z.txt summary: For example, our simulations indicate that dividing the population into two groups completely released except for taking turns on a long weekend (Fri-Tue) self-isolation once every two weeks, while protecting the 5% most sensitive population would reduce R below 1 even if ten percent of the population does not follow it. 1. Quick and accurate measure of actual coronavirus spread -as on average symptoms onset about 5.2 days after infection 30 , and households enter immediate self-isolation, immediate testing gives an accurate and near real-time measure of virus spread in the community, and could prevent the need for population survey-testing for the virus. We compare the efficiency of several key exit strategies building blocks, comparing how much they are efficient in stopping the epidemic in terms of R, while in relation to how effective they are the amount of average released business days they allow for the population. abstract: We consider and compare various exit strategy building blocks and key measures to mitigate the current SARS-CoV-2 pandemic, some already proposed as well as improvements we suggest. Our comparison is based on a computerized simulation integrating accumulated SARS-CoV-2 epidemiological knowledge. Our results stress the importance of immediate on-symptom isolation of suspected cases and household members, and the beneficial effects of prompt testing capacity. Our findings expose significant epidemic-suppression differences among strategies with seemingly similar economic cost stressing the importance of not just the portion of population and business that is released, but also the pattern. The most effective building blocks are the ones that integrate several base strategies - they allow to release large portions of the population while still achieving diminishing viral spread. However, it may come with a price on somewhat more complex schemes. For example, our simulations indicate that dividing the population into two groups completely released except for taking turns on a long weekend (Fri-Tue) self-isolation once every two weeks, while protecting the 5% most sensitive population would reduce R below 1 even if ten percent of the population does not follow it. We further simulate the contrasting approach of a stratified population release in a hope to achieve herd immunity, which for the time being seems inferior to other suggested building blocks. Knowing the tradeoff between building blocks could help optimize exit strategies to be more effective and suitable for a particular area or country, while maximizing human life as well as economic value. Given our results, we believe that pandemic can be controlled within a reasonable amount of time and at a reasonable socio-economic burden. url: https://doi.org/10.1101/2020.04.23.20072850 doi: 10.1101/2020.04.23.20072850 id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 words: 8453.0 sentences: 409.0 pages: flesch: 48.0 cache: ./cache/cord-258172-p54j4zzo.txt txt: ./txt/cord-258172-p54j4zzo.txt summary: Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . abstract: The World Health Organization declared the COVID-19 epidemic a public health emergency of international concern on March 11th, 2020, and the pandemic is rapidly spreading worldwide. COVID-19 is caused by a novel coronavirus SARS-CoV-2, which enters human target cells via angiotensin converting enzyme 2 (ACE2). We used a number of bioinformatics tools to computationally characterize ACE2 by determining its cell-specific expression in trachea, lung, and small intestine, derive its putative functions, and predict transcriptional regulation. The small intestine expressed higher levels of ACE2 mRNA than any other organ. By immunohistochemistry, duodenum, kidney and testis showed strong signals, whereas the signal was weak in the respiratory tract. Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Gene ontology analysis suggested that, besides its classical role in the renin-angiotensin system, ACE2 may be functionally associated with angiogenesis/blood vessel morphogenesis. Using a novel tool for the prediction of transcription factor binding sites we identified several putative binding sites within two tissue-specific promoters of the ACE2 gene as well as a new putative short form of ACE2. These include several interferon-stimulated response elements sites for STAT1, IRF8, and IRF9. Our results also confirmed that age and gender play no significant role in the regulation of ACE2 mRNA expression in the lung. url: https://www.ncbi.nlm.nih.gov/pubmed/33112891/ doi: 10.1371/journal.pone.0240647 id: cord-323822-jtbfpx88 author: Barnett, Brad P. title: Potential of Ocular Transmission of SARS-CoV-2: A Review date: 2020-09-01 words: 4031.0 sentences: 227.0 pages: flesch: 47.0 cache: ./cache/cord-323822-jtbfpx88.txt txt: ./txt/cord-323822-jtbfpx88.txt summary: Analysis of gene expression profiles from available datasets, published immunohistochemistry, as well as current literature was reviewed, to assess the likelihood that ocular inoculation of SARS-CoV-2 results in systemic infection. Recent findings: The ocular surface and retina have the necessary proteins, Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL) necessary to be infected with SARS-CoV-2. Summary: There is evidence that SARS-CoV-2 may either directly infect cells on the ocular surface, or virus can be carried by tears through the nasolacrimal duct to infect the nasal or gastrointestinal epithelium. From this literature search, four key proteins implicated in SARS-CoV-2 infection were identified: Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL), and datasets were utilized to analyze the expression of these proteins in ocular and non-ocular tissue. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection abstract: Purpose of review: to provide a prospective on the current mechanisms by which SARS-CoV-2 enters cells and replicates, and its implications for ocular transmission. The literature was analyzed to understand ocular transmission as well as molecular mechanisms by which SARS-CoV-2 enters cells and replicates. Analysis of gene expression profiles from available datasets, published immunohistochemistry, as well as current literature was reviewed, to assess the likelihood that ocular inoculation of SARS-CoV-2 results in systemic infection. Recent findings: The ocular surface and retina have the necessary proteins, Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL) necessary to be infected with SARS-CoV-2. In addition to direct ocular infection, virus carried by tears through the nasolacrimal duct to nasal epithelium represent a means of ocular inoculation. Summary: There is evidence that SARS-CoV-2 may either directly infect cells on the ocular surface, or virus can be carried by tears through the nasolacrimal duct to infect the nasal or gastrointestinal epithelium. url: https://www.ncbi.nlm.nih.gov/pubmed/32883010/ doi: 10.3390/vision4030040 id: cord-307303-9mzs5dl4 author: Barnett, Daniel J. title: The Application of the Haddon Matrix to Public Health Readiness and Response Planning date: 2005-02-02 words: 4303.0 sentences: 184.0 pages: flesch: 44.0 cache: ./cache/cord-307303-9mzs5dl4.txt txt: ./txt/cord-307303-9mzs5dl4.txt summary: However, in practice, public health preparedness requires additional models and tools to provide a framework to better understand and prioritize emergency readiness and response needs, as well as to facilitate solutions; this is particularly true at the local health department level. By breaking a larger problem into smaller, more manageable components, the Haddon matrix provides a practical, efficient decisionmaking and planning tool that health department leaders can use to better understand current and emerging threats, perform vulnerability assessments, prioritize and allocate readiness and response resources, and maintain institutional agility in responding to an array of public health emergencies. Applying the Haddon matrix to the threat of a dirty bomb illustrates the value of this injury prevention model as a public health readiness and response tool, even when focusing exclusively on environmental issues. abstract: State and local health departments continue to face unprecedented challenges in preparing for, recognizing, and responding to threats to the public’s health. The attacks of 11 September 2001 and the ensuing anthrax mailings of 2001 highlighted the public health readiness and response hurdles posed by intentionally caused injury and illness. At the same time, recent natural disasters have highlighted the need for comparable public health readiness and response capabilities. Public health readiness and response activities can be conceptualized similarly for intentional attacks, natural disasters, and human-caused accidents. Consistent with this view, the federal government has adopted the all-hazards response model as its fundamental paradigm. Adoption of this paradigm provides powerful improvements in efficiency and efficacy, because it reduces the need to create a complex family of situation-specific preparedness and response activities. However, in practice, public health preparedness requires additional models and tools to provide a framework to better understand and prioritize emergency readiness and response needs, as well as to facilitate solutions; this is particularly true at the local health department level. Here, we propose to extend the use of the Haddon matrix—a conceptual model used for more than two decades in injury prevention and response strategies—for this purpose. url: https://www.ncbi.nlm.nih.gov/pubmed/15866764/ doi: 10.1289/ehp.7491 id: cord-344120-7t5ce2hb author: Baroutjian, Amanda title: SARS-CoV-2 pharmacologic therapies and their safety/effectiveness according to level of evidence date: 2020-09-01 words: 5264.0 sentences: 336.0 pages: flesch: 53.0 cache: ./cache/cord-344120-7t5ce2hb.txt txt: ./txt/cord-344120-7t5ce2hb.txt summary: CONCLUSION: According to level 1 evidence reviewed here, the most effective SARS-Co-V-2 pharmacologic treatments include remdesivir for mild to severe disease, and a triple regimen therapy consisting of lopinavir-ritonavir, ribavirin and interferon beta-1b for mild to moderate disease. 20 Another randomized controlled open-label trial in 199 hospitalized patients with confirmed SARS-CoV-2 with severe COVID-19 was done to compare the clinical effectiveness of lopinavir-ritonavir to standard care alone. According to the level 1 evidence reviewed here, the most effective treatments against SARS-CoV-2, measured by time to negative RT-PCR and time to clinical improvement, are remdesivir therapy and a triple medication regimen (lopinavir-ritonavir, ribavirin, and interferon beta-1b). First, in patients with severe COVID-19, treatment with lopinavir-ritonavir showed no significant difference in time to clinical improvement, mortality at day 28, or detectable viral load compared to standard care alone. abstract: INTRODUCTION: There is a pressing need for COVID-19 transmission control and effective treatments. We aim to evaluate the safety and effectiveness of SARS-CoV-2 pharmacologic therapies as of August 2, 2020 according to study level of evidence. METHODS: PubMed, ScienceDirect, Cochrane Library, JAMA Network and PNAS were searched. The following keywords were used: ((COVID-19) OR (SARS-CoV-2)) AND ((((((therapeutics) OR (treatment)) OR (vaccine)) OR (hydroxychloroquine)) OR (antiviral)) OR (prognosis)). Results included peer-reviewed studies published in English. RESULTS: 15 peer-reviewed articles met study inclusion criteria, of which 14 were RCTs and one was a systematic review with meta-analysis. The following pharmacologic therapies were evaluated: chloroquine (CQ), hydroxychloroquine (HCQ), antivirals therapies, plasma therapy, anti-inflammatories, and a vaccine. CONCLUSION: According to level 1 evidence reviewed here, the most effective SARS-Co-V-2 pharmacologic treatments include remdesivir for mild to severe disease, and a triple regimen therapy consisting of lopinavir-ritonavir, ribavirin and interferon beta-1b for mild to moderate disease. Also, dexamethasone significantly reduced mortality in those requiring respiratory support. However, there is still a great need for detailed level 1 evidence on pharmacologic therapies. url: https://api.elsevier.com/content/article/pii/S0735675720307853 doi: 10.1016/j.ajem.2020.08.091 id: cord-252019-tbalg6k5 author: Barra, Gustavo Barcelos title: Analytical Sensitivity and Specificity of Two RT-qPCR Protocols for SARS-CoV-2 Detection Performed in an Automated Workflow date: 2020-10-12 words: 4900.0 sentences: 268.0 pages: flesch: 51.0 cache: ./cache/cord-252019-tbalg6k5.txt txt: ./txt/cord-252019-tbalg6k5.txt summary: Here, the following analytical performance characteristics of Charité and CDC protocols for SARS-CoV-2 detection were evaluated: (a) analytical specificity, which refers to the qPCR assay detecting the appropriate target sequence rather than other nonspecific targets also present in a sample [17] ; (b) PCR amplification efficiency, which is the increase in amplicon per cycle, and is highly dependent on the primers used [17, 18] ; (c) analytical sensitivity or limit of detection, which refers to the minimum number of nucleic acid copies in a sample that can be detected with 95% probability [17] ; (d) cross-reactivity with other pathogens; (e) on-going accuracy in clinical specimens, which refers to agreement between the test method and another method during the daily routine. abstract: WHO declared the novel coronavirus (COVID-19) outbreak a global pandemic on 11 March 2020. The establishment of standardized RT-qPCR protocols for respiratory secretions testing, as well as sharing of specimens, data, and information became critical. Here, we investigate the analytical performance of two interim RT-qPCR protocols (Charité and Centers for Disease Control (CDC)) for the qualitative detection of SARS-CoV-2 executed in a fully automated platform. Analytical specificity, PCR amplification efficiency, analytical sensitivity (limit of detection), and cross-reactivity were evaluated using contrived samples. The on-going accuracy was evaluated by retrospective analysis of our test results database (real clinical samples). N1, E, and a modified version of RdRP assays presented adequate analytical specificity, amplification efficiency, and analytical sensitivity using contrived samples. The three assays were applied to all individuals who requested the SARS-CoV-2 molecular test assay in our laboratory and it was observed that N1 gave more positive results than E, and E gave more positive results than RdRP (modified). The RdRP and E were removed from the test and its final version, based on N1 assay only, was applied to 30,699 Brazilian individuals (from 19 February 2020 to 8 May 2020). The aggregated test results available in the database were also presented. url: https://www.ncbi.nlm.nih.gov/pubmed/33053675/ doi: 10.3390/genes11101183 id: cord-268211-egy8rgtl author: Barrasa, Helena title: SARS-Cov-2 in Spanish Intensive Care: Early Experience with 15-day Survival In Vitoria date: 2020-04-09 words: 2681.0 sentences: 181.0 pages: flesch: 53.0 cache: ./cache/cord-268211-egy8rgtl.txt txt: ./txt/cord-268211-egy8rgtl.txt summary: Methods: We identified patients from the two public hospitals in Vitoria who were admitted to ICU with confirmed infection by SARS-CoV-2. Conclusion: This early experience with SARS-CoV-2 in Spain suggests that a strategy of right oxygenation avoiding non-invasive mechanical ventilation was life-saving. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring mechanical ventilation. Because of mortality reports in Wuhan [5] suggesting a close association, we assessed correlation between plasma procalcitonin at ICU admission and 7-day mortality. Our findings suggest that an oxygenation strategy emphasising optimisation of oxygenation, intubation based on clinical criteria of hyperventilation and avoiding ventilator-induced lung injury associated with non-invasive mechanical ventilation would be life-saving in a significant proportion of patients. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring prolonged mechanical ventilation. abstract: Abstract Purpose: Community transmission of SARS-CoV-2 was detected in Spain in February 2020, with 216% intensive care unit (ICU) capacity expanded in Vitoria by March 18th, 2020. Methods: We identified patients from the two public hospitals in Vitoria who were admitted to ICU with confirmed infection by SARS-CoV-2. Data reported here were available in March 31th, 2020. Mortality was assessed in those who completed 7-days of ICU stay. Results: We identified 48 patients (27 males) with confirmed SARS-CoV-2. Median [interquartile range (IQR)] age of patients was 63 [51-75] years. Symptoms began a median of 7 [5-12] days before ICU admission. The most common comorbidities identified were obesity (n = 48%), arterial hypertension (n = 44%) and chronic lung disease (n = 37%). All patients were admitted by hypoxemic respiratory failure and none received non-invasive mechanical ventilation. Forty-five (94%) underwent intubation, 3 HFNT, 1 (2%) extracorporeal membrane oxygenation (ECMO) and 22 (49%) required prone position. After 15 days, 14/45 (31%) intubated patients died (13% within one week), 10 (22%) were extubated, and 21/45 (47%) underwent mechanical ventilation. Six patients had documented co-infection. Procalcitonin plasma above 0.5 µg/L was associated with 16% vs. 19% (p = 0.78) risk of death after 7 days. Conclusion: This early experience with SARS-CoV-2 in Spain suggests that a strategy of right oxygenation avoiding non-invasive mechanical ventilation was life-saving. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring mechanical ventilation. After 15 days of ICU admission, half of patients remained intubated, whereas one third died. url: https://doi.org/10.1016/j.accpm.2020.04.001 doi: 10.1016/j.accpm.2020.04.001 id: cord-350094-nkzbtcfw author: Barrett, Lisa F. title: Self-Limited Gastrointestinal Bleeding in COVID-19 date: 2020-07-15 words: 649.0 sentences: 52.0 pages: flesch: 53.0 cache: ./cache/cord-350094-nkzbtcfw.txt txt: ./txt/cord-350094-nkzbtcfw.txt summary: Clinicians should be aware of a possible increased risk of GI bleeding and its complications when managing critically ill COVID-19 patients. SARS-CoV-2, a single-stranded RNA virus of the beta coronavirus genus, enters the body via the angiotensin converting enzyme 2 (ACE2) receptor [2] [3] . ACE2 is expressed in gastrointestinal (GI) epithelial cells suggesting that SARS-CoV-2 can infect and replicate in the GI tract [4] . We present a case series of six patients, most without a known source of GI bleeding, who tested positive for SARS-CoV-2 and concurrently suffered from hematochezia or melena. We recorded cases of SARS-CoV-2 infection and concurrent GI bleeding from March 1, 2020 to April 24, 2020. Coagulopathy is associated with SARS-CoV-2 infection. Given the possible increased risk of bleeding in COVID-19, therapeutic anticoagulation in infected patients should be used cautiously. This case series shows a possible increased risk of bleeding among patients with COVID-19. abstract: Abstract The most commonly reported gastrointestinal (GI) manifestations of COVID-19 include abdominal pain, diarrhea, nausea and vomiting. There is limited data regarding GI bleeding in patients with COVID-19, however, patients have been documented to present with hematochezia or melena at the onset of COVID-19 symptoms. The presence of GI bleeding in the setting of COVID-19 complicates the patient's clinical course and management of sequelae including coagulopathy. Clinicians should be aware of a possible increased risk of GI bleeding and its complications when managing critically ill COVID-19 patients. url: https://api.elsevier.com/content/article/pii/S2210740120301844 doi: 10.1016/j.clinre.2020.06.015 id: cord-309360-cpis1l4u author: Barrios-López, J. M. title: Ischaemic stroke and SARS-CoV-2 infection: A causal or incidental association? date: 2020-05-28 words: 3152.0 sentences: 235.0 pages: flesch: 42.0 cache: ./cache/cord-309360-cpis1l4u.txt txt: ./txt/cord-309360-cpis1l4u.txt summary: Results: The association between COVID-19 and stroke was probably causal in 2 patients, who presented cortical infarcts and had no relevant arterial or cardioembolic disease, but did show signs of hypercoagulability and systemic inflammation in laboratory analyses. A recent study described the cases of 3 patients with COVID-19 who presented ischaemic stroke and antiphospholipid antibodies, in addition to elevated D-dimer levels and laboratory markers of systemic inflammation. 7 A recent study reported 3 cases of severe COVID-19 and ischaemic stroke; these patients presented antiphospholipid antibodies and laboratory findings compatible with systemic inflammation and coagulopathy. 19 In patients 1 and 2 of our series (Table 1) , the likelihood of a causal relationship between COVID-19 and stroke is high, as these patients presented laboratory markers of systemic inflammation and hypercoagulability and the aetiological study found no evident cause for ischaemic stroke. abstract: Abstract Introduction Ischaemic stroke has been reported in patients with COVID-19, particularly in more severe cases. However, it is unclear to what extent this is linked to systemic inflammation and hypercoagulability secondary to the infection. Materials and methods We describe the cases of 4 patients with ischaemic stroke and COVID-19 who were attended at our hospital. Patients are classified according to the likelihood of a causal relationship between the hypercoagulable state and ischaemic stroke. We also conducted a review of studies addressing the possible mechanisms involved in the aetiopathogenesis of ischaemic stroke in these patients. Results The association between COVID-19 and stroke was probably causal in 2 patients, who presented cortical infarcts and had no relevant arterial or cardioembolic disease, but did show signs of hypercoagulability and systemic inflammation in laboratory analyses. The other 2 patients were of advanced age and presented cardioembolic ischaemic stroke; the association in these patients was probably incidental. Conclusions Systemic inflammation and the potential direct action of the virus may cause endothelial dysfunction, resulting in a hypercoagulable state that could be considered a potential cause of ischaemic stroke. However, stroke involves multiple pathophysiological mechanisms; studies with larger samples are therefore needed to confirm our hypothesis. The management protocol for patients with stroke and COVID-19 should include a complete aetiological study, with the appropriate safety precautions always being observed. url: https://api.elsevier.com/content/article/pii/S2173580820301012 doi: 10.1016/j.nrleng.2020.05.008 id: cord-254630-ed5gawoj author: Barron, Sarah P. title: Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy? date: 2020-09-17 words: 4026.0 sentences: 180.0 pages: flesch: 39.0 cache: ./cache/cord-254630-ed5gawoj.txt txt: ./txt/cord-254630-ed5gawoj.txt summary: Additionally, RFBs pose a risk of nosocomial infection transmission between patients with the identification of human proteins, deoxyribonucleic acid (DNA) and pathogenic organisms on fully reprocessed bronchoscopes despite full adherence to the guidelines. Until now, disposable or single-use flexible bronchoscopes (SUFBs) have primarily been used by anaesthetists in an ICU or peri-operative setting where they perform to an acceptable level in comparison to RFBs [12, 13] combined with the distinct advantage of a reduced risk of infection owing to their sterility [14] . In this review, the risk of infection with standard RFBs will be outlined as will the advantages of SUFBs, with comment on their cost profile compared to RFBs and attempt to suggest a rationale for their use during the COVID-19 pandemic and in a respiratory setting. abstract: The coronavirus disease (COVID-19) pandemic has highlighted the importance of reducing occupational exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reprocessing procedure for reusable flexible bronchoscopes (RFBs) involves multiple episodes of handling of equipment that has been used during an aerosol-generating procedure and thus is a potential source of transmission. Single-use flexible bronchoscopes (SUFBs) eliminate this source. Additionally, RFBs pose a risk of nosocomial infection transmission between patients with the identification of human proteins, deoxyribonucleic acid (DNA) and pathogenic organisms on fully reprocessed bronchoscopes despite full adherence to the guidelines. Bronchoscopy units have been hugely impacted by the pandemic with restructuring of pre- and post-operative areas, altered patient protocols and the reassessment of air exchange and cleaning procedures. SUFBs can be incorporated into these protocols as a means of improving occupational safety. Most studies on the efficacy of SUFBs have occurred in an anaesthetic setting so it remains to be seen whether they will perform to an acceptable standard in complex respiratory procedures such as transbronchial biopsies and cryotherapy. Here, we outline their potential uses in a respiratory setting, both during and after the current pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32944885/ doi: 10.1007/s12325-020-01495-8 id: cord-266988-72uvawth author: Barth, Rolf F. title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 date: 2020-07-14 words: 2504.0 sentences: 115.0 pages: flesch: 43.0 cache: ./cache/cord-266988-72uvawth.txt txt: ./txt/cord-266988-72uvawth.txt summary: title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 COVID-19 disease is caused by a novel coronavirus, which has been named "Severe Acute Respiratory Syndrome Corona virus-2 (SARS-CoV-2)" [2] . Our current understanding of the pathology and the pathogenesis of COVID-19 disease and SARS-CoV-2 transmission is at an early stage and much still remains to be learned [5, 6] . Therefore, the total number of autopsies performed is miniscule compared to the number of deaths, but nevertheless they are both very revealing and important in order to better understand the multi-organ involvement associated with COVID-19 infection and for the development of better treatment strategies [1, 3] . The autopsy reports that already have been published provide a solid base for a better understanding of the consequences of COVID-19 infection but much more remains to be learned about this complex disease in order to develop better treatment strategies. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32665025/ doi: 10.1186/s13000-020-00999-9 id: cord-256904-uq6gy24x author: Bartolini, A. title: Immunochromatographic assays for COVID-19 epidemiological screening: our experience date: 2020-06-02 words: 2684.0 sentences: 147.0 pages: flesch: 49.0 cache: ./cache/cord-256904-uq6gy24x.txt txt: ./txt/cord-256904-uq6gy24x.txt summary: We submitted to serological screening by two different immunochromatographic (IC) rapid testing for detection of IgG and IgM against SARS-CoV-2, 151 asymptomatic or minimally symptomatic healthcare workers previously tested positive for SARS-CoV-2 RT-PCR in order to evaluate the performance of rapid assays. Results showed discrepancies between molecular and IC results, and an inconsistency of immunoglobulins positivity patterns when compared to ELISA/CLIA results, highlighting the absolute necessity of assays performance validation before their marketing and use, in order to avoid errors in the results evaluation at both clinical and epidemiological level. Our aim was to evaluate the performances of two different IC assays, submitting to serological testing the 151 healthcare workers previously tested positive for SARS-CoV-2 RT-PCR and trying to find a correlation between the molecular method, that is considered the gold standard and rapid IC tests actually available. abstract: In March 2020, the World Health Organization (WHO) declared a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the absence of effective treatment or biomedical prevention, understanding potential post infection immunity has important implications for epidemiologic assessments. For this reason, increasing number of in vitro diagnostic companies are developing serological assays to detect antibodies against SARS-CoV-2, but most of them lack the validation by third parties in relation to their quality, limiting their usefulness. We submitted to serological screening by two different immunochromatographic (IC) rapid testing for detection of IgG and IgM against SARS-CoV-2, 151 asymptomatic or minimally symptomatic healthcare workers previously tested positive for SARS-CoV-2 RT-PCR in order to evaluate the performance of rapid assays. Results showed discrepancies between molecular and IC results, and an inconsistency of immunoglobulins positivity patterns when compared to ELISA/CLIA results, highlighting the absolute necessity of assays performance validation before their marketing and use, in order to avoid errors in the results evaluation at both clinical and epidemiological level. url: http://medrxiv.org/cgi/content/short/2020.05.28.20116046v1?rss=1 doi: 10.1101/2020.05.28.20116046 id: cord-284559-g9szoh3g author: Bartoloni, Elena title: Hypertension and SARS-Cov-2 infection: is inflammation the missing link? date: 2020-09-23 words: 616.0 sentences: 50.0 pages: flesch: 33.0 cache: ./cache/cord-284559-g9szoh3g.txt txt: ./txt/cord-284559-g9szoh3g.txt summary: The dramatic emergence of the pandemic coronavirus disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised significant medical and public health concerns for the high disease mortality rate ranging from 1% to more than 5%. 2 In fact, pre-existing cardiovascular comorbidities, including hypertension (HTN), diabetes mellitus, cerebrovascular and coronary heart disease, enhance susceptibility to SARS-CoV-2 infection and are associated with increased risk of severe disease, myocardial injury and short-term mortality rate. 4 However, due to the high prevalence of hypertension in the general population, concerns raised as to whether hypertension represents merely a concomitant risk factor or a pivotal pathogenic trigger of cardiac injury in patients with SARS-CoV2 infection. In this setting, it may be hypothesized that COVID-19associated PAMPs may act as exogenous triggers of TLR4 signalling pathway leading to inflammasome activation and inflammatory cytokine release, including interleukin-1 (Figure) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32966547/ doi: 10.1093/cvr/cvaa273 id: cord-274399-cd7cmpoj author: Barzin, Amir title: SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures date: 2020-09-29 words: 3304.0 sentences: 189.0 pages: flesch: 47.0 cache: ./cache/cord-274399-cd7cmpoj.txt txt: ./txt/cord-274399-cd7cmpoj.txt summary: This is one of the first published seroprevalence studies from North Carolina and included multicenter, primary care, and emergency care facilities serving a low-density, suburban and rural population since description of the North Carolina state index case introducing the SARS-CoV-2 respiratory pathogen to this population. Asymptomatic infection by SARS-CoV-2 (with no clinical symptoms) was examined using an Emergency Use Authorization (EUA)-approved antibody test (Abbott) for the presence of SARS-CoV-2 IgG. This study identifies a very limited seroprevalence of SARS-CoV-2 among asymptomatic individuals accessing the UNC Health system. This study employed an EUA assay performed in a CLIA-certified laboratory on a venous blood sample, with demonstrated specificity to detect antibodies only to SARS-CoV-2, not to seasonal coronaviruses. Upon arrival for SARS-CoV-2 Seroprevalence in North Carolina ® routine care or scheduled visits for enrollment into the study, patients performed a consent procedure that included reviewing recent COVID-19 clinical history using UNC IRB-approved questionnaires. abstract: Characterizing the asymptomatic spread of SARS-CoV-2 is important for understanding the COVID-19 pandemic. This study was aimed at determining asymptomatic spread of SARS-CoV-2 in a suburban, Southern U.S. population during a period of state restrictions and physical distancing mandates. This is one of the first published seroprevalence studies from North Carolina and included multicenter, primary care, and emergency care facilities serving a low-density, suburban and rural population since description of the North Carolina state index case introducing the SARS-CoV-2 respiratory pathogen to this population. To estimate point seroprevalence of SARS-CoV-2 among asymptomatic individuals over time, two cohort studies were examined. The first cohort study, named ScreenNC, was comprised of outpatient clinics, and the second cohort study, named ScreenNC2, was comprised of inpatients unrelated to COVID-19. Asymptomatic infection by SARS-CoV-2 (with no clinical symptoms) was examined using an Emergency Use Authorization (EUA)-approved antibody test (Abbott) for the presence of SARS-CoV-2 IgG. This assay as performed under CLIA had a reported specificity/sensitivity of 100%/99.6%. ScreenNC identified 24 out of 2,973 (0.8%) positive individuals among asymptomatic participants accessing health care during 28 April to 19 June 2020, which was increasing over time. A separate cohort, ScreenNC2, sampled from 3 March to 4 June 2020, identified 10 out of 1,449 (0.7%) positive participants. url: https://doi.org/10.1128/mbio.02426-20 doi: 10.1128/mbio.02426-20 id: cord-262730-1dxeg8ci author: Barón-Sánchez, J. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 words: 3510.0 sentences: 244.0 pages: flesch: 54.0 cache: ./cache/cord-262730-1dxeg8ci.txt txt: ./txt/cord-262730-1dxeg8ci.txt summary: [12] [13] [14] The olfactory alterations associated with SARS-COV-2 infection present sudden onset, are generally not accompanied by rhinorrhoea or nasal obstruction with mucus, and are of variable intensity, although patients frequently report complete loss of the sense of smell. V a r i a b l e s Participants meeting the inclusion criteria were asked to complete a questionnaire, which gathered the following data: sex; age; medical history; characteristics of olfactory/gustatory alterations (complete loss of the sense of smell/taste [anosmia/ageusia], decreased sense of smell [hyposmia], altered sense of taste [dysgeusia]); date of onset and resolution of the alterations; symptom progression; associated symptoms; close contact with a patient with COVID-19 (confirmed by PCR testing); and PCR results for COVID-19, if the test was performed. In our study, only 8.4% of individuals with olfactory/gustatory alterations undergoing PCR testing were negative for SARS-CoV-2; this supports the hypothesis that these symptoms are highly prevalent in patients with mild COVID-19. abstract: Introduction Coronavirus disease 2019 (COVID-19) has spread rapidly throughout the world. Smell and/or taste disorders have emerged as a very frequent symptom as the disease has spread in Europe. Spain is one of the European countries with the highest number of infections. Objective This study aimed to investigate the clinical progression of smell and taste disorders in Spanish patients with mild COVID-19. Methods An online survey was used to conduct a cross-sectional study of patients who presented sudden smell and/or taste disorders during the 2 months of total lockdown due to COVID-19 in Spain. Results In our sample, 91.18% of respondents with impaired smell and/or taste and who were able to undergo PCR testing were positive for SARS-CoV-2 infection. Anosmia and ageusia presented in isolation in 6.5% of participants. The remaining 93.5% presented other mild symptoms: headache (51.6%), cough (51.6%), myalgia (45.2%), asthaenia (38.7%), nasal congestion or rhinorrhoea (35.5%), fever (41.9%), low-grade fever (29.0%), odynophagia (25.8%), or diarrhoea (6.5%). The mean duration of anosmia was 8.33 days, with patients subsequently manifesting hyposmia; complete resolution occurred after a mean of 17.79 days. In 22.6% of respondents, olfactory deficits persisted. All participants recovered their sense of taste. Conclusions Olfactory and gustatory disorders are prevalent symptoms in mild COVID-19. Most patients do not present associated nasal congestion or rhinorrhoea and a small group of patients present these alterations in isolation. url: https://api.elsevier.com/content/article/pii/S2173580820302169 doi: 10.1016/j.nrleng.2020.07.007 id: cord-303609-9217t0ui author: Baselga, María Trinidad title: Trombosis y COVID-19: revisión de alcance date: 2020-09-24 words: 3233.0 sentences: 320.0 pages: flesch: 53.0 cache: ./cache/cord-303609-9217t0ui.txt txt: ./txt/cord-303609-9217t0ui.txt summary: Esta revisión de alcance (scoping review) resume y evalúa críticamente la evidencia sobre la relación entre la trombosis y el COVID-19, y se basa en una búsqueda bibliográfica sistemática de todos los artículos publicados hasta el 5 de mayo de 2020 e incluidos en las bases de datos PubMed, Scopus, Cochrane y Clinicaltrials.gov. En otros estudios se estandarizó el uso de ecografía para la detección de las complicaciones J o u r n a l P r e -p r o o f DISCUSIÓN Esta es la primera scope review que revisa los artículos que relacionan la infección por SARS-CoV-2 y las alteraciones en la coagulación, incluyendo sus repercusiones clínicas y radiológicas; en orden cronológico desde el 1 de diciembre de 2019 hasta el 5 mayo de 2020. abstract: La coronavirus disease-19 (COVID-19) ha generado la mayor crisis de salud pública de la era moderna. Se considera que el estado protrombótico inducido por la infección tiene una relación directa y de importancia sustancial con el daño agudo en el pulmón y con las complicaciones de la infección, incluida la muerte. Esta revisión de alcance (scoping review) resume y evalúa críticamente la evidencia sobre la relación entre la trombosis y el COVID-19, y se basa en una búsqueda bibliográfica sistemática de todos los artículos publicados hasta el 5 de mayo de 2020 e incluidos en las bases de datos PubMed, Scopus, Cochrane y Clinicaltrials.gov. Hemos incluido 26 artículos en la revisión, y hemos evaluado su calidad empleando la guía STROBE. Los principales síntomas que presentan los pacientes diagnosticados de COVID-19 son disnea, fiebre, tos, diarrea y vómitos. A nivel analítico destaca, en esta enfermedad, un aumento de Dímero-D, fibrinógeno, tiempo de protrombina y linfopenia. En cuanto a las pruebas radiológicas, las técnicas más usadas para el diagnóstico de tromboembolismo pulmonar, trombosis venosa profunda y otros fenómenos trombóticos; fueron la ecografía y la tomografía computarizada. Como conclusión, en la actualidad existe escasa evidencia científica con respecto a la COVID-19 y sus complicaciones trombóticas. Esta revisión resume este cuerpo de evidencia, evalúa su calidad, y ofrece conclusiones que orientan los siguientes pasos a dar en este área de investigación de enorme relevancia y crecimiento exponencial. Coronavirus disease-19 (COVID-19) has triggered the worst public health crisis of modern times. The prothrombotic state induced by the infection is considered directly and substantially related to acute lung damage and other medical complications, including death. This scoping review summarises and critically assesses the existing evidence on the association between thrombosis and COVID-19, and is based on a systematic literature search of all articles published up to 5 May 2020 included in the following databases: PubMed, Scopus, Cochrane, and Clinicaltrials.gov. A total of 25 articles were included, and their quality evaluated using STROBE guidelines. The main symptoms presented by patients that had been diagnosed with COVID-19 are dyspnoea, fever, cough, diarrhoea, and vomiting. In the laboratory findings, it is characteristic to observe an increase in D-Dimer, fibrinogen, prothrombin time, and lymphopenia. Ultrasound and computed axial tomography were the radiological techniques most used for diagnosing pulmonary thromboembolism, deep vein thrombosis, and other thrombotic phenomena. In conclusion, there is still limited scientific evidence on COVID-19 and its thrombotic complications. This review summarises the body of evidence, assesses its quality, and offers conclusions that should help in the next steps in this highly relevant and expanding research area. url: https://www.sciencedirect.com/science/article/pii/S0122726220300823?v=s5 doi: 10.1016/j.acci.2020.09.002 id: cord-104501-e5e0xrou author: Bashash, Davood title: The Prognostic Value of Thrombocytopenia in COVID-19 Patients; a Systematic Review and Meta-Analysis date: 2020-09-19 words: 2752.0 sentences: 146.0 pages: flesch: 48.0 cache: ./cache/cord-104501-e5e0xrou.txt txt: ./txt/cord-104501-e5e0xrou.txt summary: To provide a well-conceptualized viewpoint demonstrating the prognostic value of platelet count in SARS-CoV-2 infection, we performed a meta-analysis of pertinent literature to evaluate whether the emergence of thrombocytopenia could discriminate between severe and non-severe cases. Even though the results of a recent study to establish a prediction model for the prognosis of SARS-CoV-2 infection (19) introduced C reactive protein, lactic dehydrogenase, and lymphocyte count as the most valuable laboratory parameters reflecting COVID-19 severity, articles continuously introducing novel biomarkers with the ability to predict disease outcome are published daily. To provide a clear viewpoint demonstrating the prognostic value of platelet count in this novel infection, we performed a meta-analysis of pertinent literature representing information on the indicated parameter in patients with a clinically validated definition of severe disease. abstract: INTRODUCTION: Multiple lines of evidence have attested that decreased numbers of platelets may serve as a surrogate marker for poor prognosis in a wide range of infectious diseases. Thus, to provide a well-conceptualized viewpoint demonstrating the prognostic value of thrombocytopenia in COVID-19, we performed a meta-analysis of pertinent literature. METHODS: The keywords “platelet” OR “thrombocytopenia” AND “COVID-19” OR “coronavirus 2019” OR “2019-nCoV” OR “SARS-CoV-2” were searched in National Library of Medicine Medline/PubMed and Scopus between December 30, 2019, and May 9, 2020 in English without any restriction. The initial search results were first screened by title and abstract, and then full texts of relevant articles representing information on the platelet count (main outcome) with a clinically validated definition of COVID-19 severity were finally selected. To assess the existence of bias in the included studies, the funnel plot and egger plot along with egger tests were used. Also, the heterogeneity among the included studies was tested using the Chi-square test. RESULTS: The results of our meta-analysis of 19 studies, totaling 3383 COVID-19 patients with 744 (21.9%) severe cases, revealed that non-severe cases have a significantly higher number of platelets and showed that the probability of the emergence of thrombocytopenia is significantly higher in the severe cases with the pooled mean difference of -21.5 (%95 CI: -31.57, -11.43). CONCLUSION: Decreased number of platelets more commonly associates with severe COVID-19; however, whether the emergence of thrombocytopenia may result in diseases severity or the severity of the disease may decrease platelets, is open to debate. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587988/ doi: nan id: cord-341919-8gnthufw author: Basi, Saajan title: Clinical course of a 66-year-old man with an acute ischaemic stroke in the setting of a COVID-19 infection date: 2020-08-23 words: 4192.0 sentences: 221.0 pages: flesch: 50.0 cache: ./cache/cord-341919-8gnthufw.txt txt: ./txt/cord-341919-8gnthufw.txt summary: 3 There appears to be a growing correlation between COVID-19 positive patients presenting to hospital with ischaemic stroke; however, studies investigating this are in progress, with new data emerging daily. 10 The patient, in this case, illustrates the clinical relevance of understanding COVID-19, as he presented with an ischaemic stroke underlined by minimal respiratory symptoms, which progressed expeditiously, resulting in acute respiratory distress syndrome and subsequent death. Our case is an example of a new and ever-evolving clinical correlation, between patients who present with a radiological confirmed ischaemic stroke and severe COVID-19 pneumonia. As of April 2020, no comprehensive data of the relationship between ischaemic stroke and COVID-19 has been published, however early retrospective case series from three hospitals in Wuhan, China have indicated that up to 36% of COVID-19 patients had neurological manifestations, including stroke. abstract: A 66-year-old man was admitted to hospital with a right frontal cerebral infarct producing left-sided weakness and a deterioration in his speech pattern. The cerebral infarct was confirmed with CT imaging. The only evidence of respiratory symptoms on admission was a 2 L oxygen requirement, maintaining oxygen saturations between 88% and 92%. In a matter of hours this patient developed a greater oxygen requirement, alongside reduced levels of consciousness. A positive COVID-19 throat swab, in addition to bilateral pneumonia on chest X-ray and lymphopaenia in his blood tests, confirmed a diagnosis of COVID-19 pneumonia. A proactive decision was made involving the patients’ family, ward and intensive care healthcare staff, to not escalate care above a ward-based ceiling of care. The patient died 5 days following admission under the palliative care provided by the medical team. url: https://www.ncbi.nlm.nih.gov/pubmed/32843381/ doi: 10.1136/bcr-2020-235920 id: cord-331856-j0gedx43 author: Basile, K. title: Accuracy amidst ambiguity: false positive SARS-CoV-2 nucleic acid tests when COVID-19 prevalence is low date: 2020-09-30 words: 1238.0 sentences: 69.0 pages: flesch: 45.0 cache: ./cache/cord-331856-j0gedx43.txt txt: ./txt/cord-331856-j0gedx43.txt summary: In countries with a low prevalence of COVID-19 and a low pre-test probability, confirmation of positive nucleic acid test (NAT) results for SARS-CoV-2 is recommended given the potential for false positive results. [2] [3] [4] Initially, the Public Health Laboratory Network (PHLN) Australia recommended that confirmatory testing be performed on samples where SARS-CoV-2 RNA had been detected to ensure that the result was a true positive. In the context of Australia''s low prevalence of COVID-19 and thus low pre-test probability for infection, we recommend that all positive SARS-CoV-2 NAT results be confirmed by supplementary testing on the original nucleic acid extract and/or re-extraction of nucleic acid from the original sample (if available) and tested using another assay(s) with different gene targets and/or lower limits of detection 10 (Fig. 1) . abstract: nan url: https://doi.org/10.1016/j.pathol.2020.09.009 doi: 10.1016/j.pathol.2020.09.009 id: cord-262043-66qle52a author: Basit, Abdul title: Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date: 2020-05-20 words: 4866.0 sentences: 275.0 pages: flesch: 55.0 cache: ./cache/cord-262043-66qle52a.txt txt: ./txt/cord-262043-66qle52a.txt summary: Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. We designed a truncated version (tACE2) of ACE2 receptor covering the binding residues and performed protein-protein docking and molecular dynamic simulations to analyze its binding affinity for RBD and complex stability. Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) . abstract: The current pandemic of Covid-19 caused by SARS-CoV-2 is continued to spread globally and no potential drug or vaccine against it is available. Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. Thereby, blocking the S glycoprotein through potential inhibitor may interfere its interaction with ACE2 and impede its entry into the host cell. Here, we present a truncated version of human ACE2 (tACE2), comprising the N terminus region of the intact ACE2 from amino acid position 21-119, involved in binding with receptor binding domain (RBD) of SARS-CoV-2. We analyzed the in-silico potential of tACE2 to compete with intact ACE2 for binding with RBD. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. Furthermore, prediction of tACE2 soluble expression in E. coli makes it a suitable candidate to be targeted for Covid-19 therapeutics. This is the first MD simulation based findings to provide a high affinity protein inhibitor for SARS-CoV-2 S glycoprotein, an important target for drug designing against this unprecedented challenge. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1768150 doi: 10.1080/07391102.2020.1768150 id: cord-323807-e220ut9u author: Bassetti, Matteo title: The novel Chinese coronavirus (2019‐nCoV) infections: Challenges for fighting the storm date: 2020-02-05 words: 2236.0 sentences: 112.0 pages: flesch: 50.0 cache: ./cache/cord-323807-e220ut9u.txt txt: ./txt/cord-323807-e220ut9u.txt summary: Four (229E, NL63, OC43 and HKU1) are responsible for mild upper respiratory tract infections (common cold), whereas the severe acute respiratory syndrome coronavirus (SARS-CoV, which has been contained 4 ) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are able to cause atypical pneumonia. Worth noting is also that the case fatality rate of 2019-nCoV reported in the press news is lower than those previously described for SARS-CoV and MERS-CoV infections (9.5% and 40%, respectively 11 ). Lopinavir/ritonavir is available in several hospitals and has shown promising results in pre-clinical models and case series of SARS-CoV and MERS-CoV infections, 14, 15 although no high-level evidence of efficacy and safety is currently available for its use either as monotherapy or in combination with interferons or other drugs (a randomized controlled trial has been initiated in patients with 2019-nCoV pneumonia in China). abstract: Since end of December 2019, a cluster of patients with pneumonia of unknown origin was reported from Wuhan, Hubei province, China. They shared a connection with the Huanan South China Seafood Market in Wuhan, and now it has been confirmed that the disease is caused by a novel coronavirus (provisionally named 2019-nCoV). As of today (30 January 2020), 7734 cases have been confirmed in China, and 90 cases have also been cumulatively reported from Taiwan, Thailand, Vietnam, Malaysia, Nepal, Sri Lanka, Cambodia, Japan, Singapore, Republic of Korea, United Arab Emirate, United States, The Philippines, India, Australia, Canada, Finland, France, and Germany (Finland, France and Germany are the only European countries in which cases [n= 1, n = 5, and n = 4, respectively] have been reported up to date). According to the released news, the case rate fatality is 2.2% (170/7824). url: https://doi.org/10.1111/eci.13209 doi: 10.1111/eci.13209 id: cord-269756-tid8a464 author: Basso, Luis G. M. title: SARS-CoV fusion peptides induce membrane surface ordering and curvature date: 2016-11-28 words: 12194.0 sentences: 532.0 pages: flesch: 49.0 cache: ./cache/cord-269756-tid8a464.txt txt: ./txt/cord-269756-tid8a464.txt summary: Although membrane fusion promoted by class I viral glycoproteins, such as SARS-CoV Spike, human immunodeficiency virus (HIV) gp160 or influenza virus hemagglutinin (HA), has been broadly studied in recent years [16] [17] [18] [19] , many aspects of the molecular mechanism behind the virus-host cell membrane fusion remain unknown, including conformational changes of the lipid bilayers during peptide-membrane interactions. In the present study, we investigated the effects of two putative fusion peptides from SARS-CoV S glycoprotein, corresponding to residues 770-788 (SARS FP ) and 873-888 (SARS IFP ) 13, 15, 22, 23 , on the structural dynamics, physicochemical properties, and thermotropic phase behavior of lipid model membranes by differential scanning calorimetry (DSC), continuous wave (CW) and pulsed electron spin resonance (ESR) along with nonlinear least-squares (NLLS) spectral fitting 24 . abstract: Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs. DSC data showed the peptides strongly perturb the structural integrity of anionic vesicles and support the hypothesis that the peptides generate opposing curvature stresses on phosphatidylethanolamine membranes. ESR showed that both FPs increase lipid packing and head group ordering as well as reduce the intramembrane water content for anionic membranes. Therefore, bending moment in the bilayer could be generated, promoting negative curvature. The significance of the ordering effect, membrane dehydration, changes in the curvature properties and the possible role of negatively charged phospholipids in helping to overcome the high kinetic barrier involved in the different stages of the SARS-CoV-mediated membrane fusion are discussed. url: https://doi.org/10.1038/srep37131 doi: 10.1038/srep37131 id: cord-257468-woyycghi author: Basso, Trude title: Transmission of infection from non-isolated patients with COVID-19 to health care workers date: 2020-08-20 words: 1824.0 sentences: 114.0 pages: flesch: 59.0 cache: ./cache/cord-257468-woyycghi.txt txt: ./txt/cord-257468-woyycghi.txt summary: This study evaluated transmission of infection from a symptomatic patient with COVID-19 to 60 HCWs exposed ≤2 m for ≥15 minutes, or during aerosol generating procedures. Following ≥106 unique high-risk contacts, none of the HCWs tested positive for SARS-CoV-2 RNA or had developed antibodies. These results were in accordance with other reports and should reassure HCWs and further stimulate a broader evaluation of the foundation for the current practice of home-quarantine of non-symptomatic HCWs. During the Coronavirus Disease-19 (COVID-19) pandemic, the proportion of health care workers (HCWs) amongst verified, infected individuals, has been reported somewhere between 10 and 20 % [1, 2] . In this study we found that ≥106 unique close contact exposures, including 12 contacts during AGPs with a nonisolated patient with COVID-19, resulted in no SARS-CoV-2 transmissions from patient to HCWs. With one exception, all included HCWs were certain or quite certain that their adherence to the hand hygiene procedure had been proper at the time of exposure. abstract: Insufficiently protected health care workers (HCWs) defined as high-risk contacts of patients with COVID-19 are routinely quarantined. This study evaluated transmission of infection from a symptomatic patient with COVID-19 to 60 HCWs exposed ≤2 m for ≥15 minutes, or during aerosol generating procedures. Following ≥106 unique high-risk contacts, none of the HCWs tested positive for SARS-CoV-2 RNA or had developed antibodies. The HCWs reported adherence to basic infection control procedures. These results were in accordance with other reports and should reassure HCWs and further stimulate a broader evaluation of the foundation for the current practice of home-quarantine of non-symptomatic HCWs. url: https://api.elsevier.com/content/article/pii/S0195670120304023 doi: 10.1016/j.jhin.2020.08.015 id: cord-330337-d41imvo7 author: Basu, Souradip title: Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date: 2020-10-20 words: 6428.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-330337-d41imvo7.txt txt: ./txt/cord-330337-d41imvo7.txt summary: Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. The secondary structure of the wild type and the mutant proteins along with their degree of disordered residues and accessible surface area was predicted using the primary sequence of the protein. Each of the seven proteins were assigned a score of either ''-1'' or ''0'', for each of the four computational tools used for epitope prediction, where ''-1'' corresponds to any change in number or binding efficacy of antigenic determinants, that may have surfaced because of mutation and ''0'' corresponds to no changes between wild type and mutant forms. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure abstract: The SARS-CoV-2 is a positive stranded RNA virus with a genome size of ~29.9 kilobase pairs which spans 29 open reading frames. Studies have revealed that the genome encodes about 16 non-structural proteins (nsp), four structural proteins, and six or seven accessory proteins. Based on prevalent knowledge on SARS-CoV and other coronaviruses, functions have been assigned for majority of the proteins. While, researchers across the globe are engrossed in identifying a potential pharmacological intervention to control the viral outbreak, none of the work has come up with new antiviral drugs or vaccines yet. One possible approach that has shown some positive results is by treating infected patients with the plasma collected from convalescent COVID-19 patients. Several vaccines around the world have entered their final trial phase in humans and we expect that these will in time be available for application to worldwide population to combat the disease. In this work we analyse the effect of prevalent mutations in the major pathogenesis related proteins of SARS-COV2 and attempt to pinpoint the effects of those mutations on the structural stability of the proteins. Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. Our binary scoring scheme identifies L84S mutation in ORF8 as the most disruptive of the mutations under study. We believe that, the virus is under the influence of an evolutionary phenomenon similar to Muller’s ratchet where the continuous accumulation of these mutations is making the virus less virulent which may also explain the reduction in fatality rates worldwide. url: https://doi.org/10.1101/2020.10.20.347021 doi: 10.1101/2020.10.20.347021 id: cord-296219-zzg9hds0 author: Battaglini, Denise title: Neurological Manifestations of Severe SARS-CoV-2 Infection: Potential Mechanisms and Implications of Individualized Mechanical Ventilation Settings date: 2020-08-12 words: 7486.0 sentences: 369.0 pages: flesch: 33.0 cache: ./cache/cord-296219-zzg9hds0.txt txt: ./txt/cord-296219-zzg9hds0.txt summary: Within this Abbreviations: ACE2, angiotensin-converting enzyme-2; ANE, acute necrotizing encephalopathy; ARDS, acute respiratory distress syndrome; BALF, bronchoalveolar lavage fluid; BBB, blood brain-barrier; CA, Ammon''s horn; CD, cluster of differentiation; CI, confidence interval; CNS, central nervous system; CoV, coronavirus; COVID-19, coronavirus disease 2019; CT, computed tomography; CXCR, chemokine receptor; DIC, disseminated intravascular coagulation; DO 2 , oxygen delivery; DPP4, dipeptidyl dipeptidase-4; ECMO, extracorporeal membrane oxygenation; FiO 2 fraction of inspired oxygen; FOX, forkhead box; HLH, hemophagocytic lymphohistiocytosis; ICAM, intracellular adhesion molecule; ICH, intracerebral hemorrhage; ICP, intracranial pressure; IFN, interferon; MERS, Middle East respiratory syndrome; MHV, mouse hepatitis virus; MRI, magnetic resonance images; nCoV, novel coronavirus; OR, odds ratio; PaCO 2 , partial pressure of carbon dioxide; PaO 2 partial pressure of oxygen; PbtO 2 brain tissue oxygenation tension; PCR, polymerase chain reaction; PEEP, positive end-expiratory pressure; PRES posterior reversible encephalopathy syndrome; RM, recruitment maneuvers; RNA, ribonucleic acid; SARS, severe acute respiratory syndrome; TLRs, toll-like receptor; TMPRSS2 transmembrane serine protease 2; TNF, tumor necrosis factor; WHO, World Health Organization. abstract: In December 2019, an outbreak of illness caused by a novel coronavirus (2019-nCoV, subsequently renamed SARS-CoV-2) was reported in Wuhan, China. Coronavirus disease 2019 (COVID-19) quickly spread worldwide to become a pandemic. Typical manifestations of COVID-19 include fever, dry cough, fatigue, and respiratory distress. In addition, both the central and peripheral nervous system can be affected by SARS-CoV-2 infection. These neurological changes may be caused by viral neurotropism, by a hyperinflammatory and hypercoagulative state, or even by mechanical ventilation-associated impairment. Hypoxia, endothelial cell damage, and the different impacts of different ventilatory strategies may all lead to increased stress and strain, potentially exacerbating the inflammatory response and leading to a complex interaction between the lungs and the brain. To date, no studies have taken into consideration the possible secondary effect of mechanical ventilation on brain recovery and outcomes. The aim of our review is to provide an updated overview of the potential pathogenic mechanisms of neurological manifestations in COVID-19, discuss the physiological issues related to brain-lung interactions, and propose strategies for optimization of respiratory support in critically ill patients with SARS-CoV-2 pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/32903391/ doi: 10.3389/fneur.2020.00845 id: cord-290443-naulq6q7 author: Battistoni, Allegra title: Might renin–angiotensin system blockers play a role in the COVID-19 pandemic? date: 2020-04-14 words: 2219.0 sentences: 128.0 pages: flesch: 50.0 cache: ./cache/cord-290443-naulq6q7.txt txt: ./txt/cord-290443-naulq6q7.txt summary: 15, 16 Therefore, the higher ACE2 expression due to chronically medicating SARS-CoV-2-infected patients with ARB may protect them against acute lung injury by blocking the deleterious effect of angiotensin II, as well as by decreasing the production of angiotensin II by up-regulating ACE2, which in turn increases the production of angiotensin (1-7). 33-36 Moreover, even though ACEIs and ARBs might increase ACE2 levels in the lungs, this might not be relevant to SARS-CoV-2 infection. [38] [39] [40] [41] [42] [43] For the second aim, not only case series, but also autoptic exams should investigate the expression and activation of RAS components in different organs during COVID-19 infection in patients treated or not with an ACEI/ARB, also investigating ACE2 polymorphisms which could impact the affinity for the spike protein of SARS-CoV-2. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury abstract: Since December 2019, a new coronavirus, named SARS-CoV-2, has spread globally, affecting >200 000 people worldwide with the so-called COVID-19 disease. The scientific community is actively and constantly working to identify the mechanisms involved in the diffusion of this virus and the pathogenesis of the infection, with its most frequent and severe complication, namely interstitial pneumonia. To date, SARS-CoV-2 is known to enter the host cells via the angiotensin-converting enzyme 2 protein. For this reason, the hypothesis that drugs capable of increasing the expression of this protein may have a role in the spread of the virus and in the symptomatology of affected patients has taken hold. The purpose of this Editorial is to briefly show the evidence currently available in this regard and to provide ideas for future research. url: https://doi.org/10.1093/ehjcvp/pvaa030 doi: 10.1093/ehjcvp/pvaa030 id: cord-340563-hsj53inh author: Baud, David title: Using Probiotics to Flatten the Curve of Coronavirus Disease COVID-2019 Pandemic date: 2020-05-08 words: 2592.0 sentences: 137.0 pages: flesch: 31.0 cache: ./cache/cord-340563-hsj53inh.txt txt: ./txt/cord-340563-hsj53inh.txt summary: Clinical evidence shows that certain probiotic strains help to prevent bacterial and viral infections, including gastroenteritis, sepsis, and respiratory tract infections (RTIs). In one analysis of more than 8,000 preterm infants included in randomized control trials (RCTs), patients receiving enteral supplementation with probiotics showed a reduction in necrotizing enterocolitis, nosocomial sepsis, and all-cause mortality (14) . But low quality of evidence and conflicting results among different studies calls for additional well-conducted RCTs. It should be noted that not all probiotics, even those with gastrointestinal benefits, necessarily contribute in every way to reducing the risk of respiratory infection. Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial Lactobacillus plantarum DR7 improved upper respiratory tract infections via enhancing immune and inflammatory parameters: a randomized, double-blind, placebo-controlled study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32574290/ doi: 10.3389/fpubh.2020.00186 id: cord-257729-s0vo7dlk author: Bauer, Melissa title: Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date: 2020-04-20 words: 4278.0 sentences: 212.0 pages: flesch: 38.0 cache: ./cache/cord-257729-s0vo7dlk.txt txt: ./txt/cord-257729-s0vo7dlk.txt summary: T he management of obstetric patients infected with Coronavirus Disease 2019 (COVID19) due to human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires quite unique considerations-from caring for critically ill pregnant and postpartum women to protecting health care workers from exposure during the delivery hospitalization (health care providers, personnel, family members, and beyond). 4 An additional manifestation noted among patients with COVID-19 infection is the sudden loss (or reduction) of the sense of smell and taste, which is currently recommended by the American Academy of Otolaryngology-Head With increasing numbers of Coronavirus Disease 2019 (COVID 19) cases due to efficient human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United States, preparation for the unpredictable setting of labor and delivery is paramount. abstract: With increasing numbers of Coronavirus Disease 2019 (COVID19) cases due to efficient human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United States, preparation for the unpredictable setting of labor and delivery is paramount. The priorities are 2-fold in the management of obstetric patients with COVID-19 infection or persons under investigation (PUI): (1) caring for the range of asymptomatic to critically ill pregnant and postpartum women; (2) protecting health care workers and beyond from exposure during the delivery hospitalization (health care providers, personnel, family members). The goal of this review is to provide evidence-based recommendations or, when evidence is limited, expert opinion for anesthesiologists caring for pregnant women during the COVID19 pandemic with a focus on preparedness and best clinical obstetric anesthesia practice. url: https://doi.org/10.1213/ane.0000000000004856 doi: 10.1213/ane.0000000000004856 id: cord-274513-0biyfhab author: Baumgartner, M. T. title: Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19 date: 2020-07-22 words: 5076.0 sentences: 249.0 pages: flesch: 46.0 cache: ./cache/cord-274513-0biyfhab.txt txt: ./txt/cord-274513-0biyfhab.txt summary: In this study, we used an individual-based age-structured network model to assess the effective roles of different healthcare protocols such as the use of personal protection equipment and social distancing at neighborand city-level scales. Our results revealed that the model was more sensitive to changes in the parameter representing the rate of contact among people from different neighborhoods, which defends the social distancing at the city-level as the most effective protocol for the control of the disease outbreak. By varying model parameters related to these protocols, we were able to discuss better scenarios considering the delay in the infection peak and lower numbers of cases, as well as activities with a low potential to boost the outbreak. Given the specified model structure, those results forecasting early wave peaks emerged under moderate to high probabilities of the individual-level exposure to SARS-CoV-2 virus (high β), in combination with higher encountering rates among people (v and k) ( Figure 1 ; Table S1 ). abstract: The increasing number of COVID-19 cases threatens human life and requires retainment actions that control the spread of the virus in the absence of effective medical therapy or a reliable vaccine. There is a general consensus that the most efficient health protocol in the actual state is to disrupt the infection chain through social distancing, although economic interests stand against closing non-essential activities and poses a debatable tradeoff. In this study, we used an individual-based age-structured network model to assess the effective roles of different healthcare protocols such as the use of personal protection equipment and social distancing at neighbor- and city-level scales. Using as much as empirical data available in the literature, we calibrated a city model and simulated low, medium, and high parameters representing these protocols. Our results revealed that the model was more sensitive to changes in the parameter representing the rate of contact among people from different neighborhoods, which defends the social distancing at the city-level as the most effective protocol for the control of the disease outbreak. Another important identified parameter represented the use of individual equipment such as masks, face shields, and hand sanitizers like alcohol-based solutions and antiseptic products. Interestingly, our simulations suggest that some periodical activities such as going to the supermarket, gas station, and pharmacy would have little contribution to the SARS-CoV-2 spread once performed within the same neighborhood. As we can see nowadays, there is an inevitable context-dependency and economic pressure on the level of social distancing recommendations, and we reinforce that every decision must be a welfare-oriented science-based decision. url: https://doi.org/10.1101/2020.07.20.20158576 doi: 10.1101/2020.07.20.20158576 id: cord-353996-slnyun4l author: Baumgartner, M. T. title: Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil date: 2020-05-08 words: 6874.0 sentences: 350.0 pages: flesch: 52.0 cache: ./cache/cord-353996-slnyun4l.txt txt: ./txt/cord-353996-slnyun4l.txt summary: In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the cityand country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. We studied the exponential growth of time series data for over 460 cities with reported cases of infections by the new coronavirus, considering the effect of the environment, socioeconomic indicators, movement of people across the country, and social distancing. Our results show that the early spread of the new coronavirus in Brazil was mitigated by social distancing in some regions, but was also positively related to the size of the population of cities and how people moved across them. . https://doi.org/10.1101 In Great China, the ongoing COVID-19 outbreak expanded fast throughout the country and the majority of early cases reported outside of its origin had admitted recent travels to Wuhan, the core of the disease spread (Chinazzi et al., 2020) . abstract: As thousands of new cases of COVID-19 have been confirmed, there is an increasing demand to understand the factors underlying the spread of this disease. Using country-level data, we modeled the early growth in the number of cases for over 480 cities in all Brazilian states. As the main findings, we found that the percentage of people respecting social distancing protocols was the main explanatory factor for the observed growth rate of COVID-19. Those cities that presented the highest spread of the new coronavirus were also those that had lower averages of social distancing. We also underline that total population of cities and connectivity, represented by the city-level importance to the air transportation of people across the country, plays important roles in the dissemination of SARS-CoV-2. Climate and socioeconomic predictors had little contribution to the big-picture scenario. Our results show that different States had high variability in their growth rates, mostly due to quite different public health strategies to retain the outbreak of COVID-19. In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the city- and country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. Moreover, we reinforce that social distancing protocols are fundamental to avoid critical scenarios and the collapse of healthcare systems. We also predict that economic-induced decisions for relaxing social distancing might have catastrophic consequences, especially in large cities. url: http://medrxiv.org/cgi/content/short/2020.05.02.20088013v1?rss=1 doi: 10.1101/2020.05.02.20088013 id: cord-340537-pdvpmydk author: Bañon-Gonzalez, Rafael title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 words: 3682.0 sentences: 244.0 pages: flesch: 54.0 cache: ./cache/cord-340537-pdvpmydk.txt txt: ./txt/cord-340537-pdvpmydk.txt summary: Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body''s tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. abstract: Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. The practice of autopsies on people who have died from COVID-19 has been limited by the mandatory preventive measures against contagion and by the need for facilities with a level of protection against level-3 biological risk, and therefore series published to date are scarce and partial,with limited approaches (minimally invasive autopsy or needle biopsy). This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body's tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. url: https://api.elsevier.com/content/article/pii/S2445424920300200 doi: 10.1016/j.remle.2020.05.002 id: cord-338647-dtuohsf5 author: Başcı, Semih title: Outcome of COVID-19 in patients with chronic myeloid leukemia receiving tyrosine kinase inhibitors date: 2020-08-27 words: 2709.0 sentences: 169.0 pages: flesch: 55.0 cache: ./cache/cord-338647-dtuohsf5.txt txt: ./txt/cord-338647-dtuohsf5.txt summary: INTRODUCTION: In this study, we aim to report the outcome of COVID-19 in chronic myeloid leukemia (CML) patients receiving tyrosine kinase inhibitor (TKI). METHOD: The data of 16 laboratory-confirmed COVID-19 patients with CML receiving TKI and age, gender, and comorbid disease matched COVID-19 patients without cancer at a 3/1 ratio (n = 48), diagnosed between March 11, 2020 and May 22, 2020 and included in the Republic of Turkey, Ministry of Health database, were analyzed retrospectively. RESULTS: The rates of intensive care unit (ICU) admission, and mechanical ventilation (MV) support were lower in CML patients compared to the control group, however, these differences did not achieve statistical significance (p = 0.1, and p = 0.2, respectively). Moreover, the rates of ICU admission and MV support, CFR were lower and length of hospital stay was shorter in CML patients receiving TKI compared to the age, gender and comorbidity matched control group but these differences were not statistically significant. abstract: INTRODUCTION: In this study, we aim to report the outcome of COVID-19 in chronic myeloid leukemia (CML) patients receiving tyrosine kinase inhibitor (TKI). METHOD: The data of 16 laboratory-confirmed COVID-19 patients with CML receiving TKI and age, gender, and comorbid disease matched COVID-19 patients without cancer at a 3/1 ratio (n = 48), diagnosed between March 11, 2020 and May 22, 2020 and included in the Republic of Turkey, Ministry of Health database, were analyzed retrospectively. RESULTS: The rates of intensive care unit (ICU) admission, and mechanical ventilation (MV) support were lower in CML patients compared to the control group, however, these differences did not achieve statistical significance (p = 0.1, and p = 0.2, respectively). The length of hospital stay was shorter in CML patients compared with the control group; however, it was not statistically significant (p = 0.8). The case fatality rate (CFR) in COVID-19 patients with CML was 6.3%, and it was 12.8% in the control group. Although the CFR in CML patients with COVID-19 was lower compared to the control group, this difference did not achieve statistical significance (p = 0.5). When CML patients were divided into 3 groups according to the TKI, no significant difference was observed regarding the rate of ICU admission, MV support, CFR, the length of stay in both hospital and ICU (all p > 0.05). CONCLUSION: This study highlights that large scale prospective and randomized studies should be conducted in order to investigate the role of TKIs in the treatment of COVID-19. url: https://doi.org/10.1177/1078155220953198 doi: 10.1177/1078155220953198 id: cord-332268-x30svp5y author: Bearden, Donna M. title: COVID-19: a primer for healthcare providers date: 2020-05-20 words: 3692.0 sentences: 226.0 pages: flesch: 49.0 cache: ./cache/cord-332268-x30svp5y.txt txt: ./txt/cord-332268-x30svp5y.txt summary: A viral genome sequence of a novel coronavirus, currently termed SARS-CoV‑2, with a disease process called COVID-19 was released 1 week later via online resources to obtain public health support in control of spread. Perhaps the most detailed study to date, shedding light on how patients may present and progress, is an analysis of the first 99 cases of confirmed novel corona pneumonia in Wuhan [12] . Nowak and Walkowiak, in a recently released review of five in vitro studies reporting on the effect of lithium in coronavirus infections, concluded that the drug does have antiviral activity and should be explored as a potential treatment or prophylaxis for COVID-19 [24] . The authors concluded "our work suggests that remdesivir may improve disease outcomes in coronavirus patients, serve to protect health care workers in area with endemic MERS-CoV and prove valuable in preventing future epidemics " [3] . abstract: According to the World Health Organization (WHO) the China office was first notified of cases of atypical pneumonia in Wuhan City on 31 December 2019. A viral genome sequence of a novel coronavirus, currently termed SARS-CoV‑2, with a disease process called COVID-19 was released 1 week later via online resources to obtain public health support in control of spread. Since then, the virus rapidly evolved into a global pandemic. Therefore, healthcare providers need to be familiar with the clinical presentation of infected patients and measures to quickly isolate them. The prevention of nosocomial spread is paramount to proper control of COVID-19 and is reviewed. Currently, treatment is supportive. Researchers are working to develop vaccines and identify effective antiviral interventions. Those recently discussed in the literature are briefly reviewed. url: https://doi.org/10.1007/s00508-020-01678-x doi: 10.1007/s00508-020-01678-x id: cord-348727-o38uplxe author: Beaudoin-Bussières, Guillaume title: Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date: 2020-07-09 words: 920.0 sentences: 63.0 pages: flesch: 54.0 cache: ./cache/cord-348727-o38uplxe.txt txt: ./txt/cord-348727-o38uplxe.txt summary: Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. Neutralizing activity against pseudoparticles bearing the SARS-CoV S 120 glycoprotein was detected in only 25% of convalescent plasma and exhibited low potency, as 121 previously reported (Figure 2) (14) . Of note, while we observed enhanced infectivity for the 122 D614G variant compared to its WT SARS-CoV-2 S counterpart ( Figure S3A ), no major 123 differences in neutralization with convalescent plasma were detected at both time-points ( Figure 124 S3B), thus suggesting that the D614G change does not affect the overall conformation of the 125 Spike, in agreement with recent findings (18) . 126 127 The capacity to neutralize SARS-CoV-2 S WT or D614G-pseudotyped particles 128 significantly correlated with the presence of RBD-specific IgG, IgM and anti-S antibodies 129 ( Figure S4 ). Interestingly, we observed a pronounced decrease (20-30%) in the percentage of 130 patients able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 131 10 weeks after symptoms onset. abstract: In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to COVID-19 patients. The therapy has been deemed safe and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of ≥1:160 have been recommended in some convalescent plasma trials for inclusion. Here we performed repeated analyses at one-month interval on 31 convalescent individuals to evaluate how the humoral responses against the SARS-CoV-2 Spike, including neutralization, evolve over time. We observed that receptor-binding domain (RBD)-specific IgG slightly decreased between six and ten weeks after symptoms onset but RBD-specific IgM decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after symptoms resolution. url: https://doi.org/10.1101/2020.07.09.194639 doi: 10.1101/2020.07.09.194639 id: cord-356325-gk5jve0i author: Beaudoin-Bussières, Guillaume title: Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals date: 2020-10-16 words: 2143.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-356325-gk5jve0i.txt txt: ./txt/cord-356325-gk5jve0i.txt summary: Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. Of note, while we observed enhanced infectivity for the D614G variant compared to its WT SARS-CoV-2 S counterpart (see Fig. S2A in the supplemental material), no major differences in neutralization with convalescent plasma were detected at either time point (Fig. S2B) , thus suggesting that the D614G change does not affect the overall conformation of the Spike, in agreement with recent findings (17, 22) . The capacity to neutralize SARS-CoV-2 S WT-or D614G-pseudotyped particles significantly correlated with the presence of RBD-specific IgG, IgM, IgA, and anti-S antibodies (Fig. S3) . Interestingly, we observed a pronounced (20% to 30%) decrease in the proportion of convalescent individuals able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 10 weeks after the onset of symptoms. abstract: In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to coronavirus disease 2019 (COVID-19) patients. The therapy has been deemed safe, and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of ≥1:160 have been recommended in some convalescent plasma trials for inclusion. Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. We observed that the levels of receptor-binding-domain (RBD)-specific IgG and IgA slightly decreased between 6 and 10 weeks after the onset of symptoms but that RBD-specific IgM levels decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing wild-type SARS-CoV-2 S or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after resolution of symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/33067385/ doi: 10.1128/mbio.02590-20 id: cord-317227-zb434ve3 author: Beck, Bo Ram title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model date: 2020-03-30 words: 3187.0 sentences: 174.0 pages: flesch: 49.0 cache: ./cache/cord-317227-zb434ve3.txt txt: ./txt/cord-317227-zb434ve3.txt summary: title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model In this study, we applied our pre-trained MT-DTI model to identify commercially available antiviral drugs that could potentially disrupt SARS-CoV-2''s viral components, such as proteinase, RNA-dependent RNA polymerase, and/or helicase. AutoDock Vina (version 1.1.2), which is a molecular docking and virtual screening application (17) , was used to predict binding affinities (kcal/mol) between 3C-like proteinase of SARS-CoV-2 and 3,410 FDA-approved drugs. To identify potent FDA-approved drugs that may inhibit the functions of SARS-CoV-2''s core proteins, we used the MT-DTI deep learning-based model, which can accurately predict binding affinities based on chemical sequences (SMILES) and amino acid sequences (FASTA) of a target protein, without their structural information (12) . Drug-target interaction (DTI) prediction results of antiviral drugs available on markets against a novel coronavirus (SARS-CoV-2, NCBI reference sequence NC_045512.2) RNA-dependent RNA polymerase (accession YP_009725307.1). abstract: Abstract The infection of a novel coronavirus found in Wuhan of China (SARS-CoV-2) is rapidly spreading, and the incidence rate is increasing worldwide. Due to the lack of effective treatment options for SARS-CoV-2, various strategies are being tested in China, including drug repurposing. In this study, we used our pre-trained deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI) to identify commercially available drugs that could act on viral proteins of SARS-CoV-2. The result showed that atazanavir, an antiretroviral medication used to treat and prevent the human immunodeficiency virus (HIV), is the best chemical compound, showing an inhibitory potency with Kd of 94.94 nM against the SARS-CoV-2 3C-like proteinase, followed by remdesivir (113.13 nM), efavirenz (199.17 nM), ritonavir (204.05 nM), and dolutegravir (336.91 nM). Interestingly, lopinavir, ritonavir, and darunavir are all designed to target viral proteinases. However, in our prediction, they may also bind to the replication complex components of SARS-CoV-2 with an inhibitory potency with Kd < 1,000 nM. In addition, we also found that several antiviral agents, such as Kaletra (lopinavir/ritonavir), could be used for the treatment of SARS-CoV-2. Overall, we suggest that the list of antiviral drugs identified by the MT-DTI model should be considered, when establishing effective treatment strategies for SARS-CoV-2. url: https://doi.org/10.1016/j.csbj.2020.03.025 doi: 10.1016/j.csbj.2020.03.025 id: cord-018265-twp33bb6 author: Becker, Pablo D. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite the availability of antimicrobial agents and vaccines, community-acquired pneumonia remains a serious problem. Severe forms tend to occur in very young children and among the elderly, since their immune competence is eroded by immaturity and immune senescence, respectively. The main etiologic agents differ according to patient age and geographic area. Streptococcus pneumoniae, Haemophilus influenzae, respiratory syncytial virus (RSV) and parainfluenza virus type 3 (PIV-3) are the most important pathogens in children, whereas influenza viruses are the leading cause of fatal pneumonia in the elderly. Effective vaccines are available against some of these organisms. However, there are still many agents against which vaccines are not available or the existent ones are suboptimal. To tackle this problem, empiric approaches are now being systematically replaced by rational vaccine design. This is facilitated by the growing knowledge in the fields of immunology, microbial pathogenesis and host response to infection, as well as by the availability of sophisticated strategies for antigen selection, potent immune modulators and efficient antigen delivery systems. Thus, a new generation of vaccines with improved safety and efficacy profiles compared to old and new agents is emerging. In this chapter, an overview is provided about currently available and new vaccination concepts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123104/ doi: 10.1007/978-3-7643-7563-8_10 id: cord-311730-189vax2m author: Becker, Richard C. title: Covid-19 treatment update: follow the scientific evidence date: 2020-04-27 words: 4514.0 sentences: 222.0 pages: flesch: 40.0 cache: ./cache/cord-311730-189vax2m.txt txt: ./txt/cord-311730-189vax2m.txt summary: The SNS exists under the authority of the United States Department of Health and Human Services (HHS) and accepted 30 million doses of hydroxychloroquine sulfate donated by Sandoz™, the Novartis™ generics and biosimilars division, and one million doses of chloroquine phosphate donated by Bayer Pharmaceuticals™ for potential use in treating patients who were hospitalized with COVID-19 or for use in clinical trials. The adverse effects associated with taking hydroxychloroquine are similar to those observed with chloroquine and include nausea, vomiting, diarrhea, AV conduction defects, a prolonged QTc interval with torsades de pointe ventricular tachycardia, hypokalemia, hypotension and circulatory collapse. Similarly, patients with Covid-19 for whom a clinician believes that either chloroquine or hydroxychloroquine is indicated must receive information, preferably in the form of a fact sheet that clearly summarized the dose, duration of treatment, potential risks, side-effects and drug-drug interactions. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32338320/ doi: 10.1007/s11239-020-02120-9 id: cord-268098-71g1w1mc author: Beckman, M. F. title: Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date: 2020-09-15 words: 4203.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-268098-71g1w1mc.txt txt: ./txt/cord-268098-71g1w1mc.txt summary: Visualization of protein-protein interaction networks was completed using STRINGv11.0 [31] program by testing different confidence levels to identify ontologies of biological significance for the significant pathways associated with comorbidities. Possible comorbidity significant associated gene sets/pathways were checked for quality control by generating Quantile-Quantile (Q-Q) plots using observed quantiles and residual Z-scores of genes within the gene set, based on the MAGMAv1.07b publicly available Rv3.6.2 script (posthoc_qc_107a.r) [32, 33] . . https://doi.org /10.1101 was used to test the top 250 human mRNA gene expressions for each comorbidity based on available human data using NCBI GEO[39] , by only including comorbidities that had significant pathways identified by MAGMAv1.07b and VEP STRING analyses. For each comorbidity, human mRNA gene expression data corresponding to average log-fold change (aLFC) were formatted for clustering of genes identified by MAGMAv1.07b and VEP and subsequently matched to STRING protein-protein interactions. abstract: Background The COVID-19 pandemic has led to over 820,000 deaths for almost 24 million confirmed cases worldwide, as of August 27th, 2020, per WHO report. Risk factors include pre-existing conditions such as cancer, cardiovascular disease, diabetes, obesity, and cancer. There are currently no effective treatments. Our objective was to complete a meta-analysis to identify comorbidity-associated single nucleotide polymorphisms (SNPs), potentially conferring increased susceptibility to SARS-CoV-2 infection using a computational approach. Results SNP datasets were downloaded from publicly available GWAS catalog for 141 of 258 candidate COVID-19 comorbidities. Gene-level SNP analysis was performed to identify significant pathways by using MAGMA program. SNP annotation program was used to analyze MAGMA-identified genes. COVID-19 comorbidities from six disease categories were found to have significant associated pathways, which were validated by Q-Q plots (p<0.05). The top 250 human mRNA gene expressions for SNP-affected pathways, extracted from publicly accessible gene expression profiles, were evaluated for significant pathways. Protein-protein interactions of identified differentially expressed genes, visualized with STRING program, were significant (p<0.05). Gene interaction networks were found to be relevant to SARS and influenza pathogenesis. Conclusion Pathways potentially affected by or affecting SARS-CoV-2 infection were identified in underlying medical conditions likely to confer susceptibility and/or severity to COVID-19. Our findings have implications in COVID-19 treatment development. Keywords: SARS-CoV-2, COVID-19, comorbidity, susceptibility, severity url: https://doi.org/10.1101/2020.09.14.20192609 doi: 10.1101/2020.09.14.20192609 id: cord-318499-uihof6k6 author: Beddingfield, Brandon title: The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date: 2020-06-16 words: 1550.0 sentences: 100.0 pages: flesch: 54.0 cache: ./cache/cord-318499-uihof6k6.txt txt: ./txt/cord-318499-uihof6k6.txt summary: Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5β1integrin-based mechanism, and indicates that inhibiting α5β1 integrin interaction with ACE2 and the spike protein using a novel molecule ATN-161 represents a promising approach to treat COVID-19. In order to assess disruption of binding of α5β1 to SARS-CoV-2 Spike protein, 96-well plates were coated as before, but incubation with ATN-161 was performed in conjunction with 1µg/mL spike (produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH: Spike Glycoprotein Receptor Binding Domain (RBD) from SARS-Related Coronavirus 2, Wuhan-Hu-1, Recombinant from HEK293 Cells, NR-52306) in the presence of 1mM MnCl2, followed by detection with an anti-spike antibody. Inhibition of SARS-CoV-2 spike protein binding to human ACE2 by ATN-161. abstract: Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5β1integrin-based mechanism, and indicates that inhibiting α5β1 integrin interaction with ACE2 and the spike protein using a novel molecule ATN-161 represents a promising approach to treat COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32587959/ doi: 10.1101/2020.06.15.153387 id: cord-310879-b8tdug93 author: Beddingfield, Brandon J. title: In the Age of CoVID: Genomic Changes Over the Lifespan Help Explain Severe SARS-CoV-2 Disease date: 2020-10-23 words: 615.0 sentences: 47.0 pages: flesch: 62.0 cache: ./cache/cord-310879-b8tdug93.txt txt: ./txt/cord-310879-b8tdug93.txt summary: Because additional receptor interactions have been implicated in host cell invasion by previous coronaviruses, other receptors have been investigated for their potential role in SARS-CoV-2 infection. Previous studies have also The potential entry gene BSG was found to be in higher abundance in cardiorenal tissues than in the lung, though it was well expressed in all tissues examined. This is in contrast to ACE2, which was found to be expressed at low levels in lung, but higher levels in cardiorenal tissues (kidney, heart and blood vessels) across the individuals examined. Taken together, this could explain the higher levels of viral replication in lung tissue for SARS-CoV-2, even if the receptor itself is not highly expressed. Males also had an increased expression of BSG, PPIA, PPIB in endothelial cells, and higher levels of ACE2 and TMPRSS2 in the coronary artery. Airways Expression of SARS-CoV-2 Receptor, ACE2, and TMPRSS2 Is Lower in Children Than Adults and Increases with Smoking and COPD abstract: [Figure: see text] url: https://api.elsevier.com/content/article/pii/S2452302X20304435 doi: 10.1016/j.jacbts.2020.10.004 id: cord-283196-laerx0n2 author: Bedford, Juliet title: Living with the COVID-19 pandemic: act now with the tools we have date: 2020-10-08 words: 1695.0 sentences: 81.0 pages: flesch: 40.0 cache: ./cache/cord-283196-laerx0n2.txt txt: ./txt/cord-283196-laerx0n2.txt summary: The Strategic and Technical Advisory Group for Infectious Hazards (STAG-IH), the independent advisory group to the WHO Health Emergencies Programme, has reviewed information from countries around the world and has concluded that the most sound approach on the basis of current understanding is to deploy long-term strategies with a focus on preventing amplification of transmission, protecting those most at risk of severe illness, and supporting research to better understand the virus, the disease, and people''s responses to them. 2 This approach is based on three principles: understanding, trust, and participation by all population groups; decreased transmission of SARS-CoV-2 using basic epidemiological and public health interventions; and acknowledging that any potential COVID-19 vaccines and treatments will only be part of the solution and that they will best perform in conjunction with a longterm overall public health strategy. With current knowledge, even in the absence of COVID-19 vaccines or treatments and comprehensive knowledge of the immune response to SARS-CoV-2, countries can navigate pathways to reduced transmission, decreased severe illness and mortality, and less economic disruption in the short and longer term. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33038947/ doi: 10.1016/s0140-6736(20)32117-6 id: cord-297202-oup8ptya author: Beer, Martin title: SARS‐CoV‐2 vaccination—A plea for fast and coordinated action date: 2020-07-01 words: 449.0 sentences: 30.0 pages: flesch: 56.0 cache: ./cache/cord-297202-oup8ptya.txt txt: ./txt/cord-297202-oup8ptya.txt summary: If we assume that the level of herd immunity to halt the spread follows the 1 − 1/R 0 rule (Anderson, Heesterbeek, Klinkenberg, & Hollingsworth, 2020) and given conservative estimates for the basic reproduction number R 0 = 3 (Sanche et al., 2020) at least two-thirds of the world''s population must mount an effective immune response against the virus to prevent recurrent outbreaks. Yes, an R t < 0.2 would halt the spread of SARS-CoV-2 in a given population at time t, but any re-introduction of the virus could catapult us back to where we were. Unless serological surveys suggest a much higher-than-expected silent exposure of the human population to SARS-CoV-2, there is no reasonable scenario to reach the required level of herd immunity under the ''reduce spread'' paradigm that many countries have emulated. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32609415/ doi: 10.1111/zph.12740 id: cord-352230-8mazd3eu author: Beeraka, Narasimha M. title: Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date: 2020-09-18 words: 9394.0 sentences: 543.0 pages: flesch: 40.0 cache: ./cache/cord-352230-8mazd3eu.txt txt: ./txt/cord-352230-8mazd3eu.txt summary: Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. COVID-19 is a devastating disease caused by a coronavirus related to the one that caused outbreaks of Severe Acute Respiratory Syndrome (SARS) in the year 2002 (1, 2) . abstract: Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease - 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. The clinical manifestations of this disease are pneumonia, lung injury, inflammation, and severe acute respiratory syndrome (SARS). Currently, there is no vaccine or effective pharmacological agents available for the prevention/treatment of SARS-CoV2 infections. Moreover, development of a suitable vaccine is a challenging task due to antibody-dependent enhancement (ADE) and Th-2 immunopathology, which aggravates infection with SARS-CoV-2. Furthermore, the emerging SARS-CoV-2 strain exhibits several distinct genomic and structural patterns compared to other coronavirus strains, making the development of a suitable vaccine even more difficult. Therefore, the identification of novel small molecule inhibitors (NSMIs) that can interfere with viral entry or viral propagation is of special interest and is vital in managing already infected cases. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, the development of novel inhibitors of ACE2/TMPRSS2 is likely to be beneficial in combating SARS-CoV-2 infections. However, the usage of ACE-2 inhibitors to block the SARS-CoV-2 viral entry requires additional studies as there are conflicting findings and severe health complications reported for these inhibitors in patients. Hence, the current interest is shifted toward the development of NSMIs, which includes natural antiviral phytochemicals and Nrf-2 activators to manage a SARS-CoV-2 infection. It is imperative to investigate the efficacy of existing antiviral phytochemicals and Nrf-2 activators to mitigate the SARS-CoV-2-mediated oxidative stress. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. url: https://doi.org/10.3389/fimmu.2020.552925 doi: 10.3389/fimmu.2020.552925 id: cord-319555-pccqo36g author: Beggs, Clive B. title: Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study date: 2020-10-13 words: 6202.0 sentences: 260.0 pages: flesch: 52.0 cache: ./cache/cord-319555-pccqo36g.txt txt: ./txt/cord-319555-pccqo36g.txt summary: Given that COVID-19 can be transmitted by the inhalation of aerosolised respiratory droplets containing the SARS-CoV-2 virus (Beggs, 2020; Miller et al., 2020; Morawska et al., 2020; Stadnytskyi et al., 2020) , and that several studies have recovered viral RNA from hospital air samples (Chia et al., 2020; Guo et al., 2020; Jiang et al., 2020; Santarpia et al., 2020) , there is reason to believe that upper-room UVGI might be effective at "killingx201D; (inactivating) SARS-CoV-2 virions in the air, thus reducing the transmission of COVID-19 in buildings and other enclosed spaces. Because no UV irradiation experiments have to date been performed on aerosols containing the SARS-CoV-2 virus, it was necessary when undertaking the feasibility study to make assumptions regarding an appropriate value of Z ur to use in the upper-room UVGI analysis. The results for the expected and worst-case scenarios in Table 7 , strongly suggest that upper-room UVGI, if applied correctly, should be effective at disinfecting SARS-CoV-2 virions suspended in respiratory droplets in the air. abstract: As the world’s economies come out of the lockdown imposed by the COVID-19 pandemic, there is an urgent need for technologies to mitigate COVID-19 transmission in confined spaces such as buildings. This feasibility study looks at one such technology, upper-room ultraviolet (UV) air disinfection, that can be safely used while humans are present in the room space, and which has already proven its efficacy as an intervention to inhibit the transmission of airborne diseases such as measles and tuberculosis. Using published data from various sources, it is shown that the SARS-CoV-2 virus, the causative agent of COVID-19, is highly likely to be susceptible to UV-C damage when suspended in air, with a UV susceptibility constant likely to be in the region 0.377–0.590 m(2)/J, similar to that for other aerosolised coronaviruses. As such, the UV-C flux required to disinfect the virus is expected to be acceptable and safe for upper-room applications. Through analysis of expected and worst-case scenarios, the efficacy of the upper-room UV-C approach for reducing COVID-19 transmission in confined spaces (with moderate but sufficient ceiling height) is demonstrated. Furthermore, it is shown that with SARS-CoV-2, it should be possible to achieve high equivalent air change rates using upper-room UV air disinfection, suggesting that the technology might be particularly applicable to poorly ventilated spaces. url: https://doi.org/10.7717/peerj.10196 doi: 10.7717/peerj.10196 id: cord-262556-gpnp06je author: Behrens, Estuardo title: COVID-19: IFSO LAC Recommendations for the Resumption of Elective Bariatric Surgery date: 2020-08-22 words: 3197.0 sentences: 178.0 pages: flesch: 46.0 cache: ./cache/cord-262556-gpnp06je.txt txt: ./txt/cord-262556-gpnp06je.txt summary: RESULTS: The resumption of elective BMS must be a priority maybe similar to oncological surgery, when hospitals reach phase I or II, treating obesity patients in a NON-COVID area, avoiding inadvertent intrahospital contagion from healthcare provider, patients, and relatives. On December 2019, Wuhan, China, reported an outbreak of the coronavirus SARS-CoV-2 (COVID19) , an RNA virus that affects the respiratory system and has a high fatality rate especially in adults over the age of 60 and patients suffering obesity and its comorbidities [1] [2] [3] . Currently, the most effective treatment against obesity available is bariatric and metabolic surgery, which further resolves or improves the related comorbidities that are the same risk factors in developing a severe case of SARS-CoV-2. It is recommended that elective bariatric surgery be performed in medical facilities with the necessary infrastructure to treat obesity patients in a NON-COVID area. abstract: BACKGROUND: COVID-19 pandemic varies greatly and has different dynamics in every country, city, and hospital in Latin America. Obesity increases the risk of SARS-CoV-2 infection, and it is one of the independent risk factors for the most severe cases of COVID-19. Currently, the most effective treatment against obesity available is bariatric and metabolic surgery (BMS), which further resolves or improves other independent risk factors like diabetes and hypertension. OBJECTIVE: Provide recommendations for the resumption of elective BMS during COVID-19 pandemic. METHOD: This document was created by the IFSO-LAC Executive Board and a task force. Based on data collected from a survey distributed to all IFSO-LAC members that obtained 540 responses, current evidence available, and consensus reached by other scientific societies. RESULTS: The resumption of elective BMS must be a priority maybe similar to oncological surgery, when hospitals reach phase I or II, treating obesity patients in a NON-COVID area, avoiding inadvertent intrahospital contagion from healthcare provider, patients, and relatives. Same BMS indication and types of procedures as before the pandemic. Discard the presence of SARS-CoV-2 within 72 h prior to surgery. Continues laparoscopic approach. The entire team use N95 mask. Minimum hospital stays. Implement remote visits for the follow-up. CONCLUSION: Resumption of elective BMS is crucial because it is not only a weight loss operation but also resolves or improves comorbidities and appears to be an immune restorative procedure of obese patients in the medium term, offering them the same probability of contracting COVID-19 as the regular population. url: https://www.ncbi.nlm.nih.gov/pubmed/32827292/ doi: 10.1007/s11695-020-04910-9 id: cord-300395-87bl6e38 author: Behrmann, Ole title: Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification date: 2020-10-14 words: 1017.0 sentences: 140.0 pages: flesch: 61.0 cache: ./cache/cord-300395-87bl6e38.txt txt: ./txt/cord-300395-87bl6e38.txt summary: As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplifi cation (RT-RPA) technology. DOI: 10.1007/s12268-020-1458-3 © Die Autoren 2020 ó Die derzeitigen Protokolle zur Diagnose von SARS-CoV-2-Infektionen beruhen auf der quantitativen reversen Transkriptions-PCR (RT-qPCR) für den Direktnachweis der viralen RNA [1] . Alternativ sind seit einigen Jahren isotherme Verfahren -wie die loop-mediated isothermal amplifi cation (LAMP) [2] oder die recombinase polymerase amplification (RPA) [3] -verfügbar, welche der PCR hinsichtlich Sensitivität und Spezifi tät gleichwertig sind. Aufbauend auf vorhergehenden Arbeiten, in welchen der Nachweis anderer Coronaviren wie MERS-CoV [4] und Bovines Coronavirus (BCoV) [5] mittels RPA demonstriert wurde, stellen wir in diesem Artikel die Entwicklung eines RPA-Assays für den Schnellnachweis von SARS-CoV-2 vor. abstract: The COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes. url: https://www.ncbi.nlm.nih.gov/pubmed/33078045/ doi: 10.1007/s12268-020-1458-3 id: cord-285315-7r44j3q9 author: Bein, Berthold title: SARS-CoV-2/COVID-19: Empfehlungen zu Diagnostik und Therapie date: 2020-04-09 words: 2244.0 sentences: 280.0 pages: flesch: 48.0 cache: ./cache/cord-285315-7r44j3q9.txt txt: ./txt/cord-285315-7r44j3q9.txt summary: Die Case Fatality Rate (Zahl der Infizierten, die verstirbt; Letalität) von SARS-CoV-2 beträgt aktuellen Berechnungen nach nur 1,4 %, wobei das Risiko für eine symptomatische Infektion mit zunehmendem Alter ansteigt (ca. Die Surviving Sepsis Campaign (SSC) zitiert in ihren kürzlich publizierten Empfehlungen zur Behandlung von Patienten mit COVID-19 eine aktuelle Metaanalyse, in der keine Überlegenheit von speziellen "respiratory masks" (analog unseren FFP2/FFP3-Masken) gegenüber konventionellem Mund-Nasen-Schutz bezüglich einer Ansteckung von medizinischem Personal, das infektiöse Patienten betreut hatte, gefunden werden konnte [30] . Das bedeutet konkret, dass die Behandlung von Patienten mit COVID-19 zuallererst auf "Best Standard Care" beruht, also auf einer optimalen Anwendung evidenzbasierter Therapieempfehlungen, die für die Therapie des akuten Lungenversagens (Acute respiratory Distress Syndrome, ARDS) erarbeitet wurden [33] . abstract: COVID-19, a new viral disease affecting primarily the respiratory system and the lung, has caused a pandemic with serious challenges to health systems around the world. In about 20% of patients, severe symptoms occur after a mean incubation period of 5 – 6 days; 5% of patients need intensive care therapy. Morbidity is about 1 – 2%. Protecting health care workers is of paramount importance in order to prevent hospital acquired infections. Therefore, during all procedures associated with aerosol production, a personal safety equipment consisting of a FFP2/FFP3 (N95) respiratory mask, gloves, safety glasses and a waterproof overall should be used. Therapy is based on established recommendations issued for patients with acute lung injury (ARDS). Lung protective ventilation, prone position, restrictive fluid management and an adequate management of organ failures are the mainstays of therapy. In case of fulminant lung failure, veno-venous extracorporeal membrane oxygenation may be used as a rescue in experienced centres. New, experimental therapies evolve with ever increasing frequency; currently, however, there is no evidence based recommendation possible. If off-label and compassionate use of these drugs is considered, an individual benefit-risk assessment is necessary, since serious side effects have been reported. url: https://www.ncbi.nlm.nih.gov/pubmed/32274773/ doi: 10.1055/a-1146-8674 id: cord-022234-jjaqlyo5 author: Beirman, David title: A Comparative Assessment of Three Southeast Asian Tourism Recovery Campaigns: Singapore Roars: Post SARS 2003, Bali Post-the October 12, 2002 Bombing, and WOW Philippines 2003 date: 2009-11-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155472/ doi: 10.1016/b978-0-7506-7898-8.50021-7 id: cord-300191-vpc7p0d6 author: Bektaş, Osman title: The relationship between severe acute respiratory syndrome coronavirus 2 (SARS - COV - 2) pandemic and fragmented QRS date: 2020-07-22 words: 1925.0 sentences: 139.0 pages: flesch: 57.0 cache: ./cache/cord-300191-vpc7p0d6.txt txt: ./txt/cord-300191-vpc7p0d6.txt summary: OBJECTIVE: The aim of the study is to determine the frequency of fragmented QRS (FQRS) in patients with SARS COV 2. [7] In a study, evaluating patients with coronary artery disease (CAD), those with FQRS had significantly higher all cause mortality and higher frequency of adverse cardiovascular outcomes (myocardial infarction, sudden cardiac death, revascularization) [8] . The requirement for intensive care unit incresed with increasing levels of troponin in patients with SARS-COV-2 (p<0.000, Table 3 ). Moreover, a significant positive correlation was detected between serum CRP levels,heart rate and frequency of FQRS in patients with SARS-COV-2 (r=0.204, p=0.024, r=0.187 p=0.029) Lineer regression analyses revealed that serum CRP levels and heart rate were the independent predictors of presence of FQRS (Table 4 ). Fragmented QRS on a 12-lead ECG: a predictor of mortality and cardiac events in patients with coronary artery disease abstract: OBJECTIVE: The aim of the study is to determine the frequency of fragmented QRS (FQRS) in patients with SARS - COV - 2. METHODS: A total of 125 consecutive patients over 20 years of age who were hospitalized for SARS - COV - 2 between 20th March 2020 and 18th May 2020 were included in the study. The data of the patients in the inpatient ward and in the intensive care unit were recorded separately. The duration of QRS and presence of FQRS were evaluated by two experienced cardiologists. The patients were divided into two groups as FQRS positive and FQRS negative considering presence of FQRS. Moreover, the frequency of FQRS in the patients in the inpatient ward and in the intensive care unit were compared with each other. RESULTS: FQRS was found in 24% of the patients who had SARS-COV-2. There was no difference between FQRS positive and negative groups in terms of age and gender. Heart rate was higher in FQRS positive group. C-reactive protein (7.25 ± 6.65 mg/dl vs. 4.80 ± 4.48 mg/dl; p = .02) levels were also significantly higher in the FQRS positive group. In patients with SARS-COV-2, intensive care unit requirement increased with increasing levels of troponin (p < .000). A positive correlation was detected between serum CRP levels and FQRS (r = 0.204, p = .024). CONCLUSIONS: The frequency of FQRS is high in patients with SARS - COV - 2. Serum CRP levels increase with increasing frequency of FQRS in patients with SARS - COV - 2 indicating that patients with FQRS are exposed to more inflammation. Presence of FQRS in SARS - COV - 2 patients may be useful in predicting cardiovascular outcomes. url: https://www.sciencedirect.com/science/article/pii/S0022073620305008?v=s5 doi: 10.1016/j.jelectrocard.2020.07.009 id: cord-271495-5906wju4 author: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 words: 1995.0 sentences: 107.0 pages: flesch: 53.0 cache: ./cache/cord-271495-5906wju4.txt txt: ./txt/cord-271495-5906wju4.txt summary: Data and modelling supported the existence of ''superspreaders'' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. abstract: Abstract The current global propagation of COVID-19 is heterogeneous, with slow transmission continuing in many countries, and exponential propagation in others, in which the time that took to begin this explosive spread varies greatly. It is proposed that this could be explained by cascading superspreading events, in which new infections caused by a superspreader are more likely to be highly infectious. The mechanism suggested for this is related to viral loads. Exposure to high viral loads may result in infections of high intensity, which exposes new cases to high viral loads, and so on. This notion is supported by experimental veterinary research. url: https://www.ncbi.nlm.nih.gov/pubmed/32422375/ doi: 10.1016/j.ijid.2020.05.025 id: cord-304898-he57l0y7 author: Belghmaidi, Sarah title: Third Cranial Nerve Palsy Presenting with Unilateral Diplopia and Strabismus in a 24-Year-Old Woman with COVID-19 date: 2020-10-15 words: 1666.0 sentences: 104.0 pages: flesch: 49.0 cache: ./cache/cord-304898-he57l0y7.txt txt: ./txt/cord-304898-he57l0y7.txt summary: Patient: Female, 24-year-old Final Diagnosis: Third cranial nerve palsy in a women presenting COVID-19 Symptoms: Ophthalmoplegia Medication:— Clinical Procedure: — Specialty: Ophthalmology OBJECTIVE: Rare disease BACKGROUND: Coronavirus disease (COVID 19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is the causative agent of a serious disease that is of great global public health concern. We describe the case of a patient with an incomplete palsy of the left third cranial nerve sparing the pupils in the context of SARS-CoV-2 virus infection. CASE REPORT: We report the case of a 24-year-old woman with confirmed COVID-19, which presented with acute onset of diplopia and strabismus of the left eye that occurred 3 days after the start of general symptoms. A previously healthy 24-year-old woman, with no medical history (such as diabetes, high blood pressure, dyslipidemia, vasculitis, smoking, obesity, familial neurological disease, or other risk factors for ischemic ophthalmoplegia), presented to the Emergency Department for acute onset of strabismus and diplopia of the left eye, evolving for 3 days. abstract: Patient: Female, 24-year-old Final Diagnosis: Third cranial nerve palsy in a women presenting COVID-19 Symptoms: Ophthalmoplegia Medication:— Clinical Procedure: — Specialty: Ophthalmology OBJECTIVE: Rare disease BACKGROUND: Coronavirus disease (COVID 19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is the causative agent of a serious disease that is of great global public health concern. Palsy of the third cranial nerve is very rare in patients with confirmed 2019 novel coronavirus disease (COVID-19). We describe the case of a patient with an incomplete palsy of the left third cranial nerve sparing the pupils in the context of SARS-CoV-2 virus infection. CASE REPORT: We report the case of a 24-year-old woman with confirmed COVID-19, which presented with acute onset of diplopia and strabismus of the left eye that occurred 3 days after the start of general symptoms. The patient had no significant medical history. Based on detailed ophthalmic and neurological examination, acute painless incomplete palsy of the third cranial nerve was suspected. Oculo-cerebral magnetic resonance angiography was unremarkable. Blood tests revealed mild normocytic regenerative anemia. According to the Moroccan recommendations, chloroquine and azithromycin were started. After what, a quick improvement of exotropia and diplopia was observed, and complete recovery was obtained by the sixth day of treatment. No adverse effects of the treatment were noted. CONCLUSIONS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause neurological complications such as cranial nerve palsy. The pathological mechanism remains unclear. Full recovery of the ocular motricity is possible, and prognosis depends on the severity of the respiratory illness. url: https://doi.org/10.12659/ajcr.925897 doi: 10.12659/ajcr.925897 id: cord-253993-ynrthadj author: Belhassan, Assia title: Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach date: 2020-09-18 words: 1766.0 sentences: 94.0 pages: flesch: 46.0 cache: ./cache/cord-253993-ynrthadj.txt txt: ./txt/cord-253993-ynrthadj.txt summary: The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Based on all these effects, the study of interactions between chloroquine, hydroxychloroquine and the eighteen imidazole derivatives against the SARS-CoV-2 main protease are recommended. In this paper, the modeling interaction of eighteen imidazole derivatives against novel Coronavirus are performed using the molecular docking method followed by comparison with chloroquine, hydroxychloroquine interactions formed in the same binding site of SARS-CoV-2 main protease. In this study, we have tried to carry out a docking study of chemical compounds reported as potent Antiplasmodial inhibitors of imidazole derivatives based on 7-chloro-4-aminoquinoline and analogues in the active site of SARS-Cov-2 main protease, flowed by comparison with two drugs; chloroquine and hydroxychloroquine. abstract: Because of the fast increase in deaths due to Corona Viral Infection in majority region in the world, the detection of drugs potent of this infection is a major need. With this idea, docking study was executed on eighteen imidazole derivatives based on 7-chloro-4-aminoquinoline against novel Coronavirus (SARS-CoV-2). In this study, we carried out a docking study of these molecules in the active site of SARS-CoV-2 main protease. The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Because of the best energy of interaction, these three molecules could have the most potential antiviral treatment of COVID-19 than the other studied compounds. The structures with best affinity in the binding site of the protease have more than 3 cycles and electronegative atoms in the structure. This may increase the binding affinity of these molecules because of formation of π-bonds, halogen interactions and/or Hydrogen bond interactions between compounds and the enzyme. So, compounds with more cycles and electronegative atoms could have a potent inhibition of SARS-CoV-2 main protease. url: https://api.elsevier.com/content/article/pii/S0024320520312224 doi: 10.1016/j.lfs.2020.118469 id: cord-309394-vroscj3m author: Belingheri, Michael title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers date: 2020-04-07 words: 722.0 sentences: 57.0 pages: flesch: 54.0 cache: ./cache/cord-309394-vroscj3m.txt txt: ./txt/cord-309394-vroscj3m.txt summary: title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers 3 As known, the risk of exposure to coronavirus is higher among healthcare workers than other workers, due to their role in assistance and care of COVID-19 patients. Some limited data are available about previous coronavirus infections, such as severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome (MERS-CoV). Unauthorized reproduction of this article is prohibited Since the structural analysis of novel coronavirus has suggested that it would use the same mechanism of SARS-CoV, it is fundamental to consider the potential role of SARS-CoV-2 during pregnancy. [9] [10] [11] Furthermore, there is no evidence for intrauterine infection due to a vertical transmission in pregnant women affected by COVID-19. Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32730041/ doi: 10.1097/jom.0000000000001881 id: cord-285787-xvi5miqw author: Bell, Jennifer AH title: SARS and hospital priority setting: a qualitative case study and evaluation date: 2004-12-19 words: 3099.0 sentences: 177.0 pages: flesch: 50.0 cache: ./cache/cord-285787-xvi5miqw.txt txt: ./txt/cord-285787-xvi5miqw.txt summary: The purpose of this study is to describe and evaluate priority setting in a hospital in response to SARS using the ethical framework ''accountability for reasonableness''. CONCLUSIONS: ''Accountability for reasonableness'' is a framework that can be used to guide fair priority setting in health care organizations, such as hospitals. ''Accountability for reasonableness'' is an explicit ethical framework for legitimate and fair priority setting in health care [2] . The purpose of this study was to describe priority setting in a hospital in response to SARS and evaluate it using ''accountability for reasonableness''. In this section we describe one hospital''s priority setting in response to SARS by focusing on the types of decisions, the decision making process, and the supportive reasoning. ''Accountability for reasonableness'' is a framework that can be used to guide legitimate and fair priority setting in health care organizations, such as hospitals. Priority setting in a hospital critical care unit: qualitative case study abstract: BACKGROUND: Priority setting is one of the most difficult issues facing hospitals because of funding restrictions and changing patient need. A deadly communicable disease outbreak, such as the Severe Acute Respiratory Syndrome (SARS) in Toronto in 2003, amplifies the difficulties of hospital priority setting. The purpose of this study is to describe and evaluate priority setting in a hospital in response to SARS using the ethical framework 'accountability for reasonableness'. METHODS: This study was conducted at a large tertiary hospital in Toronto, Canada. There were two data sources: 1) over 200 key documents (e.g. emails, bulletins), and 2) 35 interviews with key informants. Analysis used a modified thematic technique in three phases: open coding, axial coding, and evaluation. RESULTS: Participants described the types of priority setting decisions, the decision making process and the reasoning used. Although the hospital leadership made an effort to meet the conditions of 'accountability for reasonableness', they acknowledged that the decision making was not ideal. We described good practices and opportunities for improvement. CONCLUSIONS: 'Accountability for reasonableness' is a framework that can be used to guide fair priority setting in health care organizations, such as hospitals. In the midst of a crisis such as SARS where guidance is incomplete, consequences uncertain, and information constantly changing, where hour-by-hour decisions involve life and death, fairness is more important rather than less. url: https://www.ncbi.nlm.nih.gov/pubmed/15606924/ doi: 10.1186/1472-6963-4-36 id: cord-314013-g091lv0s author: Belladonna, Maria Laura title: Potential Benefits of Tryptophan Metabolism to the Efficacy of Tocilizumab in COVID-19 date: 2020-06-19 words: 2388.0 sentences: 119.0 pages: flesch: 35.0 cache: ./cache/cord-314013-g091lv0s.txt txt: ./txt/cord-314013-g091lv0s.txt summary: Here, we briefly discuss the potentially multiple, synergistic mechanisms whereby tocilizumab might exert therapeutic activity, mostly focusing on the production of tryptophan-derived catabolites that would result from blockade of IL-6 signaling, as contextualized to the cytokine storm occurring in COVID-19 patients. If a cytokine storm occurs, the ensuing cytokine release syndrome (CRS) is typically associated with severe, rather than moderate, COVID-19, with an immunopathology being characterized by high serum levels of cytokines, CD4 + and CD8 + T (but not B) cell lymphopenia, diffused alveolar damage, pulmonary hypertension, pneumonia, and acute RDS (Pedersen and Ho, 2020) . COVID-19 is associated to a CRS referred as "cytokine storm" (A), whose reduction at lung level (the main target organ of SARS-CoV2 viral infection) may be achieved by TCZ therapy inhibiting IL-6 proinflammatory effect (B). TCZ treatment might restore a proper IDO1 activity, providing immunoactive Kyn as a ligand for AhR-dependent immune regulation, including the fostering of T-regulatory cell responses. abstract: Tocilizumab has been proposed as a means of opposing hyperinflammatory responses in intensive care patients with COVID-19. Here, we briefly discuss the potentially multiple, synergistic mechanisms whereby tocilizumab might exert therapeutic activity, mostly focusing on the production of tryptophan-derived catabolites that would result from blockade of IL-6 signaling, as contextualized to the cytokine storm occurring in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32636755/ doi: 10.3389/fphar.2020.00959 id: cord-341883-eh0aw3re author: Bellanger, Anne-Pauline title: Studying smoking benefit in farmer’s lung to understand Covid-19 date: 2020-08-11 words: 1291.0 sentences: 73.0 pages: flesch: 50.0 cache: ./cache/cord-341883-eh0aw3re.txt txt: ./txt/cord-341883-eh0aw3re.txt summary: It was observed, first in China, and then in France, that the proportion of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients was significantly lower in active smokers compared to the proportion of active smokers in the general population. The protection conferred by smoking for a respiratory disease has so far only been described for hypersensitivity pneumonitis (HP), especially for farmer''s lung, and to a lesser degree, for bird fancier''s lung. The under-representation of active smokers in SARS-CoV-2 patients suggests a protective effect of smoking, similar to that in the farmer''s lung. We chose to highlight the most obvious similarities between SARS-CoV-2 and farmer''s lung but there are probably others, especially concerning the hyperactive immune response described as ''cytokine storm''. The lack of knowledge about the mode of action of smoking in farmer''s lung disease limits comparisons with SARS-CoV-2 and more research is required. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32779722/ doi: 10.1093/occmed/kqaa147 id: cord-260618-k0y0fz7k author: Belli, Simone title: Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? date: 2020-07-01 words: 9640.0 sentences: 417.0 pages: flesch: 51.0 cache: ./cache/cord-260618-k0y0fz7k.txt txt: ./txt/cord-260618-k0y0fz7k.txt summary: Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. (2004) , and collected 256 articles indexed in the Science Citation Index (SCI) in the period March-July 2003, analyzing traditional indicators (authorship, collaboration, journals, language, document type, organization, times cited, etc.). We offer a general search in all databases available at Web of Science (WoS) platform and a deeper bibliometric analysis of recent coronavirus scientific publications indexed in its Core Collection. For the 2001-2020 period (Table 1) , the value of the TLS in proportion to the number of documents provided is especially low in countries such as Japan, South Korea, Taiwan or Brazil, with 0.46, 0.35, 0.28 and 0.38 links per document and 35.87%, 25.81%, 19.89% and 31.79% of documents resulted from international collaboration respectively. abstract: The COVID-19 pandemic is creating a global health emergency. Mapping this health emergency in scientific publications demands multiple approaches to obtain a picture as complete as possible. To progress in the knowledge of this pandemic and to control its effects, international collaborations between researchers are essentials, as well as having open and immediate access to scientific publications, what we called “coopetition”. Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. We have analyzed 18,875 articles indexed in Web of Science. We performed the descriptive statistical analysis in order to explore the performance of the more prolific countries and organizations, as well as paying attention to the last 2 years. Registers have been analyzed separately via the VOSviewer software, drawing a network of links among countries and organizations to identify the starred countries and organizations, and the strongest links of the net. We have explored the capacity of researchers to generate scientific knowledge about a health crisis emergency, and their global capacity to collaborate among them in a global emergency. We consider that science is moving rapidly to find solutions to international health problems but access to this knowledge by society is not so quick due to several limitations (open access policies, corporate interests, etc.). We have observed that papers from China in the last 3 months (from January 2020 to March 2020) have a strong impact compared with papers published in years before. The United States and China are the major producers of documents of our sample, followed by all European countries, especially the United Kingdom, Germany, the Netherlands, and France. At the same time, the leading role of Saudi Arabia, Canada or South Korea should be noted, with a significant number of documents submitted but very different dynamics of international collaboration. The proportion of international collaboration is growing in all countries in 2019–2020, which contrasts with the situation of the last two decades. The organizations providing the most documents to the sample are mostly Chinese. The percentage of open access articles on coronavirus for the period 2001–2020 is 59.2% but if we focus in 2020 the figures increase up to 91.4%, due to the commitment of commercial publishers with the emergency. url: https://doi.org/10.1007/s11192-020-03590-7 doi: 10.1007/s11192-020-03590-7 id: cord-298920-1lc2xf7u author: Bello-Perez, Melissa title: Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date: 2020-07-05 words: 6863.0 sentences: 326.0 pages: flesch: 40.0 cache: ./cache/cord-298920-1lc2xf7u.txt txt: ./txt/cord-298920-1lc2xf7u.txt summary: Along this line, the generation of these coronavirus-induced autophagosomes requires the PtdIns3P-enrichment of the ER membrane outer leaflet, and the recruitment of ZFYVE1/DFCP1 (a key protein in omegasome formation), WIPI1/2, ATG5 and LC3-II (all components of the autophagic machinery), and SQSTM1/p62 (a receptor protein for selective autophagy) [31, 50, 51] . Briefly, chloroquine, apart from disorganizing the Golgi, induces lysosomal alkalinization, which prevents amphisome/autophagosome-lysosome fusion and blocks the vesicle trafficking system [53] [54] [55] 93] , which potentially affects the replication cycle of coronavirus systemically, including their entry, which is mediated by pH-dependent endocytosis and requires a low pH for the S protein to trigger its membrane fusion activity [94, 95] . Nitazoxanide is another late-stage autophagy blocker [96] that shows high anti-SARS-CoV-2 activity in cell cultures (IC 50 : 2.12 µM) [97] , although it should be considered that its main metabolite, tizoxanide, induces autophagy by inhibiting the PI3K-AKT-MTOR pathway [98] . abstract: The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection. url: https://www.ncbi.nlm.nih.gov/pubmed/32635598/ doi: 10.3390/cells9071619 id: cord-103545-2v89ku4o author: Bellos, Ioannis title: Maternal and perinatal outcomes in pregnant women infected by SARS-CoV-2: A meta-analysis date: 2020-11-13 words: 5197.0 sentences: 333.0 pages: flesch: 48.0 cache: ./cache/cord-103545-2v89ku4o.txt txt: ./txt/cord-103545-2v89ku4o.txt summary: The following data were planned to be extracted from each of the included studies: name of first author, country, maternal age, medical history (diabetes mellitus, hypothyroidism or polycystic ovary syndrome), symptoms (fever, cough, shortness of breath, diarrhea, nausea/vomiting, myalgia, fatigue, headache, sore throat, nasal congestion, abdominal pain, chest pain), radiological signs, presence of co-infection (bacterial or influenza), laboratory tests (lymphopenia, thrombocytopenia, increased Creactive protein, procalcitonin, ferritin, liver function tests and D-dimers), type of treatment, pregnancy outcomes (fetal distress, premature rupture of membranes-PROM, placenta previa, preeclampsia, preterm birth, cesarean section, stillbirth), maternal outcomes (admission to intensive care unit-ICU or death), neonatal outcomes (gender, gestational age, birthweight, 1-minute/5-minute Apgar score, horizontal/vertical transmission, admission to ICU, mechanical ventilation, sepsis and death). As a result, the present meta-analysis was based on 16 observational studies [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] and 44 case reports/series , including a total of 920 neonates born to women with SARS-CoV-2 infection. abstract: Evidence concerning coronavirus disease-19 (covid-19) in pregnancy is still scarce and scattered. This meta-analysis aims to evaluate maternal and neonatal outcomes in covid-19 pregnancies and identify factors associated with perinatal viral transmission. Medline, Scopus, CENTRAL, Web of Science and Google Scholar databases were systematically searched to 3 June 2020. Overall, 16 observational studies and 44 case reports/series were included. Fever was the most frequent maternal symptom, followed by cough and shortness of breath, while about 15% of infected were asymptomatic. Severe disease was estimated to occur in 11% of women in case reports/series and in 7% (95% CI: 4%-10%) in observational studies. Two maternal deaths were reported. The rate of neonatal transmission did not differ between women with and without severe disease (OR: 1.94, 95% CI: 0.50-7.60). Preterm birth occurred in 29.7% and 16% (95% CI: 11%- 21%) in data obtained from case series and observational studies, respectively. Stillbirth occurred in 3 cases and 2 neonatal deaths were observed. Vertical transmission was suspected in 4 cases. Fever was the most common neonatal symptom (40%), followed by shortness of breath (28%) and vomiting (24%), while 20% of neonates were totally asymptomatic. In conclusion, the maternal and neonatal clinical course the infection is typically mild, presenting low mortality rates. The risk of vertical transmission is suggested to be low and may not be affected by the severity of maternal disease. Further large-scale studies are needed to clarify the risk factors associated with viral transmission and severe infection in the neonatal population. url: https://api.elsevier.com/content/article/pii/S0301211520307491 doi: 10.1016/j.ejogrb.2020.11.038 id: cord-318715-p6agoqu8 author: Belser, Jessica A title: Assessment of SARS-CoV-2 replication in the context of other respiratory viruses date: 2020-05-07 words: 740.0 sentences: 37.0 pages: flesch: 38.0 cache: ./cache/cord-318715-p6agoqu8.txt txt: ./txt/cord-318715-p6agoqu8.txt summary: Hui and colleagues show the susceptibility of human conjunctival explant cultures to SARS-CoV-2 infection (with higher levels of virus replication than SARS-CoV), a notable finding considering reports of ocular manifestations in some patients with confirmed COVID-19 infection, and detection of viral RNA in ocular swabs. 6 Human colorectal carcinoma epithelial cells were also found to support virus replication with SARS-CoV-2, consistent with reports of detection of viral RNA in faecal samples and other tissues from the gastrointestinal tracts of patients with confirmed COVID-19, even in the absence of gastrointestinal symptoms. Tropism of the novel coronavirus SARS-CoV-2 in human respiratory tract: an analysis in ex vivo and in vitro cultures Tropism and innate host responses of a novel avian influenza A H7N9 virus: an analysis of ex-vivo and in-vitro cultures of the human respiratory tract abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2213260020302277 doi: 10.1016/s2213-2600(20)30227-7 id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 words: 2822.0 sentences: 158.0 pages: flesch: 50.0 cache: ./cache/cord-325529-pid58g2r.txt txt: ./txt/cord-325529-pid58g2r.txt summary: METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. abstract: OBJECTIVES: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck, while the need to increase testing throughput only rises. We aim to overcome these challenges by pooling samples together, performing RNA extraction and RT-PCR in pools. METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of 8 samples in large-scale clinical tests. RESULTS: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of 8 samples, showed that test results were not significantly affected. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. CONCLUSIONS: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations. url: https://www.sciencedirect.com/science/article/pii/S1198743X20303499?v=s5 doi: 10.1016/j.cmi.2020.06.009 id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 words: 3316.0 sentences: 197.0 pages: flesch: 54.0 cache: ./cache/cord-351854-5s03f0pp.txt txt: ./txt/cord-351854-5s03f0pp.txt summary: title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. abstract: Testing for active SARS-CoV-2 infection is a fundamental tool in public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck. Here we demonstrate the reliability and efficiency of two simple pooling strategies that can increase testing capacity about 5-fold to 7.5-fold, in populations with a low infection rate. We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. url: https://doi.org/10.1101/2020.04.17.20069062 doi: 10.1101/2020.04.17.20069062 id: cord-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 words: 1174.0 sentences: 91.0 pages: flesch: 56.0 cache: ./cache/cord-283411-40ojqv1y.txt txt: ./txt/cord-283411-40ojqv1y.txt summary: title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. abstract: OBJECTIVES: Environmental surfaces have been suggested as likely contributors to the transmission of COVID-19. This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. METHODS: SARS-CoV-2 virus stability and infectivity on non-porous surfaces was tested under controlled laboratory conditions. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected by RT-PCR and infectivity was assessed by VERO E6 CPE test. RESULTS: In laboratory-controlled conditions, SARS-CoV-2 gradually lost its infectivity completely at day 4 at ambient temperature and the decay rate of viral viability on surfaces directly correlated with increase in temperature. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. None of the surface and air samples from all three sites (0/97) were found to contain infectious titers SARS-Cov-2 in tissue culture assay. CONCLUSIONS: Despite prolonged viability of SARS-CoV-2 in laboratory-controlled conditions, uncultivable viral contamination on inanimate surfaces might suggest low feasibility for indirect fomite transmission. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305322?v=s5 doi: 10.1016/j.cmi.2020.09.004 id: cord-266034-811lov8f author: Benameur, Karima title: Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020 date: 2020-09-17 words: 2447.0 sentences: 123.0 pages: flesch: 43.0 cache: ./cache/cord-266034-811lov8f.txt txt: ./txt/cord-266034-811lov8f.txt summary: CSF analysis also showed markedly increased levels of interleukin (IL)-6, IL-8, and IL-10, but severe acute respiratory syndrome coronavirus 2 was not identified in any CSF sample. Because MRI changes seen in these patients could be caused by hypercoagulability (15) or metabolic encephalopathy (16) , we propose that CSF investigation can improve the distinction between neurologic involvement of SARS-CoV-2 (or neuro-COVID) and neurologic symptoms caused by other COVID-related causes. The failure to detect CSF SARS-CoV-2 RNA does not diminish the likelihood of direct CNS infection because it is only recovered from blood in 1% of the actively infected cases (18) , and increased levels CSF IgM are also more commonly found as evidence for CNS infection than viral recovery in other encephalitides, including those for infection with Japanese encephalitis virus (19) , dengue virus (20) , human parvovirus 4 (21) , and rabies virus (22) . abstract: There are few detailed investigations of neurologic complications in severe acute respiratory syndrome coronavirus 2 infection. We describe 3 patients with laboratory-confirmed coronavirus disease who had encephalopathy and encephalitis develop. Neuroimaging showed nonenhancing unilateral, bilateral, and midline changes not readily attributable to vascular causes. All 3 patients had increased cerebrospinal fluid (CSF) levels of anti-S1 IgM. One patient who died also had increased levels of anti-envelope protein IgM. CSF analysis also showed markedly increased levels of interleukin (IL)-6, IL-8, and IL-10, but severe acute respiratory syndrome coronavirus 2 was not identified in any CSF sample. These changes provide evidence of CSF periinfectious/postinfectious inflammatory changes during coronavirus disease with neurologic complications. url: https://www.ncbi.nlm.nih.gov/pubmed/32487282/ doi: 10.3201/eid2609.202122 id: cord-325019-hznnoxw6 author: Benavides-Cordoba, Vicente title: Drug Repositioning for COVID-19 date: 2020-06-30 words: 2897.0 sentences: 165.0 pages: flesch: 45.0 cache: ./cache/cord-325019-hznnoxw6.txt txt: ./txt/cord-325019-hznnoxw6.txt summary: In this review, we present a selection of drugs, of different classes and with potential activity against COVID-19, whose trials are ongoing; and as proofs of concept, double blind, add-on event-driven, would allow proposing research that generates results in less time and preserving quality criteria for drug development and approval by regulatory agencies. Likewise, when researching new molecules in humans, it is necessary to ask several questions that could improve the designs, and avoid some failures, such as, for example, did the drug hit the target?, did the medication change the target?, what was the dose response?, and what are the characteristics of the study patients?. Hydroxychloroquine, a chloroquine analog, is a medicine widely used in the treatment of systemic autoimmune diseases 35 , being currently the most studied drug for treating COVID-19. In COVID 19, 133 clinical trials are registered, taking different degrees of severity, ranging from prophylactic use in the general population and in health workers 38 to patients with severe acute respiratory syndrome (SARS). abstract: Drug repositioning is a strategy that identifies new uses of approved drugs to treat conditions different from their original purpose. With the advance of COVID-19 and the pandemic declaration; It has become the closest alternative to reduce the advance of the virus. Antimalarial, antiviral drugs, antibiotics, glucocorticoids, monoclonal antibodies, among others, are being studied; their findings, although preliminary, could establish a starting point in the search for a solution. In this review, we present a selection of drugs, of different classes and with potential activity against COVID-19, whose trials are ongoing; and as proofs of concept, double blind, add-on event-driven, would allow proposing research that generates results in less time and preserving quality criteria for drug development and approval by regulatory agencies. url: https://doi.org/10.25100/cm.v51i2.4279 doi: 10.25100/cm.v51i2.4279 id: cord-350451-lf27iuwk author: Benedetti, Francesca title: SARS‐CoV‐2: March toward adaptation date: 2020-07-11 words: 1212.0 sentences: 79.0 pages: flesch: 44.0 cache: ./cache/cord-350451-lf27iuwk.txt txt: ./txt/cord-350451-lf27iuwk.txt summary: A third factor still subject of debate is how and how much the mutations observed in SARS-CoV-2 provide an indication of viral fitness and adaptation, and their role first into the initial phases of transmission and now during the reduction of viral spreading. The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel human pathogen, first detected in China quickly became a global health emergency, culminating with the World Health Organization publicly proclaiming the SARS-CoV-2 outbreak as a pandemic (11 March 2020) . Several reports result show that SARS-CoV-2 is rapidly moving across countries, and new mutation hotspots are emerging in different parts of the genome. Although SARS-CoV-2 is less lethal than MERS-CoV, up to 20% of the infected people develop rapidly a severe disease characterized by interstitial pneumonia and acute respiratory distress syndrome that can ultimately lead to death. Davide Zella http://orcid.org/0000-0001-5576-5770 Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant abstract: After an initial period of rising numbers of infected subjected by SARS-CoV-2 and deaths by COVID-19, currently some areas of the World are experiencing a reduction of cases. Different degrees of lockdown and social distancing measures greatly helped in limiting the spread of the disease. The contribution of other external factors like weather conditions and population density, though not as significant, seemed nonetheless to have played an additional role in shaping the course of the epidemic. A third factor still subject of debate is how and how much the mutations observed in SARS-CoV-2 provide an indication of viral fitness and adaptation, and their role first into the initial phases of transmission and now during the reduction of viral spreading. Aim of this commentary is to provide an overview of the status of the pandemic situation linking together the different factors implicated in current situation, and to summarize some strategies that could help us to better manage either a second wave of this virus or a potential new threat of similar nature. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26233 doi: 10.1002/jmv.26233 id: cord-274366-t138l6px author: Benetti, Elisa title: ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date: 2020-07-17 words: 4525.0 sentences: 247.0 pages: flesch: 49.0 cache: ./cache/cord-274366-t138l6px.txt txt: ./txt/cord-274366-t138l6px.txt summary: Taking advantage of the Network of Italian Genomes (NIG), a consortium established to generate a public database (NIG-db) containing aggregate variant frequencies data for the Italian population (http://www.nig.cineca.it/), here we describe the genetic variation of ACE2 in the Italian population, one of the newly affected countries by the SARS-CoV-2 outbreak causing COVID-19. In order to shed light on the role of ACE2 variants on interindividual variability and susceptibility to COVID-19 in Italian population we performed WES analysis on a cohort of 131 patients and 258 controls who agreed in participating to the study (see "Materials and methods"). These variants which surround residual essentials for the SARS-CoV-2 spike protein binding were predicted to likely affect the cleavage-dependent virion intake, such as the polymorphic c.2158A>G p.(Asn720Asp) (allele frequency 0.011) which lies four amino acids from the cleavage sequence of TMPRSS2 or to have a substantial impact on protein structure and spike protein interaction by MD simulation (Fig. 3a) . abstract: In December 2019, an initial cluster of interstitial bilateral pneumonia emerged in Wuhan, China. A human-to-human transmission was assumed and a previously unrecognized entity, termed coronavirus disease-19 (COVID-19) due to a novel coronavirus (SARS-CoV-2) was described. The infection has rapidly spread out all over the world and Italy has been the first European country experiencing the endemic wave with unexpected clinical severity in comparison with Asian countries. It has been shown that SARS-CoV-2 utilizes angiotensin converting enzyme 2 (ACE2) as host receptor and host proteases for cell surface binding and internalization. Thus, a predisposing genetic background can give reason for interindividual disease susceptibility and/or severity. Taking advantage of the Network of Italian Genomes (NIG), here we mined whole-exome sequencing data of 6930 Italian control individuals from five different centers looking for ACE2 variants. A number of variants with a potential impact on protein stability were identified. Among these, three more common missense changes, p.(Asn720Asp), p.(Lys26Arg), and p.(Gly211Arg) were predicted to interfere with protein structure and stabilization. Rare variants likely interfering with the internalization process, namely p.(Leu351Val) and p.(Pro389His), predicted to interfere with SARS-CoV-2 spike protein binding, were also observed. Comparison of ACE2 WES data between a cohort of 131 patients and 258 controls allowed identifying a statistically significant (P value < 0.029) higher allelic variability in controls compared with patients. These findings suggest that a predisposing genetic background may contribute to the observed interindividual clinical variability associated with COVID-19, allowing an evidence-based risk assessment leading to personalized preventive measures and therapeutic options. url: https://www.ncbi.nlm.nih.gov/pubmed/32681121/ doi: 10.1038/s41431-020-0691-z id: cord-282750-d9sb7o63 author: Benhadou, F. title: Improvement of SARS‐CoV2 symptoms following Guselkumab injection in a psoriatic patient date: 2020-05-07 words: 550.0 sentences: 28.0 pages: flesch: 44.0 cache: ./cache/cord-282750-d9sb7o63.txt txt: ./txt/cord-282750-d9sb7o63.txt summary: We read with great interest the publication of Messina et al (1) reporting the first case of SARS‐CoV2 infection in a young patient of 32‐year‐old suffering from psoriasis and psoriatic arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)‐23(2).The patient contracted the SARS‐CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)-23 2 .The patient contracted the SARS-CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. These findings support the potential role of IL-23p19 inhibitors to counteract the « cytokine storm » triggered by the SARS-CoV2 and which is potentially implicated in the severity of the symptoms 3 . abstract: We read with great interest the publication of Messina et al (1) reporting the first case of SARS‐CoV2 infection in a young patient of 32‐year‐old suffering from psoriasis and psoriatic arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)‐23(2).The patient contracted the SARS‐CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. These findings support the potential role of IL‐23p19 inhibitors to counteract the « cytokine storm » triggered by the SARS‐CoV2 and which is potentially implicated in the severity of the symptoms (3). url: https://www.ncbi.nlm.nih.gov/pubmed/32379925/ doi: 10.1111/jdv.16590 id: cord-023888-w2sbyfy2 author: Beniac, Daniel R. title: Structural Molecular Insights into SARS Coronavirus Cellular Attachment, Entry and Morphogenesis date: 2009-07-22 words: 4349.0 sentences: 238.0 pages: flesch: 57.0 cache: ./cache/cord-023888-w2sbyfy2.txt txt: ./txt/cord-023888-w2sbyfy2.txt summary: Receptor binding results in structural changes that have been observed in the spike molecule, and these appear to be the initial step in viral membrane fusion. However, despite the size differences, the SARS-CoV spike performs the same fundamental task in viral entry to the host cell as other smaller type 1 viral fusion proteins, such as the influenza hemagglutinin (HA) (~220 kD per trimer). This structural data has been modeled into a scheme to propose a mechanism for SARS-CoV spike-mediated membrane fusion (Figs. Our cryo-EM results show that it is possible for the spike to attach to three ACE2 receptors at once; this may serve to hold on to the host membrane like a tripod so as to accurately orientate the fusion core ( Fig. 3.7) . abstract: Coronavirus spikes have the largest mass of any known viral spike molecule. The spike is a type 1 viral fusion protein, a class of trimeric surface glycoprotein proteins from diverse viral families that share many common structural and functional characteristics. Fusion proteins are mainly responsible for host cell receptor recognition and subsequent membrane fusion, and may perform other roles such as virus assembly and release via budding. The conformational changes that occur in the spike of intact SARS coronavirus (SARS-CoV) when it binds to the viral receptor, angiotensin-converting enzyme 2 (ACE2) are described. Clues to the structural/functional relationships of membrane fusion have been made possible by the development of viral purification and inactivation methods, along with cryo-electron microscopy (cryo-EM) and three-dimensional (3D) image processing of many different images containing multiple views of the spikes. These methods have allowed study of the spikes while still attached to virions that are noninfectious, but fusionally competent. The receptor-binding and fusion core domains within the SARS-CoV spike have been precisely localized within the spike. Receptor binding results in structural changes that have been observed in the spike molecule, and these appear to be the initial step in viral membrane fusion. A working model for the stepwise process of receptor binding, and subsequent membrane fusion in SARS-CoV is presented. Uniquely, the large size of the SARS-CoV spike allows structural changes to be observed by cryo-EM in the native state. This provides a useful model for studying the basic process of membrane fusion in general, which forms an essential part of the function of many cellular processes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176236/ doi: 10.1007/978-3-642-03683-5_3 id: cord-305274-mcsdem7y author: Beniac, Daniel R. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 words: 5463.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-305274-mcsdem7y.txt txt: ./txt/cord-305274-mcsdem7y.txt summary: We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. The structures of ACE2 bound to a fragment of the SARS spike containing the receptor-binding domain and the pre-and postfusion configurations of the fusion core heptad repeats of the spike have been solved to atomic resolution [2, 3, [24] [25] [26] . In addition, the atomic resolution structures of two neutralizing antibodies bound to the SARS spike receptor-binding domain have been solved [27, 28] showing that blocking of the receptor binding domain, preventing attachment of virions to cell-surface ACE2, is the likely mechanism of virus neutralization by these antibodies. abstract: The SARS coronavirus (SARS-CoV) spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Previous structural studies of membrane fusion proteins have largely used crystallography of static molecular fragments, in isolation of their transmembrane domains. In this study we have produced purified, irradiated SARS-CoV virions that retain their morphology, and are fusogenic in cell culture. We used cryo-electron microscopy and image processing to investigate conformational changes that occur in the entire spike of intact virions when they bind to the viral receptor, angiotensin-converting enzyme 2 (ACE2). We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. Furthermore, our results show that receptor binding and subsequent membrane fusion are distinct steps, and that each spike can bind up to three ACE2 molecules. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/17957264/ doi: 10.1371/journal.pone.0001082 id: cord-342660-xigv4u3f author: Benotmane, I. title: In-depth virological assessment of kidney transplant recipients with COVID-19 date: 2020-06-19 words: 2499.0 sentences: 171.0 pages: flesch: 55.0 cache: ./cache/cord-342660-xigv4u3f.txt txt: ./txt/cord-342660-xigv4u3f.txt summary: We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. We thus conducted a retrospective cohort study in kidney transplant recipients (KTR) in Alsace, Grand-Est France, to determine the dynamics of nasopharyngeal and plasma viral loads and SARS-CoV-2 serology and to study their association with mortality and severe forms of COVID-19. . https://doi.org/10.1101/2020.06.17.20132076 doi: medRxiv preprint positive viral load greater than 3 log10 copies/reaction after D10, and ten patients (24.4 %) In this retrospective study conducted in a sample of 40 immunocompromised KTR hospitalized for COVID-19, we precisely determined the temporal evolution of nasopharyngeal and plasma SARS-CoV-2 loads, as well as the serological response to the virus. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread widely, causing coronavirus disease 2019 (COVID-19) and significant mortality. However, data on viral loads and antibody kinetics in immunocompromised populations are lacking. We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. In this study we examined hospitalized kidney transplant recipients with non-severe (n = 21) and severe (n =19) COVID-19. SARS-CoV-2 nasopharyngeal and plasma viral load and serological response were evaluated based on outcomes and disease severity. Ten recipients (25%) displayed persistent viral shedding 30 days after symptom onset. The SARS-CoV-2 viral load of the upper respiratory tract was not associated with severe COVID-19, whereas the plasma viral load was associated with COVID-19 severity (p=0.0087) and mortality (p=0.024). All patients harbored antibodies the second week after symptom onset that persisted for two months. We conclude that plasma viral load is associated with COVID-19 morbidity and mortality, whereas nasopharyngeal viral load is not. SARS-CoV-2 shedding is prolonged in kidney transplant recipients and the humoral response to SARS-CoV-2 does not show significant impairment in this series of transplant recipients. url: http://medrxiv.org/cgi/content/short/2020.06.17.20132076v1?rss=1 doi: 10.1101/2020.06.17.20132076 id: cord-319351-hcxbkvgd author: Benrahma, H. title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS date: 2020-06-20 words: 1547.0 sentences: 110.0 pages: flesch: 61.0 cache: ./cache/cord-319351-hcxbkvgd.txt txt: ./txt/cord-319351-hcxbkvgd.txt summary: title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp gene, N gene, and E gene in patients from diagnosis until the recovery. To date, no studies exploring the variation of RdRp, N and E genes expression of SARS-CoV-94 2 in the patient''s specimen. In this study, in first time, we analyses the epidemiological profile The LNR provide a RT-PCR to clinically suspected COVID-19 patients when they were (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019. On 2 March 2020, the Moroccan Ministry of Health confirmed the first COVID-19 case in Morocco. The new virus SARS-CoV-2 was identified in the sample of a Moroccan expatriate residing in Italy. Without a therapeutic vaccine or specific antiviral drugs, early detection and isolation become essential against novel Coronavirus. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp gene, N gene, and E gene in patients from diagnosis until the recovery. Among 859 Covid-19 RT-PCR tests realized for 285 patients, 133 cases had positive results Covid-19. 9 % of these cases present the 3 genes RdRp, N, and E, 47% only the RdRp gene, 2% with RdRp and N gene, 26% cases are positives with N gene, and 16 % with N and E gene. The analysis of the Covid-19 genes (RdRp, N, and E) dynamic reveal that more than 6% stay positive with detection of the N and E gene, and 14% with the N gene after 12 days of treatment. The median period from positive to the first negative Covid-19 RT-PCR tests was 6.8{+/-}2.24 days for 44% cases, 14.31 {+/-} 2.4 days for 30%, and 22.67 {+/-} 1.21 days for 4%. This a first description of the Moroccan COVID-19 cases and the analysis of the dynamic of the 3 genes RdRp, N, and E. The analysis of our population can help to involved in the care of patients. url: https://doi.org/10.1101/2020.06.18.20135137 doi: 10.1101/2020.06.18.20135137 id: cord-308912-2pd801t1 author: Bensimon, Cécile M. title: A qualitative study of the duty to care in communicable disease outbreaks date: 2007-12-31 words: 6458.0 sentences: 290.0 pages: flesch: 52.0 cache: ./cache/cord-308912-2pd801t1.txt txt: ./txt/cord-308912-2pd801t1.txt summary: He continued, stating that on the whole, institutions have a responsibility to provide resources and set up mechanisms with respect to ''''anything that would impact on potentially impairing healthcare workers from carrying out their duties.'''' A nurse echoed this view, stating his expectation that, ''''if I''m going to be involved in dealing with patients with some type of infectious disease, I want to know that my employer has instituted policies and procedures that are protecting my rights.'''' Many other participants agreed that ''''HCPs have the right to adequate protection,'''' and if such is not the case, ''''they should have the right to opt out, legally and ethically.'''' While many participants shared this view, several participants added the qualifier that ''''in a situation where the institution fulfills its obligation to protect these individuals, yat that point [they] can no longer respect [providers''] voluntary decision to withdraw from work and stay home.'''' A nurse stated that if someone is protected with proper equipment, ''''I don''t think you should be given a choice of saying no,'''' thus suggesting, as many others did, that HCPs ought not be able to refuse to provide care if supports are in place. abstract: Abstract Health care providers’ (HCPs’) duty to care during communicable disease outbreaks has resurfaced as an important and contentious topic. This renewed interest follows the re-emergence of communicable diseases, largely thought to have disappeared and therefore irrelevant to modern day practitioners. The 2003 SARS outbreak particularly presented propitious circumstances for reconsidering this issue. This study seeks to characterize the views of individuals on the nature and limits of this duty. The authors employed qualitative methods to gather lay and expert perspectives. Individual interviews were conducted with 67 participants consisting of HCPs, spiritual leaders, regulators, and members of the public from the greater Toronto area. Participants’ views were analyzed and organized according to three main themes, constituting a framework that combines micro-, meso-, and macro-level structures and processes: the scope of obligations of HCPs, the roles of health care institutions, and the broader social context, respectively. Our data suggest that the duty to care must be placed in a wider context to include considerations that transcend individual provider obligations. It thus follows, based on our data, that the duty to care cannot be left to personal choice or an appeal to morality based on an ethic derived entirely from individual obligations. The micro-meso-macro analytical framework that we have developed can guide the articulation of accepted norms of duty to care during epidemics and the development of policy for public health crises. It can also enhance the focus of our current expectations of HCPs’ duty during epidemics. This can be achieved by informing regulatory bodies, collaborating with policy makers and engaging the public. url: https://api.elsevier.com/content/article/pii/S027795360700411X doi: 10.1016/j.socscimed.2007.07.017 id: cord-311545-3rll9mca author: Bentley, Gillian R title: Don''t blame the BAME: Ethnic and structural inequalities in susceptibilities to COVID‐19 date: 2020-07-16 words: 2806.0 sentences: 137.0 pages: flesch: 47.0 cache: ./cache/cord-311545-3rll9mca.txt txt: ./txt/cord-311545-3rll9mca.txt summary: However, more recently, insidious and potentially racist allusions are beginning to emerge appearing to blame African Americans as somehow responsible for the relatively large number of cases and deaths from COVID-19 in the USA, stoking age-old tropes, and attributing morbidity and mortality to the behaviors and predispositions of BAME groups (Guardian, 2020b; Strings, 2020) . In reality, structural or social inequalities that affect individual vulnerabilities to SARS-CoV-2 include exposures through types of employment, whether people are working in essential transport networks carrying large numbers of people, or in small grocery shops that place BAME communities at greater risk of contracting COVID-19 ( Figure 1 ). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32677326/ doi: 10.1002/ajhb.23478 id: cord-328962-1c4vqaqr author: Benítez-Cardoza, Claudia Guadalupe title: Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug date: 2020-06-15 words: 3344.0 sentences: 184.0 pages: flesch: 54.0 cache: ./cache/cord-328962-1c4vqaqr.txt txt: ./txt/cord-328962-1c4vqaqr.txt summary: KEY FINDINGS: 20 best compounds directed to interact in ACE2 with a high probability to be safe in humans, validated by web servers of prediction of ADME and toxicity (ProTox-II and PreADMET), to difficult the interaction between ACE2 and region binding domain (RBD) of SARS-CoV-2. We use the amino acids reported in the crystallographic structure of the interaction between the S-protein-RBD of SARS-CoV-2 and ACE2 (Gln24, Asp30, His34, Tyr41, Gln42, Met82, Lys353 and Arg357 in ACE2) [10] [22] , therefore, using the crystallographic structure of ACE2 (PDB 1R42), we carried out a Docking directed to these mentioned residues using a library of compounds (EXPRESS-pick Collection from Chembridge Corp.) to select the best compounds, and that these can affect the interaction between ACE2 and SARS-CoV-2, making these results an important contribution to establishing the foundations that allow the development of a drug that optimizes the resolution of this pandemic. abstract: AIMS: The COVID-19 disease caused by the SARS-CoV-2 has become a pandemic and there are no effective treatments that reduce the contagion. It is urgent to propose new treatment options, which are more effective in the interaction between viruses and cells. In this study was to develop a search for new pharmacological compounds against the angiotensin-converting enzyme 2 (ACE2), to inhibit the interaction with SARS-CoV-2. MATERIALS AND METHODS: Docking, virtual screening using almost 500,000 compounds directed to interact in the region between the residues (Gln24, Asp30, His34, Tyr41, Gln42, Met82, Lys353, and Arg357) in ACE2. The average of ΔG(binding), the standard deviation value and the theoretical toxicity from compounds were analyzed. KEY FINDINGS: 20 best compounds directed to interact in ACE2 with a high probability to be safe in humans, validated by web servers of prediction of ADME and toxicity (ProTox-II and PreADMET), to difficult the interaction between ACE2 and region binding domain (RBD) of SARS-CoV-2. SIGNIFICANCE: In this study, 20 compounds were determined by docking focused on the region of interaction between ACE2 and RBD of SARS-CoV-2 was carried out. The compounds are publicly available to validate the effect in in vitro tests. url: https://www.sciencedirect.com/science/article/pii/S0024320520307207?v=s5 doi: 10.1016/j.lfs.2020.117970 id: cord-347263-ci6mv72z author: Berekashvili, k. title: Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients date: 2020-05-08 words: 2971.0 sentences: 223.0 pages: flesch: 56.0 cache: ./cache/cord-347263-ci6mv72z.txt txt: ./txt/cord-347263-ci6mv72z.txt summary: Methods: Over the last 6 weeks, data from four centers in New York City were collected to review the possible ischemic stroke types seen in COVID-19 positive patients. We also wanted to better describe the different ischemic stroke subtypes seen in patients with SARS-COV2 infection especially with the view to assess its unique features seen in the context of COVID-19. Two patients who presented with LVO had no prior complaints of viral illness but went on to develop a severe course of the disease. Only three patients had a severe course of the pulmonary disease prior to the neurological event requiring them to be hospitalized. The LVO cases were typically younger, had a worse neurological presentation, more severe form of viral disease and higher levels of hypercoagulability markers than the non-LVO patients. Ischemic stroke can be a presenting symptom of COVID-19 and may not always be associated with severe disease markers including in the young, minorities and healthcare workers. abstract: Objective: To describe the ischemic stroke etiopathogenesis related to COVID-19 in a cohort of NYC hospitals. Background: Extra-pulmonary involvement of COVID-19 has been reported in the hepatic, renal and hematological systems. Most neurological manifestations are non-focal but few have reported the characteristics of ischemic strokes or investigated its pathophysiology. Methods: Over the last 6 weeks, data from four centers in New York City were collected to review the possible ischemic stroke types seen in COVID-19 positive patients. Their presentation, demographics, other related vascular risk factors, associated laboratory and coagulation markers, as well as imaging and outcomes were collected. Results: In our study, age range of patients was 25-75 with no significant male preponderance. 70% presented for acute hospitalization due the stroke. About a fifth did not have common risk factors for ischemic stroke like diabetes and hypertension. None had history of atrial fibrillation or smoking. 50% had poor outcome with four ending in mortality and one in a critical condition due ARDS. All had high Neutrophil/Lymphocyte ratio except one who demonstrated some neurological recovery. In 70% of our cases, D-dimer levels were collected, and all showed mild to severe elevation. None of the emergent large vessel occlusion (LVO) cases had known cardiac risk factors but two out of five were found to have cardiac abnormalities during the course of their hospitalization. All LVOs had hypercoagulable lab markers especially elevated D-dimer and/or Fibrinogen. The LVO patients were younger and sicker with a median age of 46 and mean NIHSS of 24 as opposed to non-LVOs with a median age of 62 and mean NIHSS of 6 respectively. Conclusion: COVID-19 related ischemic events can be small vessel, branch emboli or large vessel occlusions. The latter is often associated with either a hypercoagulable state or cardio-embolism. Patient outcomes were worse when multi-organ or pulmonary system failure prevailed. Keywords: COVID-19, Acute Ischemic strokes, Emergent Large Vessel Occlusion, Mechanical Thrombectomy url: http://medrxiv.org/cgi/content/short/2020.05.03.20077206v1?rss=1 doi: 10.1101/2020.05.03.20077206 id: cord-314746-1o0rf0ii author: Bergasa-Caceres, Fernando title: Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date: 2020-08-10 words: 5038.0 sentences: 304.0 pages: flesch: 56.0 cache: ./cache/cord-314746-1o0rf0ii.txt txt: ./txt/cord-314746-1o0rf0ii.txt summary: [Image: see text] In this article, we predict the folding initiation events of the ribose phosphatase domain of protein Nsp3 and the receptor binding domain of the spike protein from the severe acute respiratory syndrome (SARS) coronavirus-2. The identification of the primary contacts along the folding pathway of viral proteins constitutes an important result for at least two reasons: (a) the sequences of the specific segments involved in the primary contacts provide a template to specify candidate peptide drugs of inhibitory effect with the maximum possible contact affinity to compete with the natural folding mechanism; and (b) it provides insight for further investigation into the subsequent folding steps leading to a fully functional viral protein, potentially providing for additional FITRs. The fact that the primary contact is defined by the interaction between two well defined amino acid sequences suggests that a strategy to develop FITR-based therapeutic drugs could be one utilizing trial peptide drugs as suggested above. abstract: [Image: see text] In this article, we predict the folding initiation events of the ribose phosphatase domain of protein Nsp3 and the receptor binding domain of the spike protein from the severe acute respiratory syndrome (SARS) coronavirus-2. The calculations employ the sequential collapse model and the crystal structures to identify the segments involved in the initial contact formation events of both viral proteins. The initial contact locations may provide good targets for therapeutic drug development. The proposed strategy is based on a drug binding to the contact location, thereby aiming to prevent protein folding. Peptides are suggested as a natural choice for such protein folding interdiction drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/32790379/ doi: 10.1021/acs.jpcb.0c03716 id: cord-277076-yvsyo4l9 author: Berger, A. title: SARS date: 2019-09-12 words: 4349.0 sentences: 215.0 pages: flesch: 45.0 cache: ./cache/cord-277076-yvsyo4l9.txt txt: ./txt/cord-277076-yvsyo4l9.txt summary: Measures including source isolation of patientswho only became infectious after onset of clinical symptomsstrict infection control in health care facilities, timely identification and quarantining of exposed contacts, and perhaps also measures to increase social distance, such as travel warnings and screening of travelers, had led to this remarkable and remarkably rapid success. A further, small SARS outbreak occurred again in Guangdong in late 2003/early 2004; molecular analysis of virus isolates from human cases and animals sampled at the same place and time confirmed that this was zoonotically acquired from Paguma larvata. The laboratory diagnosis of SARS remains a challenge; in fact, despite the rapid identification of SARS-CoV as the etiological agent, testing contributed little to the successful control of the 2003 outbreak. A negative antibody test result later than 21 days after the onset of illness is likely to indicate that no infection with SARS-CoV has taken place. abstract: Severe acute respiratory syndrome (SARS) emerged in southern China in late 2002. It first spread within Guangdong Province and then to other parts of China. Via air travelers, it quickly reached various countries around the globe, causing several major hospital outbreaks. Within weeks, the causative agent, a previously unknown coronavirus (SARS-CoV), was identified, thanks to an unprecedented international effort led by the World Health Organization (WHO). Its origin was quickly traced to wild animals traded locally for culinary purposes. Masked palm civet and some other species seem to have acted as intermediate hosts. Since then, SARS-like coronaviruses were found in different bat species in China and elsewhere, and bats are now regarded as the wildlife reservoir for SARS-CoV. Fortunately, the SARS outbreak could be contained within months. Until July 2003, it had caused 8096 cases, with 774 deaths. Once adequate measures such as isolating patients and quarantining their contacts were strictly adhered to, further transmission between human beings could be interrupted. SARS is an example of how rapidly an infectious agent can spread in the modern world. At the same time, it should serve as a showcase of how international cooperation and modern science can help to combat the spread of infectious diseases. url: https://api.elsevier.com/content/article/pii/B9780444639516006240 doi: 10.1016/b978-0-444-63951-6.00624-0 id: cord-285557-my16g91c author: Berger, A. title: Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date: 2004-01-31 words: 6381.0 sentences: 291.0 pages: flesch: 47.0 cache: ./cache/cord-285557-my16g91c.txt txt: ./txt/cord-285557-my16g91c.txt summary: This strengthened the case for the novel coronavirus being the cause of SARS, but only after it had been shown to cause a similar illness in artificially infected macaques could it be regarded as fulfilling all four of Koch''s postulates ; World Health Organisation Multicentre Collaborative Networks for Severe Acute Respiratory Syndrome Diagnosis, 2003) . Nevertheless, and despite considerable progress in this field, much remains to be done until laboratory tests become a useful tool for the management of SARS cases (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003) . An enzyme-linked immunosorbent assay (ELISA) was developed that detects antibodies in the serum of SARS patients and reliably yields positive results at around day 21 after the onset of illness (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003). abstract: Abstract An acute and often severe respiratory illness emerged in southern China in late 2002 and rapidly spread to different areas of the Far East as well as several countries around the globe. When the outbreak of this apparently novel infectious disease termed severe acute respiratory syndrome (SARS) came to an end in July 2003, it had caused over 8000 probable cases worldwide and more than 700 deaths. Starting in March 2003, the World Health Organization (WHO) organised an unprecedented international effort by leading laboratories working together to find the causative agent. Little more than one week later, three research groups from this WHO-coordinated network simultaneously found evidence of a hitherto unknown coronavirus in SARS patients, using different approaches. After Koch’s postulates had been fulfilled, WHO officially declared on 16 April 2003 that this virus never before seen in humans is the cause of SARS. Ever since, progress around SARS-associated coronavirus (SARS-CoV) has been swift. Within weeks of the first isolate being obtained, its complete genome was sequenced. Diagnostic tests based on the detection of SARS-CoV RNA were developed and made available freely and widely; nevertheless the SARS case definition still remains based on clinical and epidemiological criteria. The agent’s environmental stability, methods suitable for inactivation and disinfection, and potential antiviral compounds have been studied, and development of vaccines and immunotherapeutics is ongoing. Despite its grave consequences in humanitarian, political and economic terms, SARS may serve as an example of how much can be achieved through a well-coordinated international approach, combining the latest technological advances of molecular virology with more “traditional” techniques carried out to an excellent standard. url: https://www.ncbi.nlm.nih.gov/pubmed/14675864/ doi: 10.1016/j.jcv.2003.09.011 id: cord-286923-o4fj8kx0 author: Berhan, Yifru title: What immunological and hormonal protective factors lower the risk of COVID-19 related deaths in pregnant women? date: 2020-07-18 words: 4536.0 sentences: 212.0 pages: flesch: 34.0 cache: ./cache/cord-286923-o4fj8kx0.txt txt: ./txt/cord-286923-o4fj8kx0.txt summary: The immunological changes predominantly inclining to anti-inflammatory state, which is augmented by placental hormones'' immune modulating action, looks against with COVID-19 inflammatory reaction leading to cytokine storm and multiple organ failure. As discussed hereunder, accumulating evidence from other infections and autoimmune diseases shows that immune modulating hormones, cytokines and other anti-inflammatory endogenous ligands are determinant factors in reducing the severity of several diseases during pregnancy; which could also be the most plausible explanation for the less severity and mortality of Covid-19 in pregnant women. Despite serious concern for patients with autoimmune disease, taking their immune suppression and medications, at least 110 individuals (79% females) with rheumatoid arthritis and got infected with SARS CoV-2 (from six continents) were not as such at higher risk of mortality, probably as they were on anti-inflammatory medication; only 6(5%) persons died of COVID-19 [89] . abstract: Despite anticipated increased risk of COVID-19 and increased expression of the SARS CoV-2 receptor (ACE2), the relatively low mortality of pregnant women with COVID-19 has been an area of wonder. The immunological changes predominantly inclining to anti-inflammatory state, which is augmented by placental hormones’ immune modulating action, looks against with COVID-19 inflammatory reaction leading to cytokine storm and multiple organ failure. Unlike many other viral infections, the bilateral immune activation of COVID-19 may preferentially make pregnant women at low risk. Taking the physiological advantage of pregnant women, potential clinical trials are proposed. Quite a large number of epidemiological and obstetrics related studies have addressed the cases of women with COVID-19. However, to the best of the author's knowledge, little is done to explore the physiological internal milieu of pregnant women in relation to COVID-19. This review provides an insight into how the hormonal and immunological changes in pregnancy potentially reduce SARS-CoV-2-mediated inflammatory response. url: https://www.sciencedirect.com/science/article/pii/S0165037820301017?v=s5 doi: 10.1016/j.jri.2020.103180 id: cord-304282-om2xc4bs author: Berhan, Yifru title: Will Africa be Devastated by Covid-19 as Many Predicted? Perspective and Prospective date: 2020-05-17 words: 5345.0 sentences: 235.0 pages: flesch: 57.0 cache: ./cache/cord-304282-om2xc4bs.txt txt: ./txt/cord-304282-om2xc4bs.txt summary: Since the novel coronavirus disease 2019 (Covid-19 or SARS CoV-2 infection) has been declared as pandemic, several mathematicians and statisticians have developed different trajectory curves for Africa, with the assumption that the virus can have an exponential pattern of transmission. A very important argument is; had the Covid-19 transmission been as contagious as in Europe and USA, by this time, every health facility in Africa and other tropical countries could have been flooded with severely ill patients and deaths. The other side of the coin is; the overwhelming cases and deaths experienced in Europe and USA is despite the fact that they started to report Covid-19 confirmed cases almost same time or later than many of the countries in the tropical climate zone. An important observation was that, like the currently observed Covid-19 pandemic, the morbidity and mortality of the aforementioned influenza outbreaks were not that much spreading and killing outside the temperate zone, at least in Africa. abstract: nan url: https://doi.org/10.4314/ejhs.v30i3.17 doi: 10.4314/ejhs.v30i3.17 id: cord-335844-dybozins author: Berkowitz, Kathleen M. title: IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY date: 2020-07-11 words: 255.0 sentences: 33.0 pages: flesch: 64.0 cache: ./cache/cord-335844-dybozins.txt txt: ./txt/cord-335844-dybozins.txt summary: key: cord-335844-dybozins title: IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY cord_uid: dybozins Cleveland Clinic Foundation recently implemented a policy OF SARS-CoV-2 testing for all 9 pregnant patients with planned delivery or admitted for labor at obstetric units in Ohio. In contrast to a recent report (1) on universal screening of pregnant women residing in an 12 area of high disease prevalence, our experience derives from a population experiencing a low 13 prevalence of active disease. 14 Patients with planned delivery were tested 3-5 days prior to admission using a CDC approved 15 RT-PCR testing platform. Patients presenting 16 in spontaneous labor were tested using a rapid platform (Xpert Xpress SARS-CoV-2 (Cepheid, Screening all pregnant women admitted to 40 labor and delivery for the virus responsible for coronavirus disease 2019 Universal Screening for SARS-CoV-2 in 46 Women Admitted for Delivery Women Admitted for Delivery abstract: nan url: https://api.elsevier.com/content/article/pii/S0002937820307298 doi: 10.1016/j.ajog.2020.07.011 id: cord-323024-blc3mnbj author: Bernard-Valnet, R. title: CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology date: 2020-11-04 words: 3478.0 sentences: 226.0 pages: flesch: 49.0 cache: ./cache/cord-323024-blc3mnbj.txt txt: ./txt/cord-323024-blc3mnbj.txt summary: Methods: We checked for SARS-CoV-2 RNA by RT-qPCR, SARS-CoV-2-specific antibodies and for 48 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluids (CSF) +/sera of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological control patients (inflammatory [IND], non inflammatory [NIND], multiple sclerosis [MS]). Methods: We checked for SARS-CoV-2 mRNA by qPCR, SARS-CoV-2-specific antibodies and for 49 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluid (CSF) +/serum of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological controls (inflammatory, non inflammatory, multiple sclerosis). Thus, the main hypotheses to explain neurological complications in COVID patients point at mechanisms either related to low grade presence of the virus in the CNS, to cytokine storm or to the presence of an auto-immune response, such as anti-neuronal antibodies by analogy to what occurs in autoimmune encephalitis. We found that SARS-CoV-2 patients tend to have signs of blood brain barrier opening and possible astrocytes activation, but no strong immune response in the CSF or obvious CNS infection by the virus. abstract: Objective: Coronavirus disease (COVID-19) has been associated with a large variety of neurological disorders. However the mechanisms underlying these neurological complications remain elusive. In this study we aimed at determining whether neurological symptoms were caused by SARS-CoV-2 direct infection of by pro-inflammatory mediators. Methods: We checked for SARS-CoV-2 RNA by RT-qPCR, SARS-CoV-2-specific antibodies and for 48 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluids (CSF) +/- sera of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological control patients (inflammatory [IND], non inflammatory [NIND], multiple sclerosis [MS]). Results: We found SARS-CoV-2 RNA and antibodies specific for this virus in the CSF of 0/17 and 8/16 COVID-19 patients, respectively. The presence of SARS-CoV-2 antibodies was explained by a rupture of the blood brain barrier (passive transfer) in 6/16 (38%). An intrathecal synthesis of SARS-CoV2-specific antibodies was present in 2/16 patients. Of the four categories of tested patients, the CSF of IND exhibited the highest level of chemokines (CCL4, CCL5, CXCL8, CXCL10, CXCL12, and CXCL13), followed by the CSF of MS patients (CXCL12, and CXCL13). There was no significant difference between COVID-19 and NIND patients, even if some chemokines (CCL4, CCL5, CXCL8, andCXCL10) tended to be higher in the former. Interestingly, among COVD-19 patients, the CSF of those with a severe disease (encephalitis/encephalopathy) contained higher levels CXCL8 and CXCL10 than those with other neurological presentations. Interpretation: Our results do not show obvious SARS-CoV-2 infection of the central nervous system, but point to a mild inflammatory reaction reflecting an astrocytic reaction. Methods: We checked for SARS-CoV-2 mRNA by qPCR, SARS-CoV-2-specific antibodies and for 49 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluid (CSF) +/- serum of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological controls (inflammatory, non inflammatory, multiple sclerosis). Results: We found SARS-CoV-2 mRNA and antibodies specific for this virus in the CSF of 0/17 and 8/16 COVID-19 patients, respectively. The presence of SARS-CoV-2 antibodies was explained by a rupture of the blood brain barrier (passive transfer) in 6/16 (37,5%), but an intrathecal synthesis of SARS-CoV2-specific antibodies was present in 2/17.As compared to SARS-CoV-2-negative NIND patients, the CSF of IND patients exhibited the highest level of chemokines (CCL4, CCL5, CXCL8, CXCL10, CXCL12, and CXCL13), followed the CSF of MS patients (CXCL12, and CXCL13). There was no difference between COVID-19 patients with neurological diseases compared to NIND even if some chemokines (CCL4, CCL5, CXCL8, andCXCL10) tended to be higher than NIND. Interestingly, among COVD-19 patients, the CSF of those with a severe disease (encephalitis/encephalopathy) contained higher levels CXCL8 and CXCL10 than those with other neurological presentations. Interpretation: Our results confirm the absence of obvious SARS-CoV-2 infection of the central nervous system and point to a mild inflammatory reaction reflecting an astrocytic reaction. url: http://medrxiv.org/cgi/content/short/2020.11.01.20217497v1?rss=1 doi: 10.1101/2020.11.01.20217497 id: cord-288484-qy619tfg author: Bernard‐Valnet, R. title: Two patients with acute meningoencephalitis concomitant with SARS‐CoV‐2 infection date: 2020-05-30 words: 1138.0 sentences: 73.0 pages: flesch: 40.0 cache: ./cache/cord-288484-qy619tfg.txt txt: ./txt/cord-288484-qy619tfg.txt summary: We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. Patient 1 was a 64-year-old woman without psychiatric history, known to have had contact with SARS-CoV-2 (her husband tested positive 15 days before) and presenting for 5 days with flu-like symptoms (mild asthenia, myalgia, cough) without fever, acutely developed psychotic symptoms. Cerebral magnetic resonance imaging was normal, but her lumbar puncture was compatible with viral meningoencephalitis (Table 1) and SARS-CoV-2 was detected in her nasopharyngeal swab. A 67-year-old woman, already diagnosed with SARS-CoV-2 infection for 17 days with mild respiratory symptoms, presented an intense wake-up headache. However, CSF SARS-CoV-2 and viral/bacterial pathogen polymerase chain reaction tests were negative (Table 1 ). To conclude, we report the first temporal association between acute SARS-CoV-2 infection and aseptic encephalitis with focal neurological symptoms and signs. abstract: In December 2019, a cluster of patients with pneumonia of unknown cause led to the identification of a new strain of pandemic coronavirus called Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS-CoV outbreak, human coronaviruses are known for their neurological tropism. If respiratory complications are at the forefront of clinical presentation of SARS-CoV-2, neurological involvement remains poorly described and understood. We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. url: https://doi.org/10.1111/ene.14298 doi: 10.1111/ene.14298 id: cord-291156-zxg3dsm3 author: Bernasconi, Anna title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 words: 4600.0 sentences: 206.0 pages: flesch: 38.0 cache: ./cache/cord-291156-zxg3dsm3.txt txt: ./txt/cord-291156-zxg3dsm3.txt summary: We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. abstract: The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research. In addition to VCM, we also illustrate the data dictionary for patient’s phenotype used by the COVID-19 Host Genetic Initiative. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information. url: https://doi.org/10.1101/2020.04.29.067637 doi: 10.1101/2020.04.29.067637 id: cord-299449-226dd23u author: Bernhardt, Denise title: Neuro-oncology Management During the COVID-19 Pandemic With a Focus on WHO Grade III and IV Gliomas date: 2020-05-05 words: 4200.0 sentences: 221.0 pages: flesch: 45.0 cache: ./cache/cord-299449-226dd23u.txt txt: ./txt/cord-299449-226dd23u.txt summary: It is acknowledged that the SARS-CoV-2 pandemic will require center specific discussions of appropriate resource allocation that considers patient and provider safety, resource constraints, and a realistic evaluation of the impact of therapy upon Incurable brain tumors. This international multidisciplinary group of experts in HGG provides a risk-adapted framework for decisions in both pandemic scenarios, considering both ethical issues and resource constraints, in order to minimize the irreparable damage associated with withholding necessary treatments. We recognize that during the pandemic the challenges of ICU capacity, conservation of PPE, availability of health care professional expertise and the risk for patients'' exposure to SARS-CoV-2 may reduce the ability to provide optimal surgical management. Patients and caregivers should be included in the decision-making process as much as possible, and this should include all relevant data on chemotherapy and radiotherapy, as well as the individual risk profile associated with a potential SARS-CoV-2 infection. abstract: BACKGROUND: Because of the increased risk in cancer patients of developing complications caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), physicians have to balance the competing risks of the negative impact of the pandemic and the primary tumor. In this consensus statement, an international group of experts present mitigation strategies and treatment guidance for patients suffering from high grade gliomas (HGG) during the coronavirus disease 2019 (COVID-19) pandemic. METHOD / RESULTS: 16 international experts in the treatment of HGG contributed to this consensus-based practice recommendation including neuro-oncologists, neurosurgeons, radiation -oncologists and a medical physicist. Generally, treatment of neuro-oncological patients cannot be significantly delayed and initiating therapy should not be outweighed by COVID-19. We present detailed interdisciplinary treatment strategies for molecular subgroups in two pandemic scenarios, a scale-up phase and a crisis phase. CONCLUSION: This practice recommendation presents a pragmatic framework and consensus-based mitigation strategies for the treatment of HGG patients during the SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32369601/ doi: 10.1093/neuonc/noaa113 id: cord-355758-tk7eturq author: Berrio, Alejandro title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 words: 2175.0 sentences: 156.0 pages: flesch: 49.0 cache: ./cache/cord-355758-tk7eturq.txt txt: ./txt/cord-355758-tk7eturq.txt summary: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. abstract: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. Thermodynamic modeling of RNA stability and structure, however, indicates that RNA secondary structure within both genes in the SARS-CoV-2 genome differs from those of RaTG13, the reconstructed common ancestor, and Pan-CoV-GD (Guangdong). These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle. url: https://doi.org/10.1101/2020.09.16.300038 doi: 10.1101/2020.09.16.300038 id: cord-301974-4wn40ivq author: Berry, Jody D title: Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus date: 2004-09-01 words: 5877.0 sentences: 293.0 pages: flesch: 51.0 cache: ./cache/cord-301974-4wn40ivq.txt txt: ./txt/cord-301974-4wn40ivq.txt summary: A total of 15 l of SARS-CoV antigen (infected Vero cell lysate) or 5 g of highly purified virus is coated (per spot) for 1 h at 37 • C. c Protein specificity tests shown here were determined by Western immunoblot with purified virus and infected cell lysate under denaturing conditions (Fig. 1) . The four Western immunoblot negative, virus-neutralising mAbs were tested for their ability to bind native SARS-CoV in infected cells by immunofluorescence assay. While purified virus is clearly the optimal antigen tested in this series of experiments, the lower quality SARS-CoV-infected Vero cell lysates are, however, much easier to prepare for diagnostic assays. This paper describes the development of murine mAbs which recognise SARS-CoV antigens in ELISA, immuno-dotblot, Western immunoblot, on the surface of infected cells, and in neutralisation assays. abstract: There is a global need to elucidate protective antigens expressed by the SARS-coronavirus (SARS-CoV). Monoclonal antibody reagents that recognise specific antigens on SARS-CoV are needed urgently. In this report, the development and immunochemical characterisation of a panel of murine monoclonal antibodies (mAbs) against the SARS-CoV is presented, based upon their specificity, binding requirements, and biological activity. Initial screening by ELISA, using highly purified virus as the coating antigen, resulted in the selection of 103 mAbs to the SARS virus. Subsequent screening steps reduced this panel to seventeen IgG mAbs. A single mAb, F26G15, is specific for the nucleoprotein as seen in Western immunoblot while five other mAbs react with the Spike protein. Two of these Spike-specific mAbs demonstrate the ability to neutralise SARS-CoV in vitro while another four Western immunoblot-negative mAbs also neutralise the virus. The utility of these mAbs for diagnostic development is demonstrated. Antibody from convalescent SARS patients, but not normal human serum, is also shown to specifically compete off binding of mAbs to whole SARS-CoV. These studies highlight the importance of using standardised assays and reagents. These mAbs will be useful for the development of diagnostic tests, studies of SARS-CoV pathogenesis and vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/15234813/ doi: 10.1016/j.jviromet.2004.04.009 id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 words: 7477.0 sentences: 379.0 pages: flesch: 40.0 cache: ./cache/cord-335567-ssnvr6nj.txt txt: ./txt/cord-335567-ssnvr6nj.txt summary: In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients abstract: The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001. url: https://doi.org/10.3390/v7030996 doi: 10.3390/v7030996 id: cord-284191-05djnz4p author: Bert, Nina Le title: Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date: 2020-05-27 words: 1944.0 sentences: 103.0 pages: flesch: 53.0 cache: ./cache/cord-284191-05djnz4p.txt txt: ./txt/cord-284191-05djnz4p.txt summary: To study SARS-CoV-2 specific T cells associated with viral clearance, we collected peripheral blood of 24 individuals who recovered from mild to severe COVID-19 (demographic, clinical and virological information are summarized in Extended Data Table 1 ) and studied the T cell response against selected structural (nucleocapsid protein-NP) and non-structural proteins (NSP7 and NSP13 of ORF1) of the large SARS-CoV-2 proteome ( Figure 1A) . To confirm and further delineate the multispecificity of the NP-specific T cell response detected ex vivo in COVID-19 recovered patients, we defined in nine individuals, the distinctive sections of NP targeted by T cells. This is consistent with the findings of Grifoni et al 11 : using selected peptides, they detected ORF-1 specific T preferentially in some SARS-CoV-2 unexposed donors while T cells of COVID-19 recovered donors preferentially recognized structural proteins. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals abstract: Memory T cells induced by previous infections can influence the course of new viral infections. Little is known about the pattern of SARS-CoV-2 specific pre-existing memory T cells in human. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of ORF1) regions of SARS-CoV-2 in convalescent from COVID-19 (n=24). In all of them we demonstrated the presence of CD4 and CD8 T cells recognizing multiple regions of the NP protein. We then show that SARS-recovered patients (n=23), 17 years after the 2003 outbreak, still possess long-lasting memory T cells reactive to SARS-NP, which displayed robust cross-reactivity to SARS-CoV-2 NP. Surprisingly, we observed a differential pattern of SARS-CoV-2 specific T cell immunodominance in individuals with no history of SARS, COVID-19 or contact with SARS/COVID-19 patients (n=18). Half of them (9/18) possess T cells targeting the ORF-1 coded proteins NSP7 and 13, which were rarely detected in COVID-19- and SARS-recovered patients. Epitope characterization of NSP7-specific T cells showed recognition of protein fragments with low homology to “common cold” human coronaviruses but conserved among animal betacoranaviruses. Thus, infection with betacoronaviruses induces strong and long-lasting T cell immunity to the structural protein NP. Understanding how pre-existing ORF-1-specific T cells present in the general population impact susceptibility and pathogenesis of SARS-CoV-2 infection is of paramount importance for the management of the current COVID-19 pandemic. url: https://doi.org/10.1101/2020.05.26.115832 doi: 10.1101/2020.05.26.115832 id: cord-262863-f07v5uk8 author: Bertocchi, Ilaria title: The hidden role of NLRP3 inflammasome in obesity‐related COVID‐19 exacerbations: lessons for drug repurposing date: 2020-08-09 words: 5438.0 sentences: 252.0 pages: flesch: 30.0 cache: ./cache/cord-262863-f07v5uk8.txt txt: ./txt/cord-262863-f07v5uk8.txt summary: We and others have demonstrated that NLRP3 inflammasome over-activation is involved not only in the pathogenesis of diabesity, but also in the exacerbation of related cardiovascular injuries, including myocardial infarction, and this process is associated to an increase in the local inflammatory response. Similarly, the diabesityrelated basal activation of the NLRP3 inflammasome cascade, leading to increase in either gastrointestinal or vascular permeability, may contribute to exacerbate SARS-CoV-2 systemic diffusion and enhance the intricate mechanisms of intracellular cross talk operational in the pathogenesis of COVID-19. Up to nowadays six clinical trials (NCT04347980, NCT04325061, NCT04395105, NCT04344730, NCT04360876, NCT04327401), reported on clinicaltrials.gov are recruiting patients to test the efficacy of the corticosteroid dexamethasone, whose beneficial effects in airway inflammation has been recently demonstrated to involve lung inhibition of the activity of NLRP3 inflammasome and the release of IL-1β and IL-18 (Guan, Ma, Fan, Chen, Miao & Wu, 2020) . abstract: COVID‐19, the illness caused by SARS‐CoV‐2, has a wide‐ranging clinical spectrum that, in the worst‐case scenario, involves a rapid progression to severe acute respiratory syndrome and even death. Epidemiological data show that obesity and diabetes are among the main risk factors associated with high morbidity and mortality. The increased susceptibility to SARS‐CoV‐2 infection documented in obesity‐related metabolic derangements argues for initial defects in defense mechanisms, most likely due to an elevated systemic metabolic inflammation (“metaflammation”). The NLRP3 inflammasome is a master regulator of metaflammation and has a pivotal role in the pathophysiology of either obesity and diabetes. Here, we discuss the most recent findings suggesting contribution of NLRP3 inflammasome to the increase in complications in COVID‐19 patients with diabesity. We also review current pharmacological strategies for COVID‐19, focusing on treatments whose efficacy could be due, at least in part, to interference with the activation of the NLRP3 inflammasome. url: https://www.ncbi.nlm.nih.gov/pubmed/32776354/ doi: 10.1111/bph.15229 id: cord-280280-9jr7ekbu author: Bertoncelli, Deborah title: COVID19: potential cardiovascular issues in pediatric patients date: 2020-05-11 words: 3393.0 sentences: 181.0 pages: flesch: 36.0 cache: ./cache/cord-280280-9jr7ekbu.txt txt: ./txt/cord-280280-9jr7ekbu.txt summary: Ongoing studies and accumulated data are detailing the features and the effects of the new coronavirus disease 19 (COVID 19) in the adult population, and cardiovascular involvement is emerging as the most significant and life-threatening complication, with an increased risk of morbidity and mortality in patients with underlying cardiovascular disease. At present, though the limited data on the effects of COVID 19 in pediatric patients, children seem to count for a little proportion of SARS-COV 2 infection, and present with less severe disease and effects However infants and toddlers are at risk of developing critical course. Coronavirus disease 19 (COVID-19) is a severe acute respiratory syndrome for which the etiologic agent is the novel beta coronavirus SARS-CoV-2, first described in December 2019 in China in a cluster of patients presenting with pneumonia. The main presenting clinical feature of the disease is pneumonia, ranging from asymptomatic or mildly symptomatic to severe acute respiratory distress syndrome, but cardiovascular involvement is emerging as one of the most significant and life-threatening complications of SARS-CoV-2 infection (1, 2) . abstract: The novel severe acute respiratory syndrome coronavirus 2 (SARS-COV 2) has rapidly spread worldwide with increasing hospitalization and mortality rate. Ongoing studies and accumulated data are detailing the features and the effects of the new coronavirus disease 19 (COVID 19) in the adult population, and cardiovascular involvement is emerging as the most significant and life-threatening complication, with an increased risk of morbidity and mortality in patients with underlying cardiovascular disease. At present, though the limited data on the effects of COVID 19 in pediatric patients, children seem to count for a little proportion of SARS-COV 2 infection, and present with less severe disease and effects However infants and toddlers are at risk of developing critical course. The disease has a range of clinical presentations in children, for which the potential need for further investigation of myocardial injury and cardiovascular issues should be kept in mind to avoid misdiagnosing severe clinical entities. Overlapping with Kawasaki disease is a concern, particularly the incomplete and atypical form. We aim to summarize the initial considerations and potential cardiovascular implications of COVID-19 for children and patients with congenital heart disease. (www.actabiomedica.it) url: https://doi.org/10.23750/abm.v91i2.9655 doi: 10.23750/abm.v91i2.9655 id: cord-298967-vjyh1xvh author: Bertossi, Dario title: Safety guidelines for non‐surgical facial procedures during covid‐19 outbreak date: 2020-06-07 words: 2005.0 sentences: 130.0 pages: flesch: 51.0 cache: ./cache/cord-298967-vjyh1xvh.txt txt: ./txt/cord-298967-vjyh1xvh.txt summary: METHODS: A virtual meeting was conducted with the members (n=12) of the European Academy of Facial Plastic Surgery Focus Group to outline the safety protocol for the non‐surgical facial aesthetic procedures for aesthetic practices in order to protect the clinic staff and the patients from SARS‐CoV‐2 infection. While many medical Accepted Article practices are being run with online consultations 10 , some countries have recently decided to allow the opening of practices requiring one-on-one contact like dental, physiotherapy, for emergencies provided they strictly follow the guidelines detailing the infection control measures [12] [13] . In our largely elective field, both staff and resources should ideally be allocated through careful protocols in order to prevent COVID-19 infection. In response to this pandemic, our focus group has developed a process to stratify procedures and clinical levels with protocols that aim to minimize the risk of contagion and the diffusion of COVID-19 infection. abstract: BACKGROUND: The novel coronavirus (COVID‐19) pandemic is expected to last for an extended time, making strict safety precautions for office procedures unavoidable. The lockdown is going to be lifted in many areas, and strict guidelines detailing the infection control measures for aesthetic clinics are going to be of particular importance. METHODS: A virtual meeting was conducted with the members (n=12) of the European Academy of Facial Plastic Surgery Focus Group to outline the safety protocol for the non‐surgical facial aesthetic procedures for aesthetic practices in order to protect the clinic staff and the patients from SARS‐CoV‐2 infection. The data analysis was undertaken by thematic and iterative approach. RESULTS: Consensus guidelines for non‐surgical facial aesthetic procedures based on current knowledge are provided for three levels: precautions before visiting the clinic, precautions during the clinic visit, and precautions after the clinic visit. CONCLUSIONS: Sound infection control measures are mandatory for non‐surgical aesthetic practices all around the world. These may vary from country to country, but this logical approach can be customized according to the respective country laws and guidelines. url: https://www.ncbi.nlm.nih.gov/pubmed/32506541/ doi: 10.1111/jocd.13530 id: cord-333763-45dzsn2j author: Bestle, Dorothea title: TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells date: 2020-07-23 words: 8969.0 sentences: 441.0 pages: flesch: 49.0 cache: ./cache/cord-333763-45dzsn2j.txt txt: ./txt/cord-333763-45dzsn2j.txt summary: The data demonstrate that efficient inhibition of S cleavage by a combination of TMPRSS2 and furin inhibitors can dramatically block SARS-CoV-2 replication in human airway epithelial cells. In conclusion, our data demonstrate that both TMPRSS2 and furin cleave the SARS-CoV-2 S protein and are essential for efficient virus multicycle replication in Calu-3 human airway cells. Virus titers in supernatants were determined by TCID 50 multicycle replication of SARS-CoV-2 in Calu-3 human airway cells is strongly suppressed by inhibiting TMPRSS2 and furin activity, demonstrating that both proteases are crucial for S activation in these cells. Together, our data indicate that furin and TMPRSS2 cleave S at different sites and that cleavage by both proteases is crucial to render the S protein active for mediating virus entry and membrane fusion (Fig 6) . abstract: The novel emerged SARS-CoV-2 has rapidly spread around the world causing acute infection of the respiratory tract (COVID-19) that can result in severe disease and lethality. For SARS-CoV-2 to enter cells, its surface glycoprotein spike (S) must be cleaved at two different sites by host cell proteases, which therefore represent potential drug targets. In the present study, we show that S can be cleaved by the proprotein convertase furin at the S1/S2 site and the transmembrane serine protease 2 (TMPRSS2) at the S2′ site. We demonstrate that TMPRSS2 is essential for activation of SARS-CoV-2 S in Calu-3 human airway epithelial cells through antisense-mediated knockdown of TMPRSS2 expression. Furthermore, SARS-CoV-2 replication was also strongly inhibited by the synthetic furin inhibitor MI-1851 in human airway cells. In contrast, inhibition of endosomal cathepsins by E64d did not affect virus replication. Combining various TMPRSS2 inhibitors with furin inhibitor MI-1851 produced more potent antiviral activity against SARS-CoV-2 than an equimolar amount of any single serine protease inhibitor. Therefore, this approach has considerable therapeutic potential for treatment of COVID-19. url: https://doi.org/10.26508/lsa.202000786 doi: 10.26508/lsa.202000786 id: cord-296440-18vpg419 author: Beurnier, Antoine title: Characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who require hospitalisation date: 2020-07-30 words: 3554.0 sentences: 206.0 pages: flesch: 49.0 cache: ./cache/cord-296440-18vpg419.txt txt: ./txt/cord-296440-18vpg419.txt summary: The objective of this study was to investigate the characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who required hospitalisation during the spring 2020 outbreak in Paris, France. As the world faces the coronavirus disease 2019 (COVID-19) pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, concerns have arisen about a possible increased risk of asthma exacerbations. In Wuhan, authors pointed out a rate of 0.9% [3] , markedly lower than that in the local population; in another study investigating the clinical characteristics and allergy status of 140 patients infected by SARS-CoV-2 in Wuhan, no patient were reported as being asthmatic [3] . All adult patients hospitalized from March 15, 2020 to April 15, 2020 with a diagnosis of SARS-CoV-2 infection and reporting a history of asthma were included. Moreover, obesity, hypertension and diabetes were the most common comorbidities observed in our cohort of hospitalized asthmatics with COVID-19, which is consistent with earlier research in other patient groups [4] [23] . abstract: BACKGROUND: Viral respiratory infections are the main causes of asthma exacerbation. The susceptibility of asthmatics to develop an exacerbation when they present with severe pneumonia due to SARS-CoV-2 infection is unknown. The objective of this study was to investigate the characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who required hospitalisation during the spring 2020 outbreak in Paris, France. METHODS: A prospective cohort follow-up was carried out from March 15 to April 15, 2020 in Bicêtre Hospital, University Paris-Saclay, France. All hospitalised patients with a SARS-CoV-2 infection who reported a history of asthma were included. RESULTS: Among 768 hospitalised patients, 37 (4.8%) reported a history of asthma, which had been previously confirmed by a pulmonologist in 85% of cases. Patients were mainly female (70%), non-smokers (85%), with a median age of 54 years (interquartile range, IQR 42–67). None of them presented with an asthma exacerbation. Twenty-two (59%) had major comorbidities and 31 (84%) had a body mass index ≥25 kg·m(−2). The most common comorbidities were obesity (36%), hypertension (27%) and diabetes (19%). All patients had a confirmed diagnosis of COVID-19 pneumonia on computed tomography of the chest. Eosinopenia was a typical biologic feature with a median count of 0/mm3 (IQR 0–0). Eleven patients (30%) were admitted in intensive care unit with three death (8.1%) occurring in the context of comorbidities. CONCLUSION: Asthmatics were not overrepresented among patients with severe pneumonia due to SARS-CoV-2 infection who required hospitalisation. Worst outcomes were observed mainly in patients with major comorbidities. url: https://doi.org/10.1183/13993003.01875-2020 doi: 10.1183/13993003.01875-2020 id: cord-285896-lb8toc1m author: Beurton, Alexandra title: Limiting positive end-expiratory pressure to protect renal function in SARS-CoV-2 critically ill patients date: 2020-07-10 words: 1013.0 sentences: 66.0 pages: flesch: 55.0 cache: ./cache/cord-285896-lb8toc1m.txt txt: ./txt/cord-285896-lb8toc1m.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related pneumonia is a risk factor for acute respiratory distress syndrome (ARDS) and acute kidney injury (AKI) [1, 2] . Herein, we report our experience in SARS-CoV-2 critically ill patients before and after having modified our practices in the view of the high occurrence of AKI that needed renal replacement therapy (RRT) in the first cases we managed. During "period 1" (between 04 and 15 March 2020), all mechanically ventilated patients with confirmed SARS-CoV-2 admitted to our intensive care unit received volume-controlled ventilation with a tidal volume of 6 ml/kg of ideal body weight and PEEP stepwise increased to reach a plateau pressure below 28 cmH 2 O. Our findings suggest that changing our practices was associated with a decreased need for RRT and a lower proportion of patients with AKI KDIGO 3. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0883944120306110?v=s5 doi: 10.1016/j.jcrc.2020.07.008 id: cord-283310-5wam14aa author: Bevova, M. R. title: The New Coronavirus COVID-19 Infection date: 2020-09-09 words: 4812.0 sentences: 248.0 pages: flesch: 52.0 cache: ./cache/cord-283310-5wam14aa.txt txt: ./txt/cord-283310-5wam14aa.txt summary: Later, the pneumonia was associated with a new coronavirus; in February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus causing it. In February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus. The estimation of the case-fatality rate (portion of deaths divided by the total number of cases) for the disease varies from 1 to 7% [24, 25] depending on the sex and age composition of the population; strategies of testing, diagnostics, and treatment; bureaucratic peculiarities of healthcare in a particular country; and congestion of healthcare systems. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: In December 2019, the first cases of pneumonia of unknown etiology were found in Wuhan (China). Later, the pneumonia was associated with a new coronavirus; in February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus causing it. By March 11, 2020, when the virus had spread to 114 countries, the number of diagnosed patients had reached 118 thousand and the number of deaths was 4000, the WHO declared the outbreak of the disease a pandemic. In this review, we summarize the relevant information about the origin and spread of SARS-CoV-2, its epidemiology and diagnostics, and the clinical course and treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32929302/ doi: 10.3103/s0891416820020044 id: cord-304660-w7rs2dvt author: Bharadwaj, Shiv title: SARS-CoV-2 M(pro) inhibitors: identification of anti-SARS-CoV-2 M(pro) compounds from FDA approved drugs date: 2020-11-05 words: 4854.0 sentences: 242.0 pages: flesch: 46.0 cache: ./cache/cord-304660-w7rs2dvt.txt txt: ./txt/cord-304660-w7rs2dvt.txt summary: The top 10 screened potential compounds against SARS-CoV-2 M(pro) were then studied by re-docking, binding affinity, intermolecular interaction, and complex stability via 100 ns all atoms molecular dynamics (MD) simulation followed by post-simulation analysis, including end point binding free energy, essential dynamics, and residual correlation analysis against native crystal structure ligand N3 inhibitor. Hence, comparative molecular docking analysis of screened FDA approved drugs against N3 inhibitor suggested the potential of selected drugs to inhibit SARS-CoV-2 M pro by formation of hydrogen and non-covalent interaction with its catalytic dyad and substrate binding residues. Based on the combinatorial computational analysis, including structure-based virtual screening, molecular docking, binding free energy calculations, MD simulation and post-MD simulation analysis for the screened FDA drugs with viral protease, suggested the drugs, R428, Teniposide, VS-5584, and Setileuton with comparatively higher stability and affinity with SARS-CoV-2 M pro against N3 inhibitor via strong intermolecular interactions formation as well disturbing the conformation of viral protease active pocket. abstract: Recent outbreak of COVID-19 pandemic caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has raised serious global concern for public health. The viral main 3-chymotrypsin-like cysteine protease (M(pro)), known to control coronavirus replication and essential for viral life cycle, has been established as an essential drug discovery target for SARS-CoV-2. Herein, we employed computationally screening of Druglib database containing FDA approved drugs against active pocket of SARS-CoV-2 M(pro )using MTiopen screen web server, yields a total of 1051 FDA approved drugs with docking energy >−7 kcal/mol. The top 10 screened potential compounds against SARS-CoV-2 M(pro) were then studied by re-docking, binding affinity, intermolecular interaction, and complex stability via 100 ns all atoms molecular dynamics (MD) simulation followed by post-simulation analysis, including end point binding free energy, essential dynamics, and residual correlation analysis against native crystal structure ligand N3 inhibitor. Based on comparative molecular simulation and interaction profiling of the screened drugs with SARS-CoV-2 M(pro )revealed R428 (−10.5 kcal/mol), Teniposide (−9.8 kcal/mol), VS-5584 (−9.4 kcal/mol), and Setileuton (−8.5 kcal/mol) with stronger stability and affinity than other drugs and N3 inhibitor; and hence, these drugs are advocated for further validation using in vitro enzyme inhibition and in vivo studies against SARS-CoV-2 infection. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1842807 doi: 10.1080/07391102.2020.1842807 id: cord-256307-2b1vlda8 author: Bhardwaj, Vijay Kumar title: Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs date: 2020-11-12 words: 4556.0 sentences: 292.0 pages: flesch: 52.0 cache: ./cache/cord-256307-2b1vlda8.txt txt: ./txt/cord-256307-2b1vlda8.txt summary: RESULTS: The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated deep inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). The selected DSPD molecules (DSPD-1 to 6) were compared on different computational parameters (Docking energy, RMSD, protein-ligand interactions, MM-PBSA binding energy, Contribution energy, and SASA) to repurposed FDA approved antiviral drugs. The inbuilt published tools (ADMET and Toxicity Prediction by Komputer Assisted Technology (TOPKAT) module) and models such as the CYP2D6 Prediction, Hepatotoxic Prediction, PPB Prediction, Solubility Level, Absorption Level, 2D Polar Surface Area, AlogP98, Rat Female NTP Prediction, Rat Male NTP Prediction, Carcinogenic Potency TD50 Rat, Rat Oral LD50, Ames Prediction, DTP Prediction, Skin Irritant, and Skin Sensitization in the discovery J o u r n a l P r e -p r o o f studio package were used to calculate and analyze the pharmacokinetic profiles of DSPD molecules along with the selected FDA approved drugs [31, 32] . abstract: BACKGROUND: The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals. METHODS: We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules. RESULTS: The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated deep inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket. CONCLUSION: The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro. url: https://www.sciencedirect.com/science/article/pii/S0010482520304480?v=s5 doi: 10.1016/j.compbiomed.2020.104117 id: cord-353116-7t1prfkr author: Bhargava, Ashish title: Predictors for Severe COVID-19 Infection date: 2020-05-30 words: 2635.0 sentences: 188.0 pages: flesch: 55.0 cache: ./cache/cord-353116-7t1prfkr.txt txt: ./txt/cord-353116-7t1prfkr.txt summary: BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. abstract: BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Predictors for severe COVID-19 infection have not been well defined. Determination of risk factors for severe infection would enable identifying patients who may benefit from aggressive supportive care and early intervention. METHODS: We conducted a retrospective observational study of 197 patients with confirmed COVID-19 infection admitted to a tertiary academic medical center. RESULTS: Of 197 hospitalized patients, the mean (SD) age of the cohort was 60.6 (16.2) years, 103 (52.3%) were male and 156 (82.1%) were black. Severe COVID-19 infection was noted in 74 (37.6%) patients, requiring intubation. Patients aged above 60 were significantly more likely to have severe infection. Patients with severe infection were significantly more likely to have diabetes, renal disease, chronic pulmonary disease and had significantly higher white blood cell counts, lower lymphocyte counts, and increased C-reactive protein (CRP) compared to patients with non-severe infection. In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). Race, age and socioeconomic status were not identified as independent predictors. CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. Every 1 unit increase in CRP increased the risk of severe disease by 0.06%. url: https://www.ncbi.nlm.nih.gov/pubmed/32472676/ doi: 10.1093/cid/ciaa674 id: cord-264653-ms6zrrnd author: Bhatnagar, Tarun title: Lopinavir/ritonavir combination therapy amongst symptomatic coronavirus disease 2019 patients in India: Protocol for restricted public health emergency use date: 2020-04-28 words: 2709.0 sentences: 163.0 pages: flesch: 48.0 cache: ./cache/cord-264653-ms6zrrnd.txt txt: ./txt/cord-264653-ms6zrrnd.txt summary: In view of the earlier evidence about effectiveness of repurposed lopinavir/ritonavir against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as preliminary docking studies conducted by the ICMR-National Institute of Virology, Pune, the Central Drugs Standard Control Organization approved the restricted public health use of lopinavir/ritonavir combination amongst symptomatic COVID-19 patients detected in the country. Hospitalized adult patients with laboratory-confirmed SARS-CoV-2 infection with any one of the following criteria will be eligible to receive lopinavir/ritonavir for 14 days after obtaining written informed consent: (i) respiratory distress with respiratory rate ≥22/min or SpO(2) of <94 per cent; (ii) lung parenchymal infiltrates on chest X-ray; (iii) hypotension defined as systolic blood pressure <90 mmHg or need for vasopressor/inotropic medication; (iv) new-onset organ dysfunction; and (v) high-risk groups age >60 yr, diabetes mellitus, renal failure, chronic lung disease and immunocompromised persons. abstract: As of February 29, 2020, more than 85,000 cases of coronavirus disease 2019 (COVID-19) have been reported from China and 53 other countries with 2,924 deaths. On January 30, 2020, the first laboratory-confirmed case of COVID was reported from Kerala, India. In view of the earlier evidence about effectiveness of repurposed lopinavir/ritonavir against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as preliminary docking studies conducted by the ICMR-National Institute of Virology, Pune, the Central Drugs Standard Control Organization approved the restricted public health use of lopinavir/ritonavir combination amongst symptomatic COVID-19 patients detected in the country. Hospitalized adult patients with laboratory-confirmed SARS-CoV-2 infection with any one of the following criteria will be eligible to receive lopinavir/ritonavir for 14 days after obtaining written informed consent: (i) respiratory distress with respiratory rate ≥22/min or SpO(2) of <94 per cent; (ii) lung parenchymal infiltrates on chest X-ray; (iii) hypotension defined as systolic blood pressure <90 mmHg or need for vasopressor/inotropic medication; (iv) new-onset organ dysfunction; and (v) high-risk groups - age >60 yr, diabetes mellitus, renal failure, chronic lung disease and immunocompromised persons. Patients will be monitored to document clinical (hospital length of stay and mortality at 14, 28 and 90 days), laboratory (presence of viral RNA in serial throat swab samples) and safety (adverse events and serious adverse events) outcomes. Treatment outcomes amongst initial cases would be useful in providing guidance about the clinical management of patients with COVID-19. If found useful in managing initial SARS-CoV-2-infected patients, further evaluation using a randomized control trial design is warranted to guide future therapeutic use of this combination. url: https://doi.org/10.4103/ijmr.ijmr_502_20 doi: 10.4103/ijmr.ijmr_502_20 id: cord-345106-5szz1et3 author: Bhattacharya, D. D. title: Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2 date: 2020-09-11 words: 2348.0 sentences: 176.0 pages: flesch: 63.0 cache: ./cache/cord-345106-5szz1et3.txt txt: ./txt/cord-345106-5szz1et3.txt summary: Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Total RNA was isolated from the SARS-CoV-2-infected saliva samples using QIAamp Viral preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.09.11.20192591 doi: medRxiv preprint A total number of 53 subjects were tested positive both in NPS and saliva assay, whereas 5 samples were found only as NPS positive (Table 1) Statistically, we detected lower C T value for ORF1 gene in the saliva specimens (mean C T = 27.07; 95% confidence interval [CI], 25.62 to 28.52) than in the NPS specimens (mean C T = 28.24; 95% CI, 26.62 to 29.85) (Figure 2A) . abstract: Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings. url: https://doi.org/10.1101/2020.09.11.20192591 doi: 10.1101/2020.09.11.20192591 id: cord-353748-y1a52z8e author: Bhattacharya, Rajarshi title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 words: 3308.0 sentences: 211.0 pages: flesch: 61.0 cache: ./cache/cord-353748-y1a52z8e.txt txt: ./txt/cord-353748-y1a52z8e.txt summary: title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. abstract: Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The molecular interaction of nisin with hACE2 was investigated by homology modeling and docking studies. Further, binding efficiency of the most potent nisin H was evaluated through the interaction of hACE2:nisin H complex with RBD (receptor-binding domain) of SARS-CoV-2 and that of hACE2:RBD complex with nisin H. Here, nisin H acted as a potential competitor of RBD to access the hACE2 receptor. The study unravels for the first time that a globally used food preservative, nisin has the potential to bind to hACE2. url: https://www.sciencedirect.com/science/article/pii/S004268222030204X doi: 10.1016/j.virol.2020.10.002 id: cord-193136-7g6qr73e author: Bhattacharya, Sujit title: Visible Insights of the Invisible Pandemic: A Scientometric, Altmetric and Topic Trend Analysis date: 2020-04-22 words: 5019.0 sentences: 273.0 pages: flesch: 57.0 cache: ./cache/cord-193136-7g6qr73e.txt txt: ./txt/cord-193136-7g6qr73e.txt summary: (2018) "Google Trends shows the changes in online interest for time series in any selected term in any country or region over a selected time period, for example, a specific year, several years, 3 weeks, 4 months, 30 days, 7 days, 4 hours, 1 hour, or a specified time-frame." They argue that as the internet penetration is increasing web based search activity has become a valid indicator of public behaviour. The paper positions itself in this direction; applying various tools and techniques of scientometrics, Altmetrics and Google Trends to draw meaning from the huge volume of research papers and online activity surrounding this pandemic. The trends observed in measures like lockdown, social distancing and quarantine at global and country level showed the societal increasing concern with these aspects.The findings of this study suggests how the research and public interest has been shaped around this disease. abstract: The recent SARS-COV-2 virus outbreak has created an unprecedented global health crisis! The disease is showing alarming trends with the number of people getting infected with this disease, new cases and death rate are all highlighting the need to control this disease at the earliest. The strategy now for the governments around the globe is how to limit the spread of the virus until the research community develops treatment/drug or vaccination against the virus. The outbreak of this disease has unsurprisingly led to huge volume of research within a short period of time surrounding this disease. It has also led to aggressive social media activity on twitter, Facebook, dedicated blogs, news reports and other online sites actively involved in discussing about the various aspects of and related to this disease. It becomes a useful and challenging exercise to draw from this huge volume of research, the key papers that form the research front, its influence in the research community, and other important research insights. Similarly, it becomes important to discern the key issues that influence the society concerning this disease. The paper is motivated by this. It attempts to distinguish which are the most influential papers, the key knowledge base and major topics surrounding the research covered by COVID-19. Further it attempts to capture the society's perception by discerning key topics that are trending online. The study concludes by highlighting the implications of this study. url: https://arxiv.org/pdf/2004.10878v1.pdf doi: nan id: cord-341246-fz66z2p2 author: Bhattacharyya, Pranab J title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection date: 2020-09-28 words: 1298.0 sentences: 84.0 pages: flesch: 48.0 cache: ./cache/cord-341246-fz66z2p2.txt txt: ./txt/cord-341246-fz66z2p2.txt summary: title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection A 32-year-old primigravida at a 38-week gestation was initially admitted in cardiology isolation ward on referral by her local obstetrician for inferolateral ST-segment elevation on ECG (figure 1A) which was obtained for complaints of New York Heart Association functional class II symptoms with palpitations of a 3-day duration. As typified by this index case, TTC can mimic acute ST-segment elevation myocardial infarction and is considered to be a reversible form of cardiomyopathy characterised by a complete recovery of RWMA and LV function within weeks of presentation. 2 This is the first reported case of TTC in pregnancy as a manifestation of SARS-CoV-2 infection during this ongoing pandemic. ► The presentation of takotsubo cardiomyopathy can mimic STsegment elevation myocardial infarction but in the absence of angiographic evidence of significant obstructive coronary artery disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32988978/ doi: 10.1136/bcr-2020-239104 id: cord-254419-qw83atrx author: Bhattacharyya, Rajat title: The Interplay Between Coagulation and Inflammation Pathways in COVID-19-Associated Respiratory Failure: A Narrative Review date: 2020-08-25 words: 5900.0 sentences: 276.0 pages: flesch: 33.0 cache: ./cache/cord-254419-qw83atrx.txt txt: ./txt/cord-254419-qw83atrx.txt summary: This narrative review aims to summarize the current available evidence on the interplay between hypercoagulability, thrombo-inflammation, and pulmonary microvascular thrombosis in COVID-19 infection resulting in respiratory failure and how this information can be used to design clinical trials to optimize patient outcomes. ACE2 angiotensin-converting enzyme 2, CRP C-reactive protein, ESR erythrocyte sedimentation rate, LDH lactate dehydrogenase, NETS neutrophil extracellular traps, SARS-COV-2 severe acute respiratory syndrome coronavirus 2, TMPRSS2 transmembrane protease serine 2 shown to be at higher risk of worse outcomes [13] [14] [15] (Fig. 2) . CHD chronic heart disease, CLD chronic lung disease, CKD chronic kidney disease, DOACS direct oral anticoagulants, FDPs fibrinogen degradation products, HTN hypertension, IFN interferon, JAK Janus kinase, LDH lactate dehydrogenase, LMWH low molecular weight heparin, NSAIDS nonsteroidal anti-inflammatory drugs, PT prothrombin time, TNF tumor necrosis factor, VW Ag Von Willebrand antigen and microvascular thrombosis appears to be responsible for the clinical picture that leads to progressive multi-organ failure in a small percentage of patients, ultimately causing fatalities. abstract: The novel coronavirus disease (COVID-19) pandemic has caused an unprecedented worldwide socio-economic and health impact. There is increasing evidence that a combination of inflammation and hypercoagulable state are the main mechanisms of respiratory failure in these patients. This narrative review aims to summarize currently available evidence on the complex interplay of immune dysregulation, hypercoagulability, and thrombosis in the pathogenesis of respiratory failure in COVID-19 disease. In addition, we will describe the experience of anticoagulation and anti-inflammatory strategies that have been tested. Profound suppression of the adaptive and hyperactivity of innate immune systems with macrophage activation appears to be a prominent feature in this infection. Immune dysregulation together with endotheliitis and severe hypercoagulability results in thromboinflammation and microvascular thrombosis in the pulmonary vasculature leading to severe respiratory distress. Currently, some guidelines recommend the use of prophylactic low molecular weight heparin in all hospitalized patients, with intermediate dose prophylaxis in those needing intensive care, and the use of therapeutic anticoagulation in patients with proven or suspected thrombosis. Strong recommendations cannot be made until this approach is validated by trial results. To target the inflammatory cascade, low-dose dexamethasone appears to be helpful in moderate to severe cases and trials with anti-interleukin agents (e.g., tocilizumab, anakinra, siltuximab) and non-steroidal anti-inflammatory drugs are showing early promising results. Potential newer agents (e.g., Janus kinase inhibitor such as ruxolitinib, baricitinib, fedratinib) are likely to be investigated in clinical trials. Unfortunately, current trials are mostly examining these agents in isolation and there may be a significant delay before evidence-based practice can be implemented. It is plausible that a combination of anti-viral drugs together with anti-inflammatory and anti-coagulation medicines will be the most successful strategy in managing severely affected patients with COVID-19. url: https://doi.org/10.1007/s41030-020-00126-5 doi: 10.1007/s41030-020-00126-5 id: cord-336563-hwemigk7 author: Bhimraj, Adarsh title: Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date: 2020-04-27 words: 8308.0 sentences: 448.0 pages: flesch: 42.0 cache: ./cache/cord-336563-hwemigk7.txt txt: ./txt/cord-336563-hwemigk7.txt summary: Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . abstract: BACKGROUND: There are many pharmacologic therapies that are being used or considered for treatment of COVID-19. There is a need for frequently updated practice guidelines on their use, based on critical evaluation of rapidly emerging literature. OBJECTIVE: Develop evidence-based rapid guidelines intended to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. METHODS: IDSA formed a multidisciplinary guideline panel of infectious disease clinicians, pharmacists, and methodologists with varied areas of expertise. Process followed a rapid recommendation checklist. The panel prioritized questions and outcomes. Then a systematic review of the peer-reviewed and grey literature was conducted. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to assess the certainty of evidence and make recommendations. RESULTS: The IDSA guideline panel agreed on 7 treatment recommendations and provided narrative summaries of other treatments undergoing evaluations. CONCLUSIONS: The panel expressed the overarching goal that patients be recruited into ongoing trials, which would provide much needed evidence on the efficacy and safety of various therapies for COVID-19, given that we could not make a determination whether the benefits outweigh harms for most treatments. url: https://doi.org/10.1093/cid/ciaa478 doi: 10.1093/cid/ciaa478 id: cord-268074-9mact9br author: Bi, Qifang title: Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study date: 2020-04-27 words: 5307.0 sentences: 238.0 pages: flesch: 51.0 cache: ./cache/cord-268074-9mact9br.txt txt: ./txt/cord-268074-9mact9br.txt summary: We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We characterise differences in demographics and severity between cases identified through symptom-based surveillance and monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterise SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval, and observed reproductive number (R). This study is, to our knowledge, the first analysis of SARS-CoV-2 transmission and COVID-19 natural history based on a large primary dataset of cases and close contacts, for which the mode of surveillance (ie, symptom-based versus contact-based) was sufficiently documented and RT-PCR testing was nearly universal. Between Jan 14 and Feb 12, 2020, the Shenzhen CDC confirmed 391 cases of SARS-CoV-2 infection ( of 87) than were those detected through contact-based surveillance (tables 1, 2). abstract: BACKGROUND: Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, prompted heightened surveillance in Shenzhen, China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control measures. METHODS: From Jan 14 to Feb 12, 2020, the Shenzhen Center for Disease Control and Prevention identified 391 SARS-CoV-2 cases and 1286 close contacts. We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We estimated metrics of disease transmission and analysed factors influencing transmission risk. FINDINGS: Cases were older than the general population (mean age 45 years) and balanced between males (n=187) and females (n=204). 356 (91%) of 391 cases had mild or moderate clinical severity at initial assessment. As of Feb 22, 2020, three cases had died and 225 had recovered (median time to recovery 21 days; 95% CI 20–22). Cases were isolated on average 4·6 days (95% CI 4·1–5·0) after developing symptoms; contact tracing reduced this by 1·9 days (95% CI 1·1–2·7). Household contacts and those travelling with a case were at higher risk of infection (odds ratio 6·27 [95% CI 1·49–26·33] for household contacts and 7·06 [1·43–34·91] for those travelling with a case) than other close contacts. The household secondary attack rate was 11·2% (95% CI 9·1–13·8), and children were as likely to be infected as adults (infection rate 7·4% in children <10 years vs population average of 6·6%). The observed reproductive number (R) was 0·4 (95% CI 0·3–0·5), with a mean serial interval of 6·3 days (95% CI 5·2–7·6). INTERPRETATION: Our data on cases as well as their infected and uninfected close contacts provide key insights into the epidemiology of SARS-CoV-2. This analysis shows that isolation and contact tracing reduce the time during which cases are infectious in the community, thereby reducing the R. The overall impact of isolation and contact tracing, however, is uncertain and highly dependent on the number of asymptomatic cases. Moreover, children are at a similar risk of infection to the general population, although less likely to have severe symptoms; hence they should be considered in analyses of transmission and control. FUNDING: Emergency Response Program of Harbin Institute of Technology, Emergency Response Program of Peng Cheng Laboratory, US Centers for Disease Control and Prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/32353347/ doi: 10.1016/s1473-3099(20)30287-5 id: cord-297800-hnx213kp author: Bi, Qifang title: Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts date: 2020-03-04 words: 5363.0 sentences: 279.0 pages: flesch: 54.0 cache: ./cache/cord-297800-hnx213kp.txt txt: ./txt/cord-297800-hnx213kp.txt summary: We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We characterize differences in demographics and severity between cases identified through symptom-based surveillance and the monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterize SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval and observed reproductive number. Based on 48 pairs of cases with a clear infector-infectee relationship and time of symptom onset, we estimate that the serial interval is gamma distributed with mean 6.3 days (95% CI 5.2,7.6) and a standard deviation of 4.2 days (95% CI, 3.1,5.3) ( Figure 2B , Table S2 ). This analysis of early SARS-CoV-2 cases and their close contacts in Shenzhen China, provides insights into the natural history, transmission and control of this disease. abstract: Background Rapid spread of SARS-CoV-2 in Wuhan prompted heightened surveillance in Shenzhen and elsewhere in China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control. Methods The Shenzhen CDC identified 391 SARS-CoV-2 cases from January 14 to February 12, 2020 and 1286 close contacts. We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We estimate metrics of disease transmission and analyze factors influencing transmission risk. Findings Cases were older than the general population (mean age 45) and balanced between males (187) and females (204). Ninety-one percent had mild or moderate clinical severity at initial assessment. Three have died, 225 have recovered (median time to recovery is 21 days). Cases were isolated on average 4.6 days after developing symptoms; contact tracing reduced this by 1.9 days. Household contacts and those travelling with a case where at higher risk of infection (ORs 6 and 7) than other close contacts. The household secondary attack rate was 15%, and children were as likely to be infected as adults. The observed reproductive number was 0.4, with a mean serial interval of 6.3 days. Interpretation Our data on cases as well as their infected and uninfected close contacts provide key insights into SARS-CoV-2 epidemiology. This work shows that heightened surveillance and isolation, particularly contact tracing, reduces the time cases are infectious in the community, thereby reducing R. Its overall impact, however, is uncertain and highly dependent on the number of asymptomatic cases. We further show that children are at similar risk of infection as the general population, though less likely to have severe symptoms; hence should be considered in analyses of transmission and control. url: https://doi.org/10.1101/2020.03.03.20028423 doi: 10.1101/2020.03.03.20028423 id: cord-263123-5y8cc5eb author: Bian, Jingwei title: Anti-RAS drugs and SARS-CoV-2 infection date: 2020-04-28 words: 770.0 sentences: 56.0 pages: flesch: 56.0 cache: ./cache/cord-263123-5y8cc5eb.txt txt: ./txt/cord-263123-5y8cc5eb.txt summary: authors: Bian, Jingwei; Zhao, Rongsheng; Zhai, Suodi; Li, Zijian In addition, ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAS) and plays a key role in cardiovascular disease, especially Here, we present a completely different perspective on the relationship between SARS-CoV-2 infection and ACEI/ARB drugs. Firstly, there is no sufficient evidence to support that ACEIs and ARBs can upregulate the protein expression level of ACE2. Therefore, there is no adequate evidence to support that ACEIs/ARBs increase the risk of the SARS-CoV-2 infection by up-regulating ACE2 protein level. In addition, liver/lymph node-specific and dendritic In summary, there is currently no clear evidence indicating that anti-RAS drugs (ACEIs and ARBs) increase the risk of SARS-CoV-2 infection, as well as target organ injury. There is still no need to recommend the discontinuation of ACEIs/ARBs for hypertensive patients with or at high risk of SARS-CoV-2 infection, or the change to other antihypertensive drugs. Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19 abstract: • There is no enough evidence to indicate that ACEIs and ARBs result in ACE2 upregulation. • The level of ACE2 expression is not completely related with the risk of COVID-19 infection. • There is currently no evidence that ACEI/ARB increase risk for COVID-19 infection from clinical trials. • It is not recommended that COVID-19 patients with hypertension or normal hypertensive patients at risk for exposure to stop using ACEI/ARB or change to other antihypertensive drugs. url: https://doi.org/10.1016/j.apsb.2020.04.013 doi: 10.1016/j.apsb.2020.04.013 id: cord-280662-gakayv6e author: Bian, Jingwei title: Angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 receptor and RAS modulator date: 2020-10-13 words: 5251.0 sentences: 308.0 pages: flesch: 49.0 cache: ./cache/cord-280662-gakayv6e.txt txt: ./txt/cord-280662-gakayv6e.txt summary: Angiotensin-converting enzyme 2 (ACE2) was rapidly identified as the critical functional receptor for SARS-CoV-2. Given that ACE2 functions as both a SARS-CoV-2 receptor and a RAS modulator, the treatment for COVID-19 presents a dilemma of how to limit virus entry but protect ACE2 physiological functions. We propose five novel working modes for functional receptor for SARS-CoV-2 infection and the routes of ACE2-mediated virus entering host cells, as well as its regulatory mechanism. SARS-CoV-2 has been shown to share the same functional receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV) 4, 5 . SARS-CoV S-protein binding facilitates ADAM17-dependent ACE2 shedding and has been shown to induce viral entry into the cell 52 . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: The coronavirus disease 2019 (COVID-19) outbreak is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) was rapidly identified as the critical functional receptor for SARS-CoV-2. ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAS) and plays a key role in the cardiovascular system. Given that ACE2 functions as both a SARS-CoV-2 receptor and a RAS modulator, the treatment for COVID-19 presents a dilemma of how to limit virus entry but protect ACE2 physiological functions. Thus, an in-depth summary of the recent progress of ACE2 research and its relationship to the virus is urgently needed to provide possible solution to the dilemma. Here, we summarize the complexity and interplay between the coronavirus, ACE2 and RAS (including anti-RAS drugs). We propose five novel working modes for functional receptor for SARS-CoV-2 infection and the routes of ACE2-mediated virus entering host cells, as well as its regulatory mechanism. For the controversy of anti-RAS drugs application, we also give theoretical analysis and discussed for drug application. These will contribute to a deeper understanding of the complex mechanisms of underlying the relationship between the virus and ACE2, and provide guidance for virus intervention strategies. url: https://doi.org/10.1016/j.apsb.2020.10.006 doi: 10.1016/j.apsb.2020.10.006 id: cord-299552-rgrm8dil author: Bianchi, Martina title: Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? date: 2020-05-30 words: 2082.0 sentences: 134.0 pages: flesch: 52.0 cache: ./cache/cord-299552-rgrm8dil.txt txt: ./txt/cord-299552-rgrm8dil.txt summary: In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. In this report, a structural comparison between the Sars-CoV-2 surface proteins from different isolates with homologous proteins from closely related viruses such as those from Bat and Pangolin is described. Sars-CoV-2 E sequences differ from the homologous proteins also at positions 55-56, where the dyad Ser-Phe replaces Thr-Val (except in Bat coronavirus isolate BtKY72, accession code KY352407). In this paper, E and M proteins from 797 Sars-CoV-2 genomes have been compared to the counterparts taken from the most closely related virus also to evaluate the potential role of amino acid mutations in the epizootic origin of COVID-19. abstract: The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/32596311/ doi: 10.1155/2020/4389089 id: cord-259261-fmuozy3w author: Bickler, Stephen W. title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date: 2020-06-16 words: 2039.0 sentences: 130.0 pages: flesch: 55.0 cache: ./cache/cord-259261-fmuozy3w.txt txt: ./txt/cord-259261-fmuozy3w.txt summary: title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. We also asked the question if the differentially expressed genes between the oldest and youngest age groups encode proteins that interact with SARS-CoV-2 (see "Methods" section). Our analysis revealed eleven differentially expressed genes between the oldest and youngest age groups that encode proteins known to interact with SARS-CoV-2 (Fig. 3d) . Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts we show that expression of PRR genes and ACE2, the receptor for SARS-CoV-2 vary with age. abstract: Older aged adults and those with pre-existing conditions are at highest risk for severe COVID-19 associated outcomes. Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. Older age was associated with increased expression of PRR genes, ACE2 and four genes that encode proteins that have been shown to interact with SAR2-CoV-2 proteins. Assessment of PRR expression might provide a strategy for stratifying the risk of severe COVID-19 disease at both the individual and population levels. url: https://doi.org/10.1101/2020.06.15.134403 doi: 10.1101/2020.06.15.134403 id: cord-354148-87tpjvs6 author: Bidra, Avinash S. title: Rapid In‐Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Using Povidone‐Iodine Oral Antiseptic Rinse date: 2020-06-16 words: 3069.0 sentences: 177.0 pages: flesch: 49.0 cache: ./cache/cord-354148-87tpjvs6.txt txt: ./txt/cord-354148-87tpjvs6.txt summary: PURPOSE: To investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone‐iodine (PVP‐I) against SARS‐CoV‐2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. MATERIALS AND METHODS: The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) USA‐WA1/2020 strain, virus stock was tested against oral antiseptic solutions consisting of aqueous povidone‐iodine (PVP‐I) as the sole active ingredient. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. abstract: PURPOSE: To investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone‐iodine (PVP‐I) against SARS‐CoV‐2 (‘corona virus’) to mitigate the risk and transmission of the virus in the dental practice. MATERIALS AND METHODS: The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) USA‐WA1/2020 strain, virus stock was tested against oral antiseptic solutions consisting of aqueous povidone‐iodine (PVP‐I) as the sole active ingredient. The PVP‐I was tested at diluted concentrations of 0.5%, 1%, and 1.5%. Test media without any virus was added to 2 tubes of the compounds to serve as toxicity and neutralization controls. Ethanol (70%) was tested in parallel as a positive control, and water only as a negative control. The test solutions and virus were incubated at room temperature (22 ± 2 °C) for time periods of 15 and 30 seconds. The solution was then neutralized by a 1/10 dilution in minimum essential medium (MEM) 2% fetal bovine serum (FBS), 50 µg/mL gentamicin. Surviving virus from each sample was quantified by standard end‐point dilution assay and the log reduction value (LRV) of each compound compared to the negative (water) control was calculated. RESULTS: PVP‐I oral antiseptics at all tested concentrations of 0.5%, 1%, and 1.5%, completely inactivated SARS‐CoV‐2 within 15 seconds of contact. The 70% ethanol control group was unable to completely inactivate SARS‐CoV‐2 after 15 seconds of contact, but was able to inactivate the virus at 30 seconds of contact. CONCLUSIONS: PVP‐I oral antiseptic preparations rapidly inactivated SARS‐CoV‐2 virus in vitro. The viricidal activity was present at the lowest concentration of 0.5 % PVP‐I and at the lowest contact time of 15 seconds. This important finding can justify the use of preprocedural oral rinsing with PVP‐I (for patients and health care providers) may be useful as an adjunct to personal protective equipment, for dental and surgical specialties during the COVID‐19 pandemic. url: https://doi.org/10.1111/jopr.13209 doi: 10.1111/jopr.13209 id: cord-268809-plgip4h6 author: Bielecki, Michel title: Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date: 2020-06-29 words: 2609.0 sentences: 170.0 pages: flesch: 56.0 cache: ./cache/cord-268809-plgip4h6.txt txt: ./txt/cord-268809-plgip4h6.txt summary: We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. To our knowledge, it is unknown if lowering the viral inoculum during infection with SARS-CoV-2 or altering the mode of infection by physical means can affect the clinical course of the disease. Here, we present an outbreak at a Swiss Army Base with two very similar groups infected prior and after the implementation of stringent social distancing and hygiene A c c e p t e d M a n u s c r i p t measures (SDHMs). We describe an outbreak of SARS-CoV-2 infections in young, healthy soldiers in two spatially separated groups with almost identical baseline characteristics but different clinical courses. abstract: BACKGROUND: Social distancing and stringent hygiene seem effective in reducing the number of transmitted virus particles, and therefore the infectivity, of coronavirus disease 2019 (COVID-19) and could alter the mode of transmission of the disease. However, it is not known if such practices can change the clinical course in infected individuals. METHODS: We prospectively studied an outbreak of COVID-19 in Switzerland among a population of 508 predominantly male soldiers with a median age of 21 years. We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. RESULTS: Of the 354 soldiers infected prior to the implementation of social distancing, 30% fell ill from COVID-19. While no soldier in a group of 154, in which infections appeared after implementation of social distancing, developed COVID-19 despite the detection of viral RNA in the nose and virus-specific antibodies within this group. CONCLUSIONS: Social distancing not only can slow the spread of SARS-CoV-2 in a cohort of young, healthy adults but can also prevent the outbreak of COVID-19 while still inducing an immune response and colonizing nasal passages. Viral inoculum during infection or mode of transmission may be key factors determining the clinical course of COVID-19. url: https://doi.org/10.1093/cid/ciaa889 doi: 10.1093/cid/ciaa889 id: cord-317795-689at1qx author: Bielicki, Julia A title: Monitoring approaches for health-care workers during the COVID-19 pandemic date: 2020-07-23 words: 4876.0 sentences: 213.0 pages: flesch: 45.0 cache: ./cache/cord-317795-689at1qx.txt txt: ./txt/cord-317795-689at1qx.txt summary: One of the greatest risks to the health-care system is a high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health-care workers and the consequent lack of skilled staff to ensure a functioning local or regional response to the pandemic. 5 National and international recommendations for risk assessment and management of hospital health-care staff working with patients infected with SARS-CoV-2 are detailed and publicly available. Can rapidly deplete the workforce, particularly in cases of HCWs infected with SARS-CoV-2 exposing many colleagues or when there is uncontrolled community transmission, with HCWs exposed outside of the hospital; might not be relevant in settings where some level of PPE is universally recommended (eg, wearing surgical mask for all patient contacts) and there is high adherence to other IPC measures Specific recommendations for monitoring health-care workers for potential SARS-CoV-2 infection should be available for all staff who are expecting to see or currently managing patients with COVID-19. abstract: Health-care workers are crucial to any health-care system. During the ongoing COVID-19 pandemic, health-care workers are at a substantially increased risk of becoming infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and could come to considerable harm as a result. Depending on the phase of the pandemic, patients with COVID-19 might not be the main source of SARS-CoV-2 infection and health-care workers could be exposed to atypical patients, infected family members, contacts, and colleagues, or live in communities of active transmission. Clear strategies to support and appropriately manage exposed and infected health-care workers are essential to ensure effective staff management and to engender trust in the workplace. These management strategies should focus on risk stratification, suitable clinical monitoring, low-threshold access to diagnostics, and decision making about removal from and return to work. Policy makers need to support health-care facilities in interpreting guidance during a pandemic that will probably be characterised by fluctuating local incidence of SARS-CoV-2 to mitigate the impact of this pandemic on their workforce. url: https://www.ncbi.nlm.nih.gov/pubmed/32711692/ doi: 10.1016/s1473-3099(20)30458-8 id: cord-287448-hwsr1804 author: Bigaut, Kévin title: Guillain-Barré syndrome related to SARS-CoV-2 infection date: 2020-05-27 words: 903.0 sentences: 62.0 pages: flesch: 54.0 cache: ./cache/cord-287448-hwsr1804.txt txt: ./txt/cord-287448-hwsr1804.txt summary: Twenty-one days after the beginning of respiratory symptoms, he presented with in a rapidly progressive manner paraesthesia, hypoesthesia, and distal weakness in the lower limbs. CSF results showed normal cell count (1 × 10 6 /L), increased protein level (0.94 g/L), and negative SARS-CoV-2 on RT-PCR assay. CSF results showed subnormal cell count (6 × 10 6 /L), increased protein level (1.06 g/L), and negative SARS-CoV-2 on RT-PCR assay. We reported here 2 cases of GBS related to SARS-CoV-2 infection with neurologic improvement on IVIg, adding to few cases of GBS, one case of Miller Fisher syndrome, and one case of polyneuritis cranialis already published. 3 However, previous reports and our cases suggest that GBS associated with SARS-CoV-2 infection could start between 5 and 21 days after the SARS-CoV-2 clinical symptoms. 4 It could follow a postinfectious profile as reported on Middle East respiratory syndrome coronavirus infection in 4 patients with Bickerstaff''s encephalitis overlapping with GBS. abstract: nan url: https://doi.org/10.1212/nxi.0000000000000785 doi: 10.1212/nxi.0000000000000785 id: cord-353235-jiqhgf56 author: Bigliardi, Guido title: Middle cerebral artery ischemic stroke and COVID-19: a case report date: 2020-09-08 words: 1062.0 sentences: 82.0 pages: flesch: 49.0 cache: ./cache/cord-353235-jiqhgf56.txt txt: ./txt/cord-353235-jiqhgf56.txt summary: We present a clinical case of a patient with SARS-CoV-2 infection and respiratory symptoms, complicated with a pro-thrombotic state involving multiple vascular territories and concomitant interleukin-6 increase. Here, we report a case of a patient with SARS-CoV-2 infection that developed severe coagulopathy affecting both pulmonary and cerebral vessels. In the following days, the patient respiratory symptoms worsened with increasing need for oxygen therapy. Arterial and venous thrombotic events are recognized complications of SARS-CoV-2 infection (Klok et al. Of note, severe respiratory failure was heralded by a marked D-dimer increase 5 days earlier (Fig. 1) . This case underlines the importance of constant neurological monitoring in COVID-19 patients during ICU staying, especially in those with suspected thrombotic events, to detect possible neurological complications. High risk of thrombosis in patients with severe SARS-CoV-2 infection: a multicenter prospective cohort study Incidence of thrombotic complications in critically ill ICU patients with COVID-19 abstract: We present a clinical case of a patient with SARS-CoV-2 infection and respiratory symptoms, complicated with a pro-thrombotic state involving multiple vascular territories and concomitant interleukin-6 increase. This case underlines the possibility to develop a COVID-19-related coagulopathy. url: https://doi.org/10.1007/s13365-020-00898-1 doi: 10.1007/s13365-020-00898-1 id: cord-350686-q2bu7o4i author: Bilder, Christopher R title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 words: 539.0 sentences: 55.0 pages: flesch: 71.0 cache: ./cache/cord-350686-q2bu7o4i.txt txt: ./txt/cord-350686-q2bu7o4i.txt summary: title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people abstract: nan url: https://doi.org/10.1093/cid/ciaa774 doi: 10.1093/cid/ciaa774 id: cord-303384-bgvagdft author: Bilinska, Katarzyna title: Anosmia in COVID-19: A Bumpy Road to Establishing a Cellular Mechanism date: 2020-07-16 words: 2173.0 sentences: 124.0 pages: flesch: 49.0 cache: ./cache/cord-303384-bgvagdft.txt txt: ./txt/cord-303384-bgvagdft.txt summary: Several very recent papers contributed to explaining the key cellular steps occurring in the olfactory epithelium leading to anosmia/hyposmia (collectively known as dysosmia) initiated by SARS-CoV-2 infection. Initial hospital observations and early studies have suggested several possible mechanisms for the development of anosmia in COVID-19, including olfactory cleft syndrome, nasal obstruction and rhinorrhea, cytokine storm, direct damage to olfactory receptor neurons (ORNs), and impairment of the olfactory perception centers in the brain. The current model of olfactory dysfunction in COVID-19 is based on the already proven observation that SUS cells are the primary target of the virus and that SUSs infection initiates a series of events leading to dysosmia. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. abstract: It has become clear since the pandemic broke out that SARS-CoV-2 virus causes reduction of smell and taste in a significant fraction of COVID-19 patients. The olfactory dysfunction often occurs early in the course of the disease, and sometimes it is the only symptom in otherwise asymptomatic carriers. The cellular mechanisms for these specific olfactory disturbances in COVID-19 are now beginning to be elucidated. Several very recent papers contributed to explaining the key cellular steps occurring in the olfactory epithelium leading to anosmia/hyposmia (collectively known as dysosmia) initiated by SARS-CoV-2 infection. In this Viewpoint, we discuss current progress in research on olfactory dysfunction in COVID-19 and we also propose an updated model of the SARS-CoV-2-induced dysosmia. The emerging central role of sustentacular cells and inflammatory processes in the olfactory epithelium are particularly considered. The proposed model of anosmia in COVID-19 does not answer unequivocally whether the new coronavirus exploits the olfactory route to rapidly or slowly reach the brain in COVID-19 patients. To answer this question, new systematic studies using an infectious virus and appropriate animal models are needed. url: https://doi.org/10.1021/acschemneuro.0c00406 doi: 10.1021/acschemneuro.0c00406 id: cord-313728-08kwkbmd author: Binda, Barbara title: Follow-up and Management of Kidney Transplant Recipients During the COVID-19 Lockdown: the experience of an Italian Transplant Center, Including Two Cases of COVID-19 Pneumonia date: 2020-06-28 words: 3208.0 sentences: 170.0 pages: flesch: 39.0 cache: ./cache/cord-313728-08kwkbmd.txt txt: ./txt/cord-313728-08kwkbmd.txt summary: Conclusion In the context of a lockdown, such as that occurring in response to COVID-19, we suggest implementing remote surveillance programs in kidney transplant recipients, with the help of any available technology, and offering medical consulting and logistic support as needed. In this article, we report the strategy implemented by our KT transplant center in Central Italy to maintain follow-up of KT recipients during the lockdown response to COVID-19. Both of our COVID-19 patients had several risk factors for an unfavorable outcome of the infection: chronic immunosuppression, advanced age, cardiovascular chronic disease and, in one case, diabetes. Consistent with this, we suggest implementing remote surveillance programs in fragile populations, such as transplant recipients, with the help of any available technology (e-mail, phone calls, video calls) as soon as possible, and offering medical consulting and logistic support as needed during the COVID-19 pandemic. Case report of COVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? abstract: Abstract Background COVID-19 is a new infectious disease which emerged in China in late 2019 and is now spreading around the world. Social distancing measures were needed to reduce transmission, and lockdown included restricted access to healthcare facilities. The impact of COVID-19 on transplant recipients is unknown but, considering their immunosuppression status and associated comorbidities, they should be considered a high risk population. Methods A kidney transplant center in Central Italy implemented a strategy to maintain follow-up of kidney transplant recipients by phone and e-mail during lockdown. Telephone interviews were used administer a clinical questionnaire to patients, and e-mail was used to receive the results of diagnostic tests conducted in outpatient settings. Results From March 17 to April 23, 2020, a total of 143 kidney transplant recipients were contacted. Twenty-eight patients needed in-hospital consultation for problems unrelated to COVID-19, 3 of whom needed hospitalization. Eleven patients were managed at home for mild urinary or respiratory diseases, and one was referred to the hematologist. We identified 2 suspected cases of COVID-19 infection, and referred them to hospital care. Immunosuppressive therapy was modulated, and intravenous corticosteroids and potentially effective antiviral therapy were administered, with a favorable outcome. Conclusion In the context of a lockdown, such as that occurring in response to COVID-19, we suggest implementing remote surveillance programs in kidney transplant recipients, with the help of any available technology, and offering medical consulting and logistic support as needed. url: https://api.elsevier.com/content/article/pii/S0041134520325902 doi: 10.1016/j.transproceed.2020.06.026 id: cord-330387-7lci44w5 author: Bird, Paul title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads date: 2020-06-18 words: 1294.0 sentences: 82.0 pages: flesch: 59.0 cache: ./cache/cord-330387-7lci44w5.txt txt: ./txt/cord-330387-7lci44w5.txt summary: title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads Similarly, another study from Leicester, UK compared hospitalised and community patient SARS-CoV-2 PCR (polymerase chain reaction) positivity rates with that of staff, 2 but again, did not assess which staff groups or clinical specialties were at most risk of acquiring COVID-19. In addition, we compared the SARS-CoV-2 PCR positivity rate against ethnicity for both the HCW and household contacts combined (Fig. 1C) . 8 We then compared the SARS-CoV-2 PCR positivity rates against various demographic parameters, ethnicity and symptom patterns in both the HCWs and household contacts (n=47, Table 1 ). In summary, we have compared the SARS-CoV-2 PCR positivity rates in this HCW and household contact cohort, across different clinical roles and specialties, ethnic groups, and explored the correlation between their symptom patterns and swab viral loads. abstract: nan url: https://doi.org/10.1016/j.jinf.2020.06.035 doi: 10.1016/j.jinf.2020.06.035 id: cord-282899-kp114q7n author: Biswas, Saurav title: Blood clots in COVID-19 patients: Simplifying the curious mystery date: 2020-11-06 words: 2501.0 sentences: 138.0 pages: flesch: 38.0 cache: ./cache/cord-282899-kp114q7n.txt txt: ./txt/cord-282899-kp114q7n.txt summary: Considering the above facts and recent unusual reports, a hypothesis develops for the blood clots formation in the COVID-19 patients (Figure 1) , states that "Due to an internal injury in the endothelium of blood vessels, either directly by SARS-CoV-2 infection (coexpression and binding of the spike protein with the ACE2) or my virus-mediated inflammatory immune response, may result in vasoconstriction and the activation of coagulation and blood clotting pathways, resulting in the formation of blood clots". During COVID-19 infection, SARS-CoV-2 enters into the systemic circulation and binds with the ACE2 expressing endothelial cells (endothelium) lining the blood vessels. SO, in COVID-19 patients, the SARS-CoV-2 mediated endothelial inflammation, thrombin generation, platelet, and leukocyte recruitment, complement activation, and the initiation of innate and adaptive immune responses, forming clots, culminate in immunothrombosis, ultimately resulting in thrombotic complications, stroke, and finally death. abstract: The universal phenomenon of blood clotting is well known to be protective in external cellular/ tissue injury. However, the emergence of unusual thrombotic presentations in COVID-19 patients is the real concern. Interaction of the spike glycoprotein with ACE2 receptor present in the host cell surface mediates the entry of SARS-CoV-2 causing COVID-19 infection. New clinical findings of SARS-CoV-2 pathogenesis are coming out every day, and one such mystery is the formation of mysterious blood clots in the various tissues and organs of COVID-19 patients, which needs critical attention. To address this issue, we hypothesis that, high ACE2 expression in the endothelium of blood vessels facilitates the high-affinity binding of SARS-CoV-2 using spike protein, causing infection and internal injury inside the vascular wall of blood vessels. This viral associated injury may directly/indirectly initiate activation of coagulation and clotting cascades forming internal blood clots. However, the presence of these clots is undesirable as they are responsible for thrombosis and need to be treated with anti-thrombotic intervention. url: https://api.elsevier.com/content/article/pii/S030698772033262X doi: 10.1016/j.mehy.2020.110371 id: cord-344170-qrupbtem author: Biswas, Subrata K title: Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 date: 2020-05-24 words: 910.0 sentences: 57.0 pages: flesch: 56.0 cache: ./cache/cord-344170-qrupbtem.txt txt: ./txt/cord-344170-qrupbtem.txt summary: Variations in the genomic sequences were also observed when sequencing data from viral isolates of patients from other European and North American countries were compared with each other and with reference sequence [1] . However, this recent study [2] did not explore the association between genetic variation in SARS-CoV-2 and the severity of COVID-19. Therefore, it is an urgent need to explore the association of the mutation pattern of SARS-CoV-2 genome with the severity and fatality of COVID-19. Based on the above discussion, we hypothesize that the genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 in the population. Analysis of sequencing data of SARS-CoV-2 genome showed evidence of mutation at the beginning of the worldwide spread of COVID-19 [1] . This hypothesis can be tested by obtaining genetic sequences of SARS-CoV-2 from two groups of COVID-19 patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32464496/ doi: 10.1016/j.mehy.2020.109877 id: cord-318944-13zk6cco author: Bizzoca, Maria Eleonora title: Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date: 2020-05-27 words: 11691.0 sentences: 617.0 pages: flesch: 50.0 cache: ./cache/cord-318944-13zk6cco.txt txt: ./txt/cord-318944-13zk6cco.txt summary: The authors performed a narrative review on Severe Acute Respiratory SyndromeCoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (prevs post-COVID19) for the most common dental procedures. After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The precautions for infection control require wearing gloves, aprons, as well as eye and mouth protection (goggles and mask, such as medical masks and Filtering Face Piece or FPP) for each procedure involving direct contact with the patient body fluids. abstract: The authors performed a narrative review on Severe Acute Respiratory Syndrome- CoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (pre- vs post-COVID19) for the most common dental procedures. The outcome is forecast to help dentists to individuate for a given procedure the differences in terms of safety protocols to avoid infectious contagion (by SARS-CoV-2 and others dangerous agents). An investigation was performed on the online databases Pubmed and Scopus using a combination of free words and Medical Subject Headings (MESH) terms: “dentist” OR “oral health” AND “COVID-19” OR “SARS-CoV-2” OR “coronavirus-19”. After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The authors have highlighted the importance of knowing exactly the risk of infections in the dental practice, and to modulate correctly the use of PPE, in order to invest adequate financial resources and to avoid exposing both the dental team and patients to preventable risks. url: https://www.ncbi.nlm.nih.gov/pubmed/32471083/ doi: 10.3390/ijerph17113793 id: cord-293169-rd12xwvl author: Black, Margaret A. title: Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples date: 2020-11-07 words: 3000.0 sentences: 155.0 pages: flesch: 51.0 cache: ./cache/cord-293169-rd12xwvl.txt txt: ./txt/cord-293169-rd12xwvl.txt summary: OBJECTIVES: We validate the use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. Herein, we describe clinical validation of a new lateral flow immunoassay (LFI) test intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood. Plasma, serum, whole blood, and capillary blood (finger stick) samples from patients diagnosed with COVID-19 by PCR were tested with the 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) (Biolidics Ltd.), and the results were correlated with those obtained by enzyme-linked immunosorbent assay (ELISA), the gold standard for serologic detection of antibodies. Furthermore, we show J o u r n a l P r e -p r o o f that capillary whole blood obtained by finger stick shows comparable sensitivity for detecting anti-SARS-CoV-2 IgM and IgG antibodies as venous blood samples. abstract: OBJECTIVES: We validate the use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. We also seek to establish the value of LFI testing on blood obtained from a capillary blood sample. METHODS: Samples collected by venous blood draw and finger stick were obtained from patients with SARS-CoV-2 detected by RT-qPCR and control patients. Samples were tested with Biolidics 2019-nCoV IgG/IgM Detection Kit lateral flow immunoassay, and antibody calls were compared with ELISA. RESULTS: Biolidics LFI showed clinical sensitivity of 92% with venous blood at 7 days after PCR diagnosis of SARS-CoV-2. Test specificity was 92% for IgM and 100% for IgG. There was no significant difference in detecting IgM and IgG with Biolidics LFI and ELISA at D0 and D7 (p = 1.00), except for detection of IgM at D7 (p = 0.04). Capillary blood of SARS-CoV-2 patients showed 93% sensitivity for antibody detection. CONCLUSIONS: Clinical performance of Biolidics 2019-nCoV IgG/IgM Detection Kit is comparable to ELISA and was consistent across sample types. This provides an opportunity for decentralized rapid testing and may allow point-of-care and longitudinal self-testing for the presence of anti-SARS-CoV-2 antibodies. url: https://api.elsevier.com/content/article/pii/S0022175920302039 doi: 10.1016/j.jim.2020.112909 id: cord-287644-ay0vv27m author: Blackall, Douglas title: Rapid Establishment of a COVID‐19 Convalescent Plasma Program in a Regional Healthcare Delivery Network date: 2020-08-04 words: 3764.0 sentences: 215.0 pages: flesch: 49.0 cache: ./cache/cord-287644-ay0vv27m.txt txt: ./txt/cord-287644-ay0vv27m.txt summary: Overall, 6 major implementation "themes" were addressed: (1) registration of individual hospitals and principle investigators with a national investigational new drug research protocol, (2) collaboration with a regional blood donor center, (3) targeted recruitment of convalesced donors, (4) information technology issues related to all aspects of CCP ordering, distribution, and transfusion, (5) prioritization of patients to receive CCP, and (6) evaluation of CCP products including antibody characteristics and patient response to therapy. The Mayo IND provides specific criteria for patient inclusion in the protocol; namely, that they have positive molecular testing for SARS-CoV-2, are an adult (≥ 18 years of age), and have met defined clinical criteria qualifying them as having severe or life-threatening COVID-19. randomized controlled study, this protocol provided the infrastructure to initiate a convalescent plasma transfusion program in the SSM-STL network, which is the basis for this report. abstract: BACKGROUND: COVID‐19 convalescent plasma (CCP) represents an appealing approach to the treatment of patients with infections due to SARS‐CoV‐2. We endeavored to quickly establish a sustainable CCP transfusion program for a regional network of healthcare facilities. STUDY DESIGN AND METHODS: A regional collaborative group was activated to address the issues necessary to implementing a CCP transfusion program and making the program sustainable. A wide range of healthcare providers including physicians (critical care, infectious disease, transfusion medicine), nurses, pharmacists, laboratorians, and information technology specialists were required to make the program a success. RESULTS: The CCP implementation team initially consisted of 4 members but quickly grew to a group of nearly 20 participants based on different issues related to program implementation. Overall, 6 major implementation “themes” were addressed: (1) registration of individual hospitals and principle investigators with a national investigational new drug research protocol, (2) collaboration with a regional blood donor center, (3) targeted recruitment of convalesced donors, (4) information technology issues related to all aspects of CCP ordering, distribution, and transfusion, (5) prioritization of patients to receive CCP, and (6) evaluation of CCP products including antibody characteristics and patient response to therapy. CONCLUSION: Within 4 weeks of initiation, CCP was successfully transfused at multiple hospitals in our regional healthcare delivery system. A program infrastructure was established that will make this program sustainable into the future. This approach has broader implications for the success of multi‐institutional programs requiring rapid implementation. url: https://www.ncbi.nlm.nih.gov/pubmed/32748963/ doi: 10.1111/trf.16026 id: cord-252264-d9i19h8q author: Blackburn, Kyle M. title: Post-infectious neurological disorders date: 2020-08-30 words: 6396.0 sentences: 384.0 pages: flesch: 33.0 cache: ./cache/cord-252264-d9i19h8q.txt txt: ./txt/cord-252264-d9i19h8q.txt summary: In this review, we discuss the proposed mechanisms underlying pathogen-induced autoimmunity, and highlight the clinical presentation and treatment of several post-infectious autoimmune neurological disorders. 2 The role of infections in the pathogenesis of ''classic'' neuroimmunological disorders such as multiple sclerosis and Guillain-Barre syndrome (GBS) has been studied extensively. Here, we review the current landscape of post-infectious neurological autoimmunity, discuss proposed immunological mechanisms, highlight specific disorders strongly associated with pathogens, and review treatment considerations. Mimicry-induced autoimmunity may play an important role in GBS cases associated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. 168, 169 Furthermore, a recent systematic review determined that, among 43 post-HSE cases, no patients had experienced recurrence of herpes simplex following treatment for autoimmune encephalitis, despite the use of first and second-line immunotherapy. Guillain-Barre syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study Postinfectious Guillain-Barre syndrome related to SARS-CoV-2 infection: a case report Guillain Barre syndrome associated with COVID-19 infection: a case report abstract: A multitude of environmental factors can result in breakdown of immune tolerance in susceptible hosts. Infectious pathogens are among the most important environmental triggers in the pathogenesis of autoimmunity. Certain autoimmune disorders have a strong association with specific infections. Several neurological autoimmune disorders are thought to occur through post-infectious mechanisms. In this review, we discuss the proposed mechanisms underlying pathogen-induced autoimmunity, and highlight the clinical presentation and treatment of several post-infectious autoimmune neurological disorders. We also highlight post-infectious neurological disorders in the setting of recent outbreaks. url: https://doi.org/10.1177/1756286420952901 doi: 10.1177/1756286420952901 id: cord-339128-npfoircv author: Blair, Robert V. title: Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques date: 2020-11-07 words: 3097.0 sentences: 166.0 pages: flesch: 50.0 cache: ./cache/cord-339128-npfoircv.txt txt: ./txt/cord-339128-npfoircv.txt summary: Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. This study demonstrates that following exposure to SARS-CoV-2 aged AGMs develop a spectrum of disease, from mild to severe COVID-19, which in some cases progress to ARDS. abstract: SARS-CoV-2 induces a wide range of disease severity ranging from asymptomatic infection, to a life-threating illness, particularly in the elderly and persons with comorbid conditions. Among those persons with serious COVID-19 disease, acute respiratory distress syndrome (ARDS) is a common and often fatal presentation. Animal models of SARS-CoV-2 infection that manifest severe disease are needed to investigate the pathogenesis of COVID-19 induced ARDS and evaluate therapeutic strategies. Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. We found dramatic increases in circulating cytokines in three of four infected, aged AGMs but not in infected RMs. All of the AGMs showed increased levels of plasma IL-6 compared to baseline, a predictive marker and presumptive therapeutic target in humans infected with SARS-CoV-2 infection. Together, our results show that both RM and AGM are capable of modeling SARS-CoV-2 infection and suggest that aged AGMs may be useful for modeling severe disease manifestations including ARDS. url: https://www.sciencedirect.com/science/article/pii/S0002944020304971?v=s5 doi: 10.1016/j.ajpath.2020.10.016 id: cord-320826-o6ih2f23 author: Blairon, Laurent title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak date: 2020-07-31 words: 862.0 sentences: 56.0 pages: flesch: 53.0 cache: ./cache/cord-320826-o6ih2f23.txt txt: ./txt/cord-320826-o6ih2f23.txt summary: title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak We read with great interest the study of Chen Y et al., who analyzed, during the Chinese epidemic peak, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 105 healthcare workers (HCWs) exposed to COVID-19 patients [1] . Our purpose was to document at the end of the Belgium epidemic the seroprevalence of SARS-CoV-2 in HCWs exposed to COVID-19 at varying degrees and to compare these rates with those observed by other teams worldwide. On the same day, all asymptomatic HCWs who agreed to participate benefited from both serological and RT-qPCR SARS-CoV-2 tests. High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients COVID-19 study: 8,4% of Belgian health workers have antibodies to SARS-COV-2 n abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320305144?v=s5 doi: 10.1016/j.jinf.2020.07.033 id: cord-310857-i9v9antx author: Blaisdell, Laura L. title: Preventing and Mitigating SARS-CoV-2 Transmission — Four Overnight Camps, Maine, June–August 2020 date: 2020-09-04 words: 2583.0 sentences: 133.0 pages: flesch: 47.0 cache: ./cache/cord-310857-i9v9antx.txt txt: ./txt/cord-310857-i9v9antx.txt summary: The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020.* Shortly thereafter, closures of 124,000 U.S. public and private schools affected at least 55.1 million students through the end of the 2019-20 school year.† During the summer of 2020, approximately 82% of 8,947 U.S. overnight camps did not operate.§ In Maine, only approximately 20% of 100 overnight camps opened.¶ An overnight camp in Georgia recently reported SARS-CoV-2, the virus that causes COVID-19, transmission among campers and staff members when nonpharmaceutical interventions (NPIs) were not strictly followed (1); however, NPIs have been successfully used to mitigate SARS-CoV-2 transmission among military basic trainees (2). During June-August 2020, four overnight camps in Maine implemented several NPIs to prevent and mitigate the transmission of SARS-CoV-2, including prearrival quarantine, preand postarrival testing and symptom screening, cohorting, use of face coverings, physical distancing, enhanced hygiene measures, cleaning and disinfecting, and maximal outdoor programming. To prevent, identify, and mitigate spread of COVID-19, four Maine overnight summer camps with similar size, session duration, and camper and staff member characteristics opened with uniform NPIs, including precamp quarantine, pre-and postarrival testing and symptom screening, cohorting, and physical distancing between cohorts. abstract: The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020.* Shortly thereafter, closures of 124,000 U.S. public and private schools affected at least 55.1 million students through the end of the 2019-20 school year.† During the summer of 2020, approximately 82% of 8,947 U.S. overnight camps did not operate.§ In Maine, only approximately 20% of 100 overnight camps opened.¶ An overnight camp in Georgia recently reported SARS-CoV-2, the virus that causes COVID-19, transmission among campers and staff members when nonpharmaceutical interventions (NPIs) were not strictly followed (1); however, NPIs have been successfully used to mitigate SARS-CoV-2 transmission among military basic trainees (2). During June-August 2020, four overnight camps in Maine implemented several NPIs to prevent and mitigate the transmission of SARS-CoV-2, including prearrival quarantine, pre- and postarrival testing and symptom screening, cohorting, use of face coverings, physical distancing, enhanced hygiene measures, cleaning and disinfecting, and maximal outdoor programming. During the camp sessions, testing and symptom screening enabled early and rapid identification and isolation of attendees with COVID-19. Among the 1,022 attendees (staff members and campers) from 41 states, one territory, and six international locations, 1,010 were tested before arrival; 12 attendees who had completed a period of isolation after receiving a diagnosis of COVID-19 2 months before arrival were not tested. Four (0.4%) asymptomatic attendees received positive SARS-CoV-2 test results before arrival; these persons delayed their arrival, completed 10 days of isolation at home, remained asymptomatic, and did not receive any further testing before arrival or for the duration of camp attendance. Approximately 1 week after camp arrival, all 1,006 attendees without a previous diagnosis of COVID-19 were tested, and three asymptomatic cases were identified. Following isolation of these persons and quarantine of their contacts, no secondary transmission of SARS-CoV-2 occurred. These findings can inform similar multilayered public health strategies to prevent and mitigate the introduction and transmission of SARS-CoV-2 among children, adolescents, and adults in congregate settings, such as overnight camps, residential schools, and colleges. url: https://www.ncbi.nlm.nih.gov/pubmed/32881850/ doi: 10.15585/mmwr.mm6935e1 id: cord-333122-xw8o189s author: Blasiak, A. title: IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-08 words: 5116.0 sentences: 351.0 pages: flesch: 43.0 cache: ./cache/cord-333122-xw8o189s.txt txt: ./txt/cord-333122-xw8o189s.txt summary: IDentif.AI harnesses a quadratic relationship between therapeutic inputs (e.g. drug and dose) and biological outputs (e.g. quantifiable measurements of efficacy, safety) to experimentally pinpoint optimal combinations from large parameter spaces with a marked reduction in the number of required experiments (Fig. 1 ). The 12drug set included a broad spectrum of repurposed agents that are currently being evaluated in clinical studies for treatment of COVID-19 or being administered in conjunction with these therapies, including remdesivir (RDV), favipiravir (FPV), ritonavir (RTV), lopinavir (LPV), oseltamivir (OSV-P), dexamethasone (DEX), ribavirin (RBV), teicoplanin (TEC), losartan (LST), azithromycin (AZT), chloroquine (CQ), and hydroxychloroquine (HCQ). With a 3-order of magnitude reduction in required tests, we identified a clinically actionable list of 2-,3-, and 4-drug combinations ranked based on viral inhibition efficacy with accompanying safety data against kidney epithelial cells (Vero E6), liver epithelial cells (THLE-2) and cardiomyocytes (AC16). This study harnessed the IDentif.AI platform to interrogate a 12 drug-dose parameter space against the SARS-CoV-2 live virus to develop actionable and optimized combination therapy regimens. abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) has led to the rapid initiation of urgently needed clinical trials of repurposed drug combinations and monotherapies. These regimens were primarily relying on mechanism-of-action based selection of drugs, many of which have yielded positive in vitro but largely negative clinical outcomes. To overcome this challenge, we report the use of IDentif.AI, a platform that rapidly optimizes infectious disease (ID) combination therapy design using artificial intelligence (AI). In this study, IDentif.AI was implemented on a 12-drug candidate therapy search set representing over 530,000 possible drug combinations. IDentif.AI demonstrated that the optimal combination therapy against SARS-CoV-2 was comprised of remdesivir, ritonavir, and lopinavir, which mediated a 6.5-fold improvement in efficacy over remdesivir alone. Additionally, IDentif.AI showed hydroxychloroquine and azithromycin to be relatively ineffective. The identification of a clinically actionable optimal drug combination was completed within two weeks, with a 3-order of magnitude reduction in the number of tests typically needed. IDentif.AI analysis was also able to independently confirm clinical trial outcomes to date without requiring any data from these trials. The robustness of the IDentif.AI platform suggests that it may be applicable towards rapid development of optimal drug regimens to address current and future outbreaks. url: https://doi.org/10.1101/2020.05.04.20088104 doi: 10.1101/2020.05.04.20088104 id: cord-347119-w780f0om author: Blitz, Matthew J. title: Race/ethnicity and spatiotemporal trends in SARS-CoV-2 prevalence on obstetrical units in New York date: 2020-08-17 words: 923.0 sentences: 65.0 pages: flesch: 58.0 cache: ./cache/cord-347119-w780f0om.txt txt: ./txt/cord-347119-w780f0om.txt summary: We evaluated 7 temporal trends, regional geographic variation, and racial/ethnic disparity in SARS-CoV-8 2 prevalence among gravid women presenting to obstetrical units within a large health 9 system in New York during the COVID-19 outbreak. This retrospective study included all pregnant women who had SARS-CoV-2 testing 13 (both symptomatic and asymptomatic) at 7 hospitals within a 30-mile radius from April 14 1, 2020, before the peak of the outbreak in New York State, 4 to June 9, 2020. Of 4,811 pregnant women presenting to the 7 hospital sites after implementation of 38 universal SARS-CoV-2 testing, PCR results were obtained for 4,674 patients: 500 39 (11%) were positive. Non-Hispanic black women 50 constituted 12% (n=567) of the study population, had a test positivity rate of 14% 51 Considerable heterogeneity in SARS-CoV-2 prevalence was observed across hospitals 64 in the region (p<0.0001; Table 1 ). abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2589933320301804?v=s5 doi: 10.1016/j.ajogmf.2020.100212 id: cord-278249-vvhq9vgp author: Blot, Mathieu title: CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDS date: 2020-11-02 words: 6238.0 sentences: 346.0 pages: flesch: 45.0 cache: ./cache/cord-278249-vvhq9vgp.txt txt: ./txt/cord-278249-vvhq9vgp.txt summary: In addition, since most patients need to undergo mechanical ventilation in this context, ventilator-induced lung injury (VILI) could exacerbate tissue damage as well as local and systemic inflammation, thus acting as a "second hit." Our team has previously shown that mitochondrial alarmins (i.e., mitochondrial DNA) are released by human epithelial cells submitted to cyclic stretch, and these alarmins are also recovered from bronchoalveolar lavage (BAL) fluid obtained from either ventilated rabbits or ARDS patients. This comprehensive evaluation of systemic and pulmonary immune response showed that the higher CXCL10 concentrations in both the systemic and alveolar compartments of patients with COVID-19 ARDS were associated with a longer duration of mechanical ventilation. Finally, in both COVID-19 and non-COVID-19 patients, higher mitochondrial DNA concentrations in the plasma and ELF compartment were highly correlated with alveolar inflammation, as assessed by BALF cell count and ELF IL-8 and IL-1β concentrations. abstract: BACKGROUND: COVID-19-related ARDS has unique features when compared with ARDS from other origins, suggesting a distinctive inflammatory pathogenesis. Data regarding the host response within the lung are sparse. The objective is to compare alveolar and systemic inflammation response patterns, mitochondrial alarmin release, and outcomes according to ARDS etiology (i.e., COVID-19 vs. non-COVID-19). METHODS: Bronchoalveolar lavage fluid and plasma were obtained from 7 control, 7 non-COVID-19 ARDS, and 14 COVID-19 ARDS patients. Clinical data, plasma, and epithelial lining fluid (ELF) concentrations of 45 inflammatory mediators and cell-free mitochondrial DNA were measured and compared. RESULTS: COVID-19 ARDS patients required mechanical ventilation (MV) for significantly longer, even after adjustment for potential confounders. There was a trend toward higher concentrations of plasma CCL5, CXCL2, CXCL10, CD40 ligand, IL-10, and GM-CSF, and ELF concentrations of CXCL1, CXCL10, granzyme B, TRAIL, and EGF in the COVID-19 ARDS group compared with the non-COVID-19 ARDS group. Plasma and ELF CXCL10 concentrations were independently associated with the number of ventilator-free days, without correlation between ELF CXCL-10 and viral load. Mitochondrial DNA plasma and ELF concentrations were elevated in all ARDS patients, with no differences between the two groups. ELF concentrations of mitochondrial DNA were correlated with alveolar cell counts, as well as IL-8 and IL-1β concentrations. CONCLUSION: CXCL10 could be one key mediator involved in the dysregulated immune response. It should be evaluated as a candidate biomarker that may predict the duration of MV in COVID-19 ARDS patients. Targeting the CXCL10-CXCR3 axis could also be considered as a new therapeutic approach. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03955887 url: https://www.ncbi.nlm.nih.gov/pubmed/33138839/ doi: 10.1186/s13054-020-03328-0 id: cord-336094-ssr5y4u3 author: Blumberg, Dean A. title: Vertical Transmission of SARS-CoV-2: What is the Optimal Definition? date: 2020-06-05 words: 1423.0 sentences: 82.0 pages: flesch: 47.0 cache: ./cache/cord-336094-ssr5y4u3.txt txt: ./txt/cord-336094-ssr5y4u3.txt summary: 11 We start with several underlying assumptions (►Fig. 1) as follows: (1) the incubation period is 1 to 14 days 12,13 ; (2) intrauterine infection may potentially occur transplacentally via blood, or via transmission through swallowed or aspirated amniotic fluid; (3) maternal viremia is unlikely during the incubation period >48 hours before symptom onset and the likelihood of positive SARS-CoV-2 through RT-PCR in blood samples is low (< 1%) in COVID-19 patients 9 ; (4) intrapartum transmission may potentially occur due to exposure to maternal blood, vaginal secretions, or feces; (5) early postnatal infection may occur via the respiratory route or due to direct contact with the infected mother or other caretakers, or potential transmission through breast milk (however, to date we are not aware of any reports of viral presence in breast milk); and (6) SARS-CoV-2 virus may be transiently detected for up to 24 hours after birth due to superficial contamination or transient viremia (similar to HIV). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32503058/ doi: 10.1055/s-0040-1712457 id: cord-276870-gxtvlji7 author: Bobrowski, Tesia title: Learning from history: do not flatten the curve of antiviral research! date: 2020-07-15 words: 5089.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-276870-gxtvlji7.txt txt: ./txt/cord-276870-gxtvlji7.txt summary: Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. However, despite many experimental and clinical studies, no effective drugs or treatments have emerged to treat the previous six epidemics of bird flu, SARS, swine flu, MERS, Ebola, and Zika as well as, thus far, COVID-19. We evaluated the number of publications (in both peer-reviewed journals and ArXiv preprint servers) and the number of clinical trials performed over the course of the epidemic to estimate the engagement and success of the scientific community in response to the seven major outbreaks of the past two decades: bird flu, SARS, swine flu, MERS, Ebola, Zika, and COVID-19. abstract: Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. All six prior epidemics studied [bird flu, severe acute respiratory syndrome (SARS), swine flu, Middle East Respiratory Syndrome (MERS), Ebola, and Zika] were characterized by an initial spike of research response that flattened shortly thereafter. Unfortunately, no antiviral medications have been discovered to date as treatments for any of these diseases. By contrast, the HIV/AIDS pandemic has garnered consistent research investment since it began and resulted in drugs being developed within 7 years of its start date, with many more to follow. We argue that, to develop effective treatments for COVID-19 and be prepared for future epidemics, long-term, consistent investment in antiviral research is needed. url: https://doi.org/10.1016/j.drudis.2020.07.008 doi: 10.1016/j.drudis.2020.07.008 id: cord-315129-p31vm79o author: Bock, Jens-Ole title: Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response date: 2020-06-23 words: 3553.0 sentences: 181.0 pages: flesch: 48.0 cache: ./cache/cord-315129-p31vm79o.txt txt: ./txt/cord-315129-p31vm79o.txt summary: title: Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. Here, we use the publicly available proteomics data from this study to re-analyze the in vitro cellular consequences of SARS-CoV-2 infection by impact pathways analysis and network analysis. Cellular factors exploited by SARS-CoV-2 to gain entry into cells have recently been studied, revealing that the virus uses the angiotensin-converting enzyme 2 (ACE2) host cell receptor, together with the serine protease TMPRSS2. Host cell proteomics studies that measure changes in protein abundance following viral entry and subsequent global pathway and network analysis can shed some light on the mechanisms that are used and/or altered by the virus and may reveal novel drug targets. abstract: Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. To develop treatments that can stop or lessen the symptoms and severity of SARS-CoV-2 infection, it is critical to understand how the virus behaves inside human cells, and so far studies in this area remain scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. Here, we use the publicly available proteomics data from this study to re-analyze the in vitro cellular consequences of SARS-CoV-2 infection by impact pathways analysis and network analysis. Notably, proteins linked to the inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be altered in response to viral infection. Upregulation of inflammatory response proteins is in line with the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients and which worsens with age. url: https://doi.org/10.18632/aging.103524 doi: 10.18632/aging.103524 id: cord-275495-h60x89zi author: Bocksberger, S. title: Temporäre Hyposmie bei COVID-19-Patienten date: 2020-05-25 words: 1291.0 sentences: 145.0 pages: flesch: 58.0 cache: ./cache/cord-275495-h60x89zi.txt txt: ./txt/cord-275495-h60x89zi.txt summary: CONCLUSION: The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1–3 weeks after the onset of COVID-19 symptoms. Die im Dezember 2019 erstmalig in Wuhan, China, aufgetretene Coronaviruserkrankung (COVID-19) wird durch die Infektion mit SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), einem neuartigen RNA-β-Coronavirus, hervorgerufen und verursacht in einer Vielzahl von Fällen eine akute Atemwegsinfektion [1] . The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1-3 weeks after the onset of COVID-19 symptoms. abstract: BACKGROUND: This is a report on the high incidence of olfactory dysfunction in COVID-19 patients in the first cohort of COVID-19 patients in Germany (Webasto cluster). METHODS: Loss of sense of smell and/or taste was reported by 26 of 63 COVID-19 patients (41%), whereas only 31% of the patients experiencing hyposmia had simultaneous symptoms of rhinitis. Smell tests were performed in 14 of these patients and taste tests in 10. The measurements were conducted in a patient care setting in an early COVID-19 cohort. RESULTS: An olfactory disorder was present in 10/14 patients, before as well as after nasal decongestion. In 2 of these patients, hyposmia was the leading or only symptom of SARS-CoV‑2 infection. All tested patients reported recovery of smell and/or taste within 8 to 23 days. CONCLUSION: The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1–3 weeks after the onset of COVID-19 symptoms. There were no indications of an increased incidence of dysgeusia. These early data may help in the interpretation of COVID-19-associated hyposmia as well as in the counseling of patients, given the temporary nature of hyposmia observed in this study. Furthermore, according to the current experience, hyposmia without rhinitic obstruction can be the leading or even the only symptom of a SARS-CoV‑2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32451564/ doi: 10.1007/s00106-020-00891-4 id: cord-354080-glcq4qp9 author: Bodro, Marta title: Increased CSF levels of IL-1β, IL-6, and ACE in SARS-CoV-2–associated encephalitis date: 2020-07-01 words: 1176.0 sentences: 79.0 pages: flesch: 47.0 cache: ./cache/cord-354080-glcq4qp9.txt txt: ./txt/cord-354080-glcq4qp9.txt summary: For the latest articles, invited commentaries, and blogs from physicians around the world NPub.org/COVID19 Clinical features, serum, and CSF characteristics including cytokines and angiotensin-converting enzyme (ACE) profile from both cases are shown in the table. Three previous case reports of CNS involvement in COVID-19 suggest different pathogenic mechanisms: direct CNS infection demonstrated by detection of SARS-CoV-2 RNA in CSF, 2 recrudescence of symptoms related to previous lesions (e.g., brain infarction) in the context of systemic infection, 3 and inflammatory-mediated mechanisms resulting in acute hemorrhagic necrotizing encephalopathy. Hence, in a study of children with acute encephalitis-like syndrome, serum anti-human coronavirus-OC43 immunoglobulin M antibodies were present in 12% of patients and levels of IL-6, IL-8, monocyte chemotactic protein-1, and Granulocyte Macrophage Colony-Stimulating Factor were increased in their CSF. The main implication of these 2 patients is that physicians should be aware of COVID-19 infections presenting or predominantly manifesting as encephalitis, likely resulting from activation of inflammatory pathways with increased ILs and ACE in CSF. abstract: nan url: https://doi.org/10.1212/nxi.0000000000000821 doi: 10.1212/nxi.0000000000000821 id: cord-286029-rafcdzhm author: Bogaards, Johannes Antonie title: The potential of targeted antibody prophylaxis in SARS outbreak control: A mathematic analysis() date: 2006-05-05 words: 5574.0 sentences: 291.0 pages: flesch: 46.0 cache: ./cache/cord-286029-rafcdzhm.txt txt: ./txt/cord-286029-rafcdzhm.txt summary: METHOD: We developed a mathematical model to investigate the effects of hospital admission and targeted antibody prophylaxis on the reproduction number R, defined as the number of secondary cases generated by an index case, during different SARS outbreak scenarios. RESULTS: Assuming a basic reproduction number R(0)=3, admission of patients to hospital within 4.3 days of symptom onset is necessary to achieve outbreak control without the need to further reduce community-based transmission. Based on our model, we derived an expression for the effective reproduction number of SARS to study conditions for containment and we explored how the size and duration of an outbreak depend on the efficacy of control. Given functions for the distribution of onset-to-admission time and transmission rate before the implementation of public health measures, we define the basic reproduction number R 0 as the average number of secondary cases before intervention is in place. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) coronavirus-like viruses continue to circulate in animal reservoirs. If new mutants of SARS coronavirus do initiate another epidemic, administration of prophylactic antibodies to risk groups may supplement the stringent isolation procedures that contained the first SARS outbreak. METHOD: We developed a mathematical model to investigate the effects of hospital admission and targeted antibody prophylaxis on the reproduction number R, defined as the number of secondary cases generated by an index case, during different SARS outbreak scenarios. RESULTS: Assuming a basic reproduction number R(0)=3, admission of patients to hospital within 4.3 days of symptom onset is necessary to achieve outbreak control without the need to further reduce community-based transmission. Control may be enhanced by providing pre-exposure prophylaxis to contacts of hospitalized patients, and through contact tracing and provision of post-exposure prophylaxis. Antibody prophylaxis may also be employed to reduce R below one and thereby restrict outbreak size and duration. CONCLUSIONS: Patient isolation alone can be sufficient to control SARS outbreaks provided that the time from onset to admission is short. Antibody prophylaxis as supplemental measure generally allows for containment of higher R(0) values and restricts both the size and duration of an outbreak. url: https://api.elsevier.com/content/article/pii/S1477893906000202 doi: 10.1016/j.tmaid.2006.01.007 id: cord-259572-8n12n6ym author: Bogensperger, Christina title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report date: 2020-07-22 words: 931.0 sentences: 62.0 pages: flesch: 46.0 cache: ./cache/cord-259572-8n12n6ym.txt txt: ./txt/cord-259572-8n12n6ym.txt summary: title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. Here we present the case of a liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine preservation (NMP), which we have recently established as a routine in liver transplantation (6). abstract: Abstract The SARS-CoV-2 pandemic has changed life on a global scale. The numbers in transplantation have plumped in fear of disease transmission, recipient Covid-19 infection, priority shift and resource limitations. Covid-19 complicates transplantation since donor testing, (re)allocation of limited resources and recipient testing may exceed permissible ischemia times. Normothermic machine perfusion (NMP) helps to safely prolong liver preservation up to 38 hours. Additional time is essential under the current circumstances. Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). Donor and recipient test results for SARS-CoV-2 were negative and intensive care unit (ICU) capacity eventually available. The surgical procedure and postoperative course were uneventful. NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. url: https://doi.org/10.1016/j.transproceed.2020.07.011 doi: 10.1016/j.transproceed.2020.07.011 id: cord-256224-qprj8vlc author: Boixeda, R. title: Is chronic obstructive pulmonary disease a protective factor in SARS-CoV-2 infection? The importance of bronchodilator treatment() date: 2020-09-26 words: 1402.0 sentences: 89.0 pages: flesch: 50.0 cache: ./cache/cord-256224-qprj8vlc.txt txt: ./txt/cord-256224-qprj8vlc.txt summary: In a systematic review of infections in patients with COPD that required hospital admission, it was observed that the rhinovirus, respiratory syncytial virus (RSV), and influenza virus were the most prevalent agents, followed by parainfluenza and coronavirus. We have analyzed the prevalence of COPD in patients treated for COVID-19 in our center, specifically evaluating their baseline treatment with inhalers as a potential protective factor against SARS-CoV-2 infection. However, the use of tiotropium was significantly lower in patients with COPD who had been hospitalized for COVID-19 in relation to other cohorts of patients with stable COPD and without SARS-CoV-2 infection and controlled in primary care (12% vs. Members of the COCOHMAT (COhorte COvid del Hospital de MATaró) Group Table 1 Treatment with inhaled corticosteroids and anticholinergics in patients with COPD in series of patients hospitalized due to SARS-CoV-2, severe exacerbation of COPD, and patients in the stable phase (primary care) abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2254887420300965?v=s5 doi: 10.1016/j.rceng.2020.07.004 id: cord-313910-bwe2f7xf author: Bojadzic, Damir title: Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date: 2020-10-22 words: 7049.0 sentences: 346.0 pages: flesch: 54.0 cache: ./cache/cord-313910-bwe2f7xf.txt txt: ./txt/cord-313910-bwe2f7xf.txt summary: Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. We were able to set up a cell-free ELISA-type assay to quantify the binding of SARS-CoV-2 S protein (as well as its SARS-CoV analog) to their cognate receptors (human ACE2) and used this to screen our existing in-house compound library containing a large variety of organic dyes and a set of colorless analogs prepared as potential SMIs for costimulatory PPIs. These maintain the main molecular framework of dyes but lack the aromatic azo chromophores responsible for the color as they are replaced with amide linkers (58, 59). abstract: Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and ACE2, which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable / less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound-library that is focused on the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs identified here bind SARS-CoV-2-S and not ACE2. Selected promising compounds inhibited the entry of a SARS-CoV-2-S expressing pseudovirus into ACE2-expressing cells in concentration-dependent manner with low micromolar IC50s (6-30 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for coronavirus attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular. url: https://doi.org/10.1101/2020.10.22.351056 doi: 10.1101/2020.10.22.351056 id: cord-297974-sduz0j35 author: Bokelmann, L. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 words: 4761.0 sentences: 307.0 pages: flesch: 55.0 cache: ./cache/cord-297974-sduz0j35.txt txt: ./txt/cord-297974-sduz0j35.txt summary: Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp. abstract: Efforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can easily be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation, sophisticated laboratory equipment and trained personnel to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification). This method combines a hybridization capture-based RNA extraction of non-invasive gargle lavage samples to concentrate samples and remove inhibitors with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP does not result in false positives and single infected samples can be detected in a pool among 25 uninfected samples, thus reducing the technical cost per test to ~1 Euro per individual. url: http://medrxiv.org/cgi/content/short/2020.08.04.20168617v1?rss=1 doi: 10.1101/2020.08.04.20168617 id: cord-294501-1nf98mpb author: Bonafè, Massimiliano title: Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes date: 2020-05-03 words: 3745.0 sentences: 197.0 pages: flesch: 40.0 cache: ./cache/cord-294501-1nf98mpb.txt txt: ./txt/cord-294501-1nf98mpb.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by a high mortality of elderly men with age-related comorbidities. Consistent with this finding, the ability of DCs and macrophages to elicit CD8 + T cell response and proliferation and to release antiviral cytokines is impaired in elderly individuals [34] ; in parallel, these subjects are characterized by a reduced activity of plasmacytoid DCs, the main sources of type I IFNs, which underpin the antiviral response and provide the first-line sentinels in immune surveillance, also in the lung [35] . 4. In older men with age-related diseases, the aging-dependent reduction in ACE2 activity worsens SARS-CoV-2 infection outcomes Angiotensin-converting enzyme (ACE)2, the main SARS-CoV2 host cell receptor, plays a crucial role in virus entry into the cell, as previously demonstrated in SARS and NL63 human coronaviruses [41] . In these individuals, acute SARS-CoV-2 infection compounds their chronic, subclinical, aging-related proinflammatory state (inflamm-aging) which, together with immune senescence and the age-and gender-specific distribution of ACE2 in the airway epithelia, could blunt the antiviral response to inflammation. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by a high mortality of elderly men with age-related comorbidities. In most of these patients, uncontrolled local and systemic hyperinflammation induces severe and often lethal outcomes. The aging process is characterized by the gradual development of a chronic subclinical systemic inflammation (inflamm-aging) and by acquired immune system impairment (immune senescence). Here, we advance the hypothesis that four well-recognized features of aging contribute to the disproportionate SARS-CoV-2 mortality suffered by elderly men: i. the presence of subclinical systemic inflammation without overt disease, ii. a blunted acquired immune system and type I interferon response due to the chronic inflammation; iii. the downregulation of ACE2 (i.e. the SARS-CoV-2 receptor); and iv. accelerated biological aging. The high mortality rate of SARS-CoV-2 infection suggests that clarification of the mechanisms of inflamm-aging and immune senescence can help combat not only age-related disorders but also SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32389499/ doi: 10.1016/j.cytogfr.2020.04.005 id: cord-331547-uqmjhhna author: Bonalumi, Giorgia title: A call to action becomes practice: cardiac and vascular surgery during the COVID-19 pandemic based on the Lombardy emergency guidelines date: 2020-06-25 words: 4218.0 sentences: 226.0 pages: flesch: 50.0 cache: ./cache/cord-331547-uqmjhhna.txt txt: ./txt/cord-331547-uqmjhhna.txt summary: In Lombardy, the hub-and-spoke system was introduced to guarantee emergency and urgent cardiovascular surgery, whereas most hospitals were dedicated to patients with coronavirus disease 2019 (COVID-19). Daily morning briefings were held internally at the Monzino hospital to monitor every aspect of all in-patients (COVID-19 status, number of available beds) and to share news from the Health Care Lombardy Regional System and the national government. If the test results were positive (chest CT scan indicative of interstitial pneumonia and/or positive results from the nasal swab), the patient was transferred to a dedicated zone called the ''red area'', a separate zone with physical barriers and heavy use of personal protective equipment to protect working personnel, where only patients with COVID-19 were hospitalized. In cases of emergency surgery, the patient was considered and treated as positive for SARS-CoV-2 by the health care staff, who wore personal protective equipment, until screening results were available. abstract: OBJECTIVES: During the Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) pandemic, Northern Italy had to completely reorganize its hospital activity. In Lombardy, the hub-and-spoke system was introduced to guarantee emergency and urgent cardiovascular surgery, whereas most hospitals were dedicated to patients with coronavirus disease 2019 (COVID-19). The aim of this study was to analyse the results of the hub-and-spoke organization system. METHODS: Centro Cardiologico Monzino (Monzino) became one of the four hubs for cardiovascular surgery, with a total of eight spokes. SARS-CoV-2 screening became mandatory for all patients. New flow charts were designed to allow separated pathways based on infection status. A reorganization of spaces guaranteed COVID-19-free and COVID-19-dedicated areas. Patients were also classified into groups according to their pathological and clinical status: emergency, urgent and non-deferrable (ND). RESULTS: A total of 70 patients were referred to the Monzino hub-and-spoke network. We performed 41 operations, 28 (68.3%) of which were emergency/urgent and 13 of which were ND. The screening allowed the identification of COVID-19 (three patients, 7.3%) and non-COVID-19 patients (38 patients, 92.7%). The newly designed and shared protocols guaranteed that the cardiac patients would be divided into emergency, urgent and ND groups. The involvement of the telematic management heart team allowed constant updates and clinical discussions. CONCLUSIONS: The hub-and-spoke organization system efficiently safeguards access to heart and vascular surgical services for patients who require ND, urgent and emergency treatment. Further reorganization will be needed at the end of this pandemic when elective cases will again be scheduled, with a daily increase in the number of operations. url: https://www.ncbi.nlm.nih.gov/pubmed/32584978/ doi: 10.1093/ejcts/ezaa204 id: cord-332480-3uodkrkp author: Bonam, Srinivasa Reddy title: Adjunct immunotherapies for the management of severely ill COVID-19 patients date: 2020-04-30 words: 5440.0 sentences: 334.0 pages: flesch: 43.0 cache: ./cache/cord-332480-3uodkrkp.txt txt: ./txt/cord-332480-3uodkrkp.txt summary: Current COVID-19 data clearly highlight that cytokine storm and activated immune cell migration to the lungs characterize the early immune response to COVID-19 that causes severe lung damage and development of acute respiratory distress syndrome. 13, 14, 16, 17 Of note, similar to severely ill COVID-19 cases, elevated serum levels of IL-6, TNF-α and IFN-γ have been consistently observed in cytokine release syndrome (CRS) that is common in the patients receiving T cell-engaging immunotherapies (bispecific antibody constructs or chimeric antigen receptor (CAR) T cell therapies). A randomized Phase 1b/2, double-blind, placebo-controlled clinical trial is currently recruiting patients to investigate the therapeutic efficacy of a humanized anti-GM-CSF IgG1 monoclonal antibody TJ003234 in severely ill COVID-19 patients (NCT04341116). 68 Similarly, treatment of ten severely ill COVID-19 patients with 200 mL of convalescent plasma containing viral neutralizing antibody titers more than 1:640 (A dilution of plasma that neutralized 100 TCID 50 (50% tissue-culture-infective dose) of SARS-CoV-2) led to reduced CRP levels, undetectable viremia and improved clinical symptoms. abstract: Abstract Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has infected millions with more than 181,000 fatal cases as of 22nd April 2020. Currently, there are no specific COVID-19 therapies. Most patients depend on mechanical ventilation. Current COVID-19 data clearly highlight that cytokine storm and activated immune cell migration to the lungs characterize the early immune response to COVID-19 that causes severe lung damage and development of acute respiratory distress syndrome. In view of uncertainty associated with immunosuppressive treatments such as corticosteroids and their possible secondary effects, including risks of secondary infections, we suggest immunotherapies as an adjunct therapy in severe COVID-19 cases. Such immunotherapies based on inflammatory cytokine neutralization, immunomodulation and passive viral neutralization, not only reduce inflammation, inflammation-associated lung damage, or viral load, but could also prevent intensive care unit hospitalization and dependency on mechanical ventilation both of which are limited resources. url: https://www.ncbi.nlm.nih.gov/pubmed/32562483/ doi: 10.1016/j.xcrm.2020.100016 id: cord-220618-segffkbn author: Bonamassa, Ivan title: Geometric characterization of SARS-CoV-2 pandemic events date: 2020-07-20 words: 8692.0 sentences: 452.0 pages: flesch: 50.0 cache: ./cache/cord-220618-segffkbn.txt txt: ./txt/cord-220618-segffkbn.txt summary: Disposing of a robust and comprehensive framework to classify the SARS-CoV-2 pandemic events reported across different countries not only can enhance early [19, 20] public and governmental responses in containing the spreading and/or better absorbing the impact of a rapidly emerging epidemic outbreak, but it can further provide new information to better understand real-world epidemics and to boost the forecasting power of existing models [21] [22] [23] [24] [25] [26] [27] [28] [29] . Moving to a polar representation, we classify the plumes'' form through a set of three geometric parameters yielding two complementary rating scales for the SARS-CoV-2 pandemic types: one according to their epidemic magnitude-labeled with roman numbers from I to X for increasing strengths-and measuring the "size" of a national outbreak, and a second one according to their intensity-labeled alphabetically from A to D for increasing speed-quantifying instead the damage inflicted on the population. abstract: While the SARS-CoV-2 keeps spreading world-wide, comparing its evolution across different nations is a timely challenge of both theoretical and practical importance. The large variety of dissimilar and country-dependent epidemiological factors, in fact, makes extremely difficult to understand their influence on the epidemic trends within a unique and coherent framework. We present a geometric framework to characterize, in an integrated and low-dimensional fashion, the epidemic plume-like trajectories traced by the infection rate, $I$, and the fatality rate, $D$, in the $(I,D)$ plane. Our analysis enables the definition of an epidemiometric system based on three geometric observables rating the SARS-CoV-2 pandemic events via scales analogous to those for the magnitude and the intensity of seismic events. Being exquisitely geometric, our framework can be applied to classify other epidemic data and secondary waves, raising the possibility of designing epidemic alerts or early warning systems to enhance public and governmental responses to a rapidly emerging outbreak. url: https://arxiv.org/pdf/2007.10450v1.pdf doi: nan id: cord-302015-z2k6wuhm author: Bonardel, Claire title: Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case date: 2020-06-28 words: 1021.0 sentences: 90.0 pages: flesch: 43.0 cache: ./cache/cord-302015-z2k6wuhm.txt txt: ./txt/cord-302015-z2k6wuhm.txt summary: authors: Bonardel, Claire; Bonnerot, Mathieu; Ludwig, Marie; Vadot, Wilfried; Beaune, Gaspard; Chanzy, Bruno; Cornut, Lucie; Baysson, Hélène; Farines, Magali; Combes, Isabelle; Macheda, Gabriel; Bing, Fabrice title: Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by Covid-19. Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case Abstract In time of SARS-Cov2 pandemic, neurologists need to be vigilant for cerebrovascular complications of Covid-19. We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by . A first brain MRI performed one hour after clinical onset showed bilateral and asymmetric acute occipito-temporal infarction without visibility of the P3 segments of the posterior cerebral arteries (PCA) (Figure 2A to C). abstract: In time of SARS-Cov2 pandemic, neurologists need to be vigilant for cerebrovascular complications of Covid-19. We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by Covid-19. Differential diagnoses are discussed in front of this unusual presentation and evolution. url: https://doi.org/10.1016/j.jstrokecerebrovasdis.2020.105095 doi: 10.1016/j.jstrokecerebrovasdis.2020.105095 id: cord-345879-nbfg47x5 author: Bonaz, Bruno title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? date: 2020-07-29 words: 4072.0 sentences: 213.0 pages: flesch: 44.0 cache: ./cache/cord-345879-nbfg47x5.txt txt: ./txt/cord-345879-nbfg47x5.txt summary: title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? We hypothesize that this cytokine storm and the worsening of patients'' health status can be dampened or even prevented by specifically targeting the vagal-driven cholinergic anti-inflammatory pathway (CAP). Hence, targeting the α7nAChRs through vagus nerve stimulation (VNS) could be of interest in the management of patients with SARS-CoV-2 infection. Indeed, through the wide innervation of the organism by the vagus nerve, especially the lungs and gastrointestinal tract, VNS appears as a serious candidate for a few side effect treatment that could dampen or prevent the cytokine storm observed in COVID-19 patients with severe symptoms. Indeed, a septic shock-induced increase of TNF in the liver and the blood in mice was dampened by stimulation of the distal end cut of the vagus nerve thus arguing for an anti-inflammatory effect of vagal efferents which release acetylcholine (ACh) (Borovikova et al. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), at the origin of the worldwide COVID-19 pandemic, is characterized by a dramatic cytokine storm in some critical patients with COVID-19. This storm is due to the release of high levels of pro-inflammatory cytokines such as interleukin (IL)-1 β, IL-6, tumor necrosis factor (TNF), and chemokines by respiratory epithelial and dendritic cells, and macrophages. We hypothesize that this cytokine storm and the worsening of patients’ health status can be dampened or even prevented by specifically targeting the vagal-driven cholinergic anti-inflammatory pathway (CAP). The CAP is a concept that involves an anti-inflammatory effect of vagal efferents by the release of acetylcholine (ACh). Nicotinic acetylcholine receptor alpha7 subunit (α7nAChRs) is required for ACh inhibition of macrophage-TNF release and cytokine modulation. Hence, targeting the α7nAChRs through vagus nerve stimulation (VNS) could be of interest in the management of patients with SARS-CoV-2 infection. Indeed, through the wide innervation of the organism by the vagus nerve, especially the lungs and gastrointestinal tract, VNS appears as a serious candidate for a few side effect treatment that could dampen or prevent the cytokine storm observed in COVID-19 patients with severe symptoms. Finally, a continuous vagal tone monitoring in patients with COVID-19 could be used as a predictive marker of COVID-19 illness course but also as a predictive marker of response to COVID-19 treatment such as VNS or others. url: https://doi.org/10.1186/s42234-020-00051-7 doi: 10.1186/s42234-020-00051-7 id: cord-258905-0hgdtalg author: Bond, Katherine title: Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date: 2020-08-06 words: 3663.0 sentences: 176.0 pages: flesch: 44.0 cache: ./cache/cord-258905-0hgdtalg.txt txt: ./txt/cord-258905-0hgdtalg.txt summary: METHODS: Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). A testing panel was specifically developed to test PoCT devices for this study (Supplementary Material), consisting of 3 patient populations: (1) sera from 91 patients with SARS-CoV-2 detected by RT-PCR from upper and/or lower respiratory tract specimens; (2) sera from 36 patients with seasonal coronavirus infections or other acute infections (eg, dengue, cytomegalovirus, Epstein-Barr virus); and (3) serum from a random cohort (56 patients) of the Australian population obtained in 2018. In this study, we assessed the performance characteristics of 5 serological PoCT, a commercial ELISA, and a commercial novel sVNT against a large serum panel from a cohort of over 100 patients with RT-PCR-confirmed SARS-CoV-2. abstract: BACKGROUND: Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-of-care (PoCT) serological assays have been distributed with little premarket validation. METHODS: Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). RESULTS: Sensitivities for PoCT ranged from 51.8% (95% confidence interval [CI], 43.1%–60.4%) to 67.9% (95% CI, 59.4%–75.6%), and specificities from 95.6% (95% CI, 89.2%–98.8%) to 100.0% (95% CI, 96.1%–100.0%). ELISA sensitivity for IgA or IgG detection was 67.9% (95% CI, 59.4%–75.6%), increasing to 93.8% (95% CI, 85.0%–98.3%) for samples >14 days post symptom onset. sVNT sensitivity was 60.9% (95% CI, 53.2%–68.4%), rising to 91.2% (95% CI, 81.8%–96.7%) for samples >14 days post symptom onset, with specificity 94.4% (95% CI, 89.2%–97.5%). CONCLUSIONS: Performance characteristics for COVID-19 serological assays were generally lower than those reported by manufacturers. Timing of specimen collection relative to onset of illness or infection is crucial in reporting of performance characteristics for COVID-19 serological assays. The optimal algorithm for implementing serological testing for COVID-19 remains to be determined, particularly in low-prevalence settings. url: https://www.ncbi.nlm.nih.gov/pubmed/32761124/ doi: 10.1093/infdis/jiaa467 id: cord-336481-vrnxu217 author: Bonifácio, Lívia Pimenta title: Are SARS-CoV-2 reinfection and Covid-19 recurrence possible? a case report from Brazil date: 2020-09-18 words: 1521.0 sentences: 93.0 pages: flesch: 54.0 cache: ./cache/cord-336481-vrnxu217.txt txt: ./txt/cord-336481-vrnxu217.txt summary: Case reports have identified persistent or recurrent elimination of viral RNA in nasopharyngeal samples, raising the possibility of reinfection by SARS-CoV-2 [4] [5] [6] [7] . She also reported that the doctor who provided medical care for her on the second episode developed flu-like symptoms about a week after the contact, and Covid-19 was lately confirmed on him by means of nasopharyngeal RT-PCR. DISCUSSION Since the beginning of the Covid-19 pandemic, due to several reports of persistent detection of viral RNA by RT-PCR in a nasopharyngeal or oropharyngeal swab, but without recurrence of symptoms, the possibility of SARS-CoV-2 reinfection has been suggested and investigated by different researchers around the world 5,6,10,11 . In conclusion, this case report presents strong evidence that SARS-CoV-2 reinfection and Covid-19 recurrence, although rare, are possible. This possibility should be further investigated in patients presenting with recurrence of Covid-19 symptoms. abstract: With the large number of individuals infected and recovered from Covid-19, there is intense discussion about the quality and duration of the immunity elicited by SARS-CoV-2 infection, including the possibility of disease recurrence. Here we report a case with strong clinical, epidemiological and laboratorial evidence of, not only reinfection by SARS-CoV-2, but also clinical recurrence of Covid-19. url: https://doi.org/10.1590/0037-8682-0619-2020 doi: 10.1590/0037-8682-0619-2020 id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 words: 3770.0 sentences: 212.0 pages: flesch: 51.0 cache: ./cache/cord-324295-9c1zxjng.txt txt: ./txt/cord-324295-9c1zxjng.txt summary: Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . abstract: Bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. Transmission of highly pathogenic viruses from bats has been suspected and linked to a spectrum of emerging infectious diseases in humans and animals worldwide. Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we provide a comprehensive review on the diversity, reservoirs, and geographical distribution of the main bat viruses and their potential for cross-species transmission. url: https://www.sciencedirect.com/science/article/pii/S1201971220306809?v=s5 doi: 10.1016/j.ijid.2020.08.050 id: cord-301638-2f8r37ns author: Bonney, Glenn Kunnath title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? date: 2020-05-29 words: 709.0 sentences: 55.0 pages: flesch: 54.0 cache: ./cache/cord-301638-2f8r37ns.txt txt: ./txt/cord-301638-2f8r37ns.txt summary: title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? The rapid spread of a novel coronavirus disease (COVID-19) caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) has triggered a global pandemic. [2] The severity of AP observed varies from mild [1, 2] to severe,[43 but unfortunately accepted diagnostic criteria [4] was not used in these studies, raising the possibility that the elevated pancreatic enzymes may be due to other causes including increased gut permeability with SARS-CoV-2 infection. A study from 2010 using immunostaining found ACE2 to be highly expressed in islet cells and postulated that binding of SARS-CoV caused islet cell injury and hyperglycaemia in infected patients. [9] It is not known whether SARS-CoV-2 causes AP, whether the AP is a consequence of severe systemic inflammation and microvascular thrombosis from COVID-19 infection, or whether it is just an epiphenomenon. ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection Coronavirus Disease-19 (COVID-19) associated with severe acute pancreatitis: Case report on three family members abstract: nan url: https://api.elsevier.com/content/article/pii/S1424390320301885 doi: 10.1016/j.pan.2020.05.019 id: cord-334582-ccg27nmf author: Bonora, Benedetta Maria title: Glycaemic Control Among People with Type 1 Diabetes During Lockdown for the SARS-CoV-2 Outbreak in Italy date: 2020-05-11 words: 3846.0 sentences: 184.0 pages: flesch: 50.0 cache: ./cache/cord-334582-ccg27nmf.txt txt: ./txt/cord-334582-ccg27nmf.txt summary: CONCLUSION: Despite the limited possibility to exercise and the incumbent psychologic stress, glycaemic control improved in patients with T1D who stopped working during the lockdown, suggesting that slowing down routine daily activities can have beneficial effects on T1D management, at least in the short term. Using data collected by remote monitoring of glucose sensors, we investigated whether glycaemic control in people with type 1 diabetes (T1D) during lockdown improved or worsened. None of the patients who continued to work showed improvement in any of the measures of glucose control during the lockdown period (period 2) compared to the 3 months or the week before the SARS-CoV-2 outbreak: average glucose, standard deviation, CV%, time in hypoglycaemia, time in range and time in hyperglycaemia remained unchanged (Table 2) , as did the number of scans per day. abstract: INTRODUCTION: In late February 2020, due to the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the Italian Government closed down all educational and sport activities. In March, it introduced further measures to stop the spread of coronavirus disease (COVID-19), placing the country in a state of almost complete lockdown. We report the impact of these restrictions on glucose control among people with type 1 diabetes (T1D). METHODS: Data were collected on 33 individuals with T1D who were monitoring their glucose levels using a flash glucose monitoring device and remotely connected to the diabetes clinic on a cloud platform. We retrieved information on average glucose, standard deviation and percentage time in hypoglycaemia (< 70 mg/dl), glucose range (70–180 mg/dl) and hyperglycaemia (> 180 mg/dl). We compared glycaemic measures collected during lockdown to those collected before the SARS-CoV-2 epidemic and to the periods immediately before lockdown. RESULTS: In 20 patients who had stopped working and were at home as a result of the lockdown, overall glycaemic control improved during the first 7 days of the lockdown as compared to the weeks before the spread of SARS-CoV-2. Average glucose declined from 177 ± 45 mg/dl (week before lockdown) to 160 ± 40 mg/dl (lockdown; p = 0.005) and the standard deviation improved significantly. Time in range increased from 54.4 to 65.2% (p = 0.010), and time in hyperglycaemia decreased from 42.3 to 31.6% (p = 0.016). The number of scans per day remained unchanged. In 13 patients who continued working, none of the measures of glycaemic control changed during lockdown. CONCLUSION: Despite the limited possibility to exercise and the incumbent psychologic stress, glycaemic control improved in patients with T1D who stopped working during the lockdown, suggesting that slowing down routine daily activities can have beneficial effects on T1D management, at least in the short term. url: https://www.ncbi.nlm.nih.gov/pubmed/32395187/ doi: 10.1007/s13300-020-00829-7 id: cord-346212-mcnr7bcp author: Bonzano, Chiara title: Doxycycline: From Ocular Rosacea to COVID-19 Anosmia. New Insight Into the Coronavirus Outbreak date: 2020-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32574320/ doi: 10.3389/fmed.2020.00200 id: cord-249166-0w0t631x author: Booss-Bavnbek, Bernhelm title: Dynamics and Control of Covid-19: Comments by Two Mathematicians date: 2020-08-17 words: 7251.0 sentences: 424.0 pages: flesch: 60.0 cache: ./cache/cord-249166-0w0t631x.txt txt: ./txt/cord-249166-0w0t631x.txt summary: We give an overview of the main branches of mathematics that play a role and sketch the most frequent applications, emphasising mathematical pattern analysis in laboratory work and statistical-mathematical models in judging the quality of tests; demographic methods in the collection of data; different ways to model the evolution of the pandemic mathematically; and clinical epidemiology in attempts to develop a vaccine. A few physicians suggested that every epidemic ends because there are finally not enough people left to be infected, which is a naïve predecessor to the mathematical-epidemiologic concept of Herd Immunity (see Sect. Parallel to the entering the scene of these and other epidemics, and partly motivated by them, basically new mathematical tools of public health emerged in the first part of the 20 th Century, preceded by a few studies in the late 19 th . Dealing with large epidemics mathematically was no longer a matter of demography alone, although that continued to be the main tool for estimating number of cases and deaths. abstract: We are asking: why are the dynamics and control of Covid-19 most interesting for mathematicians and why are mathematicians urgently needed for controlling the pandemic? First we present our comments in a Bottom-up approach, i.e., following the events from their beginning as they evolved through time. They happened differently in different countries, and the main objective of the first part is to compare these evolutions in a few selected countries with each other. The second part of the article is not"country-oriented"but"problem-oriented". From a given problem we go Top-down to its solutions and their applications in concrete situations. We have organized this part by the mathematical methods that play a role in their solution. We give an overview of the main branches of mathematics that play a role and sketch the most frequent applications, emphasising mathematical pattern analysis in laboratory work and statistical-mathematical models in judging the quality of tests; demographic methods in the collection of data; different ways to model the evolution of the pandemic mathematically; and clinical epidemiology in attempts to develop a vaccine. url: https://arxiv.org/pdf/2008.07929v1.pdf doi: nan id: cord-262499-68vmdqky author: Bordi, Licia title: Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay date: 2020-10-20 words: 5037.0 sentences: 311.0 pages: flesch: 56.0 cache: ./cache/cord-262499-68vmdqky.txt txt: ./txt/cord-262499-68vmdqky.txt summary: We evaluated the use of commercial Simplexa™ COVID-19 Direct assay on OF samples from hospitalized COVID-19 patients, for identification of SARS-CoV-2 RNA, duration of viral shedding, and determining the assay specificity and sensitivity on OF samples compared to NPS and BAL samples. The first performance evaluation on clinical specimen was done by testing 41 consecutive OF samples, including 9 samples from SARS-CoV-2-negative patients, with the Simplexa™ COVID-19 Direct assay and comparing results with that obtained using RT-PCR method established by Corman VM. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. Second, results from testing on paired OF, NPS and BAL samples by Simplexa™ COVID-19 Direct assay showed almost perfect concordance for virus detection, and high correlation of Ct values. abstract: Background: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral load and shedding. Methods: Optimal assay conditions and analytical sensitivity were established for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients; 50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were also analysed. Results: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection down to 1 TCID50/mL (corresponding to 4 × 10(3) copies (cp)/mL) was observed. No crossreaction with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771–0.891), and high correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples, respectively, collected between 60 and 100 DSO. Conclusions: Simplexa™ COVID-19 Direct assays on OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to NPS for diagnosis and monitoring SARS-CoV-2 shedding. url: https://www.ncbi.nlm.nih.gov/pubmed/33092065/ doi: 10.3390/v12101184 id: cord-295957-s17z2ccf author: Bordi, Licia title: Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay date: 2020-05-04 words: 1923.0 sentences: 108.0 pages: flesch: 52.0 cache: ./cache/cord-295957-s17z2ccf.txt txt: ./txt/cord-295957-s17z2ccf.txt summary: BACKGROUND: So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. CONCLUSIONS: The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients. Moreover, to evaluate the performance of the test in a different clinical specimen, a total of 33 Broncho-Alveolar Lavage (BAL) collected for COVID-19 diagnosis between 20 March and 03 April 2020 were also analysed in parallel with the Simplexa™ COVID-19 Direct assay and the routine laboratory method, based on the WHO protocols (7, 8) , using the Abbot m2000 extraction platform. abstract: BACKGROUND: So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. OBJECTIVE: The aim of this study was to evaluate the performances of a newly designed real-time RT-PCR (Simplexa™ COVID-19 Direct assay), that is established with an all-in-one reagent mix and no separate extraction required. RESULTS: The lower limit of detection (LOD) for both target genes resulted the same: 3.2 (CI: 2.9–3.8) log10 cp/mL and 0.40 (CI: 0.2–1.5) TCID50/mL for S gene while 3.2 log10 (CI: 2.9–3.7) log10 cp/mL and 0.4 (CI: 0.2–1.3) TCID50/mL for ORF1ab. The LOD obtained with extracted viral RNA for both S gene or ORF1ab was 2.7 log10 cp/mL. Crossreactive analysis performed in 20 nasopharyngeal swabs confirmed a 100% of clinical specificity of the assay. Clinical performances of Simplexa™ COVID-19 Direct assay were assessed in 278 nasopharyngeal swabs tested in parallel with Corman's method. Concordance analysis showed an "almost perfect" agreement in SARS-CoV-2 RNA detection between the two assays, being κ = 0.938; SE = 0.021; 95% CI = 0.896-0.980. CONCLUSIONS: The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients. url: https://www.sciencedirect.com/science/article/pii/S138665322030158X?v=s5 doi: 10.1016/j.jcv.2020.104416 id: cord-327095-y2zsm8sc author: Boretti, Alberto title: Favipiravir use for SARS CoV-2 infection date: 2020-10-27 words: 2310.0 sentences: 158.0 pages: flesch: 55.0 cache: ./cache/cord-327095-y2zsm8sc.txt txt: ./txt/cord-327095-y2zsm8sc.txt summary: For the specific use against SARS CoV-2, [22] evaluated the in vitro efficacy of different drugs, from Remdesivir to Chloroquine, also including Favipiravir. Li and De Clercq [23] include Favipiravir together with Remdesivir, Galidesivir, and Ribavirin in between the existing antiviral agents'' RNA-dependent RNA polymerase inhibitors to repurpose to treat SARS CoV-2 infection. [24] also include Favipiravir, together with Chloroquine, Arbidol, and Remdesivir, all under clinical studies in China to test their efficacy and safety for SARS CoV-2 infection. Up to date, there is not enough information from specific trials to infer any conclusion on the use of Favipiravir for SARS CoV-2 infection. SARS-CoV-2: recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus Dose rationale for favipiravir use in patients infected with SARS-CoV-2 abstract: INTRODUCTION: The pandemic of SARS CoV-2 has required urgent medical treatments for numerous patients. As no specific antiviral agents were available, different off-the-shelf alternatives have been explored. OBJECTIVE: Here, we review the rationale behind the use of Favipiravir, and report of the specific studies supporting this treatment being conducted. METHODS: Here we analyze the relevant literature to conclude about the present opportunities offered by this therapeutic agent. RESULTS: This antiviral drug approved influenza in Japan since 2014, has a demonstrated in vitro activity against SARS CoV-2 and is being investigated in several trials for SARS CoV-2. Signals of benefit were shown in a small trial for SARS CoV-2. However, in another small study, there was no advantage. CONCLUSIONS: Further studies, statistically more significant, are urgently needed to understand the best opportunities offered by this treatment. url: https://doi.org/10.1007/s43440-020-00175-2 doi: 10.1007/s43440-020-00175-2 id: cord-292386-hfbgigj6 author: Borges, Lysandro Pinto title: Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil date: 2020-10-06 words: 3897.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-292386-hfbgigj6.txt txt: ./txt/cord-292386-hfbgigj6.txt summary: In order to support the ongoing public health response, all participants who tested positive for SARS-CoV-2 antibodies were contacted by phone by staff from the designated authorities to track the infection. The importance of NPIs on reducing the infection rate was observed in Vo, Italy, where prevalence estimates showed a significant decrease after a period of lockdown, suggesting that viral transmission could be effectively suppressed by combining the early isolation of detected cases with social distancing total assessed cases in that city [CI, 11.5% -21.4%]) and 12 (5.9% of the total assessed cases in that city [CI, 3.1% -10.1%]) cases; Itabaiana, that presented 55 (14.8% of the total assessed cases in that city [CI, 11.4 -18.9]) and 17 of the total assessed cases in that city (5.4% [CI, 3.1% -8.4%]) cases, being the three cities with the highest seroprevalence of SARS-CoV-2 in the state. abstract: OBJECTIVE. To estimate the prevalence of SARS-CoV-2 antibodies in an asymptomatic population in the state of Sergipe, Brazil. METHODS. This cross-sectional study with stratified sampling (sex and age) included serological immunofluorescent tests for IgM and IgG on samples from 3 046 asymptomatic individuals. Sample collection was performed in wet-markets of the 10 most populous cities of Sergipe, Brazil. Exclusion criteria included symptomatic individuals and health workers. The presence of comorbidities was registered. RESULTS. Of the 3 046 participants, 1 577 (51.8%) were female and 1 469 (48.2%) were male; the mean age was 39.76 (SD 16.83) years old. 2 921 tests were considered valid for IgM and 2 635 for IgG. Of the valid samples, 347 (11.9% [CI 10.7%–13.1%]) tested positive for IgM and 218 (8.3% [CI 7.2%–9.4%]) tested positive for IgG. Women over 40 had the highest prevalence for IgM (group C, p=0.006; group D p=0.04). The capital Aracaju displayed the highest prevalence for both antibodies; 83 (26.3% [CI 21.6%-31.6%]) tested positive for IgM and 35 (14.6% [CI 10.4%-19.7%]) for IgG. The most prevalent comorbidities were hypertension (64/123 individuals) and diabetes (29/123). CONCLUSIONS. A high prevalence of SARS-CoV-2 antibodies was found among asymptomatic persons in Sergipe. Women over 40 showed the highest rates. The capital, Aracaju, displayed the highest seroprevalence. Surveys like this one are important to understand how the virus spreads and to help authorities to plan measures to control it. Repeated serologic testing are required to track the progress of the epidemic. url: https://doi.org/10.26633/rpsp.2020.108 doi: 10.26633/rpsp.2020.108 id: cord-353274-wozwpvpq author: Borremans, B. title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date: 2020-05-20 words: 6160.0 sentences: 362.0 pages: flesch: 50.0 cache: ./cache/cord-353274-wozwpvpq.txt txt: ./txt/cord-353274-wozwpvpq.txt summary: In this study we quantified IgG and IgM antibody kinetics and RNA shedding probability during SARS-CoV-2 infection (up to 60 days post symptom onset) by drawing on published data. This formal integration approach enabled us to leverage 3,214 data points from 516 individuals with symptoms ranging from asymptomatic to critical, published in 22 studies, resulting in a quantitative synthesis of diverse data on anti-SARS-CoV-2 antibody patterns and RNA shedding during the early phase of infection. One of the goals of this study is to estimate the means and variation of IgG and IgM seroconversion times (time between symptom onset and first antibody detection) for different assays, antigens, and disease severity. . https://doi.org/10.1101/2020.05.15.20103275 doi: medRxiv preprint weighted bootstrapping procedure integrates all types of data that contain useful information about the timing of seroconversion of different antibodies in day(s) post symptom onset (dpo). The probability of detecting SARS-CoV-2 specific IgG or IgM in plasma or serum samples was estimated by integrating data on whether an individual tested positive or negative on a given dpo. abstract: Our ability to understand and mitigate the spread of SARS-CoV-2 depends largely on antibody and viral RNA data that provide information about past exposure and shedding. Five months into the outbreak there is an impressive number of studies reporting antibody kinetics and RNA shedding dynamics, but extensive variation in detection assays, study group demographics, and laboratory protocols has presented a challenge for inferring the true biological patterns. Here, we combine existing data on SARS-CoV-2 IgG, IgM and RNA kinetics using a formal quantitative approach that enables integration of 3,214 data points from 516 individuals, published in 22 studies. This allows us to determine the mean values and distributions of IgG and IgM seroconversion times and titer kinetics, and to characterize how antibody and RNA detection probabilities change during the early phase of infection. We observe extensive variation in antibody response patterns and RNA detection patterns, explained by both individual heterogeneity and protocol differences such as targeted antigen and sample type. These results provide a robust reference for clinical management of individual patients, and a foundation for the mathematical models and serological surveys that underpin public health policies. url: https://doi.org/10.1101/2020.05.15.20103275 doi: 10.1101/2020.05.15.20103275 id: cord-314793-kb319t4c author: Borroni, Barbara title: Diaphragmatic myoclonus due to SARS-CoV-2 infection date: 2020-10-22 words: 1636.0 sentences: 101.0 pages: flesch: 47.0 cache: ./cache/cord-314793-kb319t4c.txt txt: ./txt/cord-314793-kb319t4c.txt summary: Neurological signs in patients with SARS-CoV-2 have been widely reported, suggesting a neuroinvasive nature of virus [2, 3] . With the present observation, we report two cases of diaphragmatic myoclonus as neurological subacute manifestation of SARS-CoV-2 infection. The Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10072-020-04766-y) contains supplementary material, which is available to authorized users. Electromyographic recording confirmed rhythmic and synchronous contractions of the diaphragm at 3-Hz frequency as the cause of her abdominal movements (see Fig. 1 ), thus making the diagnosis of diaphragmatic myoclonus or van Leeuwenhoek''s disease [5] . Here, we draw attention to two patients who developed focal diaphragmatic myoclonus after SARS-CoV-2 infection. Indeed, three cases of generalized myoclonus due to SARS-CoV-2 infection have been recently reported [10] . With the present report of two cases, we confirm and extend the neurotropic properties of SARS-CoV-2 virus and point out to a further neurological clinical manifestation of the infection. abstract: A wide range of neurological signs and symptoms have been associated with SARS-CoV-2 infection. In the present report, we described two Italian patients diagnosed with diaphragmatic myoclonus after COVID-19. In both cases, mild lymphocytosis at cerebrospinal fluid analysis and no structural brain changes were reported. The pathophysiological origin of the myoclonus in the two cases was different. In case 1, electroencephalogram did not reveal any cortical correlates and brain imaging of the spine was unremarkable, while in case 2, cortical origin of myoclonus was demonstrated. With the present two cases, we confirm and extend the neurological manifestations of SARS-CoV-2 infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10072-020-04766-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10072-020-04766-y doi: 10.1007/s10072-020-04766-y id: cord-314948-7tnrfk24 author: Borrás, A title: Pandemia del SARS-CoV-2 y reproducción asistida date: 2020-06-19 words: 5419.0 sentences: 561.0 pages: flesch: 53.0 cache: ./cache/cord-314948-7tnrfk24.txt txt: ./txt/cord-314948-7tnrfk24.txt summary: Estas medidas fueron cruciales no sólo para permitir hospitales e instalaciones médicas tratar el aumento explosivo de pacientes con la infección por SARS-CoV-2 (denominada COVID19) , sino también para reducir la transmisión de la enfermedad, mediante estrategias de mitigación, especialmente individuales (el aislamiento). Se sugiere que la presencia de ACE2 puede ser uno de los principales determinantes de la susceptibilidad de las células a la infección por SARS-CoV-2. Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida abstract: Abstract The pandemic caused by the new SARS-CoV-2 virus has led to a process of adaptation to the new situation by society as a whole and, therefore, by assisted reproduction centres. After the acute phase of the health crisis, when activity was drastically reduced, cycles have resumed, guided by the recommendations of scientific societies. In this article, a review is presented of all the published information regarding the virus and the reproductive system, pointing out the presence of ACE2 in the female and male reproductive system, at the testicular, ovarian, endometrial and embryonic levels. In addition, a comparative analysis is carried out between the recommendations of the scientific societies regarding the screening of infection, performance standards, and general laboratory measurements. url: https://doi.org/10.1016/j.gine.2020.06.004 doi: 10.1016/j.gine.2020.06.004 id: cord-333391-6l0cpvgr author: Bortolotti, Daria title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 words: 5689.0 sentences: 309.0 pages: flesch: 57.0 cache: ./cache/cord-333391-6l0cpvgr.txt txt: ./txt/cord-333391-6l0cpvgr.txt summary: title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. abstract: Natural killer cells are important in the control of viral infections. However, the role of NK cells during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has previously not been identified. Peripheral blood NK cells from SARS-CoV and SARS-CoV-2 naïve subjects were evaluated for their activation, degranulation, and interferon-gamma expression in the presence of SARS-CoV and SARS-CoV-2 spike proteins. K562 and lung epithelial cells were transfected with spike proteins and co-cultured with NK cells. The analysis was performed by flow cytometry and immune fluorescence. SARS-CoV and SARS-CoV-2 spike proteins did not alter NK cell activation in a K562 in vitro model. On the contrary, SARS-CoV-2 spike 1 protein (SP1) intracellular expression by lung epithelial cells resulted in NK cell-reduced degranulation. Further experiments revealed a concomitant induction of HLA-E expression on the surface of lung epithelial cells and the recognition of an SP1-derived HLA-E-binding peptide. Simultaneously, there was increased modulation of the inhibitory receptor NKG2A/CD94 on NK cells when SP1 was expressed in lung epithelial cells. We ruled out the GATA3 transcription factor as being responsible for HLA-E increased levels and HLA-E/NKG2A interaction as implicated in NK cell exhaustion. We show for the first time that NK cells are affected by SP1 expression in lung epithelial cells via HLA-E/NKG2A interaction. The resulting NK cells’ exhaustion might contribute to immunopathogenesis in SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32859121/ doi: 10.3390/cells9091975 id: cord-326736-jd6fvaop author: Bosco-Lauth, Angela M. title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date: 2020-05-29 words: 922.0 sentences: 68.0 pages: flesch: 50.0 cache: ./cache/cord-326736-jd6fvaop.txt txt: ./txt/cord-326736-jd6fvaop.txt summary: title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. The first report of reverse zoonosis, or transmission from human to animal, was reported 46 from Hong Kong, where a COVID patient''s dog tested PCR positive for SARS2 multiple times 47 (Sit et al. Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of 414 COVID-19 patients in a veterinary campus Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Transmission of 422 SARS-CoV-2 in Domestic Cats abstract: The pandemic caused by SARS-CoV-2 has reached nearly every country in the world with extraordinary person-to-person transmission. The most likely original source of the virus was spillover from an animal reservoir and subsequent adaptation to humans sometime during the winter of 2019 in Wuhan Province, China. Because of its genetic similarity to SARS-CoV-1, it is likely that this novel virus has a similar host range and receptor specificity. Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. We report that cats are highly susceptible to subclinical infection, with a prolonged period of oral and nasal viral shedding that is not accompanied by clinical signs, and are capable of direct contact transmission to other cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. Further, we document that cats develop a robust neutralizing antibody response that prevented re-infection to a second viral challenge. Conversely, we found that dogs do not shed virus following infection, but do mount an anti-viral neutralizing antibody response. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. Resistance to re-exposure holds promise that a vaccine strategy may protect cats, and by extension humans, to disease susceptibility. url: https://doi.org/10.1101/2020.05.28.120998 doi: 10.1101/2020.05.28.120998 id: cord-269946-zb7gcw0m author: Boscolo-Rizzo, Paolo title: New onset of loss of smell or taste in household contacts of home-isolated SARS-CoV-2-positive subjects date: 2020-05-24 words: 1766.0 sentences: 85.0 pages: flesch: 53.0 cache: ./cache/cord-269946-zb7gcw0m.txt txt: ./txt/cord-269946-zb7gcw0m.txt summary: PURPOSE: To estimate the prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. To better estimate the burden of smell and taste impairment during COVID-19 pandemic, we searched for the prevalence of these symptoms in subjects at high risk for SARS-CoV-2 infection, i.e. household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. We previously reported the prevalence of loss of the sense of smell or taste as well as other COVID-19 symptoms in a case series of 202 home-isolated mildly symptomatic confirmed cases of SARS-CoV-2 infection [8] . The prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients was 1.5%, 22.3%, and 63.0% in subjects tested negative, non-tested, and tested positive for SARS-CoV-2 infection, respectively. However, this study showed that smell or taste impairment is quite common in not-tested household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. abstract: PURPOSE: To estimate the prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. METHODS: Cross-sectional study based on ad hoc questions. RESULTS: Of 214 mildly symptomatic COVID-19 patients managed at home under self-isolation, 179 reported to have at least one household contact, with the total number of no study participants contacts being 296. Among 175 household contacts not tested for SARS-CoV-2 infection, 67 (38.3%) had SARS-CoV-2 compatible symptoms, 39 (22.3%) had loss of smell or taste with 7 (4.0%) having loss of smell or taste in the absence of other symptoms. The prevalence of smell or taste impairment was 1.5% in patients tested negative compared to 63.0% of those tested positive for SARS-CoV-2 (p < 0.001). CONCLUSION: Smell or taste impairment are quite common in not-tested household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. This should be taken into account when estimating the burden of loss of sense of smell and taste during COVID-19 pandemic, and further highlights the value of loss of sense of smell and taste as a marker of infection. url: https://doi.org/10.1007/s00405-020-06066-9 doi: 10.1007/s00405-020-06066-9 id: cord-273311-dl9u85nh author: Boscolo‐Rizzo, Paolo title: Challenges in interpreting the diagnostic performance of symptoms to predict COVID‐19 status: the case of anosmia date: 2020-06-25 words: 430.0 sentences: 34.0 pages: flesch: 54.0 cache: ./cache/cord-273311-dl9u85nh.txt txt: ./txt/cord-273311-dl9u85nh.txt summary: Consequently, several studies have tried to estimate the sensitivity and specificity as well as the positive predictive value of self-reported new onset of smell and/or taste impairment for COVID-19 in populations of patients with flu-like symptoms. The first is that the standard diagnostic tool for diagnosis of SARS-CoV-2 infection, i.e. This article is protected by copyright. While the pooled sensitivity was 61% (95% CI, 55-68%), the pooled specificity reached 87% (95% CI, 80-92%); publication bias is possible (Figure 1b In conclusion, despite we believe that the new onset of smell and/or taste loss during COVID-19 pandemic should be considered a manifestation of SARS-CoV-2 infection until proven otherwise, sufficient to justify testing, self-isolation and the use of personal protective equipment by medical personnel interacting with these subjects, taken into account the above considerations, diagnostic performance of single symptoms should be fully understood and considered with caution when predicting SARS-CoV-2 infection in patients with flu-like symptoms. abstract: nan url: https://doi.org/10.1002/alr.22650 doi: 10.1002/alr.22650 id: cord-304139-ya3d7u9b author: Bosmann, Markus title: Complement Activation during Critical Illness: Current Findings and an Outlook in the Era of COVID-19 date: 2020-07-15 words: 2000.0 sentences: 104.0 pages: flesch: 35.0 cache: ./cache/cord-304139-ya3d7u9b.txt txt: ./txt/cord-304139-ya3d7u9b.txt summary: 230-240) report on the association between alternative complement pathway activity and better survival in patients with critical illness (3). The alternative pathway hemolytic assay (AH50) and total complement activity (CH50) tests were retrospectively analyzed in a single-center heterogeneous cohort of n = 321 patients with acute respiratory distress syndrome (33%), with suspected sepsis (63%), and on mechanical ventilation (96%). Inappropriate complement activity may result in the unloading of harmful effector functions on host cells, with the consequence of disease-causing tissue injury and organ dysfunction during critical illness. Complement activation may occur early during SARS-CoV-2 infection by the direct interaction of viral proteins with the MBL (mannose-binding lectin) and ficolin pathway, rather than the alternative pathway. In another experimental study, the host transcriptional response in SARS-CoV-2-infected A549 human lung epithelial cells included the differential expression of C3, C1R, and other complement proteins (10) . Increased alternative complement pathway function and improved survival during critical illness abstract: nan url: https://doi.org/10.1164/rccm.202005-1926ed doi: 10.1164/rccm.202005-1926ed id: cord-260673-gf028lf6 author: Bottemanne, Hugo title: Does the Coronavirus Epidemic Take Advantage of Human Optimism Bias? date: 2020-08-26 words: 3397.0 sentences: 150.0 pages: flesch: 45.0 cache: ./cache/cord-260673-gf028lf6.txt txt: ./txt/cord-260673-gf028lf6.txt summary: Building on evidence from past epidemics and three decades of research in psychology suggesting that various cognitive biases influence beliefs about life hazards, we propose that such cognitive biases have contributed to the discrepancy between early warnings about the danger of SARS-CoV-2 and slow growth of consideration for these warnings. Importantly, data collected in Western countries during the peak of the COVID 19 pandemic provides direct evidence favoring the hypothesis that unrealistic optimism has played a role in the apparent discrepancy between official warnings and individual beliefs about the consequences of the pandemic for oneself: When getting infected and infecting others became frequent events as the number of cases and deaths sharply increased, citizens in the US, Europe and the United Kingdom estimated their probability of getting infected with the virus and of subsequently infecting others as lower for themselves than for someone else (Dolinski et al., 2020; Kuper-Smith et al., 2020) . abstract: nan url: https://doi.org/10.3389/fpsyg.2020.02001 doi: 10.3389/fpsyg.2020.02001 id: cord-252818-1gms4zw3 author: Bouayed, Jaouad title: Behavioural manipulation ‐ key to the successful global spread of the new Coronavirus SARS‐Cov‐2? date: 2020-08-19 words: 2492.0 sentences: 131.0 pages: flesch: 46.0 cache: ./cache/cord-252818-1gms4zw3.txt txt: ./txt/cord-252818-1gms4zw3.txt summary: The very rapid global spread has raised the issue whether there are further multi‐dimensional consequences of SARS‐CoV‐2 infection on human behaviour, the key of its transmission. In this perspective, we highlight the possibility that COVID‐19 is facilitated by altered human social behaviour that benefits SARS‐CoV‐2 transmission, through showcasing similar virus‐induced changed behaviour by other pathogens and relating this to reports from the grey literature. Interestingly, it was also estimated that 10% of the cases are super-spreaders, resulting in 80% of viral spread, meaning that the majority of SARS-CoV-2 carriers do not appear to unaccountably transmit the virus. In this perspective, we highlighted the possibility that COVID-19 is facilitated by altered human social behaviour that benefits SARS-CoV-2 transmission (Figure 1 ). The scheme highlights the potential manipulative strategy of the novel coronavirus, resulting in viral spread, following an altered behavioural pattern in some COVID-19 patients, as a consequence of a direct impact on brain structure/function, owing to viral infiltration into the CNS, and/or via perturbation of the brain-immune axis or the gut-brain axis. abstract: Human‐ SARS‐CoV‐2 interaction can have an array of various outcomes – it could be mortal, morbid or merely carrying minor health consequences. The very rapid global spread has raised the issue whether there are further multi‐dimensional consequences of SARS‐CoV‐2 infection on human behaviour, the key of its transmission. During the coronavirus crisis, odd, abnormal, and irresponsible behaviour has been reported in COVID‐19 individuals, particularly in super‐spreaders, i.e. persons with a high viral load, thus constituting also super‐emitters. Indeed, cases of infected persons ignoring self‐confinement orders, intentionally disregarding physical distancing and multiplying social interactions, or even deliberately sneezing, spitting or coughing were reported. While it is known that some other viruses such as rabies and even influenza do change human behaviour, this remains unclear for SARS‐CoV‐2. In this perspective, we highlight the possibility that COVID‐19 is facilitated by altered human social behaviour that benefits SARS‐CoV‐2 transmission, through showcasing similar virus‐induced changed behaviour by other pathogens and relating this to reports from the grey literature. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26446 doi: 10.1002/jmv.26446 id: cord-331055-5ni0jxij author: Bouche, Pierre-Alban title: Were protective procedures against SARS-CoV-2 effective in an orthopaedic and trauma centre during the lockdown period? A retrospective study date: 2020-07-16 words: 2361.0 sentences: 151.0 pages: flesch: 51.0 cache: ./cache/cord-331055-5ni0jxij.txt txt: ./txt/cord-331055-5ni0jxij.txt summary: To take care of COVID-19 positive and negative patients, various procedures have been set up: reverse transcriptase polymerase chain reaction (RT-PCR) tests for all hospitalized patients, a specific unit for COVID-positive patients, a specific surgical room, and use of protective personal equipment. To allow the effectiveness of the procedures implemented, we evaluated the number of complications attributed to SARS-CoV-2 and the number of patients who became COVID positive during hospitalization. All elective surgery had to be stopped in order to decrease the influx of patients into hospitals and to redeploy medical and paramedical staff in different units to provide assistance in emergency departments, COVID-19 units, and intensive care units [6] . The purpose of this retrospective study was to assess the effectiveness of the guidelines implemented in our orthopaedic and trauma centre, Cochin Hospital, during the lockdown imposed in France period between March 15 and May 11, 2020. abstract: PURPOSE: The SARS-CoV-2 epidemic started in December 2019 in Wuhan. The lockdown was declared on March 16, 2020 in France. Our centre had to adapt daily practices to continue to take care of bone and soft tissue tumours and emergencies. Through this study, we wanted to assess the various procedures implemented during the lockdown period between March 17 and May 10. METHODS: A monocentric retrospective cohort study was conducted in Cochin Hospital (Paris, France). Patients included were those who had surgery during the lockdown period. To take care of COVID-19 positive and negative patients, various procedures have been set up: reverse transcriptase polymerase chain reaction (RT-PCR) tests for all hospitalized patients, a specific unit for COVID-positive patients, a specific surgical room, and use of protective personal equipment. To allow the effectiveness of the procedures implemented, we evaluated the number of complications attributed to SARS-CoV-2 and the number of patients who became COVID positive during hospitalization. RESULTS: During the lockdown period, there were 199 procedures of three types of procedures in our centre: 79 traumatology procedures (39.7%), 76 of bone and soft tissues tumours (38.2%), and 44 procedures related to infection (22.1%). We observed 13 complications (6.5%) during hospitalization, and only one patient became COVID-19 positive during the hospitalization. CONCLUSION: The COVID-19 epidemic has been a challenge for organization and adaptation to manage all COVID-19 positive and COVID negative. Through this study, we wanted to assess our procedures taken. They had been effective due to the low number of contamination and complications. url: https://www.ncbi.nlm.nih.gov/pubmed/32676776/ doi: 10.1007/s00264-020-04729-0 id: cord-290845-bf1q4k6t author: Bouchghoul, Hanane title: Do pregnant women have protective immunity against COVID‐19? date: 2020-06-24 words: 474.0 sentences: 35.0 pages: flesch: 51.0 cache: ./cache/cord-290845-bf1q4k6t.txt txt: ./txt/cord-290845-bf1q4k6t.txt summary: Thornton, in which the author relates that coronavirus disease 2019 (COVID-19) is less severe in pregnancy than the two previous coronavirus infections, SARS and Middle East respiratory syndrome. Furthermore, as SARS-CoV-2 infection can activate innate and adaptive immune responses with severe consequences, pregnant women could be preserved by the state of immunomodulation during pregnancy. In the most severe SARS-CoV-2 infections we report uncontrolled inflammatory innate responses and impaired adaptive immune responses that may lead to harmful tissue damage, both locally and systemically. 3 A cytokine profile has been reported in most severe SARS-CoV-2 infections, characterised by increased levels of cytokines and chemokines. As in patients infected with SARS-CoV-2, the serious complication is acute respiratory distress syndrome and ventilation of the mother may be difficult in the third trimester of pregnancy; it is certainly possible that the decision to delivery by an elective caesarean section was influenced by the understandable anxiety towards the potential consequences. COVID19 during pregnancy: a systematic review of reported cases abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32583553/ doi: 10.1111/1471-0528.16342 id: cord-336560-m5u6ryy9 author: Boudewijns, Robbert title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 words: 5019.0 sentences: 308.0 pages: flesch: 51.0 cache: ./cache/cord-336560-m5u6ryy9.txt txt: ./txt/cord-336560-m5u6ryy9.txt summary: Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . abstract: Since the emergence of SARS-CoV-2 causing COVID-19, the world is being shaken to its core with numerous hospitalizations and hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that productive SARS-CoV-2 infection in the lungs of mice is limited and restricted by early type I interferon responses. In contrast, we show that Syrian hamsters are highly permissive to SARS- CoV-2 and develop bronchopneumonia and a strong inflammatory response in the lungs with neutrophil infiltration and edema. Moreover, we identify an exuberant innate immune response as a key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Finally, we assess SARS-CoV- 2-induced lung pathology in hamsters by micro-CT alike used in clinical practice. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. url: https://doi.org/10.1101/2020.04.23.056838 doi: 10.1101/2020.04.23.056838 id: cord-324128-css42bsb author: Boukli, Narjis title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies date: 2020-10-21 words: 949.0 sentences: 56.0 pages: flesch: 53.0 cache: ./cache/cord-324128-css42bsb.txt txt: ./txt/cord-324128-css42bsb.txt summary: title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies The median day of IgG seroconversion is around 14 days after symptom onset (2), but a high interindividual variation has been reported, as well as contrasting performances between commercial assays (3) (4) (5) (6) . Furthermore, the 100 samples in our specificity panel were negative with the Alinity I SARS-CoV-2 IgG assay, except for one serum sample from a patient with coronavirus 229E infection, which was weakly reactive (signal-to-cutoff index ϭ 1.93; cutoff is 1.4 index), which leads to a specificity of 99%. While the clinical significance of SARS-Cov-2 antibody detection remains to be determined, our results confirm that careful evaluation of the tests on appropriate samples is required before implementing assays for routine use. abstract: Coronavirus disease 19 (COVID-19), caused by SARS-CoV-2 is a major pandemic (2).…. url: https://www.ncbi.nlm.nih.gov/pubmed/32848041/ doi: 10.1128/jcm.01352-20 id: cord-317952-4oa9hfb4 author: Bourgonje, Arno R. title: Angiotensin‐converting enzyme‐2 (ACE2), SARS‐CoV‐2 and pathophysiology of coronavirus disease 2019 (COVID‐19) date: 2020-05-17 words: 12082.0 sentences: 664.0 pages: flesch: 38.0 cache: ./cache/cord-317952-4oa9hfb4.txt txt: ./txt/cord-317952-4oa9hfb4.txt summary: ACE2 was highly expressed on lung alveolar epithelial cells and small intestinal epithelial cells, consistent with potential routes of viral transmission of SARS-CoV-2, as both respiratory and gastrointestinal systems share interfaces with the external environment. ACE2 expression in the lungs and SARS-CoV-2 viral load have been suggested to increase with age, which might provide an explanation to the higher disease severity observed in older patients with COVID-19 [35] . Both SARS-CoV-2 infection, directly mediated by ACE2 expression and activity, and superimposed disease triggers may be responsible for the observed pathological findings. Additionally, another study reported purpura and livedo racemosa in several severely affected COVID-19 patients with small vessel thrombosis with co-localization of complement and SARS-CoV-2 spike proteins on histopathology [148] .This indicates direct viral infection of the small skin vessels. Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone-inhibitors: Potential implications for coronavirus SARS-CoV-2 infected patients abstract: Angiotensin‐converting enzyme‐2 (ACE2) has been established as the functional host receptor for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the virus responsible for the current devastating worldwide pandemic of coronavirus disease 2019 (COVID‐19). ACE2 is abundantly expressed in a variety of cells residing in many different human organs. In human physiology, ACE2 is a pivotal counter‐regulatory enzyme to ACE by the breakdown of angiotensin II, the central player in the renin‐angiotensin‐aldosterone system (RAAS) and the main substrate of ACE2. Many factors have been associated with both altered ACE2 expression and COVID‐19 severity and progression, including age, sex, ethnicity, medication and several co‐morbidities, such as cardiovascular disease and metabolic syndrome. Although ACE2 is widely distributed in various human tissues and many of its determinants have been well recognised, ACE2‐expressing organs do not equally participate in COVID‐19 pathophysiology, implying that other mechanisms are involved in orchestrating cellular infection resulting in tissue damage. Reports of pathologic findings in tissue specimens of COVID‐19 patients are rapidly emerging and confirm the established role of ACE2 expression and activity in disease pathogenesis. Identifying pathologic changes caused by SARS‐CoV‐2 infection is crucially important as it has major implications for understanding COVID‐19 pathophysiology and the development of evidence‐based treatment strategies. Currently, many interventional strategies are being explored in ongoing clinical trials, encompassing many drug classes and strategies, including antiviral drugs, biological response modifiers and RAAS inhibitors. Ultimately, prevention is key to combat COVID‐19 and appropriate measures are being taken accordingly, including development of effective vaccines. In this review, we describe the role of ACE2 in COVID‐19 pathophysiology, including factors influencing ACE2 expression and activity in relation to COVID‐19 severity. In addition, we discuss the relevant pathological changes resulting from SARS‐CoV‐2 infection. Finally, we highlight a selection of potential treatment modalities for COVID‐19. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/path.5471 doi: 10.1002/path.5471 id: cord-268886-mpceglk1 author: Bourne, T. title: ISUOG Consensus Statement on rationalization of gynecological ultrasound services in context of SARS‐CoV‐2 date: 2020-04-08 words: 3086.0 sentences: 198.0 pages: flesch: 46.0 cache: ./cache/cord-268886-mpceglk1.txt txt: ./txt/cord-268886-mpceglk1.txt summary: Given the challenges of the current coronavirus (SARS-CoV-2) pandemic and to protect both patients and ultrasound providers (physicians, sonographers, allied professionals), the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) has compiled the following expert-opinion-based guidance for the rationalization of ultrasound investigations for gynecological indications. While these are extremely troublesome conditions, patients and healthcare providers should consider delaying ultrasound evaluation until resolution of the COVID-19 pandemic. Although associated symptoms (mass effect leading to pressure, bladder/bowel symptoms) are not usually acute or life-threatening, they may signal advanced ovarian cancer, in which case, it may be reasonable to recommend that ultrasound assessment should be carried out by an expert soon and appropriate treatment commenced. • Abdominopelvic ''mass'' without associated symptoms (SOON or LATER): the healthcare provider may consider delaying the ultrasound evaluation until the resolution of the pandemic if there is a known history of pelvic pathology, such as leiomyoma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32267984/ doi: 10.1002/uog.22047 id: cord-282576-mcx0xq0w author: Boutin, Catherine-Audrey title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument date: 2020-09-04 words: 1363.0 sentences: 94.0 pages: flesch: 63.0 cache: ./cache/cord-282576-mcx0xq0w.txt txt: ./txt/cord-282576-mcx0xq0w.txt summary: title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. We evaluated the concordance between the two-target cobas SARS-CoV-2 test (Roche Molecular Diagnostics, Laval, Canada) on the fully automated cobas 8800 platform authorized by Health Canada and a laboratory-developed (LD) standardized RT-PCR test using widely used primer set and probe (2, 3) in samples submitted at the diagnostic laboratory for patient care at the Centre Hospitalier de l''Université de Montréal. The correlation between Ct values obtained in the LD RT-PCR test and cobas SARS CoV-2 ORF-1 target for positive samples in both assays was good (r 2 = 0.82, data not shown). abstract: OBJECTIVE: Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown. METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. RESULTS: The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3–99.9) and 77.1 % (95 % CI, 67.7–84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7–95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75−0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3–33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2–37.1; p = 0.0009). An excellent correlation (r(2) = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r(2) = 0.82). CONCLUSION: Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform. url: https://doi.org/10.1016/j.jcv.2020.104615 doi: 10.1016/j.jcv.2020.104615 id: cord-300707-k9uk14b3 author: Bouwman, Kim M. title: Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date: 2020-09-04 words: 2328.0 sentences: 176.0 pages: flesch: 59.0 cache: ./cache/cord-300707-k9uk14b3.txt txt: ./txt/cord-300707-k9uk14b3.txt summary: Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues. The results demonstrate 104 that fully glycosylated trimeric SARS-CoV-2 RBD proteins reveal the 105 differences in ACE2 expression between cell cultures and tissue sections. A similar trend of binding intensities was observed for 214 monomeric, trimeric, and different N-glycosylated SARS-CoV-RBD proteins 215 fused to mOrange2 ( Fig S3A) . 226 227 To confirm our observations of different binding on tissues, we quantified the 228 intensities of the ACE2 antibody and SARS-CoV-1 and -2 RBD proteins, except 229 for the monomeric GnTI derived proteins as these were almost at the 230 background ( Fig 4D) . abstract: Receptor binding studies using recombinant SARS-CoV proteins have been hampered due to challenges in approaches creating spike protein or domains thereof, that recapitulate receptor binding properties of native viruses. We hypothesized that trimeric RBD proteins would be suitable candidates to study receptor binding properties of SARS-CoV-1 and -2. Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. The results demonstrate that trimeric fully glycosylated proteins are superior in receptor binding compared to monomeric and immaturely glycosylated variants. Although differences in binding to commonly used cell lines were minimal between the different RBD preparations, substantial differences were observed when respiratory tissues of experimental animals were stained. The RBD trimers demonstrated distinct ACE2 expression profiles in bronchiolar ducts and confirmed the higher binding affinity of SARS-CoV-2 over SARS-CoV-1. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues. url: https://doi.org/10.1101/2020.09.04.282558 doi: 10.1101/2020.09.04.282558 id: cord-276784-8lmg97zc author: Boziki, Marina Kleopatra title: COVID-19 Immunopathology and the Central Nervous System: Implication for Multiple Sclerosis and Other Autoimmune Diseases with Associated Demyelination date: 2020-06-04 words: 4769.0 sentences: 225.0 pages: flesch: 33.0 cache: ./cache/cord-276784-8lmg97zc.txt txt: ./txt/cord-276784-8lmg97zc.txt summary: Moreover, the management of chronic neurological diseases, such as Multiple Sclerosis (MS), underwent guided modifications, such as an Extended Interval Dose (EID) of Disease-Modifying Treatment (DMT) administration, in order to minimize patients'' exposure to the health system, thus reducing the risk of SARS-CoV-2 infection. In this review, we summarize existing evidence of key immune pathways that the SARS-CoV-2 modifies during COVID-19 and the relevant implication for MS and other autoimmune diseases with associated demyelination (such as Systemic lupus erythematosus and Antiphospholipid syndrome), including the context of potential neuroinvasion by SARS-Cov-2 and the alterations that DMT induces to the immune system. In this respect, the clinical implication of SARS-CoV-2 infection in PwMS needs to be carefully evaluated in long-term prospective studies that assess not only physical disability measurements but also cognition, patient-reported outcomes, and quality of life, thus aiming to elucidate COVID-19-related long-term effects on MS-related neurological status and beyond. abstract: In the frame of the coronavirus disease 2019 (COVID-19) pandemic, recent reports on SARS-CoV-2 potential neuroinvasion placed neurologists on increased alertness in order to assess early neurological manifestations and their potentially prognostic value for the COVID-19 disease. Moreover, the management of chronic neurological diseases, such as Multiple Sclerosis (MS), underwent guided modifications, such as an Extended Interval Dose (EID) of Disease-Modifying Treatment (DMT) administration, in order to minimize patients’ exposure to the health system, thus reducing the risk of SARS-CoV-2 infection. In this review, we summarize existing evidence of key immune pathways that the SARS-CoV-2 modifies during COVID-19 and the relevant implication for MS and other autoimmune diseases with associated demyelination (such as Systemic lupus erythematosus and Antiphospholipid syndrome), including the context of potential neuroinvasion by SARS-Cov-2 and the alterations that DMT induces to the immune system. Moreover we hereby aim to provide an overview of the possible consequences that COVID-19 may carry for the Central Nervous System (CNS) in People with MS (PwMS) and other demyelinating diseases, which are likely to pose challenges for treating Neurologists with respect to the long-term disease management of these diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32512702/ doi: 10.3390/brainsci10060345 id: cord-302806-1e99cygs author: Bozkurt, Banu title: The COVID-19 Pandemic: Clinical Information for Ophthalmologists date: 2020-04-29 words: 3685.0 sentences: 228.0 pages: flesch: 55.0 cache: ./cache/cord-302806-1e99cygs.txt txt: ./txt/cord-302806-1e99cygs.txt summary: 27 published in the journal Ophthalmology last week, viral culture and RT-PCR analysis of 64 tear samples collected simultaneously with nasopharyngeal swabs from 17 COVID-19 patients between 3 and 20 days after initial symptom onset failed to demonstrate the presence of 2019-CoV. 34 The Turkish Ministry of Health, in a guidance report entitled "Evaluation of Healthcare Workers with Patient Contact" published on March 25, 2020, identified ophthalmologic examination as a procedure requiring intensive contact, and recommended prophylaxis with hydroxychloroquine for a total of 3 days (400 mg twice on day 1, 200 mg twice daily on days 2 and 3) and 5 days of home isolation followed by a PCR test in the event of high-risk contact with COVID-19 patients without the use of personal protective equipment. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Assessing Viral Shedding and Infectivity of Tears in Coronavirus Disease 2019 (COVID-19) Patients. abstract: nan url: https://doi.org/10.4274/tjo.galenos.2020.29805 doi: 10.4274/tjo.galenos.2020.29805 id: cord-279474-c5y2lygj author: Bozzo, Caterina Prelli title: IFITM proteins promote SARS-CoV-2 infection of human lung cells date: 2020-08-18 words: 1110.0 sentences: 90.0 pages: flesch: 55.0 cache: ./cache/cord-279474-c5y2lygj.txt txt: ./txt/cord-279474-c5y2lygj.txt summary: Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) restrict numerous viral pathogens and are thought to prevent infection by severe acute respiratory syndrome coronaviruses (SARS-CoVs). In striking contrast, however, endogenous IFITM expression promoted genuine SARS-CoV-2 infection in human lung cells both in the presence and absence of interferon. Taken together, our results show that all three IFITMs prevent SARS-CoV-2 S/ACE2-mediated attachment and membrane fusion in single round pseudotype infection assays. Notably, titration experiments showed that IFITMs do not promote genuine SARS-CoV-2 247 infection in HEK239T cells over a broad range of expression levels ( Figure S4E ). (F) Quantification of the entry of VSV(luc)ΔG*-SARS-CoV-2-S by luciferase activity in HEK293T cells transiently expressing indicated proteins (IFITM mutants) and infected 24 h post-transfection with the VSVpp (MOI 0.025) for 16 h. (G) Quantification of the entry of HIV(Fluc)Δenv*-SARS-CoV-2-S by luciferase activity in HEK293T cells stably expressing indicated proteins (IFITM mutants) and ACE2 abstract: Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) restrict numerous viral pathogens and are thought to prevent infection by severe acute respiratory syndrome coronaviruses (SARS-CoVs). However, most evidence comes from single-round pseudoparticle infection of cells artificially overexpressing IFITMs. Here, we confirmed that overexpression of IFITMs blocks pseudoparticle infections mediated by the Spike proteins of β-coronaviruses including pandemic SARS-CoV-2. In striking contrast, however, endogenous IFITM expression promoted genuine SARS-CoV-2 infection in human lung cells both in the presence and absence of interferon. IFITM2 was most critical for efficient entry of SARS-CoV-2 and enhanced virus production from Calu-3 cells by several orders of magnitude. IFITMs are expressed and further induced by interferons in the lung representing the primary site of SARS-CoV-2 infection as well as in other relevant tissues. Our finding that IFITMs enhance SARS-CoV-2 infection under conditions approximating the in vivo situation shows that they may promote viral invasion during COVID-19. HIGHLIGHTS Overexpression of IFITM1, 2 and 3 restricts SARS-CoV-2 infection Endogenous IFITM1, 2 and 3 boost SARS-CoV-2 infection of human lung cells IFITM2 is critical for efficient entry of SARS-CoV-2 in Calu-3 cells url: https://doi.org/10.1101/2020.08.18.255935 doi: 10.1101/2020.08.18.255935 id: cord-272654-hh29olk7 author: Bošnjak, Berislav title: Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID-19 convalescent patients revealed by two different detection methods date: 2020-11-02 words: 6111.0 sentences: 414.0 pages: flesch: 54.0 cache: ./cache/cord-272654-hh29olk7.txt txt: ./txt/cord-272654-hh29olk7.txt summary: We used a surrogate virus neutralization test (sVNT) and SARS-CoV-2 S protein-pseudotyped vesicular stomatitis virus (VSV) vector-based neutralization assay (pVNT) to assess the degree to which serum antibodies from coronavirus disease 2019 (COVID-19) convalescent patients interfere with the binding of SARS-CoV-2 S to ACE2. Similarly, anti-SARS-CoV-2 S IgA antibodies were present in 33/37 (89.2%) of the tested sera; two samples were diagnosed as borderline positive and two as negative Fig. 1 Qualitative analysis of serum total IgG (A) and IgA (B) antibodies against SARS-CoV-2 S1 in convalescent patients with mild or severe COVID-19 and healthy controls (HC) determined by ELISA. The median sVNT titer of the mildly affected convalescent cohort was 1:180, indicating that patients with mild COVID-19 produce relatively low amounts of SASRS-CoV-2 neutralizing antibodies (Fig. 2H ). This hypothesis is further supported by a positive correlation between the duration of symptoms and total anti-SARS-CoV-2 IgG, but not IgA, antibodies in convalescent patients with mild disease (Fig. 5A, B) . abstract: Neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) block severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry into cells via surface-expressed angiotensin-converting enzyme 2 (ACE2). We used a surrogate virus neutralization test (sVNT) and SARS-CoV-2 S protein-pseudotyped vesicular stomatitis virus (VSV) vector-based neutralization assay (pVNT) to assess the degree to which serum antibodies from coronavirus disease 2019 (COVID-19) convalescent patients interfere with the binding of SARS-CoV-2 S to ACE2. Both tests revealed neutralizing anti-SARS-CoV-2 S antibodies in the sera of ~90% of mildly and 100% of severely affected COVID-19 convalescent patients. Importantly, sVNT and pVNT results correlated strongly with each other and to the levels of anti-SARS-CoV-2 S1 IgG and IgA antibodies. Moreover, levels of neutralizing antibodies correlated with the duration and severity of clinical symptoms but not with patient age. Compared to pVNT, sVNT is less sophisticated and does not require any biosafety labs. Since this assay is also much faster and cheaper, sVNT will not only be important for evaluating the prevalence of neutralizing antibodies in a population but also for identifying promising plasma donors for successful passive antibody therapy. url: https://doi.org/10.1038/s41423-020-00573-9 doi: 10.1038/s41423-020-00573-9 id: cord-256888-tdx12ccj author: Bradley, Benjamin T title: Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series date: 2020-07-16 words: 5006.0 sentences: 300.0 pages: flesch: 45.0 cache: ./cache/cord-256888-tdx12ccj.txt txt: ./txt/cord-256888-tdx12ccj.txt summary: To date, documentation of the histopathological features in fatal cases of the disease caused by SARS-CoV-2 (COVID-19) has been scarce due to sparse autopsy performance and incomplete organ sampling. 8 Post-mortem studies have shown pulmonary, renal, and small vessel injury, with particles resembling virus observed in the kidney by electron microscopy. By electron microscopy, aggregates of uniform, round enveloped particles ranging in size from around 70 nm to 100 nm with peripheral spike-like projections consistent with the morphology described for SARS-CoV-2 were observed in the lung, trachea, kidney, and large intestine of patient 8 and patient 13. [9] [10] [11] [12] We present a case series of autopsy findings in 14 patients who died after SARS-CoV-2 infection. The major histopathological observation in our series of patients who died with COVID-19 was diffuse alveolar damage-type lung injury in the acute or organising phases (12 [86%] of 14 patients). abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of an ongoing pandemic, with increasing deaths worldwide. To date, documentation of the histopathological features in fatal cases of the disease caused by SARS-CoV-2 (COVID-19) has been scarce due to sparse autopsy performance and incomplete organ sampling. We aimed to provide a clinicopathological report of severe COVID-19 cases by documenting histopathological changes and evidence of SARS-CoV-2 tissue tropism. METHODS: In this case series, patients with a positive antemortem or post-mortem SARS-CoV-2 result were considered eligible for enrolment. Post-mortem examinations were done on 14 people who died with COVID-19 at the King County Medical Examiner's Office (Seattle, WA, USA) and Snohomish County Medical Examiner's Office (Everett, WA, USA) in negative-pressure isolation suites during February and March, 2020. Clinical and laboratory data were reviewed. Tissue examination was done by light microscopy, immunohistochemistry, electron microscopy, and quantitative RT-PCR. FINDINGS: The median age of our cohort was 73·5 years (range 42–84; IQR 67·5–77·25). All patients had clinically significant comorbidities, the most common being hypertension, chronic kidney disease, obstructive sleep apnoea, and metabolic disease including diabetes and obesity. The major pulmonary finding was diffuse alveolar damage in the acute or organising phases, with five patients showing focal pulmonary microthrombi. Coronavirus-like particles were detected in the respiratory system, kidney, and gastrointestinal tract. Lymphocytic myocarditis was observed in one patient with viral RNA detected in the tissue. INTERPRETATION: The primary pathology observed in our cohort was diffuse alveolar damage, with virus located in the pneumocytes and tracheal epithelium. Microthrombi, where observed, were scarce and endotheliitis was not identified. Although other non-pulmonary organs showed susceptibility to infection, their contribution to the pathogenesis of SARS-CoV-2 infection requires further examination. FUNDING: None. url: https://doi.org/10.1016/s0140-6736(20)31305-2 doi: 10.1016/s0140-6736(20)31305-2 id: cord-307148-k1uo3fxm author: Bradshaw, Patrick C. title: COVID-19: Proposing a Ketone-Based Metabolic Therapy as a Treatment to Blunt the Cytokine Storm date: 2020-09-09 words: 20788.0 sentences: 1093.0 pages: flesch: 40.0 cache: ./cache/cord-307148-k1uo3fxm.txt txt: ./txt/cord-307148-k1uo3fxm.txt summary: R-BHB activates anti-inflammatory GPR109A signaling and inhibits the NLRP3 inflammasome and histone deacetylases, while a ketogenic diet has been shown to protect mice from influenza virus infection through a protective γδ T cell response and by increasing electron transport chain gene expression to restore energy metabolism. Others have also suggested that increasing systemic ketone levels may aid host defenses against respiratory viral infection, in part, by decreasing inflammation [1, 2] , including a recent comprehensive review [3] , while a clinical trial of the effects of a ketogenic diet on intubated SARS-CoV-2 patients has recently been registered (NCT04358835). Coronaviruses have been shown to increase the oxidation of phospholipids, which stimulate toll-like receptor 4 (TLR4) signaling on macrophages, leading to cytokine production and acute lung injury [163] , so HDAC inhibition with R-BHB appears to be a viable treatment to decrease cytokine levels and inflammation. abstract: Human SARS-CoV-2 infection is characterized by a high mortality rate due to some patients developing a large innate immune response associated with a cytokine storm and acute respiratory distress syndrome (ARDS). This is characterized at the molecular level by decreased energy metabolism, altered redox state, oxidative damage, and cell death. Therapies that increase levels of (R)-beta-hydroxybutyrate (R-BHB), such as the ketogenic diet or consuming exogenous ketones, should restore altered energy metabolism and redox state. R-BHB activates anti-inflammatory GPR109A signaling and inhibits the NLRP3 inflammasome and histone deacetylases, while a ketogenic diet has been shown to protect mice from influenza virus infection through a protective γδ T cell response and by increasing electron transport chain gene expression to restore energy metabolism. During a virus-induced cytokine storm, metabolic flexibility is compromised due to increased levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS) that damage, downregulate, or inactivate many enzymes of central metabolism including the pyruvate dehydrogenase complex (PDC). This leads to an energy and redox crisis that decreases B and T cell proliferation and results in increased cytokine production and cell death. It is hypothesized that a moderately high-fat diet together with exogenous ketone supplementation at the first signs of respiratory distress will increase mitochondrial metabolism by bypassing the block at PDC. R-BHB-mediated restoration of nucleotide coenzyme ratios and redox state should decrease ROS and RNS to blunt the innate immune response and the associated cytokine storm, allowing the proliferation of cells responsible for adaptive immunity. Limitations of the proposed therapy include the following: it is unknown if human immune and lung cell functions are enhanced by ketosis, the risk of ketoacidosis must be assessed prior to initiating treatment, and permissive dietary fat and carbohydrate levels for exogenous ketones to boost immune function are not yet established. The third limitation could be addressed by studies with influenza-infected mice. A clinical study is warranted where COVID-19 patients consume a permissive diet combined with ketone ester to raise blood ketone levels to 1 to 2 mM with measured outcomes of symptom severity, length of infection, and case fatality rate. url: https://www.ncbi.nlm.nih.gov/pubmed/33014275/ doi: 10.1155/2020/6401341 id: cord-258382-ep73us0e author: Braga, Cássia L. title: The renin–angiotensin–aldosterone system: Role in pathogenesis and potential therapeutic target in COVID‐19 date: 2020-07-13 words: 2990.0 sentences: 195.0 pages: flesch: 46.0 cache: ./cache/cord-258382-ep73us0e.txt txt: ./txt/cord-258382-ep73us0e.txt summary: 8, 9 According to Zhou et al, SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor to invade and infect cells. These proteins bud into the endoplasmic reticulum-Golgi intermediate compartment (ERGIC); new viral particles are then assembled and released to infect new target cells comes from the observation that endosomal alkalization induced by ammonium chloride inhibited SARS-CoV-2 replication. Once a hypertensive patient is infected with SARS-CoV-2, sensitization of the immune system toward an overactivation of the inflammatory response could be associated with subsequent development of cytokine storm. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS abstract: Coronavirus disease 2019 (COVID‐19), caused by the SARS‐CoV‐2 novel coronavirus, has spread worldwide causing high fatality rates. Neither a vaccine nor specific therapeutic approaches are available, hindering the fight against this disease and making better understanding of its pathogenesis essential. Despite similarities between SARS‐CoV‐2 and SARS‐CoV, the former has unique characteristics which represent a great challenge to physicians. The mechanism of COVID‐19 infection and pathogenesis is still poorly understood. In the present review, we highlight possible pathways involved in the pathogenesis of COVID‐19 and potential therapeutic targets, focusing on the role of the renin–angiotensin–aldosterone system. url: https://doi.org/10.1002/prp2.623 doi: 10.1002/prp2.623 id: cord-307815-reg04lpt author: Brancatella, Alessandro title: Is subacute thyroiditis an underestimated manifestation of SARS-CoV-2 infection? Insights from a case series date: 2020-08-11 words: 2296.0 sentences: 174.0 pages: flesch: 58.0 cache: ./cache/cord-307815-reg04lpt.txt txt: ./txt/cord-307815-reg04lpt.txt summary: After our initial description of a patient experiencing subacute thyroiditis (SAT) associated with SARS-CoV-2 infection (1), three additional case have been reported (2) (3) (4) . On March 1 st , a 38 year-old-woman underwent oropharyngeal swab for SARS-CoV-2 because of symptoms suspected for COVID-19 (Table 1) . At last evaluation (on May 10 th ), while taking prednisone 15 mg/d, patient was asymptomatic and thyroid function tests and inflammatory markers were in the normal range (Table 1) . At last evaluation (on May 18 th ), while taking 15 mg/d of prednisone, patient was asymptomatic, inflammatory markers were in the normal range, whereas thyroid function tests was consistent with subclinical hypothyroidism (Table 1) . In the present series, as well as in our previous report (1), patients experienced SAT after the resolution of distinctive symptoms of SARS-CoV-2 infection. abstract: CONTEXT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 18 million people worldwide and the pandemic is still spreading. After the first case we reported, we observed 4 additional cases of SAT related to SARS-CoV-2 infection. OBJECTIVES: To describe additional cases of SAT associated with SARS-CoV-2 infection in order to alert physicians that SAT may be a manifestation of SARS-CoV-2 infection. METHODS: We describe clinical, biochemical and imaging features of the 4 patients with SAT related to SARS-CoV-2 infection. RESULTS: All patients were female (age 29-46 years). SAT developed 16 to 36 days after the resolution of coronavirus disease 2019 (COVID-19). Neck pain radiated to the jaw and palpitations were the main presenting symptoms and were associated with fever and asthenia. One patient was hospitalized because of atrial fibrillation. Thyroid function tests (available in three subjects) were suggestive of destructive thyroiditis and inflammatory markers were high. At neck ultrasound the thyroid was enlarged, with diffuse and bilateral hypoechoic areas and (in three patients) absent vascularization at color doppler. Symptoms disappeared a few days after commencement of treatment (prednisone in three patients and ibuprofen in one). Six weeks after the onset of SAT all patients were asymptomatic and inflammatory markers had turned back to the normal range. Two patients were euthyroid while two were diagnosed with subclinical hypothyroidism. CONCLUSIONS: SAT may be an underestimated manifestation of COVID-19. Clinicians should keep in mind the possible occurrence of SAT during and after SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32780854/ doi: 10.1210/clinem/dgaa537 id: cord-313371-fdyfg0kf author: Brancatella, Alessandro title: Subacute Thyroiditis After Sars-COV-2 Infection date: 2020-05-21 words: 1612.0 sentences: 116.0 pages: flesch: 53.0 cache: ./cache/cord-313371-fdyfg0kf.txt txt: ./txt/cord-313371-fdyfg0kf.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that began in Wuhan, China, has spread rapidly worldwide and Italy has been severely affected by this outbreak. OBJECTIVES: The objective of this work is to report the first case of SAT related to SARS-CoV-2 infection. METHODS: We describe the clinical, laboratory, and imaging features of an 18-year-old woman who came to our attention for fever, neck pain radiated to the jaw, and palpitations occurring 15 days after a SARS-CoV-2–positive oropharyngeal swab. S ubacute thyroiditis (SAT) is a self-limited inflammatory thyroid disease characterized by neck pain, general symptoms, and thyroid dysfunction (1, 2) . Here, we report the first case of SAT in a patient affected by SARS-CoV-2. SAT is a self-limited, inflammatory disorder characterized by neck pain and general symptoms, often associated with thyroid dysfunction (1, 2) . SAT is usually preceded by an upper respiratory infection and usually presents in association with characteristic symptoms of viral disease. abstract: CONTEXT: Subacute thyroiditis (SAT) is a thyroid disease of viral or postviral origin. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that began in Wuhan, China, has spread rapidly worldwide and Italy has been severely affected by this outbreak. OBJECTIVES: The objective of this work is to report the first case of SAT related to SARS-CoV-2 infection. METHODS: We describe the clinical, laboratory, and imaging features of an 18-year-old woman who came to our attention for fever, neck pain radiated to the jaw, and palpitations occurring 15 days after a SARS-CoV-2–positive oropharyngeal swab. Coronavirus disease 2019 (COVID-19) had been mild and the patient had completely recovered in a few days. RESULTS: At physical examination the patient presented with a slightly increased heart rate and a painful and enlarged thyroid on palpation. At laboratory exams free thyroxine and free triiodothyronine were high, thyrotropin undetectable, and inflammatory markers and white blood cell count elevated. Bilateral and diffuse hypoechoic areas were detected at neck ultrasound. One month earlier, thyroid function and imaging both were normal. We diagnosed SAT and the patient started prednisone. Neck pain and fever recovered within 2 days and the remaining symptoms within 1 week. Thyroid function and inflammatory markers normalized in 40 days. CONCLUSIONS: We report the first case of SAT after a SARS-CoV-2 infection. We alert clinicians to additional and unreported clinical manifestations associated with COVID-19. url: https://doi.org/10.1210/clinem/dgaa276 doi: 10.1210/clinem/dgaa276 id: cord-315058-t7bq4yqw author: Brand, Samuel P C title: Forecasting the scale of the COVID-19 epidemic in Kenya date: 2020-04-14 words: 7568.0 sentences: 432.0 pages: flesch: 49.0 cache: ./cache/cord-315058-t7bq4yqw.txt txt: ./txt/cord-315058-t7bq4yqw.txt summary: Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. In the scenario with no transmission from asymptomatics the observed epidemic was dominated by cases among the working-age population (Figure 3 ), who we estimated as having high rates of assortative (i.e. within same age-group) mixing ( Figure 4 ) and a small but not negligible risk of developing symptoms of COVID-19 after infection. In this modelling study we have integrated existing data on the social structure, and mobility, of the Kenyan population with rapidly evolving estimates of the fundamental epidemiology of SARS-CoV-2 so as to make the best possible prediction of the scale of the epidemic risk that Kenya faces from the first coronavirus pandemic. abstract: Background The first COVID-19 case in Kenya was confirmed on March 13th, 2020. Here, we provide forecasts for the potential incidence rate, and magnitude, of a COVID-19 epidemic in Kenya based on the observed growth rate and age distribution of confirmed COVID-19 cases observed in China, whilst accounting for the demographic and geographic dissimilarities between China and Kenya. Methods We developed a modelling framework to simulate SARS-CoV-2 transmission in Kenya, KenyaCoV. KenyaCoV was used to simulate SARS-CoV-2 transmission both within, and between, different Kenyan regions and age groups. KenyaCoV was parameterized using a combination of human mobility data between the defined regions, the recent 2019 Kenyan census, and estimates of age group social interaction rates specific to Kenya. Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. Results We find that if person-to-person transmission becomes established within Kenya, identifying the role of subclinical, and therefore largely undetected, infected individuals is critical to predicting and containing a very significant epidemic. Depending on the transmission scenario our reproductive number estimates for Kenya range from 1.78 (95% CI 1.44 - 2.14) to 3.46 (95% CI 2.81-4.17). In scenarios where asymptomatic infected individuals are transmitting significantly, we expect a rapidly growing epidemic which cannot be contained only by case isolation. In these scenarios, there is potential for a very high percentage of the population becoming infected (median estimates: >80% over six months), and a significant epidemic of symptomatic COVID-19 cases. Exceptional social distancing measures can slow transmission, flattening the epidemic curve, but the risk of epidemic rebound after lifting restrictions is predicted to be high. url: https://doi.org/10.1101/2020.04.09.20059865 doi: 10.1101/2020.04.09.20059865 id: cord-309540-4pk5tq5w author: Brandsma, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 words: 4283.0 sentences: 268.0 pages: flesch: 54.0 cache: ./cache/cord-309540-4pk5tq5w.txt txt: ./txt/cord-309540-4pk5tq5w.txt summary: Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) in combination with Cas12 detection does not need expensive specialised equipment, is highly sensitive and specific, has a short TAT and is easy to implement and therefore could be used as an alternative for qRT-PCR (5, 6) . Since DETECTR depends on both signal amplification by RT-LAMP and reporter degradation after Cas12-dependent amplicon recognition, the assay produces a binary readout and is potentially more sensitive and specific compared to qRT-PCR (5, 6) . In this manuscript we describe the development of an in-house SARS-CoV-2 DETECTR assay, compare its performance with routine diagnostic qRT-PCR on almost 400 patient samples of three Dutch hospitals, thereby providing a first field test of this novel Cas12-mediated SARS-CoV-2 detection tool. abstract: Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Here we compare qRT-PCR with DETECTR to diagnose COVID-19 on 378 patient samples and report a 95% reproducibility. Patient sample dilution assays suggest a higher analytical sensitivity of DETECTR compared to qRT-PCR, however, this was not confirmed in a large patient cohort. The data showed that both techniques are equally sensitive in detecting SARS-CoV-2 providing an added value of DETECTR to the currently used qRT-PCR platforms. For DETECTR, different gRNAs can be used simultaneously to obviate negative results due to mutations in N-gene. Lateral flow strips, suitable as a point of care test (POCT), showed a 100% correlation to the high-throughput DETECTR assay. Importantly, DETECTR was 100% specific for SARS-CoV-2 and did not detect other human coronaviruses. As there is no need for specialized equipment, DETECTR could be rapidly implemented as a complementary technically independent approach to qRT-PCR thereby increasing the testing capacity of medical microbiological laboratories and relieving the existent PCR-platforms for routine non- SARS-CoV-2 diagnostic testing. url: http://medrxiv.org/cgi/content/short/2020.07.27.20147249v1?rss=1 doi: 10.1101/2020.07.27.20147249 id: cord-260793-bb4h255w author: Brann, David H. title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date: 2020-05-18 words: 11985.0 sentences: 604.0 pages: flesch: 53.0 cache: ./cache/cord-260793-bb4h255w.txt txt: ./txt/cord-260793-bb4h255w.txt summary: It has recently been demonstrated through single cell RNA sequencing analysis (referred to herein as scSeq) that cells from the human upper airway -including nasal RE goblet, basal and ciliated cells -express high levels of ACE2 and TMPRSS2, suggesting that these RE cell types may serve as a viral reservoir during CoV-2 infection (33) . The presence of Ace2 and Tmprss2 transcripts in mouse WOM and their (near total) absence in purified OSNs suggest that the molecular components that enable CoV-2 entry into cells are expressed in non-neuronal cell types in the mouse nasal epithelium. An independent mouse scSeq data set (obtained using the 10x Chromium platform, see Methods) revealed that olfactory sensory neurons did not express Ace2 (2 of 28769 mature OSNs were positive for Ace2), while expression was observed in a fraction of Bowman''s gland cells and HBCs ( Figure S4 , see methods). abstract: Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 – affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing and immunostaining demonstrated ACE2 expression in support cells, stem cells, and perivascular cells; in contrast, neurons in both the olfactory epithelium and bulb did not express ACE2 message or protein. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients. url: https://doi.org/10.1101/2020.03.25.009084 doi: 10.1101/2020.03.25.009084 id: cord-277239-cedoi5jr author: Bray, R. A. title: Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins date: 2020-09-03 words: 4446.0 sentences: 246.0 pages: flesch: 50.0 cache: ./cache/cord-277239-cedoi5jr.txt txt: ./txt/cord-277239-cedoi5jr.txt summary: This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. The data demonstrate that while most individuals have significant IgG responses to community coronaviruses, all pre-COVID-19 samples tested negative against the SARS-CoV-2 targets as well as to SARS and MERS S1 proteins. . https://doi.org/10.1101/2020.09.02.20185199 doi: medRxiv preprint multiplexed, solid phase assay compared to other platforms (e.g., ELISA) include the ability to assay multiple viral targets simultaneously (and thereby provide internal assay controls for coronavirus specificity), the capacity to incorporate additional SARS-CoV-2 proteins in the future, a relatively short assay time, high throughput and semiquantitative assessment of the antibody response. abstract: Transplant recipients who develop COVID-19 may be at increased risk for morbidity and mortality. Determining antibody status against SARS-CoV-2 in candidates and recipients will be important to understand the epidemiology and clinical course of COVID-19 infection in this population. There are multiple antibody tests to detect antibodies to SARS-CoV-2, but their performance varies according to their platforms and the antigenic targets, making interpretation of the results challenging. Additionally, currently available serological tests do not exclude the possibility that positive responses are due to cross reactive antibodies to community coronaviruses. This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. The antibody response to these proteins are SARS-CoV-2 specific as antibodies against four community coronaviruses do not cross-react. Assay configuration is essentially identical to the single antigen bead assays used in the majority of histocompatibility laboratories around the world and could easily be implemented into routine screening of transplant candidates and recipients. This new assay provides a novel tool to interrogate the spectrum of immune responses to SAR-CoV-2 and is uniquely suitable for use in the transplant setting. url: https://doi.org/10.1101/2020.09.02.20185199 doi: 10.1101/2020.09.02.20185199 id: cord-294134-o9bx1gn7 author: Brecher, Stephen M. title: Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2 date: 2020-07-23 words: 745.0 sentences: 44.0 pages: flesch: 51.0 cache: ./cache/cord-294134-o9bx1gn7.txt txt: ./txt/cord-294134-o9bx1gn7.txt summary: One early issue in the validation/ evaluation of antibody tests for evidence of SARS-CoV-2 infection is the possibility of cross-reacting antibodies from the plasma of patients who had been infected with one or more of the common cold coronaviruses (coronavirus 229E, HKU1, NL63, and OC43). It also ties in with issues outlined in the Infectious Diseases Society of America (IDSA) guidelines (4) and in a commentary in Lancet (5) on how to best utilize antibody test data, especially when there could be false-positive results, including cross-reacting antibodies to the four common cold coronaviruses. Although the sample size was minimal, these data are reassuring that at least for the Abbott Architect SARS-CoV-2 antibody test, plasma from patients with documented positive PCRs for these four common cold coronaviruses did not test positive for the SARS-CoV-2 IgG antibody. However, this multisite study, including data from 3 regional Veterans Affairs (VA) institutions (MA, CT, and VT) suggests that cross-reacting antibodies are not detected when testing for SARS-CoV-2 IgG antibody. abstract: The need for accurate antibody testing in patients following symptomatic or asymptomatic infections with SARS-CoV-2 is well documented.…. url: https://doi.org/10.1128/jcm.01029-20 doi: 10.1128/jcm.01029-20 id: cord-022316-mh4pslnv author: Breda, Zélia title: Safety and Security Issues Affecting Inbound Tourism in the People's Republic of China date: 2009-11-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155563/ doi: 10.1016/b978-0-7506-7898-8.50017-5 id: cord-312743-9e4yufo5 author: Breiman, Adrien title: Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 date: 2020-05-21 words: 1388.0 sentences: 66.0 pages: flesch: 45.0 cache: ./cache/cord-312743-9e4yufo5.txt txt: ./txt/cord-312743-9e4yufo5.txt summary: These observations suggested that, when produced in cells that express the A or B blood group enzymes, infectious SARS virions are decorated by the corresponding glycan antigens and that the presence of anti-A and anti-B antibodies in blood group O individuals could prevent infection by blocking virus attachment and entry. We therefore hypothesize that as they are produced in cells coexpressing the ACE2 receptor and either the αGal, NeuGc, or A/B blood group antigens, both SARS-CoV and SARS-CoV2 harbor the corresponding glycan epitopes. Likewise, impairment of transmission by the anti-blood group antibodies may not work to its full potential because of their variable titers in the population and of the high affinity of the SARS-CoV2 for ACE2 [18] , rendering its neutralization more difficult. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32437478/ doi: 10.1371/journal.ppat.1008556 id: cord-266175-4jyltfus author: Brendish, Nathan J title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 words: 5468.0 sentences: 243.0 pages: flesch: 47.0 cache: ./cache/cord-266175-4jyltfus.txt txt: ./txt/cord-266175-4jyltfus.txt summary: METHODS: We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. [5] [6] [7] [8] The aim of this trial was to assess the clinical impact and real-world diagnostic accuracy of point-of-care testing using the QIAstat-Dx Respiratory SARS-CoV-2 Panel (Qiagen, Hilden, Germany) in adults presenting with suspected COVID-19 during the first wave of the pandemic in the UK. This prospective, non-randomised, controlled trial of routine point-of-care testing for COVID-19 in hospital shows the feasibility of point-of-care testing with the QIAstat-Dx Respiratory SARS-CoV-2 Panel, and shows clinical benefits across a range of outcome measures including time to results, infection control measures, and recruitment into clinical trials compared with a control group tested by centralised laboratory PCR. abstract: BACKGROUND: The management of the COVID-19 pandemic is hampered by long delays associated with centralised laboratory PCR testing. In hospitals, these delays lead to poor patient flow and nosocomial transmission. Rapid, accurate tests are therefore urgently needed in preparation for the next wave of the pandemic. METHODS: We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. Nose and throat swab samples taken at admission from patients in the point-of-care testing group were tested with the QIAstat-Dx Respiratory SARS-CoV-2 Panel. Samples taken from patients in a contemporaneous control group were tested by laboratory PCR. The primary outcome was time to results in the full cohort. This study is registered with ISRCTN (ISRCTN14966673) and is completed. FINDINGS: Between March 20 and April 29, 2020, 517 patients were assessed for eligibility, of whom 499 were recruited to the point-of-care testing group and tested by the QIAstat-Dx Respiratory SARS-CoV-2 Panel. 555 contemporaneously identified patients were included in the control group and tested by laboratory PCR. The two groups were similar with regard to the distribution of sex, age, and ethnicity. 197 (39%) patients in the point-of-care testing group and 155 (28%) in the control group tested positive for COVID-19 (difference 11·5% [95% CI 5·8–17·2], p=0·0001). Median time to results was 1·7 h (IQR 1·6–1·9) in the point-of-care testing group and 21·3 h (16·0–27·9) in the control group (difference 19·6 h [19·0–20·3], p<0·0001). A Cox proportional hazards regression model controlling for age, sex, time of presentation, and severity of illness also showed that time to results was significantly shorter in the point-of-care testing group than in the control group (hazard ratio 4023 [95% CI 545–29 696], p<0·0001). INTERPRETATION: Point-of-care testing is associated with large reductions in time to results and could lead to improvements in infection control measures and patient flow compared with centralised laboratory PCR testing. FUNDING: University Hospitals Southampton NHS Foundation Trust. url: https://www.ncbi.nlm.nih.gov/pubmed/33038974/ doi: 10.1016/s2213-2600(20)30454-9 id: cord-261059-rcpx4god author: Brenner, Steven Robert title: Erythropoietin Induced Hemoglobin Sub‐Unit Beta may Stimulate Innate Immune RNA Virus Pattern Recognition, Suppress Reactive Oxygen Species, Reduce ACE2 Viral Doorway Opening and Neutrophil Extracellular Traps against Covid‐19 date: 2020-07-09 words: 869.0 sentences: 55.0 pages: flesch: 34.0 cache: ./cache/cord-261059-rcpx4god.txt txt: ./txt/cord-261059-rcpx4god.txt summary: Erythropoietin may stimulate innate immunity against RNA viruses, such as Covid‐19, through hemoglobin sub‐unit Beta acting on the retinoic acid inducible gene I (RIG‐1) and melanoma differentiation associated gene 5 (MDA5) viral pattern recognition receptors, causing interferon production and also maintains the vascular endothelium, a major target of SARS‐CoV‐2, possibly reducing thrombotic events which are becoming increasingly recognized complications of COVID19. Possibly hemoglobin (HB), especially subunit beta also contributed to recovery, since HB participates in innate immunity through differentially regulating the retinoic acid inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5), which are involved in viral recognition and mobilizing an interferon response. (Assessment of Endothelial and Haemostatic Changes During Severe SARS-CoV-2 Infection (Covid-Thelium), including syndecan-1, a marker of degradation of glycocalyx, D-dimers plasma levels association with thrombotic events, and von Willibrandt Factor, Viscoelastic testing and Vascular endothelial Growth Factor Receptor type 1. abstract: Erythropoietin may stimulate innate immunity against RNA viruses, such as Covid‐19, through hemoglobin sub‐unit Beta acting on the retinoic acid inducible gene I (RIG‐1) and melanoma differentiation associated gene 5 (MDA5) viral pattern recognition receptors, causing interferon production and also maintains the vascular endothelium, a major target of SARS‐CoV‐2, possibly reducing thrombotic events which are becoming increasingly recognized complications of COVID19. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32644208/ doi: 10.1002/jmv.26284 id: cord-338097-kdrq81w5 author: Brescia, Marilia D''Elboux Guimarães title: “Green July” 2020 and Another Good Reason to Quit Smoking: Help to Stop Spreading SARS-COV-2 and Save Lives! date: 2020-10-20 words: 1205.0 sentences: 83.0 pages: flesch: 64.0 cache: ./cache/cord-338097-kdrq81w5.txt txt: ./txt/cord-338097-kdrq81w5.txt summary: In Brazil, the initiative has been a great success coordinated by the Brazilian Society of Head and Neck Surgery (BSHNS), and it was expanded to one entire month, named "Green July." All around the country, besides press and television interviews and social media posts, members of the BSHNS and its accredited training centers run talks, shows and physical activities with the population to encourage healthy habits and to avoid exposure to the major risk factors associated with head and neck cancer. 2 Fortunately, for the time being, we are unaware of any Brazilian head and neck surgeons dying of SARS-Cov-2, even though the risk of severe infection to this medical specialty is quite real. Besides their individual risk for head and neck cancer, smoking is now a major risk factor for transmitting SARS-Cov 2. Tobacco Smoking a Potential Risk Factor in Transmission of COVID-19 Infection abstract: nan url: https://doi.org/10.1055/s-0040-1716571 doi: 10.1055/s-0040-1716571 id: cord-264477-2onwu92a author: Brida, Margarita title: The globe on the spotlight: Coronavirus disease 2019 (Covid-19) date: 2020-07-01 words: 1972.0 sentences: 91.0 pages: flesch: 46.0 cache: ./cache/cord-264477-2onwu92a.txt txt: ./txt/cord-264477-2onwu92a.txt summary: Our world, however, failed to learn necessary lessons from the SARS-CoV and MERS-CoV outbreaks and to invest on essential global research on ways of preventing the spread of infectious disease. The paper by Tan and Aboulhosn published in the current issue of the Journal, summarizes current knowledge regarding Covid-19 disease pandemic and its potential cardiovascular involvement, with a reference to adult congenital heart disease (ACHD) [8] . However, we are currently lacking ACHD specific data and a strict policy of social distancing employed in other parts of the world, seems to have had a positive response during the first phase of this pandemic in reducing the spread of disease and allowing for health care systems to prepare and somewhat cope with the unprecedented need. There are emerging publications regarding models of care of cardiovascular patients with infectious disease, which however are short of specific ACHD experience at present [14, 15] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32321654/ doi: 10.1016/j.ijcard.2020.04.006 id: cord-340960-abanr641 author: Brigger, D. title: Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date: 2020-09-30 words: 4479.0 sentences: 289.0 pages: flesch: 50.0 cache: ./cache/cord-340960-abanr641.txt txt: ./txt/cord-340960-abanr641.txt summary: In a mixed‐design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS‐CoV‐2 proteins and assessed the neutralizing activity of antibodies in patient sera. A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay (all collected in April 2020). Recombinantly expressed RBD has been used to establish an in-house ELISA for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in human serum samples (supplementary Fig. 1a,b) . A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay using ACE2-expressing Vero-E6 cells (34 inpatient samples, and 26 samples of medical personnel). abstract: BACKGROUND: Serological immunoassays that can identify protective immunity against SARS‐CoV‐2 are needed to adapt quarantine measures, assess vaccination responses, and evaluate donor plasma. To date, however, the utility of such immunoassays remains unclear. In a mixed‐design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS‐CoV‐2 proteins and assessed the neutralizing activity of antibodies in patient sera. METHODS: Consecutive patients admitted with confirmed SARS‐CoV‐2 infection were prospectively followed alongside medical staff and biobank samples from winter 2018/2019. An in‐house enzyme‐linked immunosorbent assay utilizing recombinant receptor‐binding domain (RBD) of the SARS‐CoV‐2 spike protein was developed and compared to three commercially available enzyme‐linked immunosorbent assays (ELISAs) targeting the nucleoprotein (N), the S1 domain of the spike protein (S1) and a lateral flow immunoassay (LFI) based on full‐length spike protein. Neutralization assays with live SARS‐CoV‐2 were performed. RESULTS: One‐thousand four‐hundred and seventy‐seven individuals were included comprising 112 SARS‐CoV‐2 positives (defined as a positive real‐time PCR result; prevalence 7.6%). IgG seroconversion occurred between day 0 and day 21. While the ELISAs showed sensitivities of 88.4% for RBD, 89.3% for S1, and 72.9% for N protein, the specificity was above 94% for all tests. Out of 54 SARS‐CoV‐2 positive individuals, 96.3% showed full neutralization of live SARS‐CoV‐2 at serum dilutions ≥1:16, while none of the 6 SARS‐CoV‐2 negative sera revealed neutralizing activity. CONCLUSIONS: ELISAs targeting RBD and S1 protein of SARS‐CoV‐2 are promising immunoassays which shall be further evaluated in studies verifying diagnostic accuracy and protective immunity against SARS‐CoV‐2. url: https://doi.org/10.1111/all.14608 doi: 10.1111/all.14608 id: cord-300716-urmogf97 author: Briguglio, Matteo title: Disentangling the Hypothesis of Host Dysosmia and SARS-CoV-2: The Bait Symptom That Hides Neglected Neurophysiological Routes date: 2020-06-05 words: 9889.0 sentences: 460.0 pages: flesch: 42.0 cache: ./cache/cord-300716-urmogf97.txt txt: ./txt/cord-300716-urmogf97.txt summary: The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. Keywords: smell, olfactory bulb, coronavirus, SARS-CoV-2, COVID-19, infections, virulence, host pathogen interactions THE SNIFFING OUT OF CORONAVIRUSES Named after their crown-like spikes, coronaviruses are large non-segmented single-stranded positive-sense enveloped RNA viruses that may spill out from animals to infect humans and cause respiratory diseases. It is urgent to discuss whether SARS-CoV-2 can gain access to the central nervous system through a nasal-nervous pathway or other routes and if the fatal respiratory failure may be associated with a neuronal injury in critical brain areas of the host. abstract: The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. The full-blown COVID-19 can lead, in susceptible individuals, to premature death because of the massive viral proliferation, hypoxia, misdirected host immunoresponse, microthrombosis, and drug toxicities. Alike other coronaviruses, SARS-CoV-2 has a neuroinvasive potential, which may be associated with early neurological symptoms. In the past, the nervous tissue of patients infected with other coronaviruses was shown to be heavily infiltrated. Patients with SARS-CoV-2 commonly report dysosmia, which has been related to the viral access in the olfactory bulb. However, this early symptom may reflect the nasal proliferation that should not be confused with the viral access in the central nervous system of the host, which can instead be allowed by means of other routes for spreading in most of the neuroanatomical districts. Axonal, trans-synaptic, perineural, blood, lymphatic, or Trojan routes can gain the virus multiples accesses from peripheral neuronal networks, thus ultimately invading the brain and brainstem. The death upon respiratory failure may be also associated with the local inflammation- and thrombi-derived damages to the respiratory reflexes in both the lung neuronal network and brainstem center. Beyond the infection-associated neurological symptoms, long-term neuropsychiatric consequences that could occur months after the host recovery are not to be excluded. While our article does not attempt to fully comprehend all accesses for host neuroinvasion, we aim at stimulating researchers and clinicians to fully consider the neuroinvasive potential of SARS-CoV-2, which is likely to affect the peripheral nervous system targets first, such as the enteric and pulmonary nervous networks. This acknowledgment may shed some light on the disease understanding further guiding public health preventive efforts and medical therapies to fight the pandemic that directly or indirectly affects healthy isolated individuals, quarantined subjects, sick hospitalized, and healthcare workers. url: https://www.ncbi.nlm.nih.gov/pubmed/32581854/ doi: 10.3389/fphys.2020.00671 id: cord-269143-8j3m03gc author: Brindisi, Giulia title: Pills to think about in allergic rhinitis children during COVID‐19 era date: 2020-07-05 words: 632.0 sentences: 39.0 pages: flesch: 45.0 cache: ./cache/cord-269143-8j3m03gc.txt txt: ./txt/cord-269143-8j3m03gc.txt summary: Allergic rhinitis (AR) is a common pediatric disease, that involves up to the 25% of children worldwide. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection in children is uncommon and often asymptomatic or mild. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children is uncommon and often asymptomatic or mild 1 . So far, we do not have data demonstrating a higher risk in the development of Coronavirus disease-19 (COVID-19) in allergic children, except for those with uncontrolled symptoms. This could help to detect affected children even with mild symptoms and limit SARS-CoV2 transmission. Instead it can be continued, as usual, in allergic children without clinical symptoms of COVID-19 and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Intranasal corticosteroids in allergic rhinitis in COVID-19 infected patients: An ARIA-EAACI statement abstract: Allergic rhinitis (AR) is a common pediatric disease, that involves up to the 25% of children worldwide. Environmental pollution, passive smoke, and many viruses are actively involved in the chronic inflammation of the nasal mucosa. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection in children is uncommon and often asymptomatic or mild. url: https://www.ncbi.nlm.nih.gov/pubmed/32627237/ doi: 10.1111/apa.15462 id: cord-030420-pgdmz69j author: Brion, Luc P. title: Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-08-13 words: 193.0 sentences: 21.0 pages: flesch: 63.0 cache: ./cache/cord-030420-pgdmz69j.txt txt: ./txt/cord-030420-pgdmz69j.txt summary: key: cord-030420-pgdmz69j title: Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) cord_uid: pgdmz69j As consistent with Lamouroux''s statement that ACE2 is low in the first trimester, ACE2 37 RNA expression is developmentally regulated with extremely low expression at 6-14 weeks, 38 although there is high expression at 24 weeks of gestation. 3 ACE2 RNA is highly expressed in 39 human villous, extravillous and syncytiotrophoblast as well as in several fetal organ cells (heart, 40 liver, and lung but not kidney) at 24 weeks of gestation. Evidence for and 65 against vertical transmission for SARS-CoV-2 (COVID-19) Clinical features of patients infected 69 with 2019 novel coronavirus in Wuhan The SARS-CoV-2 receptor ACE2 expression of 71 maternal-fetal interface and fetal organs by single-cell transcriptome study The expression and localization of 74 the human placental prorenin/renin-angiotensin system throughout pregnancy: roles in 75 trophoblast invasion and angiogenesis? Miscarriage in a Pregnant Woman With SARS-CoV-2 Infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423534/ doi: 10.1016/j.ajog.2020.08.022 id: cord-316018-zrui9i5z author: Bristow, Michael R. title: Dynamic Regulation of SARS-CoV-2 Binding and Cell Entry Mechanisms in Remodeled Human Ventricular Myocardium date: 2020-06-24 words: 3527.0 sentences: 172.0 pages: flesch: 43.0 cache: ./cache/cord-316018-zrui9i5z.txt txt: ./txt/cord-316018-zrui9i5z.txt summary: SUMMARY Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling down-regulates into the normal range. Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling downregulates into the normal range. In explanted human heart preparations from patients with end stage reduced ejection fraction heart failure (HFrEF), ACE2 enzyme activity (22) as well as gene expression at the mRNA (20,23) and protein (20,22) levels are upregulated compared to organ donor controls. F/NDC baseline data for 10 integrins previously reported to bind to ACE2 (18,19), facilitate viral internalization (17) or be associated with LV remodeling (36) or cardiac myocyte injury protection (37) . abstract: SUMMARY Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling down-regulates into the normal range. The proteases responsible for virus-cell membrane fusion were expressed but not regulated with remodeling. In addition, a new candidate for CoV-2 cell binding and entry was identified, the integrin ITGA5. The upregulation in ACE2 in remodeled LVs may explain worse outcomes in COVID-19 patients with underlying myocardial disorders, and counteracting ACE2 upregulation is a possible therapeutic approach to minimizing cardiac damage. url: https://www.ncbi.nlm.nih.gov/pubmed/32838074/ doi: 10.1016/j.jacbts.2020.06.007 id: cord-273828-557vlq9d author: Brito, Carlos Antunes title: Mechanisms and consequences of COVID-19 associated liver injury: What can we affirm? date: 2020-08-27 words: 3095.0 sentences: 166.0 pages: flesch: 50.0 cache: ./cache/cord-273828-557vlq9d.txt txt: ./txt/cord-273828-557vlq9d.txt summary: Since the first reports of coronavirus disease 2019 (COVID-19) cases in December 2019 in China, numerous papers have been published describing a high frequency of liver injury associated with severe acute respiratory syndrome coronavirus 2 infection, many of them proposing a link between these findings and patient outcomes. Recently, many papers have been published reporting gastrointestinal manifestations, including acute liver injury, with increased levels of aminotransferases, in COVID-19 patients; these manifestations have been reported more frequently in patients with severe forms of this disease. Liver injury related to SARS-CoV-2 disease has been defined by increased liver enzyme serum levels, mainly aminotransferases and bilirubin, during the infection course in patients with or without previous liver disease [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] . Wide variability in deviations of liver enzyme serum levels from normal values is observed in infected patients, with an elevation frequency ranging from 16% to 62% for aminotransferases and from 5% to 21% for bilirubin. abstract: Since the first reports of coronavirus disease 2019 (COVID-19) cases in December 2019 in China, numerous papers have been published describing a high frequency of liver injury associated with severe acute respiratory syndrome coronavirus 2 infection, many of them proposing a link between these findings and patient outcomes. Increases in serum aminotransferase levels (ranging from 16% to 62%) and bilirubin levels (ranging from 5% to 21%) have been reported and seem to be more often observed in patients with severe forms of COVID-19. Although absolute changes in these parameters are frequently seen, other variables, such as the ratio above the upper limit of normal, the onset of liver injury as a complication in severe cases and histopathological findings, reinforce that liver changes are of dubious clinical relevance in the course of this disease. Other factors must also be considered in these analyses, such as the repercussions of hemodynamic changes, the presence of thrombotic events, and, mainly, the possible drug-induced liver injury with the current, yet off-label, treatment. This paper aimed to analyze the currently available data on liver injury in patients with COVID-19. url: https://doi.org/10.4254/wjh.v12.i8.413 doi: 10.4254/wjh.v12.i8.413 id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 words: 28246.0 sentences: 1270.0 pages: flesch: 39.0 cache: ./cache/cord-315339-dcui85lw.txt txt: ./txt/cord-315339-dcui85lw.txt summary: Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . abstract: This chapter reviews the main viral pathogens of the respiratory tract, the immune responses they induce, currently available vaccines, and vaccines that are in development to control them. The main viruses responsible for acute respiratory infection in people include respiratory syncytial, influenza, human parainfluenza, human metapneumo-, human rhino-, corona-, and adenoviruses. Licensed vaccines are available only for influenza virus, with vaccines against the other pathogens either in clinical trials or in preclinical stages of development. The majority of studies evaluating respiratory virus vaccines measure serum antibody responses, because, although both cellular and humoral responses contribute to the clearance of a primary infection, neutralizing antibodies are known to protect against secondary infection. Humoral responses can be readily detected after vaccination with inactivated or subunit vaccines; however, fewer individuals seroconvert after vaccination with live vaccines. Alternative immune mechanisms such as mucosal antibody responses are probably responsible for protection by live attenuated vaccines, and immune correlates of protection are under investigation. url: https://api.elsevier.com/content/article/pii/B9780124158474000598 doi: 10.1016/b978-0-12-415847-4.00059-8 id: cord-350342-j4p8235a author: Brocato, Rebecca L. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 words: 5265.0 sentences: 283.0 pages: flesch: 49.0 cache: ./cache/cord-350342-j4p8235a.txt txt: ./txt/cord-350342-j4p8235a.txt summary: All of the SARS-CoV-2-challenged hamsters had detectable viral RNA in pharyngeal swabs at the first time point assayed, 3 dpi, and remained consistent (10 3 to 10 5 molecules of nucleocapsid using a second primer set [N2] per 100 ng RNA) throughout the duration of CyP treatment (Fig. 1C) . Viral RNA and infectious virus were detected in lung tissue from a subset of hamsters collected 13 dpi, on the day of euthanasia of moribund animals (14 to 34 dpi), or after euthanasia at 35 dpi (end of study) ( Fig. 1E and F). Electron microscopy studies were performed on lung sections of SARS-CoV-2infected, CyP-treated hamsters with various lung viral loads (Fig. 1) . Similarly, lung tissue collected at 13 dpi (end of study) indicate comparable levels of viral RNA detected (Fig. 6D ) but significantly reduced infectious virus in Centi-F1 MAb-treated animals (P ϭ 0.0002; unpaired t test) (Fig. 6E) . abstract: Animal models recapitulating human COVID-19 disease, especially severe disease, are urgently needed to understand pathogenesis and to evaluate candidate vaccines and therapeutics. Here, we develop novel severe-disease animal models for COVID-19 involving disruption of adaptive immunity in Syrian hamsters. Cyclophosphamide (CyP) immunosuppressed or RAG2 knockout (KO) hamsters were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the respiratory route. Both the CyP-treated and RAG2 KO hamsters developed clinical signs of disease that were more severe than those in immunocompetent hamsters, notably weight loss, viral loads, and fatality (RAG2 KO only). Disease was prolonged in transiently immunosuppressed hamsters and was uniformly lethal in RAG2 KO hamsters. We evaluated the protective efficacy of a neutralizing monoclonal antibody and found that pretreatment, even in immunosuppressed animals, limited infection. Our results suggest that functional B and/or T cells are not only important for the clearance of SARS-CoV-2 but also play an early role in protection from acute disease. IMPORTANCE Syrian hamsters are in use as a model of disease caused by SARS-CoV-2. Pathology is pronounced in the upper and lower respiratory tract, and disease signs and endpoints include weight loss and viral RNA and/or infectious virus in swabs and organs (e.g., lungs). However, a high dose of virus is needed to produce disease, and the disease resolves rapidly. Here, we demonstrate that immunosuppressed hamsters are susceptible to low doses of virus and develop more severe and prolonged disease. We demonstrate the efficacy of a novel neutralizing monoclonal antibody using the cyclophosphamide transient suppression model. Furthermore, we demonstrate that RAG2 knockout hamsters develop severe/fatal disease when exposed to SARS-CoV-2. These immunosuppressed hamster models provide researchers with new tools for evaluating therapies and vaccines and understanding COVID-19 pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/32900822/ doi: 10.1128/jvi.01683-20 id: cord-256699-d2tf2g7f author: Brochot, Etienne title: Comparison of different serological assays for SARS-CoV-2 in real life date: 2020-08-02 words: 1860.0 sentences: 118.0 pages: flesch: 55.0 cache: ./cache/cord-256699-d2tf2g7f.txt txt: ./txt/cord-256699-d2tf2g7f.txt summary: Using 168 samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections, we evaluated the clinical performance of 5 serological assays widely used worldwide (WANTAI®, BIORAD®, EUROIMMUN®, ABBOTT® and LIAISON®). Thus, we evaluated five commercial serological tests widely used worldwide on samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections. The assays were validated using serum samples from (i) patients hospitalized for COVID-19 (n=20), non-hospitalized patients but PCR confirmed with SARS-CoV-2 (n= 58), patients participating in screening campaigns (n= 62), and samples from patients with a history of other seasonal coronavirus infections (n= 28). For the first group, with 20 patients hospitalized for COVID-19 with a positive nasopharyngeal SARS-CoV-2 PCR, all samples were positive with these serological assays evaluated ( Figure 1A ). abstract: BACKGROUND: The emergence of the global SARS-CoV-2 pandemic required the rapid and large-scale deployment of PCR and serological tests in different formats. OBJECTIVES: Real-life evaluation of these tests is needed. Using 168 samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections, we evaluated the clinical performance of 5 serological assays widely used worldwide (WANTAI®, BIORAD®, EUROIMMUN®, ABBOTT® and LIAISON®). RESULTS: For hospitalized patients, all these assays showed a sensitivity of 100 % from day 9 after the symptoms onset. On the other hand, sensitivity was much lower for patients who did not require hospitalization for COVID-19 confirmed by PCR (from 91.6 % for WANTAI® to 69 % for LIAISON®). These differences do not seem to be due to the antigens chosen by the manufacturers but more to the test formats (IgG detection versus total antibodies). In addition, more than 50 days after a positive PCR for CoV-2-SARS the proportion of positive patients seem to decrease. We did not observe any significant cross-reactions for these techniques with the four other seasonal coronaviruses. CONCLUSION: In conclusion, the evaluation and knowledge of the serological tests used is important and should require an optimized strategy adaptation of the analysis laboratories to best meet patient’s expectations in the face of this health crisis. url: https://www.sciencedirect.com/science/article/pii/S1386653220303115?v=s5 doi: 10.1016/j.jcv.2020.104569 id: cord-322311-cg5xwx5a author: Broder, Kari title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges date: 2020-07-23 words: 773.0 sentences: 51.0 pages: flesch: 60.0 cache: ./cache/cord-322311-cg5xwx5a.txt txt: ./txt/cord-322311-cg5xwx5a.txt summary: title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges Our institution utilizes the Roche Cobas 6800 SARS-CoV-2 assay, the Cepheid GeneXpert Xpress SARS-CoV-2 assay, and a laboratory-developed test (LDT) based on a modified CDC protocol, but there is no gold standard for the diagnostic accuracy of these assays. We collected 35 positive (positivity determined per assay instructions) nasopharyngeal samples with an E target C T value of Ն30 on the Roche Cobas 6800 assay; those samples then underwent secondary testing on the Cepheid GeneXpert assay within 3 days of initial testing. One sample tested positive on the Cobas 6800 assay (C T ϭ 37.9) and negative by the GeneXpert assay and was confirmed to be negative on the LDT. Overall, the Cepheid GeneXpert Xpress SARS-CoV-2 assay and the Roche Cobas 6800 SARS-CoV-2 assay showed a high level of agreement among patients with high C T values. abstract: The SARS-CoV-2 pandemic has changed the face of the globe and upended the daily lives of billions.…. url: https://doi.org/10.1128/jcm.01187-20 doi: 10.1128/jcm.01187-20 id: cord-254668-szxhlejx author: Brogna, Barbara title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. date: 2020-06-13 words: 1885.0 sentences: 100.0 pages: flesch: 43.0 cache: ./cache/cord-254668-szxhlejx.txt txt: ./txt/cord-254668-szxhlejx.txt summary: title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. Spontaneous pneumomediastinum (SPM) and Loculated pneumothorax (LPNX) are both generally rare clinical and radiological conditions associated with Coronavirus Disease 2019 (COVID-19). We report for the first time clinical data and radiological chest CT imaging of two patients affected by COVID-pneumonia associated with early radiological findings of SPM and LPNX. It has been suggested that a dysregulation of the immune response related to SARS-CoV-2, SARS-coV or MERS-CoV infection could lead to lung injury and the clinical and radiological findings typical of ARDS 2, 20 Most of the cases of SPM and PNX described in patients with COVID-19 pneumonia and in those affected by SARS have some features in common, including the absence of smoking history 16, 19 . abstract: Spontaneous pneumomediastinum (SPM) and Loculated pneumothorax (LPNX) are both generally rare clinical and radiological conditions associated with Coronavirus Disease 2019 (COVID-19). We report for the first time clinical data and radiological chest CT imaging of two patients affected by COVID-pneumonia associated with early radiological findings of SPM and LPNX. url: https://www.sciencedirect.com/science/article/pii/S014795632030265X?v=s5 doi: 10.1016/j.hrtlng.2020.06.005 id: cord-350103-liwvhuzj author: Brooks, Nathan A. title: The role of the urologist, BCG vaccine administration, and SARS‐CoV‐2: An overview date: 2020-06-22 words: 2850.0 sentences: 144.0 pages: flesch: 39.0 cache: ./cache/cord-350103-liwvhuzj.txt txt: ./txt/cord-350103-liwvhuzj.txt summary: OBJECTIVES: To summarize the available literature regarding bacillus Calmette‐Guerin (BCG) administration, severe acute respiratory syndrome conoravirus‐2 (SARS‐CoV‐2), and the resulting clinical condition coronavirus disease (COVID‐19) in light of recent epidemiologic work suggesting decreased infection severity in BCG immunized populations while highlighting the potential role of the urologist in clinical trials and ongoing research efforts. Specifically, the epidemiologic evidence for decreased COVID‐19 morbidity in countries with BCG vaccination programs, current clinical trials for BCG vaccination to protect against COVID‐19, potential mechanisms and rationale for this protection, and the role of the urologist and urology clinic in providing support and/or leading ongoing efforts. 18 In both animal and human studies, BCG vaccination provides a non-specific benefit to the immune system, relative protection against, and reduced mortality from infections by other microbes (bacteria and viruses) which may occur by epigenetic reprogramming and induction of trained immunity. abstract: OBJECTIVES: To summarize the available literature regarding bacillus Calmette‐Guerin (BCG) administration, severe acute respiratory syndrome conoravirus‐2 (SARS‐CoV‐2), and the resulting clinical condition coronavirus disease (COVID‐19) in light of recent epidemiologic work suggesting decreased infection severity in BCG immunized populations while highlighting the potential role of the urologist in clinical trials and ongoing research efforts. MATERIALS AND METHODS: We reviewed the available literature regarding COVID‐19 and BCG vaccination. Specifically, the epidemiologic evidence for decreased COVID‐19 morbidity in countries with BCG vaccination programs, current clinical trials for BCG vaccination to protect against COVID‐19, potential mechanisms and rationale for this protection, and the role of the urologist and urology clinic in providing support and/or leading ongoing efforts. RESULTS: Epidemiologic evidence suggests that the crude case fatality rates are lower for countries with BCG vaccination compared to those without such programs. Four prospective, randomized clinical trials for BCG vaccination were identified including NCT04348370 (BADAS), NCT04327206 (BRACE), NCT04328441 (BCG‐CORONA), and NCT04350931. BCG administration may contribute to innate and adaptive immune priming with several opportunities for translational research. CONCLUSIONS: The urologist’s expertise with BCG and the infrastructure of urologic clinics may afford several opportunities for collaboration and leadership to evaluate and understand the potential role of BCG in the current COVID‐19 pandemic. url: https://doi.org/10.1002/bco2.21 doi: 10.1002/bco2.21 id: cord-349159-rndtf508 author: Brosseau, Lisa M title: Selecting Controls for Minimizing SARS-CoV-2 Aerosol Transmission in Workplaces and Conserving Respiratory Protective Equipment Supplies date: 2020-08-21 words: 5946.0 sentences: 272.0 pages: flesch: 45.0 cache: ./cache/cord-349159-rndtf508.txt txt: ./txt/cord-349159-rndtf508.txt summary: Built on the recognition that aerosol-transmissible organisms are likely to exhibit a dose–response function, such that higher exposures result from longer contact times or higher air concentrations, this control banding model offers a systematic method for identifying a set of source and pathway controls that could eliminate or reduce the need for receptor controls. From that perspective, occupational hygienists have an obligation Annals of Work Exposures and Health, 2020, 1-10 doi: 10.1093/annweh/wxaa083 Original Article to consider hazardous SARS-CoV-2 aerosols in workplace risk assessments and to encourage employers to utilize well-studied and proven source and pathway control strategies for minimizing aerosol exposures. (2019) proposed a control banding method for aerosol-transmissible diseases, such as COVID-19, for two reasons: (i) to identify those jobs at highest risk and (ii) encourage the use of source and pathway controls before resorting to personal protective equipment (PPE), for the ultimate goal of conserving PPE for those in the highest risk categories. abstract: With growing evidence of inhalation of small infectious particles as an important mode of transmission for SARS-CoV-2, workplace risk assessments should focus on eliminating or minimizing such exposures by applying the hierarchy of controls. We adapt a control banding model for aerosol-transmissible infectious disease pandemic planning to encourage the use of source and pathway controls before receptor controls (personal protective equipment). Built on the recognition that aerosol-transmissible organisms are likely to exhibit a dose–response function, such that higher exposures result from longer contact times or higher air concentrations, this control banding model offers a systematic method for identifying a set of source and pathway controls that could eliminate or reduce the need for receptor controls. We describe several examples for workers at high risk of exposure in essential or return to work categories. The goal of using control banding for such workers is to develop effective infection and disease prevention programs and conserve personal protective equipment. url: https://doi.org/10.1093/annweh/wxaa083 doi: 10.1093/annweh/wxaa083 id: cord-272135-a09bf50o author: Brouqui, Philippe title: Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease date: 2009-04-22 words: 6629.0 sentences: 370.0 pages: flesch: 48.0 cache: ./cache/cord-272135-a09bf50o.txt txt: ./txt/cord-272135-a09bf50o.txt summary: However, because the modes of infectious agent transmission are often underestimated, as was recently reported for infl uenza and SARS, 55 and because tuberculosis cannot be identifi ed without biological testing, EUNID recommends that droplet precaution should be upgraded to airborne precaution each time Situations in which a patient would need to be admitted to an HLIU • Patients with an unknown human-to-human transmittable or a potentially transmittable epidemic febrile illness that is native or imported from abroad • Patients with a known infectious disease caused by a group 3 or 4 agent* At admission of patients with HID to an emergency department • Systematically apply standard precautions and cough and respiratory etiquette • Set up at least one single room with a dedicated route and direct access, or an isolation room as recommended by EUNID for a referral hospital, † if HLIU cannot be used for ruling out HID diagnoses • Off er special training to the emergency department team • Retain close relationships with the HLIU team of the referral hospital abstract: The European Network for Infectious Diseases (EUNID) is a network of clinicians, public health epidemiologists, microbiologists, infection control, and critical-care doctors from the European member states, who are experienced in the management of patients with highly infectious diseases. We aim to develop a consensus recommendation for infection control during clinical management and invasive procedures in such patients. After an extensive literature review, draft recommendations were amended jointly by 27 partners from 15 European countries. Recommendations include repetitive training of staff to ascertain infection control, systematic use of cough and respiratory etiquette at admission to the emergency department, fluid sampling in the isolation room, and analyses in biosafety level 3/4 laboratories, and preference for point-of-care bedside laboratory tests. Children should be cared for by paediatricians and intensive-care patients should be cared for by critical-care doctors in high-level isolation units (HLIU). Invasive procedures should be avoided if unnecessary or done in the HLIU, as should chest radiography, ultrasonography, and renal dialysis. Procedures that require transport of patients out of the HLIU should be done during designated sessions or hours in secure transport. Picture archiving and communication systems should be used. Post-mortem examination should be avoided; biopsy or blood collection is preferred. url: https://www.ncbi.nlm.nih.gov/pubmed/19393960/ doi: 10.1016/s1473-3099(09)70070-2 id: cord-292015-pfvgpf7v author: Brouwer, A. F. title: SARS-CoV-2 surveillance in decedents in a large, urban medical examiner''s office date: 2020-08-07 words: 2914.0 sentences: 184.0 pages: flesch: 54.0 cache: ./cache/cord-292015-pfvgpf7v.txt txt: ./txt/cord-292015-pfvgpf7v.txt summary: We found large racial disparities in test results: despite no statistical difference in the racial distribution between those flagged and not, SARS-CoV-2 positive decedents were substantially more likely to be Black (89% vs 51%). Since mid-March (shortly after surveillance networks began detecting positive cases [7] ), WCME has been piloting daily SARS-CoV-2 surveillance by testing nasopharyngeal swabs of decedents, including both COVID-19 suspects and nonsuspects. In this analysis we compare percent positivity in WCME''s piloted SARS-Cov-2 surveillance among decedents-distinguishing between those flagged by a COVID-19 checklist and those that were not-to the percent positivity of tests among people in the surrounding catchment area. The percent positivity for SARS-CoV-2 infection among decedents flagged for testing by a COVID-19 checklist in large, urban medical examiner''s office closely mirrored percent positivity among tests in the catchment population. . https://doi.org/10.1101/2020.08.03.20162883 doi: medRxiv preprint CoV-2 test results among decedents not flagged by the COVID-19 checklist. abstract: Background: SARS-CoV-2 has become a global pandemic. Given the challenges in implementing widespread SARS-CoV-2 testing, there is increasing interest in alternative surveillance strategies. Methods: We tested nasopharyngeal swabs from 821 decedents in the Wayne County Medical Examiner's office for SARS-CoV-2. All decedents were assessed by a COVID-19 checklist, and decedents flagged by the checklist (237) were preferentially tested. A random sample of decedents not flagged by the checklist were also tested (584). We statistically analyzed the characteristics of decedents (age, sex, race, and manner of death), differentiating between those flagged by the checklist and not and between those SARS-CoV-2 positive and not. Results: Decedents were more likely to be male (70% vs 48%) and Black (55% vs 36%) than the catchment population. Seven-day average percent positivity among flagged decedents closely matched the trajectory of percent positivity in the catchment population, particularly during the peak of the outbreak (March and April). After a lull in May to mid-June, new positive tests in late June coincided with increased case detection in the catchment. We found large racial disparities in test results: despite no statistical difference in the racial distribution between those flagged and not, SARS-CoV-2 positive decedents were substantially more likely to be Black (89% vs 51%). SARS-CoV-2 positive decedents were also more likely to be older and to have died of natural causes, including of COVID-19 disease. Conclusions: Disease surveillance through medical examiners and coroners could supplement other forms of surveillance and may serve as a possible early outbreak warning sign. url: https://doi.org/10.1101/2020.08.03.20162883 doi: 10.1101/2020.08.03.20162883 id: cord-329041-coryaz2s author: Brown, Ariane J. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 words: 5934.0 sentences: 325.0 pages: flesch: 54.0 cache: ./cache/cord-329041-coryaz2s.txt txt: ./txt/cord-329041-coryaz2s.txt summary: These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. We previously reported the antiviral activity of RDV against a genetically diverse panel of human endemic, emerging and zoonotic CoV including HCoV-NL63 (alpha 1b), mouse hepatitis virus (MHV, beta 2a), SARS-CoV and related Bat CoVs WIV1 and SHC014 (beta 2b), as well as MERS-CoV and related Bat CoV HKU5 (beta 2c) (Agostini et al., 2018; Sheahan et al., 2017) . Inhibition of viral protease has also been evaluated with lopinavir, a protease inhibitor designed for human immunodeficiency virus, which like chloroquine exerts a moderate antiviral effect on CoV replication (EC 50 values: MERS-CoV 8 μM, SARS-CoV 17.1 μM, HCoV-229E 6.6 μM) (de Wilde et al., 2014) . abstract: Abstract The genetically diverse Orthocoronavirinae (CoV) family is prone to cross species transmission and disease emergence in both humans and livestock. Viruses similar to known epidemic strains circulating in wild and domestic animals further increase the probability of emergence in the future. Currently, there are no approved therapeutics for any human CoV presenting a clear unmet medical need. Remdesivir (RDV, GS-5734) is a monophosphoramidate prodrug of an adenosine analog with potent activity against an array of RNA virus families including Filoviridae, Paramyxoviridae, Pneumoviridae, and Orthocoronavirinae, through the targeting of the viral RNA dependent RNA polymerase (RdRp). We developed multiple assays to further define the breadth of RDV antiviral activity against the CoV family. Here, we show potent antiviral activity of RDV against endemic human CoVs OC43 (HCoV-OC43) and 229E (HCoV-229E) with submicromolar EC50 values. Of known CoVs, the members of the deltacoronavirus genus have the most divergent RdRp as compared to SARS- and MERS-CoV and both avian and porcine members harbor a native residue in the RdRp that confers resistance in beta-CoVs. Nevertheless, RDV is highly efficacious against porcine deltacoronavirus (PDCoV). These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/31233808/ doi: 10.1016/j.antiviral.2019.104541 id: cord-354881-7o20cn1x author: Brown, Rebecca C H title: The scientific and ethical feasibility of immunity passports date: 2020-10-16 words: 4134.0 sentences: 239.0 pages: flesch: 48.0 cache: ./cache/cord-354881-7o20cn1x.txt txt: ./txt/cord-354881-7o20cn1x.txt summary: Immunity passports could be implemented on the basis of either a laboratory test of immune response (a correlate of protection) or an immunising event (infection or vaccination), which would identify individuals less likely to get disease or transmit virus when exposed to SARS-CoV-2. 33, 34 Given the scale of the pandemic and the research into COVID-19, there is likely to be rapid progress in understanding the nature of infection and immunity such that clinical infection, with or without a measure ment of antibody response, might form the basis of a time-limited immunity passport. Evidence from previous work with seasonal coronaviruses and studies of SARS-CoV-2 vaccines in macaques suggests that previous infection or vaccination might protect from severe disease but an individual might nevertheless carry the virus at similar levels, and for a similar duration, to those previously uninfected, with an unchanged potential for transmission. abstract: There is much debate about the use of immunity passports in the response to the COVID-19 pandemic. Some have argued that immunity passports are unethical and impractical, pointing to uncertainties relating to COVID-19 immunity, issues with testing, perverse incentives, doubtful economic benefits, privacy concerns, and the risk of discriminatory effects. We first review the scientific feasibility of immunity passports. Considerable hurdles remain, but increasing understanding of the neutralising antibody response to COVID-19 might make identifying members of the community at low risk of contracting and transmitting COVID-19 possible. We respond to the ethical arguments against immunity passports and give the positive ethical arguments. First, a strong presumption should be in favour of preserving people's free movement if at all feasible. Second, failing to recognise the reduced infection threat immune individuals pose risks punishing people for low-risk behaviour. Finally, further individual and social benefits are likely to accrue from allowing people to engage in free movement. Challenges relating to the implementation of immunity passports ought to be met with targeted solutions so as to maximise their benefit. url: https://api.elsevier.com/content/article/pii/S1473309920307660 doi: 10.1016/s1473-3099(20)30766-0 id: cord-288920-xkfcc2dx author: Broxmeyer, L title: SARS: Just another viral acronym? date: 2003-08-31 words: 2362.0 sentences: 115.0 pages: flesch: 47.0 cache: ./cache/cord-288920-xkfcc2dx.txt txt: ./txt/cord-288920-xkfcc2dx.txt summary: Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. CDC began supporting the World Health Organization (WHO) in the investigation of a multi-country outbreak of the atypical pneumonia of unknown etiology (1), referred to as severe acute respiratory syndrome (SARS). Although high fever, nonproductive cough, low blood oxygen saturation, and varying degrees of respiratory distress, all found in SARS, are nothing new to the clinical picture of tuberculosis (11) , the number of TB cases in which people in the Orient die of adult respiratory distress syndrome (ARDS) is definitely on the rise (12), the same ARDS that often provokes the ''crazypaving'' appearance at thin-section CT (13). abstract: Abstract Recent observations and experimental evidence have purported that a virus causes SARS, but such viruses have been isolated in only less than half of SARS patients in some studies and virologist Vincent Plummer of Winnipeg’s National Microbiology Laboratory found that indeed 1 in 5 perfectly healthy Canadians with a history of recent travel to Asia had the virus. Therfore SARS microbiologic origins remain unclear. Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. url: https://www.sciencedirect.com/science/article/pii/S0306987703001956 doi: 10.1016/s0306-9877(03)00195-6 id: cord-255913-430lrbyx author: Brufsky, Adam title: DC/L‐SIGNs of Hope in the COVID‐19 Pandemic date: 2020-05-06 words: 1518.0 sentences: 76.0 pages: flesch: 49.0 cache: ./cache/cord-255913-430lrbyx.txt txt: ./txt/cord-255913-430lrbyx.txt summary: The current pandemic and its pleotropic effects can be explained in part by interaction between SARS‐CoV‐2 spike protein S, the ACE2/L‐SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC‐SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. The current pandemic and its pleotropic effects can be explained in part by interaction between SARS-CoV-2 spike protein S, the ACE2/L-SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC-SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. L-SIGN is expressed on human type II alveolar cells, is associated with ACE2 10 , and can enhance ACE2 mediated binding and cellular entry of viral pseudotypes expressing the spike protein S of SARS-CoV 9 . De-glycosylation reduces infectivity of viral pseudotypes expressing SARS-CoV spike protein 13 and specific asparagine glycosylation sites in three clusters within the SARS-CoV S protein appear critical for DC/L-SIGN mediated, but not ACE2 mediated, SARS Co-V pseudotype entry into cells 13 . abstract: In a rapidly evolving pandemic such as COVID‐19, theories which help unify disparate pre‐clinical and clinical observations would be useful. The current pandemic and its pleotropic effects can be explained in part by interaction between SARS‐CoV‐2 spike protein S, the ACE2/L‐SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC‐SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. Infection of the DC by SARS‐CoV‐2 can potentially explain the exuberant distal immunopathology seen in COVID‐19. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25980 doi: 10.1002/jmv.25980 id: cord-316374-mzomj1ab author: Brufsky, Adam title: Boning up: amino-bisphophonates as immunostimulants and endosomal disruptors of dendritic cell in SARS-CoV-2 infection date: 2020-06-29 words: 2774.0 sentences: 153.0 pages: flesch: 41.0 cache: ./cache/cord-316374-mzomj1ab.txt txt: ./txt/cord-316374-mzomj1ab.txt summary: Amino-bisphosphonates such as zoledronic acid (ZA) can possibly ameliorate or prevent severe COVID-19 disease by at least three distinct mechanisms: (1) as immunostimulants which could boost γδ T cell expansion, important in the acute response in the lung; (2) as DC modulators, limiting their ability to only partially activate T cells; and (3) as prenylation inhibitors of small GTPases in the endosomal pathway of the DC to prevent expulsion of lysosomes containing SARS-CoV-2 virions. Early and central infection of tissue resident dendritic cells (DC) by the SARS-CoV-2 coronavirus explain some of the immunopathology of the COVID-19 pandemic. Agents that alter endosomal pH such as hydroxychloroquine (HCQ) could be protective in SARS-CoV-2 infected DCs in maintaining the immune response as well as the lymphocyte count, as was observed in a recently reported randomized, parallel, open label, multicenter clinical trial of hydroxychloroquine (HCQ) and usual care versus usual care alone for the treatment of COVID infection [36] . abstract: Amino-bisphosphonates such as zoledronic acid (ZA) can possibly ameliorate or prevent severe COVID-19 disease by at least three distinct mechanisms: (1) as immunostimulants which could boost γδ T cell expansion, important in the acute response in the lung; (2) as DC modulators, limiting their ability to only partially activate T cells; and (3) as prenylation inhibitors of small GTPases in the endosomal pathway of the DC to prevent expulsion of lysosomes containing SARS-CoV-2 virions. Use of ZA or other amino-bisphosphonates as modulators of COVID-19 disease should be considered. url: https://doi.org/10.1186/s12967-020-02433-6 doi: 10.1186/s12967-020-02433-6 id: cord-265595-55s19mr1 author: Brug, Johannes title: Risk Perceptions and Behaviour: Towards Pandemic Control of Emerging Infectious Diseases: International Research on Risk Perception in the Control of Emerging Infectious Diseases date: 2009-01-06 words: 2318.0 sentences: 113.0 pages: flesch: 46.0 cache: ./cache/cord-265595-55s19mr1.txt txt: ./txt/cord-265595-55s19mr1.txt summary: Three papers [5] [6] [7] were the result of a European Commission funded project, called SARS-Control that was partly dedicated to exploring risk perceptions and risk communications related to SARS and other emerging infectious diseases. Effective management of new epidemic infectious disease risks in the phase that no treatment or vaccination is yet possible is largely dependent on precautionary behaviour of the population. Four of the papers present empirical mostly explorative original research on risk perceptions, knowledge, beliefs and other issues related to SARS during or after the SARS outbreak in 2003. Given the clear and present danger of newly emerging infectious disease outbreaks in the near future and the importance of the public response and precautionary actions to control the spread, additional research on risk perceptions and other behavioural determinants is warranted. Perceived threat, risk perception and efficacy beliefs related to SARS and other (emerging) infectious diseases: results of an international survey abstract: nan url: https://doi.org/10.1007/s12529-008-9000-x doi: 10.1007/s12529-008-9000-x id: cord-326568-twv2i3fb author: Bruminhent, Jackrapong title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 words: 4402.0 sentences: 245.0 pages: flesch: 48.0 cache: ./cache/cord-326568-twv2i3fb.txt txt: ./txt/cord-326568-twv2i3fb.txt summary: To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians'' diagnoses. Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. Apart from close contact with an infected case and visiting high-risk places, we found that having no medical coverage and presenting with productive cough were predictors of being diagnosed with COVID-19 among PUIs. SARS-CoV-2 is an emerging respiratory virus that commonly causes no or mild respiratory tract infection and is occasionally complicated by severe pneumonia [1] . abstract: To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians’ diagnoses. We aimed to determine characteristics among all PUIs and those with and without COVID-19. We retrospectively reviewed clinical characteristics and risk factors for laboratory-confirmed COVID-19 cases among PUIs at a tertiary care center in Bangkok, Thailand, between March 23 and April 7, 2020. Reverse transcription-polymerase chain reaction for SARS-CoV-2 RNA was performed. There were 405 evaluable PUIs; 157 (38.8%) were men, with a mean age ± SD of 36.2 ± 12.6 years. The majority (68.9%) reported no comorbidities. There were 53 (13.1%) confirmed COVID-19 cases. The most common symptoms among those were cough (73.6%), fever (58.5%), sore throat (39.6%), and muscle pain (37.4%). Among these patients, diagnoses were upper respiratory tract infection (69.8%), viral syndrome (15.1%), pneumonia (11.3%), and asymptomatic infection (3.8%). Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. COVID-19 was identified in 13% of PUIs defined per a national health authority’s case definition. History of contact with a COVID-19 patient, visiting a high-risk place, having no medical coverage, and productive cough may identify individuals at risk of COVID-19 in Thailand. url: https://www.ncbi.nlm.nih.gov/pubmed/32931517/ doi: 10.1371/journal.pone.0239250 id: cord-350134-gl3qtoug author: Brun, Gilles title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? date: 2020-05-22 words: 1006.0 sentences: 76.0 pages: flesch: 44.0 cache: ./cache/cord-350134-gl3qtoug.txt txt: ./txt/cord-350134-gl3qtoug.txt summary: title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? Since December 2019, a novel coronavirus, also called severe acute respiratory syndrome CoV-2 (SARS-CoV-2), emerged in Wuhan, China, and caused a pandemic disease . Herein, we report a case of SARS-CoV-2 brain lesions suggesting an acute demyelination. At day 7, a brain MRI revealed lesions with restricted diffusion without any hemorrhage or enhancement after gadolinium injection (figure). 4 In our case, the distribution of bilateral but asymmetrical lesions with periventricular and deep white matter involvement is rather suggestive of an acute demyelination. Although mechanisms remain obscure, our case shows the importance of the MRI in the exploration of neurologic symptoms in COVID-19. Demyelination or small-vessel CNS vasculitis might be a rare but silent complication of sedated patients with COVID-19. COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32444427/ doi: 10.1212/nxi.0000000000000777 id: cord-004634-pkrxiipo author: Brun-Buisson, Christian title: SARS: The challenge of emerging pathogens to the intensivist date: 2003-05-08 words: 1206.0 sentences: 58.0 pages: flesch: 53.0 cache: ./cache/cord-004634-pkrxiipo.txt txt: ./txt/cord-004634-pkrxiipo.txt summary: In late February 2003, the WHO issued a worldwide public health alert on the emergence of a new epidemic of acute respiratory disease first identified in Asian countries since November 2002. In a few weeks, the new agent causing this "severe acute respiratory syndrome" (SARS), a coronavirus, has been identified, sequenced, and tests have been developed for diagnosis [1] . As of the end of April 2003, about 5,000 suspected or probable cases have been reported to the WHO from 27 countries [2] , with a vast majority from inland China (57% of reported cases), which appears to be at the origin of the epidemic, and Hong Kong (32%). In North America, however, an outbreak soon occurred in Toronto, Canada, following an household epidemic which appeared secondary to contamination of a Canadian resident of Asian origin who visited relatives in Hong Kong in February 2003 [3] . Affected areas-severe acute respiratory syndrome (SARS) A Major Outbreak of Severe Acute Respiratory Syndrome in Hong Kong abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080195/ doi: 10.1007/s00134-003-1823-y id: cord-312038-g76cpjp7 author: Brunaugh, Ashlee D. title: Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date: 2020-10-07 words: 11043.0 sentences: 517.0 pages: flesch: 47.0 cache: ./cache/cord-312038-g76cpjp7.txt txt: ./txt/cord-312038-g76cpjp7.txt summary: Utilizing repurposed NIC, and with the goal of developing a therapeutically effective, rapidly scalable and globally distributable antiviral therapy to reduce the spread of SARS-CoV-2, we describe an inhalable NIC formulation that can be administered using three major models or respiratory tract delivery systems: DPI, nasal spray and nebulizer. At the highest dose tested (0.125 µg/mL NIC), Vero cells with an established MERS-CoV infection exhibited an 82.2% ± 0.8% decrease in viral load compared to untreated controls after 24-hours of exposure to NIC-hLYS particles ( Fig 1D) . While brain viral titres did not exhibit further reduction from levels noted in the preliminary efficacy study, the inoculation of Vero E6 cells with viral particles obtained from lung and brain homogenates of surviving animals resulted in no observation of CPE at any of the inoculum concentrations tested, which indicates that remaining viral particles were not active. abstract: Niclosamide (NIC) has demonstrated promising in vitro antiviral efficacy against SARS-CoV-2, the causative agent of the COVID-19 pandemic. Though NIC is already FDA-approved, the oral formulation produces systemic drug levels that are too low to inhibit SARS-CoV-2. As an alternative, direct delivery of NIC to the respiratory tract as an aerosol could target the primary site of for SARS-CoV-2 acquisition and spread. We have developed a niclosamide powder suitable for delivery via dry powder inhaler, nebulizer, and nasal spray through the incorporation of human lysozyme (hLYS) as a carrier molecule. This novel formulation exhibits potent in vitro and in vivo activity against MERS-CoV and SARS-CoV-2 and may protect against methicillin-resistance staphylococcus aureus pneumonia and inflammatory lung damage occurring secondary to CoV infections. The suitability of the formulation for all stages of the disease and low-cost development approach will ensure wide-spread utilization url: https://doi.org/10.1101/2020.09.24.310490 doi: 10.1101/2020.09.24.310490 id: cord-283034-ebely0rx author: Brunet, E title: Ileitis as the exclusive manifestation of covid-19. The first reported case date: 2020-10-19 words: 449.0 sentences: 47.0 pages: flesch: 50.0 cache: ./cache/cord-283034-ebely0rx.txt txt: ./txt/cord-283034-ebely0rx.txt summary: The patient did not report any respiratory symptoms. Two nasopharyngeal and oropharyngeal swab specimens performed before admission had been negative for SARS-CoV-2. Respiratory auscultation was strictly normal, and pain was noted on the palpation of the right lower abdominal quadrant. The patient was admitted to the gastroenterology unit after a confirmatory negative SARS-CoV-2 NAAT The patient recovered completely, with normalization of the previous blood test abnormalities. A SARS-CoV-2 control NAAT in rectal swab was negative before discharge from hospital. To our knowledge, our report is the first well-documented case of SARS-CoV-2 intestinal infection without evidence of pulmonary involvement. The multiple negative nasopharyngeal swabs plus the normal chest X-ray and CT findings rule out pulmonary infection. We report a patient with SARS-CoV-2 infection apparently limited to the bowel. In conclusion, SARS-CoV-2 may occur with an exclusive intestinal symptoms. Abdominal Pain: A Real Challenge in Novel COVID-19 Infection abstract: nan url: https://doi.org/10.1016/j.gastrohep.2020.10.001 doi: 10.1016/j.gastrohep.2020.10.001 id: cord-299783-8ti6r0eh author: Bruni, M. title: Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date: 2020-08-01 words: 3283.0 sentences: 188.0 pages: flesch: 47.0 cache: ./cache/cord-299783-8ti6r0eh.txt txt: ./txt/cord-299783-8ti6r0eh.txt summary: Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. The performances of these ELISA assays were assessed for the different viral antigens and classes of antibodies by determining ROC curves using i) a cohort of 56 sera from COVID-19 patients collected between April and June 2020 and tested positive for nasopharyngeal swabs, and ii) 436 pre-COVID-19 sera, collected between 2012 and 2015 (Supplementary Table 1 and Figure S1 ). Non-hospitalized COVID-19 subjects manifested a lower antibody titer as compared to severe ICU patients for all the tested antibody classes and viral antigens ( Figure 1B-D) . abstract: Background. Coronavirus disease-19 (COVID-19) is a respiratory illness caused by the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), a novel beta-coronavirus. Although antibody response to SARS-CoV-2 can be detected early during the infection, several outstanding questions remain to be addressed regarding magnitude and persistence of antibody titer against different viral proteins and their correlation with the strength of the immune response, as measured by serum levels of pro-inflammatory mediators. Methods. An ELISA assay has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length nucleocapsid protein (N protein). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Results. Specificity and sensitivity of the ELISA assays were high for anti-RBD IgG and IgA (92-97%) and slightly lower for IgM and the Spike and N proteins (70-85%). The ELISA allowed quantification of IgM, IgG and IgA antibody responses against all the viral antigens tested and showed a correlation between magnitude of the antibody response and disease severity. Non-hospitalized subjects showed lower antibody titers and blood pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested. Noteworthy, in non-severe COVID-19 infections, antibody titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance. Conclusions. Rapid decline in antibody titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection, suggesting that antibody-mediated protection against re-infection with SARS-CoV-2 is of short duration. These results suggest caution in use serological testing to estimate the prevalence of SARS-CoV-2 infection in the general population. url: https://doi.org/10.1101/2020.07.30.20164368 doi: 10.1101/2020.07.30.20164368 id: cord-318018-ybdkp398 author: Bruni, Margherita title: Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date: 2020-10-01 words: 5481.0 sentences: 263.0 pages: flesch: 46.0 cache: ./cache/cord-318018-ybdkp398.txt txt: ./txt/cord-318018-ybdkp398.txt summary: Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Our data show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory cytokines. Here we show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory mediators. Moreover, we showed that the vast majority of COVID-19 mildly symptomatic patients analyzed in the study halved their anti-RBD antibody titers after 4 weeks from viral negativization, thus confirming the short lifespan of humoral immune responses against SARS-CoV-2. abstract: Although antibody response to SARS-CoV-2 can be detected early during the infection, several outstanding questions remain to be addressed regarding the magnitude and persistence of antibody titer against different viral proteins and their correlation with the strength of the immune response. An ELISA assay has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length Nucleocapsid protein (N). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Non-hospitalized subjects showed lower antibody titers and blood pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested. Noteworthy, in non-severe COVID-19 infections, antibody titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance. Thus, rapid decline in antibody titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection, suggesting that antibody-mediated protection against re-infection with SARS-CoV-2 is of short duration. These results suggest caution in using serological testing to estimate the prevalence of SARS-CoV-2 infection in the general population. url: https://doi.org/10.3390/jcm9103188 doi: 10.3390/jcm9103188 id: cord-298716-pubhq564 author: Bryche, Bertrand title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date: 2020-06-16 words: 3558.0 sentences: 212.0 pages: flesch: 56.0 cache: ./cache/cord-298716-pubhq564.txt txt: ./txt/cord-298716-pubhq564.txt summary: title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. We measured the OE thickness, the OSN cilia quality (based on Golf staining) and the immune cell infiltration of the olfactory mucosa (based on the Iba1 staining) on 6 images per animal taken from 3 different slides spread along the nasal cavity. Two recent reports indicate that olfactory neurons in hamster (Sia et al., 2020) and respiratory cells in ferret (Ryan et al., 2020) may be the target of SARS-CoV-2 but these studies did not focus on the nasal cavity and they did not use double staining to clearly identify the infected cells in the OE. abstract: Anosmia is one of the most prevalent symptoms of SARS-CoV-2 infection during the COVID-19 pandemic. However, the cellular mechanism behind the sudden loss of smell has not yet been investigated. The initial step of odour detection takes place in the pseudostratified olfactory epithelium (OE) mainly composed of olfactory sensory neurons surrounded by supporting cells known as sustentacular cells. The olfactory neurons project their axons to the olfactory bulb in the central nervous system offering a potential pathway for pathogens to enter the central nervous system by bypassing the blood brain barrier. In the present study, we explored the impact of SARS-COV-2 infection on the olfactory system in golden Syrian hamsters. We observed massive damage of the OE as early as 2 days post nasal instillation of SARS-CoV-2, resulting in a major loss of cilia necessary for odour detection. These damages were associated with infection of a large proportion of sustentacular cells but not of olfactory neurons, and we did not detect any presence of the virus in the olfactory bulbs. We observed massive infiltration of immune cells in the OE and lamina propria of infected animals, which may contribute to the desquamation of the OE. The OE was partially restored 14 days post infection. Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. url: https://doi.org/10.1101/2020.06.16.151704 doi: 10.1101/2020.06.16.151704 id: cord-351314-atsuh8e2 author: Bryson-Cahn, Chloe title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 words: 1255.0 sentences: 67.0 pages: flesch: 45.0 cache: ./cache/cord-351314-atsuh8e2.txt txt: ./txt/cord-351314-atsuh8e2.txt summary: Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. abstract: Thousands of people in the United States have required testing for SARS-CoV-2. Evaluation for a special pathogen is resource intensive. We report an innovative approach to home assessment that, in collaboration with public health, enables safe evaluation and specimen collection outside the healthcare setting, avoiding unnecessary exposures and resource utilization. url: https://www.ncbi.nlm.nih.gov/pubmed/32166310/ doi: 10.1093/cid/ciaa256 id: cord-283491-y6t64pux author: Brzezinski, Dariusz title: Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date: 2020-09-27 words: 3182.0 sentences: 166.0 pages: flesch: 45.0 cache: ./cache/cord-283491-y6t64pux.txt txt: ./txt/cord-283491-y6t64pux.txt summary: Understandably, firstline research findings, including molecular structure determinations, depositions in the Protein Data Bank (PDB), 1 and related results, are often made public on BioRxiv 2 or MedRxiv 3 before formal peer review. In this paper, we present covid-19.bioreproduciblity.org, a web resource that organizes SARS-CoV-2 related structural information in a way that should be understandable and useful for a wider scientific community, and not only for structural biologists. Finally, the structures are evaluated by a team of expert structural biologists who use a combination of the mined data, validation reports, and manual inspection of the protein models and associated electron density to examine potential problems. If raw diffraction data are available, the results of automatic processing of images by HKL-3000auto are examined to verify that the structure was determined in the correct space group and at optimal resolution. abstract: The COVID‐19 pandemic has triggered numerous scientific activities aimed at understanding the SARS‐CoV‐2 virus and ultimately developing treatments. Structural biologists have already determined hundreds of experimental X‐ray, cryo‐EM, and NMR structures of proteins and nucleic acids related to this coronavirus, and this number is still growing. To help biomedical researchers, who may not necessarily be experts in structural biology, navigate through the flood of structural models, we have created an online resource, covid19.bioreproducibility.org, that aggregates expert‐verified information about SARS‐CoV‐2‐related macromolecular models. In this paper, we describe this web resource along with the suite of tools and methodologies used for assessing the structures presented therein. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32981130/ doi: 10.1002/pro.3959 id: cord-262104-oig3qrr7 author: Brüssow, Harald title: COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date: 2020-06-08 words: 7118.0 sentences: 365.0 pages: flesch: 53.0 cache: ./cache/cord-262104-oig3qrr7.txt txt: ./txt/cord-262104-oig3qrr7.txt summary: Very similar information was reported in data describing household transmission in Wuhan, where children showed a 4% infection rate compared with 17% in adults. 1.6 million tests were used to identify 1''400 SARS-CoV-2-positive cases; 1000 patients had had exposure to infected people from Hubei. In Wuhan, 105 index cases of patients suffering from moderate COVID-19 symptoms (fever, cough, fatigue) were investigated for secondary transmission to 392 household contacts. The control measures that stopped the epidemic locally have included: intense infection surveillance of incoming travelers; isolation of COVID-19 cases in hospitals; contact tracing and quarantine in holiday camps; and school closure but no lock-down, thus preventing the crisis from having a negative economic impact. Model calculations showed that the containment measures (the quarantine of exposed, and the isolation of infected persons) which depleted the number of susceptible individuals for the virus, reproduced the actually observed case development. abstract: In the absence of an efficient drug treatment or a vaccine, the control of the COVID‐19 pandemic relies on classic infection control measures. Since these means are socially disruptive and come with substantial economic loss for societies, a better knowledge of the epidemiology of the new coronavirus epidemic is crucial to achieve control at a sustainable cost, and within tolerable restrictions of civil rights. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/1462-2920.15118 doi: 10.1111/1462-2920.15118 id: cord-297168-t6zf5k99 author: Brüssow, Harald title: The Novel Coronavirus – A Snapshot of Current Knowledge date: 2020-03-06 words: 4136.0 sentences: 207.0 pages: flesch: 50.0 cache: ./cache/cord-297168-t6zf5k99.txt txt: ./txt/cord-297168-t6zf5k99.txt summary: While bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the Huanan food market in Wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. W. Tan and colleagues, who now constitute the China Novel Coronavirus Investigating and Research Team, described subsequently the isolation of further coronaviruses from three patients in Wuhan who tested negative for 18 viral and four bacterial respiratory pathogens. Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients Outside Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: Another animal to human transmission of a coronavirus occurred in December 2019 on a live animal market in the Chinese city of Wuhan causing an epidemic in China, reaching now different continents. This minireview summarizes the research literature on the virological, clinical and epidemiological aspects of this epidemic published until end of February 2020. url: https://www.ncbi.nlm.nih.gov/pubmed/32144890/ doi: 10.1111/1751-7915.13557 id: cord-302316-raf5rlkq author: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 words: 6944.0 sentences: 350.0 pages: flesch: 44.0 cache: ./cache/cord-302316-raf5rlkq.txt txt: ./txt/cord-302316-raf5rlkq.txt summary: US researchers studied the viral and cellular transcriptional response upon infection of cell cultures and in animal models with different respiratory viruses including influenza A virus and SARS-CoV-2. A French study randomizing 181 COVID-19 patients with pneumonia on hydroxychloroquine or placebo, observed, however, no significant effect of treatment on transfer to ICU, mortality, or in the prevention of development of acute respiratory distress syndrome (Mah evas et al., 2020). A total of 86 COVID-19 cases of patients from China with mild/moderate disease were randomized on the antiviral lopinavir (an inhibitor of HIV protease combined with ritonavir, which prolongs the presence of drugs in the body) or the antiviral arbidol (an influenza virus fusion inhibitor only registered in Russia) or in a control group in a 2:2:1 ratio. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial abstract: The number of people infected with SARS‐CoV‐2, and sadly dying from COVID‐19, has exploded, and so the amount of literature on the novel coronavirus and the disease it causes has increased proportionately. The case numbers in some countries are beyond the epidemic peak, but the uncertainty about a second wave keeps politicians and societies under pressure. Appropriate decision‐making and winning support from the population depends on precise scientific information rather than leaving the field to scaremongers of all proveniences. This mini‐review is an update of earlier reports (Brüssow, Microb Biotechnol 2020a;13:607; Brüssow, Microb Biotechnol 2020b; https://doi.org/10.1111/1751-7915.13592). url: https://doi.org/10.1111/1751-7915.13611 doi: 10.1111/1751-7915.13611 id: cord-332820-6qx6svs5 author: Buck, M. D. title: Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay date: 2020-07-01 words: 4095.0 sentences: 252.0 pages: flesch: 52.0 cache: ./cache/cord-332820-6qx6svs5.txt txt: ./txt/cord-332820-6qx6svs5.txt summary: The pipeline utilises a series of in-house buffers to first inactivate patient samples received from care homes and hospitals, and to then extract RNA before using a CE marked commercial kit to detect SARS-CoV-2 by RT-qPCR. Herein, we describe the use of loop mediated isothermal amplification PCR coupled with reverse transcription (RT-LAMP) as a robust method for SARS-CoV-2 detection in clinical specimens 6 . Our results demonstrate that within the CCC pipeline, RT-LAMP can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nosethroat swabs and endotracheal secretions/bronchoalveolar lavage fluid. The RT-LAMP assay reproducibility and precision were determined by extracting RNA 5 times from a confirmed COVID-19 positive patient sample through the CCC pipeline and assessing by N gene and 18S RT-LAMP in 5 independent experiments, performed by two different operators ( Figure 4D ). abstract: The ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 40,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated standard operating procedure (SOP) for high-throughput SARS- CoV-2 detection by RT-LAMP in 25 minutes that is robust, reliable, repeatable, sensitive, specific, and inexpensive. url: http://medrxiv.org/cgi/content/short/2020.06.29.20142430v1?rss=1 doi: 10.1101/2020.06.29.20142430 id: cord-311216-mfqlv3nh author: Buckley, Leo F. title: Cardiovascular Pharmacology in the Time of COVID-19: A Focus on Angiotensin-Converting Enzyme 2 date: 2020-04-13 words: 2126.0 sentences: 124.0 pages: flesch: 38.0 cache: ./cache/cord-311216-mfqlv3nh.txt txt: ./txt/cord-311216-mfqlv3nh.txt summary: Severe acute respiratory syndrome coronavirus-2019 (SARS-CoV-2), the causative virus of COVID-19, infects host cells through angiotensin-converting enzyme 2 (ACE2). We review current knowledge of the role of ACE2 in cardiovascular physiology and SARS-CoV-2 virology, as well as clinical data to inform the management of patients with or at risk for COVID-19 who require renin–angiotensin–aldosterone system inhibitor therapy. [2] [3] [4] [5] [6] [7] [8] SARS-CoV-2 infects host cells by binding to human angiotensin-converting enzyme-2 (ACE2), [9] [10] [11] a membranebound enzyme expressed in the lungs, heart, and kidneys (among many other organs). 15 It has been proposed that renin-angiotensin-aldosterone system (RAAS) inhibitors predispose to SARS-CoV-19 infection and worsen outcomes after COVID-19 by upregulating ACE2 expression. Epidemiologic studies should be performed to estimate the association of RAAS inhibitor use to risk of COVID-19 in patients with hypertension, heart failure or chronic kidney disease. Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients abstract: Coronavirus disease-2019 (COVID-19) has emerged as a pandemic affecting millions of adults. Severe acute respiratory syndrome coronavirus-2019 (SARS-CoV-2), the causative virus of COVID-19, infects host cells through angiotensin-converting enzyme 2 (ACE2). Preclinical models suggest that ACE2 upregulation confers protective effects in acute lung injury. In addition, renin–angiotensin aldosterone system inhibitors reduce adverse atherosclerotic cardiovascular disease, heart failure, and chronic kidney disease outcomes, but may increase ACE2 levels. We review current knowledge of the role of ACE2 in cardiovascular physiology and SARS-CoV-2 virology, as well as clinical data to inform the management of patients with or at risk for COVID-19 who require renin–angiotensin–aldosterone system inhibitor therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/32301766/ doi: 10.1097/fjc.0000000000000840 id: cord-277611-3iynrfzq author: Buetti, Niccolò title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 words: 810.0 sentences: 86.0 pages: flesch: 68.0 cache: ./cache/cord-277611-3iynrfzq.txt txt: ./txt/cord-277611-3iynrfzq.txt summary: In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms'' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . abstract: nan url: https://doi.org/10.1093/cid/ciaa1315 doi: 10.1093/cid/ciaa1315 id: cord-337485-nqcnd9py author: Buetti, Niccolò title: SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients date: 2020-10-16 words: 2144.0 sentences: 133.0 pages: flesch: 49.0 cache: ./cache/cord-337485-nqcnd9py.txt txt: ./txt/cord-337485-nqcnd9py.txt summary: Our objectives were to describe the viral shedding and the viral load in LRT and to determine their association with mortality in critically ill COVID-19 patients. Third, we assessed the association between viral presence in LRT and mortality using mixed-effect logistic models for clustered data adjusting for the time between symptoms'' onset and date of sampling. Our objectives were (1) to describe the viral shedding and the viral load in LRT and (2) to determine THE ASSOCIATION BETWEEN VIRAL PRESENCE AND MORTALITY in critically ill COVID-19 patients. The viral shedding in LRT lasted almost 30 days in median in critically ill patients, and the SARS-CoV-2 viral presence in the LRT was associated with the 6week mortality. Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients abstract: BACKGROUND: Data on SARS-CoV-2 load in lower respiratory tract (LRT) are scarce. Our objectives were to describe the viral shedding and the viral load in LRT and to determine their association with mortality in critically ill COVID-19 patients. METHODS: We conducted a binational study merging prospectively collected data from two COVID-19 reference centers in France and Switzerland. First, we described the viral shedding duration (i.e., time to negativity) in LRT samples. Second, we analyzed viral load in LRT samples. Third, we assessed the association between viral presence in LRT and mortality using mixed-effect logistic models for clustered data adjusting for the time between symptoms’ onset and date of sampling. RESULTS: From March to May 2020, 267 LRT samples were performed in 90 patients from both centers. The median time to negativity was 29 (IQR 23; 34) days. Prolonged viral shedding was not associated with age, gender, cardiac comorbidities, diabetes, immunosuppression, corticosteroids use, or antiviral therapy. The LRT viral load tended to be higher in non-survivors. This difference was statistically significant after adjusting for the time interval between onset of symptoms and date of sampling (OR 3.78, 95% CI 1.13–12.64, p = 0.03). CONCLUSIONS: The viral shedding in LRT lasted almost 30 days in median in critically ill patients, and the viral load in the LRT was associated with the 6-week mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/33066801/ doi: 10.1186/s13054-020-03323-5 id: cord-307436-qcdlcxyb author: Bui, L. V. title: Estimation of the incubation period of SARS-CoV-2 in Vietnam date: 2020-05-15 words: 2468.0 sentences: 158.0 pages: flesch: 52.0 cache: ./cache/cord-307436-qcdlcxyb.txt txt: ./txt/cord-307436-qcdlcxyb.txt summary: Methods: Only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset and clearly defined window of possible SARS-CoV-2 exposure were included. To assure the reliability of analysis, we selected only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset (including fever, cough, and shortness of breath) and clearly defined window of possible SARS-CoV-2 exposure. We estimated the incubation period of Vietnamese confirmed COVID-19 cases from public reported data with three parametric models, including Weibull, Gamma and Lognornal . The estimated mean of incubation period for 19 Vietnamese confirmed COVID-19 cases using Weibull distribution model is higher than that of SARS in Hong Kong and Beijing [14] and in MERS [15, 16] . Our study has several strengths, including being the first effort to estimate SAR-CoV-2 incubation period using data from Vietnamese locally transmitted cases. abstract: Objective: To estimate the incubation period of Vietnamese confirmed COVID-19 cases. Methods: Only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset and clearly defined window of possible SARS-CoV-2 exposure were included. We used three parametric forms with Hamiltonian Monte Carlo method for Bayesian Inference to estimate incubation period for Vietnamese COVID-19 cases. Leave-one-out Information Criterion was used to assess the performance of three models. Results: A total of 19 cases identified from 23 Jan 2020 to 13 April 2020 was included in our analysis. Average incubation periods estimated using different distribution model ranged from 6.0 days to 6.4 days with the Weibull distribution demonstrated the best fit to the data. The estimated mean of incubation period using Weibull distribution model was 6.4 days (95% credible interval (CI): 4.89 - 8.5), standard deviation (SD) was 3.05 (95%CI 3.05 - 5.30), median was 5.6, ranges from 1.35 to 13.04 days (2.5th to 97.5th percentiles). Extreme estimation of incubation periods is within 14 days from possible infection. Conclusion: This analysis provides evidence for an average incubation period for COVID-19 of approximately 6.4 days. Our findings support existing guidelines for 14 days of quarantine of persons potentially exposed to SARS-CoV-2. Although for extreme cases, the quarantine period should be extended up to three weeks. url: https://doi.org/10.1101/2020.05.09.20096800 doi: 10.1101/2020.05.09.20096800 id: cord-279131-1unb0z79 author: Buijsers, Baranca title: Beneficial non-anticoagulant mechanisms underlying heparin treatment of COVID-19 patients date: 2020-08-25 words: 3989.0 sentences: 219.0 pages: flesch: 30.0 cache: ./cache/cord-279131-1unb0z79.txt txt: ./txt/cord-279131-1unb0z79.txt summary: Here, we summarise potential beneficial, non-anticoagulant mechanisms underlying treatment of COVID-19 patients with heparin/LMWH, which include: (i) Inhibition of heparanase activity, responsible for endothelial leakage; (ii) Neutralisation of chemokines, and cytokines; (iii) Interference with leukocyte trafficking; (iv) Reducing viral cellular entry, and (v) Neutralisation of extracellular cytotoxic histones. In addition to functioning as anticoagulants, heparins have other therapeutic functions that are relevant for the treatment of COVID-19-associated clinical manifestations, i.e. neutralisation of inflammatory chemokines, and cytokines, such as CXCL-1, IL-6, and IL-8 that play a key role in ARDS; neutralisation of extracellular cytotoxic histones and by interfering with leukocyte trafficking [20] . Data for this review were identified by searches of PubMed, and preprint servers, and references from relevant articles using the search terms "COVID-19", "Heparin", "Non-anticoagulant functions of heparin", "Low molecular weight heparin", "ARDS", "Kidney dysfunction", "Endothelial barrier dysfunction", "Heparanase", "Heparan sulphate", "Viral entry", "Heparanase inhibition", "Inflammation", "Complement system", and "Neutrophil extracellular traps". abstract: Coronavirus disease-2019 (COVID-19) is associated with severe inflammation in mainly the lung, and kidney. Reports suggest a beneficial effect of the use of heparin/low molecular weight heparin (LMWH) on mortality in COVID-19. In part, this beneficial effect could be explained by the anticoagulant properties of heparin/LMWH. Here, we summarise potential beneficial, non-anticoagulant mechanisms underlying treatment of COVID-19 patients with heparin/LMWH, which include: (i) Inhibition of heparanase activity, responsible for endothelial leakage; (ii) Neutralisation of chemokines, and cytokines; (iii) Interference with leukocyte trafficking; (iv) Reducing viral cellular entry, and (v) Neutralisation of extracellular cytotoxic histones. Considering the multiple inflammatory and pathogenic mechanisms targeted by heparin/LMWH, it is warranted to conduct clinical studies that evaluate therapeutic doses of heparin/LMWH in COVID-19 patients. In addition, identification of specific heparin-derived sequences that are functional in targeting non-anticoagulant mechanisms may have even higher therapeutic potential for COVID-19 patients, and patients suffering from other inflammatory diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32853989/ doi: 10.1016/j.ebiom.2020.102969 id: cord-299116-1agfnjvq author: Bunders, Madeleine title: Implications of sex differences in immunity for SARS-CoV-2 pathogenesis and design of therapeutic interventions date: 2020-08-17 words: 6250.0 sentences: 333.0 pages: flesch: 45.0 cache: ./cache/cord-299116-1agfnjvq.txt txt: ./txt/cord-299116-1agfnjvq.txt summary: Emerging knowledge on the basic biological pathways that underlie differences in immune responses between women and men needs to be incorporated into research efforts on SARS-CoV-2 pathogenesis and pathology to identify targets for therapeutic interventions aimed at enhancing antiviral immune function and lung airway resilience while reducing pathogenic inflammation in COVID-19. The current Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic highlights the clinical consequences of these sex differences in antiviral immunity and tissue resilience Scully et al., 2020) , with in particular older men suffering from severe Coronavirus disease 2019 (COVID-19) and experiencing higher case mortality rates (Docherty et al., 2020; Grasselli et al., 2020; Jin et al., 2020; Salje et al., 2020) . In the following, we will address the different stages of SARS-CoV-2 pathogenesis, including viral entry and sensing, induction of antiviral immune responses and inflammation, and immune-mediated tissue-repair, in the context of critical differences in immune responses that exist between the sexes and contribute to the male-bias in development of severe COVID-19. abstract: Abstract Men present more frequently with severe manifestations of COVID-19 and are at higher risk for death. The underlying mechanisms for these differences between female and male individuals infected with SARS-CoV-2 are insufficiently understood. However, studies from other viral infections have shown that females can mount stronger immune responses against viruses than males. Emerging knowledge on the basic biological pathways that underlie differences in immune responses between women and men needs to be incorporated into research efforts on SARS-CoV-2 pathogenesis and pathology to identify targets for therapeutic interventions aimed at enhancing antiviral immune function and lung airway resilience while reducing pathogenic inflammation in COVID-19. url: https://doi.org/10.1016/j.immuni.2020.08.003 doi: 10.1016/j.immuni.2020.08.003 id: cord-325959-uqg2xkie author: Bundschuh, Christian title: Evaluation of the EDI enzyme linked immunosorbent assays for the detection of SARS-CoV-2 IgM and IgG antibodies in human plasma date: 2020-06-08 words: 2208.0 sentences: 125.0 pages: flesch: 57.0 cache: ./cache/cord-325959-uqg2xkie.txt txt: ./txt/cord-325959-uqg2xkie.txt summary: METHODS: Using EDI(TM) Novel Coronavirus COVID-19 Enzyme Linked Immunosorbent Assays (ELISAs), we measured SARS-CoV-2 IgM and IgG antibodies in 64 SARS-CoV-2 RT-PCR confirmed COVID-19 patients with serial blood samples (n=104) collected at different time points from symptom onset. low "false" positivity rates for the EDI(TM) SARS-CoV-2 IgM and IgG ELISAs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus that causes Coronavirus Disease 2019 (COVID-19), has recently emerged to cause a human pandemic. For the clinical evaluation we measured SARS-CoV-2 IgM and IgG antibodies in three different cohorts: First in a "positive cohort" of patients with SARS-CoV-2 RT-PCR confirmed 5 COVID-19 with serial blood samples at different time points from symptom onset. Furthermore, the clinical evaluation study demonstrated high "true" positivity rates in the SARS-CoV-2 RT-PCR confirmed COVID-19 patients with symptom onset after 15 days with 94.4% for IgM and 100% for IgG SARS-CoV-2 abstract: BACKGROUND: Besides SARS-CoV-2 RT-PCR testing, serological testing is emerging as additional option in COVID-19 diagnostics. Aim of this study was to evaluate novel immunoassays for detection of SARS-CoV-2 antibodies in human plasma. METHODS: Using EDI(TM) Novel Coronavirus COVID-19 Enzyme Linked Immunosorbent Assays (ELISAs), we measured SARS-CoV-2 IgM and IgG antibodies in 64 SARS-CoV-2 RT-PCR confirmed COVID-19 patients with serial blood samples (n=104) collected at different time points from symptom onset. Blood samples from 200 healthy blood donors and 256 intensive care unit (ICU) patients collected before the COVID-19 outbreak were also used. RESULTS: The positivity rates in the COVID-19 patients were 5.9% for IgM and 2.9% for IgG ≤5 days after symptom onset; Between day 5 and day 10 the positivity rates were 37.1% for IgM and 37.1% for IgG and rose to 76.4% for IgM and 82.4% for IgG after >10-15 days. After 15-22 days the “true” positivity rates were 94.4% for IgM and 100% for IgG. The “false” positivity rates were 0.5% for IgM and 1.0% for IgG in the healthy blood donors, 1.6% for IgM and 1.2% for IgG in ICU patients. CONCLUSIONS: This study shows high “true” vs. low “false” positivity rates for the EDI(TM) SARS-CoV-2 IgM and IgG ELISAs. url: https://doi.org/10.1016/j.cca.2020.05.047 doi: 10.1016/j.cca.2020.05.047 id: cord-292673-00s3wgem author: Buonaguro, Luigi title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 words: 2062.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-292673-00s3wgem.txt txt: ./txt/cord-292673-00s3wgem.txt summary: In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. Journal of Translational Medicine *Correspondence: l.buonaguro@istitutotumori.na.it 1 Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy Full list of author information is available at the end of the article SARS-CoV-2 is a positive-sense RNA virus belonging to the Orthocoronavirinae (coronavirus, CoV) family and, in particular, to the genus beta (group 2) together with the other two new human coronaviruses SARS-CoV and MERS-CoV. However, all three of them have been developed for negative-sense RNA viruses which show a significant difference in the RdRp sequence and structure compared to the positive-sense SARS-CoV-2 RNA virus. In conclusion, as for all RNA viruses, the RdRp of the newly identified positive-sense human SARS-CoV-2 RNA virus represents the most optimal target for an antiviral drug. abstract: A new human coronavirus named SARS-CoV-2 was identified in several cases of acute respiratory syndrome in Wuhan, China in December 2019. On March 11 2020, WHO declared the SARS-CoV-2 infection to be a pandemic, based on the involvement of 169 nations. Specific drugs for SARS-CoV-2 are obviously not available. Currently, drugs originally developed for other viruses or parasites are currently in clinical trials based on empiric data. In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. An accurate evaluation of RdRps from different viruses may guide the development of new drugs or the repositioning of already approved antiviral drugs as treatment of SARS-CoV-2. This can accelerate the containment of the SARS-CoV-2 pandemic and, hopefully, of future pandemics due to other emerging zoonotic RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32370758/ doi: 10.1186/s12967-020-02355-3 id: cord-327272-fspxett8 author: Buonaguro, Luigi title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 words: 1432.0 sentences: 83.0 pages: flesch: 46.0 cache: ./cache/cord-327272-fspxett8.txt txt: ./txt/cord-327272-fspxett8.txt summary: The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. The only positive-sense RNA virus, for which a very effective drug targeting specifically the RdRp is available and approved world-wide for clinical use, is hepatitis C virus (HCV). All these sequence and structural modelling evidences strongly support the concept that the SARS-CoV-2 RdRp is much more similar to the one from HCV than the one from negative-sense Influenza and Ebola RNA viruses. Therefore, repositioning of Sofosbuvir (Sovaldi®; Epclusa® by Gilead), the inhibitor of the HCV NS5B RdRp protein, as antiviral in the treatment of the SARS-CoV-2 infection has an extremely high potentiality of success, as recently postulated by others [17] , and is suggested as a potential drug for the treatment of COVID-19 in the very recent EASL-ESCMID position paper [18] . abstract: The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. Indeed, the RNA-dependent RNA-polymerases (RdRp) of the two viruses show high sequence and structural homology, supporting the likelihood of binding the Sofosbuvir molecule with similar efficiency. Such a repositioning would allow the containment of the SARS-CoV-2 pandemic and limit the progression of disease to potentially deadly COVID19. url: https://doi.org/10.1186/s13027-020-00302-x doi: 10.1186/s13027-020-00302-x id: cord-293301-7bmj8qsv author: Buonanno, Giorgio title: Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment date: 2020-04-17 words: 4387.0 sentences: 195.0 pages: flesch: 49.0 cache: ./cache/cord-293301-7bmj8qsv.txt txt: ./txt/cord-293301-7bmj8qsv.txt summary: The quanta emission rates of an asymptomatic SARS-CoV-2 infected subject, with a viral load in the mouth of 108 copies mL-1, were 10.5 quanta h-1 and 320 quanta h-1 for breathing and speaking respiratory activities, respectively, at rest. The findings in terms of quanta emission rates were then adopted in infection risk models to demonstrate its application by evaluating the number of people infected by an asymptomatic SARS-CoV-2 subject in Italian indoor microenvironments before and after the introduction of virus containment measures. In particular, airborne transmission of SARS-CoV-2 by an asymptomatic 76 subject within pharmacies, supermarkets, restaurants, banks, and post offices were simulated, and 77 the reduction in the average number of infected people from one contagious person, R0, was 78 estimated. The quanta emission rate used in the simulation of the scenario represents the average value 220 obtained from the four expiratory activities (whispered counting, voiced counting, speaking, and 221 breathing); the data are reported and discussed in the result sections. abstract: Airborne transmission is a pathway of contagion that is still not sufficiently investigated despite the evidence in the scientific literature of the role it can play in the context of an epidemic. While the medical research area dedicates efforts to find cures and remedies to counteract the effects of a virus, the engineering area is involved in providing risk assessments in indoor environments by simulating the airborne transmission of the virus during an epidemic. To this end, virus air emission data are needed. Unfortunately, this information is usually available only after the outbreak, based on specific reverse engineering cases. In this work, a novel approach to estimate the viral load emitted by a contagious subject on the basis of the viral load in the mouth, the type of respiratory activity (e.g. breathing, speaking), respiratory physiological parameters (e.g. inhalation rate), and activity level (e.g. resting, standing, light exercise) is proposed. The estimates of the proposed approach are in good agreement with values of viral loads of well-known diseases from the literature. The quanta emission rates of an asymptomatic SARS-CoV-2 infected subject, with a viral load in the mouth of 108 copies mL-1, were 10.5 quanta h-1 and 320 quanta h-1 for breathing and speaking respiratory activities, respectively, at rest. In the case of light activity, the values would increase to 33.9 quanta h-1 and 1.03×103 quanta h-1, respectively. The findings in terms of quanta emission rates were then adopted in infection risk models to demonstrate its application by evaluating the number of people infected by an asymptomatic SARS-CoV-2 subject in Italian indoor microenvironments before and after the introduction of virus containment measures. The results obtained from the simulations clearly highlight that a key role is played by proper ventilation in containment of the virus in indoor environments. url: https://doi.org/10.1101/2020.04.12.20062828 doi: 10.1101/2020.04.12.20062828 id: cord-281248-z2gisufl author: Buonsenso, Danilo title: A Pediatric Strategy for the Next Phase of the SARS–CoV-2 Pandemic date: 2020-10-09 words: 2972.0 sentences: 124.0 pages: flesch: 42.0 cache: ./cache/cord-281248-z2gisufl.txt txt: ./txt/cord-281248-z2gisufl.txt summary: Considering that most of these conditions present several overlaps with SARS-CoV-2 (Figure 1 ), this will pose challenges to pediatricians and health system to appropriately manage all these conditions and properly allocate resources, because COVID-19 will need to be considered until exclusion, in order to reduce nosocomial transmission and new outbreaks. In light of new evidences and the need to reduce as much as possible the diffusion of infectious diseases among children during the next season (because this would lead to include all cases in the differential diagnosis with COVID-19 because of similar symptoms), a reorganization of school environments should be a priority for policy makers. Therefore, even though the direct clinical impact of the SARS-COV-2 virus on children has been limited with a very low mortality rate, and the COVID-19-related pediatric inflammatory multisystem syndrome remains a relatively rare consequence of the disease, pediatricians will still need to include SARS-CoV-2 in the differential diagnosis. abstract: Although the first wave of the SARS–CoV-2 pandemic relatively spared children, the next winter season will put a strain on health systems including pediatric services. Clinical staff managing children will need to deal not only with suspected cases of COVID-19, but also with the classic infectious agents that involve children during cold seasons. It will be necessary for physicians, institutions, policy makers, and families to prepare themselves for difficulties of this phase of the pandemic. Otherwise, the same problems experienced during the first wave of SARS–CoV-2, including shortages of human resources, personal protective equipment, and uncertainty, will be exacerbated by significant issues in hospital capacity. Here we highlight the potential role of improved vaccination services, school reorganization, home–outpatient–inpatients flows and telemedicine services in order to face the coming winter season. url: https://www.ncbi.nlm.nih.gov/pubmed/33163467/ doi: 10.3389/fped.2020.582798 id: cord-289003-vov6o1jx author: Burdet, C. title: Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals date: 2018-02-28 words: 8327.0 sentences: 327.0 pages: flesch: 46.0 cache: ./cache/cord-289003-vov6o1jx.txt txt: ./txt/cord-289003-vov6o1jx.txt summary: Abstract We present here the proceedings of the 5th seminar on emerging infectious diseases, held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows: encourage research on the prediction, screening and early detection of new risks of infection; develop research and surveillance concerning transmission of pathogens between animals and humans, with their reinforcement in particular in intertropical areas ("hot-spots") via public support; pursue aid development and support in these areas of prevention and training for local health personnel, and foster risk awareness in the population; ensure adapted patient care in order to promote adherence to treatment and to epidemic propagation reduction measures; develop greater awareness and better education among politicians and healthcare providers, in order to ensure more adapted response to new types of crises; modify the logic of governance, drawing from all available modes of communication and incorporating new information-sharing tools; develop economic research on the fight against emerging infectious diseases, taking into account specific driving factors in order to create a balance between preventive and curative approaches. abstract: Abstract We present here the proceedings of the 5th seminar on emerging infectious diseases, held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows: encourage research on the prediction, screening and early detection of new risks of infection; develop research and surveillance concerning transmission of pathogens between animals and humans, with their reinforcement in particular in intertropical areas (“hot-spots”) via public support; pursue aid development and support in these areas of prevention and training for local health personnel, and foster risk awareness in the population; ensure adapted patient care in order to promote adherence to treatment and to epidemic propagation reduction measures; develop greater awareness and better education among politicians and healthcare providers, in order to ensure more adapted response to new types of crises; modify the logic of governance, drawing from all available modes of communication and incorporating new information-sharing tools; develop economic research on the fight against emerging infectious diseases, taking into account specific driving factors in order to create a balance between preventive and curative approaches. url: https://doi.org/10.1016/j.respe.2017.08.001 doi: 10.1016/j.respe.2017.08.001 id: cord-297884-a6yrtuwf author: Burke, R. M. title: Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States date: 2020-05-03 words: 7343.0 sentences: 341.0 pages: flesch: 49.0 cache: ./cache/cord-297884-a6yrtuwf.txt txt: ./txt/cord-297884-a6yrtuwf.txt summary: To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with ≥ 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members. Among 49 HCP who provided care to or came into contact with the infectious fluids of travelassociated case patients and who had at least one set of respiratory samples collected and tested for SARS-CoV-2, the secondary attack rate was 0% (95% CI: 0 -7%). abstract: Background Coronavirus disease 2019 (COVID-19), the respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. As part of initial response activities in the United States, enhanced contact investigations were conducted to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Methods Close contacts of nine early travel-related cases in the United States were identified. Close contacts meeting criteria for active monitoring were followed, and selected individuals were targeted for collection of additional exposure details and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (RT-PCR) at the Centers for Disease Control and Prevention. Results There were 404 close contacts who underwent active monitoring in the response jurisdictions; 338 had at least basic exposure data, of whom 159 had at least 1 set of respiratory samples collected and tested. Across all known close contacts under monitoring, two additional cases were identified; both secondary cases were in spouses of travel-associated case patients. The secondary attack rate among household members, all of whom had at least 1 respiratory sample tested, was 13% (95% CI: 4 - 38%). Conclusions The enhanced contact tracing investigations undertaken around nine early travel-related cases of COVID-19 in the United States identified two cases of secondary transmission, both spouses. Rapid detection and isolation of the travel-associated case patients, enabled by public awareness of COVID-19 among travelers from China, may have mitigated transmission risk among close contacts of these cases. url: https://doi.org/10.1101/2020.04.27.20081901 doi: 10.1101/2020.04.27.20081901 id: cord-324405-6uanhe2p author: Burke, Rachel M. title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 words: 6616.0 sentences: 242.0 pages: flesch: 41.0 cache: ./cache/cord-324405-6uanhe2p.txt txt: ./txt/cord-324405-6uanhe2p.txt summary: To interrupt transmission and facilitate early identification of secondary cases (i.e., transmissions of SARS-CoV-2 from the original travel-related case patient to a close contact), public health authorities at the state, county, and local levels, in consultation with subject-matter experts from the U.S. Centers for Disease Control and Prevention (CDC), mobilized rapidly to place the patients under appropriate isolation and identify contacts exposed to these patients. To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with � 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members and some healthcare personnel. abstract: Coronavirus disease 2019 (COVID-19), the respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. In response to the first cases identified in the United States, close contacts of confirmed COVID-19 cases were investigated to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Close contacts of nine early travel-related cases in the United States were identified and monitored daily for development of symptoms (active monitoring). Selected close contacts (including those with exposures categorized as higher risk) were targeted for collection of additional exposure information and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction at the Centers for Disease Control and Prevention. Four hundred four close contacts were actively monitored in the jurisdictions that managed the travel-related cases. Three hundred thirty-eight of the 404 close contacts provided at least basic exposure information, of whom 159 close contacts had ≥1 set of respiratory samples collected and tested. Across all actively monitored close contacts, two additional symptomatic COVID-19 cases (i.e., secondary cases) were identified; both secondary cases were in spouses of travel-associated case patients. When considering only household members, all of whom had ≥1 respiratory sample tested for SARS-CoV-2, the secondary attack rate (i.e., the number of secondary cases as a proportion of total close contacts) was 13% (95% CI: 4–38%). The results from these contact tracing investigations suggest that household members, especially significant others, of COVID-19 cases are at highest risk of becoming infected. The importance of personal protective equipment for healthcare workers is also underlined. Isolation of persons with COVID-19, in combination with quarantine of exposed close contacts and practice of everyday preventive behaviors, is important to mitigate spread of COVID-19. url: https://doi.org/10.1371/journal.pone.0238342 doi: 10.1371/journal.pone.0238342 id: cord-260565-cdthfl5f author: Burkle, Frederick M. title: Declining Public Health Protections within Autocratic Regimes: Impact on Global Public Health Security, Infectious Disease Outbreaks, Epidemics, and Pandemics date: 2020-04-02 words: 8816.0 sentences: 516.0 pages: flesch: 53.0 cache: ./cache/cord-260565-cdthfl5f.txt txt: ./txt/cord-260565-cdthfl5f.txt summary: While China is seeking to adhere as much as possible to the underlying norms and rules of global institutions," reemphasizing that China after SARS "perhaps [needs] to reframe health as a global public good that is available to each and every individual of the world, rather than merely as an issue of concern to nation-states." 37 In a rare openness, rarely seen before, the normally secretive Xi admitted at a meeting to coordinate the fight against the virus that China must learn from "obvious shortcomings exposed during its response." Yet given the second-guessing that always surfaces in these tragedies, "it cannot be denied that the Chinese government tried to control the narrative, another sign of irrational hubris, and as a result, the contagion was allowed to spread, contributing to equally irrational fear." A China researcher for Human Rights Watch (New York USA) noted: "authorities are as equally, if not more, concerned with silencing criticism as with containing the spread of the coronavirus. abstract: Public health emergencies of international concern, in the form of infectious disease outbreaks, epidemics, and pandemics, represent an increasing risk to the worldʼs population. Management requires coordinated responses, across many disciplines and nations, and the capacity to muster proper national and global public health education, infrastructure, and prevention measures. Unfortunately, increasing numbers of nations are ruled by autocratic regimes which have characteristically failed to adopt investments in public health infrastructure, education, and prevention measures to keep pace with population growth and density. Autocratic leaders have a direct impact on health security, a direct negative impact on health, and create adverse political and economic conditions that only complicate the crisis further. This is most evident in autocratic regimes where health protections have been seriously and purposely curtailed. All autocratic regimes define public health along economic and political imperatives that are similar across borders and cultures. Autocratic regimes are seriously handicapped by sociopathic narcissistic leaders who are incapable of understanding the health consequences of infectious diseases or the impact on their population. A cross section of autocratic nations currently experiencing the impact of COVID-19 (coronavirus disease 2019) are reviewed to demonstrate the manner where self-serving regimes fail to manage health crises and place the rest of the world at increasing risk. It is time to re-address the pre-SARS (severe acute respiratory syndrome) global agendas calling for stronger strategic capacity, legal authority, support, and institutional status under World Health Organization (WHO) leadership granted by an International Health Regulations Treaty. Treaties remain the most successful means the world has in preventing, preparing for, and controlling epidemics in an increasingly globalized world. “Honesty is worth a lot more than hope…” The Economist, February 17, 2020. url: https://doi.org/10.1017/s1049023x20000424 doi: 10.1017/s1049023x20000424 id: cord-281619-fhyamruq author: Burlacu, Alexandru title: Unpuzzling COVID-19 Prothrombotic State: Are Preexisting Thrombophilic Risk Profiles Responsible for Heterogenous Thrombotic Events? date: 2020-08-25 words: 2016.0 sentences: 112.0 pages: flesch: 32.0 cache: ./cache/cord-281619-fhyamruq.txt txt: ./txt/cord-281619-fhyamruq.txt summary: 1 The similarity between these 2 conditions is sustained by autopsy studies findings, documented immune pathogenesis, and microcirculation dysfunctions, the ability of SARS-CoV-2 to disseminate the infection in other organs and by the fact that many critically ill COVID-19 patients developed clinical symptoms of shock following a process called "viral sepsis." 2 A recent paper dealing with SARS-CoV-2 and "viral sepsis" raised alarm signals that despite the huge percentage of 71,4% of non-survivors of COVID-19 who matched the grade of overt disseminated intravascular coagulation, the concrete mechanisms of vascular thrombosis are not yet known. The hypercoagulation state consequent to SARS-COV-2 infection seems to manifest not only as pulmonary embolism, but also as other thrombotic events such as deep vein thrombosis, myocardial infarction, or ischemic stroke, 31 suggesting that the most plausible explanation has to be a pattern concerning either the patients or the virus. abstract: nan url: https://doi.org/10.1177/1076029620952884 doi: 10.1177/1076029620952884 id: cord-328680-zdwep5b2 author: Burr, Tyler title: NMDA-receptor encephalitis associated with COVID-19 infection in a toddler date: 2020-10-09 words: 897.0 sentences: 63.0 pages: flesch: 40.0 cache: ./cache/cord-328680-zdwep5b2.txt txt: ./txt/cord-328680-zdwep5b2.txt summary: Anti-NMDA receptor (NMDAR) encephalitis is characterized by mood and behavior changes, seizures, abnormal movements, autonomic instability, and encephalopathy. More recently, cases of anti-NMDAR encephalitis following viral infections have been reported, including herpes simplex virus (HSV), Japanese encephalitis virus (JEV), and now the 2019 novel coronavirus (SARS-CoV-2) 2-5 . We present the first pediatric case of SARS-CoV-2-associated anti-NMDAR Encephalitis. A post-infectious inflammatory condition following acute SARS-CoV-2, termed multisystem inflammatory syndrome in children (MIS-C), has been described. There have been two cases of anti-NMDAR encephalitis associated with SARS-CoV-2 in adults reported 5, 9 . At the time of publication, the authors are unaware of other cases of anti-NMDAR encephalitis with recent SARS-CoV-2 infection in pediatric populations. Herpes simplex virus-induced anti-N-methyl-d-aspartate receptor encephalitis: a systematic literature review with analysis of 43 cases Anti-N-methyl-D-aspartate receptor encephalitis associated with reactivated Epstein-Barr virus infection in pediatric patients: Three case reports Anti-NMDA receptor encephalitis in a psychiatric Covid-19 patient: A case report abstract: nan url: https://api.elsevier.com/content/article/pii/S0887899420303295 doi: 10.1016/j.pediatrneurol.2020.10.002 id: cord-347499-7q47jh14 author: Burrel, Sonia title: Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date: 2020-10-25 words: 1353.0 sentences: 75.0 pages: flesch: 51.0 cache: ./cache/cord-347499-7q47jh14.txt txt: ./txt/cord-347499-7q47jh14.txt summary: METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. In line with previous studies, different types of other respiratory viruses were detected together with SARS-CoV-2 among co-infected patients, including non-SARS-CoV-2 coronavirus, influenzavirus, adenovirus, rhinovirus/enterovirus, and parainfluenzavirus (Kim et al., 2020; Leuzinger et al., 2020; Lin et al., 2020a; Wee et al., 2020) . We evidenced the higher efficiency of LRT than URT samples for COVID-19 diagnosis, with a significantly higher rate of detection of SARS-CoV-2 and a 1 log-higher SARS-CoV-2 load for the majority of infected patients. In conclusion, the detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection, and LRT samples increases the accuracy of diagnosis of viral respiratory infections, including COVID-19. abstract: OBJECTIVES: We performed a study during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. A second objective consisted in the comparison of the diagnostic performances of URT and LRT samples for SARS-CoV-2 infection and to compare diagnostic performances of upper and lower respiratory tract (URT and LRT) samples for SARS-CoV-2 infection. METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. RESULTS: A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age of 50 [1-103] years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% versus 13.4%; P < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. CONCLUSION: The detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increases the accuracy of diagnosis of COVID-19. url: https://api.elsevier.com/content/article/pii/S120197122032244X doi: 10.1016/j.ijid.2020.10.040 id: cord-305770-xygg4lxu author: Busetto, Gian Maria title: SARS-CoV-2 Infection and High-Risk Non-Muscle-Invasive Bladder Cancer: Are There Any Common Features? date: 2020-06-09 words: 6963.0 sentences: 343.0 pages: flesch: 40.0 cache: ./cache/cord-305770-xygg4lxu.txt txt: ./txt/cord-305770-xygg4lxu.txt summary: Most severe cases of COVID-19 and high-risk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). Most severe cases of COVID-19 and highrisk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). When compared with COVID-19 patients without ARDS, patients with ARDS are generally older and have a higher proportion of comorbidities, and there are more observations of neutrophilia associated with lymphocytopenia, neutrophil-to-lymphocyte ratio (NLR) increase, increase in several inflammation indices (including interleukins, IL-2 and IL-6, tumor necrosis factor α, C-reactive protein and many other cytokines), elevated coagulation function and alteration of other organ dysfunction indices (liver, kidney, etc.) [4] . The following terms were the most commonly used: SARS-CoV-2, COVID-19, bladder cancer, risk factors, diabetes, obesity, aging, inflammation, cytokine, interleukin (IL), IL-6, smoking. abstract: BACKGROUND: The new severe acute respiratory syndrome virus (SARS-CoV-2) outbreak is a huge health, social and economic issue and has been declared a pandemic by the World Health Organization. Bladder cancer, on the contrary, is a well-known disease burdened by a high rate of affected patients and risk of recurrence, progression and death. SUMMARY: The coronavirus disease (COVID-19 or 2019-nCoV) often involves mild clinical symptoms but in some cases, it can lead to pneumonia with acute respiratory distress syndrome and multiorgan dysfunction. Factors associated with developing a more severe disease are increased age, obesity, smoking and chronic underlying comorbidities (including diabetes mellitus). High-risk non-muscle-invasive bladder cancer (NMIBC) progression and worse prognosis are also characterized by a higher incidence in patients with risk factors similar to COVID-19. Immune system response and inflammation have been found as a common hallmark of both diseases. Most severe cases of COVID-19 and high-risk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). Alterations in neutrophils, lymphocytes and platelets accompany the systemic inflammatory response to cancer and infections. Neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio for example have been recognized as factors related to poor prognosis for many solid tumors, including bladder cancer, and their role has been found important even for the prognosis of SARS-CoV-2 infection. KEY MESSAGES: All these mechanisms should be further analyzed in order to find new therapeutic agents and new strategies to block infection and cancer progression. Further than commonly used therapies, controlling cytokine production and inflammatory response is a promising field. url: https://www.ncbi.nlm.nih.gov/pubmed/32516772/ doi: 10.1159/000509065 id: cord-297423-iefq0fh0 author: Bushman, Dena title: Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020 date: 2020-07-17 words: 2739.0 sentences: 152.0 pages: flesch: 50.0 cache: ./cache/cord-297423-iefq0fh0.txt txt: ./txt/cord-297423-iefq0fh0.txt summary: At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS) § who had negative test results for influenza and, in some instances, other respiratory pathogens. abstract: To limit introduction of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), the United States restricted travel from China on February 2, 2020, and from Europe on March 13. To determine whether local transmission of SARS-CoV-2 could be detected, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) conducted deidentified sentinel surveillance at six NYC hospital emergency departments (EDs) during March 1-20. On March 8, while testing availability for SARS-CoV-2 was still limited, DOHMH announced sustained community transmission of SARS-CoV-2 (1). At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Using genetic sequencing, CDC determined that the sequences of most SARS-CoV-2-positive specimens resembled those circulating in Europe, suggesting probable introductions of SARS-CoV-2 from Europe, from other U.S. locations, and local introductions from within New York. These findings demonstrate that partnering with health care facilities and developing the systems needed for rapid implementation of sentinel surveillance, coupled with capacity for genetic sequencing before an outbreak, can help inform timely containment and mitigation strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32678072/ doi: 10.15585/mmwr.mm6928a5 id: cord-335172-5ig907on author: Busse, Laurence W. title: COVID-19 and the RAAS—a potential role for angiotensin II? date: 2020-04-07 words: 1668.0 sentences: 106.0 pages: flesch: 52.0 cache: ./cache/cord-335172-5ig907on.txt txt: ./txt/cord-335172-5ig907on.txt summary: Likewise, patients on angiotensin-converting enzyme (ACE) inhibitors or angiotensin receptor blockers (ARB) could be at a greater risk due to the mechanism by which SARS-CoV-2 enters the cell. First, because it normally binds to ACE2 during its degradation and hydrolysis into angiotensin-(1-7) [11] , it may compete with the SARS-CoV-2 for the ACE2 receptor (Fig. 1) . Second, the binding of AngII to the AT1 receptor has been shown to cause internalization and downregulation of ACE2 through an ERK1/2 and p38 MAP kinase pathway in both in vitro animal and in vivo human models [12, 13] . However, to date, the link between ACE inhibitors and ARBs and severity of illness of SARS-CoV-2 infection is purely speculative. Ang-2, angiotensin II; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; ACE1, angiotensinconverting-enzyme 1; ACE2, angiotensin-converting-enzyme 2; H 2 O, water; Na + , sodium Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus abstract: nan url: https://doi.org/10.1186/s13054-020-02862-1 doi: 10.1186/s13054-020-02862-1 id: cord-316658-zwxtbena author: Butler, S. E. title: Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals date: 2020-08-06 words: 3487.0 sentences: 225.0 pages: flesch: 45.0 cache: ./cache/cord-316658-zwxtbena.txt txt: ./txt/cord-316658-zwxtbena.txt summary: SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. In contrast to 168 observations in serum, nasal samples from subjects with severe disease showed little to no viral 169 neutralization, whereas subjects with elevated mucosal neutralization activity tended to have 170 experienced mild or moderate symptoms (Fig. 5b) . In contrast, the IgA-associated feature defined by nasal RBD-specific Abs binding to FcaR 226 ( Fig. 7C ) and its correlated function neutralization (Fig. 7D) were lowest in subjects with either mild or 227 severe disease, and elevated among those who recovered from moderate illness. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding 580 domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein 581 induces strong mucosal immune responses and provides long-term protection against 582 SARS-CoV infection abstract: Understanding humoral immune responses to SARS-CoV-2 infection will play a critical role in the development of vaccines and antibody-based interventions. We report systemic and mucosal antibody responses in convalescent individuals who experienced varying disease severity. Robust antibody responses to diverse SARS-CoV-2 antigens and evidence of elevated responses to endemic CoV were observed among convalescent donors. SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. Assessment of antibody-mediated effector functions revealed an inverse correlation between systemic and mucosal neutralization activity and site-dependent differences in the isotype of neutralizing antibodies. Serum neutralization correlated with systemic anti-SARS-CoV-2 IgG and IgM response magnitude, while mucosal neutralization was associated with nasal SARS-CoV-2-specific IgA. These findings begin to map how diverse Ab characteristics relate to Ab functions and outcomes of infection, informing public health assessment strategies and vaccine development efforts. url: https://www.ncbi.nlm.nih.gov/pubmed/32793926/ doi: 10.1101/2020.08.05.20168971 id: cord-348384-8cvt1fo6 author: Butsashvili, M. title: Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population date: 2020-05-19 words: 1988.0 sentences: 120.0 pages: flesch: 54.0 cache: ./cache/cord-348384-8cvt1fo6.txt txt: ./txt/cord-348384-8cvt1fo6.txt summary: This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus among Georgian population, including health care workers (HCWs). 20% of HCWs as well as other study subjects believe that SARS-COV-2 vaccine and medications do exist but are simply not available in Georgia. This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus and perceptions of preventive measures among the Georgian population, including health care workers (HCWs). We collected information on demographic data (age, gender, marital status, education, employment status), knowledge of symptoms and transmission modes of coronavirus, perceived differences between coronavirus and influenza, availability of antiviral medication and vaccination. In response to the question "Are you afraid of getting infected with SARS-COV-2?" almost half of study participants (46.3%) said "no." The majority of survey respondents correctly identified the transmission route and symptoms of the new coronavirus (96.9% and 98.0%, respectively). abstract: Introduction Georgia confirmed its first case of SARS-COV-2 infection on February 26, 2020 and by March 31, a total of 110 cases have been reported. Limited understanding about epidemics can lead to panic and disrupt public health efforts to contain transmission. It is important to understand perceptions of the population regarding the disease. This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus among Georgian population, including health care workers (HCWs). Materials and methods The online survey was conducted using a Facebook advertisement. The target was the whole country and the language used was Georgian. We collected information on demographic data, knowledge of the disease, including perceived differences between coronavirus and influenza. We also included questions to capture the populations perceptions about government preparedness to combat the new coronavirus. Results The survey was open for three days (March 2-4, 2020). 5228 participants completed the survey. Of these, 40.3% were 25-45 years old, 58.2% were female, 20.7% had university degree and 10.3% were HCWs. For 25.8% of respondents, COVID-19 and influenza are the same diseases; 10.9% did not know if they are different. The majority correctly identified the transmission route and symptoms (96.9% and 98.0%, respectively). 19.1% think that Georgia is ready for COVID 19 epidemic, while according to 55% the county is not ready, but HCWs are trying hard to respond properly. For 18% response is inadequate. There was no difference in knowledge between HCWs, non-HCWs and unemployed. 20% of HCWs as well as other study subjects believe that SARS-COV-2 vaccine and medications do exist but are simply not available in Georgia. Conclusion Given that information regarding coronavirus is changing very rapidly, the need to reach people with time-sensitive educational messages as well as prevention strategies is vital. url: http://medrxiv.org/cgi/content/short/2020.05.14.20101642v1?rss=1 doi: 10.1101/2020.05.14.20101642 id: cord-296043-jc74soom author: Butterfield, T. R. title: Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica date: 2020-09-29 words: 1650.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-296043-jc74soom.txt txt: ./txt/cord-296043-jc74soom.txt summary: Serum samples collected [≥]14 days after onset of symptoms, or [≥]14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. For all assays examined, SARS-CoV-2 real-36 time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive 37 were significantly different for samples testing antibody positive versus negative. CoV-2 antibody assays: Roche Elecsys ® Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 53 preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. When moderate, severe and 109 critical disease was grouped, for each assay there was a significant association between this 110 group and testing antibody positive: Elecsys ® Anti-SARS-CoV-2 (χ 2 =19.03, p=0.001), Architect 111 SARS-CoV-2 IgG (χ 2 =15.72, p=0.003), Euroimmun SARS-CoV-2 IgA (χ 2 =21.11, p=0.007), 112 All rights reserved. abstract: The performance of the Roche Elecsys(R) Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 IgG, Euroimmun SARS-CoV-2 IgA, Euroimmun SARS-CoV-2 IgG ELISA, and Trillium IgG/IgM rapid assays was evaluated in Jamaica, the largest country of the English-speaking Caribbean. Diagnostic sensitivities of the assays were assessed by testing serum samples from SARS-CoV-2 PCR-confirmed persons. Serum samples collected [≥]14 days after onset of symptoms, or [≥]14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. Grouping moderate to critical disease showed a significant association with a SARS-CoV-2 antibody positive result for all assays. Diagnostic specificity, assessed by testing serum samples collected during 2018-2019 from healthy persons and from persons with antibodies to a wide range of viral infections, ranged from 96.7-100.0%. For all assays examined, SARS-CoV-2 real-time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive were significantly different for samples testing antibody positive versus negative. These data from a predominantly African descent Caribbean population shows comparable diagnostic sensitivities and specificities for all testing platforms assessed and limited utility of these tests for persons with asymptomatic and mild infections. url: https://doi.org/10.1101/2020.09.27.20202655 doi: 10.1101/2020.09.27.20202655 id: cord-313275-znrvkmee author: Bwire, G. M. title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM date: 2020-06-12 words: 2965.0 sentences: 230.0 pages: flesch: 56.0 cache: ./cache/cord-313275-znrvkmee.txt txt: ./txt/cord-313275-znrvkmee.txt summary: title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM The research included studies on IgG/ IgM against SARS-CoV-2 among infants born to mother with COVID-19 published in English from December 1, 2019 onwards. On the other hand, natural passive immunity and detection of specific IgG and IgM antibodies to SARS-CoV-2 in infants born to COVID 19 confirmed mothers have been indicated in some studies where the newborns tested negative for the virus (8) . In this regard, a systematic review was conducted to determine the magnitude of IgG/ IgM in infants born to mothers with COVID-19 but tested negative for SARS-CoV-2. The median antibody levels detected in COVID-19 exposed newborns who tested negative for the virus after delivery but were born to mothers with COVID-19 were 75.49AU/mL (range: 7.25AU/mL-140.32AU/mL ) and for 3.79AU/mL (range: 0.16AU/mL-45.83AU/mL) (P = 0.0041) for anti-SARS-CoV-2 IgG and IgM, respectively. abstract: Background Currently, there is no doubt on human-to-human transmission of Coronavirus Disease 2019 (COVID-19). Now, the debates remain on whether, vertical transmission of Severe Respiratory Syndrome Virus 2 (SARS-CoV-2) and antibodies against the virus do exist. We therefore, conducted a systematic review to determine the immunoglobulin G and M (IgG/IgM) levels among infants born to mothers with COVID-19. Methods The systematic search was done using PubMed/MEDLINE and Google Scholar database. The research included studies on IgG/ IgM against SARS-CoV-2 among infants born to mother with COVID-19 published in English from December 1, 2019 onwards. Data were extracted by two independent authors in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) guidelines. We synthesized a narrative from eligible studies and performed two tailed non-parametric Mann-Whitney test to determine and compare the median IgG/IgM levels. Results In total, 486 abstracts were screened and 63 full-text articles were assessed. Of 63 articles, 6 met the inclusion criteria for qualitative analysis. Two articles were included in quantitative analysis of anti-SARS-CoV-2 IgG/ IgM levels. The median antibody levels was 75.49AU/mL (range: 7.25AU/mL- 140.32AU/mL ) and for 3.79AU/mL (range: 0.16AU/mL-45.83AU/mL) (P = 0.0041) for anti-SARS-CoV-2 IgG and IgM, respectively. Conclusion There were high levels of IgG but low IgM against SARS-CoV-2 (using <10 AU/mL as a reference range) among COVID-19 virus exposed but negative newborns. This review suggest a possible natural passive immunity (IgG/ IgM) against COVID-19 virus. url: http://medrxiv.org/cgi/content/short/2020.06.09.20127118v1?rss=1 doi: 10.1101/2020.06.09.20127118 id: cord-343128-sh77c0af author: Bwire, G. M. title: Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis date: 2020-06-12 words: 3327.0 sentences: 221.0 pages: flesch: 51.0 cache: ./cache/cord-343128-sh77c0af.txt txt: ./txt/cord-343128-sh77c0af.txt summary: title: Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted. Recent study by Wang et al (6) using 1070 clinical specimens such as bronchoalveolar lavage fluid (BLF), fibrobronchoscope brush biopsy (FBB), sputum, nasal and pharyngeal swabs, urine, feces and blood collected from 205 patients revealed a dynamic profile with high detection rate of virus from lower respiratory tract (LRT) specimens, i.e., BLF and zero detection from urogenital tract specimen, i.e., urine. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2 from different types clinical specimens using a standard diagnostic test (qRT-PCR). A systematic review protocol was developed based on the question "What is the positivity rate for SARS-CoV-2 using qRT-PCR in different types of clinical specimens". abstract: Background: Testing is one of the commendable preventive measures against coronavirus disease (COVID_19), and needs to be done using both most appropriate specimen and an accurate diagnostic test like real time reverse transcription polymerase chain reaction (qRT_PCR). However, the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS_CoV_2) RNA from different clinical specimens after onset of symptoms is not yet well established. For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted. Methods: The systematic search was done using PubMed/MEDLINE, Science direct, Google Scholar, among others. The search included studies on laboratory diagnosis of SARS_CoV_2 from different clinical specimens using PCR. Data extraction was done using Microsoft Excel spread sheet 2010 and reported according to PRISMA_P guidelines. Using Open Meta Analyst software, DerSimonian_Laird random effects analysis was performed to determine a summary estimate (positive rate [PR]/proportions) and their 95% confidence interval (95%CI). Results: A total of 8136 different clinical specimens were analyzed to detect SARS_CoV_2, with majority being nasopharyngeal swabs (69.6%). Lower respiratory tract (LRT) specimens had a PR of 71.3% (95%CI:60.3%-82.3%) while no virus was detected from the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95%CI:79.9-103.7%), followed by rectal swabs, 87.8 % (95%CI:78.6%-96.9%) then sputum, 68.1% (95%CI:56.9%-79.4%). Low PR was observed in oropharyngeal swabs, 7.6% (95%CI:5.7%-9.6%) and blood samples, 1.0% (95%CI: -0.1%-2.1%), whilst no SARS-CoV-2 was detected in urine samples. Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95%CI:31.2%-59.7%). Conclusion: In this study, SARS-CoV-2 was highly detected in lower respiratory tract specimens while there was no detected virus in urinogenital specimens. Regarding the type of clinical specimens, bronchoalveolar lavage fluid had the highest positive rate followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had a moderate detection rate. Low positive rate was recorded in oropharyngeal swab and blood sample while no virus was found in urine samples. More importantly, the virus was detected in feces, suggesting SARS-CoV-2 transmission by the fecal route. url: https://doi.org/10.1101/2020.06.11.20128389 doi: 10.1101/2020.06.11.20128389 id: cord-282817-vtzpf2wr author: Byrne, Hannah title: A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications date: 2013-10-02 words: 8419.0 sentences: 417.0 pages: flesch: 34.0 cache: ./cache/cord-282817-vtzpf2wr.txt txt: ./txt/cord-282817-vtzpf2wr.txt summary: Despite significant positive clinical results, especially in the case of hematological malignancies, adverse clinical outcomes and animal studies have highlighted underlying limitations of mAbs. Accordingly, many strategies have been developed in order to improve the specificity and control the functions of antibodies. The BiTE format potentially overcomes several limiting factors relating to the biological activity of tumor-directed bsAbs. BiTEs combine the minimal binding domains (Fv fragments) of two different mAbs fused together by a short flexible linker that allows free rotation of the two arms, and thus facilitates optimal antibody:antigen interaction [28] . bsAbs are attractive in such assays because they simplify the detection steps and are currently used for the development of simple, rapid, and highly sensitive immunoassays for the detection of bacterial and viral infectious diseases and in cancer diagnostics. CD40-targeted adenoviral gene transfer to dendritic cells through the use of a novel bispecific single-chain Fv antibody enhances cytotoxic T cell activation abstract: Artificial manipulation of antibody genes has facilitated the production of several unique recombinant antibody formats, which have highly important therapeutic and biotechnological applications. Although bispecific antibodies (bsAbs) are not new, they are coming to the forefront as our knowledge of the potential efficacy of antibody-based therapeutics expands. The next generation of bsAbs is developing due to significant improvements in recombinant antibody technologies. This review focuses on recent advances with a particular focus on improvements in format and design that are contributing to the resurgence of bsAbs, and in particular, on innovative structures applicable to next generation point-of-care (POC) devices with applicability to low resource environments. url: https://www.ncbi.nlm.nih.gov/pubmed/24094861/ doi: 10.1016/j.tibtech.2013.08.007 id: cord-318789-ylxh8vi2 author: Byrne, R. L. title: Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis. date: 2020-07-11 words: 1875.0 sentences: 133.0 pages: flesch: 62.0 cache: ./cache/cord-318789-ylxh8vi2.txt txt: ./txt/cord-318789-ylxh8vi2.txt summary: Samples were classified as RT-qPCR positive if both the internal extraction and the SARS-CoV-2 probes were detected at <40Ct. Virus copies/ml were quantified using the manufacturer''s positive control (1.67 Here we report for the first time the analytical sensitivity of saliva for the detection of SARS-CoV-2 compared to NT swab samples. In spiked saliva samples, SARS-CoV-2 can be detected with greater sensitivity in saliva compared to NT swabs by 100fold copies/ml, presumably due to the dilution factor of the amies transport medium. All saliva-positive, NT swab-negative samples in D2 (n=2) and D28 (n=1) reported low viral titre (<10 1 copies/ml) and are likely due to similar limitations outlined in the analytical sensitivity, a greater dilution factor of amies. This is in agreement with Wyllie et al., (2020) who reported that saliva had a greater sensitivity and was more likely to be constantly positive throughout the course of infection on a subset of COVID-19 hospitalised participants (n=29). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 participants than nasopharyngeal swabs abstract: RT-qPCR utilising upper respiratory swabs are the diagnostic gold standard for SARS-CoV-2 despite reported low sensitivity and limited scale up due to global shortages. Saliva is a non-invasive, equipment independent alternative to swabs. We collected 145 paired saliva and nasal/throat (NT) swabs at diagnosis (day 0) and repeated on day 2 and day 7 dependent on inpatient care and day 28 for study follow up. Laboratory cultured virus was used to determine the analytical sensitivity of spiked saliva and swabs containing amies preservation media. Self-collected saliva samples were found to be consistent, and in some cases superior when compared to healthcare worker collected NT swabs from COVID-19 suspected participants. We report for the first time the analytical limit of detection of 10-2 and 100 pfu/ml for saliva and swabs respectively. Saliva is a easily self-collected, highly sensitive specimen for the detection of SARS-CoV-2. url: http://medrxiv.org/cgi/content/short/2020.07.09.20149534v1?rss=1 doi: 10.1101/2020.07.09.20149534 id: cord-024649-y7nqz6vk author: Bösel, J. title: Neurologische Auswirkungen von COVID-19 date: 2020-05-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212508/ doi: 10.1007/s42451-020-00191-9 id: cord-258576-ywbyflas author: Bösmüller, Hans title: The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation date: 2020-06-30 words: 3628.0 sentences: 207.0 pages: flesch: 44.0 cache: ./cache/cord-258576-ywbyflas.txt txt: ./txt/cord-258576-ywbyflas.txt summary: We present the pulmonary findings in four cases of fatal COVID-19 with a spectrum of lung pathology reflecting disease course and duration, invasive therapies, and laboratory features. Based on conventional criteria, respiratory insufficiency therefore might be considered unlikely direct cause of death, but this case and recently published autopsy data indicate that pulmonary microvascular changes are an important and distinguishing feature of COVID-19 and may contribute to hypoxemia and acute cardiac insufficiency. Irrespective of the severity of pulmonary changes, however, all 4 patients showed SARS-CoV-2 RNA in lung tissues but failed to show detectable levels of viral RNA in other organs studied. The laboratory findings observed in patients 2 and 3 reflect common risk factors of fatal outcome, namely, lymphopenia; increased D-dimers; evidence of massive systemic inflammation including high levels of CRP, procalcitonin, and IL-6 during acute disease; and in the final stages massive ALT/AST elevation [1, 3, 4, 7, 11, 20] . abstract: The pandemia of coronavirus disease 2019 (COVID-19) has caused more than 355,000 confirmed deaths worldwide. However, publications on postmortem findings are scarce. We present the pulmonary findings in four cases of fatal COVID-19 with a spectrum of lung pathology reflecting disease course and duration, invasive therapies, and laboratory features. Early disease is characterized by neutrophilic, exudative capillaritis with microthrombosis and high levels of IL-1beta and IL-6. Later stages are associated with diffuse alveolar damage and ongoing intravascular thrombosis in small to medium-sized pulmonary vessels, occasionally with areas of infarction equivalents, accompanied by laboratory features of disseminated intravascular coagulation. In late stages, organizing pneumonia with extensive intra-alveolar proliferation of fibroblasts and marked metaplasia of alveolar epithelium can be observed. Viral RNA is encountered in the lung, with virus particles in endothelial cells and pneumocytes. In many patients, multi-organ failure with severe liver damage sets in finally, possibly as consequence of an early-onset pro-inflammatory cytokine storm and/or thrombotic microangiopathy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00428-020-02881-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00428-020-02881-x doi: 10.1007/s00428-020-02881-x id: cord-287372-ya5uvoki author: Böszörményi, Kinga P. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 words: 3973.0 sentences: 249.0 pages: flesch: 58.0 cache: ./cache/cord-287372-ya5uvoki.txt txt: ./txt/cord-287372-ya5uvoki.txt summary: This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. abstract: SARS-CoV-2 is a coronavirus that sparked the current COVID-19 pandemic. To stop the shattering effect of COVID-19, effective and safe vaccines, and antiviral therapies are urgently needed. To facilitate the preclinical evaluation of intervention approaches, relevant animal models need to be developed and validated. Rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis) are widely used in biomedical research and serve as models for SARS-CoV-2 infection. However, differences in study design make it difficult to compare and understand potential species-related differences. Here, we directly compared the course of SARS-CoV-2 infection in the two genetically closely-related macaque species. After inoculation with a low passage SARS-CoV-2 isolate, clinical, virological, and immunological characteristics were monitored. Both species showed slightly elevated body temperatures in the first days after exposure while a decrease in physical activity was only observed in the rhesus macaques and not in cynomolgus macaques. The virus was quantified in tracheal, nasal, and anal swabs, and in blood samples by qRT-PCR, and showed high similarity between the two species. Immunoglobulins were detected by various enzyme-linked immunosorbent assays (ELISAs) and showed seroconversion in all animals by day 10 post-infection. The cytokine responses were highly comparable between species and computed tomography (CT) imaging revealed pulmonary lesions in all animals. Consequently, we concluded that both rhesus and cynomolgus macaques represent valid models for evaluation of COVID-19 vaccine and antiviral candidates in a preclinical setting. Author summary SARS-CoV-2 infection can have a wide range of symptoms. It can cause asymptomatic or mild disease, but can also have a severe, potentially deadly outcome. Vaccines and antivirals will therefore be crucial in fighting the current COVID-19 pandemic. For testing these prophylactic and therapeutic treatments, and investigating the progression of infection and disease development, animal models play an essential role. In this study, we compare the course of SARS-CoV-2 infection in rhesus and cynomolgus macaques. Both species showed moderate disease symptoms as shown by pulmonary lesions by CT imaging. Shedding of infectious virus from the respiratory system was also documented. This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. url: https://doi.org/10.1101/2020.11.05.369413 doi: 10.1101/2020.11.05.369413 id: cord-304263-5kddk5fa author: C., Selvaa Kumar title: Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2 date: 2020-10-08 words: 3768.0 sentences: 252.0 pages: flesch: 56.0 cache: ./cache/cord-304263-5kddk5fa.txt txt: ./txt/cord-304263-5kddk5fa.txt summary: In summary, nicotine showed a profound binding affinity for the sACE2-INS1 complex than the sACE2 alone paving for the clinical trials to validate its therapeutic efficacy as a bitter compound against the SARS-CoV-2 virulence. Research studies unveiled the interaction between the structural spike 1 (S1) protein of SARS-CoV-2 with the nicotinic acetylcholine receptors (nAChRs) that are likely to intervene with its biological function (20, 21) . Thus, the insilico study performed to unveil the nicotine''s urge for binding with the soluble ACE2 with or without SARS-CoV-2 in compliance with its interaction with the known human neuronal alpha4-beta2 nicotine-acetylcholine receptor (nN-AChR). We found the reported structural protein template of ACE2-SARS-CoV-2 complex with the enlisted PDB ID: 6VW1 (24) incomplete with numerous missing amino acid residues. Structural binding characteristics of nicotine with the soluble angiotensinconverting enzyme 2 (sACE2)-SARS-CoV-2 complex in the context of its interaction with the neuronal nicotinic acetylcholine receptor (nN-AChR). abstract: The study aimed to validate the proficiency of nicotine binding with the soluble angiotensin-converting enzyme II receptor (sACE2) with or without SARS-CoV-2 in the context of its binding affinity. Modelled human sACE2 and the spike (S1) protein of Indian SARS-CoV-2 (INS1) docked with each other. On the other hand, nicotine docked with sACE2 in the presence or absence of SARS-CoV-2. Nicotine established a stable interaction with negatively charged Asp368 of sACE2, which in turn binds with amino acids like Thr362, Lys363, Thr365, Thr371, and Ala372. In the presence of nicotine, INS1 and sACE2 showed a reduced binding affinity score of -12.6 kcal/mol (Vs -15.7 kcal/mol without nicotine), and a lowered interface area of 1933.6 Å(2) (Vs 2057.3Å(2) without nicotine). The neuronal nicotinic acetylcholine receptor and angiotensin-converting enzyme 2 (ACE2) receptor showed 19.85 % sequence identity among themselves. Following these receptors possessed conserved Trp302 and Cys344 amino acids between them for nicotine binding. However, nicotine showed a higher binding affinity score of -6.33 kcal/mol for the sACE2-INS1 complex than the sACE2 alone with -5.24 kcal/mol. A lowered inhibitory constant value of 22.95µM recorded while nicotine interacted with the sACE2-INS1 complex over the sACE2 alone with 151.69 µM. In summary, nicotine showed a profound binding affinity for the sACE2-INS1 complex than the sACE2 alone paving for the clinical trials to validate its therapeutic efficacy as a bitter compound against the SARS-CoV-2 virulence. url: https://www.ncbi.nlm.nih.gov/pubmed/33052306/ doi: 10.1016/j.toxrep.2020.10.002 id: cord-262428-erlmyzwn author: CABARKAPA, Sonja title: The psychological impact of COVID-19 and other viral epidemics on frontline healthcare workers and ways to address it: A rapid systematic review date: 2020-09-17 words: 5588.0 sentences: 329.0 pages: flesch: 53.0 cache: ./cache/cord-262428-erlmyzwn.txt txt: ./txt/cord-262428-erlmyzwn.txt summary: The search strategy included terms for HCWs (e.g., nurse and doctor), mental health (e.g., wellbeing and psychological), and viral outbreaks (e.g., epidemic and pandemic). In terms of mental health impact of epidemics, HCWs represent a particularly vulnerable group due to the high risk of infection, increased work stress and fear of spreading to their families. The following search terms were used: ''health worker'', ''health care worker'', ''medical'', ''doctor'', ''nursing'', ''nurse'', ''allied health'', ''pandemic'', ''outbreak'', ''mental health'', ''mental illness'', ''psychiatric'', ''psychological'', ''coping'', ''psychosocial'', ''COVID-19'', ''coronavirus'', ''SARS'', ''MERS'' and ''Ebola''. 36, 51 At the early stages of the COVID-19 pandemic, a Wuhan study 28 found that 34.4% (342 of 994) of medical and nursing staff had mild mental health disturbances while 6.2% (62) had severe disturbances, while in another study 24 of 1,521 Chinese HCWs 14.1% had psychological abnormalities. Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 novel coronavirus disease outbreak: A cross-sectional study. abstract: BACKGROUND: As the world is battling the COVID-19 pandemic, frontline health care workers (HCWs) are among the most vulnerable groups at risk of mental health problems. The many risks to the wellbeing of HCWs are not well understood. Of the literature, there is a paucity of information around how to best prevent psychological distress, and what steps are needed to mitigate harm to HCWs’ wellbeing. METHODS: A systematic review using PRISMA methodology was used to investigate the psychological impact on HCWs facing epidemics or pandemics, using three electronic databases (PubMed, MEDLINE and CINAHL), dating back to 2002 until the 21st of August 2020. The search strategy included terms for HCWs (e.g., nurse and doctor), mental health (e.g., wellbeing and psychological), and viral outbreaks (e.g., epidemic and pandemic). Only studies with greater than 100 frontline HCWs (i.e. doctors or nurses in close proximity to infected patients) were included. RESULTS: A total of 55 studies were included, with 53 using quantitative methodology and 2 were qualitative. 50 of the quantitative studies used validated measurement tools while 5 used novel questionnaires. The studies were conducted across various countries and included people with SARS (13 studies), Ebola (1), MERS (3) and COVID-19 (38). Findings suggest that the psychological implications to HCWs are variable with several studies demonstrating an increased risk of acquiring a trauma or stress-related disorders, depression and anxiety. Fear of the unknown or becoming infected were at the forefront of the mental challenges faced. Being a nurse and being female appeared to confer greater risk. In past epidemics, the perceived stigma from family members and society heightened negative implications; predominantly stress and isolation. Coping strategies varied amongst the contrasting sociocultural settings and appeared to differ amongst doctors, nurses and other HCWs. Implemented changes, and suggestions for prevention in the future consistently highlighted the need for greater psychosocial support and clearer dissemination of disease-related information. CONCLUSION: This review can inform current and future research priorities in the maintenance of wellbeing amongst frontline HCWs. Change needs to start at the level of policy-makers to offer an enhanced variety of supports to HCWs who play a critical role during largescale disease outbreaks. Psychological implications are largely negative and require greater attention to be mitigated, potentially through the involvement of psychologists, raised awareness and better education. The current knowledge of therapeutic interventions suggests they could be beneficial but more long-term follow-up is needed. url: https://www.sciencedirect.com/science/article/pii/S2666354620301095?v=s5 doi: 10.1016/j.bbih.2020.100144 id: cord-326984-o27rp468 author: CHIEN, Jung‐Yien title: Temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome date: 2006-10-16 words: 3569.0 sentences: 202.0 pages: flesch: 53.0 cache: ./cache/cord-326984-o27rp468.txt txt: ./txt/cord-326984-o27rp468.txt summary: To improve understanding of the immuno‐pathological processes involved in lung injury associated with SARS, the temporal changes in cytokine/chemokine profiles in the sera of SARS patients were compared with those of patients with community‐acquired pneumonia (CAP), according to the degree of lung involvement. 5 In order to improve the understanding of the immuno-pathogenesis of SARS, an analysis of the dynamic changes in cytokine/chemokine profiles was undertaken in SARS patients who initially had a normal CXR, but who later progressed to typical manifestations of lung involvement. In this study, we investigated 14 SARS patients with initially normal CXR and 24 patients with non-SARS CAP, to clarify the association between temporal changes in cytokine/chemokine profiles and the severity of lung involvement during SARS. 15, 17, 18 Similar to the current study, many of the ''classic'' cytokines mediating inflammation in acute lung injury, 18 such as TNF-α and IFN-γ, were not reported to be significantly increased during SARS. abstract: Objective and background: Pathological changes in severe acute respiratory syndrome (SARS) suggest that SARS sequelae are associated with dysregulation of cytokine and chemokine production. To improve understanding of the immuno‐pathological processes involved in lung injury associated with SARS, the temporal changes in cytokine/chemokine profiles in the sera of SARS patients were compared with those of patients with community‐acquired pneumonia (CAP), according to the degree of lung involvement. Methods: Serum levels of 11 cytokines and chemokines, in 14 patients with SARS and 24 patients with CAP, were serially checked using a bead‐based multiassay system. Sera from 12 healthy subjects were used as normal controls. Results: The serum levels of interferon‐γ‐inducible protein‐10 (IP‐10), IL‐2 and IL‐6 were significantly elevated during SARS infection. In patients with CAP, but not in those with SARS, the levels of interferon‐γ, IL‐10, IL‐8 and monokine induced by interferon‐γ (MIG) were significantly elevated compared with the levels in healthy controls. Among the chemokines/cytokines, IL‐6 levels correlated most strongly with radiographic scores (r = 0.62). The elevation of IP‐10 and IL‐2 antedated the development of chest involvement and reached peak levels earlier than the radiographic scores. In contrast, the dynamic changes in IL‐6, C‐reactive protein and neutrophils occurred synchronously with the changes in radiographic scores. The mean ratio of IL‐6 to IL‐10 in SARS patients (4.84; range 0.41–21) was significantly higher than that in CAP patients (2.95; range 0.02–10.57) (P = 0.04). Conclusions: The early induction of IP‐10 and IL‐2, as well as the subsequent over‐production of IL‐6 and lack of IL‐10 production, probably contribute to the main immuno‐pathological processes involved in lung injury in SARS. These changes in cytokine/chemokine profile are remarkably different from those observed in CAP patients. url: https://www.ncbi.nlm.nih.gov/pubmed/17052299/ doi: 10.1111/j.1440-1843.2006.00942.x id: cord-326169-delehk6x author: CJ Jorgensen, Sarah title: Baricitinib: A review of pharmacology, safety and emerging clinical experience in COVID‐19 date: 2020-06-15 words: 2704.0 sentences: 180.0 pages: flesch: 44.0 cache: ./cache/cord-326169-delehk6x.txt txt: ./txt/cord-326169-delehk6x.txt summary: The lack of reliable biomarkers to monitor patients'' immune status as illness evolves complicates deployment of immunosuppressive drugs like baricitinib. In this article we review available data on baricitinib with an emphasis on immunosuppressive and antiviral pharmacology, pharmacokinetics, safety and current progress in COVID‐19 clinical trials. In population PK analyses, body weight did not have a clinically meaningful 250 impact on baricitinib clearance, however obese RA patients have been reported to have lower 251 response rates. Thrombocytosis Accepted Article 499 treatment strategies aimed at attenuating both pathogen virulence and the pro-inflammatory 500 phenotype seen in the many critically ill patients with COVID-19. 5, 9, 12, 13, 20, 56 As detailed in this 501 review, baricitinib pairs immunosuppressive properties with antiviral activity making it a logical 502 candidate for further evaluation in COVID-19 clinical trials . Baricitinib therapy in 626 COVID-19: A pilot study on safety and clinical impact Impaired type I interferon activity and exacerbated 662 inflammatory responses in severe Covid-19 patients abstract: A hyperinflammatory response to SARS‐CoV‐2 infection, reminiscent of cytokine release syndrome, has been implicated in the pathophysiology of acute respiratory distress syndrome and organ damage in patients with COVID‐19. Agents that inhibit components of the pro‐inflammatory cascade have garnered interest as potential treatment options with hopes that dampening the pro‐inflammatory process may improve clinical outcomes. Baricitinib is a reversible Janus‐associated kinase (JAK)‐inhibitor that interrupts the signaling of multiple cytokines implicated in COVID‐19 immunopathology. It may also have antiviral effects by targeting host factors that viruses rely for cell entry and by suppressing type I interferon driven angiotensin‐converting‐enzyme‐2 up regulation. However, baricitinib’s immunosuppressive effects may be detrimental during acute viral infections by delaying viral clearance and increasing vulnerability to secondary opportunistic infections. The lack of reliable biomarkers to monitor patients’ immune status as illness evolves complicates deployment of immunosuppressive drugs like baricitinib. Furthermore, baricitinib carries the risk of increased thromboembolic events which is concerning given the proclivity towards a hyper‐coagulable state in COVID‐19 patients. In this article we review available data on baricitinib with an emphasis on immunosuppressive and antiviral pharmacology, pharmacokinetics, safety and current progress in COVID‐19 clinical trials. url: https://doi.org/10.1002/phar.2438 doi: 10.1002/phar.2438 id: cord-286341-16tghl48 author: CONCHA-MEJIA, A. title: CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia date: 2020-07-24 words: 2012.0 sentences: 125.0 pages: flesch: 50.0 cache: ./cache/cord-286341-16tghl48.txt txt: ./txt/cord-286341-16tghl48.txt summary: In Colombia, the first case was diagnosed on March 6, 2020 , with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Results: We included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). In this study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Bogota, Colombia, with special emphasis on the presence of gastrointestinal symptoms. abstract: The current pandemic caused by SARS-CoV-2 has posed an important threat to the human health, healthcare systems, economy, and structure of societies. In Colombia, the first case was diagnosed on March 6, 2020 , with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Methods: Demographic and clinical data were collected, results related to the outcomes such as hospitalization time, admission to ICU, need for orotracheal intubation, and death were also included. Statistical analyses were conducted using Stata software V.15. Results: We included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). 13 (76.47%) presented with diarrhea, 29.41% with nausea/vomiting, and five (29.41%) with abdominal pain. Diarrhea in 18.06% of all those infected with SARS-CoV-2 at the time of consultation, which was the most common digestive symptom. No significant differences were observed in requirement for endotracheal intubation, hospitalization, ICU admission, and fatal outcome between the NGIS and GIS groups (p:0.671, 0.483, 1,000, and 1,000). Conclusion: In our study, patients with gastrointestinal symptoms had no significant differences in disease severity, admission to ICU or death compared to those who did not have such symptoms. url: http://medrxiv.org/cgi/content/short/2020.07.24.20161604v1?rss=1 doi: 10.1101/2020.07.24.20161604 id: cord-313829-pjscmen8 author: Caballero, A.E. title: COVID-19 in people living with diabetes: An international consensus date: 2020-07-06 words: 4355.0 sentences: 252.0 pages: flesch: 52.0 cache: ./cache/cord-313829-pjscmen8.txt txt: ./txt/cord-313829-pjscmen8.txt summary: The current clinical management of diabetes is a work in progress, requiring a shift in patient-provider interaction beyond the walls of clinics and hospitals: the use of tele-medicine when feasible, innovative patient education programs, strategies to ensure medication and glucose testing availability and affordability, as well as numerous ideas on how to improve meal plans and physical activity. It is difficult to predict but some indicators are available from the model of Harpreet In summary, while overall mortality due to COVID-19 is lower in India than in other countries, the elderly population, where most patients with diabetes, hypertension and CVD are concentrated, remains at high risk. Although it is clear that this option of care is not available to most people around the world, exploring how to improve the communication between providers and patients and families at home, in their own communities facing day to day challenges, may prove to be a more effective approach to managing the disease well beyond the COVID pandemic. abstract: The COVID-19 pandemic has added an enormous toll to the existing challenge of diabetes care world-wide. A large proportion of patients with COVID-19 requiring hospitalization and/or succumbing to the disease have had diabetes and other chronic conditions as underlying risk factors. In particular, individuals belonging to racial/ethnic minorities in the U.S. and other countries have been significantly and disproportionately impacted. Multiple and complex socioeconomic factors have long played a role in increasing the risk for diabetes and now for COVID-19. Since the pandemic began, the global healthcare community has accumulated invaluable clinical experience on providing diabetes care in the setting of COVID-19. In addition, understanding of the pathophysiological mechanisms that link these two diseases is being developed. The current clinical management of diabetes is a work in progress, requiring a shift in patient-provider interaction beyond the walls of clinics and hospitals: the use of tele-medicine when feasible, innovative patient education programs, strategies to ensure medication and glucose testing availability and affordability, as well as numerous ideas on how to improve meal plans and physical activity. Notably, this worldwide experience offers us the possibility to not only prepare better for future disasters but also transform diabetes care beyond the COVID-19 era. url: https://api.elsevier.com/content/article/pii/S1056872720304335 doi: 10.1016/j.jdiacomp.2020.107671 id: cord-320331-wtxja5i9 author: Cabbab, Iris Louise N. title: Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection date: 2020-10-08 words: 10061.0 sentences: 433.0 pages: flesch: 41.0 cache: ./cache/cord-320331-wtxja5i9.txt txt: ./txt/cord-320331-wtxja5i9.txt summary: It is important to note that since the approach of this paper is to provide current knowledge on the anatomic, physiologic and molecular bases of anti-inflammatory drug and corticosteroid action on the RAAS, this paper will not demonstrate a systematic review or meta-analysis of current clinical evidence, but will only provide insight on the probable influences of the discussed pathways on early SARS-CoV-2 infection. A correspondence by Fang et al published at The Lancet this March discussed that hypertensives and diabetics taking ACE2 inhibitor (ACEi) and angiotensin receptor blocking (ARB) drugs may be at an increased risk of infection and severity by SARS-CoV-2 and COVID-19, respectively, citing three studies wherein diabetes and hypertension were major comorbidities of patients with severe COVID-19 and of non-survivors [20] . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease 19 (COVID-19), and is genetically related to the 2003 SARS and Middle East respiratory syndrome (MERS-CoV) coronaviruses. Recent studies have reported that similar to SARS-CoV, this strain expresses a spike protein (S) with a receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2) – an enzyme expressed mostly in the endothelium, kidneys, heart, gastrointestinal tract and lungs – to facilitate viral entry and intracellular replication. Incidentally, the renin-angiotensin-aldosterone system (RAAS) is integral to physiologic control of both ACE and ACE2 expression, and is an essential system utilized by SARS-CoV-2, albeit with varying schools of thought on how it can affect viral entry. In this paper, we will review current knowledge on the RAAS and how it can be affected by non-steroidal anti-inflammatory drugs (NSAIDs) and corticosteroid use at the organ and cellular levels. We will then discuss the relevance of these interactions on organ-specific ACE2 expression, and provide scientific insights on how this mechanism can potentially affect SARS-CoV-2 infection in the early phases of disease. From the standpoint of other known viruses, we will then aim to discuss the potential uses or restrictions of these drugs in viral infection, and provide an update on relevant studies about COVID-19. url: https://doi.org/10.1016/j.virusres.2020.198190 doi: 10.1016/j.virusres.2020.198190 id: cord-352668-qjlqsb2k author: Cabello, Francisco title: Consensus on Recommendations for Safe Sexual Activity during the COVID-19 Coronavirus Pandemic date: 2020-07-20 words: 4834.0 sentences: 232.0 pages: flesch: 43.0 cache: ./cache/cord-352668-qjlqsb2k.txt txt: ./txt/cord-352668-qjlqsb2k.txt summary: Sexual activity offers numerous advantages for physical and mental health but maintains inherent risks in a pandemic situation, such as the current one caused by SARS-CoV-2. A group of experts from the Spanish Association of Sexuality and Mental Health (AESexSAME) has reached a consensus on recommendations to maintain lower-risk sexual activity, depending on one''s clinical and partner situations, based on the current knowledge of SARS-CoV-2. In all other cases (for those under quarantine, those with some clinical symptoms, health professionals in contact with COVID-19 patients, and during pregnancy), abstaining from coital/oral/anal sex, substituting it with masturbatory or virtual sexual activity to provide maximum protection from the contagion, and increasing the benefits inherent to sexual activity are recommended. Due to the ease of contagion and the lack of information about the possible transmission of SARS-CoV-2, a group of experts from the Spanish Association for Sexuality and Mental Health, covering the fields of sexology, psychiatry, psychology and medicine reached a consensus. abstract: Sexual activity offers numerous advantages for physical and mental health but maintains inherent risks in a pandemic situation, such as the current one caused by SARS-CoV-2. A group of experts from the Spanish Association of Sexuality and Mental Health (AESexSAME) has reached a consensus on recommendations to maintain lower-risk sexual activity, depending on one’s clinical and partner situations, based on the current knowledge of SARS-CoV-2. Different situations are included in the recommendations: a sexual partner passing quarantine without any symptoms, a sexual partner that has not passed quarantine, a sexual partner with some suspicious symptoms of COVID-19, a positive sexual partner with COVID-19, a pregnant sexual partner, a health professional partner in contact with COVID-19 patients, and people without a sexual partner. The main recommendations include returning to engaging in safe sex after quarantine is over (28 days based on the duration one can carry SARS-CoV-2, or 33 days for those who are >60 years old) and all parties are asymptomatic. In all other cases (for those under quarantine, those with some clinical symptoms, health professionals in contact with COVID-19 patients, and during pregnancy), abstaining from coital/oral/anal sex, substituting it with masturbatory or virtual sexual activity to provide maximum protection from the contagion, and increasing the benefits inherent to sexual activity are recommended. For persons without a partner, not initiating sexual activity with a sporadic partner is strongly recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/32698369/ doi: 10.3390/jcm9072297 id: cord-321235-h3w8827o author: Cabrera Alvargonzalez, Jorge Julio title: Pooling for SARS-CoV-2 control in care institutions date: 2020-10-12 words: 2839.0 sentences: 195.0 pages: flesch: 58.0 cache: ./cache/cord-321235-h3w8827o.txt txt: ./txt/cord-321235-h3w8827o.txt summary: The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. The rationale in this study is to develop a new strategy based on initial individual identification of positive coronavirus cases in order to organize low prevalence clusters, followed by a serial pooling strategy testing of these clusters, in order to control areas free of virus circulation, allowing them to be fully operative. During the Coronavirus pandemic, SARS-CoV-2 prevalence was obtained by individually testing of 25, 386 people from 306 Galician Care Homes: 16,477 residents, 8599 workers and 310 not specified. A global SARS-CoV-2 seroprevalence of 5% in Spain [12] and a global viral prevalence around 3% at Care Homes reported in the present study, suggest that the number of people at risk of acquiring the infection continue to be very high. abstract: BACKGROUND: Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources. The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. METHODS: A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7 and 2% prevalence. RESULTS: Distribution of SARS-CoV-2 infection at Care Homes was uneven (0–60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively). CONCLUSIONS: A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative. url: https://www.ncbi.nlm.nih.gov/pubmed/33046011/ doi: 10.1186/s12879-020-05446-0 id: cord-256375-f4vrcjr1 author: Cabrera Muras, Antonio title: Bilateral Facial Nerve Palsy associated with COVID‐19 and Epstein‐Barr Virus co‐infection date: 2020-09-30 words: 580.0 sentences: 43.0 pages: flesch: 53.0 cache: ./cache/cord-256375-f4vrcjr1.txt txt: ./txt/cord-256375-f4vrcjr1.txt summary: He was diagnosed with right peripheral facial palsy and was treated with prednisone 60 mg/24h with a tapering schedule. This patient presented with severe bilateral facial palsy, evidence of SARS-CoV-2 infection preceded by upper respiratory symptoms, and evidence of coinfection with EBV. EBV infection is responsible for 0.5%-7.5% of peripheral facial palsies, and up to 35% are bilateral [2, 3] . One of the reported patients had isolated bilateral facial palsy and was interpreted as a variant of GBS know as bifacial weakness with paresthesias [6] . SARS-CoV-2 infection should be suspected in patients with facial palsy or any suspicion of GBS in the times of COVID-19 pandemics since it may be the presenting feature in patients with mild respiratory symptoms. Bilateral facial nerve palsy associated with Epstein-Barr virus infection Bilateral facial nerve palsy associated with Epstein-Barr virus infection with a review of the literature Guillain-Barre Syndrome Associated with SARS-CoV-2 abstract: A 20‐year‐old male, with no relevant previous medical history, was admitted due to bilateral facial weakness. Two weeks before, he noticed odynophagia and fever of 39ºC without cough. He associated significant asthenia with headache, myalgia, nausea, and vomiting and he was treated with levofloxacin 500mg qd for 7 days. One week after, during an initial improvement of the respiratory symptoms, he presented acute right facial weakness. He was diagnosed with right peripheral facial palsy and was treated with prednisone 60 mg/24h with a tapering schedule. url: https://www.ncbi.nlm.nih.gov/pubmed/32997868/ doi: 10.1111/ene.14561 id: cord-307208-tw6mwa5v author: Cabrera Villegas, Antonio title: [(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2 date: 2020-09-16 words: 3341.0 sentences: 167.0 pages: flesch: 50.0 cache: ./cache/cord-307208-tw6mwa5v.txt txt: ./txt/cord-307208-tw6mwa5v.txt summary: The aim of this study was to retrospectively analyse the incidence of suspicious imaging findings of COVID-19 in PET/CT performed in asymptomatic patients referred to our Department with oncologic indications. Inclusion criteria were the following: (a) outpatients referred to Nuclear Medicine for whole-body PET/CT, (b) with [ 18 F]-FDG or [ 18 F]-fluorocholine, (c) referral was due only to oncologic indications, and (d) patients were asymptomatic for SARS-CoV-2 infection. The limitations in the diagnosis of COVID-19, together with the fact that most of the patients infected with SARS-CoV-2 are asymptomatic or present scarce symptoms, were the reason for initiating this retrospective study analysing patients scanned with PET/CT in which there were suspicious lung findings for SARS-CoV-2 infection. Our results confirm that the prevalence of SARS-CoV-2 infection is higher than the known figures, due to the relevant proportion of asymptomatic patients, some of them with lung disease, which can be diagnosed in a presymptomatic phase based on the incidental imaging findings in imaging procedures performed for completely different clinical indications. abstract: PURPOSE: Spain has been one of the most affected countries by the COVID-19 pandemic, being among the countries with worse numbers, including the death rate. However, most patients are asymptomatic, although they are very contagious. The objective of this study was to investigate the incidence in oncological patients infected with SARS-CoV-2 that are asymptomatic for COVID-19 and at home and that undergo PET/CT for oncologic indications, nonrelated to COVID-19, finding in the PET/CT lung alterations that are suggestive of SARS-CoV-2 infection. METHODS: During the period of maximum incidence of the global pandemic in one of the most affected regions of Spain, there were 145 patients that met inclusion and exclusion criteria and were included in the study. Imaging findings previously described such as ground-glass opacities with low [(18)F]-FDG uptake were considered images suspicious for SARS-CoV-2 infection. Patients with these findings were referred to RT-PCR testing and close follow-up to confirm the presence or absence of COVID-19. RESULTS: Suspicious lung imaging findings were present in 7 of 145 patients (4.8%). Five of these 7 patients were confirmed as presenting SARS-CoV-2 infection, this is, COVID-19. In the remaining two, it was not possible to confirm the presence of COVID-19 with RT-PCR, although in one of them, PET/CT allowed an early diagnosis of a lung infection related to a bacterial pneumonic infection that was promptly and adequately treated with antibiotics. CONCLUSION: These results confirm that the prevalence of SARS-CoV-2 infection is higher than suspected and that there are asymptomatic patients that are attending imaging departments to be explored for their baseline oncologic processes. In these patients, PET/CT allows an early diagnosis of COVID-19. url: https://doi.org/10.1007/s00259-020-04979-5 doi: 10.1007/s00259-020-04979-5 id: cord-316255-93srx4s7 author: Cacho, Pedro Muñoz title: Can climatic factors explain the differences in COVID-19 incidence and severity across the Spanish regions?: An ecological study date: 2020-10-13 words: 3814.0 sentences: 194.0 pages: flesch: 44.0 cache: ./cache/cord-316255-93srx4s7.txt txt: ./txt/cord-316255-93srx4s7.txt summary: Besides, temperature (February: rho = − 0.832; p < 0.001 and March: rho = − 0.904; p < 0.001), was the main climatic factor responsible for the infectivity of the coronavirus and directly contributed to a different spread of SARS-CoV-2 across the Spanish regions. To assess the possible influence on the infectivity of SARS-CoV-2 [9] [10] [11] , data on UVR (J/m 2 ), temperature (°C), and relative humidity (%) were also collected from the months with the highest infectivity (February and March 2020) to the peak of the pandemic in our country. Climatic parameters (temperature, UVR, and relative humidity) were considered as independent variables and epidemiological variables related to COVID-19 (cumulative incidence during the previous 14 days, total cases, newly diagnosed cases, hospital admissions, intensive care unit (ICU) admissions, and mortality, all referring to the period from 1 to 30 March 2020) were analyzed as dependent variables. abstract: BACKGROUND: Environmental factors play a central role in seasonal epidemics. SARS-CoV-2 infection in Spain has shown a heterogeneous geographical pattern This study aimed to assess the influence of several climatic factors on the infectivity of SARS-CoV-2 and the severity of COVID-19 among the Spanish Autonomous Communities (AA.CC.). METHODS: Data on coronavirus infectivity and severity of COVID-19 disease, as well as the climatic variables were obtained from official sources (Ministry of Health and Spanish Meteorological Agency, respectively). To assess the possible influence of climate on the development of the disease, data on ultraviolet radiation (UVR) were collected during the months before the start of the pandemic. To analyze its influence on the infectivity of SARS-CoV-2, data on UVR, temperature, and humidity were obtained from the months of highest contagiousness to the peak of the pandemic. RESULTS: From October 2019 to January 2020, mean UVR was significantly related not only to SARS-CoV-2 infection (cumulative incidence -previous 14 days- × 10(5) habitants, rho = − 0.0,666; p = 0.009), but also with COVID-19 severity, assessed as hospital admissions (rho = − 0.626; p = 0.017) and ICU admissions (rho = − 0.565; p = 0.035). Besides, temperature (February: rho = − 0.832; p < 0.001 and March: rho = − 0.904; p < 0.001), was the main climatic factor responsible for the infectivity of the coronavirus and directly contributed to a different spread of SARS-CoV-2 across the Spanish regions. CONCLUSIONS: Climatic factors may partially explain the differences in COVID-19 incidence and severity across the different Spanish regions. The knowledge of these factors could help to develop preventive and public health actions against upcoming outbreaks of the disease. url: https://doi.org/10.1186/s12940-020-00660-4 doi: 10.1186/s12940-020-00660-4 id: cord-284873-m1ehdydr author: Cadegiani, Flavio A. title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 date: 2020-07-28 words: 2536.0 sentences: 158.0 pages: flesch: 38.0 cache: ./cache/cord-284873-m1ehdydr.txt txt: ./txt/cord-284873-m1ehdydr.txt summary: title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 At the onset of the COVID-19 pandemic, mortality following infection of severe acute respiratory coronavirus (SARS-CoV-2) was thought to be solely associated with aging and pre-existing conditions; however, as the pandemic ensued, several large scale epidemiological observations eluded to additional atypical risk factors, particularly hypertension, obesity, and male gender (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) . The Renin-Angiotensin-Aldosterone System (RAAS) has been shown to be central in COVID-19, since three of the key modulators of SARS-CoV-2 infectivity-angiotensin 1-7, ACE2, and AT1-belong to the RAAS, in addition to the TMPRSS2 expression (12) (13) (14) (15) (16) (17) (18) (19) . Abnormal ACE2 expression, angiotensin II and angiotensin 1-7 imbalance, and TMPRSS2 androgen-mediated overactivity seem to be key regulators of SARS-CoV-2 infectivity, in accordance with epidemiological observations of hypertension, obesity, and male sex as being major risk factors. abstract: nan url: https://doi.org/10.3389/fmed.2020.00453 doi: 10.3389/fmed.2020.00453 id: cord-284573-w0sk622m author: Caduff, Carlo title: What Went Wrong: Corona and the World after the Full Stop date: 2020-07-21 words: 9277.0 sentences: 517.0 pages: flesch: 58.0 cache: ./cache/cord-284573-w0sk622m.txt txt: ./txt/cord-284573-w0sk622m.txt summary: Published by a group of experts without peer review on an institutional website, the report compared Covid-19 with the great pandemic of 1918, which killed over 50 million people worldwide and suggested, without any evidence, that SARS-CoV-2 was "a virus with comparable lethality to H1N1 influenza in 1918." 1 Most frightening in all this was not so much the lethality of the SARS-CoV-2 virus but the license to rush forward with predictions, abandon basic standards of science, and make dramatic claims to scare people. This extreme and unprecedented blanket approach systematically imposed on entire populations was driven by a number of factors that variously prevailed in different countries across the world: a growing sense of panic, constant media sensationalism, deep authoritarian longings, increasing political pressure to contain the spread of the virus, disturbing accounts of overwhelmed hospitals unable to cope with the surge of patients, misleading mortality calculations, and, most importantly, a trust in the power of mathematical disease modeling. abstract: This article examines the global response to the Covid‐19 pandemic. It argues that we urgently need to look beyond the virus if we want to understand the real seriousness of what is happening today. How did we end up in a space of thinking, acting, and feeling that has normalized extremes and is based on the assumption that biological life is an absolute value separate from politics? The author suggests that today's fear is fueled by mathematical disease modeling, neoliberal health policies, nervous media reporting, and authoritarian longings. url: https://www.ncbi.nlm.nih.gov/pubmed/32692890/ doi: 10.1111/maq.12599 id: cord-269563-2979u47a author: Caetano Silva-Filho, José title: The influence of ABO blood groups on COVID-19 susceptibility and severity: a molecular hypothesis based on carbohydrate-carbohydrate interactions date: 2020-08-02 words: 4614.0 sentences: 218.0 pages: flesch: 40.0 cache: ./cache/cord-269563-2979u47a.txt txt: ./txt/cord-269563-2979u47a.txt summary: Based on this survey, we hypothesize that the correlation between the ABO blood system and susceptibility to SARS-CoV-2 infection can be presumably explained by the modulation of sialic acid-containing receptors distribution on host cell surface induced by ABO antigens through carbohydrate-carbohydrate interactions, which could maximize or minimize the virus Spike protein binding to the host cell. to cell receptors, as well as (ii) the biochemical aspects of ABO blood group system and its association to infection and some circulatory conditions, we hypothesize that the influence of blood type on COVID-19 severity relies on the differential clustering of glycoproteins receptors to SARS-CoV-2 on host cell surface, induced by ABH antigens through carbohydrate-carbohydrate interactions with the glycan portions of these receptors, which could modulate virus binding to the target cell. abstract: The world is experiencing one of the most difficult moments in history with the COVID-19 pandemic, a disease caused by SARS-CoV-2, a new type of coronavirus. Virus infectivity is mediated by the binding of Spike transmembrane glycoprotein to specific protein receptors present on cell host surface. Spike is a homotrimer that emerges from the virion, each monomer containing two subunits named S1 and S2, which are related to cell recognition and membrane fusion, respectively. S1 is subdivided in domains S1A (or NTD) and S1B (or RBD), with experimental and in silico studies suggesting that the former binds to sialic acid-containing glycoproteins, such as CD147, whereas the latter binds to ACE2 receptor. Recent findings indicate that the ABO blood system modulates susceptibility and progression of infection, with type-A individuals being more susceptible to infection and/or manifestation of a severe condition. Seeking to understand the molecular mechanisms underlying this susceptibility, we carried out an extensive bibliographic survey on the subject. Based on this survey, we hypothesize that the correlation between the ABO blood system and susceptibility to SARS-CoV-2 infection can be presumably explained by the modulation of sialic acid-containing receptors distribution on host cell surface induced by ABO antigens through carbohydrate-carbohydrate interactions, which could maximize or minimize the virus Spike protein binding to the host cell. This model could explain previous sparse observations on the molecular mechanism of infection and can direct future research to better understand of COVID-19 pathophysiology. url: https://api.elsevier.com/content/article/pii/S0306987720322581 doi: 10.1016/j.mehy.2020.110155 id: cord-354458-o2kcd085 author: Caffo, Orazio title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 date: 2020-06-18 words: 630.0 sentences: 27.0 pages: flesch: 49.0 cache: ./cache/cord-354458-o2kcd085.txt txt: ./txt/cord-354458-o2kcd085.txt summary: title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 prostate cancer (PC) and risk of infection by SARSCoV-2 through a population-based study of patients with laboratory-confirmed SARS-CoV-2 infection from 68 hospitals in Veneto (1) . To further investigate this potential relationship, we identified all of the cases of COVID-19 that have occurred in metastatic castration-resistant PC (mCRPC) and metastatic castration-sensitive PC (mCSPC) patients treated in most of the high-volume referral medical oncology departments in northern Italy. The 19 high-volume medical oncology departments contributing to this study were treating a median of 80 metastatic PC patients each (range 48-230) for a total of 1,949. On the contrary, we identified a homogenous population of consecutive mCSPC/mCRPC patients treated in most of the high-volume referral medical oncology departments in northern Italy. Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (n=4532) abstract: nan url: https://api.elsevier.com/content/article/pii/S0923753420398926 doi: 10.1016/j.annonc.2020.06.005 id: cord-323940-ubazgvov author: Cafiero, Concetta title: Pharmacogenomics and Pharmacogenetics: In Silico Prediction of Drug Effects in Treatments for Novel Coronavirus SARS-CoV2 Disease date: 2020-10-13 words: 7359.0 sentences: 408.0 pages: flesch: 34.0 cache: ./cache/cord-323940-ubazgvov.txt txt: ./txt/cord-323940-ubazgvov.txt summary: Recently, pharmacogenomics (the effects of a single genetic marker) and pharmacogenetics (the collective influence of variability across the genome to modulate an individual''s drug response) have received great attention for their abilities to provide a new way to select drugs for personalized therapy (optimal dosing for maximizing drug efficacy or minimizing the risk of toxicity). 35 Search terms were "Covid-19", "novel coronavirus", "SARS-CoV2", "pharmacogenetics", "treatment/s", "adverse side effects", "therapy", "lung", "ocular", "pulmonary infection", "drugs", "drug response", "virus", "candidate drugs", "potential inhibitors", "protease inhibitors", "personalized medicine", "individual therapy", "pneumonia", "ACE", "heparin", "vasculitis", "conjunctivitis", "rhinitis", "hematological complication" and "main metabolic routes", either alone or in combination. Drugs in use as routine therapy or in clinical trials for Covid-19 include steroids and antiviral and biological humanized neutralizing antibodies against some proinflammatory cytokines, such as IL1, IL6, IFN, and TNFα, in addition to supportive measures and symptomatic treatment, according to the severity of the disease. abstract: The latest developments in precision medicine allow the modulation of therapeutic approaches in different pathologies on the basis of the specific molecular characterization of the patient. This review of the literature coupled with in silico analysis was to provide a selected screening of interactions between single-nucleotide polymorphisms (SNPs) and drugs (repurposed, investigational, and biological agents) showing efficacy and toxicityin counteracting Covid-19 infection. In silico analysis of genetic variants related to each drug was performed on such databases as PharmGKB, Ensembl Genome Browser, www.drugs.com, and SNPedia, with an extensive literature review of papers (to May 10, 2020) on Covid-19 treatments using Medline, Embase, International Pharmaceutical Abstracts, PharmGKB, and Google Scholar. The clinical relevance of SNPs, known as both drug targets and markers, considering genetic variations with known drug responses, and the therapeutic consequences are discussed. In the context of clinical treatment of Covid-19, including infection prevention, control measures, and supportive care, this review highlights the importance of a personalized approach in the final selection of therapy, which is probably essential in the management of the Covid-19 pandemic. url: https://doi.org/10.2147/pgpm.s270069 doi: 10.2147/pgpm.s270069 id: cord-291052-nstfe15a author: Cag, Yasemin title: A novel approach to managing COVID-19 patients; results of lopinavir plus doxycycline cohort date: 2020-08-27 words: 1930.0 sentences: 125.0 pages: flesch: 54.0 cache: ./cache/cord-291052-nstfe15a.txt txt: ./txt/cord-291052-nstfe15a.txt summary: This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. Second, moderate to severe cases were hospitalized and prescribed with a regimen of lopinavir plus doxycycline plus ceftriaxone for 5 days. We hospitalized moderate to severe cases and administered lopinavir combined with doxycycline and ceftriaxone to 343 patients, among whom 161 had positive PCR test results (161/343, 46.9%). We administered hydroxychloroquine to mild cases isolated at home, lopinavir plus doxycycline to hospitalized moderate to severe cases, and favipiravir in the salvage treatment. We concluded that home isolation of mild cases is an effective means to manage the burden of disease, while lopinavir plus doxycycline is an alternative to current treatment regimens for COVID-19. abstract: This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. During the study period, 2043 patients with suspected COVID-19 were admitted to the emergency department. Molecular tests indicated that 475 of these patients tested positive for COVID-19. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. The overall case fatality rate was 4.2% (20/475). url: https://www.ncbi.nlm.nih.gov/pubmed/32856202/ doi: 10.1007/s10096-020-04016-1 id: cord-317246-8c7d5ynz author: Cagetti, Maria Grazia title: Could SARS‐CoV‐2 burst the use of Non‐Invasive and Minimally Invasive treatments in paediatric dentistry? date: 2020-08-03 words: 2133.0 sentences: 128.0 pages: flesch: 46.0 cache: ./cache/cord-317246-8c7d5ynz.txt txt: ./txt/cord-317246-8c7d5ynz.txt summary: The non-invasive treatment includes the non-restorative cavity control that manages non-cavitated and cavitated active caries lesions making them cleanable and promoting their arrest through the use fluoride vehicles only. Non-operative caries treatment is mostly recommended for decayed primary teeth, but may represent a suitable alternative also for permanent teeth of children with dental anxiety or disabilities, who offer insufficient collaboration for the traditional restorative treatment. 27 The non-invasive treatment and the minimally invasive treatment are often recommended in controlling and treating dental caries in children; however, even though dentists seem to know the advantages of these strategies, the traditional caries removal and restoration therapy are still preferred. 29 In conclusion, caries treatment using the non-invasive or the minimally invasive treatments is desirable, especially since the transmission risk of SARS-CoV-2 is potentially higher in the dental environment. abstract: nan url: https://doi.org/10.1111/ipd.12679 doi: 10.1111/ipd.12679 id: cord-266888-ryvk6mte author: Cai, Guoshuai title: Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2 date: 2020-06-15 words: 1444.0 sentences: 83.0 pages: flesch: 53.0 cache: ./cache/cord-266888-ryvk6mte.txt txt: ./txt/cord-266888-ryvk6mte.txt summary: In addition, we analyzed three microarray data sets of samples derived from healthy subjects and patients with chronic obstructive pulmonary disease (COPD), including small airway epithelium samples from current smokers (from GSE5058, n = 26 [7] ), bronchial airway epithelium samples from current and former smokers (GSE37147, n = 238 [9] ), and lung samples from white patients (n = 438) who underwent lung cancer surgery at the Institut Universitaire de Cardiologie et de Pneumologie de Québec (10). We identified upregulation of pulmonary ACE2 gene expression in ever-smokers compared with nonsmokers in all data sets, irrespective of tissue subset or COPD status (Figure 1) . The significant effect of smoking on ACE2 pulmonary expression identified in this study may suggest an increased risk for viral binding and entry of SARS-CoV and SARS-CoV-2 in lungs of smokers. We further evaluated the effect of smoking on ACE2 pulmonary expression in single bronchial epithelial cells from six never-smokers and six current smokers. abstract: nan url: https://doi.org/10.1164/rccm.202003-0693le doi: 10.1164/rccm.202003-0693le id: cord-312632-g4250q6l author: Cai, Xiaofang title: Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children date: 2020-05-12 words: 4647.0 sentences: 230.0 pages: flesch: 48.0 cache: ./cache/cord-312632-g4250q6l.txt txt: ./txt/cord-312632-g4250q6l.txt summary: Five patients with non-respiratory symptoms as the first manifestation were hospitalized from the emergency department, and were later confirmed to have COVID-19, between 23 January and 20 February 2020, at the Wuhan Children''s Hospital. Severe COVID-19 was defined when the pediatric patients Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; WHO, World Health Organization; ICTV, the International Committee on Taxonomy of Viruses; MERS-CoV, Middle East respiratory syndrome coronavirus; CT, computed tomography; PICU, pediatric intensive care unit; NK, natural killer; CRRT, continuous renal replacement therapy; CRP, C-reactive protein; PCT, procalcitonin; PT, prothrombin time; APTT, activated partial thromboplastin time; IL, interleukin; EEG, electroencephalogram; ACE2, angiotensin converting enzyme 2. This might explain why case 3, who was admitted with head trauma but with no respiratory symptoms, tested positive for SARS-CoV-2 nucleic acid and his lung CT scan showed pneumonia. abstract: An outbreak of the novel coronavirus disease 2019 (COVID-19) occurred in Wuhan, China, in December 2019, which then rapidly spread to more than 80 countries. However, detailed information on the characteristics of COVID-19 in children is still scarce. Five patients with non-respiratory symptoms as the first manifestation were hospitalized from the emergency department, and were later confirmed to have COVID-19, between 23 January and 20 February 2020, at the Wuhan Children's Hospital. SARS-CoV-2 nucleic acid detection was positive for all the patients. Four of the patients were male and one was female, and their ages ranged from 2-months to 5.6 years. All lived in Wuhan. One patient had a clear history of exposure to SARS-CoV-2, one had a suspected history of exposure, while the others had no exposure history. For three of the five patients, the primary onset disease required an emergency operation or treatment, and included intussusception, acute suppurative appendicitis perforation with local peritonitis, and traumatic subdural hemorrhage with convulsion, while for the other two it was acute gastroenteritis (including one patient with hydronephrosis and a stone in his left kidney). During the course of the disease, four of the five patients had a fever, whereas one case had no fever or cough. Two patients had leukopenia, and one also had lymphopenia. In the two cases of severe COVID-19, the levels of CRP, PCT, serum ferritin, IL-6, and IL-10 were significantly increased, whereas the numbers of CD3+, CD4+, CD8+ T lymphocytes, and CD16 + CD56 natural killer cells were decreased. We also found impaired liver, kidney, and myocardial functions; the presence of hypoproteinemia, hyponatremia, and hypocalcemia; and, in one case, abnormal coagulation function. Except for one patient who had a rotavirus infection, all patients tested negative for common pathogens, including the influenza virus, parainfluenza virus, respiratory syncytial virus, adenovirus, enterovirus, mycoplasma, Chlamydia, and Legionella. Chest CT images of all the patients showed patches or ground-glass opacities in the lung periphery or near the pleura, even large consolidations. This case series is the first report to describe the clinical features of COVID-19 with non-respiratory symptoms as the first manifestation in children. url: https://doi.org/10.3389/fped.2020.00258 doi: 10.3389/fped.2020.00258 id: cord-330198-pwkxgbxk author: Cai, Xiaofang title: Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19 date: 2020-10-27 words: 4287.0 sentences: 223.0 pages: flesch: 50.0 cache: ./cache/cord-330198-pwkxgbxk.txt txt: ./txt/cord-330198-pwkxgbxk.txt summary: All febrile or suspected COVID-19 cases were referred to the fever clinic, and the others-including critically ill children-were received by the emergency department after pediatric 5-level triage. We retrospectively analyzed the clinical data of these children admitted from the emergency department to characterize thoroughly the features of COVID-19 that can be evaluated to distinguish this novel disease from pneumonia caused by other pathogens in pediatric patients. Owing to the parents'' fear that their children were infected with SARS-CoV-2, the median time from symptom onset to hospital admission was shorter for confirmed COVID-19 cases (2.0 days) than that for suspected COVID-19 cases (3.0 days) and non-COVID-19 cases (4.0 days) (P < 0.05). Moreover, serologic testing can serve as an important adjunctive method for COVID-19 diagnosis, especially when the patient is highly suspected of SARS-CoV-2 infection but is found to be negative by nucleic acid testing. abstract: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread around the world. However, approaches to distinguish COVID-19 from pneumonia caused by other pathogens have not yet been reported. We retrospectively analyzed the clinical data of 97 children with probable COVID-19. A total of 13 (13.4%) patients were confirmed positive for SARS-CoV-2 infection by nucleic acid RT-PCR testing, and 41 (42.3%) patients were found to be infected with other pathogens. Notably, no pathogen was detected in 43 (44.3%) patients. Among all patients, 25 (25.8%) had familial cluster exposure history, and 52 (53.6%) had one or more coexisting conditions. Fifteen (15.5%) patients were admitted or transferred to the PICU. In the 11 confirmed COVID-19 cases, 5 (45.5%) and 7 (63.6%) were positive for IgM and IgG against SARS-CoV-2, respectively. In 22 patients with suspected COVID-19, 1 (4.5%) was positive for IgG but negative for IgM. The most frequently detected pathogen was Mycoplasma pneumonia (29, 29.9%). One patient with confirmed COVID-19 died. Our results strongly indicated that the detection of asymptomatic COVID-19 or coexisting conditions must be strengthened in pediatric patients. These cases may be difficult to diagnose as COVID-19 unless etiologic analysis is conducted. A serologic test can be a useful adjunctive diagnostic tool in cases where SARS-CoV-2 infection is highly suspected but the nucleic acid test is negative. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available in the online version of this article at 10.1007/s11684-020-0820-7 and is accessible for authorized users. url: https://doi.org/10.1007/s11684-020-0820-7 doi: 10.1007/s11684-020-0820-7 id: cord-331897-4wnoa4l7 author: Cai, Yi title: Temporal event searches based on event maps and relationships() date: 2019-09-25 words: 10502.0 sentences: 595.0 pages: flesch: 61.0 cache: ./cache/cord-331897-4wnoa4l7.txt txt: ./txt/cord-331897-4wnoa4l7.txt summary: Experiments conducted on a real data set show that our method outperforms the baseline method Event Evolution Graph (EEG), and it can help discover certain new relationships missed by previous methods and even by human annotators. Although some work has been done to find and link incidents in news stories [4, 5] or discover event evolution graphs [6, 7] , this scholarship has only focused on time sequences and content similarity between two component events to identify the dependence relationships. To the best of our knowledge, this is the first piece of work that (1) formalizes and handles the event search problem by analyzing all temporal, content dependence and event reference relationships between events to construct an overall picture of the event''s evolution; and (2) measures the importance of events based on the interrelationships of events. abstract: To satisfy a user’s need to find and understand the whole picture of an event effectively and efficiently, in this paper we formalize the problem of temporal event searches and propose a framework of event relationship analysis for search events based on user queries. We define three kinds of event relationships: temporal, content dependence, and event reference, that can be used to identify to what extent a component event is dependent on another in the evolution of a target event (i.e., the query event). The search results are organized as a temporal event map (TEM) that serves as the whole picture about an event’s evolution or development by showing the dependence relationships among events. Based on the event relationships in the TEM, we further propose a method to measure the degrees of importance of events, so as to discover the important component events for a query, as well as the several algebraic operators involved in the TEM, that allow users to view the target event. Experiments conducted on a real data set show that our method outperforms the baseline method Event Evolution Graph (EEG), and it can help discover certain new relationships missed by previous methods and even by human annotators. url: https://doi.org/10.1016/j.asoc.2019.105750 doi: 10.1016/j.asoc.2019.105750 id: cord-303517-8971aq02 author: Cajamarca-Baron, Jairo title: SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression date: 2020-10-16 words: 9096.0 sentences: 459.0 pages: flesch: 45.0 cache: ./cache/cord-303517-8971aq02.txt txt: ./txt/cord-303517-8971aq02.txt summary: 27, 28 Among other comorbidities, chronic kidney disease is associated with in-hospital mortality, as are cancer and cerebrovascular disease, demonstrated through two meta-analyses that included over fifteen thousand patients ( Table 2) ; studies suggest that superficial fungal infections and psoriasis confer vulnerability to COVID-19; a body mass index (BMI) > 40 kg/m2 is an independent risk factor for complications from the infection; and there are discouraging results regarding underlying neurological disease and SARS-CoV-2. It is even possible that such disease-modifying therapies and their immunosuppressive effect may play a protective role during 19-COVID infection by preventing or dampening hyperimmune activity that, in some cases, could lead to clinical deterioration; there is even a report of a patient with primary progressive multiple sclerosis receiving treatment with ocrelizumab and becoming infected with SARS-CoV-2, in the context of lymphopenia and hypogammaglobulinema expected for this type of treatment, without generating major clinical complications, this hypothesis is obviously limited for now only to academic deductions and limited information. abstract: Background It is not clear whether patients with some degree of immunosuppression have worse outcomes in SARS-CoV-2 infection, compared to healthy people. Objective To carry out a narrative review of the information available on infection by SARS-CoV-2 in immunosuppressed patients, especially patients with cancer, transplanted, neurological diseases, primary and secondary immunodeficiencies. Results Patients with cancer and recent cancer treatment (chemotherapy or surgery) and SARS-CoV-2 infection have a higher risk of worse outcomes. In transplant patients (renal, cardiac and hepatic), with neurological pathologies (multiple sclerosis (MS), neuromyelitis optica (NMODS), myasthenia gravis (MG)), primary immunodeficiencies and infection with human immunodeficiency virus (HIV) in association with immunosuppressants, studies have shown no tendency for worse outcomes. Conclusion Given the little evidence we have so far, the behaviour of SARS-CoV-2 infection in immunosuppressed patients is unclear, but current studies have not shown worse outcomes, except for patients with cancer. url: https://api.elsevier.com/content/article/pii/S2173574320301295 doi: 10.1016/j.reumae.2020.08.001 id: cord-295257-iguhy1z8 author: Calcagnile, Matteo title: ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date: 2020-04-24 words: 4785.0 sentences: 253.0 pages: flesch: 49.0 cache: ./cache/cord-295257-iguhy1z8.txt txt: ./txt/cord-295257-iguhy1z8.txt summary: SARS-CoV-2 and respiratory syndrome corona virus (SARS-CoV) Spike proteins share very high phylogenetic similarities (99%), and, indeed, both viruses exploit the same human cell receptor namely angiotensin-converting enzyme 2 (ACE2), a transmembrane enzyme whose expression dominates on lung alveolar epithelial cells 6, 15, 16 . In this study we have used a combination of in silico tools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 Spike glycoprotein. Results indicate that some residues of the ACE2 interface, which are involved in the interaction with SARS-CoV-2 Spike glycoprotein can actually fluctuate (Fig. 5cd ). Indeed, in the rodent blockade of the renin-angiotensin-aldosterone system limits the acute lung injury induced by the SARS-CoV-1 spike protein 49 , suggesting that if ACE2 function is preserved (because of increased baseline expression, as especially seen in pre-menopausal women), clinical course of infection might be less severe. abstract: The current SARS covid-19 epidemic spread appears to be influenced by ethnical, geographical and sex-related factors that may involve genetic susceptibility to diseases. Similar to SARS-CoV, SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells, notably type II alveolar epithelial cells. Importantly, ACE2 gene is highly polymorphic. Here we have used in silico tools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 spike glycoprotein. We found that S19P (common in African people) and K26R (common in European people) were, among the most diffused SNPs worldwide, the only two SNPs that were able to potentially affect the interaction of ACE2 with SARS-CoV-2 spike. FireDock simulations demonstrated that while S19P may decrease, K26R might increase the ACE2 affinity for SARS-CoV-2 Spike. This finding suggests that the S19P may genetically protect, and K26R may predispose to more severe SARS-CoV-2 disease. url: https://doi.org/10.1101/2020.04.23.057042 doi: 10.1101/2020.04.23.057042 id: cord-316930-0s7k9guq author: Caldas, Lucio Ayres title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy date: 2020-09-30 words: 2901.0 sentences: 192.0 pages: flesch: 52.0 cache: ./cache/cord-316930-0s7k9guq.txt txt: ./txt/cord-316930-0s7k9guq.txt summary: title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2. At the same time, and with a MOI of 1, viruses that egressed from a previous cycle of infection were observed during the process of attachment to the cell plasma membrane ( Fig. 2A) . To approach SARS-CoV-2/cell interactions, we investigate several steps of virus infection in Vero cells at 2 and 48 hpi by SEM. These sites were appropriate to register the attachment of SARS-CoV-2 particles ( Fig. 2A ) similar to transmission electron microscopy images of the same early step of SARS-CoV infection of Vero cells 28 . Drastic vacuolization due to viral infection was previously described for other RNA viruses including SARS-CoV 20,32 . abstract: SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Here, we investigated the interaction of this new coronavirus with Vero cells using high resolution scanning electron microscopy. Surface morphology, the interior of infected cells and the distribution of viral particles in both environments were observed 2 and 48 h after infection. We showed areas of viral processing, details of vacuole contents, and viral interactions with the cell surface. Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32999356/ doi: 10.1038/s41598-020-73162-5 id: cord-272179-wvw5mmy3 author: Calderaro, Adriana title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 words: 1095.0 sentences: 70.0 pages: flesch: 53.0 cache: ./cache/cord-272179-wvw5mmy3.txt txt: ./txt/cord-272179-wvw5mmy3.txt summary: title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children abstract: OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. RESULTS: 474 samples (52.3%) were positive for at least one virus for a total of 583 viruses detected. Single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). RSV (138/583: 23.7%) and RV (130/583: 22.3%) were the most common viruses identified, followed by SARS-CoV2 (82/583: 14.1%). RSV predominates until February with 129 detections and drastically decreases in March to 9 detections. SARS-CoV-2 absent in our area until February 26, in just over a month reached 82 detections. SARS-CoV-2 was found in mixed infections only in 3 cases all observed in children younger than one year old. CONCLUSIONS: This study showed a completely different trend between SARS-CoV-2 and the "common" respiratory viruses that have seen children most affected without distinction of sex, as opposed to SARS-CoV-2 that have seen adult males the most infected. url: https://api.elsevier.com/content/article/pii/S1201971220321895 doi: 10.1016/j.ijid.2020.09.1473 id: cord-277640-vy7ex5lv author: Calderaro, Adriana title: SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date: 2020-05-14 words: 1171.0 sentences: 63.0 pages: flesch: 52.0 cache: ./cache/cord-277640-vy7ex5lv.txt txt: ./txt/cord-277640-vy7ex5lv.txt summary: The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. abstract: SARS-CoV-2 is emerged in China on December 2019 and now declared pandemic by WHO. We describe the case of an Italian 7-week-old suckling baby SARS-CoV-2-positive only by cell culture method with no clinical suspicion and/or risk factors of SARS-CoV-2 infection. The patient was referred to the hospital with signs and symptoms of infection of the upper respiratory tract before the virus was spread to the province. Nasal and pharyngeal swabs and a nasopharyngeal aspirate were used for conventional and molecular diagnostic assays not including SARS-CoV-2 virus. Bacteria referred to resident population were revealed in nasal and pharyngeal swabs. No viruses were detected using both immunofluorescence assay and nucleic acid amplification assays in the nasopharyngeal aspirate. The baby was discharged in good conditions after 3 days of hospitalization. Later a cytopathic effect on the cell monolayers currently used for respiratory viruses was observed and the viral particles were identified as Coronaviridae by transmission electron microscopy. SARS-CoV-2 was identified by RT-PCR performed both on cell culture and on the stored aliquot of the original sample. The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. url: https://api.elsevier.com/content/article/pii/S1201971220303428 doi: 10.1016/j.ijid.2020.05.035 id: cord-280671-0b1qcdwk author: Calderone, Alba title: Selective Estrogen Receptor Modulators in COVID-19: A Possible Therapeutic Option? date: 2020-07-15 words: 1555.0 sentences: 82.0 pages: flesch: 37.0 cache: ./cache/cord-280671-0b1qcdwk.txt txt: ./txt/cord-280671-0b1qcdwk.txt summary: In particular, susceptibility to SARS-CoV-2 infection is almost similar in both genders, but higher severity and mortality are observed in male patients (Wenham et al., 2020) . The previous severe acute respiratory syndromes caused by SARS-CoV and MERS-CoV were often associated with rapid viral replication, huge infiltration of inflammatory cells, and excessive production of proinflammatory cytokines (cytokine storm syndrome), leading to lung injury and respiratory distress syndrome . Moreover, pro-inflammatory cytokines, including IL-1b and IL-6, are directly induced by SARS-CoV-2 by interaction between viral components (probably nucleocapsid proteins) and toll like receptors of the host cells. Besides their potential effects on proinflammatory cytokine expression (mediated by ERs), some SERMs seem to play broader roles in inhibiting viral replication by ER-independent mechanisms. Anti-inflammatory effect of selective estrogen receptor modulators (SERMs) in microglial cells abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32765279/ doi: 10.3389/fphar.2020.01085 id: cord-320063-n9qzbnup author: Calender, Alain title: Modeling Potential Autophagy Pathways in COVID-19 and Sarcoidosis date: 2020-08-10 words: 1595.0 sentences: 75.0 pages: flesch: 34.0 cache: ./cache/cord-320063-n9qzbnup.txt txt: ./txt/cord-320063-n9qzbnup.txt summary: Of note, SARS-CoV2 protein has a high affinity for human ACE2, a membrane-bound peptidase highly expressed in the heart, lungs, digestive and renal tracts; this molecular interaction leads to a membrane fusion process and further formation of syncytia with multinucleated alveolar epithelial cells ( Figure 1 ) [7] . Different cellular receptors such as TLR3 (Toll Like Receptor 3) and RIG-1 (Retinoic Acid Inducible Gene 1) -closely related to autophagy activation in mammalian granulocyte and macrophage models -have been implicated in innate immunity response to RNA virus infections -e.g. Coronavirus, Measles, Hepatitis viruses, and Influenza virus [10] . These clinical observations raise the question of what the sensitivity of patients with sarcoidosis to respiratory viral disease is, such as that induced from SARS-CoV2 infection (COVID-19)presently being explored in several international projects [6] . abstract: ABSTRACT COVID-19 is a disease caused by coronavirus SARS-CoV2, mainly affecting the lungs. Sarcoidosis is an autoinflammatory disease characterized by the diffusion of granulomas in lung and other organs. Here, we discuss how the two diseases might involve some common mechanistic cellular pathways around the regulation of autophagy. url: https://www.sciencedirect.com/science/article/pii/S1471490620301782?v=s5 doi: 10.1016/j.it.2020.08.001 id: cord-328064-7owd28rr author: Callahan, Cody J. title: Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck date: 2020-07-23 words: 4879.0 sentences: 258.0 pages: flesch: 51.0 cache: ./cache/cord-328064-7owd28rr.txt txt: ./txt/cord-328064-7owd28rr.txt summary: We tested PCR compatibility by placing the swab head-downward after breaking it off at the break point, when present (as in a typical NP swab collection), in 3 ml of modified CDC VTM (Hanks'' balanced salt solution containing 2% heat-inactivated fetal bovine serum [FBS], 100 g/ml gentamicin, 0.5 g/ml amphotericin B [Fungizone], and 10 mg/liter phenol red [15] ) overnight to allow any PCR-inhibitory material to leach into the medium, spiking 1.5 ml with 200 copies/ml of control SARS-CoV-2 amplicon target (representing 2 times the limit of detection on our system), vortexing, and testing using the Abbott RealTime SARS-CoV-2 assay on an Abbott m2000 RealTime system platform (16) , following the same protocol as for clinical testing (37 cycles, with a cycle threshold [C T ] of Յ31.50 being reported as positive). Control and prototype swabs were placed in separate vials of VTM and transported to the BIDMC Clinical Microbiology Laboratories, where each sample was tested on the Abbott m2000 SARS-CoV-2 RT-PCR platform per the standard clinical protocol. abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a severe international shortage of the nasopharyngeal swabs that are required for collection of optimal specimens, creating a critical bottleneck blocking clinical laboratories’ ability to perform high-sensitivity virological testing for SARS-CoV-2. To address this crisis, we designed and executed an innovative, cooperative, rapid-response translational-research program that brought together health care workers, manufacturers, and scientists to emergently develop and clinically validate new swabs for immediate mass production by 3D printing. We performed a multistep preclinical evaluation of 160 swab designs and 48 materials from 24 companies, laboratories, and individuals, and we shared results and other feedback via a public data repository (http://github.com/rarnaout/Covidswab/). We validated four prototypes through an institutional review board (IRB)-approved clinical trial that involved 276 outpatient volunteers who presented to our hospital’s drive-through testing center with symptoms suspicious for COVID-19. Each participant was swabbed with a reference swab (the control) and a prototype, and SARS-CoV-2 reverse transcriptase PCR (RT-PCR) results were compared. All prototypes displayed excellent concordance with the control (κ = 0.85 to 0.89). Cycle threshold (C(T)) values were not significantly different between each prototype and the control, supporting the new swabs’ noninferiority (Mann-Whitney U [MWU] test, P > 0.05). Study staff preferred one of the prototypes over the others and preferred the control swab overall. The total time elapsed between identification of the problem and validation of the first prototype was 22 days. Contact information for ordering can be found at http://printedswabs.org. Our experience holds lessons for the rapid development, validation, and deployment of new technology for this pandemic and beyond. url: https://www.ncbi.nlm.nih.gov/pubmed/32393482/ doi: 10.1128/jcm.00876-20 id: cord-346389-gbmnoo84 author: Callender, Lauren A. title: The Impact of Pre-existing Comorbidities and Therapeutic Interventions on COVID-19 date: 2020-08-11 words: 10042.0 sentences: 514.0 pages: flesch: 40.0 cache: ./cache/cord-346389-gbmnoo84.txt txt: ./txt/cord-346389-gbmnoo84.txt summary: Here, we review immune dysfunction in response to SARS-CoV-2 infection and the impact of pre-existing comorbidities on the development of COVID-19. Furthermore, cardiovascular complications such as thromboembolic events, myocarditis, acute coronary syndrome, arrythmia, cardiogenic shock and heat failure, have been documented in COVID-19 patients without prior cardiovascular disease (71), demonstrating a significant impact of SARS-CoV-2 infection on the heart. As infection with SARS-CoV-2 results in an acute respiratory disease that can progress to ARDS, respiratory failure and potentially even death, it is reasonable to speculate that patients with pre-existing respiratory disease would be at increased risk of severe COVID-19. Consequently, it has been proposed that liver damage associated with severe COVID-19 patients is due to dysregulated innate immunity against SARS-CoV-2, or hepatoxicity in response to treatments, rather than pre-existing liver disease. Therefore, the underlying pathogenesis of chronic kidney disease may increase vulnerability to hyperinflammation and cytokine storm upon SARS-CoV-2 infection, resulting in severe COVID-19. abstract: Evidence from the global outbreak of SARS-CoV-2 has clearly demonstrated that individuals with pre-existing comorbidities are at a much greater risk of dying from COVID-19. This is of great concern for individuals living with these conditions, and a major challenge for global healthcare systems and biomedical research. Not all comorbidities confer the same risk, however, many affect the function of the immune system, which in turn directly impacts the response to COVID-19. Furthermore, the myriad of drugs prescribed for these comorbidities can also influence the progression of COVID-19 and limit additional treatment options available for COVID-19. Here, we review immune dysfunction in response to SARS-CoV-2 infection and the impact of pre-existing comorbidities on the development of COVID-19. We explore how underlying disease etiologies and common therapies used to treat these conditions exacerbate COVID-19 progression. Moreover, we discuss the long-term challenges associated with the use of both novel and repurposed therapies for the treatment of COVID-19 in patients with pre-existing comorbidities. url: https://www.ncbi.nlm.nih.gov/pubmed/32903476/ doi: 10.3389/fimmu.2020.01991 id: cord-279346-7del8d2p author: Callendret, Benoît title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 words: 10731.0 sentences: 471.0 pages: flesch: 49.0 cache: ./cache/cord-279346-7del8d2p.txt txt: ./txt/cord-279346-7del8d2p.txt summary: title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared. abstract: The SARS-CoV spike glycoprotein (S) is the main target of the protective immune response in humans and animal models of SARS. Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). The presence of both splice sites and WPRE markedly improved the immunogenicity of S-based DNA vaccines against SARS. Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. Our observations are likely to be useful for the construction of plasmid and viral vectors designed for optimal expression of intronless genes derived from cytoplasmic RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17331558/ doi: 10.1016/j.virol.2007.01.012 id: cord-257600-0plhquk9 author: Calles, Antonio title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 words: 6981.0 sentences: 353.0 pages: flesch: 47.0 cache: ./cache/cord-257600-0plhquk9.txt txt: ./txt/cord-257600-0plhquk9.txt summary: Differences in health-care systems, in the incidence and prevalence of SARS-CoV-2 infection by geographic regions, and patient access to intensive support care -including MVand treatment with antivirals or anti-IL6/IL1 agents may ultimately influence outcomes in patients with lung cancer affected by COVID-19. We aimed to describe the clinical characteristics of lung cancer patients with COVID-19 attended in a tertiary hospital in Madrid, one of the most hit regions by coronavirus in the world so far, and analyze factors associated with worse outcome, including type of treatment receiving at the time of COVID-19 diagnosis. We performed SARS-CoV-2 RT-PCR to every suspicious case and included all lung cancer patients attended at our hospital (emergency room, hospitalization, ambulatory office, day care area). Data from Wuhan, in China, showed that active cancer treatment received in the 14 days before SARS-CoV-2 infection had an increase on the risk of severe outcomes of COVID-19 (HR 4.079, 95%CI, 1.086-15.322; p = 0.037) (9) . abstract: Background: Cancer patients represent a vulnerable population for COVID-19 illness. We aimed to analyze outcomes of lung cancer patients affected by COVID-19 in a tertiary hospital of a high-incidence region during the pandemic. Methods: We annotated 23 lung cancer patients consecutively diagnosed with COVID-19 at our institution (HGUGM; Madrid, Spain) between March 4th, 2020 and May 12th, 2020. Only patients with a confirmatory SARS-CoV-2 RT-PCR were included in the study. Results: All patients had at least 1 COVID-19 related symptom; cough (48%), shortness of breath (48%), fever (39%), and low-grade fever (30%) were the most common. Time from symptoms onset to first positive SARS-CoV-2 PCR was 5.5 days (range 1–17), with 13% of cases needed from a 2nd PCR to confirm diagnosis. There was a high variability on thoracic imaging findings, with multilobar pneumonia as the most commonly found pattern (74%). Main lab test abnormalities were low lymphocytes count (87%), high neutrophil to lymphocyte ratio -NLR- (78%), and elevated inflammatory markers: fibrinogen (91%), c-reactive protein -CRP- (87%), and D-dimer (70%). In our series, hospitalization rate was 74%, 39% of patients developed acute respiratory distress syndrome (ARDS), and the case-fatality rate was 35% (8/23). 87% of patients received anti-viral treatment (87% hydroxychloroquine, 74% lopinavir/ritonavir, 13% azithromycin), 43% corticosteroids, 26% interferon-β, 4% tocilizumab, and 82% of hospitalized patients received anticoagulation. High-oxygen requirements were needed in 39% of patients, but only 1 pt was admitted for invasive MV and was discharged 42 days after admission. Multiple variables related to tumor status, clinical baseline conditions, and inflammation markers were associated with mortality but did not remain statistically significant in a multivariate model. In patients with lung cancer receiving systemic therapy (n = 242) incidence and mortality from COVID-19 were 4.5, and 2.1%, respectively, with no differences found by type of treatment. Conclusions: Lung cancer patients represent a vulnerable population for COVID-19, according to the high rate of hospitalization, onset of ARDS, and high mortality rate. Although larger series are needed, no differences in mortality were found by type of cancer treatment. Measures to minimize the risk of SARS-CoV-2 infection remain key to protect lung cancer patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33042826/ doi: 10.3389/fonc.2020.01777 id: cord-278678-ivye1qao author: Calvez, R. M. title: Molecular detection of SARS-CoV-2 using a reagent-free approach date: 2020-05-02 words: 3223.0 sentences: 186.0 pages: flesch: 55.0 cache: ./cache/cord-278678-ivye1qao.txt txt: ./txt/cord-278678-ivye1qao.txt summary: Optimisation of the heat-treatment method and inhibitory properties of UTM In a preliminary study to evaluate the best assay conditions, a range of SARS-CoV-2-positive and negative samples was selected and heat-treated at different temperatures and for different times. Each heat-treated sample was then subject to SARS-CoV-2 testing using our in-house assay derived from the CDC resource website (targeting the N-gene and using the TaqMan® Fast Virus 1-Step RT-qPCR kit from ABI). As shown in table 2 below, the ABI TaqMan® One-Step RT-qPCR mix systematically failed to detect SARS-CoV-2 in swab samples resuspended in UTM (COPAN swabs) even in the presence of viral loads greater than 1×10 6 copies/mL (003850 and 003862). Although heat-treatment of respiratory samples prior to RT-qPCR showed an attractive methodology compared to a conventional nucleic acid extraction method, the addition of an internal control is critical for quality control and successful detection of this virus if present in the patient samples. abstract: Shortage of reagents and consumables required for the extraction and molecular detection of SARS-CoV-2 RNA in respiratory samples has led many laboratories to investigate alternative approaches for sample preparation. Fomsgaard et al 2020 recently presented results using heat-processing of respiratory samples prior to RT-qPCR as an economical method enabling an extremely fast streamlining of the processes at virtually no cost. Here, we present our results using this method and highlight some major pitfalls that diagnostics laboratories should be aware of before proceeding with this technique. We first investigated various treatments using different temperatures, incubation times and sample volumes based on the above study to optimise the heat-treatment conditions. Although the initial data confirmed the published results, further investigations revealed unexpected inhibitory properties of some commonly used virus transport media (VTMs) on some commercially available RT-qPCR mixes, emphasising the critical importance of a thorough validation process to determine the most adapted reagents to be used depending on the sample types to be tested. In conclusion, although the method works, with very consistent Ct values and an excellent sensitivity when compared to a conventional RNA extraction method, it is critical to include an internal control to check each sample for potential inhibition. url: https://doi.org/10.1101/2020.04.28.20083626 doi: 10.1101/2020.04.28.20083626 id: cord-354407-zzxjv666 author: Campanacci, Valérie title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 words: 2338.0 sentences: 137.0 pages: flesch: 60.0 cache: ./cache/cord-354407-zzxjv666.txt txt: ./txt/cord-354407-zzxjv666.txt summary: title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. The crystal structure of the main (or 3CL) protease of transmissible gastroenteritis virus, a related coronavirus, has been determined and was used to construct a model of the SARS-CoV 3CL protease, facilitating future drug design against this important target (Anand et al., 2003) . In the related mouse hepatitis virus, which is a group 2 coronavirus, the SARS-CoV Nsp9 corresponds to a 12 kDa cleavage product (P1a-12) that is found preferentially in the perinuclear region of infected cells, where it co-localizes with other components of the viral replication complex (Bost et al., 2000) . abstract: The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS‐CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS‐CoV whole‐genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5 kbp in length, the largest of the known RNA viruses, and encode 20–30 mature proteins. The functions of many of these polypeptides, including the Nsp9–Nsp10 replicase‐cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS‐CoV Nsp9 protein, the first SARS‐CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8 Å resolution and belong to space group P6(1/5)22, with unit‐cell parameters a = b = 89.7, c = 136.7 Å. With two molecules in the asymmetric unit, the solvent content is 60% (V (M) = 3.1 Å(3) Da(−1)). url: https://www.ncbi.nlm.nih.gov/pubmed/12925794/ doi: 10.1107/s0907444903016779 id: cord-270049-54t3w94z author: Campione, Elena title: Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date: 2020-08-17 words: 2029.0 sentences: 113.0 pages: flesch: 53.0 cache: ./cache/cord-270049-54t3w94z.txt txt: ./txt/cord-270049-54t3w94z.txt summary: We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. 222 We performed the same analysis over the evaluated human lactoferrin (hLF)-Spike complex, 223 obtaining a binding pose superimposable to that observed for the bovine protein (Fig. 5B) . Clinical trial 397 We performed a randomized, prospective, interventional study to assess the efficacy of a liposomal Blood parameters obtained at T0 in COVID-19 group and control group were compared using t-test. abstract: The current treatments against SARS-CoV-2 have proved so far inadequate. A potent antiviral drug is yet to be discovered. Lactoferrin, a multifunctional glycoprotein, secreted by exocrine glands and neutrophils, possesses an antiviral activity extendable to SARS-Cov-2. We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. Lactoferrin induced an early viral clearance and a fast clinical symptoms recovery in addition to a statistically significant reduction of D-Dimer, Interleukin-6 and ferritin blood levels. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. Lactoferrin can be used as a safe and efficacious natural agent to prevent and treat COVID-19 infection. url: https://doi.org/10.1101/2020.08.11.244996 doi: 10.1101/2020.08.11.244996 id: cord-301590-70qmpccs author: Campos, António title: The Paradigm Shift of Ophthalmology in the COVID-19 Era date: 2020-09-14 words: 3010.0 sentences: 164.0 pages: flesch: 52.0 cache: ./cache/cord-301590-70qmpccs.txt txt: ./txt/cord-301590-70qmpccs.txt summary: CONCLUSION: It was possible to keep the ophthalmological activity during the pandemic outbreak due to the existence of a pre-scheduled fixed regimen for IVI and to the availability of personal protective equipment. We are facing a different sort of challenge now: how to accommodate the usual huge number of patients previous to the COVID-19 outbreak in the waiting rooms, while respecting the new demands from the healthcare authorities to reduce the number of waiting patients to a half or one-third. 9 Issues such as the use of personal protective equipment, the size of waiting rooms, ventilation, adherence to disinfection protocols, choose of whom to treat based on the disease natural evolution and the need to prioritize treatment visits over monitoring visits, were addressed recently. Symptomatic patients, SARS-CoV-2 positive patients and contacts, were postponed until they were RT-PCR negative, except for emergency surgeries that were performed in a COVID-dedicated OR (one room with negative pressure and special requirements 12 abstract: OBJECTIVE: To describe how a fixed regimen of intravitreal injections (IVI) was helpful to continue activity during the COVID-19 outbreak and lockdown and to address basic conditions to resume activity. METHODS: A fixed regimen of IVI was conceived to significantly reduce the number of visits while keeping a number of injections related to the best outcomes. We retrospectively collected data of surgeries performed in 2019 and in the first seven months of 2020 and from OCTs in the first semester of 2020. RESULTS: IVI per month, from January to July 2020, were 304, 291, 256, 204, 276, 297 and 322, respectively. Phacoemulsification surgeries in the same period were 397, 408, 171, 0, 304, 391 and 389. Posterior vitrectomies were 23, 21, 17, 10, 21, 28 and 25. Laser sessions were 44, 26, 33, 17, 23 and 33, respectively. OCTs dropped from a mean of 25.7 per day in the first half of March 2020 to 5.8 per day in the second half of March. A mean of 6.5 OCTs per day was made in April, rising to 19.1 in May and 39.5 in June. CONCLUSION: It was possible to keep the ophthalmological activity during the pandemic outbreak due to the existence of a pre-scheduled fixed regimen for IVI and to the availability of personal protective equipment. The air-borne nature of the peril we are facing addresses the need to evaluate the physical conditions of health facilities, including ventilation, size of waiting and consult rooms and the need to avoid elevators. url: https://doi.org/10.2147/opth.s267427 doi: 10.2147/opth.s267427 id: cord-331465-humpwwk2 author: Canaday, David H title: On setting expectations for a SARS-CoV-2 Vaccine date: 2020-06-04 words: 997.0 sentences: 67.0 pages: flesch: 45.0 cache: ./cache/cord-331465-humpwwk2.txt txt: ./txt/cord-331465-humpwwk2.txt summary: Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials abstract: The global coronavirus pandemic is unlike any other since 1918. A century of dramatic medical advances has produced a public expectation that the medical field will rapidly provide solutions to restore normalcy. In under 6 months, since SARS-CoV-2 was identified, the massive international effort to develop a SARS-CoV-2 vaccine has generated more than 140 vaccines in different stages of development with 9 already recruiting into clinical trials posted on clinicaltrials.gov. The long-term strategy to handle COVID-19 will almost certainly rely on vaccines. But, what type of protection can we realistically expect to achieve from vaccines and when? url: https://doi.org/10.1093/cid/ciaa726 doi: 10.1093/cid/ciaa726 id: cord-278106-ev1nx60h author: Cancarevic, Ivan title: Coronavirus Disease 2019 (COVID-19) in Cancer Patients date: 2020-04-26 words: 2479.0 sentences: 130.0 pages: flesch: 50.0 cache: ./cache/cord-278106-ev1nx60h.txt txt: ./txt/cord-278106-ev1nx60h.txt summary: The Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the most talked-about clinical entity in early 2020. Management presents its own set of challenges, including but not limited to, deciding whether postponing cancer treatment until the infection resolves is going to benefit the patient and how to organize all aspects of patient care when social contact is as limited as it is for patients newly diagnosed with COVID-19. found that the prevalence of cancer among patients infected with SARS-CoV-2 (COVID-19) was higher than in the general population [12] . We would strongly encourage clinicians to keep reporting any cases of cancer patients infected with SARS-CoV-2, their management, and the outcome in order to further our understanding of this complex issue. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges The treatment and outcome of a lung cancer patient infected with SARS-CoV-2 abstract: The Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the most talked-about clinical entity in early 2020. As an infection that spreads easily and has a significant mortality rate, it has caused global panic rarely seen before. Many of the measures taken by governments worldwide will have long-lasting impacts on the wellbeing of the population at large. It has been widely reported that the most vulnerable patients have been most negatively affected by SARS-CoV-2 (COVID-19). In this study, we have tried to search the currently available data on the outcomes of infected cancer patients. Most of the data points to the very challenging nature of treating such patients. Their overall outcomes seem to be worse than in the general population, and it may be difficult to differentiate which potential complications are a result of the primary oncologic disease versus the infection. Management presents its own set of challenges, including but not limited to, deciding whether postponing cancer treatment until the infection resolves is going to benefit the patient and how to organize all aspects of patient care when social contact is as limited as it is for patients newly diagnosed with COVID-19. We believe that as more data becomes available, it is going to be necessary to publish detailed guidelines on how to approach this unique clinical challenge. url: https://doi.org/10.7759/cureus.7835 doi: 10.7759/cureus.7835 id: cord-265262-r01u4jr6 author: Cannarella, Rossella title: Systemic effects of the hormonal treatment of male hypogonadism with preliminary indications for the management of COVID-19 patients date: 2020-10-13 words: 8737.0 sentences: 471.0 pages: flesch: 47.0 cache: ./cache/cord-265262-r01u4jr6.txt txt: ./txt/cord-265262-r01u4jr6.txt summary: Furthermore, recent findings on novel coronavirus disease (COVID-19) epidemiology have shown a greater mortality in male compared with female patients and a role of T in promoting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection of the host cells has been demonstrated. To accomplish the aims of the study, we performed a search on PubMed, Scopus, Ovid and Science Direct, and the following keywords were used: hypogonadism, TD, TRT, blood pressure, hypertension, ischemic heart disease, heart failure, stroke, obesity, insulin, diabetes, metabolic disorders, prostatic hyperplasia, prostate cancer, COVID-19, and SARS-CoV2. 45 In 2017, a meta-analysis including 39 randomized controlled trials (RCTs) and 10 observational studies with a total of about 5500 patients did not find any significant association between TRT and myocardial infarction, stroke, or mortality, even if the quality of the evidence was low. abstract: Male hypogonadism, defined as an inadequate production of testosterone (T), is associated with a greater morbidity and mortality. Epidemiological studies identified T deficiency as a risk factor for cardiovascular disease. Also, low serum T levels impact on glucose homeostasis through a worse glucose uptake, utilization, and disposal, and the general negative impact on metabolism. The aim of this review is to provide a comprehensive and updated overview of the effects of T replacement therapy on metabolic and cardiovascular systems and prostate tissue in patients with hypogonadism, including molecular mechanisms through which T exerts its actions. Furthermore, recent findings on novel coronavirus disease (COVID-19) epidemiology have shown a greater mortality in male compared with female patients and a role of T in promoting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection of the host cells has been demonstrated. Hence, the secondary aim of this review is to provide preliminary indications on the management in patients with COVID-19. url: https://doi.org/10.1177/2042018820966438 doi: 10.1177/2042018820966438 id: cord-203232-1nnqx1g9 author: Canturk, Semih title: Machine-Learning Driven Drug Repurposing for COVID-19 date: 2020-06-25 words: 5023.0 sentences: 257.0 pages: flesch: 52.0 cache: ./cache/cord-203232-1nnqx1g9.txt txt: ./txt/cord-203232-1nnqx1g9.txt summary: Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. abstract: The integration of machine learning methods into bioinformatics provides particular benefits in identifying how therapeutics effective in one context might have utility in an unknown clinical context or against a novel pathology. We aim to discover the underlying associations between viral proteins and antiviral therapeutics that are effective against them by employing neural network models. Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Model training excluded SARS-CoV-2 proteins and included only Phases II, III, IV and Approved level drugs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. Our results suggest multiple drug candidates, some of which complement recent findings from noteworthy clinical studies. Our in-silico approach to drug repurposing has promise in identifying new drug candidates and treatments for other viruses. url: https://arxiv.org/pdf/2006.14707v1.pdf doi: nan id: cord-309319-si5c14e8 author: Cao, Chunxiang title: Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China date: 2016-08-15 words: 4693.0 sentences: 255.0 pages: flesch: 44.0 cache: ./cache/cord-309319-si5c14e8.txt txt: ./txt/cord-309319-si5c14e8.txt summary: Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The Bayesian Maximum Entropy (BME) approach of modern geostatistics incorporates higher-order statistical estimation for space-time epidemic phenomena and has shown more accurate mapping results than those derived from linear kriging geostatistics [19] . BME provides an effective stochastic method, based on a cogent theoretical and technological strategy, to analyze relationships of SARS outbreaks in the composite space-time domain. (2) BME considers spatial heterogeneity in SARS outbreaks, which broadens the traditional epidemic research field from the temporal to space-time domain. In the case of the SARS outbreaks, we used the observations to explore general structural characteristics of the SARS S/TRF, that is, the existence of mean (or surface) trends in the space-time domain, and to explore the underlying temporal and spatial structure of the S/TRF with suitable covariance functions. abstract: Severe acute respiratory syndrome (SARS) is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/27597972/ doi: 10.1155/2016/7247983 id: cord-326427-06djb0sd author: Cao, Dongmei title: Vaginal delivery in women with COVID-19: report of two cases date: 2020-10-02 words: 2582.0 sentences: 148.0 pages: flesch: 52.0 cache: ./cache/cord-326427-06djb0sd.txt txt: ./txt/cord-326427-06djb0sd.txt summary: Because of the positive result of the maternal swabs for SARS-CoV-2 obtained on the 2nd day after sampling, we transferred the mother to the designated hospital and followed up with her by telephone interviews. Although the nucleic acid test for SARS-CoV-2 of the second patient was negative on February 29, the result was positive Delayed cord clamping and skin-to-skin contact between the mother and infant were not permitted in either case. The pregnant woman in case 2 had the typical manifestations of COVID-19, including cough, lymphopenia, and abnormal chest CT images, and her infant''s nasopharyngeal swab tested negative for SARS-CoV-2. The two cases in our study showed that there is still insufficient evidence supporting maternal-fetal vertical transmission of COVID-19 in late pregnancy, and there is no evidence that vaginal delivery would increase the possibility of neonatal infection. In conclusion, there is still insufficient evidence supporting maternal-fetus vertical transmission of COVID-19 for pregnant women in late pregnancy, and vaginal delivery may not increase the possibility of neonatal infection. abstract: BACKGROUND: During the ongoing global outbreak of COVID-19, pregnant women who are susceptible to COVID-19 should be highly concerned. The issue of vertical transmission and the possibility of neonatal infection is a major concern. CASE PRESENTATION: Case 1: A 35-year-old pregnant woman with a gestational age of 37 weeks and 6 days was admitted to our hospital at the point of giving birth. Except for the abnormalities in her chest CT image, she was asymptomatic. She had an uncomplicated spontaneous vaginal delivery, and her infant was discharged home for isolation. Because of the positive result of the maternal swabs for SARS-CoV-2 obtained on the 2nd day after sampling, we transferred the mother to the designated hospital and followed up with her by telephone interviews. Luckily, it was confirmed on February 23 that the newborn did not develop any COVID-19 symptoms after observation for 14 days after birth. Case 2: Another pregnant woman, with a gestational age of 38 weeks and 2 days, was also admitted to our hospital because of spontaneous labor with cervical dilation of 5 cm. Since she had the typical manifestations of COVID-19, including cough, lymphopenia, and abnormal chest CT images, she was highly suspected of having COVID-19. Based on the experience from case 1, we helped the mother deliver a healthy baby by vaginal delivery. On the 2nd day after delivery, the maternal nasopharyngeal swab result was positive, while the infant’s result was negative. CONCLUSION: There is still insufficient evidence supporting maternal-fetal vertical transmission for COVID-19-infected mothers in late pregnancy, and vaginal delivery may not increase the possibility of neonatal infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33008308/ doi: 10.1186/s12884-020-03281-4 id: cord-273613-cpiveo7j author: Cao, Xia title: Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date: 2020-09-29 words: 3505.0 sentences: 178.0 pages: flesch: 46.0 cache: ./cache/cord-273613-cpiveo7j.txt txt: ./txt/cord-273613-cpiveo7j.txt summary: Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Affinity maturation of STI-1499 resulted in identification of STI-2020, an antibody with a 35-fold increased affinity for the SARS-CoV-2 Spike receptor-binding domain (RBD) leading to a greater than 50-fold increase in virus neutralization potency against live WA-1/2020 and 2020001 viruses in vitro. In this study, we detail the initial discovery and profiling of a SARS-CoV-2 nAb isolated from a phage display antibody library derived from the B-cell repertoire of over 600 healthy normal individuals. Candidate nAbs were characterized for binding of Spike S1 subunit and neutralization of related clinical SARS-CoV-2 isolates. abstract: SARS-CoV-2 neutralizing antibodies represent an important component of the ongoing search for effective treatment of and protection against COVID-19. We report here on the use of a naïve phage display antibody library to identify a panel of fully human SARS-CoV-2 neutralizing antibodies. Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Both antibodies demonstrated potent protection against the pathogenic effects of the disease and a dose-dependent reduction of virus load in the lungs, reaching undetectable levels following a single dose of 500 micrograms of STI-2020. These data support continued development of these antibodies as therapeutics against COVID-19 and future use of this approach to address novel emerging pandemic disease threats. url: https://doi.org/10.1101/2020.09.27.316174 doi: 10.1101/2020.09.27.316174 id: cord-347030-yx3j6373 author: Cao, Xuetao title: COVID-19: immunopathology and its implications for therapy date: 2020-04-09 words: 1519.0 sentences: 74.0 pages: flesch: 35.0 cache: ./cache/cord-347030-yx3j6373.txt txt: ./txt/cord-347030-yx3j6373.txt summary: Most patients with COVID-19 exhibit mild to moderate symptoms, but approximately 15% progress to severe pneumonia and about 5% eventually develop acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure 1, 2 . Convalescent plasma containing neutralizing antibodies has been used to treat a small number of patients with severe disease, and preliminary results show clinical improvement in 5 of 5 critically ill patients with COVID-19 who developed ARDS 8 . High levels of pro-inflammatory cytokines may lead to shock and tissue damage in the heart, liver and kidney, as well as respiratory failure COVID-19: immunopathology and its implications for therapy Xuetao Cao 1, 2 Severe coronavirus disease 2019 (COVID-19) is characterized by pneumonia, lymphopenia, exhausted lymphocytes and a cytokine storm. In addition to the cytokine-based pathology in patients with severe COVID-19, complement activation has also been observed, indicating that complement inhibitors, if used at an early stage of the infection, may attenuate the inflammatory damage. abstract: Severe coronavirus disease 2019 (COVID-19) is characterized by pneumonia, lymphopenia, exhausted lymphocytes and a cytokine storm. Significant antibody production is observed; however, whether this is protective or pathogenic remains to be determined. Defining the immunopathological changes in patients with COVID-19 provides potential targets for drug discovery and is important for clinical management. url: https://www.ncbi.nlm.nih.gov/pubmed/32273594/ doi: 10.1038/s41577-020-0308-3 id: cord-348713-tucolje2 author: Cao, Yanan title: Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations date: 2020-02-24 words: 1570.0 sentences: 79.0 pages: flesch: 48.0 cache: ./cache/cord-348713-tucolje2.txt txt: ./txt/cord-348713-tucolje2.txt summary: Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations Yanan Cao 1 , Lin Li 1 , Zhimin Feng 1 , Shengqing Wan 1 , Peide Huang 1 , Xiaohui Sun 1 , Fang Wen 1 , Xuanlin Huang 1 , Guang Ning 1 and Weiqing Wang 1 Therefore, genetic analysis of expression quantitative trait loci (eQTLs) 8 and potential functional coding variants in ACE2 among populations are required for further epidemiological investigations of 2019-nCoV/SARS-CoV-2 spreading in East Asian (EAS) and other populations. To systematically investigate the candidate functional coding variants in ACE2 and the allele frequency (AF) differences between populations, we analyzed all the 1700 variants (Supplementary Table S1) in ACE2 gene region from the ChinaMAP (China Metabolic Analytics Project, under reviewing) and 1KGP (1000 Genomes Project) 9 databases. abstract: nan url: https://doi.org/10.1038/s41421-020-0147-1 doi: 10.1038/s41421-020-0147-1 id: cord-277491-q18b88lm author: Cao, Ying-Li title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date: 2011-02-11 words: 3988.0 sentences: 210.0 pages: flesch: 53.0 cache: ./cache/cord-277491-q18b88lm.txt txt: ./txt/cord-277491-q18b88lm.txt summary: title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus Nucleocapsid (N) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a major pathological determinant in the host that may cause host cell apoptosis, upregulate the proinflammatory cytokine production, and block innate immune responses. In the current study, we compared the N gene sequences derived from 16 different isolates of SARS-CoV and selected three novel siRNA targeting sites in the N gene, including one targeting the 3'' terminus of the gene. Overall, the above results provide strong evidence to show that all three novel siRNAs (si-N213, si-N863 and si-N1240) are specific and effective inhibitors to block the isolated SARS-CoV N gene expression. Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles Small interfering RNA effectively inhibits the expression of SARS coronavirus membrane gene at two novel targeting sites abstract: Nucleocapsid (N) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a major pathological determinant in the host that may cause host cell apoptosis, upregulate the proinflammatory cytokine production, and block innate immune responses. Therefore, N gene has long been thought an ideal target for the design of small interference RNA (siRNA). siRNA is a class of small non-coding RNAs with a size of 21-25nt that functions post-transcriptionally to block targeted gene expression. In this study, we analyzed the N gene coding sequences derived from 16 different isolates, and found that nucleotide deletions and substitutions are mainly located at the first 440nt sequence. Combining previous reports and the above sequence information, we create three novel siRNAs that specifically target the conserved and unexploited regions in the N gene. We show that these siRNAs could effectively and specifically block the isolated N gene expression in mammal cells. Furthermore, we provide evidence to show that N gene can effectively up-regulate M gene mediated interferon β (IFNβ) production, while blocking N gene expression by specific siRNA significantly reduces IFNβ gene expression. Our data indicate that the inhibitory effect of siRNA on the isolated N gene expression might be influenced by the sequence context around the targeted sites. url: https://doi.org/10.3390/molecules16021544 doi: 10.3390/molecules16021544 id: cord-272986-ebgusf3o author: Cao, Yipeng title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date: 2020-05-17 words: 4339.0 sentences: 267.0 pages: flesch: 56.0 cache: ./cache/cord-272986-ebgusf3o.txt txt: ./txt/cord-272986-ebgusf3o.txt summary: title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel. We tried to use potential mean force (PMF) to reveal the permeability of different physiological ions and water molecules in the pores of the E protein pentamer. Figure 3A shows the PMF of ions and water molecules permeating through the SARS-CoV-2 E protein pentamer pore. The free energy calculation of the ions permeating through the SARS-CoV-2 pentameric E protein channel strongly suggests that the pore has selection permeability for monovalent ions. abstract: Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is of public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 has high homology with that of severe acute respiratory syndrome coronavirus. (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Our results suggest that the pentameric E protein promotes the penetration of monovalent ions through the channel. Analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore demonstrated a clear wetting/dewetting transition with monovalent cation selectivity under transmembrane voltage, which indicates that it is a hydrophobic voltage-dependent channel. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel. url: https://doi.org/10.1101/2020.05.17.099143 doi: 10.1101/2020.05.17.099143 id: cord-266313-b518n9dx author: Cao, Yu-chen title: Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence date: 2020-04-02 words: 5542.0 sentences: 262.0 pages: flesch: 48.0 cache: ./cache/cord-266313-b518n9dx.txt txt: ./txt/cord-266313-b518n9dx.txt summary: China has also taken immediate action to put remdesivir into clinical trials with the purpose of applying it into clinical therapeutics for Corona Virus Disease 2019 (COVID-19). When we set our sights on the broad-spectrum antiviral drugs, we found that a drug unlisted, remdesivir, has demonstrated strength in trials related to MERS-CoV and Ebola virus infection. This article starts from the structure, immunogenicity, and pathogenesis of infection of the SARS-CoV-2, and then analyzes the feasibility of conducting trials and putting into clinical use of COVID-19 from the pharmacological characteristics and successful cases of remdesivir. Remdesivir (GS-5734) is a nucleoside analogues drug (Fig. 3B ) with extensive antiviral activity and effective treatment of lethal Ebola and Nipah virus infections in nonhuman primates [21] . The need of treatment on COVID-19 is urgent, so if the results of clinical trials prove it has the potential to benefit the treatment, according to China''s "Compassionate Use", remdesivir will be more immediately used in patients with severe illness. abstract: The novel coronavirus infection that initially found at the end of 2019 has attracted great attention. So far, the number of infectious cases has increased globally to more than 100 thousand and the outbreak has been defined as a pandemic situation, but there are still no “specific drug” available. Relevant reports have pointed out the novel coronavirus has 80% homology with SARS. In the difficulty where new synthesized drug cannot be applied immediately to patients, “conventional drug in new use” becomes a feasible solution. The first medication experience of the recovered patients in the US has led remdesivir to be the “specific drug”. China has also taken immediate action to put remdesivir into clinical trials with the purpose of applying it into clinical therapeutics for Corona Virus Disease 2019 (COVID-19). We started from the structure, immunogenicity, and pathogenesis of coronavirus infections of the novel coronavirus. Further, we analyzed the pharmacological actions and previous trials of remdesivir to identify the feasibility of conducting experiments on COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32247927/ doi: 10.1016/j.tmaid.2020.101647 id: cord-281393-96j70n2z author: Capai, L. title: Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020. date: 2020-09-30 words: 3684.0 sentences: 262.0 pages: flesch: 60.0 cache: ./cache/cord-281393-96j70n2z.txt txt: ./txt/cord-281393-96j70n2z.txt summary: A minimum sample size of 1814 was calculated assuming an a priori 5% IgG anti-SARS-CoV-2 seroprevalence (Salje et al., 2020) , a confidence in the estimate of 95%, a maximum allowable error in the prevalence of 1%, and a Corsican population size of 344,679 habitants based on the latest French census data (INSEE, 2020). Residual sera obtained from persons of all ages were tested for the presence of anti-SARS-CoV-2 IgG using the EUROIMMUN enzyme immunoassay kit for semiquantitative detection of IgG antibodies against S1 domain of viral spike protein (ELISA-S) (reference: In all samples with a ratio ≥ 0.8, neutralizing antibodies were detected using a VNT as previously described (Gallian et al., 2020) . To the best of our knowledge this is the first study describing the prevalence of SARS-CoV-2 antibodies in a representative sample of Corsican patients having carried out a blood analysis in biological laboratories after the COVID19 epidemic period. abstract: Our aim was to assess the seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection after the lockdown in a sample of the Corsican population. Between 16th April and 15th June 2020, 2,312 residual sera were collected from patients having carried out a blood analysis in one of the participating laboratories. Residual sera obtained from persons of all ages were tested for the presence of anti-SARS-CoV-2 IgG using the EUROIMMUN enzyme immunoassay kit for semiquantitative detection of IgG antibodies against S1 domain of viral spike protein (ELISA-S). Borderline and positive samples in ELISA-S were also tested with an in-house virus neutralization test (VNT). Prevalence values were adjusted for sex and age. A total of 1,973 residual sera samples were included in the study. The overall seroprevalence based on ELISA-S was 5.27% [95% confidence interval (CI) 4.33-6.35] and 5.46% [4.51-6.57] after adjustment. Gender was not associated with IgG detection. However, significant differences were observed between age groups (p-value = 1 E-5) and particularly for people being younger than 50 years of age (Odd ratio (OR) = 2.86 95% CI [1.80- 4.53]; p-value <0.000001*). The prevalence of neutralizing antibody titers [≥]40 was of 3% [2.28-3.84]. In conclusion the present study showed that a low seroprevalence for COVID-19 in Corsica in accordance with values reported for other French regions in which the impact of the pandemic was low. url: https://doi.org/10.1101/2020.09.29.20201368 doi: 10.1101/2020.09.29.20201368 id: cord-346197-7g5d9x57 author: Capecchi, E. title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? date: 2020-07-05 words: 859.0 sentences: 76.0 pages: flesch: 61.0 cache: ./cache/cord-346197-7g5d9x57.txt txt: ./txt/cord-346197-7g5d9x57.txt summary: title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? Since the use of nasopharyngeal aspirate (NPA) seemed to be better than nasopharyngeal swab (NS) to identify respiratory virus in paediatrics 4,5 we decided to compare these methods in detecting SARS-CoV-2 in children. . https://doi.org/10.1101/2020.07.02.20142521 doi: medRxiv preprint Considering NPA as the gold standard for detection of SARS-CoV-2, we calculated sensitivities and specificities of NS. The NS has in any case a low sensitivity in detecting SARS-CoV-2 in children when referred to NPA. Our results, the first we know are available, suggest to prefer the collection of NPA whenever possible for the detection of SARS-CoV-2 in children. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 5, 2020. abstract: The tests currently used for the direct identification of SARS-CoV-2 include specimens taken from the upper and the lower respiratory tract. In our paediatric department all children undergo both nasopharyngeal swab and nasopharyngeal aspirate, performed from both nostrils, on admission and after 24 hours. We decided to compare these two methods of detection of SARS-CoV-2. Considering nasopharyngeal aspirate as the gold standard, we calculated sensitivities and specificities of nasopharyngeal swab. Based on our results, we suggest to prefer the collection of aspirates whenever possible. url: http://medrxiv.org/cgi/content/short/2020.07.02.20142521v1?rss=1 doi: 10.1101/2020.07.02.20142521 id: cord-325559-di8lljoi author: Cappello, Francesco title: Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date: 2020-06-29 words: 5204.0 sentences: 298.0 pages: flesch: 44.0 cache: ./cache/cord-325559-di8lljoi.txt txt: ./txt/cord-325559-di8lljoi.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced disease (COVID-19) is a planetary emergency that is urging many research groups to redirect their efforts and to channel their experience towards understanding its pathogenesis. These human epitopes, in turn, can be recognized by circulating antibodies made against crossreactive microbial antigens; these antibodies behave like autoantibodies, causing the destruction of the stressed cells, representing a typical example of pathology caused by molecular mimicry and manifested as autoimmunity [30] . We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. abstract: Viruses can generate molecular mimicry phenomena within their hosts. Why should severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) not be considered one of these? Information in this short review suggests that it might be so and, thus, encourages research aiming at testing this possibility. We propose, as a working hypothesis, that the virus induces antibodies and that some of them crossreact with host’s antigens, thus eliciting autoimmune phenomena with devasting consequences in various tissues and organs. If confirmed, by in vitro and in vivo tests, this could drive researchers to find effective treatments against the virus. url: https://doi.org/10.3390/jcm9072038 doi: 10.3390/jcm9072038 id: cord-256761-rjss51sq author: Caputo, Leonardo title: Repurposing therapeutic agents and herbal medicines to defeat viral nemesis date: 2020-03-30 words: 1085.0 sentences: 69.0 pages: flesch: 43.0 cache: ./cache/cord-256761-rjss51sq.txt txt: ./txt/cord-256761-rjss51sq.txt summary: After a deep analysis and exhaustive illustration of both the rationale behind this tentative approach and related safety concern, Gurwitz suggested that data mining of clinical patient records survived to COVID-19 epidemic might be useful to assess the feasibility of sartans'' repurposing as therapeutic treatment to decrease acute respiratory distress syndrome (ARDS) and reduce the aggressiveness from severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. Obviously, repurposing old drugs for COVID-19 may start from therapeutic agents with proven efficacy against other lethal viral infections. On the other hand, the use of traditional Chinese remedies as a therapeutic approach for combating SARS-CoV has been well publicized (World Health Organization [WHO], 2003) and it was recently proposed for prevention of COVID-19 (Luo et al., 2020) . Whatever sources of drugs (natural, synthetic, or repurposed) are suggested to be used for COVID-19, their efficacy should be proven through a valid clinical trial. abstract: nan url: https://doi.org/10.1002/ddr.21668 doi: 10.1002/ddr.21668 id: cord-262575-06i2nv0t author: Caracciolo, Massimo title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome date: 2020-08-25 words: 2163.0 sentences: 139.0 pages: flesch: 40.0 cache: ./cache/cord-262575-06i2nv0t.txt txt: ./txt/cord-262575-06i2nv0t.txt summary: title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome Severe cases of COVID-19 present with serious lung inflammation, acute respiratory distress syndrome and multiorgan damage. SARS-CoV-2 infection is associated with high cytokine levels, including interleukin-6 and certain subsets of immune cells, in particular, NK, distinguished according to the cell surface density of CD56. Cytokine levels are inversely correlated with lymphocyte count, therefore cytokine release syndrome may be an impediment to the adaptive immune response against SARS-CoV-2 infection. An 85 year old male presenting in our hospital with COVID-19, whose condition was complicated by acute respiratory distress syndrome and cardiac and renal failure (with oliguria) after 25 days of hospitalization, was intubated and received canakinumab for compassionate use. The immune response, including the release of pro-inflammatory cytokines and activation of T cells, are essential for controlling the viral spread, inflammation, and tissue renewal (5, 6) . abstract: Severe cases of COVID-19 present with serious lung inflammation, acute respiratory distress syndrome and multiorgan damage. SARS-CoV-2 infection is associated with high cytokine levels, including interleukin-6 and certain subsets of immune cells, in particular, NK, distinguished according to the cell surface density of CD56. Cytokine levels are inversely correlated with lymphocyte count, therefore cytokine release syndrome may be an impediment to the adaptive immune response against SARS-CoV-2 infection. Canakinumab, a monoclonal antibody targeting IL-1β is under investigation for the treatment of severe SAR-CoV-2 infection. An 85 year old male presenting in our hospital with COVID-19, whose condition was complicated by acute respiratory distress syndrome and cardiac and renal failure (with oliguria) after 25 days of hospitalization, was intubated and received canakinumab for compassionate use. On the next day, diuresis recovered and conditions improved: high IL-6 levels and NK cells expressing CD56(bright) (associated with cytokine relase) were significantly reduced giving rise to NK CD56(dim). Patient died on day 58 with pulmonary bacterial superinfection and persistent SARS-CoV-2 positivity. In conclusion, canakinumab rescued a high risk, very elderly patient, from multiorgan damage complicating COVID-19. It may represent an useful treatment in severe cases. url: https://doi.org/10.3389/fimmu.2020.01942 doi: 10.3389/fimmu.2020.01942 id: cord-257487-xanqvdhn author: Carbajo-Lozoya, Javier title: Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date: 2012-02-10 words: 2945.0 sentences: 191.0 pages: flesch: 49.0 cache: ./cache/cord-257487-xanqvdhn.txt txt: ./txt/cord-257487-xanqvdhn.txt summary: Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. Knockdown of the cellular FK506binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. To examine whether FK506 exerts an inhibitory activity on other human coronaviruses, CaCo2 cells were infected with HCoV-NL63 at MOI = 0.004 (Herzog et al., 2008) in the presence of increasing inhibitor concentrations. In order to examine whether the cellular FK506-binding proteins FKBP1A and FKBP1B are required for virus replication, CaCo2 knockdown cell lines were established using lentiviral expression of shRNA (Sirion GmbH, Martinsried, Germany). abstract: Recent research has shown that Coronavirus (CoV) replication depends on active immunophilin pathways. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. As shown by plaque titration, qPCR, Luciferase- and green fluorescent protein (GFP) reporter gene expression, replication was diminished by several orders of magnitude. Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. url: https://doi.org/10.1016/j.virusres.2012.02.002 doi: 10.1016/j.virusres.2012.02.002 id: cord-293890-thfros7x author: Carbo, Ellen C. title: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness date: 2020-08-21 words: 2315.0 sentences: 129.0 pages: flesch: 49.0 cache: ./cache/cord-293890-thfros7x.txt txt: ./txt/cord-293890-thfros7x.txt summary: METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. Additionally, the efficacy of detection of novel coronaviruses using capture probes targeting vertebrate viruses [10] [11] known before the current pandemic was analyzed using a SARS-CoV-2 clinical sample. After extraction of human reads, FASTQ files generated for SARS-CoV-2 samples (with and without viral enrichment) were uploaded for classification and de novo assembly by the commercial webbased tool Genome Detective v1.120 (www.genomedetective.com, accessed 2020-05-11) [9] , using a reference database (generated 2019-09-21). In this study, we evaluated the performance of a metagenomic sequencing protocol for the identification of emerging viruses using clinical samples in combination with a simulated reference database. abstract: INTRODUCTION: The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness. AIM: The aim of this study is to validate a metagenomic virus discovery protocol as a tool for coronavirus pandemic preparedness. METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. RESULTS: Classification of NGS reads using Centrifuge and Genome Detective resulted in assignment of the reads to the closest relatives of the emerging coronaviruses. Low nucleotide and amino acid identity (81% and 84%, respectively, for SARS-CoV-2) in combination with up to 98% genome coverage were indicative for a related, novel coronavirus. Capture probes targeting vertebrate viruses, designed in 2015, enhanced both sequencing depth and coverage of the SARS-CoV-2 genome, the latter increasing from 71 to 98%. CONCLUSION: The model used for simulation of virus discovery enabled validation of the metagenomic sequencing protocol. The metagenomic protocol with virus probes designed before the pandemic, can assist the detection and identification of novel coronaviruses directly in clinical samples. url: https://api.elsevier.com/content/article/pii/S138665322030336X doi: 10.1016/j.jcv.2020.104594 id: cord-313537-920tgv1j author: Carbonell, Ana Piera title: Covid-19 y tromboprofilaxis: recomendaciones para nuestra práctica clínica en atención primaria date: 2020-09-18 words: 2640.0 sentences: 268.0 pages: flesch: 48.0 cache: ./cache/cord-313537-920tgv1j.txt txt: ./txt/cord-313537-920tgv1j.txt summary: Teniendo en cuenta que muchos de nuestros pacientes ya reciben terapia antitrombótica o anticoagulante, el hecho de que puedan desarrollar una infección por COVID-19 tendrá implicaciones para la elección, dosificación y control en associated with SARS-CoV-2 infection, increasing its severity and conferring a worse prognosis. La enfermedad producida por coronavirus SARS-CoV-2 (COVID19) , si bien en la mayoría de los pacientes infectados cursa con síntomas leves, en casos más severos puede progresar rápidamente y desarrollar un síndrome de dificultad respiratoria aguda, shock séptico, coagulopatía y disfunción endotelial, que son los determinantes principales de la afectación microvascular, al producir una mayor vasoconstricción, isquemia orgánica, inflamación con edema tisular asociado y un estado procoagulante que predispone a la enfermedad tromboembólica venosa (ETEV) y arterial. abstract: El nuevo coronavirus (SARS-CoV-2) es el responsable de un síndrome respiratorio agudo severo (SARS). Entre sus manifestaciones puede desarrollar una enfermedad trombótica, tanto venosa como arterial, debido a la inflamación excesiva que afecta al sistema vascular, con activación plaquetaria y disfunción endotelial, entre otros mecanismos. La trombosis se asocia a la infección producida por el SARS- CoV-2, aumentando su gravedad y confiriendo un peor pronóstico. Nuestra actuación como Médicos de Familia puede aportar acciones importantes en el manejo y control de esta severa complicación. Teniendo en cuenta que muchos de nuestros pacientes ya reciben terapia antitrombótica o anticoagulante, el hecho de que puedan desarrollar una infección por COVID-19 tendrá implicaciones para la elección, dosificación y control en su tratamiento. En este documento revisamos, con la información actualmente disponible, la relación entre enfermedad producida por el SARS-CoV-2 y trombosis, así como su manejo con un enfoque centrado en Atención Primaria. The new coronavirus (SARS-CoV-2) is responsible for a severe acute respiratory syndrome. Among its manifestations, it can develop a thrombotic disease, both venous and arterial, due to excessive inflammation that affects the vascular system, with platelet activation and endothelial dysfunction, among other mechanisms. Thrombosis is associated with SARS-CoV-2 infection, increasing its severity and conferring a worse prognosis. Our performance as Family Physicians can contribute important actions in the management and control of this severe complication. Considering that many of our patients already receive antithrombotic or anticoagulant therapy, the fact that they may develop a COVID-19 infection will have implications for the choice, dosage and control of their treatment. In this document we review, with the information currently available, the relationship between disease caused by SARS-CoV-2 and thrombosis, as well as its management with a focus on Primary Care. url: https://www.sciencedirect.com/science/article/pii/S1138359320302884?v=s5 doi: 10.1016/j.semerg.2020.07.007 id: cord-308252-qwoo7b1l author: Cardinale, Vincenzo title: Intestinal permeability changes with bacterial translocation as key events modulating systemic host immune response to SARS-CoV-2: A working hypothesis date: 2020-09-16 words: 4596.0 sentences: 229.0 pages: flesch: 36.0 cache: ./cache/cord-308252-qwoo7b1l.txt txt: ./txt/cord-308252-qwoo7b1l.txt summary: During the course of severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and 2 (SARS-CoV-2) infection, this pathway is unbalanced due to intestinal involvement and systemic inflammatory response. This review provides evidence on gut-liver axis involvement in Covid-19 as well as insights into the hypothesis that intestinal endotheliitis and permeability changes with bacterial translocation are key pathophysiologic events modulating systemic inflammatory response. Since inflammation seems to upregulate ACE2 expression [17] , it is important to understand whether patients with inflammatory bowel disease (IBD) are more susceptible to Covid-19 and the cytokine release syndrome (CRS) associated with lung injury and fatal outcome [21] . While the risk of SARS-CoV-2 infection in IBD patients depends on several universal risk factors, including social distancing [22] , older age and comorbidities have been associated with a negative outcome in IBD, whereas IBD treatments have not, highlighting that acute IBD flare prevention and inflammation reduction may avoid severe Covid-19 [23] . abstract: The microbiota-gut-liver-lung axis plays a bidirectional role in the pathophysiology of a number of infectious diseases. During the course of severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and 2 (SARS-CoV-2) infection, this pathway is unbalanced due to intestinal involvement and systemic inflammatory response. Moreover, there is convincing preliminary evidence linking microbiota-gut-liver axis perturbations, proinflammatory status, and endothelial damage in noncommunicable preventable diseases with coronavirus disease 2019 (Covid-19) severity. Intestinal damage due to SARS-CoV-2 infection, systemic inflammation-induced dysfunction, and IL-6-mediated diffuse vascular damage may increase intestinal permeability and precipitate bacterial translocation. The systemic release of damage- and pathogen-associated molecular patterns (e.g. lipopolysaccharides) and consequent immune-activation may in turn auto-fuel vicious cycles of systemic inflammation and tissue damage. Thus, intestinal bacterial translocation may play an additive/synergistic role in the cytokine release syndrome in Covid-19. This review provides evidence on gut-liver axis involvement in Covid-19 as well as insights into the hypothesis that intestinal endotheliitis and permeability changes with bacterial translocation are key pathophysiologic events modulating systemic inflammatory response. Moreover, it presents an overview of readily applicable measures for the modulation of the gut-liver axis and microbiota in clinical practice. url: https://api.elsevier.com/content/article/pii/S1590865820304692 doi: 10.1016/j.dld.2020.09.009 id: cord-331140-5b0y1xzb author: Cardona Maya, Walter D. title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health date: 2020-06-01 words: 326.0 sentences: 30.0 pages: flesch: 58.0 cache: ./cache/cord-331140-5b0y1xzb.txt txt: ./txt/cord-331140-5b0y1xzb.txt summary: key: cord-331140-5b0y1xzb title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health cord_uid: 5b0y1xzb . Recently, SARS-CoV-2 was detected in semen samples (5) . Therefore, it is not unreasonable to believe that the latest coronavirus could potentially be transmitted via semen (6) . It was also reported that angiotensin converting enzyme 2 (ACE2) is a functional receptor that mediates the entry of SARS-CoV-1 (7) and 2 (8) , and this receptor is expressed in the prostate. Perhaps in the coming years, the real effect of SARS-CoV-2 on prostatitis cases will be evaluated and scope for researching factors that cause the clinical syndrome will be expanded. Male infertility: a public health issue caused by sexually transmitted pathogens Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease SARS-CoV-2 and the Testis: similarity to other viruses and routes of infection Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32505071/ doi: 10.1016/j.mehy.2020.109914 id: cord-304791-wv4qu9xm author: Carfora, Vincenzo title: Anticoagulant treatment in COVID-19: a narrative review date: 2020-08-18 words: 3568.0 sentences: 193.0 pages: flesch: 41.0 cache: ./cache/cord-304791-wv4qu9xm.txt txt: ./txt/cord-304791-wv4qu9xm.txt summary: Besides the respiratory involvement, COVID 19 patients frequently develop a pro-coagulative state caused by virus-induced endothelial dysfunction, cytokine storm and complement cascade hyperactivation. [11] enrolled 183 consecutive COVID-19 patients and performed routine coagulation tests [PT, [8] In COVID-19-patients it is common to observe increased fibrinogen and D-Dimer levels Chen, 2020 [9] In COVID-19-patients it is common to observe variable levels of prothrombin time (PT), activated partial thromboplastin time (aPTT) and International standardized ratio (INR) Qin, 2020 [15] In COVID-19 the hyperinflammation mediated by IL-1, TNF-alfa and IL-6 leads to an increase of plasma concentrations of fibrinogen and plasminogen activator inhibitor-1 (PAI-1) Campbell, 2020 [19] In a murine model of MERS-CoV infection, increased concentrations of C5a and C5b-9 were found in sera and lung tissues. Moreover, patients with cardiovascular disease and dyslipidemia have high levels of circulating asymmetric di-methyl-arginine (ADMA) [28] , an analogue of L-arginine that inhibits NOS-3 activity [29] , and this leads to lower NO levels; this explains why endothelial dysfunction and the pro-coagulant state are more severe in this cohort of patients. abstract: The actual Coronavirus Disease (COVID 19) pandemic is due to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the coronavirus family. Besides the respiratory involvement, COVID 19 patients frequently develop a pro-coagulative state caused by virus-induced endothelial dysfunction, cytokine storm and complement cascade hyperactivation. It is common to observe diffuse microvascular thrombi in multiple organs, mostly in pulmonary microvessels. Thrombotic risk seems to be directly related to disease severity and worsens patients’ prognosis. Therefore, the correct understanding of the mechanisms underlying COVID-19 induced prothrombotic state can lead to a thorough assessment of the possible management strategies. Hence, we review the pathogenesis and therapy of COVID 19-related thrombosis disease, focusing on the available evidence on the possible treatment strategies and proposing an algorithm for the anticoagulation strategy based on disease severity. url: https://www.ncbi.nlm.nih.gov/pubmed/32809158/ doi: 10.1007/s11239-020-02242-0 id: cord-351100-llyl97ry author: Cariani, Lisa title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 words: 3248.0 sentences: 171.0 pages: flesch: 53.0 cache: ./cache/cord-351100-llyl97ry.txt txt: ./txt/cord-351100-llyl97ry.txt summary: We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. We collected cycle threshold values of the first SARS-CoV-2-positive nasopharyngeal swabs (T0) for all 182 HCWs and CT values at one week before the two negative RT-PCR tests (T1) for the 58 subjects who healed by 30 April 2020 (Figure 2 ). In the present study, we analyzed 2443 nasopharyngeal swabs from 1683 HCWs by molecular laboratory testing for suspected SARS-CoV-2 infection in a large university hospital in Milan, showing 10.8% positive HCWs. Overall, the majority of HCWs with COVID-19 were physicians, and the main reported symptoms were fever, cough, and headache. abstract: Background: Coronavirus Disease 2019 (COVID-19) has rapidly spread worldwide, becoming an unprecedented public health emergency. Rapid detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) suspected cases is crucial to control the spread of infection. We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. Methods: We retrospectively analyzed a consecutive cohort of 182 SARS-CoV-2-positive HCWs in Milan, from 16 March to 30 April 2020. Nasopharyngeal swabs were tested by RT-PCR. Results: Asymptomatic HCWs were 17.6% (32/182), and 58 healed at 30 April 2020. The median time length of negativization was 4 weeks (35% of symptomatic versus 40% of asymptomatic HCWs). Four HCWs, healed at 30 April, turned positive within three weeks during controls set up in the work unit. Three-gene positivity had the greatest variability, and increasing CT values from single- to three-gene positivity among all age groups were observed. Conclusions: Self-isolation longer than two weeks and prolonged follow-up periods for the staff returning to work after COVID-19 could be the most suitable choices to counter the SARS-CoV-2 spread. Further studies are needed to investigate infectiousness profiles among positive individuals. url: https://doi.org/10.3390/ijerph17155313 doi: 10.3390/ijerph17155313 id: cord-285822-b5itedu3 author: Carlos Marín-Gabriel, José title: Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 date: 2020-05-27 words: 7445.0 sentences: 774.0 pages: flesch: 52.0 cache: ./cache/cord-285822-b5itedu3.txt txt: ./txt/cord-285822-b5itedu3.txt summary: Promover la participación de los residentes de Aparato Digestivo en los procedimientos endoscópicos en pacientes con bajo riesgo de infección por SARS-CoV-2, siempre y cuando se disponga de los recursos necesarios que garanticen la seguridad del procedimiento. En la situación actual de alto riesgo de transmisión de la infección por SARS-CoV-2 en el entorno hospitalario, es crítico revisar los protocolos de la UE en relación con la circulación de los pacientes y acompañantes, las estrategias de cribado de COVID-19, la disponibilidad de EPI y las medidas de desinfección de las salas y equipos de endoscopia. Las sociedades firmantes de este documento se posicionan a favor de que los residentes en Aparato Digestivo continúen realizando procedimientos bajo supervisión directa en pacientes de bajo riesgo de infección por SARS-CoV-2. Para los pacientes con alta sospecha o infección confirmada por SARS-CoV2, es recomendable una desinfección en profundidad de la sala después de cada endoscopia 6 , 27 . abstract: Introduction: The COVID-19 pandemic has led to the suspension of programmed activity in most of the Endoscopy Units in our environment. The aim of this document is to facilitate the resumption of elective endoscopic activity in an efficient and safe manner. Material and methods: A series of questions considered to be of clinical and logistical relevance were formulated. In order to elaborate the answers, a structured bibliographic search was carried out in the main databases and the recommendations of the main Public Health and Digestive Endoscopy institutions were reviewed. The final recommendations were agreed upon through telematic means. Results: A total of 33 recommendations were made. The main aspects discussed are: 1) Reassessment and prioritization of the indication, 2) Restructuring of spaces, schedules and health personnel, 3) Screening for infection, 4) Hygiene measures and personal protective equipment. Conclusion: The AEG and SEED recommend restarting endoscopic activity in a phased, safe manner, adapted to local resources and the epidemiological situation of SARS-CoV-2 infection. url: https://doi.org/10.1016/j.gastrohep.2020.05.004 doi: 10.1016/j.gastrohep.2020.05.004 id: cord-339782-rybjc58j author: Carmo, Anália title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 words: 1844.0 sentences: 106.0 pages: flesch: 52.0 cache: ./cache/cord-339782-rybjc58j.txt txt: ./txt/cord-339782-rybjc58j.txt summary: The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. In men, the first negative test took 24 ± 9 days (range: 7 -46) and in women it took 25 ± 9 days (range: 9 -44), P>0.05, In an attempt to understand why some patients maintained positive tests for longer, we correlated the detection of SARS-CoV-2 RNA with the host immune response to virus infection. The lack of information regarding persistence of virus RNA and infectivity, disease severity and immune response, supports the current guidance of viral clearance confirmation prior to patient transference out of dedicated COVID-19 wards and of ending isolation in mild illness patients. abstract: COVID‐19 patients may be discharged based on clinical resolution of symptoms, and evidence for viral RNA clearance from the upper respiratory tract. Understanding the SARS‐CoV‐2 viral clearance profile is crucial to establish a re‐testing plan on discharge and ending isolation of patients. We aimed to evaluate the number of days that a patient needed to achieve undetectable levels of SARS‐CoV‐2 in upper respiratory tract specimens (nasopharyngeal swab and/or an oropharyngeal swab). The clearance and persistence of viral RNA was evaluated in two groups of positive patients: those who achieved two negative RT‐PCR tests and those who kept testing positive. Patients were organized thereafter in two subgroups, mild illness patients discharged home and inpatients who had moderate to severe illness. Results from RT‐PCR tests were then correlated with results from the evaluation of the immune response. The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32484958/ doi: 10.1002/jmv.26103 id: cord-321259-wio2b49i author: Carmona-Gutierrez, Didac title: Digesting the crisis: autophagy and coronaviruses date: 2020-05-04 words: 4350.0 sentences: 243.0 pages: flesch: 35.0 cache: ./cache/cord-321259-wio2b49i.txt txt: ./txt/cord-321259-wio2b49i.txt summary: Of note, cellular manipulation of autophagic levels during infection may also reflect desperate attempts of the cell to reestablish homeostasis, either through restriction of viral entry by actively shunting endocytosis/endosomal trafficking (possibly resulting in autophagy reduction as a sideeffect) [39] or to counteract virally induced cell death by increasing cytoprotective autophagy. Thus, the group-specific accessory proteins, which by definition are not essential for viral replication but are involved in the modulation of host cells and immune evasion [66, 67] , may represent targets for reducing the autophagy-inhibitory effects of CoVs. The FDA-approved anti-malarial drugs chloroquine and hydroxychloroquine have been suggested to be repurposed for the treatment of COVID-19 [68] [69] [70] , but this remains widely controversial [71] [72] [73] . Intriguingly, another recent preprint presents in vitro data showing that SARS-CoV-2 infection restricts autophagy and that, in turn, pro-autophagic compounds -including spermidine -may inhibit viral propagation [85] . abstract: Autophagy is a catabolic pathway with multifaceted roles in cellular homeostasis. This process is also involved in the antiviral response at multiple levels, including the direct elimination of intruding viruses (virophagy), the presentation of viral antigens, the fitness of immune cells, and the inhibition of excessive inflammatory reactions. In line with its central role in immunity, viruses have evolved mechanisms to interfere with or to evade the autophagic process, and in some cases, even to harness autophagy or constituents of the autophagic machinery for their replication. Given the devastating consequences of the current COVID-19 pandemic, the question arises whether manipulating autophagy might be an expedient approach to fight the novel coronavirus SARS-CoV-2. In this piece, we provide a short overview of the evidence linking autophagy to coronaviruses and discuss whether such links may provide actionable targets for therapeutic interventions. url: https://doi.org/10.15698/mic2020.05.715 doi: 10.15698/mic2020.05.715 id: cord-297418-36j840wm author: Carneiro Leão, Jair title: Coronaviridae ‐ old friends, new enemy! date: 2020-05-31 words: 3978.0 sentences: 263.0 pages: flesch: 53.0 cache: ./cache/cord-297418-36j840wm.txt txt: ./txt/cord-297418-36j840wm.txt summary: However, in recent years, coronaviruses have given rise to significant diseases such as severe acute respiratory syndrome (SARS-CoV) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) SARS-CoV infected 8,000 people, from 2002 to 2003 and had a mortality rate of approximately 10% (Marra et al., 2003) . On the other hand, evolutionary analysis based on the ORF1a / 1b, S and N genes suggests that SARS-CoV-2 is more likely to be a new coronavirus that has been introduced independently from animals to humans due to the inherent mutation property of coronaviruses in nature (Lam et al., 2020) . Severe acute respiratory syndrome (SARS) is a human disease associated with severe pneumonia and as noted above is caused by SARS-Coronavirus (SARS-CoV) (Drosten et al., 2003) . The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges abstract: Coronaviridae is a family of single‐stranded positive enveloped RNA viruses. This article aimed to review the history of these viruses in the last 60 years since their discovery to understand what lessons can be learned from the past. A review of the PubMed database was carried out, describing taxonomy, classification, virology, genetic recombination, host adaptation, and main symptoms related to each type of virus. SARS‐CoV‐2 is responsible for the ongoing global pandemic, SARS‐CoV and MERS‐CoV were responsible for causing severe respiratory illness and regional epidemics in the past while the four other strains of CoVs (229‐E OC43, NL63, and HKU1) circulate worldwide and normally only cause mild upper respiratory tract infections. Given the enormous diversity of coronavirus viruses in wildlife and their continuous evolution and adaptation to humans, future outbreaks would undoubtedly occur. Restricting or banning all trade in wild animals in wet markets would be a necessary measure to reduce future zoonotic infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32475006/ doi: 10.1111/odi.13447 id: cord-324892-mg2dziuw author: Carneiro, João title: CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date: 2020-06-12 words: 901.0 sentences: 76.0 pages: flesch: 48.0 cache: ./cache/cord-324892-mg2dziuw.txt txt: ./txt/cord-324892-mg2dziuw.txt summary: The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens abstract: The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing. url: https://doi.org/10.1101/2020.04.19.048991 doi: 10.1101/2020.04.19.048991 id: cord-354372-vfvnjmv1 author: Carpenito, L. title: The autopsy at the time of SARS-CoV-2: Protocol and lessons date: 2020-07-04 words: 5696.0 sentences: 256.0 pages: flesch: 51.0 cache: ./cache/cord-354372-vfvnjmv1.txt txt: ./txt/cord-354372-vfvnjmv1.txt summary: In the current pandemic scenario of SARS-CoV-2, the autopsy appears to be a crucial tool to clarify the virus target cells in human, the frameworks of organ damage and the biological mechanisms that lead to death or allow the patient to heal. To minimize the dispersion of blood and biological fluids, it is essential to always operate in the area of the autopsy table: the viscera removed from the body must be placed either on the iron section table, placed above the patient''s thighs, or in a large tray with high steel edges resting on the patient''s legs, during weighing, macroscopic examination and sampling of the viscera. Given the multiple clinical findings of neurological symptoms in patients infected with SARS-CoV-2 [22, 23] , it appears indispensable to perform the evisceration and examination of the brain and brainstem, for the completeness of the autopsy and for the very few morphological data available today on the central nervous system. abstract: A new viral disease named COVID-19 has recently turned into a pandemic. Compared to a common viral pneumonia it may evolve in an atypical way, causing the rapid death of the patient. For over two centuries, autopsy has been recognized as a fundamental diagnostic technique, particularly for new or little-known diseases. To date, it is often considered obsolete giving the inadequacy to provide samples of a quality appropriate to the sophisticated diagnostic techniques available today. This is probably one of the reasons why during this pandemic autopsies were often requested only in few cases, late and discouraged, if not prohibited, by more than one nation. This is in contrast with our firm conviction: to understand the unknown we must look at it directly and with our own eyes. This has led us to implement an autopsy procedure that allows the beginning of the autopsy shortly after death (within 1–2 h) and its rapid execution, also including sampling for ultrastructural and molecular investigations. In our experience, the tissue sample collected for diagnosis and research were of quality similar to biopsy or surgical resections. This procedure was performed ensuring staff and environmental safety. We want to propose our experience, our main qualitative results and a few general considerations, hoping that they can be an incentive to use autopsy with a new procedure adjusted to match the diagnostic challenges of the third millennium. url: https://www.ncbi.nlm.nih.gov/pubmed/32653819/ doi: 10.1016/j.anndiagpath.2020.151562 id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 words: 7248.0 sentences: 523.0 pages: flesch: 48.0 cache: ./cache/cord-271920-1dzkgt6w.txt txt: ./txt/cord-271920-1dzkgt6w.txt summary: 3 As waves of COVID-19 patients present to ED''s in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient''s exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. abstract: In December 2019 a novel viral respiratory pathogen emerged in China, ultimately named severe acute respiratory syndrome coronavirus 2 (SARS‐Co‐V‐2) with the clinical illness dubbed coronavirus disease (COVID‐19). COVID‐19 became a global pandemic in early 2020 forcing governments worldwide to enact social isolation policies with dire economic ramifications. Emergency departments (ED) encountered decreased patient volumes before some in Seattle, New York City, New Orleans, and Detroit experienced waves of COVID‐19 patients mixed with asymptomatic patients or those concerned about potential exposures. Diagnosing COVID‐19 was hampered by inadequate supplies of reagents and kits, which was compounded by clinical and radiographic features that overlap with numerous seasonal viral respiratory infections. url: https://doi.org/10.1111/acem.14048 doi: 10.1111/acem.14048 id: cord-326013-5i35zdmv author: Carpinteiro, Alexander title: Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells date: 2020-10-29 words: 3113.0 sentences: 175.0 pages: flesch: 47.0 cache: ./cache/cord-326013-5i35zdmv.txt txt: ./txt/cord-326013-5i35zdmv.txt summary: The data justify clinical studies investigating whether amitriptyline, a safe drug used clinically for almost 60 years, or other antidepressants that functionally block acid sphingomyelinase prevent SARS-CoV-2 infection. Pretreatment of the cells with 5, 10, 20, or 25 µM amitriptyline prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike for 30 min (Fig. 3B, Fig. 4A ). Treating Vero cells with neutralizing antibodies to spike or with recombinant ACE2 protein prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike (Fig. 3B, Fig. 4A Amitriptyline and other drugs with similar structure and properties have been clinically used for many years (since 1962) to treat patients with depressive disorder. Best results were obtained with venlafaxin, fluoxetine, escitalopram and mirtazipine, drugs that were also shown in the present study to inhibit acid sphingomyelinase and ceramide release upon pp-VSV-SARS-CoV-2 spike infection. abstract: The acid sphingomyelinase/ceramide system plays an important role in bacterial and viral infections. Here we report that either pharmacological inhibition of acid sphingomyelinase with amitriptyline, imipramine, fluoxetine, sertraline, escitalopram, or maprotiline, or genetic downregulation of the enzyme prevents infection of cultured cells or freshy isolated human nasal epithelial cells with SARS-CoV-2 or pseudoviral pp-VSV-SARS-CoV-2 particles expressing spike, a bona fide system mimicking SARS-CoV-2 infection. Infection activates acid sphingomyelinase and triggers a release of ceramide on the cell surface. Neutralization or consumption of surface ceramide reduces infection with pp-VSV-SARS-CoV-2 spike. Treating volunteers with a low dose of amitriptyline prevents infection of freshly isolated nasal epithelial cells with pp-VSV-SARS-CoV-2 spike. The data justify clinical studies investigating whether amitriptyline, a safe drug used clinically for almost 60 years, or other antidepressants that functionally block acid sphingomyelinase prevent SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33163980/ doi: 10.1016/j.xcrm.2020.100142 id: cord-326150-cf4rlqe5 author: Carrascosa, J M title: Manifestaciones cutáneas en el contexto de la infección por SARS-CoV-2 (COVID-19) date: 2020-08-31 words: 2443.0 sentences: 233.0 pages: flesch: 51.0 cache: ./cache/cord-326150-cf4rlqe5.txt txt: ./txt/cord-326150-cf4rlqe5.txt summary: Desde el punto de vista patogénico, la respuesta inmune desencadenada frente a la infección por SARS-CoV-2 puede resultar en efectos deletéreos, como la disfunción de las células endoteliales y la activación de las vías de la coagulación, que podrían explicar las complicaciones cardiovasculares y trombóticas que afectan a un subgrupo de pacientes. Desde el punto de vista histológico, en el conjunto de exantemas J o u r n a l P r e -p r o o f En el estudio histológico de lesiones purpúricas cutáneas se ha encontrado la presencia de una vasculopatía trombogénica pauciinflamatoria, con depósito de C5b-9 y C4d , con localización de partículas virales, lo que ha permitido proponer la existencia de un síndrome de lesión microvascular catastrófica mediada por la activación del complemento 6 . De este modo, no puede descartarse que las lesiones acrales, descritas como características por su coincidencia epidemiológica más que por pruebas microbiológicas en la mayoría de los casos, puedan no tener que ver directamente con la COVID-19. abstract: La pandemia por SARS-CoV-2 ha causado un gran impacto desde el punto de vista sanitario, económico y social. La semiología dermatológica se ha demostrado heterogénea y compleja. En la actualidad se han definido cinco grupos principales de manifestaciones cutáneas asociadas a la COVID19: lesiones acrales, exantemas vesiculares, erupciones urticariales, exantemas maculopapulares y lesiones livedoides/necróticas. Sin embargo, es probable que esta clasificación se modifique en el futuro. La clínica cutánea es probablemente el reflejo de distintas vías patogénicas con implicación variable de la infección vírica, del proceso inflamatorio, de las complicaciones vasculares o sistémicas de la enfermedad o incluso de los tratamientos administrados. El conocimiento de las manifestaciones cutáneas puede permitir un diagnóstico precoz o incluso servir como marcador pronóstico. The coronavirus 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had enormous health, economic, and social consequences. The clinical spectrum of cutaneous manifestations observed in patients with COVID-19 is both heterogeneous and complex. To date, reports have identified 5 main categories: acral lesions, vesicular rashes, urticarial rashes, maculopapular rashes, and livedoid and necrotic lesions. However, these will probably be modified as new information comes to light. Cutaneous manifestations associated with COVID-19 probably reflect the activation of pathogenic pathways by the virus or a response to inflammatory processes, vascular or systemic complications, or even treatments. Familiarity with the cutaneous manifestations of COVID-19 may enable early diagnosis or help guide prognosis. url: https://doi.org/10.1016/j.ad.2020.08.002 doi: 10.1016/j.ad.2020.08.002 id: cord-284042-awl5bb0j author: Carrascosa, J.M. title: Cutaneous Manifestations in the Context of SARS-CoV-2 Infection (COVID-19)() date: 2020-10-15 words: 3952.0 sentences: 216.0 pages: flesch: 45.0 cache: ./cache/cord-284042-awl5bb0j.txt txt: ./txt/cord-284042-awl5bb0j.txt summary: From the pathogenic point of view, the immune response triggered by infection with SARS-CoV-2 may result in harmful effects, such as endothelial cell dysfunction and activation of J o u r n a l P r e -p r o o f coagulation pathways; this may explain the cardiovascular and thrombotic complications that affect a subgroup of patients. 19 Vesicular lesions, usually monomorphic, appear early on and may at times precede other symptoms (in 15% of patients), 11 although in most cases, up to 79.2% in a series of 24 patents reported by Fernandez-Nieto et al., 20 they occur at the onset of other symptoms. 21 reported the case of a female patient who developed an urticarial rash, accompanied by odynophagia and arthralgia, before developing the full clinical manifestations of COVID-19. abstract: The coronavirus 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had enormous health, economic, and social consequences. The clinical spectrum of cutaneous manifestations observed in patients with COVID-19 is both heterogeneous and complex. To date, reports have identified 5 main categories: acral lesions, vesicular rashes, urticarial rashes, maculopapular rashes, and livedoid and necrotic lesions. However, these will probably be modified as new information comes to light. Cutaneous manifestations associated with COVID-19 probably reflect the activation of pathogenic pathways by the virus or a response to inflammatory processes, vascular or systemic complications, or even treatments. Familiarity with the cutaneous manifestations of COVID-19 may enable early diagnosis or help guide prognosis. url: https://api.elsevier.com/content/article/pii/S1578219020302754 doi: 10.1016/j.adengl.2020.10.001 id: cord-313193-q5zeoqlb author: Carrat, F. title: Seroprevalence of SARS-CoV-2 among adults in three regions of France following the lockdown and associated risk factors: a multicohort study. date: 2020-09-18 words: 4076.0 sentences: 265.0 pages: flesch: 57.0 cache: ./cache/cord-313193-q5zeoqlb.txt txt: ./txt/cord-313193-q5zeoqlb.txt summary: Methods Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE), two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA), with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE) -two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA) -with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants with a positive ELISA-S had a higher rate of self-reported symptoms than those with negative tests except for skin lesions (table 2) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint abstract: Aim To estimate the seroprevalence of SARS-CoV-2 infection in May-June 2020 after the lockdown in adults living in three regions in France and to identify the associated risk factors. Methods Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE), two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA), with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. The primary outcome was a positive anti-SARS-CoV-2 ELISA IgG result against the spike protein of the virus (ELISA-S). The secondary outcomes were a positive ELISA IgG against the nucleocapsid protein (ELISA-NP), anti-SARS-CoV-2 neutralizing antibodies titers >=40 (SN), and predicted positivity obtained from a multiple imputation model (MI). Prevalence estimates were adjusted using sampling weights and post-stratification methods. Findings Between May 4, 2020 and June 23, 2020, 16,000 participants were asked to provide DBS, and 14,628 were included in the analysis, 983 with a positive ELISA-S, 511 with a positive ELISA-NP, 424 with SN>=40 and 941 (Standard Deviation=31) with a positive MI. Adjusted estimates of seroprevalence (positive ELISA-S) were 10.0% (95%CI 9.1%;10.9%) in IDF, 9.0% (95%CI 7.7%; 10.2%) in GE and 3.1% (95%CI 2.4%; 3.7%), in NA. The adjusted prevalence of positive ELISA-NP, SN and MI were 5.7%, 5.0% and 10.0% in IDF, 6.0%, 4.3% and 8.6% in GE, and 0.6%, 1.3% and 2.5% in NA, respectively. A higher seroprevalence was observed in younger participants and when at least one child or adolescent lived in the same household. A lower seroprevalence was observed in smokers compared to non-smokers. Interpretation At the end of the lockdown the prevalence of anti-SARS-CoV-2 IgG or neutralizing antibodies remained low in the French adult population, even in regions with high reported rates of COVID-19. url: https://doi.org/10.1101/2020.09.16.20195693 doi: 10.1101/2020.09.16.20195693 id: cord-276895-p85obwp2 author: Carriazo, Sol title: Kidney disease and electrolytes in COVID-19: more than meets the eye date: 2020-07-16 words: 3633.0 sentences: 197.0 pages: flesch: 43.0 cache: ./cache/cord-276895-p85obwp2.txt txt: ./txt/cord-276895-p85obwp2.txt summary: The current issue of Clinical Kidney Journal presents 15 articles on COVID-19 and kidney disease from three continents, providing a global perspective of the impact of severe acute respiratory syndrome coronavirus 2 on electrolytes and different kidney compartments (glomeruli, tubules and vascular compartments) and presenting clinically as a syndrome of inappropriate antidiuretic hormone secretion, acute kidney injury, acute kidney disease, collapsing glomerulopathy and thrombotic microangiopathy, among others, in the context of a brand-new cardiorenal syndrome. The present issue of Clinical Kidney Journal (ckj) contains reports from the most affected countries (Figure 1 ) that illustrate the impact of SARS-CoV-2 on electrolytes and the kidneys, the different possibilities for acute renal replacement therapy (RRT) and the impact of COVID-19 in patients with pre-existing chronic kidney disease (CKD) and on chronic RRT, with emphasis on preventive measures and providing insights into therapy. abstract: COVID-19 is a global pandemic fuelled in some countries by government actions. The current issue of Clinical Kidney Journal presents 15 articles on COVID-19 and kidney disease from three continents, providing a global perspective of the impact of severe acute respiratory syndrome coronavirus 2 on electrolytes and different kidney compartments (glomeruli, tubules and vascular compartments) and presenting clinically as a syndrome of inappropriate antidiuretic hormone secretion, acute kidney injury, acute kidney disease, collapsing glomerulopathy and thrombotic microangiopathy, among others, in the context of a brand-new cardiorenal syndrome. Kidney injury may need acute dialysis that may overwhelm haemodialysis (HD) and haemofiltration capabilities. In this regard, acute peritoneal dialysis (PD) may be lifesaving. Additionally, pre-existent chronic kidney disease increases the risk of more severe COVID-19 complications. The impact of COVID-19 on PD and HD patients is also discussed, with emphasis on preventive measures. Finally, current therapeutic approaches and potential future therapeutic approaches undergoing clinical trials, such as complement targeting by eculizumab, are also presented. url: https://www.ncbi.nlm.nih.gov/pubmed/32699613/ doi: 10.1093/ckj/sfaa112 id: cord-282530-55lhjfm8 author: Carsana, Luca title: Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study date: 2020-06-08 words: 3429.0 sentences: 160.0 pages: flesch: 41.0 cache: ./cache/cord-282530-55lhjfm8.txt txt: ./txt/cord-282530-55lhjfm8.txt summary: [6] [7] [8] [9] We describe the lung histopathological findings from a large series of patients who died from COVID-19 in northern Italy, with the aim of reporting the main micro scopic pulmonary lesions associated with SARS-CoV-2 infection and severe respiratory failure. To our knowledge, these data represent the first relevant provisional information regarding tissue damage specifically induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), besides the previously described diffuse alveolar damage, a feature that characterises interstitial pneumonia regardless of infectious agent. 3, 4, 11, 14 In two autopsy studies of patients who died from SARS (eight cases from Singapore 11 and 20 cases from Toronto), 3 the predominant pattern of lung injury was diffuse alveolar damage, including the exudative and proliferative phases. In a case report of a patient who died from COVID-19 in China, the histological findings in the lungs included desquamation of pneumocytes, diffuse alveolar damage, and oedema. abstract: BACKGROUND: COVID-19 is characterised by respiratory symptoms, which deteriorate into respiratory failure in a substantial proportion of cases, requiring intensive care in up to a third of patients admitted to hospital. Analysis of the pathological features in the lung tissues of patients who have died with COVID-19 could help us to understand the disease pathogenesis and clinical outcomes. METHODS: We systematically analysed lung tissue samples from 38 patients who died from COVID-19 in two hospitals in northern Italy between Feb 29 and March 24, 2020. The most representative areas identified at macroscopic examination were selected, and tissue blocks (median seven, range five to nine) were taken from each lung and fixed in 10% buffered formalin for at least 48 h. Tissues were assessed with use of haematoxylin and eosin staining, immunohistochemical staining for inflammatory infiltrate and cellular components (including staining with antibodies against CD68, CD3, CD45, CD61, TTF1, p40, and Ki-67), and electron microscopy to identify virion localisation. FINDINGS: All cases showed features of the exudative and proliferative phases of diffuse alveolar damage, which included capillary congestion (in all cases), necrosis of pneumocytes (in all cases), hyaline membranes (in 33 cases), interstitial and intra-alveolar oedema (in 37 cases), type 2 pneumocyte hyperplasia (in all cases), squamous metaplasia with atypia (in 21 cases), and platelet–fibrin thrombi (in 33 cases). The inflammatory infiltrate, observed in all cases, was largely composed of macrophages in the alveolar lumina (in 24 cases) and lymphocytes in the interstitium (in 31 cases). Electron microscopy revealed that viral particles were predominantly located in the pneumocytes. INTERPRETATION: The predominant pattern of lung lesions in patients with COVID-19 patients is diffuse alveolar damage, as described in patients infected with severe acute respiratory syndrome and Middle East respiratory syndrome coronaviruses. Hyaline membrane formation and pneumocyte atypical hyperplasia are frequent. Importantly, the presence of platelet–fibrin thrombi in small arterial vessels is consistent with coagulopathy, which appears to be common in patients with COVID-19 and should be one of the main targets of therapy. FUNDING: None. url: https://www.ncbi.nlm.nih.gov/pubmed/32526193/ doi: 10.1016/s1473-3099(20)30434-5 id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 words: 3426.0 sentences: 227.0 pages: flesch: 51.0 cache: ./cache/cord-292347-d7xq7x5g.txt txt: ./txt/cord-292347-d7xq7x5g.txt summary: 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. abstract: nan url: https://doi.org/10.1021/acscentsci.0c00501 doi: 10.1021/acscentsci.0c00501 id: cord-264261-98h1bmb2 author: Caruana, Giorgia title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 words: 1417.0 sentences: 99.0 pages: flesch: 48.0 cache: ./cache/cord-264261-98h1bmb2.txt txt: ./txt/cord-264261-98h1bmb2.txt summary: It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients abstract: BACKGROUND: To face the current COVID-19 pandemic, diagnostic tools are essential. It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. Further studies are warranted to define the role of serological diagnosis and a possible correlation between serological response and prognosis. OBJECTIVES: To guide clinical microbiologists in the use of these diagnostic tests and clinicians in the interpretation of their results. SOURCES: A research of literature was performed through PubMed and Google Scholar using the keywords SARS-CoV-2, SARS-CoV-2 molecular diagnosis, SARS-CoV-2 immune response, SARS-CoV-2 serology/antibody testing, coronavirus diagnosis. CONTENT: The present review discusses performances, limitations and use of current and future diagnostic tests for SARS-CoV-2. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. url: https://www.ncbi.nlm.nih.gov/pubmed/32593741/ doi: 10.1016/j.cmi.2020.06.019 id: cord-354597-xubsodnk author: Carvalho, Alexandre title: SARS-CoV-2 Gastrointestinal Infection Causing Hemorrhagic Colitis: Implications for Detection and Transmission of COVID-19 Disease date: 2020-04-17 words: 2779.0 sentences: 159.0 pages: flesch: 47.0 cache: ./cache/cord-354597-xubsodnk.txt txt: ./txt/cord-354597-xubsodnk.txt summary: Recent reports from China have described concomitant digestive symptoms, such as nausea, vomiting, diarrhea, and abdominal pain, in patients with confirmed SARS-CoV-2 pulmonary infection (5) (6) (7) (8) and the presence of SARS-CoV-2 RNA in fecal samples (8, 9) . We present a case of SARS-CoV-2 gastrointestinal infection causing acute hemorrhagic colitis and signaling COVID-19 disease which endoscopy confirmed colonic injury and helped exclude other etiologies of disease. On hospital day 4, 9 days after the onset of her digestive symptoms, the patient developed a cough; nasopharyngeal swabs were sent for comprehensive viral detection, including SARS-CoV-2 RNA (Quest Diagnostics). Given the patient''s elevated C-reactive protein and persistent abdominal pain and bloody diarrhea, a flexible sigmoidoscopy was performed on hospital day 4 to evaluate for evidence of inflammatory bowel disease or ischemic colitis. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32496741/ doi: 10.14309/ajg.0000000000000667 id: cord-282539-skzosh6u author: Casadevall, Arturo title: Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date: 2020-08-17 words: 1588.0 sentences: 75.0 pages: flesch: 45.0 cache: ./cache/cord-282539-skzosh6u.txt txt: ./txt/cord-282539-skzosh6u.txt summary: The article by Wang et al in this issue of Clinical Infectious Diseases reports that neutralizing antibody titers to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus peak 4-5 weeks after the onset of symptoms and decline by 3 months [1] . The decline in neutralizing antibody titers measured by Wang et al [1] in 93.5% of the patients studied is concerning for it raises the possibility that like other coronaviruses, COVID-19 may not result in the establishment of long lasting immunity. Whereas implications of the kinetics of the antibody response to SARS-CoV-2 for long-lasting and vaccine-mediated immunity are uncertain, the results of Wang et al [1] are important for the development and use of antibody therapies. The finding that SARS-CoV-2 neutralizing titers declined relatively quickly in the Wang et al study [1] means that efforts to collect convalescent plasma with high titers of neutralizing antibody for therapy and hyper-immune globulin preparation need to be highly organized such that potential donors are contacted early in the weeks following COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32805024/ doi: 10.1093/cid/ciaa1213 id: cord-286390-ytgw3j4s author: Case, James Brett title: Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. date: 2020-07-03 words: 1659.0 sentences: 103.0 pages: flesch: 47.0 cache: ./cache/cord-286390-ytgw3j4s.txt txt: ./txt/cord-286390-ytgw3j4s.txt summary: An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We engineered an infectious molecular clone of vesicular 83 stomatitis virus (VSV) to encode the SARS-CoV-2 S protein in place of the native envelope 84 glycoprotein (G) and rescued an autonomously replication-competent virus bearing the spike. Evaluation of a novel vesicular stomatitis virus pseudotype-based assay for detection of 641 neutralizing antibody responses to SARS-CoV Vesicular stomatitis virus pseudotyped with severe acute 645 respiratory syndrome coronavirus spike protein Retroviruses pseudotyped with the severe acute respiratory 722 syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting 723 enzyme 2 abstract: Abstract Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus-reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. Comparing the neutralizing activities of various antibodies and ACE2-Fc soluble decoy protein in both assays revealed a high degree of concordance. These assays will help define correlates of protection for antibody-based countermeasures and vaccines against SARS-CoV-2. Additionally, replication-competent VSV-eGFP-SARS-CoV-2 provides a tool for testing inhibitors of SARS-CoV-2 mediated entry under reduced biosafety containment. url: https://api.elsevier.com/content/article/pii/S1931312820303620 doi: 10.1016/j.chom.2020.06.021 id: cord-265233-v5sq5epy author: Cassorla, Lydia title: Decontamination and Reuse of N95 Filtering Facepiece Respirators: Where Do We Stand? date: 2020-10-15 words: 6246.0 sentences: 470.0 pages: flesch: 47.0 cache: ./cache/cord-265233-v5sq5epy.txt txt: ./txt/cord-265233-v5sq5epy.txt summary: P ersistent shortages of filtering facepiece respirators (FFR) to protect health care workers (HCW) 1 during the current coronavirus disease 2019 (COVID-19) pandemic 2,3 has driven interest in decontamination and reuse. 8 While FFR are not superior to surgical masks for protection of HCW from seasonal flu, [9] [10] [11] [12] [13] [14] retrospective studies showed increased protection from severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1). [28] [29] [30] [31] [32] [33] [34] In 2006, the Institute of Medicine, now the National Academy of Medicine, convened a "Committee on the Development of Reusable Facemasks for Use during an Influenza Pandemic." Highlighting unpreparedness, 2 reports recommended "expeditious research and policy action" to develop personal protective equipment (PPE) designed to withstand decontamination, evidence-based performance standards, and improved coordination among regulatory agencies. Best available evidence supports moist heat, low T autoclave, MWGS, and HP-based decontamination as effective methods for SARS-CoV-2 without causing significant damage to FFR for 2-5 cycles. abstract: The coronavirus disease 2019(COVID-19) pandemic created an extraordinary demand for N95 and similarly rated filtering facepiece respirators (FFR) that remain unmet due to limited stock, production constraints, and logistics. Interest in decontamination and reuse of FFR, a product class designed for single use in health care settings, has undergone a parallel surge due to shortages. A worthwhile decontamination method must provide effective inactivation of the targeted pathogen(s), and preserve particle filtration, mask fit, and safety for a subsequent user. This discussion reviews the background of the current shortage, classification, structure, and functional aspects of FFR, and potentially effective decontamination methods along with reference websites for those seeking updated information and guidance. The most promising techniques utilize heat, hydrogen peroxide, microwave-generated steam, or ultraviolet light. Many require special or repurposed equipment and a detailed operational roadmap specific to each setting. While limited, research is growing. There is significant variation between models with regard to the ability to withstand decontamination yet remain protective. The number of times an individual respirator can be reused is often limited by its ability to maintain a tight fit after multiple uses rather than by the decontamination method itself. There is no single solution for all settings; each individual or institution must choose according to their need, capability, and available resources. As the current pandemic is expected to continue for months to years, and the possibility of future airborne biologic threats persists, the need for plentiful, effective respiratory protection is stimulating research and innovation. url: https://doi.org/10.1213/ane.0000000000005254 doi: 10.1213/ane.0000000000005254 id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 words: 11558.0 sentences: 720.0 pages: flesch: 44.0 cache: ./cache/cord-245161-xbw72k4m.txt txt: ./txt/cord-245161-xbw72k4m.txt summary: Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. abstract: Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The long persistence of viruses (hours to days) on surfaces calls for an urgent need for surface disinfection strategies to intercept virus transmission and the spread of the disease. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. This review aims to summarize the current knowledge and underlying physicochemical processes of virus transmission, in particular via fomites, and common disinfection approaches. Gaps in knowledge and needs for further research are also identified. The review focuses on SARS-CoV-2, but will supplement the discussions with related viruses. url: https://arxiv.org/pdf/2005.11443v1.pdf doi: nan id: cord-277760-i4xjk61t author: Castillo, Andrés E. title: Phylogenetic analysis of the first four SARS‐CoV‐2 cases in Chile date: 2020-04-08 words: 1208.0 sentences: 79.0 pages: flesch: 59.0 cache: ./cache/cord-277760-i4xjk61t.txt txt: ./txt/cord-277760-i4xjk61t.txt summary: To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this report, we present the sequence analysis for the first four complete genomes for SARS-CoV-2 isolates on Chilean patients. Also, a phylogenetic study was performed with worldwide SARS-CoV-2 sequences and the full genomes from Chilean isolates, to identify their genetic similarity. abstract: The current pandemic caused by the new coronavirus is a worldwide public health concern. To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. The complete genome sequences of around 450 isolates are available, and studies about similarities and differences among them and with the close related viruses that caused similar epidemics in this century. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. Our findings reveal at least two different viral variants entries to Chilean territory, coming from Europe and Asia. We also sub‐classified the isolates into variants according to punctual mutations in the genome. Our work contributes to global information about transmission dynamics and the importance to take control measures to stop the spread of the infection. url: https://doi.org/10.1002/jmv.25797 doi: 10.1002/jmv.25797 id: cord-355672-egjdy7o0 author: Castillo, Edward M. title: Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date: 2020-07-02 words: 1106.0 sentences: 67.0 pages: flesch: 49.0 cache: ./cache/cord-355672-egjdy7o0.txt txt: ./txt/cord-355672-egjdy7o0.txt summary: Initial testing protocols from the US Centers for Disease Control and Prevention (CDC) for COVID-19 for detection in patients with possible infection recommend that samples also should be first sent for influenza viruses along with respiratory panels for detection of parainfluenza virus, adenovirus, human rhinovirus, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae. 1 The problem with testing for coinfections in suspected patients is that the presence of a positive upper respiratory pathogen nucleic acid detection (RPNA) test for viruses other than SARS-CoV-2 may suggest to the clinicians alternate explanations for the patients'' symptoms. This study is a retrospective analysis of data from an academic medical center with 2 hospitals and 2 urgent care centers in San Diego, California, during the initial 2 weeks of SARS-CoV-2 testing, March 10, 2020 Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID-19) abstract: OBJECTIVES: The purpose of this study was to assess coinfection rates of coronavirus disease 2019 (COVID‐19) with other respiratory infections on presentation. METHODS: This is a retrospective analysis of data from a 2 hospital academic medical centers and 2 urgent care centers during the initial 2 weeks of testing for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) , March 10, 2020 to March 23, 2020. Testing was targeted toward high‐risk patients following US Centers for Disease Control and Prevention guidelines. Demographics include age group and sex. Laboratory test results included SARS‐CoV‐2, rapid influenza A/B, and upper respiratory pathogen nucleic acid detection. Patient demographics and coinfections are presented overall and by test results with descriptive statistics. RESULTS: Complete laboratory results from the first 2 weeks of testing were available for 471 emergency department patients and 117 urgent care center patients who were tested for SARS‐CoV. A total of 51 (8.7%) patients tested positive for COVID‐19 with only 1 of these patients also testing positive for another respiratory infection. One of the patients positive for COVID‐19 also tested positive for influenza A. Among the 537 patients who were screened and tested negative for COVID‐19, there were 33 (6.1%) patients who tested positive in the upper respiratory pathogen nucleic acid detection test. CONCLUSION: In our study investigating coinfections among 51 patients testing positive for COVID‐19, 1 patient also tested positive for influenza A. Although we found limited coinfections in our emergency department and urgent care center patient populations, further research is needed to assess potential coinfection in patients with COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32838387/ doi: 10.1002/emp2.12172 id: cord-313305-tih33rys author: Castro, Rodolfo title: COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil date: 2020-04-18 words: 838.0 sentences: 55.0 pages: flesch: 54.0 cache: ./cache/cord-313305-tih33rys.txt txt: ./txt/cord-313305-tih33rys.txt summary: We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se=82% [76-87]; Sp=97% [96-98]; DOR=168 [92-305] and SROC=0.98 [0.96-0.99]; (ii) for IgG antibodies Se=97% [90-99]; Sp=98% [97-99]; DOR=1994 [385-10334] and SROC=0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se=97% [85-99]; Sp=99% [77-100]; DOR=2649 [30-233056] and SROC=0.99 [0.98-1.00]. The aim of this study was to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. Our study reports that antigen testing and/or molecular assays using nasopharyngeal and oropharyngeal specimens had high accuracy for SARS-CoV-2 detection. abstract: Abstract The accuracy of commercially available tests for COVID-19 in Brazil remains unclear. We aimed to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. We identified 16 tests registered, mostly rapid-tests. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se=82% [76-87]; Sp=97% [96-98]; DOR=168 [92-305] and SROC=0.98 [0.96-0.99]; (ii) for IgG antibodies Se=97% [90-99]; Sp=98% [97-99]; DOR=1994 [385-10334] and SROC=0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se=97% [85-99]; Sp=99% [77-100]; DOR=2649 [30-233056] and SROC=0.99 [0.98-1.00]. These tests can be helpful for emergency testing during the COVID-19 pandemic in Brazil. However, it is important to highlight the high rate of false negative results from tests which detect SARS-CoV-2 IgM antibodies in the initial course of the disease and the scarce evidence-based validation results published in Brazil. Future studies addressing the diagnostic performance of tests for COVID-19 in the Brazilian population are urgently needed. url: https://www.sciencedirect.com/science/article/pii/S1413867020300295?v=s5 doi: 10.1016/j.bjid.2020.04.003 id: cord-340583-kjrxrk50 author: Castro‐Rodriguez, Jose A. title: Asthma and COVID‐19 in children – a systematic review and call for data date: 2020-06-18 words: 3081.0 sentences: 172.0 pages: flesch: 45.0 cache: ./cache/cord-340583-kjrxrk50.txt txt: ./txt/cord-340583-kjrxrk50.txt summary: Importantly, none of the largest epidemiological studies including children with COVID-19 reported clinical findings or underlying characteristics to help assess whether asthma -or other chronic lung diseases-constitutes a risk factor for SARS-CoV-2 infection or COVID-19 severity. Rather than a risk factor, a recent review of data in adults reported that both asthma and COPD appear to be under-represented in the comorbidities reported for patients with COVID-19, compared with global estimates of prevalence for these conditions in the general population (63) . After an extensive review of the current literature, only two reports included information on asthma as a potential risk factor for COVID-19 infection -but not severity or mortality-in children. However, the largest studies to date have been limited to a description of the number of cases by age group, and so it remains unclear whether childhood asthma -or other pediatric respiratory diseases-are associated with COVID-19 risk or severity. abstract: RATIONALE: Whether asthma constitutes a risk factor for COVID‐19 is unclear. Here we aimed to assess whether asthma, the most common chronic disease in children, is associated with higher COVID‐19 risk or severity in pediatric populations. METHODS: We performed a systematic literature search in three stages: First, we reviewed PubMed, EMBASE and CINAHL for systematic reviews of SARS‐CoV‐2 and COVID‐19 in pediatric populations, and reviewed their primary articles; second, we searched PubMed for studies on COVID‐19 or SARS‐CoV‐2 and asthma/wheeze, and evaluated whether the resulting studies included pediatric populations; third, we repeated the second search in BioRxiv.org and MedRxiv.org to find pre‐prints that may have information on pediatric asthma. RESULTS: In the first search, eight systematic reviews were found, of which five were done in pediatric populations; none of the 67 primary studies included data on pediatric asthma as a comorbidity for COVID‐19. In the second search, we found 34 results in PubMed, of which five reported asthma in adults, but none included data on children. In the third search, 25 pre‐prints in MedRxiv included data on asthma, but none on children. We found one report by the U.S. CDC stating that 40/345 (~11.5%) children with data on chronic conditions had “chronic lung diseases including asthma”, and one from a tertiary hospital in New York that reported asthma in 11/46 (~23.9%) children hospitalized for COVID‐19. CONCLUSION: There is scarcely any data on whether childhood asthma (or other pediatric respiratory diseases) constitute risk factors for SARS‐CoV‐2 infection or COVID‐19 severity. Studies are needed that go beyond counting the number of cases in the pediatric age range. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/ppul.24909 doi: 10.1002/ppul.24909 id: cord-294028-pcc6mucj author: Caussy, Cyrielle title: Obesity is Associated with Severe Forms of COVID‐19 date: 2020-05-21 words: 747.0 sentences: 42.0 pages: flesch: 56.0 cache: ./cache/cord-294028-pcc6mucj.txt txt: ./txt/cord-294028-pcc6mucj.txt summary: which reports a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2) requiring invasive mechanical ventilation. (1) , which reported a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation (IMV). The findings (1) reporting a higher IMV in severe obesity (BMI ≥ 35) versus lean patients (BMI < 25) from Lille University Center in France may not be generalizable to other centers in France or in other countries, depending on the criteria implemented for the indication of IMV in other centers (2) . However, our data tend to confirm the observation from Lille University Center of a higher requirement for IMV in severe obesity (BMI ≥ 35) compared with lean patients (81.8% vs. High prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation abstract: We have read with great interest the Brief Cutting Edge Report from Simonnet et al. which reports a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2) requiring invasive mechanical ventilation. In the context of unprecedented health crisis due to the coronavirus disease 2019 (COVID-19) outbreak, these results are of a great importance and may have major implications in public health strategy especially in western countries affected by a high prevalence of obesity. url: https://www.ncbi.nlm.nih.gov/pubmed/32314861/ doi: 10.1002/oby.22842 id: cord-336543-ydrmlujj author: Cavalli, Eugenio title: Entangling COVID-19 associated thrombosis into a secondary antiphospholipid antibody syndrome: Diagnostic and therapeutic perspectives (Review) date: 2020-06-25 words: 5813.0 sentences: 260.0 pages: flesch: 39.0 cache: ./cache/cord-336543-ydrmlujj.txt txt: ./txt/cord-336543-ydrmlujj.txt summary: We propose here that the thromboembolic events and eventually the development of DIC provoked by SARS-CoV-2 infection may represent a secondary anti-phospholipid antibody syndrome (APS). On the basis of empirical observations and emerging laboratoristic findings, we will elaborate the hypothesis that several cases of thrombotic events during cOVId-19 infection represent the clinical epiphenomenon of a viral-induced secondary anti-phospholipid antibody syndrome (APS) that, in the most severe cases, may develop as catastrophic anti-phospholipid antibody syndrome (cAPS). clinical evidence and emerging data from pathological examinations indicate that a thrombotic diathesis, potentially leading to venous thromboembolism (VTE), and to dIc in some of the most severe cases, may occur in a substantial proportion of patients with cOVId-19 infection, also in a manner independent of long-term bed rest and eventual hormonal treatment. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel β coronavirus that is the etiological agent of the pandemic coronavirus disease 2019 (COVID-19) that at the time of writing (June 16, 2020) has infected almost 6 million people with some 450,000 deaths. These numbers are still rising daily. Most (some 80%) cases of COVID-19 infection are asymptomatic, a substantial number of cases (15%) require hospitalization and an additional fraction of patients (5%) need recovery in intensive care units. Mortality for COVID-19 infection appears to occur globally between 0.1 and 0.5% of infected patients although the frequency of lethality is significantly augmented in the elderly and in patients with other comorbidities. The development of acute respiratory distress syndrome and episodes of thromboembolism that may lead to disseminated intravascular coagulation (DIC) represent the primary causes of lethality during COVID-19 infection. Increasing evidence suggests that thrombotic diathesis is due to multiple derangements of the coagulation system including marked elevation of D-dimer that correlate negatively with survival. We propose here that the thromboembolic events and eventually the development of DIC provoked by SARS-CoV-2 infection may represent a secondary anti-phospholipid antibody syndrome (APS). We will apply both Baconian inductivism and Cartesian deductivism to prove that secondary APS is likely responsible for coagulopathy during the course of COVID-19 infection. Diagnostic and therapeutic implications of this are also discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32588061/ doi: 10.3892/ijmm.2020.4659 id: cord-260054-iihgc5nr author: Cavallo, Luigi title: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date: 2020-06-08 words: 4062.0 sentences: 210.0 pages: flesch: 59.0 cache: ./cache/cord-260054-iihgc5nr.txt txt: ./txt/cord-260054-iihgc5nr.txt summary: 3D structures are now available from the Protein Data Bank (PDB) (21) for the SARS-CoV-2 S protein in the pre-fusion conformation, also bound to the ACE2 receptor (22) (23) (24) (25) (26) (27) (28) , and for the post-fusion core of its S2 subunit in the postfusion conformation (29) . We downloaded all the SARS-CoV-2 genomic sequences from the GISAID resource on April 21 st 2020, extracted from them 7,692 complete S protein sequences and identified all the point mutations occurring in at least two identical sequences (see Methods). When looking at the post-fusion conformation of the SARS-CoV-2 spike protein S2 subunit, these mutations appear more revealing. Based on a thorough analysis of the S protein sequences, that we extracted from the genomic sequences of SARS-CoV-2 reported in GISAID on April 21 st , we identified the fusion core of the HR1 as a mutational hotspot. abstract: The iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21st, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the “fusion core” of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29th, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly. url: https://doi.org/10.1101/2020.06.08.140152 doi: 10.1101/2020.06.08.140152 id: cord-306749-qetf3uur author: Caves, N.D. title: Attitudes to basic life support among medical students following the 2003 SARS outbreak in Hong Kong() date: 2005-10-10 words: 4318.0 sentences: 177.0 pages: flesch: 49.0 cache: ./cache/cord-306749-qetf3uur.txt txt: ./txt/cord-306749-qetf3uur.txt summary: This study seeks to explore whether this epidemic has altered the willingness of Hong Kong medical students to perform basic life support and mouth-to-mouth ventilation during an out-of-hospital cardiac arrest. The survey was conducted during July and August 2003, approximately two months after Hong Kong was removed from the World Health Organisation SARS Infected Areas list, and was designed to examine student confidence in BLS skills, their perceptions of the risks associated with performing BLS and their willingness to perform BLS in varying situations. Many of the previous studies investigating this issue have indicated that respondees are more reluctant to perform mouth-to-mouth ventilation than chest compressions, and have highlighted rescuers'' fears regarding transmission of the human immunodeficiency virus (HIV) in particular as a reason for not performing BLS. abstract: BACKGROUND: In 2003 severe acute respiratory syndrome (SARS) affected 1755 people in Hong Kong, including 386 health care professionals, some of whom were infected during resuscitation attempts of affected patients. This study seeks to explore whether this epidemic has altered the willingness of Hong Kong medical students to perform basic life support and mouth-to-mouth ventilation during an out-of-hospital cardiac arrest. METHODS: A questionnaire was used to survey Year 4 medical students at the end of their undergraduate anaesthesia attachment, during which basic life support (BLS) skills were taught. The survey was conducted during July and August 2003, approximately two months after Hong Kong was removed from the World Health Organisation SARS Infected Areas list, and was designed to examine student confidence in BLS skills, their perceptions of the risks associated with performing BLS and their willingness to perform BLS in varying situations. RESULTS: The response rate was over 60% (35 from a possible 54). Students were positive regarding the adequacy of their BLS training. They were concerned about disease transmission during resuscitation but were less positive regarding whether the risks had increased due to SARS. In all situations they were significantly more likely to perform mouth-to-mouth ventilation for a family member compared with a stranger (p < 0.001) and to withhold mouth-to-mouth ventilation if either vomit or blood were present in the victim's mouth. CONCLUSIONS: Hong Kong medical students feel able to perform BLS if required. They are concerned about the risk of disease transmission, including SARS, during resuscitation, but would be more likely to withhold mouth-to-mouth resuscitation in the presence of vomit or blood than due to a fear of contracting SARS. url: https://www.sciencedirect.com/science/article/pii/S0300957205002224 doi: 10.1016/j.resuscitation.2005.05.014 id: cord-273784-sr6afv60 author: Cazares, Lisa H. title: Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein date: 2020-09-23 words: 5793.0 sentences: 299.0 pages: flesch: 54.0 cache: ./cache/cord-273784-sr6afv60.txt txt: ./txt/cord-273784-sr6afv60.txt summary: The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. To determine the feasibility of targeted MS for SARS-CoV-2 diagnostics, we developed a method for the detection and quantitation of the S and NP, which employs parallel reaction monitoring (PRM) using a high-resolution Orbitrap instrument, thereby providing very high specificity. To test the ability of the PRM assay to detect S protein and NP in a relevant sample type, we spiked inactivated SARS CoV-2 virions into in vitro derived mucus. (B) PRM assay was then used to quantitate the SARS-CoV-2 protein levels in a mock sample that was created by adding an inactivated virus sample to in vitro derived mucus. Using the calibration curve from the best performing peptide for NP (DQVILLNK), the low and high SARS-CoV-2 mock samples contained on average 227 and 422 amol of NP, respectively, on column (see Figure 5A ). abstract: [Image: see text] There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected patient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as reverse transcription polymerase chain reaction (RT-PCR) are the gold standard, during the current pandemic, the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detection methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syncytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagnosis of active infection, and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of proteins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein, we report a targeted mass spectrometry assay for the detection of SARS-CoV-2 spike protein and nucleoprotein in a relevant biological matrix. Recombinant full-length spike protein and nucleoprotein were digested and proteotypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high-resolution Orbitrap instrument. A spectral library, which contained seven proteotypic peptides (four from spike protein and three from nucleoprotein) and the top three to four transitions, was generated and evaluated. From the original spectral library, we selected two best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. The PRM assay provided a limit of detection of ∼200 attomoles and a limit of quantitation of ∼ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for the detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2 × 10(5) viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially, mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the presence of SARS-CoV-2 in archived or recently collected biological fluids, in vitro-derived research materials, and wastewater samples. url: https://www.ncbi.nlm.nih.gov/pubmed/32966064/ doi: 10.1021/acs.analchem.0c02288 id: cord-270035-1e1wzdri author: Cazzaniga, Marco title: SARS-COV-2 Infection and Kawasaki Disease: Case Report of a Hitherto Unrecognized Association date: 2020-07-03 words: 2076.0 sentences: 109.0 pages: flesch: 43.0 cache: ./cache/cord-270035-1e1wzdri.txt txt: ./txt/cord-270035-1e1wzdri.txt summary: The association of Kawasaki disease and COVID-19 infection has to our knowledge been reported only once (5), we report a second case from Italy, currently the third most affected country in the world with regard to number of proven SARS-COV-2 infections. We were then contacted as reference Center for Kawasaki Disease (KD) in our Pediatric Immunology Unit: considering the clinical history (fever lasting more than 5 days, erythematous rash, labial, and conjunctival hyperemia) and the result of laboratory tests we confirmed the diagnostic suspicion of atypical/incomplete KD without coronary involvement, and started treatment with high dose intravenous immunoglobulins (IVIG) 2 g/kg and high dose acetylsalicylic acid (ASA 50 mg/kg/day). In the setting of COVID-19 there are several reports of using corticosteroids for Acute Respiratory Disease Syndrome (ARDS), but considering the not severe clinical course and presentation in our patient we did not start steroid therapy. abstract: Coronavirus-associated disease (COVID-19) was firstly reported at the end of 2019. Generally, COVID-19 seems to be a less severe disease in children than in adults. According to the current literature, children account approximately for 2% of diagnosed COVID-19 cases. Northern Italy is one of the geographical areas mainly affected by the ongoing COVID-19 pandemic. We describe a pediatric patient diagnosed and treated for atypical/incomplete Kawasaki Disease (KD) complicated with paralytic ileus, who also resulted positive for SARS-COV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32719757/ doi: 10.3389/fped.2020.00398 id: cord-306034-1u29o2id author: Cazzolla, Angela P. title: Taste and Smell Disorders in COVID-19 Patients: Role of Interleukin-6 date: 2020-08-04 words: 4014.0 sentences: 193.0 pages: flesch: 47.0 cache: ./cache/cord-306034-1u29o2id.txt txt: ./txt/cord-306034-1u29o2id.txt summary: [Image: see text] The rapid recovery of smell and taste functions in COVID-19 patients could be attributed to a decrease in interleukin-6 levels rather than central nervous system ischemic injury or viral damage to neuronal cells. To correlate interleukin-6 levels in COVID-19 patients with olfactory or gustatory dysfunctions and to investigate the role of IL-6 in the onset of these disorders, this observational study investigated 67 COVID-19 patients with taste or smell disorders or both, who did not require intensive care admission, admitted at COVID Hospital of Policlinico of Bari from March to May 2020. Interleukin-6 levels in COVID-19 patients in relation to olfactory or gustatory disorders were correlated from the time of their admission to the time of swab negativization. The aim was to monitor and to correlate IL-6 levels in laboratory-confirmed COVID-19 patients with olfactory or gustatory disorders from the time of their admission to the time of swab negativization. abstract: [Image: see text] The rapid recovery of smell and taste functions in COVID-19 patients could be attributed to a decrease in interleukin-6 levels rather than central nervous system ischemic injury or viral damage to neuronal cells. To correlate interleukin-6 levels in COVID-19 patients with olfactory or gustatory dysfunctions and to investigate the role of IL-6 in the onset of these disorders, this observational study investigated 67 COVID-19 patients with taste or smell disorders or both, who did not require intensive care admission, admitted at COVID Hospital of Policlinico of Bari from March to May 2020. Interleukin-6 was assayed in COVID-19 patients with taste or smell disturbances at the time of admission and at the time of swab negativization. At the same time, patients have been given a specific survey to evaluate the severity of taste and smell disturbances. Of 125 patients with smell or taste dysfunctions at onset of disease, 67 fulfilled the inclusion criteria, while 58 were excluded because 35 of them required intensive care admission, 5 were unable to answer, 5 died, 7 had finished chemotherapy recently, and 5 refused to participate. The evaluation of taste and smell disorders was carried out using a survey performed at the time of admission and at the time of swab negativization. Sinonasal outcome test 22 (SNOT-22) was used as a reference for olfactory function assessment, and Taste and Smell Questionnaire Section of the US NHANES 2011–2014 protocol (CDC 2013b) was used as reference for gustatory function assessment. A venous blood sample was taken for each patient to measure IL-6 levels upon entry and at swab negativization. Interleukin-6 levels in COVID-19 patients in relation to olfactory or gustatory disorders were correlated from the time of their admission to the time of swab negativization. Statistically significant correlations were obtained between the decrease of interleukin-6 levels and the improvement of smell (p value < 0.05) and taste (p = 0.047) functions at swab negativization. The acquired results demonstrate the key role of interleukin-6 in the pathogenesis of chemosensitive disorders in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32786309/ doi: 10.1021/acschemneuro.0c00447 id: cord-265170-yv04ijsm author: Ceccarelli, Giancarlo title: Probiotics and COVID-19 date: 2020-07-13 words: 1124.0 sentences: 69.0 pages: flesch: 36.0 cache: ./cache/cord-265170-yv04ijsm.txt txt: ./txt/cord-265170-yv04ijsm.txt summary: SARS-CoV-2 has been postulated to affect gut inflammation both directly and indirectly, infecting intestinal epithelial cells through the angiotensin-converting enzyme 2 (ACE2) receptor and transmembrane protease serine 2, and inducing proinflammatory chemokine and cytokine release. 7 Given this evidence, bacteriotherapy could represent a complementary resource for the prevention and restoration of SARS-CoV-2 intestinal mucosa damage through the modulation of gut microbiota and decreasing related inflammation. In other infections, such as HIV, in which intestinal inflammation and related microbiota impairment can affect gut epithelial barrier function, bacteriotherapy (through microbiota surface compounds and metabolites) to exist between different probiotic bacterial species and strains. 8, 9 We believe that studies of bacteriotherapy in SARS-CoV-2 are needed to evaluate the potential effects on intestinal mucosal inflammation and microbiome homoeostasis. In the absence of a vaccine or effective therapy for COVID-19, we agree that probiotics represent a complementary approach for the prevention and restoration of SARS-CoV-2-induced mucosal damage or inflammation through the modulation of gut microbiota. abstract: nan url: https://api.elsevier.com/content/article/pii/S2468125320301965 doi: 10.1016/s2468-1253(20)30196-5 id: cord-342084-fbtx7rwi author: Ceccarelli, Giancarlo title: IS TEICOPLANIN A COMPLEMENTARY TREATMENT OPTION FOR COVID-19? THE QUESTION REMAINS date: 2020-05-23 words: 643.0 sentences: 41.0 pages: flesch: 47.0 cache: ./cache/cord-342084-fbtx7rwi.txt txt: ./txt/cord-342084-fbtx7rwi.txt summary: We read with great interest the editorial by Baron Coronavirus (MERS-CoV), but also Ebola virus, influenza A and B viruses, and feline infectious peritonitis virus (FIPV), were reported as potential targets of teicoplanin and its chemical derivatives. Based on the aforementioned, teicoplanin has been used either as a potential antiviral agent and treatment of possible Staphylococcus aureus superinfection in our critical patients with severe SARS-CoV-2 pneumonia, since this latter may represent a major complication of respiratory viral infections. Moreover, a recent study showed that teicoplanin potently prevents the entrance of SARS-CoV2 into the cytoplasm with an IC50 of only 1.66 μM which is much lower than the routine trough serum drug concentration (approximately 7-8 μM/L). Therefore, the routinely-used teicoplanin doses adopted in our series might be considered as potentially adequate for treatment of patients with SARS-CoV2 infection. Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32454071/ doi: 10.1016/j.ijantimicag.2020.106029 id: cord-279115-eyk8sxk7 author: Cecconi, Maurizio title: Ten things we learned about COVID-19 date: 2020-06-05 words: 1621.0 sentences: 106.0 pages: flesch: 51.0 cache: ./cache/cord-279115-eyk8sxk7.txt txt: ./txt/cord-279115-eyk8sxk7.txt summary: The infection starts with the competition between the SARS-CoV-2 virions arrived in the respiratory mucosa that express high levels of ACE2 receptors and the barrier made by mucus secreted by goblet cells and moved by hair-like cilia and innate immunity reactions. Evidence from SARS-CoV-1 suggests that these viruses may block interferon-mediated antiviral immunity (Fig. 1 ). Inflammation plays a key role in the development of COVID-19 from a SARS-CoV-2 infection. Unsurprisingly for a disease characterised by an inflammatory state in response to a viral infection, venous and arterial thromboembolic complications are common in hospitalised patients [6] . Given the timing and characteristics of the antibody response (see above), appropriately validated assays are instrumental for epidemiological studies, evaluation of plasma donations (see below), assessment of memory and response to vaccine, and as a companion diagnostic in RT-PCR-negative patients. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32504103/ doi: 10.1007/s00134-020-06140-0 id: cord-323666-t7cshj05 author: Cegolon, L. title: Nasal Disinfection for the Prevention and Control of COVID-19: A Scoping Review on Potential Chemo-preventive Agents. date: 2020-08-18 words: 6187.0 sentences: 339.0 pages: flesch: 46.0 cache: ./cache/cord-323666-t7cshj05.txt txt: ./txt/cord-323666-t7cshj05.txt summary: Figure 1 reports the corresponding changes as percentage or odds; the latter detects the improvement of the index score better than the former because it is able to overcome the ceiling effects J o u r n a l P r e -p r o o f Therefore, in addition to an effective treatment for symptomatic patients, there is an urgent need to abate the carriage of SARS-CoV-2 in the human nasal cavity of asymptomatic/pre-symptomatic individuals, in order to contain the transmission of the novel coronavirus within the community. The abstracts of the original articles were explored for the following terms: mechanism(s) of action, tolerability and any evidence of toxic effects or selection of resistant strains, whether the treatment was tested in vitro (in particular against SARS-CoV-2), or reached the clinical trials stage, or is currently marketed/promoted/sold. abstract: BACKGROUND: Neither pre-exposure nor post-exposure chemo-prophylaxis agents are currently available to prevent COVID-19. On the other hand, high loads of SARS-CoV-2 are shed from the nasal cavity before and after symptoms onset. OBJECTIVE: To conduct a scoping review on the available evidence on tolerable nasal disinfectants with encouraging health outcomes against SARS-CoV-2, i.e., agents effective against at least two different viruses beyond SARS-CoV-2. METHODS: Online databases were searched to identify papers published during 2010–2020. Publications were selected if they were relevant to the scoping review. The review was narrative, describing for each treatment the mechanism(s) of action, tolerability, in vitro and in vivo evidence of the effects against SARS-CoV-2 and whether the product had been marketed. RESULTS: Eight treatments were scrutinized: hypothiocyanite, lactoferrin, N-chlorotaurine, interferon-alpha, povidone-iodine, quaternary ammonium compounds, alcohol-based nasal antiseptics and hydroxychloroquine. In vitro viricidal effect against SARS-CoV-2 was reported for povidone-iodine. Inhibition of other coronaviruses was described for lactoferrin, hydroxychloroquine and quaternary ammonium compound. No treatment has been tested against SARS-CoV-2 in randomized controlled clinical trials thus far. However, interferon-alpha, lactoferrin and hydroxychloroquine were tested in one-arm open label uncontrolled clinical trials. Oxidant activity (hypothiocyanite, N-chlorotaurine and povidone-iodine), enhancement of endocytic and lysosomal pH (quaternary ammonium compounds and hydroxychloroquine) and destruction of the viral capsid (quaternary ammonium compounds, alcohol-based nasal antiseptics) were the main mechanisms of action. Lactoferrin and interferon-alpha had subtle biological mechanisms. With the exception of N-chlorotaurine, the others are products available on the market. CONCLUSIONS: Effective and safe chemo-prophylactic drugs against SARS-CoV-2 do not exist yet but most eligible candidates are already in the market. Whilst the human nasal cavity is the port of entry for SARS-CoV-2, the mouth is involved as exit site through emission of respiratory droplets. The well-known hand-to-nose-to-hand cycle of contamination requires appropriate additional strategies for infection control. To narrow down the subsequent laboratory and clinical investigations, a case-control approach could be employed to compare the use of candidate drugs among individuals testing positive and negative to COVID-19 swabs. url: https://api.elsevier.com/content/article/pii/S1438463920305514 doi: 10.1016/j.ijheh.2020.113605 id: cord-275023-0z219rcy author: Cerofolini, Linda title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date: 2020-07-29 words: 3485.0 sentences: 198.0 pages: flesch: 44.0 cache: ./cache/cord-275023-0z219rcy.txt txt: ./txt/cord-275023-0z219rcy.txt summary: title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. In this manuscript we apply a very simple method based on a unitedresidue modelling of protein-surface interactions, to specifically address the problem of determining the orientation of the SARS-CoV-2 Spike protein Receptor Binding Domain (RBD) on a few prototypical surfaces for biomedical use. In this work, we describe the use of united-residue modelling for the prediction of the orientation of the receptor binding domain of the spike protein of the novel coronavirus SARS-CoV-2, a protein of high immunological relevance at the most commonly used surfaces for the preparation of lateral-flow immunochemical devices. abstract: The possibility of immobilizing a protein with antigenic properties on a solid support offers significant possibilities in the development of immunosensors and vaccine formulations. For both applications, the orientation of the antigen should ensure ready accessibility of the antibodies to the epitope. However, an experimental assessment of the orientational preferences necessarily proceeds through the preparation/isolation of the antigen, the immobilization on different surfaces and one or more biophysical characterization steps. To predict a priori whether favorable orientations can be achieved or not would allow one to select the most promising experimental routes, partly mitigating the time cost towards the final product. In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. These calculations can account for the experimental observation that direct immobilization on gold gives sufficient exposure of the epitope to obtain a response in immunochemical assays. url: https://doi.org/10.1016/j.bpc.2020.106441 doi: 10.1016/j.bpc.2020.106441 id: cord-343800-nbydaoac author: Cerutti, Francesco title: Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2 date: 2020-09-29 words: 1209.0 sentences: 65.0 pages: flesch: 56.0 cache: ./cache/cord-343800-nbydaoac.txt txt: ./txt/cord-343800-nbydaoac.txt summary: We evaluated the recently CE-approved rapid POCT SD-Biosensor for SARS-CoV-2 nucleoprotein detection in nasopharyngeal secretions from 330 patients admitted to the Emergency Room for a suspect of COVID-19 and travelers returning home from high risk countries. Point-of-care diagnostic tests (POCTs) for detecting viral antigens in clinical samples would be very helpful for the diagnosis of COVID-19 [2] either as mass-screening or first aid tests at the emergency room. To evaluate a recently CE-approved POCT, the STANDARD Q COVID-19 Ag (SD-Biosensor, RELAB, I), for the detection of SARS CoV-2 nucleoprotein in NP swabs in comparison with the gold standard RT-PCR. POCTs for the detection of SARS-CoV-2 J o u r n a l P r e -p r o o f antigens are quite promising; however, the principal concerns are the false-negative rate due to low viral loads [3] [4] [5] [6] [7] [8] . Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples abstract: At the time of writing, FIND has listed four CE-marked SARSCoV-2 antigen tests. We evaluated the recently CE-approved rapid POCT SD-Biosensor for SARS-CoV-2 nucleoprotein detection in nasopharyngeal secretions from 330 patients admitted to the Emergency Room for a suspect of COVID-19 and travelers returning home from high risk countries. Sensitivity, specificity, accuracy, negative and predictive values were consistent with the use of the test to mass-screening for SARS-CoV-2 surveillance. url: https://doi.org/10.1016/j.jcv.2020.104654 doi: 10.1016/j.jcv.2020.104654 id: cord-338140-p88fgojk author: Cervantes-Pérez, Enrique title: Medical Nutrition Therapy in Hospitalized Patients With SARS-CoV-2 (COVID-19) Infection in a Non-critical Care Setting: Knowledge in Progress date: 2020-10-30 words: 3964.0 sentences: 214.0 pages: flesch: 42.0 cache: ./cache/cord-338140-p88fgojk.txt txt: ./txt/cord-338140-p88fgojk.txt summary: The purpose of this review is to provide concise guidance for the nutritional management of individuals with COVID-19 based on the current literature and focused on those in the non-ICU setting or with an older age and polymorbidity, which are independently associated with malnutrition and its negative impact on mortality. Numerous cases of pneumonia caused by a new virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were initially reported in Wuhan, China, at the end of December 2019. The purpose of this review is to summarize what is known about SARS-CoV-2 infection and provide possible and potential nutritional interventions on novel coronaviruses for clinicians. Older adults and polymorbid individuals suffering from chronic and acute disease conditions are at increased risk for poor outcomes and higher mortality following infection with the COVID-19-causing virus. abstract: PURPOSE OF REVIEW: As of 13 September 2020, almost 28 million confirmed cases of COVID-19 including more than 920,000 deaths have been reported to the World Health Organization. The SARS-CoV-2 pandemic represents a potential threat to patients and healthcare systems worldwide. Patients with the worst outcomes and higher mortality are reported to include older adults, polymorbid individuals, and malnourished people in general. The purpose of this review is to provide concise guidance for the nutritional management of individuals with COVID-19 based on the current literature and focused on those in the non-ICU setting or with an older age and polymorbidity, which are independently associated with malnutrition and its negative impact on mortality. RECENT FINDINGS: Prolonged hospital stays are reported to be required for individuals with COVID-19, and longer acute setting stays may directly worsen or cause malnutrition, with severe loss of skeletal muscle mass and function, which may lead to poor quality of life and additional morbidity. Nutritional therapy is among the mainstay of therapeutic principles and one of the core contents of comprehensive treatment measures. SUMMARY: The current COVID-19 pandemic is unprecedented. The prevention, diagnosis, and treatment of malnutrition should therefore be routinely included in the management of individuals with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33125628/ doi: 10.1007/s13668-020-00337-x id: cord-297256-i9468t8v author: Cesari, Matteo title: Geriatric Medicine in Italy in the Time of Covid-19 date: 2020-04-03 words: 1645.0 sentences: 92.0 pages: flesch: 58.0 cache: ./cache/cord-297256-i9468t8v.txt txt: ./txt/cord-297256-i9468t8v.txt summary: In fact, although current data indicate that persons aged 70 years and older contribute to about the 85% of the death events in Italy, it cannot be overlooked the fact that Japan has substantially smaller figures despite being the oldest country in the world. To keep the healthcare machine running and support the colleagues overwhelmed in the management of COVID patients, there have been pediatricians working with older patients, or surgeons taking care of internal medicine issues... Geriatric medicine has produced substantial evidence showing that frail older persons require adaptations in the clinical approach, and that the environment plays a critical role for the wellbeing of the aging individual (5,6). Many older persons (with their chronic conditions and care needs) remained isolated after the SARS-CoV-2 outbreak. The same human interaction between the patient and his/her physician is lost behind the burdening personal protective equipment in COVID-19 facilities. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32346679/ doi: 10.1007/s12603-020-1354-z id: cord-269206-160ddfsc author: Ceylan, Rahmiye Figen title: Historical evidence for economic effects of COVID-19 date: 2020-06-04 words: 4555.0 sentences: 268.0 pages: flesch: 51.0 cache: ./cache/cord-269206-160ddfsc.txt txt: ./txt/cord-269206-160ddfsc.txt summary: Yet, the contagious diseases having global effects had forgotten long time ago even if there appeared some recent encounters in the past 20 The differentiating features of COVID-19 or SARS-COV2 from the recent encounters are its geographical dispersion in terms of contagion and its causalities. In an earlier attempt to comment on prospective COVID-19 effects, Barro and his friends estimated growth of national income and consumption expenditures of 42 countries between 1901 and 1929 on human capital loss due to the WWI. Due to changing labour market composition and economic conditions during and after the influenza, both productivity and overall income had declined and savings and investment potential were affected negatively. Confirming previous research on SARS, Lionello [26] indicated that rising social fear and reduction in social contact resulted in reduced supplies and reduced labour demand specifically in the services sector between 20 and 70%. Especially, shrinking services and industries facing lower labour supplies and reducing demand are expected to downsize all economic structures. abstract: Like wars and socio-politic shifts, contagious diseases have changed the economics and politics of the world throughout history. In 2020, the world faced COVID-19, a globally effective virus leading to mass losses and socio-economic panic. Due to apparent psycho-social conditions, analyzing the potential economic effects of the COVID-19 pandemic was inevitable. Thus, discussing economic effects of previous global and regional epidemics is considered beneficial. This research evaluated most of the known epidemics and their effects on economics and socio-politics by reviewing scientific literature. In addition to the vast literature and observations on the ongoing process, we assessed the potential impacts of COVID-19 and potential ways to overcome these impacts. The most urgent socio-economic measures needed to combat the negative effects of a contagious disease are related to unemployment with its income effects and security of all sectors. To prevent persistent unemployment, service, retail, and even industrial sectors need to be supported. Additionally, we discussed the need for re-organizing the funding and managerial sustainability of healthcare services to be prepared for future. url: https://www.ncbi.nlm.nih.gov/pubmed/32500243/ doi: 10.1007/s10198-020-01206-8 id: cord-257258-hu9oxea1 author: Chabner, Bruce A. title: Taking the Longer View of COVID‐19 date: 2020-04-27 words: 1810.0 sentences: 88.0 pages: flesch: 39.0 cache: ./cache/cord-257258-hu9oxea1.txt txt: ./txt/cord-257258-hu9oxea1.txt summary: In the absence of a vaccine or effective antivirals, social distancing is currently the primary public health strategy for containing the epidemic and has been successful in South Korea and China, where it was stringently employed. Regarding the chances of creating an effective vaccine against SARS-CoV-2 infection, in the U.S. the Biomedical Advanced Research and Development Authority (BARDA) of the Department of Health and Human Services is devoting significant support for two currently approved trials: a lipid nanoparticle vaccine that contains mRNAs directing the synthesis of the SARS-CoV-2 spike protein (Moderna) and an adenovirus construct of virus material co-supported by Johnson & Johnson [1] . However, vaccine development and its worldwide implementation, coupled with effective antiviral treatment, will be required to control COVID-19 and prevent another pandemic. In order to be ready for the next iteration of COVID-19, the worldwide medical community will need to cooperate in conducting extensive clinical trials of vaccines, antivirals, and immune therapies on an accelerated time scale. abstract: What are the prospects for dealing with COVID‐19 more effectively in the future? This editorial addresses the question from the perspective of long‐term control of coronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32304334/ doi: 10.1634/theoncologist.2020-0313 id: cord-296556-fr8x8j3i author: Chaccour, Carlos title: Ivermectin and COVID-19: Keeping Rigor in Times of Urgency date: 2020-04-16 words: 1400.0 sentences: 91.0 pages: flesch: 47.0 cache: ./cache/cord-296556-fr8x8j3i.txt txt: ./txt/cord-296556-fr8x8j3i.txt summary: 10 recently reported that ivermectin is a potent inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication in vitro. 13 However, even with this dose, which is 10-fold greater than those approved by the US Food and Drug Administration, the C max values reported were ∼250 ng/mL, 13 one order of magnitude lower than effective in vitro concentrations against SARS-CoV-2. Very recently, preliminary findings on a potential effect of hydroxychloroquine combined with azithromycin against SARS-CoV-2 were widely publicized, 15 leading to a surge in demand and self-medication, which resulted in serious harm in some cases and a stock shortage that jeopardized drug availability for other critical conditions for which hydroxychloroquine or chloroquine is the standard of care, that is, vivax malaria, rheumatoid arthritis, and systemic lupus erythematosus. 20, 21 Second, boosted antiretrovirals such as lopinavir/ritonavir and darunavir/cobicistat, which have been widely used against SARS-CoV-2 based on limited evidence, and a number of other drugs, are potent inhibitors of cytochrome P 450 3A4, the main metabolic pathway for ivermectin. abstract: Ivermectin and Novel Coronavirus Disease (COVID-19): Keeping Rigor in Times of Urgency. url: https://doi.org/10.4269/ajtmh.20-0271 doi: 10.4269/ajtmh.20-0271 id: cord-332178-0xyrmk5a author: Chadchan, Sangappa B. title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date: 2020-06-24 words: 2449.0 sentences: 163.0 pages: flesch: 50.0 cache: ./cache/cord-332178-0xyrmk5a.txt txt: ./txt/cord-332178-0xyrmk5a.txt summary: title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization STUDY QUESTION Is SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization? The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. WIDER IMPLICATIONS OF THE FINDINGS Expression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. Given the important function of the uterine stroma and the possibility that SARS-CoV-2 could infect the uterus, our goal here was to 101 determine whether ACE2 is expressed in endometrial stromal cells, is regulated by progesterone, 102 and is required for decidualization. Given the high ACE2 expression in the human 143 endometrium, SARS-CoV-2 may be able to enter endometrial stromal cells and elicit pathological 144 manifestations in women with COVID-19. abstract: STUDY QUESTION Is SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization? SUMMARY ANSWER ACE2 protein is highly expressed in human endometrial stromal cells during the secretory phase and is essential for human endometrial stromal cell decidualization. WHAT IS KNOWN ALREADY ACE2 is expressed in numerous human tissues including the lungs, heart, intestine, kidneys and placenta. ACE2 is also the receptor by which SARS-CoV-2 enters human cells. STUDY DESIGN, SIZE, DURATION Proliferative (n = 9) and secretory (n = 6) phase endometrium biopsies from healthy reproductive-age women and primary human endometrial stromal cells from proliferative phase endometrium were used in the study. PARTICIPANTS/MATERIALS, SETTING, METHODS ACE2 expression and localization were examined by qRT-PCR, Western blot, and immunofluorescence in both human endometrial samples and mouse uterine tissue. The effect of ACE2 knockdown on morphological and molecular changes of human endometrial stromal cell decidualization were assessed. Ovariectomized mice were treated with estrogen or progesterone to determine the effects of these hormones on ACE2 expression. MAIN RESULTS AND THE ROLE OF CHANCE In human tissue, ACE2 protein is expressed in both endometrial epithelial and stromal cells in the proliferative phase of the menstrual cycle, and expression increases in stromal cells in the secretory phase. The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. HESCs transfected with ACE2-targeting siRNA were less able to decidualize than controls, as evidenced by a lack of morphology change and lower expression of the decidualization markers PRL and IGFBP1 (P < 0.05). In mice during pregnancy, ACE2 protein was expressed in uterine epithelial and stromal cells increased through day six of pregnancy. Finally, progesterone induced expression of Ace2 mRNA in mouse uteri more than vehicle or estrogen (P < 0.05). LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Experiments assessing the function of ACE2 in human endometrial stromal cell decidualization were in vitro. Whether SARS-CoV-2 can enter human endometrial stromal cells and affect decidualization have not been assessed. WIDER IMPLICATIONS OF THE FINDINGS Expression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. If so, women with COVID-19 may be at increased risk of early pregnancy loss. STUDY FUNDINGS/COMPETING INTEREST(S) This study was supported by National Institutes of Health / National Institute of Child Health and Human Development grants R01HD065435 and R00HD080742 to RK and Washington University School of Medicine start-up funds to RK. The authors declare that they have no conflicts of interest. url: https://doi.org/10.1101/2020.06.23.168252 doi: 10.1101/2020.06.23.168252 id: cord-283193-8qj41kpp author: Chak-Yiu Lee, Andrew title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters date: 2020-09-22 words: 2326.0 sentences: 139.0 pages: flesch: 51.0 cache: ./cache/cord-283193-8qj41kpp.txt txt: ./txt/cord-283193-8qj41kpp.txt summary: title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters Utilizing Syrian hamster model, we demonstrate that the severity of pneumonia induced by intranasal inhalation of SARS-CoV-2 increases with virus inoculum. By 4 dpi, the hamsters infected with 10 2 or 10 3 PFU of SARS-90 CoV-2 also developed lung parenchymal damage which were milder than those observed in the 91 hamsters infected with 10 4 or 10 5 PFU of virus ( Figure 1D including both arteries and veins. The 133 intranasally infected hamsters had significantly higher viral load in oesophagus and stomach, but 134 no detectable virus in small intestinal tissues (n=3, Figure 2C ). In order to quantitatively compare the severity of lung damage after oral and intranasal 196 inoculation, we performed semi-quantitative histopathological evaluation of the bronchioles, 197 alveoli and blood vessels using a method modified from our previous influenza infection mouse 198 model and a reported hamster infection model (Table S1 ). abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted largely by respiratory droplets or airborne aerosols. Despite being frequently found in the immediate environment and faeces of patients, evidence supporting oral acquisition of SARS-CoV-2 is unavailable. Utilizing Syrian hamster model, we demonstrate that the severity of pneumonia induced by intranasal inhalation of SARS-CoV-2 increases with virus inoculum. SARS-CoV-2 retains its infectivity in vitro in simulated human fed-gastric and fasted-intestinal fluid after two hours. Oral inoculation with the highest intranasal inoculum(105PFU) causes mild pneumonia in 67% (4/6) of the animals with no weight loss. The lung histopathology score and viral load are significantly lower than those infected by the lowest intranasal inoculum(100PFU). However, 83% oral infection (10/12 hamsters) have similar level of detectable viral shedding from oral swabs and faeces as that of intranasally infected hamsters. Our findings indicate oral acquisition of SARS-CoV-2 can establish subclinical respiratory infection with less efficiency. url: https://www.ncbi.nlm.nih.gov/pubmed/32984855/ doi: 10.1016/j.xcrm.2020.100121 id: cord-264266-6xvj9zey author: Chakrabarti, Sankha Shubhra title: COVID-19 in India: Are Biological and Environmental Factors Helping to Stem the Incidence and Severity? date: 2020-05-09 words: 3845.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-264266-6xvj9zey.txt txt: ./txt/cord-264266-6xvj9zey.txt summary: Apart from SARS-CoV and MERS-CoV which caused severe respiratory diseases following outbreaks in 2003 and 2012, there are four endemic human corona viruses, HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1 in populations that are responsible for various types of respiratory illness which are generally self-limiting in young and immunecompetent persons [8] . It can be assumed that some degrees of sequence homology or conformational similarities among the structural proteins, especially the S protein, of SARS-CoV-2 and the endemic corona viruses (HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1) may result in cross-reactive immunity (circulating antibodies or primed T-cells) in persons with prior exposure to the latter viruses, and this may modulate the course and outcome of COVID-19. Thus, the possibility of a protective cross-immunity in the Indian population against COVID-19 cannot be ignored in explaining a rather mild effect of the current coronavirus pandemic in India in comparison to that in Europe and the USA. Therefore, cross-reactive antibodies generated as a result of infections from other human corona viruses may have a protective role in a population affected by COVID-19. abstract: The ongoing Corona virus (COVID-19) pandemic has witnessed global political responses of unimaginable proportions. Many nations have implemented lockdowns that involve mandating citizens not to leave their residences for non-essential work. The Indian government has taken appropriate and commendable steps to curtail the community spread of COVID-19. While this may be extremely beneficial, this perspective discusses the other reasons why COVID-19 may have a lesser impact on India. We analyze the current pattern of SARS-CoV-2 transmission, testing, and mortality in India with an emphasis on the importance of mortality as a marker of the clinical relevance of COVID-19 disease. We also analyze the environmental and biological factors which may lessen the impact of COVID-19 in India. The importance of cross-immunity, innate immune responses, ACE polymorphism, and viral genetic mutations are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32489695/ doi: 10.14336/ad.2020.0402 id: cord-253366-03cg831z author: Chakraborty, Hirak title: Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date: 2020-07-22 words: 5024.0 sentences: 282.0 pages: flesch: 47.0 cache: ./cache/cord-253366-03cg831z.txt txt: ./txt/cord-253366-03cg831z.txt summary: In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes abstract: The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation. url: https://api.elsevier.com/content/article/pii/S0301462220301460 doi: 10.1016/j.bpc.2020.106438 id: cord-322724-7l1668bf author: Challener, Douglas title: In Reply - Repeated testing in SARS-CoV-2 infection date: 2020-08-10 words: 472.0 sentences: 35.0 pages: flesch: 56.0 cache: ./cache/cord-322724-7l1668bf.txt txt: ./txt/cord-322724-7l1668bf.txt summary: In general, we agree that repeat testing may be helpful in certain situations of ongoing high suspicion for active infection where alternative approaches are not feasible; however, we believe that testing should not be applied indiscriminately in a resource-constrained situation. Several studies have suggested that the number of unique patient specimens tested for SARS-CoV-2 is directly related to the positive identification of the virus and that there may be a high false-negative rate of molecular testing. 2, 3 The study by Zhang et al reported 41 hospitalized patients with an initial negative PCR test who had at least one positive result on subsequent testing. 4 We agree that there may be a role for repeat testing in patients with high clinical suspicion of Low Utility of Repeat Real-Time PCR Testing for SARS-CoV-2 in Clinical Specimens Distinct characteristics of COVID-19 patients with initial rRT-PCRpositive and rRT-PCR-negative results for SARS-CoV-2 abstract: nan url: https://api.elsevier.com/content/article/pii/S0025619620309071 doi: 10.1016/j.mayocp.2020.08.006 id: cord-283413-xapzer5s author: Chan, A. K. M. title: Social media for rapid knowledge dissemination: early experience from the COVID‐19 pandemic date: 2020-03-31 words: 1213.0 sentences: 63.0 pages: flesch: 36.0 cache: ./cache/cord-283413-xapzer5s.txt txt: ./txt/cord-283413-xapzer5s.txt summary: During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2], while a recent study from Wuhan, China reported that 1716 healthcare workers were infected with COVID-19, representing 3.8% of confirmed cases [3]. During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2] . Known risks of non-peer-reviewed materials disseminated via social medial include the application of context-specific resources to unsuitable situations; engagement with biased knowledge within echo chambers'' (groups consisting of only like-minded individuals) and algorithm-driven filter bubbles that selectively display information based on user preferences [15] ; and insufficient source information available to Box 1 Criteria for the responsible use of social media disseminated information. In the current COVID-19 pandemic, social media has the potential, if responsibly and appropriately used, to provide rapid and effective dissemination routes for key information. abstract: The current COVID-19 pandemic is threatening global health. Rates of infection outside of China are rapidly increasing, with confirmed cases reported in over 160 countries as of 19 March 2020 [1]. During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2], while a recent study from Wuhan, China reported that 1716 healthcare workers were infected with COVID-19, representing 3.8% of confirmed cases [3]. During the SARS epidemic, it is likely that a lack of awareness and preparedness put healthcare workers at risk [4]. Thus, delivering rapid, reliable information that addresses critical infection control issues is of key importance, and tracheal intubation is known to be associated with a high-risk of transmission of viral infections to healthcare workers [5, 6]. url: https://doi.org/10.1111/anae.15057 doi: 10.1111/anae.15057 id: cord-325744-i3r3ff3t author: Chan, Angelina O. M. title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore date: 2004-05-17 words: 3255.0 sentences: 179.0 pages: flesch: 57.0 cache: ./cache/cord-325744-i3r3ff3t.txt txt: ./txt/cord-325744-i3r3ff3t.txt summary: title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore Aims To describe the psychological impact of severe acute respiratory syndrome (SARS) on health care workers in a regional general hospital 2 months post-outbreak. The questionnaires consisted of demographics, the General Health Questionnaire (GHQ) 28, the Impact of Events Scale (IES) and a set of questions enquiring about changes in life''s priorities and circumstances that helped them to cope with the SARS situation better. This questionnaire was developed specifically for this study, as there were no suitable scales available for measuring changes in life''s priorities and coping among health care workers as a result of SARS. From this survey, although it was perceived that the SARS situation had greatly impacted on the emotional state of health care workers, there was no significant change in the prevalence of psychiatric disorders among health care workers (35% of doctors and 25% of nurses) in this hospital who responded. abstract: Aims To describe the psychological impact of severe acute respiratory syndrome (SARS) on health care workers in a regional general hospital 2 months post-outbreak. Method Doctors and nurses were encouraged to participate. The survey consisted of self-report measures: demographics, the General Health Questionnaire (GHQ) 28 and Impact of Events Scale (IES). A questionnaire enquiring about changes in life's priorities due to SARS and circumstances that helped with coping was used. Participation was strictly voluntary and responses anonymous. Results In total 177 out of 661 (27%) participants [40 out of 113 (35%) doctors and 137 out of 544 (25%) nurses] had a GHQ 28 score ≥5. Doctors [P = 0.026, odds ratio (OR) = 1.6 and 95% confidence interval (CI) = 1.1–2.5] and single health care workers were at higher risk (P = 0.048, OR = 1.4 and 95% CI = 1.02–2.0) compared to nurses and those who were married. Approximately 20% of the participants had IES scores ≥30, indicating the presence of post-traumatic stress disorder (PTSD). Four areas were classified as more important using factor analysis: health and relationship with the family, relationship with friends/colleagues, work and spiritual. The areas for coping strategies were clear directives/precautionary measures, ability to give feedback to/obtain support from management, support from supervisors/colleagues, support from the family, ability to talk to someone and religious convictions. Support from supervisors/colleagues was a significant negative predictor for psychiatric symptoms and PTSD. Work and clear communication of directives/precautionary measures also helped reduce psychiatric symptoms. Conclusions Many health care workers were emotionally affected and traumatized during the SARS outbreak. Hence, it is important for health care institutions to provide psychosocial support and intervention for their health care workers. url: https://www.ncbi.nlm.nih.gov/pubmed/15133143/ doi: 10.1093/occmed/kqh027 id: cord-285849-jg43tcfh author: Chan, Ben Chong Pun title: Universal SARS preventive measures in an obstetrics unit: Experience of health care staff date: 2004-10-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) epidemics have affected populations in many countries, including Hong Kong. This disease is infectious, especially in hospital settings. Health care workers have expressed great concern, including those working in obstetrics wards, defined as high-risk areas. METHOD: Four weeks after implementation of universal precautionary measures at a teaching hospital in Hong Kong, a survey of the health care staff was conducted to identify their feelings and opinions. RESULTS: In spite of general knowledge about SARS epidemics and related mortality, most respondents stated that universal precautionary measures were not very necessary, especially in the obstetrics ward. In addition, respondents were generally dissatisfied with the measures, as most items imposed extra work, inconvenience, and burdens on the staff. CONCLUSION: Our findings reported the views and satisfaction levels of the front-line staff of an obstetric unit concerning precautionary measures against SARS. The importance of individualized design and implementation of infection control measures is highlighted and discussed. url: https://www.sciencedirect.com/science/article/pii/S0196655304004092 doi: 10.1016/j.ajic.2004.01.006 id: cord-306431-r83n27la author: Chan, Chak-Ming title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function date: 2009-05-04 words: 4794.0 sentences: 276.0 pages: flesch: 55.0 cache: ./cache/cord-306431-r83n27la.txt txt: ./txt/cord-306431-r83n27la.txt summary: title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function Consistent with the Vero E6 cells data (Fig. 2) , our in vivo results further validate the importance of cysteine-rich, Yxx and diacidic domains of 3a (Fig. 1A) in 3a''s pro-apoptotic function. In this study, we generated mutant 3a constructs, 3a-CS, 3a-YA and 3a-DE (Fig. 1A) , and investigated the functional significance of the cysteine-rich, Yxx and diacidic domains on 3a''s pro-apoptotic activity. We previously reported caspase-8 activation in 3a-WTexpressing Vero E6 cells , and our in vivo data also showed that cytochrome c can modulate 3a-WT-induced apoptosis . Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway abstract: The severe acute respiratory syndrome-coronavirus (SARS-CoV) caused an outbreak of atypical pneumonia in 2003. The SARS-CoV viral genome encodes several proteins which have no homology to proteins in any other coronaviruses, and a number of these proteins have been implicated in viral cytopathies. One such protein is 3a, which is also known as X1, ORF3 and U274. 3a expression is detected in both SARS-CoV infected cultured cells and patients. Among the different functions identified, 3a is a capable of inducing apoptosis. We previously showed that caspase pathways are involved in 3a-induced apoptosis. In this study, we attempted to find out protein domains on 3a that are essential for its pro-apoptotic function. Protein sequence analysis reveals that 3a possesses three major protein signatures, the cysteine-rich, Yxxϕ and diacidic domains. We showed that 3a proteins carrying respective mutations in these protein domains exhibit reduced pro-apoptotic activities, indicating the importance of these domains on 3a's pro-apoptotic function. It was previously reported that 3a possesses potassium ion channel activity. We further demonstrated that the blockade of 3a's potassium channel activity abolished caspase-dependent apoptosis. This report provides the first evidence that ion channel activity of 3a is required for its pro-apoptotic function. As ion channel activity has been reported to regulate apoptosis in different pathologic conditions, finding ways to modulate the ion channel activity may offer a new direction toward the inhibition of apoptosis triggered by SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/19398035/ doi: 10.1016/j.biocel.2009.04.019 id: cord-332680-zfn81hew author: Chan, Chieh-Kai title: Renin-Angiotensin-Aldosterone System Inhibitors and Risks of Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Systematic Review and Meta-Analysis date: 2020-09-10 words: 4301.0 sentences: 204.0 pages: flesch: 45.0 cache: ./cache/cord-332680-zfn81hew.txt txt: ./txt/cord-332680-zfn81hew.txt summary: The following variables were extracted: author, journal, publication year, study design, geographic location, participants'' details (number, study population, age, sex, and comorbidities, including hypertension, diabetes mellitus, heart failure, and chronic kidney disease), use of antihypertensive drugs, such as ACE inhibitors, ARBs, calcium-channel blockers, beta-blockers, diuretics, outcomes (including positive SARS-CoV-2 test results and disease prognosis/severity, if available). The systematic review findings of the 7 high-quality studies (with comparative data on the controls) on SARS-COV-2 infection provide the best available evidence proving that therapy with ACE inhibitors or ARBs is not associated with an increase of positive SARS-CoV-2 test result and the severity of COVID-19 disease or overall population mortality as a whole in case-population and cohort studies. ACE indicates angiotensin-converting enzyme; ARBs, angiotensin receptor blockers; BMI, body mass index; CKD, chronic kidney disease; DM, diabetes mellitus; HTN, hypertension; ICU, intensive care unit; N/A, not applicable; OHA, oral hypoglycemic agents; RAASi, renin-angiotensin-aldosterone system inhibitors; and SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. abstract: The viral spike coat protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) engages the human ACE (angiotensin-converting enzyme)2 cell surface receptor to infect the host cells. Thus, concerns arose regarding theoretically higher risk for coronavirus disease-19 (COVID-19) in patients taking ACE inhibitors/angiotensin II type 1 receptor antagonists (angiotensin receptor blockers [ARBs]). We systematically assessed case-population and cohort studies from MEDLINE (Ovid), Cochrane Database of Systematic Reviews PubMed, Embase, medRXIV, the World Health Organization database of COVID-19 publications, and ClinicalTrials.gov through June 1, 2020, with planned ongoing surveillance. We rated the certainty of evidence according to Cochrane methods and the GRADE approach. After pooling the adjusted odds ratios from the included studies, no significant increase was noted in the risk of SARS-CoV-2 infection by the use of ACEinhibitors (adjusted odds ratio, 0.95 [95% CI, 0.86–1.05]) or ARBs (adjusted odds ratio, 1.05 [95% CI, 0.97–1.14]). However, the random-effects meta-regression revealed that age may modify the SARS-CoV-2 infection risk in subjects with the use of ARBs (coefficient, −0.006 [95% CI, −0.016 to 0.004]), that is, the use of ARBs, as opposed to ACE inhibitors, specifically augmented the risk of SARS-CoV-2 infection in younger subjects (<60 yearsold). The use of ACE inhibitors might not increase the susceptibility of SARS-CoV-2 infection, severity of disease, and mortality in case-population and cohort studies. Additionally, we discovered for the first time that the use of ARBs, as opposed to ACE inhibitors, specifically augmented the risk of SARS-CoV-2 infection in younger subjects, without obvious effects on COVID-19 outcomes. url: https://doi.org/10.1161/hypertensionaha.120.15989 doi: 10.1161/hypertensionaha.120.15989 id: cord-280350-ay4cnzn5 author: Chan, Jasper F.W. title: Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus date: 2013-10-03 words: 5156.0 sentences: 259.0 pages: flesch: 45.0 cache: ./cache/cord-280350-ay4cnzn5.txt txt: ./txt/cord-280350-ay4cnzn5.txt summary: We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. Given the limited time available to develop novel anti-MERS-CoV agents in this evolving epidemic, we attempted to provide an alternative solution by identifying potential broad-spectrum antiviral agents against MERS-CoV and influenza A viruses by a small compound-based forward chemical genetics approach using chemical libraries consisting of 1280 drug compounds already marketed or having reached clinical trials in the United States, Europe, or Asia (Microsource Discovery Systems, USA). 25 We then assessed the anti-MERS-CoV activities of the identified drug compounds in cell culture by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction assay (PRA) assays, as well as drug cytotoxicity. abstract: OBJECTIVES: Middle East respiratory syndrome coronavirus (MERS-CoV) has emerged to cause fatal infections in patients in the Middle East and traveler-associated secondary cases in Europe and Africa. Person-to-person transmission is evident in outbreaks involving household and hospital contacts. Effective antivirals are urgently needed. METHODS: We used small compound-based forward chemical genetics to screen a chemical library of 1280 known drugs against influenza A virus in Biosafety Level-2 laboratory. We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. RESULTS: Ten compounds were identified as primary hits in high-throughput screening. Only mycophenolic acid exhibited low EC(50) and high selectivity index. Additionally, ribavirin and interferons also exhibited in-vitro anti-MERS-CoV activity. The serum concentrations achievable at therapeutic doses of mycophenolic acid and interferon-β1b were 60–300 and 3–4 times higher than the concentrations at which in-vitro anti-MERS-CoV activities were demonstrated, whereas that of ribavirin was ∼2 times lower. Combination of mycophenolic acid and interferon-β1b lowered the EC(50) of each drug by 1–3 times. CONCLUSIONS: Interferon-β1b with mycophenolic acid should be considered in treatment trials of MERS. url: https://www.ncbi.nlm.nih.gov/pubmed/24096239/ doi: 10.1016/j.jinf.2013.09.029 id: cord-263508-row2mn17 author: Chan, Jasper Fuk-Woo title: The emerging novel Middle East respiratory syndrome coronavirus: The “knowns” and “unknowns” date: 2013-07-21 words: 4344.0 sentences: 202.0 pages: flesch: 43.0 cache: ./cache/cord-263508-row2mn17.txt txt: ./txt/cord-263508-row2mn17.txt summary: Ten years after the devastating epidemic of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV), which resulted in a total of 774 deaths among more than 8000 confirmed cases in over 30 countries, the world is facing a new challenge posted by a "SARS-like" infection caused by another novel coronavirus emerging from the Middle East, which was originally named human coronavirus EMC/2012 (HCoV-EMC) and recently renamed by the Coronavirus Study Group of the International Committee for Taxonomy of Viruses as Middle East respiratory syndrome coronavirus (MERS-CoV). 6,7,10e14 Although the number of laboratory-confirmed cases remains limited, the severe clinical manifestations with an unusually high mortality rate of over 50%, the spread of the infection beyond the geographical confinement in the Middle East, and the epidemiological evidence of human-to-human transmission arising from the recent clusters of cases in a family in the United Kingdom (Cases 10 to 12), and in hospitals in KSA (Cases 18 to 30, 32 and 33) and France (Cases 31 and 34), have raised significant concerns on the possible emergence of another SARS-like epidemic in the near future. abstract: A novel lineage C betacoronavirus, originally named human coronavirus EMC/2012 (HCoV-EMC) and recently renamed Middle East respiratory syndrome coronavirus (MERS-CoV), that is phylogenetically closely related to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5, which we discovered in 2007 from bats in Hong Kong, has recently emerged in the Middle East to cause a severe acute respiratory syndrome (SARS)-like infection in humans. The first laboratory-confirmed case, which involved a 60-year-old man from Bisha, the Kingdom of Saudi Arabia (KSA), who died of rapidly progressive community-acquired pneumonia and acute renal failure, was announced by the World Health Organization (WHO) on September 23, 2012. Since then, a total of 70 cases, including 39 fatalities, have been reported in the Middle East and Europe. Recent clusters involving epidemiologically-linked household contacts and hospital contacts in the Middle East, Europe, and Africa strongly suggested possible human-to-human transmission. Clinical and laboratory research data generated in the past few months have provided new insights into the possible animal reservoirs, transmissibility, and virulence of MERS-CoV, and the optimal laboratory diagnostic options and potential antiviral targets for MERS-CoV-associated infection. url: https://www.sciencedirect.com/science/article/pii/S0929664613001770 doi: 10.1016/j.jfma.2013.05.010 id: cord-291847-x3b6j5d0 author: Chan, K. H. title: The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus date: 2011-10-01 words: 2305.0 sentences: 122.0 pages: flesch: 47.0 cache: ./cache/cord-291847-x3b6j5d0.txt txt: ./txt/cord-291847-x3b6j5d0.txt summary: The dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22–25°C and relative humidity of 40–50%, that is, typical air-conditioned environments. The better stability of SARS coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as Hong Kong) during the spring and in air-conditioned environments. Thus, information on the survival of the SARS coronavirus (SCoV) in the environment at different temperature and humidity conditions is of significant interest to understanding virus transmission. A recent study using surrogate coronaviruses (transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHC)) has investigated the effect of air 2 Advances in Virology (21) temperature and relative humidity on coronavirus survival on surface [18] . SARS CoV can retain its infectivity up to 2 weeks at low temperature and low humidity environment, which might facilitate the virus transmission in community as in Hong Kong which locates in subtropical area (Table 2(e)). abstract: The main route of transmission of SARS CoV infection is presumed to be respiratory droplets. However the virus is also detectable in other body fluids and excreta. The stability of the virus at different temperatures and relative humidity on smooth surfaces were studied. The dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22–25°C and relative humidity of 40–50%, that is, typical air-conditioned environments. However, virus viability was rapidly lost (>3 log(10)) at higher temperatures and higher relative humidity (e.g., 38°C, and relative humidity of >95%). The better stability of SARS coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as Hong Kong) during the spring and in air-conditioned environments. It may also explain why some Asian countries in tropical area (such as Malaysia, Indonesia or Thailand) with high temperature and high relative humidity environment did not have major community outbreaks of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/22312351/ doi: 10.1155/2011/734690 id: cord-315866-6vcts4w3 author: Chan, KC Allen title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study date: 2005-04-09 words: 2555.0 sentences: 137.0 pages: flesch: 50.0 cache: ./cache/cord-315866-6vcts4w3.txt txt: ./txt/cord-315866-6vcts4w3.txt summary: title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Therefore, in this study, we investigated the association of the ACE insertion/deletion (I/D) polymorphism of the 287 bp Alu repeat to the susceptibility to SARS and the development of adult respiratory distress syndrome (ARDS) with a larger population. The genotypic distributions and allelic frequencies of ACE I/D polymorphism in the SARS patients and control subjects are shown in table 2. abstract: BACKGROUND: It has been postulated that genetic predisposition may influence the susceptibility to SARS-coronavirus infection and disease outcomes. A recent study has suggested that the deletion allele (D allele) of the angiotensin converting enzyme (ACE) gene is associated with hypoxemia in SARS patients. Moreover, the ACE D allele has been shown to be more prevalent in patients suffering from adult respiratory distress syndrome (ARDS) in a previous study. Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. METHOD: One hundred and forty genetically unrelated Chinese SARS patients and 326 healthy volunteers were recruited. The ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Moreover, there is also no evidence that ACE I/D polymorphism is associated with the progression to ARDS or the requirement of intensive care in the SARS patients. In multivariate logistic analysis, age is the only factor associated with the development of ARDS while age and male sex are independent factors associated with the requirement of intensive care. CONCLUSION: The ACE I/D polymorphism is not directly related to increased susceptibility to SARS-coronavirus infection and is not associated with poor outcomes after SARS-coronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15819995/ doi: 10.1186/1471-2334-5-26 id: cord-326337-s0fp5z1q author: Chan, Kui K. title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date: 2020-10-19 words: 4573.0 sentences: 256.0 pages: flesch: 54.0 cache: ./cache/cord-326337-s0fp5z1q.txt txt: ./txt/cord-326337-s0fp5z1q.txt summary: Deep mutagenesis of the isolated receptor-binding domain (RBD) by yeast surface display 44 has easily identified mutations in S that retain high expression and ACE2 affinity, yet are no longer bound 45 by monoclonal antibodies and confer resistance (19) . An alternative protein-based antiviral to monoclonal antibodies is to use soluble ACE2 (sACE2) as a 56 decoy to compete for receptor-binding sites on the viral spike (6, (22) (23) (24) (25) of diverse SARS-associated betacoronaviruses that use ACE2 for entry. The sequence 162 diversity observed among natural betacoronaviruses, which display high diversity at the ACE2 binding 163 site, is therefore replicated in the deep mutational scan, which predicts the SARS-CoV-2 spike tolerates 164 substantial genetic diversity at the receptor-binding site for function. From this accessible sequence 165 diversity SARS-CoV-2 might feasibly mutate to acquire resistance to monoclonal antibodies or 166 engineered decoy receptors targeting the ACE2-binding site. abstract: The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses. url: https://doi.org/10.1101/2020.10.18.344622 doi: 10.1101/2020.10.18.344622 id: cord-285179-26ey3fm8 author: Chan, Kwok-Hung title: Cross-reactive antibodies in convalescent SARS patients'' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests date: 2013-04-10 words: 5270.0 sentences: 278.0 pages: flesch: 52.0 cache: ./cache/cord-285179-26ey3fm8.txt txt: ./txt/cord-285179-26ey3fm8.txt summary: title: Cross-reactive antibodies in convalescent SARS patients'' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests We conducted a seroprevalence study on archived sera from 94 game-food animal handlers at a wild life market, 28 SARS patients, and 152 healthy blood donors in Southern China to assess the zoonotic potential and evidence for intrusion of HCoV-EMC and related viruses into humans. 12 In order to further substantiate the hypothesis of HCoV-EMC being a zoonotic agent and elicit evidence for intrusion of HCoV-EMC and its related viruses into humans, we studied the antibody titers using immunofluorescence (IF) as screening and neutralization as confirmatory tests in at-risk groups working in a wild life market in Guangzhou of Southern China who were constantly exposed to a wide range of game food animals, SARS patients who might have acquired their infection directly from wild animals, and healthy blood donors. abstract: OBJECTIVES: A severe acute respiratory syndrome (SARS)-like disease due to a novel betacoronavirus, human coronavirus EMC (HCoV-EMC), has emerged recently. HCoV-EMC is phylogenetically closely related to Tylonycteris-bat-coronavirus-HKU4 and Pipistrellus-bat-coronavirus-HKU5 in Hong Kong. We conducted a seroprevalence study on archived sera from 94 game-food animal handlers at a wild life market, 28 SARS patients, and 152 healthy blood donors in Southern China to assess the zoonotic potential and evidence for intrusion of HCoV-EMC and related viruses into humans. METHODS: Anti-HCoV-EMC and anti-SARS-CoV antibodies were detected using screening indirect immunofluorescence (IF) and confirmatory neutralizing antibody tests. RESULTS: Two (2.1%) animal handlers had IF antibody titer of ≥1:20 against both HCoV-EMC and SARS-CoV with neutralizing antibody titer of <1:10. No blood donor had antibody against either virus. Surprisingly, 17/28 (60.7%) of SARS patients had significant IF antibody titers with 7/28 (25%) having anti-HCoV-EMC neutralizing antibodies at low titers which significantly correlated with that of HCoV-OC43. Bioinformatics analysis demonstrated a significant B-cell epitope overlapping the heptad repeat-2 region of Spike protein. Virulence of SARS-CoV over other betacoronaviruses may boost cross-reactive neutralizing antibodies against other betacoronaviruses. CONCLUSIONS: Convalescent SARS sera may contain cross-reactive antibodies against other betacoronaviruses and confound seroprevalence study for HCoV-EMC. url: https://doi.org/10.1016/j.jinf.2013.03.015 doi: 10.1016/j.jinf.2013.03.015 id: cord-341069-kngf6qpe author: Chan, Kwok-Hung title: Factors affecting stability and infectivity of SARS-CoV-2 date: 2020-07-09 words: 749.0 sentences: 54.0 pages: flesch: 67.0 cache: ./cache/cord-341069-kngf6qpe.txt txt: ./txt/cord-341069-kngf6qpe.txt summary: AIM: The aim of this study was to investigate the infectivity of SARS-CoV-2 under various environmental factors, disinfectants and different pH conditions. The viability of virus was determined after treatment with different disinfectants and pH solutions at room temperature (20∼25(o)C). SARS-CoV-2 could be detected under a wide range of pH conditions from pH4 to pH11 for several days and 1 to 2 days in stool at room temperature but lost 5 logs of infectivity. One hundred microliters of SARS-CoV-2 with 114 10 6.5 TCID 50 /ml was added into each bottles of 0.9 ml VTM and incubated at room temperature 115 (20-25 o C). When SARS-CoV-2 was added in VTM with pH ranging from 2 to 13, the virus remained 163 viable up to 6 days but lost between 2.9 and 5.33 logs of infectivity from pH5 to pH9 and up 164 to 1~2 days in pH4 and pH11 ( Table 2) . abstract: BACKGROUND: In late 2019, a novel human coronavirus, SARS-CoV-2, emerged in Wuhan, China. This virus has caused a global pandemic involving more than 200 countries. SARS-CoV-2 is highly adapted to humans and readily transmits from person-to-person. AIM: The aim of this study was to investigate the infectivity of SARS-CoV-2 under various environmental factors, disinfectants and different pH conditions. The efficacy of a variety of laboratory virus inactivation methods and home disinfectants against SARS-CoV-2 were investigated. METHODS: The residual virus in dried form or in solution was titrated on Vero E6 cell line at day 0, 1, 3, 5, and 7 after incubation at different temperatures. The viability of virus was determined after treatment with different disinfectants and pH solutions at room temperature (20∼25(o)C). FINDINGS: SARS-CoV-2 was able to retain viability for 3-5 days in dried form or 7 days in solution at room temperature. SARS-CoV-2 could be detected under a wide range of pH conditions from pH4 to pH11 for several days and 1 to 2 days in stool at room temperature but lost 5 logs of infectivity. A variety of commonly used disinfectants and laboratory inactivation procedures were found to reduce viral viability effectively. CONCLUSION: This study demonstrates the stability of SARS-CoV-2 on environmental surfaces and raises the possibility of faecal-oral transmission. Commonly used fixatives, nucleic acid extraction methods and heat inactivation were found to significantly reduce viral infectivity that could ensure hospital and laboratory safety during the COVID-19 pandemic. url: https://www.sciencedirect.com/science/article/pii/S019567012030339X?v=s5 doi: 10.1016/j.jhin.2020.07.009 id: cord-351354-10rusr6j author: Chan, Louis Y. title: Diagnostic Criteria during SARS Outbreak in Hong Kong date: 2004-06-17 words: 1947.0 sentences: 104.0 pages: flesch: 54.0 cache: ./cache/cord-351354-10rusr6j.txt txt: ./txt/cord-351354-10rusr6j.txt summary: Before the etiologic agent was identified, the diagnosis of SARS was made according to a set of clinical-epidemiologic criteria as suggested by the Centers for Disease Control and Prevention (CDC) (1-3). These criteria remained important in the initial diagnosis and prompt isolation of patients because the overall sensitivity of initial reverse transcriptase-polymerase chain reaction (RT-PCR) testing for SARSassociated coronavirus (SARS CoV) RNA on upper respiratory specimens ranged from approximately 60% to 70% (though sensitivity improved with a second test) (4, 5) . By using paired serologic testing to determine SARS-CoV infection (3), we evaluated the relative importance of the clinical-epidemiologic diagnostic criteria during an outbreak. Probable SARS case-patients were those who met the CDC clinical criteria for severe respiratory illness of unknown etiology (3), and met the epidemiologic criterion for exposure in either a close or a possible contact. Our findings showed that 5.9% of cases defined as probable SARS on the basis of clinical-epidemiologic criteria had no serologic evidence of coronavirus infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15224676/ doi: 10.3201/eid1006.030618 id: cord-309588-kw4d32dt author: Chan, Michael H.M. title: Steroid-induced osteonecrosis in severe acute respiratory syndrome: a retrospective analysis of biochemical markers of bone metabolism and corticosteroid therapy date: 2006-06-30 words: 4614.0 sentences: 245.0 pages: flesch: 46.0 cache: ./cache/cord-309588-kw4d32dt.txt txt: ./txt/cord-309588-kw4d32dt.txt summary: Summary Aim We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. Biochemical markers of bone metabolism were analysed retrospectively using serial clotted blood samples collected from each patient during the course of hospital admission to discharge and subsequent follow-up at out-patient clinic using the arbitrary time periods: (i) Day <10; (ii) Day 28-44; (iii) Day 51-84; and (iv) Day >90 after the onset of fever. Aim: We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. 9, 10 In this study, biochemical markers of bone metabolism were used retrospectively to investigate the effect of massive doses of pulse and maintenance corticosteroid therapies on patients with SARS. abstract: Summary Aim We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. Methods Seventy-one patients with a clinical diagnosis of SARS were studied according to the modified World Health Organization case definition of SARS who were involved in the SARS epidemic between 10 March and 20 June 2003. The clinical diagnosis was confirmed by serological test and/ or molecular analysis. Biochemical markers of bone metabolism were analysed retrospectively using serial clotted blood samples collected from each patient during the course of hospital admission to discharge and subsequent follow-up at out-patient clinic using the arbitrary time periods: (i) Day <10; (ii) Day 28-44; (iii) Day 51-84; and (iv) Day >90 after the onset of fever. Magnetic resonance imaging of the knee and hip joints were performed post-admission to evaluate the prevalence of osteonecrosis amongst these SARS patients. Various risk factors for the development of osteonecrosis were assessed using receiver operating characteristics curve comparison with appropriate test statistics and Spearman’s coefficients of rank correlation with biochemical bone markers. Results Biochemical markers of bone metabolism showed significant bone resorption as evidenced by a marked increase in serum C-terminal telopeptide concentration (CTx) from Day 28-44 after the onset of fever. With tapering down of corticosteroid dosage, CTx started to return to previous baseline level from Day 51 onwards, while other bone formation markers, serum osteocalcin and bone- specific alkaline phosphatase concentrations (OC and BALP, respectively), started to increase. The latter effect was even more marked after Day >90. Seven patients developed radiological evidence of osteonecrosis. The prevalence of osteonecrosis in this cohort was 9.9%. A total corticosteroid dosage of >1900mg hydrocortisone, >2000 mg methylprednisolone, >13 340 mg hydrocortisone-equivalent corticosteroid therapy, and >18 days on corticosteroid therapy were found to be significant risk factors for the subsequent development of osteonecrosis. There were also significant positive correlations amongst various biochemical bone markers in this patient cohort. Conclusion Both bone resorption and formation markers were unable to predict the subsequent development of osteonecrosis. The use of high dose of hydrocortisone or methylprednisolone for an extended duration was shown to be a significant risk factor for osteonecrosis. Its prevalence in this cohort is comparable to those reported in the literature for SARS patients with high-dose corticosteroid therapy. The Day 28–44 increase in the serum CTx coincided with the timing of corticosteroid use. The Day >51 increase in serum OC and BALP coincided with the timing of corticosteroid withdrawal. url: https://www.sciencedirect.com/science/article/pii/S003130251633940X doi: 10.1080/00313020600696231 id: cord-310687-qw164eyl author: Chan, Ming-Chin title: Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 date: 2020-09-01 words: 290.0 sentences: 21.0 pages: flesch: 60.0 cache: ./cache/cord-310687-qw164eyl.txt txt: ./txt/cord-310687-qw164eyl.txt summary: title: Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 Healthcare workers (HCWs) have been singled out, by mass screening supporters, as a high-risk group which are particularly in need to be mass-screened for the presence of SARS-CoV-2 virus or anti-SARS-CoV-2 antibodies, despite the fact that all Taiwanese If HCWs are indeed at high risk of contracting and carrying SARS-CoV-2 virus, then the current HCWs virological surveillance for COVID-19 should be able to detect SARS-CoV-2-positive cases among HCWs. Therefore, we reviewed the HCWs surveillance results at our hospital. 5 Since March 31, 2020, in consistent with Taiwan Central Epidemic Command Center''s HCWs surveillance policy, 5 all HCWs who developed fever or any respiratory symptoms were required to be tested for SARS-CoV-2 regardless of the presence of occupational exposure history or not . Taiwan Centers for Disease Control: COVID-19 statistics Taiwan Centers for Disease Control. abstract: nan url: https://api.elsevier.com/content/article/pii/S0929664620304113 doi: 10.1016/j.jfma.2020.08.037 id: cord-335375-n6q70o35 author: Chan, Paul K. S. title: Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date: 2005-07-01 words: 2186.0 sentences: 109.0 pages: flesch: 55.0 cache: ./cache/cord-335375-n6q70o35.txt txt: ./txt/cord-335375-n6q70o35.txt summary: Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. abstract: The maturation of virus-specific immunoglobulin G avidity during severe acute respiratory syndrome–associated coronavirus infection was examined. The avidity indices were low (mean ± SD, 30.8% ± 11.6%) among serum samples collected ⩽50 days after fever onset, intermediate (mean ± SD, 52.1% ± 14.1%) among samples collected between days 51 and 90, and high (mean ± SD, 78.1% ± 8.0%) among samples collected after day 90. Avidity indices of 40% and 55% could be considered as cutoff values for determination of recent (⩽50 days) and past (>65 days) infection, respectively. Measurement of antibody avidity can be used to differentiate primary infection from reexposure and to assess humoral responses to candidate vaccines url: https://www.ncbi.nlm.nih.gov/pubmed/15942907/ doi: 10.1086/430615 id: cord-307490-b4un4703 author: Chan, Sophia S.C. title: Improving older adults’ knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study date: 2007-09-30 words: 3757.0 sentences: 190.0 pages: flesch: 51.0 cache: ./cache/cord-307490-b4un4703.txt txt: ./txt/cord-307490-b4un4703.txt summary: title: Improving older adults'' knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study Objectives To assess the effectiveness of delivering a telephone health education programme dealing with anxiety levels, and knowledge and practice of measures to prevent transmission of SARS among a group of older adults with low SES. This is the first systematic study to assess the effectiveness of delivering telephone health education to older adults during the outbreak of SARS in Hong Kong. Results of the study supported that telephone health education was effective in relieving anxiety and improving knowledge of the main transmission routes of SARS in older adults, but not fostering practice of preventing SARS. This is the first systematic study to assess the effectiveness of telephone health education in improving older adults'' knowledge and practice of preventive measures during the SARS epidemic. abstract: Abstract Background The outbreak of severe acute respiratory syndrome (SARS) in Hong Kong posed many challenges for health promotion activities among a group of older adults with low socio-economic status (SES). With concerns that this vulnerable group could be at higher risk of contracting the disease or spreading it to others, the implementation of health promotion activities appropriate to this group was considered to be essential during the epidemic. Objectives To assess the effectiveness of delivering a telephone health education programme dealing with anxiety levels, and knowledge and practice of measures to prevent transmission of SARS among a group of older adults with low SES. Design Pretest/posttest design. Settings Subjects were recruited from registered members of a government subsidized social service center in Hong Kong and living in low-cost housing estates. Participants The eligibility criteria were: (1) aged 55 or above; (2) able to speak Cantonese; (3) no hearing impairment, and (4) reachable by telephone. Of the 295 eligible subjects, 122 older adults completed the whole study. Methods The interviewers approached all eligible subjects by telephone during the period of 15–25 May 2003. After obtaining the participants’ verbal consent, the interviewer collected baseline data by use of a questionnaire and implemented a health education programme. A follow-up telephone call was made a week later using the same questionnaire. Results The level of anxiety was lowered (t=3.28, p<0.001), and knowledge regarding the transmission routes of droplets (p<0.001) and urine and feaces (p<0.01) were improved after the intervention. Although statistical significant difference was found in the practice of identified preventive measures before and after intervention, influence on behavioral changes needed further exploration. Conclusion The telephone health education seemed to be effective in relieving anxiety and improving knowledge of the main transmission routes of SARS in this group, but not the practice of preventing SARS. Telephone contact appears to be a practical way of providing health education to vulnerable groups when face-to-face measure is not feasible and may be useful in raising health awareness during future outbreaks of emerging infections. url: https://www.ncbi.nlm.nih.gov/pubmed/16857203/ doi: 10.1016/j.ijnurstu.2006.04.019 id: cord-310438-744r7gc3 author: Chan, Ta-Chien title: The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date: 2010-06-25 words: 5083.0 sentences: 226.0 pages: flesch: 40.0 cache: ./cache/cord-310438-744r7gc3.txt txt: ./txt/cord-310438-744r7gc3.txt summary: This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan''s influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. The aims of this study were: (1) to evaluate the effectiveness of matching or mismatching influenza vaccine strains on influenzaassociated mortality, (2) to assess whether public health improvements during the post-SARS period might have decreased elderly mortality, and (3) to investigate molecular variation among vaccine-mismatched influenza viruses that may be associated with increased excess influenza-associated mortality. Explanatory variables for the above three outcome measures include monthly meteorological parameters (monthly means of temperature and humidity), annual periodic cycle (i.e., sine/cosine function of seasonal periodicity), monthly virus isolation rates for different subtypes/types of influenza viruses [A (H3N2) or A (H1N1) or B], matching status of different vaccine strains for each subtype/type in each of the studied years, post-SARS effect, and linear temporal monthly trends. abstract: Public health administrators do not have effective models to predict excess influenza-associated mortality and monitor viral changes associated with it. This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan's influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. A negative binomial model was developed to estimate Taiwan's monthly influenza-associated mortality among the elderly. We calculated three winter and annual excess influenza-associated mortalities [pneumonia and influenza (P&I), respiratory and circulatory, and all-cause] from the 1999–2000 through the 2006–2007 influenza seasons. Obtaining influenza virus sequences from the months/years in which death from P&I was excessive, we investigated molecular variation in vaccine-mismatched influenza viruses by comparing hemagglutinin 1 (HA1) of the circulating and vaccine strains. We found that the higher the isolation rate of A (H3N2) and vaccine-mismatched influenza viruses, the greater the monthly P&I mortality. However, this significant positive association became negative for higher matching of A (H3N2) and public health efforts with post-SARS effect. Mean excess P&I mortality for winters was significantly higher before 2003 than after that year [mean ± S.D.: 1.44±1.35 vs. 0.35±1.13, p = 0.04]. Further analysis revealed that vaccine-matched circulating influenza A viruses were significantly associated with lower excess P&I mortality during post-SARS winters (i.e., 2005–2007) than during pre-SARS winters [0.03±0.06 vs. 1.57±1.27, p = 0.01]. Stratification of these vaccine-matching and post-SARS effect showed substantial trends toward lower elderly excess P&I mortalities in winters with either mismatching vaccines during the post-SARS period or matching vaccines during the pre-SARS period. Importantly, all three excess mortalities were at their highest in May, 2003, when inter-hospital nosocomial infections were peaking. Furthermore, vaccine-mismatched H3N2 viruses circulating in the years with high excess P&I mortality exhibited both a lower amino acid identity percentage of HA1 between vaccine and circulating strains and a higher numbers of variations at epitope B. Our model can help future decision makers to estimate excess P&I mortality effectively, select and test virus strains for antigenic variation, and evaluate public health strategy effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/20592764/ doi: 10.1371/journal.pone.0011317 id: cord-347462-yz67t10x author: Chan, Tak Yeung title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 words: 3590.0 sentences: 214.0 pages: flesch: 54.0 cache: ./cache/cord-347462-yz67t10x.txt txt: ./txt/cord-347462-yz67t10x.txt summary: title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). A retrospective study was undertaken in the department of medicine and geriatrics of the hospital to evaluate the clinical course of young and elderly SARS patients. Single or paired serum samples were tested for SARS-CoV antibody in 96% (50/52) of young and 76% (19/25) of older patients. Because the proportion of patients with positive RT-PCR in stool samples was similar in two groups, fewer older patients with diarrhea probably represents a generalized paucity of symptoms rather than a different site of involvement by SARS-CoV. In the current study, similar proportions of young and older patients with SARS had RT-PCR performed, and comparable positivity rates were achieved. abstract: Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). Design: Retrospective cohort study. Setting: A community‐based, acute hospital in Hong Kong. Participants: All adult inpatients with a clinical diagnosis of SARS. Measurements: Clinical presentations, investigations, treatment, and 30‐ and 150‐day mortality. Results: There were 52 young and 25 older patients with a mean age±standard deviation of 39.5±11.7 and 72.1±7.2, respectively. Fever, chills, and diarrhea were more common in younger patients, whereas decrease in appetite and general condition occurred only in older patients. The prevalence of positive reverse‐transcriptase polymerase chain reaction for SARS‐associated coronavirus (SARS‐CoV) in nasopharyngeal secretions and stool samples was similar in the two groups. The prevalence of positive serological tests for SARS‐CoV was significantly lower in older patients (42% vs 92%, P<.001). This was largely due to incomplete testing in elderly patients. Older patients were more likely to develop secondary nosocomial infection, be admitted to an intensive care unit, and require mechanical ventilation. The cumulative 30‐ and 150‐day mortality rates were 3.8% and 7.6%, respectively, in young patients with SARS and 56% and 60%, respectively, in older patients (P<.001). Conclusion: Older patients with SARS more often presented with nonspecific symptoms, and the prognosis was poor. Reverse‐transcriptase polymerase chain reaction was useful in diagnosing SARS in older patients, but the role of serological tests in individual elderly is limited. url: https://www.ncbi.nlm.nih.gov/pubmed/15271120/ doi: 10.1111/j.1532-5415.2004.52362.x id: cord-298281-wkje5jyt author: Chan, Vinson Wai-Shun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 words: 3492.0 sentences: 271.0 pages: flesch: 54.0 cache: ./cache/cord-298281-wkje5jyt.txt txt: ./txt/cord-298281-wkje5jyt.txt summary: Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Primary outcomes of our study included urological manifestations of COVID-19, detection rates of SARS-CoV-2 viral RNA in urine and stool samples, and special considerations in urological conditions. For the urological manifestations and viral RNA detection rates, data were pool analysed using MetaXL and Microsoft Excel when there are two or more studies with at least four patients reporting the same outcome under the same definition. There were a total of 11 studies that reported the number of patients who had their urine tested for SARS-CoV-2 viral RNA. Our meta-analysis included 12 studies that reported the number of patients with stools tested for SARS-CoV-2 viral RNA. Our study showed that 5.74% of the COVID-19 patients had positive viral RNA in urine samples. abstract: PURPOSE AND OBJECTIVE: We performed a systematic review on COVID-19 and its potential urological manifestations. METHODS: A literature search was performed using combination of keywords (MeSH terms and free text words) relating to COVID-19, urology, faeces and stool on multiple databases. Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Meta-analyses were performed when there were two or more studies reporting on the same outcome. Special considerations in urological conditions that were relevant in the pandemic of COVID-19 were reported in a narrative manner. RESULTS: There were a total of 21 studies with 3714 COVID-19 patients, and urinary symptoms were absent in all of them. In patients with COVID-19, 7.58% (95% CI 3.30–13.54%) developed acute kidney injury with a mortality rate of 93.27% (95% CI 81.46–100%) amongst them. 5.74% (95% CI 2.88–9.44%) of COVID-19 patients had positive viral RNA in urine samples, but the duration of viral shedding in urine was unknown. 65.82% (95% CI 45.71–83.51%) of COVID-19 patients had positive viral RNA in stool samples, which were detected from 2 to 47 days from symptom onset. 31.6% of renal transplant recipients with COVID-19 required non-invasive ventilation, and the overall mortality rate was 15.4%. CONCLUSIONS: Acute kidney injury leading to mortality is common amongst COVID-19 patients, likely as a result of direct viral toxicity. Viral RNA positivity was detected in both urine and stool samples, so precautions are needed when we perform transurethral or transrectal procedures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00345-020-03246-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32462305/ doi: 10.1007/s00345-020-03246-4 id: cord-278682-s4gfbsqy author: Chan, W-M title: Precautions in ophthalmic practice in a hospital with a major acute SARS outbreak: an experience from Hong Kong date: 2005-04-29 words: 4131.0 sentences: 218.0 pages: flesch: 47.0 cache: ./cache/cord-278682-s4gfbsqy.txt txt: ./txt/cord-278682-s4gfbsqy.txt summary: The ultimate infectivity of the tears secretion and ocular discharge from SARS patients may bring impacts on not only the daily ophthalmic practice but also the universal infection control measures practiced by general public and health-care workers. Discard gloves, wash or alcohol-rub the hands and then put on new gloves in-between case Wear glove in high-risk procedure General categories: for all patients attending the ophthalmic outpatients in which the SARS status is not certain. In a case-control study among 254 Hong Kong health-care workers with documented exposure to SARS patients, none of the 69 staff reporting use of four infection control measures, namely mask, gloves, gowns, and hand washing, was infected. Hospital Authority guideline on infection control of Severe Acute Respiratory Syndrome (SARS) abstract: Many new infectious diseases in humans have been derived from animal sources in the past 20 years. Some are highly contagious and fatal. Vaccination may not be available and antiviral drugs are not effective enough. Infectious control is important in clinical medicine and in Ophthalmology. Severe acute respiratory syndrome (SARS), as an example, is a highly contagious respiratory disease that has recently been reported in Asia, North America, and Europe. Within a matter of weeks, the outbreak has evolved to become a global health threat and more than 30 countries have been afflicted with a novel Coronavirus strain (SARS-CoV) that is the aetiologic agent of SARS. The primary route of transmission of SARS appears involving close person-to-person contact through droplets. Ophthalmologists may be particularly susceptible to the infection as routine ophthalmic examinations like direct ophthalmoscopy and slit-lamp examination are usually performed in a setting that has close doctor–patient contact. Being the Ophthalmology Department of the only hospital in the world that has just gone through the largest outbreak of SARS, we would like to share our strategy, measures, and experiences of preventing contracting or spreading of SARS infection as an infection control model. SARS is one of the many viruses against which personnel will need protecting in an ophthalmic setting. The experiences attained and the measures established might also apply to other infectious conditions spreading by droplets such as the avian influenza with H5N1. url: https://www.ncbi.nlm.nih.gov/pubmed/15877099/ doi: 10.1038/sj.eye.6701885 id: cord-324325-rmlrhyf2 author: Chan, Wai S title: Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date: 2005-05-13 words: 3733.0 sentences: 225.0 pages: flesch: 43.0 cache: ./cache/cord-324325-rmlrhyf2.txt txt: ./txt/cord-324325-rmlrhyf2.txt summary: Immunohistochemical studies on different human tissues, including a cohort of nine autopsies, two liver biopsies and intestinal biopsies of SARS patients, further confirmed the existence of coronaviral hypothetical and structural proteins in the cytoplasm of pneumocytes and small intestinal surface enterocytes in SARS patients. In those tissue sections showing positive signals for immunohistochemical staining, we further performed immunohistochemical studies using all other antibodies tested positive in SARS-CoV-infected Vero E6 cells. The cellular distribution of SARS-CoV protein and viral genome in immunohistochemical-positive lung and small intestine sections was further evaluated by immunofluorescence-fluorescence in situ hybridization analysis (Figure 4) . 3 In Vero E6 cells, positive cytoplasmic immunohistochemical signals were detected by Figure 3 Immunohistochemical studies of antipeptide antibody SARS-AbS13a against the nucleocapsid protein on small intestine sections. In addition, in the study of tissue sections, only those cells with viral genome detected by fluorescence in situ hybridization were positive for immunohistochemical stainings for the antipeptide antibodies. abstract: Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease that haunted the world from November 2002 to July 2003. Little is known about the biology and pathophysiology of the novel coronavirus that causes SARS. The tissue and cellular distributions of coronaviral hypothetical and structural proteins in SARS were investigated. Antibodies against the hypothetical (SARS 3a, 3b, 6, 7a and 9b) and structural proteins (envelope, membrane, nucleocapsid and spike) of the coronavirus were generated from predicted antigenic epitopes of each protein. The presence of these proteins were first verified in coronavirus-infected Vero E6 tissue culture model. Immunohistochemical studies on different human tissues, including a cohort of nine autopsies, two liver biopsies and intestinal biopsies of SARS patients, further confirmed the existence of coronaviral hypothetical and structural proteins in the cytoplasm of pneumocytes and small intestinal surface enterocytes in SARS patients. With this vast array of antibodies, no signal was observed in other cell types including those organs in which reverse transcriptase-polymerase chain reactions were reported to be positive. Structural proteins and the functionally undefined hypothetical proteins were expressed in coronavirus-infected cells with distinct expression pattern in different organs in SARS patients. These antipeptide antibodies can be useful for the diagnosis of SARS at the tissue level. url: https://www.ncbi.nlm.nih.gov/pubmed/15920543/ doi: 10.1038/modpathol.3800439 id: cord-320619-r466dc5t author: Chand Dakal, Tikam title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 date: 2020-11-05 words: 3843.0 sentences: 210.0 pages: flesch: 46.0 cache: ./cache/cord-320619-r466dc5t.txt txt: ./txt/cord-320619-r466dc5t.txt summary: title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 The higher expression of integrins in lungs along with their previously known high binding affinity (∼K(D) = 4.0nM) for virus RGD motif could serve as a possible explanation for high infectivity of SARS-CoV-2. This study is the first study to present striking evidence (substantiated by existing facts in literature) favoring the role of calcium and other divalent ions (magnesium, manganese etc.) in RGD-integrins mediated virus attachment with the host cells for and that lowering the concentration of calcium and other divalent ions in lungs could be a possible mechanism to avert SARs-CoV-2 infection and invasion. A number of motifs were predicted in the spike protein sequence such as RGD (from 403-405 aa in receptor binding domain of SARS-CoV-2) ( Table 2 ). abstract: SARS-CoV-2 is a highly contagious virus that has caused serious health crisis world-wide resulting into a pandemic situation. As per the literature, the SARS-CoV-2 is known to exploit humanACE2 receptors (similar toprevious SARS-CoV-1) for gaining entry into the host cell for invasion, infection, multiplication and pathogenesis. However, considering the higher infectivity of SARS-CoV-2 along with the complex etiology and pathophysiological outcomes seen in COVID-19 patients, it seems that there may be an alternate receptor for SARS-CoV-2. I performed comparative protein sequence analysis, database based gene expression profiling, bioinformatics based molecular docking using authentic tools and techniques for unveiling the molecular basis of high infectivity of SARS-CoV-2 as compared to previous known coronaviruses. My study revealed that SARS-CoV-2 (previously known as 2019-nCoV) harbors a RGD motif in its receptor binding domain (RBD) and the motif is absent in all other previously known SARS-CoVs. The RGD motif is well known for its role in cell-attachment and cell-adhesion. My hypothesis is that the SARS-CoV-2 may be (via RGD) exploiting integrins, that have high expression in lungs and all other vital organs, for invading host cells. However, an experimental verification is required. The expression of ACE2, which is a known receptor for SARS-CoV-2, was found to be negligible in lungs. I assume that higher infectivity of SARS-CoV-2 could be due to this RGD-integrin mediated acquired cell-adhesive property. Gene expression profiling revealed that expression of integrins is significantly high in lung cells, in particular αvβ6, α5β1, αvβ8 and an ECM protein, ICAM1. The molecular docking experiment showed the RBD of spike protein binds with integrins precisely at RGD motif in a similar manner as a synthetic RGD peptide binds to integrins as found by other researchers. SARS-CoV-2 spike protein has a number of phosphorylation sites that can induce cAMP, PKC, Tyr signaling pathways. These pathways either activate calcium ion channels or get activated by calcium. In fact, integrins have calcium & metal binding sites that were predicted around and in vicinity of RGD-integrin docking site in our analysis which suggests that RGD-integrins interaction possibly occurs in calcium-dependent manner. The higher expression of integrins in lungs along with their previously known high binding affinity (∼K(D) = 4.0nM) for virus RGD motif could serve as a possible explanation for high infectivity of SARS-CoV-2. On the contrary, human ACE2 has lower expression in lungs and its high binding affinity (∼K(D)= 15nM) for spike RBD alone could not manifest significant virus-host attachment. This suggests that besides human ACE2, an additional or alternate receptor for SARS-CoV-2 is likely to exist. A highly relevant evidence never reported earlier which corroborate in favor of RGD-integrins mediated virus-host attachment is an unleashed cytokine storm which causes due to activation of TNF-α and IL-6 activation; and integrins role in their activation is also well established. Altogether, the current study has highlighted possible role of calcium and other divalent ions in RGD-integrins interaction for virus invasion into host cells and suggested that lowering divalent ion in lungs could avert virus-host cells attachment. url: https://api.elsevier.com/content/article/pii/S017129852030543X doi: 10.1016/j.imbio.2020.152021 id: cord-301535-eui41zyg author: Chandler-Brown, Devon title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 words: 4143.0 sentences: 228.0 pages: flesch: 52.0 cache: ./cache/cord-301535-eui41zyg.txt txt: ./txt/cord-301535-eui41zyg.txt summary: This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). abstract: There is currently an urgent unmet need to increase coronavirus disease 2019 (COVID-19) testing capability to effectively respond to the COVID-19 pandemic. However, the current shortage in RNA extraction reagents as well as limitations in qPCR protocols have resulted in bottlenecks in testing capacity. Herein, we describe a novel molecular diagnostic for COVID-19 based on Sanger sequencing. This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Since Sanger sequencing instruments are widespread in clinical laboratories and commonly have built-in liquid handling automation to support up to 3840 samples per instrument per day, the widespread adoption of qSanger COVID-19 diagnostics can unlock more than 1,000,000 tests per day in the US. url: https://doi.org/10.1101/2020.04.07.029199 doi: 10.1101/2020.04.07.029199 id: cord-308715-uo6h1h2e author: Chandra, Aman title: Personal protective equipment (PPE) for vitreoretinal surgery during COVID-19 date: 2020-05-12 words: 1836.0 sentences: 104.0 pages: flesch: 43.0 cache: ./cache/cord-308715-uo6h1h2e.txt txt: ./txt/cord-308715-uo6h1h2e.txt summary: SARS-CoV-2 is the recently discovered virus which has resulted in the pandemic illness known as coronavirus disease 2019 (COVID-19) [1] . Estimates for the proportion of asymptomatic patients infected with SARS-CoV-2 in different populations range between 7 and 80% [10] [11] [12] , with a substantial proportion of transmission occurring prior to illness onset [13, 14] . Gloves, disposable aprons, eye protection, fluid resistant type IIR surgical masks and slit lamp guards are recommended as personal protective equipment (PPE) for ophthalmic clinic assessment by the Royal College of Ophthalmologists [17] . Symptomatic patients with SARS tend to develop lower respiratory tract infections, suggesting aerosol transmission is important [25] . Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed Coronavirus Disease 2019 (COVID-19) in Healthcare Settings Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review abstract: nan url: https://doi.org/10.1038/s41433-020-0948-3 doi: 10.1038/s41433-020-0948-3 id: cord-310221-car394ou author: Chandrashekar, Abishek title: SARS-CoV-2 infection protects against rechallenge in rhesus macaques date: 2020-05-20 words: 2540.0 sentences: 140.0 pages: flesch: 44.0 cache: ./cache/cord-310221-car394ou.txt txt: ./txt/cord-310221-car394ou.txt summary: We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. On day 2 following challenge, both necropsied animals demonstrated multifocal regions of inflammation and evidence of viral pneumonia, including expansion of alveolar septae with mononuclear cell infiltrates, consolidation, and edema (Fig. 3, A and B) . SARS-CoV-2 infection in rhesus macaques led to humoral and cellular immune responses (Fig. 2) and provided protection against rechallenge (Fig. 5) . In summary, SARS-CoV-2 infection in rhesus macaques induced humoral and cellular immune responses and provided protective efficacy against SARS-CoV-2 rechallenge. abstract: An understanding of protective immunity to SARS-CoV-2 is critical for vaccine and public health strategies aimed at ending the global COVID-19 pandemic. A key unanswered question is whether infection with SARS-CoV-2 results in protective immunity against re-exposure. We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. Following initial viral clearance, animals were rechallenged with SARS-CoV-2 and showed 5 log(10) reductions in median viral loads in bronchoalveolar lavage and nasal mucosa compared with primary infection. Anamnestic immune responses following rechallenge suggested that protection was mediated by immunologic control. These data show that SARS-CoV-2 infection induced protective immunity against re-exposure in nonhuman primates. url: https://www.ncbi.nlm.nih.gov/pubmed/32434946/ doi: 10.1126/science.abc4776 id: cord-343365-4y9fedcr author: Chang, Christopher title: Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date: 2013-11-30 words: 7295.0 sentences: 407.0 pages: flesch: 50.0 cache: ./cache/cord-343365-4y9fedcr.txt txt: ./txt/cord-343365-4y9fedcr.txt summary: The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] . abstract: The care of patients with respiratory diseases has improved vastly in the past 50 years. In spite of that, there are still massive challenges that have not been resolved. Although the incidence of tuberculosis has decreased in the developed world, it is still a significant public health problem in the rest of the world. There are still over 2 million deaths annually from tuberculosis, with most of these occurring in the developing world. Even with the development of new pharmaceuticals to treat tuberculosis, there is no indication that the disease will be eradicated. Respiratory syncytial virus, severe acute respiratory syndrome, and pertussis are other respiratory infectious diseases with special problems of their own, from vaccine development to vaccine coverage. Asthma, one of the most common chronic diseases in children, still accounts for significant mortality and morbidity, as well as high health care costs worldwide. Even in developed countries such as the USA, there are over 4,000 deaths per year. Severe asthma presents a special problem, but the question is whether there can be one treatment pathway for all patients with severe asthma. Severe asthma is a heterogeneous disease with many phenotypes and endotypes. The gene for cystic fibrosis was discovered over 24 years ago. The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. What are the prospects for gene therapy in the twenty-first century? Autoimmune diseases of the lung pose a different set of challenges, including the development of biomarkers to diagnose and monitor the disease and biological modulators to treat the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/24293395/ doi: 10.1007/s12016-013-8399-2 id: cord-314833-6fue84x6 author: Chang, Chung-ke title: The SARS coronavirus nucleocapsid protein – Forms and functions date: 2014-01-11 words: 9459.0 sentences: 464.0 pages: flesch: 51.0 cache: ./cache/cord-314833-6fue84x6.txt txt: ./txt/cord-314833-6fue84x6.txt summary: The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. proposed a structure-based domain arrangement for SARS-CoV N protein where the NTD and CTD are sandwiched between three IDRs. Sequence alignments suggested that other coronavirus N proteins might share the same structural organization based on intrinsic disorder predictor profiles and secondary structure predictions (Fig. 2) . noticed that effective binding to RNA by MHV N protein in host cells required the presence of both the NTD and CTD (Hurst et al., 2009) , suggesting that the NTD and CTD formed a single bipartite RNA interaction site, a feature to be reiterated in the final SARS-CoV RNP model. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.” url: https://www.ncbi.nlm.nih.gov/pubmed/24418573/ doi: 10.1016/j.antiviral.2013.12.009 id: cord-342639-vf9n2vf9 author: Chang, Chung-ke title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 words: 5386.0 sentences: 243.0 pages: flesch: 42.0 cache: ./cache/cord-342639-vf9n2vf9.txt txt: ./txt/cord-342639-vf9n2vf9.txt summary: For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The nucleocapsid (N) phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD). A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization. url: https://www.ncbi.nlm.nih.gov/pubmed/23717688/ doi: 10.1371/journal.pone.0065045 id: cord-347460-9vechh4x author: Chang, Feng-Yee title: Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date: 2020-06-04 words: 8050.0 sentences: 384.0 pages: flesch: 43.0 cache: ./cache/cord-347460-9vechh4x.txt txt: ./txt/cord-347460-9vechh4x.txt summary: Three components are crucial for SARS-CoV induced diseases: 1) the role of CD8+ T cells in defense against the virus, which causes apoptosis in the infected cells, 2) interactions of the virus with macrophages and dendritic cells, which initiate the early innate and subsequent adaptive immune responses, and 3) type I interferon (IFN) system, an innate response against viral infections, which can inhibit virus replication in the early phase. Existing information suggests that the SARS-CoV-infected airways and alveolar epithelial cells secrete abundant chemokines to attract immune cell infiltrations to the lungs, including macrophages and neutrophils, thereby causing damage due to high levels of proinflammatory cytokines and other mediators secreted by these cell types. After a decade of research on coronavirus, unfortunately, still there are no licensed vaccines, effective specific antivirals, nor drug combinations supported by high-level evidence to treat the infection, especially for newly emerging strains such as SARS-COV-2 [59] . abstract: On March 11, 2020, the World Health Organization declared the worldwide spread of the infectious disease COVID-19, caused by a new strain of coronavirus, SARS-CoV-2, as a pandemic. Like in all other infectious diseases, the host immune system plays a key role in our defense against SARS-CoV-2 infection. However, viruses are able to evade the immune attack and proliferate and, in susceptible individuals, cause severe inflammatory response known as cytokine storm, particularly in the lungs. The advancement in our understanding of the mechanisms underlying the host immune responses promises to facilitate the development of approaches for prevention or treatment of diseases. Components of immune system, such as antibodies, can also be used to develop sensitive and specific diagnostic methods as well as novel therapeutic agents. In this review, we summarize our knowledge about how the host mounts immune responses to infection by SARS-CoV-2. We also describe the diagnostic methods being used for COVID-19 identification and summarize the current status of various therapeutic strategies, including vaccination, being considered for treatment of the disease. url: https://doi.org/10.1186/s12929-020-00663-w doi: 10.1186/s12929-020-00663-w id: cord-337304-2ad2m317 author: Chang, Le title: Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations date: 2020-07-17 words: 1295.0 sentences: 85.0 pages: flesch: 62.0 cache: ./cache/cord-337304-2ad2m317.txt txt: ./txt/cord-337304-2ad2m317.txt summary: Because of high rates of 2019 novel coronavirus disease in Wuhan, China, Wuhan Blood Center began screening for severe acute respiratory syndrome coronavirus 2 RNA on January 25, 2020. We screened donations in real-time and retrospectively and found plasma samples positive for viral RNA from 4 asymptomatic donors. Lei Zhao, 1 1) and detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in plasma (2, 3) , the safety of China''s blood supply became a major concern (4). By March 4, we identified 4 blood donors in Wuhan whose plasma samples tested positive for SARS-CoV-2 RNA (Figure; Appendix Table) . We tested the 4 donors multiple times, using different sample sources, including sample tubes, retained nucleic acid templates, or blood products, indicating the accuracy and validity of our results (Appendix Table) . We extracted total nucleic acids from samples on an Most reverse transcription PCR protocols for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include 2-3 targets for detection. abstract: Because of high rates of 2019 novel coronavirus disease in Wuhan, China, Wuhan Blood Center began screening for severe acute respiratory syndrome coronavirus 2 RNA on January 25, 2020. We screened donations in real-time and retrospectively and found plasma samples positive for viral RNA from 4 asymptomatic donors. url: https://doi.org/10.3201/eid2607.200839 doi: 10.3201/eid2607.200839 id: cord-261297-kbcsa9zj author: Chang, Shan-Chwen title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) date: 2005-03-31 words: 1040.0 sentences: 68.0 pages: flesch: 50.0 cache: ./cache/cord-261297-kbcsa9zj.txt txt: ./txt/cord-261297-kbcsa9zj.txt summary: title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) Severe acute respiratory syndrome (SARS) is a new infectious disease in humans caused by SARS-associated coronavirus (SARS-CoV). Liu et al reported clinical characteristics, management, and analysis of prognostic factors in patients with probable SARS who were treated at a specially designated hospital in Taipei City during the SARS epidemic from late April to July 2003. A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Clinical characteristics, management and prognostic factors in patients with probable severe acute respiratory syndrome (SARS) in a SARS center in Taiwan Temporal relationship of viral load, ribavirin, interleukin (IL)-6, IL-8, and clinical progression in patients with severe acute respiratory syndrome abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1726490109702291 doi: 10.1016/s1726-4901(09)70229-1 id: cord-285907-xoiju5ub author: Chang, Shang-Miao title: Comparative study of patients with and without SARS WHO fulfilled the WHO SARS case definition date: 2005-05-31 words: 3607.0 sentences: 192.0 pages: flesch: 59.0 cache: ./cache/cord-285907-xoiju5ub.txt txt: ./txt/cord-285907-xoiju5ub.txt summary: Abstract To differentiate severe acute respiratory syndrome (SARS) from non-SARS illness, we retrospectively compared 53 patients with probable SARS and 31 patients with non-SARS who were admitted to Mackay Memorial Hospital from April 27 to June 16, 2003. SARS patients with an initially normal chest X-ray study developed infiltrates at a mean of 5 ± 3.44 days after onset of fever (21/22 SARS vs. Severe acute respiratory syndrome (SARS) is a rapidly progressive disease caused by a novel coronavirus. Initial chest X-ray studies were normal in 22 of 53 SARS patients (41%) and 5 of 31 non-SARS patients (16%) ( Table 4 ). All except 1 of the 22 SARS patients with an initially normal chest X-ray study eventually developed abnormalities (mean FD 5 Ϯ 3.44). No non-SARS patient with an initially negative chest X-ray developed abnormalities on follow-up films. abstract: Abstract To differentiate severe acute respiratory syndrome (SARS) from non-SARS illness, we retrospectively compared 53 patients with probable SARS and 31 patients with non-SARS who were admitted to Mackay Memorial Hospital from April 27 to June 16, 2003. Fever (> 38°C) was the earliest symptom (50/53 SARS vs. 5/31 non-SARS, p < 0.0001), preceding cough by a mean of 4.5 days. The initial chest X-ray study was normal in 22/53 SARS cases versus 5/31 non-SARS cases. SARS patients with an initially normal chest X-ray study developed infiltrates at a mean of 5 ± 3.44 days after onset of fever (21/22 SARS vs. 0/5 non-SARS). Rapid radiographic progression of unifocal involvement to multifocal infiltrates was seen in 22 of 24 SARS vs. 0 of 26 non-SARS patients (p < 0.0001). Pleural effusion was not present in any SARS patients but was seen in 6 of 26 non-SARS cases (p < 0.0001). Initial lymphopenia, thrombocytopenia, and elevated lactate dehydrogenase were all more common in SARS than non-SARS (p < 0.0001). They may help differentiate SARS from non-SARS if a reliable and rapid diagnostic test is not available. url: https://www.ncbi.nlm.nih.gov/pubmed/15837019/ doi: 10.1016/j.jemermed.2004.11.022 id: cord-292580-caxb9ob9 author: Chang, Z title: RNAi therapeutics: Can siRNAs conquer SARS? date: 2005-11-10 words: 1311.0 sentences: 95.0 pages: flesch: 60.0 cache: ./cache/cord-292580-caxb9ob9.txt txt: ./txt/cord-292580-caxb9ob9.txt summary: The epidemic of the severe acute respiratory syndrome (SARS) [1] [2] [3] in 2003 heightened the necessity for us to develop strategies to cope with emerging infectious diseases. Recent work has also shown that selected siRNAs can effectively inhibit SARS-CoV replication in cultured cells. This new study provided, for the first time, the evidence that siRNAs have a significant effect on suppression of SARS-like symptoms in a macaque model. The authors'' results indicated that the SARS-CoV-infected monkeys had attenuated SARS-like symptoms when the animals were treated with siRNA duplexes. Rhesus macaque is a good model for studying human SARS-CoV infections. Although this approach is obviously not a cure for SARS since the treated animals also developed SARS symptoms, it can be used as a complementary strategy to reduce the severity of the disease and to low the viral load in patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17262907/ doi: 10.1038/sj.gt.3302682 id: cord-281254-x7ivjvti author: Chang, Zhijie title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 words: 3803.0 sentences: 256.0 pages: flesch: 56.0 cache: ./cache/cord-281254-x7ivjvti.txt txt: ./txt/cord-281254-x7ivjvti.txt summary: The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. Since SARS-CoV rep-To address the issue related to delivery of siRNAs into cells or lication also requires certain host proteins, genes from host cells living organisms, researchers have used several approaches, ininvolved in viral replication can also be selected as targets. Therefore, RNA interference this coronavirus family), siRNAs targeting different genes of can be a tool for down-regulation of gene expression in cultured SARS-CoV were used by various groups to inhibit virus gene cells as well as in living organisms. abstract: Severe acute respiratory syndrome (SARS), caused by the novel coronavirus SARS-CoV, produced a scare when it appeared in 2003 in China and later quickly spread to other countries around the world. Although it has since disappeared, its threat to human health remains. Therefore, studies on the prevention and treatment of SARS are important for dealing with epidemics of this and other infectious diseases. The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. To date, most studies on inhibition of SARS-CoV replication using small interfering RNAs (siRNAs) have been conducted in cell lines in vitro. One study using siRNAs to inhibit SARS-CoV infection in Rhesus macaques demonstrated that siRNAs were effective both prophylactically and therapeutically with no adverse effects in the animals. Challenges remaining for the application of siRNA in vivo for SARS prevention and treatment include the specificity of the siRNAs and the efficiency of delivery. However, with improvements in siRNA design and delivery methods, RNA interference has the potential to become another major weapon for combating dangerous infections due to viruses such as SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/17263585/ doi: 10.2165/00063030-200721010-00002 id: cord-327685-fymfqvp3 author: Channappanavar, Rudragouda title: Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date: 2017-05-02 words: 5834.0 sentences: 288.0 pages: flesch: 33.0 cache: ./cache/cord-327685-fymfqvp3.txt txt: ./txt/cord-327685-fymfqvp3.txt summary: In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice abstract: Human coronaviruses (hCoVs) can be divided into low pathogenic and highly pathogenic coronaviruses. The low pathogenic CoVs infect the upper respiratory tract and cause mild, cold-like respiratory illness. In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Recent studies in experimentally infected animal strongly suggest a crucial role for virus-induced immunopathological events in causing fatal pneumonia after hCoV infections. Here we review the current understanding of how a dysregulated immune response may cause lung immunopathology leading to deleterious clinical manifestations after pathogenic hCoV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28466096/ doi: 10.1007/s00281-017-0629-x id: cord-299470-sqqer16k author: Chappell, J. G. title: Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom date: 2020-08-21 words: 4491.0 sentences: 206.0 pages: flesch: 46.0 cache: ./cache/cord-299470-sqqer16k.txt txt: ./txt/cord-299470-sqqer16k.txt summary: In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. Initial SARS-CoV-2 RT-PCR testing in the UK was offered via referral to Public Health England (PHE) national and regional diagnostic laboratories, and required strict epidemiological and clinical criteria to be met, specifically a recent travel history to Hubei province or contact with a known case and 1 or more of fever, shortness of breath or new and persistent dry cough. We describe the detection of SARS-CoV-2 from 8 patients admitted to hospital with severe respiratory distress who were not tested at the time because they had no travel history or contact with someone infected and therefore did not meet the case definition applied at the time. abstract: In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea - also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger sample of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus. url: http://medrxiv.org/cgi/content/short/2020.08.18.20174623v1?rss=1 doi: 10.1101/2020.08.18.20174623 id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 words: 5782.0 sentences: 321.0 pages: flesch: 57.0 cache: ./cache/cord-351864-zozrj7w5.txt txt: ./txt/cord-351864-zozrj7w5.txt summary: Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Briefly, we show ( Figure 1 ) that we can introduce barcoded and target-specific reverse transcription primers to the samples, allowing them to hybridize to target RNA molecules already in the lysis buffer, or after a brief RNA cleanup step. Observing the target sequence directly allowed us to identify viral sequence variations in some cases ( Figure 2D ).Cross-Sample Contamination is minimal When pooling samples early on in the protocol, the main concern is that RNA molecules will be erroneously tagged due to residual free primers, or due to other artifacts during RT, PCR, or sequencing. abstract: The global SARS-CoV-2 pandemic led to a steep increase in the need for viral detection tests worldwide. Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. While automation and improved logistics can increase the capacity of these tests, they cannot exceed this lower bound dictated by one extraction and reaction per sample. Multiplexed next generation sequencing (NGS) assays provide a dramatic increase in throughput, and hold the promise of richer information on viral strains and host immune response. Here, we establish a significant improvement of existing RNA-seq detection protocols. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Thus, only one step is performed before pooling hundreds of barcoded samples for subsequent steps and further analysis. We characterize the quantitative aspects of the assay, and test ApharSeq on dozens of clinical samples in a robotic workflow. Our proposed workflow is estimated to reduce costs by 10-50 fold, labor by 5-100 fold, automated liquid handling by 5-10 fold, and reagent requirements by 100-1000 fold compared to existing testing methods. url: http://medrxiv.org/cgi/content/short/2020.08.08.20170746v1?rss=1 doi: 10.1101/2020.08.08.20170746 id: cord-268324-86a0n0dc author: Charitos, Ioannis A title: Special features of SARS-CoV-2 in daily practice date: 2020-09-26 words: 6117.0 sentences: 279.0 pages: flesch: 42.0 cache: ./cache/cord-268324-86a0n0dc.txt txt: ./txt/cord-268324-86a0n0dc.txt summary: The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia. abstract: The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. Optimal management of the Coronavirus Disease-2019 disease is evolving quickly and treatment guidelines, based on scientific evidence and experts’ opinions with clinical experience, are constantly being updated. On January 30, 2020, the World Health Organization declared the SARS-CoV-2 outbreak as a "Public Health Emergency of International Concern". The total lack of immune protection brought about a severe spread of the contagion all over the world. For this reason, diagnostic tools, patient management and therapeutic approaches have been tested along the way, in the desperate race to break free from the widespread infection and its fatal respiratory complications. Current medical knowledge and research on severe and critical patients’ management and experimental treatments are still evolving, but several protocols on minimizing risk of infection among the general population, patients and healthcare workers have been approved and diffused by International Health Authorities. url: https://www.ncbi.nlm.nih.gov/pubmed/33024749/ doi: 10.12998/wjcc.v8.i18.3920 id: cord-351218-ei8dyxfg author: Charles Bronson, Stephen title: Letter to the Editor in response to the article “Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? date: 2020-07-03 words: 549.0 sentences: 43.0 pages: flesch: 62.0 cache: ./cache/cord-351218-ei8dyxfg.txt txt: ./txt/cord-351218-ei8dyxfg.txt summary: title: Letter to the Editor in response to the article "Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? Dear Sir, I read with great interest the article by Pitocco et al titled "Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence?". The authors have pointed towards an apparent lack of involvement of type 1 diabetes patients in the COVID-19 patients'' population in the data from three studies. Also, I have come across another COVID-19 patient who was detected to have increased blood glucose levels along with ketosis for the very first-time during his admission for COVID-19. This is in line with reports where newly detected diabetes presented with ketoacidosis in COVID-19 patients. Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence? Association of Blood Glucose Control and Outcomes in Patients with COVID-19 and Pre-existing Type 2 Diabetes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32623033/ doi: 10.1016/j.diabres.2020.108306 id: cord-312027-5tntdjp9 author: Charlton, Carmen L. title: Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies date: 2020-09-22 words: 4210.0 sentences: 202.0 pages: flesch: 47.0 cache: ./cache/cord-312027-5tntdjp9.txt txt: ./txt/cord-312027-5tntdjp9.txt summary: We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. To develop a panel of positive sera from patients with COVID-19, serum samples were collected from hospitalized patients confirmed to be positive for SARS-CoV-2 upon nasopharyngeal swab or endotracheal aspirate testing by rRT-PCR. Performance characteristics of EIAs. In total, 46 samples from 28 different patients testing positive for SARS-CoV-2 by rRT-PCR and 50 negative samples from serum samples stored prior to 1 November 2019 were run on each assay. Interestingly, despite four different samples collected from patient 6 (ranging from 18 to 29 days after symptom onset), antibodies were never detected by the Roche assay. abstract: Coronavirus disease (COVID) serological tests are essential to determine the overall seroprevalence of a population and to facilitate exposure estimates within that population. We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Demographics, symptoms, comorbidities, treatment, and mortality of patients whose sera were used were also reviewed. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. Sensitivity of EIAs ranged from 50 to 100%, with only four assays having overall sensitivities of >95% after 21 days after symptom onset. Notably, cross-reactivity with other respiratory viruses (parainfluenza virus [PIV-4] [n = 5], human metapneumovirus [hMPV] [n = 3], rhinovirus/enterovirus [n = 1], CoV-229E [n = 2], CoV-NL63 [n = 2], and CoV-OC43 [n = 2]) was observed; however, overall specificity of EIAs was good (92 to 100%; all but one assay had specificity above 95%). POCTs were 0 to 100% sensitive >21 days after onset, with specificity ranging from 96 to 100%. However, many POCTs had faint banding and were often difficult to interpret. Serology assays can detect SARS-CoV-2 antibodies as early as 10 days after symptom onset. Serology assays vary in their sensitivity based on the marker (IgA/IgM versus IgG versus total) and by manufacturer; however, overall only 4 EIAs and 4 POCTs had sensitivities of >95% >21 days after symptom onset. Cross-reactivity with other seasonal coronaviruses is of concern. Serology assays should not be used for the diagnosis of acute infection but rather in carefully designed serosurveys to facilitate understanding of seroprevalence in a population and to identify previous exposure to SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32665420/ doi: 10.1128/jcm.01361-20 id: cord-322473-fmob6k0q author: Charpiat, Bruno title: Proton Pump Inhibitors are Risk Factors for Viral Infections: Even for COVID-19? date: 2020-08-10 words: 1573.0 sentences: 76.0 pages: flesch: 42.0 cache: ./cache/cord-322473-fmob6k0q.txt txt: ./txt/cord-322473-fmob6k0q.txt summary: During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more attention should be paid to the balance of risks and benefits associated with proton pump inhibitors for the following reasons. Studies have documented that proton pump inhibitors are a risk factor for rotavirus, influenza virus, norovirus, and Middle East respiratory syndrome coronavirus infections, and are associated with an increased risk of acute gastroenteritis during periods of highest circulation of enteric viruses. Given the magnitude of the SARS-CoV-2/COVID-19 pandemic, associated with the widespread misuse of PPIs, this suggests that we cannot/should not rule out the hypothesis that patients treated with PPIs may be more at risk of being infected by COVID-19. They, therefore, hypothesized that PPI treatment may also be a potential risk factor for the development of secondary infections and of acute respiratory distress syndrome in hospitalized patients with COVID-19 [12] . abstract: During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more attention should be paid to the balance of risks and benefits associated with proton pump inhibitors for the following reasons. One of the main functions of gastric juice is to inactivate swallowed microorganisms, thereby inhibiting infectious agents from reaching the intestine. Studies have documented that proton pump inhibitors are a risk factor for rotavirus, influenza virus, norovirus, and Middle East respiratory syndrome coronavirus infections, and are associated with an increased risk of acute gastroenteritis during periods of highest circulation of enteric viruses. In light of the evidence for gastrointestinal infection implying a fecal–oral transmission of SARS-CoV-2 and given the magnitude of the SARS-CoV-2/coronavirus disease 2019 pandemic, associated with the widespread misuse of proton pump inhibitors, this suggests that we should not rule out the hypothesis that patients treated with proton pump inhibitors may be more at risk of being infected by SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32779119/ doi: 10.1007/s40261-020-00963-x id: cord-335137-5qt286kc author: Chatterjee, Swapan K. title: Molecular Pathogenesis, Immunopathogenesis and Novel Therapeutic Strategy Against COVID-19 date: 2020-08-11 words: 7124.0 sentences: 369.0 pages: flesch: 47.0 cache: ./cache/cord-335137-5qt286kc.txt txt: ./txt/cord-335137-5qt286kc.txt summary: It is believed that interaction between angiotensin converting enzyme 2 (ACE2) cell receptor and viral Spike protein mediates the coronavirus entry into human respiratory epithelial cells and establishes the host tropism. The most significant surface protein is spike glycoprotein which interferes in establishing the association between the human respiratory epithelial cells to the virus via cell surface membrane receptor angiotensin-converting enzyme 2 (ACE2) and finally establishes the host tropism (Li et al., 2003) . A recent study suggests that prediction of SARS-CoV-2 spike glycoprotein structure, glycan shield pattern and pattern of glycosylation has great inference on understanding the viral camouflage as well as the outline of cell entry, and also facilitate the development of new small-molecule drugs, vaccines, antibodies, and screening of the human host targets (Song et al., 2018) . Various studies have proved that SARS-CoV-2 infection initiation and spread of disease into the host cells mainly depends upon S protein priming by TMPRSS2 (Transmembrane protease serine type 2), the serine protease. abstract: The coronavirus disease 2019 (COVID-19), is a highly contagious transmittable disease caused by a recently discovered coronavirus, pathogenic SARS-CoV-2. Followed by the emergence of highly pathogenic coronaviruses in 2003 SARS-CoV, in 2012 MERS-CoV, now in 2019 pathogenic SARS-CoV-2, is associated with a global “pandemic” situation. In humans, the effects of these viruses are correlated with viral pneumonia, severe respiratory tract infections. It is believed that interaction between angiotensin converting enzyme 2 (ACE2) cell receptor and viral Spike protein mediates the coronavirus entry into human respiratory epithelial cells and establishes the host tropism. ACE2 receptor is highly expressed in airway epithelial cells. Along with viral-receptor interaction, proteolytic cleavability of S protein has been considered as the determinant of disease severity. Several studies highlight the occurrence of impaired host immune response and expression of excessive inflammatory response especially cytokines against viral infection. The mechanisms of SARS-CoV-2 induced acute lung injury are still undefined; however, the term cytokine storm has now been recognized to be closely associated with COVID-19. The levels of inflammatory mediators from cytokine storm cause damage to the host cells. In particular, the proinflammatory cytokine IL-6 appears to be the key mediator in early phase of virus-receptor interaction; however, secreted IL-6 might not be representative of lung inflammation. Understanding the cellular, and molecular factors involved in immune dysregulation and the high virulence capacity of COVID-19 will help in potential targeted therapy against it. “Drug repurposing” and “molecular docking analysis” is considered as an attractive alternative approach in analyzing suitable drug candidates to combat SARS-CoV-2 infection. Globally, extensive research is in progress to discover a new vaccine for novel COVID-19. Moreover, our review mainly focuses on the most state-of-the-art therapeutic approach mediated by “Mannose-binding lectin (MBL).” One of the most significant molecules of innate immunity is MBL. It plays a major role in the activation of the complement system as an ante-antibody prior to the response of any particular antibody. Recombinant human MBL can be used as immunomodulators against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32850977/ doi: 10.3389/fmolb.2020.00196 id: cord-274156-c0c4rjfa author: Chau, J.P.C. title: Infection control practices among hospital health and support workers in Hong Kong date: 2010-08-31 words: 3104.0 sentences: 150.0 pages: flesch: 49.0 cache: ./cache/cord-274156-c0c4rjfa.txt txt: ./txt/cord-274156-c0c4rjfa.txt summary: We examined compliance with isolation precautions and infection control guidelines, including proper wearing of a mask, goggles/face shield, or gown; handling patient care equipment, linen, and laundry; routine and terminal cleaning; and terminal cleaning of an isolation room. Activities were recorded using an observation checklist for two patient care activities: direct (physical examination, basic and technical nursing care) and indirect (computer data entry and disinfection of equipment); and for compliance with isolation precautions and infection control guidelines laid down by the Centers for Disease Control and Prevention (CDC) and the Hong Kong Hospital Authority (HKHA). The support workers who performed this work demonstrated good compliance, though one was found not to wear a gown during the terminal cleaning of bedside equipment of a patient requiring contact precaution, and some failed to clean and disinfect environmental surfaces such as doorknobs, faucet handles and floors. abstract: Summary A report by the Hong Kong government noted that hospital infection control standards were inadequate, requiring audit, development and implementation. In addition, hospital staff needed training in infection control measures. We investigated infection control practices among 162 hospital health workers (109 nurses, 45 doctors and 8 therapists) and 44 support workers in one acute hospital and two rehabilitation hospitals using a non-blinded, observational design. We examined compliance with isolation precautions and infection control guidelines, including proper wearing of a mask, goggles/face shield, or gown; handling patient care equipment, linen, and laundry; routine and terminal cleaning; and terminal cleaning of an isolation room. One major breakdown in compliance was use of sleeveless disposable plastic aprons instead of long-sleeved gowns during procedures likely to generate splashes or sprays of blood and body fluids. In more than half of the observed episodes, participants failed to disinfect medical devices, such as stethoscopes, before re-use. Thorough cleansing of commodes between patients was also lacking. Overall compliance with local and international infection control guidelines was satisfactory, but several aspects required improvement. url: https://api.elsevier.com/content/article/pii/S019567010900468X doi: 10.1016/j.jhin.2009.10.014 id: cord-270776-oulnk1b3 author: Chau, Tai-nin title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome date: 2004-08-15 words: 2775.0 sentences: 142.0 pages: flesch: 45.0 cache: ./cache/cord-270776-oulnk1b3.txt txt: ./txt/cord-270776-oulnk1b3.txt summary: title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome Purpose To determine whether the initial chest radiograph is helpful in predicting the clinical outcome of patients with severe acute respiratory syndrome (SARS). Results Bilateral disease and involvement of more than two zones on the initial chest radiograph were associated with a higher risk of liver impairment and poor clinical outcome. Together with the clinical characteristics of SARS, such as fever and chest symptoms, and a recent history of contact with a suspected or confirmed SARS patient, radiographic evidence of infiltrates consistent with pneumonia or acute respiratory distress syndrome is important in establishing the diagnosis (5) . Studies involving patients with community-acquired pneumonia (10) , acute interstitial pneumonia (11) , or idiopathic pulmonary fibrosis (12) have shown that quantitative and qualitative changes on chest radiographs might predict clinical outcome. abstract: Purpose To determine whether the initial chest radiograph is helpful in predicting the clinical outcome of patients with severe acute respiratory syndrome (SARS). Methods Of 343 patients who met the World Health Organization’s case definition of probable SARS and who had been admitted to a regional hospital in Hong Kong, 201 patients had laboratory evidence of SARS coronavirus infection. The initial frontal chest radiographs of these 201 patients were assessed in a blinded fashion by 3 radiologists; individual findings were accepted if at least 2 of the radiologists concurred. Independent predictors of an adverse outcome, defined as the need for assisted ventilation, death, or both, were identified by multivariate analysis. Results Bilateral disease and involvement of more than two zones on the initial chest radiograph were associated with a higher risk of liver impairment and poor clinical outcome. Forty-two patients (21%) developed an adverse outcome. Multivariate analysis showed that lung involvement of more than two zones (odds ratio [OR] = 7.0; 95% confidence interval [CI]: 2.7 to 17.9), older age (OR for each decade of life = 1.5; 95% CI: 1.1 to 2.0), and shortness of breath on admission (OR = 2.8; 95% CI: 1.1 to 7.4) were independent predictors of an adverse outcome. Conclusion Frontal chest radiographs on presentation may have prognostic value in patients with SARS. url: https://www.sciencedirect.com/science/article/pii/S0002934304003146 doi: 10.1016/j.amjmed.2004.03.020 id: cord-340042-intxyu46 author: Chaudhry, Sundas Nasir title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 words: 5457.0 sentences: 260.0 pages: flesch: 43.0 cache: ./cache/cord-340042-intxyu46.txt txt: ./txt/cord-340042-intxyu46.txt summary: In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . abstract: In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Data revealed that the newly emerged SARS-CoV-2 affected more than 24,854,140 people with 838,924 deaths worldwide. Until now, no licensed immunization or drugs are present for the medication of SARS-CoV-2. The present review aims to investigate the latest developments and discuss the candidate antibodies in different vaccine categories to develop a reliable and efficient vaccine against SARS-CoV-2 in a short time duration. Besides, the review focus on the present challenges and future directions, structure, and mechanism of SARS-CoV-2 for better understanding. Based on data, we revealed that most of the vaccines are focus on targeting the spike protein (S) of COVID-19 to neutralized viral infection and develop long-lasting immunity. Up to phase-1 clinical trials, some vaccines showed the specific antigen-receptor T cell response, elicit the humoral and immune response, displayed tight binding with human-leukocytes-antigen (HLA), and recognized specific antibodies to provoke long-lasting immunity against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32926920/ doi: 10.1016/j.lfs.2020.118421 id: cord-335768-ry5boej6 author: Chauhan, Shaylika title: Comprehensive review of coronavirus disease 2019 (COVID-19) date: 2020-06-01 words: 4382.0 sentences: 242.0 pages: flesch: 55.0 cache: ./cache/cord-335768-ry5boej6.txt txt: ./txt/cord-335768-ry5boej6.txt summary: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, the capital of China''s Hubei province and has rapidly spread all over the world. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 12, 2020, as shown in Fig. 1 , this has evolved into a pandemic affecting 187 countries/regions with 1, 484, 811 cases in the world with maximum being in USA(1, 347,936) followed by 227,436 in Spain and 224, 422 in United Kingdom at the time of writing .6 It is an un-precedented global health crisis with 286,355 deaths since the virus was first reported. Severe outcomes among patients with coronavirus disease 2019 (COVID-19) d United States abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, the capital of China's Hubei province and has rapidly spread all over the world. The World Health Organization (WHO) declared the outbreak to be a Public Health Emergency of International Concern on 30 January 2020 and recognized it as a pandemic on 11 March 2020. The number of people diagnosed with COVID-19 worldwide crossed the one million mark on April 2, 2020; two million mark on April 15, 2020; three million mark on April 27,2020 and the four million mark on May 9,2020. Despite containment efforts, more than 187 countries have been affected with more than 4, 178,346 cases in the world with maximum being in USA (1, 347,936) followed by 227,436 in Spain and 224, 422 in United Kingdom as of May, 2020. COVID-19 is the latest threat to face mankind cutting across geographical barriers in a rapidly changing landscape. This review provides an update on a rapidly evolving global pandemic. As we face the threat of emerging and re-emerging infectious diseases, this is a stark reminder to invest in population health, climate change countermeasures, a global health surveillance system and effective research into identifying pathogens, their treatment and prevention and effective health delivery systems. url: https://api.elsevier.com/content/article/pii/S2319417020300871 doi: 10.1016/j.bj.2020.05.023 id: cord-327799-ngzvdd8c author: Chaumont, Claire title: The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date: 2020-09-21 words: 1796.0 sentences: 90.0 pages: flesch: 45.0 cache: ./cache/cord-327799-ngzvdd8c.txt txt: ./txt/cord-327799-ngzvdd8c.txt summary: The current global priority is to protect people from attaining the COVID-19 infection and to attend to those infected, resulting in the disruption of other activities of the health sector, such as neglected tropical disease (NTD) control and elimination programs, which, across the globe, have postponed mass drug administration (MDA) campaigns. The most obvious impact of the crisis on NTD programs relates to its effect on infection prevalence due to delayed mass drug administration campaigns. Shifts in human capital availability and transmission dynamics of SARS-CoV-2 will require national NTD programs to adopt different implementation approaches to ensure availability and use of appropriate personnel, as well as preventive measures, including social distancing, safe hygiene practices, and face masks and/or coverings. This approach could better mitigate the risk of SARS-CoV-2 transmission, but community acceptance and costs would need to be carefully considered, as well as its potential impact on coverage. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32956353/ doi: 10.1371/journal.pntd.0008680 id: cord-346530-o65m0whe author: Chaumont, H. title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection date: 2020-06-12 words: 770.0 sentences: 49.0 pages: flesch: 36.0 cache: ./cache/cord-346530-o65m0whe.txt txt: ./txt/cord-346530-o65m0whe.txt summary: title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection We report four cases of severe COVID-19 in male patients aged 50-70 with the combination of central and peripheral nervous system disorders occurring unexpectedly late after the first symptoms. Several acute neurological syndromes have been associated with SARS-CoV-2 infection, including anosmia and ageusia [1, 2] , meningoencephalitis [3, 4] , acute hemorrhagic necrotizing encephalopathy [5] , axonal or demyelinating polyradiculoneuropathy [6] [7] [8] , polyneuritis cranialis [8] . They consisted of miscellaneous symptoms such as confusion, cognitive dysfunction (memory deficit, frontal syndrome), psychiatric disorders (paranoid delusion, hallucinations), weakness, pyramidal signs, dysautonomia, swallowing dysfunction, vertical supranuclear eye palsy, upper limbs myoclonus, fasciculation and focal muscle atrophy (Table 1) . COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32533322/ doi: 10.1007/s00415-020-09986-y id: cord-308831-u5bj1sod author: Chaung, Jenna title: Coinfection with COVID‐19 and Coronavirus HKU1 – the critical need for repeat testing if clinically indicated date: 2020-04-15 words: 1008.0 sentences: 70.0 pages: flesch: 54.0 cache: ./cache/cord-308831-u5bj1sod.txt txt: ./txt/cord-308831-u5bj1sod.txt summary: COVID-19 is the latest global pandemic caused by the severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2). We describe a case of endemic HCoV co-infection with SARS-CoV-2 in a patient with COVID-19. Nasopharyngeal swabs were sent on day 1 of admission, one was positive for HCoV-HKU1 on the FilmArray Respiratory Panel (RP) (BioFire Diagnostics, bioMerieux) but another was negative for SARS-CoV-2 by RT-PCR (in-house-laboratorydeveloped test detecting the N and ORF1ab genes by primers, with LightCycler 2.0 instrument from Roche, RotKreuz, Switzerland a ) 6 . Hence, we believe that our patient experienced co-infection with both endemic HCoV-HKU1 and pandemic SARS-CoV-2. Our case illustrates the importance of maintaining a high degree of suspicion and to note that positivity for a known virus on any respiratory multiplex assay does not exclude the possibility of co-infection with SARS-CoV-2 in a patient with a compatible clinical presentation and epidemiological history. abstract: COVID‐19 is the latest global pandemic caused by severe acute respiratory syndrome coronavirus ‐2 (SARS‐CoV‐2). There have been seven pathogenic Human Coronaviruses (HCoVs) which cause respiratory infections. Common cold coronaviruses HCoV‐229E, HCoV‐OC43, HCoV‐NL63, HCoV‐HKU1 are the four endemic HCoVs. SARS‐CoV‐1, MERS‐CoV, SARS‐CoV‐2 are zoonotic emerging epidemic pathogens with significant morbidity, mortality and economic impact. The endemic HCoVs have been known to cause co‐infections or can be co‐detected with each other or with other respiratory viruses. In general, respiratory viral co‐infections are recognized more commonly today with the use of respiratory multiplex molecular diagnostic panels. Clinicians need to be aware of co‐infections among HCoVs. A high degree of suspicion in this rapidly evolving outbreak is required in order to make the diagnosis. This is vital if we are to try and contain and control the spread of the COVID‐19. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32293743/ doi: 10.1002/jmv.25890 id: cord-256688-yy7abob9 author: Chavez, Summer title: Coronavirus Disease (COVID-19): A primer for emergency physicians date: 2020-03-24 words: 6416.0 sentences: 374.0 pages: flesch: 48.0 cache: ./cache/cord-256688-yy7abob9.txt txt: ./txt/cord-256688-yy7abob9.txt summary: DISCUSSION: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing COVID-19, is primarily transmitted from person-to-person through close contact (approximately 6 ft) by respiratory droplets. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), previously referred to as 2019-nCoV, is the virus responsible for causing Coronavirus Disease 2019 (COVID-19) [3] [4] [5] [6] [7] . An emergency medicine approach to COVID-19 should focus on identifying and isolating patients at risk for infection, informing hospital infection prevention and local public health authorities, and engaging infectious disease and other specialists early in care. Emergency physicians should obtain a detailed travel history from all patients and suspect COVID-19 in patients presenting with symptoms of an acute upper respiratory illness and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Home care for patients with suspected novel coronavirus (nCoV) infection presenting with mild symptoms and management of contacts abstract: INTRODUCTION: Rapid worldwide spread of Coronavirus Disease 2019 (COVID-19) has resulted in a global pandemic. OBJECTIVE: This review article provides emergency physicians with an overview of the most current understanding of COVID-19 and recommendations on the evaluation and management of patients with suspected COVID-19. DISCUSSION: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing COVID-19, is primarily transmitted from person-to-person through close contact (approximately 6 ft) by respiratory droplets. Symptoms of COVID-19 are similar to other viral upper respiratory illnesses. Three major trajectories include mild disease with upper respiratory symptoms, non-severe pneumonia, and severe pneumonia complicated by acute respiratory distress syndrome (ARDS). Emergency physicians should focus on identifying patients at risk, isolating suspected patients, and informing hospital infection prevention and public health authorities. Patients with suspected COVID-19 should be asked to wear a facemask. Respiratory etiquette, hand washing, and personal protective equipment are recommended for all healthcare personnel caring for suspected cases. Disposition depends on patient symptoms, hemodynamic status, and patient ability to self-quarantine. CONCLUSION: This narrative review provides clinicians with an updated approach to the evaluation and management of patients presenting to the emergency department with suspected COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32265065/ doi: 10.1016/j.ajem.2020.03.036 id: cord-321819-lqyo9px1 author: Chaw, Liling title: Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei date: 2020-11-17 words: 4170.0 sentences: 215.0 pages: flesch: 47.0 cache: ./cache/cord-321819-lqyo9px1.txt txt: ./txt/cord-321819-lqyo9px1.txt summary: We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. Brunei''s thorough contact tracing provides a rare opportunity to study the epidemiologic and transmission characteristics of SARS-CoV-2 in different community settings. Among 1,755 close contacts of the COVID-19 cluster among Tablighi members in Brunei, 52 local transmissions were detected, giving an overall nonprimary attack rate of 2.9% (95% CI 2.2%-3.8%). We could not calculate the attack rate for attendees of the local religious gathering because the 3 primary cases at the event had different symptom statuses and we could not ascertain how transmission occurred. In the household setting, symptomatic casepatients had 2.7 times the risk of transmitting SARS-CoV-2 to their close contacts, compared with asymptomatic and presymptomatic case-patients (crude risk ratio 2.66 [95% CI 1.12-6.34]; Table 3 ). abstract: We report the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across different settings in Brunei. An initial cluster of SARS-CoV-2 cases arose from 19 persons who had attended the Tablighi Jama’at gathering in Malaysia, resulting in 52 locally transmitted cases. The highest nonprimary attack rates (14.8%) were observed from a subsequent religious gathering in Brunei and in households of attendees (10.6%). Household attack rates from symptomatic case-patients were higher (14.4%) than from asymptomatic (4.4%) or presymptomatic (6.1%) case-patients. Workplace and social settings had attack rates of <1%. Our analyses highlight that transmission of SARS-CoV-2 varies depending on environmental, behavioral, and host factors. We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. We propose differentiated testing strategies to account for differing transmission risk. url: https://doi.org/10.3201/eid2611.202263 doi: 10.3201/eid2611.202263 id: cord-291726-8670s4st author: Che, Xiao-yan title: A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date: 2006-07-01 words: 2584.0 sentences: 102.0 pages: flesch: 46.0 cache: ./cache/cord-291726-8670s4st.txt txt: ./txt/cord-291726-8670s4st.txt summary: Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. abstract: An asymptomatic case of severe acute respiratory syndrome (SARS) occurred early in 2004, during a community outbreak of SARS in Guangzhou, China. This was the first time that a case of asymptomatic SARS was noted in an individual with antigenemia and seroconversion. The asymptomatic case patient and the second index case patient with SARS in the 2003–2004 outbreak both worked in the same restaurant, where they served palm civets, which were found to carry SARS-associated coronaviruses. Epidemiological information and laboratory findings suggested that the findings for the patient with asymptomatic infection, together with the findings from previously reported serological analyses of handlers of wild animals and the 4 index case patients from the 2004 community outbreak, reflected a likely intermediate phase of animal-to-human transmission of infection, rather than a case of human-to-human transmission. This intermediate phase may be a critical stage for virus evolution and disease prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/16758408/ doi: 10.1086/504943 id: cord-293579-w5sub348 author: Che, Xiao-yan title: Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date: 2005-06-15 words: 2564.0 sentences: 115.0 pages: flesch: 49.0 cache: ./cache/cord-293579-w5sub348.txt txt: ./txt/cord-293579-w5sub348.txt summary: By use of Western blot analysis, indirect immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA), antigenic cross-reactivity between severe acute respiratory syndrome (SARS)—associated coronavirus (SARS-CoV) and 2 HCoVs (229E and OC43) was demonstrated in immunized animals and human serum. In the present study, we cloned the nucleocapsid genes of SARS-CoV, HCoV-229E, and HCoV-OC43 and produced specific animal antisera to determine if the nucleocapsid protein is responsible for the observed antigenic cross-reactivity. The serum samples from patients with SARS had antibody responses to SARS-CoV as well as to HCoV-229E and HCoV-OC43 when nucleocapsid proteins were used in the Western blot analysis and when CoV-infected cells were used in the IFA. Furthermore, antibodies to SARS-CoV could be detected in only 1 serum sample from a healthy donor by either IFA or nucleocapsid protein-based Western blot analysis, even though patients with SARS had antibodies to HCoV-229E and HCoV-OC43. abstract: Cross-reactivity between antibodies to different human coronaviruses (HCoVs) has not been systematically studied. By use of Western blot analysis, indirect immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA), antigenic cross-reactivity between severe acute respiratory syndrome (SARS)—associated coronavirus (SARS-CoV) and 2 HCoVs (229E and OC43) was demonstrated in immunized animals and human serum. In 5 of 11 and 10 of 11 patients with SARS, paired serum samples showed a ⩾4-fold increase in antibody titers against HCoV-229E and HCoV-OC43, respectively, by IFA. Overall, serum samples from convalescent patients who had SARS had a 1-way cross-reactivity with the 2 known HCoVs. Antigens of SARS-CoV and HCoV-OC43 were more cross-reactive than were those of SARS-CoV and HCoV-229E. url: https://www.ncbi.nlm.nih.gov/pubmed/15897988/ doi: 10.1086/430355 id: cord-350990-tywbe4o2 author: Checchi, Vittorio title: COVID‐19 dentistry‐related aspects: a literature overview date: 2020-07-05 words: 3715.0 sentences: 168.0 pages: flesch: 43.0 cache: ./cache/cord-350990-tywbe4o2.txt txt: ./txt/cord-350990-tywbe4o2.txt summary: The terms used for the identification of keywords were: COVID-19, 2019-nCov, Sars-CoV-2, COVID-19 transmission, Coronavirus pneumonia, Coronavirus infection, Severe acute respiratory syndrome, Atmospheric contamination, Droplets, Aerosol, PPE/DPI, COVID-19 guidelines, Airborne contamination, Masks and respirators, and COVID-19 dental-related aspects. Therefore, dental procedures can be considered as one of the most probable causes of Sars-CoV-2 infection because such procedures require close proximity to the patient''s mouth, possess a risk of contact with saliva, blood and other biological fluids and involve the use of instrumentation that creates large aerosols 4, 19, 20 . Moreover Sars-CoV-2 demonstrates persistent adherence, for a maximum of 9 days, to various surfaces 1, 21 ; therefore, all surfaces and instruments in a dental clinic should be considered as potential sources of virus transmission because infected droplets from saliva or aerosols could land on any exposed surface 16, 19, 22 . abstract: A new coronavirus (Sars‐CoV‐2) was detected in China at the end of 2019 and has since caused a worldwide pandemic. This virus is responsible for an acute respiratory syndrome (COVID‐19), distinguished by a potentially lethal interstitial bilateral pneumonia. Because Sars‐CoV‐2 is highly infective through airborne contamination, the high infection risk in the dental environment is a serious problem for both professional practitioners and patients. This literature overview provides a description of the clinical aspects of COVID‐19 and its transmission, while supplying valuable information regarding protection and prevention measures. url: https://doi.org/10.1111/idj.12601 doi: 10.1111/idj.12601 id: cord-331066-ediowz4s author: Chechetkin, Vladimir R. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 words: 7040.0 sentences: 416.0 pages: flesch: 57.0 cache: ./cache/cord-331066-ediowz4s.txt txt: ./txt/cord-331066-ediowz4s.txt summary: Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Therefore, the putative weakly specific assembly/packaging signals in the genomic RNA of coronaviruses should be coordinated with the parameters of the helical nucleocapsid (such as the helix pitch, inner and outer diameters) which are established by cryoelectron microscopy (cryo-EM) and other structural methods. In this article, we provide methods for the detection and comparative analysis of assembly/packaging signals in the genomic RNA of the coronaviruses SARS-CoV and SARS-CoV-2 and describe main results of our study. The abundance of quasi-periodic patterns in the genomic DNA/RNA sequences can be assessed by the spectral entropy (Balakirev et al., 2003 (Balakirev et al., , 2005 (Balakirev et al., , 2014 Chechetkin, 2011; Chechetkin & Lobzin, 1996; Chechetkin & Turygin, 1994) . abstract: The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of the ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4.4 × 10(3) N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with nonoverlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a ‘newborn’ virus. These observations may be helpful in practical medical applications and are of basic interest. Communicated by Ramaswamy H. Sarma url: https://arxiv.org/pdf/2007.10274v2.pdf doi: 10.1080/07391102.2020.1815581 id: cord-189561-jhvwozsn author: Chechetkin, Vladimr R. title: Combining Detection and Reconstruction of Periodic Motifs in Genomic Sequences with Transitional Genome Mapping date: 2020-10-14 words: 4184.0 sentences: 268.0 pages: flesch: 54.0 cache: ./cache/cord-189561-jhvwozsn.txt txt: ./txt/cord-189561-jhvwozsn.txt summary: A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences. f The distribution of k-mer lengths after TAMGI for the steps within interval 1-500 for the genome of SARS-CoV-2 (shown by crosses) and its comparison with the counterpart distribution for a random reshuffled sequence (shown by circles). The correspondence should be searched between the (generally multiple) elements of icosahedral symmetry and the character of large-scale quasi-periodic segmentation induced by weakly specific cooperative interactions between genomic RNA/DNA and capsid proteins. To sum up, TAMGI method developed in this article is quite general and can be applied to the combined detection/reconstruction of quasi-periodic motifs in the genomic RNA/DNA sequences. abstract: A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. The periodic motifs (whether tandem or sparse) are assumed to be randomly modified by point mutations and indels during molecular evolution and present in the genomes in a hidden form. TAMGI is robust with respect to patched phasing of periodic motifs induced by indels. We developed and tested the relevant theory and statistical criteria for TAMGI applications. The applications of TAMGI are illustrated by the study of hidden periodic motifs in the genomes of the severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2 (the latter coronavirus SARS-CoV-2 being responsible for the COVID-19 pandemia) packaged within filament-like helical capsid. Such ribonucleocapsid is transported into spherical membrane envelope with incorporated spike glycoproteins. Two other examples concern the genomes of viruses with icosahedral capsids, satellite tobacco mosaic virus (STMV) and bacteriophage PHIX174. A part of the quasi-periodic motifs in these viral genomes was evolved due to weakly specific cooperative interaction between genomic ssRNA/ssDNA and nucleocapsid proteins. The symmetry of the capsids leads to the natural selection of specific quasi-periodic motifs in the related genomic sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences. url: https://arxiv.org/pdf/2010.07006v1.pdf doi: nan id: cord-301251-6f2nzvhz author: Cheemarla, N. R. title: Host response-based screening to identify undiagnosed cases of COVID-19and expand testing capacity date: 2020-06-05 words: 3393.0 sentences: 215.0 pages: flesch: 64.0 cache: ./cache/cord-301251-6f2nzvhz.txt txt: ./txt/cord-301251-6f2nzvhz.txt summary: Based 25 on previous work, we hypothesized that an elevated level of the interferon inducible protein 26 CXCL10 in the nasopharynx could serve as a sensitive screen for patients with an active 27 respiratory virus infection including SARS-CoV2 2 . Protein measurements lend themselves to 30 rapid, high throughput, and point-of care diagnostic methodologies 3,4 , so this combined strategy 31 offers the potential to have a first step which is sensitive and convenient (CXCL10 assay) 32 followed by a more specific test (PCR) for a subset of screen-positive patients. . https://doi.org/10.1101/2020.06.04.20109306 doi: medRxiv preprint Previously, we found that the CXCL10 level in the NP swab viral transport medium was a useful 45 indicator of infection with many common respiratory viruses 2 , suggesting that this measurement 46 could be used to indicate which of these 376 samples were most likely to contain a virus not 47 detected by the RVP. abstract: The COVID-19 pandemic has created unprecedented challenges in diagnostic testing. At the beginning of the epidemic, a confluence of factors resulted in delayed deployment of PCR-based diagnostic tests, resulting in lack of testing of individuals with symptoms of the disease. Although these tests are now more widely available, it is estimated that a three- to ten-fold increase in testing capacity will be required to ensure adequate surveillance as communities reopen(1). In response to these challenges, we evaluated potential roles of host-response based screening in the diagnosis of COVID-19. Previous work from our group showed that the nasopharyngeal (NP) level of CXCL10, a protein produced as part of the host response to viral infection, is a sensitive predictor of respiratory virus infection across a wide spectrum of viruses(2). Here, we show that NP CXCL10 is elevated during SARS-CoV-2 infection and use a CXCL10-based screening strategy to identify four undiagnosed cases of COVID-19 in Connecticut in early March. In a second set of samples tested at the Yale New Haven Hospital, we show that NP CXCL10 had excellent performance as a rule-out test (NPV 0.99, 95% C.I. 0.985-0.997). Our results demonstrate how biomarker-based screening could be used to leverage existing PCR testing capacity to rapidly enable widespread testing for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32577694/ doi: 10.1101/2020.06.04.20109306 id: cord-255752-ofph98ac author: Chegondi, Madhuradhar title: Coronavirus Disease 2019 (COVID-19) Associated With Febrile Status Epilepticus in a Child date: 2020-08-18 words: 1615.0 sentences: 113.0 pages: flesch: 55.0 cache: ./cache/cord-255752-ofph98ac.txt txt: ./txt/cord-255752-ofph98ac.txt summary: Infection associated with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been named coronavirus disease 2019 (COVID-19). We report the case of a two-year-old child who presented to our pediatric intensive care unit with febrile status epilepticus and was diagnosed to have COVID-19 infection. The emerging literature suggests that the SARS-CoV-2 infection can affect children, including all age groups, predominantly males, and cause milder disease compared to adult patients [2, 3] . We report the case of a two-year-old child who presented to our pediatric intensive care unit (PICU) with febrile status epilepticus and was diagnosed to have COVID-19 infection. A retrospective study from China reported that common neurological symptoms in adult patients with COVID-19 include headache, dizziness, and rarely seizures [12] . Our index case illustrates that SARS-CoV-2 associated COVID-19 can present with febrile seizure and febrile status epilepticus in children. abstract: Infection associated with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been named coronavirus disease 2019 (COVID-19). The emerging literature suggests that SARS-CoV-2 infection affects children of all age groups. COVID-19 as a cause of febrile seizures and status epilepticus is not yet reported in children. We report the case of a two-year-old child who presented to our pediatric intensive care unit with febrile status epilepticus and was diagnosed to have COVID-19 infection. The child recovered fully and was discharged home after three days. url: https://www.ncbi.nlm.nih.gov/pubmed/32953347/ doi: 10.7759/cureus.9840 id: cord-337825-ujq9mxk7 author: Chen, Bin title: Overview of lethal human coronaviruses date: 2020-06-10 words: 13423.0 sentences: 761.0 pages: flesch: 51.0 cache: ./cache/cord-337825-ujq9mxk7.txt txt: ./txt/cord-337825-ujq9mxk7.txt summary: Coronaviruses are the largest +ssRNA viruses and contain at least 14 ORFs, 16 protein combines with viral RNA to form a nucleocapsid, which is involved in the replication of SARS-CoV and is the most abundant protein in virus-infected cells. MERS-CoV can infect T-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, Nanopore Targeted Sequencing, also has the potential for efficiently detecting viruses in a reasonable time. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine abstract: Coronavirus infections of multiple origins have spread to date worldwide, causing severe respiratory diseases. Seven coronaviruses that infect humans have been identified: HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Among them, SARS-CoV and MERS-CoV caused outbreaks in 2002 and 2012, respectively. SARS-CoV-2 (COVID-19) is the most recently discovered. It has created a severe worldwide outbreak beginning in late 2019, leading to date to over 4 million cases globally. Viruses are genetically simple, yet highly diverse. However, the recent outbreaks of SARS-CoV and MERS-CoV, and the ongoing outbreak of SARS-CoV-2, indicate that there remains a long way to go to identify and develop specific therapeutic treatments. Only after gaining a better understanding of their pathogenic mechanisms can we minimize viral pandemics. This paper mainly focuses on SARS-CoV, MERS-CoV, and SARS-CoV-2. Here, recent studies are summarized and reviewed, with a focus on virus–host interactions, vaccine-based and drug-targeted therapies, and the development of new approaches for clinical diagnosis and treatment. url: https://doi.org/10.1038/s41392-020-0190-2 doi: 10.1038/s41392-020-0190-2 id: cord-271339-wt5o9sgm author: Chen, Chao-Ju title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 words: 2084.0 sentences: 122.0 pages: flesch: 57.0 cache: ./cache/cord-271339-wt5o9sgm.txt txt: ./txt/cord-271339-wt5o9sgm.txt summary: The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To ensure the whole process of the COVID-19 diagnostic testing took place without a problem, we simultaneously added primers and a probe of human RNase P gene (RP gene) as an internal control in the same well with the RdRp gene assay according to the protocol from the U.S. CDC [6] (Figure 3 ). In the present report, we demonstrated our experience of relying on a protocol template from the Taiwan CDC to establish an optimized COVID-19 molecular diagnostic test within our routine services in a public health emergency. abstract: Coronavirus disease 2019 (COVID-19), the current uncontrolled outbreak of infectious disease, has caused significant challenges throughout the world. A reliable rapid diagnostic test for COVID-19 is demanded worldwide. The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we illustrate our experience of applying a protocol from the Taiwan CDC and achieving assay optimization in the immediate circumstances to meet the urgent medical and public health needs. url: https://doi.org/10.3390/diagnostics10050333 doi: 10.3390/diagnostics10050333 id: cord-343034-dzvo9v01 author: Chen, Chun-Fan title: Role of dipeptidyl peptidase-4 inhibitors in patients with diabetes infected with coronavirus-19 date: 2020-04-29 words: 1294.0 sentences: 77.0 pages: flesch: 52.0 cache: ./cache/cord-343034-dzvo9v01.txt txt: ./txt/cord-343034-dzvo9v01.txt summary: The pandemic infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is widely increasing the patients affiliated with coronavirus disease 2019 (COVID-19) from last December of 2019. Notably, whether the ACE-related inhibitors or drugs modulated ACE2 activity in affecting the viral activity and disease severity of SARS-CoV-2 is still an open question. In this article, we are focusing on the impact of ACE inhibitors (ACEI) and DPP4 inhibitors used on SARS-CoV-2 activity and discussions about those drugs that may be related to infectious condition of COVID-19 diseases. Severe acute respiratory syndrome coronavirus (SARS-CoV-1) was the first epidemic coronavirus threat infected more than 8000 people with case-fatality rate (CFR) about 11%. Previous experiments had confirmed that angiotensin-converting enzyme 2 (ACE2) is the entry receptor in SARS-CoV-1 and dipeptidyl peptidase-4 (DPP4, also known as CD26) is the entry receptor in MERS-CoV. Among numerous anti-diabetic drugs, DPP4 inhibitors might play an important role during coronavirus infection, including pandemic COVID-19. abstract: The pandemic infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is widely increasing the patients affiliated with coronavirus disease 2019 (COVID-19) from last December of 2019. It is reported that the entry receptor of SARS-CoV-2 has been confirmed to be angiotensin-converting enzyme 2 (ACE2). Notably, whether the ACE-related inhibitors or drugs modulated ACE2 activity in affecting the viral activity and disease severity of SARS-CoV-2 is still an open question. Dipeptidyl peptidase-4 (DDP-4), a well-known anti-diabetic drug, has been widely used to control the glycemic condition in patients with diabetes. In this article, we are focusing on the impact of ACE inhibitors (ACEI) and DPP4 inhibitors used on SARS-CoV-2 activity and discussions about those drugs that may be related to infectious condition of COVID-19 diseases. url: https://doi.org/10.1097/jcma.0000000000000338 doi: 10.1097/jcma.0000000000000338 id: cord-296195-m2wwlvgx author: Chen, Chung-Jen title: Toona sinensis Roem tender leaf extract inhibits SARS coronavirus replication date: 2008-10-30 words: 2541.0 sentences: 156.0 pages: flesch: 66.0 cache: ./cache/cord-296195-m2wwlvgx.txt txt: ./txt/cord-296195-m2wwlvgx.txt summary: RESULTS: Only TSL-1, the extract from tender leaf of Toona sinensis Roem was found to have an evident effect against SARS-CoV with selectivity index 12∼17. In the third study, five TCM formulae included Yin-Chiau-San, Pu-Zhi-Siau-Du-Yien, Ger-Gern-Hwang-Lein, Sang-Zhiu-Yien and Huang-Lein-Zhei-Du-Tang as well as Toona sinensis Roem tender leaf extract TSL-1 and TSL-1nm were tested against SARS-CoV. Much different from a lot of previously identified components or drugs against SARS-CoV, the tender leaf of Toona sinensis Roem has been used as a popular vegetable by Chinese people in both mainland China and Taiwan with high level of safety. To our knowledge, this is the first report to show extract from the tender leaf of Toona sinensis Roem against SARS-CoV. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. abstract: AIM OF THE STUDY: Severe acute respiratory syndrome (SARS) is a life-threatening disease caused by the SARS coronavirus (SARS-CoV). The development of new antiviral agents for SARS-CoV is an important issue. We tried to find potential resource from Traditional Chinese medicine (TCM) for development of new drugs against SARS-CoV. MATERIALS AND METHODS: Our team recruited the potential TCM formulae (also known as Kampo) from two TCM books, Shang-Han Lun (Discussion of Cold-Induced Disorders) and Wen-Bing Tiau-Bein (Differential Management of Febrile Diseases). Several herbs, which were believed to be beneficial for SARS by experienced TCM doctors were also recruited. In addition, a vegetable polular in Taiwan, China and Malaysia, the tender leaf of Toona sinensis Roem (also known as Cedrela sinensis, belongs to the family Meliacceae) was also recruited under the suggestion of botanic experts. These TCM products and plant extrats were then tested for the effectiveness against SARS-CoV in vitro. RESULTS: Only TSL-1, the extract from tender leaf of Toona sinensis Roem was found to have an evident effect against SARS-CoV with selectivity index 12∼17. CONCLUSION: This paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. Thererfore, the tender leaf of Toona sinensis Roem may be an important resource agninst SARS-CoV. url: https://www.sciencedirect.com/science/article/pii/S0378874108004200 doi: 10.1016/j.jep.2008.07.048 id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 words: 1499.0 sentences: 96.0 pages: flesch: 48.0 cache: ./cache/cord-283590-xvnv17zy.txt txt: ./txt/cord-283590-xvnv17zy.txt summary: Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People''s Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). abstract: The ongoing outbreak of COVID-19 that began in Wuhan, China, has constituted a Public Health Emergency of International Concern, with cases confirmed in multiple countries. Currently, patients are the primary source of infection. We report a confirmed case of COVID-19 whose oropharyngeal swab test of SARS-CoV-2 RNA turned positive in convalescence. This case highlights the importance of active surveillance of SARS-CoV-2 RNA for infectivity assessment. url: https://www.ncbi.nlm.nih.gov/pubmed/32147538/ doi: 10.1016/j.ijid.2020.03.003 id: cord-276017-2375ipkk author: Chen, Dongsheng title: Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date: 2020-06-14 words: 4132.0 sentences: 365.0 pages: flesch: 70.0 cache: ./cache/cord-276017-2375ipkk.txt txt: ./txt/cord-276017-2375ipkk.txt summary: Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Previous studies have proposed that animal tissues show high heterogeneity in terms of cellular composition and gene expression profiles 15 , and ACE2 is only expressed in a small proportion of specific cell populations 16 , making single cell analysis of SARS-CoV-2 target cells an attracting field to investigate. Here, we constructed the single cell atlas for livestock, poultry, pets and wildlife, then screened putative SARS-CoV-2 target cells (indicated by the co-expression patterns of SARS-CoV-2 entry receptor ACE2 and SARS-CoV-2 entry activator TMPRSS2) and systematically evaluated their susceptibility, with the aim to understand the virus transmission routes and provide clues to fight against COVID-19. abstract: A few animals have been suspected to be intermediate hosts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, a large-scale single-cell screening of SARS-CoV-2 target cells on a wide variety of animals is missing. Here, we constructed the single-cell atlas for 11 representative species in pets, livestock, poultry, and wildlife. Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Furthermore, we screened the expression patterns of receptors for 144 viruses, resulting in a comprehensive atlas of virus target cells. Taken together, our work provides a novel and fundamental strategy to screen virus target cells and susceptible species, based on single-cell transcriptomes we generated for domesticated animals and wildlife, which could function as a valuable resource for controlling current pandemics and serve as an early warning system for coping with future infectious disease threats. url: https://doi.org/10.1101/2020.06.13.149690 doi: 10.1101/2020.06.13.149690 id: cord-312899-ot5pvtbl author: Chen, F title: In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds date: 2004-09-30 words: 3161.0 sentences: 164.0 pages: flesch: 43.0 cache: ./cache/cord-312899-ot5pvtbl.txt txt: ./txt/cord-312899-ot5pvtbl.txt summary: Commercial antiviral agents and pure chemical compounds extracted from traditional Chinese medicinal herbs were screened against 10 clinical isolates of SARS coronavirus by neutralisation tests with confirmation by plaque reduction assays. Interferon-beta-1a, leukocytic interferon-alpha, ribavirin, lopinavir, rimantadine, baicalin and glycyrrhizin showed antiviral activity. We report in this study on the in vitro antiviral susceptibility of 10 isolates of SARS coronavirus to commercially available antiviral agents and pure chemical compounds including baicalin, glycyrrhizin, and chlorogenic acid extracted from traditional Chinese herbs. Further testing by neutralization tests Table 3 Comparison of antiviral activity of 10 compounds against 10 strains of SARS-CoV in fRhK4 cell line, against the prototype strains (39849) with the other 9 isolates of SARS coronavirus against the active compounds confirmed detectable inhibitory activities for leukocytic interferon-alpha, interferon-beta-1a, ribavirin, lopinavir, rimantadine, and baicalin. abstract: Abstract Effective antiviral agents are urgently needed to combat the possible return of severe acute respiratory syndrome (SARS). Commercial antiviral agents and pure chemical compounds extracted from traditional Chinese medicinal herbs were screened against 10 clinical isolates of SARS coronavirus by neutralisation tests with confirmation by plaque reduction assays. Interferon-beta-1a, leukocytic interferon-alpha, ribavirin, lopinavir, rimantadine, baicalin and glycyrrhizin showed antiviral activity. The two interferons were only active if the cell lines were pre-incubated with the drugs 16h before viral inoculation. Results were confirmed by plaque reduction assays. Antiviral activity varied with the use of different cell lines. Checkerboard assays for synergy were performed showing combinations of interferon beta-1a or leukocytic interferon-alpha with ribavirin are synergistic. Since the clinical and toxicity profiles of these agents are well known, they should be considered either singly or in combination for prophylaxis or treatment of SARS in randomised placebo controlled trials in future epidemics. url: https://www.sciencedirect.com/science/article/pii/S1386653204000551 doi: 10.1016/j.jcv.2004.03.003 id: cord-299354-rmjohbse author: Chen, Fu-Lun title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 words: 126.0 sentences: 20.0 pages: flesch: 70.0 cache: ./cache/cord-299354-rmjohbse.txt txt: ./txt/cord-299354-rmjohbse.txt summary: key: cord-299354-rmjohbse authors: Chen, Fu-Lun; Wang, Cheng-Hui; Hung, Ching-Sheng; Su, Ying-Shih; Lee, Wen-Sen title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.05.007 sha: doc_id: 299354 cord_uid: rmjohbse nan Dear Editor: The article by Jean et al. Treatment options for COVID-19: The reality and challenges Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV Recommendations and guidelines for the treatment of pneumonia in Taiwan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical characteristics of coronavirus disease 2019 in China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32505530/ doi: 10.1016/j.jmii.2020.05.007 id: cord-289332-hvakv08t author: Chen, Guoqian title: Pathogenic role of HMGB1 in SARS? date: 2004-04-30 words: 1670.0 sentences: 90.0 pages: flesch: 37.0 cache: ./cache/cord-289332-hvakv08t.txt txt: ./txt/cord-289332-hvakv08t.txt summary: High mobility group box 1 protein (HMGB1) is released by necrotic cells or activated macrophages/monocytes, and functions as a late mediator of lethal systemic and local pulmonary inflammation. In light of observations that three Chinese herbal formulations recommended for treatment of severe acute respiratory syndrome (SARS) specifically inhibited the release of HMGB1 from innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. High mobility group box 1 protein (HMGB1, formerly known as HMG-1 or amphoterin) has recently been identified as a new proinflammatory cytokine and a late mediator of inflammation, sepsis, and acute lung injury. In light of observations that several Chinese herbal remedies recommended for treatment of SARS specifically inhibited the release of HMGB1 from activated innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. abstract: High mobility group box 1 protein (HMGB1) is released by necrotic cells or activated macrophages/monocytes, and functions as a late mediator of lethal systemic and local pulmonary inflammation. Passive immunization with anti-HMGB1 antibodies confers significant protection against lethal endotoxemia, sepsis, and acute lung injury, even when antibodies are administered after the onset of these diseases. In light of observations that three Chinese herbal formulations recommended for treatment of severe acute respiratory syndrome (SARS) specifically inhibited the release of HMGB1 from innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. url: https://www.sciencedirect.com/science/article/pii/S0306987704002208 doi: 10.1016/j.mehy.2004.01.037 id: cord-352509-qrzt4zva author: Chen, Haohui title: Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak date: 2020-03-16 words: 3903.0 sentences: 223.0 pages: flesch: 63.0 cache: ./cache/cord-352509-qrzt4zva.txt txt: ./txt/cord-352509-qrzt4zva.txt summary: This study examines publicly available online search data in China to investigate the spread of public awareness of the 2019 novel coronavirus (COVID-19) outbreak. We use the continuing Wuhan coronavirus outbreak as our case study to estimate the effects of social distance and SARS memory on the spread of public awareness. The effects of social distance and SARS memory on the lead-time advantage are estimated according to Eq. 4, controlled by Euclidean distances, GDP per capita and the city''s administrative level (Table 1) . That means cities of strong SARS memory and which are closer to Wuhan in terms of Social distances develop early awareness. Through controlling for development, administrative levels, and Euclidean distances, we observe cities that were struck by SARS and have more migration to the epicentre, Wuhan, showed earlier, stronger and more durable public awareness of the outbreak. abstract: This study examines publicly available online search data in China to investigate the spread of public awareness of the 2019 novel coronavirus (COVID-19) outbreak. We found that cities that suffered from SARS and have greater migration ties to the epicentre, Wuhan, had earlier, stronger and more durable public awareness of the outbreak. Our data indicate that forty-eight such cities developed awareness up to 19 days earlier than 255 comparable cities, giving them an opportunity to better prepare. This study suggests that it is important to consider memory of prior catastrophic events as they will influence the public response to emerging threats. url: https://doi.org/10.1101/2020.03.11.20033688 doi: 10.1101/2020.03.11.20033688 id: cord-282045-pf08iakf author: Chen, Haoyan title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production date: 2020-07-08 words: 1676.0 sentences: 105.0 pages: flesch: 60.0 cache: ./cache/cord-282045-pf08iakf.txt txt: ./txt/cord-282045-pf08iakf.txt summary: title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production The percentage of these five SARS-CoV-2 entry genes was similar as ACE2, which is gradually increased in epithelial cells from normal control, CRA to CRC samples (Supplementary Fig. S3d ). Strikingly, pathways associated with virus infection, inflammation and cytokine signaling were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) . Given that IL-6 and TNF pathways were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) , we compared the IL-6 and TNF-alpha levels in peripheral blood from mild (n = 102) and severe (n = 50) COVID-19 pneumonia patients Table S3 ). Here, we first proved that the six SARS-CoV-2 entry genes, including ACE2 and TMPRSS2, are expressed in the colon epithelial cells of Chinese adults. In a word, the expression of additional five SARS-CoV-2 entry genes, virus infection, and inflammatory pathways are significantly enriched in colon epithelia cells with ACE2-positive expression. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32641705/ doi: 10.1038/s41392-020-00237-0 id: cord-288197-drto66xt author: Chen, Huijun title: Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records date: 2020-02-12 words: 3927.0 sentences: 225.0 pages: flesch: 54.0 cache: ./cache/cord-288197-drto66xt.txt txt: ./txt/cord-288197-drto66xt.txt summary: METHODS: Clinical records, laboratory results, and chest CT scans were retrospectively reviewed for nine pregnant women with laboratory-confirmed COVID-19 pneumonia (ie, with maternal throat swab samples that were positive for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) who were admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from Jan 20 to Jan 31, 2020. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy. Evidence of vertical transmission was assessed by testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in amniotic fluid, cord blood, breastmilk, and neonatal throat swab samples from six of nine patients. Based on data from this small group of patients, there is currently no evidence of vertical transmission in pregnant women who develop COVID-19 pneumonia in the third trimester. abstract: BACKGROUND: Previous studies on the pneumonia outbreak caused by the 2019 novel coronavirus disease (COVID-19) were based on information from the general population. Limited data are available for pregnant women with COVID-19 pneumonia. This study aimed to evaluate the clinical characteristics of COVID-19 in pregnancy and the intrauterine vertical transmission potential of COVID-19 infection. METHODS: Clinical records, laboratory results, and chest CT scans were retrospectively reviewed for nine pregnant women with laboratory-confirmed COVID-19 pneumonia (ie, with maternal throat swab samples that were positive for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) who were admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from Jan 20 to Jan 31, 2020. Evidence of intrauterine vertical transmission was assessed by testing for the presence of SARS-CoV-2 in amniotic fluid, cord blood, and neonatal throat swab samples. Breastmilk samples were also collected and tested from patients after the first lactation. FINDINGS: All nine patients had a caesarean section in their third trimester. Seven patients presented with a fever. Other symptoms, including cough (in four of nine patients), myalgia (in three), sore throat (in two), and malaise (in two), were also observed. Fetal distress was monitored in two cases. Five of nine patients had lymphopenia (<1·0 × 10⁹ cells per L). Three patients had increased aminotransferase concentrations. None of the patients developed severe COVID-19 pneumonia or died, as of Feb 4, 2020. Nine livebirths were recorded. No neonatal asphyxia was observed in newborn babies. All nine livebirths had a 1-min Apgar score of 8–9 and a 5-min Apgar score of 9–10. Amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples from six patients were tested for SARS-CoV-2, and all samples tested negative for the virus. INTERPRETATION: The clinical characteristics of COVID-19 pneumonia in pregnant women were similar to those reported for non-pregnant adult patients who developed COVID-19 pneumonia. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy. FUNDING: Hubei Science and Technology Plan, Wuhan University Medical Development Plan. url: https://www.ncbi.nlm.nih.gov/pubmed/32151335/ doi: 10.1016/s0140-6736(20)30360-3 id: cord-278540-gy65bvot author: Chen, I-Yin title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date: 2019-01-29 words: 4645.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-278540-gy65bvot.txt txt: ./txt/cord-278540-gy65bvot.txt summary: A recent study shows that the SARS-CoV E protein, which comprise only 76 amino acids, forms Ca 2+ -permeable ion channels and activates the NLRP3 inflammasome (Nieto-Torres et al., 2015) . To this end, we substituted amino acids Cys-127, Cys-130, and Cys-133 within the cysteine-rich domain of the SARS-CoV 3a protein with serine to generate a lentivirus expressing the ion channel activity-loss mutant, 3a-CS (Chan et al., 2009; Figure 2A) . Together, these data provide evidence that the ion channel activity of the SARS-CoV 3a protein is essential for triggering the NLRP3 inflammasome. Since mitochondrial ROS are important for NLRP3 inflammasome activation (Nakahira et al., 2011; Zhou et al., 2011) , we next stimulated BMMs with extracellular ATP or lentiviruses expressing the SARS-CoV E or 3a proteins in the presence or absence of the antioxidant, Mito-TEMPO, a scavenger that is specific for mitochondrial ROS Trnka et al., 2009) . abstract: Nod-like receptor family, pyrin domain-containing 3 (NLRP3) regulates the secretion of proinflammatory cytokines interleukin 1 beta (IL-1β) and IL-18. We previously showed that influenza virus M2 or encephalomyocarditis virus (EMCV) 2B proteins stimulate IL-1β secretion following activation of the NLRP3 inflammasome. However, the mechanism by which severe acute respiratory syndrome coronavirus (SARS-CoV) activates the NLRP3 inflammasome remains unknown. Here, we provide direct evidence that SARS-CoV 3a protein activates the NLRP3 inflammasome in lipopolysaccharide-primed macrophages. SARS-CoV 3a was sufficient to cause the NLRP3 inflammasome activation. The ion channel activity of the 3a protein was essential for 3a-mediated IL-1β secretion. While cells uninfected or infected with a lentivirus expressing a 3a protein defective in ion channel activity expressed NLRP3 uniformly throughout the cytoplasm, NLRP3 was redistributed to the perinuclear space in cells infected with a lentivirus expressing the 3a protein. K(+) efflux and mitochondrial reactive oxygen species were important for SARS-CoV 3a-induced NLRP3 inflammasome activation. These results highlight the importance of viroporins, transmembrane pore-forming viral proteins, in virus-induced NLRP3 inflammasome activation. url: https://www.ncbi.nlm.nih.gov/pubmed/30761102/ doi: 10.3389/fmicb.2019.00050 id: cord-287349-1zcq7kzx author: Chen, James title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date: 2020-07-28 words: 2959.0 sentences: 215.0 pages: flesch: 53.0 cache: ./cache/cord-287349-1zcq7kzx.txt txt: ./txt/cord-287349-1zcq7kzx.txt summary: title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. The analogous structural 234 arrangement leads us to propose that the SARS-CoV-2 RdRp may backtrack, generating a single-235 stranded RNA segment at the 3''-end that would extrude out the RdRp secondary channel 236 Table S1 ; Video S1). This aspect of helicase function could provide the NTP-296 dependent motor activity necessary to backtrack the RdRp. In cellular organisms, DdRp 297 backtracking plays important roles in many processes, including the control of pausing during 298 transcription elongation, termination, DNA repair, and fidelity (Nudler, 2012) . Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase abstract: Summary SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development. url: https://www.ncbi.nlm.nih.gov/pubmed/32783916/ doi: 10.1016/j.cell.2020.07.033 id: cord-133453-23rfdkuw author: Chen, Jiahui title: Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies date: 2020-10-13 words: 8184.0 sentences: 485.0 pages: flesch: 54.0 cache: ./cache/cord-133453-23rfdkuw.txt txt: ./txt/cord-133453-23rfdkuw.txt summary: By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. The vaccination mechanism is to stimulate the primary immune response of the human body, which will activate T cells and B cells to generate the antibodies and long-lived memory cells that prevent infectious diseases, which is one of the most effective and economical means for combating with COVID-19 at this stage. Notably, understanding how mutations have changed the SARS-CoV-2 structure, function, infectivity, activity, and virulence is of great importance for coming up with life-saving strategies in virus control, containment, prevention, and medication, especially in the antibodies and vaccines development. Next, we study the BFE changes ∆∆G induced by 39 mutations on the SARS-CoV-2 S protein RBD for the antibody Fab 2-4 (PDB: 6XEY) in Figure 6 . abstract: Antibody therapeutics and vaccines are among our last resort to end the raging COVID-19 pandemic.They, however, are prone to over 1,800 mutations uncovered by a Mutation Tracker. It is urgent to understand how vaccines and antibodies in the development would be impacted by mutations. In this work, we first study the mechanism, frequency, and ratio of mutations on the spike (S) protein, which is the common target of most COVID-19 vaccines and antibody therapies. Additionally, we build a library of antibody structures and analyze their 2D and 3D characteristics. Moreover, we predict the mutation-induced binding free energy (BFE) changes for the complexes of S protein and antibodies or ACE2. By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. We provide a strategy to prioritize the selection of mutations for designing vaccines or antibody cocktails. url: https://arxiv.org/pdf/2010.06357v1.pdf doi: nan id: cord-167889-um3djluz author: Chen, Jianguo title: A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19 date: 2020-07-04 words: 12248.0 sentences: 768.0 pages: flesch: 50.0 cache: ./cache/cord-167889-um3djluz.txt txt: ./txt/cord-167889-um3djluz.txt summary: The progress of CT image inspection based on AI usually includes the following steps: Region Of Interest (ROI) segmentation, lung tissue feature extraction, candidate infection region detection, and COVID-19 classification. Data sources Methods Country/region Huang [82] Yang [231] , WHO [216] CNN, LSTM, MLP, GRU China Hu [80, 81] The Paper [148] , WHO [216] MAE, clustering China Yang [233] Baidu [16] SEIR, LSTM China Fong [51, 52] NHC [139] SVM, PNN China Ai [3] WHO [54, 216] ANFIS, FPA China, USA Rizk [168] WHO [216] ISACL-MFNN USA, Italy, Spain Giuliani [62] Italy [144] EMTMGL Italy Ayyoubzadeh [14] Worldometer [218] , Google [201] LR, LSTM Iran Marini [129, 130] Swiss population Enerpol Switzerland Lai [110] IATA [126] , Worldpop [219] ML Global Punn [155] JHU CSSE [49] SVR, PR, DNN, LSTM, RNN Predicting commercially available antiviral drugs that may act on the novel coronavirus (sars-cov-2) through a drug-target interaction deep learning model abstract: The COVID-19 pandemic caused by the SARS-CoV-2 virus has spread rapidly worldwide, leading to a global outbreak. Most governments, enterprises, and scientific research institutions are participating in the COVID-19 struggle to curb the spread of the pandemic. As a powerful tool against COVID-19, artificial intelligence (AI) technologies are widely used in combating this pandemic. In this survey, we investigate the main scope and contributions of AI in combating COVID-19 from the aspects of disease detection and diagnosis, virology and pathogenesis, drug and vaccine development, and epidemic and transmission prediction. In addition, we summarize the available data and resources that can be used for AI-based COVID-19 research. Finally, the main challenges and potential directions of AI in fighting against COVID-19 are discussed. Currently, AI mainly focuses on medical image inspection, genomics, drug development, and transmission prediction, and thus AI still has great potential in this field. This survey presents medical and AI researchers with a comprehensive view of the existing and potential applications of AI technology in combating COVID-19 with the goal of inspiring researches to continue to maximize the advantages of AI and big data to fight COVID-19. url: https://arxiv.org/pdf/2007.02202v1.pdf doi: nan id: cord-328479-1tzysg7u author: Chen, Jianjun title: Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China date: 2020-06-21 words: 722.0 sentences: 44.0 pages: flesch: 56.0 cache: ./cache/cord-328479-1tzysg7u.txt txt: ./txt/cord-328479-1tzysg7u.txt summary: In this study, we collected swab and blood samples from pet cats and dogs in Wuhan whose owners were confirmed to have COVID-19. Swab and whole blood samples were collected from 10 cats (four female, six male) and 9 dogs (four female, five male) (Supplementary Table 1 We then conducted telephone questionnaires with the owners of the three pets. In this study, we conducted a survey for SARS-CoV-2 in pets whose owners were diagnosed with COVID-19, in 15 communities in Wuhan. Prior to our study, a preprint of a research article posted online at bioRxiv indicated that SARS-CoV-2-specific antibodies were detected in cats in Wuhan at the time of the COVID-19 epidemic (7) . In addition, pet dogs and cats in Hong Kong (8), whose owners had been diagnosed with COVID-19, tested positive for SARS-CoV-2 RNA. Collectively, these results indicate the SARS-CoV-2 can be transmitted to companion animals, possible through contact with owners carrying COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32579982/ doi: 10.1016/j.jinf.2020.06.045 id: cord-318342-eipscagh author: Chen, Juan title: The Impact of COVID-19 on Blood Glucose: A Systematic Review and Meta-Analysis date: 2020-10-05 words: 3598.0 sentences: 205.0 pages: flesch: 48.0 cache: ./cache/cord-318342-eipscagh.txt txt: ./txt/cord-318342-eipscagh.txt summary: Results: Three studies reported blood glucose and HbA1c according to the severity of COVID-19 and were included in this meta-analysis. It remains unclear regarding the effect of severity of COVID-19 infection on glycemic parameters, including blood glucose and glycated haemoglobinA1c (HbA1c). Finally, three papers were included in the meta-analysis that evaluated blood glucose and/or HbA1c levels according to the severity of COVID-19 (17) (18) (19) . The z-test result for overall effects was statistically significant (P < 0.001), indicating a significantly greater elevation in blood glucose in patients with severe COVID-19 infection than those in the mild group. In the present meta-analysis, we found that blood glucose was significantly higher in patients with severe COVID-19 than those with mild COVID-19 (WMD 2.21, 95% CI: 1.30-3.13, P < 0.001, I 2 = 0%). abstract: Background: Diabetes mellitus is considered a common comorbidity of COVID-19, which has a wide spectrum of clinical manifestations ranging from asymptomatic infection to severe respiratory symptoms and even death. However, the impact of COVID-19 on blood glucose has not been fully understood. This meta-analysis aimed to summarize available data on the association between glycemic parameters and severity of COVID-19. Methods: PubMed, EMBASE, and Cochrane Library were searched from December 1, 2019 to May 15, 2020. Observational studies investigating blood glucose or glycated hemoglobin A1c (HbA1c) according to the severity of COVID-19 were considered for inclusion. Two independent researchers extracted data from eligible studies using a standardized data extraction sheet and then proceeded to cross check the results. Data were pooled using a fixed- or random-effects model to calculate the weighted mean differences (WMDs) and 95% confidence intervals (CIs). Results: Three studies reported blood glucose and HbA1c according to the severity of COVID-19 and were included in this meta-analysis. The combined results showed that severe COVID-19 was associated with higher blood glucose (WMD 2.21, 95% CI: 1.30–3.13, P < 0.001). In addition, HbA1c was slightly higher in patients with severe COVID-19 than those with mild COVID-19, yet this difference did not reach significance (WMD 0.29, 95% CI: −0.59 to 1.16, P = 0.52). Conclusions: This meta-analysis provides evidence that severe COVID-19 is associated with increased blood glucose. This highlights the need to effectively monitor blood glucose to improve prognosis in patients infected with COVID-19. url: https://doi.org/10.3389/fendo.2020.574541 doi: 10.3389/fendo.2020.574541 id: cord-262467-epqqd8n8 author: Chen, Jun title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 words: 7596.0 sentences: 384.0 pages: flesch: 47.0 cache: ./cache/cord-262467-epqqd8n8.txt txt: ./txt/cord-262467-epqqd8n8.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 disease as originally shown in Wuhan, China, as early as documented from 1 December 2019 (ref. A recent prospective study failed to find antiviral activity or clinical benefit of this combination for the treatment of our hospitalized patients with severe COVID-19 (ref. More recently, a randomized, controlled study conducted in Wuhan, China also failed to identify beneficial effect of LPV/r beyond standard therapy in hospitalized patients with severe Covid-19 (ref. Clinical trials also showed that in patients with severe H1N1 influenza A, in the 2009 pandemic, therapy with convalescent plasma from patients who recovered, especially within 5 days of symptom onset, resulted in a lower viral load and lower mortality 66, 67 . The duration from onset of symptoms to viral clearance is significantly longer in severe and critical ill SARS-CoV-2infected patients compared with that in the mild cases 48 . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Since its first report in December 2019, despite great efforts made in almost every country worldwide, this disease continues to spread globally, especially in most parts of Europe, Iran, and the United States. Here, we update the recent understanding in clinical characteristics, diagnosis strategies, as well as clinical management of COVID-19 in China as compared to Italy, with the purpose to integrate the China experience with the global efforts to outline references for prevention, basic research, treatment as well as final control of the disease. Being the first two countries we feel appropriate to evaluate the evolution of the disease as well as the early result of the treatment, in order to offer a different baseline to other countries. It is also interesting to compare two countries, with a very significant difference in population, where the morbidity and mortality has been so different, and unrelated to the size of the country. url: https://www.ncbi.nlm.nih.gov/pubmed/32513951/ doi: 10.1038/s41419-020-2603-0 id: cord-031079-9lxhvyyb author: Chen, Li title: The effects of chloroquine and hydroxychloroquine on ACE2 related coronavirus pathology and the cardiovascular system: An evidence based review date: 2020-07-27 words: 5660.0 sentences: 354.0 pages: flesch: 47.0 cache: ./cache/cord-031079-9lxhvyyb.txt txt: ./txt/cord-031079-9lxhvyyb.txt summary: CQ and HCQ may be potential inhibitors of SARS-CoV-2 entry into host cells, which is mediated via the angiotensin-converting enzyme 2 (ACE2), and may also inhibit subsequent intracellular processes which lead to COVID-19, including damage to the cardiovascular system. CQ and HCQ could potentially be useful drugs in the treatment of COVID-19 and other ACE2 involved virus infections, but the antiviral effects of CQ and HCQ need to be tested in more well-designed clinical randomized studies and their actions on the cardiovascular system need to be further elucidated. CQ and its more soluble and less toxic metabolite HCQ are primarily used for prophylaxis and treatment of malaria, but they have also been reported to effectively inhibit the effects of certain viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza A H5N. 40, 41 Several studies have reported that 3% to 29% of COVID-19 patients develop acute respiratory distress syndrome (ARDS) which is a common complication and cause of death as a result of SARS-CoV-2 infection. abstract: The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious threat to global public health and there is currently no effective antiviral therapy. It has been suggested that Chloroquine (CQ) and hydroxychloroquine (HCQ), which were primarily employed as prophylaxis and treatment for malaria, could be used to treat COVID-19. CQ and HCQ may be potential inhibitors of SARS-CoV-2 entry into host cells, which is mediated via the angiotensin-converting enzyme 2 (ACE2), and may also inhibit subsequent intracellular processes which lead to COVID-19, including damage to the cardiovascular system. However, paradoxically, CQ and HCQ have also been reported to cause damage to the cardiovascular system. In this review, we provide a critical examination of the published evidence. CQ and HCQ could potentially be useful drugs in the treatment of COVID-19 and other ACE2 involved virus infections, but the antiviral effects of CQ and HCQ need to be tested in more well-designed clinical randomized studies and their actions on the cardiovascular system need to be further elucidated. However, even if it were to turn out that CQ and HCQ are not useful drugs in practice, further studies of their mechanism of action could be helpful in improving our understanding of COVID-19 pathology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454642/ doi: 10.1093/function/zqaa012 id: cord-348723-sf073cmj author: Chen, Liang title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 date: 2020-03-30 words: 2015.0 sentences: 104.0 pages: flesch: 51.0 cache: ./cache/cord-348723-sf073cmj.txt txt: ./txt/cord-348723-sf073cmj.txt summary: title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Angiotensin-converting enzyme 2 (ACE2), the key host cellular receptor of SARS-CoV-2, has been identified in multiple organs, but its cellular distribution in human heart is not illuminated clearly. This study performed the first state-of-art single cell atlas of adult human heart, and revealed that pericytes with high expression of ACE2 might act as the target cardiac cell of SARS-CoV-2. The finding of this study explains the high rate of severe cases among COVID-19 patients with basic cardiovascular disease; and these results also perhaps provide important reference to clinical treatment of cardiac injury among severe patients infected by SARS-CoV-2. In the present study, we investigated ACE2 expression in the adult human hearts from healthy and diseased individuals, to illuminate the potential capacity of heart infection by SARS-CoV-2. This result suggested that pericyte was a potential SARS-CoV-2 virus targeted host cell type in the human heart. abstract: A new type of pneumonia caused by a novel coronavirus SARS-CoV-2 outbreaks recently in China and spreads into many other countries. This disease, named as COVID-19, is similar to patients infected by SARS-CoV and MERS-CoV, and nearly 20% of patients developed severe condition. Cardiac injury is a prevalent complication of severe patients, exacerbating the disease severity in coronavirus disease 2019 (COVID-19) patients. Angiotensin-converting enzyme 2 (ACE2), the key host cellular receptor of SARS-CoV-2, has been identified in multiple organs, but its cellular distribution in human heart is not illuminated clearly. This study performed the first state-of-art single cell atlas of adult human heart, and revealed that pericytes with high expression of ACE2 might act as the target cardiac cell of SARS-CoV-2. The pericytes injury due to virus infection may result in capillary endothelial cells dysfunction, inducing microvascular dysfunction. And patients with basic heart failure disease showed increased ACE2 expression at both mRNA and protein levels, meaning that if infected by the virus these patients may have higher risk of heart attack and critically ill condition. The finding of this study explains the high rate of severe cases among COVID-19 patients with basic cardiovascular disease; and these results also perhaps provide important reference to clinical treatment of cardiac injury among severe patients infected by SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32227090/ doi: 10.1093/cvr/cvaa078 id: cord-350393-j80k2v21 author: Chen, Liping title: Clinical characteristics in patients with SARS‐CoV‐2/HBV co‐infection date: 2020-07-15 words: 1502.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-350393-j80k2v21.txt txt: ./txt/cord-350393-j80k2v21.txt summary: In our previous study 7 (138 cases), there were only 9 (6.1%) cases (too small) with underlying liver diseases, so no further analysis was made Accepted Article over the clinical features of COVID-19 patients with HBV infection. In this retrospective study, we expanded the sample size and aimed to evaluate the influence of SARS-CoV-2/HBV co-infection on the clinical characteristics including liver function and disease outcome. Taken into consideration that viral co-infection can exacerbate liver injury thus have a big impact on disease progression and outcome 11, 12 , we investigated the prevalence of HBV infection in COVID-19 patients and found that there was a comparable rate of SARS-CoV-2/HBV co-infection to that of general population (6.1% vs 6%). Taken together, our study is the first to elaborate on the clinical characteristics of SARS-CoV-2/HBV co-infection patients and demonstrate that the coinfection with HBV slightly affect liver function, showing no impact on the COVID-19 outcome. abstract: COVID‐19 has become a global pandemic and garnered international attention. Although the clinical features of COVID‐19 related liver injury have been investigated, there have been no reports and studies on the clinical characteristics of COVID‐19 patients co‐infected with Hepatitis B Virus (HBV). This study aimed to evaluate whether SARS‐CoV‐2/HBV co‐infection could influence liver function and the disease outcome. All 326 confirmed COVID‐19 cases in Shanghai Public Health Clinical Center (The COVID‐19 designated hospital in Shanghai, China) from January 20, 2020 to February 24, 2020 were enrolled and followed up until February 29 in this study. The clinical, laboratory data and the length of stay were collected and analyzed retrospectively. 20 patients with HBV co‐infection (6.1%) and 306 patients (93.9%) without HBV infection showed no differences in the level of liver function parameters. However, compared with HBsAg‐ patients [145.4 mg/L (103.9‐179.2)], HBsAg+ patients had a lower level of prealbumin [(102.3 mg/L (76.22‐160.2), P=.0367]. There were also no significant differences for the discharge rate and the length of stay between two groups. Taken together, we found no evidence that SARS‐CoV‐2/HBV co‐infection could aggravate liver injury or extend duration of hospitalization. url: https://www.ncbi.nlm.nih.gov/pubmed/32668494/ doi: 10.1111/jvh.13362 id: cord-268653-mje0rysp author: Chen, Miaomiao title: Changes in physiology and immune system during pregnancy and coronavirus infection: a review date: 2020-10-16 words: 2922.0 sentences: 167.0 pages: flesch: 47.0 cache: ./cache/cord-268653-mje0rysp.txt txt: ./txt/cord-268653-mje0rysp.txt summary: We explained why pregnant women are susceptible to coronavirus in terms of their adaptive changes in physiology and immune system during pregnancy, and described the associations between maternal clinical symptoms, perinatal outcomes and coronavirus infections. Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been labeled as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) on January 30, 2020 [1] [2] . Pregnant women are suspected to aspiration pneumonia because of the decreased sphincter tone in the lower esophagus, which is thought to be associated with high levels of progesterone [30] , which can reduce both pro-inflammatory and cytotoxic T cell responses. As mentioned earlier, pregnant women in their first and third trimester of pregnancy are both at the pro-inflammatory state, and the cytokine storm induced by SARS-CoV-2 in these periods may exacerbate the severity of inflammatory J o u r n a l P r e -p r o o f state, following the obstetric adverse outcomes. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the 3(rd) epidemic coronavirus after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Since December 2019, the outbreak of the Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 has aroused great attention around the world. Pregnant women and their fetuses have been concerned as a high-risk population. We explained why pregnant women are susceptible to coronavirus in terms of their adaptive changes in physiology and immune system during pregnancy, and described the associations between maternal clinical symptoms, perinatal outcomes and coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/33125977/ doi: 10.1016/j.ejogrb.2020.10.035 id: cord-350513-ho32ajsx author: Chen, Paul Chih‐Hsueh title: Re: To KF, Tong JH, Chan PK, et al. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. J Pathol 2004; 202: 157–163 date: 2004-05-07 words: 1099.0 sentences: 63.0 pages: flesch: 49.0 cache: ./cache/cord-350513-ho32ajsx.txt txt: ./txt/cord-350513-ho32ajsx.txt summary: Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. Using in situ hybridization (ISH), To et al demonstrated the presence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in pneumocytes and in the surface enterocytes of the small intestine. Supplementing their findings, we report here our recent study, which suggests that the SARS-CoV may not be exclusively located in pneumocytes, but also in pulmonary macrophages. Under low magnification, scattered cells containing dark bluish signals, which represented the SARS-CoV, were visualized ( Figure 1A , nuclear fast red counterstain) within the damaged alveolar spaces, small bronchioles, and even the vascular lumina. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Chen and Hsiao make an interesting observation on the pathology of severe acute respiratory syndrome (SARS). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15141389/ doi: 10.1002/path.1575 id: cord-320333-audnwp8t author: Chen, Qi-Lin title: Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis date: 2020-05-19 words: 5260.0 sentences: 293.0 pages: flesch: 58.0 cache: ./cache/cord-320333-audnwp8t.txt txt: ./txt/cord-320333-audnwp8t.txt summary: BACKGROUND: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. METHODS: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. The GSE121862 database is a combination of data from different experiments and institutions, and studies have suggested that single-nuclear transcriptome sequencing technology is more suitable in the kidney than other methods of gene expression analysis [25] . To compare cell receptor-related genes of SARS-CoV-2 in different tissues, high-quality single-cell transcriptome databases of the lung and small intestine were used for further analysis. For the first time from the single-cell level analysis, our results demonstrate that cell receptor-related genes of SARS-CoV-2 are differentially expressed in cell subgroups of different tissues. abstract: BACKGROUND: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. Meanwhile, the presence of B0AT1 (SLC6A19) may prevent TMPRSS2 from accessing the cutting position on ACE2. Identifying the expression of these cell receptor-related genes of SARS-CoV-2 is critical for understanding the pathogenesis of SARS-CoV-2 in various tissues, especially in the kidney. METHODS: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. RESULTS: ACE2 was significantly expressed in the S1, S2, and S3 segments of proximal tubule (PT) cells. TMPRSS2 was widely expressed in several renal tubule populations extending from the PT cells to the collection system cell type, of which intercalated cells and the distal convoluted tubule cells showed more significant expression than PT cells. Unexpectedly, although expressed on various renal tubule populations, SLC6A19 was mainly enriched in PT cells, in line with ACE2 expression. Although alveolar-type (AT) 2 cells of the lung and intestinal epithelial cells expressed ACE2 as well as PT cells, AT 2 cells significantly expressed TMPRSS2 but not SLC6A19, while all 3 genes were significantly expressed in intestinal epithelial cells. CONCLUSIONS: ACE2 was widely expressed in specific cell subgroups of various human tissues, especially in intestinal epithelial cells, kidney PT cells, and also AT 2 cells of the lung. These 3 types of cells demonstrated significant differences in the distribution of the cell receptor-related genes of SARS-CoV-2, which may indicate the diversity of cell surface structures and differences in the affinity between SARS-CoV-2 and cells. url: https://doi.org/10.1159/000508162 doi: 10.1159/000508162 id: cord-319236-gxcs77pl author: Chen, Qingyan title: Can we migrate COVID-19 spreading risk? date: 2020-08-28 words: 1478.0 sentences: 89.0 pages: flesch: 66.0 cache: ./cache/cord-319236-gxcs77pl.txt txt: ./txt/cord-319236-gxcs77pl.txt summary: However, we may have under-estimated the disease transmission by small droplets or aerosols that contain SARS-CoV-2 virus. This paper recommended wearing masks in airplanes and use partition screens in the middle of a table in a restaurant to reduce the infectioncausedbySARS-CoV-2virus. Experts so far cannot agree if SARS-CoV-2 transmission could be airborne (Lewis, 2020) , via small droplets or aerosols, although research has shown the risk. Figure 1 shows the droplet cloud that may contain SARS-CoV-2 virus with and without a screen in the middle of a table in a restaurant. The air with displacement ventilation does not mix so that the risk of inhaling airborne infectious disease virus from a neighboring student can be greatly reduced. for a long time, everyone should wear a mask to reduce infection risk although the SARS-CoV-2 virus concentration in indoor air may not be very high. Wearing mask would help as it can reduce the exposure to SARS-CoV-2 virus in air. abstract: It is well recognized that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus could be spread through touch and large droplets. However, we may have under-estimated the disease transmission by small droplets or aerosols that contain SARS-CoV-2 virus. Social distancing in public transport vehicles, such as airplanes, is not feasible. It is also not possible to wear masks in restaurant. This paper recommended wearing masks in airplanes and use partition screens in the middle of a table in a restaurant to reduce the infectioncausedbySARS-CoV-2virus. Advanced ventilation systems, such as personalized ventilation and displacement ventilation, are strongly recommended for transport vehicles and buildings. url: https://doi.org/10.1007/s11783-020-1328-8 doi: 10.1007/s11783-020-1328-8 id: cord-343143-tzuhig3f author: Chen, Rong-chang title: Treatment of Severe Acute Respiratory Syndrome With Glucosteroids The Guangzhou Experience date: 2006-06-30 words: 4649.0 sentences: 222.0 pages: flesch: 44.0 cache: ./cache/cord-343143-tzuhig3f.txt txt: ./txt/cord-343143-tzuhig3f.txt summary: Conclusion This Guangzhou retrospective study revealed that proper use of corticosteroid in confirmed critical SARS resulted in lowered mortality and shorter hospitalization stay, and was not associated with significant secondary lower respiratory infection and other complications. However, the result of a logistic regression based on the data of 152 critical SARS cases showed that steroid therapy significantly reduced the case fatality among critical SARS patients after the death-related variables were adjusted, such as age, rigor at onset, secondary lower respiratory infection, pulmonary rales, and OI grading (1, Ͻ 100; 2, Ն 100 and Ͻ 200; 3, Ն 200 and Ͻ 300; and 4, Ն 300). abstract: Study objective To investigate the efficacy and safety profiles of corticosteroid therapy in severe acute respiratory syndrome (SARS) patients. Design Four hundred one of 1,278 SARS cases treated in Guangzhou China between December 2002 and June 2003 fulfilled the diagnostic criteria issued by the World Health Organization for confirmed identification of SARS. Among them, the diagnosis of critical SARS was defined by criteria of SARS guidelines incorporated with a low oxygenation index (OI) [< 300 mm Hg]. Data of these patients retrieved from a database were retrospectively analyzed by logistic regression and Cox regression for the effect of corticosteroid therapy on death, hospitalization days, and complication presentation. Results Among the 401 SARS patients studied, 147 of 249 noncritical patients (59.0%) received corticosteroids (mean daily dose, 105.3 ± 86.1 mg) [± SD], and all survived the disease; 121 of 152 critical patients (79.6%) received corticosteroids at a mean daily dose of 133.5 ± 102.3 mg, and 25 died. Analysis of these 401 confirmed cases did not show any benefits of corticosteroid on the death rate and hospitalization days. However, when focused on 152 critical SARS cases, factors correlated with these end points indicated by univariate analysis included use of corticosteroid, age, rigor at onset, secondary respiratory infections, pulmonary rales, grading of OI, and use of invasive ventilation. After adjustment for possible confounders, treatment with corticosteroid was shown contributing to lower overall mortality, instant mortality, and shorter hospitalization stay (p < 0.05). Incidence of complications was significantly associated with the need for invasive ventilation but not with use of corticosteroids. Conclusion This Guangzhou retrospective study revealed that proper use of corticosteroid in confirmed critical SARS resulted in lowered mortality and shorter hospitalization stay, and was not associated with significant secondary lower respiratory infection and other complications. url: https://www.ncbi.nlm.nih.gov/pubmed/16778260/ doi: 10.1378/chest.129.6.1441 id: cord-257206-av2k44ig author: Chen, Ruey title: Effects of a SARS prevention programme in Taiwan on nursing staff''s anxiety, depression and sleep quality: A longitudinal survey date: 2006-02-28 words: 5064.0 sentences: 278.0 pages: flesch: 59.0 cache: ./cache/cord-257206-av2k44ig.txt txt: ./txt/cord-257206-av2k44ig.txt summary: Abstract The aim of this research is to determine the levels of anxiety, depression, and sleep quality a severe acute respiratory syndrome (SARS) nursing staff experienced before and after a SARS prevention program. Using general estimating equations (GEE) statistical analysis to control possible for affecting factors, we found that the nursing staff''s anxiety and depression along with sleep quality started to improve 2 weeks after the initiation of SARS prevention controls. This research is to describe the anxiety level, depression level, and sleep quality of nursing staff who cared for SARS patients during a sweeping epidemic and the effects of a SARS prevention program. Tables 2 and 3 show the effects of the SARS prevention program on nursing staff through their self-reported levels of anxiety and depression as well as sleep quality. abstract: Abstract The aim of this research is to determine the levels of anxiety, depression, and sleep quality a severe acute respiratory syndrome (SARS) nursing staff experienced before and after a SARS prevention program. The 116 subjects were recruited from nursing staff in the largest obligatory SARS designated treatment hospital in Taiwan. Using general estimating equations (GEE) statistical analysis to control possible for affecting factors, we found that the nursing staff's anxiety and depression along with sleep quality started to improve 2 weeks after the initiation of SARS prevention controls. From this research, we determined that nursing staff members were anxious, depressed, and they could not sleep well at the SARS outbreak. However, the systematic SARS prevention program improved these factors. When faced with these types of diseases, related international medical organizations should establish a comprehensive program to help medical professionals cope better. url: https://www.sciencedirect.com/science/article/pii/S0020748905000684 doi: 10.1016/j.ijnurstu.2005.03.006 id: cord-314321-klb8oe9q author: Chen, Serena H. title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date: 2020-04-18 words: 3168.0 sentences: 174.0 pages: flesch: 52.0 cache: ./cache/cord-314321-klb8oe9q.txt txt: ./txt/cord-314321-klb8oe9q.txt summary: Recent experimental structures of the SARS-CoV-2 S protein receptor binding domain (RBD) in complex with ACE2 provide detailed interface information [4] , [6] ; targeting this interface represents an active area of research for therapeutic development [11] . By first comparing the S protein protomer structure of SARS-CoV-2 to those from previous human coronaviruses, we identified distinct clusters for each virus in the 3-D latent space, where representative structures from these clusters highlight their differences in domain flexibility. To further understand the molecular structures of different human coronavirus S proteins and the oligomeric state of SARS-CoV-2 S protein, we deployed a custom-built deep learning architecture, a convolutional variational autoencoder (CVAE), to encode the high dimensional protein structures from the MD simulations into lower dimensional latent spaces. The size of each resulting matrix was also 191 ⇥ 191, and we merged a total of 10,000 distance matrices of the protomer and trimer of SARS-CoV-2 S protein. abstract: The emergence and rapid worldwide spread of the novel coronavirus disease, COVID-19, has prompted concerted efforts to find successful treatments. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its spike (S) protein to gain entry into host cells. Therefore, the S protein presents a viable target to develop a directed therapy. Here, we deployed an integrated artificial intelligence with molecular dynamics simulation approach to provide new details of the S protein structure. Based on a comprehensive structural analysis of S proteins from SARS-CoV-2 and previous human coronaviruses, we found that the protomer state of S proteins is structurally flexible. Without the presence of a stabilizing beta sheet from another protomer chain, two regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures. Interestingly, the region in the S2 domain was previously identified as an immunodominant site in the SARS-CoV-1 S protein. We anticipate that the molecular details elucidated here will assist in effective therapeutic development for COVID-19. url: https://doi.org/10.1101/2020.04.17.047548 doi: 10.1101/2020.04.17.047548 id: cord-300041-1d9xu4ts author: Chen, Sharon C-A title: Focus on SARS-CoV-2 and COVID-19 date: 2020-10-08 words: 1024.0 sentences: 60.0 pages: flesch: 52.0 cache: ./cache/cord-300041-1d9xu4ts.txt txt: ./txt/cord-300041-1d9xu4ts.txt summary: In contrast, more recent pandemics have been dominated by viruses such as influenza H1N1 and H3N2, localised epidemics by Ebola virus, severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1), MERS-CoV, and now, SARS-CoV-2, the causative agent of COVID-19. However, by having a single edition, with broad focus on human pathology of SARS-CoV-2 infection, we aim to provide the readers of Pathology with insights from different areas of COVID-19 diagnosis. 2 Substantive progress continues to be made in the arena of diagnostic tests for SARS-CoV-2 infection with improvements in molecular diagnostics, rapid antigen detection tests and serological assays. We continue to be faced by the risk of pandemics and we must learn from our observations at present with SARS-CoV-2 infection, and resulting COVID-19 disease. Virus isolation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnostic and research purposes Rapid deployment of pathology services to a remote Australian quarantine setting during the COVID-19 pandemic abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33121820/ doi: 10.1016/j.pathol.2020.09.010 id: cord-349031-tbof9yqi author: Chen, Shiu-Jau title: Novel Antiviral Strategies in the Treatment of COVID-19: A Review date: 2020-08-20 words: 5464.0 sentences: 303.0 pages: flesch: 43.0 cache: ./cache/cord-349031-tbof9yqi.txt txt: ./txt/cord-349031-tbof9yqi.txt summary: Fortunately, some novel antiviral strategies, such as convalescent plasma, clustered regularly interspaced short palindromic repeats (CRISPR), and mesenchymal stem cell (MSC) therapy, potentially offer an additional or alternative option or compassionate use for the people suffering from COVID-19, especially for critically ill patients, although their safety and efficacy are also under study. In this review, we explore the applications, possible mechanisms, and efficacy in successful cases using convalescent plasma, CRISPR, and MSC therapy for COVID-19 treatment, respectively. In this case series study of five critically ill patients with COVID-19 and ARDS, the administration of convalescent plasma containing neutralizing antibodies significantly improved their clinical status [53] . Under the condition that traditional drugs cannot assure their safety and efficacy for COVID-19 treatment, novel antiviral strategies, including convalescent plasma, CRISPR, and cell therapy, may be able to provide an additional or alternative option or compassionate use for the treatment of COVID-19, particular for critically ill patients. abstract: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS–CoV-2), is still a global public health problem for humans. It has caused more than 10,000,000 infections and more than 500,000 deaths in the world so far. Many scientists have tried their best to discover safe and effective drugs for the treatment of this disease; however, there are still no approved standard therapeutics or effective antiviral drugs on the market. Many new drugs are being developed, and several traditional drugs that were originally indicated or proposed for other diseases are likely to be effective in treating COVID-19, but their safety and efficacy are controversial, under study, or in clinical trial phases. Fortunately, some novel antiviral strategies, such as convalescent plasma, clustered regularly interspaced short palindromic repeats (CRISPR), and mesenchymal stem cell (MSC) therapy, potentially offer an additional or alternative option or compassionate use for the people suffering from COVID-19, especially for critically ill patients, although their safety and efficacy are also under study. In this review, we explore the applications, possible mechanisms, and efficacy in successful cases using convalescent plasma, CRISPR, and MSC therapy for COVID-19 treatment, respectively. Furthermore, the perspectives and limitations of these novel antiviral strategies are evaluated. url: https://doi.org/10.3390/microorganisms8091259 doi: 10.3390/microorganisms8091259 id: cord-271259-6kkzh1tp author: Chen, Shuai title: Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode date: 2010-01-01 words: 7826.0 sentences: 352.0 pages: flesch: 56.0 cache: ./cache/cord-271259-6kkzh1tp.txt txt: ./txt/cord-271259-6kkzh1tp.txt summary: Therefore, the N-terminal auto-processing of M(pro) appears to require only two "immature" monomers approaching one another to form an "intermediate" dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. These results indicate that N-terminal autocleavage of SARS-CoV M pro from the polyproteins only requires two "immature" proteases approaching one another to form an "intermediate" dimer structure and does not depend on the active dimer conformation existing in the mature protease. Since mutation of either of these two residues were reported to completely abolish the dimer of mature M pro , our finding raises the intriguing question of how the E290R and R298E mutants can auto-process their N-terminal GST tags when they are unable to form the active dimer structure. abstract: The main protease (M(pro)) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for transcleavage activity. However, the auto-processing mechanism of M(pro), i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” M(pro). Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature M(pro), are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and transcleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of M(pro) appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of M(pro) from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV M(pro). url: https://link.springer.com/content/pdf/10.1007/s13238-010-0011-4.pdf doi: 10.1007/s13238-010-0011-4 id: cord-343192-fkc7af9y author: Chen, Siyang title: Comment on “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ‐2 (SARS‐CoV‐2)” date: 2020-05-08 words: 1197.0 sentences: 69.0 pages: flesch: 45.0 cache: ./cache/cord-343192-fkc7af9y.txt txt: ./txt/cord-343192-fkc7af9y.txt summary: We read the article "Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)" with great interest. Although there have been several reports previously suggesting that the similar SARS-CoV-2 virus could infect neuronal cells and cause central and peripheral neurological morbidities in COVID-19 patients (3) (4) (5) , few direct detection of virus by RT-PCR in cerebrospinal fluid (CSF) has casted earlier doubt whether there is indeed a direct infection of central nervous system (CNS). It is not clear whether SARS-CoV-2 viruses can be similarly detected in endothelial cells from other severe COVID-19 patients with central neurological involvement (3). It is worthy to point out that one very recent report from a Chinese case demonstrating the presence of SARS-CoV-2 virus sequence in the CSF fluid of a COVID-19 patient presenting viral encephalitis (7) . Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) abstract: A very interesting report, for the first time, provided direct evidence that the ongoing pandemic etiological agent, SARS‐CoV‐2, may be able to directly infect central nervous system (CNS) through an endothelial route. If proven true, this may explain frequent neurological symptoms associated with severe COVID‐19 diseases. A corresponding therapeutic intervention will be urgently needed to prevent such dangerous infections of CNS and associated high mortality rate. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32383264/ doi: 10.1002/jmv.25991 id: cord-300697-p96i25uc author: Chen, Taojiang title: A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report date: 2020-09-29 words: 2182.0 sentences: 128.0 pages: flesch: 43.0 cache: ./cache/cord-300697-p96i25uc.txt txt: ./txt/cord-300697-p96i25uc.txt summary: title: A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report CASE PRESENTATION: We herein described a case of severe SARS-CoV-2 infected patient with several risk factors for poor prognosis, including male, hypertension, old age, mixed bacterial infection and multilobular infiltration on radiological imaging. After improvement of respiratory status, the onset of gastrointestinal bleeding occurred, probably resulting from direct viral invasion as evidenced by the positive findings for SARS-CoV-2 in the repeat stool specimens. Additionally, despite the clinical manifestations of coronavirus disease 2019 (COVID-19) are dominated by respiratory symptoms, evidences from recent studies have suggested that SARS-CoV-2 has the ability to actively infect and replicate in the gastrointestinal tract [3] . Herein, we described an old-aged COVID-19 patient with multiple risk factors for severe disease and ultimately died from massive GIB at Wuhan Union Hospital. abstract: BACKGROUND: SARS-CoV-2 is highly infectious and has been a significant public health threat. Despite typical manifestations of illness are dominated by respiratory symptom, some patients have concurrent gastrointestinal manifestations, including nausea, diarrhea, and vomiting. Massive gastrointestinal bleeding, however, has rarely been reported. CASE PRESENTATION: We herein described a case of severe SARS-CoV-2 infected patient with several risk factors for poor prognosis, including male, hypertension, old age, mixed bacterial infection and multilobular infiltration on radiological imaging. After improvement of respiratory status, the onset of gastrointestinal bleeding occurred, probably resulting from direct viral invasion as evidenced by the positive findings for SARS-CoV-2 in the repeat stool specimens. Although aggressive resuscitation was administered, hematochezia was uncontrolled. The patient rapidly deteriorated, suffered from cardiac arrest, and expired. CONCLUSIONS: Digestive symptoms could be severe in SARS-CoV-2 infected patients, especially for the high-risk individuals with predisposing conditions. A more thorough protocol for preventing cross-infection through faecal-oral transmission should be implemented in the process of patient care and infection control. url: https://www.ncbi.nlm.nih.gov/pubmed/32993509/ doi: 10.1186/s12876-020-01458-x id: cord-351770-cirq6pfx author: Chen, Wei title: SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia date: 2020-08-13 words: 3771.0 sentences: 226.0 pages: flesch: 54.0 cache: ./cache/cord-351770-cirq6pfx.txt txt: ./txt/cord-351770-cirq6pfx.txt summary: In this study, we analyzed the SARS-CoV-2 NAb titers in patients recently recovered from COVID-19 using a novel SARS-CoV-2 surrogate virus neutralization test (sVNT) [12] . The distribution of NAb titers in patients with COVID-19 were then plotted based on the variables of age, sex, symptom, laboratory parameters and chest CT findings at the time of admission, treatment during hospitalization and the time of blood collection for antibody analysis (Figure 1 ). Independent variables included in the OLS model included age, sex, CT score, comorbidity, laboratory parameters that associated with disease severity (CRP level and lymphocyte counts), treatment that may influence immune response to pathogen (corticosteroids and intravenous immunoglobulin) and time of blood collection for NAb analysis. In multivariate analyses, after adjustment for age, sex, comorbidity, corticosteroid treatment, CRP level, lymphocyte count and time of NAb analysis, baseline chest CT scores still strongly correlated with NAb titers in patients recovered from COVID-19 (Table 2 , p=0.02). abstract: Abstract The emerging coronavirus disease 2019 (COVID-19) has become a serious global public health threat. With more and more recovered patients, it is urgently needed for evaluation of the neutralizing antibody (NAb) in these patients. In this study, we collected blood samples from 49 patients recently recovered from COVID-19. Serum NAbs were measured using a novel surrogate virus neutralization test (sVNT). Factors associated with NAb titers were analyzed using Ordinary Least Squares regression model. The median age of the study participants was 37 years (IQR, 30.0-54.5) and 55.1% (27/49) of which were male. The median time to blood collection (for NAb analysis) from illness onset, viral clearance and discharge were 43.0 days (IQR, 36.0-50.0), 27.0 days (IQR, 20.5-37) and 17.0 days (IQR, 15.0-33.0), respectively. Patients had a median NAb titer of 1: 40 (IQR, 1:15-1:120). NAbs were not detected in two asymptomatic children who quickly cleared the virus. NAb titers were higher in patients with older age (p = 0.020), symptomatic infection (p = 0.044), more profound lung involvement (p＜0.001), abnormal C-reactive protein level (p＜0.01) and elevated lactate dehydrogenase (p = 0.019). Multivariable analysis revealed that severity of pneumonia and having comorbidity positively correlated with NAb titers in recovered patients (p = 0.02), while use of corticosteroids negatively impacted NAb titers (p = 0.01). Our study suggests that some COVID-19 patients may not have detectable NAb after recovery. SARS-CoV-2 NAb titers are positively correlated with severity of COVID-19 pneumonia. url: https://www.sciencedirect.com/science/article/pii/S0753332220308222?v=s5 doi: 10.1016/j.biopha.2020.110629 id: cord-350737-nrtrhq1f author: Chen, Xinchun title: Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date: 2004-04-01 words: 3474.0 sentences: 133.0 pages: flesch: 50.0 cache: ./cache/cord-350737-nrtrhq1f.txt txt: ./txt/cord-350737-nrtrhq1f.txt summary: A virus from the family Coronaviridae, termed "SARS coronavirus" (SARS CoV), has been identified as the cause [2] [3] [4] [5] [6] [7] , and criteria for laboratory confirmation of SARS CoV infection have been provided by WHO, on the basis of the following methods: (1) detection of SARS CoV RNA by reversetranscription polymerase chain reaction (RT-PCR); (2) serological detection of SARS CoV-related antibody; and (3) isolation of SARS CoV by cell culture [4] . Using an indirect immunofluorescence assay and parallel acute and convalescent serum samples obtained from patients with SARS, tested for IgG antibody to SARS CoV, Peiris et al. In addition, our results indicated that 9 (25.0%) of 36 patients with probable SARS CoV infection had not produced detectable anti-SARS CoV antibody by day 21 after the onset of fever; this implies that 25.0% of patients with SARS might be misdiagnosed by the laboratory confirmation guidelines that WHO currently recommends [5] . abstract: Background. Severe acute respiratory syndrome (SARS) is a novel infectious disease. No information is currently available on host-specific immunity against the SARS coronavirus (CoV), and detailed characteristics of the epidemiology of SARS CoV infection have not been identified. Methods. ELISA was used to detect antibody to SARS CoV. Reverse-transcriptase polymerase chain reaction was used to detect SARS CoV RNA. T cells in peripheral blood of patients were quantified by flow cytometry. Results. Of 36 patients with probable SARS CoV infection, 30 (83.3%) were positive for IgG antibody to SARS CoV; in contrast, only 3 of 48 patients with suspected SARS CoV infection, 0 of 112 patients with fever but without SARS, and 0 of 96 healthy control individuals were positive for it. IgG antibody to SARS CoV was first detected between day 5 and day 47 after onset of illness (mean ± SD, 18.7±10.4). Conclusion. Detection of antibody to SARS CoV is useful in the diagnosis of SARS; however, at the incubation and initial phases of the illness, serological assay is of little value, because of late seroconversion in most patients. url: https://www.ncbi.nlm.nih.gov/pubmed/15031782/ doi: 10.1086/380397 id: cord-017942-og0b2l6b author: Chen, Yi-Da title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data date: 2007 words: 3673.0 sentences: 201.0 pages: flesch: 48.0 cache: ./cache/cord-017942-og0b2l6b.txt txt: ./txt/cord-017942-og0b2l6b.txt summary: title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data In this research, we use Taiwan SARS data to investigate the differences in connectivity between personal and geographical contacts in the construction of social networks for these diseases. In 1985, Klovdahl [6] used AIDS as an example to illustrate the usefulness of Social Network Analysis (SNA) in studying the transmission of an infectious disease. However, from these two studies, we can see that incorporating geographical contacts into SNA provides us a good way to find potential connections among patients and to see the role that those geographical locations play in disease outbreaks. The studies of SNA in epidemiology primarily use personal contacts to construct social networks and model the transmission of diseases. In this research, by using Taiwan SARS data as the test dataset, we further investigate the differences in connectivity between personal and geographical contacts in the network construction for these diseases. abstract: In epidemiology, contact tracing is a process to control the spread of an infectious disease and identify individuals who were previously exposed to patients with the disease. After the emergence of AIDS, Social Network Analysis (SNA) was demonstrated to be a good supplementary tool for contact tracing. Traditionally, social networks for disease investigations are constructed only with personal contacts. However, for diseases which transmit not only through personal contacts, incorporating geographical contacts into SNA has been demonstrated to reveal potential contacts among patients. In this research, we use Taiwan SARS data to investigate the differences in connectivity between personal and geographical contacts in the construction of social networks for these diseases. According to our results, geographical contacts, which increase the average degree of nodes from 0 to 108.62 and decrease the number of components from 961 to 82, provide much higher connectivity than personal contacts. Therefore, including geographical contacts is important to understand the underlying context of the transmission of these diseases. We further explore the differences in network topology between one-mode networks with only patients and multi-mode networks with patients and geographical locations for disease investigation. We find that including geographical locations as nodes in a social network provides a good way to see the role that those locations play in the disease transmission and reveal potential bridges among those geographical locations and households. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122638/ doi: 10.1007/978-3-540-72608-1_3 id: cord-340205-cwn0gx7h author: Chen, Yih-Ting title: Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis date: 2020-07-16 words: 950.0 sentences: 57.0 pages: flesch: 43.0 cache: ./cache/cord-340205-cwn0gx7h.txt txt: ./txt/cord-340205-cwn0gx7h.txt summary: title: Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis There was no evidence of statistical heterogeneity among studies reporting AKI mortality in SARS (I2: 0.0%, p = 0.589) and MERS (I2: 0.0%, p =v0.758), but there was for COVID-19 infection (I2: 97.0%, p < 0.001) (Fig. 1 ). Possible mechanisms of higher AKI mortality following coronavirus infections are multifactorial (e.g., severe sepsis-related multiorgan failure, direct kidney involvement, and acute respiratory distress syndrome) [26] [27] [28] , although comparative pathogenesis of kidney involvement among the three infections remains unclear. A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: nan url: https://doi.org/10.1186/s13054-020-03134-8 doi: 10.1186/s13054-020-03134-8 id: cord-350015-mg5wiihj author: Chen, Yiyin title: Aging in COVID-19: Vulnerability, immunity and intervention date: 2020-10-31 words: 7489.0 sentences: 407.0 pages: flesch: 47.0 cache: ./cache/cord-350015-mg5wiihj.txt txt: ./txt/cord-350015-mg5wiihj.txt summary: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic was first reported in Wuhan, China in December 2019, moved across the globe at an unprecedented speed, and has caused a profound and yet still unfolding health and socioeconomic impacts. We hypothesize that age-related decline and dysregulation of immune function, i.e., immunosenescence and inflammaging play a major role in contributing to heightened vulnerability to severe COVID-19 outcomes in older adults. Therefore, age-associated reduction in type 1 IFN response coupled with direct viral suppression could serve as a critical innate immune mechanism that leads to poor cell mediated immunity and increased vulnerability of older adults against SARS-CoV-2 infection with therapeutic implication (Sallard et al., 2020) . On the other hand, children with COVID-19 manifested lower levels of T cell activation than adult COVID-19 patients (Moratto et al., 2020) , suggesting better immune system control and regulation in response to SARS-CoV-2 infection in children. abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic was first reported in Wuhan, China in December 2019, moved across the globe at an unprecedented speed, and has caused a profound and yet still unfolding health and socioeconomic impacts. SARS-CoV-2, a β-coronavirus, is a highly contagious respiratory pathogen that causes a disease that has been termed the 2019 coronavirus disease (COVID-19). Clinical experience thus far indicates that COVID-19 is highly heterogeneous, ranging from being asymptomatic and mild to severe and causing death. Host factors including age, sex, and comorbid conditions are key determinants of disease severity and progression. Aging itself is a prominent risk factor for severe disease and death from COVID-19. We hypothesize that age-related decline and dysregulation of immune function, i.e., immunosenescence and inflammaging play a major role in contributing to heightened vulnerability to severe COVID-19 outcomes in older adults. Much remains to be learned about the immune responses to SARS-CoV-2 infection. We need to begin partitioning all immunological outcome data by age to better understand disease heterogeneity and aging. Such knowledge is critical not only for understanding of COVID-19 pathogenesis but also for COVID-19 vaccine development. url: https://doi.org/10.1016/j.arr.2020.101205 doi: 10.1016/j.arr.2020.101205 id: cord-277342-40d24mvm author: Chen, Yu title: SARS-CoV-2: virus dynamics and host response date: 2020-03-23 words: 804.0 sentences: 57.0 pages: flesch: 53.0 cache: ./cache/cord-277342-40d24mvm.txt txt: ./txt/cord-277342-40d24mvm.txt summary: In The Lancet Infectious Diseases, Kelvin To and colleagues 4 report the viral load and antibody profiles of a cohort of 23 patients admitted to hospital with COVID-19. First, the high viral load during the early phase of illness suggests that patients could be most infectious during this period, and it might account for the high transmissibility of SARS-CoV-2. Second, age was associated with viral load in this study, which could explain the high degree of severe disease in older patients with SARS-CoV-2. 5, 6 The high viral load in elderly patients is associated not only with low immunity but also with high expression of the ACE2 receptor (the cellentry receptor for SARS-CoV-2) in older adults. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore abstract: nan url: https://api.elsevier.com/content/article/pii/S1473309920302358 doi: 10.1016/s1473-3099(20)30235-8 id: cord-311762-f6muhf3d author: Chen, Yu Wai title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates date: 2020-02-21 words: 2798.0 sentences: 183.0 pages: flesch: 60.0 cache: ./cache/cord-311762-f6muhf3d.txt txt: ./txt/cord-311762-f6muhf3d.txt summary: title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates Therefore, we are confident to prepare a structural model of the SARS-CoV-2 3CL pro by molecular modelling (Extended data 7 , Figure S1 ), which will be immediately useful for in silico development of targeted treatment. After we submitted the first draft of this study, the crystal structure of SARS-CoV-2 3CL pro was solved and released (PDB ID 6LU7), which confirms that the predicted model is good within experimental errors (Extended data 7 , Figure S2 ). By analogy, these compounds were speculated to act on SARS-CoV 3CL pro specifically, but there is as yet no crystal structure to support that, although docking studies were carried out to propose various binding modes 20-23 . • Tab S2.docx (The results of virtual screening of drugs on the active site of SARS-CoV-2 3CL pro crystal structure). abstract: We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL (pro)) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL (pro) molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes. url: https://doi.org/10.12688/f1000research.22457.1 doi: 10.12688/f1000research.22457.1 id: cord-252919-647zcjgu author: Chen, Yun title: Structure analysis of the receptor binding of 2019-nCoV date: 2020-02-17 words: 3436.0 sentences: 185.0 pages: flesch: 57.0 cache: ./cache/cord-252919-647zcjgu.txt txt: ./txt/cord-252919-647zcjgu.txt summary: We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. In this study, we analyzed the structure of spike glycoprotein RBD of 2019-nCoV and identified a unique feature that potentially allows a high affinity binding to ACE2 in human cells. There are 16 amino acid residues in SARS-CoV RBD that are directly in contact with ACE2, of which 8 are conserved in 2019-nCoV (see Fig. 1B ). Among the 16 amino acid residues in RBD of SARS that are in contact with ACE2, 14, 14, 7, and 8 are shared by SARSv, civet, bat, and 2019-nCoV, respectively (Fig. 1B) . Our study suggests unique structural features of the spike glycoprotein RBD of 2019-nCoV that confers potentially higher affinity binding for its receptor than found with SARS-CoV. abstract: Abstract 2019-nCoV is a newly identified coronavirus with high similarity to SARS-CoV. We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. The RBDs from the two viruses share 72% identity in amino acid sequences, and molecular simulation reveals highly similar ternary structures. However, 2019-nCoV has a distinct loop with flexible glycyl residues replacing rigid prolyl residues in SARS-CoV. Molecular modeling revealed that 2019-nCoV RBD has a stronger interaction with angiotensin converting enzyme 2 (ACE2). A unique phenylalanine F486 in the flexible loop likely plays a major role because its penetration into a deep hydrophobic pocket in ACE2. ACE2 is widely expressed with conserved primary structures throughout the animal kingdom from fish, amphibians, reptiles, birds, to mammals. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. 2019-nCoV is thought to be transmitted through respiratory droplets. However, since ACE2 is predominantly expressed in intestines, testis, and kidney, fecal-oral and other routes of transmission are also possible. Finally, antibodies and small molecular inhibitors that can block the interaction of ACE2 with RBD should be developed to combat the virus. url: https://doi.org/10.1016/j.bbrc.2020.02.071 doi: 10.1016/j.bbrc.2020.02.071 id: cord-297702-vxcj25sn author: Chen, Yuxin title: A comprehensive, longitudinal analysis of humoral responses specific to four recombinant antigens of SARS-CoV-2 in severe and non-severe COVID-19 patients date: 2020-09-10 words: 5253.0 sentences: 250.0 pages: flesch: 46.0 cache: ./cache/cord-297702-vxcj25sn.txt txt: ./txt/cord-297702-vxcj25sn.txt summary: We continuously monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the nucleoprotein (NP), receptor binding domain (RBD), S1 protein, and ectodomain (ECD) of the spike protein among non-severe and severe COVID-19 patients for seven weeks since disease onset. In this retrospective study, we successively monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the NP protein, RBD protein, S1 protein, and ECD protein in 19 non-severe and 7 severe COVID-19 patients during the disease progression. The severe patients and non-severe patients had comparable reduced fold of IgM, IgG, and IgA binding titer specific to RBD, ECD, S1, and NP protein and neutralization activities. Furthermore, 80.7% of the convalescent sea from COVID-19 patients displayed varying levels of neutralization activities against SARS-CoV-2, which correlated with S1-specific and ECD-specific IgA responses in non-severe patients. abstract: There is an urgent need for effective treatment and preventive vaccine to contain this devastating global pandemic, which requires a comprehensive understanding of humoral responses specific to SARS-CoV-2 during the disease progression and convalescent phase of COVID-19 patients. We continuously monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the nucleoprotein (NP), receptor binding domain (RBD), S1 protein, and ectodomain (ECD) of the spike protein among non-severe and severe COVID-19 patients for seven weeks since disease onset. Most patients generated humoral responses against NP and spike protein-related antigens but with their distinct kinetics profiles. Combined detection of NP and ECD antigens as detecting antigen synergistically improved the sensitivity of the serological assay, compared to that of using NP or RBD as detection antigen. 80.7% of convalescent sera from COVID-19 patients revealed that the varying extents of neutralization activities against SARS-CoV-2. S1-specific and ECD-specific IgA responses were strongly correlated with the neutralization activities in non-severe patients, but not in severe patients. Moreover, the neutralizing activities of the convalescent sera were shown to significantly decline during the period between 21 days to 28 days after hospital discharge, accompanied by a substantial drop in RBD-specific IgA response. Our data provide evidence that are crucial for serological testing, antibody-based intervention, and vaccine design of COVID-19. url: https://doi.org/10.1371/journal.ppat.1008796 doi: 10.1371/journal.ppat.1008796 id: cord-298639-v9yg80jw author: Chen, Yuxin title: High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients date: 2020-06-04 words: 3369.0 sentences: 178.0 pages: flesch: 51.0 cache: ./cache/cord-298639-v9yg80jw.txt txt: ./txt/cord-298639-v9yg80jw.txt summary: Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. Briefly, 96-well plates were coated with 500 ng/mL of recombinant RBD or NP protein overnight, incubating with diluted were also collected and the nasopharyngeal swab samples from these patients have been repeatedly tested as negative for SARS-CoV-2 RNA at least twice at a two-day apart. Our study proved that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. abstract: The seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was examined among 105 healthcare workers (HCWs) exposed to four patients who were laboratory confirmed with coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2 infection. These HCWs were immediately under quarantine for 14 days as soon as they were identified as close contacts. The nasopharyngeal swab samples were collected on the first and 14(th) day of the quarantine, while the serum samples were obtained on the 14(th) day of the quarantine. With the assay of enzyme immunoassay (EIA) and microneutralization assay, 17.14% (18/105) of HCWs were seropositive, while their swab samples were found to be SARS-CoV-2 RNA negative. Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32504745/ doi: 10.1016/j.jinf.2020.05.067 id: cord-306332-ug6pare2 author: Chen, Ze-Liang title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends date: 2020-05-05 words: 2008.0 sentences: 123.0 pages: flesch: 53.0 cache: ./cache/cord-306332-ug6pare2.txt txt: ./txt/cord-306332-ug6pare2.txt summary: title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends [1, 2] The 2019 novel coronavirus (2019-nCoV) caused a pneumonia outbreak, which is spreading around the country and has affected 32 provinces and regions of China as of January 27, 2020. [14, 15] Subsequent case investigations also showed that SARS-CoV had the capability to multiply and continuously undergo human-to-human transmission [Supplementary Figure 2C , http://links.lww.com/CM9/ A209]; at least four generations of cases were identified from one original patient. [18] On January 19, 2020, a cluster of cases, including 15 healthcare workers, were confirmed to have been infected via patients, confirming that 2019-nCoV also has humanto-human transmission capability. Transmission and epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected pneumonia (COVID-19): preliminary evidence obtained in comparison with 2003-SARS abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32118641/ doi: 10.1097/cm9.0000000000000776 id: cord-343502-1n0o4akm author: Chen, Zhang-Ren title: Pharmacotherapics Advice in Guidelines for COVID-19 date: 2020-06-24 words: 4051.0 sentences: 216.0 pages: flesch: 48.0 cache: ./cache/cord-343502-1n0o4akm.txt txt: ./txt/cord-343502-1n0o4akm.txt summary: SARS-CoV-2 (previously termed 2019 novel coronavirus, 2019-nCoV), a virus that causes COVID-19, likely initially transmitted from bat to human (Gorbalenya et al., 2020) , infected over 6 million people worldwide from its outbreak in December 2019 to May 2020 (China CDC, 2020; WHO, 2020a) . China, Italy, Germany, the ATS (American Thoracic Society), the SSC (Surviving Sepsis Campaign), the NIH (National Institutes of Health), the IDSA (Infectious Diseases Society of America), and the FDA (Food and Drug Administration) released guidelines and recommended several medicines for the treatment of COVID-19 (Table 1) . The majority of anti-SARS-CoV-2 virus drugs are adopted from the treatment of severe acute respiratory syndrome (SARS) or Middle East respiratory syndrome (MERS): alpha-interferon, lopinavir/ritonavir, and ribavirin. The guideline from Italy recommended remdesivir (Italian Society of Infectious and Tropical Diseases SECTION, 2020), and the FDA approved emergency use authorization (EUA) of remdesivir for the treatment of COVID-19 (FDA, 2020). abstract: Since December 2019 to May 2020, coronavirus disease 2019 (COVID-19) has infected over 6 million people worldwide. Due to its sudden and rapid outbreak, effective treatment for COVID-19 is scarce. Based on national clinical trials of novel treatments, China, Italy, Germany, and other countries and organizations have published multiple guidelines for COVID-19 and advised many medicines, such as chloroquine and tocilizumab. In this paper, we summarize the pharmacotherapy for COVID-19 according to those guidelines, highlight updates of the pharmacotherapy guidelines, and review the efficacy and safety of the indicated anti-COVID-19 drugs. url: https://doi.org/10.3389/fphar.2020.00950 doi: 10.3389/fphar.2020.00950 id: cord-026528-1ozgabwk author: Chen, Zhe title: Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination date: 2020-06-09 words: 225.0 sentences: 26.0 pages: flesch: 70.0 cache: ./cache/cord-026528-1ozgabwk.txt txt: ./txt/cord-026528-1ozgabwk.txt summary: key: cord-026528-1ozgabwk title: Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination cord_uid: 1ozgabwk We appreciate that Dr. Carosso brought up several important points about our paper, 16 which are worth discussing and clarifying. 17 We stated that we did not find SARS-CoV-2 in lower female genital tract and our 18 results may provide evidence to guide the choice of delivery method for COVID-19 19 pregnant women. However, a high incidence of cesarean sections was mentioned 22 by Dr. Carosso. It might result from concerns that SARS-CoV-2 exists in vagina. It 23 was a reasonable suspicion since SARS-CoV-2 had been identified in anal swabs, 24 urine, and tears in an early time. Review of the 2019 novel coronavirus 53 (SARS-CoV-2) based on current evidence Severe 58 COVID-19 during Pregnancy and Possible Vertical Transmission Severe Acute Respiratory Syndrome Coronavirus 2 63 (SARS-CoV-2) Vertical Transmission in Neonates Born to Mothers With 64 abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282764/ doi: 10.1016/j.ajog.2020.06.013 id: cord-282990-qb4wk4yb author: Chen, Zhuo title: Safety considerations in the bioanalytical laboratories handling specimens from coronavirus disease 2019 patients date: 2020-08-21 words: 1971.0 sentences: 113.0 pages: flesch: 48.0 cache: ./cache/cord-282990-qb4wk4yb.txt txt: ./txt/cord-282990-qb4wk4yb.txt summary: Since blood specimen is one of the most commonly analyzed sample types, viral load of SARS-CoV-2 in blood is a key issue for laboratory biosafety. Besides the above three studies, other recently published papers also demonstrated that the detection rates of SARS-CoV-2 RNA in blood from COVID-19 patients were generally low as: five of 48 (10%) [1] , two of 9 (22%) [2] and six of 41 (15%) [3] . Despite the relatively low SARS-CoV-2 viral load detected in the blood and urine of COVID-19 patients, scientists have yet to draw conclusions about the infectivity of these specimens. The Centers for Disease Control and Prevention (CDC) has issued the interim laboratory biosafety guidelines for handling COVID-19 specimens, which recommends virus inactivation prior to sample processing to reduce the risk of infection [10] . Nevertheless, only the protocol of heating at 92 • C for 15 min completely inactivated SARS-CoV-2 in respiratory specimens with much higher viral load. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32820941/ doi: 10.4155/bio-2020-0185 id: cord-314381-ltil9hwl author: Cheng, Cecilia title: The psychology behind the masks: Psychological responses to the severe acute respiratory syndrome outbreak in different regions date: 2004-03-11 words: 2253.0 sentences: 112.0 pages: flesch: 50.0 cache: ./cache/cord-314381-ltil9hwl.txt txt: ./txt/cord-314381-ltil9hwl.txt summary: The present paper proposes the influence of psychological factors on people''s cognitive, affective, and behavioral responses during the SARS outbreak. Because SARS affected a number of regions, including people from both Asian and Western cultures, did individuals from different cultures perceive and cope with the crisis in distinct manners? These results suggest a link between general coping strategies and specific health behavior to avoid contracting SARS, which applies to people in areas that were and were not affected by SARS. This commentary, together with the five articles, provides valuable information on the ways in which people from different regions of the world responded affectively, cognitively, and behaviorally to the SARS outbreak. In conclusion, this special issue highlights the role of psychological factors in people''s cognitive and behavioral responses to the SARS outbreak. abstract: Severe acute respiratory syndrome (SARS) was first reported in China, and spread to 29 regions, affecting over 8000 people worldwide. For the general public, the psychological impact of SARS may have been greater than the physical health danger of the disease. The present paper proposes the influence of psychological factors on people's cognitive, affective, and behavioral responses during the SARS outbreak. The various papers in this special issue of the Journal reveal how people have reacted during the SARS outbreak: People's general coping styles may be related to their health behavior during the outbreak. Cultural differences were evident in the perception of SARS, and individuals’ perceptual styles may have influenced their ability to cope with the outbreak. The way in which individuals coped with SARS‐related stressful events was different from their usual practices of managing daily stress. Individual differences in the adoption of preventive measures were related to the distinct susceptibility to several social‐cognitive biases. url: https://doi.org/10.1111/j.1467-839x.2004.00130.x doi: 10.1111/j.1467-839x.2004.00130.x id: cord-277796-9ddi0mm9 author: Cheng, Hao title: Organ‐protective effect of angiotensin‐converting enzyme 2 and its effect on the prognosis of COVID‐19 date: 2020-04-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This article reviews the correlation between angiotensin‐converting enzyme 2 (ACE2) and severe risk factors for coronavirus disease 2019 (COVID‐19) and the possible mechanisms. ACE2 is a crucial component of the renin‐angiotensin system (RAS). The classical RAS ACE‐Ang II‐AT1R regulatory axis and the ACE2‐Ang 1‐7‐MasR counter‐regulatory axis play an essential role in maintaining homeostasis in humans. ACE2 is widely distributed in the heart, kidneys, lungs, and testes. ACE2 antagonizes the activation of the classical RAS system and protects against organ damage, protecting against hypertension, diabetes, and cardiovascular disease. Similar to SARS‐CoV, SARS‐CoV‐2 also uses the ACE2 receptor to invade human alveolar epithelial cells. Acute respiratory distress syndrome (ARDS) is a clinical high‐mortality disease, and ACE2 has a protective effect on this type of acute lung injury. Current research shows that the poor prognosis of patients with COVID‐19 is related to factors such as sex (male), age (>60 years), underlying diseases (hypertension, diabetes, and cardiovascular disease), secondary ARDS, and other relevant factors. Because of these protective effects of ACE2 on chronic underlying diseases and ARDS, the development of spike protein‐based vaccine and drugs enhancing ACE2 activity may become one of the most promising approaches for the treatment of COVID‐19 in the future. url: https://doi.org/10.1002/jmv.25785 doi: 10.1002/jmv.25785 id: cord-275946-ofd2ipvs author: Cheng, Matthew P. title: Serodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review date: 2020-06-04 words: 5277.0 sentences: 282.0 pages: flesch: 38.0 cache: ./cache/cord-275946-ofd2ipvs.txt txt: ./txt/cord-275946-ofd2ipvs.txt summary: Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation. Appropriately designed seroepidemiologic studies will play an essential part in the public health response to the COVID-19 pandemic by characterizing transmission dynamics, refining disease burden estimates, and providing insight into the kinetics of humoral immunity to SARS-CoV-2. Serologic surveillance studies can also assess the accumulation of persons with antibody responses over time to estimate incidence of SARS-CoV-2 infection (57, 58) and can track age-and jurisdiction-specific disease susceptibility and identify at-risk populations (59) . abstract: Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. Many use cases are envisaged, including complementing molecular methods for diagnosis of active disease and estimating immunity for individuals. At the population level, carefully designed seroepidemiologic studies will aid in the characterization of transmission dynamics and refinement of disease burden estimates and will provide insight into the kinetics of humoral immunity. Yet, despite an explosion in the number and availability of serologic assays to test for antibodies against SARS-CoV-2, most have undergone minimal external validation to date. This hinders assay selection and implementation, as well as interpretation of study results. In addition, critical knowledge gaps remain regarding serologic correlates of protection from infection or disease, and the degree to which these assays cross-react with antibodies against related coronaviruses. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation. url: https://doi.org/10.7326/m20-2854 doi: 10.7326/m20-2854 id: cord-259347-3acsko74 author: Cheng, Qi title: Infectivity of human coronavirus in the brain date: 2020-05-28 words: 3981.0 sentences: 185.0 pages: flesch: 42.0 cache: ./cache/cord-259347-3acsko74.txt txt: ./txt/cord-259347-3acsko74.txt summary: A new strain of human coronaviruses (hCoVs), Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has been identified to be responsible for the current outbreak of the coronavirus disease 2019 (COVID-19). Data from multiple hACE2 transgenic mouse models has revealed that SARS-CoV detection in the brain is significantly delayed compared to that within the lung, consistent with the initial establishment of infection within the respiratory system before dissemination to the CNS [21À23]. In addition, the detection of SARS-CoV in CSF of patients with neurological manifestation has also provided direct evidence for the neuroinvasion and neurovirulence of hCoVs. However, the role of the virus in the process of the disease in acute phase as well as in the long term still remains elusive. Severe acute respiratory syndrome coronavirus infection of mice transgenic for the human Angiotensin-converting enzyme 2 virus receptor abstract: A new strain of human coronaviruses (hCoVs), Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has been identified to be responsible for the current outbreak of the coronavirus disease 2019 (COVID-19). Though major symptoms are primarily generated from the respiratory system, neurological symptoms are being reported in some of the confirmed cases, raising concerns of its potential for intracranial invasion and neurological manifestations, both in the acute phase and in the long-term. At present, it remains unclear the extent to which SARS-CoV-2 is present in the brain, and if so, its pathogenic role in the central nervous system (CNS). Evidence for neuroinvasion and neurovirulence of hCoVs has been recognised in animal and human studies. Given that SARS-CoV-2 belongs to the same family and shares characteristics in terms of receptor binding properties, it is worthwhile exploring its potential CNS manifestations. This review summarises previous findings from hCoVs in relation to the CNS, and compares these with the new strain, aiming to provide a better understanding of the effects of SARS-CoV-2 on the CNS. url: https://www.ncbi.nlm.nih.gov/pubmed/32474399/ doi: 10.1016/j.ebiom.2020.102799 id: cord-288558-rthnj6wd author: Cheng, V. C. C. title: Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date: 2004-02-15 words: 3801.0 sentences: 201.0 pages: flesch: 46.0 cache: ./cache/cord-288558-rthnj6wd.txt txt: ./txt/cord-288558-rthnj6wd.txt summary: The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. In this retrospective study, we attempt to correlate the virus load of SARS coronavirus shedding from the nasopharynx, the upper end of the aerodigestive tract, with the presence of diarrhea in a cohort of patients with SARS. abstract: The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. Data from daily hematological, biochemical, radiological, and microbiological investigations were prospectively collected, and the correlation of these findings with diarrhea was retrospectively analyzed. Sixty-nine patients (48.6%) developed diarrhea at a mean (± standard deviation [SD]) of 7.6 ± 2.6 days after the onset of symptoms. The diarrhea was most severe at a mean (±SD) of 8.8 ± 2.4 days after onset, with a maximum frequency of 24 episodes per day (median, 5 episodes; range, 3–24 episodes). A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log(10) vs. 1.8 log(10) copies/mL; P = .01) and mortality (6.2 vs. 1.7 log(10) copies/mL; P < .01). However, diarrhea was not associated with mortality. The lung and the gastrointestinal tract may react differently to SARS coronavirus infection. Additional investigation of the role of SARS coronavirus in the pathogenesis of diarrhea in patients with SARS should be conducted. url: https://www.ncbi.nlm.nih.gov/pubmed/14765337/ doi: 10.1086/382681 id: cord-270909-wb7mwklo author: Cheng, Vincent C.C. title: Absence of nosocomial transmission of coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in the pre-pandemic phase in Hong Kong date: 2020-05-24 words: 2262.0 sentences: 111.0 pages: flesch: 46.0 cache: ./cache/cord-270909-wb7mwklo.txt txt: ./txt/cord-270909-wb7mwklo.txt summary: BACKGROUND: To describe the infection control strategy to achieve zero nosocomial transmission of symptomatic coronavirus disease (COVID-19) due to SARS-CoV-2 during the pre-pandemic phase (the first 72 days after announcement of pneumonia cases in Wuhan) in Hong Kong. Pandemic infection of a coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) was declared by World Health Organization (WHO) on 11 March 2020, which is 72 days after announcement of a cluster of patients with community acquired pneumonia in Wuhan, Hubei Province by National Health Commission of the People''s Republic of China (NHCPRC), on 31 December 2019 (day 1) [1] . Up to 11 March 2020 (day 72 after the official announcement of a cluster of pneumonia of unknown etiology in Wuhan, Hubei Province, a total of 130 cases of SARS-CoV-2 infection were confirmed in Hong Kong, while the first 42 patients were reported previously [9] . abstract: BACKGROUND: To describe the infection control strategy to achieve zero nosocomial transmission of symptomatic coronavirus disease (COVID-19) due to SARS-CoV-2 during the pre-pandemic phase (the first 72 days after announcement of pneumonia cases in Wuhan) in Hong Kong. METHODS: Administrative support with the aim of zero nosocomial transmission by reducing elective clinical services, decanting wards, mobilizing isolation facilities, providing adequate personal protective equipment, coordinating laboratory network for rapid molecular diagnosis under 4-tier active surveillance for hospitalized- and out-patients, and organizing staff forum and training was implemented under the framework of preparedness plan in Hospital Authority. The trend of SARS-CoV-2 in the first 72 days was compared with that of SARS-CoV 2003. RESULTS: Up to day 72 of the epidemic, 130 (0.40%) of 32,443 patients being screened confirmed to have SARS-CoV-2 by RT-PCR. Compared with SARS outbreak in 2003, the SARS-CoV-2 case load constituted 8.9% (130 SARS-CoV-2/1458 SARS-CoV) of SARS-CoV infected cases at day 72 of the outbreak. The incidences of nosocomial acquisition of SARS-CoV per-1,000-SARS-patient-day and per-100-SARS-patient-admission were 7.9 and 16.9 respectively, which were significantly higher than the corresponding incidences of SARS-CoV-2 (zero infection, p<0.001). CONCLUSION: Administrative support to infection control could minimize the risk of nosocomial transmission of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S0196655320302807?v=s5 doi: 10.1016/j.ajic.2020.05.018 id: cord-255697-trig04hd author: Cheng, Vincent Chi-Chung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 words: 6422.0 sentences: 301.0 pages: flesch: 42.0 cache: ./cache/cord-255697-trig04hd.txt txt: ./txt/cord-255697-trig04hd.txt summary: Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. abstract: Viruses are obligatory intracellular pathogens with a simple structure consisting of assembled proteins enclosing the nucleic acid genome with or without a lipid envelope. Despite increasing availability of rapid nucleic acid amplification assays for laboratory diagnosis, effective antivirals, and safe vaccines, the control of most viral infections depends on time-honored surveillance and infection control measures. Moreover most viruses can be readily destroyed by common disinfectants. This article is focused on the epidemiology, diagnosis, and control of common and emerging viral diseases. url: https://www.sciencedirect.com/science/article/pii/B9780128036785005142 doi: 10.1016/b978-0-12-803678-5.00514-2 id: cord-299105-3ivzmiqn author: Cheng, Yi‐Qiang title: Deciphering the Biosynthetic Codes for the Potent Anti‐SARS‐CoV Cyclodepsipeptide Valinomycin in Streptomyces tsusimaensis ATCC 15141 date: 2006-03-01 words: 3774.0 sentences: 221.0 pages: flesch: 52.0 cache: ./cache/cord-299105-3ivzmiqn.txt txt: ./txt/cord-299105-3ivzmiqn.txt summary: Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors d‐α‐hydroxyisovaleric acid and l‐lactic acid. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors D-a-hydroxyisovaleric acid and L-lactic acid. The respective adenylation domains in these two modules contain novel substrate-specificity-conferring codes that might specify for a class of hydroxyl acids for the biosynthesis of the depsipeptide natural products. The key element of this approach is to sequence a certain number of random genomic clones and to identify candidate gene(s) involved in natural product biosynthesis. abstract: Valinomycin was recently reported to be the most potent agent against severe acute respiratory‐syndrome coronavirus (SARS‐CoV) in infected Vero E6 cells. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Targeted disruption of a nonribosomal peptide synthetase (NRPS) gene abolishes valinomycin production, which confirms its predicted nonribosomal‐peptide origin. Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors d‐α‐hydroxyisovaleric acid and l‐lactic acid. The respective adenylation domains in these two modules contain novel substrate‐specificity‐conferring codes that might specify for a class of hydroxyl acids for the biosynthesis of the depsipeptide natural products. url: https://www.ncbi.nlm.nih.gov/pubmed/16511823/ doi: 10.1002/cbic.200500425 id: cord-285748-us5do6c2 author: Cheng, Yongqian title: SARS-CoV-2-Related Kidney Injury: Current Concern and Challenges date: 2020-09-23 words: 5322.0 sentences: 295.0 pages: flesch: 48.0 cache: ./cache/cord-285748-us5do6c2.txt txt: ./txt/cord-285748-us5do6c2.txt summary: Currently, the diagnosis and treatment of SARS-CoV-2 infection in patients with chronic kidney disease (CKD) are still unclear. Here, we review the recent findings of characteristics of COVID-19 in CKD patients and highlight the possible mechanisms of kidney injury caused by SARS-CoV-2 infection. Controversial results also exist like another study [18] indicating that SARS-CoV-2 infection was not found significantly correlated with incremental acute renal injury or aggravate chronic kidney failure in the COVID-19 patients. Therefore, SARS-CoV-2 infection in kidney transplant patients from this study showed that such cases may be severe enough requiring intensive care admission and these patients are in high risk of disease progression and death. Another study based on single-cell analysis by Lin and colleagues [28] also found that ACE2 was enriched in proximal tubular cells which may indicate that the kidney is more susceptible to SARS-CoV-2 infection. abstract: Coronavirus disease 2019 (COVID-19) not only causes pulmonary inflammation but also causes multiple organ damages, including the kidney. ACE2, as one of the receptors for SARS-CoV-2 intrusion, is widely distributed in kidney tissues. Currently, the diagnosis and treatment of SARS-CoV-2 infection in patients with chronic kidney disease (CKD) are still unclear. Here, we review the recent findings of characteristics of COVID-19 in CKD patients and highlight the possible mechanisms of kidney injury caused by SARS-CoV-2 infection. We then discuss the emerging therapeutic approaches aimed at reducing kidney damage and protecting kidney function including virus removal, immunotherapy, supporting treatment, special blood purification therapy, etc. Problems unresolved and challenges ahead are also discussed. url: https://doi.org/10.1007/s42399-020-00529-0 doi: 10.1007/s42399-020-00529-0 id: cord-338684-po3hfibp author: Cheong, Kai Xiong title: Systematic Review of Ocular Involvement of SARS-CoV-2 in Coronavirus Disease 2019 date: 2020-09-26 words: 5033.0 sentences: 330.0 pages: flesch: 58.0 cache: ./cache/cord-338684-po3hfibp.txt txt: ./txt/cord-338684-po3hfibp.txt summary: PURPOSE OF REVIEW: Studies have reported ocular involvement in the coronavirus disease 2019 (COVID-19), with SARS-CoV-2 having been detected in ocular swab samples. Observational studies which both described ocular involvement among patients with COVID-19 and attempted to detect SARS-CoV-2 in ocular samples via RT-PCR and/or viral cultures were included. In contrast, other studies have reported the detection of SARS-CoV-2 in ocular samples from patients who did not experience ocular symptoms and signs [5, 9, 10] . reported in a retrospective case series that SARS-CoV-2 was detected in conjunctival swab samples from both eyes of two patients (6.06%) in a population of 33 patients. Seah et al., in a prospective case series of 17 patients, reported that SARS-CoV-2 could not be detected in RT-PCR of tear samples. In the studies that took serial samples, SARS-CoV-2 was reported to remain detectable up to 27 days after the onset of ocular and respiratory symptoms [16, 18] . abstract: PURPOSE OF REVIEW: Studies have reported ocular involvement in the coronavirus disease 2019 (COVID-19), with SARS-CoV-2 having been detected in ocular swab samples. This has implicated the eye as a portal of transmission. The aim of this systemic review is to summarise and discuss the current literature regarding ocular involvement of SARS-CoV-2 in COVID-19. RECENT FINDINGS: In this systematic review, the prevalence of ocular symptoms and signs was low (from 0 to 31.58%) and conjunctivitis was a relatively rare occurrence. The rate of detection of SARS-CoV-2 in the ocular swab samples was low as well and this ranged from 0 to 11.11%. The development of ocular symptoms and signs was not always accompanied by the detection of SARS-CoV-2 in the ocular swab samples. The opposite was described as well. This may reflect issues related to the characteristics of SARS-CoV-2 and of the study design. Nonetheless, the nature of research in a pandemic is that conclusions can change as more information is obtained. SUMMARY: Whilst the eye is unlikely to be a main transmission route, we need to consider the possibilities of conjunctivitis as a presenting complaint and of the eye playing a role in the transmission of SARS-CoV-2. Furthermore, we need to take the appropriate precautions in our practice. Further studies are needed to evaluate the viral tropism of SARS-CoV-2 and its role in the eyes. url: https://doi.org/10.1007/s40135-020-00257-7 doi: 10.1007/s40135-020-00257-7 id: cord-310790-3ikgmiof author: Cherrak, Sabri Ahmed title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 words: 3471.0 sentences: 226.0 pages: flesch: 50.0 cache: ./cache/cord-310790-3ikgmiof.txt txt: ./txt/cord-310790-3ikgmiof.txt summary: title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. The three compounds with highest affinity (Fig 2) for the active site are quercetin 3-rhamonoside, myricetin 3-rutinoside and rutin with binding energies of -9.7, -9,3 and -9.2 kcal.mol -1 respectively. Thirty eight flavonoids have been tested in this study by molecular docking against the active site of the SARS-CoV-2Mpro. Glycosylated flavonoids as SARS-CoV-2 Inhibitors: A molecular docking and simulation studies Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies abstract: A novel coronavirus responsible of acute respiratory infection closely related to SARS-CoV has recently emerged. So far there is no consensus for drug treatment to stop the spread of the virus. Discovery of a drug that would limit the virus expansion is one of the biggest challenges faced by the humanity in the last decades. In this perspective, to test existing drugs as inhibitors of SARS-CoV-2 main protease is a good approach. Among natural phenolic compounds found in plants, fruit, and vegetables; flavonoids are the most abundant. Flavonoids, especially in their glycosylated forms, display a number of physiological activities, which makes them interesting to investigate as antiviral molecules. The flavonoids chemical structures were downloaded from PubChem and protease structure 6LU7 was from the Protein Data Bank site. Molecular docking study was performed using AutoDock Vina. Among the tested molecules Quercetin-3-O-rhamnoside showed the highest binding affinity (-9,7 kcal/mol). Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. MD simulations were further performed to evaluate the dynamic behavior and stability of the protein in complex with the three best hits of docking experiments. Our results indicate that the rutin is a potential drug to inhibit the function of Chymotrypsin-like protease (3CL pro) of Coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/33057452/ doi: 10.1371/journal.pone.0240653 id: cord-294237-6hovffso author: Cherry, James D title: SARS: The First Pandemic of the 21(st) Century date: 2004 words: 3477.0 sentences: 192.0 pages: flesch: 56.0 cache: ./cache/cord-294237-6hovffso.txt txt: ./txt/cord-294237-6hovffso.txt summary: SARS (severe acute respiratory syndrome) was a new disease in the fall of 2002, which first occurred in Guangdong Province, China and spread to 29 countries with 8422 cases and 916 fatalities (1) (2) (3) . Moreover, cataloging the genome from human cases assisted in the search for the origin of this disease, when viruses related to the SARS-CoV were identified in animals [Himalayan palm civets (Paguma larvata) and raccoon dogs (Nyctereutes procyonoides)] in a live animal market in Shenzhen, China (12) . On the one hand, in the initial phases of the spread of SARS in Hong Kong, Singapore, and Toronto, a disproportionate number of health care workers became ill and apparent "superspreader" cases were noted (2-4, 6, 11, 14 -18) . Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens, Kowloon Bay, Hong Kong, main findings of the investigation Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15152053/ doi: 10.1203/01.pdr.0000129184.87042.fc id: cord-282338-u01qv3uc author: Cherry, James. D. title: The chronology of the 2002–2003 SARS mini pandemic date: 2004-11-05 words: 3528.0 sentences: 176.0 pages: flesch: 55.0 cache: ./cache/cord-282338-u01qv3uc.txt txt: ./txt/cord-282338-u01qv3uc.txt summary: SARS-CoV disease should be considered at a minimum in the differential diagnoses for persons requiring hospitalisation for pneumonia confirmed radiographically or acute respiratory distress syndrome without identifiable aetiology and who have one of the following risk factors in the 10 days before the onset of illness: (1) Travel to mainland China, Hong Kong, or Taiwan, or close contact with an ill person with a history of recent travel to one of these areas, or; (2) Employment in an occupation associated with a risk for SARS-CoV exposure (e.g. healthcare worker with direct patient contact or worker in a laboratory that contains live SARS-CoV) or; (3) Part of a cluster of cases of atypical pneumonia without an alternative diagnosis. abstract: Severe acute respiratory syndrome (SARS) was a new human disease in the autumn of 2002. It first occurred in Southern China in November 2002 and was transported to Hong Kong on February 21, 2003 by an infected and ill patient. Ten secondary cases spread the infection to two hospitals in Hong Kong and to Singapore, Toronto and Hanoi. In March 2003 a novel coronavirus (SARS-CoV) was found to be the causative agent. Within 11 weeks from the first SARS case in Hong Kong it had spread to an additional 27 countries or special administrative regions. The mini pandemic peaked during the last week of May 2003 and the last new probable case was on July 13, 2003. There were a total of 8096 probable cases and 774 deaths. Sixty-six per cent of the cases occurred in China, 22% in Hong Kong, 4% in Taiwan and 3% in both Singapore and Canada. Twenty-one per cent of all cases occurred in healthcare workers. url: https://www.sciencedirect.com/science/article/pii/S1526054204000788 doi: 10.1016/j.prrv.2004.07.009 id: cord-016451-k8m2xz0e author: Chertow, Daniel S. title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 words: 6141.0 sentences: 365.0 pages: flesch: 41.0 cache: ./cache/cord-016451-k8m2xz0e.txt txt: ./txt/cord-016451-k8m2xz0e.txt summary: Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection abstract: Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. These biologically diverse viruses enter and replicate within host cells triggering viral- and host-mediated damage that results in pneumonia and multiorgan failure in severe cases. Early case identification and strict infection control limit healthcare transmission. Vaccination allowed smallpox eradication and limits global measles and seasonal influenza mortality. While SARS-coronavirus (CoV) is no longer circulating, MERS-CoV and zoonotic influenza viruses, with pandemic potential, remain persistent threats. Supportive critical care is the mainstay of treatment for severe disease due to these viral infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120728/ doi: 10.1007/978-3-030-33803-9_5 id: cord-262180-t4akem15 author: Cheruiyot, Isaac title: Comment on “Encephalopathy in patients with COVID‐19: A review” date: 2020-07-11 words: 269.0 sentences: 29.0 pages: flesch: 42.0 cache: ./cache/cord-262180-t4akem15.txt txt: ./txt/cord-262180-t4akem15.txt summary: key: cord-262180-t4akem15 title: Comment on "Encephalopathy in patients with COVID‐19: A review" cord_uid: t4akem15 I read with great interest the article by Garg and colleagues on "Encephalopathy in patients with COVID-19: A review". The authors performed a review of published reports on COVID-19-associated encephalitis and encephalopathy. Encephalopathy in patients with COVID-19: a review Status of SARS-CoV-2 in cerebrospinal fluid of patients with COVID-19 and stroke Facial diplegia, a possible atypical variant of Guillain-Barré Syndrome as a rare neurological complication of SARS-CoV-2 Guillain-Barré syndrome after SARS-CoV-2 infection Guillain-Barré syndrome associated with leptomeningeal enhancement following SARS-CoV-2 infection A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 Sars-Cov-2: underestimated damage to nervous system COVID-19 encephalopathy: detection of antibodies against SARS-CoV-2 in CSF Encephalopathy and encephalitis associated with cerebrospinal fluid cytokine alterations and coronavirus disease How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis? abstract: I read with great interest the article by Garg and colleagues on "Encephalopathy in patients with COVID-19: A review". The authors performed a review of published reports on COVID-19-associated encephalitis and encephalopathy. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32603476/ doi: 10.1002/jmv.26238 id: cord-278325-ykcd7d59 author: Cheung, Carmen Ka Man title: Coronavirus Disease 2019 (COVID-19): A Haematologist''s Perspective date: 2020-07-28 words: 7672.0 sentences: 379.0 pages: flesch: 39.0 cache: ./cache/cord-278325-ykcd7d59.txt txt: ./txt/cord-278325-ykcd7d59.txt summary: Two meta-analyses showed that a lower platelet count is associated with an increased risk of severe disease and mortality in patients with COVID-19 and may serve as a marker for progression of illness [53, 54] . Experience from previous SARS patients, caused by SARS-CoV-1, suggested that coronavirus could cause thrombocytopenia by direct viral infection of bone marrow haematopoietic stem cells via CD13 or CD66a, formation of auto-antibodies and immune complexes, disseminated intravascular coagulopathy (DIC), and consumption of platelet in lung epithelium [61, 62] . The International Society on Thrombosis and Haemostasis (ISTH) suggested all patients (including non-critically ill) who require hospital admission for COVID-19 infection should receive a prophylactic dose of LMWH unless contraindicated (Table 2 ) [102] . Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 abstract: Coronavirus disease 2019 (COVID-19) is affecting millions of patients worldwide. It is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which belongs to the family Coronaviridae, with 80% genomic similarities to SARS-CoV. Lymphopenia was commonly seen in infected patients and has a correlation to disease severity. Thrombocytopenia, coagulation abnormalities, and disseminated intravascular coagulation were observed in COVID-19 patients, especially those with critical illness and non-survivors. This pandemic has caused disruption in communities and hospital services, as well as straining blood product supply, affecting chemotherapy treatment and haematopoietic stem cell transplantation schedule. In this article, we review the haematological manifestations of the disease and its implication on the management of patients with haematological disorders. url: https://www.ncbi.nlm.nih.gov/pubmed/32721958/ doi: 10.1159/000510178 id: cord-269771-hffxb7bm author: Cheung, Ka Shing title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 words: 4797.0 sentences: 263.0 pages: flesch: 51.0 cache: ./cache/cord-269771-hffxb7bm.txt txt: ./txt/cord-269771-hffxb7bm.txt summary: title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. The proportion of patients with detectable stool viral RNA was higher among those with diarrhea than those without diarrhea Table 2 including the hospital admission period, places in which the patients were recruited, sample size, age, sex, disease severity, non-gastrointestinal symptoms (fever and respiratory symptoms) on presentation, and gastrointestinal symptoms (anorexia, nausea/vomiting, diarrhea and abdominal pain/discomfort). In this meta-analysis of 4,243 COVID-19 patients from six countries, the pooled prevalence of all gastrointestinal symptoms (including anorexia, nausea/vomiting, diarrhea or abdominal pain) was 17.6%. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: Abstract Background & Aims Infection with SARS-CoV-2 causes COVID-19, which has been characterized by fever, respiratory, and gastrointestinal symptoms as well as shedding of virus RNA into feces. We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. Methods We collected data from the cohort of patients with COVID-19 in Hong Kong (n=59; diagnosis from February 2 through Feb 29, 2020), and searched PubMed, Embase, Cochrane and three Chinese databases through March 11, 2020 according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We analyzed pooled data on the prevalence of overall and individual gastrointestinal symptoms (anorexia, nausea, vomiting, diarrhea, and abdominal pain or discomfort) using a random effects model. Results Among the 59 patients with COVID-19 in Hong Kong, 15 patients (25.4%) had gastrointestinal symptoms and 9 patients (15.3%) had stool that tested positive for virus RNA. Stool viral RNA was detected in 38.5% and 8.7% among those with and without diarrhea, respectively (P=.02). The median fecal viral load was 5.1 log10cpm in patients with diarrhea vs 3.9 log10cpm in patients without diarrhea (P=.06). In a meta-analysis of 60 studies, comprising 4243 patients, the pooled prevalence of all gastrointestinal symptoms was 17.6% (95% CI, 12.3%–24.5%); 11.8% of patients with non-severe COVID-19 had gastrointestinal symptoms (95% CI, 4.1%–29.1%) and 17.1% of patients with severe COVID-19 had gastrointestinal symptoms (95% CI, 6.9%–36.7%). In the meta-analysis, the pooled prevalence of stool samples that were positive for virus RNA was 48.1% (95% CI, 38.3%–57.9%); of these samples, 70.3% of those collected after loss of virus from respiratory specimens tested positive for the virus (95% CI, 49.6%–85.1%). Conclusions In an analysis of data from the Hong Kong cohort of patients with COVID-19 and a meta-analysis of findings from publications, we found that 17.6% of patients with COVID-19 had gastrointestinal symptoms. Virus RNA was detected in stool samples from 48.1% patients—even in stool collected after respiratory samples tested negative. Healthcare workers should therefore exercise caution in collecting fecal samples or performing endoscopic procedures in patients with COVID-19—even during patient recovery. url: https://www.ncbi.nlm.nih.gov/pubmed/32251668/ doi: 10.1053/j.gastro.2020.03.065 id: cord-267388-jz5mm91w author: Cheung, Szeya title: Recurrent Acute Pancreatitis in a Patient with COVID-19 Infection date: 2020-08-24 words: 1555.0 sentences: 102.0 pages: flesch: 44.0 cache: ./cache/cord-267388-jz5mm91w.txt txt: ./txt/cord-267388-jz5mm91w.txt summary: Patient: Male, 38-year-old Final Diagnosis: Recurrent idiopathic acute pancreatitis with COVID-19 Symptoms: Nausea • severe abdominal pain • fever • vomiting Medication:— Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases • General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: The novel COVID-19 disease has infected more than 2 million people worldwide, causing more than 120 000 deaths. CONCLUSIONS: The temporal relationship between clinical presentation of acute pancreatitis and SARS-CoV-2 infection in this patient with no precipitating risk factors for pancreatitis suggests COVID-19-associated acute pancreatitis. Our review of the literature showed a few case studies that described the presentation of idiopathic acute pancreatitis in patients with concurrent SARS-CoV-2 infection [5] [6] [7] [8] [9] [10] . It is also important to note that while respiratory symptoms improve in patients with COVID-19 infection, these patients can still test positive for SARS-CoV-2 and are at risk for developing acute pancreatitis. abstract: Patient: Male, 38-year-old Final Diagnosis: Recurrent idiopathic acute pancreatitis with COVID-19 Symptoms: Nausea • severe abdominal pain • fever • vomiting Medication:— Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases • General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: The novel COVID-19 disease has infected more than 2 million people worldwide, causing more than 120 000 deaths. While the disease is known to primarily affect the respiratory system, gastrointestinal manifestations can also occur. However, little is known about the development of acute pancreatitis in COVID-19. The present report highlights a patient with no precipitating risk factors for pancreatitis who presented with recurring acute pancreatitis following the diagnosis of SARS-CoV-2 infection. CASE REPORT: An otherwise healthy 38-year-old man presented to the Emergency Department (ED) with fever and epigastric pain. Laboratory testing revealed a lipase level of 10 255 ukat/L. An abdominal ultrasound showed no gallstones. After ruling out the possible causes of acute pancreatitis, a diagnosis of idiopathic acute pancreatitis was made. He received conservative management and was discharged home after being medically stabilized. Of note, the patient tested positive for SARS-CoV-2 infection at a local testing center 1 week prior to presenting to the ED. One week following the discharge, the patient returned with recurrent severe epigastric pain. Laboratory testing showed a lipase level of 20 320 ukat/L. An abdominal CT revealed acute pancreatitis. Further workups, including abdominal ultrasound, hepatitis serology, and immunoglobulin G for autoimmune pancreatitis, were unrevealing. Repeated SARS-CoV-2 testing produced positive results. CONCLUSIONS: The temporal relationship between clinical presentation of acute pancreatitis and SARS-CoV-2 infection in this patient with no precipitating risk factors for pancreatitis suggests COVID-19-associated acute pancreatitis. Our review of the literature found a handful of reported cases of acute pancreatitis in patients with coexisting SARS-CoV-2 infection, and this report presents the first presumptive case of COVID-19-associated recurring acute pancreatitis. url: https://doi.org/10.12659/ajcr.927076 doi: 10.12659/ajcr.927076 id: cord-346032-188gnf8j author: Cheung, Ying-Kit title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 words: 4754.0 sentences: 228.0 pages: flesch: 53.0 cache: ./cache/cord-346032-188gnf8j.txt txt: ./txt/cord-346032-188gnf8j.txt summary: title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. abstract: The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. In this study, we have identified a novel HLA-A*0201 restricted epitope, N220 (LALLLLDRL), of the SARS-CoV N-protein through bioinformatics analysis. The N-protein peptide N220 shows a high binding affinity towards human MHC class I in T2-cells, and is capable of activating cytotoxic T-cells in human peripheral blood mononuclear cells (PBMCs). The application of using the N220 peptide sequence with a single-chain-trimer (SCT) approach to produce a potential DNA vaccine candidate was investigated in HLA-A2.1K(b) transgenic mice. Cytotoxicity assay clearly showed that the T-cells obtained from the vaccinated animals were able to kill the N-protein expressing cells with a cytotoxicity level of 86% in an effector cells/target cells ratio of 81:1 one week after the last vaccination, which is significantly higher than other N-protein peptides previously described. The novel immunogenic N-protein peptide revealed in the present study provides valuable information for therapeutic SARS vaccine design. url: https://api.elsevier.com/content/article/pii/S0264410X07005932 doi: 10.1016/j.vaccine.2007.05.025 id: cord-298156-d0pb1kik author: Cheval, Sorin title: Observed and Potential Impacts of the COVID-19 Pandemic on the Environment date: 2020-06-10 words: 11027.0 sentences: 569.0 pages: flesch: 47.0 cache: ./cache/cord-298156-d0pb1kik.txt txt: ./txt/cord-298156-d0pb1kik.txt summary: Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. The concept of disaster has evolved over time, and here we use an adapted Intergovernmental Panel on Climate Change (IPCC) definition: a disaster is an event, which severely alters the functioning of a community due to hazardous physical, biological or human related impacts leading to widespread adverse effects on multiple scales and systems (environment, economic, social). While negative impacts on the economy and society in general are probably huge, it is very likely that the global-scale reduction of economic activities due to the COVID-19 crisis triggers a lot of sensible improvements in environmental quality and climatic systems. abstract: Various environmental factors influence the outbreak and spread of epidemic or even pandemic events which, in turn, may cause feedbacks on the environment. The novel coronavirus disease (COVID-19) was declared a pandemic on 13 March 2020 and its rapid onset, spatial extent and complex consequences make it a once-in-a-century global disaster. Most countries responded by social distancing measures and severely diminished economic and other activities. Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. This study presents an early overview of the observed and potential impacts of the COVID-19 on the environment. We argue that the effects of COVID-19 are determined mainly by anthropogenic factors which are becoming obvious as human activity diminishes across the planet, and the impacts on cities and public health will be continued in the coming years. url: https://doi.org/10.3390/ijerph17114140 doi: 10.3390/ijerph17114140 id: cord-318262-w8oixzdg author: Chevance, A title: Ensuring mental health care during the SARS-CoV-2 epidemic in France: a narrative review date: 2020-04-22 words: 6747.0 sentences: 303.0 pages: flesch: 40.0 cache: ./cache/cord-318262-w8oixzdg.txt txt: ./txt/cord-318262-w8oixzdg.txt summary: Results: We identified four types of major vulnerabilities among patients with mental disorders during this pandemic: 1) medical comorbidities that are more frequently found among patients with mental disorders (cardiovascular and pulmonary pathologies, diabetes, obesity, etc.) which are risk factors for severe covid-19 infection; 2) age (the elderly form the population most vulnerable to the coronavirus); 3) cognitive and behavioural disorders, which can hamper compliance with confinement and hygiene measures and finally and 4) psychosocial vulnerability as a result of stigmatization and/or socio-economic difficulties. At the end of hospitalization, in particular for the population of patients in compulsory ambulatory care situations, specific case-management are organized with the possibility of home visits, in order to support patients when they get back home and to help them cope with the experience of confinement, which is liable to induce recurrences of mental disorders. abstract: Abstract Objective: The lack of resources and coordination to face the coronavirus epidemic raises concerns for the health of patients with mental disorders in a country where we still have memories of the dramatic experience of famine in psychiatric hospitals during the Second World War. This article aims to propose guidance to ensure mental health care during the SARS-CoV epidemic in France. Methods: The authors performed a narrative review identifying relevant results in the scientific and medical literature and in local initiatives in France. Results: We identified four types of major vulnerabilities among patients with mental disorders during this pandemic: 1) medical comorbidities that are more frequently found among patients with mental disorders (cardiovascular and pulmonary pathologies, diabetes, obesity, etc.) which are risk factors for severe covid-19 infection; 2) age (the elderly form the population most vulnerable to the coronavirus); 3) cognitive and behavioural disorders, which can hamper compliance with confinement and hygiene measures and finally and 4) psychosocial vulnerability as a result of stigmatization and/or socio-economic difficulties. Furthermore, the mental health healthcare system is more vulnerable than other healthcare systems. Current government plans are poorly suited to psychiatric establishments in a context of major shortages of organizational, material and human resources. In addition, a certain number of structural aspects make the psychiatric institution particularly vulnerable: many beds have been closed, wards have high densities of patients, mental health community facilities are closed, and medical teams are understaffed and poorly trained to face infectious diseases. There are also major issues when referring patients with acute mental disorders to intensive care units. To maintain the continuity of psychiatric care in this pandemic situation, several directions can be considered, in particular with the creation of "COVID+ units". These units are under the dual supervision of a psychiatrist and an internist / infectious disease specialist; all new entrants are placed in quarantine for 14 days; the nursing staff receives specific training, daily medical check-ups and close psychological support. Family visits are prohibited and replaced by videoconference. At the end of hospitalization, in particular for the population of patients in compulsory ambulatory care situations, specific case-management are organized with the possibility of home visits, in order to support patients when they get back home and to help them cope with the experience of confinement, which is liable to induce recurrences of mental disorders. The total or partial closure of community mental health facilities is particularly disturbing for patients, but a regular follow-up is possible with telemedicine and should include the monitoring of suicide risk and psycho-education strategies; developing support platforms could also be very helpful in this context. Private practice psychiatrists also have a crucial role of information towards their patients on confinement and barrier measures, and also on measures to prevent the psychological risks inherent in confinement: maintenance of regular sleep r, physical exercise, social interactions, stress management and coping strategies, prevention of addictions, etc. They should also be trained to prevent, detect and treat early warning symptoms of post-traumatic stress disorder, because their prevalence was high in the regions of China most affected by the pandemic. Discussion: French mental healthcare is now facing a great and urgent need for reorganization and must also prepare in the coming days and weeks to face an epidemic of emotional disorders due to the confinement of the general population. url: https://www.ncbi.nlm.nih.gov/pubmed/32370982/ doi: 10.1016/j.encep.2020.04.005 id: cord-354373-lldfoptb author: Chi, Jeffrey title: COVID-19 Clinical Research date: 2020-05-05 words: 2491.0 sentences: 153.0 pages: flesch: 49.0 cache: ./cache/cord-354373-lldfoptb.txt txt: ./txt/cord-354373-lldfoptb.txt summary: They can be categorized into four groups: drugs that combat SARS-CoV-2, immunomodulatory agents to counteract cytokine storm, convalescence plasma therapies and vaccines trials. They can be categorized into 1) drugs that combat SARS-CoV-2, 2) immunomodulatory agents to counteract cytokine storm, 3) convalescent plasma therapies and 4) vaccines trials (Table 1) . In vitro studies of these agents showed antiviral activities against SARS-VoV-2 and they are now repurposed for treating COVID-19 in clinical trials (Table 1) . Currently there are many ongoing clinical trials (e.g. NCT04292899, NCT04292730) to evaluate the efficacy of remdesivir in patients with mild to moderate or severe COVID-19. Sarilumab, another IL-6 receptor antagonist approved for RA, is also being studied in clinical trials (e.g. NCT04288713) in hospitalized patients with severe COVID-19 (Table 1) . As of April 19, 2020, there were 5 registered convalescent plasma therapy clinical trials in the United States for the treatment of severe and critically ill COVID-19 patients (Table 1) . abstract: INTRODUCTION: While the global COVID-19 pandemic has challenged the entire humanity and health systems, it also triggered researchers to urgently perform clinical trials to assess the safety and efficacy of many agents and modalities to combat COVID-19. As of April 22, over 650 clinical studies have been registered both in USA and internationally. Results from these studies are also coming at a brisk pace in this unprecedented emergency. AREAS COVERED: We searched the NCI website and Medline and summarize various national and international clinical trials and summarize few of the pivotal ones in this paper, including those specific to oncology population. Two hundred and eighty four studies are actively recruiting adults and children with confirmed COVID-19, including 25 are early-phase I/phase I, 72 phase II, 58 phase III, 12 phase IV, and 31 other trials. They can be categorized into four groups: drugs that combat SARS-CoV-2, immunomodulatory agents to counteract cytokine storm, convalescence plasma therapies and vaccines trials. EXPERT OPINION: It is hoped that these efforts will results in a successful treatment to COVID-19, especially in a timely fashion before the second pandemic expected in fall. It is essential to acknowledge the devotion and hard work of the clinical research team and clinical research volunteers. url: https://doi.org/10.33696/signaling.1.006 doi: 10.33696/signaling.1.006 id: cord-330607-zn4urrxc author: Chi, Qiong title: Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date: 2020-09-18 words: 3215.0 sentences: 165.0 pages: flesch: 47.0 cache: ./cache/cord-330607-zn4urrxc.txt txt: ./txt/cord-330607-zn4urrxc.txt summary: METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. abstract: BACKGROUND: Since December 2019, the coronavirus disease 2019 (COVID-19) has infected more than 12,322,000 people and killed over 556,000 people worldwide. However, Differential diagnosis remains difficult for suspected cases of COVID-19 and need to be improved to reduce misdiagnosis. METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. RESULTS: Among suspected patients, 17 were confirmed to COVID-19-positive group and 51 were distinguished to COVID-19-negative group. Patients with reduced white blood cell (WBC) count were more common in the COVID-19-positive group than in the COVID-19-negative group (29.4% vs 3.9%, P = 0.003). Subsequently, correlation analysis indicated that there was a significant inverse correlation existed between WBC count and temperature in the COVID-19-positive patients (r = − 0.587, P = 0.003), instead of the COVID-19-negative group. But reduced lymphocyte count was no different between the two groups (47.1% vs 25.5%, P = 0.096). More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). The rate of clustered infection was higher in COVID-19-positive group than COVID-19-negative group (64.7% vs 7.8%, P = 0.001). Through multiplex PCR nucleic acid testing, 2 cases of influenza A, 3 cases of influenza B, 2 cases of adenovirus, 2 cases of Chlamydia pneumonia, and 7 cases of Mycoplasma pneumoniae were diagnosed in the COVID-19-negative group. CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. Multiplex PCR nucleic acid testing helped differential diagnosis for suspected COVID-19 cases. url: https://doi.org/10.1186/s12879-020-05383-y doi: 10.1186/s12879-020-05383-y id: cord-327654-9g8zcxaa author: Chi, Xiaojing title: Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date: 2020-09-10 words: 4993.0 sentences: 302.0 pages: flesch: 51.0 cache: ./cache/cord-327654-9g8zcxaa.txt txt: ./txt/cord-327654-9g8zcxaa.txt summary: Here, using SARS-CoV-2 spike receptor-binding domain (RBD) as a bait, we generate a panel of humanized single domain antibodies (sdAbs) from a synthetic library. Competitive ligand-binding experiments suggest that the sdAbs either completely block or significantly inhibit the association between SARS-CoV-2 RBD and viral entry receptor ACE2. To determine whether sdAbs targeted different antigenic regions on the SARS-CoV-2 RBD surface, we performed a competition-binding assay using a real-time biosensor (Fig. 3) . Fc fusion sdAbs in culture supernatants were affinity purified with HiTrap Protein A HP antibody purification columns ( Supplementary Fig. 2 ) and analyzed in both reducing and non-reducing conditions in Western blot using an anti-human IgG to detect Fc. As shown in Fig. 4c , the size of the constructed intact sdAb-Fc is around 80 KDa in the non-reducing condition, but a 40 KDa monomer was observed by prior treatment in reducing condition to break disulfide bonds. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads worldwide and leads to an unprecedented medical burden and lives lost. Neutralizing antibodies provide efficient blockade for viral infection and are a promising category of biological therapies. Here, using SARS-CoV-2 spike receptor-binding domain (RBD) as a bait, we generate a panel of humanized single domain antibodies (sdAbs) from a synthetic library. These sdAbs reveal binding kinetics with the equilibrium dissociation constant (K(D)) of 0.99–35.5 nM. The monomeric sdAbs show half maximal neutralization concentration (EC(50)) of 0.0009–0.07 µg/mL and 0.13–0.51 µg/mL against SARS-CoV-2 pseudotypes, and authentic SARS-CoV-2, respectively. Competitive ligand-binding experiments suggest that the sdAbs either completely block or significantly inhibit the association between SARS-CoV-2 RBD and viral entry receptor ACE2. Fusion of the human IgG1 Fc to sdAbs improve their neutralization activity by up to ten times. These results support neutralizing sdAbs as a potential alternative for antiviral therapies. url: https://doi.org/10.1038/s41467-020-18387-8 doi: 10.1038/s41467-020-18387-8 id: cord-304201-fziv9a9k author: Chiang, Chi-Huei title: Eight-Month Prospective Study of 14 Patients With Hospital-Acquired Severe Acute Respiratory Syndrome date: 2004-11-30 words: 4220.0 sentences: 229.0 pages: flesch: 47.0 cache: ./cache/cord-304201-fziv9a9k.txt txt: ./txt/cord-304201-fziv9a9k.txt summary: CONCLUSION The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. Although several case series of SARS have been reported, 7-9 to our knowledge, a prospective clinical study including long-term follow-up assessment by chest radiography, chest high-resolution computed tomography (HRCT), and pulmonary function testing has not been reported, particularly for hospital-acquired cases. abstract: OBJECTIVE To define the clinical characteristics and clinical course of hospital-acquired severe acute respiratory syndrome (SARS). PATIENTS AND METHODS This 8-month prospective study of 14 patients with hospital-acquired SARS in Taipei, Taiwan, was conducted from April through December 2003. RESULTS The most common presenting symptoms in our 14 patients with hospital-acquired SARS were fever, dyspnea, dizziness, malaise, diarrhea, dry cough, muscle pain, and chills. Lymphopenia and elevated serum levels of lactate dehydrogenase (LDH) and C-reactive protein (CRP) were the most common initial laboratory findings. Initial chest radiographs revealed various pattern abnormalities and normal results. Five of the 14 patients required mechanical ventilation. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. Clinical severity of disease varied from mild to severe. At 8 months after disease onset, patients with mild or moderate SARS had normal findings or only focal fibrosis on chest high-resolution computed tomography. However, bilateral fibrotic changes remained in the 4 patients who had recovered from severe SARS, 1 of whom had mild restrictive ventilatory impairment. One patient with severe SARS died; she was elderly and had other comorbidities. Five additional patients had reduced diffusing capacity. CONCLUSION The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. Substantially elevated levels of LDH and CRP correlated with severe illness requiring mechanical ventilatory support. In those receiving mechanical ventilation, pulmonary function was only mildly reduced at 6 to 8 months after acute illness, consistent with the natural history of acute respiratory distress syndrome due to other causes. url: https://www.sciencedirect.com/science/article/pii/S0025619611621836 doi: 10.4065/79.11.1372 id: cord-308451-pmwmfl3w author: Chiang, Shu-Fen title: SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells date: 2010-07-27 words: 6273.0 sentences: 345.0 pages: flesch: 51.0 cache: ./cache/cord-308451-pmwmfl3w.txt txt: ./txt/cord-308451-pmwmfl3w.txt summary: In this report, we showed that spike protein of SARS virus could induce phenotypic conversion of human B cells, either from peripheral blood or B lymphoma cells, to macrophage-like cells that were steadily losing the B-cell marker CD19 and in turn expressing the macrophage-specific marker Mac-1. In conclusion, our results suggest that conversion of B cells to macrophage-like cells, similar to a pathophysiological response, could be mediated by a devastating viral ligand, in particular spike protein of SARS virus, or in combination with severe local hypoxia, which is a condition often observed in afflicted lungs of SARS patients. Our results show that spike protein of SARS displayed on recombinant baculovirus or prolonged exposure to hypoxia can trigger the conversion of peripheral B cells and B lymphoma cells into Mac-1 positive macrophage-like cells. As determined by microarray analysis, expression of CD86 (B7-2) gene was rapidly induced in B lymphoma cells within 12 h of SSDRB treatment (Fig. 4B) . abstract: Massive aggregations of macrophages are frequently detected in afflicted lungs of patients with severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection. In vitro, ectopic expression of transcription factors, in particular CCAAT/enhancer-binding protein alpha (C/EBPα) and C/EBPβ, can convert B cells into functional macrophages. However, little is known about the specific ligands responsible for such phenotype conversion. Here, we investigated whether spike protein of SARS-CoV can act as a ligand to trigger the conversion of B cells to macrophages. We transduced SARS-CoV spike protein-displayed recombinant baculovirus (SSDRB), vAtEpGS688, into peripheral B cells and B lymphoma cells. Cell surface expression of CD19 or Mac-1 (CD11b) was determined by flow cytometry. SSDRB-mediated changes in gene expression profiles of B lymphoma cells were analyzed by microarray. In this report, we showed that spike protein of SARS virus could induce phenotypic conversion of human B cells, either from peripheral blood or B lymphoma cells, to macrophage-like cells that were steadily losing the B-cell marker CD19 and in turn expressing the macrophage-specific marker Mac-1. Furthermore, we found that SSDRB enhanced the expression of CD86, hypoxia-inducible factor-1α (HIF1α), suppressor of cytokine signaling (SOCS or STAT-induced STAT inhibitor)-3, C/EBPβ, insulin-like growth factor-binding protein 3 (IGFBP3), Krüpple-like factor (KLF)-5, and CD54, without marked influence on C/EBPα or PU.1 expression in transduced cells. Prolonged exposure to hypoxia could also induce macrophage-like conversion of B cells. These macrophage-like cells were defective in phagocytosis of red fluorescent beads. In conclusion, our results suggest that conversion of B cells to macrophage-like cells, similar to a pathophysiological response, could be mediated by a devastating viral ligand, in particular spike protein of SARS virus, or in combination with severe local hypoxia, which is a condition often observed in afflicted lungs of SARS patients. url: https://www.ncbi.nlm.nih.gov/pubmed/20667598/ doi: 10.1016/j.molimm.2010.06.014 id: cord-255782-w6nfkdok author: Chikhale, Rupesh V. title: Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach date: 2020-06-22 words: 5638.0 sentences: 276.0 pages: flesch: 51.0 cache: ./cache/cord-255782-w6nfkdok.txt txt: ./txt/cord-255782-w6nfkdok.txt summary: somnifera in comparison to reference drugs (hydroxychloroquine, lopinavir and remdesivir) against two different protein targets, that is, NSP15 endoribonuclease and prefusion spike RBD from SARS-CoV-2 using in-silico docking simulation and molecular dynamics (MD) study. The top three binding energy scorer ligand to each protein, that is, QGRG, Withanoside X and Ashwagandhanolide for spike RBD and QGRG, Dihydrowithaferin A and Withanolide N for NSP15 Endoribonuclease were selected for further MD study. Therefore, in the present study 100 ns of MD simulations were performed for all selected best six docked complexes to observe how the interaction pattern of the binding site of NSP15 endoribonuclease and spike RBD from SARS CoV-2 adapts to the docked bioactive. The phytochemicals Ashwagandhanolide, QGRG and Withanoside X in complex with the SARS-CoV-2 spike protein (PDB: 6M0J) were selected for the MDS based on molecular docking study results. abstract: COVID-19 has ravaged the world and is the greatest of pandemics in modern human history, in the absence of treatment or vaccine, the mortality and morbidity rates are very high. The present investigation identifies potential leads from the plant Withania somnifera (Indian ginseng), a well-known antiviral, immunomodulatory, anti-inflammatory and a potent antioxidant plant, using molecular docking and dynamics studies. Two different protein targets of SARS-CoV-2 namely NSP15 endoribonuclease and receptor binding domain of prefusion spike protein from SARS-CoV-2 were targeted. Molecular docking studies suggested Withanoside X and Quercetin glucoside from W. somnifera have favorable interactions at the binding site of selected proteins, that is, 6W01 and 6M0J. The top-ranked phytochemicals from docking studies, subjected to 100 ns molecular dynamics (MD) suggested Withanoside X with the highest binding free energy (ΔG(bind) = −89.42 kcal/mol) as the most promising inhibitor. During MD studies, the molecule optimizes its conformation for better fitting with the receptor active site justifying the high binding affinity. Based on proven therapeutic, that is, immunomodulatory, antioxidant and anti-inflammatory roles and plausible potential against n-CoV-2 proteins, Indian ginseng could be one of the alternatives as an antiviral agent in the treatment of COVID 19. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32568012/ doi: 10.1080/07391102.2020.1778539 id: cord-308066-lrbi5198 author: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 words: 15698.0 sentences: 714.0 pages: flesch: 41.0 cache: ./cache/cord-308066-lrbi5198.txt txt: ./txt/cord-308066-lrbi5198.txt summary: The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). abstract: The uneven standards of surveillance, human- or animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. As of 2006, there appears to be little scientific, social, or political consensus that animalbased surveillance for zoonoses merits investment in international infrastructure, other than the fledgling efforts with avian influenza, or targeted nontraditional avenues of surveillance and research. url: https://www.ncbi.nlm.nih.gov/pubmed/17848073/ doi: 10.1007/978-3-540-70962-6_16 id: cord-324953-3sacf4wu author: Childs, James E. title: Introduction: Conceptualizing and Partitioning the Emergence Process of Zoonotic Viruses from Wildlife to Humans date: 2007 words: 9017.0 sentences: 379.0 pages: flesch: 40.0 cache: ./cache/cord-324953-3sacf4wu.txt txt: ./txt/cord-324953-3sacf4wu.txt summary: The process of zoonotic disease emergence can be understood by coupling knowledge of how zoonotic viruses have evolved and are maintained among their wildlife hosts, transmitted across a species barrier to cause productive infection in a taxonomically distinct secondary host, initiate a pathologic process causing disease, and, by repetitive infection within the secondary host species, result in incident morbidity or mortality of sufficient magnitude to be detected and characterized as a novel health concern of local, regional, or global significance (see the chapter by Childs, this volume). The ecologic process of zoonotic disease emergence can be schematized by four transition stages (Fig. 1 ) , of which only the first two are prerequisites for emergence: (1) contact between infectious propagules originating from the wildlife H R with individuals of a susceptible H S and (2) cross-species transmission, a transition subsuming the complex interactions of the virus infectious cycle within the H S (Nayak 2000; Childs 2004 ). abstract: This introduction provides a telegraphic overview of the processes of zoonotic viral emergence, the intricacies of host–virus interactions, and the distinct role of biological transitions and modifying factors. The process of emergence is conceptualized as two transition stages which are common and required for all disease emergence, (1) human contact with the infectious agent and (2) cross-species transmission of the agent, and two transition stages which are not required for emergence and appear unavailable to many zoonotic pathogens, (3) sustained human-to-human transmission and (4) genetic adaptation to the human host. The latter two transitions are presumably prerequisites for the pandemic emergence of a pathogen. The themes introduced herein are amplified and explored in detail by the contributors to this volume. Each author explores the mechanisms and unique circumstances by which evolution, biology, history, and current context have contrived to drive the emergence of different zoonotic agents by a series of related events; although recognizable similarities exist among the events leading to emergence the details and circumstances are never repetitive. url: https://www.ncbi.nlm.nih.gov/pubmed/17848058/ doi: 10.1007/978-3-540-70962-6_1 id: cord-308231-1t70vkxm author: Childs, S. J. title: Could Deficiencies in South African Data Be the Explanation for Its Early SARS-CoV-2 Peak? date: 2020-09-02 words: 3167.0 sentences: 191.0 pages: flesch: 64.0 cache: ./cache/cord-308231-1t70vkxm.txt txt: ./txt/cord-308231-1t70vkxm.txt summary: It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, while the second is that of an imperceptible, pre-existing, immune fraction of the population. This fact, alone, is nonetheless unable to reasonably explain the SARS-CoV-2 threshold observed in the South African data, without contemplating improbably-high, though not impossible, values. It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, denoted a, while the second is that of an imperceptible, pre-existing, immune fraction of the population, denoted b. The phenomenon of infections having been underestimated by a multiplicative factor, alone, is unable to comprehensively explain the SARS-CoV-2 peak observed in the South African data, without contemplating improbably-high values. abstract: The SARS-CoV-2 pandemic peaked very early in comparison to the thresholds predicted by an analysis of prior lockdown regimes. The most convenient explanation is that some, external factor changed the value of the basic reproduction number, r0; and there certainly are arguments for this. Other factors could, nonetheless, have played a role. This research attempts to reconcile the observed peak with the thresholds predicted by lockdown regimes similar to the one in force at the time. It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, while the second is that of an imperceptible, pre-existing, immune fraction of the population. While it is shown that it certainly is possible to manufacture the perception of an early peak as extreme as the one observed, solely by way of these two phenomena, the values need to be fairly high. The phenomena would not, by any measure, be insignificant. It also remains an inescapable fact that the early peak in infections coincided with a fairly profound change in r0; in all the contemplated scenarios of data-deficiency. url: http://medrxiv.org/cgi/content/short/2020.08.31.20185108v1?rss=1 doi: 10.1101/2020.08.31.20185108 id: cord-337700-2n9tswr8 author: Chilimuri, Sridhar title: Predictors of Mortality in Adults Admitted with COVID-19: Retrospective Cohort Study from New York City date: 2020-07-08 words: 2355.0 sentences: 146.0 pages: flesch: 51.0 cache: ./cache/cord-337700-2n9tswr8.txt txt: ./txt/cord-337700-2n9tswr8.txt summary: On multiple regression analysis, increasing odds of mortality during hospitalization was associated with older age (odds ratio [OR] 1.04; 95% confidence interval [CI], 1.01–1.06 per year increase; p < 0.0001), admission D-dimer more than 1000 nanograms per milliliter (ng/mL) (OR 3.16; 95% CI, 1.75–5.73; p<0.0001), admission C-reactive protein (CRP) levels of more than 200 milligrams per liter (mg/L) (OR 2.43; 95% CI, 1.36–4.34; p = 0.0028), and admission lymphopenia (OR 2.63; CI, 1.47–4.69; p 0.0010). CONCLUSION: In this retrospective cohort study originating in NYC, older age, admission levels of D-dimer of more than 1000 ng/mL, CRP of more than 200 mg/L and lymphopenia were associated with mortality in individuals hospitalized for COVID-19. In the final analysis, we excluded the following patients: those whose SARS-Cov-2 results were pending or whose definitive outcomes were not available at the time of the study as they were still hospitalized; and those with incomplete information. abstract: INTRODUCTION: Rapid spread of coronavirus disease 2019 (COVID-19) in the United States, especially in New York City (NYC), led to a tremendous increase in hospitalizations and mortality. There is very limited data available that associates outcomes during hospitalization in patients with COVID-19. METHODS: In this retrospective cohort study, we reviewed the health records of patients with COVID-19 who were admitted from March 9–April 9, 2020, to a community hospital in NYC. Subjects with confirmed reverse transcriptase-polymerase chain reaction (RT-PCR) of the nasopharyngeal swab for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were included. We collected data related to demographics, laboratory results, and outcome of hospitalization. Outcome was measured based on whether the patient was discharged home or died during hospitalization. RESULTS: There were 888 consecutive admissions with COVID-19 during the study period, of which 513 were excluded with pending outcome or incomplete information. We included a total of 375 patients in the study, of whom 215 (57%) survived and 160 (43%) died during hospitalization. The majority of patients were male (63%) and of Hispanic origin (66%) followed by Blacks (25%), and others (9%). Hypertension (60%) stands out to be the most common comorbidity followed by diabetes mellitus (47%), cardiovascular disease (17%), chronic kidney disease (17%), and human immunodeficiency virus/acquired immunodeficiency syndrome (9%). On multiple regression analysis, increasing odds of mortality during hospitalization was associated with older age (odds ratio [OR] 1.04; 95% confidence interval [CI], 1.01–1.06 per year increase; p < 0.0001), admission D-dimer more than 1000 nanograms per milliliter (ng/mL) (OR 3.16; 95% CI, 1.75–5.73; p<0.0001), admission C-reactive protein (CRP) levels of more than 200 milligrams per liter (mg/L) (OR 2.43; 95% CI, 1.36–4.34; p = 0.0028), and admission lymphopenia (OR 2.63; CI, 1.47–4.69; p 0.0010). CONCLUSION: In this retrospective cohort study originating in NYC, older age, admission levels of D-dimer of more than 1000 ng/mL, CRP of more than 200 mg/L and lymphopenia were associated with mortality in individuals hospitalized for COVID-19. We recommend using these risk factors on admission to triage patients to critical care units or surge units to maximize the use of surge capacity beds. url: https://www.ncbi.nlm.nih.gov/pubmed/32726241/ doi: 10.5811/westjem.2020.6.47919 id: cord-264042-4hc2i25r author: Chim, Harvey title: Severe Acute Respiratory Syndrome in a Naval Diver date: 2006-06-17 words: 2133.0 sentences: 132.0 pages: flesch: 50.0 cache: ./cache/cord-264042-4hc2i25r.txt txt: ./txt/cord-264042-4hc2i25r.txt summary: In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive. S evere acute respiratory syndrome (SARS) is an emerging infectious disease that was first reported in Guangdong Province in southern China in November 2002 and subsequently caused outbreaks in Singapore, Hong Kong, Southeast Asia, and Canada. In the week following diagnosis of SARS in this patient, only essential personnel in the diving unit were required to report to work to prevent the possible spread of SARS. abstract: Severe acute respiratory syndrome (SARS) is a highly infectious, rapidly progressive, emerging disease. Early diagnosis and preventive measures are key for treatment and minimization of secondary spread. In the context of the armed forces, aggressive containment measures are essential to prevent an outbreak. In this study, we present the first reported case, to our knowledge, of SARS in a naval diver. The special physical requirements for divers and the potential complications associated with deep sea diving necessitate extensive investigation before certification of fitness for diving after SARS. In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. Problems in the late recovery period include increased risk of diving complications (such as pulmonary barotrauma) resulting from fibrosis and scarring within the lung parenchyma, which are known complications of SARS. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive. url: https://www.ncbi.nlm.nih.gov/pubmed/16808126/ doi: 10.7205/milmed.171.6.491 id: cord-016160-ugc7ce21 author: Ching, Frank title: Bird Flu, SARS and Beyond date: 2018-03-15 words: 19410.0 sentences: 1034.0 pages: flesch: 62.0 cache: ./cache/cord-016160-ugc7ce21.txt txt: ./txt/cord-016160-ugc7ce21.txt summary: At the end of 2002, unknown to anyone in Hong Kong, another deadly virus was circulating in neighboring Guangdong Province, propagating a disease that had no name but which was preliminarily dubbed atypical pneumonia in China and later renamed Severe Acute Respiratory Syndrome, or SARS, by the World Health Organization. And now it''s been identified by all the other laboratories." 76 Also, just as Hong Kong University publicized its breakthrough before the CDC''s announcement, so the university was able to get its scientific discovery into print first, with the publication of a paper in the online Lancet on April 8, 2003, "Coronavirus as a possible cause of severe acute respiratory syndrome." The success was very much the result of a group effort, as the list of authors shows, with Malik Peiris as the lead writer, K.Y. Yuen as the last writer and others, including Guan Yi, Leo Poon, John Nicholls and K.H. Chan, in between. abstract: In the politically sensitive year of 1997, Hong Kong experienced an outbreak of avian flu when the deadly H5N1 virus unprecedentedly jumped the species barrier from chickens and infected human beings. Hong Kong decided to slaughter over a million chickens, and the virus was stopped in its tracks. In 2003, Hong Kong was the epicenter of the SARS pandemic, which originated in Guangdong province. The Faculty of Medicine played key roles in both instances, with its Microbiology Department successfully identifying a novel coronavirus as being responsible for SARS. Hong Kong learned from its experience and took action to combat the emergence of new infectious diseases. Such vigilance paid off in 2009, when swine flu swept the world, and in 2013, when a novel avian flu H7N9 emerged in China. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120366/ doi: 10.1007/978-981-10-6316-9_14 id: cord-274141-vujx538o author: Chinsembu, Kazhila C. title: Coronaviruses and Nature’s Pharmacy for the Relief of Coronavirus Disease 2019 date: 2020-10-06 words: 11338.0 sentences: 676.0 pages: flesch: 53.0 cache: ./cache/cord-274141-vujx538o.txt txt: ./txt/cord-274141-vujx538o.txt summary: De Clercq (2005 suggested that it was feasible to develop SARS-CoV fusion inhibitors analogous to enfuvirtide, a linear 36-amino acid synthetic peptide marketed under the trade name Fuzeon, an approved anti-HIV drug that inhibits the entry of the virus into cells. It was hypothesized that specific flavonoids, such as quercetin, hesperetin, and myricetin (7) and their glycosylated derivatives, may play an effective role in inhibiting SARS-CoV entry into host cells, specifically by binding with high affinity to the spike protein, helicase, and protease sites on the ACE receptor (Ngwa et al. Although the ongoing SARS-CoV-2 global pandemic should remind scientists that current options for treating life-threatening zoonotic coronavirus infections are very limited , medicinal plants offer a strong pipeline for the discovery of novel lead compounds that can be converted into new drugs to treat COVID-19. abstract: [Image: see text] url: https://doi.org/10.1007/s43450-020-00104-7 doi: 10.1007/s43450-020-00104-7 id: cord-272414-oo8kcuf3 author: Chiocchetti, Roberto title: ACE2 Expression in the Cat and the Tiger Gastrointestinal Tracts date: 2020-08-13 words: 3005.0 sentences: 161.0 pages: flesch: 52.0 cache: ./cache/cord-272414-oo8kcuf3.txt txt: ./txt/cord-272414-oo8kcuf3.txt summary: Although the evidence of ACE2-IR in the feline GIT does not necessarily indicate the possibility of viral replication and SARS-CoV-2 spread with stool, the findings in the present study could serve as an anatomical basis for additional studies considering the risk of the SARS-CoV-2 fecal-oral transmission between cats/felids, and between cats/felids and humans. Since the necessary condition for the enteric multiplication of SARS-CoV-2 is represented by the expression of its election receptor on the host cells, the present study immunohistochemically investigated the localization of ACE2 in the GIT of feline domestic (cat) and wild (tiger) species. The present study described the expression of the ACE2 receptor in the stomach and intestine of the cat and tiger for the first time and highlighted the GIT as a potential site of SARS-CoV-2 replication. abstract: Angiotensin-converting enzyme 2 (ACE2) has been identified as the functional receptor for Severe Acute Respiratory Syndrome—Coronavirus−2 (SARS-CoV-2). It has been identified in the human gastrointestinal tract (GIT), and SARS-CoV-2 has been isolated in human and animal fecal samples. The aim of the present study was to investigate the expression of ACE2 in the gastrointestinal tract of domestic (cat) and wild (tiger) felines. Samples of the pylorus, duodenum, and distal colon were collected from six cats and one tiger. The tissues were processed for immunofluorescence assay with an anti-human ACE2 antibody. Angiotensin-converting enzyme 2 was widely expressed in the gastrointestinal mucosa of the cats and the tiger. In both the species, ACE2-immunoreactivity (ACE2-IR) was expressed by the mucosal epithelial cells of the GIT and by the enteric neurons. In the cats, ACE2-IR was also expressed by the smooth muscle cells of the blood vessels and the tunica muscularis. The expression of the ACE2 receptor in enteric neurons may support the potential neurotropic properties of SARS-CoV-2. Although the evidence of ACE2-IR in the feline GIT does not necessarily indicate the possibility of viral replication and SARS-CoV-2 spread with stool, the findings in the present study could serve as an anatomical basis for additional studies considering the risk of the SARS-CoV-2 fecal-oral transmission between cats/felids, and between cats/felids and humans. url: https://doi.org/10.3389/fvets.2020.00514 doi: 10.3389/fvets.2020.00514 id: cord-264333-mgeicojq author: Chiotos, Kathleen title: Multisystem Inflammatory Syndrome in Children During the Coronavirus 2019 Pandemic: A Case Series date: 2020-05-28 words: 2490.0 sentences: 165.0 pages: flesch: 51.0 cache: ./cache/cord-264333-mgeicojq.txt txt: ./txt/cord-264333-mgeicojq.txt summary: On 6 May 2020, authors from London, England, reported clinical and laboratory features of a cluster of 8 children with hyperinflammatory shock, all of whom tested positive for SARS-CoV-2 antibodies [1] . To evaluate for incomplete Kawasaki disease/Kawasaki disease shock syndrome, an echocardiogram was performed on HD 6 that demonstrated normal biventricular systolic function (shortening fraction [SF], 38%; normal, 28%-45%) but identified right coronary artery dilation (Boston z score, 3.15). A 12-year-old male with no chronic medical conditions presented to an outside facility with a 6-day history of fever, Nasopharyngeal SARS-CoV-2 PCR was negative. Her lowest documented blood pressure within 24 hours of her PICU admission was 92/50 mm Hg. A repeat SARS-CoV-2 nasopharyngeal PCR was positive with a high cycle threshold (37.54). Further, for some patients, fever and gastrointestinal symptoms preceded the development of other "classic" clinical features of Kawasaki disease, including rash, conjunctivitis, mucous membrane changes, and extremity edema, which were variably present in our cohort. abstract: We present a series of 6 critically ill children with multisystem inflammatory syndrome in children. Key findings of this syndrome include fever, diarrhea, shock, and variable presence of rash, conjunctivitis, extremity edema, and mucous membrane changes. url: https://www.ncbi.nlm.nih.gov/pubmed/32463092/ doi: 10.1093/jpids/piaa069 id: cord-344486-iu5flbcl author: Chiotos, Kathleen title: Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2 date: 2020-09-12 words: 8595.0 sentences: 416.0 pages: flesch: 37.0 cache: ./cache/cord-344486-iu5flbcl.txt txt: ./txt/cord-344486-iu5flbcl.txt summary: In the few months since this initial publication, new evidence has emerged demonstrating the efficacy of the antiviral medication remdesivir in shortening time to clinical recovery in adults with COVID-19, while several other studies have shown ineffectiveness of hydroxychloroquine and lopinavir-ritonavir (4) (5) (6) (7) (8) . Further, additional observational studies have provided insight into the clinical epidemiology of COVID-19 in children, demonstrating that while most young patients experience mild illness, a small proportion develop severe illness associated with adverse clinical outcomes, including need for pediatric intensive care unit (PICU) admission and mortality (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) . Nevertheless, the panel recognizes that pediatric clinicians are likely to consider comorbidities when weighing the risks and benefits of antiviral therapy on a case-bycase basis, and in making these decisions may consider: 1) the available, albeit limited, pediatric COVID-19 literature; 2) risk factors associated with severe COVID-19 in adults; and 3) pre-existing medical conditions in children associated with worse clinical outcomes for other viral infections. abstract: BACKGROUND: Although Coronavirus Disease 2019 (COVID-19) is a mild infection in most children, a small proportion develop severe or critical illness. Data evaluating agents with potential antiviral activity continue to expand, such that updated guidance is needed regarding use of these agents in children. METHODS: A panel of pediatric infectious diseases physicians and pharmacists from 20 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of the best available evidence and expert opinion. RESULTS: Given the typically mild course of COVID-19 in children, supportive care alone is suggested for most cases. For children with severe illness, defined as a supplemental oxygen requirement without need for non-invasive or invasive mechanical ventilation or extra-corporeal membrane oxygenation (ECMO), remdesivir is suggested, preferably as part of a clinical trial if available. Remdesivir should also be considered for critically ill children requiring invasive or non-invasive mechanical ventilation or ECMO. A duration of 5 days is appropriate for most patients. The panel recommends against the use of hydroxychloroquine or lopinavir-ritonavir (or other protease inhibitors) for COVID-19 in children. CONCLUSIONS: Antiviral therapy for COVID-19 is not necessary for the great majority of pediatric patients. For children with severe or critical disease, this guidance offers an approach for decision-making regarding use of remdesivir. url: https://www.ncbi.nlm.nih.gov/pubmed/32918548/ doi: 10.1093/jpids/piaa115 id: cord-341620-nmrkhx5t author: Chirico, Francesco title: Can Air-Conditioning Systems Contribute to the Spread of SARS/MERS/COVID-19 Infection? Insights from a Rapid Review of the Literature date: 2020-08-20 words: 4577.0 sentences: 241.0 pages: flesch: 44.0 cache: ./cache/cord-341620-nmrkhx5t.txt txt: ./txt/cord-341620-nmrkhx5t.txt summary: Therefore, to evaluate the COVID-19 risk associated with the presence of air-conditioning systems, we conducted a rapid review of the literature concerning outbreaks of coronaviruses (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) in indoor environments. We utilized the participants-exposure-comparisons-outcome (PECOS) criteria, and we defined them according to evidence-based practice [32] -P (participants) is human subjects residing in indoor environments, E (exposure) is exposed to air-conditioning systems (HVAC), C (comparisons) is any comparison between the pathogens under study, and O (outcome) is respiratory infection outbreaks caused by SARS-CoV-1, MERS-CoV, or SARS CoV-2. A retrospective study of on outbreak involving 74 patients in the same hospital indicated that the rapid evaporation of the droplets produced by coughing in a relatively dry, air-conditioned environment, could also induce virus-laden aerosol, which was probably responsible for spreading the infection to patients who were not in the same room [35] . abstract: The airborne transmission of SARS-CoV-2 is still debated. The aim of this rapid review is to evaluate the COVID-19 risk associated with the presence of air-conditioning systems. Original studies (both observational and experimental researches) written in English and with no limit on time, on the airborne transmission of SARS-CoV, MERS-CoV, and SARS-CoV-2 coronaviruses that were associated with outbreaks, were included. Searches were made on PubMed/MEDLINE, PubMed Central (PMC), Google Scholar databases, and medRxiv. A snowball strategy was adopted to extend the search. Fourteen studies reporting outbreaks of coronavirus infection associated with the air-conditioning systems were included. All studies were carried out in the Far East. In six out the seven studies on SARS, the role of Heating, Ventilation, and Air Conditioning (HVAC) in the outbreak was indirectly proven by the spatial and temporal pattern of cases, or by airflow-dynamics models. In one report on MERS, the contamination of HVAC by viral particles was demonstrated. In four out of the six studies on SARS-CoV-2, the diffusion of viral particles through HVAC was suspected or supported by computer simulation. In conclusion, there is sufficient evidence of the airborne transmission of coronaviruses in previous Asian outbreaks, and this has been taken into account in the guidelines released by organizations and international agencies for controlling the spread of SARS-CoV-2 in indoor environments. However, the technological differences in HVAC systems prevent the generalization of the results on a worldwide basis. The few COVID-19 investigations available do not provide sufficient evidence that the SARS-CoV-2 virus can be transmitted by HVAC systems. url: https://doi.org/10.3390/ijerph17176052 doi: 10.3390/ijerph17176052 id: cord-276969-mdry8qzv author: Chirumbolo, Salvatore title: Might the many positive COVID19 subjects in Italy have been caused by resident bat‐derived zoonotic β‐coronaviruses instead of the Wuhan (China) outbreak? date: 2020-03-27 words: 865.0 sentences: 57.0 pages: flesch: 50.0 cache: ./cache/cord-276969-mdry8qzv.txt txt: ./txt/cord-276969-mdry8qzv.txt summary: Might the many positive COVID19 subjects in Italy have been caused by resident bat-derived zoonotic β-coronaviruses instead of the Wuhan (China) outbreak? The same authors concluded that the SARS-CoV2 in Italy might be present at least since September and October 2019, much before the claimed Wuhan outbreak. Questions may be raised, therefore, if, taking into account the genomic distance (or similarity) and the RNA-virus mutation rate, the "Italian" SARS-CoV2 might be the evolutionary balanced genotype (or strain) from a resident zoonotic spillover. 3 This should suggest that the cross-talk between evolution and epidemiology is closely intertwined, causing that the maintenance of an onward transmission might be crucially asThe issue of human coronaviruses virulence was recently addressed for SARS-CoV and MERS-CoV and some reports have outlined the role of coronavirus E protein in triggering an inflammatory response, cytokine storm, and/or inhibition of the innate immunity with dampening Th1 interferon-γ signaling. abstract: nan url: https://doi.org/10.1002/jmv.25777 doi: 10.1002/jmv.25777 id: cord-333498-d25qfq0f author: Chitranshi, Nitin title: Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL(pro) targeting repurposed drug candidates date: 2020-07-09 words: 5999.0 sentences: 378.0 pages: flesch: 51.0 cache: ./cache/cord-333498-d25qfq0f.txt txt: ./txt/cord-333498-d25qfq0f.txt summary: Recent release of the high-resolution crystal structure for the main proteinase 3CL pro (Protein Data Bank, PDB ID: 6Y2G), describing an additional amide bond with the α-ketoamide inhibitor pyridone ring to enhance the half-life of the compound in plasma [16] is suggested to accelerate the targeted drug discovery efforts. Since the initial stages of the SARS-CoV-2 outbreak, laboratories and hospitals around the world have sequenced viral genome data with unprecedented speed, enabling real-time understanding of this novel disease process, which will hopefully contribute to the development of novel candidate drugs. In contrast, our docking studies revealed that bilobetin, predicted almost comparable binding energy with that of amentaflavone (− 8.29 kcal/mol) suggesting that mutation in SARS-CoV-2 3CL pro could potentially disrupt hydrogen bonding or induce some conformational change that could result in alterations in the binding site thus affecting inhibitor interactions with the enzyme active site residues. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) has been initiating pandemics since the beginning of the century. In December 2019, the world was hit again by a devastating SARS episode that has so far infected almost four million individuals worldwide, with over 200,000 fatalities having already occurred by mid-April 2020, and the infection rate continues to grow exponentially. SARS coronavirus 2 (SARS-CoV-2) is a single stranded RNA pathogen which is characterised by a high mutation rate. It is vital to explore the mutagenic capability of the viral genome that enables SARS-CoV-2 to rapidly jump from one host immunity to another and adapt to the genetic pool of local populations. METHODS: For this study, we analysed 2301 complete viral sequences reported from SARS-CoV-2 infected patients. SARS-CoV-2 host genomes were collected from The Global Initiative on Sharing All Influenza Data (GISAID) database containing 9 genomes from pangolin-CoV origin and 3 genomes from bat-CoV origin, Wuhan SARS-CoV2 reference genome was collected from GeneBank database. The Multiple sequence alignment tool, Clustal Omega was used for genomic sequence alignment. The viral replicating enzyme, 3-chymotrypsin-like cysteine protease (3CL(pro)) that plays a key role in its pathogenicity was used to assess its affinity with pharmacological inhibitors and repurposed drugs such as anti-viral flavones, biflavanoids, anti-malarial drugs and vitamin supplements. RESULTS: Our results demonstrate that bat-CoV shares > 96% similar identity, while pangolin-CoV shares 85.98% identity with Wuhan SARS-CoV-2 genome. This in-depth analysis has identified 12 novel recurrent mutations in South American and African viral genomes out of which 3 were unique in South America, 4 unique in Africa and 5 were present in-patient isolates from both populations. Using state of the art in silico approaches, this study further investigates the interaction of repurposed drugs with the SARS-CoV-2 3CL(pro) enzyme, which regulates viral replication machinery. CONCLUSIONS: Overall, this study provides insights into the evolving mutations, with implications to understand viral pathogenicity and possible new strategies for repurposing compounds to combat the nCovid-19 pandemic. url: https://doi.org/10.1186/s12967-020-02448-z doi: 10.1186/s12967-020-02448-z id: cord-217961-2rczhxp2 author: Chitsaz, Mohsen title: A small molecule drug candidate targeting SARS-CoV-2 main protease date: 2020-06-16 words: 2298.0 sentences: 133.0 pages: flesch: 56.0 cache: ./cache/cord-217961-2rczhxp2.txt txt: ./txt/cord-217961-2rczhxp2.txt summary: We aligned the inhibitor on the protein and on the initial conformation of the ligand and computed structural deviations RMSDs. To observe the interaction of the inhibitor with the active site and confirming that the inhibitor stays in the active site of SARS-CoV-2 protease, we ran a simulation of 250ns that was 10 times longer than two previous MD simulations. For each of the two complexes, we analyzed the active-site by investigating all hydrophobic, H-bond, ionic and water bridge interactions of the inhibitor with SARS-Cov-2 protease and SARS-CoV protease (see Fig. 5 and Fig. 6 respectively) . We observed that the inhibitor remains in the active site for the entire duration of the simulation and maintains H-bond and water bridge contacts with GLU166 and hydrophobic Pi-Pi stacking contact with HIS41 (see Fig. 13 ). Our primary observation was that the molecule remained in the active site of SARS-CoV-2 protease for the entire duration of the simulation. abstract: A new coronavirus identified as SARS-CoV-2 virus has brought the world to a state of crisis, causing a major pandemic, claiming more than 433,000 lives and instigating major financial damage to the global economy. Despite current efforts, developing safe and effective treatments remains a major challenge. Moreover, new strains of the virus are likely to emerge in the future. To prevent future pandemics, several drugs with various mechanisms of action are required. Drug discovery efforts against the virus fall into two main categories: (a) monoclonal antibodies targeting the spike protein of the virus and blocking it from entry; (b) small molecule inhibitors targeting key proteins of the virus, interfering with replication and translation of the virus. In this study, we are presenting a computational investigation of a potential drug candidate that targets SARS-CoV-2 protease, a viral protein critical for replication and translation of the virus. url: https://arxiv.org/pdf/2006.09125v2.pdf doi: nan id: cord-290333-996tmrgo author: Chiu, Cheng-Hsun title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic date: 2020-07-23 words: 1051.0 sentences: 74.0 pages: flesch: 54.0 cache: ./cache/cord-290333-996tmrgo.txt txt: ./txt/cord-290333-996tmrgo.txt summary: title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic 7 Soon on March 23, the US Food and Drug Administration (FDA) responded that the following actions be taken: donor screening with questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2 and testing donors and/ or donor stool for SARS-CoV-2, to ensure the safety of FMT. 8e12 In addition to the recommended testing procedures, all the screening protocols include questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2. Safety alert regarding use of fecal microbiota for transplantation and additional safety protections pertaining to SARS-CoV-2 and COVID-19 Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward Additional safety protections relating to COVID-19 for faecal microbiota transplant (FMT) products Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0929664620303405 doi: 10.1016/j.jfma.2020.07.028 id: cord-312170-p2yrbosz author: Chiu, Man-Chun title: Suggested management of immunocompromized kidney patients suffering from SARS date: 2003-10-24 words: 832.0 sentences: 57.0 pages: flesch: 55.0 cache: ./cache/cord-312170-p2yrbosz.txt txt: ./txt/cord-312170-p2yrbosz.txt summary: The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial. The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial, and little is known worldwide about the treatment for SARS kidney transplant patients. It seems children suffered much less from the infection than adults, although some adolescents could have severe lung involvement [3, 4, 5] . In Hong Kong, 7 of 19 adult ESRD patients on haemodialysis or peritoneal dialysis infected with SARS died (C.B. Leung et al., pers. Paediatric nephrologists should be on the alert for SARS, because we have to care for a group of immunocompromised patients including those transplant children. Cumulative number of reported probable cases of severe acute respiratory syndrome (SARS) www Clinical presentations and outcome of severe acute respiratory syndrome in children Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong Treatment of severe acute respiratory syndrome with convalescent plasma abstract: The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial. Herein we report our experience in treating approximately 40 SARS children and adolescents. Treatment of SARS kidney patients is limited. Paediatric nephrologists should be on the alert for SARS in order to care for immunocompromised patients. Precautions should be made for both staff and patients with protective measures for infection control. url: https://www.ncbi.nlm.nih.gov/pubmed/14663579/ doi: 10.1007/s00467-003-1325-8 id: cord-324638-gwd8qin6 author: Chiu, Rossa WK title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 words: 3360.0 sentences: 152.0 pages: flesch: 49.0 cache: ./cache/cord-324638-gwd8qin6.txt txt: ./txt/cord-324638-gwd8qin6.txt summary: We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. abstract: BACKGROUND: We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS) based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR). In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay. METHODS: An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics) was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen) for quantitative performance, analytical sensitivity and precision. RESULTS: The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method. CONCLUSION: As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method. url: https://www.ncbi.nlm.nih.gov/pubmed/16466582/ doi: 10.1186/1471-2334-6-20 id: cord-350212-448mv4lt author: Chiuppesi, Flavia title: Development of a Multi-Antigenic SARS-CoV-2 Vaccine Using a Synthetic Poxvirus Platform date: 2020-07-17 words: 7728.0 sentences: 446.0 pages: flesch: 52.0 cache: ./cache/cord-350212-448mv4lt.txt txt: ./txt/cord-350212-448mv4lt.txt summary: We demonstrate that these sMVA vectors stimulate robust SARS-CoV-2 antigen-speci c humoral and cellular immunity in mice, including potent NAb. These results emphasize the value of a novel vaccine platform based on synthetic DNA to e ciently produce recombinant poxvirus vectors and warrant further pre-clinical and clinical testing of a multiantigenic sMVA vaccine candidate to control the ongoing SARS-CoV-2 pandemic and its devastating consequences. In response to the ongoing global SARS-CoV-2 pandemic, we used this novel vaccine platform to rapidly produce sMVA vectors co-expressing SARS-CoV-2 S and N antigens and show that these vectors can induce potent SARS-CoV-2 antigen-speci c humoral and cellular immune responses in mice, including potent NAb. These results highlight the feasibility to e ciently produce recombinant MVA vectors from chemically synthesized DNA and to rapidly develop a synthetic poxvirusbased vaccine candidate to prevent SARS-CoV-2 infection. abstract: Modified Vaccinia Ankara (MVA) is a highly attenuated poxvirus vector that is widely used to develop vaccines for infectious diseases and cancer. We developed a novel vaccine platform based on a unique three-plasmid system to efficiently generate recombinant MVA vectors from chemically synthesized DNA. In response to the ongoing global pandemic caused by SARS coronavirus-2 (SARS-CoV-2), we used this novel vaccine platform to rapidly produce fully synthetic MVA (sMVA) vectors co-expressing SARS-CoV-2 spike and nucleocapsid antigens, two immunodominant antigens implicated in protective immunity. Mice immunized with these sMVA vectors developed robust SARS-CoV-2 antigen-specific humoral and cellular immune responses, including potent neutralizing antibodies. These results demonstrate the potential of a novel vaccine platform based on synthetic DNA to efficiently generate recombinant MVA vectors and to rapidly develop a multi-antigenic poxvirus-based SARS-CoV-2 vaccine candidate. url: https://www.ncbi.nlm.nih.gov/pubmed/32702732/ doi: 10.21203/rs.3.rs-40198/v1 id: cord-326045-x8xntne7 author: Chng, Shu-Sin title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate date: 2004-12-20 words: 1254.0 sentences: 78.0 pages: flesch: 60.0 cache: ./cache/cord-326045-x8xntne7.txt txt: ./txt/cord-326045-x8xntne7.txt summary: title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate Synthesis of intermediate 1 and analogues proceeded via a highly diastereoselective indium-mediated allylation of α-aminoaldehydes. Based on these findings, it was suggested that the HRV 3C pro inhibitor, AG7088, could serve as a good starting point for modifications leading to an efficient and bio-available inhibitor for the SARS-CoV M pro and other coronavirus main proteinases. The synthesis of 1 in our group has proceeded via the highly stereoselective indium-mediated allylation reaction of N-protected valinal as illustrated in Scheme 2. 8 In addition, when we performed the same indium-mediated allylation reaction on N-t-butyloxycarbonyl-L L-valinal, we obtained the homoallylic alcohol as an 87:13 mixture of syn/anti isomers (Scheme 4). The critical step in the synthesis involved a highly diastereoselective indium-mediated allylation reaction. abstract: AG7088 was identified as a good starting point for modification, leading to an efficient and bio-available inhibitor for the SARS coronavirus main proteinase (SARS-CoV M(pro)). Synthesis of intermediate 1 and analogues proceeded via a highly diastereoselective indium-mediated allylation of α-aminoaldehydes. url: https://api.elsevier.com/content/article/pii/S0040403904023895 doi: 10.1016/j.tetlet.2004.10.146 id: cord-304321-y177sqee author: Cho, Ryan H. W. title: Pearls of experience for safe and efficient hospital practices in otorhinolaryngology—head and neck surgery in Hong Kong during the 2019 novel coronavirus disease (COVID-19) pandemic date: 2020-05-15 words: 4375.0 sentences: 192.0 pages: flesch: 43.0 cache: ./cache/cord-304321-y177sqee.txt txt: ./txt/cord-304321-y177sqee.txt summary: We hope that our experiences will serve as pearls for otolaryngologists and other healthcare personnel working in institutes that serve large numbers of patients every day, particularly with regard to the sharing of clinical and administrative tasks during the COVID-19 pandemic. In 2003 outbreak of SARS in Hong Kong, the initial phase of outbreak began in Prince of Wales Hospital with a carrier of coronavirus in a medical ward causing widespread infection to patients and medical staff through the use of nebulizer for bronchodilators which facilitated the transmission of the virus through aerosol spread. Health seminars on COVID-19, which were organized by the infection control team to all hospital staff on daily basis across the whole month, provided a direct platform from which to educate healthcare personnel about the virus, its mode of transmission, the course of the disease, management and the mortality rate. abstract: The 2019 novel coronavirus disease (COVID-19) epidemic originated in Wuhan, China and spread rapidly worldwide, leading the World Health Organization to declare an official global COVID-19 pandemic in March 2020. In Hong Kong, clinicians and other healthcare personnel collaborated closely to combat the outbreak of COVID-19 and minimize the cross-transmission of disease among hospital staff members. In the field of otorhinolaryngology—head and neck surgery (OHNS) and its various subspecialties, contingency plans were required for patient bookings in outpatient clinics, surgeries in operating rooms, protocols in wards and other services. Infected patients may shed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) particles into their environments via body secretions. Therefore, otolaryngologists and other healthcare personnel in this specialty face a high risk of contracting COVID-19 and must remain vigilant when performing examinations and procedures involving the nose and throat. In this article, we share our experiences of the planning and logistics undertaken to provide safe and efficient OHNS practices over the last 2 months, during the COVID-19 pandemic. We hope that our experiences will serve as pearls for otolaryngologists and other healthcare personnel working in institutes that serve large numbers of patients every day, particularly with regard to the sharing of clinical and administrative tasks during the COVID-19 pandemic. url: https://doi.org/10.1186/s40463-020-00427-4 doi: 10.1186/s40463-020-00427-4 id: cord-017668-my2l85bn author: Cho, Yeon-Jin title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction date: 2005 words: 2084.0 sentences: 140.0 pages: flesch: 60.0 cache: ./cache/cord-017668-my2l85bn.txt txt: ./txt/cord-017668-my2l85bn.txt summary: title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction We present a new method that generates prediction rules for SARS-CoV protease cleavage sites. Experimental results show that the method could generate new rules for cleavage site prediction, which are more general and accurate than consensus patterns. In this paper, we present new approaches to rule generation for the cleavage site prediction, and the rule is represented in an explicit form such as "if L@p2 and R@p3, then cleavage". We used the methods of rule extraction from neural networks and knowledge-based genetic algorithms in this paper. used feed-forward neural networks for SARS-CoV cleavage site analysis [11] . Domain knowledge was obtained by extracting rules from consensus patterns, decision tree and neural networks. Finally, we compare the rule performances between decision tree, neural network and knowledge-based genetic algorithm (KBGA). We presented a new method that generates rules and improves quality of the rules with the subject of SARS-CoV protease cleav-age site prediction. abstract: Cleavage site prediction is an important issue in molecular biology. We present a new method that generates prediction rules for SARS-CoV protease cleavage sites. Our method includes rule extraction from a trained neural network and then enhancing the extracted rules by genetic evolution to improve its quality. Experimental results show that the method could generate new rules for cleavage site prediction, which are more general and accurate than consensus patterns. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122303/ doi: 10.1007/11553939_111 id: cord-262338-ipvzugo8 author: Choi, Jun-Yong title: The pathogenesis and alternative treatment of SARS-CoV2 date: 2020-05-03 words: 1153.0 sentences: 69.0 pages: flesch: 55.0 cache: ./cache/cord-262338-ipvzugo8.txt txt: ./txt/cord-262338-ipvzugo8.txt summary: The scientific community has identified the culprit of the shock wave as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) (1). Since 2002, however, newly merged hCoV causes fever, dyspnea, and often organ failure, which bestow SARS (severe acute respiratory syndrome) to otherwise benign hCoV (5) . During the MERS-CoV and SARS-CoV outbreaks, most patients died of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS), a severe case of ALI (11) . Fortunately, the mortality of SARS-CoV2 infection, which is related to ALI or ARDS, is lower than those of the other two outbreaks (13) . As yet, however, no evidence is available that, if administered to patients on the principles of traditional Asian medicine, the medicinal herbs show effectiveness against ALI caused by SARS-CoV2 infection. The time comes to examine whether antiinflammatory medicinal herbs give a medical benefit to patients infected by SARS-CoV2. abstract: nan url: https://api.elsevier.com/content/article/pii/S2213422020300536 doi: 10.1016/j.imr.2020.100421 id: cord-332716-1d89j7jh author: Choi, Marcelo title: El SRAA y el SARS-CoV-2: el acertijo a resolver date: 2020-05-27 words: 3334.0 sentences: 366.0 pages: flesch: 59.0 cache: ./cache/cord-332716-1d89j7jh.txt txt: ./txt/cord-332716-1d89j7jh.txt summary: Uno de los temas que ha generado debate se vincula con la asociación entre la terapia antihipertensiva con inhibidores del sistema renina-angiotensina-aldosterona (SRAA) y la infección por el virus SARS-CoV-2. Para ingresar a las células el coronavirus interactúa, utilizando como receptor, con la ECA2 y serina-proteasas transmembrana de tipo II (TMPRSS2) ubicadas en la superficie celular del huésped (7) . Los estudios clínicos llevados a cabo hasta el día de hoy no han demostrado que existen diferencias entre ambos tratamientos en términos de aumento del riesgo de infección por SARS-CoV-2 o de desarrollo de resultados graves en pacientes con COVID-19 (27) (28) (29) (30) (31) . Si bien existe evidencia in vitro de que el SARS-CoV-2 se une a los receptores ECA2 y que éstos se encuentran aumentados en presencia de IECA o ARA-II, no hay evidencia al momento de que la exposición a estos fármacos facilite la entrada del coronavirus ni que produzcan un mayor riesgo de COVID-19. abstract: Resumen El 31 de diciembre de 2019 se reportó el primer caso de COVID-19 en Wuhan, China, y desde entonces ha habido un interés creciente y sin precedentes por conocer todos los aspectos vinculados con esta nueva enfermedad. Uno de los temas que ha generado debate se vincula con la asociación entre la terapia antihipertensiva con inhibidores del sistema renina-angiotensina-aldosterona (SRAA) y la infección por el virus SARS-CoV-2. Si bien muchas preguntas siguen hoy día sin poder ser respondidas, la intención de este comunicado es informar a los profesionales de la salud acerca del estado actual de conocimiento. Dado que este es un tema en constante evolución, se recomienda su actualización a medida que se presenten nuevas evidencias. A continuación, daremos revisión a los estudios preclínicos y clínicos que relacionan el coronavirus con el SRAA. Abstract The first case of COVID-19 was reported on 31 December 2019 in Wuhan, China. Ever since there has been unprecedented and growing interest in learning about all aspects of this new disease. Debate has been generated as to the association between antihypertensive therapy with renin-angiotensin-aldosterone system (RAAS) inhibitors and SARS-CoV-2 infection. While many questions as yet remain unanswered, the aim of this report is to inform health professionals about the current state of knowledge. Because this is an ever-evolving topic, the recommendation is that it be updated as new evidence becomes available. Below, we provide a review of pre-clinical and clinical studies that link coronavirus to the RAAS. url: https://www.sciencedirect.com/science/article/pii/S1889183720300568?v=s5 doi: 10.1016/j.hipert.2020.05.005 id: cord-270278-d61n3v90 author: Choi, S.M.Y. title: Enhancing legal preparedness for the prevention and control of infectious diseases: Experience from severe acute respiratory syndrome in Hong Kong date: 2009-03-31 words: 4224.0 sentences: 193.0 pages: flesch: 45.0 cache: ./cache/cord-270278-d61n3v90.txt txt: ./txt/cord-270278-d61n3v90.txt summary: This article shares Hong Kong''s experience in reforming its public health legislation to: (1) update terminology and re-organize provisions in accordance with modern public health disease control principles and control mechanisms for disease; (2) enhance responsiveness for better preparedness and flexibility in handling emergent infections; (3) ensure appropriate checks and balances to coercive powers; and (4) introduce emergency powers for the handling of public health emergencies. During the outbreak of SARS in 2003, the Quarantine and Prevention of Disease Ordinance 2 (QPDO) of the laws of Hong Kong was the legal tool that provided the legal framework for the prevention and control of infectious diseases of public health importance in Hong Kong. This article shares Hong Kong''s experience in reforming its public health legislation, leading to the passing of the Prevention and Control of Disease Ordinance 4 in order to strengthen the capacity of law to support strategy in the control of infectious diseases. abstract: Summary The use of legislation as a health protection tool forms an important and distinct aspect in the arena of public health. A review of Hong Kong's infectious disease legislation was conducted with a view to updating the legal framework for the prevention of infectious diseases, in order to strengthen the capacity of law to support strategy in the control of infectious diseases. This article shares Hong Kong's experience in reforming its public health legislation to: (1) update terminology and re-organize provisions in accordance with modern public health disease control principles and control mechanisms for disease; (2) enhance responsiveness for better preparedness and flexibility in handling emergent infections; (3) ensure appropriate checks and balances to coercive powers; and (4) introduce emergency powers for the handling of public health emergencies. url: https://www.ncbi.nlm.nih.gov/pubmed/19264334/ doi: 10.1016/j.puhe.2009.01.004 id: cord-345854-f0dq94j1 author: Chong, Wai Po title: The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date: 2006-05-04 words: 1770.0 sentences: 116.0 pages: flesch: 54.0 cache: ./cache/cord-345854-f0dq94j1.txt txt: ./txt/cord-345854-f0dq94j1.txt summary: We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). In this study, we hypothesized that the polymorphisms of the cytokine genes, i.e. IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C, might be associated with SARS. We tested our hypotheses in 476 SARS patients and 449 healthy controls and found that polymorphism of IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner. The frequencies of genotypes and alleles of the 4 single nucleotide polymorphisms (SNPs) were compared between the SARS patients and healthy controls by 3 × 2 and 2 × 2 chi square test respectively. Our case-control study genotyped the 4 SNPs IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C in 476 Chinese patients with SARS and 449 healthy controls. Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection abstract: BACKGROUND: Cytokines play important roles in antiviral action. We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: A case-control study was carried out in 476 Chinese SARS patients and 449 healthy controls. We tested the polymorphisms of IFN-γ,TNF-α and IL-10 for their associations with SARS. RESULTS: IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner (P < 0.001). Individuals with IFN-γ +874 AA and AT genotype had a 5.19-fold (95% Confidence Interval [CI], 2.78-9.68) and 2.57-fold (95% CI, 1.35-4.88) increased risk of developing SARS respectively. The polymorphisms of IL-10 and TNF-α were not associated with SARS susceptibility. CONCLUSION: IFN-γ +874A allele was shown to be a risk factor in SARS susceptibility. url: https://www.ncbi.nlm.nih.gov/pubmed/16672072/ doi: 10.1186/1471-2334-6-82 id: cord-296271-85io9yvy author: Chong, Woon H. title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) date: 2020-07-28 words: 784.0 sentences: 54.0 pages: flesch: 54.0 cache: ./cache/cord-296271-85io9yvy.txt txt: ./txt/cord-296271-85io9yvy.txt summary: title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) 1 A study of 701 SARS-CoV-2 patients by Cheng and colleagues demonstrated that in-hospital mortality increased by almost three-fold in those who had AKI. 2 We report a patient with SARS-CoV-2 who developed AKI likely secondary to rhabdomyolysis and discuss the possible association between cytokine storm as the etiology. A case series of SARS-CoV-related rhabdomyolysis showed the development of AKI with peak CK levels ranging from 7,500 to 340,000 IU/L. 3 Jin and colleagues were the first to describe a 60-year-old man who was admitted with RT-PCR confirmed SARS-CoV-2 pneumonia and developed rhabdomyolysis on day 9 th of hospital admission. A retrospective study of 171 SARS-CoV-2 patients showed that CK of more than 185 IU/L, AKI, and requirement of RRT was associated with an increase in mortality. abstract: nan url: https://doi.org/10.1016/j.amjms.2020.07.032 doi: 10.1016/j.amjms.2020.07.032 id: cord-270788-w0pewq52 author: Chou, Chih-Fong title: A novel cell-based binding assay system reconstituting interaction between SARS-CoV S protein and its cellular receptor date: 2004-11-05 words: 4759.0 sentences: 241.0 pages: flesch: 64.0 cache: ./cache/cord-270788-w0pewq52.txt txt: ./txt/cord-270788-w0pewq52.txt summary: A binding epitope with lesser degree of glycosylation and native conformation was localized by using rabbit anti-sera raised against five denatured recombinant S protein fragments expressed in Escherichia coli. Cells were washed once with PBS and three times with PBS containing 500 mM NaCl. To test whether the anti-sera from SARS patients or raised against S protein fragments can block the binding between CHO-SG and Vero E6, dislodged CHO-SG cells were preincubated with the anti-serum to be tested at 4 • C for 1 h. The CHO-G cells resisted the PBS wash but were detached by the solutions containing supplemented NaCl. In contrast, the binding between CHO-SG and Vero E6 could resist up to 1M NaCl. We sought to investigate the binding specificity of this interaction by testing whether the serum from a recovered SARS patient (P8 in Tan et al., 2004a ) and a goat anti-ACE2 antibody could block the interaction. abstract: Severe acute respiratory syndrome (SARS), a life-threatening disease, is caused by the newly identified virus SARS coronavirus (SARS-CoV). In order to study the spike (S) protein of this highly contagious virus, we established a clonal cell-line, CHO-SG, from the Chinese hamster ovary cells that stably expresses C-terminally EGFP-tagged SARS-CoV S protein (S-EGFP). The ectodomain of the S glycoprotein is localized on the surface of CHO-SG cells with N-acetyl-glucosamine-terminated carbohydrate structure. CHO-SG cells associated tightly with Vero E6 cells, a SARS-CoV receptor (ACE2) expressing cell-line, and the interaction remained stable under highly stringent condition (1 M NaCl). This interaction could be blocked by either the serum from a SARS convalescent patient or a goat anti-ACE2 antibody, indicating that the interaction is specific. A binding epitope with lesser degree of glycosylation and native conformation was localized by using rabbit anti-sera raised against five denatured recombinant S protein fragments expressed in Escherichia coli. One of the sera obtained from the fragment encompassing amino acids 48-358 significantly blocked the interaction between CHO-SG and Vero E6 cells. The region is useful for studying neutralizing antibodies in future vaccine development. This paper describes an easy and safe cell-based assay suitable for studying the binding between SARS-CoV S protein and its receptor. url: https://api.elsevier.com/content/article/pii/S0166093404002654 doi: 10.1016/j.jviromet.2004.09.008 id: cord-309650-6xz9gjq0 author: Chou, Roger title: Update Alert 4: Epidemiology of and Risk Factors for Coronavirus Infection in Health Care Workers date: 2020-09-11 words: 1472.0 sentences: 95.0 pages: flesch: 45.0 cache: ./cache/cord-309650-6xz9gjq0.txt txt: ./txt/cord-309650-6xz9gjq0.txt summary: Specific risk factors for SARS-CoV-2 transmission among health care workers in a university hospital Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers Prevalence of SARS-CoV-2 infection among health care workers in a tertiary community hospital Asymptomatic infection by SARS-CoV-2 in healthcare workers: a study in a large teaching hospital in Wuhan, China Dynamic of SARS-CoV-2 RT-PCR positivity and seroprevalence among high-risk health care workers and hospital staff Risk factors of healthcare workers with Corona Virus Disease 2019: a retrospective cohort study in a designated hospital of Wuhan in China Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 Novel Coronavirus Disease outbreak: a cross-sectional study Analysis of the infection status of the health care workers in Wuhan during the COVID-19 outbreak: A cross-sectional study SARS-CoV-2 infection among healthcare workers in a hospital in abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32915642/ doi: 10.7326/l20-1134 id: cord-313345-zwe3tmq0 author: Chou, Roger title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings date: 2020-07-20 words: 602.0 sentences: 40.0 pages: flesch: 43.0 cache: ./cache/cord-313345-zwe3tmq0.txt txt: ./txt/cord-313345-zwe3tmq0.txt summary: title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings Masks for prevention of respiratory virus infections, including SARS-CoV-2, in health care and community settings: a living rapid review Facemasks and hand hygiene to prevent influenza transmission in households: a cluster randomized trial Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study A case-control study on the risk factors of severe acute respiratory syndromes among health care workers Factors associated with transmission of severe acute respiratory syndrome among health-care workers in Singapore Surgical mask vs N95 respirator for preventing influenza among health care workers: a randomized trial A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. N95 Respirators vs medical masks for preventing influenza among health care personnel: a randomized clinical trial abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32687391/ doi: 10.7326/l20-0948 id: cord-326320-flfrdrbi author: Choudhary, Shalki title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date: 2020-08-29 words: 4675.0 sentences: 280.0 pages: flesch: 56.0 cache: ./cache/cord-326320-flfrdrbi.txt txt: ./txt/cord-326320-flfrdrbi.txt summary: title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 The multi-targeting potential of generated analogues was explored against various targets involved in the pathogenesis of COVID-19 including SARS-CoV-2 SP, ACE2, furin, TMPRSS2 (in viral attachment) and 3CLPro (in viral replication). A cutoff value of 3 was used for the screening of compounds based on synthetic possibility and topranked molecules were submitted to structure-guided drug binding analysis such as molecular docking studies. All these molecules were docked against SARS-CoV-2 SP-ACE2 complex, furin, TMPRSS2 and main protease (3CLPro) and the binding affinity of their docked complexes was also calculated in terms of MM-GBSA score. J o u r n a l P r e -p r o o f 44 A combination of scaffold morphing and a structure-based drug designing approach was successfully utilized to identify putative multi-targeting analogues of arbidol against COVID-19. abstract: The rapid emergence of a novel coronavirus, SARS-coronavirus 2 (SARS-CoV-2), originated from Wuhan, China, imposed a global health emergency. Angiotensin-converting enzyme 2 (ACE2) receptor serves as an entry point for this deadly virus while the proteases like furin, transmembrane protease serine 2 (TMPRSS2) and 3 chymotrypsin-like protease (3CLpro) are involved in the further processing and replication of SARS-CoV-2. The interaction of SP with ACE2 and these proteases results in the SARS-CoV-2 invasion and fast epidemic spread. The small molecular inhibitors are reported to limit the interaction of SP with ACE2 and other proteases. Arbidol, a membrane fusion inhibitor approved for influenza virus is currently undergoing clinical trials against COVID-19. In this context, we report some analogues of arbidol designed by scaffold morphing and structure-based designing approaches with a superior therapeutic profile. The representative compounds A_BR4, A_BR9, A_BR18, A_BR22 and A_BR28 restricted the interaction of SARS-CoV-2 SP with ACE2 and host proteases furin and TMPRSS2. For 3CLPro, Compounds A_BR5, A_BR6, A_BR9 and A_BR18 exhibited high binding affinity, docking score and key residue interactions. Overall, A_BR18 and A_BR28 demonstrated multi-targeting potential against all the targets. Among these top-scoring molecules A_BR9, A_BR18, A_BR22 and A_BR28 were predicted to confer favorable ADME properties. url: https://www.sciencedirect.com/science/article/pii/S0168170220310534?v=s5 doi: 10.1016/j.virusres.2020.198146 id: cord-334891-4jgtxg07 author: Choudhury, Abhigyan title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 words: 2926.0 sentences: 169.0 pages: flesch: 54.0 cache: ./cache/cord-334891-4jgtxg07.txt txt: ./txt/cord-334891-4jgtxg07.txt summary: This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. abstract: The worldwide outbreak of COVID-19 pandemic caused by SARS-CoV-2 leads to loss of mankind and global economic stability. The continuous spreading of the disease and its pathogenesis takes millions of lives of peoples and the unavailability of appropriate therapeutic strategy makes it much more severe. Toll-like receptors (TLRs) are the crucial mediators and regulators of host immunity. The role of several TLRs in immunomodulation of host by SARS-CoV-2 is recently demonstrated. However, the functionality of human intracellular TLRs including TLR3,7,8 and 9 is still being untested for sensing of viral RNA. This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. url: https://doi.org/10.1101/2020.11.11.377713 doi: 10.1101/2020.11.11.377713 id: cord-356021-lr3wj8we author: Choudhury, Chinmayee title: Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease date: 2020-06-01 words: 6858.0 sentences: 346.0 pages: flesch: 53.0 cache: ./cache/cord-356021-lr3wj8we.txt txt: ./txt/cord-356021-lr3wj8we.txt summary: With the arrival of the very first structure (6LU7) of this protein in PDB (Jin et al., 2020) , several groups have come up with interesting strategies such as artificial intelligence based de novo design (Bung et al., 2020) , repurposing existing drugs that can bind this protein or virtually screening large chemical databases to identify peptide like small molecules (Pant et al., 2020) , natural products such as Moroccan medicinal plants products (Aanouz et al., 2020) , against this protein (Islam et al., 2020; Sarma et al., 2020) , identification of Andrographolide as a potential inhibitor of SARS-CoV-2 main protease through in silico screening (Enmozhi et al., 2020) using molecular docking, molecular dynamics simulations and PCA based quantitative structureactivity relationship (QSAR) for pattern recognition of the best ligands (Islam et al., 2020) , to mention a few. abstract: The recent pandemic of severe acute respiratory syndrome–coronavirus2 (SARS-CoV-2) infection (COVID-19) has put the world on serious alert. The main protease of SARS-CoV-2 (SARS-CoV-2-M(Pro)) cleaves the long polyprotein chains to release functional proteins required for replication of the virus and thus is a potential drug target to design new chemical entities in order to inhibit the viral replication in human cells. The current study employs state of art computational methods to design novel molecules by linking molecular fragments which specifically bind to different constituent sub-pockets of the SARS-CoV-2-M(Pro) binding site. A huge library of 191678 fragments was screened against the binding cavity of SARS-CoV-2-M(Pro) and high affinity fragments binding to adjacent sub-pockets were tailored to generate new molecules. These newly formed molecules were further subjected to molecular docking, ADMET filters and MM-GBSA binding energy calculations to select 17 best molecules (named as MP-In1 to MP-In17), which showed comparable binding affinities and interactions with the key binding site residues as the reference ligand. The complexes of these 17 molecules and the reference molecule with SARS-CoV-2-M(Pro), were subjected to molecular dynamics simulations, which assessed the stabilities of their binding with SARS-CoV-2-M(Pro). Fifteen molecules were found to form stable complexes with SARS-CoV-2-M(Pro). These novel chemical entities designed specifically according to the pharmacophoric requirements of SARS-CoV-2-M(Pro) binding pockets showed good synthetic feasibility and returned no exact match when searched against chemical databases. Considering their interactions, binding efficiencies and novel chemotypes, they can be further evaluated as potential starting points for SARS-CoV-2 drug discovery. [Image: see text] Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32452282/ doi: 10.1080/07391102.2020.1771424 id: cord-323643-lu3ngt6r author: Chow, C.B. title: Post-SARS infection control in the hospital and clinic date: 2004-11-05 words: 4449.0 sentences: 252.0 pages: flesch: 53.0 cache: ./cache/cord-323643-lu3ngt6r.txt txt: ./txt/cord-323643-lu3ngt6r.txt summary: The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. PAEDIATRIC Summary The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. 17 Despite great concerns, compliance to infection control precautions by community general practitioners in Hong Kong lagged behind their hospital counterparts -97.7% had not worn masks at all times, a third did not wash their hands after seeing/examining a patient and half did not wear gowns. In a study looking into factors affecting nosocomial infection in Hong Kong, it was found that all HCWs consistently used N95s or surgical masks and perceived that the inadequacy of personal protective equipment (PPE) supply, infection control training <2 h and inconsistent use of goggles, gowns, gloves and caps were significant independent risk factors for SARS infection. abstract: The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. Triage, early case detection followed by prompt isolation and quarantine are major preventive measures. Respiratory tract infections are the most common childhood illnesses and paediatric SARS poses special problems in diagnosis because of its non-specific presentation. The main lessons learnt from the outbreak were: (1) despite well established guidelines on infection control precautions, poor understanding of underlying principles and deficiencies in compliance are common among healthcare professionals, especially during emergencies; (2) even a slight lapse can be fatal; and (3) over-protection can be counterproductive. Hence it is important to: (1) be protected to protect others; (2) be vigilant and prepared for emerging infections; (3) be proficient and scrupulous in infection control measures; (4) be apposite and practical on personal protective equipments to ensure sustainability; and (5) be dutiful and prompt in informing of potential threats and work closely with others. url: https://api.elsevier.com/content/article/pii/S1526054204000752 doi: 10.1016/j.prrv.2004.07.006 id: cord-258223-8dhtwf03 author: Chow, Cristelle title: The Next Pandemic: Supporting COVID-19 Frontline Doctors Through Film Discussion date: 2020-09-05 words: 4749.0 sentences: 185.0 pages: flesch: 41.0 cache: ./cache/cord-258223-8dhtwf03.txt txt: ./txt/cord-258223-8dhtwf03.txt summary: Themes derived from the film included preparedness, blame, and the impact on healthcare workers and public, which were further discussed to include concerns regarding current local readiness levels given global connectivity, the need for international cooperation, and the effects of blame such as racism and prejudice. These rich discussions demonstrate the pivotal role health humanities has in times of uncertainty such as an emerging infectious disease outbreak by providing timely pandemic education and supporting reflective learning. Hence, as the world experiences the current COVID-19 pandemic situation, this study aims to describe the use of a short film and post-film discussion to educate and support frontline doctorsin-training during an acute emerging infectious disease outbreak. While the focus of this study was on the implementation of a timely film screening and discussion, the themes that emerged from the guided reflections were insightful and can inform future pandemic-preparedness efforts for frontline healthcare staff. abstract: This paper describes an innovative just-in-time health humanities programme to educate and provide support to COVID-19 frontline doctors-in-training. The programme incorporates small-group screening of the Netflix documentary, The Next Pandemic from the Explained series, followed by a one-hour facilitated discussion to explore themes surrounding the current pandemic and its impact on frontline doctors in a tertiary paediatric hospital in Singapore. Themes derived from the film included preparedness, blame, and the impact on healthcare workers and public, which were further discussed to include concerns regarding current local readiness levels given global connectivity, the need for international cooperation, and the effects of blame such as racism and prejudice. The association with culture; the current impact on healthcare workers, physician-patient relationships, and the public including the role of social media, the government and associated public reactions were also explored. These rich discussions demonstrate the pivotal role health humanities has in times of uncertainty such as an emerging infectious disease outbreak by providing timely pandemic education and supporting reflective learning. url: https://www.ncbi.nlm.nih.gov/pubmed/32889676/ doi: 10.1007/s10912-020-09662-2 id: cord-289038-15yp9uqy author: Chow, Jonathan Tak-Sum title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date: 2020-08-26 words: 5312.0 sentences: 445.0 pages: flesch: 62.0 cache: ./cache/cord-289038-15yp9uqy.txt txt: ./txt/cord-289038-15yp9uqy.txt summary: The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. Another recent study used a high-throughput reporter screen of miRNA from human and mouse respiratory epithelial cells to identify hsa-miR-127-3p, hsa-miR-486-5p, and hsa-miR-593-5p as contributors to the antiviral defence against influenza A virus by targeting the genomes of the H3N2 and attenuated PR8 (H1N1) viral strains [16] . Given the wealth of evidence supporting a role for miRNA in host cell antiviral defence mechanisms, we sought to identify human miRNA that have the potential to target the SARS-CoV-2 genome. DEA of Calu3 cells infected with SARS-CoV revealed that only hsa-miR-155-3p (upregulated) and hsa-let-7a-3p (downregulated) out of the 128 miRNA we identified in this study, were differentially expressed ( Figure 4B ). abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus, is responsible for the coronavirus disease 2019 (COVID-19) pandemic of 2020. Experimental evidence suggests that microRNA can mediate an intracellular defence mechanism against some RNA viruses. The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. We hypothesize that high expression of specific coronavirus-targeting microRNA in lung epithelia may protect against infection and viral propagation, conversely, low expression may confer susceptibility to infection. We have identified 128 human microRNA with potential to target the SARS-CoV-2 genome, most of which have very low expression in lung epithelia. Six of these 128 microRNA are differentially expressed upon in vitro infection of SARS-CoV-2. Additionally, 28 microRNA also target the SARS-CoV genome while 23 microRNA target the MERS-CoV genome. We also found that a number of microRNA are commonly identified in two other studies. Further research into identifying bona fide coronavirus targeting microRNA will be useful in understanding the importance of microRNA as a cellular defence mechanism against pathogenic coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32858958/ doi: 10.3390/genes11091002 id: cord-326273-6rp12py3 author: Chow, Kuan-Chih title: Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date: 2004-04-01 words: 3202.0 sentences: 190.0 pages: flesch: 45.0 cache: ./cache/cord-326273-6rp12py3.txt txt: ./txt/cord-326273-6rp12py3.txt summary: Previous reports have indicated that patients with severe acute respiratory syndrome (SARS)–associated coronavirus infection could develop atypical pneumonia with fulminant pulmonary edema. Severe acute respiratory syndrome (SARS) is an acute infectious disease that affects primarily the lower respiratory tract, with clinical manifestations of atypical pneumonia with dry cough, persistent fever, progressive dyspnea, and, sometimes, the abrupt deterioration of lung function [1] [2] [3] [4] [5] and the ensuing oxygen deprivation-associated systemic organ failures. Nevertheless, when antisense oligonucleotide probes specific to the replicase-encoding (REP) region of the SARS viral genome were used to determine the presence of virus, the intensity of the in situ hybridization signal decreased substantially compared with that detected by probes to the N and M regions ❚Image 2D❚ ❚Table 3❚. B, By using in situ hybridization and antisense oligonucleotide probes specific to the nucleic acid binding protein-encoding (N) and membrane protein-encoding (M) regions of the severe acute respiratory syndrome (SARS) viral genome, the SARS viral signal was detected in the enlarged and multinucleated cell (arrow, purple blue precipitates). abstract: Previous reports have indicated that patients with severe acute respiratory syndrome (SARS)–associated coronavirus infection could develop atypical pneumonia with fulminant pulmonary edema. However, the target cells of SARS viral infection have not been characterized in detail. We report the pathologic findings of the lung in 3 cases of SARS. Chest radiographs at 2 to 3 weeks of infection revealed an atypical pneumonia with pulmonary consolidation, a clinical characteristic of SARS infection. The presence of the SARS virus was determined by nested reverse transcription–polymerase chain reaction (RT-PCR), and the infected cells were identified by in situ hybridization in open-lung biopsy and postmortem necropsy specimens. Expression of SARS virus–encoded RNA was detected in all 3 cases by RT-PCR, and the SARS viral signal was localized in pneumocytes by using in situ hybridization. url: https://www.ncbi.nlm.nih.gov/pubmed/15080310/ doi: 10.1309/c0edu0raqbtxbhce id: cord-309556-xv3413k1 author: Chow, Ryan D. title: The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date: 2020-04-15 words: 5761.0 sentences: 373.0 pages: flesch: 53.0 cache: ./cache/cord-309556-xv3413k1.txt txt: ./txt/cord-309556-xv3413k1.txt summary: In aggregate, these analyses showed that the age-associated genes with functional roles in SARS-CoV are expressed in specific cell types of the human lung. Of note, the overlap between lung ageassociated genes and SARS-CoV-2 regulated genes was statistically significant across all 3 cell lines (Figure 6d-f) , suggesting a degree of similarity between the transcriptional changes associated with aging and with SARS-CoV-2 infection. Among the age-associated genes that were induced by SARS-CoV-2 infection, the majority of these genes increase in expression with age (Cluster 1) (Figure 6g-i) . To identify a consensus set of age-associated genes that are regulated by SARS-CoV-2 infection, we integrated the analyses from all 3 cell lines. By integrating these data with single cell transcriptomes of human lung tissue, we further pinpointed the specific cell types that normally express the age-associated genes. abstract: Since the emergence of SARS-CoV-2 in December 2019, Coronavirus Disease-2019 (COVID-19) has rapidly spread across the globe. Epidemiologic studies have demonstrated that age is one of the strongest risk factors influencing the morbidity and mortality of COVID-19. Here, we interrogate the transcriptional features and cellular landscapes of the aging human lung through integrative analysis of bulk and single-cell transcriptomics. By intersecting these age-associated changes with experimental data on host interactions between SARS-CoV-2 or its relative SARS-CoV, we identify several age-associated factors that may contribute to the heightened severity of COVID-19 in older populations. We observed that age-associated gene expression and cell populations are significantly linked to the heightened severity of COVID-19 in older populations. The aging lung is characterized by increased vascular smooth muscle contraction, reduced mitochondrial activity, and decreased lipid metabolism. Lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts, pericytes and CD4+ Tcm cells increase in abundance with age. Several age-associated genes have functional effects on SARS-CoV replication, and directly interact with the SARS-CoV-2 proteome. Interestingly, age-associated genes are heavily enriched among those induced or suppressed by SARS-CoV-2 infection. These analyses illuminate potential avenues for further studies on the relationship between the aging lung and COVID-19 pathogenesis, which may inform strategies to more effectively treat this disease. url: https://doi.org/10.1101/2020.04.07.030684 doi: 10.1101/2020.04.07.030684 id: cord-342557-a7q8vp8m author: Chowdhury, Surid Mohammad title: Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date: 2020-10-23 words: 3554.0 sentences: 232.0 pages: flesch: 54.0 cache: ./cache/cord-342557-a7q8vp8m.txt txt: ./txt/cord-342557-a7q8vp8m.txt summary: [Image: see text] Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Peptides that showed higher S protein-binding affinity compared to the α-helix (AH) of the ACE2 peptidase were further analyzed with molecular dynamics (MD) simulation and the structure− activity relationship (SAR) in order to achieve a high-affinity binder for the S protein. 30 Initially, stepwise multiple linear regression (MLR) was performed considering these properties as variables to predict the calculated binding affinity of the test peptides with the RBD of the SARS CoV-2 spike protein. All 51 peptides were docked to the RBD of the SARS CoV-2 spike protein using PatchDock. Various residues including Glu484, Tyr449, and Tyr505 present in the ACE2 binding site of the RBD were involved in noncovalent interaction with the antiviral peptides ( Figure 1a) . abstract: [Image: see text] Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Based on the binding affinity and interaction, 15 peptides were selected, which showed higher affinity compared to the α-helix of the human ACE2 receptor. Molecular dynamics simulation demonstrated that two peptides, S2P25 and S2P26, were the most promising candidates, which could potentially block the entry of SARS-CoV-2. Tyr489 and Tyr505 residues present in the “finger-like” projections of the RBD were found to be critical for peptide interaction. Hydrogen bonding and hydrophobic interactions played important roles in prompting peptide–protein binding and interaction. Structure–activity relationship indicated that peptides containing aromatic (Tyr and Phe), nonpolar (Pro, Gly, Leu, and Ala), and polar (Asn, Gln, and Cys) residues were the most significant contributors. These findings can facilitate the rational design of selective peptide inhibitors targeting the spike protein of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33095007/ doi: 10.1021/acs.jpcb.0c05621 id: cord-256270-7e8zlt3t author: Choy, Ka-Tim title: Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro date: 2020-04-03 words: 2745.0 sentences: 147.0 pages: flesch: 44.0 cache: ./cache/cord-256270-7e8zlt3t.txt txt: ./txt/cord-256270-7e8zlt3t.txt summary: We evaluated the in vitro antiviral effect of compounds that were previously reported to inhibit coronavirus replication and compounds that are currently under evaluation in clinical trials for SARS-CoV-2 patients. We report the antiviral effect of remdesivir, lopinavir, homorringtonine, and emetine against SARS-CoV-2 virus in Vero E6 cells with the estimated 50% effective concentration at 23.15 μM, 26.63 μM, 2.55 μM and 0.46 μM, respectively. Among the 16 compounds we tested, remdesivir, lopinavir, homoharringtonine, and emetine dihydrochloride were found to inhibit SARS-CoV-2 replication in Vero E6 cells with EC 50 under 100 μM (Table 1) . Importantly, we observed that some of the compounds currently undergoing clinical trials such as ribavirin, favipiravir, oseltamivir, or baloxavir showed no apparent antiviral effect against the SARS-CoV-2 virus in vitro at concentrations under 100 μM (Table 1) . abstract: An escalating pandemic by the novel SARS-CoV-2 virus is impacting global health and effective therapeutic options are urgently needed. We evaluated the in vitro antiviral effect of compounds that were previously reported to inhibit coronavirus replication and compounds that are currently under evaluation in clinical trials for SARS-CoV-2 patients. We report the antiviral effect of remdesivir, lopinavir, homorringtonine, and emetine against SARS-CoV-2 virus in Vero E6 cells with the estimated 50% effective concentration at 23.15 μM, 26.63 μM, 2.55 μM and 0.46 μM, respectively. Ribavirin or favipiravir that are currently evaluated under clinical trials showed no inhibition at 100 μM. Synergy between remdesivir and emetine was observed, and remdesivir at 6.25 μM in combination with emetine at 0.195 μM may achieve 64.9% inhibition in viral yield. Combinational therapy may help to reduce the effective concentration of compounds below the therapeutic plasma concentrations and provide better clinical benefits. url: https://api.elsevier.com/content/article/pii/S016635422030200X doi: 10.1016/j.antiviral.2020.104786 id: cord-340970-389t032s author: Choy, Wai-Yan title: Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development date: 2004-06-01 words: 3526.0 sentences: 172.0 pages: flesch: 51.0 cache: ./cache/cord-340970-389t032s.txt txt: ./txt/cord-340970-389t032s.txt summary: Background: The S (spike) protein of the etiologic coronavirus (CoV) agent of severe acute respiratory syndrome (SARS) plays a central role in mediating viral infection via receptor binding and membrane fusion between the virion and the host cell. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. The rabbit and monkey antisera against the synthetic peptides were diluted to 1:40-fold with PBS, and 10 L of each diluted serum was added to a well of the slide that was coated with SARS-CoV-infected African green monkey kidney Vero cells and incubated at 37°C for 1 h. The first batch of the rabbit and monkey antisera against the six synthetic peptides was collected 1 week after the second immunization and was tested for antibody specificity against the corresponding antigen (either conjugatefree or KLH-conjugated peptide) by ELISA analysis. abstract: Background: The S (spike) protein of the etiologic coronavirus (CoV) agent of severe acute respiratory syndrome (SARS) plays a central role in mediating viral infection via receptor binding and membrane fusion between the virion and the host cell. We focused on using synthetic peptides for developing antibodies against SARS-CoV, which aimed to block viral invasion by eliciting an immune response specific to the native SARS-CoV S protein. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. These synthetic peptides were used to immunize both rabbits and monkeys. Antisera collected 1 week after the second immunization were analyzed by ELISA and tested for antibody specificity against SARS-CoV by immunofluorescent confocal microscopy. Results: Four of our six synthetic peptides (S2, S3, S5, and S6) elicited SARS-CoV-specific antibodies, of which S5 (residues 788–820) and S6 (residues 1002–1030) exhibited immunogenic responses similar to those found in a parallel investigation using truncated recombinant protein analogs of the SARS-CoV S protein. This suggested that our S5 and S6 peptides may represent two minimum biologically active sequences of the immunogenic regions of the SARS-CoV S protein. Conclusions: Synthetic peptides can elicit specific antibodies to SARS-CoV. The study provides insights for the future development of SARS vaccine via the synthetic-peptide-based approach. url: https://www.ncbi.nlm.nih.gov/pubmed/15044316/ doi: 10.1373/clinchem.2003.029801 id: cord-325421-1ysn0kyr author: Christensen, Johanna title: Covid-19 Viremia, Serologies and Clinical Course in a Case Series of Transplant Recipients date: 2020-09-03 words: 2551.0 sentences: 169.0 pages: flesch: 56.0 cache: ./cache/cord-325421-1ysn0kyr.txt txt: ./txt/cord-325421-1ysn0kyr.txt summary: In this preliminary report, we find that immunocompromised transplant patients had higher rates of RNAemia (67%) than reported in the general population (15%), seeming absence of allo-immune injury despite systemic inflammation and formation of IgG overtime after recovery from infection. 8, 9 J o u r n a l P r e -p r o o f In this first case series, we report the characteristics, inflammatory immune response, biomarkers of graft injury along with SARS-CoV-2 RNAemia and serological response in a small cohort of kidney/liver transplant patients. Between, March 2020 and May 2020, six symptomatic kidney transplant recipients presented to the Virginia Commonwealth University hospital and tested positive for SARS-CoV-2. While it is not yet established if J o u r n a l P r e -p r o o f seroconversion confers immunity in the general population, 8, 9 the low re-infection rates and early reports of favorable efficacy of convalescent plasma in patients with severe COVID-19 manifestations [15] [16] [17] [18] suggest that this may be true. abstract: Here we report a single-center cohort of 6 patients (4 kidney-only, and 2 simultaneous liver/kidney transplants) diagnosed with COVID-19 at a median of 1.9 years (range=0.2-9.3 years) post-transplant. Five (of 6) patients required inpatient admission, two patients (mortality=33%) died. Among those with mortality, an increased concentration of inflammatory biomarkers [interleukin-6 (IL6) and C-reactive protein] was noted with a lack of response to IL-6 blockade, remdesivir and/or convalescent plasma. None of the kidney-only transplants (4/6; 67%) had elevation in plasma donor-derived cell-free DNA above the previously published cut-off of 1% suggesting absence of significant allo-immune injury. Four (of 5) admitted patients had detectable SARS-CoV-2 (severe acute respiratory syndrome–coronavirus 2) in blood on samples obtained at/during hospitalization. Of the 4 discharged patients, two patients with undetectable virus on repeat nasopharyngeal swabs had seroconversion with positive SARS-CoV-2 IgG formation at 30-48 days post-infection. One patient had prolonged shedding of virus on nasopharyngeal swab at 28 days post-discharge despite lack of symptoms. In this preliminary report, we find that immunocompromised transplant patients had higher rates of RNAemia (67%) than reported in the general population (15%), seeming absence of allo-immune injury despite systemic inflammation and formation of IgG overtime after recovery from infection. url: https://doi.org/10.1016/j.transproceed.2020.08.042 doi: 10.1016/j.transproceed.2020.08.042 id: cord-279520-zccd1mq5 author: Christian, Michael D. title: Possible SARS Coronavirus Transmission during Cardiopulmonary Resuscitation date: 2004-02-17 words: 4047.0 sentences: 199.0 pages: flesch: 45.0 cache: ./cache/cord-279520-zccd1mq5.txt txt: ./txt/cord-279520-zccd1mq5.txt summary: Infection of healthcare workers with the severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to occur primarily by either contact or large respiratory droplet transmission. We investigated a possible cluster of SARS-CoV infections in healthcare workers who used contact and droplet precautions during attempted cardiopulmonary resuscitation of a SARS patient. On the basis of the results of this investigation and previous reports of SARS transmission during aerosol-generating procedures, a systematic approach to the problem is outlined, including the use of the following: 1) administrative controls, 2) environmental engineering controls, 3) personal protective equipment, and 4) quality control. However, despite the use of infection control precautions and personal protective equipment designed to prevent contact and droplet transmission, episodes of SARS-CoV transmission to health-care workers have continued to occur under certain circumstances. We present the results of an investigation of the first reported transmission of SARS-CoV to healthcare workers that occurred during attempted cardiopulmonary resuscitation of a completely unresponsive SARS patient. abstract: Infection of healthcare workers with the severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to occur primarily by either contact or large respiratory droplet transmission. However, infrequent healthcare worker infections occurred despite the use of contact and droplet precautions, particularly during certain aerosol-generating medical procedures. We investigated a possible cluster of SARS-CoV infections in healthcare workers who used contact and droplet precautions during attempted cardiopulmonary resuscitation of a SARS patient. Unlike previously reported instances of transmission during aerosol-generating procedures, the index case-patient was unresponsive, and the intubation procedure was performed quickly and without difficulty. However, before intubation, the patient was ventilated with a bag-valve-mask that may have contributed to aerosolization of SARS-CoV. On the basis of the results of this investigation and previous reports of SARS transmission during aerosol-generating procedures, a systematic approach to the problem is outlined, including the use of the following: 1) administrative controls, 2) environmental engineering controls, 3) personal protective equipment, and 4) quality control. url: https://www.ncbi.nlm.nih.gov/pubmed/15030699/ doi: 10.3201/eid1002.030700 id: cord-327263-d5mmeu96 author: Christoff, A. P. title: Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2 date: 2020-09-05 words: 4134.0 sentences: 258.0 pages: flesch: 49.0 cache: ./cache/cord-327263-d5mmeu96.txt txt: ./txt/cord-327263-d5mmeu96.txt summary: Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint detect clear differences due to dilution alone, with point estimates from 0.43 to 0.61 Cq. In practice, observational data from 246 positive patients generated point estimates of mean Cq differences between individual tests and their corresponding pools ranging from 0.1 to 2.09 Cq. While such values are hardly significant in terms of analytical sensitivity, the expected counterparts for traditional pooling would range from 3.3 to 5 Cq under optimal amplification conditions. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint of diagnostic samples for SARS-CoV-2 can also perform swab pool analysis using the same detection methods and infrastructure already in use. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint CONCLUSION Pool testing is a major alternative for large-scale screening of SARS-CoV-2 in low prevalence populations. abstract: Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Here, we describe a pooling procedure in which nasopharyngeal swabs are pooled together at the time of sample collection (swab pooling), decreasing laboratory manipulation and minimizing dilution of the viral RNA present in the samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96.9% to 100%) and a specificity of 99.8% (Cr.I. 99.4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0.1 Cq (Cr.I. -0.98 to 1.17) to 2.09 Cq (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1.26%). This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Finally, these data demonstrate that swab pooling can significantly minimize sample dilution and sensitivity issues commonly seen in its traditional counterpart. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations. url: https://doi.org/10.1101/2020.09.03.20187732 doi: 10.1101/2020.09.03.20187732 id: cord-302442-jhio7mrl author: Chrzanowski, Wojciech title: Can Stem Cells Beat COVID-19: Advancing Stem Cells and Extracellular Vesicles Toward Mainstream Medicine for Lung Injuries Associated With SARS-CoV-2 Infections date: 2020-05-26 words: 4158.0 sentences: 180.0 pages: flesch: 38.0 cache: ./cache/cord-302442-jhio7mrl.txt txt: ./txt/cord-302442-jhio7mrl.txt summary: Stem cell therapies and, more recently, their secreted extracellular vesicles (EVs), are emerging as new promising treatments, which could attenuate inflammation but also regenerate the lung damage caused by COVID-19. In this review article, we outline the mechanisms of cytokine storm and lung damage caused by SARS-CoV-2 virus leading to COVID-19 disease and how mesenchymal stem cells (MSCs) and their secreted EVs can be utilized to tackle this damage by harnessing their regenerative properties, which gives them potential enhanced clinical utility compared to other investigated pharmacological treatments. The safety profile and efficacy of MSCs are well-established based on the results from a number of completed clinical studies investigating the therapeutic potential of these therapies in lung diseases such as ARDS (Matthay et al., 2019; and bronchopulmonary dysplasia (Namba, 2019) , cardiovascular diseases (Kim et al., 2015; Suvakov et al., 2020) , diabetes (Thakkar et al., 2015; Cho et al., 2018) , and spinal cord injury (Xu and Yang, 2019) . abstract: A number of medicines are currently under investigation for the treatment of COVID-19 disease including anti-viral, anti-malarial, and anti-inflammatory agents. While these treatments can improve patient's recovery and survival, these therapeutic strategies do not lead to unequivocal restoration of the lung damage inflicted by this disease. Stem cell therapies and, more recently, their secreted extracellular vesicles (EVs), are emerging as new promising treatments, which could attenuate inflammation but also regenerate the lung damage caused by COVID-19. Stem cells exert their immunomodulatory, anti-oxidant, and reparative therapeutic effects likely through their EVs, and therefore, could be beneficial, alone or in combination with other therapeutic agents, in people with COVID-19. In this review article, we outline the mechanisms of cytokine storm and lung damage caused by SARS-CoV-2 virus leading to COVID-19 disease and how mesenchymal stem cells (MSCs) and their secreted EVs can be utilized to tackle this damage by harnessing their regenerative properties, which gives them potential enhanced clinical utility compared to other investigated pharmacological treatments. There are currently 17 clinical trials evaluating the therapeutic potential of MSCs for the treatment of COVID-19, the majority of which are administered intravenously with only one clinical trial testing MSC-derived exosomes via inhalation route. While we wait for the outcomes from these trials to be reported, here we emphasize opportunities and risks associated with these therapies, as well as delineate the major roadblocks to progressing these promising curative therapies toward mainstream treatment for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32574317/ doi: 10.3389/fbioe.2020.00554 id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 words: 2971.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-261279-6mef38eo.txt txt: ./txt/cord-261279-6mef38eo.txt summary: RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. abstract: BACKGROUND: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. METHODS: We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. CONCLUSIONS: The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32031583/ doi: 10.1093/clinchem/hvaa029 id: cord-336517-v7z62tld author: Chu, Hsu-Feng title: Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine date: 2018-08-20 words: 5193.0 sentences: 324.0 pages: flesch: 59.0 cache: ./cache/cord-336517-v7z62tld.txt txt: ./txt/cord-336517-v7z62tld.txt summary: Further studies suggest that PEDV PL2 pro exhibits much higher DUB activity than that of SARS-and MERS-CoV PL pro s and can be inhibited by the anti-leukemia drug 6-thioguanine (6TG). Previous studies suggested that the Ubl domain was not involved in the catalytic activity of SARS-and MERS-CoV PL pro s (Chou et al., 2012; Clasman et al., 2017) . Overall, the secondary, tertiary and quaternary structures of the PEDV PL2 pro catalytic core are similar to those of SARS-and MERS-CoV PL pro s, even though their sequence identity is only 22-25% (Fig. S1 ). In contrast, previous studies suggested that the binding site of 6TG for SARS-and MERS-CoV PL pro s may be near the catalytic triad''s cysteine residue due to its competitive pattern of inhibition Chou et al., 2008) . Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin abstract: Porcine epidemic diarrhea virus (PEDV) is a coronavirus (CoV) discovered in the 1970s that infects the intestinal tract of pigs, resulting in diarrhea and vomiting. It can cause extreme dehydration and death in neonatal piglets. In Asia, modified live attenuated vaccines have been used to control PEDV infection in recent years. However, a new strain of PEDV that belongs to genogroup 2a appeared in the USA in 2013 and then quickly spread to Canada and Mexico as well as Asian and European countries. Due to the less effective protective immunity provided by the vaccines against this new strain, it has caused considerable agricultural and economic loss worldwide. The emergence of this new strain increases the importance of understanding PEDV as well as strategies for inhibiting it. Coronaviral proteases, including main proteases and papain-like proteases, are ideal antiviral targets because of their essential roles in viral maturation. Here we provide a first description of the expression, purification and structural characteristics of recombinant PEDV papain-like protease 2, moreover present our finding that 6-thioguanine, a chemotherapeutic drug, in contrast to its competitive inhibition on SARS- and MERS-CoV papain-like proteases, is a noncompetitive inhibitor of PEDV papain-like protease 2. url: https://www.sciencedirect.com/science/article/pii/S0166354218302183 doi: 10.1016/j.antiviral.2018.08.011 id: cord-337812-arivkkj0 author: Chu, Ling-Hon Matthew title: Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry date: 2006-03-07 words: 6860.0 sentences: 286.0 pages: flesch: 52.0 cache: ./cache/cord-337812-arivkkj0.txt txt: ./txt/cord-337812-arivkkj0.txt summary: To screen the substrate specificity of SARS-CoV 3CL pro in a rapid and highthroughput manner in contrast to the traditional tedious procedures, we applied the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis in combination with the novel "cartridge replacement" solid-phase peptide synthesis approach to investigate the biological significance of amino acid residues in the P2, P3, P4, P1¢, P2¢, and P3¢ positions that are flanking the conserved Gln residue in the P1 position at the SARS-CoV 3CL pro cleavage site (Schechter and Berger 1967; Fan et al. In this study, we used MALDI-TOF MS analysis in combination with the solid-phase peptide synthesis approach to examine the biological significance of amino acid residues in a total of six target positions at the SARS-CoV 3CL pro cleavage sites, including the P2, P3, and P4 positions at the amino side of the P1 position; and the P1¢, P2¢, and P3¢ positions at the carboxyl side of the P1 position (Table 1) . abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CL(pro)) mediates extensive proteolytic processing of replicase polyproteins, and is considered a promising target for anti-SARS drug development. Here we present a rapid and high-throughput screening method to study the substrate specificity of SARS-CoV 3CL(pro). Six target amino acid positions flanking the SARS-CoV 3CL(pro) cleavage site were investigated. Each batch of mixed peptide substrates with defined amino acid substitutions at the target amino acid position was synthesized via the “cartridge replacement” approach and was subjected to enzymatic cleavage by recombinant SARS-CoV 3CL(pro). Susceptibility of each peptide substrate to SARS-CoV 3CL(pro) cleavage was monitored simultaneously by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The hydrophobic pocket in the P2 position at the protease cleavage site is crucial to SARS-CoV 3CL(pro)-specific binding, which is limited to substitution by hydrophobic residue. The binding interface of SARS-CoV 3CL(pro) that is facing the P1′ position is suggested to be occupied by acidic amino acids, thus the P1′ position is intolerant to acidic residue substitution, owing to electrostatic repulsion. Steric hindrance caused by some bulky or β-branching amino acids in P3 and P2′ positions may also hinder the binding of SARS-CoV 3CL(pro). This study generates a comprehensive overview of SARS-CoV 3CL(pro) substrate specificity, which serves as the design basis of synthetic peptide-based SARS-CoV 3CL(pro) inhibitors. Our experimental approach is believed to be widely applicable for investigating the substrate specificity of other proteases in a rapid and high-throughput manner that is compatible for future automated analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/16600962/ doi: 10.1110/ps.052007306 id: cord-277498-hdhq99k2 author: Chua, Melvin L.K. title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic date: 2020-05-15 words: 3345.0 sentences: 158.0 pages: flesch: 45.0 cache: ./cache/cord-277498-hdhq99k2.txt txt: ./txt/cord-277498-hdhq99k2.txt summary: title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic These scenarios would be considered high-risk for SARS-CoV-2 transmission, and the HCW consulting the patient would require full personal protection equipment (PPE) consisting of N95 mask, surgical gowns, gloves, and goggles/face shields 16 . Following the completion of treatment any patient with direct contact with a SARS-CoV-2 infected individual or who has personally tested positive or has symptoms of COVID-19 should not be seen in an oncology clinic for a follow-up visit. When it is challenging to distinguish between post-treatment edema and residual tumor on imaging, a detailed physical exam including endoscopy may be required, and as aforementioned, full PPE is required to protect the HCW from transmission of SARS-CoV-2 through aerosolization during NPL. Herein, we focused on the impact of this pandemic on the management of head and neck cancer patients who are undergoing or have completed radiation treatment. abstract: The SARS-CoV-2 pandemic has significantly impacted healthcare delivery around the world. Elective procedures and routine follow-ups have been cancelled and/or converted to tele-health visits by many systems. In this article, we focus on recommendations for the surveillance of head and neck cancer patients during and following radiotherapy treatment. We synthesized information from clinical evidence, existing recommendations from the NCCN, and variations in practice between multiple academic tertiary cancer centers to develop the proposed guidance. url: https://www.ncbi.nlm.nih.gov/pubmed/32426556/ doi: 10.1016/j.adro.2020.04.031 id: cord-290414-8i8g0xdc author: Chuan, Ong Sze title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? date: 2020-06-21 words: 398.0 sentences: 32.0 pages: flesch: 62.0 cache: ./cache/cord-290414-8i8g0xdc.txt txt: ./txt/cord-290414-8i8g0xdc.txt summary: title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? Unlike face masks which provided some protection against both aerosols and droplets, slit lamp shields conferred protection only against direct large droplet transmission, with a limited role in reducing aerosol transmission risk. The SARS-CoV-2 is primarily transmitted via respiratory droplets, contact with 1 contaminated surfaces, or free-floating aerosols. We attempted to replicate the 5 spread of infected aerosols and large droplets in the clinical setting of a slit lamp 6 examination, to evaluate the efficacy of protective equipment in reducing the risk of viral 7 4 The experimental setup ( Figure S1 , available online at 12 www.aaojournal.org) consisted of a slit lamp (B900 Slit Lamp, Haag-Streit Holding AG, 13 Switzerland), a mannequin face which represented the ophthalmologist, and a spray bottle at 14 the chin rest which represented respiratory particle production from the patient. abstract: Unlike face masks which provided some protection against both aerosols and droplets, slit lamp shields conferred protection only against direct large droplet transmission, with a limited role in reducing aerosol transmission risk. url: https://doi.org/10.1016/j.ophtha.2020.06.031 doi: 10.1016/j.ophtha.2020.06.031 id: cord-353479-kwi8zxo6 author: Chuang, H.-L. title: Impact of enhanced infection control procedures on clinical outcome following resuscitation attempts date: 2007-11-30 words: 2902.0 sentences: 144.0 pages: flesch: 39.0 cache: ./cache/cord-353479-kwi8zxo6.txt txt: ./txt/cord-353479-kwi8zxo6.txt summary: Other strict hospital ICMs in period 2 included the following: (i) all new admissions were required to be examined by our emergency department''s SARS screening team; (ii) all febrile patients were required to be admitted to the fever screening ward regardless of their diagnoses; (iii) unnecessary contact between HCWs was restricted and regular meetings and conferences were cancelled; (iv) each step of the standard operating procedure was strictly audited during resuscitation. There were also more emergency resuscitations performed without intubation and a higher number of ''do not resuscitate'' orders signed during resuscitation in the period of strict implementation of ICMs. These changes resulted in an abnormal situation in which the hospital''s facilities were adversely affected and the ability of the hospital to provide patients with medical care during the SARS outbreak was reduced. abstract: Summary The impact of infection control measures (ICMs) on emergency resuscitation during an outbreak is unclear. The purpose of this retrospective observational study was to investigate the outcomes of emergency resuscitation after implementation of ICMs. Data were collected for the period 1 January to 4 July in 2003 from a 1732-bed tertiary care hospital in central Taiwan. Non-trauma patients who required emergency resuscitation were classified into two groups: before (period 1), and after (period 2), the date on which strict ICMs were implemented. The analysis variables included demographic data of patients, place of resuscitation, number of participating resuscitators, response time and duration of resuscitation, fever, pneumonia status and results of resuscitation. The response time was unchanged but the number of patient resuscitations without an emergency intubation, rapid sequence intubation or a ‘do not resuscitate’ order increased from 88 (24.4%), 23 (6.4%) and 16 (4.4%) in period 1 to 103 (33.0%), 32 (10.3%) and 29 (9.3%) in period 2, respectively. The failure rate of resuscitation was significantly higher in period 2 (odds ratio: 1.59, 95% confidence interval: 1.17–2.16). The number of emergency resuscitations in patients with fever or pneumonia was not significantly different between these two periods. In conclusion, strict ICM implementation appeared to play a role in the increased failure rate in emergency resuscitation. Normal provision of healthcare to patients and adequate protection of healthcare workers during emergency resuscitation will be of paramount importance during the next outbreak of a highly contagious disease. url: https://api.elsevier.com/content/article/pii/S0195670107002940 doi: 10.1016/j.jhin.2007.08.015 id: cord-331563-4yvfdqbq author: Chughtai, Abrar Ahmad title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis date: 2013-05-31 words: 5634.0 sentences: 312.0 pages: flesch: 51.0 cache: ./cache/cord-331563-4yvfdqbq.txt txt: ./txt/cord-331563-4yvfdqbq.txt summary: title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis BACKGROUND: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). RESULTS: Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). This study aimed to examine available policies and guidelines around the use of masks and respirator for HCWs, for the prevention of influenza, SARS and TB; and to describe areas of consistency and inconsistency between guidelines, as well as gaps, with reference to the WHO and the CDC guidelines. Health care organizations and countries have different policies and guidelines around mask and respirator use for influenza, SARS and TB. abstract: BACKGROUND: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). This study aimed to examine available policies and guidelines around the use of masks and respirators in HCWs and to describe areas of consistency between guidelines, as well as gaps in the recommendations, with reference to the WHO and the CDC guidelines. METHODS: Policies and guidelines related to mask and respirator use for the prevention of influenza, SARS and TB were examined. Guidelines from the World Health Organization (WHO), the Center for Disease Control and Prevention (CDC), three high-income countries and six low/middle-income countries were selected. RESULTS: Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). However, for pandemic influenza and SARS, the WHO recommends mask use in low risk and respirators in high risk situations, whereas, the CDC recommends respirators in both low and high risk situations. Amongst the nine countries reviewed, there are variations in the recommendations for all three diseases. While, some countries align with the WHO recommendations, others align with those made by the CDC. The choice of respirator and the level of filtering ability vary amongst the guidelines and the different diseases. Lastly, none of the policies discuss reuse, extended use or the use of cloth masks. CONCLUSION: Currently, there are significant variations in the policies and recommendations around mask and respirator use for protection against influenza, SARS and TB. These differences may reflect the scarcity of level-one evidence available to inform policy development. The lack of any guidelines on the use of cloth masks, despite widespread use in many low and middle-income countries, remains a policy gap. Health organizations and countries should jointly evaluate the available evidence, prioritize research to inform evidence gaps, and develop consistent policy on masks and respirator use in the health care setting. url: https://www.ncbi.nlm.nih.gov/pubmed/23725338/ doi: 10.1186/1756-0500-6-216 id: cord-276857-i948aq4b author: Chung, Grace TY title: A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date: 2005-10-18 words: 2331.0 sentences: 129.0 pages: flesch: 50.0 cache: ./cache/cord-276857-i948aq4b.txt txt: ./txt/cord-276857-i948aq4b.txt summary: We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [8, 12] . In this study, we demonstrate the feasibility of the adoption of allelic discrimination assays based on the use of fluorogenic oligonucleotide probes for the genotyping of SARS-CoV isolates. Our study has clearly demonstrated the feasibility of using allelic discrimination assays as a method for genetic characterization of SARS-CoV genotypes in patients. Genotype of SARS-CoV culture isolates from 30 patients determined by Taqman Allelic Discrimination assays Petric M, Skowronski DM abstract: BACKGROUND: The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. METHODS: Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. RESULTS: Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort. CONCLUSION: We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/16229749/ doi: 10.1186/1471-2334-5-87 id: cord-334717-zg9f19p8 author: Chung, Mina K. title: SARS-CoV-2 and ACE2: The biology and clinical data settling the ARB and ACEI controversy date: 2020-08-06 words: 6048.0 sentences: 311.0 pages: flesch: 45.0 cache: ./cache/cord-334717-zg9f19p8.txt txt: ./txt/cord-334717-zg9f19p8.txt summary: Angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) have been reported to increase ACE2 expression in animal models, and worse outcomes are reported in patients with co-morbidities commonly treated with these agents, leading to controversy during the COVID-19 pandemic over whether these drugs might be helpful or harmful. Recently there has been controversy over whether use of angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) might be harmful in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with cardiovascular disease, hypertension, or diabetes mellitus under treatment with these agents. SARS-CoV-2, the coronavirus causing COVID-19, enters host cells via binding of the virus spike protein to angiotensin-converting enzyme 2 (ACE2). In a study of 2877 hospitalized patients with COVID-19, 850 had hypertension of which 183 were treated with renin-angiotensin-aldosterone system inhibitors (RAASi) and 527 were not; RAASi use was not associated with severity of disease or mortality [66] . abstract: BACKGROUND: SARS-CoV-2 enters cells by binding of its spike protein to angiotensin-converting enzyme 2 (ACE2). Angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) have been reported to increase ACE2 expression in animal models, and worse outcomes are reported in patients with co-morbidities commonly treated with these agents, leading to controversy during the COVID-19 pandemic over whether these drugs might be helpful or harmful. METHODS: : Animal, in vitro and clinical data relevant to the biology of the renin-angiotensin system (RAS), its interaction with the kallikrein-kinin system (KKS) and SARS-CoV-2, and clinical studies were reviewed. FINDINGS AND INTERPRETATION: SARS-CoV-2 hijacks ACE2to invade and damage cells, downregulating ACE2, reducing its protective effects and exacerbating injurious Ang II effects. However, retrospective observational studies do not show higher risk of infection with ACEI or ARB use. Nevertheless, study of the RAS and KKS in the setting of coronaviral infection may yield therapeutic targets. url: https://www.ncbi.nlm.nih.gov/pubmed/32771682/ doi: 10.1016/j.ebiom.2020.102907 id: cord-023510-gd4phncm author: Chuo, Hsin-You title: Theme Park Visitors’ Responses to the SARS Outbreak in Taiwan date: 2007-05-02 words: 5264.0 sentences: 230.0 pages: flesch: 48.0 cache: ./cache/cord-023510-gd4phncm.txt txt: ./txt/cord-023510-gd4phncm.txt summary: 1. Can a significant discriminant function be developed to interpret the differences between respondents who did and did not visit theme parks during the SARS outbreak period in Taiwan on the basis of their personal characteristics? In addition to the information of respondents'' general demographics, their patronage frequency in the last year and whether they visited theme parks in the period of the SARS outbreak, the question content also consisted of scale items to measure ''''benefit sought,'''' ''''product involvement,'''' and ''''risk perception.'''' Ten individual benefit scale items were derived from Pearce''s (1993) Leisure Ladder Model for theme park visitors. Thus, on the one hand, whether or not the respondents visited theme parks during the SARS outbreak was adopted to be the dependant (criterion) variable; on the other, respondents'' age, their patronage frequency in the last year, and the factors condensed from scale items of respondents'' risk perception, benefit sought, and product involvement were adopted to be the independent variables (predictors) in the developing discriminant function. abstract: The purpose of this study is to examine empirically different characteristics between theme park visitors who did and did not visit theme parks during the SARS outbreak period in Taiwan. The data consisting of 1,255 respondents were obtained from visitors to the five leading theme parks. Discriminant analysis was used to analyze respondents’ characteristics such as age, benefit sought, product involvement, and risk perception to examine significant differences between the two categories of respondents. Results of this study showed that younger or more frequent visitors more likely continued to visit theme parks during the SARS outbreak. Besides, visitors who continued to visit theme parks perceived greater infectious risk than those who did not visit theme parks during the SARS outbreak. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170396/ doi: 10.1016/s1745-3542(06)03006-2 id: cord-322913-sq9mq6f1 author: Ciabattini, Annalisa title: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date: 2020-11-06 words: 8068.0 sentences: 363.0 pages: flesch: 33.0 cache: ./cache/cord-322913-sq9mq6f1.txt txt: ./txt/cord-322913-sq9mq6f1.txt summary: The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of innate and adaptive immune responses, and the lack of a clear correlate of protection, make the design of vaccination strategies for older people extremely challenging (Fig. 3 ). abstract: The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the vaccination of older people. The development of a vaccine against SARS-CoV-2 tailored for the elderly population faces the challenge of the poor immune responsiveness of the older population due to immunosenescence, comorbidities, and pharmacological treatments. Moreover, it is likely that the inflammaging phenotype associated with age could both influence vaccination efficacy and exacerbate the risk of COVID-19-related “cytokine storm syndrome” with an overlap between the factors which impact vaccination effectiveness and those that boost virulence and worsen the prognosis of SARS-CoV-2 infection. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. In the ongoing effort in vaccine development, different SARS-CoV-2 vaccine candidates have been developed, tested in pre-clinical and clinical studies and are undergoing clinical testing, but only a small fraction of these are currently being tested in the older fraction of the population. Recent advances in systems biology integrating clinical, immunologic, and omics data can help to identify stable and robust markers of vaccine response and move towards a better understanding of SARS-CoV-2 vaccine responses in the elderly. url: https://doi.org/10.1007/s00281-020-00821-0 doi: 10.1007/s00281-020-00821-0 id: cord-342396-n3txsvf7 author: Ciaglia, Elena title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children date: 2020-04-23 words: 1701.0 sentences: 83.0 pages: flesch: 47.0 cache: ./cache/cord-342396-n3txsvf7.txt txt: ./txt/cord-342396-n3txsvf7.txt summary: title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children In another case control study conducted in the north eastern Chinese Han population, the serum ACE2 activity negatively correlated with body mass index (BMI), pulse pressure, and estrogen levels in female EH (essential hypertension) patients (14) . Cases of coronavirus disease 2019 (COVID-19) among children in China have been less severe than those in adults, according to a new study. Now, circulating level of ACE2 may have prognostic effect in monitoring COVID-infection, and the genetic analysis of ACE2 polymorphisms might be a key element of individualized care for its prevention, diagnosis, and treatment. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32391299/ doi: 10.3389/fped.2020.00206 id: cord-017903-92hnaiyc author: Cieslak, Theodore J. title: Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date: 2018-07-07 words: 7492.0 sentences: 335.0 pages: flesch: 46.0 cache: ./cache/cord-017903-92hnaiyc.txt txt: ./txt/cord-017903-92hnaiyc.txt summary: These two facilities cared for seven Ebola virus disease (EVD) patients during the 2014-2016 outbreak, while another two were cared for at the National Institutes of Health''s Special Clinical Studies Unit, which had also developed HLCC capability. First, patients harboring diseases caused by pathogens that require handling under BSL-4 conditions in the laboratory would seem to be obvious candidates for clinical management under HLCC conditions. Lujo virus, an Old World arenavirus closely related to Lassa, was first described in 2008 as the cause of a single outbreak of viral hemorrhagic fever involving five patients in Lusaka, Zambia, and Johannesburg, South Africa (the name, Lujo, derives from the two cities) [20] . It would seem prudent to manage patients potentially harboring such diseases under HLCC conditions when feasible and to handle their causative viruses in a BSL-4 laboratory. abstract: High-level containment care involves the management of patients with highly hazardous communicable diseases in specialized biocontainment units possessing a unique collection of engineering, administrative, and personnel controls. These controls are more stringent than those found in conventional airborne infection isolation rooms and provide additional safeguards against nosocomial disease transmission. Borne amidst a convergence of events in 1969, the employment of HLCC units was validated during the 2014–2016 Ebola virus disease outbreak, and the United States (as well as many other nations) is in the process of expanding its HLCC capacity. Beyond Ebola, however, the specific diseases that might warrant care in a HLCC unit remain unclear. We review here the fascinating history of HLCC and of biocontainment units and make recommendations regarding those highly hazardous communicable diseases that might optimally be managed in these units. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122591/ doi: 10.1007/978-3-319-77032-1_1 id: cord-340305-jtvn9tlm author: Cimolai, Nevio title: A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19 date: 2020-09-19 words: 5105.0 sentences: 294.0 pages: flesch: 40.0 cache: ./cache/cord-340305-jtvn9tlm.txt txt: ./txt/cord-340305-jtvn9tlm.txt summary: At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Others have found strong correlations between neutralizing antibodies and EIA-detected antibodies to various SARS-CoV-2 antigens [41, 42] .Some have found diversity in immune responses contingent on the nature of presenting disease [38, 43] . With the availability of viral antigen, most scientists in the know-how would be able to fashion a test for antibody determination in short order and most would likely choose an enzyme immunoassay (EIA) (or nearly equivalent non-enzymebased assay) for its potential of automation and widespread use. Sensitive and specific detection of low-level antibody responses in mild Middle East Respiratory Syndrome coronavirus infections A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients abstract: Until either efficacious therapy or vaccination for COVID-19 is achieved, there will be a need to regain world economic stability while yet controlling the pandemic with current approaches. For those infected thus far, there is a prevailing perspective that devising recognition for protective immunity will progressively allow segments of society to return to some functionality more than is existing. At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Serum neutralizing antibody more easily fulfills the latter requisite, but current live virus methods for neutralization prevent large-scale application. It is conceivable that the exposure of previously infected individuals can allow for the definition of protective thresholds of neutralizing antibody. Thereafter, many other antibody assays will be able to screen for surrogate protection after correlations with protective neutralizing antibody are made. Specificity of common antibody tests would benefit from confirmatory blocking systems or confirmatory immunoblotting fingerprints with well-defined antigen(s). The opportunity for the scientific community to make these assessments is evident in the current context of the COVID-19 epidemic given the large numbers of infected individuals worldwide. Such information will also be vital to guide vaccine development and/or immunotherapy. url: https://doi.org/10.1007/s42399-020-00533-4 doi: 10.1007/s42399-020-00533-4 id: cord-352146-i4ezsclf author: Cimolai, Nevio title: Efficacy of povidone‐iodine to reduce viral load date: 2020-07-31 words: 580.0 sentences: 43.0 pages: flesch: 52.0 cache: ./cache/cord-352146-i4ezsclf.txt txt: ./txt/cord-352146-i4ezsclf.txt summary: (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. While povidone-iodine may be the main ingredient in the specific mouthwash preparation, there are often a number of unlisted ingredients (e.g., alcohol) which can potentially provide both antisepsis and RT-PCR inhibition. As another form of control, however, it would be of relevance to see what the lavage properties of gargling in itself have for reducing viral load in those samples assessed. COVID-19, povidone-iodine, quantitation, respiratory, SARS-CoV-2 Is povidone-iodine mouthwash effective against SARS-CoV-2? abstract: Martinez-Lamas et al. (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. Chin et al. (2020) have also proposed some efficacy for the antiviral properties of povidone-iodine in another context. Both of these findings offer some promise for implementing povidone-iodine as a tool for prevention. Their findings are also consistent with the use of halogens generally as coronavirus antivirals (Cimolai 2020a). The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. Although clinical samples are often extracted prior to amplification, a number of inhibitors may be present that may not be removed sufficiently. url: https://doi.org/10.1111/odi.13557 doi: 10.1111/odi.13557 id: cord-300319-9k8zseao author: Cinatl Jr., J. title: Infection of cultured intestinal epithelial cells with severe acute respiratory syndrome coronavirus date: 2004 words: 3017.0 sentences: 159.0 pages: flesch: 42.0 cache: ./cache/cord-300319-9k8zseao.txt txt: ./txt/cord-300319-9k8zseao.txt summary: To identify a model for the study of intestinal pathogenesis of severe acute respiratory syndrome (SARS) we tested the sensitivity of six human intestinal epithelial cell lines to infection with SARS coronavirus (SARS-CoV). In both cell lines, SARS-CoV infection deregulated expression of cellular genes which may be important for the intestinal pathogenesis of SARS. To investigate whether ACE2 is a functional receptor for SARS-CoV in intestinal epithelial cell cultures, the cells were pre-treated for 60 min at 37°C with goat antibody directed against the human ACE2 ectodomain (R&D Systems; Wiesbaden-Nordenstadt, Germany). SARS-CoV infection of Caco-2 cells up-regulated OAS2 and MXA but not PKR genes. The discrepancy between transcriptional activation of IFN-induced genes and the ability of SARS-CoV to replicate in Caco-2 cells could be explained by the existence of a specific viral mechanism for escaping IFNinduced anti-viral effects common to most viruses [28] . This justifies the use of intestinal cell lines as a model to study the direct effects of SARS-CoV infection on gene expression in permissive human cells. abstract: To identify a model for the study of intestinal pathogenesis of severe acute respiratory syndrome (SARS) we tested the sensitivity of six human intestinal epithelial cell lines to infection with SARS coronavirus (SARS-CoV). In permissive cell lines, effects of SARS-CoV on cellular gene expression were analysed using high-density oligonucleotide arrays. Caco-2 and CL-14 cell lines were found to be highly permissive to SARS-CoV, due to the presence of angiotensin-converting enzyme 2 as a functional receptor. In both cell lines, SARS-CoV infection deregulated expression of cellular genes which may be important for the intestinal pathogenesis of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15316659/ doi: 10.1007/s00018-004-4222-9 id: cord-294933-oc2glu4a author: Cinesi Gómez, César title: Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date: 2020-06-19 words: 5643.0 sentences: 337.0 pages: flesch: 45.0 cache: ./cache/cord-294933-oc2glu4a.txt txt: ./txt/cord-294933-oc2glu4a.txt summary: The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations. abstract: Abstract Coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by a newly emergent coronavirus, that was first recognized in Wuhan, China, in December 2019. Currently, the World Health Organization (WHO) has defined the infection as a global pandemic and there is a health and social emergency for the management of this new infection. While most people with COVID-19 develop only mild or uncomplicated illness, approximately 14% develop severe disease that requires hospitalization and oxygen support, and 5% require admission to an intensive care unit. In severe cases, COVID-19 can be complicated by the acute respiratory distress syndrome (ARDS), sepsis and septic shock, and multiorgan failure. This consensus document has been prepared on evidence-informed guidelines developed by a multidisciplinary panel of health care providers from four Spanish scientific societies (Spanish Society of Intensive Care Medicine [SEMICYUC], Spanish Society of Pulmonologists [SEPAR], Spanish Society of Emergency [SEMES], Spanish Society of Anesthesiology, Reanimation, and Pain [SEDAR]) with experience in the clinical management of patients with COVID-19 and other viral infections, including SARS, as well as sepsis and ARDS. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. This consensus guidance should serve as a foundation for optimized supportive care to ensure the best possible chance for survival and to allow for reliable comparison of investigational therapeutic interventions as part of randomized controlled trials. url: https://www.sciencedirect.com/science/article/pii/S217357272030120X doi: 10.1016/j.medine.2020.03.002 id: cord-262159-8y0q45gr author: Ciorba, Andrea title: Don’t forget ototoxicity during the SARS-CoV-2 (Covid-19) pandemic! date: 2020-07-10 words: 956.0 sentences: 59.0 pages: flesch: 41.0 cache: ./cache/cord-262159-8y0q45gr.txt txt: ./txt/cord-262159-8y0q45gr.txt summary: Aim of this communication is to remind clinical professionals to be aware of ototoxic side effects of several specific drugs proposed for the treatment of the new virus SARS-CoV-2 (Covid-19). In particular, chloroquine and hydroxychloroquine have been widely promoted and used during the pandemic; 2,3 however, in the past, data in the literature have suggested that in many treated cases side effects such as sensorineural hearing loss, tinnitus, and/or persistent imbalance were common. However, ototoxicity has been reported among the possible side effects of the adenosine nucleotide analogues; 5, 6 specifically, data in the literature report that patients may develop irreversible unilateral or bilateral hearing loss and tinnitus due to the use of these drugs, usually after a few weeks of administration. 7, 8 Lopinavir, a nucleoside reverse-transcriptase inhibitor, proposed in the treatment of SARS-CoV-2 infections, has been related to the onset of sensorineural hearing loss, 9 after several weeks of administration. abstract: Aim of this communication is to remind clinical professionals to be aware of ototoxic side effects of several specific drugs proposed for the treatment of the new virus SARS-CoV-2 (Covid-19). In particular, chloroquine and hydroxychloroquine, azithromycin, as well as antiviral drugs such as remdesivir, favipiravir and lopinavir can all present potential ototoxic side effects. The data in the literature do not offer specific information on their potential synergetic effects nor on their interactions. url: https://doi.org/10.1177/2058738420941754 doi: 10.1177/2058738420941754 id: cord-338798-xsun927w author: Ciorba, Andrea title: Ototoxicity prevention during the SARS-CoV-2 (Covid-19) emergency date: 2020-10-17 words: 499.0 sentences: 37.0 pages: flesch: 42.0 cache: ./cache/cord-338798-xsun927w.txt txt: ./txt/cord-338798-xsun927w.txt summary: • To remind the risk of ototoxicity when using chloroquine and hydroxychloroquine, in particular as prophylactic agents against SARS-CoV-2, during the pandemic. • Healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. eventually adequate treatment is established (3) (4) (5) . Pure tone audiometry represents the main instrument for the identification and classification of hearing impairment; however, Otoacoustic Emissions (OAEs) are reported to be very sensitive in evaluating early manifestations of cochlear damages (6), as ototoxic drugs typically affect primarily outer hair cells (1, (3) (4) (5) . Therefore, healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. Clearly, even without a fatal condition, it is important to avoid the onset of ototoxic manifestations, especially when chloroquine and hydroxychloroquine are administered with a prophylaxis intent. abstract: • To remind the risk of ototoxicity when using chloroquine and hydroxychloroquine, in particular as prophylactic agents against SARS-CoV-2, during the pandemic. • Otoacoustic Emissions (OAEs) are reported to be very sensitive in evaluating early manifestations of cochlear ototoxic damages. • Healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. url: https://api.elsevier.com/content/article/pii/S2213716520302617 doi: 10.1016/j.jgar.2020.09.030 id: cord-252804-u7tz6xzz author: Ciotti, Marco title: COVID-19 Outbreak: An Overview date: 2020-04-07 words: 3558.0 sentences: 186.0 pages: flesch: 50.0 cache: ./cache/cord-252804-u7tz6xzz.txt txt: ./txt/cord-252804-u7tz6xzz.txt summary: Inoculation of bronchoalveolar lavage fluid obtained from patients with pneumonia of unknown origin into human airway epithelial cells and Vero E6 and Huh7 cell lines led to the isolation of a novel coronavirus, SARS-CoV-2, previously named 2019-nCov [1] . As soon as on January 7, 2020, the Chinese health authorities had declared that a novel coronavirus was responsible for this outbreak of pneumonia in Wuhan, a European network of academic and public laboratories designed an rRT-PCR protocol based on the comparison and alignment of previously available SARS-CoV and bat-related coronavirus genome sequences as well as five sequences derived from the novel coronavirus SARS-CoV-2 made available by the Chinese authorities [23] . Regarding the sites under positive selective pressure found on the Spike glycoprotein, the results have shown that amino acid position 536 in COVID-19 has an Asn residue, while the Bat SARS-like coronavirus has a Gln 4 DOI: 10.1159/000507423 residue; the SARS virus, instead, has an Asp residue. Phylogenetic analysis of the SARS-CoV-2 genomes showed that the novel coronavirus responsible for the pneumonia outbreak in Wuhan, China, belongs to the Betacoronavirus genus, subgenus Sarbecovirus [37] . abstract: BACKGROUND: In late December 2019, Chinese health authorities reported an outbreak of pneumonia of unknown origin in Wuhan, Hubei Province. SUMMARY: A few days later, the genome of a novel coronavirus was released (http://virological.org/t/novel-2019-coronavirus-genome/319; Wuhan-Hu-1, GenBank accession No. MN908947) and made publicly available to the scientific community. This novel coronavirus was provisionally named 2019-nCoV, now SARS-CoV-2 according to the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. SARS-CoV-2 belongs to the Coronaviridae family, Betacoronavirus genus, subgenus Sarbecovirus. Since its discovery, the virus has spread globally, causing thousands of deaths and having an enormous impact on our health systems and economies. In this review, we summarize the current knowledge about the epidemiology, phylogenesis, homology modeling, and molecular diagnostics of SARS-CoV-2. KEY MESSAGES: Phylogenetic analysis is essential to understand viral evolution, whereas homology modeling is important for vaccine strategies and therapies. Highly sensitive and specific diagnostic assays are key to case identification, contact tracing, identification of the animal source, and implementation of control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/32259829/ doi: 10.1159/000507423 id: cord-283440-8du0s33p author: Ciuca, Ioana M title: COVID-19 in Children: An Ample Review date: 2020-06-25 words: 5636.0 sentences: 313.0 pages: flesch: 45.0 cache: ./cache/cord-283440-8du0s33p.txt txt: ./txt/cord-283440-8du0s33p.txt summary: The aim of this review was to describe the current knowledge about coronavirus disease 2019 (COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) in children, from epidemiological, clinical, and laboratory perspectives, including knowledge on the disease course, treatment, and prognosis. This review highlights that COVID-19 in children is similar to the disease in the adult population, but with particularities regarding clinical manifestations, laboratory test results, chest imaging, and treatment. It started at the end of 2019, when many adult patients with a new form of pneumonia that was frequently fatal were admitted to Chinese hospitals; this illness was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [11] [12] [13] This study aimed to review the current data on SARS-CoV-2 infection in children, from epidemiological, clinical, and laboratory perspectives, including data on the disease course, treatment, and prognosis. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: The aim of this review was to describe the current knowledge about coronavirus disease 2019 (COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) in children, from epidemiological, clinical, and laboratory perspectives, including knowledge on the disease course, treatment, and prognosis. An extensive literature search was performed to identify papers on COVID-19 (SARS-CoV-2 infection) in children, published between January 1, 2020 and April 1, 2020. There were 44 relevant papers on COVID-19 in children. The results showed that COVID-19 occurs in 0.39–12.3% of children. Clinical signs and symptoms are comparable to those in adults, but milder forms and a large percentage of asymptomatic carriers are found among children. Elevated inflammatory markers are associated with complications and linked to various co-infections. Chest computed tomography (CT) scans in children revealed structural changes similar to those found in adults, with consolidations surrounded by halos being somewhat specific for children with COVID-19. The recommended treatment includes providing symptomatic therapy, with no specific drug recommendations for children. The prognosis is much better for children compared to adults. This review highlights that COVID-19 in children is similar to the disease in the adult population, but with particularities regarding clinical manifestations, laboratory test results, chest imaging, and treatment. The prognosis is much better for children compared to adults, but with the progression of the pandemic; the cases in children might change in the future. url: https://doi.org/10.2147/rmhp.s257180 doi: 10.2147/rmhp.s257180 id: cord-275454-an8xvow3 author: Clark, Andrew E title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date: 2020-09-28 words: 1607.0 sentences: 87.0 pages: flesch: 48.0 cache: ./cache/cord-275454-an8xvow3.txt txt: ./txt/cord-275454-an8xvow3.txt summary: We read with interest the study appearing in this issue by Li et al, who utilized a pooled sample strategy and a point-of-care (POC) reverse transcriptase-polymerase chain reaction (RT-PCR) assay for screening asymptomatic airline passengers arriving from areas of high SARS-CoV-2 prevalence. At the time of this writing, 2 reference laboratories in the United States (Quest Diagnostics and LabCorp) have received emergency use authorizations from the US Food and Drug Administration to use pooled specimens for SARS-CoV-2 detection [2] . In this work, pooling was performed in a 10:1 ratio, meaning 10 patient specimens were combined and tested using a single SARS-CoV-2 assay. At our institution, we are aware of patients who underwent preprocedure SARS-CoV2 screening utilizing the same assay deployed in this work, only to be diagnosed with active, symptomatic COVID-19 within 5 days of testing. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32986122/ doi: 10.1093/cid/ciaa1145 id: cord-256156-mywhe6w9 author: Clausen, Thomas Mandel title: SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date: 2020-09-14 words: 8965.0 sentences: 562.0 pages: flesch: 59.0 cache: ./cache/cord-256156-mywhe6w9.txt txt: ./txt/cord-256156-mywhe6w9.txt summary: We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. In this report, we show that the ectodomain of the SARS-CoV-2 spike (S) protein interacts with cell surface HS through the Receptor Binding Domain (RBD) in the S1 subunit. Adjacent to the ACE2 binding site and exposed in the RBD lies a group of positively-charged amino acid residues that represents a potential site that could interact with heparin or heparan sulfate ( Fig. 1A and Suppl. The SARS-CoV-2 spike protein depends on cellular heparan sulfate for cell binding. Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin abstract: We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Docking studies suggest a heparin/heparan sulfate-binding site adjacent to the ACE2 binding site. Both ACE2 and heparin can bind independently to spike protein in vitro and a ternary complex can be generated using heparin as a scaffold. Electron micrographs of spike protein suggests that heparin enhances the open conformation of the RBD that binds ACE2. On cells, spike protein binding depends on both heparan sulfate and ACE2. Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. We suggest a model in which viral attachment and infection involves heparan sulfate-dependent enhancement of binding to ACE2. Manipulation of heparan sulfate or inhibition of viral adhesion by exogenous heparin presents new therapeutic opportunities. url: https://www.ncbi.nlm.nih.gov/pubmed/32970989/ doi: 10.1016/j.cell.2020.09.033 id: cord-311758-wof4yi39 author: Clauw, Daniel J. title: Considering the potential for an increase in chronic pain after the COVID-19 pandemic date: 2020-06-03 words: 3182.0 sentences: 165.0 pages: flesch: 43.0 cache: ./cache/cord-311758-wof4yi39.txt txt: ./txt/cord-311758-wof4yi39.txt summary: The experience of living within this pandemic has disrupted daily life across all sectors, including those living with chronic pain (CP), those infected with the coronavirus Severe Acute Respiratory Syndrome (SARS)-CoV2, healthcare providers and essential workers, as well as those who remained physically healthy. Specific possibilities might include: (1) CP as part of a postviral syndrome or the result of viral-associated organ damage; (2) worsening of CP due to exacerbation of preexisting pain physical or mental complaints; and (3) CP newly triggered in individuals not infected with COVID by exacerbation of risk factors (poor sleep, inactivity, fear, anxiety, and depression). In a small study of 22 subjects (21 of whom were healthcare workers) infected during the SARS epidemic, a chronic post-SARS syndrome consisting of fatigue, diffuse myalgia, depression, and nonrestorative sleep persisted for almost 2 years. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32501861/ doi: 10.1097/j.pain.0000000000001950 id: cord-341453-9yrvjlpx author: Clay, Candice C title: Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses date: 2014-03-19 words: 8130.0 sentences: 395.0 pages: flesch: 48.0 cache: ./cache/cord-341453-9yrvjlpx.txt txt: ./txt/cord-341453-9yrvjlpx.txt summary: The aim of this study was to determine how the peripheral and mucosal immune responses to SARS-CoV infection compare in the aged and juvenile nonhuman primate host and to determine how this may impact viral replication levels. No virus was detected in any sample collected from either age group at 10 d.p.i. To determine if advanced age correlated with increased severity of lung pathology, a comprehensive histological analysis of the respiratory tract following SARS-CoV infection was conducted in aged and juvenile animals. To determine how mucosal cytokines in SARS-CoV infection compared to systemic responses and how age may impact mucosal cytokine expression; the inflammatory protein profile was evaluated by bead-based arrays in standardized-collected lung tissue from the proximal portion of the right caudal lobe. Although no age-dependent differences were observed in the frequency of naïve (CD45RA + CCR7+) CD8 T cells in peripheral blood, there were significantly lower levels of these cells in the lung and lymph node of aged animals during SARS-CoV infection ( Figure 6A -C; unpaired student T-tests). abstract: BACKGROUND: Many respiratory viruses disproportionately impact the elderly. Likewise, advanced age correlated with more adverse disease outcomes following severe acute respiratory syndrome coronavirus (SARS-CoV) infection in humans. We used an aged African green monkey SARS-CoV infection model to better understand age-related mechanisms of increased susceptibility to viral respiratory infections. Nonhuman primates are critical translational models for such research given their similarities to humans in immune-ageing as well as lung structure. RESULTS: Significant age- and infection-dependent differences were observed in both systemic and mucosal immune compartments. Peripheral lymphocytes, specifically CD8 T and B cells were significantly lower in aged monkeys pre- and post- SARS-CoV infection, while neutrophil and monocyte numbers were not impacted by age or infection status. Serum proinflammatory cytokines were similar in both age groups, whereas significantly lower levels of IL-1beta, IL-18, IL-6, IL-12 and IL-15 were detected in the lungs of SARS-CoV-infected aged monkeys at either 5 or 10 days post infection. Total lung leukocyte numbers and relative frequency of CD8 T cells, B cells, macrophages and dendritic cells were greatly reduced in the aged host during SARS-CoV infection, despite high levels of chemoattractants for many of these cells in the aged lung. Dendritic cells and monocytes/macrophages showed age-dependent differences in activation and chemokine receptor profiles, while the CD8 T cell and B cell responses were significantly reduced in the aged host. In examination of viral titers, significantly higher levels of SARS-CoV were detected in the nasal swabs early, at day 1 post infection, in aged as compared to juvenile monkeys, but virus levels were only slightly higher in aged animals by day 3. Although there was a trend of higher titers in respiratory tissues at day 5 post infection, this did not reach statistical significance and virus was cleared from all animals by day 10, regardless of age. CONCLUSIONS: This study provides unique insight into how several parameters of the systemic and mucosal immune response to SARS-CoV infection are significantly modulated by age. These immune differences may contribute to deficient immune function and the observed trend of higher SARS-CoV replication in aged nonhuman primates. url: https://doi.org/10.1186/1742-4933-11-4 doi: 10.1186/1742-4933-11-4 id: cord-325261-bdumhy5b author: Clemente, Valentino title: Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19 date: 2020-05-15 words: 7815.0 sentences: 380.0 pages: flesch: 44.0 cache: ./cache/cord-325261-bdumhy5b.txt txt: ./txt/cord-325261-bdumhy5b.txt summary: Since viral PLPs are used by coronaviruses to both replicate and to antagonize the innate immune response, they are considered important therapeutic targets for coronavirus infections and thus may be of interest for future COVID-19 treatment strategies. The multifunctional activities of PLPs, namely as cysteine proteases, DUBs and deISGylating enzymes, play two important roles in coronavirus pathogenesis: the first involves the production of non-structural proteins (nsp) required for the replication process and the second consists of blocking the innate immune system of the infected host cell. Since it is known that cellular antiviral pathways include (de)ubiquitination within their regulatory mechanisms [14, 15] , PLPs are believed to contribute to infection pathogenesis by using their intrinsic DUB and deISGylating activities to antagonize the activation of the host cell innate immune response [5] . Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression abstract: Following the outbreak of novel severe acute respiratory syndrome (SARS)-coronavirus (CoV)2, the majority of nations are struggling with countermeasures to fight infection, prevent spread and improve patient survival. Considering that the pandemic is a recent event, no large clinical trials have been possible and since coronavirus specific drug are not yet available, there is no strong consensus on how to treat the coronavirus disease 2019 (COVID-19) associated viral pneumonia. Coronaviruses code for an important multifunctional enzyme named papain-like protease (PLP), that has many roles in pathogenesis. First, PLP is one of the two viral cysteine proteases, along with 3-chymotripsin-like protease, that is responsible for the production of the replicase proteins required for viral replication. Second, its intrinsic deubiquitinating and deISGylating activities serve to antagonize the host’s immune response that would otherwise hinder infection. Both deubiquitinating and deISGylating functions involve the removal of the small regulatory polypeptides, ubiquitin and ISG15, respectively, from target proteins. Ubiquitin modifications can regulate the innate immune response by affecting regulatory proteins, either by altering their stability via the ubiquitin proteasome pathway or by directly regulating their activity. ISG15 is a ubiquitin-like modifier with pleiotropic effects, typically expressed during the host cell immune response. PLP inhibitors have been evaluated during past coronavirus epidemics, and have showed promising results as an antiviral therapy in vitro. In this review, we recapitulate the roles of PLPs in coronavirus infections, report a list of PLP inhibitors and suggest possible therapeutic strategies for COVID-19 treatment, using both clinical and preclinical drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/32429099/ doi: 10.3390/ijms21103492 id: cord-315328-8g40ukml author: Clementi, Nicola title: Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection date: 2020-06-19 words: 2275.0 sentences: 115.0 pages: flesch: 50.0 cache: ./cache/cord-315328-8g40ukml.txt txt: ./txt/cord-315328-8g40ukml.txt summary: In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In the current study, we assessed its anti-SARS-CoV-2 activity in vitro to give a preclinical background to clinical trials evaluating the possible therapeutic role of IFN-β-1a in patients with coronavirus disease 2019 (COVID-19). Vero E6 cells were treated with concentrations ranging from 5000 to 0.01 IU/mL of IFN-β-1a 1 hour after inoculation with SARS-CoV-2 and monitored for cytopathic effect and real-time-PCR quantitative evaluation at 48, 72, and 96 hours after infection. Our in vitro observations shed light for the first time on that antiviral activity of IFN-β-1a against SARS-CoV-2 when administered after the infection of cells, highlighting its possible efficacy in an early therapeutic setting. abstract: The ongoing coronavirus disease 2019 pandemic has forced the clinical and scientific community to try drug repurposing of existing antiviral agents as a quick option against severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2). Under this scenario, interferon (IFN) β-1a, whose antiviral potential is already known, and which is a drug currently used in the clinical management of multiple sclerosis, may represent as a potential candidate. In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32559285/ doi: 10.1093/infdis/jiaa350 id: cord-320401-itltvh3f author: Clementi, Nicola title: NARINGENIN IS A POWERFUL INHIBITOR OF SARS-CoV-2 INFECTION IN VITRO date: 2020-10-20 words: 1495.0 sentences: 85.0 pages: flesch: 51.0 cache: ./cache/cord-320401-itltvh3f.txt txt: ./txt/cord-320401-itltvh3f.txt summary: In the present insight, we highlight novel experimental evidence that the flavanone Naringenin, targeting the endo-lysosomal Two-Pore Channels (TPCs), could be added to the list of potential weapons against SARS-CoV-2 infection and COVID-19 disease. Noteworthy, our recent evidence has shown that the activity of human TPC channels can be inhibited by the natural flavonoid compound Naringenin (Nar) [4] , one of the main flavonoids present in the human diet. Images showed that Nar treatment did not cause toxicity on uninfected cells at any of the tested concentrations and DMSO (vehicle) did not significantly affect SARS-CoV-2 replication (Fig.1D-E) . Of note, results indicated a strong decrease of CPE (>90%) at 48hpi when Vero E6 cells were treated with 250 and 62.5 μM Nar (Fig.1E) . Differences between treated samples (n=4, n=3 at 72hpi) and controls (untreated infected cells, n=4, not shown) were significant Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? abstract: [Figure: see text] Schematic representation of TPC2 role, investigated through genetic ablation and drug blocker, in the inhibition of Coronaviruses release into the cells. url: https://www.sciencedirect.com/science/article/pii/S1043661820315632?v=s5 doi: 10.1016/j.phrs.2020.105255 id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 words: 4259.0 sentences: 224.0 pages: flesch: 54.0 cache: ./cache/cord-337198-4sors3bg.txt txt: ./txt/cord-337198-4sors3bg.txt summary: In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . abstract: While the SARS-CoV-2 pandemic is heavily hitting the world, it is of extreme importance that significant in vitro observations guide the quick set up of clinical trials. In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. This suggests that only a combined prophylactic and therapeutic use of hydroxychloroquine may be effective in limiting viral replication in patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32754147/ doi: 10.3389/fmicb.2020.01704 id: cord-308760-xonuu04p author: Clerici, Bianca title: A case of newly diagnosed immune thrombocytopenia in the COVID-19 era date: 2020-11-12 words: 2165.0 sentences: 116.0 pages: flesch: 47.0 cache: ./cache/cord-308760-xonuu04p.txt txt: ./txt/cord-308760-xonuu04p.txt summary: First-line treatment options for ITP include corticosteroids and intravenous immunoglobulin (IvIg); of the two, corticosteroids induce a more persistent increase in platelet count, and appear more suitable in this case. In this patient, the benefits of a rapid increase in platelet count must be weighed against the risk of deterioration of the ongoing viral infection, of superimposed hospital-acquired infections, of liver impairment, and of venous thromboembolic events, which might be favored by ITP itself [6, 7] , the treatment with a TPO-RA [8] , the suspected presence of a neoplasm, the length of hospitalization and SARS-CoV-2 infection [9, 10] . The impact of the anti-CD20 activity of Rituximab on the course of SARS-CoV-2 infection in a patient on steroid treatment was unknown and particularly worrisome given the crucial role of humoral immunity in infection contrast [11, 12] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33180223/ doi: 10.1007/s11739-020-02553-3 id: cord-274945-6p5de7o2 author: Clevers, Hans title: COVID-19: organoids go viral date: 2020-06-01 words: 1375.0 sentences: 86.0 pages: flesch: 51.0 cache: ./cache/cord-274945-6p5de7o2.txt txt: ./txt/cord-274945-6p5de7o2.txt summary: Indeed, enterocytes generated in ASC derived, small intestinal organoid cultures allowed cultivation of multiple human norovirus strains. There is no robust in vitro model beyond the use of ex vivo bronchus explant cultures for assessing the infectivity of emerging flu viruses in humans. Penninger and colleagues 7 demonstrated that SARS CoV2 could directly infect capillary organoids and kidney organoids, both established from human iPSCs. These observations may explain the spread of the virus through the body and the loss of kidney function in severely ill individuals. All three studies reported that the most common cell type of the intestinal epithelium, the enterocyte, is readily infected, suggesting that the intestine is a poten tial site of SARS CoV2 replication. Differentiated human airway organoids to assess infectivity of emerging influenza virus TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes Infection of bat and human intestinal organoids by SARS-CoV-2 abstract: The coronavirus disease-19 (COVID-19) pandemic underscores the threat posed by newly emerging viruses. Understanding the biology of novel viruses rests in large part on in vitro models that allow viral replication. Human and animal organoids are now proving their value as an experimental virology platform. url: https://doi.org/10.1038/s41580-020-0258-4 doi: 10.1038/s41580-020-0258-4 id: cord-222664-4qyrtzhu author: Coban, Mathew title: Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date: 2020-07-06 words: 11220.0 sentences: 638.0 pages: flesch: 46.0 cache: ./cache/cord-222664-4qyrtzhu.txt txt: ./txt/cord-222664-4qyrtzhu.txt summary: We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors; S/Ace2, Tmprss2, Cathepsins L and K, and Mpro to prevent binding, membrane fusion and replication of the virus, respectively. Using a computational pipeline that aimed to expeditiously identify lead compounds against COVID-19, we combined compound library preparation, molecular modeling, and structure simulations to generate an ensemble of conformations and increase high quality docking outcomes against two essential SARS-CoV-2 viral proteins and their host protein interactions; S/Ace2, Tmprss2, Cathepsin L and K, and M pro that are known to control both viral binding, entry and virus replication (Fig. 1A) . abstract: COVID-19 is a devastating respiratory and inflammatory illness caused by a new coronavirus that is rapidly spreading throughout the human population. Over the past 6 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has already infected over 11.6 million (25% located in United States) and killed more than 540K people around the world. As we face one of the most challenging times in our recent history, there is an urgent need to identify drug candidates that can attack SARS-CoV-2 on multiple fronts. We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors; S/Ace2, Tmprss2, Cathepsins L and K, and Mpro to prevent binding, membrane fusion and replication of the virus, respectively. All together we generated an ensemble of structural conformations that increase high quality docking outcomes to screen over>6 million compounds including all FDA-approved drugs, drugs under clinical trial (>3000) and an additional>30 million selected chemotypes from fragment libraries. Our results yielded an initial set of 350 high value compounds from both new and FDA-approved compounds that can now be tested experimentally in appropriate biological model systems. We anticipate that our results will initiate screening campaigns and accelerate the discovery of COVID-19 treatments. url: https://arxiv.org/pdf/2007.02557v1.pdf doi: nan id: cord-031289-uxoz0xhk author: Coccolini, Federico title: SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients date: 2020-05-18 words: 1326.0 sentences: 98.0 pages: flesch: 51.0 cache: ./cache/cord-031289-uxoz0xhk.txt txt: ./txt/cord-031289-uxoz0xhk.txt summary: title: SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients The present article represents the very first positive result describing the presence of the virus in peritoneal fluid during an emergency surgical procedure in a COVID-19 sick patient. Interestingly, the nasal swab contained less SARS-CoV-2 RNA virus compared to the viral fluid that scored positive in 2 targets out of 3. This indicates that the viral load in the peritoneal fluid was higher compared to the upper respiratory material and suggests that the surgical operation was indeed a procedure at risk of infection. As no information exist about the virus passage to peritoneal cavity and fluids, present data may suggest that potentially all people even those with mild to moderate respiratory symptoms by SARS-CoV-2 could present viral load in peritoneal fluid, thus increasing the exposure and contagion risks for the entire surgical staff.Peritoneal fluid contamination with blood of feces may interfere with the virus detection. abstract: BACKGROUND: The excretion pathomechanisms of SARS-CoV-2 are actually unknown. No certain data exist about viral load in the different body compartments and fluids during the different disease phases. MATERIAL AND METHODS: Specific real-time reverse transcriptase–polymerase chain reaction targeting 3 SARS-CoV-e genes were used to detect the presence of the virus. RESULTS: SARS-CoV-2 was detected in peritoneal fluid at a higher concentration than in respiratory tract. CONCLUSION: Detection of SARS-CoV-2 in peritoneal fluid has never been reported. The present article represents the very first positive result describing the presence of the virus in peritoneal fluid during an emergency surgical procedure in a COVID-19 sick patient. This article thus represents a warning for increasing the level of awareness and protection for surgeon especially in emergency surgical setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7467036/ doi: 10.1097/sla.0000000000004030 id: cord-328000-i9tzr13z author: Cockrell, Adam S. title: Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date: 2018-07-24 words: 11004.0 sentences: 519.0 pages: flesch: 44.0 cache: ./cache/cord-328000-i9tzr13z.txt txt: ./txt/cord-328000-i9tzr13z.txt summary: Three different strategies were employed for development of SARS-CoV mouse models: (i) different mouse species (or subspecies) were challenged with wildtype human SARS-CoV isolates in order to find a model that allows for replication and reflects severe respiratory disease symptoms observed in infected human patients; (ii) mice were genetically engineered to modify the host receptor, which facilitated productive SARS-CoV replication and pathogenesis; and (iii) adaptive evolution of wild-type SARS-CoV to a chosen mouse species was done to enhance pathogenesis, and associated clinical phenotypes in vivo. To adapt SARS-CoV to cause severe acute respiratory disease in mouse lungs, 6-week-old female BALB/c mice were intra-nasally infected with the clinical Urbani isolate (Roberts et al. Virus infection studies in CC mouse lines, including SARS-CoV, have led to mapping of high and low host response alleles as they relate to development of clinical signs of disease following viral pathogenesis (Bottomly et al. abstract: The emergence of highly pathogenic human coronaviruses (hCoVs) in the last two decades has illuminated their potential to cause high morbidity and mortality in human populations and disrupt global economies. Global pandemic concerns stem from their high mortality rates, capacity for human-to-human spread by respiratory transmission, and complete lack of approved therapeutic countermeasures. Limiting disease may require the development of virus-directed and host-directed therapeutic strategies due to the acute etiology of hCoV infections. Therefore, understanding how hCoV–host interactions cause pathogenic outcomes relies upon mammalian models that closely recapitulate the pathogenesis of hCoVs in humans. Pragmatism has largely been the driving force underpinning mice as highly effective mammalian models for elucidating hCoV–host interactions that govern pathogenesis. Notably, tractable mouse genetics combined with hCoV reverse genetic systems has afforded the concomitant manipulation of virus and host genetics to evaluate virus–host interaction networks in disease. In addition to assessing etiologies of known hCoVs, mouse models have clinically predictive value as tools to appraise potential disease phenotypes associated with pre-emergent CoVs. Knowledge of CoV pathogenic potential before it crosses the species barrier into the human population provides a highly desirable preclinical platform for addressing global pathogen preparedness, an overarching directive of the World Health Organization. Although we recognize that results obtained in robust mouse models require evaluation in non-human primates, we focus this review on the current state of hCoV mouse models, their use as tractable complex genetic organisms for untangling complex hCoV–host interactions, and as pathogenesis models for preclinical evaluation of novel therapeutic interventions. url: https://doi.org/10.1007/s00335-018-9760-9 doi: 10.1007/s00335-018-9760-9 id: cord-312367-24huwt3y author: Coelho, Camila title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 words: 3351.0 sentences: 210.0 pages: flesch: 49.0 cache: ./cache/cord-312367-24huwt3y.txt txt: ./txt/cord-312367-24huwt3y.txt summary: As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). As viral proteases, following polymerases, are the most prominent targets for antiviral drug design [9] , here we describe initial biochemical screenings with recombinant purified SARS-CoV-2 M pro performed in order to define possible candidates which could serve as lead compounds for the design of future COVID-19 therapies. In order to contribute to the ongoing worldwide research and development efforts to contain COVID-19, we cloned, expressed recombinantly in E.coli BL21(DE3) and purified an important drug target of SARS-CoV-2, its main protease (M pro ). From these obtained compounds, esculetin-4-carboxylic acid ethyl ester (IC 50 = 46 μM in M pro inhibition assays), a coumarin derivative and natural product, demonstrated an EC 50 of 112 μM (median toxic concentration TC 50 >800μM) in Vero-cell SARS-CoV assays [13] and MP576 (IC 50 = 2.5 μM), a quinolinecarboxylate, demonstrated an EC 50 of 7 μM (TC 50 >50μM) [15, 17] , thus validating the M pro biochemical screening approach for the development of SARS-CoV drugs. abstract: The Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic represents a global challenge. SARS-CoV-2's ability to replicate in host cells relies on the action of its non-structural proteins, like its main protease (M(pro)). This cysteine protease acts by processing the viruses' precursor polyproteins. As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). A fluorescent assay was used to identify inhibitors in a compound library containing known drugs, bioactive molecules and natural products. These screens led to the identification of 13 inhibitors with IC(50) values ranging from 0.2 μM to 23 μM. The screens confirmed several known SARS-CoV M(pro) inhibitors as inhibitors of SARS-CoV-2 M(pro), such as the organo-mercuric compounds thimerosal and phenylmercuric acetate. Benzophenone derivatives could also be identified among the most potent screening hits. Additionally, Evans blue, a sulfonic acid-containing dye, could be identified as an M(pro) inhibitor. The obtained compounds could be of interest as lead compounds for the development of future SARS-CoV-2 drugs. url: https://doi.org/10.1371/journal.pone.0240079 doi: 10.1371/journal.pone.0240079 id: cord-260854-v7wgb6mr author: Colafrancesco, Serena title: COVID-19 gone bad: A new character in the spectrum of the hyperferritinemic syndrome? date: 2020-05-05 words: 3340.0 sentences: 160.0 pages: flesch: 37.0 cache: ./cache/cord-260854-v7wgb6mr.txt txt: ./txt/cord-260854-v7wgb6mr.txt summary: The severe form of COVID-19 share several clinical and laboratory features with four entities gathered under the term "hyperferritinemic syndrome" and including macrophage activation syndrome (MAS), adult-onset Still''s disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS) and septic shock. COVID-19 systemic inflammatory reaction and "hyperferritinemic syndromes" are all characterized by high serum ferritin and a life-threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi-organ failure. In this review, we analyze the possible epidemiological and molecular mechanisms responsible for hyper-inflammation in patients with severe COVID-19 and we underline the similarities between this condition and "hyperferritinemic syndromes" which would allow considering this entity as the fifth member of the spectrum of inflammatory conditions. The umbrella term "hyperferritinemic syndrome" encompasses four clinical conditions, macrophage activation syndrome (MAS), adult-onset Still''s disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS), and septic shock, all characterized by high serum ferritin and a life -threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi -organ failure [1] . abstract: The severe form of COVID-19 share several clinical and laboratory features with four entities gathered under the term “hyperferritinemic syndrome” and including macrophage activation syndrome (MAS), adult-onset Still's disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS) and septic shock. COVID-19 systemic inflammatory reaction and “hyperferritinemic syndromes” are all characterized by high serum ferritin and a life-threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi-organ failure. In this review, we analyze the possible epidemiological and molecular mechanisms responsible for hyper-inflammation in patients with severe COVID-19 and we underline the similarities between this condition and “hyperferritinemic syndromes” which would allow considering this entity as the fifth member of the spectrum of inflammatory conditions. url: https://api.elsevier.com/content/article/pii/S156899722030135X doi: 10.1016/j.autrev.2020.102573 id: cord-288553-fez60jyn author: Colaneri, Marta title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. date: 2020-03-19 words: 537.0 sentences: 37.0 pages: flesch: 53.0 cache: ./cache/cord-288553-fez60jyn.txt txt: ./txt/cord-288553-fez60jyn.txt summary: title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. Health care workers are at increased risk of acquiring COVID-19 infection, possibly due to direct contact with the patients. In this regard, studies suggest that surfaces and suspensions can carry HCoVs, increasing the risk of contact transmission that could lead to hospital acquired HCoVs infections [4, 5] Since February 21, 2020, when the first autochthonous case in Italy was confirmed, an overwhelming number of SARS-CoV-2 infections is continuously being detected, exceeding 8,000 cases at the time of writing. Fondazione IRCCS Policlinico San Matteo, Pavia, is a 1,300-bed tertiary teaching hospital in Northern Italy and a national SARS-CoV-2 referral center. Survival of human coronaviruses 229E and OC43 in suspension and after drying on surfaces: A possible source of hospital-acquired infections Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0195670120301171?v=s5 doi: 10.1016/j.jhin.2020.03.018 id: cord-353615-9aj5yxkd author: Colaneri, Marta title: Running out of bullets: the challenging management of acute hepatitis and SARS‐COV‐2 from the SMatteo COvid19 Registry (SMACORE) date: 2020-07-17 words: 1604.0 sentences: 89.0 pages: flesch: 45.0 cache: ./cache/cord-353615-9aj5yxkd.txt txt: ./txt/cord-353615-9aj5yxkd.txt summary: Since several of the currently administered drugs against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are possibly hepatotoxic, the management of patients with COVID‐19 and liver failure is still an almost unexplored field. Beyond the well-known catastrophic pulmonary effects of coronavirus disease 2019 , the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has also been associated with a significant damage to other organ systems, including kidney, heart, vessels and liver (1) (2) (3) (4) (5) . et al (12) , patients with SARS-CoV-2 and chronic HBV co-infection with liver injury and coagulation dysfunction were more likely to develop severe illness and had higher mortality. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: A retrospective study Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection abstract: Liver impairment is frequent in patients with novel coronavirus disease (COVID‐19) and direct viral tropism for the liver has been proven. Since several of the currently administered drugs against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are possibly hepatotoxic, the management of patients with COVID‐19 and liver failure is still an almost unexplored field. Taking this challenging case of acute HBV with persistent hyperbilirubinemia and SARS‐COV‐2 infection with respiratory distress as a starting point, we here loop through this condition. Where the available therapeutic options are scarce, we here propose hemoperfusion (HP) as an attractive alternative to both delay any late‐stage progression of hyper inflammation process in COVID‐19 and remove the toxins involved in acute liver failure. url: https://doi.org/10.1111/liv.14609 doi: 10.1111/liv.14609 id: cord-288998-0by0bkgs author: Colarusso, Chiara title: A lesson from a saboteur: high molecular weight kininogen (HMWK) impact in COVID‐19 date: 2020-06-04 words: 3857.0 sentences: 211.0 pages: flesch: 45.0 cache: ./cache/cord-288998-0by0bkgs.txt txt: ./txt/cord-288998-0by0bkgs.txt summary: In the attempt to understand how the virus spreads and how to pharmacologically abolish it, it was highlighted that SARS‐CoV‐2 infects human cells by means of angiotensin converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2) and SARS‐CoV‐2 main protease (M(pro)). Our attention has been focused on the role of ACE2 in that its blockade by the virus increases Bradykinin and its metabolites, well known to facilitate inflammation in the lung (responsible for cough and fever), facilitate both the coagulation and complement system, three mechanisms that are typical of angioedema, cardiovascular dysfunction and sepsis, pathologies which symptoms occur in COVID‐19 patients. Once SARS-CoV-2 binds to ACE2 , the enzyme is blocked, therefore, leading to what we are actually assisting in terms of high blood pressure in COVID-19 patients and pulmonary edema up to angioedema, which underlies the fact that physiologically ACE2 cleaves several bioactive peptides, among which [des-Arg 9 ]bradykinin ([des-Arg 9 ]BK) (Vickers et al. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a newly identified coronavirus which has spread from China to the rest of the world causing the pandemic coronavirus disease 19 (COVID‐19). It has fatality rate that floats from 5 to 15% and the symptoms are fever, cough, myalgia and/or fatigue up to dyspnea, responsible for hospitalization and in most of the cases of artificial oxygenation. In the attempt to understand how the virus spreads and how to pharmacologically abolish it, it was highlighted that SARS‐CoV‐2 infects human cells by means of angiotensin converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2) and SARS‐CoV‐2 main protease (M(pro)). Once bound to its receptor ACE2, the other two proteases, in concert with the receptor‐mediated signaling, allow virus replication and spread throughout the body. Our attention has been focused on the role of ACE2 in that its blockade by the virus increases Bradykinin and its metabolites, well known to facilitate inflammation in the lung (responsible for cough and fever), facilitate both the coagulation and complement system, three mechanisms that are typical of angioedema, cardiovascular dysfunction and sepsis, pathologies which symptoms occur in COVID‐19 patients. Thus, we propose to pharmacologically block the kallikrein‐kinin system upstream bradykinin and the ensuing inflammation, coagulation and complement activation by means of lanadelumab, which is a clinically approved drug for hereditary angioedema. url: https://www.ncbi.nlm.nih.gov/pubmed/32497257/ doi: 10.1111/bph.15154 id: cord-323831-1qadv7r1 author: Coleman, H title: Severe acute respiratory syndrome coronavirus-2 in post-laryngectomy patients: case series of four patients date: 2020-06-23 words: 1999.0 sentences: 125.0 pages: flesch: 53.0 cache: ./cache/cord-323831-1qadv7r1.txt txt: ./txt/cord-323831-1qadv7r1.txt summary: OBJECTIVE: To report our experience of diagnosis, investigation and management in patients who had undergone laryngectomy secondary to previous squamous cell carcinoma, who were subsequently infected with severe acute respiratory syndrome coronavirus-2 during the coronavirus disease 2019 pandemic. CASE REPORTS: Four post-laryngectomy patients with laboratory-proven severe acute respiratory syndrome coronavirus-2 infection were admitted to our institution from 1 March to 1 May 2020. 2 There is no published evidence to date on the post-operative and ward management of this group of patients with laboratory-proven SARS-CoV-2 infection. 3 Here, we present our experience of the diagnosis, investigation and management of SARS-CoV-2 positive, post-laryngectomy patients, who attended our institution between 1 March and 1 May 2020, during the Covid-19 pandemic. Patient one, a 50-year-old female, was an in-patient on the ENT ward, who was progressing well 2 weeks following total laryngectomy, bilateral neck dissection and pectoralis major flap reconstruction for a tumour-node staged T 3 N 2c moderately differentiated supraglottic SCC. abstract: OBJECTIVE: To report our experience of diagnosis, investigation and management in patients who had undergone laryngectomy secondary to previous squamous cell carcinoma, who were subsequently infected with severe acute respiratory syndrome coronavirus-2 during the coronavirus disease 2019 pandemic. CASE REPORTS: Four post-laryngectomy patients with laboratory-proven severe acute respiratory syndrome coronavirus-2 infection were admitted to our institution from 1 March to 1 May 2020. All patients displayed symptoms of coronavirus disease 2019 and underwent investigations, including swab and serum sampling, and chest X-ray where indicated. All were managed conservatively on dedicated coronavirus disease 2019 wards and were discharged without the requirement of higher level care. CONCLUSION: It is hypothesised that laryngectomy may offer a protective effect against severe or critical disease in severe acute respiratory syndrome coronavirus-2 infection. We hope sharing our experience will aid all practitioners in the management of this, often intimidating, cohort of patients. url: https://doi.org/10.1017/s0022215120001310 doi: 10.1017/s0022215120001310 id: cord-293315-kx4x2g24 author: Colmenero, I. title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases date: 2020-06-20 words: 2530.0 sentences: 162.0 pages: flesch: 43.0 cache: ./cache/cord-293315-kx4x2g24.txt txt: ./txt/cord-293315-kx4x2g24.txt summary: title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases CONCLUSIONS: Although the clinical and histopathological features were similar to other forms of chilblains, the presence of viral particles in the endothelium and the histological evidence of vascular damage, support a causal relation of the lesions with SARS‐CoV‐2. 4 Most patients have been negative for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) when tested by PCR of nasopharyngeal and oropharyngeal swabs, and less than 50% have a history of exposure to positive household contacts or previous history of mild upper respiratory or gastrointestinal symptoms. Lymphocytic vascular damage was the hallmark feature in biopsies from our 7 patients with COVID-19 related chilblains. 25 We have demonstrated the presence of viral particles within endothelial cells in lesional skin biopsies from patients presenting with chilblains during the COVID-19 pandemic. Chilblain-like lesions: a case series of 41 patients during the COVID-19 pandemic abstract: BACKGROUND: Chilblains ("COVID toes") are being seen with increasing frequency in children and young adults during the COVID‐19 pandemic. Detailed histopathological descriptions of COVID‐19 chilblains have not been reported, and causality of SARS‐CoV‐2 has not been established yet. OBJECTIVE: To describe histopathological features of Covid‐19 chilblains and explore the presence of SARS‐CoV‐2 in the tissue. METHODS: We examined skin biopsies from 7 paediatric patients presenting with chilblains during the COVID‐19 pandemic. Immunohistochemistry for SARS‐CoV‐2 was performed in all cases and electron microscopy in one. RESULTS: Histopathology showed variable degrees of lymphocytic vasculitis ranging from endothelial swelling and endothelialitis to fibrinoid necrosis and thrombosis. Purpura, superficial and deep perivascular lymphocytic inflammation with perieccrine accentuation, oedema, and mild vacuolar interface damage were also seen. SARS‐CoV‐2 immunohistochemistry was positive in endothelial cells and epithelial cells of eccrine glands. Coronavirus particles were found in the cytoplasm of endothelial cells on electron microscopy. CONCLUSIONS: Although the clinical and histopathological features were similar to other forms of chilblains, the presence of viral particles in the endothelium and the histological evidence of vascular damage, support a causal relation of the lesions with SARS‐CoV‐2. Endothelial damage induced by the virus could be the key mechanism in the pathogenesis of COVID‐19 chilblains and perhaps also in a group of patients severely affected by COVID‐19 presenting with features of microangiopathic damage. url: https://www.ncbi.nlm.nih.gov/pubmed/32562567/ doi: 10.1111/bjd.19327 id: cord-307113-mu3ow7m4 author: Colmenero, I. title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors date: 2020-09-30 words: 415.0 sentences: 33.0 pages: flesch: 53.0 cache: ./cache/cord-307113-mu3ow7m4.txt txt: ./txt/cord-307113-mu3ow7m4.txt summary: title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors The size and shape of the particle shown in our paper fit with other descriptions of SARS‐CoV‐2, but there may be a bias in interpretation. The size and shape of the particle shown in our paper fit with other descriptions of SARS-CoV-2, but there may be a bias in interpretation. After the publication of our series, new evidence is rising favouring a causal role for SARS-CoV-2 in COVID chilblains. Positive immunohistochemistry for SARS-CoV has been reported by different authors in cutaneous biopsies of COVID chilblains using antibodies directed against different parts of the virus, 3, 4 and SARS-CoV-2 RNA-positive cells have been demonstrated by RNAscope. SARS-CoV-2 endothelial infection causes COVID-19 chilblains: histopathological, immunohistochemical and ultrastructural study of seven paediatric cases Chilblains and COVID-19: why SARS-CoV-2 endothelial infection is questioned. abstract: We fully agree that the interpretation of electron microscopy findings can be challenging, even for experts. Differences between viral pathogens and normal subcellular organelles may be subtle, and some cellular components can masquerade as viruses. The size and shape of the particle shown in our paper fit with other descriptions of SARS‐CoV‐2, but there may be a bias in interpretation. url: https://doi.org/10.1111/bjd.19579 doi: 10.1111/bjd.19579 id: cord-355283-ny1ju7vc author: Colombo, L. title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism date: 2020-08-12 words: 1953.0 sentences: 95.0 pages: flesch: 40.0 cache: ./cache/cord-355283-ny1ju7vc.txt txt: ./txt/cord-355283-ny1ju7vc.txt summary: title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism Although the most known feature of SARS-CoV-2 associated infection is a mild to severe pneumonia, increasing evidence suggests the existence of an infection-associated risk of both arterial and venous thromboembolism (VTE), but the exact magnitude of this phenomenon is still unknown. Only a few months have passed since the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19) , have spread all over the world, resulting in more than 17 million cases, more than 670,000 infection-related deaths [1] and a global health threat that has no comparison in the last decades. High incidence of venous thromboembolic events in anticoagulated severe COVID-19 patients abstract: BACKGROUND: . Although the most known feature of SARS-CoV-2 associated infection is a mild to severe pneumonia, increasing evidence suggests the existence of an infection-associated risk of both arterial and venous thromboembolism (VTE), but the exact magnitude of this phenomenon is still unknown. Given that, it is important for the Emergency Physician to remember that a SARS-CoV-2 associated respiratory failure con be caused not only by the pulmonary parenchymal inflammation that characterizes the pneumonia, but also by an associated pulmonary thromboembolism. CASE REPORT: . A healthy 73-years old woman admitted to the ED for dyspnea, fever and thoracic pain. Cardiac ultrasound, electrocardiogram and clinical findings suggested a diagnosis of cardiogenic obstructive shock due to acute pulmonary embolism, successfully treated with thrombolysis. A CT angiography confirmed the pulmonary embolism (EP) diagnosis and showed bilateral pneumonia, caused by SARS-CoV-2 infection. CONCLUSION: . Considering the high prevalence of thromboembolic events in COVID-19 patients it is mandatory for the emergency physician to systematically evaluate signs of pulmonary thromboembolism, in order to perform the most patient-tailored therapy as soon as possible. url: https://www.ncbi.nlm.nih.gov/pubmed/32834988/ doi: 10.1016/j.rmcr.2020.101185 id: cord-266480-u8o4eitu author: Colubri, Andrés title: Preventing outbreaks through interactive, experiential real-life simulations date: 2020-09-02 words: 3167.0 sentences: 173.0 pages: flesch: 45.0 cache: ./cache/cord-266480-u8o4eitu.txt txt: ./txt/cord-266480-u8o4eitu.txt summary: Operation Outbreak (OO) is an educational curriculum and simulation platform that uses Bluetooth to spread a virtual "pathogen" in real-time across smartphones in close proximity. The app-generated data from these simulations represented the "ground truth" of the mock outbreaks, captured several essential features of SARS-CoV-2, and allowed us to observe behavioral changes among participants--many of which are now being mirrored in real life. Our 2018 SMA Ebola simulation first showed how student social-distancing could affect an "outbreak''s" trajectory ( Figure 2A More detailed data from the 2019 simulation allowed us to reconstruct transmission chains over time and identify important features of the outbreak, such as the existence of two super-spreaders causing 4 and 5 secondary infections early in the game ( Figure 2C ). We envision OO as playing two key roles: (1) as a pedagogical platform for teaching fundamentals of pandemic response that are vital for the public to understand and (2) as a novel system for simulating outbreaks and evaluating real-world mitigation strategies, including those needed to restart in-person education. abstract: Operation Outbreak (OO) is a simulation platform that teaches students how pathogens spread and the impact of interventions, thereby facilitating the safe re-opening of schools. In addition, OO generates data to inform epidemiological models and prevent future outbreaks. Before SARS-CoV-2 was reported we repeatedly simulated a virus with similar features, correctly predicting many human behaviors later observed during the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32905783/ doi: 10.1016/j.cell.2020.08.042 id: cord-328644-odtue60a author: Comandatore, Francesco title: Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date: 2020-05-28 words: 6535.0 sentences: 301.0 pages: flesch: 50.0 cache: ./cache/cord-328644-odtue60a.txt txt: ./txt/cord-328644-odtue60a.txt summary: These variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded RNA viruses -as in the case of SARS-CoV-2 (Sanjuán and Domingo-Calap 2016) , which has a single, positive-strand RNA genome. To have a better insight on the history and spread of the COVID-19 pandemic in Italy and thanks to the sequences deposited in the Gisaid database, we identified 7 non synonymous mutations that are differentially frequent in Italian SARS-CoV-2 strains respect to strains circulating globally. Our analysis allowed us to identify 7 positions in four proteins that present drastic changes in amino acid frequencies when comparing Italian sequences with worldwide sequences available on Gisaid.org on April, 10, 2020 ( Figure 1 ). abstract: The SARS-CoV-2 pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. One of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. Such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. In this work we identified and traced over time 7 amino acid variants that are present with high frequency in Italy and Europe, but that were absent or present at very low frequencies during the first stages of the epidemic in China and the initial reports in Europe. The analysis of these variants helps defining 6 phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. In the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage. url: https://doi.org/10.1101/2020.04.30.071027 doi: 10.1101/2020.04.30.071027 id: cord-316345-a1cirnya author: Comas, Carmina title: COVID‐19 and pregnancy: An opportunity to correct an historic gender bias date: 2020-08-02 words: 1447.0 sentences: 74.0 pages: flesch: 40.0 cache: ./cache/cord-316345-a1cirnya.txt txt: ./txt/cord-316345-a1cirnya.txt summary: Unfortunately, this bias seems to be maintained in the COVID‐19 epidemic: most current guidelines for diagnosing SARS‐CoV‐2 infection during pregnancy apply the same standard criteria as for the general population. Unfortunately, this bias seems to be maintained in the COVID-19 epidemic: most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population. This pandemic is an opportunity to begin redressing this historic gender bias against pregnant women, and to achieve this, we recommend two actions that are easy to implement, and would have a large impact. Indeed, despite significant variation in protocols between hospitals, most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population, namely performing one of the available molecular tests, such as quantitative reverse transcription polymerase chain reaction. abstract: Current literature and clinical guidelines do not include pregnant women as an a priori risk group for COVID‐19. However, a gender vision of health begs the question: Why are pregnant women not considered a risk group for COVID‐19? The answer is clear: historically, most community scientific studies have not considered female gender, or pregnancy as a state, to be a focus of special interest or effort. Unfortunately, this bias seems to be maintained in the COVID‐19 epidemic: most current guidelines for diagnosing SARS‐CoV‐2 infection during pregnancy apply the same standard criteria as for the general population. url: https://www.ncbi.nlm.nih.gov/pubmed/32706391/ doi: 10.1002/jmv.26350 id: cord-279940-i2rgjpxf author: Comentale, Giuseppe title: Sars-Cov-2 interference in HEME production: is it the time for an early predictive biomarker? date: 2020-06-29 words: 1348.0 sentences: 65.0 pages: flesch: 43.0 cache: ./cache/cord-279940-i2rgjpxf.txt txt: ./txt/cord-279940-i2rgjpxf.txt summary: In particular, thrombosis seems to drive the entire disease course: Sars-Cov-2 infection triggers a large thrombophilic response that results in diffuse occlusion of the smaller vessels, especially in the lungs where the result is a wide thrombotic microangiopathy [5] explaining the radiologic "ground glass" pattern. Furthermore, as IL-1 was shown to be a major culprit in the development of many cardiovascular diseases [11] , its involvement in the Sars-Cov-2 infection could explain the high mortality and morbidity rate among cardiopathic patients. Identifying the mechanisms by which Sars-Cov-2 damages the human body, focusing on the structural proteins, could be a possible strategy to finding an effective solution. From this point of view, Sars-Cov-2 seems to be very similar to malaria: many clinical and scientific reports have shown that Covid-19, not only can be successfully treated with chloroquine but also, like malaria, appears to be diagnosed much more frequently in blood group A patients [14] . abstract: nan url: https://doi.org/10.1007/s00109-020-01945-4 doi: 10.1007/s00109-020-01945-4 id: cord-285960-1zuhilmu author: Conly, John title: Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic date: 2020-08-06 words: 4921.0 sentences: 209.0 pages: flesch: 41.0 cache: ./cache/cord-285960-1zuhilmu.txt txt: ./txt/cord-285960-1zuhilmu.txt summary: The report by the World Health Organization (WHO) Joint Mission on Coronavirus Disease 2019 (COVID-19) in China supports person-to-person droplet and fomite transmission during close unprotected contact with the vast majority of the investigated infection clusters occurring within families, with a household secondary attack rate varying between 3 and 10%, a finding that is not consistent with airborne transmission. Based on the scientific evidence accumulated to date, our view is that SARS-CoV-2 is not spread by the airborne route to any significant extent and the use of particulate respirators offers no advantage over medical masks as a component of personal protective equipment for the routine care of patients with COVID-19 in the health care setting. The findings from multiple systematic reviews and meta analyses over the last decade have not demonstrated any significant difference in the clinical effectiveness of particulate respirators compared to the use of medical masks when used by HCWs in multiple health care settings for the prevention of respiratory virus infections, including influenza [57] [58] [59] . abstract: Currently available evidence supports that the predominant route of human-to-human transmission of the SARS-CoV-2 is through respiratory droplets and/or contact routes. The report by the World Health Organization (WHO) Joint Mission on Coronavirus Disease 2019 (COVID-19) in China supports person-to-person droplet and fomite transmission during close unprotected contact with the vast majority of the investigated infection clusters occurring within families, with a household secondary attack rate varying between 3 and 10%, a finding that is not consistent with airborne transmission. The reproduction number (R(0)) for the SARS-CoV-2 is estimated to be between 2.2–2.7, compatible with other respiratory viruses associated with a droplet/contact mode of transmission and very different than an airborne virus like measles with a R(0) widely cited to be between 12 and 18. Based on the scientific evidence accumulated to date, our view is that SARS-CoV-2 is not spread by the airborne route to any significant extent and the use of particulate respirators offers no advantage over medical masks as a component of personal protective equipment for the routine care of patients with COVID-19 in the health care setting. Moreover, prolonged use of particulate respirators may result in unintended harms. In conjunction with appropriate hand hygiene, personal protective equipment (PPE) used by health care workers caring for patients with COVID-19 must be used with attention to detail and precision of execution to prevent lapses in adherence and active failures in the donning and doffing of the PPE. url: https://www.ncbi.nlm.nih.gov/pubmed/32762735/ doi: 10.1186/s13756-020-00779-6 id: cord-280147-xvzi1i0v author: Consoli, Letizia title: 2019 novel coronavirus (COVID-19) pneumonia complications: the importance of lung ultrasound date: 2020-06-19 words: 1386.0 sentences: 76.0 pages: flesch: 46.0 cache: ./cache/cord-280147-xvzi1i0v.txt txt: ./txt/cord-280147-xvzi1i0v.txt summary: Herein, we report a case of a patient affected by COVID-19 pneumonia referred in the emergency department of our institution on April 4, 2020, with peculiar lung ultrasound findings. In January 2020, Chinese scientists isolated a novel coronavirus from patients affected by viral pneumonia, denominated severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), and in February 2020, the World Health Organization designated as COVID-19 the coronavirus disease caused by SARS-COV-2. As indicated in a report from the Chinese Center for Disease Control and Prevention on 44,500 SARS-COV-2 patients, severe respiratory symptoms were found in 14% of cases, characterized by dyspnea, hypoxia, or > 50% lung involvement on imaging. On the other hand, ultrasound may produce a real-time and dynamic evaluation, even in Convex array probe showed the absence pleural sliding at the left lung with a "barcode sign" at the M-mode evaluation cases with critical complications of severe COVID-19 pneumonia, such as pneumothorax. abstract: In December 2019, a novel coronavirus (SARS-Cov-2) was first reported in Wuhan, China, and rapidly spread around the world, leading to an international emerging public health emergency. As reported from Chinese experiences, approximately 20% of patients had a severe course, requiring intensive care, with an overall case fatality rate of 2.3%. In diagnosis, chest computed tomography most commonly showed ground-glass opacity with or without consolidative patterns. Herein, we report a case of a patient affected by COVID-19 pneumonia referred in the emergency department of our institution on April 4, 2020, with peculiar lung ultrasound findings. url: https://www.ncbi.nlm.nih.gov/pubmed/32562109/ doi: 10.1007/s40477-020-00494-3 id: cord-351555-hsgsuor2 author: Constantinou, Constantina title: Developing a holistic contingency plan: Challenges and dilemmas for cancer patients during the COVID‐19 date: 2020-07-20 words: 7593.0 sentences: 406.0 pages: flesch: 48.0 cache: ./cache/cord-351555-hsgsuor2.txt txt: ./txt/cord-351555-hsgsuor2.txt summary: Zhang et al, 21 reported that patients who had their last anti-tumor treatment (including chemotherapy, immunotherapy, and radiation) within 14 days prior to infection with SARS-CoV-2 had a significantly increased risk of developing severe events (HR = 4.079, 95% CI 1.086-15.322, P = .037). 37, 38 In order to achieve this, in the most affected areas medical specialists, including oncologists, were asked to provide their assistance in managing patients suffering from COVID-19 requiring hospitalization in ICUs or in the departments of infectious or respiratory diseases or general internal medicine. 40 Currently, there are no official reports of how the treatment of cancer patients has been affected by the lack of resources and limited access to healthcare due to the COVID-19 pandemic in most afflicted countries. The decision should be based on the cancer type and stage, the clinical condition of the patient, the treatment indicated for the condition, the patient''s response to anticancer therapy, and the potential risks for an infection with SARS-CoV-2. abstract: During the first quarter of 2020 the world is experiencing a pandemic of Severe Acute Respiratory Syndrome‑Coronavirus‑2 (SARS‑CoV‑2), a novel beta coronavirus that is responsible for the 2019 novel coronavirus disease (COVID‐19). The COVID‐19 pandemic revealed that healthcare systems around the world were not prepared to deal with either the direct effects of the pandemic or with the indirect effects that are imposed on the health of patients with chronic disorders such as cancer patients. Some challenges and dilemmas currently faced during the pandemic include the management of cancer patients during the treatment and follow‐up phases, the assessment of the safety of treatments currently used for the management of SARS‑CoV‑2 for use in cancer patients, the development of psychoeducation and emotional support for cancer patients and the safe conduct of clinical trials involving participation of cancer patients. Evidence from the literature supports the need for the urgent development of a holistic contingency plan which will include clear guidelines for the protection and comprehensive care of cancer patients. The implementation of such a plan is expected to have many beneficial effects by mainly minimizing the increased morbidity and mortality of cancer patients that could result as an adverse consequence of the COVID‐19 or future pandemics. url: https://doi.org/10.1002/cam4.3271 doi: 10.1002/cam4.3271 id: cord-305270-vos341i1 author: Conte, Luana title: Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection date: 2020-06-29 words: 2455.0 sentences: 152.0 pages: flesch: 39.0 cache: ./cache/cord-305270-vos341i1.txt txt: ./txt/cord-305270-vos341i1.txt summary: title: Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection 16 Targeting the gut-lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection keywords: anti-inflammatory effects, COVID-19 infection, gut-lung microbiota aixs, high-fibre diet, probiotics, SARS-CoV-2 Among dietary supplements, potential new treatments against COVID-19 infection could be based on probiotics, 17, 22 which might not only reduce colonisation by pathogenic species but also increase commensal bacterial growth in the respiratory tract. Although there is no clinical evidence that targeting the gut-lung microbiota axis would play a therapeutic role in COVID-19 infection, we believe that the manipulation of microbial patterns through the use of probiotics, prebiotics and a high-fibre diet may help to reduce cell inflammation, maintain a healthy gut microbial diversity and strengthen the immune system. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 1 is a 2019 novel coronavirus, which only in the European area has led to more than 300,000 cases with at least 21,000 deaths. This manuscript aims to speculate that the manipulation of the microbial patterns through the use of probiotics and dietary fibers consumption may contribute to reduce inflammation and strengthen the immune system response in COVID-19 infection. The reviews of this paper are available via the supplemental material section. url: https://www.ncbi.nlm.nih.gov/pubmed/32600125/ doi: 10.1177/1753466620937170 id: cord-313265-lff5cajm author: Conway, Michael J. title: Identification of coronavirus sequences in carp cDNA from Wuhan, China date: 2020-03-16 words: 918.0 sentences: 61.0 pages: flesch: 61.0 cache: ./cache/cord-313265-lff5cajm.txt txt: ./txt/cord-313265-lff5cajm.txt summary: Severe acute respiratory syndrome (SARS)‐like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. SARS-like virus sequences that were highly homologous to SARS-CoV-2 were identified in two separate complementary DNA (cDNA) pools. Tblastn analysis using this sequence identified two cDNA clones that were highly homologous to SARS-like coronaviruses. The first cDNA pool was made from Carassius auratus (crucian carp) blastulae embryonic cell line and contained a sequence of 152 amino acids that covered 2% of the SARS-CoV-2 genome and was 93.42% The second cDNA pool was made from Ctenopharyngodon idella (grass carp) head kidney and contained a sequence of 88 amino acids that covered 1% of the SARS-CoV-2 genome and was 93.18% identical. Protein and nucleic acid alignments of each cDNA clone were performed to compare with the most related coronavirus sequences (Figures 1 and 2) . abstract: Severe acute respiratory syndrome (SARS)‐like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. The first pool was from a Carassius auratus (crusian carp) cell line and the second was from Ctenopharyngodon idella (grass carp) head kidney tissue. BLAST analysis suggests that these sequences belong to SARS‐like coronaviruses, and that they are not evolutionarily conserved in other species. Investigation of the submitting laboratories revealed that two laboratories from the Institute of Hydrobiology at the Chinese Academy of Sciences in Wuhan, China performed the research and submitted the cDNA libraries to GenBank. This institution is very close in proximity to the Wuhan South China Seafood Wholesale Market where SARS‐CoV‐2 first amplified in the human population. It is possible that these sequences are an artifact of the bioinformatics pipeline that was used. It is also possible that SARS‐like coronaviruses are a common environmental pathogen in the region that may be in aquatic habitats. url: https://www.ncbi.nlm.nih.gov/pubmed/32159234/ doi: 10.1002/jmv.25751 id: cord-263538-0wozg085 author: Cooch, P. B. title: Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date: 2020-10-23 words: 4440.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-263538-0wozg085.txt txt: ./txt/cord-263538-0wozg085.txt summary: Conclusions: Supervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, paired with infection mitigation strategies (e.g., masking, physical distancing, stable cohorts, and hand hygiene), comprise a comprehensive strategy for safe school reopening. We hypothesized that supervised self-collection of anterior nares and saliva samples for the purpose of SARS-CoV-2 surveillance would be acceptable and feasible for kindergarten through 8 th grade children, their household contacts, and camp staff, and that camp staff could assist with collection supervision. 17 To our knowledge, this is the first study to describe self-collected anterior nares SARS-CoV-2 testing among children, or any participants in a school-like setting. In conclusion, we demonstrated excellent feasibility and acceptability of a serial surveillance SARS-CoV-2 testing approach with supervised anterior nares self-collection in 5-14 year-old children, their household contacts, and staff, during indoor summer camp. abstract: Background and Objectives: Testing strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in school settings are needed to assess the efficacy of infection mitigation strategies and inform school reopening policies. We hypothesized that supervised serial self-collected non-nasopharyngeal testing in summer camp settings would be acceptable and feasible. Methods: We performed a cohort study at two urban day camps for kindergarten-8th graders in June and July 2020. Eligible participants were campers, up to two adult household contacts, and camp staff. We assessed participation rates for providing, at two time points, supervised, self-collected anterior nares samples for reverse transcription polymerase chain reaction (RT-PCR) and saliva samples for antibody testing. We qualitatively assessed testing feasibility and adherence to stated camp infection mitigation strategies. Results: 76% (186/246) of eligible participants consented. The cohort completing both rounds of testing (n=163) comprised 67 campers, 76 household contacts, and 20 staff. Among those present, 100% of campers and staff completed test collection at both time points. Testing was feasible to implement, including staff participation supervising camper test collection. No virus was detected by RT-PCR; seven participants had antibodies. Observed adherence to stated camp mitigation policies for masking, physical distancing, and stable cohorting was generally high. Conclusions: Supervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. This strategy for testing and the observed infection mitigation practices comprise potential core components for safe school reopening. url: https://doi.org/10.1101/2020.10.21.20214338 doi: 10.1101/2020.10.21.20214338 id: cord-259863-ndclxrm7 author: Cooke, William R. title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases date: 2020-05-15 words: 728.0 sentences: 69.0 pages: flesch: 56.0 cache: ./cache/cord-259863-ndclxrm7.txt txt: ./txt/cord-259863-ndclxrm7.txt summary: title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases We present our experience of managing two cases of SARS-CoV-2 infection in very preterm pregnancy. SARS-CoV-2 infection causing type 1 respiratory failure was presumed. A multidisciplinary (obstetric, anaesthetic and intensivist) decision was made for delivery by caesarean section, to facilitate invasive ventilation of the woman. SARS-CoV-2 RNA swab from the patient was positive, and from the baby was negative. SARS-CoV-2 RNA swab from the mother was positive, and from the baby was negative. To date 3 cases of severe SARS-CoV-2 infection in very preterm pregnancy (<32 weeks) have been published; all underwent caesarean section for maternal resuscitation; one woman died [1] [2] [3] . 1. Both women deteriorated within 24 hours of presentation: we recommend early administration of corticosteroids for fetal maturation. A case of 2019 Novel Coronavirus in a pregnant woman with preterm delivery abstract: nan url: https://doi.org/10.1016/j.ejogrb.2020.05.025 doi: 10.1016/j.ejogrb.2020.05.025 id: cord-311125-v9ddes3c author: Cooper, Keiland W. title: COVID-19 and the chemical senses: supporting players take center stage date: 2020-07-01 words: 9480.0 sentences: 510.0 pages: flesch: 49.0 cache: ./cache/cord-311125-v9ddes3c.txt txt: ./txt/cord-311125-v9ddes3c.txt summary: Given data suggesting that ACE2 is necessary for SARS-CoV2 to infect host cells, researchers have used a variety of approaches to discern the pattern of expression of ACE2 and other viral entry proteins across the tissue landscape, with the goal of inferring possible target cells and disease mechanisms. It remains unclear whether SARS-CoV-2 (given that it likely does not directly infect OSNs, and thus cannot pass directly through the olfactory nerve, see However, scSeq and immunostaining of the mouse OB has revealed -as in the nose -that bulb neurons do not express detectable levels of ACE2 ( Figure 2 ) . This model suggests that neural function is altered indirectly due to sequelae of SARS-CoV-2 infection of peripheral support cells, including (but not limited to) local inflammation and changes in OSN gene expression and ciliary structure. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia abstract: Abstract The main neurological manifestation of COVID-19 is loss of smell or taste. The high incidence of smell loss without significant rhinorrhea or nasal congestion suggests that SARS-CoV-2 targets the chemical senses through mechanisms distinct from those used by endemic coronaviruses or other common cold-causing agents. Here we review recently developed hypotheses about how SARS-CoV-2 might alter the cells and circuits involved in chemosensory processing and thereby change perception. Given our limited understanding of SARS-CoV-2 pathogenesis, we propose future experiments to elucidate disease mechanisms and highlight the relevance of this ongoing work to understanding how the virus might alter brain function more broadly. url: https://doi.org/10.1016/j.neuron.2020.06.032 doi: 10.1016/j.neuron.2020.06.032 id: cord-347356-uc9dqhyq author: Cooper, TJ title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 words: 3949.0 sentences: 228.0 pages: flesch: 54.0 cache: ./cache/cord-347356-uc9dqhyq.txt txt: ./txt/cord-347356-uc9dqhyq.txt summary: OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The aim of this systematic review was to identify studies that discuss PLHIV who have been infected with SARS-CoV-2 and that report whether coinfection results in a greater risk of adverse outcomes and, furthermore, whether controlled HIV infection vs. A comprehensive literature search was carried out in Global Health, SCOPUS, Medline and EMBASE to identify articles that discussed HIV-positive patients and the clinical implications of HIV infection in COVID-19 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines [13] . [21] , also highlighted a case study of a HIV patient with SARS-CoV2 co-infection, diagnosis of viral pneumonia was made on clinical examination and chest CT findings. abstract: OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). METHODS: We conducted a systematic review using the Preferred Reporting Items for Systematic Reviews and Meta‐analysis (PRISMA) guidelines. A comprehensive literature search was conducted in Global Health, SCOPUS, Medline and EMBASE using pertinent key words and Medical Subject Headings (MeSH) terms relating to coronavirus disease 2019 (COVID‐19) and HIV. A narrative synthesis was undertaken. Articles are summarized in relevant sections. RESULTS: Two hundred and eighty‐five articles were identified after duplicates had been removed. After screening, eight studies were analysed, totalling 70 HIV‐infected patients (57 without AIDS and 13 with AIDS). Three themes were identified: (1) controlled HIV infection does not appear to result in poorer COVID‐19 outcomes, (2) more data are needed to determine COVID‐19 outcomes in patients with AIDS and (3) HIV‐infected patients presenting with COVID‐19 symptoms should be investigated for superinfections. CONCLUSIONS: Our findings suggest that PLHIV with well‐controlled disease are not at risk of poorer COVID‐19 disease outcomes than the general population. It is not clear whether those with poorly controlled HIV disease and AIDS have poorer outcomes. Superimposed bacterial pneumonia may be a risk factor for more severe COVID‐19 but further research is urgently needed to elucidate whether PLHIV are more at risk than the general population. url: https://doi.org/10.1111/hiv.12911 doi: 10.1111/hiv.12911 id: cord-309089-ex9nh1yi author: Coperchini, Francesca title: The Cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system date: 2020-05-11 words: 6132.0 sentences: 303.0 pages: flesch: 43.0 cache: ./cache/cord-309089-ex9nh1yi.txt txt: ./txt/cord-309089-ex9nh1yi.txt summary: Since the first reports on COVID-19 disease, it appeared clear that Acute respiratory distress syndrome (ARDS) accounted for a significant number of deaths among infected patients and that ARDS should be regarded as the hallmark immune-mediated clinical consequence in SARS-CoV-2, similarly to what described for SARS-CoV and MERS-CoV infections [11] . As shown by previous data in the literature, increased circulating levels of pro-inflammatory cytokines (eg, Interferon γ, interleukin (IL-) 1B, IL-6, IL-12) and chemokines (CXCL10, and CCL2) are associated with pulmonary inflammation and extensive lung involvement in SARS patients, similarly to what happens in MERS-CoV infection [13] . In mice infected with SARS-CoV, the clinical features of the syndrome showed an age-dependent increase in severity (similarly to what observed in humans), which was related to an increased level of pro-inflammatory cytokines and chemokines, paralleled by a reduction in T-cell responses [78] . abstract: In 2019-2020 a new coronavirus named SARS-CoV-2 was identified as the causative agent of a several acute respiratory infection named COVID-19, which is causing a worldwide pandemic. There are still many unresolved questions regarding the pathogenesis of this disease and especially the reasons underlying the extremely different clinical course, ranging from asymptomatic forms to severe manifestations, including the Acute Respiratory Distress Syndrome (ARDS). SARS-CoV-2 showed phylogenetic similarities to both SARS-CoV and MERS-CoV viruses, and some of the clinical features are shared between COVID-19 and previously identified beta-coronavirus infections. Available evidence indicate that the so called “cytokine storm” an uncontrolled over-production of soluble markers of inflammation which, in turn, sustain an aberrant systemic inflammatory response, is a major responsible for the occurrence of ARDS. Chemokines are low molecular weight proteins with powerful chemoattractant activity which play a role in the immune cell recruitment during inflammation. This review will be aimed at providing an overview of the current knowledge on the involvement of the chemokine/chemokine-receptor system in the cytokine storm related to SARS-CoV-2 infection. Basic and clinical evidences obtained from previous SARS and MERS epidemics and available data from COVID-19 will be taken into account. url: https://www.sciencedirect.com/science/article/pii/S1359610120300927?v=s5 doi: 10.1016/j.cytogfr.2020.05.003 id: cord-344842-9cfbb7p6 author: Coppola, Maurizio title: Potential Unconventional Medicines for the Treatment of SARS-CoV-2 date: 2020-05-19 words: 723.0 sentences: 43.0 pages: flesch: 45.0 cache: ./cache/cord-344842-9cfbb7p6.txt txt: ./txt/cord-344842-9cfbb7p6.txt summary: Adem and colleagues in their virtual screening based molecular docking study reported a potential binding affinity exerted by various bioflavonoids at the active site of the MPro, the main protease of the SARS-CoV-2 [1] . Potential inhibition properties were studied using the Molegro Virtual Docker Program and some flavonoids, in particular hesperidin, rutin, and diosmin showed a better affinity for the MPro than nelfinavir [1] . Rutin showed the second strongest binding energy at the active site of the MPro with a MoLDock score of −176.2740 and a HBond of −21.2402. Recently, Caly and colleagues reported a potential antiretroviral activity of the anti-parasitic agent ivermectin against SARS-CoV-2 virus. Despite the absence of clinical evidences regarding some potential anti-SARS-CoV-2 drugs, preliminar information reported by researchers suggest anyhow further studies in order to evaluate the clinical effects as well as the possibility to synthesize derivatives with stronger antiretroviral properties. abstract: nan url: https://doi.org/10.1055/a-1170-4624 doi: 10.1055/a-1170-4624 id: cord-312670-hi3fjne4 author: Corman, V. M. title: Coronaviren als Ursache respiratorischer Infektionen date: 2019-08-27 words: 2307.0 sentences: 257.0 pages: flesch: 49.0 cache: ./cache/cord-312670-hi3fjne4.txt txt: ./txt/cord-312670-hi3fjne4.txt summary: Zusätzlich zu diesen ständig im Menschen zirkulierenden Varianten wurden in den vergangenen Jahren zwei CoV im Menschen gefunden, nämlich SARS-CoV und MERS-CoV, die aus dem Tierreservoir auf den Menschen übergegangen sind und bei einem deutlich größeren Anteil der Infizierten schwere virale Pneumonien mit tödlichem Verlauf auslösen [25, 28] . Obwohl die Mehrzahl der Infektionen mit den vier endemischen CoV nur leichte Atemwegserkrankungen verursacht, können alle HCoV auch schwere Hier steht eine Anzeige. Inwiefern diese sekundären Infektionen auf die intensivmedizinische Behandlung und Beatmung zurückzuführen sind oder ein spezifisches grundsätzliches Risiko einer CoV-Infektion darstellen, ist noch nicht verstanden. Jedoch ist eine spezifische Labordiagnostik bei Verdacht auf eine Infektion mit endemi-schen CoV bei harmlosem Verlauf und Patienten ohne besonderes Risiko für die Entstehung von Komplikationen auch nicht indiziert. Bei der typischerweise unspezifischen Klinik von MERS-CoV-Infektionen sollte auch die Möglichkeit einer Infektion mit anderen Pathogenen in Betracht gezogen werden [26] . RKI (2015) Schwere respiratorische Erkrankungen in Verbindung mit Middle East Respiratory Syndrome Coronavirus (MERS-CoV). abstract: BACKGROUND: There are six human pathogenic coronaviruses (CoV), which mainly cause infections of the respiratory system. In everyday clinical practice, it is helpful to know the relevance and characteristics of these pathogens. OBJECTIVE: To present the epidemiology, clinical picture and differences of human pathogenic CoV and to provide information on the diagnostics and treatment of patients suspected of having CoV infections. MATERIAL AND METHODS: Selective literature search, presentation of results and discussion of fundamental works and expert recommendations, including publications by the World Health Organization (WHO), the European Centre for Disease Prevention and Control (ECDC) and the Robert Koch Institute. RESULTS: The four endemic human CoVs (HCoV-NL63, HCoV-229E, HCoV-OC43 and HCoV-HKU1) mainly cause mild respiratory tract infections. In addition to these four endemic HCoV, the two epidemic CoV, severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV can cause severe pneumonia. The SARS-CoV has not been detected in humans in the last 15 years and MERS-CoV has been circulating mainly on the Arabian Peninsula since 2012; however, neither a specific treatment nor approved vaccines exist for any of the six human pathogenic CoVs. CONCLUSION: All six human CoVs can be diagnosed using RT-PCR on respiratory specimens but this is rarely necessary for the four endemic strains. In current clinical practice SARS-CoV has no importance as it has not been detected in humans for 15 years; however, a possible MERS-CoV infection should be taken into account in patients with typical symptoms and travel history to endemic regions. In this case, rapid diagnostic and general hygiene practices are important to prevent further transmission. url: https://doi.org/10.1007/s00108-019-00671-5 doi: 10.1007/s00108-019-00671-5 id: cord-317608-otd81rvy author: Corman, Victor M. title: SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission date: 2020-05-27 words: 1245.0 sentences: 75.0 pages: flesch: 56.0 cache: ./cache/cord-317608-otd81rvy.txt txt: ./txt/cord-317608-otd81rvy.txt summary: Oral swabs, sputum, and blood samples from 18 asymptomatic and symptomatic patients with SARS‐CoV‐2 infection were examined using RT‐PCR testing in order to assess the risk of transfusion‐related transmission. In asymptomatic patients as well as patients with flu‐like symptoms and fever, no SARS‐CoV‐2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • In asymptomatic patients as well as patients with flulike symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • As patients with symptoms of infectious disease will not be admitted to blood donation, the risk for transfusion transmission of SARS-CoV-2 seems to be negligible. In asymptomatic patients who are eligible for blood donation as well as patients with flu-like symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. abstract: Oral swabs, sputum, and blood samples from 18 asymptomatic and symptomatic patients with SARS‐CoV‐2 infection were examined using RT‐PCR testing in order to assess the risk of transfusion‐related transmission. In asymptomatic patients as well as patients with flu‐like symptoms and fever, no SARS‐CoV‐2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. As patients with symptoms of infectious disease will not be admitted to blood donation, the risk for transfusion transmission of SARS‐CoV‐2 seems to be negligible. url: https://www.ncbi.nlm.nih.gov/pubmed/32361996/ doi: 10.1111/trf.15841 id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 words: 4046.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-353342-2n6kqyeo.txt txt: ./txt/cord-353342-2n6kqyeo.txt summary: title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: Background. The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. Methods. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. Results. One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 10(6) (6 × 10(10)) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 10(4) copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. Conclusions. The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26565003/ doi: 10.1093/cid/civ951 id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 words: 4584.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-327259-7o7fs4yb.txt txt: ./txt/cord-327259-7o7fs4yb.txt summary: We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . abstract: qRT-PCR is the gold standard technique available for SARS-CoV-2 detection. However, the long test run time and costs associated with this type of molecular testing are a challenge in the actual pandemic scenario. Due to high testing demand, pooling sample strategy is an interesting approach to allow cost savings. We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). Although the sensitivity reduction in samples pooled with 32 individuals was observed, the high-test sensitivity is maintained even when 16 and 8 samples were pooled. The in silico analysis showed high-cost savings in populations with positive rates lower than 15.0% according to the pool size. This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. Our data confirmed that mathematical modeling is a powerful strategy to improve the pooling approach for SARS-CoV-2 mass testing around the world while maintaining high sensitivity and robustness. url: http://medrxiv.org/cgi/content/short/2020.08.16.20167536v1?rss=1 doi: 10.1101/2020.08.16.20167536 id: cord-264976-6n9cdex6 author: Corse, Tanner title: Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date: 2020-10-18 words: 6080.0 sentences: 266.0 pages: flesch: 41.0 cache: ./cache/cord-264976-6n9cdex6.txt txt: ./txt/cord-264976-6n9cdex6.txt summary: The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. abstract: In the ongoing COVID-19 pandemic, all COVID-19 patients are naïve patients as it is the first-time humans have been exposed to the SARS-CoV-2 virus. As with exposure to many viruses, individuals with pre-existing, compromised immune systems may be at increased risk of developing severe symptoms and/or dying because of (SARS-CoV-2) infection. To learn more about such individuals, we conducted a search and review of published reports on the clinical characteristics and outcomes of COVID-19 patients with pre-existing, compromised immune systems. Here we present our review of patients who possess pre-existing primary antibody deficiency (PAD) and those who are organ transplant recipients on maintenance immunosuppressants. Our review indicates different clinical outcomes for the patients with pre-existing PAD, depending on the underlying causes. For organ transplant recipients, drug-induced immune suppression alone does not appear to enhance COVID-19 mortality risk - rather, advanced age, comorbidities, and the development of secondary complications appears required. url: https://doi.org/10.7150/ijms.50537 doi: 10.7150/ijms.50537 id: cord-270919-0hldozml author: Cortey, Martí title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date: 2020-05-17 words: 1063.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-270919-0hldozml.txt txt: ./txt/cord-270919-0hldozml.txt summary: title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%. 54 The aim of the present study was to determine the amino acid substitutions in viral 55 proteins that were widely present in available sequences of SARS-CoV-2, relating them 56 to the known chronology of the pandemic. abstract: The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%. url: https://doi.org/10.1101/2020.05.16.099499 doi: 10.1101/2020.05.16.099499 id: cord-314694-g0pes5o3 author: Cortiula, F. title: Managing COVID-19 in the oncology clinic and avoiding the distraction effect date: 2020-03-19 words: 1163.0 sentences: 69.0 pages: flesch: 49.0 cache: ./cache/cord-314694-g0pes5o3.txt txt: ./txt/cord-314694-g0pes5o3.txt summary: The safety and management of cancer patients in the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is urgent and most cancer clinics need to establish a contingency plan. The authors suggest that postponing adjuvant chemotherapy or elective surgery for less aggressive cancers should be considered and that the increased risk for personal protection provisions should be emphasized for patients with cancer or cancer survivors. Furthermore, more intensive surveillance or treatment should be considered for those patients with cancer who are infected with SARS-CoV-2. Re-allocating an excessive amount of health care personnel, both nurses and doctors, to the COVID-19 triage and management may stretch an already fragile system and potentially leave uncovered some vital activities, such as treatment administration, surgeries and inpatient assistance. 5 Patients with advanced disease, and no suggestive symptoms of COVID-19, should keep receiving planned chemotherapy or radiotherapy treatment, without unnecessary delays. Risk of COVID-19 for patients with cancer abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0923753420363730 doi: 10.1016/j.annonc.2020.03.286 id: cord-310692-8fuj9td2 author: Coste, A. T. title: Indication for SARS-CoV-2 serology: first month follow-up date: 2020-07-03 words: 1536.0 sentences: 99.0 pages: flesch: 51.0 cache: ./cache/cord-310692-8fuj9td2.txt txt: ./txt/cord-310692-8fuj9td2.txt summary: Our laboratory performed a prospective surveillance of the SARS-CoV-2 serologic test requested during the first 5 weeks, by specifically looking at rate of the different accepted indications. For the 303 serologies requested by hospital-based physicians working in tertiary hospitals or clinics, 94 were positive (31%), 205 were negative (68%), and four were undetermined (13%). They had specific directives in their hospital to systematically perform a SARS-CoV-2 RT-PCR screening and serology to any patient arriving at the hospital. The residuals symptoms with no documented or negative RT-PCR (indication N°6.4) appeared to be very important for patient care but was totally unexpected, since on 14 th April, when we started the SARS-CoV-2 serology, the occurrence of such post-infectious complications were not yet reported [5] . This work may serve as a seed for international guidelines regarding the indications of SARS-CoV-2 serology for patients care. abstract: SARS-CoV-2 detection is mainly performed by RT-PCR but recently serological tests were made available. A first one month follow-up of the SARS-CoV-2 serology records was performed in our laboratory to precise the diversity and proportion of the SARS-CoV-2 serology test indications and to identify new valid indications (meningoencephalitis, vasculitis, etc) url: http://medrxiv.org/cgi/content/short/2020.06.30.20140715v1?rss=1 doi: 10.1101/2020.06.30.20140715 id: cord-277889-8u685f45 author: Costela-Ruiz, Víctor J. title: SARS-CoV-2 infection: the role of cytokines in COVID-19 disease date: 2020-06-02 words: 9212.0 sentences: 552.0 pages: flesch: 49.0 cache: ./cache/cord-277889-8u685f45.txt txt: ./txt/cord-277889-8u685f45.txt summary: The majority of patients infected with COVID-19 have normal or reduced white cell counts and lymphocytopenia, and those with severe disease have shown significantly elevated levels of neutrophils, dimer-D, and urea in blood, with a continuing decrease in lymphocytes. detected elevated levels of the antagonistic receptor of IL-1 (IL-1Ra) in 14 severe cases of COVID-19, and this marker has been associated with increased viral load, loss of pulmonary function, lung damage, and mortality risk [55] . observed that its expression during infection with an influenza virus had negative effects on CD8 + memory T cells [71] .Various studies of COVID-19 patients have detected elevated IL-4 levels as part of the cytokine storm associated with severe respiratory symptoms [16, 17, 43, 72] . Elevated IL-17 levels have been reported in patients with SARS-CoV-2 as part of the cytokine storm [17] , and they have been associated with the viral load and disease severity [56] . abstract: COVID-19 disease, caused by infection with SARS-CoV-2, is related to a series of physiopathological mechanisms that mobilize a wide variety of biomolecules, mainly immunological in nature. In the most severe cases, the prognosis can be markedly worsened by the hyperproduction of mainly proinflammatory cytokines, such as IL-1, IL-6, IL-12, IFN-γ, and TNF-α, preferentially targeting lung tissue. This study reviews published data on alterations in the expression of different cytokines in patients with COVID-19 who require admission to an intensive care unit. Data on the implication of cytokines in this disease and their effect on outcomes will support the design of more effective approaches to the management of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S135961012030109X?v=s5 doi: 10.1016/j.cytogfr.2020.06.001 id: cord-312633-cks6aij2 author: Cotten, Matthew title: Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus date: 2013-05-17 words: 4063.0 sentences: 229.0 pages: flesch: 55.0 cache: ./cache/cord-312633-cks6aij2.txt txt: ./txt/cord-312633-cks6aij2.txt summary: Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events. We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. A map of the primer mapping positions Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus and the predicted PCR products using EMC/2012 as the target is shown in Figure 1 , panel A. A ML phylogenetic tree inferred from the whole genome alignment indicated that the 3 novel human beta-CoVs sequences (England1, England/Qatar/2012, and EMC/2012) clustered closely, forming a monophyletic lineage that falls into group 2c (Figure 3 , panel A, Appendix, wwwnc.cdc.gov/EID/article/19/5/13-0057-F3.htm). abstract: A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient’s sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events. url: https://www.ncbi.nlm.nih.gov/pubmed/23693015/ doi: 10.3201/eid1905.130057 id: cord-300117-rlpzejjt author: Coutard, B. title: The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade date: 2020-02-10 words: 3021.0 sentences: 146.0 pages: flesch: 50.0 cache: ./cache/cord-300117-rlpzejjt.txt txt: ./txt/cord-300117-rlpzejjt.txt summary: In the case of human-infecting coronaviruses such as HCoV-OC43 (Le Coupanec et al., 2015) , MERS-CoV (Millet and Whittaker, 2014) , and HKU1 (Chan et al., 2008) the spike protein has been demonstrated to be cleaved at an S1/S2 cleavage site (Fig. 2) generating the S1 and S2 subunits. The furin-like S2′ cleavage site at KR↓SF with P1 and P2 basic residues and a P2′ hydrophobic Phe (Seidah and Prat, 2012) , downstream of the IFP is identical between the 2019-nCoV and SARS-CoV (Fig. 2) . However, in the other less pathogenic circulating human CoV, the S2′ cleavage site only exhibits a monobasic R↓S sequence (Fig. 2) with no basic residues at either P2 and/or P4 needed to allow furin cleavage, suggesting a less efficient cleavage or higher restriction at the entry step depending on the cognate proteases expressed by target cells. abstract: In 2019, a new coronavirus (2019-nCoV) infecting Humans has emerged in Wuhan, China. Its genome has been sequenced and the genomic information promptly released. Despite a high similarity with the genome sequence of SARS-CoV and SARS-like CoVs, we identified a peculiar furin-like cleavage site in the Spike protein of the 2019-nCoV, lacking in the other SARS-like CoVs. In this article, we discuss the possible functional consequences of this cleavage site in the viral cycle, pathogenicity and its potential implication in the development of antivirals. url: https://www.sciencedirect.com/science/article/pii/S0166354220300528 doi: 10.1016/j.antiviral.2020.104742 id: cord-268169-xry3nhzt author: Couturier, Aymeric title: Indirect effects of severe acute respiratory syndrome coronavirus 2 on the kidney in coronavirus disease patients date: 2020-05-22 words: 3084.0 sentences: 175.0 pages: flesch: 47.0 cache: ./cache/cord-268169-xry3nhzt.txt txt: ./txt/cord-268169-xry3nhzt.txt summary: Among patients hospitalized for novel coronavirus disease (COVID-19), between 10 and 14% develop an acute kidney injury and around half display marked proteinuria and haematuria. Collapsing glomerulopathy is a peculiar form of focal segmental glomerulosclerosis (FSGS) [6] that has been well characterized in patients infected by human immunodeficiency virus (HIV) type 1 [7] . In order to better characterize the relationship between SARS-CoV-2 infection and collapsing FSGS, we performed an RT-PCR assay on the renal tissue specimen from Patient 1. Our results are in line with a recent inpress report that describes the presence of collapsing glomerulopathy and tubulointerstitial lesions in living COVID-19 patients of African origin, homozygous for APOL1 risk allele G1 and evidence of chronicity on kidney biopsy [12] . Although our findings do not definitely rule out a direct infection of kidney cells by SARS-CoV-2, COVID-19-related collapsing FSGS appears to be related to a viral-induced inflammatory response against a peculiar genetic background. abstract: Among patients hospitalized for novel coronavirus disease (COVID-19), between 10 and 14% develop an acute kidney injury and around half display marked proteinuria and haematuria. Post-mortem analyses of COVID-19 kidney tissue suggest that renal tubular cells and podocytes are affected. Here we report two cases of collapsing glomerulopathy and tubulointerstitial lesions in living COVID-19 patients. Despite our use of sensitive reverse transcription polymerase chain reaction techniques in this study, we failed to detect the virus in blood, urine and kidney tissues. Our observations suggest that these kidney lesions are probably not due to direct infection of the kidney by severe acute respiratory syndrome coronavirus 2. url: https://doi.org/10.1093/ckj/sfaa088 doi: 10.1093/ckj/sfaa088 id: cord-311066-62edsbfc author: Cox, Brian J. title: Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date: 2020-06-24 words: 2926.0 sentences: 172.0 pages: flesch: 61.0 cache: ./cache/cord-311066-62edsbfc.txt txt: ./txt/cord-311066-62edsbfc.txt summary: Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5''-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. Some RNAs, especially non-coding RNAs, generally lack a poly-A tail, which could explain poor detection of TRS independent sgmRNAs. Using published sequencing data of ribosome depleted total RNA from SARS-CoV-2 infected cells and animals (Blanco-Melo et al., 2020) , I aligned these against the viral genome (Figure 2) . Using the aligned reads, I generated transcript models using stringtie, which identified multiple spliced species that aligned with the TRS-L templated events (Figure 2) . Split reads also identified TRS-independent sgmRNAs. In support of my observations on SARS-CoV-2, I also assessed SARS-CoV and MERs transcriptional data, two other human pathogenic CoV. I also identified the TIR motif, a novel sequence element (ATTGGC) flanking the spliced regions of TRS independent sgmRNAs in both SARS-CoV-2 and SARS-CoV. abstract: In the last twenty years, three separate coronaviruses have left their typical animal hosts and became human pathogens. An area of research interest is coronavirus transcription regulation that uses an RNA-RNA mediated template-switching mechanism. It is not known how different transcriptional stoichiometries of each viral gene are generated. Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5’-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. TRS independent transcripts were detected as likely non-polyadenylated. Additionally, a novel conserved sequence motif was discovered at either end of the TRS independent splice junctions. While similar both SARS viruses generated similar TRS independent transcripts they were more abundant in SARS-CoV-2. TRS independent gene regulation requires investigation to determine its relationship to viral pathogenicity. url: https://doi.org/10.1101/2020.06.24.169144 doi: 10.1101/2020.06.24.169144 id: cord-278542-vqp6ec6e author: Coyne, Carolyn title: Recommendations for future university pandemic responses: What the first COVID-19 shutdown taught us date: 2020-08-27 words: 2562.0 sentences: 148.0 pages: flesch: 45.0 cache: ./cache/cord-278542-vqp6ec6e.txt txt: ./txt/cord-278542-vqp6ec6e.txt summary: Successes and failures along the way highlighted how the autonomous nature of the American academic research enterprise and skillsets normally required of university leaders were ill-suited to mounting an emergency response. Here, as faculty from medical centers in the United States, we draw lessons from these experiences and apply them as we plan for the next possible COVID-19-induced shutdown as well as other large-scale pandemics and emergencies at universities in the United States and throughout the world. In addition, students (and faculty) with children or other dependents required homeschooling and alternative care plans that conflicted with classes they either were enrolled in or taught. Other swiftly implemented decisions included accommodating research groups who possessed expertise to work on SARS-CoV-2 while creating protocols such as social distancing and PPE use for their safety. In addition, institutions need to consider the needs of laboratory staff and trainees and include them in the decision-making process. abstract: The SARS-CoV-2 epidemic challenged universities and other academic institutions to rapidly adapt to urgent and life-threatening situations. It forced most institutions to shut down nearly every aspect of their research and educational enterprises. In doing so, university leaders were thrust into unchartered waters and forced them to make unprecedented decisions. Successes and failures along the way highlighted how the autonomous nature of the American academic research enterprise and skillsets normally required of university leaders were ill-suited to mounting an emergency response. Here, as faculty from medical centers in the United States, we draw lessons from these experiences and apply them as we plan for the next possible COVID-19-induced shutdown as well as other large-scale pandemics and emergencies at universities in the United States and throughout the world. url: https://www.ncbi.nlm.nih.gov/pubmed/32853196/ doi: 10.1371/journal.pbio.3000889 id: cord-270880-azslipmp author: Cozzupoli, Grazia Maria title: Possible Retinal Impairment Secondary to Ritonavir Use in SARS-CoV-2 Patients: A Narrative Systematic Review date: 2020-08-22 words: 2813.0 sentences: 153.0 pages: flesch: 44.0 cache: ./cache/cord-270880-azslipmp.txt txt: ./txt/cord-270880-azslipmp.txt summary: Seven single cases and one case series, reporting a total of 10 patients affected by retinal changes secondary to long-term ritonavir treatment, were included in the review. Although a recent randomized trial [3] involving hospitalized adult patients with confirmed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection has not shown significant benefits with lopinavir/ritonavir treatment beyond standard care, this protease inhibitor association is used in worldwide hospitals [4] . us, we conducted a narrative systematic review of the published reports describing the clinical features and imaging signs associated with ritonavirinduced retinal toxicity. Anyway, it is not illogical to hypothesize that the retinal toxic effects of both long-term hydroxychloroquine [32] and ritonavir therapies might appear also after short-term treatments, as in the case of SARS-CoV-2 patients, enhanced by the deterioration of renal and hepatic clearance function, respectively. e authors report a case of bull''s eye maculopathy pattern in an HIV-positive patient, being treated with ritonavir for 13 years. abstract: Some reports described a possible ritonavir-related retinal toxicity. The objective of this research was to review and analyze previous studies conducted on ritonavir administration and retinal impairment in a narrative synthesis. PubMed was used to perform a systematic review of ritonavir effects and retinal damage. All studies up to December 2019 were considered. Seven single cases and one case series, reporting a total of 10 patients affected by retinal changes secondary to long-term ritonavir treatment, were included in the review. Variable degrees of outer retina and retinal pigment epithelium changes were detected in most of the patients, with two patients showing macular telangiectasia, four patients presenting intraretinal crystal deposits, two patients disclosing a bull's eye maculopathy, and two patients revealing midperipheral bone spicule-like pigment changes. In the present study, we hypothesized that the use of ritonavir in life-saving treatments of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pneumonia might expose these patients to the risk of developing a retinotoxicity. We aimed to alert ophthalmologists on the importance of recognizing ritonavir-induced retinal impairment in SARS-CoV-2 patients. These findings are the target for personalized medicine. url: https://doi.org/10.1155/2020/5350494 doi: 10.1155/2020/5350494 id: cord-275420-zkxyxiv5 author: Crabtree, Scott J. title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States date: 2020-07-23 words: 1190.0 sentences: 67.0 pages: flesch: 50.0 cache: ./cache/cord-275420-zkxyxiv5.txt txt: ./txt/cord-275420-zkxyxiv5.txt summary: title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States This case study highlights the role of a multidisciplinary Infection Prevention team in the identification of the first community-transmitted SARS-CoV-2 case at a large, tertiary referral center in the United States. By rounding on the hospital units such teams can serve vital infection prevention, antibiotic stewardship, and disease surveillance functions. Through the coordinated efforts of UCD''s multidisciplinary infection prevention (IP) program, the patient was identified as a possible COVID-19 case and obtained SARS-CoV-2 testing. During rounds, each patient is reviewed through the electronic medical record and via discussion with the bedside nurse to evaluate for possible infection prevention and antimicrobial stewardship interventions. The patient''s case was discussed with her bedside nurse, who confirmed that SARS-CoV-2 was considered by her primary team, but given the absence of exposures, testing for this agent was not pursued. abstract: This case study highlights the role of a multidisciplinary Infection Prevention team in the identification of the first community-transmitted SARS-CoV-2 case at a large, tertiary referral center in the United States. By rounding on the hospital units such teams can serve vital infection prevention, antibiotic stewardship, and disease surveillance functions. url: https://www.ncbi.nlm.nih.gov/pubmed/32698916/ doi: 10.1017/ice.2020.360 id: cord-263456-lqe1yckv author: Craney, Arryn R. title: Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-07-23 words: 2902.0 sentences: 177.0 pages: flesch: 54.0 cache: ./cache/cord-263456-lqe1yckv.txt txt: ./txt/cord-263456-lqe1yckv.txt summary: We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. On 4 February 2020, the Centers for Disease Control and Prevention (CDC) received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for an RT-PCR assay to detect SARS-CoV-2 in a range of respiratory specimens (5) . In this study, we compared the diagnostic performances of the cobas 6800 and Panther Fusion high-throughput RT-PCR systems for the detection of SARS-CoV-2 RNA in 389 NP swab specimens, the predominant specimen type employed for SARS-CoV-2 RT-PCR (4). However, to the best of our knowledge, no study has evaluated the performance characteristics of the Panther Fusion SARS-CoV-2 RT-PCR assay or directly compared two high-throughput systems. In conclusion, the cobas 6800 and Panther Fusion systems and their associated SARS-CoV-2 tests are comparable in terms of their performance characteristics in the clinical setting. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as the cause of a worldwide pandemic. Many commercial SARS-CoV-2 reverse transcription-PCR (RT-PCR) assays have received Emergency Use Authorization from the U.S. Food and Drug Administration. However, there are limited data describing their performance, in particular the performance of high-throughput SARS-CoV-2 RT-PCR systems. We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. The overall agreement between the platforms was 96.4% (375/389). Cohen’s kappa analysis rated the strength of agreement between the two platforms as “almost perfect” (κ = 0.922; standard error, 0.051). Furthermore, there was no significant difference between corresponding cycle threshold values generated on the two systems (P value = 0.88; Student’s t test). Taken together, these data imply that the two platforms can be considered comparable in terms of their clinical performance. We believe that this information will be useful for those who have already adopted these platforms or are seeking to implement high-throughput RT-PCR testing to stem the SARS-CoV-2 pandemic. url: https://doi.org/10.1128/jcm.00890-20 doi: 10.1128/jcm.00890-20 id: cord-334309-rddznfax author: Craver, Randall title: Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) date: 2020-05-13 words: 1672.0 sentences: 118.0 pages: flesch: 46.0 cache: ./cache/cord-334309-rddznfax.txt txt: ./txt/cord-334309-rddznfax.txt summary: title: Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) Postmortem nasopharyngeal swabs detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) known to cause coronavirus disease 2019 (COVID-19). Myocardial damage, myocarditis, and cardiomyopathy is often referred to in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] [2] [3] [4] [5] [6] . There is little information regarding cardiac complications in children [11] [12] [13] We present a previously healthy 17 year male old dying suddenly with an eosinophilic myocarditis (EM) in which a nasopharyngeal swab detected SARS-CoV-2 at autopsy (Figs. The question of whether this is a direct complication of SARS-CoV-2 infection, or if this is an idiopathic eosinophilic myocarditis in which the stress of the COVID-19 contributed to the cardiac decompensation cannot be answered definitively at this time. abstract: Background: Cardiac damage is frequently referred to in patients with SARS-CoV-2, is usually diagnosed by enzyme elevations, and is generally thought to be due to underlying coronary artery disease. There are references to cardiomyopathies accompanying coronavirus, but there has been no histologic confirmation. Case report: A previously healthy 17 year male old presented in full cardiac arrest to the emergency department after a 2 day history of headache, dizziness, nausea and vomiting. Autopsy demonstrated an enlarged flabby heart with eosinophilic myocarditis. There was no interstitial pneumonia or diffuse alveolar damage. Postmortem nasopharyngeal swabs detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) known to cause coronavirus disease 2019 (COVID-19). No other cause for the eosinophilic myocarditis was elucidated. Conclusion: Like other viruses, SARS-CoV-2 may be associated with fulminant myocarditis. url: https://www.ncbi.nlm.nih.gov/pubmed/32401577/ doi: 10.1080/15513815.2020.1761491 id: cord-315448-bosazmlm author: Crawford, Katharine H D title: Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection date: 2020-09-30 words: 3872.0 sentences: 267.0 pages: flesch: 54.0 cache: ./cache/cord-315448-bosazmlm.txt txt: ./txt/cord-315448-bosazmlm.txt summary: Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post symptom onset from a prospective cohort of 32 recovered individuals with asymptomatic, mild, or moderate-severe disease. Most of these studies have reported that over the first three months, antibodies targeting spike decline several fold from a peak reached a few weeks post symptom onset [5, 7, 19] , suggesting that the early dynamics of the antibody response to SARS-CoV-2 are similar to those for other acute viral infections. A c c e p t e d M a n u s c r i p t 5 Here we build on these studies by measuring both the neutralizing and binding antibody levels in serial plasma samples from 32 SARS-CoV-2-infected individuals across a range of disease severity with follow-up as long as 152 days post symptom onset. abstract: Most individuals infected with SARS-CoV-2 develop neutralizing antibodies that target the viral spike protein. Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post symptom onset from a prospective cohort of 32 recovered individuals with asymptomatic, mild, or moderate-severe disease. Neutralizing antibody titers declined an average of about four-fold from one to four months post symptom onset. This decline in neutralizing antibody titers was accompanied by a decline in total antibodies capable of binding the viral spike or its receptor-binding domain. Importantly, our data are consistent with the expected early immune response to viral infection, where an initial peak in antibody levels is followed by a decline to a lower plateau. Additional studies of long-lived B-cells and antibody titers over longer time frames are necessary to determine the durability of immunity to SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33000143/ doi: 10.1093/infdis/jiaa618 id: cord-332723-rz1iilsv author: Creager, Hannah M. title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date: 2020-07-06 words: 1474.0 sentences: 114.0 pages: flesch: 60.0 cache: ./cache/cord-332723-rz1iilsv.txt txt: ./txt/cord-332723-rz1iilsv.txt summary: Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10-7 dilution. Ten-fold serial dilutions of a natural nasopharyngeal swab specimen with known high positivity for SARS-CoV-2 RNA (E gene detected at a cycle threshold (Ct) of 16.6 by the cobas SARS-CoV-2 assay) were prepared with a diluent of pooled NPS. Comparison of SARS-CoV-2 Detection from Nasopharyngeal Swab Samples by the Roche cobas(R) 6800 SARS-CoV-2 Test and a Laboratory-Developed Real-Time RT-PCR test abstract: We evaluated the performance of the BioFire® Respiratory Panel 2.1 (RP2.1) in the detection of SARS CoV-2 in comparison against three other SARS CoV-2 EUA assays. In these studies, the RP2.1 panel had 98% positive percent agreement (48/49) and 100% negative percent agreement (49/49). Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10-7 dilution. Overall, these studies suggest that the BioFire® RP2.1 assay can be used to detect acute cases of SARS CoV2 in addition to patients with low viral titer later in disease presentation. url: https://doi.org/10.1016/j.jcv.2020.104538 doi: 10.1016/j.jcv.2020.104538 id: cord-326406-n0qi6gs8 author: Creed, Marina title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. date: 2020-05-19 words: 1801.0 sentences: 111.0 pages: flesch: 48.0 cache: ./cache/cord-326406-n0qi6gs8.txt txt: ./txt/cord-326406-n0qi6gs8.txt summary: title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. Here, we report a 59-year-old woman with aquaporin-4-positive (AQPR4+) neuromyelitis Optica treated with rituximab who developed mild respiratory symptoms with COVID-19, despite B cell depletion at the time of infection. To infect the host, SARS-CoV-2 uses the viral receptors ACE2 and TMPRSS2, which are membrane associated proteins expressed in many cells throughout the body, particularly the respiratory system 2 . Most cases are mild, but in a number of patients, the disease evolves into an acute respiratory distress syndrome (ARDS) 3 or a dysregulated immune system state leading to cytokine storm, most often in older adults, requiring intensive care and resulting in increased mortality 4 . Here, we describe an AQPR4+ NMOSD patient treated with rituximab who developed mild COVID-19 infection despite B cell depletion. abstract: Coronavirus disease 2019 (COVID-19) is caused by the novel coronavirus SARS-CoV-2, which affects the lung and other organs. After an incubation period of 3-14 days, the infection presents with symptoms of variable severity, from mild flu-like disease to severe pneumonia and cytokine storm with increased mortality. Immunosuppressed patients may have higher risk of adverse outcomes; hence, there is an urgent need to evaluate the immune response and clinical outcomes of SARS-CoV-2 infection in these patients. Here, we report a 59-year-old woman with aquaporin-4-positive (AQPR4+) neuromyelitis Optica treated with rituximab who developed mild respiratory symptoms with COVID-19, despite B cell depletion at the time of infection. url: https://doi.org/10.1016/j.msard.2020.102199 doi: 10.1016/j.msard.2020.102199 id: cord-344266-ug2uew71 author: Crema, E. title: The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission date: 2020-08-07 words: 3951.0 sentences: 215.0 pages: flesch: 54.0 cache: ./cache/cord-344266-ug2uew71.txt txt: ./txt/cord-344266-ug2uew71.txt summary: Currently, this phenomenon has gained tragic relevance due to the uncontrolled dispersion of the Covid-19 throughout the planet, since airborne transmission is one of the forms of viral contamination, as well as the direct reception of drops exhaled by a contaminated person and the contact with infected surfaces. A relevant study issued in the journal Nature revealed the existence of the RNA of the SARS-COV-2 in aerosols collected from the air of several closed environments and open places of two hospitals in Wuhan dedicated only to patients infected with Covid-19 (12) . This indication is based only on old studies about the direct transmission by larger drops, dangerously ignoring the contamination by the virus airborne in droplets that remain suspended in the air for several hours, and even days after the environment has been visited by an infected person. abstract: Background This paper presents a global analysis of the SARS-COV-2 outbreak in Brazil. Amazonian States have a much higher contamination rate than the southern and southeastern States. So far, no explanation has been provided for this striking difference that can shed light on the airborne transmission of the virus. Minimizing airborne transmission, health authorities recommend two meters as a safe distance. However, recent experiments reveal that this can be the main form of contagion. There is a lack of theoretical explanation on how airborne transmission works. Methods To investigate the spread of SARS-COV-2 in different macro environments, we analyzed the daily official data on the evolution of COVID-19 in Brazil. We compared our epidemiologic results obtained in States with very different climatic characteristics, and that had adopted, almost simultaneously, similar social isolation measures. To understand the virus spread, it was necessary to calculate theoretically the movement and behavior in the air of saliva droplets. Findings The transmission of SARS-COV-2 is much faster in the Amazon rainforest region. Our theoretical calculations explain and support the empirical results observed in recent experiments that demonstrate the relevance of aerial transmission of the coronavirus. Interpretation An onset of collective immunity may have been achieved with a contamination rate of about 15% of the Amazonian population. If confirmed, this result will have an essential impact on the management of the pandemic across the planet. The airborne transmission played a decisive role in the striking difference in the evolution of the pandemic among Brazilian regions. Air humidity is the most important climatic factor in viral spreading, while usual ambient temperatures do not have strong influence. There is no safe indoor distance for the coronavirus transmission. So, mask and eye protection are essential. url: http://medrxiv.org/cgi/content/short/2020.08.06.20169433v1?rss=1 doi: 10.1101/2020.08.06.20169433 id: cord-306675-kwrm8whn author: Crespo Sabarís, R title: “SARS-CoV-2: una presentación peculiar” date: 2020-05-08 words: 813.0 sentences: 77.0 pages: flesch: 63.0 cache: ./cache/cord-306675-kwrm8whn.txt txt: ./txt/cord-306675-kwrm8whn.txt summary: El 27 de marzo se contacta con el paciente que refiere seguir con algunas lesiones y prurito, pero no se modifica tratamiento, aunque el día 30 acude muy nervioso y desde la consulta de enfermería se envían las fotografías 1 y 2 (figuras 1 y 2) al médico titular, que está haciendo teletrabajo, y al apreciar en las mismas componente inflamatorio y lesiones de rascado, se indica administrar metilprednisolona y dexcloreniramina parenterales, con mejoría en menos de una hora, y se pautan 5 días de tratamiento con prednisona de 30 mg, se aumenta la hidroxicina cambiándose cetirizina por rupatadina. Se sabe que estas lesiones, además de por la propia infección vírica, se pueden observar tras los tratamientos para la COVID19, pero esto no se cumple en el caso que nos ocuoa, por lo que hay una relación directa entre la propia infección y las lesiones, como en diversas infecciones víricas 6 , aunque todavía no se conoce su patogenia exacta. abstract: nan url: https://api.elsevier.com/content/article/pii/S1138359320301404 doi: 10.1016/j.semerg.2020.05.001 id: cord-322957-clf8f90t author: Crespo, Javier title: Resumption of activity in gastroenterology departments. Recommendations by SEPD, AEEH, GETECCU and AEG date: 2020-04-28 words: 5297.0 sentences: 364.0 pages: flesch: 51.0 cache: ./cache/cord-322957-clf8f90t.txt txt: ./txt/cord-322957-clf8f90t.txt summary: The general objectives of these recommendations include: • To protect our patients against the risks of infection with SARS-CoV-2 and to provide them with high-quality care. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. abstract: Abstract The set of measures proposed by SEPD, AEEH, GETECCU and AEG are aimed to help departments in their resumption of usual activity. We have prepared a number of practical recommendations regarding patient management and the stepwise resumption of healthcare activity. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. The general objectives of these recommendations include: • To protect our patients against the risks of infection with SARS-CoV-2 and to provide them with high-quality care. • To protect all healthcare professionals against the risks of infection with SARS-CoV-2. • To resume normal functioning of our departments in a setting of ongoing risk for infection with SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S2444382420300717 doi: 10.1016/j.gastre.2020.04.001 id: cord-279363-4almssg6 author: Crespo, Roland Mojica title: Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión date: 2020-05-16 words: 5181.0 sentences: 512.0 pages: flesch: 59.0 cache: ./cache/cord-279363-4almssg6.txt txt: ./txt/cord-279363-4almssg6.txt summary: En ese momento, a este nuevo coronavirus se le llamó 2019-nCoV (del inglés: 2019-novel coronavirus) y fue identificado por las autoridades sanitarias chinas como el agente causal de estos casos de neumonía atípica 1,3,4 . Hacia final de mes, el día 30 de enero la OMS declaró la enfermedad causada por el nuevo coronavirus como una emergencia de salud pública de preocupación internacional, ya que para aquel momento se habían reportado casos en todas las regiones de la OMS en solo un mes 9,11 . Concretamente la RNVE en su informe n°29 del día 7 de mayo enumera los principales síntomas presentados por el conjunto de la población española, hasta la fecha y a base de una muestra de 217,543 casos, de la siguiente manera: Entre estos hallazgos, es comúnmente observar la leucopenia y linfopenia, siendo esta última característica de COVID-19. abstract: Resumen A finales de diciembre del 2019, se reportaron una serie de casos de neumonía atípica, en ese momento, de origen desconocido en Wuhan, China. Días más tarde se identificó al agente etiológico como un nuevo coronavirus. A este nuevo coronavirus, se le llamó SARS-CoV-2 y a la enfermedad que produce se le denominó COVID-19. El origen de este nuevo virus se presume zoonótico siendo los murciélagos su probable vector. Debido al acelerado número de contagios y muertes que se produjeron primero en China y posteriormente alrededor del mundo, la infección de este virus pasó rápidamente de ser un brote aislado en una región china, a convertirse en una emergencia sanitaria de preocupación internacional y posteriormente, en una pandemia. El propósito de esta revisión es estudiar la información más relevante y actual del patógeno, así como la epidemiología, patología, características clínicas, transmisión, prevención y tratamiento de la enfermedad. Abstract In late December 2019, some cases of atypical pneumonia, at that time of unknown origin, were reported in Wuhan, China. Days later, the etiologic agent was identified as a new coronavirus. This new coronavirus was called SARS-CoV-2 and the disease it produces was named COVID-19. The origin of this new virus is presumed zoonotic, with bats being its probable vector. Due to the rapid number of infections and deaths that occurred first in China and later around the world, the infection of this virus quickly went from being an isolated outbreak in a Chinese region to becoming a health emergency of international concern and later, a pandemic. The purpose of this review is to study the most relevant and current information on the pathogen, as well as epidemiology, pathology, clinical features, transmission, prevention, and treatment of the disease. url: https://www.sciencedirect.com/science/article/pii/S1138359320301714?v=s5 doi: 10.1016/j.semerg.2020.05.010 id: cord-265813-2onv9mvl author: Criado, Paulo Ricardo title: Are the cutaneous manifestations during or due to SARS-CoV-2 infection/COVID-19 frequent or not? Revision of possible pathophysiologic mechanisms date: 2020-06-02 words: 5143.0 sentences: 262.0 pages: flesch: 39.0 cache: ./cache/cord-265813-2onv9mvl.txt txt: ./txt/cord-265813-2onv9mvl.txt summary: RESULTS: The pathophysiology of the disease is multifactorial: association with innate immune response, hypercoagulability state, lung tissue damage, neurological and/or gastrointestinal tract involvement, monocytic/macrophage activation syndrome, culminating in exaggerated cytokine secretion, called "cytokine storm", which leads to worsening and death. Until the present day, the cardinal points in severe COVID-19 are upregulated innate immune human response; hypercoagulable state; polymorphous clinical manifestations, due to pulmonary tissue damage, neurological and/ or gastrointestinal tract involvement; and fatal outcome in severe cases of macrophage activation syndrome-like (MAS) [102] . Excessive activation of inflammatory mediators creating a "cytokine storm", leading to damage to the endothelium; formation of multiple thromboses in the microvasculature of the skin; changes in the cellular component of immunity with activation of the complement system, as well as, the possibility of direct entry of SARS-CoV-2 entry via receptor ACE2 and protease TMPRSS2 in the human endothelial cell in dermal blood vessels cannot be excluded such as possible mechanisms if the possibility of virus circulation in the blood is proved. abstract: BACKGROUND: SARS-Cov-2 is a single-stranded RNA virus, a Betacoronavirus, composed of 16 non-structural proteins, with specific roles in replication of coronaviruses. The pathogenesis of COVID-19 is not yet fully understood. The virus and host factors interplay among distinct outcomes of infected patients. METHODS: Using MeSH (Medical Subject Headings) in PubMed, authors searched for articles cotaining information on COVID-19 and the skin. RESULTS: The pathophysiology of the disease is multifactorial: association with innate immune response, hypercoagulability state, lung tissue damage, neurological and/or gastrointestinal tract involvement, monocytic/macrophage activation syndrome, culminating in exaggerated cytokine secretion, called “cytokine storm”, which leads to worsening and death. These systemic conditions may be associated with cutaneous lesions, that have polymorphic aspects, where at histopathological level show involvement in different skin changes. These lesions may be associated with multisystemic manifestations that could occur due to angiotensin-converting enzyme 2 receptor and transmembrane serine protease action, allowing the pulmonary infection and possibly skin manifestation. Several reports in literature show cutaneous lesions similar to chilblain, urticarial eruptions, diffuse or disseminated erythema, livedo racemosa, blue toe syndrome, retiform purpura, vesicle trunk, purpuric exanthema or exanthema with clinical aspects of symmetrical drug-related intertriginous and flexural exanthema (SDRIFE) and others. CONCLUSIONS: This review describes the complexity of Covid-19, pathophysiological and clinical aspects, dermatological finding and other dermatological conditions associated with SARS-CoV-2 infection or COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32488318/ doi: 10.1007/s00011-020-01370-w id: cord-347553-d7q6u7vj author: Criado, Paulo Ricardo title: Lessons from dermatology about inflammatory responses in Covid‐19 date: 2020-07-12 words: 5067.0 sentences: 326.0 pages: flesch: 40.0 cache: ./cache/cord-347553-d7q6u7vj.txt txt: ./txt/cord-347553-d7q6u7vj.txt summary: The antithrombotic effect of chloroquine analogues has been attributed to a range of mechanisms, including reduction in red blood cell aggregation, inhibition of platelet aggregation and adhesion, reduction in blood viscosity and enhancement of antiplatelet activity 86 Hydroxychloroquine and chloroquine were indicated for treat patients with COVID-19, under in vitro effects due to capacity as 87 : (a) an inhibitor of endocytic pathways through an elevation of endosomal pH, and (b) these drugs shown to interfere with the terminal glycosylation of angiotensin-converting enzyme-2 (ACE2), which acts as a plasma membrane receptor for both SARS-CoV and SARS-CoV-2. 61 99 Procoagulant factors, such F I G U R E 5 Clinical outcomes in SARS-CoV-2 infected patients/Covid-19, immune system responses, systemic and possible cutaneous manifestations.① The outcome spectrum is probably related to intrinsic host factors. ③ In a selected group of patients, with moderate and severe Covid-19, some authors proposed that a genetic background in these subjects might determinate one new immune response as ④ ''second wave'' of cytokines production, the ''CSS'' in response to the SARS-CoV-2 infection, similar to Macrophage Activation Syndrome (MAS-like/sHLH). abstract: The SARS‐Cov‐2 is a single‐stranded RNA virus composed of 16 non‐structural proteins (NSP 1‐16) with specific roles in the replication of coronaviruses. NSP3 has the property to block host innate immune response and to promote cytokine expression. NSP5 can inhibit interferon (IFN) signalling and NSP16 prevents MAD5 recognition, depressing the innate immunity. Dendritic cells, monocytes, and macrophages are the first cell lineage against viruses' infections. The IFN type I is the danger signal for the human body during this clinical setting. Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. In Covid‐19 the pathogenesis is not yet fully understood, but viral and host factors seem to play a key role. Important points in severe Covid‐19 are characterized by an upregulated innate immune response, hypercoagulopathy state, pulmonary tissue damage, neurological and/or gastrointestinal tract involvement, and fatal outcome in severe cases of macrophage activation syndrome, which produce a ‘cytokine storm’. These systemic conditions share polymorphous cutaneous lesions where innate immune system is involved in the histopathological findings with acute respiratory distress syndrome, hypercoagulability, hyperferritinemia, increased serum levels of D‐dimer, lactic dehydrogenase, reactive‐C‐protein and serum A amyloid. It is described that several polymorphous cutaneous lesions similar to erythema pernio, urticarial rashes, diffuse or disseminated erythema, livedo racemosa, blue toe syndrome, retiform purpura, vesicles lesions, and purpuric exanthema or exanthema with clinical aspects of symmetrical drug‐related intertriginous and flexural exanthema. This review describes the complexity of Covid‐19, its pathophysiological and clinical aspects. url: https://doi.org/10.1002/rmv.2130 doi: 10.1002/rmv.2130 id: cord-325197-j1uo8qmf author: Crimi, Ettore title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 words: 6066.0 sentences: 342.0 pages: flesch: 34.0 cache: ./cache/cord-325197-j1uo8qmf.txt txt: ./txt/cord-325197-j1uo8qmf.txt summary: Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. The goal of the review was to provide an appropriate pathogenic scenario in which epigenetic-sensitive mechanisms and epidrugs may be clinically useful to stratify risk and treatment of patients in ICU affected by severe viral respiratory infections. Here, we give an update on clinical evidence about the usefulness of novel and FDA-approved drugs interfering with epigenetic pathways, which were applied to ICU patients affected by highly pathogenic strains of influenza virus and CoV, with a particular interest about the novel SARS-CoV-2 (Table 4 ). abstract: The emergence of highly pathogenic strains of influenza virus and coronavirus (CoV) has been responsible for large epidemic and pandemic outbreaks characterised by severe pulmonary illness associated with high morbidity and mortality. One major challenge for critical care is to stratify and minimise the risk of multi-organ failure during the stay in the intensive care unit (ICU). Epigenetic-sensitive mechanisms, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) methylation, histone modifications, and non-coding RNAs may lead to perturbations of the host immune-related transcriptional programmes by regulating chromatin structure and gene expression patterns. Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. For example, Middle East respiratory syndrome-CoV and H5N1 can affect host antigen presentation through DNA methylation and histone modifications. The same mechanisms would presumably occur in patients with coronavirus disease 2019, in which tocilizumab may epigenetically reduce microvascular damage. Targeting epigenetic pathways by immune modulators (e.g. tocilizumab) or repurposed drugs (e.g. statins) may provide novel therapeutic opportunities to control viral–host interaction during critical illness. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. url: https://api.elsevier.com/content/article/pii/S0007091220305638 doi: 10.1016/j.bja.2020.06.060 id: cord-266702-6oxtlzqo author: Cristelo, Cecília title: SARS-CoV-2 and Diabetes: New Challenges for the Disease date: 2020-05-22 words: 4054.0 sentences: 241.0 pages: flesch: 47.0 cache: ./cache/cord-266702-6oxtlzqo.txt txt: ./txt/cord-266702-6oxtlzqo.txt summary: Emerging evidence demonstrates that the correct management of diabetes in those patients infected with SARS-CoV-2 is of utmost importance for the viral disease progression, therefore, the importance of blood glucose control will also be addressed. In vitro and in vivo studies showed that angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for SARS-CoV virus [7, 8] . It has been confirmed in some clinical studies that the long-term use of ACEIs or ARBs by patients is not associated with an increased risk of SARS-CoV-2 infection, neither of developing severe COVID-19 or even with a higher risk of in-hospital death [40] [41] [42] . In the case of SARS-CoV-2 the same transient damage in the pancreas has already been documented [44] , and given its higher infectivity and affinity for the ACE2 receptor, there is increased concern relative to the complications caused by hyperglycemia, as well as the long-term effects of the infection on recovered patients. abstract: A novel small enveloped RNA virus with the typical characteristic of the family to which it belongs, a crown, hence the name coronavirus, appeared in December 2019 in Wuhan, China, and subdued the world to its influence. The particular severity of the disease and higher mortality rates in patients with associated morbidities, including hypertension, obesity and diabetes, increases the concern over the consequences of this pandemic. In this review, the features of SARS-CoV-2 will be addressed, as well as the reasons why it poses a particular challenge to diabetic patients. We will also highlight the recent treatment strategies being explored to control this pandemic. Emerging evidence demonstrates that the correct management of diabetes in those patients infected with SARS-CoV-2 is of utmost importance for the viral disease progression, therefore, the importance of blood glucose control will also be addressed. url: https://doi.org/10.1016/j.diabres.2020.108228 doi: 10.1016/j.diabres.2020.108228 id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 words: 4826.0 sentences: 219.0 pages: flesch: 52.0 cache: ./cache/cord-329504-91te3nu8.txt txt: ./txt/cord-329504-91te3nu8.txt summary: A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. abstract: During the COVID-19 pandemic, structural biologists have rushed to solve the structures of the 28 proteins encoded by the SARS-CoV-2 genome in order to understand the viral life cycle and enable structure-based drug design. In addition to the 200 structures from SARS-CoV previously solved, 367 structures covering 16 of the viral proteins have been released in the span of only 6 months. These structural models serve as basis for research worldwide to understand how the virus hijacks human cells, for structure-based drug design and to aid in the development of vaccines. However, errors often occur in even the most careful structure determination - and are even more common among these structures, which were solved under immense pressure. From the beginning of the pandemic, the Coronavirus Structural Taskforce has categorized, evaluated and reviewed all of these experimental protein structures in order to help downstream users and original authors. Our website also offers improved models for many key structures, which have been used by Folding@Home, OpenPandemics, the EU JEDI COVID-19 challenge, and others. Here, we describe our work for the first time, give an overview of common problems, and describe a few of these structures that have since acquired better versions in the worldwide Protein Data Bank, either from new data or as depositor re-versions using our suggested changes. url: https://doi.org/10.1101/2020.10.07.307546 doi: 10.1101/2020.10.07.307546 id: cord-265277-ymvrserl author: Crooke, Stephen N. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 words: 4620.0 sentences: 249.0 pages: flesch: 52.0 cache: ./cache/cord-265277-ymvrserl.txt txt: ./txt/cord-265277-ymvrserl.txt summary: A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. abstract: A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Using increasingly stringent selection criteria to select peptides with significant HLA promiscuity and predicted antigenicity, we identified 41 potential T cell epitopes (5 HLA class I, 36 HLA class II) and 6 potential B cell epitopes, respectively. Docking analysis and binding predictions demonstrated enrichment for peptide binding to HLA-B (class I) and HLA-DRB1 (class II) molecules. Overlays of predicted B cell epitopes with the structure of the viral spike (S) glycoprotein revealed that 4 of 6 epitopes were located in the receptor-binding domain of the S protein. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development. Significance Statement The novel coronavirus SARS-CoV-2 recently emerged from China, rapidly spreading and ushering in a global pandemic. Despite intensive research efforts, our knowledge of SARS-CoV-2 immunology and the proteins targeted by the immune response remains relatively limited, making it difficult to rationally design candidate vaccines. We employed a suite of bioinformatic tools, computational algorithms, and structural modeling to comprehensively analyze the entire SARS-CoV-2 proteome for potential T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen. url: https://doi.org/10.1101/2020.05.14.093757 doi: 10.1101/2020.05.14.093757 id: cord-323092-j2u0ny2u author: Crosby, James C. title: COVID‐19: A review of therapeutics under investigation date: 2020-04-19 words: 3896.0 sentences: 270.0 pages: flesch: 51.0 cache: ./cache/cord-323092-j2u0ny2u.txt txt: ./txt/cord-323092-j2u0ny2u.txt summary: The World Health Organization (WHO) has released general guidelines for managing the illness caused by the virus (COVID-19), which includes supportive care similar to other viral pneumonias: airway and respiratory support, empiric antibiotics for secondary bacterial infection, and acute respiratory distress syndrome (ARDS) management. 2 While these treatments are thought to offer the best chance of survival for the approximately 20% of COVID-19 cases that progress to severe disease, limited health care resources and the speed at which the pandemic has developed are pressuring clinicians and scientists to provide therapeutics that specifically target SARS-CoV-2 and improve mortality. 32, 33 There are a number of promising studies that have demonstrated shorter hospital stays, lower mortality rates, and reduced viral loads in SARS-CoV-1 and H1N1 influenza infected patients treated with convalescent plasma. There is another single ongoing observational trial examining the efficacy of anti-SARS-CoV-2 inactivated convalescent plasma in COVID-19 patients, the results of which remain to be seen. abstract: The COVID‐19 outbreak has disrupted global health care networks and caused thousands of deaths and an international economic downturn. Multiple drugs are being used on patients with COVID‐19 based on theoretical and in vitro therapeutic targets. Several of these therapies have been studied, but many have limited evidence behind their use, and clinical trials to evaluate their efficacy are either ongoing or have not yet begun. This review summarizes the existing evidence for medications currently under investigation for treatment of COVID‐19, including remdesivir, chloroquine/hydroxychlorquine, convalescent plasma, lopinavir/ritonavir, IL‐6 inhibitors, corticosteroids, and angiotensin‐converting enzyme inhibitors. url: https://www.ncbi.nlm.nih.gov/pubmed/32838367/ doi: 10.1002/emp2.12081 id: cord-344909-0o55l4iy author: Cross, Robert W. title: Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date: 2020-10-14 words: 5711.0 sentences: 291.0 pages: flesch: 49.0 cache: ./cache/cord-344909-0o55l4iy.txt txt: ./txt/cord-344909-0o55l4iy.txt summary: However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Differences in clinical parameters of the LD-treated group with untreated control animals from this study or historical control animals were minimal; however, the lack of infectious SARS-CoV-2 in the BAL samples from all of the LD-treated animals and reduced lung pathology suggest that an antiviral effect was present despite the lower concentration of neutralizing antibodies in the dose of convalescent sera administered. PRNT50 assays were performed on pooled convalescent sera from AGMs challenged with the homologous isolate of SARS-CoV-2 in previous studies (Cross et al., 2020; Woolsey et al., 2020) compared with control animals on day 2 post infection (d) and abstract: Passive transfer of convalescent plasma or serum is a time-honored strategy for treating infectious diseases. Human convalescent plasma containing antibodies against SARS-CoV-2 is currently being used to treat COVID-19 patients. However, most patients have been treated outside of randomized clinical trials making it difficult to determine the efficacy of this approach. Here, we assessed the efficacy of convalescent sera in a newly developed African green monkey model of COVID-19. Groups of SARS-CoV-2-infected animals were treated with pooled convalescent sera containing either high or low to moderate anti-SARS-CoV-2 neutralizing antibody titers. Differences in viral load and disease pathology were minimal between monkeys that received the lower titer convalescent sera and untreated controls. However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Our data support human studies suggesting that convalescent plasma therapy is an effective strategy if donors with high level of antibodies against SARS-CoV-2 are employed and if recipients are at an early stage of disease. url: https://doi.org/10.1101/2020.10.14.340091 doi: 10.1101/2020.10.14.340091 id: cord-302146-51hof7it author: Cross, Thomas J. title: Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date: 2020-05-15 words: 3668.0 sentences: 196.0 pages: flesch: 50.0 cache: ./cache/cord-302146-51hof7it.txt txt: ./txt/cord-302146-51hof7it.txt summary: Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery. Molecular modeling is an important tool for guiding inhibitor discovery, making it possible to evaluate large numbers of candidate drugs in silico to select experimental targets; however, standard approaches screen against only one version of the protein, typically the reference or wild-type (WT) sequence. Here we characterize all 79 known variants of M pro as of 29 April, 2020, and analyze trends in amino acid substitutions and the resulting structural changes using network analysis and molecular modeling. Analysis of active site networks (ASN) from M pro variants suggests differences in active site flexibility and cohesion that may serve to guide the design of robust, mutation-resistant inhibitors. abstract: The SARS-CoV-2 main protease (Mpro) is essential to viral replication and cleaves highly specific substrate sequences, making it an obvious target for inhibitor design. However, as for any virus, SARS-CoV-2 is subject to constant selection pressure, with new Mpro mutations arising over time. Identification and structural characterization of Mpro variants is thus critical for robust inhibitor design. Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Residue substitution is widely distributed, with some tendency toward larger and more hydrophobic residues. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery. url: https://doi.org/10.1101/2020.05.15.097493 doi: 10.1101/2020.05.15.097493 id: cord-267308-rgqjolue author: Crovetto, F. title: SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY date: 2020-06-19 words: 1432.0 sentences: 91.0 pages: flesch: 52.0 cache: ./cache/cord-267308-rgqjolue.txt txt: ./txt/cord-267308-rgqjolue.txt summary: Introduction: Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. We evaluated the seroprevalence and clinical presentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pregnant women in the first and third trimester. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. abstract: Introduction: Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. Most COVID-19 cases published were in the third trimester of pregnancy, which could reflect reporting bias, higher risk of infection or increased disease severity in late pregnancy. Seroprevalence studies may allow reliable estimates of the susceptibility to infection and clinical spectrum since they include asymptomatic and mild infections not tested for PCR. We evaluated the seroprevalence and clinical presentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pregnant women in the first and third trimester. Methods: The study was approved by the Institutional Review Board at each institution and informed consent was obtained. We recruited 874 consecutive pregnancies attending for first trimester screening (10-16 weeks of gestation, n=372) or delivery (n=502) from April 14 to May 5. All women were interviewed with a structured questionnaire for COVID-19 symptoms two months prior to sampling. SARS-CoV-2 IgG and IgM/IgA antibodies were tested (COVID-19 VIRCLIA Monotest, Vircell Microbiologist, Spain; reported sensitivity 70% IgG and 89% IgM/IgA, and specificity 89% and 99% respectively). Indeterminate results were re-tested (VITROS Immunodiagnostic Products Anti-SARS-CoV2 Total Tests, Ortho Clinical Diagnostics, USA; 100% sensitivity and specificity) and re-classified as positive or negative. Women with COVID-19 were diagnosed and managed according to standard protocols and guidelines3,4. Statistical differences were tested using the {chi}2 test or Student t-test as appropriate (p<0.05). Results: A total of 125 of 874 women (14.3%) were positive for either IgG or IgM/IgA SARS-CoV-2 antibodies, 54/372 (14.5%) in the first and 71/502 (14.1%) in the third trimester. A total of 75/125 (60%) reported no symptoms of COVID-19 in the past 2 months, whereas 44 (35.2%) reported one or more symptoms, of which 31 (24.8%) had at least 3 symptoms or anosmia and 8 (6.4%) dyspnea. Overall, 7 women (5.6%) were admitted for persistent fever despite paracetamol and dyspnea, of which 3 had signs of pneumonia on chest radiography. All 3 had criteria for severity (bilateral chest condensation, respiratory rate>30 and leukopenia) and required oxygen support but not critical care or mechanical ventilation, and they were all discharged well. The rates of symptomatic infection, hospital admission or dyspnea were significantly higher in third trimester women (Table and Figure). Discussion: The 14.3% seroprevalence of SARS-COV-2 in pregnant women in this study was substantially larger than the contemporary rates of PCR positive cases (0.78%) reported for women 20-40y in Barcelona. The data confirm that COVID-19 is asymptomatic in the majority of pregnant women6 and illustrate the value of seroprevalence studies to capture the high proportion of asymptomatic or mild infections. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. However, the proportion of infections with symptoms or dyspnea was remarkably higher in the third trimester, and these results are in line with COVID-19 registries, reporting that 81% of hospitalized women were in late pregnancy or peripartum. These results provide reassuring information that, even in settings with a high prevalence, SARS-CoV-2 infection in pregnancy mostly presents with asymptomatic or mild clinical forms. The susceptibility to infection seemed to be the same in the first and the third trimesters of gestation. The data further suggest that, as with other respiratory viruses, COVID-19 could be more severe and require increased surveillance in late pregnancy. These findings should be confirmed and extended with larger consecutive prevalence studies in pregnancy. url: http://medrxiv.org/cgi/content/short/2020.06.17.20134098v1?rss=1 doi: 10.1101/2020.06.17.20134098 id: cord-331060-b3z1zb4t author: Cruickshank, Marilyn title: COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic date: 2020-06-04 words: 2291.0 sentences: 107.0 pages: flesch: 53.0 cache: ./cache/cord-331060-b3z1zb4t.txt txt: ./txt/cord-331060-b3z1zb4t.txt summary: Some of this includes the extent to which humans develop a protective immune response to COVID-19 via antibodies (The World Health Organization, 2020), the extent to which asymptomatic people can spread the infection (Bai et al., 2020; Kimball et al., 2020) , whether the use of face masks by asymptomatic members of the community can affect transmission (Feng et al., 2020) , the significance of the loss of smell as an early predictive or differential symptom of disease, the role of herd immunity and whether infection confers immunity, and if so, for how long. Once the number of new cases have stabilised, there can be a move to mitigation strategies which might not necessarily stop the spread, but can help to protect those most at risk of severe disease by isolating suspected cases and their households, while continuing to implement social distancing measures for older people and others at high risk. abstract: The year 2020 will mark a once‐in‐a‐century global event: the outbreak and pandemic of COVID‐19. On the 31 December 2019 the World Health Organization (WHO) reported a cluster of pneumonia‐like cases of a novel coronavirus zoonosis in Wuhan City, Hubei Province, China. The outbreak was due to a new or novel coronavirus, which would later be called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2). url: https://doi.org/10.1111/jocn.15365 doi: 10.1111/jocn.15365 id: cord-352123-0bflqj1c author: Csiszar, Anna title: Companion animals likely do not spread COVID-19 but may get infected themselves date: 2020-08-07 words: 4752.0 sentences: 225.0 pages: flesch: 51.0 cache: ./cache/cord-352123-0bflqj1c.txt txt: ./txt/cord-352123-0bflqj1c.txt summary: Recent evidence suggests that SARS-CoV-2, similar to other coronaviruses, can infect several species of animals, including companion animals such as dogs, cats, and ferrets although their viral loads remain low. In late March 2020, the Federal Agency for the Safety of the Food Chain (FASFC) in Belgium reported that a pet cat was diagnosed to be infected with SARS-CoV-2 [21, 22] , showing that felines living in the household of people with COVID-19 are at risk of contracting the disease and may potentially spread the virus. On April 23, it was reported that two pet cats in New York state have tested positive for the SARS-CoV-2, which are the first confirmed COVID-19 cases in companion animals in the USA [22] . In the current SARS-CoV-2 pandemic, the situation is rapidly evolving and in the light of the recent evidence, we should be aware of the possibility that humans can be potentially infected with COVID-19 by animals, including by pet cats, dogs, or other domesticated species. abstract: Coronavirus disease 2019 (COVID-19) is a highly contagious infectious disease caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). From the epidemiological data, the picture emerges that the more severe etiopathologies among COVID-19 patients are found in elderly people. The risk of death due to COVID-19 increases exponentially with age. Eight out of 10 COVID-19 related deaths occur in people older than 65 years of age. Older patients with comorbid conditions such as hypertension, heart failure, diabetes mellitus, asthma, chronic obstructive pulmonary disease, and cancer have a much higher case fatality rate. Governments and public health authorities all over the world have realized that protections of vulnerable older adults should be a priority during the COVID-19 pandemic. COVID-19 is a zoonotic disease. The SARS-CoV-2 virus was originally transmitted likely from a bat or a pangolin to humans. Recent evidence suggests that SARS-CoV-2, similar to other coronaviruses, can infect several species of animals, including companion animals such as dogs, cats, and ferrets although their viral loads remain low. While the main source of infection transmission therefore is human to human, there are a few rare cases of pets contracting the infection from a SARS-CoV-2-infected human. Although there is no evidence that pets actively transmit SARS-CoV-2 via animal-to-human transmission, senior pet ownership potentially may pose a small risk to older adults by (1) potentially enabling animal-to-human transmission of SARS-CoV-2 in the most vulnerable population and (2) by increasing the exposition risk for the elderly due to the necessity to care for the pet and, in the case of dogs, to take them outside the house several times per day. In this overview, the available evidence on SARS-CoV-2 infection in pets is considered and the potential for spread of COVID-19 from companion animals to older individuals and the importance of prevention are discussed. url: https://doi.org/10.1007/s11357-020-00248-3 doi: 10.1007/s11357-020-00248-3 id: cord-317628-1inxq7t5 author: Cuccarese, Michael F. title: Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date: 2020-08-14 words: 9573.0 sentences: 487.0 pages: flesch: 43.0 cache: ./cache/cord-317628-1inxq7t5.txt txt: ./txt/cord-317628-1inxq7t5.txt summary: We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. We used these capabilities to rapidly develop high-throughput-ready disease models for both SARS-CoV-2 viral infection and the resulting cytokine storm, and immediately launched large-scale drug screens that recapitulated known effective and ineffective therapies and, more importantly, identified several new potential treatments for both SARS-CoV-2 infection and COVID-19-associated cytokine storm. To define the model, we evaluated the effect of SARS-CoV-2 infection in multiple cell types, of which three resulted in robust phenoprints as compared to either mock infected or inactivated virus control populations: Calu3 (a lung adenocarcinoma line), Vero (an immortalized interferondeficient African green monkey kidney line 55 ), and primary Human Renal Cortical Epithelium (HRCE) (Fig. 5C, Fig. S6D ). abstract: Development of accurate disease models and discovery of immune-modulating drugs is challenged by the immune system’s highly interconnected and context-dependent nature. Here we apply deep-learning-driven analysis of cellular morphology to develop a scalable “phenomics” platform and demonstrate its ability to identify dose-dependent, high-dimensional relationships among and between immunomodulators, toxins, pathogens, genetic perturbations, and small and large molecules at scale. High-throughput screening on this platform demonstrates rapid identification and triage of hits for TGF-β- and TNF-α-driven phenotypes. We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. The presented library of images, deep learning features, and compound screening data from immune profiling and COVID-19 screens serves as a deep resource for immune biology and cellular-model drug discovery with immediate impact on the COVID-19 pandemic. url: https://doi.org/10.1101/2020.08.02.233064 doi: 10.1101/2020.08.02.233064 id: cord-013269-u1e0kzmm author: Cucinotta, Domenico title: Primum non nocere (first do no harm). The SARS-CoV-2 pandemic course in oldest in Italy date: 2020-05-11 words: 1602.0 sentences: 94.0 pages: flesch: 54.0 cache: ./cache/cord-013269-u1e0kzmm.txt txt: ./txt/cord-013269-u1e0kzmm.txt summary: Maybe a bad strategy and lack of timely intervention togheter with concurrent social events, comorbidities of oldest persons, bed rest, inadequate nutritional support and drugs'' side effects and infection of health professionals proved fatal for many. Different opinions among scientists, as occurred recently in COVID-19 pandemia in Italy, combined with the difficulties due to comorbidities and dependency of oldest persons have resulted in strategic errors, a significant part of which proved fatal for the patient and catastrofic for the society. On January 18 the Medical Literature Guide Amedeo (1) drowes the attention to a study of the Imperial College of London on the real high number of cases in Wuhan and on 23 the Chinese government put millions of people in quarantine, with severe travel restriction starting from 25. bas a consequence of the lack of a timely intervention with no appropriate prevention methodologies, virus entered into hospitals, nursing homes, day centers and doctor''s offices. et al Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China abstract: Dramatic outcomes of Covid-19 pandemia in Italy, in particular in the North, must be discussed. Maybe a bad strategy and lack of timely intervention togheter with concurrent social events, comorbidities of oldest persons, bed rest, inadequate nutritional support and drugs’ side effects and infection of health professionals proved fatal for many. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569649/ doi: 10.23750/abm.v91i2.9624 id: cord-272009-yxjhfg7m author: Cui, Jie title: Evolutionary Relationships between Bat Coronaviruses and Their Hosts date: 2007-10-17 words: 3543.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-272009-yxjhfg7m.txt txt: ./txt/cord-272009-yxjhfg7m.txt summary: Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. abstract: Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002–2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/18258002/ doi: 10.3201/eid1310.070448 id: cord-265242-y8t37p0b author: Cui, Wei title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date: 2003-09-15 words: 1782.0 sentences: 112.0 pages: flesch: 64.0 cache: ./cache/cord-265242-y8t37p0b.txt txt: ./txt/cord-265242-y8t37p0b.txt summary: title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS. means ‫ע‬ SD The differences in the mean values between patients with SARS and healthy control subjects were estimated with Student''s t test, with a limit of significance of 0.05. The mean lymphocyte count of patients with SARS was significantly lower than that of healthy control subjects ( ; table 1) . The results of lymphocyte immunophenotyping demonstrated that the absolute counts of all lymphocyte subsets declined in patients with SARS (table 2) . Our study shows that the absolute counts of CD4 + T cells and CD8 + T cells have clinical significance in patients with SARS and that surveillance of lymphocytes and lymphocyte subsets is helpful in the diagnosis and treatment of SARS. abstract: In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. CD4(+) T lymphocyte levels were reduced in 100% of patients, CD8(+) T lymphocyte levels were reduced in 87%, B lymphocyte levels were reduced in 76%, and natural killer cell levels were reduced in 55%. Our data suggested that these patients' immune systems were impaired during the course of SARS. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/12955652/ doi: 10.1086/378587 id: cord-291113-iizj932l author: Cumbo, Enzo title: Alternative Methods of Sterilization in Dental Practices Against COVID-19 date: 2020-08-08 words: 7441.0 sentences: 273.0 pages: flesch: 40.0 cache: ./cache/cord-291113-iizj932l.txt txt: ./txt/cord-291113-iizj932l.txt summary: It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. abstract: SARS-CoV-2, and several other microorganisms, may be present in nasopharyngeal and salivary secretions in patients treated in dental practices, so an appropriate clinical behavior is required in order to avoid the dangerous spread of infections. COVID-19 could also be spread when patients touches a contaminated surface with infected droplets and then touch their nose, mouth, or eyes. It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be addressed to problems related to the spreading of infections due to air and surface contamination. The effectiveness of conventional cleaning and disinfection procedures may be limited by several factors; first of all, human operator dependence seems to be the weak aspect of all procedures. The improvement of these conventional methods requires the modification of human behavior, which is difficult to achieve and sustain. As alternative sterilization methods, there are some that do not depend on the operator, because they are based on devices that perform the entire procedure on their own, with minimal human intervention. In conclusion, continued efforts to improve the traditional manual disinfection of surfaces are needed, so dentists should consider combining the use of proper disinfectants and no-touch decontamination technologies to improve sterilization procedures. url: https://doi.org/10.3390/ijerph17165736 doi: 10.3390/ijerph17165736 id: cord-352737-3ttrx3lf author: Cunha, Lucas Leite title: Remodeling of the Immune Response With Aging: Immunosenescence and Its Potential Impact on COVID-19 Immune Response date: 2020-08-07 words: 6824.0 sentences: 337.0 pages: flesch: 37.0 cache: ./cache/cord-352737-3ttrx3lf.txt txt: ./txt/cord-352737-3ttrx3lf.txt summary: Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Interestingly, polymorphonuclear leucocytes from the elderly are less capable of modulating the triggering receptor expressed on myeloid cell-1 (TREM-1)-induced oxidative bursts, suggesting that TREM-1 signal transduction altered with aging may be one of the mediators of the decrease in microbicidal potential of innate immune cells in older adults (41) . abstract: Elderly individuals are the most susceptible to an aggressive form of coronavirus disease (COVID-19), caused by SARS-CoV-2. The remodeling of immune response that is observed among the elderly could explain, at least in part, the age gradient in lethality of COVID-19. In this review, we will discuss the phenomenon of immunosenescence, which entails changes that occur in both innate and adaptive immunity with aging. Furthermore, we will discuss inflamm-aging, a low-grade inflammatory state triggered by continuous antigenic stimulation, which may ultimately increase all-cause mortality. In general, the elderly are less capable of responding to neo-antigens, because of lower naïve T cell frequency. Furthermore, they have an expansion of memory T cells with a shrinkage of the T cell diversity repertoire. When infected by SARS-CoV-2, young people present with a milder disease as they frequently clear the virus through an efficient adaptive immune response. Indeed, antibody-secreting cells and follicular helper T cells are thought to be effectively activated in young patients that present a favorable prognosis. In contrast, the elderly are more prone to an uncontrolled activation of innate immune response that leads to cytokine release syndrome and tissue damage. The failure to trigger an effective adaptive immune response in combination with a higher pro-inflammatory tonus may explain why the elderly do not appropriately control viral replication and the potential clinical consequences triggered by a cytokine storm, endothelial injury, and disseminated organ injury. Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32849623/ doi: 10.3389/fimmu.2020.01748 id: cord-265260-n6wm54wz author: Cuong, Hoang Quoc title: Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-09-25 words: 2074.0 sentences: 120.0 pages: flesch: 56.0 cache: ./cache/cord-265260-n6wm54wz.txt txt: ./txt/cord-265260-n6wm54wz.txt summary: RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. In this study, the assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master showed positive results from a single reaction of triplicate in the three days of 4.8 copies/reaction ( Table 3) . In this study, we reported the comparative analysis of laboratory screening for SARS-CoV-2 among three primer-probe sets in two different master mixes (Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master). abstract: BACKGROUND: There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. METHODS: We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master. RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19. url: https://doi.org/10.1155/2020/7610678 doi: 10.1155/2020/7610678 id: cord-291194-cl3nu5cm author: DURDAĞI, Serdar title: Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target date: 2020-06-21 words: 2146.0 sentences: 136.0 pages: flesch: 54.0 cache: ./cache/cord-291194-cl3nu5cm.txt txt: ./txt/cord-291194-cl3nu5cm.txt summary: One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC''s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. The small molecules from NCGC-NIH Chemical Genomics Center Pharmaceutical Collection (i.e. NPC library) were used in virtual screening studies at the active site of developed TMPRSS2 model target protein. Interestingly, benzquercin was also found as potent hit compounds in our previous virtual screening study using same protocol against another important cellentry target of SARS-CoV-2 Spike/ACE2 (Durdagi et al., 2020) . In this study, a virtual drug repurposing study was performed to identify new compounds against TMPRSS2 which is an important target for the entry of the SARS-CoV-2 to the host cell. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike Receptor-Binding Domain Bound with ACE2 COVID19 Target Proteins: A Virtual Drug Repurposing Study abstract: Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32595355/ doi: 10.3906/biy-2005-112 id: cord-302527-n53d5en0 author: Dadlani, Shashi title: SARS-CoV-2 Transmission in a Dental Practice in Spain: After the Outbreak date: 2020-06-29 words: 2425.0 sentences: 148.0 pages: flesch: 54.0 cache: ./cache/cord-302527-n53d5en0.txt txt: ./txt/cord-302527-n53d5en0.txt summary: SARS-CoV-2 is a human-to-human viral infection [4, 5] transmitted through airborne droplets from talking, coughing, or sneezing [6] or by touching or coming into contact with contaminated surfaces that are then transmitted to oral, nasal, and mucosal membranes [7] . During the coronavirus outbreak, dentists in Spain and other countries were recommended to only attend dental emergencies under strict measures wearing specific professional protection equipment to minimize the risk and maintain social distancing [12] . SARS-CoV-2 has been identified in the saliva of infected patients [14] , suggesting that the aerosols generated during dental procedures from an infected person can be extremely contagious. ese droplets can remain in the area even after the patient has left the clinic, leading to infection of dental professionals via contaminated surfaces [15] . e inhalation of airborne particles and aerosol particles during dental treatments on patients with SARS-CoV-2 is a very high-risk procedure where dentists can be exposed to the virus. abstract: The World Health Organization declared a pandemic on March 11, 2020, due to a virus named SARS-CoV-2 discovered in Wuhan, China, in December 2019. Many countries have been hit hard including Spain, with the highest number of healthcare workers being infected (>50,000). A lack of personal protective equipment and protocols at the time of the outbreak led to many fatalities. Although few of these healthcare workers are dental professionals, this community required protective measures as well. Fortunately, there are no reported cases of SARS-CoV-2 transmission in dental practices. Dental professionals were advised only to treat dental emergencies, and such cases were screened via telephone to maintain social distancing. Nevertheless, new protocols and measures are needed as dental professionals return to normal practice after weeks of confinement in many countries. Relatively, few articles have discussed the management of dental practice during the SARS-CoV-2 with no known articles on postpandemic outbreak guidelines. Though some protocols and measures are the same, there are also many differences. Here, we describe protocols and measures for dental practice in Spain in accordance with the Spanish Health Ministry. url: https://www.ncbi.nlm.nih.gov/pubmed/32676111/ doi: 10.1155/2020/8828616 id: cord-325419-15vm22d8 author: Dai, C. L. title: Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity date: 2020-10-15 words: 4227.0 sentences: 238.0 pages: flesch: 46.0 cache: ./cache/cord-325419-15vm22d8.txt txt: ./txt/cord-325419-15vm22d8.txt summary: All multivariate models included race/ethnicity as an independent variable, with demographic factors (age; age-squared; sex), socioeconomic factors (insurance; neighborhood rates of poverty, crowded housing, limited English proficiency, and minority), and comorbidities (Charlson Comorbidity Index score; hypertension; and obesity) as covariates. Minority populations including Hispanic, Black, Asian, NH/PI and AI/AN had increased odds of SARS-CoV-2 infection compared to Whites in unadjusted and adjusted analysis ( race/ethnicity with White patients as the reference category. Minority races/ethnicities were not consistently associated with increased odds for COVID-19 hospitalization, until adjusting for demographics, comorbidities, insurance status and neighborhood characteristics. Race/ethnicity was associated with SARS-CoV-2 infection and COVID-19 hospitalization, with adjusted odds of both outcomes highest among Hispanics and NH/PI patients. The significant associations of minority races/ethnicities with SARS-CoV-2 infection and COVID-19-related hospitalization builds on previous analyses of Black and Hispanic patients(24-27). abstract: Background Data on the characteristics of COVID-19 patients disaggregated by race/ethnicity remain limited. We evaluated the sociodemographic and clinical characteristics of patients across the major racial/ethnic groups and assessed their associations with COVID-19 outcomes. Methods This retrospective cohort study analyzed patients who were tested for SARS-CoV-2 in a large, integrated health system spanning California, Oregon, and Washington between March 1 and August 30, 2020. Sociodemographic and clinical characteristics were obtained from electronic health records. Odds of SARS-CoV-2 infection, COVID-19 hospitalization, and in-hospital death were assessed with multivariate logistic regression. Findings 289,294 patients with known race/ethnicity were tested for SARS-CoV-2 by PCR, of whom 27.5% were non-White minorities. 15,605 persons tested positive, with minorities representing 58.0%. Disparities were widest among Hispanics, who represented 40.5% of infections but 12.8% of those tested. Hispanics were generally younger and had fewer comorbidities except diabetes than White patients. Of the 3,197 patients hospitalized, 58.9% were non-White. 459 patients died, of whom 49.8% were minorities. Racial/ethnic distributions of outcomes across the health system tracked with state-level statistics. Increase odds of testing positive and hospitalization were associated with all minority races/ethnicities except American Indian/Alaska Native. Highest odds of testing SARS-CoV-2 positive was for Hispanic patients (OR [95% CI]: 3.68 [3.52-3.84]) and highest odds of COVID-19 hospitalization was for Native Hawaiian/Pacific Islander patients (2.13 [1.48 - 3.06]). Hispanic patients also exhibited increased morbidity including need for mechanical ventilation. In multivariate modeling, Hispanic race/ethnicity was associated with increased odds of hospital mortality (1.75 [1.15-2.67]) among patients over age 70, but hospital mortality was not increased for any race/ethnicity sub-population in the multivariate model. Interpretation Major healthcare disparities were evident, especially among Hispanics who tested positive at a higher rate, and despite younger in age, required excess hospitalization and need for mechanical ventilation compared to their expected demographic proportions. As characteristics of patients varying between race/ethnicity, targeted, culturally-responsive interventions are needed to address the increased risk of poor outcomes among minority populations with COVID-19. Funding Biomedical Advanced Research and Development Authority; National Center for Advancing Translational Sciences url: https://doi.org/10.1101/2020.10.14.20212803 doi: 10.1101/2020.10.14.20212803 id: cord-303832-1kcqhgjw author: Dai, Manman title: Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date: 2020-09-06 words: 834.0 sentences: 49.0 pages: flesch: 66.0 cache: ./cache/cord-303832-1kcqhgjw.txt txt: ./txt/cord-303832-1kcqhgjw.txt summary: Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. ABSTRACT 21 Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that 22 fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. In this study, we detected the titer (50% tissue culture infectious dose/mL, TCID 50 /mL) of 35 viable SARS-CoV-2 attached on salmon or untreated SARS-CoV-2 in culture medium stored at 36 4°C, the temperature in refrigerators or cold rooms for the temporary storage of fish, or 25°C, the 37 regular room temperature, respectively, using end-point titration assay on Vero E6 cells as 38 described previously (8). As shown in Figure A and B, salmon-attached SARS-CoV-2 remained 39 viable at 4°C and 25°C for 8 and 2 days, respectively, while the untreated SARS-CoV-2 in 40 culture medium remained infectious at 4°C and 25°C for more than 8 days. abstract: Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. Here we showed that salmon-attached SARS-CoV-2 at 4°C could remain infectious for more than one week, suggesting that fish-attached SARS-CoV-2 may be a source of transmission. url: https://doi.org/10.1101/2020.09.06.284695 doi: 10.1101/2020.09.06.284695 id: cord-281686-edpyn8fd author: Dalamaga, Maria title: 19 treatment regimens? date: 2020-05-08 words: 1448.0 sentences: 89.0 pages: flesch: 35.0 cache: ./cache/cord-281686-edpyn8fd.txt txt: ./txt/cord-281686-edpyn8fd.txt summary: These agents could attenuate ARDS and help control SARS-CoV-2 via multiple mechanisms including: 1) inhibition of viral replication; 2) decrease of iron availability; 3) upregulation of B cells; 4) improvement of the neutralizing anti-viral antibody titer; 5) inhibition of endothelial inflammation and 6) prevention of pulmonary fibrosis and lung decline via reduction of pulmonary iron accumulation. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. It could also be reasonable to speculate that iron chelators may prevent the development of pulmonary fibrosis and lung function decline following COVID-19 infection. abstract: The pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to global health. Currently, no specific prophylactic and therapeutic treatment is available. No evidence from randomized clinical trials (RCTs) that a treatment may ameliorate the clinical outcome of patients with COVID-19 exists with the only exception of preliminary evidence from remdesivir trials. Here, we present evidence from the literature and a compelling hypothesis on the potential immunomodulatory, iron chelating and anti-oxidant effects of iron chelators in the treatment of COVID-19 and its complications. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. Iron chelators exhibit iron chelating, antiviral and immunomodulatory effects in vitro and in vivo, particularly against RNA viruses. These agents could attenuate ARDS and help control SARS-CoV-2 via multiple mechanisms including: 1) inhibition of viral replication; 2) decrease of iron availability; 3) upregulation of B cells; 4) improvement of the neutralizing anti-viral antibody titer; 5) inhibition of endothelial inflammation and 6) prevention of pulmonary fibrosis and lung decline via reduction of pulmonary iron accumulation. Both retrospective analyses of data in electronic health records, as well as proof of concept studies in humans and large RCTs are needed to fully elucidate the efficacy and safety of iron chelating agents in the therapeutic armamentarium of COVID-19, probably as an adjunctive treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32418885/ doi: 10.1016/j.metabol.2020.154260 id: cord-259933-ggx4v0bz author: Dalan, Rinkoo title: The ACE-2 in COVID-19: Foe or Friend? date: 2020-04-27 words: 4187.0 sentences: 225.0 pages: flesch: 44.0 cache: ./cache/cord-259933-ggx4v0bz.txt txt: ./txt/cord-259933-ggx4v0bz.txt summary: The SARS-CoV-2, a positive strand RNA virus, has been seen to infect humans through the angiotensin converting enzyme -2 (ACE-2) receptor [9] . In individuals with hypertension, diabetes, and other cardiovascular disorders with vascular complications, the renin angiotensin system (RAS) is known to be activated with an increase in ACE activity and a downregulation of ACE-2. Therefore, it may be assumed that the inherent downregulation of the ACE-2-Ang-(1-7)-Mas axis (as seen in metabolic conditions) is exacerbated in the COVID-19 state because (i) the virus uses the peptidase domain of the enzyme for entry into the cells and (ii) there is a decrease in ACE-2 with an increase in ACE [9] . Individuals with underlying hypertension, type 2 diabetes, or cardiovascular disease are at higher risk for respiratory failure and mortality in COVID-19. abstract: COVID-19 is a rapidly spreading outbreak globally. Emerging evidence demonstrates that older individuals and people with underlying metabolic conditions of diabetes mellitus, hypertension, and hyperlipidemia are at higher risk of morbidity and mortality. The SARS-CoV-2 infects humans through the angiotensin converting enzyme (ACE-2) receptor. The ACE-2 receptor is a part of the dual system renin-angiotensin-system (RAS) consisting of ACE-Ang-II-AT (1) R axis and ACE-2-Ang-(1–7)-Mas axis. In metabolic disorders and with increased age, it is known that there is an upregulation of ACE-Ang-II-AT (1) R axis with a downregulation of ACE-2-Ang-(1–7)-Mas axis. The activated ACE-Ang-II-AT1R axis leads to pro-inflammatory and pro-fibrotic effects in respiratory system, vascular dysfunction, myocardial fibrosis, nephropathy, and insulin secretory defects with increased insulin resistance. On the other hand, the ACE-2-Ang-(1–7)-Mas axis has anti-inflammatory and antifibrotic effects on the respiratory system and anti-inflammatory, antioxidative stress, and protective effects on vascular function, protects against myocardial fibrosis, nephropathy, pancreatitis, and insulin resistance. In effect, the balance between these two axes may determine the prognosis. The already strained ACE-2-Ang-(1–7)-Mas in metabolic disorders is further stressed due to the use of the ACE-2 by the virus for entry, which affects the prognosis in terms of respiratory compromise. Further evidence needs to be gathered on whether modulation of the renin angiotensin system would be advantageous due to upregulation of Mas activation or harmful due to the concomitant ACE-2 receptor upregulation in the acute management of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32340044/ doi: 10.1055/a-1155-0501 id: cord-299520-2khjhows author: Dalla Volta, Alberto title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures date: 2020-08-18 words: 2422.0 sentences: 115.0 pages: flesch: 50.0 cache: ./cache/cord-299520-2khjhows.txt txt: ./txt/cord-299520-2khjhows.txt summary: title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures We conducted a surveillance for SARS-CoV-2 infection among the staff members of the Medical Oncology Unit of ASST Spedali Civili in Brescia, one of the Italian areas most affected by the SARS-CoV-2 pandemic. Since last February 24, 2020, the Medical Oncology Unit of ASST Spedali Civili in Brescia put in place most of the protective measures that were subsequently acknowledged to be effective in preventing viral infection among healthcare professionals (HCPs) and patients (3) (4) (5) . The Medical Oncology Unit of ASST Spedali Civili of Brescia is located in one of the Italian areas that were most affected by the SARS-CoV-2 infection, and the hospital had to allocate the majority of its beds to patients with severe virus-related diseases. abstract: Patients with cancer are at a higher risk of developing serious disease-related complications in case of contracting SARS-CoV-2. Oncology units should implement all possible preventive measures to reduce the risk of viral transmission by healthcare professionals (HCPs) to patients. We conducted a surveillance for SARS-CoV-2 infection among the staff members of the Medical Oncology Unit of ASST Spedali Civili in Brescia, one of the Italian areas most affected by the SARS-CoV-2 pandemic. The aim of this study was to demonstrate whether the recommended preventive measures, promptly implemented by the unit, have been effective in reducing the spread of the virus among the HCPs. Between February 24 and May 19, 2020, SARS-CoV-2 infection was detected in 10 out of 76 healthy HCPs (13%). Six of them developed a symptomatic disease, leading to home quarantine, and four remained asymptomatic. The infection was revealed when a serology test was performed on all staff members of the unit. In seven HCPs, in which it was possible to trace the person-to-person infection, the contagion occurred as a result of unprotected contacts or partially protected with surgical masks. In particular, four asymptomatic HCPs did not stop working, but a widespread outbreak in the unit was avoided. Adherence to the recommended preventive strategies, in particular, wearing of surgical masks by both the HCPs and the patients, is effective in reducing and preventing the viral spread. url: https://doi.org/10.3389/fonc.2020.01574 doi: 10.3389/fonc.2020.01574 id: cord-315756-g6g34uvh author: Danchin, A. title: Immunity after COVID-19: protection or sensitization ? date: 2020-05-23 words: 4278.0 sentences: 249.0 pages: flesch: 62.0 cache: ./cache/cord-315756-g6g34uvh.txt txt: ./txt/cord-315756-g6g34uvh.txt summary: Then we use a compartmental epidemic model structured by immunity level (taken here as age classes) that we fit on available data; this allows to derive quantitative insights into the future number of severe cases and deaths. Note that in both cases the results depend on the total epidemic infection rate, which is between α t = 5.7% (present) and the group immunity rate 1 − 1/R 0 (i.e., 70% for R 0 = 3.3). Note first that the relatively controlled nature of the 2003 SARS epidemic did not allow us to draw conclusions on how the 2003 epidemic influenced the infected (too few cases); by contrast, if a sensitizing process in the immune response triggered by SARS-CoV-2 exists, the pandemic nature of the 2019/20 COVID-19 outbreak will likely have noticeable effects on the overall population health state. abstract: Motivated by historical and present clinical observations, we discuss the possible unfavorable evolution of the immunity (similar to documented antibody-dependent enhancement scenarios) after a first infection with COVID-19. More precisely we ask the question of how the epidemic outcomes are affected if the initial infection does not provide immunity but rather sensitization to future challenges. We first provide background comparison with the 2003 SARS epidemic. Then we use a compartmental epidemic model structured by immunity level (taken here as age classes) that we fit on available data; this allows to derive quantitative insights into the future number of severe cases and deaths. url: http://medrxiv.org/cgi/content/short/2020.05.21.20108860v1?rss=1 doi: 10.1101/2020.05.21.20108860 id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 words: 5318.0 sentences: 244.0 pages: flesch: 42.0 cache: ./cache/cord-330131-yfhrmbvx.txt txt: ./txt/cord-330131-yfhrmbvx.txt summary: In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. abstract: nan url: https://doi.org/10.1111/1462-2920.15025 doi: 10.1111/1462-2920.15025 id: cord-317333-unrd76bo author: Danesh, Ali title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date: 2011-01-05 words: 5467.0 sentences: 278.0 pages: flesch: 48.0 cache: ./cache/cord-317333-unrd76bo.txt txt: ./txt/cord-317333-unrd76bo.txt summary: Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) . abstract: Type I interferons (IFNs) are essential to the clearance of viral diseases, however, a clear distinction between genes upregulated by direct virus–cell interactions and genes upregulated by secondary IFN production has not been made. Here, we investigated differential gene regulation in ferrets upon subcutaneous administration of IFN-α2b and during SARS-CoV infection. In vivo experiments revealed that IFN-α2b causes STAT1 phosphorylation and upregulation of abundant IFN response genes (IRGs), chemokine receptors, and other genes that participate in phagocytosis and leukocyte transendothelial migration. During infection with SARS-CoV not only a variety of IRGs were upregulated, but also a significantly broader range of genes involved in cell migration and inflammation. This work allowed dissection of several molecular signatures present during SARS-CoV which are part of a robust IFN antiviral response. These signatures can be useful markers to evaluate the status of IFN responses during a viral infection and specific features of different viruses. url: https://www.sciencedirect.com/science/article/pii/S0042682210006380 doi: 10.1016/j.virol.2010.10.002 id: cord-316946-bxfdq8e1 author: Danion, François title: The Good, the Bad, and the Hoax: When Publication Instantaneously Impacts Treatment Strategies for COVID-19 date: 2020-07-22 words: 762.0 sentences: 50.0 pages: flesch: 49.0 cache: ./cache/cord-316946-bxfdq8e1.txt txt: ./txt/cord-316946-bxfdq8e1.txt summary: In Strasbourg University Hospital, France, which was severely affected by the SARS-CoV-2 epidemic at the beginning of March 2020, we analyzed the consumption of antiviral agents according to the emergence of relevant scientific data. The treatment strategies in our center, outside clinical trials, included standard of care alone or in combination with lopinavir-ritonavir or hydroxychloroquine (HCQ) in off-label utilization and without grading of the recommendations. Despite the major limitations of this study-including no outcome data on clinical efficacy or safety, the small number of patients enrolled, and the absence of randomization-we experienced a dramatic increase in our HCQ prescriptions following this publication (Fig. 1) . Following the publication of a large observational study on 22 May showing no beneficial effect of HCQ, this treatment regimen is not authorized anymore in France outside clinical trials (6) . Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial abstract: The COVID-19 pandemic is an unprecedented situation with physicians awaiting information on therapeutic advances to an extent hardly ever seen in medical history.…. url: https://www.ncbi.nlm.nih.gov/pubmed/32513798/ doi: 10.1128/aac.01127-20 id: cord-342145-cq6xe5r7 author: Dao Thi, Viet Loan title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 words: 9311.0 sentences: 507.0 pages: flesch: 58.0 cache: ./cache/cord-342145-cq6xe5r7.txt txt: ./txt/cord-342145-cq6xe5r7.txt summary: The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital''s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ). abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions. url: https://www.ncbi.nlm.nih.gov/pubmed/32719001/ doi: 10.1126/scitranslmed.abc7075 id: cord-307285-bxy0zsc7 author: Dar Odeh, Najla title: COVID-19: Present and Future Challenges for Dental Practice date: 2020-04-30 words: 4708.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-307285-bxy0zsc7.txt txt: ./txt/cord-307285-bxy0zsc7.txt summary: Realizing the severity of outcomes associated with this disease and its high rate of transmission, dentists were instructed by regulatory authorities, such as the American Dental Association, to stop providing treatment to dental patients except those who have emergency complaints. In vitro studies have shown that azithromycin is active against Zika and Ebola viruses, [18] [19] [20] and is able to prevent severe respiratory tract infections when administrated to patients suffering viral infection [12] However, the efficacy of azithromycin in combination with hydroxychloroquine in the treatment of COVID-19 patients has not been confirmed yet [21, 22] , and more studies are needed to further investigate its clinical effects. Following the recommended cross-infection control procedures, spreading awareness based on evidence and not misconceptions, identifying emergency cases indicated for dental treatment, and practicing effective tele-dentistry when needed can all be helpful for dental patients and community as a whole. abstract: COVID-19 was declared a pandemic by the World Health Organization, with a high fatality rate that may reach 8%. The disease is caused by SARS-CoV-2 which is one of the coronaviruses. Realizing the severity of outcomes associated with this disease and its high rate of transmission, dentists were instructed by regulatory authorities, such as the American Dental Association, to stop providing treatment to dental patients except those who have emergency complaints. This was mainly for protection of dental healthcare personnel, their families, contacts, and their patients from the transmission of virus, and also to preserve the much-needed supplies of personal protective equipment (PPE). Dentists at all times should competently follow cross-infection control protocols, but particularly during this critical time, they should do their best to decide on the emergency cases that are indicated for dental treatment. Dentists should also be updated on how this pandemic is related to their profession in order to be well oriented and prepared. This overview will address several issues concerned with the COVID-19 pandemic that directly relate to dental practice in terms of prevention, treatment, and orofacial clinical manifestations. url: https://www.ncbi.nlm.nih.gov/pubmed/32366034/ doi: 10.3390/ijerph17093151 id: cord-000333-4prvgmvt author: Darbyshire, Philip title: Nursing heroism in the 21(st )Century'' date: 2011-02-16 words: 5166.0 sentences: 275.0 pages: flesch: 63.0 cache: ./cache/cord-000333-4prvgmvt.txt txt: ./txt/cord-000333-4prvgmvt.txt summary: Gary Carr, who was a Nurse Practitioner at the AIDS Clinic at San Francisco General Hospital, described the perverse ambivalence of a wider community that lauds and praises nurses for their ''heroic efforts'' in the face of such public health crises. When, two decades later, SARS emerged as a potentially lethal viral infection, nurses and health care staff again faced considerable dangers as they strove to treat patients and protect their communities. In addition, Hall and colleagues in the US reported that: "Nursing assistants working in long-term care facilities have the highest incidence of workplace violence of any American worker". Perhaps if we return to the definition of heroism as ''providing service in the face of extreme personal danger'', then our Emergency Department nurses should allow themselves to feel, at least somewhat heroic. So too, the health, wellbeing, safety and experiences of patients, clients and families are dependent upon the often invisible and overlooked caring practices of nurses. abstract: BACKGROUND: The Vivian Bullwinkel Oration honours the life and work of an extraordinary nurse. Given her story and that of her World War II colleagues, the topic of nursing heroism in the 21(st )century could not be more germane. DISCUSSION: Is heroism a legitimate part of nursing, or are nurses simply 'just doing their job' even when facing extreme personal danger? In this paper I explore the place and relevance of heroism in contemporary nursing. I propose that nursing heroism deserves a broader appreciation and that within the term lie many hidden, 'unsung' or 'unrecorded' heroisms. I also challenge the critiques of heroism that would condemn it as part of a 'militarisation' of nursing. Finally, I argue that nursing needs to be more open in celebrating our heroes and the transformative power of nursing achievements. SUMMARY: The language of heroism may sound quaint by 21(st )Century standards but nursing heroism is alive and well in the best of our contemporary nursing ethos and practice. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048573/ doi: 10.1186/1472-6955-10-4 id: cord-302111-kg0dmgq0 author: Darden, Dijoia B. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 words: 4492.0 sentences: 257.0 pages: flesch: 34.0 cache: ./cache/cord-302111-kg0dmgq0.txt txt: ./txt/cord-302111-kg0dmgq0.txt summary: Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. abstract: This review will briefly examine the clinical presentation and important immunology of viral pneumonia with a focus on severe acute respiratory syndrome coronavirus 2 (coronavirus disease 2019). DATA SOURCES, STUDY SELECTION, DATA EXTRACTION, AND DATA SYNTHESIS: The most relevant, original and review literature were assessed for inclusion in this review. Sources included the Centers for Disease Control and Prevention, World Health Organization, and PubMed. CONCLUSIONS: Pneumonia is a leading cause of hospitalization and death worldwide, with viral etiologies being very common. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Symptoms of viral pneumonia include common respiratory tract infection symptoms of cough, fever, and shortness of breath. Immunologic changes include up-regulation of airway pro-inflammatory cytokines and pathogen- and damage-associated molecular patterns contributing to cytokine and genomic changes. Coronavirus disease 2019 clinical presentation is typical of viral pneumonia with an increased prevalence of early pulmonary infiltrates and lymphopenia. Principles of early coronavirus disease 2019 management and isolation as well as potential therapeutic approaches to the emerging pandemic are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32426751/ doi: 10.1097/cce.0000000000000109 id: cord-314171-431buxxr author: Dariya, Begum title: Understanding novel COVID-19: its impact on organ failure and risk assessment for diabetic and cancer patients date: 2020-05-06 words: 6892.0 sentences: 421.0 pages: flesch: 51.0 cache: ./cache/cord-314171-431buxxr.txt txt: ./txt/cord-314171-431buxxr.txt summary: In this review article, we have presented the effect of SARS-CoV-2 infection in comorbid patients and discussed organ failure caused by this virus. The mRNA and protein ACE2 expression levels are higher in these patients with cardiac disease, creating an increased risk for severe COVID-19 complications, including heart failure. After SARS-CoV-2 binds with ACE2, the virus degrades it, and thus the free angiotensin II induces acute lung injury [58] . Thus, targeting the binding site of the ACE2 receptor and SARS-CoV-2 with antibodies or therapeutic drugs might provide a successful treatment strategy. Moreover, this also increases the level of soluble ACE2 that competitively binds with SARS-CoV-2, causing delayed entry of the virus into cells and protecting against lung injury. The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 abstract: The current pandemic outbreak of COVID-19 originated from Wuhan, China. It is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significant mortality and morbidity rate. The severe risk factors are commonly detected in patients of older age and with medical comorbidities like cancer and diabetes. Scientists and doctors have scrambled to gain knowledge about the novel virus and its pathophysiology in order to discover possible therapeutic regimens and vaccines for COVID-19. The therapeutic strategies like targeting the viral genome emphasize the promising approach to target COVID-19. Additionally, blocking the receptor, ACE2 via the neutralizing antibodies for viral escape that prevents it from entering into the cells provides another therapeutic regimen. In this review article, we have presented the effect of SARS-CoV-2 infection in comorbid patients and discussed organ failure caused by this virus. Based on the data available from the scientific literature and ongoing clinical trials, we have focused on therapeutic strategies. We hope that we would fill the gaps that puzzled the researchers and clinicians with the best of our knowledge collected for the betterment of the patients for the coming future. url: https://doi.org/10.1016/j.cytogfr.2020.05.001 doi: 10.1016/j.cytogfr.2020.05.001 id: cord-022003-cvawdes6 author: Darling, Robert G. title: Future Biological and Chemical Weapons date: 2015-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152330/ doi: 10.1016/b978-0-323-28665-7.00080-7 id: cord-303216-1pbuywz6 author: Das, Gaurav title: Neurological Insights of COVID-19 Pandemic date: 2020-04-22 words: 2872.0 sentences: 155.0 pages: flesch: 54.0 cache: ./cache/cord-303216-1pbuywz6.txt txt: ./txt/cord-303216-1pbuywz6.txt summary: If scientific reports relevant to the SARS-CoV-2 virus are noted, it can be seen that the virus owes much of its killer properties to its unique structure that has a stronger binding affinity with the human angiotensin-converting enzyme 2 (hACE2) protein, which the viruses utilize as an entry point to gain accesses to its hosts. The intriguing part though is that recently reported studies have noted altered mental health in some COVID-19 patients showing symptoms like anosmia and ageusia thereby indicating a neuroinvasive nature of the virus. The neurological manifestations of SARS-CoV-2 have been recently recognized from CT scan images and MRI scan of the brain of a patient who contracted COVID-19 and showed symptoms of necrotizing hemorrhagic encephalopathy. The brain reportedly, like most other organs, expresses the hACE2 considered to be the entry point of the SARS-CoV-2 viruses in humans and is therefore not immune to viral infection. abstract: The novel coronavirus SARS-CoV-2, which was identified after a recent outbreak in Wuhan, China, in December 2019, has kept the whole world in tenterhooks due to its severe life-threatening nature of the infection. The virus is unlike its previous counterparts, SARS-CoV and MERS-CoV, or anything the world has encountered before both in terms of virulence and severity of the infection. If scientific reports relevant to the SARS-CoV-2 virus are noted, it can be seen that the virus owes much of its killer properties to its unique structure that has a stronger binding affinity with the human angiotensin-converting enzyme 2 (hACE2) protein, which the viruses utilize as an entry point to gain accesses to its hosts. Recent reports suggest that it is not just the lung that the virus may be targeting; the human brain may soon emerge as the new abode of the virus. Already instances of patients with COVID-19 have been reported with mild (anosmia and ageusia) to severe (encephalopathy) neurological manifestations, and if that is so, then it gives us more reasons to be frightened of this killer virus. Keeping in mind that the situation does not worsen from here, immediate awareness and more thorough research regarding the neuroinvasive nature of the virus is the immediate need of the hour. Scientists globally also need to up their game to design more specific therapeutic strategies with the available information to counteract the pandemic. In this Viewpoint, we provide a brief outline of the currently known neurological manifestations of COVID-19 and discuss some probable ways to design therapeutic strategies to overcome the present global crisis. url: https://doi.org/10.1021/acschemneuro.0c00201 doi: 10.1021/acschemneuro.0c00201 id: cord-292657-gq3965se author: Das, Piyanki title: Decoding the global outbreak of COVID-19: the nature is behind the scene date: 2020-06-22 words: 5030.0 sentences: 221.0 pages: flesch: 43.0 cache: ./cache/cord-292657-gq3965se.txt txt: ./txt/cord-292657-gq3965se.txt summary: The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. abstract: The sudden emergence of SARS-CoV-2 causing the global pandemic is a major public health concern. Though the virus is considered as a novel entity, it is not a completely new member. It is just a new version of previously emerged human SARS corona virus. The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. The evolution of the virus has been occurred by the continuous process of molecular genetic manipulation, through mutation, deletion and genetic recombinationevents. Different host body environment acts as the supportive system for the pathogen which creates extreme selective pressure. By the process of genetic evolution the pathogen developes new characters. Then the new version of the virus has been naturally selected by susceptible human host and adapt itself inside the host body causing deadly effect. Moreover, extreme environmental stability helps in the process of viral survival outside the host and its transmission. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. url: https://www.ncbi.nlm.nih.gov/pubmed/32656307/ doi: 10.1007/s13337-020-00605-y id: cord-259340-1ir19s25 author: Das, Rohit Pritam title: Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date: 2020-07-01 words: 1640.0 sentences: 128.0 pages: flesch: 51.0 cache: ./cache/cord-259340-1ir19s25.txt txt: ./txt/cord-259340-1ir19s25.txt summary: Here the authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The B-cell epitopic regions present in SARS-CoV-2 S protein were identified using BcePred prediction server (https://webs.iiitd.edu.in/cgibin/bcepred/) [17] . Molecular docking was performed between the predicted peptides and MHC representative structures using PatchDock web server [22, 23, 24] . Interaction of both TLR2 and TLR4 structures with the predicted peptides were performed using PatchDock web server [22, 23, 24] . This study is focused on the prediction of effective epitopes from Spike protein of SARS-CoV-2. abstract: Novel corona virus disease 2019 (COVID-19) is emerging as a pandemic situation and declared as a global health emergency by WHO. Due to lack of specific medicine and vaccine, viral infection has gained a frightening rate and created a devastating state across the globe. Here the authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. We have predicted a 9-mer peptide as representative of both B-cell and T-cell epitopic region along with suitable properties such as antigenic and non-allergenic. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The present study may helpful to step forward in the development of vaccine candidates against COVID-19. url: https://doi.org/10.1101/2020.07.01.150805 doi: 10.1101/2020.07.01.150805 id: cord-301026-spgidqh3 author: Das, Shaoli title: In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data date: 2020-06-30 words: 4169.0 sentences: 190.0 pages: flesch: 43.0 cache: ./cache/cord-301026-spgidqh3.txt txt: ./txt/cord-301026-spgidqh3.txt summary: Next, using the available drug perturbational data sets from the Broad Institute Connectivity map (CMAP project 14 , we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. To get a pathway-based estimation instead of individual genes, we calculated ssGSEA scores for the differentially enriched pathways in COVID-19 or SARS infection for all drug-treated cell lines at different dose/time points. Thereafter, combining the potential human interactome of SARS-CoV-2 from a recently published study 9 and SARS-CoV-1-interacting proteins curated in another publication 8 with drug target databases 10, 11 , drug perturbational data sets 14 , and drug sensitivity screening data sets 15 , we propose a map of the drugs that can be effective in COVID-19 treatment. Next, using the available drug perturbational data sets from the Broad Institute CMAP project, we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) continues to affect a growing number of populations in different parts of the world. In the current situation, drug repurposing is a viable strategy to combat COVID-19. The drugs targeting the host receptors that interact with SARS-CoV-2 are possible candidates. However, assessment of their effectiveness in COVID-19 patients is necessary before prioritizing them for further study. We attempted to shortlist the candidate drugs using an in-silico approach. First, we analysed two published transcriptomic data sets of COVID-19- and SARS-infected patients compared to healthy individuals to find the key pathways altered after infection. Then, using publicly available drug perturbational data sets in human cell lines from the Broad Institute Connectivity Map (CMAP), we assessed the effects of the approved drugs on the altered pathways. We also used the available pharmacogenomic data sets from the Genomics of Drug Sensitivity in Cancer (GDSC) portal to assess the effects of the altered pathways on resistance or sensitivity to the drugs in human cell lines. Our analysis identified many candidate drugs, some of which are already being investigated for treatment of COVID-19 and can serve as a basis for prioritizing additional viable candidate drugs for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32702730/ doi: 10.21203/rs.3.rs-39128/v1 id: cord-263576-pn2zieek author: Das, Sourav title: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study date: 2020-05-13 words: 5000.0 sentences: 266.0 pages: flesch: 54.0 cache: ./cache/cord-263576-pn2zieek.txt txt: ./txt/cord-263576-pn2zieek.txt summary: Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. Hydroxychloroquine, a promising candidate for the treatment of the current pandemic due to SARS-CoV-2 (Gautret et al., 2020) , has been found to bind within the active site of the protease through p-sulphur interaction with MET165, p-sigma with GLN189, alkyl hydrophobic with LEU167 and PRO168, and van der Waals interactions with other residues as shown in Figure 2c . Curcumin, a potent bioactive molecule binds in the active site of SARS-CoV-2 M pro (Figure 3a ) through hydrogen bonding with GLY143 and GLN192, p-sulphur, p-sigma interactions with CYS145 and PRO168, respectively, along with other non-covalent interactions such as van der Waals interactions with other residues as shown in the 2 D plot (Figure Table 1 . abstract: A new strain of a novel infectious disease affecting millions of people, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a pandemic by the World Health Organization (WHO). Currently, several clinical trials are underway to identify specific drugs for the treatment of this novel virus. The inhibition of the SARS-CoV-2 main protease is necessary for the blockage of the viral replication. Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. All the studied molecules could bind to the active site of the SARS-CoV-2 protease (PDB: 6Y84), out of which rutin (a natural compound) has the highest inhibitor efficiency among the 33 molecules studied, followed by ritonavir (control drug), emetine (anti-protozoal), hesperidin (a natural compound), lopinavir (control drug) and indinavir (anti-viral drug). All the molecules, studied out here could bind near the crucial catalytic residues, HIS41 and CYS145 of the main protease, and the molecules were surrounded by other active site residues like MET49, GLY143, HIS163, HIS164, GLU166, PRO168, and GLN189. As this study is based on molecular docking, hence being particular about the results obtained, requires extensive wet-lab experimentation and clinical trials under in vitro as well as in vivo conditions. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32362245/ doi: 10.1080/07391102.2020.1763201 id: cord-266113-3fp46sov author: Dashti‐Khavidaki, Simin title: Considerations for Statin Therapy in Patients with COVID‐19 date: 2020-05-04 words: 1352.0 sentences: 88.0 pages: flesch: 42.0 cache: ./cache/cord-266113-3fp46sov.txt txt: ./txt/cord-266113-3fp46sov.txt summary: Current coronavirus pandemic named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third coronavirus outbreak during the current century after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses.1 Acute respiratory distress syndrome (ARDS) is an immunopathologic event and main cause of death following COVID-19. The main mechanism of ARDS is uncontrolled systemic inflammatory response and cytokine storm following release of proinflammatory cytokines (such as interferons (IFN), interleukines (IL), tumor necrosis factor (TNF)-α) and chemokines.2-3 So, some Chinese researchers proposed or used anti-inflammatory agents in the treatment regimen of patients with COVID-19.3-4. The current coronavirus pandemic is an outbreak of coronavirus disease 2019 (COVID19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2, 23 Thus, initiating statins in patients with COVID-19 may increase the risk and severity of myopathies and acute kidney injury. abstract: Current coronavirus pandemic named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third coronavirus outbreak during the current century after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses.1 Acute respiratory distress syndrome (ARDS) is an immunopathologic event and main cause of death following COVID-19. The main mechanism of ARDS is uncontrolled systemic inflammatory response and cytokine storm following release of proinflammatory cytokines (such as interferons (IFN), interleukines (IL), tumor necrosis factor (TNF)-α) and chemokines.2-3 So, some Chinese researchers proposed or used anti-inflammatory agents in the treatment regimen of patients with COVID-19.3-4. url: https://www.ncbi.nlm.nih.gov/pubmed/32267560/ doi: 10.1002/phar.2397 id: cord-224516-t5zubl1p author: Daubenschuetz, Tim title: SARS-CoV-2, a Threat to Privacy? date: 2020-04-21 words: 4799.0 sentences: 214.0 pages: flesch: 46.0 cache: ./cache/cord-224516-t5zubl1p.txt txt: ./txt/cord-224516-t5zubl1p.txt summary: We furthermore discuss the issues with privacy that can occur during a crisis such as this global pandemic and what can be done to ensure information security and hence appropriate data protection. When we are considering the example of doctors treating their patients, we can use the framework of contextual integrity to reason about the appropriate information flow as follows: the patient is both the sender and the subject of the data exchange, the doctor is the receiver, the information type is the patient''s medical information, the transmission principle includes, most importantly, doctor-patient confidentiality aside from public health issues. In Germany, the authority for disease control and prevention, the Robert Koch Institute (RKI), made headlines on March 18, 2020, as it became public that telecommunication provider Telekom had shared an anonymized set of mobile phone movement data to monitor citizens'' mobility in the fight against SARS-CoV-2. abstract: The global SARS-CoV-2 pandemic is currently putting a massive strain on the world's critical infrastructures. With healthcare systems and internet service providers already struggling to provide reliable service, some operators may, intentionally or unintentionally, lever out privacy-protecting measures to increase their system's efficiency in fighting the virus. Moreover, though it may seem all encouraging to see the effectiveness of authoritarian states in battling the crisis, we, the authors of this paper, would like to raise the community's awareness towards developing more effective means in battling the crisis without the need to limit fundamental human rights. To analyze the current situation, we are discussing and evaluating the steps corporations and governments are taking to condemn the virus by applying established privacy research. url: https://arxiv.org/pdf/2004.10305v1.pdf doi: nan id: cord-287682-97fquq16 author: Daubin, Cédric title: Is a COPD patient protected against SARS-CoV-2 virus? date: 2020-10-03 words: 745.0 sentences: 55.0 pages: flesch: 50.0 cache: ./cache/cord-287682-97fquq16.txt txt: ./txt/cord-287682-97fquq16.txt summary: In addition, cigarette smoke and COPD were reported to up-regulate Angiotensin-converting enzyme 2 (ACE-2) expression, which plays a key role in the pathogenesis of SARS-CoV-2 in lower airways [2] . Considering a significant inverse relationship between ACE-2 gene expression and the severity of COPD [2] , one hypothesis could be that COPD protects against SARS-CoV-2 through a TMPRSS2 inhibitor activity or by an a downregulation of the inflammatory pathway limiting severe forms of infection. Interestingly, as reported by Halpin et al., inhaled corticosteroids, used by COPD patients can reduce the risk of viral infection. Therefore, inhaled corticosteroids in combination with bronchodilators could limit expression or activity of transmenbrane serine protease TMPRSS2 which facilitates SARS-CoV-2 entry in cells. Surprisingly current smokers (i.e., a large part of COPD patients) could be protected against SARS-CoV-2 infection [4] . Sin DD (2020) ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19 abstract: nan url: https://api.elsevier.com/content/article/pii/S0399077X20307137 doi: 10.1016/j.medmal.2020.09.015 id: cord-321267-ihd30qi0 author: Daughton, Christian G. title: Natural experiment concept to accelerate the Re-purposing of existing therapeutics for Covid-19 date: 2020-05-15 words: 5350.0 sentences: 263.0 pages: flesch: 45.0 cache: ./cache/cord-321267-ihd30qi0.txt txt: ./txt/cord-321267-ihd30qi0.txt summary: Proposed here is a new but simple concept that would capitalize on the opportunity presented by the on-going natural experiment involving the collection of data from epidemiological surveillance screening and diagnostic testing for clinical treatment. These drug usage data would be collected for several major test groups those who test positive for active SARS-CoV-2 infection (using molecular methods) and those who test negative for current infection but also test positive for past infection (using serologic antibody tests). (1) As Covid-19 epidemiological surveillance screening and diagnostic testing proceeds, a national database would be continually populated with drug usage data collected from each case among three different combinations of sub-groups based upon whether they tested positive or negative for active SARS-CoV-2 infection or tested positive for past SARS-CoV-2 infection (see Table 1 ). abstract: One of the many questions with respect to controlling the novel coronavirus pandemic is whether existing drugs can be re-purposed (re-positioned) for the prevention or treatment of Covid-19 - or for any future epidemic. The usefulness of existing approaches for re-purposing range from computational modeling to clinical trials. These are often time-consuming, resource intensive, and prone to failure. Proposed here is a new but simple concept that would capitalize on the opportunity presented by the on-going natural experiment involving the collection of data from epidemiological surveillance screening and diagnostic testing for clinical treatment. The objective would be to also collect for each Covid-19 case the patient's prior usage of existing therapeutic drugs. These drug usage data would be collected for several major test groups - those who test positive for active SARS-CoV-2 infection (using molecular methods) and those who test negative for current infection but also test positive for past infection (using serologic antibody tests). Patients from each of these groups would also be categorized with respect to where they resided on the spectrum of morbidities (from no or mild symptomology to severe). By comparing the distribution of normalized usage data for each drug within each group, drugs that are more associated with particular test groups could be revealed as having potential prophylactic, therapeutic, or contraindicated effects with respect to disease progression. These drugs could then be selected as candidates for further evaluation in fighting Covid-19. Also summarized are some of the numerous attributes, advantages, and limitations of the proposed concept, all pointing to the need for further discussion and evaluation. url: https://www.sciencedirect.com/science/article/pii/S2590113320300109?v=s5 doi: 10.1016/j.gloepi.2020.100026 id: cord-255101-l5ssz750 author: Daval, Mary title: Efficacy of local budesonide therapy in the management of persistent hyposmia in COVID-19 patients without signs of severity: A structured summary of a study protocol for a randomised controlled trial date: 2020-07-20 words: 8946.0 sentences: 919.0 pages: flesch: 63.0 cache: ./cache/cord-255101-l5ssz750.txt txt: ./txt/cord-255101-l5ssz750.txt summary: Objectif principal: Evaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. L''objectif de cet essai randomisé contrôlé, bicentrique, est d''évaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. Evaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. abstract: OBJECTIVES: To assess the efficacy of local intranasal treatment with budesonide (nasal irrigation), in addition to olfactory rehabilitation, in the management of loss of smell in COVID-19 patients without signs of severity and with persistent hyposmia 30 days after the onset of symptoms. To search for an association between the presence of an obstruction on MRI and the severity of olfactory loss, at inclusion and after 30 days of treatment. TRIAL DESIGN: Two center, open-label, 2-arm (1:1 ratio) parallel group randomized controlled superiority trial. PARTICIPANTS: Inclusion criteria - Patient over 18 years of age; - Patient with a suspected SARS-CoV-2 infection, whether or not confirmed by PCR, or close contact with a PCR-confirmed case, typical chest CT scan (unsystematic frosted glass patches with predominantly sub-pleural appearance, and at a later stage, alveolar condensation without excavation or nodules or masses) or positive serology ; - Patient with isolated sudden onset hyposmia persisting 30 days after the onset of symptoms of CoV-2 SARS infection; - Affiliate or beneficiary of a social security scheme; - Written consent to participate in the study. Non-inclusion criteria - Known hypersensitivity to budesonide or any of the excipients; - Hemostasis disorder or epistaxis; - Oral-nasal and ophthalmic herpes virus infection; - Long-term corticosteroid treatment; - Treatment with potent CYP3A4 inhibitors (e.g., ketoconazole, itraconazole, voriconazole, posaconazole, clarithromycin, telithromycin, nefazodone and HIV protease inhibitors); - Severe forms of SARS-CoV-2 with respiratory or other signs; - Hyposmia persisting for more than 90 days after the onset of symptoms - Other causes of hyposmia found on interrogation or MRI; - Patient benefiting from a legal protection measure; - Pregnant or breastfeeding women. The participants will be recruited from: Hôpital Fondation Adolphe de Rothschild and Hôpital Lariboisière in Paris, France INTERVENTION AND COMPARATOR: Intervention: Experimental group: Nasal irrigation with budesonide and physiological saline (Budesonide 1mg/2mL diluted in 250mL of physiological saline 9°/00): 3 syringes of 20mL in each nasal cavity, morning and evening, for 30 days, in addition to olfactory rehabilitation twice a day. Control group: Nasal irrigation with physiological saline 9°/00 only: 3 syringes of 20cc in each nasal cavity, morning and evening, for 30 days, in addition to olfactory rehabilitation twice a day. MAIN OUTCOMES: Percentage of patients with an improvement of more than 2 points on the ODORATEST score after 30 days of treatment. RANDOMISATION: Patients will be randomized (1:1) between the experimental and control groups, using the e-CRF. The randomization list will be stratified by centre. BLINDING (MASKING): Participants and caregivers are aware of the group assignment. People assessing the outcomes are blinded to the group assignment Numbers to be randomised (sample size) 120 patients are planned to be randomized into two groups of 60 patients. TRIAL STATUS: MDL_2020_10. Version number 2, May 22, 2020. Recruitment started on May 22, 2020. The trial will finish recruiting by August 2020. TRIAL REGISTRATION: EUDRACT number: 2020-001667-85; date of trial registration: 15 May 2020 Protocol registered on ClinicalTrial.gov, registration number: NCT04361474; date of trial registration: 24 April 2020. FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. url: https://www.ncbi.nlm.nih.gov/pubmed/32690074/ doi: 10.1186/s13063-020-04585-8 id: cord-346403-fuxs1axy author: Davanzo, G. G. title: SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes date: 2020-09-28 words: 3490.0 sentences: 214.0 pages: flesch: 59.0 cache: ./cache/cord-346403-fuxs1axy.txt txt: ./txt/cord-346403-fuxs1axy.txt summary: We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARSCoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Since CD4 + T lymphocytes orchestrate innate and adaptive immune responses 19, 20 , infection of CD4 + T cells by SARS-CoV-2 might explain lymphocytopenia and dysregulated inflammatory response in severe COVID-19 patients. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as coronavirus disease-2019 (COVID-19). SARS-CoV-2 infects the lungs and may cause several immune-related complications such as lymphocytopenia and cytokine storm which are associated with the severity of the disease and predict mortality . The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is not fully understood. Here we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS- CoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. Once inside T helper cells, SARS-CoV-2 assembles viral factories, impairs cell function and may cause cell death. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID- 19 patients. url: http://medrxiv.org/cgi/content/short/2020.09.25.20200329v1?rss=1 doi: 10.1101/2020.09.25.20200329 id: cord-268484-hf4zflsy author: Davanzo, Riccardo title: Breast feeding at the time of COVID-19: do not forget expressed mother’s milk, please date: 2020-04-06 words: 726.0 sentences: 49.0 pages: flesch: 57.0 cache: ./cache/cord-268484-hf4zflsy.txt txt: ./txt/cord-268484-hf4zflsy.txt summary: In the context of the coronavirus disease (COVID-19) prevention and cure, a remarkable issue, particularly in maternity hospitals, is represented by the risk of mother to child transmission by a breastfeeding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive woman. Moreover, Chinese colleagues who have recently coped with COVID-19 just do not consider the breast feeding option, nor the use of expressed breast milk for newborn infants. Thus, the author seems to implicitly endorse the use of expressed mother''s milk, although in the flow chart contained in the online supplementary appendix, he contradictorily warns just against breast feeding for all SARS-CoV-2-positive mothers at delivery. In conclusion, protocols applied in maternity hospitals to prevent COVID-2 should consider, as far as possible, the promotion of breast feeding, without disregarding the feasible option of expressing mother''s milk. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32253201/ doi: 10.1136/archdischild-2020-319149 id: cord-285111-qjclp51i author: Davanzo, Riccardo title: Breastfeeding and coronavirus disease‐2019: Ad interim indications of the Italian Society of Neonatology endorsed by the Union of European Neonatal & Perinatal Societies date: 2020-04-26 words: 3616.0 sentences: 209.0 pages: flesch: 53.0 cache: ./cache/cord-285111-qjclp51i.txt txt: ./txt/cord-285111-qjclp51i.txt summary: The Italian Society on Neonatology (SIN) after reviewing the limited scientific knowledge on the compatibility of breastfeeding in the COVID‐19 mother and the available statements from Health Care Organizations has issued the following indications that have been endorsed by the Union of European Neonatal & Perinatal Societies (UENPS). • If a breastfeeding mother and her newborn infant are managed jointly, measures aimed at preventing the transmission of the viral infection should be put in place: avoid kissing the neonate, protect him from adult coughing and respiratory secretions (wear a mask during feeding and intimate contact with the baby), wash hands, in particular, before feeding, suspend visits. We recognize that this guidance might be subject to change in the future when further knowledge will be acquired about the COVID-19 pandemic, its perinatal transmission, and clinical characteristics of cases of neonatal SARS-CoV-2 infection. abstract: The recent COVID‐19 pandemic has spread to Italy with heavy consequences on public health and economics. Besides the possible consequences of COVID‐19 infection on a pregnant woman and the fetus, a major concern is related to the potential effect on neonatal outcome, the appropriate management of the mother–newborn dyad, and finally the compatibility of maternal COVID‐19 infection with breastfeeding. The Italian Society on Neonatology (SIN) after reviewing the limited scientific knowledge on the compatibility of breastfeeding in the COVID‐19 mother and the available statements from Health Care Organizations has issued the following indications that have been endorsed by the Union of European Neonatal & Perinatal Societies (UENPS). If a mother previously identified as COVID‐19 positive or under investigation for COVID‐19 is asymptomatic or paucisymptomatic at delivery, rooming‐in is feasible, and direct breastfeeding is advisable, under strict measures of infection control. On the contrary, when a mother with COVID‐19 is too sick to care for the newborn, the neonate will be managed separately and fed fresh expressed breast milk, with no need to pasteurize it, as human milk is not believed to be a vehicle of COVID‐19. We recognize that this guidance might be subject to change in the future when further knowledge will be acquired about the COVID‐19 pandemic, the perinatal transmission of SARS‐CoV‐2, and clinical characteristics of cases of neonatal COVID‐19. url: https://doi.org/10.1111/mcn.13010 doi: 10.1111/mcn.13010 id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 words: 3255.0 sentences: 193.0 pages: flesch: 59.0 cache: ./cache/cord-262485-sx2q5ol4.txt txt: ./txt/cord-262485-sx2q5ol4.txt summary: The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. abstract: With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency. url: https://doi.org/10.1101/2020.06.08.139477 doi: 10.1101/2020.06.08.139477 id: cord-305511-gdpxvqkk author: Dave, Gaurav S. title: High affinity interaction of Solanum tuberosum and Brassica juncea residue smoke water compounds with proteins involved in coronavirus infection date: 2020-08-11 words: 3194.0 sentences: 222.0 pages: flesch: 48.0 cache: ./cache/cord-305511-gdpxvqkk.txt txt: ./txt/cord-305511-gdpxvqkk.txt summary: Phytoconstituents that possess remarkable pharmacological activity were selected as reported from Solanum tuberosum and Brassica juncea residue smoke water (Dave et al., 2018) and Ligand library was prepared of potential molecules to be used for the docking study with human, SARS-CoV and SARS-CoV-2 proteins as given in Table 1 (Sakai et al., 2014) , SARS-CoV-S in complex with ACE2 (PDB: 2AJF) (Li et al., 2005; Micholas & Jeremy, 2020) , PLpro (PDB: 3E9S) , SARS-CoV-2 3CLpro (PDB: 6LU7) , SARS-CoVRdRp (PDB: 6NUR) (Elfiky, 2020) , SARS-CoV-2 spike glycoprotein structure (SARS-CoV-2-S) (PDB: 6VSB) (Grifoni et al., 2020) , binding complex of human ACE2 and RBD (PDB: 6VW1) (Qiu et al., 2020) , SARS-CoV-2-S (closed) (PDB: 6VXX) (Walls et al., 2020) , SARS-CoV-2-S with one S B (open) (PDB: 6VYB) (Walls et al., 2020) and Human angiotensin-converting enzyme 2 (ACE2) (PDB: 1R42) (Jia et al., 2009) are selected for the present study as target proteins ( Figure 1 ). abstract: The world is in an immediate need of treatment for coronavirus disease (COVID‐19). Chronic exposure of hydroxychloroquine in the treatment of COVID‐19 may have multiple adverse effects on human physiology, such as cardiac arrhythmias. Natural compounds need to be evaluated as treatment and preventive agents in coronavirus infection. A total of 30 compounds of Solanum tuberosum and Brassica juncea residue smoke water were selected for the virtual screening against SARS‐CoV‐1, SARS‐CoV‐2 and cellular proteins involved in the mechanism of infection. Docking analysis identified lead molecules with favorable binding energy, number of poses and hydrogen bond interactions, which indicates the effective modulation of ACE2 and TMPRSS2 receptors. Results indicated (a) curcumenol, (b) N‐desmethylselegiline, (c) phentermine and (d) sphingolipid derivatives as a selective and potent candidates in comparison to hydroxychloroquine for COVID‐19 treatment. Our in silico findings, therefore, warrant further in vitro validations of the selected compounds for the discovery of novel preventive and therapeutic drug against SARS‐CoV‐2 infection. url: https://doi.org/10.1002/ptr.6796 doi: 10.1002/ptr.6796 id: cord-295034-em6z8mlu author: Daverey, Achlesh title: COVID-19: Eco-friendly hand hygiene for human and environmental safety date: 2020-11-11 words: 1896.0 sentences: 125.0 pages: flesch: 40.0 cache: ./cache/cord-295034-em6z8mlu.txt txt: ./txt/cord-295034-em6z8mlu.txt summary: Frequent handwashing with soap and the use of alcohol-based hand sanitizers is recommended by WHO for hand hygiene and to prevent the spread of COVID-19. However, there are safety concerns associated with the use of soaps and alcohol-based hand sanitizers. Therefore, the review aims to highlight the health and environmental concerns associated with the frequent use of soaps/detergents and alcohol-based hand sanitizers amid COVID-19. The potential of some of the natural detergents and sanitizing agents as eco-friendly alternatives to petrochemical-based soaps and alcohol-based hand rubs for hand hygiene are discussed. Overall, all these properties of plant-derived natural soaps and detergents have the potential to replace the synthetic detergents and alcohol-based sanitizers. Economical production of biosurfactants and extraction of bioactive antimicrobial agents from the plants will play a crucial role in their commercial application and sustainability as eco-friendly soaps and hand sanitizers and therefore further research is needed in this direction. abstract: The Coronavirus disease-2019 (COVID-19) outbreak is caused by a highly pathogenic novel coronavirus (SARS-CoV-2). To date, there is no prescribed medicine for COVID-19. Frequent handwashing with soap and the use of alcohol-based hand sanitizers is recommended by WHO for hand hygiene and to prevent the spread of COVID-19. However, there are safety concerns associated with the use of soaps and alcohol-based hand sanitizers. Therefore, the review aims to highlight the health and environmental concerns associated with the frequent use of soaps/detergents and alcohol-based hand sanitizers amid COVID-19. The potential of some of the natural detergents and sanitizing agents as eco-friendly alternatives to petrochemical-based soaps and alcohol-based hand rubs for hand hygiene are discussed. The market of soaps and hand sanitizers is expected to grow in the coming years and therefore, future research should be directed to develop eco-friendly soaps and hand sanitizers for human and environmental safety. url: https://www.sciencedirect.com/science/article/pii/S2213343720311039?v=s5 doi: 10.1016/j.jece.2020.104754 id: cord-275108-snqbrxgr author: Daverio, Marco title: Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date: 2020-05-22 words: 505.0 sentences: 31.0 pages: flesch: 51.0 cache: ./cache/cord-275108-snqbrxgr.txt txt: ./txt/cord-275108-snqbrxgr.txt summary: We read with interest the article by Cowling and Aiello [1] about the use of proactive public health measures to help slow the spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over the world. Furthermore, the numbers of individuals infected are difficult to estimate, owing to the presence of both SARS-CoV-2-positive asymptomatic individuals and symptomatic, self-isolating individuals in whom nasopharyngeal swab samples were not obtained. It may seem a waste of resources but knowing people''s serological status regarding SARS-CoV-2 could allow those who were previously infected to return to work and restart the world economy before the entire pandemic is over. We therefore suggest, along with all the necessary public preventive measures, performing target testing for SARS-CoV-2 antibodies in particular subpopulations, for example, young and healthy persons who can actively work. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32442248/ doi: 10.1093/infdis/jiaa283 id: cord-253933-29tedkf8 author: David, Abel P. title: Tracheostomy guidelines developed at a large academic medical center during the COVID‐19 pandemic date: 2020-04-27 words: 3038.0 sentences: 163.0 pages: flesch: 42.0 cache: ./cache/cord-253933-29tedkf8.txt txt: ./txt/cord-253933-29tedkf8.txt summary: 1 As an aerosol-generating procedure (AGP), tracheostomy is associated with high droplet and particle generation, placing health care providers at increased risk for transmission of respiratory viral infections. Factors relevant to our review included optimal timing of tracheostomy, duration of viral shedding in patients with COVID-19, risk to procedural teams from aerosol generation during tracheostomy, ICU capacity, and availability of PPE. In the context of the current pandemic, Tay et al conducted a literature review of tracheostomies performed during the SARS epidemic and concluded the following: (a) proper PPE (N95 mask, surgical cap, gown, goggles, and gloves) is of utmost importance; (b) surgical tracheostomy is preferably performed in a negative pressure ICU room by experienced providers with meticulous planning and seamless communication; (c) aerosol generation should be minimized through patient paralysis, ventilation hold during creation of tracheal window, and utilization of HEPA-filtered suction systems. abstract: BACKGROUND: During the SARS‐CoV‐2 pandemic, tracheostomy may be required for COVID‐19 patients requiring long‐term ventilation in addition to other conditions such as airway compromise from head and neck cancer. As an aerosol‐generating procedure, tracheostomy increases the exposure of health care workers to COVID‐19 infection. Performing surgical tracheostomy and tracheostomy care requires a strategy that mitigates these risks and maintains the quality of patient care. METHODS: This study is a multidisciplinary review of institutional tracheostomy guidelines and clinical pathways. Modifications to support clinical decision making in the context of COVID‐19 were derived by consensus and available evidence. RESULTS: Modified guidelines for all phases of tracheostomy care at an academic tertiary care center in the setting of COVID‐19 are presented. DISCUSSION: During the various phases of the COVID‐19 pandemic, clinicians must carefully consider the indications, procedural precautions, and postoperative care for tracheostomies. We present guidelines to mitigate risk to health care workers while preserving the quality of care. url: https://doi.org/10.1002/hed.26191 doi: 10.1002/hed.26191 id: cord-257105-vrwuaknf author: Davies, Julie title: Neuropilin-1 as a new potential SARS-CoV-2 infection mediator implicated in the neurologic features and central nervous system involvement of COVID-19 date: 2020-09-15 words: 2642.0 sentences: 141.0 pages: flesch: 47.0 cache: ./cache/cord-257105-vrwuaknf.txt txt: ./txt/cord-257105-vrwuaknf.txt summary: Preclinical studies have suggested that neuropilin-1 (NRP1), which is a transmembrane receptor that lacks a cytosolic protein kinase domain and exhibits high expression in the respiratory and olfactory epithelium, may also be implicated in COVID-19 by enhancing the entry of SARS-CoV-2 into the brain through the olfactory epithelium. This study presents a detailed in silico analysis of the expression of nrP1 in the human brain, highlighting the potential role of nrP1 as an additional SarS-coV-2 infection mediator in the CNS via NRP1-expressing cells. Given this newly identified role of nrP1 in enhancing SarS-coV-2 entry into the cnS, characterizing the precise expression of nrP1 in the human brain becomes important in the context of the neurologic involvement of coVid-19. Finally, the parolfactory gyri which receive inputs from the olfactory bulb and provide input to the limbic system, also exhibit nrP1 expression, and so their potential involvement in the SarS-coV-2 infection of the cnS merits further research. abstract: Infection by the severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) is the cause of the new viral infectious disease (coronavirus disease 2019; COVID-19). Emerging evidence indicates that COVID-19 may be associated with a wide spectrum of neurological symptoms and complications with central nervous system (CNS) involvement. It is now well-established that entry of SARS-CoV-2 into host cells is facilitated by its spike proteins mainly through binding to the angiotensin-converting enzyme 2 (ACE-2). Preclinical studies have suggested that neuropilin-1 (NRP1), which is a transmembrane receptor that lacks a cytosolic protein kinase domain and exhibits high expression in the respiratory and olfactory epithelium, may also be implicated in COVID-19 by enhancing the entry of SARS-CoV-2 into the brain through the olfactory epithelium. In the present study, we expand on these findings and demonstrate that the NRP1 is also expressed in the CNS, including olfactory-related regions such as the olfactory tubercles and paraolfactory gyri. This furthers supports the potential role of NRP1 as an additional SARS-CoV-2 infection mediator implicated in the neurologic manifestations of COVID-19. Accordingly, the neurotropism of SARS-CoV-2 via NRP1-expressing cells in the CNS merits further investigation. url: https://www.ncbi.nlm.nih.gov/pubmed/33000221/ doi: 10.3892/mmr.2020.11510 id: cord-283253-qdq4mfz3 author: Davlantes, Elizabeth title: Notes from the Field: COVID-19 Prevention Practices in State Prisons — Puerto Rico, 2020 date: 2020-08-21 words: 657.0 sentences: 42.0 pages: flesch: 43.0 cache: ./cache/cord-283253-qdq4mfz3.txt txt: ./txt/cord-283253-qdq4mfz3.txt summary: These results followed implementation in mid-March of a protocol (2) for the diagnosis, management, and prevention of COVID-19 in all Puerto Rico Department of Correction and Rehabilitation prisons based on CDC''s interim guidance on management of COVID-19 in correctional and detention facilities (3) . To minimize SARS-CoV-2 transmission from newly incarcerated persons, all state prison intakes in Puerto Rico now occur at a single location, in the municipality of Bayamon. During March 16-July 31, 2020, 1,340 persons entered Puerto Rico Department of Correction and Rehabilitation prisons, and two (0.1%) had positive SARS-CoV-2 RT-PCR test results. If any group member exhibits COVID-19 symptoms, which are defined according to CDC guidelines (4), the symptomatic person is isolated in the prison''s medical facility, and the entire group is quarantined until the symptomatic person receives a negative SARS-CoV-2 RT-PCR result. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32817601/ doi: 10.15585/mmwr.mm6933a4 id: cord-305959-x061q8t7 author: Davoudi-Monfared, Effat title: A Randomized Clinical Trial of the Efficacy and Safety of Interferon β-1a in Treatment of Severe COVID-19 date: 2020-08-20 words: 4733.0 sentences: 280.0 pages: flesch: 50.0 cache: ./cache/cord-305959-x061q8t7.txt txt: ./txt/cord-305959-x061q8t7.txt summary: As the primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 ± 5.8 versus 8.3 ± 4.9 days, respectively, P = 0.95). The vital signs at the time of hospital admission were not statistically different, except respiratory rate was significantly higher in the IFN group (22 versus 20, respectively, P ϭ 0.009). As a primary outcome, the time to clinical response was not significantly different between the IFN and control groups (9.7 Ϯ 5.8 versus 8.3 Ϯ 4.9 days, respectively, P ϭ 0.95), which is shown in the Kaplan-Meier plot (Fig. 2) . On day 0, there was no significant difference between the groups in terms of the components Interferon ␤-1a in Treatment of Severe COVID19 Antimicrobial Agents and Chemotherapy of this scale. The present study was the first randomized, open-label, controlled trial that assessed the efficacy and safety of IFN ␤-1a in the treatment of patients diagnosed with severe COVID-19. abstract: To the best of our knowledge, there is no published study on the use of interferon β-1a (IFN β-1a) in the treatment of severe COVID-19. In this randomized clinical trial, the efficacy and safety of IFN β-1a were evaluated in patients with severe COVID-19. Forty-two patients in the interferon group received IFN β-1a in addition to the national protocol medications (hydroxychloroquine plus lopinavir-ritonavir or atazanavir-ritonavir). Each 44-μg/ml (12 million IU/ml) dose of interferon β-1a was subcutaneously injected three times weekly for two consecutive weeks. The control group consisted of 39 patients who received only the national protocol medications. The primary outcome of the study was time to reach clinical response. Secondary outcomes were duration of hospital stay, length of intensive care unit stay, 28-day mortality, effect of early or late administration of IFN on mortality, adverse effects, and complications during the hospitalization. Between 29 February and 3 April 2020, 92 patients were recruited, and a total of 42 patients in the IFN group and 39 patients in the control group completed the study. As the primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 ± 5.8 versus 8.3 ± 4.9 days, respectively, P = 0.95). On day 14, 66.7% versus 43.6% of patients in the IFN group and the control group, respectively, were discharged (odds ratio [OR], 2.5; 95% confidence interval [CI], 1.05 to 6.37). The 28-day overall mortality was significantly lower in the IFN than the control group (19% versus 43.6%, respectively, P = 0.015). Early administration significantly reduced mortality (OR, 13.5; 95% CI, 1.5 to 118). Although IFN did not change the time to reach the clinical response, adding it to the national protocol significantly increased discharge rate on day 14 and decreased 28-day mortality. (This study is in the Iranian Registry of Clinical Trials under identifier IRCT20100228003449N28.) url: https://doi.org/10.1128/aac.01061-20 doi: 10.1128/aac.01061-20 id: cord-258152-3udtsvga author: Dawood, Ali Adel title: Tunicamycin, an anticancer drug and inhibitor of N- linked glycosylation proteins is reliable to treat COVID-19 date: 2020-10-20 words: 2965.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-258152-3udtsvga.txt txt: ./txt/cord-258152-3udtsvga.txt summary: The glycans in some proteins play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. SARS-CoV is one of the viruses contain N-linked glycoproteins which are glycosylated by the transfer of core oligosaccharides from a dolichol pyrophosphate carrier to asparagine residues on the polypeptide [2] . Furthermore, HE protein of MHV was found to be modified by N-linked glycosylation and was inhibited by tunicamycin but not monensin. The inhibition Nlinked glycosylation of SARS-CoV 8ab protein by tunicamycin is not completely understood [33, 34] . HE and 8ab proteins of SARS-CoV glycosylation are inhibited by tunicamycin. Since tunicamycin has long been used as an anti-cancer and can inhibit glycoproteins of coronaviruses, we recommend using this drug to treat the SARS-CoV-2. abstract: SARS-CoV-2 outbreaks remains a medical and economic challenge, due to the lack of a suitable drug or vaccine. The glycans in some proteins play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. Tunicamycin and anticancer drug inhibit the N- linked glycans. Our study aimed to find out the mechanism action of tunicamycin on the viral glycoproteins. The growth of coronavirus in the presence inhibitor tunicamycin resulted in the production of spikeless, non-infectious virions which were devoid of S protein. We concluded that tunicamycin inhibits E2, S, and M glycoproteins of coronaviruses. Tunicamycin is also diminished glycosylation od PTMs such as HE, and 8 ab of SARS-CoV. Finally, we recommend using this drug to treat the SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0882401020309529 doi: 10.1016/j.micpath.2020.104586 id: cord-355899-wd00f8cw author: Dawson, E. D. title: Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses date: 2020-09-04 words: 5841.0 sentences: 294.0 pages: flesch: 48.0 cache: ./cache/cord-355899-wd00f8cw.txt txt: ./txt/cord-355899-wd00f8cw.txt summary: This study reports on the VaxArray CoV SeroAssay linear dynamic range, limit of detection, specificity, reproducibility, accuracy, and investigates assay performance on a retrospective set of 263 blinded, de-identified human serum and plasma specimens to demonstrate positive and negative percent agreement to a mixed reference method of RT-PCR on a patient-matched specimen and collection date prior to the COVID-19 outbreak. A total of 132 serum samples known to be negative for the presence of antibodies to SARS-CoV-2 based on date of collection prior to December 2019, including 33 specimens from pediatric donors age 2-16, were analyzed via the standard VaxArray CoV SeroAssay procedure at a 1:100 dilution in PBB. To assess reproducibility and accuracy, a pooled human serum sample positive for antibodies to SARS-CoV-2, and also known to be reactive to the SARS antigen and the 4 endemic Table 3 shows the % CV in the back-calculated concentration value obtained on each relevant capture antigen for all 216 replicate measurements over all 3 days and all three lots of slides, with values ranging from 7 to 19 %CV for the 9 antigens. abstract: Rapid, sensitive, and precise multiplexed assays for serological analysis during candidate COVID-19 vaccine development would streamline clinical trials. The VaxArray Coronavirus (CoV) SeroAssay quantifies IgG antibody binding to 9 pandemic, potentially pandemic, and endemic human CoV spike antigens in 2 hours with automated results analysis. IgG antibodies in serum bind to the CoV spike protein capture antigens printed in a microarray format and are labeled with a fluorescent anti-species IgG secondary label. The assay demonstrated excellent lower limits of quantification ranging from 0.3 to 2.0 ng/mL and linear dynamic ranges of 76 to 911-fold. Average precision of 11% CV and accuracy (% recovery) of 92.5% over all capture antigens were achieved over 216 replicates representing 3 days and 3 microarray lots. Clinical performance on 263 human serum samples (132 SARS-CoV-2 negatives and 131 positives based on donor-matched RT-PCR and/or date of collection) produced 98.5% PPA (sensitivity) and 100% NPA (specificity). url: http://medrxiv.org/cgi/content/short/2020.09.03.20179598v1?rss=1 doi: 10.1101/2020.09.03.20179598 id: cord-325609-n6dpac6i author: Dawson, Kathryn L. title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 - single center experience. date: 2020-06-13 words: 1512.0 sentences: 79.0 pages: flesch: 49.0 cache: ./cache/cord-325609-n6dpac6i.txt txt: ./txt/cord-325609-n6dpac6i.txt summary: title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 single center experience. Over the 12-month period preceding the SARS-CoV-2 related stay-at-home order, a total of 4 patients followed by the ACHD service at the University of Washington Medical Center with defects of various severities died in an acute setting. We believe that this change in emergency department volume, combined with the acute increase in mortality reported in this case series, emphasizes the potential adverse outcomes of delayed presentations in medically complex patients. These cases highlight the need for public education regarding the imperative to present for medical care when symptoms would have merited emergency treatment prior to the pandemic, particularly amongst our most vulnerable populations. It also highlights the need for routine follow-up care for patients with congenital heart disease, even in the presence of clinical stability, to assess for subclinical symptom burdens that may herald future acute presentations. abstract: Abstract Fear of acquiring severe acute respiratory syndrome coronavirus 2 infection is a major contributor to under-utilization of the healthcare system during the current pandemic. In this report, we describe 4 cases of unexpected deaths that occurred within a short time period in adult congenital heart disease patients without warning symptoms. url: https://doi.org/10.1016/j.jaccas.2020.06.013 doi: 10.1016/j.jaccas.2020.06.013 id: cord-266695-ktbgm0p9 author: Dawson, Liza title: SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date: 2020-06-04 words: 1452.0 sentences: 109.0 pages: flesch: 50.0 cache: ./cache/cord-266695-ktbgm0p9.txt txt: ./txt/cord-266695-ktbgm0p9.txt summary: have recently argued that researchers should consider conducting SARS-CoV-2 human challenge studies to hasten vaccine development [1] . However, we disagree that SARS-CoV-2 challenge studies are ethically appropriate at this time, for three reasons: 1) current scientific knowledge of SARS-CoV-2 infection is insufficient to manage risks; 2) autonomous decision-making, while necessary, does not override concerns about risk; and 3) undertaking challenge studies now would imperil confidence in the research enterprise, potentially undermining the global response to the COVID-19 pandemic. Current scientific knowledge is insufficient to manage the risks of severe disease or death of volunteers in SARS-CoV-2 human challenge studies, especially in terms of selecting low risk volunteers [2] . It is not obvious that the possible benefits of developing a successful vaccine in less time justify the risks SARS-CoV-2 challenge studies, as Eyal and colleagues suggest. However, conducting SARS-CoV-2 human challenge trials now unjustifiably threatens both the well-being of volunteers and confidence in the research enterprise. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32496536/ doi: 10.1093/infdis/jiaa314 id: cord-020769-elzkwyz0 author: Day, Brennan title: The new normal: lessons learned from SARS for corporations operating in emerging markets date: 2004-07-01 words: 6422.0 sentences: 312.0 pages: flesch: 55.0 cache: ./cache/cord-020769-elzkwyz0.txt txt: ./txt/cord-020769-elzkwyz0.txt summary: This paper uses the recent SARS epidemic as a background to highlight the importance of crisis planning, particularly in emerging economies, and suggests how organizations can address these concerns. This paper will start by presenting background information on the SARS epidemic and the impact on organizations, especially those operating in emerging markets. Since emerging markets are increasingly important to the world economy and are at the same time susceptible to outbreaks of infectious diseases, we need to understand how we are linked together on an interdependent global level. If just three of the Asian emerging economies -China, India, and Indonesia -are able to maintain this growth rate of 6 percent per year, the Organisation for Economic Co-operation and Development (OECD) has estimated that by 2010 approximately 700 million people in those countries will have an average income equivalent to that of Spain today. abstract: The modern industrialized world was completely caught off guard by the recent SARS outbreak. Fortunately, for most organizations, the impact has been short lived, but management has been provided with a reminder of the impact of the external environment in a world of ever increasing globalization. As seen with the SARS outbreak, a lack of preparedness can have devastating effects on business and warrant inclusion in a business definition of a crisis. This paper uses the recent SARS epidemic as a background to highlight the importance of crisis planning, particularly in emerging economies, and suggests how organizations can address these concerns. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147509/ doi: 10.1108/00251740410542357 id: cord-291393-iht5zndl author: De Angelis, Giulia title: Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features date: 2020-10-19 words: 2704.0 sentences: 133.0 pages: flesch: 47.0 cache: ./cache/cord-291393-iht5zndl.txt txt: ./txt/cord-291393-iht5zndl.txt summary: METHODS: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Because of substantial pneumonia-related morbidity and mortality [3] , testing for SARS-CoV-2 infection of patients who meet the suspected-case definition for COVID-19 [4] is central for their management. We comparatively explored the clinical features of 165 patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia admitted to COVID-19 wards of the Fondazione Policlinico A. We tested the hypothesis that negative patients did not differ from SARS-CoV-2 RNA positive patients by comparing features of 165 cases with clinically diagnosed 2019-nCoV pneumonia in our hospital. abstract: BACKGROUND: Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel etiologic agent of viral pneumonia. We aimed to compare clinical features of 165 Italian patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia. METHODS: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Before admission to a hospital ward, patients underwent RT-PCR based SARS-CoV-2 RNA detection in their nasopharyngeal swab samples. RESULTS: Of 165 patients studied, 119 had positive RT-PCR results and 46 were RT-PCR negative for 2 days or longer (i.e., when the last swab sample was obtained). The median age was 70 years (IQR, 58–78), and 123 (74.6%) of 165 patients had at least one comorbidity. The majority of patients (101/165, 61.2%) had a mild pneumonia, and the remaining patients (64/165, 38.8%) a severe/critical pneumonia. We did not find any substantial difference in symptoms, incubation periods, and radiographic/CT abnormalities as well as in many of the biological abnormalities recorded. However, at multivariable analysis, higher concentrations of hemoglobin (OR, 1.34; 95% CI, 1.11–1.65; P = 0.003) and lower counts of leukocytes (OR, 0.81; 95% CI, 0.72–0.90; P < 0.001) were statistically associated with confirmed COVID-19 diagnosis. While mortality rates were similar, patients with confirmed diagnosis were more likely to receive antivirals (95% vs 19.6%, P < 0.001) and to develop ARDS (63% vs 37%, P = 0.003) than those with unconfirmed COVID-19 diagnosis. CONCLUSIONS: Our findings suggest that unconfirmed 2019-nCoV pneumonia cases may be actually COVID-19 cases and that clinicians should be cautious when managing patients with presentations compatible with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33076874/ doi: 10.1186/s12879-020-05504-7 id: cord-344382-vge4ho2v author: De Flora, Silvio title: Rationale for the use of N‐acetylcysteine in both prevention and adjuvant therapy of COVID‐19 date: 2020-08-11 words: 4995.0 sentences: 271.0 pages: flesch: 41.0 cache: ./cache/cord-344382-vge4ho2v.txt txt: ./txt/cord-344382-vge4ho2v.txt summary: 5 Elderly individuals maintain a chronic low level of inflammation that is associated with oxidative stress and inflammatory cytokine production, a condition that increases the severity of viral infections in this population and that could be attenuated by administration of antioxidants. 36 A randomized, double-blind, placebo-controlled, prospective clinical trial in 5 ICUs in the USA and Canada showed that the intravenous administration of NAC (70 mg/ kg body weight), every 8 hours for 10 days, effectively repleted GSH in red blood cells, decreased the number of days of acute lung injury, and significantly increased the cardiac index. 50 NAC inhibited the pulmonary inflammation and edema as well as myeloperoxidase (MPO) activity, total cells, neutrophils, macrophages, TNF-α, IL-6, IL-1β, and chemokine (C-X-C motif) ligand-10 (CXCL-10) in the bronchoalveolar lavage fluid and reduced the levels of toll-like receptor 4 (TLR4) protein and mRNA in the lungs of BALB/c mice inoculated intranasally with A/swine/HeBei/012/2008/ H9N2 influenza virus. abstract: COVID‐19 may cause pneumonia, acute respiratory distress syndrome, cardiovascular alterations, and multiple organ failure, which have been ascribed to a cytokine storm, a systemic inflammatory response, and an attack by the immune system. Moreover, an oxidative stress imbalance has been demonstrated to occur in COVID‐19 patients. N‐ Acetyl‐L‐cysteine (NAC) is a precursor of reduced glutathione (GSH). Due to its tolerability, this pleiotropic drug has been proposed not only as a mucolytic agent, but also as a preventive/therapeutic agent in a variety of disorders involving GSH depletion and oxidative stress. At very high doses, NAC is also used as an antidote against paracetamol intoxication. Thiols block the angiotensin‐converting enzyme 2 thereby hampering penetration of SARS‐CoV‐2 into cells. Based on a broad range of antioxidant and anti‐inflammatory mechanisms, which are herein reviewed, the oral administration of NAC is likely to attenuate the risk of developing COVID‐19, as it was previously demonstrated for influenza and influenza‐like illnesses. Moreover, high‐dose intravenous NAC may be expected to play an adjuvant role in the treatment of severe COVID‐19 cases and in the control of its lethal complications, also including pulmonary and cardiovascular adverse events. url: https://doi.org/10.1096/fj.202001807 doi: 10.1096/fj.202001807 id: cord-351092-b01o6f69 author: De Francesco, Maria A. title: Pneumocystis jirevocii and SARS-CoV-2 Co-Infection: A Common Feature in Transplant Recipients? date: 2020-09-18 words: 2229.0 sentences: 126.0 pages: flesch: 39.0 cache: ./cache/cord-351092-b01o6f69.txt txt: ./txt/cord-351092-b01o6f69.txt summary: Here we describe, for the first time in Europe, a fatal case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii in a kidney transplant recipient. Pneumocystis jirevocii pneumonia is an opportunistic infection affecting patients with cellular immunity defects due to human immunodeficiency virus (HIV) infections or iatrogenic immunosuppression [15, 16] . Here, we report the fatal case of a SARS-CoV-2 and Pneumocystis jirevocii co-infection in a kidney transplant recipient. This is, to the best of our knowledge, the first case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii reported in Europe in a kidney transplant recipient. Pneumocystis jirevocii pneumonia in immunocompromised patients: Delayed diagnosis and poor outcomes in non-HIV infected individuals Acute respiratory failure due to Pneumocystis pneumonia in patients without human immunodeficiency virus infection: Outcome and associated features Critical care management and outcome of severe Pneumocystis pneumonia in patients with and without HIV infection abstract: COVID-19 might potentially give rise to a more severe infection in solid organ transplant recipients due to their chronic immunosuppression. These patients are at a higher risk of developing concurrent or secondary bacterial and fungal infections. Co-infections can increase systemic inflammation influencing the prognosis and the severity of the disease, and can in turn lead to an increased need of mechanical ventilation, antibiotic therapy and to a higher mortality. Here we describe, for the first time in Europe, a fatal case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii in a kidney transplant recipient. url: https://www.ncbi.nlm.nih.gov/pubmed/32962148/ doi: 10.3390/vaccines8030544 id: cord-278129-bpuyrsza author: De Haan, Cornelis A. M. title: Hosting the severe acute respiratory syndrome coronavirus: specific cell factors required for infection date: 2006-06-27 words: 4481.0 sentences: 216.0 pages: flesch: 47.0 cache: ./cache/cord-278129-bpuyrsza.txt txt: ./txt/cord-278129-bpuyrsza.txt summary: As with all viruses, the severe acute respiratory syndrome coronavirus (SARS‐CoV) utilizes specific host cell factors during its infection cycle. In this short review we focus on the severe acute respiratory syndrome coronavirus (SARS-CoV) describing what is currently known of the cell''s contributions during the successive phases of the infection cycle, i.e. entry, replication and assembly (Fig. 1) . Amino acids 270-510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensinconverting enzyme 2 Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry abstract: As with all viruses, the severe acute respiratory syndrome coronavirus (SARS‐CoV) utilizes specific host cell factors during its infection cycle. Some of these factors have been identified and are now increasingly scrutinized as targets to intervene with infection. In this brief review, we describe the current understanding of how the SARS‐CoV is able to use the cellular machinery for its replication. url: https://www.ncbi.nlm.nih.gov/pubmed/16803585/ doi: 10.1111/j.1462-5822.2006.00744.x id: cord-353237-rob4ems7 author: De Maio, Antonio title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? date: 2020-05-18 words: 2861.0 sentences: 148.0 pages: flesch: 43.0 cache: ./cache/cord-353237-rob4ems7.txt txt: ./txt/cord-353237-rob4ems7.txt summary: title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? The virus has been detected in the lungs and immune cells of patients who have succumbed to the infection, consistent with direct injury to the pulmonary tissue and activation of the immune response. Experimental animal studies about the response to sepsis have suggested that early interventions are critical to ameliorate the condition, such as source control of the infection or injury (Cauvi et al. In this regard, hyperbaric oxygen therapy (HBOT) that consists of exposure to 100% oxygen under increased atmospheric pressure up to 2.4 atm could be a great resource to improve the outcome from the infection when it is administered at early stages as soon as a reduction of arterial oxygen concentration is detected. Indeed, experimental animal studies have shown that an initial HBOT improved dramatically the outcome from sepsis, which was correlated with a reduction of the inflammatory response triggered by the initial insult (Halbach et al. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32424591/ doi: 10.1007/s12192-020-01121-0 id: cord-298482-r7lallv0 author: De Maio, Flavio title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis date: 2020-09-04 words: 1739.0 sentences: 86.0 pages: flesch: 54.0 cache: ./cache/cord-298482-r7lallv0.txt txt: ./txt/cord-298482-r7lallv0.txt summary: title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. The amino acid sequence of the SARS-CoV-2 Envelope protein was extracted, and the NMR structure of the 119 homologous protein of SARS-CoV (PDB code: 2MM4) was used as a template. In Figure 1B and 1C, the two predicted monomeric E full length protein structure models have been 159 constructed and show N-terminal (blue), transmembrane (green), C-terminal domains (red) as well as the 160 amino acid variants (yellow). In order to verify the potential implications of the altered amino acid sequence, the binding pose of the two 174 C-terminus octapeptides belonging to SARS-CoV and SARS-CoV-2 were determined and compared with 175 the crystallographic structure of the complex PALS1-CRB1[31]. abstract: The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations. url: https://doi.org/10.1016/j.micinf.2020.08.006 doi: 10.1016/j.micinf.2020.08.006 id: cord-349311-yo4up42r author: De Maria, Andrea title: High prevalence of olfactory and taste disorder during SARS‐CoV‐2 infection in outpatients date: 2020-05-17 words: 741.0 sentences: 47.0 pages: flesch: 46.0 cache: ./cache/cord-349311-yo4up42r.txt txt: ./txt/cord-349311-yo4up42r.txt summary: Here we comment on Sun and coll Metaanlysis with particular nuance to olfactory and taste disorders that very often herald SARS-CoV-2 in our country, particularly in outpatients, and are not reported so far in the medical literature from China. Limited or no information has been so far gathered on the majority of milder cases of SARS-CoV-2-disease that are cared for at home since they are not progressing to respiratory insufficiency and hospitalization/ventilation. In addition, profound olfactory and taste disorder (OTD), that has been reported to be frequent in hospitalized patients in Italy, 7 is not reported in China or other areas, 2,3,5 and correspondingly fails to be reported in the meta-analysis. Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: a single arm metaanalysis Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study abstract: Prevalent symptoms of SARS-CoV-2 in reports and metaanalyses refer to cough, fatigue, myalgia and respiratory distress. These represent clinically acknowledged relevant findings of valuable importance, particularly with the requirement for ventilation and hospital bed occupancy in ICUs. There is however a wide discordance with the actual picture of clinical presentation and symptoms in Italy. Here we comment on Sun and coll Metaanlysis with particular nuance to olfactory and taste disorders that very often herald SARS-CoV-2 in our country, particularly in outpatients, and are not reported so far in the medical literature from China. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32383174/ doi: 10.1002/jmv.25995 id: cord-338225-8dlxnpcn author: De Meyer, Sandra title: Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date: 2020-05-29 words: 329.0 sentences: 27.0 pages: flesch: 60.0 cache: ./cache/cord-338225-8dlxnpcn.txt txt: ./txt/cord-338225-8dlxnpcn.txt summary: Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. abstract: Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. There are currently no definitive data on the safety and efficacy of DRV/cobicistat for treatment of COVID-19. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Remdesivir, used as a positive control, showed potent antiviral activity (EC50 =0.38μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32479865/ doi: 10.1016/j.ijid.2020.05.085 id: cord-332150-j76726no author: De Stefano, Ludovico title: A “Window of Therapeutic Opportunity” for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019 date: 2020-10-06 words: 3616.0 sentences: 166.0 pages: flesch: 28.0 cache: ./cache/cord-332150-j76726no.txt txt: ./txt/cord-332150-j76726no.txt summary: The main challenge for effective administration of anti-cytokine therapy in COVID-19 will be therefore to better define a precise "window of therapeutic opportunity." Only considering a more specific set of criteria able to integrate information on direct viral damage, the cytokine burden, and the patient''s immune vulnerability, it will be possible to decide, carefully balancing both benefits and risks, the appropriateness of using immunosuppressive drugs even in patients affected primarily by an infectious disease. Discovery of virus and host genomic factors will undoubtedly support risk stratification and targeted treatment; however, as genomic studies require long times before entering clinical practice, it is urgent to integrate easily accessible information on the dynamics and pathogenicity of the immune response during the different phases of SARS-CoV-2 infection. Accordingly, longitudinal immune profiling of hospitalized COVID-19 cases with different outcomes has recently shown that, despite similar levels of inflammatory cytokines in the first 10 days from symptom onset, patients with less severe disease evolution also express mediators of wound healing and tissue repair (41) . abstract: The effects of cytokine inhibition in the different phases of the severe coronavirus disease 2019 (COVID-19) are currently at the center of intense debate, and preliminary results from observational studies and case reports offer conflicting results thus far. The identification of the correct timing of administration of anti-cytokine therapies and other immunosuppressants in COVID-19 should take into account the intricate relationship between the viral burden, the hyperactivation of the innate immune system and the adaptive immune dysfunction. The main challenge for effective administration of anti-cytokine therapy in COVID-19 will be therefore to better define a precise “window of therapeutic opportunity.” Only considering a more specific set of criteria able to integrate information on direct viral damage, the cytokine burden, and the patient’s immune vulnerability, it will be possible to decide, carefully balancing both benefits and risks, the appropriateness of using immunosuppressive drugs even in patients affected primarily by an infectious disease. url: https://doi.org/10.3389/fimmu.2020.572635 doi: 10.3389/fimmu.2020.572635 id: cord-290677-3gdcyrrz author: De Virgiliis, Francesco title: Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19 date: 2020-08-25 words: 6108.0 sentences: 278.0 pages: flesch: 34.0 cache: ./cache/cord-290677-3gdcyrrz.txt txt: ./txt/cord-290677-3gdcyrrz.txt summary: In line with these findings, virus-induced airway hyperresponsiveness in humans seems to be mediated by the vagus nerve 53 , raising the possibility that the dyspnoea and respiratory failure observed in patients with severe COVID-19 is exacerbated by neuroimmune crosstalk in the lungs. A plausible hypothesis is that these NAMs act in concert with neuronal cells to control inflammation, and that malfunctioning of this system in older or immunocompromised people could contribute to the cytokine storm and ARDS in patients with severe COVID-19 or other respiratory virus infections. In the context of SARS-CoV-2 infection, specific tissueresident macrophages that are involved in modulating inflammation following viral infection are in close contact with vagal fibres innervating the lungs, and this ''neuroimmune synapse'' could be one of the keys to controlling aberrant inflammation in patients with severe COVID-19. abstract: COVID-19 is an infectious disease caused by the coronavirus SARS-CoV-2, which was first reported in Wuhan, China, in December 2019 and has caused a global pandemic. Acute respiratory distress syndrome (ARDS) is a common feature of severe forms of COVID-19 and can lead to respiratory failure, especially in older individuals. The increasing recognition of the neurotropic potential of SARS-CoV-2 has sparked interest in the role of the nervous system in respiratory failure in people with COVID-19. However, the neuroimmune interactions in the lung in the context of ARDS are poorly understood. In this Perspectives article, we propose the concept of the neuroimmune unit as a critical determinant of lung function in the context of COVID-19, inflammatory conditions and ageing, focusing particularly on the involvement of the vagus nerve. We discuss approaches such as neurostimulation and pharmacological neuromodulation to reduce tissue inflammation with the aim of preventing respiratory failure. url: https://www.ncbi.nlm.nih.gov/pubmed/32843733/ doi: 10.1038/s41582-020-0402-y id: cord-313756-2pqpk3v7 author: De Vriese, An S. title: In Reply to ‘Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?’ date: 2020-06-27 words: 292.0 sentences: 25.0 pages: flesch: 54.0 cache: ./cache/cord-313756-2pqpk3v7.txt txt: ./txt/cord-313756-2pqpk3v7.txt summary: key: cord-313756-2pqpk3v7 title: In Reply to ''Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?'' cord_uid: 2pqpk3v7 In a small group of hemodialysis patients with confirmed SARS-CoV-2 infection, we reported that the presence of anti-SARS-CoV-2 IgG overlaps by several weeks with detectable viral RNA in the upper airways (1) . Viral load was highest during the first week of illness, suggesting that patients are most infectious during this period. It remains unclear whether the lower viral loads during the following weeks associate with a clinically relevant transmissibility of SARS-CoV-2 requiring further quarantining. We measured anti-SARS-CoV-2 IgG with a N protein-based ELISA (NovaLisa, NovaTec). Dudreuilh and Moutzouris suggest that the combination with a S protein-based assay may provide additional information. IgG Antibody Response to SARS-CoV-2 Infection and Viral RNA Persistence in Patients on Maintenance Hemodialysis Clinical performance of different SARS-CoV-2 IgG antibody tests abstract: nan url: https://doi.org/10.1053/j.ajkd.2020.06.005 doi: 10.1053/j.ajkd.2020.06.005 id: cord-305564-dj3vj4tk author: DeDiego, Marta L. title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date: 2008-07-01 words: 6065.0 sentences: 287.0 pages: flesch: 53.0 cache: ./cache/cord-305564-dj3vj4tk.txt txt: ./txt/cord-305564-dj3vj4tk.txt summary: All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR abstract: Recombinant severe acute respiratory virus (SARS-CoV) variants lacking the group specific genes 6, 7a, 7b, 8a, 8b and 9b (rSARS-CoV-Δ[6-9b]), the structural gene E (rSARS-CoV-ΔE), and a combination of both sets of genes (rSARS-CoV-Δ[E,6-9b]) have been generated. All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. Furthermore, in Vero E6 cells, all the viruses showed the formation of particles with the same morphology as the wt virus, indicating that these proteins do not have a high impact in the final morphology of the virions. Nevertheless, in the absence of E protein, release of virus particles efficacy was reduced. Viruses lacking E protein grew about 100-fold lower than the wt virus in lungs of Tg infected mice but did not grow in the brains of the same animals, in contrast to the rSARS-CoV-Δ[6-9b] virus, which grew almost as well as the wt in both tissues. Viruses lacking E protein were highly attenuated in the highly sensitive hACE-2 Tg mice, in contrast to the minimal rSARS-CoV-Δ[6-9b] and wt viruses. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. url: https://doi.org/10.1016/j.virol.2008.03.005 doi: 10.1016/j.virol.2008.03.005 id: cord-342220-lrqt2gcw author: Dearlove, Bethany title: A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants date: 2020-09-22 words: 7874.0 sentences: 415.0 pages: flesch: 49.0 cache: ./cache/cord-342220-lrqt2gcw.txt txt: ./txt/cord-342220-lrqt2gcw.txt summary: Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute While the evolutionary rate is likely to decrease over time (18) , it is important to monitor the introduction of any mutation that may compromise the potential efficacy of vaccine candidates derived from the first available SARS-CoV-2 sequences. In S, only site 614 was estimated to be under diversifying selection in a majority of subsampled alignments (58%); evidence of diversifying selection indicates that genetic diversity increases in the viral population (i.e., there was a higher proportion of mutations causing an amino acid change than not at site 614, or, the nonsynonymous/synonymous substitution rates ratio, dN/dS, was over 1, P < 0.1) (SI Appendix, Fig. S4 ). abstract: The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages. url: https://doi.org/10.1073/pnas.2008281117 doi: 10.1073/pnas.2008281117 id: cord-261110-cnj0e0s9 author: Debarnot, Claire title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date: 2011-02-25 words: 2656.0 sentences: 169.0 pages: flesch: 64.0 cache: ./cache/cord-261110-cnj0e0s9.txt txt: ./txt/cord-261110-cnj0e0s9.txt summary: This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. We present X-ray diffraction data from these SARS-CoV nsp10-nsp16 crystals. The purified SARS-CoV nsp10-nsp16 complex was analyzed by 12% SDS-PAGE and stained using Coomassie Blue. Lane MK, molecular-weight markers; lane 1, 2 mg nsp10-nsp16 protein complex eluted from the Strep-Tactin column. The nsp10-nsp16 complex eluted from the Strep-Tactin column was analyzed on a 16/60 S200 gel-filtration column and the elution of protein and nucleic acid was followed by measuring the absorption at 280 nm (blue) and 260 nm (orange), respectively. The purified SARS-CoV nsp10-nsp16 complex was loaded onto a 4-12% NuPAGE gel and stained using Coomassie Blue. We have crystallized a complex of the SARS-CoV nsp10 and nsp16 proteins. abstract: To date, the SARS coronavirus is the only known highly pathogenic human coronavirus. In 2003, it was responsible for a large outbreak associated with a 10% fatality rate. This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. The crystal structure of nsp16 is unknown. Nsp16 is an RNA-cap AdoMet-dependent (nucleoside-2′-O-)-methyltransferase that is only active in the presence of nsp10. In this paper, the expression, purification and crystallization of nsp10 in complex with nsp16 are reported. The crystals diffracted to a resolution of 1.9 Å resolution and crystal structure determination is in progress. url: http://journals.iucr.org/f/issues/2011/03/00/nj5077/nj5077.pdf doi: 10.1107/s1744309111002867 id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 words: 14927.0 sentences: 720.0 pages: flesch: 49.0 cache: ./cache/cord-324324-8ybfiz8f.txt txt: ./txt/cord-324324-8ybfiz8f.txt summary: In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. abstract: The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S0378113520302935 doi: 10.1016/j.vetmic.2020.108693 id: cord-312036-5867bc6i author: Decker, Annegrit title: Prolonged SARS‐CoV‐2 shedding and mild course of COVID‐19 in a patient after recent heart transplantation date: 2020-06-09 words: 1943.0 sentences: 142.0 pages: flesch: 49.0 cache: ./cache/cord-312036-5867bc6i.txt txt: ./txt/cord-312036-5867bc6i.txt summary: Here, we present a 62‐year old male COVID‐19 patient with recent heart transplantation who developed only mild symptoms, but had prolonged virus shedding, and summarize the available data on COVID‐19 in cardiac allograft recipients. [5] [6] [7] Here, we report a mild course of SARS-CoV-2 infection with prolonged virus persistence in a patient only five months after heart transplantation. In fact, in 71.8 % of patients with COVID-19 after heart transplant, immunosuppressive agents have been (partially) discontinued or reduced in dose (Table 1) , thus potentially increasing the risk of organ rejection. 19 In our case, continuation of the immunosuppressant regime was associated with a mild course of COVID-19, though we observed a transient increase in CRP and IL-6. Although the cardiovascular system seems to be a critical target site of SARS-CoV-2 infection, a mild course of COVID-19 is possible even in a high-risk patient after recent heart transplantation. abstract: In the coronavirus disease 2019 (COVID‐19) pandemic, organ transplant recipients are considered to be at high risk for unfavorable outcome. However, in particular the role of immunosuppression in patients infected with SARS‐CoV‐2 remains undetermined. Here, we present a 62‐year old male COVID‐19 patient with recent heart transplantation who developed only mild symptoms, but had prolonged virus shedding, and summarize the available data on COVID‐19 in cardiac allograft recipients. Initially the patient presented with a transient episode of fever and sore throat but no other symptoms, in particular no cough or dyspnea at rest. After diagnosis, immunosuppression was continued unchanged. On day 7, temperature increased again with concurrent mild rise of CRP, IL‐6 and proBNP levels. Hydroxychloroquine was started and continued for 7 days. While the patient had no clinical symptoms anymore 20 days after initial presentation, virus culture of throat swabs on days 18 and 21 confirmed active virus replication and SARS‐CoV‐2 PCR remained positive on day 35 with copy numbers similar to the onset of infection. In conclusion, immunosuppression regimen in transplant recipients with mild COVID‐19 associated symptoms may be continued unchanged. However, it may contribute to delayed virus PCR conversion and thus possible prolonged infectivity. url: https://www.ncbi.nlm.nih.gov/pubmed/32519406/ doi: 10.1111/ajt.16133 id: cord-280958-36ytqapi author: Decker, Summer J title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 words: 3513.0 sentences: 266.0 pages: flesch: 63.0 cache: ./cache/cord-280958-36ytqapi.txt txt: ./txt/cord-280958-36ytqapi.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs. METHODS: We developed a 3D-printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (p=0.05 and p=0.05) as well as the NeuMoDx assay (p=0.401 and p=0.484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901). CONCLUSIONS: 3DP swabs were equivalent to standard FLNP in three testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. url: https://doi.org/10.1093/cid/ciaa1366 doi: 10.1093/cid/ciaa1366 id: cord-269526-3npk3u5t author: Dehghanbanadaki, Hojat title: Bibliometric analysis of global scientific research on Coronavirus (COVID-19) date: 2020-05-23 words: 3305.0 sentences: 174.0 pages: flesch: 52.0 cache: ./cache/cord-269526-3npk3u5t.txt txt: ./txt/cord-269526-3npk3u5t.txt summary: Methods: We extracted all COVID-19 documents indexed in the Scopus from December 1, 2019, to April 1, 2020, without any language limitation and determined their bibliometric characteristics, including document type, open accessibility status, citation counting, H-index, top cited documents, the most productive countries, institutions and journals, international collaboration, the most frequent terms and keywords, journal bibliographic coupling and cocitations. The most frequent terms were COVID (n = 983 repeats), patient (n = 741 repeats), SARS-CoV (n = 593 repeats), China (n = 497 repeats), case (n = 464 repeats), nCoV (n = 417 repeats), outbreak (n = 355 repeats), infection (n = 344 repeats), novel coronavirus (n = 324 repeats), Wuhan (n = 269 repeats), Coronavirus (n =243 repeats), virus (n = 204 repeats), pneumonia (n = 195 repeats), Coronavirus disease (n = 170 repeats), treatment (n = 162 repeats), transmission (n = 158 repeats), study (n = 156 repeats), data (n = 151 repeats), country (n = 137 repeats), and epidemic (n = 136 repeats). abstract: Background: Since the outbreak of the novel coronavirus disease from Wuhan, China, in early December 2019, many scientists focused on this infection to find a way to deal with it. Due to the dramatic scientific growth in this field, we conducted a scientometric study to gain a better understanding of the scientific literature on COVID-19. Methods: We extracted all COVID-19 documents indexed in the Scopus from December 1, 2019, to April 1, 2020, without any language limitation and determined their bibliometric characteristics, including document type, open accessibility status, citation counting, H-index, top cited documents, the most productive countries, institutions and journals, international collaboration, the most frequent terms and keywords, journal bibliographic coupling and cocitations. Results: A total of 923 documents on COVID-19 were retrieved, of which 418 were original articles. All documents had received 2551 citations with an average citation of 2.76 per document and an h-index of 23. China ranked first with 348 documents, followed by the United States (n = 160). The Lancet and BMJ Clinical Research Ed published the most documents (each with 74 documents) and 2 institutions (University of Hong Kong and Huazhong University of Science and Technology) ranked first in this regard. In addition, the present study analyzed the top 25 highly-cited documents (those that had received 70% of all citations). Conclusion: This study highlighted the focused subjects on various aspects of COVID-19 literature such as pathogenesis, epidemiology, transmission, diagnosis, treatment, prevention, and its complications. url: https://doi.org/10.34171/mjiri.34.51 doi: 10.34171/mjiri.34.51 id: cord-343415-lj2trn85 author: Del Barba, Paolo title: COVID‐19 cardiac involvement in a 38‐day old infant date: 2020-06-18 words: 996.0 sentences: 61.0 pages: flesch: 47.0 cache: ./cache/cord-343415-lj2trn85.txt txt: ./txt/cord-343415-lj2trn85.txt summary: We report the case of an infant who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and developed mild cardiovascular inflammation, a novelty for patients of very young age, that contributes to defining the puzzling nature of this disease in pediatric patients. 1 COVID-19 may indeed have cardiac complications, including myocarditis, 2 and up to 31% of children have myocardial enzyme elevation, mainly creatine kinase MB, despite no specific sign or symptom of clinical cardiac disease. For the first time, we report the case of an infant affected by COVID-19 with documented mild cardiac involvement. The chest computed tomograpghy scan was not performed, thus avoiding the exposure to Abbreviations: ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. We suggest that SARS-CoV-2 cardiac involvement should always be taken into account also in children; while our case was mild, it might be of concern especially in patients with other underlying conditions. abstract: The spectrum of clinical manifestations of coronavirus disease 2019 in children is yet to be fully elucidated. We report the case of an infant who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and developed mild cardiovascular inflammation, a novelty for patients of very young age, that contributes to defining the puzzling nature of this disease in pediatric patients. The potential cardiovascular involvement of SARS‐CoV‐2 in children should always be taken into account. url: https://www.ncbi.nlm.nih.gov/pubmed/32558285/ doi: 10.1002/ppul.24895 id: cord-274028-dvsvtsn0 author: Del Brutto, Oscar H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 words: 1217.0 sentences: 74.0 pages: flesch: 60.0 cache: ./cache/cord-274028-dvsvtsn0.txt txt: ./txt/cord-274028-dvsvtsn0.txt summary: Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . abstract: A sudden increase in adult mortality associated with respiratory diseases was noticed in Atahualpa (a rural Ecuadorian village), coinciding with the introduction of SARS-CoV-2 in the region. From a total of 1,852 individuals aged ≥18 years, 40 deaths occurred between January and June, 2020. In addition, a seroprevalence survey showed that 45% of the adult population have SARS-CoV-2 antibodies. Verbal autopsies revealed SARS-CoV-2 as the most likely cause of death in 29 cases. The mean age of suspected or confirmed SARS-CoV-2 cases was 76.9 ± 12.1 years, while that of those dying from unrelated causes was 60.3 ± 20.4 years (p = 0.003). The overall mortality rate was 21.6 per 1,000 population (95% C.I.: 15.9 – 29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 – 22.4). This configures a 266% of excess mortality when compared to 5.9 per 1,000 (95% C.I.: 3.3 – 10.6) deaths from other causes. When SARS-CoV-2 mortality rate was calculated in individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47.8 – 98.4). After peaking in April and May, mortality significantly decreased. It is possible that the high proportion of infected individuals and the resulting herd immunity contributed to the observed reduction in mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/32781165/ doi: 10.1016/j.ijid.2020.08.003 id: cord-325498-4yciuh1n author: Del Brutto, Oscar H. title: Incident SARS-CoV-2 Infection and a Shared Latrine date: 2020-07-22 words: 649.0 sentences: 38.0 pages: flesch: 55.0 cache: ./cache/cord-325498-4yciuh1n.txt txt: ./txt/cord-325498-4yciuh1n.txt summary: title: Incident SARS-CoV-2 Infection and a Shared Latrine Incident SARS-CoV-2 Infection and a Shared Latrine. In a recent serosurvey, we found that the use of open latrines (instead of flushing toilet systems) was significantly associated with seropositivity to SARS-CoV-2 on lateral flowbased antibody testing (BIOHIT Health Care Ltd., Cheshire, United Kingdom), suggesting a contributory role for fecal-oral transmission of the disease, as previously proposed by others. Here, we present a cluster of incident cases of SARS-CoV-2 involving a woman who lived alone (house A), and a five-member family (house B) who were seronegative during the first survey. Two weeks after our baseline serosurvey, a 22-year-old grandson of the old woman moved into Atahualpa from Guayaquil (a heavily infected urban center), staying at her house and using the shared latrine. There were no other incident cases in the entire block, where only one person in a distant house had tested positive at baseline, and several other inhabitants of other houses remained seronegative (Figure 2, left) . abstract: Incident SARS-CoV-2 Infection and a Shared Latrine. url: https://doi.org/10.4269/ajtmh.20-0793 doi: 10.4269/ajtmh.20-0793 id: cord-285168-qkadqohe author: Delatorre, Edson title: Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries date: 2020-04-23 words: 2551.0 sentences: 149.0 pages: flesch: 55.0 cache: ./cache/cord-285168-qkadqohe.txt txt: ./txt/cord-285168-qkadqohe.txt summary: Here, we estimate the probable onset date of the community spread of SARS-CoV-2 from the cumulative number of deaths reported during the early stage of the epidemic in Western Europe and the Americas. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analyzed between the middle of January and early February 2020, thus long before community transmission was officially recognized and control measures were implemented. In some countries (Italy and Netherlands) community transmission was traced long before (2-4 weeks) the first confirmed SARS-CoV-2 infection case; while in others (Spain, France, United Kingdom, Germany, and Belgium) the onset date roughly coincides with the time of detection of the first imported cases (Figure 1 ). That quite long period of cryptic community transmission (> 4 weeks) in all analyzed countries draws attention to the great challenge of tracking the early global spread of SARS-CoV-2 and supports that control measures should be adopted at least as soon as first imported cases are detected in a new geographic region. abstract: The SARS-CoV-2 rapidly spread around the world during 2020, but the precise time in which the virus began to spread locally is currently unknown for most countries. Here, we estimate the probable onset date of the community spread of SARS-CoV-2 from the cumulative number of deaths reported during the early stage of the epidemic in Western Europe and the Americas. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analyzed between the middle of January and early February 2020, thus long before community transmission was officially recognized and control measures were implemented. url: https://doi.org/10.1101/2020.04.20.20073007 doi: 10.1101/2020.04.20.20073007 id: cord-290056-x74cq2k5 author: Delgado-Roche, Livan title: Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection date: 2020-04-30 words: 1910.0 sentences: 103.0 pages: flesch: 43.0 cache: ./cache/cord-290056-x74cq2k5.txt txt: ./txt/cord-290056-x74cq2k5.txt summary: title: Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection Some authors suggest that the onset of severe lung injury in SARS-CoV infected patients depends on activation of the oxidative stress machinery that is coupled with innate immunity and activates transcription factors, such as NF-κB, resulting in an exacerbated proinflammatory host response (14) . Activation of the PI3K/Akt signaling pathway may lead to a delay in Oxidative stress -NF-kB -toll-like receptor (mainly TL4) signaling pathways, triggered by viral pathogens like SARS-CoV, may further amplify the host inflammatory response, ultimately leading to acute lung injury. In conclusion, literature evidence suggests that oxidative stress and chronic low-grade inflammation in the lungs are associated with aging and may contribute to age-related immune dysfunction and mortality risk in aged patients affected by respiratory virus infections, such as SARS-CoV-2. abstract: Abstract The emergence of viral respiratory pathogens with pandemic potential, such as severe acute respiratory syndrome coronavirus (SARS-CoV), the pathogenic agent of Covid-19, represent a serious health problem worldwide. Respiratory viral infections are, in general, associated with cytokine production, inflammation, cell death, and other pathophysiological processes, which could be link with a redox imbalance or oxidative stress. These phenomena are substantially increased during aging. Actually, severity and mortality risk of SARS-CoV-2 infection or Covid-19 disease have been associated with the age. The aim of the present work was to contribute with the understanding of the possible link between oxidative stress and the pathogenesis, severity and mortality risk in patients affected by SARS-CoV infection. url: https://api.elsevier.com/content/article/pii/S0188440920305403 doi: 10.1016/j.arcmed.2020.04.019 id: cord-302733-rfuyd041 author: Dellicour, Simon title: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date: 2020-10-21 words: 3727.0 sentences: 165.0 pages: flesch: 41.0 cache: ./cache/cord-302733-rfuyd041.txt txt: ./txt/cord-302733-rfuyd041.txt summary: At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. We generated a time-scaled phylogenetic tree using a rapid maximum likelihood approach 16 and subsequently ran a preliminary discrete phylogeographic analysis along this tree to identify internal nodes and descending clades that likely correspond to distinct introductions into the Belgian territory ( Fig. 1, S2 ). We used the continuous diffusion model 13 available in BEAST 1.10 14 to perform a spatially-explicit (or "continuous") phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. abstract: Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement. url: https://doi.org/10.1101/2020.05.05.078758 doi: 10.1101/2020.05.05.078758 id: cord-262911-e9z00y3b author: Delpino, M. Victoria title: SARS-CoV-2 Pathogenesis: Imbalance in the Renin-Angiotensin System Favors Lung Fibrosis date: 2020-06-12 words: 2806.0 sentences: 132.0 pages: flesch: 38.0 cache: ./cache/cord-262911-e9z00y3b.txt txt: ./txt/cord-262911-e9z00y3b.txt summary: In addition to its functions in regulating blood pressure, AngII plays a pivotal role in signaling cellular and molecular events that are considered critical in the pathogenesis of pulmonary fibrosis, such as: (i) inflammation (promoting production of proinflammatory cytokines such as IL-6, and IL-8 by macrophages), (ii) the production of reactive oxygen species (ROS) among infected-alveolar epithelial cells followed by its apoptosis, and (iii) the proliferation, migration, and differentiation of fibroblasts to myofibroblasts capable of synthesize smooth muscle alpha-actin (α-SMA) and produce extracellular matrix (collagen and fibronectin) through a mechanism mediated by autocratic trans-activation of TGF-β in the fibroblast itself (Wolf et al., 1992; Kagami et al., 1994; Jia, 2016) . In contrast, the Ang1-7 peptide, after interacting with its cellular receptor Mas, exhibits the ability to inhibit proapoptotic signaling in alveolar epithelial cells, promote autophagy, andtogether with the ACE2 receptor-counteract the profibrotic effects, reducing both TGF-β mediated collagen expression, as well as the transition from fibroblasts to myofibroblasts (Iwata et al., 2005; Zeng et al., 2009; Zhou et al., 2016) . abstract: nan url: https://doi.org/10.3389/fcimb.2020.00340 doi: 10.3389/fcimb.2020.00340 id: cord-337220-yv7qdvzi author: Demeke, Addis title: Biosensor and molecular-based methods for the detection of human coronaviruses: A review date: 2020-09-08 words: 2215.0 sentences: 128.0 pages: flesch: 39.0 cache: ./cache/cord-337220-yv7qdvzi.txt txt: ./txt/cord-337220-yv7qdvzi.txt summary: This assay involves simultaneous 130 reverse transcription and isothermal amplification using loop-mediated amplification (RT-131 LAMP) for RNA, followed by Cas12 detection of predefined coronavirus sequences, after which 132 cleavage of a reporter molecule confirms detection of the E and N genes of SARS-CoV-2. Rapid lateral flow-based assays for anti-COVID-19 antibodies (IgM and IgG) are under 147 development which will play an important role in the epidemiological investigation of the 148 disease [9] . Therefore, the convalescent plasma has been used as 155 therapy for the treatment of critically ill COVID-19 patients [26, 27] The biosensor was developed by using a spike protein of SARS-CoV-2 immobilized onto the 237 FET graphene sheet (a two-dimensional sheet of hexagonal oriented carbon atom) with 1-pyrene 238 butyric acid N-hydroxy succinimide ester (PBASE) (Figure 1) . Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription 473 loop-mediated isothermal amplification assay abstract: The ongoing crisis due to the global pandemic caused by a highly contagious coronavirus (Coronavirus disease – 2019; COVID-19) and the lack of either proven effective therapy or a vaccine has made diagnostic a valuable tool in disease tracking and prevention. The complex nature of this newly emerging virus calls for scientists’ attention to find the most reliable, highly sensitive, and selective detection techniques for better control or spread of the disease. Reverse transcriptase-polymerase chain reaction (RT-PCR) and serology-based tests are currently being used. However, the speed and accuracy of these tests may not meet the current demand; thus, alternative technology platforms are being developed. Nano biosensor technology platforms have been established as a promising diagnostic tool for rapid and accurate detection of viruses as well as other life-threatening diseases even in resource-limited settings. This review aims to provide a short overview of recent advancements in molecular and biosensor-based diagnosis of viruses, including the human coronaviruses, and highlight the challenges and future perspectives of these detection technologies. url: https://doi.org/10.1016/j.mcp.2020.101662 doi: 10.1016/j.mcp.2020.101662 id: cord-196129-3zfeamgs author: Demertzis, Konstantinos title: Flattening the COVID-19 Curve: The"Greek"case in the Global Pandemic date: 2020-10-09 words: 5639.0 sentences: 238.0 pages: flesch: 46.0 cache: ./cache/cord-196129-3zfeamgs.txt txt: ./txt/cord-196129-3zfeamgs.txt summary: Focusing on the peculiarities of the disease spreading in Greece, both in epidemiological and in implementation terms, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. Within this context, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. This paper studied the COVID-19 temporal spread in Greece and proposed an innovative, realistic, and highly reliable methodology for forecasting the flattening of the curve, based on the spline and logistic regression algorithm, along with the complex network analysis. abstract: The global crisis caused by the COVID-19 pandemic, in conjunction with the economic consequences and the collapse of health systems, has raised serious concerns in Europe, which is the most affected continent by the pandemic since it recorded 2,388,694 cases and 190,091 deaths (39.6% of the worldwide total), of which 71.7% (136,238) are in the United Kingdom (43,414), Italy (34,708), France (29,778), and Spain (28,338). Unlike other countries, Greece, with about 310 confirmed cases and 18 deaths per million, is one bright exception in the study and analysis of this phenomenon. Focusing on the peculiarities of the disease spreading in Greece, both in epidemiological and in implementation terms, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. Also, it proposes a hybrid spline regression and complex network model of social distance measures evaluating and interpreting the spread of the disease. The overall approach contributes to decision making and support of the public health system and to the fight against the pandemic. url: https://arxiv.org/pdf/2010.12040v1.pdf doi: nan id: cord-311766-m9yv4qkm author: Demey, Baptiste title: Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date: 2020-05-07 words: 1754.0 sentences: 92.0 pages: flesch: 49.0 cache: ./cache/cord-311766-m9yv4qkm.txt txt: ./txt/cord-311766-m9yv4qkm.txt summary: Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection. abstract: In order to fight the SARS-CoV-2 pandemic infection, there is a growing need and demand for diagnostic tools that are complementary and different from the RT-PCR currently in use. Multiple serological tests are or will be very soon available but need to be evaluated and validated. We have thus tested 4 immunochromatographic tests for the detection of antibodies to SARS-CoV-2. In addition, we assessed the kinetics of antibody appearance using these assays in 22 patients after they were tested positive by RT-PCR. We observed great heterogeneity in antiboy detection post-symptom onset. The median antibody detection time was between 8 and 10 days according to the manufacturers. All the tests showed a sensitivity of 60 to 80% on day 10 and 100% on day 15. In addition, a single cross-reaction was observed with other human coronavirus infections. Thus, immunochromatographic tests for the detection of anti-SARS-CoV-2 antibodies may have their place for the diagnostic panel of COVID-19. url: https://api.elsevier.com/content/article/pii/S0163445320302449 doi: 10.1016/j.jinf.2020.04.033 id: cord-326718-jboiufoq author: Deming, Meagan E. title: COVID-19 and Lessons to Be Learned from Prior Coronavirus Outbreaks date: 2020-07-17 words: 2539.0 sentences: 121.0 pages: flesch: 41.0 cache: ./cache/cord-326718-jboiufoq.txt txt: ./txt/cord-326718-jboiufoq.txt summary: In addition, three novel CoVs have emerged as zoonotic human infections in the past 17 years; SARS-CoV, Middle East respiratory syndrome CoV (MERS-CoV), and the 2019 novel CoV (SARS-CoV-2) (2) have each been associated with lower respiratory symptoms, progressing in a subset of individuals to acute respiratory distress syndrome (ARDS) and death. Interestingly NL63, an hCoV that also uses angiotensin converting enzyme 2 as the host receptor, but typically causes mild upper respiratory disease, was the cause of a cluster of severe pediatric pneumonias in China in 2018, during which half of the patients were identified with viruses containing a specific substitution in the spike glycoprotein that enhanced binding to and entry via angiotensin converting enzyme 2 (4). It can be hypothesized that the spike glycoprotein of SARS-CoV-2, with its PERSPECTIVE structural similarity and higher affinity binding to angiotensin converting enzyme 2, provokes a similar mechanism of lung pathology leading to ARDS with severe COVID-19. abstract: nan url: https://doi.org/10.1513/annalsats.202002-149ps doi: 10.1513/annalsats.202002-149ps id: cord-336742-42ebj3gi author: Demmler, Gail J title: Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future date: 2003-07-31 words: 3156.0 sentences: 177.0 pages: flesch: 55.0 cache: ./cache/cord-336742-42ebj3gi.txt txt: ./txt/cord-336742-42ebj3gi.txt summary: The disease, severe acute respiratory syndrome (SARS), spread quickly and caused numerous deaths, as well as public panic. The first report of the new disease, given the name "severe acute respiratory syndrome" (SARS), was received by WHO on February 11 from the Chinese Ministry of Health, which documented that 305 cases and 5 deaths had occurred in the Guangdon Province. 2, 5 By March 5, secondary probable SARS cases were identified among healthcare workers in Hanoi, and at the urging of Dr. Urbani and his colleagues, Vietnam closed the hospital to new patients and visitors on March 11. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: Clinical features of index patient and initial contacts Identification of a novel coronavirus in patients with severe acute respiratory syndrome abstract: Abstract During the first part of 2003, the world experienced the first epidemic of the 21st century with the emergence of a new and readily transmissible disease. The disease, severe acute respiratory syndrome (SARS), spread quickly and caused numerous deaths, as well as public panic. This article provides a brief review of the initial history of the epidemiology, as well as of the clinical definition, occurrence in the pediatric population, etiology, prevention, drug studies, and considerations for the future. url: https://api.elsevier.com/content/article/pii/S1045187003000566 doi: 10.1016/s1045-1870(03)00056-6 id: cord-354950-kmpbdvof author: Demurtas, Olivia C. title: Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date: 2016-02-05 words: 8651.0 sentences: 406.0 pages: flesch: 51.0 cache: ./cache/cord-354950-kmpbdvof.txt txt: ./txt/cord-354950-kmpbdvof.txt summary: Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. In addition, the WHO guidelines for SARS diagnosis, developed during the outbreak in 2003, suggested the use of N-based ELISA for specific IgG detection as confirmatory test of SARS-CoV infection (World Health Organization [WHO] , 2003 SARS: Laboratory diagnostic tests) due to the ability of the host to mount an early antibody response against the N protein (Che et al., 2004) . As the plant-derived recombinant M protein, the M RLV was also specifically recognized by the mouse anti-M pAb ( Figure 6C ) that had previously validated by Immunofluorescence Antibody Assay (IFA) in SARS CoV infected Vero cells (Carattoli et al., 2005) . abstract: Severe acute respiratory syndrome (SARS) is a dangerous infection with pandemic potential. It emerged in 2002 and its aetiological agent, the SARS Coronavirus (SARS-CoV), crossed the species barrier to infect humans, showing high morbidity and mortality rates. No vaccines are currently licensed for SARS-CoV and important efforts have been performed during the first outbreak to develop diagnostic tools. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. For the M protein, this is the first description of production in plants, while for plant-derived N protein we demonstrate that it is recognized by sera of patients from the SARS outbreak in Hong Kong in 2003. The availability of recombinant N and M proteins from plants opens the way to further evaluation of their potential utility for the development of diagnostic and protection/therapy tools to be quickly manufactured, at low cost and with minimal risk, to face potential new highly infectious SARS-CoV outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/26904039/ doi: 10.3389/fpls.2016.00054 id: cord-270515-bfjdvfuq author: Deng, Chu-Xia title: The global battle against SARS-CoV-2 and COVID-19 date: 2020-03-15 words: 1052.0 sentences: 52.0 pages: flesch: 54.0 cache: ./cache/cord-270515-bfjdvfuq.txt txt: ./txt/cord-270515-bfjdvfuq.txt summary: Compared with its close related coronavirus family member SARS-CoV and MERS-CoV, which infected 8096 and 2494 people in year 2003 and year 2012, respectively, the outbreak of COVID-19 is much more serious with its high virulence. Zheng indicated that SARS-CoV-2 is an emerging new coronavirus that causes a global threat, and summarized the key events occurred during the early outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients, the possible transmission pathways of the virus, the Zhou and Zhao pointed out the great importance of using therapeutic neutralizing antibodies (NAbs) to control the spread and re-emergence of SARS-CoV-2 and assert that the development of NAbs therefore should be a high priority in near future [5] . Understanding the knowledge, attitudes and behaviors of residents towards COVID-19 during the early stage of disease outbreak could help the authority effectively implement preventive and control measures. Traditional Chinese Medicine in the Treatment of Patients Infected with 2019-New Coronavirus (SARS-CoV-2): A Review and Perspective abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32226284/ doi: 10.7150/ijbs.45587 id: cord-262936-yo6jf3ng author: Deng, Jia-gang title: Carry forward advantages of traditional medicines in prevention and control of outbreak of COVID-19 pandemic date: 2020-06-02 words: 2941.0 sentences: 131.0 pages: flesch: 39.0 cache: ./cache/cord-262936-yo6jf3ng.txt txt: ./txt/cord-262936-yo6jf3ng.txt summary: This paper manly reviews the achievements of the implementation of the epidemic prevention and control plan, advances of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. After the outbreak of COVID-19, the research team of GXUCM responded actively, and the application for two special science and technology projects to prevent and control pneumonia caused by SARS-CoV-2 in Guangxi in 2020 was approved, including Sino-Singapore cooperation for evaluating the effectiveness and application of Guangxi Zhuang/Yao medicines against In summary, this paper manly contents achievements of the implementation of the epidemic prevention and control plan, advance of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. abstract: Members of the China-ASEAN Joint Laboratory for International Cooperation in Traditional Medicine Research used the video conference platform to exchange and discuss the advantages of traditional medicine through the form of score exchange and report, and research and develop the amount and issues of the therapeutic COVID-19 products of concern. This paper manly reviews the achievements of the implementation of the epidemic prevention and control plan, advances of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. The authors believe that the declaration of the (10+3) special meeting of national leaders on epidemic prevention and control should raise the medical and pharmaceutical issues of common concern. It is the responsibility of our joint laboratory members to accelerate the development of traditional medicine research and industry. Also the authors believe that this exchange will certainly promote the development of the cause of cooperation. url: https://www.sciencedirect.com/science/article/pii/S1674638420300484?v=s5 doi: 10.1016/j.chmed.2020.05.003 id: cord-281081-rifr5uub author: Deng, Junhua title: Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date: 2020-05-07 words: 1515.0 sentences: 86.0 pages: flesch: 55.0 cache: ./cache/cord-281081-rifr5uub.txt txt: ./txt/cord-281081-rifr5uub.txt summary: In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. The results showed that no SARS-CoV-2-specific antibodies were detected in above species of animals including pangolin which has been reported as an intermediate host of SARS-CoV-2 (Kangpeng Xiao, 2020) . After confirming the specificity, sensitivity and suitability of SARS-CoV-2 ELISA kit for different species of experimental animals, clinical serum samples from domestic livestock (pig, cow, sheep, horse), poultry (chicken, duck, goose), experimental animal (mice, rat and rhesus monkey), companion animal (dog and cat) and wild animals (camel, fox, mink, alpaca, ferret, bamboo rat, peacock, eagle, tiger rhinoceros, pangolin, leopard cat, jackal, giant panda, masked civet, porcupine, bear, yellow-throated marten, weasel, red pandas and wild boar) were used for antibody detection. abstract: The pandemic SARS‐CoV‐2 has been reported in 123 countries with more than 5,000 patients died from it. However, the original and intermediate hosts of the virus remain unknown. In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. More importantly, companion animals including pet dogs (including one dog the SARS‐CoV‐2 patient kept and two dogs which had close contact with it) and cats, street dogs and cats also showed serological negative to SARS‐CoV‐2, which relieved the public concerns for the pets as SARS‐CoV‐2 carriers. url: https://doi.org/10.1111/tbed.13577 doi: 10.1111/tbed.13577 id: cord-271813-nroflfmc author: Deng, Wang title: Positive results for patients with COVID-19 discharged form hospital in Chongqing, China date: 2020-06-19 words: 2423.0 sentences: 145.0 pages: flesch: 46.0 cache: ./cache/cord-271813-nroflfmc.txt txt: ./txt/cord-271813-nroflfmc.txt summary: METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Among them, 61 patients had positive results of SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (RT-PCR) test, which provided the important information and clinical evidence for the improved management of patients recovered from COVID-19. The study revealed the clinical features of recovered patients with the recurrence of positive results of SARS-CoV-2.Multi-site screening including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. abstract: BACKGROUND: Since December 2019, over 80,000 patients with coronavirus disease 2019 (COVID-19) have been confirmed in China. With the increasing number of recovered patients, more attention should be paid to the follow-up of these patients. METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. Among the 576 patients, 61 patients (10.6%) had positive RT-PCR test results of SARS-CoV-2. We aimed to analyze the demographics, clinical characteristics and treatment of 61 patients. RESULTS: These positive patients were characterized by older age, chronic medical illness and mild conditions. 38 (62.3%) patients who were asymptomatic without abnormalities on chest radiographs were found in the positive with COVID-19. Also, they showed positive results of stool or sputum specimens with negative results of nasal and pharyngeal swab specimens. The median duration of positive result of SARS-CoV-2 was varied from 3 days to 35 days in the patients discharged from hospital with no family member infection. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Our findings provide the important information and clinical evidence for the improved management of patients recovered from COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32560694/ doi: 10.1186/s12879-020-05151-y id: cord-300174-5pt9jmyz author: Deng, Wei title: Therapeutic efficacy of Pudilan Xiaoyan Oral Liquid (PDL) for COVID-19 in vitro and in vivo date: 2020-05-08 words: 1242.0 sentences: 84.0 pages: flesch: 56.0 cache: ./cache/cord-300174-5pt9jmyz.txt txt: ./txt/cord-300174-5pt9jmyz.txt summary: 4 Twelve SARS-CoV-2infected hACE2 mice were randomly assigned to the two groups, PDL-treated group and model control group. Next, the viral RNA copies of lung were significantly reduced in SARS-CoV-2-infected hACE2 mice with PDL treatment compared with model control group at 3 dpi (****p < 0.0001, t = 27.94, df = 4) and 5 dpi (p = 0.0021) (Fig. 1c) . These data indicated that PDL had a potent inhibitory effect against SARS-CoV-2 in vitro and in vivo, as well as improved the weight loss caused by the viral replication. To evaluate the efficacy of PDL against pneumonia caused by SARS-CoV-2 infection, the histopathological changes were observed in PDL-treated mice and control mice. These data indicated that the pneumonia in SARS-CoV-2-infected hACE2 mice was relieved after PDL treatment. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32385228/ doi: 10.1038/s41392-020-0176-0 id: cord-312434-yx24golq author: Deng, Ziqin title: Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research date: 2020-09-23 words: 6219.0 sentences: 294.0 pages: flesch: 49.0 cache: ./cache/cord-312434-yx24golq.txt txt: ./txt/cord-312434-yx24golq.txt summary: Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. Therefore, in order to accurately, effectively and systematically reveal connections within the human coronavirus field, our study applied bibliometrics and visualization methods to analyze human coronaviruses-related publications and citations, countries and affiliations, as well as journal performance, author impact and keyword cooccurrence cluster. According to these keywords, human coronavirus diseases like "SARS, " "MERS" and COVID-19 may have something worthwhile for comparison with other "infectious diseases" like "influenza" in their epidemiological characteristics; "healthcare workers, " "transmission, " "surveillance, " "quarantine, " or "isolation" may be the focuses of these studies, which can help to promote current disease control and prevention measures. abstract: Human coronaviruses, which can cause a range of infectious diseases, have been studied for nearly 60 years. The field has gained renewed interest from researchers around the world due to the COVID-19 outbreak in late 2019. Despite a large amount of research, little is known about the knowledge structure and developing trends of this topic. Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. The results show that research on human coronavirus is dominated by SARS-CoV. Although there have been many publications, only 626 publications (4.1% of total) have more than 100 citations. The top 20 journals with most publications account for 20.6% of total publications and 41% of total citations. In addition to the United States and some European countries, many Asian and African countries are involved in this research, with China holding an important position in this area. Leading researchers from various fields of human coronavirus research are listed to facilitate collaboration and promote effective disease prevention and control. The keywords co-occurrence analysis reveals that the research focus on virology, public health, drugs and other hotspot fields, and uncovers changes in the direction of coronavirus research. The research map on human coronavirus obtained by our analysis are expected to help researchers to efficiently and effectively explore COVID-19. url: https://doi.org/10.3389/fcimb.2020.581404 doi: 10.3389/fcimb.2020.581404 id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 words: 7332.0 sentences: 345.0 pages: flesch: 38.0 cache: ./cache/cord-304498-ty41xob0.txt txt: ./txt/cord-304498-ty41xob0.txt summary: Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. abstract: In order to survive and propagate, RNA viruses must achieve a balance between the capacity for adaptation to new environmental conditions or host cells with the need to maintain an intact and replication competent genome. Several virus families in the order Nidovirales, such as the coronaviruses (CoVs) must achieve these objectives with the largest and most complex replicating RNA genomes known, up to 32 kb of positive-sense RNA. The CoVs encode sixteen nonstructural proteins (nsp 1–16) with known or predicted RNA synthesis and modification activities, and it has been proposed that they are also responsible for the evolution of large genomes. The CoVs, including murine hepatitis virus (MHV) and SARS-CoV, encode a 3′-to-5′ exoribonuclease activity (ExoN) in nsp14. Genetic inactivation of ExoN activity in engineered SARS-CoV and MHV genomes by alanine substitution at conserved DE-D-D active site residues results in viable mutants that demonstrate 15- to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other RNA viruses. Thus nsp14-ExoN is essential for replication fidelity, and likely serves either as a direct mediator or regulator of a more complex RNA proofreading machine, a process previously unprecedented in RNA virus biology. Elucidation of the mechanisms of nsp14-mediated proofreading will have major implications for our understanding of the evolution of RNA viruses, and also will provide a robust model to investigate the balance between fidelity, diversity and pathogenesis. The discovery of a protein distinct from a viral RdRp that regulates replication fidelity also raises the possibility that RNA genome replication fidelity may be adaptable to differing replication environments and selective pressures, rather than being a fixed determinant. url: https://www.ncbi.nlm.nih.gov/pubmed/21593585/ doi: 10.4161/rna.8.2.15013 id: cord-258844-b4d79m1f author: Denning, M. title: DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY date: 2020-07-18 words: 3793.0 sentences: 237.0 pages: flesch: 49.0 cache: ./cache/cord-258844-b4d79m1f.txt txt: ./txt/cord-258844-b4d79m1f.txt summary: Methods From 22nd March 2020 to 18th June 2020, healthcare workers from the United Kingdom, Poland, and Singapore were invited to participate using a self-administered questionnaire comprising the Safety Attitudes Questionnaire (SAQ), Oldenburg Burnout Inventory (OLBI) and Hospital Anxiety and Depression Scale (HADS) to evaluate safety culture, burnout and anxiety/depression. Significant predictors of burnout included patient-facing roles: doctor (OR 2.10; 95% CI 1.49-2.95), nurse (OR 1.38; 95% CI 1.04-1.84), and other clinical staff (OR 2.02; 95% CI 1.45-2.82); being redeployed (OR 1.27; 95% CI 1.02-1.58), bottom quartile SAQ score (OR 2.43; 95% CI 1.98-2.99), anxiety (OR 4.87; 95% CI 3.92-6.06) and depression (OR 4.06; 95% CI 3.04-5.42). This study aims to describe the prevalence and predictors of burnout, anxiety and depression in healthcare workers during the Covid-19 pandemic. The survey consisted of four parts; demographic questions followed by 3 validated psychometric instruments; the Safety Attitudes Questionnaire, Oldenburg Burnout Inventory and Hospital Anxiety and Depression Scale. abstract: Background The Covid-19 pandemic has placed unprecedented pressure on healthcare systems and workers around the world. Such pressures may impact on working conditions, psychological wellbeing and perception of safety. In spite of this, no study has assessed the relationship between safety attitudes and psychological outcomes. Moreover, only limited studies have examined the relationship between personal characteristics and psychological outcomes during Covid-19. Methods From 22nd March 2020 to 18th June 2020, healthcare workers from the United Kingdom, Poland, and Singapore were invited to participate using a self-administered questionnaire comprising the Safety Attitudes Questionnaire (SAQ), Oldenburg Burnout Inventory (OLBI) and Hospital Anxiety and Depression Scale (HADS) to evaluate safety culture, burnout and anxiety/depression. Multivariate logistic regression was used to determine predictors of burnout, anxiety and depression. Results Of 3,537 healthcare workers who participated in the study, 2,364 (67%) screened positive for burnout, 701 (20%) for anxiety, and 389 (11%) for depression. Significant predictors of burnout included patient-facing roles: doctor (OR 2.10; 95% CI 1.49-2.95), nurse (OR 1.38; 95% CI 1.04-1.84), and other clinical staff (OR 2.02; 95% CI 1.45-2.82); being redeployed (OR 1.27; 95% CI 1.02-1.58), bottom quartile SAQ score (OR 2.43; 95% CI 1.98-2.99), anxiety (OR 4.87; 95% CI 3.92-6.06) and depression (OR 4.06; 95% CI 3.04-5.42). Factors significantly protective for burnout included being tested for SARS-CoV-2 (OR 0.64; 95% CI 0.51-0.82) and top quartile SAQ score (OR 0.30; 95% CI 0.22-0.40). Significant factors associated with anxiety and depression, included burnout, gender, safety attitudes and job role. Conclusion Our findings demonstrate a significant burden of burnout, anxiety, and depression amongst healthcare workers. A strong association was seen between SARS-CoV-2 testing, safety attitudes, gender, job role, redeployment and psychological state. These findings highlight the importance of targeted support services for at risk groups and proactive SARS-CoV-2 testing of healthcare workers. url: http://medrxiv.org/cgi/content/short/2020.07.16.20155622v1?rss=1 doi: 10.1101/2020.07.16.20155622 id: cord-258011-19yfwvki author: Deprest, Jan title: SARS‐CoV2 (COVID‐19) infection: is fetal surgery in times of national disasters reasonable? date: 2020-04-22 words: 2087.0 sentences: 123.0 pages: flesch: 48.0 cache: ./cache/cord-258011-19yfwvki.txt txt: ./txt/cord-258011-19yfwvki.txt summary: 10 From a fetal intervention perspective, we need to appreciate that doing an invasive procedure in a SARS-CoV2 positive woman potentially increases the risk of vertical transmission, similar to what was observed in HIV positive women prior to the introduction of antiviral therapies. With open fetal surgery, the risk of mother-child transmission is likely higher than with needle and fetoscopic procedures as the fetus is exposed to more maternal blood and the fetal skin integrity is usually breached in these interventions. SARS-CoV2 negative patients planned to undergo fetal intervention should be informed that exposure to healthcare professionals, other patients or hospital staff increases their risk of contracting the virus. 5 The risk for an asymptomatic SARS-CoV2-positive pregnant mother to progress to overt COVID-19 disease is unknown, though most sources quote it as ''low'' and not higher than health-and age-equivalent women. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes abstract: Even though the global COVID‐19 pandemic may affect how medical care is delivered in general, most countries try to maintain steady access for women to routine pregnancy care, including fetal anomaly screening. This means that, also during this pandemic, fetal anomalies will be detected, and that discussions regarding invasive genetic testing and possibly fetal therapy will need to take place. For patients, concerns about Severe Acute Respiratory Syndrome‐Corona Virus 2 will add to the anxiety caused by the diagnosis of a serious fetal anomaly. Yet, also for fetal medicine teams the situation gets more complex as they must weigh up the risks and benefits to the fetus as well as the mother, while managing a changing evidence base and logistic challenges in their healthcare system. url: https://doi.org/10.1002/pd.5702 doi: 10.1002/pd.5702 id: cord-319022-1twsxzcd author: Desai, Antonio title: The role of anti-hypertensive treatment, comorbidities and early introduction of LMWH in the setting of COVID-19: A retrospective, observational study in Northern Italy() date: 2020-09-25 words: 2874.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-319022-1twsxzcd.txt txt: ./txt/cord-319022-1twsxzcd.txt summary: BACKGROUND: There is a great deal of debate about the role of cardiovascular comorbidities and the chronic use of antihypertensive agents (such as ACE-I and ARBs) on mortality on COVID-19 patients. The aim of the study was to evaluate the role of chronic treatment with ACE-I or ARBs and other clinical predictors on in-hospital mortality in a cohort of COVID-19 patients. As for today, there are discordant results regarding the use of either angiotensin converting enzyme inhibitors (ACE-I) or angiotensin II receptor blockers (ARBs) as for their possible impact on COVID-19 mortality. We found that ACE-I, which acts by inhibiting the conversion from angiotensin I to angiotensin II, showed a trend in protecting from mortality from COVID-19 and was significant in delaying mortality as shown by multivariate Cox regression analysis unlike ARBs, which antagonize the effects of angiotensin II on its receptors 2,3 . Association of Inpatient Use of Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers with Mortality Among Patients With Hypertension Hospitalized With COVID-19 abstract: BACKGROUND: There is a great deal of debate about the role of cardiovascular comorbidities and the chronic use of antihypertensive agents (such as ACE-I and ARBs) on mortality on COVID-19 patients. Of note, ACE2 is responsible for the host cell entry of the virus. METHOD: We extracted data on 575 consecutive patients with laboratory-confirmed SARS-CoV-2 infection admitted to the Emergency Department (ED) of Humanitas Center, between February 21 and April 14, 2020. The aim of the study was to evaluate the role of chronic treatment with ACE-I or ARBs and other clinical predictors on in-hospital mortality in a cohort of COVID-19 patients. RESULTS: Multivariate analysis showed that a chronic intake of ACE-I was associated with a trend in reduction of mortality (OR: 0.53; 95% CI: 0.27–1.03; p = 0.06). Increased age (ORs ranging from 3.4 to 25.2 and to 39.5 for 60–70, 70–80 and > 80 years vs < 60) and cardiovascular comorbidities (OR: 1.90; 95% CI: 1.1–3.3; p = 0.02) were confirmed as important risk factors for COVID-19 mortality. Timely treatment with low-molecular-weight heparin (LMWH) in ED was found to be protective (OR: 0.36; 95% CI: 0.21–0.62; p < 0.0001). CONCLUSIONS: This study can contribute to understand the reasons behind the high mortality rate of patients in Lombardy, a region which accounts for >50% of total Italian deaths. Based on our findings, we support that daily intake of antihypertensive medications in the setting of COVID-19 should not be discontinued and that a timely LMWH administration in ED has shown to decrease in-hospital mortality. url: https://doi.org/10.1016/j.ijcard.2020.09.062 doi: 10.1016/j.ijcard.2020.09.062 id: cord-271919-pbs95hy0 author: Desenclos, Jean-Claude title: Introduction of SARS in France, March–April, 2003 date: 2004-02-17 words: 3412.0 sentences: 145.0 pages: flesch: 56.0 cache: ./cache/cord-271919-pbs95hy0.txt txt: ./txt/cord-271919-pbs95hy0.txt summary: For patients who fulfilled the definition of a probable case, respiratory secretion specimens were taken from the nose, throat, or sputum to detect for SARS-associated coronovirus (CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (7) at the National Reference Center for Influenza (Northern France), Institut Pasteur, Paris. As recommended by WHO, this follow-up included the passengers who sat within two rows of a SARS case-patient on the Air France Hanoi-Paris flight of March 22 and 23, 2003 (14) . Passengers on a flight in which a person with a symptomatic probable case had traveled were informed publicly through the media and mail of the potential exposure and advised to call the emergency service phone number to be evaluated and admitted to the closest university-affiliated infectious disease ward if a fever of >38°C developed within 10 days of the flight. abstract: We describe severe acute respiratory syndrome (SARS) in France. Patients meeting the World Health Organization definition of a suspected case underwent a clinical, radiologic, and biologic assessment at the closest university-affiliated infectious disease ward. Suspected cases were immediately reported to the Institut de Veille Sanitaire. Probable case-patients were isolated, their contacts quarantined at home, and were followed for 10 days after exposure. Five probable cases occurred from March through April 2003; four were confirmed as SARS coronavirus by reverse transcription–polymerase chain reaction, serologic testing, or both. The index case-patient (patient A), who had worked in the French hospital of Hanoi, Vietnam, was the most probable source of transmission for the three other confirmed cases; two had been exposed to patient A while on the Hanoi-Paris flight of March 22–23. Timely detection, isolation of probable cases, and quarantine of their contacts appear to have been effective in preventing the secondary spread of SARS in France. url: https://www.ncbi.nlm.nih.gov/pubmed/15030682/ doi: 10.3201/eid1002.030351 id: cord-294812-nnlzwaf1 author: Desforges, Marc title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 words: 7096.0 sentences: 318.0 pages: flesch: 36.0 cache: ./cache/cord-294812-nnlzwaf1.txt txt: ./txt/cord-294812-nnlzwaf1.txt summary: However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . abstract: In humans, viral infections of the respiratory tract are a leading cause of morbidity and mortality worldwide. Several recognized respiratory viral agents have a neuroinvasive capacity since they can spread from the respiratory tract to the central nervous system (CNS). Once there, infection of CNS cells (neurotropism) could lead to human health problems, such as encephalitis and long-term neurological diseases. Among the various respiratory viruses, coronaviruses are important pathogens of humans and animals. Human Coronaviruses (HCoV) usually infect the upper respiratory tract, where they are mainly associated with common colds. However, in more vulnerable populations, such as newborns, infants, the elderly, and immune-compromised individuals, they can also affect the lower respiratory tract, leading to pneumonia, exacerbations of asthma, respiratory distress syndrome, or even severe acute respiratory syndrome (SARS). The respiratory involvement of HCoV has been clearly established since the 1960s. In addition, for almost three decades now, the scientific literature has also demonstrated that HCoV are neuroinvasive and neurotropic and could induce an overactivation of the immune system, in part by participating in the activation of autoreactive immune cells that could be associated with autoimmunity in susceptible individuals. Furthermore, it was shown that in the murine CNS, neurons are the main target of infection, which causes these essential cells to undergo degeneration and eventually die by some form of programmed cell death after virus infection. Moreover, it appears that the viral surface glycoprotein (S) represents an important factor in the neurodegenerative process. Given all these properties, it has been suggested that these recognized human respiratory pathogens could be associated with the triggering or the exacerbation of neurological diseases for which the etiology remains unknown or poorly understood. url: https://doi.org/10.1007/978-81-322-1777-0_6 doi: 10.1007/978-81-322-1777-0_6 id: cord-266511-g5h4tazp author: Deslandes, A title: SARS-COV-2 was already spreading in France in late December 2019 date: 2020-05-03 words: 1369.0 sentences: 93.0 pages: flesch: 58.0 cache: ./cache/cord-266511-g5h4tazp.txt txt: ./txt/cord-266511-g5h4tazp.txt summary: We report here a case of a patient hospitalized in December 2019 in our intensive care, of our hospital in the north of Paris, for hemoptysis with no etiological diagnosis and for which RT-PCR was performed retrospectively on the stored respiratory sample which confirmed the diagnosis of COVID-19 infection. After its onset in December 2019 in China, the new coronavirus (SARS-COV-2) spreads widely in several countries, causing COVID-19 illness. 8 Clinical symptomatology between COVID-19 and ILIis similar,we therefore decided retrospectively to look for SARS-COV2 in respiratory samples collected in the intensive care units (ICUs) of our hospital near Paris. We reviewed medical record of ICUs patients admitted for ILI between December 2, 2019 and January 16, 2020, with a negative RT-PCR performed at admission. Samples taken from patients with both ILI symptoms (fever higher than 38.5°C, cough, rhinitis, sore throat or myalgia) and ground glass opacity according to their medical record underwent SARS-COV-2 RT-PCR. abstract: Abstract The COVID-19 epidemic is believed to have started in late January 2020 in France. We report here a case of a patient hospitalized in December 2019 in our intensive care, of our hospital in the north of Paris, for hemoptysis with no etiological diagnosis and for which RT-PCR was performed retrospectively on the stored respiratory sample which confirmed the diagnosis of COVID-19 infection. Based on this result, it appears that the COVID-19 epidemic started much earlier. url: https://www.sciencedirect.com/science/article/pii/S0924857920301643?v=s5 doi: 10.1016/j.ijantimicag.2020.106006 id: cord-280423-v3r7vo0o author: Desmazes‐Dufeu, Nadine title: Discordant courses of COVID‐19 in a cohabiting couple of lung transplant recipients date: 2020-07-31 words: 1771.0 sentences: 107.0 pages: flesch: 52.0 cache: ./cache/cord-280423-v3r7vo0o.txt txt: ./txt/cord-280423-v3r7vo0o.txt summary: Solid organ transplant recipients are perceived to be at increased risk of severe COVID‐19 due to their chronic use of immunosuppressive drugs (ISDs) and to their associated conditions. We report here two cases of COVID‐19 in a cohabiting couple of lung transplant recipients for cystic fibrosis, who had different ISDs management and who developed discordant courses of their disease. We report here two cases of synchronic COVID-19 in a cohabiting couple of lung transplant recipients for cystic fibrosis but who had discordant courses of their disease. 13 While lymphopenia and lower CD4 + and CD8 + lymphocytes count have been associated with worst outcome and prolonged viral shedding in the general population of COVID-19 patients, 14 other reports suggested that ISDs per se might diminish the "cytokine storm" underlying the development of acute respiratory distress syndrome (ARDS) and subsequent mortality. abstract: COVID‐19 is a novel infectious disease caused by SARS‐CoV‐2 that emerged in late 2019 and which is now a pandemic. Solid organ transplant recipients are perceived to be at increased risk of severe COVID‐19 due to their chronic use of immunosuppressive drugs (ISDs) and to their associated conditions. Scarce data are available on the optimized management of ISDs in these patients and on its impact on presentation, clinical course, viral shedding, and outcome. We report here two cases of COVID‐19 in a cohabiting couple of lung transplant recipients for cystic fibrosis, who had different ISDs management and who developed discordant courses of their disease. Our findings suggest that the degree of their immunosuppression might be a reason for their different course and that ISDs might prove partially protective. url: https://www.ncbi.nlm.nih.gov/pubmed/32654244/ doi: 10.1111/tid.13410 id: cord-355122-x3v80bdp author: Desterke, Christophe title: PPARγ cistrome repression during activation of lung monocyte-macrophages in severe COVID-19 date: 2020-09-25 words: 7873.0 sentences: 368.0 pages: flesch: 43.0 cache: ./cache/cord-355122-x3v80bdp.txt txt: ./txt/cord-355122-x3v80bdp.txt summary: Overall, these results demonstrate for the first time, the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte / macrophage-mediated inflammatory storm. A differentially expressed gene (DEG) analysis was performed on lung biopsies from COVID-19 patients and healthy donors; this revealed widespread repression of many gene pathways in COVID-19 lungs (Supplemental Figures 4A-4B) , which could affect major functionalities of the cells in this organ. Specifically, the gene-set enrichment analysis (performed using the ''hallmarks'' gene set of the MsigDB database) highlighted repression of the mitosis spindle and p53 pathway (cell cycle gatekeeper) in samples of COVID-19 lungs compared to those of healthy donors (NES = -3.45 and -2.77, respectively, with p-value<0.001, Supplemental Figure 5A ). Mononuclear cells, monocytes, and macrophages were found in positions similar to the COVID-19 lung samples, suggesting major infiltrations in this tissue (Supplemental Figure 4E ) and confirming the results of the ''xcell'' immune score analysis (Supplemental Figure 4C ). abstract: The molecular mechanisms of cytokine storm in patients with severe COVID-19 infections are poorly understood. To uncover these events, we performed transcriptome analyses of lung biopsies from COVID-19 patients, revealing a gene enrichment pattern similar to that of PPARγ-knockout macrophages. Single-cell gene expression analysis of bronchoalveolar lavage fluids revealed a characteristic trajectory of PPARγ-related disturbance in the CD14+/CD16+ cells. We identified a correlation with the disease severity and the reduced expression of several members of the PPARγ complex such as EP300, RXRA, RARA, SUMO1, NR3C1, CCDC88A. CHIP-seq analyses confirmed repression of the PPARγ-RXRA-NR3C1 cistrome in COVID-19 lung samples. Further analysis of protein-protein networks highlighted an interaction between the PPARγ-associated protein SUMO1 and a nucleoprotein of the SARS virus. Overall, these results demonstrate for the first time, the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte / macrophage-mediated inflammatory storm. url: https://www.ncbi.nlm.nih.gov/pubmed/33015591/ doi: 10.1016/j.isci.2020.101611 id: cord-311264-zn7ydrvh author: Deurenberg-Yap, M. title: The Singaporean response to the SARS outbreak: knowledge sufficiency versus public trust date: 2005-06-17 words: 3445.0 sentences: 159.0 pages: flesch: 50.0 cache: ./cache/cord-311264-zn7ydrvh.txt txt: ./txt/cord-311264-zn7ydrvh.txt summary: In this paper, the informing seeking and processing mindset of Singaporeans during a severe outbreak situation is assessed by testing the level of knowledge on SARS and its preventive/ control measures following the earlier communication efforts and subsequent public education campaign. More than nine out of 10 respondents thought that infection control measures undertaken at hospitals were Overall, the public trust index was high at 11.4 out of a maximum score of 14, with no significant difference between gender, age groups and educational levels. First, while knowledge about infection control measures undertaken at TTSH was low (mean per cent score of 20 ± 16%), the level of confidence was high, with 82% of the respondents expressing confidence in the hospital''s ability to deal with SARS. abstract: During the outbreak of severe acute respiratory syndrome (SARS) in Singapore from 1 March to 11 May 2003, various national prevention and control measures were undertaken to control and eliminate the transmission of the infection. During the initial period of the epidemic, public communication was effected through press releases and media coverage of the epidemic. About a month into the epidemic, a public education campaign was mounted to educate Singaporeans on SARS and adoption of appropriate behaviours to prevent the spread of the disease. A survey was conducted in late April 2003 to assess Singaporeans' knowledge about SARS and infection control measures, and their concerns and anxiety in relation to the outbreak. The survey also sought to assess their confidence in the ability of various institutions to deal with SARS and their opinion on the seemingly tough measures enforced. The study involved 853 adults selected from a telephone-sampling frame. Stratified sampling was used to ensure adequate representation from major ethnic groups and age groups. The study showed that the overall knowledge about SARS and control measures undertaken was low (mean per cent score of 24.5 ± 8.9%). While 82% of respondents expressed confidence in measures undertaken by Tan Tock Seng Hospital (the hospital designated to manage SARS), only 36% had confidence in nursing homes. However, >80% of the public agreed that the preventive and control measures instituted were appropriate. Despite the low knowledge score, the overall mean satisfaction score of the government's response to SARS was 4.47 (out of possible highest score of 5.00), with >93% of adult Singaporeans indicating that they were satisfied or very satisfied with the government's response to SARS. Generally, Singaporeans had a high level of public trust (satisfaction with government, confidence in institutions, deeming government measures appropriate), scoring 11.4 out of possible maximum of 14. The disparity between low knowledge on the one hand and high confidence and trust in the actions of the government on the other suggests that Singaporeans do not require high knowledge sufficiency to be confident in measures undertaken by the government to control the SARS crisis. url: https://www.ncbi.nlm.nih.gov/pubmed/15964886/ doi: 10.1093/heapro/dai010 id: cord-287410-boxxlopy author: Devi, Arpita title: In silico designing of multi-epitope vaccine construct against human coronavirus infections date: 2020-08-10 words: 7189.0 sentences: 446.0 pages: flesch: 60.0 cache: ./cache/cord-287410-boxxlopy.txt txt: ./txt/cord-287410-boxxlopy.txt summary: Band T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. To predict the probable immune response of the designed multi-epitope vaccine construct in human immune system, in silico immune simulations were conducted using the C-ImmSim server (http://150.146.2.1/C-IMMSIM/index.php) (Rapin et al., 2010) . C-ImmSim is a novel in silico approach for the study of the mammalian immune system The tool is a combination of a mesoscopic scale simulator of the immune system with machine learning techniques for molecular-level predictions of major histocompatibility complex (MHC)-peptide-binding interactions, linear B-cell epitope discovery, and protein-protein potential estimation. The antigenicity of the vaccine construct including the adjuvant sequence and His-tag was predicted by the VaxiJen 2.0 server to be 0.6452 with a bacteria model at a threshold of 0.4. abstract: Single stranded RNA viruses were known to cause variety of diseases since many years and are gaining much importance due to pandemic after the identification of a novel corona virus (severe acute respiratory syndrome-coronavirus (SARS-CoV-2)). Seven coronaviruses (CoVs) are known to infect humans and they are OC43 CoV, NL63 CoV, HKU1 CoV, Middle East respiratory syndrome, SARS CoV, and SARS CoV-2. Virus replication weakens the immune system of host thereby altering T-cell count and much of interferon response. Although no vaccine or therapeutic treatment has been approved till now for CoV infection, trials of vaccine against SARS CoV-2 are in progress. One of the epitopes used for vaccine production is of the spike protein on the surface of virus. The work focuses on designing of multi-epitope vaccine construct for treatment of seven human CoV infections using the epitopes present on the spike protein of human CoVs. To address this, immuno-informatics techniques have been employed to design multi-epitope vaccine construct. B- and T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. The tertiary structure of the vaccine construct along with the adjuvant has been modelled and the physiochemical properties have been predicted. The multi-epitope vaccine construct has antigenic and non-allergenic property. After validation, refinement and disulphide engineering of the vaccine construct, molecular docking with toll-like receptors (TLRs) have been performed. Molecular dynamics simulation in aqueous environment predicted that the vaccine-TLRs complexes were stable. The vaccine construct is predicted to be able to trigger primary immune response in silico. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1804460 doi: 10.1080/07391102.2020.1804460 id: cord-325377-g68onkjt author: Dey, Anusree title: COVID-19: Scientific Overview of the global Pandemic date: 2020-10-28 words: 1515.0 sentences: 108.0 pages: flesch: 60.0 cache: ./cache/cord-325377-g68onkjt.txt txt: ./txt/cord-325377-g68onkjt.txt summary: COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics. According to the global data as well as the early estimates from China, both old 69 J o u r n a l P r e -p r o o f age and comorbidities may render the patients at higher risk of developing severe disease or 70 death due to COVID-19 infection, perhaps due to a weaker immune functioning [8, 10] . Interestingly, in an independent study, researchers have found 124 three blood based biomarkers which can predict disease severity at least ten days in advance 125 with more than 90% accuracy, based on a database of 485 infected patients from Wuhan, 126 abstract: COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. Genome sequence of the virus revealed that it’s a new zoonotic virus which might have evolved by jumping from bats to humans with one or more intermediate hosts. The immediate availability of the sequence information in public domain has accelerated development of quantitative-reverse-transcription PCR based diagnostics. Besides, numbers of clinical trials have been prioritized globally for testing new vaccines and treatments against this disease. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics. url: https://doi.org/10.1016/j.nmni.2020.100800 doi: 10.1016/j.nmni.2020.100800 id: cord-298301-p1zj6jg9 author: Dey, Lopamudra title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date: 2020-09-03 words: 6298.0 sentences: 387.0 pages: flesch: 49.0 cache: ./cache/cord-298301-p1zj6jg9.txt txt: ./txt/cord-298301-p1zj6jg9.txt summary: title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins A total of 1326 potential human target proteins of SARS-CoV-2 have been predicted by the proposed ensemble model and validated using gene ontology and KEGG pathway enrichment analysis. In this article, we have tried to predict the target human proteins of the SARS-CoV-2 virus based on their protein sequences combining amino acid composition, pseudo amino acid composition, and conjoint triad features using machine learning techniques. Subsequently, after feature reduction, we have used some popular supervised learning algorithms such as Support Vector Machine (SVM), Naive Bayes (NB), Random Forest (RF) and K-Nearest Neighbor (KNN) along with a deep multi-layer perceptron model and ensemble techniques (Voting classifier, XGBoost, AdaBoost) for classification and prediction. A total of 3 sets of sequence-based features, namely, amino acid composition, conjoint triad, and pseudo amino acid composition of the human proteins are considered to train the machine learning models. abstract: BACKGROUND: COVID-19 (Coronavirus Disease-19), a disease caused by the SARS-CoV-2 virus, has been declared as a pandemic by the World Health Organization on March 11, 2020. Over 15 million people have already been affected worldwide by COVID-19, resulting in more than 0.6 million deaths. Protein-protein interactions (PPIs) play a key role in the cellular process of SARS-CoV-2 virus infection in the human body. Recently a study has reported some SARS-CoV-2 proteins that interact with several human proteins while many potential interactions remain to be identified. METHOD: In this article, various machine learning models are built to predict the PPIs between the virus and human proteins that are further validated using biological experiments. The classification models are prepared based on different sequence-based features of human proteins like amino acid composition, pseudo amino acid composition, and conjoint triad. RESULT: We have built an ensemble voting classifier using SVM(Radial), SVM(Polynomial), and Random Forest technique that gives a greater accuracy, precision, specificity, recall, and F1 score compared to all other models used in the work. A total of 1326 potential human target proteins of SARS-CoV-2 have been predicted by the proposed ensemble model and validated using gene ontology and KEGG pathway enrichment analysis. Several repurposable drugs targeting the predicted interactions are also reported. CONCLUSION: This study may encourage the identification of potential targets for more effective anti-COVID drug discovery. url: https://www.sciencedirect.com/science/article/pii/S2319417020301360?v=s5 doi: 10.1016/j.bj.2020.08.003 id: cord-279255-v861kk0i author: Dhama, Kuldeep title: Coronavirus Disease 2019–COVID-19 date: 2020-06-24 words: 23862.0 sentences: 1164.0 pages: flesch: 44.0 cache: ./cache/cord-279255-v861kk0i.txt txt: ./txt/cord-279255-v861kk0i.txt summary: Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . Health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel CoV (originally named 2019-nCoV), which was first identified in Wuhan City, Hubei Province, China, on 12 December 2019. abstract: In recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32580969/ doi: 10.1128/cmr.00028-20 id: cord-327063-ea7a1xfl author: Dhama, Kuldeep title: SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus date: 2020-08-02 words: 11048.0 sentences: 600.0 pages: flesch: 48.0 cache: ./cache/cord-327063-ea7a1xfl.txt txt: ./txt/cord-327063-ea7a1xfl.txt summary: The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARSand MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease. Further research exploring the SARS-CoV-2 associated zoonosis and mechanisms accounting for its initial transmission from animals to humans, will lead to sort out the spread of this virus as well as design and develop appropriate prevention and control strategies to counter COVID-19. The present comprehensive manuscript presents an overview on COVID-19, an emerging SARS-CoV-2 infectious disease while focusing mainly on the events and circumstantial evidences with regards to this virus jumping the species barriers, sharing a few lessons learned from SARS-and MERS-CoVs, zoonotic spillover events (zoonosis), acquiring transmission ability to infect humans, and adopting appropriate preventive and control measures [42] . abstract: Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome - Coronavirus-2) of the family Coronaviridae, appeared in China in December 2019. This disease was declared as posing Public Health International Emergency by World Health Organization on January 30, 2020, attained the status of a very high-risk category on February 29, and now having a pandemic status (March 11). COVID-19 has presently spread to more than 215 countries/territories while killing nearly 0.62 million humans out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost 15 million as of July 22, 2020, within a short period of just a few months. Researchers worldwide are pacing with high efforts to counter the spread of this virus and to design effective vaccines and therapeutics/drugs. Few of the studies have shown the potential of the animal-human interface and zoonotic links in the origin of SARS-CoV-2. Exploring the possible zoonosis and revealing the factors responsible for its initial transmission from animals to humans will pave ways to design and implement effective preventive and control strategies to counter the COVID-19. The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARS- and MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease. url: https://api.elsevier.com/content/article/pii/S1477893920303264 doi: 10.1016/j.tmaid.2020.101830 id: cord-253124-s3pa4n8a author: Dhamad, Ahmed E. title: COVID-19: molecular and serological detection methods date: 2020-10-07 words: 3370.0 sentences: 188.0 pages: flesch: 50.0 cache: ./cache/cord-253124-s3pa4n8a.txt txt: ./txt/cord-253124-s3pa4n8a.txt summary: Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. And the top keywords that searched were: COVID-19, SARS-CoV-2, coronavirus, genomic RNA, protein structure, ACE2, transmission, symptoms, molecular detection methods, serological detection methods, rRT-PCR, ID NOW COVID-19, isothermal amplification, CRISPR, SARS-CoV-2 DETECTR, LAMP, recombinase polymerase amplification (RPA), Lateral flow assay (LFA) and Enzyme-linked immunosorbent assay (ELISA). In this method (e.g., SARS-CoV-2 DETECTR), the RNA virus is extracted from a specimen and designated regions of N2, E, RP genes are amplified at 62 C for 20 min by specific primes through Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) approach Lamb et al., 2020; Hong et al., 2004) . Unlike molecular methods, serological methods (also called antibody tests) can be applied to detect past and current SARS-CoV-2 infection and monitor the progress of the disease periods and immune response. abstract: Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods. url: https://doi.org/10.7717/peerj.10180 doi: 10.7717/peerj.10180 id: cord-333200-yka7wfbi author: Dhampalwar, Swapnil title: Treatment armamentarium of COVID-19: Evolving strategies & evidence so far date: 2020-07-16 words: 1253.0 sentences: 82.0 pages: flesch: 48.0 cache: ./cache/cord-333200-yka7wfbi.txt txt: ./txt/cord-333200-yka7wfbi.txt summary: Keeping up with this current pace of information, we review the clinical studies of different therapeutic options available to treat SARS-CoV-2. (20) Since, these studies with CQ & HCQ have different therapeutic regimens, heterogenous study population, unequal arms to compare, ill-defined outcomes, and non-reproducible results; further randomized trials are needed before recommending the routine use of HCQ in mild COVID-19. Since Favipiravir and Lopinavir-ritonavir did not provide significant benefits in viral clearance or clinical improvement in severe disease, further randomized trials are necessary before recommending these drugs in clinical practice. A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an openlabel non-randomized clinical trial No Evidence of Rapid Antiviral Clearance or Clinical Benefit with the Combination of Hydroxychloroquine and Azithromycin in Patients with Severe COVID-19 Infection abstract: The outbreak of SARS-CoV-2 started in Hubei province of China in December 2019 and rapidly spread all over the world. It has infected more than 7 million people worldwide and has pushed half of the world in a state of lockdown. There is an urgent unmet need of interventions both for prevention & treatment of this disease and more than 500 clinical trials are ongoing in this regard. At present, no study with robust methodology have clearly demonstrated benefits of Hydroxycholoquine for treatment, pre-exposure prophylaxis in healthcare workers or post exposure prophylaxis in COVID-19. Remdesivir has been shown to have modest benefits in moderate to severe disease, if administered early. Given the rapid pace of clinical information and discoveries, it is important for clinicians to be up to date with the latest, evidence-based treatment options available for this novel disease. Keeping up with this current pace of information, we review the clinical studies of different therapeutic options available to treat SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0973688320301018 doi: 10.1016/j.jceh.2020.07.001 id: cord-024080-eh3ztsv5 author: Dheda, Keertan title: Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date: 2020-04-17 words: 3953.0 sentences: 214.0 pages: flesch: 44.0 cache: ./cache/cord-024080-eh3ztsv5.txt txt: ./txt/cord-024080-eh3ztsv5.txt summary: Recent data from infections in special contexts such as cruise liners (9) and in close contacts of COVID-19 patients (10) have demonstrated that SARS-CoV-2-specific RT-PCR may be positive in the early phase of the disease, and that viral shedding in the asymptomatic phase and in the early prodromal phase can be considerable. (19) This false negativity phenomenon may be due to several factors, including a low viral load below the detection limit of the assay, low sample volume or cellular mass during acquisition, sampling location (upper versus lower respiratory tract), sample degradation during transport or storage, sample processing methodology and the timing of sampling in relation to the stage of the disease (RT-PCR positivity may progressively increase during the course of the disease). In patients with more severe diseases, including those with lower respiratory tract infection, but also in individuals with mild disease, high viral loads can be detected often for several days after the resolution of symptoms. abstract: Coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 is a global pandemic that has resulted in over 1.5 million confirmed cases and close to 100,000 deaths. In the majority of symptomatic cases COVID-19 results in a mild disease predominantly characterised by upper respiratory tract symptoms. Reverse transcription polymerase chain reaction (RT-PCR), using a nasopharyngeal sample, is the mainstay of diagnosis, but there is an ~30% false negative rate early in the disease and in patients with mild disease. RT-PCR positivity can persist for several days after a resolution of symptoms. IgM and IgG antibody responses become positive several days after the onset of symptoms, and robust antibody responses are detectable in the second week of illness. Antibody-based immunoassays have a limited role in the diagnosis of early symptomatic disease. However, their incremental benefit over RT-PCR in the first 2 weeks of illness is currently being clarified in ongoing studies. Such assays may be useful for surveillance purposes. However, their role in potentially selecting individuals that may benefit from vaccination, or as a biomarker identifying persons that could be redeployed into essential employment roles are being investigated. Rapid antibody-based immunoassays that detect viral antigen in nasopharyngeal samples are being developed and evaluated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187744/ doi: 10.18772/26180197.2020.v2nsia1 id: cord-320149-3q4q98a6 author: Di Carlo, Davide Tiziano title: Exploring the clinical association between neurological symptoms and COVID-19 pandemic outbreak: a systematic review of current literature date: 2020-08-01 words: 3482.0 sentences: 196.0 pages: flesch: 39.0 cache: ./cache/cord-320149-3q4q98a6.txt txt: ./txt/cord-320149-3q4q98a6.txt summary: An increasing body of evidence suggests that patients with the coronavirus disease (COVID-19) might have a heterogeneous spectrum of neurological symptoms METHODS: A systematic search of two databases was performed for studies published up to May 29th, 2020. The pathophysiology of this association is under investigation and warrants additional studies, Physicians should be aware of this possible association because during the epidemic period of COVID-19, early recognition of neurologic manifestations otherwise not explained would raise the suspect of acute respiratory syndrome coronavirus 2 infection. Our systematic review of 2499 patients reported the occurrence of a wide spectrum of neurologic complications in hospitalized patients with laboratory-confirmed COVID-19 infection, supporting the possible neuroinvasive potential of SARS-CoV-2. Recently, several case reports described the occurrence of ischemic and hemorrhagic stroke (see supplementary material 1), confirming the association of cerebrovascular complications with severe COVID-19 infection, older age, and the presence of multiple comorbidity [46, 47] . abstract: OBJECT: The novel severe acute respiratory syndrome (SARS)-CoV-2 outbreak has been declared a pandemic in March, 2020. An increasing body of evidence suggests that patients with the coronavirus disease (COVID-19) might have a heterogeneous spectrum of neurological symptoms METHODS: A systematic search of two databases was performed for studies published up to May 29th, 2020. PRISMA guidelines were followed. RESULTS: We included 19 studies evaluating 12,157 patients with laboratory-confirmed COVID-19 infections. The median age of patients was 50.3 (IQR 11.9), and the rate of male patients was 50.6% (95% CI 49.2–51.6%). The most common reported comorbidities were hypertension and diabetes (31.1%, 95% CI 30–32.3% and 13.5%, 95% CI 12.3–14.8%, respectively). Headache was reported in 7.5% of patients (95% CI 6.6–8.4%), and dizziness in 6.1% (95% CI 5.1–7.1%). Hypo/anosmia, and gustatory dysfunction were reported in 46.8 and 52.3%, of patients, respectively. Symptoms related to muscular injury ranged between 15 and 30%. Three studies reported radiological confirmed acute cerebrovascular disease in 2% of patients (95% CI 1.6–2.4%). CONCLUSIONS: These data support accumulating evidence that a significant proportion of patients with COVID-19 infection develop neurological manifestations, especially olfactory, and gustatory dysfunction. The pathophysiology of this association is under investigation and warrants additional studies, Physicians should be aware of this possible association because during the epidemic period of COVID-19, early recognition of neurologic manifestations otherwise not explained would raise the suspect of acute respiratory syndrome coronavirus 2 infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00415-020-09978-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00415-020-09978-y doi: 10.1007/s00415-020-09978-y id: cord-315970-m5o962yw author: Di Ciaula, Agostino title: COVID‐19, internists and resilience: the north‐south Italy outbreak. date: 2020-06-01 words: 3971.0 sentences: 220.0 pages: flesch: 48.0 cache: ./cache/cord-315970-m5o962yw.txt txt: ./txt/cord-315970-m5o962yw.txt summary: The rates of infected subjects and deaths in Italy (whole country and regional level) per 100,000 residents were calculated considering the official number of residents derived from the National Institute of Statistics (ISTAT). Figure 1 summarizes the daily progression in the cumulative number of COVID-19 positive subjects and in the incidence of deaths related to COVID-19 in southern and northern Italy, since the start of the outbreak. On the national "lockdown" day (March 12), in northern Italy there was a total of 14,335 infected patients and 997 COVID-19 related deaths. Following the COVID-19 outbreak, the local Apulian government firstly increased the number of available beds in the units of intensive care, pneumology, and infectious diseases across the Region. In the most affected regions (northern Italy, mainly Lombardy) serious concerns existed about the effective capacity of the national health system to adequately face the burden of disease. abstract: According to data from the World Health Organization, Italy has been particularly affected by the ongoing COVID‐19 pandemic. On April 1(st) 2020, Italy gained, at a world level, the highest number of total confirmed cases (n=110,574) and deaths (n=13,155) since the beginning of the outbreak. The number of cases raised exponentially, reaching a total of 227,364 infected subjects and 32,330 deaths on May, 20. The distribution of infected subjects and deaths, however, was not homogeneous, being respectively about 7‐times and 12‐times higher in northern‐ than in southern regions url: https://doi.org/10.1111/eci.13299 doi: 10.1111/eci.13299 id: cord-268224-5tbb8df1 author: Di Gioacchino, Andrea title: The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date: 2020-08-27 words: 7109.0 sentences: 412.0 pages: flesch: 62.0 cache: ./cache/cord-268224-5tbb8df1.txt txt: ./txt/cord-268224-5tbb8df1.txt summary: Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven, in the N protein coding region, both by the viral codon bias and by the high value of the CpG content, leading to a loss in CpG. Finally we use a model of the viral gene evolution under human host pressure, characterized by the CpG force, to study synonymous mutations, and in particular those which change CpG content, observed since the SARS-CoV-2 entered the human population (Sec. 2.3). We first compute the global force on CpG dinucleotides for SARS-Cov-2 and a variety of other viruses from the Coronaviridae family affecting humans or other mammals (bat, pangolin), see Fig. 1a , using as null model the nucleotide usage calculated from human genome [22] (see Methods Sec. 4.2) 1 . abstract: COVID-19 can lead to acute respiratory syndrome in patients, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We find that CpG relative abundance, which we characterize by an adequate force parameter taking into account statistical constraints acting on the genome at the nucleotidic and amino-acid levels is, on the overall, low compared to other pathogenic betacoronaviruses. However, the CpG force widely fluctuates along the genome, with particularly low value, comparable to the circulating seasonal HKU1, in the Spike protein (S) coding region and high value, comparable to SARS and MERS, in the highly expressed nucleocapside (N) coding regions, whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3’UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven, in the N protein coding region, both by the viral codon bias and by the high value of the CpG content, leading to a loss in CpG. Sequence motifs preceding these CpG-loss-associated loci match recently identified binding patterns of the Zinc finger Anti-viral Protein. url: https://www.ncbi.nlm.nih.gov/pubmed/32511407/ doi: 10.1101/2020.05.06.074039 id: cord-256351-q8lkhklw author: Di Giorgio, Angelo title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy date: 2020-05-12 words: 1377.0 sentences: 77.0 pages: flesch: 48.0 cache: ./cache/cord-256351-q8lkhklw.txt txt: ./txt/cord-256351-q8lkhklw.txt summary: title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy Twenty-six per cent (n= 39) developed mild/moderate respiratory symptoms likely due to an underlying SARS-CoV-2 infection; however, since the NPS was not carried out, they were classified as suspected cases of COVID-19. cases; the majority of them (3/4 patients, 75%) presented with a mild or moderate clinical phenotype (1 was asymptomatic) whilst 1 patient died ; this patient had risk factors for complicated COVID-19 described in the general population, including old age and associated comorbidities. We previously reported our review of past outbreaks of coronavirus infections and our preliminary experience with these patients followed in our center, and we suggested that immunocompromised patients (adults and children) are not at increased risk of COVID-19 complicated course compared to the general population (3). However we recently reported the uneventful course of patients with inflammatory bowel disease who were under IS or immunomodulating drugs, including antimetabolites, during the SARS-CoV-2 epidemic (4). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32413378/ doi: 10.1016/j.jhep.2020.05.008 id: cord-258067-par61wwh author: Di Martino, Marcello title: Elective Surgery During the SARS-CoV-2 Pandemic (COVID-19): A Morbimortality Analysis and Recommendations on Patient Prioritisation and Security Measures date: 2020-06-20 words: 3464.0 sentences: 178.0 pages: flesch: 42.0 cache: ./cache/cord-258067-par61wwh.txt txt: ./txt/cord-258067-par61wwh.txt summary: Conclusions The patients undergoing the surgical procedures showed high rates of COVID-19 infection and postoperative complications, especially the patients with oncological diseases. The following variables were analysed: age; sex; functional status (defined according to the ECOG scale) (21); personal background; diagnosis; type of surgical intervention; the timing of SARS-CoV-2 infection; the treatment required (Table 1) ; the severity of the respiratory infection (according to the BRCSS) (20) ; and postoperative complications (according to the Dindo-Clavien classification) (19) . Ten (16.9%) of the oncological patients, one (1%) of those operated on electively for benign diseases and four (7%) of the urgent surgery group presented with a SARS-CoV-2 infection, with statistically significant differences in the infection rate of the three groups (p = 0.004) ( Table 2) . Patients undergoing elective surgery before and during the peak of the COVID-19 pandemic showed a high rate of postoperative complications, with a SARS-CoV-2 infection rate of up to 16% in patients undergoing oncologic surgical procedures. abstract: Abstract Introduction The spread of the SARS-CoV-2 infection (COVID-19) has required adaptation by hospitals affected by the pandemic, which has caused a reduction in elective surgical activity. Methods Retrospective study of patients operated on in the previous month and during the peak of the pandemic. We analysed the COVID-19 infection rate, the severity of respiratory infection according to the Brescia respiratory COVID-19 severity scale, the adopted therapeutic measures and the overall postoperative complications. Results From 17th February to 31st March 2020, there was a progressive decrease in surgical activity, with only 213 patients operated on. This comprised 59 (27.8%) elective operations for oncological diseases, 97 (45.5%) elective operations for benign diseases and 57 (26.7%) as urgent procedures. There was a progressive increase in the rate of infection by COVID-19, with a total of 15 cases (7%). This included 10 patients (16.9%) in the elective group for oncological disease, 1 (1%) in the elective surgery group for benign disease and 4 (7%) in the urgent surgery group (P <.001). Five patients presented with a severe respiratory infection, of which 4 were affected by oncological disease. There were 3 deaths (1.4%), which were all due to the worsening of a respiratory infection. Conclusions The patients undergoing the surgical procedures showed high rates of COVID-19 infection and postoperative complications, especially the patients with oncological diseases. Local resumption of surgical activity must be based on the prioritisation of the cases to be operated on, respecting certain premises of security and optimisation of the available resources. url: https://api.elsevier.com/content/article/pii/S2173507720301216 doi: 10.1016/j.cireng.2020.06.005 id: cord-281528-xy8j5jiv author: Di Paola, Luisa title: The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date: 2020-06-17 words: 6715.0 sentences: 402.0 pages: flesch: 56.0 cache: ./cache/cord-281528-xy8j5jiv.txt txt: ./txt/cord-281528-xy8j5jiv.txt summary: All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein. We also provided biophysical evidence based on the elastic network modeling (ENM) approach, combined with perturbation-response scanning (PRS) 36 that AMRs in both viruses acted as a mediator of intermolecular allostery between the S protein and ACE2. The map of the participation coefficient projected onto the ribbon structure of the SARS-CoV/ACE2 complex ( Figure 1C ) shows an active region (P > 0) in the junction between the fusion peptide and the trimeric bulk phase of the spike protein. abstract: [Image: see text] SARS-CoV-2 has caused the largest pandemic of the twenty-first century (COVID-19), threatening the life and economy of all countries in the world. The identification of novel therapies and vaccines that can mitigate or control this global health threat is among the most important challenges facing biomedical sciences. To construct a long-term strategy to fight both SARS-CoV-2 and other possible future threats from coronaviruses, it is critical to understand the molecular mechanisms underlying the virus action. The viral entry and associated infectivity stems from the formation of the SARS-CoV-2 spike protein complex with angiotensin-converting enzyme 2 (ACE2). The detection of putative allosteric sites on the viral spike protein molecule can be used to elucidate the molecular pathways that can be targeted with allosteric drugs to weaken the spike-ACE2 interaction and, thus, reduce viral infectivity. In this study, we present the results of the application of different computational methods aimed at detecting allosteric sites on the SARS-CoV-2 spike protein. The adopted tools consisted of the protein contact networks (PCNs), SEPAS (Affinity by Flexibility), and perturbation response scanning (PRS) based on elastic network modes. All of these methods were applied to the ACE2 complex with both the SARS-CoV2 and SARS-CoV spike proteins. All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein. url: https://doi.org/10.1021/acs.jproteome.0c00273 doi: 10.1021/acs.jproteome.0c00273 id: cord-268425-xg8xnjf9 author: DiNicolantonio, James J. title: Harnessing Adenosine A2A Receptors as a Strategy for Suppressing the Lung Inflammation and Thrombotic Complications of COVID-19: Potential of Pentoxifylline and Dipyridamole date: 2020-07-02 words: 3891.0 sentences: 251.0 pages: flesch: 41.0 cache: ./cache/cord-268425-xg8xnjf9.txt txt: ./txt/cord-268425-xg8xnjf9.txt summary: 5 Importantly, neutrophils, whose activation and transit into lung interstitial tissue and alveolar space is a key mediator of the respiratory distress syndrome associated with COVID-19, are highly responsive to the functionally suppressive effects of A2AR, as are the endothelial cells whose activation attracts and enables transendothelial passage of activated neutrophils. Most studies with DIP have focused on its platelet-stabilizing effects -which presumably could provide some protection from SARS-CoV-2''s pro-thrombotic effects -but experimental studies also show that DIP can act on neutrophils to suppress superoxide production, adhesion to endothelial cells, and, in a mouse model of anti-phospholipid syndrome (a sometime feature of COVID-19), NETosis formation. 79 Supplemental glucosamine may likewise up-regulate the type 1 interferon responses to viruses, while exerting anti-inflammatory effects that render it protective in rodent models of sepsis and lung inflammation induced by LPS or cigarette smoke. abstract: Counterproductive lung inflammation and dysregulated thrombosis contribute importantly to the lethality of advanced COVID-19. Adenosine A2A receptors (A2AR), expressed by a wide range of immune cells, as well as endothelial cells and platelets, exert cAMP-mediated anti-inflammatory and anti-thrombotic effects that potentially could be highly protective in this regard. The venerable drug pentoxifylline (PTX) exerts both anti-inflammatory and antithrombotic effects that reflect its ability to boost the responsiveness of A2AR to extracellular adenosine. The platelet-stabilizing drug dipyridamole (DIP) blocks intracellular uptake of extracellularly-generated adenosine, thereby up-regulating A2AR signaling in a way that should be functionally complementary to the impact of PTX in that regard. Moreover, DIP has recently been reported to slow the cellular replication of SARS-CoV-2 in clinically feasible concentrations. Both PTX and DIP are reasonably safe, well-tolerated, widely available, and inexpensive drugs. When COVID-19 patients can be treated within several days of symptom onset, using PTX + DIP in conjunction with hydroxychloroquine (HCQ) and an antibiotic - azithromycin (AZM) or doxycycline – might be warranted. HCQ and AZM can suppress SARS-CoV-2 proliferation in vitro and may slow the cell-to-cell spread of the virus; a large case series evaluating this combination in early-stage patients reported an impressively low mortality rate. However, whereas HCQ and AZM can promote QT interval lengthening and may be contraindicated in more advanced COVID-19 entailing cardiac damage, doxycycline has no such effect and exerts a potentially beneficial anti-inflammatory action. In contrast to HCQ, we propose that the combination of PTX + DIP can be used in both early and advanced stages of COVID-19. Concurrent use of certain nutraceuticals – yeast beta-glucan, zinc, vitamin D, spirulina, phase 2 inducers, N-acetylcysteine, glucosamine, quercetin, and magnesium – might also improve therapeutic outcomes in COVID-19. url: https://api.elsevier.com/content/article/pii/S0306987720317382 doi: 10.1016/j.mehy.2020.110051 id: cord-262726-lfuxhlki author: Diallo, Aïssatou Bailo title: Daytime variation in SARS-CoV-2 infection and cytokine production date: 2020-09-11 words: 1156.0 sentences: 77.0 pages: flesch: 51.0 cache: ./cache/cord-262726-lfuxhlki.txt txt: ./txt/cord-262726-lfuxhlki.txt summary: Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. Importance The implication of circadian rhythm (CR) in pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recently anticipated. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. abstract: S. Ray and A. Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). In addition to its key role in the regulation of biological functions, the circadian rhythm has been suggested as a regulator of viral infections. Specifically, the time of day of infection was found critical for illness progression, as has been reported for influenza, respiratory syncytial and parainfluenza type 3 viruses. We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. The circadian gene expression of Bmal1 and Clock genes was investigated with q-RTPCR. Monocytes were infected with SARS-CoV-2 virus strain and viral infection was investigated by One-Step qRT-PCR and immunofluorescence. Interleukin (IL)-6, IL-1β and IL-10 levels were also measured in supernatants of infected monocytes. Using Cosinor analysis, we showed that Bmal1 and Clock transcripts exhibited circadian rhythm in monocytes with an acrophase and a bathyphase at Zeitgeber Time (ZT)6 and ZT17. After forty-eight hours, the amount of SARS-CoV-2 virus increased in the monocyte infected at ZT6 compared to ZT17. The high virus amount at ZT6 was associated with significant increased release in IL-6, IL-1β and IL-10 compared to ZT17. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. They support consideration of circadian rhythm in SARS-CoV-2 disease progression and we propose circadian rhythm as a novel target for managing viral progression. Importance The implication of circadian rhythm (CR) in pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recently anticipated. The time of day of infection is critical for illness progression as reported for influenza, respiratory syncytial and parainfluenza type 3 viruses. In this study, we wondered if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells affected by Covid-19, were regulated by CR. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. They support consideration of circadian rhythm in SARS-CoV-2 disease progression and we propose circadian rhythm as a novel target for managing viral progression. url: https://doi.org/10.1101/2020.09.09.290718 doi: 10.1101/2020.09.09.290718 id: cord-257789-pdybfft6 author: Diamond, Betty title: SARS-CoV-2 and interferon blockade date: 2020-11-09 words: 3583.0 sentences: 200.0 pages: flesch: 43.0 cache: ./cache/cord-257789-pdybfft6.txt txt: ./txt/cord-257789-pdybfft6.txt summary: We propose that SARS-CoV-2 activates the innate immune system through the renin-angiotensin and kallikrein-bradykinin pathways, blocks interferon production and reduces an effective adaptive immune response. Here we propose that the systemic inflammation seen in Covid-19 patients results from the activation of two intersecting systems, the renin-angiotensin system (RAS) and the kallikrein-bradykinin system (Diamond 2020) . The engagement of these pathways helps explain how severe Covid-19 infection is characterized by massive inflammation in multiple target organs, a poor anti-viral response with little production of interferon, and little participation of the adaptive immune system. As we have hypothesized that some of the inflammation induced in severe, and perhaps even moderate, Covid-19 is the result of dysregulation of the RAS and kallikrein-bradykinin pathways, the associated players serve as potential therapeutic targets ( Fig. 1 ) As mentioned above, ACE inhibitors and AT1 blockers (ARBs) are approved and safe drugs. abstract: The response to viral infection generally includes an activation of the adaptive immune response to produce cytotoxic T cells and neutralizing antibodies. We propose that SARS-CoV-2 activates the innate immune system through the renin-angiotensin and kallikrein-bradykinin pathways, blocks interferon production and reduces an effective adaptive immune response. This model has therapeutic implications. url: https://www.ncbi.nlm.nih.gov/pubmed/33167852/ doi: 10.1186/s10020-020-00231-w id: cord-331786-wgt7kg6f author: Diego-Martin, Borja title: Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date: 2020-10-13 words: 7034.0 sentences: 326.0 pages: flesch: 45.0 cache: ./cache/cord-331786-wgt7kg6f.txt txt: ./txt/cord-331786-wgt7kg6f.txt summary: For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. abstract: The current CoVid-19 crisis is revealing the strengths and the weaknesses of the world’s capacity to respond to a global health crisis. A critical weakness has resulted from the excessive centralization of the current biomanufacturing capacities, a matter of great concern, if not a source of nationalistic tensions. On the positive side, scientific data and information have been shared at an unprecedented speed fuelled by the preprint phenomena, and this has considerably strengthened our ability to develop new technology-based solutions. In this work we explore how, in a context of rapid exchange of scientific information, plant biofactories can serve as a rapid and easily adaptable solution for local manufacturing of bioreagents, more specifically recombinant antibodies. For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. For the design of the antibodies we took advantage, among other data sources, of the DNA sequence information made rapidly available by other groups in preprint publications. mAbs were all engineered as single-chain fragments fused to a human gamma Fc and transiently expressed using a viral vector. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Our results indicate that gram amounts of anti-SARS-CoV-2 antibodies could be easily produced in little more than 6 weeks in repurposed greenhouses with little infrastructure requirements using N. benthamiana as production platform. Similar procedures could be easily deployed to produce diagnostic reagents and, eventually, could be adapted for rapid therapeutic responses. url: https://doi.org/10.1101/2020.10.13.331306 doi: 10.1101/2020.10.13.331306 id: cord-335347-vxl2flbn author: Diercks, Gillian R. title: Asymptomatic COVID-19 Infection in a Child with Nasal Foreign Body date: 2020-05-08 words: 1914.0 sentences: 104.0 pages: flesch: 40.0 cache: ./cache/cord-335347-vxl2flbn.txt txt: ./txt/cord-335347-vxl2flbn.txt summary: Aerosolized SARS-CoV-2 viral particles have been shown to remain viable for up to 3 hours 10 , raising concern about risk of exposure for healthcare workers during aerosol generating procedures (APGs), including endoscopy, in the nasal cavity, nasopharynx and upper airway. Prior to bringing the patient to the operating room, COVID-19 testing was pursued given concerns about the potential for asymptomatic infection in the pediatric population, and generation of aerosolized respiratory secretions during nasal endoscopy, suctioning and foreign body removal, in order to optimize protection of the perioperative care team and surgical staff. Preoperative planning and SARS-CoV2 testing is of particular importance for the pediatric population given the high proportion of SARS-CoV-2 infected children who are asymptomatic or exhibit minimal symptoms of COVID-19, but who may harbor significant viral loads in the nasopharynx and upper airway, placing healthcare workers at particular risk. abstract: While children, particularly infants, are susceptible to severe and critical COVID-19 disease, over 55% of pediatric cases are present in asymptomatic or mildly symptomatic children. Aerosolized SARS-CoV-2 viral particles remain viable for up to 3 hours, raising concern about risk to healthcare workers during aerosol generating procedures (APGs) in the airway and nasopharynx. Herein we describe the first case of a nasal foreign body in an asymptomatic child with SARS-CoV-2 infection. We discuss management of this child and highlight the importance of considering asymptomatic infection and preoperative testing when planning procedures of the airway in the COVID-19 era. url: https://doi.org/10.1016/j.ijporl.2020.110092 doi: 10.1016/j.ijporl.2020.110092 id: cord-282771-iwpx02v3 author: Dietzel, Steffen title: A joint action in times of pandemic: the German BioImaging recommendations for operating imaging core facilities during the SARS‐Cov‐2 emergency date: 2020-06-24 words: 2242.0 sentences: 140.0 pages: flesch: 55.0 cache: ./cache/cord-282771-iwpx02v3.txt txt: ./txt/cord-282771-iwpx02v3.txt summary: To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS‐CoV‐2 between users and staff. The outcome of this workshop, the first version of the "German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic" was published on the GerBI-GMB website a few days after the meeting. The aim of these recommendations is to help protecting users and staff working in a low-safety environment (mostly biosafety level 1) from accidental contagion by yet unidentified, asymptomatic SARS-CoV-2 carriers, and are based on our current still fragmentary knowledge of this virus. Thus, all surfaces that might get touched by different users during operating a microscope are to be disinfected before and after each usage to avoid potential spread of SARS-CoV-2 via this route. German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic abstract: Operating shared resource laboratories (SRL) in times of pandemic is a challenge for research institutions. In a multi‐user, high‐turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS‐CoV‐2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus‐free. These recommendations may prove useful for other types of SRLs. url: https://doi.org/10.1002/cyto.a.24178 doi: 10.1002/cyto.a.24178 id: cord-281717-kzd9vvci author: Digard, Paul title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 words: 4473.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-281717-kzd9vvci.txt txt: ./txt/cord-281717-kzd9vvci.txt summary: CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . abstract: CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development, and if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the newly emerged SARS-CoV-2 genome was characterised in the context of other coronaviruses. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. While ORF10 is only present in the genomes of a subset of coronaviruses, E is essential for virus replication. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. Phylogeny indicates that this is an ancestrally-derived trait reflecting their origin in bats, rather than something selected for after zoonotic transfer. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine. url: https://doi.org/10.1101/2020.05.08.083816 doi: 10.1101/2020.05.08.083816 id: cord-300696-alpztpzw author: Dilek, Tugce Damla title: THE IMPACT OF SARS-COV 2 ON THE ANXIETY LEVELS OF SUBJECTS AND ON THE ANXIETY AND DEPRESSION LEVELS OF THEIR PARENTS date: 2020-10-26 words: 4238.0 sentences: 215.0 pages: flesch: 60.0 cache: ./cache/cord-300696-alpztpzw.txt txt: ./txt/cord-300696-alpztpzw.txt summary: This study was conducted to evaluate the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety depression status of their parents. In this study, we aimed to evaluate the the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety -depression status of their parents. Disease flares, problems about reaching the hospitals, and medication, any history of contact with confirmed SARS-CoV2 infections of self or family members, encounters with digital screen, workout program, caring about diet, use of vitamins, direct exposure to sunlight, obeying the 14 rules recommended by the Ministry of Health and similar issues were questioned in the survey. The patient and control groups were compared according to STAI scores to investigate the anxiety status during SARS-CoV2 pandemic. abstract: BACKGROUND: The Severe Acute Respiratory Syndrome-CoV2 outbreak was announced a pandemic by the World Health Organization on March 11th, 2020. Both the pandemic itself and the restrictions were thought to create some psychological problems especially in patients with chronic illnesses such as Multiple Sclerosis (MS). This study was conducted to evaluate the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety - depression status of their parents. METHODS: This study was performed on a group of pediatric MS patients aged 8-18 years in Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, and Child Neurology Department. Thirty patients with MS and their 30 parents were enrolled to the study. The control group consisted of 49 healthy, age- and sex-matched children and their 49 parents. The patients (and their parents) were asked to complete a web-based survey evaluating access to health care and other changes in daily life between March 11(th), 2020 and June 1st, 2020. The State-Trait Anxiety Inventory (STAI) [which is composed of two parts; S-anxiety (STAI-S) and T-anxiety (STAI-T)] was administrated to the patients and healthy controls and the results were compared between the two groups to assess their anxiety levels. The Hospital Anxiety and Depression Scale (HAD) [which is composed of two parts; HAD-anxiety (HAD-A) and HAD-depression (HAD-D)] was also given to all parents. The results of the HAD tests were compared between the two groups statistically. RESULTS: The results of the web-based survey showed that 4 of 9 (44.4 %) patients, who had a regular workout program, left the program and 13 (43.3 %) patients put on weight during the pandemic. Twenty-two patients (73.3 %) could not get direct exposure to sunlight because of the curfew. Therefore, approximately half of the patients started to take vitamin D supplement. Most of the patients (80 %) thought that they had higher risk and believed that they would have severe symptoms compared to healthy people. Twenty one (70%) patients disrupted their regular health checks and the most frequent causes were identified as closure of policlinics to routine patient care (33%) and concerns of getting SARS-CoV2 infection (26,6 %). Two of 3 patients who had an MS attack did not go to the doctor during this period. The mean STAI-S scores in MS patients were significantly higher compared to the healthy controls (p=<0.001). The level of S-anxiety in all patients was higher compared to the cut off value.The mean HAD A score was found to be significantly higher in them compared to the parents of healthy individuals (p= 0.001). CONCLUSION: Our results showed that children with MS had negative changes in daily life and high anxiety levels during the pandemic. Since MS patients have also psychiatric comorbidities, they may need psychosocial support especially in this period. Besides, establishment of separate health centers to be used during pandemics for children with chronic illnesses such as MS may be recommended to facilitate access to health care. url: https://www.sciencedirect.com/science/article/pii/S2211034820306696?v=s5 doi: 10.1016/j.msard.2020.102595 id: cord-334584-xh41koro author: Dilucca, Maddalena title: Temporal evolution and adaptation of SARS-COV 2 codon usage date: 2020-05-29 words: 3955.0 sentences: 210.0 pages: flesch: 56.0 cache: ./cache/cord-334584-xh41koro.txt txt: ./txt/cord-334584-xh41koro.txt summary: Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), non-structural 3C-like proteinase (3CLpro), ssRNA-binding protein (RBP), 2''-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase, RNA-dependent RNA polymerase (RdRp), Nsp7, Nsp8, and exonuclease ExoN. An EN C plot analysis was performed to estimate the relative contributions of mutational bias and natural selection in shaping CUB of 13 genes encoding proteins that are crucial for SARS-CoV-2. For the funtionally important genes in each genome, we calculated the average values of CAI and ENC over time, as compared to the reference SARS-CoV-2 sequence (WSM). Based on the SiD combined with the CAI results ( Figure 5 ), we suggest that SARS-CoV-2, over time, has preferentially accumulated mutations in its genome which correspond to codons that adapt better to the human host. abstract: The outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. In this study, we compared 15,259 SARS-CoV-2 genomes isolated from 60 countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), non-structural 3C-like proteinase (3CLpro), ssRNA-binding protein (RBP), 2’-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase, RNA-dependent RNA polymerase (RdRp), Nsp7, Nsp8, and exonuclease ExoN. As a general rule, we find that SARS-CoV-2 genome tends to diverge over time by accumulating mutations on its genome and, specifically, on the coding sequences for proteins N and S. Interestingly, different patterns of codon usage were observed among these genes. Genes S, Nsp7, NSp8, tend to use a norrower set of synonymous codons that are better optimized to the human host. Conversely, genes E and M consistently use a broader set of synonymous codons, which does not vary with respect to the reference genome. We identified key SARS-CoV-2 genes (S, N, ExoN, RNase, RdRp, Nsp7 and Nsp8) suggested to be causally implicated in the virus adaptation to the human host. url: https://doi.org/10.1101/2020.05.29.123976 doi: 10.1101/2020.05.29.123976 id: cord-333453-v3gap8kj author: Dima, Mirabela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 words: 3020.0 sentences: 173.0 pages: flesch: 52.0 cache: ./cache/cord-333453-v3gap8kj.txt txt: ./txt/cord-333453-v3gap8kj.txt summary: The novel coronavirus officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Virus generated a pandemic, which erupted in Hubei, Wuhan, China and quickly spread throughout the world, [1, 2] has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. The clinic where the patient was born discharged her and the mother on April 6, 2020 both being negative for SARS-CoV-2 (RT-PCR test). On April 15, after 3 days of observing cough, lethargy, loss of appetite, jaundice, and constant fever, the mother presented in emergency room with the newborn, both being tested positive for SARS-CoV-2. [10] We believe it is important in the current epidemiologic context to mention that all 3 patients were discharged from the clinic where they were born with SARS-CoV-2 negative tests (RT-PCR), which were taken in conformity with our national protocol regarding COVID-19. abstract: RATIONALE: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, which quickly spread throughout the world, has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. Although pediatric cases are rare, the group age under 12 months has been in general more susceptible to develop severe forms of the disease compared with the patients in the age interval of 1 to 18 years. PATIENT CONCERNS: Three newborns have been tested positive for SARS-CoV-2 infection. One of them presented bilateral decreased air entry, while the other 2 had no respiratory symptomatology. All 3 developed diaper erythema and oral candidiasis. DIAGNOSIS: For building up the report, newborns that were positive for coronavirus disease 2019 (COVID-19) infection were included in the case series. The chest X-ray of the symptomatic patient revealed a medium degree of hilar parenchymal infiltration and a slight infiltration of the visceral pleura. INTERVENTIONS: The patients were admitted in our isolated neonatology ward. All of them received antifungal treatment for the oral candidiasis and topic cream for diaper erythema. The symptomatic patient also received prophylactic antibiotherapy, human immunoglobulins, aminophylline, and parenteral nutrition. OUTCOMES: All 3 neonates were discharged after 2 consecutive negative tests for SARS-CoV-2. Patients 1 and 2 fully recovered, whereas the condition of patient 3 improved. LESSONS: Even if there are only a few reported cases of neonates infected with COVID-19 and most of them present mild manifestations, newborns need a more careful insight because of the nonspecific symptomatology. url: https://www.ncbi.nlm.nih.gov/pubmed/32871986/ doi: 10.1097/md.0000000000021284 id: cord-256633-vls23fu5 author: Dimeglio, Chloé title: The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France date: 2020-04-29 words: 1336.0 sentences: 88.0 pages: flesch: 63.0 cache: ./cache/cord-256633-vls23fu5.txt txt: ./txt/cord-256633-vls23fu5.txt summary: We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. Our statistical model for predicting the spread of SARS-CoV-2 in France is based on a diffusion and transmission coefficient that varies with an individual''s age, the likelihood of contagion, and two administration parameters (confinement and quarantine). Figures 1.b, 1 .c, 1.d, 1.e showed predictions of new cases per day depending on the SARS-CoV-2 seroprevalence before and after the containment phase. Our data indicate that seroprevalence must reach approximately 50% after total deconfinement on May 11 or a gradual exit phase over several months starting on May 11 if an infection rebound is to be avoided (Figure 1 .d, 1.e and Figure 2 .b). abstract: A new virus, SARS-CoV-2, has spread world-wide since December 2019, probably affecting millions of people and killing thousands. Failure to anticipate the spread of the virus now seriously threatens many health systems. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. url: https://api.elsevier.com/content/article/pii/S0163445320302425 doi: 10.1016/j.jinf.2020.04.031 id: cord-268335-mfcjldu3 author: Dimeglio, Chloé title: Children are protected against SARS-CoV-2 infection date: 2020-05-20 words: 556.0 sentences: 38.0 pages: flesch: 56.0 cache: ./cache/cord-268335-mfcjldu3.txt txt: ./txt/cord-268335-mfcjldu3.txt summary: Chloé Dimeglio 1,2* , Jean-Michel Mansuy 2 , Sandrine Charpentier 3,4 , Isabelle Claudet 4,5 , and Jacques Izopet 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. As infants and young children infected with respiratory tract viruses are particularly at risk of hospitalization (3) the paucity of pediatric patients with COVID-19 has raised many questions for clinicians, epidemiologists and scientists. The study previously published by Lancet Infectious Disease has important implications for the clinical management of these patients and the social distancing needed to prevent virus transmission (4). The abovementioned study has found that children are susceptible to SARS-CoV-2 infection, but rarely display any physical signs of the disease. The most important finding emerging from this analysis is the clear evidence that children are less susceptible to SARS-CoV-2 infection than adults. While children have been regarded as facilitators of virus transmission, we now need to identify the mechanism which protects them, at least partially, against SARS-CoV-2 infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32454427/ doi: 10.1016/j.jcv.2020.104451 id: cord-017070-05vlz5dn author: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 words: 6662.0 sentences: 299.0 pages: flesch: 38.0 cache: ./cache/cord-017070-05vlz5dn.txt txt: ./txt/cord-017070-05vlz5dn.txt summary: These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121542/ doi: 10.1007/978-1-59745-569-5_34 id: cord-303377-lkewcf8a author: Dimke, H. title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date: 2020-05-27 words: 4112.0 sentences: 205.0 pages: flesch: 52.0 cache: ./cache/cord-303377-lkewcf8a.txt txt: ./txt/cord-303377-lkewcf8a.txt summary: Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. A total of 87 clinical sample specimens were chosen based on SARS-CoV-2 status from the Cobas ® 6800 system and used to evaluate the analytical sensitivity, specificity and accuracy of our in-house SARS-CoV-2 RT-qPCR assay after RNA purification using the Maxwell ® RSC 48 and AGPC methods. The AGPC method delivers high analytical sensitivity, specificity and accuracy for SARS-CoV-2 testing To evaluate whether conventional AGPC based extraction of RNA could serve as a viable alternative to automated systems with respect to reliability and accuracy, we isolated RNA using the AGPC method from 87 clinical specimens (oropharyngeal or nasopharyngeal swabs) with known SARS-CoV-2 status (57 positive and 30 negative), and performed a side-by-side comparison with the identical samples extracted on a Maxwell ® RSC 48 instrument. abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 remains essential for tracking and containing the rapid spread of the virus. However, due to increased global demand, kits and proprietary reagents for RNA extraction are limited, which markedly reduce SARS-CoV-2 testing capabilities in many countries. Here, we explore the use of conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA purification as an alternative to commercial automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical oropharyngeal or nasopharyngeal swab specimens were extracted by AGPC and compared to the commercial platforms, the Maxwell(R) RSC 48 instrument for automated RNA extraction and the fully integrated diagnostic system, the Cobas(R)6800 apparatus. Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, we find that the AGPC method is easily scalable and implemented in conventional laboratories. Taken together, these data identify conventional AGPC-based RNA extraction as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2, when automated systems, kits and reagents are not readily available. url: http://medrxiv.org/cgi/content/short/2020.05.26.20099440v1?rss=1 doi: 10.1101/2020.05.26.20099440 id: cord-284829-dge21g0g author: Dinakaran, Damodharan title: Neuropsychiatric aspects of COVID-19 Pandemic: A Selective Review date: 2020-05-30 words: 2288.0 sentences: 174.0 pages: flesch: 38.0 cache: ./cache/cord-284829-dge21g0g.txt txt: ./txt/cord-284829-dge21g0g.txt summary: In this selective review, the authors present the neuropsychiatric manifestations and postulated mechanisms of COVID-19. Though the most common presentation is a self limiting viral illness with fever and dry cough, severe infection is reported in 15-20% of the affected population (26) . In about 5% of the severely ill patients, Acute Respiratory Distress Syndrome (ARDS), Multi organ involvement and septic shock leads to further clinical deterioration. Acute polyradiculopathy (Guillain Barre Syndrome -GBS) has been reported related to SARS-CoV-2 infection (41) (42) (43) (44) (45) (46) . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain Barre syndrome associated with COVID-19 infection: A case report abstract: Corona virus disease (COVID-19) has been declared as a controllable pandemic by the World Health Organization (WHO). COVID-19 though is a predominantly respiratory illness; it can also affect brain and other organs like kidneys, heart and liver. Neuropsychiatric manifestations are common during viral pandemics but are not effectively addressed. Fever and cough are common symptoms only in infected individuals but headache and sleep disturbances are common even in uninfected general public. In this selective review, the authors report the available evidence of neuropsychiatric morbidity during the current COVID-19 crisis. The authors also discuss the postulated neuronal mechanisms of the corona virus infection sequelae. url: https://doi.org/10.1016/j.ajp.2020.102188 doi: 10.1016/j.ajp.2020.102188 id: cord-348777-pk9y6vfp author: Ding, Cheng title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 words: 3609.0 sentences: 190.0 pages: flesch: 46.0 cache: ./cache/cord-348777-pk9y6vfp.txt txt: ./txt/cord-348777-pk9y6vfp.txt summary: title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Our observational results revealed that corticosteroid therapy had no positive effect on the durations of SARS-CoV-2 RNA clearance among patients with mild COVID-19. Results from this study suggested that patients with mild COVID-19 may not benefit from corticosteroid therapy in terms of the duration of SARS-CoV-2 clearance. abstract: INTRODUCTION: In December, 2019, an outbreak of the coronavirus disease 2019 (COVID-19), which was caused by a novel coronavirus, started in Wuhan, China. So far, there is limited clinical evidence on the effect of corticosteroid therapy for this disease. This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. METHODS: Patients with mild COVID-19 were enrolled from two medical centers in China between January 13, 2020 and February 29, 2020. Baseline characteristics and durations of RNA clearance were compared between the corticosteroid and non-corticosteroid therapy groups. The independent effects of corticosteroid therapy on the duration of RNA clearance were estimated by generalized linear models. RESULTS: Of 82 patients with a mild infection, 40 patients were male (48.8%), with a median age of 49 years (interquartile range, IQR 36–61). Among those patients, 36 patients (43.9%) received corticosteroid therapy. The adjusted multivariate models showed that the effects of corticosteroids were non-significant on the durations of onset to first RNA clearance [β 2.48, 95% CI (95% confidence interval) − 0.42 to 5.38, P = 0.0926] and to persistent RNA clearance (β 1.54, 95% CI − 1.41 to 4.48, P = 0.3016), and durations of therapy to first RNA clearance (β 2.16, 95% CI − 0.56 to 4.89, P = 0.1184) and to persistent RNA clearance (β 1.22, 95% CI − 1.52 to 3.95, P = 0.3787). CONCLUSIONS: Corticosteroid therapy in patients with mild COVID-19 was not associated with the duration of SARS-CoV-2 clearance, suggesting that the use of corticosteroids may not be beneficial for patients with mild COVID-19 and should be prudently recommended in clinical practice. However, further studies are needed to verify the findings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40121-020-00337-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32986226/ doi: 10.1007/s40121-020-00337-y id: cord-346263-8znpqcth author: Ding, Huiling title: Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu date: 2014-04-13 words: 9976.0 sentences: 415.0 pages: flesch: 44.0 cache: ./cache/cord-346263-8znpqcth.txt txt: ./txt/cord-346263-8znpqcth.txt summary: This essay examines how Chinese governments, local communities, and overseas Chinese in North America responded to the perceived health risks of Severe Acute Respiratory Syndrome (SARS) and H1N1 flu through the use of public and participatory rhetoric about risk and quarantines. One instance of mandatory quarantine is the widespread use of community entry surveillance tools such as temperature monitoring and health registration forms to identify floating people returning from severely SARS affected regions such as Guangdong or Beijing. As a sharp contrast to Asian American and Asian Canadian''s use of coerced quarantines as responses to racial targeting in SARS, overseas Chinese from H1N1 epicenters implemented voluntary quarantines when travelling back to China to reduce potential health risks they might have posed to local communities and the nation. abstract: This essay examines how Chinese governments, local communities, and overseas Chinese in North America responded to the perceived health risks of Severe Acute Respiratory Syndrome (SARS) and H1N1 flu through the use of public and participatory rhetoric about risk and quarantines. Focusing on modes of security and quarantine practices, I examine how globalization and the social crises surrounding SARS and H1N1 flu operated to regulate differently certain bodies and areas. I identify three types of quarantines (mandatory, voluntary, and coerced) and conduct a transnational comparative analysis to investigate the relationships among quarantines, rhetoric, and public communication. I argue that health authorities must openly acknowledge the legitimacy of public input and actively seek public support regarding health crises. Only by collaborating with concerned communities and citizens and by providing careful guidance for public participation can health institutions ensure the efficacy of quarantine orders during emerging epidemics. url: https://doi.org/10.1007/s10912-014-9282-8 doi: 10.1007/s10912-014-9282-8 id: cord-319519-mb9ofh12 author: Ding, J. title: A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes'' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date: 2020-07-02 words: 7247.0 sentences: 474.0 pages: flesch: 52.0 cache: ./cache/cord-319519-mb9ofh12.txt txt: ./txt/cord-319519-mb9ofh12.txt summary: The algorithm establishes the shortest path between 118 the candidate genes and the known host interacting proteins with SARS-CoV-2 and calculates an 119 overall connectivity score for the network (a smaller value represents a greater connectivity) ( Fig 120 1 and Supplementary Table S1 ). The network-informed analysis presented in this paper, 262 revealed that 1) the top GO biological function associated with HLH genes is neutrophil 263 degranulation, consistent with a recent report highlighting the undervalued role of neutrophils in 264 HLH 36 ; 2) HLH genes are significantly enriched with the SARS-CoV-2 human interactome; 3) the 265 top-ranked HLH gene, AP3B1, has roles in cargo loading of type II pneumocytes, where it may 266 interact with SARS-CoV-2 to disturb surfactant physiological functions to promote 267 inflammation/pro-coagulation activities; 4) diseases/syndromes-associated with increased release 268 of Neutrophil Extracellular Traps (NETs) may predict vulnerable populations, including those 269 affecting children. abstract: Abnormal coagulation and an increased risk of thrombosis are features of severe COVID-19, with parallels proposed with hemophagocytic lymphohistiocytosis (HLH), a life-threating condition associated with hyperinflammation. The presence of HLH was described in severely ill patients during the H1N1 influenza epidemic, presenting with pulmonary vascular thrombosis. We tested the hypothesis that genes causing primary HLH regulate pathways linking pulmonary thromboembolism to the presence of SARS-CoV-2 using novel network-informed computational algorithms. This approach led to the identification of Neutrophils Extracellular Traps (NETs) as plausible mediators of vascular thrombosis in severe COVID-19 in children and adults. Taken together, the network-informed analysis led us to propose the following model: the release of NETs in response to inflammatory signals acting in concert with SARS-CoV-2 damage the endothelium and direct platelet-activation promoting abnormal coagulation leading to serious complications of COVID-19. The underlying hypothesis is that genetic and/or environmental conditions that favor the release of NETs may predispose individuals to thrombotic complications of COVID-19 due to an increase risk of abnormal coagulation. This would be a common pathogenic mechanism in conditions including autoimmune/infectious diseases, hematologic and metabolic disorders. url: http://medrxiv.org/cgi/content/short/2020.07.01.20144121v1?rss=1 doi: 10.1101/2020.07.01.20144121 id: cord-334833-7gv1c7we author: Ding, Yanqing title: The clinical pathology of severe acute respiratory syndrome (SARS): a report from China date: 2003-07-01 words: 2615.0 sentences: 138.0 pages: flesch: 48.0 cache: ./cache/cord-334833-7gv1c7we.txt txt: ./txt/cord-334833-7gv1c7we.txt summary: The pulmonary lesions included bilateral extensive consolidation, localized haemorrhage and necrosis, desquamative pulmonary alveolitis and bronchitis, proliferation and desquamation of alveolar epithelial cells, exudation of protein and monocytes, lymphocytes and plasma cells in alveoli, hyaline membrane formation, and viral inclusion bodies in alveolar epithelial cells. Systemic vasculitis included oedema, localized fibrinoid necrosis, and infiltration of monocytes, lymphocytes, and plasma cells into vessel walls in the heart, lung, liver, kidney, adrenal gland, and the stroma of striated muscles. With regard to the aetiology and pathogenesis of SARS, this study has demonstrated extensive pulmonary consolidation; significant pulmonary oedema; localized haemorrhage and necrosis; widespread hyaline membrane formation; a local inflammatory reaction consisting mostly of monocytes, lymphocytes, and plasma cells; desquamation of bronchial and alveolar epithelial cells; numerous multinucleate and mononuclear giant cells in pulmonary alveoli in two cases; and typical viral inclusion bodies in epithelial cells in alveoli in all the three cases. abstract: In order to investigate the clinical pathology of severe acute respiratory syndrome (SARS), the autopsies of three patients who died from SARS in Nan Fang Hospital Guangdong, China were studied retrospectively. Routine haematoxylin and eosin (H&E) staining was used to study all of the tissues from the three cases. The lung tissue specimens were studied further with Macchiavello staining, viral inclusion body staining, reticulin staining, PAS staining, immunohistochemistry, ultrathin sectioning and staining, light microscopy, and transmission electron microscopy. The first symptom was hyperpyrexia in all three cases, followed by progressive dyspnoea and lung field shadowing. The pulmonary lesions included bilateral extensive consolidation, localized haemorrhage and necrosis, desquamative pulmonary alveolitis and bronchitis, proliferation and desquamation of alveolar epithelial cells, exudation of protein and monocytes, lymphocytes and plasma cells in alveoli, hyaline membrane formation, and viral inclusion bodies in alveolar epithelial cells. There was also massive necrosis of splenic lymphoid tissue and localized necrosis in lymph nodes. Systemic vasculitis included oedema, localized fibrinoid necrosis, and infiltration of monocytes, lymphocytes, and plasma cells into vessel walls in the heart, lung, liver, kidney, adrenal gland, and the stroma of striated muscles. Thrombosis was present in small veins. Systemic toxic changes included degeneration and necrosis of the parenchyma cells in the lung, liver, kidney, heart, and adrenal gland. Electron microscopy demonstrated clusters of viral particles, consistent with coronavirus, in lung tissue. SARS is a systemic disease that injures many organs. The lungs, immune organs, and systemic small vessels are the main targets of virus attack, so that extensive consolidation of the lung, diffuse alveolar damage with hyaline membrane formation, respiratory distress, and decreased immune function are the main causes of death. Copyright © 2003 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/12845623/ doi: 10.1002/path.1440 id: cord-023862-fakapdcc author: Dinman, Jonathan D. title: Programmed –1 Ribosomal Frameshifting in SARS Coronavirus date: 2009-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In coronaviruses such as the SARS coronavirus (SARS-CoV), programmed −1 ribosomal frameshifting (−1 PRF) is used to direct the synthesis of immediate early proteins, e.g., RNA-dependent RNA polymerase (RDRP) and proteases, that are thought to prepare the infected cell for takeover by the virus. Unlike other RNA viruses which make their structural proteins first, this class of proteins is synthesized after −1 PRF, from subgenomic mRNAs produced subsequent to production of RDRP. Also unique among the coronaviruses is the inclusion of mRNA structural elements that do not appear to be essential for frameshifting. Understanding the differences between –1 PRF signals from coronaviruses and other viruses will enhance our understanding of –1 PRF in general, and will be instructive in designing new classes of antiviral therapeutics. In this chapter we summarize current knowledge and add additional insight to the function of the programmed –1 ribosomal frameshift signal present in the SARS-associated coronavirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176209/ doi: 10.1007/978-3-642-03683-5_5 id: cord-344246-sf9cymhc author: Diriba, Kuma title: The effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and the possibility of vertical maternal–fetal transmission: a systematic review and meta-analysis date: 2020-09-04 words: 5141.0 sentences: 253.0 pages: flesch: 46.0 cache: ./cache/cord-344246-sf9cymhc.txt txt: ./txt/cord-344246-sf9cymhc.txt summary: Previous outbreaks of coronaviruses include the severe acute respiratory syndrome (SARS)-CoV epidemic in 2003 [2] and the Middle East respiratory syndrome (MERS)-CoV in 2012 [3] , while the newly emergent coronavirus, initially referred to as 2019-nCoV and subsequently termed SARS-CoV-2, the disease it produces has been termed COVID-19, which causes respiratory infection and can progress to severe pneumonia and, in a small number of cases, death [4] . A systematic review and meta-analysis was aimed to assess the effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and its possibility of vertical maternal-fetal transmission following the methodological framework suggested by Arksey and O''Malley [15] . The primary outcome variable of this study was the pregnancy outcomes observed, listed as follows: preterm birth (PTB; either before 37 or 34 weeks of gestation), preeclampsia, preterm prelabor rupture of membranes, (pPROM), fetal growth restriction (FGR), miscarriage, maternal death, mode of delivery and other clinical feature, laboratory findings and coexisting disease. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes abstract: BACKGROUND: Coronavirus is challenging the global health care system from time to time. The pregnant state, with alterations in hormone levels and decreased lung volumes due to a gravid uterus and slightly immunocompromised state may predispose patients to a more rapidly deteriorating clinical course and can get a greater risk of harm for both the mother and fetus. Therefore, this systematic review was aimed to assess the effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and its possibility of vertical maternal–fetal transmission. METHODS: A systematic search was conducted on PubMed, Web of Science, Embase, Google Scholar and the Cochrane Library until the end of April. All authors independently extracted all necessary data using excel spreadsheet form. Only published articles with fully accessible data on pregnant women infected with SARS-CoV, MARS-CoV, and SARS-CoV-2 were included. Data on clinical manifestations, maternal and perinatal outcomes were extracted and analyzed. RESULT: Out of 879 articles reviewed, 39 studies involving 1316 pregnant women were included. The most common clinical features were fever, cough, and myalgia with prevalence ranging from 30 to 97%, while lymphocytopenia and C-reactive protein were the most common abnormal laboratory findings (55–100%). Pneumonia was the most diagnosed clinical symptom of COVID-19 and non-COVID-19 infection with prevalence ranged from 71 to 89%. Bilateral pneumonia (57.9%) and ground-glass opacity (65.8%) were the most common CT imaging reported. The most common treatment options used were hydroxychloroquine (79.7%), ribavirin (65.2%), and oxygen therapy (78.8%). Regarding maternal outcome, the rate of preterm birth < 37 weeks of gestation was 14.3%, preeclampsia (5.9%), miscarriage (14.5%, preterm premature rupture of membranes (9.2%) and fetal growth restriction (2.8%). From the total coronavirus infected pregnant women, 56.9% delivered by cesarean, 31.3% admitted to ICU, while 2.7% were died. Among the perinatal outcomes, fetal distress rated (26.5%), neonatal asphyxia rated (1.4%). Only, 1.2% of neonates had apgar score < 7 at 5 min. Neonate admitted to ICU was rated 11.3%, while the rate of perinatal death was 2.2%. In the current review, none of the studies reported transmission of CoV from the mother to the fetus in utero during the study period. CONCLUSION: Coronavirus infection is more likely to affect pregnant women. Respiratory infectious diseases have demonstrated an increased risk of adverse maternal obstetrical complications than the general population due to physiological changes occurred during pregnancy. None of the studies reported transmission of CoV from the mother to the fetus in utero, which may be due to a very low expression of angiotensin-converting enzyme-2 in early maternal–fetal interface cells. url: https://www.ncbi.nlm.nih.gov/pubmed/32887660/ doi: 10.1186/s40001-020-00439-w id: cord-267613-hsc2x36j author: Dittmar, Mark title: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date: 2020-06-19 words: 7558.0 sentences: 452.0 pages: flesch: 50.0 cache: ./cache/cord-267613-hsc2x36j.txt txt: ./txt/cord-267613-hsc2x36j.txt summary: Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. Previous studies found that the antiviral drug remdesivir, which was developed against the RNA-dependent RNA polymerase of Ebola virus, was also active against SARS-CoV-2 in vitro, with promising results in clinical trials (5) (6) (7) . Both cepharanthine and tetrandrine were previously shown to have antiviral activity against the human coronavirus OC43 and in recent studies on SARS-CoV-2 in Vero cell screens (13, 62, 63) . Strikingly, the activities of all of these drugs is similar in the two cell lines suggesting the same target and mechanism-of-action and that Cyclosporine would block SARS-CoV-2 in diverse infected tissues in vivo. abstract: There are an urgent need for antivirals to treat the newly emerged SARS-CoV-2. To identify new candidates we screened a repurposing library of ~3,000 drugs. Screening in Vero cells found few antivirals, while screening in human Huh7.5 cells validated 23 diverse antiviral drugs. Extending our studies to lung epithelial cells, we found that there are major differences in drug sensitivity and entry pathways used by SARS-CoV-2 in these cells. Entry in lung epithelial Calu-3 cells is pH-independent and requires TMPRSS2, while entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent endosomal proteases. Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. These antivirals reveal essential host targets and have the potential for rapid clinical implementation. url: https://doi.org/10.1101/2020.06.19.161042 doi: 10.1101/2020.06.19.161042 id: cord-286084-2275xvxb author: Dixit, Alok title: Ivermectin: Potential Role as Repurposed Drug for COVID-19 date: 2020-08-19 words: 2238.0 sentences: 113.0 pages: flesch: 45.0 cache: ./cache/cord-286084-2275xvxb.txt txt: ./txt/cord-286084-2275xvxb.txt summary: Currently there is no effective treatment for coronavirus infection; major effort is to develop vaccine against the virus and development of therapeutic drugs for the disease. IVM is shown to be effective in vitro against RNA and deoxyribonucleic acid (DNA) viruses, including human immunodeficiency virus-1 (HIV-1), dengue virus (DENV), influenza, Venezuelan equine encephalitis virus (VEEV) and Zika virus (14) . Currently, remdesivir is a promising potential therapy for COVID-19 due to its broad-spectrum and potent in vitro activity against several novel coronavirus (nCoVs), including SARS-CoV-2 with EC 50 (half maximal effective concentration) and EC 90 (concentration to induce 90% maximal response) values of 0.77 μM and 1.76 μM, respectively (8). IVM which is a widely used as antiparasitic drug has shown to have antiviral activity in in vitro studies against HIV, dengue, influenza, VEEV and Zika virus. Studies are available for its use against RNA virus and have also been tested for its effectiveness against SARS-CoV-2 in vitro. abstract: Severe acute respiratory illness caused by 2019 novel coronavirus (2019-nCoV), officially named severe acute respiratory syndrome coronavirus (SARS-CoV-2) in late December 2019 is an extremely communicable disease. World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) as a pandemic as it has spread to at least 200 countries in a short span of time. Being a new disease there is lack of information about pathogenesis and proliferation pathways of this new coronavirus. Currently there is no effective treatment for coronavirus infection; major effort is to develop vaccine against the virus and development of therapeutic drugs for the disease. The development of genome-based vaccine and therapeutic antibodies require thorough testing for safety and will be available after some time. In the meanwhile, the available practical approach is to repurpose existing therapeutic agents, with proven safety record as a rapid response measure for the current pandemic. Here we discuss the presently used repurposed drugs for COVID-19 and the potential for ivermectin (IVM) to be used as a therapeutic option in COVID-19. url: https://doi.org/10.21315/mjms2020.27.4.15 doi: 10.21315/mjms2020.27.4.15 id: cord-291517-ifei60ly author: Dixon, Luke title: COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia date: 2020-05-26 words: 1835.0 sentences: 118.0 pages: flesch: 43.0 cache: ./cache/cord-291517-ifei60ly.txt txt: ./txt/cord-291517-ifei60ly.txt summary: title: COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia OBJECTIVE: To describe a novel case of coronavirus disease 2019 (COVID-19)-associated acute necrotizing encephalopathy (ANE) in a patient with aplastic anemia where there was early brain stem-predominant involvement. Nasopharyngeal swab testing for severe acute respiratory syndrome coronavirus (SARS-CoV-2) was positive, and CT during admission demonstrated diffuse swelling of the brain stem. 2 Here, we report a further case of possible COVID-19-related necrotizing hemorrhagic encephalopathy associated with early brain stem involvement. Extensive abnormal signal and microhemorrhage were found in a symmetrical distribution within the dorsolateral putamina, ventrolateral thalamic nuclei, subinsular regions, splenium of the corpus callosum, cingulate gyri, and subcortical Glossary ANE = acute necrotizing encephalopathy; COVID-19 = coronavirus disease 2019; GCS = Glasgow Coma Score; GTCS = generalized tonic-clonic seizure; SARS-CoV-2 = severe acute respiratory syndrome coronavirus 2. abstract: OBJECTIVE: To describe a novel case of coronavirus disease 2019 (COVID-19)-associated acute necrotizing encephalopathy (ANE) in a patient with aplastic anemia where there was early brain stem-predominant involvement. METHODS: Evaluation of cause, clinical symptoms, and treatment response. RESULTS: A 59-year-old woman with a background of transfusion-dependent aplastic anemia presented with seizures and reduced level of consciousness 10 days after the onset of subjective fever, cough, and headache. Nasopharyngeal swab testing for severe acute respiratory syndrome coronavirus (SARS-CoV-2) was positive, and CT during admission demonstrated diffuse swelling of the brain stem. She required intubation and mechanical ventilation for airway protection, given her reduced level of consciousness. The patient's condition deteriorated, and MRI on day 6 demonstrated worsening brain stem swelling with symmetrical hemorrhagic lesions in the brain stem, amygdalae, putamina, and thalamic nuclei. Appearances were consistent with hemorrhagic ANE with early brain stem involvement. The patient showed no response to steroid therapy and died on the eighth day of admission. CONCLUSIONS: COVID-19 may be associated with an acute severe encephalopathy and, in this case, was considered most likely to represent an immune-mediated phenomenon. As the pandemic continues, we anticipate that the spectrum of neurologic presentation will broaden. It will be important to delineate the full clinical range of emergent COVID-19-related neurologic disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32457227/ doi: 10.1212/nxi.0000000000000789 id: cord-343966-bfon094h author: Djaparidze, L. title: SARS-CoV-2 waves in Europe: A 2-stratum SEIRS model solution date: 2020-10-13 words: 9878.0 sentences: 605.0 pages: flesch: 61.0 cache: ./cache/cord-343966-bfon094h.txt txt: ./txt/cord-343966-bfon094h.txt summary: Almost every other finding in this paper also came from this tool: Immune level estimation sensitivity analysis (e.g. change Ro and fit); Estimating the spreading day if only one non-communitarian spreader is assumed (i.e. change initial spreading day until fitted initial spreaders is 1); Finding that Do=2 coupled with Eo=5 can explain the multiple valleys after lockdowns observed in the 1-day moving average daily death curves (i.e. fitting a dozen of different pairs of Do and Eo); Include lack of IgG in asymptomatic when predicting reported serology ratio (i.e. add TAK variable and equation); Estimate the proportion of asymptomatic for <60 and >60 (i.e. change proportions and fit until predicted asymptomatic to symptomatic ratio in Spain matches the reported = 1); Estimate that the proportion of SARS-CoV-2 positive reported deaths that are "with" the virus is 15% (i.e. add testing positive period parameter and yearly probability of dying for other causes to the predicted sars-cov2 positive deaths and lower IFR_vul until predicted serology ratio matches again); Estimate the minimum value of IFR_vul to have another wave in Brussels or the maximum that avoids the low one in Stockholm (i.e. change IFR_vul and fit until the second wave appears or disappears); Hypothesize that an early wave of a D614 like variant can be the cause of low mortality in most locations in Asia (i.e. fit with an hypothetical lower IFR_vul competing strain and then simulate setting the dominant spreading event 60 days earlier). abstract: In order to design actionable SARS-CoV-2 strategies, we extended the SEIRS model to support stratified isolation levels for healthy <60 and vulnerable individuals. At first, we forced isolation levels to be uniform, showing that daily deaths curves of all metropolitan areas in the analysis can be fitted using homogeneous Ro=3.3. In the process, we established the possibility that an extremely short infectiousness period of 2 days coupled with 5 days exposure may be responsible for the multiple deaths valleys observed during the weeks following lockdowns. Regardless of the infectiousness period, we realized that is possible to infer non-uniform isolation levels for healthy <60 and vulnerable by forcing the model to match the <60 to >60 age serology ratio reported in seroprevalence studies. Since the serology ratio is more robust than absolute values, we argue immunity level estimations made in this way (Madrid 43%; Catalonia 24%; Brussels 73%; and Stockholm 65%) are closer to reality. In locations where we did not find reliable serology, we performed immunity estimations assuming Spain serology ratio (Paris: 24%; London: 34%). We predict that, with the exception of Brussels, no location can return to normal life without having a second wave (albeit in Stockholm a smaller one). For locations far from the herd immunity threshold (HIT) we searched what isolation values allow to return to normal life in 90 days minimizing final deaths, shockingly all found isolations for healthy <60 were negative (i.e. coronavirus parties minimize final deaths). Then, assuming an ideal 1-day long vaccination campaign with a 77% efficacy vaccine, we compared predicted final deaths of those 90-day strategies for all possible vaccination dates with a 180-day long vaccine waiting strategy that imposes 0.40 mandatory isolation to healthy <60 and results in 0.65 isolation to vulnerable. We found that 180-day of mandatory isolations to healthy <60 (i.e. schools and workplaces closed) produces more final deaths if the vaccination date is later than (Madrid: March 7 2021; Catalonia: Dec 26 2020; Paris: Jan 12 2021; London: Jan 25 2021). We conclude that our 2-stratum SEIRS model is suitable to predict SARS-CoV-2 epidemic behavior and can be used to minimize covid-19 disease and isolations related damages. url: https://doi.org/10.1101/2020.10.09.20210146 doi: 10.1101/2020.10.09.20210146 id: cord-266885-a5fdeuvv author: Dlotko, P. title: Covid-19 clinical data analysis using Ball Mapper date: 2020-04-15 words: 2957.0 sentences: 207.0 pages: flesch: 64.0 cache: ./cache/cord-266885-a5fdeuvv.txt txt: ./txt/cord-266885-a5fdeuvv.txt summary: In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. Our target will be to locate any clusters of patients with particularly high value of variable 2 (positively of SARS-Cov-2 result), patients that have been admitted to a regular ward, semi intensive or intensive care unit. Our task is to present how the predictive variables 2, 3, 4 and 5 (SARS-Cov-2 result, standard ward, semi intensive care and intensive care admission) changes over P by examining how they change over the obtained Ball Mapper graph. The obtained Ball Mapper graph suggest that the patients, which are likely to have positive result for SARS-Cov2, have quite similar values coming from the blood tests. . Figure 6 : Ball Mapper graph for normalized data colored by the patients who required Intensive Care Unit. abstract: In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. We observe that patients with the virus and in particularly patients who end up in Intensive Care Unit have quite narrow values of those parameters. Please note that this is a preliminary work and it need to be validated on much larger dataset which we are trying to acquire at the moment. url: http://medrxiv.org/cgi/content/short/2020.04.10.20061374v1?rss=1 doi: 10.1101/2020.04.10.20061374 id: cord-305234-nclk7bbo author: Do, Mytrang H. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 words: 146.0 sentences: 19.0 pages: flesch: 58.0 cache: ./cache/cord-305234-nclk7bbo.txt txt: ./txt/cord-305234-nclk7bbo.txt summary: key: cord-305234-nclk7bbo authors: Do, Mytrang H.; Minkis, Kira; Petukhova, Tatyana A.; Lipner, Shari R. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.06.983 sha: doc_id: 305234 cord_uid: nclk7bbo nan . Furthermore, the patient''s mouth and nose are often exposed We hope that these suggestions provide the best possible protection for dermatologic efficiency particle air, RT-PCR, reverse transcription-polymerase chain reaction, SARS-CoV-2, 81 severe acute respiratory syndrome coronavirus 2 Head and neck surgery is a high-risk procedure for COVID-19 87 transmission and there is a need for a preventive strategy to protect professionals Detection of SARS-CoV-2 in Different Types of Clinical 4. American College of Surgeons. COVID-19: Considerations for Optimum Surgeon 19/clinical-guidance/surgeon-protection American Academy of Dermatology. Reopening the dermatologic surgery office in the abstract: nan url: https://api.elsevier.com/content/article/pii/S0190962220320831 doi: 10.1016/j.jaad.2020.06.983 id: cord-294304-9w6zt778 author: Doanvo, Anhvinh title: Machine Learning Maps Research Needs in COVID-19 Literature date: 2020-09-16 words: 5506.0 sentences: 283.0 pages: flesch: 50.0 cache: ./cache/cord-294304-9w6zt778.txt txt: ./txt/cord-294304-9w6zt778.txt summary: The projection values of COVID-19 abstracts on PC2 were lower and associated with 11 emergent COVID-19 clinical-, modeling-or field-based (CMF) research -such as observational, 12 clinical, and epidemiological studies -exemplified by stem terms "patient", "pandem", "estim", 13 and "case". 14 Furthermore, we developed a framework that improves upon existing bibliometric studies 15 in three key ways; namely, our approach (1) maps connections between publications by relying 16 directly on the abstracts instead of the narrow information gained from metadata as in other 17 bibliometric analyses, including those from other fields 9,10 ; (2) uses ML to explore latent 18 semantic information of vast scale and complexity to identify hidden trends; and (3) does not 19 rely on any a priori knowledge of what topics we expect coronavirus literature to cover but 20 rather highlights them without any preconceived assumptions. abstract: As of August 2020, thousands of COVID-19 (coronavirus disease 2019) publications have been produced. Manual assessment of their scope is an overwhelming task, and shortcuts through metadata analysis (e.g., keywords) assume that studies are properly tagged. However, machine learning approaches can rapidly survey the actual text of publication abstracts to identify research overlap between COVID-19 and other coronaviruses, research hotspots, and areas warranting exploration. We propose a fast, scalable, and reusable framework to parse novel disease literature. When applied to the COVID-19 Open Research Dataset (CORD-19), dimensionality reduction suggests that COVID-19 studies to date are primarily clinical-, modeling- or field-based, in contrast to the vast quantity of laboratory-driven research for other (non-COVID-19) coronavirus diseases. Furthermore, topic modeling indicates that COVID-19 publications have focused on public health, outbreak reporting, clinical care, and testing for coronaviruses, as opposed to the more limited number focused on basic microbiology, including pathogenesis and transmission. url: https://www.sciencedirect.com/science/article/pii/S2666389920301641?v=s5 doi: 10.1016/j.patter.2020.100123 id: cord-297684-9q3oopaz author: Dobaño, Carlota title: Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date: 2020-06-12 words: 5198.0 sentences: 226.0 pages: flesch: 41.0 cache: ./cache/cord-297684-9q3oopaz.txt txt: ./txt/cord-297684-9q3oopaz.txt summary: The Receptor-Binding Domain (RBD) of the spike (S) glycoprotein of SARS-CoV-2, the leading vaccine candidate target, was selected as the primary antigen to develop the initial qSAT assay because (i) S is one of the most immunogenic surface proteins together with the nucleocapsid protein (N) (20) (ii) RBD is the fragment of the virus that mediates binding to the host receptor ACE2 in the lung cells (21) (iii) antibodies to RBD correlate with neutralizing antibodies (20)(22) that could be associated with protection based on studies of other coronaviruses and animal models (23) (24) (25) (26) , and (iv) an ELISA based on this same protein has received FDA approval for COVID-19 serology (11) . We developed three novel multiplex immunoassays for quantifying IgM, IgA and IgG to eight SARS-CoV-2 protein constructs and evaluated by machine learning classification algorithms the performance of several isotype/antigen combinations to detect any positive antibody response to infection, obtaining specificities of 100% and sensitivities of 94.94% (≥14 days since symptoms onset) or 96.08% (≥21 days since symptoms onset), and very high predictability (AUC ≥0.99). abstract: Reliable serological tests are required to determine the prevalence of antibodies against SARS-CoV-2 antigens and to characterise immunity to the disease in order to address key knowledge gaps in the context of the COVID-19 pandemic. Quantitative suspension array technology (qSAT) assays based on the xMAP Luminex platform overcome the limitations of rapid diagnostic tests and ELISA with their higher precision, dynamic range, throughput, miniaturization, cost-efficacy and multiplexing capacity. We developed three qSAT assays to detect IgM, IgA and IgG to a panel of eight SARS-CoV-2 antigens including spike (S), nucleoprotein (N) and membrane (M) protein constructs. The assays were optimized to minimize processing time and maximize signal to noise ratio. We evaluated the performance of the assays using 128 plasmas obtained before the COVID-19 pandemic (negative controls) and 115 plasmas from individuals with SARS-CoV-2 diagnosis (positive controls), of whom 8 were asymptomatic, 58 had mild symptoms and 49 were hospitalized. Pre-existing IgG antibodies recognizing N, M and S2 proteins were detected in negative controls suggestive of cross-reactive to common cold coronaviruses. The best performing antibody isotype/antigen signatures had specificities of 100% and sensitivities of 94.94% at ≥14 days since the onset of symptoms and 96.08% at ≥21 days since the onset of symptoms, with AUC of 0.992 and 0.999, respectively. Combining multiple antibody markers as assessed by qSAT assays has the highest efficiency, breadth and versatility to accurately detect low-level antibody responses for obtaining reliable data on prevalence of exposure to novel pathogens in a population. Our assays will allow gaining insights into antibody correlates of immunity required for vaccine development to combat pandemics like the COVID-19. url: https://doi.org/10.1101/2020.06.11.147363 doi: 10.1101/2020.06.11.147363 id: cord-311477-gm0vg53l author: Doboszewska, Urszula title: Targeting zinc metalloenzymes in COVID‐19 date: 2020-07-15 words: 6194.0 sentences: 327.0 pages: flesch: 49.0 cache: ./cache/cord-311477-gm0vg53l.txt txt: ./txt/cord-311477-gm0vg53l.txt summary: We attempt to integrate data on the effects of agents targeting zinc fingers in viral metalloenzymes (zinc fingers targeting agents), which cause removal of zinc from the proteins, thus destabilizing the proteins and leading to increased intracellular concentration of zinc ions, and other agents which induce changes in intracellular levels of zinc (zinc ionophores), with data on consequences of altered level of intracellular zinc, with a focus on SARS-CoV-2 and related pathogens. Chloroquine, an old antimalarial drug (Blount, 1967) , was demonstrated to block virus infection at low micromolar concentration in Vero E6 cells infected with SARS-CoV-2 , thus suggesting the possible use of chloroquine in patients with COVID-19. With regard to COVID-19, a novel drug would target labile zinc fingers in SARS-CoV-2 proteins, thus destroying the proteins and producing an increase in intracellular concentration of zinc ions. abstract: Several lines of evidence support a link between the essential element zinc and the coronavirus disease 2019 (COVID‐19). An important fact is that zinc is present in proteins of humans and of viruses. Some zinc sites in viral enzymes may serve as drug targets and may liberate zinc ions, thus leading to changes in intracellular concentration of zinc ions, while increased intracellular zinc may induce biological effects in both the host and the virus. Drugs such as chloroquine may contribute to increased intracellular zinc. Moreover, clinical trials on the use of zinc alone or in addition to other drugs in the prophylaxis/treatment of COVID‐19 are ongoing. Thereby, we aim to discuss the rationale for targeting zinc metalloenzymes with regard to COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32671829/ doi: 10.1111/bph.15199 id: cord-349029-zyfop43z author: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 words: 4596.0 sentences: 233.0 pages: flesch: 48.0 cache: ./cache/cord-349029-zyfop43z.txt txt: ./txt/cord-349029-zyfop43z.txt summary: In order to estimate how effective these strategies will be, we will need a better understanding of the role of asymptomatic individuals in SARS-CoV-2 spread and the effect the proportion and relative infectiousness of asymptomatics have on the time course of the epidemic. In this paper, we study a compartmental epidemic model that includes asymptomatic infections to determine the role that asymptomatic individuals might play in the spread of SARS-CoV-2. We apply our model to data from SARS-CoV-2 epidemics in California, Florida, New York, and Texas, finding that a large number of infections in these states are unreported and that relaxing social distancing measures too early will cause a rapid spike in infections driven in part by these hidden infections. For the SARS-CoV epidemics examined here, the model predicts that there are far more asymptomatic or unreported cases at the peak of the infection, suggesting that there might be widespread community transmission if stay-at-home orders are relaxed too early. abstract: SARS-CoV-2 started causing infections in humans in late 2019 and has spread rapidly around the world. While the number of symptomatically infected and severely ill people is high and has overwhelmed the medical systems of many countries, there is mounting evidence that some of the rapid spread of this virus has been driven by asymptomatic infections. In this study, we use a compartmental mathematical model of a viral epidemic that includes asymptomatic infection to examine the role of asymptomatic individuals in the spread of the infection. We apply the model to epidemics in California, Florida, New York, and Texas, finding that asymptomatic infections far outnumber reported symptomatic infections at the peak of the epidemic in all four states. The model suggests that relaxing of social distancing measures too quickly could lead to a rapid rise in the number of cases, driven in part by asymptomatic infections. url: https://doi.org/10.1371/journal.pone.0236976 doi: 10.1371/journal.pone.0236976 id: cord-293615-f1e6hs11 author: Dockery, Dominique M. title: The Ocular Manifestations and Transmission of COVID-19; Recommendations for Prevention date: 2020-05-08 words: 903.0 sentences: 48.0 pages: flesch: 52.0 cache: ./cache/cord-293615-f1e6hs11.txt txt: ./txt/cord-293615-f1e6hs11.txt summary: Abstract Background Coronavirus disease-2019 (COVID-19), caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been linked to ocular signs and symptoms in several case reports. Research has demonstrated that SARS-CoV-2 is spread primarily through close contact via respiratory droplets, but there is the possibility for ocular transmission with the conjunctiva as a conduit as well as a source of infection. Discussion Ocular manifestations of SARS-CoV-2 include follicular conjunctivitis and have been repeatedly noted as an initial or subsequent symptom of COVID-19 positive patients. Particularly in patients with ocular manifestations, there is evidence that the virus may present in tears based on the detection of SARS-CoV-2 in conjunctival swab samples via reverse transcription polymerase chain reaction (RT-PCR). The conjunctivitis was noted to resolve at day 20 and the patient continued to have daily viral 109 SARS-CoV-2 RNA detection in ocular samples until day 21. abstract: Abstract Background Coronavirus disease-2019 (COVID-19), caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been linked to ocular signs and symptoms in several case reports. Research has demonstrated that SARS-CoV-2 is spread primarily through close contact via respiratory droplets, but there is the possibility for ocular transmission with the conjunctiva as a conduit as well as a source of infection. Discussion Ocular manifestations of SARS-CoV-2 include follicular conjunctivitis and have been repeatedly noted as an initial or subsequent symptom of COVID-19 positive patients. Particularly in patients with ocular manifestations, there is evidence that the virus may present in tears based on the detection of SARS-CoV-2 in conjunctival swab samples via reverse transcription polymerase chain reaction (RT-PCR). The virus may therefore be transmittable from the ocular surface to a new host via contact with the ocular mucosa, tears, or subsequent fomites. Conclusions All healthcare professionals should ask patients about ocular symptoms consistent with SARS-CoV-2, use eye protection such as goggles or face shields as part of the standard personal protective equipment (PPE) for high-risk patients in addition to wearing of masks both by the patient and provider, and should consider tears to be potentially infectious. url: https://api.elsevier.com/content/article/pii/S073646792030398X doi: 10.1016/j.jemermed.2020.04.060 id: cord-337444-pqoq8aew author: Doi, Kent title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series date: 2020-07-03 words: 988.0 sentences: 55.0 pages: flesch: 43.0 cache: ./cache/cord-337444-pqoq8aew.txt txt: ./txt/cord-337444-pqoq8aew.txt summary: title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series Through high-throughput screening of 1017 existing drugs, a clinically available serine protease inhibitor nafamostat mesylate was identified as a potent inhibitor of Middle East respiratory syndrome coronavirus entry into human epithelial cells [2] . Eleven adults with reverse transcriptase polymerase chain reaction-confirmed SARS-CoV-2 infection were admitted to the intensive care unit (ICU) at The University of Tokyo Hospital between April 6 and April 21, 2020, and treated with nafamostat mesylate in combination with favipiravir. Although the number of patients in this case series was very small, this low mortality rate suggests that combination treatment of favipiravir and nafamostat mesylate may be effective for critically ill Covid-19 patients. A clinical trial for the combination treatment of nafamostat mesylate and favipiravir against Covid-19 will be initiated in Japan (jRCTs031200026). Nafamostat mesylate blocks activation of SARS-CoV-2: new treatment option for COVID-19 abstract: nan url: https://doi.org/10.1186/s13054-020-03078-z doi: 10.1186/s13054-020-03078-z id: cord-255458-81ugj38k author: Doll, Michelle E. title: Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests date: 2020-05-11 words: 1169.0 sentences: 77.0 pages: flesch: 48.0 cache: ./cache/cord-255458-81ugj38k.txt txt: ./txt/cord-255458-81ugj38k.txt summary: title: Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests Infectious disease physicians designated each patient with high or low probability based on the following clinical criteria consistent with reported literature 7 : (1) exposure to SARS-CoV-2; (2) symptoms of COVID-19, including hypoxia, respiratory or gastrointestinal symptoms, or fever; (3) leukopenia; (4) chest imaging; (5) lack of other explanatory diagnosis. Overall, 70 inpatients with initially negative SARS-CoV-2 testing underwent repeat testing for ongoing clinical concerns between March 2 and April 4, 2020. Early interval retesting of patients with a high pretest probability for SARS-CoV-2 as part of a formal protocol was performed from March 31, 2020, through April 7, 2020. The patient who tested positive 6 days after a negative result was deemed "low probability" when re-evaluated for that repeat test. 3, 4 However, cases of high probability symptomatic patients with false-negative testing early in the course of illness have been reported. abstract: nan url: https://doi.org/10.1017/ice.2020.224 doi: 10.1017/ice.2020.224 id: cord-309619-glb2y82u author: Domingo, Pere title: The four horsemen of a viral Apocalypse: The pathogenesis of SARS-CoV-2 infection (COVID-19) date: 2020-07-29 words: 9353.0 sentences: 508.0 pages: flesch: 40.0 cache: ./cache/cord-309619-glb2y82u.txt txt: ./txt/cord-309619-glb2y82u.txt summary: Severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 lights the wick by infecting alveolar epithelial cells (AECs) and downregulating the angiotensin converting enzyme-2 (ACE2)/angiotensin (Ang-1–7)/Mas1R axis. SARS-CoV induces the signal transducer and activator of transcription 1 TACE TNF-a converting enzyme TBK1 TANK-binding kinase 1 TLR toll-like receptor TMPRSS2 type II transmembrane serine protease TNF-a tumor necrosis alpha TRAF3 TNF receptor-associated factor 3 XCR1 XCL1 (Chemokine [C motif] ligand 1) and XCL3 (Chemokine [C motif] ligand 3) receptor production of double-membrane vesicles that lack PRRs and can then replicate in these vesicles [18] . COVID-19 patients have high serum levels of inflammatory cytokines, including interleukin (IL)-2, IL-7, IL-10, granulocyte-colony stimulating factor (G-CSF), interferon gamma-induced protein (IP)-10, monocyte chemoattractant protein (MCP)-1, macrophage SARS-CoV-2 infects primarily type II pneumocytes through binding to the ACE2 receptor. ACE2 = Angiotensin-converting enzyme 2; SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2; Ang II = Angiotensin II; ROS = Reactive oxygen species; AT1R = Angiotensin 1 receptor; ADAM17 = A disintegrin and metalloproteinase domain 17; TNF-a = Tumor necrosis factor alpha; TMPRSS2 = transmembrane protease serine 2. abstract: The pathogenesis of coronavirus disease 2019 (COVID-19) may be envisaged as the dynamic interaction between four vicious feedback loops chained or happening at once. These are the viral loop, the hyperinflammatory loop, the non-canonical renin-angiotensin system (RAS) axis loop, and the hypercoagulation loop. Severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 lights the wick by infecting alveolar epithelial cells (AECs) and downregulating the angiotensin converting enzyme-2 (ACE2)/angiotensin (Ang-1–7)/Mas1R axis. The viral feedback loop includes evading the host's innate response, uncontrolled viral replication, and turning on a hyperactive adaptative immune response. The inflammatory loop is composed of the exuberant inflammatory response feeding back until exploding in an actual cytokine storm. Downregulation of the ACE2/Ang-(1–7)/Mas1R axis leaves the lung without a critical defense mechanism and turns the scale to the inflammatory side of the RAS. The coagulation loop is a hypercoagulable state caused by the interplay between inflammation and coagulation in an endless feedback loop. The result is a hyperinflammatory and hypercoagulable state producing acute immune-mediated lung injury and eventually, adult respiratory distress syndrome. url: https://doi.org/10.1016/j.ebiom.2020.102887 doi: 10.1016/j.ebiom.2020.102887 id: cord-308288-3ewdy5l3 author: Domingues, Renan Barros title: First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease date: 2020-06-20 words: 1163.0 sentences: 67.0 pages: flesch: 48.0 cache: ./cache/cord-308288-3ewdy5l3.txt txt: ./txt/cord-308288-3ewdy5l3.txt summary: However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74–100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs. The viral genome was demonstrated by RT-PCR technique in cerebrospinal fluid sample (CSF), suggesting that the virus has the ability to infect central nervous system (CNS) [1] . However, no case has been described of an association between SARS-COV-2 and CNS demyelinating disease so far. This case report suggests a possible association between CNS focal symptoms compatible with demyelinating disease and SARS-COV-2 infection. abstract: The association between coronaviruses and central nervous system (CNS) demyelinating lesions has been previously shown. However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. SARS-COV-2 was previously detected in cerebrospinal fluid (CSF) sample of a patient with encephalitis. However, the virus identity was not confirmed by deep sequencing of SARS-COV-2 detected in the CSF. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74–100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs. url: https://doi.org/10.1007/s00415-020-09996-w doi: 10.1007/s00415-020-09996-w id: cord-266444-rw94yls8 author: Dominguez Andres, Ana title: SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date: 2020-08-19 words: 5639.0 sentences: 305.0 pages: flesch: 44.0 cache: ./cache/cord-266444-rw94yls8.txt txt: ./txt/cord-266444-rw94yls8.txt summary: The interactome and proteome studies identified cellular processes affected by SARS-CoV-2 infection or specific viral proteins, notably innate immune signaling (19, 20, 23, (28) (29) (30) , ubiquitin ligase activities (19, 20, 23, (28) (29) (30) , p38 mitogenactivated protein kinase (MAPK) signaling (19, 20, 23, (28) (29) (30) . To assess if there were notable differences in the intensity of the changes in protein abundance in response to proteasome inhibition, we calculated relative changes in protein abundance between control and ORF9c-expressing cells from both the DMSO and MG132 conditions for proteins associated with IFN signaling or the ubiquitin proteasome (UBP) system and antigen presentation (Fig. 2D ). In contrast to the proteomic results that revealed predominant downregulation of proteins following ORF9c expression, RNA-seq analysis showed a similar number of transcripts were increased or decreased in the presence or absence of MG132 (Fig. 3A, table S2 ). abstract: Disrupted antiviral immune responses are associated with severe COVID-19, the disease caused by SAR-CoV-2. Here, we show that the 73-amino-acid protein encoded by ORF9c of the viral genome contains a putative transmembrane domain, interacts with membrane proteins in multiple cellular compartments, and impairs antiviral processes in a lung epithelial cell line. Proteomic, interactome, and transcriptomic analyses, combined with bioinformatic analysis, revealed that expression of only this highly unstable small viral protein impaired interferon signaling, antigen presentation, and complement signaling, while inducing IL-6 signaling. Furthermore, we showed that interfering with ORF9c degradation by either proteasome inhibition or inhibition of the ATPase VCP blunted the effects of ORF9c. Our study indicated that ORF9c enables immune evasion and coordinates cellular changes essential for the SARS-CoV-2 life cycle. One-sentence summary SARS-CoV-2 ORF9c is the first human coronavirus protein localized to membrane, suppressing antiviral response, resembling full viral infection. url: https://doi.org/10.1101/2020.08.18.256776 doi: 10.1101/2020.08.18.256776 id: cord-315415-3aotsb2g author: Dong, Jianbo title: Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2 date: 2020-10-20 words: 7194.0 sentences: 427.0 pages: flesch: 57.0 cache: ./cache/cord-315415-3aotsb2g.txt txt: ./txt/cord-315415-3aotsb2g.txt summary: In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19. (c) The binding of VHH-Fcs and ACE2 to Expi293 cells expressing SARS-CoV-2 S1 wild type (WT) or mutant proteins (del1-del5) were assessed by flow cytometry following FITC-conjugated secondary antibody treatment. Based on the binding and epitope binning data, we constructed 3D docking models that predicted the interactions between SARS-CoV-2 S1 RBD, ACE2 and lead VHH-Fcs (Fig. 2e) . Next, we tested whether the combination of individual VHHs binding to different S1 RBD epitopes into bi-specific antibody molecules would yield synergistic effects in SARS-CoV-2 binding and S/ACE2 blocking. abstract: SARS-CoV-2 is a newly emergent coronavirus, which has adversely impacted human health and has led to the COVID-19 pandemic. There is an unmet need to develop therapies against SARS-CoV-2 due to its severity and lack of treatment options. A promising approach to combat COVID-19 is through the neutralization of SARS-CoV-2 by therapeutic antibodies. Previously, we described a strategy to rapidly identify and generate llama nanobodies (VHH) from naïve and synthetic humanized VHH phage libraries that specifically bind the S1 SARS-CoV-2 spike protein, and block the interaction with the human ACE2 receptor. In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33082473/ doi: 10.1038/s41598-020-74761-y id: cord-354030-8tfg881h author: Dong, Rong title: Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date: 2020-07-28 words: 7983.0 sentences: 442.0 pages: flesch: 52.0 cache: ./cache/cord-354030-8tfg881h.txt txt: ./txt/cord-354030-8tfg881h.txt summary: The realm of immunoinformatics tools considers the mechanism of the host immune response to yield additional methodologies in the design of vaccine against diseases are cost-effective and convenient, as in silico predictions can reduce the number of experiments needed (13, 14) . In this present, we employed immunoinformatics to predict multiple immunogenic proteins from the SARS-CoV-2 proteome and thereby design a multi-epitope vaccine. developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . A vaccine based on the spike protein could induce antibodies to block SARS-COV-2 binding and fusion or neutralize virus infection (18) , as well as induce harmful immune responses that cause liver damage (19) . To design an effective vaccine, we selected the SARS-CoV-2 protein through the above-mentioned methods for epitope prediction. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach abstract: COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1–14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded, positive (+) sense RNA beta coronavirus. The development of a vaccine for SARS-CoV-2 is an urgent need worldwide. Immunoinformatics approaches are both cost-effective and convenient, as in silico predictions can reduce the number of experiments needed. In this study, with the aid of immunoinformatics tools, we tried to design a multi-epitope vaccine that can be used for the prevention and treatment of COVID-19. The epitopes were computed by using B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) base on the proteins of SARS-CoV-2. A vaccine was devised by fusing together the B cell, HTL, and CTL epitopes with linkers. To enhance the immunogenicity, the β-defensin (45 mer) amino acid sequence, and pan-HLA DR binding epitopes (13aa) were adjoined to the N-terminal of the vaccine with the help of the EAAAK linker. To enable the intracellular delivery of the modeled vaccine, a TAT sequence (11aa) was appended to C-terminal. Linkers play vital roles in producing an extended conformation (flexibility), protein folding, and separation of functional domains, and therefore, make the protein structure more stable. The secondary and three-dimensional (3D) structure of the final vaccine was then predicted. Furthermore, the complex between the final vaccine and immune receptors (toll-like receptor-3 (TLR-3), major histocompatibility complex (MHC-I), and MHC-II) were evaluated by molecular docking. Lastly, to confirm the expression of the designed vaccine, the mRNA of the vaccine was enhanced with the aid of the Java Codon Adaptation Tool, and the secondary structure was generated from Mfold. Then we performed in silico cloning. The final vaccine requires experimental validation to determine its safety and efficacy in controlling SARS-CoV-2 infections. url: https://doi.org/10.3389/fimmu.2020.01784 doi: 10.3389/fimmu.2020.01784 id: cord-333682-ktbnrkwh author: Dong, Yunzhu title: Antibodies in the breast milk of a maternal woman with COVID-19 date: 2020-07-03 words: 1332.0 sentences: 82.0 pages: flesch: 58.0 cache: ./cache/cord-333682-ktbnrkwh.txt txt: ./txt/cord-333682-ktbnrkwh.txt summary: A maternal woman was positive for SARS-CoV-2 tested in throat swabs but negative tested in other body fluids, and she had IgG and IgA detected in breast milk. Although clinical and laboratory characteristics, and outcomes of pregnant women with COVID-19 have been reported [4], there are no continuously monitored data about the viral loads in several body fluids of the maternal women that would bring potential risks of SARS-CoV-2 infection to neonates [8] . The titers of IgG antibody in breast milk were 2.34, 3.02, 2.84, 2.79, and 3.35, respectively, when three SARS-CoV-2 negative maternal woman''s breast milk were tested as control (mean titer 0.98) (Figure 1, panel D) . (D) Titers of IgG antibody to SARS-CoV-2 in maternal woman''s breast milk determined using ELISA. abstract: A maternal woman was positive for SARS-CoV-2 tested in throat swabs but negative tested in other body fluids, and she had IgG and IgA detected in breast milk. Her infant negative for SARS-CoV-2 at birth had elevated IgG in serum but quickly decayed. These findings suggest that breastfeeding might have the potential benefit to the neonates. url: https://www.ncbi.nlm.nih.gov/pubmed/32552365/ doi: 10.1080/22221751.2020.1780952 id: cord-342731-rilr45yb author: Donia, Ahmed title: RNA interference as a promising treatment against SARS-CoV-2 date: 2020-09-01 words: 844.0 sentences: 58.0 pages: flesch: 55.0 cache: ./cache/cord-342731-rilr45yb.txt txt: ./txt/cord-342731-rilr45yb.txt summary: Previous study also reported the production of plasmid-mediated small interfering RNAs (siRNAs) to target the viral RNA polymerase, which successfully inhibited the cytopathic effects of SARS-CoV on Vero cells (Wang et al. The genomic and the subgenomic mRNAs of coronaviruses have an identical 5′ leader sequence (via a unique mechanism called discontinuous transcription) and common 3′-ends, a unique feature in coronavirus replication. The siRNA targeting the leader sequence reduced the abundance of mRNA and protein expression levels of the reporter genes in 293 T cell line. They also found that the siRNA targeting the leader sequence could inhibit the replication of SARS-CoV via silencing gene expression in Vero E6 cells. Additionally, siRNA targeting the leader sequence exhibited a much potent inhibitory effect on the replication of SARS-CoV than the siRNAs targeting the spike gene made (Enjuanes et al. ) siRNA targeting the leader sequence of SARS-CoV inhibits virus replication abstract: Until now, there is no current vaccine or treatment against SARS-CoV-2. There are previous successful RNAi studies performed on SARS-CoV. Therefore, similar line of investigation against SARS-CoV-2 could be successful. url: https://doi.org/10.1007/s10123-020-00146-w doi: 10.1007/s10123-020-00146-w id: cord-330868-7ocseuz3 author: Donnelly, Christl A title: Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong date: 2003-05-24 words: 3812.0 sentences: 167.0 pages: flesch: 47.0 cache: ./cache/cord-330868-7ocseuz3.txt txt: ./txt/cord-330868-7ocseuz3.txt summary: Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Key epidemiological determinants of the magnitude and timescale of the epidemic (figure 1) include the interval between infection and onset of symptoms and between onset and hospital admission, the degree and duration of the infectiousness of the agent, and the extent of contact and mixing between infectious and susceptible people enabling transmission of the virus. If ␥ distribution is assumed, the estimated distributions and case fatality rate varied as a function of patients'' age, but not the time from onset to admission (figure 2). abstract: BACKGROUND: Health authorities worldwide, especially in the Asia Pacific region, are seeking effective public-health interventions in the continuing epidemic of severe acute respiratory syndrome (SARS). We assessed the epidemiology of SARS in Hong Kong. METHODS: We included 1425 cases reported up to April 28, 2003. An integrated database was constructed from several sources containing information on epidemiological, demographic, and clinical variables. We estimated the key epidemiological distributions: infection to onset, onset to admission, admission to death, and admission to discharge. We measured associations between the estimated case fatality rate and patients’age and the time from onset to admission. FINDINGS: After the initial phase of exponential growth, the rate of confirmed cases fell to less than 20 per day by April 28. Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. The mean incubation period of the disease is estimated to be 6.4 days (95% Cl 5.2–7.7). The mean time from onset of clinical symptoms to admission to hospital varied between 3 and 5 days, with longer times earlier in the epidemic. The estimated case fatality rate was 13.2% (9.8–16.8) for patients younger than 60 years and 43.3% (35.2–52.4) for patients aged 60 years or older assuming a parametric γ distribution. A non-parametric method yielded estimates of 6.8% (4.0–9.6) and 55.0% (45.3–64.7), respectively. Case clusters have played an important part in the course of the epidemic. INTERPRETATION: Patients’age was strongly associated with outcome. The time between onset of symptoms and admission to hospital did not alter outcome, but shorter intervals will be important to the wider population by restricting the infectious period before patients are placed in quarantine. Published online May 7, 2003 http://image.thelancet.com/extras/03art4453web.pdf url: https://www.ncbi.nlm.nih.gov/pubmed/12781533/ doi: 10.1016/s0140-6736(03)13410-1 id: cord-311926-n7co0jtu author: Donà, Daniele title: COVID-19 Pandemic: Perspective of an Italian Tertiary Care Pediatric Center date: 2020-09-01 words: 3176.0 sentences: 132.0 pages: flesch: 51.0 cache: ./cache/cord-311926-n7co0jtu.txt txt: ./txt/cord-311926-n7co0jtu.txt summary: Predicting a rapid spread of the SARS-CoV-2 virus within our region, the Department for Women''s and Children''s Health promptly decided (i) to revise the distribution of the clinical areas in order to create both designated COVID-19 and COVID-19-free areas with their own access, (ii) to reinforce infection prevention control (IPC) measures for all healthcare workers and administrative staff and (iii) to adopt the new "double-gate approach": a phone call pre-triage and nasopharyngeal swab for SARS-CoV-2 detection before the admission of all patients and caregivers. • to ensure the protection of the healthcare workers, as the top priority; • to rigorously implement all the conventional rules emanated by the WHO for preventing the infection • to minimize the risk of admitting into hospital asymptomatic COVID-19 positive patients; • to adapt/transform some hospital areas in order to be able to admit and treat suspected/confirmed; COVID-19 pediatric patients Predicting a rapid spread of the SARS-CoV-2 virus within our region, in the afternoon of February 24th the Chief Executive Officer (CEO) of Padua University Hospital called for an emergency meeting with all the department chairmen and the mandates received were: abstract: Since February 2020, Italy has been faced with the dramatic spread of novel Coronavirus SARS-CoV-2. This impetuous pandemic infection forced many hospitals to reorganize their healthcare systems. Predicting a rapid spread of the SARS-CoV-2 virus within our region, the Department for Women’s and Children’s Health promptly decided (i) to revise the distribution of the clinical areas in order to create both designated COVID-19 and COVID-19-free areas with their own access, (ii) to reinforce infection prevention control (IPC) measures for all healthcare workers and administrative staff and (iii) to adopt the new “double-gate approach”: a phone call pre-triage and nasopharyngeal swab for SARS-CoV-2 detection before the admission of all patients and caregivers. Between 21 February 2020 till 04 May 2020, only seven physicians, two nurses and two of the administrative staff resulted positive, all during the first week of March. No other cases of intra-department infection were documented among the healthcare workers since all the preventive procedures described above were implemented. It is predicted that similar situations can happen again in the future, and thus, it is necessary to be more prepared to deal with them than we were at the beginning of this COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32882820/ doi: 10.3390/healthcare8030311 id: cord-327933-u0fcs3yg author: Doná, Daniele title: Pediatric transplantation in Europe during the COVID‐19 pandemic: early impact on activity and healthcare date: 2020-08-12 words: 2634.0 sentences: 142.0 pages: flesch: 41.0 cache: ./cache/cord-327933-u0fcs3yg.txt txt: ./txt/cord-327933-u0fcs3yg.txt summary: Indeed, although severe outcomes (including deaths) have been reported in the pediatric population 6 , relatively fewer children with COVID-19 require hospitalization or admission to the intensive care unit (ICU) 7 . The survey included relevant questions to: i) assess pediatric transplantation activity, including living-donation issues; ii) identify the protocols adopted to prevent and manage SARS-CoV-2 infection at the hospital level; iii) evaluate the impact of these practices on the healthcare of transplanted children; and iv), describe the management of confirmed COVID-19 cases among the special population of pediatric transplant recipients and candidates. In eight centers (44%) outpatient visits were performed only after a telephone pretriage excluding epidemiological (e.g., close contact with a known COVID-19 case) and clinical risk factors (e.g., ongoing fever or respiratory symptoms in the patient or in the caregiver) for SARS-CoV-2 infection. Due to lack of experience in treating affected pediatric transplant patients, hospital admission criteria for suspected and confirmed COVID-19 cases varied between ERN-TransplantChild centers. abstract: The current pandemic SARS‐CoV‐2 virus has required an unusual allocation of resources that can negatively impact of chronically ill patients and high‐complexity procedures. Across the European reference network on pediatric transplantation (ERN‐TransplantChild) we conducted a survey to investigate the impact of the COVID‐19 outbreak on pediatric transplant activity and healthcare practices in both solid organ transplantation (SOT) and hematopoietic stem cell (HSCT) transplantation. The replies of 30 professionals from 18 centers in Europe were collected. Twelve of 18 centers (67%) showed a reduction in their usual transplant activity. Additionally, outpatient visits have been modified, restricted to selected ones and to the use of telemedicine tools has increased. Additionally, a total of 14 COVID‐19 pediatric transplanted patients were identified at the time of the survey, including eight transplant recipients and six candidates for transplantation. Only two moderate‐severe cases were reported, both in HSCT setting. These survey results demonstrate the limitations in healthcare resources for pediatric transplantation patients during early stages of this pandemic. COVID‐19 disease is a major worldwide challenge for the field of pediatric transplantation, where there will be a need for systematic data collection, encouraging regular discussions to address the long‐term consequences for pediatric transplantation candidates, recipients and their families. url: https://www.ncbi.nlm.nih.gov/pubmed/32786120/ doi: 10.1111/ctr.14063 id: cord-291588-tp89j1kk author: Dorche, Maryam Sharifian title: Neurological complications of coronavirus infection; a comparative review and lessons learned during the COVID-19 pandemic date: 2020-08-07 words: 5579.0 sentences: 431.0 pages: flesch: 42.0 cache: ./cache/cord-291588-tp89j1kk.txt txt: ./txt/cord-291588-tp89j1kk.txt summary: During the current pandemic, 370 patients with SARS-CoV-2 infection out of 37 studies (Table 3) were reported to suffer from AIS or transient ischemic attack (TIA). (145) Acute Necrotizing Encephalopathy(ANE) which was reported in 8 patients (Table 3) with COVID-19 is a distinct entity defined as rapid onset of neurological symptoms often secondary to a viral infection such as herpes viruses and influenza. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series Evolution and resolution of brain involvement associated with SARS-CoV2 infection: A close Clinical -Paraclinical follow up study of a case EEG Findings in Acutely Ill Patients Investigated for SARS-CoV-2/COVID-19: A Small Case Series Preliminary Report. Guillain-Barré syndrome in a patient infected with SARS-CoV-2, a case report Guillain-Barré Syndrome as a Neurological Complication of Novel COVID-19 Infection: A Case Report and Review of the Literature abstract: INTRODUCTION: Coronavirus disease-19 (COVID-19) pandemic continues to grow all over the world. Several studies have been performed, focusing on understanding the acute respiratory syndrome and treatment strategies. However, there is growing evidence indicating neurological manifestations occur in patients with COVID-19. Similarly, the other coronaviruses (CoV) epidemics; severe acute respiratory syndrome (SARS-CoV-1) and Middle East respiratory syndrome (MERS-CoV) have been associated with neurological complications. METHODS: This systematic review serves to summarize available information regarding the potential effects of different types of CoV on the nervous system and describes the range of clinical neurological complications that have been reported thus far in COVID-19. RESULTS: Two hundred and twenty-five studies on CoV infections associated neurological manifestations in human were reviewed. Of those, 208 articles were pertinent to COVID-19. The most common neurological complaints in COVID-19 were anosmia, ageusia, and headache, but more serious complications, such as stroke, impairment of consciousness, seizures, and encephalopathy, have also been reported. CONCLUSION: There are several similarities between neurological complications after SARS-CoV-1, MERS-CoV and COVID-19, however, the scope of the epidemics and number of patients are very different. Reports on the neurological complications after and during COVID-19 are growing on a daily basis. Accordingly, comprehensive knowledge of these complications will help health care providers to be attentive to these complications and diagnose and treat them timely. url: https://api.elsevier.com/content/article/pii/S0022510X20304226 doi: 10.1016/j.jns.2020.117085 id: cord-310605-r63sg73c author: Dorward, D. A. title: Tissue-specific tolerance in fatal Covid-19 date: 2020-07-04 words: 4482.0 sentences: 256.0 pages: flesch: 39.0 cache: ./cache/cord-310605-r63sg73c.txt txt: ./txt/cord-310605-r63sg73c.txt summary: Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. As analysis of SARS-CoV-2 RNA confirmed presence in numerous organs, detailed histological analysis of multiple tissues was undertaken on every patient to determine the associated pathological consequences and inflammatory responses. The present study shows that fatal Covid-19 is associated with variable but widespread distribution of viral RNA and protein but with a discordant inflammatory response to local viral presence, both between and within tissues, demonstrating tissue-specific tolerance of SARS-CoV-2. abstract: Successful host defence against a pathogen can involve resistance or tolerance, with implications for prioritising either antimicrobial or immunomodulatory therapeutic approaches. Hyper-inflammation occurs in Covid-19 and is associated with worse outcomes. The efficacy of dexamethasone in preventing mortality in critical Covid-19 suggests that inflammation has a causal role in death. Whether this deleterious inflammation is primarily a direct response to the presence of SARS-CoV-2 requiring enhanced resistance, or an independent immunopathologic process necessitating enhanced tolerance, is unknown. Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. We found that inflammation and organ dysfunction in fatal Covid-19 did not map to the widespread tissue and cellular distribution of SARS-CoV-2 RNA and protein, both between and within tissues. A monocyte/myeloid-rich vasculitis was identified in the lung, along with an influx of macrophages/monocytes into the parenchyma. In addition, stereotyped abnormal reticulo-endothelial responses (reactive plasmacytosis and iron-laden macrophages) were present and dissociated from the presence of virus in lymphoid tissues. Our results support virus-independent immunopathology being one of the primary mechanisms underlying fatal Covid-19. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. url: https://doi.org/10.1101/2020.07.02.20145003 doi: 10.1101/2020.07.02.20145003 id: cord-346546-yffwd0dc author: Douangamath, Alice title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date: 2020-05-27 words: 4059.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-346546-yffwd0dc.txt txt: ./txt/cord-346546-yffwd0dc.txt summary: To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. For 113 another series of hit compounds, containing a N-chloroacetyl piperidinyl-4-carboxamide 114 motif (Table S2 ) which displays lower reactivity and were not frequent hitters in previous 115 screens, we attempted crystallization despite their absence of labelling in the stringent 116 The bound fragments comprehensively sample all subsites of the active 287 site revealing diverse expansion vectors, and the electrophiles provide extensive, systematic 288 as well as serendipitous, data for designing covalent compounds. Crystal structure of SARS-CoV-2 main protease 763 provides a basis for design of improved alpha-ketoamide inhibitors abstract: COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments was progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. url: https://doi.org/10.1101/2020.05.27.118117 doi: 10.1101/2020.05.27.118117 id: cord-315968-q2rxj90s author: Douglas, Jennifer E. title: Management of a Unique Sinonasal Undifferentiated Carcinoma Subtype in the Era of SARS-CoV-2 date: 2020-10-05 words: 1379.0 sentences: 80.0 pages: flesch: 43.0 cache: ./cache/cord-315968-q2rxj90s.txt txt: ./txt/cord-315968-q2rxj90s.txt summary: Sinonasal undifferentiated carcinoma (SNUC) represents a rare malignancy of the sinonasal tract, a unique subset of which has never been previously reported in the otolaryngology literature and is characterized by inactivation of the SMARCB (INI-1) tumor suppressor gene. Here we present the case of an individual who was diagnosed with a sinonasal mass during the SARS-CoV-2 pandemic, which was ultimately found to be SMARCB (INI-1)-deficient sinonasal carcinoma. While SNUC has itself a poor prognosis, a subset of sinonasal neoplasms with inactivation of the SMARCB (INI-1) tumor suppressor gene exhibits particularly treatment-recalcitrant disease. Here we present the case of an individual with a sinonasal mass who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma and the unique management required during the SARS-CoV-2 pandemic. Here we present the case of an individual initially diagnosed with nasal polyps who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma during the SARS-CoV-2 pandemic and the unique management required. abstract: The novel coronavirus (SARS-CoV-2) pandemic has influenced the timeliness of care for patients with both common and rare conditions, particularly those affecting high-risk operative sites such as the upper aerodigestive tract. Sinonasal undifferentiated carcinoma (SNUC) represents a rare malignancy of the sinonasal tract, a unique subset of which has never been previously reported in the otolaryngology literature and is characterized by inactivation of the SMARCB (INI-1) tumor suppressor gene. This subtype exhibits a particularly poor prognosis and is characterized pathologically by its rhabdoid appearance. Here we present the case of an individual who was diagnosed with a sinonasal mass during the SARS-CoV-2 pandemic, which was ultimately found to be SMARCB (INI-1)-deficient sinonasal carcinoma. Advanced imaging was deferred in the interest of limiting the patient's exposure to the virus, and expedited operative management was performed which facilitated prompt referral for adjuvant chemoradiation. The SARS-CoV-2 pandemic presents unique challenges, but the work-up of high-risk lesions must be prioritized; this continues to be paramount as SARS-CoV-2 resurges in many cities across the USA. url: https://doi.org/10.1159/000511713 doi: 10.1159/000511713 id: cord-350959-bsbz3a1l author: Dovey, Zachary title: Impact of COVID-19 on Prostate Cancer Management: Guidelines for Urologists date: 2020-06-16 words: 5079.0 sentences: 241.0 pages: flesch: 47.0 cache: ./cache/cord-350959-bsbz3a1l.txt txt: ./txt/cord-350959-bsbz3a1l.txt summary: There is also epidemiological evidence that PCa patients have increased incidence and mortality from SARS-CoV-2 infection due to gender differences, age, and higher propensity for risk factors (eg, respiratory disease, obesity, hypertension, and smoking status). Patient summary Prostate cancer patients can be followed up remotely until the severe acute respiratory syndrome coronavirus 2 pandemic resolves, but higher-risk cases may have treatment expedited to limit any negative impact on prostate cancer outcomes. As shown in Table 2 , PCa patients with either diabetes or hypertension should seek advice from their physicians to optimize their treatment, especially if this includes ACE inhibitors or ARBs [32] , to reduce their risk of SARS-CoV-2 infection and morbidity. Tewari Prostate cancer (PCa) patients may have an increased risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. abstract: Abstract Context The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has resulted in a global health emergency, the like of which has never been seen before. Prostate cancer (PCa) services across the globe have been on hold due to changing medical and surgical priorities. There is also epidemiological evidence that PCa patients have increased incidence and mortality from SARS-CoV-2 infection due to gender differences, age, and higher propensity for risk factors (eg, respiratory disease, obesity, hypertension, and smoking status). Objective To contribute to the emerging body of knowledge on the risks of SARS-CoV-2 infection to PCa patients and, in the face of PCa treatment delays, provide evidence-based recommendations for ongoing management of specific PCa patient groups. Evidence acquisition A literature search was performed using all sources (MEDLINE, EMBASE, ScienceDirect, Cochrane Libraries, and Web of Science) as well as the media to harness emerging data on the SARS-CoV-2 pandemic and its influence on PCa. Eligibility criteria were originality of data and relevance to PCa management. The authors note that during these unprecedented times, retrospective data are constantly being updated from multiple sources globally. Evidence synthesis A total of 72 articles and data sources were found initially. Owing to repetition, lack of originality, or nonrelevance, six articles were rejected, leaving 23 retrospective studies, seven basic science research articles, 15 societal and journal guidelines, and 21 epidemiological data sources, from countries at different stages of SARS-CoV-2 pandemic. These were analyzed qualitatively to produce evidence-based guidelines for the management of PCa patients at different stages of the patient journey, with strategies to reduce the risk of viral spread. Conclusions PCa patients may have an increased risk of SARS-CoV-2 infection as well as morbidity and mortality if infected. Once appropriately triaged, and to reduce viral spread, PCa patients can have surveillance by telemedicine, and institute lifestyle changes and social quarantining measures. If risk stratification suggests that treatment should be planned, androgen deprivation therapy can be started, or potentially surgery or radiation therapy is possible on a case-by-case basis. Patient summary Prostate cancer patients can be followed up remotely until the severe acute respiratory syndrome coronavirus 2 pandemic resolves, but higher-risk cases may have treatment expedited to limit any negative impact on prostate cancer outcomes. url: https://www.sciencedirect.com/science/article/pii/S2666168320351120?v=s5 doi: 10.1016/j.euros.2020.05.005 id: cord-256023-21b5hanj author: Dowdell, A. K. title: Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon date: 2020-08-04 words: 3829.0 sentences: 246.0 pages: flesch: 56.0 cache: ./cache/cord-256023-21b5hanj.txt txt: ./txt/cord-256023-21b5hanj.txt summary: We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Genomic sequencing is rapidly emerging as an orthogonal strategy to RT-PCR for outbreak monitoring as the sequence specificity uncovered in individual SARS-CoV-2 isolates has shown significant utility for the epidemiological investigation of outbreak origins as well as the early identification of possible functional changes to the virus that may affect transmission rates or associated clinical outcomes. In order to assess the heterogeneity of SARS-CoV-2 genomes across OR, a total of 204 nasopharyngeal swab patient specimens (representing 188 unique patients) were sequenced from diverse clinical sites across OR. Next, we sought to determine whether sequence variants in the isolated SARS-CoV-2 genomes were associated with differential clinical manifestation of COVID-19 in the patients. abstract: The first reported case of COVID-19 in the State of Oregon occurred in late February 2020, with subsequent outbreaks occurring in the populous Portland metro area but also with significant outbreaks in less-populous and rural areas. Here we report viral sequences from 188 patients across the hospitals and associated clinics in the Providence Health System in the State of Oregon dating back to the early days of the outbreak. We show a significant shift in dominant clade lineages over time in Oregon, with the rapid emergence and dominance of Spike D614G-positive variants. We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Lastly, we show that SARS-CoV-2 genomic information may offer additional utility in combination with clinical covariates in the prediction of acute disease phenotypes. url: https://doi.org/10.1101/2020.07.30.20160069 doi: 10.1101/2020.07.30.20160069 id: cord-350935-p6euuop3 author: Doğan, Tunca title: CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date: 2020-09-15 words: 7066.0 sentences: 298.0 pages: flesch: 45.0 cache: ./cache/cord-350935-p6euuop3.txt txt: ./txt/cord-350935-p6euuop3.txt summary: We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. In this project, we aimed to address the current shortcomings by developing a comprehensive open access biomedical system entitled CROssBAR via integrating various biological databases to each other, inferring the missing relations between existing data points, and constructing informative knowledge graphs based on specific biomedical components/terms such as a disease/phenotype, biological process, gene/protein and drug/compound, or specific combinations of them. abstract: Systemic analysis of available large-scale biological and biomedical data is critical for developing novel and effective treatment approaches against both complex and infectious diseases. Owing to the fact that different sections of the biomedical data is produced by different organizations/institutions using various types of technologies, the data are scattered across individual computational resources, without any explicit relations/connections to each other, which greatly hinders the comprehensive multi-omics-based analysis of data. We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. As a use-case study, we constructed CROssBAR COVID-19 KGs (available at: https://crossbar.kansil.org/covid_main.php) that incorporate relevant virus and host genes/proteins, interactions, pathways, phenotypes and other diseases, as well as known and completely new predicted drugs/compounds. Our COVID-19 graphs can be utilized for a systems-level evaluation of relevant virus-host protein interactions, mechanisms, phenotypic implications and potential interventions. url: https://doi.org/10.1101/2020.09.14.296889 doi: 10.1101/2020.09.14.296889 id: cord-348202-6we8e60b author: Drake, Daniel H. title: Echo in Pandemic: Front Line Perspective, Expanding Role of Ultrasound and Ethics of Resource Allocation date: 2020-04-10 words: 4115.0 sentences: 308.0 pages: flesch: 40.0 cache: ./cache/cord-348202-6we8e60b.txt txt: ./txt/cord-348202-6we8e60b.txt summary: During a declared health care crisis, providers must be familiar with the ethical principles, organizational structure, practical application, and gravity of limited resource allocation. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Echocardiography has been most useful for 1) initial assessment of patients with respiratory complaints who are seen in the COVID-19 evaluation pathway but may have another etiology for their symptoms, 2) assessment of cardiac function in critical care patients, where SARS-CoV-2 associated cardiomyopathy is prevalent and 3) volume assessment of patients with acute respiratory distress syndrome (ARDS), where sparing unnecessary fluids is mandatory. Ethical Considerations for Decision Making Regarding Allocation of Mechanical Ventilators During a Severe Influenza Pandemic or Other Public Health Emergency abstract: Abstract The grave clinical context of the pandemic must be understood. Italy is immersed in COVID-19. Most of the world will soon follow. The United States currently has the most documented cases of COVID-19 of any nation. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. COVID-19 patients frequently require mechanical support for adequate oxygenation. A severe shortfall of ventilators is predicted. Of equal concern is the projected shortage of trained professionals required to care for patients on mechanical ventilation. Ultrasonography is proving to be a valuable tool for identifying the pulmonary manifestations and progression of COVID-19. Lung ultrasound also facilitates successful weaning from mechanical ventilation. Ultrasonography of the lung, pleura and diaphragm are easily mastered by experienced echocardiographers. Echocardiography has an established role for optimal fluid management and recognition of cardiac disease including SARS-CoV-2 associated acute cardiomyopathy. Cardiologists, anesthesiologists, sonographers, and all providers should be prepared to commit their full spectrum of skills to mitigate the consequences of the pandemic. We should also be prepared to collaborate and cross-train to expand professional services as necessary. During a declared health care crisis, providers must be familiar with the ethical principles, organizational structure, practical application, and gravity of limited resource allocation. url: https://www.sciencedirect.com/science/article/pii/S0894731720302182?v=s5 doi: 10.1016/j.echo.2020.04.007 id: cord-354763-odzrco6q author: Drake, John M. title: Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date: 2006-12-20 words: 5739.0 sentences: 283.0 pages: flesch: 46.0 cache: ./cache/cord-354763-odzrco6q.txt txt: ./txt/cord-354763-odzrco6q.txt summary: We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. We also retrospectively explore the effect of societal learning during the 2003 outbreak of SARS in Singapore, using weekly data on the time between onset of symptoms and removal of infectious individuals. Finally, we discuss societal and epidemiological factors that might affect societal learning, we observe that a difficult task during the early stages of an outbreak is to estimate the learning rate and suggest that the rate estimated here might be used as prior information in future outbreaks, and we conclude by recommending rapid investment in research at the time of initial detection when actions taken to reduce disease spread can be most efficient and cost effective. abstract: BACKGROUND: Rapid response to outbreaks of emerging infectious diseases is impeded by uncertain diagnoses and delayed communication. Understanding the effect of inefficient response is a potentially important contribution of epidemic theory. To develop this understanding we studied societal learning during emerging outbreaks wherein patient removal accelerates as information is gathered and disseminated. METHODS AND FINDINGS: We developed an extension of a standard outbreak model, the simple stochastic epidemic, which accounts for societal learning. We obtained expressions for the expected outbreak size and the distribution of epidemic duration. We found that rapid learning noticeably affects the final outbreak size even when learning exhibits diminishing returns (relaxation). As an example, we estimated the learning rate for the 2003 outbreak of severe acute respiratory syndrome (SARS) in Singapore. Evidence for relaxation during the first eight weeks of the outbreak was inconclusive. We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. By contrast, the expected outbreak size for societal learning twice as effective was 116 cases. CONCLUSION: These results show that the rate of societal learning can greatly affect the final size of disease outbreaks, justifying investment in early warning systems and attentiveness to disease outbreak by both government authorities and the public. We submit that the burden of emerging infections, including the risk of a global pandemic, could be efficiently reduced by improving procedures for rapid detection of outbreaks, alerting public health officials, and aggressively educating the public at the start of an outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/17183647/ doi: 10.1371/journal.pone.0000020 id: cord-345992-3ij1vbqp author: Drosten, Christian title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 words: 1746.0 sentences: 98.0 pages: flesch: 42.0 cache: ./cache/cord-345992-3ij1vbqp.txt txt: ./txt/cord-345992-3ij1vbqp.txt summary: Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Inactivated severe acute respiratory syndrome-associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Highly sensitive methods for virus detection, such as reverse transcription-polymerase chain reaction (RT-PCR) are required to confirm SARS in the acute phase and prevent transmission. First, laboratories had to correctly detect the four samples containing >9,400 copies of viral RNA per milliliter, a concentration well above the detection limit of published and commercial nucleic acid amplification tests (NAT) for SARS-CoV, (6, 7, (10) (11) (12) . Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Of 58 participants, 51 correctly detected virus in all samples >9,400 RNA copies per milliliter and none in negative samples. Commercial test kits significantly improved the outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/15663861/ doi: 10.3201/eid1012.040416 id: cord-297327-19dfgfz6 author: Drożdżal, Sylwester title: COVID-19: Pain Management in Patients with SARS-CoV-2 Infection—Molecular Mechanisms, Challenges, and Perspectives date: 2020-07-20 words: 5672.0 sentences: 319.0 pages: flesch: 41.0 cache: ./cache/cord-297327-19dfgfz6.txt txt: ./txt/cord-297327-19dfgfz6.txt summary: Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, nonPutative mechanisms of myalgia and headache during viral infection. Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, non-steroidal inflammatory drugs or analgosedation [52] . Recently, concerns about the possible higher frequency of adverse effects and exacerbation of symptoms of viral respiratory tract infections, such as COVID-19, in patients treated with NSAIDs have been raised [67] . There are reports of a significantly higher use of opioids because of sedation requirements during respiratory failure caused by SARS-CoV-2, which highlights the importance of undertaking a study aiming to determine efficacious and safe procedures of pain management in patients with COVID-19. abstract: Since the end of 2019, the whole world has been struggling with the pandemic of the new Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Available evidence suggests that pain is a common symptom during Coronavirus Disease 2019 (COVID-19). According to the World Health Organization, many patients suffer from muscle pain (myalgia) and/or joint pain (arthralgia), sore throat and headache. The exact mechanisms of headache and myalgia during viral infection are still unknown. Moreover, many patients with respiratory failure get admitted to the intensive care unit (ICU) for ventilatory support. Pain in ICU patients can be associated with viral disease itself (myalgia, arthralgia, peripheral neuropathies), may be caused by continuous pain and discomfort associated with ICU treatment, intermittent procedural pain and chronic pain present before admission to the ICU. Undertreatment of pain, especially when sedation and neuromuscular blocking agents are used, prone positioning during mechanical ventilation or extracorporeal membrane oxygenation (ECMO) may trigger delirium and cause peripheral neuropathies. This narrative review summarizes current knowledge regarding challenges associated with pain assessment and management in COVID-19 patients. A structured prospective evaluation should be undertaken to analyze the probability, severity, sources and adequate treatment of pain in patients with COVID-19 infection. url: https://doi.org/10.3390/brainsci10070465 doi: 10.3390/brainsci10070465 id: cord-252528-rgnhfcbx author: Du, Fenghe title: COVID-19: the role of excessive cytokine release and potential ACE2 down-regulation in promoting hypercoagulable state associated with severe illness date: 2020-07-16 words: 8437.0 sentences: 359.0 pages: flesch: 30.0 cache: ./cache/cord-252528-rgnhfcbx.txt txt: ./txt/cord-252528-rgnhfcbx.txt summary: • Anti-inflammatory therapies, including tocilizumab, chloroquine, and hydroxychloroquine, which can be promising treatment to control excessive cytokine release in severe COVID-19, have the potential to reduce the risk of vascular thrombotic events, but more clinical data are needed for optimum instruction of drug use and drug selection. By interpreting the pathological mechanisms, we aim to illustrate that excessive pro-inflammatory cytokine release and potential ACE2 down-regulation can promote the hypercoagulable state in severe COVID19 , and propose that the anti-inflammatory medications, as well as ACEI/ARB, can benefit severe COVID-19 patients by reducing the risk of vascular thrombotic events. abstract: [Image: see text] url: https://doi.org/10.1007/s11239-020-02224-2 doi: 10.1007/s11239-020-02224-2 id: cord-332555-jfqlkd72 author: Du, Hengzhi title: The potential effects of DPP‐4 inhibitors on cardiovascular system in COVID‐19 patients date: 2020-07-26 words: 1411.0 sentences: 96.0 pages: flesch: 41.0 cache: ./cache/cord-332555-jfqlkd72.txt txt: ./txt/cord-332555-jfqlkd72.txt summary: similar outer membrane spike glycoproteins among the coronavirus, it is possible that DPP-4 might also be a functional receptor of SARS-CoV-2. It has been reported that membrane-associated human DPP-4, as a functional MERS-CoV receptor, interacted with MERS-CoV through the spike glycoprotein S1b domain to facilitate the entry of MERS-CoV. Evidence from severely ill patients with COVID-19 suggested that the release of cytokines and chemokines was delayed in respiratory epithelial cells, dendritic cells (DCs) and macrophages at the early stage of SARS-CoV-2 infection. 17 Similar findings were also observed in SARS-CoV and MERS-CoV infected human airway epithelial cells, THP-1 cells, human peripheral blood monocyte-derived macrophages and DCs. 18 Although inflammation initially only damages limited organs, such as the lungs, an over-activated inflammatory response will spread all over the body rapidly, including the heart. Meanwhile, DPP-4 inhibitors could inhibit the over-activated inflammatory caused by SARS-CoV-2 and thus improve cardiovascular function. The potential effects of DPP-4 inhibitors on cardiovascular system in COVID-19 patients abstract: With the outbreak of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the public healthcare systems are facing great challenges. Coronavirus disease 2019 (COVID‐19) could develop into severe pneumonia, acute respiratory distress syndrome and multi‐organ failure. Remarkably, in addition to the respiratory symptoms, some COVID‐19 patients also suffer from cardiovascular injuries. Dipeptidyl peptidase‐4 (DPP‐4) is a ubiquitous glycoprotein which could act both as a cell membrane‐bound protein and a soluble enzymatic protein after cleavage and release into the circulation. Despite angiotensin‐converting enzyme 2 (ACE2), the recently recognized receptor of SARS‐CoV and SARS‐CoV‐2, which facilitated their entries into the host, DPP‐4 has been identified as the receptor of middle east respiratory syndrome coronavirus (MERS‐CoV). In the current review, we discussed the potential roles of DPP‐4 in COVID‐19 and the possible effects of DPP‐4 inhibitors on cardiovascular system in patients with COVID‐19. url: https://doi.org/10.1111/jcmm.15674 doi: 10.1111/jcmm.15674 id: cord-319089-hxpoy4gd author: Du, Li title: Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews date: 2020-09-18 words: 2219.0 sentences: 150.0 pages: flesch: 51.0 cache: ./cache/cord-319089-hxpoy4gd.txt txt: ./txt/cord-319089-hxpoy4gd.txt summary: title: Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews BACKGROUND: The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has emerged to be the biggest global health threat worldwide. METHODS: Two independent reviewers will conduct comprehensively searches in PubMed, EMBASE.com, Web of Science, the Cochrane Library, Chinese biomedical literature database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wan fang Database, Chongqing VIP (CQVIP). Prevalence of stress, anxiety, depression among the general population during the COVID-19 pandemic: a systematic review and meta-analysis The psychological and mental impact of coronavirus disease 2019 (COVID-19) on medical staff and general public: a systematic review and meta-analysis Prevalence of depression, anxiety, and insomnia among healthcare workers during the COVID-19 pandemic: a systematic review and meta-analysis Psychological effects caused by the COVID-19 pandemic in health professionals: a systematic review with meta-analysis abstract: BACKGROUND: The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has emerged to be the biggest global health threat worldwide. COVID-19 marks the emergence of the third large-scale epidemic related to the coronavirus, after SARS-CoV in 2002 and Middle-East respiratory syndrome coronavirus (MERSCoV) in 2012. The pandemic has had a harmful effect on the public mental health, especially on depression. Increasing systematic reviews (SRs) of coronavirus were focusing on depression. However, the methodological quality of these SRs is unclear. Therefore, to evaluate and compare the normativity of report of SR, we conducted a comprehensive overview of depression during the SARS, MERS, and COVID-19 pandemics. METHODS: Two independent reviewers will conduct comprehensively searches in PubMed, EMBASE.com, Web of Science, the Cochrane Library, Chinese biomedical literature database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wan fang Database, Chongqing VIP (CQVIP). Reference lists of articles, gray literature, and conference proceedings will also be searched. We will extract the data and assess the methodological quality using the Assessment of Multiple Systematic Reviews-2 (AMSTAR-2) measurement tool and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. General characteristics of the eligible SRs will be summarized and described. We will provide AMSTAR-2 and PRISMA assessments in tabular form for each review, the total percentage of each item will be calculated. Endnote X8 and EXCEL will be used. RESULTS: Using the draft search strategy of databases, 8 SRs met the a priori criteria and were included. The overview of SRs will be published in a peer-reviewed journal. CONCLUSION: Our overview will be a comprehensive synthesis of the existing systemic review on depression with SARS, MERS, and COVID-19. PROTOCOL REGISTRATION: INPLASY202080003 url: https://www.ncbi.nlm.nih.gov/pubmed/32957366/ doi: 10.1097/md.0000000000022235 id: cord-308583-vtmwv8zl author: Du, Qishi title: Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase date: 2005-02-15 words: 3856.0 sentences: 225.0 pages: flesch: 63.0 cache: ./cache/cord-308583-vtmwv8zl.txt txt: ./txt/cord-308583-vtmwv8zl.txt summary: In this research we study the cleavage mechanism, the properties of the relevant chemical bonds, and the catalytic interactions between the octapeptides and the SARS CoV M pro using molecular mechanical and quantum chemical simulations to provide useful insights for the chemical modification. The docking calculation between SARS CoV M pro and the octapeptide AVLQSGFR was performed using the molecular although still bound to the active site, the peptide has lost its cleavability after its scissile bond was modified from a hybrid peptide bond to a strong bond. Fig. 5B is the contour map of differential electronic density of the peptide bond Gln-Ser in the octapeptide AVLQSGFR, obtained by subtracting the electron density in the gaseous phase from the electron density in the background [23] of SARS CoV M pro and solvent water molecules. For the peptide inhibitor of proteinase, the chemical modification to cleavable octapeptide should focus on the scissile peptide bond between R 1 and R 1 0 to be cleaved by SARS CoV M pro . abstract: Abstract Severe acute respiratory syndrome (SARS) is a respiratory disease caused by a newly found virus, called SARS coronavirus. In this study, the cleavage mechanism of the SARS coronavirus main proteinase (Mpro or 3CLpro) on the octapeptide NH2-AVLQ↓SGFR-COOH was investigated using molecular mechanics and quantum mechanics simulations based on the experimental structure of the proteinase. It has been observed that the catalytic dyad (His-41/Cys-145) site between domains I and II attracts the π electron density from the peptide bond Gln–Ser, increasing the positive charge on C(CO) of Gln and the negative charge on N(NH) of Ser, so as to weaken the Gln–Ser peptide bond. The catalytic functional group is the imidazole group of His-41 and the S in Cys-145. Nδ1 on the imidazole ring plays the acid–base catalytic role. Based on the “distorted key theory” [K.C. Chou, Anal. Biochem. 233 (1996) 1–14], the possibility to convert the octapeptide to a competent inhibitor has been studied. It has been found that the chemical bond between Gln and Ser will become much stronger and no longer cleavable by the SARS enzyme after either changing the carbonyl group CO of Gln to CH2 or CF2 or changing the NH of Ser to CH2 or CF2. The octapeptide thus modified might become an effective inhibitor or a potential drug candidate against SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15691506/ doi: 10.1016/j.ab.2004.10.003 id: cord-337962-9le56say author: Duan, Fuyu title: Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2 date: 2020-08-20 words: 5337.0 sentences: 262.0 pages: flesch: 51.0 cache: ./cache/cord-337962-9le56say.txt txt: ./txt/cord-337962-9le56say.txt summary: Here, we used directed differentiation of human pluripotent stem cells (hPSCs) to establish a lung and macrophage co-culture system and model the host-pathogen interaction and immune response caused by SARS-CoV-2 infection. Recent studies (Liao et al., 2020; Xu et al., 2020) on immunity of COVID-19 patients indicate that the cells damaged by SARS-CoV-2 infection induced innate in ammation in the lungs that is largely mediated by pro-in ammatory macrophages and granulocytes. To further characterize at the transcriptomic level the response of iLung and iMφ following viral infection, scRNA-seq was performed on the co-cultures with SARS-CoV-2 pseudo virus infection and the analysis revealed that a set of anti-in ammatory factors and anti-viral activity related genes, such as CCL26, CCL13, ISG15, IFITM2 and IFITM3, were clearly upregulated when cultures contained M2-iMφ ( Figure 4A and C, Figures S8A) . abstract: Dysfunctional immune responses contribute critically to the progression of Coronavirus Disease-2019 (COVID-19) from mild to severe stages including fatality, with pro-inflammatory macrophages as one of the main mediators of lung hyper-inflammation. Therefore, there is an urgent need to better understand the interactions among SARS-CoV-2 permissive cells, macrophage, and the SARS-CoV-2 virus, thereby offering important insights into new therapeutic strategies. Here, we used directed differentiation of human pluripotent stem cells (hPSCs) to establish a lung and macrophage co-culture system and model the host-pathogen interaction and immune response caused by SARS-CoV-2 infection. Among the hPSC-derived lung cells, alveolar type II and ciliated cells are the major cell populations expressing the viral receptor ACE2 and co-effector TMPRSS2, and both were highly permissive to viral infection. We found that alternatively polarized macrophages (M2) and classically polarized macrophages (M1) had similar inhibitory effects on SARS-CoV-2 infection. However, only M1 macrophages significantly up-regulated inflammatory factors including IL-6 and IL-18, inhibiting growth and enhancing apoptosis of lung cells. Inhibiting viral entry into target cells using an ACE2 blocking antibody enhanced the activity of M2 macrophages, resulting in nearly complete clearance of virus and protection of lung cells. These results suggest a potential therapeutic strategy, in that by blocking viral entrance to target cells while boosting anti-inflammatory action of macrophages at an early stage of infection, M2 macrophages can eliminate SARS-CoV-2, while sparing lung cells and suppressing the dysfunctional hyper-inflammatory response mediated by M1 macrophages. url: https://doi.org/10.21203/rs.3.rs-62758/v1 doi: 10.21203/rs.3.rs-62758/v1 id: cord-328003-yovp8squ author: Duan, Liangwei title: The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date: 2020-10-07 words: 7346.0 sentences: 386.0 pages: flesch: 46.0 cache: ./cache/cord-328003-yovp8squ.txt txt: ./txt/cord-328003-yovp8squ.txt summary: Here, we provide a comprehensive overview of the wealth of research related to the SARS-CoV-2 S glycoprotein biosynthesis, structure, function, and antigenicity, aiming to provide useful insights into the design and development of the S protein-based vaccines as well as therapeutics to prevent or treat the ongoing global spread of SARS-CoV-2/COVID-19. Prefusion structures of human coronavirus HKU1 (HCoV-HKU1) and mouse hepatitis virus S protein ectodomains without two consecutive proline mutations reveal only fully closed conformation (37, 42) , similar to that observed for a full-length, wild-type prefusion form of the SARS-CoV-2 S glycoprotein (41) . Therefore, SARS-CoV-2 evades immune surveillance also through conformational masking, which is well-documented for HIV-1 (43, 44) ; while at the same time, the S protein could transiently sample the functional state to engage ACE2, consistent with the notion that the fusion glycoprotein of highly pathogenic viruses have evolved to perform its functions while evading host neutralizing antibody responses. abstract: The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a grave threat to global public health and imposes a severe burden on the entire human society. Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion and entry into the host cell. Surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of the S protein-based vaccines as well as therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/33117378/ doi: 10.3389/fimmu.2020.576622 id: cord-268895-m97zsodx author: Duan, Ping title: Safety considerations during return to work in the context of stable COVID-19 epidemic control: an analysis of health screening results of all returned staff from a hospital date: 2020-09-18 words: 3217.0 sentences: 161.0 pages: flesch: 45.0 cache: ./cache/cord-268895-m97zsodx.txt txt: ./txt/cord-268895-m97zsodx.txt summary: In total, 4729 returned staff from Zhongnan Hospital of Wuhan University, Wuhan, China were examined for COVID-19, and the basic information, radiology and laboratory test results were obtained and systematically analysed. The 4729 returned staff, all from Zhongnan Hospital of Wuhan University, underwent comprehensive SARS-CoV-2 screening, including SARS-CoV-2 nucleic acid test, antibody detection, chest CT scan, body temperature measurement and recording of infection characteristics. Among 172 people with abnormal first physical examination results, we observed that 170 cases (98.84%) were negative in the first SARS-CoV-2 nucleic acid test, but one of which was positive by RT-PCR at the time of reexamination. In summary, we efficiently identified asymptomatic infections through extensive health screening of all returned staff from a hospital in a short period of time, combined with a variety of inspection methods (including nucleic acid test for SARS-CoV-2, antibody detection and chest CT scan), and emphasising the presence of asymptomatic infections in the general population. abstract: In March 2020, China had periodically controlled the coronavirus disease-19 (COVID-19) epidemic. We reported the results of health screening for COVID-19 among returned staff of a hospital and conducted a summary analysis to provide valuable experience for curbing the COVID-19 epidemic and rebound. In total, 4729 returned staff from Zhongnan Hospital of Wuhan University, Wuhan, China were examined for COVID-19, and the basic information, radiology and laboratory test results were obtained and systematically analysed. Among the 4729 employees, medical staff (62.93%) and rear-service personnel (30.73%) were the majority. The results of the first physical examination showed that 4557 (96.36%) were normal, 172 (3.64%) had abnormal radiological or laboratory test results. After reexamination and evaluation, four were at high risk (asymptomatic infections) and were scheduled to transfer to a designated hospital, and three were at low risk (infectivity could not be determined) and were scheduled for home isolation observation. Close contacts were tracked and managed by the Center for Disease Control and Prevention (CDC) in China. Asymptomatic infections are a major risk factor for returning to work. Extensive health screening combined with multiple detection methods helps to identify asymptomatic infections early, which is an important guarantee in the process of returning to work. url: https://www.ncbi.nlm.nih.gov/pubmed/32943130/ doi: 10.1017/s0950268820002150 id: cord-342221-xvrpx9p8 author: Duan, Qing title: Reovirus, isolated from SARS patients date: 2003 words: 1783.0 sentences: 103.0 pages: flesch: 55.0 cache: ./cache/cord-342221-xvrpx9p8.txt txt: ./txt/cord-342221-xvrpx9p8.txt summary: In this report, reovirus was isolated from throat swabs of SARS patients, including the first case in Beijing and her mother. SCV was isolated in lung tissue collected at autopsy from her father, and the first isolate in Beijing was named the BJO 1 strain of SARS-associated coronavirus, whose genome sequence has been determined [4] . Isolation of reovirus: To isolate viruses associated with SARS, we inoculated the clinical specimen (material from throat swabs) obtained from the first patient with SARS admitted to hospital in Beijing onto Hep-2 cells. We isolated the virus in throat swab specimen from the first case in Beijing and her mother, and initially considered it as a possible variant of SCv, but the PCR test failed to amplify DNA from it. Electron microscopy (EM) examination of Hep-2 cells and Vero-E6 cells infected with the virus isolated from throat swab specimens of the first case in Beijing revealed characteristic reovirus particles with a size of about 60-80 urn in diameter. abstract: Beijing has been severely affected by SARS, and SARS-associated coronavirus has been confirmed as its cause. However, clinical and experimental evidence implicates the possibility of co-infection. In this report, reovirus was isolated from throat swabs of SARS patients, including the first case in Beijing and her mother. Identification with the electron microscopy revealed the characteristic features of reovirus. 24 of 38 samples from other SARS cases were found to have serologic responses to the reovirus. Primers designed for reovirus have amplified several fragments of DNA, one of which was sequenced (S2 gene fragment), which indicates it as a unique reovirus (orthoreovirus). Preliminary animal experiment showed that inoculation of the reovirus in mice caused death with atypical pneumonia. Nevertheless, the association of reovirus with SARS outbreak requires to be further investigated. url: https://www.ncbi.nlm.nih.gov/pubmed/32214706/ doi: 10.1007/bf03184165 id: cord-343317-97n1j0jj author: Duan, Xiaohua title: Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date: 2020-05-02 words: 3776.0 sentences: 222.0 pages: flesch: 56.0 cache: ./cache/cord-343317-97n1j0jj.txt txt: ./txt/cord-343317-97n1j0jj.txt summary: Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. The organoids infected with SARS-CoV-2 pseudo-entry virus at MOI=0.01 showed a strong signal at 24 hpi (Fig. 2a) . The mRNAs of SARS-CoV-2 pseudo-entry virus, including VSV-NS, VSV-N, and VSV-M, were detected in all five cell populations (Fig. 2f) , but not in the uninfected COs (Extended Data Fig. 2f) . Immunohistochemistry detected luciferase in ACE2 + and Villin + cells, suggesting these are permissive to SARS-CoV-2 pseudo-entry virus infection in vivo (Fig. 2k) . Next, we adapted hPSC-COs to a high throughput screening platform and probed the Prestwick FDA-approved drug library to identify drug candidates capable of blocking SARS-CoV-2 pseudo-virus infection. abstract: The current COVID-19 pandemic is caused by SARS-coronavirus 2 (SARS-CoV-2). There are currently no therapeutic options for mitigating this disease due to lack of a vaccine and limited knowledge of SARS-CoV-2 biology. As a result, there is an urgent need to create new disease models to study SARS-CoV-2 biology and to screen for therapeutics using human disease-relevant tissues. COVID-19 patients typically present with respiratory symptoms including cough, dyspnea, and respiratory distress, but nearly 25% of patients have gastrointestinal indications including anorexia, diarrhea, vomiting, and abdominal pain. Moreover, these symptoms are associated with worse COVID-19 outcomes1. Here, we report using human pluripotent stem cell-derived colonic organoids (hPSC-COs) to explore the permissiveness of colonic cell types to SARS-CoV-2 infection. Single cell RNA-seq and immunostaining showed that the putative viral entry receptor ACE2 is expressed in multiple hESC-derived colonic cell types, but highly enriched in enterocytes. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. We used hPSC-derived COs in a high throughput platform to screen 1280 FDA-approved drugs against viral infection. Mycophenolic acid and quinacrine dihydrochloride were found to block the infection of SARS-CoV-2 pseudo-entry virus in COs both in vitro and in vivo, and confirmed to block infection of SARS-CoV-2 virus. This study established both in vitro and in vivo organoid models to investigate infection of SARS-CoV-2 disease-relevant human colonic cell types and identified drugs that blocks SARS-CoV-2 infection, suitable for rapid clinical testing. url: https://doi.org/10.1101/2020.05.02.073320 doi: 10.1101/2020.05.02.073320 id: cord-284625-to6w5hm2 author: Duan, Xiaopei title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 words: 3347.0 sentences: 183.0 pages: flesch: 55.0 cache: ./cache/cord-284625-to6w5hm2.txt txt: ./txt/cord-284625-to6w5hm2.txt summary: Given the concept of the early diagnosis and treatment of SARS-CoV-2, this article mainly focused on the 25 initial laboratory-confirmed patients in the Luoyang area, discussing their imaging features and clinical characteristics. From January 10 to February 8, 2020, 25 patients with laboratory-confirmed SARS-CoV-2 infection in the area of Luoyang, Henan Province, China, were enrolled in the study. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. A woman who is the wife of the patient 3 and mother of patient 22 had two negative PCR results, but the lesions in her lung had the same progression, and the blood test also confirmed the SARS-CoV-2 infection. abstract: PURPOSE: To summarize the chest CT imaging and clinical features of the initial COVID-19 patients and provide a clinical diagnostic method that is more effective and can be performed earlier. METHODS: This retrospective study investigated the clinical, laboratory and imaging information of 25 patients in the Luoyang area. There were 15 (60%) male and 10 (40%) female patients ranging from 24 to 88 years old (52 ± 19.30). Data were analyzed by Microsoft Excel and are expressed as the mean ± standard deviation or percentage. RESULTS: Thirteen (52%) patients had been in Wuhan or were in contact with people who had been in Wuhan, and ten (40%) patients were infected by their families or colleagues. The median time from initial symptoms to diagnosis was 7 days. Ninety-two percent of patients had respiratory symptoms, and 8% of them had digestive symptoms. Fever (92%), cough (60%) and fatigue (56%) were the most common symptoms. Most patients had a normal or reduced WBC (96%), reduced lymphocyte count (60%), increased CRP (48%) and increased ESR (44%). Ground glass opacity (GGO) was the typical radiological finding on chest CT. CONCLUSION: Characteristic chest CT imaging features could appear earlier than the viral nucleic acid assay results. url: https://www.ncbi.nlm.nih.gov/pubmed/32458125/ doi: 10.1007/s11604-020-00988-4 id: cord-321768-oevswvvd author: Duan, Ya-qi title: Deficiency of Tfh Cells and Germinal Center in Deceased COVID-19 Patients date: 2020-08-07 words: 2307.0 sentences: 125.0 pages: flesch: 51.0 cache: ./cache/cord-321768-oevswvvd.txt txt: ./txt/cord-321768-oevswvvd.txt summary: In this study, we examined the immune cell compositions in the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients and 4 focal organizing pneumonia (FOP) patients who underwent lung surgery and served as controls. In contrast to the FOP patients, Tfh cells and germinal center formation were largely absent in the draining hilar lymph nodes in the deceased COVID-19 patients. Characterization of compositions of the immune cells within the lung tissues and draining hilar lymph nodes from the postmortem specimens might provide valuable insights on how the immune responses in the deceased patients were dysregulated and offer new strategies for treatment. To gain insight into the human immune responses during a fatal SARS-CoV2 infection, we performed postmortem autopsy studies of the immune cell compositions within the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients, and 4 FOP patients who underwent lung surgery served as controls. abstract: The COVID-19 pandemic caused by SARS-CoV2 is characterized by a remarkable variation in clinical severity ranging from a mild illness to a fatal multi-organ disease. Understanding the dysregulated human immune responses in the fatal subjects is critical for management of COVID-19 patients and the pandemic. In this study, we examined the immune cell compositions in the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients and 4 focal organizing pneumonia (FOP) patients who underwent lung surgery and served as controls. We found a dominant presence of macrophages and a general deficiency of T cells and B cells in the lung tissues from deceased COVID-19 patients. In contrast to the FOP patients, Tfh cells and germinal center formation were largely absent in the draining hilar lymph nodes in the deceased COVID-19 patients. This was correlated with reduced IgM and IgG levels compared to convalescent COVID-19 patients. In summary, our data highlight a defect of germinal center structure in deceased COVID-19 patients leading to an impaired humoral immunity. Understanding the mechanisms of this deficiency will be one of the key points for the management of this epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32767259/ doi: 10.1007/s11596-020-2225-x id: cord-284091-1dj4yxkz author: Duart, Gerard title: SARS-CoV-2 envelope protein topology in eukaryotic membranes date: 2020-09-09 words: 2892.0 sentences: 155.0 pages: flesch: 45.0 cache: ./cache/cord-284091-1dj4yxkz.txt txt: ./txt/cord-284091-1dj4yxkz.txt summary: In this report, we studied the E protein topology from the new SARS-CoV-2 virus both in microsomal membranes and in mammalian cells. Computer-assisted analysis of the SARS-CoV-2 E protein amino acid sequence using seven popular prediction methods showed that all membrane protein prediction algorithms except MEMSAT-SVM suggested the presence of one transmembrane (TM) segment located roughly around amino acids 12 to 39 (table 1) , which is not predicted as a cleavable signal sequence according to SignalP-5.0 [7] . Since multiple topologies have been reported for previous coronavirus E proteins [13] [14] [15] [16] [17] , SARS-CoV-2 E protein insertion into the microsomal membranes in two opposite orientations cannot be discounted, but according to our data being dominant an Nt lum /Ct cyt orientation. As shown in figure 2c, E protein (NST) was efficiently glycosylated when microsomal membranes were added to the translation mixture cotranslationally (lane 4). Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells abstract: Coronavirus E protein is a small membrane protein found in the virus envelope. Different coronavirus E proteins share striking biochemical and functional similarities, but sequence conservation is limited. In this report, we studied the E protein topology from the new SARS-CoV-2 virus both in microsomal membranes and in mammalian cells. Experimental data reveal that E protein is a single-spanning membrane protein with the N-terminus being translocated across the membrane, while the C-terminus is exposed to the cytoplasmic side (Nt(lum)/Ct(cyt)). The defined membrane protein topology of SARS-CoV-2 E protein may provide a useful framework to understand its interaction with other viral and host components and contribute to establish the basis to tackle the pathogenesis of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32898469/ doi: 10.1098/rsob.200209 id: cord-263365-ymnbktm5 author: Dube, Geoffrey K. title: COVID‐19 infection in pancreas transplant recipients date: 2020-06-09 words: 2494.0 sentences: 168.0 pages: flesch: 51.0 cache: ./cache/cord-263365-ymnbktm5.txt txt: ./txt/cord-263365-ymnbktm5.txt summary: 1 Clinical manifestations of COVID-19, the disease caused by SARS-CoV-2, range from asymptomatic infection to mild upper respiratory tract symptoms or viral pneumonia. We present here the first four cases of COVID-19 disease reported in PT recipients, with one case being a presumptive diagnosis based on suggestive symptoms and known nosocomial exposure in the absence of confirmatory PCR testing for SARS-CoV-2. First, the main presenting symptoms in our PT recipients (fever in 100%, cough in 75%) were similar to what is reported in the non-transplant population. The clinical deterioration of patient 3 after 10 days highlights the importance of close monitoring of suspected or confirmed COVID-19 in PT recipients followed in the outpatient setting until complete symptom resolution. When our patients informed us of symptoms consistent with COVID-19 infection, we held mycophenolate in 3 of our patients and temporarily held tacrolimus in 1 patient on monotherapy, a strategy similar to that employed in other solid organ transplant recipients at our center. abstract: Coronavirus Disease 2019 (COVID‐19) has become a pandemic since first being described in January 2020. Clinical manifestations in non‐transplant patients range from asymptomatic infection to severe pneumonia with acute respiratory distress syndrome, multiorgan system failure and death. Limited reports in kidney transplant recipients suggest similar characteristics in that population. We report here the first case series of COVID‐19 infection occurring in pancreas transplant recipients. url: https://doi.org/10.1111/tid.13359 doi: 10.1111/tid.13359 id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 words: 13885.0 sentences: 845.0 pages: flesch: 44.0 cache: ./cache/cord-294108-uvnh0s9r.txt txt: ./txt/cord-294108-uvnh0s9r.txt summary: [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. abstract: The deadly pandemic, coronavirus disease 2019 (COVID‐19), caused due to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has paralyzed the world. Although significant methodological advances have been made in the field of viral detection/diagnosis with 251 in vitro diagnostic tests receiving emergency use approval by the US‐FDA, little progress has been made in identifying curative or preventive therapies. This review discusses the current trends and potential future approaches for developing COVID‐19 therapeutics, including repurposed drugs, vaccine candidates, immune‐modulators, convalescent plasma therapy, and antiviral nanoparticles/nanovaccines/combinatorial nanotherapeutics to surmount the pandemic viral strain. Many potent therapeutic candidates emerging via drug‐repurposing could significantly reduce the cost and duration of anti‐COVID‐19 drug development. Gene/protein‐based vaccine candidates that could elicit both humoral and cell‐based immunity would be on the frontlines to prevent the disease. Many emerging nanotechnology‐based interventions will be critical in the fight against the deadly virus by facilitating early detection and enabling target oriented multidrug therapeutics. The therapeutic candidates discussed in this article include remdesivir, dexamethasone, hydroxychloroquine, favilavir, lopinavir/ritonavir, antibody therapeutics like gimsilumab and TJM2, anti‐viral nanoparticles, and nanoparticle‐based DNA and mRNA vaccines. url: https://doi.org/10.1002/adtp.202000172 doi: 10.1002/adtp.202000172 id: cord-356174-40k6m7l0 author: Ducloyer, Mathilde title: Complete post-mortem data in a fatal case of COVID-19: clinical, radiological and pathological correlations date: 2020-08-06 words: 2874.0 sentences: 176.0 pages: flesch: 46.0 cache: ./cache/cord-356174-40k6m7l0.txt txt: ./txt/cord-356174-40k6m7l0.txt summary: A reverse-transcription polymerase chain reaction test was positive for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using a nasopharyngeal swab sample. Post-mortem virology studies detected the presence of SARS-CoV-2 (B.1 lineage) in the nasopharynx, plasma, lung biopsies, pleural effusion and faeces confirming the persistence of viral ribonucleic acid 48 h after death. This case is one of the first to describe complete post-mortem data for a COVID-19 death and highlights the ability of PMCT to detect severe involvement of the lungs before autopsy in an apparently natural death. The present pathology results are concordant with previously reported findings and reinforce the disease pathogenesis hypothesis of combined viral replication with an inappropriate immune response. Concerning the post-mortem virology data, this case demonstrated that RNA from SARS-CoV-2 was still detectable in blood, faeces, the lungs and the upper airways more than 48 h after death. abstract: A 75-year-old man presented to a French hospital with a 4-day fever after returning from a coronavirus disease-19 (COVID-19) cluster region. A reverse-transcription polymerase chain reaction test was positive for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using a nasopharyngeal swab sample. After he returned home and a telephone follow-up, he was found deceased 9 days after first showing symptoms. Whole-body, non-enhanced, post-mortem computed tomography (PMCT) and a forensic autopsy were performed approximately 48 h after death, with sanitary precautions. The PMCT showed bilateral and diffuse crazy-paving lung opacities, with bilateral pleural effusions. Post-mortem virology studies detected the presence of SARS-CoV-2 (B.1 lineage) in the nasopharynx, plasma, lung biopsies, pleural effusion and faeces confirming the persistence of viral ribonucleic acid 48 h after death. Microscopic examination showed that severe lung damage was responsible for his death. The main abnormality was diffuse alveolar damage, associated with different stages of inflammation and fibrosis. This case is one of the first to describe complete post-mortem data for a COVID-19 death and highlights the ability of PMCT to detect severe involvement of the lungs before autopsy in an apparently natural death. The present pathology results are concordant with previously reported findings and reinforce the disease pathogenesis hypothesis of combined viral replication with an inappropriate immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/32767018/ doi: 10.1007/s00414-020-02390-1 id: cord-333239-nj5dma98 author: Ducrest, P. J. title: Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2 date: 2020-10-13 words: 1771.0 sentences: 121.0 pages: flesch: 63.0 cache: ./cache/cord-333239-nj5dma98.txt txt: ./txt/cord-333239-nj5dma98.txt summary: Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). The aim of this study is to develop and evaluate the performance of a new IgM/IgG rapid diagnostic test (RDT) based on lateral flow assay (LFA) technology, in a high COVID-19 prevalence setting using gold standard RT-PCR as well as an Electro-chemiluminescence immunoassay (ECLIA) Elecsys® Anti-SARS-CoV-2 total Ig (Roche, Switzerland). The key finding of the present evaluation study, using an unmatched case-control design including 73.5% of negative control samples, is that the diagnostic accuracy of IgG/IgM RDT on plasma samples when compared to RT-PCR or ECLIA is the same and displayed a SE of 100%, a SP of 93% and a NPV of 100%. abstract: There is an urgent need in rapid diagnostic test (RDT) to detect antibodies against SARS-CoV-2. We have developed a rapid and simple point-of-care lateral flow immunoassay (LFIA) detecting IgM and IgG against SARS-CoV-2 in 10 minutes. The aim of this study is to evaluate the diagnostic performance of this RDT. RT-PCR positive plasma samples (n=35) for SARS-CoV-2 and 97 negative control samples were studied. Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). This IgG/IgM RDT done in plasma displays a high diagnostic accuracy for SARS-CoV-2 IgG/IgM in high COVID-19 prevalence settings. Its use could be considered in the absence of routine diagnostic serology facilities for samples collected between 10 and 180 days after symptoms onset. url: https://doi.org/10.1101/2020.10.09.20209866 doi: 10.1101/2020.10.09.20209866 id: cord-340579-cvze15cj author: Dudley, Joseph P title: Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date: 2020-03-31 words: 1430.0 sentences: 74.0 pages: flesch: 46.0 cache: ./cache/cord-340579-cvze15cj.txt txt: ./txt/cord-340579-cvze15cj.txt summary: There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 abstract: We analyzed age- and sex-specific morbidity and mortality data from SARS-COV-2 pandemic in China and Republic of Korea (ROK). Data from China exhibit a Gaussian distribution with peak morbidity in the 50-59 years cohort, while the ROK data have a bimodal distribution with highest morbidity in the 20-29 years cohort. url: https://doi.org/10.1093/cid/ciaa354 doi: 10.1093/cid/ciaa354 id: cord-294700-pb5k21da author: Dulek, Daniel E title: Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute COVID-19 in Pediatric Patients date: 2020-08-18 words: 14522.0 sentences: 835.0 pages: flesch: 38.0 cache: ./cache/cord-294700-pb5k21da.txt txt: ./txt/cord-294700-pb5k21da.txt summary: Although the majority of SARS-CoV-2 infections in pediatric populations result in minimal or mild COVID-19 in the acute phase of infection, a small subset of children develop severe and even critical disease in this phase with concomitant inflammation that may benefit from immunomodulation. The framework presented herein offers an approach to decision-making regarding immunomodulatory therapy for severe or critical pediatric COVID-19 and is informed by currently available data, while awaiting results of placebo-controlled randomized clinical trials. Given the lack of available results from randomized-controlled trials of immunomodulatory therapy in children with COVID-19, the risk-benefit ratio for most pediatric patients points toward supportive care as the key management strategy. In the absence of such opportunity, and recognizing that definitive evidence is lacking, consideration for use of immunomodulatory agents in cases of SARS-CoV-2 infection with clinical and biochemical evidence of cytokine storm physiology (e.g., features of secondary HLH) should be limited to patients with clear evidence of critical COVID-19 disease and risk for multi-organ failure. abstract: BACKGROUND: Immune-mediated lung injury and systemic hyperinflammation are characteristic of severe and critical coronavirus disease 2019 (COVID-19) in adults. Although the majority of SARS-CoV-2 infections in pediatric populations result in minimal or mild COVID-19 in the acute phase of infection, a small subset of children develop severe and even critical disease in this phase with concomitant inflammation that may benefit from immunomodulation. Therefore, guidance is needed regarding immunomodulatory therapies in the setting of acute pediatric COVID-19. This document does not provide guidance regarding the recently emergent multisystem inflammatory syndrome in children (MIS-C). METHODS: A multidisciplinary panel of pediatric subspecialty physicians and pharmacists with expertise in infectious diseases, rheumatology, hematology/oncology, and critical care medicine was convened. Guidance statements were developed based on best available evidence and expert opinion. RESULTS: The panel devised a framework for considering the use of immunomodulatory therapy based on an assessment of clinical disease severity and degree of multi-organ involvement combined with evidence of hyperinflammation. Additionally, the known rationale for consideration of each immunomodulatory approach and the associated risks and benefits was summarized. CONCLUSIONS: Immunomodulatory therapy is not recommended for the majority of pediatric patients, who typically develop mild or moderate COVID-19. For children with severe or critical illness, the use of immunomodulatory agents may be beneficial. The risks and benefits of such therapies are variable and should be evaluated on a case-by-case basis with input from appropriate specialty services. When available, the panel strongly favors immunomodulatory agent use within the context of clinical trials. The framework presented herein offers an approach to decision-making regarding immunomodulatory therapy for severe or critical pediatric COVID-19 and is informed by currently available data, while awaiting results of placebo-controlled randomized clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32808988/ doi: 10.1093/jpids/piaa098 id: cord-270935-t9pym9k0 author: Dumyati, Ghinwa title: Does Universal Testing for COVID-19 Work for Everyone? date: 2020-08-15 words: 2681.0 sentences: 179.0 pages: flesch: 55.0 cache: ./cache/cord-270935-t9pym9k0.txt txt: ./txt/cord-270935-t9pym9k0.txt summary: Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. Dr. Jump reports support for this work in part through the Cleveland Geriatric Research 50 While there is general agreement that increased access to testing is important for personal and 23 public health, the selection and use of diagnostic tests to mitigate COVID-19 infections in post-24 acute and long-term care settings is complex and should be tailored to individual sites. Because he met the nursing 36 home''s enhanced screening criteria for COVID-19 (Table 1) , 1 he was placed on transmission-37 based precautions and a laboratory test for SARS-CoV-2 was ordered. abstract: Abstract The COVID-19 pandemic has been especially devastating among nursing home residents, with both the health circumstances of individual residents as well as communal living settings contributing to increased morbidity and mortality. Preventing the spread of COVID-19 infection requires a multipronged approach that includes early identification of infected residents and healthcare personnel, compliance with infection prevention and control measures, cohorting infected residents, and furlough of infected staff. Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. We review the tests available to diagnose COVID-19 infections, the implications of universal testing for nursing home staff and residents, interpretation of test results, issues around repeat testing, and incorporation of test results as part of a long-term response to the COVID-19 pandemic. We propose a structured approach for facility-wide testing of resident and staff and provide alternatives if testing capacity is limited, emphasizing contact tracing. Nursing homes with strong screening protocols for residents and staff, that engage in contact tracing for new cases, and that continue to remain vigilant about infection prevent and control practices, may better serve their residents and staff by thoughtful use of symptom- and risk-based testing strategies. url: https://www.sciencedirect.com/science/article/pii/S1525861020307039?v=s5 doi: 10.1016/j.jamda.2020.08.013 id: cord-317355-z5tk3v3b author: Dunker, Susanne title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread date: 2020-10-13 words: 1954.0 sentences: 139.0 pages: flesch: 62.0 cache: ./cache/cord-317355-z5tk3v3b.txt txt: ./txt/cord-317355-z5tk3v3b.txt summary: title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread Air samples collected at our measuring station in Leipzig and purified pollen were analyzed for SARS-CoV-2 typical signals or for virus-induced cytopathic effects, to test if the virus could bind to bioaerosols and if so, whether these complexes are infectious. We therefore aimed at investigating whether SARS-CoV-2 can bind to pollen or other kind of particulate matter within bioaerosols sampled at our station in Leipzig and if so, whether these complexes are infectious. In none of these samples SARS-CoV-2 typical For a detailed analysis of a possible correlation between concentrations of the most abundant pollen, particulate matter and registered Covid-19 cases, a correlation matrix was created with R (package "PerformanceAnalytics") (Fig. 2) . abstract: The SARS-CoV-2 pandemic co-occurred with pollen season in Europe 2020 and recent studies suggest a potential link between both. Air samples collected at our measuring station in Leipzig and purified pollen were analyzed for SARS-CoV-2 typical signals or for virus-induced cytopathic effects, to test if the virus could bind to bioaerosols and if so, whether these complexes are infectious. The results show that neither air samples nor purified pollen were infectious or could act as carrier for virus particles. url: https://api.elsevier.com/content/article/pii/S0048969720364111 doi: 10.1016/j.scitotenv.2020.142881 id: cord-307702-n74wvika author: Durant, Thomas J S title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 words: 2811.0 sentences: 162.0 pages: flesch: 44.0 cache: ./cache/cord-307702-n74wvika.txt txt: ./txt/cord-307702-n74wvika.txt summary: METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. abstract: BACKGROUND: Coronavirus Disease 2019 (COVID-19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19. METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. RESULTS: Between February 2, 2020 and April 11, 2020, there were 873,397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization. CONCLUSION: Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability. url: https://doi.org/10.1093/jalm/jfaa121 doi: 10.1093/jalm/jfaa121 id: cord-322885-ob5euspo author: Durdagi, Serdar title: Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date: 2020-09-09 words: 10818.0 sentences: 656.0 pages: flesch: 54.0 cache: ./cache/cord-322885-ob5euspo.txt txt: ./txt/cord-322885-ob5euspo.txt summary: One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. Radiation-damage-free SFX method which enables obtaining the novel high-resolution ambient-temperature structures of the binding pocket of Mpro provides an unprecedented opportunity for identification of highly effective inhibitors for drug repurposing by using a hybrid approach that combines structural and in silico methods. We determined two radiation-damage-free SFX crystal structures of SARS-CoV-2 Mpro in two crystal forms at 1.9 Å and 2.1 Å resolutions with the following PDB IDs: 7CWB and 7CWC, respectively (Fig. 1A, B) (Supplementary Table 1&2 The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al., They reveal novel active site residue conformations and dynamics at atomic level, revealing several differences compared to the prior ambient-temperature structure of SARS-CoV-2 Mpro that was obtained at a home X-ray source (Fig. 1A, B ). abstract: The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray crystallography. We employed detailed molecular simulations of selected known main protease inhibitors with the structures and compared binding modes and energies. The combined structural biology and molecular modeling studies not only reveal the dynamics of small molecules targeting main protease but will also provide invaluable opportunities for drug repurposing and structure-based drug design studies against SARS-CoV-2. One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. url: https://doi.org/10.1101/2020.09.09.287987 doi: 10.1101/2020.09.09.287987 id: cord-291281-ygrh8ces author: Durner, J. title: Critical Questions when Interpreting Coronavirus PCR Diagnostics date: 2020-06-14 words: 1912.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-291281-ygrh8ces.txt txt: ./txt/cord-291281-ygrh8ces.txt summary: In contrast to other PCR examinations, or laboratory medical analyses, currently SARS-CoV-2 diagnostic information about the device or the detection limit / sensitivity is not usually provided by the laboratory. Using a protocol without purification of viral RNA, i.e. the Munich Extraction Protocol (MEP) [2] , we could show that the type of transport medium had little influence on the detection sensitivity of SARS-CoV-2 in the PCR (Table 1) . By using this system, the sensitivity could be increased by at least one more dilution step compared to the use of commercial purification methods in PCR (Table 3) . . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 1 Comparison of different types of transport media for their influence on the detectability of SARS-CoV-2. . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 2 Comparison of different purification systems for their influence on the detectability of SARS-CoV-2 (Cp = crossing point). abstract: The results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work. url: http://medrxiv.org/cgi/content/short/2020.06.11.20127241v1?rss=1 doi: 10.1101/2020.06.11.20127241 id: cord-033010-o5kiadfm author: Durojaye, Olanrewaju Ayodeji title: Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date: 2020-10-02 words: 8125.0 sentences: 375.0 pages: flesch: 53.0 cache: ./cache/cord-033010-o5kiadfm.txt txt: ./txt/cord-033010-o5kiadfm.txt summary: RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Our current study took advantage of the availability of the SARS CoV main proteinase amino acid sequence to map out the nucleotide coding region for the same protein in the 2019-nCoV. The predicted secondary structure composition shows a high degree of alpha helix and beta sheets, respectively, occupying 45 and 47% of the total residues with the percentage loop occupancy at 8% regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology. abstract: BACKGROUND: The 2019-nCoV which is regarded as a novel coronavirus is a positive-sense single-stranded RNA virus. It is infectious to humans and is the cause of the ongoing coronavirus outbreak which has elicited an emergency in public health and a call for immediate international concern has been linked to it. The coronavirus main proteinase which is also known as the 3C-like protease (3CLpro) is a very important protein in all coronaviruses for the role it plays in the replication of the virus and the proteolytic processing of the viral polyproteins. The resultant cytotoxic effect which is a product of consistent viral replication and proteolytic processing of polyproteins can be greatly reduced through the inhibition of the viral main proteinase activities. This makes the 3C-like protease of the coronavirus a potential and promising target for therapeutic agents against the viral infection. RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Comparative physiochemical studies were carried out on the resultant target protein and its template while selected HIV protease inhibitors were docked against the protein binding sites which contained no co-crystallized ligand. CONCLUSION: In line with results from this study which has shown great consistency with other scientific findings on coronaviruses, we recommend the administration of the selected HIV protease inhibitors as first-line therapeutic agents for the treatment of the current coronavirus epidemic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529470/ doi: 10.1186/s43042-020-00081-5 id: cord-265191-unk6rt7u author: Durrani, Muhammad title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report date: 2020-06-22 words: 1818.0 sentences: 109.0 pages: flesch: 40.0 cache: ./cache/cord-265191-unk6rt7u.txt txt: ./txt/cord-265191-unk6rt7u.txt summary: title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report Among the respiratory viral pathogens, the Coronaviridae family and its genera coronaviruses have been implicated as having neurotropic and neuroinvasive capabilities in human hosts.1 Despite previous strains of coronaviruses exhibiting neurotropic and neuroinvasive capabilities, little is known about the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its involvement with the central nervous system (CNS). CONCLUSION: The patient underwent further workup and treatment with intravenous corticosteroids with improvement of symptoms and a discharge diagnosis of ATM secondary to SARS-CoV-2. 11 Additionally, the first case report of acute infectious myelitis associated with concurrent SARS-CoV-2 was only recently described. Our patient met the inclusion criteria for diagnosis of ATM based on bilateral motor symptoms and autonomic dysfunction with bladder incontinence along with evidence of CSF lymphocytic pleocytosis and characteristic MRI findings while ruling out other infectious, autoimmune, and connective tissue etiologies. abstract: INTRODUCTION: Respiratory viral illnesses are associated with diverse neurological complications, including acute transverse myelitis (ATM). Among the respiratory viral pathogens, the Coronaviridae family and its genera coronaviruses have been implicated as having neurotropic and neuroinvasive capabilities in human hosts.1 Despite previous strains of coronaviruses exhibiting neurotropic and neuroinvasive capabilities, little is known about the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its involvement with the central nervous system (CNS). The current pandemic has highlighted the diverse clinical presentation of SARS-CoV-2 including a possible link to CNS manifestation with disease processes such as Guillain-Barré syndrome and cerebrovascular disease. It is critical to shed light on the varied neurological manifestation of SARS-CoV-2 to ensure clinicians do not overlook at-risk patient populations and are able to provide targeted therapies appropriately. CASE REPORT: While there are currently no published reports on post-infectious ATM secondary to SARS-CoV-2, there is one report of parainfectious ATM attributed to SARS-CoV-2 in pre-print. Here, we present a case of infectious ATM attributed to SARS-CoV-2 in a 24-year-old male who presented with bilateral lower-extremity weakness and overflow urinary incontinence after confirmed SARS-CoV-2 infection. Magnetic resonance imaging revealed non-enhancing T2-weighted hyperintense signal abnormalities spanning from the seventh through the twelfth thoracic level consistent with acute myelitis. CONCLUSION: The patient underwent further workup and treatment with intravenous corticosteroids with improvement of symptoms and a discharge diagnosis of ATM secondary to SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32926682/ doi: 10.5811/cpcem.2020.6.48462 id: cord-269766-arjoemla author: Dutescu, R. Michael title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 words: 2141.0 sentences: 124.0 pages: flesch: 57.0 cache: ./cache/cord-269766-arjoemla.txt txt: ./txt/cord-269766-arjoemla.txt summary: title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. To clarify this, we tested the tear fluid of confirmed hospitalized SARS-CoV-2 patients by PCR using a method not previously used for the collection of tear samples. In this study, we could confirm SARS-CoV-2 RNA positive tear samples by PCR in as many as 28% of determined SARS-CoV-2 patients by oropharyngeal swabs. 13 In a more recent cross-sectional study, only 1 (1.38%) conjunctival swab of 72 confirmed SARS-CoV-2 cases was tested positive. abstract: This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. Tear samples obtained with a laboratory capillary and oropharyngeal swabs were analyzed by real-time PCR using the Altona SARS-CoV-2 Assay or the Roche SARS-CoV-2 LightMix PCR, depending on the availability. Patient history was documented, and ophthalmoscopy was used to assess for ocular surface disease. RESULTS: Of all 18 patients recruited in April 2020, 5 suffered from respiratory failure and were submitted to an intensive care unit. None of our patients had signs of viral conjunctivitis although all patients in intensive care showed chemosis and conjunctival hyperemia because of third-spacing or fluid overload. The presence of coronavirus RNA was confirmed by PCR in 5 of 18 patients (28%) in tears and 72% for oropharyngeal swabs. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. This does not automatically indicate viral shedding in ocular tissue or contagiousness of tear fluid. url: https://doi.org/10.1097/ico.0000000000002562 doi: 10.1097/ico.0000000000002562 id: cord-300040-rvrp5zvv author: Dutta, Noton Kumar title: Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine date: 2008-06-15 words: 4681.0 sentences: 255.0 pages: flesch: 54.0 cache: ./cache/cord-300040-rvrp5zvv.txt txt: ./txt/cord-300040-rvrp5zvv.txt summary: We constructed eukaryotic expression plasmid encoding N [(N1 (nucleotide: 1-1269), N2 (nucleotide: 1-327), and N3 (nucleotide: 328-1296)) gene fragments of the SARS-CoV and compared their individual potential immune responses in BALB/c mice for use in the development of SARS vaccine candidates. In this report, we detected SARS-Cov N1 and N3 protein-specific immune response induced by pVAX-N1 and N3 DNA vaccination, respectively, and found significantly high titres of specific antibody and specific cell mediated immunity compared to control. These results indicate that N protein, which naturally exists in virus particles after binding of viral RNA, was able to induce strong humoral and cellular immune responses when induced by DNA vaccine, and it might be a prospective candidate gene for development of SARS-CoV vaccine. showed that expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization. The expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization abstract: It is believed today that nucleocapsid protein (N) of severe acute respiratory syndrome (SARS)-CoV is one of the most promising antigen candidates for vaccine design. In this study, three fragments [N1 (residues: 1–422); N2 (residues: 1–109); N3 (residues: 110–422)] of N protein of SARS-CoV were expressed in Escherichia coli and analyzed by pooled sera of convalescence phase of SARS patients. Three gene fragments [N1 (1–1269 nt), N2 (1–327 nt) and N3 (328–1269 nt)—expressing the same proteins of N1, N2 and N3, respectively] of SARS-N were cloned into pVAX-1 and used to immunize BALB/c mice by electroporation. Humoral (by enzyme-linked immunosorbent assay, ELISA) and cellular (by cell proliferation and CD4(+):CD8(+) assay) immunity was detected by using recombinant N1 and N3 specific antigen. Results showed that N1 and N3 fragments of N protein expressed by E. coli were able to react with sera of SARS patients but N2 could not. Specific humoral and cellular immunity in mice could be induced significantly by inoculating SARS-CoV N1 and N3 DNA vaccine. In addition, the immune response levels in N3 were significantly higher for antibody responses (IgG and IgG1 but not IgG2a) and cell proliferation but not in CD4(+):CD8(+) assay compared to N1 vaccine. The identification of antigenic N protein fragments has implications to provide basic information for the design of DNA vaccine against SARS-CoV. The present results not only suggest that DNA immunization with pVax-N3 could be used as potential DNA vaccination approaches to induce antibody in BALB/c mice, but also illustrates that gene immunization with these SARS DNA vaccines can generate different immune responses. url: https://www.ncbi.nlm.nih.gov/pubmed/18440652/ doi: 10.1016/j.imlet.2008.03.003 id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 words: 4061.0 sentences: 244.0 pages: flesch: 49.0 cache: ./cache/cord-352720-z1cvjc2y.txt txt: ./txt/cord-352720-z1cvjc2y.txt summary: While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. abstract: BACKGROUND: South America has become the epicenter of coronavirus pandemic. It seems that asymptomatic population may contribute importantly to the spread of the disease. Transmission from asymptomatic pregnant patients’ needs to be characterized in larger population cohorts and symptom assessment needs to be standardized. OBJECTIVE: To assess the prevalence of SARS CoV-2 infection in an unselected obstetrical population and to describe their presentation and clinical evolution. METHODS: A cross-sectional study was designed. Medical records of pregnant women admitted at the Obstetrics & Gynecology department of Clínica Dávila for labor & delivery, between April 27(th) and June 7(th), 2020 were reviewed. All patients were screened with RT-PCR for SARS CoV-2 at admission. After delivery, positive cases were inquired by the researchers for clinical symptoms presented before admission and clinical evolution. All neonates born from mothers with confirmed SARS CoV-2 were isolated and tested for SARS CoV-2 infection. RESULTS: A total of 586 patients were tested for SARS CoV-2 during the study period. Outcomes were obtained from 583 patients which were included in the study. Thirty-seven pregnant women had a positive test for SARS CoV-2 at admission. Cumulative prevalence of confirmed SARS CoV-2 infection was 6.35% (37/583) [CI 95%: 4.63–8.65]. From confirmed cases, 43.2% (16/37) were asymptomatic. From symptomatic patients 85.7% (18/21) had mild symptoms and evolved without complications and 14.3% (3/21) presented severe symptoms requiring admission to intensive care unit. Only 5.4% (2/37) of the neonates born to mothers with a positive test at admission had a positive RT-PCR for SARS CoV-2. CONCLUSION: In our study nearly half of pregnant patients with SARS CoV-2 were asymptomatic at the time of delivery. Universal screening, in endemic areas, is necessary for adequate patient isolation, prompt neonatal testing and targeted follow-up. url: https://www.ncbi.nlm.nih.gov/pubmed/32991621/ doi: 10.1371/journal.pone.0239887 id: cord-264614-2x7cdul3 author: Díaz-Guio, Diego Andrés title: COVID-19: Biosafety in the Intensive Care Unit date: 2020-08-27 words: 3857.0 sentences: 228.0 pages: flesch: 49.0 cache: ./cache/cord-264614-2x7cdul3.txt txt: ./txt/cord-264614-2x7cdul3.txt summary: PURPOSE OF REVIEW: COVID-19 is a new, highly transmissible disease to which healthcare workers (HCWs) are exposed, especially in the intensive care unit (ICU). This article aims to show the different strategies to prevent the widespread of the disease to critical care healthcare workers based on the review of the recent literature and the author''s experience with the personal protective equipment (PPE) in the care of patients with COVID-19 and work on human factors in crisis management. Nonetheless, to date, there is no robust evidence that medical masks are inferior to N95/FFP2 respirators for protecting healthcare workers against laboratory-confirmed COVID-19 during patients care and non-AGPs [31] . While personal protective equipment is an essential part of safety to prevent SARS-CoV-2 transmission, it must be employed appropriately, together with frequent hand hygiene, and mastering specific techniques and non-technical skills like awareness, closed-loop communication, leadership, team working, appropriate resource management, and cognitive aids [14, 34] . abstract: PURPOSE OF REVIEW: COVID-19 is a new, highly transmissible disease to which healthcare workers (HCWs) are exposed, especially in the intensive care unit (ICU). Information related to protection mechanisms is heterogeneous, and the infected HCWs’ number is increasing. This review intends to summarize the current knowledge and practices to protect ICU personnel during the patient management process in the context of the current pandemic. RECENT FINDINGS: The transmission mechanisms of SARS-CoV-2 are mainly respiratory droplets, aerosols, and contact. The virus can last for a few hours suspended in the air and be viable on surfaces for several days. Some procedures carried out in the ICU can generate aerosols. The shortage of respirators, such as the N95, has generated an increase in the demand for other protective equipment in critical care settings. SUMMARY: The probability of transmission depends on the characteristics of the pathogen, the availability of quality personal protective equipment, and the human factors associated with the performance of health workers. It is necessary to have knowledge of the virus and availability of the best possible personal protection equipment, develop skills for handling equipment, and develop non-technical skills during all intensive care process; this can be achieved through structured training. url: https://doi.org/10.1007/s40475-020-00208-z doi: 10.1007/s40475-020-00208-z id: cord-273182-djb0ozrt author: Díez, José María title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-09-09 words: 4326.0 sentences: 260.0 pages: flesch: 50.0 cache: ./cache/cord-273182-djb0ozrt.txt txt: ./txt/cord-273182-djb0ozrt.txt summary: Recently, we reported cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2 and MERS-CoV with Flebogamma R DIF 5 and 10% and Gamunex R -C, two currently available intravenous IGs (IVIG) [23] . Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2 and MERS-CoV by: ELISA techniques; and well-established neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT 50 titers ranging from 4.5 to >5 (Figure 2 ). This neutralizing activity correlates with the cross-reactivity to different coronavirus antigens observed in ELISA-binding assays with IVIG, as shown in a previous study [23] . • Intravenous immunoglobulin products were tested against severe acute respiratory syndrome coronavirus 2 in cell culture neutralization assays. abstract: Background: Cross-reactivity against human coronaviruses with Flebogamma(®) DIF and Gamunex(®)-C, two available intravenous immunoglobulins (IVIG), has been reported. In this study, these IVIG were tested for neutralization activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). Materials & methods: Neutralization capacity of lots of IVIG manufactured prior to COVID-19 pandemic was assessed against these viruses in cell culture. Infectivity neutralization was quantified by percent reduction in plaque-forming units and/or cytopathic/cytotoxic methods. Results: All IVIG preparations showed neutralization of SARS-CoV-2 isolates. All IVIG lots produced neutralization of SARS-CoV. No IVIG preparation showed significant neutralizing activity against MERS-CoV. Conclusion: The tested IVIG contain antibodies with significant in vitro cross-neutralization capacity against SARS-CoV-2 and SARS-CoV, but not MERS-CoV. These preparations are currently under evaluation as potential therapies for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32900263/ doi: 10.2217/imt-2020-0220 id: cord-254318-w8wrn9lx author: Díez, José-María title: Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens date: 2020-05-13 words: 2687.0 sentences: 167.0 pages: flesch: 48.0 cache: ./cache/cord-254318-w8wrn9lx.txt txt: ./txt/cord-254318-w8wrn9lx.txt summary: MATERIAL & METHODS: Gamunex(®)-C and Flebogamma(®) DIF (Grifols) intravenous immunoglobulin (IVIG) products were tested using ELISA techniques for antibodies against several antigens of human common betacoronaviruses that may crossreact with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Gamunex R -C (Grifols Therapeutics, Inc., NC, USA) and Flebogamma R DIF (Instituto Grifols S.A., Barcelona, Spain) IVIGs were tested for crossreactivity against several betacoronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 antigens, using ELISA techniques. Even with this uncertainty, in the context of the current health emergency (pandemic), the potential of IVIG as a therapy for COVID-19 is already being evaluated in a number of studies involving patients with severe SARS-CoV-2 viral infections including pneumonia [28] [29] [30] . • This is the first time that currently available intravenous immunoglobulins have been reported to contain antibodies that crossreact against antigens of SARS-CoV-2 and other coronaviruses. abstract: AIM: There is a critical need for effective therapies that are immediately available to control the spread of COVID-19 disease. MATERIAL & METHODS: Gamunex(®)-C and Flebogamma(®) DIF (Grifols) intravenous immunoglobulin (IVIG) products were tested using ELISA techniques for antibodies against several antigens of human common betacoronaviruses that may crossreact with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. RESULTS: Both IVIGs showed consistent reactivity to components of the tested viruses. Positive crossreactivity was seen in SARS-CoV, middle east respiratory syndrome-CoV and SARS-CoV-2. For SARS-CoV-2, positive reactivity was observed at IVIG concentrations ranging from 100 μg/ml with Gamunex-C to 1 mg/ml with Flebogamma 5% DIF. CONCLUSION: Gamunex-C and Flebogamma DIF contain antibodies reacting against SARS-CoV-2 antigens. Studies to confirm the utility of IVIG preparations for COVID-19 management may be warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/32397847/ doi: 10.2217/imt-2020-0095 id: cord-296237-i9cti2ok author: Díez, José-María title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-06-19 words: 3741.0 sentences: 220.0 pages: flesch: 51.0 cache: ./cache/cord-296237-i9cti2ok.txt txt: ./txt/cord-296237-i9cti2ok.txt summary: Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. Recently, cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2, and MERS-CoV has been reported with currently available intravenous immunoglobulins (IVIG) such as Gamunex-C and Flebogamma DIF 19 . In this study, the neutralization capacity of the IVIG products Gamunex-C and Flebogamma DIF against these epidemic human coronaviruses -SARS-CoV, SARS-CoV-2, and MERS-CoV-was evaluated. Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2, and MERS-CoV by: i) ELISA techniques; and ii) well-stablished neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT50 titers ranging from 4.5 to >5 (Figure 2 ). abstract: Background There is a crucial need for effective therapies that are immediately available to counteract COVID-19 disease. Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. In this study, the same products were tested for neutralization activity against SARS-CoV-2, SARS-CoV and MERS-CoV and their potential as an antiviral therapy. Methods The neutralization capacity of six selected lots of IVIG was assessed against SARS-CoV-2 (two different isolates), SARS-CoV and MERS-CoV in cell cultures. Infectivity neutralization was measured by determining the percent reduction in plaque-forming units (PFU) and by cytopathic effects for two IVIG lots in one of the SARS-CoV-2 isolates. Neutralization was quantified using the plaque reduction neutralization test 50 (PRNT50) in the PFU assay and the half maximal inhibitory concentration (IC50) in the cytopathic/cytotoxic method (calculated as the minus log10 dilution which reduced the viral titer by 50%). Results All IVIG preparations showed neutralization of both SARS-CoV-2 isolates, ranging from 79 to 89.5% with PRNT50 titers from 4.5 to >5 for the PFU method and ranging from 47.0%-64.7% with an IC50 ~1 for the cytopathic method. All IVIG lots produced neutralization of SARS-CoV ranging from 39.5 to 55.1 % and PRNT50 values ranging from 2.0 to 3.3. No IVIG preparation showed significant neutralizing activity against MERS-CoV. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. However, no neutralization capacity was demonstrated against MERS-CoV. These preparations are currently available and may be immediately useful for COVID-19 management. url: https://doi.org/10.1101/2020.06.19.160879 doi: 10.1101/2020.06.19.160879 id: cord-281241-k1adcls8 author: Döhla, M. title: Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date: 2020-04-18 words: 1991.0 sentences: 127.0 pages: flesch: 59.0 cache: ./cache/cord-281241-k1adcls8.txt txt: ./txt/cord-281241-k1adcls8.txt summary: Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. We therefore evaluated a rapid antibody IgG/IgMebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. Thirty-nine randomly selected individuals at the centre were tested simultaneously using the SARS-CoV-2 rapid test and the gold standard RT-qPCR method (Altona Diagnostics). The rapid test used for evaluation is a qualitative IgG/IgM detection system to test for a current or past infection of SARS-CoV-2. abstract: OBJECTIVE: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. The gold standard is a quantitative polymerase chain reaction (qPCR)–based system taking several hours to confirm positivity. For effective public health containment measures, this time span is too long. We therefore evaluated a rapid test in a high-prevalence community setting. STUDY DESIGN: Thirty-nine randomly selected individuals at a COVID-19 screening centre were simultaneously tested via qPCR and a rapid test. Ten previously diagnosed individuals with known SARS-CoV-2 infection were also analysed. METHODS: The evaluated rapid test is an IgG/IgM–based test for SARS-CoV-2 with a time to result of 20 min. Two drops of blood are needed for the test performance. RESULTS: Of 49 individuals, 22 tested positive by repeated qPCR. In contrast, the rapid test detected only eight of those positive correctly (sensitivity: 36.4%). Of the 27 qPCR-negative individuals, 24 were detected correctly (specificity: 88.9%). CONCLUSION: Given the low sensitivity, we recommend not to rely on an antibody-based rapid test for public health measures such as community screenings. url: https://www.sciencedirect.com/science/article/pii/S0033350620301141 doi: 10.1016/j.puhe.2020.04.009 id: cord-353524-3w970ycx author: Dömling, Alexander title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 words: 3942.0 sentences: 237.0 pages: flesch: 52.0 cache: ./cache/cord-353524-3w970ycx.txt txt: ./txt/cord-353524-3w970ycx.txt summary: Given that SARS-CoV-2 and SARS-CoV share very high identical sequence in their 3CLpro, these HIV protease inhibitors are currently again repurposed for the treatment of COVID-19 (Chinese Clinical Trial Registry: ChiCTR2000029539). 30, 31 The interplay of the ACE receptor in cardiovascular diseases (with the well-known drug class of ACE inhibitors) and as the docking point for SARS-CoV-2 cellular infection is a current point of intense debate and research. For example, the crystal structure of SARS-CoV-2 N protein RNA-binding domain was just published and will give structural insight as a potential drug target. Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure-based drug design study Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites abstract: SARS-CoV-2 (previously 2019-nCoV or Wuhan coronavirus) caused an unprecedented fast-spreading worldwide pandemic. Although currently with a rather low mortality rate, the virus spread rapidly over the world using the modern world’s traffic highways. The coronavirus (CoV) family members were responsible for several deadly outbreaks and epidemics during the last decade. Not only governments but also the scientific community reacted promptly to the outbreak, and information is shared quickly. For example, the genetic fingerprint was shared, and the 3D structure of key proteins was rapidly solved, which can be used for the discovery of potential treatments. An overview is given on the current knowledge of the spread, disease course, and molecular biology of SARS-CoV-2. We discuss potential treatment developments in the context of recent outbreaks, drug repurposing, and development timelines. url: https://www.sciencedirect.com/science/article/pii/S2451929420301959 doi: 10.1016/j.chempr.2020.04.023 id: cord-312697-ffxcze6c author: Dübel, Stefan title: Rekombinante, vollständig humane Antikörper zur Behandlung akuter COVID-19 date: 2020-06-26 words: 1015.0 sentences: 129.0 pages: flesch: 41.0 cache: ./cache/cord-312697-ffxcze6c.txt txt: ./txt/cord-312697-ffxcze6c.txt summary: COVID-19 (coronavirus disease 2019) ist eine akute schwere virale Erkrankung der oberen Atemwege und Lungen, die vom neuartigen SARS-CoV-2-Virus hervorgerufen wird und zum ersten Mal in Wuhan (China) Ende 2019 beschrieben wurde. Solche Antikörper sind eine komplementäre Ergänzung zu den derzeit laufenden Virus-Impfstoff-Entwicklungen, da sie mit sehr hoher Wahrscheinlichkeit auch den bereits an COVID-19 erkrankten Patienten helfen können. Dies könnte sehr schnell gehen: Aufgrund der großen Erfolge rekombinanter Antikörperwirkstoffe (fast 100 zugelassene Medikamente) stehen dafür zudem bereits heute umfangreiche Produktionskapazitäten und defi nierte Produktionsprozesse zur Verfügung, während diese bei einem neuartigen Impfstoff aus Viruskomponenten erst noch zeitaufwendig entwickelt, skaliert und zugelassen werden müssen. Auf Basis dieser Erfahrungen begannen wir im Februar dieses Jahres in Braunschweig an der TU und parallel an deren Ausgründung YUMAB GmbH mit Arbeiten zu dem Ziel, vollständig menschliche Antikörper zu entwickeln, welche die SARS-CoV-2-Infektion verhindern können. So konnte bisher ein sehr großer Satz von mehr als 750 komplett menschlichen monoklonalen Antikörpern gegen das SARS-CoV-2-Spike(S)-Protein gefunden und sequenziert werden. abstract: nan url: https://doi.org/10.1007/s12268-020-1404-4 doi: 10.1007/s12268-020-1404-4 id: cord-328113-eczjjc2v author: D’Alessandro, Angelo title: Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level date: 2020-07-30 words: 4662.0 sentences: 237.0 pages: flesch: 40.0 cache: ./cache/cord-328113-eczjjc2v.txt txt: ./txt/cord-328113-eczjjc2v.txt summary: Subjects seen at Columbia University Irving Medical Center/New York−Presbyterian Hospital included 33 COVID-19-positive patients, as determined by SARS-CoV-2 nucleic acid testing of nasopharyngeal swabs; in this group, the severity of the disease was inferred from serum levels of IL-6, which were determined by CLIAcertified ELISA-based measurements. Sera of COVID-19 patients, especially those with IL-6 levels >10 pg/mL, contained increased levels of multiple proteins in the acute phase response that is initiated by IL-6specifically components of the coagulation and complement cascades (top enriched pathway, p-value: 1.6 × 10 −31 ; Figure 2 ). Other RBC-derived proteins (i.e., band 3, anion exchanger 1 (AE1; the most abundant RBC membrane protein), peroxiredoxins 2 and 6, catalase, and Journal of Proteome Research pubs.acs.org/jpr Article biliverdin reductase B) correlated significantly with HBA and HBB levels, despite not reaching significance when compared to COVID-19-negative subjects, suggesting that minimal hemolysis was present in a subset of the most severely ill patients in our study ( Figure 4A ), perhaps due to mechanical ventilation or other iatrogenic interventions−including the sample collection protocol adopted in this study. abstract: [Image: see text] Over 5 million people around the world have tested positive for the beta coronavirus SARS-CoV-2 as of May 29, 2020, a third of which are in the United States alone. These infections are associated with the development of a disease known as COVID-19, which is characterized by several symptoms, including persistent dry cough, shortness of breath, chills, muscle pain, headache, loss of taste or smell, and gastrointestinal distress. COVID-19 has been characterized by elevated mortality (over 100 thousand people have already died in the US alone), mostly due to thromboinflammatory complications that impair lung perfusion and systemic oxygenation in the most severe cases. While the levels of pro-inflammatory cytokines such as interleukin-6 (IL-6) have been associated with the severity of the disease, little is known about the impact of IL-6 levels on the proteome of COVID-19 patients. The present study provides the first proteomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to markers of inflammation and renal function. As a function of IL-6 levels, we identified significant dysregulation in serum levels of various coagulation factors, accompanied by increased levels of antifibrinolytic components, including several serine protease inhibitors (SERPINs). These were accompanied by up-regulation of the complement cascade and antimicrobial enzymes, especially in subjects with the highest levels of IL-6, which is consistent with an exacerbation of the acute phase response in these subjects. Although our results are observational, they highlight a clear increase in the levels of inhibitory components of the fibrinolytic cascade in severe COVID-19 disease, providing potential clues related to the etiology of coagulopathic complications in COVID-19 and paving the way for potential therapeutic interventions, such as the use of pro-fibrinolytic agents. Raw data for this study are available through ProteomeXchange with identifier PXD020601. url: https://doi.org/10.1021/acs.jproteome.0c00365 doi: 10.1021/acs.jproteome.0c00365 id: cord-340908-8q7i5ds3 author: D’Ambrosi, Riccardo title: Guidelines for Resuming Elective Hip and Knee Surgical Activity Following the COVID-19 Pandemic: An Italian Perspective date: 2020-10-13 words: 1838.0 sentences: 116.0 pages: flesch: 46.0 cache: ./cache/cord-340908-8q7i5ds3.txt txt: ./txt/cord-340908-8q7i5ds3.txt summary: 1. Facility requirement: All diagnosis and treatment activities related to surgery for patients not infected with SARS-CoV-2 must be performed in a COVID-19-free environment. 3. Patient selection: Patient selection must take into account age, urgency of treatment, risk of exposure to SARS-CoV-2, American Society of Anesthesiologists (ASA) classification, comorbidity, socio-professional situation, and the possibility of performing post-operative physiotherapy [7, 13] . (However, if these patients did have surgery, the procedure must take place in a separate environment within the hospital and with adequate assessment of the risk to healthcare staff and planning to optimize their ability to avoid infection.) Also, patients classified as ASA I or ASA II had priority for intervention regardless of the urgency of the treatment. The complete program including surgical treatment, post-operative physiotherapy management, and follow-up must be discussed and planned with the patient before surgery. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33071683/ doi: 10.1007/s11420-020-09809-w id: cord-265111-d44ireu5 author: D’Ardes, Damiano title: Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids date: 2020-08-31 words: 3103.0 sentences: 148.0 pages: flesch: 45.0 cache: ./cache/cord-265111-d44ireu5.txt txt: ./txt/cord-265111-d44ireu5.txt summary: A longer duration of COVID-19 with delayed clinical healing (symptom-free) occurred in patients presenting at admission a lower PaO(2)/FiO(2) ratio (p < 0.001), a more severe clinical presentation (p = 0.001) and a lower lymphocyte count (p = 0.035). All adult patients were diagnosed with COVID-19 according to World Health Organization (WHO) interim guidance: they had clinical symptoms of COVID-19 and confirmation of SARS-CoV-2 infection through instrumental signs and a positive result on RT-PCR assays of nasopharyngeal swab specimens. The specific inclusive criteria were as follows: (1) patients confirmed by positive detection of SARS-CoV-2 RNA from nasopharyngeal/throat swabs by RT-PCR with clinical data suggesting for COVID-19, (2) patients aged more than 18 years old and (3) patients with a known date of performing different RT-PCR assays. Disease severity and lower lymphocyte levels at admission also predict longer SARS-CoV-2 viral shedding. abstract: The diffusion of SARS-CoV-2, starting from China in December 2019, has led to a pandemic, reaching Italy in February 2020. Previous studies in Asia have shown that the median duration of SARS-CoV-2 viral shedding was approximately 12–20 days. We considered a cohort of patients recovered from COVID-19 showing that the median disease duration between onset and end of COVID-19 symptoms was 27.5 days (interquartile range (IQR): 17.0–33.2) and that the median duration between onset of symptoms and microbiological healing, defined by two consecutive negative nasopharyngeal swabs, was 38 days (IQR: 31.7–50.2). A longer duration of COVID-19 with delayed clinical healing (symptom-free) occurred in patients presenting at admission a lower PaO(2)/FiO(2) ratio (p < 0.001), a more severe clinical presentation (p = 0.001) and a lower lymphocyte count (p = 0.035). Moreover, patients presenting at admission a lower PaO(2)/FiO(2) ratio and more severe disease showed longer viral shedding (p = 0.031 and p = 0.032, respectively). In addition, patients treated with corticosteroids had delayed clinical healing (p = 0.013). url: https://www.ncbi.nlm.nih.gov/pubmed/32878286/ doi: 10.3390/microorganisms8091327 id: cord-313460-oao2zppd author: D’Ardes, Damiano title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection date: 2020-05-11 words: 878.0 sentences: 57.0 pages: flesch: 60.0 cache: ./cache/cord-313460-oao2zppd.txt txt: ./txt/cord-313460-oao2zppd.txt summary: title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection We describe the case of a 65-year-old woman who clinically recovered from COVID-19 but showed persistent infection with SARS-CoV-2 for 51 days. Although the patient had clinically recovered and had been transferred from our acute department to a unit for clinically stable patients, the nasopharyngeal swabs for SARS-CoV-2 continued to be positive until the end of April (swabs taken in mid-April, 22 April and 30 April), an interval of around 51 days from the onset of symptoms on 10 March. In contrast to the 15-20 days usually described as the average duration of mild COVID-19 disease, in this case we demonstrated SARS-CoV-2 positivity which lasted for over 50 days even though the patient was clinically well 2 weeks after the onset of symptoms. Positive RT-PCR test results in patients recovered from COVID-19 abstract: In December 2019, an outbreak of a new coronavirus (SARS-CoV-2) was reported in Hubei province in China. The disease has since spread worldwide and the World Health Organization declared it a pandemic on 11 March 2020. We describe the case of a 65-year-old woman who clinically recovered from COVID-19 but showed persistent infection with SARS-CoV-2 for 51 days. LEARNING POINTS: A case of persistent infection with SARS-CoV-2 is described. Some tests may pick up viral RNA fragments, giving a false positive result. The quarantining of infected patients to limit possible SARS-CoV-2 spread is important. url: https://www.ncbi.nlm.nih.gov/pubmed/32523924/ doi: 10.12890/2020_001707 id: cord-004204-cpub9oah author: D’Cunha, Colin title: SARS: Lessons Learned from a Provincial Perspective date: 2004-01-01 words: 1538.0 sentences: 93.0 pages: flesch: 55.0 cache: ./cache/cord-004204-cpub9oah.txt txt: ./txt/cord-004204-cpub9oah.txt summary: T o say that SARS was a unique threat, and one that challenged public health and the entire health system in Ontario could be viewed as somewhat of an understatement. Never had the modern public health or the health care system been put to such a test or been put under such pressure to respond as during the two phases of SARS outbreaks earlier this year. The very uniqueness and stress that the SARS outbreaks placed on our system inevitably revealed the weaknesses and the areas where change or fortification in our public health defenses was needed in order for us to meet successfully future challenges. Funding for public health services in Ontario is based on a mixed model with municipal and provincial partners contributing to the funding. Other public health professionals should be cross-trained in communicable disease management to create additional surge capacity. A Report of the National Advisory Committee on SARS and Public Health abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976128/ doi: 10.1007/bf03403629 id: cord-269009-0i2bvt77 author: D’Souza, Rohan title: A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID‐19 date: 2020-08-05 words: 3295.0 sentences: 205.0 pages: flesch: 36.0 cache: ./cache/cord-269009-0i2bvt77.txt txt: ./txt/cord-269009-0i2bvt77.txt summary: Should patients develop coronavirus disease (COVID‐19) pneumonia requiring hospital admission for treatment of hypoxia, the risk for thromboembolic complications increases greatly. 2 As pregnancy is a prothrombotic state, the possibility of an increased risk of thrombosis in pregnant women with COVID-19 has become an area of concern, and a number of international organiPatients with severe COVID-19 may be at risk for pulmonary thromboembolic complications through at least two distinct mechanisms -immunothrombosis and hospital-associated venous thromboembolism (VTE). 12 A recent study of patients with severe COVID-19 demonstrated a correlation between IL-6 and fibrinogen levels, 3 further supporting the theory that massive activation of the acute phase response, with increased production of coagulation factors, appears to be the predominant prothrombotic mechanism in COVID-19. A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID-19 abstract: Those who are infected with Severe Acute Respiratory Syndrome‐related CoronaVirus‐2 are theoretically at increased risk of venous thromboembolism during self‐isolation if they have reduced mobility or are dehydrated. Should patients develop coronavirus disease (COVID‐19) pneumonia requiring hospital admission for treatment of hypoxia, the risk for thromboembolic complications increases greatly. These thromboembolic events are the result of at least two distinct mechanisms – microvascular thrombosis in the pulmonary system (immunothrombosis) and hospital‐associated venous thromboembolism. Since pregnancy is a prothrombotic state, there is concern regarding the potentially increased risk of thrombotic complications among pregnant women with COVID‐19. To date, however, pregnant women do not appear to have a substantially increased risk of thrombotic complications related to COVID‐19. Nevertheless, several organizations have vigilantly issued pregnancy‐specific guidelines for thromboprophylaxis in COVID‐19. Discrepancies between these guidelines reflect the altruistic wish to protect patients and lack of high‐quality evidence available to inform clinical practice. Low molecular weight heparin (LMWH) is the drug of choice for thromboprophylaxis in pregnant women with COVID‐19. However, its utility in non‐pregnant patients is only established against venous thromboembolism, as LMWH may have little or no effect on immunothrombosis. Decisions about initiation and duration of prophylactic anticoagulation in the context of pregnancy and COVID‐19 must take into consideration disease severity, outpatient vs inpatient status, temporal relation between disease occurrence and timing of childbirth, and the underlying prothrombotic risk conferred by additional comorbidities. There is currently no evidence to recommend the use of intermediate or therapeutic doses of LMWH in thromboprophylaxis, which may increase bleeding risk without reducing thrombotic risk in pregnant patients with COVID‐19. Likewise, there is no evidence to comment on the role of low‐dose aspirin in thromboprophylaxis or of anti‐cytokine and antiviral agents in preventing immunothrombosis. These unanswered questions are being studied within the context of clinical trials. url: https://doi.org/10.1111/aogs.13962 doi: 10.1111/aogs.13962 id: cord-292387-2xv3wgaq author: D′Agostino, Armando title: Brief Psychotic Disorder During the National Lockdown in Italy: An Emerging Clinical Phenomenon of the COVID-19 Pandemic date: 2020-08-06 words: 4555.0 sentences: 240.0 pages: flesch: 44.0 cache: ./cache/cord-292387-2xv3wgaq.txt txt: ./txt/cord-292387-2xv3wgaq.txt summary: Approximately 2 months after the COVID-19 outbreak in Lombardy and 50 days into national lockdown, we began to hospitalize patients with brief psychotic episodes at a remarkable rate. We report a case series of all consecutive patients admitted to the 2 psychiatric inpatient units of the San Paolo University Hospital who were discharged with a diagnosis of BPD during the COVID-19 pandemic lockdown in Milan, Italy (March 9 to May 18). In order to standardize the evaluation criteria, the following set of instruments was employed: the Brief Psychiatric Rating Scale (BPRS) 20 was performed as a global measure of psychopathology upon admission and at discharge; the presence of stressful life events in the 12 months before the lockdown was assessed using Paykel''s interview for recent life events 21 ; the Structured Clinical Interview for DSM (SCID-II) 22 was performed to evaluate the presence of a personality disorder; and the Temperament and Character Inventory-240 items (TCI-240) 23 was administered to investigate personality dimensions. abstract: The impact of the COVID-19 pandemic on psychosis remains to be established. Here we report 6 cases (3 male and 3 female) of first-episode psychosis (FEP) admitted to our hospital in the second month of national lockdown. All patients underwent routine laboratory tests and a standardized assessment of psychopathology. Hospitalization was required due to the severity of behavioral abnormalities in the context of a full-blown psychosis (the Brief Psychiatric Rating Scale [BPRS] = 75.8 ± 14.6). Blood tests, toxicological urine screening, and brain imaging were unremarkable, with the exception of a mild cortical atrophy in the eldest patient (male, 73 years). All patients were negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout their stay, but 3 presented the somatic delusion of being infected. Of note, all 6 cases had religious/spiritual delusions and hallucinatory contents. Despite a generally advanced age (53.3 ± 15.6), all patients had a negative psychiatric history. Rapid discharge (length of stay = 13.8 ± 6.9) with remission of symptoms (BPRS = 27.5 ± 3.1) and satisfactory insight were possible after relatively low-dose antipsychotic treatment (Olanzapine-equivalents = 10.1 ± 5.1 mg). Brief psychotic disorder/acute and transient psychotic disorder diagnoses were confirmed during follow-up visits in all 6 cases. The youngest patient (female, 23 years) also satisfied the available criteria for brief limited intermittent psychotic symptoms. Although research on larger populations is necessary, our preliminary observation suggests that intense psychosocial stress associated with a novel, potentially fatal disease and national lockdown restrictions might be a trigger for FEP. url: https://www.ncbi.nlm.nih.gov/pubmed/32761196/ doi: 10.1093/schbul/sbaa112 id: cord-288639-wy07nao0 author: Earnest, Arul title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore date: 2005-05-11 words: 2797.0 sentences: 152.0 pages: flesch: 50.0 cache: ./cache/cord-288639-wy07nao0.txt txt: ./txt/cord-288639-wy07nao0.txt summary: title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore BACKGROUND: The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make real-time predictions on the number of beds occupied in Tan Tock Seng Hospital, during the recent SARS outbreak. The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make realtime predictions on the number of beds occupied in TTSH during the SARS outbreak, starting from 14 Mar 2003, when the CDC was activated, to 31 May 2003 when Singapore was declared SARS free. To the best of our knowledge, this is the first study to suggest the application of a known statistical method such as the ARIMA model, to predict and monitor the utilization of hospital isolation beds during the recent SARS outbreak in Singapore, for which Tan Tock Seng Hospital was the Admissions, predicted and actual number of beds occupied abstract: BACKGROUND: The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make real-time predictions on the number of beds occupied in Tan Tock Seng Hospital, during the recent SARS outbreak. METHODS: This is a retrospective study design. Hospital admission and occupancy data for isolation beds was collected from Tan Tock Seng hospital for the period 14(th )March 2003 to 31(st )May 2003. The main outcome measure was daily number of isolation beds occupied by SARS patients. Among the covariates considered were daily number of people screened, daily number of people admitted (including observation, suspect and probable cases) and days from the most recent significant event discovery. We utilized the following strategy for the analysis. Firstly, we split the outbreak data into two. Data from 14(th )March to 21(st )April 2003 was used for model development. We used structural ARIMA models in an attempt to model the number of beds occupied. Estimation is via the maximum likelihood method using the Kalman filter. For the ARIMA model parameters, we considered the simplest parsimonious lowest order model. RESULTS: We found that the ARIMA (1,0,3) model was able to describe and predict the number of beds occupied during the SARS outbreak well. The mean absolute percentage error (MAPE) for the training set and validation set were 5.7% and 8.6% respectively, which we found was reasonable for use in the hospital setting. Furthermore, the model also provided three-day forecasts of the number of beds required. Total number of admissions and probable cases admitted on the previous day were also found to be independent prognostic factors of bed occupancy. CONCLUSION: ARIMA models provide useful tools for administrators and clinicians in planning for real-time bed capacity during an outbreak of an infectious disease such as SARS. The model could well be used in planning for bed-capacity during outbreaks of other infectious diseases as well. url: https://www.ncbi.nlm.nih.gov/pubmed/15885149/ doi: 10.1186/1472-6963-5-36 id: cord-262766-ndn6iwre author: Easom, Nicholas title: 68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit date: 2020-03-06 words: 2964.0 sentences: 145.0 pages: flesch: 45.0 cache: ./cache/cord-262766-ndn6iwre.txt txt: ./txt/cord-262766-ndn6iwre.txt summary: Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. In addition, many mild respiratory viral infections were managed as influenza 10 , with significant resource implications, both for healthcare services and patients Here we describe our experience of the first 68 patients we have tested for SARS-CoV-2 at a Regional Infectious Diseases unit (RIDU) in the UK. Specialist Infectious Diseases consultant-delivered assessment of a group of patients who predominantly have mild illness is unlikely to be sustainable, especially as the case-definition broadens to include a wider geographical area and/or COVID-19 patients requiring inpatient care becomes more common in the UK. abstract: Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. We report our case series of 68 patients, reviewed by Infectious Diseases Consultants at a Regional Infectious Diseases Unit in the UK. We prospectively evaluated our service between the 29th Jan 2020 and 24th Feb 2020. Demographic, clinical, epidemiological and laboratory data were collected. We have compared clinical features and subsequent diagnosis between well patients not requiring admission for clinical reasons or antimicrobials with those assessed as needing either admission or antimicrobial treatment. Final microbiological diagnoses included SARS-CoV-2 (COVID-19), Mycoplasma pneumonia, influenza A, RSV, non SARS/MERS coronaviruses, rhinovirus/enterovirus. 9/68 were treated with antimicrobials, 15/68 were admitted to a negative pressure room of whom 5/68 were admitted solely due to an inability to isolate at home. Patients requiring either admission on clinical grounds or antimicrobials (14/68) were similar to those not requiring admission or antimicrobials, with modestly more fever and shortness of breath in the clinically admitted / antimicrobial group. The most commonly prescribed antimicrobials were doxycycline, moxifloxacin and oseltamivir. The majority of patients had mild illness which did not require a clinical intervention to manage. This finding supports a community testing approach supported by clinicians to review the proportion of more unwell patients. url: https://doi.org/10.1101/2020.02.29.20029462 doi: 10.1101/2020.02.29.20029462 id: cord-322385-sc2vxxnn author: Ebinger, J. title: SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers date: 2020-08-04 words: 3672.0 sentences: 205.0 pages: flesch: 38.0 cache: ./cache/cord-322385-sc2vxxnn.txt txt: ./txt/cord-322385-sc2vxxnn.txt summary: Main Outcomes: Using Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection. Recognizing the range of factors that might influence antibody status in a given individual, we focused our study on not only estimating seroprevalence but also on identifying factors associated with seropositivity and relative antibody levels within the following three categories: (1) pre-existing demographic and clinical characteristics; (2) potential Covid-19 illness related exposures; and, (3) Covid-19 illness related response variables (i.e. different types of self-reported symptoms). In adjusted analyses, we compared differences between serology status (i.e. antibody positive versus negative) in each variable of interest, grouped into one of three categories: (1) preexisting demographic and clinical characteristics (e.g. age, gender, ethnicity, race, and selfreported medical comorbidities); (2) Covid-19 related exposures (e.g. self-reported medical diagnosis of Covid-19 illness, household member with Covid-19 illness, number of people living in the home including children, type of home dwelling, etc); and, (3) Covid-19 related response variables (e.g. self-reported fever, chills, dry cough, anosmia, nausea, myalgias, etc.). abstract: Importance: Antibody testing is important for understanding patterns of exposure and potential immunity to SARS-CoV-2. Prior data on seroprevalence have been subject to variations in selection of individuals and nature as well as timing of testing in relation to exposures. Objective: We sought to determine the extent of SARS-CoV-2 seroprevalance and the factors associated with seroprevelance across a diverse cohort of healthcare workers. Design: Observational cohort study of healthcare workers, including SARS-CoV-2 serology testing and participant questionaires. Participants: A diverse and unselected population of adults (n=6,062) employed in a multi-site healthcare delivery system located in Los Angeles County, including individuals with direct patient contact and others with non-patient-oriented work functions. Exposure: Exposure and infection with the SARS-CoV-2 virus, as determined by seropositivity. Main Outcomes: Using Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection. Results: We observed a seroprevalence rate of 4.1%, with anosmia as the most prominently associated self-reported symptom in addition to fever, dry cough, anorexia, and myalgias. After adjusting for potential confounders, pre-existing medical conditions were not associated with antibody positivity. However, seroprevalence was associated with younger age, Hispanic ethnicity, and African-American race, as well as presence of either a personal or household member having a prior diagnosis of Covid-19. Importantly, African American race and Hispanic ethnicity were associated with antibody positivity even after adjusting for personal Covid-19 diagnosis status, suggesting the contribution of unmeasured structural or societally factors. Notably, number of people, or children, in the home was not associated with antibody positivity. Conclusion and Relevance: The demographic factors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace. The size and diversity of our study population, combined with robust survey and modeling techniques, provide a vibrant picture of the demographic factors, exposures, and symptoms that can identify individuals with susceptibility as well as potential to mount an immune response to Covid-19. url: https://doi.org/10.1101/2020.07.31.20163055 doi: 10.1101/2020.07.31.20163055 id: cord-319706-2e9jrv0s author: Ebinger, Joseph E. title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 words: 4904.0 sentences: 219.0 pages: flesch: 40.0 cache: ./cache/cord-319706-2e9jrv0s.txt txt: ./txt/cord-319706-2e9jrv0s.txt summary: For all patients considered to have Covid-19, based on direct or documented laboratory test result and suggestive signs and/or symptoms, we obtained information from the electronic health record (EHR) and verified data for the following demographic and clinical characteristics: age at the time of diagnosis; sex; race; ethnicity; smoking status defined as current versus prior, never, or unknown; comorbidities, including obesity, as clinically assessed and documented by a provider with ICD-10 coding; and, chronic use of angiotensin converting enzyme (ACE) inhibitor or angiotensin II receptor blocker (ARB) medications. For the primary outcome of illness severity, categorized by escalating levels of care (i.e., hospitalization, intensive care, intubation), the pre-existing characteristics that demonstrated statistical significance in age-and sex-adjusted models included older age, male sex, African American race, obesity, hypertension, diabetes mellitus, and the Elixhauser comorbidity score ( Table 2 ; Fig 3) . abstract: IMPORTANCE: Certain individuals, when infected by SARS-CoV-2, tend to develop the more severe forms of Covid-19 illness for reasons that remain unclear. OBJECTIVE: To determine the demographic and clinical characteristics associated with increased severity of Covid-19 infection. DESIGN: Retrospective observational study. We curated data from the electronic health record, and used multivariable logistic regression to examine the association of pre-existing traits with a Covid-19 illness severity defined by level of required care: need for hospital admission, need for intensive care, and need for intubation. SETTING: A large, multihospital healthcare system in Southern California. PARTICIPANTS: All patients with confirmed Covid-19 infection (N = 442). RESULTS: Of all patients studied, 48% required hospitalization, 17% required intensive care, and 12% required intubation. In multivariable-adjusted analyses, patients requiring a higher levels of care were more likely to be older (OR 1.5 per 10 years, P<0.001), male (OR 2.0, P = 0.001), African American (OR 2.1, P = 0.011), obese (OR 2.0, P = 0.021), with diabetes mellitus (OR 1.8, P = 0.037), and with a higher comorbidity index (OR 1.8 per SD, P<0.001). Several clinical associations were more pronounced in younger compared to older patients (P(interaction)<0.05). Of all hospitalized patients, males required higher levels of care (OR 2.5, P = 0.003) irrespective of age, race, or morbidity profile. CONCLUSIONS AND RELEVANCE: In our healthcare system, greater Covid-19 illness severity is seen in patients who are older, male, African American, obese, with diabetes, and with greater overall comorbidity burden. Certain comorbidities paradoxically augment risk to a greater extent in younger patients. In hospitalized patients, male sex is the main determinant of needing more intensive care. Further investigation is needed to understand the mechanisms underlying these findings. url: https://doi.org/10.1371/journal.pone.0236240 doi: 10.1371/journal.pone.0236240 id: cord-289522-7u3d6nfc author: Ebrahimi, Mina title: COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population date: 2020-10-17 words: 2460.0 sentences: 161.0 pages: flesch: 45.0 cache: ./cache/cord-289522-7u3d6nfc.txt txt: ./txt/cord-289522-7u3d6nfc.txt summary: title: COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population This review compared coronavirus disease 2019 (COVID-19) laboratory findings, comorbidities, and clinical outcomes in patients from the general population versus medical staff to aid diagnosis of COVID-19 in a more timely, efficient, and accurate way. Two reviewers separately extracted the data from included studies, considering key characteristics including author, publication year, country, type of study, sample size, laboratory findings, comorbidities, and final clinical outcomes. Further analysis revealed the frequency of clinical manifestations in infected medical staff were similar to patients in the general public (Table 3) . The findings of this COVID-19 meta-analysis review revealed that the normal or abnormal outcome of a patient''s laboratory results may shed light on the stage of the disease and its progression. Laboratory findings, signs and symptoms, clinical outcomes of Patients with COVID-19 Infection: An updated systematic review and meta-analysis abstract: This review compared coronavirus disease 2019 (COVID-19) laboratory findings, comorbidities, and clinical outcomes in patients from the general population versus medical staff to aid diagnosis of COVID-19 in a more timely, efficient, and accurate way. Electronic databases were searched up to 23(rd) March, 2020. The initial search yielded 6,527 studies. Following screening, 24 studies were included [18 studies (11,564 cases) of confirmed COVID-19 cases in the general public, and 6 studies (394 cases) in medical staff] in this review. Significant differences were observed in white blood cell counts (p < 0.001), lymphocyte counts (p < 0.001), platelet counts (p = 0.04), procalcitonin levels (p < 0.001), lactate dehydrogenase levels (p < 0.001), and creatinine levels (p = 0.03) when comparing infected medical staff with the general public. The mortality rate was higher in the general population than in medical staff (8% versus 2%). This review showed that during the early stages of COVID-19, laboratory findings alone may not be significant predictors of infection and may just accompany increasing C-reactive protein levels, erythrocyte sedimentation rates, and lactate dehydrogenase levels. In the symptomatic stage, the lymphocyte and platelet counts tended to decrease. Elevated D-dimer fibrin degradation product was associated with poor prognosis. url: https://doi.org/10.24171/j.phrp.2020.11.5.02 doi: 10.24171/j.phrp.2020.11.5.02 id: cord-312849-vgzvpwz9 author: Eckbo, Eric J. title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples date: 2020-11-10 words: 1421.0 sentences: 74.0 pages: flesch: 48.0 cache: ./cache/cord-312849-vgzvpwz9.txt txt: ./txt/cord-312849-vgzvpwz9.txt summary: title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of SARS-CoV-2 in nasopharyngeal swabs. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RdRP and E genes. This report describes the results of an independent evaluation of the performance characteristics of the BioFire COVID-19 Test and the RP2.1 for detection of SARS-CoV-2. The BioFire COVID-19 Test and Respiratory Panel 2.1 are easy-to-use, highly sensitive, and rapid assays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. This evaluation demonstrates that the assays perform comparably to our laboratory developed real-time PCR assay, with 100% agreement in testing results for clinical specimens and acceptable performance at their stated limits of detection. abstract: The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of SARS-CoV-2 in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and bacterial pathogens can be detected. Both tests have received emergency use authorization from the U.S. Food & Drug Administration and Interim Order authorization from Health Canada for use in clinical laboratories. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RdRP and E genes. A total of 78 tests were performed using the BioFire COVID-19 Test, including 30 clinical specimens and 48 tests in a limit of detection (LoD) study; 57 tests were performed using the RP2.1 for evaluation of SARS-CoV-2 detection, including 30 clinical specimens and 27 tests for LoD. Results showed 100% concordance between the BioFire assays and the laboratory-developed test for all clinical samples tested, and acceptable performance of both BioFire assays at their stated limits of detection. Conclusively, the BioFire COVID-19 Test and RP2.1 are highly sensitive assays that can be effectively used in the clinical laboratory for rapid SARS-CoV-2 testing. url: https://api.elsevier.com/content/article/pii/S0732889320306374 doi: 10.1016/j.diagmicrobio.2020.115260 id: cord-265682-yac7kzaf author: Eden, John-Sebastian title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-04-10 words: 1847.0 sentences: 99.0 pages: flesch: 53.0 cache: ./cache/cord-265682-yac7kzaf.txt txt: ./txt/cord-265682-yac7kzaf.txt summary: Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is directly linked to the Iranian epidemic, from where genomic data are currently lacking. abstract: The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32296544/ doi: 10.1093/ve/veaa027 id: cord-331701-izkz1hz4 author: Eden, John-Sebastian title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-03-17 words: 1271.0 sentences: 70.0 pages: flesch: 50.0 cache: ./cache/cord-331701-izkz1hz4.txt txt: ./txt/cord-331701-izkz1hz4.txt summary: Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is linked to the Iranian epidemic, from where genomic data is currently lacking. abstract: The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. url: https://doi.org/10.1101/2020.03.15.992818 doi: 10.1101/2020.03.15.992818 id: cord-288660-z0k2ui3y author: Edler, Alice A. title: Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology date: 2006-02-28 words: 2409.0 sentences: 135.0 pages: flesch: 48.0 cache: ./cache/cord-288660-z0k2ui3y.txt txt: ./txt/cord-288660-z0k2ui3y.txt summary: Abstract Avian flu, influenza A subtype H5N1, is an emergent and virulent disease that poses a threat to the health and safety of the world community. Avian flu is responsible for the current outbreak in Asia; H5N1 has now displayed probable human-to-human transmission; it could be a harbinger of a global epidemic. Subtype H5N1, currently known as avian or bird flu, is of particular interest because of its increasing pathogenicity and ability to form a new viral subtype to which there is no native immunity in human hosts. However, if individuals are infected, the current case-fatality rate for avian flu is thought to be greater than 50% in humans [2] and greater than 90% in birds and other mammals. The key to addressing the threat of avian flu in all populations, including anesthesiologists, is prevention of the disease and containment of its spread through traditional, public health preparedness: basic hygiene, Universal Precautions, and special procedures designed to prevent exposure and contain infection in health-care settings. abstract: Abstract Avian flu, influenza A subtype H5N1, is an emergent and virulent disease that poses a threat to the health and safety of the world community. Avian flu is 1 of more than 25 influenza A viruses that reside primarily in birds but also infect humans and other mammals. Avian flu is responsible for the current outbreak in Asia; H5N1 has now displayed probable human-to-human transmission; it could be a harbinger of a global epidemic. Anesthesiologists are exposed to a risk for infection when they are involved in airway instrumentation of infected patients. Given the evidence of emerging resistance to common antiviral agents used to treat H5N1 influenza virus and limited supply of H5N1 vaccine, prevention is our best protection. The following article will detail the virology and preventive public health practices for H5N1. This knowledge can also be used to define and prevent other yet unidentified infectious threats. url: https://www.sciencedirect.com/science/article/pii/S0952818005003557 doi: 10.1016/j.jclinane.2005.12.004 id: cord-344017-qldawc8m author: Edouard, S. title: Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France date: 2020-11-11 words: 4013.0 sentences: 191.0 pages: flesch: 48.0 cache: ./cache/cord-344017-qldawc8m.txt txt: ./txt/cord-344017-qldawc8m.txt summary: Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. In this study, we are reporting our experience to develop an indirect immunofluorescent assay (IFA) for the detection of anti-SARS-CoV-2 antibodies that we implemented before any other serological test was available in France. ELISA To compare our IFA with commercial ELISA IgG, we randomly selected 70 sera with possible cross-reactivity (including 45 sera with possible nonspecific serological interference and 25 sera from patients diagnosed with common others human coronavirus), 30 sera collected before the pandemic and 100 sera from our cohort of SARS-CoV-2-infected patients among all the sera that we tested by IFA. Some other studies also reported an earlier serological response in severe compared to mild SARS-CoV-2 infection [5, 20, 25] that is consistent with the earlier seroconversion that we found in patients with poor clinical outcome (PClinO). abstract: An indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. IFA presented substantial agreement (86%) with ELISA EUROIMMUN SARS-CoV-2 IgG kit (Cohen’s Kappa = 0.61). The presence of antibodies was then measured at 3% before a 5-day evolution up to 47% after more than 15 days of evolution. We observed that the rates of seropositivity as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that detection anti-SARS-CoV-2 antibodies is useful as a marker associated with COVID-19 severity. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10096-020-04104-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33179133/ doi: 10.1007/s10096-020-04104-2 id: cord-255229-w2xtxo9a author: Edson, Daniel C title: Identification of SARS-CoV-2 in a Proficiency Testing Program date: 2020-07-20 words: 2048.0 sentences: 151.0 pages: flesch: 48.0 cache: ./cache/cord-255229-w2xtxo9a.txt txt: ./txt/cord-255229-w2xtxo9a.txt summary: OBJECTIVES: At the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States, testing was limited to the Centers for Disease Control and Prevention–developed reverse transcription polymerase chain reaction assay. METHODS: The American Proficiency Institute sent 2 test samples to 346 clinical laboratories in order to assess the accuracy of SARS-CoV-2 assays. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. In this report we present the results of the first US study of SARS-CoV-2 accuracy by API participant laboratories from the 2020 First Test Event. abstract: OBJECTIVES: At the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States, testing was limited to the Centers for Disease Control and Prevention–developed reverse transcription polymerase chain reaction assay. The urgent and massive demand for testing prompted swift development of assays to detect SARS-CoV-2. The objective of this study was to assess the accuracy of these newly developed tests. METHODS: The American Proficiency Institute sent 2 test samples to 346 clinical laboratories in order to assess the accuracy of SARS-CoV-2 assays. The positive sample, containing 5,175 viral copies/mL, was fully extractable with SARS-CoV-2 viral capsid protein and RNA. The negative sample, with 3,951 viral copies/mL, contained recombinant virus particles with sequences for targeting human RNAase P gene sequences. RESULTS: Of the laboratories submitting results, 97.4% (302/310) correctly detected the virus when present and 98.3% (296/301) correctly indicated when the virus was not present. Among incorrect results reported in this proficiency challenge, 76.9% (10/13) were likely related to clerical error. This accounts for 1.6% (10/611) of all reported results. CONCLUSIONS: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. url: https://doi.org/10.1093/ajcp/aqaa128 doi: 10.1093/ajcp/aqaa128 id: cord-271090-91lzr4tz author: Edwards, Kathryn M. title: Anticipating SARS-CoV-2 Vaccine Testing, Licensure, and Recommendations for Use date: 2020-06-19 words: 2694.0 sentences: 142.0 pages: flesch: 47.0 cache: ./cache/cord-271090-91lzr4tz.txt txt: ./txt/cord-271090-91lzr4tz.txt summary: Because of concerns raised about enhanced disease after wild virus infection in animal studies following vaccination against severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and Middle East respiratory syndromecoronavirus (MERS-CoV) (9, 10), experts have met and proposed immunologic criteria to be evaluated in animals and humans to detect and consequently reduce the risk of enhanced disease (11) . Some of the Phase 1 studies evaluating SARS-CoV-2 vaccines have also included individuals >65 years of age to assess safety and immunogenicity in this population, which is at greater risk for severe COVID-19 disease. With SARS-CoV-2 vaccines, Phase 2 studies are planned to expand the safety profile and to assess immune responses in larger numbers of subjects. The Phase 3 efficacy trials planned for SARS-CoV-2 vaccines in the United States are expected to enroll 20,000 to 30,000 individuals, the numbers projected to be necessary to determine whether the vaccines will prevent significant disease over a period of 6 months follow-up. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0022347620307514?v=s5 doi: 10.1016/j.jpeds.2020.06.048 id: cord-278812-5jps95q9 author: Edwards, Sarah J L title: Anthroponotic risk of SARS-CoV-2, precautionary mitigation, and outbreak management date: 2020-07-02 words: 658.0 sentences: 52.0 pages: flesch: 57.0 cache: ./cache/cord-278812-5jps95q9.txt txt: ./txt/cord-278812-5jps95q9.txt summary: Following early reports of anthroponotic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and mixed messages over anthroponotic risk, some pets were reportedly abandoned to fend for them selves or killed. Evidence of infection of animals with SARS-CoV-2 has been shown experimentally both in vivo and in vitro for mammals including monkeys, cats, ferrets, rabbits, foxes, and hamsters, while bioinformatic studies also predict infectivity of pigs and wild boar among other mammals. 6 Additional experimental inoculation of animals would not help because small sample sizes and bioinformatic studies alone cannot confirm that a whole species is incapable of being infected by SARS-CoV-2. Sufficient evidence exists of anthroponosis of SARS-CoV-2 on which to base precautionary steps to mitigate the risks it poses. Infection and rapid transmission of SARS-CoV-2 in ferrets Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Potential fecal transmission of SARS-CoV-2: current evidence and implications for public health SARS-CoV-2 infection in farmed minks, the Netherlands abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32838345/ doi: 10.1016/s2666-5247(20)30086-0 id: cord-276057-427ji6ze author: Effenberger, Maria title: Faecal calprotectin indicates intestinal inflammation in COVID-19 date: 2020-04-20 words: 907.0 sentences: 56.0 pages: flesch: 52.0 cache: ./cache/cord-276057-427ji6ze.txt txt: ./txt/cord-276057-427ji6ze.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-RNA was detected in the faeces in ~50% of patients with COVID-19 3 5 6 ; SARS-CoV-2 viral particles were observed by electron microscopy in stool samples from two patients without diarrhoea 2 ; and one study reported SARS-CoV-2 infection of the oesophagus, stomach, duodenum and rectum. 7 In this pilot study, we explored a relation between GI symptoms, intestinal inflammation (determined by FC) and faecal SARS-CoV-2-RNA in hospitalised patients with COVID-19 who did not require intensive care measures. We report evidence that SARS-CoV-2 infection in patients with COVID-19 indeed instigates an inflammatory response in the gut, as evidenced by diarrhoea, elevated FC (largely expressed by neutrophil granulocytes 7 ) and a systemic IL-6 response. Faecal SARS-CoV-2 RNA was not detected during acute diarrhoea but could be detected in asymptomatic patients with or without previous diarrhoeal symptoms. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32312790/ doi: 10.1136/gutjnl-2020-321388 id: cord-346758-pi1hf6xg author: Egerup, P. title: Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns date: 2020-09-15 words: 3802.0 sentences: 304.0 pages: flesch: 54.0 cache: ./cache/cord-346758-pi1hf6xg.txt txt: ./txt/cord-346758-pi1hf6xg.txt summary: Two smaller case reports from China documented SARS-CoV-2 antibodies in newborns with COVID-19 positive mothers indicating possible vertical transmission. This study aimed to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns. We here report the results of a prospective cohort study with unselected serological testing in 1,313 parturient women, 1,189 partners and 1,206 newborns to identify if SARS-CoV-2 infection is associated with obstetric and neonatal complications. The serum from the blood samples from women, partners and newborns were analyzed for SARS-CoV-2 antibodies (IgM and IgG). There was no significant difference between pre-pregnancy characteristics in relation to SARS-CoV-2 antibodies, except blood type and that women with antibodies reported more COVID-19-like symptoms (p=0.025). In this prospective cohort study with serological testing of parturient women, partners and newborns we found no association between COVID-19 and obstetric-or neonatal complications. abstract: Background: Only few studies have focused on serological testing for SARS-CoV-2 in pregnant women and no previous study has investigated the frequency in partners. The aim was to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns. Methods: From April 4th to July 3rd, 2020, all parturient women, their partners and newborns were invited to participate in the study. Participating women and partners had a pharyngeal swab and a blood sample taken at admission and immediately after delivery a blood sample was drawn from the umbilical cord. The swabs were analyzed for SARS-CoV-2 RNA by PCR and the blood samples were analyzed for SARS-CoV-2 antibodies. Full medical history, obstetric- and neonatal information were available. Results: A total of 1,361 parturient women, 1,236 partners and 1,342 newborns participated in the study. No associations between previous COVID-19 disease and obstetric- or neonatal complications were found. The adjusted serological prevalence was 2.9% in women and 3.8% in partners. The frequency of blood type A was significantly higher in women with antibodies compared to women without antibodies. 17 newborns had SARS-CoV-2 IgG antibodies, and none had IgM antibodies. Full serological data from 1,052 families showed an absolute risk of infection of 0.37 if the partner had antibodies. Only 55% of individuals with antibodies reported symptoms. Conclusion: This large prospective cohort study reports no association between COVID-19 and obstetric- or neonatal complications. The family pattern showed a substantial increase in absolute risk for women living with a partner with antibodies. url: https://doi.org/10.1101/2020.09.14.20191106 doi: 10.1101/2020.09.14.20191106 id: cord-315685-ute3dxwu author: Ehaideb, Salleh N. title: Evidence of a wide gap between COVID-19 in humans and animal models: a systematic review date: 2020-10-06 words: 5542.0 sentences: 352.0 pages: flesch: 48.0 cache: ./cache/cord-315685-ute3dxwu.txt txt: ./txt/cord-315685-ute3dxwu.txt summary: The systematic search identified 101 studies and 326 preprints, of which 400 articles were excluded because they were reviews, non-original articles, unrelated to the COVID-19 infection, or experimental animals that do not support SARS-CoV-2 replication such as pigs, ducks, and chickens ( Fig. 1 and Additional file 2). The aims were to investigate the pathogenesis of COVID-19 (n = 15), testing drugs and vaccines (n = 14), the host Table 1 Search strategy and selection criteria We searched the MEDLINE, as well as BioRxiv and MedRxiv preprint servers for original research describing or using an animal model of SARS-CoV-2 induced COVID published in English from January 1, 2020, to May 20, 2020. We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). abstract: BACKGROUND: Animal models of COVID-19 have been rapidly reported after the start of the pandemic. We aimed to assess whether the newly created models reproduce the full spectrum of human COVID-19. METHODS: We searched the MEDLINE, as well as BioRxiv and MedRxiv preprint servers for original research published in English from January 1 to May 20, 2020. We used the search terms (COVID-19) OR (SARS-CoV-2) AND (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). Inclusion criteria were the establishment of animal models of COVID-19 as an endpoint. Other inclusion criteria were assessment of prophylaxis, therapies, or vaccines, using animal models of COVID-19. RESULT: Thirteen peer-reviewed studies and 14 preprints met the inclusion criteria. The animals used were nonhuman primates (n = 13), mice (n = 7), ferrets (n = 4), hamsters (n = 4), and cats (n = 1). All animals supported high viral replication in the upper and lower respiratory tract associated with mild clinical manifestations, lung pathology, and full recovery. Older animals displayed relatively more severe illness than the younger ones. No animal models developed hypoxemic respiratory failure, multiple organ dysfunction, culminating in death. All species elicited a specific IgG antibodies response to the spike proteins, which were protective against a second exposure. Transient systemic inflammation was observed occasionally in nonhuman primates, hamsters, and mice. Notably, none of the animals unveiled a cytokine storm or coagulopathy. CONCLUSIONS: Most of the animal models of COVID-19 recapitulated mild pattern of human COVID-19 with full recovery phenotype. No severe illness associated with mortality was observed, suggesting a wide gap between COVID-19 in humans and animal models. url: https://www.ncbi.nlm.nih.gov/pubmed/33023604/ doi: 10.1186/s13054-020-03304-8 id: cord-320092-0qnvydux author: Ehsani, Sepehr title: COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date: 2020-10-16 words: 7536.0 sentences: 406.0 pages: flesch: 45.0 cache: ./cache/cord-320092-0qnvydux.txt txt: ./txt/cord-320092-0qnvydux.txt summary: An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. c The position of the disulfide bonds in the sequence of the mature human hepcidin is illustrated along with the potential palmitoylation residues (ten cysteines) of the cytoplasmic tail of the SARS-CoV-2 spike protein. If the sequence similarity reported here is actually playing a significant role at the cellular level, could it be that, although the cellular localizations appear to be different based on current knowledge, the SARS-CoV-2 spike protein cytoplasmic tail can partly mimic the structure of hepcidin and interact with ferroportin? In addition, a notyet-fully-established link of relevance here is the observations of a Kawasaki-disease-like systemic vasculitis syndrome in children infected with the novel Fig. 3 Summary of salient facets of coronavirus spike protein and human hepcidin biology. abstract: The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail. Here we report a distant sequence similarity between the cysteine-rich cytoplasmic tail of the coronavirus spike protein and the hepcidin protein that is found in humans and other vertebrates. Hepcidin is thought to be the key regulator of iron metabolism in humans through its inhibition of the iron-exporting protein ferroportin. An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. The question of possible homology and an evolutionary connection between the viral spike protein and hepcidin is not assessed in this report, but some scenarios for its study are discussed. url: https://doi.org/10.1186/s13062-020-00275-2 doi: 10.1186/s13062-020-00275-2 id: cord-262415-cj4pjuuc author: Eiros, R. title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers date: 2020-07-14 words: 4634.0 sentences: 282.0 pages: flesch: 49.0 cache: ./cache/cord-262415-cj4pjuuc.txt txt: ./txt/cord-262415-cj4pjuuc.txt summary: title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers The present study was designed to search for evidence of pericardial and myocardial involvement after past SARS-CoV-2 infection comprehensively studied by clinical assessment, laboratory tests, electrocardiography and cardiac magnetic resonance (CMR) imaging. Overall, the drug therapy aimed at Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. 10 This study examined the prevalence of pericarditis and of myocarditis in a cohort of SARS-CoV-2 positive health-care workers in Salamanca, Spain. However, the strength of this study is the addition of non-hospitalized participants and also the inclusion of participants diagnosed of past SARS-CoV-2 infection through serology, who also had a high prevalence of pericarditis and myocarditis. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. abstract: Background: Cardiac sequelae of past SARS-CoV-2 infection are still poorly documented. We conducted a cross-sectional study in health-care workers to report evidence of pericarditis and myocarditis after SARS-CoV-2 infection. Methods We studied 139 health-care workers with confirmed past SARS-CoV-2 infection (103 diagnosed by RT-PCR and 36 by serology). Participants underwent clinical assessment, electrocardiography, laboratory tests including immune cell profiling and cardiac magnetic resonance (CMR) imaging. Pericarditis was diagnosed when classical criteria were present, and the diagnosis of myocarditis was based on the updated CMR Lake-Louise-Criteria. Results: Median age was 52 years (IQR 41-57), 100 (72%) were women, and 23 (16%) were previously hospitalized for Covid-19 pneumonia. At examination (10.4 [9.3-11.0] weeks after infection-like symptoms), all participants presented hemodynamic stability. Chest pain, dyspnoea or palpitations were observed in 58 (42%) participants; electrocardiographic abnormalities in 69 (50%); NT-pro-BNP was elevated in 11 (8%); troponin in 1 (1%); and CMR abnormalities in 104 (75%). Isolated pericarditis was diagnosed in 4 (3%) participants, myopericarditis in 15 (11%) and isolated myocarditis in 36 (26%). Participants diagnosed by RT-PCR were more likely to still present symptoms than participants diagnosed by serology (73 [71%] vs 18 [50%]; p=0.027); nonetheless, the prevalence of pericarditis or myocarditis was high in both groups (44 [43%] vs 11 [31%]; p=0.238). Most participants (101 [73%]) showed altered immune cell counts in blood, particularly decreased eosinophil (37 [27%]; p<0.001) and increased CD4-CD8-/loT alpha beta-cell numbers (24 [17%]; p<0.001). Pericarditis was associated with elevated CD4-CD8-/loT alpha beta-cell numbers (p=0.011), while participants diagnosed with myopericarditis or myocarditis had lower (p<0.05) plasmacytoid dendritic cell, NK-cell and plasma cell counts and lower anti-SARS-CoV-2-IgG antibody levels (p=0.027). Conclusions: Pericarditis and myocarditis with clinical stability are frequent long after SARS-CoV-2 infection, even in presently asymptomatic subjects. These observations will probably apply to the general population infected and may indicate that cardiac sequelae might occur late in association with an altered (delayed) innate and adaptative immune response. url: http://medrxiv.org/cgi/content/short/2020.07.12.20151316v1?rss=1 doi: 10.1101/2020.07.12.20151316 id: cord-349485-iomk99lv author: Eis-Hübinger, Anna M. title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples date: 2020-04-22 words: 1633.0 sentences: 103.0 pages: flesch: 56.0 cache: ./cache/cord-349485-iomk99lv.txt txt: ./txt/cord-349485-iomk99lv.txt summary: title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples To rapidly identify unrecognized cases in hospitals in an efficient, resource-saving and cost effective manner we propose an ad hoc laboratory-based surveillance approach for SARS-CoV-2. It is based upon minipool (MP) testing of nucleic acid preparations of respiratory samples submitted to laboratories for routine diagnostics. The workflow comprises individual nucleic acid (NA) extraction of respiratory samples, pooling of extracted NA samples in batches of 10 and SARS-CoV-2 specific real-time RT-PCR. We report a diagnostic workflow for the laboratory-based surveillance of SARS-CoV-2 in a rapid and cost effective manner. From a public health perspective an easy to establish and cost effective laboratory-based screening strategy may assist in rapid case detection, surveillance and ultimately in a better understanding of this epidemic (7) . abstract: BACKGROUND: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019 and subsequently caused a pandemic. Surveillance is important to better appreciate this evolving pandemic and to longitudinally monitor the effectiveness of public health measures. OBJECTIVES: We aimed to provide a rapid, easy to establish and costeffective laboratory-based surveillance tool for SARS-CoV-2. Study design: We used minipools of RNA prepared from nucleic acid extractions of routine respiratory samples. We technically validated the assay and distributed the protocol within an informal network of five German university laboratories. RESULTS: We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany from 17.02.2020- 10.03.2020. One minipool reacted positive and after resolution one individual sample tested SARS-COV-2 positive. This sample was from a hospitalized patient not suspected of having contracted SARS-CoV-2. CONCLUSIONS: Our approach of a laboratory-based surveillance for SARSCoV-2 using minipools proved its concept is easily adaptable and resource-saving. It might assist not only public health laboratories in SARS-CoV-2 surveillance. url: https://doi.org/10.1016/j.jcv.2020.104381 doi: 10.1016/j.jcv.2020.104381 id: cord-324800-l8xl4g2a author: Eisenberg, Michael L. title: Coronavirus Disease 2019 (COVID-19) and men’s reproductive health date: 2020-04-22 words: 682.0 sentences: 45.0 pages: flesch: 54.0 cache: ./cache/cord-324800-l8xl4g2a.txt txt: ./txt/cord-324800-l8xl4g2a.txt summary: As the COVID-19 pandemic rages across the world, the scientific community continues to study the pathophysiology of SARS-Cov-2 virus to guide transmission, susceptibility, and treatment. While cardiac, ocular, and neurologic symptoms of the COVID-19 have been reported, the reproductive implications of coronavirus infection remain unknown. Indeed, the current report was not able to assess any changes in semen quality among the participants thus it remains unknown how and if the fecundability of infected men is impaired. In addition, as more than 80% of those who are infected by the coronavirus are asymptomatic, the reproductive implications for these men would likely be favorable but also remains unknown. But given the current impact of the pandemic on the world, the likelihood the virus will remain for some time, and that over 100 million babies are born every year, the reproductive implications of SARS-Cov-2 should be further studied. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0015028220303861?v=s5 doi: 10.1016/j.fertnstert.2020.04.039 id: cord-327214-kcbxyhhh author: Eketunde, Adenike O title: A Review of Postmortem Findings in Patients With COVID-19 date: 2020-07-28 words: 2725.0 sentences: 139.0 pages: flesch: 43.0 cache: ./cache/cord-327214-kcbxyhhh.txt txt: ./txt/cord-327214-kcbxyhhh.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus originated in Wuhan, China, and has spread rapidly across the world. According to Merad and Martin''s study, the hyper inflammation in severe COVID-19 patients shared similarities with cytokine release syndromes, including macrophages activation syndrome. Minimally invasive autopsies of three COVID-19 patients in Chongqing, China revealed damage to the alveolar structure with minor serous and fibrin exudation and hyaline membrane formation [8] . The hypercoagulable state has been linked to a poor prognosis in patients with severe COVID-19, which leads to a microthrombi formation in the lungs, lower limbs, hands, brain, heart, liver, and kidneys, as a result of the activation of the coagulation pathway. There is a strong association with the hyperinflammatory state, which can be explained by most of the signs and symptoms that are exhibited by COVID-19 patients, including most of the pathological findings. Fatal eosinophilic myocarditis in a healthy 17-year-old male with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2c) abstract: Multiple public health problems have been caused by various coronavirus strains over the last few years, such as the middle eastern respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and COVID-19. COVID-19, which is also known as coronavirus disease 2019, was first detected in Wuhan, China, and has significantly impacted people's health and lives. Additionally, it has led to a pandemic, and the virus has spread to over 121 countries worldwide. There is numerous information available regarding this virus. A detailed and extensive study of the morphological and histopathological findings will help understand and diagnose the disease. As it is a new disease, it is challenging to understand the mechanism of the action and disease pathology due to the limited availability of data from autopsies or biopsies. However, as the detailed mechanism of injury remains unclear, this paper aims to review the postmortem gross and histopathological findings of various organs that have been affected with coronavirus, focusing on the pulmonary, cardiac, and hematologic findings. This paper emphasizes the postmortem findings of the effect of the coronavirus disease on multiple organ systems. Advance search of the keywords on PubMed was used, limiting the search to the last five years. The eligible article is narrowed based on relevance containing postmortem findings of the novel virus; COVID-19. A total of 25 full-text articles were selected and used in the review of this paper. url: https://www.ncbi.nlm.nih.gov/pubmed/32864262/ doi: 10.7759/cureus.9438 id: cord-344884-dcoq9srf author: El Otmani, H. title: Neuro-COVID-19: What are we talking about? date: 2020-06-06 words: 879.0 sentences: 60.0 pages: flesch: 51.0 cache: ./cache/cord-344884-dcoq9srf.txt txt: ./txt/cord-344884-dcoq9srf.txt summary: Q2 In a very short time after the onset of the COVID-19 infection, a ''''flood'''' of reports regarding SARS-Cov-2 related neurological manifestations were published. While more than three and a half million individuals are affected worldwide to date, most arguments of COVID-19related neurological manifestations are supported by case reports or small series [1] [2] [3] . On the other hand, a review of the available data shows that the implication of the SARS-Cov-2 virus as a direct cause of neurological complications is not established yet. In support to this, to date, only 2 cases of meningitis or encephalitis with evidence of viral SARS-Cov-2 detection in CSF are reported [6, 7] . So far, a dozen of COVID-19-related Guillain-Barré syndromes (GBS) have been reported, which seems to be marginal compared to the high prevalence of infected individuals [10] . Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Neurologic Features in Severe SARS-CoV-2 Infection abstract: nan url: https://doi.org/10.1016/j.neurol.2020.05.004 doi: 10.1016/j.neurol.2020.05.004 id: cord-314942-eym2rh8v author: El Tabaa, Manar Mohammed title: New putative insights into neprilysin (NEP)-dependent pharmacotherapeutic role of roflumilast in treating COVID-19 date: 2020-10-01 words: 7634.0 sentences: 473.0 pages: flesch: 48.0 cache: ./cache/cord-314942-eym2rh8v.txt txt: ./txt/cord-314942-eym2rh8v.txt summary: Being a highly selective phosphodiesterase-4 inhibitors (PDE4i), roflumilast acts by enhancing the level of cyclic adenosine monophosphate (cAMP), that probably potentiates its anti-inflammatory action via increasing neprilysin (NEP) activity. Because activating NEP was previously reported to mitigate several airway inflammatory ailments; this review thoroughly discusses the proposed NEP-based therapeutic properties of roflumilast, which may be of great importance in curing COVID-19. Additionally, breaking ET-1 by NEP will prolong the anti-inflammatory effect of 716 roflumilast via maintaining the high cAMP level which is underscored to play an 717 important role in improving the immune system of highly risk COVID-19 groups 718 (Graf et al., 1995; Raker et al., 2016) . Degrading ET-1 can also inhibit pulmonary fibrosis via blocking the ET-1-induced transforming growth factor-β1 (TGF-β1), and at the same time, maintain the high level of cAMP which may contribute for long-term anti-inflammatory effect of roflumilast. abstract: Nowadays, coronavirus disease 2019 (COVID-19) represents the most serious inflammatory respiratory disease worldwide. Despite many proposed therapies, no effective medication has yet been approved. Neutrophils appear to be the key mediator for COVID-19-associated inflammatory immunopathologic, thromboembolic and fibrotic complications. Thus, for any therapeutic agent to be effective, it should greatly block the neutrophilic component of COVID-19. One of the effective therapeutic approaches investigated to reduce neutrophil-associated inflammatory lung diseases with few adverse effects was roflumilast. Being a highly selective phosphodiesterase-4 inhibitors (PDE4i), roflumilast acts by enhancing the level of cyclic adenosine monophosphate (cAMP), that probably potentiates its anti-inflammatory action via increasing neprilysin (NEP) activity. Because activating NEP was previously reported to mitigate several airway inflammatory ailments; this review thoroughly discusses the proposed NEP-based therapeutic properties of roflumilast, which may be of great importance in curing COVID-19. However, further clinical studies are required to confirm this strategy and to evaluate its in vivo preventive and therapeutic efficacy against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33011243/ doi: 10.1016/j.ejphar.2020.173615 id: cord-299911-v95pf3eg author: El-Ghiaty, Mahmoud A. title: Cytochrome P450-mediated drug interactions in COVID-19 patients: current findings and possible mechanisms date: 2020-06-26 words: 5319.0 sentences: 272.0 pages: flesch: 37.0 cache: ./cache/cord-299911-v95pf3eg.txt txt: ./txt/cord-299911-v95pf3eg.txt summary: Based on the conclusions drawn from the currently rapidly evolving knowledge about COVID-19, our hypothesis is built on the potential modulation of CYPs activity by the inflammatory environment provoked by SARS-CoV-2 infection, as well as the pathologic involvement of the liver which harbors the majority of the drug metabolizing enzymes (DMEs). Systemic inflammation and immune response represent a substantial element in many acute and chronic diseases which is strongly implicated in altering drug pharmacokinetics through, mainly, modulating the expression and activity of DMEs. As a main contributor to the metabolic biotransformation of most drugs, CYPs are widely involved in such disease-drug interactions [19] . For decades, IL-6 has been recognized as the major inflammatory element that provokes a significant repressive effect on the expression and activity of different CYPs. Human recombinant interleukin 6 (rhIL-6) has shown concentration-dependent blocking of phenobarbital-mediated induction of CYP2B1/2 mRNA and activity in rat hepatocytes [48] . abstract: At the end of 2019, the entire world has witnessed the birth of a new member of coronavirus family in Wuhan, China. Ever since, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has swiftly invaded every corner on the planet. By the end of April 2020, almost 3.5 million cases have been reported worldwide, with a death toll of about 250000 deaths. It is currently well-recognized that patient’s immune response plays a pivotal role in the pathogenesis of Coronavirus Disease 2019 (COVID-19). This inflammatory element was evidenced by its elevated mediators that, in severe cases, reach their peak in a cytokine storm. Together with the reported markers of liver injury, such hyperinflammatory state may trigger significant derangements in hepatic cytochrome P450 metabolic machinery, and subsequent modulation of drug clearance that may result in unexpected therapeutic/toxic response. We hypothesize that COVID-19 patients are potentially vulnerable to a significant disease-drug interaction, and therefore, suitable dosing guidelines with therapeutic drug monitoring should be implemented to assure optimal clinical outcomes. url: https://www.sciencedirect.com/science/article/pii/S0306987720311750?v=s5 doi: 10.1016/j.mehy.2020.110033 id: cord-292367-ocbsmmt6 author: El-Masri, Maher M. title: Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date: 2012-02-29 words: 3089.0 sentences: 134.0 pages: flesch: 49.0 cache: ./cache/cord-292367-ocbsmmt6.txt txt: ./txt/cord-292367-ocbsmmt6.txt summary: Such comparison is intended to provide a surrogate measure of the influence that strict enforcement of infection control strategies during the SARS outbreak may have had on the risk of HAIs. Methods A retrospective chart review was conducted on the medical records of 400 intensive care patients who were admitted to the ICU three months before and during the 2003 SARS outbreak. The intent of such comparison is to provide a surrogate measure of the influence that strict enforcement of infection control guidelines might have had on the risk of developing HAIs. A retrospective chart review was conducted on the medical records of 400 patients who were admitted to the intensive care unit of a community-based hospital in Southwestern Ontario. abstract: Summary Background Although strict adherence to infection control strategies is recognised as the simplest and most cost effective method to prevent the spread of healthcare associated infections (HAIs), measurement of the direct impact that such adherence may have on the risk of developing such infections has always been a challenge. Purpose The purpose of this study was to compare the risk of HAIs before and during the SARS outbreak. Such comparison is intended to provide a surrogate measure of the influence that strict enforcement of infection control strategies during the SARS outbreak may have had on the risk of HAIs. Methods A retrospective chart review was conducted on the medical records of 400 intensive care patients who were admitted to the ICU three months before and during the 2003 SARS outbreak. Results The rate of HAIs was higher in the pre-SARS period than the SARS period. Specifically, 61.7% of all reported infections were diagnosed in the pre-SARS period. The rate of HAIs in the pre-SARS period was 14.5% as opposed to 9% during the SARS period. Adjusted logistic regression analysis suggested that the odds of HAIs were 2.2 times higher in the pre-SARS period as compared to the SARS period (OR =2.2; 95%CI =1.08–4.49). Conclusion Our findings suggest that strict enforcement of infection control strategies may have a positive impact on the efforts to minimise the risk of HAIs. These findings carry a clinical significance that shall not be ignored with regard to our overall efforts to minimise the risk of developing HAIs in the ICU. url: https://doi.org/10.1016/j.iccn.2011.10.003 doi: 10.1016/j.iccn.2011.10.003 id: cord-296950-9dldbs6o author: El-Zein, Rayan S title: COVID-19-associated meningoencephalitis treated with intravenous immunoglobulin date: 2020-09-06 words: 1832.0 sentences: 122.0 pages: flesch: 43.0 cache: ./cache/cord-296950-9dldbs6o.txt txt: ./txt/cord-296950-9dldbs6o.txt summary: Neurologic manifestations in patients infected with SARS-CoV-2 have been reported such as anosmia, ageusia, ataxia, seizures, haemorrhagic necrotising encephalopathy, and Guillain-Barré syndrome. The SARS-CoV-2 CSF PCR was negative; however, a high index of suspicion remained due to the temporal relationship of his current symptoms and the recent COVID-19 pneumonia. Our report describes a case of encephalitis associated with SARS-CoV-2 which showed clinical improvement with IVIg therapy. Moriguchi et al 5 described what appears to be the first case of COVID-19-associated meningoencephalitis presenting with convulsions and confirmed with a positive SARS-CoV-2 CSF PCR; their patient had abnormal MRI findings of the medial temporal lobe and was treated with favipiravir. Paniz-Mondolfi et al 6 reported a case of COVID-19-associated pneumonia in a 74 years old with Parkinson''s who succumbed to his illness on day 11; however, SARS-CoV-2 was found in the brain capillary endothelium and neuronal cell bodies on postmortem examination. abstract: A 40-year-old man presented with altered mental status after a recenthospitalisation for COVID-19 pneumonia. Cerebrospinal fluid (CSF) analysis showed lymphocytosis concerning for viral infection. The CSF PCR for SARS-CoV-2 was negative, yet this could not exclude COVID-19 meningoencephalitis. During hospitalisation, the patient’s mentation deteriorated further requiring admission to the intensive care unit (ICU). Brain imaging and electroencephalogram (EEG) were unremarkable. He was, thus, treated with intravenous immunoglobulin (IVIg) for 5 days with clinical improvement back to baseline. This case illustrates the importance of considering COVID-19’s impact on the central nervous system (CNS). Haematogenous, retrograde axonal transport, and the effects of cytokine storm are the main implicated mechanisms of CNS entry of SARS-CoV-2. While guidelines remain unclear, IVIg may be of potential benefit in the treatment of COVID-19-associated meningoencephalitis. url: https://doi.org/10.1136/bcr-2020-237364 doi: 10.1136/bcr-2020-237364 id: cord-286365-fy0a8mb4 author: ElHawary, Hassan title: Bibliometric Analysis of Early COVID-19 Research: The Top 50 Cited Papers date: 2020-10-13 words: 2619.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-286365-fy0a8mb4.txt txt: ./txt/cord-286365-fy0a8mb4.txt summary: CONCLUSION: By highlighting the characteristics of the top 50 cited COVID-19-related articles, the authors hope to disseminate information that could assist researchers to identify the important topics, study characteristics, and gaps in the literature. To that end, the goal of this study was to present a bibliometric analysis to identify and dissect the characteristics of the top 50 cited COVID-19-related articles published early on following the outbreak. 62 The majority of the highly cited research assessed COVID-19''s clinical presentation and disease description while only 7 papers discussed potential treatment. While this limitation is present with any bibliometric analysis, the main goal of this study was to highlight the characteristics of the highly cited research articles early during the COVID-19 pandemic and the dynamic nature of citation count should not diminish the value of the information presented here. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: INTRODUCTION: The COVID-19 pandemic is rapidly evolving with the number of cases exponentially rising. The research scientific community has reacted promptly as evidenced by an outstanding number of COVID-19 related publications. As the number of scientific publications rapidly rises, there is a need to dissect the factors that lead to highly impactful publications. To that end, the present paper summarizes the characteristics of the top 50 cited COVID-19-related publications that emerged early during the pandemic. METHODS: A systematic search of the Web of Science, Scopus, and Google Scholar was performed, using keywords related to COVID-19 and SARS-CoV-19. Two independent authors reviewed all the search results, screening for the top 50 cited COVID-19-related articles. Inclusion criteria comprised any publication on COVID-19 or the SARS-CoV-2 virus. Data extracted included the type of study, journal, number of citations, number of authors, country of publication, and study content. RESULTS: As of May 29th, the top 50 cited articles were cited 63849 times during the last 4 months. On average, 14 authors contributed to each publication. Over half of the identified articles were published in only 3 journals. Furthermore, 42% and 26% of the identified articles were retrospective case series and correspondence/viewpoints, respectively, while only 1 article was a randomized controlled trial. In terms of content, almost half (48%) of the identified publications reported clinical/radiological findings while only 7 out of the 50 articles investigated potential treatments. CONCLUSION: By highlighting the characteristics of the top 50 cited COVID-19-related articles, the authors hope to disseminate information that could assist researchers to identify the important topics, study characteristics, and gaps in the literature. url: https://doi.org/10.1177/1178633720962935 doi: 10.1177/1178633720962935 id: cord-307489-2liu4anc author: Elavia, Nasha title: An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia date: 2020-05-23 words: 1321.0 sentences: 72.0 pages: flesch: 43.0 cache: ./cache/cord-307489-2liu4anc.txt txt: ./txt/cord-307489-2liu4anc.txt summary: title: An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia Clinical presentation and severity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) varies greatly amongst patients, as supported by recent literature. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) presenting with atypical gastrointestinal symptoms in a patient with SARS-CoV-2 infection. This atypical presentation of PE is unique to our case and highlights the significance of a high index of clinical suspicion for SARS-CoV-2 and its associated thrombogenic effect, even in patients with atypical symptoms. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) in a patient with SARS-CoV-2 pneumonia who mainly presented with gastrointestinal symptoms. Our patient however presented mainly with gastrointestinal symptoms, which have been reported with SARS-CoV-2; however, with significant hypoxia in the absence of a respiratory viral syndrome although with a low pretest probability for PE, we decided to further evaluate the patient for hypoxia. abstract: Clinical presentation and severity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) varies greatly amongst patients, as supported by recent literature. This poses an ongoing challenge in the diagnostic and therapeutic approach for managing these patients. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) presenting with atypical gastrointestinal symptoms in a patient with SARS-CoV-2 infection. This atypical presentation of PE is unique to our case and highlights the significance of a high index of clinical suspicion for SARS-CoV-2 and its associated thrombogenic effect, even in patients with atypical symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/32596069/ doi: 10.7759/cureus.8249 id: cord-340535-78bpvtuf author: Elbay, Rümeysa Yeni title: Depression, Anxiety, Stress Levels of Physicians and Associated Factors In Covid-19 Pandemics date: 2020-05-27 words: 2429.0 sentences: 131.0 pages: flesch: 50.0 cache: ./cache/cord-340535-78bpvtuf.txt txt: ./txt/cord-340535-78bpvtuf.txt summary: AIM: To investigate anxiety, stress, and depression levels of physicians during the Covid-19 outbreak and explored associated factors in both clinical and general site. Factors found to be associated with higher DAS-21 total scores in frontline workers were as follows: increased weekly working hours, increased number of Covid-19 patients cared for, lower level of support from peers and supervisors, lower logistic support, and lower feelings of competence during Covid-19 related tasks. In an early study investigating immediate psychological response during Covid-19 epidemic among general population in China, 53.8% of participants rated the psychological impact of the outbreak as moderate or severe (1) . In another study investigating long term psychological effects of SARS outbreak on healthcare workers, 23% of staff were found to have moderate or severe depressive symptoms in a 3year follow-up (4) . Based on this perspective, here, we aimed to investigate anxiety, stress and depression levels of physicians during Covid-19 outbreak and explored associated factors in both clinical and general site. abstract: AIM: To investigate anxiety, stress, and depression levels of physicians during the Covid-19 outbreak and explored associated factors in both clinical and general site. METHODS: An online survey is conducted to asses psychological responses of healthcare workers and related factors during Covid-19 outbreak. It is consisted of three subsections covering the following areas: 1) sociodemographic data 2) information on individuals` working condition 3) Depression Anxiety and Stress Scale-21 (DAS-21). RESULTS: Of all 442 participants, 286 (64.7%) had symptoms of depression, 224 (51.6%) anxiety, and 182 (41.2%) stress. Being female, young, and single, having less work experience, working in frontline were associated with higher scores, whereas having a child was associated with lower scores in each subscale. Factors found to be associated with higher DAS-21 total scores in frontline workers were as follows: increased weekly working hours, increased number of Covid-19 patients cared for, lower level of support from peers and supervisors, lower logistic support, and lower feelings of competence during Covid-19 related tasks. CONCLUSIONS: Our findings highlight the factors which need to be taken into consideration to protect the mental wellbeing of doctors while fighting with a disaster that has major impacts on society worldwide. url: https://doi.org/10.1016/j.psychres.2020.113130 doi: 10.1016/j.psychres.2020.113130 id: cord-264326-teahway7 author: Eleftheriou, Phaedra title: In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus date: 2020-05-29 words: 5403.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-264326-teahway7.txt txt: ./txt/cord-264326-teahway7.txt summary: According to docking analysis the most promising results were found for HCV protease, DPP-4, α-thrombin and coagulation Factor Xa known inhibitors, with several of them exhibiting estimated free binding energy lower than −8.00 kcal/mol and better prediction results than reference compounds. Since the 3D structure of the active site of the enzyme is crucial for catalytic activity, we proceeded to a comparison of the SARS-CoV-2 main protease, Mpro, with the HIV-1 protease, the HCV protease (NS3 protein) and the human proteases DPP-4, thrombin, Factor Xa, renin and ACE, which constitute known drug targets with approved inhibitors. The structural similarity between the SARS-CoV-2 protease and some of the selected proteases, in combination with the existence of the same amino acids at certain positions of the substrate cleavage site, such as Ser at the P1'' position of the recognition sequence of the HCV protease and thrombin are promising features in the effort to identify effective SARS-CoV-2 protease inhibitors among the approved drugs of the selected proteases. abstract: The coronavirus disease, COVID-19, caused by the novel coronavirus SARS-CoV-2, which first emerged in Wuhan, China and was made known to the World in December 2019 turned into a pandemic causing more than 126,124 deaths worldwide up to April 16th, 2020. It has 79.5% sequence identity with SARS-CoV-1 and the same strategy for host cell invasion through the ACE-2 surface protein. Since the development of novel drugs is a long-lasting process, researchers look for effective substances among drugs already approved or developed for other purposes. The 3D structure of the SARS-CoV-2 main protease was compared with the 3D structures of seven proteases, which are drug targets, and docking analysis to the SARS-CoV-2 protease structure of thirty four approved and on-trial protease inhibitors was performed. Increased 3D structural similarity between the SARS-CoV-2 main protease, the HCV protease and α-thrombin was found. According to docking analysis the most promising results were found for HCV protease, DPP-4, α-thrombin and coagulation Factor Xa known inhibitors, with several of them exhibiting estimated free binding energy lower than −8.00 kcal/mol and better prediction results than reference compounds. Since some of the compounds are well-tolerated drugs, the promising in silico results may warrant further evaluation for viral anticipation. DPP-4 inhibitors with anti-viral action may be more useful for infected patients with diabetes, while anti-coagulant treatment is proposed in severe SARS-CoV-2 induced pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/32485894/ doi: 10.3390/molecules25112529 id: cord-290429-0d34abdo author: Elengoe, Asita title: COVID-19 Outbreak in Malaysia date: 2020-06-17 words: 1332.0 sentences: 105.0 pages: flesch: 61.0 cache: ./cache/cord-290429-0d34abdo.txt txt: ./txt/cord-290429-0d34abdo.txt summary: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic outbreak emerged in December 2019 from Wuhan City, Hubei Province, China and spread to the rest of the world. They reported that the virus had 96.3% genetic similarity with a Yunnan bat coronavirus RaTG13 and 70% homology with severe acute respiratory syndrome coronavirus (SARS-CoV) [2] . On the 12 th January 2020, the World Health Organization (WHO) announced the cause of this epidemic outbreak was a novel coronavirus discovered in 2019 (2019-nCoV) or SARS-CoV-2 and named the disease coronavirus disease 2019 (COVID-19) [3] . Coronavirus COVID-19 cases spiked across Asia after a mass gathering in Malaysia. The origin, transmission, and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak -An update on the status Epidemiology, causes, clinical manifestation and diagnosis, prevention, and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review abstract: In 2020 a significant threat to public health emerged. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic outbreak emerged in December 2019 from Wuhan City, Hubei Province, China and spread to the rest of the world. This disease was named COVID-19 by World Health Organization. To date (17(th) April 2020) a total of 2,230,439 cases of COVID-19; 150,810 cases of deaths and 564,210 recovered cases have been reported worldwide. In this review the SARS-CoV-2 morphology, pathogenic mechanism, similarities and differences between SARS-CoV and Middle East Respiratory Syndrome and severe acute respiratory syndrome, transmission mode, diagnosis, treatment, and preventive measures were investigated. The outbreak of COVID-19 from a Malaysian perspective was explored and mental health care during the COVID-19 outbreak was explored. To date, there is no vaccine or no specific treatment for COVID-19. Therefore, preventive measures are very important to prevent and control the rapid spread of the SARS-CoV-2 virus. Preparedness should be a priority for future pandemic outbreaks. url: https://doi.org/10.24171/j.phrp.2020.11.3.08 doi: 10.24171/j.phrp.2020.11.3.08 id: cord-296692-t5p09le8 author: Elgin, T.G. title: The changing landscape of SARS-CoV-2: Implications for the maternal-infant dyad date: 2020-09-07 words: 5325.0 sentences: 303.0 pages: flesch: 47.0 cache: ./cache/cord-296692-t5p09le8.txt txt: ./txt/cord-296692-t5p09le8.txt summary: In December of 2019 cases of an unknown viral pneumonia were reported from Wuhan, Hubei, China Although much uncertainty remains, regarding the natural history and demographics of COVID19 , the virus appears to primarily cause infection in adults over 51 with case fatality rates increasing dramatically with age [5] . There are, however, emerging case reports of pregnant mothers who test positive for COVID-19 infection and who remain either completely asymptomatic [23] and or manifest mild symptoms in the subsequent 24 hours following delivery. Although clinical evidence is lacking, the case numbers to date of COVID-19 in pregnancy remain very low [32] and case reports of two neonates who tested positive for SARS-CoV-2 shortly after birth lends some credence to the concern. Vertical transmission of coronavirus disease 19 (COVID-19) from infected pregnant mothers to neonates: A review An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes abstract: The COVID-19 pandemic represents the greatest challenge to date faced by the medical community in the 21st century. The rate of rapid dissemination, magnitude of viral contagiousness, person to person transmission at an asymptomatic phase of illness pose a unique and dangerous challenge for all patients, including neonatal and obstetric patients. Although scientific understanding of the pathophysiology of the disease, nature of transmission, and efficacy of mitigation strategies is growing, neither a cure or vaccine have been developed. While COVID-19 is primarily a disease of older patients, infection is now seen across all age demographics with reports of illness in pregnant patients and infants. Altered hormone status and predominance of Th-2 immune helper cells may result in increased predisposition to SARS-CoV-2. Case reports of pregnant patients demonstrate a clinical presentation comparable to non-pregnant adults, but evidence of vertical transmission to the fetus is controversial. Neonatal reports demonstrate an inconsistent and non-specific phenotype, and it is often difficult to separate COVID-19 from the underlying conditions of prematurity or bacterial infection. The development of international registries to enable risk profiling of COVID-19 positive pregnant mothers and/or their offspring may facilitate the development of enhanced mitigation strategies, medical treatments and effective vaccinations. url: https://doi.org/10.3233/npm-200460 doi: 10.3233/npm-200460 id: cord-274184-hm516x6p author: Elli, Luca title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 words: 4843.0 sentences: 280.0 pages: flesch: 50.0 cache: ./cache/cord-274184-hm516x6p.txt txt: ./txt/cord-274184-hm516x6p.txt summary: From the abovementioned reasons we must deduce that: -in high SARS-CoV-2 incidence areas where PCR assays are not extensively performed, Covid-19 cannot be ruled out by simple clinical examination or epidemiological link; -the greatest amount of efforts and precautions are required to minimize the spread of the disease and to preserve medical staff from infection. In our current situation, which is characterized by high incidence of Covid-19 and relative scarcity of surveillance assays in asymptomatic subjects, for the abovementioned reasons we recommend different modalities of individual protection based on a strict clinical and epidemiological stratification of patients with potential SARS-CoV-2 infection undergoing endoscopic examination. In this setting, regardless of the classification of patients (high/low-risk, , in order to prevent the medical staff from becoming infected, we suggest high-performance personal protection equipment, i.e. a N95 or FFP2/FFP3 respirator, a hairnet, a double pair of gloves, a disposable waterproof surgical gown, a face shield (which we prefer because it allows to protect, and then spare, respirators) or goggles, and work safety clogs (Table 1) . abstract: A dramatic SARS-Cov-2 outbreak is hitting Italy hard. To face the new scenario all the hospitals have been re-organised in order to reduce all the outpatient services and to devote almost all their personnel and resources to the management of Covid-19 patients. As a matter of fact, all the services have undergone a deep re-organization guided by: the necessity to reduce exams, to create an environment that helps reduce the virus spread, and to preserve the medical personnel from infection. In these days a re-organization of the endoscopic unit, sited in a high-incidence area, has been adopted, with changes to logistics, work organization and patients selection. With the present manuscript, we want to support gastroenterologists and endoscopists in the organization of a “new” endoscopy unit that responds to the “new” scenario, while remaining fully aware that resources availability and local circumstances may extremely vary from unit to unit. url: https://www.sciencedirect.com/science/article/pii/S1590865820301730?v=s5 doi: 10.1016/j.dld.2020.04.018 id: cord-310623-zbjgr9jk author: Ellington, Sascha title: Characteristics of Women of Reproductive Age with Laboratory-Confirmed SARS-CoV-2 Infection by Pregnancy Status — United States, January 22–June 7, 2020 date: 2020-06-26 words: 2985.0 sentences: 160.0 pages: flesch: 45.0 cache: ./cache/cord-310623-zbjgr9jk.txt txt: ./txt/cord-310623-zbjgr9jk.txt summary: These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation compared with nonpregnant women, but their risk for death is similar. These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation * https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html. In contrast, however, ICU admission and receipt of mechanical ventilation are distinct proxies for illness severity (8) , and after adjusting for age, presence of underlying conditions, and race/ethnicity, the risks for both (N = 91,412) , by pregnancy status, age group, and race/ethnicity, and relative risk for these outcomes comparing pregnant women to nonpregnant women aged 15-44 years -United States, January 22-June 7, 2020 Among reproductive-age women with SARS-CoV-2 infection, pregnancy was associated with hospitalization and increased risk for intensive care unit admission, and receipt of mechanical ventilation, but not with death. abstract: As of June 16, 2020, the coronavirus disease 2019 (COVID-19) pandemic has resulted in 2,104,346 cases and 116,140 deaths in the United States.* During pregnancy, women experience immunologic and physiologic changes that could increase their risk for more severe illness from respiratory infections (1,2). To date, data to assess the prevalence and severity of COVID-19 among pregnant U.S. women and determine whether signs and symptoms differ among pregnant and nonpregnant women are limited. During January 22-June 7, as part of COVID-19 surveillance, CDC received reports of 326,335 women of reproductive age (15-44 years) who had positive test results for SARS-CoV-2, the virus that causes COVID-19. Data on pregnancy status were available for 91,412 (28.0%) women with laboratory-confirmed infections; among these, 8,207 (9.0%) were pregnant. Symptomatic pregnant and nonpregnant women with COVID-19 reported similar frequencies of cough (>50%) and shortness of breath (30%), but pregnant women less frequently reported headache, muscle aches, fever, chills, and diarrhea. Chronic lung disease, diabetes mellitus, and cardiovascular disease were more commonly reported among pregnant women than among nonpregnant women. Among women with COVID-19, approximately one third (31.5%) of pregnant women were reported to have been hospitalized compared with 5.8% of nonpregnant women. After adjusting for age, presence of underlying medical conditions, and race/ethnicity, pregnant women were significantly more likely to be admitted to the intensive care unit (ICU) (aRR = 1.5, 95% confidence interval [CI] = 1.2-1.8) and receive mechanical ventilation (aRR = 1.7, 95% CI = 1.2-2.4). Sixteen (0.2%) COVID-19-related deaths were reported among pregnant women aged 15-44 years, and 208 (0.2%) such deaths were reported among nonpregnant women (aRR = 0.9, 95% CI = 0.5-1.5). These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation compared with nonpregnant women, but their risk for death is similar. To reduce occurrence of severe illness from COVID-19, pregnant women should be counseled about the potential risk for severe illness from COVID-19, and measures to prevent infection with SARS-CoV-2 should be emphasized for pregnant women and their families. url: https://doi.org/10.15585/mmwr.mm6925a1 doi: 10.15585/mmwr.mm6925a1 id: cord-285711-2utcn0hw author: Elliott, Robert title: COVID-19 Related Mortality During Management of a Hepatic Abscess date: 2020-09-22 words: 2071.0 sentences: 102.0 pages: flesch: 48.0 cache: ./cache/cord-285711-2utcn0hw.txt txt: ./txt/cord-285711-2utcn0hw.txt summary: Declared a pandemic by the World Health Organization on March 11th, 2020, COVID-19 has challenged healthcare systems to limit the spread of community and hospital-acquired of disease. In the setting of an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), healthcare systems have been challenged to limit in-hospital transmission of the virus; a task noted to be incredibly difficult given the suggestion of what appears to be fairly high viral transmissibility (3, 4) . We presented a case of a patient death from SARS-CoV-2 infection prior to the implementation of universal masking. In addition, now having lived this experience with universal masking, we question: (1) if there might be a survival advantage to short-interval masking during the height of seasonal influenza activity and (2) if there may be a benefit to expanded use of N95 respirators in the IR suite during AGP-type interventions performed on individuals presenting with respiratory infections not limited to Covid-19. abstract: The coronavirus disease (COVID-19) is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which originated in the capital city of the Hubei Province, Wuhan, China in late 2019. Declared a pandemic by the World Health Organization on March 11th, 2020, COVID-19 has challenged healthcare systems to limit the spread of community and hospital-acquired of disease. This article uses a patient case to highlight the importance of infection control during the height of the SARS-CoV-2 surge at a Level I affiliated community hospital in Western New York. url: https://www.ncbi.nlm.nih.gov/pubmed/32982611/ doi: 10.1016/j.jradnu.2020.09.001 id: cord-035292-pan415s7 author: Elmessaoudi-Idrissi, Mohcine title: Structure-guided discovery approach identifies potential lead compounds targeting M(pro) of SARS-CoV-2 date: 2020-11-11 words: 1758.0 sentences: 125.0 pages: flesch: 53.0 cache: ./cache/cord-035292-pan415s7.txt txt: ./txt/cord-035292-pan415s7.txt summary: Targeting the SARS-CoV-2 M(pro) crystal structure (PDB ID: 6LU7) a combination of in silico screening, molecular docking, and dynamic approaches, a set of 5000 compounds of the ZINC database were screened. As a result, we identified and ranked the top 20 compounds based on the scores of ligand-interaction, their drug-likeness properties, and their predicted antiviral efficacies. Taking the advantage of the main protease (M pro ) structure that became available recently [14] , we carried out a virtual in silico screening of nearly 5000 ZINC compound database to identify new inhibitors targeting the SARS-CoV-2. The docking simulations showed, by a ranking of binding energies score, that compound 2-[2-(2Fig. 1 Structure of SARS-CoV-2 main protease M pro . Based on our computational strategy, the pharmacokinetic properties and drug-likeness of the top 20 ranked scoring molecules that show the potential of M pro inhibitors of the SARS-CoV-2 are shown in supplementary table 1. abstract: The ongoing coronavirus disease 19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become fatal for the world with affected population crossing over 25 million in more than 217 countries, consequently declared a global pandemic by the World Health Organization. Unfortunately, neither specific prophylactic or therapeutic drugs nor vaccines are available. To address the unmet medical needs, we explored a strategy identifying new compounds targeting the main protease (M(pro)) of SARS-CoV-2. Targeting the SARS-CoV-2 M(pro) crystal structure (PDB ID: 6LU7) a combination of in silico screening, molecular docking, and dynamic approaches, a set of 5000 compounds of the ZINC database were screened. As a result, we identified and ranked the top 20 compounds based on the scores of ligand-interaction, their drug-likeness properties, and their predicted antiviral efficacies. The prominent drug-like and potent inhibitory compounds are 2-[2-(2-aminoacetyl) aminoacetyl] amino-3-(4-hydroxyphenyl)-propanamide (ZINC000004762511), 6′-fluoroaristeromycin (ZINC000001483267) and cyclo (L-histidyl-L-histidyl) (ZINC000005116916) scaffolds. Further in vitro and in vivo validations are required to demonstrate anti-SARS-CoV-2 activities. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13337-020-00627-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656896/ doi: 10.1007/s13337-020-00627-6 id: cord-350189-2su7oqbz author: Elmén, Joacim title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 words: 5415.0 sentences: 322.0 pages: flesch: 55.0 cache: ./cache/cord-350189-2su7oqbz.txt txt: ./txt/cord-350189-2su7oqbz.txt summary: A priori, this suggests that LNA may be used to increase the functional half-life of siRNA in vivo by two different mechanisms, e.g. by enhancing the resistance of the constituent RNA strands against degradation by single-stranded RNases and by stabilizing the siRNA duplex structure that is critical for activity. Next, we examined the effect of making single RNA to LNA exchanges at base-paired positions in the antisense strand of the firefly luciferase siLNA1. Although we cannot exclude that these modifications somehow prevent loading of the antisense strand into RISC, we believe this to be unlikely given the functionality of many significantly more modified siLNAs. Rather, as these positions are all close to the site where RNA target cleavage occurs [between pos. The SARS siRNA (Table 1) has identical closing base-pairs at both ends (A:U) making it likely that enough of both the antisense and sense strand would be incorporated into RISC to observe activity on the respective targets. abstract: Therapeutic application of the recently discovered small interfering RNA (siRNA) gene silencing phenomenon will be dependent on improvements in molecule bio-stability, specificity and delivery. To address these issues, we have systematically modified siRNA with the synthetic RNA-like high affinity nucleotide analogue, Locked Nucleic Acid (LNA). Here, we show that incorporation of LNA substantially enhances serum half-life of siRNA's, which is a key requirement for therapeutic use. Moreover, we provide evidence that LNA is compatible with the intracellular siRNA machinery and can be used to reduce undesired, sequence-related off-target effects. LNA-modified siRNAs targeting the emerging disease SARS, show improved efficiency over unmodified siRNA on certain RNA motifs. The results from this study emphasize LNA's promise in converting siRNA from a functional genomics technology to a therapeutic platform. url: https://www.ncbi.nlm.nih.gov/pubmed/15653644/ doi: 10.1093/nar/gki193 id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 words: 7523.0 sentences: 353.0 pages: flesch: 47.0 cache: ./cache/cord-255495-xnoppq3y.txt txt: ./txt/cord-255495-xnoppq3y.txt summary: It is possible that this "Trojan horse" strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this "silence" time period and then started to re-spread again. The fact that SARS-CoV-2 can be present within the vacuoles or double membrane vesicles (DMVs) within the host cells was proven by the careful post-mortem histopathological analysis of the renal samples of patients with COVID-19 by light microscopy, electron microscopic examination, and immunostaining (Farkash et al., 2020; Su et al., 2020) . Is this "Trojan horse" strategy of the release of the SARS-CoV-2-loaded exosomes or EDMVs represent a reasonable explanation for the appearance of the viral RNA in the recovered COVID-19 patients 7-14 day post discharge? abstract: We propose here that one of the potential mechanisms for the relapse of the COVID-19 infection could be a cellular transport pathway associated with the release of the SARS-CoV-2-loaded exosomes and other extracellular vesicles. It is possible that this “Trojan horse” strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this “silence” time period and then started to re-spread again. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32643586/ doi: 10.1080/07391102.2020.1790426 id: cord-303659-mzez7v4d author: Elsayed, Sarah M title: The Possibility and Cause of Relapse After Previously Recovering From COVID-19: A Systematic Review date: 2020-09-05 words: 3203.0 sentences: 195.0 pages: flesch: 54.0 cache: ./cache/cord-303659-mzez7v4d.txt txt: ./txt/cord-303659-mzez7v4d.txt summary: There are reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial clearance of the virus. There have been reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial documented clearance of the virus. The publications included COVID-19 positive patient data and the relapse of disease was confirmed by PCR; the full text was available for these publications. Data were collected in the following categories when available: Study design; Study country; Patient demographics; Clinical signs and symptoms; Laboratory findings; Imaging studies; Dynamics of the oropharyngeal swab test; Treatment of the first presentation; The clinical picture of relapse; Day of a positive result after confirmed negative We tabulated the data using Microsoft Excel (2010, Microsoft Corp, Redmond, WA). The study reports a total of 11 patients (6 females and 5 males), all from China, who tested positive for COVID-19. abstract: The severe acute respiratory distress syndrome coronavirus-2 (SARS-Cov-2) is a novel coronavirus that is believed to be mainly transmitted via droplet and contact transmission. While research is focusing on epidemiology, transmission, vaccine development, and therapeutics for coronavirus disease 2019 (COVID-19), there is a possibility of disease relapse. There are reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial clearance of the virus. Objective This systematic review aims to identify the trends of COVID-19 relapse, the effects of co-morbidities on it, and associated mortality rates. Methods We conducted a systematic search during March and April 2020 for research articles on the relapse of COVID-19 using two primary databases, PubMed and Embase. Results A total of 13 eligible studies were screened of which 11 (case reports) were eligible for data extraction. The earliest to report relapse was after two days of discharge and the latest was 22 days after discharge. The mean number of days to relapse was 12 days and the median number was seven days. There was incomplete information about comorbidities. No mortalities were reported at the time of the study. url: https://www.ncbi.nlm.nih.gov/pubmed/33042702/ doi: 10.7759/cureus.10264 id: cord-260180-kojb8efv author: Elsoukkary, Sarah S. title: Autopsy Findings in 32 Patients with COVID-19: A Single-Institution Experience date: 2020-09-17 words: 4600.0 sentences: 269.0 pages: flesch: 49.0 cache: ./cache/cord-260180-kojb8efv.txt txt: ./txt/cord-260180-kojb8efv.txt summary: METHODS: We report the clinicopathologic findings from 32 autopsy studies conducted on patients who died of COVID-19 including routine gross and microscopic examination with applicable special and immunohistochemical staining techniques. The purpose of this study is to describe clinical and pathologic findings in major organ systems of patients who died from SARS-CoV-2 infection. In this study, we described the unique and multisystem clinical and pathologic findings in 32 autopsies of patients who died from the novel coronavirus, SARS-CoV-2. On histologic examination, we observed findings secondary to the patients'' preexisting conditions in the heart, lungs, liver, and kidneys, as well as changes secondary to SARS-CoV-2 infection such as various stages of DAD and multiple thromboemboli in large and small vessels in multiple organs. While the lung findings are most significant for the majority of those infected, other organ systems are frequently involved including with widespread microscopic thromboses in numerous organs, as well as liver, kidney, and lymph node pathology. abstract: BACKGROUND: A novel coronavirus, SARS-CoV-2, was identified in Wuhan, China in late 2019. This virus rapidly spread around the world causing disease ranging from minimal symptoms to severe pneumonia, which was termed coronavirus disease (i.e., COVID). Postmortem examination is a valuable tool for studying the pathobiology of this new infection. METHODS: We report the clinicopathologic findings from 32 autopsy studies conducted on patients who died of COVID-19 including routine gross and microscopic examination with applicable special and immunohistochemical staining techniques. RESULTS: SARS-CoV-2 infection was confirmed by nasopharyngeal RT-PCR in 31 cases (97%) and by immunohistochemical staining for SARS-CoV-2 spike-protein in the lung in the remaining 1 case (3%). The ethnically diverse cohort consisted of 22 males and 10 females with a mean age of 68 years (range: 30–100). Patients most commonly presented with cough (17 [55%]), shortness of breath (26 [81%]), and a low-grade fever (17 [55%]). Thirty-one (97%) of the patients had at least 1 comorbidity (mean = 4). Twenty-eight patients (88%) had widespread thromboembolic disease, as well as diffuse alveolar damage (30 [94%]), diabetic nephropathy (17 [57%]) and acute tubular injury. Patterns of liver injury were heterogeneous, featuring 10 (36%) with frequent large basophilic structures in sinusoidal endothelium, and increased immunoblast-like cells in lymph nodes. CONCLUSION: This series of autopsies from patients with COVID-19 confirms the observation that the majority of severely affected patients have significant pulmonary pathology. However, many patients also have widespread microscopic thromboses, as well as characteristic findings in the liver and lymph nodes. url: https://doi.org/10.1159/000511325 doi: 10.1159/000511325 id: cord-351691-3egwvb59 author: Elzupir, Amin O. title: Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 date: 2020-10-23 words: 2948.0 sentences: 181.0 pages: flesch: 52.0 cache: ./cache/cord-351691-3egwvb59.txt txt: ./txt/cord-351691-3egwvb59.txt summary: This study investigates the inhibitory effect of SARS-CoV-2 3-chymotrypsin-like protease (3CL(pro)) using caffeine and caffeine-containing pharmaceuticals (3CPs) based on molecular dynamics simulations and free energy calculations by means of molecular mechanics-Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics-generalized-Born surface area (MMGBSA). Of these 3CPs, seven drugs approved by the US-Food and Drug Administration have shown a good binding affinity to the catalytic residues of 3CL(pro) of His(41) and Cys(145): caffeine, theophylline, dyphylline, pentoxifylline, linagliptin, bromotheophylline and istradefylline. This study demonstrates the inhibitory effect of 3CL pro by means of approved caffeine and caffeine-containing pharmaceuticals (3CPs) using the molecular docking approach. An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations abstract: In December 2019, a new coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the outbreak of a pulmonary disease called COVID-19, which killed thousands of people worldwide. Therefore, the necessity to find out the potential therapeutic pharmaceuticals is imperious. This study investigates the inhibitory effect of SARS-CoV-2 3-chymotrypsin-like protease (3CL(pro)) using caffeine and caffeine-containing pharmaceuticals (3CPs) based on molecular dynamics simulations and free energy calculations by means of molecular mechanics-Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics-generalized-Born surface area (MMGBSA). Of these 3CPs, seven drugs approved by the US-Food and Drug Administration have shown a good binding affinity to the catalytic residues of 3CL(pro) of His(41) and Cys(145): caffeine, theophylline, dyphylline, pentoxifylline, linagliptin, bromotheophylline and istradefylline. Their binding affinity score ranged from –4.9 to –8.6 kcal/mol. The molecular dynamic simulation in an aqueous solution of docked complexes demonstrated that the 3CPs conformations bound to the active sites of 3CL(pro) during 200 ns molecular dynamics simulations. The free energy of binding also confirms the stability of the 3CPs–3CL(pro) complexes. To our knowledge, this in silico study shows for the first time very inexpensive drugs available in large quantities that can be potential inhibitors against 3CL(pro). In particular, the repurposing of linagliptin, and caffeine are recommended for COVID-19 treatment after in vitro, in vivo and clinical trial validation. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1835732 doi: 10.1080/07391102.2020.1835732 id: cord-253468-pf0xubii author: Emara, Mohamed H title: Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients date: 2020-09-02 words: 986.0 sentences: 57.0 pages: flesch: 58.0 cache: ./cache/cord-253468-pf0xubii.txt txt: ./txt/cord-253468-pf0xubii.txt summary: title: Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients We hereby present the data of 3 patients presented to our OPD and were admitted as diabetic ketoacidosis (DKA) and 2-3 days later they developed manifestations suggestive of and proved by swabbing as positive cases. Chest auscultation and chest X ray were unremarkable and hence chest CT scan was requested ( Figure 1 ) and showed picture suggestive of mild-moderate COVID-19, swabbing was done and came positive Case 2: A 51-year-old male, presented by dizziness over last 2-3 days and when examined found to have high RBS and ketonuria, and hence admitted as KDA, and was acidotic (PH 7). A 62-year-old male patient who was not compliant with his medicines over the last 2 months, presented for renewal of medicine without any clinical manifestations, found to have panic RBS measurement, and was positive for urine ketones. abstract: We present three diabetic patients cases presented with kentonuria as the presenting manifestation of SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S0306987720324828 doi: 10.1016/j.mehy.2020.110226 id: cord-304544-tqtdjh2m author: Enes, Ak title: Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date: 2020-06-20 words: 3745.0 sentences: 189.0 pages: flesch: 49.0 cache: ./cache/cord-304544-tqtdjh2m.txt txt: ./txt/cord-304544-tqtdjh2m.txt summary: Comparison of transcriptome of NHBE cells 24 hours after mock-infection and SARS-CoV-2 infection demonstrated that most genes that respond to infection were upregulated (320 genes) rather than being downregulated (115 genes).While upregulated genes were enriched in signalling pathways related to virus response, downregulated genes are related to kidney development. Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. Upregulated MMPs and chemokines demonstrate the response generated by NHBE cells to trigger the immune system, these two subgroups of genes are further discussed below comparatively in SARS-CoV-2 and H1N1 infection. Interestingly, none of the IL-17 ligands were expressed in detectable amounts in NHBE cells, and none of the ligands or receptors were upregulated in response to virus infection, therefore the positive feedback loop is likely to be initiated by activation of NFκB via other signalling pathways. abstract: SARS-CoV-2 virus, the pathogen that causes Covid-19 disease, emerged in Wuhan region in China in 2019, infected more than 4M people and is responsible for death of at least 300K patients globally as of May 2020. Identification of the cellular response mechanisms to viral infection by SARS-CoV-2 may shed light on progress of the disease, indicate potential drug targets, and make design of new test methods possible. In this study, we analysed transcriptomic response of normal human bronchial epithelial cells (NHBE) to SARS-CoV-2 infection and compared the response to H1N1 infection. Comparison of transcriptome of NHBE cells 24 hours after mock-infection and SARS-CoV-2 infection demonstrated that most genes that respond to infection were upregulated (320 genes) rather than being downregulated (115 genes).While upregulated genes were enriched in signalling pathways related to virus response, downregulated genes are related to kidney development. We mapped the upregulated genes on KEGG pathways to identify the mechanisms that mediate the response. We identified canonical NFκB, TNF and IL-17 pathways to be significantly upregulated and to converge to NFκB pathway via positive feedback loops. Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. Our results also indicate that immune response system is activated at the early stage of the infection and orchestrated by a crosstalk of signalling pathways. Finally, we compared transcriptomic SARS-CoV-2 response to H1N1 response in NHBE cells to elucidate the virus specificity of the response and virus specific extracellular proteins expressed by NHBE cells. url: https://doi.org/10.1101/2020.06.20.163006 doi: 10.1101/2020.06.20.163006 id: cord-270123-m8utyd1m author: Enmozhi, Sukanth Kumar title: Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach date: 2020-05-05 words: 3873.0 sentences: 187.0 pages: flesch: 49.0 cache: ./cache/cord-270123-m8utyd1m.txt txt: ./txt/cord-270123-m8utyd1m.txt summary: This paper evaluates the compound Andrographolide from Andrographis paniculata as a potential inhibitor of the main protease of SARS-COV-2 (Mpro) through in silico studies such as molecular docking, target analysis, toxicity prediction and ADME prediction. And upon certain in vitro and some clinical data chloroquine phosphate and hydroxychloroquine sulphate was advised to be the treatment for COVID-19 and enough randomized trials on these compounds to be provided and allowed the administration of the above drugs to be used for emergency (https://www.fda.gov/emergency-use-authori-zation#covidtherapeutics). Though there are many targets are found for the treatment of COVID-19, the main protease (M pro ) of SARS-CoV-2 was chosen due to interest of treating infected patients, to stop the multiplication of virus within the cells, through which M pro was involved in the release of polypeptides which are functional extensive proteolysis and cleavage of the enzyme itself from the sites of genome, pp1a and ppa1ab . abstract: SARS-CoV-2 virus which caused the global pandemic the Coronavirus Disease- 2019 (COVID-2019) has infected about 1,203,959 patients and brought forth death rate about 64,788 among 206 countries as mentioned by WHO in the month of April 2020. The clinical trials are underway for Remdesivir, an investigational anti-viral drug from Gilead Sciences. Antimalarial drugs such as Chloroquine and Hydroxychloroquine derivatives are being used in emergency cases; however, they are not suitable for patients with conditions like diabetes, hypertension and cardiac issues. The lack of availability of approved treatment for this disease calls forth the scientific community to find novel compounds with the ability to treat it. This paper evaluates the compound Andrographolide from Andrographis paniculata as a potential inhibitor of the main protease of SARS-COV-2 (Mpro) through in silico studies such as molecular docking, target analysis, toxicity prediction and ADME prediction. Andrographolide was docked successfully in the binding site of SARS-CoV-2 Mpro. Computational approaches also predicts this molecule to have good solubility, pharmacodynamics property and target accuracy. This molecule also obeys Lipinski’s rule, which makes it a promising compound to pursue further biochemical and cell based assays to explore its potential for use against COVID-19. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1760136 doi: 10.1080/07391102.2020.1760136 id: cord-021805-2j07zw6q author: Epstein, Jonathan H. title: Emerging Diseases in Bats date: 2018-09-28 words: 4160.0 sentences: 214.0 pages: flesch: 50.0 cache: ./cache/cord-021805-2j07zw6q.txt txt: ./txt/cord-021805-2j07zw6q.txt summary: 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152049/ doi: 10.1016/b978-0-323-55228-8.00040-0 id: cord-302939-z0071rwa author: Erdeve, Ömer title: The Turkish Neonatal Society proposal for the management of COVID-19 in the neonatal intensive care unit date: 2020-06-19 words: 3955.0 sentences: 203.0 pages: flesch: 48.0 cache: ./cache/cord-302939-z0071rwa.txt txt: ./txt/cord-302939-z0071rwa.txt summary: • NICUs should prepare emergency plans for COVID-19 to ensure the optimal management of potential victims • The assigned team should coordinate the hospitalization and maintenance of the patient with suspected COVID-19 • In the presence of high-risk factors, it is recommended that the newborn should be admitted and taken into an isolation ward in the NICU as soon as possible • Samples of the patient should be taken by staff that is trained and designated by the NICU • Newborns may be born prematurely and the most common non-specific initial symptoms include respiratory distress, shortness of breath, cyanosis, increased heart rate, lethargy, fever, feeding intolerance and vomiting • The SARS-CoV-2 has not been detected in breast milk, but the choice to breastfeed should be the mother''s and the families • There is no effective anti-coronavirus treatment yet and treatment is generally supportive abstract: Due to immaturity of immune function and the possibility of mother-fetal vertical and aerosol transmissions, neonates are particularly susceptible to the new coronavirus (SARS-CoV-2). Perinatal-neonatal departments should cooperate closely and take integrated approaches, and neonatal intensive care units (NICU) should prepare emergency plans for the coronavirus disease 2019 (COVID-19) as far as possible, so as to ensure the optimal management and treatment of potential victims. During the epidemic of COVID-19, the emergency response plan for the NICU should be based on the actual situation, including diagnosis, isolation, and treatment, as well as available equipment and staffing, and take into account the psychosocial needs of the families and neonatal care staff. In this context of the COVID-19 pandemic, the Turkish Neonatal Society has proposed a protocol with the evidence available at the time of preparation to handle neonates with SARS-CoV-2 infections and outbreaks in NICUs. We hope that this proposal can provide valuable information so medical workers do not have to enter the battlefield alone. At this moment, sharing resources, experiences and lessons, regardless of who you are, is our only chance to win. url: https://doi.org/10.14744/turkpediatriars.2020.43788 doi: 10.14744/turkpediatriars.2020.43788 id: cord-271014-xzpvupms author: Erikstrup, Christian title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 words: 2366.0 sentences: 177.0 pages: flesch: 57.0 cache: ./cache/cord-271014-xzpvupms.txt txt: ./txt/cord-271014-xzpvupms.txt summary: title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. abstract: BACKGROUND: The pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has tremendous consequences for our societies. Knowledge of the seroprevalence of SARS-CoV-2 is needed to accurately monitor the spread of the epidemic and to calculate the infection fatality rate (IFR). These measures may help the authorities to make informed decisions and adjust the current societal interventions. The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. METHODS: Danish blood donors aged 17–69 years giving blood April 6 to May 3 were tested for SARS-CoV-2 immunoglobulin M and G antibodies using a commercial lateral flow test. Antibody status was compared between geographical areas and an estimate of the IFR was calculated. The seroprevalence was adjusted for assay sensitivity and specificity taking the uncertainties of the test validation into account when reporting the 95% confidence intervals (CI). RESULTS: The first 20,640 blood donors were tested and a combined adjusted seroprevalence of 1.9% (CI: 0.8-2.3) was calculated. The seroprevalence differed across areas. Using available data on fatalities and population numbers a combined IFR in patients younger than 70 is estimated at 89 per 100,000 (CI: 72-211) infections. CONCLUSIONS: The IFR was estimated to be slightly lower than previously reported from other countries not using seroprevalence data. The IFR is likely several fold lower than the current estimate. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. url: https://doi.org/10.1093/cid/ciaa849 doi: 10.1093/cid/ciaa849 id: cord-320308-pzex799x author: Erol, Adnan title: Role of oxidized LDL-induced “trained macrophages” in the pathogenesis of COVID-19 and benefits of pioglitazone: A hypothesis date: 2020-05-12 words: 1916.0 sentences: 129.0 pages: flesch: 43.0 cache: ./cache/cord-320308-pzex799x.txt txt: ./txt/cord-320308-pzex799x.txt summary: CONCLUSIONS: When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. CARD9 is critical adaptor protein and a central integrator in innate immune cell activation that triggers the inflammatory signaling pathway in response to viral infection. Consequently, while SARS-CoV-infection in oxLDL-trained macrophages cannot produce protective type I interferons, they readily potentiates existing low-grade inflammation through ASC-mediated caspase-1 activation [10, 11] . All COVID-19 patients who develop severe respiratory failure display hyper-inflammatory responses with features of either immune dysregulation or macrophage activation syndrome. The information provided here must match the contributors'' statement in the manuscript.Importance of oxidized lipid-trained macrophages in the severity of COVID-19Adnan Erol Comment Role of the funding source Please disclose any funding sources and their role, if any, in the writing of the manuscript or the decision to submit it for publication. abstract: BACKGROUND AND AIMS: Older adults and people who have cardiovascular disorders (their common pathogenetic mechanism is progressive atherosclerosis) are at higher risk for severe illness from COVID-19 (coronavirus disease 2019). Their common pathogenetic mechanism is progressive atherosclerosis in which oxLDL (oxidized LDL) plays major role. Receptor-mediated uptake of oxLDL by the monocyte-derived macrophages activates the long-term epigenetic reprogramming of innate immunity, which is termed “trained immunity.” The aim of this work is to investigate the mechanisms and treatment possibilities that can control the activities of these specific macrophages. METHODS: Search in Medline and PubMed relevant articles on the trained immunity and cytokine storm of COVID-19. CONCLUSIONS: When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. Therefore, blocking macrophage training by pioglitazone, a thiazolidinedione, could control the hyperactivation that the virus would trigger. url: https://www.ncbi.nlm.nih.gov/pubmed/32470851/ doi: 10.1016/j.dsx.2020.05.007 id: cord-253431-fjds5cdr author: Erukainure, Ochuko L. title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. (Labiatae) date: 2020-11-03 words: 6198.0 sentences: 344.0 pages: flesch: 46.0 cache: ./cache/cord-253431-fjds5cdr.txt txt: ./txt/cord-253431-fjds5cdr.txt summary: title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. Ligand-protein interactions between viral protein (SARS-CoV-2 spike protein), the host receptor target (ACE2) and Harpagide 5-O-b-D-glucopyranoside are presented in Figures 5-7 . Harpagide 5-O-b-D-glucopyranoside displayed a good binding in complex with the host receptor target, initiation and termination sequence of the viral spike protein messenger RNA compared to all studied standard drugs with binding affinities of À7.5, À6.4 and 6.3 kcal mol À1 respectively (Table 5) . In the present study, we investigated the epidemiology of COVID-19 and the potentials of harpagide 5-O-b-D-glucopyranoside, a new iridoid glycoside isolated from C. At molecular level, the viral envelope spike (S) protein of SARS-CoV-2 and angiotensin converting enzyme 2 receptor within the host are central to COVID-19 pathogenesis and response to therapeutic interventions among other biological factors . abstract: The global spread of the coronavirus infections disease − 2019 (COVID-19) and the search for new drugs from natural products particularly from plants are receiving much attention recently. In this study, the therapeutic potential of a new iridoid glycoside isolated from the leaves of Clerodendrum volubile against COVID-19 was investigated. Harpagide 5-O-β-D-glucopyranoside (HG) was isolated, characterised and investigated for its druglikeness, optimized geometry, and pharmacokinetics properties. Its immunomodulatory was determined by chemiluminescence assay using polymorphonuclear neutrophils (PMNs) in addition to T-cell proliferation assay. In silico analysis was used in determining its molecular interaction with severe acute respiratory syndrome coronavirus-2 (SARS-COV-2). HG displayed potent druglikeness properties, with no inhibitory effect on cytochrome P(450) (1A2, 2C19, 2C9, 2D6 and 3A4) and a predicted LD(50) of 2000 mg/kg. Its (1)H-NMR chemical shifts showed a little deviation of 0.01 and 0.11 ppm for H-4 and H-9, respectively. HG significantly suppressed oxidative bursts in PMNs, while concomitantly inhibiting T-cell proliferation. It also displayed a very strong binding affinity with the translation initiation and termination sequence sites of spike (S) protein mRNA of SARS-COV-2, its gene product, and host ACE2 receptor. These results suggest the immunomodulatory properties and anti-SARS-COV-2 potentials of HG which can be explored in the treatment and management of COVID-19. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1840439 doi: 10.1080/07391102.2020.1840439 id: cord-280043-bm0qkrod author: Esagian, Stepan M. title: Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic date: 2020-06-04 words: 4217.0 sentences: 214.0 pages: flesch: 38.0 cache: ./cache/cord-280043-bm0qkrod.txt txt: ./txt/cord-280043-bm0qkrod.txt summary: As the coronavirus disease 2019 (COVID-19) outbreak has rapidly evolved into a global pandemic, abdominal organ transplantation programs are currently facing multiple challenges. According to the report of the first case series from China, a significant proportion of patients (23.7%) suffered from comorbidities, which are commonly seen in abdominal transplant candidates, including hypertension (15.0%), diabetes mellitus (7.2%), hepatitis B infection (2.1%), cancer (0.9%), chronic kidney disease (0.7%) and immunodeficiency (0.2%) (7) . Although data for abdominal organ transplant candidates and recipients are still limited, emerging reports have indicated that these patients may present with atypical COVID-19 manifestations. These guidelines address three potential standpoints the epidemic confronts transplantation systems with; first, the risk of donor-derived SARS-CoV-2 infection, which although has not been reported thus far in neither organ or blood product recipients, extensive donor screening protocols have been implemented in many transplant centers in pandemic areas. abstract: As the coronavirus disease 2019 (COVID-19) outbreak has rapidly evolved into a global pandemic, abdominal organ transplantation programs are currently facing multiple challenges. Transplant candidates and recipients are considered high-risk populations for severe disease and death due to COVID-19 as a result of their numerous underlying comorbidities, advanced age and impaired immune function. Emerging reports of atypical and delayed clinical presentations in these patients generate further concerns for widespread disease transmission to medical personnel and the community. The striking similarities between COVID-19 and other outbreaks that took place over the past two decades, like Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome, highlight the severity of the situation and dictate that extra measures should be taken by the transplant programs to avoid adverse outcomes. Transplant organizations are currently calling for strict screening and isolation protocols to be established in all transplant programs, for both organ donors and recipients. As the situation escalates, more radical measures might be necessary, including a temporary hold on non-urgent transplantations, resulting in serious ethical dilemmas between the survival of these patients and the safety of the community. Further data about these special populations could result in more individualized guidelines for abdominal organ transplantation in the era of COVID-19. url: https://doi.org/10.3389/fmed.2020.00287 doi: 10.3389/fmed.2020.00287 id: cord-315064-2mgv9j6n author: Escher, Felicitas title: Detection of viral SARS‐CoV‐2 genomes and histopathological changes in endomyocardial biopsies date: 2020-06-12 words: 3813.0 sentences: 241.0 pages: flesch: 48.0 cache: ./cache/cord-315064-2mgv9j6n.txt txt: ./txt/cord-315064-2mgv9j6n.txt summary: Accordingly, we prospectively analysed endomyocardial biopsies (EMBs) from a cohort of 104 samples of patients with suspected myocarditis or unexplained heart disease for the presence of SARS-CoV-2 RNA by RT-qPCR and hints for histopathological injury. Up to 8 EMBs each of 104 patients [mean age: 57.90 ± 16.37 years; left ventricular ejection fraction (LVEF): 33.7 ± 14.6%, sex: n = 79 male/25 female] with suspected myocarditis or unexplained heart failure were analysed between 3 February and 26 March 2020 in German clinical centres in accordance with SARS-CoV2 spread in Germany. In this study, we established for the first time the evidence of SARS-CoV-2 genome detection in 5 of 104 EMBs of patients with suspected myocarditis or unexplained heart failure. Our finding of SARS-CoV-2 genome detection in EMBs of patients suffering from myocarditis/inflammatory cardiomyopathy cannot rule out or confirm the infection of cardiac cells but revealed incremental insights into organ-specific infection of SARS-CoV-2 using possibly macrophage migration as a shuttle from the lung to the heart. abstract: AIMS: Since December 2019, the novel coronavirus SARS‐CoV‐2 has spread rapidly throughout China and keeps the world in suspense. Cardiovascular complications with myocarditis and embolism due to COVID‐19 have been reported. SARS‐CoV‐2 genome detection in the heart muscle has not been demonstrated so far, and the underlying pathophysiological mechanisms remain to be investigated. METHODS AND RESULTS: Endomyocardial biopsies (EMBs) of 104 patients (mean age: 57.90 ± 16.37 years; left ventricular ejection fraction: 33.7 ± 14.6%, sex: n = 79 male/25 female) with suspected myocarditis or unexplained heart failure were analysed. EMB analysis included histology, immunohistochemistry, and detection of SARS‐CoV‐2 genomes by real‐time reverse transcription polymerase chain reaction in the IKDT Berlin, Germany. Among 104 EMBs investigated, five were confirmed with SARS‐CoV‐2 infected by reverse real‐time transcriptase polymerase chain reaction. We describe patients of different history of symptoms and time duration. Additionally, we investigated histopathological changes in myocardial tissue showing that the inflammatory process in EMBs seemed to permeate vascular wall leading to small arterial obliteration and damage. CONCLUSIONS: This is the first report that established the evidence of SARS‐CoV‐2 genomes detection in EMBs. In these patients, myocardial injury ischaemia may play a role, which could explain the ubiquitous troponin increases. EMB‐based identification of the cause of myocardial injury may contribute to explain the different evolution of complicated SARS‐CoV‐2‐infection and to design future specific and personalized treatment strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32529795/ doi: 10.1002/ehf2.12805 id: cord-293136-lfwqzf8m author: Escosa‐García, Luis title: Ten key points about COVID‐19 in children: the shadows on the wall date: 2020-08-13 words: 3631.0 sentences: 241.0 pages: flesch: 52.0 cache: ./cache/cord-293136-lfwqzf8m.txt txt: ./txt/cord-293136-lfwqzf8m.txt summary: It was initially named Pediatric multisystem inflammatory syndrome (PIMS) temporally associated with COVID-19 by the Royal College of Paediatrics and Child Health (RCPCH) 18 To date, some cases of neonatal SARS-CoV-2 infection have been reported 27 28 . Recent data from a German study indicate that viral loads in the very young (age group 0-6 years) do not significantly differ from those of adults 44 To put it briefly, SARS-CoV-2 PCR of nasopharyngeal swab is considered the gold standard diagnostic test for acute COVID-19 disease. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center''s observational study Characteristics and Outcomes of Children With Coronavirus Disease 2019 (COVID-19) Infection Admitted to US and Canadian Pediatric Intensive Care Units abstract: The pandemic of the new coronavirus disease (COVID‐19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), initially described in China, is challenging the healthcare systems of all countries. Every emerging disease raises many questions with a scarcity of answers since all its characteristics are still being discovered. In the case of SARS‐CoV‐2, most of the literature comes from adult patients. Children seem to be less affected. Pediatric patients diagnosed with COVID‐19 disease usually suffer a mild illness, with low risk of complications or mortality. Defining the role of children in the transmission of SARS‐CoV‐2 is critical as some national infection control decisions involving children, such as school closures or social distancing, will probably impact the dynamics of the virus. To aid in the knowledge on COVID‐19 in children, this work presents an expert review of the literature published from January 1 to April 20, 2020, including peer‐reviewed and pre‐print non‐peer‐reviewed studies, along with some relevant articles afterwards, summarizing ten key points that characterize the disease in children. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/ppul.25025 doi: 10.1002/ppul.25025 id: cord-305104-jk6ai1od author: Escribese, María M title: Cross‐sectional pilot study exploring the feasibility of a rapid SARS‐CoV‐2 immunization test in health and non‐healthcare workers date: 2020-08-05 words: 1265.0 sentences: 70.0 pages: flesch: 52.0 cache: ./cache/cord-305104-jk6ai1od.txt txt: ./txt/cord-305104-jk6ai1od.txt summary: All rights reserved Cross-sectional pilot study exploring the feasibility of a rapid SARS-CoV-2 immunization test in healthcare and non-healthcare workers To the Editor: We aimed to generate an immune response map to SARS-CoV-2 in a very specific population of a Medical School were both healthcare workers and non-healthcare workers cohabit, and elucidate the main risk factors that can be associated with COVID-19 diagnosis in each population. Additionally, this pilot study provides the knowledge and the positive controls (healthcare workers with positive RT-PCR) for the development of future methodological strategies aiming to set up new immunological tests for herd immunity follow-up (ELISA, neutralization assays, etc.).This will be helpful if we take into account the shortage of commercial kits for SARS-CoV-2 immunological tests during the pandemic, and the limitations of these tests in terms of specificity and sensitivity (5, 6)(). abstract: nan url: https://doi.org/10.1111/all.14545 doi: 10.1111/all.14545 id: cord-349504-oqpjqgv4 author: Escudero, Dolores title: Análisis de SARS-CoV-2 en el aire de una UCI dedicada a pacientes Covid-19 date: 2020-10-10 words: 1627.0 sentences: 140.0 pages: flesch: 66.0 cache: ./cache/cord-349504-oqpjqgv4.txt txt: ./txt/cord-349504-oqpjqgv4.txt summary: Algunos estudios han documentado que el SARS-CoV-2 puede permanecer en el aire generado por aerosoles hasta 3 horas (7) demostrándose la presencia de genoma viral en el aire y filtros de los hospitales. El estudio se realizó a finales de mayo del 2020 en 5 boxes diferentes de la UCI (Tabla 1), colocando los equipos de extracción en el suelo, cerca de la cabeza del paciente y lo más alejado posible de la salida de aire, recogiéndo las muestras de aire durante un tiempo de 2-4 horas. El análisis mediante RT-PCR cuantitativa no mostró en ningún caso detección del genoma de SARS-CoV-2 en las muestras recogidas por los dos métodos descritos, por lo que en nuestro estudio no hemos podido demostrar la presencia de SARS-CoV-2 en el aire de la UCI ni en la planta de hospitalización. En nuestra UCI todos los boxes estaban equipados con presión negativa de -10 pascales y un intercambio de 15-20 ciclos/h de aire lo cual puede justificar la ausencia de RNA del SARS-CoV-2 en nuestra investigación. abstract: nan url: https://doi.org/10.1016/j.medin.2020.09.004 doi: 10.1016/j.medin.2020.09.004 id: cord-281699-pxof67pl author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-08-13 words: 3089.0 sentences: 169.0 pages: flesch: 55.0 cache: ./cache/cord-281699-pxof67pl.txt txt: ./txt/cord-281699-pxof67pl.txt summary: In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are not under selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene, and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors ( Fig. 1) . abstract: SARS-CoV-2 is a betacoronavirus responsible for human cases of COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load in both regions without selective pressure and across the genome, compared to nsp7, 8, and 12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates, and nsp14 mutations as potential predictors for high mutability strains. url: https://doi.org/10.1101/2020.08.12.248732 doi: 10.1101/2020.08.12.248732 id: cord-331076-ak481qew author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 words: 3858.0 sentences: 192.0 pages: flesch: 52.0 cache: ./cache/cord-331076-ak481qew.txt txt: ./txt/cord-331076-ak481qew.txt summary: In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are under less selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020a) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors (Fig. 1) . Three of the five most common nsp14 mutations, namely 18060C>T, 18736T>C and 18877C>T are associated with increases in both genome-wide mutational load, as well as MoE status, an alternative indicator of mutational rate and virus evolution. abstract: SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains. url: https://doi.org/10.7717/peerj.10181 doi: 10.7717/peerj.10181 id: cord-283699-c4jjdj5o author: Eslami, Gholamali title: The impact of sofosbuvir/daclatasvir or ribavirin in patients with severe COVID-19 date: 2020-08-19 words: 3476.0 sentences: 188.0 pages: flesch: 51.0 cache: ./cache/cord-283699-c4jjdj5o.txt txt: ./txt/cord-283699-c4jjdj5o.txt summary: With the national standard COVID-19 treatment protocol at the time being lopinavir/ritonavir 200/50 mg two tablets every 12 h plus hydroxychloroquine 400 mg daily, it was decided to conduct a two-arm trial where both arms would receive the standard protocol in addition to either ribavirin or sofosbuvir/ daclatasvir. In this open-label trial, the effects of sofosbuvir/daclatasvir and ribavirin in patients with severe COVID-19 were measured. The time required before observing clinical improvement was significantly less in patients treated with sofosbuvir/daclatasvir, and the side effects of the medication, such as GI bleeding and anaemia, were lower than in the group receiving ribavirin. In this open-label study, treatment of patients with severe COVID-19 with sofosbuvir/daclatasvir was significantly more effective than ribavirin through improved clinical symptoms, lower mortality rates, a shorter duration of both ICU and hospital stays, and fewer side effects. abstract: OBJECTIVES: Sofosbuvir and daclatasvir are direct-acting antivirals highly effective against hepatitis C virus. There is some in silico and in vitro evidence that suggests these agents may also be effective against SARS-CoV-2. This trial evaluated the effectiveness of sofosbuvir in combination with daclatasvir in treating patients with COVID-19. METHODS: Patients with a positive nasopharyngeal swab for SARS-CoV-2 on RT–PCR or bilateral multi-lobar ground-glass opacity on their chest CT and signs of severe COVID-19 were included. Subjects were divided into two arms with one arm receiving ribavirin and the other receiving sofosbuvir/daclatasvir. All participants also received the recommended national standard treatment which, at that time, was lopinavir/ritonavir and single-dose hydroxychloroquine. The primary endpoint was time from starting the medication until discharge from hospital with secondary endpoints of duration of ICU stay and mortality. RESULTS: Sixty-two subjects met the inclusion criteria, with 35 enrolled in the sofosbuvir/daclatasvir arm and 27 in the ribavirin arm. The median duration of stay was 5 days for the sofosbuvir/daclatasvir group and 9 days for the ribavirin group. The mortality in the sofosbuvir/daclatasvir group was 2/35 (6%) and 9/27 (33%) for the ribavirin group. The relative risk of death for patients treated with sofosbuvir/daclatasvir was 0.17 (95% CI 0.04–0.73, P = 0.02) and the number needed to treat for benefit was 3.6 (95% CI 2.1–12.1, P < 0.01). CONCLUSIONS: Given these encouraging initial results, and the current lack of treatments proven to decrease mortality in COVID-19, further investigation in larger-scale trials seems warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/32812051/ doi: 10.1093/jac/dkaa331 id: cord-288025-skkpkqw6 author: Eslami, Hadi title: The role of environmental factors to transmission of SARS-CoV-2 (COVID-19) date: 2020-05-15 words: 4860.0 sentences: 269.0 pages: flesch: 54.0 cache: ./cache/cord-288025-skkpkqw6.txt txt: ./txt/cord-288025-skkpkqw6.txt summary: Human-to-human transmission of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs most often when people are in the incubation stage of the disease or are carriers and have no symptoms. Therefore, in this study, was discussed the role of environmental factors and conditions such as temperature, humidity, wind speed as well as food, water and sewage, air, insects, inanimate surfaces, and hands in COVID-19 transmission. This study aimed to investigate the effect and role of various factors, including environmental factors (climate change, water transfer, air, and food), disinfection of surfaces, and hands in the transmission and prevalence of COVID-19 pandemics. The most well-known methods of surface disinfection to remove SARS-CoV-2 virus are, in short, the use of ethyl alcohol (62-70%), or hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%, dilution ratio 1 to 50) with a contact time of 1 min (Henwood 2020; WHO 2014) . abstract: The current outbreak of the novel coronavirus disease 2019 (COVID-19) in more than 250 countries has become a serious threat to the health of people around the world. Human-to-human transmission of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs most often when people are in the incubation stage of the disease or are carriers and have no symptoms. Therefore, in this study, was discussed the role of environmental factors and conditions such as temperature, humidity, wind speed as well as food, water and sewage, air, insects, inanimate surfaces, and hands in COVID-19 transmission. The results of studies on the stability of the SARS-CoV-2 on different levels showed that the resistance of this virus on smooth surfaces was higher than others. Temperature increase and sunlight can facilitate the destruction of SARS-COV-2 and the stability of it on surfaces. When the minimum ambient air temperature increases by 1 °C, the cumulative number of cases decreases by 0.86%. According to the latest evidence, the presence of coronavirus in the sewer has been confirmed, but there is no evidence that it is transmitted through sewage or contaminated drinking water. Also, SARS-COV-2 transmission through food, food packages, and food handlers has not been identified as a risk factor for the disease. According to the latest studies, the possibility of transmitting SARS-COV-2 bioaerosol through the air has been reported in the internal environment of ophthalmology. The results additionally show that infectious bio-aerosols can move up to 6 feet. There have been no reports of SARS-COV-2 transmission by blood-feeding arthropods such as mosquitoes. url: https://doi.org/10.1186/s13568-020-01028-0 doi: 10.1186/s13568-020-01028-0 id: cord-342024-kaku49xd author: Espejo, Andrea P title: Review of Current Advances in Serologic Testing for COVID-19 date: 2020-06-25 words: 6480.0 sentences: 373.0 pages: flesch: 50.0 cache: ./cache/cord-342024-kaku49xd.txt txt: ./txt/cord-342024-kaku49xd.txt summary: • The use of total antibody or simultaneous IgG/IgM measurements (regardless of method) significantly adds sensitivity to reverse transcription polymerase chain reaction testing protocols early post onset of symptoms and becomes the most accurate diagnostic test at later time points. The SP, RBD, and NP proteins appear to be the main targets of the humoral immune response in coronavirus infections including SARS-CoV-2 and were the antigens used in the majority of the serologic assays examined in this literature review. Overall, while these results are similar to that reported in a review of serologic testing for MERS-CoV and SARS-CoV, they may have been affected by choice of target antigens, the various immunoassay kits, and the level of detail of case history used to categorize the time of sample acquisition post onset of symptoms. abstract: OBJECTIVES: To examine and summarize the current literature on serologic methods for the detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: A literature review was performed using searches in databases including PubMed, medRxiv, and bioRxiv. Thirty-two peer-reviewed papers and 23 preprints were examined. RESULTS: The studies included lateral flow immunoassay, enzyme-linked immunosorbent assay, chemiluminescence immunoassay, and neutralizing antibody assays. The use of all major SARS-CoV-2 antigens was demonstrated to have diagnostic value. Assays measuring total antibody reactivity had the highest sensitivity. In addition, all the methods provided opportunities to characterize the humoral immune response by isotype. The combined use of IgM and IgG detection resulted in a higher sensitivity than that observed when detecting either isotype alone. Although IgA was rarely studied, it was also demonstrated to be a sensitive marker of infection, and levels correlated with disease severity and neutralizing activity. CONCLUSIONS: The use of serologic testing, in conjunction with reverse transcription polymerase chain reaction testing, was demonstrated to significantly increase the sensitivity of detection of patients infected with SARS-CoV-2. There was conflicting evidence regarding whether antibody titers correlated with clinical severity. However, preliminary investigations indicated some immunoassays may be a surrogate for the prediction of neutralizing antibody titers and the selection of recovered patients for convalescent serum donation. url: https://www.ncbi.nlm.nih.gov/pubmed/32583852/ doi: 10.1093/ajcp/aqaa112 id: cord-348360-20eq5meh author: Esposito, Dominic title: Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date: 2020-06-04 words: 3438.0 sentences: 158.0 pages: flesch: 49.0 cache: ./cache/cord-348360-20eq5meh.txt txt: ./txt/cord-348360-20eq5meh.txt summary: To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Thus, the work presented here is intended to provide a robust method for those wishing to reliably produce SARS CoV-2 spike protein in quantities sufficient for serology assays, structural biology, or simply to better understand some of the production variables affecting the yield. Nevertheless, the approaches outlined here allowed us to improve the production yield of spike protein significantly by modifying cell culture temperature and harvest time, as well as improving the purification process. To produce SARS-CoV-2 antigens for the development of serology assays, we initially followed standard procedures for secreted protein production: transfection using the manufacturer''s protocols, expression at 37°C, harvest at three days post-transfection, tangential flow filtration of the culture supernatant, immobilized metal ion chromatography with linear gradient elution, and size exclusion chromatography. abstract: The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots. url: https://www.ncbi.nlm.nih.gov/pubmed/32504802/ doi: 10.1016/j.pep.2020.105686 id: cord-340279-bq5owwot author: Espíndola, Otávio de Melo title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date: 2020-06-04 words: 285.0 sentences: 37.0 pages: flesch: 52.0 cache: ./cache/cord-340279-bq5owwot.txt txt: ./txt/cord-340279-bq5owwot.txt summary: key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection abstract: Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. This finding points to the need for the development of more sensitive molecular tests and the investigation of other neurotropic pathogens to exclude concurrent neuroinfection. url: https://doi.org/10.1016/j.ijid.2020.05.123 doi: 10.1016/j.ijid.2020.05.123 id: cord-347965-zluu0i41 author: Essahib, Wafaa title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts date: 2020-09-21 words: 1684.0 sentences: 114.0 pages: flesch: 58.0 cache: ./cache/cord-347965-zluu0i41.txt txt: ./txt/cord-347965-zluu0i41.txt summary: title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts PURPOSE: To visualize SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. RESULTS: SARS-CoV-2 host receptors ACE2 and CD147 are present on the membrane of trophectoderm, epiblast and hypoblast cells in human blastocysts. The aim of our study was to visualize SARS-CoV-2 receptors ACE2 and CD147 on human oocytes and blastocysts. In pre (5 days post fertilization (dpf5) and (dpf6))-and peri (dpf7)-implantation blastocysts, CD147 and ACE2 are present on the membrane of trophectoderm and hypoblast cells, which will both contribute to the embryonic part of the placenta (chorion). The presence of the receptors ACE2 and CD147, especially on the membrane, implicates that SARS-CoV-2 is theoretically able to bind and infect human oocytes and pre-and periimplantation embryos. Samples were washed in 2% BSA/PBS before Fig. 1 Immunofluorescent staining and confocal microscopy for SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. abstract: PURPOSE: To visualize SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. METHODS: Immunohistochemistry and confocal microscopy on human primary oocytes and pre (5 days post fertilization (dpf5) and (dpf6))- and peri (dpf7)-implantation blastocysts donated to research. RESULTS: SARS-CoV-2 host receptors ACE2 and CD147 are present on the membrane of trophectoderm, epiblast and hypoblast cells in human blastocysts. CD147 is also present on the oolemma. CONCLUSION: Theoretically, the earliest stages of embryonic development may be vulnerable for SARS-CoV-2 infection. url: https://doi.org/10.1007/s10815-020-01952-x doi: 10.1007/s10815-020-01952-x id: cord-277399-0w8is9xm author: Esteves, Sandro C. title: SARS‐CoV‐2 pandemic and repercussions for male infertility patients: A proposal for the individualized provision of andrological services date: 2020-05-22 words: 4160.0 sentences: 216.0 pages: flesch: 38.0 cache: ./cache/cord-277399-0w8is9xm.txt txt: ./txt/cord-277399-0w8is9xm.txt summary: The prolonged lockdown of health facilities providing non‐urgent gamete cryopreservation—as currently recommended by many reproductive medicine entities and regulatory authorities due to the SARS‐CoV‐2 pandemic will be detrimental for subgroups of male infertility patients. These groups include infertility patients (eg, azoospermic and cryptozoospermic) undergoing medical or surgical treatment to improve sperm quantity and quality, as well as males of reproductive age affected by inflammatory and systemic auto‐immune diseases who are about to start treatment with gonadotoxic drugs or who are under remission. Sperm banking should be considered in men with HH who respond to therapy, that is, have viable spermatozoa in the ejaculate, in particular, when the continuation of gonadotropin therapy during the SARS-CoV-2 pandemic is neither possible (eg, due to economic or logistic reasons), nor desired. We propose remedies to mitigate the consequences of a prolonged cessation of andrological services due to the SARS-CoV-2 pandemic to vulnerable subgroups of male infertility patients. abstract: The prolonged lockdown of health facilities providing non‐urgent gamete cryopreservation—as currently recommended by many reproductive medicine entities and regulatory authorities due to the SARS‐CoV‐2 pandemic will be detrimental for subgroups of male infertility patients. We believe the existing recommendations should be promptly modified and propose that the same permissive approach for sperm banking granted for men with cancer is expanded to other groups of vulnerable patients. These groups include infertility patients (eg, azoospermic and cryptozoospermic) undergoing medical or surgical treatment to improve sperm quantity and quality, as well as males of reproductive age affected by inflammatory and systemic auto‐immune diseases who are about to start treatment with gonadotoxic drugs or who are under remission. In both scenarios, the “fertility window” may be transitory; postponing diagnostic semen analysis and sperm banking in these men could compromise the prospects of biological parenthood. Moreover, we provide recommendations on how to continue the provision of andrological services in a considered manner and a safe environment. Our opinion is timely and relevant given the fact that fertility services are currently rated as of low priority in most countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32357288/ doi: 10.1111/andr.12809 id: cord-341670-o1v63zg8 author: Estevez-Ordonez, Dagoberto title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage date: 2020-05-20 words: 887.0 sentences: 59.0 pages: flesch: 54.0 cache: ./cache/cord-341670-o1v63zg8.txt txt: ./txt/cord-341670-o1v63zg8.txt summary: title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage Postoperative cerebrospinal fluid (CSF) samples were also tested for SARS-CoV-2 viral ribonucleic acid (RNA), which was not detected. CSF sample was obtained on hospital day 6, 5 d after testing positive for SARS-CoV-2 and evaluated by RT-qPCR. At 20 d, no one involved in her care has reported symptoms of infection with COVID-19 or has tested positive for SARS-CoV-2. Testing of CSF in a SARS-CoV-2-infected patient is also reported here, which to our knowledge has not been documented in the peered-reviewed literature. The present approach to the management of this patient with aSAH may provide some insight when caring for patients with urgent/emergent surgical pathologies in the setting of SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges abstract: nan url: https://doi.org/10.1093/neuros/nyaa197 doi: 10.1093/neuros/nyaa197 id: cord-285647-9tegcrc3 author: Estrada, Ernesto title: Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date: 2020-08-17 words: 9179.0 sentences: 533.0 pages: flesch: 59.0 cache: ./cache/cord-285647-9tegcrc3.txt txt: ./txt/cord-285647-9tegcrc3.txt summary: By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19. 25, 26 Therefore, we assume here that perturbations produced by SARS-CoV-2 proteins on the human PPI network are propagated by means of diffusive processes. Here, we propose the use of a time-fractional diffusion model on the PPI network of proteins targeted by SARS-CoV-2. We now consider how a perturbation produced by SARS-CoV-2 on a protein mainly expressed in the lungs can be propagated to proteins mainly located in other tissues (see Table S4 in the supplementary material) by a subdiffusive process. Here, we have studied the particular case in which the time-fractional diffusion equation produces a subdiffusive regime, with the use of α = 3/4 in the network of human proteins targeted by SARS-CoV-2. abstract: The coronavirus 2019 (COVID-19) respiratory disease is caused by the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which uses the enzyme ACE2 to enter human cells. This disease is characterized by important damage at a multi-organ level, partially due to the abundant expression of ACE2 in practically all human tissues. However, not every organ in which ACE2 is abundant is affected by SARS-CoV-2, which suggests the existence of other multi-organ routes for transmitting the perturbations produced by the virus. We consider here diffusive processes through the protein–protein interaction (PPI) network of proteins targeted by SARS-CoV-2 as an alternative route. We found a subdiffusive regime that allows the propagation of virus perturbations through the PPI network at a significant rate. By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32872802/ doi: 10.1063/5.0015626 id: cord-335648-lbmhprjn author: Estrich, Cameron G. title: Estimating COVID-19 prevalence and infection control practices among US dentists date: 2020-10-15 words: 4197.0 sentences: 207.0 pages: flesch: 49.0 cache: ./cache/cord-335648-lbmhprjn.txt txt: ./txt/cord-335648-lbmhprjn.txt summary: Dentists from every US state (n = 2,195) answered questions about COVID-19–associated symptoms, SARS-CoV-2 infection, mental and physical health conditions, and infection control procedures used in their primary dental practices. As early as March 2020, Journal of Dental Research published the infection control guidelines that dentists at Wuhan University used, 7 and, in April and May 2020, the American Dental Association (ADA) and the Centers for Disease Control and Prevention (CDC), respectively, released interim guidance on infection control protocols and changes to the practice and office environments. In this article, we used the first month of study data to estimate the prevalence of COVID-19 among US dentists and to determine the rate of compliance with CDC and ADA infection prevention and control procedures. 14, 15 Respondents who reported providing oral health care in the past month were asked about infection prevention or control procedures in their primary dental practice. abstract: BACKGROUND: Understanding the risks associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during oral health care delivery and assessing mitigation strategies for dental offices are critical to improving patient safety and access to oral health care. METHODS: The authors invited licensed US dentists practicing primarily in private practice or public health to participate in a web-based survey in June 2020. Dentists from every US state (n = 2,195) answered questions about COVID-19–associated symptoms, SARS-CoV-2 infection, mental and physical health conditions, and infection control procedures used in their primary dental practices. RESULTS: Most of the dentists (82.2%) were asymptomatic for 1 month before administration of the survey; 16.6% reported being tested for SARS-CoV-2; and 3.7%, 2.7%, and 0% tested positive via respiratory, blood, and salivary samples, respectively. Among those not tested, 0.3% received a probable COVID-19 diagnosis from a physician. In all, 20 of the 2,195 respondents had been infected with SARS-CoV-2; weighted according to age and location to approximate all US dentists, 0.9% (95% confidence interval, 0.5 to 1.5) had confirmed or probable COVID-19. Dentists reported symptoms of depression (8.6%) and anxiety (19.5%). Enhanced infection control procedures were implemented in 99.7% of dentists’ primary practices, most commonly disinfection, COVID-19 screening, social distancing, and wearing face masks. Most practicing dentists (72.8%) used personal protective equipment according to interim guidance from the Centers for Disease Control and Prevention. CONCLUSIONS: COVID-19 prevalence and testing positivity rates were low among practicing US dentists. This indicates that the current infection control recommendations may be sufficient to prevent infection in dental settings. PRACTICAL IMPLICATIONS: Dentists have enhanced their infection control practices in response to COVID-19 and may benefit from greater availability of personal protective equipment. ClinicalTrials.gov: NCT04423770. url: https://www.ncbi.nlm.nih.gov/pubmed/33071007/ doi: 10.1016/j.adaj.2020.09.005 id: cord-278960-3xw4qjoy author: Evangelista, A. T. title: The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 date: 2020-05-20 words: 3833.0 sentences: 170.0 pages: flesch: 51.0 cache: ./cache/cord-278960-3xw4qjoy.txt txt: ./txt/cord-278960-3xw4qjoy.txt summary: The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. In temperate regions of the globe, the incidence of respiratory enveloped viruses, such as influenza and endemic human coronaviruses peak in winter months, usually in January and February, which is considered due to indoor social crowding with droplet and contact transmission and the added effect of low indoor relative humidity (RH). abstract: The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. Patients admitted to a pediatric hospital with worsening respiratory symptoms were tested using a multiplex PCR assay from nasopharyngeal swabs. The additive seasonal effects of outdoor temperatures and indoor relative humidity (RH) were evaluated. The 8-year average peak activity of human coronaviruses occurred in the first week of January, when droplet and contact transmission was enabled by the low indoor RH of 20-30%. Previous studies have shown that an increase in RH to 50% has been associated with markedly reduced viability and transmission of influenza virus and animal coronaviruses. As disease incidence was reduced by 50% in early March, to 75% in early April, to greater than 99% at the end of April, a relationship was observed from colder temperatures in January with a low indoor RH to a gradual increase in outdoor temperatures in April with an indoor RH of 45-50%. As a lipid-bound, enveloped virus with similar size characteristics to endemic human coronaviruses, SARS-CoV-2 should be subject to the same dynamics of reduced viability and transmission with increased humidity. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. url: http://medrxiv.org/cgi/content/short/2020.05.15.20103416v1?rss=1 doi: 10.1101/2020.05.15.20103416 id: cord-317622-o10ntfi8 author: Evans, Ronald M. title: Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing date: 2020-09-11 words: 4646.0 sentences: 230.0 pages: flesch: 39.0 cache: ./cache/cord-317622-o10ntfi8.txt txt: ./txt/cord-317622-o10ntfi8.txt summary: In patients, severity of liver disease correlates inversely with VDR expression, levels of vitamin D, and metabolites (Oh et al., 2020) , and hepatocellular injury directly with progressive COVID-19 (Henry et al., 2020; Ji et al., 2020) . Similar effects were observed in non-lung models; e.g., vitamin D deficiency (or VDR knockout) was associated with increased renin and Ang II (and IL-6 and TGFb) levels in diabetic mice (Zhang et al., 2008) . Human intestinal organoids (ACE2 expressing), suggesting a gut enterocyte reservoir for SARS-CoV-2, fuel viral spread and cytokine response in COVID-19 pathogenesis, another potential enteric-phase inflammatory hurdle to oral vitamin D administration (Clevers, 2020) . Heightened basal RAS (e.g., reduced ACE2 expression, higher Ang II levels) activation and inflammatory states (Ajilore and Thames, 2020; Albert and Ridker, 2004; Suthanthiran et al., 2000; Vinciguerra and Greco, 2020) , reported in African Americans, are associated with severe COVID-19 outcomes and relevant risk co-morbidities (e.g., hypertension, diabetes), some linked to vitamin D deficiency (Rostand, 2010; Yancy, 2020) . abstract: SARS-CoV-2 pneumonitis can quickly strike to incapacitate the lung, leading to severe disease and sometimes death. In this perspective, we suggest that vitamin D deficiency and the failure to activate the vitamin D receptor (VDR) can aggravate this respiratory syndrome by igniting a wounding response in stellate cells of the lung. The FDA-approved injectable vitamin D analog, paricalcitol, suppresses stellate cell-derived murine hepatic and pancreatic pro-inflammatory and pro-fibrotic changes. Therefore, we suggest a possible parallel program in the pulmonary stellate cells of COVID-19 patients and propose repurposing paricalcitol infusion therapy to restrain the COVID-19 cytokine storm. This proposed therapy could prove important to people of color who have higher COVID-19 mortality rates and lower vitamin D levels. url: https://doi.org/10.1016/j.cmet.2020.09.007 doi: 10.1016/j.cmet.2020.09.007 id: cord-261307-qmh3wtqo author: Evans, Scott E. title: Inducible Epithelial Resistance against Coronavirus Pneumonia in Mice date: 2020-10-17 words: 658.0 sentences: 38.0 pages: flesch: 44.0 cache: ./cache/cord-261307-qmh3wtqo.txt txt: ./txt/cord-261307-qmh3wtqo.txt summary: , a single PUL-042 treatment significantly improved survival of otherwise lethal SARS-CoV infection and significantly reduced the lung MERS-CoV burden 3 days after challenge, congruent with our prior work demonstrating a consistent correlation between survival advantage and reduced pathogen burden. Although it is suspected that a second pandemic wave may arise concurrently with seasonal influenza, a patient with a virus-like illness can be preemptively treated with PUL-042 with the expectation that she or he will appreciate a benefit, whether the syndrome results from SARS-CoV-2, influenza A, both viruses, or another pathogen. The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents the latest threat to global health security, and the pressure to identify effective therapeutics during this pandemic is immense. After an early report of a "cytokine storm" in patients with coronavirus disease (COVID-19) , there is increased interest in anti-IL-6 therapy as a treatment option, with ill-defined criteria for use (1). Inducible epithelial resistance against acute Sendai virus infection prevents chronic asthma-like lung disease in mice abstract: nan url: https://doi.org/10.1165/rcmb.2020-0247le doi: 10.1165/rcmb.2020-0247le id: cord-325936-rwxg187r author: Eyal, Nir title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 words: 2220.0 sentences: 115.0 pages: flesch: 51.0 cache: ./cache/cord-325936-rwxg187r.txt txt: ./txt/cord-325936-rwxg187r.txt summary: To minimize risk to participants, live SARS-CoV-2 vaccine challenge trials would need to recruit participants who, in the-likely-event of infection, would remain at relatively low fatality risk. Shortly after HIV sterilizing cure trials transplanted allogenic stem cell in participants, with well over a thousand times the fatal risk of SARS-Cov-2 infection in healthy young participants [17, 18] , AIDS activist David Evans interviewed the participants of these risky trials and concluded, "We should recognize their great capacity to understand the risks they may confront as research participants and, after a careful ethical and scientific review, respect the motivations of those who decide that the benefits of knowing that their contributions may help others outweighs the risks" [19] . That is not the case for COVID-19, which means that adequately communicating about and assessing potential risks and benefits of participating in a challenge study and ensuring appropriate informed consent may be impossible. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32591984/ doi: 10.1007/s10461-020-02953-8 id: cord-285159-gytebbua author: Eydoux, Cecilia title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 words: 3603.0 sentences: 215.0 pages: flesch: 59.0 cache: ./cache/cord-285159-gytebbua.txt txt: ./txt/cord-285159-gytebbua.txt summary: Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). abstract: The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) emergence in 2003 introduced the first serious human coronavirus pathogen to an unprepared world. To control emerging viruses, existing successful anti(retro)viral therapies can inspire antiviral strategies, as conserved viral enzymes (eg., viral proteases and RNA-dependent RNA polymerases) represent targets of choice. Since 2003, much effort has been expended in the characterization of the SARS-CoV replication/transcription machinery. Until recently, a pure and highly active preparation of SARS-CoV recombinant RNA synthesis machinery was not available, impeding target-based high throughput screening of drug candidates against this viral family. The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. This phylogenetic relatedness highlights the potential use of conserved replication enzymes to discover inhibitors against this significant pathogen, which in turn, contributes to scientific preparedness against emerging viruses. Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. The screening of a small (1,520 compounds) chemical library of FDA-approved drugs demonstrates the robustness of our assay and will allow to speed-up drug repositioning or novel drug discovery against the SARS-CoV-2. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights - A new SARS-CoV non radioactive RNA polymerase assay is described - The robotized assay is suitable to identify RdRp inhibitors based on HTS url: https://doi.org/10.1101/2020.07.07.192005 doi: 10.1101/2020.07.07.192005 id: cord-263583-a1zon98c author: Fabbris, Cristoforo title: Is oro/nasopharyngeal swab for SARS-CoV-2 detection a safe procedure? Complications observed among a case series of 4876 consecutive swabs date: 2020-10-13 words: 760.0 sentences: 52.0 pages: flesch: 52.0 cache: ./cache/cord-263583-a1zon98c.txt txt: ./txt/cord-263583-a1zon98c.txt summary: In this paper we present the complications encountered in a series of healthworkers who underwent oro/nasopharyngeal swab for detection of SARS-CoV-2. All patients underwent sampling with a sterile collection Citoswab® (Citotest Labware Manufacturing Co., LTD) All reports, possible complications and clinical information were noted from registries of the infectious disease units and medical records. One patient, affected by diabetes mellitus and neutropenia, developed septal abscess (case 2) and another, who later was observed to have septal deviation, had severe anterior and posterior bleeding from an arterial point of the olfactory area, possibly arising from the anterior ethmoidal artery (case 3) requiring surgical cauterization. However arterial rupture can give catastrophic bleed as seen in one patient: we suspect the septal deviation may have misled the swabbing process to the upper part of nares where trauma to the anterior ethmoidal artery may have occurred. In conclusion, oro/nasopharyngeal swabs are safe procedures to detect SARS-CoV-2 infection. abstract: nan url: https://doi.org/10.1016/j.amjoto.2020.102758 doi: 10.1016/j.amjoto.2020.102758 id: cord-298056-svwtfshi author: Fabio, Ciceri title: Early predictors of clinical outcomes of COVID-19 outbreak in Milan, Italy date: 2020-06-12 words: 3319.0 sentences: 169.0 pages: flesch: 46.0 cache: ./cache/cord-298056-svwtfshi.txt txt: ./txt/cord-298056-svwtfshi.txt summary: Multivariable analysis showed older age, coronary artery disease, cancer, low lymphocyte count and high RALE score as factors independently associated with an increased risk of mortality. CONCLUSION: In a large cohort of COVID-19 patients of European origin, main risk factors for mortality were older age, comorbidities, low lymphocyte count and high RALE. 14 In this report we describe the demographical, clinical, radiological and laboratory characteristics, as well as the clinical outcomes and the risk factors for mortality, of the first 500 patients with COVID-19 admitted to San Raffaele Scientific Institute, a tertiary care academic hospital in Milan, Italy. With a clinical observation longer than one months from the last patient admitted, w e were able to identify early predictors of mortality related to patient characteristics, radiological and laboratory findings at hospital admission for COVID-19. abstract: BACKGROUND: National health-system hospitals of Lombardy faced a heavy burden of admissions for acute respiratory distress syndromes associated with coronavirus disease (COVID-19). Data on patients of European origin affected by COVID-19 are limited. METHODS: All consecutive patients aged ≥18 years, coming from North-East of Milan's province and admitted at San Raffaele Hospital with COVID-19, between February 25th and March 24th, were reported, all patients were followed for at least one month. Clinical and radiological features at admission and predictors of clinical outcomes were evaluated. RESULTS: Of the 500 patients admitted to the Emergency Unit, 410 patients were hospitalized and analyzed: median age was 65 (IQR 56–75) years, and the majority of patients were males (72.9%). Median (IQR) days from COVID-19 symptoms onset was 8 (5–11) days. At hospital admission, fever (≥ 37.5 °C) was present in 67.5% of patients. Median oxygen saturation (SpO2) was 93% (range 60–99), with median PaO(2)/FiO(2) ratio, 267 (IQR 184–314). Median Radiographic Assessment of Lung Edema (RALE) score was 9 (IQR 4–16). More than half of the patients (56.3%) had comorbidities, with hypertension, coronary heart disease, diabetes and chronic kidney failure being the most common. The probability of overall survival at day 28 was 66%. Multivariable analysis showed older age, coronary artery disease, cancer, low lymphocyte count and high RALE score as factors independently associated with an increased risk of mortality. CONCLUSION: In a large cohort of COVID-19 patients of European origin, main risk factors for mortality were older age, comorbidities, low lymphocyte count and high RALE. url: https://www.sciencedirect.com/science/article/pii/S1521661620304563?v=s5 doi: 10.1016/j.clim.2020.108509 id: cord-256020-wrui3i2l author: Fadaka, Adewale Oluwaseun title: Understanding the epidemiology, pathophysiology, diagnosis and management of SARS-CoV-2 date: 2020-08-26 words: 7097.0 sentences: 465.0 pages: flesch: 49.0 cache: ./cache/cord-256020-wrui3i2l.txt txt: ./txt/cord-256020-wrui3i2l.txt summary: The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The disease is caused by SARS-CoV-2, a zoonotic pathogen that acquired mutations as it crossed the species barrier from bat to pangolin enabling it to infect humans. 5 The clinical symptoms of COVID-19 include fever, cough, and pneumonia, which makes the disease enormously dangerous with a high case fatality rate. 11 Symptoms of human SARS-CoV-1 infections include headache, fever and respiratory complications such as cough, dyspnea, and pneumonia. 81 The main goal of SARS-CoV-2 diagnosis is to accurately detect the virus and to minimize further transmissions by timely isolation and treatment of infected patients. 112 This implies that variation in ACE-2 expression in COVID-19 patients is likely to affect susceptibility, symptoms and intervention outcomes following SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations abstract: The emergence of coronavirus disease 2019 (COVID-19) in December 2019 has resulted in over 20 million cases and 741,808 deaths globally, affecting more than 200 countries. COVID-19 was declared a pandemic on 11 March 2020 by the World Health Organization. The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). There is limited information on COVID-19, and treatment has so far focused on supportive care and use of repurposed drugs. COVID-19 can be transmitted via person-to-person contact through droplet spread. Some of the recommended precautionary measures to reduce the rate of disease spread include social distancing, good hygiene practices, and avoidance of crowded areas. These measures are effective because the droplets are heavy and can only travel approximately 1 meter in the air, settling quickly on fixed surfaces. Promising strategies to combat SARS-CoV-2 include discovery of therapeutic targets/drugs and vaccines. In this review, we summarize the epidemiology, pathophysiology, and diagnosis of COVID-19. We also address the mechanisms of action of approved repurposed drugs for therapeutic management of the disease. url: https://doi.org/10.1177/0300060520949077 doi: 10.1177/0300060520949077 id: cord-281684-m3m4mhye author: Fagre, Anna C. title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date: 2020-09-28 words: 3707.0 sentences: 212.0 pages: flesch: 47.0 cache: ./cache/cord-281684-m3m4mhye.txt txt: ./txt/cord-281684-m3m4mhye.txt summary: title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. However, to date, there has been only a gross histological analysis of the lung pathological changes following infection and the impact of SARS-CoV-2 neutralizing antibody clones on lung immune infiltrates has yet to be fully assessed. Those antibody clones that blocked the interaction of the RBD with ACE2 and bound to native spike protein were then tested for neutralization of SARS-CoV-2 in a cytopathic effect (CPE) assay with Vero E6 cells. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity abstract: The emergence of COVID-19 has led to a pandemic that has caused millions of cases of disease, variable morbidity and hundreds of thousands of deaths. Currently, only remdesivir and dexamethasone have demonstrated limited efficacy, only slightly reducing disease burden, thus novel approaches for clinical management of COVID-19 are needed. We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. Administration of the lead antibody clone to Syrian hamsters challenged with SARS-CoV-2 significantly reduced viral load and histopathology score in the lungs. Moreover, the antibody interrupted monocyte infiltration into the lungs, which may have contributed to the reduction of disease severity by limiting immunopathological exacerbation. The use of this antibody could provide an important therapy for treatment of COVID-19 patients. url: https://doi.org/10.1101/2020.09.25.313601 doi: 10.1101/2020.09.25.313601 id: cord-257584-v38tjof3 author: Fahmi, Muhamad title: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date: 2020-03-03 words: 2933.0 sentences: 180.0 pages: flesch: 49.0 cache: ./cache/cord-257584-v38tjof3.txt txt: ./txt/cord-257584-v38tjof3.txt summary: Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45). abstract: The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV. url: https://doi.org/10.1016/j.meegid.2020.104272 doi: 10.1016/j.meegid.2020.104272 id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 words: 4842.0 sentences: 263.0 pages: flesch: 54.0 cache: ./cache/cord-279576-wt4crton.txt txt: ./txt/cord-279576-wt4crton.txt summary: Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . abstract: The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. In the interest of economy, time and availability of chemicals and consumables, the SYBR Green-based detection was implemented to establish a convenient assay. Therefore, we adapted one of WHO recommended Taqman-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results suggest that SYBR-Green detection represents a reliable cost-effective alternative to increase the testing capacity. url: https://doi.org/10.1101/2020.05.13.093609 doi: 10.1101/2020.05.13.093609 id: cord-316080-y6ypbdtu author: Fajnzylber, J. M. title: SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality date: 2020-07-17 words: 1701.0 sentences: 124.0 pages: flesch: 53.0 cache: ./cache/cord-316080-y6ypbdtu.txt txt: ./txt/cord-316080-y6ypbdtu.txt summary: We quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. Amongst the participants hospitalized with COVID-19, higher prevalence of detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. Amongst hospitalized individuals, the majority still 92 had detectable SARS-CoV-2 RNA at the time of initial sample collection, including 50% with variable, individuals with detectable plasma, nasopharyngeal or sputum viral loads had 124 significantly lower absolute lymphocyte counts, and higher CRP and IL-6 levels compared to 125 those without detectable plasma viremia (Fig 2b-d) . . https://doi.org/10.1101/2020.07.15.20131789 doi: medRxiv preprint DISCUSSION 151 We report a comprehensive analysis of SARS-CoV-2 respiratory tract, plasma, and urine viral 152 loads of 235 participants who were either hospitalized with COVID-19, evaluated as 153 symptomatic outpatients, or had recovered from COVID-19 disease. abstract: The relationship between SARS-CoV-2 viral load and risk of disease progression remains largely undefined in coronavirus disease 2019 (COVID-19). We quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. SARS-CoV-2 plasma RNA was detected in 27% of hospitalized participants and 13% of outpatients diagnosed with COVID-19. Amongst the participants hospitalized with COVID-19, higher prevalence of detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. SARS-CoV-2 viral loads, especially plasma viremia, were associated with increased risk of mortality. SARS-CoV-2 viral load may aid in the risk stratification of patients with COVID-19 and its role in disease pathogenesis should be further explored. url: https://doi.org/10.1101/2020.07.15.20131789 doi: 10.1101/2020.07.15.20131789 id: cord-316095-jzyb4jn5 author: Falahchai, Mehran title: Dental care management during the COVID‐19 outbreak date: 2020-09-19 words: 5601.0 sentences: 369.0 pages: flesch: 50.0 cache: ./cache/cord-316095-jzyb4jn5.txt txt: ./txt/cord-316095-jzyb4jn5.txt summary: Sixteen English papers were enrolled to answer questions about procedures that are allowed to perform during the COVID‐19 outbreak, patients who are in priority to receive dental care services, the conditions and necessities for patient admission, waiting room and operatory room, and personal protective equipment (PPE) that is necessary for dental clinicians and the office staff. Considering the generation of high amounts of droplets and aerosols during routine dental procedures, the conventional protective measures that are routinely followed by dental clinicians are no longer efficient for prevention of COVID-19 transmission. Urgent dental treatments include management of conditions that require immediate attention such as alleviation of severe pain with/without the risk of infection and balancing the patient load in the hospital emergency departments. According to the data acquired from the screening questionnaires, patients who need emergency/urgent dental treatment can be divided into three groups of apparently healthy, suspected, and confirmed cases. abstract: AIM: The level of preparedness of the healthcare system plays an important role in management of coronavirus disease 2019 (COVID‐19). This study attempted to devise a comprehensive protocol regarding dental care during the COVID‐19 outbreak. METHODS AND RESULT: Embase, PubMed, and Google Scholar were searched until March 2020 for relevant papers. Sixteen English papers were enrolled to answer questions about procedures that are allowed to perform during the COVID‐19 outbreak, patients who are in priority to receive dental care services, the conditions and necessities for patient admission, waiting room and operatory room, and personal protective equipment (PPE) that is necessary for dental clinicians and the office staff. CONCLUSION: Dental treatment should be limited to patients with urgent or emergency situation. By screening questionnaires for COVID‐19, patients are divided into three groups of (a) apparently healthy, (b) suspected for COVID‐19, and (c) confirmed for COVID‐19. Separate waiting and operating rooms should be assigned to each group of patients to minimize the risk of disease transmission. All groups should be treated with the same protective measures with regard to PPE for the dental clinicians and staff. url: https://doi.org/10.1111/scd.12523 doi: 10.1111/scd.12523 id: cord-270661-e83xe4sp author: Falahi, Shahab title: Transmission routes for SARS-COV-2 infection: Review of Evidence date: 2020-10-06 words: 1274.0 sentences: 90.0 pages: flesch: 57.0 cache: ./cache/cord-270661-e83xe4sp.txt txt: ./txt/cord-270661-e83xe4sp.txt summary: Subsequent studies have shown that the virus is also present in saliva; given the evidence of virus transmission from asymptomatic individuals(1) and the presence of the virus in saliva, it has been suggested that even secretory droplets during normal speeching may be a route to transmit SARS-COV-2 (2). In a number of studies, the SARS-CoV-2 genome was identified in blood samples from a number of patients with COVID-19 (15, 16) , and subsequently raised the question: Is SARS-CoV-2 transmitted through transfusion? In a study, all blood samples of asymptomatic people with COVID-19 were negative for SARS-COV-2 PCR and RNAemia was detected in severe and symptomatic cases. Sexual transmission: SARS-COV-2 is present in saliva and feces, and in theory it is possible to transmit through oral-anal intercourse (17) but this sexual habit is not common, so it is unlikely that this route will be a significant mean of transmission. abstract: • Airborne transmission of SARS-COV-2 emphasizes the importance of using face masks in public, crowded and closed places as the most important preventive measure. • household contact tracing of index COVID-19 cases can be applied as important part of COVID-19 control programs. • Vertical transmission of SARS-COV-2 seems possible, but the risk is very low. • in theory, SARS-COV-2 may transmit through oral-anal intercourse, it is unlikely that this route will be a significant mean of transmission. • similarity of SARS-COV-2 with SARS, supports the hypothesis of non-transmission through blood. url: https://www.sciencedirect.com/science/article/pii/S205229752030130X?v=s5 doi: 10.1016/j.nmni.2020.100778 id: cord-340357-gyvvcnuf author: Fallahi, Hamid Reza title: Being a front-line dentist during the Covid-19 pandemic: a literature review date: 2020-04-24 words: 3777.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-340357-gyvvcnuf.txt txt: ./txt/cord-340357-gyvvcnuf.txt summary: This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. The purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the CDC and the ADA guidelines. Due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for 2019-nCoV infection. 2019-nCoV transmission in dental settings occurs through four major routes: (1) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials; abstract: Coronavirus is an enveloped virus with positive-sense single-stranded RNA. Coronavirus infection in humans mainly affects the upper respiratory tract and to a lesser extent the gastrointestinal tract. Clinical symptoms of coronavirus infections can range from relatively mild (similar to the common cold) to severe (bronchitis, pneumonia, and renal involvement). The disease caused by the 2019 novel coronavirus (2019-nCoV) was called Covid-19 by the World Health Organization in February 2020. Face-to-face communication and consistent exposure to body fluids such as blood and saliva predispose dental care workers at serious risk for 2019-nCoV infection. As demonstrated by the recent coronavirus outbreak, information is not enough. During dental practice, blood and saliva can be scattered. Accordingly, dental practice can be a potential risk for dental staff, and there is a high risk of cross-infection. This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. url: https://doi.org/10.1186/s40902-020-00256-5 doi: 10.1186/s40902-020-00256-5 id: cord-273685-oxvfxmtr author: Fan, Qihong title: Anal swab findings in an infant with COVID‐19 date: 2020-03-17 words: 1250.0 sentences: 89.0 pages: flesch: 61.0 cache: ./cache/cord-273685-oxvfxmtr.txt txt: ./txt/cord-273685-oxvfxmtr.txt summary: In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in pharyngeal swab and anal swab were compared. In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in pharyngeal swab and anal swab were compared. The oropharyngeal specimen showed negative result for SARS-CoV-2 on the 14th day after onset of the illness. However, the anal swab was still positive for SARS-CoV-2 on the 28th day after the onset of the illness. COVID-19, Anal swab, SARS-CoV-2, Fecal-oral transmission confirmed in China with at least 3042 reported deaths. Several reports noted that the stool specimens from the patients with COVID-19 were positive for the novel SARS-CoV-2. However, the anal swabs remained positive for SARS-CoV-2 on the 28th day after the onset of the illness (Table 1) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: INTRODUCTION: The transmission pathways of coronavirus disease 2019 (COVID‐19) remain not completely clear. In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in pharyngeal swab and anal swab were compared. CASE PRESENTATION: A 3‐month‐old girl was admitted to our hospital with COVID‐19. Her parents had both been diagnosed with COVID‐19. The results of pharyngeal swab and anal swab of the little girl were recorded and compared during the course of the disease. The oropharyngeal specimen showed negative result for SARS‐CoV‐2 on the 14th day after onset of the illness. However, the anal swab was still positive for SARS‐CoV‐2 on the 28th day after the onset of the illness. CONCLUSION: The possibility of fecal‐oral transmission of COVID‐19 should be assessed. Personal hygiene during home quarantine merits considerable attention. url: https://doi.org/10.1002/ped4.12186 doi: 10.1002/ped4.12186 id: cord-337297-fkw8780t author: Fan, Siyuan title: Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study date: 2020-07-10 words: 4698.0 sentences: 267.0 pages: flesch: 41.0 cache: ./cache/cord-337297-fkw8780t.txt txt: ./txt/cord-337297-fkw8780t.txt summary: Methods: This retrospective single-center case series analyzed critically ill patients with COVID-19 at the intensive care unit of Tongji Hospital, Wuhan, China from February 5 to April 2, 2020. Herein, we conducted a retrospective study to analyze the neurological manifestations of critically ill patients with COVID-19 in intensive care units (ICU) to explore various pathophysiological mechanisms that could contribute to neurological complications in these patients. COVID-19, corona virus disease 2019; AIS, acute ischemic stroke; WBC, white blood cell; ALT, alanine transaminase, cTnI, High-sensitive cardiac troponin I; NT-proBNP, N-terminal prohormone of brain natriuretic peptide; LDL-C, low-density-lipoprotein cholesterol; aPTT, activated partial thromboplastin time; hsCRP, high sensitivity C-reactive protein; LDH, lactate dehydrogenase; IQR, interquartile range. The clinical spectrum of neurological complications in critically ill patients with COVID-19 was broad, including delirium, acute ischemic stroke, intracerebral hemorrhage, hypoxic-ischemic brain injury, flaccid paralysis and rhabdomyolysis. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: Background: The complications of coronavirus disease 2019 (COVID-19) involved multiple organs or systems, especially in critically ill patients. We aim to investigate the neurological complications in critically ill patients with COVID-19. Methods: This retrospective single-center case series analyzed critically ill patients with COVID-19 at the intensive care unit of Tongji Hospital, Wuhan, China from February 5 to April 2, 2020. Demographic data, clinical and laboratory findings, comorbidities and treatments were collected and analyzed. Results: Among 86 patients with confirmed COVID-19, 54 patients (62.8%) were male, and the mean (SD) age was 66.6 (11.1) years. Overall, 65% patients presented with at least one neurological symptom. Twenty patients (23.3%) had symptoms involving the central nervous system, including delirium, cerebrovascular diseases and hypoxic-ischemic brain injury, while 6 patients (7%) had neuromuscular involvement. Seven of 86 patients exhibited new stroke and 6 (7%) cases were ischemic. A significantly higher prevalence of antiphospholipid antibodies was observed in patients with ischemic stroke than in those without stroke (83.3 vs. 26.9%, p < 0.05). Patients with ischemic stroke were more likely to have a higher myoglobulin level, and a lower hemoglobin level. Conclusions: The clinical spectrum of neurological complications in critically ill patients with COVID-19 was broad. Stroke, delirium and neuromuscular diseases are common neurological complications of COVID-19. Physicians should pay close attention to neurological complications in critically ill patients with COVID-19. url: https://doi.org/10.3389/fneur.2020.00806 doi: 10.3389/fneur.2020.00806 id: cord-318204-t024w7h6 author: Fang, Ferric C title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date: 2020-06-08 words: 2976.0 sentences: 218.0 pages: flesch: 51.0 cache: ./cache/cord-318204-t024w7h6.txt txt: ./txt/cord-318204-t024w7h6.txt summary: As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection abstract: Diagnostic testing has played and will continue to play a major role in the COVID-19 pandemic. The ability to detect the SARS-CoV-2 coronavirus in respiratory secretions is essential to determine when an individual is infected and potentially infectious to others. Viral detection is used for the identification, management and isolation of individual patients. Viral detection is also used to determine when the virus has entered a community and how rapidly it is spreading. As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. Here we discuss questions commonly asked by clinicians about COVID-19 diagnostic testing. url: https://www.ncbi.nlm.nih.gov/pubmed/32511679/ doi: 10.1093/cid/ciaa742 id: cord-277188-t33nw4zb author: Fang, Jie title: Efficacy of Early Combination Therapy With Lianhuaqingwen and Arbidol in Moderate and Severe COVID-19 Patients: A Retrospective Cohort Study date: 2020-09-18 words: 4641.0 sentences: 227.0 pages: flesch: 46.0 cache: ./cache/cord-277188-t33nw4zb.txt txt: ./txt/cord-277188-t33nw4zb.txt summary: RESULTS: The early combined usage of LHQW and Arbidol can significantly accelerate the recovery of patients with moderate COVID-19 by reducing the time to conversion to nucleic acid negativity, the time to chest CT improvement, and the length of hospital stay. One case report of four patients with mild or severe COVID-19 in Shanghai (China) found that combining antiviral drugs (lopinavir/ ritonavir or Arbidol) with TCM (Shufengjiedu capsule) resulted in a significant improvement in clinical symptoms . In conclusion, this retrospective study demonstrated that the early administration of LHQW + Arbidol combination therapy could significantly accelerate recovery in patients with moderate COVID-19 by reducing the time to conversion to nucleic acid Frontiers in Pharmacology | www.frontiersin.org September 2020 | Volume 11 | Article 560209 negativity, the time to chest CT improvement and the length of hospital stay. abstract: OBJECTIVE: Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan City, China, coronavirus disease 2019 (COVID-19) has become a global pandemic. However, no special therapeutic drugs have been identified for COVID-19. The aim of this study was to search for drugs to effectively treat COVID-19. MATERIALS AND METHODS: We conducted a retrospective cohort study with a total of 162 adult inpatients (≥18 years old) from Ruijin Hospital (Shanghai, China) and Tongji Hospital (Wuhan, China) between January 27, 2020, and March 10, 2020. The enrolled COVID-19 patients were first divided into the Lianhuaqingwen (LHQW) monotherapy group and the LHQW + Arbidol combination therapy group. Then, these two groups were further classified into moderate and severe groups according to the clinical classification of COVID-19. RESULTS: The early combined usage of LHQW and Arbidol can significantly accelerate the recovery of patients with moderate COVID-19 by reducing the time to conversion to nucleic acid negativity, the time to chest CT improvement, and the length of hospital stay. However, no benefit was observed in severe COVID-19 patients treated with the combination of LHQW + Arbidol. In this study, both Arbidol and LHQW were well tolerated without serious drug-associated adverse events. CONCLUSION: The early combined usage of LHQW and Arbidol may accelerate recovery and improve the prognosis of patients with moderate COVID-19. url: https://doi.org/10.3389/fphar.2020.560209 doi: 10.3389/fphar.2020.560209 id: cord-346092-fo83f99f author: Fang, Li‐Qun title: Geographical spread of SARS in mainland China date: 2009-06-05 words: 2763.0 sentences: 126.0 pages: flesch: 50.0 cache: ./cache/cord-346092-fo83f99f.txt txt: ./txt/cord-346092-fo83f99f.txt summary: Objectives To describe the spatiotemporal diffusion of the severe acute respiratory syndrome (SARS) epidemic in mainland China, and to analyse the spatial pattern of SARS transmission from the Beijing epicentre to its neighbouring areas. SARS cases that got infected in Beijing but were reported in three provinces surrounding Beijing were mapped, and logistic regression using a ''case–control'' design at the county level was performed to analyse the impact of travel‐related risk factors in the diffusion pattern. Results The SARS epidemic in mainland China spanned a large geographical extent but clustered in two areas: first in Guangdong Province, and about 3 months later in Beijing with its surrounding areas in Shanxi Province, Inner Mongolia Autonomic Region, Hebei Province and Tianjin. Using the tracking analysis, we identified geographic features associated with SARS outbreaks in mainland We found that 34 SARS cases became infected in Beijing and travelled to the Inner Mongolia Autonomic Region, Shanxi Province or Hebei Province after onset, and were reported by hospitals outside Beijing. abstract: Objectives To describe the spatiotemporal diffusion of the severe acute respiratory syndrome (SARS) epidemic in mainland China, and to analyse the spatial pattern of SARS transmission from the Beijing epicentre to its neighbouring areas. Methods Probable SARS cases occurring between November 2002 and May 2003 in mainland China were compiled from different sources and geo‐coded into a geographical information database based on onset location. Spatial analyses including kernel density estimation, and spatial statistical and tracking analyses were performed to characterise the spatiotemporal distribution of SARS cases based on onset location/date. SARS cases that got infected in Beijing but were reported in three provinces surrounding Beijing were mapped, and logistic regression using a ‘case–control’ design at the county level was performed to analyse the impact of travel‐related risk factors in the diffusion pattern. Results The SARS epidemic in mainland China spanned a large geographical extent but clustered in two areas: first in Guangdong Province, and about 3 months later in Beijing with its surrounding areas in Shanxi Province, Inner Mongolia Autonomic Region, Hebei Province and Tianjin. Counties in the neighbourhood of Beijing that were crossed by a national highway or inter‐provincial freeway showed the highest risk of acquiring SARS infections, even after correction for population density and medical staff density. Being intersected by a railway did not significantly associate with risk of SARS. Conclusions This study provides the first complete documentation of the spatial and temporal characteristics of the SARS epidemic in mainland China. Our analyses confirmed that SARS had benefited from national highways and inter‐provincial freeways for its spread from epicentres to neighbouring areas, whereas trains showed no significant association. This knowledge may be important for the control of re‐emerging SARS, or other future emerging human‐to‐human transmittable infections. url: https://doi.org/10.1111/j.1365-3156.2008.02189.x doi: 10.1111/j.1365-3156.2008.02189.x id: cord-274279-f99nd3dx author: Fantini, Jacques title: Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection date: 2020-04-03 words: 4442.0 sentences: 271.0 pages: flesch: 56.0 cache: ./cache/cord-274279-f99nd3dx.txt txt: ./txt/cord-274279-f99nd3dx.txt summary: Using a combination of structural and molecular modelling approaches, this study showed that chloroquine (CLQ), one of the drugs currently under investigation for SARS-CoV-2 treatment, binds sialic acids and gangliosides with high affinity. A ganglioside-binding site in the Nterminal domain (NTD) of the spike (S) glycoprotein of SARS-CoV-2 was identified, and CLQ was shown to be a potential blocker of the S-ganglioside interaction which occurs in the first step of the viApril 10, 2020; 14:43 ] ral replication cycle (i.e. attachment to the surface of respiratory cells, mediated by the S protein). At this stage, attachment of the NTD to the ganglioside-rich microdomain involved the whole interface (i.e. Table 1 Energy of interaction of each amino acid residue of SARS-CoV-2 spike protein in contact with GM1 molecules. As CLQ and CLQ-OH are potential therapies for SARS-CoV-2 infection, it is important to check whether the amino acid residues identified as critical for ganglioside binding are conserved among clinical isolates. abstract: ABSTRACT The recent emergence of the novel pathogenic SARS-coronavirus 2 (SARS-CoV-2) is responsible for a worldwide pandemic. Given the global health emergency, drug repositioning is the most reliable option to design an efficient therapy for infected patients without delay. The first step of the viral replication cycle [i.e. attachment to the surface of respiratory cells, mediated by the spike (S) viral protein] offers several potential therapeutic targets. The S protein uses the angiotension-converting enzyme-2 (ACE-2) receptor for entry, but also sialic acids linked to host cell surface gangliosides. Using a combination of structural and molecular modelling approaches, this study showed that chloroquine (CLQ), one of the drugs currently under investigation for SARS-CoV-2 treatment, binds sialic acids and gangliosides with high affinity. A new type of ganglioside-binding domain at the tip of the N-terminal domain of the SARS-CoV-2 S protein was identified. This domain (111–158), which is fully conserved among clinical isolates worldwide, may improve attachment of the virus to lipid rafts and facilitate contact with the ACE-2 receptor. This study showed that, in the presence of CLQ [or its more active derivative, hydroxychloroquine (CLQ-OH)], the viral S protein is no longer able to bind gangliosides. The identification of this new mechanism of action of CLQ and CLQ-OH supports the use of these repositioned drugs to cure patients infected with SARS-CoV-2. The in-silico approaches used in this study might also be used to assess the efficiency of a broad range of repositioned and/or innovative drug candidates before clinical evaluation. url: https://api.elsevier.com/content/article/pii/S0924857920301102 doi: 10.1016/j.ijantimicag.2020.105960 id: cord-347121-5drl3xas author: Farah, I. title: A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform. date: 2020-09-29 words: 16886.0 sentences: 784.0 pages: flesch: 48.0 cache: ./cache/cord-347121-5drl3xas.txt txt: ./txt/cord-347121-5drl3xas.txt summary: The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The platform is a proven research ecosystem used by universities, biotech, and bioinformatics organizations to share and analyze omics data and can be used for a variety of use cases; from precision medicine, drug discovery, translational science to building data repositories, and tackling a disease outbreak. Our approach is designed to provide healthcare professionals with an urgently needed platform to find and analyze genetic data, and securely and anonymously share sensitive patient data to fight the disease outbreak. Among other use-cases, the provided platform can be used to rapidly study SARS-CoV-2, including analyses of the host response to COVID-19 disease, establish a multi-institutional collaborative datahub for rapid response for current and future pandemics, characterizing potential co-infections, and identifying potential therapeutic targets for preclinical and clinical development. abstract: Under public health emergencies, particularly an early epidemic, it is fundamental that genetic and other healthcare data is shared across borders in both a timely and accurate manner before the outbreak of a global pandemic. However, although the COVID-19 pandemic has created a tidal wave of data, most patient data is siloed, not easily accessible, and due to low sample size, largely not actionable. Based on the precision medicine platform Shivom, a novel and secure data sharing and data analytics marketplace, we developed a versatile pandemic preparedness platform that allows healthcare professionals to rapidly share and analyze genetic data. The platform solves several problems of the global medical and research community, such as siloed data, cross-border data sharing, lack of state-of-the-art analytic tools, GDPR-compliance, and ease-of-use. The platform serves as a central marketplace of 'discoverability'. The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The bioinformatics marketplace contains some preinstalled COVID-19 pipelines to analyze virus- and host genomes without the need for bioinformatics expertise. The platform will be the quickest way to rapidly gain insight into the association between virus-host interactions and COVID-19 in various populations which can have a significant impact on managing the current pandemic and potential future disease outbreaks. url: https://doi.org/10.1101/2020.09.28.20203257 doi: 10.1101/2020.09.28.20203257 id: cord-313344-rqvi2ksc author: Farcas, Gabriella A. title: Fatal Severe Acute Respiratory Syndrome Is Associated with Multiorgan Involvement by Coronavirus date: 2005-01-15 words: 2427.0 sentences: 104.0 pages: flesch: 46.0 cache: ./cache/cord-313344-rqvi2ksc.txt txt: ./txt/cord-313344-rqvi2ksc.txt summary: Severe acute respiratory syndrome (SARS) is characterized by pulmonary compromise; however, patients often have evidence of other organ dysfunction that may reflect extrapulmonary dissemination of SARS coronavirus (SARS-CoV). The purpose of the present study was to investigate the presence of SARS-CoV, the degree of viral dissemination, and the viral loads in multiple organ samples from all patients who died of SARS during the Toronto outbreak (March to September 2003) and underwent a postmortem examination and compare the results with those found in patients who died of other causes during the outbreak. A total of 212 discrete postmortem organ samples, including lung, liver, spleen, kidney, small bowel, large bowel, lymph nodes, heart, and skeletal muscle, were prospectively collected from the 21 patients who died of SARS and underwent autopsies. abstract: Severe acute respiratory syndrome (SARS) is characterized by pulmonary compromise; however, patients often have evidence of other organ dysfunction that may reflect extrapulmonary dissemination of SARS coronavirus (SARS-CoV). We report on the distribution and viral load of SARS-CoV in multiple organ samples from patients who died of SARS during the Toronto outbreak. SARS-CoV was detected in lung (100%), bowel (73%), liver (41%), and kidney (38%) in 19 patients who died of SARS, with the highest viral loads observed in lung (1.0 × 10(10) copies/g) and bowel (2.7 × 10(9) copies/g). Fatal SARS was associated with multiorgan viral dissemination in a distribution that has implications for disease manifestation, viral shedding, and transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/15609228/ doi: 10.1086/426870 id: cord-340260-z13aa1wk author: Farewell, V. T. title: SARS incubation and quarantine times: when is an exposed individual known to be disease free? date: 2005-10-19 words: 4727.0 sentences: 232.0 pages: flesch: 55.0 cache: ./cache/cord-340260-z13aa1wk.txt txt: ./txt/cord-340260-z13aa1wk.txt summary: For the data set of averaged times, Figure 1 presents the proÿle likelihoods, L * P (M ), based on the gamma, log-normal and log-gamma models discussed in Section 2. For the truncated gamma model, the proÿle likelihood never drops below 60 per cent suggesting that any value of M greater than the maximum time observed, 14, is plausible. For public health purposes, it could therefore be argued that, based only on such data and an assumed log-normal model, that a quarantine time of 20 days might be necessary to ensure that SARS cases were not released ''too early''. Finally, to show the e ect of more extreme interval-censoring, we consider extending the set of data in Table II by including additional SARS cases from Hong Kong whose period of possible exposure, which deÿnes the width of the interval within which their incubation time lies, is thought to be less than 10 days rather than 5 days. abstract: The setting of a quarantine time for an emerging infectious disease will depend on current knowledge concerning incubation times. Methods for the analysis of information on incubation times are investigated with a particular focus on inference regarding a possible maximum incubation time, after which an exposed individual would be known to be disease free. Data from the Hong Kong SARS epidemic are used for illustration. The incorporation of interval‐censored data is considered and comparison is made with percentile estimation. Results suggest that a wide class of models for incubation times should be considered because the apparent informativeness of a likelihood depends on the choice and generalizability of a model. There will usually remain a probability of releasing from quarantine some infected individuals and the impact of early release will depend on the size of the epidemic. Copyright © 2005 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16237660/ doi: 10.1002/sim.2206 id: cord-354353-hyz0gmpz author: Farhangrazi, Z. Shadi title: Airborne Particulate Matter and SARS-CoV-2 Partnership: Virus Hitchhiking, Stabilization and Immune Cell Targeting — A Hypothesis date: 2020-09-24 words: 2465.0 sentences: 108.0 pages: flesch: 38.0 cache: ./cache/cord-354353-hyz0gmpz.txt txt: ./txt/cord-354353-hyz0gmpz.txt summary: While long-term exposure to air pollutants such as PM 2.5 and nitrous dioxide contributes to persistent inflammatory responses and cardiopulmonary diseases (7) , which might increase vulnerability to COVID-19, it is also plausible that depending on the environment SARS-CoV-2 "hitchhiking" on airborne PM pollutants might be an additional mechanism for spreading the infection. In summary, although long-term exposure to polluted air might increase vulnerability to COVID-19 through prior adverse cellular effects of settled PM (24), our proposed "hitchhiking" hypothesis offers an additional multi-mechanistic pathogenic process through delivery of low viral titres with diverse PM-virus composites and is applicable to both indoor and outdoor situations, where the pathogenic severity is dependent on PM concentration, composition, shape and size as well as the infectious viral load. Contrary to the suggestions that long-term exposure to PM might increase vulnerability to SAR-CoV-2 infection, inhaled PM might promote some forms of immunity to the virus in some individuals. abstract: nan url: https://doi.org/10.3389/fimmu.2020.579352 doi: 10.3389/fimmu.2020.579352 id: cord-322641-mz0b91xr author: Farnsworth, Christopher W title: SARS-CoV-2 Serology: Much Hype, Little Data date: 2020-04-28 words: 1566.0 sentences: 96.0 pages: flesch: 48.0 cache: ./cache/cord-322641-mz0b91xr.txt txt: ./txt/cord-322641-mz0b91xr.txt summary: In response to a lack of COVID-19 testing the FDA issued guidance regarding serologic assays, stating that although manufacturers could use the Emergency Use Authorization (EUA) pathway for approval, serologic assays could also be marketed in the US bypassing this approval process (2) . Serology has been suggested to play three roles in the COVID-19 pandemic; 1) diagnosis, 2) identification of convalescent plasma donors, 3) screening populations with the purpose of determining exposure and immunity. If the prevalence of COVID-19 in the population is 20% a test with a sensitivity and specificity of 98% will make the value of a positive result (PPV) 92.5% (Figure 1 ). The importance of specificity of serologic tests for screening low prevalence populations was recently demonstrated in a non-peer reviewed publication (11) . The authors found that 1.5% of those screened were positive for SARS-CoV-2 antibodies and, after analysis, found the estimated prevalence to be 2.4%. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32343775/ doi: 10.1093/clinchem/hvaa107 id: cord-007567-vst954ef author: Farquharson, Carolyn title: Responding to the severe acute respiratory syndrome (SARS) outbreak: Lessons learned in a Toronto emergency department() date: 2003-06-04 words: 4228.0 sentences: 234.0 pages: flesch: 57.0 cache: ./cache/cord-007567-vst954ef.txt txt: ./txt/cord-007567-vst954ef.txt summary: 3 Epidemiologic evidence indicates that transmission of the illness occurs with close person-toperson contact (to household members, health care workers, or nearby patients who were not protected by contact or respiratory isolation precautions) and through droplet secretions. In an effort to deal with the transmission and onset of illness within health care and community settings, the province of Ontario designated a Provincial Operations Centre (POC), which was responsible for issuing directives to hospitals about patient care and infection control practices. Some had normal chest radiography with no infiltrates demonstrated (yet) but had symptoms of fever, headache, myalgia, and malaise, and 1 of 3 distinct exposures: they had either traveled to Vietnam, China, Hong Kong, Singapore, or Taiwan; they had been exposed to a person with SARS; or they had been a health care worker, patient, or visitor in a hospital in the GTA where there had been recorded cases of SARS transmission. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119307/ doi: 10.1067/men.2003.109 id: cord-354619-pftjhtpo author: Farronato, Marco title: A Call for Action to Safely Deliver Oral Health Care during and Post COVID-19 Pandemic date: 2020-09-15 words: 5041.0 sentences: 258.0 pages: flesch: 49.0 cache: ./cache/cord-354619-pftjhtpo.txt txt: ./txt/cord-354619-pftjhtpo.txt summary: The oral cavity is purported to be one of the main host sites, both for entry and transmission, implicated in SARS-CoV-2 spread either through contact, droplet, aerosols, or saliva. Evidence suggests that the classic mechanism of transmission, contact and droplet spread, can be contained mostly by isolating symptomatic patients and by the use of facial masks/facial coverings, which de facto provides a physical barrier to the oral cavity and nose, the primary source of infection for droplets and larger aerosol particles. Following the above proposed guidelines, no cases COVID-19 disease transmission after single or multiple dental consultations was registered among the DHCW or patients. Classified as operative and non-operative, depending on their ability to work in the oral cavity or/and provide an essential outside support, the DHCW and the patients visiting the dental practice are undeniably at higher risk of SARS-CoV-2 infection and further transmission [41] . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started just a couple of months ago and it grew rapidly causing several deaths and morbidities. The mechanism behind the transmission of the virus is still not completely understood despite a multitude of new specific manuscripts being published daily. This article highlights the oral cavity as a possible viral transmission route into the body via the Angiotensin converting enzyme 2 receptor. It also provides guidelines for routine protective measures in the dental office while delivering oral health care. url: https://doi.org/10.3390/ijerph17186704 doi: 10.3390/ijerph17186704 id: cord-334099-rtv6xm90 author: Farrow, Robert title: Early Multi-organ Point-of-Care Ultrasound Evaluation of Respiratory Distress During SARS-CoV-2 Outbreak: Case Report date: 2020-04-15 words: 2039.0 sentences: 121.0 pages: flesch: 44.0 cache: ./cache/cord-334099-rtv6xm90.txt txt: ./txt/cord-334099-rtv6xm90.txt summary: 1, 2 In our early experience during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, with multiple patients presenting with acute dyspnea of suspected parenchymal Highland Hospital / Alameda Health System, Department of Emergency Medicine, Oakland, California pulmonary pathology, we found that the prompt differentiation between an underlying cardiac versus pulmonary source can be instrumental in both triage and early resuscitation. Herein we present a case of SARS-CoV-2 related multifocal pneumonia diagnosed by POCUS in the ED during the initial triage of a return ED visit, which highlights its clinical utility and our proposed imaging pathway for evaluating patients with acute dyspnea during the current SARS-CoV-2 outbreak. While the majority of patients infected with SARS-CoV-2 will experience only mild illness, a subset will progress to multifocal pneumonia, acute respiratory distress syndrome, and cardiomyopathy [10] [11] [12] pathologies that can be identified rapidly with POCUS. abstract: INTRODUCTION: Coronavirus disease 2019 (COVID-19) is caused by the virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several case series from Italy and China have highlighted the lung ultrasound findings of this disease process and may demonstrate its clinical utility during the current pandemic. CASE REPORT: We present a case of a COVID-19 patient who presented to the emergency department twice within a 24-hour period with rapidly progressing illness. A multi-organ point-of-care ultrasound (POCUS) evaluation was used on the return visit and assisted clinical decision-making. DISCUSSION: A multi-organ POCUS exam allows for quick assessment of acute dyspnea in the emergency department. As the lung involvement of COVID-19 is primarily a peripheral process it is readily identifiable via lung ultrasound. We believe that when applied efficiently and safely a POCUS exam can reduce clinical uncertainty and potentially limit the use of other imaging modalities when treating patients with COVID-19. CONCLUSION: This case highlights the utility of an early multiorgan point-of-care assessment for patients presenting with moderate respiratory distress during the severe SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32426653/ doi: 10.5811/cpcem.2020.4.47524 id: cord-273351-vq3budip author: Farré, Núria title: Prolonged QT Interval in SARS-CoV-2 Infection: Prevalence and Prognosis date: 2020-08-21 words: 4368.0 sentences: 238.0 pages: flesch: 51.0 cache: ./cache/cord-273351-vq3budip.txt txt: ./txt/cord-273351-vq3budip.txt summary: A prolonged QTc was independently associated with a higher mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. QTc prolongation was defined as an increase of at least one millisecond in QTc compared to baseline QTc. According to the protocol at our center at the time of the study, treatment with hydroxychloroquine and azithromycin was recommended to all patients. The variables included in the model were age, baseline QTc > 480 ms, chronic kidney disease, treatment with azithromycin and hydroxychloroquine, ischemic chronic disease, atrial fibrillation or flutter, heart failure, and the presence of any cardiovascular risk factor. Although these differences could be due to a more severe presentation in a group of elderly comorbid patients, SARS-CoV-2 infection could be the cause of this prolonged QTc interval, either as a direct effect of the virus or through systemic inflammation. A prolonged QTc was independently associated with a higher risk of mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. abstract: Background: The prognostic value of a prolonged QT interval in SARS-Cov2 infection is not well known. Objective: To determine whether the presence of a prolonged QT on admission is an independent factor for mortality in SARS-Cov2 hospitalized patients. Methods: Single-center cohort of 623 consecutive patients with positive polymerase-chain-reaction test (PCR) to SARS Cov2, recruited from 27 February to 7 April 2020. An electrocardiogram was taken on these patients within the first 48 h after diagnosis and before the administration of any medication with a known effect on QT interval. A prolonged QT interval was defined as a corrected QT (QTc) interval >480 milliseconds. Patients were followed up with until 10 May 2020. Results: Sixty-one patients (9.8%) had prolonged QTc and only 3.2% had a baseline QTc > 500 milliseconds. Patients with prolonged QTc were older, had more comorbidities, and higher levels of immune-inflammatory markers. There were no episodes of ventricular tachycardia or ventricular fibrillation during hospitalization. All-cause death was higher in patients with prolonged QTc (41.0% vs. 8.7%, p < 0.001, multivariable HR 2.68 (1.58–4.55), p < 0.001). Conclusions: Almost 10% of patients with COVID-19 infection have a prolonged QTc interval on admission. A prolonged QTc was independently associated with a higher mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. An electrocardiogram should be included on admission to identify high-risk SARS-CoV-2 patients. url: https://doi.org/10.3390/jcm9092712 doi: 10.3390/jcm9092712 id: cord-257191-u5xnmsv8 author: Farshi, Esmaeil title: Investigation of immune cells on elimination of pulmonary‐Infected COVID‐19 and important role of innate immunity, phagocytes date: 2020-09-18 words: 2540.0 sentences: 128.0 pages: flesch: 53.0 cache: ./cache/cord-257191-u5xnmsv8.txt txt: ./txt/cord-257191-u5xnmsv8.txt summary: [4] [5] [6] [7] [8] Lethal disease in BALB/c mice infected with a mouse-adapted strain of SARS-CoV, MA15, showed a lack of activation of innate immune response, resulting in a barely detectable antivirus T cell response. 8 On the other hand, aged BALB/c mice that were infected with a human clinical isolate of SARS-CoV (Urbani strain) successfully eliminated the invasive virus within 1 week post-infection; these mice exhibited high and prolonged levels of viral replication, signs consistent with clinical symptoms, and pathologic changes in the lung resembling those seen in elderly SARS patients. In this study, we attempted to identify the types of immune cells that contribute to clearing COVID-19 during the acute phase of the infection in mice models plus human. Cellular immune responses to severe acute respiratory syndrome coronavirus (SARS-CoV) infection in senescent BALB/c mice: CD4+ T cells are important in control of SARS-CoV infection abstract: We identified types of immune cells that contribute to clearing COVID‐19 during the acute phase of the infection in mouse model and human. Our results suggest that both innate and adaptive immune responses are essential for controlling COVID‐19 infection. Mild infection report of children by COVID‐19 comparing adults' infection causes conclusion of higher resistance of immune system of children comparing adults. Our results show innate immune system including phagocytes contribute severely to the elimination of COVID‐19 in both mouse model and human. Our results also show the elimination of COVID‐19 required the activation of B cells by CD4+ T cells. CD4+ T cells play an important role in elimination of COVID‐19 in primary effection. We measured IgM and IgG in all patients including adults and kids (human) and found IgM and IgG in kids patients are much higher than other adults patients. It causes production of much more natural antibodies in kids' bodies to protect them against COVID‐19 that shows reason of mild effection of kids comparing adults. Our observations have important ramifications for the development of novel vaccination and medicine strategies to alleviate COVID‐19. The most important result is for producing any vaccine for COVID‐19, increasing and producing these factors must be included: (a) Phagocytes (IgM and IgG), (b) T Cells, and (c) White Cells. url: https://doi.org/10.1002/rmv.2158 doi: 10.1002/rmv.2158 id: cord-291613-pfgy9ztl author: Farshidpour, Maham title: A brief review of liver injury in patients with Corona Virus Disease-19 during the pandemic date: 2020-07-03 words: 1536.0 sentences: 77.0 pages: flesch: 40.0 cache: ./cache/cord-291613-pfgy9ztl.txt txt: ./txt/cord-291613-pfgy9ztl.txt summary: Corona Virus Disease (COVID)-19 is a respiratory viral infection caused by a newly emergent coronavirus, Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2), which started in Wuhan, China, in December 2019 and has since evolved into a pandemic with a global risk to human health [1] . Although abnormal liver enzymes were regularly described as an extrapulmonary clinical feature, and almost one half of patients experienced grades of hepatic injury [6] [7] [8] [9] , liver damage in patients with SARS infections was primarily manifested in the mild and moderate elevation of alanine and/or aspartate aminotransferases (ALT and AST) with some degree of hypoalbuminemia and hyperbilirubinemia during the early stage of the illness [10, 11] . In this brief review article, we summarized the characteristics and mechanism of liver injury in patients with SARS-CoV-2 infection, with the hope of guiding further study on this important topic. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: a retrospective study abstract: The novel coronavirus Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) infection has been mostly leading to respiratory distress syndrome, but liver injury has also been documented. The mechanism of liver injury is limited and poorly understood. However, the hepatic injury could be due to a consequence of systemic inflammatory response, viral infection of hepatocytes, or as a result of intensive care treatment or drug toxicity. Based on the current studies, this review article emphasizes on the demographic and potential mechanisms of Corona Virus Disease (COVID)-19-related liver dysfunction url: https://doi.org/10.1007/s12664-020-01068-1 doi: 10.1007/s12664-020-01068-1 id: cord-122092-gdyt02er author: Fatehi, Farzad title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date: 2020-10-18 words: 10080.0 sentences: 511.0 pages: flesch: 55.0 cache: ./cache/cord-122092-gdyt02er.txt txt: ./txt/cord-122092-gdyt02er.txt summary: Comparison of different scenarios is based on tissue damage and viral load, highlighting the impact(s) of antibodies and adaptive cell-mediated immune response on infection dynamics. Surprisingly, our model also suggests that early treatment by either therapy alone can actually increase the duration of infection compared with a later therapy start, likely because suppressing virus production results in a reduced immune response. The model also includes non-structural proteins that are important for the viral life cycle, such as the replicase-transcriptase complex (RTC), and keeps track of the numbers of gRNAs (and subgenomic sgRNAs) at different stages of the replication process. We have included additional reactions into the model that describe remdesivir binding to the RTC complexes on the gRNAs and sgRNAs to capture this (see SI for details), and track the effect of a given, fixed number of remdesivir molecules per cell on the release of viral particles from an infected host cell. abstract: Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in the absence of treatment. This is contrasted with the profiles obtained after variation of model parameters pertinent to the immune response, such as effector cell and antibody proliferation rates, mimicking disease progression in immunocompromised patients. These profiles are then compared with disease progression in the presence of antiviral and convalescent plasma therapy against COVID-19 infections. The model reveals that using both therapies in combination can be very effective in reducing the length of infection, but these synergistic effects decline with a delayed treatment start. Conversely, early treatment with either therapy alone can actually increase the duration of infection, with infectious virions still present after the decline of other markers of infection. This suggests that usage of these treatments should remain carefully controlled in a clinical environment. url: https://arxiv.org/pdf/2010.08957v1.pdf doi: nan id: cord-312444-c1dz5o85 author: Faure‐Bardon, V title: How should we treat pregnant women infected with SARS‐CoV‐2? date: 2020-05-14 words: 1827.0 sentences: 133.0 pages: flesch: 50.0 cache: ./cache/cord-312444-c1dz5o85.txt txt: ./txt/cord-312444-c1dz5o85.txt summary: (Hydroxy) chloroquine has been used in SARS-CoV-2-infected humans with highly controversial results 14,15 but several phase 3 studies are underway to analyse its efficacy both as a cure for patients at each stage of the disease and as a preventive measure. Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with severe coronavirus disease (COVID-19) -Full Text View -ClinicalTrials Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with moderate coronavirus disease (COVID-19) compared to standard of care treatment -Full Text View -ClinicalTrials The efficacy of different anti-viral drugs in COVID 19 infected patients -Full Text View -ClinicalTrials In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine versus placebo in COVID-19 patients at risk for severe disease -Full Text View -ClinicalTrials abstract: The health crisis caused by the novel SARS-cov-2 (formally called 2019-nCoV) related pandemic requires urgent action, including a necessary therapeutic response. Pregnant women are just as exposed as the general population and should not be excluded, because of their status, from discussions on effective and well tolerated candidate treatments. url: https://doi.org/10.1111/1471-0528.16270 doi: 10.1111/1471-0528.16270 id: cord-317379-ljdaj80d author: Faure‐Bardon, V. title: Anatomical and timely assessment of protein expression of angiotensin‐converting enzyme 2, SARS‐CoV‐2 specific receptor, in fetal and placental tissues: new insight for perinatal counseling date: 2020-08-15 words: 2190.0 sentences: 157.0 pages: flesch: 54.0 cache: ./cache/cord-317379-ljdaj80d.txt txt: ./txt/cord-317379-ljdaj80d.txt summary: Beyond theoretical assessment of risk and pathways for vertical transmission, the low incidence of perinatal infections might relate to a lower expression of ACE2 in the placenta and targeted organs. We aimed to evaluate protein expression of ACE2 both in placentas and in all fetal organs from pregnancies not infected with SARS-CoV2 at various gestational ages. Seven placentas were analyzed including 5 from the cases described above, 1 from a 7 weeks''-miscarriage, and 1 from a symptomatic infected pregnant woman with positive SARS-CoV2 RT-PCR delivered by cesarean section at 34 weeks''. These results broaden the insight on likelihood, pathways and morbidities of vertical transmission of SARS-CoV-2, providing a unique anatomical and timely validation of the protein distributions in fetal organs and placentas. The marked placental presence of the specific SARS-CoV2 receptor, ACE2, and its absence from the amnion suggests that ascending vertical transmission could mainly occur following rupture of the amniotic membranes. abstract: Infection with SARS‐CoV2 does not spare pregnant women and the possibility of vertical transmission which might lead to fetal damages is pending. OBJECTIVE: We hypothesized that the observed low incidence of perinatal infection could be related to a low expression of the membrane receptor for SARS‐CoV2, ACE2, in the fetal‐placental unit. We evaluated protein expression of ACE2 both in placentas and fetal organs from non‐infected pregnancies across gestation. METHODS: Discovery study. Immunocytochemistry analysis for ACE2 in organs and placentas were performed in May 2020, in samples from a registered biobank. Five cases of medical termination of pregnancy performed at between 15 and 38 weeks’ in healthy women. Paraffin‐embedded tissues (kidneys, brain, lungs, intestinal tract, heart). Matching tissues from 8‐year‐old children (N=4) were tested as controls. Seven placentas including those of the 5 cases, 1 of a 7‐week miscarriage and 1 of a symptomatic SARS‐COV2 pregnancy at 34 weeks. Tissues’ sections were incubated with rabbit monoclonal anti‐ACE2. Protein expression of ACE2 was detected by immunochemistry. RESULTS: ACE2 expression was detected in fetal kidneys, rectum and ileum across gestation and similarly in the pediatric control. It was barely detectable in lungs at 15 weeks’ and not found thereafter. In the pediatric control, ACE2 was only detectable in type 2 pneumocytes. No ACE2 expression was found in the cerebral ependymal, parenchyma nor in cardiac tissues ACE2 was expressed in syncitiotrophoblast and cytotrophoblast from 7th weeks’ onwards and across gestation but not in the amnion. Similar intensity and distribution of ACE2 staining were identified in the mother's SARS‐CoV2 placenta. CONCLUSIONS: Marked placental expression of ACE2 provides a rationale for vertical transmission at cellular level. Absence of ACE2 expression in the fetal brain and heart is reassuring on the risk of congenital malformation. Clinical follow‐up of infected pregnant women and their children are needed to validate these observations. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32798244/ doi: 10.1002/uog.22178 id: cord-326916-bakwk4tm author: Fauver, Joseph R. title: Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States date: 2020-05-07 words: 5556.0 sentences: 323.0 pages: flesch: 53.0 cache: ./cache/cord-326916-bakwk4tm.txt txt: ./txt/cord-326916-bakwk4tm.txt summary: To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. To delineate the roles of domestic and international virus spread in the emergence of new United States COVID-19 outbreaks, we sequenced SARS-CoV-2 viruses collected from cases identified in Connecticut. We sequenced SARS-CoV-2 genomes from nine of the first COVID-19 cases reported in Connecticut, with sample collection dating from March 6-14, 2020 (Data S1). By combining daily passenger volumes ( Figure 2B ) with COVID-19 prevalence at the travel route origin (Figures 2C and 2D) and accounting for differences in reporting rates, we found that the domestic and international SARS-CoV-2 importation risk started to increase dramatically at the beginning of March 2020 ( Figure 2E ). abstract: The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance. url: https://doi.org/10.1016/j.cell.2020.04.021 doi: 10.1016/j.cell.2020.04.021 id: cord-312997-wcqdksfg author: Favresse, Julien title: Clinical performance of the Elecsys electrochemiluminescent immunoassay for the detection of SARS-CoV-2 total antibodies date: 2020-06-02 words: 651.0 sentences: 44.0 pages: flesch: 47.0 cache: ./cache/cord-312997-wcqdksfg.txt txt: ./txt/cord-312997-wcqdksfg.txt summary: In the context of COVID-19, a wide range of serology immunoassays with different SARS-CoV-2 antigen recognition and antibody specificity have been developed to complement RT-PCR assays [1] . This study is the first to report the external validation of a new electrochemiluminescent immunoassay (ECLIA) test, the Elecsys anti-SARS-CoV-2 from Roche Diagnostics ® . This retrospective study was conducted from May 6 to 12, 2020 at the clinical biology Analyses of serum samples obtained 28 days or more after symptom onset provided a sensitivity of 96.7% (95%CI: 82.8-99.9%) and 100% (95%CI: 88.9-100%) with the manufacturer and the optimized cut-off, respectively (Figure 1) . The optimal ROC cut-off showed excellent clinical performance 14 days or more following RT-PCR positivity or following the onset of COVID-19 symptoms. abstract: nan url: https://doi.org/10.1093/clinchem/hvaa131 doi: 10.1093/clinchem/hvaa131 id: cord-344356-up53a0k4 author: Feaster, Matt title: High Proportion of Asymptomatic SARS-CoV-2 Infections in 9 Long-Term Care Facilities, Pasadena, California, USA, April 2020 date: 2020-10-17 words: 956.0 sentences: 62.0 pages: flesch: 53.0 cache: ./cache/cord-344356-up53a0k4.txt txt: ./txt/cord-344356-up53a0k4.txt summary: Our analysis of coronavirus disease prevalence in 9 long-term care facilities demonstrated a high proportion (40.7%) of asymptomatic infections among residents and staff members. Infection control measures in congregate settings should include mass testing–based strategies in concert with symptom screening for greater effectiveness in preventing the spread of severe acute respiratory syndrome coronavirus 2. Early in the COVID-19 pandemic, the supply of both nasopharyngeal swabs and test kits for SARS-CoV-2 rRT-PCR testing in the United States was extremely limited and made available only for symptomatic persons meeting certain criteria determined by the Centers for Disease Control and Prevention (CDC) (12). Our findings demonstrate a high prevalence of both symptomatic and asymptomatic COVID-19 infection among residents and staff in 9 LTCFs. Because the potential for asymptomatic transmission of SARS-CoV-2 is concerning, for greater effectiveness, infection control efforts in LTCFs should include both mass testing-based strategies and symptom screening. abstract: Our analysis of coronavirus disease prevalence in 9 long-term care facilities demonstrated a high proportion (40.7%) of asymptomatic infections among residents and staff members. Infection control measures in congregate settings should include mass testing–based strategies in concert with symptom screening for greater effectiveness in preventing the spread of severe acute respiratory syndrome coronavirus 2. url: https://www.ncbi.nlm.nih.gov/pubmed/32614768/ doi: 10.3201/eid2610.202694 id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 words: 5433.0 sentences: 276.0 pages: flesch: 43.0 cache: ./cache/cord-344970-ud1lhkyi.txt txt: ./txt/cord-344970-ud1lhkyi.txt summary: Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). abstract: Coronaviruses are enveloped, single-stranded, positive-sense RNA viruses that can infect animal and human hosts. The infection induces mild or sometimes severe acute respiratory diseases. Nowadays, the appearance of a new, highly pathogenic and lethal coronavirus variant, SARS-CoV-2, responsible for a pandemic (COVID-19), represents a global problem for human health. Unfortunately, only limited approaches are available to treat coronavirus infections and a vaccine against this new coronavirus variant is not yet available. The plasma membrane microdomain lipid rafts have been found by researchers to be involved in the replication cycle of numerous viruses, including coronaviruses. Indeed, some pathogen recognition receptors for coronaviruses as for other viruses cluster into lipid rafts, and it is therefore conceivable that the first contact between virus and host cells occurs into these specialized regions, representing a port of cell entry for viruses. Recent data highlighted the peculiar pro-viral or anti-viral role played by autophagy in the host immune responses to viral infections. Coronaviruses, like other viruses, were reported to be able to exploit the autophagic machinery to increase their replication or to inhibit the degradation of viral products. Agents known to disrupt lipid rafts, such as metil-β-cyclodextrins or statins, as well as autophagy inhibitor agents, were shown to have an anti-viral role. In this review, we briefly describe the involvement of lipid rafts and autophagy in coronavirus infection and replication. We also hint how lipid rafts and autophagy may represent a potential therapeutic target to be investigated for the treatment of coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32849425/ doi: 10.3389/fmicb.2020.01821 id: cord-329240-atisrhas author: Fedorenko, Aliza title: Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date: 2020-06-16 words: 4493.0 sentences: 233.0 pages: flesch: 50.0 cache: ./cache/cord-329240-atisrhas.txt txt: ./txt/cord-329240-atisrhas.txt summary: Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic. To study virus survival in microdroplets deposited on a smooth inanimate surface, we sprayed Phi6, MS2, and PhiX174 viruses suspended in three media -human saliva, water, and SM bufferon glass-bottom 12-well plates (Fig. 1, Methods) . The observation that at a given RH, the microscopic hydration conditions of deposited droplets of various media can differ so widely (see along the rows of Fig. 3 ) suggests that RH does not directly affect virus stability and infectivity in drying microdroplets deposited on surfaces, but rather RH indirectly affects survival through its effect on physicochemical conditions at the scale that matters for viruses (~ µm). abstract: The novel coronavirus respiratory syndrome (COVID-19) has now spread worldwide. The relative contribution of viral transmission via fomites is still unclear. SARS-CoV-2 has been shown to survive on inanimate surfaces for several days, yet the factors that determine its survival on surfaces are not well understood. Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. We measured virus viability in human saliva microdroplets, SM buffer, and water following deposition on glass surfaces at various relative humidities (RH). Although saliva microdroplets dried out rapidly at all tested RH levels (unlike SM that remained hydrated at RH ≥ 57%), survival of all three viruses in dry saliva microdroplets was significantly higher than in water or SM. Thus, RH and hydration conditions are not sufficient to explain virus survival, indicating that the suspended medium, and association with saliva components in particular, likely affect physicochemical properties that determine virus survival. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic. url: https://doi.org/10.1101/2020.06.15.152983 doi: 10.1101/2020.06.15.152983 id: cord-331871-colmj7uk author: Feehan, A. K. title: Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020 date: 2020-06-24 words: 1227.0 sentences: 88.0 pages: flesch: 60.0 cache: ./cache/cord-331871-colmj7uk.txt txt: ./txt/cord-331871-colmj7uk.txt summary: Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. This study was designed to estimate SARS-CoV-2 infections in Orleans and Jefferson Parishes (O/JP) and the COVID-19 related IFR by race. . https://doi.org/10.1101/2020.06.23.20138321 doi: medRxiv preprint was used to calculate "presumed recovered." IFR was calculated by dividing cumulative deaths by race, reported by the Louisiana Department of Health, by "presumed recovered" individuals. 2018 population estimates are indicated in Table 1 and multiplied by weighted seroprevalence (percent IgG+) to generate the number of "presumed recovered." Reported deaths are divided by "presumed recovered" to calculate the IFR, which was 1.63% overall. abstract: Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. Infections were highly variable by ZIP and differed by race. Overall census-weighted prevalence was 7.8% and the calculated infection fatality rate was 1.63%. url: http://medrxiv.org/cgi/content/short/2020.06.23.20138321v1?rss=1 doi: 10.1101/2020.06.23.20138321 id: cord-275604-5u4kikov author: Feehan, Amy K. title: Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 date: 2020-11-17 words: 1417.0 sentences: 88.0 pages: flesch: 51.0 cache: ./cache/cord-275604-5u4kikov.txt txt: ./txt/cord-275604-5u4kikov.txt summary: Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. We estimated SARS-CoV-2 infections in Orleans and Jefferson Parishes, Louisiana, USA, and determined the COVID-19-related IFR by race. io) considered >50 characteristics, including social determinants of health and US Census population Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. Study participants for whom either or both tests were positive were considered to be infected with SARS-CoV-2. Our study found the overall SARS-CoV-2 exposure rate in this area to be 7.8% and confirmed a recent report of overrepresentation of Black persons with COVID-19 in the New Orleans area (5) . abstract: Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. Infections were highly variable by ZIP code and differed by race/ethnicity. Overall census-weighted seroprevalence was 6.9%, and the calculated infection fatality ratio was 1.63%. url: https://www.ncbi.nlm.nih.gov/pubmed/32731911/ doi: 10.3201/eid2611.203029 id: cord-295455-km0qcmlh author: Fehr, Anthony R. title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 words: 5467.0 sentences: 309.0 pages: flesch: 46.0 cache: ./cache/cord-295455-km0qcmlh.txt txt: ./txt/cord-295455-km0qcmlh.txt summary: The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Originally described as ADP-ribose-1 00 -phosphatases, both cellular and viral macrodomains enzymatically remove mono-and poly-ADP-ribose from proteins, supporting the notion that protein ADP-ribosylation is a component of the antiviral response. It was unclear how these mutations affected this protein, as neither mutant affected PAR binding and it was unknown whether alphaviruses'' macrodomains had de-ADP-ribosylating activity. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites The conserved macrodomains of the nonstructural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases abstract: Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families ​all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis. url: https://api.elsevier.com/content/article/pii/S0966842X17302603 doi: 10.1016/j.tim.2017.11.011 id: cord-259223-6b07qiw2 author: Feitosa, Eduardo L title: COVID-19: Rational discovery of the therapeutic potential of Melatonin as a SARS-CoV-2 main Protease Inhibitor date: 2020-07-30 words: 6844.0 sentences: 322.0 pages: flesch: 40.0 cache: ./cache/cord-259223-6b07qiw2.txt txt: ./txt/cord-259223-6b07qiw2.txt summary: Molecular docking studies described the binding sites and the interaction energies of 74 Mpro-ligand complexes deposited in the Protein Data Bank (PDB). The search for structural similarity used the 10 hit molecules that presented the best interaction energies (Kcal/mol) measured in the docking study among all 74 ligand-Mpro complexes from PDB. The selected hits (top 10 best-scored compounds identified by previous docking study), as well as their respective similar binders, were docked into SARS-CoV-2 main protease (Mpro) with unliganded active site (PDB id: 6Y84). The interaction between melatonin and Mpro (Figure 4) improved the values of binding energy and created a new perspective for a molecule with high therapeutic potential over the COVID-19 pathology to act, so far, only in more severe cases of the disease. To understand the need to clinically evaluate melatonin against Cov-2, we should make a brief introduction to infectious and physiopathological characteristics related mainly to the viral cycle and host immune response in the COVID-19 ( Figure 5) . abstract: The SARS-CoV-2 spread quickly across the globe. The World Health Organization (WHO) on March 11 declared COVID-19 a pandemic. The mortality rate, hospital disorders and incalculable economic and social damages, besides the unproven efficacy of the treatments evaluated against COVID-19, raised the need for immediate control of this disease. Therefore, the current study employed in silico tools to rationally identify new possible SARS-CoV-2 main protease (Mpro) inhibitors. That is an enzyme conserved among the coronavirus species; hence, the identification of an Mpro inhibitor is to make it a broad-spectrum drug. Molecular docking studies described the binding sites and the interaction energies of 74 Mpro-ligand complexes deposited in the Protein Data Bank (PDB). A structural similarity screening was carried out in order to identify possible Mpro ligands that show additional pharmacological properties against COVID-19. We identified 59 hit compounds and among them, melatonin stood out due to its prominent immunomodulatory and anti-inflammatory activities; it can reduce oxidative stress, defence cell mobility and efficiently combat the cytokine storm and sepsis. In addition, melatonin is an inhibitor of calmodulin, an essential intracellular component to maintain angiotensin-converting enzyme 2 (ACE-2) on the cell surface. Interestingly, one of the most promising hits in our docking study was melatonin. It revealed better interaction energy with Mpro compared to ligands in complexes from PDB. Consequently, melatonin can have response potential in early stages for its possible effects on ACE-2 and Mpro, although it is also promising in more severe stages of the disease for its action against hyper-inflammation. These results definitely do not confirm antiviral activity, but can rather be used as a basis for further preclinical and clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32922174/ doi: 10.7150/ijms.48053 id: cord-343515-fad1yyqx author: Felgenhauer, Ulrike title: Inhibition of SARS–CoV-2 by type I and type III interferons date: 2020-10-09 words: 2934.0 sentences: 157.0 pages: flesch: 53.0 cache: ./cache/cord-343515-fad1yyqx.txt txt: ./txt/cord-343515-fad1yyqx.txt summary: For SARS-CoV-2 (dark gray bars), statistically significant negative correlation coefficients (CC) were obtained for both cell lines, indicating that viral replication is increasingly inhibited by IFN-a. Observations were similar when the input MOI was reduced to 0.001 (Fig. S1 ), except that titers of SARS-CoV-1 in Calu-3 cells were already very low in the absence of any IFN-a, resulting in a nonsignificant effect of additional IFN. Our data thus indicate that (i) if anything, ruxolitinib is an enhancer rather than an inhibitor of SARS-CoV-2 multiplication, and (ii) the boosting effect is most likely due to inhibition of the antiviral JAK/ STAT signaling pathway, because it is not present in the IFN induction-deficient Vero E6 cells. For the statistical testing of the dose-response effect of IFN (type I and III) against SARS-coronaviruses, the typical regression procedures were not applicable because of several values below the detection limit and some ties in the data. abstract: The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS–CoV-2) is the causative agent of the devastating COVID-19 lung disease pandemic. Here, we tested the inhibitory activities of the antiviral interferons of type I (IFN-α) and type III (IFN-λ) against SARS–CoV-2 and compared them with those against SARS–CoV-1, which emerged in 2003. Using two mammalian epithelial cell lines (human Calu-3 and simian Vero E6), we found that both IFNs dose-dependently inhibit SARS–CoV-2. In contrast, SARS–CoV-1 was restricted only by IFN-α in these cell lines. SARS–CoV-2 generally exhibited a broader IFN sensitivity than SARS–CoV-1. Moreover, ruxolitinib, an inhibitor of IFN-triggered Janus kinase/signal transducer and activator of transcription signaling, boosted SARS–CoV-2 replication in the IFN-competent Calu-3 cells. We conclude that SARS–CoV-2 is sensitive to exogenously added IFNs. This finding suggests that type I and especially the less adverse effect–prone type III IFN are good candidates for the management of COVID-19. url: https://doi.org/10.1074/jbc.ac120.013788 doi: 10.1074/jbc.ac120.013788 id: cord-301157-tu3iig9o author: Felsenstein, Susanna title: Presentation, Treatment Response and Short-Term Outcomes in Paediatric Multisystem Inflammatory Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS) date: 2020-10-14 words: 7843.0 sentences: 455.0 pages: flesch: 45.0 cache: ./cache/cord-301157-tu3iig9o.txt txt: ./txt/cord-301157-tu3iig9o.txt summary: Whilst most children and young people develop mild symptoms, recent reports suggest a novel paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS). Since the advent of the Coronavirus Disease 2019 (COVID-19) pandemic, dominated by respiratory disease and evolution of acute respiratory distress syndrome (ARDS), cardiovascular compromise, excessive systemic inflammation and coagulopathy in adults [1] [2] [3] , several countries affected by the coronavirus disease [4] pandemic have reported an unusually high number of cases of children hospitalized due to a multisystem inflammatory condition, at times requiring intensive care (Table S1) . Temporal distribution of paediatric inflammatory multisystem syndrome temporally associated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (PIMS-TS) cases of this cohort, in relation to COVID-19 like presentations to hospitals in England. The peak of presentations of children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 followed the peak of presentations of patients, adult and paediatric, to English Emergency Departments, with a lag of 4-6 weeks (Figure adapted from https://www.gov.uk/government/news/weekly-covid-19-surveillance-report-published; week 30). abstract: The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible for Coronavirus Disease 2019 (COVID-19). Whilst most children and young people develop mild symptoms, recent reports suggest a novel paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS). Case definition and classification are preliminary, treatment is empiric and disease-associated outcomes are unclear. Here, we report 29 patients with PIMS-TS who were diagnosed, admitted and treated in the English North West between March and June 2020. Consistent with patterns observed internationally, cases peaked approximately 4 weeks after the initial surge of COVID-19-like symptoms in the UK population. Clinical symptoms included fever (100%), skin rashes (72%), cardiovascular involvement (86%), conjunctivitis (62%) and respiratory involvement (21%). Some patients had clinical features partially resembling Kawasaki disease (KD), toxic shock syndrome and cytokine storm syndrome. Male gender (69%), black, Asian and other minority ethnicities (BAME, 59%) were over-represented. Immune modulating treatment was used in all, including intravenous immunoglobulin (IVIG), corticosteroids and cytokine blockers. Notably, 32% of patients treated with IVIG alone went into remission. The rest required additional treatment, usually corticosteroids, with the exception of two patients who were treated with TNF inhibition and IL-1 blockade, respectively. Another patient received IL-1 inhibition as primary therapy, with associated rapid and sustained remission. Randomized and prospective studies are needed to investigate efficacy and safety of treatment, especially as resources of IVIG may be depleted secondary to high demand during future waves of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33066459/ doi: 10.3390/jcm9103293 id: cord-354531-7klivhut author: Feng, Liqiang title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques date: 2020-08-21 words: 8295.0 sentences: 482.0 pages: flesch: 58.0 cache: ./cache/cord-354531-7klivhut.txt txt: ./txt/cord-354531-7klivhut.txt summary: title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques In an attempt to develop a prophylactic vaccine against SARS-CoV-2, we constructed a replication-incompetent recombinant adenovirus, Ad5-S-nb2, that can efficiently express SARS-CoV-2 S protein in infected cells (Fig. 1a) . All non-vaccinated macaques showed no serum neutralizing activities (<1:50) against SARS-CoV-2 either before or 7 days after challenge (Fig. 4f) (Fig. 4g) . This study demonstrated that candidate vaccine Ad5-S-nb2 can elicit S-specific antibody and CMI responses in rodents and in NHPs. A single IM injection with a low-dose of 1 × 10 10 vp Ad5-S-nb2 can confer effective protection against SAR-CoV-2 challenge in aged Chinese rhesus macaques. Consistently, other studies in rhesus macaques also showed that the immune responses elicited by a primary SARS-CoV-2 infection or inactivated whole virus effectively protected against SARS-CoV-2 challenge without observing ADE 18, 19, 29, 30 . abstract: The rapid spread of coronavirus SARS-CoV-2 greatly threatens global public health but no prophylactic vaccine is available. Here, we report the generation of a replication-incompetent recombinant serotype 5 adenovirus, Ad5-S-nb2, carrying a codon-optimized gene encoding Spike protein (S). In mice and rhesus macaques, intramuscular injection with Ad5-S-nb2 elicits systemic S-specific antibody and cell-mediated immune (CMI) responses. Intranasal inoculation elicits both systemic and pulmonary antibody responses but weaker CMI response. At 30 days after a single vaccination with Ad5-S-nb2 either intramuscularly or intranasally, macaques are protected against SARS-CoV-2 challenge. A subsequent challenge reveals that macaques vaccinated with a 10-fold lower vaccine dosage (1 × 10(10) viral particles) are also protected, demonstrating the effectiveness of Ad5-S-nb2 and the possibility of offering more vaccine dosages within a shorter timeframe. Thus, Ad5-S-nb2 is a promising candidate vaccine and warrants further clinical evaluation. url: https://doi.org/10.1038/s41467-020-18077-5 doi: 10.1038/s41467-020-18077-5 id: cord-307536-qeo5dfxg author: Feng, Ye title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date: 2020-06-30 words: 998.0 sentences: 69.0 pages: flesch: 58.0 cache: ./cache/cord-307536-qeo5dfxg.txt txt: ./txt/cord-307536-qeo5dfxg.txt summary: title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19. Based on both the epitope counts and HLA score, we 250 eventually selected 13 T-cell epitopes-only vaccine peptides. abstract: A new coronavirus SARS-CoV-2 has caused over 9.2 million infection cases and 475758 deaths worldwide. Due to the rapid dissemination and the unavailability of specific therapy, there is a desperate need for vaccines to combat the epidemic of SARS-CoV-2. An in silico approach based on the available virus genome was applied to identify 19 high immunogenic B-cell epitopes and 499 human-leukocyte-antigen (HLA) restricted T-cell epitopes. Thirty multi-epitope peptide vaccines were designed by iNeo Suite, and manufactured by solid-phase synthesis. Docking analysis showed stable hydrogen bonds of epitopes with their corresponding HLA alleles. When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. The ratio of IFN-γ-secreting lymphocytes in CD4+ or CD8+ cells in the peptides-immunized mice were higher than that in the control mice. There were also a larger number of IFN-γ-secreting T cells in spleen in the peptides-immunized mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. The obtained vaccine peptides successfully elicited specific humoral and cellular immune responses in mice. Primate experiments and clinical trial are urgently required to validate the efficacy and safety of these vaccine peptides. Importance So far, a new coronavirus SARS-CoV-2 has caused over 9.2 million infection cases and 475758 deaths worldwide. Due to the rapid dissemination and the unavailability of specific therapy, there is a desperate need for vaccines to combat the epidemic of SARS-CoV-2. Different from the development approaches for traditional vaccines, the development of our peptide vaccine is faster and simpler. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19. url: https://doi.org/10.1101/2020.03.03.962332 doi: 10.1101/2020.03.03.962332 id: cord-327681-c2kmog0g author: Feng, Zhilan title: Timely identification of optimal control strategies for emerging infectious diseases() date: 2009-07-07 words: 4608.0 sentences: 282.0 pages: flesch: 51.0 cache: ./cache/cord-327681-c2kmog0g.txt txt: ./txt/cord-327681-c2kmog0g.txt summary: RESULTS: Stage-specific infection rate estimates from cases hospitalized before quarantine began exceed those from the entire outbreak, but are qualitatively similar: infectiousness was negligible until symptom onset, and increased 10-fold from prodrome to acute illness. Our model resembles theirs (Fig. 1 ), but we distinguish the prodrome and acute respiratory phase and allow infected people to become infectious before or after becoming ill, at rates-products of contact rates and probabilities of transmission on contact-that may differ among stages. A Mathematica TM notebook that evaluates these expressions for user-supplied parameter values, comparing the impact of non-pharmaceutical interventions on any disease transmitted by close contact, is available from the Table 1 Parameter estimates (b represents infection, r isolation efficiency, f hospitalization; subscripts E, P and R refer to pre-symptomatic, prodrome, and acute respiratory stage) from fitting predicted to observed cumulative admissions to TTSH during the first 30 days of the outbreak (cf. abstract: BACKGROUND: Health authorities must rely on quarantine, isolation, and other non-pharmaceutical interventions to contain outbreaks of newly emerging human diseases. METHODS: We modeled a generic disease caused by a pathogen apparently transmitted by close interpersonal contact, but about which little else is known. In our model, people may be infectious while incubating or during their prodrome or acute illness. We derived an expression for [Formula: see text] , the reproduction number, took its partial derivatives with respect to control parameters, and encoded these analytical results in a user-friendly Mathematica™ notebook. With biological parameters for SARS estimated from the initial case series in Hong Kong and infection rates from hospitalizations in Singapore, we determined [Formula: see text] 's sensitivity to control parameters. RESULTS: Stage-specific infection rate estimates from cases hospitalized before quarantine began exceed those from the entire outbreak, but are qualitatively similar: infectiousness was negligible until symptom onset, and increased 10-fold from prodrome to acute illness. Given such information, authorities might instead have emphasized a strategy whose efficiency more than compensates for any possible reduction in efficacy. CONCLUSIONS: In future outbreaks of new human diseases transmitted via close interpersonal contact, it should be possible to identify the optimal intervention early enough to facilitate effective decision-making. url: https://doi.org/10.1016/j.jtbi.2009.03.006 doi: 10.1016/j.jtbi.2009.03.006 id: cord-285574-i0dh1u5i author: Ferini-Strambi, Luigi title: COVID-19 and neurological disorders: are neurodegenerative or neuroimmunological diseases more vulnerable? date: 2020-07-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Neurological disorders and coronavirus 2019 (COVID-19) pandemic are two conditions with a recent well-documented association. Intriguing evidences showed that COVID-19 infection can modify clinical spectrum of manifested neurological disorders but also it plays a crucial role in the development of future diseases as long-tem consequences. In this viewpoint review, we aimed to assess the vulnerability to SARS-CoV-2 infection and development of COVID-19 among neurological disorders. With this in mind, we tested the hypothesis that age rather than neuropathology itself could be decisive in neurodegenerative diseases such as Parkinson’s disease, whereas neuropathology rather than age may be critical in neuroimmunological diseases such as Multiple Sclerosis. Highlighting the role of potential susceptibility or protection factors from this disastrous infection, we also stratify the risk for future neurodegeneration. url: https://doi.org/10.1007/s00415-020-10070-8 doi: 10.1007/s00415-020-10070-8 id: cord-351736-4x5u4qsy author: Fernandez-Garcia, Cristina title: Severe COVID-19 During Pregnancy and the Subsequent Premature Delivery date: 2020-09-19 words: 556.0 sentences: 44.0 pages: flesch: 62.0 cache: ./cache/cord-351736-4x5u4qsy.txt txt: ./txt/cord-351736-4x5u4qsy.txt summary: Only a few case of SARS-CoV-2 infection in preterm neonates delivered by mothers with COVID-19 have been reported till date. We report the cases of three premature babies delivered by two mothers with severe COVID-19 pneumonia, whose condition deteriorated to the point that necessitated the use of mechanical ventilation on the mothers as well as accelerated child delivery of the mothers. There have been very few reports of preterm delivery in mothers with COVID-19 and most babies have tested negative to SARS-CoV-2. 3, 4 In the few reported neonates who tested positive to SARS-CoV-2 via PCR, there is no evidence of in utero transmission, since infection in the immediate neonatal period could not be completely excluded. 5, 6 Preterm delivery was required in the three cases described in this report, since the mothers developed severe COVID-19 pneumonia. There was no evidence of in utero transmission, such that all the babies (3) tested negative to SARS-CoV-2 immediately after birth and at 24 hours, 5, and 14 days of life. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1875957220301455?v=s5 doi: 10.1016/j.pedneo.2020.09.005 id: cord-294262-yvbufnf4 author: Fernandez-Nieto, D. title: Comment on: “To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out. Characterization of herpetic lesions in hospitalized COVID-19 patients.” date: 2020-06-22 words: 538.0 sentences: 40.0 pages: flesch: 59.0 cache: ./cache/cord-294262-yvbufnf4.txt txt: ./txt/cord-294262-yvbufnf4.txt summary: All 15 patients presented typical clinical lesions and symptoms of herpes 39 simplex/zoster. In spite of performing PCR tests for SARS-CoV-2 from the 42 content of the vesicles in only three patients, the results were all negative. Regarding vesicular rashes or varicella-like COVID-19 exanthems 3 , we previously 44 reported four cases in which we performed both PCR multiplex for herpesvirus and rt-45 PCR for SARS-CoV-2, directly from the content of the vesicles. This reasonably rules out a role of herpes 47 viruses 3 , and a potential infective ability of SARS-CoV-2 through the vesicles. In our current experience, the diagnosis of 55 herpesvirus infection in COVID-19 patients does not usually involve diagnostic doubts, 56 due to the clinical presentation and reported symptoms being typical of the disease, 57 even when lesions are extensive (Figure 1) . abstract: nan url: https://api.elsevier.com/content/article/pii/S0190962220311610 doi: 10.1016/j.jaad.2020.06.063 id: cord-335364-qwjuzebd author: Fernandez-Rivas, G. title: Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave date: 2020-06-26 words: 4200.0 sentences: 233.0 pages: flesch: 51.0 cache: ./cache/cord-335364-qwjuzebd.txt txt: ./txt/cord-335364-qwjuzebd.txt summary: title: Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave Methods: IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22nd, 2020) by chemiluminescence assays. IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22 nd , 2020) by chemiluminescence assays. Hence, in this study we analyzed the SARS-CoV-2 IgG seroprevalence in Healthcare workers of the Northern Metropolitan Area of Barcelona, Spain. From May 4th to May 22 nd , 2020, all Healthcare workers of the ICS-Northern Metropolitan Area of Barcelona (n=9315) were offered to have serum testing performed for SARS-CoV-2 IgG antibodies. abstract: Background: The rapid spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) around the world has caused a global pandemic, infecting millions of individuals worldwide, with an unprecedented impact in health care systems worldwide. Healthcare workers are one of the risk groups that need to be well characterized due to their strategic role in the management of patients, presently and in prevention of healthcare needs for future outbreaks. This study presents the results of the first SARS-CoV-2 seroprevalence study in the Northern Metropolitan Area of Barcelona, Spain. Methods: IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22nd, 2020) by chemiluminescence assays. Results: A total of 779 of 7563 (10.3%) healthcare workers had detectable anti-SARS-CoV-2 IgG (specific for either S1/S2 or N antigens). No significant differences were observed between those working at primary care or at the reference hospital. Interestingly, in 29 (8.53%) of the previously confirmed positive reverse-transcriptase polymerase chain reaction (rRT-PCR) patients SARS-CoV-2 IgG (S1/S2 or recombinant N antigen) were negative. Conclusion: Seroprevalence of anti-SARS-CoV-2 IgG in the healthcare workers of the Nord Metropolitan Area of Barcelona was significantly increased in comparison with the general population in the same geographical area. These results give us an important insight for a better understanding of SARS-CoV-2 epidemiology, in a collective that is essential for the response against this pandemic. url: https://doi.org/10.1101/2020.06.24.20135673 doi: 10.1101/2020.06.24.20135673 id: cord-270888-8j17ul7k author: Fernández-González, Sara Mª title: ¿Infección Por Sars-Cov-2 Como Desencadenante De Un Síndrome Inflamatorio Sistémico? date: 2020-09-09 words: 862.0 sentences: 90.0 pages: flesch: 50.0 cache: ./cache/cord-270888-8j17ul7k.txt txt: ./txt/cord-270888-8j17ul7k.txt summary: Desde entonces este síndrome se ha conocido con diferentes nomenclaturas y, desde Mayo, se conoce como Paediatric inflammatory multisystem syndrome temporally associated with severe J o u r n a l P r e -p r o o f acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PIMS-TS) [3] [4] [5] . Presentamos el caso de un niño de 4 años con síndrome de respuesta inflamatoria sistémica e IgG positiva para SARS-CoV-2 con IgM y reacción en cadena de la polimerasa (PCR) sobre muestra de frotis nasofaríngeo negativas. Tras 24 horas de inicio de tratamiento presentó una mejoría clínica progresiva con desaparición del exantema, edema e hiperemia conjuntival, así como normalización de constantes (frecuencia cardiaca 71 lpm y tensión arterial 97/52 mmHg, p50) y parámetros analíticos, a excepción de trombocitosis reactiva (plaquetas 579000/L) Estuvo ingresado durante 9 días en planta de hospitalización, hasta completar 7 días de antibioterapia intravenosa en espera de resultados de cultivos y mejoría de parámetros analíticos, manteniéndose estable a nivel hemodinámico y respiratorio sin necesitar soporte vasoactivo ni respiratorio. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33008679/ doi: 10.1016/j.eimc.2020.07.012 id: cord-270112-o2exvfy5 author: Ferrarese, Carlo title: An Italian multicenter retrospective-prospective observational study on neurological manifestations of COVID-19 (NEUROCOVID) date: 2020-05-19 words: 2465.0 sentences: 103.0 pages: flesch: 31.0 cache: ./cache/cord-270112-o2exvfy5.txt txt: ./txt/cord-270112-o2exvfy5.txt summary: We report here the description of a multicenter retrospective-prospective observational study promoted by the Italian Society of Neurology (SIN), involving the Italian Neurological Departments, who will consecutively recruit patients with neurological symptoms and/or signs, occurred at the onset or as a complication of COVID-19. A comprehensive data collection, in the form of electronic case report form (eCRF), will register all possible neurological manifestations involving central nervous systems, peripheral nerves, and muscles, together with clinical, laboratory (including cerebrospinal fluid, if available), imaging, neurological, neurophysiological, and neuropsychological data. More specifically, the aims are to gather data on the following: (1) the appearance of neurologic symptoms and/or signs at COVID-19 onset or during the disease course, (2) the exams performed for the diagnosis of the neurological involvement, (3) the clinical course of both the COVID-19 infection and the neurological events, but also the occurrence of possible long-term neurological complications within a 6-month period of follow-up. abstract: Neurological manifestations of COVID-19 have been described in both single case reports and retrospective scanty case series. They may be linked to the potential neurotropism of the SARS-COV-2 virus, as previously demonstrated for other coronaviruses. We report here the description of a multicenter retrospective-prospective observational study promoted by the Italian Society of Neurology (SIN), involving the Italian Neurological Departments, who will consecutively recruit patients with neurological symptoms and/or signs, occurred at the onset or as a complication of COVID-19. Hospitalized patients will be recruited either in neurological wards or in COVID wards; in the latter cases, they will be referred from other specialists to participant neurologists. Outpatients with clinical signs of COVID and neurological manifestations will be also referred to participating neurologists from primary care physicians. A comprehensive data collection, in the form of electronic case report form (eCRF), will register all possible neurological manifestations involving central nervous systems, peripheral nerves, and muscles, together with clinical, laboratory (including cerebrospinal fluid, if available), imaging, neurological, neurophysiological, and neuropsychological data. A follow-up at hospital discharge (in hospitalized patients), and for all patients after 3 and 6 months, is also planned. We believe that this study may help to intercept the full spectrum of neurological manifestations of COVID-19 and, given the large diffusion at national level, can provide a large cohort of patients available for future more focused investigations. Similar observational studies might also be proposed at international level to better define the neurological involvement of COVID-19. url: https://doi.org/10.1007/s10072-020-04450-1 doi: 10.1007/s10072-020-04450-1 id: cord-255665-srvz2ay0 author: Ferrari, Marco title: COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions date: 2020-10-14 words: 2481.0 sentences: 156.0 pages: flesch: 45.0 cache: ./cache/cord-255665-srvz2ay0.txt txt: ./txt/cord-255665-srvz2ay0.txt summary: title: COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions The study included all patients undergoing surgery under general anesthesia for HNC at two Italian tertiary referral academic hospitals during the peak of the pandemic diffusion of to an internal "grey zone" of COVID-19 surveillance, submitted to further blood tests, chest CT, and nasal/nasopharyngeal swab while maintaining strict isolation. The following data were extracted from institutional databases: patient-related including the 2-week post-discharge period) was considered as the gold standard evaluation (i.e. patients developing symptoms attributed to COVID-19 through nucleic acid-based test on respiratory secretions in this time frame were considered as "false negative" of the screening; abstract: Background Preoperative screening had a key role in planning elective surgical activity for head and neck cancer (HNC) during the COVID-19 pandemic. Methods All patients undergoing surgery for HNC at two Italian referral hospitals (University of Padua and National Cancer Institute [NCI]) during the peak of the COVID-19 epidemic in Italy were included. Accuracy of screening protocols was assessed. Results In the Padua protocol, 41 patients were screened by pharyngeal swab. The entire sample (100%) was admitted to surgery, diagnostic accuracy was 100%. In the NCI protocol, 23 patients underwent a telephone interview, blood test, and chest CT. Twenty patients (87%) were negative and were directly admitted to surgery. In the remaining 3 (13%), pharyngeal swab was performed. The screening was repeated until a negative chest CT was found. Diagnostic accuracy was 85%. Conclusions Dedicated screening protocols for COVID-19 allow to safely perform elective HNC surgery. url: https://www.sciencedirect.com/science/article/pii/S1368837520304796?v=s5 doi: 10.1016/j.oraloncology.2020.105043 id: cord-355175-uo9fx6jy author: Ferrazzi, E title: Vaginal delivery in SARS‐CoV‐2‐infected pregnant women in Northern Italy: a retrospective analysis date: 2020-05-28 words: 3176.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-355175-uo9fx6jy.txt txt: ./txt/cord-355175-uo9fx6jy.txt summary: Data were collected from the clinical records using a standardised questionnaire on maternal general characteristics, any medical or obstetric co‐morbidity, course of pregnancy, clinical signs and symptoms, treatment of COVID 19 infection, mode of delivery, neonatal data and breastfeeding. Conclusions Although postpartum infection cannot be excluded with 100% certainty, these findings suggest that vaginal delivery is associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. Another clinical series of 11 women with COVID 19 infection who had successful deliveries (10 caesarean and 1 vaginal) has been reported: in all the newborns, the 2019-nCoV nucleic acid test was negative. This paper reports the obstetric outcome of a cohort of COVID-19-affected pregnant women and the rate of SARS-CoV-2 positivity in newborns according to mode of delivery and breastfeeding status. Although postpartum infection cannot be excluded, our study also suggests that vaginal delivery may be associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. abstract: OBJECTIVE: To report mode of delivery and immediate neonatal outcome in women infected with COVID‐19. DESIGN: Retrospective study. SETTING: Twelve hospitals in northern Italy. PARTICIPANTS: Pregnant women with COVID‐19‐confirmed infection who delivered. EXPOSURE: COVID 19 infection in pregnancy. METHODS: SARS‐CoV‐2‐infected women who were admitted and delivered from 1 to 20 March 2020 were eligible. Data were collected from the clinical records using a standardised questionnaire on maternal general characteristics, any medical or obstetric co‐morbidity, course of pregnancy, clinical signs and symptoms, treatment of COVID 19 infection, mode of delivery, neonatal data and breastfeeding. MAIN OUTCOME AND MEASURES: Data on mode of delivery and neonatal outcome. RESULTS: In all, 42 women with COVID‐19 delivered at the participating centres; 24 (57.1%, 95% CI 41.0–72.3) delivered vaginally. An elective caesarean section was performed in 18/42 (42.9%, 95% CI 27.7–59.0) cases: in eight cases the indication was unrelated to COVID‐19 infection. Pneumonia was diagnosed in 19/42 (45.2%, 95% CI 29.8–61.3) cases: of these, 7/19 (36.8%, 95% CI 16.3–61.6) required oxygen support and 4/19 (21.1%, 95% CI 6.1–45.6) were admitted to a critical care unit. Two women with COVID‐19 breastfed without a mask because infection was diagnosed in the postpartum period: their newborns tested positive for SARS‐Cov‐2 infection. In one case, a newborn had a positive test after a vaginal operative delivery. CONCLUSIONS: Although postpartum infection cannot be excluded with 100% certainty, these findings suggest that vaginal delivery is associated with a low risk of intrapartum SARS‐Cov‐2 transmission to the newborn. TWEETABLE ABSTRACT: This study suggests that vaginal delivery may be associated with a low risk of intrapartum SARS‐Cov‐2 transmission to the newborn. url: https://www.ncbi.nlm.nih.gov/pubmed/32339382/ doi: 10.1111/1471-0528.16278 id: cord-267762-mzon01fd author: Ferreira, A. title: Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection. date: 2020-06-29 words: 2939.0 sentences: 167.0 pages: flesch: 51.0 cache: ./cache/cord-267762-mzon01fd.txt txt: ./txt/cord-267762-mzon01fd.txt summary: Methods: By analyzing the Portuguese anonymized data on private and public based medical prescriptions we have identified all cases chronically receiving HCQ for the management of diseases such as systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. Cross linking the two sets of data has allowed us to compare the proportion of HCQ chronic treatment (at least 2 grams per month) in laboratory confirmed cases of SARS-CoV-2 infection with laboratory confirmed negative cases. Several in vitro studies have shown chloroquine phosphate and hydroxychloroquine sulphate (HCQ) to be effective in both preventing and treating SARS-CoV-2 infection in isolated cells (1) (2) (3) . By analyzing these sets of data, we were able to detect all patients with SARS-CoV-2 confirmed infections and all clinically suspected but non-confirmed patients between Mars 2, 2020 (the date of the first Portuguese case) and the moment of the analysis. The proportion of HCQ chronic treatment was higher in negative patients is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: Background: Hydroxychloroquine sulphate (HCQ) is being scrutinized for repositioning in the treatment and prevention of SARS-Cov-2 infection. This antimalarial drug is also chronically used to treat patients with autoimmune diseases. Methods: By analyzing the Portuguese anonymized data on private and public based medical prescriptions we have identified all cases chronically receiving HCQ for the management of diseases such as systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. Additionally, we have detected all laboratory confirmed cases of SARS-CoV-2 infection and all laboratory confirmed negative cases in the Portuguese population (mandatorily registered in a centrally managed database). Cross linking the two sets of data has allowed us to compare the proportion of HCQ chronic treatment (at least 2 grams per month) in laboratory confirmed cases of SARS-CoV-2 infection with laboratory confirmed negative cases. Results: Out of 26,815 SARS-CoV-2 positive patients, 77 (0.29%) were chronically treated with HCQ, while 1,215 (0.36%) out of 333,489 negative patients were receiving it chronically (P=0.04). After adjustment for age, sex, and chronic treatment with corticosteroids and/or immunosuppressants, the odds ratio of SARS-CoV-2 infection for chronic treatment with HCQ has been 0.51 (0.37-0.70). Conclusions: Our data suggest that chronic treatment with HCQ confer protection against SARS-CoV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.06.26.20056507v1?rss=1 doi: 10.1101/2020.06.26.20056507 id: cord-295121-4xemmaqt author: Ferreira, Eliane de Oliveira title: Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date: 2020-09-29 words: 2301.0 sentences: 117.0 pages: flesch: 40.0 cache: ./cache/cord-295121-4xemmaqt.txt txt: ./txt/cord-295121-4xemmaqt.txt summary: The outbreak caused by the novel coronavirus SARS-CoV-2 and its associated symptoms, termed COVID-19 disease, originally in Wuhan, China in 2019, has rapidly become a global pandemic (Park, 2020) . Although some of those risk factors for CDI are also related to higher probability rates of mortality in severe SARS-CoV-2 infection, the limited number of CDI cases reported among COVID-19 patients is somewhat surprising. The authors emphasized that when CDI is present as a co-infection with COVID-19 and the diarrhea persists, therapy can be difficult because of the SARS-CoV-2 infection. The dearth of studies regarding secondary infections, such as Clostridioides difficile, in COVID-19 patients makes it difficult to measure the effect of the pandemic on antimicrobial stewardship programs and on long term antimicrobial resistance. In conclusion, it seems highly likely that cases of CDI are being under-reported among COVID-19 patients and the increased use of antibiotics may, in part, be responsible. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33133048/ doi: 10.3389/fmicb.2020.581343 id: cord-330061-q4xi260z author: Ferreira, João Guimarães title: Pneumothorax as a late complication of COVID-19 date: 2020-08-31 words: 2421.0 sentences: 151.0 pages: flesch: 48.0 cache: ./cache/cord-330061-q4xi260z.txt txt: ./txt/cord-330061-q4xi260z.txt summary: We present a typical laboratory confirmed case of COVID-19 pneumonia, that was hospitalized due to hypoxemia but did not require mechanical ventilation. On the other hand, patients with more severe disease comprise 14% of the cases, with progressive tachypnea and dyspnea after five to eight days from the beginning of the symptoms, low blood oxygen saturation, and/or lung infiltrates in > 50% of the lungs. Regarding laboratory abnormalities in patients with COVID-2019 infections, the most frequent findings for those who need admission to the intensive care unit are leukocytosis, higher neutrophil count, lymphopenia, increased values of CRP, LDH, aminotransferases, total bilirubin, creatinine, cardiac troponin, procalcitonin and D-dimer. Herein, we present a typical and laboratory confirmed case of COVID-19 pneumonia, with clinical course deterioration during the third week of the disease due to a massive hypertensive pneumothorax with no known previous risk factor. Spontaneous pneumothorax and subcutaneous emphysema in COVID-19 patient: case report abstract: In late 2019, a novel coronavirus initially related to a cluster of severe pneumonia cases in China was identified. COVID-19 cases have rapidly spread to multiple countries worldwide. We present a typical laboratory confirmed case of COVID-19 pneumonia, that was hospitalized due to hypoxemia but did not require mechanical ventilation. Although initially the patient was evaluated with a favorable outcome, in the third week of the disease, the symptomatology deteriorated due to a massive hypertensive pneumothorax with no known previous risk factor. Since the first cases of COVID-19 have been described, pneumothorax was characterized as a potential, though uncommon, complication. It has been reported that diffuse alveolar injury caused by SARS-CoV-2 can cause alveolar rupture, produce air leakage and interstitial emphysema. Although uncommon, pneumothorax should be listed as a differential diagnosis for COVID-19 patients with sudden respiratory decompensation. As a life-threatening event, it requires prompt recognition and expeditious treatment. url: https://doi.org/10.1590/s1678-9946202062061 doi: 10.1590/s1678-9946202062061 id: cord-326983-h6gdck2u author: Ferretti, Andrew P. title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 words: 5634.0 sentences: 274.0 pages: flesch: 56.0 cache: ./cache/cord-326983-h6gdck2u.txt txt: ./txt/cord-326983-h6gdck2u.txt summary: We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). abstract: Developing effective strategies to prevent or treat COVID-19 requires understanding the natural immune response to SARS-CoV-2. We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8+ T cells of COVID-19 patients. In total, we identified 3–8 epitopes for each of the six most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8+ T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S1074761320304477 doi: 10.1016/j.immuni.2020.10.006 id: cord-312559-ygh507x2 author: Fiesco-Sepulveda, K. Y. title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review date: 2020-05-22 words: 1890.0 sentences: 177.0 pages: flesch: 60.0 cache: ./cache/cord-312559-ygh507x2.txt txt: ./txt/cord-312559-ygh507x2.txt summary: title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, meta-analyses 248 using Latin American cases would also be ideal for determining how COVID-19 could affect this 249 region, which has some differences, such as lower average age or higher exposure to respiratory 250 infections than other regions like Europe (Amariles et al., 2020a). (2020) concluded that the novel virus could come from a bat SARS-like coronavirus isolate, 168 which is in agreement with reports from the GISAID database Clinical features of patients infected 644 with 2019 novel coronavirus in Wuhan The novel coronavirus (SARS-CoV-2) emergency and the role of timely and 674 effective national health surveillance Complete genome sequence of a 2019 novel coronavirus (SARS-COV-2) strain isolated 792 in Nepal. abstract: This paper aimed to give the visibility of Latin American researchers' contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than four months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on April 10, 2020, showed 1224 documents published by authors with 1797 affiliations from 80 countries. 25.4%, 24.0%, and 12.6% of these national affiliations were from China, Europe, and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on April 10, 2020, we searched different databases, such as Scopus, PubMed, and Web of Science, finding that the contribution of this region was 2.7% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social, and environmental considerations, bioinformatics, and epidemiology. url: https://doi.org/10.1101/2020.05.16.20104422 doi: 10.1101/2020.05.16.20104422 id: cord-315152-v3l33up6 author: Figlerowicz, Magdalena title: First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia date: 2020-07-01 words: 1701.0 sentences: 114.0 pages: flesch: 57.0 cache: ./cache/cord-315152-v3l33up6.txt txt: ./txt/cord-315152-v3l33up6.txt summary: title: First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia We present the case of a six-year-old girl with severe COVID-19, in whom SARS-CoV-2 was successfully eliminated after convalescent plasma transfusion. In December 2019, a novel coronavirus disease (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) arose unexpectedly in China. In pediatric patients with a severe or critical course of COVID-19, acute respiratory distress syndrome (ARDS) can occur; toxic shock is also observed. Here, we present a case of using a J o u r n a l P r e -p r o o f convalescent plasma transfusion as a therapeutic method for severe pediatric COVID-19associated aplastic anemia. We present a case of using convalescent plasma in the therapy of a child with severe COVID-19. Effectiveness of convalescent plasma therapy in severe COVID-19 patients abstract: We present the case of a six-year-old girl with severe COVID-19, in whom SARS-CoV-2 was successfully eliminated after convalescent plasma transfusion. Children show a variable clinical course of COVID-19, from asymptomatic to critical. In our patient, we diagnosed COVID-19-associated aplastic anemia with severe pancytopenia. The correlation between SARS-CoV-2 infection with aplastic anemia remains unclear. At the beginning of the disease, we used antiviral drugs and immune modulators as therapy but without any positive results. After providing a transfusion of convalescent plasma, the elimination of SARS-CoV-2 was observed. We did not observe any adverse events of this treatment. The girl still has a diagnosis of aplastic anemia and requires specialist therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/32636116/ doi: 10.1016/j.transci.2020.102866 id: cord-282878-8qgsq2km author: Fignani, Daniela title: SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date: 2020-10-23 words: 7565.0 sentences: 359.0 pages: flesch: 43.0 cache: ./cache/cord-282878-8qgsq2km.txt txt: ./txt/cord-282878-8qgsq2km.txt summary: Finally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the β-cell line EndoC-βH1 and in primary human pancreatic islets. To address this question, we screened the ACE2 expression pattern in human pancreata obtained from adult non-diabetic multiorgan donors and in the insulin-producing human β-cell line EndoC-βH1, using different methodologies, multiple reagents, and publicly available or in-house generated RNA sequencing datasets. Here, we adopted multiple technologies and reagents to thoroughly analyse presence of ACE2, both at mRNA and protein level, in order to evaluate its expression and localization in pancreatic tissue samples obtained from adult non-diabetic multiorgan donors from the INNODIA EUnPOD biobank collection, in enzymatic-and LCM-isolated primary adult human pancreatic islets and in human β-cell line EndoC-βH1. Importantly, a recent report showed that human pancreatic islets can be infected in vitro by SARS-CoV-2 (23), supporting our observations of a specific tropism of the virus due to ACE2 expression. abstract: Increasing evidence demonstrated that the expression of Angiotensin I-Converting Enzyme type 2 (ACE2), is a necessary step for SARS-CoV-2 infection permissiveness. In the light of the recent data highlighting an association between COVID-19 and diabetes, a detailed analysis aimed at evaluating ACE2 expression pattern distribution in human pancreas is still lacking. Here, we took advantage of INNODIA network EUnPOD biobank collection to thoroughly analyse ACE2, both at mRNA and protein level, in multiple human pancreatic tissues and using several methodologies. Using multiple reagents and antibodies, we showed that ACE2 is expressed in human pancreatic islets, where it is preferentially expressed in subsets of insulin producing β-cells. ACE2 is also is highly expressed in pancreas microvasculature pericytes and moderately expressed in rare scattered ductal cells. By using different ACE2 antibodies we showed that a recently described short-ACE2 isoform is also prevalently expressed in human β-cells. Finally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the β-cell line EndoC-βH1 and in primary human pancreatic islets. Taken together, our data indicate a potential link between SARS-CoV-2 and diabetes through putative infection of pancreatic microvasculature and/or ductal cells and/or through direct β-cell virus tropism. url: https://doi.org/10.1101/2020.07.23.208041 doi: 10.1101/2020.07.23.208041 id: cord-028989-w50thois author: Figueira Gonçalves, Juan Marco title: Clinical challenges in chronic obstructive pulmonary disease in patients who suffered SARS-CoV-2 infection() date: 2020-07-10 words: 2005.0 sentences: 100.0 pages: flesch: 44.0 cache: ./cache/cord-028989-w50thois.txt txt: ./txt/cord-028989-w50thois.txt summary: Reported complications of SARS-CoV-2 infection, such as extensive pneumonia/acute lung damage or adult acute respiratory distress syndrome, the occurrence of myocarditis/cardiac arrhythmias or the development of thromboembolic 2/7 episodes are events that may worsen the baseline condition of the COPD patient surviving the process, having to take into account their existence when planning their outpatient follow-up. Despite the lack of sufficient evidence at the moment, the results reported to date and the pathogenic mechanisms plausibly involved, make it advisable to consider this aspect in those patients with COPD who, after hospital discharge, develop in the medium to long term an increase in dyspnoea not justified by spirometric parameters. In the SARS-CoV-1 epidemic, some of the survivors developed avascular necrosis, pulmonary fibrosis, and dyslipidaemia after viral infection 15, 16 , which may have a relevant impact on those patients who already had some underlying respiratory or cardiovascular condition. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351405/ doi: 10.1016/j.medcle.2020.04.012 id: cord-298850-tgxfki7n author: Figuero-Pérez, Luis title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab date: 2020-10-15 words: 1027.0 sentences: 84.0 pages: flesch: 49.0 cache: ./cache/cord-298850-tgxfki7n.txt txt: ./txt/cord-298850-tgxfki7n.txt summary: title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab Several studies have proposed that anti-IL-6 receptor antibodies, such as tocilizumab, play an important role in the treatment of severe acute respiratory infection associated with SARS-CoV-2. We present a case report of a 51-year-old man diagnosed with severe respiratory infection associated with SARS-CoV-2 that was refractory to antiviral and anti-IL-6 treatment, with a favourable clinical outcome and analytical improvement after treatment with anti-IL-1 (anakinra). We present the case of a 51-year-old patient with bilateral pneumonia secondary to SARS-CoV-2 infection refractory to treatment with tocilizumab who showed improvement after treatment with anakinra. The "cytokine storm" secondary to SARS-CoV-2 infection determines severe COVID-19 disease. 3 The use of anti-IL-6 antibodies in the treatment of SARS-CoV-2 infection is currently under study, being one of the current pillars of COVID-19 disease treatment. abstract: SARS-CoV-2 is a new RNA virus which causes coronavirus disease 2019 (COVID-19), declared a pandemic by the World Health Organization (WHO). It triggers an atypical pneumonia that can progress to multiorgan failure. COVID-19 can cause dysregulation of the immune system, triggering an inflammatory response, and simulate haemophagocytic lymphohistiocytosis. Several studies have proposed that anti-IL-6 receptor antibodies, such as tocilizumab, play an important role in the treatment of severe acute respiratory infection associated with SARS-CoV-2. However, the role of anti-IL-1 receptor antibodies, such as anakinra, in the treatment of COVID-19 has not been established. We present a case report of a 51-year-old man diagnosed with severe respiratory infection associated with SARS-CoV-2 that was refractory to antiviral and anti-IL-6 treatment, with a favourable clinical outcome and analytical improvement after treatment with anti-IL-1 (anakinra). url: https://api.elsevier.com/content/article/pii/S2173574320301313 doi: 10.1016/j.reumae.2020.06.008 id: cord-339009-wcoch07b author: File, Thomas M. title: Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date: 2012-08-23 words: 6023.0 sentences: 324.0 pages: flesch: 50.0 cache: ./cache/cord-339009-wcoch07b.txt txt: ./txt/cord-339009-wcoch07b.txt summary: Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world. abstract: Severe acute respiratory syndrome (SARS) is a newly emerged infection that is caused by a previously unrecognized virus–a novel coronavirus designated as SARS-associated coronavirus (SARS-CoV). From November 2002 to July 2003 the cumulative number of worldwide cases was >8000, with a mortality rate of close to 10%. The mortality has been higher in older patients and those with co-morbidities. SARS has been defined using clinical and epidemiological criteria and cases are considered laboratory-confirmed if SARS coronavirus is isolated, if antibody to SARS coronavirus is detected, or a polymerase chain reaction test by appropriate criteria is positive. At the time of writing (24 May 2004), no specific therapy has been recommended. A variety of treatments have been attempted, but there are no controlled data. Most patients have been treated throughout the illness with broad-spectrum antimicrobials, supplemental oxygen, intravenous fluids, and other supportive measures. Transmission of SARS is facilitated by close contact with patients with symptomatic infection. The majority of cases have been reported among healthcare providers and family members of SARS patients. Since SARS-CoV is contagious, measures for prevention center on avoidance of exposure, and infection control strategies for suspected cases and contacts. This includes standard precautions (hand hygiene), contact precautions (gowns, goggles, gloves) and airborne precautions (negative pressure rooms and high efficiency masks). In light of reports of new cases identified during the winter of 2003–4 in China, it seems possible that SARS will be an important cause of pneumonia in the future, and the screening of outpatients at risk for SARS may become part of the pneumonia evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/15813661/ doi: 10.2165/00151829-200504020-00003 id: cord-324651-8teb5jrn author: Filippini, Antonio title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date: 2020-04-30 words: 2052.0 sentences: 97.0 pages: flesch: 43.0 cache: ./cache/cord-324651-8teb5jrn.txt txt: ./txt/cord-324651-8teb5jrn.txt summary: title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? In the present opinion article we highlight evidence from different laboratories to drive the attention of the scientific community on the role played by endo-lysosomal Two-Pore Channels (TPCs) in viral infection. In particular, cross linking our recent data and existing literature, we focus on evidence indicating that virus intracellular pathway could be targeted by a novel occurring TPCs inhibitor, the flavonoid Naringenin. Intriguingly, our recent evidence has shown that the activity of human TPC channels can be inhibited by a natural flavonoid compound, in fact present in citruses and tomatoes, Naringenin (Pafumi et al., 2017) . In conclusion, these considerations offer a perspective on specific molecular targets, TPCs, and underpin a role for Naringenin as pharmacological blockade of SARS-CoV-2 infectivity providing further support for exploration of TPCs inhibition as novel antiviral therapy. abstract: nan url: https://doi.org/10.3389/fmicb.2020.00970 doi: 10.3389/fmicb.2020.00970 id: cord-320902-1hfxju5f author: Filocamo, Giovanni title: Use of anakinra in severe COVID-19: a case report date: 2020-05-11 words: 1440.0 sentences: 88.0 pages: flesch: 46.0 cache: ./cache/cord-320902-1hfxju5f.txt txt: ./txt/cord-320902-1hfxju5f.txt summary: As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still''s disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient''s critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). abstract: Abstract Coronavirus Disease 19 is a global healthcare emergency with high lethality rate. Relevant inflammatory cytokine storm is associated with severity of disease and IL1 inhibition is a cornerstone treatment for hyperinflammatory diseases. We present here the case of a patient with critical COVID-19 successfully treated with IL-1 receptor antagonist (anakinra). url: https://api.elsevier.com/content/article/pii/S1201971220303337 doi: 10.1016/j.ijid.2020.05.026 id: cord-312702-fruzsn26 author: Finch, Courtney L. title: Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date: 2020-05-14 words: 2785.0 sentences: 167.0 pages: flesch: 46.0 cache: ./cache/cord-312702-fruzsn26.txt txt: ./txt/cord-312702-fruzsn26.txt summary: title: Characteristic and quantifiable COVID-19-like abnormalities in CTand PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) Based on the rather limited X-97 ray findings in the lungs of reported NHP models of SARS-CoV-2 infection with either 98 mild or no clinical signs (11, 25, 27-29), we turned to high-resolution chest CT and 99 Increases in PCLH or PCLH/LV 169 were not seen in the mock-exposed macaques over the entire study (Figure 8a A key advantage of quantifiable CT chest imaging readout over serial euthanasia 212 studies, in addition to potentially reduced experimental animal numbers, is the ability not 213 only to evaluate between-group differences, but also to compare severity and duration of 214 disease at higher resolution in single animals and even in isolated parenchymal areas 215 sequentially. follow-up confirmation of these pilot results in this model of mild-moderate COVID-19 233 is needed to further establish quantifiable lung CT as a reliable disease readout and to 234 forge imaging-pathologic correlates in macaques euthanized at peak radiographic 235 abnormality. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing an exponentially increasing number of coronavirus disease 19 (COVID-19) cases globally. Prioritization of medical countermeasures for evaluation in randomized clinical trials is critically hindered by the lack of COVID-19 animal models that enable accurate, quantifiable, and reproducible measurement of COVID-19 pulmonary disease free from observer bias. We first used serial computed tomography (CT) to demonstrate that bilateral intrabronchial instillation of SARS-CoV-2 into crab-eating macaques (Macaca fascicularis) results in mild-to-moderate lung abnormalities qualitatively characteristic of subclinical or mild-to-moderate COVID-19 (e.g., ground-glass opacities with or without reticulation, paving, or alveolar consolidation, peri-bronchial thickening, linear opacities) at typical locations (peripheral>central, posterior and dependent, bilateral, multi-lobar). We then used positron emission tomography (PET) analysis to demonstrate increased FDG uptake in the CT-defined lung abnormalities and regional lymph nodes. PET/CT imaging findings appeared in all macaques as early as 2 days post-exposure, variably progressed, and subsequently resolved by 6–12 days post-exposure. Finally, we applied operator-independent, semi-automatic quantification of the volume and radiodensity of CT abnormalities as a possible primary endpoint for immediate and objective efficacy testing of candidate medical countermeasures. url: https://www.ncbi.nlm.nih.gov/pubmed/32511338/ doi: 10.1101/2020.05.14.096727 id: cord-313349-ikjivfce author: Finsterer, Josef title: Causes of hypogeusia/hyposmia in SARS‐CoV2 infected patients date: 2020-04-20 words: 1132.0 sentences: 85.0 pages: flesch: 49.0 cache: ./cache/cord-313349-ikjivfce.txt txt: ./txt/cord-313349-ikjivfce.txt summary: It is well appreciated that SARS‐CoV2 does not exclusively affect the lungs.(1,2) Virus‐RNA can be detected in most of the body compartments, including the cerebrospinal fluid (CSF).(3) Neurological manifestations have been recently investigated in a retrospective study of 214 SARS‐CoV2‐infected patients.(1) This article is protected by copyright. A further argument against hypothesis one is that SARS-CoV2-associated meningitis is rare Accepted Article but smelling/taste abnormalities are frequent. In COVID-19 patients, ACE2-expressing cells of the taste buds and/or olfactory epithelium might be targeted by SARS-Cov2 via a cytopathic effect. 15 Besides the hypothesis of a cytopathic effect on neurosensory cells, the high incidence of smell and/or taste loss in COVID-19 patients might thus reflect the impact of SARS-Cov2 on the synthesis of neurotransmitters (notably serotonin and dopamine) by ACE2-expressing cells. In summary, the most likely cause for transient hypogeusia and hyposmia in SARS-CoV2-infected patients is a direct contact and interaction of the virus with gustatory receptors or olfactory receptor cells. abstract: It is well appreciated that SARS‐CoV2 does not exclusively affect the lungs.(1,2) Virus‐RNA can be detected in most of the body compartments, including the cerebrospinal fluid (CSF).(3) Neurological manifestations have been recently investigated in a retrospective study of 214 SARS‐CoV2‐infected patients.(1) This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25903 doi: 10.1002/jmv.25903 id: cord-266710-3wdy16tw author: Fintelman-Rodrigues, Natalia title: Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production date: 2020-09-21 words: 4822.0 sentences: 298.0 pages: flesch: 55.0 cache: ./cache/cord-266710-3wdy16tw.txt txt: ./txt/cord-266710-3wdy16tw.txt summary: Molecular dynamics analysis revealed that the root mean square deviation (RMSD) for the SARS-CoV-2 Mpro backbone presented different conformations in complex with ATV or LPV (see Fig. S3 ). As a control, the activity of SARS-CoV-2 Mpro in fractions from infected cells was evaluated by treatment with RTV, which inhibited activity in the molecular range of 31 to 38 kDa without a change in the 70-kDa region (Fig. 2 , RTV lanes). Since the results regarding the pharmacologic activity of ATV and ATV/RTV against SARS-CoV-2 replication in Vero cells were promising, we next investigated whether the proposed drug therapies could inhibit virus replication in a human epithelial pulmonary cell line (A549). We highlight ATV and ATV/RTV because our assay readout to quantify infectious virus particles reveals (i) a good profile of antiviral activity, (ii) higher potencies in respiratory cells, and (iii) the ability to reduce levels of proinflammation mediator in monocytes. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is already responsible for far more deaths than previous pathogenic coronaviruses (CoVs) from 2002 and 2012. The identification of clinically approved drugs to be repurposed to combat 2019 CoV disease (COVID-19) would allow the rapid implementation of potentially life-saving procedures. The major protease (Mpro) of SARS-CoV-2 is considered a promising target, based on previous results from related CoVs with lopinavir (LPV), an HIV protease inhibitor. However, limited evidence exists for other clinically approved antiretroviral protease inhibitors. Extensive use of atazanavir (ATV) as antiretroviral and previous evidence suggesting its bioavailability within the respiratory tract prompted us to study this molecule against SARS-CoV-2. Our results show that ATV docks in the active site of SARS-CoV-2 Mpro with greater strength than LPV, blocking Mpro activity. We confirmed that ATV inhibits SARS-CoV-2 replication, alone or in combination with ritonavir (RTV) in Vero cells and a human pulmonary epithelial cell line. ATV/RTV also impaired virus-induced enhancement of interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-α) levels. Together, our data strongly suggest that ATV and ATV/RTV should be considered among the candidate repurposed drugs undergoing clinical trials in the fight against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32759267/ doi: 10.1128/aac.00825-20 id: cord-311782-d2t8bzio author: Fiore, Josè Ramòn title: Results from a survey in healthy blood donors in South Eastern Italy indicate that we are far away from herd immunity to SARS‐CoV‐2 date: 2020-08-13 words: 1725.0 sentences: 95.0 pages: flesch: 53.0 cache: ./cache/cord-311782-d2t8bzio.txt txt: ./txt/cord-311782-d2t8bzio.txt summary: We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general population three months after the local start of the epidemic. In our study, we confirm a low rate of antibodies against SARS-CoV-2 on a group of blood donors from a geographical region with a moderate incidence (187 cases/100.000 inhabitants vs the national data of 390 infections/100.000 inhabitants); our results are at variance with those observed in other regions of Italy. abstract: Here we present results from a survey on anti‐SARS‐CoV‐2 seroprevalence in healthy blood donors from a low incidence COVID‐19 area (Apulia region, South Eastern Italy). Among 904 subjects tested, only in 9 cases (0.99%) antibodies against SARS‐CoV‐2 were demonstrated. All the 9 seropositive patients were negative for the research of viral RNA by RT‐PCR in nasopharyngeal swabs. These data, along with those recently reported from other countries, clearly show that we are very far from herd immunity and that the containment measures are at the moment the only realistic instrument we have to slow the spread of the pandemic. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26425 doi: 10.1002/jmv.26425 id: cord-313356-ninzeazy author: Fiorillo, Luca title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 words: 3803.0 sentences: 248.0 pages: flesch: 53.0 cache: ./cache/cord-313356-ninzeazy.txt txt: ./txt/cord-313356-ninzeazy.txt summary: title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention abstract: Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. This certainly generates insecurity and fear in people, with an important psychological component that is not to be underestimated at this stage of the pandemic. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. As this was a current study, there are still not many sources in the literature, and scientific strategies are moving towards therapy and diagnosis, rather than knowing the characteristics of the virus. Such an article could be an aid to summarize virus features and formulate new guidelines and anti-spread strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32365891/ doi: 10.3390/ijerph17093132 id: cord-312663-hhd5f823 author: Fiorino, Gionata title: Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date: 2020-03-24 words: 2199.0 sentences: 109.0 pages: flesch: 52.0 cache: ./cache/cord-312663-hhd5f823.txt txt: ./txt/cord-312663-hhd5f823.txt summary: The outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. IBD patients are severely worried about the impact of their disease and medications on the risk and the prognosis of COVID-19, and many of them are forced to come to hospital because of active disease, complications and drug administration. Patients scheduled for a follow-up visit are required to stay at home and to complete a questionnaire about IBD symptoms and quality of life, together with their routine laboratory tests, to the nurse and the dedicated doctor, who give recommendations and information about therapy and follow-up procedures. Based on the assumption that the risk of coronavirus infection is not different between the general population and IBD patients, but that IBD flares are difficult to manage in this situation, we advise all patients to continue their therapies, especially if in remission. abstract: The outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. This is the first pandemic caused by a coronavirus in history. More than 150 000 confirmed cases worldwide are reported involving the SARS-CoV2, with more than 5000 COVID-19-related deaths on March 14, 2020. Fever, chills, cough, shortness of breath, generalised myalgia, malaise, drowsiness, diarrhoea, confusion, dyspnoea, and bilateral interstitial pneumonia are the common symptoms. No therapies are available, and the only way to contain the virus spread is to regularly and thoroughly clean one’s hands with an alcohol-based hand rub or wash them with soap and water, to maintain at least 1 m [3 feet] distance from anyone who is coughing or sneezing, to avoid touching eyes, nose, and mouth, and to stay home if one feels unwell. No data are available on the risk of COVID-19 and outcomes in inflammatory bowel disease [IBD] patients. Outbreak restrictions can impact on the IBD care. We aim to give a viewpoint on how operationally to manage IBD patients and ensure quality of care in the current pandemic era. url: https://www.ncbi.nlm.nih.gov/pubmed/32211765/ doi: 10.1093/ecco-jcc/jjaa058 id: cord-330266-uypjqif7 author: Firpo, Mason R. title: Targeting Polyamines Inhibits Coronavirus Infection by Reducing Cellular Attachment and Entry date: 2020-09-23 words: 5471.0 sentences: 330.0 pages: flesch: 51.0 cache: ./cache/cord-330266-uypjqif7.txt txt: ./txt/cord-330266-uypjqif7.txt summary: To determine if coronaviruses are susceptible to polyamine depletion, we treated Vero-E6 cells with doses of DFMO ranging from 750 μM to 5 mM for 4 days prior to infection with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.1 plaque forming units (pfu) per cell. To determine if DFMO-mediated virus restriction was a result of polyamine depletion, we treated BHK-R cells with DFMO and, at the time of infection, supplemented with the individual polyamines putrescine, spermidine, and spermine at 1 μM, a level that did not affect cellular viability ( Figure 2A ). We observed that DFMO reduced viral titers and that supplementation with any of the individual polyamines rescued virus replication to untreated levels ( Figure 2C ). 19 We observed no changes in plaque size ( Figure 3A ) or morphology ( Figure 3B ) with DFMO supplementation to the media, suggesting that DFMO was not sufficiently antiviral when applied to cells after infection and highlighting that DFMO must be applied prophylactically to reduce coronavirus replication. abstract: [Image: see text] Coronaviruses first garnered widespread attention in 2002 when the severe acute respiratory syndrome coronavirus (SARS-CoV) emerged from bats in China and rapidly spread in human populations. Since then, Middle East respiratory syndrome coronavirus (MERS-CoV) emerged and still actively infects humans. The recent SARS-CoV-2 outbreak and the resulting disease (coronavirus disease 2019, COVID19) have rapidly and catastrophically spread and highlighted significant limitations to our ability to control and treat infection. Thus, a basic understanding of entry and replication mechanisms of coronaviruses is necessary to rationally evaluate potential antivirals. Here, we show that polyamines, small metabolites synthesized in human cells, facilitate coronavirus replication and the depletion of polyamines with FDA-approved molecules significantly reduces coronavirus replication. We find that diverse coronaviruses, including endemic and epidemic coronaviruses, exhibit reduced attachment and entry into polyamine-depleted cells. We further demonstrate that several molecules targeting the polyamine biosynthetic pathway are antiviral in vitro. In sum, our data suggest that polyamines are critical to coronavirus replication and represent a highly promising drug target in the current and any future coronavirus outbreaks. url: https://doi.org/10.1021/acsinfecdis.0c00491 doi: 10.1021/acsinfecdis.0c00491 id: cord-252767-as841xo0 author: Fischer, Bastian title: SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, March to June 2020 date: 2020-07-16 words: 2028.0 sentences: 110.0 pages: flesch: 49.0 cache: ./cache/cord-252767-as841xo0.txt txt: ./txt/cord-252767-as841xo0.txt summary: We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. To determine an approximation of the actual rate of people who have recovered from COVID-19, representative of the German population, we determined the anti-SARS-CoV-2 IgG seroprevalence of regular blood donors resident in three different German federal states between March and June 2020. The Figure shows the anti-SARS-CoV-2 IgG distribution in blood donors with equivocal (ratio: ≥ 0.8 to < 1.1) and clearly seropositive (ratio: ≥ 1.1) test results. Distribution of anti-SARS-CoV-2 IgG ratios of blood donors with seropositive and equivocal test results, Germany, March-June 2020, (n = 3,186) abstract: Most cases of coronavirus disease 2019 are mild or asymptomatic. Therefore, many cases remain unrecorded. We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. The IgG seroprevalence was 0.91% (95% confidence interval (CI): 0.58–1.24) overall, ranging from 0.66% (95% CI: 0.13–1.19) in Hesse to 1.22% (95% CI: 0.33–2.10) in Lower-Saxony. url: https://www.ncbi.nlm.nih.gov/pubmed/32700672/ doi: 10.2807/1560-7917.es.2020.25.28.2001285 id: cord-293517-8derad2p author: Fischer, Johannes C. title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update date: 2020-10-30 words: 191.0 sentences: 21.0 pages: flesch: 70.0 cache: ./cache/cord-293517-8derad2p.txt txt: ./txt/cord-293517-8derad2p.txt summary: key: cord-293517-8derad2p authors: Fischer, Johannes C.; Zänker, Kurt; van Griensven, Martijn; Schneider, Marion; Kindgen-Milles, Detlef; Knoefel, Wolfram Trudo; Lichtenberg, Artur; Tamaskovics, Balint; Djiepmo-Njanang, Freddy Joel; Budach, Wilfried; Corradini, Stefanie; Ganswindt, Ute; Häussinger, Dieter; Feldt, Torsten; Schelzig, Hubert; Bojar, Hans; Peiper, Matthias; Bölke, Edwin; Haussmann, Jan; Matuschek, Christiane title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update journal: Eur J Med Res cord_uid: 8derad2p High activity natural killer cell during target attack. Footprint of previously attached natural killer cell can be identified by patchy membrane residuals on the target cell surface. When will NK-cells join the cellular immune cascade to fight SARS-CoV-2? The role of passive immunization in the age of SARS-CoV-2: an update Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Fischer et al. Eur J Med Res (2020) 25:53 abstract: An amendment to this paper has been published and can be accessed via the original article. url: https://www.ncbi.nlm.nih.gov/pubmed/33126916/ doi: 10.1186/s40001-020-00449-8 id: cord-255888-znfgh78m author: Fisher, Dale title: Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date: 2020-08-18 words: 1816.0 sentences: 110.0 pages: flesch: 58.0 cache: ./cache/cord-255888-znfgh78m.txt txt: ./txt/cord-255888-znfgh78m.txt summary: SARS-CoV-2 was detected on workers and environmental samples, including a cutting board used to slice imported salmon. We have assessed the survival of SARS-CoV-2 on refrigerated and frozen meat and salmon over 3 weeks to assess the potential of outbreaks being seeded by imported contaminated food. The clusters of infection of COVID-19 among workers in slaughterhouses and meat processing facilities in many countries can be attributed to factors that promote transmission of virus directly between workers, such as crowding, poor ventilation, and shouting in close proximity due to high ambient noise levels. With a significant burden of virus present in infected workers and the environment then contamination of meat with SARS-CoV-2 is possible during butchering and processing. Our laboratory work has shown that SARS-CoV-2 can survive the time and temperatures associated with transportation and storage conditions associated with international food trade. We believe it is possible that contaminated imported food can transfer virus to workers as well as the environment. abstract: An explanation is required for the re-emergence of COVID-19 outbreaks in regions with apparent local eradication. Recent outbreaks have emerged in Vietnam, New Zealand and parts of China where there had been no cases for some months. Importation of contaminated food and food packaging is a feasible source for such outbreaks and a source of clusters within existing outbreaks. Such events can be prevented if the risk is better appreciated. url: https://doi.org/10.1101/2020.08.17.255166 doi: 10.1101/2020.08.17.255166 id: cord-010050-utbrf4ad author: Fisher, Dale A title: Preventing local transmission of SARS: lessons from Singapore date: 2003-06-02 words: 2363.0 sentences: 134.0 pages: flesch: 54.0 cache: ./cache/cord-010050-utbrf4ad.txt txt: ./txt/cord-010050-utbrf4ad.txt summary: 4 Instituting this Preventing local transmission of SARS: lessons from Singapore Clinical record At 11:30 on 8 April 2003, a 64-year-old man presented to the National University Hospital emergency department (ED) complaining of light headedness for 3 days, and dry cough and body aches for 2 days. Australia must ensure rapid identification of a potential index case at points of initial contact in hospitals, community clinics and general practices across the country. 1, 2 In countries with the resources to implement full and effective contact and respiratory isolation for all suspect patients, local transmission of the virus has been almost non-existent. Provided there is consistent early identification of imported suspect cases, then Australia''s healthcare system can manage these patients with appropriate isolation to prevent secondary transmission. Each health jurisdiction in Australia must have a plan for managing a local SARS outbreak, which should include prompt hospital and community responses, and an ability to meet potential needs at short notice. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168499/ doi: 10.5694/j.1326-5377.2003.tb05358.x id: cord-333042-icgsbelo author: Fisher, Kiva A. title: Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities — United States, July 2020 date: 2020-09-11 words: 3405.0 sentences: 186.0 pages: flesch: 49.0 cache: ./cache/cord-333042-icgsbelo.txt txt: ./txt/cord-333042-icgsbelo.txt summary: Restricting the analysis to participants without known close contact with a person with confirmed COVID-19, case-patients were more likely to report dining at a restaurant (aOR = 2.8, 95% CI = 1.9-4.3) or going to a bar/coffee shop (aOR = 3.9, 95% CI = 1.5-10.1) than were control-participants. For each reported activity, participants were asked to quantify degree of adherence to recommendations such as wearing a face mask of any kind or social distancing among other persons at that location, with response options ranging from "none" to "almost all." Descriptive and statistical analyses were performed to compare case-patients with control-participants, assessing differences in demographic characteristics, community exposures, and close contact. In addition to dining at a restaurant, case-patients were more likely to report going to a bar/coffee shop, but only when the analysis was restricted to participants without close contact with persons with known COVID-19 before illness onset. abstract: Community and close contact exposures continue to drive the coronavirus disease 2019 (COVID-19) pandemic. CDC and other public health authorities recommend community mitigation strategies to reduce transmission of SARS-CoV-2, the virus that causes COVID-19 (1,2). Characterization of community exposures can be difficult to assess when widespread transmission is occurring, especially from asymptomatic persons within inherently interconnected communities. Potential exposures, such as close contact with a person with confirmed COVID-19, have primarily been assessed among COVID-19 cases, without a non-COVID-19 comparison group (3,4). To assess community and close contact exposures associated with COVID-19, exposures reported by case-patients (154) were compared with exposures reported by control-participants (160). Case-patients were symptomatic adults (persons aged ≥18 years) with SARS-CoV-2 infection confirmed by reverse transcription-polymerase chain reaction (RT-PCR) testing. Control-participants were symptomatic outpatient adults from the same health care facilities who had negative SARS-CoV-2 test results. Close contact with a person with known COVID-19 was more commonly reported among case-patients (42%) than among control-participants (14%). Case-patients were more likely to have reported dining at a restaurant (any area designated by the restaurant, including indoor, patio, and outdoor seating) in the 2 weeks preceding illness onset than were control-participants (adjusted odds ratio [aOR] = 2.4; 95% confidence interval [CI] = 1.5-3.8). Restricting the analysis to participants without known close contact with a person with confirmed COVID-19, case-patients were more likely to report dining at a restaurant (aOR = 2.8, 95% CI = 1.9-4.3) or going to a bar/coffee shop (aOR = 3.9, 95% CI = 1.5-10.1) than were control-participants. Exposures and activities where mask use and social distancing are difficult to maintain, including going to places that offer on-site eating or drinking, might be important risk factors for acquiring COVID-19. As communities reopen, efforts to reduce possible exposures at locations that offer on-site eating and drinking options should be considered to protect customers, employees, and communities. url: https://www.ncbi.nlm.nih.gov/pubmed/32915165/ doi: 10.15585/mmwr.mm6936a5 id: cord-265278-wf5pbvvt author: Fishman, Jay A. title: Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation date: 2020-09-17 words: 5266.0 sentences: 317.0 pages: flesch: 40.0 cache: ./cache/cord-265278-wf5pbvvt.txt txt: ./txt/cord-265278-wf5pbvvt.txt summary: In transplant recipiAfter infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viral replication ensues in the respiratory epithelium, followed by viremia and systemic spread to organs by means of the angiotensin-converting-enzyme 2 receptor. 22 Graft rejection and toxic effects from calcineurin inhibitors may be difficult to distinguish from The varied presentation of SARS-CoV-2 infection reflects diversity in host immune responses, notably in immunosuppressed transplant recipients. Although the use of antiinflammatory drugs (e.g., high-dose glucocorticoids or interleukin-6 receptor antagonists) in solid-organ transplant recipients may have the additional benefit of protecting against rejection among patients who are receiving tapering courses of the immunosuppressive agents, especially when calcineurin inhibitors are discontinued because of severe disease, their efficacy in the context of solidorgan transplantation warrants testing in clinical trials. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32937051/ doi: 10.1056/nejmcpc2004982 id: cord-295864-kwdvais7 author: Flahault, Antoine title: Has China faced only a herald wave of SARS-CoV-2? date: 2020-03-27 words: 271.0 sentences: 24.0 pages: flesch: 63.0 cache: ./cache/cord-295864-kwdvais7.txt txt: ./txt/cord-295864-kwdvais7.txt summary: key: cord-295864-kwdvais7 journal: The Lancet cord_uid: kwdvais7 Serosurveys should be seen as polls before elections; they can be repeated several times, 3 week after week, to monitor the epidemic precisely. There is no reason to wait for the end of the epidemic before doing serosurveys. The results would be tremendously informative to China, first and foremost, and to the entire international community, on the risk of big secondary epidemic waves. The attack rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) calculated by mathe matical models, from estimates of the basic reproduction number, R0, of 2-3, suggests that 50-60% of the population should eventually be infected because the population seems to be entirely naive to the new virus. COVID-19) advice for the public Director-General''s opening remarks at the media briefing on COVID-19 -28 A WHO-UNICEF-Lancet Commission abstract: nan url: https://api.elsevier.com/content/article/pii/S0140673620305213 doi: 10.1016/s0140-6736(20)30521-3 id: cord-280915-yk872yaz author: Flaherman, Valerie J title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 words: 1528.0 sentences: 98.0 pages: flesch: 54.0 cache: ./cache/cord-280915-yk872yaz.txt txt: ./txt/cord-280915-yk872yaz.txt summary: In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. abstract: Infant outcomes after maternal SARS-CoV-2 infection are not well-described. In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. url: https://doi.org/10.1093/cid/ciaa1411 doi: 10.1093/cid/ciaa1411 id: cord-264814-v4wnmg03 author: Flanagan, Katie L. title: Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date: 2020-10-02 words: 15130.0 sentences: 700.0 pages: flesch: 44.0 cache: ./cache/cord-264814-v4wnmg03.txt txt: ./txt/cord-264814-v4wnmg03.txt summary: Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure. abstract: There are currently around 200 SARS-CoV-2 candidate vaccines in preclinical and clinical trials throughout the world. The various candidates employ a range of vaccine strategies including some novel approaches. Currently, the goal is to prove that they are safe and immunogenic in humans (phase 1/2 studies) with several now advancing into phase 2 and 3 trials to demonstrate efficacy and gather comprehensive data on safety. It is highly likely that many vaccines will be shown to stimulate antibody and T cell responses in healthy individuals and have an acceptable safety profile, but the key will be to confirm that they protect against COVID-19. There is much hope that SARS-CoV-2 vaccines will be rolled out to the entire world to contain the pandemic and avert its most damaging impacts. However, in all likelihood this will initially require a targeted approach toward key vulnerable groups. Collaborative efforts are underway to ensure manufacturing can occur at the unprecedented scale and speed required to immunize billions of people. Ensuring deployment also occurs equitably across the globe will be critical. Careful evaluation and ongoing surveillance for safety will be required to address theoretical concerns regarding immune enhancement seen in previous contexts. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. We provide details of some of the frontrunner vaccines and discuss potential issues including adverse effects, scale-up and delivery. url: https://doi.org/10.3389/fimmu.2020.579250 doi: 10.3389/fimmu.2020.579250 id: cord-314822-lmoc0xwi author: Flegel, Willy A. title: CoVID‐19 insights from transfusion medicine date: 2020-07-08 words: 1746.0 sentences: 113.0 pages: flesch: 52.0 cache: ./cache/cord-314822-lmoc0xwi.txt txt: ./txt/cord-314822-lmoc0xwi.txt summary: 5 The first analyses of patients with CoVID-19 in Wuhan, China did not report a substantial need for blood transfusion. In rapid reporting succession, patients with CoVID-19 infection have been documented to develop cold agglutinin disease, 11 the relatively more common autoimmune haemolytic anaemia 12, 13 or immune thrombocytopenia 14 and their combination as Evans syndrome. 23, 24 The safety profile has to be established, particularly for patients in early stage CoVID-19, where convalescent plasma, if safe, may be most effective. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and Transfusion Medicine: reflections from Italy Blood component use in critical care in patients with COVID-19 infection: a single centre experience Improved clinical symptoms and mortality on severe/critical COVID-19 patients utilizing convalescent plasma transfusion Relationship between ABO blood group distribution and clinical characteristics in patients with COVID-19 More on ''Association between ABO blood groups and risk of SARS-CoV-2 pneumonia'' More on ''Association between ABO blood groups and risk of SARS-CoV-2 pneumonia'' abstract: The emergence of CoVID‐19 infection in the first months of 2020 resulted in a massive surge in admissions to hospitals and intensive care units due to the nature of the respiratory pathophysiology. In some countries, health care systems were rapidly overwhelmed, while in others their hospitals coped with the first wave and all patients received the level of care needed, depending upon both the containment measured and the level of development of the heath care systems. url: https://www.ncbi.nlm.nih.gov/pubmed/32640485/ doi: 10.1111/bjh.17005 id: cord-300024-169g2ih5 author: Flemming, S. title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-05-26 words: 299.0 sentences: 24.0 pages: flesch: 52.0 cache: ./cache/cord-300024-169g2ih5.txt txt: ./txt/cord-300024-169g2ih5.txt summary: key: cord-300024-169g2ih5 title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 cord_uid: 169g2ih5 Abdominal fluid (ascites), bile, liver and gall bladder samples were collected during emergency cholecystectomy of a critically ill patient suffering from COVID-19. Tracheal secretion and throat swab samples were collected immediately prior to surgery as positive controls. All samples were tested for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (PCR) using validated primers 5 . PCR tests revealed strongly positive results for SARS-CoV-2 RNA in tracheal secretion as well as in throat swab samples, with cycle threshold values of 20 and 25, respectively. The remaining samples all tested negative for SARS-CoV-2 suggesting that the virus does not spread to the abdominal cavity, bile and abdominal organs. A stool sample obtained one day after surgery also tested negative. Recommendations for general surgery activities in a pandemic scenario (SARS-CoV-2) abstract: nan url: https://doi.org/10.1002/bjs.11713 doi: 10.1002/bjs.11713 id: cord-309304-glcxrh7t author: Flemming, Sven title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date: 2020-09-19 words: 596.0 sentences: 37.0 pages: flesch: 43.0 cache: ./cache/cord-309304-glcxrh7t.txt txt: ./txt/cord-309304-glcxrh7t.txt summary: title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 Nevertheless, these recommendations should be critically challenged since only the transmission of human papillomavirus from patient to surgeon by surgical smoke (aerosols) has been reported in a very small number of cases. Several recent studies have shown that fecal samples of COVID-19 patients can be positive for SARS-CoV-2, suggesting potential fecal oral transmission and thus a higher risk for gastrointestinal surgeons 3 . The purpose of our case report was to share actual clinical observations and results from a critically ill patient suffering from COVID-19 pneumonia who required emergency surgical treatment. These results have since been supported by a second case report showing negative PCR of peritoneal fluid in a COVID-19 patient who needed emergency surgery due to acute appendicitis. abstract: nan url: https://doi.org/10.1002/bjs.11898 doi: 10.1002/bjs.11898 id: cord-316670-x9x54fxw author: Flinck, Heini title: Comparison of two fully automated tests detecting antibodies against nucleocapsid N and spike S1/S2 proteins in COVID-19 date: 2020-08-29 words: 1869.0 sentences: 108.0 pages: flesch: 52.0 cache: ./cache/cord-316670-x9x54fxw.txt txt: ./txt/cord-316670-x9x54fxw.txt summary: Based on our results, the SARS-CoV-2 antibodies can be quite reliable detected 2 weeks after NAAT positivity and 3 weeks after the symptom onset with both tests. In this paper, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. N protein based tests may be more sensitive to detect past COVID-19, but S protein may be a possible target for neutralizing antibodies, and SARS-CoV-2 antibodies against that antigen may better predict the protective immunity (Walls et al. In this study, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. Response of anti-SARS-CoV-2 total antibodies to nucleocapsid antigen in COVID-19 patients: a longitudinal study abstract: Automated assays for detecting SARS-CoV-2 antibodies in COVID-19 diagnostics have recently come available. We compared the performance of the Elecsys® Anti-SARS-CoV-2 and LIAISON® SARS-CoV-2 S1/S2 IgG tests. The seroconversion panel comprised of 120 samples from 13 hospitalized COVID-19 patients. For the sensitivity and specificity testing, samples from COVID-19 outpatients >15 days after positive NAAT result (n = 35), and serum control samples collected before the COVID-19 era (n = 161) were included in the material. Samples for the detection of possible cross-reactions were also tested. Based on our results, the SARS-CoV-2 antibodies can be quite reliable detected 2 weeks after NAAT positivity and 3 weeks after the symptom onset with both tests. However, since some COVID-19 patients were positive only with Elecsys®, the antibodies should be screened against N-antigen (Elecsys®), and reactive samples confirmed with S antigen (LIAISON®), but the both results should be reported. In some COVID-19 patients the serology can remain negative. url: https://api.elsevier.com/content/article/pii/S0732889320305745 doi: 10.1016/j.diagmicrobio.2020.115197 id: cord-016897-t71f10kv author: Flores, Marco V. title: Preventing Airborne Disease Transmission: Implications for Patients During Mechanical Ventilation date: 2013-05-29 words: 3661.0 sentences: 196.0 pages: flesch: 46.0 cache: ./cache/cord-016897-t71f10kv.txt txt: ./txt/cord-016897-t71f10kv.txt summary: We discuss the risk of transmitting these procedures and the strategies for mechanical ventilation in future airborne epidemics with special consideration given to the issue of protecting health care workers (HCWs). In contrast to the situation regarding severe acute respiratory syndrome (SARS) or tuberculosis prevention in HCWs, little attention has been given to the importance of HCWs personal protective equipment (PPE) (gowns, gloves, masks) for prevention and management of infl uenza. There is also potential for NIV to reduce the need for intubation in patients with infl uenza pneumonia or chronic respiratory disease, facilitate extubation, and widen the provision of ventilator support outside the intensive care unit (ICU). Evaluation of droplet dispersion during non-invasive ventilation, oxygen therapy, nebulizer treatment and chest physiotherapy in clinical practice: implications for management of pandemic infl uenza and other airbone infections Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review abstract: The organisms causing respiratory infections such as influenza are spread in droplets or aerosols or by direct or indirect contact with contaminated surfaces. Certain medical procedures have been termed aerosol generating because they are associated with high or augmented inspiratory and expiratory flows, which can increase microbial dissemination. Invasive ventilation maneuvers and noninvasive ventilation (NIV) fall into that category. We discuss the risk of transmitting these procedures and the strategies for mechanical ventilation in future airborne epidemics with special consideration given to the issue of protecting health care workers (HCWs). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121330/ doi: 10.1007/978-3-7091-1496-4_34 id: cord-310624-3kojrkz7 author: Flores-Alanis, Alejandro title: The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789 date: 2020-08-27 words: 3064.0 sentences: 181.0 pages: flesch: 56.0 cache: ./cache/cord-310624-3kojrkz7.txt txt: ./txt/cord-310624-3kojrkz7.txt summary: In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved. abstract: OBJECTIVE: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved. url: https://doi.org/10.1186/s13104-020-05242-8 doi: 10.1186/s13104-020-05242-8 id: cord-319013-oytqcifa author: Focosi, Daniele title: Convalescent Plasma Therapy for COVID-19: State of the Art date: 2020-08-12 words: 7474.0 sentences: 335.0 pages: flesch: 41.0 cache: ./cache/cord-319013-oytqcifa.txt txt: ./txt/cord-319013-oytqcifa.txt summary: In the first retrospective, randomized controlled trial published to date, 39 patients in New York with severe COVID-19 were transfused with 2 units of ABO-type matched CP with anti-Spike antibody titers of Ն1:320 (measured by a two-step Spike proteindirected ELISA). CP (9 to 13 ml/kg from donors with S-RBD IgG titer of Ն1:640) was associated with a negative SARS-CoV-2 PCR test at 72 h in 87.2% of the CP group versus 37.5% of the BSC group, but clinical improvement at 28 days was statistically different only in patients with severe, but not in life-threatening, disease (104) . Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol Anti-SARS-CoV-2 virus antibody levels in convalescent plasma of six donors who have recovered from COVID-19 abstract: Convalescent plasma (CP) therapy has been used since the early 1900s to treat emerging infectious diseases; its efficacy was later associated with the evidence that polyclonal neutralizing antibodies can reduce the duration of viremia. Recent large outbreaks of viral diseases for which effective antivirals or vaccines are still lacking has renewed the interest in CP as a life-saving treatment. The ongoing COVID-19 pandemic has led to the scaling up of CP therapy to unprecedented levels. Compared with historical usage, pathogen reduction technologies have now added an extra layer of safety to the use of CP, and new manufacturing approaches are being explored. This review summarizes historical settings of application, with a focus on betacoronaviruses, and surveys current approaches for donor selection and CP collection, pooling technologies, pathogen inactivation systems, and banking of CP. We additionally list the ongoing registered clinical trials for CP throughout the world and discuss the trial results published thus far. url: https://www.ncbi.nlm.nih.gov/pubmed/32792417/ doi: 10.1128/cmr.00072-20 id: cord-337602-5evfkk70 author: Focosi, Daniele title: Anti‐A Isohemagglutinin titers and SARS‐CoV2 neutralization: implications for children and convalescent plasma selection date: 2020-06-09 words: 1163.0 sentences: 55.0 pages: flesch: 44.0 cache: ./cache/cord-337602-5evfkk70.txt txt: ./txt/cord-337602-5evfkk70.txt summary: . Most importantly, the Italian-Spanish genome-wide association study identified the rs657152 polymorphism in the ABO locus on chromosome 9q34 (and only another polymorphism in chromosome 3p21.31) as the only susceptibility locus for respiratory failure in COVID-19 (6) , suggesting that, in addition to disease acquisition, ABO blood group could also affect disease severity. If confirmed, this hypothesis will have implications for convalescent plasma therapy, since anti-A1 IgG could confer additional benefit over anti-SARS-CoV2 neutralizing antibodies: in fact, while preserving ABO match compatibility, it could be wiser to prefer blood group O donors for CP in COVID-19. All rights reserved Accepted Article considered that hyperimmune serum, arising from pooled diverse ABO groups, contains far lower anti-A isoagglutinin titer than an average O-group convalescent donation. The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis abstract: I read with interest the recent article by Li et al (1) detailing the risk for COVID‐19 pneumonia and ABO blood group. After demonstration that group O healthcare workers were less likely to become infected with SARS‐CoV (2), a research group proved that anti‐A blood group natural isoagglutinins inhibit SARS‐CoV entry into competent cells (3) and could opsonize viral particles leading to complement‐mediated neutralization (4). Since SARS‐CoV2 uses the same receptor as SARS‐CoV, anti‐A isoagglutinins are expected to have similar effects against SARS‐CoV2: accordingly, clusters of glycosylation sites exist proximal to the receptor‐binding motif of the SARS‐CoV and SARS‐CoV2 S protein (5). url: https://www.ncbi.nlm.nih.gov/pubmed/32516462/ doi: 10.1111/bjh.16932 id: cord-325669-6kjlcakt author: Fogacci, Silvia title: Management of pregnancy-related hypertensive disorders in patients infected with SARS CoV-2: pharmacological and clinical issues date: 2020-09-10 words: 3373.0 sentences: 186.0 pages: flesch: 38.0 cache: ./cache/cord-325669-6kjlcakt.txt txt: ./txt/cord-325669-6kjlcakt.txt summary: The purpose of the current review is to highlight the safety of drug treatment for COVID -19 in pregnant women treated with anti-hypertensive medications. In accordance with the European Society of Cardiology (ESC) guidelines for the management of CV diseases during pregnancy, 100-150 mg/day acetylsalicylic acid (aspirin) should be recommended to pregnant women with a high or moderate risk to develop pre-eclampsia (class I; level of evidence A) [17] . In accordance with the American Heart Association (AHA) recommendations [25] , methyldopa should only be prescribed in cases of severe hypertension during pregnancy, considering potential maternal and fetal side effects (class I; level of evidence A). In accordance with the latest ESC guidelines for the management of CV disease during the COVID-19 pandemic, drug-drug interactions should be considered before administering azithromycin in patients treated with LMWH [37] , despite possible beneficial effects by azithromycin in patients infected with SARS-CoV-2 [48] . abstract: AIMS: Coronavirus-19 disease (COVID-19) continues to spread throughout the world. It is known that among patients with hypertension, diabetes, chronic respiratory disease, or cardiovascular diseases, COVID-19 is associated with greater morbidity and mortality compared with patients without these conditions. This correlation is of great importance in pregnant women affected by COVID-19, since it usually leads to the development of a serious clinical complication. In particular, managing hypertensive disorders in pregnancy can be problematic because antihypertensive medications may interact pharmacologically with drugs used to treat COVID-19. This review focuses on the safety of drug treatment for COVID-19 in pregnant women treated with antihypertensive medication. METHODS AND RESULTS: Several databases were searched to identify relevant literature. A few antihypertensive drugs and antithrombotic treatments are known for having a beneficial effect in the management of hypertension and hypertensive disorders in pregnancy. In this review, we focus on the expected drug–drug interactions with the experimental agents most often used to treat COVID-19. CONCLUSIONS: The current indications for the management of hypertension-related disorders in pregnancy maintain their validity, while the risk of pharmacological interaction with the currently tested anti-SARS-CoV-2 medications is relatively low. url: https://doi.org/10.1093/ehjcvp/pvaa105 doi: 10.1093/ehjcvp/pvaa105 id: cord-302358-vou46eie author: Fomsgaard, Anna S title: An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage date: 2020-03-30 words: 1720.0 sentences: 114.0 pages: flesch: 58.0 cache: ./cache/cord-302358-vou46eie.txt txt: ./txt/cord-302358-vou46eie.txt summary: With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98°C prior to the RT-qPCR reaction. Analysis of SARS-CoV-2 positive and negative oropharyngeal swaps using the SensiFAST TM kit showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy when samples were heat-processed for 5 min. Analysis of the clinical samples using the RealStar® SARS-CoV-2 RT-PCR kit showed significant inhibition of the RT-qPCR reaction (Figure 1 ) except when the MagNA Pure and QIACube purified samples were used. Moreover, this positive result could not be confirmed by any other NA purification method or SARS-CoV-2 specific RT-qPCR assay and therefore we cannot confirm if this patient sample is truly positive for COVID-19 using the QIACube purification system or false negative using the MagNA Pure system. abstract: Abstract The World Health Organisation has declared a pandemic caused by the newly discovered SARS-CoV-2. Due to growing demand for reagents used for SARS-CoV-2 RNA extraction for subsequent molecular diagnostics, there is a worldwide risk of kit- and/or reagent-shortages for extraction. With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98°C prior to the RT-qPCR reaction. url: https://doi.org/10.1101/2020.03.27.20044495 doi: 10.1101/2020.03.27.20044495 id: cord-265228-afbkp3wm author: Fomsgaard, Anna S. title: An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020 date: 2020-04-09 words: 1797.0 sentences: 103.0 pages: flesch: 57.0 cache: ./cache/cord-265228-afbkp3wm.txt txt: ./txt/cord-265228-afbkp3wm.txt summary: The comparison of the SensiFAST Probe No-ROX One-Step Real-time PCR results using the simplified workflow to both NA purification systems is shown in Table 1 , Table 2 Comparison of results obtained with the SensiFAST Probe No-ROX One-Step Real-time PCR a assay on clinical samples, which were prior subjected to various minimal processing methods or nucleic acid extractions b , Denmark, 2020 (n = 87 patient samples c ) SARS-CoV-2 positive and negative oropharyngeal swab-samples heat-processed for 5 min at 98 °C before the RT-qPCR reaction showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy compared with MagNA Pure 96 purified samples when using the SensiFAST assay ( Table 1 ). Due to the alarmingly low accessibility to NA purification reagents and kits, we show an alternative to the MagNA Pure purification step with simple heating for 5 min at 98 °C that results in a sensitivity, specificity, and accuracy of 97.4% (95% CI: 86.2-99.9), 100.0% (95% CI: 84.6-100.0) and 98.3% (95% CI: 91.1-99.9), respectively, using the SensiFAST SARS-CoV-2 RT-qPCR assay (Supplementary Data). abstract: The World Health Organization has declared COVID-19 caused by the newly discovered SARS-CoV-2 a pandemic. Due to growing demand for reagents and/or kits to extract SARS-CoV-2 RNA for subsequent RT-qPCR diagnostics, there is a worldwide risk of shortages. With a detection sensitivity of 97.4% (95% CI: 86.2–99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 min at 98 °C before a commonly-used RT-qPCR procedure. url: https://doi.org/10.2807/1560-7917.es.2020.25.14.2000398 doi: 10.2807/1560-7917.es.2020.25.14.2000398 id: cord-275926-rj23z7po author: Fontanella, Marco M. title: Neurosurgical practice during the SARS-CoV-2 pandemic: a worldwide survey date: 2020-05-05 words: 4013.0 sentences: 234.0 pages: flesch: 52.0 cache: ./cache/cord-275926-rj23z7po.txt txt: ./txt/cord-275926-rj23z7po.txt summary: 3. Institutional plans for the SARS-CoV-2 outbreak: any special measures adopted for SARS-CoV-2 positive neurosurgical patients were investigated, i.e. their screening rate and method, any changes in surgical indications, planning and activity for oncologic procedures, non-emergency surgeries, and subarachnoid hemorrhages (SAHs). The same correlation was found with regards to the medical perception of disease activity (Q2) in different countries, and only few respondents (3%) claimed their country was not facing the outbreak during the time period studied: among them, neurosurgeons from Germany were probably the most "wrong", since their country had between 10 4 to 10 5 SARS-CoV2 patients during the study period (Fig. 4A) . 5 India and Pakistan have been reported to be the world''s best respondents to the SARS-COV-2 pandemic, 22-24 thus reflecting high rates of neurosurgical activity reorganizations. abstract: Abstract Background and Objective The SARS-CoV-2 pandemic has consistently changed medical practice throughout specialties, regardless of their contribution in facing the disease itself. We surveyed neurosurgeons worldwide to investigate the situation they are experiencing. Design and participants A 17-question, web-based survey was administered to neurosurgeons worldwide through the WFNS and the Neurosurgery Cocktail from March 28 to April 5, 2020 by web link or e-mail invitation. Questions were divided into three subgroups: general information, health system organization, and institutional plans for the SARS-CoV-2 outbreak. Collected data was initially elaborated using Survey Monkey® software. Country specific data were extracted from the WHO website. Statistical analysis was performed using R version 3.6.3. Results Of the 446 respondents, most were from Italy (20%), India (19%), and Pakistan (5%). Surgical activity was significantly reduced in most centers (79%) and dedicated in-hospital routes were created for SARS-CoV-2 patients (58%). Patient screening was performed only when there were symptoms (57%) and not routinely before surgery (18%). The preferred methods included a nasopharyngeal swab and chest x-ray. Health professionals were rarely screened (20%) and sometimes, even if SARS-CoV-2 positive, were asked to work if asymptomatic (26%). Surgical planning was changed in most institutions (92%), while indications were modified for non-urgent procedures (59%) and remained unchanged for subarachnoid hemorrhages (85%). Conclusions Most neurosurgeons worldwide reported work reorganization and practices that respond to current international guidelines. Differences in practice might be related to the perception of the pandemic and significant differences in the health systems. Sharing data and experiences will be of paramount importance to address the present moment and challenges in the near future. url: https://www.sciencedirect.com/science/article/pii/S1878875020309141?v=s5 doi: 10.1016/j.wneu.2020.04.204 id: cord-328683-zvabpty9 author: Fontanet, A. title: SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission date: 2020-06-29 words: 4046.0 sentences: 224.0 pages: flesch: 56.0 cache: ./cache/cord-328683-zvabpty9.txt txt: ./txt/cord-328683-zvabpty9.txt summary: Methods: Between 28-30 April 2020, a retrospective cohort study was conducted among pupils, their parents and relatives, and staff of primary schools exposed to SARS-CoV-2 in February and March 2020 in a city north of Paris, France. Seroepidemiological studies are thus needed to determine the extent of infection in children and to decipher the role they may play in transmission To our knowledge, the number of SARS-CoV-2 secondary transmissions in school setting documented in scientific literature is limited, with very few or no secondary cases in investigations in . The epidemic curve, based on symptoms experienced by participants with SARS-CoV-2 antibodies, had no specific pattern, and transmission does not appear to have been impacted by the closure of schools for holidays on February 14 (end of week 7) ( Figure 2A ). They differ however from the results of the study performed in the high school of the same city in France, in which 38% of pupils, 43% of teaching staff and 59% of nonteaching staff who participated in the investigation had anti-SARS-CoV-2 antibodies 27 . abstract: Background: The extent of SARS-CoV-2 transmission among pupils in primary schools and their families is unknown. Methods: Between 28-30 April 2020, a retrospective cohort study was conducted among pupils, their parents and relatives, and staff of primary schools exposed to SARS-CoV-2 in February and March 2020 in a city north of Paris, France. Participants completed a questionnaire that covered sociodemographic information and history of recent symptoms. A blood sample was tested for the presence of anti-SARS-CoV-2 antibodies using a flow-cytometry-based assay. Results: The infection attack rate (IAR) was 45/510 (8.8%), 3/42 (7.1%), 1/28 (3.6%), 76/641 (11.9%) and 14/119 (11.8%) among primary school pupils, teachers, non-teaching staff, parents, and relatives, respectively (P = 0.29). Prior to school closure on February 14, three SARS-CoV-2 infected pupils attended three separate schools with no secondary cases in the following 14 days among pupils, teachers and non-teaching staff of the same schools. Familial clustering of cases was documented by the high proportion of antibodies among parents and relatives of infected pupils (36/59 = 61.0% and 4/9 = 44.4%, respectively). In children, disease manifestations were mild, and 24/58 (41.4%) of infected children were asymptomatic. Interpretation: In young children, SARS-CoV-2 infection was largely mild or asymptomatic and there was no evidence of onwards transmission from children in the school setting. url: http://medrxiv.org/cgi/content/short/2020.06.25.20140178v1?rss=1 doi: 10.1101/2020.06.25.20140178 id: cord-270355-5mljrk1h author: Fontanet, Arnaud title: Les enseignements du SRAS date: 2007-02-28 words: 2339.0 sentences: 166.0 pages: flesch: 61.0 cache: ./cache/cord-270355-5mljrk1h.txt txt: ./txt/cord-270355-5mljrk1h.txt summary: Points essentiels Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l''homme; d''où l''importance d''une détection précoce par la surveillance des foyers épidémiques inhabituels. Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l''homme ; d''où l''importance d''une détection précoce par la surveillance des foyers épidémiques inhabituels. Un même scénario est plausible dans le contexte de la grippe aviaire, où les virus directement contractés au contact des volailles n''ont heureusement pas encore (ou exceptionnellement) été à l''origine de transmission interhumaine [11] . Modes de transmission, durée d''incubation et période de contagiosité ont été rapidement connus [12] , avant même que l''agent infectieux ne soit identifié, ce qui a permis d''instaurer des mesures de prévention efficaces associant protection contre les germes respiratoires, isolement des cas, quarantaine des contacts, et restriction des déplacements. abstract: Key points Given that viruses may not have adapted to human-to-human transmission during their initial emergence in humans, they may thus be easier to control; accordingly, early detection by surveillance of unusual outbreaks is essential. Our healthcare systems are very vulnerable to viruses with a particular tropism for hospital personnel. International collaboration by teams of epidemiologists as well as virologists was the key to success against SARS (severe acute respiratory syndrome). We were lucky in the fight against SARS, the virus was in fact moderately transmissible and then only after the onset of symptoms. It was thus possible to isolate cases before they became contagious. SARS provided a good “dress rehearsal” and educated the public authorities about the issues of infectious pandemics. The specific types of new epidemics cannot be predicted but they are inevitable. Points essentiels Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l'homme; d'où l'importance d'une détection précoce par la surveillance des foyers épidémiques inhabituels. Nos systèmes de santé sont très vulnérables face à des virus ayant un tropisme particulier pour le personnel hospitalier. La collaboration internationale, tant pour les équipes d'épidémiologistes que de virologues, a été la clef du succès de la lutte contre le SRAS (Syndrome respiratoire aigu sévère). Nous avons eu beaucoup de chance avec le SRAS: le virus était finalement peu transmissible, et seulement après le début des symptômes, permettant d'identifier et d'isoler les cas avant la période contagieuse. L'épidémie de SRAS a servi de “répétition générale”, permettant la prise de conscience par les pouvoirs publics des enjeux posés par les pandémies d'origine infectieuse. De nouvelles épidémies, quelles qu'elles soient, sont inéluctables. url: https://api.elsevier.com/content/article/pii/S075549820600114X doi: 10.1016/j.lpm.2006.12.005 id: cord-352228-dzkf7c7l author: Fontanet, Arnaud title: Cluster of COVID-19 in northern France: A retrospective closed cohort study date: 2020-04-23 words: 4248.0 sentences: 225.0 pages: flesch: 54.0 cache: ./cache/cord-352228-dzkf7c7l.txt txt: ./txt/cord-352228-dzkf7c7l.txt summary: Methods: Between 30 March and 4 April 2020, we conducted a retrospective closed cohort study among pupils, their parents and siblings, as well as teachers and non-teaching staff of a high-school located in Oise. Participants completed a questionnaire that covered history of fever and/or respiratory symptoms since 13 January 2020 and had blood tested for the presence of anti-SARS-CoV-2 antibodies. Interpretation: The relatively low IAR observed in an area where SARS-CoV-2 actively circulated weeks before confinement measures indicates that establishing herd immunity will take time, and that lifting these measures in France will be long and complex. Using a combination of serologic assays with high sensitivity and specificity for anti-SARS-CoV-2 antibodies, we conducted a retrospective closed cohort study. This is, to our knowledge, the first study estimating by antibody detection the IAR of SARS-CoV-2 infection in a community affected by COVID-19, and the fist description of a COVID-19 outbreak in a school. abstract: Background: The Oise department in France has been heavily affected by COVID-19 in early 2020. Methods: Between 30 March and 4 April 2020, we conducted a retrospective closed cohort study among pupils, their parents and siblings, as well as teachers and non-teaching staff of a high-school located in Oise. Participants completed a questionnaire that covered history of fever and/or respiratory symptoms since 13 January 2020 and had blood tested for the presence of anti-SARS-CoV-2 antibodies. The infection attack rate (IAR) was defined as the proportion of participants with confirmed SARS-CoV-2 infection based on antibody detection. Blood samples from two blood donor centres collected between 23 and 27 March 2020 in the Oise department were also tested for presence of anti-SARS-CoV-2 antibodies. Findings: Of the 661 participants (median age: 37 years), 171 participants had anti-SARS-CoV-2 antibodies. The overall IAR was 25.9% (95% confidence interval (CI) = 22.6-29.4), and the infection fatality rate was 0% (one-sided 97.5% CI = 0-2.1). Nine of the ten participants hospitalised since mid-January were in the infected group, giving a hospitalisation rate of 5.3% (95% CI = 2.4-9.8). Anosmia and ageusia had high positive predictive values for SARS-CoV-2 infection (84.7% and 88.1%, respectively). Smokers had a lower IAR compared to non-smokers (7.2% versus 28.0%, P <0.001). The proportion of infected individuals who had no symptoms during the study period was 17.0% (95% CI = 11.2-23.4). The proportion of donors with anti-SARS-CoV-2 antibodies in two nearby blood banks of the Oise department was 3.0% (95% CI = 1.1-6.4). Interpretation: The relatively low IAR observed in an area where SARS-CoV-2 actively circulated weeks before confinement measures indicates that establishing herd immunity will take time, and that lifting these measures in France will be long and complex. url: https://doi.org/10.1101/2020.04.18.20071134 doi: 10.1101/2020.04.18.20071134 id: cord-308234-4obggisp author: Ford, Nathan title: Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID‐19: initial assessment date: 2020-04-15 words: 2845.0 sentences: 137.0 pages: flesch: 45.0 cache: ./cache/cord-308234-4obggisp.txt txt: ./txt/cord-308234-4obggisp.txt summary: RESULTS: From an initial screen of 433 titles, two randomized trials and 24 observational studies provided clinical outcome data on the use of antiretroviral drugs; most studies reported outcomes using LPV/r as treatment. The use of lopinavir/ritonavir (LPV/r) has been supported by data from in vitro studies, animal models and positive clinical outcomes when LPV/r was given to patients infected with severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) diseases also caused by coronaviruses [2] [3] [4] [5] . Lopinavir/ritonavir (LPV/r) is included in rapid guidance issued by researchers from Wuhan University based on clinical use during prior epidemics of severe acute respiratory syndrome (SARS) and MERS coronavirus (CoV) infections [6] . This systematic review identified two randomized trials and 21 observational studies provided clinical outcome data on the use of LPV/r for the treatment of COVID-19, SARS and MERS. abstract: INTRODUCTION: Several antiretroviral drugs are being considered for the treatment of COVID‐19, the disease caused by a newly identified coronavirus, (SARS‐CoV‐2). We systematically reviewed the clinical outcomes of using antiretroviral drugs for the prevention and treatment of coronaviruses and planned clinical trials. METHODS: Three databases were screened from inception to 30 March 2020 for studies reporting clinical outcomes of patients with SARS, MERS or COVID‐19 treated with antiretrovirals. RESULTS: From an initial screen of 433 titles, two randomized trials and 24 observational studies provided clinical outcome data on the use of antiretroviral drugs; most studies reported outcomes using LPV/r as treatment. Of the 21 observational studies reporting treatment outcomes, there were three studies among patients with SARS, six studies among patients with MERS and 12 studies among patients with COVID‐19. In one randomized trial 99 patients with severe COVID‐19 illness were randomized to receive LPV/r (400/100 mg twice a day) and 100 patients to standard of care for 14 days: LPV/r was not associated with a statistically significant difference in time to clinical improvement, although LPV/r given within 12 days of symptoms was associated with shorter time to clinical improvement; 28 day mortality was numerically lower in the LPV/r group (14/99) compared to the control group (25/100), but this difference was not statistically significant. The second trial found no benefit. The certainty of the evidence for the randomized trials was low. In the observational studies 3 out of 361 patients who received LPV/r died; the certainty of evidence was very low. Three studies reported a possible protective effect of LPV/r as post‐exposure prophylaxis. Again, the certainty of the evidence was very low due to uncertainty due to limited sample size. CONCLUSIONS: On the basis of the available evidence it is uncertain whether LPV/r and other antiretrovirals improve clinical outcomes or prevent infection among patients at high risk of acquiring COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32293807/ doi: 10.1002/jia2.25489 id: cord-315289-4x229n8n author: Foresta, C. title: Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome date: 2020-09-16 words: 3417.0 sentences: 166.0 pages: flesch: 43.0 cache: ./cache/cord-315289-4x229n8n.txt txt: ./txt/cord-315289-4x229n8n.txt summary: Although it is assumed that older men have more comorbidities than women of similar age, a tentative hypothesis to explain these epidemiologic findings is the role of the angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 engages ACE2 in alveolar epithelial On the top of the figure, epidemiological data from the Italian Ministry of Health are reported, with respective gender distribution of cases and deaths. The lack of increased ACE2 pool in men due to low estrogens would favor the ACE pathway (red arrows) in the RAS axis, which further promotes tissue injury and disease severity in men, compared with women with the same viral load cells as the entry receptor and employs the serine protease TMPRSS2 for S protein priming [8, 9] . Altogether, available evidence points toward two not-mutually exclusive mechanisms in differential gender susceptibility to COVID-19 by sex hormonal regulation of the two main actors in SARS-CoV-2 infection: ACE2 and TMPRSS2. abstract: BACKGROUND: The recent emergence of COVID-19 poses a global health emergency. One of the most frequently reported data is sex-related severity and mortality: according to the last available analysis on 239,709 patients in Italy, lethality is 17.7% in men and 10.8% in women, with 59% of total deaths being men. Interestingly, the infection rate is lower in males than in females, with 45.8% and 54.2% of positive cases, respectively, suggesting that gender-related factor may worsen disease evolution. A tentative hypothesis to explain these findings is the role of angiotensin-converting enzyme 2 (ACE2) and serine protease TMPRSS2 involved in viral infection. PURPOSE: In this review, we summarize the available evidence pointing to gender-related differences in ACE2 and TMPRSS2 expression, from both genetic and endocrine points of view. RESULTS: Altogether, available evidence points toward two not-mutually exclusive mechanisms in gender susceptibility to COVID-19 by sex hormonal regulation of ACE2 and TMPRSS2. On one hand, ACE2 expression could be increased in women, either by estrogens or constitutively by X chromosome inactivation escape or by reduced methylation, providing a larger reservoir of ACE2 to maintain the fundamental equilibrium of RAS regulatory axis. On the other, low levels of androgens in women may keep at low levels TMPRSS2 expression, representing a further protective factor for the development of COVID-19 infection, despite the increased expression of ACE2, which represents the Trojan horse for SARS-CoV-2 entry. CONCLUSIONS: Both mechanisms consistently point to the role of sex hormones and sex chromosomes in the differential severity and lethality of COVID-19 in men and women. url: https://doi.org/10.1007/s40618-020-01383-6 doi: 10.1007/s40618-020-01383-6 id: cord-311377-ffkwis40 author: Forns, Xavier title: Inmunosupresión en el trasplante hepático en la era Covid-19 date: 2020-06-12 words: 3930.0 sentences: 344.0 pages: flesch: 50.0 cache: ./cache/cord-311377-ffkwis40.txt txt: ./txt/cord-311377-ffkwis40.txt summary: La presencia de linfopenia con neutrofilia, niveles elevados de IL-6, incremento de la proteína C reactiva así como el hallazgo de niveles elevados de citoquinas asociadas a la inmunidad innata como IP-10, MCP-1, MIP-1α y TNFα sugieren que ésta juega un papel muy importante en la respuesta inflamatoria asociada a la infección (que también se observó con el SARS-CoV y MERS-CoV) y por tanto, sea responsable de la evolución hacia la gravedad de Covid La respuesta efectora inmune innata contra los virus se basa mayoritariamente en el interferón (IFN-1) (23). En caso de enfermedad grave Covid 19, la substitución temporal de anticalcineurínicos y micofenolato mofetilo (MMF) por GC permite a estos pacientes evitar efectos indeseables secundarios a la interacción de dichos inmunosupresores con los múltiples medicamentos que reciben para el tratamiento de la infección por SARS-Cov 2. abstract: Abstract SARS CoV-2 infection has produced a pandemic with serious consequences for our health care system. Although liver transplant patients represent only a minority of the population, the hepatologists who follow these patients have tried to coordinate efforts to produce a protocol the management of immunosuppression during SARS Cov-2 infection. Although there are no solid studies to support general recommendations, experiences with other viral infections (hepatitis C, cytomegalovirus) suggest that management of immunosuppression without mycophenolate mofetil or m-Tor inhibitors (drugs that are also associated with leukopenia and lymphopenia) may be beneficial. It is also important to pay attention to possible drug interactions, especially in the case of tacrolimus, with some of the treatments with antiviral effect given in the context of COVID 19 (lopinavir/ritonavir, azithromycin). Finally, the immunosuppressive effect of immunomodulating drugs (tocilizumab and similar) administered to patients with severe lung disease should be taken into account. The mechanisms of action of the different immunosuppressive drugs are reviewed in this article, as well as their potential effect on Cov-2 SARS infection, and suggests guidelines for the management of immunosuppression. url: https://api.elsevier.com/content/article/pii/S0210570520302156 doi: 10.1016/j.gastrohep.2020.06.003 id: cord-325863-3t73v4ng author: Foss, Francine M. title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib date: 2020-06-25 words: 1989.0 sentences: 113.0 pages: flesch: 45.0 cache: ./cache/cord-325863-3t73v4ng.txt txt: ./txt/cord-325863-3t73v4ng.txt summary: title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib We report a mild and attenuated SARS CoV-2 infection in a patient who is 17 months post stem cell transplantation and maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia. Due to the signal transduction role that the JAK-STAT pathway plays in mediating Immune-effector cell activation, there has been interest in pursuing inhibitors of this pathway as potential therapeutic agents in mitigating COVID19-associated lung inflammation 9, 10 . We recently diagnosed COVID19 infection in a patient who was on oral ruxolitinib for management of graft-vs-host disease after allogeneic stem cell transplant and report on his presentation and the evolution of his clinical course. Our patient was 17 months post stem cell transplantation and was maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia, throughout his clinical course with successful attenuation of symptoms. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has a high death rate in patients with comorbidities or in an immunocompromised state. We report a mild and attenuated SARS CoV-2 infection in a patient who is 17 months post stem cell transplantation and maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia. url: https://www.sciencedirect.com/science/article/pii/S2152265020303128?v=s5 doi: 10.1016/j.clml.2020.06.014 id: cord-270399-yfko8mpc author: Foster, Allison title: It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date: 2020-10-15 words: 3390.0 sentences: 210.0 pages: flesch: 47.0 cache: ./cache/cord-270399-yfko8mpc.txt txt: ./txt/cord-270399-yfko8mpc.txt summary: title: It''s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury In this report, we discuss a unique case of an HIV-positive patient in New York City who presented with a 2-week history of worsening fatigue, cough, dyspnea, and myalgias and was found to have COVID-19 pneumonia and acute kidney injury. The pathophysiologic mechanisms of acute kidney injury, SARS-CoV-2 renal tropism, and the impact of highly active antiretroviral therapy on COVID-19 pneumonia are discussed. 20 Whether directly through involvement of SARS-CoV-2 interaction with ACE-2 receptor or indirectly from causing hypotension from an undetermined mechanism, this patient''s decline in renal function can be attributed to his acute infection with COVID-19. [24] [25] [26] Our patient''s exceptional clinical course despite having HIV lends to the idea that his HAART regimen as well as his azithromycin use prior to presentation may have decreased the total amount of SARS-CoV-2 viral replication in both the renal parenchyma and pulmonary tissue resulting in a rapid recovery and subsequent hospital discharge. abstract: The SARS-Cov-2/COVID-19 pandemic in early 2020 has had a devastating impact on health systems around the world. While viral pneumonia remains the most common complication, reports are surfacing of cases with neurological, cardiac, and renal involvement. Even less is known about the implications in special high-risk populations. In this report, we discuss a unique case of an HIV-positive patient in New York City who presented with a 2-week history of worsening fatigue, cough, dyspnea, and myalgias and was found to have COVID-19 pneumonia and acute kidney injury. He was managed for severe uremic metabolic acidosis and electrolyte abnormalities with emergent hemodialysis and supportive therapy with subsequent improvement. Direct involvement of SARS-CoV-2 and pneumonia-induced rhabdomyolysis were identified as the precipitating factors of his acute kidney injury. The pathophysiologic mechanisms of acute kidney injury, SARS-CoV-2 renal tropism, and the impact of highly active antiretroviral therapy on COVID-19 pneumonia are discussed. We highlight the importance of clinician awareness of this potentially fatal complication of COVID-19 pneumonia, particularly in the HIV-positive population as early recognition and management can have favorable outcomes. url: https://doi.org/10.1177/2050313x20965423 doi: 10.1177/2050313x20965423 id: cord-324255-ize21we2 author: Fouchier, Ron A. M. title: Koch''s postulates fulfilled for SARS virus date: 2003 words: 769.0 sentences: 44.0 pages: flesch: 47.0 cache: ./cache/cord-324255-ize21we2.txt txt: ./txt/cord-324255-ize21we2.txt summary: Severe acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003). S evere acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003) . We inoculated two macaques with Vero-cellcultured SCV isolated from a fatal SARS case, and monitored their clinical signs, virus excretion and antibody response. The macaques excreted virus from the nose and throat at 2-6 d.p.i., as shown by polymerase chain reaction with reverse transcription (RT-PCR) and by virus isolation (see supplementary information). At gross necropsy, one macaque had severe multifocal pulmonary consolidation, and SCV infection was detected in lung tissue by RT-PCR and virus isolation. However, these were not present in SCV-inoculated macaques (results not shown), were not found consistently in SARS patients, and do not usually cause the lesions associated with SARS. abstract: Severe acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003). Here we provide proof from experimental infection of cynomolgus macaques (Macaca fascicularis) that the newly discovered SARS-associated coronavirus (SCV) is the aetiological agent of this disease. Our understanding of the aetiology of SARS will expedite the development of diagnostic tests, antiviral therapies and vaccines, and may allow a more concise case definition for this emerging disease. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/423240a) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/12748632/ doi: 10.1038/423240a id: cord-307842-7q2jd0mf author: Fox, Alisa title: Robust and specific secretory IgA against SARS-CoV-2 detected in human milk date: 2020-10-26 words: 467.0 sentences: 40.0 pages: flesch: 58.0 cache: ./cache/cord-307842-7q2jd0mf.txt txt: ./txt/cord-307842-7q2jd0mf.txt summary: The SARS-CoV-2 immune response in human milk has not yet been examined, though protecting infants and young children from COVID-19 is critical for limiting community transmission, and preventing serious illness and death. Milk samples were initially evaluated for IgA binding reactivity by human IgA-specific ELISA to the 88 full trimeric SARS-CoV-2 Spike (Fig. 1) . It was evident that all samples obtained from COVID-19-89 recovered donors (100%), in undiluted form, exhibited binding activity significantly above that of the 90 pre-pandemic control milk samples, which did exhibit some low-level non-specific or cross-reactive 91 activity (Fig. 1a) . It was found 92 that all COVID-19-recovered samples exhibited endpoint titers significantly higher than control samples evident that most of the samples contained SARS-CoV-2-reactive IgA without necessarily containing 146 measurable IgG and/or IgM, which particularly in the case of IgG, would likely be derived in large part 147 from the serum. abstract: The SARS-CoV-2 immune response in human milk has not yet been examined, though protecting infants and young children from COVID-19 is critical for limiting community transmission, and preventing serious illness and death. Here, milk samples from 8 COVID-19-recovered and 7 COVID-19-suspected donors were tested for antibody (Ab) binding to the SARS-CoV-2 Spike protein. All samples exhibited significant specific IgA reactivity to the full Spike, while 80% exhibited significant IgA and secretory (s)Ab binding to the receptor binding domain (RBD). Additionally, 67% of samples exhibited IgG and/or IgM binding to RBD. IgA and sAb titers were highly correlated, indicating most IgA to be sIgA. Overall, these data indicate that a robust sIgA-dominant SARS-CoV-2 Ab response in human milk after infection should be expected in a significant majority of individuals. Further research is highly warranted to determine Ab functionality, and the potential for exploiting extracted milk sIgA for therapeutic use. url: https://doi.org/10.1016/j.isci.2020.101735 doi: 10.1016/j.isci.2020.101735 id: cord-301779-y07xjnpe author: Fox, Sharon E title: Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans date: 2020-05-27 words: 3284.0 sentences: 174.0 pages: flesch: 44.0 cache: ./cache/cord-301779-y07xjnpe.txt txt: ./txt/cord-301779-y07xjnpe.txt summary: INTERPRETATION: We identify key pathological states, including thrombotic and microangiopathic pathology in the lungs, that contributed to death in patients with severe COVID-19 and decompensation in this demographic. Evidence before this study We reviewed the single study of autopsy in a COVID-19 positive patient by Z Xu and colleagues, published in this journal, and reports of pathology from severe acute respiratory syndrome (SARS) coronavirus and similar viral infections by J Nicholls. Previous evidence [10] [11] [12] [13] [14] reports viral infection causing activation of both maladaptive cytokine pathways and a platelet response, and our findings suggest that these immune functions might be related to severe forms of COVID-19. We do not have evidence of direct infection of megakaryocytes by SARS-CoV-2, but the abundance of these cells in the lungs at autopsy is probably related to the abundance of small, sometimes platelet-rich thrombi, and foci of haemorrhage. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly across the USA, causing extensive morbidity and mortality, particularly in the African American community. Autopsy can considerably contribute to our understanding of many disease processes and could provide crucial information to guide management of patients with coronavirus disease 2019 (COVID-19). We report on the relevant cardiopulmonary findings in, to our knowledge, the first autopsy series of ten African American decedents, with the cause of death attributed to COVID-19. METHODS: Autopsies were performed on ten African American decedents aged 44–78 years with cause of death attributed to COVID-19, reflective of the dominant demographic of deaths following COVID-19 diagnosis in New Orleans. Autopsies were done with consent of the decedents' next of kin. Pulmonary and cardiac features were examined, with relevant immunostains to characterise the inflammatory response, and RNA labelling and electron microscopy on representative sections. FINDINGS: Important findings include the presence of thrombosis and microangiopathy in the small vessels and capillaries of the lungs, with associated haemorrhage, that significantly contributed to death. Features of diffuse alveolar damage, including hyaline membranes, were present, even in patients who had not been ventilated. Cardiac findings included individual cell necrosis without lymphocytic myocarditis. There was no evidence of secondary pulmonary infection by microorganisms. INTERPRETATION: We identify key pathological states, including thrombotic and microangiopathic pathology in the lungs, that contributed to death in patients with severe COVID-19 and decompensation in this demographic. Management of these patients should include treatment to target these pathological mechanisms. FUNDING: None. url: https://www.sciencedirect.com/science/article/pii/S2213260020302435 doi: 10.1016/s2213-2600(20)30243-5 id: cord-316179-kmdxltie author: Fozouni, P. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 words: 8244.0 sentences: 507.0 pages: flesch: 58.0 cache: ./cache/cord-316179-kmdxltie.txt txt: ./txt/cord-316179-kmdxltie.txt summary: Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. When the SARS-CoV-2 sequence became public in January 2020, we set out to develop a Cas13-based direct-detection assay for viral RNA that would avoid the need for amplification and enable point-of-care testing. We tested the performance of the device for detecting SARS-CoV-2 RNA using the triple-crRNA Cas13a assay and a dilution series with full viral RNA isolated from supernatants of infected Vero CCL-81 cells . (B) RNPs made with crRNA 2 and crRNA 4 individually and in combination (50 nM total RNP concentration for each reaction) were tested against 2.9 x 10 5 copies/µL (480 fM) of SARS-CoV-2 IVT N gene RNA, and compared to fluorescence from no target RNA RNP alone controls ("RNP 2," "RNP 4," and "RNP 2+4"). abstract: The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre- symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ~100 copies/L sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2. url: https://doi.org/10.1101/2020.09.28.20201947 doi: 10.1101/2020.09.28.20201947 id: cord-343090-dsjq98ks author: Fragkou, Paraskevi C. title: Review of trials currently testing treatment and prevention of COVID-19 date: 2020-05-23 words: 2027.0 sentences: 153.0 pages: flesch: 46.0 cache: ./cache/cord-343090-dsjq98ks.txt txt: ./txt/cord-343090-dsjq98ks.txt summary: OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. property to achieve at least 10-fold higher concentrations in epithelial lung fluid than in 202 serum, have led researchers to repurpose them against SARS-CoV-2 (Table 1, Table S1 observations the antifibrotic agent pirfenidone is being evaluated in at least three randomised 215 clinical trials for its efficacy in the prevention of post-COVID-19 pneumonia fibrosis (Table 216 1, Table S1 ). Among the eligible treatment studies, 310 children recruitment (i.e.< 14 years old) was reported in 7 clinical trials in total: 1 testing 311 darunavir with cobicistat (NCT04252274); 2 on human stem cells transfusion 312 (ChiCTR2000029606, ChiCTR2000030944); 1 testing hydroxycholoroquine (EudraCT 313 Phase IV and phase III treatment trials were the most commonly reported interventional study 319 types (n=40, 20% and n=35, 18% respectively) as demonstrated in Table 3 . abstract: BACKGROUND: As COVID-19 cases continue to rise globally, evidence from large randomised controlled trials is still lacking. Currently, numerous trials testing potential treatment and preventative options are undertaken all over the world. OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. Additionally, we evaluated the quality of the retrieved studies. DATA SOURCES: Clinicaltrials.gov, the Chinese Clinical Trial Registry and the European Union Clinical Trials Register were systematically searched. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. No language, country or study design restrictions were applied. We excluded withdrawn or cancelled studies and trials not reporting therapeutic or preventative strategies for COVID-19. PARTICIPANTS: and interventions: No restrictions in terms of participants’ age and medical background or type of intervention were enforced. METHODS: The registries were searched using the term “coronavirus” or “COVID-19” from their inception until 26(th) March 2020.Additional manual search of the registries was also performed. Eligible studies were summarised and tabulated. Interventional trials were methodologically analysed, excluding expanded access studies and trials testing Traditional Chinese Medicine. RESULTS: In total, 309 trials evaluating therapeutic management options, 23 studies assessing preventive strategies and 3 studies examining both were retrieved. Finally, 214 studies were methodologically reviewed. Interventional treatment studies were mostly randomised (n=150, 76%) and open-label (n=73, 37%) with a median number of planned inclusions of 90 (IQR 40-200). Major categories of interventions that are currently being investigated are discussed. CONCLUSION: Numerous clinical trials have been registered since the onset of the COVID-19 pandemic. Summarised data on these trials will assist physicians and researchers to promote patient care and guide future research efforts for COVID-19 pandemic containment. url: https://www.sciencedirect.com/science/article/pii/S1198743X20302962?v=s5 doi: 10.1016/j.cmi.2020.05.019 id: cord-336782-0zkb39v1 author: Fraile Gutiérrez, V. title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine date: 2020-11-02 words: 6658.0 sentences: 394.0 pages: flesch: 47.0 cache: ./cache/cord-336782-0zkb39v1.txt txt: ./txt/cord-336782-0zkb39v1.txt summary: title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine The disease caused by SARS-CoV-2 (COVID-19) is characterized by pneumonia clinical presentation with fever and cough accompanied by multifocal nodular (round or oval) ground-glass opacities in the lungs that can progress to acute respiratory distress syndrome (ARDS) and requires admission to an Intensive Care Medicine Service (ICMS) in a high percentage of patients. Ultrasound can be a very useful tool during the management of the COVID-19 pandemic because it provides real-time non-invasive bedside images of patients admitted to intensive care units (ICU). • It is superior to the simple x-ray for the detection of pneumothorax, pleural effusion, pneumonia, interstitial syndrome, and for the differential diagnosis of acute dyspnea • In the thoracic ultrasound, the clinical signs are the determinant factor regarding the interpretation of the data obtained. abstract: The clinical picture of SARS-CoV-2 infection (COVID-19) is characterized in its more severe form, by an acute respiratory failure which can worsen to pneumonia and acute respiratory distress syndrome (ARDS), and get complicated with thrombotic events and heart dysfunction. Therefore, admission to the Intensive Care Unit (ICU) is common. Ultrasound, which has become an everyday tool in the ICU, can be very useful during COVID-19 pandemic, since it provides the clinician with information which can be interpreted and integrated within a global assessment during the physical examination. A description of some of the potential applications of ultrasound is depicted in this document, in order to supply the physicians taking care of these patients with a adapted guide to the intensive care setting. Some of its applications since ICU admission include verification of the correct position of the endotracheal tube, contribution to safe cannulation of lines, and identification of complications and thrombotic events. Furthermore, pleural and lung ultrasound can be an alternative diagnostic test to assess the degree of involvement of the lung parenchyma by means of the evaluation of specific ultrasound patterns, identification of pleural effusions and barotrauma. Echocardiography provides information of heart involvement, detects cor pulmonale and shock states. url: https://www.sciencedirect.com/science/article/pii/S2173572720301752 doi: 10.1016/j.medine.2020.10.002 id: cord-270458-7imgvale author: Franchini, Massimo title: The impact of the SARS‐CoV‐2 outbreak on the safety and availability of blood transfusions in Italy date: 2020-04-13 words: 1525.0 sentences: 78.0 pages: flesch: 50.0 cache: ./cache/cord-270458-7imgvale.txt txt: ./txt/cord-270458-7imgvale.txt summary: The CNS has already released since 22 January 2020 a recommendation outlining preventative measures for the transmission of SARS-CoV-2 by transfusion of labile blood components related to travels from the People''s Republic of China. On 2 March 2020, following the recommendations of the European Centre for Disease Prevention and Control (ECDC) [9] and reflecting the decrees of the Italian government, the CNS updated the prevention measures, reducing the period of temporary deferral of donors from the previous 28 to 14 days. Following the declaration of the government of the widespread dissemination of the SARS-CoV-2 infection in Italy, the last update of the CNS on 10 March 2020 extended these measures to the whole national territory of Italy. In Fig. 1 , the trend of positive cases for SARS-CoV-2 infection in Italy, updated on 20 March 2020, is reported with a concise chronology of the main documents released and the trend of blood donations in the same period. abstract: Coronaviruses are enveloped single-stranded RNA viruses belonging to the family of Coronaviridae. While initial research focused on their ability to cause enzootic infections, infections which have emerged in the past two decades demonstrate their ability to cross the species barrier and infect humans [1,2]. The ensuing epidemics have included Severe Acute Respiratory Syndrome (SARS) in 2002 and the more recent Middle East Respiratory Syndrome (MERS) in 2012, and have resulted in severe disease burden, mortality and economic disruption [3]. A novel flu-like coronavirus, emerging towards the end of 2019 and subsequently named SARS-CoV-2, has been associated with an epidemic initially focused in Wuhan, China. url: https://doi.org/10.1111/vox.12928 doi: 10.1111/vox.12928 id: cord-337753-olc00glo author: Franco, D. title: Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. date: 2020-08-04 words: 2737.0 sentences: 160.0 pages: flesch: 52.0 cache: ./cache/cord-337753-olc00glo.txt txt: ./txt/cord-337753-olc00glo.txt summary: The protocol EC-CNBI-202-04-46 was approved by the National Committee on Bioethics of Research of Panama to use de-identified epidemiological data to analyze SARS-CoV-2 transmission and spread, as well as to sequence the complete genome of SARS-CoV-2 from Gorgas Memorial Institute of Health Studies (GMI)''s confirmed cases. . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama detected the first SARS-CoV-2 infection one month after Brazil 15 , being the 11 th country with confirmed cases in Latin America (Supplementary Figure 2) . To characterize the distribution of genetic lineages in Panama, we generated 313 SARS-CoV-2 sequences, which represents 7.4 % of the total confirmed cases by April 15 th (Supplementary Figure 4A Figure 4A ). . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama has the most confirmed SARS-CoV-2 infections and associated fatalities in Central America, although control strategies were rapidly implemented at the beginning of the outbreak. abstract: Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease control strategies. We investigated the early transmission patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number (Rt) using date of symptom onset in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission clusters is crucial to interrupt local transmission of SARS-CoV-2 in a region. url: https://doi.org/10.1101/2020.07.31.20160929 doi: 10.1101/2020.07.31.20160929 id: cord-311144-tumtzad8 author: Franco-Muñoz, Carlos title: Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date: 2020-09-17 words: 2822.0 sentences: 163.0 pages: flesch: 54.0 cache: ./cache/cord-311144-tumtzad8.txt txt: ./txt/cord-311144-tumtzad8.txt summary: A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016) . The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with J o u r n a l P r e -p r o o f Journal Pre-proof 80-100% of the reported sequences ( Fig. 2A) . abstract: SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests. url: https://www.ncbi.nlm.nih.gov/pubmed/32950697/ doi: 10.1016/j.meegid.2020.104557 id: cord-274341-vrwmxwvm author: Frank, Carlos Henrique Michiles title: Guillain–Barré Syndrome Associated with SARS-CoV-2 Infection in a Pediatric Patient date: 2020-07-12 words: 1744.0 sentences: 96.0 pages: flesch: 42.0 cache: ./cache/cord-274341-vrwmxwvm.txt txt: ./txt/cord-274341-vrwmxwvm.txt summary: We report the case of a 15-year-old male patient presenting frontal headaches with retro-orbital pain accompanied by fever evolving to weakness and pain of the lower limbs, which ascended to upper limbs. Here, we report a pediatric case involving a progressive acute symmetrical paralysis of the lower and upper limbs, with an upward evolution, which was possibly related to SARS-CoV-2 infection. Given the patient''s clinical history of a rapidly progressive symmetrical weakness with supporting electroneurography findings, a recent SARS-CoV-2 infection confirmed through the PCR test, negative microbiologic results for other etiologies in CSF and normal MRI, a diagnosis of GBS associated with COVID-19 was made. According to the most recently published systematic review on neurological manifestations in patients with COVID-19, studies have shown data ranging from common, non-specific symptoms to more complex and life-threatening conditions, such as cerebrovascular diseases, encephalopathies and GBS [5] . abstract: We report the case of a 15-year-old male patient presenting frontal headaches with retro-orbital pain accompanied by fever evolving to weakness and pain of the lower limbs, which ascended to upper limbs. A COVID-19 rapid test (IgG and IgM) and nasopharyngeal swab polymerase chain reaction (PCR) was positive for SARS-CoV-2. The blood tests, cerebral spinal fluid (CSF) analysis and CSF aerobic culture revealed no abnormalities. PCR testing of the CSF was negative for the most prevalent etiologies as well as for SARS-CoV-2. Electroneurography study was compatible with the acute motor axonal neuropathy variant of Guillain–Barré syndrome. No cases involving young patients have been presented to date. Therefore, this is the first reported pediatric case of SARS-CoV-2 infection associated with GBS. Evidence reveals that SARS-CoV-2 infection is not limited to the respiratory tract. Neurotropism could explain this important neurologic manifestation of COVID-19 in children. url: https://www.ncbi.nlm.nih.gov/pubmed/32653906/ doi: 10.1093/tropej/fmaa044 id: cord-299432-lbv69du4 author: Franklin, Alan B. title: Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen date: 2020-05-12 words: 2104.0 sentences: 126.0 pages: flesch: 56.0 cache: ./cache/cord-299432-lbv69du4.txt txt: ./txt/cord-299432-lbv69du4.txt summary: Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal waste water treatment plants into the natural aquatic environment where potential wildlife hosts become infected. Here, we propose a plausible mechanism where SARS-CoV-2, the pathogen causing the disease COVID-19, could spillover from infected humans into novel wildlife hosts in North America. While the primary risk associated with the current COVID-19 outbreak appears to be humanto-human transmission of SARS-CoV-2, we believe the existing evidence also supports the plausibility of novel coronaviruses, such as SARS-CoV-2, spilling over to new wildlife hosts through fecal shedding by infected humans and introduction to the natural aquatic environment via the waste water treatment system. abstract: Abstract There is evidence that the current outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, is of animal origin. As with a number of zoonotic pathogens, there is a risk of spillover into novel hosts. Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal waste water treatment plants into the natural aquatic environment where potential wildlife hosts become infected. We use the existing literature on human coronaviruses, including SARS CoV, to support the potential pathways and mechanisms in the conceptual model. Although we focus on North America, our conceptual model could apply to other parts of the globe as well. url: https://www.ncbi.nlm.nih.gov/pubmed/32416535/ doi: 10.1016/j.scitotenv.2020.139358 id: cord-019048-29wzpwvr author: Franks, Teri J. title: Coronavirus date: 2013-08-26 words: 2805.0 sentences: 135.0 pages: flesch: 47.0 cache: ./cache/cord-019048-29wzpwvr.txt txt: ./txt/cord-019048-29wzpwvr.txt summary: From discovery to mid-September 2013, HCoV-EMC, renamed MERS-CoV, (de Groot 2013 ) caused 132 laboratory-confi rmed cases of severe acute pneumonia including 58 deaths. Certain structural proteins are common to all coronaviruses: the spike glycoprotein S, an envelope glycoprotein that mediates receptor-binding and membrane fusion; the envelope spanning glycoprotein M, which contributes to the thickness of the envelop; the envelope protein E, which has been identifi ed as a virulence factor SARS-CoV ; and the nucleocapsid protein N, with its function in genome encapsidation, RNA synthesis and translation, and as a type I interferon antagonist ( Fig. 13 .2 ). Initial signs and symptoms of SARS are nonspecifi c and common, which generates a wide differential diagnosis of respiratory pathogens including infl uenza virus, parainfl uenza Fig. 13.4 Acute-phase DAD in SARS patient. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection abstract: Name of Virus: Coronavirus url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124098/ doi: 10.1007/978-3-642-40605-8_13 id: cord-322044-4eejzpmn author: Frediansyah, Andri title: Remdesivir and its antiviral activity against COVID-19: A systematic review date: 2020-08-07 words: 613.0 sentences: 55.0 pages: flesch: 47.0 cache: ./cache/cord-322044-4eejzpmn.txt txt: ./txt/cord-322044-4eejzpmn.txt summary: title: Remdesivir and its antiviral activity against COVID-19: A systematic review BACKGROUND: To summarize the antiviral activities of remdesivir against SARS-CoV-2, the causative agent of COVID-19. Although remdesivir has been used as a compassionate drug for treating COVID-19 patients, it has only moderate efficacy. CONCLUSION: Although remdesivir has shown potent antiviral activities, more efficacy assessments are urgently warranted in clinical trials. The first randomized, double-blind, placebo-controlled, multicenter clinical trial was 175 reported on April 29, 2020 [48] . Prophylactic 341 and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of 342 MERS-CoV infection Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2 Compassionate use 355 of remdesivir for patients with severe Covid-19 The authors whose names are listed immediately below report the following details of affiliation or involvement in an organization or entity with a financial or non-financial interest in the subject matter or materials discussed in this manuscript. abstract: BACKGROUND: To summarize the antiviral activities of remdesivir against SARS-CoV-2, the causative agent of COVID-19. METHODS: Available publications were systematically explored on some databases and gray literature was examined. Publications were discussed narratively. RESULTS: Remdesivir inhibits SARS-CoV-2 replication, reduces viral load, and exerts protective effects in SARS-CoV-2 infected animals. Remdesivir also reduces the pathological process, alleviates mild symptoms, and improves pulmonary lesions in SARS-CoV-2-infecetd animals. Although remdesivir has been used as a compassionate drug for treating COVID-19 patients, it has only moderate efficacy. CONCLUSION: Although remdesivir has shown potent antiviral activities, more efficacy assessments are urgently warranted in clinical trials. url: https://www.sciencedirect.com/science/article/pii/S2213398420301810?v=s5 doi: 10.1016/j.cegh.2020.07.011 id: cord-285053-ah9z9luw author: Freedman, David O title: In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks date: 2020-09-25 words: 2057.0 sentences: 106.0 pages: flesch: 58.0 cache: ./cache/cord-285053-ah9z9luw.txt txt: ./txt/cord-285053-ah9z9luw.txt summary: This review presents a comprehensive table summarizing all peer-reviewed or public health publication of flights with likely, possible or unproven in-flight SARS-CoV-2 transmission from 24 January 2020 to 21 September 2020. Two likely secondary cases (one seated in Row 40 with 5 index cases) had negative Day 0 PCR testing and were PCR+ on Day 14; pre-flight transmission shortly before the relatively short flight cannot be ruled out. A number of these flights have carried COVID-19 cases, 5 but no national databases or unified international registries documenting evacuation flights or their passenger loads are publicly available, and few data have been published to date. On flights N-R with the rigid masking policies (meals served) of Emirates Airlines, no secondary cases were identified on Day 14 screening despite 58 passengers who were PCR+ on a total of 5 flights of 8 hours each with ∼1500-2000 passengers. abstract: The absence of large numbers of published in-flight transmissions of SARS-CoV-2 is not definitive evidence of safety. All peer-reviewed publications of flights with possible transmission are categorized by the quantity of transmission. Three mass transmission flights without masking are contrasted to 5 with strict masking and 58 cases with zero transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/32975554/ doi: 10.1093/jtm/taaa178 id: cord-318957-gp5drg71 author: Freedman, Matthew title: Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography date: 2004-06-30 words: 756.0 sentences: 52.0 pages: flesch: 53.0 cache: ./cache/cord-318957-gp5drg71.txt txt: ./txt/cord-318957-gp5drg71.txt summary: title: Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography Abstract Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. A computer-aided detection system has been developed that marks locations on chest radiographs of minimal areas of pneumonia. It has been tested on a small series of chest radiographs with minimal SARS pneumonia and provided 88% sensitivity with 1.3 false-positive marks per image. Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. In this process of early detection, the chest radiograph is used as the primary screening method for people presenting with symptoms of potential SARS pneumonia. Severe Acute Respiratory Syndrome: radiographic review of 40 probable cases in Toronto Severe Acute Respiratory Syndrome: radiographic appearances and pattern of progression in 138 patients abstract: Abstract Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. It is highly contagious and has a high mortality rate. It is unresponsive to antibiotics and the main methods of control involve barrier isolation. Because of these features, early diagnosis is required for control of the disease. Unlike other forms of severe pneumonia, the initial presenting chest radiograph may not disclose the pneumonia. A computer-aided detection system has been developed that marks locations on chest radiographs of minimal areas of pneumonia. It has been tested on a small series of chest radiographs with minimal SARS pneumonia and provided 88% sensitivity with 1.3 false-positive marks per image. url: https://www.sciencedirect.com/science/article/pii/S0531513104007563 doi: 10.1016/j.ics.2004.03.323 id: cord-272734-kawim93f author: Freire-Paspuel, Byron title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date: 2020-05-22 words: 1243.0 sentences: 92.0 pages: flesch: 60.0 cache: ./cache/cord-272734-kawim93f.txt txt: ./txt/cord-272734-kawim93f.txt summary: title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies The CDC designed 2019-nCoV CDC EUA kit (IDT, USA) is based on N1 and N2 probes to detect SARS-CoV-2 that have received positive evaluation on recent reports (1) (2) (3) , and and RNase P as an RNA extraction quality control. Other kit avalaible in the market is nCoV-QS (MiCo BioMed; South Corea) that include probes "ORF3a" and "N" probes for SARS-CoV-2 detection but no probe for RNA extraction quality control, with no EUA approval neither from FDA (USA) nor from Korean CDC (4,5,6). Both CoV-QS and 2019-nCoV CDC EUA kits were used at SARS-CoV-2 diagnosis laboratory "LabGal" at "Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos" at Puerto Ayora in Galapagos Islands (Ecuador), where we considered this validation necessary to guarantee the sensibility of SARS-CoV-2 during the surveillance. abstract: BACKGROUND: Several qPCR kits are available for SARS-CoV-2 diagnosis, mostly lacking of evaluation due to covid19 emergency. OBJECTIVE: We evaluated nCoV-QS (MiCo BioMed) kit using CDC kit as gold standard. RESULTS: We found limitations for nCoV-QS: 1) lower sensitivity 2) lack of RNA quality control probe. CONCLUSIONS: Validation studies should be implemented for any SARS-CoV-2 RT-qPCR commercial kit to prevent unreliable diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/32485473/ doi: 10.1016/j.jcv.2020.104454 id: cord-332510-x3znuwc0 author: Freire-Álvarez, Eric title: COVID-19-associated encephalitis successfully treated with combination therapy date: 2020-11-01 words: 1901.0 sentences: 117.0 pages: flesch: 38.0 cache: ./cache/cord-332510-x3znuwc0.txt txt: ./txt/cord-332510-x3znuwc0.txt summary: We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. Conclusion: This case report indicates that COVID-19 may present as an encephalitis syndrome mimicking acute demyelinating encephalomyelitis that could be amenable to therapeutic modulation. Despite most of the patients with altered mental in this cohort had a brain MRI performed, they did not observe any case of acute disseminated encephalomyelitis, an immune mediated disease that often occurs following viral infections [12] . The negative RT-PCR CSF results for SARS-CoV-2 along with the hyperinflammatory systemic response observed and the impressive findings in the MRI after therapy with immunoglobulins and tocilizumab suggest an acute disseminated encephalomyelitis. abstract: Background Acute encephalitis can occur in different viral diseases due to infection of the brain or by an immune mechanism. Severe novel coronavirus disease 2019 (COVID-19) is associated with a major immune inflammatory response with cytokine upregulation including interleukin 6 (IL-6). We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. Case Report: A 39-year-old-man was brought to the Emergency Department with drowsiness, mental disorientation, intermittent fever and headache. A brain magnetic resonance imaging showed extensive involvement of the brain including cortical and subcortical right frontal regions, right thalamus, bilateral temporal lobes and cerebral peduncles, with no leptomeningeal enhancement. Cerebrospinal fluid (CSF) showed a leukocyte count of 20/µL (90% lymphocytes), protein level of 198 mg/dL, and glucose of 48 mg/dL. SARS-CoV-2 was detected in nasopharyngeal swabs by reverse-transcriptase-PCR (RT-PCR) but it was negative in the CSF. Remarkable laboratory findings in blood tests included low lymphocyte count and elevated ferritin, IL-6 and D-dimer. He had a complicated clinical course requiring mechanical ventilation. Intravenous immunoglobulins and cytokine blockade with tocilizumab, an IL-6 receptor antagonist, were added considering acute demyelinating encephalomyelitis. The patient made a full recovery, suggesting that it could have been related to host inflammatory response. Conclusion This case report indicates that COVID-19 may present as an encephalitis syndrome mimicking acute demyelinating encephalomyelitis that could be amenable to therapeutic modulation. url: https://doi.org/10.1016/j.clinpr.2020.100053 doi: 10.1016/j.clinpr.2020.100053 id: cord-313316-l147b7jk author: Freudenthal, Bernard title: Misuse of SARS-CoV-2 testing in symptomatic health-care staff in the UK date: 2020-10-22 words: 1110.0 sentences: 72.0 pages: flesch: 57.0 cache: ./cache/cord-313316-l147b7jk.txt txt: ./txt/cord-313316-l147b7jk.txt summary: An initiative to screen asymptomatic health-care workers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was timely and logical, 1 and contrasted markedly with the UK Government''s testing strategy stated. His opened-out presentation of a brain does not show the paired lateral ventricles and the foramen of Monro, as several authors erroneously down, and the way to do that is to get the amount of testing up". Overzealous redirection of self-isolating staff back to work before they had completed sufficient self-isolation to exclude infectivity was therefore likely to increase spread of the virus to other staff and to patients or care-receivers in a substantial number of cases, especially given the high prevalence and likelihood of SARS-CoV-2 infection among exposed health-care workers during the epidemic. 5 We believe a symptom-agnostic testing approach for SARS-CoV-2 among HCWs is an effective measure of reducing viral transmission. 1 We agree that use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing among health-care workers (HCWs) solely to reduce absenteeism is inappro priate. abstract: nan url: https://api.elsevier.com/content/article/pii/S0140673620321474 doi: 10.1016/s0140-6736(20)32147-4 id: cord-308358-2bap7iih author: Friedland, Robert P title: The role for the metagenome in the pathogenesis of COVID-19 date: 2020-10-07 words: 1126.0 sentences: 57.0 pages: flesch: 39.0 cache: ./cache/cord-308358-2bap7iih.txt txt: ./txt/cord-308358-2bap7iih.txt summary: A common factor associated with aging and other COVID-19 risk factors is the dysbiosis of gut microbiota and resulting low grade inflammation with loss of epithelial barrier function [5] . Germ free animals have defective immune systems and the gut microbiota influences pathogen dissemination, inflammation, organ damage and mortality in murine pneumonia [9] . Changes in diet with aging may well influence short chain fatty acid production, affecting immune homeostasis, barrier function and severity of COVID-19. However, in cases of severe disease of COVID-19, it is the innate response and not the unregulated adaptive immune response via T cells that results in morbidity and death. The influence of the microbiota on immune processes in COVID19 infection may be assessed with metagenomic analysis of nasal, oral and intestinal communities, as well as metabolomics. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals abstract: nan url: https://api.elsevier.com/content/article/pii/S2352396420303959 doi: 10.1016/j.ebiom.2020.103019 id: cord-290776-l6ajq6vp author: Frithiof, Robert title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients date: 2020-09-29 words: 986.0 sentences: 71.0 pages: flesch: 58.0 cache: ./cache/cord-290776-l6ajq6vp.txt txt: ./txt/cord-290776-l6ajq6vp.txt summary: title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients Patients infected with SARS-CoV-2 requiring intensive care due to coronavirus disease 2019 (COVID-19) frequently develop acute kidney injury (AKI) [1] , but the underlying mechanisms are poorly explored. In this report, SARS-CoV-2 RNA levels were prospectively investigated in urine of patients with upper or lower airway swab test PCR-verified COVID-19, admitted to a Swedish intensive care unit (ICU, n = 81). Nucleic acid was extracted from urine samples using NucliSENS® eMAG® (bioMerieux), and the amount of viral RNA was quantitated by detection of SARS-CoV-2 E and N-genes using real-time RT-PCR according to previously described protocols [5, 6] . In this cohort, SARS-CoV-2 RNA was not more frequently detected in urine of patients that died or developed acute kidney injury. abstract: nan url: https://doi.org/10.1186/s13054-020-03302-w doi: 10.1186/s13054-020-03302-w id: cord-340811-w4x4falm author: Frizzelli, Annalisa title: What happens to people’s lungs when they get coronavirus disease 2019? date: 2020-05-11 words: 1779.0 sentences: 106.0 pages: flesch: 46.0 cache: ./cache/cord-340811-w4x4falm.txt txt: ./txt/cord-340811-w4x4falm.txt summary: Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: The novel coronavirus SARS-CoV-2 was first identified in Wuhan in December 2019 as cause of the consequent novel coronavirus disease 2019 (COVID-19). The virus has since spread worldwide. The clinical presentation following human infection ranges from a mild upper respiratory tract infection to severe acute respiratory distress syndrome and sepsis. We reviewed literature using Pubmed to identify relevant English-language articles published until April 15, 2020. Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. We summarized what SARS-CoV-2 infection means for the lungs. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420938/ doi: 10.23750/abm.v91i2.9574 id: cord-254395-tu4aqczj author: Froggatt, Heather M. title: Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL(pro) Reporter Assay date: 2020-10-27 words: 4200.0 sentences: 254.0 pages: flesch: 50.0 cache: ./cache/cord-254395-tu4aqczj.txt txt: ./txt/cord-254395-tu4aqczj.txt summary: This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. With the aim of generating a protease reporter compatible with SARS-CoV-2 and other present and future coronaviruses to support viral inhibitor screening, we selected CoV 3CL pro as our protease target. (C) Quantification of fluorescence from 293T cells 48 h after transfection with each FlipGFP reporter and either the SARS-CoV-2 3CL pro or an influenza virus protein (A/PR8/1834 NP). To observe whether these FlipGFP constructs background fluoresced without CoV 3CL pro activity, we transfected cells with each reporter or a superfolder GFP (sfGFP) expression plasmid. Development of a FlipGFP CoV 3CL pro reporter-based assay for protease inhibitor screening in human cells. abstract: In late 2019, a human coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged, likely from a zoonotic reservoir. This virus causes COVID-19, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA-approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available, and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of the highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CL(pro). 3CL(pro) is an attractive target for antiviral therapeutics, as it is essential for processing newly translated viral proteins and the viral life cycle cannot be completed without protease activity. In this work, we report a new assay to identify inhibitors of 3CL(pro). Our reporter is based on a green fluorescent protein (GFP)-derived protein that fluoresces only after cleavage by 3CL(pro). This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread. IMPORTANCE The COVID-19 pandemic has already led to more than 700,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CL(pro). This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32843534/ doi: 10.1128/jvi.01265-20 id: cord-299927-ixuvy2g4 author: Frontera, Jennifer title: Global Consortium Study of Neurological Dysfunction in COVID-19 (GCS-NeuroCOVID): Study Design and Rationale date: 2020-05-22 words: 4851.0 sentences: 229.0 pages: flesch: 30.0 cache: ./cache/cord-299927-ixuvy2g4.txt txt: ./txt/cord-299927-ixuvy2g4.txt summary: As the COVID-19 pandemic evolves worldwide, reports of a spectrum of mild to severe neurological syndromes among patients infected with SARS-CoV-2 are emerging, including headache, anosmia, ageusia, seizures, coma, encephalitis, Guillain-Barre syndrome, and acute cerebrovascular events including ischemic stroke, intracerebral hemorrhage, and cerebral venous sinus thromboses [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] . [15] reported that 84% (49/58) of patients with severe SARS-CoV-2 infection and acute respiratory distress syndrome had neurological symptoms including encephalopathy, agitation and confusion, and corticospinal tract signs. We established the Global Consortium to Study Neurological dysfunction in COVID-19 patients (GCS-NeuroCOVID) and promptly launched a tiered research program with an early, pragmatic, and nimble design to enable successful implementation during a global pandemic crisis when healthcare systems are stressed. The primary outcome in Tier 1 is the prevalence of new clinical neurological syndromes in SARS-CoV-2 patients including: new onset headache, anosmia/ageusia, clinical seizures/status epilepticus, strokes (ischemic and hemorrhagic), meningitis/encephalitis, hypoxic/ischemic injury, acute encephalopathy, coma, myelopathy, neuropathy, and dysautonomia/sympathetic storming. abstract: BACKGROUND: As the COVID-19 pandemic developed, reports of neurological dysfunctions spanning the central and peripheral nervous systems have emerged. The spectrum of acute neurological dysfunctions may implicate direct viral invasion, para-infectious complications, neurological manifestations of systemic diseases, or co-incident neurological dysfunction in the context of high SARS-CoV-2 prevalence. A rapid and pragmatic approach to understanding the prevalence, phenotypes, pathophysiology and prognostic implications of COVID-19 neurological syndromes is urgently needed. METHODS: The Global Consortium to Study Neurological dysfunction in COVID-19 (GCS-NeuroCOVID), endorsed by the Neurocritical Care Society (NCS), was rapidly established to address this need in a tiered approach. Tier-1 consists of focused, pragmatic, low-cost, observational common data element (CDE) collection, which can be launched immediately at many sites in the first phase of this pandemic and is designed for expedited ethical board review with waiver-of-consent. Tier 2 consists of prospective functional and cognitive outcomes assessments with more detailed clinical, laboratory and radiographic data collection that would require informed consent. Tier 3 overlays Tiers 1 and 2 with experimental molecular, electrophysiology, pathology and imaging studies with longitudinal outcomes assessment and would require centers with specific resources. A multicenter pediatrics core has developed and launched a parallel study focusing on patients ages <18 years. Study sites are eligible for participation if they provide clinical care to COVID-19 patients and are able to conduct patient-oriented research under approval of an internal or global ethics committee. Hospitalized pediatric and adult patients with SARS-CoV-2 and with acute neurological signs or symptoms are eligible to participate. The primary study outcome is the overall prevalence of neurological complications among hospitalized COVID-19 patients, which will be calculated by pooled estimates of each neurological finding divided by the average census of COVID-19 positive patients over the study period. Secondary outcomes include: in-hospital, 30 and 90-day morality, discharge modified Rankin score, ventilator-free survival, ventilator days, discharge disposition, and hospital length of stay. RESULTS: In a one-month period (3/27/20–4/27/20) the GCS-NeuroCOVID consortium was able to recruit 71 adult study sites, representing 17 countries and 5 continents and 34 pediatrics study sites. CONCLUSIONS: This is one of the first large-scale global research collaboratives urgently assembled to evaluate acute neurological events in the context of a pandemic. The innovative and pragmatic tiered study approach has allowed for rapid recruitment and activation of numerous sites across the world—an approach essential to capture real-time critical neurological data to inform treatment strategies in this pandemic crisis. url: https://doi.org/10.1007/s12028-020-00995-3 doi: 10.1007/s12028-020-00995-3 id: cord-271027-4omocd8q author: Fronza, R. title: Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak date: 2020-05-01 words: 5723.0 sentences: 309.0 pages: flesch: 55.0 cache: ./cache/cord-271027-4omocd8q.txt txt: ./txt/cord-271027-4omocd8q.txt summary: While it is possible to reason that observed variation in the number and severity of cases stem from the initial number of infected individuals, the difference in the testing policies and social aspects of community transmissions, the factors that could explain high discrepancy in areas with a similar level of healthcare still remain unknown. A generalized Poisson model was fitted to estimate the association among the data showing the number of infected cases per million and the atmospheric factors. Binary classifier based on an artificial neural network (ANN) was implemented to test the capacity of the atmospheric variables to predict the epidemic escalation of the number of positive cases per million on the basis of a combination of where l= PM2.5, PM10, NH 3 dM A l and O 3 . The expected number of infected cases in the total of 107 Italian provinces were predicted for the months of March (Spring), June (Summer), September (Autumn) and December (Winter) using the real measured values for PM2.5 and O 3 atmospheric factors from 2018 seasonal datasets. abstract: The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing coronavirus disease 2019 (COVID-19) reached over two million confirmed cases worldwide, and numbers are still growing at a fast rate. The majority of new infections are now being reported outside of China, where the outbreak officially originated in December 2019 in Wuhan. Despite the wide outbreak of the infection, a remarkable asymmetry is observed in the number of cases and in the distribution of the severity of the COVID-19 symptoms in patients with respect to the countries/regions. In the early stages of a new pathogen outbreak, it is critical to understand the dynamics of the infection transmission, in order to follow contagion over time and project the epidemiological situation in the near future. While it is possible to reason that observed variation in the number and severity of cases stem from the initial number of infected individuals, the difference in the testing policies and social aspects of community transmissions, the factors that could explain high discrepancy in areas with a similar level of healthcare still remain unknown. Here we introduce a binary classifier based on an artificial neural network that can help in explaining those differences and that can be used to support the design of containment policies. We propose that air pollutants, and specifically particulate matter (PM) 2.5 and ozone, are oppositely related with the SARS-CoV-2 infection frequency and could serve as surrogate markers to complement the infection outbreak anticipation. url: https://doi.org/10.1101/2020.04.26.20080846 doi: 10.1101/2020.04.26.20080846 id: cord-273074-k8m917i4 author: Fu, Chao-Yang title: Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens date: 2005-12-01 words: 1662.0 sentences: 91.0 pages: flesch: 50.0 cache: ./cache/cord-273074-k8m917i4.txt txt: ./txt/cord-273074-k8m917i4.txt summary: title: Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot and neutralization test results showed that the IgY obtained was of a high purity and had a strong reactive activity with a neutralization titer of 1:640. In this study, we have successfully immunized specific pathogen-free (SPF) chickens, and then purified a high-titer anti-SARS coronavirus yolk immunoglobulin (IgY) with neutralizing activity against SARS coronavirus. The activity of IgY in sera and yolks diluted at 1:200 in phosphate buffer saline (PBS) from immunized animals was assessed using an indirect ELISA assay as described previously (Huang et al., 2005) (Fig. 1) . The development of high-titer anti-SARS coronavirus IgY described in this study would appear to have potential as a new anti-SARS biological product for passive immunization, as it effectively neutralized the SARS coronavirus. abstract: Severe acute respiratory syndrome (SARS) is a recently discovered viral disease, characterized by fever, cough, acute fibrinous pneumonia and high infectivity. Specific pathogen-free (SPF) chickens were immunized with inactivated SARS coronavirus and their eggs were harvested at regular intervals. Yolk immunoglobulin (IgY) was extracted using the water dilution method, followed by further purification on a Sephadex G-75 column. SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot and neutralization test results showed that the IgY obtained was of a high purity and had a strong reactive activity with a neutralization titer of 1:640. Lyophilization and stability tests showed that lyophilized anti-SARS coronavirus IgY had promising physical properties, with no significant reduction in reactive activity and good thermal stability. All these data suggest that the anti-SARS coronavirus IgY could be a new useful biological product for specific antiviral therapy against SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/16325277/ doi: 10.1016/j.jviromet.2005.10.027 id: cord-289101-ko1knslk author: Fu, Weihui title: An open-label, randomized trial of the combination of IFN-κ plus TFF2 with standard care in the treatment of patients with moderate COVID-19 date: 2020-09-20 words: 6194.0 sentences: 315.0 pages: flesch: 48.0 cache: ./cache/cord-289101-ko1knslk.txt txt: ./txt/cord-289101-ko1knslk.txt summary: Our previous clinical pilot study indicated that aerosol inhalation of IFN-k plus TFF2 is a safe treatment and is able to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby resulting in an early release from hospitalization without induction of a proinflammatory response [20] . This study demonstrated that the combination inhalation of IFN-k and TFF2 is able to shorten the time of viral RNA negative conversion and CT improvement, and facilitating patients early discharge from the hospital, in the absence of induction of a proinflammatory response and treatment-related adverse events. The primary endpoint was a significantly shorter time (Mean 3¢80 days, 95% CI 2¢07À5¢53) from the start of the study treatment to viral RNA negative conversion for SARS-CoV-2 in all clinical samples, including nasopharyngeal swabs, throat swabs and stool swabs, in experimental group than in control group (7¢40 days, 95% CI 4¢57À10¢23) (p = 0¢031), and difference between means was 3¢60 days (Fig. 2A) . abstract: BACKGROUND: Epidemic outbreaks caused by SARS-CoV-2 are worsening around the world, and there are no target drugs to treat COVID-19. IFN-κ inhibits the replication of SARS-CoV-2; and TFF2 is a small secreted polypeptide that promotes the repair of mucosal injury and reduces the inflammatory responses. We used the synergistic effect of both proteins to treat COVID-19. METHODS: We conducted an open-label, randomized, clinical trial involving patients with moderate COVID-19. Patients were assigned in a 1:1 ratio to receive either aerosol inhalation treatment with IFN-κ and TFF2 every 24 h for six consecutive dosages in addition to standard care (experimental group) or standard care alone (control group). The primary endpoint was the time until a viral RNA negative conversion for SARS-CoV-2 in all clinical samples. The secondary clinical endpoint was the time of CT imaging improvement. Data analysis was performed per protocol. This study was registered with chictr.org.cn, ChiCTR2000030262. FINDINGS: Between March 23 and May 23 of 2020, 86 COVID-19 patients with symptoms of moderate illness were recruited, and 6 patients were excluded due to not matching the inclusion criteria (patients with pneumonia through chest radiography). Among the remaining 80 patients, 40 patients were assigned to experimental group, and the others were assigned to control group to only receive standard care. Efficacy and safety were evaluated for both groups. The time of viral RNA negative conversion in experimental group (Mean, 3·80 days, 95% CI 2·07–5·53), was significantly shorter than that in control group (7·40 days, 95% CI 4·57 to 10·23) (p = 0.031), and difference between means was 3·60 days. The percentage of patients in experimental group with reversion to negative viral RNA was significantly increased compared with control group on all sampling days (every day during the 12-day observation period) (p = 0·037). For the secondary endpoint, the experimental group had a significantly shorter time until improvement was seen by CT (Mean 6·21 days, N = 38/40, 95% CI 5·11–7·31) than that in control group (8·76 days, N = 34/40, 95% CI 7·57–9·96) (p = 0.002), and difference between means was 2·55 days. No discomfort or complications during aerosol inhalation were reported to the nurses by any experimental patients. INTERPRETATION: In conclusion, we found that aerosol inhalation of IFN-κ plus TFF2 in combination with standard care is safe and superior to standard care alone in shortening the time up to viral RNA negative conversion in all clinical samples. In addition, the patients in experimental group had a significantly shortened CT imaging improvement time than those in control group. This study suggested that this combination treatment is able to facilitate clinical improvement (negative for virus, improvement by CT, reduced hospitalization stay) and thereby result in an early release from the hospital. These data support the need for exploration with a large-scale trial of IFN-κ plus TFF2 to treat COVID-19. FUNDING: Funding was provided by the National Natural Science Foundation of China, National Major Project for Control and Prevention of Infectious Disease in China, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission. url: https://doi.org/10.1016/j.eclinm.2020.100547 doi: 10.1016/j.eclinm.2020.100547 id: cord-347225-gh51ag2x author: Fu, Weihui title: A clinical pilot study on the safety and efficacy of aerosol inhalation treatment of IFN-κ plus TFF2 in patients with moderate COVID-19 date: 2020-07-29 words: 4921.0 sentences: 233.0 pages: flesch: 46.0 cache: ./cache/cord-347225-gh51ag2x.txt txt: ./txt/cord-347225-gh51ag2x.txt summary: INTERPRETATION: Aerosol inhalation of IFN-κ plus TFF2 is a safe treatment and is likely to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby achieves an early release from hospitalization. Therefore, to evaluate the efficacy and safety of intranasal inhalation of TFF2 and IFN-k protein for SARS-CoV-2 infection, we conducted an open-label, nonrandomized, clinical trial in adult patients hospitalized with moderate COVID-19 disease in China. In this trial, any AE from the beginning of aerosol inhalation to 5 days after the end of the last aerosol inhalation were taken as an adverse event during treatment (TEAE); The secondary objective of the pilot study was to evaluate the clinical efficacy of IFN-k plus TFF2 as compared to the control group as assessed by days of hospitalization staying, CT imaging improvement and cough relief time and negative reversion of viral RNA after 10 days of treatment. abstract: BACKGROUND: The outbreak of a new coronavirus (SARS-CoV-2) poses a great challenge to global public health. New and effective intervention strategies are urgently needed to combat the disease. METHODS: We conducted an open-label, non-randomized, clinical trial involving moderate COVID-19 patients according to study protocol. Patients were assigned in a 1:2 ratio to receive either aerosol inhalation treatment with IFN-κ and TFF2, every 48 h for three consecutive dosages, in addition to standard treatment (experimental group), or standard treatment alone (control group). The end point was the time to discharge from the hospital. This study is registered with chictr.org.cn, ChiCTR2000030262. FINDINGS: A total of thirty-three eligible COVID-19 patients were enrolled from February 1, 2020 to April 6, 2020, eleven were assigned to the IFN-κ plus TFF2 group, and twenty-two to the control group. Safety and efficacy were evaluated for both groups. No treatment-associated severe adverse effects (SAE) were observed in the group treated with aerosol inhalation of IFN-κ plus TFF2, and no significant differences in the safety evaluations were observed between experimental and control groups. CT imaging was performed in all patients with the median improvement time of 5(.)0 days (IQR 3(.)0–9(.)0) in the experimental group versus 8(.)5 days (IQR 3(.)0–17(.)0) in the control group (p<0(.)05). In addition, the experimental group had a significant shorten median time in cough relief (4(.)5 days [IQR 2(.)0–7(.)0]) than the control group did (10(.)0 days [IQR 6(.)0–21(.)0])(p<0(.)005), in viral RNA reversion of 6(.)0 days (IQR 2(.)0–13(.)0) in the experimental group vs 9.5 days (IQR 3(.)0–23(.)0) in the control group (p < 0(.)05), and in the median hospitalization stays of 12(.)0 days (IQR 7.0–20.0) in the experimental group vs 15(.)0 days (IQR 10.0–25.0) in the control group (p<0(.)001), respectively. INTERPRETATION: Aerosol inhalation of IFN-κ plus TFF2 is a safe treatment and is likely to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby achieves an early release from hospitalization. These data support to explore a scale-up trial with IFN-κ plus TFF2. FUNDING: National Major Project for Control and Prevention of Infectious Disease in China, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission. url: https://doi.org/10.1016/j.eclinm.2020.100478 doi: 10.1016/j.eclinm.2020.100478 id: cord-285848-37dmv4ep author: Fu, Xiao-Wei title: Review of possible psychological impacts of COVID-19 on frontline medical staff and reduction strategies date: 2020-08-06 words: 4405.0 sentences: 195.0 pages: flesch: 42.0 cache: ./cache/cord-285848-37dmv4ep.txt txt: ./txt/cord-285848-37dmv4ep.txt summary: A large number of studies have reported that infectious epidemic diseases, such as severe acute respiratory syndrome (SARS), induce considerable psychological pressure that continues to impact frontline medical personnel a full year after such incidences [1] . In this paper, we present the findings of a review of studies that have investigated the psychological pressure and causes of stress associated with previous outbreaks of infectious diseases, such as SARS and influenza A (H1N1). The association between nurses'' perceived Stress from SARS and their corresponding 13 Chan et al [15] Hong Kong Questionnaires A total of 8 of the 42 Hong Kong public hospitals Perceived health status during the SARS epidemic 14 Kim et al [18] Seoul and in Kyung-gi province psychological interventions targeting frontline medical staff prior to the outbreak of epidemic infectious diseases in the future to reduce or avoid the pressures and impacts of these epidemics on them. abstract: Like soldiers, frontline medical staff provide a first line of defense and have played a critical role in responses to the outbreak of coronavirus disease-2019 in December 2019. It is important to acknowledge the considerable pressure placed on frontline medical staff in the face of a new type of coronavirus that is highly infectious and for which no specific treatment is available. Here, we review the various kinds of psychological problems afflicting frontline medical staff who are combatting the severe acute respiratory syndrome epidemic. These include anxiety, insomnia, depression, interpersonal difficulties, and post-traumatic stress disorder syndrome. We further present a summary of countermeasures for alleviating these problems based on our findings. These countermeasures include ensuring the provision of adequate protective gear for frontline medical staff, developing timely and clear guidelines, strengthening social support, and providing clear criteria and additional training, focusing on the choice of frontline medical staff. An understanding of the psychological impacts of an epidemic situation and of relevant countermeasures will contribute to reducing the psychological pressures on frontline medical staff. Consequently, they will be able to cope better with outbreaks of infectious diseases in the future, to reduce the psychological pressure of the front-line medical staff, and to improve the treatment level. url: https://www.ncbi.nlm.nih.gov/pubmed/32874973/ doi: 10.12998/wjcc.v8.i15.3188 id: cord-284376-plwyjhl8 author: Fu, Xinmiao title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 words: 14726.0 sentences: 782.0 pages: flesch: 49.0 cache: ./cache/cord-284376-plwyjhl8.txt txt: ./txt/cord-284376-plwyjhl8.txt summary: All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In contrast, corticosteroid use within the month before sampling was not different between The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis. abstract: • Cumulative confirmed cases in China were well fitted with Boltzmann function. • Potential total numbers of confirmed cases in different regions were estimated. • Key dates indicating minimal daily number of new confirmed cases were estimated. • Cumulative confirmed cases of 2003 SARS-CoV were well fitted to Boltzmann function. • The Boltzmann function was, for the first time, applied to epidemic analysis. url: https://api.elsevier.com/content/article/pii/S0163445320300980 doi: 10.1016/j.jinf.2020.02.019 id: cord-261415-qxl14j2m author: Fu, Yajing title: Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools date: 2020-03-03 words: 2594.0 sentences: 140.0 pages: flesch: 41.0 cache: ./cache/cord-261415-qxl14j2m.txt txt: ./txt/cord-261415-qxl14j2m.txt summary: In addition, given that uncontrolled pulmonary inflammation is likely a leading cause of fatality in SARS-CoV-2 infection, we also attempt to speculate possible therapeutic interventions that may be applied to attenuate inflammatory responses in order to reduce mortality (Fig. 2) . In SARS-CoV infection, viroporin 3a has also been shown to trigger the activation of NLRP3 (NOD-like receptor protein 3) inflammasome and the secretion of IL-1b in bone marrowderived macrophages, suggesting the induction of cell pyroptosis , which can cause the release of large amounts of proinflammatory factors (Fink and Cookson 2005) . However, previous studies in animal models have shown that in SARS-CoV infection, such anti-S protein-neutralizing antibodies (anti-S-IgG) can also cause severe lung injury by altering inflammatory responses (Liu et al. This animal study suggests that despite viral suppression, the presence of anti-spike protein antibody at the acute stage of SARS-CoV infection can actually cause severe acute lung injury that persists until the late stages. abstract: Currently there is no effective antiviral therapy for SARS-CoV-2 infection, which frequently leads to fatal inflammatory responses and acute lung injury. Here, we discuss the various mechanisms of SARS-CoV-mediated inflammation. We also assume that SARS-CoV-2 likely shares similar inflammatory responses. Potential therapeutic tools to reduce SARS-CoV-2-induced inflammatory responses include various methods to block FcR activation. In the absence of a proven clinical FcR blocker, the use of intravenous immunoglobulin to block FcR activation may be a viable option for the urgent treatment of pulmonary inflammation to prevent severe lung injury. Such treatment may also be combined with systemic anti-inflammatory drugs or corticosteroids. However, these strategies, as proposed here, remain to be clinically tested for effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/32125642/ doi: 10.1007/s12250-020-00207-4 id: cord-343569-9th5bcv0 author: Fu, Yu-Zhi title: SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response date: 2020-10-27 words: 3403.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-343569-9th5bcv0.txt txt: ./txt/cord-343569-9th5bcv0.txt summary: [28] [29] [30] To identify SARS-CoV-2 proteins that may inhibit the RLR-mediated induction of downstream antiviral genes, we constructed 17 SARS-CoV-2 protein expression clones and screened for candidates that inhibit the Sendai virus (SeV, an RNA virus)-induced activation of the IFNβ promoter in HEK293 cells by reporter assays (Fig. 1A) . In reporter assays, ectopic expression of the M protein dose-dependently inhibited the SeV-induced activation of We next performed ELISA experiments and found that the secretion of IFN-β and TNF-α following SeV infection or poly (I:C) transfection was also impaired in HEK293-M cells (Fig. 1G ). These results suggest that the M protein impairs the recruitment of TRAF3, TBK1 and IRF3 to the MAVS complex, leading to the inhibition of the innate antiviral response. In this study, we identified the SARS-CoV-2 M protein as a factor underlying the inhibition of host antiviral innate immunity by directly targeting the central adaptor MAVS in the RLR-mediated induction of type I IFNs. Several lines of evidence suggest that M directly targets MAVS to inhibit the innate immune response. abstract: A novel SARS-related coronavirus (SARS-CoV-2) has recently emerged as a serious pathogen that causes high morbidity and substantial mortality. However, the mechanisms by which SARS-CoV-2 evades host immunity remain poorly understood. Here, we identified SARS-CoV-2 membrane glycoprotein M as a negative regulator of the innate immune response. We found that the M protein interacted with the central adaptor protein MAVS in the innate immune response pathways. This interaction impaired MAVS aggregation and its recruitment of downstream TRAF3, TBK1, and IRF3, leading to attenuation of the innate antiviral response. Our findings reveal a mechanism by which SARS-CoV-2 evades the innate immune response and suggest that the M protein of SARS-CoV-2 is a potential target for the development of SARS-CoV-2 interventions. url: https://doi.org/10.1038/s41423-020-00571-x doi: 10.1038/s41423-020-00571-x id: cord-297787-t9neub6d author: Fu, Ziyang title: Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date: 2020-07-18 words: 2152.0 sentences: 149.0 pages: flesch: 64.0 cache: ./cache/cord-297787-t9neub6d.txt txt: ./txt/cord-297787-t9neub6d.txt summary: The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19. The in-vitro 85 IC50 of GRL0617 against SARS-COV-2 PLpro was 2.1 ± 0.2 μM, suggesting a promising lead 86 compound and therefore it was subjected to further structural and mechanistic studies ( Fig. 2A) . Taken together, our NMR and X-ray analysis indicates that GRL0617 162 is a potent PPI (protein-protein interaction) inhibitor for PLpro blocking the binding of ISG15. Our co-crystal structure of PLpro C111S in complex with the potent 175 inhibitor GRL0617 validated that SARS-COV-2 PLpro is a druggable target. Based on the structure, GRL0617 resides in the S3/S4 site of PLpro, naturally it will also 179 inhibit the processing of viral polyproteins of SARS-CoV-2 since these viral polyproteins share the 180 same substrate cleavage sequence with Ub and ISG15. The SARS-coronavirus papain-like 257 protease: structure, function and inhibition by designed antiviral compounds abstract: SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease has been implicated in virus maturation, dysregulation of host inflammation and antiviral immune responses. We showed that PLpro preferably cleaves the K48-ubiquitin linkage while also being capable of cleaving ISG15 modification. The multiple functions of PLpro render it a promising drug target. Therefore, we screened an FDA-approved drug library and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising IC50 of 2.1 μM. The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. NMR data indicate that GRL0617 blocks the binding of ISG15 to PLpro. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19. One Sentence Summary Co-crystal structure of PLpro in complex with GRL0617 reveals the druggability of PLpro for SARS-CoV-2 treatment. url: https://doi.org/10.1101/2020.07.17.208959 doi: 10.1101/2020.07.17.208959 id: cord-354534-0b7zwzjv author: Fuccillo, E title: Olfactory disorders in coronavirus disease 2019 patients: a systematic literature review date: 2020-09-15 words: 2847.0 sentences: 161.0 pages: flesch: 43.0 cache: ./cache/cord-354534-0b7zwzjv.txt txt: ./txt/cord-354534-0b7zwzjv.txt summary: The patients, intervention, comparison and outcomes (''PICO'') criteria for the review were considered as follows: (1) patientspatients with SARS-CoV-2 infection certified on laboratory tests who underwent a clinical evaluation of smell impairment using anamnestic data, a smell questionnaire and/or olfactory tests; (2) interventionclinical evaluation of olfactory disorders; (3) comparisondifferent methods of evaluating olfactory function (subjective and objective); and (4) outcomeprevalence and characteristics of olfactory dysfunction in Covid-19 patients. The reported data show that smell dysfunction was, overall, more prevalent in patients investigated with validated questionnaires and/or tests with odorants (Table 3 ), compared to PubMed (("COVID" OR "COVID-19" OR "SARS-COV-2" OR "coronavirus")) AND ("smell" or "anosmia" or "dysosmia" or "hyposmia" or "parosmia" or "olfaction" or "olfactory") The Journal of Laryngology & Otology individuals evaluated using anamnestic data, simple surveys and/or non-validated questionnaires. abstract: OBJECTIVE: Recent scientific literature has widely described a possible major role of smell dysfunction as a specific symptom of coronavirus disease 2019. This systematic review may provide a more holistic approach to current knowledge of the disease. METHODS: A systematic review was completed using Embase, PubMed and Web of Science databases that considered original articles focused on olfactory evaluation in coronavirus disease 2019 patients, published between March and May 2020, in English language. RESULTS: From the 483 research papers initially identified, 32 original studies were selected, comprising a total of 17 306 subjects with a laboratory confirmed diagnosis of coronavirus disease 2019. Individual study sample sizes ranged from 6 to 6452 patients. This comprehensive analysis confirmed that olfactory disorders represent an important clinical feature in coronavirus disease 2019, with a prevalence of 11–100 per cent in included patients, although there was heterogeneity in terms of assessment tools and population selection criteria. CONCLUSION: The results indicate that an accurate clinical evaluation should be carried out using structured questionnaires and tests with olfactory substances. url: https://doi.org/10.1017/s0022215120002005 doi: 10.1017/s0022215120002005 id: cord-328074-pcvdr052 author: Fuereder, Thorsten title: Circumnavigating the challenges of COVID-19 in oncology date: 2020-05-07 words: 1842.0 sentences: 83.0 pages: flesch: 40.0 cache: ./cache/cord-328074-pcvdr052.txt txt: ./txt/cord-328074-pcvdr052.txt summary: authors: Fuereder, Thorsten; Gunsilius, Eberhard; Bartsch, Rupert; Hilbe, Wolfgang At this time, patients with haematological malignancies may well be the most threatened patient population as many are heavily immunosuppressed due to the underlying disease, their treatment, or both, and thus are highly susceptible to severe complications if infected with SARS CoV-2. The European Society of Medical Oncology (ESMO) has meanwhile provided comprehensive guidelines for the management and treatment of lung cancer patients in the SARS CoV-2 era [6] : High priority in stage IV lung cancer remains the initiation of firstor second-line chemotherapy, immunotherapy or TKI therapy. Based on these findings the interleukin-6 inhibitor tocilizumab, which is used for the treatment of severe CPI (and CAR-T cells) induced adverse events, is currently being evaluated in clinical trials in patients with COVID-19. Therefore, no recommendations can be given to delay CPI therapy for cancer patients during the SARS CoV-2 pandemic [7] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32382356/ doi: 10.1007/s12254-020-00611-2 id: cord-328762-2b1pl8jr author: Fuest, Matthias title: Postmortem conjunctival and nasopharyngeal swabs in SARS‐CoV‐2 infected and uninfected patients date: 2020-08-06 words: 888.0 sentences: 60.0 pages: flesch: 64.0 cache: ./cache/cord-328762-2b1pl8jr.txt txt: ./txt/cord-328762-2b1pl8jr.txt summary: The specifity of ocular tissue/fluid in detecting SARS-CoV-2 was very low in comparison with standard sample collection from nasopharyngeal swabs (NPS) (Ulhaq & Soraya 2020) . To date, no data are available on the postmortem prevalence of virus RNA in ocular and pharyngeal tissue in SARS-CoV-2 patients. Accordingly, in a prospective cohort study, potential corneal donors (uninfected with negative premortem NPS) in our institution had postmortem conjunctival (COS) and NPS taken starting March 17, 2020. SARS-CoV-2 RNA was not detected in any postmortem NPS or COS in the uninfected group. The absence of virus RNA in our postmortem swabs agrees with the literature on premortem samples, where only 3/315 COS = 0.95% (compared to NPS 604/849 = 71.1%) were positive even in symptomatic eyes, indicating that the human conjunctiva is not a typical site of SARS-CoV-2 replication (Lu et al. All these SARS-CoV-2 patients were diagnosed by premortem positive NPS. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32767497/ doi: 10.1111/aos.14559 id: cord-320912-jfeu4tho author: Fukui, M. title: Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models date: 2020-06-12 words: 11777.0 sentences: 786.0 pages: flesch: 59.0 cache: ./cache/cord-320912-jfeu4tho.txt txt: ./txt/cord-320912-jfeu4tho.txt summary: This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection dynamics, even with large populations. . https://doi.org/10.1101/2020.06.11.20128058 doi: medRxiv preprint Figure 3 plots the predicted ranking of infection cases given the estimated negative binomial (NB) distribution, in addition to the log-log plots and estimated power law (PL) distributions. The mean is set to the same value as power law case, R 0 = 2.5, Figure 4a shows 10 sample paths of infected population generated through the simulation of the model with α = 1.1. abstract: While they are rare, superspreading events (SSEs), wherein a few primary cases infect an extraordinarily large number of secondary cases, are recognized as a prominent determinant of aggregate infection rates (R0). Existing stochastic SIR models incorporate SSEs by fitting distributions with thin tails, or finite variance, and therefore predicting almost deterministic epidemiological outcomes in large populations. This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection dynamics, even with large populations. That is, the timing and magnitude of outbreaks will be unpredictable. While such uncertainties have social costs, we also find that they on average decrease the herd immunity thresholds and the cumulative infections because per-period infection rates have decreasing marginal effects. Our findings have implications for social distancing interventions: targeting SSEs reduce not only the average rate of infection (R0) but also its uncertainty. To understand this effect, and to improve inference of the average reproduction numbers under fat tails, estimating the tail distribution of SSEs is vital. url: http://medrxiv.org/cgi/content/short/2020.06.11.20128058v1?rss=1 doi: 10.1101/2020.06.11.20128058 id: cord-311333-shvtfxog author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-05-28 words: 414.0 sentences: 37.0 pages: flesch: 70.0 cache: ./cache/cord-311333-shvtfxog.txt txt: ./txt/cord-311333-shvtfxog.txt summary: title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. Nasopharyngeal swab, sputum and saliva samples were collected from 9 patients who 69 were admitted to our hospital after a diagnosis of COVID-19. Saliva as a 187 non-invasive specimen for detection of SARS-CoV-2 Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva Detection of noroviruses in fecal specimens by direct RT-PCR 195 without RNA purification abstract: Rapid detection of SARS-CoV-2 is critical for the diagnosis of coronavirus disease 2019 (COVID-19) and preventing the spread of the virus. A novel “2019 Novel Coronavirus Detection Kit (nCoV-DK)” halves detection time by eliminating the steps of RNA extraction and purification. We evaluated concordance between the nCoV-DK and direct PCR. The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. The overall concordance rate of the virus detection between the two methods was 94.4% (95% CI, 86.2-98.4). Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. url: https://doi.org/10.1101/2020.05.27.120410 doi: 10.1101/2020.05.27.120410 id: cord-340410-s9haq8y1 author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-06-26 words: 1072.0 sentences: 81.0 pages: flesch: 68.0 cache: ./cache/cord-340410-s9haq8y1.txt txt: ./txt/cord-340410-s9haq8y1.txt summary: The virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct PCR and nCoV-DK, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. The nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. The 2019 Novel Coronavirus Detection Kit (nCoV-DK, Shimadzu Corporation, Kyoto, Japan) eliminates the steps of RNA extraction and purification by using the Ampdirect TM technology (Nishimura et al., 2010) , thus significantly reducing the time required for sample preparation and PCR detection from more than 2 hours to about 1 hour. We herein compared efficacy of the nCoV-DK with the direct PCR method requiring RNA extraction and purification. Particularly, it should be noted saliva is a reliable tool to detect the virus by the nCoV-KD even without process of RNA extraction and purification. abstract: Abstract Rapid detection of SARS-CoV-2 is critical for the diagnosis of coronavirus disease 2019 (COVID-19) and preventing the spread of the virus. A novel “2019 Novel Coronavirus Detection Kit (nCoV-DK)” halves detection time by eliminating the steps of RNA extraction and purification. We evaluated concordance between the nCoV-DK and direct PCR. The virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct PCR and nCoV-DK, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. The nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. url: https://doi.org/10.1016/j.ijid.2020.06.074 doi: 10.1016/j.ijid.2020.06.074 id: cord-296551-efqt3tw2 author: Fukushi, Shuetsu title: Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry Mediated by SARS Coronavirus Spike Proteins date: 2007-11-28 words: 1670.0 sentences: 100.0 pages: flesch: 56.0 cache: ./cache/cord-296551-efqt3tw2.txt txt: ./txt/cord-296551-efqt3tw2.txt summary: Severe acute respiratory syndrome (SARS) coronavirus (CoV) contains a spike (S) protein that binds to a receptor molecule (angiotensin-converting enzyme 2; ACE2), induces membrane fusion, and serves as a neutralizing epitope. To study the functions of the S protein, we describe here the generation of SARS-CoV S protein-bearing vesicular stomatitis virus (VSV) pseudotype using a VSV∆G∗/GFP system in which the G gene is replaced by the green fluorescent protein (GFP) gene (VSV-SARS-CoV-St19/GFP). Thus, VSV pseudotyped with SARS-CoV S protein is useful for developing a rapid detection system for neutralizing antibody specific for SARS-CoV infection as well as studying the S-mediated cell entry of SARS-CoV. In addition to a significant advantage of the VSV-SARS-St19/GFP for safe and rapid analyses of infection, the VSV⌬G*/SEAP system, in which the G gene is replaced with the secreted alkaline phosphatase (SEAP) gene, may be superior to high-throughput quantitative analysis of S-mediated cell entry. Mix serially diluted VSV-SARS-St19/GFP with DMEM-5%FCS and inoculate the mixture into Vero E6 cells seeded in 96-well culture plates. abstract: Severe acute respiratory syndrome (SARS) coronavirus (CoV) contains a spike (S) protein that binds to a receptor molecule (angiotensin-converting enzyme 2; ACE2), induces membrane fusion, and serves as a neutralizing epitope. To study the functions of the S protein, we describe here the generation of SARS-CoV S protein-bearing vesicular stomatitis virus (VSV) pseudotype using a VSV∆G∗/GFP system in which the G gene is replaced by the green fluorescent protein (GFP) gene (VSV-SARS-CoV-St19/GFP). Partial deletion of the cytoplasmic domain of SARS-CoV S protein (SARS-CoV-St19) allowed efficient incorporation into the VSV particle that enabled the generation of a high titer of pseudotype virus. Neutralization assay with anti-SARS-CoV antibody revealed that VSV-SARS-St19/GFP pseudotype infection is mediated by SARS-CoV S protein. The VSV∆G∗/SEAP system, which secretes alkaline phosphatase instead of GFP, was also generated as a VSV pseudotype having SARS-CoV S protein (VSV-SARS-CoV-St19/SEAP). This system enabled high-throughput analysis of SARS-CoV S protein-mediated cell entry by measuring alkaline phosphatase activity. Thus, VSV pseudotyped with SARS-CoV S protein is useful for developing a rapid detection system for neutralizing antibody specific for SARS-CoV infection as well as studying the S-mediated cell entry of SARS-CoV. url: https://doi.org/10.1007/978-1-59745-181-9_23 doi: 10.1007/978-1-59745-181-9_23 id: cord-317591-qa6oxy4j author: Fukushima, Akiko title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 words: 3605.0 sentences: 196.0 pages: flesch: 53.0 cache: ./cache/cord-317591-qa6oxy4j.txt txt: ./txt/cord-317591-qa6oxy4j.txt summary: To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells. abstract: OBJECTIVE: Severe acute respiratory syndrome (SARS) is a severe pulmonary infectious disease caused by a novel coronavirus. To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). METHOD: Chimeric DNA-RNA hammerhead ribozyme targeting MHV and SARS-CoV were designed and synthesized. To confirm its activity, in vitro cleavage reactions were performed with the synthesized ribozyme. Effects of the chimeric ribozyme were evaluated on multiplication of MHV. Effects of the chimeric ribozyme on expression of SARS-CoV were evaluated in cultured 3T3 cells. RESULT: The synthetic ribozyme cleaved the synthetic target MHV and SARS-CoV RNA into fragments of predicted length. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited the expression of SARS-CoV RNA in 3T3 cells transfected with the recombinant plasmid. The chimeric DNA-RNA ribozyme targeting SARS-CoV significantly inhibited MHV viral activity and expression of recombinant SARS RNA in vitro. CONCLUSION: These findings indicate that the synthetic chimeric DNA-RNA ribozyme could provide a feasible treatment for SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/19420961/ doi: 10.1159/000215946 id: cord-312950-ggywr91e author: Fuller, Julie title: Surveillance for Febrile Respiratory Infections during Cobra Gold 2003 date: 2006-05-17 words: 1855.0 sentences: 99.0 pages: flesch: 43.0 cache: ./cache/cord-312950-ggywr91e.txt txt: ./txt/cord-312950-ggywr91e.txt summary: The Naval Health Research Center conducted laboratory-based surveillance for febrile respiratory infections at the 2003 Cobra Gold Exercise in Thailand. To ease these concerns, the Naval Health Research Center (NHRC), with an 8-year history of surveillance and diagnosis of febrile respiratory illness (FRI) within active duty continental United States and deployed forces, was tasked with conducting laboratory-based, active surveillance for respiratory illnesses (including SARS) during the exercise, with the intent of early recognition and response. 7, 8 As concerns over SARS importation were eased with implementation of surveillance, valuable information on circulating respiratory pathogens during such an exercise was collected. Supplies, including viral transport medium, swabs (sterile Dacron), preprinted subject identification labels, FRI log sheets, and informed consent/case forms, were provided to both units. Of the 16 diagnostic specimens received, seven (44%) tested positive for influenza A, 2 (13%) for coronavirus OC43, 2 (13%) for respiratory syncytial virus, and 1 (6%) for rhinovirus. abstract: The Naval Health Research Center conducted laboratory-based surveillance for febrile respiratory infections at the 2003 Cobra Gold Exercise in Thailand. Seventeen individuals met the case definition for febrile respiratory illness, and diagnostic specimens were obtained from 16. Laboratory testing identified influenza A for 44%; sequence analysis demonstrated that these were Fujian-like influenza strains, which represented the predominant strain found globally in 2003/2004. Other pathogens identified included coronavirus OC43, respiratory syncytial virus, and rhinovirus. Logistical challenges were overcome as laboratory-supported febrile respiratory illness surveillance was conducted during a military training exercise. With heightened concern over the potential for another global influenza pandemic, such surveillance could prove critical for the detection of emerging influenza and respiratory pathogen strains with potential for importation to the United States. url: https://www.ncbi.nlm.nih.gov/pubmed/16761881/ doi: 10.7205/milmed.171.5.357 id: cord-273492-i483r91m author: Fulzele, Sadanand title: COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile date: 2020-05-09 words: 3637.0 sentences: 233.0 pages: flesch: 51.0 cache: ./cache/cord-273492-i483r91m.txt txt: ./txt/cord-273492-i483r91m.txt summary: In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Based on the above reports, we did in silico analysis of miRNAs targeting SARS and COVID-19 (recent isolates from different regions) to understand the pathophysiology and identify novel therapeutic targets. In a previous report, host cellular miRNAs-181 binds to the ORF-4 region at the viral genome of porcine reproductive and respiratory syndrome virus (PRRSV) to inhibit its replication [17] . Both KEGG and GO pathway analysis revealed that COVID-19 targeting human cellular miRNAs are involved in the number of age-related complications. abstract: The World health organization (WHO) declared Coronavirus disease 2019 (COVID-19) a global pandemic and a severe public health crisis. Drastic measures to combat COVID-19 are warranted due to its contagiousness and higher mortality rates, specifically in the aged patient population. At the current stage, due to the lack of effective treatment strategies for COVID-19 innovative approaches need to be considered. It is well known that host cellular miRNAs can directly target both viral 3'UTR and coding region of the viral genome to induce the antiviral effect. In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. We found 848 common miRNAs targeting the SARS genome and 873 common microRNAs targeting the COVID-19 genome. Out of a total of 848 miRNAs from SARS, only 558 commonly present in all COVID-19 isolates. Interestingly, 315 miRNAs are unique for COVID-19 isolates and 290 miRNAs unique to SARS. We also noted that out of 29 COVID-19 isolates, 19 isolates have identical miRNA targets. The COVID-19 isolates, Netherland (EPI_ISL_422601), Australia (EPI_ISL_413214), and Wuhan (EPI_ISL_403931) showed six, four, and four unique miRNAs targets, respectively. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Recent studies also suggested that some of the human miRNAs targeting COVID-19 decreased with aging and underlying conditions. GO and KEGG identified impaired signaling pathway may be due to low abundance miRNA which might be one of the contributing factors for the increasing severity and mortality in aged individuals and with other underlying conditions. Further, in vitro and in vivo studies are needed to validate some of these targets and identify potential therapeutic targets. url: https://doi.org/10.14336/ad.2020.0428 doi: 10.14336/ad.2020.0428 id: cord-322650-q8inhgtr author: Fung, Yin-Wan Wendy title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date: 2004-08-15 words: 1132.0 sentences: 64.0 pages: flesch: 50.0 cache: ./cache/cord-322650-q8inhgtr.txt txt: ./txt/cord-322650-q8inhgtr.txt summary: title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15356838/ doi: 10.1086/422887 id: cord-267856-t3ksa18w author: Funk, Colin D. title: A Novel Strategy to Mitigate the Hyperinflammatory Response to COVID-19 by Targeting Leukotrienes date: 2020-08-06 words: 4340.0 sentences: 232.0 pages: flesch: 43.0 cache: ./cache/cord-267856-t3ksa18w.txt txt: ./txt/cord-267856-t3ksa18w.txt summary: We offer a simple treatment paradigm using two generic drugs targeting the hyperinflammatory response that characterizes the turning point from mild to severe/critical COVID-19 by targeting leukotriene biosynthesis with zileuton (Zyflo(®) controlled release formulation) and antagonism of the cysteinyl leukotriene 1 receptor with montelukast (Singulair(®)). By targeting vascular permeability, immune modulating and general inflammation-dampening effects at the CysLT 1 level with montelukast (Dahleń et al., 1981; Maeba et al., 2005; Capra et al., 2007; Tahan et al., 2008; Khodir et al., 2014) and LT biosynthesis with the 5-lipoxygenase inhibitor zileuton, to block both arms of the LT pathway ( Figure 2 ) and remove ligands for another key receptor regulating vascular permeability, CysLT 2 (Moos et al., 2008) , as well as inflammatory cell recruitment and endothelial cell adhesion via BLT 1 receptor (Ford-Hutchinson et al., 1980; Tager et al., 2003; Taube et al., 2006; Sasaki and Yokomizo, 2019) , there is a sound scientific basis for alleviating disease progression from mild to severe-critical stages of COVID-19 (Figures 1 and 2) . abstract: SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) has wreaked havoc during the global pandemic of 2020 infecting millions and leaving over a half million dead. As a new virus, not previously in the human population, but with similarities to other coronaviruses causing severe acute respiratory distress syndrome (SARS/ARDS), and no known treatments, the race to re-purpose existing drugs and to enlist novel therapeutics is underway. In the half-year since the first cases, we have acquired substantial knowledge of this virus and the clinical course of COVID-19 progression. Results from early clinical trials have revealed two treatments (remdesivir, dexamethasone) that mitigate disease progression but clearly, there is much room for improvement. Initial case reports indicated many succumb to COVID-19 of hypoxic respiratory failure due to ARDS. However, ensuing studies revealed an atypical, immune cell-sequestered, vasculature-inflamed state leading to multiorgan thrombotic complications and end organ failure likely due to hyperinflammatory host responses. This Perspective focuses on a potential mechanism for a key COVID-19 disease progression turning point related to vascular and airway inflammation. The leukotriene lipid mediators have been overlooked with discussion centering on cytokine storms unleashing the deadly form of COVID-19. Leukotrienes possess some of the most potent known activities on immune cell trafficking and vascular leakage. We offer a simple treatment paradigm using two generic drugs targeting the hyperinflammatory response that characterizes the turning point from mild to severe/critical COVID-19 by targeting leukotriene biosynthesis with zileuton (Zyflo(®) controlled release formulation) and antagonism of the cysteinyl leukotriene 1 receptor with montelukast (Singulair(®)). url: https://www.ncbi.nlm.nih.gov/pubmed/32848802/ doi: 10.3389/fphar.2020.01214 id: cord-269835-mz7i66qp author: Furfaro, Federica title: SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date: 2020-06-11 words: 7275.0 sentences: 295.0 pages: flesch: 38.0 cache: ./cache/cord-269835-mz7i66qp.txt txt: ./txt/cord-269835-mz7i66qp.txt summary: The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with inflammatory bowel disease (IBD) who need to undergo endoscopic procedures. In particular, recommendations regarding the use of personal protective equipment to prevent COVID-19 transmission, both for patients and health-care professionals, are proposed and different scenarios in endoscopic IBD management are evaluated to suggest when endoscopy could be rescheduled and replaced by alternative biomarkers. The panel of experts con sidered possible aerosolization during colonoscopy, in particular during the insertion and removal of instruments through the biopsy channel and the presence of the virus in the stool and advised on the use of N95 masks for lower gastrointestinal procedures as a precautionary measure to protect the endoscopist from the risk of possible COVID-19 transmission from the patient if infected by SARS-CoV-2 (ref. abstract: The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with inflammatory bowel disease (IBD) who need to undergo endoscopic procedures. Several preventive measures must be taken to avoid the spread of infection among health-care professionals and patients with IBD, including the use of personal protective equipment, greater attention to endoscopic room hygiene and rescheduling of non-urgent procedures. This Perspective aims to provide a guide based on the Italian and French experience to better face the difficulties encountered by endoscopists during this global health emergency. In particular, recommendations regarding the use of personal protective equipment to prevent COVID-19 transmission, both for patients and health-care professionals, are proposed and different scenarios in endoscopic IBD management are evaluated to suggest when endoscopy could be rescheduled and replaced by alternative biomarkers. url: https://www.ncbi.nlm.nih.gov/pubmed/32528139/ doi: 10.1038/s41575-020-0319-3 id: cord-138656-8iyynbup author: Furuyama, Taima N. title: Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant date: 2020-06-20 words: 3036.0 sentences: 172.0 pages: flesch: 61.0 cache: ./cache/cord-138656-8iyynbup.txt txt: ./txt/cord-138656-8iyynbup.txt summary: title: Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant From November 2002 to May 2004, SARS-CoV-1 (Severe Acute Respiratory Syndrome caused by Coronavirus type 1) affected 26 countries worldwide, accounted 8,096 confirmed cases and 774 deaths (9.6% fatality ratio) (Drosten et al., 2003; Ksiazek et al., 2003; Lee et al., 2003; Peiris et al., 2003; Zhong et al., 2003 ; Centers for Disease Control and Prevention -Department of Health and Human Services, 2004; World Health Organization, 2004; Centers for Disease Control and Prevention, 2017) . MERS-CoV (Middle East Respiratory Syndrome caused by Coronavirus) spread to 27 countries around the globe, totalizing 2,519 confirmed cases and 866 deaths (34.4% fatality ratio) continuously since April 2012 (Zaki et al., 2012; Hijawi et al., 2013; Centers for Disease Control and Prevention, 2019; World Health Organization, 2019 , 2020b . If there is a correlation between the D614G variant prevalence and higher SARS-CoV-2 transmission, then the epidemiological data might reveal a significant correlation between D614G prevalence and the growth rate coefficients of epidemic curves globally. abstract: The COVID-19 pandemic started in Wuhan, China, and caused the worldwide spread of the RNA virus SARS-CoV-2, the causative agent of COVID-19. Because of its mutational rate, wide geographical distribution, and host response variance this coronavirus is currently evolving into an array of strains with increasing genetic diversity. Most variants apparently have neutral effects for disease spread and symptoms severity. However, in the viral Spike protein, which is responsible for host cell attachment and invasion, an emergent variant, containing the amino acid substitution D to G in position 614 (D614G), was suggested to increase viral infection capability. To test whether this variant has epidemiological impact, the temporal distributions of the SARS-CoV-2 samples bearing D or G at position 614 were compared in the USA, Asia and Europe. The epidemiological curves were compared at early and late epidemic stages. At early stages, where containment measures were still not fully implemented, the viral variants are supposed to be unconstrained and its growth curves might approximate the free viral dynamics. Our analysis shows that the D614G prevalence and the growth rates of COVID-19 epidemic curves are correlated in the USA, Asia and Europe. Our results suggest a selective sweep that can be explained, at least in part, by a propagation advantage of this variant, in other words, that the molecular level effects of D614G have sufficient impact on population transmission dynamics as to be detected by differences in rate coefficients of epidemic growth curves. url: https://arxiv.org/pdf/2006.11609v1.pdf doi: nan id: cord-322837-tqgwgvo0 author: Gable, Lance title: Legal and Ethical Implications of Wastewater SARS-CoV-2 Monitoring for COVID-19 Surveillance date: 2020-06-24 words: 1909.0 sentences: 104.0 pages: flesch: 47.0 cache: ./cache/cord-322837-tqgwgvo0.txt txt: ./txt/cord-322837-tqgwgvo0.txt summary: Even if reliability and efficacy are established, limits on sample and data collection, use, and sharing, must also be considered to prevent undermining privacy and autonomy in order to implement these public health strategies consistent with legal and ethical considerations. The proposed use of wastewater screening to detect SARS-CoV-2 viral RNA has the potential to greatly enhance our technical capabilities to identify, track, pinpoint, and quantify 32 Second, public health authorities could use this information to justify increased testing among people living in homes or working at sites close to where the virus has been found in wastewater, or to implement neighborhood-wide screening programs in these areas. Wastewater screening for SARS-CoV-2 could provide an important tool to detect new outbreaks of COVID-19 and to target resources to intervene to stop the spread of the disease; however, scientific research must establish the efficacy of such testing in identifying communitybased COVID-19 infections before its use can be considered as the basis for public policy. abstract: Scientists have observed that molecular markers for COVID-19 can be detected in wastewater of infected communities both during an outbreak and, in some cases, before the first case is confirmed. The CDC and other government entities are considering whether to add community surveillance through wastewater monitoring to assist in tracking disease prevalence and guiding public health responses to the COVID-19 pandemic. This scientific breakthrough may lead to many useful potential applications for tracking disease, intensifying testing, initiating social distancing or quarantines, and even lifting restrictions once a cessation of infection is detected and confirmed. Yet, new technologies developed in response to a public health crisis may raise difficult legal and ethical questions about how such technologies may impact both the public health and civil liberties of the population. This Article describes recent scientific evidence regarding COVID-19 detection in wastewater, identifying public health benefits that may result from this breakthrough, as well as the limitations of existing data. The Article then assesses the legal and ethical implications of implementing policy based on positive sewage signals. It concludes that the first step to implementing legal and ethical wastewater monitoring is to develop scientific understanding. Even if reliability and efficacy are established, limits on sample and data collection, use, and sharing, must also be considered to prevent undermining privacy and autonomy in order to implement these public health strategies consistent with legal and ethical considerations. url: https://doi.org/10.1093/jlb/lsaa039 doi: 10.1093/jlb/lsaa039 id: cord-256147-lfwytlj3 author: Gabriella, di Mauro title: SARS-Cov-2 infection: response of human immune system and possible implications for the rapid test and treatment date: 2020-04-16 words: 1645.0 sentences: 81.0 pages: flesch: 50.0 cache: ./cache/cord-256147-lfwytlj3.txt txt: ./txt/cord-256147-lfwytlj3.txt summary: Considering the clinical impact of the new outbreak, it is highly important to study the potential responses of the human immune system during the SARS-CoV-2 infection as well as the role of virus-specific T cells and by B-lymphocytes. In order to apply a rapid test able to detect the presence of specific IgM and IgG for SARS-CoV-2, it is important to consider that the IgM values tend to disappear within 2 weeks since the beginning of the infection. The sensitivity and specificity of these tests were evaluated on 397 blood samples from patients who tested positive for the nasopharyngeal swab for SARS-CoV-2 infection and on 128 patients who tested negative and asymptomatic but potentially at risk of developing the infection based on epidemiological criteria [7] . The results of the study showed that out of 397 blood samples from patients with a SARS-CoV-2 infection, 352 tested positive. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis abstract: The new coronavirus outbreak is an ongoing pandemic that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The new coronavirus SARS-Cov-2 belongs to the subfamily of β−coronaviruses and shares 79.5% of the genetic sequence of SARS-CoV, the causative agent of the epidemic that started in 2002 and ended in 2004. Considering the clinical impact of the new outbreak, it is highly important to study the potential responses of the human immune system during the SARS-CoV-2 infection as well as the role of virus-specific T cells and by B-lymphocytes. Moreover, specific data on the production of IgG and IgM is crucial to allow the rapid identification of the infection. In this paper we also described the importance of sensitive and specific rapid test for SARS-CoV-2. Indeed, this test represents an important immunological tool aimed at identifying the precise phase of the infection in order to undertake a more appropriate pharmacological treatment. Lastly, we provided an overview of pharmacological treatments aimed to reduce inflammatory processes underlying the infection and the need for the discovery of a new vaccine against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32311668/ doi: 10.1016/j.intimp.2020.106519 id: cord-280029-g1k3zlax author: Gabutti, Giovanni title: Coronavirus: Update Related to the Current Outbreak of COVID-19 date: 2020-04-08 words: 5006.0 sentences: 271.0 pages: flesch: 53.0 cache: ./cache/cord-280029-g1k3zlax.txt txt: ./txt/cord-280029-g1k3zlax.txt summary: The World Health Organization (WHO) has officially named the infection coronavirus disease 2019 (COVID-19), and the virus has been classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS is caused by a virus that emerged in southern China in November 2002 and led to [ 8000 human infections and 774 deaths in 37 countries in the 2002-2003 period [3] ; MERS is related to a virus detected for the first time in Saudi Arabia in 2012, responsible for 2494 laboratoryconfirmed cases of infection and 858 deaths since September 2012 [4] . On January 11 and 12, 2020, the WHO received further details and information from the Chinese National Health Commission regarding the possible association of this epidemic with exposure in a fish market in Wuhan, and the Chinese authorities shared the genetic sequence of a new coronavirus, subsequently identified as SARS-CoV-2 [14] . abstract: In December 2019, some cases of viral pneumonia were epidemiologically related to a new coronavirus in the province of Hubei, China. Subsequently, there has been an increase in infections attributable to this virus throughout China and worldwide. The World Health Organization (WHO) has officially named the infection coronavirus disease 2019 (COVID-19), and the virus has been classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This appears to be a virus from Rhinolophus bats, but the intermediate host has not yet been identified. The mechanism of infection of SARS-CoV-2 is not yet known; it appears to have affinity for cells located in the lower airways, where it replicates. The interhuman transmission of coronaviruses mainly occurs through saliva droplets and direct and indirect contact via surfaces. As of March 10, 2020, the number of cases worldwide was 113,702. Along with severe acute respiratory syndrome (SARS) and Middle Eastern respiratory syndrome (MERS), COVID-19 appears to cause a severe clinical picture in humans, ranging from mild malaise to death by sepsis/acute respiratory distress syndrome. The prognosis is worse in elderly patients with comorbidities. To date, there is no specific therapy for COVID-19. Prevention of SARS-CoV-2 infection implies strategies that limit the spread of the virus. WHO and other international and national bodies have developed continuously updated strategic objectives and provisions to contain the spread of the virus and infection. url: https://doi.org/10.1007/s40121-020-00295-5 doi: 10.1007/s40121-020-00295-5 id: cord-273314-p1dlzoh1 author: Gadiparthi, Chiranjeevi title: Gastrointestinal Bleeding in Patients with Severe SARS-CoV-2 date: 2020-06-04 words: 1464.0 sentences: 88.0 pages: flesch: 45.0 cache: ./cache/cord-273314-p1dlzoh1.txt txt: ./txt/cord-273314-p1dlzoh1.txt summary: Gastrointestinal symptoms are common and frequently reported in Coronavirus Disease-2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, GIB in COVID-19 patients poses unique challenges to patients due to high-risk of concomitant respiratory failure and to endoscopy personnel due to risk of airborne transmission during endoscopic procedures. GI bleeding (GIB) in patients with SARS-CoV-2 poses unique challenges, especially for endoscopists and other procedural staff because of the potential for aerosol spread. In this article, we report 3 hospitalized patients with SARS-CoV-2 infection with GIB and acute blood loss anemia with focus on management strategies. She tested positive for SARS-CoV-2 by RT-PCR assay and developed acute hypoxic respiratory failure requiring supplemental oxygen of 15 L per minute via a nonrebreather mask. On hospital day 5, the patient developed recurrent GIB with a large amount of melena and bright red blood per rectum with hemodynamic instability requiting intensive care unit (ICU) transfer. abstract: Gastrointestinal symptoms are common and frequently reported in Coronavirus Disease-2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is unclear if SARS-CoV-2 is associated with increased risk of gastrointestinal bleeding (GIB). Nevertheless, GIB in COVID-19 patients poses unique challenges to patients due to high-risk of concomitant respiratory failure and to endoscopy personnel due to risk of airborne transmission during endoscopic procedures. Many management issues related to COVID-19 are still being studied. In this case series, we attempt to discuss the important clinical implications related to the management of GIB in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32516204/ doi: 10.14309/ajg.0000000000000719 id: cord-353594-z1vxamvp author: Gagiannis, Daniel title: Clinical, Serological, and Histopathological Similarities Between Severe COVID-19 and Acute Exacerbation of Connective Tissue Disease-Associated Interstitial Lung Disease (CTD-ILD) date: 2020-10-02 words: 4997.0 sentences: 246.0 pages: flesch: 40.0 cache: ./cache/cord-353594-z1vxamvp.txt txt: ./txt/cord-353594-z1vxamvp.txt summary: Since we observed similarities between COVID-19 and interstitial lung disease in connective tissue disease (CTD-ILD), we investigated features of autoimmunity in SARS-CoV-2-associated respiratory failure. Patients or their relatives had given written informed consent to routine diagnostic procedures (serology, bronchoscopy, radiology) as well as (partial) autopsy in the case of death, respectively, as well as to the scientific use of data and tissue samples in the present study. Our finding that significant ANA titers and/or detection of specific autoantibodies are found in most patients who develop ARDS raises the question if there is a comparable mechanism of lung damage between SARS-CoV-2 infection and exacerbating autoimmune disease. Our observation of CTD-associated autoantibodies together with the CTD-like radiologic and histopathologic lung findings in severe cases of COVID-19 point towards a possible dysregulation of the immune response upon SARS-CoV-2 infection that might fuel organizing pneumonia and trigger interstitial fibrosis, with deleterious effects on the functional outcome in long-term survivors. abstract: BACKGROUND AND OBJECTIVES: Understanding the pathophysiology of respiratory failure in coronavirus disease 2019 (COVID-19) is indispensable for development of therapeutic strategies. Since we observed similarities between COVID-19 and interstitial lung disease in connective tissue disease (CTD-ILD), we investigated features of autoimmunity in SARS-CoV-2-associated respiratory failure. METHODS: We prospectively enrolled 22 patients with RT-PCR-confirmed SARS-CoV-2 infection and 10 patients with non-COVID-19-associated pneumonia. Full laboratory testing was performed including autoantibody (AAB; ANA/ENA) screening using indirect immunofluorescence and immunoblot. Fifteen COVID-19 patients underwent high-resolution computed tomography. Transbronchial biopsies/autopsy tissue samples for histopathology and ultrastructural analyses were obtained from 4/3 cases, respectively. RESULTS: Thirteen (59.1%) patients developed acute respiratory distress syndrome (ARDS), and five patients (22.7%) died from the disease. ANA titers ≥1:320 and/or positive ENA immunoblots were detected in 11/13 (84.6%) COVID-19 patients with ARDS, in 1/9 (11.1%) COVID-19 patients without ARDS (p = 0.002) and in 4/10 (40%) patients with non-COVID-19-associated pneumonias (p = 0.039). Detection of AABs was significantly associated with a need for intensive care treatment (83.3 vs. 10%; p = 0.002) and occurrence of severe complications (75 vs. 20%, p = 0.03). Radiological and histopathological findings were highly heterogeneous including patterns reminiscent of exacerbating CTD-ILD, while ultrastructural analyses revealed interstitial thickening, fibroblast activation, and deposition of collagen fibrils. CONCLUSIONS: We are the first to report overlapping clinical, serological, and imaging features between severe COVID-19 and acute exacerbation of CTD-ILD. Our findings indicate that autoimmune mechanisms determine both clinical course and long-term sequelae after SARS-CoV-2 infection, and the presence of autoantibodies might predict adverse clinical course in COVID-19 patients. url: https://doi.org/10.3389/fimmu.2020.587517 doi: 10.3389/fimmu.2020.587517 id: cord-300963-1n1f8mf2 author: Gajendran, Mahesh title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date: 2020-10-12 words: 6681.0 sentences: 350.0 pages: flesch: 46.0 cache: ./cache/cord-300963-1n1f8mf2.txt txt: ./txt/cord-300963-1n1f8mf2.txt summary: Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient''s age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. abstract: The current outbreak of COVID-19 pandemic caused by SARS-CoV-2 has affected nearly 188 countries. Patients with severe COVID-19 are more commonly elderly and suffer from comorbidities such as hypertension, diabetes mellitus, coronary artery disease, chronic pulmonary disease, obesity, and cancer. Inflammatory bowel disease (IBD) affects as many as 6.8 million people globally, and a significant proportion of them are treated with immunosuppressants. Hence, there is an ongoing concern over the impact of COVID-19 on IBD patients and their susceptibility to it. So far, there are about 1439 IBD patients in the Surveillance Epidemiology of Coronavirus under Research Exclusion (SECURE-IBD) registry reported to be infected with SARS-CoV-2. There are many unique challenges and dilemmas that need to be taken into account when managing an IBD patient with COVID-19. The management of each patient should be individualized. The IBD societies and experts have strongly recommended that patients should not discontinue their IBD medications. If the patients have symptoms of COVID-19 or IBD flare-up, they are recommended to call their IBD physician first to discuss their medication. In addition, IBD patients are urged to practice social distancing strictly to minimize the chances of infection. As COVID-19 is rapidly evolving, our experience and understanding of its impact on the IBD population may potentially change in the near future. url: https://doi.org/10.20524/aog.2020.0547 doi: 10.20524/aog.2020.0547 id: cord-352433-sts48u9i author: Galanti, Marta title: Direct Observation of Repeated Infections With Endemic Coronaviruses date: 2020-07-07 words: 3824.0 sentences: 170.0 pages: flesch: 41.0 cache: ./cache/cord-352433-sts48u9i.txt txt: ./txt/cord-352433-sts48u9i.txt summary: BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. However, in Korea, as reported by the Korean Centers for Disease Control and Prevention, viable SARS-CoV-2 was not isolated in cell culture of respiratory samples from potentially reinfected individuals [5] ; thus, these subsequent positive results may have been due to inactive genetic material detected by molecular testing. abstract: BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. METHODS: Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. RESULTS: During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the betacoronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity, but found strong association between symptom severity and belonging to the same family. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32692346/ doi: 10.1093/infdis/jiaa392 id: cord-252600-bvh1o64r author: Galasiti Kankanamalage, Anushka C. title: Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date: 2018-04-25 words: 4752.0 sentences: 254.0 pages: flesch: 54.0 cache: ./cache/cord-252600-bvh1o64r.txt txt: ./txt/cord-252600-bvh1o64r.txt summary: We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). abstract: Abstract There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography. url: https://www.ncbi.nlm.nih.gov/pubmed/29544147/ doi: 10.1016/j.ejmech.2018.03.004 id: cord-313489-i969aqn9 author: Galbadage, Thushara title: Does COVID-19 Spread Through Droplets Alone? date: 2020-04-24 words: 2342.0 sentences: 126.0 pages: flesch: 50.0 cache: ./cache/cord-313489-i969aqn9.txt txt: ./txt/cord-313489-i969aqn9.txt summary: Social or physical distancing helps reduce the transmission of respiratory droplets containing SARS-CoV-2 and slows the incidence of the disease by reducing the opportunities for potential viral exposures. Precautions to prevent the spread by droplets as recommended by both the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) are to (1) wash hands with soap, (2) avoid touching viral entry points, such as eyes, nose, and mouth, (3) cover the mouth when coughing or sneezing, (4) wear a facemask if sick and (5) practice social distancing by putting 6 feet of distance between individuals. The ability of SARS-CoV-2 to remain viable longer on surfaces taken together with its higher virulence in establishing an infection makes it very likely that this coronavirus uses other modes of transmission in addition to respiratory droplets (Figure 1) . abstract: nan url: https://doi.org/10.3389/fpubh.2020.00163 doi: 10.3389/fpubh.2020.00163 id: cord-354261-gdvawnp6 author: Gale, Chris title: National active surveillance to understand and inform neonatal care in COVID-19 date: 2020-06-14 words: 1626.0 sentences: 92.0 pages: flesch: 46.0 cache: ./cache/cord-354261-gdvawnp6.txt txt: ./txt/cord-354261-gdvawnp6.txt summary: Vertical transmission of SARS-CoV-2 has yet to be definitively established; neonatal infection with the virus has been detected in the first days after birth to mothers with COVID-19 1 ; however, this could represent early horizontal transmission. For more complete case ascertainment, this BPSU surveillance will link with other related data sources, including ongoing UKOSS surveillance of COVID-19 in pregnancy for maternal cases, Mothers and Babies: Reducing Risk through Audits and Confidential Enquiries across the UK (MBRRACE-UK), for neonatal deaths and stillbirths, and Public Health England (PHE), Health Protection Scotland, Public Health Wales and the Health and Social Care Public Health Agency in Northern Ireland. Active surveillance through established national systems such as the BPSU and UKOSS with very high population-based case ascertainment is among the simplest, quickest and most efficient way to obtain the accurate population level incidence data and to determine true infection rates, clinical characteristics and outcomes, which are needed to inform optimal perinatal and neonatal care. abstract: nan url: https://doi.org/10.1136/archdischild-2020-319372 doi: 10.1136/archdischild-2020-319372 id: cord-309317-cgs0sui7 author: Galeotti, Caroline title: Autoimmune and inflammatory diseases following COVID-19 date: 2020-06-04 words: 1624.0 sentences: 80.0 pages: flesch: 44.0 cache: ./cache/cord-309317-cgs0sui7.txt txt: ./txt/cord-309317-cgs0sui7.txt summary: Emerging reports show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection precedes the appearance of various autoimmune and autoinflammatory diseases, including paediatric inflammatory multisystemic syndrome (PIMS) or multisystem inflammatory syndrome in children (MIS-C), thus adding to the growing mystery of this virus and raising questions about the nature of its link with autoimmune and autoinflammatory sequelae. Several emerging reports show that coronavirus disease 2019 (COVID-19), a pandemic respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), could lead to autoimmune and autoinflammatory diseases, such as paedi atric inflammatory multisystemic syndrome (PIMS; which includes Kawasaki-like disease, Kawasaki disease shock syndrome, toxic shock syndrome, myocarditis and macrophage activation syndrome) in children [1] [2] [3] [4] [5] [6] . In the USA, the New York City Health Department on 4 May 2020 reported that 15 children aged 2-15 years had presented with symptoms of MIS-C, including persistent fever and increased levels of inflammatory markers, and many also had rash, abdominal pain, vomiting or diarrhea; ten of the 15 child ren were positive for SARS-CoV-2 infection 6 . abstract: Emerging reports show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection precedes the appearance of various autoimmune and autoinflammatory diseases, including paediatric inflammatory multisystemic syndrome (PIMS) or multisystem inflammatory syndrome in children (MIS-C), thus adding to the growing mystery of this virus and raising questions about the nature of its link with autoimmune and autoinflammatory sequelae. url: https://doi.org/10.1038/s41584-020-0448-7 doi: 10.1038/s41584-020-0448-7 id: cord-352905-ge3u32hm author: Galimberti, Sara title: Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2 date: 2020-09-02 words: 5383.0 sentences: 231.0 pages: flesch: 45.0 cache: ./cache/cord-352905-ge3u32hm.txt txt: ./txt/cord-352905-ge3u32hm.txt summary: Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Translated in the COVID-19 context, if TKIs would sustain the coronavirus infection or replication, we might expect to observe a significant increase of TTV load during treatment of our patients with nilotinib. In the second phase of our study, we employed the NanoString technology for analyzing the expression of 770 inflammationand immunity-related genes in five CML patients before and after 6 months of treatment with imatinib, with the aim of testing the impact of this TKI on the possible immunological control of viral infection. Considering that it has been proven that at diagnosis, the immunity of these patients is severely impaired (63) , the low infection rate observed during the 2020 pandemic could prove that TKIs play an antiviral role or, at least, could not impair the host response against the new coronavirus. abstract: SARS-CoV-2 is the viral agent responsible for the pandemic that in the first months of 2020 caused about 400,000 deaths. Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Very few cases of COVID-19 have been reported in Ph+ ALL and in CML Italian cohorts; authors suggested that this low rate of infections might depend on the use of TKIs, but the biological causes of this phenomenon remain unknown. In this study, the CML model was used to test if TKIs would sustain or not the viral replication and if they could damage patient immunity. Firstly, the infection and replication rate of torquetenovirus (TTV), whose load is inversely proportional to the host immunological control, have been measured in CML patients receiving nilotinib. A very low percentage of subjects were infected at baseline, and TTV did not replicate or at least showed a low replication rate during the follow-up, with a mean load comparable to the measured one in healthy subjects. Then, after gene expression profiling experiments, we found that several “antiviral” genes, such as CD28 and IFN gamma, were upregulated, while genes with “proviral” action, such as ARG-1, CEACAM1, and FUT4, were less expressed during treatment with imatinib, thus demonstrating that TKIs are not detrimental from the immunological point of view. To sum up, our data could offer some biological explanations to the low COVID-19 occurrence in Ph+ ALL and CML patients and sustain the use of TKIs in COVID-19, as already proposed by several international ongoing studies. url: https://doi.org/10.3389/fonc.2020.01428 doi: 10.3389/fonc.2020.01428 id: cord-280774-r2xm164s author: Gallizzi, Romina title: Management of pernio‐like cutaneous manifestations in children during the outbreak of covid‐19. date: 2020-09-19 words: 2083.0 sentences: 128.0 pages: flesch: 47.0 cache: ./cache/cord-280774-r2xm164s.txt txt: ./txt/cord-280774-r2xm164s.txt summary: The increased number of cases of pernio-like lesions compared to the cases per year we usually observe, the mild temperatures of those months in Southern Italy and the concomitant lockdown, led us to hypothesize a possible correlation with SARS-CoV-2 infection. This is useful to highlight, as in our case, the D-dimer of our patients was weakly increased, a condition perfectly correlated with the mild symptoms of SARS-CoV-2 putative infection presented. In a report of 19 adolescent patients with a clinical diagnosis of pernio-like lesions nasopharyngeal swab and IgG serology for SARS-CoV-2 nucleocapsid protein were negative. Why some children who come into contact with the SARS-CoV-2 do not develop striking respiratory symptoms but present pernio-like lesions with negativity on diagnostic tests? This pathogenic mechanism could explain the appearance of pernio-like lesions due to SARS-CoV-2 infection. In conclusion, we think there is a correlation between pernio-like lesions and SARS-CoV-2 infection, but further studies are needed to prove it. abstract: BACKGROUND: During the outbreak of COVID‐19 many pernio‐like lesions have been increasingly reported. The aim of the study is to describe our management of these skin manifestations and to evaluate a possible correlation to SARS‐CoV‐2 infection. METHODS: All patients underwent clinical and laboratory tests to detect a possible underlying connective disease and also to specific SARS‐CoV‐2 investigations such as oropharyngeal swab and IgG‐IgM serology. RESULTS: Nine patients aged between five and fifteen years old were evaluated. Skin lesions observed were purplish, erythematous and oedematous, in some cases painful and itchy. Six out of nine had respiratory and systemic symptoms (cough, nasal congestion, chills, fever, asthenia) that preceded cutaneous findings of approximately two weeks. Concerning blood exams, three out of nine had D‐dimer weakly increased, four had ANA positivity: two with a title 1:160, one with 1:320 and one with 1:5120 and a speckled pattern. The latter patient had also ENA SS‐A positive and RF positivity, confirmed at a second check, so as to allow us to make a diagnosis of connective tissue disease. Four out of nine had aPL positivity (IgM). Reactants acute phase were all negative. Oropharyngeal swabs and serology tests for SARS‐CoV‐2 was negative (borderline in one patient for IgM). No treatment was needed. CONCLUSIONS: Even if we do not have enough data to prove it, we hypothesize a correlation between pernio‐like lesions and SARS‐CoV‐2 infection for an increased number of these lesions described during the pandemic and also because such manifestations appeared when temperatures were mild and patients were at home in isolation for the lockdown. Many questions remain open about interaction host‐virus. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32949449/ doi: 10.1111/dth.14312 id: cord-340857-teq5txm9 author: Galloro, Giuseppe title: SAFETY IN DIGESTIVE ENDOSCOPY PROCEDURES IN THE COVID ERA RECOMMENDATIONS IN PROGRES OF THE ITALIAN SOCIETY OF DIGESTIVE ENDOSCOPY date: 2020-05-13 words: 3414.0 sentences: 177.0 pages: flesch: 49.0 cache: ./cache/cord-340857-teq5txm9.txt txt: ./txt/cord-340857-teq5txm9.txt summary: Based on the most recent scientific literature and strong statements by the most prestigious international health institutions, the Italian Society of Digestive Endoscopy has drawn up some recommendations about the use of personal protective equipment, the correct way of dressing and undressing of endoscopists and nurses, before and after digestive endoscopy procedures. In addition the CDC and some other Authors detected the virus in the feces of CoViD-19 positive patients (in up to 54% of the cases), suggesting a potential fecal-oral transmission (31, 32) . A recent ad-interim guidance, about the preventive measures of infection control (shown in table 3 ) and about the right use of appropriate PPE for healthcare workers performing endoscopy on subjects with CoViD-19, has been published by the WHO (45) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus infected pneumonia in Wuhan, China. abstract: The new corona virus disease has started in Wuhan - China at the end of 2019 and quickly spread with a pandemic trend across the rest of the world. The scientific community is making an extraordinary effort to study and control the situation, but the results are just partial. Based on the most recent scientific literature and strong statements by the most prestigious international health institutions, the Italian Society of Digestive Endoscopy has drawn up some recommendations about the use of personal protective equipment, the correct way of dressing and undressing of endoscopists and nurses, before and after digestive endoscopy procedures. In addition, some other important indications are given to reduce the risk of contamination of healthcare providers during endoscopic activities, in the setting of a pandemic. Nevertheless, because of the very quick evolution of our knowledge on this issue, these recommendations must be considered as evolving, because they could change in a short time. url: https://api.elsevier.com/content/article/pii/S1590865820301912 doi: 10.1016/j.dld.2020.05.002 id: cord-307885-butuv3n1 author: Galvani, Alison P. title: Emerging Infections: What Have We Learned from SARS? date: 2004-07-17 words: 1195.0 sentences: 71.0 pages: flesch: 44.0 cache: ./cache/cord-307885-butuv3n1.txt txt: ./txt/cord-307885-butuv3n1.txt summary: As is typical of an emerging disease, no vaccines or drugs to combat SARS existed, making quarantine, patient isolation, travel restrictions, and contact precautions the only means of limiting transmission. Previously, similar models had guided public health policy, for example, in halting an outbreak of hoof and mouth disease in the United Kingdom in 2001 (5, 6) . The case-fatality rate is a key determinant of the public health impact of an emerging disease and was high for SARS at approximately 15% (11) . The success with which WHO coordinated the global collaboration in containing SARS galvanized the World Health Assembly to grant WHO greater authority to verify outbreaks, conduct investigations of outbreak severity, and evaluate the adequacy of control measures. Transmission dynamics of the etiological agent of severe acute respiratory syndrome (SARS) in Hong Kong: the impact of public health interventions Infectious diseases of humans: dynamics and control abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15338569/ doi: 10.3201/eid1007.040166 id: cord-301106-qskwujpa author: Gambato, Martina title: Clinical implications of COVID-19 in patients with chronic liver disease and liver tumor date: 2020-06-05 words: 1665.0 sentences: 81.0 pages: flesch: 44.0 cache: ./cache/cord-301106-qskwujpa.txt txt: ./txt/cord-301106-qskwujpa.txt summary: On March 31st of this year, the World Health Organization (WHO) declared a pandemic infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing 2019 coronavirus disease (COVID-19). A single case of acute chronic liver failure secondary to SARS-CoV-2 infection in a decompensated alcoholic cirrhotic patient was recently reported. Overall, the reported data are not yet enough for us to know the risk of infection in patients with existing chronic liver disease, or the impact of COVID-19 on their liver status and outcomes. Patients with liver cancer are another special population often coming to the hospital for treatment and monitoring, who may be at higher risk of contracting COVID-19, especially if they are receiving chemotherapy or immunotherapy. In conclusion, liver damage during SARS-CoV-2 infection has been reported quite frequently, especially in patients who developed severe COVID-19 disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32504266/ doi: 10.1007/s13304-020-00804-8 id: cord-289905-dvl2pud2 author: Gan, Rosemary title: COVID-19 as a Viral Functional ACE2 Deficiency Disorder with ACE2 Related Multi-organ Disease date: 2020-06-23 words: 4355.0 sentences: 215.0 pages: flesch: 33.0 cache: ./cache/cord-289905-dvl2pud2.txt txt: ./txt/cord-289905-dvl2pud2.txt summary: Appreciating the clear differences between SARS and COVID-19 in presentation, poor prognostic indicators related to individuals'' co-morbid status, and biochemical and radiologic profiles, a novel disease model may assist in: 1) the early recognition of atypical (non-respiratory) presentations of disease; 2) early prophylactic treatment intervention for individuals at risk of severe and critical disease which could take place 6 in the community; 3) revised management of pulmonary complications including those related to prone posturing and ventilation protocols; 4) allowing better utilisation of data collated at a global level in the absence of an evidence-based disease model at this time; 5) identification of different markers of disease progression in at-risk individuals. An upregulation of ACE2 expressing cells related to chronic ATII elevation [18] or treatment with ACEinhibitors [19] , may increase the infective potential of SARS-CoV-2 in this group as a consequence of the duality of ACE2 functioning as both a receptor for viral entry to cells and as an enzyme. abstract: SARS-CoV-2, the agent of COVID-19, shares a lineage with SARS-CoV-1, and a common fatal pulmonary profile but with striking differences in presentation, clinical course, and response to treatment. In contrast to SARS-CoV-1 (SARS), COVID-19 has presented as an often bi-phasic, multi-organ pathology, with a proclivity for severe disease in the elderly and those with hypertension, diabetes and cardiovascular disease. Whilst death is usually related to respiratory collapse, autopsy reveals multi-organ pathology. Chronic pulmonary disease is underrepresented in the group with severe COVID-19. A commonality of aberrant renin angiotensin system (RAS) is suggested in the at-risk group. The identification of angiotensin-converting-enzyme 2 (ACE2) as the receptor allowing viral entry to cells precipitated our interest in the role of ACE2 in COVID-19 pathogenesis. We propose that COVID-19 is a viral multisystem disease, with dominant vascular pathology, mediated by global reduction in ACE2 function, pronounced in disease conditions with RAS bias toward angiotensin-converting-enzyme (ACE) over ACE2. It is further complicated by organ specific pathology related to loss of ACE2 expressing cells particularly affecting the endothelium, alveolus, glomerulus and cardiac microvasculature. The possible upregulation in ACE2 receptor expression may predispose individuals with aberrant RAS status to higher viral load on infection and relatively more cell loss. Relative ACE2 deficiency leads to enhanced and protracted tissue, and vessel exposure to angiotensin II, characterised by vasoconstriction, enhanced thrombosis, cell proliferation and recruitment, increased tissue permeability, and cytokine production (including IL-6) resulting in inflammation. Additionally, there is a profound loss of the “protective” angiotensin (1-7), a vasodilator with anti-inflammatory, anti-thrombotic, antiproliferative, antifibrotic, anti-arrhythmic, and antioxidant activity. Our model predicts global vascular insult related to direct endothelial cell damage, vasoconstriction and thrombosis with a disease specific cytokine profile related to angiotensin II rather than “cytokine storm”. Our proposed mechanism of lung injury provides an explanation for early hypoxia without reduction in lung compliance and suggests a need for revision of treatment protocols to address vasoconstriction, thromboprophylaxis, and to minimize additional small airways and alveolar trauma via ventilation choice. Our model predicts long term sequelae of scarring/fibrosis in vessels, lungs, renal and cardiac tissue with protracted illness in at-risk individuals. It is hoped that our model stimulates review of current diagnostic and therapeutic intervention protocols, particularly with respect to early anticoagulation, vasodilatation and revision of ventilatory support choices. url: https://doi.org/10.1016/j.mehy.2020.110024 doi: 10.1016/j.mehy.2020.110024 id: cord-308507-hp6m6qrn author: Gan, Yi-Ru title: Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase date: 2005-10-19 words: 1570.0 sentences: 98.0 pages: flesch: 62.0 cache: ./cache/cord-308507-hp6m6qrn.txt txt: ./txt/cord-308507-hp6m6qrn.txt summary: The results demonstrate that, compared with other compounds reported so far, AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus, and that no detectable toxicity is observed on Vero cells under the condition of experimental concentration. These authors had done studies of docking the octapeptide to SARS-CoV M pro based on the three-dimensional structure of SARS coronavirus main proteinase obtained by Anand et al. The binding results obtained through docking study [10] and structural bioinformatics [7] show that the octapeptide AVLQSGFR is bound to the SARS proteinase through six hydrogen bonds. The present study was initiated in an attempt to conduct an in-depth examination of the antiviral activity of the octapeptide AVLQSGFR against SARS-associated coronavirus by biochemical experimental approaches. We also detected the effect of the octapeptide AVLQSGFR on replication of SARS-associated coronavirus in Vero cells (Fig. 2) . abstract: The outbreak of SARS, a life-threatening disease, has spread over many countries around the world. So far there is no effective drug for the treatment of SARS. Stimulated by the binding mechanism of SARS-CoV M(pro) with the octapeptide AVLQSGFR reported recently as well as the “Chou's distorted key” theory, we synthesized the octapeptide AVLQSGFR for conducting various biochemical experiments to investigate the antiviral potential of the octapeptide against SARS coronavirus (BJ-01). The results demonstrate that, compared with other compounds reported so far, AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus, and that no detectable toxicity is observed on Vero cells under the condition of experimental concentration. url: https://www.ncbi.nlm.nih.gov/pubmed/16242214/ doi: 10.1016/j.peptides.2005.09.006 id: cord-033244-u05rw6sk author: Ganesamoorthi, Arimanickam title: Non-availability of anesthesia scavenging system and decontamination of the outflow gas from the anesthesia machine during this COVID-19 pandemic date: 2020-10-06 words: 984.0 sentences: 57.0 pages: flesch: 45.0 cache: ./cache/cord-033244-u05rw6sk.txt txt: ./txt/cord-033244-u05rw6sk.txt summary: The HMEF/HEPA filter can be connected to the AGS, even if the anesthesia machine ventilator is used for prolonged ventilation of critically ill patients, like an ICU ventilator when a shortage arises in this COVID-19 pandemic (COVID-19: Usage of Dräger anaesthesia devices for long-term ventilation dated 19 may 2020, 2020). Authors'' contributions AG conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable and contributed to the writing and editing of the final version of the manuscript. ViVi conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable, and contributed to the review of literature, and writing and editing of the final version of the manuscript. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7537952/ doi: 10.1186/s42077-020-00096-5 id: cord-103497-1ls2dvzy author: Ganier, C title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date: 2020-05-29 words: 1427.0 sentences: 90.0 pages: flesch: 53.0 cache: ./cache/cord-103497-1ls2dvzy.txt txt: ./txt/cord-103497-1ls2dvzy.txt summary: title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). The ACE2 receptor has been shown to mediate uptake of the virus responsible for COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in human cells (Hoffmann, Kleine-Weber, Schroeder, et al. In order to define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). abstract: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a wide range of systemic manifestations. Several observations support a role for vascular endothelial dysfunction in the pathogenesis including an increased incidence of thrombotic events and coagulopathy and the presence of vascular risk factors as an independent predictor of poor prognosis. It has recently been reported that endothelitis is associated with viral inclusion bodies suggesting a direct role for SARS-CoV-2 in the pathogenesis. The ACE2 receptor has been shown to mediate SARS-CoV-2 uptake and it has been proposed that CD147 (BSG) can function as an alternative cell surface receptor. To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). We found that CD147 (BSG) but not ACE2 is detectable in vascular endothelial cells within single cell sequencing datasets derived from multiple tissues in healthy individuals. This implies that either ACE2 is not expressed in healthy tissue but is instead induced in response to SARS-Cov2 or that SARS-Cov2 enters endothelial cells via an alternative receptor such as CD147. url: https://doi.org/10.1101/2020.05.29.123513 doi: 10.1101/2020.05.29.123513 id: cord-274680-6pui91uu author: Gao, Chun title: Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date: 2020-10-14 words: 2206.0 sentences: 151.0 pages: flesch: 52.0 cache: ./cache/cord-274680-6pui91uu.txt txt: ./txt/cord-274680-6pui91uu.txt summary: 5 Many studies have found that older patients have a higher risk of having a severe case and they have a higher death rate from COVID-19, which may be related to a weaker host immune response for antiviral defense and an uncontrolled proinflammatory cytokine storm. [10] [11] Therefore, this retrospective study aimed to analyze the clinical characteristics of COVID-19 patients who experienced prolonged viral shedding and to investigate the contributing risk factors. This is a comprehensive report of 112 COVID-19 patients investigating the distinct characteristics and risk factors for prolonged SARS-CoV-2 viral RNA shedding. In our study, we found that COVID-19 patients with prolonged viral shedding were older (p<0.001) and presented with a higher rate of hypertension (p<0.001). This study focused on investigating the risk factors for COVID-19 patients with prolonged viral shedding. In summary, in this study, we investigated the distinct dynamics of the inflammatory response in COVID-19 patients with prolonged viral RNA shedding. abstract: Since December 2019, Coronavirus Disease 2019 (COVID-19) has emerged as a global pandemic. We aimed to investigate the clinical characteristics and analyzed the risk factors for prolonged viral RNA shedding. We retrospectively collected data from 112 hospitalized COVID-19 patients in a single center in Wuhan, China. Factors associated with prolonged viral RNA shedding (≥28 days) were investigated. Forty-nine (43.8%) patients had prolonged viral RNA shedding. Patients with prolonged viral shedding were older and had a higher rate of hypertension. Proinflammatory cytokines, including interleukin-2R (IL-2R) and tumor necrosis factor-α (TNF-α), were significantly elevated in patients with prolonged viral shedding. Multivariate analysis revealed that hypertension, older age, lymphopenia and elevated serum IL-2R were independent risk factors for prolonged viral shedding. This comprehensive investigation revealed the distinct characteristics between patients with or without prolonged viral RNA shedding. Hypertension, older age, lymphopenia and high levels of proinflammatory cytokines may be correlated with prolonged viral shedding. url: https://api.elsevier.com/content/article/pii/S1521661620307713 doi: 10.1016/j.clim.2020.108611 id: cord-271371-qs7zge3l author: Gao, Jia title: Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-07-28 words: 2217.0 sentences: 139.0 pages: flesch: 57.0 cache: ./cache/cord-271371-qs7zge3l.txt txt: ./txt/cord-271371-qs7zge3l.txt summary: As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligandand protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (M(pro)) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of M(pro). We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 M(pro). Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs. Nevertheless, using this fragment-based approach is a feasible strategy for repurposing low-molecular-weight drugs targeting SARS-CoV-2 M pro . abstract: [Image: see text] The coronavirus disease pandemic caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the global healthcare system. As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligand- and protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (M(pro)) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of M(pro). We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 M(pro). Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs. url: https://doi.org/10.1021/acs.jpclett.0c01894 doi: 10.1021/acs.jpclett.0c01894 id: cord-297439-xg0pkjrh author: Gao, Jing title: The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China date: 2020-04-22 words: 2030.0 sentences: 120.0 pages: flesch: 62.0 cache: ./cache/cord-297439-xg0pkjrh.txt txt: ./txt/cord-297439-xg0pkjrh.txt summary: Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and lasting positive nucleic acid test result in patients recovered from pneumonia. The CT image is used to assess the disease progress, whereas the continued two times of negative results from SARS-CoV-2 nucleic acid detection had been considered as a criterion for ending antiviral treatment. Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and showed the suspected SARS-CoV-2 carrier. On day 16, the 4th result of nucleic acid in throat swab changed to negative, whereas it was positive in sputum ( Fig. 1) , thus continued the antiviral treatment with interferon inhalation and lopinavir/ ritonavir. On day 8 and day 10, SARS-CoV-2 nucleic acid in throat swab were shown the negative at that two time, and the repeated chest CT image showed that the infection range was declined a lot (Fig. 1) . abstract: The novel coronavirus disease (COVID-19) outbreak started in December 2019 in Wuhan, China, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The CT image is used to assess the disease progress, whereas the continued two times of negative results from SARS-CoV-2 nucleic acid detection had been considered as a criterion for ending antiviral treatment. We compared the two COVID-19 cases with similar backgrounds and CT image repeated intervals under treatment. Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and lasting positive nucleic acid test result in patients recovered from pneumonia. It may be contributed to recognize the disease and improve prevention. url: https://doi.org/10.1186/s12931-020-01363-7 doi: 10.1186/s12931-020-01363-7 id: cord-266090-f40v4039 author: Gao, Wei title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system date: 2020-08-03 words: 2737.0 sentences: 177.0 pages: flesch: 51.0 cache: ./cache/cord-266090-f40v4039.txt txt: ./txt/cord-266090-f40v4039.txt summary: title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system According to the report presented by the World Health Organization, a new member of viruses, namely, coronavirus, shortly 2019-nCoV, which arised in Wuhan, China, on January 7, 2020, has been introduced to the literature. Whereas the obtained results show the effectiveness of the theoretical method considered for the governing system, the results also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. The obtained results show the effectiveness of the theoretical method considering the governing system and also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. In this subsection, by using VIM we numerically investigate the Bats-Hosts-Reservoir-People coronavirus model. Modeling the dynamics of novel coronavirus (2019-nCov) with fractional derivative Application of variational iteration method to nonlinear differential equations of fractional order abstract: According to the report presented by the World Health Organization, a new member of viruses, namely, coronavirus, shortly 2019-nCoV, which arised in Wuhan, China, on January 7, 2020, has been introduced to the literature. The main aim of this paper is investigating and finding the optimal values for better understanding the mathematical model of the transfer of 2019-nCoV from the reservoir to people. This model, named Bats-Hosts-Reservoir-People coronavirus (BHRPC) model, is based on bats as essential animal beings. By using a powerful numerical method we obtain simulations of its spreading under suitably chosen parameters. Whereas the obtained results show the effectiveness of the theoretical method considered for the governing system, the results also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. url: https://www.ncbi.nlm.nih.gov/pubmed/32834818/ doi: 10.1186/s13662-020-02831-6 id: cord-331878-ww9fu8ey author: Gao, Xiaopan title: Crystal structure of SARS-CoV-2 papain-like protease date: 2020-09-02 words: 3510.0 sentences: 222.0 pages: flesch: 58.0 cache: ./cache/cord-331878-ww9fu8ey.txt txt: ./txt/cord-331878-ww9fu8ey.txt summary: The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. We then determined the structure of SARS-CoV-2 PLpro complex by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The initial hydrolysis rate was plotted as the function of inhibitor concentration and the plot was fitted by the equation Y=Bottom+(Top-Bottom)/(1+(X/IC 50 )) using software GraphPad. To gain structural and biochemical insight into SARS-CoV-2 PLpro domain (nsp3 746-1063aa, Supporting Information Fig. S1 ), we expressed two PLpro variants. For example, several crystal structures of SARS-CoV-2 PLpro C111S mutant complexed by various non-covalent inhibitors have been recently deposited in Protein Data Bank (PDB ID: 7JIT, 7JIR and 7JIV), which support our assertion. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors abstract: The pandemic of coronavirus disease 2019 (COVID-19) is changing the world like never before. This crisis is unlikely contained in the absence of effective therapeutics or vaccine. The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology, inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development. In this study, we sought to provide structural frameworks for PLpro inhibitor design. We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111S, which shares many structural features of SARS-CoV PLpro. This crystal form has unique packing, high solvent content and reasonable resolution 2.5 Å, hence provides a good possibility for fragment-based screening using crystallographic approach. We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture. We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARS-CoV-2 with the IC(50) of 2.2±0.3 μmol/L. We then determined the structure of SARS-CoV-2 PLpro complex by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The binding of GRL0617 induces closure of the BL2 loop and narrows the substrate binding cleft, whereas the binding of a tetrapeptide substrate enlarges the cleft. Hence, our results suggest a mechanism of GRL0617 inhibition, that GRL0617 not only occupies the substrate pockets, but also seals the entrance to the substrate binding cleft hence prevents the binding of the LXGG motif of the substrate. url: https://www.ncbi.nlm.nih.gov/pubmed/32895623/ doi: 10.1016/j.apsb.2020.08.014 id: cord-351644-pl7xpivx author: Gao, Yelei title: Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis date: 2020-04-17 words: 4712.0 sentences: 336.0 pages: flesch: 55.0 cache: ./cache/cord-351644-pl7xpivx.txt txt: ./txt/cord-351644-pl7xpivx.txt summary: We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. Data extracted included: 1) Basic information: title, first author, publication year and study design; 2) participants: baseline characteristics and sample size; and 3) results: proportions of individuals using telemedicine for different contents of consultation (e.g. symptoms, therapy and prevention, policy, public service), details of screening of suspected cases, the provision of advice given to people who had symptoms or contact history, and the limitations of telemedicine. https://doi.org/10.1101/2020.04.14.20065664 doi: medRxiv preprint proportion of consultation on public issues (including disease knowledge, epidemic situation and public issues of COVID-19/SARS). abstract: Background: As COVID-19 has become a global pandemic, early prevention and control of the epidemic is extremely important. Telemedicine, which includes medical advice given over telephone, Internet, mobile phone applications or other similar ways, may be an efficient way to reduce transmission and pressure on medical institutions. Methods: We searched MEDLINE, Web of science, Embase, Cochrane, CBM, CNKI and Wanfang databases for literature on the use of telemedicine for COVID-19, SARS and MERS. from their inception to March 31st, 2020. We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. We conducted meta-analyses on the main outcomes of the studies. Results: A total of 2041 articles were identified after removing duplicates. After reading the full texts, we finally included nine studies. People were most concerned about symptoms (64.2%), epidemic situation and public problems (14.5%), and psychological problems (10.3%) during COVID-19 epidemic. During the SARS epidemic, the proportions of people asking for consultation for symptoms, prevention and therapy, and psychological problems were 35.0%, 22.0%, and 23.0%, respectively. Two studies demonstrated that telemedicine can be used to screen the suspected patients and give advice. One study emphasized the limited possibilities to follow up people calling hotlines and difficulties in identifying all suspect cases. Conclusions: Telemedicine services should focus on the issues that the public is most concerned about, such as then symptoms, prevention and treatment of the disease, and provide reasonable advice to patients with symptoms or people with epidemic history. Keywords：COVID-19; SARS; MERS; telemedicine; rapid review url: https://doi.org/10.1101/2020.04.14.20065664 doi: 10.1101/2020.04.14.20065664 id: cord-350949-ystkjdwk author: Gao, Yi-jie title: Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date: 2020-08-03 words: 4518.0 sentences: 274.0 pages: flesch: 55.0 cache: ./cache/cord-350949-ystkjdwk.txt txt: ./txt/cord-350949-ystkjdwk.txt summary: The meta-analysis showed the following results: the incidence of severe case or death was 12, 95% CI: 0.03-0.20, I 2 = 0%, P = 0.006; the incidence of fever was 51, 95% CI: 0.35-0.67, I 2 = 89%, P < 0.00001; the incidence of cough was 31, 95% CI: 0.23-0.39, I 2 = 38%, P < 0.00001; the incidence of lymphopenia was 49, 95% CI: 0.29-0.70, I 2 = 83%, P < 0.00001; the incidence of positive CT findings was 71, 95% CI: 0.49-0.93, I 2 = 90%, P < 0.00001; the incidence of coexisting disorders was 33, 95% CI: 0.21-0.44, I 2 = 70%, P < 0.00001; the incidence of preterm labor was 23, 95% CI: 0.14-0.32, I 2 = 21%, P < 0.00001; the incidence of caesarean section was 65, 95% CI: 0.42-0.87, I 2 = 90%, P < 0.00001; the incidence of fetal distress was 29, 95% CI: 0.08-0.49, I 2 = 68%, P = 0.007; the incidence of neonatal asphyxia or neonatal death or stillbirth was 9, 95% CI: − 0.03-0.21, I 2 = 0%, P = 0.14; the incidence of neonatal infection was 12, 95% CI: − 0.01-0.26, I 2 = 0%, P = 0.06; and SARS-CoV-2 testing of breast milk was only mentioned in the study by Chen H (2020.2.12), and the incidence was 0, which cannot be calculated by metaanalysis. abstract: BACKGROUND: The recent COVID-19 outbreak in Wuhan, China, has quickly spread throughout the world. In this study, we systematically reviewed the clinical features and outcomes of pregnant women with COVID-19. METHODS: PubMed, Web of Science, EMBASE and MEDLINE were searched from January 1, 2020, to April 16, 2020. Case reports and case series of pregnant women infected with SARS-CoV-2 were included. Two reviewers screened 366 studies and 14 studies were included. Four reviewers independently extracted the features from the studies. We used a random-effects model to analyse the incidence (P) and 95% confidence interval (95% CI). Heterogeneity was assessed using the I(2) statistic. RESULTS: The meta-analysis included 236 pregnant women with COVID-19. The results were as follows: positive CT findings (71%; 95% CI, 0.49–0.93), caesarean section (65%; 95% CI, 0.42–0.87), fever (51%; 95% CI, 0.35–0.67), lymphopenia (49%; 95% CI, 0.29–0.70), coexisting disorders (33%; 95% CI, 0.21–0.44), cough (31%; 95% CI, 0.23–0.39), fetal distress (29%; 95% CI, 0.08–0.49), preterm labor (23%; 95% CI, 0.14–0.32), and severe case or death (12%; 95% CI, 0.03–0.20). The subgroup analysis showed that compared with non-pregnant patients, pregnant women with COVID-19 had significantly lower incidences of fever (pregnant women, 51%; non-pregnant patients, 91%; P < 0.00001) and cough (pregnant women, 31%; non-pregnant patients, 67%; P < 0.0001). CONCLUSIONS: The incidences of fever, cough and positive CT findings in pregnant women with COVID-19 are less than those in the normal population with COVID-19, but the rate of preterm labor is higher among pregnant with COVID-19 than among normal pregnant women. There is currently no evidence that COVID-19 can spread through vertical transmission. url: https://doi.org/10.1186/s12879-020-05274-2 doi: 10.1186/s12879-020-05274-2 id: cord-253245-433mg0ke author: Gao, Zhiru title: A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date: 2020-08-05 words: 1854.0 sentences: 100.0 pages: flesch: 55.0 cache: ./cache/cord-253245-433mg0ke.txt txt: ./txt/cord-253245-433mg0ke.txt summary: A recent study reported that four medical workers aged 30-36 years who had re-detectable positive (RP) for SARS-CoV-2 within 5-13 days after being cured and discharged, indicating that some of the recovered patients may still be virus carriers, which caused widespread concern (Lan et al., 2020). Although the results of the three nucleic acid tests were negative for the patient, there were viral residue in the lungs, so even if the patient was discharged, we supposed that virus would transfer positive again after a period of time (Yao et al., 2020) . In addition, initial studies reported that the SARS-CoV-2 RNA could be detected in the feces of 81.8% recovered patients (54/66), even in those with negative throat swabs (Ling et al., 2020) . In other words, even if sometimes the virus nucleic acid tested by RT-PCR is positive in the recovery phase of COVID-19, it will not cause a more serious condition, and antiviral therapy may not be required in most patients. abstract: A large number of coronavirus disease 2019 (COVID-19) patients have been cured and discharged due to timely and effective treatments. While some discharged patients have been found re-positive nucleic acid again in the recovery phase. Until now, there is still a great challenge to its infectivity and the specific potential mechanism which need further discussion. However, more intensive attention should be paid to the prognosis of the recovered patients. In this review, we mainly focus on the characteristics, potential reasons, infectivity, and outcomes of re-detectable positive patients, thereby providing some novel insights into the cognition of COVID-19. url: https://doi.org/10.1016/j.meegid.2020.104494 doi: 10.1016/j.meegid.2020.104494 id: cord-324102-75v4ebag author: Garcia Rodriguez, Alejandro title: SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? Case report date: 2020-10-06 words: 1728.0 sentences: 110.0 pages: flesch: 49.0 cache: ./cache/cord-324102-75v4ebag.txt txt: ./txt/cord-324102-75v4ebag.txt summary: title: SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? BACKGROUND: There are no published cases of tonic-clonic seizures and posterior bilateral blindness during pregnancy and Severe Acute Respiratory Syndrome (SARS) Coronavirus (COV) 2 (SARS-COV-2) infection. CONCLUSION: The authors conclude that SARS COV-2 infection could promote brain endothelial damage and facilitate neurological complications during pregnancy. That is the reason why we present a case report of a pregnant woman infected with SARS-COV-2 who showed seizures and sudden blindness. Therefore, we consider that SARS-COV-2 infection during pregnancy could increase the risk of suffering posterior reversible leukoencephalopathy or preeclampsia/eclampsia syndrome. To our knowledge, this is the first report of a patient with COVID-19 presenting preeclampsia associated with eclampsia versus posterior reversible leukoencephalopathy without alarm signs or symptoms. We consider further studies are needed to confirm that SARS-COV-2 infection is a risk factor to develop neurological complications of pregnant woman during pregnancy. abstract: BACKGROUND: There are no published cases of tonic-clonic seizures and posterior bilateral blindness during pregnancy and Severe Acute Respiratory Syndrome (SARS) Coronavirus (COV) 2 (SARS-COV-2) infection. We do not just face new and unknown manifestations, but also how different patient groups are affected by SARS-COV-2 infection, such as pregnant women. Coronavirus Disease 2019 (COVID-19), preeclampsia, eclampsia and posterior reversible leukoencephalopathy share endothelium damage and similar pathophysiology. CASE PRESENTATION: A 35-year-old pregnant woman was admitted for tonic-clonic seizures and SARS-COV-2 infection. She had a normal pregnancy control and no other symptoms before tonic-clonic seizures development. After a Caesarean section (C-section) she developed high blood pressure, and we initiated antihypertensive treatment with labetalol, amlodipine and captopril. Few hours later she developed symptoms of cortical blindness that resolved in 72 h with normal brain computed tomography (CT) angiography. CONCLUSION: The authors conclude that SARS COV-2 infection could promote brain endothelial damage and facilitate neurological complications during pregnancy. url: https://www.ncbi.nlm.nih.gov/pubmed/33023500/ doi: 10.1186/s12884-020-03275-2 id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 words: 7354.0 sentences: 355.0 pages: flesch: 47.0 cache: ./cache/cord-103787-qhftb6d7.txt txt: ./txt/cord-103787-qhftb6d7.txt summary: Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. abstract: We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics. url: https://api.elsevier.com/content/article/pii/S1525157810605752 doi: 10.1016/s1525-1578(10)60575-2 id: cord-310636-y7n22ykt author: Garcia-Beltran, W. F. title: COVID-19 neutralizing antibodies predict disease severity and survival date: 2020-10-20 words: 10879.0 sentences: 545.0 pages: flesch: 47.0 cache: ./cache/cord-310636-y7n22ykt.txt txt: ./txt/cord-310636-y7n22ykt.txt summary: A quantitative ELISA that measures IgG, IgM, and IgA antibodies to the receptor binding domain (RBD) of SARS-CoV-2 and a high-throughput neutralization assay using lentiviral vectors pseudotyped with SARS-CoV-2 and WIV1-CoV were developed to assess neutralization potency and cross-neutralizing responses. We determined the sensitivity and specificity of this assay by assessing anti-RBD antibody levels in a cohort of SARS-CoV-2-infected patient serum samples collected between 14 to 42 days after symptom onset ( n = 85) in order to maximize seropositivity for IgG, IgM, and IgA. Anti-RBD IgG, IgM, and IgA levels were measured for each sample by interpolation on to the standard curve and a receiver operating curve (ROC) analysis was used to determined optimal cut-offs that distinguished SARS-CoV-2-infected patients from pre-pandemic controls ( Figure 2C ). However, a principle components analysis (PCA) that included demographic data, pre-existing medical conditions, laboratory data, treatments received, anti-RBD antibody levels and neutralization titers but not clinical outcomes demonstrated clustering of patients by the severity cohorts ( Figure 4A ). abstract: COVID-19 exhibits variable symptom severity ranging from asymptomatic to life-threatening, yet the relationship between severity and the humoral immune response is poorly understood. We examined antibody responses in 113 COVID-19 patients and found that severe cases resulting in intubation or death exhibited increased inflammatory markers, lymphopenia, and high anti-RBD antibody levels. While anti-RBD IgG levels generally correlated with neutralization titer, quantitation of neutralization potency revealed that high potency was a predictor of survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting protection from reinfection by this strain. However, SARS-CoV-2 sera was unable to cross-neutralize a highly-homologous pre-emergent bat coronavirus, WIV1-CoV, that has not yet crossed the species barrier. These results highlight the importance of neutralizing humoral immunity on disease progression and the need to develop broadly protective interventions to prevent future coronavirus pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/33106822/ doi: 10.1101/2020.10.15.20213512 id: cord-284387-cjziykrz author: Garcia-Castrillo, Luis title: European Society For Emergency Medicine position paper on emergency medical systems’ response to COVID-19 date: 2020-05-04 words: 2346.0 sentences: 125.0 pages: flesch: 44.0 cache: ./cache/cord-284387-cjziykrz.txt txt: ./txt/cord-284387-cjziykrz.txt summary: Second, protective measures by health services, especially in public and open environments like emergency departments (EDs) where isolation of potentially infected patients is a real challenge or clinical wards is vital [10] . Clinical care of suspected patients with COVID-19 should focus on early recognition, and immediate isolation, as well as appropriate infection prevention measures and control measures with care taken to optimise supportive care. (1) An informative, coordinated campaign for public and healthcare professionals, focused on mechanisms of contagion [4] , personal protection equipment (PPE) use, and a clinical pathway for the suspected patients infected with COVID-19. (5) The development and implementation of cleaning protocols, considering that coronavirus has been isolated on inanimate objects, and healthcare workers were infected by SARS, even without direct contact with sick patients [15] . The patient, relative or general practitioner may alert the emergency number indicating that a potential case of SARS-CoV-2 infection with severe symptoms is seeking care. abstract: The 2019 novel coronavirus acute respiratory epidemic is creating a stressed situation in all the health systems of the affected countries. Emergency medical systems and specifically the emergency departments as the front line of the health systems are suffering from overload and severe working conditions, the risk of contagion and transmission of the health professionals adds a substantial burden to their daily work. Under the perspective of European Society For Emergency Medicine, the recommendations provided by the health authorities are reviewed focus on the emergency department’s activity. url: https://doi.org/10.1097/mej.0000000000000701 doi: 10.1097/mej.0000000000000701 id: cord-330807-abi8pra7 author: Garcia-Pachon, Eduardo title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization date: 2020-07-04 words: 1471.0 sentences: 96.0 pages: flesch: 52.0 cache: ./cache/cord-330807-abi8pra7.txt txt: ./txt/cord-330807-abi8pra7.txt summary: title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization INTRODUCTION: The prevalence of asthma in patients hospitalized with SARS-CoV-2 has been studied and varies widely in the different series. METHODS AND RESULTS: A total of 218 patients (58% of those who tested positive) did not require hospitalization; they had a median age of 45 years (IQR 34–57) and 57% were female. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. For this reason we have analyzed the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay [12] for SARS-CoV-2 and did not require hospital admission. abstract: INTRODUCTION: The prevalence of asthma in patients hospitalized with SARS-CoV-2 has been studied and varies widely in the different series. However, the prevalence in SARS-infected patients not requiring hospitalization is not known. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. METHODS AND RESULTS: A total of 218 patients (58% of those who tested positive) did not require hospitalization; they had a median age of 45 years (IQR 34–57) and 57% were female. Six patients (2.8%) had a previous diagnosis of asthma. Only one patient developed a mild aggravation of asthma symptoms associated with SARS-CoV-2 infection. CONCLUSIONS: Few patients with asthma were infected by SARS-CoV-2, and this infection was not a significant cause of asthma exacerbation. url: https://www.sciencedirect.com/science/article/pii/S0954611120302249?v=s5 doi: 10.1016/j.rmed.2020.106084 id: cord-347731-eqxn6auk author: Garcia‐Cremades, Maria title: Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date: 2020-05-12 words: 5430.0 sentences: 333.0 pages: flesch: 50.0 cache: ./cache/cord-347731-eqxn6auk.txt txt: ./txt/cord-347731-eqxn6auk.txt summary: The data sources included were (i) longitudinal clinical, pharmacokinetic (PK), and virologic data from patients with severe acute respiratory syndrome‐2 (SARS‐CoV‐2) infection who received HCQ with or without azithromycin (n = 116), (ii) in vitro viral replication data and SARS‐CoV‐2 viral load inhibition by HCQ, (iii) a population PK model of HCQ, and (iv) a model relating chloroquine PKs to corrected QT (QTc) prolongation. 12 The drug effect over time on viral replication rate was established by simulating unbound plasma concentrations or unbound lung tissue concentrations using a previously defined partition coefficient (10 2.45 ; HCQ unbound fraction assumed to be ~ 50%) and using the established in vitro sigmoidal efficacy parameters. 3, 9, 10 Viral kinetics were estimated from in vitro replication rate of severe acute respiratory syndrome-coronavirus (SARS-CoV)-1 and unbound drug concentration in plasma and lungs were simulated with HCQ PK model. abstract: Hydroxychloroquine (HCQ) is a promising candidate for Coronavirus disease of 2019 (COVID‐19) treatment. The optimal dosing of HCQ is unknown. Our goal was to integrate historic and emerging pharmacological and toxicity data to understand safe and efficacious HCQ dosing strategies for COVID‐19 treatment. The data sources included were (i) longitudinal clinical, pharmacokinetic (PK), and virologic data from patients with severe acute respiratory syndrome‐2 (SARS‐CoV‐2) infection who received HCQ with or without azithromycin (n = 116), (ii) in vitro viral replication data and SARS‐CoV‐2 viral load inhibition by HCQ, (iii) a population PK model of HCQ, and (iv) a model relating chloroquine PKs to corrected QT (QTc) prolongation. A mechanistic PK/virologic/QTc model for HCQ was developed and externally validated to predict SARS‐CoV‐2 rate of viral decline and QTc prolongation. SARS‐CoV‐2 viral decline was associated with HCQ PKs (P < 0.001). The extrapolated patient half‐maximal effective concentration (EC(50)) was 4.7 µM, comparable to the reported in vitro EC(50s). HCQ doses > 400 mg b.i.d. for ≥5 days were predicted to rapidly decrease viral loads, reduce the proportion of patients with detectable SARS‐CoV‐2 infection, and shorten treatment courses, compared with lower dose (≤ 400 mg daily) regimens. However, HCQ doses > 600 mg b.i.d. were also predicted to prolong QTc intervals. This prolongation may have clinical implications warranting further safety assessment. Due to COVID‐19's variable natural history, lower dose HCQ regimens may be indistinguishable from controls. Evaluation of higher HCQ doses is needed to ensure adequate safety and efficacy. url: https://doi.org/10.1002/cpt.1856 doi: 10.1002/cpt.1856 id: cord-347308-l19snjyf author: García-Howard, Marcos title: Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 date: 2020-08-06 words: 3095.0 sentences: 170.0 pages: flesch: 47.0 cache: ./cache/cord-347308-l19snjyf.txt txt: ./txt/cord-347308-l19snjyf.txt summary: Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. Additionally, during hospitalization, the patient and her mother were included in a collaborative study of genomic medicine for identifying genetic variants causing hyperimmunity due to SARS-CoV-2 infection. abstract: Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. No detailed temporally associated neurological complications have been documented in pediatric case series so far. Case description: We present the case of a 3-months-old girl with non-febrile repeated seizures in a COVID-19 family setting. The infant started with a mild fever and cough that lasted for 2 days. At day 6 from onset, the girl presented with two focal motor seizures with impaired consciousness and awareness. All investigations ruled out signs of meningo-encephalitis or active epilepsy, including normal electroencephalogram and cerebral magnetic resonance imaging. PCR from nasal and throat swabs was positive for SARS-CoV-2. Remarkably, blood ferritin and D-dimer levels were increased. At day 9, the infant presented another afebrile motor seizure, and levetiracetam dose was modified there was a favorable response within 3 months of the follow-up. Much interest has been raised with regards to host genetic determinants to disease severity and susceptibility to COVID-19. We thus performed whole exome sequencing, revealing a pathogenic frameshift mutation in the PRRT2 gene in both the mother and the infant. The mother had presented two late infantile febrile convulsions with normal outcome afterwards. Discussion: The hyperimmune response described in adult cases with COVID-19 can be seen in infants, even in the absence of respiratory symptoms. Moreover, COVID-19 may present in infants as non-febrile seizures, triggering early onset seizures in infants with a genetic predisposition. In this pandemic situation, precision medicine using massive sequencing can shed light on underlying molecular mechanisms driving the host response to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32850563/ doi: 10.3389/fped.2020.00507 id: cord-337127-pc9hez28 author: García-Salido, Alberto title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a date: 2020-09-30 words: 989.0 sentences: 68.0 pages: flesch: 52.0 cache: ./cache/cord-337127-pc9hez28.txt txt: ./txt/cord-337127-pc9hez28.txt summary: title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a The immune response to SARS-CoV-2 infection appears to be a critical factor in the development and prognosis of COVID-19 patients 2 . In children, severe forms of the disease like the pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 appears to be related with some immune dysregulation 3 . We study in this report three children with severe SARS-CoV-2 infection. As can be seen in Figure 1 children with SARS-CoV-2 show levels of CD64 expression that are higher than in previous published reports of bacterial or viral infections or autoinflammatory diseases 5 . In summary, we describe the immunophenotype of three children with severe SARS-CoV-2 infection. Neutrophil CD64 expression as a longitudinal biomarker for severe disease and acute infection in critically ill patients abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0210569120303193?v=s5 doi: 10.1016/j.medin.2020.09.003 id: cord-355294-gifsqph6 author: García-Suárez, Julio title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study date: 2020-10-08 words: 4736.0 sentences: 300.0 pages: flesch: 46.0 cache: ./cache/cord-355294-gifsqph6.txt txt: ./txt/cord-355294-gifsqph6.txt summary: title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study METHODS: In this population-based registry study, we collected de-identified data on clinical characteristics, treatment and outcomes in adult patients with hematologic malignancies and confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection within the Madrid region of Spain. This case series included consecutive patients with hematologic malignancies aged ≥ 18 years who received a confirmed diagnosis of COVID-19 in the emergency departments, hospital wards (patients infected while hospitalized) or outpatient clinics of these Madrid hospitals up to May 25, 2020. Potential prognostic factors were collected including pre-infection patient characteristics (age, sex, comorbidities, type of hematologic malignancy and therapy), COVID-19 clinical severity, treatments and care setting. Clinical severity of COVID-19 was worse, and mortality rates were higher among older patients and those with a greater number of comorbidities and varied by type of hematologic malignancy and active antineoplastic treatment. abstract: BACKGROUND: Patients with cancer have been shown to have a higher risk of clinical severity and mortality compared to non-cancer patients with COVID-19. Patients with hematologic malignancies typically are known to have higher levels of immunosuppression and may develop more severe respiratory viral infections than patients with solid tumors. Data on COVID-19 in patients with hematologic malignancies are limited. Here we characterize disease severity and mortality and evaluate potential prognostic factors for mortality. METHODS: In this population-based registry study, we collected de-identified data on clinical characteristics, treatment and outcomes in adult patients with hematologic malignancies and confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection within the Madrid region of Spain. Our case series included all patients admitted to 22 regional health service hospitals and 5 private healthcare centers between February 28 and May 25, 2020. The primary study outcome was all-cause mortality. We assessed the association between mortality and potential prognostic factors using Cox regression analyses adjusted for age, sex, comorbidities, hematologic malignancy and recent active cancer therapy. RESULTS: Of 833 patients reported, 697 were included in the analyses. Median age was 72 years (IQR 60–79), 413 (60%) patients were male and 479 (69%) and 218 (31%) had lymphoid and myeloid malignancies, respectively. Clinical severity of COVID-19 was severe/critical in 429 (62%) patients. At data cutoff, 230 (33%) patients had died. Age ≥ 60 years (hazard ratios 3.17–10.1 vs < 50 years), > 2 comorbidities (1.41 vs ≤ 2), acute myeloid leukemia (2.22 vs non-Hodgkin lymphoma) and active antineoplastic treatment with monoclonal antibodies (2·02) were associated with increased mortality; conventional chemotherapy showed borderline significance (1.50 vs no active therapy). Conversely, Ph-negative myeloproliferative neoplasms (0.33) and active treatment with hypomethylating agents (0.47) were associated with lower mortality. Overall, 574 (82%) patients received antiviral therapy. Mortality with severe/critical COVID-19 was higher with no therapy vs any antiviral combination therapy (2.20). CONCLUSIONS: In this series of patients with hematologic malignancies and COVID-19, mortality was associated with higher age, more comorbidities, type of hematological malignancy and type of antineoplastic therapy. Further studies and long-term follow-up are required to validate these criteria for risk stratification. url: https://doi.org/10.1186/s13045-020-00970-7 doi: 10.1186/s13045-020-00970-7 id: cord-333520-v2sb90rc author: Gardin, Chiara title: Could Mesenchymal Stem Cell-Derived Exosomes Be a Therapeutic Option for Critically Ill COVID-19 Patients? date: 2020-08-26 words: 10154.0 sentences: 466.0 pages: flesch: 36.0 cache: ./cache/cord-333520-v2sb90rc.txt txt: ./txt/cord-333520-v2sb90rc.txt summary: Exosomes derived from mesenchymal stem cells (MSCs) are being explored for the management of a number of diseases that currently have limited or no therapeutic options, thanks to their anti-inflammatory, immunomodulatory, and pro-angiogenic properties. Next, we describe some of the most significant clinical evidence of the successful use of MSC-derived exosomes in animal models of lung and heart injuries, which might strengthen our hypothesis in terms of their utility for also treating critically ill COVID-19 patients. Recently, MSC-derived exosomes have been demonstrated to have comparable and even greater effects than cells themselves in improving inflammation and injury in a variety of pre-clinical lung disease models, including ALI/ARDS (Table 1) . From the studies discussed above, it emerged that the rationale for using MSC-derived exosomes, MVs, or EVs in ALI/ARDS is based on several processes, many of which are shared with those identified in the parent MSCs. These include immunomodulation and anti-inflammatory properties on host tissue, reduction of the permeability of alveolar epithelium and endothelium, improvement of alveolar fluid clearance, enhancement of macrophage phagocytosis, and tissue repair through direct mitochondrial transfer with host cells (Figure 2 ). abstract: Coronavirus disease 2019 (COVID-19) is a pandemic viral disease originated in Wuhan, China, in December 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The severe form of the disease is often associated with acute respiratory distress syndrome (ARDS), and most critically ill patients require mechanical ventilation and support in intensive care units. A significant portion of COVID-19 patients also develop complications of the cardiovascular system, primarily acute myocardial injury, arrhythmia, or heart failure. To date, no specific antiviral therapy is available for patients with SARS-CoV-2 infection. Exosomes derived from mesenchymal stem cells (MSCs) are being explored for the management of a number of diseases that currently have limited or no therapeutic options, thanks to their anti-inflammatory, immunomodulatory, and pro-angiogenic properties. Here, we briefly introduce the pathogenesis of SARS-CoV-2 and its implications in the heart and lungs. Next, we describe some of the most significant clinical evidence of the successful use of MSC-derived exosomes in animal models of lung and heart injuries, which might strengthen our hypothesis in terms of their utility for also treating critically ill COVID-19 patients. url: https://doi.org/10.3390/jcm9092762 doi: 10.3390/jcm9092762 id: cord-313117-0qur0isb author: Gardinassi, Luiz G. title: Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse date: 2020-06-26 words: 3565.0 sentences: 177.0 pages: flesch: 35.0 cache: ./cache/cord-313117-0qur0isb.txt txt: ./txt/cord-313117-0qur0isb.txt summary: To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. In addition, our approach also detected increased signals of monocytes (Figure 1B) , dendritic cells ( Figure 1C ) and of the mitochondrial respiratory electron transport chain in SARS-CoV-2 infection (Figure 1A) , suggesting a critical role of metabolic pathways for the immune response of COVID-19 patients. abstract: The current pandemic of coronavirus disease 19 (COVID-19) has affected millions of individuals and caused thousands of deaths worldwide. The pathophysiology of the disease is complex and mostly unknown. Therefore, identifying the molecular mechanisms that promote progression of the disease is critical to overcome this pandemic. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. Here, we provide novel perspectives on the pathophysiology of COVID-19 using robust functional approaches to analyze public transcriptome datasets. In addition, we compared the transcriptional signature of COVID-19 patients with individuals infected with SARS-CoV-1 and Influenza A (IAV) viruses. We identified a core transcriptional signature induced by the respiratory viruses in peripheral leukocytes, whereas the absence of significant type I interferon/antiviral responses characterized SARS-CoV-2 infection. We also identified the higher expression of genes involved in metabolic pathways including heme biosynthesis, oxidative phosphorylation and tryptophan metabolism. A BTM-driven meta-analysis of bronchoalveolar lavage fluid (BALF) from COVID-19 patients showed significant enrichment for neutrophils and chemokines, which were also significant in data from lung tissue of one deceased COVID-19 patient. Importantly, our results indicate higher expression of genes related to oxidative phosphorylation both in peripheral mononuclear leukocytes and BALF, suggesting a critical role for mitochondrial activity during SARS-CoV-2 infection. Collectively, these data point for immunopathological features and targets that can be therapeutically exploited to control COVID-19. url: https://doi.org/10.3389/fimmu.2020.01636 doi: 10.3389/fimmu.2020.01636 id: cord-296356-qkvafy69 author: Garman, Elspeth title: SARS Proteomics Reveals Viral Secrets date: 2005-11-30 words: 1306.0 sentences: 74.0 pages: flesch: 51.0 cache: ./cache/cord-296356-qkvafy69.txt txt: ./txt/cord-296356-qkvafy69.txt summary: The structure of the mutagenic base pair in the confines of a closed polymerase complex exposes some of those strategies. (2005) In a worldwide cooperative research effort involving a multidisciplinary approach, structural and functional characterization of the SARS virus and its host interactions has been swiftly pursued. By sequence alignment and structural comparison with all known H2A domains, as well as examination of functional data, the authors conjecture that proteins from this superfamily form an emerging group of nucleotide phosphatases, all with similar functionality. This has two pivotal consequences for understanding the biology of the virus: A systematic approach is essential, and, even more importantly, a deeper structural and functional knowledge of the many complexes that the SARS CoV proteins form with one another and with proteins of the host organisms will be required-research that is still in its infancy. abstract: Worldwide cooperative efforts to understand the biology of the SARS coronavirus have already born significant fruit. In a further advance, the X-ray structure of a domain of nonstructural protein 3 is reported by Saikatendu et al. (2005) in this issue of Structure. url: https://api.elsevier.com/content/article/pii/S0969212605003540 doi: 10.1016/j.str.2005.10.004 id: cord-331496-5xak7z6b author: Garnett, Emily title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 words: 3450.0 sentences: 187.0 pages: flesch: 43.0 cache: ./cache/cord-331496-5xak7z6b.txt txt: ./txt/cord-331496-5xak7z6b.txt summary: We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. In this study, we describe validation of one of the first assays to receive EUA on an automated platform, the Vitros Anti-SARS-CoV-2 Total (CoV2T; Ortho Clinical Diagnostics) antibody assay, for screening of previous exposure to SARS-CoV-2 in our patient population. Seroconversion in our patient population was assessed by correlation of chart review of 55 patients known to be positive for SARS-CoV-2 by RT-PCR and known date of symptom onset with sample reactivity by the CoV2T assay. Specimens from 14 patients with acute infections, previously tested to be negative for SARS-CoV-2 by RT-PCR but positive for another respiratory viral infection by molecular analysis, were nonreactive by the CoV2T assay. abstract: OBJECTIVES: Evaluation of serostatus against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as an important tool in identification of exposure to coronavirus disease 2019 (COVID-19). We report on the validation of the Vitros Anti–SARS-CoV-2 Total (CoV2T) assay for qualitative serologic testing of SARS-CoV-2 antibodies. METHODS: We performed validation studies according to Commission of Office Laboratories Accreditation guidelines, using samples previously tested for SARS-CoV-2 by reverse transcription–polymerase chain reaction (RT-PCR). We evaluated precision, analytical interferences, and cross-reactivity with other viral infections; evaluated concordance with molecular and other serologic testing; and evaluated seroconversion. RESULTS: The Vitros CoV2T assay exhibited acceptable precision and did not exhibit cross-reactivity with other acute respiratory virus infections. The CoV2T assay exhibited 100% negative predictive agreement (56/56) and 71% positive predictive agreement (56/79) with RT-PCR across all patient samples and was concordant with other serologic assays. Concordance with RT-PCR was 97% more than 7 days after symptom onset. The CoV2T assay was robust to icterus and lipemia but had interference from significant hemolysis. CONCLUSIONS: The Vitros CoV2T assay was successfully validated in our laboratory. We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. url: https://doi.org/10.1093/ajcp/aqaa157 doi: 10.1093/ajcp/aqaa157 id: cord-267588-ruuzr6l1 author: Garnett, Lauren title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 words: 3093.0 sentences: 156.0 pages: flesch: 51.0 cache: ./cache/cord-267588-ruuzr6l1.txt txt: ./txt/cord-267588-ruuzr6l1.txt summary: This study aimed to examine the efficacy of six different swabs that are commonly found in hospital settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima), along with more readily available alternative transport mediums (DMEM, PBS, 100% ethanol, 0.9% normal saline and VTM) for their use in molecular detection of SARS-CoV-2. Therefore, our results suggest that the cotton and wood For the portion of the study focusing on alternative transport media, we assessed the ability of DMEM, PBS, 0.9% Normal Saline, and 100% ethanol compared to VTM to be used as medium for the preservation and recovery of viral RNA to be quantified by molecular detection. Despite finding similar levels of viral RNA collected using different swabs and transport media, there is variation when evaluating different respiratory clinical samples while testing for SARS-CoV-2. abstract: On March 11, 2020, the World Health Organization (WHO) assessed COVID-19, caused by SARS-CoV-2, as a pandemic. As of June 1, 2020, SARS-CoV-2 has had a documented effect of over 6 million cases world-wide, amounting to over 370,000 deaths (World Health Organization, 2020. Novel Coronavirus (COVID-19) Situation. http://https://covid19.who.int/). Consequently, the high demand for testing has resulted in a depletion of commercially available consumables, including the recommended swabs and viral transport media (VTM) required for nasopharyngeal sampling. Therefore, the potential use of unvalidated alternatives must be explored to address the global shortage of testing supplies. To tackle this issue, we evaluated the utility of different swabs and transport mediums for the molecular detection of SARS-CoV-2. This study compared the performance of six swabs commonly found in primary and tertiary health care settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6” cotton tipped applicators, and HOLOGIC Aptima) for their efficacy in testing for SARS-CoV-2. Separately, the molecular detection of SARS-CoV-2 was completed from different transport mediums (DMEM, PBS, 100 % ethanol, 0.9 % normal saline and VTM), which were kept up to three days at room temperature (RT). The results indicate that there is no meaningful difference in viral yield from different swabs and most transport mediums for the collection and detection of SARS-CoV-2, indicating swab and medium alternatives could be used if supplies run out. url: https://api.elsevier.com/content/article/pii/S0166093420301993 doi: 10.1016/j.jviromet.2020.113947 id: cord-275088-wbqznzj7 author: Garrido, Pablo F. title: The Lord of the NanoRings: cyclodextrins and the battle against SARS-CoV-2 date: 2020-07-25 words: 9649.0 sentences: 535.0 pages: flesch: 44.0 cache: ./cache/cord-275088-wbqznzj7.txt txt: ./txt/cord-275088-wbqznzj7.txt summary: This includes the encapsulation and transport of specific drugs, as adjuvants to stabilize proteins, vaccines or other molecules involved in the infection, as cholesterol trappers to destabilize the virus envelope, as carriers for RNA therapies, as direct antiviral drugs and even to rescue blood coagulation upon heparin treatment. Modified Cyclodextrins in general antiviral formulations Not only native CDs but also CD derivates have been studied as potential drugdelivery platforms to treat several viral diseases. The inclusion conjugates release sACE2 after entering the body via atomization or other drug delivery means, and the released sACE2 would combine with SARS-CoV-2 S-proteins to block the virus''s ability to infect and destroy human cells. Recently, we discuss the mechanism and production of cyclodextrin-soluble angiotensin-converting enzyme 2 (CD-sACE2) inclusion compounds in the treatment of SARS-CoV-2 infections by blocking S-proteins. abstract: A handful of singular structures and laws can be observed in nature. They are not always evident but, once discovered, it seems obvious how to take advantage of them. In chemistry, the discovery of reproducible patterns stimulates the imagination to develop new functional materials and technological or medical applications. Two clear examples are helical structures at different levels in biological polymers as well as ring and spherical structures of different size and composition. Rings are intuitively observed as holes able to thread elongated structures. A large number of real and fictional stories have rings as inanimate protagonists. The design, development or just discovering of a special ring has often been taken as a symbol of power or success. Several examples are the Piscatory Ring wore by the Pope of the Catholic Church, the NBA Championship ring and the One Ring created by the Dark Lord Sauron in the epic story The Lord of the Rings. In this work, we reveal the power of another extremely powerful kind of rings to fight against the pandemic which is currently affecting the whole world. These rings are as small as ∼1 nm of diameter and so versatile that they are able to participate in the attack of viruses, and specifically SARS-CoV-2, in a large range of different ways. This includes the encapsulation and transport of specific drugs, as adjuvants to stabilize proteins, vaccines or other molecules involved in the infection, as cholesterol trappers to destabilize the virus envelope, as carriers for RNA therapies, as direct antiviral drugs and even to rescue blood coagulation upon heparin treatment. “One ring to rule them all. One ring to find them. One ring to bring them all and in the darkness bind them.” J. R. R. Tolkien url: https://www.ncbi.nlm.nih.gov/pubmed/32717282/ doi: 10.1016/j.ijpharm.2020.119689 id: cord-274090-eab7i4f6 author: Gaspari, Valeria title: Can Covid‐19 be a sexually transmitted disease? Posterity will judge date: 2020-05-24 words: 566.0 sentences: 31.0 pages: flesch: 47.0 cache: ./cache/cord-274090-eab7i4f6.txt txt: ./txt/cord-274090-eab7i4f6.txt summary: The knowledge of all possible modes of transmission of SARS-CoV-2 infection is the key to improving both the identification of the asymptomatic population and the necessary isolation measures in order to further flatten the curve. The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients (66.67%) has already been demonstrated in recent studies in Wuhan, without being statistically related to gastrointestinal symptoms and/or disease severity. Moreover, the positivity for SARS-CoV-2 on vaginal swab raises the possibility of both sexual and mother-to-child transmission 7 , although further studies are needed on these issues since no definitive proofs have been found. A further step would be adding SARS-CoV-2 serology, pharyngeal, anal and vaginal swabs to our usual STD screening also in the asymptomatic population, in order to identify positive cases and to confirm the SARS-CoV-2 orogenital route of transmission. SARS-CoV-2 possible contamination of genital area: implications for sexual and vertical transmission routes abstract: nan url: https://doi.org/10.1111/dth.13676 doi: 10.1111/dth.13676 id: cord-344778-2p1mm3vg author: Gasparri, Maria Luisa title: Changes in breast cancer management during the Corona Virus Disease 19 pandemic: an international survey of the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) date: 2020-05-29 words: 2685.0 sentences: 165.0 pages: flesch: 47.0 cache: ./cache/cord-344778-2p1mm3vg.txt txt: ./txt/cord-344778-2p1mm3vg.txt summary: The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. Two-hundred and fifty-two/377 (67%) responders considered chemotherapy as being riskier for developing severe COVID-19-related complications compared to surgery and radiation therapy. The reported cases of patients diagnosed with SARS-CoV-2 during BC treatment or within 14 days following treatment are 10%, 7% and 4% for chemotherapy, surgery and radiation therapy, respectively. This large international survey among breast cancer centres showed that the COVID-19 pandemic affected management of BC patients, including treatment modifications, longer waiting times and increased use of genomic profile analysis. Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic abstract: BACKGROUND: Corona Virus Disease 19 (COVID-19) had a worldwide negative impact on healthcare systems, which were not used to coping with such pandemic. Adaptation strategies prioritizing COVID-19 patients included triage of patients and reduction or re-allocation of other services. The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. METHODS: A survey was developed by a multidisciplinary group on behalf of European Breast Cancer Research Association of Surgical Trialists and distributed via breast cancer societies. One reply per breast unit was requested. RESULTS: In ten days, 377 breast centres from 41 countries completed the questionnaire. RT-PCR testing for SARS-CoV-2 prior to treatment was reported by 44.8% of the institutions. The estimated time interval between diagnosis and treatment initiation increased for about 20% of institutions. Indications for primary systemic therapy were modified in 56% (211/377), with upfront surgery increasing from 39.8% to 50.7% (p<0.002) and from 33.7% to 42.2% (p<0.016) in T1cN0 triple-negative and ER-negative/HER2-positive cases, respectively. Sixty-seven percent considered that chemotherapy increases risks for developing COVID-19 complications. Fifty-one percent of the responders reported modifications in chemotherapy protocols. Gene-expression profile used to evaluate the need for adjuvant chemotherapy increased in 18.8%. In luminal-A tumours, a large majority (68%) recommended endocrine treatment to postpone surgery. Postoperative radiation therapy was postponed in 20% of the cases. CONCLUSIONS: Breast cancer management was considerably modified during the COVID-19 pandemic. Our data provide a base to investigate whether these changes impact oncologic outcomes. url: https://api.elsevier.com/content/article/pii/S0960977620301132 doi: 10.1016/j.breast.2020.05.006 id: cord-255552-k1retwa4 author: Gassen, Nils C. title: Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date: 2020-04-15 words: 1208.0 sentences: 73.0 pages: flesch: 39.0 cache: ./cache/cord-255552-k1retwa4.txt txt: ./txt/cord-255552-k1retwa4.txt summary: Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Targeting of these pathways by exogenous administration of spermidine, AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS-CoV-2 propagation by 85, 88, and >99%, respectively. In the case of highly pathogenic Middle East respiratory syndrome 57 (MERS)-CoV, we recently showed that autophagy is limited by a virus-induced AKT1-dependent 58 activation of the E3-ligase S-phase kinase-associated protein 2 (SKP2), which targets the key autophagy 59 initiating protein Beclin-1 (BECN1) for proteasomal degradation (10). Direct blocking of the negative BECN1 regulator SPK2 by previously 175 described inhibitors SMIP004, SMIP004-7, valinomycin, and niclosamide (10) showed SARS-CoV-2 176 growth inhibition from 50 (SMIP004, SMIP004-7) to over 99% in case of valinomycin and niclosamide 177 (Figure 4a, lower panel, Figure S3d,e) . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses an acute threat to public health and the world economy, especially because no approved specific drugs or vaccines are available. Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. Here we show that SARS-CoV-2 infection limits autophagy by interfering with multiple metabolic pathways and that compound-driven interventions aimed at autophagy induction reduce SARS-CoV-2 propagation in vitro. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Infection also downregulates autophagy-inducing spermidine, and facilitates AKT1/SKP2-dependent degradation of autophagy-initiating Beclin-1 (BECN1). Targeting of these pathways by exogenous administration of spermidine, AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS-CoV-2 propagation by 85, 88, and >99%, respectively. In sum, SARS-CoV-2 infection causally diminishes autophagy. A clinically approved and well-tolerated autophagy-inducing compound shows potential for evaluation as a treatment against SARS-CoV-2. url: https://doi.org/10.1101/2020.04.15.997254 doi: 10.1101/2020.04.15.997254 id: cord-302920-jkr438p9 author: Gasser, Romain title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date: 2020-10-09 words: 423.0 sentences: 31.0 pages: flesch: 48.0 cache: ./cache/cord-302920-jkr438p9.txt txt: ./txt/cord-302920-jkr438p9.txt summary: key: cord-302920-jkr438p9 title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 cord_uid: jkr438p9 Characterization of the humoral response to SARS-CoV-2, the etiological agent of Covid-19, is essential to help control the infection. In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. In this study, we selected plasma from a cohort of Covid-19 convalescent patients and selectively depleted immunoglobulin A, M or G before testing the remaining neutralizing capacity of the depleted plasma. This observation may help design efficient antibody-based COVID-19 therapies and may also explain the increased susceptibility to SARS-CoV-2 of autoimmune patients receiving therapies that impair the production of IgM. Decline of humoral 409 responses against SARS-CoV-2 Spike in convalescent individuals Potent neutralizing 413 antibodies from COVID-19 patients define multiple targets of vulnerability abstract: Characterization of the humoral response to SARS-CoV-2, the etiological agent of Covid-19, is essential to help control the infection. In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. However, the specific role of each immunoglobulin isotype in the overall neutralizing capacity is still not well understood. In this study, we selected plasma from a cohort of Covid-19 convalescent patients and selectively depleted immunoglobulin A, M or G before testing the remaining neutralizing capacity of the depleted plasma. We found that depletion of immunoglobulin M was associated with the most substantial loss of virus neutralization, followed by immunoglobulin G. This observation may help design efficient antibody-based COVID-19 therapies and may also explain the increased susceptibility to SARS-CoV-2 of autoimmune patients receiving therapies that impair the production of IgM. url: https://doi.org/10.1101/2020.10.09.333278 doi: 10.1101/2020.10.09.333278 id: cord-271404-tu8u1b1d author: Gaunkar, Ridhima B title: COVID-19 in Smokeless Tobacco Habitués: Increased Susceptibility and Transmission date: 2020-06-25 words: 3088.0 sentences: 154.0 pages: flesch: 49.0 cache: ./cache/cord-271404-tu8u1b1d.txt txt: ./txt/cord-271404-tu8u1b1d.txt summary: Smokeless tobacco (SLT) consumption is of particular concern in countries in South Asia with high population densities, as it facilitates exposure to SARS-CoV-2 within or between communities by the act of public spitting. SLT-induced higher expression of angiotensin-converting enzyme 2 receptors along with the presence of furin in the oral mucosa and dysfunctional immune responses among SLT habitués increase viral dissemination and an individual''s susceptibility to COVID-19. There has not been much research on the increased risk of contracting COVID-19 for smokeless tobacco (SLT) users, although the use of these products is widely prevalent in South Asia and the Western Pacific region. The known action of the enzyme furin and the nicotine-induced increased expression of the ACE2 receptor result in COVID-19 viral tropism to the oral mucosal tissues in smokeless tobacco habitués [11] [12] [13] [14] [15] [16] [17] [18] [19] . abstract: As the coronavirus disease (COVID-19) pandemic continues to sweep across the globe, the world is responding by implementing public awareness campaigns, social distancing measures, and other preventive strategies to arrest the spread of this lethal disease. Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacts a heavy toll on patients with existing comorbidities. Smokeless tobacco (SLT) consumption is of particular concern in countries in South Asia with high population densities, as it facilitates exposure to SARS-CoV-2 within or between communities by the act of public spitting. Salivary droplets generated in this act are a potential threat because they can transmit this airborne infection. Moreover, large gatherings at tobacco retail outlets, frequent hand-to-mouth contact, and sharing of apparatus by SLT habitués could also aid in increasing the spread of SARS-CoV-2. SLT-induced higher expression of angiotensin-converting enzyme 2 receptors along with the presence of furin in the oral mucosa and dysfunctional immune responses among SLT habitués increase viral dissemination and an individual’s susceptibility to COVID-19. Issuing rigorous regulations to restrict the use of various forms of SLT products and the obnoxious act of spitting in public can assist in arresting the spread of COVID-19. Widespread education campaigns enlightening the community regarding the adverse effects of SLT consumption and its relationship with COVID-19, along with providing effective assistance to quit for those who are addicted, would decrease the spread of COVID-19. url: https://doi.org/10.7759/cureus.8824 doi: 10.7759/cureus.8824 id: cord-307701-fujejfwb author: Gaurav, Shubham title: Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date: 2020-06-07 words: 2069.0 sentences: 111.0 pages: flesch: 54.0 cache: ./cache/cord-307701-fujejfwb.txt txt: ./txt/cord-307701-fujejfwb.txt summary: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the cause of the novel human Corona Virus Disease COVID-19, first reported on November 17 th , 2019 in Wuhan, China [12] . In addition to structural and NSPs, SARS-CoV-2 genome also codes for at least two other viroporin candidates (other than the E protein), namely ORF3a and ORF8 [3] . Moreover, the 29-nucleotide deleted SARS CoV-1 strain had a 23-fold less viral replication as compared to its wild type, suggesting that this mutation effectively attenuated the virus. abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. Studies on SARS-CoV-2 are being carried out at an unprecedented rate to tackle this threat. Genomics studies, in particular, are indispensable to elucidate the dynamic nature of the RNA genome of SARS-CoV-2. RNA viruses are marked by their unique ability to undergo high rates of mutation in their genome, much more frequently than their hosts, which diversifies their strengths qualifying them to elude host immune response and amplify drug resistance. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. In addition to multiple point mutations, we found a remarkable similarity between relatively common mutations of 36-nucleotide deletion in ORF8 of SARS-CoV-2. Our results corroborate with the earlier reported 29-nucleotide deletion in SARS, which was frequent during the early stage of human-to-human transmission. The results will be useful to understand the biology of SARS-CoV-2 and itsattenuation for vaccine development. url: https://doi.org/10.1101/2020.06.06.137604 doi: 10.1101/2020.06.06.137604 id: cord-252286-377y9aqx author: Gauss, Tobias title: Preliminary pragmatic lessons from the SARS-CoV-2 pandemic from France date: 2020-05-13 words: 2161.0 sentences: 132.0 pages: flesch: 43.0 cache: ./cache/cord-252286-377y9aqx.txt txt: ./txt/cord-252286-377y9aqx.txt summary: Abstract The first wave of the SARS-CoV-2 pandemic required an unprecedented and historic increase in critical care capacity on a global scale in France. The SARS-CoV-2 pandemic requires an unprecedented and historic increase in critical care capacity on a global scale. The ongoing fight against the pandemic and potential resurgence of the virus made it compelling for the authors to share specific concepts for the management of critical care surge capacity. One particularity of any exceptional situation (mass casualty, pandemic, etc.) is the activation of a structured crisis mode during which authority lies within the crisis committee, relying on a chain of command and clearly defined principles of control. ICU/HDU capacities management required conscious effort to preserve protected space for non-SARS-CoV-2 critical care and respond to the evolving situation. Training was essential to prepare healthcare professionals in the first days of the pandemic for PPE use, airway management, cleaning, cardiac arrest, etc. abstract: Abstract The first wave of the SARS-CoV-2 pandemic required an unprecedented and historic increase in critical care capacity on a global scale in France. Authors and members from the ACUTE and REANIMATION committees of the French Society of Anaesthesiology and Critical Care (SFAR) wished to share experience and insights gained during the first weeks of this pandemic. These were summarised following the World Health Organisation Response Checklist and detailed according to the subsequent subheadings: 1. Command and Control, 2. Communication, 3. Safety and Security, 4. Triage, 5. Surge Capacity, 6. Continuity of essential services, 7. Human resources, 8. Logistics and supply management, 9. Training/Preparation, 10. Psychological comfort for patients and next of kin, 11. Learning and 12. Post disaster recovery. These experience-based recommendations, consensual across all members from both committees of our national society, establish a practical framework for medical teams, either spared by the first wave of severe COVID patients or preparing for the second one. url: https://www.ncbi.nlm.nih.gov/pubmed/32405518/ doi: 10.1016/j.accpm.2020.05.005 id: cord-280979-0vaarrji author: Gauttier, V. title: Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date: 2020-08-14 words: 4302.0 sentences: 227.0 pages: flesch: 40.0 cache: ./cache/cord-280979-0vaarrji.txt txt: ./txt/cord-280979-0vaarrji.txt summary: These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Altogether, these data showed that optimized peptide vaccination against selected SARS-CoV-2 epitopes elicits robust and broad Th1-biased immunogenicity against several structural (S, M, N) and non-structural proteins in HLA-A2 expressing mice and that several peptides induce viral-specific memory CD8 T cells displaying all characteristics of T lymphocyte sentinels in barrier tissues. Using sequence design through reverse vaccinology selection approach based on previous CoVs knowledge on immunodominant epitopes and computational immunology optimization, we developed a combination of 12 CD8 T cell synthetic peptides originating from 11 SARS-CoV-2 structural and non-structural proteins capable to cover HLA polymorphism with high coverage globally and to induce immunogenicity to different proteins independently of HLA alleles expression. abstract: The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which enters the body principally through the nasal and larynx mucosa and progress to the lungs through the respiratory tract. SARS-CoV-2 replicates efficiently in respiratory epithelial cells motivating the development of alternative and rapidly scalable vaccine inducing mucosal protective and long-lasting immunity. We have previously developed an immunologically optimized multi-neoepitopes-based peptide vaccine platform which has already demonstrated tolerance and efficacy in hundreds of lung cancer patients. Here, we present a multi-target CD8 T cell peptide COVID-19 vaccine design targeting several structural (S, M, N) and non-structural (NSPs) SARS-CoV-2 proteins with selected epitopes in conserved regions of the SARS-CoV-2 genome. We observed that a single subcutaneous injection of a serie of epitopes induces a robust immunogenicity in-vivo as measured by IFNγ ELIspot. Upon tetramer characterization we found that this serie of epitopes induces a strong proportion of virus-specific CD8 T cells expressing CD103, CD44, CXCR3 and CD49a, the specific phenotype of tissue-resident memory T lymphocytes (Trm). Finally, we observed broad cellular responses, as characterized by IFNγ production, upon restimulation with structural and non-structural protein-derived epitopes using blood T cells isolated from convalescent asymptomatic, moderate and severe COVID-19 patients. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Statement of Significance Humoral and cellular adaptive immunity are different and complementary immune defenses engaged by the body to clear viral infection. While neutralizing antibodies have the capacity to block virus binding to its entry receptor expressed on human cells, memory T lymphocytes have the capacity to eliminate infected cells and are required for viral clearance. However, viruses evolve quickly, and their antigens are prone to mutations to avoid recognition by the antibodies (phenomenon named ‘antigenic drift’). This limitation of the antibody-mediated immunity could be addressed by the T-cell mediated immunity, which is able to recognize conserved viral peptides from any viral proteins presented by virus-infected cells. Thus, by targeting several proteins and conserved regions on the genome of a virus, T-cell epitope-based vaccines are less subjected to mutations and may work effectively on different strains of the virus. We designed a multi-target T cell-based vaccine containing epitope regions optimized for CD8+ T cell stimulation that would drive long-lasting cellular immunity with high specificity, avoiding undesired effects such as antibody-dependent enhancement (ADE) and antibody-induced macrophages hyperinflammation that could be observed in subjects with severe COVID-19. Our in-vivo results showed that a single injection of selected CD8 T cell epitopes induces memory viral-specific T-cell responses with a phenotype of tissue-resident memory T cells (Trm). Trm has attracted a growing interest for developing vaccination strategies since they act as immune sentinels in barrier tissue such as the respiratory tract and the lung. Because of their localization in tissues, they are able to immediately recognize infected cells and, because of their memory phenotypes, they rapidly respond to viral infection by orchestrating local protective immune responses to eliminate pathogens. Lastly, such multiepitope-based vaccination platform uses robust and well-validated synthetic peptide production technologies that can be rapidly manufactured in a distributed manner. url: https://doi.org/10.1101/2020.08.14.240093 doi: 10.1101/2020.08.14.240093 id: cord-343715-y594iewi author: Gavriatopoulou, Maria title: Organ-specific manifestations of COVID-19 infection date: 2020-07-27 words: 8765.0 sentences: 447.0 pages: flesch: 38.0 cache: ./cache/cord-343715-y594iewi.txt txt: ./txt/cord-343715-y594iewi.txt summary: Patients infected with this new coronavirus present with a variety of symptoms, which range from asymptomatic disease to mild and moderate symptoms (mild pneumonia), severe symptoms (dyspnoea, hypoxia, or > 50% lung involvement on imaging) and symptoms of critical illness (acute respiratory distress syndrome, respiratory failure, shock or multiorgan system dysfunction). A large retrospective observational study from China showed that among 214 hospitalized patients with confirmed SARS-CoV-2 infection, 36.4% had neurological manifestations [114] . The correlation of disease severity with neurological symptoms was confirmed by another retrospective study from France, reporting a prevalence of 84% of neurological manifestations in 58 hospitalized patients with acute respiratory distress syndrome (ARDS) due to COVID-19 [115] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: Although COVID-19 presents primarily as a lower respiratory tract infection transmitted via air droplets, increasing data suggest multiorgan involvement in patients that are infected. This systemic involvement is postulated to be mainly related to the SARS-CoV-2 virus binding on angiotensin-converting enzyme 2 (ACE2) receptors located on several different human cells. Lung involvement is the most common serious manifestation of the disease, ranging from asymptomatic disease or mild pneumonia, to severe disease associated with hypoxia, critical disease associated with shock, respiratory failure and multiorgan failure or death. Among patients with COVID-19, underlying cardiovascular comorbidities including hypertension, diabetes and especially cardiovascular disease, has been associated with adverse outcomes, whereas the emergence of cardiovascular complications, including myocardial injury, heart failure and arrhythmias, has been associated with poor survival. Gastrointestinal symptoms are also frequently encountered and may persist for several days. Haematological complications are frequent as well and have been associated with poor prognosis. Furthermore, recent studies have reported that over a third of infected patients develop a broad spectrum of neurological symptoms affecting the central nervous system, peripheral nervous system and skeletal muscles, including anosmia and ageusia. The skin, the kidneys, the liver, the endocrine organs and the eyes are also affected by the systemic COVID-19 disease. Herein, we provide a comprehensive overview of the organ-specific systemic manifestations of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32720223/ doi: 10.1007/s10238-020-00648-x id: cord-284526-a5kgo4ct author: Gavriilaki, Eleni title: Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses date: 2020-08-27 words: 6004.0 sentences: 319.0 pages: flesch: 32.0 cache: ./cache/cord-284526-a5kgo4ct.txt txt: ./txt/cord-284526-a5kgo4ct.txt summary: Experience from previous coronaviruses has triggered hypotheses on the role of endothelial dysfunction in the pathophysiology of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which are currently being tested in preclinical and clinical studies. Recent evidence suggests that signs and symptoms of severe coronavirus disease-2019 (COVID-19) infection resemble the clinical phenotype of endothelial dysfunction and share mutual pathophysiological mechanisms [1] . Experience from previous coronaviruses has triggered studies testing hypotheses on the role of the endothelial dysfunction in patients with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Α high rate of VTE (43%, mainly PE) overall was reported in another series of 150 ICU patients in which patients with COVID-19associated acute respiratory distress syndrome (ARDS) had higher rates of thrombotic complications compared with non-COVID-19-ARDS [65] . Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection abstract: PURPOSE OF REVIEW: To review current literature on endothelial dysfunction with previous coronaviruses, and present available data on the role of endothelial dysfunction in coronavirus disease-2019 (COVID-19) infection in terms of pathophysiology and clinical phenotype RECENT FINDINGS: Recent evidence suggests that signs and symptoms of severe COVID-19 infection resemble the clinical phenotype of endothelial dysfunction, implicating mutual pathophysiological pathways. Dysfunction of endothelial cells is believed to mediate a variety of viral infections, including those caused by previous coronaviruses. Experience from previous coronaviruses has triggered hypotheses on the role of endothelial dysfunction in the pathophysiology of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which are currently being tested in preclinical and clinical studies. SUMMARY: Endothelial dysfunction is the common denominator of multiple clinical aspects of severe COVID-19 infection that have been problematic for treating physicians. Given the global impact of this pandemic, better understanding of the pathophysiology could significantly affect management of patients. url: https://doi.org/10.1007/s11906-020-01078-6 doi: 10.1007/s11906-020-01078-6 id: cord-283948-rb9rrkxb author: Gavriilidis, Paschalis title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series date: 2020-06-25 words: 1595.0 sentences: 105.0 pages: flesch: 48.0 cache: ./cache/cord-283948-rb9rrkxb.txt txt: ./txt/cord-283948-rb9rrkxb.txt summary: title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series Currently, the first articles reporting outcomes of liver transplant recipients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are published. The aim of the present study was to summarise the reported evidence of liver transplant recipients infected by SARS-CoV-2 during the global pandemic. A systematic literature search of articles published from inception until April 2020 performed in EMBASE, MED-LINE (PubMed), Cochrane Library, and Google Scholar databases using free text and MeSH terms (corona virus, COVID-19, liver transplantation, liver transplant recipients, global pandemic of COVID-19, severe acute respiratory syndrome, SARS). Of note, D''Antiga reported that children liver transplant recipients although immunosuppressed were not at increased risk to develop severe COVID-19 compared with the general population [7] . abstract: The pandemic of coronavirus disease 2019 (COVID-19) changed the surgical everyday practice overnight. Currently, the first articles reporting outcomes of liver transplant recipients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are published. The aim of the present study was to summarise the existing evidence of impact of COVID-19 global pandemic on liver transplant recipients. Electronic databases were searched in accordance with Preferred Reporting Items in Systematic Reviews and Meta-Analyses (PRISMA). Five studies were selected from a pool of 12 studies with a total of 854 liver transplant recipients of whom 700 were children and the rest 154 were adults. The present evidence, based on case reports and series demonstrated lower mortality in liver transplant recipients compared to general population. url: https://www.ncbi.nlm.nih.gov/pubmed/32655733/ doi: 10.14740/jocmr4223 id: cord-302821-b9ikg0xy author: Gawałko, Monika title: COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications date: 2020-09-01 words: 3685.0 sentences: 209.0 pages: flesch: 34.0 cache: ./cache/cord-302821-b9ikg0xy.txt txt: ./txt/cord-302821-b9ikg0xy.txt summary: Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. The pathophysiology of COVID-19 related AF is not well understood and proposed putative mechanisms include a reduction in angiotensin-converting enzyme 2 (ACE2) receptor availability, CD147-and sialic acid-spike protein interaction, enhanced inflammatory signalling eventually culmination in inflammatory cytokine storm, direct viral endothelial damage, electrolytes and acid-base balance abnormalities in the acute phase of severe illness and increased adrenergic drive.(28) (Fig. 1) . abstract: Coronavirus disease 2019 (COVID-19) is a novel, highly transmittable and severe strain disease, which has rapidly spread worldwide. Despite epidemiological evidence linking COVID-19 withcardiovascular diseases, little is knownabout whether and how COVID-19 influences atrial fibrillation(AF), the most prevalent arrhythmia in clinical practice. Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. url: https://www.sciencedirect.com/science/article/pii/S2352906720303298?v=s5 doi: 10.1016/j.ijcha.2020.100631 id: cord-258722-1o6zhnnj author: Gbinigie, Kome title: Should azithromycin be used to treat COVID-19? A rapid review date: 2020-05-13 words: 3320.0 sentences: 193.0 pages: flesch: 50.0 cache: ./cache/cord-258722-1o6zhnnj.txt txt: ./txt/cord-258722-1o6zhnnj.txt summary: In vivo and in vitro studies were included assessing the safety and effectiveness of azithromycin for treatment of COVID-19, and/or the activity of azithromycin against SARS-CoV-2. In another pre-print, Andreania and colleagues 13 report the results of an in vitro study assessing the activity of azithromycin and hydroxychloroquine against SARS-CoV-2. In vivo research effectiveness Only one trial was identified on the effectiveness of azithromycin for the treatment of COVID-19, conducted by Gautret and colleagues in France and reported in a pre-print 14 (see Table 1 ). The same research team that conducted the in vivo study included in this review conducted a singlearm trial of 80 patients who tested positive for SARS-CoV-2 and showed mild symptoms, 17 to further assess the effectiveness of the combined hydroxychloroquine/azithromycin treatment regime. No in vivo studies were identified assessing the safety or effectiveness of azithromycin as a standalone treatment for COVID-19. abstract: BACKGROUND: There are no established effective treatments for COVID-19. While novel drugs are being developed, azithromycin has been identified as a candidate treatment in the interim. AIM: To review the evidence for the effectiveness and safety of azithromycin in treating COVID-19. DESIGN & SETTING: A rapid review of the literature was conducted. METHOD: Electronic searches were conducted on 16 April 2020 of PubMed, TRIP, EPPI COVID Living Map, MedRxiv, GoogleScholar, and Google. In vivo and in vitro studies were included assessing the safety and effectiveness of azithromycin for treatment of COVID-19, and/or the activity of azithromycin against SARS-CoV-2. In vivo studies needed to include a comparator group. RESULTS: Three studies were identified, two in vitro and one in vivo, which were suitable for inclusion. All three were published as pre-prints. The in vitro studies revealed conflicting results, with one finding anti-SARS-CoV-2 activity for azithromycin alone, while the other found activity against SARS-CoV-2 only when azithromycin was combined with hydroxychloroquine. A small trial of 36 patients, with high risk of bias, found superior viral clearance in patients with COVID-19 treated with azithromycin and hydroxychloroquine combined, compared with hydroxychloroquine alone. CONCLUSION: There is no evidence to support the use of azithromycin for the treatment of COVID-19 outside of the context of clinical trials, unless it is used to treat bacterial super-infection. There is extremely limited evidence of a possible synergy between azithromycin and hydroxychloroquine. The adverse events profile of azithromycin in the context of COVID-19 has not yet been established. Well-conducted clinical trials are urgently needed in this area. url: https://www.ncbi.nlm.nih.gov/pubmed/32398343/ doi: 10.3399/bjgpopen20x101094 id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 words: 5103.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-255738-r8zfdsix.txt txt: ./txt/cord-255738-r8zfdsix.txt summary: Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric''s group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel''s group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. abstract: The severe acute respiratory syndrome (SARS) outbreak in 2002, which had a high morbidity rate and caused worldwide alarm, remains untreated today even though SARS was eventually isolated and controlled. Development and high-throughput screening of efficacious drugs is therefore critical. However, currently there remains a lack of such a safe system. Here, the generation and characterization of the first selectable, SARS–coronavirus (SARS–CoV)-based replicon cell line which can be used for screening is described. Partial SARS–CoV cDNAs and antibiotic resistance/reporter gene DNA were generated and assembled in vitro to produce the replicon transcription template, which was then transcribed in vitro to generate the replicon RNA. The latter was introduced into a mammalian cell line and the transfected cells were selected for by antibiotic application. For the antibiotic-resistant cell lines thus generated, the expression of reporter gene was ensured by continued monitoring using fluorescent microscopy and flow cytometry. The suitability of this replicon cell line in drug screening was demonstrated by testing the inhibitory effect of several existing drugs and the results demonstrate that the SARS–CoV replicon cell lines provide a safe tool for the identification of SARS–CoV replicase inhibitors. The replicon cell lines thus developed can be applied to high-throughput screening for anti-SARS drugs without the need to grow infectious SARS–CoV. url: https://api.elsevier.com/content/article/pii/S0042682206007410 doi: 10.1016/j.virol.2006.10.016 id: cord-314311-xbpb9nfi author: Ge, Huipeng title: The epidemiology and clinical information about COVID-19 date: 2020-04-14 words: 5263.0 sentences: 325.0 pages: flesch: 55.0 cache: ./cache/cord-314311-xbpb9nfi.txt txt: ./txt/cord-314311-xbpb9nfi.txt summary: In November 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong, China, and resulted in more than 8000 infections and 774 deaths in 37 countries. This review makes a comprehensive introduction about this disease, including the genome structure and receptor of SARS-CoV-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of COVID-19. The clinical manifestations of SARS-CoV-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. The COVID-19 patients around the world were diagnosed based on World Health Organization interim guidance [65] , and China updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in Chinese) according to epidemic situation and improved awareness of disease. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: In December 2019, pneumonia of unknown cause occurred in Wuhan, Hubei Province, China. On 7 January 2020, a novel coronavirus, named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was identified in the throat swab sample of one patient. The World Health Organization (WHO) announced the epidemic disease caused by SARS-CoV-2 as coronavirus disease 2019 (COVID-19). Currently, COVID-19 has spread widely around the world, affecting more than seventy countries. China, with a huge burden of this disease, has taken strong measures to control the spread and improve the curative rate of COVID-19. In this review, we summarized the epidemiological characteristics, clinical features, diagnosis, treatment, and prognosis of COVID-19. A comprehensive understanding will help to control the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32291542/ doi: 10.1007/s10096-020-03874-z id: cord-295733-f3rt1fyk author: Ge, Tianxiang title: Evaluation of disinfection procedures in a designated hospital for COVID-19 date: 2020-08-22 words: 2492.0 sentences: 142.0 pages: flesch: 49.0 cache: ./cache/cord-295733-f3rt1fyk.txt txt: ./txt/cord-295733-f3rt1fyk.txt summary: When compared with previous study, more places that could be potentially contaminated by COVID-19 patients were sampled for viral RNA detection, such as the flush button of the toilet bowl, medical refuse transfer trolley, elevators, and the examination rooms for these patients. These areas could not be used for non-COVID-19 patients until all the environmental samples collected were negative for SARS-CoV-2 RNA detection. In this study, surface samples collected from the examination rooms were all negative for SARS-CoV-2 RNA detection, and the samples collected from isolation wards and other places were also negative for viral RNA detection, which indicated that the terminal disinfection was effective. Other researches had revealed the presence of SARS-CoV-2 RNA in aerosol, which indicated the air could be contaminated by the virus, and patients could be infected in the isolation wards [12, 28] . Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) has spread globally and been a public health emergency worldwide. It is important to reduce the risk of healthcare associated infections among the healthcare workers and patients. This study aimed to investigate the contamination of environment in isolation wards and sewage, and assess the quality of routine disinfection procedures in our hospital. METHODS: Routine disinfection procedures were performed three-times a day in general isolation wards and six-times a day in isolated ICU wards in our hospital. Environmental surface samples and sewage samples were collected for viral RNA detection. SARS-CoV-2 RNA detection were performed with quantitative reverse transcription PCR (qRT-PCR). RESULTS: A total of 163 samples were collected from February 6th to April 4th. Among 122 surface samples, two were positive for SARS-CoV-2 RNA detection. One was collected from the flush button of the toilet bowl, and the other was collected from a hand-basin. Although 10 of the sewage samples were positive for viral RNA detection, all positive samples were negative for viral culture. CONCLUSION: These results revealed the routine disinfection procedures in our hospital were effective in reducing the potential risk of healthcare associated infection. Two surface samples were positive for viral detection, suggesting that more attention should be paid when disinfecting places easy to be ignored. url: https://www.sciencedirect.com/science/article/pii/S0196655320308129?v=s5 doi: 10.1016/j.ajic.2020.08.028 id: cord-342362-j7vuoer6 author: Gegúndez-Fernández, José A title: Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19 date: 2020-04-25 words: 3525.0 sentences: 354.0 pages: flesch: 53.0 cache: ./cache/cord-342362-j7vuoer6.txt txt: ./txt/cord-342362-j7vuoer6.txt summary: Conclusiones: Durante la pandemia COVID-19, la atención a los potenciales riesgos de salud para la población ocasionados por el coronavirus deberá prevalecer sobre la posible progresión de enfermedades oculares comunes. Recoge recomendaciones de máximos para la atención a pacientes oftalmológicos, tanto COVID positivos como negativos, durante la pandemia por coronavirus SARS-CoV-2. Durante este periodo la atención a los potenciales riesgos de salud para la población general ocasionados por la pandemia COVID-19 debe primar sobre la posible progresión de enfermedades tales como el glaucoma crónico, la retinopatía diabética, la degeneración macular asociada a la edad (DMAE), enfermedades corneales e inflamatorias, entre otras. Las precauciones tomadas para la elaboración de los derivados hemáticos serán las propias establecidas según el informe de la AEMPS 20 de 23/mayo/2013 sobre el uso de Plasma Rico en Plaquetas (PRP) y teniendo en cuenta los criterios de exclusión del Anexo II del Real Decreto 21 1088/2005, el cual especifica que pacientes con infecciones se excluirán durante y como mínimo las dos semanas posteriores al restablecimiento clínico completo de una enfermedad infecciosa y tras la desaparición de síntomas, incluyendo fiebre superior a 38ºC y afección pseudogripal, donde podríamos clasificar la infección por SARS-CoV-2. abstract: ABSTRACT Objective: Minimize exposure to the SARS-CoV-2, reduce the chances of cross-transmission between patients and healthcare personnel, and prevent the development of postoperative complications from the management of patients with eye diseases during the 2019 coronavirus disease pandemic (COVID -19). Methods: COVID-19 literature review and consensus establishment between different Spanish ophthalmology societies in order to provide guidelines and recommendations of maximum resources primarily conditioned by the state of alert, confinement and social distancing that occurs in Spain since March 16, 2020. Results: The recommendations will promote the adoption of action and protection measures for eye care in outpatient clinics, surgical areas and hospitalization, for unconfirmed (asymptomatic and symptomatic) and confirmed COVID-19 patients. Measures must be adapted to the circumstances and availability of Personal Protective Equipment (PPE) in each of the centers and Autonomous Communities, which will be updated according to the pandemic phases and the measures adopted by the Spanish Government. Conclusions: During the COVID-19 pandemic, attention to the potential health risks to the population caused by coronavirus should prevail over the possible progression of the common eye diseases. Ophthalmologists and other eye care professionals must assume a possible progression of these diseases due to the impossibility of adequate patient follow-up. url: https://www.ncbi.nlm.nih.gov/pubmed/32409243/ doi: 10.1016/j.oftal.2020.04.002 id: cord-306881-wrd2rhjz author: Gehrie, Eric title: Transfusion Service Response to the COVID-19 Pandemic date: 2020-06-25 words: 3296.0 sentences: 140.0 pages: flesch: 44.0 cache: ./cache/cord-306881-wrd2rhjz.txt txt: ./txt/cord-306881-wrd2rhjz.txt summary: In this article, we highlight "best practices" that have emerged during the pandemic, focusing on management of blood supply and blood bank operations, rapid incorporation of COVID-19 convalescent plasma into blood bank inventory, and changes to the approach to the patient requiring therapeutic apheresis. Extrapolation from previous experience with SARS-CoV, Middle Eastern respiratory syndrome, and influenza, and with the strong backing of statements by AABB, the Centers for Disease Control and Prevention, and the Food and Drug Administration (FDA), as well as the preliminary experience of other areas that were afflicted by COVID-19 prior to its wide spread in the United States, blood bankers were able to convince most stakeholders that the true risk to the blood supply was not SARS-CoV-2 itself, but rather social distancing practices resulting in an interruption to the critically needed blood supply. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32584950/ doi: 10.1093/ajcp/aqaa111 id: cord-314135-udce22id author: Geisslinger, Franz title: Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? date: 2020-07-06 words: 6414.0 sentences: 379.0 pages: flesch: 46.0 cache: ./cache/cord-314135-udce22id.txt txt: ./txt/cord-314135-udce22id.txt summary: The responsible virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causes the coronavirus disease 2019 (COVID-19), which is mainly characterized by fever, cough and shortness of breath. We summarize the available literature on COVID-19 suggesting an increased risk for severe disease progression in cancer patients, and we discuss the possibility that SARS-CoV-2 could contribute to cancer development. The main symptoms of COVID-19, the lung disease following SARS-CoV-2 infection are fever, cough, shortness of breath and respiratory distress syndrome with risk for septic shock. Preliminary evidence suggests that such a cytokine storm in response to infection with SARS-CoV-2 is a major factor, promoting severe COVID-19 progress and subsequently disease fatality [8, 12] . Chemotherapy-and radiation therapy-induced immunosuppression is a major risk factor for cancer patients to acquire a severe and probably fatal SARS-CoV-2 infection. Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: Relation to the acute lung injury and pathogenesis of SARS † abstract: The world is currently suffering from a pandemic which has claimed the lives of over 230,000 people to date. The responsible virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causes the coronavirus disease 2019 (COVID-19), which is mainly characterized by fever, cough and shortness of breath. In severe cases, the disease can lead to respiratory distress syndrome and septic shock, which are mostly fatal for the patient. The severity of disease progression was hypothesized to be related to an overshooting immune response and was correlated with age and comorbidities, including cancer. A lot of research has lately been focused on the pathogenesis and acute consequences of COVID-19. However, the possibility of long-term consequences caused by viral infections which has been shown for other viruses are not to be neglected. In this regard, this opinion discusses the interplay of SARS-CoV-2 infection and cancer with special focus on the inflammatory immune response and tissue damage caused by infection. We summarize the available literature on COVID-19 suggesting an increased risk for severe disease progression in cancer patients, and we discuss the possibility that SARS-CoV-2 could contribute to cancer development. We offer lines of thought to provide ideas for urgently needed studies on the potential long-term effects of SARS-CoV-2 infection. url: https://doi.org/10.3390/ph13070143 doi: 10.3390/ph13070143 id: cord-271723-8qoozmgk author: Gelman, Ram title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents date: 2020-06-18 words: 6269.0 sentences: 304.0 pages: flesch: 37.0 cache: ./cache/cord-271723-8qoozmgk.txt txt: ./txt/cord-271723-8qoozmgk.txt summary: title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents The ongoing severe acute respiratory syndrome pandemic caused by the novel coronavirus 2 (SARS-CoV-2) is associated with high morbidity and mortality rates, and it has created a pressing global need for effective antiviral therapies against it. Potential therapeutic approaches have been proposed to target various steps in the viral infectious process, including a SARS-CoV-2 S-protein-based vaccine, a TMPRSS2 inhibitor aiming to block the priming of the viral S protein, an anti-ACE2 antibody to block the surface receptor, and a soluble ACE2 analogue which competitively binds with SARS-CoV-2 to slow viral entry into cells and decrease viral spread [27] . receptor, which may also be associated with the antiviral immune response Dipeptidyl peptidase 4 (DPP4), also known as CD26, is a 110 kDa transmembrane glycoprotein expressed on the surface of a wide variety of epithelial cells and some lymphocytes. abstract: The ongoing severe acute respiratory syndrome pandemic caused by the novel coronavirus 2 (SARS-CoV-2) is associated with high morbidity and mortality rates, and it has created a pressing global need for effective antiviral therapies against it. COVID-19 disease pathogenesis is characterized by an initial virus-mediated phase, followed by inappropriate hyperactivation of the immune system leading to organ damage. Targeting of the SARS-CoV-2 viral receptors is being explored as a therapeutic option for these patients. In this paper, we summarize several potential receptors associated with the infectivity of SARS-CoV-2 and discuss their association with the immune-mediated inflammatory response. The potential for the development of resistance towards antiviral drugs is also presented. An algorithm-based platform to improve the efficacy of and overcome resistance to viral receptor blockers through the introduction of personalized variability is described. This method is designed to ensure sustained antiviral effectiveness when using SARS-CoV-2 receptor blockers. url: https://www.ncbi.nlm.nih.gov/pubmed/32490731/ doi: 10.1080/22221751.2020.1776161 id: cord-326498-8oa5gkrp author: Gemmati, Donato title: COVID-19 and Individual Genetic Susceptibility/Receptivity: Role of ACE1/ACE2 Genes, Immunity, Inflammation and Coagulation. Might the Double X-Chromosome in Females Be Protective against SARS-CoV-2 Compared to the Single X-Chromosome in Males? date: 2020-05-14 words: 9876.0 sentences: 474.0 pages: flesch: 40.0 cache: ./cache/cord-326498-8oa5gkrp.txt txt: ./txt/cord-326498-8oa5gkrp.txt summary: Firstly, SARS-CoV-2 has a strong interaction with the human ACE2 receptor, which plays an essential role in cell entry together with transmembrane serine protease 2 (TMPRSS2); it is interesting to note that the ACE2 gene lays on the X-chromosome, thus allowing females to be potentially heterozygous and differently assorted compared to men who are definitely hemizygous. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. abstract: In December 2019, a novel severe acute respiratory syndrome (SARS) from a new coronavirus (SARS-CoV-2) was recognized in the city of Wuhan, China. Rapidly, it became an epidemic in China and has now spread throughout the world reaching pandemic proportions. High mortality rates characterize SARS-CoV-2 disease (COVID-19), which mainly affects the elderly, causing unrestrained cytokines-storm and subsequent pulmonary shutdown, also suspected micro thromboembolism events. At the present time, no specific and dedicated treatments, nor approved vaccines, are available, though very promising data come from the use of anti-inflammatory, anti-malaria, and anti-coagulant drugs. In addition, it seems that males are more susceptible to SARS-CoV-2 than females, with males 65% more likely to die from the infection than females. Data from the World Health Organization (WHO) and Chinese scientists show that of all cases about 1.7% of women who contract the virus will die compared with 2.8% of men, and data from Hong Kong hospitals state that 32% of male and 15% of female COVID-19 patients required intensive care or died. On the other hand, the long-term fallout of coronavirus may be worse for women than for men due to social and psychosocial reasons. Regardless of sex- or gender-biased data obtained from WHO and those gathered from sometimes controversial scientific journals, some central points should be considered. Firstly, SARS-CoV-2 has a strong interaction with the human ACE2 receptor, which plays an essential role in cell entry together with transmembrane serine protease 2 (TMPRSS2); it is interesting to note that the ACE2 gene lays on the X-chromosome, thus allowing females to be potentially heterozygous and differently assorted compared to men who are definitely hemizygous. Secondly, the higher ACE2 expression rate in females, though controversial, might ascribe them the worst prognosis, in contrast with worldwide epidemiological data. Finally, several genes involved in inflammation are located on the X-chromosome, which also contains high number of immune-related genes responsible for innate and adaptive immune responses to infection. Other genes, out from the RAS-pathway, might directly or indirectly impact on the ACE1/ACE2 balance by influencing its main actors (e.g., ABO locus, SRY, SOX3, ADAM17). Unexpectedly, the higher levels of ACE2 or ACE1/ACE2 rebalancing might improve the outcome of COVID-19 in both sexes by reducing inflammation, thrombosis, and death. Moreover, X-heterozygous females might also activate a mosaic advantage and show more pronounced sex-related differences resulting in a sex dimorphism, further favoring them in counteracting the progression of the SARS-CoV-2 infection. url: https://doi.org/10.3390/ijms21103474 doi: 10.3390/ijms21103474 id: cord-287338-pws42iay author: Gendelman, Omer title: Continuous hydroxychloroquine or colchicine therapy does not prevent infection with SARS-CoV-2: Insights from a large healthcare database analysis date: 2020-05-05 words: 2016.0 sentences: 107.0 pages: flesch: 46.0 cache: ./cache/cord-287338-pws42iay.txt txt: ./txt/cord-287338-pws42iay.txt summary: As such, in this study, we investigated whether a chronic baseline use of anti-inflammatory medications (namely, hydroxychloroquine and colchicine) could provide a potentially beneficial effect in preventing or, at least partially, mitigating the burden of the SARS-CoV-2 infection. In the present study, we have utilized "real-world data" to explore the associations between subjects positive for SARS-COV-2, different underlying co-morbidities and medications, which were not administered for anti-viral treatment purposes. In a population-based study evaluating the clinical characteristics of 1,482 patients hospitalized with COVID-19 in the USA [19] the majority of patients were males (54.4%) with a similar pattern of underlying comorbidities, most commonly hypertension (49.7%), followed by obesity (48.3%), DM (28.3%), and cardiovascular disease (27.8%). Concerning the alleged anti-viral activities of hydroxychloroquine [23] and its potential protective role against infections [24] , the existing scholarly literature reports contrasting findings even though to date no RCT has shown an unequivocal advantage in preventing or improving the major outcomes in COVID-19 patients [25, 26] . abstract: BACKGROUND: Some disease-modifying agents commonly used to treat patients with rheumatic diseases/autoimmune disorders, such as hydroxychloroquine and colchicine, are under investigation as potential therapies for the “coronavirus disease 2019” (COVID-19). However, the role of such agents as prophylactic tools is still not clear. METHODS: This is a retrospective study based on a large healthcare computerized database including all patients that were screened for the “Severe Acute Respiratory Syndrome Coronavirus type 2” (SARS-CoV-2) in the study period from February 23rd 2020 to March 31st 2020. A comparison was conducted between subjects tested positive for SARS-CoV-2 and those found negative in terms of rate of administration of hydroxychloroquine/colchicine therapy. RESULTS: An overall sample of 14,520 subjects were screened for SARS-CoV-2 infection and 1317 resulted positive. No significant difference was found in terms of rates of usage of hydroxychloroquine or colchicine between those who were found positive for SARS-CoV-2 and those who were found negative (0.23% versus 0.25% for hydroxychloroquine, and 0.53% versus 0.48% for colchicine, respectively). CONCLUSION: These findings raise doubts regarding the protective role of these medications in the battle against SARS-CoV-2 infection. url: https://doi.org/10.1016/j.autrev.2020.102566 doi: 10.1016/j.autrev.2020.102566 id: cord-270218-578lsck9 author: Gentile, Davide title: Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study date: 2020-04-23 words: 5872.0 sentences: 300.0 pages: flesch: 46.0 cache: ./cache/cord-270218-578lsck9.txt txt: ./txt/cord-270218-578lsck9.txt summary: On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pro (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pr (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. To further validate the pharmacophore model descriptors, validate the poses and binding energies, and comprehensively investigate the interactions of the new ligands within the catalytic site of the protease, we conducted a parallel docking study, with Autodock4, and MD simulations on those compounds (1-17) that showed a better affinity (Table 1) . abstract: The current emergency due to the worldwide spread of the COVID-19 caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness has not yet been assessed. The main protease (M(pro)) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent M(pro) inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by a hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed this study to highlight some crucial aspects. Seventeen potential SARS-CoV-2 M(pro) inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent. url: https://www.ncbi.nlm.nih.gov/pubmed/32340389/ doi: 10.3390/md18040225 id: cord-268330-mo5myrz4 author: Gentile, Pietro title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia date: 2020-04-29 words: 4618.0 sentences: 239.0 pages: flesch: 47.0 cache: ./cache/cord-268330-mo5myrz4.txt txt: ./txt/cord-268330-mo5myrz4.txt summary: title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia [1] , reported exceptional outcomes in improved pulmonary functional activity, into seven patients who suffered Coronavirus Disease 2019 (COVID19) after an intravenous administration of clinical-grade mesenchymal stem cells (MSCs). [1] , 7 SARS-CoV-2 positive patients, with COVID-19 pneumonia (study group), showed a great improving pulmonary functional activity after an intravenous administration of clinical-grade MSCs [1] . The rationale of the present work is to suggest the possibility to use autologous or allogeneic adipose-derived stromal stem cells (ASCs) (in the last case after decellularization and with good manufacturing practices -GMPlaboratory approval) intravenously or directly through a ventilation mask (aerosol). In the last case, it could be possible to donate human adipose tissue to GMP, EMA, or FDA Laboratory or bank to isolate SVFs and ASCs and re-infuse the cellular product obtained, as certified drugs, in COVID-19 patients. abstract: nan url: https://doi.org/10.1080/14712598.2020.1761322 doi: 10.1080/14712598.2020.1761322 id: cord-320815-p9oh54nt author: Gentile, Pietro title: Research progress on Mesenchymal Stem Cells (MSCs), Adipose-Derived Mesenchymal Stem Cells (AD-MSCs), Drugs, and Vaccines in Inhibiting COVID-19 Disease date: 2020-10-01 words: 4718.0 sentences: 234.0 pages: flesch: 46.0 cache: ./cache/cord-320815-p9oh54nt.txt txt: ./txt/cord-320815-p9oh54nt.txt summary: Additionally, recent studies reported improved respiratory activity after intravenous administration of MSCs into patients affected by coronavirus disease 2019 (COVID-19) caused by the Coronavirus 2 (SARS-CoV-2) suggesting their role as anti-viral therapy. In this literature review, the role of regenerative strategies through MSCs, AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. In this current review, the role of regenerative strategies through MSCs, focusing on AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. Two clinical trials (EUCTR2020-001364-29-ES and EUCTR2020-001266-11-ES) were registered in April 2020, after the pandemic situation produced by COVID-19 but the last one (EUCTR2019-002688-89-ES) based on the possibility "To assess the feasibility, safety, and tolerability of the administration of HCR040, a drug whose active substance is HC016, allogeneic adiposederived adult mesenchymal stem cells expanded and pulsed with H2O2, in patients with acute respiratory distress syndrome. abstract: Mesenchymal Stem Cells (MSCs), and Adipose-Derived Mesenchymal Stem Cells (AD-MSCs) have been used for many years in regenerative medicine for clinical and surgical applications. Additionally, recent studies reported improved respiratory activity after intravenous administration of MSCs into patients affected by coronavirus disease 2019 (COVID-19) caused by the Coronavirus 2 (SARS-CoV-2) suggesting their role as anti-viral therapy. Severe COVID-19 patients usually progress to acute respiratory distress syndrome, sepsis, metabolic acidosis that is difficult to correct, coagulation dysfunction, multiple organ failure, and even death in a short period after onset. Currently, there is still a lack of clinically effective drugs for such patients. The high secretory activity, the immune-modulatory effect, and the homing ability make MSCs and in particular AD-MSCs both a potential tool for the anti-viral drug-delivery in the virus microenvironment and potential cellular therapy. AD-MSCs as the most important exponent of MSCs are expected to reduce the risk of complications and death of patients due to their strong anti-inflammatory and immune-modulatory capabilities, which can improve microenvironment, promote neovascularization and enhance tissue repair capabilities. In this literature review, the role of regenerative strategies through MSCs, AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33014532/ doi: 10.14336/ad.2020.0711 id: cord-332970-atwz3rgf author: Gentile, Pietro title: Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease date: 2020-05-09 words: 2635.0 sentences: 133.0 pages: flesch: 52.0 cache: ./cache/cord-332970-atwz3rgf.txt txt: ./txt/cord-332970-atwz3rgf.txt summary: title: Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease A recent and interesting study reported improved respiratory activity after intravenous administration of mesenchymal stem cells (MSCs) into patients affected by coronavirus disease 2019 (COVID-19). The MSCs could represent an effective, autologous and safe therapy, and therefore, sharing these published results, here is reported the potential use possibilities in COVID-19 of the most common MSCs represented by Adipose Stem Cells (ASCs). Robert Chunhua Zhao''s group [1] reported in a recent study, published in March 2020, an interesting improvement in pulmonary functional activity, into 7 patients affected by Coronavirus Disease 2019 (COVID-19) after a intravenous administration of clinical-grade mesenchymal stem cells (MSCs). In the preliminary study of Robert Chunhua Zhao''s group [1] , 7 patients affected by SARS-CoV-2, with COVID-19 pneumonia displayed a sensible improvement pulmonary function after several intravenous infusion of clinicalgrade MSCs [1] . abstract: A recent and interesting study reported improved respiratory activity after intravenous administration of mesenchymal stem cells (MSCs) into patients affected by coronavirus disease 2019 (COVID-19). These outcomes displayed that intravenous infiltration of MSCs is a safe and efficacy treatment for COVID-19 pneumonia, a severe acute respiratory illness caused by the coronavirus 2 (SARS-CoV-2). Only 7 patients were treated, but with extraordinary results, opening a new strategy in COVID-19 therapy. Currently, no specific therapies against SARS-CoV-2 are available. The MSCs therapy outcomes reported, are striking, as these cells inhibit the over-activation of the immune system, promoting endogenous repair, by improving the lung microenvironment after the SARS-CoV-2 infection. The MSCs could represent an effective, autologous and safe therapy, and therefore, sharing these published results, here is reported the potential use possibilities in COVID-19 of the most common MSCs represented by Adipose Stem Cells (ASCs). url: https://www.ncbi.nlm.nih.gov/pubmed/32489692/ doi: 10.14336/ad.2020.0422 id: cord-257399-p6of5fno author: Gentry, Chris A title: Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date: 2020-09-21 words: 4529.0 sentences: 196.0 pages: flesch: 42.0 cache: ./cache/cord-257399-p6of5fno.txt txt: ./txt/cord-257399-p6of5fno.txt summary: METHODS: This retrospective cohort study included de-identified information of all veterans in the US Veterans Health Administration clinical administrative database aged 18 years or older with rheumatoid arthritis, systemic lupus erythematosus, or associated rheumatological conditions (based on International Classification of Diseases, 10th edition, diagnostic codes) who were alive on March 1, 2020. We aimed to examine whether patients with rheuma tological conditions receiving chronic hydroxy chloroquine therapy are at less risk of developing SARS-CoV-2 infection compared with a propensity-matched group of patients not receiving hydroxychloroquine. Our study takes advantage of a setting in which a specific group of patients has been receiving chronic hydroxy chloroquine over several months to years as a novel virus emerges among the population, setting up an ideal premise to test the hypothesis that hydroxychloroquine might be effective in preventing SARS-CoV-2 infection. abstract: BACKGROUND: Hydroxychloroquine is one of several agents being evaluated in the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We aimed to examine whether patients with rheumatological conditions receiving chronic hydroxychloroquine therapy are at less risk of developing SARS-CoV-2 infection than those not receiving hydroxychloroquine. METHODS: This retrospective cohort study included de-identified information of all veterans in the US Veterans Health Administration clinical administrative database aged 18 years or older with rheumatoid arthritis, systemic lupus erythematosus, or associated rheumatological conditions (based on International Classification of Diseases, 10th edition, diagnostic codes) who were alive on March 1, 2020. A propensity score was calculated for each patient, and each patient who was receiving hydroxychloroquine was matched to two patients who were not receiving hydroxychloroquine (controls). The primary endpoint was the proportion of patients with PCR-confirmed SARS-CoV-2 infection among those receiving chronic hydroxychloroquine versus the propensity-matched patients not receiving chronic hydroxychloroquine between March 1 and June 30, 2020. Secondary outcomes were hospital admission associated with SARS-CoV-2 infection; intensive care requirement associated with SARS-CoV-2 infection; mortality associated with SARS-CoV-2 infection; and overall rates of any hospital admission and mortality (ie, all cause). Multivariate logistic regression analysis was done to determine independent variables for the development of active SARS-CoV-2 infection. FINDINGS: Between March 1 and June 30, 2020, 10 703 patients receiving hydroxychloroquine and 21 406 patients not receiving hydroxychloroquine were included in the primary analysis. The incidence of active SARS-CoV-2 infections during the study period did not differ between patients receiving hydroxychloroquine and patients not receiving hydroxychloroquine (31 [0·3%] of 10 703 vs 78 [0·4%] of 21 406; odds ratio 0·79, 95% CI 0·52–1·20, p=0·27). There were no significant differences in secondary outcomes between the two groups in patients who developed active SARS-CoV-2 infection. For all patients in the study, overall mortality was lower in the hydroxychloroquine group than in the group of patients who did not receive hydroxychloroquine (odds ratio 0·70, 95% CI 0·55–0·89, p=0·0031). In multivariate logistic regression analysis, receipt of hydroxychloroquine was not associated with the development of active SARS-CoV-2 infection (odds ratio 0·79, 95% CI 0·51–1·42). INTERPRETATION: Hydroxychloroquine was not associated with a preventive effect against SARS-CoV-2 infection in a large group of patients with rheumatological conditions. FUNDING: None. url: https://api.elsevier.com/content/article/pii/S2665991320303052 doi: 10.1016/s2665-9913(20)30305-2 id: cord-352741-0pdeehai author: Geramizadeh, Bita title: Histopathologic Findings of Coronavirus in Lung: A Mini-Review date: 2020-10-12 words: 2158.0 sentences: 143.0 pages: flesch: 44.0 cache: ./cache/cord-352741-0pdeehai.txt txt: ./txt/cord-352741-0pdeehai.txt summary: In this report, we will review the published reports about the histopathologic findings of lung tissue in the patients infected with SARS-CoV-2 in comparison with 2 other coronaviruses that have caused outbreaks, ie, SARS-CoV-1 and MERS-CoV. The keywords for searching were "lung," " pulmonary," and CoVs, ie, "severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2])," "coronavirus disease (COVID-19)," "pathology," "biopsy," "autopsy," "histopathology," "severe acute respiratory syndrome (SARS)," and "Middle East Respiratory syndrome (MERS)." Histological examination of lung in rare cases reported from SARS-CoV-2 showed "edema, bilateral diffuse alveolar damage with cellular fibromyxoid exudates, desquamation of pneumocytes and hyaline membrane formation," indicating acute respiratory distress syndrome. 19 One histopathologic finding in the new SARS-CoV-2infected lung disease that has not been reported in the previous epidemics of coronaviruses is the presence of pulmonary fibrosis that can be indicative of future pulmonary dysfunction if the patient recovers. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore abstract: Coronaviruses (CoVs) are important human and animal pathogens. There have been several outbreaks of lung involvement by this category of viruses in the world, ie, severe acute respiratory syndrome (SARS-CoV-1) in 2002 and 2003, the Middle East respiratory syndrome (MERS-CoV) in 2012, and the new coronavirus (2019-nCoV) outbreak of pneumonia from Wuhan, China, since December 2019. There have been several studies about the clinical features and imaging features, but very few reports have been published about pathologic findings in lung tissue, which was partly because of the lack of tissue diagnosis secondary to suddenness of the outbreak. Overall, less than 30 reports have been published in the literature about histologic findings of lung in these viruses, so far. In this report, we will review the published reports about the histopathologic findings of lung tissue in the patients infected with SARS-CoV-2 in comparison with 2 other coronaviruses that have caused outbreaks, ie, SARS-CoV-1 and MERS-CoV. url: https://doi.org/10.1177/2632010x20951823 doi: 10.1177/2632010x20951823 id: cord-330701-k68b0wqe author: Gerc, Vjekoslav title: Cardiovascular Diseases (CVDs) in COVID-19 Pandemic Era date: 2020-06-17 words: 5521.0 sentences: 282.0 pages: flesch: 48.0 cache: ./cache/cord-330701-k68b0wqe.txt txt: ./txt/cord-330701-k68b0wqe.txt summary: AIM: The aim of this study is to retreive published papers about COVID-19 infection deposited in PubMed data base and analyzed current results of investigations regarding morbidity and mortality rates as consequences of COVID-19 infection and opinions of experts about treatment of afected patients with COVID-19 who have Cardiovascular diseases (CVDs). COVID-19 infection is caused by a new beta-coronavirus, which the WHO has called (SARS-CoV-2) -Severe Acute Respiratory Syndrome. Initially, the main complications of COVID-19 were thought to be lung-related, then it was quickly observed that COVID-19 is attacking many organs, including the heart muscle, vascular endothelium and the cardiovascular system in general, increasing morbidity and mortality, especially in patients with other cardiovascular risk factors presented (hypertension, diabetes, obesity, cerebrovascular and renal disease). In Wuhan, according to reports of Chinese physicians, in patients infected with COVID-19 and with acute coronary syndrome, the complete clinical picture was very severe and associated with high mortality (9) . abstract: INTRODUCTION: COVID-19 is the disease caused by an infection of the SARS-CoV-2 virus, previously known as 2019 Novel Coronavirus (2019-nCoV) respiratory disease. World Health Organization (WHO) declared the official name as COVID-19 in February 2020 and in 11(th) March 2020 declared COVID-19 as Global Pandemic. In June 6(th) 2020, over 7 million cases registered in the world, recovered 3.4 million and death over 402.000. AIM: The aim of this study is to retreive published papers about COVID-19 infection deposited in PubMed data base and analyzed current results of investigations regarding morbidity and mortality rates as consequences of COVID-19 infection and opinions of experts about treatment of afected patients with COVID-19 who have Cardiovascular diseases (CVDs). METHODS: It’s used method of descriptive analysis of the published papers with described studies about Corona virus connected with CVDs. RESULTS: After searching current scientific literature (on PubMed till today is deposited more than 1.000 papers about COVID-19 with consequences in almost every medical disciplines), we have acknowledged that till today not any Evidence Based Medicine (EBM) study in the world. Also, there are no unique proposed ways of treatments and drugs to protect patients, especially people over 65 years old, who are very risk group to be affected with COVID-19, including patients with CVDs. Vaccine against COVID-19 is already produced and being in phases of testing in praxis in treatment of COVID-19 at affected patients, but the opinions of experts and common people whole over the world about vaccination are full of controversis. CONCLUSION: Frequent hand washing, avoiding crowds and contact with sick people, and cleaning and disinfecting frequently touched surfaces can help prevent coronavirus infections are the main proposal of WHO experts in current Guidelines, artefacts stored on a web site. Those preventive measures at least can help to everybody, including also the patients who have evidenced CVDs in their histories of illness. Authors analyzed most important dilemmas about all aspects of CVDs, including etipathogenesis, treatment with current drugs and use of potential discovered vaccines against COVID-19 infection, described in scientific papers deposited in PubMed data base. url: https://www.ncbi.nlm.nih.gov/pubmed/32843866/ doi: 10.5455/msm.2020.32.158-164 id: cord-326888-0p8nctpy author: Gercina, Anne Caroline title: What is the best mouthrinse against Coronaviruses? date: 2020-08-13 words: 548.0 sentences: 49.0 pages: flesch: 42.0 cache: ./cache/cord-326888-0p8nctpy.txt txt: ./txt/cord-326888-0p8nctpy.txt summary: (1) Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post‐surgical infectious complications. The person-to-person transmission of SARS-CoV-2 may occur directly or indirectly through saliva, and a preoperational use of antimicrobial mouthwash is considered to reduce the number of oral microbes. 1 Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post-surgical infectious complications. All rights reserved Even assuming that 1% of hydrogen peroxide is the best alternative to prevent transmission during oral procedures, its use on postoperative does not seem to be necessary. The purpose of rinsing 1% hydrogen peroxide is to protect the professional from avoiding transmission during the procedure from patients already infected by SARS-CoV-2. Comparison of In Vitro Inactivation of SARS CoV-2 with Hydrogen Peroxide and Povidone-Iodine Oral Antiseptic Rinses abstract: The person‐to‐person transmission of SARS‐CoV‐2 may occur directly or indirectly through saliva, and a preoperational use of antimicrobial mouthwash is considered to reduce the number of oral microbes. (1) Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post‐surgical infectious complications. url: https://www.ncbi.nlm.nih.gov/pubmed/32837535/ doi: 10.1111/ors.12549 id: cord-290851-1e5e033r author: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 words: 2742.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-290851-1e5e033r.txt txt: ./txt/cord-290851-1e5e033r.txt summary: Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection abstract: Viruses enter the host cell by binding cellular receptors that allow appropriate delivery of the viral genome. Although the horizontal propagation of viruses feeds the continuous emergence of novel pathogenic viruses, the genetic variation of cellular receptors can represent a challenging barrier. The SARS coronavirus, henipaviruses and filoviruses are zoonotic RNA viruses that use bats as their reservoir. Their lethality for man has fostered extensive research both on the cellular receptors they use and their entry pathways. These studies have allowed new insights into the diversity of the molecular mechanisms underlying both virus entry and pathogenesis. url: https://doi.org/10.1016/j.coviro.2011.05.014 doi: 10.1016/j.coviro.2011.05.014 id: cord-318184-atlslk0e author: Germain, N. title: Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France date: 2020-09-11 words: 2380.0 sentences: 173.0 pages: flesch: 60.0 cache: ./cache/cord-318184-atlslk0e.txt txt: ./txt/cord-318184-atlslk0e.txt summary: We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. First identified in Wuhan (China), in early January 2020, the new severe acute respiratory syndrome virus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID19) , rapidly spread to other countries worldwide causing an unprecedented pandemic 1 . Taking into account the information available, the French Biomedicine Agency updated the guidance on SARS-CoV-2 transmission risk via donated organs and tissues on March 5, 2020 and recommended to exclude donors with symptoms suggestive of COVID-19 (fever, cough, etc.) and donors who had stayed or traveled to high risk regions within the prior 28 days, or . Archived blood specimens collected on the day of donation for donor screening of infectious diseases were retrospectively tested for SARS-CoV-2 antibodies (Fig.2 ). abstract: Background: The COVID-19 pandemic has altered organ and tissue donations as well as transplantation practices. SARS-CoV-2 serological tests could help in the selection of donors. We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. Methods: 235 tissue donors at the Lille Tissue bank between November 1, 2019 and March 16, 2020 were included. Archived serum samples were tested for SARS-CoV-2 antibodies using two FDA-approved kits. Results: Most donors were at higher risks for severe COVID-19 illness including age over 65 years (142/235) and/or presence of co-morbidities (141/235). According to the COVID-19 risk assessment of transmission, 183 out of 235 tissue donors presented with a low risk level and 52 donors with an intermediate risk level of donor derived infection. Four out of the 235 (1.7%) tested specimens were positive for anti-SARS-CoV-2 antibodies: 2 donors with anti-N protein IgG and 2 other donors with anti-S protein total Ig. None of them had both type of antibodies. Conclusion: Regarding the seroprevalence among tissue donors, we concluded that the transmission probability to recipient via tissue products was very low at the beginning of the outbreak. url: http://medrxiv.org/cgi/content/short/2020.09.11.20192518v1?rss=1 doi: 10.1101/2020.09.11.20192518 id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 words: 1794.0 sentences: 117.0 pages: flesch: 59.0 cache: ./cache/cord-341838-lkz8ro90.txt txt: ./txt/cord-341838-lkz8ro90.txt summary: The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. abstract: Little is known about the clinical outcomes of HIV patients infected with SARS-CoV-2. We describe 47 patients referred to our hospital between 21 February and 16 April 2020 with proven/probable COVID-19, 45 (96%) of whom fully recovered and two died. url: https://doi.org/10.1093/cid/ciaa579 doi: 10.1093/cid/ciaa579 id: cord-351224-jeedo5mc author: GeurtsvanKessel, Corine H. title: An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment date: 2020-07-06 words: 3046.0 sentences: 153.0 pages: flesch: 46.0 cache: ./cache/cord-351224-jeedo5mc.txt txt: ./txt/cord-351224-jeedo5mc.txt summary: The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. Despite the differences in sensitivity, all laboratory assays had sufficient positive predictive value (PPV) in COVID-19 hospitalized patients when assuming an expected seroprevalence in this population of ≥50% (Table 1) , or when using serology as an adjunct to RT-PCR testing to monitor the clinical course of illness. To determine specificity of the assays, we used a well-defined panel of 147 serum and plasma samples from 147 individuals exposed to human coronaviruses (HCoV-229E, NL63 or OC43), SARS, MERS), or with a range of other respiratory viruses ( Sensitivity was calculated by using a total of 187 sera from 107 individuals in the Netherlands, in whom COVID-19 was confirmed by RT-PCR and antibodies were detected by PRNT50. abstract: The world is entering a new era of the COVID-19 pandemic in which there is an increasing call for reliable antibody testing. To support decision making on the deployment of serology for either population screening or diagnostics, we present a detailed comparison of serological COVID-19 assays. We show that among the selected assays there is a wide diversity in assay performance in different scenarios and when correlated to virus neutralizing antibodies. The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. The large variety of available serological assays requires proper assay validation before deciding on deployment of assays for specific applications. url: https://doi.org/10.1038/s41467-020-17317-y doi: 10.1038/s41467-020-17317-y id: cord-320535-fo4lzcav author: Geyer, Howard L. title: Movement Disorders in COVID-19: Whither Art Thou? date: 2020-08-12 words: 1662.0 sentences: 86.0 pages: flesch: 37.0 cache: ./cache/cord-320535-fo4lzcav.txt txt: ./txt/cord-320535-fo4lzcav.txt summary: The paucity of movement disorders associated with COVID-19 is particularly striking when contrasted with the neurologic syndrome which affected over a million people worldwide in the aftermath of the 1918 "Spanish" influenza, termed by Constanin von Economo encephalitis lethargica. That encephalitis was associated with a wide range of movement disorders, of which post-encephalitic parkinsonism is the best known, although other manifestations in the acute phase included dystonia, tremor, chorea, myoclonus, and oculomasticatory myorhythmia [6, 7] . Although encephalitis has been described as a cardinal neurological manifestation of COVID-19 during the acute phase of illness [8, 9] , we have yet to encounter any of these associated movement disorder presentations. (In the time since this write-up was first prepared, patients with acute movement disorders and COVID-19 have been reported exiguously; we know of four such reports, which describe myoclonus [10, 11] , a hypokinetic-rigid syndrome [12] , and tremor/ataxia [13] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32864184/ doi: 10.5334/tohm.553 id: cord-292274-upwn9o2m author: Ghaffari, Abdi title: COVID-19 Serological Tests: How Well Do They Actually Perform? date: 2020-07-04 words: 4648.0 sentences: 244.0 pages: flesch: 44.0 cache: ./cache/cord-292274-upwn9o2m.txt txt: ./txt/cord-292274-upwn9o2m.txt summary: While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . Typically, RDT test strips use a drop of blood to detect the presence of patient antibodies (IgG, IgM, or IgA) produced against a specific SARS-CoV-2 antigen ( Figure 2 ). Critics point to gaps in our understanding of immune response to COVID-19 infection, including the ability of serological tests to detect neutralizing antibodies and the capacity of the immune system to provide long-term immunity against SARS-CoV-2. abstract: In only a few months after initial discovery in Wuhan, China, SARS-CoV-2 and the associated coronavirus disease 2019 (COVID-19) have become a global pandemic causing significant mortality and morbidity and implementation of strict isolation measures. In the absence of vaccines and effective therapeutics, reliable serological testing must be a key element of public health policy to control further spread of the disease and gradually remove quarantine measures. Serological diagnostic tests are being increasingly used to provide a broader understanding of COVID-19 incidence and to assess immunity status in the population. However, there are discrepancies between claimed and actual performance data for serological diagnostic tests on the market. In this study, we conducted a review of independent studies evaluating the performance of SARS-CoV-2 serological tests. We found significant variability in the accuracy of marketed tests and highlight several lab-based and point-of-care rapid serological tests with high levels of performance. The findings of this review highlight the need for ongoing independent evaluations of commercialized COVID-19 diagnostic tests. url: https://www.ncbi.nlm.nih.gov/pubmed/32635444/ doi: 10.3390/diagnostics10070453 id: cord-325473-hrdanbn1 author: Ghahremanpour, Mohammad M. title: Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date: 2020-08-28 words: 2915.0 sentences: 205.0 pages: flesch: 56.0 cache: ./cache/cord-325473-hrdanbn1.txt txt: ./txt/cord-325473-hrdanbn1.txt summary: 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 5 Thus, M pro is viewed as a promising target for anti SARS-CoV-2 drug design; it has been the focus of several studies since the pandemic has emerged. For instance, a molecular docking study suggested remdesivir as a potential therapeutic that could be used against SARS-CoV-2, 10 which was supported experimentally by an EC50 value of 23 μM in an infected-cell assay. Structural Basis for the Inhibition of SARS-CoV-2 Main Protease by Antineoplastic Drug Carmofur Crystal Structure of SARS-CoV-2 Main Protease Provides a Basis for Design of Improved α-Ketoamide Inhibitors Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition Structure-based Design of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease Targeting the SARS-CoV-2 Main Protease to Repurpose Drugs for abstract: A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 42 drugs emerged as top candidates, and after visual analyses of the predicted structures of their complexes with Mpro, 17 were chosen for evaluation in a kinetic assay for Mpro inhibition. Remarkably 14 of the compounds at 100-μM concentration were found to reduce the enzymatic activity and 5 provided IC50 values below 40 μM: manidipine (4.8 μM), boceprevir (5.4 μM), lercanidipine (16.2 μM), bedaquiline (18.7 μM), and efonidipine (38.5 μM). Structural analyses reveal a common cloverleaf pattern for the binding of the active compounds to the P1, P1’, and P2 pockets of Mpro. Further study of the most active compounds in the context of COVID-19 therapy is warranted, while all of the active compounds may provide a foundation for lead optimization to deliver valuable chemotherapeutics to combat the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32869018/ doi: 10.1101/2020.08.28.271957 id: cord-332065-afq26621 author: Ghanchi, Hammad title: Racial Disparity Amongst Stroke Patients During the Coronavirus Disease 2019 Pandemic date: 2020-09-10 words: 2855.0 sentences: 151.0 pages: flesch: 46.0 cache: ./cache/cord-332065-afq26621.txt txt: ./txt/cord-332065-afq26621.txt summary: The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting with stroke during the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A statistically significant increase in the number of Black and Hispanic patients presenting with strokes was noted in California, Pacific hospitals, Western hospitals, and all hospitals in the United States during various months studied comparing 2020 to 2019. Given the recent pandemic and racial disparity among patients afflicted with SARS-CoV-2 and the possible link of this virus and cerebrovascular accidents (CVA), we sought to analyze whether there was a disparity for stroke patients presenting to hospitals during this time using the Get with the Guidelines (GWTG) National Stroke Database. The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting to our institution with stroke during the COVID-19 pandemic caused by SARS-CoV-2. abstract: Introduction The global coronavirus disease 2019 (COVID-19) pandemic has had deleterious effects on our healthcare system. Lockdown measures have decreased the number of patients presenting to the hospital for non-respiratory illnesses, such as strokes. Moreover, there appears to be a racial disparity among those afflicted with the virus. We sought to assess whether this disparity also existed for patients presenting with strokes. Methods The Get with the Guidelines National Stroke Database was reviewed to assess patients presenting with a final diagnosis of ischemic stroke, transient ischemic attack (TIA), subarachnoid hemorrhage (SAH), or spontaneous/nontraumatic intraparenchymal hemorrhage (IPH). The period of February - May 2020 was chosen given the surge of patients affected with the virus and national shutdowns. Data from this same time during 2019 was used as the control population. Our hospital numbers and four additional regions were assessed (California hospitals, Pacific State hospitals, Western Region hospitals, and all hospitals in the United States). Patients were categorized by race (White, Black/African American, Asian, Native American, Hispanic) in each cohort. The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting with stroke during the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results A downward trend in total number of patients was noted in all five regional cohorts assessed. A statistically significant increase in the number of Black and Hispanic patients presenting with strokes was noted in California, Pacific hospitals, Western hospitals, and all hospitals in the United States during various months studied comparing 2020 to 2019. A statistically significant increase in the Hispanic population was noted in February and March in all California hospitals (p=0.005 and 0.02, respectively) and Pacific Coast hospitals (p=0.005 and 0.039, respectively). The Western region and all national hospitals noted a significant increase in strokes in the Hispanic population in April (p=0.039 and 0.023, respectively). A statistically significant increase of strokes in the Black population was noted in April in Pacific hospitals, Western region hospitals, and all national hospitals (p=0.039, 0.03, and 0.03, respectively). Conclusion The COVID-19 pandemic has adversely affected certain racial groups more than others. A similar increase is noted in patients presenting with strokes in these specific racial populations. Moreover, lack of testing for the SARS-CoV-2 virus may be missing a possible link between racial disparity for patients infected with the virus and patients presenting with stroke. The authors advocate for widespread testing for all patients to further assess this correlation. url: https://doi.org/10.7759/cureus.10369 doi: 10.7759/cureus.10369 id: cord-351896-j6h02ab5 author: Ghannam, Malik title: Neurological involvement of coronavirus disease 2019: a systematic review date: 2020-06-19 words: 5060.0 sentences: 271.0 pages: flesch: 40.0 cache: ./cache/cord-351896-j6h02ab5.txt txt: ./txt/cord-351896-j6h02ab5.txt summary: The following search strategy was implemented and these keywords and their synonyms (in the all fields) were combined in each database as follows: ("COVID 19" OR "coronavirus") AND ("brain" OR "CNS" OR "spinal cord" OR "nerve" OR "neurologic" OR "stroke" OR "cerebrovascular" OR "cerebral vein thrombosis" OR "sinus thrombosis" OR "Intracerebral hemorrhage" OR "hemorrhage" OR "myelitis" OR "GBS" OR "Guillain Barre syndrome" OR "neuropathy" OR "radiculopathy" OR "cranial neuropathy" OR "myopathy" OR "myositis" OR "rhabdomyolysis" OR "encephalitis" OR "encephalopathy" OR "meningitis" OR "meningoencephalitis" OR "seizure" OR "convulsion" OR "epilepsy") [ Fig. 1 ]. [11] For each study, the following descriptive, microbiological, and clinical information was extracted: patient demographic data, SARS-CoV-2 testing from nasal swab and CSF, neurological symptoms and signs and their onset in relation to respiratory or gastrointestinal (GI) symptoms or anosmia or dysgeusia, any neurological investigations and CSF or any other relevant laboratory testing (such as CK, LDH, CRP, D-dimer, lupus anticoagulant, fibrinogen, ganglioside antibodies), neurological diagnosis, occurrence of respiratory failure (defined as need for intubation, abnormal PO2 in blood gas, or Glasgow Coma Scale score less than or equal 8), treatments administered for the neurological diagnosis, and final outcome. abstract: BACKGROUND: In December 2019, unexplained cases of pneumonia emerged in Wuhan, China, which were found to be secondary to the novel coronavirus SARS-CoV-2. On March 11, 2020, the WHO declared the Coronavirus Disease 2019 (COVID-2019) outbreak, a pandemic. OBJECTIVE: To clarify the neurological complications of SARS-CoV-2 infection including the potential mechanisms and therapeutic options. METHODS: We conducted a systematic literature search from December 01, 2019 to May 14, 2020 using multiple combinations of keywords from PubMed and Ovid Medline databases according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We included articles with cases of COVID-19 where neurological involvement was evident. RESULTS: We were able to identify 82 cases of COVID-19 with neurological complications. The mean age was 62.3 years. 37.8% of the patients were women (n = 31). 48.8% of the patients (n = 40) had cerebrovascular insults, 28% (n = 23) had neuromuscular disorders, and 23% of the patients (n = 19) had encephalitis or encephalopathy. CONCLUSIONS: Neurological manifestations of COVID-19 are not rare, especially large vessel stroke, Guillain–Barre syndrome, and meningoencephalitis. Moving forward, further studies are needed to clarify the prevalence of the neurological complications of SARS-CoV-2 infection, investigate their biological backgrounds, and test treatment options. Physicians should be cautious not to overlook other neurological diagnoses that can mimic COVID-19 during the pandemic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00415-020-09990-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32561990/ doi: 10.1007/s00415-020-09990-2 id: cord-285426-iyl12ber author: Ghavami, Shaghayegh Baradaran title: IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date: 2020-09-08 words: 1967.0 sentences: 111.0 pages: flesch: 47.0 cache: ./cache/cord-285426-iyl12ber.txt txt: ./txt/cord-285426-iyl12ber.txt summary: Interestingly, in the recent pandemic of coronavirus disease (COVID19) , and the SARS-CoV epidemic in 2003, while the fecal samples of these patients were positive for the virus, they did not present any severe respiratory distress syndrome (4). Remarkably, the angiotensin-converting enzyme-2 (ACE2) is the receptor for SARS-CoV-2 and it is expressed in different organs including the lungs, testis and ileum. showed that when rheumatoid arthritis patients were treated with anti-TNF-α biologicals (infliximab, adalimumab, and certolizumab pegol), the expression of IFN-α-regulated genes was increased in the peripheral blood mononuclear cell (PBMC) compared to the control group. Besides, in IBD patients, particularly those who are under anti-TNF-α treatment, the host innate immune system interferes more efficiently with viral replication cycle and the clinical presentations are more moderate (9, 12) . Are patients with inflammatory bowel disease at increased risk for Covid-19 infection? abstract: Inflammatory bowel diseases (IBDs) are chronic disorders of the gastrointestinal tract. The goal of IBD treatment is to reduce the inflammation period and induce long-term remission. Use of anti-inflammatory drugs including corticosteroids, immunosuppressants and biologicals, is often the first step in the treatment of IBD. Therefore, IBD patients in pandemic of infectious diseases are considered a high-risk group. The public believes that IBD patients are at a higher risk in the current coronavirus 2 pandemic. Nevertheless, these patients may experience mild or moderate complications compared to healthy people. This might be because of particular anti-TNF-α treatment or any immunosuppressant that IBD patients receive. Moreover, these patients might be silent carrier for the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32779446/ doi: 10.22074/cellj.2020.7603 id: cord-218639-ewkche9r author: Ghavasieh, Arsham title: Multiscale statistical physics of the Human-SARS-CoV-2 interactome date: 2020-08-21 words: 3175.0 sentences: 184.0 pages: flesch: 48.0 cache: ./cache/cord-218639-ewkche9r.txt txt: ./txt/cord-218639-ewkche9r.txt summary: Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing strategies. Similarly, they have been used for characterizing the interactions between viral and human proteins in case of SARS-CoV-2 [13] [14] [15] , providing insights into the structure and function of the virus 16 and identifying drug repurposing strategies 17, 18 . Instead, we model the propagation of perturbations from viral nodes through the whole system, using bio-chemical and regulatory dynamics, to obtain the spreading patterns and compare the average impact of viruses on human proteins. Our results shed light on the unexplored aspects of SARS-CoV-2, from the perspective of statistical physics of complex networks, and the presented framework opens the doors for further theoretical developments aiming to characterize structure and dynamics of virus-host interactions, as well as grounds for further experimental investigation and potentially novel clinical treatments. abstract: Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing strategies. However, our knowledge of (dis)similarities between this one and other viral agents is still very limited. Here we compare the novel coronavirus PPI network against 45 known viruses, from the perspective of statistical physics. Our results show that classic analysis such as percolation is not sensitive to the distinguishing features of viruses, whereas the analysis of biochemical spreading patterns allows us to meaningfully categorize the viruses and quantitatively compare their impact on human proteins. Remarkably, when Gibbsian-like density matrices are used to represent each system's state, the corresponding macroscopic statistical properties measured by the spectral entropy reveals the existence of clusters of viruses at multiple scales. Overall, our results indicate that SARS-CoV-2 exhibits similarities to viruses like SARS-CoV and Influenza A at small scales, while at larger scales it exhibits more similarities to viruses such as HIV1 and HTLV1. url: https://arxiv.org/pdf/2008.09649v1.pdf doi: nan id: cord-344012-npob20n0 author: Gheblawi, Mahmoud title: Angiotensin-Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System: Celebrating the 20th Anniversary of the Discovery of ACE2 date: 2020-05-08 words: 10479.0 sentences: 569.0 pages: flesch: 39.0 cache: ./cache/cord-344012-npob20n0.txt txt: ./txt/cord-344012-npob20n0.txt summary: ACE2 (angiotensin-converting enzyme 2) has a multiplicity of physiological roles that revolve around its trivalent function: a negative regulator of the renin-angiotensin system, facilitator of amino acid transport, and the severe acute respiratory syndrome-coronavirus (SARS-CoV) and SARS-CoV-2 receptor. Our review summarizes the progress over the past 20 years, highlighting the critical role of ACE2 as the novel SARS-CoV-2 receptor and as the negative regulator of the renin-angiotensin system, together with implications for the coronavirus disease 2019 pandemic and associated cardiovascular diseases. 21, 22 Ongoing global efforts are focused on manipulating the ACE2/Ang 1-7 axis to curtail SARS-CoV-2 infection while affording maximal protective effects against lung and cardiovascular damage in patients with In this review, we summarize the diverse roles of ACE2, highlighting its role as the SARS-CoV-2 receptor and negative regulator of the RAS, and the implications for the COVID-19 pandemic. abstract: ACE2 (angiotensin-converting enzyme 2) has a multiplicity of physiological roles that revolve around its trivalent function: a negative regulator of the renin-angiotensin system, facilitator of amino acid transport, and the severe acute respiratory syndrome-coronavirus (SARS-CoV) and SARS-CoV-2 receptor. ACE2 is widely expressed, including, in the lungs, cardiovascular system, gut, kidneys, central nervous system, and adipose tissue. ACE2 has recently been identified as the SARS-CoV-2 receptor, the infective agent responsible for coronavirus disease 2019, providing a critical link between immunity, inflammation, ACE2, and cardiovascular disease. Although sharing a close evolutionary relationship with SARS-CoV, the receptor-binding domain of SARS-CoV-2 differs in several key amino acid residues, allowing for stronger binding affinity with the human ACE2 receptor, which may account for the greater pathogenicity of SARS-CoV-2. The loss of ACE2 function following binding by SARS-CoV-2 is driven by endocytosis and activation of proteolytic cleavage and processing. The ACE2 system is a critical protective pathway against heart failure with reduced and preserved ejection fraction including, myocardial infarction and hypertension, and against lung disease and diabetes mellitus. The control of gut dysbiosis and vascular permeability by ACE2 has emerged as an essential mechanism of pulmonary hypertension and diabetic cardiovascular complications. Recombinant ACE2, gene-delivery of Ace2, Ang 1–7 analogs, and Mas receptor agonists enhance ACE2 action and serve as potential therapies for disease conditions associated with an activated renin-angiotensin system. rhACE2 (recombinant human ACE2) has completed clinical trials and efficiently lowered or increased plasma angiotensin II and angiotensin 1-7 levels, respectively. Our review summarizes the progress over the past 20 years, highlighting the critical role of ACE2 as the novel SARS-CoV-2 receptor and as the negative regulator of the renin-angiotensin system, together with implications for the coronavirus disease 2019 pandemic and associated cardiovascular diseases. url: https://doi.org/10.1161/circresaha.120.317015 doi: 10.1161/circresaha.120.317015 id: cord-341000-9xs8aukq author: Ghiasvand, Fereshteh title: Symmetrical polyneuropathy in Coronavirus Disease 2019 (COVID-19) date: 2020-05-15 words: 1425.0 sentences: 96.0 pages: flesch: 42.0 cache: ./cache/cord-341000-9xs8aukq.txt txt: ./txt/cord-341000-9xs8aukq.txt summary: The knowledge around the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still evolving with the cases increasing globally. A case series presented data of four Severe Acute Respiratory Syndrome (SARS) patients who developed polyneuropathy, myopathy, or both approximately three weeks after the onset of SARS with a probable diagnosis of critical-illness polyneuropathy (CIP) and/or critical-illness myopathy (CIM) [9] . A case of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported with developing weakness and numbness in lower limbs and inability to walk with a likely diagnosis of critical illness polyneuropathy (CIP) [10] . Since no symptoms were present before the development of COVID-19 and toxic neuropathy was excluded after a review of all her medications, critical illness polyneuropathy (CIP) and Guillain-Barré syndrome (GBS) were considered to be the J o u r n a l P r e -p r o o f most likely diagnosis. abstract: The outbreak of the novel coronavirus that began in late December 2019 was announced as a pandemic by the World Health Organization as the number of cases is increasing exponentially throughout the globe. We present a patient with confirmed SARS-CoV-2 pneumonia developing symmetric polyneuropathy. To our knowledge, extrapulmonary clinical presentations of 2019 novel coronavirus disease (COVID-19) have rarely been reported. This case highlights the possible association between SARS-CoV-2 infection and nervous system involvement. url: https://api.elsevier.com/content/article/pii/S2214250920301232 doi: 10.1016/j.idcr.2020.e00815 id: cord-287172-h8zoplkm author: Ghobrial, Moheb title: The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date: 2020-10-21 words: 7020.0 sentences: 315.0 pages: flesch: 55.0 cache: ./cache/cord-287172-h8zoplkm.txt txt: ./txt/cord-287172-h8zoplkm.txt summary: To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. Notably, the top regulated pathways included inflammation, angiogenesis, coagulation, cell-extracellular matrix interaction, viral-host interaction, vascular metabolism, blood-brain-barrier permeability, and reactive oxygen species (ROS) in both the adult and the fetal brain endothelium ( Together, these data reveal that CTSB is highly expressed in various endothelial cell clusters of the fetal and adult human brain and that pathways downstream of CTSB might provide a suggestive explanation of some of the neurovascular symptoms observed in COVID-19 abstract: A large number of hospitalized COVID-19 patients show neurological symptoms such as ischemic- and hemorrhagic stroke as well as encephalitis, and SARS-CoV-2 can directly infect endothelial cells leading to endotheliitis across multiple vascular beds. These findings suggest an involvement of the brain- and peripheral vasculature in COVID-19, but the underlying molecular mechanisms remain obscure. To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. We observed a distinct expression pattern of the cathepsins B (CTSB) and -L (CTSL) - which are able to substitute for the ACE2 co-receptor TMPRSS2 - in the human vasculature with CTSB being mainly expressed in the brain vasculature and CTSL predominantly in the peripheral vasculature, and these observations were confirmed at the protein level in the Human Protein Atlas and using immunofluorescence stainings. This expression pattern of SARS-CoV-2 viral-entry associated proteases and SARS-CoV-2 interaction partners was also present in endothelial cells and microglia in the fetal brain, suggesting a developmentally established SARS-CoV-2 entry machinery in the human vasculature. At both the adult and fetal stages, we detected a distinct pattern of SARS-CoV-2 entry associated genes’ transcripts in brain vascular endothelial cells and microglia, providing a potential explanation for an inflammatory response in the brain endothelium upon SARS-CoV-2 infection. Moreover, CTSB was co-expressed in adult and fetal brain endothelial cells with genes and pathways involved in innate immunity and inflammation, angiogenesis, blood-brain-barrier permeability, vascular metabolism, and coagulation, providing a potential explanation for the role of brain endothelial cells in clinically observed (neuro)vascular symptoms in COVID-19 patients. Our study serves as a publicly available single-cell atlas of SARS-CoV-2 related entry factors and interaction partners in human and mouse brain endothelial- and perivascular cells, which can be employed for future studies in clinical samples of COVID-19 patients. url: https://doi.org/10.1101/2020.10.10.334664 doi: 10.1101/2020.10.10.334664 id: cord-310230-9wfb43gt author: Ghorbani, Mahdi title: Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date: 2020-06-27 words: 3479.0 sentences: 220.0 pages: flesch: 56.0 cache: ./cache/cord-310230-9wfb43gt.txt txt: ./txt/cord-310230-9wfb43gt.txt summary: Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body. The focus of this article is to elucidate the differences between the interface of SARS-COV and nCOV-2019 with ACE2 to understand with atomic resolution the interaction mechanism and hotspot residues at the RBD/ACE2 interface using long-timescale molecular dynamics (MD) simulation. The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019 and all its mutant complexes were investigated by the MMPBSA method. Computational Simulations Reveal the Binding Dynamics between Human ACE2 and the Receptor Binding Domain of SARS-CoV-2 Spike Protein abstract: The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion’s surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious. url: https://www.ncbi.nlm.nih.gov/pubmed/32637962/ doi: 10.1101/2020.06.27.175448 id: cord-344064-l3u4l3se author: Ghosh, Rajesh title: Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves date: 2020-11-03 words: 8644.0 sentences: 453.0 pages: flesch: 51.0 cache: ./cache/cord-344064-l3u4l3se.txt txt: ./txt/cord-344064-l3u4l3se.txt summary: Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. The leaves of the traditional medicinal plant Torreya nucifera contains eight well-known diterpenoids (18-hydroxyferruginol, hinokiol, ferruginol, 18-oxoferruginol, O-acetyl-18hydroxyferruginol, methyl dehydroabietate, isopimaric acid, kayadiol) and four biflavonoids (amentoflavone, bilobetin, ginkgetin, sciadopitysin) ( Figure 1 ) (Ryu et al., 2010) . Overall, molecular docking studies clearly revealed that selected three biflavonoids (amentoflavone, bilobetin and ginkgetin) interacted with two key residues (His41 and Cys145) of Mpro via alkyl bond(s) interactions ( Figure 2 ). Overall, this study showed that three important biflavonoids of Torreya nucifera leaves (amentoflavone, bilobetin and ginkgetin) can act as SARS CoV-2 Mpro inhibitors. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study abstract: SARS CoV-2 is the causative agent of the pandemic disease COVID-19. There is an urgent need for effective drugs or vaccines which can effectively combat this outbreak. The main protease (Mpro), a key component for the SARS CoV-2 replication, is considered to be one of the important drug targets for developing anti-COVID-19 drugs. This SARS CoV-2 Mpro/cysteine protease has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight diterpenoids and four biflavonoids derived from the leaf of Torreya nucifera show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these phytochemicals exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To understand this fact, here, we have adopted various in-silico approaches. Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. Only three biflavonoids (amentoflavone, bilobetin and ginkgetin) were selected by comparing their binding affinities with N3 and lopinavir. They interacted with two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these three Mpro-biflavonoid complexes are highly stable and share a similar degree of compactness. Besides, these complexes experience less conformational fluctuations and more expansion than Mpro-N3 and/or Mpro-lopinavir complex. MM-GBSA and H-bond analysis further corroborated these findings. Altogether, our study suggested that these three biflavonoids could possibly inhibit the proteolytic/catalytic activity of SARS CoV-2 Mpro and might be useful for COVID-19 treatment. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33140695/ doi: 10.1080/07391102.2020.1841680 id: cord-315388-8sv00zqz author: Ghosh, Ritwik title: Famotidine against SARS-CoV2: A hope or hype? date: 2020-06-06 words: 1097.0 sentences: 65.0 pages: flesch: 40.0 cache: ./cache/cord-315388-8sv00zqz.txt txt: ./txt/cord-315388-8sv00zqz.txt summary: In the absence of a specific anti-viral or vaccine against the novel severe acute respiratory syndrome-corona virus (SARS-CoV2), "repurposing" of old time-tested medications are being tried. Through binding with H 2 R and modulating the effector pathways mediated by protein kinase A (PKA), famotidine potentially regulates innate and adaptive immune responses. Comparison of immunomodulative effects of the histamine-2 receptor antagonists cimetidine, ranitidine, and famotidine on peripheral blood mononuclear cells in gastric cancer patients Histamine Receptor 2 is Required to Suppress Innate Immune Responses to Bacterial Ligands in Patients with Inflammatory Bowel Disease The effect of histamine type 2 receptor antagonists on human immunodeficiency virus (HIV) replication: identification of a new class of antiviral agents A placebocontrolled trial of ranitidine in patients with early human immunodeficiency virus infection Effects of the H2-receptor antagonist famotidine on the pharmacokinetics of atazanavir-ritonavir with or without tenofovir in HIV-infected patients abstract: nan url: https://api.elsevier.com/content/article/pii/S0025619620305437 doi: 10.1016/j.mayocp.2020.05.027 id: cord-347104-h168kqjn author: Ghosh, Ritwik title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection date: 2020-11-11 words: 2596.0 sentences: 184.0 pages: flesch: 38.0 cache: ./cache/cord-347104-h168kqjn.txt txt: ./txt/cord-347104-h168kqjn.txt summary: title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection J o u r n a l P r e -p r o o f It has recently reported a case of a young man presenting with bilateral severe optic neuritis and myelitis, determined to be simultaneously SARS-CoV-2 and MOG IgG antibody positive, i.e. a variant of NMOSD. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. abstract: Neuromyelitis optica spectrum disorder (NMOSD) is a disabling autoimmune astrocytopathic channelopathy, characterized by the presence of pathogenic antibodies to aquaporin-4 (AQP-4) water channels. Several viral infections including HIV, influenza virus, varicella zoster virus, and Epstein Barr virus, among others, have been alleged to trigger NMOSD in both immunocompetent and immunocompromised individuals. Neurological manifestations of coronavirus infectious disease of 2019 (COVID-19) have been ever evolving and the spectrum of neuraxial involvement is broadening. Albeit it may affect any area of the neural axis, the involvement of the spinal cord is rare compared to that of the brain and of the peripheral nervous system. Cases with acute longitudinally extensive transverse myelitis (LETM) have been recently reported in SARS-CoV-2 infection but did not fulfill the international consensus diagnostic criteria for NMOSD. AQP-4-antibody-seropositive NMOSD following SARS-CoV-2 infection had not yet been reported. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. He was finally diagnosed to be a case of seropositive NMOSD which presented as area postrema syndrome. The response to immunomodulatory drugs was excellent. url: https://www.sciencedirect.com/science/article/pii/S0165572820307001?v=s5 doi: 10.1016/j.jneuroim.2020.577439 id: cord-336561-llwjsds8 author: Ghosh, Sanhita title: siRNA could be a potential therapy for COVID-19 date: 2020-04-22 words: 743.0 sentences: 51.0 pages: flesch: 60.0 cache: ./cache/cord-336561-llwjsds8.txt txt: ./txt/cord-336561-llwjsds8.txt summary: Thus, the sequence coding for nsp5 can be treated as a potential target for RNAi using siRNA based therapeutics. Further, Alnylam Pharmaceuticals (USA) has designed and synthesized over 350 siRNA targeting highly conserved regions of the available SARS-CoV-2 genome (Hodgson, 2020) . In this context, Conti and co-researchers have demonstrated an in vitro testing of poly (amidoamine) dendrimer nanocarriers for the potential aerosol-based delivery system of siRNA onto lung epithelial cells (Conti et al., 2014) . Thus, for the treatment of COVID-19 siRNA based therapy can be developed against the novel coronavirus SARS-CoV-2, where siRNAs can hit the highly conserved region of SARS-CoV-2 RNA and also can act as an inhibitor to suppress the genetic disorders of the lungs. The cytopathic effect (CPE) was observed in Vero cells when it was infected with SARS and reduced the CPE after siRNA treatment. Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32398976/ doi: 10.17179/excli2020-1328 id: cord-304584-jxha3rz8 author: Giacomo, Di title: SARS-COV-2 infection in cancer patients undergoing checkpoint blockade: clinical course and outcome date: 2020-05-03 words: 425.0 sentences: 35.0 pages: flesch: 51.0 cache: ./cache/cord-304584-jxha3rz8.txt txt: ./txt/cord-304584-jxha3rz8.txt summary: The potential interplay between Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) infection and treatment with immune-checkpoint inhibitors (ICI) of cancer patients is presently unknown. Two subsequent swabs tested negative on April 3 and 4 for SARS-CoV-2 infection ( Figure 1) ; thus, the patient was considered cured from COVID-19 and she will resume ICI-therapy shortly. Undoubtedly, no general conclusion can be drawn from the positive outcome of these two patients on the reciprocal interplay between ICI therapy and SARS-CoV-2 infection. Nevertheless, these findings seem to suggest that treatment with ICI is a doable approach during the COVID-19 pandemic, and that SARS-CoV-2 infection does not seem to represent an obstacle to grant cancer patients the best treatment according to their clinical setting. SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerasechain-reaction (rRT-PCR) testing positive (★) or negative (✪). SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerase-chainreaction (rRT-PCR) testing positive (★) or negative (✪). abstract: nan url: https://api.elsevier.com/content/article/pii/S095980492030229X doi: 10.1016/j.ejca.2020.04.026 id: cord-339436-0k73tlna author: Giagulli, Vito Angelo title: Worse progression of COVID‐19 in men: Is Testosterone a key factor? date: 2020-06-11 words: 7894.0 sentences: 520.0 pages: flesch: 40.0 cache: ./cache/cord-339436-0k73tlna.txt txt: ./txt/cord-339436-0k73tlna.txt summary: Considering that low serum T levels induce detrimental effects on cardiovascular system and predispose to impaired immune response, endothelial dysfunction and systemic inflammation, respectively 28 , herein, we will overview on possible putative mechanisms by which circulating T might affect the prognosis in men with COVID-19 (Table 1) . All rights reserved adipose tissue dysfunction and male hypogonadism, even if subclinical, are associated with higher circulating levels of cytokine (IL-6, IL-1 and TNF-alpha), endothelial dysfunction 163 , and amplified thrombosis risk, possibly prompting to detrimental clinical consequences in case of SARS-CoV-2 infection. It may affect baseline respiratory function, thus increasing the risk of mechanical ventilation requirement once the infection occurred; increase the number of baseline comorbidities, consequently predisposing to poor prognosis or death as certificated by epidemiological studies; fosters hormonal imbalance (decline in circulating serum T and increase in serum estrogen concentration) which are involved in the fine regulation of immune system and coagulative homeostasis in case of infection, and predispose men to poor effective immune response, cytokine dysregulation; endothelial dysfunction and thrombosis. abstract: BACKGROUND: The novel Severe Acute Respiratory Syndrome Coronavirus (SARS‐CoV‐2) disease 2019 (COVID‐19) seems to have a worse clinical course among infected men compared to women, thus, highlighting concerns about gender predisposition to serious prognosis. Therefore, androgens, particularly testosterone (T), could be suspected as playing a critical role in driving this excess of risk. However, gonadal function in critically ill men is actually unknown, mainly because serum T concentration is not routinely measured in clinical practice, even more in this clinical context. OBJECTIVE: To overview on possible mechanisms by which serum T levels could affect the progression of COVID‐19 in men. METHODS: Authors searched PubMed/Medline, Web of Science, EMBASE, Cochrane Library, Google, and Institutional websites for medical subheading terms and free text words referred to “SARS‐CoV‐2”, “COVID‐19”, “testosterone”, “male hypogonadism”, “gender” “immune system”, “obesity”, “thrombosis” until May 19(th) 2020. RESULTS: T, co‐regulating the expression of angiotensin‐converting enzyme 2 and transmembrane protease serine 2 in host cells, may facilitate SARS‐CoV‐2 internalization. Instead, low serum T levels may predispose to endothelial dysfunction, thrombosis and defective immune response, leading to both impaired viral clearance and systemic inflammation. Obesity, one of the leading causes of severe prognosis in infected patients, is strictly associated with functional hypogonadism, and may consistently strengthen the aforementioned alterations, ultimately predisposing to serious respiratory and systemic consequences. DISCUSSION AND CONCLUSION: T in comparison to estrogen may predispose men to a widespread COVID‐19 infection. Low serum levels of T, which should be supposed to characterize the hormonal milieu in seriously ill individuals, may predispose men, especially aged men, to poor prognosis or death. Further studies are needed to confirm these pathophysiological assumptions and to promptly identify adequate therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32524732/ doi: 10.1111/andr.12836 id: cord-329825-e9mepqvn author: Giamarellos-Bourboulis, Evangelos J. title: Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date: 2020-04-21 words: 3756.0 sentences: 177.0 pages: flesch: 47.0 cache: ./cache/cord-329825-e9mepqvn.txt txt: ./txt/cord-329825-e9mepqvn.txt summary: Immune responses of critically ill patients with sepsis can be classified into three patterns: macrophage-activation syndrome (MAS) (Kyriazopoulou et al., 2017) , sepsis-induced immunoparalysis characterized by low expression of the human leukocyte antigen D related (HLA-DR) on CD14 monocytes (Lukaszewicz et al., 2009) , and an intermediate functional state of the immune system lacking obvious dysregulation. Abbreviations are as follows: ALT, alanine aminotransferase; aPTT, activated partial thromboplastin time; AST, aspartate aminotransferase; APACHE, acute physiology and chronic health evaluation; CCI, Charlson''s comorbidity index; INR, international normalized ratio; PSI, pneumonia severity index; SD, standard deviation; SOFA, sequential organ failure assessment Immune classification of patients with SARS-CoV-2 was performed by using the tools suggested for bacterial sepsis, i.e., ferritin more than 4,420 ng/mL for MAS (Kyriazopoulou et al., 2017) , and HLA-DR molecules on CD14 monocytes lower than 5,000, in the absence of elevated ferritin, for the immune dysregulation phenotype (Lukaszewicz et al., 2009) . abstract: Proper management of COVID-19 mandates better understanding of disease pathogenesis. The sudden clinical deterioration 7–8 days after initial symptom onset suggests that severe respiratory failure (SRF) in COVID-19 is driven by a unique pattern of immune dysfunction. We studied immune responses of 54 COVID-19 patients, 28 of whom had SRF. All patients with SRF displayed either macrophage activation syndrome (MAS) or very low human leukocyte antigen D related (HLA-DR) expression accompanied by profound depletion of CD4 lymphocytes, CD19 lymphocytes, and natural killer (NK) cells. Tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) production by circulating monocytes was sustained, a pattern distinct from bacterial sepsis or influenza. SARS-CoV-2 patient plasma inhibited HLA-DR expression, and this was partially restored by the IL-6 blocker Tocilizumab; off-label Tocilizumab treatment of patients was accompanied by increase in circulating lymphocytes. Thus, the unique pattern of immune dysregulation in severe COVID-19 is characterized by IL-6-mediated low HLA-DR expression and lymphopenia, associated with sustained cytokine production and hyper-inflammation. url: https://api.elsevier.com/content/article/pii/S1931312820302365 doi: 10.1016/j.chom.2020.04.009 id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 words: 6678.0 sentences: 441.0 pages: flesch: 54.0 cache: ./cache/cord-269726-z0frgm7s.txt txt: ./txt/cord-269726-z0frgm7s.txt summary: Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . abstract: Can a patient diagnosed with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) be infected again? This question is still unsolved. We tried to analyze local and literature cases with a positive respiratory swab after recovery. We collected data from symptomatic patients diagnosed with SARS-CoV-2 infection in the Italian Umbria Region that, after recovery, were again positive for SARS-CoV-2 in respiratory tract specimens. Samples were also assessed for infectivity in vitro. A systematic review of similar cases reported in the literature was performed. The study population was composed of 9 patients during a 4-month study period. Among the new positive samples, six were inoculated in Vero-E6 cells and showed no growth and negative molecular test in culture supernatants. All patients were positive for IgG against SARS-CoV-2 nucleoprotein and/or S protein. Conducting a review of the literature, 1350 similar cases have been found. The presumptive reactivation occurred in 34.5 days on average (standard deviation, SD, 18.7 days) after COVID-19 onset, when the 5.6% of patients presented fever and the 27.6% symptoms. The outcome was favorable in 96.7% of patients, while the 1.1% of them were still hospitalized at the time of data collection and the 2.1% died. Several hypotheses have been formulated to explain new positive respiratory samples after confirmed negativity. According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo. url: https://doi.org/10.1007/s10096-020-04057-6 doi: 10.1007/s10096-020-04057-6 id: cord-311848-8n9ee57a author: Giesen, Nicola title: Evidence-based Management of COVID-19 in Cancer Patients – Guideline by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) date: 2020-09-21 words: 7678.0 sentences: 516.0 pages: flesch: 48.0 cache: ./cache/cord-311848-8n9ee57a.txt txt: ./txt/cord-311848-8n9ee57a.txt summary: It was prepared by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) by critically reviewing the currently available data on SARS-CoV-2 and COVID-19 in cancer patients applying evidence-based medicine criteria. We do not 285 recommend to delay/discontinue radiotherapy, targeted therapy, endocrine therapy or surgery in 286 cancer patients without suspected/confirmed SARS-CoV-2 infection (DII u ) as no impact on mortality 287 of such prior treatments was seen in several large cohort studies of 20, 31, 40, 94 288 In patients with COVID-19, it is strongly recommended to delay/discontinue chemotherapy, if 289 possible, as chemotherapy within two weeks of admission was a major risk factor for severe COVID-290 19 in a large Chinese cohort study (AII u ). Clinical characteristics and risk factors 38 associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, 39 retrospective, cohort study abstract: Since its first detection in China in late 2019 the novel coronavirus SARS-CoV-2 and the associated infectious disease COVID-19 continue to have a major impact on global health care and clinical practice. Cancer patients, in particular those with haematological malignancies, seem to be at an increased risk for a severe course of infection. Deliberations to avoid or defer potentially immunosuppressive therapies in these patients need to be balanced against the overarching goal of providing optimal antineoplastic treatment. This poses a unique challenge to treating physicians. This guideline provides evidence-based recommendations regarding prevention, diagnostics and treatment of SARS-CoV-2 infection and COVID-19 as well as strategies towards safe antineoplastic care during the COVID-19 pandemic. It was prepared by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) by critically reviewing the currently available data on SARS-CoV-2 and COVID-19 in cancer patients applying evidence-based medicine criteria. url: https://www.sciencedirect.com/science/article/pii/S0959804920304937?v=s5 doi: 10.1016/j.ejca.2020.09.009 id: cord-334278-ajdjfzd2 author: Gilis, M. title: Caractéristiques de la COVID-19 chez les patients âgés de 75 ans et plus, hospitalisés date: 2020-09-30 words: 2156.0 sentences: 222.0 pages: flesch: 75.0 cache: ./cache/cord-334278-ajdjfzd2.txt txt: ./txt/cord-334278-ajdjfzd2.txt summary: Matériels et méthodes Il s''agit d''une étude prospective observationnelle descriptive monocentrique incluant tous les patients hospitalisés, initialement hors réanimation, avec une COVID-19 confirmée par RT-PCR et/ou par imagerie scanographique entre le 3 mars et le 24 avril 2020. Conclusion Sur la période de mars 2020 alors que l''épidémie de SARS-CoV-2 a touché la France de plein fouet, les virus respiratoires classiques ont rapidement disparu tandis que la COVID-19 touchait plus du tiers des personnes consultant pour un syndrome grippal dans un centre de dépistage hospitalier francilien. Matériels et méthodes Dans notre hôpital, les soignants symptomatiques étaient systématiquement testés par une RT-PCR SARS-CoV2 sur frottis rhinopharyngé. Les soignants COVID avaient été plus souvent en contact avec un cas confirmé d''infection à SARS-CoV-2 (75 % vs 63 %, p < 0,001) mais n''étaient pas plus souvent affectés dans les unités COVID (16 % vs 12 %, p = 0,17). abstract: Introduction Les personnes âgées comptent parmi le groupe de population le plus touché et le plus à risque de développer une forme grave de la COVID-19. La symptomatologie est parfois frustrée et aspécifique dans cette population. L’objectif est de comparer les caractéristiques d’une population ≥75 ans hospitalisée pour une COVID-19 à celles d’une population<75 ans, en incluant la mortalité toute cause à 28jours du début des signes cliniques. Matériels et méthodes Il s’agit d’une étude prospective observationnelle descriptive monocentrique incluant tous les patients hospitalisés, initialement hors réanimation, avec une COVID-19 confirmée par RT-PCR et/ou par imagerie scanographique entre le 3 mars et le 24 avril 2020. Pour tous les patients, étaient recueillies de façon standardisée des variables démographiques, cliniques et paracliniques. Tous les patients ont eu un suivi clinique et/ou téléphonique jusqu’à j28 du début des signes cliniques. Les caractéristiques des patients de ≥75 ans sont comparées à celles des patients<75 ans (tests du Chi2 et exact de Fisher ; la valeur p <0,05 est considérée comme statistiquement significative). Résultats Ont été hospitalisés 436 patients (femmes : 196 [45 %] ; âge moyen : 69±18 ans ; patients ≥75 ans : 186 [43 %]). Le délai moyen entre le début des symptômes et l’hospitalisation était de 5,8±5jours. Le score moyen de Charlson était de 5,7 (±3). Cinquante-quatre patients (12 %) ont été transférés en réanimation (âge moyen : 67±18 ans). Soixante-dix-neuf patients sont décédés (18 %) dont 7 après leur transfert en réanimation. À l’admission, les patients ≥75 ans présentaient moins souvent des symptômes ORL (8 % vs 16 %, p <0,01), une toux (70 % vs 81 %, p <0,012) et une dyspnée (44 % vs 56 %, p =0,013). À noter qu’ils présentaient aucun signe respiratoire dans 11 % des cas vs dans 5,6 % chez les plus jeunes (p =0,047). Une chute les jours précédant l’hospitalisation, un syndrome confusionnel et une atteinte digestive fébrile étaient plus souvent retrouvés chez les patients ≥75 ans (respectivement, 22 % vs 4 %, p <0,001 ; 19 % vs 5 %, p <0,001 et 6 % vs 2 %, p =0,015). Les transferts en réanimation étaient moins fréquents chez les patients ≥75 ans (6 % vs 18 %, p <0,001), la mortalité toute cause à 28jours y est en revanche plus élevée (30 % vs 8 %, p <0,001). Conclusion Comparés aux<75 ans, les patients ≥75 ans ont moins souvent des symptômes respiratoires et plus souvent des symptômes classiquement retrouvés dans la population gériatrique, quelle que soit l’étiologie : chute, confusion et troubles digestifs. En période d’épidémie, il est important de prendre en compte ces spécificités gériatriques afin de mettre en place les précautions complémentaires adaptées et de réaliser un test diagnostique du virus SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0399077X2030295X doi: 10.1016/j.medmal.2020.06.131 id: cord-334735-up81jotp author: Gillissen, Adrian title: Das schwere akute Atemwegssyndrom (SARS) date: 2003 words: 1298.0 sentences: 139.0 pages: flesch: 58.0 cache: ./cache/cord-334735-up81jotp.txt txt: ./txt/cord-334735-up81jotp.txt summary: Severe acute respiratory syndrome (SARS) is a viral disease, observed primarily in Southern China in November 2002, with variable flu-like symptoms and pneumonia, in approx. Weitere Fälle wurden aus Vietnam, Singapur und den USA (hier mation about a new syndrome by the end of February 2003, after the first cases outside the Republic of China had been observed. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong Identification of a novel coronavirus in patients with severe acute respiratory syndrome Guideline on management of severe acute respiratory syndrome (SARS) A novel coronavirus associated with severe acute respiratory syndrome SARS: imaging of severe acute respiratory syndrome Coronavirus as possible cause of severe acute respiratory syndrome A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS): infection control Dieses Prinzip ist bei den Neuraminidaseinhibitoren zur Therapie der Influenza bekannt und klinisch umgesetzt [7, 9, 21] . abstract: Severe acute respiratory syndrome (SARS) is a viral disease, observed primarily in Southern China in November 2002, with variable flu-like symptoms and pneumonia, in approx. 5% leading to death from respiratory distress syndrome (RDS). The disease was spread over more than 30 states all over the globe by SARS-virus-infected travelers. WHO and CDC received first information about a new syndrome by the end of February 2003, after the first cases outside the Republic of China had been observed. A case in Hanoi, Vietnam, led to the first precise information about the new disease entity to WHO, by Dr. Carlo Urbani, a co-worker of WHO/Doctors without Borders, who had been called by local colleagues to assist in the management of a patient with an unknown severe disease by the end of February 2003. Dr. Urbani died from SARS, as did many other health care workers. In the meantime, more than 7,000 cases have been observed worldwide, predominantly in China and Hong Kong, but also in Taiwan, Canada, Singapore, and the USA, and many other countries, and more than 600 of these patients died from RDS. Since the beginning of March 2003, when WHO and CDC started their activities, in close collaboration with a group of international experts, including the Bernhard-Nocht-Institute in Hamburg and the Department of Virology in Frankfurt/Main, a previously impossible success in the disclosure of the disease was achieved. Within only 8 weeks of research it was possible to describe the infectious agent, a genetically modified coronavirus, including the genetic sequence, to establish specific diagnostic PCR methods and to find possible mechanisms for promising therapeutic approaches. In addition, intensifying classical quarantine and hospital hygiene measures, it was possible to limit SARS in many countries to sporadic cases, and to reduce the disease in countries such as Canada and Vietnam. This review article summarizes important information about many issues of SARS (May 15th, 2003). url: https://www.ncbi.nlm.nih.gov/pubmed/12811416/ doi: 10.1007/s00063-003-1271-z id: cord-296981-tded20ih author: Gilmore, Kerry title: In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date: 2020-10-05 words: 3162.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-296981-tded20ih.txt txt: ./txt/cord-296981-tded20ih.txt summary: We report in vitro efficacy of Artemisia annua extracts as well as artemisinin, artesunate, and artemether against SARS-CoV-2. Subsequent concentration-response studies using a high-throughput antiviral assay, based on immunostaining of SARS-CoV-2 spike glycoprotein, revealed that pretreatment and treatment with extracts, artemisinin, and artesunate inhibited SARS-CoV-2 infection of VeroE6 cells. The selectivity index (SI), calculated based on treatment and cell viability assays, was highest for artemisinin (54), and roughly equal for the extracts (5-10), artesunate (6) and artemether (<7). annua extracts, as well as pure artemisinin, artesunate, and artemether are active against SARS-CoV-2 in vitro. To initially screen whether extracts and pure artemisinin were active against SARS-CoV-2, their antiviral activity was tested by pretreating VeroE6 cells at different time points during 120 minutes with selected concentrations of the extracts or compounds prior to infection with the first European SARS-CoV-2 isolated in München (SARS-CoV-2/human/Germany/BavPat 1/2020). abstract: Effective and affordable treatments for patients suffering from coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are needed. We report in vitro efficacy of Artemisia annua extracts as well as artemisinin, artesunate, and artemether against SARS-CoV-2. The latter two are approved active pharmaceutical ingredients of anti-malarial drugs. Proof-of-concept for prophylactic efficacy of the extracts was obtained using a plaque-reduction assay in VeroE6 cells. Subsequent concentration-response studies using a high-throughput antiviral assay, based on immunostaining of SARS-CoV-2 spike glycoprotein, revealed that pretreatment and treatment with extracts, artemisinin, and artesunate inhibited SARS-CoV-2 infection of VeroE6 cells. In treatment assays, artesunate (50% effective concentration (EC50): 7 μg/mL) was more potent than the tested plant extracts (128-260 μg/mL) or artemisinin (151 μg/mL) and artemether (>179 μg/mL), while generally EC50 in pretreatment assays were slightly higher. The selectivity index (SI), calculated based on treatment and cell viability assays, was highest for artemisinin (54), and roughly equal for the extracts (5-10), artesunate (6) and artemether (<7). Similar results were obtained in human hepatoma Huh7.5 cells. Peak plasma concentrations of artesunate exceeding EC50 values can be achieved. Clinical studies are required to further evaluate the utility of these compounds as COVID-19 treatment. url: https://doi.org/10.1101/2020.10.05.326637 doi: 10.1101/2020.10.05.326637 id: cord-267115-6jqdi417 author: Giobbe, Giovanni Giuseppe title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 words: 8080.0 sentences: 408.0 pages: flesch: 47.0 cache: ./cache/cord-267115-6jqdi417.txt txt: ./txt/cord-267115-6jqdi417.txt summary: Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . abstract: Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global public health emergency. COVID-19 typically manifests as a respiratory illness but an increasing number of clinical reports describe gastrointestinal (GI) symptoms. This is particularly true in children in whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. By contrast, fetuses seem to be rarely affected by COVID-19, although the virus has been detected in placentas of affected women. These observations raise the question of whether the virus can infect and replicate within the stomach once ingested. Moreover, it is not yet clear whether active replication of SARS-CoV-2 is possible in the stomach of children or in fetuses at different developmental stages. Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. Gastric organoids recapitulate human stomach with linear increase of gastric mucin 5AC along developmental stages, and expression of gastric markers pepsinogen, somatostatin, gastrin and chromogranin A. In order to investigate SARS-CoV-2 infection with minimal perturbation and under steady-state conditions, we induced a reversed polarity in the gastric organoids (RP-GOs) in suspension. In this condition of exposed apical polarity, the virus can easily access viral receptor angiotensin-converting enzyme 2 (ACE2). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, where viral nucleoprotein is expressed in cells undergoing programmed cell death, while the efficiency of infection is significantly lower in fetal organoids. The RP-GOs derived from pediatric patients show sustained robust viral replication of SARS-CoV-2, compared with organoids derived from fetal stomachs. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. However, the virus can efficiently infect gastric epithelium in pediatric patients, suggesting that the stomach might have an active role in fecal-oral transmission of SARS-CoV-2. url: https://doi.org/10.1101/2020.06.24.167049 doi: 10.1101/2020.06.24.167049 id: cord-291176-evb6yt0r author: Giorgi Rossi, Paolo title: Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date: 2020-08-27 words: 4559.0 sentences: 213.0 pages: flesch: 46.0 cache: ./cache/cord-291176-evb6yt0r.txt txt: ./txt/cord-291176-evb6yt0r.txt summary: In this report, based on the cohort of all residents in the province of Reggio Emilia who were SARS-CoV-2-positive at nasal and pharyngeal swab and with symptoms (COVID-19 cases) since the inception of the epidemic, we describe patient characteristics and explore their role as putative prognostic factors in predicting the occurrence of hospital admission or death. We considered the following patient characteristics: age, sex, place of birth (Italy or abroad), time span (in days) from symptom onset to diagnosis/ hospitalization, and comorbidities, whose prognostic role was explored both singly (chronic obstructive pulmonary disease, arrhythmia, diabetes, coronary heart disease, heart failure, vascular diseases, obesity) and by computing the Charlson Comorbidity Index, which provides an overall measure of an individual patient''s complexity [12] . While in this study we focused on the risk of hospitalization and death in a cohort of COVID-19 patients diagnosed during the epidemic in Northern Italy, it also provided us with the opportunity to describe the pattern of distribution of the disease in the whole population. abstract: This is a population-based prospective cohort study on archive data describing the age- and sex-specific prevalence of COVID-19 and its prognostic factors. All 2653 symptomatic patients tested positive for SARS-CoV-2 from February 27 to April 2, 2020 in the Reggio Emilia province, Italy, were included. COVID-19 cumulative incidence, hospitalization and death rates, and adjusted hazard ratios (HR) with 95% confidence interval (95% CI) were calculated according to sociodemographic and clinical characteristics. Females had higher prevalence of infection than males below age 50 (2.61 vs. 1.84 ‰), but lower in older ages (16.49 vs. 20.86 ‰ over age 80). Case fatality rate reached 20.7% in cases with more than 4 weeks follow up. After adjusting for age and comorbidities, men had a higher risk of hospitalization (HR 1.4 95% CI 1.2 to 1.6) and of death (HR 1.6, 95% CI 1.2 to 2.1). Patients over age 80 compared to age < 50 had HR 7.1 (95% CI 5.4 to 9.3) and HR 27.8 (95% CI 12.5 to 61.7) for hospitalization and death, respectively. Immigrants had a higher risk of hospitalization (HR 1.3, 95% CI 0.99 to 1.81) than Italians and a similar risk of death. Risk of hospitalization and of death were higher in patients with heart failure, arrhythmia, dementia, coronary heart disease, diabetes, and hypertension, while COPD increased the risk of hospitalization (HR 1.9, 95% CI 1.4 to 2.5) but not of death (HR 1.1, 95% CI 0.7 to 1.7). Previous use of ACE inhibitors had no effect on risk of death (HR 0.97, 95% CI 0.69 to 1.34). Identified susceptible populations and fragile patients should be considered when setting priorities in public health planning and clinical decision making. url: https://doi.org/10.1371/journal.pone.0238281 doi: 10.1371/journal.pone.0238281 id: cord-269071-jbxbknyt author: Giorgianni, Andrea title: Transient acute-onset tetraparesis in a COVID-19 patient date: 2020-06-02 words: 785.0 sentences: 44.0 pages: flesch: 42.0 cache: ./cache/cord-269071-jbxbknyt.txt txt: ./txt/cord-269071-jbxbknyt.txt summary: Since the main organic, infectious, and immunomediated causes of acute-onset flaccid tetraparesis have been excluded from the anamnestic, neuroradiological, and laboratory data recorded, we can hypothesize that SARS-CoV-2 had a promoter role in the onset of the tetraparetic clinical presentation. A first-reported case of postinfective acute transverse myelitis has been described in the literature [2] , suggesting that spinal cord can be the target of SARS-CoV-2 infection. Therefore, we can deduce that the neuro-shocking and neuro-irritative effect of SARS-CoV-2, in addition to hyperglycemic neuro-stress, can have a promoting and synergistic role in the manifestation of the tetraparetic transient acute clinic. As described in this case, the neuroinvasive and neurotrophic potential of SARS-CoV-2 could have a synergistic and promoter role in determining neuro-irritative and neuro-shocking effects, without necessarily causing neuroimaging evident organic damage. Acute myelitis after SARS-CoV-2 infection: a case report abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32488194/ doi: 10.1038/s41393-020-0493-8 id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 words: 15827.0 sentences: 874.0 pages: flesch: 56.0 cache: ./cache/cord-350286-n7ylgqfu.txt txt: ./txt/cord-350286-n7ylgqfu.txt summary: The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . abstract: Recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 9,00,000 cases of SARS-CoV-2 infection and more than 47,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted that the COVID-19 is a pandemic now. The multiple sequence alignment data correlated with the already published reports on the SARS-CoV-2 evolution and indicated that this virus is closely related to the bat Severe Acute Respiratory Syndrome-like coronavirus (bat SARS-like CoV) and the well-studied Human SARS coronavirus (SARS CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for Nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins were shown to contain molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of the SARS-CoV-2 proteome will have important implications for the structural and non-structural biology of SARS or SARS-like coronaviruses. Significance The infection caused by a novel coronavirus (SARS-CoV-2) that causes severe respiratory disease with pneumonia-like symptoms in humans is responsible for the current COVID-19 pandemic. No in-depth information on structures and functions of SARS-CoV-2 proteins is currently available in the public domain, and no effective anti-viral drugs and/or vaccines are designed for the treatment of this infection. Our study provides the first comparative analysis of the order- and disorder-based features of the SARS-CoV-2 proteome relative to human SARS and bat CoV that may be useful for structure-based drug discovery. url: https://doi.org/10.1101/2020.03.13.990598 doi: 10.1101/2020.03.13.990598 id: cord-311523-erntrh3p author: Gisondi, P title: Dermatologists and SARS‐CoV‐2: The impact of the pandemic on daily practice date: 2020-04-22 words: 2757.0 sentences: 150.0 pages: flesch: 43.0 cache: ./cache/cord-311523-erntrh3p.txt txt: ./txt/cord-311523-erntrh3p.txt summary: Since the first case of "pneumonia of unknown aetiology" was diagnosed at the Wuhan Jinyintan Hospital in China on 30 December 2019, what was recognised thereafter as "severe acute respiratory syndrome coronavirus 2" (SARS‐CoV‐2) has spread over the four continents, causing the respiratory manifestations of Coronavirus disease‐19 (COVID‐ 19) and satisfying the epidemiological criteria for a label of "pandemic." The ongoing SARS‐CoV‐2 pandemic is having a huge impact on dermatological practice including the marked reduction of face‐to‐face consultations in favour of teledermatology, the uncertainties concerning the outcome of COVID‐19 infection in patients with common inflammatory disorders such as psoriasis or atopic dermatitis receiving immunosuppressive/immunomodulating systemic therapies; the direct involvement of dermatologists in COVID‐19 care for patients assistance and new research needs to be addressed. abstract: Since the first case of “pneumonia of unknown aetiology” was diagnosed at the Wuhan Jinyintan Hospital in China on 30 December 2019, what was recognised thereafter as “severe acute respiratory syndrome coronavirus 2” (SARS‐CoV‐2) has spread over the four continents, causing the respiratory manifestations of Coronavirus disease‐19 (COVID‐ 19) and satisfying the epidemiological criteria for a label of “pandemic.” The ongoing SARS‐CoV‐2 pandemic is having a huge impact on dermatological practice including the marked reduction of face‐to‐face consultations in favour of teledermatology, the uncertainties concerning the outcome of COVID‐19 infection in patients with common inflammatory disorders such as psoriasis or atopic dermatitis receiving immunosuppressive/immunomodulating systemic therapies; the direct involvement of dermatologists in COVID‐19 care for patients assistance and new research needs to be addressed. It is not known yet, if skin lesions and derangement of the skin barrier could make it easier for SARS‐CoV‐2 to transmit via indirect contact; it remains to be defined if specific mucosal or skin lesions are associated with SARS‐CoV‐2 infection, although some unpublished observations indicate the occurrence of a transient varicelliform exanthema during the early phase of the infection. SARS‐CoV‐2 is a new pathogen for humans that is highly contagious, can spread quickly, and is capable of causing enormous health, economic and societal impacts in any setting. The consequences may continue long after the pandemic resolves, and new management modalities for dermatology may originate from the COVID‐19 disaster. Learning from experience may help to cope with future major societal changes. url: https://doi.org/10.1111/jdv.16515 doi: 10.1111/jdv.16515 id: cord-287220-mpnuhqwg author: Giuliani, C. title: Breastfeeding during the COVID-19 pandemic: suggestions on behalf of Woman Study Group of AMD date: 2020-05-30 words: 2758.0 sentences: 161.0 pages: flesch: 50.0 cache: ./cache/cord-287220-mpnuhqwg.txt txt: ./txt/cord-287220-mpnuhqwg.txt summary: Woman Study Group of AMD, after reviewing current knowledge about COVID-19 vertical transmission and the compatibility of breastfeeding in COVID-19 mother, the available recommendations from Health Care Organizations and main experts opinions, issued the following suggestions on breastfeeding during the COVID-19 pandemic, addressed both to mothers with and without diabetes It should be considered that following suggestions may change in the future when more evidence is acquired regarding SARS-Cov2 infection. Chen Y et al 5 reported four cases of live born infants, born to pregnant women with the COVID-19 infection in Wuhan: newborns had no clinical signs of disease and were tested negative for the virus at delivery. 14 Moreover, some experts speculate that, similar to the 2002-2003 SARS-Co-V epidemic 15 , specific SARS-CoV-2 antibodies pass via the breast milk from the COVID-19 mother to the infant within a few days after the onset of the disease, possibly moderating the clinical expression of infant''s infection 16 . abstract: Abstract SARS-Cov2 infection has recently spread to Italy with important consequences on pregnancy management, mother and child health and mother-child contact. Breastfeeding improves the health of mother and child and reduces risk of neonatal infection with other pathogens that are likely to cause serious illness. To date no evidence confirmed COVID-19 vertical transmission from infected pregnant mother to their fetus. However it is well known that an infected mother can transmit the COVID-19 virus through respiratory droplets during breastfeeding or intimate contact. Thus, the mothers with known or suspected COVID-19 should adhere to standard and contact precautions during breastfeeding. Woman Study Group of AMD, after reviewing current knowledge about COVID-19 vertical transmission and the compatibility of breastfeeding in COVID-19 mother, the available recommendations from Health Care Organizations and main experts opinions, issued the following suggestions on breastfeeding during the COVID-19 pandemic, addressed both to mothers with and without diabetes It should be considered that following suggestions may change in the future when more evidence is acquired regarding SARS-Cov2 infection. url: https://api.elsevier.com/content/article/pii/S0168822720304897 doi: 10.1016/j.diabres.2020.108239 id: cord-282043-cs1oyohu author: Giustino, Gennaro title: Coronavirus and Cardiovascular Disease, Myocardial Injury, and Arrhythmia: JACC Focus Seminar date: 2020-10-27 words: 1923.0 sentences: 114.0 pages: flesch: 27.0 cache: ./cache/cord-282043-cs1oyohu.txt txt: ./txt/cord-282043-cs1oyohu.txt summary: Both direct viral infection and indirect injury resulting from inflammation, endothelial activation, and microvascular thrombosis occur in the context of coronavirus disease 2019. Although originally believed to be a syndrome characterized by acute lung injury, respiratory failure, and death, it is now apparent that severe coronavirus disease 2019 (COVID-19) is further characterized by exuberant cytokinemia, with resultant endothelial inflammation, microvascular thrombosis, and multiorgan failure (2) . Myocardial injury can be detected in w25% of hospitalized patients with COVID-19 and is associated with an increased risk of mortality. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Acute myocardial injury in patients hospitalized with COVID-19 infection: a review Characteristics and clinical significance of myocardial injury in patients with severe coronavirus disease 2019 abstract: The cardiovascular system is affected broadly by severe acute respiratory syndrome coronavirus 2 infection. Both direct viral infection and indirect injury resulting from inflammation, endothelial activation, and microvascular thrombosis occur in the context of coronavirus disease 2019. What determines the extent of cardiovascular injury is the amount of viral inoculum, the magnitude of the host immune response, and the presence of co-morbidities. Myocardial injury occurs in approximately one-quarter of hospitalized patients and is associated with a greater need for mechanical ventilator support and higher hospital mortality. The central pathophysiology underlying cardiovascular injury is the interplay between virus binding to the angiotensin-converting enzyme 2 receptor and the impact this action has on the renin-angiotensin system, the body’s innate immune response, and the vascular response to cytokine production. The purpose of this review was to describe the mechanisms underlying cardiovascular injury, including that of thromboembolic disease and arrhythmia, and to discuss their clinical sequelae. url: https://www.sciencedirect.com/science/article/pii/S0735109720364949 doi: 10.1016/j.jacc.2020.08.059 id: cord-340984-blkhfhe2 author: Gklinos, Panagiotis title: Neurological manifestations of COVID-19: a review of what we know so far date: 2020-05-26 words: 2665.0 sentences: 139.0 pages: flesch: 45.0 cache: ./cache/cord-340984-blkhfhe2.txt txt: ./txt/cord-340984-blkhfhe2.txt summary: Prompt diagnosis and immediate management of the neurological manifestations of the novel coronavirus will not only improve the prognosis of COVID-19 patients but will also prevent the dissemination of the disease due to misdiagnosed cases. COVID-19 is confirmed to be caused by a novel coronavirus (2019 novel coronavirus, 2019-nCoV) and presents with symptoms similar to those of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. However, neurological manifestations of the novel coronavirus are not precepted by all clinicians, thus, leading to inappropriate management of COVID-19 patients presenting with non-specific neurological symptoms initially. This article aims to review the cases, which reported neurological symptoms at presentation or during the course of the disease and discuss the potential mechanisms of Central Nervous System (CNS) involvement in COVID-19. The other study is a retrospective case series in Wuhan, China, which reported the neurological symptoms of COVID-19 patients [13] . abstract: Coronavirus disease 2019 (COVID‐19) has become a pandemic disease globally. While it mostly presents with respiratory symptoms, it has already been found that it could manifest with a series of neurological symptoms as well, either at presentation or during the course of the disease. Symptoms vary from non-specific such as headache or dizziness to more specific such as convulsions and cerebrovascular disease (CVD). This study aims to give an overview of the neurological manifestations of COVID-19 and discuss the potential pathogenetic mechanisms of central nervous system (CNS) involvement. Clinicians and especially internists, neurologists, and infectious disease specialists should be aware of these symptoms and able to recognize them early. Prompt diagnosis and immediate management of the neurological manifestations of the novel coronavirus will not only improve the prognosis of COVID-19 patients but will also prevent the dissemination of the disease due to misdiagnosed cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32458197/ doi: 10.1007/s00415-020-09939-5 id: cord-326254-8dlxsf57 author: Glasbey, T. title: Flawed disinfectant recommendations during a pandemic date: 2020-06-15 words: 907.0 sentences: 53.0 pages: flesch: 46.0 cache: ./cache/cord-326254-8dlxsf57.txt txt: ./txt/cord-326254-8dlxsf57.txt summary: We are deeply concerned over the recommendations in the paper by Kampf [1] recently published in this journal as to what disinfectants are appropriate for use with respect to surface disinfection in the setting of the current Coronavirus pandemic. In that recent paper [1] , the author also suggests that the use of disinfectants containing benzalkonium chloride may be problematic as ''data obtained with benzalkonium chloride at reasonable contact times were conflicting. of Kampf are also diametrically opposed to the United States EPA recommendations for suitable disinfectant products given on their List N: ''Products with Emerging Viral Pathogens and Human Coronavirus claims for use against SARS-CoV-2'' [5] . Here, any disinfectant recommended for use against SARS-CoV-2 is required to be included the Australian Register of Therapeutic Goods (ARTG), and the manufacturer or product sponsor is required to hold suitable efficacy data against either the SARS-CoV-2 virus or recognised surrogate [8] . abstract: nan url: https://api.elsevier.com/content/article/pii/S2590088920300342 doi: 10.1016/j.infpip.2020.100070 id: cord-279861-gk8cow8k author: Glasser, John W. title: Modeling and public health emergency responses: Lessons from SARS date: 2011-01-28 words: 4361.0 sentences: 196.0 pages: flesch: 40.0 cache: ./cache/cord-279861-gk8cow8k.txt txt: ./txt/cord-279861-gk8cow8k.txt summary: By overestimating the potential of managing contacts versus cases, moreover, we may even have inadvertently contributed to a lingering misunderstanding of means by which this epidemic was controlled that will affect their future responses to newly-emerging infectious diseases. Given the assumptions outlined above, together with a gamma distribution, these results suggest that for a disease with ℜ 0 = 3, isolation that was 100% effective in blocking transmission could prevent ℜ 0 − 1 infections (and thus lead to epidemic control) if implemented up to 5.2 days after symptom onset, on average (Fig. 1) . Knowledgeable public health practitioners might have cautioned against overestimating the potential impact of managing contacts of SARS patients, and interpreted observations suggesting that infected people were not particularly infectious until acutely ill as an indication for managing cases instead. abstract: Modelers published thoughtful articles after the 2003 SARS crisis, but had limited if any real-time impact on the global response and may even have inadvertently contributed to a lingering misunderstanding of the means by which the epidemic was controlled. The impact of any intervention depends on its efficiency as well as efficacy, and efficient isolation of infected individuals before they become symptomatic is difficult to imagine. Nonetheless, in exploring the possible impact of quarantine, the product of efficiency and efficacy was varied over the entire unit interval. Another mistake was repeatedly fitting otherwise appropriate gamma distributions to times to event regardless of whether they were stationary or not, particularly onset-isolation intervals whose progressive reduction evidently contributed to SARS control. By virtue of their unknown biology, newly-emerging diseases are more challenging than familiar human scourges. Influenza, for example, recurs annually and has been modeled more thoroughly than any other infectious disease. Moreover, models were integrated into preparedness exercises, during which working relationships were established that bore fruit during the 2009 A/H1N1 pandemic. To provide the most accurate and timely advice possible, especially about the possible impact of measures designed to control diseases caused by novel human pathogens, we must appreciate the value and difficulty of policy-oriented modeling. Effective communication of insights gleaned from modeling SARS will help to ensure that policymakers involve modelers in future outbreaks of newly-emerging infectious diseases. Accordingly, we illustrate the increasingly timely care-seeking by which, together with increasingly accurate diagnoses and effective isolation, SARS was controlled via heuristic arguments and descriptive analyses of familiar observations. url: https://www.sciencedirect.com/science/article/pii/S1755436511000028 doi: 10.1016/j.epidem.2011.01.001 id: cord-345356-gn1iwis0 author: Glebov, Oleg O. title: Understanding SARS‐CoV‐2 endocytosis for COVID‐19 drug repurposing date: 2020-06-02 words: 3502.0 sentences: 175.0 pages: flesch: 35.0 cache: ./cache/cord-345356-gn1iwis0.txt txt: ./txt/cord-345356-gn1iwis0.txt summary: Given that most viruses use endocytosis to enter the host cell, mechanistic investigation of SARS‐CoV‐2 infection needs to consider the diversity of endocytic pathways available for SARS‐CoV‐2 entry in the human lung epithelium. Taken together, the above evidence suggests that SARS-CoV-2 may employ distinct endocytic pathways for cell entry in the upper and lower respiratory tract (Fig. 1) . This approach would allow tracking of the virus in relation to other endocytic pathways and also to investigate the effect of viral infection on the general membrane trafficking network of the host cell. Taken together, the combination of adequate cell models with the newly developed SARS-CoV-2 toolkit and established tools of membrane trafficking research is well-poised to deliver a key insight into the mechanisms underlying COVID-19 infection. Furthermore, considering that various viruses may use the same endocytic pathways of the host cell [15] , targeting viral entry at the point of endocytosis holds a more general promise for the development of broad-spectrum antiviral drugs [51] . abstract: The quest for the effective treatment against coronavirus disease 2019 pneumonia caused by the severe acute respiratory syndrome (SARS)‐coronavirus 2(CoV‐2) coronavirus is hampered by the lack of knowledge concerning the basic cell biology of the infection. Given that most viruses use endocytosis to enter the host cell, mechanistic investigation of SARS‐CoV‐2 infection needs to consider the diversity of endocytic pathways available for SARS‐CoV‐2 entry in the human lung epithelium. Taking advantage of the well‐established methodology of membrane trafficking studies, this research direction allows for the rapid characterisation of the key cell biological mechanism(s) responsible for SARS‐CoV‐2 infection. Furthermore, 11 clinically approved generic drugs are identified as potential candidates for repurposing as blockers of several potential routes for SARS‐CoV‐2 endocytosis. More broadly, the paradigm of targeting a fundamental aspect of human cell biology to protect against infection may be advantageous in the context of future pandemic outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32428379/ doi: 10.1111/febs.15369 id: cord-272956-0yumc7em author: Gnavi, Roberto title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 words: 1772.0 sentences: 90.0 pages: flesch: 51.0 cache: ./cache/cord-272956-0yumc7em.txt txt: ./txt/cord-272956-0yumc7em.txt summary: Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. abstract: Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. url: https://doi.org/10.1093/cid/ciaa634 doi: 10.1093/cid/ciaa634 id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 words: 3924.0 sentences: 251.0 pages: flesch: 56.0 cache: ./cache/cord-354733-qxivrhj8.txt txt: ./txt/cord-354733-qxivrhj8.txt summary: Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. abstract: Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a retrospective cohort of COVID-19 patients at the Johns Hopkins Hospital were assessed for RNA and infectious virus shedding. Whole genome sequencing confirmed the virus genotype in patients with prolonged viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false negative standard of care PCR results. Recovery of infectious virus was associated with Ct values of 18.8 {+/-} 3.4. Prolonged viral RNA shedding was associated with recovery of infectious virus in specimens collected up to 20 days after the first positive result in patients who were symptomatic at the time of specimen collection. The use of Ct values and clinical symptoms provides a more accurate assessment of the potential for infectious virus shedding. url: https://doi.org/10.1101/2020.08.05.20168963 doi: 10.1101/2020.08.05.20168963 id: cord-346670-34wfy52f author: Gobeil, Sophie M-C. title: D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date: 2020-10-12 words: 7065.0 sentences: 359.0 pages: flesch: 57.0 cache: ./cache/cord-346670-34wfy52f.txt txt: ./txt/cord-346670-34wfy52f.txt summary: Most structures of the SARS-CoV-2 S ectodomain currently available include two mutations, one to disrupt the furin cleavage site (RRAR to GSAS = S-GSAS), and a double proline mutation (PP) of residues 986-987, designed to prevent conformational change to the post-fusion state (Wrapp et al., 2020) . While the SARS-CoV-2 S ectodomain construct that includes mutations of residues K986 and V987, between the HR1 and CH subdomains (S2 domain), to prolines (PP) (named S-GSAS/PP in this study) (Figure 1 ) is widely used in the field, the origin of this PP construct was based upon the stabilization of the pre-fusion conformation of other coronavirus spikes (Pallesen et al., 2017; Walls et al., 2020; Wrapp et al., 2020) . Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 b sheet ( Figure 7C, S8B) . abstract: The SARS-CoV-2 spike (S) protein is the target of vaccine design efforts to end the COVID-19 pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic, and are now the dominant form worldwide. Here, we analyze the D614G mutation in the context of a soluble S ectodomain construct. Cryo-EM structures, antigenicity and proteolysis experiments suggest altered conformational dynamics resulting in enhanced furin cleavage efficiency of the G614 variant. Furthermore, furin cleavage altered the conformational dynamics of the Receptor Binding Domains (RBD) in the G614 S ectodomain, demonstrating an allosteric effect on the RBD dynamics triggered by changes in the SD2 region, that harbors residue 614 and the furin cleavage site. Our results elucidate SARS-CoV-2 spike conformational dynamics and allostery, and have implications for vaccine design. Highlights SARS-CoV-2 S ectodomains with or without the K986P, V987P mutations have similar structures, antigenicity and stability. The D614G mutation alters S protein conformational dynamics. D614G enhances protease cleavage susceptibility at the S protein furin cleavage site. Cryo-EM structures reveal allosteric effect of changes at the S1/S2 junction on RBD dynamics. url: https://doi.org/10.1101/2020.10.11.335299 doi: 10.1101/2020.10.11.335299 id: cord-286290-85l99l13 author: Goddard, N.L. title: Lessons learned from SARS: The experience of the Health Protection Agency, England date: 2005-11-16 words: 3393.0 sentences: 155.0 pages: flesch: 44.0 cache: ./cache/cord-286290-85l99l13.txt txt: ./txt/cord-286290-85l99l13.txt summary: Lessons learned from mounting a UK response to SARS included: the importance of international collaboration; formation of a UK-wide, multidisciplinary Task Force; flexible case reporting mechanisms; integration of surveillance and laboratory data; generation of prompt and web-accessible guidance and advice; availability of surge capacity; and contingency planning. The global response to SARS provided new opportunities for the UK to collaborate with WHO (Geneva and Western Pacific Region), a number of public health organisations in south east Asia, as well as national public health centres such as the Centers for Disease Control and Prevention in the USA and Health Canada. Surveillance arrangements were revised during the outbreak to encourage initial alerting to HPA Regional Offices and ensure that local public health authorities were aware of the potential cases. 3. Flexible case reporting mechanisms need to be implemented at central, regional and local level during an evolving outbreak to inform appropriate public health measures. abstract: The United Kingdom was assessed as a low risk country throughout the 2003 global SARS outbreaks. Despite this, 368 reports of potential SARS cases were made to the Health Protection Agency (HPA) between March and July 2003. The public health actions undertaken in response to these reports, the establishment of reporting mechanisms and the development of guidance documents were substantial. Lessons learned from mounting a UK response to SARS included: the importance of international collaboration; formation of a UK-wide, multidisciplinary Task Force; flexible case reporting mechanisms; integration of surveillance and laboratory data; generation of prompt and web-accessible guidance and advice; availability of surge capacity; and contingency planning. Lessons learned are being incorporated into the HPA's preparedness to prevent and control future newly emerging infectious disease threats. url: https://api.elsevier.com/content/article/pii/S0033350605002386 doi: 10.1016/j.puhe.2005.10.003 id: cord-264057-z5arb1k5 author: Goel, S. title: Preparations and limitations for prevention of severe acute respiratory syndrome in a tertiary care centre of India date: 2007-05-18 words: 2753.0 sentences: 190.0 pages: flesch: 59.0 cache: ./cache/cord-264057-z5arb1k5.txt txt: ./txt/cord-264057-z5arb1k5.txt summary: This short-term observational study of infection control practice was performed in the medical emergency outpatient department (EMOPD) of a tertiary-care hospital in India when threatened by an outbreak of severe acute respiratory syndrome (SARS). Infection control measures such as fumigation and cleaning were noted, as was the EMOPD laboratory function, use of personnel protection and display of information on infectious diseases. The EMOPDs in key hospitals need be able to screen for infectious diseases, especially in view of the threats from SARS and Avian influenza. The need to screen all patients with suspected infectious disease in the medical emergency outpatient department (EMOPD), and for control and prevention of infection, was recognized. In addition, the patient/attendant load, patient flow, and medical staff practice were observed, and information displayed on SARS or other infectious diseases was noted. abstract: This short-term observational study of infection control practice was performed in the medical emergency outpatient department (EMOPD) of a tertiary-care hospital in India when threatened by an outbreak of severe acute respiratory syndrome (SARS). An investigator attended the lobby daily to screen patients with symptoms for SARS. Patient/attendant load, patient flow, medical staff working practices and position in the EMOPD were observed. Infection control measures such as fumigation and cleaning were noted, as was the EMOPD laboratory function, use of personnel protection and display of information on infectious diseases. A total of 162 (7.4%) of the 2165 patients surveyed had respiratory symptoms but no cases of SARS were found. The flow of patients and their attendants was not systematic. No laboratory tests for SARS were available, and no educational material on SARS was displayed. The EMOPDs in key hospitals need be able to screen for infectious diseases, especially in view of the threats from SARS and Avian influenza. url: https://www.sciencedirect.com/science/article/pii/S019567010700062X doi: 10.1016/j.jhin.2007.02.015 id: cord-308857-otsrexqu author: Goel, Saurav title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 words: 10608.0 sentences: 526.0 pages: flesch: 47.0 cache: ./cache/cord-308857-otsrexqu.txt txt: ./txt/cord-308857-otsrexqu.txt summary: This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. abstract: The world is witnessing tumultuous times as major economic powers including the US, UK, Russia, India, and most of Europe continue to be in a state of lockdown. The worst-hit sectors due to this lockdown are sales, production (manufacturing), transport (aerospace and automotive) and tourism. Lockdowns became necessary as a preventive measure to avoid the spread of the contagious and infectious “Coronavirus Disease 2019” (COVID-19). This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. We also offer perspectives on future considerations on climate change, outsourced versus indigenous manufacturing, automation, and antimicrobial resistance. Overall, this paper attempts to identify key areas where manufacturing can be employed to address societal challenges such as COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2468519420300604?v=s5 doi: 10.1016/j.mtchem.2020.100300 id: cord-332592-bfqsyiyf author: Goette, Andreas title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation date: 2020-09-26 words: 3539.0 sentences: 261.0 pages: flesch: 41.0 cache: ./cache/cord-332592-bfqsyiyf.txt txt: ./txt/cord-332592-bfqsyiyf.txt summary: title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation Coronavirus disease 2019 (COVID-19) is a viral disease induced by severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2), which may cause an acute respiratory distress syndrome (ARDS). Here, we can present a case of cytokine release syndrome induced by SARS-CoV-2 causing multiorgan failure and death. In summary, the present case shows that severe COVID-19 induces CRS associated with ARDS, acute kidney failure, liver pathologies, vascular intimal inflammation, pulmonary arterial, and venous thromboses and an inflammatory atrial cardiomyopathy. In the present case, we can show that COVID-19 can induce the occurrences of ARDS, which was associated with pulmonary embolism, as well as thrombogenesis, in pulmonary veins and the right atrial appendage. In addition to COVID-19-induced ARDS, CRS might be associated with pulmonary artery, as well as vein thromboses, atrial fibrillation, sinus node dysfunction, right atrial clot formation, and inflammatory invasion of autonomic atrial nerve ganglia. abstract: Coronavirus disease 2019 (COVID-19) is a viral disease induced by severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2), which may cause an acute respiratory distress syndrome (ARDS). First reports have shown that elevated levels of inflammatory cytokines might be involved in the development of organ dysfunction in COVID-19. Here, we can present a case of cytokine release syndrome induced by SARS–CoV-2 causing multiorgan failure and death. Of note, we can report on pulmonary vein thromboses as potential source of cerebrovascular embolic events. Furthermore, we present a specific form of an isolated inflammatory atrial cardiomyopathy encompassing atrial myocardium, perivascular matrix, as well as atrial autonomic nerve ganglia, causing atrial fibrillation, sinus node arrest, as well as atrial clot formation in the right atrial appendage. An associated acute glomerulonephritis caused acute kidney failure. Furthermore, all the described pathologies of organs and vessels were associated with increased local expression of interleukin-6 and monocyte chemoattractant protein-1 (MCP-1). This report provides new evidence about fatal pathologies and summarizes the current knowledge about organ manifestations observed in COVID-19. url: https://doi.org/10.1055/s-0040-1716717 doi: 10.1055/s-0040-1716717 id: cord-278182-75u57fw1 author: Goh, Gerard Kian-Meng title: Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids date: 2020-03-31 words: 4613.0 sentences: 253.0 pages: flesch: 58.0 cache: ./cache/cord-278182-75u57fw1.txt txt: ./txt/cord-278182-75u57fw1.txt summary: A model to classify and predict the levels of respective respiratory and fecal-oral transmission potentials of the various viruses was built before the outbreak of MERS-CoV using AI and empirically-based molecular tools to predict the disorder level of proteins. Using the percentages of intrinsic disorder (PID) of the nucleocapsid (N) and membrane (M) proteins of CoV, the model easily clustered the viruses into three groups with the SARS-CoV (M PID = 8%, N PID = 50%) falling into Category B, in which viruses have intermediate levels of both respiratory and fecal-oral transmission potentials. In 2011-2012, just before the outbreak of the Middle Eastern Respiratory Syndrome (MERS-CoV), we built an empirically-based model that measures the percentage of intrinsic disorder (PID) of the membrane (M) and nucleocapsid (N) proteins in viruses [5, 6] . abstract: The coronavirus (CoV) family consists of viruses that infects a variety of animals including humans with various levels of respiratory and fecal-oral transmission levels depending on the behavior of the viruses' natural hosts and optimal viral fitness. A model to classify and predict the levels of respective respiratory and fecal-oral transmission potentials of the various viruses was built before the outbreak of MERS-CoV using AI and empirically-based molecular tools to predict the disorder level of proteins. Using the percentages of intrinsic disorder (PID) of the nucleocapsid (N) and membrane (M) proteins of CoV, the model easily clustered the viruses into three groups with the SARS-CoV (M PID = 8%, N PID = 50%) falling into Category B, in which viruses have intermediate levels of both respiratory and fecal-oral transmission potentials. Later, MERS-CoV (M PID = 9%, N PID = 44%) was found to be in Category C, which consists of viruses with lower respiratory transmission potential but with higher fecal-oral transmission capabilities. Based on the peculiarities of disorder distribution, the SARS-CoV-2 (M PID = 6%, N PID = 48%) has to be placed in Category B. Our data show however, that the SARS-CoV-2 is very strange with one of the hardest protective outer shell, (M PID = 6%) among coronaviruses. This means that it might be expected to be highly resilient in saliva or other body fluids and outside the body. An infected body is likelier to shed greater numbers of viral particles since the latter is more resistant to antimicrobial enzymes in body fluids. These particles are also likelier to remain active longer. These factors could account for the greater contagiousness of the SARS-CoV-2 and have implications for efforts to prevent its spread. url: https://www.ncbi.nlm.nih.gov/pubmed/32244041/ doi: 10.1016/j.micpath.2020.104177 id: cord-332539-v1bfm57x author: Gohl, Daryl M. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 words: 5048.0 sentences: 246.0 pages: flesch: 55.0 cache: ./cache/cord-332539-v1bfm57x.txt txt: ./txt/cord-332539-v1bfm57x.txt summary: Several variants of the ARTIC protocol exist in which the pooled SARS-CoV-2 amplicons from a sample are taken through a NGS library preparation protocol (using either ligation or tagmentation-based approaches) in which sample-specific barcodes are added, and are then sequenced using either short-read (Illumina) or long-read (Oxford Nanopore, PacBio) technologies. We sequenced these samples using Illumina''s Nextera DNA Flex Enrichment protocol using a respiratory virus oligo panel containing probes for SARS-CoV-2, the ARTIC v3 tiled primers, and a novel tailed amplicon method designed to reduce cost and streamline the preparation of SARS-CoV-2 sequencing libraries. For the Illumina DNA Flex Enrichment protocol, SARS-CoV-2 genome coverage was more complete for samples with lower N1 and N2 Cts (ranging from ~20-30) at comparable read depths and coverage thresholds than with amplicon approaches, similar to the BEI WA isolate data ( Figure 3C , Supplemental Figure S2 -S3). abstract: The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries. Here we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach and represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing. url: https://doi.org/10.1101/2020.05.11.088724 doi: 10.1101/2020.05.11.088724 id: cord-317820-od9l7p1r author: Goker Bagca, Bakiye title: Overview of the COVID-19 and JAK/STAT Pathway Inhibition: Ruxolitinib Perspective date: 2020-06-20 words: 3961.0 sentences: 233.0 pages: flesch: 41.0 cache: ./cache/cord-317820-od9l7p1r.txt txt: ./txt/cord-317820-od9l7p1r.txt summary: The virus, which is the cause of the COVID-19 was named as Severe Acute Respiratory Syndromerelated Coronavirus (SARS-CoV-2) by Coronaviridae Study Group of the International Committee on Taxonomy of Viruses (Figure 1a) . As an expected result of SARS-CoV-2 infection, it was reported cytokine storm syndrome triggered by the dysregulated immunity in numerous patients. There are clinical studies including baricitinib, tofacitinib, and ruxolitinib JAK inhibitors against cytokine storm caused by COVID-19. It is reported that tocilizumab which is an approved IL6 receptor antagonist, treatment reduced cytokine release syndrome symptoms in severe patients COVID-19 [66] . It is reported that the usage of ruxolitinib suppresses cytokine levels and JAK/STAT pathway in Epstein-Barr Virus (EBV) -associated hemophagocytic lymphohistiocytosis [71] . In this context, it is clear that ruxolitinib, which is used especially in older age patients, has an important potential in overcoming complications that are caused by over activation of the immune system which is triggered through JAK/STAT signaling pathway. abstract: Ruxolitinib is the first approved JAK1 and JAK2 inhibitor. It inhibits the JAK / STAT pathway which is one of the main cellular signaling pathways especially regulates inflammatory response. COVID-19 is an urgent pandemic situation caused by SARS-CoV-2 infection. This review firstly presents an overview of SARS-CoV-2 and COVID-19, and then it focuses on the potential efficacy of ruxolitinib in this infection. The possible targets of ruxolitinib are determined by using genetic alterations that have been reported in COVID-19 patients. The potential effectiveness of ruxolitinib is suggested by evaluating the interactions of these potential targets which are directly affected by the ruxolitinib or JAK/STAT pathway. url: https://doi.org/10.1016/j.cytogfr.2020.06.013 doi: 10.1016/j.cytogfr.2020.06.013 id: cord-296676-2anl2agl author: Goldberg, Michael F. title: Neuroradiologic manifestations of COVID-19: what the emergency radiologist needs to know date: 2020-08-21 words: 4158.0 sentences: 213.0 pages: flesch: 43.0 cache: ./cache/cord-296676-2anl2agl.txt txt: ./txt/cord-296676-2anl2agl.txt summary: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global pandemic with a wide spectrum of clinical signs and symptoms. These neurologic manifestations were more common in severely affected patients, tended to occur early in the disease course, and could be the initial, presenting clinical evidence of COVID-19 [4] . Lastly, the authors note that ECMO alone (in the absence of SARS-CoV-2 infection) is a risk factor for intracranial hemorrhage, further limiting the generalizability of this small case series. Regardless, prior studies that evaluated neuroimaging findings of patients infected with other members of the Betacoronavirus genus have also demonstrated significant abnormalities, including intracranial hemorrhage and evidence of acute disseminated encephalomyelitis (ADEM), which could represent sequelae of inflammatory response and/or direct CNS infection [50, 51] . On behalf of the CoCo Neurosciences study group (2020) Retrospective observational study of brain magnetic resonance imaging findings in patients with acute SARS-CoV-2 infection and neurological manifestations abstract: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global pandemic with a wide spectrum of clinical signs and symptoms. Neurologic manifestations are relatively common, with severe cases often demonstrating striking findings on neuroimaging. Because the neuroradiologic findings may be the first evidence of COVID-19, the emergency radiologist has a critical role to play in not only the detection and management of the disease but also in the safety of other patients and hospital staff. Therefore, radiologists, especially those who specialize in emergency radiology, need to be aware of the neuroradiologic manifestations of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32822060/ doi: 10.1007/s10140-020-01840-y id: cord-351011-v4zmksio author: Golden, Joseph W. title: Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date: 2020-07-09 words: 4650.0 sentences: 268.0 pages: flesch: 52.0 cache: ./cache/cord-351011-v4zmksio.txt txt: ./txt/cord-351011-v4zmksio.txt summary: In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. In comparison with the normal lung architecture in uninfected control animals, infected mice necropsied on day 3, and those succumbing to disease on days 5-11, had varying levels of lung injury including area of lung consolidation characterized by inflammation/expansion of 145 alveolar septa with fibrin, edema and mononuclear leukocytes and infiltration of vessel walls by numerous mononuclear leukocytes (Fig 3A, Fig S4, and Table S1 ). Importantly, in our study some animals at the lower dose survived infection despite significant Infection of K18-hACE2 mice by SARS-CoV-2 produces a disease similar to that observed in acute human cases, with development of an acute lung injury associated with edema, production 285 of inflammatory cytokines and the accumulation of mononuclear cells in the lung. abstract: The emergence of SARS-CoV-2 has created an international health crisis. Small animal models mirroring SARS-CoV-2 human disease are essential for medical countermeasure (MCM) development. Mice are refractory to SARS-CoV-2 infection due to low affinity binding to the murine angiotensin-converting enzyme 2 (ACE2) protein. Here we evaluated the pathogenesis of SARS-CoV-2 in male and female mice expressing the human ACE2 gene under the control of the keratin 18 promotor. In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. Vasculitis was the most prominent finding in the lungs of infected mice. Transcriptomic analysis from lungs of infected animals revealed increases in transcripts involved in lung injury and inflammatory cytokines. In the lower dose challenge groups, there was a survival advantage in the female mice with 60% surviving infection whereas all male mice succumbed to disease. Male mice that succumbed to disease had higher levels of inflammatory transcripts compared to female mice. This is the first highly lethal murine infection model for SARS-CoV-2. The K18-hACE2 murine model will be valuable for the study of SARS-CoV-2 pathogenesis and the assessment of MCMs. url: https://doi.org/10.1101/2020.07.09.195230 doi: 10.1101/2020.07.09.195230 id: cord-308800-b8gtwdxc author: Goldhaber-Fiebert, Sara N. title: Low-flow Nasal Cannula and Potential Nosocomial Spread of COVID-19 date: 2020-05-18 words: 573.0 sentences: 46.0 pages: flesch: 53.0 cache: ./cache/cord-308800-b8gtwdxc.txt txt: ./txt/cord-308800-b8gtwdxc.txt summary: 8 Even with single-occupancy rooms, healthcare providers could be exposed to or spread SARS-CoV-2 after touching contaminated surfaces surrounding unsuspected COVID-19 patients presenting for other reasons. Some institutions have begun covering low-flow nasal cannula, at least in certain contexts, 10 11 though discussions with peers across specialities and institutions suggest that practice is far from uniform and is often limited to known COVID-19 patients. 11 By a conservative estimate, if 10% of the occupants of the roughly one-million hospital beds in the US are on low-flow nasal cannula oxygen on any given day, that translates into 100,000 patients in US hospitals whose treatment may also be adding to nosocomial spread of SARS-CoV-2. With many governments currently encouraging everyone to wear cloth masks in public to decrease spread, our healthcare systems should likewise consider the potential risks from the constant blowing of uncovered, loose-fitting, low-flow nasal cannula oxygen. abstract: nan url: https://api.elsevier.com/content/article/pii/S0007091220303615 doi: 10.1016/j.bja.2020.05.011 id: cord-275521-dlp055z8 author: Goldman, Emanuel title: Exaggerated risk of transmission of COVID-19 by fomites date: 2020-07-03 words: 737.0 sentences: 42.0 pages: flesch: 58.0 cache: ./cache/cord-275521-dlp055z8.txt txt: ./txt/cord-275521-dlp055z8.txt summary: A clinically significant risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission by fomites (inanimate surfaces or objects) has been assumed on the basis of studies that have little resemblance to real-life scenarios. The longest survival (6 days) of severe acute respiratory syndrome coronavirus (SARS-CoV) on surfaces was done by placing a very large initial virus titre sample (10⁷ infectious virus particles) on the surface being tested. 1 Another study that claimed survival of 4 days used a similarly large sample (10⁶ infectious virus particles) on the surface. 3 Yet another study found long survival (5 days) of human coronavirus 229E on surfaces with what I would still consider a substantially large viral load (10³ plaque-forming units) in a cell lysate. For example, in the studies that used a sample of 10⁷, 10⁶, and 10⁴ particles of infectious virus on a small surface area, 1-3 these concentrations are a lot higher than those in droplets in real-life situations, with the amount of virus actually deposited on surfaces likely to be several orders of magnitude smaller. abstract: nan url: https://api.elsevier.com/content/article/pii/S1473309920305612 doi: 10.1016/s1473-3099(20)30561-2 id: cord-255365-fog62qdu author: Goldstein, Neal D. title: On the importance of early testing even when imperfect in a pandemic such as COVID-19 date: 2020-08-03 words: 1482.0 sentences: 83.0 pages: flesch: 49.0 cache: ./cache/cord-255365-fog62qdu.txt txt: ./txt/cord-255365-fog62qdu.txt summary: bias in identified cases of SARS-CoV-2 infections will vary in the face of unknown data surrounding test sensitivity and specificity. The true prevalence of COVID-19 will vary in the tested population (e.g., whether a drive-thru public event, clinical referral, group home, etc.), therefore we allowed for a hypothetical range from 0% to 50%. When the true prevalence of COVID-19 infection is low, as at the start of a pandemic, there will be a greater number of false positives, even under excellent specificity. If we assume 25% prevalence of disease in the tested population, we could realistically anticipate between 0 and 75 false positive results, and between 0 and 100 false negative results per 1000 tests. Serosurveys employing antibody assays can thereby inform public health surveillance regarding the extent of the population who have been infected at any point with SARS-CoV-2, and track herd immunity thresholds. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2590113320300158 doi: 10.1016/j.gloepi.2020.100031 id: cord-281216-7t647fww author: Goldust, Mohamad title: Performing dermoscopy in the COVID‐19 pandemic date: 2020-05-05 words: 499.0 sentences: 43.0 pages: flesch: 56.0 cache: ./cache/cord-281216-7t647fww.txt txt: ./txt/cord-281216-7t647fww.txt summary: A novel coronavirus (SARS-CoV-2) that has recently emerged from China in late 2019 has become a global pandemic. Recent data has suggested that SARS -COV2 can remain viable in aerosols for multiple hours. However, cross-infection is a significant concern with contact dermoscopy especially during a viral pandemic. to disinfect hands with 60-70% isopropyl alcohol, provide verbal consents, and wear surgical masks before entering procedure rooms. It is advisable to wear adequate eye protection (goggles or visor) considering that exposed mucous membranes and unprotected eyes can increase the risk of SARS-CoV2 transmission. 4 Mucous membrane dermoscopy should only be performed when the examination has fundamental significance for therapeutic decisions. Aerosol and Surface Stability of SARSCoV-2 as Compared with SARS-CoV-1 Identifying gram-positive cocci on dermatoscopes and smartphone adapters using MALDI-TOF MS: a cross-sectional study 2019-nCoV transmission through the ocular surface must not be ignored abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32367660/ doi: 10.1111/dth.13506 id: cord-255325-tl5fm2yu author: Goletic, Teufik title: Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date: 2020-06-19 words: 1726.0 sentences: 95.0 pages: flesch: 49.0 cache: ./cache/cord-255325-tl5fm2yu.txt txt: ./txt/cord-255325-tl5fm2yu.txt summary: Objectives of this research were: To share obtained sequences of the complete genome of SARS-CoV-2 strains from clinical samples of BiH patients diagnosed with COVID-19, and To contribute to the understanding of the interaction of molecular and classical epidemiology findings of COVID 19 in BH and the whole region and give recommendations for the improvement of prevention and future measures. Livno and Banja Luka samples WGS was performed according to the ARTIC amplicon sequencing protocol for MinION for nCoV-2019, which uses two primer pools to generate the sequence, as described elsewhere [7] . The constructed phylogenetic tree in Figure 2 indicates probable multiple independent introduction events as reflected by clustering of each single BiH sequence in a separate cluster, highlighted with red (Livno, EPI_ISL_462753), green (Banja Luka, EPI_ISL_462990), blue (Sarajevo, EPI_ISL_467300) and purple (Tuzla, EPI_ISL_463893). abstract: Whole Genome Sequence of four samples from COVID-19 outbreaks was done in two laboratories in Bosnia and Herzegovina (Veterinary Faculty Sarajevo and Alea Genetic Center). All four BiH sequences cluster mainly with European ones (Italy, Austria, France, Sweden, Cyprus, England). The constructed phylogenetic tree indicates probable multiple independent introduction events. The success of future containment measures concernig new introductions will be highly challenging for country due to the significant proportion of BH population living abroad. url: https://doi.org/10.1101/2020.06.19.160606 doi: 10.1101/2020.06.19.160606 id: cord-314676-ndke9agh author: Gollapalli, Pavan title: Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 date: 2020-11-04 words: 7090.0 sentences: 338.0 pages: flesch: 51.0 cache: ./cache/cord-314676-ndke9agh.txt txt: ./txt/cord-314676-ndke9agh.txt summary: title: Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 The top hit molecules from this screening were then docked to the SARS-CoV-2 spike glycoprotein RBD-ACE2 interface, after which molecular dynamic simulations of the top scored compound and a reference ligand were performed to compare their binding affinities. To focus on the role of amino acid residues Asn501B and Tyr41A, we performed a docking simulation of the top 5 ligands at the interface of the spike glycoprotein RBD-hACE2 complex (amino acid residues were taken from PDBSum) by setting exhaustiveness to 100 (supplementary material, Table 7 and Figure 4) . The docking calculations at the spike glycoprotein RBD-hACE2 interface showed an even better binding energy and formation of H-bond interactions, and the detailed interaction analysis for the top 5 ligands is reported in Table 2 . abstract: SARS-CoV-2 has become a pandemic causing a serious global health concern. The absence of effective drugs for treatment of the disease has caused its rapid spread on a global scale. Similarly to the SARS-CoV, the SARS-CoV-2 is also involved in a complex interplay with the host cells. This infection is characterized by a diffused alveolar damage consistent with the Acute Respiratory Disease Syndrome (ARDS). To explore the complex mechanisms of the disease at the system level, we used a network medicine tools approach. The protein-protein interactions (PPIs) between the SARS-CoV and the associated human cell proteins are crucial for the viral pathogenesis. Since the cellular entry of SARS-CoV-2 is accomplished by binding of the spike glycoprotein binding domain (RBD) to the human angiotensin-converting enzyme 2 (hACE2), a molecule that can bind to the spike RDB-hACE2 interface could block the virus entry. Here, we performed a virtual screening of 55 compounds to identify potential molecules that can bind to the spike glycoprotein and spike-ACE2 complex interface. It was found that the compound ethyl 1-{3-[(2,4-dichlorobenzyl) carbamoyl]-1-ethyl-6-fluoro-4-oxo-1,4-dihydro-7-quinolinyl}-4-piperidine carboxylate (the S54 ligand) and ethyl 1-{3-[(2,4-dichlorobenzyl) carbamoyl]-1-ethyl-6-fluoro-4-oxo-1,4-dihydro-7-quinolinyl}-4 piperazine carboxylate (the S55 ligand) forms hydrophobic interactions with Tyr41A, Tyr505B and Tyr553B, Leu29A, Phe495B, respectively of the spike glycoprotein, the hotspot residues in the spike glycoprotein RBD-hACE2 binding interface. Furthermore, molecular dynamics simulations and free energy calculations using the MM-GBSA method showed that the S54 ligand is a stronger binder than a known SARS-CoV spike inhibitor SSAA09E3 (N-(9,10-dioxo-9, 10-dihydroanthracen-2-yl) benzamide). Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33146070/ doi: 10.1080/07391102.2020.1841681 id: cord-287628-lzqsh3jf author: Gomersall, Charles D. title: Transmission of SARS to healthcare workers. The experience of a Hong Kong ICU date: 2006-02-25 words: 2608.0 sentences: 151.0 pages: flesch: 58.0 cache: ./cache/cord-287628-lzqsh3jf.txt txt: ./txt/cord-287628-lzqsh3jf.txt summary: CONCLUSIONS: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff exposure times and a sub-standard physical environment. Conclusions: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff If our protective measures were effective when fully developed and rigorously applied, then the logical con-clusion is that intensive care units should have strategies in place to prevent infection of healthcare workers; all staff should be fully aware of the procedures and be fully trained in the use of protective equipment. In summary, our data indicate that, with infection control measures, the risk to ICU healthcare workers of acquiring SARS is low, despite prolonged exposure to patients with SARS. abstract: OBJECTIVE: To describe the extent and temporal pattern of transmission of severe acute respiratory syndrome (SARS) to intensive care unit staff. DESIGN: Retrospective observational cohort study. SETTING: University hospital intensive care unit, caring solely for patients with SARS or suspected to have SARS. PARTICIPANTS: Thirty-five doctors and 152 nurses and healthcare assistants who worked in the ICU during the SARS epidemic. Interventions: Infection control measures designed to prevent transmission of disease to staff were implemented. MEASUREMENTS AND RESULTS: Sixty-seven patients with SARS were admitted to the intensive care unit. Four nurses and one healthcare assistant contracted SARS, with three of these developing symptoms within 10 days of admission of the first patient with SARS. Doctors were exposed to patients with SARS for a median (IQR) of 284 (97–376) h, while nurses and healthcare assistants were exposed for a median (IQR) of 119 (57–166) h. The ICU did not meet international standards for physical space or ventilation. CONCLUSIONS: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff exposure times and a sub-standard physical environment. ELECTRONIC SUPPLEMENTARY MATERIAL: The electronic reference of this article is http://dx.doi.org/10.1007/s00134-006-0081-1 The online full-text version of this article includes electronic supplementary material. This material is available to authorised users and can be accessed by means of the ESM button beneath the abstract or in the structured full-text article. To cite or link to this article you can use the above reference. url: https://www.ncbi.nlm.nih.gov/pubmed/16505989/ doi: 10.1007/s00134-006-0081-1 id: cord-300046-orlga9qf author: Gomes da Silva, J. title: Health literacy of inland population in the mitigation phase 3.2. of COVID-19''s pandemic in Portugal - a descriptive cohort study date: 2020-05-14 words: 5399.0 sentences: 273.0 pages: flesch: 48.0 cache: ./cache/cord-300046-orlga9qf.txt txt: ./txt/cord-300046-orlga9qf.txt summary: Globally, younger individuals, females, graduates and the Non-Risk Group presented higher relative frequencies of the correct answer along COVID-19''s Questionnaire. However, three exceptions were observed: the Undergraduate Group and the Risk-Group had a high relative frequency stating that COVID-19 has a cure and in mentioning "Social Isolation" as an important preventive measure to adopt when compared to the Graduate Group and the Non-Risk Group, respectively. Males have higher relative frequency in answering the correct number of SNS24 and in stating that children can get sick and transmit the infection by SARS-CoV-2 when compared to females ( Table 2 -Supplementary information). Nonparametric tests reveal a statistically significant association regarding variable "Age", "Gender" and "Risk Factor", with younger individuals, females and individuals from Risk-Group stating more often the correct answer. Nonparametric tests reveal a statistically significant association regarding variable "Gender" and "Risk Factor", with males and individuals from Non-Risk Group answering the correct number. abstract: Background: COVID-19 is a respiratory disease transmitted through respiratory droplets with a high transmission rate. There's still no effective and approved antiretroviral treatment or vaccine, thus, preventive measures are the main key to contain this pandemic. Portugal is now in phase 3.2 of the mitigation of COVID-19, being imperative to understand the health literacy of our country and how to prevent the lack of information, through community empowerment. Material and methods: A cross-sectional study with a cohort from a primary care facility was conducted. We collected demographic and epidemiological data and carried out a questionnaire by phone call. Descriptive statistics and nonparametric tests were used to assess associations between the independent variables and the level of health literacy. The level of significance was set at p<0.05. Results: Our cohort includes 222 subjects (median age: 62 years old), mostly females (131), undergraduate (193) and with at least one risk factor for COVID-19 (144). Globally, younger individuals, females, graduates and the Non-Risk Group appear to have higher levels of health literacy, with some exceptions to this pattern. Conclusions: We observe a well-informed population. However, being a pandemic situation, we intend to identify and correct outliers/misconceptions. This work allows a perspective of the current state/pattern of health literacy as well as its possible predictors. Furthermore, this study makes aware of how relevant the specific communication approaches are. Further studies to understand the predictors of health literacy are necessary. Key-Words: COVID-19, pandemic, SARS-CoV2, Portugal, Health literacy. url: https://doi.org/10.1101/2020.05.11.20098061 doi: 10.1101/2020.05.11.20098061 id: cord-305742-wf6qxplf author: Gomez, Santiago A. title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 words: 3457.0 sentences: 176.0 pages: flesch: 53.0 cache: ./cache/cord-305742-wf6qxplf.txt txt: ./txt/cord-305742-wf6qxplf.txt summary: In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. abstract: The magnified infectious power of the SARS–CoV–2 virus compared to its precursor SARS–CoV is intimately linked to an enhanced ability in the mutated virus to find available hydrogen bond sites in the host cells. This characteristic is acquired during virus evolution because of the selective pressure exerted at the molecular level. We pinpoint the specific residue (in the virus) to residue (in the cell) contacts during the initial recognition and binding and show that the virus· · · cell interaction is mainly due to an extensive network of hydrogen bonds and to a large surface of non–covalent interactions. In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. url: https://doi.org/10.1002/cbic.202000618 doi: 10.1002/cbic.202000618 id: cord-273626-zy8qjaai author: Gong, Shu‐ran title: The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models date: 2018-07-28 words: 3257.0 sentences: 183.0 pages: flesch: 56.0 cache: ./cache/cord-273626-zy8qjaai.txt txt: ./txt/cord-273626-zy8qjaai.txt summary: This illness has been named Middle East respiratory syndrome and the pathogen (MERS-CoV) has been shown to be a type of coronavirus that is highly related to SARS-CoV. Another suitable and well-established model is the common marmoset (Saguinus mystax), which can show more severe clinical signs than rhesus macaques when infected with MERS-CoV. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Middle East Respiratory Syndrome Coronavirus (MERS-CoV) origin and animal reservoir Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques Studies of severe acute respiratory syndrome coronavirus pathology in human cases and animal models Infection, replication, and transmission of middle east respiratory syndrome Coronavirus in Alpacas abstract: In humans, infection with the coronavirus, especially the severe acute respiratory syndrome coronavirus (SARS‐CoV) and the emerging Middle East respiratory syndrome coronavirus (MERS‐CoV), induces acute respiratory failure, resulting in high mortality. Irregular coronavirus related epidemics indicate that the evolutionary origins of these two pathogens need to be identified urgently and there are still questions related to suitable laboratory animal models. Thus, in this review we aim to highlight key discoveries concerning the animal origin of the virus and summarize and compare current animal models. url: https://doi.org/10.1002/ame2.12017 doi: 10.1002/ame2.12017 id: cord-305266-fuaq4ujb author: Gong, Yue title: Early Research on COVID-19: A Bibliometric Analysis date: 2020-08-05 words: 2118.0 sentences: 125.0 pages: flesch: 44.0 cache: ./cache/cord-305266-fuaq4ujb.txt txt: ./txt/cord-305266-fuaq4ujb.txt summary: In this review, we found that because of the rapid response of researchers worldwide, the number of COVID-19-related publications showed a high growth trend in the first ten days of February; among these, the largest number of studies originated in China, the country most affected by pandemic in its early stages. The Coronavirus Study Group 4 (CSG) of the International Committee on Taxonomy of Viruses designated the causative 5 virus as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease, 6 which subsequently spread globally, was named coronavirus disease of 2019 7 COVID-19, covering topics such as etiology, diagnosis, epidemiology, treatment, 24 prognosis, nursing, prevention and control, were available in the PubMed and China 25 national knowledge infrastructure (CNKI) databases. Escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in Hong Kong abstract: Abstract In December 2019, an outbreak of pneumonia, which was named COVID-2019, emerged as a global health crisis. Scientists worldwide are engaged in attempts to elucidate the transmission and pathogenic mechanisms of the causative coronavirus. COVID-19 was declared a pandemic by the World Health Organization in March 2020, making it critical to track and review the state of research on COVID-19 to provide guidance for further investigations. Here, bibliometric and knowledge mapping analyses of studies on COVID-19 were performed, including more than 1500 papers on COVID-19 available in the PubMed and CNKI databases from January 1, 2020 to March 8, 2020. In this review, we found that because of the rapid response of researchers worldwide, the number of COVID-19-related publications showed a high growth trend in the first ten days of February; among these, the largest number of studies originated in China, the country most affected by pandemic in its early stages. Our findings revealed that the epidemic situation and data accessibility of different research teams have caused obvious difference in emphases of the publications. Besides, there was an unprecedented level of close cooperation and information sharing within the global scientific community relative to previous coronavirus research. We combed and drew the knowledge map of the SARS-CoV-2 literature, explored early status of research on etiology, pathology, epidemiology, treatment, prevention, and control, and discussed knowledge gaps that remain to be urgently addressed. Future perspectives on treatment, prevention, and control were also presented to provide fundamental references for current and future coronavirus research. url: https://www.sciencedirect.com/science/article/pii/S2666675820300278?v=s5 doi: 10.1016/j.xinn.2020.100027 id: cord-259699-48jg7ci7 author: González-Calatayud, Dra Mariel title: Observational study of the suspected or confirmed cases of sars COV-2 infection needing emergency surgical intervention during the first months of the pandemic in a third level hospital: Case series date: 2020-10-24 words: 2797.0 sentences: 131.0 pages: flesch: 46.0 cache: ./cache/cord-259699-48jg7ci7.txt txt: ./txt/cord-259699-48jg7ci7.txt summary: METHOD: We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial biomarkers (first five days of hospitalization), days of hospital stay, days in the Intensive Care Unit and reason for discharge. We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial laboratory tests (first five days of hospitalization): ferritin, D-dimer, total leucocyte count, total lymphocyte count, lymphocytes (%), platelets, lactate dehydrogenase, fibrinogen, and procalcitonin; we also considered days of hospital stay (DOHS), days in the Intensive Care Unit (ICU), and reason for discharge. Indeed, it has been decided to reduce elective surgical treatment, we have also observed that patients undergoing emergency surgery with suspicion or confirmation of SARS-Cov-2 infection have significant mortality depending on the performed surgical procedure, without relevant findings regarding biomarkers. abstract: Approximately 28, 404, 603 surgical events have been suspended in the 12 peak weeks of the COVID-19 pandemic. The aim of this study was to report all the surgically intervened patients with suspected or confirmed SARS CoV-2 infection from April 1 to July 31, 2020, and to estimate their prognosis in the Surgical Therapy Department of a third level hospital in Mexico. METHOD: We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial biomarkers (first five days of hospitalization), days of hospital stay, days in the Intensive Care Unit and reason for discharge. RESULTS: 42 patients have been surgically intervened, with a total of 49 surgeries. For Otolaringology and General Surgery, there were more deceased cases than alive cases; while for Thoracic Surgery, and Obstetrics and Gynecology, there were more alive cases than deceased ones (36% and 0% deceased, respectively), with statistically significant differences (p = 0.014). With regard to mortality for each group of surgical procedure, patients who underwent C-section or pleurostomy had a mortality rate of 0%; the mortality rate for patients who underwent tracheostomy was 52%; patients who underwent laparotomy had a mortality rate of 54%; for those who underwent debridement, the mortality rate was 100%; which show significant differences, with a p value of 0.03. DISCUSSION: we identified an overall mortality rate of 42.8%, with a significant difference between treating departments and type of surgical procedure. This can be explained because many of the General Surgery patients, in addition to their infectious process by COVID-19, had another complication, like sepsis, In the same way, we can say that pregnant patients are healthy and have a physiological condition. Finally, patients undergoing an open tracheostomy had solely pulmonary complications. CONCLUSION: There is no doubt that we face an unknown condition for which we have been learning tests along the way. This sample of cases undergoing surgery at the beginning of the COVID-19 pandemic can provide clues on relevant results that we must consider for future cases. url: https://www.sciencedirect.com/science/article/pii/S2049080120303939?v=s5 doi: 10.1016/j.amsu.2020.10.038 id: cord-338744-2kizbzns author: González-Castro, A. title: Síndrome post-cuidados intensivos después de la pandemia por SARS-CoV-2 date: 2020-04-27 words: 465.0 sentences: 48.0 pages: flesch: 57.0 cache: ./cache/cord-338744-2kizbzns.txt txt: ./txt/cord-338744-2kizbzns.txt summary: El mundo está inmerso en una pandemia por SARS-CoV-2 que Q2 está llevando a los sistemas sanitarios al borde del colapso y a las unidades de cuidados intensivos a trabajar por encima de su capacidad. Dentro de este panorama general, los servicios de cuidados intensivos deben de estar alertados para identificar «la cola de la primera oleada», que englobará un síndrome post-cuidados intensivos (SPCI) de una gran magnitud y con características especiales. En circunstancias normales el SPCI afecta al 30-50% de nuestros pacientes 3 y sus secuelas pueden persistir incluso más allá de los 5 años tras el alta hospitalaria, especialmente en la recuperación del síndrome respiratorio agudo 4 . Si otras condiciones nos mostraron que hasta el 16% de los familiares no habían reducido el nivel de depresión al año del alta 5 ¿estaremos preparados para el SPCI-post Working experiences of nurses during the Middle East respiratory syndrome outbreak Functional disability 5 years after acute respiratory distress syndrome abstract: nan url: https://doi.org/10.1016/j.medin.2020.04.011 doi: 10.1016/j.medin.2020.04.011 id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 words: 3999.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-277357-lpurk7pe.txt txt: ./txt/cord-277357-lpurk7pe.txt summary: title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. abstract: The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×10(5) DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32790779/ doi: 10.1371/journal.pone.0237418 id: cord-314024-n6l2804j author: Gonçalves, Antonio title: Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date: 2020-04-07 words: 2091.0 sentences: 130.0 pages: flesch: 54.0 cache: ./cache/cord-314024-n6l2804j.txt txt: ./txt/cord-314024-n6l2804j.txt summary: We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We 162 considered a simple case where the drug effectiveness is assumed to be constant after therapy 163 initiation (see methods) and we calculated the minimal efficacy that would be needed to 164 generate more than 2 logs of viral decline at peak viral load in the 13 studied patients (Fig. 1) . For a putative 167 treatment initiated at the time of infection, symptom onset, or 3 days post symptom onset, a 168 median efficacy of at least 60, 90 and 99% in reducing viral replication would be needed, 169 respectively, to generate more than 2 log of decline in the peak viral load (Fig. 1) . abstract: We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer viral growth parameters and predict the effects of antiviral treatments. In order to reduce peak viral load by more than 2 logs, drug efficacy needs to be greater than 80% if treatment is administered after symptom onset; an efficacy of 50% could be sufficient if treatment is initiated before symptom onset. Given their pharmacokinetic/pharmacodynamic properties, current investigated drugs may be in a range of 20-70% efficacy. They may help control virus if administered very early, but may not have a major effect in severe patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32511641/ doi: 10.1101/2020.04.04.20047886 id: cord-304479-uxp1kg86 author: Goodarzi, Pedram title: Coronavirus disease 2019 (COVID-19): Immunological approaches and emerging pharmacologic treatments date: 2020-08-08 words: 8098.0 sentences: 434.0 pages: flesch: 41.0 cache: ./cache/cord-304479-uxp1kg86.txt txt: ./txt/cord-304479-uxp1kg86.txt summary: Finally, recently, a case report study from Japan shows that orally inhaled ciclesonide alleviates the local inflammation in the lung of patients with COVID-19 pneumonia and inhibits the propagation of the virus by antiviral activity [60] . In the same way, a recent case-report study showed that the adoptive transfer therapy of human umbilical cord blood derived-mesenchymal stem cells (hUCMSCs) to a Chinese female patient afflicted with acute COVID19 syndromes improved her laboratory tests and CT images [69] . In vitro evidence of activity against SARS-CoV-2 in infected Vero E6 cells reported with high concentrations of the drug [104, 105, 142] FPV significantly improved the latency to relief for pyrexia and cough [99] FPV in patients with COVID-19 led to decrease of viral load and significant improvement in chest imaging compared with the control arm [98] abstract: The SARS-CoV-2 virus is an etiological agent of pandemic COVID-19, which spreads rapidly worldwide. No proven effective therapies currently exist for this virus, and efforts to develop antiviral strategies for the treatment of COVID-19 are underway. The rapidly increasing understanding of SARS-CoV-2 virology provides a notable number of possible immunological procedures and drug targets. However, gaps remain in our understanding of the pathogenesis of COVID-19. In this review, we describe the latest information in the context of immunological approaches and emerging current antiviral strategies for COVID-19 treatment. url: https://api.elsevier.com/content/article/pii/S1567576920323092 doi: 10.1016/j.intimp.2020.106885 id: cord-288255-p8uzrsbd author: Goossens, Gijs H. title: Obesity and COVID-19: A Perspective from the European Association for the Study of Obesity on Immunological Perturbations, Therapeutic Challenges, and Opportunities in Obesity date: 2020-08-13 words: 7043.0 sentences: 333.0 pages: flesch: 36.0 cache: ./cache/cord-288255-p8uzrsbd.txt txt: ./txt/cord-288255-p8uzrsbd.txt summary: authors: Goossens, Gijs H.; Dicker, Dror; Farpour-Lambert, Nathalie J.; Frühbeck, Gema; Mullerova, Dana; Woodward, Euan; Holm, Jens-Christian Evidence from studies in humans indicates that people with obesity are characterized by systemic low-grade inflammation, higher susceptibility to infections, dampened immune response to infectious agents, as well as higher morbidity and mortality associated with infections, and demonstrate an impaired immune response to vaccinations and antimicrobial treatment [25] [26] [27] [28] . Together, these findings imply that evaluation of cytokine profiles and immune cell subsets in patients with SARS-CoV-2 infection, and a deeper understanding of the underlying processes, will significantly contribute to better treatment strategies and clinical management of COVID-19 [37] . At the same time, the rapidly emerging clinical data require ongoing scrutiny to understand not only the risks and benefits of single drugs to tackle COVID-19, but also the interaction with pharmacological agents commonly used in people with obesity and related NCDs, including type 2 diabetes and cardiovascular diseases, who are especially at risk of or hospitalized with SARS-CoV-2 infection. abstract: Accumulating evidence suggests that obesity is a major risk factor for the initiation, progression, and outcomes of coronavirus disease 2019 (COVID-19). The European Association for the Study of Obesity (EASO), as a scientific and medical society dedicated to the promotion of health and well-being, is greatly concerned about the concomitant obesity and COVID-19 pandemics and their impact on health and society at large. In this perspective, we will address the inherent immunological perturbations and alterations in the renin-angiotensin-aldosterone system in patients with obesity and COVID-19, and discuss how these impairments may underlie the increased susceptibility and more detrimental outcomes of COVID-19 in people with obesity. Clearly, this has important implications for preventive measures, vaccination, and future therapeutic strategies to combat COVID-19. Furthermore, we will highlight important knowledge gaps and provide suggestions for future research and recommendations for policy actions. Since many new reports on COVID-19 rapidly appear, the present perspective should be seen as a focus for discussion to drive forward further understanding, research initiatives, and clinical management of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32791497/ doi: 10.1159/000510719 id: cord-356090-oj3d9ail author: Gorgun, D. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 words: 6065.0 sentences: 277.0 pages: flesch: 51.0 cache: ./cache/cord-356090-oj3d9ail.txt txt: ./txt/cord-356090-oj3d9ail.txt summary: Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. In this study, using a large set of simulations, we describe how the SARS-CoV2 FP binds mammalian cellular membranes and characterize, at atomic details, lipid-protein interactions important for the stability of the bound state. abstract: Infection of human cells by the SARS-CoV2 relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas. In 60% of the simulations, the FP reaches a stable, membrane-bound configuration where the peptide deeply penetrated into the membrane. Clustering of the results reveals two major membrane binding modes, the helix-binding mode and the loop-binding mode. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In the helix-binding mode, the helix is stabilized in an oblique angle with respect to the membrane with its N-terminus tilted towards the membrane core. Analysis of the FP-lipid interactions shows the involvement of specific residues of the helix in membrane binding previously described as the fusion active core residues. Taken together, the results shed light on a key step involved in SARS-CoV2 infection with potential implications in designing novel inhibitors. SIGNIFICANCE A key step in cellular infection by the SARS-CoV2 virus is its attachment to and penetration into the plasma membrane of human cells. These processes hinge upon the membrane interaction of the viral fusion peptide, a segment exposed by the spike protein upon its conformational changes after encountering the host cell. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. url: https://doi.org/10.1101/2020.10.27.357350 doi: 10.1101/2020.10.27.357350 id: cord-348748-rxyh58eu author: Gorospe, Luis title: COVID-19: Thoracic Diagnostic Interventional Procedures in Troubled Times() date: 2020-09-07 words: 1272.0 sentences: 64.0 pages: flesch: 49.0 cache: ./cache/cord-348748-rxyh58eu.txt txt: ./txt/cord-348748-rxyh58eu.txt summary: Some publications have addressed the clinical management of cancer patients in the current SARS-CoV-2 pandemic, but there are no specific guidelines for performing thoracic diagnostic interventional procedures in patients with tumors who are also infected with SARS-CoV-2. Because of this situation, most of the hospital''s clinical activity (like many other centers throughout the country) was focused on the treatment of Covid-19 patients, and large numbers of medical personnel (including pulmonologists, medical oncologists and radiation therapists, thoracic surgeons, pathologists, and radiologists) had been recruited from different departments of the center for the care and management of these patients. 15 Recent articles have reminded us how important it is for radiology departments to be prepared for COVID-19 (from the indication of chest X-rays or CT to the protection of their staff), 16 but there are no specific guidelines for performing diagnostic thoracic interventional procedures in patients with tumor lesions who are also infected with SARS-CoV-2. abstract: nan url: https://api.elsevier.com/content/article/pii/S1579212920302172 doi: 10.1016/j.arbr.2020.08.008 id: cord-331680-qlzhtxs0 author: Goryachev, A.N. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 words: 4106.0 sentences: 200.0 pages: flesch: 51.0 cache: ./cache/cord-331680-qlzhtxs0.txt txt: ./txt/cord-331680-qlzhtxs0.txt summary: In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. abstract: Data on potential effectiveness and prospects of treatment of new coronavirus infection of COVID-19 caused by virus SARS-CoV-2 with the help of antisense oligonucleotides acting against RNA of virus on an in vitro model are given. The ability of antisense oligonucleotides to suppress viral replication in diseases caused by coronaviruses using the example of SARS and MERS is shown. The identity of the initial regulatory section of RNA of various coronaviruses was found within 50 - 100 nucleotides from the 5’-end, which allows using antisense suppression of this RNA fragment. A new RNA fragment of the virus present in all samples of coronovirus SARS-CoV-2 has been identified, the suppression of which with the help of an antisense oligonucleotide can be effective in the treatment of COVID-19. The study of the synthesized antisense oligonucleotide 5’ - AGCCGAGTGACAGCC ACACAG, complementary to the selected virus RNA sequence, was carried out. The low toxicity of the preparations of this group in the cell culture study and the ability to reduce viral load at high doses according to real time-PCR data are shown. The cytopathogenic dose exceeds 2 mg / ml. At a dosage of 1 mg / ml, viral replication is reduced by 5-13 times. Conclusions are made about the prospects of this direction and the feasibility of using the inhalation way of drug administration into the body. url: https://doi.org/10.1101/2020.11.02.363598 doi: 10.1101/2020.11.02.363598 id: cord-279563-4lu1n0s7 author: Gorzalski, Andrew J. title: High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date: 2020-06-10 words: 1720.0 sentences: 116.0 pages: flesch: 47.0 cache: ./cache/cord-279563-4lu1n0s7.txt txt: ./txt/cord-279563-4lu1n0s7.txt summary: The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). CONCLUSIONS: The higher analytical sensitivity may explain the assay''s ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. To assess differences in analytical sensitivity between real-time PCR and TMA, we performed a limit-ofdetection (LoD) study by creating a dilution series of purified / quantified SARS-CoV-2 genomic material either in VTM or APTIMA collection matrix. Noting the sensitivity difference demonstrated by the LoD study, we sought to assess the performance of TMA on specimens previously tested by RT-PCR for SARS-CoV-2. The Hologic Panther SARS-CoV-2 transcription mediated amplification test showed higher analytical sensitivity when compared to real time PCR for the detection of SARS-CoV-2. abstract: BACKGROUND: As the demand for laboratory testing for SARS-CoV-2 increases, additional varieties of testing methodologies are being considered. While real time polymerase chain reaction (RT-PCR) has performed as the main method for virus detection, other methods are becoming available, including transcription mediated amplification (TMA). The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). OBJECTIVES: We sought to compare the sensitivity and specificity of the Aptima SARS-CoV-2 Assay to RTPCR as a means of SARS-CoV-2 detection in a diagnostic setting. STUDY DESIGN: We performed a limit-of-detection study (LoD) to assess the analytical sensitivity of TMA and RT-PCR. This preceded a comparison of the methods using previously evaluated clinical specimens (nasopharyngeal swabs) using 116 human specimens tested by both methodologies. Specimens included sixty-one (61) specimens found reactive by real-time PCR, fifty-one (51) found non-reactive, and four (4) deemed inconclusive. RESULTS: The Aptima SARS-CoV-2 Assay showed a markedly higher analytical sensitivity than RT-PCR by LoD study. Evaluation of clinical specimens resulted in fewer inconclusive results by the SARS-CoV-2 assay, leading to potentially higher clinical sensitivity. CONCLUSIONS: The higher analytical sensitivity may explain the assay’s ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. TMA provides an effective, highly sensitive means of detection of SARS-CoV-2 in nasopharyngeal specimens. url: https://www.sciencedirect.com/science/article/pii/S1386653220302432?v=s5 doi: 10.1016/j.jcv.2020.104501 id: cord-277260-7se220oz author: Gosain, Rohit title: COVID-19 and Cancer: a Comprehensive Review date: 2020-05-08 words: 5926.0 sentences: 306.0 pages: flesch: 39.0 cache: ./cache/cord-277260-7se220oz.txt txt: ./txt/cord-277260-7se220oz.txt summary: Since the emergence of the first case in Wuhan, China, in December 2019, tremendous research efforts have been underway to understand the mechanisms of infectivity and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a fatal virus responsible for abysmal survival outcomes. Data from China thus far have shown that cancer patients infected with COVID-19 are at 3.5 times the risk of requiring mechanical ventilation or ICU admission, compared to the general population [9•] . The CALAVI trial will be initiated as a randomized global clinical trial to assess the potential of acalabrutinib in the treatment of the cytokine storm associated with severely ill COVID-19 patients [86] . An exploratory meta-analysis of 32 studies showed evidence of reduced mortality after receiving various doses of convalescent plasma in patients with severe acute respiratory infections of viral etiology [92] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China abstract: PURPOSE OF REVIEW: The outbreak of the novel coronavirus disease 2019 (COVID-19) has emerged to be the biggest global health threat worldwide, which has now infected over 1.7 million people and claimed more than 100,000 lives around the world. Under these unprecedented circumstances, there are no well-established guidelines for cancer patients. RECENT FINDINGS: The risk for serious disease and death in COVID-19 cases increases with advancing age and presence of comorbid health conditions. Since the emergence of the first case in Wuhan, China, in December 2019, tremendous research efforts have been underway to understand the mechanisms of infectivity and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a fatal virus responsible for abysmal survival outcomes. To minimize the mortality rate, it becomes prudent to identify symptoms promptly and employ treatments appropriately. Even though no cure has been established, multiple clinical trials are underway to determine the most optimal strategy. Managing cancer patients under these circumstances is rather challenging, given their vulnerable status and the aggressive nature of their underlying disease. SUMMARY: In this comprehensive review, we discuss the impact of COVID-19 on health and the immune system of those affected, reviewing the latest treatment approaches and ongoing clinical trials. Additionally, we discuss challenges faced while treating cancer patients and propose potential approaches to manage this vulnerable population during this pandemic. url: https://doi.org/10.1007/s11912-020-00934-7 doi: 10.1007/s11912-020-00934-7 id: cord-287991-10jz1dz2 author: Goshen-Lago, Tal title: The Potential Role of Immune Alteration in the Cancer–COVID19 Equation—A Prospective Longitudinal Study date: 2020-08-26 words: 4497.0 sentences: 235.0 pages: flesch: 47.0 cache: ./cache/cord-287991-10jz1dz2.txt txt: ./txt/cord-287991-10jz1dz2.txt summary: Conclusion: Our results indicate a similar rate of asymptomatic COVID19 infection in cancer patients and healthcare workers in a longitudinal study throughout the pandemic time. During the study interval, there was no documented symptomatic case of COVID19 among the recruited participants, nor in the general patient population of the cancer center or in the healthcare workers cohort. Furthermore, when analyzing the myeloid lineage, we found a substantial increase in myeloid cells in cancer patients compared to healthcare workers (both SARS-CoV-2 IgG-), in line with previous studies [11, 12] . Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. abstract: SIMPLE SUMMARY: Despite lack of concrete evidence, cancer patients were considered at the onset of the COVID19 pandemic as high-risk population for COVID19 infection. However, current evidence is inconclusive and the potential role of cancer or anti-neoplastic treatments in COVID19 course remains to be elucidated. Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents the host response to the SARS-COV2 may lessen symptom severity. Delineating COVID-19 infection trends in asymptomatic healthcare workers as well as a cohort of cancer patients who are on active anti-cancer treatment will lend credence to tailor future healthcare policy in the next phases of the pandemic. ABSTRACT: Background: The risk of cancer patients to develop COVID19 infection is unclear. We aimed to prospectively study cancer patients and oncology healthcare workers for COVID19 serology. In IgG+ cases, immune profile was determined to portray the pattern of immune response to SARS-CoV2. Methods: Cancer patients on active treatment and healthcare workers were enrolled. During the study period (3/2020–6/2020), demographic data and blood were collected at three time points. Expression of IgG, IgM, and IgA were assessed. In SARS-CoV-2 IgG+ cases and matched negative cases, we performed mass cytometry time of flight (CyTOF) analysis on the basis of the expression of surface markers. Results: The study included 164 cancer patients on active intravenous treatment and 107 healthcare workers at the cancer center. No symptomatic cases were reported during the study period. Serology analysis revealed four IgG+ patients (2.4%) and two IgG+ healthcare workers (1.9%)—all were asymptomatic. CyTOF analysis demonstrated substantial reduction in myeloid cells in healthcare workers who were SARS-CoV-2 IgG+ compared to those who were SARS-CoV-2 IgG-, whereas in cancer patients, the reduction was relatively milder (≈50% reduction in SARS-CoV-2 IgG+ cancer patients compared with ≈90% reduction in SARS-CoV-2 IgG+ workers). Conclusion: Our results indicate a similar rate of asymptomatic COVID19 infection in cancer patients and healthcare workers in a longitudinal study throughout the pandemic time. Due to differential immune cell profiles of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may play a role in COVID19 course and representation. The immunological perspective of cancer treatments on the risk for COVID19 infection should be further explored. url: https://doi.org/10.3390/cancers12092421 doi: 10.3390/cancers12092421 id: cord-257408-ejhhk1iu author: Goss, Matthew B. title: The Pediatric Solid Organ Transplant Experience with COVID‐19: An Initial Multi‐Center, Multi‐Organ Case Series date: 2020-09-18 words: 2294.0 sentences: 146.0 pages: flesch: 46.0 cache: ./cache/cord-257408-ejhhk1iu.txt txt: ./txt/cord-257408-ejhhk1iu.txt summary: CONCLUSIONS: Our multi‐institutional experience suggests the prognoses of pediatric transplant recipients infected with COVID‐19 may mirror those of immunocompetent children, with infrequent hospitalization and minimal treatment, if any, required. Many adult centers (2) (3) (4) have suggested that transplant recipients are at particular risk for an arduous clinical course given their immunocompromised state, though highly associated comorbidities exist as confounders and appear to play a significant role in COVID-19 outcomes for the transplant subpopulation (5) . Data were collected via institutions'' respective electronic medical record systems and were reviewed for patient characteristics, history of recent exposure, timing of presentation, symptomatology, laboratory values, immunosuppression management, antiviral treatment strategies, and clinical outcomes. To date, the bulk of the literature examining COVID-19 following transplant is adult focused, with pediatric reports limited to single patient experiences. Comorbidities associated with a severe COVID-19 clinical phenotype among adult transplant recipients, e.g. hypertension, obesity, and diabetes, (14) are less prevalent in the pediatric population. abstract: BACKGROUND: The clinical course of COVID‐19 in pediatric solid organ transplant recipients remains ambiguous. Though preliminary experiences with adult transplant recipients have been published, literature centered on the pediatric population is limited. We herein report a multi‐center, multi‐organ cohort analysis of COVID‐19 positive transplant recipients ≤ 18 years at time of transplant. METHODS: Data were collected via institutions’ respective electronic medical record systems. Local review boards approved this cross‐institutional study. RESULTS: Among 5 transplant centers, 26 patients (62% male) were reviewed with a median age of 8 years. 6 were heart recipients, 8 kidney, 10 liver, and 2 lung. Presenting symptoms included cough (n=12 (46%)), fever (n=9 (35%)), dry/sore throat (n=3 (12%)), rhinorrhea (n=3 (12%)), anosmia (n=2 (8%)), chest pain (n=2 (8%)), diarrhea (n=2 (8%)), dyspnea (n=1 (4%)), and headache (n=1 (4%)). Six patients (23%) were asymptomatic. No patient required supplemental oxygen, intubation, or ECMO. Eight patients (31%) were hospitalized at time of diagnosis, 3 of whom were already admitted for unrelated problems. Post‐transplant immunosuppression was reduced for only 2 patients (8%). All symptomatic patients recovered within 7 days. CONCLUSIONS: Our multi‐institutional experience suggests the prognoses of pediatric transplant recipients infected with COVID‐19 may mirror those of immunocompetent children, with infrequent hospitalization and minimal treatment, if any, required. url: https://doi.org/10.1111/petr.13868 doi: 10.1111/petr.13868 id: cord-262068-9ixq8hwb author: Gottardi, Andrea De title: Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection date: 2020-06-10 words: 1773.0 sentences: 119.0 pages: flesch: 49.0 cache: ./cache/cord-262068-9ixq8hwb.txt txt: ./txt/cord-262068-9ixq8hwb.txt summary: The data that support the findings of this study are available from the corresponding author, upon Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection SUMMARY We present here the case of a 62-year-old man, who was referred to the emergency department with fever and cough for 3 days. Therefore, due to the potential clinical efficacy for COVID-19 patients [11] and based on SARS clinical cases in 2003 [12] , and before the publication of the LOTUS China trial [13] , we started a treatment with lopinavir 200 mg and ritonavir 50 mg 2-0-2, and hydroxychloroquine 200 mg twice daily. Clinical data available so far indicate that up to 53% of the patients with COVID-19 present increased levels of transaminases during the infection and that liver injury is apparently associated with the severity of respiratory symptoms [14, 15] . abstract: SUMMARY We present here the case of a 62-year-old man, who was referred to the emergency department with fever and cough for 3 days. He underwent liver transplantation 4 years earlier due to HCV and NASH-related cirrhosis with hepatocellular carcinoma. At admission he was in reduced general conditions. Nasopharyngeal smear specimen resulted positive for SARS-CoV-2 infection. Pulmonary low-dose CT-scan revealed bilateral subpleural ground-glass infiltrates. O2 saturation was 93%. A treatment with lopinavir/ritonavir and hydroxychloroquine twice daily was started. The patient received also cefepime and remained in isolation. Seven days later imaging showed a progression of the pulmonary infiltrates. Cefepime was replaced by meropenem. During the following 3 days the fever resolved, and the general conditions of the patient significantly improved. Consequently, treatment with lopinavir/ritonavir and hydroxychloroquine was stopped. The evolution of SARS-CoV-2 interstitial pneumonia in this immunosuppressed patient was moderate to severe and liver injury was not clinically significant. Despite its limitations, this case report confirm that the liver may be only mildly affected during SARS-CoV-2 infection, also in liver transplanted patients. Further studies are needed to assess whether the outcome of SARS-CoV-2 infection is worse in immunosuppressed patients than in the general population. url: https://doi.org/10.1016/j.clinre.2020.05.014 doi: 10.1016/j.clinre.2020.05.014 id: cord-315617-mhm9wh9q author: Gottschalk, René title: Bioterrorism: is it a real threat? date: 2004-09-02 words: 3326.0 sentences: 142.0 pages: flesch: 43.0 cache: ./cache/cord-315617-mhm9wh9q.txt txt: ./txt/cord-315617-mhm9wh9q.txt summary: However, it is the developments over the past years that are causing the greatest concern: new threats to the security of nations are emerging in the form of terrorist organizations that seem to increasingly explore novel ways of spreading terror [1] . Terrorists will know that using highly infectious agents such as the smallpox virus for biological attacks might well mean their spread also to their own followers because they do not have smallpox vaccine or other preventative measures available. tuberculosis, Nipah virus) Third highest priority agents include emerging pathogens that could be engineered for mass dissemination in the future because of: -availability -ease of production and dissemination -potential for high morbidity and mortality rates and major health impact in the aftermath of the 2001 anthrax attacks, with numerous letters allegedly containing B. abstract: The Geneva Protocol of 1925 commits the signatory nations to refraining from the use of biological weapons. However, the terrorist assaults of September 2001 and, subsequently, the anthrax-containing letters are cause for great concerns: new threats to the security of nations are expected, as terrorist organizations seem to increasingly explore novel ways of spreading terror. In this context, naturally emerging diseases such as SARS, monkeypox or West Nile fever assume new importance because it is difficult to distinguish between natural epidemics and possible bioweapon assaults. Great efforts on the part of governments and public health authorities are necessary to counteract these threats. url: https://www.ncbi.nlm.nih.gov/pubmed/15349775/ doi: 10.1007/s00430-004-0228-z id: cord-303539-gimz41yb author: Goudouris, Ekaterini S. title: Laboratory diagnosis of COVID-19() date: 2020-08-31 words: 3605.0 sentences: 220.0 pages: flesch: 45.0 cache: ./cache/cord-303539-gimz41yb.txt txt: ./txt/cord-303539-gimz41yb.txt summary: DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. 25 Some studies report patients with mild (or even asymptomatic) COVID-19 present lower levels of SARS-CoV-2-specific antibodies or may even do not develop detectable levels, while patients with more severe conditions have higher levels of these. 38 The data presented suggest that the diagnosis of COVID-19 should be based on clinical manifestations, contact history, imaging tests, laboratory tests, and not only on serological tests and the search for the genetic material of the virus. The gold standard for the diagnosis of SARS-CoV-2 infection is the identification of viral genetic material by RT-PCR, in different samples, with greater sensitivity in bronchoalveolar lavage and nasopharyngeal swab. abstract: OBJECTIVES: This was a non-systematic review of the literature on the laboratory diagnosis of COVID-19. DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic” OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. SUMMARY OF FINDINGS: Tests for the etiological agent identify genetic material of SARS-CoV-2 or humoral responses to it. The gold standard for diagnosis is the identification of viral genome targets by real-time polymerase chain reaction (RT-PCR) in respiratory tract materials during the first week of symptoms. Serological tests should be indicated from the second week of symptoms onwards. A wide range of different tests is available, with variable sensitivity and specificity, most of which require validation. Laboratory tests such as complete blood count, C-reactive protein (CRP), D-dimer, clotting tests, lactic dehydrogenase (LDH), ferritin, and procalcitonin identify risk of disease with greater severity, thromboembolic complications, myocardial damage, and/or worse prognosis. Imaging tests may be useful for diagnosis, especially when there is a compatible clinical picture, and other tests presented negative results or were unavailable. CONCLUSIONS: The identification of genetic material of the virus by RT-PCR is the gold standard test, but its sensitivity is not satisfactory. The diagnosis of COVID-19 should be based on clinical data, epidemiological history, tests for etiological diagnosis, and tests to support the diagnosis of the disease and/or its complications. New diagnostic methods with higher sensitivity and specificity, as well as faster results, are necessary. url: https://api.elsevier.com/content/article/pii/S0021755720301996 doi: 10.1016/j.jped.2020.08.001 id: cord-305755-6jup93v4 author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date: 2020-07-22 words: 6708.0 sentences: 328.0 pages: flesch: 50.0 cache: ./cache/cord-305755-6jup93v4.txt txt: ./txt/cord-305755-6jup93v4.txt summary: In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analyzed by MS/MS with a short gradient. To foster the development of alternative detection methods for SARS-CoV-2, we performed a proof-of-concept study to assess the potential of MS/MS for proteotyping SARS-CoV-2: (i) in simulated nasal swabs containing different quantities of viral peptides and (ii) in nasopharyngeal swabs from COVID-19 diagnosed patients. abstract: [Image: see text] Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry. url: https://www.ncbi.nlm.nih.gov/pubmed/32697082/ doi: 10.1021/acs.jproteome.0c00535 id: cord-351321-6d2mn5ok author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date: 2020-06-19 words: 6241.0 sentences: 294.0 pages: flesch: 52.0 cache: ./cache/cord-351321-6d2mn5ok.txt txt: ./txt/cord-351321-6d2mn5ok.txt summary: Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. To assess the performance of shotgun MS-based proteomics in detecting SARS-CoV-2 peptides in a background matrix consisting of nasopharyngeal swab protein material, we experimentally created tryptic peptidomes from i) a purified virus solution obtained from Vero E6 cells infected with a SARS-CoV-2 reference strain, and ii) nasopharyngeal swabs obtained from two healthy volunteers (Figure 1) . Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analysed by MS/MS with a short gradient. abstract: Rapid but yet sensitive, specific and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostic that would not require specific reagents are worth to investigate not only for fighting the COVID-19 pandemic, but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry. url: https://doi.org/10.1101/2020.06.19.161000 doi: 10.1101/2020.06.19.161000 id: cord-263532-q044i7ym author: Goyal, Bhupesh title: Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy date: 2020-05-13 words: 6017.0 sentences: 402.0 pages: flesch: 54.0 cache: ./cache/cord-263532-q044i7ym.txt txt: ./txt/cord-263532-q044i7ym.txt summary: In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M(pro) on its dimerization and, thus, catalytic activity. The individual monomers of SARS-CoV M pro are enzymatically inactive, and two strategies have been employed to develop inhibitors against this enzyme: (i) molecules targeting the substrate binding pocket to block the catalytic activity, and (ii) dimerization inhibitors. 14, 15 In the present review, literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M pro on its dimerization and, thus, catalytic activity are compiled. The various mutation analyses, N-terminal truncation studies, and MD simulation studies that highlighted key residues of SARS-CoV M pro involved in the stabilization of the catalytically active dimeric structure of the enzyme are listed in Table 2 and are arranged in chronological order. abstract: [Image: see text] A new coronavirus (CoV) caused a pandemic named COVID-19, which has become a global health care emergency in the present time. The virus is referred to as SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) and has a genome similar (∼82%) to that of the previously known SARS-CoV (SARS coronavirus). An attractive therapeutic target for CoVs is the main protease (M(pro)) or 3-chymotrypsin-like cysteine protease (3CL(pro)), as this enzyme plays a key role in polyprotein processing and is active in a dimeric form. Further, M(pro) is highly conserved among various CoVs, and a mutation in M(pro) is often lethal to the virus. Thus, drugs targeting the M(pro) enzyme significantly reduce the risk of mutation-mediated drug resistance and display broad-spectrum antiviral activity. The combinatorial design of peptide-based inhibitors targeting the dimerization of SARS-CoV M(pro) represents a potential therapeutic strategy. In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M(pro) on its dimerization and, thus, catalytic activity. We believe that the present review will stimulate research in this less explored yet quite significant area. The effect of the COVID-19 epidemic and the possibility of future CoV outbreaks strongly emphasize the urgent need for the design and development of potent antiviral agents against CoV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32402186/ doi: 10.1021/acscombsci.0c00058 id: cord-261615-p81l6zvz author: Grabbe, Stephan title: Systemische Immunsuppression in Zeiten von COVID‐19: Müssen wir umdenken? date: 2020-08-21 words: 2089.0 sentences: 202.0 pages: flesch: 36.0 cache: ./cache/cord-261615-p81l6zvz.txt txt: ./txt/cord-261615-p81l6zvz.txt summary: Über eine mögliche therapeutische Wirksamkeit von Chloroquin oder Hydroxychloroquin bei einer COVID-19-Erkrankung wurde bereits in der Laienpresse spekuliert, sodass diese Substanzen vielfach als unkritisch für die Dauerbehandlung von Patienten mit Autoimmunerkrankungen angesehen werden. In der Klinik scheint jedoch die langfristige therapeutische Einnahme von Hydroxychloroquin in Patienten mit systemischem LE nicht vor einer Covid-19-Erkrankung oder einem schweren Verlauf zu schützen [30, 31] . Somit gibt es derzeit keine Hinweise, dass die Therapie mit Chloroquin oder Hydroxychloroquin negative oder schützende Effekte auf eine SARS-CoV-2-Infektion hat oder den Infektionsverlauf ändert. Grundsätzlich gibt es derzeit keine Datenlage für eine generelle Reduktion oder Pausierung einer Immunsuppression bei Patienten mit Autoimmunerkrankungen, da das Risiko einer Untertherapie dieser zumeist schweren Erkrankungen deutlich höher als das eines aggravierten Infektionsverlaufs einer COVID-19-Erkrankung ist. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: Die aktuelle SARS‐CoV‐2 Pandemie gefährdet vor allem ältere Menschen mit kardiopulmonalen und metabolischen Vorerkrankungen. In aktueller Diskussion ist jedoch auch, ob Patienten unter immunsuppressiver Therapie ebenfalls ein höheres Risiko haben, im Fall einer COVID‐19‐Erkrankung einen schweren Krankheitsverlauf zu erleiden. Grundsätzlich gibt es derzeit jedoch keine Datenlage für eine generelle Reduktion oder Pausierung einer Immunsuppression bei Patienten mit Autoimmunerkrankungen in Zeiten der SARS‐CoV‐2‐Pandemie. Da es jedoch derzeit weder eine wirksame Therapie, noch einen entsprechenden Impfschutz gibt, sollten wir uns gezielt mit der Problematik chronisch‐immunsupprimierter Patienten beschäftigen. Um Risiken für Patienten zu minimieren, sollte die Indikation für eine solche Therapie mit besonderer Sorgfalt gestellt werden. Insbesondere sollten Immuntherapeutika, die langfristige Effekte erzeugen (zum Beispiel Rituximab) mit besonderer Vorsicht eingesetzt werden. Demgegenüber könnten immunmodulierende Substanzen, die keine Immunsuppression induzieren (zum Beispiel systemische Immunglobuline, Doxycyclin) oder die intrinsische Wirkungen auf SARS‐CoV‐2 haben (Calcineurininhibitoren, Chloroquin, Hydroxychloroquin), eine sinnvolle Alternative darstellen. url: https://doi.org/10.1111/ddg.14194_g doi: 10.1111/ddg.14194_g id: cord-283380-l60yyr6l author: Grabbe, Stephan title: Systemic immunosuppression in times of COVID‐19: Do we need to rethink our standards? date: 2020-08-02 words: 2577.0 sentences: 123.0 pages: flesch: 35.0 cache: ./cache/cord-283380-l60yyr6l.txt txt: ./txt/cord-283380-l60yyr6l.txt summary: However, it is also currently under discussion whether patients under immunosuppressive therapy also have a higher risk of suffering a severe course of the COVID-19 disease. However, in clinical practice, long-term therapeutic use of hydroxychloroquine in patients with systemic lupus erythematosus does not appear to protect against covid-19 disease or a severe course of the disease [30, 31] . Therefore, the authors recommend that this therapy option should be considered especially in patients with other risk factors for a severe course of SARS-CoV-2 infection. Essentially, there is currently no data available for a general reduction or pause of immunosuppression in patients with autoimmune diseases, since the risk of an insufficient therapy of these mostly severe diseases is clearly higher than that of an aggravated course of COVID-19 disease. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: The current SARS‐CoV‐2 pandemic particularly endangers older people with pre‐existing cardiopulmonary and metabolic conditions. However, it is also currently under discussion whether patients under immunosuppressive therapy also have a higher risk of suffering a severe course of the COVID‐19 disease. In principle though, there is currently no data available for a general reduction or pause of immunosuppression in patients with autoimmune diseases because of the SARS‐CoV‐2 pandemic. However, since there is currently neither an effective therapy nor corresponding vaccination protection, the indication for a prolonged immunosuppressive therapy should be made with special care. In particular, immunotherapeutic agents that produce long‐term effects (e.g., rituximab) should be used with special caution. In contrast, immunomodulating substances that do not suppress antiviral immunity (e.g. systemic immunoglobulins, doxycycline), or that have intrinsic effects on SARS‐CoV‐2 (calcineurin inhibitors, chloroquine, hydroxychloroquine) may be useful alternatives. url: https://www.ncbi.nlm.nih.gov/pubmed/32743938/ doi: 10.1111/ddg.14194 id: cord-327247-dbcacphq author: Grace, Sherry L. title: The Occupational and Psychosocial Impact of SARS on Academic Physicians in Three Affected Hospitals date: 2011-04-12 words: 3019.0 sentences: 154.0 pages: flesch: 46.0 cache: ./cache/cord-327247-dbcacphq.txt txt: ./txt/cord-327247-dbcacphq.txt summary: The survey that was developed was based on a literature review and input from key health care professionals and included items on sociodemographic variables (sex, age, specialty, number and ages of children, number of years in practice, and ethnocultural background); health status; attitudes and perceptions toward SARS; SARSrelated coping methods, concerns, and symptoms; and effects on personal relationships and changes to work resulting from the SARS outbreak. On a scale from 1 (a lot) to 5 (not at all), physicians perceived that their work had been seriously affected by the SARS outbreaks (mean‫,97.1ס‬ SD‫.)98.0ס‬ Ways in which their work had been affected included: interruptions to teaching and education (84.5%, N‫,)361ס‬ unwillingness of patients to attend outpatient clinics (79.8%, N‫,)451ס‬ infection control precautions (77.2%, N‫,)941ס‬ inability to see outpatients (71.0%, N‫,)731ס‬ inability to perform regular activities (51.8%, N‫,)001ס‬ interruptions to research (51.8%, N‫,)001ס‬ new involvement in SARS-related work (8.8%, N‫,)71ס‬ and inability to enter work due to symptoms (4.1%, N‫.)8ס‬ abstract: A cross-sectional anonymous survey was administered to all directory-listed physicians within a network of three large teaching hospitals that provided care to SARS patients in Toronto. One hundred ninety-three physicians participated, 23% of whom provided direct care to SARS patients. A significantly higher rate of psychological distress was seen among physicians providing direct care to SARS patients (45.7%) than among those not providing direct care (17.7%), and physicians providing direct care reported feeling more stigmatized. Several physicians (10.9%) reported entering the hospital despite experiencing identified SARS symptoms. The most frequent SARS concerns were about the care of non-SARS patients following suspension of nonessential services and loss of physician income. url: https://api.elsevier.com/content/article/pii/S0033318205700499 doi: 10.1176/appi.psy.46.5.385 id: cord-348455-vcxalkeo author: Graham, N. R. title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 words: 4105.0 sentences: 283.0 pages: flesch: 62.0 cache: ./cache/cord-348455-vcxalkeo.txt txt: ./txt/cord-348455-vcxalkeo.txt summary: title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. We first piloted our antigen preps for the RBD-S IgG screening assay using serum 81 samples from a PCR-confirmed severe COVID-19 patient (defined as admission to the Intensive 82 Care Unit, ICU) who was admitted to the hospital 10 days following symptom onset and based 83 on an early report suggesting that SARS-CoV-2 could trigger antibody responses in this 84 timeframe (24). Anti-S titers in patients with a negative RBD-S test were 138 generally low and in RBD-positive samples, followed the same trends as RBD-reactivity, 139 providing further confirmation of robust serological responses to SARS-CoV-2 during acute 140 COVID-19. abstract: SARS-CoV-2 is the newly emerged virus responsible for the global COVID-19 pandemic. There is an incomplete understanding of the host humoral immune response to SARS-CoV-2 during acute infection. Host factors such as age and sex as well the kinetics and functionality of antibody responses are important factors to consider as vaccine development proceeds. The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. In a cross-sectional study of anti-RBD-S antibodies in COVID-19 patients we found equivalent levels in male and female patients and no age-related deficiencies even out to 93 years of age. The anti-RBD-S response was evident as little as 6 days after onset of symptoms and for at least 5 weeks after symptom onset. Anti-RBD-S IgG, IgM, and IgA responses were simultaneously induced within 10 days after onset, but isotype-specific kinetics differed such that anti-RBD-S IgG was most sustained over a 5-week period. The kinetics and magnitude of neutralizing antibody formation strongly correlated with that seen for anti-RBD-S antibodies. Our results suggest age- and sex- related disparities in COVID-19 fatalities are not explained by anti-RBD-S responses. The multi-isotype anti-RBD-S response induced by live virus infection could serve as a potential marker by which to monitor vaccine-induced responses. url: http://medrxiv.org/cgi/content/short/2020.07.15.20154443v1?rss=1 doi: 10.1101/2020.07.15.20154443 id: cord-277487-jgbjxgh1 author: Graham, Simon P. title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-06-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Here, we compared the immunogenicity of one or two doses of ChAdOx1 nCoV-19 in both mice and pigs. Whilst a single dose induced antigen-specific antibody and T cells responses, a booster immunisation enhanced antibody responses, particularly in pigs, with a significant increase in SARS-CoV-2 neutralising titres. url: https://doi.org/10.1101/2020.06.20.159715 doi: 10.1101/2020.06.20.159715 id: cord-353826-owoec2ud author: Graham, Simon P. title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-07-27 words: 5496.0 sentences: 269.0 pages: flesch: 53.0 cache: ./cache/cord-353826-owoec2ud.txt txt: ./txt/cord-353826-owoec2ud.txt summary: Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Analysis of SARS-CoV-2 S proteinspecific murine splenocyte responses by IFN-γ ELISpot assay showed no statistically significant difference between the primeonly and prime-boost vaccination regimens, in either strain of mouse (Fig. 1a) . SARS-CoV-2 S protein-specific antibody responses following ChAdOx1 nCoV-19 prime-only and prime-boost vaccination regimens in mice and pigs SARS-CoV-2 S protein-specific antibody titres in serum were determined by ELISA using recombinant soluble trimeric S (FL-S) and receptor binding domain (RBD) proteins. Small animal models have variable success in predicting vaccine efficacy in larger animals but are an important To analyse SARS-CoV-2 S-specific T cell responses, all mice were sacrificed on day 49 for isolation of splenocytes and pigs were blood sampled longitudinally to isolate PBMC. abstract: Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Here, we compared the immunogenicity of one or two doses of ChAdOx1 nCoV-19 in both mice and pigs. Whilst a single dose induced antigen-specific antibody and T cells responses, a booster immunisation enhanced antibody responses, particularly in pigs, with a significant increase in SARS-CoV-2 neutralising titres. url: https://doi.org/10.1038/s41541-020-00221-3 doi: 10.1038/s41541-020-00221-3 id: cord-272702-7uc4ozjy author: Graham, T. G. W. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 words: 8061.0 sentences: 483.0 pages: flesch: 59.0 cache: ./cache/cord-272702-7uc4ozjy.txt txt: ./txt/cord-272702-7uc4ozjy.txt summary: We therefore tested whether we could detect SARS-CoV-2 RNA by adding 1 μ l of each swab sample to 20 μ l TaqPath reactions containing the N1, N2, and RNase P (RP) probes ( Fig 2A) . Taken together, these results show that RT-qPCR with BEARmix can detect SARS-CoV-2 in clinical samples, either using purified RNA or by direct addition of swab samples, albeit with somewhat less sensitivity than commercial TaqPath master mix. To evaluate a complete protocol in which swab samples are collected into PK solution and then added directly to BEARmix RT-PCRs, we prepared contrived swab samples in which live virus was mixed with pathogenfree human nasal fluid prior to dilution into either DNA/RNA Shield, VCM containing 0.4 mg/ml proteinase K, or a solution of 0.4 mg/ml proteinase K in water (Fig 6) . Here we have developed simple, academic laboratory-derived methods for RNA extraction, direct sample addition, and RT-PCR detection that provide low-cost alternatives to the use of commercial kits (Fig 8) . abstract: Re-opening of communities in the midst of the ongoing COVID-19 pandemic has ignited a second wave of infections in many places around the world. Mitigating the risk of reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. To this end, we evaluated several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods. First, we show that isopropanol precipitation provides an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, we evaluate direct addition of NP swab samples to RT-qPCR reactions without an RNA extraction step. We describe a simple, inexpensive swab collection solution suitable for direct addition, which we validate using contrived swab samples. Third, we describe an open-source master mix for RT-qPCR and show that it permits detection of viral RNA in NP swab samples. Lastly, we show that an end-point fluorescence measurement provides an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, inexpensive methods has the potential to significantly reduce the time and expense of COVID-19 testing. url: https://doi.org/10.1101/2020.09.16.20193466 doi: 10.1101/2020.09.16.20193466 id: cord-268406-3v309r41 author: Grajewski, Rafael S. title: A missing link between SARS‐CoV‐2 and the eye?: ACE2 expression on the ocular surface date: 2020-06-12 words: 668.0 sentences: 53.0 pages: flesch: 53.0 cache: ./cache/cord-268406-3v309r41.txt txt: ./txt/cord-268406-3v309r41.txt summary: We applaud Lange et al.1 for their extensive efforts to analyse entry factors for severe acute respiratory syndrome coronavirus (SARS-CoV-2) into conjunctival epithelial cells covering the ocular surface, which is an important albeit controversially discussed issue1,2 . A missing link between SARS-CoV-2 and the eye?: ACE2 expression on the ocular surface Before incubation with the primary antibody, tissue was subjected to heat-induced epitope retrieval using Target Retrieval Solution pH 9 (catalog #S2367; Dako). The location of ACE2 expression at the ocular surface enables direct contact of SARS-CoV-2 with conjunctival cells, raising the question how often this occurs and if protective mechanisms of tears and conjunctiva might prevent conjunctivitis to happen more frequently. 6 In summary, our results provide an important addition to the results of Lange et al 1 and other works by clearly demonstrating specific ACE2 expression in conjunctival epithelial cells, providing the receptor for direct entry of SARS-CoV-2. abstract: We applaud Lange et al.1 for their extensive efforts to analyse entry factors for severe acute respiratory syndrome coronavirus (SARS-CoV-2) into conjunctival epithelial cells covering the ocular surface, which is an important albeit controversially discussed issue1,2 . This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26136 doi: 10.1002/jmv.26136 id: cord-301633-t8s4s0wo author: Gralinski, Lisa E. title: Return of the Coronavirus: 2019-nCoV date: 2020-01-24 words: 3938.0 sentences: 186.0 pages: flesch: 51.0 cache: ./cache/cord-301633-t8s4s0wo.txt txt: ./txt/cord-301633-t8s4s0wo.txt summary: Similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections, patients exhibited symptoms of viral pneumonia including fever, difficulty breathing, and bilateral lung infiltration in the most severe cases [1] . A range of disease has been observed highlighted by fever, dry cough, shortness of breath, and leukopenia; patients have included mild cases needing supportive care to severe cases requiring extracorporeal membrane oxygenation; however, compared to SARS-CoV (10% mortality) and MERS-CoV (35% mortality), the 2019-nCoV appears to be less virulent at this point with the exception of the elderly and those with underlying health conditions. In the early part of the outbreak, the absence of infection in health care workers argued for inefficient human to human spread and distinguished 2019-nCoV from both SARS-CoV and MERS-CoV. abstract: The emergence of a novel coronavirus (2019-nCoV) has awakened the echoes of SARS-CoV from nearly two decades ago. Yet, with technological advances and important lessons gained from previous outbreaks, perhaps the world is better equipped to deal with the most recent emergent group 2B coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/31991541/ doi: 10.3390/v12020135 id: cord-335938-hscgmis5 author: Gralinski, Lisa E. title: Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury date: 2013-08-06 words: 7816.0 sentences: 370.0 pages: flesch: 42.0 cache: ./cache/cord-335938-hscgmis5.txt txt: ./txt/cord-335938-hscgmis5.txt summary: The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. To model system-wide behaviors following SARS-CoV infection, we performed a dose-response study that included biological sampling at multiple time points, transcriptional and proteomic systems biology data, and mathematical modeling algorithms to identify signaling networks associated with progression from severe to lethal disease outcomes. These data demonstrate the successful use of highly refined modeling algorithms to identify and validate novel genes and pathways that play critical roles in SARS-CoV pathogenesis and the development of ALI following virus infection in the lung. Similar changes in the urokinase, coagulation, and fibrinolysin pathway expression signatures are noted following highly pathogenic SARS-CoV and influenza virus infections (see Fig. S5B and S6 in the supplemental material), arguing for a con-served role for these pathways in virus-induced end-stage lung diseases, like ALI and ARDS. abstract: Systems biology offers considerable promise in uncovering novel pathways by which viruses and other microbial pathogens interact with host signaling and expression networks to mediate disease severity. In this study, we have developed an unbiased modeling approach to identify new pathways and network connections mediating acute lung injury, using severe acute respiratory syndrome coronavirus (SARS-CoV) as a model pathogen. We utilized a time course of matched virologic, pathological, and transcriptomic data within a novel methodological framework that can detect pathway enrichment among key highly connected network genes. This unbiased approach produced a high-priority list of 4 genes in one pathway out of over 3,500 genes that were differentially expressed following SARS-CoV infection. With these data, we predicted that the urokinase and other wound repair pathways would regulate lethal versus sublethal disease following SARS-CoV infection in mice. We validated the importance of the urokinase pathway for SARS-CoV disease severity using genetically defined knockout mice, proteomic correlates of pathway activation, and pathological disease severity. The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. url: https://doi.org/10.1128/mbio.00271-13 doi: 10.1128/mbio.00271-13 id: cord-344227-rdlinzrn author: Gralinski, Lisa E. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 words: 6557.0 sentences: 309.0 pages: flesch: 43.0 cache: ./cache/cord-344227-rdlinzrn.txt txt: ./txt/cord-344227-rdlinzrn.txt summary: As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. abstract: Acute respiratory distress syndrome (ARDS) is immune-driven pathologies that are observed in severe cases of severe acute respiratory syndrome coronavirus (SARS-CoV) infection. SARS-CoV emerged in 2002 to 2003 and led to a global outbreak of SARS. As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Using this model, we investigated the role of the complement system during SARS-CoV infection. We observed activation of the complement cascade in the lung as early as day 1 following SARS-CoV infection. To test whether this activation contributed to protective or pathologic outcomes, we utilized mice deficient in C3 (C3(–/–)), the central component of the complement system. Relative to C57BL/6J control mice, SARS-CoV-infected C3(–/–) mice exhibited significantly less weight loss and less respiratory dysfunction despite equivalent viral loads in the lung. Significantly fewer neutrophils and inflammatory monocytes were present in the lungs of C3(–/–) mice than in C56BL/6J controls, and subsequent studies revealed reduced lung pathology and lower cytokine and chemokine levels in both the lungs and the sera of C3(–/–) mice than in controls. These studies identify the complement system as an important host mediator of SARS-CoV-induced disease and suggest that complement activation regulates a systemic proinflammatory response to SARS-CoV infection. Furthermore, these data suggest that SARS-CoV-mediated disease is largely immune driven and that inhibiting complement signaling after SARS-CoV infection might function as an effective immune therapeutic. url: https://doi.org/10.1128/mbio.01753-18 doi: 10.1128/mbio.01753-18 id: cord-340486-wydlqq2z author: Grandbastien, Manon title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation date: 2020-06-27 words: 2102.0 sentences: 132.0 pages: flesch: 50.0 cache: ./cache/cord-340486-wydlqq2z.txt txt: ./txt/cord-340486-wydlqq2z.txt summary: title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation Conclusion Our results demonstrate that asthmatic patients appeared not to be at risk for severe SARS-CoV-2 pneumonia. Moreover, SARS-CoV-2 pneumonia did not induce severe asthma exacerbation. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. The propensity score allows analyzing 245 an observational nonrandomized study so that it mimics some of the particular 246 characteristics of a randomized controlled trial as it accounts for systematic differences in 247 baseline characteristics between asthmatic and non-asthmatic subjects when estimating the 248 effect of asthma on severe COVID-19 outcomes. This suggests that the risk factors for hospitalization in our patients were 390 related more to the risk factors of SARS-CoV-2 pneumonia than to asthma. abstract: Abstract Background Viral infections are known to exacerbate asthma in adults. Previous studies have found few asthmatics among SARS-CoV-2 pneumonia cases. However, the relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. Objective We assessed the frequency of asthma exacerbation in asthmatic patients hospitalized for SARS-CoV-2 pneumonia and compared symptoms laboratory and radiological findings in asthmatic and non-asthmatic patients with SARS-CoV-2 pneumonia. Methods We included 106 patients between March 4 and April 6, 2020, who were hospitalized in the Chest Diseases Department of Strasbourg University Hospital; 23 were asthmatics. To assess the patients’ asthma status, three periods were defined: the last month before the onset of COVID-19 symptoms (p1), pre-hospitalization (p2) and during hospitalization (p3). Severe asthma exacerbations were defined according to GINA guidelines during p1 and p2. During p3, we defined severe asthma deterioration as the onset of breathlessness and wheezing requiring systemic corticosteroids and inhaled beta-2-agonist. Results We found no significant difference between asthmatics and non-asthmatics in terms of severity (length of stay, maximal oxygen flow needed, non-invasive ventilation requirement and ICU transfer). 52.2% of the asthmatic patients were Gina 1. One patient had a severe exacerbation during p1, two patients during p2, and five patients were treated with systemic corticosteroids and inhaled beta-2-agonist during p3. Conclusion Our results demonstrate that asthmatic patients appeared not to be at risk for severe SARS-CoV-2 pneumonia. Moreover, SARS-CoV-2 pneumonia did not induce severe asthma exacerbation. url: https://doi.org/10.1016/j.jaip.2020.06.032 doi: 10.1016/j.jaip.2020.06.032 id: cord-349659-6drnriun author: Grant, Benjamin D. title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents date: 2020-07-01 words: 3203.0 sentences: 207.0 pages: flesch: 57.0 cache: ./cache/cord-349659-6drnriun.txt txt: ./txt/cord-349659-6drnriun.txt summary: title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents In this work, we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. 10 Antigen detecting ELISAs were previously developed in 2004 for SARS-CoV-1, with limits of detection of approximately 50 pg/mL and clinical sensitivity as a function of days since onset that was significantly better than the useful time window for the current generation of SARS-CoV-2 serology assays. A dose response curve was generated for the half-strip LFA using two commercially available SARS-CoV-2 nucleocapsid (N) proteins, from Genemedi and Genscript. Analytical Chemistry pubs.acs.org/ac Article and determination of realistic limits of detection for a full strip LFA in multiple sample matrices will help point the way toward the best approach for an antigen detecting LFA for SARS-CoV-2. In this paper, we present a half-strip LFA for the detection of nucleocapsid protein of SARS-CoV-2. abstract: [Image: see text] The SARS-CoV-2 pandemic has created an unprecedented need for rapid diagnostic testing to enable the efficient treatment and mitigation of COVID-19. The primary diagnostic tool currently employed is reverse transcription polymerase chain reaction (RT-PCR), which can have good sensitivity and excellent specificity. Unfortunately, implementation costs and logistical problems with reagents during the global SARS-CoV-2 pandemic have hindered its universal on demand adoption. Lateral flow assays (LFAs) represent a class of diagnostic that, if sufficiently clinically sensitive, may fill many of the gaps in the current RT-PCR testing regime, especially in low- and middle-income countries (LMICs). To date, many serology LFAs have been developed, though none meet the performance requirements necessary for diagnostic use cases, primarily due to the relatively long delay between infection and seroconversion. However, on the basis of previously reported results from SARS-CoV-1, antigen-based SARS-CoV-2 assays may have significantly better clinical sensitivity than serology assays. To date, only a very small number of antigen-detecting LFAs have been developed. Development of a half-strip LFA is a useful first step in the development of any LFA format. In this work, we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. We have tested this LFA in buffer and measured an LOD of 0.65 ng/mL (95% CI of 0.53 to 0.77 ng/mL) ng/mL with recombinant antigen using an optical reader with sensitivity equivalent to a visual read. Further development, including evaluating the appropriate sample matrix, will be required for this assay approach to be made useful in a point of care setting, though this half-strip LFA may serve as a useful starting point for others developing similar tests. url: https://doi.org/10.1021/acs.analchem.0c01975 doi: 10.1021/acs.analchem.0c01975 id: cord-340656-ltd6ueoi author: Grant, Michael C. title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date: 2020-06-23 words: 3435.0 sentences: 199.0 pages: flesch: 48.0 cache: ./cache/cord-340656-ltd6ueoi.txt txt: ./txt/cord-340656-ltd6ueoi.txt summary: title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries Furthermore, with few included studies (30 in the largest and most recent [12] ), the range of symptoms were limited and the estimates of prevalence are likely to be upwardly biased because only unwell patients (largely those admitted to hospital) were tested in the early phase of the outbreak. We excluded case reports, articles which failed to disaggregate symptoms in adult and paediatric cohorts, studies of patients with prior respiratory infections (e.g. tuberculosis) or co-infections with other viruses (e.g. similar viruses SARS-CoV-1 or HCoV-EMC/2012, etc) and articles which we are unable to translate to English in a timely fashion. Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: A retrospective single center analysis Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms abstract: BACKGROUND: To limit the spread of SARS-CoV-2, an evidence-based understanding of the symptoms is critical to inform guidelines for quarantining and testing. The most common features are purported to be fever and a new persistent cough, although the global prevalence of these symptoms remains unclear. The aim of this systematic review is to determine the prevalence of symptoms associated with COVID-19 worldwide. METHODS: We searched PubMed, Embase, CINAHL, AMED, medRxiv and bioRxiv on 5(th) April 2020 for studies of adults (>16 years) with laboratory test confirmed COVID-19. No language or publication status restrictions were applied. Data were independently extracted by two review authors into standardised forms. All datapoints were independently checked by three other review authors. A random-effects model for pooling of binomial data was applied to estimate the prevalence of symptoms, subgrouping estimates by country. I(2) was used to assess inter-study heterogeneity. RESULTS: Of 851 unique citations, 148 articles were included which comprised 24,410 adults with confirmed COVID-19 from 9 countries. The most prevalent symptoms were fever (78% [95% CI 75%-81%]; 138 studies, 21,701 patients; I(2) 94%), a cough (57% [95% CI 54%-60%]; 138 studies, 21,682 patients; I(2) 94%) and fatigue (31% [95% CI 27%-35%]; 78 studies, 13,385 patients; I(2) 95%). Overall, 19% of hospitalised patients required non-invasive ventilation (44 studies, 6,513 patients), 17% required intensive care (33 studies, 7504 patients), 9% required invasive ventilation (45 studies, 6933 patients) and 2% required extra-corporeal membrane oxygenation (12 studies, 1,486 patients). The mortality rate was 7% (73 studies, 10,402 patients). CONCLUSIONS: We confirm that fever and cough are the most prevalent symptoms of adults infected by SARS-CoV-2. However, there is a large proportion of infected adults which symptoms-alone do not identify. url: https://doi.org/10.1371/journal.pone.0234765 doi: 10.1371/journal.pone.0234765 id: cord-304356-jyp9gjh9 author: Grant, Rogan A. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 words: 7453.0 sentences: 427.0 pages: flesch: 44.0 cache: ./cache/cord-304356-jyp9gjh9.txt txt: ./txt/cord-304356-jyp9gjh9.txt summary: We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. abstract: Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation. This manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/ One sentence summary SARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19. url: https://doi.org/10.1101/2020.08.05.238188 doi: 10.1101/2020.08.05.238188 id: cord-292544-m7jyydf1 author: Grau-Pujol, Berta title: Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial date: 2020-07-29 words: 4575.0 sentences: 257.0 pages: flesch: 50.0 cache: ./cache/cord-292544-m7jyydf1.txt txt: ./txt/cord-292544-m7jyydf1.txt summary: OBJECTIVES: The aim of this study is to assess the efficacy of the use of pre-exposure prophylaxis (PrEP) with hydroxychloroquine against placebo in healthcare workers with high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in reducing their risk of coronavirus disease 2019 (COVID-19) disease during an epidemic period. As secondary endpoints, we will obtain: i) the SARS-CoV-2 seroconversion in the PrEP group compared to placebo during the 6 months of follow-up in healthcare workers with negative serology at day 0; ii) the occurrence of any adverse event related with hydroxychloroquine treatment; iii) the incidence of SARS-CoV-2 infection and COVID-19 among healthcare workers in the non-PrEP group, among the total of healthcare workers included in the non-PrEP group during the study period; iv) the risk ratio for the different clinical, analytical and microbiological conditions to develop COVID-19; v) a repository of serum samples obtained from healthcare workers confirmed COVID-19 cases for future research on blood markers to predict SARS-CoV-2 infection. abstract: OBJECTIVES: The aim of this study is to assess the efficacy of the use of pre-exposure prophylaxis (PrEP) with hydroxychloroquine against placebo in healthcare workers with high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in reducing their risk of coronavirus disease 2019 (COVID-19) disease during an epidemic period. As secondary objectives, we would like to: i) assess the efficacy of the use of PrEP with hydroxychloroquine against placebo in healthcare workers with high risk of SARS-CoV-2 infection in reducing their risk of exposure to SARS-CoV-2 (defined by seroconversion) during an epidemic period, ii) evaluate the safety of PrEP with hydroxychloroquine in adults, iii) describe the incidence of SARS-CoV-2 infection among healthcare workers at high risk of SARS-CoV-2 infection, iv) identify clinical, analytical and microbiological predictors of COVID-19 among healthcare workers at high risk of SARS-CoV-2 infection, v) set up a repository of serum samples obtained from healthcare workers at high risk of SARS-CoV-2 infection for future research on blood markers to predict SARS-CoV-2 infection. TRIAL DESIGN: Multicentre double-blind parallel design (ratio 1:1) randomized controlled clinical trial. PARTICIPANTS: Approximately 440 healthcare workers of four Spanish hospitals (Hospital Clínic of Barcelona, Hospital de la Santa Creu i Sant Pau of Barcelona, Hospital Plató of Barcelona, Hospital General de Granollers, Barcelona) will be recruited. Participants are considered to be at high-risk of SARS-CoV-2 infection due to their frequent contact with suspected and confirmed cases of COVID-19. For eligibility, healthcare workers with 18 years old or older working at least 3 days a week in a hospital with both negative SARS-CoV-2 polymerase chain reaction (PCR) assays and serological COVID-19 rapid diagnostic tests (RDT) are invited to participate. Participants with any of the following conditions are excluded: pregnancy, breastfeeding, ongoing antiviral, antiretroviral or corticosteroids treatment, chloroquine or hydroxychloroquine uptake the last month or any contraindication to hydroxychloroquine treatment. INTERVENTION AND COMPARATOR: Intervention group (PrEP): participants will receive the standard of care and will take 400mg of hydroxychloroquine (2 tablets of 200 mg per Dolquine® tablet) daily the first four consecutive days, followed by 400 mg weekly for a period of 6 months. Control group: participants will receive placebo tablets with identical physical appearance to hydroxychloroquine 200 mg (Dolquine®) tablets following the same treatment schedule of the intervention group. Both groups will be encouraged to use the personal protection equipment (PPE) for COVID-19 prevention according to current hospital guidelines. MAIN OUTCOMES: The primary endpoint will be the number of confirmed cases of a COVID-19 (defined by a positive PCR for SARS-CoV-2 or symptoms compatible with COVID-19 with seroconversion) in the PrEP group compared to the placebo group at any time during the 6 months of the follow-up in healthcare workers with negative SARS-CoV-2 PCR and serology at day 0. As secondary endpoints, we will obtain: i) the SARS-CoV-2 seroconversion in the PrEP group compared to placebo during the 6 months of follow-up in healthcare workers with negative serology at day 0; ii) the occurrence of any adverse event related with hydroxychloroquine treatment; iii) the incidence of SARS-CoV-2 infection and COVID-19 among healthcare workers in the non-PrEP group, among the total of healthcare workers included in the non-PrEP group during the study period; iv) the risk ratio for the different clinical, analytical and microbiological conditions to develop COVID-19; v) a repository of serum samples obtained from healthcare workers confirmed COVID-19 cases for future research on blood markers to predict SARS-CoV-2 infection. RANDOMISATION: Participants meeting all eligibility requirements will be allocated to one of the two study arms (PrEP with hydroxychloroquine or non-PrEP control group) in a 1:1 ratio using simple randomisation with computer generated random numbers. BLINDING (MASKING): Participants, doctors and nurses caring for participants, and investigators assessing the outcomes will be blinded to group assignment. NUMBERS TO BE RANDOMISED (SAMPLE SIZE): Each intervention group will have 220 participants, giving a total of 440 participants. TRIAL STATUS: The current protocol version is 1.5, 2(nd) of June 2020. Two hundred and seventy-fiveparticipants were recruited and completed first month follow-up until date. The estimated sample size could not be reached yet due to the declining national epidemic curve. Thus, 275 is the total number of participants included until date. The study has been suspended (26(th) of June) until new epidemic curve occurs. TRIAL REGISTRATION: This trial was registered on April 2(nd) 2020 at clinicaltrials.gov with the number NCT04331834. FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. url: https://doi.org/10.1186/s13063-020-04621-7 doi: 10.1186/s13063-020-04621-7 id: cord-282858-zikoui4h author: Graudenz, Gustavo Silveira title: SARS-CoV-2. Long Distance Airborne Transmission and its Public Health Implications date: 2020-11-02 words: 1665.0 sentences: 87.0 pages: flesch: 42.0 cache: ./cache/cord-282858-zikoui4h.txt txt: ./txt/cord-282858-zikoui4h.txt summary: Its predecessor, SARS-CoviD-1, the agent that caused Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003, showed strong evidence of opportunistic airborne transmission in different environments, such as collective housing environments (8) , indoor environments such as airplanes (9), and health service institutions (10) . (12) that suggested transmission of SARS-CoV-2 through infected surfaces and contaminated individual protection equipment as well as long distance environment contamination. In health care settings, the Center for Disease Control''s recommendations for prevention of airborne transmission include maintaining a negative pressure environment, fine filtering of exhaust air from infected patients'' rooms, maintaining high air exchange rates (12 air exchanges per hour), shutting recirculation ducts, and establishing pressure cascades (2) in these settings until further evidence of long distance transmission is obtained Unfortunately, these precautionary measures have not yet been applied in most health care facilities in Brazil. Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus abstract: nan url: https://doi.org/10.6061/clinics/2020/e2343 doi: 10.6061/clinics/2020/e2343 id: cord-255515-7se14455 author: Graudenzi, Alex title: Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date: 2020-07-06 words: 8275.0 sentences: 450.0 pages: flesch: 53.0 cache: ./cache/cord-255515-7se14455.txt txt: ./txt/cord-255515-7se14455.txt summary: To dissect the mechanisms underlying the observed inflation of variants in SARS-CoV-2 genome, we present the largest up-to-date analysis of intra-host genomic diversity, which reveals that the majority of samples present a complex sublineage architecture, due to the interplay between host-related mutational processes and transmission dynamics. Strikingly, our analysis allowed to identify three non-overlapping mutational signatures, i.e., specific distributions of nucleotide substitutions, which are observed in distinct clusters of samples in a mutually exclusive fashion, suggesting the presence of host-related mutational processes. Finally, the analysis of homoplasies, i.e., (low-frequency) variants shared across distinct viral lineages and unlikely due to infection events, demonstrate that a high number of mutations can independently emerge in multiple samples, due to mutational hotspots often related to signatures or, possibly, to positive (functional) selection. abstract: To dissect the mechanisms underlying the observed inflation of variants in SARS-CoV-2 genome, we present the largest up-to-date analysis of intra-host genomic diversity, which reveals that the majority of samples present a complex sublineage architecture, due to the interplay between host-related mutational processes and transmission dynamics. Strikingly, the deconvolution of the entire set of intra-host variants reveals the existence of mutually exclusive viral mutational signatures, which prove that distinct hosts differently respond to SARS-CoV-2 infections. In particular, two signatures are likely ruled by APOBEC and Reactive Oxygen Species (ROS), which induce hypermutation in a significant number of samples, and appear to be affected by severe purifying selection. Conversely, several mutations linked to low-rate mutational processes appear to transit to clonality in the population, eventually leading to the definition of new viral genotypes and to an increase of overall genomic diversity. Finally, we demonstrate that a high number of variants are observed in samples associated to independent lineages, likely due to signature-related mutational hotspots or to positive selection. url: https://doi.org/10.1101/2020.07.06.189944 doi: 10.1101/2020.07.06.189944 id: cord-293852-r72c6584 author: Greco, S. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 words: 8163.0 sentences: 468.0 pages: flesch: 40.0 cache: ./cache/cord-293852-r72c6584.txt txt: ./txt/cord-293852-r72c6584.txt summary: Different studies found that the values of cardiac Troponins were increased in COVID-19 patients with more severe disease [4, 5, [68] [69] [70] , indicating an association of SARS-CoV-2 with myocardial damage. Moreover, the single-cell RNA-sequencing (scRNAseq) approach has been used to profile the SARS-CoV-2 host-response in the PBMCs of COVID-19 patients, and to comprehensively characterize the immunological changes [124] [125] [126] [127] [128] [129] [130] . However, SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) induced cytotoxic effects and RNA-seq findings highlighted significant transcriptional changes in gene pathways related to cellular metabolism and immune response [131] [132] [133] . This analysis also revealed several host-derived lncRNAs differentially expressed in COVID-19 patient-derived lung tissue, and in SARS-CoV-2 infected epithelial cells, including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and NEAT1 (nuclear-enriched autosomal transcript 1) [151] (Fig. 5) . abstract: COronaVIrus Disease 19 (COVID-19) is caused by the infection of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Although the main clinical manifestations of COVID-19 are respiratory, many patients also display acute myocardial injury and chronic damage to the cardiovascular system. Understanding both direct and indirect damage caused to the heart and the vascular system by SARS-CoV-2 infection is necessary to identify optimal clinical care strategies. The homeostasis of the cardiovascular system requires a tight regulation of the gene expression, which is controlled by multiple types of RNA molecules, including RNA encoding proteins (messenger RNAs) (mRNAs) and those lacking protein-coding potential, the noncoding-RNAs. In the last few years, dysregulation of noncoding-RNAs has emerged as a crucial component in the pathophysiology of virtually all cardiovascular diseases. Here we will discuss the potential role of noncoding RNAs in COVID-19 disease mechanisms and their possible use as biomarkers of clinical use. url: https://www.ncbi.nlm.nih.gov/pubmed/33129318/ doi: 10.1186/s12967-020-02582-8 id: cord-325910-qiay8n43 author: Green, D. A. title: Clinical Performance of SARS-CoV-2 Molecular Testing date: 2020-05-08 words: 3945.0 sentences: 201.0 pages: flesch: 56.0 cache: ./cache/cord-325910-qiay8n43.txt txt: ./txt/cord-325910-qiay8n43.txt summary: In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19. For the time-dependent analysis of conversion rates, we considered "initially positive" 216 patients with any "Detected" or "Indeterminate" SARS-CoV-2 result obtained during the 217 first calendar day of testing rather than the first positive test, to reduce bias due to 218 nasopharyngeal sampling inadequacy (Table 1) . Considering ''Detected'' and "Indeterminate" as 239 positive, 1,471 repeat-tested patients had one or more SARS-CoV-2 positive results over 240 time; only 61.9% were positive on the initial test and only 69.3% had a positive result on 241 the first day (Table 1) . abstract: Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the test clinical performance is poorly understood. From 3/10/2020-5/1/2020 NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed in 3,432 patients, of which 2,413 had negative and 1,019 had positive first day results. Repeat-tested patients were more likely to be older, male, African-American or Hispanic, and to have severe disease. Among the patients with initially negative results, 18.6% became positive upon repeat-testing. Only 58.1% of any-time positive patients had a result of "detected" on the first test. The clinical sensitivity of COVID-19 molecular assays is estimated between 66.2% and 95.6%, depending on the unknown number of false negative results in single-tested patients. Conversion to a negative result is unlikely to occur before 15 to 20 days after initial testing or 20-30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Forty-nine initially-positive patients converted to negative and then back to positive in subsequent days. Conversion from first day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19. url: http://medrxiv.org/cgi/content/short/2020.05.06.20093575v1?rss=1 doi: 10.1101/2020.05.06.20093575 id: cord-294372-pec1886j author: Greene, Dina N. title: Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date: 2020-10-15 words: 1698.0 sentences: 103.0 pages: flesch: 60.0 cache: ./cache/cord-294372-pec1886j.txt txt: ./txt/cord-294372-pec1886j.txt summary: Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. In the United States, surveillance data suggest that mean age of infected patients is decreasing compared to the early stages of the COVID-19 pandemic. We used SARS-CoV-2 testing data from a national reference laboratory to characterize the age distribution of detected cases between March and July of 2020. Surveillance data in the United States have shown a trend toward decreasing age among persons with laboratory-confirmed SARS-CoV-2 infection. This study found a similar pattern among patients tested by a national reference laboratory, with the median age among patients testing positive being five years lower in June and early July compared to March and April. abstract: BACKGROUND: Understanding and monitoring the demographics of SARS-CoV-2 infection can inform strategies for prevention. Surveillance monitoring has suggested that the age distribution of people infected with SARS-CoV-2 has changed since the pandemic began, but no formal analysis has been performed. METHODS: Retrospective review of SARS-CoV-2 molecular testing results from a national reference laboratory was performed. Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Additionally, a sub-analysis compared changing age distributions between inpatients and outpatients. RESULTS: There were 277,601 test results of which 19320 (7.0%) were positive. The median age of infected people declined over time (p < 0.0005). In March-April, the median age of positive people was 40.8 years (Interquartile range (IQR): 29.0–54.1). In June-July, the median age of positive people was 35.8 years (IQR: 24.0–50.2). The positivity rate of patients under 50 increased from 6.0 to 10.6 percent and the positivity rate for those over 50 decreased from 6.3 to 5.0 percent between the early and late periods. The trend was only observed for outpatient populations. CONCLUSIONS: We confirm that there is a trend toward decreasing age among persons with laboratory-confirmed SARS-CoV-2 infection, but that these trends seem to be specific to the outpatient population. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. This calls for caution in interpretation of routine surveillance data until testing patterns stabilize. url: https://doi.org/10.1371/journal.pone.0240783 doi: 10.1371/journal.pone.0240783 id: cord-294921-h44tct43 author: Greninger, Alexander L. title: The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience date: 2020-07-23 words: 2744.0 sentences: 121.0 pages: flesch: 55.0 cache: ./cache/cord-294921-h44tct43.txt txt: ./txt/cord-294921-h44tct43.txt summary: Dr. Greninger was working in his research lab, assembling data for an early February grant for funding to understand the function of his favorite coronavirus gene (orf3a) in SARS-CoV-2, while Dr. Jerome continued splitting time between clinical virology and his work at the Fred Hutchinson Cancer Research Center on gene therapies for persistent viruses. From mid-January until the end of February, we received respiratory specimens from about 15 different persons under investigation for COVID-19 for respiratory virus panel testing, but each of them tested negative for SARS-CoV-2, not only at the CDC but also in our lab as we continued the evaluation of our assay. We could not report results from our assay development and validation studies, but our clinicians soon became disappointed by the 5-to 7-day turnaround time for clinical results from the CDC, during which patients waited in isolation for test results. abstract: In early March 2020, the University of Washington Medical Center clinical virology laboratory became one of the first clinical laboratories to offer testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When we first began test development in mid-January, neither of us believed there would be more than 2 million confirmed SARS-CoV-2 infections nationwide or that we would have performed more than 150,000 real-time PCR (RT-PCR) tests, with many more to come. This article will be a chronological summary of how we rapidly validated tests for SARS-CoV-2, increased our testing capacity, and addressed the many problems that came up along the way. url: https://doi.org/10.1128/jcm.01416-20 doi: 10.1128/jcm.01416-20 id: cord-285430-o086q2qa author: Gribble, Karleen title: Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date: 2020-07-25 words: 2622.0 sentences: 150.0 pages: flesch: 51.0 cache: ./cache/cord-285430-o086q2qa.txt txt: ./txt/cord-285430-o086q2qa.txt summary: BACKGROUND: In an effort to prevent infants being infected with SARS-CoV-2, some governments, professional organisations, and health facilities are instituting policies that isolate newborns from their mothers and otherwise prevent or impede breastfeeding. WEIGHING OF RISKS IS NECESSARY IN POLICY DEVELOPMENT: Such policies are risky as was shown in the early response to the HIV pandemic where efforts to prevent mother to child transmission by replacing breastfeeding with infant formula feeding ultimately resulted in more infant deaths. In the COVID-19 pandemic, the risk of maternal SARS-CoV-2 transmission needs to be weighed against the protection skin-to-skin contact, maternal proximity, and breastfeeding affords infants. However, mothers and infants present a special situation as the risk of mother-to-child transmission of SARS-CoV-2 needs to be weighed against the protection from infectious diseases and the support for bonding and caregiving provided by close maternal proximity and breastfeeding. abstract: BACKGROUND: In an effort to prevent infants being infected with SARS-CoV-2, some governments, professional organisations, and health facilities are instituting policies that isolate newborns from their mothers and otherwise prevent or impede breastfeeding. WEIGHING OF RISKS IS NECESSARY IN POLICY DEVELOPMENT: Such policies are risky as was shown in the early response to the HIV pandemic where efforts to prevent mother to child transmission by replacing breastfeeding with infant formula feeding ultimately resulted in more infant deaths. In the COVID-19 pandemic, the risk of maternal SARS-CoV-2 transmission needs to be weighed against the protection skin-to-skin contact, maternal proximity, and breastfeeding affords infants. CONCLUSION: Policy makers and practitioners need to learn from the mistakes of the HIV pandemic and not undermine breastfeeding in the COVID-19 pandemic. It is clear that in order to maximise infant health and wellbeing, COVID-19 policies should support skin-to-skin contact, maternal proximity, and breastfeeding. url: https://doi.org/10.1186/s13006-020-00306-8 doi: 10.1186/s13006-020-00306-8 id: cord-349428-i2s41kl7 author: Griffin, Ian title: The Impact of COVID-19 Infection on Labor and Delivery, Newborn Nursery, and Neonatal Intensive Care Unit: Prospective Observational Data from a Single Hospital System date: 2020-06-13 words: 4416.0 sentences: 228.0 pages: flesch: 53.0 cache: ./cache/cord-349428-i2s41kl7.txt txt: ./txt/cord-349428-i2s41kl7.txt summary: The study population consisted of maternal-infant dyads whose mothers were identified to be either COVID-19 positive or persons under investigation (PUI) before their admission to labor and delivery (L&D) or at any time before their discharge. Obstetric patients who were COVID-19 positive or PUIs were cared for in a designated suite of single-person airborne infection isolation (AIIRs) negative pressure rooms separate from the main L&D unit through delivery and the postpartum period, while awaiting testing for COVID-19 or if they had tested positive for COVID-19. If a mother tested positive for COVID-19 and newborn infants had been immediately separated at birth from their mother, neonatal isolation precautions were suspended after two negative polymerase chain reaction (PCR)-based nasopharyngeal swab tests, performed at 48 hours and at 5 days of life, respectively. abstract: Objective Since its emergence in late 2019, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the novel coronavirus that causes novel coronavirus disease 2019 (COVID-19), has spread globally. Within the United States, some of the most affected regions have been New York, and Northern New Jersey. Our objective is to describe the impact of COVID-19 in a large delivery service in Northern New Jersey, including its effects on labor and delivery (L&D), the newborn nursery, and the neonatal intensive care unit (NICU). Materials and Methods Between April 21, 2020 and May 5, 2020, a total of 78 mothers (3.6% of deliveries) were identified by screening history or examination to either be COVID-19 positive or possible positives (persons under investigation). Of the mothers who were tested after admission to L&D, 28% tested positive for SARS-CoV-2. Discussion Isolation between mother and infant was recommended in 62 cases, either because the mother was positive for SARS-CoV-2 or because the test was still pending. Fifty-four families (87%) agreed to isolation and separation. The majority of infants, 51 (94%), were initially isolated on the newborn nursery. Six needed NICU admission. No infants had clinical evidence of symptomatic COVID-19 infection. Fourteen infants whose mothers were positive for SARS-CoV-2, and who had been separated from the mother at birth were tested for SARS-CoV-2 postnatally. All were negative. Results COVID-19 posed a significant burden to mothers, infants, and staff over the 5-week study period. The yield from screening mothers for COVID-19 on L&D was high. Most families accepted the need for postnatal isolation and separation of mother and newborn. Conclusion Our study suggests that the transmission of SARS-CoV-2 from mother to her fetus/newborn seems to be uncommon if appropriate separation measures are performed at birth. Key Points: The yield of targeted testing for SARS-CoV-2, on mothers on Labor and Delivery is high. Agreement to separation of mothers and infants to reduce transmission of SARS-CoV-2 was high. The incidence of symptomatic COVID-19 in newborns is low, if appropriate separation occurs at birth. url: https://www.ncbi.nlm.nih.gov/pubmed/32534458/ doi: 10.1055/s-0040-1713416 id: cord-294429-isivkz8b author: Grifoni, Alba title: Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals date: 2020-05-20 words: 10250.0 sentences: 589.0 pages: flesch: 55.0 cache: ./cache/cord-294429-isivkz8b.txt txt: ./txt/cord-294429-isivkz8b.txt summary: To test for the generation of SARS-CoV-2 CD4 + and CD8 + T cell responses following infection, we initially recruited 20 adult patients who had recovered from COVID-19 disease ( Table 1) . Initial definition and assessment of human antigen-specific SARS-CoV-2 T cell responses are best made with direct ex vivo T cell assays using broad-based epitope pools, such as MPs, and assays capable of detecting T cells of unknown cytokine polarization and functional attributes. Data from both the epitope MPs and protein peptide pool experiments can be interpreted in the context of previously reported T cell response immunodominance patterns observed for other coronaviruses, particularly the SARS and MERS viruses, which have been studied in humans, HLA-transgenic mice, wild-type mice and other species. (C) Correlation of SARS-CoV-2−specific CD4 + T cells detected using the epitope prediction approach (CD4_R MP) compared against the sum total of all antigen pools of overlapping peptides (excluding spike), run with samples from the same donors in two different experiment series. abstract: Summary Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide ‘megapools’, circulating SARS-CoV-2−specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike and N proteins each accounted for 11-27% of the total CD4+ response, with additional responses commonly targeting nsp3, nsp4, ORF3a and ORF8, among others. For CD8+ T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2−reactive CD4+ T cells in ∼40-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32473127/ doi: 10.1016/j.cell.2020.05.015 id: cord-266168-hxu5u5op author: Grimaud, Emilie title: Delayed acute bronchiolitis in infants hospitalized for COVID‐19 date: 2020-07-10 words: 406.0 sentences: 33.0 pages: flesch: 48.0 cache: ./cache/cord-266168-hxu5u5op.txt txt: ./txt/cord-266168-hxu5u5op.txt summary: To the Editor, Because of the infant''s history, a chest X-ray was performed and returned normal. A term eutrophic male with otherwise unremarkable neonatal history was referred for poorly tolerated high fever at age 2 months. The respiratory and clinical examination findings including hemodynamics were normal. RT-PCR testing of a nasopharyngeal swab was positive for SARS-CoV-2 but negative for RSV and IV. The chest X-ray was normal, and no lung ultrasonography was performed. These two cases of COVID-19 in infants hospitalized for poorly tolerated high fever and neurological symptoms in whom acute bronchiolitis developed following a delay of 2 to 8 days suggest that SARS-CoV-2 infection may cause acute bronchiolitis in the absence of a viral coinfection such as RSV. Pneumonia is the most common respiratory illness among symptomatic children with COVID-19. Infection and rapid transmission of SARS-CoV-2 in Ferrets Wheezing rhinovirus illnesses in early life predict asthma development in high-risk children abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32779885/ doi: 10.1002/ppul.24946 id: cord-277440-9nehpbg2 author: Grimm, Christian title: Could an endo-lysosomal ion channel be the Achilles heel of SARS-CoV2? date: 2020-05-06 words: 1326.0 sentences: 82.0 pages: flesch: 55.0 cache: ./cache/cord-277440-9nehpbg2.txt txt: ./txt/cord-277440-9nehpbg2.txt summary: Genetic ablation of TPCs or TPC blockers have been previously shown to affect trafficking of both viruses and bacterial toxins through the endo-lysosomal system, reducing infectivity, including, e.g. cholera toxin, diphtheria toxin, Pasteurella multocida toxin, Anthrax toxin, Ebola virus, and MERS-CoV [5] [6] [7] . Indeed, it has been demonstrated before that SARS-CoV, like EBOV, displays late cell entry kinetics and that transport to NPC1+ (Niemann-Pick C1 protein) late endo-lysosomes is a rate-defining step [9] . The two-pore channels (TPC1, TPC2) are required by viruses such as EBOV (Ebola virus), MERS-CoV and SARS-CoV, orchestrating the interplay of virus and endolysosomal milieus such as trafficking from early to late endosomes, fusion of late endosomes with lysosomes, and facilitating releasing of viral RNA into the cytoplasm. abstract: The ongoing SARS-CoV2 outbreak has developed into a global pandemic. Despite previous outbreaks of SARS-CoV and the related MERS-CoV in recent years, neither a vaccine nor any other medication for an effective treatment are currently available. Endo-lysosomal two-pore cation channels have now emerged as potential novel targets for SARS-CoV treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32402856/ doi: 10.1016/j.ceca.2020.102212 id: cord-267436-mivxm8oh author: Groneberg, David A title: Treatment and vaccines for severe acute respiratory syndrome date: 2005-03-10 words: 5913.0 sentences: 317.0 pages: flesch: 44.0 cache: ./cache/cord-267436-mivxm8oh.txt txt: ./txt/cord-267436-mivxm8oh.txt summary: The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. 31 The results of a randomised clinical study in Guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose (400-600 mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. Search terms were "severe acute respiratory syndrome", "SARS", "treatment", "coronavirus", "infection", "SARS coronavirus", "vaccination", and "antiviral". Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus abstract: The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002–2003 outbreak, is a coronavirus that was unknown before the outbreak. Although many different treatments were used during the outbreak, none were implemented in a controlled fashion. Thus, the optimal treatment for SARS is unknown. Since the outbreak, much work has been done testing new agents against SARS using in-vitro methods and animal models. In addition, global research efforts have focused on the development of vaccines against SARS. Efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another SARS outbreak occur. url: https://api.elsevier.com/content/article/pii/S1473309905013071 doi: 10.1016/s1473-3099(05)01307-1 id: cord-304815-3datxv8j author: Gronvall, Gigi Kwik title: The Scientific Response to a Pandemic date: 2006-02-24 words: 1522.0 sentences: 92.0 pages: flesch: 49.0 cache: ./cache/cord-304815-3datxv8j.txt txt: ./txt/cord-304815-3datxv8j.txt summary: More than 150 scientists and public health practitioners from 25 countries gathered in Lyon, France, to hear speakers from the WHO, the European Commission, scientific journals, Interpol, and public health networks-many of the institutions and individuals who will likely play key roles in the global response to the next pandemic. By discussing the biosafety and biosecurity challenges presented by past epidemics such as SARS, participants recognized the importance of scientific and public health collaboration in combating disease-and the need to plan. Researchers will need to share biological samples between laboratories, sometimes internationally; decision makers and journalists will want the latest information, which may not be peer reviewed; and researchers will risk contracting the disease they research, which could then spread outside of the laboratory. Scientists need access to samples from patients and laboratories in order to conduct research and public health surveillance, as well as to develop diagnostic tests. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/16738708/ doi: 10.1371/journal.ppat.0020009 id: cord-325991-dktffiaa author: Gross, Oliver title: COVID-19-associated nephritis: early warning for disease severity and complications? date: 2020-05-06 words: 593.0 sentences: 41.0 pages: flesch: 45.0 cache: ./cache/cord-325991-dktffiaa.txt txt: ./txt/cord-325991-dktffiaa.txt summary: title: COVID-19-associated nephritis: early warning for disease severity and complications? COVID-19-associated nephritis: early warning for disease severity and complications? Here we report that analysis of a urine sample on admission to hospital can be used to detect systemic capillary leak syndrome, which can be a predictor of fluid overload, respiratory failure, need for ICU admission, and death. Three of these patients had coincidentally submitted urine samples in the few weeks before their infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On the basis of these findings, we generated an algorithm for early detection of COVID-19-associated nephritis and to assess the risk of respiratory decompensation by capillary leak syndrome (figure). In summary, the respiratory tract is the gateway for SARS-CoV-2 infection, but we postulate that COVID-19associated nephritis, which can be easily screened for through a simple and inexpensive urine sample analysis, might help predict complications. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0140673620310412 doi: 10.1016/s0140-6736(20)31041-2 id: cord-266648-962r0vm8 author: Grossberg, Laurie B title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date: 2020-07-03 words: 3613.0 sentences: 234.0 pages: flesch: 50.0 cache: ./cache/cord-266648-962r0vm8.txt txt: ./txt/cord-266648-962r0vm8.txt summary: title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic Although data in patients with IBD contracting COVID-19 are still limited, both providers and patients have particular concerns regarding the risk of infection with SARS-CoV-2 and how to manage their medications during the COVID-19 pandemic. Information regarding risk factors, prevention, routine care (including office visits, testing, endoscopy, and surgery), and medication management of patients with IBD in the setting of COVID-19 was collected from each reference and is summarized in the Results. 10, 11 Other organizations, including the American Gastroenterological Association doi: 10.1093/ibd/izaa174 Published online 3 July 2020 (AGA), the Gastroenterological Society of Australia, and the European Crohn''s and Colitis Organisation (ECCO), agree that there are no data to support an increased risk of infection among patients with IBD. abstract: nan url: https://doi.org/10.1093/ibd/izaa174 doi: 10.1093/ibd/izaa174 id: cord-280628-ok62havd author: Groß, Sonja title: SARS-CoV-2 receptor ACE2-dependent implications on the cardiovascular system: From basic science to clinical implications date: 2020-04-30 words: 4453.0 sentences: 252.0 pages: flesch: 43.0 cache: ./cache/cord-280628-ok62havd.txt txt: ./txt/cord-280628-ok62havd.txt summary: COVID-19 requires the collaboration of nearly 200 countries to curb the spread of SARS-CoV-2 while gaining time to explore and improve treatment options especially for cardiovascular disease (CVD) and immunocompromised patients, who appear to be at high-risk to die from cardiopulmonary failure. Since the coronavirus disease (COVID19) is still an emerging pandemic with more than 2.1 million confirmed cases worldwide [1] , special focus is currently directed towards the understanding of why people are hospitalized, receive intensive care, and frequently die as a consequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. While higher mortality rates among CVD patients are also associated with other respiratory diseases (especially influenza virus-induced flu or previous SARS epidemics), the question was put forward, whether people treated for heart-related illness are more prone to SARS-CoV-2 viral infection, based on first epidemiological evidence, but particularly based on the presumed upregulation of the SARS-CoV-2 entry receptor. abstract: The current COVID-19 pandemic started several months ago and is still exponentially growing in most parts of the world – this is the most recent and alarming update. COVID-19 requires the collaboration of nearly 200 countries to curb the spread of SARS-CoV-2 while gaining time to explore and improve treatment options especially for cardiovascular disease (CVD) and immunocompromised patients, who appear to be at high-risk to die from cardiopulmonary failure. Currently unanswered questions are why elderly people, particularly those with pre-existing comorbidities seem to exhibit higher mortality rates after SARS-CoV-2 infection and whether intensive care becomes indispensable for these patients to prevent multi-organ failure and sudden death. To face these challenges, we here summarize the molecular insights into viral infection mechanisms and implications for cardiovascular disease. Since the infection starts in the upper respiratory system, first flu-like symptoms develop that spread throughout the body. The wide range of affected organs is presumably based on the common expression of the major SARS-CoV-2 entry-receptor angiotensin-converting enzyme 2 (ACE2). Physiologically, ACE2 degrades angiotensin II, the master regulator of the renin-angiotensin-aldosterone system (RAAS), thereby converting it into vasodilatory molecules, which have well-documented cardio-protective effects. Thus, RAAS inhibitors, which may increase the expression levels of ACE2, are commonly used for the treatment of hypertension and CVD. This, and the fact that SARS-CoV-2 hijacks ACE2 for cell-entry, have spurred controversial discussions on the role of ACE2 in COVID-19 patients. In this review, we highlight the state-of-the-art knowledge on SARS-CoV-2-dependent mechanisms and the potential interaction with ACE2 expression and cell surface localization. We aim to provide a list of potential treatment options and a better understanding of why CVD is a high risk factor for COVID-19 susceptibility and further discuss the acute as well as long-term cardiac consequences. url: https://www.ncbi.nlm.nih.gov/pubmed/32360703/ doi: 10.1016/j.yjmcc.2020.04.031 id: cord-296767-mgr32ftl author: Große, Karsten title: SARS‐CoV‐2 as an extrahepatic precipitator of acute‐on‐chronic liver failure date: 2020-05-29 words: 295.0 sentences: 27.0 pages: flesch: 45.0 cache: ./cache/cord-296767-mgr32ftl.txt txt: ./txt/cord-296767-mgr32ftl.txt summary: key: cord-296767-mgr32ftl cord_uid: mgr32ftl We read with great interest the report by Qiu and colleages reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. As ACLF following hepatic versus extrahepatic insults may differ in presentation, course, and prognosis, we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. To the Editor We read with great interest the report by Qiu et al 1 reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. 1 As ACLF following hepatic vs extrahepatic insults may differ in presentation, course and prognosis, 2 we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. Acute on chronic liver failure from novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acute-on-chronic liver failure precipitated by hepatic injury is distinct from that precipitated by extrahepatic insults Multiorgan and renal tropism of SARS-CoV-2 abstract: We read with great interest the report by Qiu and colleages reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. Based on elevated transaminases, jaundice, and coagulopathy, the authors discuss hepatic virus entry and systemic inflammation as possible underlying mechanisms. As ACLF following hepatic versus extrahepatic insults may differ in presentation, course, and prognosis, we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. url: https://doi.org/10.1111/liv.14540 doi: 10.1111/liv.14540 id: cord-321308-rwxhdg8r author: Grubaugh, Nathan D. title: Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear date: 2020-07-03 words: 1505.0 sentences: 87.0 pages: flesch: 60.0 cache: ./cache/cord-321308-rwxhdg8r.txt txt: ./txt/cord-321308-rwxhdg8r.txt summary: While clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown. Following the emergence of SARS-CoV-2 in China in late 2019, and the rapid expansion of the COVID-19 pandemic in 2020, questions about viral evolution have come tumbling after. They present compelling data that an amino acid change in the virus'' spike protein, D614G, emerged early during the pandemic, and viruses containing G614 are now dominant in many places around the world. In support of their hypothesis, the authors provided evidence that clinical samples from G614 infections have a higher levels of viral RNA, and produced higher titers in pseudoviruses from in vitro experiments; results that now seem to be corroborated by others [e.g. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry abstract: Abstract Korber et al. (2020) found that a SARS-CoV-2 variant in the spike protein, D614G, rapidly became dominant around the world. While clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown. url: https://api.elsevier.com/content/article/pii/S0092867420308175 doi: 10.1016/j.cell.2020.06.040 id: cord-354103-4dldgqzf author: Grubic, Andrew D title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 words: 4869.0 sentences: 266.0 pages: flesch: 47.0 cache: ./cache/cord-354103-4dldgqzf.txt txt: ./txt/cord-354103-4dldgqzf.txt summary: While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a "stress test" to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. On the same day, the United States Surgeon General echoed the recommendation from the American College of Surgeons and urged hospitals and healthcare systems to consider suspending elective surgical procedures during the outbreak of COVID-19. This pandemic started with identification of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent from a cluster of pneumonias in the Hubei providence of China in December 2019. On March 25, 2000, American College of Surgeons released the guidelines for emergency general surgery in COVID-19 positive patients or those at high clinical suspicion for COVID infection. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases abstract: One-hundred years after the 1918-19 H1N1 flu pandemic and 10 years after the 2009 H1N1 flu pandemic, another respiratory virus has now inserted itself into the human population. Severe acute respiratory syndrome coronavirus has become a critical challenge to global health with immense economic and social disruption. In this article we review salient aspects of the coronavirus disease 2019 (COVID-19) outbreak that are relevant to surgical practice. The emphasis is on considerations during the pre-operative and post-operative periods as well as the utility and limitations of COVID-19 testing. The focus of the media during this pandemic is centered on predictive epidemiologic curves and models. While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a “stress test” to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. As recently pointed out by Dr. Anthony Fauci, the virus decides the timelines in the models. However, the models can also change based on our decisions and behavior. It is our role as surgeons, to make every effort to bend the curves against the virus’ will. url: https://doi.org/10.4240/wjgs.v12.i6.259 doi: 10.4240/wjgs.v12.i6.259 id: cord-285700-9q6vwoct author: Grzelak, Ludivine title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. date: 2020-04-24 words: 6520.0 sentences: 392.0 pages: flesch: 53.0 cache: ./cache/cord-285700-9q6vwoct.txt txt: ./txt/cord-285700-9q6vwoct.txt summary: title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. Here, we performed a pilot study to assess the levels of anti-SARS-CoV-2 antibodies in samples taken from 491 preepidemic individuals, 51 patients from Hopital Bichat (Paris), 209 pauci-symptomatic individuals in the French Oise region and 200 contemporary Oise blood donors. To avoid redundancy, we focused LIPS analysis to N, selecting it for its sensitivity regarding an intracellular viral protein not targeted by NAbs and S1 as it is described as a target of most NAbs. To establish the specificity of the assay, we first analyzed the same series of 40 sera we used for S-Flow and found all of the sera to be negative (Fig. S3 ). Sera from pre-epidemic individuals sampled between 2017 and 2019 (first row), hospitalized cases with confirmed COVID-19 (second row), paucisymptomatics individual from the Crépy-en-Vallois epidemic cluster (third row) and healthy blood donors (last row) were surveyed for anti-SARS-Cov-2 antibodies using four serological assays. abstract: It is of paramount importance to evaluate the prevalence of both asymptomatic and symptomatic cases of SARS-CoV-2 infection and their antibody response profile. Here, we performed a pilot study to assess the levels of anti-SARS-CoV-2 antibodies in samples taken from 491 pre- epidemic individuals, 51 patients from Hopital Bichat (Paris), 209 pauci-symptomatic individuals in the French Oise region and 200 contemporary Oise blood donors. Two in-house ELISA assays, that recognize the full-length nucleoprotein (N) or trimeric Spike (S) ectodomain were implemented. We also developed two novel assays: the S-Flow assay, which is based on the recognition of S at the cell surface by flow-cytometry, and the LIPS assay that recognizes diverse antigens (including S1 or N C- terminal domain) by immunoprecipitation. Overall, the results obtained with the four assays were similar, with differences in sensitivity that can be attributed to the technique and the antigen in use. High antibody titers were associated with neutralisation activity, assessed using infectious SARS-CoV- 2 or lentiviral-S pseudotypes. In hospitalized patients, seroconversion and neutralisation occurred on 5-14 days post symptom onset, confirming previous studies. Seropositivity was detected in 29% of pauci-symptomatic individuals within 15 days post-symptoms and 3 % of blood of healthy donors collected in the area of a cluster of COVID cases. Altogether, our assays allow for a broad evaluation of SARS-CoV2 seroprevalence and antibody profiling in different population subsets. url: http://medrxiv.org/cgi/content/short/2020.04.21.20068858v1?rss=1 doi: 10.1101/2020.04.21.20068858 id: cord-260624-rqjeacow author: Gu, Jiang title: Multiple organ infection and the pathogenesis of SARS date: 2005-08-01 words: 5320.0 sentences: 271.0 pages: flesch: 51.0 cache: ./cache/cord-260624-rqjeacow.txt txt: ./txt/cord-260624-rqjeacow.txt summary: SARS viral particles and genomic sequence were detected in a large number of circulating lymphocytes, monocytes, and lymphoid tissues, as well as in the epithelial cells of the respiratory tract, the mucosa of the intestine, the epithelium of the renal distal tubules, the neurons of the brain, and macrophages in different organs. In situ hybridization demonstrated SARS viral sequences in the cytoplasm of a large number of intact and degenerating epithelial cells of the lungs as well as in the scanty infiltrating lymphocytes and clustered macrophages ( Fig. 1, C and D) . (C) In situ hybridization of SARS genomic sequence of the lung from a SARS victim who died 62 d after the onset of high fever detected a large number of pulmonary epithelial cells (small arrows) that contained the virus. In the autopsy samples, in situ hybridization and EM demonstrated virus-infected immune cells in the circulating blood, spleen, lymph nodes, and lymphoid tissue of various organs. abstract: After >8,000 infections and >700 deaths worldwide, the pathogenesis of the new infectious disease, severe acute respiratory syndrome (SARS), remains poorly understood. We investigated 18 autopsies of patients who had suspected SARS; 8 cases were confirmed as SARS. We evaluated white blood cells from 22 confirmed SARS patients at various stages of the disease. T lymphocyte counts in 65 confirmed and 35 misdiagnosed SARS cases also were analyzed retrospectively. SARS viral particles and genomic sequence were detected in a large number of circulating lymphocytes, monocytes, and lymphoid tissues, as well as in the epithelial cells of the respiratory tract, the mucosa of the intestine, the epithelium of the renal distal tubules, the neurons of the brain, and macrophages in different organs. SARS virus seemed to be capable of infecting multiple cell types in several organs; immune cells and pulmonary epithelium were identified as the main sites of injury. A comprehensive theory of pathogenesis is proposed for SARS with immune and lung damage as key features. url: https://www.ncbi.nlm.nih.gov/pubmed/16043521/ doi: 10.1084/jem.20050828 id: cord-277307-wabruzfs author: Gu, Wei title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 words: 1096.0 sentences: 79.0 pages: flesch: 66.0 cache: ./cache/cord-277307-wabruzfs.txt txt: ./txt/cord-277307-wabruzfs.txt summary: In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region abstract: In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel-related. Cases were significantly associated with travel to Europe or New York (odds ratio 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe. url: https://doi.org/10.1093/cid/ciaa599 doi: 10.1093/cid/ciaa599 id: cord-294527-fct2y5vn author: Guadarrama-Ortiz, Parménides title: Neurological Aspects of SARS-CoV-2 Infection: Mechanisms and Manifestations date: 2020-09-04 words: 8820.0 sentences: 441.0 pages: flesch: 37.0 cache: ./cache/cord-294527-fct2y5vn.txt txt: ./txt/cord-294527-fct2y5vn.txt summary: The human infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern that has caused more than 16.8 million new cases and 662,000 deaths as of July 30, 2020. Although coronavirus disease 2019 (COVID-19), which is associated with this virus, mainly affects the lungs, recent evidence from clinical and pathological studies indicates that this pathogen has a broad infective ability to spread to extrapulmonary tissues, causing multiorgan failure in severely ill patients. In this context, SARS-CoV-2 can also cause viral meningitis and encephalitis, as demonstrated by a recent report of a 64-yearold patient with laboratory-confirmed COVID-19 who presented neurologic manifestations during the infection, including lethargy, clonus, and pyramidal signs in the lower limbs as well as stiff neck and Brudzinski sign (76) . Future studies are required to evaluate the serologic features of anti-glycolipid antibodies in patients with COVID-19 to elucidate possible mechanisms underlying the association between SARS-CoV-2 infection and Guillain-Barré syndrome. abstract: The human infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern that has caused more than 16.8 million new cases and 662,000 deaths as of July 30, 2020. Although coronavirus disease 2019 (COVID-19), which is associated with this virus, mainly affects the lungs, recent evidence from clinical and pathological studies indicates that this pathogen has a broad infective ability to spread to extrapulmonary tissues, causing multiorgan failure in severely ill patients. In this regard, there is increasing preoccupation with the neuroinvasive potential of SARS-CoV-2 due to the observation of neurological manifestations in COVID-19 patients. This concern is also supported by the neurotropism previously documented in other human coronaviruses, including the 2002–2003 SARS-CoV-1 outbreak. Hence, in the current review article, we aimed to summarize the spectrum of neurological findings associated with COVID-19, which include signs of peripheral neuropathy, myopathy, olfactory dysfunction, meningoencephalitis, Guillain-Barré syndrome, and neuropsychiatric disorders. Furthermore, we analyze the mechanisms underlying such neurological sequela and discuss possible therapeutics for patients with neurological findings associated with COVID-19. Finally, we describe the host- and pathogen-specific factors that determine the tissue tropism of SARS-CoV-2 and possible routes employed by the virus to invade the nervous system from a pathophysiological and molecular perspective. In this manner, the current manuscript contributes to increasing the current understanding of the neurological aspects of COVID-19 and the impact of the current pandemic on the neurology field. url: https://doi.org/10.3389/fneur.2020.01039 doi: 10.3389/fneur.2020.01039 id: cord-339576-0d6sa9pe author: Guallar, María Pilar title: Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date: 2020-06-14 words: 1380.0 sentences: 79.0 pages: flesch: 56.0 cache: ./cache/cord-339576-0d6sa9pe.txt txt: ./txt/cord-339576-0d6sa9pe.txt summary: Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure abstract: Abstract A relationship between the infecting dose and the risk of disease severity has not been demonstrated for SARS-CoV-2 infection. Here, we report three clusters of individuals that were exposed to diverse inoculi in Madrid and overall developed divrgent clinical forms of COVID-19. Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. url: https://api.elsevier.com/content/article/pii/S1201971220304707 doi: 10.1016/j.ijid.2020.06.035 id: cord-286713-14i38xtt author: Guarner, Jeannette title: Three Emerging Coronaviruses in Two Decades: The Story of SARS, MERS, and Now COVID-19 date: 2020-02-13 words: 1179.0 sentences: 71.0 pages: flesch: 58.0 cache: ./cache/cord-286713-14i38xtt.txt txt: ./txt/cord-286713-14i38xtt.txt summary: As a matter of fact, the characteristic electron microscopy appearance was the clue to amplify and sequence nucleic acids from Dr Urbani''s (one of the health care providers who died of severe acute respiratory syndrome [SARS] in 2003) respiratory specimen using a consensus coronavirus primer. The virus was ultimately named SARS-CoV, as febrile patients had severe acute respiratory syndrome and could present with pneumonia and lower respiratory symptoms such as cough and dyspnea. Nine years later, a new coronavirus that causes respiratory disease appeared in the Middle East, thus the name of MERS-CoV. Symptoms of MERS-CoV are nonspecific, but many patients end up with severe acute respiratory distress. SARS-CoV-2 will cause many more deaths than its predecessors, even though the mortality rate is lower than MERS-CoV infections, because there have been so many more cases. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: nan url: https://doi.org/10.1093/ajcp/aqaa029 doi: 10.1093/ajcp/aqaa029 id: cord-337179-qytruuif author: Guazzi, Marco title: The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients date: 2020-05-21 words: 1887.0 sentences: 109.0 pages: flesch: 43.0 cache: ./cache/cord-337179-qytruuif.txt txt: ./txt/cord-337179-qytruuif.txt summary: title: The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients The main clinical manifestation of SARS-CoV-2 is severe acute respiratory syndrome which yields to inflammatory reaction and alveolar fluid floading ultimately impairing gas exchange. We gained previous experience on the effects of renin-angiotensin system inhibition on the pulmonary function of HF patients showing a protective effect on the perturbed gas exchange and lung fluid handling, i.e. alveolar capillary stress-failure, an effect especially observed with enalapril treatment, with a positive but statistically not signfiicnat trend for losartan 11, 12 . Based on this, we outline how renin angiotensin blockers may interact with the lung fluid handling and gas diffusion process in patients with HF infected by SARS-CoV-2, and propose areas for further research. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32438449/ doi: 10.1002/ejhf.1910 id: cord-314070-8qz23nn4 author: Gubbi, Sriram title: Catecholamine physiology and its implications in patients with COVID-19 date: 2020-10-28 words: 5313.0 sentences: 296.0 pages: flesch: 31.0 cache: ./cache/cord-314070-8qz23nn4.txt txt: ./txt/cord-314070-8qz23nn4.txt summary: The risk factors for severe COVID-19 are diverse, yet closely resemble the clinical manifestations of catecholamine excess states (eg, hypertension, cardiovascular disease, immune dysregulation, and hyperglycaemia), suggesting a potentially common basis for disease. 6 Consequently, catecholamine excess states such as PPGL can cause substantial dysregulation of physiological systems, and lead to pronounced changes in pulmonary (vasoplegia), coronary (myocardial infarction), cerebro vascular (stroke), and remaining systemic vascular tone (hypertension), as well as myocardial disease (cardio myopathies), tachyarrhythmias (benign and fatal), hyper coagulability (thromboem bolism), immune dysreg u lation (cytokine storm), and diabetogenic states; these outcomes are the same as the risk factors that lead to adverse outcomes from COVID-19. 19 Increased concentrations of these cytokines and their downstream acute phase reactants (eg, ferritin) have been associated with a higher likelihood of severe disease and mortality in patients with 20 Catecholamines augment the production of IL-6, IL-10, and other cytokines through a self-amplifying feed-forward loop within myeloid cells, an effect mediated through α1-adrenoceptors. abstract: The risk factors for severe COVID-19 are diverse, yet closely resemble the clinical manifestations of catecholamine excess states (eg, hypertension, cardiovascular disease, immune dysregulation, and hyperglycaemia), suggesting a potentially common basis for disease. Unfortunately, severe illness (eg, respiratory failure, compromised cardiac function, and shock) incurred by COVID-19 hinders the direct study of catecholamines in these patients, especially among those on multiple medications or those on adrenaline or noradrenaline infusions, or both. Phaeochromocytoma and paraganglioma (PPGL) are tumours that secrete catecholamines, namely adrenaline and noradrenaline, often in excess. PPGL are well studied disease processes in which the effects of catecholamines are easily discernible and therefore their potential biochemical and physiological influences in patients with COVID-19 can be explored. Because catecholamines are expected to have a role in patients with critical illness, patients on vasopressor infusions, and patients who sustain some acute and chronic physical stresses, the challenges involved in the management of catecholamine excess states are directly relevant to the treatment of patients with COVID-19. In this Personal View, we discuss the complex interplay between catecholamines and COVID-19, and the management of catecholamine excess states, while referencing relevant insights derived from the study of PPGL. url: https://api.elsevier.com/content/article/pii/S2213858720303429 doi: 10.1016/s2213-8587(20)30342-9 id: cord-350904-wyg8ikph author: Gubernatorova, E.O. title: IL-6: relevance for immunopathology of SARS-CoV-2 date: 2020-05-20 words: 8298.0 sentences: 410.0 pages: flesch: 35.0 cache: ./cache/cord-350904-wyg8ikph.txt txt: ./txt/cord-350904-wyg8ikph.txt summary: In turn, SARS-CoV-2 infection of recruited immune cells may increase their apoptosis and exacerbate lymphocytosis [32, 33] , and, finally, may lead in some patients to life-threatening conditions, such as respiratory distress syndrome, cytokine storm, and secondary hemophagocytic lymphohistiocytosis. Interestingly, patients requiring intensive care and invasive lung ventilation display negative correlation between IL-6, TNF and IL-1b concentrations and CD4 + and CD8 + T cell counts [75] , confirming previous studies in animal models, which suggested that cytokine storm actually dampens adaptive immunity against SARS-CoV infection [76] . Taking together, Angiotensin II accumulation due to SARS-CoV-2-mediated ACE2 downregulation may cause Angiotensin 1 receptor downstream activation of NADPH oxidase, which, in turn, leads to elevated ROS production and to induction of transcriptional mechanisms that directly promote IL-6 expression, implicated in inflammation-induced injury and immunopathology. abstract: COVID-19 mortality is strongly associated with the development of severe pneumonia and acute respiratory distress syndrome with the worst outcome resulting in cytokine release syndrome and multiorgan failure. It is becoming critically important to identify at the early stage of the infection those patients who are prone to develop the most adverse effects. Elevated systemic interleukin-6 levels in patients with COVID-19 are considered as a relevant parameter in predicting most severe course of disease and the need for intensive care. This review discusses the mechanisms by which IL-6 may possibly contribute to disease exacerbation and the potential of therapeutic approaches based on anti-IL-6 biologics. url: https://api.elsevier.com/content/article/pii/S1359610120301088 doi: 10.1016/j.cytogfr.2020.05.009 id: cord-273382-7w8fli6w author: Guderian, Daniela B. title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling date: 2020-09-07 words: 3941.0 sentences: 242.0 pages: flesch: 45.0 cache: ./cache/cord-273382-7w8fli6w.txt txt: ./txt/cord-273382-7w8fli6w.txt summary: title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling Five typical surgical intervention techniques (mechanical stress with a passive instrument with and without suction, CO(2) laser treatment, drilling and bipolar electrocoagulation) were examined and compared regarding resulting particle release. The aim of the presented study was therefore to develop an experimental setup for the simultaneous assessment of aerosol and particle formation in various typical ENT interventions. Similarly, no particle or aerosol formation was detected during mechanical impact by use of a passive instrument in direct tissue contact with additional suction (cf. The laser treatment of the tissue did not lead to a detectable particle formation at any of the three points in time of the analysis (see Fig. 3 , third line). abstract: INTRODUCTION: Based on current knowledge, the SARS-CoV-2 is transmitted via droplet, aerosols and smear infection. Due to a confirmed high virus load in the upper respiratory tract of COVID-19 patients, there is a potential risk of infection for health care professionals when performing surgical procedures in this area. The aim of this study was the semi-quantitative comparison of ENT-typical interventions in the head and neck area with regard to particle and aerosol generation. These data can potentially contribute to a better risk assessment of aerogenic SARS-CoV-2-transmission caused by medical procedures. MATERIALS AND METHODS: As a model, a test chamber was created to examine various typical surgical interventions on porcine soft and hard tissues. Simultaneously, particle and aerosol release were recorded and semi-quantitatively evaluated time-dependently. Five typical surgical intervention techniques (mechanical stress with a passive instrument with and without suction, CO(2) laser treatment, drilling and bipolar electrocoagulation) were examined and compared regarding resulting particle release. RESULTS: Neither aerosols nor particles could be detected during mechanical manipulation with and without suction. The use of laser technique showed considerable formation of aerosol. During drilling, mainly solid tissue particles were scattered into the environment (18.2 ± 15.7 particles/cm(2)/min). The strongest particle release was determined during electrocoagulation (77.2 ± 30.4 particles/cm(2)/min). The difference in particle release between electrocoagulation and drilling was significant (p < 0.05), while particle diameter was comparable. In addition, relevant amounts of aerosol were released during electrocoagulation (79.6% of the maximum flue gas emission during laser treatment). DISCUSSION: Our results demonstrated clear differences comparing surgical model interventions. In contrast to sole mechanical stress with passive instruments, all active instruments (laser, drilling and electrocoagulation) released particles and aerosols. Assuming that particle and aerosol exposure is clinically correlated to the risk of SARS-CoV-2-transmission from the patient to the physician, a potential risk for health care professionals for infection cannot be excluded. Especially electrocautery is frequently used for emergency treatment, e.g., nose bleeding. The use of this technique may, therefore, be considered particularly critical in potentially infectious patients. Alternative methods may be given preference and personal protective equipment should be used consequently. url: https://www.ncbi.nlm.nih.gov/pubmed/32895799/ doi: 10.1007/s00405-020-06330-y id: cord-330121-eadu2ba3 author: Gudmundsdottir, Ágústa title: Inactivation of SARS‐CoV‐2 and HCoV‐229E in vitro by ColdZyme® a medical device mouth spray against common cold date: 2020-09-25 words: 1628.0 sentences: 114.0 pages: flesch: 58.0 cache: ./cache/cord-330121-eadu2ba3.txt txt: ./txt/cord-330121-eadu2ba3.txt summary: It contains glycerol and minor amounts of purified cold-adapted trypsin 5 The entry of coronaviruses into host cells is mediated by the spike (S) glycoprotein that forms homo-trimers protruding from the virus surface 11 . Based on the results presented in this study, CZ-MD was found to inactivate SARS-CoV-2 (98.3%) and HCoV-229E (99.9%) in vitro (Table I) Coronaviruses cause about one-third of the common cold cases 4 Entry of coronaviruses into susceptible cells requires receptor-binding of the S protein and it''s proteolytic processing by host cell proteases that occurs in a concerted action to promote virus-cell fusion 3 . However, the in vitro study presented here clearly demonstrates that the CZ-MD (containing cod trypsin) inactivates SARS-CoV-2 and HCoV-229E. Although the in vitro results presented cannot be directly translated into clinical efficacy, the study indicates that CZ-MD might offer a protective barrier against coronaviruses such as SARS-CoV-2 and a decreased risk of COVID-19 transmission. abstract: BACKGROUND: The COVID‐19 pandemic calls for effective and safe treatments. SARS‐CoV‐2 causing COVID‐19 actively replicates in the throat, unlike SARS‐CoV, and shows high pharyngeal viral shedding even in patients with mild symptoms of the disease. HCoV‐229E is one of four coronaviruses causing the common cold. In this study, the efficacy of ColdZyme® (CZ‐MD), a medical device mouth spray, was tested against SARS‐CoV‐2 and HCoV‐229E in vitro. The CZ‐MD provides a protective glycerol barrier containing cod trypsin as an ancillary component. Combined, these ingredients can inactivate common cold viruses in the throat and mouth. The CZ‐MD is believed to act on the viral surface proteins that would perturb their entry pathway into cells. The efficacy and safety of the CZ‐MD has been demonstrated in clinical trials on the common cold. METHOD OF STUDY: The ability of the CZ‐MD to inactivate SARS‐CoV‐2 and HCoV‐229E was tested using an in vitro virucidal suspension test (ASTM E1052). RESULTS: CZ‐MD inactivated SARS‐CoV‐2 by 98.3% and HCoV‐229E by 99.9%. CONCLUSION: CZ‐MD mouth spray can inactivate the respiratory coronaviruses SARS‐CoV‐2 and HCoV‐229E in vitro. Although the in vitro results presented cannot be directly translated into clinical efficacy, the study indicates that CZ‐MD might offer a protective barrier against SARS‐CoV‐2 and a decreased risk of COVID‐19 transmission. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32975843/ doi: 10.1002/jmv.26554 id: cord-294120-8fxrqorg author: Guebre-Xabier, Mimi title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date: 2020-08-19 words: 866.0 sentences: 78.0 pages: flesch: 64.0 cache: ./cache/cord-294120-8fxrqorg.txt txt: ./txt/cord-294120-8fxrqorg.txt summary: title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. And, hACE2 receptor 158 inhibition titers of 649, 1,410, and 1,320 in 2.5, 5, and 25 µg NVX-CoV2373 dose groups 159 respectively were 5.2 -11.2-fold higher than in convalescent sera ( Figure 1C) . Finally, 160 SARS-CoV-2 GMT neutralization antibody titers of 17,920 -23,040 CPE 100 in 161 immunized macaques, were 7.9 -10.1-fold higher than in convalescent sera ( Figure 162 1D) . To evaluate the potential efficacy of NVX-CoV2373 vaccine, macaques were 165 challenged with SARS-CoV-2 virus in upper and lower airways. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 214 elicits immunogenicity in baboons and protection in mice These interests do not alter the authors adherence to policies on 209 sharing data and materials. abstract: There is an urgent need for a safe and protective vaccine to control the global spread of SARS-CoV-2 and prevent COVID-19. Here, we report the immunogenicity and protective efficacy of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length SARS-CoV-2 spike (S) glycoprotein stabilized in the prefusion conformation. Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. Following intranasal and intratracheal challenge with SARS-CoV-2, immunized macaques were protected against upper and lower infection and pulmonary disease. These results support ongoing phase 1/2 clinical studies of the safety and immunogenicity of NVX-CoV2327 vaccine (NCT04368988). Highlights Full-length SARS-CoV-2 prefusion spike with Matrix-M1™ (NVX-CoV2373) vaccine. Induced hACE2 receptor blocking and neutralizing antibodies in macaques. Vaccine protected against SARS-CoV-2 replication in the nose and lungs. Absence of pulmonary pathology in NVX-CoV2373 vaccinated macaques. url: https://doi.org/10.1101/2020.08.18.256578 doi: 10.1101/2020.08.18.256578 id: cord-336909-nnxa5ant author: Guedez-López, Gladys Virginia title: Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2 date: 2020-08-17 words: 3246.0 sentences: 159.0 pages: flesch: 52.0 cache: ./cache/cord-336909-nnxa5ant.txt txt: ./txt/cord-336909-nnxa5ant.txt summary: The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. RT-qPCR tests presented a high specificity with a low probability of false positive; however, sensitivity relies on different factors as specimen site, method of collection, viral load and time from the onset of symptoms [3, 7] . Detection rate of IgM, IgG and IgM/IgG antibodies against SARS-CoV-2 with the three ICT strip assays in positive and negative RT-PCR patients along three periods of time since the onset of symptoms is shown in Table 3 . Detection rates of total antibodies (IgM/IgG) obtained with Sienna® and Wondfo® by the two groups of patients along the three stages since the symptoms onset are collected in Table 4 . In this study, we have investigated the diagnostic value of detection of SARS-CoV-2 IgM and IgG antibodies in different stages of the disease, using three ICT strip assays, in comparison with RT-qPCR. abstract: Lateral flow immunoassays (LFIA) for rapid detection of specific antibodies (IgM and IgG) against SARS-CoV-2 in different human specimens have been developed in response to the pandemic. The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. A total of 145 serum samples from 145 patients with clinical suspicion of COVID-19 were collected: all of the samples were tested with Sienna®, 117 with Wondfo® and 89 with Prometheus®. The overall results of sensitivity, specificity, positive predictive value and negative predictive value obtained were as follows: 64.4%, 75%, 85.5% and 47.8% with Sienna®; 45.2%, 81.8%, 80.5% and 47.4% with Wondfo® and 75.5%, 12.5%, 51.4% and 29.4% with Prometheus®. The accuracy of the test for Sienna®, Wondfo® and Prometheus® was 67.6%, 59% and 47.2%, with a prevalence of COVID-19 of 69.7%, 62.4% and 55.1% respectively. Sensitivity of the three tests (Sienna®, Wondfo® and Prometheus® respectively) along the three different stages was 36.6%, 18.8% and 68.6% in the early stage (first week); 81.3%, 74.1% and 90.9% in the intermediate stage (second week) and 100%, 83.3% and 100% in the late stage (third week). The results demonstrate that even though Prometheus® presented a high sensitivity, the specificity was notably lower than the other two tests. Sienna® showed the greatest contrast between sensitivity and specificity, achieving the best accuracy, followed by Wondfo®. The sensitivity of the three ICT assays was higher in late stages of the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-04010-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32808111/ doi: 10.1007/s10096-020-04010-7 id: cord-255284-ffh1jl40 author: Guery, B title: Syndrome respiratoire aigu sévère date: 2003-06-30 words: 2809.0 sentences: 291.0 pages: flesch: 65.0 cache: ./cache/cord-255284-ffh1jl40.txt txt: ./txt/cord-255284-ffh1jl40.txt summary: Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d''isoler l''agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l''épidémie. Deux éléments notables sont évoqués dans cette publication, tout d''abord le fait que seuls les patients atteints de SARS ont des anticorps témoignant du fait que ce virus circule pour la première fois. À noter que cette faculté existe chez un Coronavirus porcin entraînant des pathologies respiratoires mais, aucun lien de parenté entre ces deux virus n''a été mis en évidence. Dans le cas du SARS, les premières analyses montrent que la contamination nécessite un contact prolongé et répété avec un malade présentant une symptomatologie pulmonaire. ont montré la présente d''ARN du Coronavirus responsable du SARS dans les selles des patients [4] . abstract: Résumé Le syndrome respiratoire aigu sévère (severe acute respiratory syndrome, SARS) est apparu à l’automne 2002 dans la province de Guangdong en Chine. L’épidémie s’est rapidement propagée à travers le monde pour toucher, courant avril, plus de 26 pays avec un total de cas à cette même date proche de 3500 cas. La symptomatologie associe des formes modérées se manifestant par une fièvre, une hypoxie, avec des formes de gravité majeure responsables de syndrome de détresse aigue nécessitant l’hospitalisation en unité de réanimation. Des formes digestives ont aussi récemment été décrites. Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d’isoler l’agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l’épidémie. Cette revue rassemble l’ensemble des données actuellement disponibles sur le SARS, de l’histoire de l’épidémie aux propositions thérapeutiques disponibles en date d’avril 2003. Abstract In the Fall of 2002 a report from Guangdong Province in China showed the occurrence of an outbreak of atypical pneumonia. This outbreak rapidly progressed from China to Hong Kong, Singapore, Toronto, and the USA, to more than 25 countries worldwide and almost 3500 cases to date in april 2003. The clinical features associate a fever with mild respiratory symptoms which can progress to a typical acute respiratory distress syndrome requiring intensive care unit admission. Enteric forms with diarrhea were recently described in Hong Kong. The medical community responded very rapidly and united in front of this major health crisis. In a couple weeks, the agent, a new Coronavirus was isolated, therapeutic guidelines were proposed and measures to limit the outbreak diffusion were started worldwide. We summarize here the history of the outbreak, the clinical, laboratory and radiological features of SARS. April 2003 therapeutic guidelines are also reported. url: https://www.sciencedirect.com/science/article/pii/S0399077X03002002 doi: 10.1016/s0399-077x(03)00200-2 id: cord-337557-ct43uoir author: Guetl, Katharina title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia date: 2020-10-27 words: 855.0 sentences: 58.0 pages: flesch: 46.0 cache: ./cache/cord-337557-ct43uoir.txt txt: ./txt/cord-337557-ct43uoir.txt summary: title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia (4, 5) Here, we report SARS-CoV-2 positive viral culture 7 weeks after onset of COVID-19 in a patient with an underlying immunosuppressive disorder, so-called X chromosome-linked agammaglobulinemia (XLA), demonstrating the potential of prolonged SARS-CoV-2 spreading beyond widely accepted isolation precautions. On April 15, five days after tocilizumab and convalescent plasma administration and five weeks after the initial diagnosis of COVID-19, SARS-CoV-2 RNA was not detectable for the first time. The patient showed progressive clinical recovery, but an alternating course of three negative followed by three positive SARS-CoV-2 RT-PCR results was subsequently observed. In summary, we have to assume that in our patient shedding of infectious SARS-CoV-2 stopped between week 7 and 10 of disease. abstract: nan url: https://api.elsevier.com/content/article/pii/S0163445320306848 doi: 10.1016/j.jinf.2020.10.025 id: cord-304899-vruq4r7z author: Guihot, Amélie title: Syndrome respiratoire aigu sévère : une épidémie singulière de pneumonie virale date: 2004-03-31 words: 2706.0 sentences: 261.0 pages: flesch: 63.0 cache: ./cache/cord-304899-vruq4r7z.txt txt: ./txt/cord-304899-vruq4r7z.txt summary: L''agent infectieux étiologique a rapidement été identifié comme étant un nouveau Coronavirus, baptisé Coronavirus associé au Sras (Sras-CoV).La transmission du virus est interhumaine, par les particules respiratoires principalement. n Chine du Sud-Est, au début de l''année 2003, une épidémie de pneumopathie hautement contagieuse et potentiellement mortelle a été signalée par les autorités sanitaires chinoises.Cette entité clinique d''étiologie inconnue a été baptisée Syndrome respiratoire aigu sévère (Sras) par l''Organisation mondiale de la santé (OMS). La ribavirine est un analogue nucléosidique utilisé comme anti-viral dans le traitement de l''hépatite C chronique (Rébétol ® ), en association avec l''interféron α .La ribavirine possédant une activité in vitro contre plusieurs virus respiratoires (virus syncytial respiratoire, virus de la grippe), elle a été utilisée empiriquement par plusieurs équipes chez des patients atteints de Sras. abstract: Résumé Agent infectieux Le Syndrome respiratoire aigu sévère (Sras) est une pneumopathie fébrile initialement observée en Chine à la fin de l’année 2002. L’agent infectieux étiologique a rapidement été identifié comme étant un nouveau Coronavirus, baptisé Coronavirus associé au Sras (Sras-CoV). La transmission du virus est interhumaine, par les particules respiratoires principalement. Clinique et traitement La gravité clinique est variable, allant de la simple fièvre au syndrome de détresse respiratoire aigu. Il n’existe pas de traitement spécifique. Cependant, la ribavirine combinée à des corticoïdes a été utilisée avec succès dans un certain nombre de cas. Épidémiologie Au cours du premier semestre de l’année 2003, la dissémination du virus a été extrêmement rapide, évoluant sur un mode pandémique, contaminant plus de 8000 patients, dont 774 en sont décédés. Le réservoir viral, probablement d’origine animale, reste inconnu à ce jour. L’épidémie semble être actuellement jugulée, mais des ré-émergences sporadiques ou épidémiques sont possibles et ont été décrites en Chine dans la province de Guangdong début janvier 2004. Summary Infectious agent The severe acute respiratory syndrome (SARS) is a febrile pneumonia initially observed in China at the end of 2002. The infectious agent has rapidly been identified as a new coronavirus, baptised SARS-associated coronavirus (CoV-SARS). Transmission is inter-human, via respiratory particles mainly. Clinical presentation and treatment The clinical presentation is highly variable, from a mild fever to an acute respiratory distress syndrome. There is no specific treatment. Ribavirin associated with steroids have been used with success in numerous cases. Epidemiology During the first half of 2003, the spreading of the virus has been very fast, with a pandemic mode of evolution. More than 8 000 people were infected and 774 died. The reservoir of the virus, which may be animal, is still unknown. The epidemic seems to be controlled, but sporadic or epidemic re-emergences may occur and have been observed in China duting January 2004. url: https://api.elsevier.com/content/article/pii/S0755498204985818 doi: 10.1016/s0755-4982(04)98581-8 id: cord-299499-66qh3r75 author: Guilamo-Ramos, Vincent title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 words: 4199.0 sentences: 218.0 pages: flesch: 42.0 cache: ./cache/cord-299499-66qh3r75.txt txt: ./txt/cord-299499-66qh3r75.txt summary: In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. abstract: Evidence regarding the important role of adolescents and young adults (AYA) in accelerating and sustaining coronavirus disease 2019 (COVID-19) outbreaks is growing. Furthermore, data suggest two known factors that contribute to high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmissibility—presymptomatic transmission and asymptomatic case presentations—may be amplified in AYA. However, AYA have not been prioritized as a key population in the public health response to the COVID-19 pandemic. Policy decisions that limit public health attention on AYA and are driven by the assumption of insignificant forward transmission from AYA pose a risk to inadvertently reinvigorate local transmission dynamics. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. url: https://www.ncbi.nlm.nih.gov/pubmed/32894747/ doi: 10.1093/cid/ciaa1348 id: cord-285449-frft2h85 author: Guillon, Patrice title: Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies date: 2008-09-25 words: 6026.0 sentences: 293.0 pages: flesch: 54.0 cache: ./cache/cord-285449-frft2h85.txt txt: ./txt/cord-285449-frft2h85.txt summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) is a highly pathogenic emergent virus which replicates in cells that can express ABH histo-blood group antigens. We observed that the S protein/angiotensin-converting enzyme 2-dependent adhesion of these cells to an angiotensin-converting enzyme 2 expressing cell line was specifically inhibited by either a monoclonal or human natural anti-A antibodies, indicating that these antibodies may block the interaction between the virus and its receptor, thereby providing protection. We present data indicating that the S protein/ACE2-mediated adhesion between cells expressing ACE2 and cells coexpressing the S protein and the A histo-blood group antigen can be specifically blocked by anti-A antibodies. To further evaluate the potential effect of the ABO polymorphism on the epidemiology of SARS, we present a model of its transmission dynamics that takes into account the effect of the protection by anti-histo-blood group natural antibodies. abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) is a highly pathogenic emergent virus which replicates in cells that can express ABH histo-blood group antigens. The heavily glycosylated SARS-CoV spike (S) protein binds to angiotensin-converting enzyme 2 which serves as a cellular receptor. Epidemiological analysis of a hospital outbreak in Hong Kong revealed that blood group O was associated with a low risk of infection. In this study, we used a cellular model of adhesion to investigate whether natural antibodies of the ABO system could block the S protein and angiotensin-converting enzyme 2 interaction. To this aim, a C-terminally EGFP-tagged S protein was expressed in chinese hamster ovary cells cotransfected with an α1,2-fucosyltransferase and an A-transferase in order to coexpress the S glycoprotein ectodomain and the A antigen at the cell surface. We observed that the S protein/angiotensin-converting enzyme 2-dependent adhesion of these cells to an angiotensin-converting enzyme 2 expressing cell line was specifically inhibited by either a monoclonal or human natural anti-A antibodies, indicating that these antibodies may block the interaction between the virus and its receptor, thereby providing protection. In order to more fully appreciate the potential effect of the ABO polymorphism on the epidemiology of SARS, we built a mathematical model of the virus transmission dynamics that takes into account the protective effect of ABO natural antibodies. The model indicated that the ABO polymorphism could contribute to substantially reduce the virus transmission, affecting both the number of infected individuals and the kinetics of the epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/18818423/ doi: 10.1093/glycob/cwn093 id: cord-325014-n7mnhk2v author: Gujski, Mariusz title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 words: 4892.0 sentences: 254.0 pages: flesch: 49.0 cache: ./cache/cord-325014-n7mnhk2v.txt txt: ./txt/cord-325014-n7mnhk2v.txt summary: As the time window for a positive RT-PCR result is short, serological testing, which provides information about whether a person has been exposed to SARS-CoV-2, may be useful for epidemiological purposes to detect the overall burden of previous infection in a given community. The aim of this study was to determine the prevalence of current and past SARS-CoV-2 infections among police employees, a high-risk population due to their professional duties, during the COVID-19 epidemic. Neither sex (p =0.155) nor other variables listed in Figure 2 were significantly associated with the IgG results ( Figure 2 A logistic regression model predicting a positive anti-SARS-CoV-2 IgM+IgA index was developed (Cox and Snell R Square at 0.015 andNagelkerke R Square at 0.033). After including all variables listed in Figures 1 and 2 along with the number of registered cases and deaths due to COVID-19 (per 10,000 inhabitants), only 4 variables showed a correlation with a positive anti-SARS-CoV-2 IgM+IgA index. abstract: Background: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to determine the prevalence of current and past SARS-CoV-2 infections among police employees. Methods: This cross-sectional survey was undertaken among 5082 police employees from Mazowieckie Province, Poland. RT-PCR testing for current SARS-CoV-2 infection and serological tests (ELISA) for the presence of anti-SARS-CoV-2 IgM+IgA and IgG antibodies were performed. Results: All RT-PCR tests were negative. The anti-SARS-CoV-2 IgM+IgA index was positive (>8) in 8.9% of participants, including 11.2% women and 7.7% men (p < 0.001). Equivocal IgM+IgA index (6–8) was found in 9.8% of participants, including 11.9% women and 8.7% men (p < 0.001). The IgG index was positive (>6) in 4.3% and equivocal (4–6) in 13.2% of participants. A higher odds of positive IgM+IgA index was found in women vs. men (OR: 1.742) and police officers vs. civilian employees (OR: 1.411). Participants aged ≥60 years had a higher odds of positive IgG index vs. those aged 20–29 years (OR: 3.309). Daily vaping also increased the odds of positive IgG index (OR: 2.058). Conclusions: The majority of Polish police employees are seronegative for SARS-CoV-2 infection. Vaping and older age (≥60 years) were associated with a higher risk of SARS-CoV-2 infection. url: https://doi.org/10.3390/jcm9103245 doi: 10.3390/jcm9103245 id: cord-286870-92eckkhk author: Gul, Seref title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials date: 2020-08-05 words: 6577.0 sentences: 387.0 pages: flesch: 50.0 cache: ./cache/cord-286870-92eckkhk.txt txt: ./txt/cord-286870-92eckkhk.txt summary: title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials The FDA-approved drug library was used to screen for the identification of molecules with high affinity to the active site of 3CL pro and nsp8 binding site of RdRp ( Figure 1 ). We also determined critical residues responsible for the high binding affinity of drugs to the protease, which may help to develop novel inhibitor molecules through rational drug design and quantitative structure-activity relationship (QSAR) studies. Conservation of these interactions during MD simulations and their contribution to BFE suggests that ergotamine can stably interact with the nsp8 binding site of RdRp. These results indicate that ergotamine and dihydroergotamine are possible candidates for further in vitro testing and clinical evaluation as an anti-SARS-CoV-2 agents. abstract: Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxychloroquine. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CL(pro)) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CL(pro) based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1802346 doi: 10.1080/07391102.2020.1802346 id: cord-338775-gh3a0wuf author: Gulersen, Moti title: Histopathological evaluation of placentas after diagnosis of maternal SARS-CoV-2 infection date: 2020-08-15 words: 2512.0 sentences: 152.0 pages: flesch: 44.0 cache: ./cache/cord-338775-gh3a0wuf.txt txt: ./txt/cord-338775-gh3a0wuf.txt summary: Study Design Retrospective cohort study of women diagnosed with SARS-CoV-2 infection who delivered at a single center from April 9th to April 27th, 2020, and had placental specimens reviewed by pathology. Histopathological characteristics were evaluated in each placenta and the incidence of these findings were compared between placentas after diagnosis of maternal SARS-CoV-2 infection and historical controls, as well as between placentas from patients with or without typical symptoms related to infection. Conclusions Based on our data, there are no significant placental histopathological changes that occur after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared to a gestational age-matched historical control group. The results of our study did not demonstrate significant placental histopathological changes 229 occurring after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared 230 to a gestational-age-matched historical control group with a similar incidence of antepartum or Pathology for examination or due to history of melanoma. abstract: Abstract Background The impact of maternal SARS-CoV-2 infection on placental histopathology is not well known. Objectives To determine if significant placental histopathological changes occur after diagnosis of SARS-CoV-2 infection in pregnancy and whether these changes are correlated with the presence or absence of symptoms associated with infection. Study Design Retrospective cohort study of women diagnosed with SARS-CoV-2 infection who delivered at a single center from April 9th to April 27th, 2020, and had placental specimens reviewed by pathology. Women with singleton gestations and laboratory-confirmed SARS-CoV-2 infection were eligible for inclusion. Historical controls selected from a cohort of women who delivered 6 months prior to the study period were matched in a 1:1 fashion by week of gestation at delivery. Histopathological characteristics were evaluated in each placenta and the incidence of these findings were compared between placentas after diagnosis of maternal SARS-CoV-2 infection and historical controls, as well as between placentas from patients with or without typical symptoms related to infection. Statistical analysis included use of Wilcoxon rank sum test and Fisher’s exact test for comparison of categorical and continuous variables. Statistical significance was defined as P value < 0.05. Results A total of 50 placentas after diagnosis of maternal SARS-CoV-2 infection and 50 historical controls were analyzed. Among placentas from patients diagnosed with SARS-CoV-2 infection, 3 (6%) were preterm (33 3/7, 34 6/7 and 36 6/7 weeks of gestation), 16 (32%) were from patients with typical symptoms related to infection and 34 (68%) were from patients without typical symptoms related to the infection. All patients had diagnosis of SARS-CoV-2 infection in the third trimester. Decidual vasculopathy was not visualized in any of the placentas from patients diagnosed with SARS-CoV-2 infection. There was no statistically significant difference in placental histopathological characteristics between the groups. SARS-CoV-2 testing for all neonates at 24 hours of life was negative. Conclusions Based on our data, there are no significant placental histopathological changes that occur after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared to a gestational age-matched historical control group. Similar incidences of histopathological findings were also discovered when comparing placentas from patients with SARS-CoV-2 infection with or without the presence of symptoms typically related to infection. url: https://www.sciencedirect.com/science/article/pii/S2589933320301798?v=s5 doi: 10.1016/j.ajogmf.2020.100211 id: cord-280392-ij5gtesw author: Gultom, Mitra title: Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date: 2020-11-10 words: 2253.0 sentences: 140.0 pages: flesch: 50.0 cache: ./cache/cord-280392-ij5gtesw.txt txt: ./txt/cord-280392-ij5gtesw.txt summary: In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. The AEC 131 cultures from 12 different species (rhesus macaque, cat, ferret, dog, rabbit, pig, cattle, goat, llama, 132 camel, and two neotropical bats) were inoculated with 10.000 TCID50 of either IAV or IDV and incubated 133 at 33°C and 37°C. For IDV we observed 137 antigen-positive cells in all AEC model, except for rhesus macaque and one of the neotropical bat 138 species, indicating that the AEC cultures were all well-differentiated and susceptible to virus infection. In the viral sequences in the 96 hpi samples from virus-infected 156 rhesus macaque and cat AEC cultures, we observed no obvious signs of nucleotide transitions that lead 157 to nonsynonymous mutations compared to the respective inoculums ( Fig. 3) , irrespective of 158 temperature and animal species. abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally, and the number of cases continues to rise all over the world. Besides humans, the zoonotic origin, as well as intermediate and potential spillback host reservoirs of SARS-CoV-2 are unknown. To circumvent ethical and experimental constraints, and more importantly, to reduce and refine animal experimentation, we employed our airway epithelial cell (AEC) culture repository composed of various domesticated and wildlife animal species to assess their susceptibility to SARS-CoV-2. In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. We observed that SARS-CoV-2 only replicated efficiently in monkey and cat AEC culture models. Whole-genome sequencing of progeny virus revealed no obvious signs of nucleotide transitions required for SARS-CoV-2 to productively infect monkey and cat epithelial airway cells. Our findings, together with the previously reported human-to-animal spillover events warrants close surveillance to understand the potential role of cats, monkeys, and closely related species as spillback reservoirs for SARS-CoV-2. url: https://doi.org/10.1101/2020.11.10.374587 doi: 10.1101/2020.11.10.374587 id: cord-314687-kyj6etnc author: Gunalan, Vithiagaran title: A putative diacidic motif in the SARS-CoV ORF6 protein influences its subcellular localization and suppression of expression of co-transfected expression constructs date: 2011-10-25 words: 4918.0 sentences: 222.0 pages: flesch: 45.0 cache: ./cache/cord-314687-kyj6etnc.txt txt: ./txt/cord-314687-kyj6etnc.txt summary: Following this, a mammalian expression plasmid pXJ3''-ORF6 was transfected into Vero E6 cells and Confocal microscopy showed that the ORF6 protein localized to a similar population of intracellular vesicles. These alanine substitution mutants were cloned into the same vector as the wildtype ORF6 gene and titrated against the nsp8 gene, by co-transfection of Vero E6 cells with plasmids encoding for myc-nsp8 and either 2 g pXJ3'' ORF6 Figure 3 The ORF6 protein exerts a transcriptional effect on nsp8 expression. This indicated that the reduction in the suppression of the expression of co-transfected myc-nsp8 by ORF6A53-56 was significant, and therefore that the putative diacidic motif defined by amino acids 53-56 has a role to play in this ability of the ORF6 protein. This indicated that the putative diacidic motif from amino acids 53-56, in addition to being involved in the suppression of the expression of co-transfected myc-nsp8, is also involved in the subcellular localization of the ORF6 protein and therefore these 2 phenomena may be linked. abstract: BACKGROUND: The ORF6 protein is one of the eight accessory proteins of the severe acute respiratory syndrome coronavirus (SARS-CoV). Numerous properties of ORF6 have been documented and this study focuses on two of these, namely, its ability to suppress the expression of co-transfected expression constructs and its subcellular localization to vesicular structures. RESULTS: Using a transient transfection system, ORF6's ability to suppress the expression of co-transfected expression constructs was measured in a quantitative manner. While ORF6 does not have a global effect on protein synthesis, quantitative real-time PCR revealed that it down-regulated the mRNA level of the co-transfected myc-nsp8 gene. Furthermore, alanine substitution of a diacidic cluster motif (aa53-56) in the ORF6 gene caused a reduction in the suppression of expression of co-transfected myc-nsp8 gene. Our previous study revealed that ORF6 localized to vesicular structures in SARS-CoV infected Vero E6 cells. Here, ORF6 was observed to be localized to similar vesicular structures in Vero E6 cells which have been transiently transfected with a mammalian expression plasmid encoding for untagged ORF6. ORF6 showed partial colocalization with cellular proteins CD63 and Lamp1, suggesting that the vesicular structures may be a subpopulation of endosomal/lysosomal vesicles. The alanine substitution of the diacidic cluster motif also altered the subcellular localization of the ORF6 protein, indicating a potential relationship between the subcellular localization of the ORF6 protein and its ability to suppress the expression of co-transfected expression constructs. CONCLUSIONS: By combining quantitative real-time PCR and transient transfection system, a simple and safe method is established to measure ORF6's ability to suppress the expression of co-transfected myc-nsp8. In addition, immunofluorescence analysis revealed that the subcellular localization of ORF6 when expressed on its own is similar to that observed in SARS-CoV infected cells. Through the use of these two assays, a putative diacidic motif in the ORF6 protein was found to influence its subcellular localization and ability to suppress the expression of co-transfected expression constructs. url: https://www.ncbi.nlm.nih.gov/pubmed/22026976/ doi: 10.1186/1756-0500-4-446 id: cord-273367-gl266pvt author: Gunawardana, M. title: Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date: 2020-07-28 words: 5731.0 sentences: 417.0 pages: flesch: 59.0 cache: ./cache/cord-273367-gl266pvt.txt txt: ./txt/cord-273367-gl266pvt.txt summary: Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. Subject 557 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on 558 symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but 559 tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A) . abstract: Background The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the associated coronavirus disease 2019 (COVID-19) have precipitated a global pandemic heavily challenging our social behavior, economy, and healthcare infrastructure. Public health practices currently represent the primary interventions for managing the spread of the pandemic. We hypothesized that frequent, longitudinal workplace disease surveillance would represent an effective approach to controlling SARS-CoV-2 transmission among employees and their household members, reducing potential economic consequences and loss of productivity of standard isolation methods, while providing new insights into viral-host dynamics. Methodology and Findings On March 23, 2020 a clinical study (OCIS-05) was initiated at a small Southern California organization. Results from the first 3 months of the ongoing study are presented here. Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. Only participants testing negative were allowed to enter the "safe zone" workplace facility. Optional blood samples were collected at baseline and throughout the 3-month study. Serum virus-specific antibody concentrations (IgG, IgM, and IgA) were measured using a selective, sensitive, and quantitative ELISA assay developed in house. A COVID-19 infection model, based on traditional SEIR compartmental models combined with Bayesian non-linear mixed models and modern machine learning, was used to predict the number of employees and household members who would have become infected in the absence of workplace surveillance. Two study participants were found to be infected by SARS-CoV-2 during the study. One subject, a household member, tested positive clinically by RT-qPCR prior to enrollment and experienced typical COVID-19 symptoms that did not require hospitalization. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. A single, unrelated employee became positive for SARS-CoV-2 RNA over the course of the study, but remained asymptomatic with low associated viral RNA copy numbers. The participant did not have detectable serum IgM and IgG concentrations, and IgA concentrations decayed rapidly (half-life: 1.3 d). The employee was not allowed entry to the safe zone workplace until testing negative three consecutive times over 7 d. No other employees or household members contracted COVID-19 over the course of the study. Our model predicted that under the current prevalence in Los Angeles County without surveillance intervention, up to 7 employees (95% CI = 3-10) would have become infected with at most 1 of them requiring hospitalizations and 0 deaths. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. The surveillance plan outlined here is scalable and transferrable. The study represents a powerful example on how an innovative public health initiative can be dovetailed with scientific discovery. url: https://doi.org/10.1101/2020.07.25.20160812 doi: 10.1101/2020.07.25.20160812 id: cord-329473-dtlwjndn author: Guo, Ao-Xiang title: The clinical characteristics and mortal causes analysis of COVID-19 death patients date: 2020-04-15 words: 3279.0 sentences: 240.0 pages: flesch: 63.0 cache: ./cache/cord-329473-dtlwjndn.txt txt: ./txt/cord-329473-dtlwjndn.txt summary: Therefore, we supposed that the expression of ACE2 and TMPRSS2 in human tissues could be used to explain the clinical characteristics of COVID-19 patients, including coexisting disorders, direct causes of death and initial symptoms. Our results also proved that coexisting disorders of hypertension and heart disease and initial symptoms of dyspnea were significantly higher in death patients, which was consistent with the one previous study [7] . While that ACE2 was highly expressed in heart may be related with the attack of SARS-CoV-2 in heart, which may lead to the initial symptoms of palpitate and chest tightness in some patients, and the direct causes of death including circulatory failure, heart disease and cardiac arrest. The expression of the SARS-CoV-2 targets in these important organs such as lung, heart, liver and kidney may help to explain the clinical characteristics of death patients. abstract: Abstract Purpose: Currently, COVID-19 is causing a large number of deaths globally. However, few researches focused on the clinical features of death patients. This study conducted a retrospective analysis of clinical characteristics and mortal causes in Chinese COVID-19 death patients. Patients and methods: The clinical characteristics of death patients were collected from publicized by local health authorities in China. Expressions of virus targets in human organs were obtained from GTEx database. Results: 159 patients from 24 provinces in China were recruited in our study, including 26 young patients under 60 and 133 aged 60 or older. The median age was 71 years, which indicated that most death patients were elderly. More male patients died of COVID-19 than females (1.65 fold). Hypertension was the most common coexisting disorder and respiratory failure was the most common direct cause of death. Fever (71.19%) and cough (55.08%) were the predominant presenting symptoms. There was one asymptomatic patient. In addition, by comparing young and old patients, heart disease was identified as an important risk factor for death in the aged patients. ACE2 and TMPRSS2 were the targets of SARS-CoV-2, we analyzed their expression in different organs. TMPRSS2 and ACE2 had a high expression in the organs which had corresponding clinical features in death patients. Conclusion: Male, age and heart disease were the main risk factors of death. Beside, asymptomatic patients with serious coexisting disorders may also die of SARS-CoV-2. Thus, more attention should be paid to the old patients with heart disease and asymptomatic patients in the treatment . Keywords: COVID-19, SARS-Cov-2, death, coexisting disorder, cause of death url: https://doi.org/10.1101/2020.04.12.20062380 doi: 10.1101/2020.04.12.20062380 id: cord-261834-x5ltmj30 author: Guo, Cheng-Xian title: Epidemiological and clinical features of pediatric COVID-19 date: 2020-08-06 words: 3438.0 sentences: 195.0 pages: flesch: 48.0 cache: ./cache/cord-261834-x5ltmj30.txt txt: ./txt/cord-261834-x5ltmj30.txt summary: METHODS: A retrospective study was conducted on children with a definite diagnosis of COVID-19 in mainland China using the web crawler technique to collect anonymous COVID-19 updates published by local health authorities. In this report, we conducted a retrospective review of COVID-19 features in 341 pediatric patients with ages between 0 and 14 years with the overall goal of providing data that could help in the development of guidelines for the prevention and treatment of pediatric COVID-19. This retrospective review was conducted in children aged 0-14 years with a definite diagnosis of COVID-19 from local health authorities between January 15, 2020, and March 15, 2020, in mainland China. Although there is relatively ample information available for adult COVID-19 patients, our knowledge and analysis of the epidemiology and clinical characteristics of pediatric COVID-19 is quite limited. The data was obtained from local China health authorities thus unable to compare the epidemiological and clinical data from US and European studies in children with COVID-19. abstract: BACKGROUND: COVID-19 is an extremely severe infectious disease. However, few studies have focused on the epidemiological and clinical characteristics of pediatric COVID-19. This study conducted a retrospective review of the epidemiological and clinical features of COVID-19 in children. METHODS: A retrospective study was conducted on children with a definite diagnosis of COVID-19 in mainland China using the web crawler technique to collect anonymous COVID-19 updates published by local health authorities. RESULTS: Three hundred forty-one children aged 4 days to 14 years with a median age of 7 years were included. Sixty-six percent of pediatric patients were infected via family members with COVID-19. The median incubation period was 9 days (interquartile range, 6 to 13). Asymptomatic cases accounted for 5.9%, of which 30% had abnormal chest radiologic findings. A majority of pediatric COVID-19 cases showed mild to moderate clinical features, and only a few developed severe or critical diseases (0.6% and 0.3%, respectively). Fever (77.9%) and cough (32.4%) were the predominant presenting symptoms of pediatric COVID-19. The pediatric patients had fewer underlying diseases and complications than adults. The treatment modalities for pediatric COVID-19 patients were not as complex as those of adult COVID-19 patients. The overall prognosis of pediatric COVID-19 was benign with a decent recovery. The median time from onset to cure was 16 days (interquartile range, 13 to 21). CONCLUSIONS: Compared to adults, COVID-19 in children has distinct features of epidemiology and clinical manifestations. The findings from this study might help to guide the development of measures to prevent and treat this ongoing global pandemic. TRIAL REGISTRATION: Chinese Clinical Trial Registry (chictr.org.cn) identifier: ChiCTR2000030464. url: https://doi.org/10.1186/s12916-020-01719-2 doi: 10.1186/s12916-020-01719-2 id: cord-270698-9w3ap3gz author: Guo, Hua title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date: 2020-05-13 words: 2496.0 sentences: 142.0 pages: flesch: 59.0 cache: ./cache/cord-270698-9w3ap3gz.txt txt: ./txt/cord-270698-9w3ap3gz.txt summary: title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. Consistent results were observed by binding affinity assays between SARSand SARSr-CoV spike proteins and receptor molecules from bats and humans. In a host-virus arms race situation, the genes involved tend to display dN/dS ratios Codon-based analysis of molecular evolution 536 Bat ACE2 and SARSr-CoV spike sequences were analyzed for positive selection. Identification of key amino acid 671 residues required for horseshoe bat angiotensin-I converting enzyme 2 to function as a 672 receptor for severe acute respiratory syndrome coronavirus abstract: The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we have identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiency in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS- and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that these residues were under strong positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics. It further proves that R. sinicus is the natural host of SARSr-CoVs. Importance Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoV in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS- and SARSr-CoV infection but with different binding affinity to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity of spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests a long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease. url: https://doi.org/10.1101/2020.05.13.093658 doi: 10.1101/2020.05.13.093658 id: cord-260376-29ih5c9v author: Guo, Jian-Ping title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 words: 2994.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-260376-29ih5c9v.txt txt: ./txt/cord-260376-29ih5c9v.txt summary: title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera. abstract: We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. We probed these membranes with four pairs of acute and convalescent sera from recovered SARS cases. We correlated positively reacting peptides with the in vitro SARS-CoV neutralizing activity of the samples. We found that convalescent sera with high neutralizing activity recognized exclusively only a limited number of peptides on the membranes. This suggests that antibodies against the epitopes represented by these peptides could be responsible for much of the SARS-CoV neutralizing activity. The findings have implications for monitoring humoral responses to SARS-CoV as well as for developing a successful SARS vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/15207612/ doi: 10.1016/j.virol.2004.04.017 id: cord-203191-7ftg6bfx author: Guo, Kai title: Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data date: 2020-05-16 words: 3729.0 sentences: 184.0 pages: flesch: 43.0 cache: ./cache/cord-203191-7ftg6bfx.txt txt: ./txt/cord-203191-7ftg6bfx.txt summary: title: Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA approved drugs and pre-clinical small-molecule compounds by integrating the gene expression perturbation data by chemicals from the Library of Integrated Network-Based Cellular Signatures (LINCS) project with publically available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We also collected a list of differentially expressed genes (DEGs) in SARS-CoV-2-infected lung BALF using a bulk RNA-Seq analysis to compare against the single-cell-based data. Repurposing analysis in severe COVID-19 patients 60 potent drugs were also selected in severe cases compared to controls (severe vs healthy group) according to their average CS between the replicates, and 25 of them involved in more than one cell subtype ( Figure 2B , Supplementary Tables S8 & S9) . abstract: With more than 3.8 million people infected Coronavirus Disease 2019 (COVID-19), caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a critical threat to human health. There is no proven vaccine or specific drug to date, which highlights the urgent need for rapid development of therapeutics for COVID-19. To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA approved drugs and pre-clinical small-molecule compounds by integrating the gene expression perturbation data by chemicals from the Library of Integrated Network-Based Cellular Signatures (LINCS) project with publically available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We identified 281 FDA approved drugs that have the potential to be effective against SARS-CoV-2 infection, 10 of which are currently undergoing clinical trials to evaluate their efficacy against COVID-19. In conclusion, we have identified a list of repurposable anti-SARS- CoV-2 drugs using a systems biology approach. url: https://arxiv.org/pdf/2005.07856v1.pdf doi: nan id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 words: 3486.0 sentences: 181.0 pages: flesch: 55.0 cache: ./cache/cord-354943-wxhbwcfr.txt txt: ./txt/cord-354943-wxhbwcfr.txt summary: METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. abstract: BACKGROUND: The emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. The current method of detection involves a quantitative polymerase chain reaction (qPCR)–based technique, which identifies the viral nucleic acids when present in sufficient quantity. False-negative results can be achieved and failure to quarantine the infected patient would be a major setback in containing the viral transmission. We aim to describe the time kinetics of various antibodies produced against the 2019 novel coronavirus (SARS-CoV-2) and evaluate the potential of antibody testing to diagnose COVID-19. METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. 208 plasma samples were collected from 82 confirmed and 58 probable cases (qPCR negative but with typical manifestation). The diagnostic value of IgM was evaluated in this cohort. RESULTS: The median duration of IgM and IgA antibody detection was 5 (IQR, 3–6) days, while IgG was detected 14 (IQR, 10–18) days after symptom onset, with a positive rate of 85.4%, 92.7%, and 77.9%, respectively. In confirmed and probable cases, the positive rates of IgM antibodies were 75.6% and 93.1%, respectively. The detection efficiency by IgM ELISA is higher than that of qPCR after 5.5 days of symptom onset. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). CONCLUSIONS: The humoral response to SARS-CoV-2 can aid in the diagnosis of COVID-19, including subclinical cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32198501/ doi: 10.1093/cid/ciaa310 id: cord-320165-1b6sycgv author: Guo, Qirui title: Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date: 2020-09-09 words: 6762.0 sentences: 425.0 pages: flesch: 54.0 cache: ./cache/cord-320165-1b6sycgv.txt txt: ./txt/cord-320165-1b6sycgv.txt summary: S100A8/A9 specific inhibitor, Paquinimod, significantly reduced the number of neutrophils activated by the coronavirus, inhibited viral replication and rescued lung damage a result of SARS-CoV-2 infection. The whole genome wide RNA-seq analysis of the lungs from infected rhesus macaques showed that a number of transcripts were induced or inhibited at day 3 and day 5 after SARS-CoV-2 infection (Supplementary Figure 1A) . Similar to the data from rhesus macaque experiments, compared to other alarmins, S100A8 was robustly induced by SARS-CoV-2 but not by IAV infection in mice ( Figure 2E ). The expression of these B cell related genes was rescued or induced by Paquinimod during MHV infection, which was confirmed by qRT-PCR analysis ( Figure 3M ). Moreover, both Paquinimod and Resatorvid suppressed the activation of coronavirus related neutrophils in lung during SARS-CoV-2 infection ( Figure 4D ). abstract: The SARS-CoV-2 pandemic poses an unprecedented public health crisis. Accumulating evidences suggest that SARS-CoV-2 infection causes dysregulation of immune system. However, the unique signature of early immune responses remains elusive. We characterized the transcriptome of rhesus macaques and mice infected with SARS-CoV-2. Alarmin S100A8 was robustly induced by SARS-CoV-2 in animal models as well as in COVID-19 patients. Paquinimod, a specific inhibitor of S100A8/A9, could reduce inflammatory response and rescue the pneumonia with substantial reduction of viral titers in SASR-CoV-2 infected animals. Remarkably, Paquinimod treatment resulted in 100% survival of mice in a lethal model of mouse coronavirus (MHV) infection. A novel group of neutrophils that contributed to the uncontrolled inflammation and onset of COVID-19 were dramatically induced by coronavirus infections. Paquinimod treatment could reduce these neutrophils and regain antiviral responses, unveiling key roles of S100A8/A9 and noncanonical neutrophils in the pathogenesis of COVID-19, highlighting new opportunities for therapeutic intervention. url: https://doi.org/10.1101/2020.09.09.288704 doi: 10.1101/2020.09.09.288704 id: cord-307932-7t41wvw3 author: Guo, Xiaoqin title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers date: 2020-02-14 words: 1854.0 sentences: 115.0 pages: flesch: 58.0 cache: ./cache/cord-307932-7t41wvw3.txt txt: ./txt/cord-307932-7t41wvw3.txt summary: title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers METHODS: A long-term prospective cohort study followed 34 SARS-CoV-infected healthcare workers from a hospital with clustered infected cases during the 2002-2003 SARS outbreak in Guangzhou, China, with a 13-year follow-up. Non-linear exponential decay models were used to estimate the average decay rates of the antibody CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In our cohort, we found that two healthcare workers might have been misdiagnosed with 236 SARS, as the IgG antibodies against both the whole virus and N199 antigen was persistently 237 lower than the cutoff value, for these two patients. Collectively, based on our results, we can infer that the IgG against SARS-CoV can persist at CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: BACKGROUND: The ongoing worldwide outbreak of the 2019-nCoV is markedly similar to the severe acute respiratory syndrome (SARS) outbreak 17 years ago. During the 2002-2003 SARS outbreak, healthcare workers formed a special population of patients. Although virus-specific IgG play important roles in virus neutralization and prevention against future infection, limited information is available regarding the long term persistence of IgG after infection with SARS-like coronavirus. METHODS: A long-term prospective cohort study followed 34 SARS-CoV-infected healthcare workers from a hospital with clustered infected cases during the 2002-2003 SARS outbreak in Guangzhou, China, with a 13-year follow-up. Serum samples were collected annually from 2003-2015. Twenty SARS-CoV-infected and 40 non-infected healthcare workers were enrolled in 2015, and their serum samples were collected. All sera were tested for IgG antibodies with ELISA using whole virus and a recombinant nucleocapsid protein of SARS-CoV, as a diagnostic antigen. RESULTS: Anti SARS-CoV IgG was found to persist for up to 12 years. IgG titers typically peaked in 2004, declining rapidly from 2004-2006, and then continued to decline at a slower rate. IgG titers in SARS-CoV-infected healthcare workers remained at a significantly high level until 2015. Patients treated with corticosteroids at the time of infection were found to have lower IgG titers than those without. CONCLUSIONS: IgG antibodies against SARS-CoV can persist for at least 12 years. The presence of SARS-CoV IgG might provide protection against SARS-CoV and other betacoronavirus. This study provides valuable information regarding humoral immune responses against SARS-CoV and the 2019-nCoV. url: https://doi.org/10.1101/2020.02.12.20021386 doi: 10.1101/2020.02.12.20021386 id: cord-346987-fbqqf00i author: Guo, Yongwen title: Controls of SARS-CoV-2 transmission in orthodontic practice date: 2020-06-05 words: 4660.0 sentences: 244.0 pages: flesch: 47.0 cache: ./cache/cord-346987-fbqqf00i.txt txt: ./txt/cord-346987-fbqqf00i.txt summary: ABSTRACT The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted worldwide concerns because of its high person-to-person infectivity and lethality, and it was labeled as a pandemic as the rapid increase of confirmed cases in most areas around the world became evident. Although the spread of COVID-19 has been effectively controlled in China and many areas have gradually resumed work and classes, orthodontic participants are still under high risks of SARS-CoV-2 infection. What''s more, the close contact between dental staffs and patients as well as the droplets and aerosols generated during treatment containing saliva and blood further increase the risk of SARS-CoV-2 transmission in dental practice 5 . We must constantly bear in mind that the threat of infection is not visible which poses a challenge on the orthodontic practice thus effective control measures should be taken to prevent the transmission of SARS-CoV-2 and protect both practitioners and patients from the COVID-19. abstract: ABSTRACT The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted worldwide concerns because of its high person-to-person infectivity and lethality, and it was labeled as a pandemic as the rapid increase of confirmed cases in most areas around the world became evident. The SARS-CoV-2 is mainly transmitted through respiratory droplets and close contact. There are also evidences of transmission through aerosols and digestive tracts. Since orthodontic treatment involves large population who need routine return-visits, it was significantly affected and suspended because of the COVID-19 pandemic and the shutdown of the dental clinics and hospitals. Although the spread of COVID-19 has been effectively controlled in China and many areas have gradually resumed work and classes, orthodontic participants are still under high risks of SARS-CoV-2 infection. This is due to the asymptomatic carriers of SARS-CoV-2 or patients in the incubation period may cause the cross infection between orthodontic practitioners and patients. The close proximity between the practitioners and the patients, and the generation of droplets and aerosols that contain saliva and blood during treatment further increase the risks of transmission. In this review, we summarized the preventive strategies for controls of SARS-CoV-2 transmission to protect both staffs and patients during the orthodontic practice. url: https://doi.org/10.1016/j.ajodo.2020.05.006 doi: 10.1016/j.ajodo.2020.05.006 id: cord-298172-iyxyennq author: Guo, Youjia title: Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date: 2020-10-02 words: 4557.0 sentences: 295.0 pages: flesch: 49.0 cache: ./cache/cord-298172-iyxyennq.txt txt: ./txt/cord-298172-iyxyennq.txt summary: Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Among them, two antibodies were shown to attenuate the interaction of spike proteins with ACE2 and neutralized infection of VeroE6/TMPRSS2 cells by SARS-CoV-2. Mice were immunized with these recombinant spike proteins to generate antibodies against the SARS-CoV-2 virus, followed by cell fusion to generate a hybridoma-producing antibody. The performance of our antibodies in IP experiments prompted us to examine whether they were capable of inhibiting spike-ACE2 binding or even neutralizing SARS-CoV-2 infection. Our antibodies, S1D7 and S3D8, have been shown to attenuate the interaction of spike proteins with ACE2 and neutralize infection of VeroE6/TM2 cells by SARS-CoV-2. abstract: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a global pandemic since its first outbreak in the winter of 2019. An extensive investigation of SARS-CoV-2 is critical for disease control. Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. However, the need for dedicated monoclonal antibodies in molecular pathology research is not fully addressed. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Our monoclonal antibodies are of mouse origin, making them compatible with the experimental immunoassay setups commonly used in basic molecular biology research laboratories, and large-scale production and easy distribution are guaranteed by conventional mouse hybridoma technology. url: https://doi.org/10.1101/2020.10.01.323220 doi: 10.1101/2020.10.01.323220 id: cord-271536-pscw933i author: Guo, Zhen-Dong title: Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020 date: 2020-07-17 words: 1685.0 sentences: 100.0 pages: flesch: 61.0 cache: ./cache/cord-271536-pscw933i.txt txt: ./txt/cord-271536-pscw933i.txt summary: To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. Furthermore, we found that rates of positivity differed by air sampling site, which reflects the distribution of virus-laden aerosols in the wards ( Figure 2 , panel A). SARS-CoV-2 aerosol was detected at all 3 sampling sites; rates of positivity were 35.7% (5/14) near air outlets, 44.4% (8/18) in patients'' rooms, and 12.5% Figure 2 (1/8) in the doctors'' office area. First, SARS-CoV-2 was widely distributed in the air and on object surfaces in both the ICU and GW, implying a potentially high infection risk for medical staff and other close contacts. abstract: To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. Contamination was greater in intensive care units than general wards. Virus was widely distributed on floors, computer mice, trash cans, and sickbed handrails and was detected in air ≈4 m from patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32275497/ doi: 10.3201/eid2607.200885 id: cord-302541-0upiu6iq author: Gupta, Abhishek title: Lockdown—the only solution to defeat COVID-19 date: 2020-05-06 words: 575.0 sentences: 35.0 pages: flesch: 62.0 cache: ./cache/cord-302541-0upiu6iq.txt txt: ./txt/cord-302541-0upiu6iq.txt summary: As it is a new strain of coronavirus and little is known about its behaviour except its potential for transmission while being asymptomatic during an incubation period of up to 14 days and its sensitivity to heat, Sophie Bushwick, technology editor at Scientific American, a science magazine, stated on 20 March 2020 that asymptomatic people with COVID-19 have a higher viral load. A lockdown period depends upon the virus'' faster decay rate which is directly related to the melting point of the outer protective lipid bilayers of SARS-CoV2. In the case of SARS-CoV2 being zoonotic, it is presumed that the melting point of its lipid layer should be around 40°C, resulting in its faster decay during the summer. Because coronavirus is transmitted from host to host only, keeping it away from a host for longer than its incubation period through a lockdown can cause its own death and defeat COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32377056/ doi: 10.1007/s13410-020-00826-3 id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 words: 5174.0 sentences: 385.0 pages: flesch: 57.0 cache: ./cache/cord-276908-9jthjf24.txt txt: ./txt/cord-276908-9jthjf24.txt summary: In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. abstract: Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease‐2019 (COVID‐19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID‐19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS‐CoV‐2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present‐day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding. url: https://www.ncbi.nlm.nih.gov/pubmed/32835089/ doi: 10.1002/slct.202001709 id: cord-317906-u5z5cpfk author: Gupta, Ishita title: Atypical Neurological Manifestations of COVID-19 date: 2020-06-08 words: 2184.0 sentences: 163.0 pages: flesch: 58.0 cache: ./cache/cord-317906-u5z5cpfk.txt txt: ./txt/cord-317906-u5z5cpfk.txt summary: The novel coronavirus (SARS-CoV-2), belonging to a group of RNA-enveloped viruses and believed to be transmitted by aerosol route, is a worldwide pandemic. However, to our knowledge, there are minimal studies on the neurological manifestations in SARS-CoV-2 positive patients. Our review aims to identify the various neurological manifestations in SARS-CoV-2 positive patients, which could be an added advantage in the early diagnosis and prevention of further complications of the nervous system. Other non-neurological symptoms were diarrhea, anorexia, myalgia, sore throat, dyspnea, chest pain, fatigue, headache, arthralgia, nausea, and vomiting (see Figure 2 and Table 3 ) [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] . The presentation of olfactory symptoms in SARS-CoV-2-affected patients is due to the fact that the illness spreads through the cribriform plate, which is in close proximity to the olfactory region [30] . Neurological manifestations in COVID-19 caused by SARS-CoV-2 abstract: The novel coronavirus (SARS-CoV-2), belonging to a group of RNA-enveloped viruses and believed to be transmitted by aerosol route, is a worldwide pandemic. Many studies have described typical clinical manifestations such as fever, cough, fatigue, diarrhea, and nasal congestion. However, to our knowledge, there are minimal studies on the neurological manifestations in SARS-CoV-2 positive patients. Our review aims to identify the various neurological manifestations in SARS-CoV-2 positive patients, which could be an added advantage in the early diagnosis and prevention of further complications of the nervous system. url: https://doi.org/10.7759/cureus.8518 doi: 10.7759/cureus.8518 id: cord-330717-uzrxtgrg author: Gupta, Madhu title: The need for COVID-19 research in low- and middle-income countries date: 2020-07-01 words: 1840.0 sentences: 96.0 pages: flesch: 40.0 cache: ./cache/cord-330717-uzrxtgrg.txt txt: ./txt/cord-330717-uzrxtgrg.txt summary: We therefore propose research in three broad areas as urgently needed to inform responses in lowand middle-income countries: transmission patterns of SARS-CoV-2, the clinical characteristics of the disease, and the impact of pandemic prevention and response measures. Targeted research activities should be done to help mitigate the potential burden of COVID-19 in lowand middle-income countries without diverting the limited human resources, funding, or medical supplies from response activities. We propose three broad research questions to inform public health and policy responses to COVID-19 in LMICs: (1) how do the patterns of SARS-CoV-2 transmission differ in resource-poor settings? A more thorough understanding of the relationship between climate, seasonality, and virus transmissibility could provide insights into the potential course of the pandemic in LMICs that tend to be warmer and more humid, supporting preparedness and response efforts in these settings. abstract: In the early months of the pandemic, most reported cases and deaths due to COVID-19 occurred in high-income countries. However, insufficient testing could have led to an underestimation of true infections in many low- and middle-income countries. As confirmed cases increase, the ultimate impact of the pandemic on individuals and communities in low- and middle-income countries is uncertain. We therefore propose research in three broad areas as urgently needed to inform responses in low- and middle-income countries: transmission patterns of SARS-CoV-2, the clinical characteristics of the disease, and the impact of pandemic prevention and response measures. Answering these questions will require a multidisciplinary approach led by local investigators and in some cases additional resources. Targeted research activities should be done to help mitigate the potential burden of COVID-19 in low- and middle-income countries without diverting the limited human resources, funding, or medical supplies from response activities. url: https://doi.org/10.1186/s41256-020-00159-y doi: 10.1186/s41256-020-00159-y id: cord-337032-s4g4g80w author: Gupta, Manoj Kumar title: In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date: 2020-04-15 words: 3964.0 sentences: 191.0 pages: flesch: 52.0 cache: ./cache/cord-337032-s4g4g80w.txt txt: ./txt/cord-337032-s4g4g80w.txt summary: Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ''SARS-CoV2 E'' protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. By considering the above information, in the present study, authors employed computational approach for identifying the best possible structure of the ''SARS-CoV2 E'' protein present in the PDB database to understand its structure and function as well as its behaviour towards various phytochemicals. Subsequently, molecular docking of the ''SARS-CoV2 E'' protein with ligands having 250 conformations using the AutoDock tool revealed that the best ten phytochemicals with minimal binding energy are TIP006452 (Belachinal), TIP005365 (Macaflavanone E), TIP003272 (Vibsanol B), TIP003258 (14 R à ,15-Epoxyvibsanin C), TIP005363 (Macaflavanone C), TIP000749 (Luzonoid D), TIP008605 (Grossamide K), TIP009461 ((-)-Blestriarene C), TIP005366 (Macaflavanone F) and TIP005783 (Dolichosterone). abstract: Recent outbreak of Coronavirus disease (COVID-19) pandemic around the world is associated with ‘severe acute respiratory syndrome’ (SARS-CoV2) in humans. SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. Thus, there is always a quest to inhibit these ion channels, which in turn may help in controlling diseases caused by SARS-CoV2 in humans. Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ‘SARS-CoV2 E’ protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. However, after binding with Belachinal, Macaflavanone E, and Vibsanol B, the random motion of the human ‘SARS-CoV2 E’ protein gets reduced, this, in turn, inhibits the function of the ‘SARS-CoV2 E’ protein. It is pertinent to note that two amino acids, namely VAL25 and PHE26, play a key role while interacting with these three phytochemicals. As these three phytochemicals, namely, Belachinal, Macaflavanone E & Vibsanol B, have passed the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) property as well as ‘Lipinski’s Rule of 5s’, they may be utilized as drugs in controlling disease caused via SARS-COV2, after further investigation. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1751300 doi: 10.1080/07391102.2020.1751300 id: cord-352059-1bjskqyg author: Gupta, Nivedita title: Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories date: 2020-04-28 words: 4174.0 sentences: 224.0 pages: flesch: 53.0 cache: ./cache/cord-352059-1bjskqyg.txt txt: ./txt/cord-352059-1bjskqyg.txt summary: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, which is the apex laboratory for viral diagnosis and research in India, optimized the conventional and real-time PCR assays targeting different genomic regions of SARS-CoV-2 and initiated testing of suspected cases. Before initiating testing of clinical specimens from suspected cases of SARS-CoV-2, each VRDL shared results from the rRT-PCR runs performed with positive and negative controls with the apex laboratory (NIV, Pune). Expansion of testing capabilities and selection of testing laboratories for SARS-CoV-2: Following the increase in the load of screening samples from suspected cases with symptoms and travel history to China or asymptomatic persons with travel history to Wuhan after January 15, 2020, it was decided that strategically located VRDLs needed to start testing for SARS-CoV-2 in addition to Thereafter, NCDC, Delhi, initiated independent testing; however, results were shared with ICMR on a daily basis. abstract: BACKGROUND & OBJECTIVES: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. METHODS: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. RESULTS: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. INTERPRETATION & CONCLUSIONS: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs. url: https://www.ncbi.nlm.nih.gov/pubmed/32242875/ doi: 10.4103/ijmr.ijmr_594_20 id: cord-339786-elrzlbsg author: Gurala, Dhineshreddy title: Acute Liver Failure in a COVID-19 Patient Without any Preexisting Liver Disease date: 2020-08-26 words: 2058.0 sentences: 117.0 pages: flesch: 51.0 cache: ./cache/cord-339786-elrzlbsg.txt txt: ./txt/cord-339786-elrzlbsg.txt summary: Studies and data so far on coronavirus infections from China, Singapore, and other countries showed that liver enzymes elevation could be seen in 20-50% of cases. In another study published in the Lancet in February 2020 by Huang et al., an increase in aspartate aminotransferase (AST) was observed in 62% in intensive care unit (ICU) patients compared to 25% in non-ICU patients, indicating that more severe disease correlates with worsening of liver enzymes [10] . Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. In summary, we describe the first case of acute liver failure caused by the COVID-19 infection. abstract: In December 2019, an outbreak of novel coronavirus started in Wuhan, China, which gradually spread to the entire world. The World Health Organization (WHO) on February 11, 2020, officially announced the name for the disease as coronavirus disease 2019, abbreviated as COVID-19. It is caused by severe respiratory distress syndrome coronavirus 2 (SARS-CoV-2). The WHO declared SARS-CoV-2 as a pandemic on March 11, 2020. SARS-CoV-2 mainly causes fever as well as respiratory symptoms such as cough and shortness of breath. Gastrointestinal/hepatic sequelae such as diarrhea, nausea, vomiting, and elevated liver enzymes have been reported as well. Studies and data so far on coronavirus infections from China, Singapore, and other countries showed that liver enzymes elevation could be seen in 20-50% of cases. More severe disease can correlate with the worsening of liver enzymes. However, acute liver failure in patients with COVID-19 has not been described. Herein we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. url: https://doi.org/10.7759/cureus.10045 doi: 10.7759/cureus.10045 id: cord-259566-qtlq7a6l author: Guraya, Salman Yousuf title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article date: 2020-06-23 words: 2421.0 sentences: 150.0 pages: flesch: 39.0 cache: ./cache/cord-259566-qtlq7a6l.txt txt: ./txt/cord-259566-qtlq7a6l.txt summary: title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article Benefits of delaying elective and non-urgent surgery outweighs the risk of performing surgical procedures on patients with asymptomatic or active COVID-19 disease. Limiting the number of operating room personnel, use of disposable instruments, small trocar incisions, negative pressure environment, and setting energy devices at low modes can help reduce disease transmission during laparoendocsopic procedures. This write up provides a brief account of the impact of the COVID-19, big data analytics of response of medical personnel in curtailing and understanding the disease process and the consensus guidelines for carrying out laparoscopic and endoscopic procedures. -Limiting the number of operating room personnel, use of disposable instruments, negative pressure air flow, and setting electrocautery energy devices at low modes can possibly reduce disease transmission during laparoendocsopic procedures. abstract: The current dreadful pandemic of coronavirus disease (COVID-19) is playing havoc with humanity, socio-communal systems and economic reservoirs worldwide. Certain countries have managed to curtail COVID-19 crisis to some extent, however, a great majority still remains helpless in containing this outbreak. Rapidly evolving disease patterns and complex epidemiology of COVID-19 necessitate a tailored approach by medical experts in dealing with this devastating outbreak. Similar to other medical disciplines, surgical associations and societies have developed a tailored approach of patients’ selection and planning with improvised endolaparoscopic practice during the COVID-19 pandemic. Non-essential and non-urgent surgical procedures are deferred till this outbreak is abated. Benefits of delaying elective and non-urgent surgery outweighs the risk of performing surgical procedures on patients with asymptomatic or active COVID-19 disease. Laparoendoscopic procedures increase the risk of aerosol exposure, disease transmission and contamination. Limiting the number of operating room personnel, use of disposable instruments, small trocar incisions, negative pressure environment, and setting energy devices at low modes can help reduce disease transmission during laparoendocsopic procedures. This write up provides a brief account of the impact of the COVID-19, big data analytics of response of medical personnel in curtailing and understanding the disease process and the consensus guidelines for carrying out laparoscopic and endoscopic procedures. url: https://api.elsevier.com/content/article/pii/S1743919120305094 doi: 10.1016/j.ijsu.2020.06.027 id: cord-265128-i0d4lxko author: Gurung, Arun Bahadur title: Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M(pro) enzyme through in silico approach date: 2020-05-22 words: 2234.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-265128-i0d4lxko.txt txt: ./txt/cord-265128-i0d4lxko.txt summary: Among coronaviruses, the main protease (M(pro)) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 M(pro) enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 M(pro), SARS-CoV M(pro) and MERS-CoV M(pro) were studied using molecular docking. Structure-based drug design primarily relies on molecular docking to identify lead molecules against the target proteins from chemical libraries [12, 13] . The natural products such as traditional medicines and plant-derived compounds (phytochemicals) are the rich sources of promising antiviral drugs [14] . The binding energies and inhibition constants of the phytochemicals with the SARS-CoV-2 M pro enzyme were compared with that of a set of twelve FDA approved antiviral drugs-a) Viral abstract: A new SARS coronavirus (SARS-CoV-2) belonging to the genus Betacoronavirus has caused a pandemic known as COVID-19. Among coronaviruses, the main protease (M(pro)) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. There are no human proteases with similar cleavage specificity and therefore, inhibitors are highly likely to be nontoxic. Therefore, targeting the SARS-CoV-2 M(pro) enzyme with small molecules can block viral replication. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 M(pro) enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 M(pro), SARS-CoV M(pro) and MERS-CoV M(pro) were studied using molecular docking. Bonducellpin D was identified as the best lead molecule which shows higher binding affinity (−9.28 kcal/mol) as compared to the control (−8.24 kcal/mol). The molecular binding was stabilized through four hydrogen bonds with Glu166 and Thr190 as well as hydrophobic interactions via eight residues. The SARS-CoV-2 M(pro) shows identities of 96.08% and 50.65% to that of SARS-CoV M(pro) and MERS-CoV M(pro) respectively at the sequence level. At the structural level, the root mean square deviation (RMSD) between SARS-CoV-2 M(pro) and SARS-CoV M(pro) was found to be 0.517 Å and 0.817 Å between SARS-CoV-2 M(pro) and MERS-CoV M(pro). Bonducellpin D exhibited broad-spectrum inhibition potential against SARS-CoV M(pro) and MERS-CoV M(pro) and therefore is a promising drug candidate, which needs further validations through in vitro and in vivo studies. url: https://doi.org/10.1016/j.lfs.2020.117831 doi: 10.1016/j.lfs.2020.117831 id: cord-347366-0gier0lu author: Gurwitz, David title: Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics date: 2020-03-04 words: 1917.0 sentences: 105.0 pages: flesch: 45.0 cache: ./cache/cord-347366-0gier0lu.txt txt: ./txt/cord-347366-0gier0lu.txt summary: A tentative suggestion based on existing therapeutics, which would likely be resistant to new coronavirus mutations, is to use available angiotensin receptor 1 (AT1R) blockers, such as losartan, as therapeutics for reducing the aggressiveness and mortality from SARS‐CoV‐2 virus infections. These tentative suggestions were based on the observation that SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor binding domain for its spike protein (Lu et al., 2020; Wan, Shang, Graham, Baric, & Li, 2020) , similarly to the coronavirus strain implicated in the 2002-2003 SARS epidemic (Dimitrov, 2003; Ge et al., 2013; Li et al., 2003; Prabakaran et al 2004; Turner, Hiscox, & Hooper, 2004) . The tentative suggestion to apply AT1R antagonists such as losartan and telmisartan as SARS-CoV-2 therapeutics for treating patients prior to the development of acute respiratory syndrome remains unproven until tried. abstract: At the time of writing this commentary (February 2020), the coronavirus COVID‐19 epidemic has already resulted in more fatalities compared with the SARS and MERS coronavirus epidemics combined. Therapeutics that may assist to contain its rapid spread and reduce its high mortality rates are urgently needed. Developing vaccines against the SARS‐CoV‐2 virus may take many months. Moreover, vaccines based on viral‐encoded peptides may not be effective against future coronavirus epidemics, as virus mutations could make them futile. Indeed, new Influenza virus strains emerge every year, requiring new immunizations. A tentative suggestion based on existing therapeutics, which would likely be resistant to new coronavirus mutations, is to use available angiotensin receptor 1 (AT1R) blockers, such as losartan, as therapeutics for reducing the aggressiveness and mortality from SARS‐CoV‐2 virus infections. This idea is based on observations that the angiotensin‐converting enzyme 2 (ACE2) very likely serves as the binding site for SARS‐CoV‐2, the strain implicated in the current COVID‐19 epidemic, similarly to strain SARS‐CoV implicated in the 2002–2003 SARS epidemic. This commentary elaborates on the idea of considering AT1R blockers as tentative treatment for SARS‐CoV‐2 infections, and proposes a research direction based on datamining of clinical patient records for assessing its feasibility. url: https://www.ncbi.nlm.nih.gov/pubmed/32129518/ doi: 10.1002/ddr.21656 id: cord-329318-eo8auo1f author: Gusarov, Sergey title: COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2 date: 2020-10-26 words: 3971.0 sentences: 217.0 pages: flesch: 46.0 cache: ./cache/cord-329318-eo8auo1f.txt txt: ./txt/cord-329318-eo8auo1f.txt summary: [Image: see text] Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. In this study, we propose a novel set of drug screening descriptors based on COSMO-RS σ-profiles, augmented by dipole moment and induced charge of the phosphorus atom, to evaluate the chemical similarity of the drugs with nucleotides, as RNA replication transcription initiation activators. A novel set of descriptors based on COSMO-RS σ-profiles and chemical thermodynamics is proposed and evaluated using PCA for the initial screening of a series of nucleotides and nucleotide-analog RdRp replication inhibitor drugs to help accelerate the discovery of COVID-19 treatments. The PCA results show that the novel σ-profile-based descriptor set I clearly correlates the leading COVID-19 drugs remdesivir and EIDD-2801 in monophosphate forms and highlights weaker correlations with drugs that have been reported to exhibit anti-SARS-CoV-2 activity. abstract: [Image: see text] Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. We propose novel descriptors based on a COSMO-RS (short for conductor-like screening model for real solvents) σ-profiles for enhanced drug screening enabled by machine learning (ML). The descriptors’ performance is hereby illustrated for nucleotide analogue drugs that inhibit the ribonucleic acid-dependent ribonucleic acid polymerase, key to viral transcription and genome replication. The COSMO-RS-based descriptors account for both chemical reactivity and structure, and are more effective for ML-based screening than fingerprints based on molecular structure and simple physical/chemical properties. The descriptors are evaluated using principal component analysis, an unsupervised ML technique. Our results correlate with the active monophosphate forms of the leading drug remdesivir and the prospective drug EIDD-2801 with nucleotides, followed by other promising drugs, and are superior to those from molecular structure-based descriptors and molecular docking. The COSMO-RS-based descriptors could help accelerate drug discovery for the treatment of emerging diseases. url: https://doi.org/10.1021/acs.jpclett.0c02836 doi: 10.1021/acs.jpclett.0c02836 id: cord-306414-2dv3qced author: Gutierrez, Lucas title: Deciphering the TCR Repertoire to Solve the COVID-19 Mystery date: 2020-06-20 words: 6993.0 sentences: 368.0 pages: flesch: 42.0 cache: ./cache/cord-306414-2dv3qced.txt txt: ./txt/cord-306414-2dv3qced.txt summary: Advances in sequencing technologies and single-cell immune profiling can be leveraged to monitor adaptive immune responses in COVID-19 patients and guide future SARS-CoV-2 immunotherapy and biomarker development. Whether the aged and less diverse TCR repertoire impacts the ability to generate a sufficiently robust T cell response against SARS-CoV-2 in older patients remains to be studied. The development of faster and cheaper sequencing technologies, augmented by the advances in computational tools, support the feasibility of using TCR analyses not only to track SARS-CoV-2specific T cell expansion post-COVID-19 infection or in the course of treating patients with COVID-19, but also to establish certain features of the TCR repertoire architecture as predictive biomarkers for patients'' clinical outcome. Thus, a comprehensive characterization of the dynamics and composition of the TCR repertoires to SARS-CoV-2 infection can largely contribute to the evolving understanding of the functional and mechanistic involvement of the adaptive immune cell response and potentially guide the design of effective treatment. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected several millions and killed more than quarter of a million worldwide to date. Important questions have remained unanswered: why some patients develop severe disease, while others do not; and what roles do genetic variabilities play in the individual immune response to this viral infection. Here, we discuss the critical role T cells play in the orchestration of the antiviral response underlying the pathogenesis of the disease, COVID-19. We highlight the scientific rationale for comprehensive and longitudinal TCR analyses in COVID-19 and reason that analyzing TCR repertoire in COVID-19 patients would reveal important findings that may explain the outcome disparity observed in these patients. Finally, we provide a framework describing the different strategies, the advantages, and the challenges involved in obtaining useful TCR repertoire data to advance our fight against COVID-19. url: https://doi.org/10.1016/j.tips.2020.06.001 doi: 10.1016/j.tips.2020.06.001 id: cord-285739-0enn5bzn author: Gutiérrez Rodríguez, José title: Variables asociadas a mortalidad en una población de pacientes mayores de 80 años y con algún grado de dependencia funcional hospitalizados por COVID-19 en un Servicio de Geriatría date: 2020-07-16 words: 3924.0 sentences: 356.0 pages: flesch: 52.0 cache: ./cache/cord-285739-0enn5bzn.txt txt: ./txt/cord-285739-0enn5bzn.txt summary: Ese mismo día, tras un gran esfuerzo organizativo se abren las plantas para pacientes con COVID-19 en nuestro centro hospitalario: un total de 38 camas destinadas a pacientes mayores de 80 años con infección por coronavirus, que precisan hospitalización por presentar insuficiencia respiratoria aguda o descompensación de patología de base y que, en caso de empeoramiento clínico, no serían subsidiarios de beneficio de ingreso en UCI por sufrir algún grado de dependencia funcional y/o deterioro cognitivo 22 . En este ámbito asistencial, los objetivos de este trabajo han sido: a) estudiar las características epidemiológicas, clínica, analíticas y radiológicas de pacientes mayores de 80 años con algún grado de dependencia funcional y/o deterioro cognitivo ingresados con COVID-19 confirmado por diagnóstico de laboratorio, b) determinar la tasa de mortalidad, c) analizar las variables clínicas, terapéuticas, funcionales y mentales que se asocian a mayor riesgo de mortalidad. abstract: ABSTRACT Objective: The SARS-CoV-2 pandemic conditions high mortality rates in hospitalized elderly. Currently, a few studies include octogenarian patients and none of them analyze the impact of functional status on this health outcome. Our objective is to describe the characteristics of patients older than 80 years hospitalized for “coronavirus disease 2019” (COVID-19), to determine the mortality rate and to identify associated factors. Material and methods: Prospective observational study carried out on patients over 80 years admitted for COVID-19 in a Geriatrics Service. Sociodemographic, clinical, functional, mental, analytical, radiological, therapeutic and healthcare variables were collected. The factors associated with in-hospital lethality were analyzed by bivariate analysis. Results: 58 cases with laboratory-confirmed COVID-19 were included, mean age 88,3±5,4 years, 69% women, 65,5% moderate-severe cognitive impairment and previous Barthel index 40,66±36. The main symptoms were fever (60,3%), dyspnea (53,4%) and deterioration of functional condition (50%). The most frequent comorbidities were cardiovascular disease (75,9%), hypertension (HT) (74,1%) and chronic kidney disease (CKD) (50%). A mortality rate of 41,4% was detected and the associated factors were: severe functional dependence (OR=3,8 [1,2-12,2]), moderate-severe cognitive impairment (OR= 4,9 [1-25,4]) and CKD (OR=3,2 [1,1-9,7]). Conclusion: High mortality rates are observed in older patients hospitalized for COVID-19, with a higher risk of dying in those with severe functional dependence or cognitive impairment. These findings reinforce the value of Geriatric Assessment to develop strategies to adapt diagnostic and therapeutic decision-making and to optimize care for elderly patients in the event of a new epidemic outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32736821/ doi: 10.1016/j.regg.2020.07.002 id: cord-287247-vv0zc0gd author: Gutman, Julie R. title: Malaria and Parasitic Neglected Tropical Diseases: Potential Syndemics with COVID-19? date: 2020-06-01 words: 4248.0 sentences: 236.0 pages: flesch: 41.0 cache: ./cache/cord-287247-vv0zc0gd.txt txt: ./txt/cord-287247-vv0zc0gd.txt summary: With many LMICs implementing movement restrictions or ordering their populations to stay at home to limit SARS-CoV-2 transmission, the threat to essential health services is likely to be immediate, causing delays to diagnosis and treatment for other diseases, including malaria and NTDs. During the Ebola epidemic in West Africa, there were substantial reductions in all-cause outpatient visits and patients treated with antimalarial drugs 2 ; modeling the potential for similar disruptions in malaria control due to COVID-19 suggests that there could be up to an estimated 769,000 deaths due to malaria in 2020 (approximately double the number seen in 2018), mostly among children younger than 5 years. 58 Thus, coinfection with parasitic NTDs could result in altered risks and severity of clinical manifestations of SARS-CoV-2 infection, with the potential for decreased development of immunity with increased viral loads. abstract: The COVID-19 pandemic, caused by SARS-CoV-2, have surpassed 5 million cases globally. Current models suggest that low- and middle-income countries (LMICs) will have a similar incidence but substantially lower mortality rate than high-income countries. However, malaria and neglected tropical diseases (NTDs) are prevalent in LMICs, and coinfections are likely. Both malaria and parasitic NTDs can alter immunologic responses to other infectious agents. Malaria can induce a cytokine storm and pro-coagulant state similar to that seen in severe COVID-19. Consequently, coinfections with malaria parasites and SARS-CoV-2 could result in substantially worse outcomes than mono-infections with either pathogen, and could shift the age pattern of severe COVID-19 to younger age-groups. Enhancing surveillance platforms could provide signals that indicate whether malaria, NTDs, and COVID-19 are syndemics (synergistic epidemics). Based on the prevalence of malaria and NTDs in specific localities, efforts to characterize COVID-19 in LMICs could be expanded by adding testing for malaria and NTDs. Such additional testing would allow the determination of the rates of coinfection and comparison of severity of outcomes by infection status, greatly improving the understanding of the epidemiology of COVID-19 in LMICs and potentially helping to mitigate its impact. url: https://doi.org/10.4269/ajtmh.20-0516 doi: 10.4269/ajtmh.20-0516 id: cord-290378-h4cof32m author: Guy, Tiphaine title: High-flow nasal oxygen: a safe, efficient treatment for COVID-19 patients not in an ICU date: 2020-08-28 words: 1389.0 sentences: 77.0 pages: flesch: 54.0 cache: ./cache/cord-290378-h4cof32m.txt txt: ./txt/cord-290378-h4cof32m.txt summary: SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. Patients infected with SARS-CoV-2 can develop severe pneumonia and respiratory failure, which often require treatment in intensive care units (ICU) in Western European countries (2) . This report describes the use of HFNO to manage SARS-CoV-2 infected patients with respiratory failure on the pulmonology ward rather than in an ICU. The theoretical risk of virus aerosolization resulted in early published reports of critically ill SARS-CoV-2-infected patients in China not recommending the use of HFNO or non-invasive ventilation until the patient had been cleared of COVID-19 (4). While these results should be confirmed in larger studies, we believe that our data strongly suggest that SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. abstract: SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. The technique appears to be safe for HCWs and could well liberate critical ICU resources. url: https://www.ncbi.nlm.nih.gov/pubmed/32859678/ doi: 10.1183/13993003.01154-2020 id: cord-279406-wwdqh9qs author: Guzman, Norberto A. title: A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy date: 2020-07-30 words: 17172.0 sentences: 835.0 pages: flesch: 33.0 cache: ./cache/cord-279406-wwdqh9qs.txt txt: ./txt/cord-279406-wwdqh9qs.txt summary: To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses. It would be beneficial to have a sample processing method before separation, to isolate and concentrate the intended viruses or EVs. Immunoaffinity capillary electrophoresis has already been proven to be a useful technology to isolate, separate, and quantify cell-free molecules of biological interest based on the specificity and selectivity not only of antibody reagents, but also of lectin and aptamer reagents, quantifying molecules ranging from microgram/milliliter to femtogram/milliliter [25, 54, 55, 57, 75] . abstract: Biomarker detection for disease diagnosis, prognosis, and therapeutic response is becoming increasingly reliable and accessible. Particularly, the identification of circulating cell-free chemical and biochemical substances, cellular and subcellular entities, and extracellular vesicles has demonstrated promising applications in understanding the physiologic and pathologic conditions of an individual. Traditionally, tissue biopsy has been the gold standard for the diagnosis of many diseases, especially cancer. More recently, liquid biopsy for biomarker detection has emerged as a non-invasive or minimally invasive and less costly method for diagnosis of both cancerous and non-cancerous diseases, while also offering information on the progression or improvement of disease. Unfortunately, the standardization of analytical methods to isolate and quantify circulating cells and extracellular vesicles, as well as their extracted biochemical constituents, is still cumbersome, time-consuming, and expensive. To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. Isolation and concentration of analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. When compared to other existing methods, the process of this affinity capture, enrichment, release, and separation of one or a panel of biomarkers can be carried out on-line with the advantages of being rapid, automated, and cost-effective. Additionally, it has the potential to demonstrate high analytical sensitivity, specificity, and selectivity. As the potential of liquid biopsy grows, so too does the demand for technical advances. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses. url: https://doi.org/10.3390/biomedicines8080255 doi: 10.3390/biomedicines8080255 id: cord-327459-tyhy784d author: Gómez-Rial, J. title: A strategy targeting monocyte-macrophage differentiation to avoid pulmonary complications in SARS-Cov2 infection date: 2020-04-23 words: 785.0 sentences: 51.0 pages: flesch: 35.0 cache: ./cache/cord-327459-tyhy784d.txt txt: ./txt/cord-327459-tyhy784d.txt summary: Gómez-Rial J, MD 1,2 , Martinón-Torres F, MD, Phd, Assoc Prof 1 The immune dysregulation and cytokine storm observed in severe COVID-19 cases has led to the trial of licensed RA drugs such as Chloroquine, IL-1/IL-6 blockers, TNF or Janus kinase inhibitors in COVID-19 patients [1] In addition we propose that blockade of granulocyte macrophage-colony stimulating factor (GM-CSF) may be an effective strategy to prevent pulmonary complications and fatality in SARS-Cov2 infection. and inflammation-related phenotypic changes in peripheral blood monocytes, and correlation with acute respiratory distress syndrome (ARDS) in severe patients [5] Furthermore, single-cell RNA sequencing of lung bronchoalveolar immune cells infection [6] If these findings are confirmed, they would indicate that in SARS-Cov2, similarly to SARS-Cov1, acute lethal disease is produced by delayed and dysregulated type I interferon response and pulmonary accumulation of inflammatory monocytemacrophages, which are mainly responsible for immunopathology [6, 7] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32335290/ doi: 10.1016/j.clim.2020.108442 id: cord-298505-r7ihqb96 author: Górski, Andrzej title: Sepsis, Phages, and COVID-19 date: 2020-10-15 words: 3735.0 sentences: 226.0 pages: flesch: 47.0 cache: ./cache/cord-298505-r7ihqb96.txt txt: ./txt/cord-298505-r7ihqb96.txt summary: In fact, in addition to data obtained in experimental animals, there are already reports of successful phage therapy in patients with sepsis [2] . Phage therapy efficacy has also been studied in a mouse model of neonatal sepsis caused by Escherichia coli, Klebsiella pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Citrobacter freundii and Moraxella catarrhalis. High effectiveness of phage therapy in the treatment of experimental sepsis induced by multidrug resistant P. Further progress in phage therapy of sepsis has recently been achieved by introducing engineered phages used to treat a patient with a disseminated drug resistant mycobacterial infection. In recent years, a number of reports derived from experimental studies in animals and human clinics have suggested the potential value of phage therapy in the treatment of sepsis. The anti-inflammatory and the immunomodulating properties of phages could also be useful in the treatment of severe COVID-19 syndrome including viral sepsis (Table 2) . abstract: Phage therapy has emerged as a potential novel treatment of sepsis for which no decisive progress has been achieved thus far. Obviously, phages can help eradicate local bacterial infection and bacteremia that may occur in a syndrome. For example, phages may be helpful in correcting excessive inflammatory responses and aberrant immunity that occur in sepsis. Data from animal studies strongly suggest that phages may indeed be an efficient means of therapy for experimentally induced sepsis. In recent years, a number of reports have appeared describing the successful treatment of patients with sepsis. Moreover, novel data on the anti-viral potential of phages may be interpreted as suggesting that phages could be used as an adjunct therapy in severe COVID-19. Thus, clinical trials assessing the value of phage therapy in sepsis, including viral sepsis, are urgently needed. url: https://www.ncbi.nlm.nih.gov/pubmed/33076482/ doi: 10.3390/pathogens9100844 id: cord-326532-2ehuuvnx author: Götzinger, Florian title: COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study date: 2020-06-25 words: 5321.0 sentences: 282.0 pages: flesch: 46.0 cache: ./cache/cord-326532-2ehuuvnx.txt txt: ./txt/cord-326532-2ehuuvnx.txt summary: This study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across Europe to inform physicians and health-care service planning during the ongoing pandemic. Significant risk factors for requiring ICU admission in multivariable analyses were being younger than 1 month (odds ratio 5·06, 95% CI 1·72–14·87; p=0·0035), male sex (2·12, 1·06–4·21; p=0·033), pre-existing medical conditions (3·27, 1·67–6·42; p=0·0015), and presence of lower respiratory tract infection signs or symptoms at presentation (10·46, 5·16–21·23; p<0·0001). For this cohort study, European members of the Paediatric Tuberculosis Network European Trials Group (ptbnet)-which currently includes 304 clinicians and researchers, most of whom are based at tertiary or quaternary paediatric infectious diseases or paediatric pulmonology units, across 128 paediatric health-care institutions in 31 European countries [15] [16] [17] [18] [19] [20] -were invited to contribute cases of confirmed SARS-CoV-2 infection that had been managed at or managed remotely by their health-care institution (including individuals admitted to other hospitals or identified during community screening) before or during the study period. abstract: BACKGROUND: To date, few data on paediatric COVID-19 have been published, and most reports originate from China. This study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across Europe to inform physicians and health-care service planning during the ongoing pandemic. METHODS: This multicentre cohort study involved 82 participating health-care institutions across 25 European countries, using a well established research network—the Paediatric Tuberculosis Network European Trials Group (ptbnet)—that mainly comprises paediatric infectious diseases specialists and paediatric pulmonologists. We included all individuals aged 18 years or younger with confirmed SARS-CoV-2 infection, detected at any anatomical site by RT-PCR, between April 1 and April 24, 2020, during the initial peak of the European COVID-19 pandemic. We explored factors associated with need for intensive care unit (ICU) admission and initiation of drug treatment for COVID-19 using univariable analysis, and applied multivariable logistic regression with backwards stepwise analysis to further explore those factors significantly associated with ICU admission. FINDINGS: 582 individuals with PCR-confirmed SARS-CoV-2 infection were included, with a median age of 5·0 years (IQR 0·5–12·0) and a sex ratio of 1·15 males per female. 145 (25%) had pre-existing medical conditions. 363 (62%) individuals were admitted to hospital. 48 (8%) individuals required ICU admission, 25 (4%) mechanical ventilation (median duration 7 days, IQR 2–11, range 1–34), 19 (3%) inotropic support, and one (<1%) extracorporeal membrane oxygenation. Significant risk factors for requiring ICU admission in multivariable analyses were being younger than 1 month (odds ratio 5·06, 95% CI 1·72–14·87; p=0·0035), male sex (2·12, 1·06–4·21; p=0·033), pre-existing medical conditions (3·27, 1·67–6·42; p=0·0015), and presence of lower respiratory tract infection signs or symptoms at presentation (10·46, 5·16–21·23; p<0·0001). The most frequently used drug with antiviral activity was hydroxychloroquine (40 [7%] patients), followed by remdesivir (17 [3%] patients), lopinavir–ritonavir (six [1%] patients), and oseltamivir (three [1%] patients). Immunomodulatory medication used included corticosteroids (22 [4%] patients), intravenous immunoglobulin (seven [1%] patients), tocilizumab (four [1%] patients), anakinra (three [1%] patients), and siltuximab (one [<1%] patient). Four children died (case-fatality rate 0·69%, 95% CI 0·20–1·82); at study end, the remaining 578 were alive and only 25 (4%) were still symptomatic or requiring respiratory support. INTERPRETATION: COVID-19 is generally a mild disease in children, including infants. However, a small proportion develop severe disease requiring ICU admission and prolonged ventilation, although fatal outcome is overall rare. The data also reflect the current uncertainties regarding specific treatment options, highlighting that additional data on antiviral and immunomodulatory drugs are urgently needed. FUNDING: ptbnet is supported by Deutsche Gesellschaft für Internationale Zusammenarbeit. url: https://www.sciencedirect.com/science/article/pii/S2352464220301772 doi: 10.1016/s2352-4642(20)30177-2 id: cord-348696-86nbwon2 author: Güemes-Villahoz, Noemi title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review date: 2020-08-18 words: 4199.0 sentences: 216.0 pages: flesch: 43.0 cache: ./cache/cord-348696-86nbwon2.txt txt: ./txt/cord-348696-86nbwon2.txt summary: title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review A multicenter study which documented potential risk factors for SARS-CoV-2 transmission in patients requiring intubation [7] reported that unprotected eye contact with secretions from infected patients was the most predictive variable for transmission to healthcare workers. A recent study evaluated the ocular tropism of SARS-CoV-2 in patients with confirmed COVID-19. Of the 56 subjects investigated there was only one patient who gave a history of prior pterygium surgery, with conjunctivitis and a positive PCR result from the conjunctival swab highlighting the importance of an intact ocular surface in resisting virus invasion [25] . Despite ocular complications not being a common clinically detectable manifestation of SARS-CoV-2 infection, recent evidence suggests that ocular exposure may represent a major transmission route for the virus. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection SARS-CoV-2 RNA detection in tears and conjunctival secretions of COVID-19 patients with conjunctivitis abstract: SARS-CoV-2 is a highly transmissible virus that spreads mainly via person-to-person contact through respiratory droplets, or through contact with contaminated objects or surfaces from an infected person. At present we are passing through a phase of slow and painful understanding of the origin, epidemiological profile, clinical spectrum, and risk profile of the virus. To the best of our knowledge there is only limited and contradictory evidence concerning SARS-CoV-2 transmission through other routes. Importantly, the eye may constitute not only a potential site of virus replication but also an alternative transmission route of the virus from the ocular surface to the respiratory and gastrointestinal tract. It is therefore imperative to gain a better insight into the potential ophthalmological transmission route of the virus and establish directions on best practice and future models of care for ophthalmological patients. This review article critically evaluates available evidence on the ophthalmological mode of viral transmission and the value of earlier identification of the virus on the eye. More evidence is urgently needed to better evaluate the need for protective measures and reliable ocular diagnostic tests to diminish further pandemic spread. url: https://doi.org/10.1007/s12325-020-01442-7 doi: 10.1007/s12325-020-01442-7 id: cord-354134-gb2pf5kb author: Güemes-Villahoz, Noemi title: Conjunctivitis in COVID-19 patients: frequency and clinical presentation date: 2020-08-29 words: 3461.0 sentences: 170.0 pages: flesch: 41.0 cache: ./cache/cord-354134-gb2pf5kb.txt txt: ./txt/cord-354134-gb2pf5kb.txt summary: Given the current situation of the SARS-CoV-2 pandemic, describing the clinical characteristics of conjunctivitis associated with the novel coronavirus has relevant implications in the future identification of suspected COVID-19 patients and the differential diagnosis from other forms viral conjunctivitis. A study analyzing a sample of 1099 patients hospitalized for COVID-19 disease in China found a prevalence of conjunctivitis symptoms of only 0.8% and other small series have reported a prevalence around 3% [4, 6, 7] . Despite our study showed no difference in the clinical presentation of conjunctivitis in male and female, we found that conjunctivitis was more frequent in males with moderate COVID-19 and women with mild disease. A better understanding of the ocular manifestations of the virus will assist in early identification of SARS-CoV-2infected cases, prioritizing diagnostic testing in patients with clinical findings compatible with conjunctivitis associated with COVID-19. abstract: PURPOSE: The purpose of this study was to evaluate the frequency and clinical presentation of conjunctivitis in hospitalized patients with COVID-19. METHODS: A cross-sectional study was conducted at the Hospital Clinico San Carlos of Madrid, Spain. A total of 301 subjects from the COVID admission unit with laboratory-confirmed SARS-CoV-2 infection were included. The presence and clinical characteristics of conjunctivitis were evaluated. Laboratory, radiological, and clinical results in patients with and without conjunctivitis stratified by sex were analyzed. RESULTS: Of the 301 subjects included, 180 patients (59.8%) were male and the median age was 72 years (IQ 59–82). Overall, 35 patients (11.6%) were diagnosed with acute conjunctivitis. We found no relationship between the COVID-19 severity score and the presence of conjunctivitis (P = 0.17). However, conjunctivitis was more frequent in males with moderate clinical severity and in women classified as clinically mild. The natural history of the disease seems to be a rapid self-limited conjunctivitis that improves without treatment and does not affect visual acuity nor associate short-term complications. CONCLUSIONS: Approximately, 1 out of 10 hospitalized non-critical COVID-19 patients presents conjunctivitis during the disease. Compared with other viral conjunctivitis, we found distinctive clinical findings that could guide defining and differentiating conjunctivitis in COVID-19 patients. TRIAL REGISTRATION NUMBER: 20/336_E_COVID [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32860573/ doi: 10.1007/s00417-020-04916-0 id: cord-314926-4bltio08 author: Ha, Le Dang title: Lack of SARS Transmission among Public Hospital Workers, Vietnam date: 2004-02-17 words: 2096.0 sentences: 99.0 pages: flesch: 48.0 cache: ./cache/cord-314926-4bltio08.txt txt: ./txt/cord-314926-4bltio08.txt summary: The severe acute respiratory syndrome (SARS) outbreak in Vietnam was amplified by nosocomial spread within hospital A, but no transmission was reported in hospital B, the second of two designated SARS hospitals. Our study documents lack of SARS-associated coronavirus transmission to hospital B workers, despite variable infection control measures and the use of personal protective equipment. In conclusion, we found no evidence of SARS-CoV transmission among hospital B workers, despite contact with laboratory-confirmed SARS case-patients and variable infection control practices and use of personal protective equipment. This finding may be explained by differences in infection control practices, use of personal protective equipment (including masks for patients as well as healthcare workers), nursing style, environmental features, and clinical factors such as severity of illness and the absence of a highly infectious SARS-CoV spreader. abstract: The severe acute respiratory syndrome (SARS) outbreak in Vietnam was amplified by nosocomial spread within hospital A, but no transmission was reported in hospital B, the second of two designated SARS hospitals. Our study documents lack of SARS-associated coronavirus transmission to hospital B workers, despite variable infection control measures and the use of personal protective equipment. url: https://www.ncbi.nlm.nih.gov/pubmed/15030695/ doi: 10.3201/eid1002.030707 id: cord-288231-vg8bwed9 author: Haagmans, Bart L. title: The Application of Genomics to Emerging Zoonotic Viral Diseases date: 2009-10-26 words: 3406.0 sentences: 146.0 pages: flesch: 35.0 cache: ./cache/cord-288231-vg8bwed9.txt txt: ./txt/cord-288231-vg8bwed9.txt summary: Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. abstract: Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/19855817/ doi: 10.1371/journal.ppat.1000557 id: cord-351649-87g7g5au author: Haagmans, Bart L. title: SARS date: 2009-01-30 words: 6736.0 sentences: 298.0 pages: flesch: 40.0 cache: ./cache/cord-351649-87g7g5au.txt txt: ./txt/cord-351649-87g7g5au.txt summary: Because the disease in macaques caused by SARS-CoV infection was pathologically similar to that seen in human patients with SARS, and since the virus should induce highly cross-reactive neutralizing antibodies to protect against newly emerging viruses related to SARS-CoV and protect both the gastrointestinal and respiratory tract in the absence of significant side effects. African green monkeys immunized via the respiratory tract with two doses of a recombinant Newcastle disease virus encoding the S protein developed a relatively high titer of SARS-CoV neutralizing antibodies and upon challenge demonstrated a 1000-fold zoonotic coronaviruses. Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies abstract: Abstract Five years after the first severe acute respiratory syndrome (SARS) outbreak, several candidate SARS-coronavirus (CoV) vaccines are at various stages of preclinical and clinical development. Based on the observation that SARSCoV infection is efficiently controlled upon passive transfer of antibodies directed against the spike (S) protein of SARS-CoV, vaccines containing the S protein have been formulated. Animals immunized with inactivated whole virus vaccines or live-recombinant vaccines expressing the SARS-CoV S protein (e.g., using rabies virus, vesicular stomatitis virus, bovine parainfluenza virus type 3, adenovirus, or attenuated vaccinia virus MVA as a vector), as well as mice immunized with DNA vaccines expressing the S protein gene all developed neutralizing antibodies to SARS-CoV and were protected against SARS-CoV challenge. Although much effort has been focused on developing a SARS vaccine, the commercial viability of such a vaccine for SARS-CoV will ultimately depend on whether the virus re-emerges in the near future. This vaccine should induce highly cross-reactive neutralizing antibodies to protect against newly emerging viruses related to SARS-CoV and protect both the gastrointestinal and respiratory tract in the absence of significant side effects. Given the fact that in the previous outbreak mainly the elderly succumbed to the infection, special attention should be given to vaccines that are able to efficiently protect aged individuals. url: https://api.elsevier.com/content/article/pii/B9780123694089000366 doi: 10.1016/b978-0-12-369408-9.00036-6 id: cord-260191-0u0pu0br author: Haas, W. title: „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date: 2004-05-29 words: 2431.0 sentences: 335.0 pages: flesch: 51.0 cache: ./cache/cord-260191-0u0pu0br.txt txt: ./txt/cord-260191-0u0pu0br.txt summary: Abstract Some emerging infectious diseases have recently become endemic in Germany.Others remain confined to specific regions in the world.Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms.Several of these emerging infections will be explained.HIV is an example for an imported pathogen which has become endemic in Germany.SARS and avian influenza are zoonoses with the potential to spread from person to person.Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain.Outbreaks of dengue fever in endemic areas are reflected in increased infec-gehäuften Erkrankungen bei Rückkehrern wieder.West-Nil-Virus-Erkrankungen kommen derzeit nur als importierte Erkrankungen in Deutschland vor.Wichtig ist,diese Erkrankungen frühzeitig in die differenzialdiagnostischen Überlegungen des Klinikers einzubeziehen,um die erforderlichen Maßnahmen zur Diagnostik,Therapie und zum Infektionsschutz rechtzeitig einleiten zu können.Dies erfordert ein gutes Zusammenspiel mit dem Labor und dem öffentlichen Gesundheitsdienst. abstract: Some emerging infectious diseases have recently become endemic in Germany. Others remain confined to specific regions in the world. Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms. Several of these emerging infections will be explained. HIV is an example for an imported pathogen which has become endemic in Germany. SARS and avian influenza are zoonoses with the potential to spread from person to person. Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain. Outbreaks of dengue fever in endemic areas are reflected in increased infections in travelers returning from these areas. Currently, West-Nile-virus infections are only imported into Germany. The timely implementation of diagnostic, therapeutic and infection control measures requires physicians to include these diseases in their differential diagnosis. To achieve this goal, good cooperation between physicians, laboratories and the public health service is essential. url: https://www.ncbi.nlm.nih.gov/pubmed/15107983/ doi: 10.1007/s00108-004-1199-2 id: cord-291747-3du4jluy author: Habashy, Noha H. title: The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking date: 2020-11-11 words: 1341.0 sentences: 91.0 pages: flesch: 57.0 cache: ./cache/cord-291747-3du4jluy.txt txt: ./txt/cord-291747-3du4jluy.txt summary: title: The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking We evaluated the predicted anti-SARS-CoV-2 effect of major royal jelly protein (MRJP)2 and MRJP2 isoform X1, which recently showed high efficacy against other enveloped RNA-viruses (HCV and HIV). Since the end of 2019 to the present, severe acute respiratory syndrome 47 coronavirus 2 (SARS-CoV-2) has caused widespread infection and is considered 48 a threat to public health security. SARS-CoV-2, severe 865 acute respiratory syndrome-related coronavirus; nsps, non-structural proteins. Structural and 661 molecular modelling studies reveal a new mechanism of action of 662 chloroquine and hydroxychloroquine against SARS-CoV-2 infection The potential antiviral effect of major royal jelly protein2 and its 835 isoform X1 against severe acute respiratory syndrome coronavirus 2 836 (SARS-CoV-2): Insight on their sialidase activity and molecular 837 docking abstract: Severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 is a newly emerging type of CoV. We evaluated the predicted anti-SARS-CoV-2 effect of major royal jelly protein (MRJP)2 and MRJP2 isoform X1, which recently showed high efficacy against other enveloped RNA-viruses (HCV and HIV). Some in-silico analyses have been performed to predict the impact of these proteins on viral entry, replication, and complications. These proteins have shown a high potency in sialic acid hydrolysis from the lung cells (WI-38) surface. Docking analysis showed that these proteins have a high binding affinity to viral receptor-binding sites in the receptor-binding domain, causing attachment prevention. Moreover, MRJPs can exert an inhibitory influence, via different mechanisms, for SARS-CoV-2 non-structural proteins (main and papain proteases, RNA replicase, RNA-dependent RNA polymerase, and methyltransferase). Also, they can bind to hemoglobin-binding sites on viral-nsps and prevent their hemoglobin attack. Thus, MRJP2 and MRJP2 X1 can be a promising therapy for SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S1756464620305065 doi: 10.1016/j.jff.2020.104282 id: cord-262250-o7qhncic author: Habel, J. R. title: Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype date: 2020-08-19 words: 6206.0 sentences: 308.0 pages: flesch: 57.0 cache: ./cache/cord-262250-o7qhncic.txt txt: ./txt/cord-262250-o7qhncic.txt summary: Using peptide-HLA-I tetramers, we performed direct ex vivo tetramer enrichment to define the frequency and activation profiles of the responding SARS-CoV2-specific CD8 + T-cells in acute and convalescent COVID-19 patients and in prepandemic PBMCs, tonsil and lung tissues from uninfected donors. 17.20176370 doi: medRxiv preprint To further probe the the responsiveness of A2/SARS-CoV-2 CD8 + T-cells from uninfected versus convalescent COVID-19 donors, PBMCs or tonsil cells were stimulated with the S 269 and Orf1ab 3183 peptides and cultured in vitro for 10 days. Our findings show that, while ''early memory'' CD8 + T-cells can be detected in convalescent HLA-A*02:01 COVID-19 patients at frequencies ∼5-fold higher than those from pre-pandemic samples, the SARS-CoV-2-specific response was ∼10-fold lower than that found regularly for CD8 + T-cells directed at IAV or EBV epitopes. Even so, it is the case that SARS-CoV-2-specific CD8 + T-cells were found in all COVID-19 acute and convalescent donors, and in stored pre-pandemic PBMC and tonsil samples (but not lung tissues) from HLA-A*02:01 children, mature adults and the elderly. abstract: An improved understanding of human T-cell-mediated immunity in COVID-19 is important if we are to optimize therapeutic and vaccine strategies. Experience with influenza shows that infection primes CD8+ T-cell memory to shared peptides presented by common HLA types like HLA-A2. Following re-infection, cross-reactive CD8+ T-cells enhance recovery and diminish clinical severity. Stimulating peripheral blood mononuclear cells from COVID-19 convalescent patients with overlapping peptides from SARS-CoV-2 Spike, Nucleocapsid and Membrane proteins led to the clonal expansion of SARS-CoV-2-specific CD8+ and CD4+ T-cells in vitro, with CD4+ sets being typically robust. For CD8+ T-cells taken directly ex vivo, we identified two HLA-A*02:01-restricted SARS-CoV-2 epitopes, A2/S269-277 and A2/Orf1ab3183-3191. Using peptide-HLA tetramer enrichment, direct ex vivo assessment of the A2/S269+CD8+ and A2/Orf1ab3183+CD8+ populations indicated that the more prominent A2/S269+CD8+ set was detected at comparable frequency (1.3x10-5) in acute and convalescent HLA-A*02:01+ patients. But, while the numbers were higher than those found in uninfected HLA-A*02:01+ donors (2.5x10-6), they were low when compared with frequencies for influenza-specific (A2/M158) and EBV-specific (A2/BMLF1280) (1.38x10-4) populations. Phenotypic analysis ex vivo of A2/S269+CD8+ T-cells from COVID-19 convalescents showed that A2/S269+CD8+ T-cells were predominantly negative for the CD38, HLA-DR, PD-1 and CD71 activation markers, although the majority of total CD8+ T-cells were granzyme and/or perforin-positive. Furthermore, the bias towards naive, stem cell memory and central memory A2/S269+CD8+ T-cells rather than effector memory populations suggests that SARS-CoV2 infection may be compromising CD8+ T-cell activation. Priming with an appropriate vaccine may thus have great value for optimizing protective CD8+ T-cell immunity in COVID-19. url: https://doi.org/10.1101/2020.08.17.20176370 doi: 10.1101/2020.08.17.20176370 id: cord-349923-cja8i0hw author: Habibzadeh, Parham title: The Novel Coronavirus: A Bird''s Eye View date: 2020-02-05 words: 2444.0 sentences: 143.0 pages: flesch: 50.0 cache: ./cache/cord-349923-cja8i0hw.txt txt: ./txt/cord-349923-cja8i0hw.txt summary: C oronaviruses typically result in respiratory and enteric infections affecting both animals and humans, and were considered relatively benign to humans before the severe acute respiratory syndrome (SARS-CoV) outbreak in 2002 and 2003 in China. [1] [2] [3] [4] A decade later, Middle East respiratory syndrome coronavirus (MERS-CoV), another pathogenic coronavirus with a clinical picture reminiscent of SARS, was isolated in patients presenting with pneumonia in the Middle Eastern countries. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. abstract: The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. With a death toll exceeding that of the SARS-CoV outbreak back in 2002 and 2003 in China, 2019-nCoV has led to a public health emergency of international concern, putting all health organizations on high alert. Herein, we present on an overview of the currently available information on the pathogenesis, epidemiology, clinical presentation, diagnosis, and treatment of this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32020915/ doi: 10.15171/ijoem.2020.1921 id: cord-280924-g6062fwk author: Hachim, Mahmood Yaseen title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date: 2020-06-10 words: 2851.0 sentences: 147.0 pages: flesch: 42.0 cache: ./cache/cord-280924-g6062fwk.txt txt: ./txt/cord-280924-g6062fwk.txt summary: title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. To effectively address the ongoing COVID-19 pandemic, there is a recognized need for a framework for rapid identification of novel targets for diagnostic and therapeutic interventions as well as determine clinically approved drugs with high potential for repurposed use against SARS-CoV-2. In this study, we have applied this approach, and our findings have identified IFITM3 as an early upregulated gene and indicate that valproic acid enhances IFITM3 mRNA expression and antiviral action. Our toxicogenomic analysis showed that valproic acid increased the mRNA expression of IFITM3, supporting a new report that the SARS-CoV-2-human protein-protein interaction map showed that valproic acid might be a potential repurposing drug for COVID-19 (34) . abstract: Current guidelines for COVID-19 management recommend the utilization of various repurposed drugs. Despite ongoing research toward the development of a vaccine against SARS-CoV-2, such a vaccine will not be available in time to contribute to the containment of the ongoing pandemic. Therefore, there is an urgent need to develop a framework for the rapid identification of novel targets for diagnostic and therapeutic interventions. We analyzed publicly available transcriptomic datasets of SARS-CoV infected humans and mammals to identify consistent differentially expressed genes then validated in SARS-CoV-2 infected epithelial cells transcriptomic datasets. Comprehensive toxicogenomic analysis of the identified genes to identify possible interactions with clinically proven drugs was carried out. We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. These findings indicate that analysis of publicly available transcriptomic and toxicogenomic data represents a rapid approach for the identification of novel targets and molecules that can modify the action of such targets during the early phases of emerging infections like COVID-19. url: https://doi.org/10.3389/fimmu.2020.01372 doi: 10.3389/fimmu.2020.01372 id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 words: 3698.0 sentences: 205.0 pages: flesch: 44.0 cache: ./cache/cord-310920-itqwhi6a.txt txt: ./txt/cord-310920-itqwhi6a.txt summary: Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. abstract: RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets. url: https://api.elsevier.com/content/article/pii/S1046202320301249 doi: 10.1016/j.ymeth.2020.06.013 id: cord-353475-dtn7h1gj author: Haddad, Hazem title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 words: 1462.0 sentences: 103.0 pages: flesch: 64.0 cache: ./cache/cord-353475-dtn7h1gj.txt txt: ./txt/cord-353475-dtn7h1gj.txt summary: In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. To understand the early steps of COVID-19 infection, we predicted miRNAs sequences targeting the submitted 29903bp of viral ss-RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 complete genomic RNA sequence) from the isolate of Wuhan-Hu-J o u r n a l P r e -p r o o f 1. abstract: MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5′ to 3′ that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. url: https://www.ncbi.nlm.nih.gov/pubmed/32839745/ doi: 10.1016/j.ncrna.2020.08.002 id: cord-340008-2efzyki4 author: Haddadi, Kaveh title: Coronavirus Disease 2019: Latest Data on Neuroinvasive Potential date: 2020-09-17 words: 3581.0 sentences: 209.0 pages: flesch: 42.0 cache: ./cache/cord-340008-2efzyki4.txt txt: ./txt/cord-340008-2efzyki4.txt summary: Similar to other respiratory viruses, severe acute respiratory syndrome coronavirus (SARS-COV-2) may enter the brain via the hematogenous or neuronal route; however, only a few reports are available on the neurological complications of COVID-19. Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel coronavirus, originated in China in December 2019 and rapidly progressed into an epidemic infection, such that the World Health Organization (WHO) termed this calamitous virus "coronavirus disease 2019 (COVID-19)". Indeed, while the bulk of research conducted and published thus far has focused on the mechanisms whereby SARS-CoV-2 targets the respiratory system, more recent investigations have reported disconcerting evidence of the entrance of this new coronavirus into the CNS via different ways, resulting in significant damage to this system or even death due to its infection. Some investigators in China reported that more than 30% of their 214 patients with COVID-19 presented with neurological signs and symptoms; they, therefore, concluded that SARS-CoV-2 might attack the CNS through blood or retrograde neuronal routes, causing the destruction of the CNS. abstract: Coronavirus disease 2019 (COVID-19) is a pandemic infection. Similar to other respiratory viruses, severe acute respiratory syndrome coronavirus (SARS-COV-2) may enter the brain via the hematogenous or neuronal route; however, only a few reports are available on the neurological complications of COVID-19. Encephalopathy is a significant neurological complication of COVID-19. We herein present an update on the virology, neurological pathogenesis, and neuroinvasive potential of coronaviruses and briefly discuss the latest findings on SARS-CoV-2 neuroinfection. The reports thus far indicate that the access of SARS-CoV into host cells is bolstered chiefly by a cellular receptor, angiotensin-converting enzyme 2, and that SARS-CoV-2 may induce some neurological manifestations via direct or indirect mechanisms. Further research is required to shed sufficient light on the impact on the central nervous system and altered mental status in patients with COVID-19. Indeed, a better understanding of the pathways of SARS-CoV-2 neuroinvasion would further clarify the neurological pathogenesis and manifestations of coronaviruses and enhance the management and treatment of this group of patients. In the current epidemic era of COVID-19, health care staff should strongly become aware of SARS-CoV-2 infection as an essential diagnosis to get away misdiagnosis and prevention of transmission. url: https://doi.org/10.30476/ijms.2020.85980.1561 doi: 10.30476/ijms.2020.85980.1561 id: cord-328246-boxsf2sz author: Hadi-Alijanvand, Hamid title: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes date: 2020-07-27 words: 10124.0 sentences: 563.0 pages: flesch: 55.0 cache: ./cache/cord-328246-boxsf2sz.txt txt: ./txt/cord-328246-boxsf2sz.txt summary: 48 In the current study, the input structures for PISA to predict the dissociation free energy of the complex are FoldX-generated mutant 3D structures of ACE2 in association with the RBD of the S1 protein. Free energy of ACE2 binding to RBD of SARS-CoV-2 spike protein 1 is also estimated in the current work by using MM-GBSA approach for mutations in ACE2 that are reported for Iranian ethnic groups by NAMD 2.13. In the current study, we predict the effect of 240 widespread missense mutations in the ACE2 gene reported for different human populations and especially eight ones specific for Iranian ethnic populations on the binding affinity between ACE2 and S1 RBD of SARS-CoV-2 with different computational approaches from bioinformatic methods to a thermodynamic integration procedure. We report the predicted affinities of 240 mutated versions of ACE2 to S1 of SARS-CoV-2 using the mentioned fast structure-based computational methods in Figure 1 . abstract: [Image: see text] A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for the ACE2 gene. In the current study, we predict the affinity of many ACE2 variants for binding to S1 protein using different computational approaches. The dissociation process of S1 from some variants of ACE2 is studied in the current work by molecular dynamics approaches. We study the relation between structural dynamics of ACE2 in closed and open states and its affinity for S1 protein of SARS-CoV-2. url: https://doi.org/10.1021/acs.jproteome.0c00348 doi: 10.1021/acs.jproteome.0c00348 id: cord-321580-3ru92tra author: Hadler, James L title: Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? date: 2020-09-07 words: 1134.0 sentences: 71.0 pages: flesch: 51.0 cache: ./cache/cord-321580-3ru92tra.txt txt: ./txt/cord-321580-3ru92tra.txt summary: The initial country-level responses to SARS-CoV-2 have provided substantial evidence of their collective impact on the COVID-19 pandemic and, incidentally, on seasonal influenza epidemics. As a country, it has perhaps the largest influenza sentinel surveillance system in the world, including active testing for influenza, and it was the first country to implement highly successful NPIs against SARS-CoV-2, giving it the best opportunity to see a possible change in influenza before the expected seasonal decline. To know what might happen with influenza this coming fall and winter, we need to know what has happened prospectively in southern hemisphere countries, especially those that like the US have used fewer NPI''s and used them with less rigor and, correspondingly, been less successful in controlling SARS-CoV-2 transmission. Nonpharmaceutical interventions used to control COVID-19 reduced seasonal influenza transmission in China abstract: nan url: https://doi.org/10.1093/infdis/jiaa571 doi: 10.1093/infdis/jiaa571 id: cord-356030-bbj4r81i author: Haehner, Antje title: Predictive Value of Sudden Olfactory Loss in the Diagnosis of COVID-19 date: 2020-06-11 words: 2041.0 sentences: 105.0 pages: flesch: 53.0 cache: ./cache/cord-356030-bbj4r81i.txt txt: ./txt/cord-356030-bbj4r81i.txt summary: The aim of this study was to investigate the frequency of olfactory loss in an outpatient population who presented to a coronavirus testing center during a 2-week period and to evaluate the diagnostic value of the symptom "sudden smell loss" for screening procedures. METHODS: In this cross-sectional controlled cohort study, 500 patients who presented with symptoms of a common cold to a corona testing center and fulfilled corona testing criteria completed a standardized diagnostic questionnaire which included the patients'' main symptoms, time course, and an additional self-assessment of the patients'' current smell, taste function, and nasal breathing compared to the level before the onset of symptoms. CONCLUSION: Considering the high frequency of smell loss in non-hospitalized COVID-19 patients, acute olfactory impairment should be recognized as an early symptom of the disease and should be tested for on a regular basis. abstract: INTRODUCTION: Recent reports suggest that sudden smell loss might be a symptom of SARS-CoV-2 infection. The aim of this study was to investigate the frequency of olfactory loss in an outpatient population who presented to a coronavirus testing center during a 2-week period and to evaluate the diagnostic value of the symptom “sudden smell loss” for screening procedures. METHODS: In this cross-sectional controlled cohort study, 500 patients who presented with symptoms of a common cold to a corona testing center and fulfilled corona testing criteria completed a standardized diagnostic questionnaire which included the patients' main symptoms, time course, and an additional self-assessment of the patients' current smell, taste function, and nasal breathing compared to the level before the onset of symptoms. RESULTS: Out of the 500 patients, 69 presented with olfactory loss. Twenty-two of them subsequently tested positive for SARS-CoV-2. Only 12 out of the patients without olfactory loss tested positive, resulting in a frequency of 64.7% for the symptom “sudden smell loss” in COVID-19 patients. Compared to COVID-19 patients without smell loss, they were significantly younger and less severely affected. Changes in nasal airflow were significantly more pronounced in SARS-CoV-2 negative patients with olfactory complaints compared to the patients with smell loss who tested positive for SARS-CoV-2. By excluding patients with a blocked nose, the symptom “sudden smell loss” can be attested a high specificity (97%) and a sensitivity of 65% with a positive predictive value of 63% and negative predictive value of 97% for COVID-19. CONCLUSION: Considering the high frequency of smell loss in non-hospitalized COVID-19 patients, acute olfactory impairment should be recognized as an early symptom of the disease and should be tested for on a regular basis. In contrast to other acute viral smell impairment, COVID-19-associated smell loss seems to be only rarely accompanied by a severely blocked nose. url: https://www.ncbi.nlm.nih.gov/pubmed/32526759/ doi: 10.1159/000509143 id: cord-258708-da6x5rxa author: Hafiane, Anouar title: SARS-CoV-2 and the cardiovascular system date: 2020-07-16 words: 4033.0 sentences: 253.0 pages: flesch: 43.0 cache: ./cache/cord-258708-da6x5rxa.txt txt: ./txt/cord-258708-da6x5rxa.txt summary: The coronavirus disease COVID-19 is a public health emergency caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In COVID-19, particular attention has been given to the role of angiotensin-(Ang) converting enzyme 2 (ACE2), and the binding site for SARS-CoV-2 cellular entry (3). One of the clinical features of patients infected with SARS-CoV-2 included abnormal features such as acute cardiac injury (12%) (22) . Significance of the SARS-CoV-2 infection in the CV system is reflected through incidences of acute myocardial injury, arrhythmias, ACS, sepsis, septic shock, viral myocarditis, and heart failure. Coronavirus Disease 2019 (COVID-19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin-Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection 19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin‐Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection abstract: The coronavirus disease COVID-19 is a public health emergency caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 infection uses the angiotensin-converting enzyme 2 (ACE2) receptor, and typically spreads through the respiratory tract. Invading viruses can elicit an exaggerated host immune response, frequently leading to a cytokine storm that may be fueling some COVID-19 death. This response contributes to multi-organ dysfunction. Accumulating data points to an increased cardiovascular disease morbidity, and mortality in COVID-19 patients. This brief review explores potential available evidence regarding the association between COVID-19, and cardiovascular complications. url: https://api.elsevier.com/content/article/pii/S0009898120303430 doi: 10.1016/j.cca.2020.07.019 id: cord-272211-nkv6irr7 author: Hagan, Liesl M. title: Mass Testing for SARS-CoV-2 in 16 Prisons and Jails — Six Jurisdictions, United States, April–May 2020 date: 2020-08-21 words: 3012.0 sentences: 143.0 pages: flesch: 41.0 cache: ./cache/cord-272211-nkv6irr7.txt txt: ./txt/cord-272211-nkv6irr7.txt summary: To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. In May 2020, CDC requested data from 15 jurisdictions (the Federal Bureau of Prisons [BOP], 10 state prison systems, and four city or county jails), describing SARS-CoV-2 mass testing events † and cases identified before mass testing. High SARS-CoV-2 prevalence detected during mass testing events in a convenience sample of correctional and detention facilities suggests that symptom-based testing underestimates the number of COVID-19 cases in these settings. abstract: Preventing coronavirus disease 2019 (COVID-19) in correctional and detention facilities* can be challenging because of population-dense housing, varied access to hygiene facilities and supplies, and limited space for isolation and quarantine (1). Incarcerated and detained populations have a high prevalence of chronic diseases, increasing their risk for severe COVID-19-associated illness and making early detection critical (2,3). Correctional and detention facilities are not closed systems; SARS-CoV-2, the virus that causes COVID-19, can be transmitted to and from the surrounding community through staff member and visitor movements as well as entry, transfer, and release of incarcerated and detained persons (1). To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. Six jurisdictions reported SARS-CoV-2 prevalence of 0%-86.8% (median = 29.3%) from mass testing events in 16 adult facilities. Before mass testing, 15 of the 16 facilities had identified at least one COVID-19 case among incarcerated or detained persons using symptom-based testing, and mass testing increased the total number of known cases from 642 to 8,239. Case surveillance from symptom-based testing has likely underestimated SARS-CoV-2 prevalence in correctional and detention facilities. Broad-based testing can provide a more accurate assessment of prevalence and generate data to help control transmission (4). url: https://doi.org/10.15585/mmwr.mm6933a3 doi: 10.15585/mmwr.mm6933a3 id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 words: 9036.0 sentences: 483.0 pages: flesch: 43.0 cache: ./cache/cord-279691-v5kpmk0b.txt txt: ./txt/cord-279691-v5kpmk0b.txt summary: Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). abstract: Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/23202524/ doi: 10.3390/v4113245 id: cord-266031-tlrsco40 author: Haghani, Milad title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCoV literature date: 2020-09-21 words: 7993.0 sentences: 356.0 pages: flesch: 51.0 cache: ./cache/cord-266031-tlrsco40.txt txt: ./txt/cord-266031-tlrsco40.txt summary: To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. The decision on which general database to use (e.g. Web of Science (WoS) or Scopus) was mainly made on the basis of the number of indexed Covid-19 studies in particular, as the sector of the coronavirus literature that is currently emerging (compared to the literatures on SARS and MERS that have already stabilised). In this cluster, one can observe terms such as those associated with general public health including "wold health organisation", "public health", "public The map of keyword co-occurrences associated with the Covid-19 literature health service", "global health", as well as those associated with disease outbreaks including "emergency", "health risk" "epidemics", "pandemic", "outbreak", "viral diseases", "virus infection", "communicable disease", "transmission", "travel". abstract: During the current century, each major coronavirus outbreak has triggered a quick and immediate surge of academic publications on its respective topic. The spike in research publications following the 2019 Novel Coronavirus (Covid-19) outbreak, however, has been like no other. The global crisis caused by the Covid-19 pandemic has mobilised scientific efforts at an unprecedented scale. In less than 5 months, more than 12,000 research items and in less than seven months, more than 30,000 items were indexed, while it is projected that the number could exceed 80,000 by the end of 2020, should the current trend continues. With the health crisis affecting all aspects of life, research on Covid-19 seems to have become a focal point of interest across many academic disciplines. Here, scientometric aspects of the Covid-19 literature are analysed and contrasted with those of the two previous major coronavirus diseases, i.e., Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The focus is on the co-occurrence of key-terms, bibliographic coupling and citation relations of journals and collaborations between countries. Interesting recurring patterns across all three literatures were discovered. All three outbreaks have commonly generated three distinct cohorts of studies: (i) studies linked to public health response and epidemic control, (ii) studies on chemical constitution of the virus; and (iii) studies related to treatment, vaccine and clinical care. While studies affiliated with category (i) seem to have been relatively earliest to emerge, they have overall received relatively smaller number of citations compared to publications the two other categories. Covid-19 studies seem to have been disseminated across a broader variety of journals and across a more diverse range of subject areas. Clear links are observed between the geographical origins of each outbreak as well as the local geographical severity of each outbreak and the magnitude of research originated from regions. Covid-19 studies also display the involvement of authors from a broader variety of countries compared to SARS and MERS. Considering the speed at which the Covid-19-related literature is accumulating, an interesting dimension that warrants further exploration could be to assess if the quality and rigour of these publications have been affected. url: https://www.ncbi.nlm.nih.gov/pubmed/32981988/ doi: 10.1007/s11192-020-03706-z id: cord-300078-svu06v9c author: Haghani, Milad title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date: 2020-06-01 words: 6365.0 sentences: 298.0 pages: flesch: 52.0 cache: ./cache/cord-300078-svu06v9c.txt txt: ./txt/cord-300078-svu06v9c.txt summary: To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. Figures A1 and A2 in the Appendix illustrate the map associated with the SARS literature overlaid respectively with the average year of publication and average number of citations associated with the studies where these keywords have occurred. Maps of term occurrences based on the analysis of the title and abstract of studies on SARS, MERS and Covid-19 have also been presented in Figures 7, 8 and 9 respectively. An inspection of the maps overlaid with the average year of publications for SARS and MERS in Figures A1 and A3 in the Appendix suggests that, on average, this cohort of studies are generally the last to emerge in the published domain compared to the two other major clusters, but they receive relatively high citations on average (according to Figures A2, A4 and A6). abstract: During the current century, each major coronavirus outbreak has triggered a quick and immediate surge of academic publications on this topic. The spike in research publications following the 2019 Novel Coronavirus (Covid-19) outbreak, however, has been like no other. The global crisis caused by the Covid-19 pandemic has mobilised scientific efforts in an unprecedented way. In less than five months, more than 12,000 research items have been indexed while the number increasing every day. With the crisis affecting all aspects of life, research on Covid-19 seems to have become a focal point of interest across many academic disciplines. Here, scientometric aspects of the Covid-19 literature are analysed and contrasted with those of the two previous major Coronavirus diseases, i.e. Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The focus is on the co-occurrence of key-terms, bibliographic coupling and citation relations of journals and collaborations between countries. Certain recurring patterns across all three literatures were discovered. All three outbreaks have commonly generated three distinct and major cohort of studies: (i) studies linked to the public health response and epidemic control, (ii) studies associated with the chemical constitution of the virus and (iii) studies related to treatment, vaccine and clinical care. While studies affiliated with the category (i) seem to have been the first to emerge, they overall received least numbers of citations compared to those of the two other categories. Covid-19 studies seem to have been distributed across a broader variety of journals and subject areas. Clear links are observed between the geographical origins of each outbreak or the local geographical severity of each outbreak and the magnitude of research originated from regions. Covid-19 studies also display the involvement of authors from a broader variety of countries compared to SARS and MRS. url: https://doi.org/10.1101/2020.05.31.126813 doi: 10.1101/2020.05.31.126813 id: cord-343029-85ga6r7d author: Haghpanah, Abdolreza title: Potential mechanisms of SARS‐CoV‐2 action on male gonadal function and fertility: Current status and future prospects date: 2020-10-27 words: 4375.0 sentences: 218.0 pages: flesch: 43.0 cache: ./cache/cord-343029-85ga6r7d.txt txt: ./txt/cord-343029-85ga6r7d.txt summary: The aim of this review was to provide new insights into different possible mechanisms of involvement of male gonads with SARS‐CoV‐2 including investigating the ACE2 axis in testis, hormonal alterations in patients with COVID‐19, possible formation of anti‐sperm antibodies (ASA) and subsequently immunological infertility as a complication of SARS‐CoV‐2 infection. Considering the fact that the testis is highly enriched in ACE2 receptors and its vulnerability to SARS-CoV-2 invasion, detectable changes in semen analysis, alteration in sex hormones balance and, most importantly, anti-sperm antibodies (ASA) formation and sperm DNA fragmentation are considered to play a major role in male infertility. Search phrases used for different databases strategy included the following: "severe acute respiratory syndrome coronavirus 2", "2019 nCoV", "SARS-CoV-2", "coronavirus", "COVID-19", "reproductive system", "fertility", "infertility", "germ cells", "gamete", "spermatogonia", "spermatogenesis" "spermatozoa", "spermatozoan", "testis", "Sertoli cells", "Leydig cells", "Androgen", "steroidogenesis", "spermiogenesis", "spermiation", "development", "fertilization", "gonadal function", "sex hormones", "angiotensin-converting enzyme 2 receptor", "ACE2", "anti-sperm antibodies", "ASA", "sperm DNA fragmentation index", "DFI", and "semen analysis". abstract: The novel coronavirus was recognised in December 2019 and caught humanity off guard. The virus employs the angiotensin‐converting enzyme 2 (ACE2) receptor for entry into human cells. ACE2 is expressed on different organs, which is raising concern as to whether these organs can be infected by the virus or not. The testis appears to be an organ enriched with levels of ACE2, while the possible mechanisms of involvement of the male reproductive system by SARS‐CoV‐2 are not fully elucidated. The major focus of the present studies is on the short‐term complications of the coronavirus and gains importance on studying the long‐term effects, including the possible effects of the virus on the male reproductive system. The aim of this review was to provide new insights into different possible mechanisms of involvement of male gonads with SARS‐CoV‐2 including investigating the ACE2 axis in testis, hormonal alterations in patients with COVID‐19, possible formation of anti‐sperm antibodies (ASA) and subsequently immunological infertility as a complication of SARS‐CoV‐2 infection. Finally, we suggest measuring the sperm DNA fragmentation index (DFI) as a determiner of male fertility impairment in patients with COVID‐19 along with other options such as sex‐related hormones and semen analysis. Invasion of SARS‐CoV‐2 to the spermatogonia, Leydig cells and Sertoli cells can lead to sex hormonal alteration and impaired gonadal function. Once infected, changes in ACE2 signalling pathways followed by oxidative stress and inflammation could cause spermatogenesis failure, abnormal sperm motility, DNA fragmentation and male infertility. url: https://www.ncbi.nlm.nih.gov/pubmed/33108833/ doi: 10.1111/and.13883 id: cord-291561-sxvgue36 author: Haixu, Liang title: Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date: 2019-11-25 words: 10271.0 sentences: 543.0 pages: flesch: 50.0 cache: ./cache/cord-291561-sxvgue36.txt txt: ./txt/cord-291561-sxvgue36.txt summary: A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/31778686/ doi: 10.1016/j.jinf.2019.11.014 id: cord-353391-o0s2h0y0 author: Haj Bloukh, Samir title: A Look Behind the Scenes at COVID-19: National Strategies of Infection Control and Their Impact on Mortality date: 2020-08-04 words: 9925.0 sentences: 539.0 pages: flesch: 54.0 cache: ./cache/cord-353391-o0s2h0y0.txt txt: ./txt/cord-353391-o0s2h0y0.txt summary: To investigate the importance of serum vitamin D levels, median age, temperature, and humidity we compare infection control measures and their impact on COVID-19-related fatalities in Portugal, Sweden, and Switzerland ( Figure 1 ). A study compared community-wide mask compliance in relation to the number of confirmed SARS-CoV-2 cases/fatalities in Hong Kong, Singapore, and other countries [29] . This mask-wearing strategy combined with social distancing, personal hygiene, cancellation of social gatherings, use of the home office, and school closures resulted in the effective control of the SARS-CoV-2 transmission compared to other neighboring countries [29] . We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. abstract: (1) Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began spreading across the globe in December and, as of 9 July 2020, had inflicted more than 550,000 deaths. Public health measures implemented to control the outbreak caused socio-economic havoc in many countries. The pandemic highlighted the quality of health care systems, responses of policymakers in harmony with the population, and socio-economic resilience factors. We suggest that different national strategies had an impact on mortality and case count. (2) Methods: We collected fatality data for 17 countries until 2 June 2020 from public data and associated these with implemented containment measures. (3) Results: The outcomes present the effectiveness of control mechanisms in mitigating the virus for selected countries and the UAE as a special case. Pre-existing conditions defined the needed public health strategies and fatality numbers. Other pre-existing conditions, such as temperature, humidity, median age, and low serum 25-hydroxyvitamin D (25(OH)D) concentrations played minor roles and may have had no direct impact on fatality rates. (4) Conclusions: Prevention, fast containment, adequate public health strategies, and importance of indoor environments were determining factors in mitigating the pandemic. Development of public health strategies adapted to pre-existing conditions for each country and community compliance with implemented policies ensure the successful control of pandemics. url: https://doi.org/10.3390/ijerph17155616 doi: 10.3390/ijerph17155616 id: cord-291719-1ku6cmwj author: Hajjo, Rima title: A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date: 2020-10-06 words: 6493.0 sentences: 315.0 pages: flesch: 41.0 cache: ./cache/cord-291719-1ku6cmwj.txt txt: ./txt/cord-291719-1ku6cmwj.txt summary: METHODS: We developed and employed a systems biology workflow capable of identifying small-molecule antiviral drugs and vaccines that can boast immunity and affect a wide variety of viral disease pathways to protect from the fatal consequences of emerging viruses. RESULTS: Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. Herein, we describe a unique drug and vaccine repurposing workflow, and list high confidence proteins and pharmacological classes of compounds, that work as BCG mimics at the system level by inducing beneficial long lasting trained immune response. Earlier studies suggested that the documented beneficial off-target effects of BCG in protecting from non-TB infections, including perhaps COVID-19, involve a potentiation of innate immune responses through epigenetic mechanisms (56) (57) (58) . abstract: PURPOSE: Coronavirus disease 2019 (COVID-19) is expected to continue to cause worldwide fatalities until the World population develops ‘herd immunity’, or until a vaccine is developed and used as a prevention. Meanwhile, there is an urgent need to identify alternative means of antiviral defense. Bacillus Calmette–Guérin (BCG) vaccine that has been recognized for its off-target beneficial effects on the immune system can be exploited to boast immunity and protect from emerging novel viruses. METHODS: We developed and employed a systems biology workflow capable of identifying small-molecule antiviral drugs and vaccines that can boast immunity and affect a wide variety of viral disease pathways to protect from the fatal consequences of emerging viruses. RESULTS: Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. We have identified small-molecule BCG mimics, including antiviral drugs such as raltegravir and lopinavir as high confidence hits. Strikingly, our top hits emetine and lopinavir were independently validated by recent experimental findings that these compounds inhibit the growth of SARS-CoV-2 in vitro. CONCLUSIONS: Our results provide systems biology support for using BCG and small-molecule BCG mimics as putative vaccine and drug candidates against emergent viruses including SARS-CoV-2. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11095-020-02930-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/33025261/ doi: 10.1007/s11095-020-02930-9 id: cord-262635-fdwd99ah author: Hajra Martínez, Ismael El title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus date: 2020-08-07 words: 238.0 sentences: 25.0 pages: flesch: 63.0 cache: ./cache/cord-262635-fdwd99ah.txt txt: ./txt/cord-262635-fdwd99ah.txt summary: key: cord-262635-fdwd99ah title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus cord_uid: fdwd99ah abdominal CT scan, a thickening of the terminal ileum was observed suggesting the presence of acute ileitis. The patient received empirical treatment with ciprofloxacin and metronidazole without any improvement. Microbiological stool examinations were negative, also for SARS-CoV-2 rRT-PCR test. April 29 th , the study was completed with an ileo-colonoscopy with ileal biopsy. The mucosa of ileum and colon was macroscopically normal, and the biopsy showed no damage. However, RT-PCR test on ileal tissue was positive for SARS-CoV-2 RNA. We repeated the SARS-CoV-2 rRT-PCR test on nasopharyngeal swab and it again came back negative. The patient improved over the next few days without any specific treatment. Evidence for Gastrointestinal Infection of SARS-CoV-2 Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis abstract: nan url: https://api.elsevier.com/content/article/pii/S0016508520350198 doi: 10.1053/j.gastro.2020.05.101 id: cord-341234-2zgfcrwc author: Hallak, Jorge title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil date: 2020-09-02 words: 3614.0 sentences: 178.0 pages: flesch: 41.0 cache: ./cache/cord-341234-2zgfcrwc.txt txt: ./txt/cord-341234-2zgfcrwc.txt summary: title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil Recently, a group of 27 experts from 15 countries and five continents has argued that postponing andrological services and male infertility care during the COVID-19 pandemic could permanently compromise the prospects of biological parenthood for ''time-sensitive'' patients, thus resulting in a devastating psychological impact on men undergoing fertility-related treatment (1) . A recent probabilistic pilot study conducted in seven districts of the city of São Paulo to estimate the prevalence of herd immunity showed that about 5.2% individuals had SARS-CoV-2 IgG antibodies, corresponding to an overall infection rate We reiterate that andrological services and male infertility care cannot be considered low priority during the current SARS-CoV-2 pandemic, particularly for the most vulnerable patients, like those with cancer, patients using immunosuppressive therapy, and the azoospermic/cryptozoospermic men under medical or post-surgical treatment to improve spermatogenesis. abstract: nan url: https://doi.org/10.1590/s1677-5538.ibju.2020.06.03 doi: 10.1590/s1677-5538.ibju.2020.06.03 id: cord-273064-c58nf9vb author: Hallowell, Benjamin D. title: Severe Acute Respiratory Syndrome Coronavirus 2 Prevalence, Seroprevalence, and Exposure among Evacuees from Wuhan, China, 2020 date: 2020-09-17 words: 3519.0 sentences: 168.0 pages: flesch: 47.0 cache: ./cache/cord-273064-c58nf9vb.txt txt: ./txt/cord-273064-c58nf9vb.txt summary: At arrival in the United States and again at the quarantine facility, evacuees were asked to complete a US Traveler''s Health Declaration form disclosing any symptoms; they were also screened for illness and fever, asked about symptoms in the past 72 hours, and asked about any high-risk exposures (including working in or visiting healthcare settings; caring for or visiting persons with fever, respiratory illness, or a confirmed COVID-19 diagnosis; or visiting any live animal markets) in Wuhan in the past 14 days. The survey captured information on demographics, clinical signs/ symptoms, travel outside of Hubei Province, face mask use, limitation of time spent in public, and past high-risk exposures (including contact with confirmed COVID-19 case-patients; persons with fever, acute respiratory illness, or both; healthcare and laboratory facilities; and animals and live animal markets). abstract: To determine prevalence of, seroprevalence of, and potential exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among a cohort of evacuees returning to the United States from Wuhan, China, in January 2020, we conducted a cross-sectional study of quarantined evacuees from 1 repatriation flight. Overall, 193 of 195 evacuees completed exposure surveys and submitted upper respiratory or serum specimens or both at arrival in the United States. Nearly all evacuees had taken preventive measures to limit potential exposure while in Wuhan, and none had detectable SARS-CoV-2 in upper respiratory tract specimens, suggesting the absence of asymptomatic respiratory shedding among this group at the time of testing. Evidence of antibodies to SARS-CoV-2 was detected in 1 evacuee, who reported experiencing no symptoms or high-risk exposures in the previous 2 months. These findings demonstrated that this group of evacuees posed a low risk of introducing SARS-CoV-2 to the United States. url: https://www.ncbi.nlm.nih.gov/pubmed/32620182/ doi: 10.3201/eid2609.201590 id: cord-257751-n7w1psr4 author: Halperin, Daniel T. title: Coping With COVID-19: Learning From Past Pandemics to Avoid Pitfalls and Panic date: 2020-06-30 words: 6378.0 sentences: 386.0 pages: flesch: 57.0 cache: ./cache/cord-257751-n7w1psr4.txt txt: ./txt/cord-257751-n7w1psr4.txt summary: As we wrestle with how best to mitigate COVID-19, it is imperative to concur on the likely main drivers of transmission (notably, infection clusters resulting from prolonged indoor respiratory exposure) in order to clearly explain risk and to determine the most effective, realistic behavioral and other means to reduce illness and mortality. What is clear, based on evidence from several countries (and despite media attention to statistically anomalous cases of healthy and younger victims), is that severe outcomes and deaths from COVID-19 are overwhelmingly associated with preexisting (and especially multiple) serious illnesses such as diabetes and heart disease, [14] [15] [16] more so in men and particularly when exacerbated by obesity and smoking. Moreover, the fact that between 96% (in the United States 16 ) and more than 99% (in Italy 14 ) of COVID-19-related deaths, at any age, have occurred in persons with preexisting conditions could suggest that even very old but otherwise healthy people may not be at greatly elevated risk of dying from the disease. abstract: It is imperative to concur on the main transmission routes of COVID-19 to explain risk and determine the most effective means to reduce illness and mortality. We must avoid generating irrational fear and maintain a broader perspective in the pandemic response, including assessing the possibility for substantial unintended consequences. url: https://doi.org/10.9745/ghsp-d-20-00189 doi: 10.9745/ghsp-d-20-00189 id: cord-278260-3o91v72a author: Halstead, Scott B title: COVID 19 Vaccines: Should we fear ADE? date: 2020-08-12 words: 2331.0 sentences: 178.0 pages: flesch: 44.0 cache: ./cache/cord-278260-3o91v72a.txt txt: ./txt/cord-278260-3o91v72a.txt summary: Within months large numbers of vaccinated children developed a severe breakthrough disease, called "atypical measles." [6] A similar outcome, "vaccine associated enhanced respiratory disease (VAERD)," was observed in infants, 4 -12 months of age, who were given formalininactivated respiratory syncytial virus (RSV) and a few months later infected by RSV. The biological behavior of some coronaviruses in non-human species together with evidence that human coronavirus antibodies enhanced infection of SARS or MERS CoVs in Fc receptor-bearing cells, in vitro, have led to speculations that ADE contributes to disease severity in humans. [11] It has been reported that high levels of SARS CoV-1 IgG antibodies circulated in severe SARS cases and that anti-S IgG neutralizing antibody (NAb) responses developed significantly faster after the onset of clinical symptoms in fatal compared with recovered cases leading some to attribute enhanced tissue damage to ADE. With others, we conclude that the differences in clinical, epidemiological and pathological features of SARS and DENV diseases suggest that iADE does not contribute to the severity of natural human coronavirus infections. abstract: Might COVID 19 vaccines sensitize humans to antibody dependent enhanced (ADE) breakthrough infections? This outcome is unlikely because coronavirus diseases in humans lack the clinical, epidemiological, biological or pathological attributes of ADE disease exemplified by the dengue viruses (DENV). In contrast to DENV, SARS and MERS CoVs predominantly infect respiratory epithelium, not macrophages. Severe disease centers on older persons with pre-existing conditions and not young infants or individuals with previous coronavirus infections. Live virus challenge of animals given SARS or MERS vaccines has resulted in vaccine hypersensitivity reactions (VAH), similar to those in humans given inactivated measles or respiratory syncytial virus vaccines. Safe and effective COVID 19 vaccines must avoid VAH. url: https://www.ncbi.nlm.nih.gov/pubmed/32785649/ doi: 10.1093/infdis/jiaa518 id: cord-260247-akujsk0s author: Hamed, Ehab title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar date: 2020-11-02 words: 962.0 sentences: 79.0 pages: flesch: 56.0 cache: ./cache/cord-260247-akujsk0s.txt txt: ./txt/cord-260247-akujsk0s.txt summary: title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar The group suggested recurrent positive rt-PCR results of more than 21 days following the resolution of symptoms as criteria for reinfection. Utilising the criteria set by the COCOREC study group, this record-based study reports on the cases with recurrent positive RT-PCR nasopharyngeal swab for SARS-CoV-2 results in primary health care corporation (PHCC) settings in Qatar. The study population included patients attending with documented SARS-CoV-2 rt-PCR results during the study period. What are the rates of recurrent rt-PCR SARS-CoV-2 positive results of more than 21 days, and what are the population characteristics? No previous studies reported to the rates of recurrent positive rt-PCR for SARS-CoV-2 infections. Given the extensive reporting of the SARS-CoV-2 infections, the number of case reports of recurrent positive and reinfection to date is extremely low, which agrees with our findings. abstract: nan url: https://api.elsevier.com/content/article/pii/S0163445320306915 doi: 10.1016/j.jinf.2020.10.029 id: cord-268206-ino9srb6 author: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 words: 6067.0 sentences: 330.0 pages: flesch: 46.0 cache: ./cache/cord-268206-ino9srb6.txt txt: ./txt/cord-268206-ino9srb6.txt summary: Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. In the current SARS-COV-2 pandemic, Wu and McGoogan (2020) showed that patients with chronic diseases, including diabetes, were at higher risk for severe COVID-19 infection and mortality. The former (S) is the wild type which is milder while the latter (L) is the novel one which resulted in high binding affinity between SARS-COV-2 virus with angiotensin-converting enzyme 2 receptor in human cells. The use of convalescent plasma was recommended before as an important treatment during outbreaks of Ebola virus, Middle East respiratory syndrome coronavirus, SARS-COV-1, H5N1 avian influenza, and H1N1 influenza (Zhou et al. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. abstract: Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. By the declaration of WHO, COVID-19 outbreak considered as a public health problem of international concern. The aim of this study is to provide a comprehensive view on COVID-19 and the future expectations to control virus progression. Patients with liver disease, diabetes, high blood pressure, and obesity are more susceptible to the incidence of COVID-19 infection. So, there is a rapid need for disease diagnosis, vaccine development, and drug discovery to detect, prevent, and treat this sudden and lethal virus. Real-time polymerase chain reaction (RT-PCR) is considered as a rapid, accurate, and specific tool for disease diagnosis. Under this emergency situation that the world facing against COVID-19, there are about 15 potential vaccine candidates tested globally based on messenger RNA, DNA-based, nanoparticle, synthetic, and modified virus-like particle. Certain drugs that are clinically approved for other diseases were tested against COVID-19 as chloroquine, hydroxychloroquine, ivermectin, favipiravir, ribavirin, and remdesivir. Convalescent plasma transfusion and traditional herbal medicine were also taken into consideration. Due to the absence of effective treatment or vaccines against COVID-19 so far, the precautionary measures according to WHO’s strategic objectives are the only way to confront this crisis. Governments should adopt national medical care programs to reduce the risk of exposure to any future viral outbreaks especially to patients with pre-existing medical conditions. url: https://doi.org/10.1186/s42269-020-00341-9 doi: 10.1186/s42269-020-00341-9 id: cord-263616-igprqlqr author: Hamid, Hytham K. S. title: Considerations for transanal surgery during COVID‐19 pandemic date: 2020-07-15 words: 148.0 sentences: 19.0 pages: flesch: 56.0 cache: ./cache/cord-263616-igprqlqr.txt txt: ./txt/cord-263616-igprqlqr.txt summary: key: cord-263616-igprqlqr authors: Hamid, Hytham K. title: Considerations for transanal surgery during COVID‐19 pandemic date: 2020-07-15 journal: J Surg Oncol DOI: 10.1002/jso.26085 sha: doc_id: 263616 cord_uid: igprqlqr nan To the Editor, Elective colorectal cancer surgery at the oncologic hub of Lombardy inside a pandemic COVID-19 area Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis Prolonged presence of SARS-CoV-2 viral RNA in faecal samples Evidence for gastrointestinal infection of SARS-CoV-2 Detection of SARS-CoV-2 in different types of clinical specimens Isolation of 2019-nCoV from a stool specimen of a laboratory-confirmed case of the coronavirus disease 2019 (COVID-19) Detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child Coronavirus disease (COVID-19) in a paucisymptomatic patient: epidemiological and clinical challenge in settings with limited community transmission abstract: nan url: https://doi.org/10.1002/jso.26085 doi: 10.1002/jso.26085 id: cord-277659-afysef1e author: Hamilton, F. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 words: 3096.0 sentences: 203.0 pages: flesch: 53.0 cache: ./cache/cord-277659-afysef1e.txt txt: ./txt/cord-277659-afysef1e.txt summary: Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCW''s). In this paper, we report the kinetics and performance of this assay in three populations: confirmed (PCR +ve) and suspected COVID-19 patients, confirmed (PCR +ve) healthcare workers, and pre-pandemic controls with respiratory infection. The sensitivity of the Abbott SARS-CoV-2 IgG assay was estimated with 95% Confidence Intervals at different time points post symptom onset (DISCOVER patients) or first PCR positive result (healthcare workers). abstract: Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). Pre-pandemic respiratory infection sera were tested as negative controls. The sensitivity of the assay was calculated at different time points (<5 days, 5-9 days, 10-14 days, 15-19 days, >20 days, >42 days), and compared between cohorts. Results: Performance of the Abbot Architect SARS-CoV-2 assay varied significantly between cohorts. For PCR confirmed hospitalised patients (n = 114), early sensitivity was low: <5 days: 44.4% (95%CI: 18.9%-73.3%), 5-9 days: 32.6% (95%CI, 20.5%-47.5%), 10-14 days: 65.2% (95% CI 44.9%-81.2%), 15-20 days: 66.7% (95% CI: 39.1%-86.2%) but by day 20, sensitivity was 100% (95%CI, 86.2-100%). In contrast, 17 out of 114 symptomatic healthcare workers tested at >20 days had negative results, generating a sensitivity of 85.1% (95%CI, 77.4% - 90.5%). All pre-pandemic sera were negative, a specificity of 100%. Seroconversion rates were similar for PCR positive and PCR negative hospitalised cases. Conclusions: The sensitivity of the Abbot Architect SARS-CoV-2 IgG assay increases over time, with sensitivity not peaking until 20 days post symptoms. Performance varied markedly by setting, with sensitivity significantly worse in symptomatic healthcare workers than in the hospitalised cohort. Clinicians, policymakers, and patients should be aware of the reduced sensitivity in this setting. url: http://medrxiv.org/cgi/content/short/2020.07.03.20145722v1?rss=1 doi: 10.1101/2020.07.03.20145722 id: cord-341776-y7kpp10x author: Hamm, C. title: Zusammenhang zwischen Angiotensinblockade und Influenza-A-Inzidenz date: 2020-06-05 words: 286.0 sentences: 45.0 pages: flesch: 51.0 cache: ./cache/cord-341776-y7kpp10x.txt txt: ./txt/cord-341776-y7kpp10x.txt summary: key: cord-341776-y7kpp10x cord_uid: y7kpp10x So wird unter anderem diskutiert, ob Medikamente, die auf das Renin-Angiotensin-Aldosteron-System (RAAS) wirken, für eine Infektion mit Coronaviren sensibilisieren. Bekannt ist, dass ACE2-Rezeptoren bei Influenza-A-induzierten Lungenschäden, insbesondere beim schweren akuten respiratorischen Syndrom (SARS), eine wichtige Rolle spielen. Ziel der im Folgenden vorgestellten epidemiologischen Studie war es daher, den Zusammenhang zwischen der Häufigkeit einer Influenzainfektion und der Therapie mit ACE-Hemmern bzw. Obwohl nicht sicher ist, ob diese Beobachtung auch auf SARS-CoV-2 übertragbar ist, ist sie in der derzeitigen Pandemieunsicherheit ein Beitrag, der bei eingeschränkten Therapieoptionen hohe Aufmerksamkeit hervorrufen muss. Wenn das Risiko zu erkranken geringer ist, verläuft dann die Erkrankung auch anders? Insgesamt stützt diese Beobachtung derzeit sicherlich die Empfehlung aller kardiologischen und Hypertoniefachgesellschaften [5] , die Therapie mit ACE-Hemmern oder ARB auch in Zeiten der COVID-19-Pandemie uneingeschränkt fortzuführen. Renin-angiotensin-aldosterone system blockers and the risk of Covid-19 Renin-angiotensin-aldosteronesysteminhibitors and risk of Covid-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32504298/ doi: 10.1007/s00108-020-00827-8 id: cord-348773-ulnc9gdv author: Hammoud, H. title: Post mortem pathological findings in COVID-19 cases: A Systematic Review date: 2020-10-14 words: 5075.0 sentences: 341.0 pages: flesch: 54.0 cache: ./cache/cord-348773-ulnc9gdv.txt txt: ./txt/cord-348773-ulnc9gdv.txt summary: Methods: A systematic search of electronic databases (PubMed, ScienceDirect, Google scholar, Medrxiv & Biorxiv) was carried out from December 2019 to August, 15th 2020, for journal articles of different study designs reporting postmortem pathological findings in COVID-19 cases. Articles were included if they met the following eligibility criteria: (1) addressed pathological reports of COVID-19 autopsies or postmortem cases, (2) involved human subjects (at least one case), (3) all study designs were involved (case report, case series, cross-sectional, case-control, randomized and non-randomized studies), (4) no language restrictions were applied. (13, 19, 20, 22-32, 34, 38-41, 44-65, 67) Regarding the included organs, this review described the histopathology of different organs as follows; Lung and pulmonary system was the most common described organ in 42 articles, ( is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Regarding the postmortem pulmonary pathology, our review showed that different histopathological findings had been identified among COVID-19 cases. abstract: Abstract Background: The current COVID-19 pandemic is considered one of the most serious public health crisis over the last few decades. Although the disease can result in diverse, multiorgan pathology, there have been very few studies addressing the postmortem pathological findings of the cases. Active autopsy amid this pandemic could be an essential tool for diagnosis, surveillance, and research. Objective: To provide a total picture of the SARS-CoV-2 histopathological features of different body organs in postmortem autopsies through a systematic search of the published literature. Methods: A systematic search of electronic databases (PubMed, ScienceDirect, Google scholar, Medrxiv & Biorxiv) was carried out from December 2019 to August, 15th 2020, for journal articles of different study designs reporting postmortem pathological findings in COVID-19 cases. PRISMA guidelines were used for reporting the review. Results: A total of 50 articles reporting 430 cases were included in our analysis. Postmortem pathological findings were reported for different body organs, pulmonary system (42 articles), cardiovascular system ( 23 articles), hepatobiliary system (22 articles), kidney (16 articles), spleen, and lymph nodes (12 articles), and central nervous system (7 articles). In lung samples, diffuse alveolar damage (DAD) was the most commonly reported findings in 239 cases (84.4%). Myocardial hypertrophy (87 cases by 51.2%), arteriosclerosis (121 cases by 62%), and steatosis ( 118 cases by 59.3%) were the most commonly reported pathological findings in the heart, kidney, and hepatobiliary system respectively. Conclusion: Autopsy examination as an investigation tool could help in a better understanding of SARS-CoV-2 pathophysiology, diagnosis, management, and subsequently improving patient care. Keywords: SARS-CoV-2, Histopathology, Autopsy, forensic pathology, COVID-19 url: http://medrxiv.org/cgi/content/short/2020.10.11.20210849v1?rss=1 doi: 10.1101/2020.10.11.20210849 id: cord-339381-vvh06d2c author: Han, Deheng title: SARS‐CoV‐2 was found in the bile juice from a patient with severe COVID‐19 date: 2020-06-12 words: 967.0 sentences: 60.0 pages: flesch: 57.0 cache: ./cache/cord-339381-vvh06d2c.txt txt: ./txt/cord-339381-vvh06d2c.txt summary: In the case report, the novel coronavirus was found in the bile specimen from a patient with severe COVID‐19 by real‐time fluorescent RT‐PCR. SARS-CoV-2 was found in the bile juice from a patient with severe COVID-19 Coronavirus disease 2019 (Covid-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to 163 countries/areas since December 2019. Previous studies have reported that the SARS-CoV-2 could be detected in sputum, faeces, tears, urine and other specimens of infected patients [3, 4] . In the case report, the novel coronavirus was found in the bile specimen from a patient with severe Covid-19. In view of the patient''s medical history, the attending doctor considered bile duct obstruction as one of the reasons for liver function failure. To our knowledge, this is the first case in which bile juice SARS-CoV-2 was detected. abstract: SARS‐CoV‐2 has infected over 170,000 people worldwide and was associated with substantial mortality. Previous studies have reported that the SARS‐CoV‐2 could be detected in sputum, faeces, urine and other specimens from COVID‐19 patients. In the case report, the novel coronavirus was found in the bile specimen from a patient with severe COVID‐19 by real‐time fluorescent RT‐PCR. In addition, much higher viral load in the bile juice than in the sputum indicated that a false positive error in the specimen was hardly possible. As far as we know, it is the first report about SARS‐CoV‐2 in the bile juice. We would love to share the information to other researchers. The report may have a significant impact on the clinical management and public health decision making. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26169 doi: 10.1002/jmv.26169 id: cord-275993-isff6lp2 author: Han, Dong P title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date: 2004-08-15 words: 5598.0 sentences: 308.0 pages: flesch: 52.0 cache: ./cache/cord-275993-isff6lp2.txt txt: ./txt/cord-275993-isff6lp2.txt summary: Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. S-protein of coronaviruses, which is thought to function as a trimer (Delmas and Laude, 1990) , is responsible for both binding to cellular receptors and inducing membrane fusion for virus entry into target cells (Collins et al., 1982; Godet et al., 1994; Kubo et al., 1994) . Despite difficulties in detecting S-protein directly by immunoassays, proteins expressed from both pcDNA-S and pHCMV-S constructs were able to pseudotype MuLV particles to produce SARS pseudoviruses that could readily infect Vero E6 cells (Fig. 3A) . To assess whether SARS pseudoviruses we generated could be used to quantify virus-neutralizing antibodies, we examined their susceptibility to convalescent sera from SARS-CoV-infected patients. Pseudotyping of murine leukemia virus with the envelope glycoproteins of HIV generates a retroviral vector with specificity of infection for CD4-expressing cells abstract: The etiological agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus SARS-CoV. Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. Accordingly, S-protein plays an important role in virus infection cycle and is the primary target of neutralizing antibodies. To begin to understand its biochemical and immunological properties, we expressed both full-length and ectodomain of the protein in various primate cells. Our results show that the protein has an electrophoretic mobility of about 160–170 kDa. The protein is glycosylated with high mannose and/or hybrid oligosaccharides, which account for approximately 30 kDa of the apparent protein mass. The detection of S-protein by immunoassays was difficult using human convalescent sera, suggesting that the protein may not elicit strong humoral immune response in virus-infected patients. We were able to pseudotype murine leukemia virus particles with S-protein and produce SARS pseudoviruses. Pseudoviruses infected Vero E6 cells in a pH-independent manner and the infection could be specifically inhibited by convalescent sera. Consistent with low levels of antibodies against S-protein, neutralizing activity was weak with 50% neutralization titers ranging between 1:15 to 1:25. To facilitate quantifying pseudovirus-infected cells, which are stained blue with X-Gal, we devised an automated procedure using an ELISPOT analyzer. The high-throughput capacity of this procedure and the safety of using SARS pseudoviruses should make possible large-scale analyses of neutralizing antibody responses against SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/15262502/ doi: 10.1016/j.virol.2004.05.017 id: cord-294136-e69ao8j0 author: Han, Dongsheng title: COVID-19: Insight into the asymptomatic SARS-COV-2 infection and transmission date: 2020-08-27 words: 5215.0 sentences: 263.0 pages: flesch: 42.0 cache: ./cache/cord-294136-e69ao8j0.txt txt: ./txt/cord-294136-e69ao8j0.txt summary: successfully isolated SARS-CoV-2 from throat swabs of two asymptomatic patients in a cell culture of Caco-2 cells, suggesting the potential for presymptomatic transmission [16] ; (5) Increasing studies show clear epidemiological evidence of human-to-human asymptomatic spread of COVID-19 (described in the following section); (6) Asymptomatic infection tends to be, but is not only, identified among young people (<20 years old) [14, 15, [17] [18] [19] ; And (7) the majority (>90%) of asymptomatic patients appears to have a milder clinical course during hospitalization [15] , but the severity of the symptoms of the secondary patients infected by SARS-COV-2 from asymptomatic patients varies based on their physical constitution [2, 20] . As the transmission of SARS-COV-2 may occur in the early course of infection and a high viral load in respiratory samples could be detected [13] , RT-PCR testing for this virus is more suitable for screening at earlier stages of infection in key populations, such as patients with obvious symptoms and close contacts of asymptomatic patients [35] . abstract: The existence of a substantial but unclear number of asymptomatic SARS-COV-2 patients worldwide has raised concerns among global public health authorities. In this review, according to the published literature, we provided the evidence that asymptomatic infections can result in person-to-person transmission. Four studies suggested that the virus can be transmitted by asymptomatic patients for at least two consecutive generations, indicating its strong infectivity. Asymptomatic infection tends to be, but is not only, identified among young people (<20 years old). The majority of asymptomatic patients appear to have a milder clinical course during hospitalization, but the severity of the symptoms of the secondary patients infected by SARS-COV-2 from asymptomatic patients varies with their physical constitution. The proportion of asymptomatic individuals among all confirmed cases widely differed (from 1.95% to 87.9%) according to the study setting and the populations studied. The increasing large-scale tests are expected to give more information about the true number of asymptomatic infections in the population. In China and other countries, various guidelines for management of asymptomatic cases have been issued. Importantly, early detection, early reporting, early isolation and early treatment of asymptomatic patients require the joint efforts of policy makers, clinicians, technicians, epidemiologists, virologists and patients. url: https://doi.org/10.7150/ijbs.48991 doi: 10.7150/ijbs.48991 id: cord-265350-k9yus2sv author: Han, Guan-Zhu title: Pangolins Harbor SARS-CoV-2-Related Coronaviruses date: 2020-04-06 words: 1217.0 sentences: 94.0 pages: flesch: 59.0 cache: ./cache/cord-265350-k9yus2sv.txt txt: ./txt/cord-265350-k9yus2sv.txt summary: Several recent studies identified SARS-CoV-2-related viruses in Malayan pangolins (Manis javanica), providing new insights into the host distribution and evolution of SARS-CoV-2-related viruses [3] [4] [5] [6] [7] . SARS-CoV and SARS-CoV-2 have been taxonomically classified into a single viral species, Severe acute respiratory syndrome-related coronavirus [8] . Whereas SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), two highly contagious CoVs that emerged in humans during the past two decades, might ultimately have bat origins, both of them were introduced into human populations through intermediate hosts [9] . Phylogenetic analysis based on the synonymous sites of RBD, whose evolution is less likely to be influenced by natural selection, shows that RaTG13 is more closely related to SARS-CoV-2 than are the GD pangolin CoVs (Figure 1B) , indicating that the high amino acid similarity between the GD pangolin CoVs and SARS-CoV-2 in the RBD might be due to convergent evolution [3] . abstract: The pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has posed a severe threat to global public health. Yet, the origin of SARS-CoV-2 remains mysterious. Several recent studies (e.g., Lam et al ., Xiao et al .) identified SARS-CoV-2-related viruses in pangolins, providing novel insights into the evolution and diversity of SARS-CoV-2-related viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32544437/ doi: 10.1016/j.tim.2020.04.001 id: cord-351625-1we9wi1g author: Han, Huan title: Descriptive, Retrospective Study of the Clinical Characteristics of Asymptomatic COVID-19 Patients date: 2020-10-07 words: 4062.0 sentences: 245.0 pages: flesch: 48.0 cache: ./cache/cord-351625-1we9wi1g.txt txt: ./txt/cord-351625-1we9wi1g.txt summary: Since asymptomatic patients may be a greater risk of virus transmission than symptomatic patients, public health interventions and a broader range of testing may be necessary for the control of COVID-19. IMPORTANCE Asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a potential problem for pandemic control through public health strategies. Since asymptomatic patients have no clinical symptoms which can easily prevent timely diagnosis and treatment, they may cause a greater risk of virus transmission than symptomatic patients, which poses a major challenge to infection control. Thus far, many studies have analyzed the clinical characteristics of SARS-CoV-2-infected patients presenting levels of illness ranging from mild to severely critical (10, 11) . In this study, we enrolled 25 asymptomatic and 27 symptomatic COVID-19 patients and performed systematic analysis of different clinical characteristics. In this study, we systematically compared different complete blood counts, serum biochemistries, and immunologic responses from SARS-CoV-2-infected asymptomatic and symptomatic individuals. abstract: Since the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China, it has rapidly spread around the world. Persons with asymptomatic disease exhibit viral shedding, resulting in transmission, which presents disease control challenges. However, the clinical characteristics of these asymptomatic individuals remain elusive. We collected samples of 25 asymptomatic and 27 symptomatic COVID-19 patients. Viral titers of throat swabs were determined by quantitative reverse transcription-PCR (qRT-PCR). COVID-19 IgG and IgM were examined. Complete blood counts were determined, and serum biochemistry panels were performed. Cytokines, including gamma interferon (IFN-γ), tumor necrosis factor alpha (TNF-α), interleukin 2 (IL-2), IL-4, IL-6, and IL-10 were evaluated. T cell, B cell, and NK cell counts were measured using flow cytometry. Although similar viral loads were detected, asymptomatic patients had significantly faster virus turnover than symptomatic patients. Additionally, asymptomatic patients had higher counts of lymphocytes, T cells, B cells, and NK cells. While liver damage was observed in symptomatic patients, as indicated by elevated liver enzymes and decreased liver-synthesized proteins in the blood, asymptomatic patients showed normal liver measurements. Lactate dehydrogenase, a COVID-19 risk factor, was significantly lower in asymptomatic patients. These results suggest that asymptomatic COVID-19 patients had normal clinical indicators and faster viral clearance than symptomatic patients. Lymphocytes may play a role in their asymptomatic phenotype. Since asymptomatic patients may be a greater risk of virus transmission than symptomatic patients, public health interventions and a broader range of testing may be necessary for the control of COVID-19. IMPORTANCE Asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a potential problem for pandemic control through public health strategies. Our results demonstrate that asymptomatic COVID-19 patients have better outcomes than symptomatic patients. This may have been due to more active cellular immune responses and normal liver function. Since asymptomatic patients have no clinical symptoms which can easily prevent timely diagnosis and treatment, they may cause a greater risk of virus transmission than symptomatic patients, which poses a major challenge to infection control. Evidence suggests that nonpharmaceutical public health interventions, like social distancing and face mask ordinances, play important roles in the control of COVID-19. Looking forward, it may be necessary to proceed cautiously while reopening businesses in areas of epidemicity to prevent potential waves of COVID-19 in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/33028689/ doi: 10.1128/msphere.00922-20 id: cord-303941-3lg1bzsi author: Han, Hui-Ju title: Bats as reservoirs of severe emerging infectious diseases date: 2015-07-02 words: 4679.0 sentences: 244.0 pages: flesch: 56.0 cache: ./cache/cord-303941-3lg1bzsi.txt txt: ./txt/cord-303941-3lg1bzsi.txt summary: Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Currently, bats have been considered to be natural reservoirs of SARS-CoV, MERS-CoV, NiV, HeV, Ebola virus, and Marburg viruses. The viruses discussed above tend to be restricted to certain geographic regions with a particular bat reservoir, such as HeV and NiV associated with flying foxes in Australia and Southeast Asia and Ebola virus associated with Egyptian fruit bats in Africa. Bats have been proposed as the natural reservoirs of viruses causing severe diseases in humans, such as NiV and HeV in Southeast Asia and Australia, Ebola and Marburg viruses in Africa, SARS-CoV in Asia and MERS-CoV in Middle East. abstract: Abstract In recent years severe infectious diseases have been constantly emerging, causing panic in the world. Now we know that many of these terrible diseases are caused by viruses originated from bats (Table 1), such as Ebola virus, Marburg, SARS coronavirus (SARS-CoV), MERS coronavirus (MERS-CoV), Nipah virus (NiV) and Hendra virus (HeV). These viruses have co-evolved with bats due to bats’ special social, biological and immunological features. Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Humans may also become infected with viruses through aerosol by intruding into bat roosting caves or via direct contact with bats, such as catching bats or been bitten by bats. url: https://api.elsevier.com/content/article/pii/S016817021500177X doi: 10.1016/j.virusres.2015.05.006 id: cord-344038-20n74z3o author: Han, Mi Seon title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 words: 1548.0 sentences: 110.0 pages: flesch: 67.0 cache: ./cache/cord-344038-20n74z3o.txt txt: ./txt/cord-344038-20n74z3o.txt summary: In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate''s clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother''s respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . abstract: We report changes in viral load over time in a 27-day old neonate with COVID-19 who presented with fever, cough, and vomiting. SARS-CoV-2 RNA was detected in the nasopharynx, oropharynx, stool, saliva, plasma, and urine. The highest viral RNA copies in nasopharynx decreased over time while viral load in stool remained high. url: https://www.ncbi.nlm.nih.gov/pubmed/32297925/ doi: 10.1093/cid/ciaa447 id: cord-301115-sedfbjlw author: Han, Mingfeng title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date: 2020-08-28 words: 4577.0 sentences: 255.0 pages: flesch: 53.0 cache: ./cache/cord-301115-sedfbjlw.txt txt: ./txt/cord-301115-sedfbjlw.txt summary: title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity The results of our analysis demonstrated that the initial SARS-CoV-2 RNA loads varied in patients, but were comparable in different patient groups stratified by age, gender, comorbidities and disease severity. We compared the measured SARS-CoV-2 RNA levels in sputum specimens from COVID-19 patients at admission among groups divided according to age, sex, underlying diseases and disease severity (Fig. 2a) . a, b The measured SARS-CoV-2 RNAs levels in sputum (a) and throat swab (b) specimens from COVID-19 patients at admission were compared according to the age, sex, comorbidity, and the disease severity. In this study, we analyzed the clinical features including SARS-CoV-2 RNA load and immunological characteristics of peripheral blood in a patient cohort with COVID-19 from Anhui Province, China. abstract: The magnitude of SARS-CoV-2 infection, the dynamic changes of immune parameters in patients with the novel coronavirus disease (COVID-19) and their correlation with the disease severity remain unclear. The clinical and laboratory results from 154 confirmed COVID-19 patients were collected. The SARS-CoV-2 RNA levels in patients were estimated using the Ct values of specific RT-PCR tests. The lymphocyte subsets and cytokine profiles in the peripheral blood were analyzed by flow cytometry and specific immunoassays. 154 confirmed COVID-19 patients were clinically examined up to 4 weeks after admission. The initial SARS-CoV-2 RNA Ct values at admission varied, but were comparable in the patient groups classified according to the age, gender, underlying diseases, and disease severity. Three days after admission, significant higher Ct values were found in severe cases. Significantly reduced counts of T cells and T cell subsets were found in patients with old age and underlying diseases at admission and were characteristic for the development of severe COVID-19. Severe COVID-19 developed preferentially in patients with underlying compromised immunity and was not associated with initial virus levels. Higher SARS-CoV-2 RNA levels in severe cases were apparently a result of impaired immune control associated with dysregulation of inflammation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00430-020-00693-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32860073/ doi: 10.1007/s00430-020-00693-z id: cord-255895-6at9gelt author: Han, Namshik title: Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date: 2020-08-25 words: 4736.0 sentences: 269.0 pages: flesch: 52.0 cache: ./cache/cord-255895-6at9gelt.txt txt: ./txt/cord-255895-6at9gelt.txt summary: We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Importantly, treatment of Calu-3 and Vero E6 cell lines with Proguanil and Sulfasalazine led to a significant downregulation of the mRNA of key cytokines (Figures 4G-J and S8), which are dictated by the p38/MAPK signalling pathway and shown to become elevated during SARS-CoV-2 infection and replication (CXCL3, IFNB1 and TNF-A). Here we have used a series of computational approaches, including bespoke methods for data integration, network analysis, computer simulation and machine learning, to identify novel SARS-CoV-2 induced pathways that could be targeted therapeutically by repurposing existing and approved drugs ( Figure S9 ). abstract: The global outbreak of SARS-CoV-2 necessitates the rapid development of new therapies against COVID-19 infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Using artificial neural network analysis we classified these 200 drugs into 9 distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (130) and immune response (70). A subset of drugs implicated in viral replication were tested in cellular assays and two (proguanil and sulfasalazine) were shown to inhibit replication. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials. url: https://doi.org/10.1101/2020.08.24.265496 doi: 10.1101/2020.08.24.265496 id: cord-330849-yt44k88m author: Han, Rachel H. title: Planning for Mental Health Needs During COVID-19 date: 2020-10-08 words: 5521.0 sentences: 262.0 pages: flesch: 39.0 cache: ./cache/cord-330849-yt44k88m.txt txt: ./txt/cord-330849-yt44k88m.txt summary: The purpose of this article, written from the perspective of military medical planners, is to present available data on the prevalence of specific mental health concerns and conditions from previous recent pandemics and COVID-19, as well as to provide data-informed recommendations for meeting the psychological needs of affected individuals. A combination of the following keywords in the title and/or abstract was used in searches of literature on the Southeast Asian Respiratory Syndrome (SARS), H1N1 influenza (H1N1), Middle Eastern Respiratory Syndrome (MERS), Ebola, and COVID-19 pandemics: mental health OR mental illness OR psychiatry OR psychology OR therapist OR PTSD OR posttraumatic OR post-traumatic stress disorder OR behavioral health OR anxiety [disorder] OR GAD OR depression/depressed OR complex grief AND data analysis OR statistic* OR prevalence OR percentage OR increase OR decrease. abstract: PURPOSE OF REVIEW: The ability to effectively prepare for and respond to the psychological fallout from large-scale disasters is a core competency of military mental health providers, as well as civilian emergency response teams. Disaster planning should be situation specific and data driven; vague, broad-spectrum planning can contribute to unprepared mental health teams and underserved patient populations. Herein, we review data on mental health sequelae from the twenty-first century pandemics, including SARS-CoV2 (COVID-19), and offer explanations for observed trends, insights regarding anticipated needs, and recommendations for preliminary planning on how to best allocate limited mental health resources. RECENT FINDINGS: Anxiety and distress, often attributed to isolation, were the most prominent mental health complaints during previous pandemics and with COVID-19. Additionally, post-traumatic stress was surprisingly common and possibly more enduring than depression, insomnia, and alcohol misuse. Predictions regarding COVID-19’s economic impact suggest that depression and suicide rates may increase over time. SUMMARY: Available data suggest that the mental health sequelae of COVID-19 will mirror those of previous pandemics. Clinicians and mental health leaders should focus planning efforts on the negative effects of isolation, particularly anxiety and distress, as well as post-traumatic stress symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/33030637/ doi: 10.1007/s11920-020-01189-6 id: cord-313099-rpdlk1b6 author: Han, Xiaoyu title: Severe Acute Respiratory Syndrome Coronavirus 2 among Asymptomatic Workers Screened for Work Resumption, China date: 2020-09-17 words: 1154.0 sentences: 77.0 pages: flesch: 55.0 cache: ./cache/cord-313099-rpdlk1b6.txt txt: ./txt/cord-313099-rpdlk1b6.txt summary: After the outbreak in Wuhan, China, we assessed 29,299 workers screened for severe acute respiratory syndrome coronavirus 2 by reverse transcription PCR. We noted 18 (0.061%) cases of asymptomatic infection; 13 turned negative within 8.0 days, and 41 close contacts tested negative. A s the population of Wuhan, China, returns to work, asymptomatic cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being discovered among workers receiving health checkups for work resumption. We report on cases of asymptomatic SARS-CoV-2 infection among persons during work resumption screening in Wuhan. Among 29,299 persons screened by RT-PCR, we confirmed 18 (0.061%) cases of SARS-CoV-2 infection. Half the cases in our study showed negative IgM and IgG at the time of positive RT-PCR, suggesting recent infections (<14 days). In addition, 13 cases had negative RT-PCR assays <8 (range 3-14) days, suggesting a favorable prognosis for persons with asymptomatic infections. In addition, all 41 close contacts of the asymptomatic case-patients tested negative by RT-PCR. abstract: After the outbreak in Wuhan, China, we assessed 29,299 workers screened for severe acute respiratory syndrome coronavirus 2 by reverse transcription PCR. We noted 18 (0.061%) cases of asymptomatic infection; 13 turned negative within 8.0 days, and 41 close contacts tested negative. Among 6 contacts who had serologic tests, none were positive. url: https://www.ncbi.nlm.nih.gov/pubmed/32553070/ doi: 10.3201/eid2609.201848 id: cord-323072-4rsgeag7 author: Han, Xueqing title: The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date: 2004-12-01 words: 3741.0 sentences: 185.0 pages: flesch: 54.0 cache: ./cache/cord-323072-4rsgeag7.txt txt: ./txt/cord-323072-4rsgeag7.txt summary: Since the outbreak of SARS in 2003, several laboratory diagnostic methods have been established, including real-time RT-PCR assay, whole-virus-based immunofluorescence assay (IFA), recombinant protein-based enzyme-linked immunosorbent assay (ELISA) and immunochromatographic tests, antigencapturing enzyme-linked immunosorbent assay, and Western blot (WB) assay. To test whether the recombinant M protein is effective as an ELISA antigen for detecting SARS-CoV patient serum, the sera from four healthy people and four SARS patients were used. Detection results of eight human sera by ELISA using purified recombinant M protein as antigen.# 1-4: sera from four healthy people, respectively, # 5-8: sera from four SARS patients, respectively. The results were in complete accordance with those of other assays, thus indicating that the recombinant M protein may be useful as an ELISA antigen for detecting specific antibodies to SARS-CoV in human sera. Recombinant protein-based enzyme-linked imunosorbent assay and immunochromatographic tests for detection of immunoglobulin G antibodies to severe acute respiratory syndrome (SARS) coronavirus in SARS patients abstract: High-level protein expression is an important means of obtaining large amounts of viral proteins to investigate further their biological properties. To express the membrane (M) protein of SARS–CoV at high-level in vitro, the M gene fragment was amplified and cloned it into the Pichia Pastoris expression vector pPICZαA. SDS–PAGE and Western blotting analysis of the induced products of recombinant yeast transformant indicated that successful high-level expression of M protein was achieved, and that the expression product was similar antigenically to the natural protein. Purified recombinant M protein was used subsequently as an ELISA antigen for detection of eight serum samples screened previously by whole virus ELISA and immunofluorescence assay, and consistent results were obtained. These findings suggest that the recombinant M protein may be useful as a diagnostic reagent. url: https://api.elsevier.com/content/article/pii/S0166093404002472 doi: 10.1016/j.jviromet.2004.08.015 id: cord-295142-5sqkdpi8 author: Han, Y. title: The active lung microbiota landscape of COVID-19 patients date: 2020-08-23 words: 3028.0 sentences: 199.0 pages: flesch: 47.0 cache: ./cache/cord-295142-5sqkdpi8.txt txt: ./txt/cord-295142-5sqkdpi8.txt summary: The bronchoalveolar lavage fluid (BALF), containing microenvironment information on bronchioles and lung alveoli from the lower respiratory tract, is one of key sample types for characterizing the host inflammatory response and microbiota of COVID-19 patients as lung is one of main organs for the infection of SARS-CoV-2 (7, 8) . In this study, we systematically profiled the transcriptionally active microbiota landscape in BALF from COVID-19 patients and healthy individuals, identified microorganism composition in healthy individuals and COVID-19 patients, found disease-specific active microbes in the COVID-19 patient group, revealed the interaction between several bacteria or viruses and SARS-CoV-2. The diversity analysis revealed that the infection of SARS-CoV-2 probably caused a different lung microbiota composition in the COVID-19 patient group compared with the healthy group. Our study provides insight into the active microbiota in the lungs of COVID-19 patients and will contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. abstract: With the outbreak of COVID-19 causing by SARS-CoV-2, the interaction between the host and SARS-CoV-2 was widely studied. However, it is unclear whether and how SARS-CoV-2 infection affects lung microflora, which contributes to COVID-19 complications. Here, we analyzed the metatranscriptomic data of bronchoalveolar lavage fluid (BALF) of 19 COVID-19 patients and 23 healthy controls from 6 independent projects and detailed the active microbiota landscape in both healthy individuals and COVID-19 patients. The infection of SARS-CoV-2 could deeply change the lung microbiota, evidenced by the -diversity, {beta}-diversity and species composition analysis based on bacterial microbiota and virome. Pathogens (such as Klebsiella oxytoca causing pneumonia as well), immunomodulatory probiotics (such as Lactic Acid Bacteria and Faecalibacterium prausnitzii, a butyrate producer) and Tobacco mosaic virus (TMV) were enriched in the COVID-19 group, suggesting a severe microbiota dysbiosis. The significant correlation between Rothia mucilaginosa, TMV and SARS-CoV-2 revealed drastic inflammatory battles between the host, SARS-CoV-2 and other microbes in the lungs. Notably, TMV only existed in the COVID-19 group, while Human respirovirus 3 only existed in the healthy group. Our study provides insight into the active microbiota in the lungs of COVID-19 patients and will contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. url: http://medrxiv.org/cgi/content/short/2020.08.20.20144014v1?rss=1 doi: 10.1101/2020.08.20.20144014 id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 words: 5268.0 sentences: 330.0 pages: flesch: 48.0 cache: ./cache/cord-354536-c9v9kbw8.txt txt: ./txt/cord-354536-c9v9kbw8.txt summary: This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. abstract: Since the end of 2019, a new type of coronavirus pneumonia (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading rapidly throughout the world. Previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32714083/ doi: 10.7150/ijms.47836 id: cord-277870-o79wph9r author: Han, Yanqiang title: Potential inhibitors for the novel coronavirus (SARS-CoV-2) date: 2020-09-18 words: 3814.0 sentences: 171.0 pages: flesch: 45.0 cache: ./cache/cord-277870-o79wph9r.txt txt: ./txt/cord-277870-o79wph9r.txt summary: In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. In this study, we chose 3CL Mpro as the therapeutic target to ab initio investigate its inhibition mechanism and binding ability of these most promising drug molecules by ligand-protein docking program (Rosetta) and molecular dynamics (MD) simulations. Through molecular docking and kinetic analysis, we found that for repurposed drugs, the Chloroquine molecule has the strongest interaction with the 3CL Mpro, indicating that Chloroquine is the best potential inhibitor for SARS-CoV-2, followed by Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir. For docking and binding analysis, seven clinically approved inhibitors (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) were selected from previous reported virtual screening works or were found to be highly effective in the control of SARS-CoV-2 infection in vitro [6, 12] . abstract: The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition. url: https://doi.org/10.1093/bib/bbaa209 doi: 10.1093/bib/bbaa209 id: cord-319590-f9qcabcx author: Han, Yanxiao title: Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date: 2020-04-14 words: 2768.0 sentences: 176.0 pages: flesch: 58.0 cache: ./cache/cord-319590-f9qcabcx.txt txt: ./txt/cord-319590-f9qcabcx.txt summary: Molecular dynamics simulations revealed that the α-helical peptides maintain their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. 17 In this work, we design and simulate several peptide inhibitors against SARS-CoV-2, which included components from the virus-binding domains of ACE2; based on the recently released crystal structure (PDB code: 6M17 9 ). We have also designed other inhibitors that are closer to the ACE2 protein, whose parts are connected by peptide bonds, and which contain all 15 residues that initially bind to RBD in the 6M17 crystal structure. To examine how these potential inhibitors bind to RBD of SARS-CoV-2, we prepared these systems in the initial position known from the crystal structure (PDB: 6M17) and simulated them in physiological solution (Methods), as shown in Figure 2a −d. In Figure 2a , 200 ns long simulations showed that the helical structure of inhibitor 1 deforms from the left sideloose end unfolding, although it still binds to the RBD of SARS-CoV-2. abstract: [Image: see text] Peptide inhibitors against the SARS-CoV-2 coronavirus, currently causing a worldwide pandemic, are designed and simulated. The inhibitors are mostly formed by two sequential self-supporting α-helices (bundle) extracted from the protease domain (PD) of angiotensin-converting enzyme 2 (ACE2), which bind to the SARS-CoV-2 receptor binding domains. Molecular dynamics simulations revealed that the α-helical peptides maintain their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. To provide a multivalent binding to the SARS-CoV-2 receptors, many such peptides could be attached to the surfaces of nanoparticle carriers. The proposed peptide inhibitors could provide simple and efficient therapeutics against the COVID-19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32286790/ doi: 10.1021/acsnano.0c02857 id: cord-271211-frkk6w0a author: Han, Yu title: The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID‐19): A Chinese perspective date: 2020-03-12 words: 2110.0 sentences: 139.0 pages: flesch: 55.0 cache: ./cache/cord-271211-frkk6w0a.txt txt: ./txt/cord-271211-frkk6w0a.txt summary: The Chinese government has taken emergency measures to control the outbreak and has undertaken initial steps in the diagnosis and treatment of 2019 novel coronavirus infection disease (COVID‐19). A study in South Korea showed that many environmental surfaces of patients with MERS were contaminated by MERS-CoV, and virus RNA was detected from environmental surfaces within 5 days after the last positive PCR of patients'' respiratory samples. 12 Guangzhou CDC also found SARS-CoV-2 in the house of a confirmed patient, 13 which serves as evidence of contact transmission. 20 The Lancet also reminded doctors not to ignore SARS-CoV-2 transmission via ocular surfaces as infected droplets and bodily fluids may easily contaminate the human conjunctival epithelium. 27 A study showed that during the outbreak of SARS-CoV, of all exposed health care workers, 7.5% were asymptomatic SARSpositive cases. SARS-CoV-2 viral load in upper respiratory specimens of infected patients abstract: 2019 novel coronavirus (SARS‐CoV‐2), which originated in Wuhan, China, has attracted the world's attention over the last month. The Chinese government has taken emergency measures to control the outbreak and has undertaken initial steps in the diagnosis and treatment of 2019 novel coronavirus infection disease (COVID‐19). However, SARS‐CoV‐2 possesses powerful pathogenicity as well as transmissibility and still holds many mysteries that are yet to be solved, such as whether the virus can be transmitted by asymptomatic patients or by mothers to their infants. Our research presents selected available cases of COVID‐19 in China to better understand the transmission and diagnosis regarding this infectious disease. url: https://doi.org/10.1002/jmv.25749 doi: 10.1002/jmv.25749 id: cord-284366-snajbvr9 author: Han, Zhiyong title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 words: 2017.0 sentences: 133.0 pages: flesch: 61.0 cache: ./cache/cord-284366-snajbvr9.txt txt: ./txt/cord-284366-snajbvr9.txt summary: [3] [4] [5] The diagnosis of COVID-19 considers clinical symptoms, GGO lesions in chest CT or Xray images, and positive RT-PCR test results for the presence of SARS-CoV-2 RNA in patient samples. For example, the guidelines of the National Health Commission of China state that patients must meet the following 4 benchmarks before they can be discharged: (i) be afebrile for at least 3 consecutive days, (ii) have significantly improved respiratory function, (iii) produce two negative SARS-CoV-2 RT-PCR test results at least 24 hours apart, and (iv) have significant improvement in lung GGO lesions determined by chest CT or X-ray imaging. In Table 1 , we summarize the information about patients who tested positive for SARS-CoV-2 RNA in post-discharge, follow-up examinations in China as described in the 12 published reports. Our analysis indicates that many of the discharged patients tested positive for SARS-CoV-2 RNA when feces or anal swabs were employed, even though they tested negative at the same time when nasopharyngeal or oropharyngeal or sputum samples were examined. abstract: In the ongoing COVID‐19 pandemic, one potential cause of concern is that some discharged COVID‐19 patients are testing positive again for SARS‐CoV‐2 RNA. To better understand what is happening and to provide public health policy planners and clinicians timely information, we have searched and reviewed published studies about discharged patients testing positive again for the SARS‐CoV‐2 RNA. Our search found 12 reports, all of which described patients in China. Our review of these reports indicates the presence of discharged patients who remain asymptomatic but test positive. However, it is unclear whether they are contagious because a positive RT‐PCR test does not necessarily indicate the presence of replicating and transmissible virus. Our review suggests the need for timely, parallel testing of different samples, including for example, fecal specimens, from COVID‐19 patients before and after they are discharged from hospitals. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26250 doi: 10.1002/jmv.26250 id: cord-304016-4o2bpedp author: Hanage, William P. title: COVID-19: US federal accountability for entry, spread, and inequities—lessons for the future date: 2020-11-02 words: 5701.0 sentences: 249.0 pages: flesch: 49.0 cache: ./cache/cord-304016-4o2bpedp.txt txt: ./txt/cord-304016-4o2bpedp.txt summary: In this article we assess the impact of missteps by the Federal Government in three specific areas: the introduction of the virus to the US and the establishment of community transmission; the lack of national COVID-19 workplace standards and enforcement, and lack of personal protective equipment (PPE) for workplaces as represented by complaints to the Occupational Safety and Health Administration (OSHA) which we find are correlated with deaths 16 days later (ρ = 0.83); and the total excess deaths in 2020 to date already total more than 230,000, while COVID-19 mortality rates exhibit severe—and rising—inequities in race/ethnicity, including among working age adults. Finally, despite the initial federal failure to report COVID-19 data by race/ethnicity [6] , a combination of specific studies, state reporting, investigative journalism, and data trackers has revealed that a persistent feature of the pandemic has been the existence of racial/ethnic inequities in cases, hospitalizations, and mortality, especially with regard to increased risk among US Black, Latinx, and American Indian/Alaska Native populations compared to the US white non-Hispanic population [3-5, 7, 8, 69, 70] . abstract: The United States (US) has been among those nations most severely affected by the first—and subsequent—phases of the pandemic of COVID-19, the disease caused by SARS-CoV-2. With only 4% of the worldwide population, the US has seen about 22% of COVID-19 deaths. Despite formidable advantages in resources and expertise, presently the per capita mortality rate is over 585/million, respectively 2.4 and 5 times higher compared to Canada and Germany. As we enter Fall 2020, the US is enduring ongoing outbreaks across large regions of the country. Moreover, within the US, an early and persistent feature of the pandemic has been the disproportionate impact on populations already made vulnerable by racism and dangerous jobs, inadequate wages, and unaffordable housing, and this is true for both the headline public health threat and the additional disastrous economic impacts. In this article we assess the impact of missteps by the Federal Government in three specific areas: the introduction of the virus to the US and the establishment of community transmission; the lack of national COVID-19 workplace standards and enforcement, and lack of personal protective equipment (PPE) for workplaces as represented by complaints to the Occupational Safety and Health Administration (OSHA) which we find are correlated with deaths 16 days later (ρ = 0.83); and the total excess deaths in 2020 to date already total more than 230,000, while COVID-19 mortality rates exhibit severe—and rising—inequities in race/ethnicity, including among working age adults. url: https://www.ncbi.nlm.nih.gov/pubmed/33136249/ doi: 10.1007/s10654-020-00689-2 id: cord-333264-jdvb8px4 author: Hanke, Leo title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date: 2020-09-04 words: 6380.0 sentences: 380.0 pages: flesch: 51.0 cache: ./cache/cord-333264-jdvb8px4.txt txt: ./txt/cord-333264-jdvb8px4.txt summary: Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. The S ectodomain was purified from filtered supernatant on Streptactin XT resin (IBA Lifesciences), followed by size-exclusion chromatography on a Superdex 200 in 5 mM Tris pH 8, 200 mM NaCl. The RBD domain (RVQ-VNF) of SARS-CoV-2 was cloned upstream of an enterokinase cleavage site and a human IgG1 Fc. This plasmid was used to transiently transfect FreeStyle 293F cells using the FreeStyle MAX reagent. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 abstract: SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the ‘up’ and ‘down’ conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32887876/ doi: 10.1038/s41467-020-18174-5 id: cord-171703-n22tr8f2 author: Hanmo, Li title: Robust estimation of SARS-CoV-2 epidemic at US counties date: 2020-10-22 words: 13227.0 sentences: 452.0 pages: flesch: 65.0 cache: ./cache/cord-171703-n22tr8f2.txt txt: ./txt/cord-171703-n22tr8f2.txt summary: In this work, we propose a robust approach of integrating test data and death toll to estimate COVID-19 transmission characteristics by a Susceptible, Infectious, Resolving (but not infectious), Deceased and reCovered (SIRDC) model initially studied in 7 . We have developed a novel approach to integrate test data and death toll to estimate probability of contracting COVID-19, as well as the time-dependent transmission rate and the number of active infectious individuals at the county level in the US. Furthermore, when we reduce the infectious period by 10% (or equivalently 4.5 days in total), while the transmission rate (β t in SIRDC model) is held the same, the PoC SARS-CoV-2 is reduced by 5 times for 26 counties in Washington and 146 counties in Texas, shown in Extended Data Figure 4 . abstract: The COVID-19 outbreak is asynchronous at US counties. Mitigating the COVID-19 transmission requires not only the state and federal level order of protection measures such as social distancing and testing, but also public's awareness of the time-dependent risk and reactions at county and community levels. We propose a robust approach to estimate the heterogeneous progression of SARS-CoV-2 at all US counties having no less than 2 COVID-19 associated deaths, and we develop the daily probability of contracting (PoC) SARS-CoV-2 for a susceptible individual to quantify the risk of SARS-CoV-2 transmission in community. We found that shortening only $5%$ of the infectious period of SARS-CoV-2 can reduce around $39%$ (or $78$K, $95%$ CI: $[66$K $, 89$K $]$) of the COVID-19 associated deaths in the US as of 20 September 2020. Our findings also indicate that the reduction of infection and deaths by shortened infectious period is more pronounced for areas with the effective reproduction number close to 1, suggesting that testing should be used along with other mitigation measures, such as social distancing and facial mask wearing, to reduce the transmission rate. Our deliverable includes a dynamic county-level map for local officials to determine optimal policy responses, and for public to better understand the risk of contracting SARS-CoV-2 on each day. url: https://arxiv.org/pdf/2010.11514v1.pdf doi: nan id: cord-338541-0yiuh017 author: Hannan, Md. Abdul title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response date: 2020-07-10 words: 4302.0 sentences: 244.0 pages: flesch: 42.0 cache: ./cache/cord-338541-0yiuh017.txt txt: ./txt/cord-338541-0yiuh017.txt summary: title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response As a healthy practice, calorie restriction in the form of intermittent fasting (IF) in several clinical settings has been reported to promote several health benefits, including priming of the immune response. A comprehensive review has therefore been planned to highlight the beneficial role of fasting in immunity and autophagy, that underlie the possible defense against SARS-CoV-2 infection. In this review, we revisit the current knowledge of fasting as a possible important mediator that is involved in the diverse pathophysiological phenomena, including host immune response, autophagy, and the pathogenesis of SARS-CoV-2 infection. During adaptive immunity, autophagy plays an important role in major histocompatibility complex (MHC)-antigen presentation, lymphocyte development, thymic selection, inflammatory signaling, and cytokine regulation [10] . abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative pathogen of deadly Coronavirus disease-19 (COVID-19) pandemic, which emerged as a major threat to public health across the world. Although there is no clear gender or socioeconomic discrimination in the incidence of COVID-19, individuals who are older adults and/or with comorbidities and compromised immunity have a relatively higher risk of contracting this disease. Since no specific drug has yet been discovered, strengthening immunity along with maintaining a healthy living is the best way to survive this disease. As a healthy practice, calorie restriction in the form of intermittent fasting (IF) in several clinical settings has been reported to promote several health benefits, including priming of the immune response. This dietary restriction also activates autophagy, a cell surveillance system that boosts up immunity. With these prevailing significance in priming host defense, IF could be a potential strategy amid this outbreak to fighting off SARS-CoV-2 infection. Currently, no review so far available proposing IF as an encouraging strategy in the prevention of COVID-19. A comprehensive review has therefore been planned to highlight the beneficial role of fasting in immunity and autophagy, that underlie the possible defense against SARS-CoV-2 infection. The COVID-19 pathogenesis and its impact on host immune response have also been briefly outlined. This review aimed at revisiting the immunomodulatory potential of IF that may constitute a promising preventive approach against COVID-19. url: https://api.elsevier.com/content/article/pii/S0165247820303497 doi: 10.1016/j.imlet.2020.07.001 id: cord-269564-r5mmsnbx author: Hans, Diana title: Rapidly Fatal Infections date: 2008-05-31 words: 7549.0 sentences: 426.0 pages: flesch: 46.0 cache: ./cache/cord-269564-r5mmsnbx.txt txt: ./txt/cord-269564-r5mmsnbx.txt summary: Reports have suggested a mortality rate of 30% to 70% despite aggressive treatment [35] TSS is most commonly caused by Staphylococcus aureus and group A streptococcus. Unfortunately, complicated group A streptococcus infections are shown to have a high mortality rate despite aggressive antibiotic therapy, and penicillin has been shown to have limited effects if not initiated early in the disease. Fifty-three percent of the patients were positive for MRSA, and the risk factors associated with colonization included recent antibiotic use (within 3 months), hospitalization within the past year, skin or soft tissue infection on admission, and HIV infection [68] . PVL-positive S aureus pneumonia typically occurred in younger patients (median age, 14.8 years) who were previously healthy, and 75% were found to have had a viral infection in the preceding days. Two deadly viral infections that have emerged in recent years include severe acute respiratory syndrome (SARS) and influenza A (H5N1), also known as avian influenza or bird flu. abstract: Emergency physicians are trained to separate “sick” from “not sick” patients during their training. Nevertheless, every emergency physician will face situations in which early intervention is critical to their patient's outcome. Infectious diseases are responsible for many of these potentially poor outcomes. This article discusses early identification and treatment for several rapidly fatal infections, including two newly identified travel-related illnesses. url: https://www.sciencedirect.com/science/article/pii/S0733862708000047 doi: 10.1016/j.emc.2008.01.003 id: cord-343185-lbmbp9ca author: Hansen, C. B. title: SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals date: 2020-07-29 words: 5349.0 sentences: 332.0 pages: flesch: 51.0 cache: ./cache/cord-343185-lbmbp9ca.txt txt: ./txt/cord-343185-lbmbp9ca.txt summary: Here we have developed novel flexible ELISA-based assays for specific detection of SARS-CoV-2 antibodies against the receptor-binding domain (RBD): An antigen sandwich-ELISA relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Detection of IgM, IgA and IgG antibodies against SARS-CoV-2 protein N was evaluated by analyzing 136 positive samples and 174 negative controls and ROC curve analyses were assessed to estimate the assay performance . To provide a better insight into antibody seroconversion during SARS-CoV-2 infection and reactivity against different locations on protein S and protein N, we conducted IgM, IgA and IgG detection in 90 positive samples against 14 protein fragments and short peptides located on the protein S and protein N structures, full-length RBD, protein S and protein N (Figure 2A ). We have developed an ELISA-based platform for detection SARS-CoV-2 antibodies comprising an indirect RBD S-ELISA for pan Ig detection and direct ELISAs for in-depth analyses of the IgM, IgA and IgG isotype responses towards RBD and protein N. abstract: Globally, the COVID-19 pandemic has had extreme consequences for the healthcare system and calls for diagnostic tools to monitor and understand the transmission, pathogenesis and epidemiology, as well as to evaluate future vaccination strategies. Here we have developed novel flexible ELISA-based assays for specific detection of SARS-CoV-2 antibodies against the receptor-binding domain (RBD): An antigen sandwich-ELISA relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Their performance was evaluated in a cohort of 350 convalescent participants with previous COVID-19 infection, ranging from asymptomatic to critical cases. We mapped the antibody responses to different areas on protein N and S and showed that the IgM, A and G antibody responses against RBD are significantly correlated to the disease severity. These assays-and the data generated from them-are highly relevant for diagnostics and prognostics and contribute to the understanding of long-term COVID-19 immunity. url: http://medrxiv.org/cgi/content/short/2020.07.27.20162321v1?rss=1 doi: 10.1101/2020.07.27.20162321 id: cord-320158-6dh9e5rg author: Hansen, Richard title: Adaptations to the current ECCO/ESPGHAN guidelines on the management of paediatric acute severe colitis in the context of the COVID-19 pandemic: a RAND appropriateness panel date: 2020-09-01 words: 5593.0 sentences: 284.0 pages: flesch: 37.0 cache: ./cache/cord-320158-6dh9e5rg.txt txt: ./txt/cord-320158-6dh9e5rg.txt summary: CONCLUSION: Our COVID-19-specific adaptations to paediatric ASC guidelines using a RAND panel generally support existing recommendations, particularly the use of corticosteroids and escalation to infliximab, irrespective of SARS-CoV-2 status. [10] [11] [12] Panellists rated the appropriateness of specific interventions at various time points during a patient''s admission with ASC (admission, first-line therapy, rescue therapy, continued medical therapy on discharge and surgery) in the context of their SARS-CoV-2 swab status and the presence or absence of symptoms or signs of COVID-19 infection. After the second round of voting, agreement was present for all scenarios (DI<1) except two, both relating to SARS-CoV-2positive patients with symptoms or signs of infection; the use of ciclosporin with corticosteroids as rescue therapy and the use of prophylactic anticoagulation after discharge A detailed list of all scenarios, complete with median score, appropriateness rating and DI is shown in online supplementary table 2. abstract: OBJECTIVE: Paediatric acute severe colitis (ASC) management during the novel SARS-CoV-2/COVID-19 pandemic is challenging due to reliance on immunosuppression and the potential for surgery. We aimed to provide COVID-19-specific guidance using the European Crohn’s and Colitis Organisation/European Society for Paediatric Gastroenterology, Hepatology and Nutrition guidelines for comparison. DESIGN: We convened a RAND appropriateness panel comprising 14 paediatric gastroenterologists and paediatric experts in surgery, rheumatology, respiratory and infectious diseases. Panellists rated the appropriateness of interventions for ASC in the context of the COVID-19 pandemic. Results were discussed at a moderated meeting prior to a second survey. RESULTS: Panellists recommended patients with ASC have a SARS-CoV-2 swab and expedited biological screening on admission and should be isolated. A positive swab should trigger discussion with a COVID-19 specialist. Sigmoidoscopy was recommended prior to escalation to second-line therapy or colectomy. Methylprednisolone was considered appropriate first-line management in all, including those with symptomatic COVID-19. Thromboprophylaxis was also recommended in all. In patients requiring second-line therapy, infliximab was considered appropriate irrespective of SARS-CoV-2 status. Delaying colectomy due to SARS-CoV-2 infection was considered inappropriate. Corticosteroid tapering over 8–10 weeks was deemed appropriate for all. After successful corticosteroid rescue, thiopurine maintenance was rated appropriate in patients with negative SARS-CoV-2 swab and asymptomatic patients with positive swab but uncertain in symptomatic COVID-19. CONCLUSION: Our COVID-19-specific adaptations to paediatric ASC guidelines using a RAND panel generally support existing recommendations, particularly the use of corticosteroids and escalation to infliximab, irrespective of SARS-CoV-2 status. Consideration of routine prophylactic anticoagulation was recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/32873696/ doi: 10.1136/gutjnl-2020-322449 id: cord-296054-s8pibdeg author: Hanson, K. E. title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 date: 2020-10-21 words: 2452.0 sentences: 125.0 pages: flesch: 51.0 cache: ./cache/cord-296054-s8pibdeg.txt txt: ./txt/cord-296054-s8pibdeg.txt summary: title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 We prospectively compared health care worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of coronavirus disease 2019 (COVID-19) in 354 patients. More cases were detected by the use of NPS (n = 80) and saliva (n = 81) than by the use of ANS (n = 70), but no single specimen type detected all severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Larger studies that compare the performance of patient self-collected ANS and straight saliva to health care worker-collected NPS for SARS-CoV-2 detection are needed. Therefore, we performed a prospective comparative study to evaluate the performance of patient self-collected ANS and saliva versus that of health care providercollected NPS for SARS-CoV-2 diagnostic testing. This study represents one of the largest prospective comparisons of specimen types to date and demonstrates excellent agreement between provider-collected NPS and patient self-collected saliva and ANS. abstract: We prospectively compared health care worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of coronavirus disease 2019 (COVID-19) in 354 patients. The percent positive agreement between NPS and ANS or saliva was 86.3% (95% confidence interval [CI], 76.7 to 92.9%) and 93.8% (95% CI, 86.0 to 97.9%), respectively. The percent negative agreement was 99.6% (95% CI, 98.0 to 100.0%) for NPS versus ANS and 97.8% (95% CI, 95.3 to 99.2%) for NPS versus saliva. More cases were detected by the use of NPS (n = 80) and saliva (n = 81) than by the use of ANS (n = 70), but no single specimen type detected all severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32817233/ doi: 10.1128/jcm.01824-20 id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 words: 10179.0 sentences: 681.0 pages: flesch: 47.0 cache: ./cache/cord-296588-q2716lda.txt txt: ./txt/cord-296588-q2716lda.txt summary: OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. abstract: BACKGROUND: Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE: The IDSA’s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings, and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS: IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS: The panel agreed on 15 diagnostic recommendations. CONCLUSIONS: Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered low to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32556191/ doi: 10.1093/cid/ciaa760 id: cord-337973-djqzgc1k author: Hao, Siyuan title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date: 2020-08-28 words: 2624.0 sentences: 166.0 pages: flesch: 54.0 cache: ./cache/cord-337973-djqzgc1k.txt txt: ./txt/cord-337973-djqzgc1k.txt summary: title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Our observation that SARS-CoV-2 was unable to infect epithelial cells from the 299 basolateral side supports that the viral entry receptor ACE2 is polarly expressed at the apical 300 side 30, 31 . We 332 determined that 1 pfu of SARS-CoV-2 in Vero-E6 cells has a particle (viral genome copy) 333 number of 820, suggesting that a load of 2.46 x 10 5 particles is required to productively infect 1 334 cm 2 of the airway epithelium, which is much higher than the small DNA virus parvovirus human 335 bocavirus 1 (HBoV1) we studied 55 . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates throughout human airways. The polarized human airway epithelium (HAE) cultured at an airway-liquid interface (HAE-ALI) is an in vitro model mimicking the in vivo human mucociliary airway epithelium and supports the replication of SARS-CoV-2. However, previous studies only characterized short-period SARS-CoV-2 infection in HAE. In this study, continuously monitoring the SARS-CoV-2 infection in HAE-ALI cultures for a long period of up to 51 days revealed that SARS-CoV-2 infection was long lasting with recurrent replication peaks appearing between an interval of approximately 7-10 days, which was consistent in all the tested HAE-ALI cultures derived from 4 lung bronchi of independent donors. We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Notably, virus infection immediately damaged the HAE, which is demonstrated by dispersed Zonula occludens-1 (ZO-1) expression without clear tight junctions and partial loss of cilia. Importantly, we identified that SARS-CoV-2 productive infection of HAE requires a high viral load of 2.5 × 105 virions per cm2 of epithelium. Thus, our studies highlight the importance of a high viral load and that epithelial renewal initiates and maintains a recurrent infection of HAE with SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32869024/ doi: 10.1101/2020.08.27.271130 id: cord-307811-6e3j0pn7 author: Hao, Wei title: Binding of the SARS-CoV-2 Spike Protein to Glycans date: 2020-07-02 words: 5665.0 sentences: 299.0 pages: flesch: 54.0 cache: ./cache/cord-307811-6e3j0pn7.txt txt: ./txt/cord-307811-6e3j0pn7.txt summary: Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. Previous studies of many other viruses suggested that SARS-CoV-2 S protein may use other molecules on host cell surface as attachment factors to facilitate binding to the high-affinity receptor ACE2. 36 A recent study suggested that HS may bind to the receptor binding domain (RBD, the C-terminal region of the S1 subunit, Fig. 2 ) of the SARS-CoV-2 spike protein and change its conformation. 38 In this study, we systematically examined and compared the binding of the SARS-CoV-2 S protein subunits, full-length molecule and its trimer to different HS using microarray experiments (Fig. 2) . In addition to binding protein-based receptors, many viruses can interact with cell surface glycans, including GAGs and sialic acid-containing oligosaccharides. abstract: The pandemic of SARS-CoV-2 has caused a high number of deaths in the world. To combat it, it is necessary to develop a better understanding of how the virus infects host cells. Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. In this study, we examined and compared the binding of the subunits and spike (S) proteins of SARS-CoV-2 and SARS-CoV, MERS-CoV to these glycans. Our results revealed that the S proteins and subunits can bind to HS in a sulfation-dependent manner, the length of HS is not a critical factor for the binding, and no binding with sialic acid residues was detected. Overall, this work suggests that HS binding may be a general mechanism for the attachment of these coronaviruses to host cells, and supports the potential importance of HS in infection and in the development of antiviral agents against these viruses. url: https://doi.org/10.1101/2020.05.17.100537 doi: 10.1101/2020.05.17.100537 id: cord-297941-7yut9vt4 author: Haq, M. title: Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan date: 2020-09-30 words: 2709.0 sentences: 210.0 pages: flesch: 61.0 cache: ./cache/cord-297941-7yut9vt4.txt txt: ./txt/cord-297941-7yut9vt4.txt summary: In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV2 antibodies and the risk factors of COVID 19 in healthcare-workers but little is known from developing countries. Methods: This cross-sectional study was conducted on prevalence of SARS CoV2 antibody and risk factors for seropositivity in HCWs in tertiary care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan. To our knowledge this is the first study of assessing SARS-CoV-2 antibodies of HCWs form both public and private tertiary care hospitals in Peshawar, Pakistan. To our knowledge this is the first study on prevalence of SARS CoV-2 antibodies in HCW of tertiary care hospitals in Pakistan. The risk of becoming positive for SARS-CoV-2 antibodies did not increase with history of direct contact with COVID patients within or outside the hospital. abstract: Background: High number of SARS CoV2 infected patients has overburdened healthcare delivery system, particularly in low-income countries. In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV2 antibodies and the risk factors of COVID 19 in healthcare-workers but little is known from developing countries. Methods: This cross-sectional study was conducted on prevalence of SARS CoV2 antibody and risk factors for seropositivity in HCWs in tertiary care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan. Findings: The overall seroprevalence of SARS CoV2 antibodies was 30.7% (CI, 27.8 to 33.6) in 1011 HCWs. Laboratory technicians had the highest seropositivity (50.0%, CI, 31.8 to 68.1). Risk analysis revealed that wearing face-mask and observing social-distancing within a family could reduce the risk (OR:0.67. p<0.05) and (OR:0.73. p<0.05) while the odds of seropositivity were higher among those attending funeral and visiting local-markets (OR:1.83. p<0.05) and (OR:1.66. p<0.01). In Univariable analysis, being a nursing staff and a paramedical staff led to higher risk of seropositivity (OR:1.58. p< 0.05), (OR:1.79. p< 0.05). Fever (OR:2.36, CI, 1.52 to 3.68) and loss of smell (OR:2.95, CI: 1.46 to 5.98) were significantly associated with increased risk of seropositivity (p<0.01). Among the seropositive HCWs, 165 (53.2%) had no symptoms at all while 145 (46.8%) had one or more symptoms. Interpretation: The high prevalence of SARS CoV2 antibodies in HCWs warrants for better training and use of protective measure to reduce their risk. Early detection of asymptomatic HCWs may be of special importance because they are likely to be potential threat to others during the active phase of viremia. Funding: Prime Foundation Pakistan. url: https://doi.org/10.1101/2020.09.29.20203125 doi: 10.1101/2020.09.29.20203125 id: cord-293564-6xtg8uqt author: Hara, Tasuku title: Infection risk in a gastroenterological ward during a nosocomial COVID‐19 infection event date: 2020-04-22 words: 453.0 sentences: 35.0 pages: flesch: 48.0 cache: ./cache/cord-293564-6xtg8uqt.txt txt: ./txt/cord-293564-6xtg8uqt.txt summary: A case of presumably nosocomial COVID‐19 was detected in the gastroenterological ward; however, appropriate precautions against contact and droplet prevented a subsequent infection cluster. To assess the risk of COVID-19 infection, the exposure-risk category and underlying conditions and their relationship with a positive PCR result were examined. Exposure-risk categories, which is based on whether patients and healthcare professionals use personal protective equipment, were assessed using Interim U.S. Guidance for Risk The basic reproduction number (R0: the number of people a single patient is expected to infect) for COVID-19 is estimated at 2.2 (1.4-3.9). 6,7 Therefore, the CCI was used in this study to assess the risk conferred by underlying diseases for COVID-19. No patient in the low-exposure risk category or with high-risk underlying conditions was infected with SARS-CoV-2 at this hospital. The authors thank all members of the Department of Gastroenterology and Hepatology, Fukuchiyama City Hospital. abstract: The coronavirus disease (COVID‐19) first emerged in Wuhan, China, in December 2019 and rapidly infected a large number of individuals, and disease clusters have spread worldwide. A case of presumably nosocomial COVID‐19 was detected in the gastroenterological ward; however, appropriate precautions against contact and droplet prevented a subsequent infection cluster. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25853 doi: 10.1002/jmv.25853 id: cord-264772-v3a2qmj5 author: Harada, Kouji H. title: Letter to the Editor on “An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)”, Back to Basics date: 2020-06-18 words: 509.0 sentences: 37.0 pages: flesch: 48.0 cache: ./cache/cord-264772-v3a2qmj5.txt txt: ./txt/cord-264772-v3a2qmj5.txt summary: authors: Harada, Kouji H.; Harada Sassa, Mariko; Yamamoto, Naomichi Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)" highlights an imperative need for research on SARS-CoV-2 in environmental sciences. Here we highlight research showing the importance of basic sanitations to control the spread of infectious diseases applicable to the prevention of COVID-19. 4 The aerosol transmission route for SARS-CoV-2 in aerosols 5 means effective ventilation, including both natural and mechanical ventilation, is an important, easy and basic way to reduce risk of transmission. 8 A case study of the nosocomial spread of SARS in a Vietnam hospital with 33 SARS patients during the 2003 SARS outbreak demonstrated the effectiveness of face masks, gloves, hand sanitizer, and cross-ventilation in the hospital in reducing cross-infection rates. Although comparisons of the cost-effectiveness of basic versus advanced technologies are not yet available, COVID-19 cases in low-and middle-income countries are rapidly rising. abstract: nan url: https://doi.org/10.1021/acs.est.0c02850 doi: 10.1021/acs.est.0c02850 id: cord-259968-cr3zf4oa author: Harb, Roa title: Evaluation of Three Commercial Automated Assays for the Detection of anti-SARS-CoV-2 Antibodies date: 2020-08-06 words: 255.0 sentences: 29.0 pages: flesch: 49.0 cache: ./cache/cord-259968-cr3zf4oa.txt txt: ./txt/cord-259968-cr3zf4oa.txt summary: key: cord-259968-cr3zf4oa cord_uid: cr3zf4oa The Diasorin assay detects IgG antibodies to the S1 and S2 subunits of the spike protein and the signal is expressed in arbitrary units (AU/mL). The Roche assay detects total antibodies to the nucleocapsid protein and the signal is reported as a cutoff index (COI). Cutoffs for positive samples by the Abbott, Diasorin, and Roche assays are ≥ 1.4, ≥ 15 AU/mL, and ≥ 1.0 COI, respectively. Clinical performance of the roche sars-cov-2 serologic assay Clinical performance of the elecsys electrochemiluminescent immunoassay for the detection of sars-cov-2 total antibodies Performance characteristics of four high-throughput immunoassays for detection of igg antibodies against sars-cov-2 Middle, values for Diasorin SARS-CoV-2 IgG for expected negative (n=344) and expected positive (n=65) specimens. Right, values for Roche SARS-CoV-2 total antibodies for expected negative (n=141) and expected positive (n=65) specimens. B) Distribution of anti-SARS-CoV-2 antibody results in expected positive specimens at 0-11 (n=12) abstract: nan url: https://doi.org/10.1093/clinchem/hvaa193 doi: 10.1093/clinchem/hvaa193 id: cord-329944-ywusapij author: Harbourt, D. title: Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing date: 2020-07-03 words: 2103.0 sentences: 150.0 pages: flesch: 62.0 cache: ./cache/cord-329944-ywusapij.txt txt: ./txt/cord-329944-ywusapij.txt summary: title: Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing Skin, currency, and clothing samples were exposed to SARS-CoV-2 under laboratory conditions and incubated at three different temperatures (4C, 22C, and 37C). Herein, we model the stability of SARS-CoV-2 77 across animal skin, paper currency, and clothing. . https://doi.org/10.1101/2020.07.01.20144253 doi: medRxiv preprint 9 190 SARS-CoV-2 remained viable at 37°C on skin samples for up to 8 h (Fig 1 and Fig 2) . Significant differences 200 were observed in virus stability between the skin samples and all other tested surfaces (Fig S2) . The results in this study demonstrate the continued inverse relationship between virus stability 259 and temperature which is seen both in the laboratory and in the field when evaluating different was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: A new coronavirus (SARS-CoV-2) emerged in the winter of 2019 in Wuhan, China, and rapidly spread around the world. The extent and efficiency of SARS-CoV-2 pandemic is far greater than previous coronaviruses that emerged in the 21st Century. Here, we modeled stability of SARS-CoV-2 on skin, paper currency, and clothing to determine if these surfaces may factor in the fomite transmission dynamics of SARS-CoV-2. Skin, currency, and clothing samples were exposed to SARS-CoV-2 under laboratory conditions and incubated at three different temperatures (4C, 22C, and 37C). Stability was evaluated at 0 hours (h), 4 h, 8 h, 24 h, 72 h, 96 h, 7 days, and 14 days post-exposure. SARS-CoV-2 was shown to be stable on skin through the duration of the experiment at 4C (14 days). Virus remained stable on skin for at least 96 h at 22C and for at least 8h at 37C. There were minimal differences between the tested currency samples. The virus remained stable on the $1 U.S.A. Bank Note for at least 96 h at 4C while viable virus was not detected on the $20 U.S.A. Bank Note samples beyond 72 h. The virus remained stable on both Bank Notes for at least 8 h at 22C and 4 h at 37C. Clothing samples were similar in stability to the currency with the virus being detected for at least 96 h at 4C and at least 4 h at 22C. No viable virus was detected on clothing samples at 37C after initial exposure. This study confirms the inverse relationship between virus stability and temperature. Furthermore, virus stability on skin demonstrates the need for continued hand hygiene practices to minimize fomite transmission both in the general population as well as workplaces where close contact is common. url: https://doi.org/10.1101/2020.07.01.20144253 doi: 10.1101/2020.07.01.20144253 id: cord-280231-jo3grxd5 author: Hardenberg, Jan‐Hendrik title: Covid‐19, ACE2 and the kidney date: 2020-08-02 words: 3901.0 sentences: 285.0 pages: flesch: 55.0 cache: ./cache/cord-280231-jo3grxd5.txt txt: ./txt/cord-280231-jo3grxd5.txt summary: Corona-virus disease 2019 (Covid-19) is a global pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 15 A cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter collectrin (also known as B 0 AT1), with or without the receptor SARS-CoV2 binding domain (RBD), of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 F I G U R E 1 Evolution of the "anginotensin converting enzyme" (ACE) family. 25 That Covid-19 patients develop acute kidney injury (AKI) would not be a surprise. Progressive respiratory failure, not renal failure, is the primary T A B L E 1 A brief overview of Covid-19 patients, acute kidney injury (AKI) and renal-replacement therapies (RRT) Stepwise multivariate binary logistic regression analyses showed that severity of pneumonia was the risk factor most commonly associated with lower odds of proteinuric or haematuric remission and recovery from AKI. abstract: We are confronted with the most dramatic pandemic world-wide for the past 100 years. We are armed "to-the-teeth" compared to 1918, we know the agent, the genomic sequence, the bodily entry, the proliferation rate, the damage pathogenesis, and the very nature of our enemy. We can identify its bodily presence and our resistance to it in terms of neutralizing antibody production. Nonetheless, the disease has laid lame the great nations of the current world and crippled the less fortunate countries. The primary disease features are not the kidney. However, the entry point has much to do with renal and cardiovascular disease. The kidney is a common target of corona-virus (SARS-CoV2) disease; the longer-term consequences could be as well. url: https://www.ncbi.nlm.nih.gov/pubmed/32662161/ doi: 10.1111/apha.13539 id: cord-344204-qq2vqzc2 author: Hariharan, Apurva title: The Role and Therapeutic Potential of NF-kappa-B Pathway in Severe COVID-19 Patients date: 2020-11-07 words: 5647.0 sentences: 307.0 pages: flesch: 47.0 cache: ./cache/cord-344204-qq2vqzc2.txt txt: ./txt/cord-344204-qq2vqzc2.txt summary: Severe presentations of COVID-19 such as severe pneumonia and acute respiratory distress syndrome (ARDS) have been associated with the post-viral activation and release of cytokine/chemokines which leads to a "cytokine storm" causing inflammatory response and destruction, mainly affecting the lungs. Immunomodulation at the level of NF-κB activation and inhibitors of NF-κB (IκB) degradation along with TNF-α inhibition will potentially result in a reduction in the cytokine storm and alleviate the severity of COVID-19. During previous coronavirus outbreaks, such as SARS-CoV and the Middle East Respiratory syndrome coronavirus (MERS-CoV) , it was reported that viral proteins such as nsp1, nsp3a, nsp7a, spike, and nucleocapsid protein all caused excessive NF-κB activation, possibly contributing to severe disease and high case-fatality rate (DeDiego et al. Herein, we review current literature on the effect of SARS-nCoV-2 infection on NF-κB activation and discuss the potential therapeutic role of inhibitors of this pathway in the treatment of COVID-19. abstract: Coronavirus disease 2019 (COVID-19) pandemic has affected health care systems worldwide. Severe presentations of COVID-19 such as severe pneumonia and acute respiratory distress syndrome (ARDS) have been associated with the post-viral activation and release of cytokine/chemokines which leads to a “cytokine storm” causing inflammatory response and destruction, mainly affecting the lungs. COVID-19 activation of transcription factor, NF-kappa B (NF-κB) in various cells such as macrophages of lung, liver, kidney, central nervous system, gastrointestinal system and cardiovascular system leads to production of IL-1, IL-2, IL-6, IL-12, TNF-α, LT-α, LT-β, GM-CSF, and various chemokines. The sensitised NF-κB in elderly and in patients with metabolic syndrome makes this set of population susceptible to COVID-19 and their worse complications, including higher mortality. Immunomodulation at the level of NF-κB activation and inhibitors of NF-κB (IκB) degradation along with TNF-α inhibition will potentially result in a reduction in the cytokine storm and alleviate the severity of COVID-19. Inhibition of NF-κB pathway has a potential therapeutic role in alleviating the severe form of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33159646/ doi: 10.1007/s10787-020-00773-9 id: cord-255498-npk4zv4i author: Harikrishnan, Pandurangan title: Saliva as a Potential Diagnostic Specimen for COVID-19 Testing date: 2020-06-11 words: 1779.0 sentences: 113.0 pages: flesch: 54.0 cache: ./cache/cord-255498-npk4zv4i.txt txt: ./txt/cord-255498-npk4zv4i.txt summary: Various clinical specimens like blood, pharyngeal swabs, saliva, anal swabs and urine showed the presence of the virus in infected patients. WHO recommends specimens from upper respiratory tract like nasopharyngeal (NP), oropharyngeal (OP) swab or wash in ambulatory patients, and lower respiratory specimens like sputum, endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease for the quantitative assessment of SARS-CoV-2 RNA level through real-time reverse transcription polymerase chain reaction (rRT-PCR). 17 Azzi et al collected saliva from 25 COVID-19 patients (confirmed by NP swabs) through the drooling technique and all were tested positive for the presence of SARS-CoV-2, while there was an inverse association between lactate dehydrogenase (LDH) and Cycle threshold (Ct) values (considered as semiquantitative indicators of viral load). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. abstract: The current outbreak of the highly contagious, animal origin SARS-CoV-2 virus causes the disease COVID-19. The disease is globally pandemic and as per World Health Organization (WHO) has spread to 235 countries. There is global lockdown for containment of the virus transmission. Testing of symptomatic patients, healthcare workers and suspected individuals and mass screening is vital. WHO recommends nasopharyngeal (NP) and oropharyngeal (OP) swab for the quantitative assessment of SARS-CoV-2 RNA level through real-time reverse transcription polymerase chain reaction (rRT-PCR). The virus is shown to be consistently present in saliva and rRTPCR of saliva specimens and have advantages over NP and OP swabs such as self-collection of saliva, avoidance of healthcare workers for specimen collection, cost-effectiveness, etc. This article explores the current literature and suggests saliva as an emerging potential diagnostic specimen for COVID-19 testing. url: https://www.ncbi.nlm.nih.gov/pubmed/32541273/ doi: 10.1097/scs.0000000000006724 id: cord-336012-8klkojpo author: Harilal, Divinlal title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 words: 3040.0 sentences: 144.0 pages: flesch: 45.0 cache: ./cache/cord-336012-8klkojpo.txt txt: ./txt/cord-336012-8klkojpo.txt summary: Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. abstract: Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. url: https://doi.org/10.1101/2020.06.06.138339 doi: 10.1101/2020.06.06.138339 id: cord-309986-p7pqla6l author: Harkin, Timothy J title: Delayed diagnosis of COVID-19 in a 34-year-old man with atypical presentation date: 2020-05-18 words: 2110.0 sentences: 118.0 pages: flesch: 52.0 cache: ./cache/cord-309986-p7pqla6l.txt txt: ./txt/cord-309986-p7pqla6l.txt summary: [1] [2] [3] Infection with SARS-CoV-2 is confirmed by real-time RT-PCR, typically done on naso pharyngeal (NP) swabs or, less commonly, samples from the lower respiratory tract, including broncho alveolar lavage (BAL). 5 Here, we present a man who developed rapidly progressive pulmonary disease and, following two negative NP tests, was diagnosed with COVID-19 on the basis of broncho scopic biopsy and BAL after 9 days of illness. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course. normal in the first 48 h (appendix p 1), serum and BAL galactomannan were negative, and the pathological finding of acute lung injury in the lesion was already present on day 2, which argue against this explanation. abstract: nan url: https://api.elsevier.com/content/article/pii/S2213260020302320 doi: 10.1016/s2213-2600(20)30232-0 id: cord-353329-ju3vwlow author: Haroon, Khawaja Hassan title: COVID-19 Related Cerebrovascular Thromboembolic Complications in Three Young Patients date: 2020-09-28 words: 2006.0 sentences: 128.0 pages: flesch: 56.0 cache: ./cache/cord-353329-ju3vwlow.txt txt: ./txt/cord-353329-ju3vwlow.txt summary: We describe clinical, radiological and laboratory findings of three young patients who presented with ischemic stroke and cerebral venous sinus thrombosis to our hospital within the first few weeks of COVID-19 outbreak. His CT of the brain, CT angiogram and CT perfusion ( Fig. 1a -e) showed acute established infarct in the right frontal lobe and basal ganglia, large matched defect in the right MCA territory and occlusion of right CCA and right terminal ICA with no evidence of dissection as well as lung findings suggestive of COVID-19 pneumonia. He was transferred to medical ICU for close monitoring and his follow-up non-contrast CT of the head (Fig. 1f ) revealed large right MCA territory infarct. Our first and second patient showed significant arterial lesions, while the third patient showed a high burden of cerebral venous sinus thrombosis with raised D-dimers and inflammatory markers, leading to stroke. abstract: Coronavirus disease 2019 (COVID-19) is a viral illness, caused by the novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). It is currently affecting millions of people worldwide and is associated with coagulopathy, both in the venous and arterial systems. The proposed mechanism being excessive inflammation, platelet activation, endothelial dysfunction, and stasis. As an ongoing pandemic declared by WHO in March 2020, health systems worldwide are experiencing significant challenges with COVID-19-related complications. It has been noticed that patients with COVID-19 are at greater risk of thrombosis. url: https://doi.org/10.1159/000511179 doi: 10.1159/000511179 id: cord-289520-i6pv90s9 author: Harris, Carlyn title: An evidence-based framework for priority clinical research questions for COVID-19 date: 2020-03-31 words: 4699.0 sentences: 282.0 pages: flesch: 46.0 cache: ./cache/cord-289520-i6pv90s9.txt txt: ./txt/cord-289520-i6pv90s9.txt summary: RESULTS: From the research objectives for SARS-CoV and MERS-CoV, ten themes in the literature were identified: Clinical characterisation, prognosis, diagnosis, clinical management, viral pathogenesis, epidemiological characterisation, infection prevention and control/transmission, susceptibility, psychosocial, and aetiology. Outbreaks, especially of novel agents, create a pressing need to collect data on clinical characterization, treatment, and validation of new diagnostics to inform rapid public health response. We compared our findings to the 2018 systematic review on SARS and MERS to determine which questions have already been addressed, what information is lacking, and provide recommendations for data sharing and clinical study designs to be conducted during the current outbreak. These observational studies are practical in the fast-paced outbreak setting, as they are easier than randomised controlled The First Few X (FFX) WHO Protocol https://www.who.int/publications-detail/the-first-few-x-(ffx)-cases-and-contact-investigation-protocol-for-2019-novel-coronavirus-(2019-ncov)-infection) What are the risk factors for death or severe illness? abstract: BACKGROUND: On 31 December, 2019, the World Health Organization China Country Office was informed of cases of pneumonia of unknown aetiology. Since then, there have been over 75 000 cases globally of the 2019 novel coronavirus (COVID-19), 2000 deaths, and over 14 000 cases recovered. Outbreaks of novel agents represent opportunities for clinical research to inform real-time public health action. In 2018, we conducted a systematic review to identify priority research questions for Severe Acute Respiratory Syndrome-related coronavirus (SARS-CoV) and Middle East Respiratory Syndrome-related coronavirus (MERS-CoV). Here, we review information available on COVID-19 and provide an evidenced-based framework for priority clinical research in the current outbreak. METHODS: Three bibliographic databases were searched to identify clinical studies published on SARS-CoV and MERS-CoV in the outbreak setting. Studies were grouped thematically according to clinical research questions addressed. In February 2020, available information on COVID19 was reviewed and compared to the results of the SARS-CoV and MERS-CoV systematic review. RESULTS: From the research objectives for SARS-CoV and MERS-CoV, ten themes in the literature were identified: Clinical characterisation, prognosis, diagnosis, clinical management, viral pathogenesis, epidemiological characterisation, infection prevention and control/transmission, susceptibility, psychosocial, and aetiology. For COVID19, some information on clinical presentation, diagnostic testing, and aetiology is available but many clinical research gaps have yet to be filled. CONCLUSIONS: Based on a systematic review of other severe coronaviruses, we summarise the state of clinical research for COVID-19, highlight the research gaps, and provide recommendations for the implementation of standardised protocols. Data based on internationally standardised protocols will inform clinical practice real-time. url: https://www.ncbi.nlm.nih.gov/pubmed/32257173/ doi: 10.7189/jogh.10-011001 id: cord-299093-zp07aqpm author: Harrison, Andrew G. title: Mechanisms of SARS-CoV-2 transmission and pathogenesis date: 2020-10-14 words: 6389.0 sentences: 385.0 pages: flesch: 46.0 cache: ./cache/cord-299093-zp07aqpm.txt txt: ./txt/cord-299093-zp07aqpm.txt summary: Thus, evasion of IFN signaling by SARS-CoV-2 and impaired IFN production in J o u r n a l P r e -p r o o f human peripheral blood immune cells might contribute to the productive viral replication, transmission, and severe pathogenesis during COVID-19, although further testing is warranted to fully dissect these putative evasion pathways [95] . For instance, Krt18-hACE2 and betaactin-hACE2-transgenic mice rapidly succumb to SARS-CoV-2 infection with lung infiltration of inflammatory immune cells inducing severe pulmonary disease, accompanied by evident thrombosis and anosmia, which partially recapitulate human COVID-19 [114] [115] . Furthermore, upon viral challenge, lymphocytes have expanded in rhesus macaque models around 5 dpi with complementary B-cell responses against SARS-CoV-2 Spike appearing 10-15 dpi in blood samples [125] ; expansion of these adaptive immune compartments was analogous to those observed in COVID-19 patients [37, 125, [132] [133] [134] . abstract: The emergence of SARS-coronavirus 2 (SARS-CoV-2) marks the third highly pathogenic coronavirus to spill over into the human population. SARS-CoV-2 is highly transmissible with a broad tissue tropism that is likely perpetuating the pandemic. However, important questions remain regarding its transmissibility and pathogenesis. In this review, we summarize current SARS-CoV-2 research, with an emphasis on transmission, tissue tropism, viral pathogenesis, and immune antagonism. We further present advances in animal models that are important for understanding the pathogenesis of SARS-CoV-2, vaccine development, and therapeutic testing. When necessary, comparisons are made from studies with SARS to provide further perspectives on COVID-19, as well as draw inferences for future investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/33132005/ doi: 10.1016/j.it.2020.10.004 id: cord-314796-bek92zs9 author: Hartung, Hans-Peter title: COVID-19 and management of neuroimmunological disorders date: 2020-05-22 words: 1313.0 sentences: 82.0 pages: flesch: 36.0 cache: ./cache/cord-314796-bek92zs9.txt txt: ./txt/cord-314796-bek92zs9.txt summary: The pathogen was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the diseasecoronavirus disease 2019 (COVID-19) -has caused the first recorded non-influenza pandemic. On the basis of their presumed mode of action and evidence from their use in patients, β-interferons, glatiramer acetate and teriflunomide are safe in COVID-19 because they do not cause relevant immunosuppression or increase the risk of viral infections. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. The complement-blocking mAb eculizumab, which is approved for treatment of NMOSD, has not been associated with an increased risk of viral infections. However, COVID-19 affects the management of patients with neurological diseases in many ways. abstract: The importance of reported neurological manifestations of coronavirus disease 2019 (COVID-19) is still unclear. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. url: https://doi.org/10.1038/s41582-020-0368-9 doi: 10.1038/s41582-020-0368-9 id: cord-259200-65b267ic author: Harypursat, Vijay title: Six weeks into the 2019 coronavirus disease outbreak: it is time to consider strategies to impede the emergence of new zoonotic infections date: 2020-05-05 words: 1705.0 sentences: 77.0 pages: flesch: 47.0 cache: ./cache/cord-259200-65b267ic.txt txt: ./txt/cord-259200-65b267ic.txt summary: Subsequent to the severe acute respiratory syndrome (SARS) outbreak in China 2003, and the Middle East respiratory syndrome (MERS) outbreak in the Middle East in 2012, global concerns regarding the pathogenicity and epidemic/pandemic potential of novel human coronaviruses began to emerge, with some experts predicting that novel coronaviruses could likely again cross the species barrier and present humans with future pandemic-potential infections. 2019-nCoV is the seventh coronavirus species that is now known to infect humans, is also zoonotic in origin, and is the causative organism for the current viral pneumonia epidemic in China. The complete ban on market trading and sale of wild game meat in China on January 26th, 2020 will help prevent zoonotic transmission of 2019-nCoV in the current epidemic and, to a certain degree, help prevent emergence of new zoonotic infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32097202/ doi: 10.1097/cm9.0000000000000760 id: cord-265598-4h3wx81q author: Hasan, Abdulkarim title: Histopathology Laboratory Paperwork as a Potential Risk of COVID-19 Transmission among the Lab Personnel date: 2020-08-06 words: 2230.0 sentences: 121.0 pages: flesch: 50.0 cache: ./cache/cord-265598-4h3wx81q.txt txt: ./txt/cord-265598-4h3wx81q.txt summary: Methods We tracked paper-based forms from time of test ordering till the release of the pathology report by calculating the time taken for the papers to reach the lab and the exposure of each staff group to the received papers from both high and moderate COVID-19 risk areas. Conclusion More than 80% of the manual paper request forms will take less than 24 hours to be handled by laboratory personnel; carrying a high potential risk for viral transmission. In this study we focused on defining the major hospital departments that request histopathology (by frequency and percent), measuring the time from handling the paper by clinician staff till handling by laboratory personnel, and comparing the possibility of COVID-19 transmission by paperwork to laboratory personnel, according to their exposure time to these papers. More studies are required to detect stability of the SARS-COV-2 on different surfaces and the potential risk of COVID-19 transmission through papers. abstract: ABSTRACT. Background Healthcare workers have a higher risk of acquiring COVID-19 infection. The process of requesting pathology investigations is usually handled manually through the paper-based forms. We evaluated the potential of paper-based request forms to transmit COVID-19 to laboratory staff to make recommendations for dealing with hospital paperwork in a post COVID-19 world. Methods We tracked paper-based forms from time of test ordering till the release of the pathology report by calculating the time taken for the papers to reach the lab and the exposure of each staff group to the received papers from both high and moderate COVID-19 risk areas. Results Four hundred and thirty two (83%) out of 520 forms were received in the laboratory within 24 hours. The remaining 88 (17%) forms took 24 hours or more to be handled by lab personnel. The mean daily exposure time to the paperwork for various laboratory staff was as follows - receptionists: 2.7 minutes, technicians: 5.5 minutes and pathologists: 54.6 minutes. Conclusion More than 80% of the manual paper request forms will take less than 24 hours to be handled by laboratory personnel; carrying a high potential risk for viral transmission. We recommend replacing hardcopy paper-based request forms with electronic requests that could be printed in the laboratory if required. The other option would be to sterilize received papers to ensure the safety of the laboratory personnel. More studies are required to detect stability of the SARS-COV-2 on the different surfaces and the potential risk of COVID-19 transmission through papers. url: https://api.elsevier.com/content/article/pii/S2590088920300457 doi: 10.1016/j.infpip.2020.100081 id: cord-315754-dq2empne author: Hasan, Anwarul title: A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin date: 2020-04-22 words: 4662.0 sentences: 272.0 pages: flesch: 50.0 cache: ./cache/cord-315754-dq2empne.txt txt: ./txt/cord-315754-dq2empne.txt summary: Angiotensin-converting enzyme-2 (ACE-2) is one of the most important receptors on the cell membrane of the host cells (HCs) which its interaction with spike protein (SP) with a furin-cleavage site results in the SARS-CoV-2 invasion. Genomic analysis of the new CoV has shown that its SP differs from that of other viruses (Du et al., 2017; Li, 2016) , indicating that the protein has a site activated by a HC enzyme called furin (Millet & Whittaker, 2015) (Figure 1 ). The furin activation site (FAS) makes the new CoV much different in cell entry than SARS, and probably affects the stability of the virus and, consequently, the transmission process (Li et al., 2015; Millet & Whittaker, 2014; Yamada & Liu, 2009) . A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 abstract: The widespread antigenic changes lead to the emergence of a new type of coronavirus (CoV) called as severe acute respiratory syndrome (SARS)-CoV-2 that is immunologically different from the previous circulating species. Angiotensin-converting enzyme-2 (ACE-2) is one of the most important receptors on the cell membrane of the host cells (HCs) which its interaction with spike protein (SP) with a furin-cleavage site results in the SARS-CoV-2 invasion. Hence, in this review, we presented an overview on the interaction of ACE-2 and furin with SP. As several kinds of CoVs, from various genera, have at their S1/S2 binding site a preserved site, we further surveyed the role of furin cleavage site (FCS) on the life cycle of the CoV. Furthermore, we discussed that the small molecular inhibitors can limit the interaction of ACE-2 and furin with SP and can be used as potential therapeutic platforms to combat the spreading CoV epidemic. Finally, some ongoing challenges and future prospects for the development of potential drugs to promote targeting specific activities of the CoV were reviewed. In conclusion, this review may pave the way for providing useful information about different compounds involved in improving the effectiveness of CoV vaccine or drugs with minimum toxicity against human health. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1754293 doi: 10.1080/07391102.2020.1754293 id: cord-297786-jz1d1m2e author: Hasan, Md. Mahbub title: Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date: 2020-08-26 words: 3271.0 sentences: 187.0 pages: flesch: 54.0 cache: ./cache/cord-297786-jz1d1m2e.txt txt: ./txt/cord-297786-jz1d1m2e.txt summary: Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Then, we studied the variants present in different isolates of Bangladesh to investigate the pattern of mutations, identify UMs, and discuss the pseudo-effect of these mutations on the structure and function of encoded proteins, with their role in pathogenicity. To understand the SARS-CoV-2 viral transmission in Bangladesh, we performed phylogenetic analysis on the selected 207 viral genomes reported from different districts of Bangladesh along with selected 467 globally submitted sequences as reported from 42 countries and 6 continents ( Figure 1 ). abstract: Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. Nearly 0.4 million mutations were identified so far in ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Phylogenetic analyses indicates that in Bangladesh, SARS-CoV-2 viruses might arrived through infected travelers from European countries, and the GR clade was found as predominant in this region. We found 2602 mutations including 1602 missense mutations, 612 synonymous mutations, 36 insertions and deletions with 352 other mutations types. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (95.6%) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M and N of genomes, having nucleotide shift at G614 (n=459), were significantly higher (p≤0.001) than those having mutation at D614 (n=215). Previously reported frequent mutations such as P4715L, D614G, R203K, G204R and I300F were also prevalent in Bangladeshi isolates. Additionally, 87 unique amino acid changes were revealed and were categorized as originating from different cities of Bangladesh. The analyses would increase our understanding of variations in virus genomes circulating in Bangladesh and elsewhere and help develop novel therapeutic targets against SARS-CoV-2. url: https://doi.org/10.1101/2020.08.25.267658 doi: 10.1101/2020.08.25.267658 id: cord-278123-mq56em3z author: Hasan, Mohammad Rubayet title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 words: 3924.0 sentences: 259.0 pages: flesch: 58.0 cache: ./cache/cord-278123-mq56em3z.txt txt: ./txt/cord-278123-mq56em3z.txt summary: Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. abstract: To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR to detect SARS-CoV-2 in nasopharyngeal swabs without RNA extraction. Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. The results were compared to that of standard approach that involves RNA extraction. Incubation of specimens at 65°C for 10 minutes along with the use of TaqPath(™) 1-Step RT-qPCR Master Mix provides higher analytical sensitivity for detection of SARS-CoV-2 RNA than many other conditions tested. The optimized direct RT-qPCR approach demonstrated a limit of detection of 6.6x10(3) copy/ml and high reproducibility (co-efficient of variation = 1.2%). In 132 nasopharyngeal specimens submitted for SARS-CoV-2 testing, the sensitivity, specificity and accuracy of our optimized approach were 95%, 99% and 98.5%, respectively, with reference to the standard approach. Also, the RT-qPCR C(T) values obtained by the two methods were positively correlated (Pearson correlation coefficient r = 0.6971, p = 0.0013). The rate of PCR inhibition by the direct approach was 8% compared to 9% by the standard approach. Our simple approach to detect SARS-CoV-2 RNA by direct RT-qPCR may help laboratories continue testing for the virus despite reagent shortages or expand their testing capacity in resource limited settings. url: https://doi.org/10.1371/journal.pone.0236564 doi: 10.1371/journal.pone.0236564 id: cord-333547-88dkh6xd author: Hasan, Shadi W. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 words: 3980.0 sentences: 220.0 pages: flesch: 54.0 cache: ./cache/cord-333547-88dkh6xd.txt txt: ./txt/cord-333547-88dkh6xd.txt summary: Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. A limited number of studies have shown that the shedding period of SARS-CoV-2 in stool samples varies considerably, and can still be detected up to 27.9 ± 10.7 days after infection in some cases [9, 11] . Consequently, the main objectives of this study were: (i) to detect the presence of SARS-CoV-2 virus in municipal (untreated) wastewater and treated effluents of wastewater treatment plants (WWTPs) in the UAE; (ii) to quantify the viral concentration in viral gene copies per liter; and (iii) to explore whether these measurements mirror infections in the population in order to comment on the utility of this method to track the epidemiology of the disease. abstract: Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. This study reports SARS-CoV-2 viral load in wastewater influents and treated effluents of 11 wastewater treatment plants (WWTPs), as well as untreated wastewater from 38 various locations, in the United Arab Emirates (UAE) in May and June 2020. Composite samples collected over twenty-four hours were thermally deactivated for safety, followed by viral concentration using ultrafiltration, RNA extraction using commercially available kits, and viral quantification using RT-qPCR. Furthermore, estimates of the prevalence of SARS-CoV-2 infection in different regions were simulated using Monte Carlo. Results showed that the viral load in wastewater influents from these WWTPs ranged from 7.50E+02 to over 3.40E+04 viral gene copies/L with some plants having no detectable viral RNA by RT-qPCR. The virus was also detected in 85% of untreated wastewater samples taken from different locations across the country, with viral loads in positive samples ranging between 2.86E+02 and over 2.90E+04 gene copies/L. It was also observed that the precautionary measures implemented by the UAE government correlated with a drop in the measured viral load in wastewater samples, which were in line with the reduction of COVID-19 cases reported in the population. Importantly, none of the 11 WWTPs’ effluents tested positive during the entire sampling period, indicating that the treatment technologies used in the UAE are efficient in degrading SARS-CoV-2, and confirming the safety of treated re-used water in the country. SARS-CoV-2 wastewater testing has the potential to aid in monitoring or predicting an outbreak location and can shed light on the extent viral spread at the community level. url: https://doi.org/10.1016/j.scitotenv.2020.142929 doi: 10.1016/j.scitotenv.2020.142929 id: cord-255264-2kj961en author: Hasan, Syed Shahzad title: Social distancing and the use of PPE by community pharmacy personnel: Does evidence support these measures? date: 2020-05-01 words: 2233.0 sentences: 104.0 pages: flesch: 45.0 cache: ./cache/cord-255264-2kj961en.txt txt: ./txt/cord-255264-2kj961en.txt summary: While the United States adopted a universal mask approach and Turkey recommended the use of masks and protective goggles for their pharmacy personnel, almost all of the countries recommended against routine use of face mask and other PPE (gloves or aprons/gowns), except when dealing with suspected COVID-19 patients or performing activities requiring close contact (unable to maintain recommended social distance) with the patients. Though the observation from such case study cannot be regarded as conclusive, the assumption, for now, should be that airborne transmission of SARS-CoV-2 is possible unless being discredited in the future, and therefore we opine that the wearing of appropriate PPE is of utmost importance for healthcare workers, including community pharmacy personnel dealing with individuals may or may not be infected on a day-to-day basis, regardless if they manage to observe social distancing in their workplace or if they perform close contact activities. abstract: Community pharmacists are one of the most accessible healthcare professionals and are often served as the first point of contact when it comes to minor ailments and health advice. As such, community pharmacists can play a vital role in a country's response to various preventative and public health measures amid the COVID-19 pandemic. Given the essential nature of community pharmacy as a health service, community pharmacies are unlikely to shut down in any foreseeable lockdown scenario. It is therefore important to assess the preventative measure directives for community pharmacies that are in place to safeguard community pharmacy personnel from SARS-CoV-2 in the various parts of the world. Upon reviewing the recommendations of 15 selected countries across five continents (Asia, Europe, Oceania, North America, and Africa) on social distancing and the use of personal protective equipment (PPE) in community pharmacies, we found inconsistencies in the recommended social distance to be practiced within the community pharmacies. There were also varying recommendations on the use of PPE by the pharmacy personnel. Despite the differences in the recommendations, maintaining recommended social distance and the wearing of appropriate PPE is of utmost importance for healthcare workers, including community pharmacy personnel dealing with day-to-day patient care activities, though full PPE should be worn when dealing with suspected COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32387229/ doi: 10.1016/j.sapharm.2020.04.033 id: cord-279223-qvih5qas author: Hascoët, Jean-Michel title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 words: 3057.0 sentences: 165.0 pages: flesch: 50.0 cache: ./cache/cord-279223-qvih5qas.txt txt: ./txt/cord-279223-qvih5qas.txt summary: Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Thus, although the mother was considered cleared at 6 weeks after the onset of infection, which was confirmed by negative nasopharyngeal and stool SARS-CoV-2 RT-PCR tests after delivery, we tested stool and pharynx swab samples from asymptomatic baby-girl D. Two additional babies and their mothers were tested at birth because the mothers had symptomatic infection, documented with positive SARS-CoV-2 RT-PCR results, at 28 and 31 days before delivery, respectively. Despite the first newborn was asymptomatic and the screening performed as part of routine systematic testing, SARS-CoV-2 RNA detection through early nasopharyngeal sampling and the persistent detection of virus in stool strongly suggest possible vertical maternofetal infection. abstract: Background: Despite the pandemic, data are limited regarding COVID-19 infection in pregnant women and newborns. This report aimed to bring new information about presentation that could modify precautionary measures for infants born of mothers with a remote history of COVID-19. Methods: We report two infants with possible maternofetal transmission, and four mothers without immunologic reactions. Data were collected from the patient files. Results: One mother exhibited infection signs 10 days before uncomplicated delivery, with negative RT-PCR and no antibody detection thereafter. Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Both newborns were asymptomatic but tested positive for nasopharyngeal and stool RT-PCR at 1 and 3 days of age for the first one and at 1 day of age for stool analysis for the second one. Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28- and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Conclusion: These observations raise concerns regarding contamination risk by asymptomatic newborns and the efficacy of immunologic reactions in pregnant mothers, questioning the reliability of antibody testing during pregnancy. url: https://doi.org/10.3389/fped.2020.568979 doi: 10.3389/fped.2020.568979 id: cord-270743-yyl50z94 author: Haseli, Sara title: Reply to “MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss” date: 2020-06-10 words: 619.0 sentences: 40.0 pages: flesch: 47.0 cache: ./cache/cord-270743-yyl50z94.txt txt: ./txt/cord-270743-yyl50z94.txt summary: title: Reply to "MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss" We read with great interest the letter by Eliezer and Hautefort discussing our recent report in Academic Radiology of magnetic resonance imaging (MRI) findings in a patient with coronavirus disease-2019 (Covid-19) and enumerating the possible mechanisms of SARS-CoV-2-induced anosmia 1 . In the apparent absence of anatomical changes on MRI and to assess a putative loss of neuronal function in anosmia of Covid-19, we performed 18 FDG PET/CT scan in a patient with isolated anosmia under neutral olfactory condition, which revealed hypoactivity of the left orbitofrontal cortex, thus suggesting a probable neuroinvasive mechanism for anosmia of Covid-19 8 . MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. abstract: nan url: https://api.elsevier.com/content/article/pii/S1076633220303044 doi: 10.1016/j.acra.2020.05.025 id: cord-276139-l13hbucu author: Hashem, A. M. title: Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients date: 2020-09-23 words: 4628.0 sentences: 272.0 pages: flesch: 57.0 cache: ./cache/cord-276139-l13hbucu.txt txt: ./txt/cord-276139-l13hbucu.txt summary: Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Here, we studied the kinetics of SARS-CoV-2 specific antibodies to S1 and N viral proteins in blood samples collected between 4 to 70 days post-symptoms onset from a cohort of 87 COVID-19 patients with different disease presentations (i.e. mild, moderate or severe) or outcomes (i.e. survival vs death). Comparing the kinetics of antibody response in COVID-19 patients who had fatal outcomes to those who survived the infection also showed that early induction of anti-N IgG and IgM during the first 15 days post-disease onset is indicative of fatal outcomes (Figure 4c) . In this study we studied the characteristics and kinetics of SARS-CoV-2 specific antibody response (nAbs, IgG and IgM) in a series of serum samples collected from a total of 87 confirmed COVID-19 hospitalized patients over a period of 70 days post-symptoms onset. abstract: The Coronavirus Disease 2019 (COVID-19), caused by the novel SARS-CoV-2, continues to spread globally with significantly high morbidity and mortality rates. Immunological surrogate markers, in particular antigen-specific responses, are of unquestionable value for clinical management of patients with COVID-19. Here, we investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing capabilities in hospitalized patients with RT-PCR confirmed COVID-19 infection. Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Notably, anti-S and -N IgG, peaked 20-40 day after disease onset, and were still detectable for at least up to 70 days, with nAbs observed during the same time period. Moreover, nAbs titers were strongly correlated with IgG antibodies. Significantly higher levels of nAbs as well as anti-S1 and N IgG and IgM antibodies were found in patients with more severe clinical presentations, patients requiring admission to intensive care units (ICU) or those with fatal outcomes. Interestingly, lower levels of antibodies, particularly anti-N IgG and IgM in the first 15 days after symptoms onset, were found in survivors and those with mild clinical presentations. Collectively, these findings provide new insights into the characteristics and kinetics of antibody responses in COVID-19 patients with different disease severity. url: http://medrxiv.org/cgi/content/short/2020.09.21.20198309v1?rss=1 doi: 10.1101/2020.09.21.20198309 id: cord-341101-5yvjbr5q author: Hashem, Anwar M. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 words: 4823.0 sentences: 275.0 pages: flesch: 43.0 cache: ./cache/cord-341101-5yvjbr5q.txt txt: ./txt/cord-341101-5yvjbr5q.txt summary: While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro abstract: The rapidly spreading Coronavirus Disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2), represents an unprecedented serious challenge to the global public health community. The extremely rapid international spread of the disease with significant morbidity and mortality made finding possible therapeutic interventions a global priority. While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. Recent publications have re-examined the use of Chloroquine (CQ) and/or Hydroxychloroquine (HCQ) as a potential therapeutic option for these patients. In an attempt to explore the evidence that supports their use in COVID-19 patients, we comprehensively reviewed the previous studies which used CQ or HCQ as an antiviral treatment. Both CQ and HCQ demonstrated promising in vitro results, however, such data have not yet been translated into meaningful in vivo studies. While few clinical trials have suggested some beneficial effects of CQ and HCQ in COVID-19 patients, most of the reported data are still preliminary. Given the current uncertainty, it is worth being mindful of the potential risks and strictly rational the use of these drugs in COVID-19 patients until further high quality randomized clinical trials are available to clarify their role in the treatment or prevention of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32387694/ doi: 10.1016/j.tmaid.2020.101735 id: cord-260644-5moccf8c author: Hashemi, Seyed Ahmad title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date: 2020-11-07 words: 2174.0 sentences: 149.0 pages: flesch: 67.0 cache: ./cache/cord-260644-5moccf8c.txt txt: ./txt/cord-260644-5moccf8c.txt summary: title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Some researchers evaluated and compared the whole genome sequence of SARS-CoV-2 isolated in various parts of the world and identified some mutations. The high-frequency mutations of the SARS-CoV-2 genome were seen in nsp6, RNA polymerase, helicase, membrane glycoprotein, RNA primase, nucleocapsid phosphoprotein, and spike protein genes (Yin, 2020) . In the first step, we used the sequence of S protein of SARS-CoV-2, published in Gene bank with accession number MT252819.1, for appropriate restriction endonuclease selection and primer design. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity abstract: In late 2019, an outbreak of respiratory disease named COVID-19 started in the world. To date, thousands of cases of infection are reported worldwide. Most researchers focused on epidemiology and clinical features of COVID-19, and a small part of studies was performed to evaluate the genetic characteristics of this virus. Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Using bioinformatics databases and software, we designed the PCR-RFLP method for D614G mutation detection. We evaluated 144 SARS-CoV-2 positive samples isolated in six months in Northeastern Iran. Our results showed that the prevalent type is S-D in our isolates, and a small number of isolated belongs to the S-G type. Of 144 samples, 127 (88.2%) samples have belonged to type S-D, and 13 (9%) samples typed S-G. The first S-G type was detected on 2020 June 10. We have little information about the prevalence of D614G mutation, and it seems that the reason is the lack of cheap and fast methods. We hope that this method will provide more information on the prevalence and epidemiology of D614G mutations worldwide. url: https://api.elsevier.com/content/article/pii/S1567134820304561 doi: 10.1016/j.meegid.2020.104625 id: cord-278945-q5lzf5o4 author: Hashemi, Seyed Ahmad title: Report of death in children with SARS‐CoV‐2 and Human metapneumovirus (hMPV) co‐infection: is hMPV the trigger? date: 2020-08-07 words: 1285.0 sentences: 88.0 pages: flesch: 55.0 cache: ./cache/cord-278945-q5lzf5o4.txt txt: ./txt/cord-278945-q5lzf5o4.txt summary: To investigate the presence of other respiratory viruses, we performed a panel of virus detection through PCR and RT‐PCR tests to detect influenza virus, parainfluenza virus, Human metapneumovirus, Human bocavirus, adenovirus, and respiratory syncytial virus on nasopharyngeal swabs of all 74 SARS‐CoV‐2 positive dead patients. Although surveys confirmed that children could be infected with SARS-CoV-2 (1-3), there is evidence showing people more than 50 years old are more susceptible to the COVID-19. Case presentation Blood tests, including blood cell differential count, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) were performed for all patients admitted to the hospital with suspicion of infection with SARS-CoV-2. Besides, all patients underwent a chest CT scan that is the most sensitive test for COVID-19 identification (5, 6) , and SARS-COV-2 detection was performed using real-time PCR. We found the influenza virus, Human bocavirus, respiratory syncytial virus, parainfluenza virus, and hMPV in some SARS-CoV-2 positive samples. abstract: In the last month of 2019, a new virus called SARS‐CoV‐2 was discovered in Wuhan, China. This virus causes a wide range of symptoms, and respiratory tract illness is the most common disorder. To investigate the presence of other respiratory viruses, we performed a panel of virus detection through PCR and RT‐PCR tests to detect influenza virus, parainfluenza virus, Human metapneumovirus, Human bocavirus, adenovirus, and respiratory syncytial virus on nasopharyngeal swabs of all 74 SARS‐CoV‐2 positive dead patients. Here we report an interesting finding of the co‐infection of SARS‐CoV‐2 and Human metapneumovirus (hMPV) in three deceased children in North Khorasan Province, Iran. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26401 doi: 10.1002/jmv.26401 id: cord-277509-khvuiwl1 author: Hashemi, Seyyed Alireza title: Ultra-sensitive viral glycoprotein detection NanoSystem toward accurate tracing SARS-CoV-2 in biological/non-biological media date: 2021-01-01 words: 5375.0 sentences: 283.0 pages: flesch: 52.0 cache: ./cache/cord-277509-khvuiwl1.txt txt: ./txt/cord-277509-khvuiwl1.txt summary: The working electrode of developed sensor is activated upon coating a layer of coupled graphene oxide (GO) with sensitive chemical compounds along with gold nanostars (Au NS) that can detect the trace of viruses in any aquatic biological media (e.g., blood, saliva and oropharyngeal/ nasopharyngeal swab) through interaction with active functional groups of their glycoproteins. Herein, we have addressed this demand via developing a rapid and highly sensitive diagnostic kit that do not require any extraction or biological marker and can detect trace of different kinds of pathogenic animal/human viruses such as SARS-CoV-2, infectious bronchitis virus (IBV), avian influenza and Newcastle Disease Virus (LaSota and V4 strains) via active functional groups of their viral glycoproteins upon demonstration of differentiable fingerprints of each virus at diverse voltage positions. abstract: Rapid person-to-person transfer of viruses such as SARS-CoV-2 and their occasional mutations owing to the human activity and climate/ecological changes by the mankind led to creation of wrecking worldwide challenges. Such fast transferable pathogens requiring practical diagnostic setups to control their transfer chain and stop sever outbreaks in early stages of their appearance. Herein, we have addressed this urgent demand by designing a rapid electrochemical diagnostic kit composed of fixed/screen printed electrodes that can detect pathogenic viruses such as SARS-CoV-2 and/or animal viruses through the differentiable fingerprint of their viral glycoproteins at different voltage positions. The working electrode of developed sensor is activated upon coating a layer of coupled graphene oxide (GO) with sensitive chemical compounds along with gold nanostars (Au NS) that can detect the trace of viruses in any aquatic biological media (e.g., blood, saliva and oropharyngeal/nasopharyngeal swab) through interaction with active functional groups of their glycoproteins. The method do not require any extraction and/or biomarkers for detection of target viruses and can identify trace of different pathogenic viruses in about 1 min. The nanosensor also demonstrated superior limit of detection (LOD) and sensitivity of 1.68 × 10(−22) μg mL(−1) and 0.0048 μAμg.mL(−1). cm(−2), respectively, toward detection of SARS-CoV-2 in biological media, while blind clinical evaluations of 100 suspected samples furtherly confirmed the superior sensitivity/specificity of developed nanosystem toward rapid identification of ill people even at incubation and prodromal periods of illness. url: https://doi.org/10.1016/j.bios.2020.112731 doi: 10.1016/j.bios.2020.112731 id: cord-255972-u7v0es5w author: Hashikawa, Andrew title: Child Care in the Time of COVID-19: A Period of Challenge and Opportunity. date: 2020-07-17 words: 4036.0 sentences: 229.0 pages: flesch: 49.0 cache: ./cache/cord-255972-u7v0es5w.txt txt: ./txt/cord-255972-u7v0es5w.txt summary: Existing CFOC standards do not address the new concerns expressed by ECE workers during the pandemic, which include: determining the risks for ECE workers, establishing whether physical distancing in young children is feasible and effective, providing more details about cleaning and disinfecting, defining new group size requirements, defining the proper use of SARS-CoV-2 screening tests, handling readmission of children with symptoms or positive COVID-19 tests, and establishing guidelines for temperature checks (type of thermometer, fever threshold for exclusion, when to take temperatures after the initial screening). Even though there remain gaps in COVID-19 specific information that need further research, there is an important role for pediatric health experts to provide some structured guidance based on both expert group consensus and best available evidence to assist ECE directors in operating their programs and in providing consistent messaging to parents. abstract: nan url: https://doi.org/10.1016/j.jpeds.2020.07.042 doi: 10.1016/j.jpeds.2020.07.042 id: cord-305581-0bqxwh1o author: Hassan, Sk. Sarif title: Molecular phylogeny and missense mutations of envelope proteins across coronaviruses date: 2020-09-12 words: 2000.0 sentences: 109.0 pages: flesch: 57.0 cache: ./cache/cord-305581-0bqxwh1o.txt txt: ./txt/cord-305581-0bqxwh1o.txt summary: The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations. In the Table 1 , total number of available CoV genomes of respective hosts as well as distinct number of envelope proteins are presented. It is noted that the envelope (E) protein of the CoVs of Pangolin and Chimpanzee are found to be 100% conserved as presented in Table 1 and consequently no mutation was found over there. Among 79 available complete CoV genomes of Bat, twenty-five sequences possess various mutations in the three domains of the E protein as presented in the Fig.2 . Based on mutation characteristics and amino acid conservations over the E proteins across various host CoVs, this report predicts potential close kins of human SARS-CoV2 as the Pangolin-CoV and Bat-CoV which was also reported in a recent study [21] . abstract: Envelope (E) protein is one of the structural viroporins (76–109 amino acids) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the β-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations. url: https://api.elsevier.com/content/article/pii/S0888754320309095 doi: 10.1016/j.ygeno.2020.09.014 id: cord-306085-gnrnsxej author: Hassan, Sk. Sarif title: SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences date: 2020-07-05 words: 963.0 sentences: 69.0 pages: flesch: 67.0 cache: ./cache/cord-306085-gnrnsxej.txt txt: ./txt/cord-306085-gnrnsxej.txt summary: The envelope protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane domain and (C)-terminus in 15 (0.414%) genomes among 3617 available SARS-CoV2 genomes. Here, we present the non-synonymous mutations of the envelope protein over the available 3617 SARS-CoV2 genomes (Table 1) . It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contain the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes.  In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617 on which the present study of mutation over the envelope protein is made. More precisely, it is to be mentioned that 10(0.386\%) out of 2588 genomes from the USA, 3(0.806\%) from Asia, 1 (0.348\%) from Europe and 1 (0.274\%) from Oceania contain the missense mutations over the envelope proteins of SARS-CoV2 genomes. abstract: Abstract In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane domain and (C)-terminus in 15 (0.414%) genomes among 3617 available SARS-CoV2 genomes. More precisely, it is to be mentioned that 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contain the missense mutations over the envelope proteins of SARS-CoV2 genomes. The C-terminus motif DLLV has been changed to DFLV and YLLV in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1. url: https://www.sciencedirect.com/science/article/pii/S0888754320307345?v=s5 doi: 10.1016/j.ygeno.2020.07.001 id: cord-312999-3erodkv9 author: Hassan, Sk. Sarif title: Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date: 2020-09-06 words: 3920.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-312999-3erodkv9.txt txt: ./txt/cord-312999-3erodkv9.txt summary: SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Based on the mutations, conserved and non-conserved residues in ORF10 proteins are identified and marked in different colors in (Figure There are altogether 22 distinct missense mutations which were examined across 22 unique ORF10 variants of SARS-CoV-2. abstract: The global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection. url: https://doi.org/10.1101/2020.09.06.284976 doi: 10.1101/2020.09.06.284976 id: cord-338055-2d6n4cve author: Hassan, Sk. Sarif title: A unique view of SARS-CoV-2 through the lens of ORF8 protein date: 2020-08-26 words: 5942.0 sentences: 322.0 pages: flesch: 55.0 cache: ./cache/cord-338055-2d6n4cve.txt txt: ./txt/cord-338055-2d6n4cve.txt summary: In this present study, we identified the distinct mutations present across unique variants of the SARS-CoV-2 ORF8 and classified them according to their predicted effect on the host, i.e disease or neutral and the consequences on protein structural stability. The ORF8 sequences of SARS-CoV-2, Bat-CoV RaTG13 and Pangolin-CoV have almost the same positive and negative charged amino acids, therefore we can say that probably they have similar kind of electrostatic and hydrophobic interactions, 135 which also contribute to the functionality of the proteins. • QKV07730.1: The T11A mutation occurred as the second mutation in this sequence, which was predicted to be of disease-increasing type and the polarity was changed from hydrophilic to hydrophobic, hence the structure and 305 function of the protein are expected to differ. abstract: Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8. url: https://doi.org/10.1101/2020.08.25.267328 doi: 10.1101/2020.08.25.267328 id: cord-297127-nhgm09db author: Hasseli, Rebecca title: National registry for patients with inflammatory rheumatic diseases (IRD) infected with SARS-CoV-2 in Germany (ReCoVery): a valuable mean to gain rapid and reliable knowledge of the clinical course of SARS-CoV-2 infections in patients with IRD date: 2020-09-02 words: 4093.0 sentences: 218.0 pages: flesch: 45.0 cache: ./cache/cord-297127-nhgm09db.txt txt: ./txt/cord-297127-nhgm09db.txt summary: OBJECTIVES: Patients with inflammatory rheumatic diseases (IRD) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be at risk to develop a severe course of COVID-19. 2 In this situation, patients with inflammatory rheumatic diseases (IRD) may face a particular risk as their disease, especially when clinically active, and their immunomodulatory treatment may impact the course of COVID-19 infection. However, firm knowledge of the course of SARS-CoV-2 infection in patients with IRD is missing, and therefore, evidence-based recommendations for the management of COVID-19 in patients with rheumatic disorders and antirheumatic treatments are lacking. As necessary data cannot be extracted from clinical charts or health insurance records, the DGRh and the Justus-Liebig University Giessen decided to establish a web-based registry, which allows a rapid and timely collection of IRD cases with confirmed SARS-CoV-2 infections in Germany to analyse the clinical course of SARS-CoV-2 infections in patients with IRD and to develop guidance for the management of patients with IRD during the COVID-19 pandemic. abstract: OBJECTIVES: Patients with inflammatory rheumatic diseases (IRD) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be at risk to develop a severe course of COVID-19. The influence of immunomodulating drugs on the course of COVID-19 is unknown. To gather knowledge about SARS-CoV-2 infections in patients with IRD, we established a registry shortly after the beginning of the pandemic in Germany. METHODS: Using an online questionnaire (www.COVID19-rheuma.de), a nationwide database was launched on 30 March 2020, with appropriate ethical and data protection approval to collect data of patients with IRD infected with SARS-CoV-2. In this registry, key clinical and epidemiological parameters—for example, diagnosis of IRD, antirheumatic therapies, comorbidities and course of the infection—are documented. RESULTS: Until 25 April 2020, data from 104 patients with IRD infected with SARS-CoV-2 were reported (40 males; 63 females; 1 diverse). Most of them (45%) were diagnosed with rheumatoid arthritis, 59% had one or more comorbidities and 42% were treated with biological disease-modifying antirheumatic drugs. Hospitalisation was reported in 32% of the patients. Two-thirds of the patients already recovered. Unfortunately, 6 patients had a fatal course. CONCLUSIONS: In a short time, a national registry for SARS-CoV2-infected patients with IRD was established. Within 4 weeks, 104 cases were documented. The registry enables to generate data rapidly in this emerging situation and to gain a better understanding of the course of SARS-CoV2-infection in patients with IRD, with a distinct focus on their immunomodulatory therapies. This knowledge is valuable for timely information of physicians and patients with IRD, and shall also serve for the development of guidance for the management of patients with IRD during this pandemic. url: https://doi.org/10.1136/rmdopen-2020-001332 doi: 10.1136/rmdopen-2020-001332 id: cord-322562-3gvsn9vf author: Hatada, Ryo title: Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) date: 2020-06-15 words: 4813.0 sentences: 295.0 pages: flesch: 55.0 cache: ./cache/cord-322562-3gvsn9vf.txt txt: ./txt/cord-322562-3gvsn9vf.txt summary: Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). As illustrated in a recent book of in silico drug design, 8 the fragment molecular orbital (FMO) method 9−12 provides an efficient tool for performing ab initio quantum-chemical calculations for biomolecular systems and accurately analyzing their intermolecular interactions in terms of the interfragment interaction energies (IFIEs). Table 1 compiles the results of IFIE and decomposed contributions (PIEDA) interacting with Fragment 1 of the ligand, where the listing threshold is set as 2.0 kcal/mol The distance between the main chain >CO of Thr190 and the N−H part of Fragment 1 is as close as 1.99 Å as illustrated in Figure 6 , suggesting that they are forming a typical hydrogen bond. abstract: [Image: see text] The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson–Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/32539372/ doi: 10.1021/acs.jcim.0c00283 id: cord-329840-f3dsu36p author: Hati, Sanchita title: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date: 2020-05-11 words: 2497.0 sentences: 173.0 pages: flesch: 51.0 cache: ./cache/cord-329840-f3dsu36p.txt txt: ./txt/cord-329840-f3dsu36p.txt summary: In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. In the backdrop of significant mortality rate for SARS-CoV-2 (hereinafter referred to as CoV-2) infection, it is important to know if the thiol-disulfide balance plays any role on the binding of the spike glycoprotein on to the host cell receptor protein ACE2. Using these reported structures, molecular dynamics simulations and electrostatic field calculations were performed to explore the impact of thioldisulfide balance on CoV/CoV-2 and ACE2 binding affinities. The structural and dynamical changes due to the change in the redox states of cysteines in the interacting proteins were analyzed and their effects on binding free energies were studied. abstract: The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress. url: https://doi.org/10.1101/2020.05.07.083147 doi: 10.1101/2020.05.07.083147 id: cord-330478-g9n2mfni author: Hattenbach, Lars-Olof title: Krisenstrategien der Kliniken während der Pandemie date: 2020-07-01 words: 1540.0 sentences: 184.0 pages: flesch: 41.0 cache: ./cache/cord-330478-g9n2mfni.txt txt: ./txt/cord-330478-g9n2mfni.txt summary: authors: Hattenbach, Lars-Olof; Reinhard, Thomas; Walter, Peter; Roider, Johannes; Feltgen, Nicolas; Hesse, Lutz; Schrecker, Jens; Eter, Nicole Hintergrund Die SARS-CoV-2(Severe Acute Respiratory Syndrome Coronavirus 2)-Pandemie hat während der ersten Monate des Jahres 2020 weltweit zu tiefgreifenden Veränderungen der medizinischen Versorgung mit massiven Einschränkungen bei chirurgischen Eingriffen und nichtdringlichen ambulanten wie stationären Behandlungen geführt [1] [2] [3] [4] . Jüngere Publikationen zeigen jedoch, dass das Risiko einer Ansteckung durch Tränenflüssigkeit selbst bei COVID-19-Patienten eher gering ist und auch die Häufigkeit des Auftretens einer Konjunktivitis nur bei etwa 1 % liegt [12] [13] [14] . Despite the challenge of a significant shift of medical resources during the SARS-CoV-2 pandemic, medically urgently necessary ophthalmological treatments are continuously provided by maximum care clinics; however, based on currently available data, it cannot be ruled out whether treatment of emergency patients was delayed during the pandemic. abstract: BACKGROUND: The SARS-CoV‑2 pandemic has led worldwide to substantial limitations in healthcare systems. This article describes the recent developments and measures from March through May 2020, which have contributed to the maintenance of ophthalmological care at in-patient departments of ophthalmology. METHODS: PubMed literature search, own data, interhospital survey. RESULTS: The rapid implementation of infection and hygiene control measures and adaptation of standard operating procedures (SOP) to minimize the risk of infection, along with prioritized urgent and emergency care combined with postponement of elective procedures enabled the continuous care of ophthalmological patients. CONCLUSION: Despite the challenge of a significant shift of medical resources during the SARS-CoV‑2 pandemic, medically urgently necessary ophthalmological treatments are continuously provided by maximum care clinics; however, based on currently available data, it cannot be ruled out whether treatment of emergency patients was delayed during the pandemic. url: https://doi.org/10.1007/s00347-020-01162-x doi: 10.1007/s00347-020-01162-x id: cord-328381-bfvdhai8 author: Hattermann, K. title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus date: 2005-01-13 words: 1829.0 sentences: 103.0 pages: flesch: 60.0 cache: ./cache/cord-328381-bfvdhai8.txt txt: ./txt/cord-328381-bfvdhai8.txt summary: In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown). abstract: In order to define and characterize target cells of SARS-coronavirus (SARS-CoV) we studied the susceptibility of 23 different permanent and primary eukaryotic cell lines to SARS-coronavirus. Beneath Vero E6 cells SARS- Coronavirus infection could also be demonstrated in two pig cell lines (POEK, PS) and one human cell line (Huh-7) using the indirect immunofluorescence assay and a newly established quantitative real-time PCR. In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. Our results show that there is a correlation between the abundance of ACE2 mRNA and SARS-CoV susceptibility. url: https://www.ncbi.nlm.nih.gov/pubmed/15645376/ doi: 10.1007/s00705-004-0461-1 id: cord-295946-p9enjxiq author: Hattori, Shin-ichiro title: GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection date: 2020-08-20 words: 7044.0 sentences: 390.0 pages: flesch: 54.0 cache: ./cache/cord-295946-p9enjxiq.txt txt: ./txt/cord-295946-p9enjxiq.txt summary: We assessed various newly generated compounds that target the main protease (M(pro)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. When VeroE6 cells were exposed to SARS-CoV-2 WK-521 at a multiplicity of infection (MOI) of 0.05 and cultured in the presence of various concentrations of the two indole chloropyridinyl esters GRL-0820 and GRL-0920, the compounds were found to be highly potent against SARS-CoV-2 WK-521 with 50% effective concentration (EC 50 ) values of 15 Ϯ 18 and 2.8 Ϯ 0.3 M, respectively, using RNA-qPCR (Table 1) . When VeroE6 TMPRSS2 cells were exposed to SARS-CoV-2 WK-521 and cultured in the presence of various concentrations of lopinavir and nelfinavir, many virus-infected cells were seen at 1 and 10 M and stained in green, indicating that these two compounds had no detectable antiviral activity in the assay. abstract: We assessed various newly generated compounds that target the main protease (M(pro)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. Here, we show that two indole-chloropyridinyl-ester derivatives, GRL-0820 and GRL-0920, exerted potent activity against SARS-CoV-2 in cell-based assays performed using VeroE6 cells and TMPRSS2-overexpressing VeroE6 cells. While GRL-0820 and the nucleotide analog remdesivir blocked SARS-CoV-2 infection, viral breakthrough occurred. No significant anti-SARS-CoV-2 activity was found for several compounds reportedly active against SARS-CoV-2 such as lopinavir, nelfinavir, nitazoxanide, favipiravir, and hydroxychroloquine. In contrast, GRL-0920 exerted potent activity against SARS-CoV-2 (50% effective concentration [EC(50)] = 2.8 μM) and dramatically reduced the infectivity, replication, and cytopathic effect of SARS-CoV-2 without significant toxicity as examined with immunocytochemistry. Structural modeling shows that indole and chloropyridinyl of the derivatives interact with two catalytic dyad residues of M(pro), Cys145 and His41, resulting in covalent bonding, which was verified using high-performance liquid chromatography–mass spectrometry (HPLC/MS), suggesting that the indole moiety is critical for the anti-SARS-CoV-2 activity of the derivatives. GRL-0920 might serve as a potential therapeutic for coronavirus disease 2019 (COVID-19) and might be optimized to generate more-potent anti-SARS-CoV-2 compounds. url: https://doi.org/10.1128/mbio.01833-20 doi: 10.1128/mbio.01833-20 id: cord-254900-fg5wd0nh author: Havenga, M.J.E. title: Serum‐free transient protein production system based on adenoviral vector and PER.C6 technology: High yield and preserved bioactivity date: 2007-12-13 words: 7456.0 sentences: 339.0 pages: flesch: 48.0 cache: ./cache/cord-254900-fg5wd0nh.txt txt: ./txt/cord-254900-fg5wd0nh.txt summary: Because of these features it can be envisioned that the use of adenoviral vectors results in higher protein yields derived from mammalian cells cultured in suspension as compared to current DNA transfection protocols for which processes at scale like cell uptake and nuclear localization, present major technical hurdles. Based on the data obtained thus far it was concluded that an DE1/DE2A adenoviral vector can be efficiently produced at 348C on PER.E2A cells and can subsequently serve as a tranducing agent for PER.C6 cells without inducing viral backbone replication or high level viral capsid protein expression in human A549 indicator cells. As shown in Figure 2C the yield of SARS anti-body produced did not significantly differ demonstrating that cleared vector stock directly harvested from he PER.E2A cell line can be used for production of recombinant protein without compromising yield. abstract: Stable E1 transformed cells, like PER.C6, are able to grow at scale and to high cell densities. E1‐deleted adenoviruses replicate to high titer in PER.C6 cells whereas subsequent deletion of E2A from the vector results in absence of replication in PER.C6 cells and drastically lowers the expression of adenovirus proteins in such cells. We therefore considered the use of an ΔE1/ΔE2 type 5 vector (Ad5) to deliver genes to PER.C6 cells growing in suspension with the aim to achieve high protein yield. To evaluate the utility of this system we constructed ΔE1/ΔE2 vector carrying different classes of protein, that is, the gene coding for spike protein derived from the Coronavirus causing severe acute respiratory syndrome (SARS‐CoV), a gene coding for the SARS‐CoV receptor or the genes coding for an antibody shown to bind and neutralize SARS‐CoV (SARS‐AB). The ΔE1/ΔE2A‐vector backbones were rescued on a PER.C6 cell line engineered to constitutively over express the Ad5 E2A protein. Exposure of PER.C6 cells to low amounts (30 vp/cell) of ΔE1/ΔE2 vectors resulted in highly efficient (>80%) transduction of PER.C6 cells growing in suspension. The efficient cell transduction resulted in high protein yield (up to 60 picogram/cell/day) in a 4 day batch production protocol. FACS and ELISA assays demonstrated the biological activity of the transiently produced proteins. We therefore conclude that ΔE1/ΔE2 vectors in combination with the PER.C6 technology may provide a viable answer to the increasing demand for high quality, high yield recombinant protein. Biotechnol. Bioeng. 2008;100: 273–283. © 2007 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/18512821/ doi: 10.1002/bit.21757 id: cord-316215-4mj7n0ax author: Haveri, Anu title: Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020 date: 2020-03-19 words: 2968.0 sentences: 156.0 pages: flesch: 53.0 cache: ./cache/cord-316215-4mj7n0ax.txt txt: ./txt/cord-316215-4mj7n0ax.txt summary: Suspicion of COVID-19 led to her direct transfer to the Lapland Central Hospital in Rovaniemi, where she was isolated and sampled on 28 and 29 January for laboratory confirmation of SARS-CoV-2 infection ( Figure 1 ). SARS-CoV-2 infection was confirmed from nasopharyngeal samples on 29 January by the Helsinki University Hospital Laboratory (HUSLAB), and further confirmed at the Finnish Institute for Health and Welfare (THL) ( Table) . Presence of serum IgM and IgG antibodies against SARS-CoV-2 was analysed by immunofluorescence assays (IFA) based on Vero E6 cells infected with passage 4 of the patient''s isolate SARS-CoV-2/ Finland/1/2020 virus and transferred onto microscope slides and fixed with acetone ( Figure 2 ). Western blot of mock-and SARS-CoV-2 infected Vero E6 cells using patient serum collected 20 days after onset of symptoms, Finland, January-February 2020 No neutralising SARS-CoV-2 antibodies were detected in the close contacts nor in the control population samples collected during 2019 in Finland. abstract: The first case of coronavirus disease (COVID-19) in Finland was confirmed on 29 January 2020. No secondary cases were detected. We describe the clinical picture and laboratory findings 3–23 days since the first symptoms. The SARS-CoV-2/Finland/1/2020 virus strain was isolated, the genome showing a single nucleotide substitution to the reference strain from Wuhan. Neutralising antibody response appeared within 9 days along with specific IgM and IgG response, targeting particularly nucleocapsid and spike proteins. url: https://doi.org/10.2807/1560-7917.es.2020.25.11.2000266 doi: 10.2807/1560-7917.es.2020.25.11.2000266 id: cord-288284-fghu8ouc author: Hawryluck, Laura title: Clinical review: SARS – lessons in disaster management date: 2005-01-13 words: 4269.0 sentences: 182.0 pages: flesch: 45.0 cache: ./cache/cord-288284-fghu8ouc.txt txt: ./txt/cord-288284-fghu8ouc.txt summary: Infectious diseases, whether they be natural (e.g. SARS [severe acute respiratory syndrome] and influenza) or the result of bioterrorism, have the potential to create a large influx of critically ill into our already strained hospital systems. Core to any disaster management plan are leaders with clear responsibilities to coordinate efforts and develop policies to contain the disease; to coordinate resource allocation and manpower; to advise and share information regarding infection control and treatment; to share data and research endeavours; to maintain staff morale; and to provide information to various levels of government, health care institutions, front-line workers and the public [1, 13] . The model we propose (Fig. 1 ) is one of a Central Critical Care Crisis Team, composed of leaders of different subteams of multidisciplinary professionals responsible for domains of crucial importance: clinical management, infection control, education, communication, team morale, manpower and system thinking, data collection, research and, finally, lobbying to ensure resources are available to meet critical care needs. abstract: Disaster management plans have traditionally been required to manage major traumatic events that create a large number of victims. Infectious diseases, whether they be natural (e.g. SARS [severe acute respiratory syndrome] and influenza) or the result of bioterrorism, have the potential to create a large influx of critically ill into our already strained hospital systems. With proper planning, hospitals, health care workers and our health care systems can be better prepared to deal with such an eventuality. This review explores the Toronto critical care experience of coping in the SARS outbreak disaster. Our health care system and, in particular, our critical care system were unprepared for this event, and as a result the impact that SARS had was worse than it could have been. Nonetheless, we were able to organize a response rapidly during the outbreak. By describing our successes and failures, we hope to help others to learn and avoid the problems we encountered as they develop their own disaster management plans in anticipation of similar future situations. url: https://www.ncbi.nlm.nih.gov/pubmed/16137388/ doi: 10.1186/cc3041 id: cord-277313-5f5lrn3c author: Hayakawa, Satoshi title: Covid‐19 pandemic and pregnancy date: 2020-08-10 words: 4622.0 sentences: 280.0 pages: flesch: 51.0 cache: ./cache/cord-277313-5f5lrn3c.txt txt: ./txt/cord-277313-5f5lrn3c.txt summary: 20 However, fortunately, clinical data suggest no deleterious outcomes of pregnant women who are infected with COVID-19 during pregnancy compared with those infected with SARS-CoV or MERS. In another report from Wuhan, of 13 pregnant women who developed COVID-19 during pregnancy, one woman delivered a dead fetus at 34 weeks of gestation, but the cause of fetal death was speculated to be severe maternal pneumonia and multiple organ failure rather than viral infection of the fetus. 22 Another report showed that 3 of 33 pregnant women who developed COVID-19 during pregnancy in Wuhan showed evidence of intrauterine infection by cord blood PCR test. While early studies showed no evidence of vertical transmission of SARS-CoV-2 from mother-to-child in late pregnancy, 21 recent reports have shown possible in utero transmission. Coronavirus disease 2019 (COVID-19) in pregnant women: A report based on 116 cases abstract: At the end of 2019, a new coronavirus disease, COVID‐19, emerged and quickly spread around the world. Severe acute respiratory syndrome Coronavirus 2 (SARS‐CoV‐2), the causative virus of this disease, belongs to the β‐coronavirus family, together with SARS and middle east respiratory syndrome, and has similar biological characteristics to these viruses. For obstetricians, the susceptibility and prognoses of pregnant women and the effects of the infection on the fetus have been the focus of attention; however, at present, the seriousness of the disease in pregnant women is not apparent, and COVID‐19 does not increase the rate of miscarriage, stillbirth, preterm labor or teratogenicity. Even so, carriers might transmit SARS‐CoV‐2 to pregnant women. Thus, we must keep in mind that all medical personnel must understand and maintain standard precautions in their clinical and laboratory practices. url: https://www.ncbi.nlm.nih.gov/pubmed/32779342/ doi: 10.1111/jog.14384 id: cord-252428-w6tsf478 author: Hayashi, Takuma title: Highly conserved binding region of ACE2 as a receptor for SARS-CoV-2 between humans and mammals date: 2020-09-29 words: 2696.0 sentences: 158.0 pages: flesch: 52.0 cache: ./cache/cord-252428-w6tsf478.txt txt: ./txt/cord-252428-w6tsf478.txt summary: The multiple sequence alignments of the ACE2 proteins shows high homology and complete conservation of the five amino acid residues: 353-KGDFR-357 with humans, dogs, cats, tigers, minks, and other animals, except for snakes. (B) The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks. The multiple sequence alignments of the sampled ACE2 proteins revealed high homology and high conservation of the five amino acid residues: 353-KGDFR-357 with specific reference to humans, dogs, cats, tigers, minks, and other animals, except for snakes ( Figure 1 (A) and Supplementary Materials). The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks (Figure 1(B) ). abstract: Several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection transmitted from human owners to their dogs have recently been reported. The first ever case of SARS-CoV-2 transmission from a human owner to a domestic cat was confirmed on March 27, 2020. A tiger from a zoo in New York, USA, was also reportedly infected with SARS-CoV-2. It is believed that SARS-CoV-2 was transmitted to tigers from their caretakers, who were previously infected with this virus. On May 25, 2020, the Dutch Minister of Agriculture, Nature and Food Quality reported that two employees were infected with SARS-CoV-2 transmitted from minks. These reports have influenced us to perform a comparative analysis among angiotensin-converting enzyme 2 (ACE2) homologous proteins for verifying the conservation of specific protein regions. One of the most conserved peptides is represented by the peptide “353-KGDFR-357 (H. sapiens ACE2 residue numbering), which is located on the surface of the ACE2 molecule and participates in the binding of SARS-CoV-2 spike receptor binding domain (RBD). Multiple sequence alignments of the ACE2 proteins by ClustalW, whereas the three-dimensional structure of its binding region for the spike glycoprotein of SARS-CoV-2 was assessed by means of Spanner, a structural homology modeling pipeline method. In addition, evolutionary phylogenetic tree analysis by ETE3 was used. ACE2 works as a receptor for the SARS-CoV-2 spike glycoprotein between humans, dogs, cats, tigers, minks, and other animals, except for snakes. The three-dimensional structure of the KGDFR hosting protein region involved in direct interactions with SARS-CoV-2 spike RBD of the mink ACE2 appears to form a loop structurally related to the human ACE2 corresponding protein loop, despite of the reduced available protein length (401 residues of the mink ACE2 available sequence vs 805 residues of the human ACE2). The multiple sequence alignments of the ACE2 proteins shows high homology and complete conservation of the five amino acid residues: 353-KGDFR-357 with humans, dogs, cats, tigers, minks, and other animals, except for snakes. Where the information revealed from our examinations can support precision vaccine design and the discovery of antiviral therapeutics, which will accelerate the development of medical countermeasures, the World Health Organization recently reported on the possible risks of reciprocal infections regarding SARS-CoV-2 transmission from animals to humans. url: https://www.ncbi.nlm.nih.gov/pubmed/32921279/ doi: 10.1080/01652176.2020.1823522 id: cord-342915-r9kv67we author: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 words: 5748.0 sentences: 281.0 pages: flesch: 33.0 cache: ./cache/cord-342915-r9kv67we.txt txt: ./txt/cord-342915-r9kv67we.txt summary: Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. abstract: Progress in the development of antivirals for non‐influenza respiratory viruses has been slow with the result that many unmet medical needs and few approved agents currently exist. This commentary selectively reviews examples of where specific agents have provided promising clinical benefits in selected target populations and also considers potential therapeutics for emerging threats like the SARS and Middle East respiratory syndrome coronaviruses. Recent studies have provided encouraging results in treating respiratory syncytial virus infections in lung transplant recipients, serious parainfluenza virus and adenovirus infections in immunocompromised hosts, and rhinovirus colds in outpatient asthmatics. While additional studies are needed to confirm the efficacy and safety of the specific agents tested, these observations offer the opportunity to expand therapeutic studies to other patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/24215380/ doi: 10.1111/irv.12173 id: cord-334624-chnibsa1 author: Hayn, Manuel title: Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date: 2020-10-30 words: 5355.0 sentences: 432.0 pages: flesch: 57.0 cache: ./cache/cord-334624-chnibsa1.txt txt: ./txt/cord-334624-chnibsa1.txt summary: Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation. SARS-CoV-1 ORF6 is about 4-fold less potent in antagonizing type I IFN signaling (Fig. 243 4b) but induces higher levels of autophagy (Fig. 4c) . Examination of the functional conservation showed that SARS-CoV-2 Nsp15 was less 319 efficient in blocking innate immune activation, both type I IFN induction and signaling, than SARS-320 Hepatitis C virus viruses to block anti-viral autophagic turnover 50 and thus may represent a common studies will see more mechanistic data to explain the molecular details of the impact of SARS-CoV-2 343 proteins on innate immune activation. abstract: The innate immune system constitutes a powerful barrier against viral infections. However, it may fail because successful emerging pathogens, like SARS-CoV-2, evolved strategies to counteract it. Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Mechanistic analyses show that autophagy and type I IFN responses are effectively counteracted at different levels. For example, Nsp14 induces loss of the IFN receptor, whereas ORF3a disturbs autophagy at the Golgi/endosome interface. Comparative analyses revealed that antagonism of type I IFN and autophagy is largely conserved, except that SARS-CoV-1 Nsp15 is more potent in counteracting type I IFN than its SARS-CoV-2 ortholog. Altogether, however, SARS-CoV-2 counteracts type I IFN responses and autophagy much more efficiently than type II and III IFN signaling. Consequently, the virus is relatively resistant against exogenous IFN-α/β and autophagy modulation but remains highly vulnerable towards IFN-γ and -λ treatment. In combination, IFN-γ and -λ act synergistically, and drastically reduce SARS-CoV-2 replication at exceedingly low doses. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation. url: https://doi.org/10.1101/2020.10.15.340612 doi: 10.1101/2020.10.15.340612 id: cord-288153-2qsh2dlk author: Hays, Priya title: Clinical sequelae of the novel coronavirus: does COVID-19 infection predispose patients to cancer? date: 2020-05-27 words: 4322.0 sentences: 225.0 pages: flesch: 41.0 cache: ./cache/cord-288153-2qsh2dlk.txt txt: ./txt/cord-288153-2qsh2dlk.txt summary: Major signaling pathways implicated in aberrant cellular growth are activated, the ensuing cytokine storm weakens the immune system response to tumors, and patients may develop cancer as a result of superimposed mutagenic and/or carcinogenic events. There may be a distinct association between novel coronavirus infection and the onset of cancer through the activation of the MAPK and JAK-STAT signaling pathways and the NF-κB transcription factor. The turning on of oncogenic signaling pathways and the acute inflammatory response that results upon coronavirus infection can be hypothesized as being cancer inducing, or leading to the risk of developing cancer, especially if the patient has a superimposed mutagenic or carcinogenic event occurring concomitantly, even if the virus does not cause a chronic infection like viruses such as HCV, HCV and EBV. Oncologic sequelae of the novel coronavirus • Viral infection induces a robust immune response, a ''cytokine storm'' leading to tissue damage and inflammation, which may predispose to cancer. abstract: As cancer patients are clinically known to be predisposed to COVID-19 infection, a corollary question of whether COVID-19 infection predisposes to cancer is explored. This article seeks to establish an association between novel coronavirus sequelae and cancer. A literature review on COVID-19 mechanisms of action, molecular responses it elicits upon infection and tumorigenesis pathways is conducted to establish this association. Major signaling pathways implicated in aberrant cellular growth are activated, the ensuing cytokine storm weakens the immune system response to tumors, and patients may develop cancer as a result of superimposed mutagenic and/or carcinogenic events. Future work needs to be performed to support this hypothesis, both in in vitro models and preclinical studies. COVID-19 patients may need to be monitored post-infection for developing cancer. url: https://doi.org/10.2217/fon-2020-0300 doi: 10.2217/fon-2020-0300 id: cord-313246-2gtiqrnj author: Hazra, Aniruddha title: Coinfections with SARS-CoV-2 and other respiratory pathogens date: 2020-07-03 words: 801.0 sentences: 52.0 pages: flesch: 50.0 cache: ./cache/cord-313246-2gtiqrnj.txt txt: ./txt/cord-313246-2gtiqrnj.txt summary: 3 The same specimen can be tested via RT-PCR for a respiratory panel (RP) of other common pathogens, including adenovirus, coronavirus 229E/HKU1/NL63/OC43, human metapneumovirus, influenza A/B, parainfluenza 1-4, respiratory syncytial virus, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, and rhinovirus/enterovirus (BioFire FilmArray respiratory panel 2). This report examines patients with influenza-like illness symptoms who were simultaneously tested for SARS-CoV-2 and the above panel from March 12, 2020, through April 15, 2020. During the observed period, 2,535 specimens were simultaneously tested for SARS-CoV-2 and RP pathogens on 2,458 symptomatic patients. Notably, the median age of coinfected patients was nearly 20 years younger than those only infected with SARS-CoV-2. During the study period, the Illinois Department of Public Health noted a decline in influenza tests positivity from 14.9% to 1.6% between the weeks ending March 14, 2020, and April 11, 2020, respectively. Rates of coinfection between SARS-CoV-2 and other respiratory pathogens abstract: nan url: https://doi.org/10.1017/ice.2020.322 doi: 10.1017/ice.2020.322 id: cord-330692-rqwkkfp0 author: He, Daihai title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date: 2020-06-26 words: 727.0 sentences: 50.0 pages: flesch: 56.0 cache: ./cache/cord-330692-rqwkkfp0.txt txt: ./txt/cord-330692-rqwkkfp0.txt summary: title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom We found that the on-going COVID-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. The fast spread and high fatality of the coronavirus disease 2019 (COVID-19) remind us of the first pandemic in last century, the 1918-19 influenza pandemic. A comparison between the YLLs for COVID-19 and 1918-19 influenza should be conducted, because YLL is the other important indicator of the severity of a pandemic. If we assume a 0.5% IFR for COVID-19 in 2020 and a 2% infection fatality rate in 1918, we may calculate and compare the infections based on reported deaths which should be more reliable than reported cases. abstract: Abstract We compare the COVID-19 pandemic and 1918-19 influenza pandemic in United Kingdom. We found that the on-going COVID-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. We discussed the similar characteristics between these two pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32599281/ doi: 10.1016/j.ijid.2020.06.075 id: cord-264148-qpcvxwti author: He, Feng title: Coronavirus disease 2019: What we know? date: 2020-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In late December 2019, a cluster of unexplained pneumonia cases has been reported in Wuhan, China. A few days later, the causative agent of this mysterious pneumonia was identified as a novel coronavirus. This causative virus has been temporarily named as severe acute respiratory syndrome coronavirus 2 and the relevant infected disease has been named as coronavirus disease 2019 (COVID‐19) by the World Health Organization, respectively. The COVID‐19 epidemic is spreading in China and all over the world now. The purpose of this review is primarily to review the pathogen, clinical features, diagnosis, and treatment of COVID‐19, but also to comment briefly on the epidemiology and pathology based on the current evidence. url: https://www.ncbi.nlm.nih.gov/pubmed/32170865/ doi: 10.1002/jmv.25766 id: cord-299899-is815pol author: He, Jingjing title: Proportion of asymptomatic coronavirus disease 2019 (COVID‐19): a systematic review and meta‐analysis date: 2020-07-21 words: 2576.0 sentences: 191.0 pages: flesch: 46.0 cache: ./cache/cord-299899-is815pol.txt txt: ./txt/cord-299899-is815pol.txt summary: The pooled proportion of asymptomatic infection among 1152 COVID‐19 children from 11 studies is 27.7% (95% CI: 16.4–42.7%), which is much higher than patients from all aged groups. However, patients infected with SARS-CoV-2 could also be asymptomatic, confirmed by positive Nucleic acid testing results during the illness. While a variety of studies on asymptomatic infection have been reported, the proportion of asymptomatic patients in confirmed COVID-19 cases is not well characterized. Original articles reporting asymptomatic infection in confirmed COVID-19 patients were included for meta-analysis. Noticeably, one study from Wuhan showed that 98/1021(9.6%) nucleic acid testing negative patients had lgG positive results, suggesting possible recovery from asymptomatic SARS-CoV-2 infection 54 . Characteristics of asymptomatic patients with SARS-CoV-2 infection in Jinan, China. Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha, China. Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection abstract: OBJECTIVE: We aim to systematically review the characteristics of asymptomatic infection in the coronavirus disease 2019 (COVID‐19). METHODS: PubMed and EMBASE were electronically searched to identify original studies containing the rate of asymptomatic infection in COVID‐19 patients before 20 May 2020. Then mate‐analysis was conducted using R version 3.6.2. RESULTS: A total of 50155 patients from 41 studies with confirmed COVID‐19 were included. The pooled percentage of asymptomatic infection is 15.6% (95% CI: 10.1%‐23.0%). Ten included studies contain the number of pre‐symptomatic patients, who were asymptomatic at screening point and developed symptoms during follow‐up. The pooled percentage of pre‐symptomatic infection among 180 initially asymptomatic patients is 48.9% (95% CI: 31.6‐66.2%). The pooled proportion of asymptomatic infection among 1152 COVID‐19 children from 11 studies is 27.7% (95% CI: 16.4–42.7%), which is much higher than patients from all aged groups. Abnormal CT features are common in asymptomatic COVID‐19 infection. For 36 patients from 4 studies that CT results were available, 15 (41.7%) patients had bilateral involvement and 14 (38.9%) had unilateral involvement in CT results. Reduced white blood cell count, increased lactate dehydrogenase, and increased C‐reactive protein were also recorded. CONCLUSION: About 15.6% of confirmed COVID‐19 patients are asymptomatic. Nearly half of the patients with no symptoms at detection time will develop symptoms later. Children are likely to have a higher proportion of asymptomatic infection than adults. Asymptomatic COVID‐19 patients could have abnormal laboratory and radiational manifestations which can be used as screening strategies to identify asymptomatic infection. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32691881/ doi: 10.1002/jmv.26326 id: cord-277186-sj8ngpk8 author: He, Qigai title: Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA date: 2005-04-19 words: 4192.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-277186-sj8ngpk8.txt txt: ./txt/cord-277186-sj8ngpk8.txt summary: Specific binding of the MAb S-A5D5 to both purified N195 and SARS CoV nucleocapsid antigen was effectively inhibited by human SARS positive serum and guinea pig anti-N195 serum. The monoclonal antibodies were characterized by SARS CoV-infected Vero cells and nucleocapsid-spike fusion protein-based IFA, Western blot, and N195 proteinbased ELISA. The isotype of the promising monoclonal antibody, designated as S-A5D5, was determined and was further applied to develop a specific and sensitive antigen capture ELISA for the detection of SARS CoV. The specific reactivity of the MAb S-A5D5 with purified N195 protein (Fig. 3A ) was identical to that of the human SARS positive serum (Fig. 3B) , while no reaction was observed when non-antibody secreting hybridoma was tested (Fig. 3C) . Therefore, this antigen capture ELISA, based on MAb to N protein, might provide a more sensitive method for early detection of SARS CoV infection. abstract: This report describes the production of several MAbs against N195 protein, a major immunodomain of SARS CoV nucleocapsid protein [He, Q., Chong, K.H., Chang, H.H., Leung, B., Ling, A.E., Wei, T., Chan, S.W., Ooi, E.E., Kwang, J., 2004. Development of a Western blot assay for detection of antibodies against coronavirus causing severe acute respiratory syndrome. Clin. Diagn. Lab. Immunol. 11 (2) 417–422.]. One representative IgG1 monoclonal antibody (MAb), S-A5D5, was selected and characterized. S-A5D5 reacted specifically react with both recombinant and native nucleocapsid protein of SARS CoV. The reactivity of S-A5D5 with purified N195 protein and utilization of the MAb as a detector antibody to develop an antigen capture ELISA was assessed. As little as 37.5 pg of purified N protein and 50 TCID(50) of SARS CoV could be detected by the antigen capture ELISA. Specific binding of the MAb S-A5D5 to both purified N195 and SARS CoV nucleocapsid antigen was effectively inhibited by human SARS positive serum and guinea pig anti-N195 serum. The N protein in N195-spike recombinant baculovirus-infected Sf-9 cells could also be identified. N protein was detected in 18 IFA IgM-positive serum samples collected from SARS confirmed patients, but not in nine samples collected from SARS recovery patient. No false positive results were given when 60 samples from healthy individuals were tested, and no cross-reaction occurred when infectious bronchitis virus (IBV), chicken coronavirus, was tested. This monoclonal antibody-based antigen capture ELISA is thus a powerful tool for early diagnosis of SARS CoV infection. url: https://api.elsevier.com/content/article/pii/S0166093405000856 doi: 10.1016/j.jviromet.2005.03.004 id: cord-255586-wshvvgxg author: He, Shengyang title: Clinical characteristics of “re-positive” discharged COVID-19 pneumonia patients in Wuhan, China date: 2020-10-15 words: 2920.0 sentences: 163.0 pages: flesch: 45.0 cache: ./cache/cord-255586-wshvvgxg.txt txt: ./txt/cord-255586-wshvvgxg.txt summary: The demographic features, clinical symptoms, laboratory results, comorbidities, co-infections, treatments, illness severities and chest CT scan results of 267 patients were collected from 1st January to 15th February 2020. | (2020) 10:17365 | https://doi.org/10.1038/s41598-020-74284-6 www.nature.com/scientificreports/ disease progression, no differences were found, suggesting this group of COVID-19 patients could be difficult to detect by using standard clinical data. All raw clinical and laboratory results were collected from electronic medical records system of the Central Hospital of Wuhan, followed by a follow up visit up to 14 days (also known as the discharge quarantine) to test for a re-positive nucleic acid assay. Definition of "re-positive": when a confirmed COVID-19 patient is detected SARS-CoV-2 RNA positive during the 14 days post-discharge quarantine (random test timing). Since understanding of the mechanisms of SARS-CoV-2 infection is still lacking, a careful discharge protocol should be applied (e.g. negative results of the nucleic acid tests of respiratory pathogens for 3 consecutive times), and post-discharge quarantine should be strictly observed, especially for severe and critical COVID-19 patients. abstract: To analyze the clinical characteristics of re-positive discharged COVID-19 patients and find distinguishing markers. The demographic features, clinical symptoms, laboratory results, comorbidities, co-infections, treatments, illness severities and chest CT scan results of 267 patients were collected from 1st January to 15th February 2020. COVID-19 was diagnosed by RT-PCR. Clinical symptoms and nucleic acid test results were collected during the 14 days post-hospitalization quarantine. 30 out of 267 COVID-19 patients were detected re-positive during the post-hospitalization quarantine. Re-positive patients could not be distinguished by demographic features, clinical symptoms, laboratory results, comorbidities, co-infections, treatments, chest CT scan results or subsequent clinical symptoms. However, re-positive rate was found to be correlated to illness severity, according the Acute Physiology and Chronic Health Evaluation II (APACHE II) severity-of-disease classification system, and the confusion, urea, respiratory rate and blood pressure (CURB-65) score. Common clinical characteristics were not able to distinguish re-positive patients. However, severe and critical cases classified high according APACHE II and CURB-65 scores, were more likely to become re-positive after discharge. url: https://doi.org/10.1038/s41598-020-74284-6 doi: 10.1038/s41598-020-74284-6 id: cord-254855-gmy9zyad author: He, Sijia title: PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date: 2020-07-06 words: 1700.0 sentences: 94.0 pages: flesch: 51.0 cache: ./cache/cord-254855-gmy9zyad.txt txt: ./txt/cord-254855-gmy9zyad.txt summary: Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. Together, these results demonstrate that PSGL-1 expression in the virus-producer cells severely diminishes the infectivity of virions bearing SARS coronavirus S proteins. We and other previously reported that PSGL-1-mediated inhibition of virion infectivity is through steric hindrance of particle attachment to target cells, which does not depend on the presence of viral envelope glycoproteins (1, 5) . We performed a virion attachment assay and observed that the lentiviral particles pseudotyped with SARS-CoV or SARS-CoV-2 S protein produced from PSGL-1-expressing cells were impaired in their ability to attach to target cells (Fig. 2D) . These results demonstrate that the presence of PSGL-1 on virus particles can structurally hinder virion interaction with the target cells even in the presence of remaining S proteins, consistent with previous studies of PSGL-1 and HIV-1 infection (1, 5) . abstract: P-selectin glycoprotein ligand-1 (PSGL-1) is a cell surface glycoprotein that binds to P-, E-, and L-selectins to mediate the tethering and rolling of immune cells on the surface of the endothelium for cell migration into inflamed tissues. PSGL-1 has been identified as an interferon-γ (INF-γ)-regulated factor that restricts HIV-1 infectivity, and has recently been found to possess broad-spectrum antiviral activities. Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. These findings suggest that PSGL-1 may potentially inhibit coronavirus replication in PSGL-1+ cells. url: https://www.ncbi.nlm.nih.gov/pubmed/32511349/ doi: 10.1101/2020.05.01.073387 id: cord-334443-3pyu8ucs author: He, Yu title: Public health might be endangered by possible prolonged discharge of SARS-CoV-2 in stool date: 2020-03-05 words: 1015.0 sentences: 61.0 pages: flesch: 55.0 cache: ./cache/cord-334443-3pyu8ucs.txt txt: ./txt/cord-334443-3pyu8ucs.txt summary: According to a recent report, since December 8 2019, a novel identified coronavirus, SARS-CoV-2(previously named as 2019-nCOV) is causing outbreak of pneumonia in Wuhan, China and become the major concern throughout the world [1] . Those early reports may not represent actual rate of gastrointestinal symptoms caused by SARS-CoV-2, because in early stages of the outbreak, the limited resources for detection were only provided to those patients with severe symptoms like respiratory distress syndrome. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Detection and monitoring of SARS coronavirus in the plasma and peripheral blood lymphocytes of patients with severe acute respiratory syndrome abstract: • The published data, which showed the COVID-19 patients with low digestive. • manifestation, might be misleading. Case with negative URT test showed positive in. • rectal scarab which challenge the isolation protocol. • As fomite transmission caused clusters of infection of SARS, adequate disinfection. • operations should be adopted in SARS-CoV-2 outbreak. url: https://doi.org/10.1016/j.jinf.2020.02.031 doi: 10.1016/j.jinf.2020.02.031 id: cord-301693-3hsu2u1k author: He, Yuwen title: Value of Viral Nucleic Acid in Sputum and Feces and Specific IgM/IgG in Serum for the Diagnosis of Coronavirus Disease 2019 date: 2020-08-06 words: 3551.0 sentences: 184.0 pages: flesch: 53.0 cache: ./cache/cord-301693-3hsu2u1k.txt txt: ./txt/cord-301693-3hsu2u1k.txt summary: To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We undertook a study on the viral nucleic acids of SARS-CoV-2 in swabs (nasal, pharyngeal), sputum and feces, as well as antibodies in the serum of COVID-19 patients admitted to the First Affiliated Hospital of Guangzhou Medical University, China. abstract: A new type of coronavirus-induced pneumonia eventually termed “coronavirus disease 2019” (COVID-19) was diagnosed in patients in Wuhan (Hubei Province, China) in December 2019, and soon spread worldwide. To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We also recommend for the application of serological test to assist in confirming SARS-CoV-2 infection judged by viral nucleic acid test, especially when COVID-19-related symptoms have appeared and the viral nucleic acid test was negative. Our findings are critical for the diagnosis of SARS-CoV-2 infection and for determining deadline of restriction measures to prevent transmission caused by convalescent patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32850506/ doi: 10.3389/fcimb.2020.00445 id: cord-323514-jaom3p6s author: He, Yuxian title: A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date: 2006-05-26 words: 4007.0 sentences: 182.0 pages: flesch: 48.0 cache: ./cache/cord-323514-jaom3p6s.txt txt: ./txt/cord-323514-jaom3p6s.txt summary: Abstract The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has two major functions: interacting with the receptor to mediate virus entry and inducing protective immunity. Coincidently, the receptor-binding domain (RBD, residues 318–510) of SAR-CoV S protein is a major antigenic site to induce neutralizing antibodies. We also demonstrated that the RBD-Fc bearing R441A mutation could not bind to soluble and cell-associated angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV and failed to block S protein-mediated pseudovirus entry, indicating that this point mutation also disrupted the receptor-binding motif (RBM) in the RBD. In this study, we used the RBD-Fc as a model to study how a single residue mutation in the RBD can abolish the major function of full-length S protein, since this molecule can efficiently bind to the receptor ACE2 and contains multiple conformation-dependent epitopes (Conf I-VI) capable of inducing highly potent neutralizing antibodies [29] . abstract: Abstract The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has two major functions: interacting with the receptor to mediate virus entry and inducing protective immunity. Coincidently, the receptor-binding domain (RBD, residues 318–510) of SAR-CoV S protein is a major antigenic site to induce neutralizing antibodies. Here, we used RBD-Fc, a fusion protein containing the RBD and human IgG1 Fc, as a model in the studies and found that a single amino acid substitution in the RBD (R441A) could abolish the immunogenicity of RBD to induce neutralizing antibodies in immunized mice and rabbits. With a panel of anti-RBD mAbs as probes, we observed that R441A substitution was able to disrupt the majority of neutralizing epitopes in the RBD, suggesting that this residue is critical for the antigenic structure responsible for inducing protective immune responses. We also demonstrated that the RBD-Fc bearing R441A mutation could not bind to soluble and cell-associated angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV and failed to block S protein-mediated pseudovirus entry, indicating that this point mutation also disrupted the receptor-binding motif (RBM) in the RBD. Taken together, these data provide direct evidence to show that a single amino acid residue at key position in the RBD can determine the major function of SARS-CoV S protein and imply for designing SARS vaccines and therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/16615996/ doi: 10.1016/j.bbrc.2006.03.139 id: cord-323908-8dgngwmw author: He, Zhesheng title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date: 2020-05-31 words: 881.0 sentences: 61.0 pages: flesch: 59.0 cache: ./cache/cord-323908-8dgngwmw.txt txt: ./txt/cord-323908-8dgngwmw.txt summary: title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity. These compounds could serve as potential anti-SARS-CoV-2 lead molecules for further drug studies to combat COVID-19. The interactions between the gold atom with the binding pockets of proteins were studied by density functional theory (DFT) calculations. abstract: SARS-CoV-2 has emerged as a world public health threat. Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. Gold cluster could significantly inhibit 3CLpro of SARS-COV-2. Phenyl isothiocyanate and Vitamin K3 could well suppress the activity of 3CLpro. For Mpro inhibition, IC50 of auranofin, Vitamin K3, phenyl isothiocyanate, gold cluster are about 0.51μM, 7.96μM, 10.13μM, 1.61μM, respectively. These compounds may be with potentials for treatment SARS-CoV-2 virus replication. Especially for FDA approved auranofin, it is an anti-inflammation drug in clinic, thus it may with strong potential to inhibit virus replication and suppress the inflammation damage in COVID-19 patients. Gold cluster is with better safety index and well anti-inflammation in vitro/vivo, therefore it is with potential to inhibit virus replication and suppress the inflammation damage caused by COVID-19 virus. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity. url: https://doi.org/10.1101/2020.05.28.120642 doi: 10.1101/2020.05.28.120642 id: cord-320829-uepneyug author: He, Zhongping title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 words: 2631.0 sentences: 138.0 pages: flesch: 59.0 cache: ./cache/cord-320829-uepneyug.txt txt: ./txt/cord-320829-uepneyug.txt summary: title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS abstract: INTRODUCTION: Severe acute respiratory syndrome (SARS) caused large outbreaks of atypical pneumonia in 2003, with the largest localized outbreak occurring in Beijing, China. Lymphopenia was prominent amongst the laboratory abnormalities reported in acute SARS. METHODS: The effect of SARS on peripheral blood lymphocytes and their subsets was examined in 271 SARS coronavirus-infected individuals. RESULTS: There was a significant decrease in the CD45+, CD3+, CD4+, CD8+, CD19+ and CD16+/56+ cell counts over the five weeks of the SARS illness although CD4+/CD8+ ratios did not change significantly. The lymphopenia was prolonged, reaching a nadir during days 7–9 in the second week of illness before returning towards normal after five weeks, with the lowest mean CD4+ cell count of 317 cells × 10(6)/L at day 7, and CD8+ cell count of 239 cells × 10(6)/L at day 8. Patients with more severe clinical illness, or patients who died, had significantly more profound CD4+ and CD8+ lymphopenia. DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Possible reasons for the SARS-associated lymphopenia may be direct infection of lymphocytes by SARS-CoV, lymphocyte sequestration in the lung or cytokine-mediated lymphocyte trafficking. There may also be immune-mediated lymphocyte destruction, bone marrow or thymus suppression, or apoptosis. url: https://api.elsevier.com/content/article/pii/S120197120500072X doi: 10.1016/j.ijid.2004.07.014 id: cord-340883-zf8jbhdl author: He, Zhongping title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 words: 2892.0 sentences: 119.0 pages: flesch: 56.0 cache: ./cache/cord-340883-zf8jbhdl.txt txt: ./txt/cord-340883-zf8jbhdl.txt summary: title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) caused a large outbreak of pneumonia in Beijing, China, in 2003. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. RESULTS: SARS-CoV detection rates in sera were highest in the first 9 days of illness, whereas detection was highest in throat washes 5–14 days after onset of symptoms. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. Fecal samples were frequently SARS-CoV RT-PCR positive beyond 40 days, and occasional sera still had SARS-CoV detected after 3 weeks of illness. CONCLUSION: In the context of an extensive outbreak with major pressure on hospital resources, patient self-collected samples are an alternative to nasopharyngeal aspirates for laboratory confirmation of SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/17386116/ doi: 10.1186/1743-422x-4-32 id: cord-032751-pmclolvh author: Head, Katharine J. title: A National Survey Assessing SARS-CoV-2 Vaccination Intentions: Implications for Future Public Health Communication Efforts date: 2020-09-23 words: 5086.0 sentences: 305.0 pages: flesch: 48.0 cache: ./cache/cord-032751-pmclolvh.txt txt: ./txt/cord-032751-pmclolvh.txt summary: Research Question 2: What are the SARS-CoV-2 vaccine behavioral intentions of adults in the U.S. when a health care provider recommends the vaccine? Importantly, because vaccine intent and/or need may be different for people who were previously infected with SARS-CoV-2 and perceived threat variables (discussed below) are usually only measured for future threats, only participants who answered "no" to the question "do you believe that you''ve had COVID-19" are included in the current study (n = 3,159). Step 3 of the hierarchical regression model, with all variables included, less education was associated with lower intent to receive a SARS-CoV-2 vaccine. The health belief variables that were significant in the full regression model were all positively associated with intent to receive a SARS-CoV-2 vaccine. abstract: With SARS-CoV-2 vaccines under development, research is needed to assess intention to vaccinate. We conducted a survey (N = 3,159) with U.S. adults in May 2020 assessing SARS-CoV-2 vaccine intentions, intentions with a provider recommendation, and sociodemographic and psychosocial variables. Participants had high SARS-CoV-2 vaccine intentions (M = 5.23/7-point scale), which increased significantly with a provider recommendation (M = 5.47). Hierarchical linear regression showed that less education and working in health care were associated with lower intent, and liberal political views, altruism, and COVID-19-related health beliefs were associated with higher intent. This work can inform interventions to increase vaccine uptake, ultimately reducing COVID-19-related morbidity and mortality. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520657/ doi: 10.1177/1075547020960463 id: cord-353731-7xn7m662 author: Heaton, Brook E. title: SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date: 2020-08-18 words: 2233.0 sentences: 139.0 pages: flesch: 51.0 cache: ./cache/cord-353731-7xn7m662.txt txt: ./txt/cord-353731-7xn7m662.txt summary: sgRNA sequencing data indicated that the host gene with the highest probability of being 125 required for SARS-CoV-2 infection was the serine/arginine-rich protein kinase, SRPK1 126 ( Figure 1B) . We next wanted to define the degree to which inhibition of SRPK1 mediated N 141 phosphorylation would affect viral replication, especially since other non-SRPK1 kinases 142 have been predicted to be responsible for SARS-CoV-2 protein phosphorylation 12,13 . SRPIN340 treatment of cells infected with the 183 alphacoronavirus 229E (which is only distantly related to betacoronavirus SARS-CoV-2) 184 inhibited the virus by more than 1,000-fold at non-toxic concentrations of the drug ( Figure 185 2G-H). Human papillomavirus type 1 E1^E4 protein is a potent 533 inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits 534 phosphorylation of host SR proteins and of the viral transcription and replication 535 regulator E2 abstract: Antiviral therapeutics against SARS-CoV-2 are needed to treat the pandemic disease COVID-19. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. Here, we performed a genome-wide screen in human lung epithelial cells to identify potential host therapeutic targets. We report that the kinase SRPK1, together with the closely related SRPK2, are jointly essential for SARS-CoV-2 replication; inhibition of SRPK1/2 with small molecules led to a dramatic decrease (more than 100,000-fold) in SARS-CoV-2 virus production in immortalized and primary human lung cells. Subsequent biochemical studies revealed that SPRK1/2 phosphorylate the viral nucleocapsid (N) protein at sites highly conserved across human coronaviruses and, due to this conservation, even a distantly related coronavirus was highly sensitive to an SPRK1/2 inhibitor. Together, these data suggest that SRPK1/2-targeted therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases. url: https://doi.org/10.1101/2020.08.14.251207 doi: 10.1101/2020.08.14.251207 id: cord-313174-ig0h2s6l author: Hecht, Jonathon L. title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers date: 2020-08-02 words: 4188.0 sentences: 244.0 pages: flesch: 52.0 cache: ./cache/cord-313174-ig0h2s6l.txt txt: ./txt/cord-313174-ig0h2s6l.txt summary: title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers Herein, we describe 19 placentas from mothers with COVID-19 studied for gross and histopathologic findings, viral expression by in situ hybridization (ISH) and immunohistochemistry (IHC), and ACE2 and TMPRSS2 expression by IHC. Ten placentas of COVID-19 negative mothers (delivered either before the pandemic or with negative tests) with clinical histories focusing on infections by an RNA virus (one case each of Zika exposure, HIV infection, and Hepatitis C infection), two cases of intrauterine fetal demise, and with histopathologies associated with congenital infections and coagulopathies (one case each of high stage and grade acute chorioamnionitis, high grade maternal vascular malperfusion (MVM), high grade fetal vascular malperfusion (FVM), high grade villitis of unknown etiology (VUE), chronic histiocytic intervillositis, and multiple intervillous thrombi) were identified from the pathology database using this diagnostic terminology and used as this set of controls. abstract: Congenital infection of SARS-CoV-2 appears to be exceptionally rare despite many cases of COVID-19 during pregnancy. Robust proof of placental infection requires demonstration of viral localization within placental tissue. Only two of the few cases of possible vertical transmission have demonstrated placental infection. None have shown placental expression of the ACE2 or TMPRSS2 protein, both required for viral infection. We examined 19 COVID-19 exposed placentas for histopathologic findings, and for expression of ACE2, and TMPRSS2 by immunohistochemistry. Direct placental SARS-CoV-2 expression was studied by two methods—nucleocapsid protein expression by immunohistochemistry, and RNA expression by in situ hybridization. ACE2 membranous expression in the syncytiotrophoblast (ST) of the chorionic villi is predominantly in a polarized pattern with expression highest on the stromal side of the ST. In addition, cytotrophoblast and extravillous trophoblast express ACE2. No ACE2 expression was detected in villous stroma, Hofbauer cells, or endothelial cells. TMPRSS2 expression was only present weakly in the villous endothelium and rarely in the ST. In 2 of 19 cases, SARS-CoV-2 RNA was present in the placenta focally in the ST and cytotrophoblast. There was no characteristic histopathology present in our cases including the two placental infections. We found that the placenta is capable of being infected but that this event is rare. We propose one explanation could be the polarized expression of ACE2 away from the maternal blood and pronounced paucity of TMPRSS2 expression in trophoblast. url: https://doi.org/10.1038/s41379-020-0639-4 doi: 10.1038/s41379-020-0639-4 id: cord-343357-5nhyumxl author: Heegaard, Peter M. H. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 words: 3446.0 sentences: 180.0 pages: flesch: 46.0 cache: ./cache/cord-343357-5nhyumxl.txt txt: ./txt/cord-343357-5nhyumxl.txt summary: We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. abstract: The ongoing COVID-19 pandemic caused by infection with SARS-CoV-2 has created an urgent need for animal models to enable study of basic infection and disease mechanisms and for development of vaccines, therapeutics, and diagnostics. Most research on animal models for COVID-19 has been directed toward rodents, transgenic rodents, and non-human primates. The primary focus has been on the angiotensin-converting enzyme 2 (ACE2), which is a host cell receptor for SARS-CoV-2. Among investigated species, irrespective of ACE2 spike protein binding, only mild (or no) disease has occurred following infection with SARS-CoV-2, suggesting that ACE2 may be necessary for infection but is not sufficient to determine the outcome of infection. The common trait of all species investigated as COVID models is their healthy status prior to virus challenge. In contrast, the vast majority of severe COVID-19 cases occur in people with chronic comorbidities such as diabetes, obesity, and/or cardiovascular disease. Healthy pigs express ACE2 protein that binds the viral spike protein but they are not susceptible to infection with SARS-CoV-2. However, certain pig breeds, such as the Ossabaw pig, can reproducibly be made obese and show most aspects of the metabolic syndrome, thus resembling the more than 80% of the critically ill COVID-19 patients admitted to hospitals. We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. url: https://doi.org/10.3389/fmicb.2020.573756 doi: 10.3389/fmicb.2020.573756 id: cord-331428-6pvr2vew author: Heffernan, Kevin S. title: Exercise as medicine for COVID-19: on PPAR with emerging pharmacotherapy date: 2020-08-17 words: 1835.0 sentences: 107.0 pages: flesch: 34.0 cache: ./cache/cord-331428-6pvr2vew.txt txt: ./txt/cord-331428-6pvr2vew.txt summary: Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating peroxisome proliferator-activated receptor alpha (PPARα), possibly contributing to lipotoxicity, inflammation and untoward respiratory effects. While we all eagerly await the development of a vaccine, scientists and clinicians have begun exploring "off-label" use of various drugs with that hope that strategic repurposing may help manage and treat COVID-19.(1) Fenofibrate (a peroxisome proliferator-activated receptor alpha agonist) is one such medication that holds promise given its favorable effects on inflammation and endothelial function. This paper will explore the hypothesis that exercise may be a useful adjuvant in a setting of COVID-19 management/rehabilitation due to its effects on PPAR and vascular endothelial function. (3) Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating PPAR, possibly contributing to lipotoxicity and untoward respiratory effects. Peroxisome Proliferator-Activated Receptor α Agonists Increase Nitric Oxide Synthase Expression in Vascular Endothelial Cells abstract: Coronavirus disease 2019 (COVID-19) may have a metabolic origin given strong links with risk factors such as lipids and glucose and co-morbidities such as obesity and type 2 diabetes mellitus. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein mediates viral cellular entry via the ACE2 receptor. The cytoplasmic tail of this spike protein is heavily palmitoylated. Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating peroxisome proliferator-activated receptor alpha (PPARα), possibly contributing to lipotoxicity, inflammation and untoward respiratory effects. Disruption of this process may affect palmitoylation of SARS-CoV spike protein and thus infectivity and viral assembly. COVID-19 is also increasingly being recognized as a vascular disease, with several studies noting prominent systemic endothelial dysfunction. The pathogenesis of endothelial dysfunction may also be linked to COVID-19-mediated metabolic and inflammatory effects. Herein, exercise will be compared to fenofibrate as a possible therapeutic strategy to bolster resilience against (and help manage recovery from) COVID-19. This paper will explore the hypothesis that exercise may be a useful adjuvant in a setting of COVID-19 management/rehabilitation due to its effects on PPARα and vascular endothelial function. url: https://www.ncbi.nlm.nih.gov/pubmed/33017906/ doi: 10.1016/j.mehy.2020.110197 id: cord-325112-7ie23c7f author: Heimer, Carol A. title: The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date: 2018-10-04 words: 10440.0 sentences: 448.0 pages: flesch: 43.0 cache: ./cache/cord-325112-7ie23c7f.txt txt: ./txt/cord-325112-7ie23c7f.txt summary: Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Thus although the long silence of the Chinese government was not technically a violation of the IHR, it nevertheless appeared dishonest and inappropriate to the international community, undermining rather than supporting emerging cooperative norms and in fact harming global public health by allowing the new disease to spread beyond China''s borders. abstract: The SARS epidemic that broke out in late 2002 in China’s Guangdong Province highlighted the difficulties of reliance on state‐provided information when states have incentives to conceal discrediting information about public health threats. Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Through information leveraging, technically sufficient information then becomes socially sufficient information. Thus it is especially information initially categorized as non‐knowledge – including suppressed data, rumour, unverified evidence, and unofficial information – that creates pressure for the renegotiation of information orders. The argument and evidence of the article also address broader issues about how international law and global norms are realigned, how global norms change, and how social groups manage risk. url: https://www.ncbi.nlm.nih.gov/pubmed/30288737/ doi: 10.1111/1468-4446.12495 id: cord-337712-ylqgraos author: Heinz, Franz X. title: Profile of SARS-CoV-2 date: 2020-10-30 words: 6028.0 sentences: 301.0 pages: flesch: 44.0 cache: ./cache/cord-337712-ylqgraos.txt txt: ./txt/cord-337712-ylqgraos.txt summary: Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . abstract: The recent emergence of a new coronavirus (severe acute respiratory syndrome coronavirus‑2, SARS-CoV-2) that is transmitted efficiently among humans and can result in serious disease and/or death has become a global threat to public health and economy. In this article, we describe some of the most important characteristics of this new virus (including gaps in our understanding) and provide a perspective of ongoing activities for developing virus-specific countermeasures, such as vaccines and antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/33125580/ doi: 10.1007/s00508-020-01763-1 id: cord-292250-jjhpwgfa author: Heinz, Nicole title: A case of an Infant with SARS‐CoV‐2 hepatitis early after liver transplantation date: 2020-06-25 words: 1294.0 sentences: 80.0 pages: flesch: 45.0 cache: ./cache/cord-292250-jjhpwgfa.txt txt: ./txt/cord-292250-jjhpwgfa.txt summary: We present a case of a pediatric liver transplant recipient diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection four days after receiving a living donor liver allograft from her mother. The team decision to proceed with the transplant contemplated the rate of progression of chronic liver failure, the risk of patient mortality before the epidemic abated, the perceived lower risk at the onset of the epidemic compared to the weeks/months ahead and the fact that neither the donor nor recipient demonstrated signs or symptoms of SARS-CoV-2 infection. Follow-up evaluation in the outpatient clinic on POD 30 was notable for resolution of all symptoms including diarrhea, but liver enzymes were again elevated in the setting of a subtherapeutic tacrolimus trough (Table 1, Figure 2) . On POD 36 the patient remained clinically well, liver enzymes had improved and tacrolimus trough was at target. A case of an Infant with SARS-CoV-2 hepatitis early after liver transplantation abstract: We present a case of a pediatric liver transplant recipient diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection four days after receiving a living donor liver allograft from her mother. The recipient was a 6‐month‐old with end‐stage liver disease due to biliary atresia and failed Kasai. The infant had an uncomplicated implantation, excellent graft function and down‐trending liver enzymes until developing fevers, diarrhea, and moderate respiratory distress requiring non‐invasive respiratory support. SARS‐CoV‐2 testing (nasal swab Polymerase Chain Reaction) was positive on post‐operative day (POD) 4. Liver enzymes peaked ~1000 U/L (5‐fold higher than the previous day) on POD 6. Histology demonstrated a mixed picture of moderate acute hepatitis and classical elements of mild to moderate acute cellular rejection. Her hepatitis and respiratory symptoms improved coincident with completing treatment with hydroxychloroquine, reduced immunosuppression, and intravenous gamma globulin (IVIG). url: https://doi.org/10.1111/petr.13778 doi: 10.1111/petr.13778 id: cord-282108-hhnnloxp author: Heister, Paula M. title: Pharmacological hypothesis: TPC2 antagonist tetrandrine as a potential therapeutic agent for COVID‐19 date: 2020-09-15 words: 4037.0 sentences: 253.0 pages: flesch: 49.0 cache: ./cache/cord-282108-hhnnloxp.txt txt: ./txt/cord-282108-hhnnloxp.txt summary: The putative mechanism of action of tetrandrine that underlies its potential use as a coronavirus disease 2019 (COVID-19) treatment is its ability to block the two-pore channel 2 (TPC2) in host cells and thus inhibit virus replication at low micromolar concentrations. While this paper was in preparation, a large-scale study exploring SARS-CoV-2 human protein-protein interactions to identify potential therapeutic candidates identified verapamil as a contender, but initial in vitro screening did not show a promising effect at the concentrations used. If indicated by the above, clinical trials to investigate tetrandrine''s potential, using an established oral dose, as an acute therapeutic or prophylactic agent against SARS-CoV-2 infection, provided safety can be confirmed for the particular length of use. 7. If indicated by the above, clinical trials to investigate the potential role of established calcium channel blockers as therapeutic agents in SARS-CoV-2 infection. abstract: More than ten million patients worldwide have been diagnosed with coronavirus disease 19 (COVID‐19) to date (WHO situation report, 1st July 2020). There is no vaccine to prevent infection with the causative organism, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), nor a cure. In the struggle to devise potentially useful therapeutics in record time, the repurposing of existing compounds is a key route of action. In this hypothesis paper, we argue that the bisbenzylisoquinoline and calcium channel blocker tetrandrine, originally extracted from the plant Stephania tetrandra and utilized in traditional Chinese medicine, may have potential in the treatment of COVID‐19 and should be further investigated. We collate and review evidence for tetrandrine's putative mechanism of action in viral infection, specifically its recently discovered antagonism of the two‐pore channel 2 (TPC2). While tetrandrine's particular history of use provides a very limited pharmacological dataset, there is a suggestion from the available evidence that it could be effective at doses used in clinical practice. We suggest that further research to investigate this possibility should be conducted. url: https://doi.org/10.1002/prp2.653 doi: 10.1002/prp2.653 id: cord-325282-20l9xcmg author: Helal, Mohamed A. title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date: 2020-09-16 words: 6739.0 sentences: 365.0 pages: flesch: 53.0 cache: ./cache/cord-325282-20l9xcmg.txt txt: ./txt/cord-325282-20l9xcmg.txt summary: title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The entry of the virus into host cells is facilitated by binding of its transmembrane spike (S) protein with angiotensin-converting enzyme 2 (ACE-2) receptor (Hoffmann et al., 2020) . To understand the mechanism of interaction of the SARS-CoV-2 spike protein with the CD147 receptor, we have performed a four-stage in-silico study. The recently reported crystal structure of SARS-Cov-2 spike protein complex with ACE2 (PDB ID: 6LZG) reveals that the virus utilizes the external subdomain of the spike Receptor Binding Domain (RBD) to recognize the human ACE2 receptor . abstract: Lymphopenia is considered one of the most characteristic clinical features of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. Since T lymphocytes display a very low expression level of hACE2, a novel receptor might be involved in the entry of SARS-CoV-2 into T cells. The transmembrane glycoprotein CD147 is highly expressed by activated T lymphocytes, and was recently proposed as a probable route for SARS-CoV-2 invasion. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The results showed that this binding is dominated by electrostatic interactions involving residues Arg403, Asn481, and the backbone of Gly502. The overall binding arrangement shows the CD147 C-terminal domain interacting with the spike external subdomain in the grove between the short antiparallel β strands, β1’ and β2’, and the small helix α1’. This proposed interaction was further confirmed using MD simulation and binding free energy calculation. These data contribute to a better understanding of the mechanism of infection of SARS-CoV-2 to T lymphocytes and could provide valuable insights for the rational design of adjuvant treatment for COVID-19. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32936048/ doi: 10.1080/07391102.2020.1822208 id: cord-297432-2edncbgn author: Helleberg, Marie title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 words: 2390.0 sentences: 139.0 pages: flesch: 46.0 cache: ./cache/cord-297432-2edncbgn.txt txt: ./txt/cord-297432-2edncbgn.txt summary: A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. abstract: The antiviral drug remdesivir has been shown clinically effective for treatment of COVID-19. We here demonstrate suppressive but not curative effect of remdesivir in an immunocompromised patient. A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. During two 10-day courses of remdesivir starting 24 and 45 days after fever onset, pneumonia and spiking fevers remitted, but relapsed after discontinuation. Kinetics of temperature, C-reactive protein, and lymphocyte counts mirrored the remitting/relapsing SARS-CoV-2 infection. Combination therapy or longer treatment duration may be needed in immunocompromised patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32702095/ doi: 10.1093/infdis/jiaa446 id: cord-255415-sr81j7my author: Heller, Lindsay K. title: Mustela Vison ACE2 Functions as a Receptor for Sars-Coronavirus date: 2006 words: 1487.0 sentences: 97.0 pages: flesch: 62.0 cache: ./cache/cord-255415-sr81j7my.txt txt: ./txt/cord-255415-sr81j7my.txt summary: However, SARS-CoV-like viruses isolated from palm civets appeared to be under strong selective pressure and are genetically most similar to viruses infecting humans early in the outbreak. Human, palm civet, rat, mouse, chicken, and mink ACE2 were compared to identify differences that are important in species specificity and to discern regions within ACE2 that may impact its function as a SARS-CoV receptor. Expression of ACE2 RNA in SARS-CoV susceptible human (Huh7, HEK293T), African green monkey (VeroE6), and Mv1Lu cell lines 7 was analyzed by RT-PCR (chapter 4.8 this volume). 7 The complete open reading frame of human ACE2 (hACE2) or mvACE2 was amplified from RNA isolated from the Huh7 or Mv1Lu cell line, respectively. Our data demonstrate that mvACE2 RNA is expressed by SARS-CoV susceptible Mv1Lu cells, that it is closely related to palm civet ACE2, and that mvACE2 is a functional receptor for SARS-CoV. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037586/ doi: 10.1007/978-0-387-33012-9_90 id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 words: 9290.0 sentences: 516.0 pages: flesch: 51.0 cache: ./cache/cord-286298-pn9nwl64.txt txt: ./txt/cord-286298-pn9nwl64.txt summary: Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. abstract: A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers. url: https://www.ncbi.nlm.nih.gov/pubmed/32344679/ doi: 10.3390/jcm9041225 id: cord-252456-971d0sir author: Hemida, Maged Gomaa title: The SARS-CoV-2 outbreak from a one health perspective date: 2020-03-16 words: 4824.0 sentences: 244.0 pages: flesch: 55.0 cache: ./cache/cord-252456-971d0sir.txt txt: ./txt/cord-252456-971d0sir.txt summary: The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . abstract: The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. The virus shares a high level of identity with some bat coronaviruses and is recognised as a potentially zoonotic virus. We are utilizing the One Health concept to understand the emergence of the virus, as well as to point to some possible control strategies that might reduce the spread of the virus across the globe; thus, containment of such virus would be possible. url: https://api.elsevier.com/content/article/pii/S2352771420300185 doi: 10.1016/j.onehlt.2020.100127 id: cord-327454-o1mrpgvj author: Hemmati-Dinarvand, Farshad title: Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV date: 2020-05-06 words: 3200.0 sentences: 168.0 pages: flesch: 47.0 cache: ./cache/cord-327454-o1mrpgvj.txt txt: ./txt/cord-327454-o1mrpgvj.txt summary: Instead, the extremely pathogenic CoVs, containing Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), mostly contaminate lower airways and lead to pneumonia (5) . Based on the genomic structure and phylogenetic analysis, the family Coronaviridae is currently classified into two subfamilies, Sarbecovirus containing SARS-CoV are two major zoonotic pathogenic coronaviruses (Table 1) . Accordingly, the International Committee on Taxonomy of Viruses named it severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently reported that between the SARS-CoV genome sequence and the novel coronavirus exist 82% similarity, thus, named 2019-nCoV by WHO (18) . This theory may be indicating that 2019-nCoV uses the same SARS-CoV mechanism i.e. through angiotensin-converting enzyme2 (ACE2) receptor and the TMPRSS2 protease to infect the human cells. Sequence analysis has shown that some of the 2019-nCoV clusters and bat-associated SARS76 CoV viruses (SARSr-CoV) can use the ACE2 receptor to enter the host cell. abstract: Abstract At the end of the year 2019, the novel coronavirus (2019-nCoV) was spreading in Wuhan, China, and the outbreak process has a high speed. It was recognized as a pandemic by the World Health Organization (WHO) on 11 March 2020. Coronaviruses are enveloped and single-stranded RNA that have several families including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The pathogenesis mechanism and disease outcomes of SARS and MERS are now clear to some extent, but little information is available for 2019-nCoV. This newly identified corona virus infection represents flu-like symptoms, but usually the first symptoms are fever and dry cough. There has been no specific treatment against 2019-nCoV up to now, and physicians only apply supportive therapy. In the present article, we made an attempt to review the behavior of the virus around the world, epidemiology, a pathway for influx into the host cells, clinical presentation, as well as the treatments currently in use and future approaches; nitazoxanide may be our dream drug. We hope that this review has a positive impact on public knowledge for helping to deal with the 2019-nCoV and move one step forward toward its treatment in the near future. url: https://api.elsevier.com/content/article/pii/S0188440920305506 doi: 10.1016/j.arcmed.2020.04.022 id: cord-299560-np6nfvf2 author: Hendaus, Mohamed A. title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date: 2020-05-20 words: 2789.0 sentences: 166.0 pages: flesch: 53.0 cache: ./cache/cord-299560-np6nfvf2.txt txt: ./txt/cord-299560-np6nfvf2.txt summary: Replication of SARS-CoV-2 depends on the viral RNAdependent RNA polymerase (RdRp) (Elfiky & Azzam, 2020) which is the most probable target of the investigational nucleotide analogue remdesivir (RDV) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . RDV exhibits broad-spectrum antiviral activity against RNA viruses, and former studies with RdRps from Ebola virus (EBOV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have shown that delayed chain-termination is RDV''s conceivable mechanism of action ( Figure 2 ) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . On April 29, 2020, Gilead revealed results from the openlabel, Phase 3 SIMPLE trial evaluating 5-day and 10-day dosing durations of the investigational antiviral remdesivir in hospitalized patients with severe manifestations of COVID-19 disease. abstract: The pandemic of COVID-19 (Coronavirus Disease-2019) is an extremely contagious respiratory illness due to a novel coronavirus, SARS-CoV-2. Certain drugs have several protein targets and many illnesses share overlapping molecular paths. In such cases, reusing drugs for more than one objective and finding their novice uses can considerably decrease the time in finding new cures for unforeseen diseases. Remdesivir has been recently a strong candidate for the treatment of Covid-19. In this commentary, we have portrayed the structure of the coronavirus in a simple way as well as the site where remdesivir acts. We have also displayed the ongoing clinical trials, as well as a published study that was conducted on compassionate base. The covid-19 pandemic might wean down by the end of summer 2020, but the risk of seasonality exists. Therefore, future disposal of agents such as remdesivir might be crucial for ensuring an efficient treatment, decrease mortality and allow early discharge. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1767691 doi: 10.1080/07391102.2020.1767691 id: cord-282560-tofppr3b author: Henderson, Jack A. title: Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors date: 2020-09-21 words: 6242.0 sentences: 332.0 pages: flesch: 56.0 cache: ./cache/cord-282560-tofppr3b.txt txt: ./txt/cord-282560-tofppr3b.txt summary: Here, we report the pK(a) calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. 14, 15 Our previous work employing the hybrid-solvent based continuous constant pH molecular dynamics (CpHMD) simulations 16 demonstrated that the elucidation of proton-coupled conformational dynamics offers a deeper understanding of the structure-dynamics-function relationships 17 and inhibition mechanisms 18-20 of aspartyl proteases. We performed pH replica-exchange CpHMD simulations to estimate the pKa values of Asp/Glu/His/Cys/Lys side chains and assess possible proton-coupled dynamics in SARS-CoV, SARS-CoV-2, and MERS-CoV PLpros. To provide support for the protonation states determined by GB-CpHMD titrations and test the proton-coupled dynamics of the BL2 loop, we performed conventional all-atom fixed-charge MD simulations of SARS-CoV-2 PLpro with the catalytic side chains fixed in the charged states and Cys270 fixed in the protonated or deprotonated state. abstract: Broad-spectrum antiviral drugs are urgently needed to stop the Coronavirus Disease 2019 pandemic and prevent future ones. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is related to the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which have caused the previous outbreaks. The papain-like protease (PLpro) is an attractive drug target due to its essential roles in the viral life cycle. As a cysteine protease, PLpro is rich in cysteines and histidines, and their protonation/deprotonation modulates catalysis and conformational plasticity. Here, we report the pK(a) calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. The calculated pK(a)’s support the catalytic roles of the Cys–His–Asp triad. We also found that several residues can switch protonation states at physiological pH among which is C270/271 located on the flexible blocking loop 2 (BL2) of SARS-CoV-2/CoV PLpro. Simulations revealed that the BL2 can open and close depending on the protonation state of C271/270, consistent with the most recent crystal structure evidence. Interestingly, despite the lack of an analogous cysteine, BL2 in MERS-CoV PLpro is also very flexible, challenging a current hypothesis. These findings are supported by the all-atom fixed-charge simulations and provide a starting point for more detailed studies to assist the structure-based design of broad-spectrum inhibitors against CoV PLpros. url: https://doi.org/10.1063/5.0020458 doi: 10.1063/5.0020458 id: cord-022266-nezgzovk author: Henderson, Joan C. title: Tourism and Health Crises date: 2009-11-16 words: 7964.0 sentences: 394.0 pages: flesch: 52.0 cache: ./cache/cord-022266-nezgzovk.txt txt: ./txt/cord-022266-nezgzovk.txt summary: Such situations and approaches to their resolution represent the subject of this chapter in which health risks when traveling and on arrival at destinations are considered, with a section devoted to infectious diseases affecting humans and animals and birds. Health is a major public and private concern in general and a key element in destination choice and visitor satisfaction, with individuals and the tourism industry likely to shun environments where there might be a risk to tourist well-being. Some studies have concluded that the health of as many as 50% of participants is impaired by the experience of international tourism (Dawood, 1989) and the rise in foreign travel has been accompanied by an increased incidence of disease, especially that of a tropical nature (Connor, 2005) . Some initiatives to minimize unnecessary dangers and avoid serious injuries in the fi eld of adventure tourism are operator accreditation schemes, strict health and safety rules, codes of conduct, staff training and the education and prior assessment of participants (Bentley and Page, 2001) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155505/ doi: 10.1016/b978-0-7506-7834-6.50008-9 id: cord-023140-ytal7wog author: Henderson, Joan C. title: Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore date: 2004-12-09 words: 3949.0 sentences: 163.0 pages: flesch: 48.0 cache: ./cache/cord-023140-ytal7wog.txt txt: ./txt/cord-023140-ytal7wog.txt summary: title: Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore The sudden outbreak of severe acute respiratory syndrome (SARS) in Singapore in 2003 was a grave crisis for the tourism industry as a whole and highlights the importance of effectively managing and planning for such occurrences. It focuses on how the epidemic impacted on Singapore''s hotel sector and management reactions to it, affording insights into the problems caused by outbreaks of infectious disease at destinations and possible responses. The epidemic of SARS in 2003 was an exceptional crisis for Singapore''s hotels and an exacting test for its managers, in which advances to near normality were dictated by outside developments and agencies as much as their own efforts. Managing a health-related crisis: severe acute respiratory syndrome (SARS) in Singapore Chaos, crises and disasters: a strategic approach to crisis management in the tourism industry abstract: The sudden outbreak of severe acute respiratory syndrome (SARS) in Singapore in 2003 was a grave crisis for the tourism industry as a whole and highlights the importance of effectively managing and planning for such occurrences. This study looks at the particular consequences of the infectious virus for the hotel sector and reactions to the challenges posed. Further health‐related crises seem inevitable in the modern world and some guidelines for dealing with these are proposed, based on the Singapore experience and an existing framework for tourism crisis management. Copyright © 2004 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167073/ doi: 10.1002/jtr.505 id: cord-293367-0fe62h2f author: Henderson, Lauren A. title: American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS‐C) Associated with SARS‐CoV‐2 and Hyperinflammation in COVID‐19. Version 1 date: 2020-07-23 words: 6229.0 sentences: 333.0 pages: flesch: 41.0 cache: ./cache/cord-293367-0fe62h2f.txt txt: ./txt/cord-293367-0fe62h2f.txt summary: Since its initial description in December 2019 in Wuhan China, coronavirus disease 2019 , caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly evolved into a worldwide pandemic affecting millions of lives.(1) Unlike adults, the vast majority of children with COVID-19 have mild symptoms. Reports in the literature and unpublished observations by members of the panel both note that some patients with MIS-C can decompensate rapidly; however, the risk factors that predispose patients to such severe and progressive illness have not been identified.(10, 13) Accordingly, children with abnormal vital signs, concerning physical examination findings, significantly elevated inflammatory markers, or signs of cardiac involvement will need to be admitted to the hospital for supportive care while Tier 2 testing is completed. abstract: OBJECTIVE: To provide guidance on the management of Multisystem Inflammatory Syndrome in Children (MIS‐C), a condition characterized by fever, inflammation, and multiorgan dysfunction that manifests late in the course of SARS‐CoV‐2 infection. The Task Force also provided recommendations for children with hyperinflammation during COVID‐19, the acute, infectious phase of SARS‐CoV‐2 infection. METHODS: The Task Force was composed of 9 pediatric rheumatologists, 2 adult rheumatologists, 2 pediatric cardiologists, 2 pediatric infectious disease specialists, and 1 pediatric critical care physician. Preliminary statements addressing clinical questions related to MIS‐C and hyperinflammation in COVID‐19 were developed based on evidence reports. Consensus was built through a modified Delphi process that involved 2 rounds of anonymous voting and 2 webinars. A 9‐point scale was used to determine the appropriateness of each statement (1‐3, inappropriate; 4‐6, uncertain; 7‐9, appropriate), and consensus was rated as low (L), moderate (M), or high (H) based on dispersion of the votes along the numeric scale. Approved guidance statements had to be classified as appropriate with moderate or high levels of consensus, which were pre‐specified prior to voting. RESULTS: A total of 128 statements were approved by the Task Force, which were refined into 40 final guidance statements accompanied by a flow diagram depicting the diagnostic pathway for MIS‐C. CONCLUSION: Our understanding of SARS‐CoV‐2‐related syndromes in the pediatric population continues to evolve. This guidance document reflects currently available evidence coupled with expert opinion but is meant to be modified as additional data become available. url: https://doi.org/10.1002/art.41454 doi: 10.1002/art.41454 id: cord-325593-ww2vq3n4 author: Hendren, Nicholas S. title: Unique Patterns of Cardiovascular Involvement in COVID-19 date: 2020-05-14 words: 1298.0 sentences: 71.0 pages: flesch: 35.0 cache: ./cache/cord-325593-ww2vq3n4.txt txt: ./txt/cord-325593-ww2vq3n4.txt summary: However, to our knowledge, a framework describing the variable presentations of cardiac involvement in COVID-19 within the broader spectrum of symptomatic SARS-CoV-2 infection has not been previously proposed. First, the prevalence of mixed cardiopulmonary disease as assessed by elevated cardiac troponin levels, is variable, but occurs in 10-25% of patients hospitalized with COVID-19 3, 4 . ACovCS with cardiac predominate disease may be more apparent at hospital presentation relative to mixed cardiopulmonary disease because the predominate cardiac manifestations (e.g. chest pain due to a myocardial infarction) often results in symptoms which lead patients to seek emergent care. Just as there is variability in cardiac presentations of COVID-19, SARS-CoV-2 infection overall has a wide spectrum of disease penetrance with many patients displaying few to no symptoms, while an unfortunate minority develop severe life limiting disease. Other factors which may influence the variable presentation of COVID-19 include mutations in the circulating SARS-CoV-2 virus though it remains uncertain whether such observations explain the regional differences in the outcomes of COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32417379/ doi: 10.1016/j.cardfail.2020.05.006 id: cord-344853-s2p2csrx author: Hendren, Nicholas S. title: Description and Proposed Management of the Acute COVID-19 Cardiovascular Syndrome date: 2020-04-16 words: 6688.0 sentences: 357.0 pages: flesch: 34.0 cache: ./cache/cord-344853-s2p2csrx.txt txt: ./txt/cord-344853-s2p2csrx.txt summary: A substantial minority of patients hospitalized develop an acute COVID-19 cardiovascular syndrome, which can manifest with a variety of clinical presentations but often presents as an acute cardiac injury with cardiomyopathy, ventricular arrhythmias, and hemodynamic instability in the absence of obstructive coronary artery disease. S ince the index cases were first reported in Wuhan, China, in December 2019, coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic infecting >1 million individuals by early April 2020. In this document, we focus on a prominent myocarditis-like syndrome involving acute myocardial injury often associated with reduced left ventricular ejection fraction in the absence of obstructive coronary artery disease. Additional studies, including collection of endomyocardial tissue by biopsy and autopsy studies, are required to delineate the pattern and proportion of ACovCS related to acute myocarditis versus general myocardial injury caused by systemic cytokine dysregulation. abstract: Coronavirus disease 2019 (COVID-19) is a rapidly expanding global pandemic caused by severe acute respiratory syndrome coronavirus 2, resulting in significant morbidity and mortality. A substantial minority of patients hospitalized develop an acute COVID-19 cardiovascular syndrome, which can manifest with a variety of clinical presentations but often presents as an acute cardiac injury with cardiomyopathy, ventricular arrhythmias, and hemodynamic instability in the absence of obstructive coronary artery disease. The cause of this injury is uncertain but is suspected to be related to myocarditis, microvascular injury, systemic cytokine-mediated injury, or stress-related cardiomyopathy. Although histologically unproven, severe acute respiratory syndrome coronavirus 2 has the potential to directly replicate within cardiomyocytes and pericytes, leading to viral myocarditis. Systemically elevated cytokines are also known to be cardiotoxic and have the potential to result in profound myocardial injury. Prior experience with severe acute respiratory syndrome coronavirus 1 has helped expedite the evaluation of several promising therapies, including antiviral agents, interleukin-6 inhibitors, and convalescent serum. Management of acute COVID-19 cardiovascular syndrome should involve a multidisciplinary team including intensive care specialists, infectious disease specialists, and cardiologists. Priorities for managing acute COVID-19 cardiovascular syndrome include balancing the goals of minimizing healthcare staff exposure for testing that will not change clinical management with early recognition of the syndrome at a time point at which intervention may be most effective. This article aims to review the best available data on acute COVID-19 cardiovascular syndrome epidemiology, pathogenesis, diagnosis, and treatment. From these data, we propose a surveillance, diagnostic, and management strategy that balances potential patient risks and healthcare staff exposure with improvement in meaningful clinical outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/32297796/ doi: 10.1161/circulationaha.120.047349 id: cord-257533-i85dyg8n author: Henn, Wolfram title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity date: 2020-06-23 words: 1070.0 sentences: 60.0 pages: flesch: 45.0 cache: ./cache/cord-257533-i85dyg8n.txt txt: ./txt/cord-257533-i85dyg8n.txt summary: title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity Although healthcare systems around the world currently are fully absorbed with the day-today challenge of slowing down the spread of the SARS-CoV-2 virus, ongoing research makes it very likely that a protective vaccine will be developed within a rather short period of time [1, 2] . Given the unprecedented public attention to the issue, these criteria must be medically adequate, socially fair, transparent, verifiable, and easily understandable for non-experts, in order to bridge thehopefully short but anyway relevant-initial shortage of vaccine supply without creating social discomfort or even unrest. As current data clearly show that COVID-19 mortality is strongly associated with age [7] , it should be the leading and also easily verifiable medical parameter for the distribution of the expected vaccine during an initial scarcity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32600909/ doi: 10.1016/j.vaccine.2020.06.058 id: cord-295545-ruxz77i8 author: Hennighausen, Lothar title: Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date: 2020-05-11 words: 1660.0 sentences: 108.0 pages: flesch: 55.0 cache: ./cache/cord-295545-ruxz77i8.txt txt: ./txt/cord-295545-ruxz77i8.txt summary: The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2. A study in pneumocytes demonstrated that ACE2 expression is induced by interferons (Ziegler, 2020) , possibly through the transcription factors Signal Transducer and Activator of Transcription (STAT) 1 and 2, as the authors suggest. Ace2 mRNA levels vary widely between cell types, with high expression detected in lactating mammary and intestinal tissues ( Figure 1A -B) and Type II Pneumocytes (Ziegler, 2020) . To explore the possibility that Ace2 gene expression in SARS-CoV-2 target cells is regulated not only by interferons but also by a range of cytokines through the family of STAT transcription factors, we mined available scRNA-seq data (Ziegler, 2020) (Table 1) . abstract: ACE2, in concert with the protease TMPRSS2, binds the novel coronavirus SARS-CoV-2 and facilitates its cellular entry. The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. Viral RNA was also detected in breast milk (Wu et al., 2020), raising the possibility that ACE2 expression is under the control of cytokines through the JAK-STAT pathway. Here we show that Ace2 expression in mammary tissue is induced during pregnancy and lactation, which coincides with the establishment of a candidate enhancer. The prolactin-activated transcription factor STAT5 binds to tandem sites that coincide with activating histone enhancer marks and additional transcription components. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2. url: https://doi.org/10.1101/2020.05.11.089045 doi: 10.1101/2020.05.11.089045 id: cord-352863-6cttilm8 author: Hennighausen, Lothar title: Activation of the SARS-CoV-2 receptor Ace2 through JAK/STAT-dependent enhancers during pregnancy date: 2020-09-06 words: 3450.0 sentences: 197.0 pages: flesch: 55.0 cache: ./cache/cord-352863-6cttilm8.txt txt: ./txt/cord-352863-6cttilm8.txt summary: Expression of the ACE2 gene in type II pneumocytes is activated by interferons (Ziegler et al., 2020) , opening the possibility that the cytokine storm in COVID-19 patients, and peptide hormones in general, might lead to increased levels of ACE2 in a range of putative SARS-CoV-2 target tissues. Next, we mined RNA-seq data from our lab and demonstrated increased Ace2 expression throughout pregnancy and lactation ( Figure 1B ) with a pattern similar to that of other prolactin-regulation genes (Lee et al., 2018; Yamaji et al., 2013) . Our study directly demonstrates that the Ace2 gene is expressed in mammary tissue and activated during pregnancy and lactation through intronic enhancers built on the transcription factor STAT5. While SARS-CoV-2 has been detected in breast milk in at least seven studies and our research has demonstrated that its receptor ACE2 is present in mammary tissue and highly induced during lactation, the impact of these findings on COVID-19 requires further investigations. abstract: ACE2 binds the coronavirus SARS-CoV-2 and facilitates its cellular entry. Interferons activate ACE2 expression in pneumocytes, suggesting a critical role of cytokines in SARS-CoV-2 target cells. Viral RNA was detected in breast milk in at least seven studies, raising the possibility that ACE2 is expressed in mammary tissue during lactation. Here we show that Ace2 expression in mouse mammary tissue is induced during pregnancy and lactation, which coincides with the activation of intronic enhancers. These enhancers are occupied by the prolactin-activated transcription factor STAT5 and additional regulatory factors, including Polymerase II. Deletion of Stat5a results in decommissioning of the enhancers and an 83% reduction of Ace2 mRNA. We also demonstrate that Ace2 expression increases during lactation in lung, but not in kidney and intestine. JAK/STAT components are present in a range of SARS-CoV-2 target cells opening the possibility that cytokines contribute to the viral load and extrapulmonary pathophysiology. url: https://www.ncbi.nlm.nih.gov/pubmed/32966801/ doi: 10.1016/j.celrep.2020.108199 id: cord-350101-t34myl7l author: Henrique Braz‐Silva, Paulo title: SARS‐CoV‐2: What can saliva tell us? date: 2020-05-11 words: 887.0 sentences: 47.0 pages: flesch: 46.0 cache: ./cache/cord-350101-t34myl7l.txt txt: ./txt/cord-350101-t34myl7l.txt summary: The World Health Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. In addition to the diagnosis itself, the study of saliva in cases of COVID-19 will help understanding its pathogenesis, since it has been recently reported that epithelial cells of the oral cavity showed abundant expression of the angiotensin-converting enzyme II (ACE2), a receptor playing a key role in the entry of SARS-CoV-2 into the cells (Xu et al., 2020) . Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: A diagnostic validity study abstract: An epidemic pneumonia was first reported in the city of Wuhan, China, in the end of December 2019, had its aetiological agent identified as a new coronavirus (Zhu et al., 2020). The World Health Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32311181/ doi: 10.1111/odi.13365 id: cord-343273-zaaraiy7 author: Hensley, Lisa E. title: Interferon-β 1a and SARS Coronavirus Replication date: 2004-02-17 words: 1009.0 sentences: 58.0 pages: flesch: 49.0 cache: ./cache/cord-343273-zaaraiy7.txt txt: ./txt/cord-343273-zaaraiy7.txt summary: Here, we report that recombinant human interferon (IFN)-β 1a potently inhibits SARS coronavirus replication in vitro. The IFN-β 1a preparation employed in this study was selected because it is currently used as part of the most effective treatment regimen for relapsing forms of multiple sclerosis (8) , and more importantly, because it was shown to have antiviral activity (as measured in a vesicular stomatitis virus cytopathic assay system) 14 times greater than the currently available treatment using IFN-β 1b (9) . In the current study, Vero E6 cells were treated with concentrations (5,000 to 500,000 IU/mL) of IFN-β 1a either 24 h before or 1 h after inoculation with the SARS-CoV (multiplicity of infection 0.1 PFU/cell), and monitored for cytopathic effect and production of infectious SARS-CoV at 24, 48, and 72 h postinfection. Production of infectious SARS-CoV was potently inhibited (>99.5% or 2.00 log 10 PFU/mL) at 24 h postinfection by pretreatment of Vero E6 cells with IFN-β 1a at all concentrations tested (Figure 1 ). abstract: A global outbreak of severe acute respiratory syndrome (SARS) caused by a novel coronavirus began in March 2003. The rapid emergence of SARS and the substantial illness and death it caused have made it a critical public health issue. Because no effective treatments are available, an intensive effort is under way to identify and test promising antiviral drugs. Here, we report that recombinant human interferon (IFN)-β 1a potently inhibits SARS coronavirus replication in vitro. url: https://www.ncbi.nlm.nih.gov/pubmed/15030704/ doi: 10.3201/eid1002.030482 id: cord-346763-xdfl659q author: Herman, A. title: Drug reaction with eosinophilia and systemic symptoms syndrome in a patient with COVID‐19 date: 2020-08-13 words: 1319.0 sentences: 68.0 pages: flesch: 50.0 cache: ./cache/cord-346763-xdfl659q.txt txt: ./txt/cord-346763-xdfl659q.txt summary: We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. According to the scoring system for classifying DRESS cases (RegiSCAR) reported by Kardaun et al., 1 a drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome was diagnosed as follows: fever ≥38.5°C (0), enlarged lymph nodes (0), eosinophilia (1), atypical lymphocytes (1), skin rash extent >50% body surface area (1), skin rash suggesting DRESS (1), biopsy suggesting DRESS (0), organ involvement (liver, kidney, lung) (2), resolution ≥15 days (0), viral titers (HBV/HCV) negative (1) . Drug reaction with eosinophilia and systemic symptoms syndrome (DRESS) syndrome associated with azithromycin presenting like septic shock: a case report Drug reaction with eosinophilia and systemic symptoms (DRESS) associated with azithromycin in acute Epstein-Barr virus infection abstract: Skin rashes associated with COVID-19 include eruptions induced by drugs prescribed for management of this infection. We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. A 50-year-old man was admitted to the intensive care unit for pneumonia with acute respiratory distress syndrome. COVID-19 was confirmed by positive RT-PCR SARS-CoV-2 on nasopharyngeal swabs and later by positive IgM and IgG antibodies against SARS-CoV-2 (114,5 AU/mL). In the context of fever >38,5°C, nine days after admission, the patient developed a generalized maculopapular rash on more than 70% of his body surface area with oedema of hands and face (Fig.1). Azithromycin and hydroxychloroquine had been initiated 18 and 17 days respectively prior to the skin eruption. url: https://doi.org/10.1111/jdv.16838 doi: 10.1111/jdv.16838 id: cord-285469-b61y9ezi author: Hernández-Fernández, Francisco title: Cerebrovascular disease in patients with COVID-19: neuroimaging, histological and clinical description date: 2020-07-09 words: 7007.0 sentences: 368.0 pages: flesch: 42.0 cache: ./cache/cord-285469-b61y9ezi.txt txt: ./txt/cord-285469-b61y9ezi.txt summary: The aim of our study is to describe the clinical characteristics, laboratory findings, neuroimaging and available pathological anatomy data, as well as the presentation, therapeutic management and clinical outcomes of patients with acute CVD in a healthcare setting with a high incidence of transmission of this virus. We registered all hospitalized patients with COVID-19 reported during this period, and included all patients diagnosed with acute CVD, both ischaemic and haemorrhagic, treated consecutively by neurology, neurosurgery and the intensive care unit. Bivariates studies were designed to contrast the main variables among CVD patients, between ischaemic/haemorrhagic subtypes within the COVID-19 group, and to assess clinical prognosis. The other three haemorrhagic cases were detected on varying days of clinical evolution because having been intubated, sedated and treated for SARS-CoV-2 infection, the neurological manifestations were masked prior to tracheal extubation, when difficulty arousing these patients was observed. abstract: Since the appearance of the first case of coronavirus disease 2019 (COVID-19) a pandemic has emerged affecting millions of people worldwide. Although the main clinical manifestations are respiratory, an increase in neurological conditions, specifically acute cerebrovascular disease, has been detected. We present cerebrovascular disease case incidence in hospitalized patients with SARS-CoV-2 infection. Patients were confirmed by microbiological/serological testing, or on chest CT semiology. Available data on comorbidity, laboratory parameters, treatment administered, neuroimaging, neuropathological studies and clinical evolution during hospitalization, measured by the modified Rankin scale, were analysed. A bivariate study was also designed to identify differences between ischaemic and haemorrhagic subtypes. A statistical model of binary logistic regression and sensitivity analysis was designed to study the influence of independent variables over prognosis. In our centre, there were 1683 admissions of patients with COVID-19 over 50 days, of which 23 (1.4%) developed cerebrovascular disease. Within this group of patients, cerebral and chest CT scans were performed in all cases, and MRI in six (26.1%). Histological samples were obtained in 6/23 cases (two brain biopsies, and four arterial thrombi). Seventeen patients were classified as cerebral ischaemia (73.9%, with two arterial dissections), five as intracerebral haemorrhage (21.7%), and one leukoencephalopathy of posterior reversible encephalopathy type. Haemorrhagic patients had higher ferritin levels at the time of stroke (1554.3 versus 519.2, P = 0.004). Ischaemic strokes were unexpectedly frequent in the vertebrobasilar territory (6/17, 35.3%). In the haemorrhagic group, a characteristic radiological pattern was identified showing subarachnoid haemorrhage, parieto-occipital leukoencephalopathy, microbleeds and single or multiple focal haematomas. Brain biopsies performed showed signs of thrombotic microangiopathy and endothelial injury, with no evidence of vasculitis or necrotizing encephalitis. The functional prognosis during the hospital period was unfavourable in 73.9% (17/23 modified Rankin scale 4–6), and age was the main predictive variable (odds ratio = 1.5; 95% confidence interval 1.012–2.225; P = 0.043). Our series shows cerebrovascular disease incidence of 1.4% in patients with COVID-19 with high morbidity and mortality. We describe pathological and radiological data consistent with thrombotic microangiopathy caused by endotheliopathy with a haemorrhagic predisposition. url: https://doi.org/10.1093/brain/awaa239 doi: 10.1093/brain/awaa239 id: cord-300774-5mrkmctl author: Hernández-Mora, Miguel Górgolas title: Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date: 2020-10-25 words: 4340.0 sentences: 230.0 pages: flesch: 50.0 cache: ./cache/cord-300774-5mrkmctl.txt txt: ./txt/cord-300774-5mrkmctl.txt summary: INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . abstract: INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). However, there are no consistent data whom might benefit most from it. METHODS: We provided tocilizumab on a compassionate-use basis to patients with SSP hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. Primary endpoint was intubation or death after 24 hours of its administration. Patients received at least one dose of 400 mg intravenous tocilizumab during March 8-2020, through April 20-2020. RESULTS: A total of 207 patients were studied and 186 analysed. The mean age was 65 years and 68% were male. A co-existing condition was present in 68 % of cases. Death prognostic factors were older age, higher IL-6, D-dimer and high sensitivity C reactive protein (HSCRP), lower total lymphocytes and severe disease requiring higher oxygen support. The primary endpoint (intubation or death) was significantly worst (37% vs 13%, p < 0·001) in those receiving the drug when the oxygen support was high (FiO2 > 0.5%). CONCLUSIONS: Tocilizumab is well tolerated in patients with severe SARS-CoV-2 pneumonia, but it has a limited effect on the evolution of cases with high oxygen support needs. url: https://www.sciencedirect.com/science/article/pii/S1201971220322499?v=s5 doi: 10.1016/j.ijid.2020.10.045 id: cord-347968-jhnr8k3j author: Herrera, David title: Is the oral cavity relevant in SARS-CoV-2 pandemic? date: 2020-06-23 words: 3388.0 sentences: 140.0 pages: flesch: 36.0 cache: ./cache/cord-347968-jhnr8k3j.txt txt: ./txt/cord-347968-jhnr8k3j.txt summary: CONCLUSIONS: Antiseptic mouth rinses, such as those containing cetylpyridinium chloride or povidone-iodine, may be able to decrease the severity of COVID-19 by reducing oral viral load in infected subjects and decreasing the risk of transmission by limiting viral load in droplets, generated in normal life, or in aerosols, produced during dental procedures. The information presented in this narrative review supports the use of antiseptic mouth rinses, both as a single preprocedural use and as daily use during a limited period of time, to impact the transmission and/or pathogenicity of SARS-CoV-2, since they have shown to reduce the oral viral load and, therefore, they may reduce the severity of the disease in an infected subject and may reduce the risk of transmission, by reducing the viral load in aerosols, expelled during dental procedures, or in droplets generated when breathing, talking, sneezing, coughing, etc. abstract: OBJECTIVES: Recent scientific evidences suggest a relevant role of the oral cavity in the transmission and pathogenicity of SARS-CoV-2. METHODS: A literature search was performed in PubMed, up to April 30, 2020, focusing on SARS-CoV-2, COVID-19, oral cavity, and antimicrobial agents. RESULTS: Oral viral load of SARS-CoV-2 has been associated with the severity of COVID-19, and thus, a reduction in the oral viral load could be associated with a decrease in the severity of the condition. Similarly, a decrease in the oral viral load would diminish the amount of virus expelled and reduce the risk of transmission, since (i) during the first 10 days, the virus mainly accumulates at the nasal, oral, and pharyngeal area; (ii) the number of angiotensin-converting enzyme (ACE2) receptor is greater in the salivary glands as compared with the lungs; and (iii) salivary droplets represent the most relevant transmission route. To reduce the oral viral load, antiseptic agents may be used, although the evidence on its efficacy is indirect and weak. CONCLUSIONS: Antiseptic mouth rinses, such as those containing cetylpyridinium chloride or povidone-iodine, may be able to decrease the severity of COVID-19 by reducing oral viral load in infected subjects and decreasing the risk of transmission by limiting viral load in droplets, generated in normal life, or in aerosols, produced during dental procedures. Well-designed clinical and preclinical research must be conducted to support these hypotheses. CLINICAL RELEVANCE: Antiseptic mouth rinses may help in decreasing the severity of COVID-19 and in reducing the risk of transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/32577830/ doi: 10.1007/s00784-020-03413-2 id: cord-294644-xuafsnxm author: Herrmann, Burkhard L. title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten date: 2020-08-13 words: 1028.0 sentences: 121.0 pages: flesch: 55.0 cache: ./cache/cord-294644-xuafsnxm.txt txt: ./txt/cord-294644-xuafsnxm.txt summary: title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten Patients with newly diagnosed COVID-19 (coronavirus disease 2019) develop antibodies against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The prevalence of 1.2% of SARS-CoV-2-IgG-antibodies and consequently the rate of infection in asymptomatic outpatients in Northrhine-Westfalia (Germany) is low. Inwiefern sich im Rahmen einer ambulanten Vorstellung (Einzugsgebiet Nordrhein-Westfalen [NRW], Deutschland) SARS-CoV-2-IgG-AK im Screening nachweisen lassen, wurde in einer monozentrischen prospektiven Erhebung an 415 Patienten ohne zurückliegenden wissentlichen Kontakt mit SARS-CoV-2 oder COVID-19 untersucht. Alle Patienten willigten in die Untersuchung ein und gaben an, zum Zeitpunkt der Abnahme unter keinen Symptomen einer akuten Infektion wie Husten, Fieber oder Dyspnoe zu leiden. Alle Patienten wurden durch den Autor eigenständig anamnestiziert und verneinten einen Kontakt mit Menschen, die positiv auf SARS-CoV-2 getestet wurden oder an COVID-19 erkrankt sind. Mit einer Prävalenz von 1,2% wurden SARS-CoV-2-AK in der Studienpopulation (ambulante, asymptomatische Patienten) nachgewiesen. abstract: Patients with newly diagnosed COVID-19 (coronavirus disease 2019) develop antibodies against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). To date, few data have been obtained of the prevalence of SARS-CoV-2-antibodies in general population and in asymptomatic outpatients in Germany. From March 26 to June 4 2020, 415 asymptomatic outpatients were tested prospectively in Northrhine-Westfalia (Germany), to detect SARS-CoV-2-IgG-antibodies. In case of a positive result, anti-SARS-CoV-2-IgA was determined additionally. 5 of 415 asymptomatic outpatients had positive SARS-CoV-2-IgG-antibodies with a calculated prevalence of 1.2%. Reference range of anti-SARS-CoV-2-IgA and IgG was defined as ratio for negative < 0.8, borderline 0.8—1.1 and > 1.1 positive. The mean concentration of SARS-CoV-2-IgG-antibodies of the positive 5 outpatients was lower than in symptomatic patients with COVID-19 (n = 12) and positive PCR of SARS-CoV-2 (3.04 ± 2.58 versus 8.05 ± 6.70; p = 0.002). 4 of 5 patients had elevated SARS-CoV-2-IgA-antibodies (1.61 ± 0.82). In 408 screening-outpatients with negative anti-SARS-CoV-2-ELISA-IgG (< 0.8), the mean ratio was 0.25 ± 0.13. Two patients were in the borderline range (0.83 and 0.86). The prevalence of 1.2% of SARS-CoV-2-IgG-antibodies and consequently the rate of infection in asymptomatic outpatients in Northrhine-Westfalia (Germany) is low. The impact of virus neutralisation by antibodies and consequently immunization is the challenge of further investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/32780376/ doi: 10.1007/s15006-020-0750-y id: cord-344316-mwnnmwnw author: Herst, C.V. title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design date: 2020-04-28 words: 3495.0 sentences: 194.0 pages: flesch: 49.0 cache: ./cache/cord-344316-mwnnmwnw.txt txt: ./txt/cord-344316-mwnnmwnw.txt summary: title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors'' CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. Wilson We set out to see if we could drive CTL expansion directed against NP43-53 to occur after vaccinating C57BL/6 mice with Ebola Zaire NP43-53 (VYQVNNLEEIC), 50 and to subsequently conduct an in-vivo EBOV challenge study to see if this peptide was protective. We show here that the H2-D b restricted epitopes VSV (RGYVYQGL) and OVA (SIINFEKL), when administered to C57BL/6 mice, each produce a CD8+ We used this adjuvanted microsphere peptide vaccine platform to immunize C57BL/6 mice with NP43-53, the CTL+ class I peptide antigen from the Ebola Ziare NP protein identified as protective by Wilson et al. abstract: The 2013-2016 West Africa EBOV epidemic was the biggest EBOV outbreak to date. An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. The dominant response (25/26 subjects) was specific to the EBOV nucleocapsid protein (NP). It has been suggested that epitopes on the EBOV NP could form an important part of an effective T-cell vaccine for Ebola Zaire. We show that a 9-amino-acid peptide NP44-52 (YQVNNLEEI) located in a conserved region of EBOV NP provides protection against morbidity and mortality after mouse adapted EBOV challenge. A single vaccination in a C57BL/6 mouse using an adjuvanted microsphere peptide vaccine formulation containing NP44-52 is enough to confer immunity in mice. Our work suggests that a peptide vaccine based on CD8+ T-cell immunity in EBOV survivors is conceptually sound and feasible. Nucleocapsid proteins within SARS-CoV-2 contain multiple class I epitopes with predicted HLA restrictions consistent with broad population coverage. A similar approach to a CTL vaccine design may be possible for that virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32418793/ doi: 10.1016/j.vaccine.2020.04.034 id: cord-337093-7pxfzuq0 author: Hess, David C. title: COVID-19-Related Stroke date: 2020-05-07 words: 1846.0 sentences: 118.0 pages: flesch: 49.0 cache: ./cache/cord-337093-7pxfzuq0.txt txt: ./txt/cord-337093-7pxfzuq0.txt summary: The SARS-CoV-2 virus binds to angiotensin-converting enzyme 2 (ACE2) present on brain endothelial and smooth muscle cells. Depletion of ACE2 by SARS-CoV-2 may tip the balance in favor of the "harmful" ACE1/angiotensin II axis and promote tissue injury including stroke. There is a rationale to continue to treat with tissue plasminogen activator for COVID-19-related stroke and low molecular weight heparinoids may reduce thrombosis and mortality in sepsis-induced coagulopathy. The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) via its spike (S) protein [9] . The depletion of ACE2 by the SARS-CoV-2 virus coupled with the age-related decline in ACE2 and increase of ACE-1-Ang II tips the balance in favor of ACE-1/ angiotensin II with proinflammatory and organ damaging effects. Binding to and depletion of ACE2 may tip the RAS balance in favor of the ACE-1-angiotensin II-AT1 axis and contribute to endothelial dysfunction, organ damage, and stroke. abstract: The COVID-19 pandemic is associated with neurological symptoms and complications including stroke. There is hypercoagulability associated with COVID-19 that is likely a “sepsis-induced coagulopathy” and may predispose to stroke. The SARS-CoV-2 virus binds to angiotensin-converting enzyme 2 (ACE2) present on brain endothelial and smooth muscle cells. ACE2 is a key part of the renin angiotensin system (RAS) and a counterbalance to angiotensin-converting enzyme 1 (ACE1) and angiotensin II. Angiotensin II is proinflammatory, is vasoconstrictive, and promotes organ damage. Depletion of ACE2 by SARS-CoV-2 may tip the balance in favor of the “harmful” ACE1/angiotensin II axis and promote tissue injury including stroke. There is a rationale to continue to treat with tissue plasminogen activator for COVID-19-related stroke and low molecular weight heparinoids may reduce thrombosis and mortality in sepsis-induced coagulopathy. url: https://doi.org/10.1007/s12975-020-00818-9 doi: 10.1007/s12975-020-00818-9 id: cord-315462-u2dj79yw author: Hewitt, Judith A. title: ACTIVating Resources for the COVID-19 Pandemic: In vivo Models for Vaccines and Therapeutics date: 2020-10-01 words: 8953.0 sentences: 469.0 pages: flesch: 44.0 cache: ./cache/cord-315462-u2dj79yw.txt txt: ./txt/cord-315462-u2dj79yw.txt summary: The selection of appropriate animal models of infection, disease manifestation, and efficacy measurements is important for vaccines and therapeutics to be compared under ACTIV''s umbrella using Master Protocols with standardized endpoints and assay readouts. Models of SARS-CoV-2 infection include mice (ACE2 transgenic strains, mouse adapted virus, and AAV transduced ACE2 mice), hamsters, rats, ferrets and non-human primates (NHPs). Following infection by the intranasal route, golden Syrian Hamsters demonstrate clinical features, viral kinetics, histopathological changes, and immune responses that closely mimic the mild to moderate disease described in human COVID-19 patients (Chan et al., 2020b; Imai et al., 2020; Sia et al., 2020) . In an initial study of SARS-CoV-2 infection of hACE2-hamsters, clinical signs were observed including elevated body temperatures, slow or reduced mobility, weight loss and mortality (1 out of 4 animals). Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease. abstract: The Preclinical Working Group of Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV), a public-private partnership spearheaded by the National Institutes of Health, was charged with identifying, prioritizing, and communicating SARS-CoV-2 preclinical resources. Reviewing SARS-CoV-2 animal model data facilitates standardization and harmonization and informs knowledge gaps and prioritization of limited resources. To date, mouse, hamster, ferret, guinea pig, and non-human primates have been investigated. Several species are permissive for SARS-CoV-2 replication, often exhibiting mild disease with resolution, reflecting most human COVID-19 cases. More severe disease develops in a few models, some associated with advanced age, a risk factor for human disease. This review provides a snapshot that recommends the suitability of models for testing vaccines and therapeutics, which may evolve as our understanding of COVID-19 disease biology improves. COVID-19 is a complex disease and individual models recapitulate certain aspects of disease; therefore, the coordination and assessment of animal models is imperative. url: https://www.sciencedirect.com/science/article/pii/S1931312820305217?v=s5 doi: 10.1016/j.chom.2020.09.016 id: cord-336117-hit4kza8 author: Heymann, D.L. title: Emerging Infections, the International Health Regulations, and Macro-Economy date: 2014-02-27 words: 3357.0 sentences: 130.0 pages: flesch: 46.0 cache: ./cache/cord-336117-hit4kza8.txt txt: ./txt/cord-336117-hit4kza8.txt summary: Under the IHR, countries are able to work transparently with WHO and its scientific experts and collaborating laboratories to conduct joint risk assessments of public health events such as outbreaks of infectious diseases; to make evidence-based recommendations to help prevent or control their international spread; and, by providing valid and transparent information to national focal points, to help prevent unnecessary panic and misunderstanding about risk. Precautionary measures to prevent international spread of the infection were immediately recommended by the WHO -it was first recommended that persons who were ill with similar symptoms and contact with geographic areas where outbreaks were occurring defer their travel until they were well. The IHR 1969 were revised in 2005, incorporating many of the lessons learned during the SARS outbreak, and now ensure broader disease coverage, and in addition require countries to develop core capacities in public health laboratory and epidemiology in order to detect and respond to diseases where and when it occurs, and before it spreads internationally (Box 1). abstract: When breaches in the species barrier between animals and humans result in crossover of animal infections to humans, the result is an emerging infectious disease. Emerging infections have the potential to cause severe human illness and death, and to spread among human populations and across geographic borders. Direct costs associated with emerging infections are often high, caused by prolonged patient management, hospitalization, and convalescence. Indirect costs are caused by absenteeism from work, death, and permanent removal from the workforce. There may be additional costs if precautionary prevention measures are required, based on the known or potential risk. These costs result from culling and prohibited trade in animals and animal-based products if infected animals are a continuing threat to humans; or from postponement or cancellation of travel and tourism if transmission in the general population is uncontrolled. Emerging infections sometimes cause panic and/or fear because of misunderstanding of the risk, and can lead to actions that result in economic loss similar to that caused by legitimate public health precautionary measures. They include reactions such as avoiding animal-based foods mistakenly thought to be the source of infection; unnecessary cancelling travel plans to avoid geographic areas where there is a perception of risk of infection; and/or unwarranted culling of animals or destruction of animal-based foods. If the misunderstanding is transmitted widely by the press or through social media networks, the negative economic impact can be amplified. Economic loss caused by these perceived risks can generally not be disentangled from the losses causes by public health measures that may be in place, but it is thought that at times they add significantly to the economic burden. The International Health Regulations (IHR) were designed to respond to the international spread of infectious disease outbreaks in a manner that prevents unnecessary negative economic impacts. Agreed by all Member States of the World Health Organization in 2005, they are a legally binding global agreement with the specific purpose of ensuring maximum security against the international spread of diseases, with a minimum interference in world traffic and trade. They reflect current understanding of infectious disease risks, especially those that emerge at the animal/human interface; the realization that infectious diseases cannot be stopped from entering countries at borders; the vast increase in access to information through the internet; and globalization that increases the speed with which infectious diseases spread. Under the IHR, countries are able to work transparently with WHO and its scientific experts and collaborating laboratories to conduct joint risk assessments of public health events such as outbreaks of infectious diseases; to make evidence-based recommendations to help prevent or control their international spread; and, by providing valid and transparent information to national focal points, to help prevent unnecessary panic and misunderstanding about risk. url: https://www.sciencedirect.com/science/article/pii/B9780123756787006246 doi: 10.1016/b978-0-12-375678-7.00624-6 id: cord-009153-zxx4m1kz author: Heymann, David L title: Dangerous pathogens in the laboratory: from smallpox to today''s SARS setbacks and tomorrow''s polio-free world date: 2004-05-15 words: 2790.0 sentences: 147.0 pages: flesch: 48.0 cache: ./cache/cord-009153-zxx4m1kz.txt txt: ./txt/cord-009153-zxx4m1kz.txt summary: THE LANCET • Vol 363 • May 15, 2004 • www.thelancet.com COMMENTARY Less than a year after an unprecedented international public-health effort interrupted human-to-human transmission of the coronavirus that causes severe acute respiratory syndrome (SARS-CoV), some human beings are again infected. 2 Auspiciously, the new SARS cases are occurring as WHO''s Biosafety Advisory Group prepares to examine the long-term containment of poliovirus stocks, the risks of which will rapidly increase after interruption of transmission and the ending of immunisation with oral poliovirus vaccine. 3 The recent outbreak of nine cases of SARS in China, with one death, underlines again the challenges of maintaining appropriate biosafety conditions in laboratories working with dangerous pathogens. During the SARS outbreak last year, many specimens were obtained from human cases of SARS COMMENTARY Dangerous pathogens in the laboratory: from smallpox to today''s SARS setbacks and tomorrow''s polio-free world and sent to many different national and international laboratories for various studies. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135754/ doi: 10.1016/s0140-6736(04)16234-x id: cord-308736-kpz0o1ag author: Heßling, Martin title: Ultraviolet irradiation doses for coronavirus inactivation – review and analysis of coronavirus photoinactivation studies date: 2020-05-14 words: 2826.0 sentences: 156.0 pages: flesch: 45.0 cache: ./cache/cord-308736-kpz0o1ag.txt txt: ./txt/cord-308736-kpz0o1ag.txt summary: Methods: Coronavirus inactivation experiments with ultraviolet light performed in the past were evaluated to determine the UV radiation dose required for a 90% virus reduction. To answer the important question regarding SARS-CoV-2 and other coronaviruses as to which irradiation doses are needed for inactivation, the existing coronavirus photoinactivation results of the last 60 years have been reviewed and analyzed in this study. In most studies, the authors did not intend to investigate the log-reduction doses of coronaviruses, but rather virus inactivation in various applications. Most authors did not measure the UVC absorption properties of their biological materials because it was of no importance for their research task; thus, it is almost impossible to extract the role of the absorption in the calculation of the necessary irradiation doses for a 90% virus reduction. To date, UVC radiation has been effective against all coronaviruses in all published investigations, although the absorption properties of the sample media reduced inactivation success. abstract: Background: To slow the increasing global spread of the SARS-CoV-2 virus, appropriate disinfection techniques are required. Ultraviolet radiation (UV) has a well-known antiviral effect, but measurements on the radiation dose necessary to inactivate SARS-CoV-2 have not been published so far. Methods: Coronavirus inactivation experiments with ultraviolet light performed in the past were evaluated to determine the UV radiation dose required for a 90% virus reduction. This analysis is based on the fact that all coronaviruses have a similar structure and similar RNA strand length. Results: The available data reveals large variations, which are apparently not caused by the coronaviruses but by the experimental conditions selected. If these are excluded as far as possible, it appears that coronaviruses are very UV sensitive. The upper limit determined for the log-reduction dose (90% reduction) is approximately 10.6 mJ/cm(2) (median), while the true value is probably only 3.7 mJ/cm(2) (median). Conclusion: Since coronaviruses do not differ structurally to any great exent, the SARS-CoV-2 virus – as well as possible future mutations – will very likely be highly UV sensitive, so that common UV disinfection procedures will inactivate the new SARS-CoV-2 virus without any further modification. url: https://www.ncbi.nlm.nih.gov/pubmed/32547908/ doi: 10.3205/dgkh000343 id: cord-296657-mymndjvd author: Higuchi, Yusuke title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 words: 3509.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-296657-mymndjvd.txt txt: ./txt/cord-296657-mymndjvd.txt summary: The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. Three cycles of screening resulted in an identification of mutant ACE2 clones with more than 100-fold higher binding affinity to the RBD and lower half-maximal inhibitory concentration (IC50) for SARS-CoV-2 pseudotyped lentivirus as well as authentic virus. We engineered ACE2 to bind the RBD of the SARS-CoV-2 spike protein with the combination of surface display of mutagenized library and fluorescence-activated cell sorting (FACS) to perform the evolution in 293T human cells. abstract: The SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor via receptor binding domain (RBD) to enter into the cell. Inhibiting this interaction is a main approach to block SARS-CoV-2 infection and it is required to have high affinity to RBD independently of viral mutation for effective protection. To this end, we engineered ACE2 to enhance the affinity with directed evolution in human cells. Three cycles of random mutation and cell sorting achieved more than 100-fold higher affinity to RBD than wild-type ACE2. The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. url: https://doi.org/10.1101/2020.09.16.299891 doi: 10.1101/2020.09.16.299891 id: cord-294582-flkjekyo author: Hijikata, Atsushi title: Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs date: 2020-05-25 words: 4238.0 sentences: 232.0 pages: flesch: 49.0 cache: ./cache/cord-294582-flkjekyo.txt txt: ./txt/cord-294582-flkjekyo.txt summary: In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Among these methods, SBDR is the most promising to find Abbreviations ACE2, angiotensin I-converting enzyme 2; MERS, Middle East respiratory syndrome; RBD, receptor-binding domain; SARS-CoV, severe acute respiratory syndrome coronavirus; SBDR, structure-based drug repositioning; WHO, World Health Organization. Also, the structural models of the complexes between SARS-CoV-2 proteins and potential drugs were proposed by comparing the ligand molecules of the proteins and approved, experimental, or natural drugs. A total of 11 ligand molecules were matched to 21 approved/experimental and 5 natural drugs, and the complex models of the SARS-CoV-2 proteins with several promising drugs, those with high similarity score or placed in higher ranking, were constructed as follows. abstract: The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID‐19) caused by the novel coronavirus SARS‐CoV‐2 a pandemic. There is, however, no confirmed anti‐COVID‐19 therapeutic currently. In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Our theoretical models suggest several drugs, such as carfilzomib, sinefungin, tecadenoson, and trabodenoson, that could be further investigated for their potential for treating COVID‐19. url: https://doi.org/10.1002/1873-3468.13806 doi: 10.1002/1873-3468.13806 id: cord-283579-aejbfk3l author: Hilda, Awoyelu Elukunbi title: Phyloevolutionary analysis of SARS-CoV-2 in Nigeria date: 2020-06-14 words: 1708.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-283579-aejbfk3l.txt txt: ./txt/cord-283579-aejbfk3l.txt summary: Conclusion The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. Knowledge on the outbreak and spread of SARS-CoV-2 in Nigeria would help in providing preventive measures and reduce transmission among populations at risk. Comparative analysis of strains within clades was performed on Geneious Prime (https://www.geneious.com/) based on statistical analysis to determine positions in the genomic sequences from Nigeria that significantly differ between other strain. Figures 2a -g showed consensus similarities and variants between 3 strains from Wuhan, China and Nigeria, including human SARS-CoV-2 human genome. Comparative analysis of the strain from Nigeria, 2 strains from Wuhan sharing the same clade and the reference human SARS-CoV-2 genome was done. The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. abstract: Abstract Background Phyloepidemiologic approaches have given specific insight to understanding emergence and evolution of infection. Knowledge on the outbreak and spread of SARS-CoV-2 in Nigeria would assist in providing preventive measures to reduce transmission among populations at risk. Therefore, this study aimed at investigating the evolution of SARS-CoV-2 in Nigeria. Materials and Method A total of 39 complete genomes of SARS-CoV-2 were retrieved from the GISAID EpiFluTM database on March 29th 2020 to investigate its evolution in Nigeria. Sequences were selected based on the travel history of the patient and the collection date. Other sequences were not selected because they were short, contained artefacts, not from original source or had insufficient information. Evolutionary history was inferred using Maximum Likelihood method based on the General Time Reversible model. Phylogenetic tree was constructed to determine the common ancestor of each strain. Results The phylogenetic analysis showed the strain in Nigeria clustered in a monophyletic clade with a Wuhan sublineage. Nucleotide alignment also showed a 100% similarity indicating a common origin of evolution. Comparative analysis showed 27,972 (93.6%) identical sites and 97.6% pairwise identity with the consensus. Conclusion The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. Preventive measures that can limit the spread of the infection among populations at risk should be implemented. url: https://doi.org/10.1016/j.nmni.2020.100717 doi: 10.1016/j.nmni.2020.100717 id: cord-266016-555e3ndo author: Hildenwall, Helena title: Paediatric COVID‐19 admissions in a region with open schools during the two first months of the pandemic date: 2020-06-21 words: 969.0 sentences: 53.0 pages: flesch: 54.0 cache: ./cache/cord-266016-555e3ndo.txt txt: ./txt/cord-266016-555e3ndo.txt summary: While it appears that most children get mild symptoms if they become infected with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) (1), there have been concerns that they may present with high viral loads and contribute to asymptomatic transmission (2) . We carried out a two-month review of paediatric admissions aged 0-17 years who tested positive for SARS-CoV-2 in the Stockholm region, where approximately 514,000 (24%) of all Swedish children live. A total of 63 admitted children aged 0-17 years tested positive for SARS-CoV-2 during the study period. Infants represented more than half of all symptomatic admissions (16/30, 53%) whereas the proportion of all SARS-CoV-2 positive admitted children Paediatric admissions accounted for a minor part of the total admissions due to COVID-19 as a primary diagnosis during the first two months of the pandemic in Stockholm (30/4347, 0.7%). abstract: According to the United Nations Educational, Science and Cultural Organization, 194 countries had implemented country‐wide school closures by April 1(st) 2020 in an effort to combat the COVID‐19 pandemic. It’s estimated that those closures affected 91.3% of students across the globe. However, Sweden adopted a different approach to the strict lockdowns imposed elsewhere and day care centres and schools for children up to 15 years of age remained open. The strategy decision to shift schools to distance learning only for children aged 16 years and older was influenced by multiple factors, including the potential impact on school closures on the availability of the healthcare work force, the increasing evidence of mainly mild infections among children and the potential negative consequences of school closures for younger children. url: https://www.ncbi.nlm.nih.gov/pubmed/32567145/ doi: 10.1111/apa.15432 id: cord-346658-ij5sr88p author: Hilgenfeld, Rolf title: Sometimes Intermediates Do the Job! date: 2006-04-07 words: 1196.0 sentences: 73.0 pages: flesch: 60.0 cache: ./cache/cord-346658-ij5sr88p.txt txt: ./txt/cord-346658-ij5sr88p.txt summary: The mode of binding of this inhibitor to the target enzyme was found to be related (although not identical) to what had been seen earlier in a complex between the rhinovirus (HRV-2) 3C proteinase and compound AG7088 (Figure 1A) , a vinylogous ethyl ester developed by Agouron Inc. The structural insight along with information on the flexibility of the enzyme [9] enabled researchers world-wide to use structure-based design [5] and virtual screening methods [10] to prepare new inhibitors of the SARS-CoV M pro . Several lopinavir derivatives showed somewhat improved binding affinities, but it came as a big surprise that some of the intermediate benzotriazole esters resulting from the activation of the acid components by HBTU were nanomolar inhibitors of the M pro ! The discovery of compounds binding noncovalently to the M pro may, in the end, constitute a more important milestone on the way to clinically useful inhibitors of the coronavirus main proteinase than identification of the acylating agents. abstract: The SARS coronavirus main proteinase is a prime target for antiviral therapy. In this issue of Chemistry & Biology, Wu et al. describe potent inhibition of the enzyme by benzotriazole esters, which were originally obtained as intermediates in the synthesis of lopinavir derivatives [1]. url: https://api.elsevier.com/content/article/pii/S1074552106000883 doi: 10.1016/j.chembiol.2006.03.002 id: cord-328960-46zui1sl author: Hillen, Hauke S. title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 words: 4541.0 sentences: 285.0 pages: flesch: 62.0 cache: ./cache/cord-328960-46zui1sl.txt txt: ./txt/cord-328960-46zui1sl.txt summary: Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). abstract: The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present the cryo-electron microscopic structure of the SARS-CoV-2 RdRp in its replicating form. The structure comprises the viral proteins nsp12, nsp8, and nsp7, and over two turns of RNA template-product duplex. The active site cleft of nsp12 binds the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the RNA duplex as it exits. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged ‘sliding poles’ that may enable processive replication of the long coronavirus genome. Our results will allow for a detailed analysis of the inhibitory mechanisms used by antivirals such as remdesivir, which is currently in clinical trials for the treatment of coronavirus disease 2019 (COVID-19). url: https://doi.org/10.1101/2020.04.27.063180 doi: 10.1101/2020.04.27.063180 id: cord-331517-o5ejfq86 author: Hirayama, Takehisa title: Guillain-Barré syndrome after COVID-19 in Japan date: 2020-10-29 words: 2135.0 sentences: 148.0 pages: flesch: 47.0 cache: ./cache/cord-331517-o5ejfq86.txt txt: ./txt/cord-331517-o5ejfq86.txt summary: We report the first case of Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection in Japan. In previous reports, most patients with SARS-CoV-2-infection-related GBS had lower limb predominant symptoms, and antiganglioside antibody tests were negative. Our findings support the notion that non-immune abnormalities such as hyperinflammation following cytokine storms and microvascular disorders due to vascular endothelial damage may lead to neurological symptoms in patients with SARS-CoV-2 infection. 4 In the present report, we discuss a case of axonal-type GBS associated with SARS-CoV-2 infection, where the patient was tested for various antiganglioside antibodies. Furthermore, we review the cases of SARS-CoV-2-infection-related GBS reported to date, in order to provide insight into the clinical characteristics and pathological mechanisms underlying the disease. In conclusion, our report supports the notion that patients with GBS associated with SARS-CoV-2 infection tend to test negative for antiganglioside antibodies. ► Patients with Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection may test negative for many known antiganglioside antibodies. abstract: We report the first case of Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection in Japan. A 54-year-old woman developed neurological symptoms after SARS-CoV-2 infection. We tested for various antiganglioside antibodies, that had not been investigated in previous cases. The patient was diagnosed with GBS based on neurological and electrophysiological findings; no antiganglioside antibodies were detected. In previous reports, most patients with SARS-CoV-2-infection-related GBS had lower limb predominant symptoms, and antiganglioside antibody tests were negative. Our findings support the notion that non-immune abnormalities such as hyperinflammation following cytokine storms and microvascular disorders due to vascular endothelial damage may lead to neurological symptoms in patients with SARS-CoV-2 infection. Our case further highlights the need for careful diagnosis in suspected cases of GBS associated with SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33122241/ doi: 10.1136/bcr-2020-239218 id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 words: 3105.0 sentences: 184.0 pages: flesch: 55.0 cache: ./cache/cord-258250-zueo1xfa.txt txt: ./txt/cord-258250-zueo1xfa.txt summary: title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . abstract: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is determined by reverse-transcription PCR (RT-PCR) in routine clinical practice. In the current pandemic situation, a more rapid and high-throughput method is in growing demand. Here, we validated the performance of a new antigen test (LUMIPULSE) based on the chemiluminescence enzyme immunoassay. A total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients, 231 individual samples from 4 infected patients and 215 non-infected individuals) were analyzed for SARS-CoV-2 by quantitative RT-PCR (RT-qPCR) and then subjected to LUMIPULSE. We determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of RT-qPCR. Further, we compared the viral loads and antigen levels in serial samples from seven infected patients. When using RT-qPCR as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313). In specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with RT-qPCR, respectively. This concordance declined with lower viral loads. In the serially followed patients, the antigen levels showed a steady decline along with viral clearance. This gradual decline was in contrast with the abrupt “positive-to-negative” and “negative-to-positive” status changes observed with RT-qPCR, particularly in the late phase of infection. In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. url: https://doi.org/10.1016/j.ijid.2020.08.029 doi: 10.1016/j.ijid.2020.08.029 id: cord-269519-8hr8wyrr author: Hirotsu, Yosuke title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 words: 1599.0 sentences: 113.0 pages: flesch: 54.0 cache: ./cache/cord-269519-8hr8wyrr.txt txt: ./txt/cord-269519-8hr8wyrr.txt summary: Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. abstract: BACKGROUND: Severe acute respiratory coronavirus 2 (SARS-CoV-2) has spread and caused death worldwide. Preventive measures and infection control are underway, and some areas show signs of convergence. Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. OBJECTIVES: We aim to investigate the incidence of causative viruses and pathogens in patients. STUDY DESIGN: We collected 191 nasopharyngeal swabs from patients with cold-like symptoms in Japan. All samples were subjected to multiplex PCR with the FilmArray Respiratory Panel and reverse transcription PCR (RT-PCR) to detect SARS-CoV-2. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). Of these, we frequently identified human rhinoviruses/enteroviruses (5.8%, n=11), human metapneumovirus (3.7%, n=7), coronavirus 229E (2.1%, n=4) and coronavirus OC43 (1.6%, n=3); while no influenza viruses were detected. RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. CONCLUSIONS: Co-infection with SARS-CoV-2 and other viruses was not observed. Causative viruses remain prevalent after implementing preventive measures. SARS-CoV-2 differs from influenza viruses in its infectivity. url: https://doi.org/10.1016/j.jcv.2020.104543 doi: 10.1016/j.jcv.2020.104543 id: cord-278987-3s5p9yw6 author: Hirotsu, Yosuke title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship date: 2020-04-17 words: 517.0 sentences: 45.0 pages: flesch: 55.0 cache: ./cache/cord-278987-3s5p9yw6.txt txt: ./txt/cord-278987-3s5p9yw6.txt summary: title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship The patient stayed in room A for 3 days, during which he had the SARS-CoV-2 infection. SARS-CoV-2 is detectable in several types of clinical samples including bronchial lavage fluid, nasopharyngeal swab, pharyngeal swab, sputum, saliva, and feces. 4, 5 Transmission of SARS-CoV-2 via surfaces in hospitals is of great concern to medical staff and patients. 6 A recent study showed that environmental contamination can occur via contact with patients with SARS-CoV-2 and upper respiratory tract symptoms. Double-quencher probes improved the detection sensitivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by one-step RT-PCR Surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient All authors report no conflicts of interest relevant to this article. abstract: nan url: https://doi.org/10.1017/ice.2020.144 doi: 10.1017/ice.2020.144 id: cord-356364-ipi81ce3 author: Ho, Bo-Lin title: Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date: 2015-12-14 words: 5038.0 sentences: 277.0 pages: flesch: 62.0 cache: ./cache/cord-356364-ipi81ce3.txt txt: ./txt/cord-356364-ipi81ce3.txt summary: In the present study, MERS-CoV main protease (M(pro)) is expressed; the dimerization of the protein and its relationship to catalysis are investigated. The colorimetry-based peptide substrate, TSAVLQ-para-nitroanilide (TQ6-pNA) (purity 95-99% by HPLC; GL Biochem Ltd, Shanghai, China), was used to measure the proteolytic activity of MERS-CoV M pro and its mutants throughout the course of the study as described previously [25, 28] . In addition, although the K d values of wild-type SARS-CoV M pro without or with substrates show no significant difference (Table 2) , it was possible to detect substrate-induced dimerization at a protein concentration of 1 μM by AEC [33] . Biochemical and AUC studies indicated that MERS-CoV M pro shows almost the same proteolytic activity as SARS-CoV M pro ; although it is a monomer in aqueous buffer and displays substrate-induced dimerization (Fig 6) . abstract: BACKGROUND: A highly pathogenic human coronavirus (CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), has emerged in Jeddah and other places in Saudi Arabia, and has quickly spread to European and Asian countries since September 2012. Up to the 1(st) October 2015 it has infected at least 1593 people with a global fatality rate of about 35%. Studies to understand the virus are necessary and urgent. In the present study, MERS-CoV main protease (M(pro)) is expressed; the dimerization of the protein and its relationship to catalysis are investigated. METHODS AND RESULTS: The crystal structure of MERS-CoV M(pro) indicates that it shares a similar scaffold to that of other coronaviral M(pro) and consists of chymotrypsin-like domains I and II and a helical domain III of five helices. Analytical ultracentrifugation analysis demonstrated that MERS-CoV M(pro) undergoes a monomer to dimer conversion in the presence of a peptide substrate. Glu169 is a key residue and plays a dual role in both dimerization and catalysis. The mutagenesis of other residues found on the dimerization interface indicate that dimerization of MERS-CoV M(pro) is required for its catalytic activity. One mutation, M298R, resulted in a stable dimer with a higher level of proteolytic activity than the wild-type enzyme. CONCLUSIONS: MERS-CoV M(pro) shows substrate-induced dimerization and potent proteolytic activity. A critical assessment of the residues important to these processes provides insights into the correlation between dimerization and catalysis within the coronaviral M(pro) family. url: https://doi.org/10.1371/journal.pone.0144865 doi: 10.1371/journal.pone.0144865 id: cord-299835-92karhpl author: Ho, Khek Y. title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date: 2004-02-17 words: 3524.0 sentences: 163.0 pages: flesch: 52.0 cache: ./cache/cord-299835-92karhpl.txt txt: ./txt/cord-299835-92karhpl.txt summary: title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. abstract: Background. Severe acute respiratory syndrome (SARS) is a newly recognized infectious disease that has recently emerged in East Asia and North America. Although the clinical features of acute infection have been well described, mildly symptomatic or asymptomatic infections have not been well characterized. Objective. To assess the spectrum of illness in health-care workers (HCWs). Methods. A prospective seroepidemiologic cohort study was conducted on 372 HCWs in a large teaching hospital in Singapore who were both exposed and not exposed to patients with SARS. Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Results. A total of 21 patients with SARS were treated at our hospital. They were associated with transmission to 14 staff members, patients, and visitors in our hospital. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. All seropositive HCWs had been exposed either directly or indirectly to patients with SARS. No asymptomatic, nonexposed staff members were found to be seropositive. There was a trend towards protection for HCWs who, while fully protected, had had contact with patients with SARS. Conclusions. Although the majority of cases of SARS are associated with pneumonia, a small number of mildly symptomatic individuals do seroconvert. HCWs who are exposed to patients with SARS can be infected with SARS, regardless of the intensity of exposure. This has implications for surveillance and infection control planning, in the event that SARS returns next winter. url: https://www.ncbi.nlm.nih.gov/pubmed/14767817/ doi: 10.1086/381558 id: cord-345296-4z7yfj5s author: Ho, Mei-Shang title: Neutralizing Antibody Response and SARS Severity date: 2005-11-17 words: 4600.0 sentences: 190.0 pages: flesch: 42.0 cache: ./cache/cord-345296-4z7yfj5s.txt txt: ./txt/cord-345296-4z7yfj5s.txt summary: Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. To adjust the time effects and other covariates of interest, the relationship between antibody titer, based on logarithmic transformation of base 2 (serum dilution) and other potential factors, i.e., age, sex, infection source, and duration of illness, was quantified by linear mixed models (18) , which took into account the correlation between repeated measurements of each study participants. In the model, patients with a more severe clinical course had earlier and higher antibody responses; we then examined the death rate of the early responders (Table 6 ). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways abstract: Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. With a linear mixed model, neutralizing antibody titer was shown to peak between week 5 and week 8 after onset and to decline thereafter, with a half-life of 6.4 weeks. Patients with a longer illness showed a lower neutralizing antibody response than patients with a shorter illness duration (p = 0.008). When early responders were compared with most patients, who seroconverted on and after week 3 of illness, the small proportion (17.4%) of early responders (antibody detectable within 2 weeks) had a higher death rate (29.6% vs. 7.8%) (Fisher exact test, p = 0.004), had a shorter survival time of <2 weeks (Fisher exact test, p = 0.013), and were more likely to be > 60 years of age (Fisher exact test, p = 0.01). Our findings have implications for understanding the pathogenesis of SARS and for SARS vaccine research and development. url: https://www.ncbi.nlm.nih.gov/pubmed/16318725/ doi: 10.3201/eid1111.040659 id: cord-281793-tj4m01s4 author: Ho, Mitchell title: Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date: 2020-05-20 words: 3745.0 sentences: 203.0 pages: flesch: 51.0 cache: ./cache/cord-281793-tj4m01s4.txt txt: ./txt/cord-281793-tj4m01s4.txt summary: Crossreactive antibodies (e.g., 47D11, S309, and VHH-72) that bind highly conserved epitopes on the RBDs of SARS-CoV and SARS-CoV-2 could have broad neutralization activities against viral infection. The receptor binding domain (RBD) of the SARS-CoV-2 S protein contains several novel residues that might be introduced through recombination with the pangolin coronavirus, indicating a possible critical step in the evolution of the ability of SARS-CoV-2 to infect humans [10] . isolated a human monoclonal antibody (named "rRBD-15") that inhibits the interaction of the RBD of SARS-CoV-2 and the ACE2 and neutralizes the pseudovirus infection [5] . The structure complex of 47D11 and the RBD (or the S1/S protein) would reveal a novel conserved site on the RBD for broad-neutralizing antibodies against SARSr-CoVs. In addition to 47D11, another human antibody (S309) isolated from memory B cells of a SARS survivor infected in 2003 neutralizes SARS-CoV-2 [18] . abstract: SARS-CoV-2 gains entry to human cells through its spike (S) protein binding to angiotensin-converting enzyme 2 (ACE2). Therefore, the receptor binding domain (RBD) of the S protein is the primary target for neutralizing antibodies. Selection of broad-neutralizing antibodies against SARS-CoV-2 and SARS-CoV is attractive and might be useful for treating not only COVID-19 but also future SARS-related CoV infections. Broad-neutralizing antibodies, such as 47D11, S309, and VHH-72, have been reported to target a conserved region in the RBD of the S1 subunit. The S2 subunit required for viral membrane fusion might be another target. Due to their small size and high stability, single-domain antibodies might have the ability to be administered by an inhaler making them potentially attractive therapeutics for respiratory infections. A cocktail strategy combining two (or more) antibodies that recognize different parts of the viral surface that interact with human cells might be the most effective. url: https://doi.org/10.1093/abt/tbaa009 doi: 10.1093/abt/tbaa009 id: cord-323871-2hx4fuk2 author: Ho, Sheau Ling title: Structural bioinformatics analysis of free cysteines in protein environments date: 2009-03-14 words: 3244.0 sentences: 198.0 pages: flesch: 59.0 cache: ./cache/cord-323871-2hx4fuk2.txt txt: ./txt/cord-323871-2hx4fuk2.txt summary: For non-membrane proteins: the hydrophobic residues such as leucine, valine, isoleucine and alanine were more frequently seen in the spatial neighborhood around free cysteines; the same was observed for the aromatic phenylalanine residue. Thus, we applied a structure-base sequence alignment of these nine coronavirus main proteinases to identify any spatial correspondences involving cysteine among them. It can be observed that this multiple sequences alignment figure shows a strong conservation of hydrophobic residues (valine, leucine, isoleucine, alanine phenylalanine and proline) and small residues (serine and glycine) in proximity to cysteine residues. A superimposition (stereo image) of the structures of SARS 3CLpro demonstrates that cysteine residues not only favor positioning in a hydrophobic environment but also develop hunched posture in the surroundings of aromatic residues, see Fig. 3 . abstract: Cysteine has been considered as a “hydrophilic” amino acid because of its pK(a) and its ability to form (weak) hydrogen bonds. However, cysteines are found mostly in hydrophobic environments, either in S–S (disulphide) form or in free cysteine form. When free cysteines are found on the surface of proteins, they are often involved in catalytic residues, as in cysteine proteases, P-loop phosphatases, etc. Additionally, a unique property of cysteines is that their side-chain volume is different from all other amino acids. This study is focused on the discrimination between structural versus active free cysteines based on a local environment analysis which does not appear to have been attempted previously. We have demonstrated the corresponding structural positions associated with free cysteines in their three-dimensional localization environment. We examined protein samples including nine, sequenced, coronavirus proteases and cysteine-rich non-membrane proteins. Our present study shows that the sequential environments of free cysteines of coronavirus proteases are rather hydrophobic and that the free cysteines of non-membrane proteases have a higher amount of contacts to hydrophobic residues and lower amount of contacts to polar or charged residues. url: https://doi.org/10.1016/j.jtice.2008.07.015 doi: 10.1016/j.jtice.2008.07.015 id: cord-298083-4h3tg6hg author: Ho, Tin-Yun title: Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein date: 2004-01-23 words: 3557.0 sentences: 208.0 pages: flesch: 56.0 cache: ./cache/cord-298083-4h3tg6hg.txt txt: ./txt/cord-298083-4h3tg6hg.txt summary: In order to analyze the antigenicity and receptor-binding ability of SARS-CoV S protein, we expressed the S protein in Escherichia coli using a pET expression vector. By biotinylated ELISA and Western blot using biotin-labeled S protein as the probe, we identified 130-kDa and 140-kDa proteins in Vero cells that might be the cellular receptors responsible for SARS-CoV infection. Taken together, these results suggested that recombinant S protein exhibited the antigenicity and receptor-binding ability, and it could be a good candidate for further developing SARS vaccine and anti-SARS therapy. These data suggested that comparison of primary amino acid sequences does not provide insight into the receptor-binding specificity or antigenic properties of SARS-CoV S protein. To analyze the antigenicity of recombinant S protein, we performed Western blot and ELISA using sera from SARS patients or from spike-immunized rabbits. abstract: Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a novel coronavirus and causing worldwide outbreaks. SARS coronavirus (SARS-CoV) is an enveloped RNA virus, which contains several structural proteins. Among these proteins, spike (S) protein is responsible for binding to specific cellular receptors and is a major antigenic determinant, which induces neutralizing antibody. In order to analyze the antigenicity and receptor-binding ability of SARS-CoV S protein, we expressed the S protein in Escherichia coli using a pET expression vector. After the isopropyl-β-d-thiogalactoside induction, S protein was expressed in the soluble form and purified by nickel-affinity chromatography to homogeneity. The amount of S protein recovered was 0.2–0.3 mg/100 ml bacterial culture. The S protein was recognized by sera from SARS patients by ELISA and Western blot, which indicated that recombinant S protein retained its antigenicity. By biotinylated ELISA and Western blot using biotin-labeled S protein as the probe, we identified 130-kDa and 140-kDa proteins in Vero cells that might be the cellular receptors responsible for SARS-CoV infection. Taken together, these results suggested that recombinant S protein exhibited the antigenicity and receptor-binding ability, and it could be a good candidate for further developing SARS vaccine and anti-SARS therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/14706633/ doi: 10.1016/j.bbrc.2003.11.180 id: cord-339514-0aa58pi6 author: Ho, Yu title: Assembly of human severe acute respiratory syndrome coronavirus-like particles date: 2004-06-11 words: 2662.0 sentences: 140.0 pages: flesch: 53.0 cache: ./cache/cord-339514-0aa58pi6.txt txt: ./txt/cord-339514-0aa58pi6.txt summary: Viral particles of human severe acute respiratory syndrome coronavirus (SARS CoV) consist of three virion structural proteins, including spike protein, membrane protein, and envelope protein. In this report, virus-like particles were assembled in insect cells by the co-infection with recombinant baculoviruses, which separately express one of these three virion proteins. Sucrose gradient purification followed by Western blot analysis and immunogold labeling showed that the spike protein could be incorporated into the virus like particle also. Recombinant baculoviruses encoding E, M, and S protein genes were used to infect Sf21 insect cell, and the expression of each protein was checked by Western blot at 4 dpi (data not shown). The packaging signal of coronavirus RNA was previously identified by using defective interfering viral particles [26] , since the SARS-CoV is a highly infectious virus, it would be much more feasible to identify this signal by using VLPs. Moreover, S protein-containing VLPs should be able to specifically target to the host cell of the SARS CoV and serve as a safe and efficient tool to deliver Western analysis confirmed the presence of S and E proteins mainly in fractions 16-18. abstract: Viral particles of human severe acute respiratory syndrome coronavirus (SARS CoV) consist of three virion structural proteins, including spike protein, membrane protein, and envelope protein. In this report, virus-like particles were assembled in insect cells by the co-infection with recombinant baculoviruses, which separately express one of these three virion proteins. We found that the membrane and envelope proteins are sufficient for the efficient formation of virus-like particles and could be visualized by electron microscopy. Sucrose gradient purification followed by Western blot analysis and immunogold labeling showed that the spike protein could be incorporated into the virus like particle also. The construction of engineered virus-like particles bearing resemblance to the authentic one is an important step towards the development of an effective vaccine against infection of SARS CoV. url: https://www.sciencedirect.com/science/article/pii/S0006291X04008253 doi: 10.1016/j.bbrc.2004.04.111 id: cord-342456-5gp3cry0 author: Hoagland, Daisy A. title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 words: 4511.0 sentences: 240.0 pages: flesch: 48.0 cache: ./cache/cord-342456-5gp3cry0.txt txt: ./txt/cord-342456-5gp3cry0.txt summary: Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. abstract: To interfere with the biology of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, we focused on restoring the transcriptional response induced by infection. Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. Here we demonstrate the successful identification of compounds that display efficacy in blocking SARS-CoV-2 replication based on their ability to counteract the virus-induced transcriptional landscape. These compounds were found to potently reduce viral load despite having no impact on viral entry or modulation of the host antiviral response in the absence of virus. RNA-Seq profiling implicated the induction of the cholesterol biosynthesis pathway as the underlying mechanism of inhibition and suggested that targeting this aspect of host biology may significantly reduce SARS-CoV-2 viral load. url: https://doi.org/10.1101/2020.07.12.199687 doi: 10.1101/2020.07.12.199687 id: cord-281948-xv7vuypd author: Hoang, Ansel title: COVID-19 in 7780 pediatric patients: A systematic review date: 2020-06-26 words: 4065.0 sentences: 235.0 pages: flesch: 47.0 cache: ./cache/cord-281948-xv7vuypd.txt txt: ./txt/cord-281948-xv7vuypd.txt summary: We included published or in press peer-reviewed cross-sectional, case series, and case reports providing clinical signs, imaging findings, and/or laboratory results of pediatric patients who were positive for COVID-19. Data collected included the type of article (e.g., case series), country of origin, number of pediatric patients, demographic information, and all clinical symptoms (e. Compared to that review and other COVID-19 pediatric systematic reviews, [18À21] this manuscript has several key advantages: (1) we summarize 131 studies that includes 7780 children from 26 different countries, (2) this report synthesizes underlying pediatric medical conditions and delineates bacterial and viral coinfections, (3) we quantitatively describe clinical symptoms and imaging findings, (4) herein, we conglomerate the mean and standard deviation of frequently used laboratory analytes in COVID-19 positive children, (5) our report presents antiviral therapies by specific agents, and (6) our systematic review offers a preliminary comparison of patients with/without MIS-C. abstract: BACKGROUND: Studies summarizing the clinical picture of COVID-19 in children are lacking. This review characterizes clinical symptoms, laboratory, and imaging findings, as well as therapies provided to confirmed pediatric cases of COVID-19. METHODS: Adhering to PRISMA guidelines, we searched four medical databases (PubMed, LitCovid, Scopus, WHO COVID-19 database) between December 1, 2019 to May 14, 2020 using the keywords “novel coronavirus”, “COVID-19” or “SARS-CoV-2”. We included published or in press peer-reviewed cross-sectional, case series, and case reports providing clinical signs, imaging findings, and/or laboratory results of pediatric patients who were positive for COVID-19. Risk of bias was appraised through the quality assessment tool published by the National Institutes of Health. PROSPERO registration # CRD42020182261. FINDINGS: We identified 131 studies across 26 countries comprising 7780 pediatric patients. Although fever (59·1%) and cough (55·9%) were the most frequent symptoms 19·3% of children were asymptomatic. Patchy lesions (21·0%) and ground-glass opacities (32·9%) depicted lung radiograph and computed tomography findings, respectively. Immunocompromised children or those with respiratory/cardiac disease comprised the largest subset of COVID-19 children with underlying medical conditions (152 of 233 individuals). Coinfections were observed in 5.6% of children and abnormal laboratory markers included serum D-dimer, procalcitonin, creatine kinase, and interleukin-6. Seven deaths were reported (0·09%) and 11 children (0·14%) met inclusion for multisystem inflammatory syndrome in children. INTERPRETATION: This review provides evidence that children diagnosed with COVID-19 have an overall excellent prognosis. Future longitudinal studies are needed to confirm our findings and better understand which patients are at increased risk for developing severe inflammation and multiorgan failure. FUNDING: Parker B. Francis and pilot grant from 2R25-HL126140. Funding agencies had no involvement in the study. url: https://api.elsevier.com/content/article/pii/S2589537020301772 doi: 10.1016/j.eclinm.2020.100433 id: cord-334162-j8m2zqbr author: Hoechter, D. J. title: Besonderheiten der kardiopulmonalen Reanimation zu Zeiten von SARS-CoV-2 date: 2020-07-15 words: 1385.0 sentences: 181.0 pages: flesch: 42.0 cache: ./cache/cord-334162-j8m2zqbr.txt txt: ./txt/cord-334162-j8m2zqbr.txt summary: Als Beispiel seien hier die Empfehlungen der Deutscher Gesellschaft für Anaesthesiologie und Intensivmedizin (DGAI) und des Berufsverbands Deutscher Anästhesisten (BDA) zu den Besonderheiten des Atemwegsmanagements bei Patienten mit vermuteter oder gesicherter COVID-19-Erkrankung und bei Patienten ohne Infektion während der Coronapandemie genannt [13] . Besteht bei dem Patienten ein begründeter oder bestätigter Verdacht auf COVID-19 sollen Laienhelfer, die über keine Schutzausrüstung verfügen, auf die Thoraxkompressionen verzichten und ggf. Dabei wird angenommen, dass es bei der Defibrillation wahrscheinlich zu keiner oder allenfalls zu einer kurzzeitigen und geringen Aerosolbildung kommt und die mittlerweile flächendeckende Nutzung von Klebepads den Anwender Distanz zum Patienten halten lässt. Bei innerklinischen Reanimationen von Patienten mit vermuteter oder bestätigter Infektion mit SARS-CoV-2 sollen folgende Besonderheiten hervorgehoben werden: Die Verwendung von Frühwarnsystemen (wie beispielsweise dem "early warning score") wird verstärkt empfohlen, um kritisch kranke Patienten frühzeitig zu erkennen und die Notwendigkeit zur Durchführung einer Reanimation möglichst zu vermeiden [5, 10] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32671430/ doi: 10.1007/s00101-020-00814-6 id: cord-350817-tmszrtju author: Hoepel, Willianne title: Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date: 2020-07-13 words: 5626.0 sentences: 296.0 pages: flesch: 47.0 cache: ./cache/cord-350817-tmszrtju.txt txt: ./txt/cord-350817-tmszrtju.txt summary: Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. Taken together, these data demonstrate that anti-Spike IgG immune complexes generated from serum of severely ill COVID-19 patients induce a strong pro-inflammatory response by (otherwise immunosuppressive) human M2 macrophages, which is characterized by high production of classical cytokine storm mediators such as IL-1β, IL-6, IL-8, and TNF. As shown in Figure 4A , the used human macrophage model highly expressed all FcγRs. To determine whether FcγRs are involved in activation by anti-Spike immune complexes, we blocked the different FcγRs with specific antibodies during stimulation, and analyzed cytokine production. In conclusion, our data show that anti-Spike IgG from serum of severely ill COVID-19 patients strongly amplifies pro-inflammatory responses by human macrophages, and can contribute to subsequent endothelial barrier disruption and thrombosis. abstract: For yet unknown reasons, severely ill COVID-19 patients often become critically ill around the time of activation of adaptive immunity. Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. The excessive inflammatory capacity of this anti-Spike IgG is related to glycosylation changes in the IgG Fc tail. Moreover, the hyper-inflammatory response induced by anti-Spike IgG can be specifically counteracted in vitro by use of the active component of fostamatinib, an FDA- and EMA-approved therapeutic small molecule inhibitor of Syk. One sentence summary Anti-Spike IgG promotes hyper-inflammation. url: https://doi.org/10.1101/2020.07.13.190140 doi: 10.1101/2020.07.13.190140 id: cord-300964-knc0ruou author: Hoffman, Tove title: Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 date: 2020-04-14 words: 2546.0 sentences: 139.0 pages: flesch: 54.0 cache: ./cache/cord-300964-knc0ruou.txt txt: ./txt/cord-300964-knc0ruou.txt summary: We evaluated a commercially available test developed for rapid (within 15 minutes) detection of SARS-CoV-2-specific IgM and IgG by 29 PCR-confirmed COVID-19 cases and 124 negative controls. In the present study, we evaluated a commercially available assay, the COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China), developed for detection of SARS-CoV-2-specific antibodies. None of the 24 healthy volunteers, without any known history of SARS-CoV-2 infection/COVID-19, tested positive for IgM or IgG. In this study we evaluated a commercial rapid test for detection of SARS-CoV-2-specific IgM and IgG. If this was the case for one or more of the included patients, the actual sensitivities should be higher, i.e. when evaluated only on samples known to contain detectable levels of SARS-CoV-2-specific IgM and/or IgG. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis abstract: COVID-19 is the most rapidly growing pandemic in modern time, and the need for serological testing is most urgent. Although the diagnostics of acute patients by RT-PCR is both efficient and specific, we are also crucially in need of serological tools for investigating antibody responses and assessing individual and potential herd immunity. We evaluated a commercially available test developed for rapid (within 15 minutes) detection of SARS-CoV-2-specific IgM and IgG by 29 PCR-confirmed COVID-19 cases and 124 negative controls. The results revealed a sensitivity of 69% and 93.1% for IgM and IgG, respectively, based solely on PCR-positivity due to the absence of a serological gold standard. The assay specificities were shown to be 100% for IgM and 99.2% for IgG. This indicates that the test is suitable for assessing previous virus exposure, although negative results may be unreliable during the first weeks after infection. More detailed studies on antibody responses during and post infection are urgently needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32363011/ doi: 10.1080/20008686.2020.1754538 id: cord-274852-84m62t4x author: Hogan, Catherine A. title: Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019 date: 2020-10-17 words: 1083.0 sentences: 62.0 pages: flesch: 46.0 cache: ./cache/cord-274852-84m62t4x.txt txt: ./txt/cord-274852-84m62t4x.txt summary: To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. The study period corresponded to the onset of the 2019-2020 respiratory virus season, during which the number of cases of influenza A, influenza B, and respiratory syncytial virus increased and the frequency To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. Our pooled screening strategy for investigating local community transmission of SARS-CoV-2 in the San Francisco Bay area of California during late 2019 during the onset of the respiratory virus season identified no COVID-19 cases. abstract: To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. We found no evidence of earlier infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32620178/ doi: 10.3201/eid2610.202296 id: cord-335077-ievtvhge author: Hogan, Catherine A. title: Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens date: 2020-07-23 words: 2217.0 sentences: 115.0 pages: flesch: 52.0 cache: ./cache/cord-335077-ievtvhge.txt txt: ./txt/cord-335077-ievtvhge.txt summary: The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. The aim of this study was to evaluate the test performance characteristics of the Accula SARS-CoV-2 test in a clinical setting against a high-complexity reference standard. The manufacturer''s instructions comprise the following steps: collection of NP swab, lysis of viral particles in SARS-CoV-2 buffer, transfer of nucleic acid solution to a test cassette that contains internal process positive and negative controls, reverse transcription of viral RNA to cDNA, nucleic acid amplification, and detection by lateral flow. We included 100 samples (50 positive, 50 negative) previously tested by the SHC-LDT and subsequently tested with the Accula SARS-CoV-2 POCT. In individuals with moderate to high pretest probability of SARS-CoV-2, reflex testing of negative samples on a separate EUA assay should be performed. abstract: Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. The aim of this study was to assess the test performance of the Accula SARS-CoV-2 test. The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen’s kappa coefficient. Overall percent agreement between the assays was 84.0% (95% confidence interval [CI], 75.3 to 90.6%), PPA was 68.0% (95% CI, 53.3 to 80.5%), and the kappa coefficient was 0.68 (95% CI, 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test and showed low viral load burden, with a median cycle threshold value of 37.7. NPA was 100% (95% CI, 94.2 to 100%). Compared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false-negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings and for confirmatory testing in individuals with moderate to high pretest probability of SARS-CoV-2 who test negative on Accula. url: https://www.ncbi.nlm.nih.gov/pubmed/32461285/ doi: 10.1128/jcm.01072-20 id: cord-270122-xijsj0d8 author: Hogan, Robert Edward title: COVID-19 in Patients With Seizures and Epilepsy: Interpretation of Relevant Knowledge of Presenting Signs and Symptoms date: 2020-08-24 words: 1636.0 sentences: 92.0 pages: flesch: 42.0 cache: ./cache/cord-270122-xijsj0d8.txt txt: ./txt/cord-270122-xijsj0d8.txt summary: Realizing the need for current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and clinical presentation of COVID-19, especially in relationship to patients with seizures and epilepsy. Overall, findings indicate seizures and epilepsy are rare, especially in mild COVID-19 cases, but may occur in more severe cases later in the disease course. Realizing both the need for and limitation of current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and COVID-19, especially in relationship to patients with seizures and epilepsy. 27 As compared to population-based studies of the initial clinical presentation of COVID-19, studies in patients with seizures and epilepsy are lacking. While a neuroinvasive mechanism of SARS-CoV-2 virus CNS infection remains a postulated cause of clinical neurological disease, 16 investigation of new-onset neurological impairments associated with COVID-19 found lack of evidence for direct acute insult of SARS-CoV-19 virus to the CNS. abstract: There are an increasing number of clinical studies for COVID-19, with several large cohort studies documenting initial signs and symptoms. Realizing the need for current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and clinical presentation of COVID-19, especially in relationship to patients with seizures and epilepsy. There is no evidence from cohort studies in the general population that seizures are worsened in COVID-19. However, relative lack of cohort studies in patients with a history of epileptic seizures limit conclusions about effects of COVID-19 patients with epilepsy. Overall, findings indicate seizures and epilepsy are rare, especially in mild COVID-19 cases, but may occur in more severe cases later in the disease course. Caregivers should be vigilant in assessing for possible seizures, especially in patients with systemic effects of severe COVID-19 infections. url: https://doi.org/10.1177/1535759720948549 doi: 10.1177/1535759720948549 id: cord-327431-dnppshnv author: Hognon, Cécilia title: Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date: 2020-05-27 words: 2460.0 sentences: 133.0 pages: flesch: 48.0 cache: ./cache/cord-327431-dnppshnv.txt txt: ./txt/cord-327431-dnppshnv.txt summary: In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. 28, 37 In this letter, we report an extended all-atom molecular dynamics (MD) study of the interactions produced between a dimeric SUD domain and a short RNA G4 sequence. To further examine the conformational space spanned by the G4/SUD complex, and in particular the role of the RNA in favoring the dimerization and the structure of the interface, we resorted to enhanced sampling MD simulations to obtain the 2D free energy profile along two relevant collective variables: first, the distance between G4 and SUD, and second, the separation between the two SUD subdomains. abstract: Coronaviruses may produce severe acute respiratory syndrome (SARS). As a matter of fact, a new SARS-type virus, SARS-CoV-2, is responsible of a global pandemic in 2020 with unprecedented sanitary and economic consequences for most countries. In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. Our results evidence two stable binding modes involving an interaction site spanning either the protein dimer interface or only one monomer. The free energy profile unequivocally points to the dimer mode as the thermodynamically favored one. The effect of these binding modes in stabilizing the protein dimer was also assessed, being related to its biological role in assisting SARS viruses to bypass the host protective response. This work also constitutes a first step of the possible rational design of efficient therapeutic agents aiming at perturbing the interaction between SARS Unique Domain and guanine quadruplexes, hence enhancing the host defenses against the virus. TOC GRAPHICS url: https://doi.org/10.1101/2020.04.07.029447 doi: 10.1101/2020.04.07.029447 id: cord-347818-93ixqyfp author: Hojyo, Shintaro title: How COVID-19 induces cytokine storm with high mortality date: 2020-10-01 words: 4508.0 sentences: 214.0 pages: flesch: 39.0 cache: ./cache/cord-347818-93ixqyfp.txt txt: ./txt/cord-347818-93ixqyfp.txt summary: Thus, IL-6 serves as a possible mechanism of treatment for severe COVID-19 patients, raising the possibility that one therapeutic option for the disease may be targeting excessive inflammation caused by IL-6 receptor (IL-6R) signaling with monoclonal antibody therapy or treatment with chemical modulators to block the signaling cascade while maintaining a sufficient antiviral primary immune response. IL-6-STAT3 signaling as a potential cause of the ARDS via cytokine storms in COVID-19 patients IL-6 amplifier, machinery for excessive inflammation SARS-CoV-2 infection induces the endocytosis of ACE2 together with SARS-CoV in target cells including epithelial cells and endothelial cells, resulting in an increase of serum angiotensin II (Ang II) levels due to the reduction of ACE2 surface expression (Fig. 1) [17, 48] . abstract: The newly emerging coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, but has rapidly spread all over the world. Some COVID-19 patients encounter a severe symptom of acute respiratory distress syndrome (ARDS) with high mortality. This high severity is dependent on a cytokine storm, most likely induced by the interleukin-6 (IL-6) amplifier, which is hyper-activation machinery that regulates the nuclear factor kappa B (NF-κB) pathway and stimulated by the simultaneous activation of IL-6-signal transducer and activator of transcription 3 (STAT3) and NF-κB signaling in non-immune cells including alveolar epithelial cells and endothelial cells. We hypothesize that IL-6-STAT3 signaling is a promising therapeutic target for the cytokine storm in COVID-19, because IL-6 is a major STAT3 stimulator, particularly during inflammation. We herein review the pathogenic mechanism and potential therapeutic targets of ARDS in COVID-19 patients. url: https://doi.org/10.1186/s41232-020-00146-3 doi: 10.1186/s41232-020-00146-3 id: cord-310291-z79x349o author: Holland, LaRinda A. title: An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) date: 2020-07-01 words: 1052.0 sentences: 67.0 pages: flesch: 52.0 cache: ./cache/cord-310291-z79x349o.txt txt: ./txt/cord-310291-z79x349o.txt summary: title: An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) Here, we report on early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sentinel surveillance in Tempe, Arizona. Genomic characterization identified an isolate encoding a 27-amino-acid in-frame deletion in accessory protein ORF7a, the ortholog of SARS-CoV immune antagonist ORF7a/X4. In anticipation of COVID-19 spreading in Arizona, we initiated a surveillance effort for the local emergence of SARS-CoV-2 starting 24 January 2020. To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we performed next-generation sequencing (NGS; Illumina NextSeq, 2ϫ76) directly on specimen RNA, thereby avoiding cell culture passage and potentially associated mutations. We found that the SARS-CoV-2 AZ-ASU2923 genome has an 81-nucleotide (nt) deletion in the ORF7a gene, resulting in a 27-amino-acid in-frame deletion (Fig. 2B) . Severe acute respiratory syndrome coronavirus gene 7 products contribute to virus-induced apoptosis abstract: On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona (3rd case in the US) (1).…. url: https://doi.org/10.1128/jvi.00711-20 doi: 10.1128/jvi.00711-20 id: cord-273918-knlc3bxh author: Holmes, Emily A title: Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science date: 2020-04-15 words: 10279.0 sentences: 452.0 pages: flesch: 35.0 cache: ./cache/cord-273918-knlc3bxh.txt txt: ./txt/cord-273918-knlc3bxh.txt summary: 1,2 Furthermore, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, might infect the brain or trigger immune responses that have additional adverse effects on brain function and mental health in patients with Research funders and researchers must deploy resources to understand the psychological, social, and neuroscientific effects of the COVID-19 pandemic. We use the term mental health sciences to reflect the many different disciplines, including, but not limited to, psychology, psychiatry, clinical medicine, behavioural and social sciences, and neuroscience, that will need to work together in a multidisciplinary fashion together with people with lived experience of mental health issues or COVID-19 to address these research priorities. abstract: The coronavirus disease 2019 (COVID-19) pandemic is having a profound effect on all aspects of society, including mental health and physical health. We explore the psychological, social, and neuroscientific effects of COVID-19 and set out the immediate priorities and longer-term strategies for mental health science research. These priorities were informed by surveys of the public and an expert panel convened by the UK Academy of Medical Sciences and the mental health research charity, MQ: Transforming Mental Health, in the first weeks of the pandemic in the UK in March, 2020. We urge UK research funding agencies to work with researchers, people with lived experience, and others to establish a high level coordination group to ensure that these research priorities are addressed, and to allow new ones to be identified over time. The need to maintain high-quality research standards is imperative. International collaboration and a global perspective will be beneficial. An immediate priority is collecting high-quality data on the mental health effects of the COVID-19 pandemic across the whole population and vulnerable groups, and on brain function, cognition, and mental health of patients with COVID-19. There is an urgent need for research to address how mental health consequences for vulnerable groups can be mitigated under pandemic conditions, and on the impact of repeated media consumption and health messaging around COVID-19. Discovery, evaluation, and refinement of mechanistically driven interventions to address the psychological, social, and neuroscientific aspects of the pandemic are required. Rising to this challenge will require integration across disciplines and sectors, and should be done together with people with lived experience. New funding will be required to meet these priorities, and it can be efficiently leveraged by the UK's world-leading infrastructure. This Position Paper provides a strategy that may be both adapted for, and integrated with, research efforts in other countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32304649/ doi: 10.1016/s2215-0366(20)30168-1 id: cord-312340-hpuoren5 author: Holstein, Sarah A. title: Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button date: 2020-06-02 words: 1964.0 sentences: 91.0 pages: flesch: 40.0 cache: ./cache/cord-312340-hpuoren5.txt txt: ./txt/cord-312340-hpuoren5.txt summary: Given the expected duration of the pandemic, it is imperative that treatment of the patient''s cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Given the expected duration of the pandemic, it is imperative that treatment of the patient''s cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Despite the barriers that lead to this low rate of participation, clinical trials remain the cornerstone for improving oncology patient outcomes through the development of new therapies. To this end, there are many groups, including ASCO and the American Society of Hematology, that have created registries in order to collect data on outcomes of oncology patients infected with SARS-CoV-2. It is imperative that comprehensive immune profiling studies be performed to evaluate the immune responses in these patient populations and that oncology patients be included in COVID-19 clinical trials. abstract: The COVID‐19 pandemic has far‐reaching ramifications for patients undergoing cancer treatment. Oncologists and institutions have adjusted treatment practices and, in many cases, significantly curtailed clinical trial conduct. Whether these adjustments mitigate the risk of COVID‐19 complications without jeopardizing treatment of the cancer is unknown. Given the expected duration of the pandemic, it is imperative that treatment of the patient's cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. url: https://doi.org/10.1002/cpt.1920 doi: 10.1002/cpt.1920 id: cord-344901-mgnaprgt author: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 words: 112.0 sentences: 18.0 pages: flesch: 67.0 cache: ./cache/cord-344901-mgnaprgt.txt txt: ./txt/cord-344901-mgnaprgt.txt summary: key: cord-344901-mgnaprgt authors: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 journal: Ophthalmologe DOI: 10.1007/s00347-020-01097-3 sha: doc_id: 344901 cord_uid: mgnaprgt nan Der Augenarzt, Dr. Li Wenliang, war in China einer der ersten, der auf eine "SARS-ähnliche" Epidemie hinwies. Er selbst hat sich an einem asymptomatischen Glaukom-Patienten infiziert und ist an Komplikationen der Erkrankung verstorben [3] . Insbesondere Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection The China Medical Treatment Expert Group for Covid-19, Guan W et al (2020) Clinical characteristics of Coronavirus disease 2019 in China Chinese doctor, silenced after warning of outbreak, dies from Coronavirus abstract: nan url: https://doi.org/10.1007/s00347-020-01097-3 doi: 10.1007/s00347-020-01097-3 id: cord-290068-s1gdbsfx author: Hon, KLE title: Clinical presentations and outcome of severe acute respiratory syndrome in children date: 2003-05-17 words: 1900.0 sentences: 117.0 pages: flesch: 55.0 cache: ./cache/cord-290068-s1gdbsfx.txt txt: ./txt/cord-290068-s1gdbsfx.txt summary: title: Clinical presentations and outcome of severe acute respiratory syndrome in children In addition, we treated patients who had moderate symptoms of high fluctuating fever and notable malaise with intravenous ribavirin (20 mg/kg daily, given in three doses) and hydrocortisone (2 mg/kg every 6 h) immediately after admission. Lymphopenia (0·3-3·0ϫ10 9 /L) was reported in all patients, but the teenagers were generally more severely affected than the younger children. 2, 3 Ribavirin is a broad-spectrum antiviral agent and has been used for treatment of severe respiratory syncytial virus infection in We noted two distinct patterns of clinical presentation among the children we studied. On this basis, we did an open-label study in which oral gabapentin 300 mg thrice daily was given for every other chemotherapy treatment in nine patients with breast cancer. The patient reported severe nausea after the first two chemotherapy treatments. abstract: Hong Kong has been severely affected by severe acute respiratory syndrome (SARS). Contact in households and healthcare settings is thought to be important for transmission, putting children at particular risk. Most data so far, however, have been for adults. We prospectively followed up the first ten children with SARS managed during the early phase of the epidemic in Hong Kong. All the children had been in close contact with infected adults. Persistent fever, cough, progressive radiographic changes of chest and lymphopenia were noted in all patients. The children were treated with high-dose ribavirin, oral prednisolone, or intravenous methylprednisolone, with no short-term adverse effects. Four teenagers required oxygen therapy and two needed assisted ventilation. None of the younger children required oxygen supplementation. Compared with adults and teenagers, SARS seems to have a less aggressive clinical course in younger children. url: https://www.sciencedirect.com/science/article/pii/S0140673603133648 doi: 10.1016/s0140-6736(03)13364-8 id: cord-289282-4oz6r7op author: Hon, Kam Lun title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date: 2020-06-01 words: 3558.0 sentences: 269.0 pages: flesch: 58.0 cache: ./cache/cord-289282-4oz6r7op.txt txt: ./txt/cord-289282-4oz6r7op.txt summary: title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS abstract: Many respiratory viral infections such as influenza and measles result in severe acute respiratory symptoms and epidemics. In the spring of 2003, an epidemic of coronavirus pneumonia spread from Guangzhou to Hong Kong and subsequently to the rest of the world. The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. In the summer of 2012, epidemic of pneumonia occurred again in Saudi Arabia which was subsequently found to be caused by another novel coronavirus. WHO coined the term MERS (Middle East respiratory syndrome) to denote the Middle East origin of the novel virus (MERS‐CoV). In the winter of 2019, another outbreak of pneumonia occurred in Wuhan, China which rapidly spread globally. Yet another novel coronavirus was identified as the culprit and has been named SARS‐CoV‐2 due to its similarities with SARS‐CoV, and the disease as coronavirus disease‐2019. This overview aims to compare and contrast the similarities and differences of these three major episodes of coronavirus outbreak, and conclude that they are essentially the same viral respiratory syndromes caused by similar strains of coronavirus with different names. Coronaviruses have caused major epidemics and outbreaks worldwide in the last two decades. From an epidemiological perspective, they are remarkably similar in the mode of spread by droplets. Special focus is placed on the pediatric aspects, which carry less morbidity and mortality in all three entities. url: https://doi.org/10.1002/ppul.24810 doi: 10.1002/ppul.24810 id: cord-326864-i1r3bv4p author: Hon, Kam Lun title: Coronavirus disease 2019 (COVID-19): latest developments in potential treatments date: 2020-06-29 words: 6265.0 sentences: 370.0 pages: flesch: 46.0 cache: ./cache/cord-326864-i1r3bv4p.txt txt: ./txt/cord-326864-i1r3bv4p.txt summary: 4 COVID-19 is a respiratory tract infection that causes mild symptoms in the majority of cases, but can also lead to ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 : latest developments in potential treatments drugsincontext.com mortality and morbidity. SARS-CoV is closely related to civet and bat CoVs, but it is phylogenetically divergent from other coronaviruses associated with human infections, including ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com OC43, NL63, 229E, and HKU1. In a clinical trial involving 199 patients with laboratory-confirmed SARS-CoV-2 infection, lopinavir-ritonavir treatment was not associated with any clinical improvements compared with standard care. 25 Long and colleagues reported that corticosteroid therapy using methylprednisolone, dexamethasone, and hydrocortisone was beneficial in treating ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com SARS-CoV patients, 78 and significantly prolonged survival time in clinical cases. abstract: Many viral respiratory infections can cause severe acute respiratory symptoms leading to mortality and morbidity. In the spring of 2003, the severe acute respiratory syndrome (SARS) outbreak caused by SARS-CoV spread globally. In the summer of 2012, the Middle East respiratory syndrome (MERS) outbreak caused by MERS-CoV occurred in Saudi Arabia. In the winter of 2019, the coronavirus disease 2019 (COVID-19) outbreak caused by a novel coronavirus SARS-CoV-2 occurred in China which rapidly spread worldwide causing a global pandemic. Up until 27 May 2020, there are 5.5 million confirmed cases of COVID-19 and 347,587 COVID-19 related deaths worldwide, and there has also been an unprecedented increase in socioeconomic and psychosocial issues related to COVID-19. This overview aims to review the current developments in preventive treatments and therapies for COVID-19. The development of vaccines for SARS-CoV-2 is ongoing and various clinical trials are currently underway around the world. It is hoped that existing antivirals including remdesivir and lopinavir-ritonavir might have roles in the treatment of COVID-19, but results from trials thus far have not been promising. COVID-19 causes a mild respiratory disease in the majority of cases, but in some cases, cytokine activation causes sepsis and acute respiratory distress syndrome, leading to morbidity and mortality. Immunomodulatory treatments and biologics are also being actively explored as therapeutics for COVID-19. On the other hand, the use of steroidal and nonsteroidal anti-inflammatory drugs (NSAIDs) has been discouraged based on concerns about their adverse effects. Over the past two decades, coronaviruses have caused major epidemics and outbreaks worldwide, whilst modern medicine has been playing catch-up all along. url: https://www.ncbi.nlm.nih.gov/pubmed/32655654/ doi: 10.7573/dic.2020-4-15 id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 words: 3616.0 sentences: 192.0 pages: flesch: 51.0 cache: ./cache/cord-287228-0qm939ve.txt txt: ./txt/cord-287228-0qm939ve.txt summary: In one study including 70 patients with COVID-19, 21% clinically recovered patients with two consecutive negative results of nucleic acid detection experienced a later positive testing for SARS-CoV-2, and the longest duration of viral RNA positivity in this study was 45 days following infection [4] . A total of 2860 COVID-19 patients were hospitalized and followed in this hospital since the epidemic, and those with persistent or intermittent viral RNA positivity in respiratory samples (including the nasopharyngeal, oropharyngeal and sputum samples) for at least 4 weeks were included in our study, regardless of the age and their clinical status. However, in most of these studies, PCR testing was used as a marker to indicate the existence of virus, and patients with positive viral RNA was considered infectious though they have been infected for months without further clinical symptoms. abstract: Prolonged presence of viral nucleic acid was reported in certain patients with coronavirus disease 2019 (COVID-19), with unclear clinical and epidemiological significance. We here described the clinical and epidemiological characteristics of 37 recovered COVID-19 patients with prolonged presence of viral RNA in Wuhan, China. For those who had been discharged and re-admitted, their close contacts outside the hospital were traced and evaluated. The median age of the 37 patients was 62 years (IQR 50, 68), and 24 (64.9%) were men. They had common or severe COVID-19. With prolonged positive RT-PCR, most patients were clinically stable, 29 (78.4%) denied any symptoms. A total of 431 PCR tests were carried out, with each patient at a median of 8 time points. The median time of PCR positivity to April 18 was 78 days (IQR 67.7, 84.5), and the longest 120 days. 22 of 37 patients had been discharged at a median of 44 days (IQR 22.3, 50) from disease onset, and 9 had lived with their families without personal protections for a total of 258 person-days and no secondary infection was identified through epidemiological investigation, nucleic acid and antibody screening. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT–PCR. Those patients who have clinically recovered and whose disease course has exceeded four weeks were associated with very limited infectiousness. Reconsideration of disease control in such patients is needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32981485/ doi: 10.1080/22221751.2020.1827983 id: cord-333863-mtljy3s6 author: Hong, Nan title: Evaluation of ocular symptoms and tropism of SARS‐CoV‐2 in patients confirmed with COVID‐19 date: 2020-04-26 words: 4033.0 sentences: 232.0 pages: flesch: 53.0 cache: ./cache/cord-333863-mtljy3s6.txt txt: ./txt/cord-333863-mtljy3s6.txt summary: Patients with COVID-19 may show prodromal symptom of conjunctivitis in cases where eye goggles were not worn while in close proximity with COVID-19 positive patients, leading to suggestions that ocular exposure might be a potential route of SARS-CoV-2 infection (Lu et al. Previously hospitalized patients (admission date from 19 January to 29 February 2020) in the isolation ward of the First Affiliated Hospital of Zhejiang University, diagnosed as COVID-19 positive based on their clinical symptoms and positive SARS-CoV-2 test results of their sputum swab specimens, were the target subject population. After the onset of COVID-19, the mean scores of the SEEQ and OSDI questionnaires were significantly raised, suggesting a degraded ocular surface condition (Table 2) . In our study, fifteen subjects (27%) reported new onset ocular irritation symptoms or aggravated pre-existing ocular surface irritation symptoms after infection of SARS-CoV-2. abstract: PURPOSE: The SARS‐CoV‐2 RNA has been detected in tears and conjunctival samples from infected individuals. Conjunctivitis is also reported in a small number of cases. We evaluated ocular symptoms and ocular tropism of SARS‐CoV‐2 in a group of patients with COVID‐19. METHOD: Fifty‐six patients infected with SARS‐CoV‐2 were recruited as subjects. Relevant medical histories were obtained from the electronic medical record system. Ocular history and ocular symptoms data were obtained by communicating directly with the subjects. The Ocular Surface Disease Index (OSDI) and Salisbury Eye Evaluation Questionnaire (SEEQ) were used to assess the anterior ocular surface condition before and after the onset of disease. RESULTS: Patients classified as severe COVID‐19 cases were more likely to have hypertension compared to mild cases (p = 0.035). Of the 56 subjects, thirteen patients (23%) were infected in Wuhan, 32 patients (57%) were community‐infected, 10 patients (18%) were unknown origin, 1 (2%) was a physician likely infected by a confirmed patient. Three patients wore face mask with precaution when contacting the confirmed patients. Fifteen (27%) had aggravated ocular symptoms, of which 6 (11%) had prodromal ocular symptoms before disease onset. The differences in mean scores of OSDI questionnaire and SEEQ between before and after onset of COVID‐19 were all significant (p < 0.05 for both). CONCLUSIONS: Ocular symptoms are relatively common in COVID‐19 disease and may appear just before the onset of respiratory symptoms. Our data provided the anecdotal evidences of transmission of SARS‐CoV‐2 via ocular surface. url: https://www.ncbi.nlm.nih.gov/pubmed/32336042/ doi: 10.1111/aos.14445 id: cord-269522-38dhwggn author: Hong, Xia title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() date: 2009-08-27 words: 4269.0 sentences: 243.0 pages: flesch: 56.0 cache: ./cache/cord-269522-38dhwggn.txt txt: ./txt/cord-269522-38dhwggn.txt summary: title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() OBJECTIVE: To measure the incidence and impact of posttraumatic stress disorder (PTSD) in a cohort of 70 subjects with severe acute respiratory syndrome (SARS). To study the impact of PTSD, we used the Impact of Event Scale (IES), Zung Self-Rating Anxiety Scale (SAS), Zung Self-Rating Depression Scale (SDS), Symptom Checklist 90 (SCL-90), Short Form-36 (SF-36 Health Survey) and Social Disability Screening Schedule (SDSS). In one study of 63 survivors of SARS at 3 months postdischarge from hospital in Singapore, the rate of possible PTSD, inferred from an Impact of Event Scale (IES) Score of N26, was 41.7% [15] . In a study of 195 survivors of SARS at 1 month postdischarge from hospital in Hong Kong, 10% to 18% of them reported symptoms related to PTSD [16] . abstract: OBJECTIVE: To measure the incidence and impact of posttraumatic stress disorder (PTSD) in a cohort of 70 subjects with severe acute respiratory syndrome (SARS). METHODS: Clinical assessments of PTSD were conducted at 2, 7, 10, 20 and 46 months after discharge from medical hospitalization for treatment of SARS. Diagnoses of PTSD were established by a trained psychiatrist using the Chinese Classification of Mental Disorders (CCMD-III) and Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) criteria. To study the impact of PTSD, we used the Impact of Event Scale (IES), Zung Self-Rating Anxiety Scale (SAS), Zung Self-Rating Depression Scale (SDS), Symptom Checklist 90 (SCL-90), Short Form-36 (SF-36 Health Survey) and Social Disability Screening Schedule (SDSS). RESULTS: Of the 68 subjects who finished at least two follow-up interviews, 30 developed PTSD over the study period (44.1%). Scores on IES, SAS, SDS and SCL-90 (P<.0001) were higher, and functional impairment as measured by SF-36 (P<.0001) and SDSS was more severe (P=.0073) for subjects with PTSD. CONCLUSION: PTSD occurs in a significant percentage of subjects who recover from SARS, and the occurrence of PTSD predicts persistent psychological distress and diminished social functioning in the 4 years after SARS treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/19892213/ doi: 10.1016/j.genhosppsych.2009.06.008 id: cord-330597-nftwj0d5 author: Hopfer, Helmut title: Hunting coronavirus by transmission electron microscopy – a guide to SARS‐CoV‐2‐associated ultrastructural pathology in COVID‐19 tissues date: 2020-09-27 words: 4636.0 sentences: 328.0 pages: flesch: 48.0 cache: ./cache/cord-330597-nftwj0d5.txt txt: ./txt/cord-330597-nftwj0d5.txt summary: Using micrographs from infected cell cultures and autopsy tissues, we show how coronavirus replication affects ultrastructure and put the morphological findings in the context of viral replication, which induces extensive remodelling of the intracellular membrane systems. To better understand the ultrastructural morphology of SARS-CoV-2 infection and COVID-19, we will first briefly discuss the pathogenesis of COVID-19 and coronavirus replication in general and then examine the TEM findings in more detail. All rights reserved Coronaviruses including SARS-CoV-2 and the morphological changes associated with replication can be visualised by TEM in infected cell lines (figure 3A-G) [81] [82] [83] [84] [85] 87, 88] or organoids [96, 97] . Based on the cell culture findings outlined above, we expect to find the same SARS-CoV-2 morphology and distribution in vesicles of autopsy and biopsy tissues of COVID-19 patients. abstract: Transmission electron microscopy has become a valuable tool to investigate tissues of COVID‐19 patients because it allows visualisation of SARS‐CoV‐2, but the “virus‐like particles” described in several organs have been highly contested. Because most electron microscopists in pathology are not accustomed to analysing viral particles and subcellular structures, our review aims to discuss the ultrastructural changes associated with SARS‐CoV‐2 infection and COVID‐19 with respect to pathology, virology, and electron microscopy. Using micrographs from infected cell cultures and autopsy tissues, we show how coronavirus replication affects ultrastructure and put the morphological findings in the context of viral replication, which induces extensive remodelling of the intracellular membrane systems. Virions assemble by budding into the endoplasmic reticulum‐Golgi intermediate complex and are characterized by electron dense dots of cross‐sections of the nucleocapsid inside the viral particles. Physiological mimickers such as multivesicular bodies or coated vesicles serve as perfect decoys. Compared to other in‐situ techniques, transmission electron microscopy is the only method to visualize assembled virions in tissues and will be required to prove SARS‐CoV‐2 replication outside the respiratory tract. In practice, documenting in tissues the characteristic features seen in infected cell cultures, seems to be much more difficult than anticipated. In our view, the hunt for coronavirus by transmission electron microscopy is still on. url: https://doi.org/10.1111/his.14264 doi: 10.1111/his.14264 id: cord-264919-0jlg2gkc author: Hopp, Marie-Thérèse title: Unravelling the debate on heme effects in COVID-19 infections date: 2020-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-CoV-2 outbreak was recently declared a worldwide pandemic. Infection triggers the respiratory tract disease COVID-19, which is accompanied by serious changes of clinical biomarkers such as hemoglobin and interleukins. The same parameters are altered during hemolysis, which is characterized by an increase in labile heme. We present two approaches that aim at analyzing a potential link between available heme and COVID-19 pathogenesis. Four COVID-19 related proteins, i.e. the host cell proteins ACE2 and TMPRSS2 as well as the viral protein 7a and S protein, were identified as potential heme binders. We also performed a detailed analysis of the common pathways induced by heme and SARS-CoV-2 by superimposition of knowledge graphs covering heme biology and COVID-19 pathophysiology. Herein, focus was laid on inflammatory pathways, and distinct biomarkers as the linking elements. Finally, the results substantially improve our understanding of COVID-19 infections and disease progression of patients with different clinical backgrounds and expand the diagnostic and treatment options. url: https://doi.org/10.1101/2020.06.09.142125 doi: 10.1101/2020.06.09.142125 id: cord-274591-p34kk4up author: Horby, Peter W, title: Prospects for Emerging Infections in East and Southeast Asia 10 Years after Severe Acute Respiratory Syndrome date: 2013-06-17 words: 4265.0 sentences: 156.0 pages: flesch: 36.0 cache: ./cache/cord-274591-p34kk4up.txt txt: ./txt/cord-274591-p34kk4up.txt summary: The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The SARS epidemic provided a dramatic demonstration of the weaknesses in national and global capacities to detect and respond to emerging infectious diseases, and it was in many ways a watershed event that had a transformative effect on many of the clinical, public health, and other professionals involved. Surveillance and response capacities have improved in the last decade, and East and Southeast Asia are far better prepared to detect and respond to emerging infectious diseases. abstract: It is 10 years since severe acute respiratory syndrome (SARS) emerged, and East and Southeast Asia retain a reputation as a hot spot of emerging infectious diseases. The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The region is now better able to detect and respond to emerging infectious diseases than it was a decade ago, but the tools and methods to produce sufficiently refined assessments of the risks of disease emergence are still lacking. Given the continued scale and pace of change in East and Southeast Asia, it is vital that capabilities for predicting, identifying, and controlling biologic threats do not stagnate as the memory of SARS fades. url: https://doi.org/10.3201/eid1906.121783 doi: 10.3201/eid1906.121783 id: cord-320627-7vi6skvh author: Horejsh, Douglas title: A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry date: 2005-01-19 words: 3725.0 sentences: 172.0 pages: flesch: 48.0 cache: ./cache/cord-320627-7vi6skvh.txt txt: ./txt/cord-320627-7vi6skvh.txt summary: We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. In this report, we describe the construction of molecular beacon-conjugated beads that we have called ''BeadCons'', whose specific hybridization with complementary target sequences can be resolved by flow cytometry (see Figure 1 ). In the multiplex detection experiment, the test sample contained 0.5 ml of the positive oligo DNA (100 mM stock) diluted in 9.5 ml of a complex mixture of oligonucleotides (equimolar levels of 10 mM each, equalling a 100 mM total concentration; sequences listed in Supplementary Table 1 ). abstract: Molecular beacons are dual-labelled probes that are typically used in real-time PCR assays, but have also been conjugated with solid matrices for use in microarrays or biosensors. We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. For this array system, molecular beacons were conjugated with microspheres using a biotin-streptavidin linkage. A bridged conjugation method using streptavidin increased the signal-to-noise ratio, allowing for further discrimination of target quantitation. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. Considering that routine flow cytometers are able to detect up to four fluorescent channels, this novel assay may allow for the specific multiplex detection of a nucleic acid panel in a single tube. url: https://www.ncbi.nlm.nih.gov/pubmed/15659574/ doi: 10.1093/nar/gni015 id: cord-328409-px92ff89 author: Hornuss, Daniel title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 words: 1575.0 sentences: 172.0 pages: flesch: 42.0 cache: ./cache/cord-328409-px92ff89.txt txt: ./txt/cord-328409-px92ff89.txt summary: After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Als Diagnostik der Wahl zur schnellen Identifikation von COVID-19-Fällen hat sich dabei die PCR-Analyse auf SARS-CoV-2 aus tiefen nasopharyngealen oder oropharyngealen Abstrichen etabliert [3] . abstract: Patient history and clinical findings A 46-year old construction worker presented at the emergency department with two orthostatic syncopes. The patient complained of prolonged fever and coughs for 7 days which had not improved after oral treatment with sultamicillin for 5 days, prescribed by the patient’s general practitioner. Physical examination showed high blood pressure due to previously known hypertension. Other vital signs without pathological findings. Pulmonary auscultation showed basal soft crackling noises of the left lung Findings and Diagnosis Laboratory examination showed increased values for LDH, pro-BNP and CRP and normal values for leucocytes and procalcitonin. Conventional X-Ray of the chest showed bipulmonal lateral atypical infiltrates. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. Again, SARS-CoV-2-RNA was not detected. A CT-scan of the chest showed bipulmonal lateral ground-glass attenuation, again typical for COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Therapy and Course of events The patient was admitted for evaluation of syncopes and suspect of COVID-19 associated pneumonia. The patient was prophylactically isolated while the result of SARS-CoV-2-PCR from a deep oral swab was pending. Suspecting a possible secondary bacterial infection at the beginning, intravenous antibiotic treatment with ampicillin/sulbactam was initiated. While further examinations showed no indication for bacterial infection, antibiotics were discontinued after 3 days. Due to clinical recovery antiviral therapy was not performed after confirming the diagnosis. The patient was discharged 17 days after onset of first symptoms without any requirements for further isolation. Conclusion This casuistic describes a case of COVID-19 associated pneumonia presenting with typical clinical features, laboratory and radiological findings. Detection of viral RNA was not successful from deep oral swab-samples despite repeated attempts. Finally, PCR-analysis of sputum confirmed the diagnosis. Analysis of deeper airway samples (sputum, bronchoalveolar lavage, tracheal secretions) or stool for SARS-CoV-2 should be performed in cases of evident clinical suspicion of COVID-19 and negative PCR results from deep oral swabs. url: https://doi.org/10.1055/a-1170-6061 doi: 10.1055/a-1170-6061 id: cord-333465-cha7ndv5 author: Horspool, A. M. title: Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date: 2020-08-31 words: 4309.0 sentences: 286.0 pages: flesch: 52.0 cache: ./cache/cord-333465-cha7ndv5.txt txt: ./txt/cord-333465-cha7ndv5.txt summary: Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations. We evaluated anti-193 SARS-CoV-2 antibody production to 3 antigens (RBD, N, and S1) in 82 in-patients 194 Table 1 ) by developing a novel rapid-ELISA technique. Our survey of SARS-CoV-2 positive patients demonstrated that antibody (IgG) 198 production to RBD, N, and S1 proteins developed over the first 10 to 20 days post-199 symptom onset (Figure 1a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. To accurately assess 223 differences in antibody production independently of disease outcome, we quantified anti-224 SARS-CoV-2 IgG production in patients who survived infection grouped by biological sex, 225 . . https://doi.org/10.1101/2020.08.24.20180877 doi: medRxiv preprint significantly increased in patients that did not survive SARS-CoV-2 infection compared to 272 those that did (Figure 4d ). abstract: The SARS-CoV-2 pandemic is continuing to impact the global population. This study was designed to assess the interplay of antibodies with the systemic cytokine response in SARS-CoV-2 patients. We demonstrate that significant anti-SARS-CoV-2 antibody production to Receptor Binding Domain (RBD), Nucleocapsid (N), and Spike S1 subunit (S1) of SARS-CoV-2 develops over the first 10 to 20 days of infection. The majority of patients produced antibodies against all three antigens (219/255 SARS-CoV-2 positive patient specimens, 86%) suggesting a broad response to viral proteins. Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations. To better understand the systemic immune response, we analyzed the production of 20 cytokines by SARS-CoV-2 patients over the course of infection. Cytokine analysis of SARS-CoV-2 positive patients exhibited increases in proinflammatory markers (IL-6, IL-8, IL-18) and chemotactic markers (IP-10, SDF-1, MIP-1{beta}, MCP-1, and eotaxin) relative to healthy individuals. Patients who succumbed to infection produced decreased IL-2, IL-4, IL-12, IL-13, RANTES, TNF-, GRO-, and MIP-1 relative to patients who survived infection. We also observed that the chemokine CXCL13 was particularly elevated in patients that succumbed to infection. CXCL13 is involved in B cell activation, germinal center development, and antibody maturation, and we observed that CXCL13 levels in blood trended with anti-SARS-CoV-2 antibody production. Furthermore, patients that succumbed to infection produced high CXCL13 and also tended to have high ratio of nucleocapsid to RBD antibodies. This study provides insights into SARS-CoV-2 immunity implicating the magnitude and specificity of response in relation to patient outcomes. url: https://doi.org/10.1101/2020.08.24.20180877 doi: 10.1101/2020.08.24.20180877 id: cord-292209-d1ty9etr author: Horta, Bernardo L title: Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date: 2020-10-29 words: 4330.0 sentences: 247.0 pages: flesch: 53.0 cache: ./cache/cord-292209-d1ty9etr.txt txt: ./txt/cord-292209-d1ty9etr.txt summary: Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. The present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in 133 sentinel cities throughout Brazil, as part of the EPICOVID-19 study (www.epicovid19brasil.org). In summary, the analyses of the three waves of national serological surveys in Brazil showed important inequalities in the prevalence of antibodies against SARS-CoV-2 according to family wealth, education and ethnic groups. Yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against SARS-CoV-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. abstract: OBJECTIVES. To investigate socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in the 27 federative units of Brazil. METHODS. In this cross-sectional study, three household surveys were carried out on May 14-21, June 4-7, and June 21-24, 2020 in 133 Brazilian urban areas. Multi-stage sampling was used to select 250 individuals in each city to undergo a rapid antibody test. Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. Principal component analyses of assets was used to classify socioeconomic position into five wealth quintiles. Poisson regression was used for the analyses. RESULTS. 25 025 subjects were tested in the first, 31 165 in the second, and 33 207 in the third wave of the survey, with prevalence of positive results equal to 1.4%, 2.4%, and 2.9% respectively. Individuals in the poorest quintile were 2.16 times (95% confidence interval 1.86; 2.51) more likely to test positive than those in the wealthiest quintile, and those with 12 or more years of schooling had lower prevalence than subjects with less education. Indigenous individuals had 4.71 (3.65; 6.08) times higher prevalence than whites, as did those with black or brown skin color. Adjustment for region of the country reduced the prevalence ratios according to wealth, education and ethnicity, but results remained statistically significant. CONCLUSIONS. The prevalence of antibodies against SARS-CoV-2 in Brazil shows steep class and ethnic gradients, with lowest risks among white, educated and wealthy individuals. url: https://doi.org/10.26633/rpsp.2020.135 doi: 10.26633/rpsp.2020.135 id: cord-331617-1ytcd0ax author: Horvath, Karl title: Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date: 2020-05-15 words: 2635.0 sentences: 331.0 pages: flesch: 55.0 cache: ./cache/cord-331617-1ytcd0ax.txt txt: ./txt/cord-331617-1ytcd0ax.txt summary: Da weitgehend alle zur Diagnose eingesetzten Tests nicht vollständig fehlerfrei funktionieren, ist auch bei der Testung auf Vorliegen von SARS-CoV-2 spezifischen AK damit zu rechnen, dass es einen Anteil von Personen gibt, der vom Test falsch klassifiziert wird. Wie groß dieser jeweilig falsch klassifizierte Anteil an allen getesteten Personen ist, d.h. wie sicher ein positives oder negatives Testresultat ist, ist abhängig von der Sensitivität und Spezifität des jeweiligen Tests sowie von der gegebenen Vortestwahrscheinlichkeit. Mit anderen Worten beschreibt die Vortestwahrscheinlichkeit das Risiko, dass bei einer bisher ungetesteten Person eine SARS-CoV-2 Infektion vorliegt bzw. Zu bedenken ist auch, dass sich die Prävalenz einer SARS-CoV-2 Infektion und damit die Vortestwahrscheinlichkeit mit Fortschreiten der Pandemie ändern wird. Auch bei nahezu idealen Testeigenschaften sind bei geringer Vortestwahrscheinlichkeit (wie sie bei der Testung von Personen ohne Symptome und Risikofaktoren für eine SARS-CoV-2 Infektion besteht) positive Testresultate häufig falsch. abstract: INTRODUCTION: In the context of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the detection of virus-specific antibodies (AB) will play an increasing role. The presence or absence of such antibodies can potentially lead to considerations regarding immunity and infection. ISSUE: How reliable are inferences from positive or negative test results regarding the actual presence of SARS-CoV-2 specific antibodies? METHODS: Calculation of the probability that, depending on the pretest probability (prevalence of SARS-CoV-2 infection) and test properties, antibodies are present or absent in the case of positive or negative test results. RESULTS: Sensitivity and specificity of different SARS-CoV-2 AB test systems vary between 53 % and 94 % and between 91 % and 99.5 %, respectively. When using a test with high test quality, the positive predictive value (PPV) is 42 % and 7 9%, respectively, with a pre-test probability of 1 % to 5 %, as can currently be assumed for the general population in Austria or Germany. For persons with an increased pre-test probability of 20 %, e. g. persons from high-risk professions, the PPW is 95 %, with a pre-test probability of 80 % the PPW is almost 100 %. The negative predictive value (NPV) is at least 99.7 % for persons with a low pre-test probability of up to 5 % and 79.1 % for persons with a pre-test probability of 80 %. When using test systems with lower sensitivity and specificity, the reliability of the results decreases considerably. The PPV is 5.9 % with a pre-test probability of 1 %. CONCLUSIONS: A sufficiently high sensitivity and specificity are prerequisites for the application of antibody test systems. Positive test results are often false if the pre-test probability is low. Depending on the assumed prevalence of a SARS-CoV-2 infection, there are substantial differences in the significance of a concrete test result for the respective affected persons. url: https://doi.org/10.1016/j.zefq.2020.05.005 doi: 10.1016/j.zefq.2020.05.005 id: cord-297775-ug4ovsws author: Hosie, Margaret J title: Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date: 2020-09-23 words: 1997.0 sentences: 118.0 pages: flesch: 54.0 cache: ./cache/cord-297775-ug4ovsws.txt txt: ./txt/cord-297775-ug4ovsws.txt summary: High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. Recent reports from Dutch mink farms of both mink-to-cat and mink-tohuman transmission of the virus provide support for this scenario (5, 9) We used a range of laboratory techniques to show that two domestic cats from households with suspected cases of COVID-19, and which displayed either mild or severe respiratory disease, were infected with SARS-CoV-2. As we do not have the owner''s virus sequence, we cannot determine whether the observed mutations in cat 2''s viral genome arose in a human prior to transmission. Table 1 details the SNPs observed in the cat 2 viral genome, and their frequency in the existing UK human population and among existing feline SARS-CoV-2 sequences. abstract: Two cats from different COVID-19-infected households in the UK were found to be infected with SARS-CoV-2 from humans, demonstrated by immunofluorescence, in situ hybridisation, reverse transcriptase quantitative PCR and viral genome sequencing. Lung tissue collected post-mortem from cat 1 displayed pathological and histological findings consistent with viral pneumonia and tested positive for SARS-CoV-2 antigens and RNA. SARS-CoV-2 RNA was detected in an oropharyngeal swab collected from cat 2 that presented with rhinitis and conjunctivitis. High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. An analysis of cat 2’s viral genome together with nine other feline-derived SARS-CoV-2 sequences from around the world revealed no shared catspecific mutations. These findings indicate that human-to-cat transmission of SARS-CoV-2 occurred during the COVID-19 pandemic in the UK, with the infected cats developing mild or severe respiratory disease. Given the versatility of the new coronavirus, it will be important to monitor for human-to-cat, cat-to-cat and cat-to-human transmission. url: https://doi.org/10.1101/2020.09.23.309948 doi: 10.1101/2020.09.23.309948 id: cord-274286-07arhrv9 author: Hosier, H. title: First case of placental infection with SARS-CoV-2 date: 2020-05-05 words: 3935.0 sentences: 237.0 pages: flesch: 50.0 cache: ./cache/cord-274286-07arhrv9.txt txt: ./txt/cord-274286-07arhrv9.txt summary: Conclusion: This case demonstrates, for the first time, SARS-CoV-2 invasion of the placenta, highlighting the potential for severe morbidity among pregnant women with Covid-19. Levels of anti-SARS-CoV-2 IgG and IgM antibodies in the case study patient were among the highest observed in 56 Covid-19 + patients admitted to Yale New Haven Hospital. This report describes a case of second-trimester Covid-19 associated with preeclampsia and SARS-CoV-2 infection of the placenta. Further studies of placenta from women with Covid-19 may help address whether this is a histological feature associated with placental SARS-CoV-2 infection. RNA was extracted from homogenized placenta, umbilical cord, fetal lungs, heart kidney tissues (27-160 mg; stored in formalin) and maternal oral, nasal, and rectal swabs, saliva, urine, plasma, and serum post-operatively and tested for the presence of SARS-CoV-2 and human RNase P using the US CDC qRT-PCR assay as described 7 . abstract: Background: The effects of Covid-19 in pregnancy remain relatively unknown. We present a case of second trimester pregnancy with symptomatic Covid-19 complicated by severe preeclampsia and placental abruption. Methods: We analyzed placenta for the presence of SARS-CoV-2 through molecular and immunohistochemical assays and by and electron microscopy, and we measured the maternal antibody response in blood to this infection. Results: SARS-CoV-2 localized predominantly to syncytiotrophoblast cells at the maternal-fetal interface of the placenta. Histological examination of the placenta revealed a dense macrophage infiltrate, but no evidence for vasculopathy typically associated with preeclampsia. Conclusion: This case demonstrates, for the first time, SARS-CoV-2 invasion of the placenta, highlighting the potential for severe morbidity among pregnant women with Covid-19. url: http://medrxiv.org/cgi/content/short/2020.04.30.20083907v1?rss=1 doi: 10.1101/2020.04.30.20083907 id: cord-032811-sdbj26ca author: Hosoki, Koa title: Reply date: 2020-09-29 words: 666.0 sentences: 50.0 pages: flesch: 52.0 cache: ./cache/cord-032811-sdbj26ca.txt txt: ./txt/cord-032811-sdbj26ca.txt summary: They suggest that suppression of angiotensin-converting enzyme-2 (ACE-2) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could impair the hydrolysis of des-Arg 9 -bradykinin and stimulate the bradykinin receptor type 1 (BKB1) pathway to induce leakage of fluid into the lungs. 4 However, other studies suggest that SARS-CoV-2 may upregulate the expression of ACE-2 in patients with coronavirus disease 2019 (COVID-19) or influenza pneumonia in alveolar epithelial cells, endothelial cells, and lymphocytes in perivascular tissue than in uninfected control autopsy lung. 7 We favor a third hypothesis, where excessive and prolonged secretion of type I and type III IFNs in the airways contributes to loss of lung epithelial barrier function during COVID-19 and other RNA virus infections (Fig 1, A) . Because IFN-l contributes to loss of lung epithelial barrier function, 8 we hypothesize that entry of SARS-CoV-2 via ACE-2 can stimulate secretion of IFN-l and induce leakage of fluid into the lungs (Fig 1, A) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522701/ doi: 10.1016/j.jaci.2020.09.008 id: cord-310299-isdsestc author: Hosseini, Akram A. title: Delirium as a presenting feature in COVID-19: neuroinvasive infection or autoimmune encephalopathy? date: 2020-06-09 words: 981.0 sentences: 84.0 pages: flesch: 46.0 cache: ./cache/cord-310299-isdsestc.txt txt: ./txt/cord-310299-isdsestc.txt summary: 1 We report two cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) infection with acute onset of altered mental status and delirium with normal respiration and metabolic balance in the first 48 hours. Despite normal brain CT at 48 hours, MRI on day 6 showed three hyperintense foci on diffusion-weighted images, but no overt restriction, consistent with T2-shine-through suggesting cellular infiltration/inflammation or small infarcts ( Figure 1 ). 1,2 However, there is currently no report of limbic encephalitis associated with COVID-19 that presented with delirium in the absence of respiratory, metabolic or systemic features, while patients may be hidden sources of spreading the virus in busy clinical settings. The detection of SARS-CoV2 in the CSF in a patient with meningo-encephalitis supports neurotropic and neuroinvasive potential of the virus 2 presumably through the blood vesselrich meninges once the blood brain barrier is damaged. Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) abstract: nan url: https://doi.org/10.1016/j.bbi.2020.06.012 doi: 10.1016/j.bbi.2020.06.012 id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 words: 3784.0 sentences: 222.0 pages: flesch: 46.0 cache: ./cache/cord-292751-tk1oggi9.txt txt: ./txt/cord-292751-tk1oggi9.txt summary: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. Early diagnosis of COVID-19 is the most critical step to treat infection. The diagnostic tools are generally molecular methods, serology and viral culture. Recently CRISPR-based method has been investigated to diagnose and treat coronavirus infection. The emergence of 2019-nCoV during the influenza season, has led to the extensive use of antibiotics and neuraminidase enzyme inhibitors, taken orally and intravenously. Currently, antiviral inhibitors of SARS and MERS spike proteins, neuraminidase inhibitors, anti-inflammatory drugs and EK1 peptide are the available therapeutic options for SARS-CoV-2 infected individuals. In addition, Chloroquine, which was previously used for malarial and autoimmune disease, has shown efficacy in the 2019-nCoV infection treatment. In severe hypoxaemia, a combination of antibiotics, α-interferon, lopinavir and mechanical ventilation can effectively mitigate the symptoms. Comprehensive knowledge on the innate and adaptive immune responses, will make it possible to propose potent antiviral drugs with their effective therapeutic measures for the prevention of viral infection. This therapeutic strategy will help patients worldwide to protect themselves against severe and fatal viral infections, that potentially can evolve and develop drug resistance, and to reduce mortality rates. url: https://doi.org/10.1016/j.virol.2020.08.011 doi: 10.1016/j.virol.2020.08.011 id: cord-331277-fjsuo3yy author: Hoste, Alexis C.R. title: Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: A screening tool and a point-of-care test date: 2020-08-11 words: 2407.0 sentences: 136.0 pages: flesch: 52.0 cache: ./cache/cord-331277-fjsuo3yy.txt txt: ./txt/cord-331277-fjsuo3yy.txt summary: Two serological tools based on a Double Recognition assay (Enzyme-Linked Immunosorbent Assay, DR-ELISA and Lateral Flow Assay, DR-LFA) to detect total antibodies to SARS-CoV-2, have been developed based on the recombinant nucleocapsid protein. Therefore, the aim of the present work was the development of serological tools to determine the presence of antibodies against SARS-CoV-2 in the population, as an indicator of an ongoing or previous infection. In the current study, a Double Recognition Enzyme-Linked Immunosorbent Assay (DR-ELISA) was developed to determine the presence of immunoglobulins of different classes (IgG, IgM and IgA) to SARS-CoV-2 in human serum, to support the diagnosis of COVID-19. In the present study, we developed two serological assays using the recombinant N protein Table 1, a group of 14 serum samples from early days post infection, positive to COVID-19 by respiratory-PCR yet still negative in the commercial serological assay (with seroconversion a few days later) were also tested in our assays. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 8 million people worldwide, becoming a pandemic. Detecting antibodies against SARS-CoV-2 is of utmost importance and a good indicator of exposure and circulation of the virus within the general population. Two serological tools based on a Double Recognition assay (Enzyme-Linked Immunosorbent Assay, DR-ELISA and Lateral Flow Assay, DR-LFA) to detect total antibodies to SARS-CoV-2, have been developed based on the recombinant nucleocapsid protein. A total of 1065 serum samples, including positive for COVID-19 and negative samples from healthy donors or infected with other respiratory pathogens, were analyzed. The results showed values of sensitivity between 91.2%–100%, and specificity of 100%–98.2%, for DR-LFA and DR-ELISA, respectively. No cross-reactivity against seasonal coronavirus (HCoV-NL63, HCoV-229E, HCoV-HKU1, HCoV-OC43) was found. These results demonstrate the importance of serology as a complementary tool to PCR, for follow up of recovered patients and identification of asymptomatic individuals. url: https://doi.org/10.1016/j.diagmicrobio.2020.115167 doi: 10.1016/j.diagmicrobio.2020.115167 id: cord-255413-8o884nyp author: Hotez, Peter J. title: The Potential Role of Th17 Immune Responses in Coronavirus Immunopathology and Vaccine-induced Immune Enhancement date: 2020-04-17 words: 1707.0 sentences: 104.0 pages: flesch: 35.0 cache: ./cache/cord-255413-8o884nyp.txt txt: ./txt/cord-255413-8o884nyp.txt summary: From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. Beyond direct virus-induced pathology, immune enhancement associated with eosinophilic infiltration and immunopathology is a potential safety concern linked to first-generation vaccines to prevent severe acute respiratory syndrome (SARS) (12) . While vaccinia and other vectored vaccines induce substantial immune enhancement in both the lungs and liver of experimental animals (20) (21) (22) (23) (24) , which in some cases have been linked to viral expression of the N protein (15) , none of these studies specifically examined Th17 responses. A double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge Severe acute respiratory syndrome-associated coronavirus vaccines formulated with delta inulin adjuvants provide enhanced protection while ameliorating lung eosinophilic immunopathology abstract: Increasing evidence points to host Th17 inflammatory responses as contributing to the severe lung pathology and mortality of lower respiratory tract infections from coronaviruses. This includes host inflammatory and cytokine responses to COVID-19 caused by the SARS-2 coronavirus (SARS CoV2). From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. Here we summarize evidence suggesting there may be partial overlap between the underlying immunopathologic processes linked to both coronavirus infection and vaccination, and a role for Th17 in immune enhancement and eosinophilic pulmonary immunopathology. Such findings help explain the link between viral-vectored coronavirus vaccines and immune enhancement and its reduction through alum adjuvants. Additional research may also clarify links between COVID-19 pulmonary immunopathology and heart disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32305501/ doi: 10.1016/j.micinf.2020.04.005 id: cord-256303-bpa571ys author: Hotez, Peter J. title: Will COVID-19 become the next neglected tropical disease? date: 2020-04-10 words: 564.0 sentences: 32.0 pages: flesch: 61.0 cache: ./cache/cord-256303-bpa571ys.txt txt: ./txt/cord-256303-bpa571ys.txt summary: The daily World Health Organization (WHO) Coronavirus Situation Reports highlight the rapid spread of COVID-19 across Europe, the United States, and many of the advanced nations in East Asia [1] . If SARS CoV2 becomes a major respiratory virus pathogen in resource-poor countries of the tropics and subtropics, we might envision unprecedented levels of global morbidity and mortality. Accordingly, PLOS Neglected Tropical Diseases will consider articles from the community of scientists and public health experts in Asia, Africa, and Latin America now shifting their efforts to combat the COVID-19 pandemic. However, as John Lennon once said, "life is what happens to you while you''re busy making other plans," and on that basis we now invite our community of NTD scientists to submit COVID-19 papers on what may become a global health terror on a scale that rivals or even exceeds some of the world''s major neglected tropical diseases. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32275667/ doi: 10.1371/journal.pntd.0008271 id: cord-260412-yjr83ef6 author: Hotez, Peter J. title: Developing a low-cost and accessible COVID-19 vaccine for global health date: 2020-07-29 words: 2322.0 sentences: 117.0 pages: flesch: 43.0 cache: ./cache/cord-260412-yjr83ef6.txt txt: ./txt/cord-260412-yjr83ef6.txt summary: Our group is developing a two-pronged approach to advance recombinant protein-based vaccines to prevent COVID-19 caused by SARS-CoV-2 and other coronavirus infections. One vaccine is based on a yeast-derived (Pichia pastoris) recombinant protein comprised of the receptor-binding domain (RBD) of the SARS-CoV formulated on alum and referred to as the CoV RBD219-N1 Vaccine. In addition to their low cost and suitability for use in public immunization programs in lowand middle-income countries, we pursued RBD recombinant protein-based vaccines as a technology to maximize safety relative to other platforms, such as virus vectors that have previously been found to induce immune enhancement. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1), a SARS Vaccine Candidate Potential for developing a SARS-CoV receptor-binding domain (RBD) recombinant protein as a heterologous human vaccine against coronavirus infectious disease (COVID)-19 Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1) Formulated with Alum Induces Protective Immunity and Reduces Immune Enhancement abstract: nan url: https://doi.org/10.1371/journal.pntd.0008548 doi: 10.1371/journal.pntd.0008548 id: cord-307858-274a699i author: Hotez, Peter J. title: COVID-19 vaccines: neutralizing antibodies and the alum advantage date: 2020-06-04 words: 1331.0 sentences: 64.0 pages: flesch: 40.0 cache: ./cache/cord-307858-274a699i.txt txt: ./txt/cord-307858-274a699i.txt summary: A chemically inactivated virus vaccine (PiCoVacc) and a recombinant proteinbased vaccine (CoV-RBD219N1) were recently shown to elicit high levels of protective immunity in rhesus macaques or in mice against homologous virus challenge with SARS-CoV-2 or SARS-CoV, respectively 2,3 . Similarly, mice vaccinated with CoV-RBD219N1, based on the recombinant RBD protein of SARS-CoV, which is now investigated as a COVID-19 vaccine candidate, exhibited virus-neutralizing antibody titres between 640 and 1,280 upon SARS-CoV homologous viral challenge 3 . Therefore, an emerging story in COVID-19 vaccine development is the potential importance of inducing high levels of neutralizing antibodies to the S protein or its RBD. A key finding so far is that aluminium adjuvant formulations, such as those used for PiCoVacc and CoV-RBD219N1, appear to promote high titres of neutralizing antibody. A potential concern about the use of aluminium adjuvants is based on the claim that T H 2-type immune responses might promote vaccine-enhanced respiratory disease (VAERD) 9 . abstract: Achieving high levels of neutralizing antibodies to the spike protein of SARS-CoV-2 in a safe manner is likely to be crucial for an effective vaccine. Here, we propose that aluminium-based adjuvants might hold the key to this. url: https://doi.org/10.1038/s41577-020-0358-6 doi: 10.1038/s41577-020-0358-6 id: cord-031001-x4iiqq5e author: Hou, Fan Fan title: Personnel protection strategy for healthcare workers in Wuhan during the COVID-19 epidemic date: 2020-07-20 words: 2512.0 sentences: 127.0 pages: flesch: 51.0 cache: ./cache/cord-031001-x4iiqq5e.txt txt: ./txt/cord-031001-x4iiqq5e.txt summary: DESIGN: During the COVID-19 pandemic, 943 healthcare staff sent from Guangzhou to Wuhan to care for patients with suspected/confirmed COVID-19 received infection precaution training before their mission and were equipped with Level 2/3 personal protective equipment (PPE), in accordance with guidelines from the National Health Commission of China. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53 out of 1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126 out of 2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53/1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126/2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively (Table 3) . abstract: OBJECTIVE: To identify the effectiveness of a personnel protection strategy in protection of healthcare workers from SARS-CoV-2 infection. DESIGN: During the COVID-19 pandemic, 943 healthcare staff sent from Guangzhou to Wuhan to care for patients with suspected/confirmed COVID-19 received infection precaution training before their mission and were equipped with Level 2/3 personal protective equipment (PPE), in accordance with guidelines from the National Health Commission of China. We conducted a serological survey on the cumulative attack rate of SARS-CoV-2 among the healthcare workers sent to Wuhan and compared the seropositive rate to that in local healthcare workers from Wuhan and Jingzhou. RESULTS: Serial tests for SARS-CoV-2 RNA and tests for SARS-CoV-2 immunoglobulin M and G after the 6-8 week mission revealed a zero cumulative attack rate. Among the local healthcare workers in Wuhan and Jingzhou of Hubei Province, 2.5% (113 out of 4495) and 0.32% (10 out of 3091) had RT-PCR confirmed COVID-19, respectively. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53 out of 1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126 out of 2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively. CONCLUSIONS AND RELEVANCE: Our study confirmed that adequate training/PPE can protect medical personnel against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454919/ doi: 10.1093/pcmedi/pbaa024 id: cord-339012-4juhmjaj author: Hou, Wei title: Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date: 2020-07-28 words: 6756.0 sentences: 344.0 pages: flesch: 48.0 cache: ./cache/cord-339012-4juhmjaj.txt txt: ./txt/cord-339012-4juhmjaj.txt summary: Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and "synaptic clefts" between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The detected sets of differential expressed genes (DEGs) for PEDV and MRV were analyzed by gene set enrichment analysis (GSEA) using functional bioinformatic programs to retrieve biological processes (pathways and Gene Ontology terms [GO-term]) and associations with chemical compounds, including drugs. abstract: The transcriptional response in Vero cells (ATCC® CCL-81) infected with the coronavirus Porcine Epidemic Diarrhea Virus (PEDV) was measured by RNAseq analysis 4 and 6 hours after infection. Differential expressed genes (DEGs) in PEDV infected cells were compared to DEGs responding in Vero cells infected with Mammalian Orthoreovirus (MRV). Functional analysis of MRV and PEDV DEGs showed that MRV increased the expression level of several cytokines and chemokines (e.g. IL6, CXCL10, IL1A, CXCL8 [alias IL8]) and antiviral genes (e.g. IFI44, IFIT1, MX1, OASL), whereas for PEDV no enhanced expression was observed for these “hallmark” antiviral and immune effector genes. Pathway and Gene Ontology “enrichment analysis” revealed that PEDV infection did not stimulate expression of genes able to activate an acquired immune response, whereas MRV did so within 6h. Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). PEDV also down-regulated expression of Ectodysplasin A, a cytokine of the TNF-family able to activate the canonical NFKB-pathway responsible for transcription of inflammatory genes like IL1B, TNF, CXCL8 and PTGS2. The only 2 cytokine genes found up-regulated by PEDV were Cardiotrophin-1, an IL6-type cytokine with pleiotropic functions on different tissues and types of cells, and Endothelin 2, a neuroactive peptide with vasoconstrictive properties. Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and “synaptic clefts” between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The information in this study describing a “very early” response of epithelial cells to an infection with a coronavirus may provide pharmacologists, immunological and medical specialists additional insights in the underlying mechanisms of coronavirus associated severe clinical symptoms including those induced by SARS-CoV-2. This may help them to fine-tune therapeutic treatments and apply specific approved drugs to treat COVID-19 patients. url: https://doi.org/10.1101/2020.07.28.224576 doi: 10.1101/2020.07.28.224576 id: cord-350855-gofzhff7 author: Hou, Yixuan J. title: SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract date: 2020-05-27 words: 3416.0 sentences: 222.0 pages: flesch: 50.0 cache: ./cache/cord-350855-gofzhff7.txt txt: ./txt/cord-350855-gofzhff7.txt summary: High-sensitivity RNA in situ mapping revealed the highest ACE2 expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) vs distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. We measured the relative infectivity of the SARS-CoV-2 GFP virus in primary 283 cells based on the average peak titers and observed that infectivity exhibited the same 284 pattern as the ACE2 expression levels from the upper to lower respiratory tract ( Figure 285 6Bi-6Biv). Gene 1230 expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human 1231 airway epithelial cells and lung tissue abstract: Summary The mode of acquisition and causes for the variable clinical spectrum of COVID-19 remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore SARS-CoV-2 pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest ACE2 expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) vs distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis. url: https://doi.org/10.1016/j.cell.2020.05.042 doi: 10.1016/j.cell.2020.05.042 id: cord-252232-vgq6gjpx author: Hou, Yuxuan title: Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date: 2010-06-22 words: 3208.0 sentences: 159.0 pages: flesch: 57.0 cache: ./cache/cord-252232-vgq6gjpx.txt txt: ./txt/cord-252232-vgq6gjpx.txt summary: Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry. abstract: The discovery of SARS-like coronavirus in bats suggests that bats could be the natural reservoir of SARS-CoV. However, previous studies indicated the angiotensin-converting enzyme 2 (ACE2) protein, a known SARS-CoV receptor, from a horseshoe bat was unable to act as a functional receptor for SARS-CoV. Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. The results show that ACE2s of Myotis daubentoni and Rhinolophus sinicus support viral entry mediated by the SARS-CoV S protein, albeit with different efficiency in comparison to that of the human ACE2. Further, the alteration of several key residues either decreased or enhanced bat ACE2 receptor efficiency, as predicted from a structural modeling study of the different bat ACE2 molecules. These data suggest that M. daubentoni and R. sinicus are likely to be susceptible to SARS-CoV and may be candidates as the natural host of the SARS-CoV progenitor viruses. Furthermore, our current study also demonstrates that the genetic diversity of ACE2 among bats is greater than that observed among known SARS-CoV susceptible mammals, highlighting the possibility that there are many more uncharacterized bat species that can act as a reservoir of SARS-CoV or its progenitor viruses. This calls for continuation and expansion of field surveillance studies among different bat populations to eventually identify the true natural reservoir of SARS-CoV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-010-0729-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-010-0729-6 doi: 10.1007/s00705-010-0729-6 id: cord-329200-o5hxpl8f author: Houlihan, Catherine F title: The complexities of SARS-CoV-2 serology date: 2020-09-23 words: 1010.0 sentences: 60.0 pages: flesch: 40.0 cache: ./cache/cord-329200-o5hxpl8f.txt txt: ./txt/cord-329200-o5hxpl8f.txt summary: Our understanding of individual and population-level immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains incomplete and developing reliable serological assays to detect previous infection has been an intense focus of the global scientific effort. For public health planning we need scalable assays validated against large banks of samples from individuals who had proven seasonal (non-severe acute respiratory syndrome) coronaviruses and those who had well characterised symptomatic and asymptomatic confirmed SARS-CoV-2 infection. In The Lancet Infectious Diseases, the National SARS-CoV-2 Serology Assay Evaluation Group 1 provide the first large comparative investigation of the performance of four widely available commercial assays and a single in-house assay. Antibody responses to SARS-CoV-2 are predominantly directed at the spike glycoprotein, which the virus requires for entry, and the nucleocapsid protein, which binds the viral RNA genome. 2,3 The DiaSorin, Siemens, and in-house assays measured these potentially protective antibodies, with the inhouse ELISA using trimerised spike protein, which shows a high correlation with neutralisation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32979317/ doi: 10.1016/s1473-3099(20)30699-x id: cord-278176-o9glkhyv author: Houng, Huo-Shu H title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 words: 4782.0 sentences: 226.0 pages: flesch: 54.0 cache: ./cache/cord-278176-o9glkhyv.txt txt: ./txt/cord-278176-o9glkhyv.txt summary: The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. It was demonstrated that the RT-PCR assay with 91% amplification efficiency could be used for consistent detect ion of the SARS-CoV viral RNA extracted from samples containing as little as 0.005 pfu per reaction with an anticipated C T value of 40 cycles (data not shown). It was demonstrated in this study that the cloned pHCV1 plasmid could be used to replace viral cDNA as a stable and rational SARS-CoV copy number standard for the SARS-CoV RT-PCR assay. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: The severe acute respiratory syndrome (SARS) epidemic originating from China in 2002 was caused by a previously uncharacterized coronavirus that could be identified by specific RT-PCR amplification. Efforts to control future SARS outbreaks depend on the accurate and early identification of SARS-CoV infected patients. A real-time fluorogenic RT-PCR assay based on the 3′-noncoding region (3′-NCR) of SARS-CoV genome was developed as a quantitative SARS diagnostic tool. The ideal amplification efficiency of a sensitive SARS-CoV RT-PCR assay should yield an E value (PCR product concentration increase per amplification cycle) equal to 2.0. It was demonstrated that the 3′-NCR SARS-CoV based RT-PCR reactions could be formulated to reach excellent E values of 1.81, or 91% amplification efficacy. The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The viral genomic copy (or genomic equivalences, GE) per infectious unit (GE/pfu) of SARS-CoV used in this study was also established to be approximate 1200–1600:1. The assay’s detection sensitivity could reach 0.005 pfu or 6–8 GE per assay. It was preliminarily demonstrated that the assay could efficiently detect SARS-CoV from clinical specimens of SARS probable and suspected patients identified in Taiwan. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. url: https://www.ncbi.nlm.nih.gov/pubmed/15234807/ doi: 10.1016/j.jviromet.2004.04.008 id: cord-267960-r5m7o9dp author: Hourdel, Véronique title: Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date: 2020-09-25 words: 4466.0 sentences: 211.0 pages: flesch: 51.0 cache: ./cache/cord-267960-r5m7o9dp.txt txt: ./txt/cord-267960-r5m7o9dp.txt summary: In this study, we aimed at implementing an ampliconbased sequencing approach to obtain SARS-CoV-2 consensus genomes directly from clinical specimens, adaptable into the field conditions, with the two easily manageable nextgeneration sequencers, the nanopore MinION and the Illumina iSeq100 TM system. Sputum specimens and respective isolates RNA extracts were tested with the SARS-CoV-2 real-time RdRP gene duplex reverse transcription (RT)-PCR developed by the French National Reference Center for Respiratory Viruses and the real-time E gene RT-PCR from the Charité protocol (see WHO Coronavirus disease COVID-19 technical guidance: Laboratory testing for 2019-nCoV in humans, available from https://www.who. Globally, using our amplicon-based approach, combined with the MinION platform, we were able to obtain the near fulllength genome of the studied viral specimens in around 8 h, from samples to sequences data. Viral consensus genomic sequences were rapidly and easily obtained for the two SARS-CoV-2 clinical specimens and their respective isolates, by using the two different sequencing platforms, MinION and iSeq100 TM system. abstract: Global human health is increasingly challenged by emerging viral threats, especially those observed over the last 20 years with coronavirus-related human diseases, such as the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS). Recently, in late December 2019, a novel Betacoronavirus, SARS-CoV-2, originating from the Chinese city of Wuhan, emerged and was then identified as the causative agent of a new severe form of pneumonia, COVID-19. Real-time genome sequencing in such viral outbreaks is a key issue to confirm identification and characterization of the involved pathogen and to help establish public health measures. Here, we implemented an amplicon-based sequencing approach combined with easily deployable next-generation sequencers, the small and hand-held MinION sequencer and the latest most compact Illumina sequencer, the iSeq100(TM) system. Our results highlighted the great potential of the amplicon-based approach to obtain consensus genomes of SARS-CoV-2 from clinical samples in just a few hours. Both these mobile next-generation sequencers are proven to be efficient to obtain viral sequences and easy to implement, with a minimal laboratory environment requirement, providing useful opportunities in the field and in remote areas. url: https://www.ncbi.nlm.nih.gov/pubmed/33101244/ doi: 10.3389/fmicb.2020.571328 id: cord-291642-xfkdxnfb author: Howley, Fergal title: Late presentation of ‘Lemierre’s syndrome’: how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic date: 2020-10-10 words: 2575.0 sentences: 148.0 pages: flesch: 42.0 cache: ./cache/cord-291642-xfkdxnfb.txt txt: ./txt/cord-291642-xfkdxnfb.txt summary: title: Late presentation of ''Lemierre''s syndrome'': how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic We describe an atypical case of Lemierre''s syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe an atypical case of Lemierre''s syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe a severe case of Lemierre''s syndrome, requiring ICU admission and intubation, where presentation and initiation of treatment were delayed by the SARS-CoV-2 pandemic. abstract: The SARS-CoV-2 outbreak has disrupted the delivery of routine healthcare services on a global scale. With many regions suspending the provision of non-essential healthcare services, there is a risk that patients with common treatable illnesses do not receive prompt treatment, leading to more serious and complex presentations at a later date. Lemierre’s syndrome is a potentially life-threatening and under-recognised sequela of an oropharyngeal or dental infection. It is characterised by septic embolisation of the gram-negative bacillus Fusobacterium necrophorum to a variety of different organs, most commonly to the lungs. Thrombophlebitis of the internal jugular vein is frequently identified. We describe an atypical case of Lemierre’s syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/33040042/ doi: 10.1136/bcr-2020-239269 id: cord-353873-88ud20oq author: Hoyler, Marguerite M. title: The importance of challenges in COVID-19 screening and testing in the obstetric patient population date: 2020-05-28 words: 539.0 sentences: 37.0 pages: flesch: 49.0 cache: ./cache/cord-353873-88ud20oq.txt txt: ./txt/cord-353873-88ud20oq.txt summary: We reviewed with interest the recent article and accompanying infographic published by Herman and colleagues regarding anesthesia management of the obstetric patient in the era of COVID-19. [1] We commend the authors for a compelling visual summary of strategies to help care for patients as well as protect obstetric anesthesia providers from possible SARS-CoV-2 transmission. These observations support a low threshold for testing parturients for COVID-19, even if they present with symptoms that occur in normal pregnancy; this is particularly important in communities with high rates of SARS-CoV-2 infection. As part of obstetric anesthesia care considerations, and particularly in communities and institutions with high burdens of SARS-CoV-2 infection, it may be prudent to routinely manage parturients as high risk for COVID-19 infection and to encourage conservative measures that J o u r n a l P r e -p r o o f abstract: nan url: https://doi.org/10.1016/j.jclinane.2020.109938 doi: 10.1016/j.jclinane.2020.109938 id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 words: 16737.0 sentences: 847.0 pages: flesch: 45.0 cache: ./cache/cord-291916-5yqc3zcx.txt txt: ./txt/cord-291916-5yqc3zcx.txt summary: abstract: Over the past two decades, there have been two major outbreaks where the crossover of animal Betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In December 2019, a global public health concern started with the emergence of a new strain of coronavirus (SARS-CoV-2 or 2019 novel coronavirus, 2019-nCoV) which has rapidly spread all over the world from its origin in Wuhan, China. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes human SARS-CoV, MERS and two other human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1. The fatality rate of SARS-CoV-2 is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed SARS-CoV-2 to be highly contagious. Based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of SARS-CoV-2 infections in comparison with those caused by SARS-CoV and MERS-CoV. Moreover, the possible impact of weather conditions on the transmission of SARS-CoV-2 is also discussed. Therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches. url: https://doi.org/10.3390/ijerph17165648 doi: 10.3390/ijerph17165648 id: cord-291459-m56dy8us author: Hraiech, Sami title: Lack of viral clearance by the combination of hydroxychloroquine and azithromycin or lopinavir and ritonavir in SARS-CoV-2-related acute respiratory distress syndrome date: 2020-05-24 words: 1152.0 sentences: 64.0 pages: flesch: 52.0 cache: ./cache/cord-291459-m56dy8us.txt txt: ./txt/cord-291459-m56dy8us.txt summary: In order to evaluate these results in intensive care unit (ICU) patients, we retrospectively assessed in moderate-to-severe ARDS the efficacy of hydroxychloroquine-azithromycin combination regarding viral disappearance at both day 6 of the treatment and day 6 of evolution of ARDS as compared with patients treated with lopinavir-ritonavir and a control group without any anti-viral treatment. Negative nasopharyngeal PCR for SARS-CoV-2 at day 6 following the initiation of treatment were observed in 5 (38%) patients from the lopinavir-ritonavir group as compared with 3 (18%) patients from the hydroxychloroquine-azithromycin group and 2 (20%) from the control group (p = 0.39). At day 6 following ARDS onset, PCR was negative in only 9 patients, 5 from the lopinavir-ritonavir group, 2 from the hydroxychloroquine-azithromycin group and 2 from the control group. abstract: nan url: https://doi.org/10.1186/s13613-020-00678-4 doi: 10.1186/s13613-020-00678-4 id: cord-299781-9d5g5xaw author: Hrusak, Ondrej title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment date: 2020-04-07 words: 2377.0 sentences: 128.0 pages: flesch: 49.0 cache: ./cache/cord-299781-9d5g5xaw.txt txt: ./txt/cord-299781-9d5g5xaw.txt summary: title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment While we should not underestimate the risk of developing a more severe course of COVID-19 than observed here, the intensity of preventive measures should not cause delays or obstructions in oncological treatment. The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causing the Coronavirus Disease (COVID-19) pandemic in 2020 was identified in December, 2019. 11 To evaluate this, we used a flash survey to determine whether there was current evidence that pediatric patients with cancer in SARS-CoV-2 affected areas had been tested for this virus or had developed severe COVID-19 disease. More research is needed to better understand the epidemiology of SARS-CoV-2 infection and COVID-19 in pediatric patients with cancer or other immunocompromised children. abstract: Abstract Introduction Since the beginning of COVID-19 pandemics, it is known that the severe course of the disease occurs mostly among elderly, whereas it is rare among children and young adults. Comorbidities, in particular diabetes and hypertension, clearly associated with age, besides obesity and smoke are strongly associated with the need of intensive treatment and a dismal outcome. A weaker immunity of the elderly has been proposed as a possible explanation of this uneven age distribution. Along the same line, anecdotal information from Wuhan, China mentioned a severe course of COVID-19 in a child treated for leukemia. Aim and methods We made a flash survey on COVID19 incidence and severity among children on anticancer treatment. Respondents were asked by email to fill in a short web based survey. Results We received reports from 25 countries, where approximately 10,000 patients at risk are followed. At the time of the survey, over 200 of these children were tested, nine of whom were positive for COVID-19. Eight of the nine cases had asymptomatic to mild disease and one was just diagnosed with COVID-19. We also discuss preventive measures that are in place or should be taken as well as treatment options in immunocompromised children with COVID-19. Conclusion Thus, even children receiving anti-cancer chemotherapy may have a mild or asymptomatic course of COVID-19. While we should not underestimate the risk of developing a more severe course of COVID-19 than observed here, the intensity of preventive measures should not cause delays or obstructions in oncological treatment. url: https://doi.org/10.1016/j.ejca.2020.03.021 doi: 10.1016/j.ejca.2020.03.021 id: cord-269707-titu9lm4 author: Hsieh, Ching-Lin title: Structure-based design of prefusion-stabilized SARS-CoV-2 spikes date: 2020-07-23 words: 2125.0 sentences: 122.0 pages: flesch: 50.0 cache: ./cache/cord-269707-titu9lm4.txt txt: ./txt/cord-269707-titu9lm4.txt summary: Here, we characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting ~10-fold higher expression than its parental construct and the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2. In addition to salt bridges, filling loosely packed hydrophobic cores that allow the protein to refold can help stabilize the prefusion state, as shown by previous cavity-filling substitutions in RSV F and HIV-1 Env (12, 20, 22) . Adding one disulfide (S884C/A893C) to a single proline variant (F817P) also reduced the expression level, although the quaternary structure of the spikes was well maintained (table S2, Combo40). HexaPro expressed 9.8-fold higher than S-2P, had ~5°C increase in Tm, and retained the trimeric prefusion conformation (Fig. 3D) . abstract: The COVID-19 pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. Here, we characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting ~10-fold higher expression than its parental construct and the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2. url: https://doi.org/10.1126/science.abd0826 doi: 10.1126/science.abd0826 id: cord-322451-cwpz4akv author: Hsin, Dena Hsin-Chen title: Heroes of SARS: professional roles and ethics of health care workers date: 2004-07-27 words: 3598.0 sentences: 200.0 pages: flesch: 66.0 cache: ./cache/cord-322451-cwpz4akv.txt txt: ./txt/cord-322451-cwpz4akv.txt summary: To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. In a number of countries in order to encourage HCW, the government and the public started to give the title of ''hero'' to nurses and doctors who are working in the frontline of SARS outbreak. While the ethical ideal of self-less sacrifice of life for curing disease is promoted in the public image and media, discussions with HCW in several countries suggests that being a hero is not what modern medical practice is for some HCWs. Most HCWs in Taiwan are working in the commercial hospital, where the hirer pushes them to focus their effort of work on business competition rather than the basic role of helpers to human''s health. Nurses'' professional care obligation and their attitudes towards SARS infection control measures in Taiwan during and after the 2003 epidemic abstract: Objectives. To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. Methods. Descriptive discussion of media reports, analysis of ethical principles and political decisions discussed in the outbreak, with particular emphasis on the events in mainland China and Taiwan. Results. There were differences in the way that Taiwan and mainland China responded to the SARS epidemic, however, both employed techniques of hospital quarantine. After early policy mistakes in both countries HCWs were called heroes. The label ‘hero’ may not be appropriate for the average HCW when faced with the SARS epidemic, although a number of self-less acts can be found. The label was also politically convenient. Conclusions. A middle ground for reasonable expectations from HCW when treating diseases that have serious risk of infection should be expected. While all should act according to the ethic of beneficence not all persons should be expected to be martyrs for society. url: https://api.elsevier.com/content/article/pii/S0163445304001410 doi: 10.1016/j.jinf.2004.06.005 id: cord-255476-p0gyyl3c author: Hsu, Albert L. title: Placental SARS‐CoV‐2 in a Pregnant Woman with Mild COVID‐19 Disease date: 2020-08-04 words: 3310.0 sentences: 232.0 pages: flesch: 53.0 cache: ./cache/cord-255476-p0gyyl3c.txt txt: ./txt/cord-255476-p0gyyl3c.txt summary: Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality.(1) COVID‐19 manifestations appear similar between pregnant and non‐pregnant women.(2) OBJECTIVES/STUDY DESIGN: We present a case of placental SARS‐CoV‐2 virus in a woman with mild COVID‐19 disease, then review the literature. Evidence of placental COVID‐19 raises concern for placental vasculopathy (potentially leading to fetal growth restriction and other pregnancy complications) and possible vertical transmission – especially for pregnant women who may be exposed to COVID‐19 in early pregnancy. In this case study, we present a case of placental SARS-CoV-2 virus in a woman with an uncomplicated pregnancy and mild COVID-19 disease. To date, there is still no other published work about SARS-CoV-2 virus by immunohistochemistry in the placentas of women with mild COVID-19 disease. Despite her having mild COVID-19 disease in pregnancy, we demonstrate placental vasculopathy and presence of SARS-CoV-2 virus across the placenta. Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of the placenta in pregnancies with COVID-19 positive mothers and neonates at birth abstract: BACKGROUND: The full impact of COVID‐19 on pregnancy remains uncharacterized. Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality.(1) COVID‐19 manifestations appear similar between pregnant and non‐pregnant women.(2) OBJECTIVES/STUDY DESIGN: We present a case of placental SARS‐CoV‐2 virus in a woman with mild COVID‐19 disease, then review the literature. RT‐PCR was performed to detect SARS‐CoV‐2. Immunohistochemistry staining was performed with specific monoclonal antibodies to detect SARS‐CoV‐2 antigen or to identify trophoblasts. RESULTS: A 29 year‐old multigravida presented at 40‐4/7 weeks for labor induction. With myalgias two days prior, she tested positive for SARS‐CoV‐2. We demonstrate maternal vascular malperfusion, with no fetal vascular malperfusion, as well as SARS‐CoV‐2 virus in chorionic villi endothelial cells, and also rarely in trophoblasts. CONCLUSIONS: To our knowledge, this is the first report of placental SARS‐CoV‐2 despite mild COVID‐19 disease (no symptoms of COVID‐19 aside from myalgias); patient had no fever, cough, or shortness of breath, but only myalgias and sick contacts. Despite her mild COVID‐19 disease in pregnancy, we demonstrate placental vasculopathy and presence of SARS‐CoV‐2 virus across the placenta. Evidence of placental COVID‐19 raises concern for placental vasculopathy (potentially leading to fetal growth restriction and other pregnancy complications) and possible vertical transmission – especially for pregnant women who may be exposed to COVID‐19 in early pregnancy. This raises important questions of whether future pregnancy guidance should include stricter pandemic precautions, such as screening for a wider array of COVID‐19 symptoms, increased antenatal surveillance, and possibly routine COVID‐19 testing throughout pregnancy. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26386 doi: 10.1002/jmv.26386 id: cord-290257-2u228xe9 author: Hsu, Chih-Cheng title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan date: 2006-05-05 words: 3081.0 sentences: 170.0 pages: flesch: 51.0 cache: ./cache/cord-290257-2u228xe9.txt txt: ./txt/cord-290257-2u228xe9.txt summary: title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan This paper assesses factors related to public health nurses'' confidence in managing community SARS control programs. The third section contained questions (using 10-point Likert scale: 1 5 the worst to 10 5 the best) about the effectiveness of the nurse''s institution in managing the SARS epidemic, including the nurse''s assessment of (1) the institutional functioning on community home quarantine, (2) the quality of training received for controlling infectious disease outbreaks, and (3) the adequacy of support (for both manpower and financing) received from superior health agencies force commander said the epidemic situation was stable and advised people to return to their routine. In summary, public health nurses'' confidence in the control of a SARS outbreak and people''s compliance with quarantine measures are 2 major factors that can affect the success of a SARS-control program. abstract: BACKGROUND: Taiwan experienced one of the most serious outbreaks of severe acute respiratory syndrome (SARS) during the 2003 epidemic. Public health nurses faced unprecedented challenges in implementing an extensive quarantine policy to prevent disease spread. Their professional confidence, however, was shattered during the SARS crisis. This paper assesses factors related to public health nurses' confidence in managing community SARS control programs. METHODS: In May 2003, we sent structured questionnaires to all 361 health centers in Taiwan and asked the public health nurses responsible for epidemic control to complete. A total of 312 completed surveys were returned for a response rate of 86.4%. Descriptive methods and logistic regression were used to analyze the data. RESULTS: Most public health nurses (71.9%) expressed a general lack of confidence in handling the SARS epidemic. Confidence was significantly associated with perceived epidemic severity (OR, 0.58; 95% CI: 0.35-0.99), daily epidemic updates (OR, 2.26; 95% CI: 1.28-3.98), and number of cases in the community (OR, 2.21; 95% CI: 1.13-4.31). CONCLUSION: Nurses' individual risk perception and prompt update of epidemic information significantly affect levels of professional confidence, a key factor influencing quarantine implementation success. Strategies to promote productive interagency collaboration and advocate participatory policy making involving health workers at all levels are needed to control effectively infectious disease outbreaks. url: https://www.sciencedirect.com/science/article/pii/S0196655306000794 doi: 10.1016/j.ajic.2005.11.008 id: cord-340651-g3518bq2 author: Hsu, Chung-Hua title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study date: 2007-05-29 words: 3363.0 sentences: 210.0 pages: flesch: 62.0 cache: ./cache/cord-340651-g3518bq2.txt txt: ./txt/cord-340651-g3518bq2.txt summary: title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study The cases were too few to be conclusive, the initial observations seem to indicate NHM appears to be safe in non-criticallly ill patients and clinical trials are feasible in the setting of pandemic outbreaks. In view of the possible beneficial effect of NHM on SARS or SARS-like infectious diseases, we conducted this randomized, double-blind clinical trial with placebo-control to examine its effectiveness. To our knowledge, this is the first double-blind and placebo-controlled clinical pilot study on supplementary treatment of SARS or SAR-like diseases. abstract: Natural herbal medicine (NHM) has been used to control infectious diseases for thousands of years. In view of the possible beneficial effect of NHM on SARS, we conducted this study to examine whether NHM is of any benefit as a supplementary treatment of SARS or SARS-like infectious disease. This was a randomized, double-blind, placebo-controlled trial. Twenty-eight patients fulfilled the WHO inclusion criteria and our exclusion criteria. All enrolled patients received routine western-medicine treatment. Patients were randomly allocated to one of the three supplementary treatment groups: NHM A (Group A, n = 9) NHM B (Group B, n = 9) or placebo (Group C, n = 10). Chest X-ray was done every 1 or 2 days for every patient. Reading radiologists use a standard 0–3 scoring system (0: no infiltration; 1: focal haziness or even small patchy lesion; 2: ground glass picture; 3: lobar consolidation) according to the severity of infiltration in each lung field (three lung fields in both right and left lungs). The main outcome measurements were the improving chest radiographic scores (IRS) and the duration (days) till improvement (DI). One patient from the placebo group passed away. Patients from NHM A took less days before showing improvement (6.7 ± 1.8) compared with placebo group (11.2 ± 4.9), which showed statistical significance (P = 0.04). The cases were too few to be conclusive, the initial observations seem to indicate NHM appears to be safe in non-criticallly ill patients and clinical trials are feasible in the setting of pandemic outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/18830453/ doi: 10.1093/ecam/nem035 id: cord-298079-hgdyxk98 author: Hsu, Jeffrey J. title: Heart Transplantation in the Early Phase of the COVID‐19 Pandemic: A Single‐Center Case Series date: 2020-07-12 words: 2096.0 sentences: 126.0 pages: flesch: 53.0 cache: ./cache/cord-298079-hgdyxk98.txt txt: ./txt/cord-298079-hgdyxk98.txt summary: Here, we describe our center''s experience with orthotopic heart transplantation (OHT) in one of the country''s pandemic epicenters, where we performed eight OHTs in the first two months after community spread began in late February 2020. 3 Further, the effects of SARS-CoV-2 in highly immunosuppressed patients in the early post-transplant period are currently unclear. Current recommendations from the International Society of Heart and Lung Transplantation (ISHLT) is for all potential donors to undergo PCR-based testing for SARS-CoV-2. In our eight cases performed during the period of pandemic onset (Table) , none have become infected with SARS-CoV-2 to date, despite the growing number of cases in Los Angeles (Figure 1) . Similarly, the impact of SARS-CoV-2 infection in a patient with a newly transplanted cardiac graft is unclear, as to our knowledge, there are have yet to be any cases reported at the time of this communication. More evidence is needed to determine the risks of SARS-CoV-2 infection in newly transplanted patients. abstract: The infectious disease Coronavirus Disease 2019 (COVID‐19) was declared a pandemic by the World Health Organization in March 2020. The impact of COVID‐19 on solid organ transplantations, including heart transplantation, is currently unclear. Many transplant programs have been forced to swiftly re‐evaluate and adapt their practices, leading to a marked decrease in transplants performed. This trend has been due to various factors, including increased donor COVID‐19 screening scrutiny and recipient waiting list management in anticipation of COVID‐19 critical care surge capacity planning. In the face of these unknown variables, determining when and how to proceed with transplantation in our population of patients with end‐stage cardiomyopathies is challenging. Here, we describe our center’s experience with orthotopic heart transplantation (OHT) in one of the country’s pandemic epicenters, where we performed eight OHTs in the first two months after community spread began in late February 2020. url: https://doi.org/10.1111/ctr.14042 doi: 10.1111/ctr.14042 id: cord-254072-evgw0as5 author: Hsu, Li-Yang title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts date: 2003-06-17 words: 2240.0 sentences: 129.0 pages: flesch: 52.0 cache: ./cache/cord-254072-evgw0as5.txt txt: ./txt/cord-254072-evgw0as5.txt summary: title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts We describe the clinical, laboratory, and radiologic features of the index patient and the patient''s initial contacts affected with probable SARS. According to the World Health Organization, a suspected case of SARS is defined as documented fever (temperature >38°C), lower respiratory tract symptoms, and contact with a person believed to have had SARS or history of travel to an area of documented transmission. We describe the clinical features of the index patient in Singapore and the patient''s initial group of contacts affected with probable SARS. Nine days after admission, the patient began to improve clinically, the laboratory abnormalities returned towards normal, and the chest x-ray abnormalities stabilized and resolved. When the index patient was seen in early March, the clinical features and highly infectious nature of SARS were not known. abstract: Severe acute respiratory syndrome (SARS) is an emerging viral infectious disease. One of the largest outbreaks of SARS to date began in Singapore in March 2003. We describe the clinical, laboratory, and radiologic features of the index patient and the patient’s initial contacts affected with probable SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/12781012/ doi: 10.3201/eid0906.030264 id: cord-297463-mmmwi8de author: Hsu, You-Ren title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors date: 2013-03-15 words: 934.0 sentences: 61.0 pages: flesch: 58.0 cache: ./cache/cord-297463-mmmwi8de.txt txt: ./txt/cord-297463-mmmwi8de.txt summary: title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect the SARS coronavirus (SARS-CoV) nucleocapsid protein interaction without fluorescent labeling. We demonstrated AlGaN/GaN was highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleic acid-protein interaction. Here, we demonstrated using the AlGaN/GaN HEMT-based sensors to detect the SARS-CoV CTD s protein. Here, we demonstrated that the AlGaN/GaN HEMTs also have the capability of detecting nucleic acid-protein interaction with high sensitivity. The detection limit of AlGaN/GaN HEMTs sensor for SARS-CoV N protein of dsDNA immobilized device was 0.003 nM, and two orders lower than AMPs immobilized nanowire FET 17 . In summary, AlGaN/GaN HEMTs can detect the nucleic acid binding protein at a low detection limit. abstract: AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect the SARS coronavirus (SARS-CoV) nucleocapsid protein interaction without fluorescent labeling. The detection limit in our system was approximately 0.003 nM of protein sample. Our result showed that this technique was more competitive than isotope-labeling EMSA. We demonstrated AlGaN/GaN was highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleic acid-protein interaction. url: https://www.ncbi.nlm.nih.gov/pubmed/32288936/ doi: 10.1149/05006.0239ecst id: cord-330944-54xmnum8 author: Hsu, You-Ren title: Investigation of C-terminal domain of SARS nucleocapsid protein–Duplex DNA interaction using transistors and binding-site models date: 2014-03-31 words: 3927.0 sentences: 248.0 pages: flesch: 58.0 cache: ./cache/cord-330944-54xmnum8.txt txt: ./txt/cord-330944-54xmnum8.txt summary: AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. With a quantitative analysis of the signals from the sensors through binding-site models, we are able to reveal how many binding sites are on the receptor (dsDNA) for certain ligands (SARS-N protein) and what the dissociation constants are for ligand-receptor complexes. The chemical reaction for the surface-immobilized receptor (dsDNA) and the free ligand (SARS-N protein-CTD) in bulk solution can be expressed as the following equations: Therefore, we conclude that for a one-binding-site model, the most significant change of the surface coverage ratio is within the range of the ligand concentration between one order higher and one order lower than the value of the dissociation constant. abstract: AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). The sensing signals were the drain current change of the HEMTs induced by the protein–dsDNA binding. Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. Two dissociation constants, K(D1) = 0.0955 nM, K(D2) = 51.23 nM, were obtained by fitting the experimental results into the two-binding-site model. The result shows that this technique is more competitive than isotope-labeling electrophoretic mobility shift assay (EMSA). We demonstrated that AlGaN/GaN HEMTs were highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleotide–protein interaction. url: https://www.sciencedirect.com/science/article/pii/S0925400513014378 doi: 10.1016/j.snb.2013.11.087 id: cord-279754-95zawygq author: Hsu, Yu-Chen title: Risk and Outbreak Communication: Lessons from Taiwan''s Experiences in the Post-SARS Era date: 2017-04-01 words: 3387.0 sentences: 161.0 pages: flesch: 46.0 cache: ./cache/cord-279754-95zawygq.txt txt: ./txt/cord-279754-95zawygq.txt summary: After the SARS outbreak, Taiwan''s Centers for Disease Control (Taiwan CDC) followed the WHO outbreak communication guidelines on trust, early announcements, transparency, informing the public, and planning, in order to reform its risk communication systems. After the SARS outbreak, Taiwan''s Centers for Disease Control (CDC) followed the WHO outbreak communication guidelines-on trust, announcing early, transparency, informing the public, and planning-to reform its risk communication systems. In order to analyze the efficiency of risk communication on influenza vaccination, Taiwan CDC has monitored the toll-free hotline to identify topics that are of most concern to the public (eg, who are the target population, where to get the shot, adverse event reporting). The government of Taiwan has demonstrated considerable improvement in its risk communication practices during public health emergencies since the SARS outbreak in 2003. abstract: In addition to the impact of a disease itself, public reaction could be considered another outbreak to be controlled during an epidemic. Taiwan's experience with SARS in 2003 highlighted the critical role played by the media during crisis communication. After the SARS outbreak, Taiwan's Centers for Disease Control (Taiwan CDC) followed the WHO outbreak communication guidelines on trust, early announcements, transparency, informing the public, and planning, in order to reform its risk communication systems. This article describes the risk communication framework in Taiwan, which has been used to respond to the 2009-2016 influenza epidemics, Ebola in West Africa (2014-16), and MERS-CoV in South Korea (2015) during the post-SARS era. Many communication strategies, ranging from traditional media to social and new media, have been implemented to improve transparency in public communication and promote civic engagement. Taiwan CDC will continue to maintain the strengths of its risk communication systems and resolve challenges as they emerge through active evaluation and monitoring of public opinion to advance Taiwan's capacity in outbreak communication and control. Moreover, Taiwan CDC will continue to implement the IHR (2005) and to promote a global community working together to fight shared risks and to reach the goal of “One World, One Health.” url: https://www.ncbi.nlm.nih.gov/pubmed/28418746/ doi: 10.1089/hs.2016.0111 id: cord-307460-v6xgkg1p author: Hsu, Yu-Lung title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan date: 2020-06-13 words: 220.0 sentences: 26.0 pages: flesch: 64.0 cache: ./cache/cord-307460-v6xgkg1p.txt txt: ./txt/cord-307460-v6xgkg1p.txt summary: key: cord-307460-v6xgkg1p authors: Hsu, Yu-Lung; Lin, Hsiao-Chuan; Wei, Hsiu-Mei; Lai, Huan-Cheng; Hwang, Kao-Pin title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan cord_uid: v6xgkg1p Therefore, we believe that, all things being equal, the transmission of SARS CoV-2 differs 32 between tropical and non-tropical regions. This is because countries greatly 34 differ with respect to population density, disease burden, health care quality, infection control Stability of SARS coronavirus in human specimens and 42 environment and its sensitivity to heating and UV irradiation Epidemiology and clinical 45 presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 46 3 years using a novel multiplex real-time PCR method The pediatric burden of human coronaviruses 49 evaluated for twenty years Coronaviruses in the Pediatric Population Hsu 57 and Hsiao-Chuan Lin interpreted data Distribution of COVID-19 patients around the world 64 Distribution of local cases of COVID-19 in Taiwan abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32544431/ doi: 10.1016/j.tmaid.2020.101790 id: cord-321691-46la29tm author: Hsueh, Po-Ren title: SARS Antibody Test for Serosurveillance date: 2004-09-17 words: 2800.0 sentences: 133.0 pages: flesch: 44.0 cache: ./cache/cord-321691-46la29tm.txt txt: ./txt/cord-321691-46la29tm.txt summary: A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. Such surveillance may be key to tracking the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) because mild and asymptomatic cases of SARS-CoV infection that do not meet the World Health Organization''s case definition (1) have been identified by immunoassays (2) (3) (4) , and SARS-CoV-like viruses have been isolated from wild mammals (5) . The diagnostic sensitivity of the peptide ELISA was 100% on a panel of 69 convalescent-phase serum samples from SARS patients provided as a reference panel by the Center for Disease Control, Department of Health, Taiwan. The peptide ELISA was evaluated for specificity on serum samples drawn from patients associated with typical and atypical respiratory pathogens other than SARS-CoV (National Taiwan University Hospital). abstract: A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. The assay was developed by epitope mapping, using synthetic peptides from the spike, membrane, and nucleocapsid protein sequences of SARS-associated coronavirus. The new peptide ELISA consistently detected seroconversion by week 2 of onset of fever, and seropositivity remained through day 100. Specificity was 100% on normal blood donor samples, on serum samples associated with infection by other pathogens, and on an interference panel. The peptide-based test has advantages of safety, standardization, and automation over previous immunoassays for SARS. The assay was used for a retrospective survey of healthy healthcare workers in Taiwan who treated SARS patients. Asymptomatic seroconversions were detected in two hospitals that had nosocomial disease. url: https://www.ncbi.nlm.nih.gov/pubmed/15498156/ doi: 10.3201/eid1009.040101 id: cord-294854-rvrgcugn author: Hu, Biying title: The cytokine storm and COVID‐19 date: 2020-06-27 words: 2781.0 sentences: 187.0 pages: flesch: 47.0 cache: ./cache/cord-294854-rvrgcugn.txt txt: ./txt/cord-294854-rvrgcugn.txt summary: An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread throughout the world 1 . It has been reported that a cytokine storm is Accepted Article associated with the deterioration of many infectious diseases, including severe acute respiratory syndrome (SARS) 3 and Middle East respiratory syndrome (MERS) 4 . It is considered to be the main cause of disease severity and death in Accepted Article COVID-19 patients 5 , and is related to high levels of circulating cytokines, severe lymphopenia, thrombosis, and massive mononuclear cell infiltration in multiple organs 21 . Anakinra, an IL-1 receptor antagonist that blocks the activity of pro-inflammatory cytokines IL-1α and IL-1β, has been reported to improve respiratory function and increase the survival rate of COVID-19 patients 73 . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of Accepted Article coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) abstract: Coronavirus disease 2019 (COVID‐19), which began in Wuhan, China in December 2019 has caused a large global pandemic and poses a serious threat to public health. More than four million cases of COVID‐19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), have been confirmed as of May 11, 2020. SARS‐CoV‐2 is a highly pathogenic and transmissible coronavirus that primarily spreads through respiratory droplets and close contact. A growing body of clinical data suggests that a cytokine storm is associated with COVID‐19 severity and is also a crucial cause of death from COVID‐19. In the absence of antivirals and vaccines for COVID‐19, there is an urgent need to understand the cytokine storm in COVID‐19. Here, we have reviewed the current understanding of the features of SARS‐CoV‐2 and the pathological features, pathophysiological mechanisms, and treatments of the cytokine storm induced by COVID‐19. Additionally, we suggest that the identification and treatment of the cytokine storm are important components for rescuing patients with severe COVID‐19. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32592501/ doi: 10.1002/jmv.26232 id: cord-353914-zzla4frm author: Hu, Bo title: Cardiac involvement of COVID-19: Looking forward to novel discoveries and clinically valuable evidence() date: 2020-09-01 words: 423.0 sentences: 36.0 pages: flesch: 42.0 cache: ./cache/cord-353914-zzla4frm.txt txt: ./txt/cord-353914-zzla4frm.txt summary: Since the Coronavirus Disease-2019 (COVID-19) outbreak, several clinical studies [1] [2] [3] have discovered the evidence of myocardial injury as significant elevation of cardiac troponin among the infected patients, especially those required intensive care. From our experiences, myocardial injury is almost in COVID-19 patients of severe and critical types and/or with underlying cardiovascular diseases [1] [2] [3] . Currently, the number of infected people has reached 3.6 million, while cases with myocarditis were extremely rare in the published clinical studies and case reports. In line with our study [1] , although SARS-CoV-2 infection can be detected in myocardial tissue, cardiac involvement of COVID-19 is possibly more integrated with systemic disorders. Clinical investigation of SARS-CoV-2 myocarditis should focus on young patients without any underlying cardiovascular diseases. We look forward to novel discoveries and clinically valuable evidence regarding to cardiac involvement of COVID-19. Suspected myocardial injury in patients with COVID-19: evidence from front-line clinical observation in Wuhan, China abstract: nan url: https://doi.org/10.1016/j.ijcard.2020.05.049 doi: 10.1016/j.ijcard.2020.05.049 id: cord-304480-azosg1tt author: Hu, Donghua title: Studies on the interactions of Ti-containing polyoxometalates (POMs) with SARS-CoV 3CL(pro) by molecular modeling date: 2006-09-05 words: 2363.0 sentences: 162.0 pages: flesch: 62.0 cache: ./cache/cord-304480-azosg1tt.txt txt: ./txt/cord-304480-azosg1tt.txt summary: The ligand-receptor interaction of POMs/3CL pro generally causes energy decreasing and conformation changing; accordingly these changes should influence the enzyme catalytic activity of the SARS-CoV 3CL pro . What is more, during the course of POMs/SARS-CoV 3CL pro complex formation, the atom charge loading properties and the electrostatic characteristic are very vital elements that keep the enzyme-inhibitor interaction. The investigation results show that: (1) POMs interact with the 3CL pro receptor in enzyme active site region, with several polarized residues including the enzyme catalyst residues of His41/Cys145; (2) The total binding energies of the five POM/SARS-CoV 3CL pro complexes lead to the following order of complex stability: 1,2-PTi 2 /3CL pro > 1,4-PTi 2 /3CL pro > 1,5-PTi 2 /3CL pro > 1,6-PTi 2 /3CL pro > 1,11-PTi 2 /3CL pro . (3) Electrostatic energy and hydrogen bond interaction contribute much to the enzyme-inhibitor complex formation between POMs and SARS-CoV 3CL pro . abstract: Ti-containing α-Keggin polyoxometalates (POMs) have been proved with properties of both anti-tumor and anti-HIV (human immunodeficiency virus). The potential anti-SARS (severe acute respiratory syndrome) activity of the POMs [α-PTi(2)W(10)O(40)](7−) isomers was investigated in this paper by molecular modeling method. The SARS 3c like protease, namely the SARS 3CL(pro) is the key function protease for virus replication as well as transcription and thus can be taken as one of the key targets for anti-SARS drug design. Affinity/Insight II was used to explore possible binding locations for POMs/3CL(pro) interaction. Charges in the POMs were obtained from density-functional theory (DFT) method. The results show that POMs bind with 3CL(pro) in the active site region with high affinity; POMs are more prone to bind with 3CL(pro) than with some organic compounds; for the POMs/3CL(pro)complex, the OTi(2) in POMs is the vital element for electrostatic interaction, and the electrostatic binding energy is strong enough to keep the complex stable. url: https://api.elsevier.com/content/article/pii/S0162013406002315 doi: 10.1016/j.jinorgbio.2006.08.013 id: cord-292880-zegtr19k author: Hu, Fuying title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 date: 2020-08-13 words: 3794.0 sentences: 242.0 pages: flesch: 52.0 cache: ./cache/cord-292880-zegtr19k.txt txt: ./txt/cord-292880-zegtr19k.txt summary: title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 Here, we reviewed medical records of patients with laboratory-confirmed COVID-19 in Tianmen, a city in Hubei province adjacent to Wuhan, to describe the clinical features, epidemiological characteristics and risk factors associated with prolonged viral shedding of COVID-19. Time from illness onset to hospital admission (P < 0.001), radiographic extent (P = 0.002), lymphocyte count (P = 0.038), albumin (P = 0.046), hs-CRP (P = 0.010), and prescription of antibiotics (P < 0.001), arbidol (P = 0.020), oseltamivir (P <0.001), corticosteroid (P < 0.001) and immunoglobulin (P < 0.001) were also associated with prolonged viral shedding. In the present study, we described the epidemiological and clinical characteristics of patients in Tianmen city, Hubei province, and concluded that delayed admission, and prescription of corticosteroid and oseltamivir were significantly associated with prolonged viral shedding. abstract: INTRODUCTION: Coronavirus Disease 2019 (COVID‐19) has spread worldwide, and it has reached to more than 14.5 million cases. Although Hubei province is the epicenter of China, little is known about epidemiological and clinical features of COVID‐19 in other areas in Hubei province around Wuhan. In addition, the virological data, particularly the factors associated with viral shedding of COVID‐19 has not been well described. OBJECTIVE: To describe the epidemiological and clinical features of patients with COVID‐19 in Tianmen city, and identify risk factors associated with prolonged viral shedding of COVID‐19. METHODS: Inpatients with COVID‐19 admitted before February 9, 2020 were included. Characteristics were compared between patients with early and late viral RNA shedding. Multivariate cox regression model was used to investigate variables associated with prolonged viral shedding. RESULTS: One hundred and eighty‐three patients were included. About 8.2% patients were categorized as critical degree of severity. All patients received antiviral therapy, with arbidol and interferon being the commonest. About 38.3% and 16.9% patients were treated with corticosteroid and immunoglobulin, respectively. Time from onset to admission (HR = 0.829, P < 0.001), and administration of corticosteroid (HR = 0.496, P = 0.002), arbidol (HR = 2.605, P = 0.008) and oseltamivir (HR = 0.416, P < 0.001) were independently associated with duration of viral shedding. CONCLUSION: Symptoms of patients from Tianmen are relatively mild. Treatment should be started as early as possible, but corticosteroid and oseltamivir should be initiated with caution. In addition, clinical trials on arbidol should be conducted to demonstrate its effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/32750201/ doi: 10.1111/crj.13243 id: cord-277739-eb4z3u66 author: Hu, Ke title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial date: 2020-05-16 words: 3665.0 sentences: 195.0 pages: flesch: 48.0 cache: ./cache/cord-277739-eb4z3u66.txt txt: ./txt/cord-277739-eb4z3u66.txt summary: title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial In the latest publication, Lianhuaqingwen (LH) capsule (Shijiazhuang Yiling Pharmaceutical Co. Ltd., Shijiazhuang, China) was a manufactured product of the traditional Chinese medicine formula marketed in China that could significantly inhibit SARS-CoV-2 replication, alter the viral morphology and confer anti-inflammatory activity in vitro . On the basis of usual treatment, we sought to explore the safety and efficacy of LH capsules in patients with Covid-19 by conducting a multicenter randomized controlled trial in mainland China. Eligibility criteria consisted of the following: 1) Laboratory-confirmed cases with according to the Protocol for Diagnosis and Treatment of Novel Coronarvirus Pneumonia (4 th edition) which was issued by the National Health Commission (General Office Of The National Health And Health Commission, 2020) (Panel 1); 2) Being symptomatic (either having fever, coughing, or fatigue) plus radiologic abnormalities consistent with pneumonia; 3) Patients aged 18 years or greater of either sex. abstract: BACKGROUND: Coronavirus disease 2019 (Covid-19) has resulted in a global outbreak. Few existing targeted medications are available. Lianhuaqingwen (LH) capsule, a repurposed marketed Chinese herb product, has been proven effective for influenza. PURPOSE: To determine the safety and efficacy of LH capsule in patients with Covid-19. METHODS: We did a prospective multicenter open-label randomized controlled trial on LH capsule in confirmed cases with Covid-19. Patients were randomized to receive usual treatment alone or in combination with LH capsules (4 capsules, thrice daily) for 14 days. The primary endpoint was the rate of symptom (fever, fatigue, coughing) recovery. RESULTS: We included 284 patients (142 each in treatment and control group) in the full-analysis set. The recovery rate was significantly higher in treatment group as compared with control group (91.5% vs. 82.4%, P=0.022). The median time to symptom recovery was markedly shorter in treatment group (median: 7 vs. 10 days, P<0.001). Time to recovery of fever (2 vs. 3 days), fatigue (3 vs. 6 days) and coughing (7 vs. 10 days) was also significantly shorter in treatment group (all P<0.001). The rate of improvement in chest computed tomographic manifestations (83.8% vs. 64.1%, P<0.001) and clinical cure (78.9% vs. 66.2%, P=0.017) was also higher in treatment group. However, both groups did not differ in the rate of conversion to severe cases or viral assay findings (both P>0.05). No serious adverse events were reported. CONCLUSION: In light of the safety and effectiveness profiles, LH capsules could be considered to ameliorate clinical symptoms of Covid-19. url: https://www.sciencedirect.com/science/article/pii/S0944711320300738?v=s5 doi: 10.1016/j.phymed.2020.153242 id: cord-269825-k685efoh author: Hu, Parker title: Early comprehensive testing for COVID-19 is essential to protect trauma centers date: 2020-07-01 words: 3286.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-269825-k685efoh.txt txt: ./txt/cord-269825-k685efoh.txt summary: We recorded the daily number of trauma patients diagnosed with SARS-CoV-2 infection, the presence of clinical symptoms or radiological signs of COVID-19, and the results of verbal symptom screen (for new admissions). Positive verbal screen results, presence of ground glass opacities on admission chest CT, and presence of clinical symptoms were not significantly different in patients with or without SARS-CoV-2 infection (p > 0.05). [14] [15] [16] While the position is becoming well defined for those patients with known, established disease, there is little available data to guide trauma centers that may be required to treat significant numbers of asymptomatic infected new patients during this ongoing crisis. The screening and testing procedure in the trauma bay subsequently identified four additional SARS-CoV-2-infected patients. All new trauma patients should be regarded as SARS-CoV-2 positive until testing can be completed to minimize exposures to staff and limit nosocomial spread of disease. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic presents a threat to health care systems worldwide. Trauma centers may be uniquely impacted, given the need for rapid invasive interventions in severely injured and the growing incidence of community infection. We discuss the impact that SARS-CoV-2 has had in our trauma center and our steps to limit the potential exposures. METHODS: We performed a retrospective evaluation of the trauma service, from March 16 to 30, following the appearance of SARS-CoV-2 in our state. We recorded the daily number of trauma patients diagnosed with SARS-CoV-2 infection, the presence of clinical symptoms or radiological signs of COVID-19, and the results of verbal symptom screen (for new admissions). The number of trauma activations, admissions, and census, as well as staff exposures and infections, was recorded daily. RESULTS: Over the 14-day evaluation period, we tested 85 trauma patients for SARS-CoV-2 infection, and 21 (25%) were found to be positive. Sixty percent of the patients in the trauma/burn intensive care unit were infected with SARS-CoV-2. Positive verbal screen results, presence of ground glass opacities on admission chest CT, and presence of clinical symptoms were not significantly different in patients with or without SARS-CoV-2 infection (p > 0.05). Many infected patients were without clinical symptoms (9/21, 43%) or radiological signs on admission (18/21, 86%) of COVID-19. CONCLUSION: Forty-five percent of trauma patients are asymptomatic at the time of SARS-CoV-2 diagnosis. Respiratory symptoms, as well as verbal screening (recent fevers, shortness of breath, cough, international travel, and close contact with known SARS-CoV-2 carriers), are inaccurate in the trauma population. These findings demonstrate the need for comprehensive rapid testing of all trauma patients upon presentation to the trauma bay. LEVEL OF EVIDENCE: Diagnostic tests or criteria, level III, Therapeutic/care management, level IV. url: https://doi.org/10.1097/ta.0000000000002870 doi: 10.1097/ta.0000000000002870 id: cord-340163-ex03l0pc author: Hu, Tingting title: A comparison of COVID-19, SARS and MERS date: 2020-08-19 words: 7908.0 sentences: 459.0 pages: flesch: 53.0 cache: ./cache/cord-340163-ex03l0pc.txt txt: ./txt/cord-340163-ex03l0pc.txt summary: In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The latest diagnostic criteria of COVID-19, SARS and MERS including clinical presentations, labora tory diagnosis and radiological feature Latest treatment and prevention methods of Published in a peer-reviewed article Availability of the full text publication Availability of the paper in English According to a study among 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China, the male-to-female ratio was 1.06:1, and the median age was 56 years (interquartile range, 42-68; range, 22-92 years) (Wu & McGoogan, 2020; Wang et al., 2020) . CXR findings In the early phase, CXR of COVID-19 patients is not highly recommended for clinical diagnosis because of its low sensitivity in detecting SARS-CoV-2 pneumonia. abstract: In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 19 May 2020, a total of 4,731,458 individuals were reported as infected with SARS-CoV-2 among 213 countries, areas or territories with recorded cases, and the overall case-fatality rate was 6.6% (316,169 deaths among 4,731,458 recorded cases), according to the World Health Organization. Studies have shown that SARS-CoV-2 is notably similar to (severe acute respiratory syndrome coronavirus) SARS-CoV that emerged in 2002–2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) that spread during 2012, and these viruses all contributed to global pandemics. The ability of SARS-CoV-2 to rapidly spread a pneumonia-like disease from Hubei Province, China, throughout the world has provoked widespread concern. The main symptoms of coronavirus disease 2019 (COVID-19) include fever, cough, myalgia, fatigue and lower respiratory signs. At present, nucleic acid tests are widely recommended as the optimal method for detecting SARS-CoV-2. However, obstacles remain, including the global shortage of testing kits and the presentation of false negatives. Experts suggest that almost everyone in China is susceptible to SARS-CoV-2 infection, and to date, there are no effective treatments. In light of the references published, this review demonstrates the biological features, spread, diagnosis and treatment of SARS-CoV-2 as a whole and aims to analyse the similarities and differences among SARS-CoV-2, SARS-CoV and MERS-CoV to provide new ideas and suggestions for prevention, diagnosis and clinical treatment. url: https://doi.org/10.7717/peerj.9725 doi: 10.7717/peerj.9725 id: cord-277014-iz8jo44e author: Hu, Weihua title: Disorders of sodium balance and its clinical implications in COVID-19 patients: a multicenter retrospective study date: 2020-10-16 words: 3643.0 sentences: 202.0 pages: flesch: 43.0 cache: ./cache/cord-277014-iz8jo44e.txt txt: ./txt/cord-277014-iz8jo44e.txt summary: This study indicates that severity of the disease, the length of stay in the hospital of surviving patients, and mortality were higher among COVID-19 patients with sodium balance disorders. CONCLUSION: Sodium balance disorder, particularly hyponatremia, is a common condition among hospitalized patients with COVID-19 in Hubei, China, and it is associated with a higher risk of severe illness and increased in-hospital mortality. reported hyponatremia to be much common (50%) amongst hospitalized COVID-19 patients in the United States [13] , and recently study further suggested that serum sodium concentration was inversely correlated with IL-6, and hyponatremia was associated with a more severe outcome of COVID-19 disease [14] . The associative disorders of serum sodium balance, their clinical characteristics, severity, and outcomes in SARS-CoV-2 infected patients have not been established. It was revealed that disease severity, the length of hospital stay for surviving patients, and mortality were high among COVID-19 patients with sodium balance disorders. abstract: BACKGROUND: The worldwide spread of SARS-CoV-2 has infected millions of people leading to over 0.3 million mortalities. The disruption of sodium homeostasis, tends to be a common occurrence in patients with COVID-19. METHODS AND RESULTS: A total of 1,254 COVID-19 patients comprising 124 (9.9%) hyponatremic patients (under 135 mmol/L) and 30 (2.4%) hypernatremic patients (over 145 mmol/L) from three hospitals in Hubei, China, were enrolled in the study. The relationships between sodium balance disorders in COVID-19 patients, its clinical features, implications, and the underlying causes were presented. Hyponatremia patients were observed to be elderly, had more comorbidities, with severe pneumonic chest radiographic findings. They were also more likely to have a fever, nausea, higher leukocyte and neutrophils count, and a high sensitivity C-reactive protein (HS-CRP). Compared to normonatremia patients, renal insufficiency was common in both hyponatremia and hypernatremia patients. In addition, hyponatremia patients required extensive treatment with oxygen, antibiotics, and corticosteroids. The only significant differences between the hypernatremia and normonatremia patients were laboratory findings and clinical complications, and patients with hypernatremia were more likely to use traditional Chinese medicine for treatment compared to normonatremia patients. This study indicates that severity of the disease, the length of stay in the hospital of surviving patients, and mortality were higher among COVID-19 patients with sodium balance disorders. CONCLUSION: Sodium balance disorder, particularly hyponatremia, is a common condition among hospitalized patients with COVID-19 in Hubei, China, and it is associated with a higher risk of severe illness and increased in-hospital mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/33064253/ doi: 10.1007/s11739-020-02515-9 id: cord-334518-mjr6u7ak author: Hu, X. title: Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection date: 2020-05-23 words: 5158.0 sentences: 294.0 pages: flesch: 51.0 cache: ./cache/cord-334518-mjr6u7ak.txt txt: ./txt/cord-334518-mjr6u7ak.txt summary: To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on the serial upper respiratory samples from an asymptomatic carrier, and the insistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. . https://doi.org/10.1101/2020.05.20.20108530 doi: medRxiv preprint As described in the Materials and Methods, we developed a rapid and simple RT-LAMP assay to detect SARS-CoV-2 RNA, and positive reactions resulted in a color change from purple to blue due to decreased magnesium concentration in the presence of extensive Bst DNA polymerase activity, while negative reactions retained the purple color. abstract: Background The outbreak of SARS-CoV-2 urgently requires sensitive and convenient COVID-19 diagnostics to assure the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2 in both qualified laboratories and point-of-care settings. Methods Patients with suspected COVID-19 and close contacts between Jan 26 and April 8, 2020, were recruited from two hospitals. Respiratory samples were collected and tested with LAMP and the results were compared with those obtained by RT-qPCR. The inconsistent samples between these two methods were subjected to next-generation sequencing for confirmation. In addition, we tested the RT-LAMP on an asymptomatic COVID-19 carrier and patients with other respiratory viral infections. Results We finally collected a cohort of 129 cases (329 nasopharyngeal swabs) and the independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). RT-LAMP was validated to be accurate (overall sensitivity and specificity: 88.89% and 99.00%; positive and negative predictive values: 94.74% and 97.78%) and diagnostically useful (positive and negative likelihood ratios: 88.89 and 0.11). RT-LAMP showed an increased sensitivity (88.89% vs 81.48%) and high consistency (kappa 0.92) compared with RT-qPCR for SARS-CoV-2 screening while requiring only constant temperature heating and visual inspection. The median time required for RT-LAMP was less than 1 h from sample to result. Further analyses indicated that RT-LAMP was feasible for asymptomatic patients and did not cross-react with other respiratory pathogen infections. Conclusion The RT-LAMP assay offers a rapid, sensitive and straightforward detection for SARS-CoV-2 infection, which could aid the expansion of COVID-19 testing in the public domain and hospitals. url: https://doi.org/10.1101/2020.05.20.20108530 doi: 10.1101/2020.05.20.20108530 id: cord-294069-7zr77r71 author: Hu, Xiaowen title: The distribution of SARS-CoV-2 contamination on the environmental surfaces during incubation period of COVID-19 patients date: 2020-09-30 words: 2527.0 sentences: 136.0 pages: flesch: 50.0 cache: ./cache/cord-294069-7zr77r71.txt txt: ./txt/cord-294069-7zr77r71.txt summary: In this study, we sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the environmental surfaces during the incubation period of coronavirus disease 2019 (COVID-19) patients. In addition, we synchronously sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the SARS-CoV-2 distribution on the environmental surfaces during the incubation period of COVID-19 patients. Then, medical staffs stayed in hotel immediately sampled their nasopharyngeal swabs and environmental surfaces, and transferred them to the hospital for further diagnosis Additionally, the frequency of washing behaviors of patients at the quarantine room, including face washing, hands washing, tooth brushing, bathing and excrement, were shown in Table 2 . Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient abstract: Roles of environmental factors in transmission of COVID-19 have been highlighted. In this study, we sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the environmental surfaces during the incubation period of coronavirus disease 2019 (COVID-19) patients. Fifteen sites were sampled from the quarantine room, distributing in the functional areas such as bedroom, bathroom and living room. All environmental surface samples were collected with sterile polyester-tipped applicator pre-moistened in viral transport medium and tested for SARS-CoV-2. Overall, 34.1% of samples were detected positively for SARS-CoV-2. The positive rates of Patient A, B and C, were 46.2%, 0 and 61.5%, respectively. SARS-CoV-2 was detected positively in bedroom and bathroom, with the positive rate of 50.0% and 46.7%, respectively. In contrast, living room had no positive sample detected. Environmental contamination of SARS-CoV-2 distributes widely during the incubation period of CCOVID-19, and the positive rates of SARS-CoV-2 on environmental surfaces are relatively high in bathroom and bedroom. url: https://doi.org/10.1016/j.ecoenv.2020.111438 doi: 10.1016/j.ecoenv.2020.111438 id: cord-312652-zhccmfgw author: Hu, Xiumei title: Impact of Heat-Inactivation on the detection of SARS-CoV-2 IgM and IgG Antibody by ELISA date: 2020-06-20 words: 3001.0 sentences: 176.0 pages: flesch: 50.0 cache: ./cache/cord-312652-zhccmfgw.txt txt: ./txt/cord-312652-zhccmfgw.txt summary: According to Chinese Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (Trial Version 7), SARS-CoV-2 specific IgM becomes detectable around 3-5 days after onset and IgG reaches a titration of at least 4-fold increase during convalescence compared with the acute [9] . In order to establish a safe and accurate method for detecting SARS-CoV-2 specific antibodies, we retrospectively assessed the impact of sera heat-inactivation at 56℃ for 30 minutes on the levels of SARS-CoV-2 IgM or IgG antibodies. Therefore, our analysis provide evidence that sera inactivated by heating at 56℃ for 30 minutes could reduce the risk of virus contamination, and would not impair the detection efficacy of SARS-CoV-2 IgM or IgG testing using this ELISA assay. In summary, sera inactivated by heating at 56℃ for 30 minutes could minimize the risk of virus contamination and did not impair the positive detection rate using SARS-CoV-2 antibody detection kit (ELISA-immunoassay) and eventually represents a valuable contribution to a safer COVID-19 serological diagnosis. abstract: BACKGROUND: To establish a safe and accurate method for detecting SARS-CoV-2 IgM and IgG, we assessed the impact of sera after heat-inactivation on the SARS-CoV-2 IgM and IgG levels measured by ELISA-immunoassay. METHODS: The serum samples of 62 patients with COVID-19 and 18 healthy controls were collected in Hankou’s Hospital of Wuhan from February 27 to March 6, 2020. Before and after the samples were inactivated, the levels of IgM and IgG antibodies were measured. RESULTS: The indexes of antibodies after inactivated were significantly higher than those in fresh sera, while the positive rates in all participants or in patients with COVID-19 did not change. The positive coincidence rate, negative coincidence rate and total coincidence rate of IgM antibodies before and after inactivation were 100.00% (55/55), 96.00% (24/25) and 98.75% (79/80), respectively (κ=0.971, P<0.001), while those for IgG antibodies were 98.21% (55/56), 91.67% (22/24) and 98.75% (79/80) respectively (κ=0.910, P<0.001). These results showed a good consistency. CONCLUSIONS: Heating-activation does not decrease the diagnostic efficacy of SARS-CoV-2 IgM or IgG antibodies. Sera inactivated by heating at 56℃ for 30 minutes should be recommended to minimize the risk of virus contamination of laboratory staff. url: https://doi.org/10.1016/j.cca.2020.06.032 doi: 10.1016/j.cca.2020.06.032 id: cord-346555-3hrbea6d author: Hu, Xiumei title: Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS‐CoV‐2 date: 2020-06-28 words: 1187.0 sentences: 80.0 pages: flesch: 50.0 cache: ./cache/cord-346555-3hrbea6d.txt txt: ./txt/cord-346555-3hrbea6d.txt summary: Since many coronaviruses are sensitive to heat, heating inactivation of samples at 56°C prior to testing is considered a possible method to reduce the risk of transmission, but the effect of heating on the measurement of SARS‐CoV‐2 antibodies is still unclear. CONCLUSION: Our results indicate that heat inactivation of serum at 56°C for 30 minutes interferes with the immunoanalysis of antibodies to SARS‐CoV‐2. The current outbreak of coronavirus disease 2019 (COVID19) caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is posing a serious threat to public health. The signal intensity of the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before and after heat inactivation The changes in the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before (blue dot) and after heat inactivation (red dot) Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS-CoV-2 abstract: BACKGROUND: The detection of serum antibodies to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is emerging as a new tool for the coronavirus disease 2019 (COVID‐19) diagnosis. Since many coronaviruses are sensitive to heat, heating inactivation of samples at 56°C prior to testing is considered a possible method to reduce the risk of transmission, but the effect of heating on the measurement of SARS‐CoV‐2 antibodies is still unclear. METHODS: By comparing the levels of SARS‐CoV‐2 antibodies before and after heat inactivation of serum at 56°C for 30 minutes using a quantitative fluorescence immunochromatographic assay RESULTS: We showed that heat inactivation significantly interferes with the levels of antibodies to SARS‐CoV‐2. The IgM levels of all the 34 serum samples (100%) from COVID‐19 patients decreased by an average level of 53.56%. The IgG levels were decreased in 22 of 34 samples (64.71%) by an average level of 49.54%. Similar changes can also be observed in the non–COVID‐19 disease group (n = 9). Of note, 44.12% of the detected IgM levels were dropped below the cutoff value after heating, suggesting heat inactivation can lead to false‐negative results of these samples. CONCLUSION: Our results indicate that heat inactivation of serum at 56°C for 30 minutes interferes with the immunoanalysis of antibodies to SARS‐CoV‐2. Heat inactivation prior to immunoanalysis is not recommended, and the possibility of false‐negative results should be considered if the sample was pre‐inactivated by heating. url: https://doi.org/10.1002/jcla.23411 doi: 10.1002/jcla.23411 id: cord-276957-pk33dl8q author: Hu, Xuejiao title: Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection date: 2020-08-26 words: 5649.0 sentences: 287.0 pages: flesch: 47.0 cache: ./cache/cord-276957-pk33dl8q.txt txt: ./txt/cord-276957-pk33dl8q.txt summary: To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. The detection results obtained using the RT-LAMP assay showed good concordance with those obtained using the RT-qPCR In Cohort I, 35 of 37 nasopharyngeal swabs from 24 COVID-19 patients were confirmed to be SARS-CoV-2 positive according to the criteria of RT-qPCR (28 samples) and NGS confirmation (7 samples) (see Table S3 in the supplemental material). Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on serial upper respiratory samples from an asymptomatic carrier, and the inconsistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak urgently necessitates sensitive and convenient COVID-19 diagnostics for the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2. Patients with suspected COVID-19 and close contacts were recruited from two hospitals between 26 January and 8 April 2020. Respiratory samples were collected and tested using RT-LAMP, and the results were compared with those obtained by reverse transcription-quantitative PCR (RT-qPCR). Samples yielding inconsistent results between these two methods were subjected to next-generation sequencing for confirmation. RT-LAMP was also applied to an asymptomatic COVID-19 carrier and patients with other respiratory viral infections. Samples were collected from a cohort of 129 cases (329 nasopharyngeal swabs) and an independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). The RT-LAMP assay was validated to be accurate (overall sensitivity and specificity of 88.89% and 99.00%, respectively) and diagnostically useful (positive and negative likelihood ratios of 88.89 and 0.11, respectively). RT-LAMP showed increased sensitivity (88.89% versus 81.48%) and high consistency (kappa, 0.92) compared to those of RT-qPCR for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection. The time required for RT-LAMP was less than 1 h from sample preparation to the result. In addition, RT-LAMP was feasible for use with asymptomatic patients and did not cross-react with other respiratory pathogens. The developed RT-LAMP assay offers rapid, sensitive, and straightforward detection of SARS-CoV-2 infection and may aid the expansion of COVID-19 testing in the public domain and hospitals. IMPORTANCE We developed a visual and rapid reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay targeting the S gene for SARS-CoV-2 infection. The strength of our study was that we validated the RT-LAMP assay using 481 clinical respiratory samples from two prospective cohorts of suspected COVID-19 patients and on the serial samples from an asymptomatic carrier. The developed RT-LAMP approach showed an increased sensitivity (88.89%) and high consistency (kappa, 0.92) compared with those of reverse transcription-quantitative PCR (RT-qPCR) for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection, facilitating SARS-CoV-2 screening in well-equipped labs as well as in the field. The time required for RT-LAMP was less than 1 h from sample preparation to the result (more than 2 h for RT-qPCR). This study showed that the RT-LAMP assay was a simple, rapid, and sensitive approach for SARS-CoV-2 infection and can facilitate COVID-19 diagnosis, especially in resource-poor settings. url: https://www.ncbi.nlm.nih.gov/pubmed/32848011/ doi: 10.1128/msphere.00808-20 id: cord-309898-sju15hev author: Hu, Yiwen title: Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date: 2020-11-02 words: 4295.0 sentences: 219.0 pages: flesch: 50.0 cache: ./cache/cord-309898-sju15hev.txt txt: ./txt/cord-309898-sju15hev.txt summary: The key result of our work is that both, the overall flexibility of upward RBD and the mobility ratio of RBDs in different conformations, represent two significant factors that show a positive scaling with virus lethality and an inverse correlation with the infection rate. Figure 2 depicts data that shows that the lowest-frequency normal modes of MERS-CoV, SARS-CoV and SARS-CoV-2 spike proteins are all associated with a swing motion of upward receptor-binding domain (RBD) to different extents. Figure 4 provides a correlation diagram for MERS-CoV, SARS-CoV and SARS-CoV-2 spike protein, where the overall flexibility of upward RBD is evaluated by the average fluctuation of open-state RBD and the mobility ratio is quantified as the ratio of maximum fluctuations over upward and downward RBDs. The data shows that both factors have positive correlation with case fatality rate and inverse relationship with the virus infectivity. abstract: The novel coronavirus disease, COVID-19, has spread rapidly around the world. Its causative virus, SARS-CoV-2, enters human cells through the physical interaction between the receptor-binding domain (RBD) of its spike protein and the human cell receptor ACE2. Here, we provide a novel way in understanding coronavirus spike proteins, connecting their nanomechanical features – specifically its vibrational spectrum and quantitative measures of mobility – with virus lethality and infection rate. The key result of our work is that both, the overall flexibility of upward RBD and the mobility ratio of RBDs in different conformations, represent two significant factors that show a positive scaling with virus lethality and an inverse correlation with the infection rate. Our analysis shows that epidemiological virus properties can be linked directly to pure nanomechanical, vibrational aspects, offering an alternative way of screening new viruses and mutations, and potentially exploring novel ways to prevent infections from occurring. url: https://www.ncbi.nlm.nih.gov/pubmed/33163958/ doi: 10.1016/j.matt.2020.10.032 id: cord-267533-nmgtan4e author: Hu, Zhigang title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 words: 3605.0 sentences: 214.0 pages: flesch: 46.0 cache: ./cache/cord-267533-nmgtan4e.txt txt: ./txt/cord-267533-nmgtan4e.txt summary: By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin. abstract: Coronavirus disease 2019 (COVID-19) with the infection of SARS-CoV-2 has become a serious pandemic worldwide. However, only few studies focused on risk factors of prolonged SARS-CoV-2 RNA detection among patients with COVID-19. We included 206 adult patients with laboratory-confirmed COVID-19 from two hospitals between 23 Jan and 1 April 2020. Least absolute shrinkage and selection operator (LASSO) analysis was used to screen out independent risk factors of SARS-CoV-2 RNA detection. By multivariate binomial logistic regression analysis and Cox regression analysis, we further determined the associations between SARS-CoV-2 RNA detection and potential risk factors. All patients had two negative SARS-CoV-2 tests with 33 days of median duration of SARS-CoV-2 RNA detection (interquartile range: 25.2–39 days). LASSO and binomial logistic regression analyses suggested that delayed hospital admission (adjusted OR = 3.70, 95% CI: 1.82–7.50), hypokalemia, and subpleural lesion (adjusted OR = 4.32, 95% CI: 1.10–16.97) were associated with prolonged SARS-CoV-2 RNA detection. By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. Early hospital admission shortened 5.73 days of mean duration of SARS-CoV-2 RNA detection than delayed hospital admission after adjusting confounding factors. Our study demonstrated that delayed hospital admission and subpleural lesion were associated with prolonged SARS-CoV-2 RNA detection among patients with COVID-19. The use of high-dose corticosteroids should be interpreted with extreme caution in treating COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33123934/ doi: 10.1007/s10096-020-04085-2 id: cord-342938-rzhsnkn4 author: Huang, Bo-Ruei title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan date: 2020-06-30 words: 977.0 sentences: 68.0 pages: flesch: 52.0 cache: ./cache/cord-342938-rzhsnkn4.txt txt: ./txt/cord-342938-rzhsnkn4.txt summary: title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan 1, 2 Here, we report a unique case of influenza B virus co-infection with SARS-CoV-2 in Taiwan. The co-infection of influenza virus and SARS-CoV-2 is unusual, and to date, most reported cases are from China. Beside co-infection of influenza virus, increased co-infection of other virus or bacteria had also been reported among In our case, the newly developed dry cough and fever during hospitalization was the warning sign and the subsequent chest image confirmed clinical deterioration, which prompted the initiation of hydroxychloroquine. Single dose baloxavir marboxil was also superior to oseltamivir in reducing the viral load one day after the initiation of the trial regimen in patients with uncomplicated influenza. The clinical characteristics of pneumonia patients co-infected with 2019 novel coronavirus and influenza virus in Wuhan Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1684118220301523?v=s5 doi: 10.1016/j.jmii.2020.06.011 id: cord-313028-0nhgxoim author: Huang, Chaolin title: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China date: 2020-01-24 words: 4784.0 sentences: 248.0 pages: flesch: 49.0 cache: ./cache/cord-313028-0nhgxoim.txt txt: ./txt/cord-313028-0nhgxoim.txt summary: INTERPRETATION: The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Following the pneumonia cases of unknown cause reported in Wuhan and considering the shared history of exposure to Huanan seafood market across the patients, an epidemiological alert was released by the local health authority on Dec 31, 2019, and the market was shut down on Jan 1, 2020. 16 Secondary infection was diagnosed if the patients had clinical symptoms or signs of nosocomial pneumonia or bacteraemia, and was combined with a positive culture of a new pathogen from a lower respiratory tract specimen (including the sputum, transtracheal aspirates, or bronchoalveolar lavage fluid, or from blood samples taken ≥48 h after admission). In view of the high amount of cytokines induced by SARS-CoV, 22, 24 MERS-CoV, 25, 26 and 2019-nCoV infections, corticosteroids were used frequently for treatment of patients with severe illness, for possible benefit by reducing inflammatory-induced lung injury. abstract: BACKGROUND: A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients. METHODS: All patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by WHO and the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not. FINDINGS: By Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0–58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0–13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα. INTERPRETATION: The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies. FUNDING: Ministry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission. url: https://www.sciencedirect.com/science/article/pii/S0140673620301835 doi: 10.1016/s0140-6736(20)30183-5 id: cord-322908-e3gok0ot author: Huang, Fangfang title: A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19) date: 2020-05-20 words: 5056.0 sentences: 275.0 pages: flesch: 42.0 cache: ./cache/cord-322908-e3gok0ot.txt txt: ./txt/cord-322908-e3gok0ot.txt summary: In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19. In this review, we summarized potential Chinese herbal medicines ( Table 2 ) that may treat COVID-19 by targeting proteins such as Spike protein, ACE2, 3CLpro, PLpro and RdRp. We also predicted the binding affinities between these compounds and COVID-19 related targets by molecular docking, with a focus on six compounds: quercetin, andrographolide, glycyrrhizic acid, baicalin, patchouli alcohol, and luteolin. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: The epidemic of pneumonia (COVID-19) caused by novel coronavirus (SARS-CoV-2) infection has been listed as a public health emergency of international concern by the World Health Organization (WHO), and its harm degree is defined as a global “pandemic”. At present, the efforts of various countries focus on the rapid diagnosis and isolation of patients, as well as to find a treatment that can combat the most serious impact of the disease. The number of reported COVID-19 virus infections is still increasing. Unfortunately, no drugs or vaccines have been approved for the treatment of human coronaviruses, but there is an urgent need for in-depth research on emerging human infectious coronaviruses. Clarification transmission routes and pathogenic mechanisms, and identification of potential drug treatment targets will promote the development of effective prevention and treatment measures. In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. This review summarizes the epidemiological characteristics, pathogenesis, virus structure and targeting strategies of COVID-19. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1043661820312378?v=s5 doi: 10.1016/j.phrs.2020.104929 id: cord-278951-vxrwrzlj author: Huang, Hsien-Hao title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak date: 2006-12-31 words: 2736.0 sentences: 128.0 pages: flesch: 56.0 cache: ./cache/cord-278951-vxrwrzlj.txt txt: ./txt/cord-278951-vxrwrzlj.txt summary: title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak Background The immediate and long-term impact of severe acute respiratory syndrome (SARS) outbreak on emergency department (ED) visits and hospital expenditures for these visits has not been thoroughly investigated. 14 This study found that a substantial mean reduction in the number of ED visits occurred during the SARS epidemic, with a peak of 51.6% and a mean of 32.1% (95% CI of the mean difference, 27.6-36.6%) during the 4-month (April-July) epidemic period in a designated SARS hospital in Taiwan ( Figure 1 ). The higher total cost for each patient during the SARS epidemic was primarily attributed to increases in the number of laboratory investigations, radiographic examinations, ancillary procedures and medications required ( Figure 5 ). abstract: Background The immediate and long-term impact of severe acute respiratory syndrome (SARS) outbreak on emergency department (ED) visits and hospital expenditures for these visits has not been thoroughly investigated. The objectives of this retrospective observational study investigated the impact of SARS outbreak on ED visits and the cost of these visits in a designated SARS medical center. Methods Data related to the total number of ED visits and their costs were collected for the SARS epidemic period in 2003 and the same period in the preceding year in 2002. Data collected included total number of ED visits, services provided, triage categories, and total expenditures for all patients. Data for before and during the outbreak were retrieved and compared. Results At the peak of the SARS epidemic, the reduction in daily ED visits reached 51.6% of pre-epidemic numbers (p < 0.01). In pediatric, trauma and non-trauma patients, the maximum mean decreases in number of visits were 80.0% (p < 0.01), 57.6% (p < 0.01) and 40.8% (p < 0.01), respectively. In triage 1, 2 and 3 patients, the maximum mean decreases were 18.1% (p < 0.01), 55.9% (p < 0.01) and 53.7% (p < 0.01), respectively. The maximum decrease in total costs was 37.7% (p < 0.01). The maximum mean costs per patient increased 35.9% (p < 0.01). The proportions of increases in mean costs for each patient were attributed to laboratory investigations (31.4%), radiography (21.9%) and medications (29.5%). Conclusion The SARS outbreak resulted in a marked reduction in the number of ED visits which persisted for 3 months after the end of the epidemic. Total cost of treating individual patients showed a simultaneous marked increase, while overall operational costs in the ED showed a marked decrease. The increased total cost for each patient was attributed to the increased number of diagnostic procedures to screen for possible SARS in the ED. url: https://www.ncbi.nlm.nih.gov/pubmed/16440068/ doi: 10.1016/s0929-6646(09)60106-6 id: cord-260697-oepk0b1d author: Huang, J. title: COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches date: 2020-08-01 words: 5734.0 sentences: 353.0 pages: flesch: 50.0 cache: ./cache/cord-260697-oepk0b1d.txt txt: ./txt/cord-260697-oepk0b1d.txt summary: We applied the Synthetic Minority Oversampling Technique (SMOTE) to overcome the rare recurring events in certain age groups and performed Virtual Twins (VT) analysis facilitated by random forest regression for medical treatment-recurrence classification. Here, we report the clinical, radiological, laboratory, and drug treatment findings of 93 recurring patients from 414 patients in Shenzhen, along with our machine learning approaches for identifying the best drug combinations that reduce recurring rates in all population, different age groups and obese patients. The interaction among age, hospitalization delay and drug treatment on SARS-CoV-2 recurring rate is shown in Figure 3 . Interestingly, we found out that the combination of anti-influenza virus drug, oseltamivir, with Interferon/Lopinavir/Ritonavir/Arbidol, has very good outcome (recurring rate of 0.172), supporting the hypothesis of co-infection of influenzas and SARS-CoV-2. . https://doi.org/10.1101/2020.07.29.20164699 doi: medRxiv preprint Supplement Table Table S1 : Clinical characteristics, laboratory findings, treatments, and outcomes of Covid-19 patients with and without recurrence of SARS-CoV-2 PCR positivity during hospitalization. abstract: Various medical treatments for COVID-19 are attempted. After patients are discharged, SARS-CoV-2 recurring cases are reported and the recurrence could profoundly impact patient healthcare and social economics. To date, no data on the effects of medical treatments on recurrence has been published. We analyzed the treatment data of combinations of ten different drugs for the recurring cases in a single medical center, Shenzhen, China. A total of 417 patients were considered and 414 of them were included in this study (3 deaths) with mild-to-critical COVID-19. Patients were treated by 10 different drug combinations and followed up for recurrence for 28 days quarantine after being discharged from the medical center between February and May, 2020. We applied the Synthetic Minority Oversampling Technique (SMOTE) to overcome the rare recurring events in certain age groups and performed Virtual Twins (VT) analysis facilitated by random forest regression for medical treatment-recurrence classification. Among those drug combinations, Methylprednisolone/Interferon/Lopinavir/Ritonavir/Arbidol led to the lowest recurring rate (0.133) as compared to the average recurring rate (0.203). For the younger group (age 20-27) or the older group (age 60-70), the optimal drug combinations are different, but the above combination is still the second best. For obese patients, the combination of Ribavirin/Interferon/Lopinavir/Ritonavir/Arbidol led to the lowest recurring rate for age group of 20-50, whereas the combination of Interferon/Lopinavir/Ritonavir/Arbidol led to lowest recurring rate for age group of 50-70. The insights into combinatorial therapy we provided here shed lights on the use of a combination of (biological and chemical) anti-virus therapy and/or anti-cytokine storm as a potentially effective therapeutic treatment for COVID-19. url: http://medrxiv.org/cgi/content/short/2020.07.29.20164699v1?rss=1 doi: 10.1101/2020.07.29.20164699 id: cord-301556-f3m9gwvo author: Huang, Jessie title: SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response date: 2020-09-18 words: 6737.0 sentences: 319.0 pages: flesch: 49.0 cache: ./cache/cord-301556-f3m9gwvo.txt txt: ./txt/cord-301556-f3m9gwvo.txt summary: Serially passaging these epithelial spheres generated >10 30 iAT2s per starting sorted tdTomato+ cell over 225 days in culture (Hurley et al., 2020) , generating cells that maintained expression of AT2 marker genes including surfactants as shown by single cell RNA sequencing (scRNA-Seq) ( Figure 1C -D, Figure S1 ) and providing a stable source of human primary-like AT2 cells for viral infection disease modeling. Compared to other published datasets of SARS-CoV-2 infection models in Calu-3, J o u r n a l P r e -p r o o f A549-ACE2, and primary (non-alveolar) normal human bronchial epithelium (NHBE) (Blanco-Melo et al., 2020) , iAT2s were able to uniquely capture the downregulation of AT2-specific programs, such as decreased surfactant gene expression and loss of lamellar body gene ontology (GO) terms (comparative gene set enrichment based on lung-related GO biological processes; Figure S3 ). abstract: A hallmark of severe COVID-19 pneumonia is SARS-CoV-2 infection of the facultative progenitors of lung alveoli, the alveolar epithelial type 2 cells (AT2s). However, inability to access these cells from patients, particularly at early stages of disease, limits an understanding of disease inception. Here we present an in vitro human model that simulates the initial apical infection of alveolar epithelium with SARS-CoV-2, using induced pluripotent stem cell-derived AT2s that have been adapted to air-liquid interface culture. We find a rapid transcriptomic change in infected cells, characterized by a shift to an inflammatory phenotype with upregulation of NF-kB signaling and loss of the mature alveolar program. Drug testing confirms the efficacy of remdesivir as well as TMPRSS2 protease inhibition, validating a putative mechanism used for viral entry in alveolar cells. Our model system reveals cell-intrinsic responses of a key lung target cell to SARS-CoV-2 infection and should facilitate drug development. url: https://api.elsevier.com/content/article/pii/S1934590920304598 doi: 10.1016/j.stem.2020.09.013 id: cord-293765-xpc4yizb author: Huang, Jia-Ling title: Th2 predominance and CD8+ memory T cell depletion in patients with severe acute respiratory syndrome() date: 2005-02-24 words: 5149.0 sentences: 250.0 pages: flesch: 53.0 cache: ./cache/cord-293765-xpc4yizb.txt txt: ./txt/cord-293765-xpc4yizb.txt summary: To define the dynamics of the immune spectrum in SARS, serum levels of cytokines, chemokines, immunoglobulins, complement and specific antibodies against SARS-associated coronavirus (SARS-CoV) were assayed by enzyme-linked immunosorbent assay (ELISA), and phenotypes of peripheral lymphocytes were analyzed by flow cytometry in 95 SARS-infected patients. IL-10 levels in the serum of SARS patients were continuously elevated for the 5 months observed in this study (2.47-4 .57 times that of normal control levels; Fig. 1C , P < 0.001, correlation coefficient = 0.514, one-way ANOVA; minimum detectable dose < 3.9 pg/ml). In this study, we found that infection with SARS-CoV triggered vigorous immune disturbances characterized by the following: (1) typical anti-viral nonspecific and specific humoral responses; (2) perturbation of cytokine and chemokine levels; and (3) severe impairment of cellular immunity, including lymphopenia in acute phase and loss of CD8+ memory T cells in convalescent phase. abstract: The immune spectrum of severe acute respiratory syndrome (SARS) is poorly understood. To define the dynamics of the immune spectrum in SARS, serum levels of cytokines, chemokines, immunoglobulins, complement and specific antibodies against SARS-associated coronavirus (SARS-CoV) were assayed by enzyme-linked immunosorbent assay (ELISA), and phenotypes of peripheral lymphocytes were analyzed by flow cytometry in 95 SARS-infected patients. Results showed that interleukin (IL)-10 and transforming growth factor β (TGF-β) were continuously up-regulated during the entirety of SARS. Regulated on activation normally T cell-expressed and secreted (RANTES) levels were decreased, while monocyte chemoattractant protein-1 (MCP-1) was elevated in acute patients. Immunoglobulins and complement were elevated during the first month of SARS. Both serum-positive rates and titers of specific IgM and IgG antibodies responding to SARS-CoV peaked at days 41–60 from the onset of SARS. CD4+ and CD8+ T lymphocytes decreased significantly in acute-phase. CD3+CD8+CD45RO+ T lymphocytes were decreased by 36.78% in the convalescent patients. Conclusion: SARS-CoV seemed to elicit effective humoral immunity but inhibited cellular immunity, especially CD8+ memory T lymphocytes over time. Prolonged overproduction of IL-10 and TGF-β may play an important role in the disease. url: https://api.elsevier.com/content/article/pii/S1286457905000304 doi: 10.1016/j.micinf.2004.11.017 id: cord-330200-l6bnxi40 author: Huang, Jianping title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 words: 4472.0 sentences: 306.0 pages: flesch: 59.0 cache: ./cache/cord-330200-l6bnxi40.txt txt: ./txt/cord-330200-l6bnxi40.txt summary: title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. abstract: ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. DESIGN Retrospective, observational case series. SETTING Wenzhou Sixth Peoples Hospital PARTICIPANTS Thirty-three patients with laboratory confirmed SARS-CoV-2 pneumonia admitted to hospital. Data were collected from January 27 to April 10, 2020. MAIN OUTCOME MEASURES Throat swabs, sputum, stool, and blood samples were collected, and viral load was measured by reverse transcription PCR (RT-PCR). Specific IgM and IgG against spike protein (S), spike protein receptor binding domain (RBD), and nucleocapsid (N) were analyzed. RESULTS At the early stages of symptom onset, SARS-CoV-2 viral load is higher in throat swabs and sputum, but lower in stool. The median (IQR) time of undetectable viral RNA in throat swab, sputum, and stool was 18.5 (13.25-22) days, 22 (18.5-27.5) days, and 17 (11.5-32) days, respectively. In sputum, 17 patients (51.5%) had undetectable viral RNA within 22 days (short persistence), and 16 (48.5%) had persistent viral RNA more than 22 days (long persistence). Three patients (9.1%) had a detectable relapse of viral RNA in sputum within two weeks of their discharge from the hospital. One patient had persistent viral RNA for 59 days or longer. The median (IQR) seroconversion time of anti-S IgM, anti-RBD IgM, and anti-N IgM was 10.5 (7.75-15.5) days, 14 (9-24) days, and 10 (7-14) days, respectively. The median (IQR) seroconversion time of anti-S IgG, anti-RBD IgG, and anti-N IgG was 10 (7.25-16.5) days, 13 (9-17) days, and 10 (7-14) days, respectively. By week 8 after symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels were 4-times higher in convalescence than in acute phase. SARS-CoV-2 RNA coexisted with antibodies for more than 50 days. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients. CONCLUSION This study adds important new information about the features of viral load and antibody dynamics of SARS-CoV-2. It is clear from these results that the viral RNA persists in sputum and stool specimens for a relatively long time in many patients. Anti-RBD may also serve as a potential protective antibody against SARS-CoV-2 infection, as viral persistence appears to be related to anti-RBD levels. Earlier treatment intervention also appears to be a factor in viral persistence. url: http://medrxiv.org/cgi/content/short/2020.04.22.20071258v1?rss=1 doi: 10.1101/2020.04.22.20071258 id: cord-302608-fw4pmaoc author: Huang, Jiao-Mei title: Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 words: 1890.0 sentences: 125.0 pages: flesch: 57.0 cache: ./cache/cord-302608-fw4pmaoc.txt txt: ./txt/cord-302608-fw4pmaoc.txt summary: However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. The host specificity of virus particle is determined by amino acid sequence of RBD and is usually dissimilar among different CoVs. Therefore, RBD is a core determinant for tissue tropism and host range of CoVs. This article presents SARS-CoV-2 phylogenetic trees, comparison and analysis of genome, spike protein, and RBD amino acid sequences of different CoVs, deducing source and etiology of COVID-19 and evolutionary relationship among SARS-CoV-2 in human. The S-protein amino acid sequence identity between SARS-CoV-2 and related beta-CoVs showed that bat/Yunnan/RaTG13 shares highest similarity of 97.43%. abstract: The recent global outbreak of viral pneumonia designated as Coronavirus Disease 2019 (COVID-19) by coronavirus (SARS-CoV-2) has threatened global public health and urged to investigate its source. Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13) and clustered together in phylogenetic tree. Furthermore, RaTGl3 also showed 97.43% spike protein similarity with SARS-CoV-2 suggesting that RaTGl3 is the closest strain. However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. In short, our findings propose that homologous recombination has been occurred between bat and pangolin CoVs that triggered cross-species transmission and emergence of SARS-CoV-2, and, during the ongoing outbreak, SARS-CoV-2 is still evolving for its adaptability. url: https://doi.org/10.1101/2020.03.16.993816 doi: 10.1101/2020.03.16.993816 id: cord-341970-pho6dksc author: Huang, Jun title: Immunization with SARS-CoV S DNA vaccine generates memory CD4(+) and CD8(+) T cell immune responses date: 2006-06-05 words: 4417.0 sentences: 259.0 pages: flesch: 64.0 cache: ./cache/cord-341970-pho6dksc.txt txt: ./txt/cord-341970-pho6dksc.txt summary: In the present study, mice were immunized i.m. with SARS-CoV S DNA vaccine, and three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses when the cells were stimulated in vitro with a pool of peptides overlapping entire SARS spike protein. Moreover, mice boosted with SARS S DNA vaccine exhibited a 3-30-fold increase in the frequency of IFN-␥-producing cells in spleens (P < 0.01) and lymph nodes (P < 0.05), respectively (Fig. 1) , compared with the prime immunization. To further ascertain whether the frequency of SARS-CoV S specific CD4 + and CD8 + T cell responses was increased after boost vaccination, mice were boosted i.m. with SARS-CoV S DNA vaccine, seven days after injection, IFN-␥-and IL-2-producing CD4 + and CD8 + T cells were determined in lymph nodes, spleen and lungs. abstract: An effective vaccine for severe acute respiratory syndrome (SARS) will probably require the generation and maintenance of both humoral and cellular immune responses. It has been reported that after natural infection in humans and immunization in animals with SARS-CoV vaccine, antibody is produced and persistent for a long period of time. In the present study, mice were immunized i.m. with SARS-CoV S DNA vaccine, and three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses when the cells were stimulated in vitro with a pool of peptides overlapping entire SARS spike protein. The results show that prime-immunization with SARS-CoV S DNA vaccine can induce both CD4(+) and CD8(+) T cell responses. Boosting with the same vaccine enhances CD4(+) and CD8(+) T cell responses in both lymphoid and nonlymphoid organs and were persistent over two months. The SARS-CoV S-specific CD4(+) and CD8(+) T cells were CD62L(−), a marker for memory cells, and −30 to 50% of the cells expressed IL-7Rα (CD127), a marker for the capacity of effector cells to develop into memory cells. In addition, immunization with the DNA vaccine elicited high levels of antibody production. Taken together, these data demonstrate that immunization with SARS-CoV S DNA vaccine can generate antigen-specific humoral and cellular immune responses that may contribute to long-term protection. url: https://www.ncbi.nlm.nih.gov/pubmed/16621188/ doi: 10.1016/j.vaccine.2006.03.058 id: cord-262145-i29e3fge author: Huang, Kuan-Ying A. title: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date: 2020-10-19 words: 2949.0 sentences: 207.0 pages: flesch: 61.0 cache: ./cache/cord-262145-i29e3fge.txt txt: ./txt/cord-262145-i29e3fge.txt summary: A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. The MAbs with 161 strong anti-RBD binding have a relatively long heavy chain CDR3 length (50% 162 binding concentration <0.5 µg/ml versus >0.5 µg/ml, p=0.03, two-tailed Mann-163 Whitney test; Supplemental Figure 3 The 32 anti-spike glycoprotein MAbs were systematically examined by plaque 173 reduction neutralisation (PRNT) assay for neutralisation of wild type SARS-CoV-2 174 virus (see methods; summarised in Table 1 ). Potent neutralising antibodies to the RBD of SARS-CoV-2 spike glycoprotein were 188 identified and we thus analyse the blockade of the ACE2-RBD interaction by anti-189 RBD antibodies in two assays ( Figure 3 , Table 1 The structure of VHH72-Fc bound to RBD is known (17) and its footprint on the 198 RBD does not overlap that of ACE2, so inhibition is thought to occur by steric 199 hindrance. abstract: Serological and plasmablast responses and plasmablast-derived IgG monoclonal antibodies (MAbs) have been analysed in three COVID-19 patients with different clinical severities. Potent humoral responses were detected within 3 weeks of onset of illness in all patients and the serological titre was elicited soon after or concomitantly with peripheral plasmablast response. An average of 13.7% and 13.0% of plasmablast-derived MAbs were reactive with virus spike glycoprotein or nucleocapsid, respectively. A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. Fourteen of 32 anti-spike MAbs, including five anti-RBD, three anti-non-RBD S1 and six anti-S2, neutralised wild-type SARS-CoV-2 in independent assays. Anti-RBD MAbs were further grouped into four cross-inhibiting clusters, of which six antibodies from three separate clusters blocked the binding of RBD to ACE2 and five were neutralising. All ACE2-blocking anti-RBD antibodies were isolated from two patients with prolonged fever, which is compatible with substantial ACE2-blocking response in their sera. At last, the identification of non-competing pairs of neutralising antibodies would offer potential templates for the development of prophylactic and therapeutic agents against SARS-CoV-2. url: https://doi.org/10.1101/2020.08.28.267526 doi: 10.1101/2020.08.28.267526 id: cord-267246-hq7g62p5 author: Huang, Su-Hua title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism date: 2015-07-31 words: 3422.0 sentences: 190.0 pages: flesch: 41.0 cache: ./cache/cord-267246-hq7g62p5.txt txt: ./txt/cord-267246-hq7g62p5.txt summary: title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism METHODS: This study identified SARS-CoV ORF6-interacting proteins using the phage displayed human lung cDNA libraries, and examined the association of ORF6–host factor interaction with Type I IFN antagonism. RESULTS: The highest affinity clone to ORF6 displayed the C-terminal domain of NPIPB3 (nuclear pore complex interacting protein family, member B3; also named as phosphatidylinositol-3-kinase-related kinase SMG-1 isoform 1 homolog). The nucleotide sequences of the C terminus (amino acid residues 936e1050) of NPIPB3 (Accession Number Q92617) fused with the coat protein of ORF6-interacting phage clone 40 was amplified using PCR, and then cloned into bacterial expression vector pET32a for coimmunoprecipitation in vitro and mammalian expression vector pDsRed1-C (BD Biosciences Clontech) for colocalization assay. abstract: BACKGROUND/PURPOSE: Severe acute respiratory syndrome coronavirus (SARS-CoV) proteins including ORF6 inhibit Type I interferon (IFN) signaling. METHODS: This study identified SARS-CoV ORF6-interacting proteins using the phage displayed human lung cDNA libraries, and examined the association of ORF6–host factor interaction with Type I IFN antagonism. After the fifth round of biopanning with Escherichia coli-synthesized ORF6-His tagged protein, the relative binding affinity of phage clones to ORF6 was determined using direct enzyme-linked immunosorbent assay. RESULTS: The highest affinity clone to ORF6 displayed the C-terminal domain of NPIPB3 (nuclear pore complex interacting protein family, member B3; also named as phosphatidylinositol-3-kinase-related kinase SMG-1 isoform 1 homolog). The coimmunoprecipitation assay demonstrated the direct binding of ORF6 to the C-terminal domain of NPIPB3 in vitro. Confocal imaging revealed a close colocalization of SARS-CoV ORF6 protein with NPIPB3 in human promonocytes. The dual luciferase reporter assay showed that the C-terminal domain of NPIPB3 attenuated the antagonistic activity of SARS-CoV ORF6 on IFN-β-induced ISRE (IFN stimulated response element)-responsive firefly luciferase activity. In addition, confocal imaging and Western blotting assays revealed that the increases in STAT-1 nuclear translocation and phosphorylation occurred in the transfected cells expressing both genes of ORF6 and NPIPB3, but not in the ORF6-expressing cells in response to IFN-β. CONCLUSION: The overexpression of NPIPB3 restored the IFN-β responses in SARS-CoV ORF6 expressing cells, indicating that the interaction of SARS CoV ORF6 and NPIPB3 reduced Type I IFN antagonism by SARS-CoV ORF6. url: https://www.sciencedirect.com/science/article/pii/S1684118215008051 doi: 10.1016/j.jmii.2015.07.002 id: cord-277619-83bve5z0 author: Huang, Victoria W. title: Head and neck survivorship care in the times of the SARS‐CoV‐2 pandemic date: 2020-05-02 words: 2306.0 sentences: 127.0 pages: flesch: 49.0 cache: ./cache/cord-277619-83bve5z0.txt txt: ./txt/cord-277619-83bve5z0.txt summary: In this present commentary, we discuss the unique mental health challenges and burdens of patients with head and neck cancer in the times of the SARS‐CoV‐2 pandemic and approaches to mitigate these stressors through telemedicine to reduce future burdens to the patient and the health care system. With the uncertainties of the SARS-CoV-2 pandemic and a head and neck cancer (HNC) diagnosis, the potential mental health consequences of such delays to treatment warrant further discussion. 24 With HNC patients already a vulnerable population, delaying treatment in the times of the SARS-CoV-2 pandemic can place additional strain on the mental health and QOL of patients, resulting in future burdens on the health care system. With examples of utilizing technology from China, providers need to address the mental health burden of a HNC diagnosis for patients who are being asked to delay treatment to ensure comprehensive cancer care. abstract: With the arrival of the coronavirus disease (SARS‐CoV‐2) in the United States, care practice paradigms have drastically changed. Data from China suggest that the new virus poses additional risks as case fatality of patients with cancer was higher at 5.6% compared to 2.3% of the general population. There are three proposed major strategies to address care for patients with cancer in this SARS‐CoV‐2 pandemic with postponing treatment for those with stable cancer, increasing personal protection provisions for patients with cancer, and increasing monitoring if a patient becomes infected with SARS‐CoV‐2. In this present commentary, we discuss the unique mental health challenges and burdens of patients with head and neck cancer in the times of the SARS‐CoV‐2 pandemic and approaches to mitigate these stressors through telemedicine to reduce future burdens to the patient and the health care system. url: https://www.ncbi.nlm.nih.gov/pubmed/32358880/ doi: 10.1002/hed.26235 id: cord-309074-pys4aa60 author: Huang, Victoria W. title: Telehealth in the times of SARS-CoV-2 infection for the Otolaryngologist date: 2020-05-30 words: 2644.0 sentences: 154.0 pages: flesch: 48.0 cache: ./cache/cord-309074-pys4aa60.txt txt: ./txt/cord-309074-pys4aa60.txt summary: OBJECTIVE: In response to the American Academy of Otolaryngology – Head and Neck Surgery''s recommendations to limit patient care activities in the times of SARS-CoV-2, many elective surgeries have been canceled without patient clinics transitioning to virtual visits. In response to these evolving needs, the American Academy of Otolaryngology -Head and Neck Surgery (AAO-HNS) telemedicine committee has put forth new recommendations to prioritize novel applications of telehealth to help limit coronavirus disease pandemic spread while maintaining quality care 8 . As testing in the U.S. becomes more available in this era of SARS-CoV-2, telemedicine continues to take the main role of "forward triage", evaluating patients with respiratory symptoms before they arrive in hospitals 23 With the AAO-HNS recommending all otolaryngologists to limit patient care activities to time-sensitive, urgent, and emergent medical conditions, elective surgeries have been canceled with many outpatient clinics rescheduling appointments and transitioning to virtual visits 7, 8 . abstract: OBJECTIVE: In response to the American Academy of Otolaryngology – Head and Neck Surgery’s recommendations to limit patient care activities in the times of SARS-CoV-2, many elective surgeries have been canceled without patient clinics transitioning to virtual visits. With regulations for telemedicine loosened, new possibilities for the practice of otolaryngology have opened. To address the uncertain duration of this pandemic, a review was conducted of current literature on use of telemedicine services in the current SARS-CoV-2 pandemic and in previous national emergencies to reveal the role telemedicine can play for otolaryngology practices. DATA SOURCES: Pubmed articles with an independent search query were utilized. METHODS: Literature review performed by one author searched for all published English-language literature on telehealth in the SARS-CoV-2 era. Articles were considered for discussion if they provided relevant developments for telemedicine in the context of the SARS-CoV-2 pandemic. RESULTS: Telemedicine can be up-scaled in the current SARS-CoV-2 pandemic where exposure containment is of the utmost priority. With patient interaction possible through virtual communication, telemedicine allows continued patient care while minimizing the risk of viral spread. In the realm of otolaryngology, telemedicine has been used in the past during disasters with other studies demonstrating high diagnostic concordance with inpatient visits. Many institutions have recognized the potential for such care as they begin utilize both virtual visits and in-person care during this pandemic. CONCLUSION: To limit the spread of SARS-CoV-2, we support the AAO-HNS recommendation for the adoption of novel ways to employ telemedicine in this era. Many emergency departments and health care systems have the infrastructure necessary for synchronous video telemedicine visits that can be leveraged to provide quality care with patients. With the continued need to socially distance, telemedicine can protect both physicians and patients from unnecessary exposure to the virus. url: https://www.sciencedirect.com/science/article/pii/S2095881120300676?v=s5 doi: 10.1016/j.wjorl.2020.04.008 id: cord-337854-5ogip9tz author: Huang, Wanqiu title: The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology date: 2020-07-02 words: 1020.0 sentences: 67.0 pages: flesch: 53.0 cache: ./cache/cord-337854-5ogip9tz.txt txt: ./txt/cord-337854-5ogip9tz.txt summary: In our study, we developed an improved strategy, termed as nestRPA (nest recombinase polymerase amplification), which could greatly improve the sensitivity of nucleic acid detection for SARS-CoV-2 than RPA or qPCR. Using nestRPA technology, we found that positive plasmid containing SARS-CoV-2 with the concentration of 1 copy/ul could also be stably detected by Fragment 5 and nucleic acid detection results were negative using qPCR. Our results suggested that the ultra-sensitive nucleic acid detection technique has important implications for early identification of those asymptomatic carriers infected with SARS-CoV-2. In addition, many experts of COVID-19 prevention and treatment clearly pointed out that the inaccurate sample collection were also one of the important reasons for the false negative result of SARS-CoV-2 nucleic acid [6] [7] [8] . If all the links in the detection of SARS-CoV-2 nucleic acid could be strictly administrated, false negative could be completely eliminated, and the discontinuation of isolation will no longer be a dilemma for us. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320304564?v=s5 doi: 10.1016/j.jinf.2020.06.075 id: cord-344636-go5cw92q author: Huang, Wei E. title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 words: 4771.0 sentences: 253.0 pages: flesch: 61.0 cache: ./cache/cord-344636-go5cw92q.txt txt: ./txt/cord-344636-go5cw92q.txt summary: In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample. abstract: The pandemic coronavirus SARS‐CoV‐2 in the world has caused a large infected population suffering from COVID‐19. To curb the spreading of the virus, WHO urgently demanded an extension of screening and testing; thus, a rapid and simple diagnostic method is needed. We applied a reverse transcription‐loop‐mediated isothermal amplification (RT‐LAMP) to achieve the detection of SARS‐CoV‐2 in 30 min. We designed four sets of LAMP primers (6 primers in each set), targeting the viral RNA of SARS‐CoV‐2 in the regions of orf1ab, S gene and N gene. A colorimetric change was used to report the results, which enables the outcome of viral RNA amplification to be read by the naked eye without the need of expensive or dedicated instrument. The sensitivity can be 80 copies of viral RNA per ml in a sample. We validated the RT‐LAMP method in a hospital in China, employing 16 clinic samples with 8 positives and 8 negatives. The testing results are consistent with the conventional RT‐qPCR. In addition, we also show that one‐step process without RNA extraction is feasible to achieve RNA amplification directly from a sample. This rapid, simple and sensitive RT‐LAMP method paves a way for a large screening at public domain and hospitals, particularly regional hospitals and medical centres in rural areas. url: https://www.ncbi.nlm.nih.gov/pubmed/32333644/ doi: 10.1111/1751-7915.13586 id: cord-325657-s2vdazq0 author: Huang, Yan-Jang S. title: SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge date: 2020-07-17 words: 1589.0 sentences: 105.0 pages: flesch: 46.0 cache: ./cache/cord-325657-s2vdazq0.txt txt: ./txt/cord-325657-s2vdazq0.txt summary: Three widely distributed species of mosquito; Aedes aegypti, Ae. albopictus and Culex quinquefasciatus, representing the two most significant genera of arbovirus vectors that infect people, were tested. In this study, the susceptibility of three mosquito species, Ae. aegypti, Ae. albopictus and Cx. quinquefasciatus, were determined through the intrathoracic inoculation with SARS-CoV-2. No virus was detected in the 277 inoculated mosquitoes collected and titrated at time points beyond 24 h, suggesting a rapid loss of infectivity and the lack of replication after injection. Based upon the lack of detectable infectious virus in any of the 277 samples collected at all time points beyond 24 h post-inoculation, we conclude that SARS-CoV-2 is unable to replicate in mosquitoes and that even if a mosquito fed on a person with virus in the blood, that the mosquito would not be a vector if feeding on a naïve host. abstract: This research addresses public speculation that SARS-CoV-2 might be transmitted by mosquitoes. The World Health Organization has stated “To date there has been no information nor evidence to suggest that the new coronavirus could be transmitted by mosquitoes”. Here we provide the first experimental data to investigate the capacity of SARS-CoV-2 to infect and be transmitted by mosquitoes. Three widely distributed species of mosquito; Aedes aegypti, Ae. albopictus and Culex quinquefasciatus, representing the two most significant genera of arbovirus vectors that infect people, were tested. We demonstrate that even under extreme conditions, SARS-CoV-2 virus is unable to replicate in these mosquitoes and therefore cannot be transmitted to people even in the unlikely event that a mosquito fed upon a viremic host. url: https://doi.org/10.1038/s41598-020-68882-7 doi: 10.1038/s41598-020-68882-7 id: cord-330067-ujhgb3b0 author: Huang, Yi title: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes date: 2007-10-02 words: 3007.0 sentences: 168.0 pages: flesch: 55.0 cache: ./cache/cord-330067-ujhgb3b0.txt txt: ./txt/cord-330067-ujhgb3b0.txt summary: To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. In CoVDB, with the aim of facilitating gene retrieval, we tried to unify the naming of these non-structural proteins from different groups of coronaviruses. When we compared their putative amino acid sequences to the corresponding ones in other group 1 coronavirus genomes using BLAST, as well as searching for conserved domains using motifscan, results showed that the putative proteins encoded by these ORFs belonged to a protein family in Pfam originally assigned as ''Corona_NS3b'' (accession number PF03053). database, CoVDB, of annotated coronavirus genes and genomes, which offers efficient batch sequence retrieval and analysis. abstract: The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/17913743/ doi: 10.1093/nar/gkm754 id: cord-351532-2yd4wg9v author: Huang, Yin-Qiu title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study date: 2020-07-14 words: 5739.0 sentences: 260.0 pages: flesch: 48.0 cache: ./cache/cord-351532-2yd4wg9v.txt txt: ./txt/cord-351532-2yd4wg9v.txt summary: title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study The proportion of patients with SARS-CoV-2 nucleic acid negativity in the LPV/r+IFN-α-treated group (61.1%) was higher than the RBV+ IFN-α-treated group (51.5%) and the RBV+LPV/r+IFN-α-treated group (46.9%) at day 14; however, the difference between these groups was calculated to be statistically insignificant. The office of National Health Commission of the People''s Republic of China, and the National Administration Bureau of Traditional Chinese Medicine have jointly issued different versions of the "Guidelines for diagnosis and treatment of novel coronavirus pneumonia", in which LPV/r, IFNa, and RBV are recommended for on-trial use in patients with COVID-19. abstract: BACKGROUND: Currently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, causing an unprecedented pandemic. However, there is no specific antiviral therapy for coronavirus disease 2019 (COVID-19). We conducted a clinical trial to compare the effectiveness of three antiviral treatment regimens in patients with mild to moderate COVID-19. METHODS: This was a single-center, randomized, open-labeled, prospective clinical trial. Eligible patients with mild to moderate COVID-19 were randomized into three groups: ribavirin (RBV) plus interferon-α (IFN-α), lopinavir/ritonavir (LPV/r) plus IFN-α, and RBV plus LPV/r plus IFN-α at a 1:1:1 ratio. Each patient was invited to participate in a 28-d follow-up after initiation of an antiviral regimen. The outcomes include the difference in median interval to SARS-CoV-2 nucleic acid negativity, the proportion of patients with SARS-CoV-2 nucleic acid negativity at day 14, the mortality at day 28, the proportion of patients re-classified as severe cases, and adverse events during the study period. RESULTS: In total, we enrolled 101 patients in this study. Baseline clinical and laboratory characteristics of patients were comparable among the three groups. In the analysis of intention-to-treat data, the median interval from baseline to SARS-CoV-2 nucleic acid negativity was 12 d in the LPV/r+IFN-α-treated group, as compared with 13 and 15 d in the RBV+IFN-α-treated group and in the RBV+LPV/r+ IFN-α-treated group, respectively (p=0.23). The proportion of patients with SARS-CoV-2 nucleic acid negativity in the LPV/r+IFN-α-treated group (61.1%) was higher than the RBV+ IFN-α-treated group (51.5%) and the RBV+LPV/r+IFN-α-treated group (46.9%) at day 14; however, the difference between these groups was calculated to be statistically insignificant. The RBV+LPV/r+IFN-α-treated group developed a significantly higher incidence of gastrointestinal adverse events than the LPV/r+ IFN-α-treated group and the RBV+ IFN-α-treated group. CONCLUSIONS: Our results indicate that there are no significant differences among the three regimens in terms of antiviral effectiveness in patients with mild to moderate COVID-19. Furthermore, the combination of RBV and LPV/r is associated with a significant increase in gastrointestinal adverse events, suggesting that RBV and LPV/r should not be co-administered to COVID-19 patients simultaneously. CLINICAL TRIAL REGISTRATION: www.ClinicalTrials.gov, ID: ChiCTR2000029387. Registered on January 28, 2019. url: https://www.ncbi.nlm.nih.gov/pubmed/32765274/ doi: 10.3389/fphar.2020.01071 id: cord-268370-kfjujs4z author: Huang, Yu-Tung title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study date: 2009-05-31 words: 3292.0 sentences: 173.0 pages: flesch: 48.0 cache: ./cache/cord-268370-kfjujs4z.txt txt: ./txt/cord-268370-kfjujs4z.txt summary: title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study The purpose of this study was to explore the effect of the SARS outbreak on hospitalization for chronic ambulatory-care-sensitive conditions (ACSCs) in Taiwan. Methods We applied a population-based interrupted time series study design and used the time series auto-regressive integrated moving-average model to compare the actual and predicted admission rates of seven selected chronic ACSCs. The analyses were based on National Health Insurance hospital inpatient claims data from 1997 to 2003. We applied a population-based interrupted time series design to compare the actual with predicted hospitalization for ACSCs after the SARS outbreak, to identify conditions with increased hospitalization that might have been caused by untimely or inappropriate primary care during the SARS outbreak. We found that the actual hospitalization rates for six selected ACSCs, particularly respiratory conditions, were significantly lower than their predicted rates for at least 1 month during the SARS period. abstract: Background/Purpose In 2003, the severe acute respiratory syndrome (SARS) outbreak resulted in 8096 probable cases and 774 deaths in 26 countries. The purpose of this study was to explore the effect of the SARS outbreak on hospitalization for chronic ambulatory-care-sensitive conditions (ACSCs) in Taiwan. Methods We applied a population-based interrupted time series study design and used the time series auto-regressive integrated moving-average model to compare the actual and predicted admission rates of seven selected chronic ACSCs. The analyses were based on National Health Insurance hospital inpatient claims data from 1997 to 2003. Results The impact of SARS on ACSCs after the outbreak varied among seven selected chronic conditions. Hospitalization for respiratory conditions was significantly lower than the predicted values, whereas hospitalization for diabetes was significantly higher than the predicted values after the outbreak. Conclusion Admission rates for most ACSCs, except for diabetes, did not change in the post-SARS period. The reductions in outpatient utilization during the SARS outbreak did not appear to affect adversely admissions for most ACSCs. url: https://doi.org/10.1016/s0929-6646(09)60082-6 doi: 10.1016/s0929-6646(09)60082-6 id: cord-329011-spiuqngp author: Huang, Yuan title: Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date: 2020-08-03 words: 6045.0 sentences: 340.0 pages: flesch: 53.0 cache: ./cache/cord-329011-spiuqngp.txt txt: ./txt/cord-329011-spiuqngp.txt summary: The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. A large number of glycosylated S proteins cover the surface of SARS-CoV-2 and bind to the host cell receptor angiotensinconverting enzyme 2 (ACE2), mediating viral cell entry [8] . The SARS-CoV-2 S protein is highly conserved among all human coronaviruses (HCoVs) and is involved in receptor recognition, viral attachment, and entry into host cells. Structure of the S1 subunit The binding of virus particles to cell receptors on the surface of the host cell is the initiation of virus infection; therefore, receptor recognition is an important determinant of viral entry and a drug design target. Therefore, the development of antibodies targeting this functional motif may cross-bind and neutralize these two viruses and related CoVs. Antiviral peptides prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infection. abstract: Coronavirus disease 2019 is a newly emerging infectious disease currently spreading across the world. It is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. The S1 subunit contains a receptor-binding domain that recognizes and binds to the host receptor angiotensin-converting enzyme 2, while the S2 subunit mediates viral cell membrane fusion by forming a six-helical bundle via the two-heptad repeat domain. In this review, we highlight recent research advance in the structure, function and development of antivirus drugs targeting the S protein. url: https://doi.org/10.1038/s41401-020-0485-4 doi: 10.1038/s41401-020-0485-4 id: cord-351662-rmkcb6o3 author: Huang, Zhifeng title: Characteristics and roles of SARS‐CoV‐2 specific antibodies in patients with different severities of COVID‐19 date: 2020-07-24 words: 2855.0 sentences: 179.0 pages: flesch: 54.0 cache: ./cache/cord-351662-rmkcb6o3.txt txt: ./txt/cord-351662-rmkcb6o3.txt summary: We aimed to quantify the levels of SARS‐CoV‐2‐specific IgM, IgA, and IgG antibodies, identify changes in them based on COVID‐19 severity, and establish the significance of combined antibody detection. The rise times for specific IgM and IgG levels are different, and combined detection could be more advantageous in the diagnosis of COVID-19 [5] . In this study, SARS-CoV-2-specific IgM, IgA, and IgG levels were measured in patients with varying severities of COVID-19, the relationship between specific antibody levels and disease severity was classified, and the significance of combined antibody detection was clarified, providing a reference for the clinical diagnosis of COVID-19. We also found that while IgA and IgG levels were significantly higher in the severe & critical patients than in moderate patients, there was no difference in IgM between the two groups. Levels of IgA and IgG were higher in severe & critical COVID-19 patients than in moderate COVID-19 patients, while IgM levels were no different between the two groups. abstract: BACKGROUND: The diagnosis of COVID‐19 relies mainly on viral nucleic acid detection, but false negatives can lead to missed diagnosis and misdiagnosis. SARS‐CoV‐2‐specific antibody detection is convenient, safe, and highly sensitive. IgM and IgG are commonly used to serologically diagnose COVID‐19; however, the role of IgA is not well known. We aimed to quantify the levels of SARS‐CoV‐2‐specific IgM, IgA, and IgG antibodies, identify changes in them based on COVID‐19 severity, and establish the significance of combined antibody detection. METHODS: COVID‐19 patients, divided into a severe & critical group and a moderate group, and non‐COVID‐19 patients with respiratory disease were included in this study. A chemiluminescence method was used to detect the levels of SARS‐CoV‐2‐specific IgM, IgA, and IgG in the blood samples from the three groups. Epidemiological characteristics, symptoms, blood test results, and other data were recorded for all patients. RESULTS: Compared to the traditional IgM–IgG combined antibodies, IgA–IgG combined antibodies are better for diagnosing COVID‐19. During the disease process, IgA appeared first and disappeared last. All three antibodies had significantly higher levels in COVID‐19 patients than in non‐COVID‐19 patients. IgA and IgG were also higher for severe & critical disease than for moderate disease. All antibodies were at or near low levels at the time of tracheal extubation in critical patients. CONCLUSIONS: Detection of SARS‐CoV‐2‐specific combined IgA–IgG antibodies is advantageous in diagnosing COVID‐19. IgA detection is suitable during early and late stages of the disease. IgA and IgG levels correspond to disease severity. url: https://doi.org/10.1111/cei.13500 doi: 10.1111/cei.13500 id: cord-277490-xrgnt6l5 author: Huang, Zhongwei title: Optimal temperature zone for the dispersal of COVID-19 date: 2020-05-16 words: 424.0 sentences: 33.0 pages: flesch: 57.0 cache: ./cache/cord-277490-xrgnt6l5.txt txt: ./txt/cord-277490-xrgnt6l5.txt summary: Abstract It is essential to know the environmental parameters within which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can survive to understand its global dispersal pattern. Our findings suggest that there is an optimal climatic zone in which the concentration of SARS-CoV-2 markedly increases in the ambient environment (including the surfaces of objects). The aerodynamic characteristics and propagation of SARS-CoV-2 in aerosols have been reported (Liu et al., 2020) . Therefore, it is essential to understand the survival of SARS-CoV-2 in the ambient environment to prevent COVID-19. Transmission of a 2009 Pandemic Influenza Virus Shows a Sensitivity to Temperature and Humidity Similar to That of an H3N2 Seasonal Strain Evidence that higher temperatures are associated with lower incidence of COVID-19 in pandemic state, cumulative cases reported up to Association between ambient temperature and COVID-19 infection in 122 cities from China abstract: Abstract It is essential to know the environmental parameters within which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can survive to understand its global dispersal pattern. We found that 60.0% of the confirmed cases of coronavirus disease 2019 (COVID-19) occurred in places where the air temperature ranged from 5 °C to 15 °C, with a peak in cases at 11.54 °C. Moreover, approximately 73.8% of the confirmed cases were concentrated in regions with absolute humidity of 3 g/m3 to 10 g/m3. SARS-CoV-2 appears to be spreading toward higher latitudes. Our findings suggest that there is an optimal climatic zone in which the concentration of SARS-CoV-2 markedly increases in the ambient environment (including the surfaces of objects). These results strongly imply that the COVID-19 pandemic may spread cyclically and outbreaks may recur in large cities in the mid-latitudes in autumn 2020. url: https://api.elsevier.com/content/article/pii/S0048969720330047 doi: 10.1016/j.scitotenv.2020.139487 id: cord-320511-qnxj7d9l author: Hueston, Linda title: The antibody response to SARS-CoV-2 infection date: 2020-08-27 words: 3106.0 sentences: 180.0 pages: flesch: 47.0 cache: ./cache/cord-320511-qnxj7d9l.txt txt: ./txt/cord-320511-qnxj7d9l.txt summary: METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for IgG, IgA and IgM was developed, and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Diagnosis is primarily by detecting SARS-CoV-2-specific RNA by nucleic acid testing (NAT), but this has limitations, including the possibility of false-negative results due to low virus load in patients with minimal disease, inadequate respiratory tract sampling or mutations in the target sequence, and false-positive results due to contamination or nonspecific amplification. The objective of this study was to develop and evaluate an immunofluorescent antibody (IFA) test for SARS-CoV-2-specific IgG, IgM and IgA, and apply it to document the serological response in individuals with confirmed COVID-19. Since the start of the epidemic in Australia, the Public Health Laboratory Network recommended collecting acute and convalescent sera for serological assays on individuals being tested for SARS-CoV-2 infection, in addition to respiratory tract samples for NAT, though this has not been universally adopted [5] . abstract: BACKGROUND: Testing for SARS-CoV-2-specific antibodies has become an important tool, complementing nucleic acid tests (NATs) for diagnosis and for determining the prevalence of COVID-19 in population serosurveys. The magnitude and persistence of antibody responses are critical for assessing the duration of immunity. METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for IgG, IgA and IgM was developed, and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay. RESULTS: 2753 individuals were eligible for the study (126 NAT positive, prevalence 4·6%). The median ‘window period’ from illness onset to appearance of antibody was 10·2 days (range 5·8 – 14·4). The sensitivity and specificity of either SARS-CoV-2 IgG, IgA or IgM when collected 14 days or more after symptom onset was 91·3% (95% CI 84·9-95·6) and 98·9% (98·4-99·3), respectively. The negative predictive value was 99·6% (99·3-99·8). The positive predictive value of detecting any antibody class was 79·9% (73·3-85·1); this increased to 96·8% (90·7-99·0) for the combination of IgG and IgA. CONCLUSIONS: Measurement of SARS-CoV-2-specific antibody by IFA is an accurate method to diagnose COVID-19. Serological testing should be incorporated into diagnostic algorithms for SARS-CoV-2 infection to identify additional cases where NAT was not performed, and resolve cases where false-negative and false-positive NATs are suspected. The majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established. url: https://doi.org/10.1093/ofid/ofaa387 doi: 10.1093/ofid/ofaa387 id: cord-342144-awtiqxx5 author: Hufert, F. title: Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie date: 2020-04-01 words: 3305.0 sentences: 352.0 pages: flesch: 48.0 cache: ./cache/cord-342144-awtiqxx5.txt txt: ./txt/cord-342144-awtiqxx5.txt summary: Ein klinischer Nutzen konnte beim Einsatz der eigentlich für die Behandlung von Humane-Immundefizienz(HIV)-Infektionen verwendeten Proteaseinhibitoren Lopinavir und Ritonavir (Kaletra ® ) zur Therapie des SARS-CoV nachgewiesen werden [6] . Im Dezember 2019 trat in China erstmalig ein neues Coronavirus auf, das zunächst als 2019-nCoV bezeichnet wurde und nach aktueller Nomenklatur des International Committee on Taxonomy of Viruses (ICTV) nun als SARS-CoV-2 bezeichnet wird [7] . So ist der kombinierte Einsatz der Proteaseinhibitoren Lopinavir und Ritonavir bei SARS-CoV-Patienten von klinischem Nutzen [6] . Eine weitere Studie mit MERS-CoV-Infizierten wird in Saudi-Arabien durchgeführt, bei der mit Lopinavir/Ritonavir plus Interferon-β behandelt wird [30] ; Daten zu den Ergebnissen liegen noch nicht vor. konnte gezeigt werden, dass die zelluläre Protease TMPRSS2 für die Infektiosität von SARS-CoV-2 essenziell ist und eine Hemmung dieser Protease mithilfe von Camostat-Mesilat die Vermehrung des Virus u. abstract: In December 2019 a new human coronavirus emerged in Wuhan, China, which is known as SARS-CoV‑2. The clinical course of the disease known as coronavirus disease 2019 (COVID-19) ranges from mild respiratory symptoms to severe lung failure. The virus is currently rapidly spreading around the world and pushing health systems to the limits of their capacity due to the exponential increase in the number of cases. The origin of SARS-CoV‑2 lies in the bat coronavirus pool and has now emerged in the human population due to interspecies transmission. Molecular diagnostic methods have been established in a very short time and a number of clinical studies on the effectiveness of different antiviral drugs are ongoing. The development of a vaccine using different approaches is also under investigation. Considering the high number of cases and mortality rates of up to 9% there is an urgent need for action. This article summarizes the current state of knowledge on human coronaviruses with a strong focus on the current data on SARS-CoV‑2. Due to the daily changing level of knowledge, the article reflects the status up to 21 March 2020. url: https://doi.org/10.1007/s00112-020-00910-2 doi: 10.1007/s00112-020-00910-2 id: cord-007713-611sp7uo author: Hughes, J. M. title: Emerging infectious diseases: the public’s view of the problem and what should be expected from the public health community date: 2005 words: 2683.0 sentences: 135.0 pages: flesch: 43.0 cache: ./cache/cord-007713-611sp7uo.txt txt: ./txt/cord-007713-611sp7uo.txt summary: In 2003 alone, a newly recognized coronavirus spread across five continents sickening more than 8,000 people and causing 774 deaths from a new disease designated severe acute respiratory syndrome (SARS) [4] , the exotic animal trade resulted in the first cases of human monkeypox in the Western hemisphere [5] , and highly pathogenic strains of avian influenza virus killed humans and devastated the poultry industry in parts of Asia [6] -further heightening fears of pandemic influenza. Improving preparedness and response: lessons learned from recent outbreaks -Strengthening existing and developing new national and international partnerships -Training and educating a multidisciplinary workforce -Ensuring "full use" of investments -Encouraging transparency and political will -Fostering a global commitment to address inequities -Developing and implementing preparedness plans and research agendas -Proactively communicating with health professionals, the media, and the public While the first line of defense in controlling an outbreak remains strong national surveillance systems that can readily detect outbreaks, the SARS experience highlighted the importance of global disease detection efforts [13] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121075/ doi: 10.1007/3-211-29981-5_17 id: cord-270837-xvauo76d author: Hui, David S. title: The 1-Year Impact of Severe Acute Respiratory Syndrome on Pulmonary Function, Exercise Capacity, and Quality of Life in a Cohort of Survivors date: 2005-10-31 words: 5821.0 sentences: 284.0 pages: flesch: 54.0 cache: ./cache/cord-270837-xvauo76d.txt txt: ./txt/cord-270837-xvauo76d.txt summary: Our assessment included: lung volume (total lung capacity [TLC], vital capacity, residual volume, functional residual capacity), spirometry (FVC, FEV1), diffusing capacity of the lung for carbon monoxide (Dlco), inspiratory and expiratory respiratory muscle strength, 6-min walk distance (6MWD), chest radiographs (CXRs), and HRQoL by Medical Outcomes Study 36-Item Short-Form General Health Survey questionnaire. The lung function tests at 12 months showed significantly lower percentage of predicted FVC, VC, TLC, RV, and Dlco in survivors who required ICU support than those who were treated on medical wards, although no significant difference was noted for 6MWD and respiratory muscle strength between the two groups ( Table 5) . The 1-year lung function indexes (percentage of predicted FVC, VC, TLC, RV, and Dlco) in survivors who required ICU support were remarkably lower than those of patients who were treated on medical wards, although no significant differences were noted for 6MWD, respiratory muscle strength, and health status between the two groups. abstract: Objective To examine pulmonary function, exercise capacity, and health-related quality of life (HRQoL) among severe acute respiratory syndrome (SARS) survivors. Methods We evaluated survivors with confirmed SARS at the Prince of Wales Hospital, Hong Kong, at 3, 6, and 12 months after symptom onset. Our assessment included: lung volume (total lung capacity [TLC], vital capacity, residual volume, functional residual capacity), spirometry (FVC, FEV1), diffusing capacity of the lung for carbon monoxide (Dlco), inspiratory and expiratory respiratory muscle strength, 6-min walk distance (6MWD), chest radiographs (CXRs), and HRQoL by Medical Outcomes Study 36-Item Short-Form General Health Survey questionnaire. Results Ninety-seven patients completed the serial assessments. There were 39 male and 58 female patients, and 63 patients (70%) were health-care workers (mean age, 36.9 years [SD, 9.5 years]; body mass index, 23.7 kg/m2 [SD, 4.0 kg/m2]). At 1 year, 27 patients (27.8%) had abnormal CXR findings. Four patients (4.1%), 5 patients (5.2%), and 23 patients (23.7%) had FVC, TLC, and Dlco values < 80% of predicted values, respectively. The 6MWD at 12 months was 511.0 m (SD, 89.8 m), which was higher than at 3 months (mean difference, 47.0 m; 95% confidence interval [CI], 31.8 to 62.1 m; p < 0.01) but not different from 6 months (mean difference, 9.7 m; 95% CI, − 4.4 to 23.8 m; p = 0.18). The 6MWD was lower than that for normal control subjects of the same age groups, and there was impairment of HRQoL at 12 months. Patients who required ICU admission (n = 31) showed higher CXR scores (1.6 [SD, 3.1]; vs 0.4 [SD, 1.1]; p = 0.04) and lower percentage of predicted FVC, TLC, and Dlco than those who did not, but there were no differences in 6MWD and health status. Conclusion Significant impairment in Dlco was noted in 23.7% of survivors 1 year after illness onset. Exercise capacity and health status of SARS survivors were remarkably lower than those of a normal population. url: https://api.elsevier.com/content/article/pii/S0012369215526299 doi: 10.1378/chest.128.4.2247 id: cord-270857-8424oq4x author: Hui, David S. title: Exhaled Air Dispersion During Oxygen Delivery Via a Simple Oxygen Mask date: 2007-08-31 words: 4034.0 sentences: 186.0 pages: flesch: 50.0 cache: ./cache/cord-270857-8424oq4x.txt txt: ./txt/cord-270857-8424oq4x.txt summary: We studied the dispersion of exhaled air through a simple oxygen mask applied to a human patient simulator (HPS) during the delivery of different oxygen flow in a room free of air currents. 7 As part of our influenza pandemic preparedness, we studied the safety of oxygen therapy by examining exhaled air dispersion from a simple oxygen mask attached to a human patient simulator (HPS) during the delivery of oxygen at different levels of flow. 33 Using a laser visualization technique and a mathematical model that was different from the one used in the current study for data analysis, we have previously shown a maximal dispersion distance of approximately 0.4 m during the application of oxygen at 4 L/min via a simple mask to the HPS, which was programmed at a respiratory rate of 12 breaths/min and a tidal volume of 0.5 L. abstract: Background Pneumonia viruses such as influenza may potentially spread by airborne transmission. We studied the dispersion of exhaled air through a simple oxygen mask applied to a human patient simulator (HPS) during the delivery of different oxygen flow in a room free of air currents. Methods The HPS represented a 70-kg adult male individual in a semi-sitting position on a hospital bed inclined at 45°. A simple oxygen mask was fitted to the HPS in the normal fashion. The head, neck, and internal airways of the HPS were configured to allow realistic airflow modeling in the airways and around the face. The HPS was programmed to breathe at a respiratory rate of 14 breaths/min with a tidal volume of 0.5 L. Airflow was marked with intrapulmonary smoke for visualization. A leakage jet plume was revealed by a laser light-sheet, and images were captured by high-resolution video. Smoke concentration in the exhaled plume was estimated from the total light intensity scattered by smoke particles. Findings A jet plume of air leaked through the side vents of the simple oxygen mask to lateral distances of 0.2, 0.22, 0.3, and 0.4 m from the sagittal plane during the delivery of oxygen at 4, 6, 8, and 10 L/min, respectively. Coughing could extend the dispersion distance beyond 0.4 m. Conclusion Substantial exposure to exhaled air occurs generally within 0.4 m from patients receiving supplemental oxygen via a simple mask. Health-care workers should take precautions when managing patients with community-acquired pneumonia of unknown etiology that is complicated by respiratory failure. url: https://api.elsevier.com/content/article/pii/S0012369215374481 doi: 10.1378/chest.07-0636 id: cord-290758-kz0qfy3r author: Hui, David S. title: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China date: 2020-02-29 words: 1305.0 sentences: 68.0 pages: flesch: 51.0 cache: ./cache/cord-290758-kz0qfy3r.txt txt: ./txt/cord-290758-kz0qfy3r.txt summary: title: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -The latest 2019 novel coronavirus outbreak in Wuhan, China The 2019-nCoV infection in Wuhan appears clinically milder than SARS or MERS overall in terms of severity, case fatality rate and transmissibility, which increases the risk of cases remaining undetected. The rapid identification and containment of a novel coronavirus virus in a short period of time is a reassuring and a commendable achievement by China''s public health authorities and reflects the increasing global capacity to detect, identify, define and contain new outbreaks. The latest analysis show that the Wuhan CoV cluster with the SARS CoV.10 (Novel coronavirus -China (01) Whilst several important aspects of MERS-CoV epidemiology, virology, mode of transmission, pathogenesis, diagnosis, clinical features, have been defined, there remain many unanswered questions, including source, transmission and epidemic potential. abstract: nan url: https://api.elsevier.com/content/article/pii/S1201971220300114 doi: 10.1016/j.ijid.2020.01.009 id: cord-333368-kjrk8nn9 author: Huizinga, Gabrielle P title: The Collision of Meta-Inflammation and SARS-CoV-2 Pandemic Infection date: 2020-09-03 words: 5490.0 sentences: 347.0 pages: flesch: 47.0 cache: ./cache/cord-333368-kjrk8nn9.txt txt: ./txt/cord-333368-kjrk8nn9.txt summary: While obesity and diabetes may complicate the delivery of supportive care in critical illness regardless of the underlying disease, lessons learned from the interaction of obesity with other systemic inflammatory syndromes suggest that obesity modifies biologic factors related to SARS-CoV-2 infection and the COVID-19 syndrome. In seasonal and pandemic influenza, however, obese individuals may be more susceptible to severe viral respiratory disease even if they mount a serologic response to vaccination 25 A c c e p t e d M a n u s c r i p t 11 Along with possible impairments in pathogen clearance, obese hosts are more likely to experience the breakdown of respiratory epithelium during a pulmonary infection, which leads to increased fluid in the airway space. abstract: The COVID-19 pandemic has forced us to consider the physiologic role of obesity in the response to infectious disease. There are significant disparities in morbidity and mortality by sex, weight and diabetes status. Numerous endocrine changes might drive these varied responses to SARS-CoV-2 infection including hormone and immune mediators, hyperglycemia, leukocyte responses, cytokine secretion, and tissue dysfunction. Studies of patients with severe COVID-19 disease have revealed the importance of innate immune responses in driving immunopathology and tissue injury. In this review we will describe the impact of the metabolically induced inflammation (meta-inflammation) that characterizes obesity on innate immunity. We consider that obesity-driven dysregulation of innate immune responses may drive organ injury in development of severe COVID-19 and impair viral clearance. url: https://doi.org/10.1210/endocr/bqaa154 doi: 10.1210/endocr/bqaa154 id: cord-271815-yr1dq258 author: Hulkower, Rachel L. title: Inactivation of surrogate coronaviruses on hard surfaces by health care germicides date: 2011-06-30 words: 4178.0 sentences: 222.0 pages: flesch: 47.0 cache: ./cache/cord-271815-yr1dq258.txt txt: ./txt/cord-271815-yr1dq258.txt summary: Methods The efficacy of health care germicides against 2 surrogate coronaviruses, mouse hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), was tested using the quantitative carrier method on stainless steel surfaces. This study was undertaken using the carrier method to evaluate 6 chemical germicides commonly used in health care settings for their efficacy in reducing infectivity of coronaviruses on environmental surfaces. The efficacy of 6 hospital surface germicides was tested against 2 coronaviruses, MHV and TGEV, used as surrogates for SARS-CoV. 3, 15, 17, 24 The results of this study show that, of the commonly used hospital germicides tested, only the ethanol-based germicides were able to achieve this level of reduction of infectious virus after 1 minute of contact time. Studies of hospital germicide efficacy against adenovirus 8 using the same carrier-based method with 1-minute contact times found greater log 10 reduction factors by OPA (4.37) than were observed in this study for TGEV (2.27) and MHV (1.71). abstract: Background In the 2003 severe acute respiratory syndrome outbreak, finding viral nucleic acids on hospital surfaces suggested surfaces could play a role in spread in health care environments. Surface disinfection may interrupt transmission, but few data exist on the effectiveness of health care germicides against coronaviruses on surfaces. Methods The efficacy of health care germicides against 2 surrogate coronaviruses, mouse hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), was tested using the quantitative carrier method on stainless steel surfaces. Germicides were o-phenylphenol/p-tertiary amylphenol) (a phenolic), 70% ethanol, 1:100 sodium hypochlorite, ortho-phthalaldehyde (OPA), instant hand sanitizer (62% ethanol), and hand sanitizing spray (71% ethanol). Results After 1-minute contact time, for TGEV, there was a log10 reduction factor of 3.2 for 70% ethanol, 2.0 for phenolic, 2.3 for OPA, 0.35 for 1:100 hypochlorite, 4.0 for 62% ethanol, and 3.5 for 71% ethanol. For MHV, log10 reduction factors were 3.9 for 70% ethanol, 1.3 for phenolic, 1.7 for OPA, 0.62 for 1:100 hypochlorite, 2.7 for 62% ethanol, and 2.0 for 71% ethanol. Conclusion Only ethanol reduced infectivity of the 2 coronaviruses by >3-log10 after 1 minute. Germicides must be chosen carefully to ensure they are effective against viruses such as severe acute respiratory syndrome coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/21256627/ doi: 10.1016/j.ajic.2010.08.011 id: cord-329454-69z28yli author: Humar, Atul title: Severe acute respiratory syndrome and the liver date: 2004-01-30 words: 1889.0 sentences: 117.0 pages: flesch: 45.0 cache: ./cache/cord-329454-69z28yli.txt txt: ./txt/cord-329454-69z28yli.txt summary: Liver enzyme abnormalities are common in SARS patients, although hepatic impair-ment has not been reported to be a prominent feature of this illness. However, this is the first report to associate hepatic SCoV infection and liver pathologic features. Defining the basis for susceptibility to severe inflammatory outcomes after coronavirus infection has obvious implications for the study and treatment of clinical SARS. Although the exact mechanisms for resistance and susceptibility to MHV3 coronavirus infection have not be determined, studies have shown that in resistant mice, infection leads to a T helper type 1 (TH1)-dominant response that, through the production of interferon, neutralizing antibodies, and cytotoxic T cells, results in viral clearance. A novel coronaviruses associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/14767979/ doi: 10.1002/hep.20069 id: cord-322007-xy66t0ls author: Humbert, S title: COVID-19 as a cause of immune thrombocytopenia date: 2020-05-20 words: 946.0 sentences: 71.0 pages: flesch: 49.0 cache: ./cache/cord-322007-xy66t0ls.txt txt: ./txt/cord-322007-xy66t0ls.txt summary: ITP has been described during the course of several viral infections: HIV, EBV, CMV, HCV but only once during severe acute respiratory distress coronavirus 2 (SARS-CoV-2) [2] . As immune thrombocytopenia was the most relevant diagnosis and due to severe bleeding, we started prednisone (1 mg/kg/day) and one course of intravenous immunoglobulins 1 g/kg. We describe here the second case of SARS-CoV-2-induced ITP. COVID-19 is caused by SARS-CoV-2, responsible for severe pneumonia in less than 20% of cases. COVID-19 thrombocytopenia could be secondary to direct platelet-virus interaction via pathogen recognition receptors (PRR). In our case, thrombocytopenia is lower than what is usually observed during COVID-19 and may be secondary to an immune-related mechanism. The suddenness and severity of thrombocytopenia could be explained by the patient''s advanced age as coronavirus induced higher antibodies production in older people [10] . Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 abstract: nan url: https://doi.org/10.1016/j.medmal.2020.05.003 doi: 10.1016/j.medmal.2020.05.003 id: cord-312561-9o2fhi6e author: Hung, I.F.N. title: Viral Loads in Clinical Specimens and SARS Manifestations date: 2004-09-17 words: 3328.0 sentences: 171.0 pages: flesch: 51.0 cache: ./cache/cord-312561-9o2fhi6e.txt txt: ./txt/cord-312561-9o2fhi6e.txt summary: A retrospective viral load study was performed on clinical specimens from 154 patients with laboratory-confirmed severe acute respiratory syndrome (SARS); the specimens were prospectively collected during patients'' illness. Viral load in nasopharyngeal aspirates (n = 142) from day 10 to day 15 after onset of symptoms was associated with oxygen desaturation, mechanical ventilation, diarrhea, hepatic dysfunction, and death. We compared the viral load in these specimens with the presence or absence of diarrhea, oxygen desaturation, mechanical ventilation, lymphopenia, hepatic dysfunction, abnormal urinalysis findings, and death rate by chi-square or Fisher exact test for categorical variables and by Mann-Whitney U test for continuous variables. A high viral load in serum was also associated with oxygen desaturation, mechanical ventilation, hepatic dysfunction, and death (all p < 0.01) but not with diarrhea or abnormal urinalysis findings. The importance of SARS-CoV as a respiratory pathogen is supported by the strong association of viral load in NPA with oxygen desaturation, mechanical ventilation, and death. abstract: A retrospective viral load study was performed on clinical specimens from 154 patients with laboratory-confirmed severe acute respiratory syndrome (SARS); the specimens were prospectively collected during patients' illness. Viral load in nasopharyngeal aspirates (n = 142) from day 10 to day 15 after onset of symptoms was associated with oxygen desaturation, mechanical ventilation, diarrhea, hepatic dysfunction, and death. Serum viral load (n = 53) was associated with oxygen desaturation, mechanical ventilation, and death. Stool viral load (n = 94) was associated with diarrhea, and urine viral load (n = 111) was associated with abnormal urinalysis results. Viral replications at different sites are important in the pathogenesis of clinical and laboratory abnormalities of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15498155/ doi: 10.3201/eid1009.040058 id: cord-314734-ai0hz4uq author: Hung, Ivan Fan-Ngai title: SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: a case series date: 2020-06-12 words: 4595.0 sentences: 248.0 pages: flesch: 56.0 cache: ./cache/cord-314734-ai0hz4uq.txt txt: ./txt/cord-314734-ai0hz4uq.txt summary: Thus, the Diamond Princess cruise ship, which was quarantined because of an onboard outbreak of COVID-19 in February, 2020, provides an opportunity to define the shedding pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient antibody responses before and after the onset of symptoms. Participants were prospectively screened by quantitative RT-PCR (RT-qPCR) of nasopharyngeal and throat swabs, and serum IgG and IgM against internal nucleoprotein and the surface spike receptor-binding protein (RBD) of SARS-CoV-2 at baseline (upon entering quarantine) and on days 4, 8, and 12 of quarantine. Evidence before this study We searched PubMed on March 14, 2020, with no date restrictions, for articles in English, using the terms "Covid-19", "coronavirus", "antibody", "viral load", "cruise ship", "quarantine", "shedding", and "seroconversion". By Feb 20, 2020, 76 passengers from Hong Kong were hospitalised in Japan after testing positive for SARS-CoV-2 by throat swab RT-PCR, of whom two individuals died from complications of the infection (appendix). abstract: BACKGROUND: A cruise ship is a closed-off environment that simulates the basic functioning of a city in terms of living conditions and interpersonal interactions. Thus, the Diamond Princess cruise ship, which was quarantined because of an onboard outbreak of COVID-19 in February, 2020, provides an opportunity to define the shedding pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient antibody responses before and after the onset of symptoms. METHODS: We recruited adult (≥18 years) passengers from Hong Kong who had been on board the Diamond Princess cruise ship docked in Yokohama, Japan in February, 2020. All participants had been found to be negative for SARS-CoV-2 by RT-PCR 4 days before disembarking and were transferred to further quarantine in a public estate in Hong Kong, where they were recruited. Participants were prospectively screened by quantitative RT-PCR (RT-qPCR) of nasopharyngeal and throat swabs, and serum IgG and IgM against internal nucleoprotein and the surface spike receptor-binding protein (RBD) of SARS-CoV-2 at baseline (upon entering quarantine) and on days 4, 8, and 12 of quarantine. FINDINGS: On Feb 22, 2020, 215 adults were recruited, of whom nine (4%; 95% CI 2–8) were positive for SARS-CoV-2 by RT-qPCR or serology and were hospitalised. Of these nine patients, nasopharyngeal swab RT-qPCR was positive in eight patients (89%; 57–99) at baseline. All nine patients were positive for anti-RBD IgG by day 8. Eight (89%; 57–99) were simultaneously positive for nasopharyngeal swab RT-PCR and anti-RBD IgG. One patient who was positive for anti-RBD IgG and had a negative viral load had multifocal peripheral ground-glass changes on high-resolution CT that were typical of COVID-19. Five patients (56%; 27–81) with ground-glass changes on high-resolution CT were found to have higher anti-nucleoprotein-IgG OD values on day 8 and 12 and anti-RBD IgG OD value on day 12 than patients without ground-glass changes. Six (67%; 35–88) patients remained asymptomatic throughout the 14-day quarantine period. INTERPRETATION: Patients with COVID-19 can develop asymptomatic lung infection with viral shedding and those with evidence of pneumonia on imaging tend to have an increased antibody response. Positive IgG or IgM confirmed infection of COVID-19 in both symptomatic and asymptomatic patients. A combination of RT-PCR and serology should be implemented for case finding and contact tracing to facilitate early diagnosis, prompt isolation, and treatment. FUNDING: Shaw Foundation Hong Kong; Sanming-Project of Medicine (Shenzhen); High Level-Hospital Program (Guangdong Health Commission). url: https://doi.org/10.1016/s1473-3099(20)30364-9 doi: 10.1016/s1473-3099(20)30364-9 id: cord-331835-nuhrd92z author: Hung, Kevin K. C. title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date: 2018-11-27 words: 4011.0 sentences: 201.0 pages: flesch: 51.0 cache: ./cache/cord-331835-nuhrd92z.txt txt: ./txt/cord-331835-nuhrd92z.txt summary: title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. This case study will use the example of the Metropole Hotel in Hong Kong in the international spread of Severe Acute Respiratory Syndrome (SARS) in 2003, and the effect of the government mandated quarantine of the Metropark Hotel during the swine flu 2009 in Hong Kong. After the SARS outbreak in Hong Kong the health authority established the Guidelines for Hotels in Preventing Severe Acute Respiratory Syndrome (SARS) [24] abstract: BACKGROUND: The global travel and tourism industry has been rapidly expanding in the past decades. The traditional focus on border screening, and by airline and cruise industries may be inadequate due to the incubation period of an infectious disease. This case study highlights the potential role of the hotel industry in epidemic preparedness and response. METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. RESULTS: The Metropole Hotel hastened the international spread of the 2003 SARS outbreak by the index case infecting visitors from Singapore, Vietnam, Canada as well as local people via close contact with the index case and the environmental contamination. The one-week quarantine of more than 300 guests and staff at the Metropark Hotel during the 2009 H1N1 swine flu exposed gaps in the partnership with the hotel industry. The subsequent guidelines for the hotel industry from the Centre of Health Protection focused largely on the maintenance of hygiene within the hotel premises. CONCLUSION: Positive collaborations may bring about effective preparedness across the health and the tourism sectors for future epidemics. Regular hygiene surveillance at hotel facilities, and developing coordination mechanism for impending epidemics on the use of screening, swift reporting and isolation of infected persons may help mitigate the impact of future events. Preparedness and contingency plans for infectious disease control for the hotel industry requires continuous engagement and dialogue. url: https://www.ncbi.nlm.nih.gov/pubmed/30482214/ doi: 10.1186/s12992-018-0438-6 id: cord-256572-sqz8yc7b author: Huo, Jiandong title: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date: 2020-05-06 words: 5378.0 sentences: 313.0 pages: flesch: 59.0 cache: ./cache/cord-256572-sqz8yc7b.txt txt: ./txt/cord-256572-sqz8yc7b.txt summary: The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Potent nanomolar affinity neutralising human monoclonal antibodies against the SARS-CoV RBD have been identified that attach at the ACE2 receptor binding site (including M396, CR3014 and 80R (Ter Meulen et al., 2006; Sui et al., 2004; Zhu et al., 2007) ). We determined the crystal structure of the SARS-CoV-2 RBD-CR3022 Fab complex (see Methods and Table S3 ) to investigate the relationship between the binding epitopes of ACE2 and CR3022. Full interpretation of the detailed interactions between CR3022 and the RBD was enabled by the second crystal form which diffracted to high resolution, 2.4 Å, and the structure of which was refined to give an R-work/R-free of 0.213/0.239 and good stereochemistry (Methods, Table S3, Figure S5 ). abstract: There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment. Highlights CR3022 neutralises SARS-CoV-2 Neutralisation is by destroying the prefusion SPIKE conformation This antibody may have therapeutic potential alone or with one blocking receptor attachment url: https://doi.org/10.1101/2020.05.05.079202 doi: 10.1101/2020.05.05.079202 id: cord-293946-4bquxdqa author: Huong, Nguyen Quynh title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date: 2020-08-10 words: 6229.0 sentences: 292.0 pages: flesch: 51.0 cache: ./cache/cord-293946-4bquxdqa.txt txt: ./txt/cord-293946-4bquxdqa.txt summary: In this study we investigated the presence and diversity of coronavirus sequences in the field rat trade distribution chain, wildlife farms specializing in raising rodents for human consumption, and bat guano "farms" and roosts near human dwellings to better understand the natural hosts of coronaviruses and the risk for these interfaces to facilitate spillover into humans. Out of 70 sites, coronavirus positives were detected at 58 including 100% (24/24) of live rat trade sites, 60.7% (17/28) of rodent wildlife farm sites, 94.1% (16/17) of bat guano farm sites, and at the one natural pteropid bat roost. Significant findings of this study are the high proportion of coronavirus positive wildlife (bats and rodents) and the increasing proportion of positives found along the rat trade supply chain from sub-interfaces close to the capture site (rat traders) to restaurants. abstract: Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this viral family as a zoonotic public health threat. To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013–2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151). Coronaviruses were also detected in rodents on the majority of wildlife farms sampled (60.7%, 17/28). These coronaviruses were found in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are raised on wildlife farms for human consumption as food. We identified six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including the Alpha-, Beta-, and Gammacoronaviruses. Our analysis also suggested either mixing of animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and avian coronaviruses were detected in rodent feces on wildlife farms. The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spillover to people. url: https://www.ncbi.nlm.nih.gov/pubmed/32776964/ doi: 10.1371/journal.pone.0237129 id: cord-256092-bph9ys72 author: Hussain, Aneela N. title: Role of testosterone in COVID-19 patients - a double-edged sword? date: 2020-09-17 words: 1574.0 sentences: 93.0 pages: flesch: 43.0 cache: ./cache/cord-256092-bph9ys72.txt txt: ./txt/cord-256092-bph9ys72.txt summary: Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Lower levels of testosterone result in the upregulation of ACE2 and TMPRSS2 receptors, facilitating SARS-CoV-1 entry into the alveolar cells, and deregulating a lung-protective pathway (4) . Thereby we hypothesize that low testosterone levels in males have a direct correlation with the severity of disease and a worse outcome in COVID-19. Patients with low testosterone have reportedly developed severe manifestations requiring assisted ventilation because of the upregulation of ACE-2 receptors in lower respiratory cells, increased risk of lung damage, and respiratory muscle catabolism. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China abstract: COVID-19 affects males twice as frequently as females with significantly increased severity and mortality. Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. The gradual decline in total and free testosterone levels has a direct correlation with serious pulmonary complications requiring advanced care (ICU, ventilators, ECMO, etc.). SARS-CoV-2 utilizes Angiotensin-Converting Enzyme II (ACE2) for entry in the host cell, and Transmembrane Protease, Serine 2 (TMPRSS2) to prime spike protein of SARS-CoV-2. Testosterone induces ACE-2 expression, a critical pulmonary protective enzyme. Low testosterone levels in males have a direct correlation with the high probability of ICU admission and the worse disease outcome (ARDS, duration of ICU stay, mortality). On the contrary, however, high testosterone levels can lead to thrombosis which is also one of the fatal manifestations in COVID-19 patients. A critical evaluation of the serum testosterone and its relevance to COVID-19 is warranted to re-evaluate strategies to effectively triage, prioritize, and manage high-risk patients for ICU admission, survival outcomes, targeted solutions, and operational algorithms. url: https://api.elsevier.com/content/article/pii/S0306987720321915 doi: 10.1016/j.mehy.2020.110287 id: cord-346930-gl573ip9 author: Hussain, Azhar title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date: 2020-05-24 words: 4177.0 sentences: 207.0 pages: flesch: 45.0 cache: ./cache/cord-346930-gl573ip9.txt txt: ./txt/cord-346930-gl573ip9.txt summary: Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. Since the emergence of the virus in China in December of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the globe resulting in the current global pandemic. Arbidol (also known as Umifenovir) is a promising repurposed antiviral agent with a unique mechanism of action targeting the S protein/ACE2 interaction and inhibiting membrane fusion of the viral envelope to the host cell [7] . abstract: As a new decade began, COVID-19 quickly gained importance as it became the cause of the current global pandemic. Research has been focusing on studying the structure of SARS-CoV-2 and investigates possible pharmaceutical approaches. With the number of cases increasing every day, globally, multiple drugs are being researched as possible candidates. Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. Furthermore, several supplements have also been documented in being utilized as treatment of COVID-19. The exact mechanism and efficacy of current candidate drugs are still being explored through clinical trials. Despite the advancements in current research with emerging treatments, social distancing and engaging in preventative measures remains crucial to attempt to prevent the occurrence of more cases and deaths, worldwide. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. url: https://doi.org/10.7759/cureus.8260 doi: 10.7759/cureus.8260 id: cord-315288-fcx4q6mp author: Hussain, Mohammed Hassan title: Tracheal swab from front of neck airway for SARS-CoV-2; a bronchial foreign body date: 2020-08-27 words: 1566.0 sentences: 105.0 pages: flesch: 62.0 cache: ./cache/cord-315288-fcx4q6mp.txt txt: ./txt/cord-315288-fcx4q6mp.txt summary: We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. Patients with front of neck airways, either in the form of a laryngectomy or tracheostomy stoma site, present a challenge in terms of testing for SARS-CoV-2. There is a need for clear guidance on how to test patients with front of neck airways for SARS-CoV-2. abstract: We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. A qualified nurse was performing a routine SARS-CoV-2 swab on a 51-year-old woman, fitted with a tracheostomy in the recent past following a craniotomy. This was part of the discharging protocol to a nursing home. During the sampling, part of the swab stylet snapped and was inadvertently dropped through the tracheostomy site. Initial CT imaging was reported as showing no signs of a foreign body but some inflammatory changes. Bedside flexible endoscopy through the tracheostomy site revealed the swab in a right lobar bronchus. This was subsequently removed by flexible bronchoscopy. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. url: https://doi.org/10.1136/bcr-2020-237787 doi: 10.1136/bcr-2020-237787 id: cord-344658-4z2697q6 author: Hutasoit, Novana title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology date: 2020-08-29 words: 2469.0 sentences: 132.0 pages: flesch: 54.0 cache: ./cache/cord-344658-4z2697q6.txt txt: ./txt/cord-344658-4z2697q6.txt summary: title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology The primary intention was to alleviate the tendency of SARS-CoV-2 (COVID-19) virus to linger longer on touch surfaces that attract high-to-medium volume human contact, such as the push plates used in publicly accessed buildings and hospitals. This work showcases the capability of cold-spray as a potential copper-coating solution for different in-use parts and components that can act as sources for the spread of the virus. In this work the authors have deposited copper coatings onto the stainless steel push-plates in a matter of 7 mins only, which is a marvellous demonstration of the application of the cold spray coating process for ongoing and future challenges arising from the pandemic. Table 1 and Fig. 2 presents the viricidal activity results of SARS-CoV-2 virus when exposed to three different metallic surfaces and compared with COVID-19 only and positive control solutions. abstract: In this work, cold-spray technique was employed for rapid coating of copper on in-use steel parts. The primary intention was to alleviate the tendency of SARS-CoV-2 (COVID-19) virus to linger longer on touch surfaces that attract high-to-medium volume human contact, such as the push plates used in publicly accessed buildings and hospitals. The viricidal activity test revealed that 96% of the virus was inactivated within 2-hrs, which was substantially shorter than the time required for stainless steel to inactivate the virus to the same level. Moreover, it was found that the copper-coated samples significantly reduces the lifetime of COVID-19 virus to less than 5-hrs. The capability of the cold-spray technique to generate antiviral copper coating on the existing touch surface eliminates the need for replacing the entire touch surface application with copper material. Furthermore, with a short manufacturing time to produce coatings, the re-deployment of copper-coated parts can be accomplished in minutes, thereby resulting in significant cost savings. This work showcases the capability of cold-spray as a potential copper-coating solution for different in-use parts and components that can act as sources for the spread of the virus. url: https://doi.org/10.1016/j.mfglet.2020.08.007 doi: 10.1016/j.mfglet.2020.08.007 id: cord-293715-lipme817 author: Hutchison, Lisa title: Neuropsychiatric Symptoms in an Adolescent Boy with Multisystem Inflammatory Syndrome in Children (MIS-C) date: 2020-06-30 words: 3230.0 sentences: 175.0 pages: flesch: 44.0 cache: ./cache/cord-293715-lipme817.txt txt: ./txt/cord-293715-lipme817.txt summary: BACKGROUND: Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID-19) is an emergent syndrome affecting children globally in the wake of the SARS-CoV-2 pandemic. METHOD: This case describes a 14-year-old boy who developed prominent neuropsychiatric symptoms including delirium followed by impairments in executive functioning in the context of MIS-C with positive SARS-CoV-2 antibodies. The recent SARS-CoV-2 pandemic has been associated with emergence of a new syndrome referred to as Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID19) . Given the paucity of knowledge concerning this syndrome''s effect on the nervous system, the intent of this case report is to describe the neuropsychiatric symptoms in one 14-year-old boy presenting with multisystem inflammatory syndrome and positive SARS-CoV-2 antibodies. Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicenter cohort abstract: BACKGROUND: Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID-19) is an emergent syndrome affecting children globally in the wake of the SARS-CoV-2 pandemic. The clinical presentation has similarities to Kawasaki disease and toxic shock syndrome. As knowledge of the cardiac and gastrointestinal manifestations has been emerging, little is known about the impact on the brain. METHOD: This case describes a 14-year-old boy who developed prominent neuropsychiatric symptoms including delirium followed by impairments in executive functioning in the context of MIS-C with positive SARS-CoV-2 antibodies. These symptoms improved in correlation with improvements in inflammatory markers. RESULTS: Neuropsychiatric manifestations including confusion, irritability, and headaches have been reported in pediatric patients with MIS-C. Potential mechanisms include direct neurotropic effect of SARS-CoV-2, secondary effects of systemic inflammation, and/or adverse side effects of treatment. CONCLUSIONS: MIS-C is a novel and poorly understood syndrome related to SARS-CoV-2 with effects on multiple organ systems including the central nervous system. As additional cases are reported and research expands, so too will our understanding of the neuropsychiatric manifestations. Better understanding of the underlying pathophysiology would aid in determining targeted interventions. url: https://doi.org/10.1016/j.psym.2020.06.015 doi: 10.1016/j.psym.2020.06.015 id: cord-341474-06113cn0 author: Huynh, Tien title: In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease date: 2020-05-14 words: 5393.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-341474-06113cn0.txt txt: ./txt/cord-341474-06113cn0.txt summary: Besides the identification of several high-potency drugs and/or molecules, we unveiled the consensus binding mechanism that a ligand prefers to bind the "anchor" site of the Mpro pocket, which might facilitate the future design and optimization of an inhibitor for the SARS-CoV-2''s Mpro. To verify the docking results, as an example, we further performed the MD simulation to investigate the stability of entecavir''s pose with the best affinity score inside the Mpro pocket (Figure 5a ). As shown in Figure 3c , our docking result verifies that the Boc group indeed occupies the "anchor" site, further validating the binding mechanisms discovered in this work for stabilizing the ligand inside the Mpro''s pocket. We found that the docking affinity scores of several molecules (such as nelfinavir and entecavir) are very close to those of the ligands found experimentally (N3 and O6K), and their binding stabilities with the Mpro were verified in MD simulations. abstract: [Image: see text] Currently, the new coronavirus disease 2019 (COVID-19) is a global pandemic without any well-calibrated treatment. To inactivate the SARS-CoV-2 virus that causes COVID-19, the main protease (Mpro) that performs key biological functions in the virus has been the focus of extensive studies. With the fast-response experimental efforts, the crystal structures of Mpro of the SARS-CoV-2 virus have just become available recently. Herein, we theoretically investigated the mechanism of binding between the Mpro’s pocket and various marketed drug molecules being tested in clinics to fight COVID-19 that show promising outcomes. By combining the existing experimental results with our computational ones, we revealed an important ligand binding mechanism of the Mpro, demonstrating that the binding stability of a ligand inside the Mpro pocket can be significantly improved if part of the ligand occupies its so-called “anchor” site. Along with the highly potent drugs and/or molecules (such as nelfinavir) revealed in this study, the newly discovered binding mechanism paves the way for further optimizations and designs of Mpro’s inhibitors with a high binding affinity. url: https://www.ncbi.nlm.nih.gov/pubmed/32406687/ doi: 10.1021/acs.jpclett.0c00994 id: cord-275257-upj8mvzn author: Hwang, E. Shelley title: Surgical Oncologists and the COVID-19 Pandemic: Guiding Cancer Patients Effectively through Turbulence and Change date: 2020-06-14 words: 8495.0 sentences: 389.0 pages: flesch: 40.0 cache: ./cache/cord-275257-upj8mvzn.txt txt: ./txt/cord-275257-upj8mvzn.txt summary: Perspectives are provided on: (1) maintaining a safe environment for surgical oncology care; (2) redirecting the multidisciplinary model to guide surgical decisions; (3) harnessing telemedicine to accommodate requisite physical distancing; (4) understanding interactions between SARS CoV-2 and cancer therapy; (5) considering the ethical impact of professional guidelines for surgery prioritization; and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. The panel provides perspectives on: (1) creating a safe environment for surgical oncology care, (2) redirecting the multidisciplinary model to guide surgical decisions, (3) harnessing telemedicine to accommodate requisite physical distancing, (4) understanding interactions between SARS CoV-2 and cancer therapy, (5) considering the ethical impact of professional guidelines for surgery prioritization, and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. abstract: BACKGROUND: The COVID-19 pandemic has posed extraordinary demands from patients, providers, and health care systems. Despite this, surgical oncologists must maintain focus on providing high-quality, empathetic care for the almost 2 million patients nationally who will be diagnosed with operable cancer this year. The focus of hospitals is transitioning from initial COVID-19 preparedness activities to a more sustained approach to cancer care. METHODS: Editorial Board members provided observations of the implications of the pandemic on providing care to surgical oncology patients. RESULTS: Strategies are presented that have allowed institutions to successfully prepare for cancer care during COVID-19, as well as other strategies that will help hospitals and surgical oncologists manage anticipated challenges in the near term. Perspectives are provided on: (1) maintaining a safe environment for surgical oncology care; (2) redirecting the multidisciplinary model to guide surgical decisions; (3) harnessing telemedicine to accommodate requisite physical distancing; (4) understanding interactions between SARS CoV-2 and cancer therapy; (5) considering the ethical impact of professional guidelines for surgery prioritization; and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. CONCLUSIONS: Until an effective vaccine becomes available for widespread use, it is imperative that surgical oncologists remain focused on providing optimal care for our cancer patients while managing the demands that the COVID-19 pandemic will continue to impose on all of us. url: https://doi.org/10.1245/s10434-020-08673-6 doi: 10.1245/s10434-020-08673-6 id: cord-294122-ou3wj4rz author: Hwang, Stephen W title: Population mortality during the outbreak of Severe Acute Respiratory Syndrome in Toronto date: 2007-05-29 words: 2944.0 sentences: 177.0 pages: flesch: 51.0 cache: ./cache/cord-294122-ou3wj4rz.txt txt: ./txt/cord-294122-ou3wj4rz.txt summary: BACKGROUND: Extraordinary infection control measures limited access to medical care in the Greater Toronto Area during the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak. The objective of this study was to determine if the period of these infection control measures was associated with changes in overall population mortality due to causes other than SARS. METHODS: Observational study of death registry data, using Poisson regression and interrupted time-series analysis to examine all-cause mortality rates (excluding deaths due to SARS) before, during, and after the SARS outbreak. An interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak. The interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak in 2003, as indicated by the fact that the observed rates remained almost entirely within the 95% CI for the predicted rates. abstract: BACKGROUND: Extraordinary infection control measures limited access to medical care in the Greater Toronto Area during the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak. The objective of this study was to determine if the period of these infection control measures was associated with changes in overall population mortality due to causes other than SARS. METHODS: Observational study of death registry data, using Poisson regression and interrupted time-series analysis to examine all-cause mortality rates (excluding deaths due to SARS) before, during, and after the SARS outbreak. The population of Ontario was grouped into the Greater Toronto Area (N = 2.9 million) and the rest of Ontario (N = 9.3 million) based upon the level of restrictions on delivery of clinical services during the SARS outbreak. RESULTS: There was no significant change in mortality in the Greater Toronto Area before, during, and after the period of the SARS outbreak in 2003 compared to the corresponding time periods in 2002 and 2001. The rate ratio for all-cause mortality during the SARS outbreak was 0.99 [95% Confidence Interval (CI) 0.93–1.06] compared to 2002 and 0.96 [95% CI 0.90–1.03] compared to 2001. An interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak. CONCLUSION: Limitations on access to medical services during the 2003 SARS outbreak in Toronto had no observable impact on short-term population mortality. Effects on morbidity and long-term mortality were not assessed. Efforts to contain future infectious disease outbreaks due to influenza or other agents must consider effects on access to essential health care services. url: https://www.ncbi.nlm.nih.gov/pubmed/17535440/ doi: 10.1186/1471-2458-7-93 id: cord-349117-xfir3m5p author: Hyseni, Inesa title: Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays date: 2020-09-10 words: 8298.0 sentences: 403.0 pages: flesch: 52.0 cache: ./cache/cord-349117-xfir3m5p.txt txt: ./txt/cord-349117-xfir3m5p.txt summary: After fully characterising lentiviral pseudotypes bearing the SARS-CoV-2 spike protein, we employed them in pseudotype-based neutralisation assays in order to profile the neutralising activity of human serum samples from an Italian sero-epidemiological study. SARS CoV-2 strain 2019-nCov/Italy wild-type virus (LV), which was handled in a level 3 bio-containment facility (BSL 3), was used as positive control in order to evaluate the spike glycoprotein expression, while a ∆-envelope pseudotype, prepared with the same procedure, was used as a negative control. To verify the expression of the spike protein in the SARS-CoV-2 pseudotypes, the spike was detected by Western blot; sera from convalescent SARS-CoV-2 patients, which have been shown to have a high neutralising titre in microneutralisation with a live virus, were used as the primary antibody, and goat anti-Human IgG as the secondary antibody. abstract: The recent outbreak of a novel Coronavirus (SARS-CoV-2) and its rapid spread across the continents has generated an urgent need for assays to detect the neutralising activity of human sera or human monoclonal antibodies against SARS-CoV-2 spike protein and to evaluate the serological immunity in humans. Since the accessibility of live virus microneutralisation (MN) assays with SARS-CoV-2 is limited and requires enhanced bio-containment, the approach based on “pseudotyping” can be considered a useful complement to other serological assays. After fully characterising lentiviral pseudotypes bearing the SARS-CoV-2 spike protein, we employed them in pseudotype-based neutralisation assays in order to profile the neutralising activity of human serum samples from an Italian sero-epidemiological study. The results obtained with pseudotype-based neutralisation assays mirrored those obtained when the same panel of sera was tested against the wild type virus, showing an evident convergence of the pseudotype-based neutralisation and MN results. The overall results lead to the conclusion that the pseudotype-based neutralisation assay is a valid alternative to using the wild-type strain, and although this system needs to be optimised and standardised, it can not only complement the classical serological methods, but also allows serological assessments to be made when other methods cannot be employed, especially in a human pandemic context. url: https://www.ncbi.nlm.nih.gov/pubmed/32927639/ doi: 10.3390/v12091011 id: cord-320612-vam0bli3 author: Höring, Steffen title: Management of a Hospital-Wide COVID-19 Outbreak Affecting Patients and Healthcare Workers date: 2020-10-26 words: 3403.0 sentences: 190.0 pages: flesch: 48.0 cache: ./cache/cord-320612-vam0bli3.txt txt: ./txt/cord-320612-vam0bli3.txt summary: Here, we report a large nosocomial outbreak of SARS-CoV-2 that occurred at a satellite hospital of the University Hospital Aachen, Germany, with 26 patients and 21 healthcare workers infected. Considering the numerous COVID-19 cases among patients and HCW, a hospital-wide screening was initiated on April 8 for all remaining SARS-CoV-2-negative patients and entire hospital staff. On the other hand, we analyzed the first cases among hospital staff, starting with the potential index nurse tested positive for SARS-CoV-2 on the 6th of April. By the time the outbreak emerged, the hospital policy already comprised preemptive infection control measures in order to prevent intrahospital spread of SARS-CoV-2. The second route of transmission addressed by our measures was infected HCW, who potentially spread SARS-CoV-2 to patients as well as to their co-workers. In the post-outbreak period, we have continued to screen all patients on their day of admission and all geriatric inpatients once weekly for SARS-CoV-2 in order to detect new cases timely. abstract: To the best of our knowledge, here, we describe the first hospital-wide outbreak of SARS-CoV-2 that occurred in Germany in April 2020. We aim to share our experience in order to facilitate the management of nosocomial COVID-19 outbreaks in healthcare facilities. All patients and hospital workers were screened for SARS-CoV-2 repeatedly. An infection control team on the side was installed. Strict spatial separation of patients and intensified hygiene training of healthcare workers (HCW) were initiated. By the time of reporting, 26 patients and 21 hospital workers were infected with a cluster of cases in the geriatric department. Fourteen patients developed COVID-19 consistent symptoms and five patients with severe pre-existing medical conditions died. The outbreak was successfully contained after intensified infection control measures were implemented and no further cases among patients were detected over a period of 14 days. Strict application of standard infection control measures proved to be successful in the management of nosocomial SARS-CoV-2 outbreaks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42399-020-00597-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s42399-020-00597-2 doi: 10.1007/s42399-020-00597-2 id: cord-291809-b7sosrc7 author: Iacovoni, Attilio title: A case series of Novel-Coronavirus infection in heart transplantation from two centers in the pandemic area in the North of Italy date: 2020-06-26 words: 2482.0 sentences: 163.0 pages: flesch: 53.0 cache: ./cache/cord-291809-b7sosrc7.txt txt: ./txt/cord-291809-b7sosrc7.txt summary: BACKGROUND Little is known about the coronavirus SARS-CoV-2 disease (COVID-19) in solid organ transplanted patients. (5) It has been speculated that 10 SARS-CoV-2 damages the host through two overlapping mechanisms, the first is the direct damage 11 of the virus itself, the second is an abnormal host response that may lead to a cytokine storm Aim of this study is to report a series of heart transplanted patients with SARS-CoV-2 infection 3 from two Heart Transplant Centers in the North of Italy describing clinical characteristics, 4 prognosis and the impact of COVID-19 on heart transplant programs. The high case fatality rate observed in heart transplanted patients may be due 3 to the characteristics of the cohort evaluated in the analysis. These characteristics may therefore explain the 12 higher incidence SARS-CoV-2 infection, the more severe clinical presentation and the higher 13 mortality rate in transplanted patients. Case report of COVID-19 in a kidney transplant recipient: Does 21 immunosuppression alter the clinical presentation? abstract: BACKGROUND Little is known about the coronavirus SARS-CoV-2 disease (COVID-19) in solid organ transplanted patients. We here report a series of heart transplanted patients with COVID-19 from two centers of Italy. METHODS All heart transplanted patients of Transplant Centers of Bergamo and Torino with a microbiologically confirmed SARS-CoV-2 infection were enrolled. Data collection included clinical presentation, laboratory and radiological findings, treatment and outcome. Follow-up was performed by visit or phone. RESULTS From February to March 2020 twenty-six heart transplanted patients (age 62±12 years; 77% males; time from transplant 10±10 years; 69% with comorbidities) had a microbiologically confirmed COVID-19. The most frequent symptom was fever, followed by cough. Seventeen patients had a pneumonia, 8 of them severe pneumonia. Seven patients died (27%) and 17 (65%) were hospitalized. Discontinuation of immunosuppression was associated with death (71 vs 21%, p=0.02). Conversely, all patients receiving steroids survived (p<0.001). Patients who received heart transplantation during COVID-19 outbreak survived and no acute graft rejection occurred. Patients who died were older than survivors, had a longer time from transplant and a worse clinical presentation at diagnosis. The current regimen enabled the prolonged survival and function of orthotopic cardiac xenografts in altogether 6 of 8 baboons, of which 4 were now added. These results exceed the threshold set by the Advisory Board of the International Society for Heart and Lung Transplantation. CONCLUSIONS COVID-19 has a significant impact on long term heart transplanted patients. Conversely, SARS-CoV-2 infection seems to have a limited influence on more recent transplants. Our experience may suggest that heart transplantation programs can be maintained even during the pandemic phase if specific and tailored paths to prevent and to limit virus transmission are provided. url: https://doi.org/10.1016/j.healun.2020.06.016 doi: 10.1016/j.healun.2020.06.016 id: cord-328289-3h3kmjlz author: Iadecola, Costantino title: Effects of COVID-19 on the nervous system date: 2020-08-19 words: 6524.0 sentences: 349.0 pages: flesch: 40.0 cache: ./cache/cord-328289-3h3kmjlz.txt txt: ./txt/cord-328289-3h3kmjlz.txt summary: Another Parkinson''s disease patient with obesity, hypertension and diabetes, exhibited at autopsy, in addition to hypoxic-ischemic neuronal damage, microhemorrhages, white matter lesions and enlarged perivascular spaces, but no evidence of SARS-CoV-2 in the brain (Kantonen et al., 2020) . The encephalopathy is most likely a consequence of systemic factors, such as cytokine sickness, hypoxia and metabolic dysfunction due to peripheral organ failure, while the strokes seem to be related more to hypercoagulability and endothelial injury than to SARS-CoV-2 vasculitis affecting brain vessels. In some cases, the possibility of a SARS-CoV-2 encephalitis could not be ruled out based on the potential for the virus to infect neurons (Song et al., 2020) , but definitive clinical and pathological evidence of neurotropism is lacking. abstract: Summary Neurological complications have emerged as a significant cause of morbidity and mortality in the ongoing COVID-19 pandemic. Beside respiratory insufficiency, many hospitalized patients exhibit neurological manifestations, ranging from headache and loss of smell, to confusion and disabling strokes. COVID-19 is also anticipated to take a toll on the nervous system in the long term. Here we will provide a critical appraisal of the potential for neurotropism and mechanisms of neuropathogenesis of SARS-CoV-2, as they relate to the acute and chronic neurological consequences of the infection. Finally, we will examine potential avenues for future research and therapeutic development. url: https://api.elsevier.com/content/article/pii/S0092867420310709 doi: 10.1016/j.cell.2020.08.028 id: cord-261414-vqvctafm author: Ian Gallicano, G. title: Molecular targeting of vulnerable RNA sequences in SARS CoV-2: identifying clinical feasibility date: 2020-11-12 words: 3032.0 sentences: 230.0 pages: flesch: 58.0 cache: ./cache/cord-261414-vqvctafm.txt txt: ./txt/cord-261414-vqvctafm.txt summary: Here we show that siRNAs and miRNAs inhibit SARS CoV-2 spike protein production in a dose-dependent manner in both HEK293 cells and a primary human airway tracheal cell line. Two cell types, HEK293 cells and primary human tracheal cells (hpTCs) were employed to test the hypothesis that siRNAs or miRNAs could suppress SARS CoV-2 spike expression. As a result, electroporation was used to introduce spike cDNA into hpTCs. Twenty four hours after electroporation of spike plasmid, 200 nM of each small RNA (the concentration seen to virtually completely suppress spike in HEK293 cells) was transfected resulting in marked reduction in spike protein expression in both siRNA1 + 2 and miRNA1 + 2 samples (Fig. 3A) . The data in Fig. 3B , C reveal that siRNA1/NT (non-transfection reagent) suppressed spike protein production in a dose-dependent manner in HEK293 cells (Fig. 3B ). abstract: Covid-19 (SARS CoV-2) has become a deadly, world-wide pandemic. Although most who are infected survive, complications from the virus can be pronounced and long-lasting. To date, of all the respiratory viruses including influenza and coronaviruses, only influenza has had a drug (i.e., Tamiflu) specifically targeted to treat and prevent infection. As a result, additional agents that specifically target viral production and are clinically feasible are needed to alleviate respiratory viral infections. The idea of using a miRNA/siRNA molecular approach for treating various diseases was postulated over a decade ago; however, only within the past few years has it become feasible. One technological advancement has been the molecular linkage of lipophilic moieties to mi/siRNAs in order to bypass the need for enveloping these inhibitory RNAs in lipid-based transfection reagents, which could irritate the airway if inhaled. Here we show that siRNAs and miRNAs inhibit SARS CoV-2 spike protein production in a dose-dependent manner in both HEK293 cells and a primary human airway tracheal cell line. We also show that this inhibition is equally robust using a clinically relevant siRNA that does not need to be prepped with a transfection reagent. url: https://doi.org/10.1038/s41434-020-00210-0 doi: 10.1038/s41434-020-00210-0 id: cord-263945-yli5suxb author: Iancu, Gabriela Mariana title: Viral exanthema as manifestation of SARS-CoV-2 infection: A case report date: 2020-08-28 words: 2216.0 sentences: 142.0 pages: flesch: 47.0 cache: ./cache/cord-263945-yli5suxb.txt txt: ./txt/cord-263945-yli5suxb.txt summary: RATIONALE: The clinical manifestations of the SARS-CoV-2 infection are mainly respiratory but the virus can cause a variety of symptoms. PATIENT CONCERNS: We present the case of SARS-CoV-2 infection in a previously healthy woman who presented with respiratory symptoms and developed anosmia, diarrhea, and an erythematous maculo-papular rash on day 15 from symptom onset. [6] Pathogenetically, the appearance of cutaneous lesions during the SARS-CoV-2 infection can be explained by an immune response initiated by the viral nucleotides which activate Langerhans cells with the secondary involvement of keratinocytes (maculopapular, urticarial and chicken pox-like rashes), by microthrombi formation and cutaneous vasculopathy (chilblain lesions, livedo reticularis, erythema multiforme-like rash, gangrene), or by reaction to the medication administered (urticaria, erythroderma, erythema multiforme, etc.). [7, 8] We report a case of disseminated exanthema that appeared after 15 days of treatment for SARS-CoV-2 infection in a patient without other medical and dermatological problems in the past. abstract: RATIONALE: The clinical manifestations of the SARS-CoV-2 infection are mainly respiratory but the virus can cause a variety of symptoms. Dermatological findings are less well-characterized. Data is scarce on their timing, type and correlation with the immune response. PATIENT CONCERNS: We present the case of SARS-CoV-2 infection in a previously healthy woman who presented with respiratory symptoms and developed anosmia, diarrhea, and an erythematous maculo-papular rash on day 15 from symptom onset. DIAGNOSIS: The nasopharyngeal swab tested by real time PCR for COVID-19 was positive. We interpreted this as a viral exanthema likely caused by an immune response to SARS-CoV-2 nucleotides. INTERVENTIONS: She was treated with Hydroxychloroquine, Azithromycin and Lopinavir/Ritonavir, and the rash with topical corticosteroids. OUTCOMES: All symptoms resolved except for anosmia which persisted for 6 weeks. At the 4- and 6-weeks follow-up the IgG titers for SARS-CoV-2 were high. LESSONS: We must consider that SARS-CoV-2 has a multi-organ tropism. In our case, the SARS-CoV-2 infection had lung, nasopharyngeal, neurological, digestive, and skin manifestations. Identifying the different manifestations is useful for understanding the extent of SARS-CoV-2 infection. We not only present a rare manifestation but also suggest that cutaneous manifestations may correlate with immunity. url: https://www.ncbi.nlm.nih.gov/pubmed/32871902/ doi: 10.1097/md.0000000000021810 id: cord-331094-22366b81 author: Ianevski, Aleksandr title: Potential Antiviral Options against SARS-CoV-2 Infection date: 2020-06-13 words: 6822.0 sentences: 424.0 pages: flesch: 49.0 cache: ./cache/cord-331094-22366b81.txt txt: ./txt/cord-331094-22366b81.txt summary: We also screened 136 safe-in-man broad-spectrum antivirals against the SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. After the initial screening, we identified apilimod, emetine, amodiaquine, obatoclax, homoharringtonine, salinomycin, arbidol, posaconazole and nelfinavir as compounds that rescued virus-infected cells from death (AUC from 285 to 585; Table S1 ). We next profiled transcriptional responses to nelfinavir, amodiaquine or both drugs in virus-or mock-infected Vero-E6 cells at 24 h. Anti-SARS-CoV-2 activity of safe-in man broad-spectrum antivirals in Vero-E6 cells. Here, we found that combinations of nelfinavir with salinomycin, amodiaquine, obatoclax, emetine or homoharringtonine were synergistic against SARS-CoV-2 in Vero-E6 cells. Thus, the amodiaquine and nelfinavir combination could result in better efficacy and decreased toxicity for the treatment of SARS-CoV-2 and perhaps other viral infections. Transcriptomic analysis of mock-and SARS-CoV-2-infected Vero-E6 cells treated with nelfinavir, amodiaquine or both drugs. abstract: As of June 2020, the number of people infected with severe acute respiratory coronavirus 2 (SARS-CoV-2) continues to skyrocket, with more than 6.7 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. However, developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent sera and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here, we developed a neutralization assay using SARS-CoV-2 strain and Vero-E6 cells. We identified the most potent sera from recovered patients for the treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against the SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that a combination of orally available virus-directed nelfinavir and host-directed amodiaquine exhibited the highest synergy. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32545799/ doi: 10.3390/v12060642 id: cord-348855-lnltoj1n author: Iannaccone, Giulia title: Weathering the Cytokine Storm in COVID-19: Therapeutic Implications date: 2020-06-29 words: 4669.0 sentences: 207.0 pages: flesch: 37.0 cache: ./cache/cord-348855-lnltoj1n.txt txt: ./txt/cord-348855-lnltoj1n.txt summary: The exaggerated cytokine release in response to viral infection, a condition known as cytokine release syndrome (CRS) or cytokine storm, is emerging as the mechanism leading to ARDS and MOF in COVID-19, thus endorsing the hypothesis that properly timed anti-inflammatory therapeutic strategies could improve patients'' clinical outcomes and prognosis. CS are the cornerstone of treatments for cytokine storms and macrophage activation syndrome in autoimmune/autoinflammatory diseases [18] ; in the COVID-19 scenario they may be useful in the more severe forms of CRS to curb the systemic inflammatory response and prevent the occurrence of ARDS, if appropriately timed [10, 19] , 20]. Tocilizumab is now already included in many practice guidelines for COVID-19 management, especially for the treatment of critically ill patients with severe refractory hypoxemia in a later stage after the high-viral-load initial phase all over the world, while we wait for more definite data from multiple ongoing clinical trials [42] . abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged in Wuhan, Hubei-China, as responsible for the coronavirus disease 2019 (COVID-19) and then spread rapidly worldwide. While most individuals remain asymptomatic or develop only mild symptoms, approximately 5% develop severe forms of COVID-19 characterized by acute respiratory distress syndrome (ARDS) and multiple-organ failure (MOF) that usually require intensive-care support and often yield a poor prognosis. SUMMARY: The pathophysiology of COVID-19 is far from being completely understood, and the lack of effective treatments leads to a sense of urgency to develop new therapeutic strategies based on pathophysiological assumptions. The exaggerated cytokine release in response to viral infection, a condition known as cytokine release syndrome (CRS) or cytokine storm, is emerging as the mechanism leading to ARDS and MOF in COVID-19, thus endorsing the hypothesis that properly timed anti-inflammatory therapeutic strategies could improve patients' clinical outcomes and prognosis. KEY MESSAGES: The objective of this article is to explore and comment on the potential role of the promising immunomodulatory therapies using pharmacological and nonpharmacological approaches to overcome the dysregulated proinflammatory response in COVID-19. url: https://doi.org/10.1159/000509483 doi: 10.1159/000509483 id: cord-254120-1q8tqeg7 author: Iannone, Primiano title: The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness. date: 2020-04-11 words: 3240.0 sentences: 207.0 pages: flesch: 47.0 cache: ./cache/cord-254120-1q8tqeg7.txt txt: ./txt/cord-254120-1q8tqeg7.txt summary: The WHO, ECDC and CDC have issued conflicting guidelines on the use of respiratory filters (N95) by HCWs. Methods We searched PubMed, Embase and The Cochrane Library from the inception to March 21, 2020 to identify randomized controlled trials (RCTs) comparing N95 respirators versus surgical masks for prevention of COVID-19 or any other respiratory infection among HCWs. The grading of recommendations, assessment, development, and evaluation (GRADE) was used to evaluate the quality of evidence. However, wearing N95 respirators can prevent 73 more (95% CI 46-91) clinical respiratory infections per 1000 HCWs compared to surgical masks (2 RCTs; 2594 patients; low quality of evidence). We therefore conducted a systematic review aimed at assessing the efficacy of N95 respirators versus surgical masks for the prevention of respiratory tract infections transmission among HCWs. The evidence from the review can then be used for the development of an appropriate GRADE framework for public health policy guidelines. abstract: Background Protecting Health Care Workers (HCWs) during routine care of suspected or confirmed COVID-19 patients is of paramount importance to halt the SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus-2) pandemic. The WHO, ECDC and CDC have issued conflicting guidelines on the use of respiratory filters (N95) by HCWs. Methods We searched PubMed, Embase and The Cochrane Library from the inception to March 21, 2020 to identify randomized controlled trials (RCTs) comparing N95 respirators versus surgical masks for prevention of COVID-19 or any other respiratory infection among HCWs. The grading of recommendations, assessment, development, and evaluation (GRADE) was used to evaluate the quality of evidence. Findings Four RCTs involving 8736 HCWs were included. We did not find any trial specifically on prevention of COVID-19. However, wearing N95 respirators can prevent 73 more (95% CI 46-91) clinical respiratory infections per 1000 HCWs compared to surgical masks (2 RCTs; 2594 patients; low quality of evidence). A protective effect of N95 respirators in laboratory-confirmed bacterial colonization (RR= 0.41; 95%CI 0.28-0.61) was also found. A trend in favour of N95 respirators was observed in preventing laboratory-confirmed respiratory viral infections, laboratory-confirmed respiratory infection, and influenza like illness. Interpretation We found no direct high quality evidence on whether N95 respirators are better than surgical masks for HCWs protection from SARS-CoV-2. However, low quality evidence suggests that N95 respirators protect HCWs from clinical respiratory infections. This finding should be contemplated to decide the best strategy to support the resilience of healthcare systems facing the potentially catastrophic SARS-CoV-2 pandemic. url: https://doi.org/10.1101/2020.04.06.20054841 doi: 10.1101/2020.04.06.20054841 id: cord-273426-55vu6b3u author: Iba, Toshiaki title: Coagulopathy of Coronavirus Disease 2019 date: 2020-05-26 words: 4536.0 sentences: 257.0 pages: flesch: 31.0 cache: ./cache/cord-273426-55vu6b3u.txt txt: ./txt/cord-273426-55vu6b3u.txt summary: Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. (Crit Care Med 2020; XX:00-00) Key Words: coagulopathy; coronavirus; coronavirus disease 2019; disseminated intravascular coagulation; hypercoagulability; thromboembolism I ncreasing communications worldwide have reported that hospitalized, critically ill coronavirus disease 2019 (COVID-19) patients are frequently developing laboratory abnormalities compatible with hypercoagulability and clinically a high prevalence of thromboembolic events (1). abstract: Recent studies have reported a high prevalence of thrombotic events in coronavirus disease 2019. However, the significance of thromboembolic complications has not been widely appreciated. The purpose of this review is to provide current knowledge of this serious problem. DESIGN: Narrative review. DATA SOURCES: Online search of published medical literature through PubMed using the term “COVID-19,” “SARS,” “acute respiratory distress syndrome,” “coronavirus,” “coagulopathy,” “thrombus,” and “anticoagulants.” STUDY SELECTION AND DATA EXTRACTION: Articles were chosen for inclusion based on their relevance to coagulopathy and thrombosis in coronavirus disease 2019, and anticoagulant therapy. Reference lists were reviewed to identify additional relevant articles. DATA SYNTHESIS: Coronavirus disease 2019 is associated with a strikingly high prevalence of coagulopathy and venous thromboembolism that may contribute to respiratory deterioration. Monitoring coagulation variables is important, as abnormal coagulation tests are related to adverse outcomes and may necessitate adjuvant antithrombotic interventions. In the initial phase of the infection, d-dimer and fibrinogen levels are increased, while activated partial prothrombin time, prothrombin time, and platelet counts are often relatively normal. Increased d-dimer levels three times the upper limit of normal may trigger screening for venous thromboembolism. In all hospitalized patients, thromboprophylaxis using low-molecular-weight heparin is currently recommended. The etiology of the procoagulant responses is complex and thought to be a result of specific interactions between host defense mechanisms and the coagulation system. Although the coagulopathy is reminiscent of disseminated intravascular coagulation and thrombotic microangiopathy, it has features that are markedly distinct from these entities. CONCLUSIONS: Severe acute respiratory syndrome coronavirus 2/coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. d-dimers and fibrinogen levels should be monitored, and all hospitalized patients should undergo thromboembolism prophylaxis with an increase in therapeutic anticoagulation in certain clinical situations. url: https://www.ncbi.nlm.nih.gov/pubmed/32467443/ doi: 10.1097/ccm.0000000000004458 id: cord-312684-3i2r2ahr author: Iba, Toshiaki title: Coagulopathy in COVID‐19 date: 2020-06-18 words: 3630.0 sentences: 213.0 pages: flesch: 39.0 cache: ./cache/cord-312684-3i2r2ahr.txt txt: ./txt/cord-312684-3i2r2ahr.txt summary: For example, the coronavirus that caused severe acute respiratory syndrome (SARS) in 2002 (SARS-CoV-1) were reported to be associated with thrombocytopenia (55%), thrombocytosis (49%), and prolonged activated partial thromboplastin time (aPTT) (63%), but the incidence of bleeding was not high [5, 6] . In this respect, Chinese experts noted that in severe cases, patients can develop acute respiratory distress syndrome (ARDS), with coagulation predominant-type coagulopathy [9] . The excess production of proinflammatory cytokines, increased levels of damage-associated molecular patterns (DAMPs), the stimulation of cell-death mechanisms and vascular endothelial damage are the major causes of coagulation disorder in any severe infection (Fig. 1) . The major targets of the SARS-CoV-2 are the lung epithelial cell, lymphocyte, and the vascular endothelial cell, and these findings can explain that the clinical presentation of severe COVID-19 is characterized by ARDS, shock, and coagulopathy [12, 47] . abstract: The COVID‐19 pandemic has become an urgent issue in every country. Based on recent reports, the most severely ill patients present with coagulopathy, and disseminated intravascular coagulation (DIC)‐like massive intravascular clot formation is frequently seen in this cohort. Therefore, coagulation tests may be considered useful to discriminate severe cases of COVID‐19. The clinical presentation of COVID‐19‐associated coagulopathy is organ dysfunction primarily, while hemorrhagic events are less frequent. Changes in hemostatic biomarkers represented by increase in D‐dimer and fibrin/fibrinogen degradation products indicate the essence of coagulopathy is massive fibrin formation. In comparison with bacterial‐sepsis‐associated coagulopathy/DIC, prolongation of prothrombin time, and activated partial thromboplastin time, and decrease in antithrombin activity is less frequent and thrombocytopenia is relatively uncommon in COVID‐19. The mechanisms of the coagulopathy are not fully elucidated, however. It is speculated that the dysregulated immune responses orchestrated by inflammatory cytokines, lymphocyte cell‐death, hypoxia, and endothelial damage are involved. Bleeding tendency is uncommon, but the incidence of thrombosis in COVID‐19 and the adequacy of current recommendations regarding standard venous thromboembolic dosing are uncertain. url: https://www.ncbi.nlm.nih.gov/pubmed/32558075/ doi: 10.1111/jth.14975 id: cord-268827-qwcbvtna author: Ibanez, Agustin title: COVID-19 in older people with cognitive impairment in Latin America date: 2020-08-18 words: 1465.0 sentences: 88.0 pages: flesch: 49.0 cache: ./cache/cord-268827-qwcbvtna.txt txt: ./txt/cord-268827-qwcbvtna.txt summary: 9 If SARS-CoV-2 can impair proteostasis through ORF8 binding and cause dysregulated endoplasmic reticulum protein traffick ing, then α-synuclein could aggregate uncontrollably. The COVID-19 pandemic in Latin America and Caribbean countries (LACs) has failed to capture the attention exiguous. 7 Many hospitals in LACs have inadequate protective equipment and there is scarce support for health-care workers who become sick. implemented control measures, is third highest among LACs. The public health conditions in these countries are complex and pose unique challenges; one underlying explanation for the surge in cases might be a large informal economy, in which workers need to leave their house every day to clean other households or to stand, for instance, at crowded traffic corners to sell their goods or shine shoes. For instance, with 20% of over 11 000 health workers in Mexico ill with COVID-19-one of the highest rates in the world-hospital staffing is and attract the resources necessary to control it. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1474442220302702 doi: 10.1016/s1474-4422(20)30270-2 id: cord-312160-2820aftb author: Ibrahim, Mahmoud A.A. title: In silico Drug Discovery of Major Metabolites from Spices as SARS-CoV-2 Main Protease Inhibitors date: 2020-10-08 words: 2443.0 sentences: 162.0 pages: flesch: 51.0 cache: ./cache/cord-312160-2820aftb.txt txt: ./txt/cord-312160-2820aftb.txt summary: Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). The binding energies of the investigated spices compounds with SARS-CoV-2 M pro were estimated using molecular mechanical-generalized Born surface area (MM-GBSA) approach with modified GB model (igb=2) implemented in AMBER16 software [27] . The physicochemical parameters of the most promising natural spices as SARS-CoV-2 M pro inhibitors were predicted using the online Molinspiration cheminformatics software %ABS was estimated as follows [28] : The online web-based tools of SwissTargetPredicition (http://www.swisstargetprediction.ch) were applied to predict the biological targets for the most promising natural spices as SARS-CoV-2 M pro inhibitors. Since the main protease of SARS-CoV-2 (M pro ) plays a critical role in the viral replication process, structure-based computational modeling of ligand-receptor interactions and molecular dynamics has been used to screen metabolites from common spices as potential M pro inhibitors. abstract: Coronavirus Disease 2019 (COVID-19) is an infectious illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), originally identified in Wuhan, China (December 2019) and has since expanded into a pandemic. Here, we investigate metabolites present in several common spices as possible inhibitors of COVID-19. Specifically, 32 compounds isolated from 14 cooking seasonings were examined as inhibitors for SARS-CoV-2 main protease (M(pro)), which is required for viral multiplication. Using a drug discovery approach to identify possible antiviral leads, in silico molecular docking studies were performed. Docking calculations revealed a high potency of salvianolic acid A and curcumin as M(pro) inhibitors with binding energies of −9.7 and −9.2 kcal/mol, respectively. Binding mode analysis demonstrated the ability of salvianolic acid A and curcumin to form nine and six hydrogen bonds, respectively with amino acids proximal to M(pro)'s active site. Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). Molecular mechanics-generalized Born surface area energy calculations revealed greater salvianolic acid A affinity for the enzyme over curcumin and lopinavir with energies of −44.8, −34.2 and −34.8 kcal/mol, respectively. Using a STRING database, protein-protein interactions were identified for salvianolic acid A included the biochemical signaling genes ACE, MAPK14 and ESR1; and for curcumin, EGFR and TNF. This study establishes salvianolic acid A as an in silico natural product inhibitor against the SARS-CoV-2 main protease and provides a promising inhibitor lead for in vitro enzyme testing. url: https://www.sciencedirect.com/science/article/pii/S0010482520303772?v=s5 doi: 10.1016/j.compbiomed.2020.104046 id: cord-331109-a8e7r80d author: Ibrahim, Yassmin S. title: Case Report: Paralytic Ileus: A Potential Extrapulmonary Manifestation of Severe COVID-19 date: 2020-08-31 words: 2354.0 sentences: 160.0 pages: flesch: 48.0 cache: ./cache/cord-331109-a8e7r80d.txt txt: ./txt/cord-331109-a8e7r80d.txt summary: We report two cases of SARS-CoV-2 infection complicated by paralytic ileus. Several authors have postulated that the angiotensin-converting enzyme 2 receptors, the host receptors for COVID-19, that are present on enterocytes in both the small and large bowel might mediate viral entry and resultant inflammation. We describe two cases of severe COVID-19 pneumonia who developed paralytic ileus during their disease course, which may represent one of the luminal manifestations of severe SARS-CoV-2 infection. 7 A review of 29 studies noted that 12% of patients with SARS-CoV-2 infection had gastrointestinal symptoms, including diarrhea, nausea, and vomiting. In conclusion, we report paralytic small and large bowel ileus as a complication of COVID-19. The added value of the present case report is the detailed histopathological evidence supporting a role for COVID-19-induced micro-thrombosis, thereby compromising microcirculatory function and resultant colonic bowel dilatation and perforation in the first patient. abstract: The COVID-19 pandemic has recently spread worldwide, presenting primarily in the form of pneumonia or other respiratory disease. In addition, gastrointestinal manifestations have increasingly been reported as one of the extrapulmonary features of the virus. We report two cases of SARS-CoV-2 infection complicated by paralytic ileus. The first patient was a 33-year-old man who was hospitalized with severe COVID-19 pneumonia requiring ventilator support and intensive care. He developed large bowel dilatation and perforation of the mid-transverse colon, and underwent laparotomy and colonic resection. Histopathology of the resected bowel specimen showed acute inflammation, necrosis, and hemorrhage, supporting a role for COVID-19–induced micro-thrombosis leading to perforation. The second patient was a 33-year-old man who had severe COVID-19 pneumonia, renal failure, and acute pancreatitis. His hospital course was complicated with paralytic ileus, and he improved with conservative management. Both cases were observed to have elevated liver transaminases, which is consistent with other studies. Several authors have postulated that the angiotensin-converting enzyme 2 receptors, the host receptors for COVID-19, that are present on enterocytes in both the small and large bowel might mediate viral entry and resultant inflammation. This is a potential mechanism of paralytic ileus in cases of severe COVID-19 infection. Recognizing paralytic ileus as a possible complication necessitates timely diagnosis and management. url: https://doi.org/10.4269/ajtmh.20-0894 doi: 10.4269/ajtmh.20-0894 id: cord-268453-87b298uk author: Ibáñez, Sebastián title: Hydroxychloroquine and chloroquine in COVID-19: should they be used as standard therapy? date: 2020-06-03 words: 3500.0 sentences: 150.0 pages: flesch: 48.0 cache: ./cache/cord-268453-87b298uk.txt txt: ./txt/cord-268453-87b298uk.txt summary: In the absence of a vaccine and specifically designed antivirals, the medical community has proposed the use of various previously available medications in order to reduce the number of patients requiring prolonged hospitalizations, oxygen therapy, and mechanical ventilation and to decrease mortality from coronavirus disease 2019 (COVID-19). HCQ was, in vitro, at least as effective as chloroquine in inhibiting SARS-CoV-2 infection, although it should be noted that studies on its mechanisms of action are not as extensive as with CQ [30] . The evidence for the use of hydroxychloroquine or chloroquine in COVID-19 is not good so far, not only because of the negative results of most of the studies but also because of their design, when publishing results of a very low number of patients, when reporting favorable results but without having a control group that allows comparison, when choosing results for which it will be very difficult to find significant differences, such as mortality, or for which their clinical relevance is uncertain. abstract: The pandemic of the new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has urged the nations to an unprecedented world-wide reaction, including an accelerated exploration of therapeutic options. In the absence of a vaccine and specifically designed antivirals, the medical community has proposed the use of various previously available medications in order to reduce the number of patients requiring prolonged hospitalizations, oxygen therapy, and mechanical ventilation and to decrease mortality from coronavirus disease 2019 (COVID-19). Hydroxychloroquine and chloroquine are among the proposed drugs and are the most widely used so far, despite the lack of robust evidence on their usefulness. The objective of this article is to review and discuss the possible role of these drugs in the therapy of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32495226/ doi: 10.1007/s10067-020-05202-4 id: cord-304457-8g36h1bz author: Idelsis, E.-M. title: Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date: 2020-08-01 words: 5862.0 sentences: 330.0 pages: flesch: 47.0 cache: ./cache/cord-304457-8g36h1bz.txt txt: ./txt/cord-304457-8g36h1bz.txt summary: Conclusions: In a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly negativized the virus on day 4 of treatment when comparing with IFN-alpha2b. The RT-PCR after treatment with IFNs on day 14 for hospital discharges was negative to SARS-CoV-2 in 100% and 91% of patients of HeberFERON and control cohorts, respectively. These results confirm the validity of early intervention with the treatment of IFNs in patients with COVID-19, whereas demonstrated in the trial, the combination of type I and type II IFNs impacts strongly in the reduction of the risk for a severe disease likely through the efficient implementation of a timely controlled inflammatory antiviral response against the SARS-CoV-2 infection. Evaluation of the Effect and Safety of HeberFERON vs Heberon Alpha in Patients Infected with Corona Virus SARS-CoV-2 (Study ESPERANZA/HOPE): TRIALS abstract: Abstract Objectives: IFN-alpha2b and IFN-gamma combination has demonstrated favorable pharmacodynamics for genes underlying antiviral activity which might be involved in the defense of the organism from a SARS-CoV-2 infection. Considering this we conducted a randomized controlled clinical trial for efficacy and safety evaluation of subcutaneous IFN-alpha2b and IFN-gamma administration in patients positive to SARS-CoV-2. Methods: We enrolled 19-82 years-old inpatients at the Military Central Hospital Luis Diaz Soto, Havana, Cuba. They were hospitalized after confirmed diagnosis for SARS-CoV-2 RNA by real-time reverse transcription polymerase chain reaction. Patients were randomly assigned in a 1:1 ratio to receive either, subcutaneous treatment with a co-lyophilized combination of 3.0 MIU IFN-alpha2b and 0.5 MIU IFN-gamma (HeberFERON, CIGB, Havana, Cuba), twice a week for two weeks, or thrice a week intramuscular injection of 3.0 MIU IFN-alpha2b (Heberon Alpha R, CIGB, Havana, Cuba). Additionally, all patients received lopinavir-ritonavir 200/50 mg every 12 h and chloroquine 250 mg every 12 h (standard of care). The primary endpoints were the time to negativization of viral RNA and the time to progression to severe COVID-19, from the start of treatment. The protocol was approved by the Ethics Committee on Clinical Investigation from the Hospital and the Center for the State Control of Medicines, Equipment and Medical Devices in Cuba. Informed consent was obtained from each participant. Results: A total of 79 patients with laboratory-confirmed SARS-CoV-2 infection, including symptomatic or asymptomatic conditions, fulfilled the inclusion criteria and underwent randomization. Thirty-three subjects were assigned to the HeberFERON group, and 33 to the Heberon Alpha R group. Sixty-three patients were analyzed for viral negativization, of them 78.6% in the HeberFERON group negativized the virus after 4 days of treatment versus 40.6% of patients in the Heberon Alpha R groups (p=0.004). Time to reach the negativization of the SARS-CoV-2 measured by RT-PCR in real time was of 3.0 and 5.0 days for the HeberFERON and Heberon Alpha R groups, respectively. A significant improvement in the reduction of time for negativization was attributable to HeberFERON (p=0.0027, Log-rank test) with a Hazard Ratio of 3.2 and 95% CI of 1.529 to 6.948, as compared to Heberon Alpha R treated group. Worsening of respiratory symptoms was detected in two (6.6%) and one (3.3%) patients in HeberFERON and IFN-alpha2b groups, respectively. None of the subjects transit to severe COVID-19 during the study or the epidemiological follow-up for 21 more days. RT-PCR on day 14 after the start of the treatment was negative to SARS-CoV-2 in 100% and 91% of patients of the combination of IFNs and IFN-alpha2b, respectively. Negativization for HeberFERON treated patients was related to a significant increase in lymphocytes counts and an also significant reduction in CRP as early as 7 days after commencing the therapeutic schedule. All the patients in both cohorts recover by day 14 and were in asymptomatic condition and laboratory parameters return to normal values by day 14 after treatment initiation. Adverse events were identified in 31.5% of patients, 28.5% in the control group, and 34.4% in the HeberFERON group, and the most frequent were headaches (17.4%). Conclusions: In a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly negativized the virus on day 4 of treatment when comparing with IFN-alpha2b. Heberon Alpha R also showed efficacy for the treatment of the viral infection. Both treatments were safe and positively impact on the resolution of the symptoms. None of the patients developed severe COVID-19. Key words: COVID-19, treatment, drug, virus negativization, antiviral, interferon combination, SARS CoV-2. url: https://doi.org/10.1101/2020.07.29.20164251 doi: 10.1101/2020.07.29.20164251 id: cord-268283-eja8fkwv author: Iftikhar, Hafsa title: Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach date: 2020-06-09 words: 4811.0 sentences: 235.0 pages: flesch: 45.0 cache: ./cache/cord-268283-eja8fkwv.txt txt: ./txt/cord-268283-eja8fkwv.txt summary: In this regard, several recent studies have been conducted using computational methods to screen libraries of approved drugs or drug-like molecules to identify potential inhibitors of different viral proteins, particularly, RdRp and 3CL-protease [13] [14] [15] [16] [17] . Here, we applied a computer aided drug discovery approach by targeting three important enzymes (RdRp, 3CL-protease and helicase) of SARS-CoV-2 and identified three FDA-approved drugs and three other drug-like molecules as potential therapeutics. In this study, we used a virtual screening based strategy to identify already approved drugs or drug-like molecules that can bind to any of the three key viral enzymes, 3CL-protease, RdRp and helicase, and potentially inhibit the function of these enzymes. In our studies we performed computational screening by targeting three important enzymes of SARS-CoV-2 including RdRp, 3CL-protease and helicase, to identify not only the already approved drugs for repurposing but also the drug candidates or lead structures that can be chemically modified to develop potential drugs. abstract: The recent outbreak of coronavirus disease-19 (COVID-19) continues to drastically affect healthcare throughout the world. To date, no approved treatment regimen or vaccine is available to effectively attenuate or prevent the infection. Therefore, collective and multidisciplinary efforts are needed to identify new therapeutics or to explore effectiveness of existing drugs and drug-like small molecules against SARS-CoV-2 for lead identification and repurposing prospects. This study addresses the identification of small molecules that specifically bind to any of the three essential proteins (RdRp, 3CL-protease and helicase) of SARS-CoV-2. By applying computational approaches we screened a library of 4574 compounds also containing FDA-approved drugs against these viral proteins. Shortlisted hits from initial screening were subjected to iterative docking with the respective proteins. Ranking score on the basis of binding energy, clustering score, shape complementarity and functional significance of the binding pocket was applied to identify the binding compounds. Finally, to minimize chances of false positives, we performed docking of the identified molecules with 100 irrelevant proteins of diverse classes thereby ruling out the non-specific binding. Three FDA-approved drugs showed binding to 3CL-protease either at the catalytic pocket or at an allosteric site related to functionally important dimer formation. A drug-like molecule showed binding to RdRp in its catalytic pocket blocking the key catalytic residues. Two other drug-like molecules showed specific interactions with helicase at a key domain involved in catalysis. This study provides lead drugs or drug-like molecules for further in vitro and clinical investigation for drug repurposing and new drug development prospects. url: https://www.sciencedirect.com/science/article/pii/S0010482520302079 doi: 10.1016/j.compbiomed.2020.103848 id: cord-298679-w0yp4u19 author: Iftimie, Simona title: Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date: 2020-09-03 words: 3587.0 sentences: 184.0 pages: flesch: 48.0 cache: ./cache/cord-298679-w0yp4u19.txt txt: ./txt/cord-298679-w0yp4u19.txt summary: Logistic regression analyses showed that fever, pneumonia, acute respiratory distress syndrome, diabetes mellitus and cancer were the variables that showed independent and statistically significant associations with mortality. This is one of the first studies to describe the factors associated with mortality in patients infected with SARS-CoV-2 in Spain, and one of the few in the Mediterranean area. The objective of the present study has been to characterize our patients'' epidemiology and to identify the risk factors associated with mortality for this disease in our geographical area. Logistic regression analyses showed that the presence of fever, pneumonia, acute respiratory distress syndrome, type 2 diabetes mellitus and cancer were the only variables that showed an independent and statistically significant association with mortality when they were adjusted for differences in age, gender, smoking status and alcohol intake (Tables 2 and 3) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: Spain is one of the countries that has suffered the most from the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the strain that causes coronavirus disease 2019 (COVID-19). However, there is a lack of information on the characteristics of this disease in the Spanish population. The objective of this study has been to characterize our patients from an epidemiological point of view and to identify the risk factors associated with mortality in our geographical area. We performed a prospective, longitudinal study on 188 hospitalized cases of SARS-Cov-2 infection in Hospital Universitari de Sant Joan, in Reus, Spain, admitted between 15(th) March 2020 and 30(th) April 2020. We recorded demographic data, signs and symptoms and comorbidities. We also calculated the Charlson and McCabe indices. A total of 43 deaths occurred during the study period. Deceased patients were older than the survivors (77.7 ± 13.1 vs. 62.8 ± 18.4 years; p < 0.001). Logistic regression analyses showed that fever, pneumonia, acute respiratory distress syndrome, diabetes mellitus and cancer were the variables that showed independent and statistically significant associations with mortality. The Charlson index was more efficient than the McCabe index in discriminating between deceased and survivors. This is one of the first studies to describe the factors associated with mortality in patients infected with SARS-CoV-2 in Spain, and one of the few in the Mediterranean area. We identified the main factors independently associated with mortality in our population. Further studies are needed to complete and confirm our findings. url: https://doi.org/10.1371/journal.pone.0234452 doi: 10.1371/journal.pone.0234452 id: cord-306177-5wefp31y author: Iheagwam, Franklyn Nonso title: Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants date: 2020-09-12 words: 4804.0 sentences: 251.0 pages: flesch: 42.0 cache: ./cache/cord-306177-5wefp31y.txt txt: ./txt/cord-306177-5wefp31y.txt summary: e Unites States Food and Drug Administration-(USFDA-) approved drugs [26] , drugbank [27, 28] , traditional Ayurvedic, Chinese and natural medicine [20, [28] [29] [30] [31] , dark chemical matter, and fooDB [25] are some of the ZINC database subsets that have been rigourously screened for molecules to combat SARS-CoV-2 with main protease, RNA-dependent RNA polymerase, and angiotensin-converting enzyme-2 as the major therapeutic targets. Hence, this study analysed a plethora of natural products (NPs) from African medicinal plants with known bioactivities in human as therapeutic candidates targeting and inhibiting SARS-CoV-2 RNA synthesis, replication, structural protein function, and host-specific receptors/enzymes. In the course of drug discovery, structure-based virtual screening is a computational approach utilised to identify promising novel small chemical ligands from curated chemical compound databases with potential activity against drug targets [48] . abstract: The COVID-19 pandemic, which started in Wuhan, China, has spread rapidly over the world with no known antiviral therapy or vaccine. Interestingly, traditional Chinese medicine helped in flattening the pandemic curve in China. In this study, molecules from African medicinal plants were analysed as potential candidates against multiple SARS-CoV-2 therapeutic targets. Sixty-five molecules from the ZINC database subset (AfroDb Natural Products) were virtually screened with some reported repurposed therapeutics against six SARS-CoV-2 and two human targets. Molecular docking, druglikeness, absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the best hits were further simulated. Of the 65 compounds, only three, namely, 3-galloylcatechin, proanthocyanidin B1, and luteolin 7-galactoside found in almond (Terminalia catappa), grape (Vitis vinifera), and common verbena (Verbena officinalis), were able to bind to all eight targets better than the reported repurposed drugs. The findings suggest these molecules may play a role as therapeutic leads in tackling this pandemic due to their multitarget activity. url: https://doi.org/10.1155/2020/1878410 doi: 10.1155/2020/1878410 id: cord-326581-31trqhi1 author: Ihling, Christian title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients date: 2020-06-22 words: 1147.0 sentences: 81.0 pages: flesch: 54.0 cache: ./cache/cord-326581-31trqhi1.txt txt: ./txt/cord-326581-31trqhi1.txt summary: title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. 2 On the basis of the prospective goals of this coalition, the aim of this "proof-of-principle" study is to highlight the potential of MS in identifying SARS-CoV-2 proteins, even from highly diluted samples, such as gargle solutions of COVID-19 patients. All samples had been classified as SARS-CoV-2-positive by three reverse-transcription and quantitative polymerase chain reaction (RT-qPCR) analyses identifying E-, S-, and N-gene RNAs. For protein precipitation, 1 mL of acetone (−20°C) was added to 750 μL of gargle solution and stored overnight at −20°C. We present a protein MS-based method to specifically detect SARS-CoV-2 virus proteins from highly diluted gargle solutions of COVID-19 patients. Using this approach, we were able to identify peptides originating from SARS-CoV-2 nucleoprotein in gargle solution samples. abstract: [Image: see text] Mass spectrometry (MS) can deliver valuable diagnostic data that complement genomic information and allow us to increase our current knowledge of the COVID-19 disease caused by the SARS-CoV-2 virus. We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. The protocol consists of an acetone precipitation and tryptic digestion of proteins contained within the gargle solution, followed by a targeted MS analysis. Our methodology identifies unique peptides originating from SARS-CoV-2 nucleoprotein. Building on these promising initial results, faster MS protocols can now be developed as routine diagnostic tools for COVID-19 patients. Data are available via ProteomeXchange with identifier PXD019423. url: https://doi.org/10.1021/acs.jproteome.0c00280 doi: 10.1021/acs.jproteome.0c00280 id: cord-284498-54j6ys8s author: Ihsanullah, Ihsanullah title: Coronavirus 2 (SARS-CoV-2) in water environments: Current status, challenges and research opportunities date: 2020-10-16 words: 5702.0 sentences: 398.0 pages: flesch: 47.0 cache: ./cache/cord-284498-54j6ys8s.txt txt: ./txt/cord-284498-54j6ys8s.txt summary: Some of the significant challenges and research opportunities are the development of standard techniques for the detection and quantification of SARS-CoV-2 in the water phase, assessment of favorable environments for its survival and decay in water; and development of effective strategies for elimination of the novel virus from water. Development of effective standard techniques for the detection and quantification of SARS-CoV-2 in water, assessment of the existing water purification technologies and development of novel advanced water treatment systems are major challenges and open research opportunities. Furthermore, careful surveillance of water and wastewater to be used as an early warning tool for such outbreaks in future, understanding the survival and decay mechanism of the novel virus in water and wastewater, analysis of potential pathways of SARS-CoV-2 into water bodies are other potential research opportunities for environmental researchers [40] [41] [42] [43] [44] . abstract: The outbreak of COVID-19 has posed enormous health, social, environmental and economic challenges to the entire human population. Nevertheless, it provides an opportunity for extensive research in various fields to evaluate the fate of the crisis and combat it. The apparent need for imperative research in the biological and medical field is the focus of researchers and scientists worldwide. However, there are some new challenges and research opportunities in the field of water and wastewater treatment concerning the novel coronavirus 2 (SARS-CoV-2). This article briefly summarizes the latest literature reporting the presence of SARS-CoV-2 in water and wastewater/sewage. Furthermore, it highlights the challenges, potential opportunities and research directions in the water and wastewater treatment field. Some of the significant challenges and research opportunities are the development of standard techniques for the detection and quantification of SARS-CoV-2 in the water phase, assessment of favorable environments for its survival and decay in water; and development of effective strategies for elimination of the novel virus from water. Advancement in research in this domain will help to protect the environment, human health, and managing this type of pandemic in the future. url: https://api.elsevier.com/content/article/pii/S2214714420306127 doi: 10.1016/j.jwpe.2020.101735 id: cord-035163-tqh5wv12 author: Ijaz, M. Khalid title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date: 2020-09-08 words: 6841.0 sentences: 345.0 pages: flesch: 46.0 cache: ./cache/cord-035163-tqh5wv12.txt txt: ./txt/cord-035163-tqh5wv12.txt summary: In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan City, China, late in December 2019 is an example of an emerging zoonotic virus that threatens public health and international travel and commerce. When such a virus emerges, there is often insufficient specific information available on mechanisms of virus dissemination from animal-to-human or from person-to-person, on the level or route of infection transmissibility or of viral release in body secretions/excretions, and on the survival of virus in aerosols or on surfaces. The effectiveness of available virucidal agents and hygiene practices as interventions for disrupting the spread of infection and the associated diseases may not be clear for the emerging virus. In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485481/ doi: 10.7717/peerj.9914 id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 words: 6845.0 sentences: 375.0 pages: flesch: 51.0 cache: ./cache/cord-312996-qzu8pkyt.txt txt: ./txt/cord-312996-qzu8pkyt.txt summary: Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. abstract: The COVID-19 pandemic caused by the SARS-CoV-2 Coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a countrys population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology - multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct applicable to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 Coronavirus detection (Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; 1) ease of sampling, 2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution. url: http://medrxiv.org/cgi/content/short/2020.08.22.20176669v1?rss=1 doi: 10.1101/2020.08.22.20176669 id: cord-352580-l6vkzja0 author: Iltaf, Samar title: Frequency of Neurological Presentations of Coronavirus Disease in Patients Presenting to a Tertiary Care Hospital During the 2019 Coronavirus Disease Pandemic date: 2020-08-18 words: 2266.0 sentences: 130.0 pages: flesch: 42.0 cache: ./cache/cord-352580-l6vkzja0.txt txt: ./txt/cord-352580-l6vkzja0.txt summary: Background Coronavirus disease 2019 (COVID-19), caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), usually presents clinically with cough, fever, shortness of breath, and loss of taste and/or smell. COVID-19 can also present with neurologic signs and symptoms, including headache, hyposmia/anosmia, encephalopathy, meningoencephalitis, Guillain-Barré syndrome, stroke, and seizure. This subjective survey addressed 10 neurological manifestations of COVID-19: headache, altered sensation, nausea and vomiting, sudden hemiparesis (stroke), numbness and paresthesia, vertigo, ataxia, seizure, encephalitis/meningitis, Guillain-Barré Syndrome (GBS), and myelitis. Our study confirmed that headache (6%), altered level of consciousness and encephalopathy (2%), hemiparesis (stroke; 0.6%), GBS (0.3%) and seizure (0.3%) were the most frequently reported neurological presentations [5, 6, 7, 8] . A case study reported that a patient positive for SARS-CoV-2 presented with isolated sudden onset anosmia but no other symptoms of COVID-19 [11] . abstract: Background Coronavirus disease 2019 (COVID-19), caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), usually presents clinically with cough, fever, shortness of breath, and loss of taste and/or smell. COVID-19 can also present with neurologic signs and symptoms, including headache, hyposmia/anosmia, encephalopathy, meningoencephalitis, Guillain-Barré syndrome, stroke, and seizure. Viral transmission occurs through aerosols generated when an infected person coughs, sneezes, or exhales and by direct touching of contaminated surfaces. The present study evaluated the frequency of neurologic presentations of coronavirus disease in patients presenting at a tertiary care hospital during the COVID-19 pandemic. Methodology This cross-sectional study included 350 inpatients and outpatients (self-isolated) with polymerase chain reaction-confirmed SARS-CoV-2 infection who presented at Dow International Medical College of Karachi between March and June 2020. Of these 350 patients, 68 (18.9%) presented with neurological signs and symptoms and were further evaluated. The data were analyzed statistically using IBM Statistical Product and Service Solutions (SPSS) for Windows, version 20.0 (IBM Corp., Armonk, NY). Results The 350 patients with SARS-CoV-2 infection included 245 (70%) men and 105 (30%) women; of these, 262 (74.9%) were married, and 88 (25.1%) were unmarried. Patients ranged in age from 17 to 88 years (mean ± standard deviation, 49.5 ± 17.4 years), with 68 (18.9%) having neurological manifestations. Headache was the most frequent neurological symptom, reported in 21 (6%) patients, followed by vertigo in 12 patients (3.4%), numbness/paresthesia in 11 (3.1%), altered level of consciousness in seven (2%), hyposmia/anosmia in five (1.4%), and encephalitis in three (0.9%). Other symptoms included sudden hemiparesis (stroke) in two patients (0.6%), flaccid paralysis due to Guillain-Barre syndrome in one (0.3%), and seizure in one (0.3%). Conclusion Neurological involvement is not infrequent in patients with COVID-19. Neurologic manifestations should be carefully monitored in infected patients. COVID-19 should be suspected in patients presenting with neurological abnormalities and should be included in the differential diagnosis to prevent further virus transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/32953353/ doi: 10.7759/cureus.9846 id: cord-312619-7jpf81yz author: Ilyas, Sadia title: Disinfection technology and strategies for COVID-19 hospital and bio-medical waste management date: 2020-08-12 words: 5989.0 sentences: 263.0 pages: flesch: 48.0 cache: ./cache/cord-312619-7jpf81yz.txt txt: ./txt/cord-312619-7jpf81yz.txt summary: The exposure to COVID-waste may potentially increase the virus spread by increasing the reproductive number (R 0 ) from its determined range between 2.2 to 3.58 Thus, effective management of COVID-waste including the appropriate disinfect and disposal techniques are necessary to control the pandemic spread, which has not been focused yet albeit posing a similar threat as SARS-CoV-2 itself can have to the public health. The present article reviews the disinfection technologies to control/prevent the novel coronavirus spread and the proper management of COVID-waste including the effective strategies and reprocessing possibilities of the used items. Not only the COVID-waste generated by the hospitals, health centers, and self-quarantines, but the waste generated during the disinfection of public area or, where an infected person visited have been directed to treat as medical waste and collection of those waste in double-packed designated bags are mandatory before sending to burning at the high-temperature incinerator facility. abstract: Abstract The isolation wards, institutional quarantine centers, and home quarantine are generating a huge amount of bio-medical waste (BMW) worldwide since the outbreak of novel coronavirus disease-2019 (COVID-19). The personal protective equipment, testing kits, surgical facemasks, and nitrile gloves are the major contributors to waste volume. Discharge of a new category of BMW (COVID-waste) is of great global concern to public health and environmental sustainability if handled inappropriately. It may cause exponential spreading of this fatal disease as waste acts as a vector for SARS-CoV-2, which survives up to 7 days on COVID-waste (like facemasks). Proper disposal of COVID-waste is therefore immediately requires to lower the threat of pandemic spread and for sustainable management of the environmental hazards. Henceforth, in the present article, disinfection technologies for handling COVID-waste from its separate collection to various physical and chemical treatment steps have been reviewed. Furthermore, policy briefs on the global initiatives for COVID-waste management including the applications of different disinfection techniques have also been discussed with some potential examples effectively applied to reduce both health and environmental risks. This article can be of great significance to the strategy development for preventing/controlling the pandemic of similar episodes in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32822917/ doi: 10.1016/j.scitotenv.2020.141652 id: cord-290948-cuu78cvl author: Imbert, Isabelle title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date: 2008-02-05 words: 7091.0 sentences: 356.0 pages: flesch: 53.0 cache: ./cache/cord-290948-cuu78cvl.txt txt: ./txt/cord-290948-cuu78cvl.txt summary: Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. abstract: Many genetic and mechanistic features distinguish the coronavirus replication machinery from that encoded by most other RNA viruses. The coronavirus replication/transcription complex is an assembly of viral and, most probably, cellular proteins that mediate the synthesis of both the unusually large (∼30 kb) RNA genome and an extensive set of subgenomic mRNAs. The viral components of the complex are encoded by the giant replicase gene, which is expressed in the form of two polyproteins (pp1a and pp1ab) that are processed into 16 cleavage products (nonstructural proteins 1–16). Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. We demonstrate the existence of a complex network of interactions involving all 16 nonstructural proteins. Our results both confirmed previously described associations and identified novel heterodimerizations. The interaction map thus provides a sum of the interactions that may occur at some point during coronavirus RNA synthesis and provides a framework for future research. url: https://doi.org/10.1016/j.virusres.2007.11.017 doi: 10.1016/j.virusres.2007.11.017 id: cord-011813-lm105z6n author: Imperiale, Michael J. title: Recurring Themes date: 2020-07-08 words: 309.0 sentences: 28.0 pages: flesch: 68.0 cache: ./cache/cord-011813-lm105z6n.txt txt: ./txt/cord-011813-lm105z6n.txt summary: to ask whether mSphere would be interested in publishing a summary of a conference being held at that time in Singapore to commemorate the 20th anniversary of the first Nipah virus outbreak. Having attended a similar conference on Ebola and other emerging infectious diseases a couple of years earlier, I knew that the topics of discussion and the information presented at such a meeting are of interest and importance to the microbial sciences community. I therefore told Benhur that we were absolutely interested: the report from the Nipah@20 conference is published with this editorial (1). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was beginning its journey from Wuhan, China to the rest of the world, and as of the time I am writing this, well over 10 million cases and half a million deaths have been reported. As the authors of the Nipah@20 conference summary note, the similarities in terms of what the world needs to respond to such emerging diseases are many. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343984/ doi: 10.1128/msphere.00633-20 id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 words: 8002.0 sentences: 414.0 pages: flesch: 37.0 cache: ./cache/cord-298036-2zurc60t.txt txt: ./txt/cord-298036-2zurc60t.txt summary: Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . abstract: Apoptosis, necroptosis and pyroptosis represent three major regulated cell death modalities. Apoptosis features cell shrinkage, nuclear fragmentation and cytoplasm-blebbing. Necroptosis and pyroptosis exhibit osmotic imbalances in the cell accompanied by early membrane ruptures, which morphologically resembles necrosis. Importantly, these two lytic cell death forms facilitate the release of damage associated molecular patterns into the extracellular space leading to inflammatory response. Whereas, during apoptosis, the membrane integrity is preserved and the apoptotic cell is removed by neighbouring cells ensuring the avoidance of immune-stimulation. Viruses comprise a versatile group of intracellular pathogens, which elicit various strategies to infect and to propagate. Viruses are recognized by a myriad of pathogen recognition receptors in the human cells, which consequently lead to activation of the immune system and in certain circumstances cell-autonomous cell death. Importantly, the long-standing view that a cell death inducing capacity of a virus is equal to its pathogenic potential seems to be only partially valid. The altruistic cell death of an infected cell may serve the whole organism by ultimately curbing the way of virus manufacturing. In fact, several viruses express “anti-cell death” proteins to avoid this viral-defence mechanism. Conversely, some viruses hijack cell death pathways to selectively destroy cell populations in order to compromise the immune system of the host. This review discusses the pros and cons of virus induced cell death from the perspective of the host cells and attempts to provide a comprehensive overview of the complex network of cell death signalling in virus infection. url: https://api.elsevier.com/content/article/pii/S0898656820302497 doi: 10.1016/j.cellsig.2020.109772 id: cord-293056-kz3w0nfh author: Indes, Jeffrey E. title: Early Experience with Arterial Thromboembolic Complications in Patents with COVID-19 date: 2020-08-28 words: 1933.0 sentences: 125.0 pages: flesch: 51.0 cache: ./cache/cord-293056-kz3w0nfh.txt txt: ./txt/cord-293056-kz3w0nfh.txt summary: A retrospective case-control study design was used to identify, characterize and evaluate potential risk factors for arterial thromboembolic disease in SARS-CoV-2 positive patients. Although not statistically significant, in patients with arterial thromboembolism, patients who were SARS-CoV-2 positive compared to those testing negative or not tested tended to be male (66.7 % v. Treatment of arterial thromboembolic disease in the COVID-19 positive patients included open thromboembolectomy in 6 patients (40%), anticoagulation alone in 4 (26.7%) and 5 (33.3%) did not require or their overall illness severity precluded additional treatment. The SARS-CoV-2 positive group included patients with a range of COVID-19 16 symptomatology (mild to severe) as well as those tested as part of routine preoperative 17 preparation. Patients with arterial thrombosis who were SARS-CoV-10 2 positive had significantly higher D-dimer levels, BMI, were younger, and less often on 11 antiplatelet medications as compared to patients who were SARS-CoV-2 negative or not tested. abstract: INTRODUCTION: Little is known about the arterial complications and hypercoagulability associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We sought to characterize our experience with arterial thromboembolic complications in patients with hospitalized for coronavirus disease 2019 (COVID-19). METHODS: All patients admitted from March 1 to April 20, 2020 and who underwent carotid, upper, lower and aortoiliac arterial duplex, CT angiogram or MRA for suspected arterial thrombosis were included. A retrospective case-control study design was used to identify, characterize and evaluate potential risk factors for arterial thromboembolic disease in SARS-CoV-2 positive patients. Demographics, characteristics and laboratory values were abstracted and analyzed. RESULTS: During the study period, 424 patients underwent 499 arterial duplex, CT angiogram or MRA imaging studies with overall 9.4% positive for arterial thromboembolism. Of the 40 patients with arterial thromboembolism, 25 (62.5%) were SARS-CoV-2 negative or admitted for unrelated reasons and 15 (37.5%) were SARS-CoV-2 positive. The odds ratio for arterial thrombosis in COVID-19 was 3.37 (95% CI 1.68 – 6.78, p=0.001). Although not statistically significant, in patients with arterial thromboembolism, patients who were SARS-CoV-2 positive compared to those testing negative or not tested tended to be male (66.7 % v. 40.0%, p=0.191), have a less frequent history of former or active smoking (42.9% vs 68.0%, p=0.233) and have a higher white blood cell count (WBC 14.5 vs. 9.9, p=0.208). While the SARS-CoV-2 positive patients trended toward a higher the neutrophil-to-lymphocyte ratio (8.9 vs. 4.1, p=0.134), CPK level (359.0 vs. 144.5, p=0.667), CRP level (24.2 vs. 13.8, p=0.627), LDH level (576.5 vs. 338.0, p=0.313) and ferritin level (974.0 vs. 412.0, p=0.47), these did not reach statistical significance. Patients with arterial thromboembolic complications and SARS-CoV-2 positive when compared to SARS-CoV-2 negative or admitted for unrelated reasons were younger (64 vs. 70 years, p=0.027), had a significantly higher body mass index (BMI) (32.6 vs. 25.5, p=0.012), a higher D-dimer at the time of imaging (17.3 vs. 1.8, p=0.038), a higher average in hospital D-dimer (8.5 vs. 2.0, p=0.038), a greater distribution of patients with clot in the aortoiliac location (5 vs. 1, p=0.040), less prior use of any antiplatelet medication (21.4% vs. 62.5%, p=0.035) and a higher mortality rate (40.0 % vs. 8.0%, p=0.041). Treatment of arterial thromboembolic disease in the COVID-19 positive patients included open thromboembolectomy in 6 patients (40%), anticoagulation alone in 4 (26.7%) and 5 (33.3%) did not require or their overall illness severity precluded additional treatment. CONCLUSIONS: Patients with SAR-CoV-2 are at risk for acute arterial thromboembolic complications despite a lack of conventional risk factors. A hyperinflammatory state may be responsible for this phenomenon with a preponderance for aortoiliac involvement. These findings provide an early characterization of arterial thromboembolic disease in SARS-CoV-2 patients. url: https://www.sciencedirect.com/science/article/pii/S0741521420318796?v=s5 doi: 10.1016/j.jvs.2020.07.089 id: cord-290895-tb0xald0 author: Indu, Purushothaman title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach date: 2020-10-26 words: 2632.0 sentences: 155.0 pages: flesch: 53.0 cache: ./cache/cord-290895-tb0xald0.txt txt: ./txt/cord-290895-tb0xald0.txt summary: title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. RESULTS: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥ -8 kcal/mol. In this study, FDA J o u r n a l P r e -p r o o f approved small molecule antiviral drugs were screened against protein targets of SARS-CoV-2 using a computational based approach. In our study, other screened antiviral drugs such as Indinavir, Tipranavir, and Pibrentasvir showed dock energy value more than -8 kcal/mol and these drugs might also serve as an inhibitors of Mpro target of SARS-CoV-2. abstract: BACKGROUND: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to find out the drugs for COVID-19 treatment from existing FDA approved antiviral drugs. In this study, FDA approved small molecule antiviral drugs were repurposed against the major viral proteins of SARS-CoV-2. METHODS: The 3D structures of FDA approved small molecule antiviral drugs were retrieved from PubChem. Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. Furthermore, lead molecules were individually docked against protein targets using AutoDock 4.0.1 software and their drug-likeness and ADMET properties were evaluated. RESULTS: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥ -8 kcal/mol. Similarly Indinavir showed the highest binding energy of -11.5 kcal/mol against the target protein RdRp and Dolutegravir, Elbasvir, Tipranavir, Taltegravir, Grazoprevir, Daclatasvir, Glecaprevir, Ledipasvir, Pibrentasvir and Velpatasvir showed a binding energy value in range from -8 to -11.2 kcal/mol. The antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine also exhibited good bioavailability and drug-likeness properties. CONCLUSION: This study suggests that the screened small molecule antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine could serve as potential drugs for the treatment of COVID-19 with further validation studies. url: https://api.elsevier.com/content/article/pii/S1876034120307127 doi: 10.1016/j.jiph.2020.10.015 id: cord-254821-px4fe7mn author: Infantino, Maria title: Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date: 2020-05-10 words: 1224.0 sentences: 67.0 pages: flesch: 42.0 cache: ./cache/cord-254821-px4fe7mn.txt txt: ./txt/cord-254821-px4fe7mn.txt summary: Sixty‐one COVID‐19 patients and 64 patients from a control group were tested by iFlash1800 CLIA analyzer for anti‐SARS CoV‐2 antibodies IgM and IgG. The more relaxed rules of the FDA''s "Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency" issued on 16 March 2020, 9 has allowed the market easier access to these tests as well as easier and faster diagnostics, but the lack of control in the production process is also dangerous making these tests potentially less reliable. 11 The aim of the this study was to assess the diagnostic performance of a novel fully automated CLIA for the quantitative detection of anti-SARS-CoV-2 IgM and IgG antibodies. 16 As with most existing studies on the diagnostic performance of the SARS-CoV-2 antibodies, our preliminary data showed that most COVID-19 patients have both IgM and IgG, and only few of them have isolated IgG or IgM antibodies. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Assessment of immune response to SARS-CoV-2 with fully-automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays abstract: A pandemic of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been spreading throughout the world. Though molecular diagnostic tests are the gold standard for COVID‐19, serological testing is emerging as a potential surveillance tool, in addition to its complementary role in COVID‐19 diagnostics. Indubitably quantitative serological testing provides greater advantages than qualitative tests but today there is still little known about serological diagnostics and what the most appropriate role quantitative tests might play. Sixty‐one COVID‐19 patients and 64 patients from a control group were tested by iFlash1800 CLIA analyzer for anti‐SARS CoV‐2 antibodies IgM and IgG. All COVID‐19 patients were hospitalized in San Giovanni di Dio Hospital (Florence, Italy) and had a positive oro/nasopharyngeal swab reverse‐transcription polymerase chain reaction result. The highest sensitivity with a very good specificity performance was reached at a cutoff value of 10.0 AU/mL for IgM and of 7.1 for IgG antibodies, hence near to the manufacturer's cutoff values of 10 AU/mL for both isotypes. The receiver operating characteristic curves showed area under the curve values of 0.918 and 0.980 for anti‐SARS CoV‐2 antibodies IgM and IgG, respectively. iFlash1800 CLIA analyzer has shown highly accurate results for the anti‐SARS‐CoV‐2 antibodies profile and can be considered an excellent tool for COVID‐19 diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/32330291/ doi: 10.1002/jmv.25932 id: cord-271751-46oo9xv5 author: Ingraham, Nicholas E. title: Shining a light on the evidence for hydroxychloroquine in SARS-CoV-2 date: 2020-04-28 words: 1112.0 sentences: 77.0 pages: flesch: 51.0 cache: ./cache/cord-271751-46oo9xv5.txt txt: ./txt/cord-271751-46oo9xv5.txt summary: Chloroquine and hydroxychloroquine seem effective in killing SARS-CoV in vitro [1, 3] . Recent reports show it also may be effective at killing SARS-CoV-2-infected cells in vitro [4] . To date, no pre-clinical studies have evaluated the efficacy of hydroxychloroquine in the current SARS-CoV-2 pandemic. A recent article published in Chinese found no benefit with chloroquine in a 1:1 randomized trial with 30 patients [6] . Until data from randomized controlled trials are available, we suggest caution utilizing hydroxychloroquine off label for patients with COVID-19. There are currently no evidence supporting hydroxychloroquine as prophylaxis, but unfortunately these data are being extrapolated to the indication potentially resulting in drug shortages for patients with rheumatic diseases who require this medication. Preliminary study of hydroxychloroquine sulfate in treating common coronavirus disease (COVID-19) patients in 2019 Hydroxychloroquine and azithromycin as a treatment of COVID-19: preliminary results of an open-label nonrandomized clinical trial abstract: nan url: https://doi.org/10.1186/s13054-020-02894-7 doi: 10.1186/s13054-020-02894-7 id: cord-283197-jjye8t6j author: Ingraham, Nicholas E. title: Fact Versus Science Fiction: Fighting Coronavirus Disease 2019 Requires the Wisdom to Know the Difference date: 2020-04-29 words: 1870.0 sentences: 107.0 pages: flesch: 42.0 cache: ./cache/cord-283197-jjye8t6j.txt txt: ./txt/cord-283197-jjye8t6j.txt summary: This commentary uses a recent study of hydroxychloroquine to demonstrate the dire need for randomized clinical trials, but more importantly, to explore the potential consequences of misinformation, how fear fuels its impact, and offer guidance to maintain scientific integrity without relinquishing hope. As of March 25, there remains no randomized control trial in humans with evidence that chloroquine or hydroxychloroquine is beneficial in SARS-CoV or SARS-CoV-2. Premature acceptance of efficacy is not new (swine flu vaccination [10] or recombinant human activated protein C [11] ), but it is these prior experiences that influence current standards to require high quality and often multiple randomized control trials to change practice. However, despite warnings from healthcare leaders and public health agencies, there continues to be a premature adoption of hydroxychloroquine as treatment based on limited preclinical data and misinformed interpretation of a nonrandomized study. abstract: nan url: https://doi.org/10.1097/cce.0000000000000108 doi: 10.1097/cce.0000000000000108 id: cord-309370-g8d3w7it author: Insausti-García, Alfredo title: Papillophlebitis in a COVID-19 patient: Inflammation and hypercoagulable state date: 2020-07-30 words: 2083.0 sentences: 119.0 pages: flesch: 40.0 cache: ./cache/cord-309370-g8d3w7it.txt txt: ./txt/cord-309370-g8d3w7it.txt summary: We believe that the inflammatory reaction and the coagulation alteration present in our patient due to Sars-Cov2 coronavirus may have acted as risk factors for the development of papillophlebitis. It has been suggested to result from idiopathic inflammation of retinal vascular and, possibly of the capillaries of the optic disc; however it is mandatory to work out a hypercoagulable state (hereditary or acquired thrombophilia factors), vasculitic syndromes, blood hyperviscosity, and other recognized systemic vascular inflammatory disorders. On left eye fundus examination, and color and red free retinographies, severe inflammation of the optic nerve head was observed accompanied by retinal venous vasodilatation and tortuosity, cotton-wool spots and moderate superficial hemorrhages in all four quadrants. 8 In addition to the respiratory tract infection and to these acute ocular manifestations, the current pandemic caused by the SARS-CoV-2 is associated with coagulation activation and a disproportionate systemic inflammatory response. abstract: INTRODUCTION: Papillophlebitis is a rare condition characterized by venous congestion and optic disc edema, which has been suggested to occur as a consequence of inflammation of the retinal veins or, possibly, the capillaries of the optic disc, leading to venous insufficiency and compression of the central retina vein. The disease affects healthy young adults and commonly has a benign course, however, if complications such as macular edema or ischemia appears, treatment should be instituted immediately to avoid poor prognosis. CASE REPORT: A 40-year old white male patient consulted for a slight decrease in the sensitivity of the visual field in his left eye (OS). Visual acuities (VA) were 20/20 in both eyes. OS fundus examination showed dilated and tortuous retinal vessels, disc edema, and retinal hemorrhages. The patient was diagnosed with papillophlebitis. OS VA decreased to 20/200 due to macular edema, and he was treated with a intravitreal dexamethasone implant. An exhaustive and interdisciplinary exploration process was performed, identifying a recent disease and recovery of Covid-19 as the only factor of inflammation and coagulation alteration. Other systemic diseases were excluded. We also describe a rapid decrease in disc and macular edema after intravitreal dexametasone injection, which could support the inflammatory hypothesis. CONCLUSION: The importance of this case lies in the possible association of papillophlebitis with the new Covid-19 disease. We believe that the inflammatory reaction and the coagulation alteration present in our patient due to Sars-Cov2 coronavirus may have acted as risk factors for the development of papillophlebitis. url: https://doi.org/10.1177/1120672120947591 doi: 10.1177/1120672120947591 id: cord-307860-iqk1yiw4 author: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 words: 9856.0 sentences: 668.0 pages: flesch: 57.0 cache: ./cache/cord-307860-iqk1yiw4.txt txt: ./txt/cord-307860-iqk1yiw4.txt summary: Structures retrieved from PDB (August 12, 2020) were analyzed for relevant information on COVID-19 infection, synthesis of new inhibitors, SARS-CoV-2 interaction with host receptors, and the neutralizing antibodies interactions with spike glycoprotein. The first X-ray structure found (PDB ID 6LU7) belongs to the nonstructural protein 5 (3C-like protease) of the SARS-CoV-2 in complex with the Michael acceptor-based inhibitor N3 (PRD_002214). There is a cryo-EM crystal structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp12/nsp8/nsp7) with the antiviral drug remdesivir (PDB ID 7BV2) [37] . Previous studies on the crystal structures of SARS-CoV S glycoprotein mutants neutralized by 80R-specific antibodies have been considered a hope for the immunotherapeutic Fig. 8 The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites abstract: Many research teams all over the world focus their research on the SARS-CoV-2, the new coronavirus that causes the so-called COVID-19 disease. Most of the studies identify the main protease or 3C-like protease (M(pro)/3CL(pro)) as a valid target for large-spectrum inhibitors. Also, the interaction of the human receptor angiotensin-converting enzyme 2 (ACE2) with the viral surface glycoprotein (S) is studied in depth. Structural studies tried to identify the residues responsible for enhancement/weaken virus-ACE2 interactions or the cross-reactivity of the neutralizing antibodies. Although the understanding of the immune system and the hyper-inflammatory process in COVID-19 are crucial for managing the immediate and the long-term consequences of the disease, not many X-ray/NMR/cryo-EM crystals are available. In addition to 3CL(pro), the crystal structures of other nonstructural proteins offer valuable information for elucidating some aspects of the SARS-CoV-2 infection. Thus, the structural analysis of the SARS-CoV-2 is currently mainly focused on three directions—finding M(pro)/3CL(pro) inhibitors, the virus-host cell invasion, and the virus-neutralizing antibody interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10930-020-09933-w) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/33098476/ doi: 10.1007/s10930-020-09933-w id: cord-342453-1vj9p7vm author: Ip, A. title: Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study date: 2020-08-25 words: 4165.0 sentences: 325.0 pages: flesch: 48.0 cache: ./cache/cord-342453-1vj9p7vm.txt txt: ./txt/cord-342453-1vj9p7vm.txt summary: Methods: We examined the association between outpatient hydroxychloroquine exposure and the subsequent progression of disease among mildly symptomatic non-hospitalized patients with documented SARS-CoV-2 infection. [15] [16] [17] [18] In this multi-center observational cohort study we report progression from mildly symptomatic SARS-CoV-2 infection diagnosed as an outpatient progressing to subsequent need for in-patient hospitalization according to outpatient exposure to hydroxychloroquine. This retrospective, observational, multicenter cohort study within the Hackensack Meridian Health network (HMH) utilized EHR-derived data of patients with documented SARS-CoV-2 infection who received care initially within an outpatient setting. Our primary objective was to evaluate the association between hydroxychloroquine exposure and subsequent need for hospitalization in a population of patients with documented SARS-CoV-2 infection diagnosed in the outpatient setting. In this multicenter retrospective observational cohort study of mildly symptomatic outpatients with polymerase chain reaction documented SARS-CoV-2 infection, we noted an association (OR 0.53; 95% CI, 0.29, 0.95) between outpatient exposure to hydroxychloroquine and a reduction in subsequent need for hospitalization. abstract: Background: Hydroxychloroquine has not been associated with improved survival among hospitalized COVID-19 patients in the majority of observational studies and similarly was not identified as an effective prophylaxis following exposure in a prospective randomized trial. We aimed to explore the role of hydroxychloroquine therapy in mildly symptomatic patients diagnosed in the outpatient setting. Methods: We examined the association between outpatient hydroxychloroquine exposure and the subsequent progression of disease among mildly symptomatic non-hospitalized patients with documented SARS-CoV-2 infection. The primary outcome assessed was requirement of hospitalization. Data was obtained from a retrospective review of electronic health records within a New Jersey USA multi-hospital network. We compared outcomes in patients who received hydroxychloroquine with those who did not applying a multivariable logistic model with propensity matching. Results: Among 1274 outpatients with documented SARS-CoV-2 infection 7.6% were prescribed hydroxychloroquine. In a 1067 patient propensity matched cohort, 21.6% with outpatient exposure to hydroxychloroquine were hospitalized, and 31.4% without exposure were hospitalized. In the primary multivariable logistic regression analysis with propensity matching there was an association between exposure to hydroxychloroquine and a decreased rate of hospitalization from COVID-19 (OR 0.53; 95% CI, 0.29, 0.95). Sensitivity analyses revealed similar associations. QTc prolongation events occurred in 2% of patients prescribed hydroxychloroquine with no reported arrhythmia events among those with data available. Conclusions: In this retrospective observational study of SARS-CoV-2 infected non-hospitalized patients hydroxychloroquine exposure was associated with a decreased rate of subsequent hospitalization. Additional exploration of hydroxychloroquine in this mildly symptomatic outpatient population is warranted. url: http://medrxiv.org/cgi/content/short/2020.08.20.20178772v1?rss=1 doi: 10.1101/2020.08.20.20178772 id: cord-307213-i8yijbiu author: Ip, Jonathan Daniel title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date: 2020-11-02 words: 1043.0 sentences: 82.0 pages: flesch: 58.0 cache: ./cache/cord-307213-i8yijbiu.txt txt: ./txt/cord-307213-i8yijbiu.txt summary: title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. A total of 28 serial respiratory specimens from 12 patients were successfully sequenced 49 using nanopore and Illumina sequencing. Temporal profiles of 310 viral load in posterior oropharyngeal saliva samples and serum antibody responses during 311 infection by SARS-CoV-2: an observational cohort study A neutralizing human antibody 370 binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Viral load dynamics and disease 397 severity in patients infected with SARS-CoV-2 in Zhejiang province, China abstract: OBJECTIVES: SARS-CoV-2 has evolved rapidly into several genetic clusters. However, data on mutations during the course of infection are scarce. This study aims to determine viral genome diversity in serial samples of COVID-19 patients. METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. Sanger sequencing was then performed to confirm the single nucleotide polymorphisms. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. A 75-year-old patient with severe disease had a mutation, G22017T, identified in the second specimen. The frequency of G22017T increased from ≤5% (nanopore: 3.8%; Illumina: 5%) from first respiratory tract specimen (sputum) to ≥60% (nanopore: 67.7%; Illumina: 60.4%) in the second specimen (saliva; collected 2 days after the 1(st) specimen). The difference in G22017T frequency was also confirmed by Sanger sequencing. G22017T corresponds to W152L amino acid mutation in the spike protein which was only found in <0.03% of the sequences deposited into a public database. Spike amino acid residue 152 is located within the N-terminal domain, which mediates the binding of a neutralizing antibody. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. Our study demonstrated that monitoring of serial specimens is important in identifying hotspots of mutations, especially those occurring at neutralizing epitopes which may affect the therapeutic efficacy of monoclonal antibodies. url: https://doi.org/10.1016/j.cmi.2020.10.030 doi: 10.1016/j.cmi.2020.10.030 id: cord-349821-5ykwwq75 author: Ippolito, G. title: Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date: 2006-09-09 words: 6497.0 sentences: 257.0 pages: flesch: 35.0 cache: ./cache/cord-349821-5ykwwq75.txt txt: ./txt/cord-349821-5ykwwq75.txt summary: The term ''highly infectious diseases'' describes infections caused by pathogens that are transmissible from person to person, cause severe or life-threatening illness; present a serious hazard in healthcare settings and in the community; and require specific control measures, which may include management of cases in a highly secure isolation unit. In Canada, where SARS ''paralysed the Greater Toronto Area healthcare system for weeks'' [27] , and the Toronto public health department investigated 2132 potential cases of SARS, identified over 23,000 contacts as requiring quarantine and logged more than 316,000 calls on its SARS hotline [28] , a national review commission identified systemic deficiencies in response capacity, including ''inadequacies in institutional outbreak management protocols, infection control and infectious disease surveillance'', and found that these deficiencies resulted at least in part from failure to implement lessons learned from earlier public health emergencies [22] . abstract: In the last 2 decades, successive outbreaks caused by new, newly recognised and resurgent pathogens, and the risk that high-consequence pathogens might be used as bioterrorism agents amply demonstrated the need to enhance capacity in clinical and public health management of highly infectious diseases. In this article we review these recent and current threats to public health, whether naturally occurring or caused by accidental or intentional release. Moreover, we discuss some components of hospital preparedness for, and response to, infectious disease of the emergencies in developed countries. The issues of clinical awareness and education, initial investigation and management, surge capacity, communication, and caring for staff and others affected by the emergency are discussed. We also emphasise the importance of improving the everyday practice of infection control by healthcare professionals. url: https://www.ncbi.nlm.nih.gov/pubmed/16964581/ doi: 10.1007/s00018-006-6309-y id: cord-307070-tqxvu3pu author: Iqbal, Phool title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date: 2020-09-20 words: 2758.0 sentences: 150.0 pages: flesch: 49.0 cache: ./cache/cord-307070-tqxvu3pu.txt txt: ./txt/cord-307070-tqxvu3pu.txt summary: However, improvement was observed in the clinical condition of the patients who were managed as per COVID-19 protocol based upon the clinical signs and symptoms after correlating with diagnostic chest imaging studies. The infectious disease team advised testing with COVID-19 serology (immunoglobulin (Ig) M and IgG antibodies through lateral flow assay), the results of which were positive, indicating recent infection. The infectious disease team was consulted and based upon his clinical presentation and previous investigations, the patient was maintained on the local management protocol for COVID-19 infection. Moreover, biomarkers such as CRP, ferritin, lymphocyte counts, lactate dehydrogenase, and N-terminal pro b-type natriuretic peptide, along with radiological findings in CXR or features such as unilateral or bilateral pneumonia, ground-glass opacities, or consolidations in a chest CT scan, can suggest COVID-19 infection even in such patients where RT-PCR alone is negative [4] . abstract: Since the declaration of coronavirus disease 2019 (COVID-19) disease as a pandemic by the World Health Organization (WHO), it has been a challenge to the whole medical community. Researchers and clinicians have been trying to explain and explore its mechanism and pathophysiology to get a better understanding of this disease, as it has exhausted the healthcare resources and has impacted human life in general. Many tests have been developed including polymerase chain reaction (PCR) of the virus and rapid diagnostic testing in patients based on IgM/IgG serology. But owing to variable sensitivity and specificity of these tests, it has created a challenging situation to proceed with the further management plan. We are reporting a case series where we experienced the dilemma of diagnosing COVID-9 disease in our patients and further plan of care. url: https://www.ncbi.nlm.nih.gov/pubmed/33101802/ doi: 10.7759/cureus.10555 id: cord-274602-q9i2k304 author: Iqbal, Yousaf title: Psychiatric presentation of patients with acute SARS-CoV-2 infection: a retrospective review of 50 consecutive patients seen by a consultation-liaison psychiatry team date: 2020-09-10 words: 3717.0 sentences: 231.0 pages: flesch: 45.0 cache: ./cache/cord-274602-q9i2k304.txt txt: ./txt/cord-274602-q9i2k304.txt summary: BACKGROUND: Reports of psychiatric morbidity associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection tend to be limited by geography and patients'' clinical status. AIMS: To describe the psychiatric morbidity associated with SARS-CoV-2 infection (confirmed by real-time polymerase chain reaction) in referrals to a consultation-liaison psychiatry service in Qatar. 12 Finally, all current studies in hospital settings have restricted themselves to symptomatic patients with COVID-19, although psychiatric consultation-liaison services will also be referred patients who have tested positive for SARS-CoV-2 but are physically asymptomatic. The current study aimed to complement existing data by characterising the psychiatric morbidity associated with acute SARS-CoV-2 infection in patients referred to a consultation-liaison psychiatry service in Qatar. As such it offers a broad clinical picture of the psychiatric problems associated with acute SARS-CoV-2 infection, occurring in a general hospital setting, and including patients who are symptomatic and asymptomatic for COVID-19 infection. abstract: BACKGROUND: Reports of psychiatric morbidity associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection tend to be limited by geography and patients’ clinical status. Representative samples are needed to inform service planning and research. AIMS: To describe the psychiatric morbidity associated with SARS-CoV-2 infection (confirmed by real-time polymerase chain reaction) in referrals to a consultation-liaison psychiatry service in Qatar. METHOD: Retrospective review of 50 consecutive referrals. RESULTS: Most patients were male. Median age was 39.5 years. Thirty-one patients were symptomatic (upper respiratory tract symptoms or pneumonia) for coronavirus disease 2019 (COVID-19) and 19 were asymptomatic (no characteristic physical symptoms of COVID-19 infection). Seventeen patients (34%) had a past psychiatric history including eight with bipolar I disorder or psychosis, all of whom relapsed. Thirty patients (60%) had physical comorbidity. The principal psychiatric diagnoses made by the consultation-liaison team were delirium (n = 13), psychosis (n = 9), acute stress reaction (n = 8), anxiety disorder (n = 8), depression (n = 8) and mania (n = 8). Delirium was confined to the COVID-19 symptomatic group (the exception being one asymptomatic patient with concurrent physical illness). The other psychiatric diagnoses spanned the symptomatic and asymptomatic patients with COVID. One patient with COVID-19 pneumonia experienced an ischaemic stroke. Approximately half the patients with mania and psychosis had no past psychiatric history. Three patients self-harmed. The commonest psychiatric symptoms were sleep disturbance (70%), anxiety (64%), agitation (50%), depressed mood (42%) and irritability (36%). CONCLUSIONS: A wide range of psychiatric morbidity is associated with SARS-CoV-2 infection and is seen in symptomatic and asymptomatic individuals. Cases of psychosis and mania represented relapses in people with schizophrenia and bipolar disorder and also new onset cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32907692/ doi: 10.1192/bjo.2020.85 id: cord-277110-e27lm7rr author: Iria, Neri title: Major cluster of pediatric “ true ” primary chilblains during the COVID‐19 pandemic: a consequence of lifestyle changes due to lockdown date: 2020-06-13 words: 2903.0 sentences: 181.0 pages: flesch: 52.0 cache: ./cache/cord-277110-e27lm7rr.txt txt: ./txt/cord-277110-e27lm7rr.txt summary: We reported demographical, laboratory and clinical features, history of close contact with COVID‐19 patients, presence of similar skin lesions in other family members, precipitating and risk factors for chilblain onset. All rights reserved In April 2020, we observed a growing number of chilblain-like manifestations similar to coldinduced lesions during the pandemic, with the opportunity to study 8 cases, 2 children and 6 adolescents, and report here our results. The aim of this study is to verify whether the chilblain-like lesions were a cutaneous clue for SARS-CoV-2 infection or due to other causes. All rights reserved -PCR-assay on blood samples for Parvovirus B19 DNA and Enterovirus RNA -PCR-assay on skin biopsy for Parvovirus B19, Mycoplasma pneumoniae and SARS-CoV-2 was performed in a single patient (12.5%). Various cutaneous findings were observed in adults infected with COVID-19 and, simultaneously, a marked increase of chilblain-like lesions occurred worldwide among children during the COVID-19 pandemic 10, 11 In our cases we exclude SARS-CoV-2 infection. abstract: BACKGROUND: Over the last months, during the COVID‐19 pandemic, a growing number of chilblain‐like lesions was reported mainly in children, rarely in young adults. The relationship with SARS‐CoV‐2 infection was postulated, often without any laboratory, instrumental or clinical confirmation. The disclosure of information about chilblain‐like lesions as a COVID‐19 manifestation in social media has created concern in children’s families and pediatricians OBJECTIVES: to verify whether the chilblain‐like lesions were caused by SARS‐CoV‐2 infection. METHODS: prospective study on a case series including children who presented with acral lesions at the Pediatric Dermatology Outpatient and Pediatric Emergency Unit of the University of Bologna, from April 1 to April 30, 2020. We reported demographical, laboratory and clinical features, history of close contact with COVID‐19 patients, presence of similar skin lesions in other family members, precipitating and risk factors for chilblain onset. RESULTS: We evaluated 8 patients (5 females, 3 males) aged between 11 and 15 years. We excluded acute or previous SARS‐CoV‐2 infection with RT‐PCR nasopharyngeal swab, serum antibody levels using chemiluminescent immunoassays. Other acute infections causing purpuric lesions at the extremities were negative in all patients. Skin lesion biopsy for histological and immunohistochemical evaluation was made in two cases and was consistent with chilblain. PCR‐assay on skin lesion biopsy for Parvovirus B19, Mycoplasma pneumoniae and SARS‐CoV‐2 was performed in a patient and resulted negative. We identified common precipitating and risk factors: physical (cold and wet extremities, low BMI), cold and wet indoor and outdoor environment, behaviors, habits, lifestyle. We therefore reached a diagnosis of primary chilblains. CONCLUSIONS: During the COVID‐19 pandemic, a “cluster” of primary chilblains developed in predisposed subjects, mainly teenagers, due to to cold exposure in the lockdown period. Laboratory findings support our hypothesis, although it is also possible that an unknown infectious trigger may have contributed to the pathogenesis. url: https://doi.org/10.1111/jdv.16751 doi: 10.1111/jdv.16751 id: cord-272653-01wck9f3 author: Isaacs, David title: Apocalypse perhaps date: 2020-08-24 words: 1894.0 sentences: 133.0 pages: flesch: 59.0 cache: ./cache/cord-272653-01wck9f3.txt txt: ./txt/cord-272653-01wck9f3.txt summary: The exact starting date of the novel coronavirus pandemic COVID-19 will never be known, but China informed the World Health Organization (WHO) about the disease on New Year''s Eve, 31 December 2019. Transmission of severe acute respiratory syndrome (SARS)-CoV-2, the virus that causes COVID-19, was accelerated by traditional travel of 3 billion people for 40 days before the Chinese New Year on 25 January 2020. 2,3 When the Australian Chief Medical Officer activated the pandemic emergency response plan, weeks before the World Health Organization declared a pandemic, the Government was legally obliged to act. 12 The authors conclude that staff were being infected through community transmission and that PPE was effective in protecting front-line health-care workers. At a time when world leaders want to blame each other for aspects of the COVID-19 pandemic, the war metaphor is particularly menacing. Managing mental health challenges faced by healthcare workers during covid=19 pandemic abstract: nan url: https://doi.org/10.1111/jpc.15011 doi: 10.1111/jpc.15011 id: cord-341648-z4lflkmo author: Isaacs, David title: To what extent do children transmit SARS‐CoV‐2 virus? date: 2020-06-16 words: 576.0 sentences: 50.0 pages: flesch: 63.0 cache: ./cache/cord-341648-z4lflkmo.txt txt: ./txt/cord-341648-z4lflkmo.txt summary: A current child care outbreak in Sydney was initiated and spread by infected adults. 6 An unreviewed study of 15 New South Wales schools found nine staff and nine students who had tested positive for SARS-CoV-2. 7 It is possible that asymptomatic and mildly infected children are important transmitters of SARS-CoV-2, but the evidence to date suggests children rarely spread the virus. 8 Studies suggest school closures in China, Hong Kong and Singapore had little or no effect on control of the 2003 outbreak with the related SARS virus, which like infection with SARS-CoV-2 was much milder in children than adults. 9 In conclusion, the available evidence to date suggests children are unlikely to be major transmitters of SARSEpidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China School closure and management practices during coronavirus outbreaks including COVID-19: A systematic review abstract: nan url: https://doi.org/10.1111/jpc.14937 doi: 10.1111/jpc.14937 id: cord-291024-9g4om4sf author: Isakbaeva, Elmira T. title: SARS-associated Coronavirus Transmission, United States date: 2004-02-17 words: 3669.0 sentences: 160.0 pages: flesch: 53.0 cache: ./cache/cord-291024-9g4om4sf.txt txt: ./txt/cord-291024-9g4om4sf.txt summary: To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. To that end, we obtained serial biologic specimens and clinical and exposure data for 5 to 10 weeks after onset of illness from seven laboratory-confirmed U.S. SARS patients and their household contacts. We detected SARS-CoV in fecal and respiratory specimens and found that SARS case-patients may have high concentrations of virus in stools during the 2nd week of illness and continue to shed the virus in feces until at least 26 days after onset of symptoms. All upper respiratory specimens in the first 2 weeks after onset were negative for SARS-CoV by RT-PCR; this finding differs from a report in Hong Kong, where viral RNA was detected in nasopharyngeal aspirates of 68% of case-patients at day 14 (21) . abstract: To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. SARS-CoV was detected in a day-14 sputum specimen from one case-patient and in five stool specimens from two case-patients. In one case-patient, SARS-CoV persisted in stool for at least 26 days after symptom onset. The highest amounts of virus were in the day-14 sputum sample and a day-14 stool sample. Residual respiratory symptoms were still present in recovered SARS case-patients 2 months after illness onset. Possible transmission of SARS-CoV occurred in one household contact, but this person had also traveled to a SARS-affected area. The data suggest that SARS-CoV is not always transmitted efficiently. Laboratory diagnosis of SARS-CoV infection is difficult; thus, sputum and stool specimens should be included in the diagnostic work-up for SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15030687/ doi: 10.3201/eid1002.030734 id: cord-279765-sb1ifyfx author: Isakova-Sivak, Irina title: A promising inactivated whole-virion SARS-CoV-2 vaccine date: 2020-10-15 words: 1083.0 sentences: 52.0 pages: flesch: 44.0 cache: ./cache/cord-279765-sb1ifyfx.txt txt: ./txt/cord-279765-sb1ifyfx.txt summary: In this regard, the study by Shengli Xia and colleagues 7 is timely because it provides valuable evidence for the safety and immunogenicity of a β-propiolactone inactivated aluminium hydroxideadjuvanted whole-virion SARS-CoV-2 vaccine candidate developed by China National Biotec Group and the Beijing Institute of Biological Products (BBIBP-CorV), which was tested in randomised, double-blind, placebocontrolled phase 1/2 clinical trials in healthy individuals aged 18 years and older. Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Effect of an inactivated vaccine against SARS-CoV-2 on safety and immunogenicity outcomes: interim analysis of 2 randomized clinical trials Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBIBP-CorV: a randomised, double-blind, placebo-controlled, phase 1/2 trial abstract: nan url: https://doi.org/10.1016/s1473-3099(20)30832-x doi: 10.1016/s1473-3099(20)30832-x id: cord-338517-1mxcssjj author: Ishay, Yuval title: Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date: 2020-08-26 words: 7387.0 sentences: 399.0 pages: flesch: 40.0 cache: ./cache/cord-338517-1mxcssjj.txt txt: ./txt/cord-338517-1mxcssjj.txt summary: The phage display method, allowing rapid and wide display of proteins directly correlated to their associated genes, can detect NAbs against SARS-CoV from both naïve and immune antibody libraries, capable of blocking the binding of S1 domain, thereby showing virus neutralization and prophylaxis capability either in vitro or in the animal models (31, 33, 36) . Another method, possibly allowing the production and utilization of existing NAbs, may include the use of Epstein-Barr virus (EBV) transformation of human B cells to improve the isolation of NAbs from the memory B cells harvested from the SARS-CoV infected patients (11) . Experimental and clinical data on the use of convalescent plasma products and humanized monoclonal antibodies for H5N1 influenza infection have also shown positive outcomes, and this treatment was proposed as a mean for overcoming anti-viral drug resistance (62, 79, 80) . In a study involving 20 patients with severe pandemic influenza A (H1N1) 2009 virus infection, administration of convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality (81) . abstract: The immune response against SARS‐CoV‐2 is comprised of both cellular and humoral arms. While current diagnostic methods are mainly based on PCR, they suffer from insensitivity. Therefore, antibody‐based serological tests are being developed to achieve higher sensitivity and specificity. Current efforts in treating SARS‐CoV‐2 infection include blocking of viral entry into the host cells, prohibiting viral replication and survival in the host cells, or reducing the exaggerated host immune response. Administration of convalescent plasma containing anti‐viral antibodies was proposed to improve the outcome in severe cases. In this paper, we review some of the aspects associated with the development of antibodies against SARS‐CoV‐2 and their potential use for improved diagnosis and therapy. url: https://doi.org/10.1002/hep4.1600 doi: 10.1002/hep4.1600 id: cord-311948-3v311fnd author: Ishiguro, Takashi title: Clinical Course and Findings of 14 Patients with COVID-19 Compared with 5 Patients with Conventional Human Coronavirus Pneumonia date: 2020-08-27 words: 2614.0 sentences: 183.0 pages: flesch: 56.0 cache: ./cache/cord-311948-3v311fnd.txt txt: ./txt/cord-311948-3v311fnd.txt summary: Because her symptoms, laboratory data, and radiological findings were mild with patchy GGOs detectable only by CT ( Figure 11 ), we did not administer antibiotics or antivirals, and she remained in stable condition during hospitalization. Only one of the SARS-CoV-2 pneumonia patients was in severe condition on admission (Table 3) , but 5 patients worsened during hospitalization, and one patient (Case 5) required HFNC therapy. Abnormal X-ray shadows were not detectable in 4 (36.3%) of the 11 SARS-CoV-2 pneumonia patients throughout their course, but abnormal shadows were found in the other patients on admission or during hospitalization. 10 Abnormal shadows were not detected on initial chest X-ray in 5 of our 11 patients with SARS-CoV-2 pneumonia. (11) We administered ritonavir/lopinavir to 5 of the 11 SARS-CoV-2 pneumonia patients, and chest X-ray findings gradually began to improve 3 days after the initiation of these agents in 3 patients. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: OBJECTIVE: To clarify what future problems must be resolved and how clinical findings of SARS-CoV-2 infection differ from those of cHCoV infection. METHODS: Patients and Methods Clinical characteristics of 14 patients with laboratory-confirmed Coronavirus disease 2019 (COVID-19) and 5 patients with cHCoV pneumonia admitted to our institution and treated up to March 8, 2020, were retrospectively analyzed. RESULTS: On admission, 10 patients had pneumonia, 5 of whom had pulmonary shadows detectable only via computed tomography (CT). During hospitalization, another patient with no pulmonary shadows on admission developed pneumonia. In total, 11 (78.6%) of the 14 patients developed pneumonia, indicating its high prevalence in COVID-19. During hospitalization, the patients’ symptoms spontaneously relapsed and resolved, and gastrointestinal symptoms were frequently found. C-reactive protein values showed correlation with the patients’ clinical courses. Ritonavir/lopinavir were administered to 5 patients whose respiratory conditions worsened during admission, all of whom improved. However, the pneumonia in the 6 other patients improved without antivirals. None of the 14 patients died, whereas 5 other patients with cHCoV pneumonia were in respiratory failure on admission, and one patient (20%) died. CONCLUSION: Both SARS-CoV-2 and cHCoV can cause severe pneumonia. Problems for future resolution include whether antiviral agents administered in cases of mild or moderate severity can reduce the number of severe cases, and whether antivirals administered in severe cases can reduce mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/32874906/ doi: 10.1016/j.rmcr.2020.101207 id: cord-335377-zrbn637z author: Ishimaru, Daniella title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date: 2012-12-26 words: 7699.0 sentences: 376.0 pages: flesch: 52.0 cache: ./cache/cord-335377-zrbn637z.txt txt: ./txt/cord-335377-zrbn637z.txt summary: Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. We further show that kissing dimer formation plays a role in frameshift-stimulation and modulates the relative abundance of full-length and subgenomic viral RNAs. Plasmids containing wild-type pseudoknot as well as the ÁS3 pk mutant were described in Plant et al (1) . Our previous NMR analysis of exchangeable imino protons of the SARS-CoV pseudoknot ( Figure 1A , wild-type pk) provided unequivocal evidence for the existence of Stem 3 (1). Surprisingly, in the context of the SARS-CoV Stem 3 sequence, 5 0 -cuug-3 0 tetraloop-capped mutants readily formed extended duplex structures as revealed by native gel and NMR analysis. abstract: Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/23275571/ doi: 10.1093/nar/gks1361 id: cord-276481-os1nf3cs author: Ishizaki, Tatsuro title: Estimation of the impact of providing outpatients with information about SARS infection control on their intention of outpatient visit date: 2004-09-30 words: 4930.0 sentences: 171.0 pages: flesch: 38.0 cache: ./cache/cord-276481-os1nf3cs.txt txt: ./txt/cord-276481-os1nf3cs.txt summary: Abstract To examine the effect of provision of information about the infection control in the specific infection disease treatment unit in a city hospital on the outpatient''s intention of outpatient service use, respondents who underwent outpatient medical care at the hospital (N = 821) were asked whether or not they intended to continue the outpatient visit at the hospital if a severe acute respiratory syndrome (SARS) patient was admitted to the unit. This study examined the effect of providing outpatients with information about SARS infection control in the infectious disease treatment unit in a community hospital on their intention to continue outpatient visits, and estimated the cumulative total number of outpatients as well as the cumulative total expenditures for outpatient care at the hospital during a 180-day period after the admission of a SARS patient to the hospital. abstract: Abstract To examine the effect of provision of information about the infection control in the specific infection disease treatment unit in a city hospital on the outpatient’s intention of outpatient service use, respondents who underwent outpatient medical care at the hospital (N = 821) were asked whether or not they intended to continue the outpatient visit at the hospital if a severe acute respiratory syndrome (SARS) patient was admitted to the unit. Although 56% of respondents replied that they could continue to visit the department if a SARS patient was admitted to the unit in the hospital before they read the information, the proportion of those who intended to continue outpatient care significantly increased by 15% after they read it. The logistic regression analyses revealed that respondents who had frequently visited the outpatient department (P < 0.001), those who felt relieved by reading the information about the unit (P < 0.001), and those who did not worry about nosocomial SARS infection inside the hospital (P < 0.001) were significantly more likely to reply that they would continue outpatient visits. We estimated that admission of a SARS patient to the unit would result in a 20% decrease in the cumulative total number of outpatients in the hospital during a 180-day interval after admission of a SARS patient to the unit, and the cumulative total number of outpatients increased by 7% after they read the information. This study suggests that providing outpatients with appropriate information about SARS infection control in the hospital had a statistically significant and substantial impact on the outpatients’ intention to continue outpatient visits at the hospital. url: https://api.elsevier.com/content/article/pii/S0168851004000910 doi: 10.1016/j.healthpol.2004.04.008 id: cord-252714-idlyl4ga author: Islam, M. Saiful title: Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis date: 2020-05-15 words: 5654.0 sentences: 348.0 pages: flesch: 51.0 cache: ./cache/cord-252714-idlyl4ga.txt txt: ./txt/cord-252714-idlyl4ga.txt summary: 1,2 Outbreaks of newly emerging or remerging infectious diseases present a unique challenge and a threat to healthcare providers (HCPs) and other frontline responders due to limited understanding of the emerging threat and reliance on infection prevention and control (IPC) measures that may not consider all transmission dynamics of the emerging pathogens. We searched publications in English on ''PubMed'' and Google Scholar for the period between January 1 and April 27, 2020, using the following search terms: "2019-nCoV" or "COVID-19" or "2019 novel coronavirus" or "SARS-CoV-2." To identify COVID-19 IPC guidelines, we visited the websites of the international public health agencies such as CDC, ECDC, WHO, as well as the Australian Government Department of Health, the Bureau of Disease Prevention and Control of the National Health Commission of the People''s Republic of China, and Public Health England. abstract: OBJECTIVE: In the current absence of a vaccine for COVID-19, public health responses aim to break the chain of infection by focusing on the mode of transmission. We reviewed the current evidence on the transmission dynamics and on pathogenic and clinical features of COVID-19 to critically identify any gaps in the current infection prevention and control (IPC) guidelines. METHODS: In this study, we reviewed global COVID-19 IPC guidelines by organizations such as the World Health Organization (WHO), the US Centers for Disease Control and Prevention (CDC), and the European Centre for Disease Prevention and Control (ECDC). Guidelines from 2 high-income countries (Australia and United Kingdom) and from 1 middle-income country (China) were also reviewed. We searched publications in English on ‘PubMed’ and Google Scholar. We extracted information related to COVID-19 transmission dynamics, clinical presentations, and exposures that may facilitate transmission. We then compared these findings with the recommended IPC measures. RESULTS: Nosocomial transmission of SARS-CoV-2 in healthcare settings occurs through droplets, aerosols, and the oral–fecal or fecal–droplet route. However, the IPC guidelines fail to cover all transmission modes, and the recommendations also conflict with each other. Most guidelines recommend surgical masks for healthcare providers during routine care and N95 respirators for aerosol-generating procedures. However, recommendations regarding the type of face mask varied, and the CDC recommends cloth masks when surgical masks are unavailable. CONCLUSION: IPC strategies should consider all the possible routes of transmission and should target all patient care activities involving risk of person-to-person transmission. This review may assist international health agencies in updating their guidelines. url: https://www.ncbi.nlm.nih.gov/pubmed/32408911/ doi: 10.1017/ice.2020.237 id: cord-339524-r0a6a1jw author: Islam, M. T. title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades date: 2020-10-13 words: 2518.0 sentences: 157.0 pages: flesch: 60.0 cache: ./cache/cord-339524-r0a6a1jw.txt txt: ./txt/cord-339524-r0a6a1jw.txt summary: title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2. 137 A set of 15 primers ( Table 1) was designed based on the ARMS for differentiating six major 138 clades of SARS-CoV-2: S, L, V, G, GH, and GR. Hence, the single-variant specific PCRs were able to identify the 228 SARS-CoV-2 positive sample containing GR-clade of the virus. This study proposes a simple and exclusive ARMS-based SNP-discriminating method using 257 conventional PCR to establish multiplex-assays in detecting SARS-CoV-2 mutation clades. abstract: Tracing the globally circulating SARS-CoV-2 mutants is essential for the outbreak alerts and far-reaching epidemiological surveillance. The available technique to identify the phylogenetic clades through high-throughput sequencing is costly, time-consuming, and labor-intensive that hinders the viral genotyping in low-income countries. Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized in the primer concentration (0.2-0.6 M) and annealing temperature (56-60{degrees}C) of PCR using 3-5 ng/l cDNA template synthesized upon random- and oligo(dT)-primer based reverse transcription. The different primer concentration for the triplex and quadruplex adjusted to different strengths ensured an even amplification with a maximum resolution of all targeted amplicons. The targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of our designed primers. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2. url: https://doi.org/10.1101/2020.10.08.20209692 doi: 10.1101/2020.10.08.20209692 id: cord-339352-c9uh8vjx author: Islam, Muhammad Torequl title: Environmental Integrants Affecting the Spreadability of SARS-CoV-12 date: 2020-07-28 words: 772.0 sentences: 61.0 pages: flesch: 54.0 cache: ./cache/cord-339352-c9uh8vjx.txt txt: ./txt/cord-339352-c9uh8vjx.txt summary: The SARS-CoVs can survive in water and remain infectious for long periods (days to weeks), therefore, these may affect people and other animals if aerosols are generated (Casanova et al. It has been demonstrated that SARS-CoVs have low stability in the environment, very sensitive to oxidants (e.g., chlorine) and are inactivated significantly faster in water. However, SARS-CoV-2 has been found in the fecal samples and anal swabs of some patients, therefore, there is a possibility of fecal-oral (including waterborne) transmission of this virus (Rosa et al. Additionally, it is also necessary to study all the environmental components that affecting the survival, replication, spreadability or transmission and pathogenicity of SARS-CoV-2 in human and other animals. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Selenium and RNA virus interactions: Potential implications for SARS-CoV-2 infection (COVID-19) TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32725583/ doi: 10.1007/s12560-020-09435-z id: cord-308370-9av7qw10 author: Islam, Rajib title: A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 date: 2020-05-12 words: 5675.0 sentences: 333.0 pages: flesch: 49.0 cache: ./cache/cord-308370-9av7qw10.txt txt: ./txt/cord-308370-9av7qw10.txt summary: To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. The aim of this study is to explore and identify the binding affinities and interactions of these antiviral phytochemicals against the main protease of SARS-CoV-2 using computational and statistical tools. In this study, a-ketoamide-11r is considered as a control ligand because it is recently reported as a good inhibitor against main protease , which shows binding affinity of -7.8 kcal/mol. Among the studied 40 phytochemicals, hypericin, cyanidin 3-glucoside, baicalin, glabridin, and a-ketoamide-11r show the highest binding affinity and strong interactions with both or at least one of the catalytic residues (Cys145 and His41) of the main protease. abstract: The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the R(2) value of 0.842 for the training set and 0.753 for the test set. Our proposed MLR model can predict the favorable binding energy compared with the binding energy detected from molecular docking. ADMET analysis demonstrates that these candidates appear to be safer inhibitors. Our comprehensive computational and statistical analysis show that these selected phytochemicals can be used as potential inhibitors against the SARS-CoV-2. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1761883 doi: 10.1080/07391102.2020.1761883 id: cord-320490-3jmo35jc author: Ismail, Saba title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 words: 6688.0 sentences: 412.0 pages: flesch: 52.0 cache: ./cache/cord-320490-3jmo35jc.txt txt: ./txt/cord-320490-3jmo35jc.txt summary: In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . abstract: The COVID-19 pandemic caused by SARS-CoV-2 is a public-health emergency of international concern and thus calling for the development of safe and effective therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for vaccine, antibodies and inhibitor development because of many roles it plays in attachment, fusion and entry into the host cell. In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in solution aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel analytical tool axial frequency distribution (AFD). Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus has the potential to be considered in experimental studies. url: https://doi.org/10.1101/2020.04.05.026005 doi: 10.1101/2020.04.05.026005 id: cord-332374-cbiw6yvb author: Israeli, Ofir title: Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date: 2020-06-10 words: 1051.0 sentences: 77.0 pages: flesch: 55.0 cache: ./cache/cord-332374-cbiw6yvb.txt txt: ./txt/cord-332374-cbiw6yvb.txt summary: Very recently, two studies [6] [7] used a direct no-buffer RT-qPCR approach which identified > 90% of the tested clinical samples. In this study, we tested the diagnostic efficiency following thermal inactivation (65°C for 30min and 95°C for 10min) without addition of lysis buffers ("no buffer") or following lysis by three buffers (Virotype, QuickExtract and 2% Triton-X-100) and compared it to diagnosis after standard RNA extraction. Samples included buffers spiked with SARS-CoV-2, at concentrations 0.1-100,000 PFU/ml and 30 clinical samples, previously diagnosed as positive (20) and negative (10). The limit of detection was 1 PFU/ml: In this concentration samples in the no buffer mode and Virotype at 95°C were not detected, while the RNA extraction mode averaged the lowest critical threshold ( Ct=29.8) followed by QuickExtract and Triton. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step abstract: SARS-CoV-2 genetic identification is based on viral RNA extraction prior to RT-qPCR assay, however recent studies support the elimination of the extraction step. Herein, we assessed the RNA extraction necessity, by comparing RT-qPCR efficacy in several direct approaches vs. the gold standard RNA extraction, in detection of SARS-CoV-2 from laboratory samples as well as clinical Oro-nasopharyngeal SARS-CoV-2 swabs. Our findings show advantage for the extraction procedure, however a direct no-buffer approach might be an alternative, since it identified up to 70% of positive clinical specimens. url: https://doi.org/10.1101/2020.06.10.144196 doi: 10.1101/2020.06.10.144196 id: cord-283749-j4600733 author: Itoyama, Satoru title: ACE1 polymorphism and progression of SARS date: 2004-10-22 words: 2975.0 sentences: 152.0 pages: flesch: 53.0 cache: ./cache/cord-283749-j4600733.txt txt: ./txt/cord-283749-j4600733.txt summary: Angiotensin converting enzyme (ACE1) insertion/deletion (I/D) polymorphism was previously reported to show association with the adult respiratory distress syndrome, which is also thought to play a key role in damaging the lung tissues in SARS cases. Despite the small sample size, the frequency of the D allele was significantly higher in the hypoxemic group than in the non-hypoxemic group (p =0.013), whereas there was no significant difference between the SARS cases and controls, irrespective of a contact history. Genotypic distribution and allele frequency of the ACE I/D polymorphism in SARS cases and controls with or without contact history to SARS patients were compared (Table 4 ). The ACE insertion/deletion polymorphism has also been reported to be a risk factor of the diseases mentioned above [17] and this might be associated with systemic angiopathy and influence progression of SARS in the lung. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore abstract: Abstract We have hypothesized that genetic predisposition influences the progression of SARS. Angiotensin converting enzyme (ACE1) insertion/deletion (I/D) polymorphism was previously reported to show association with the adult respiratory distress syndrome, which is also thought to play a key role in damaging the lung tissues in SARS cases. This time, the polymorphism was genotyped in 44 Vietnamese SARS cases, with 103 healthy controls who had had a contact with the SARS patients and 50 controls without any contact history. SARS cases were divided into either non-hypoxemic or hypoxemic groups. Despite the small sample size, the frequency of the D allele was significantly higher in the hypoxemic group than in the non-hypoxemic group (p =0.013), whereas there was no significant difference between the SARS cases and controls, irrespective of a contact history. ACE1 might be one of the candidate genes that influence the progression of pneumonia in SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15381116/ doi: 10.1016/j.bbrc.2004.08.208 id: cord-345493-3bb1zuqp author: Itoyama, Satoru title: Identification of an alternative 5′‐untranslated exon and new polymorphisms of angiotensin‐converting enzyme 2 gene: Lack of association with SARS in the Vietnamese population date: 2005-06-03 words: 3331.0 sentences: 172.0 pages: flesch: 54.0 cache: ./cache/cord-345493-3bb1zuqp.txt txt: ./txt/cord-345493-3bb1zuqp.txt summary: We analyzed genetic variations of angiotensin‐converting enzyme 2 (ACE2), considering that it might influence patients'' susceptibility to severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) or development of SARS as a functional receptor. © 2005 Wiley‐Liss, Inc. We analyzed genetic variations of angiotensinconverting enzyme 2 (ACE2), considering that it might influence patients'' susceptibility to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) or development of SARS as a functional receptor. A case control study involving 44 SARS cases, 16 anti-SARS-CoV antibodypositive contacts, 87 antibody-negative contacts, and 50 non-contacts in Vietnam, failed to obtain any evidence that the ACE2 gene polymorphisms are involved in the disease process in the population. Using the PCR-based cloning procedure, we identified for the first time an alternative exon upstream of the original exon 1 of ACE2 that is expressed in various organs, including the lung and trachea, primary-cultured bronchial epithelial cells, and the small intestine. abstract: We analyzed genetic variations of angiotensin‐converting enzyme 2 (ACE2), considering that it might influence patients' susceptibility to severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) or development of SARS as a functional receptor. By cloning of the full‐length cDNA of the ACE2 gene in the lung, where replication occurs on SARS‐CoV, it was shown that there are different splicing sites. All exons including the new alternative exon, exon‐intron boundaries, and the corresponding 5′‐flanking region of the gene were investigated and 19 single nucleotide polymorphisms (SNPs) were found. Out of these, 13 SNPs including one non‐synonymous substitution and three 3′‐UTR polymorphisms were newly identified. A case control study involving 44 SARS cases, 16 anti‐SARS‐CoV antibody‐positive contacts, 87 antibody‐negative contacts, and 50 non‐contacts in Vietnam, failed to obtain any evidence that the ACE2 gene polymorphisms are involved in the disease process in the population. Nevertheless, identification of new 5′‐untranslated exon and new SNPs is considered helpful in investigating regulation of ACE2 gene expression in the future. © 2005 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/15937940/ doi: 10.1002/ajmg.a.30779 id: cord-345092-1ztfcpsb author: Iwasaki, Masae title: Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications date: 2020-10-08 words: 11428.0 sentences: 550.0 pages: flesch: 44.0 cache: ./cache/cord-345092-1ztfcpsb.txt txt: ./txt/cord-345092-1ztfcpsb.txt summary: Severe patients of COVID-19 often develop acute respiratory distress syndrome and multiple organ dysfunction/failure with high mortality that may be closely related to the hyper-proinflammatory status called the "cytokine storm." Massive cytokines including interleukin-6, nuclear factor kappa B (NFκB), and tumor necrosis factor alpha (TNFα) released from SARS-CoV-2-infected macrophages and monocytes lead inflammation-derived injurious cascades causing multi-organ injury/failure. ARB/ACE-I, angiotensin receptor blocker/ACE2 inhibitor; AT1aR, angiotensin receptor subtype 1a; C3, complement component 3; E-cadherin, epithelial cadherin; gp130, glycoprotein 130; IL, interleukin; JAK, Janus kinase; MAPK, mitogenactivated protein kinase; MCP-1, monocyte chemoattractant protein 1; mIL-6R, membrane interleukin 6 receptor; MMP9, matrix metallopeptidase 9; MyD88, myeloid differentiation primary response 88; NFκB, nuclear factor kappa-light-chain-enhancer of activated B cells; NFκB, nuclear factor kappa B; PI3K/Akt, phosphoinositide-3-kinase/protein Kinase B; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; sIL-6R, soluble interleukin 6 receptor; SOCS3, the suppressor of cytokine signaling-3; STAT3, signal transducers and activators of transcription; sTNFα, soluble tumor necrosis factor alpha; Tfh, follicular helper T cell; Th0, naive T cell; Th17, T helper 17 cell; TMPRSS2, transmembrane protease serine 2; TNFα, tumor necrosis factor alpha; TPO, thrombopoietin; VEGF, vascular endothelial growth factor. abstract: The widespread occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a pandemic of coronavirus disease 2019 (COVID-19). The S spike protein of SARS-CoV-2 binds with angiotensin-converting enzyme 2 (ACE2) as a functional “receptor” and then enters into host cells to replicate and damage host cells and organs. ACE2 plays a pivotal role in the inflammation, and its downregulation may aggravate COVID-19 via the renin-angiotensin system, including by promoting pathological changes in lung injury and involving inflammatory responses. Severe patients of COVID-19 often develop acute respiratory distress syndrome and multiple organ dysfunction/failure with high mortality that may be closely related to the hyper-proinflammatory status called the “cytokine storm.” Massive cytokines including interleukin-6, nuclear factor kappa B (NFκB), and tumor necrosis factor alpha (TNFα) released from SARS-CoV-2-infected macrophages and monocytes lead inflammation-derived injurious cascades causing multi-organ injury/failure. This review summarizes the current evidence and understanding of the underlying mechanisms of SARS-CoV-2, ACE2 and inflammation co-mediated multi-organ injury or failure in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33029758/ doi: 10.1007/s10753-020-01337-3 id: cord-275439-cdlcv1c9 author: Iwasaki, S. title: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date: 2020-05-19 words: 1850.0 sentences: 130.0 pages: flesch: 66.0 cache: ./cache/cord-275439-cdlcv1c9.txt txt: ./txt/cord-275439-cdlcv1c9.txt summary: We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in nine COVID-19 patients. SARS-CoV-2 was detected in saliva in 8 of 9 (89%) patients and in all 11 samples taken within 2 weeks after disease onset. The diagnosis of COVID-19 is made by PCR testing of samples collected by nasopharyngeal or oropharyngeal swabs, with the nasopharyngeal route being the standard with a sensitivity for the virus in the range of 52-71% [1] [2] [3] [4] [5] . demonstrated the saliva to be more sensitive for SARS-CoV-2 detection patients than nasopharyngeal swabs 14 . We prospectively compared SARS-CoV-2 detection between nasopharyngeal samples and saliva samples in 9 patients with COVID-19. Our results were consistent to these data; the virus was detected in all the saliva samples taken within 2 weeks after symptom onset. Data are shown as mean ± SD (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in nine COVID-19 patients. SARS-CoV-2 was detected in saliva in 8 of 9 (89%) patients and in all 11 samples taken within 2 weeks after disease onset. Viral load was equivalent at earlier time points but declined in saliva than nasopharyngeal samples. PCR negativity was also concordant in all 27 saliva samples from 24 patients between nasopharyngeal and saliva samples. These results suggest that saliva is a reliable noninvasive alternative to nasopharyngeal swabs and facilitate widespread PCR testing in the face of shortages of swabs and protective equipment without posing a risk to healthcare workers. url: https://doi.org/10.1101/2020.05.13.20100206 doi: 10.1101/2020.05.13.20100206 id: cord-025980-85jbwmfv author: Iwasaki, Sumio title: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date: 2020-06-04 words: 626.0 sentences: 42.0 pages: flesch: 61.0 cache: ./cache/cord-025980-85jbwmfv.txt txt: ./txt/cord-025980-85jbwmfv.txt summary: We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in 76 patients including ten coronavirus disease 2019 (COVID-19) patients. Figure 1C shows To our knowledge, a few studies compared viral load between nasopharyngeal and saliva samples. The viral loads were 5-times higher in saliva than in nasopharyngeal samples in one study (5) , whereas they were lower in saliva in two studies (6, 8) . Our results showed that the viral load was equivalent at earlier time points but lower in saliva than in nasopharyngeal samples at convalescent phase. Saliva is more sensitive for SARS-CoV-2 detectionin COVID-19 patients than nasopharyngeal swabs. Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7270800/ doi: 10.1016/j.jinf.2020.05.071 id: cord-010384-wyp7hrde author: Iwen, Peter C title: Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-04-10 words: 1633.0 sentences: 64.0 pages: flesch: 40.0 cache: ./cache/cord-010384-wyp7hrde.txt txt: ./txt/cord-010384-wyp7hrde.txt summary: The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184424/ doi: 10.1093/labmed/lmaa018 id: cord-272450-8a3ir06y author: Iwen, Peter C title: Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 words: 1732.0 sentences: 68.0 pages: flesch: 40.0 cache: ./cache/cord-272450-8a3ir06y.txt txt: ./txt/cord-272450-8a3ir06y.txt summary: The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32190890/ doi: 10.1093/ajcp/aqaa047 id: cord-312884-anlp8lab author: Iyer, Gayatri R. title: Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants date: 2020-09-04 words: 6268.0 sentences: 317.0 pages: flesch: 44.0 cache: ./cache/cord-312884-anlp8lab.txt txt: ./txt/cord-312884-anlp8lab.txt summary: Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. The aim of the present study was to identify variants in these five selected candidate genes from the clinical exome data available with us for more than 100 individuals and make an attempt to classify them as relevant to the present COVID-19 aetiopathology, especially for the Indian population. The selected candidate gene variants were assessed in our internal cohort of 103 individuals, who had earlier provided consent, to perform a pilot study on the susceptibility and disease severity of Indians for COVID-19. Since host genetic polymorphisms have been demonstrated to be associated with vulnerability to human infection, in this study five candidate genes-ACE2, TMPRSS2, CD209, IFITM3, and MUC5B-were selected based on their relevance to the current pandemic. abstract: Introduction: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has spread around the globe. Susceptibility has been associated with age, biological sex, and other prior existing health conditions. However, host genes are involved in viral infectivity and pathogenicity, and polymorphisms in these could be responsible for the interethnic/interindividual variability observed in infection and progression of COVID-19. Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. Results: A total of 497 polymorphisms were identified in the five selected genes in the exomes analyzed. Thirty-eight polymorphisms identified in our cohort have been reported earlier in literature and have functional significance or association with health conditions. These variants were classified into three groups: protective, susceptible, and responsible for comorbidities. Discussion and Conclusion: The two polymorphisms described in literature as risk inducing are rs35705950 in MUC5B gene and TMPRSS2 haplotype (rs463727, rs34624090, rs55964536, rs734056, rs4290734, rs34783969, rs11702475, rs35899679, and rs35041537) were absent in our cohort explaining the slower infectivity of the disease in this part of India. The 38 functional variants identified can be used as a predisposition panel for the COVID-19 infectivity and progression and stratify individuals as “high or low risk,” which would help in planning appropriate surveillance and management protocols. A larger study from different regions of India is warranted to validate these results. url: https://doi.org/10.3389/fgene.2020.00861 doi: 10.3389/fgene.2020.00861 id: cord-342538-5bwsm290 author: Izquierdo Lara, R. W. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 words: 5031.0 sentences: 281.0 pages: flesch: 56.0 cache: ./cache/cord-342538-5bwsm290.txt txt: ./txt/cord-342538-5bwsm290.txt summary: Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina). abstract: The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community. url: https://doi.org/10.1101/2020.09.21.20198838 doi: 10.1101/2020.09.21.20198838 id: cord-345139-gyvlikye author: Izquierdo-Domínguez, Adriana title: Pérdida del sentido del olfato durante la pandemia COVID-19 date: 2020-06-12 words: 2888.0 sentences: 290.0 pages: flesch: 54.0 cache: ./cache/cord-345139-gyvlikye.txt txt: ./txt/cord-345139-gyvlikye.txt summary: Mientras que la función olfatoria normal se define como normosmia, los trastornos cuantitativos se clasifican en pérdida parcial (hiposmia) o total (anosmia) del olfato 4 . Se habla de estudio cuantitativo al referirse a la cantidad de olor necesitado para ser detectado (umbral olfativo) y tiene por objeto el estudio de las variaciones olfativas en función de la concentración de la sustancia olorosa y de la cantidad de los olores detectados, dando un resultado de anosmia (pérdida total), hiposmia (pérdida parcial) o normosmia (olfato normal). Durante la pandemia COVID-19, se aconseja a aquellos pacientes con pérdida repentina y grave del sentido del olfato, iniciar medidas de distanciamiento social, aislamiento domiciliario preventivo y realizar pruebas de diagnóstico para el SARS-CoV-2 cuando sea posible. abstract: nan url: https://doi.org/10.1016/j.medcli.2020.06.006 doi: 10.1016/j.medcli.2020.06.006 id: cord-347813-9vfwl7c0 author: Jackson, M. L. title: Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2 date: 2020-07-02 words: 3783.0 sentences: 224.0 pages: flesch: 47.0 cache: ./cache/cord-347813-9vfwl7c0.txt txt: ./txt/cord-347813-9vfwl7c0.txt summary: Interventions considered were (a) encouraging telecommuting; (b) reducing contacts to seniors and nursing home residents; (c) modest reductions to contacts outside of the home; (d) encouraging self-isolation of persons with COVID-19 symptoms; (e) rapid testing and household quarantining. This report presents findings from an agent-based model of SARS-CoV-2 transmission that can help guide decisions about mitigating the impact of COVID-19 during this re-opening. 6 The per-contact probability of transmitting SARS-CoV-2 in homes and in non-home settings was estimated by fitting simulated daily COVID-19 hospitalizations to hospitalizations in King County from 28 February -27 May 2020, in the presence of social distancing interventions as actually implemented in King County. Rather than estimating the impact of generic reductions in Reff, this report uses an agent-based model to estimate the impact of specific policies on SARS-CoV-2 transmission and COVID-19 hospitalizations. 15 used also agent-based models to explore the impact of combinations of social distancing measures on SARS-CoV-2 transmission. abstract: Background After many jurisdictions have implemented intensive social distancing to suppress SARS-CoV-2 transmission, the challenge now is to mitigate the ongoing COVID-19 epidemic without overburdening economic and social activities. This report explores low-impact interventions to mitigate SARS-CoV-2 with a minimum of social and economic disruption. Methods An agent-based model simulated the population of King County, Washington, with agents that interact in homes, schools, workplaces, and other community sites. SARS-CoV-2 transmission probabilities were estimated by fitting simulated to observed hospital admissions from February-May 2020. Interventions considered were (a) encouraging telecommuting; (b) reducing contacts to seniors and nursing home residents; (c) modest reductions to contacts outside of the home; (d) encouraging self-isolation of persons with COVID-19 symptoms; (e) rapid testing and household quarantining. Results Individual interventions are not expected to have a large impact on COVID-19 hospitalizations. No intervention reduced COVID-19 hospitalizations by more than 12.7% (95% confidence interval [CI], 12.0% to 13.3%). Removing all interventions would result in nearly 42,000 COVID-19 hospitalizations between June 2020 and January 2021, with peak hospital occupancy exceeding available beds 6-fold. Combining the interventions is predicted to reduce total hospitalizations by 48% (95% CI, 47-49%), with peak COVID-19 hospital occupancy of 70% of total beds. Targeted school closures can further reduce the peak occupancy. Conclusions Combining low-impact interventions may mitigate the course of the COVID-19 epidemic, keeping hospital burden within the capacity of the healthcare system. Under this approach SARS-CoV-2 can spread through the community, moving toward herd immunity, while minimizing social and economic disruption. url: http://medrxiv.org/cgi/content/short/2020.06.30.20143735v1?rss=1 doi: 10.1101/2020.06.30.20143735 id: cord-312486-rumqopg0 author: Jacob, Chaim Oscar title: On the genetics and immunopathogenesis of COVID-19 date: 2020-09-10 words: 11514.0 sentences: 579.0 pages: flesch: 44.0 cache: ./cache/cord-312486-rumqopg0.txt txt: ./txt/cord-312486-rumqopg0.txt summary: The question is whether ACE2 expression levels are pertinent to SARS-CoV-2 infection only in the tissues relevant to viral entry and the lungs as its major target, [44, 45] or, given that COVID-19 in its severe form is a systemic disease with multi-organ disfunction [46, 47] , ACE2 expression levels may be important in multiple organs and tissues other than those of the respiratory system. However, the activation of multiple complement pathways, dysregulated neutrophil responses, endothelial injury, and hypercoagulability appear to be interlinked with SARS-CoV-2 infection and instead serve to drive the severity of the disease [91] . Regarding SLE, the prototypic systemic autoimmune disease, a group of investigators suggested that inherent epigenetic dysregulation causing hypomethylation and overexpression of ACE2, the functional receptor for SARS-CoV-2, might facilitate viral J o u r n a l P r e -p r o o f entry, viremia, and increased likelihood of cytokine storm in such patients [153] . abstract: Most severe cases with COVID-19, especially those with pulmonary failure, are not a consequence of viral burden and/or failure of the ‘adaptive’ immune response to subdue the pathogen by utilizing an adequate ‘adaptive’ immune defense. Rather it is a consequence of immunopathology, resulting from imbalanced innate immune response, which may not be linked to pathogen burden at all. In fact, it might be described as an autoinflammatory disease. The Kawasaki-like disease seen in children with SARS-CoV-2 exposure might be another example of similar mechanism. url: https://api.elsevier.com/content/article/pii/S1521661620307518 doi: 10.1016/j.clim.2020.108591 id: cord-337105-jlmh79qv author: Jacob, Fadi title: Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date: 2020-09-21 words: 9954.0 sentences: 567.0 pages: flesch: 53.0 cache: ./cache/cord-337105-jlmh79qv.txt txt: ./txt/cord-337105-jlmh79qv.txt summary: We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. QPCR analysis also showed higher levels of ACE2 and TMPRSS2 expression in CPOs at 50 DIV and 100 DIV than in hippocampal organoids ( Figure S2D ) Together, these results show that our CPOs exhibit a similar transcriptome as adult human choroid plexus tissue and express markers for choroid plexus epithelial cells and SARS-CoV-2 receptors, representing a suitable experimental model to study SARS-CoV-2 infection. Our finding that dysregulated gene expression varies widely among hepatocyte, intestinal, and choroid plexus organoids infected with SARS-CoV-2 suggests unique responses in different cell types and highlights the need for diverse human cellular model systems when studying the disease. abstract: Neurological complications are common in patients with COVID-19. While SARS-CoV-2, the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function are not well understood. Here we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found that neurons and astrocytes were sparsely infected, but choroid plexus epithelial cells underwent robust infection. We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our findings provide evidence for selective SARS-CoV-2 neurotropism and support the use of hiPSC-derived brain organoids as a platform to investigate SARS-CoV-2 infection susceptibility of brain cells, mechanisms of virus-induced brain dysfunction, and treatment strategies. url: https://www.sciencedirect.com/science/article/pii/S193459092030463X?v=s5 doi: 10.1016/j.stem.2020.09.016 id: cord-317693-l08q2lhp author: Jacob, Michelle Cristine Medeiros title: Animal-based food systems are unsafe: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fosters the debate on meat consumption date: 2020-07-07 words: 3262.0 sentences: 173.0 pages: flesch: 49.0 cache: ./cache/cord-317693-l08q2lhp.txt txt: ./txt/cord-317693-l08q2lhp.txt summary: CONCLUSION: To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases (5) . Uses of bushmeat vary from COMMENTARY SNAPSHOT SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases. To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. FNS, food and nutrition security; SARS, severe acute respiratory syndrome subsistence-based rural consumption and subsistencecommercial hunting to a luxury commodity in urban areas (18) . abstract: OBJECTIVE: The current pandemic restarts a debate on permanently banning wildlife consumption in an effort to prevent further public health threats. In this commentary, we offer two ideas to enhance the discussion on foodborne zoonotic diseases in food systems. DESIGN: First, we focus on the probable consequences that the loss of access to wildlife could cause to the status of food and nutrition security of many people in developing countries that rely on bushmeat to subsist. Second, we argue that all animal-based food systems, especially the ones based on intensive husbandry, present food safety threats. CONCLUSION: To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. url: https://doi.org/10.1017/s1368980020002657 doi: 10.1017/s1368980020002657 id: cord-325460-4fhegc0z author: Jacobs, Werner title: Fatal lymphocytic cardiac damage in coronavirus disease 2019 (COVID‐19): autopsy reveals a ferroptosis signature date: 2020-09-22 words: 3977.0 sentences: 241.0 pages: flesch: 39.0 cache: ./cache/cord-325460-4fhegc0z.txt txt: ./txt/cord-325460-4fhegc0z.txt summary: Immunohistochemical staining with E06, a monoclonal antibody binding to oxidized phosphatidylcholine (reflecting lipid peroxidation during ferroptosis), was positive in morphologically degenerating and necrotic cardiomyocytes adjacent to the infiltrate of lymphocytes, near arteries, in the epicardium and myocardium. We examined the patient''s myocardial tissue for markers of ferroptosis, an iron-catalysed form of regulated cell death that occurs through excessive peroxidation of polyunsaturated fatty acids and is also proposed to detrimentally contribute to some forms of ischaemia-reperfusion injury, stroke, and degenerative diseases. Renal tissue from the COVID-19 patient with myocarditis and multiple organ dysfunction syndrome showed morphological signs of acute tubular necrosis, intratubular oxalate crystals, as well as E06 positivity in proximal tubuli (A). By comparison, in the case of sudden death due to myocarditis of other aetiology, immunohistochemical staining with E06 (B) and anti-4-HNE antibody (D) in the renal tissue showed no presence of these ferroptosis markers (non-specific staining in the corticomedullary junction is also present on control stains). abstract: AIMS: Cardiovascular complications, including myocarditis, are observed in coronavirus disease 2019 (COVID‐19). Major cardiac involvement is a potentially lethal feature in severe cases. We sought to describe the underlying pathophysiological mechanism in COVID‐19 lethal cardiogenic shock. METHODS AND RESULTS: We report on a 48‐year‐old male COVID‐19 patient with cardiogenic shock; despite extracorporeal life support, dialysis, and massive pharmacological support, this rescue therapy was not successful. Severe acute respiratory syndrome coronavirus 2 RNA was detected at autopsy in the lungs and myocardium. Histopathological examination revealed diffuse alveolar damage, proliferation of type II pneumocytes, lymphocytes in the lung interstitium, and pulmonary microemboli. Moreover, patchy muscular, sometimes perivascular, interstitial mononuclear inflammatory infiltrates, dominated by lymphocytes, were seen in the cardiac tissue. The lymphocytes ‘interlocked’ the myocytes, resulting in myocyte degeneration and necrosis. Predominantly, T‐cell lymphocytes with a CD4:CD8 ratio of 1.7 infiltrated the interstitial myocardium, reflecting true myocarditis. The myocardial tissue was examined for markers of ferroptosis, an iron‐catalysed form of regulated cell death that occurs through excessive peroxidation of polyunsaturated fatty acids. Immunohistochemical staining with E06, a monoclonal antibody binding to oxidized phosphatidylcholine (reflecting lipid peroxidation during ferroptosis), was positive in morphologically degenerating and necrotic cardiomyocytes adjacent to the infiltrate of lymphocytes, near arteries, in the epicardium and myocardium. A similar ferroptosis signature was present in the myocardium of a COVID‐19 subject without myocarditis. In a case of sudden death due to viral myocarditis of unknown aetiology, however, immunohistochemical staining with E06 was negative. The renal proximal tubuli stained positively for E06 and also hydroxynonenal (4‐HNE), a reactive breakdown product of the lipid peroxides that execute ferroptosis. In the case of myocarditis of other aetiology, the renal tissue displayed no positivity for E06 or 4‐HNE. CONCLUSIONS: The findings in this case are unique as this is the first report on accumulated oxidized phospholipids (or their breakdown products) in myocardial and renal tissue in COVID‐19. This highlights ferroptosis, proposed to detrimentally contribute to some forms of ischaemia–reperfusion injury, as a detrimental factor in COVID‐19 cardiac damage and multiple organ failure. url: https://doi.org/10.1002/ehf2.12958 doi: 10.1002/ehf2.12958 id: cord-285362-7dc2gox0 author: Jacot, Damien title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses date: 2020-09-07 words: 1229.0 sentences: 86.0 pages: flesch: 59.0 cache: ./cache/cord-285362-7dc2gox0.txt txt: ./txt/cord-285362-7dc2gox0.txt summary: title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses We analyzed SARS-CoV-2 viral loads from 22''323 RT-PCR results according to samples types, gender, age, and health units. Quantitative reverse transcription polymerase chain reaction (RT-PCR) represents a 24 key diagnostic tool for patients with suspected SARS-CoV-2 infection. The report of RT-PCR SARS-CoV-2 viral loads raised also several 38 questions regarding the use of this information for the laboratory as an internal quality assessment 39 tool, as well as (i) to predict contagiousness of patients and hence to guide epidemiological 40 decisions, especially for hospitalized patients and (ii) to predict the patient prognosis and assess for the E-gene PCR was those described by Corman and colleague (4) . Clinical progression and 218 viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study SARS-CoV-2 Viral Load in Upper 224 Respiratory Specimens of Infected Patients abstract: RT-PCRs to detect SARS-CoV-2 RNA is key to manage the COVID-19 pandemic. We analyzed SARS-CoV-2 viral loads from 22’323 RT-PCR results according to samples types, gender, age, and health units. Viral load did not show any difference across age and appears to be a poor predictor of disease outcome. SARS-CoV-2 viral load showed similar high viral loads than the one observed for RSV and influenza B. The importance of viral load to predict contagiousness and to assess disease progression is discussed. url: https://doi.org/10.1016/j.micinf.2020.08.004 doi: 10.1016/j.micinf.2020.08.004 id: cord-035274-hu8zshq8 author: Jadali, Zohreh title: Neurologic manifestations of COVID-19: what can we learn from other coronaviruses date: 2020-11-11 words: 703.0 sentences: 57.0 pages: flesch: 43.0 cache: ./cache/cord-035274-hu8zshq8.txt txt: ./txt/cord-035274-hu8zshq8.txt summary: Like other coronaviruses, SARS-CoV-2 is neurotropic and may spread to the nervous system via similar mechanisms. Neurotropic and neuroinvasive properties of SARS-CoV-2 are supported by several observations including the presence of virus particles in the cerebrospinal fluid of patients with significant nervous system symptoms [3] . Currently, it is difficult to distinguish whether neurological complications of COVID-19 are a consequence of direct or indirect effects of viral infection. Another mechanism relies on blood circulation and angiotensin-converting enzyme 2 (ACE2) receptors that are expressed on glial cells, neurons, and capillary endothelium and are involved in virus entry [4] . Molecular mimicry that could be associated with the development of autoimmunity is another mechanism by which SARS-CoV-2 may trigger an immune response against nervous system-specific proteins [5] . Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ACE2: Angiotensin-converting enzyme 2 COVID-19 and SARS-Cov-2 infection: pathophysiology and clinical effects on the nervous system The author(s) read and approved the final manuscript. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656222/ doi: 10.1186/s41983-020-00240-w id: cord-350821-0qfoc553 author: Jahromi, Reza title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date: 2020-06-01 words: 1941.0 sentences: 113.0 pages: flesch: 46.0 cache: ./cache/cord-350821-0qfoc553.txt txt: ./txt/cord-350821-0qfoc553.txt summary: title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 In this study, we present the effect of surfactants on coronavirus (SARS-CoV-2) virucidal efficiency in sanitizing fluids. Sodium dodecylbenzenesulfonate (SDBS), sodium laureth sulfate (SLS), and two commercial dish soap and liquid hand soap were studied with the goal of evaporation rate reduction in sanitizing liquids to maximize surface contact time. Twelve fluids with different recipes composed of ethanol, isopropanol, SDBS, SLS, glycerin, and water of standardized hardness (WSH) were tested for their evaporation time and virucidal efficiency. Twelve sanitizing fluids with different recipes, as shown in Table 1 , were prepared to examine the effect of individual components and mixtures on evaporation rate and SARS-CoV-2 virucidal efficiency of the solutions. Furthermore, the addition of 3% dish soap to the ethanol solution (S1) increased the evaporation time by about 63% from 24 to 39 s (of fluid S9), as shown in Figure 2 . abstract: Our surrounding environment, especially often-touched contaminated surfaces, plays an important role in the transmission of pathogens in society. The shortage of effective sanitizing fluids, however, became a global challenge quickly after the coronavirus disease-19 (COVID-19) outbreak in December 2019. In this study, we present the effect of surfactants on coronavirus (SARS-CoV-2) virucidal efficiency in sanitizing fluids. Sodium dodecylbenzenesulfonate (SDBS), sodium laureth sulfate (SLS), and two commercial dish soap and liquid hand soap were studied with the goal of evaporation rate reduction in sanitizing liquids to maximize surface contact time. Twelve fluids with different recipes composed of ethanol, isopropanol, SDBS, SLS, glycerin, and water of standardized hardness (WSH) were tested for their evaporation time and virucidal efficiency. Evaporation time increased by 17-63% when surfactant agents were added to the liquid. In addition, surfactant incorporation enhanced the virucidal efficiency between 15-27% according to the 4-field test in the EN 16615:2015 European Standard method. Most importantly, however, we found that surfactant addition provides a synergistic effect with alcohols to inactivate the SARS-CoV-2 virus. This study provides a simple, yet effective solution to improve the virucidal efficiency of commonly used sanitizers. url: https://doi.org/10.1101/2020.05.29.124107 doi: 10.1101/2020.05.29.124107 id: cord-146679-g7qioapl author: Jaimes, Javier A. title: Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses date: 2020-02-14 words: 3652.0 sentences: 181.0 pages: flesch: 55.0 cache: ./cache/cord-146679-g7qioapl.txt txt: ./txt/cord-146679-g7qioapl.txt summary: title: Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses To obtain an initial assessment of shared and/or specific features of the 2019-nCoV spike (S) envelope glycoprotein, a protein sequence alignment was performed to compare the sequence of the Wuhan-Hu-1 strain of the novel coronavirus with that of the closely related human SARS-CoV S strain Tor2 sequence ( Supplementary Fig. 1 ). The relatively high degree of sequence identity for the RBD is consistent with the view that 2019-nCoV, like SARS-CoV, may use ACE2 as its host cell receptor, The composition of residues found at the two known coronavirus S cleavage sites was performed using alignment data ( Fig. 2B and C). abstract: The 2019 novel coronavirus (2019-nCoV) is currently causing a widespread outbreak centered on Hubei province, China and is a major public health concern. Taxonomically 2019-nCoV is closely related to SARS-CoV and SARS-related bat coronaviruses, and it appears to share a common receptor with SARS-CoV (ACE-2). Here, we perform structural modeling of the 2019-nCoV spike glycoprotein. Our data provide support for the similar receptor utilization between 2019-nCoV and SARS-CoV, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains, which we predict to be proteolytically-sensitive. We suggest this loop confers fusion activation and entry properties more in line with MERS-CoV and other coronaviruses, and that the presence of this structural loop in 2019-nCoV may affect virus stability and transmission. url: https://arxiv.org/pdf/2002.06196v1.pdf doi: nan id: cord-291991-on70zzn0 author: Jaimes, Javier A. title: Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site date: 2020-05-28 words: 1700.0 sentences: 93.0 pages: flesch: 58.0 cache: ./cache/cord-291991-on70zzn0.txt txt: ./txt/cord-291991-on70zzn0.txt summary: Here we provide context and clarify the role of the novel SARS-CoV-2 S1/S2 cleavage site in virus 90 emergence and infection, and perform a direct assessment of the proteases cleaving this site by use of 91 biochemical assays. To directly address the proteases cleaving the SARS-CoV-2 S1/S2 site, we used a biochemical peptide 95 cleavage assay (Jaimes et al., 2019), which was previously used to screen emerging influenza viruses 96 (Straus and Whittaker, 2017) . The comparative data with SARS-CoV S1/S2 site reveals that the acquisition of the 4 109 amino acid insert distinctively broadens the activating protease repertoire of the SARS-CoV-2 S1/S2 110 cleavage site to all major classes of proteolytic enzymes known to potentially activate coronavirus S 111 proteins. Activation of the SARS coronavirus spike 195 protein via sequential proteolytic cleavage at two distinct sites A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at 258 the S1/S2 cleavage site of the spike protein abstract: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread to the entire world within a few months. The origin of SARS-CoV-2 has been related to the lineage B Betacoronavirus SARS-CoV and SARS-related coronaviruses found in bats. Early characterizations of the SARS-CoV-2 genome revealed the existence of a distinct 4 amino acid insert within the spike (S) protein (underlined, SPRRAR↓S), at the S1/S2 site located at the interface between the S1 receptor binding subunit and the S2 fusion subunit. Notably, this insert appears to be a distinguishing feature among SARS-related sequences and introduces a potential cleavage site for the protease furin. Here, we investigate the potential role of this novel S1/S2 cleavage site and present direct biochemical evidence for proteolytic processing by a variety of proteases. We discuss these findings in the context of the origin of SARS-CoV-2, viral stability and transmission. url: https://api.elsevier.com/content/article/pii/S2589004220303977 doi: 10.1016/j.isci.2020.101212 id: cord-339570-vf79fefg author: Jain, Vidhi title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists date: 2020-06-22 words: 352.0 sentences: 27.0 pages: flesch: 50.0 cache: ./cache/cord-339570-vf79fefg.txt txt: ./txt/cord-339570-vf79fefg.txt summary: title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists While the former highlighted the importance of human secretions like tears as a potential source of transmission of the virus, the latter explored the possibility of SARS-CoV-2 in amniotic membrane grafts. The amniotic membrane, while having great potential for healing ophthalmologic wounds, was recently shown to be RT-PCR positive for viral RNA in two critically ill pregnant females with COVID-19 [3] . While there is no confirmed data on the survival of SARS CoV-2 in cryopreserved amniotic membranes, it is clear that temperature strongly influences viral persistence (>2 weeks survival at 4°C vs only 2 days at 20°C) [5] . In light of these findings, we strongly suggest ophthalmologists to observe extreme caution while handling body fluids and placental membranes during the current COVID-19 pandemic. Amniotic membrane harvesting during COVID-19 pandemic Detection of SARS-COV-2 in placental and fetal membrane samples abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32572187/ doi: 10.1038/s41433-020-1051-5 id: cord-303069-ss6g3jkg author: Jakhar, Renu title: An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date: 2020-05-26 words: 3379.0 sentences: 202.0 pages: flesch: 52.0 cache: ./cache/cord-303069-ss6g3jkg.txt txt: ./txt/cord-303069-ss6g3jkg.txt summary: A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. The aim of this study is to analyze envelope protein strains using in silico approaches looking for the conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine [22, 23, 24] . Envelope protein from the SARS-CoV-2 was analyzed using the IEDB MHC-1 binding prediction tool to predict the T cell epitope suggested interacting with different types of MHC Class I alleles. Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus abstract: COVID-19 is a new viral emergent human disease caused by a novel strain of Coronavirus. This virus has caused a huge problem in the world as millions of the people are affected with this disease in the entire world. We aimed to design a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system and can be used later to create a new peptide vaccine that could replace conventional vaccines. A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. Then we docked the best predicted CTL epitopes with HLA alleles. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. Potentially continuous B cell epitopes were predicted using tools from IEDB. The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. We found these CTL epitopes to be T helper epitopes also. The B cell epitope, SRVKNL and T cell epitope, FLAFVVFLL were suggested to become a universal candidate for peptide-based vaccine against COVID-19. We hope to confirm our findings by adding complementary steps of both in vitro and in vivo studies to support this new universal predicted candidate. url: https://doi.org/10.1101/2020.05.26.115790 doi: 10.1101/2020.05.26.115790 id: cord-269101-7altkx5u author: Jakhmola Mani, Ruchi title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study date: 2020-10-28 words: 4934.0 sentences: 270.0 pages: flesch: 50.0 cache: ./cache/cord-269101-7altkx5u.txt txt: ./txt/cord-269101-7altkx5u.txt summary: title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study An amazing herb, Nigella sativa, having antiviral, antihypertensive, antidiarrhoeal, analgesics, and anti-bacterial properties, needs to be explored for its efficacy against SARS-CoV-2, the causative agent of COVID-19. sativa bioactive constituents were similar to the pathways followed in SARS-COV-2 pathology, like renin-angiotensin system, kidney functions, regulation of blood circulation, blood vessel diameter, etc. To study the effectiveness of N.sativa against SARS-CoV-2, protein interactions studies were carried out for receptors predicted via swiss target prediction for this plant''s bioactive constituents, to understand their beneficial effect on SARS-CoV-2 in humans. sativa bioactive constituents by protein interaction and docking studies as well as proven their binding efficiency with ACE2 receptor and now this can be studied further in wet lab and be formulated as the medicine to combat the deadly disease COVID-19. abstract: COVID-19, emerged at the end of 2019 have dramatically threatened the health, economy, and social mobility of people around the world and till date no medication is available for its treatment. An amazing herb, Nigella sativa, having antiviral, antihypertensive, anti- diarrhoeal, analgesics, and anti-bacterial properties, needs to be explored for its efficacy against SARS-CoV-2, the causative agent of COVID-19. In-silico studies were carried out to understand the role of its bioactive constituents in COVID-19 treatment and prevention. Firstly, the disease network was prepared by using ACE2 (Angiotensin-II receptor), as it is the entry site for virus. It was used to decipher the mechanism of SARS-COV-2 infection in humans. Second, the target receptors for N. sativa were predicted and protein interaction studies were conducted. Further, docking studies were also performed to analyse it for treatment purpose as well. This study concludes that pathways undertaken by N. sativa bioactive constituents were similar to the pathways followed in SARS-COV-2 pathology, like renin-angiotensin system, kidney functions, regulation of blood circulation, blood vessel diameter, etc. Also, in docking studies, the constituents of N. sativa, α-hederin, Thymohydroquinone and Thymoquinone were observed to be efficiently binding to ACE2. Also, the bioactive phytoconstituents are involved in molecular pathways like HIF1, VEGF, IL-17, AGE-RAGE, chemokine and calcium signaling pathways which can be majorly helpful in combating hypoxia and inflammation caused due to compromised immune system and oxidative stress. Therefore, N. sativa standardized extract having the above phytoconstituents could be useful in COVID-19 and hence opens a new treatment line. url: https://doi.org/10.1080/07391102.2020.1839560 doi: 10.1080/07391102.2020.1839560 id: cord-278721-g5zqebju author: Jakhmola, Shweta title: Comorbidity Assessment Is Essential During COVID-19 Treatment date: 2020-08-04 words: 3748.0 sentences: 233.0 pages: flesch: 45.0 cache: ./cache/cord-278721-g5zqebju.txt txt: ./txt/cord-278721-g5zqebju.txt summary: Our study revealed that deaths associated with cardiovascular diseases and diabetes are highly significant (p < 0.0001) compared to hospitalized in countries like Italy, France, and Spain unlike the Netherlands. Deaths from kidney diseases (Italyp < 0.0001; Swedenp < 0.0001; Netherlandsp = 0.0001; Francep = 0.0033) and neurological ailments (Francep = 0.0001; Netherlandsp < 0.0001) are significantly higher than the total hospitalized patients affected by the particular comorbidity. The information about numbers of hospitalized or deceased COVID-19 patients with associated comorbidities from individual countries was already provided in their respective reports. The death proportions due to Heart Diseases including, cardiovascular diseases and hypertension, were significantly higher (p < 0.0001) compared to the total hospitalized patients in Italy, Sweden, and Spain. Notably we found that heart diseases, including hypertension along with cardiovascular diseases, are the most frequent association with SARS-CoV2 infection in most countries (Italy, France, Spain, and Sweden) except the Netherlands. abstract: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV2 is associated with various comorbidities; cardiovascular diseases, hypertension, diabetes, liver, lung diseases, and neurological ailments. The majority of the dysfunctions mentioned above are often associated with endothelial deterioration, indicating that endothelium can be the target of SARS-CoV2. Our study is an exclusive observational study that quantitatively analyses COVID-19 related comorbidities. We retrieved the data of % population of COVID-19 hospitalized and deceased patients with associated comorbidities from publicly accessible portals of the five European countries. A two tailed t-test enabled us to determine the significant proportions of deaths compared to hospitalized patients with associated comorbidity. Our study revealed that deaths associated with cardiovascular diseases and diabetes are highly significant (p < 0.0001) compared to hospitalized in countries like Italy, France, and Spain unlike the Netherlands. Deaths from kidney diseases (Italy- p < 0.0001; Sweden- p < 0.0001; Netherlands- p = 0.0001; France- p = 0.0033) and neurological ailments (France- p = 0.0001; Netherlands- p < 0.0001) are significantly higher than the total hospitalized patients affected by the particular comorbidity. We have noted that deaths due to liver diseases are least associated with COVID-19 among all comorbidities. Intriguingly, immunodeficiency shows mixed outcomes in death proportions compared to the hospital admitted individuals. Besides, the treatment regime involves drugs like losartan, ACE inhibitors, angiotensin-receptor blockers, Remdesivir, Chloroquine, Hydroxychloroquine, etc. may modulate the severity of the comorbidities. These comorbidities can create chaos in the existing healthcare system and may worsen the disease outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/32903640/ doi: 10.3389/fphys.2020.00984 id: cord-295041-5vpawtef author: Jakhmola, Shweta title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 words: 5012.0 sentences: 310.0 pages: flesch: 39.0 cache: ./cache/cord-295041-5vpawtef.txt txt: ./txt/cord-295041-5vpawtef.txt summary: Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. abstract: Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Additionally, transmembrane serine protease 2 (TMPRSS2) and furin facilitate virus entry into the host. Besides, the probable routes of virus entry into the nervous system include the hematogenic pathway, through the vagus, the olfactory nerve, or the enteric nervous system. However, the trajectory of SARS-CoV-2 to the brain needs investigation. Furthermore, a Th17-mediated cytokine storm is seen in COVID-19 cases with higher levels of IL-1β/2/7/8/9/10/17, GM-CSF, IFN-γ, TNF-α, CXCL-10, MCP1, and MIP1α/β. Some cytokines can cross the blood-brain barrier and activate the brain’s immune cells to produce neural cytokines, leading to neuronal dysfunctions. Nonetheless, most of the neurological conditions developed due to viral infections may not have effective and registered treatments. Although, some antivirals may inhibit the virus-mediated pathogenesis and prove to be suitable in COVID-19 treatment. Therefore, clinicians’ and researchers’ collective expertise may unravel the potential of SARS-CoV-2 infection to prevent short-term and long-term CNS damage. url: https://doi.org/10.1007/s42399-020-00522-7 doi: 10.1007/s42399-020-00522-7 id: cord-276797-86hc3lbi author: Jamieson, Denise J. title: Emerging infectious disease outbreaks: Old lessons and new challenges for obstetrician-gynecologists date: 2006-06-30 words: 7263.0 sentences: 417.0 pages: flesch: 50.0 cache: ./cache/cord-276797-86hc3lbi.txt txt: ./txt/cord-276797-86hc3lbi.txt summary: Objective The purpose of this study was to summarize 3 recent high-profile infectious disease threats that have affected the United States: severe acute respiratory syndrome, West Nile virus, and anthrax. Results The 3 emerging infectious diseases pose very different threats: Severe acute respiratory syndrome is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. This systematic review summarizes 3 recent, highprofile infectious disease threats that have affected the United States: (1) SARS, (2) West Nile virus, and (3) anthrax. The 3 emerging infectious disease threats that are described in this systematic review pose very different and novel health threats: SARS is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. abstract: Objective The purpose of this study was to summarize 3 recent high-profile infectious disease threats that have affected the United States: severe acute respiratory syndrome, West Nile virus, and anthrax. Study design A systematic review was conducted with the use of Medline searches, searches of the Centers for Disease Control and Prevention website, and review by experts at the Centers for Disease Control and Prevention. Results The 3 emerging infectious diseases pose very different threats: Severe acute respiratory syndrome is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. Conclusion All 3 outbreaks highlight the importance of obstetrician-gynecologists keeping current with new information as it emerges. In this global environment, it is likely that novel disease threats will continue to emerge in the United States. url: https://www.ncbi.nlm.nih.gov/pubmed/16731070/ doi: 10.1016/j.ajog.2005.06.062 id: cord-339726-eg0hajzl author: Jamrozik, Euzebiusz title: Coronavirus Human Infection Challenge Studies: Assessing Potential Benefits and Risks date: 2020-08-25 words: 3643.0 sentences: 154.0 pages: flesch: 40.0 cache: ./cache/cord-339726-eg0hajzl.txt txt: ./txt/cord-339726-eg0hajzl.txt summary: Novel research designs, particularly where such studies might be controversial as in the case of SARS-CoV-2 HCS, require especially careful ethical evaluation including rigorous risk-benefit assessments as well as timely, thorough, public engagement ( WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020; Bambery et al. To be ethically acceptable, SARS-CoV-2 HCS would need to have multiple risk minimization strategies in place, including (i) selection of low risk participants (e.g., healthy young adults 1 ), (ii) careful strain selection and development, (iii) careful titration of viral dose, (iv) early diagnosis and availability of all necessary medical care, (v) long-term follow-up of participants, (vi) compensation for any lasting harms, and (vii) stringent infection control including measures to protect and screen research staff for infection (WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020). Tensions between public health and vaccine research priorities: A comparative modelling assessment of the risks and benefits of SARS-CoV-2 vaccine field trials versus human challenge studies abstract: Human infection challenge studies (HCS) have been proposed as a means to accelerate SARS-CoV2 vaccine development and thereby help to mitigate a prolonged global public health crisis. A key criterion for the ethical acceptability of SARS-CoV2 HCS is that potential benefits outweigh risks. Although the assessment of risks and benefits is meant to be a standard part of research ethics review, systematic comparisons are particularly important in the context of SARS-CoV2 HCS in light of the significant potential benefits and harms at stake as well as the need to preserve public trust in research and vaccines. In this paper we explore several considerations that should inform systematic assessment of SARS-CoV-2 HCS. First, we detail key potential benefits of SARS-CoV-2 HCS including, but not limited to, those related to the acceleration of vaccine development. Second, we identify where modelling is needed to inform risk-benefit (and thus ethical) assessments. Modelling will be particularly useful in (i) comparing potential benefits and risks of HCS with those of vaccine field trials under different epidemiological conditions and (ii) estimating marginal risks to HCS participants in light of the background probabilities of infection in their local community. We highlight interactions between public health policy and research priorities, including situations in which research ethics assessments may need to strike a balance between competing considerations. url: https://doi.org/10.1007/s11673-020-10030-x doi: 10.1007/s11673-020-10030-x id: cord-284978-vh1x6pg9 author: Jang, Hongje title: Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date: 2013-02-18 words: 2968.0 sentences: 160.0 pages: flesch: 53.0 cache: ./cache/cord-284978-vh1x6pg9.txt txt: ./txt/cord-284978-vh1x6pg9.txt summary: Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . abstract: Ein einfaches Testsystem auf der Basis von Graphenoxid (GO) ermöglicht das Screening selektiver Inhibitoren einer Helicase des Hepatitis‐C‐Virus (HCV) zusammen mit Inhibitoren eines SARS‐Coronavirus (SARS‐CoV) (siehe Schema). In einem einzelnen Screen wurden fünf hochselektive Inhibitoren der HCV‐Helicase gefunden, die ortholog zur SARS‐CoV‐Helicase sind. Einige dieser Treffer wurden mit dem gleichen GO‐Assay validiert.[Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32313317/ doi: 10.1002/ange.201209222 id: cord-307556-k2lavvca author: Jang, Hongje title: Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date: 2013-02-18 words: 2983.0 sentences: 154.0 pages: flesch: 53.0 cache: ./cache/cord-307556-k2lavvca.txt txt: ./txt/cord-307556-k2lavvca.txt summary: Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . abstract: A GO‐to solution: A simple graphene oxide (GO)‐based assay to screen for selective inhibitors of a hepatitis C virus (HCV) helicase along with inhibitors of a severe acute respiratory syndrome coronavirus (SARS CoV) helicase was tested (see scheme). A single screen found five inhibitors highly selective for the HCV helicase orthologous to the SARS CoV helicase. Some of these hits were validated using the same GO‐based assay.[Image: see text] url: https://doi.org/10.1002/anie.201209222 doi: 10.1002/anie.201209222 id: cord-286014-cc99e24x author: Jang, T.-N title: Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases date: 2003-11-05 words: 3025.0 sentences: 201.0 pages: flesch: 56.0 cache: ./cache/cord-286014-cc99e24x.txt txt: ./txt/cord-286014-cc99e24x.txt summary: To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). The first probable SARS patient in Taiwan returned from China via Hong Kong early in the global outbreak in February 2003. 7 We analyse the clinical, laboratory, and radiological features of patients with probable SARS who were seen at the Shin Kong Wu Ho-Su Memorial Hospital (SKMH) in Taipei, Taiwan. 16 In our study, SARS-associated coronavirus RNA was detected in oropharyngeal swabs by RT-PCR in 16 (55.1%) of 29 patients at initial presentation. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome in Singapore: clinical features of index patient and initial contacts Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China abstract: Objectives. To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). Methods. Between March 28 and June 30 '2003, 29 patients with probable SARS seen at Shin Kong Wu Ho-Su Memorial Hospital, Taipei, were analysed. Results. Presenting symptoms included fever (100%), cough (69.0%), chills or rigor (62.1%), and shortness of breath (41.4%). Mean days to defervescence were 6.8±2.9 days, but fever recurred in 15 patients (51.7%) at 10.9±3.4 days. Common laboratory features included lymphopenia (72.4%), thrombocytopenia (34.5%) and elevated C-reactive protein (CRP), lactate dehydrogenase (LDH), and aspartate aminotransferase (AST) (93.1, 62.1, 44.8%, respectively). All patients except one had initial abnormal chest radiographs and 20 (69.0%) had radiological worsening at 7.5±2.6 days. Nine patients (31.0%) subsequently required mechanical ventilation with four deaths (13.8%). Most patients with clinical deterioration responded to pulse corticosteroid therapy (14 out of 17) but six complicated with nosocomial infections. The risk factors associated with severe disease were presence of diarrhoea, high peak LDH and CRP, high AST and creatine kinase on admission and high peak values. Conclusions. Prudent corticosteroid use, vigilant microbiological surveillance and appropriate antibiotics coverage are the key to successful treatment. url: https://api.elsevier.com/content/article/pii/S0163445303001804 doi: 10.1016/j.jinf.2003.09.004 id: cord-300138-1s87msv2 author: Jang, Youngeun title: Olfactory and taste disorder: The first and only sign in a patient with SARS-CoV-2 pneumonia date: 2020-04-20 words: 706.0 sentences: 47.0 pages: flesch: 55.0 cache: ./cache/cord-300138-1s87msv2.txt txt: ./txt/cord-300138-1s87msv2.txt summary: 3 Recently, Giacomelli et al 4 reported that 20 of 59 (33.9%) of SARS-CoV-2-positive hospitalized patients had an olfactory or taste disorder. 4 SARS-CoV-2 can be transmitted in the asymptomatic or paucisymptomatic stages; therefore, olfactory and taste disorders can be significant signs for its early detection to control transmission. He had been self-quarantined for 14 days since March 12 due to close contact with a confirmed SARS-CoV-2-positive patient, who was his cohabitant. Although he had no clinical symptoms or signs of COVID-19 such as fever, myalgia, cough, and sore throat, on March 26 (the final day of his quarantine) he was confirmed positive based on a polymerase chain reaction (PCR) test (Rdrp gene, cycle threshold value of 30.28 on sputum and 33.47 on nasopharyngeal and oropharyngeal swab). This case of a SARS-CoV-2-positive patient with radiologically proven pneumonia on chest CT, who presented with only olfactory and taste disorders and no other clinical manifestations, suggests that previous cases with asymptomatic infections could have been misclassified. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32307026/ doi: 10.1017/ice.2020.151 id: cord-017354-cndb031c author: Janies, D. title: Large-Scale Phylogenetic Analysis of Emerging Infectious Diseases date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Microorganisms that cause infectious diseases present critical issues of national security, public health, and economic welfare. For example, in recent years, highly pathogenic strains of avian influenza have emerged in Asia, spread through Eastern Europe, and threaten to become pandemic. As demonstrated by the coordinated response to Severe Acute Respiratory Syndrome (SARS) and influenza, agents of infectious disease are being addressed via large-scale genomic sequencing. The goal of genomic sequencing projects are to rapidly put large amounts of data in the public domain to accelerate research on disease surveillance, treatment, and prevention. However, our ability to derive information from large comparative genomic datasets lags far behind acquisition. Here we review the computational challenges of comparative genomic analyses, specifically sequence alignment and reconstruction of phylogenetic trees. We present novel analytical results on two important infectious diseases, Severe Acute Respiratory Syndrome (SARS) and influenza. SARS and influenza have similarities and important differences both as biological and comparative genomic analysis problems. Influenza viruses (Orthymxyoviridae) are RNA based. Current evidence indicates that influenza viruses originate in aquatic birds from wild populations. Influenza has been studied for decades via well-coordinated international efforts. These efforts center on surveillance via antibody characterization of the hemagglutinin (HA) and neuraminidase (N) proteins of the circulating strains to inform vaccine design. However, we still do not have a clear understanding of (1) various transmission pathways such as the role of intermediate hosts like swine and domestic birds and (2) the key mutation and genomic recombination events that underlie periodic pandemics of influenza. In the past 30 years, sequence data from HA and N loci has become an important data type. In the past year, full genomic data has become prominent. These data present exciting opportunities to address unanswered questions in influenza pandemics. SARS is caused by a previously unrecognized lineage of coronavirus, SARS-CoV, which like influenza has an RNA based genome. Although SARS-CoV is widely believed to have originated in animals, there remains disagreement over the candidate animal source that lead to the original outbreak of SARS. In contrast to the long history of the study of influenza, SARS was only recognized in late 2002 and the virus that causes SARS has been documented primarily by genomic sequencing. In the past, most studies of influenza were performed on a limited number of isolates and genes suited to a particular problem. Major goals in science today are to understand emerging diseases in broad geographic, environmental, societal, biological, and genomic contexts. Synthesizing diverse information brought together by various researchers is important to find out what can be done to prevent future outbreaks [JON03]. Thus comprehensive means to organize and analyze large amounts of diverse information are critical. For example, the relationships of isolates and patterns of genomic change observed in large datasets might not be consistent with hypotheses formed on partial data. Moreover when researchers rely on partial datasets, they restrict the range of possible discoveries. Phylogenetics is well suited to the complex task of understanding emerging infectious disease. Phylogenetic analyses can test many hypotheses by comparing diverse isolates collected from various hosts, environments, and points in time and organizing these data into various evolutionary scenarios. The products of a phylogenetic analysis are a graphical tree of ancestor–descendent relationships and an inferred summary of mutations, recombination events, host shifts, geographic, and temporal spread of the viruses. However, this synthesis comes at a price. The cost of computation of phylogenetic analysis expands combinatorially as the number of isolates considered increases. Thus, large datasets like those currently produced are commonly considered intractable. We address this problem with synergistic development of heuristics tree search strategies and parallel computing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121896/ doi: 10.1007/978-3-540-74331-6_2 id: cord-305931-0pgu2gvh author: Janus, Scott E title: COVID19: a case report of thrombus in transit date: 2020-06-17 words: 1431.0 sentences: 85.0 pages: flesch: 43.0 cache: ./cache/cord-305931-0pgu2gvh.txt txt: ./txt/cord-305931-0pgu2gvh.txt summary: In view of the fact that the utility of tissue plasminogen activator in this population is not well studied, we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. 4 Although the utility of tissue plasminogen activator (TPA) for thrombus in transit in other clinical settings has previously been reported, 5 the literature regarding cardiovascular events in SARS-CoV-2 remains scarce; we therefore describe the case of a 64-year-old male who presented with Learning points SARS-CoV-2 pneumonia, who was found to have extensive clot in transit on echocardiography and underwent successful lytic therapy. In view of the fact that the utility of TPA in this population is not well studied, 10 we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. abstract: BACKGROUND: The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused significant morbidity and mortality, not only through devastating lung injury, but also due to multiple malfunctions in the cardiovascular system. The primary aetiology is believed to be mediated through lung alveolar injury; however, a few published reports have linked SARS-CoV-2 to significant organ dysfunction, venous thrombo-embolism, and coagulopathy. In view of the fact that the utility of tissue plasminogen activator in this population is not well studied, we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. CASE SUMMARY: We discuss a patient admitted with SARS-CoV-2 pneumonia. Due to the development of dramatic hypoxia, he underwent echocardiography which demonstrated extensive thrombus in transit. He received successful thrombolytic therapy with tissue plasminogen activator, with subsequent improvement in oxygenation. The patient was successfully discharged home on 2 L of oxygen via nasal cannula, and continues to improve at follow-up with his cardiologist and primary care physician. CONCLUSION: This case not only highlights embolic causes of hypoxia in SARS-CoV-2, but demonstrates the important utility of an echocardiogram and tissue plasminogen activator in this population. url: https://www.ncbi.nlm.nih.gov/pubmed/33089047/ doi: 10.1093/ehjcr/ytaa189 id: cord-349477-3qhpu7v0 author: Jarynowski, A. title: An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland date: 2020-10-15 words: 7012.0 sentences: 438.0 pages: flesch: 51.0 cache: ./cache/cord-349477-3qhpu7v0.txt txt: ./txt/cord-349477-3qhpu7v0.txt summary: Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. Demographic (like age, mobility, migration etc.), social ("income","PiS_support") and COVID-related factors (population size,forest_density,population_density,arrival_SARS) are the ground for our proposal of proper sanitary staff allocation. The aim of this paper is an exploratory and preliminary quantitative evaluation of the geographical spread on the level of county/poviat (NUTS-4) of SARS-CoV-2 virus (and COVID-19 disease caused by it) in Poland during the Spring wave of infections. The main statistical approach is calculating multiple regressions with Akaike selection criteria on the SARS-CoV-2 arrival time to each poviat and the number of COVID-19 cases based on socio-economic variables. abstract: Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. We showed that immigration and the logarithm of general mobility is the best predictor of SARS-CoV-2 arrival times, while emigration, industrialization and air quality explain the most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats. url: https://doi.org/10.1101/2020.10.14.20090985 doi: 10.1101/2020.10.14.20090985 id: cord-338979-ew046wcr author: Jasti, Madhu title: A review of pathophysiology and neuropsychiatric manifestations of COVID-19 date: 2020-06-03 words: 2972.0 sentences: 167.0 pages: flesch: 44.0 cache: ./cache/cord-338979-ew046wcr.txt txt: ./txt/cord-338979-ew046wcr.txt summary: This novel coronavirus reportedly had symptoms resembling that of Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV) seen in the year 2003 [3] . A recently published study that looked at 214 cases of severe coronavirus illness treated in Wuhan during the early phase of the global pandemic reported that about 36% of patients displayed neurological symptoms [11] . There have been a fair number of reports suggesting SARS-CoV-2 infecting the neurons, raising questions about the direct effects of the virus on the brain that play a role in patients'' deaths. By contrast, there have been a few case reports which mention no penetrance of virus into the central nervous system as evidenced by the absence of SARS-CoV-2 in CSF and that the CNS effects are secondary to elevated inflammatory markers as CSF analyses during the acute stage showed pleocytosis with increased IL-8 and TNF-α concentrations [17] . abstract: INTRODUCTION: The outbreak of coronavirus disease 2019 (COVID-19) has become one of the most serious pandemics of the recent times. Since this pandemic began, there have been numerous reports about the COVID-19 involvement of the nervous system. There have been reports of both direct and indirect involvement of the central and peripheral nervous system by the virus. OBJECTIVE: To review the neuropsychiatric manifestations along with corresponding pathophysiologic mechanisms of nervous system involvement by the COVID-19. BACKGROUND: Since the beginning of the disease in humans in the later part of 2019, the coronavirus disease 2019 (COVID-19) pandemic has rapidly spread across the world with over 2,719,000 reported cases in over 200 countries [World Health Organization. Coronavirus disease 2019 (COVID-19) situation report-96.,]. While patients typically present with fever, shortness of breath, sore throat, and cough, neurologic manifestations have been reported, as well. These include the ones with both direct and indirect involvement of the nervous system. The reported manifestations include anosmia, ageusia, central respiratory failure, stroke, acute inflammatory demyelinating polyneuropathy (AIDP), acute necrotizing hemorrhagic encephalopathy, toxic–metabolic encephalopathy, headache, myalgia, myelitis, ataxia, and various neuropsychiatric manifestations. These data were derived from the published clinical data in various journals and case reports. CONCLUSION: The neurological manifestations of the COVID-19 are varied and the data about this continue to evolve as the pandemic continues to progress. url: https://www.ncbi.nlm.nih.gov/pubmed/32494854/ doi: 10.1007/s00415-020-09950-w id: cord-351694-nb7230s1 author: Jatt, Lauren P. title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings date: 2020-06-16 words: 1522.0 sentences: 79.0 pages: flesch: 44.0 cache: ./cache/cord-351694-nb7230s1.txt txt: ./txt/cord-351694-nb7230s1.txt summary: title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings We describe a widespread laboratory surveillance program for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) at an integrated medical campus that includes a tertiary-care center, a skilled nursing facility, a rehabilitation treatment center, and temporary shelter units. As part of its coronavirus disease 2019 (COVID-19) response, VAGLAHS implemented a widespread laboratory surveillance program for SARS-CoV-2 in both hospital and residential facilities. Finally, on March 31, the laboratory at VALBHS initiated SARS-CoV-2 testing using the cobas system and began accepting specimens from other VA facilities, substantially increasing testing capacity and further decreasing turnaround time to a median of 1 day (IQR, 1-1). On April 3 and April 6, 57 residents who originally tested negative but lived in the same SNF unit as the SARS-CoV-2 positive individuals were retested, and 2 additional asymptomatic cases were identified. abstract: We describe a widespread laboratory surveillance program for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) at an integrated medical campus that includes a tertiary-care center, a skilled nursing facility, a rehabilitation treatment center, and temporary shelter units. We identified 22 asymptomatic cases of SARS-CoV-2 and implemented infection control measures to prevent SARS-CoV-2 transmission in congregate settings. url: https://www.ncbi.nlm.nih.gov/pubmed/32539876/ doi: 10.1017/ice.2020.301 id: cord-283352-0l1ggmhx author: Javelot, H title: Panic and pandemic: narrative review of the literature on the links and risks of panic disorder as a consequence of the SARS-CoV-2 pandemic date: 2020-08-10 words: 4437.0 sentences: 191.0 pages: flesch: 36.0 cache: ./cache/cord-283352-0l1ggmhx.txt txt: ./txt/cord-283352-0l1ggmhx.txt summary: Abstract Although the ''panic'' word has been abundantly linked to the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic in the press, in the scientific literature very few studies have considered whether the current epidemic could predispose to the onset or the aggravation of panic attacks or panic disorder. The current SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic is likely to induce, beyond its potentially dramatic impact on health, serious psychological consequences, particularly in terms of the often reported "panic" state it triggered, and the medical disorder potentially linked to this state, i.e., panic disorder [1] [2] [3] [4] [5] . In this review, we propose to address : (i) the way in which the international literature has used to date the terminology of "panic" in relation to the SARS-CoV-2 pandemic, (ii) the very concept of panic attack, panic disorder and the specificity of the respiratory component frequently associated with it, (iii) and finally, a synthesis of the links and risk factors between COVID-19 and "respiratory" panic disorder. abstract: Abstract Although the ‘panic’ word has been abundantly linked to the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic in the press, in the scientific literature very few studies have considered whether the current epidemic could predispose to the onset or the aggravation of panic attacks or panic disorder. Indeed, most studies thus far have focused on the risk of increase and aggravation of other psychiatric disorders as a consequence of the SARS-CoV-2 epidemic, such as obsessive-compulsive disorder (OCD), post-traumatic stress disorder (PTSD), and generalized anxiety disorder (GAD). Yet, risk of onset or aggravation of panic disorder, especially the subtype with prominent respiratory symptoms, which is characterized by a fear response conditioning to interoceptive sensations (e.g., respiratory), and hypervigilance to these interoceptive signals, could be expected in the current situation. Indeed, respiratory symptoms, such as coughs and dyspnea, are among the most commonly associated with the SARS-CoV-2 (59-82% and 31-55%, respectively), and respiratory symptoms are associated with a poor illness prognosis. Hence given that some etiological and maintenance factors associated with panic disorder – i.e., fear conditioning to abnormal breathing patterns attributable or not to the COVID-19 (coronavirus disease 2019), as well as hypervigilance towards breathing abnormalities – are supposedly more prevalent, one could expect an increased risk of panic disorder onset or aggravation following the COVID-19 pandemic in people who were affected by the virus, but also those who were not. In people with the comorbidity (i.e., panic disorder or panic attacks and the COVID-19), it is particularly important to be aware of the risk of hypokalemia in specific at-risk situations or prescriptions. For instance, in the case of salbutamol prescription, which might be overly used in patients with anxiety disorders and COVID-19, or in patients presenting with diarrhea and vomiting. Hypokalemia is associated with an increased risk of torsade de pointe, thus caution is required when prescribing specific psychotropic drugs, such as the antidepressants citalopram and escitalopram, which are first-line treatments for panic disorder, but also hydroxyzine, aiming at anxiety relief. The results reviewed here highlight the importance of considering and further investigating the impact of the current pandemic on the diagnosis and treatment of panic disorder (alone or comorbid with the COVID-19). url: https://api.elsevier.com/content/article/pii/S0013700620301895 doi: 10.1016/j.encep.2020.08.001 id: cord-301943-qdtfjdxr author: Javelot, H title: Panique et pandémie: revue de la littérature sur les liens entre le trouble panique et l''épidémie à SARS-CoV-2 date: 2020-05-21 words: 4740.0 sentences: 393.0 pages: flesch: 53.0 cache: ./cache/cord-301943-qdtfjdxr.txt txt: ./txt/cord-301943-qdtfjdxr.txt summary: Résumé L''état de panique associé à la pandémie liée au SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) incite à s''interroger sur les troubles anxieux que cette situation pourrait générer ou aggraver. D''éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d''hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l''infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. D''éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d''hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l''infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. abstract: Résumé L’état de panique associé à la pandémie liée au SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) incite à s’interroger sur les troubles anxieux que cette situation pourrait générer ou aggraver. Si la littérature a déjà fourni des projections généralistes en la matière, les données concrètes concernent à ce stage davantage le trouble de stress post-traumatique et le trouble obsessionnel compulsif, tandis que quelques évaluations s’intéressent au cadre nosographie du trouble anxieux généralisé. Le trouble panique ne se voit que peu ou pas cité et l’évocation de la « panique », au sens social, la supplante largement. Bien que d’une légitimité clinique encore débattue, le trouble panique qualifié de « respiratoire » pourrait se voir augmenter en nombre et/ou être intensifié chez les patients qui en présentent déjà. D’éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d’hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l’infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. L’hypokaliémie est associée à un risque accru de torsade de pointe, il convient donc également d’être prudent en matière de prescription de psychotropes à risque : comme avec le citalopram et l’escitalopram, des antidépresseurs indiqués dans le trouble panique, ou encore l’hydroxyzine, à visée anxiolytique. Ces données sont de nature à resituer l’importance de la prise en considération du trouble panique dans le cadre de la pandémie en cours. Abstract Although the ‘panic’ word has been abundantly linked to the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic in the press, in the scientific literature very few studies have considered whether the current epidemic could predispose to the onset or the aggravation of panic attacks or panic disorder. Indeed, most studies thus far have focused on the risk of increase and aggravation of other psychiatric disorders as a consequence of the SARS-CoV-2 epidemic, such as obsessive-compulsive disorder (OCD), post-traumatic stress disorder (PTSD), and generalized anxiety disorder (GAD). Yet, risk of onset or aggravation of panic disorder, especially the subtype with prominent respiratory symptoms, which is characterized by a fear response conditioning to interoceptive sensations (e.g., respiratory), and hypervigilance to these interoceptive signals, could be expected in the current situation. Indeed, respiratory symptoms, such as coughs and dyspnea, are among the most commonly associated with the SARS-CoV-2 (59-82 % and 31-55 %, respectively), and respiratory symptoms are associated with a poor illness prognosis. Hence given that some etiological and maintenance factors associated with panic disorder – i.e., fear conditioning to abnormal breathing patterns attributable or not to the COVID-19 (coronavirus disease 2019), as well as hypervigilance towards breathing abnormalities – are supposedly more prevalent, one could expect an increased risk of panic disorder onset or aggravation following the COVID-19 epidemic in people who were affected by the virus, but also those who were not. In people with the comorbidity (i.e., panic disorder or panic attacks and the COVID-19), it is particularly important to be aware of the risk of hypokalemia in specific at-risk situations or prescriptions. For instance, in the case of salbutamol prescription, which might be overly used in patients with anxiety disorders and COVID-19, or in patients presenting with diarrhea and vomiting. Hypokalemia is associated with an increased risk of torsade de pointe, thus caution is required when prescribing specific psychotropic drugs, such as the antidepressants citalopram and escitalopram, which are first-line treatments for panic disorder, but also hydroxyzine, aiming at anxiety reduction. The results reviewed here highlight the importance of considering and further investigating the impact of the current pandemic on the diagnosis and treatment of panic disorder (alone or comorbid with the COVID-19). url: https://api.elsevier.com/content/article/pii/S0013700620300956 doi: 10.1016/j.encep.2020.05.010 id: cord-328209-uc37poce author: Javid, Babak title: Impact of population mask wearing on Covid-19 post lockdown date: 2020-04-16 words: 1251.0 sentences: 67.0 pages: flesch: 44.0 cache: ./cache/cord-328209-uc37poce.txt txt: ./txt/cord-328209-uc37poce.txt summary: Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high, the reduction on deaths was dramatic as the effective R approached 1, as might be expected after aggressive social-distancing measures such as wide-spread lockdowns. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high (Fig. 1a) , the reduction on deaths was dramatic as the effective R approached 1 (Fig. 1b) , as might be expected after aggressive socialdistancing measures such as wide-spread lockdowns 5 . abstract: COVID-19, caused by SARS-CoV2 is a rapidly spreading global pandemic. Although precise transmission routes and dynamics are unknown, SARS-CoV2 is thought primarily to spread via contagious respiratory droplets. Unlike with SARS-CoV, maximal viral shedding occurs in the early phase of illness, and this is supported by models that suggest 40-80% of transmission events occur from pre- and asymptomatic individuals. One widely-discussed strategy to limit transmission of SARS-CoV2, particularly from presymptomatic individuals, has been population-level wearing of masks. Modelling for pandemic influenza suggests some benefit in reducing total numbers infected with even 50% mask-use. COVID-19 has a higher hospitalization and mortality rate than influenza, and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. We derived a simplified SIR model to investigate the effects of near-universal mask-use on COVID-19 assuming 8 or 16% mask efficacy. We decided to model, in particular, the impact of masks on numbers of critically-ill patients and cumulative mortality, since these are parameters that are likely to have the most severe consequences in the COVID-19 pandemic. Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high, the reduction on deaths was dramatic as the effective R approached 1, as might be expected after aggressive social-distancing measures such as wide-spread lockdowns. One major concern with COVID-19 is its potential to overwhelm healthcare infrastructures, even in resource-rich settings, with one third of hospitalized patients requiring critical-care. We incorporated this into our model, increasing death rates for when critical-care resources have been exhausted. Our simple model shows that modest efficacy of masks could avert substantial mortality in this scenario. Importantly, the effects on mortality became hyper-sensitive to mask-wearing as the effective R approaches 1, i.e. near the tipping point of when the infection trajectory is expected to revert to exponential growth, as would be expected after effective lockdown. Our model suggests that mask-wearing might exert maximal benefit as nations plan their post-lockdown strategies and suggests that mask-wearing should be included in further more sophisticated models of the current pandemic. url: https://doi.org/10.1101/2020.04.13.20063529 doi: 10.1101/2020.04.13.20063529 id: cord-354900-bzv4yhqi author: Jawhara, Samir title: How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections date: 2020-10-12 words: 3691.0 sentences: 162.0 pages: flesch: 34.0 cache: ./cache/cord-354900-bzv4yhqi.txt txt: ./txt/cord-354900-bzv4yhqi.txt summary: During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. This short review focuses on the role of baker''s yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available. Of note, the SARS-CoV-2 particles first invade the respiratory mucosa and infect other cell types, causing a series of immune responses and the overproduction of cytokines ''cytokine storm'' , which may be related to the critical condition of COVID-19 patients [21] . abstract: The emergence of the novel coronavirus SARS-CoV-2, which causes severe respiratory tract infections in humans (COVID-19), has become a global health concern. One of the most worrying features of COVID-19 is a phenomenon known as the “cytokine storm”, which is a rapid overreaction of the immune system. Additionally, coagulation abnormalities, thrombocytopenia and digestive symptoms, including anorexia, vomiting, and diarrhea, are often observed in critically ill patients with COVID-19. Baker’s yeast β-glucan, a natural immunomodulatory component derived from Saccharomyces cerevisiae, primes the immune system to respond better to any microbial infection. Our previous studies have shown that oral administration of yeast β-glucans decreased the diarrhoea, modulated cytokine expression, and reduced the intestinal inflammation. Additionally, we showed that β-glucan fractions decreased coagulation in plasma and reduced the activation of platelets. During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. Additionally, β-glucan can be used to strengthen the immune defence in healthy individuals prior to any possible viral infections. This short review focuses on the role of baker’s yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available. url: https://doi.org/10.1186/s13099-020-00385-2 doi: 10.1186/s13099-020-00385-2 id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 words: 13003.0 sentences: 770.0 pages: flesch: 44.0 cache: ./cache/cord-300399-21xozruq.txt txt: ./txt/cord-300399-21xozruq.txt summary: This review paper examines current molecular diagnostic tools (Fig. 1) , such as amplification-based (including CRISPR-Cas based), antibody and antigen tests, and sequencing, utilized for the detection of SARS-CoV-2. In addition, we also discuss sample preparation aspects that are relevant to wider utilization and point-of-care (POC) deployment of COVID-19 diagnostic tests (PCR, isothermal amplification, and sequencing-including library preparation). RT-PCR broadly involves four steps-lysis of SARS-CoV-2 in the sample, purification of the viral RNA, reverse transcription to complementary DNA (cDNA), and amplification of specific regions of the cDNA, and finally, optical detection of the amplified cDNA. The assay can detect the virus from respiratory swab samples with sensitivity comparable to that of the US Centers for Disease Control and Prevention (CDC) SARS-CoV-2 real-time RT-PCR assay in 30-40 min. Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples abstract: The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification–, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting. url: https://www.ncbi.nlm.nih.gov/pubmed/33073312/ doi: 10.1007/s00216-020-02958-1 id: cord-263457-puf8gjir author: Jayarangaiah, Apoorva title: COVID-19-Associated Coagulopathy: An Exacerbated Immunothrombosis Response date: 2020-07-31 words: 5552.0 sentences: 374.0 pages: flesch: 34.0 cache: ./cache/cord-263457-puf8gjir.txt txt: ./txt/cord-263457-puf8gjir.txt summary: Activated leukocytes potentiate a procoagulant state via release of intravascular tissue factor, platelet activation, NETosis, and inhibition of anticoagulant mechanisms. 4, 5 The predominant underlying mechanism in COVID-19-related mortality is hypothesized to be widespread tissue damage and endothelial injury from an overactivated immune system via exaggerated T-cell responses and increased cytokine secretion, leading to a cytokine storm. 70 In conclusion, a viral-mediated coagulant state culminates in the presence of endothelial injury and dysfunction and cytokine-driven inflammatory conditions, leading to activation of TF-mediated thrombosis. The current COVID-19 pandemic has resurrected the concept of immunothrombosis as it is a relevant model to demonstrate the potentiating effects of the immune system and the coagulation system and the detrimental effects associated with their unrestrained activation, as evidenced by microthrombi and overt venous and arterial thrombi (Figure 4 ). A procoagulant state in COVID-19 is the result of a direct viral-related endothelial injury, leukocyte-and cytokinemediated platelet activation, TF release, and NETosis augmented by an unchecked activation of the complement system. abstract: Since the onset of the global pandemic in early 2020, coronavirus disease 2019 (COVID-19) has posed a multitude of challenges to health care systems worldwide. In order to combat these challenges and devise appropriate therapeutic strategies, it becomes of paramount importance to elucidate the pathophysiology of this illness. Coronavirus disease 2019, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), is characterized by a dysregulated immune system and hypercoagulability. COVID-associated coagulopathy (CAC) was recognized based on profound d-dimer elevations and evidence of microthrombi and macrothrombi, both in venous and arterial systems. The underlying mechanisms associated with CAC have been suggested, but not clearly defined. The model of immunothrombosis illustrates the elaborate crosstalk between the innate immune system and coagulation. The rendering of a procoagulant state in COVID-19 involves the interplay of many innate immune pathways. The SARS-CoV2 virus can directly infect immune and endothelial cells, leading to endothelial injury and dysregulation of the immune system. Activated leukocytes potentiate a procoagulant state via release of intravascular tissue factor, platelet activation, NETosis, and inhibition of anticoagulant mechanisms. Additional pathways of specific relevance in CAC include cytokine release and complement activation. All these mechanisms have recently been reported in COVID-19. Immunothrombosis provides a comprehensive perspective of the several synergistic pathways pertinent to the pathogenesis of CAC. url: https://doi.org/10.1177/1076029620943293 doi: 10.1177/1076029620943293 id: cord-253252-s8fm5rfa author: Jayaweera, Mahesh title: Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy date: 2020-06-13 words: 14098.0 sentences: 573.0 pages: flesch: 45.0 cache: ./cache/cord-253252-s8fm5rfa.txt txt: ./txt/cord-253252-s8fm5rfa.txt summary: This review paper intends to outline the literature concerning the transmission of viral-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. There have been myriads of hypotheses corroborating that certain threshold levels of humidity, temperature, sunlight, and ventilation will speed up the virus-laden droplet and aerosol transmission, aggravating the spread of the SARS-CoV disease (Morawska, 2006) . Nevertheless, the effectiveness of the use of masks for the control of SARS-CoV-2-laden aerosol transmission from an infected person to a susceptible host is uncertain and not fully conceivable. Researchers have speculated that both droplets and aerosols generated from non-violent and violent expirations of SARS-CoV-2-infected people may be responsible for the nonnosocomial and nosocomial transmission of COVID-19 disease. abstract: The practice of social distancing and wearing masks has been popular worldwide in combating the contraction of COVID-19. Undeniably, although such practices help control the COVID-19 pandemic to a greater extent, the complete control of viral-laden droplet and aerosol transmission by such practices is poorly understood. This review paper intends to outline the literature concerning the transmission of viral-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. The case studies that have come out in different countries have, with prima facie evidence, manifested that the airborne transmission plays a profound role in contracting susceptible hosts. Interestingly, the nosocomial transmission by airborne SARS-CoV-2 viral-laden aerosols in healthcare facilities may be plausible. Hence, clearly defined, science-based administrative, clinical, and physical measures are of paramount importance to eradicate the COVID-19 pandemic from the world. url: https://www.ncbi.nlm.nih.gov/pubmed/32569870/ doi: 10.1016/j.envres.2020.109819 id: cord-315453-mbv8vb2r author: Jean, Shio-Shin title: Old and re-purposed drugs for the treatment of COVID-19 date: 2020-06-01 words: 3462.0 sentences: 169.0 pages: flesch: 40.0 cache: ./cache/cord-315453-mbv8vb2r.txt txt: ./txt/cord-315453-mbv8vb2r.txt summary: EXPERT OPINION: Although strong evidence of well-designed randomized controlled studies regarding COVID-19 therapy is presently lacking, remdesivir, teicoplanin, hydroxychloroquine (not in combination with azithromycin), and ivermectin might be effective antiviral drugs and are deemed promising candidates for controlling SARS-CoV-2. In future, clinical trials regarding a combination of potentially effective drugs against SARS-CoV-2 need to be conducted to establish the optimal regimen for the treatment of patients with moderate-to-severe COVID-19. Recently, US Food and Drug Administration (FDA) approved the phase 3, double-blind ODYSSEY study (ClinicalTrials.gov Identifier: NCT04326426, initiated on 12 April 2020) to investigate the efficacy and safety of tradipitant at a dosage of 85 mg orally twice daily for the treatment of inflammatory lung injury following critical COVID-19 infection [35] . Apart from remdesivir that was shown to have acceptable clinical efficacy against moderate-to-severe COVID-19 and acceptable side effects, the potential antiviral drugs that are likely useful in the treatment of patients with mild-to-moderate COVID-19 included hydroxychloroquine, teicoplanin, and ivermectin. abstract: INTRODUCTION: The coronavirus disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed since December 2019. It has caused a global pandemic with more than three hundred thousand case fatalities. However, apart from supportive care by respirators, no standard medical therapy is validated. AREAS COVERED: This paper presents old drugs with potential in vitro efficacy against SARS-CoV-2. The in vitro database, adverse effects, and potential toxicities of these drugs are reviewed regarding their feasibility of clinical prescription for the treatment of patients with COVID-19. To obtain convincing recommendations, we referred to opinions from the US National Institute of Health regarding drugs repurposed for COVID-19 therapy. EXPERT OPINION: Although strong evidence of well-designed randomized controlled studies regarding COVID-19 therapy is presently lacking, remdesivir, teicoplanin, hydroxychloroquine (not in combination with azithromycin), and ivermectin might be effective antiviral drugs and are deemed promising candidates for controlling SARS-CoV-2. In addition, tocilizumab might be considered as the supplementary treatment for COVID-19 patients with cytokine release syndrome. In future, clinical trials regarding a combination of potentially effective drugs against SARS-CoV-2 need to be conducted to establish the optimal regimen for the treatment of patients with moderate-to-severe COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32419524/ doi: 10.1080/14787210.2020.1771181 id: cord-321867-7n88rl6p author: Jee, J. title: Oncologic Immunomodulatory Agents in Patients with Cancer and COVID-19 date: 2020-08-12 words: 3944.0 sentences: 259.0 pages: flesch: 49.0 cache: ./cache/cord-321867-7n88rl6p.txt txt: ./txt/cord-321867-7n88rl6p.txt summary: A recent retrospective study found a possible trend toward worse outcomes associated with corticosteroid use in cancer patients, although no analysis was performed to correct for possible selection bias in which sicker patients received those medications [11] . For all analyses we considered the number of patients who developed a primary composite endpoint of respiratory failure (use of nonrebreather, high-flow nasal oxygen, or mechanical ventilation) or death within 28 days of SARS-CoV-2 diagnosis. When patients were stratified by level of respiratory support, corticosteroid use was associated with worse outcomes in the pre-2L oxygen cohort (HR 2.3, 95% CI 1.1-4.9), a trend not observed in the post-2L oxygen (HR 0.9, 95% CI 0.4-1.9) and post-critical cohorts (HR 0.8, 95% CI 0.5-1.4), though these additional analyses were limited by All rights reserved. . https://doi.org/10.1101/2020.08.11.20145458 doi: medRxiv preprint from neutropenia 60 to 180 days prior to SARS-CoV-2 diagnosis did not have worse outcomes. abstract: Background Corticosteroids, anti-CD20 agents, immunotherapies, and cytotoxic chemotherapy are commonly used in the treatment of patients with cancer. How these agents impact patients with cancer who are infected with SARS-CoV-2 remains unclear. Methods We retrospectively investigated associations between SARS-CoV-2-associated respiratory failure or death with receipt of the aforementioned medications and with pre-COVID-19 neutropenia. The study included all cancer patients diagnosed with SARS-CoV-2 at Memorial Sloan Kettering Cancer Center until June 2, 2020 (N=820). We controlled for cancer-related characteristics known to predispose to worse COVID-19. To address that more acutely ill patients receive therapeutic corticosteroids, we examined patient subsets based on different levels of respiratory support: <=2 L/min supplemental oxygen, >2L/min supplemental oxygen, and advanced respiratory support prior to death. Results Corticosteroid administration was associated with worse outcomes in the pre-2L supplemental oxygen cohort; no statistically significant difference was observed in the >2L/min supplemental oxygen and post-critical cohorts. Interleukin-6 (IL-6) and C-reactive protein (CRP) levels were lower, and ferritin levels were higher, after corticosteroid administration. In patients with metastatic thoracic cancer, 9 of 25 (36%) and 10 of 31 (32%) had respiratory failure or death among those who did and did not receive immunotherapy, respectively. Seven of 23 (30%) and 52 of 187 (28%) patients with hematologic cancer had respiratory failure or death among those who did and did not receive anti-CD20 therapy, respectively. Chemotherapy itself was not associated with worse outcomes, but pre-COVID-19 neutropenia was associated with worse COVID-19 course. Relative prevalence of chemotherapy-associated neutropenia in previous studies may account for different conclusions regarding the risks of chemotherapy in patients with COVID-19. In the absence of prospective studies and evidence-based guidelines, our data may aid providers looking to assess the risks and benefits of these agents in caring for cancer patients in the COVID-19 era. url: https://doi.org/10.1101/2020.08.11.20145458 doi: 10.1101/2020.08.11.20145458 id: cord-342340-q6j7vy8u author: Jefferies, Sarah title: COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study date: 2020-10-14 words: 5717.0 sentences: 281.0 pages: flesch: 43.0 cache: ./cache/cord-342340-q6j7vy8u.txt txt: ./txt/cord-342340-q6j7vy8u.txt summary: METHODS: We did a descriptive epidemiological study of all laboratory-confirmed and probable cases of COVID-19 and all patients tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New Zealand from Feb 2 to May 13, 2020, after which time community transmission ceased. Demographic features and disease outcomes, transmission patterns (source of infection, outbreaks, household transmission), time-to-event intervals, and testing coverage were described over five phases of the response, capturing different levels of non-pharmaceutical interventions. This descriptive epidemiological study examined a cohort of all confirmed and probable COVID-19 cases and all people tested for SARS-CoV-2 infection in New Zealand up to May 13, 2020 , which marked the easing of the most restrictive non-pharmaceutical interventions, after which community transmission ceased. abstract: BACKGROUND: In early 2020, during the COVID-19 pandemic, New Zealand implemented graduated, risk-informed national COVID-19 suppression measures aimed at disease elimination. We investigated their impacts on the epidemiology of the first wave of COVID-19 in the country and response performance measures. METHODS: We did a descriptive epidemiological study of all laboratory-confirmed and probable cases of COVID-19 and all patients tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New Zealand from Feb 2 to May 13, 2020, after which time community transmission ceased. We extracted data from the national notifiable diseases database and the national SARS-CoV-2 test results repository. Demographic features and disease outcomes, transmission patterns (source of infection, outbreaks, household transmission), time-to-event intervals, and testing coverage were described over five phases of the response, capturing different levels of non-pharmaceutical interventions. Risk factors for severe outcomes (hospitalisation or death) were examined with multivariable logistic regression and time-to-event intervals were analysed by fitting parametric distributions using maximum likelihood estimation. FINDINGS: 1503 cases were detected over the study period, including 95 (6·3%) hospital admissions and 22 (1·5%) COVID-19 deaths. The estimated case infection rate per million people per day peaked at 8·5 (95% CI 7·6–9·4) during the 10-day period of rapid response escalation, declining to 3·2 (2·8–3·7) in the start of lockdown and progressively thereafter. 1034 (69%) cases were imported or import related, tending to be younger adults, of European ethnicity, and of higher socioeconomic status. 702 (47%) cases were linked to 34 outbreaks. Severe outcomes were associated with locally acquired infection (crude odds ratio [OR] 2·32 [95% CI 1·40–3·82] compared with imported), older age (adjusted OR ranging from 2·72 [1·40–5·30] for 50–64 year olds to 8·25 [2·59–26·31] for people aged ≥80 years compared with 20–34 year olds), aged residential care residency (adjusted OR 3·86 [1·59–9·35]), and Pacific peoples (adjusted OR 2·76 [1·14–6·68]) and Asian (2·15 [1·10–4·20]) ethnicities relative to European or other. Times from illness onset to notification and isolation progressively decreased and testing increased over the study period, with few disparities and increasing coverage of females, Māori, Pacific peoples, and lower socioeconomic groups. INTERPRETATION: New Zealand's response resulted in low relative burden of disease, low levels of population disease disparities, and the initial achievement of COVID-19 elimination. FUNDING: Ministry of Business Innovation and Employment Strategic Scientific Investment Fund, and Ministry of Health, New Zealand. url: https://www.sciencedirect.com/science/article/pii/S2468266720302255 doi: 10.1016/s2468-2667(20)30225-5 id: cord-307242-e20gtx0z author: Jegouic, Sophie M. title: Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date: 2020-05-22 words: 3454.0 sentences: 177.0 pages: flesch: 52.0 cache: ./cache/cord-307242-e20gtx0z.txt txt: ./txt/cord-307242-e20gtx0z.txt summary: Similar western blot analysis of total protein extracts following induction of logarithmic phase E.coli cultures with IPTG confirmed the expression of His-tagged S antigen of the predicted molecular weight in all cases ( Figure 3 , upper panel). Nevertheless, we found that S protein fragments prepared for gel electrophoresis using non-reducing loading buffer could be used successfully for epitope mapping of 2 S reactive monoclonal antibodies, 3G9, an unpublished mouse mAb generated to SARS S, and CR3022, a human mAb also isolated originally to SARS [19] but shown to cross-react with SARS-CoV-2. To provide an additional level of validation and to add epitope specificity to the data, 2 of the sera scoring positive by S1 ELISA were used as probes on western blots using full length S expressed in insect cells (cf. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain ( RBD219-N1 ), a SARS Vaccine Candidate abstract: The newly emergent SARS-CoV-2 coronavirus is closely related to SARS-CoV which emerged in 2002. Studies on coronaviruses in general, and SARS in particular, have identified the virus spike protein (S) as being central to virus tropism, to the generation of a protective antibody response and to the unambiguous detection of past infections. As a result of this centrality SARS-CoV-2 S protein has a role in many aspects of research from vaccines to diagnostic tests. We describe a number of recombinant forms of SARS-CoV-2 S expressed in commonly available expression systems and their preliminary use in diagnostics and epitope mapping. These sources may find use in the current and future analysis of the virus and the Covid-19 disease it causes. url: https://doi.org/10.1101/2020.05.21.109298 doi: 10.1101/2020.05.21.109298 id: cord-353200-5csewb1k author: Jehi, Lara title: Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date: 2020-08-11 words: 4344.0 sentences: 226.0 pages: flesch: 40.0 cache: ./cache/cord-353200-5csewb1k.txt txt: ./txt/cord-353200-5csewb1k.txt summary: OBJECTIVE: To characterize a large cohort of patients hospitalized with COVID-19, their outcomes, develop and validate a statistical model that allows individualized prediction of future hospitalization risk for a patient newly diagnosed with COVID-19. DESIGN: Retrospective cohort study of patients with COVID-19 applying a least absolute shrinkage and selection operator (LASSO) logistic regression algorithm to retain the most predictive features for hospitalization risk, followed by validation in a temporally distinct patient cohort. MEASUREMENTS: Demographic, clinical, social influencers of health, exposure risk, medical co-morbidities, vaccination history, presenting symptoms, medications, and laboratory values were collected on all patients, and considered in our model development. Hospitalization risk prediction and outcomes in COVID-19 PLOS ONE | https://doi.org/10.1371/journal.pone.0237419 August 11, 2020 2 / 15 ethical restrictions by the Cleveland clinic regulatory bodies including the institutional review Board and legal counsel. We also develop and validate a statistical model that can assist with individualized prediction of hospitalization risk for a patient with COVID-19. abstract: BACKGROUND: Coronavirus Disease 2019 is a pandemic that is straining healthcare resources, mainly hospital beds. Multiple risk factors of disease progression requiring hospitalization have been identified, but medical decision-making remains complex. OBJECTIVE: To characterize a large cohort of patients hospitalized with COVID-19, their outcomes, develop and validate a statistical model that allows individualized prediction of future hospitalization risk for a patient newly diagnosed with COVID-19. DESIGN: Retrospective cohort study of patients with COVID-19 applying a least absolute shrinkage and selection operator (LASSO) logistic regression algorithm to retain the most predictive features for hospitalization risk, followed by validation in a temporally distinct patient cohort. The final model was displayed as a nomogram and programmed into an online risk calculator. SETTING: One healthcare system in Ohio and Florida. PARTICIPANTS: All patients infected with SARS-CoV-2 between March 8, 2020 and June 5, 2020. Those tested before May 1 were included in the development cohort, while those tested May 1 and later comprised the validation cohort. MEASUREMENTS: Demographic, clinical, social influencers of health, exposure risk, medical co-morbidities, vaccination history, presenting symptoms, medications, and laboratory values were collected on all patients, and considered in our model development. RESULTS: 4,536 patients tested positive for SARS-CoV-2 during the study period. Of those, 958 (21.1%) required hospitalization. By day 3 of hospitalization, 24% of patients were transferred to the intensive care unit, and around half of the remaining patients were discharged home. Ten patients died. Hospitalization risk was increased with older age, black race, male sex, former smoking history, diabetes, hypertension, chronic lung disease, poor socioeconomic status, shortness of breath, diarrhea, and certain medications (NSAIDs, immunosuppressive treatment). Hospitalization risk was reduced with prior flu vaccination. Model discrimination was excellent with an area under the curve of 0.900 (95% confidence interval of 0.886–0.914) in the development cohort, and 0.813 (0.786, 0.839) in the validation cohort. The scaled Brier score was 42.6% (95% CI 37.8%, 47.4%) in the development cohort and 25.6% (19.9%, 31.3%) in the validation cohort. Calibration was very good. The online risk calculator is freely available and found at https://riskcalc.org/COVID19Hospitalization/. LIMITATION: Retrospective cohort design. CONCLUSION: Our study crystallizes published risk factors of COVID-19 progression, but also provides new data on the role of social influencers of health, race, and influenza vaccination. In a context of a pandemic and limited healthcare resources, individualized outcome prediction through this nomogram or online risk calculator can facilitate complex medical decision-making. url: https://www.ncbi.nlm.nih.gov/pubmed/32780765/ doi: 10.1371/journal.pone.0237419 id: cord-321549-r7bmtloy author: Jendrny, Paula title: Scent dog identification of samples from COVID-19 patients – a pilot study date: 2020-07-23 words: 3459.0 sentences: 184.0 pages: flesch: 52.0 cache: ./cache/cord-321549-r7bmtloy.txt txt: ./txt/cord-321549-r7bmtloy.txt summary: METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. As dogs can be trained quickly, the aim of the present study was to test the concept of using dogs reliably and in real-time to discriminate between samples of SARS-CoV-2 infected patients and non-infected controls. The individuals were only tested for SARS-CoV-2 virus and therefore one cannot exclude that a former infection, especially with another human coronavirus like HCoV-OC43 resulted in false positive indications of the dogs and that cross detection occurred. Detection dogs were able to discriminate respiratory secretions of infected SARS-CoV-2 individuals from those of healthy controls with high rates of sensitivity and specificity. abstract: BACKGROUND: As the COVID-19 pandemic continues to spread, early, ideally real-time, identification of SARS-CoV-2 infected individuals is pivotal in interrupting infection chains. Volatile organic compounds produced during respiratory infections can cause specific scent imprints, which can be detected by trained dogs with a high rate of precision. METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. RESULTS: The dogs were able to discriminate between samples of infected (positive) and non-infected (negative) individuals with average diagnostic sensitivity of 82.63% (95% confidence interval [CI]: 82.02–83.24%) and specificity of 96.35% (95% CI: 96.31–96.39%). During the presentation of 1012 randomised samples, the dogs achieved an overall average detection rate of 94% (±3.4%) with 157 correct indications of positive, 792 correct rejections of negative, 33 incorrect indications of negative or incorrect rejections of 30 positive sample presentations. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. This data may form the basis for the reliable screening method of SARS-CoV-2 infected people. url: https://www.ncbi.nlm.nih.gov/pubmed/32703188/ doi: 10.1186/s12879-020-05281-3 id: cord-270257-5f95gve3 author: Jeon, Sangeun title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date: 2020-03-28 words: 1145.0 sentences: 79.0 pages: flesch: 53.0 cache: ./cache/cord-270257-5f95gve3.txt txt: ./txt/cord-270257-5f95gve3.txt summary: Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. In near future, these already FDA-approved drugs could be further developed following clinical trials in order to provide additional therapeutic options for patients with COVID-19. We screened approximately 3,000 FDA-and IND-approved drug library against SARS-CoV to identify antiviral drug candidates (manuscript in preparation). Among the 48 drugs that were evaluated in our study, 24 drugs showed potential antiviral activities against SARS-CoV-2 with IC 50 values in Second, ciclesonide is another interesting drug candidate for further development although its antiviral potency was much lower (IC 50 = 4.33 µM) than niclosamide. Prior to our evaluation of 48 drugs against SARS-CoV-2 infection, we also tested antiviral activity of several other drugs based on the cytopathic effect of the virus in the presence of each drug ( Figure 2 ). abstract: COVID-19 is an emerging infectious disease and was recently declared as a pandemic by WHO. Currently, there is no vaccine or therapeutic available for this disease. Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. We found a total of 24 drugs which exhibited antiviral efficacy (0.1 μM < IC50 < 10 μM) against SARS-CoV-2. In particular, two FDA-approved drugs - niclosamide and ciclesonide – were notable in some respects. These drugs will be tested in an appropriate animal model for their antiviral activities. In near future, these already FDA-approved drugs could be further developed following clinical trials in order to provide additional therapeutic options for patients with COVID-19. url: https://doi.org/10.1101/2020.03.20.999730 doi: 10.1101/2020.03.20.999730 id: cord-346008-6v2gdz4a author: Jeong, Areum title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea date: 2020-06-02 words: 1152.0 sentences: 84.0 pages: flesch: 52.0 cache: ./cache/cord-346008-6v2gdz4a.txt txt: ./txt/cord-346008-6v2gdz4a.txt summary: title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea Due to close contact during examination, frequent exposure to tears and ocular discharge, and the inevitable sharing of equipment, ophthalmologists and patients are at a higher risk of SARS-CoV-2 infection. To prevent the transmission of COVID-19 in clinics, we follow steps based on three levels of control measures: administrative control, environmental control, and the use of personal protective equipment (PPE). If any of the aforementioned conditions are met, the patient is masked, isolated, and instructed to visit the COVID-19 screening center for reverse transcription polymerase chain reaction. Patients who have fever but negative test results postpone the appointment or attend the clinic. To reduce the exposure time, all patients should wear a mask in the waiting room. Characteristics of ocular findings of patients with coronavirus disease 2019 (COVID-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32537958/ doi: 10.3947/ic.2020.52.2.226 id: cord-276493-hoaxv5e0 author: Jeong, Gi Uk title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 words: 5687.0 sentences: 363.0 pages: flesch: 56.0 cache: ./cache/cord-276493-hoaxv5e0.txt txt: ./txt/cord-276493-hoaxv5e0.txt summary: With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. abstract: The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies. url: https://doi.org/10.3389/fmicb.2020.01723 doi: 10.3389/fmicb.2020.01723 id: cord-342776-hkjhqgie author: Jewett, Anahid title: The Potential Effect of Novel Coronavirus SARS-CoV-2 on NK Cells; A Perspective on Potential Therapeutic Interventions date: 2020-07-10 words: 3612.0 sentences: 159.0 pages: flesch: 41.0 cache: ./cache/cord-342776-hkjhqgie.txt txt: ./txt/cord-342776-hkjhqgie.txt summary: While studies on SARS-CoV-2 effects on immune cell function continue to progress, we know very little about the significance of depletion of key immune effectors by the virus in the mortality and morbidity of the disease. It also underscores the necessity for the future comprehensive studies of NK cells in SARS-CoV-2 infected individuals and animal models to better understand the role and significance of reported NK cell depletion and functional inactivation in disease morbidity and mortality, in hope to design effective therapeutic interventions for the disease. In particular, in the peripheral blood of patients that were infected with SARS, it was noted that there were significantly lower numbers of natural killer (NK) cells compared to healthy subjects (14) . As mentioned above the infectious agent of COVID-19 disease depletes NK cells in the peripheral blood, and potentially even in the lung tissues of patients, thereby, disabling and depleting the core immune effectors necessary to remove the virus and regulate uncontrolled immune activation. abstract: Coronavirus-induced disease-2019 (COVID-19) continues to cause significant morbidity and mortality worldwide. While studies on SARS-CoV-2 effects on immune cell function continue to progress, we know very little about the significance of depletion of key immune effectors by the virus in the mortality and morbidity of the disease. This commentary outlines what is the reported literature thus far on the effect of virus on NK cells known to kill virally infected cells. It also underscores the necessity for the future comprehensive studies of NK cells in SARS-CoV-2 infected individuals and animal models to better understand the role and significance of reported NK cell depletion and functional inactivation in disease morbidity and mortality, in hope to design effective therapeutic interventions for the disease. url: https://doi.org/10.3389/fimmu.2020.01692 doi: 10.3389/fimmu.2020.01692 id: cord-026811-6bdzut3d author: Jha, Ashish K. title: Emerging Treatment and Prevention Strategies against COVID-19: A Brief Update date: 2020-05-16 words: 2684.0 sentences: 148.0 pages: flesch: 45.0 cache: ./cache/cord-026811-6bdzut3d.txt txt: ./txt/cord-026811-6bdzut3d.txt summary: We have highlighted here the potential therapeutic role of remdesivir, chloroquine/ hydroxychloroquine (HCQ), lopinavir/ritonavir, and convalescent plasma in patients with SARS-CoV-2 infection. However, interpretation of the result of this study is limited by the lack of a randomized control group, small sample size, exclusion of serious cases (creatinine clearance <30 mL/min and >five-time elevation of serum aminotransferase), variable duration of remdesivir administration, noncollection of viral load data, adverse effects, and short-term follow-up. Early results obtained from more than 100 patients enrolled in studies conducted in the China showed the superiority of chloroquine compared with the controls in terms of reduction of exacerbation of pneumonia, duration of symptoms, and delay of viral clearance, all in the absence of severe side effects. A systematic review and exploratory meta-analysis from 32 studies of SARS coronavirus infection and severe influenza showed a statistically significant reduction in the pooled odds of mortality following treatment with convalescent plasma compared with placebo (odds ratio = 0.25; 95% confidence interval [CI]:0.14-0.45; I[2] = 0%). abstract: Patients with novel coronavirus disease 2019 (COVID-19) are at significantly increased risk for mortality and morbidity. Current management remains supportive care, ranging from symptomatic outpatient management to full–intensive care support, including intravenous fluids, invasive, and non-invasive oxygen supplementation. In patients with septic shock, treatment with antibiotics and vasopressors are recommended to keep mean arterial pressure (MAP) ≥ 65 mm Hg and lactate < 2 mmol/L. Because of the lack of effectiveness and possible adverse effects, routine corticosteroids should be avoided unless they are indicated for another reason (exacerbation of asthma or chronic obstructive pulmonary disease [COPD], and septic shock in whom fluids and vasopressors do not restore hemodynamic stability). There is currently no sufficient evidence of efficacy of hydroxychloroquine/chloroquine, remdesivir, and other antivirals in the treatment or prevention of COVID-19. Limited evidence shows that COVID-19 convalescent plasma can be used as a treatment of COVID-19 without the occurrence of severe adverse events. Drug regulatory agencies granted an emergency-use authorization of chloroquine/hydroxychloroquine and remdesivir to treat patients when a clinical trial is not available or participation is not feasible. Chloroquine and hydroxychloroquine are associated with QT interval prolongation and life-threatening cardiac arrhythmia in patients with pre-existing cardiovascular disease. Guidelines are issued for use of convalescent plasma in patients with serious or immediately life-threatening COVID-19. Data from several ongoing randomized controlled trials will provide further evidence regarding the safety and efficacy of these drugs for the treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295303/ doi: 10.1055/s-0040-1712547 id: cord-341415-g781zhu6 author: Jhaveri, Kenar D. title: Thrombotic microangiopathy in a patient with COVID-19 date: 2020-06-07 words: 1002.0 sentences: 86.0 pages: flesch: 51.0 cache: ./cache/cord-341415-g781zhu6.txt txt: ./txt/cord-341415-g781zhu6.txt summary: We describe a patient with coronavirus disease 2019 (COVID-19) and clinically significant kidney biopsy proven thrombotic microangiopathy(TMA). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was confirmed in the patient by reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay or serologic testing at our center. On day 20, the patient underwent a kidney biopsy that revealed severe acute thrombotic microangiopathy with cortical necrosis (Figure 1 ). While beta 2 glycoprotein-1 IgM levels were elevated, other laboratory and clinical features of anti-phospholipid antibody were absent( Table 2) . We report the first case of TMA associated with SARS-CoV-2 with presence of diffuse cortical necrosis and widespread microthrombi in the kidney biopsy. Physicians treating patients with COVID-19 should keep microangiopathic disease in the differential diagnosis when systemic findings of hemolysis are present along with thrombocytopenia and AKI. Coagulopathy and Antiphospholipid Antibodies in Patients with Covid-19 Acute Kidney injury in patients hospitalized with COVID abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0085253820306293?v=s5 doi: 10.1016/j.kint.2020.05.025 id: cord-305591-ir3wz6nr author: Ji, Danyang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 words: 5138.0 sentences: 315.0 pages: flesch: 55.0 cache: ./cache/cord-305591-ir3wz6nr.txt txt: ./txt/cord-305591-ir3wz6nr.txt summary: We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). We confirm Gquadruplex structure forming in the top-ranked PQSs by multiple spectroscopic assays in vitro and characterize the crosstalk between G-quadruplexes and viral helicase by microscale thermophoresis (MST) and molecular docking. Our analysis of Gquadruplex-forming sequences in SARS-CoV-2 provides insights into the design of anti-viral treatment by targeting the viral helicase and G-quadruplex structures. Interestingly, PQSs at positions 13385 and 24268 with the highest G-scores indicating high probability to adopt G-quadruplex structures only share high sequence similarity to the bat CoVs (see Supplementary Information S1 available online at https://academic.oup.com/bib and Table 2 ). In comparison, our G-quadruplex search across the genome of SARS-CoV-2 also identified a number of GG PQSs. PQS at position 13385 was confirmed to adopt G-quadruplex structures, which also contains a [GAAAG] sequence in the middle ( Table 1 ). abstract: The outbreak caused by the novel coronavirus SARS-CoV-2 has been declared a global health emergency. G-quadruplex structures in genomes have long been considered essential for regulating a number of biological processes in a plethora of organisms. We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). Detailed analysis of SARS-CoV-2 PQSs revealed their locations in the open reading frames of ORF1 ab, spike (S), ORF3a, membrane (M) and nucleocapsid (N) genes. Identical PQSs were also found in the other members of the Coronaviridae family. The top-ranked PQSs at positions 13385 and 24268 were confirmed to form RNA G-quadruplex structures in vitro by multiple spectroscopic assays. Furthermore, their direct interactions with viral helicase (nsp13) were determined by microscale thermophoresis. Molecular docking model suggests that nsp13 distorts the G-quadruplex structure by allowing the guanine bases to be flipped away from the guanine quartet planes. Targeting viral helicase and G-quadruplex structure represents an attractive approach for potentially inhibiting the SARS-CoV-2 virus. url: https://doi.org/10.1093/bib/bbaa114 doi: 10.1093/bib/bbaa114 id: cord-260772-n5q2yi7j author: Ji, Dong title: Reply to: ‘No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease’ date: 2020-05-06 words: 405.0 sentences: 34.0 pages: flesch: 57.0 cache: ./cache/cord-260772-n5q2yi7j.txt txt: ./txt/cord-260772-n5q2yi7j.txt summary: title: Reply to: ''No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease'' Secondly, this is in keeping to our hypothesis that dysregulated hepatic innate immunity in patients with MAFLD contribute to the pathogenesis of COVID-19. 2 The liver is enriched with innate immune cells (such as macrophages, natural killer, natural killer T, and γδ T cells) 3 and due to its rich blood supply from the small bowel, circulation of the virus via the hepatic reticular system is expected. Hepatic innate immunity populations are potent cytokine producers and there are reports that obesity and NAFLD were associated with increased production of pro-inflammatory cytokines like TNF-α by adipose cells and Kupffer cells. No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease of the link between the dysregulated hepatic innate immunity and COVID-19. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0168827820302853?v=s5 doi: 10.1016/j.jhep.2020.04.039 id: cord-332458-2kwfcgz9 author: Ji, Henry title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus date: 2020-03-25 words: 1101.0 sentences: 58.0 pages: flesch: 34.0 cache: ./cache/cord-332458-2kwfcgz9.txt txt: ./txt/cord-332458-2kwfcgz9.txt summary: title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. abstract: A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. Our approach entails utilizing SARS-CoV-2 Spike antigen-expressing, non-replicating cells as carriers and presenters of immunogenic antigens, so called “I-cells”. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. Another advantage of this strategy is that the manufacturing process is scalable and yields uniform cell products allowing for “off-the-shelf” frozen supply availability. To prevent engraftment and proliferation of the cells after administration, the cells will be irradiated post-harvesting abolishing in vivo replication potential. Specifically, immunoreactive Spike-1 proteins from SARS-CoV-2 are expressed on the surface of irradiated target I-cells. Utilizing this innovative strategy, these viral antigen-displaying decoy cells will be developed as a vaccine to protect against COVID-19 disease. url: https://api.elsevier.com/content/article/pii/S2590098620300130 doi: 10.1016/j.medidd.2020.100026 id: cord-349210-8t4a5qqo author: Ji, Ping title: Immunomodulatory Therapeutic Proteins in COVID‐19: Current Clinical Development and Clinical Pharmacology Considerations date: 2020-08-10 words: 7698.0 sentences: 436.0 pages: flesch: 40.0 cache: ./cache/cord-349210-8t4a5qqo.txt txt: ./txt/cord-349210-8t4a5qqo.txt summary: Immunomodulatory biological therapies are being evaluated in clinical trials for the management of the systemic inflammatory response and pulmonary complications in patients with advanced stages of COVID‐19. A randomized, open-label, controlled trial for the efficacy and safety of adalimumab in patients with elevated TNF-α levels in the critical stages of severe COVID-19 is ongoing in Shanghai, China, with the main outcome of time to clinical improvement. A Phase 2 trial of the efficacy and safety of infliximab was initiated to evaluate whether early institution of TNF-α inhibitor therapy in patients with severe COVID-19 infections could prevent further clinical deterioration and reduce the need for advanced cardiorespiratory support and early mortality at a 5 mg/kg IV single dose. extrinsic factors ( Route of administration: As described before, the immunomodulatory therapeutic proteins currently in clinical trials for the treatment of COVID-19 mostly are directed towards patients with moderate and severe stages of the disease. abstract: The COVID‐19 pandemic caused by infection with SARS‐CoV‐2 has led to more than 600,000 deaths worldwide. Patients with severe disease often experience acute respiratory distress characterized by upregulation of multiple cytokines. Immunomodulatory biological therapies are being evaluated in clinical trials for the management of the systemic inflammatory response and pulmonary complications in patients with advanced stages of COVID‐19. In this review, we summarize the clinical pharmacology considerations in the development of immunomodulatory therapeutic proteins for mitigating the heightened inflammatory response identified in COVID‐19. This article is protected by copyright. All rights reserved url: https://doi.org/10.1002/jcph.1729 doi: 10.1002/jcph.1729 id: cord-335538-thd5oaef author: Ji, Xiaoyang title: TWIRLS, a knowledge‐mining technology, suggests a possible mechanism for the pathological changes in the human host after coronavirus infection via ACE2 date: 2020-07-13 words: 5274.0 sentences: 252.0 pages: flesch: 46.0 cache: ./cache/cord-335538-thd5oaef.txt txt: ./txt/cord-335538-thd5oaef.txt summary: First, TWIRLS can process and summarize the massive biomedical literature on coronaviruses, and then collect, classify, and analyze reported coronavirus studies to reveal host-related entities based on the distribution of specific genes in the text of the articles. We obtained text data (referred to as the local samples) from all related peer reviewed articles published by human researchers that contained the keyword "coronavirus" including the title, abstracts, and author and affiliation information (total 3,182,687 words). TWIRLS first calculates the specific co-distribution between CSHGs in local samples, then determines the distance between each pair of CSSEs and performs dichotomy clustering according to the linkage relationship between CSSEs and CSHGs. This step classified the 623 entities into 32 categories represented as C0-C31 (see category number in Table S1 , Sheet 1 second column). Interestingly, CSHGs in the 2 connections of ACE2 and DPP4 associated with category C5 were also enriched in category C3, inferring that the information summarized in category C3 probably describes the underlying mechanisms of the pathological changes after coronavirus infection. abstract: Faced with the current large‐scale public health emergency, collecting, sorting, and analyzing biomedical information related to the “SARS‐CoV‐2” should be done as quickly as possible to gain a global perspective, which is a basic requirement for strengthening epidemic control capacity. However, for human researchers studying viruses and hosts, the vast amount of information available cannot be processed effectively and in a timely manner, particularly if our scientific understanding is also limited, which further lowers the information processing efficiency. We present TWIRLS (Topic‐wise inference engine of massive biomedical literatures), a method that can deal with various scientific problems, such as liver cancer, acute myeloid leukemia, and so forth, which can automatically acquire, organize, and classify information. Additionally, this information can be combined with independent functional data sources to build an inference system via a machine‐based approach, which can provide relevant knowledge to help human researchers quickly establish subject cognition and to make more effective decisions. Using TWIRLS, we automatically analyzed more than three million words in more than 14,000 literature articles in only 4 hr. We found that an important regulatory factor angiotensin‐converting enzyme 2 (ACE2) may be involved in host pathological changes on binding to the coronavirus after infection. On triggering functional changes in ACE2/AT2R, the cytokine homeostasis regulation axis becomes imbalanced via the Renin‐Angiotensin System and IP‐10, leading to a cytokine storm. Through a preliminary analysis of blood indices of COVID‐19 patients with a history of hypertension, we found that non‐ARB (Angiotensin II receptor blockers) users had more symptoms of severe illness than ARB users. This suggests ARBs could potentially be used to treat acute lung injury caused by coronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32657473/ doi: 10.1002/ddr.21717 id: cord-275482-ncrhb75f author: Jia, Hong Peng title: Infection of Human Airway Epithelia by Sars Coronavirus is Associated with ACE2 Expression and Localization date: 2006 words: 2141.0 sentences: 110.0 pages: flesch: 42.0 cache: ./cache/cord-275482-ncrhb75f.txt txt: ./txt/cord-275482-ncrhb75f.txt summary: In contrast with results in polarized epithelia, poorly differentiated primary human tracheobronchial epithelia or A549 cells grown on tissue culture plastic expressed little ACE2 mRNA or protein. (D) β-galactosidase levels determined in primary human airway epithelia cultured under ALI or resubmerged conditions that were infected from the apical with SARS-S protein pseudotyped FIV. These results indicated that SARS-CoV infects undifferentiated human airway epithelial cells poorly or not at all, while well-differentiated conduction airway epithelia are susceptible. Our studies revealed the novel observation that SARS-CoV infection of human airway epithelia is dependent upon the state of epithelial differentiation and ACE2 mRNA and protein expression. In conclusion, studies in models of human airway epithelial differentiation and polarity reveal that SARS-CoV infects well-differentiated cells from the apical surface and preferentially exits from the apical side. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037581/ doi: 10.1007/978-0-387-33012-9_85 id: cord-024020-6opgzgcj author: Jia, Hongpeng title: Sustained research fund and dedicated research center for preparing next pandemic date: 2020-04-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The current COVID-19 pandemic caused by the SARS-CoV-2 virus is imposing a great threat to human lives and international panic that is not seen since WWII, resulting in financial crisis, daily life disturbance, transportation shutdown, industry disruption, and countries/cities lockdown in every corner of the globe. The inability to effectively contain the virus indicates that our investment and attention in research, prevention, and treatment development for this type of deadly viruses is insufficient, considering it has been 17 years since the brother coronavirus, SARS-CoV outbreak. The biggest lesson learned from the acrimonious past experiences is that humans quickly lose memory and do not continue to support related research when a pandemic is gone. It is the very time for the government, industry, and private foundations to work together to respond to this wake-up call and to take extraordinary measures to sustain the research support and establish comprehensive research centers. Only this level response may give us a hope to prepare the future and adequately deal with the next potential pandemic caused by emerging devastating viral infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184470/ doi: 10.1093/pcmedi/pbaa012 id: cord-290066-umthoftd author: Jia, Xingwang title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 date: 2020-10-08 words: 518.0 sentences: 41.0 pages: flesch: 55.0 cache: ./cache/cord-290066-umthoftd.txt txt: ./txt/cord-290066-umthoftd.txt summary: title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 We read with interest that antibody testing using a rapid immunochromatographic assay is reliable in the diagnosis of severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ) infection 1 . positive antibody results could be eliminated after five times dilution with normal human serum, when the RF level was lower than 10 IU/mL. The false positive antibody results could also be eliminated after 5 times dilution with normal human serum. Although the RT-PCR test has become the standard method for the diagnosis of SARS-CoV-2 infection, false-negative rates have been reported. Therefore, the combination of serum IgM/IgG antibody detection, the nucleic acid test, CT scan and clinical features improves the accuracy of COVID-19 diagnosis. Reliability and usefulness of a rapid IgM-IgG antibody test for the diagnosis of SARS-CoV-2 infection: A preliminary report abstract: nan url: https://api.elsevier.com/content/article/pii/S0163445320306496 doi: 10.1016/j.jinf.2020.10.007 id: cord-353777-t8q99tlq author: Jia, Yong title: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date: 2020-04-11 words: 3217.0 sentences: 180.0 pages: flesch: 58.0 cache: ./cache/cord-353777-t8q99tlq.txt txt: ./txt/cord-353777-t8q99tlq.txt summary: The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020. The discrepant phylogenies for the spike protein and its 23 receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARSDespite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that 25 leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27 th January 2020 from 26 abstract: Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and raises the alarm that the ongoing vaccine development may become futile in future epidemic if more mutations were identified. Highlights Based on the currently available genome sequence data, we proved that SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak. The spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. We confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020. url: https://doi.org/10.1101/2020.04.09.034942 doi: 10.1101/2020.04.09.034942 id: cord-288010-i9zrojoo author: Jia, Yuanyuan title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China date: 2020-05-15 words: 1132.0 sentences: 64.0 pages: flesch: 58.0 cache: ./cache/cord-288010-i9zrojoo.txt txt: ./txt/cord-288010-i9zrojoo.txt summary: title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China 6 However, limited studies on full-length genome characterization of SARS-CoV-2 from COVID-19 cases imported from abroad. Here, we characterized the genotype and mutation characteristics of SARS-CoV-2 isolated from eight imported cases from abroad in Yunnan, China. To further characterize the characteristics of virus variation, the sequence analyses based on SARS-CoV-2 full-length nucleotide and amino acid sequences was performed using the strain Wuhan-Hu-1 (Genbank no. Moreover, three novel mutations, including D1962V in nsp3 from the strain YN_Im03, L1375F in nsp3 and A829T in S protein from the isolate YN_Im04 were first identified in this study according to the comparison with 11,231 genomic sequences available at GISAID on 4/26/2020. In summary, we characterized the full-length genomes of SARS-CoV-2 strains from eight COVID-19 cases imported from abroad in Yunnan, China. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320302917?v=s5 doi: 10.1016/j.jinf.2020.05.016 id: cord-303135-rx21ajiw author: Jian, Li title: Perspective: COVID-19, implications of nasal diseases and consequences for their management date: 2020-05-01 words: 1723.0 sentences: 82.0 pages: flesch: 47.0 cache: ./cache/cord-303135-rx21ajiw.txt txt: ./txt/cord-303135-rx21ajiw.txt summary: This leads us to the question whether treatment in patients with allergic rhinitis, normally INCS, or in severe patients with CRSwNP, nowadays including biologics to suppress type 2 immune reactions, should be continued in case of a SARS-CoV-2 infection. SARS-CoV-2 may also infect patients with severe asthma and CRSwNP, who might be under treatment with a type 2 biologic drug such as dupilumab, omalizumab, or mepolizumab. However, we begin to recognize that diseases of the upper airways or their management by corticosteroids and biologics do not seem to increase the risk of infection nor the risk for severe COVID-19. In research perspective, because the airway passage of nose and nasopharynx is the main entry for respiratory viruses including the SARS-CoV 2, the expression and its regulation of the ACE2 receptor and the TMPRSS2 protease are key topics for research and targets for interventions. SARS-CoV-2 entry genes are most highly expressed in nasal goblet and ciliated cells within human airways abstract: nan url: https://doi.org/10.1016/j.jaci.2020.04.030 doi: 10.1016/j.jaci.2020.04.030 id: cord-298216-iq7fenxm author: Jiang, Chao title: Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season date: 2020-05-13 words: 1618.0 sentences: 114.0 pages: flesch: 44.0 cache: ./cache/cord-298216-iq7fenxm.txt txt: ./txt/cord-298216-iq7fenxm.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to sweep the world, causing infection of millions and death of hundreds of thousands. The respiratory disease that it caused, COVID-19 (stands for coronavirus disease in 2019), has similar clinical symptoms with other two CoV diseases, severe acute respiratory syndrome and Middle East respiratory syndrome (SARS and MERS), of which causative viruses are SARS-CoV and MERS-CoV, respectively. This is a discussion and comparison of the virus structures, transmission characteristics, clinical symptoms, diagnosis, pathological changes, treatment and prevention of the two kinds of viruses, CoVs and IAVs. It hopes to provide information for practitioners in the medical field during the epidemic season. In December 2019, a novel coronavirus, SARS-CoV-2, caused a pneumonia epidemic 44 in Wuhan, Hubei province of China. Lung pathology of severe 567 acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Molecular pathology analyses of two fatal 572 human infections of avian influenza A(H7N9) virus abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to sweep the world, causing infection of millions and death of hundreds of thousands. The respiratory disease that it caused, COVID-19 (stands for coronavirus disease in 2019), has similar clinical symptoms with other two CoV diseases, severe acute respiratory syndrome and Middle East respiratory syndrome (SARS and MERS), of which causative viruses are SARS-CoV and MERS-CoV, respectively. These three CoVs resulting diseases also share many clinical symptoms with other respiratory diseases caused by influenza A viruses (IAVs). Since both CoVs and IAVs are general pathogens responsible for seasonal cold, in the next few months, during the changing of seasons, clinicians and public heath may have to distinguish COVID-19 pneumonia from other kinds of viral pneumonia. This is a discussion and comparison of the virus structures, transmission characteristics, clinical symptoms, diagnosis, pathological changes, treatment and prevention of the two kinds of viruses, CoVs and IAVs. It hopes to provide information for practitioners in the medical field during the epidemic season. url: https://doi.org/10.1016/j.micinf.2020.05.005 doi: 10.1016/j.micinf.2020.05.005 id: cord-340351-ee8wjp5u author: Jiang, Fa-Chun title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms date: 2020-09-17 words: 1090.0 sentences: 83.0 pages: flesch: 57.0 cache: ./cache/cord-340351-ee8wjp5u.txt txt: ./txt/cord-340351-ee8wjp5u.txt summary: We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. Approximately 3 hours after the 2 patients were identified as positive for SARS-CoV-2 RNA, we sampled the environmental surfaces of the 2 rooms in the centralized quarantine hotel in which they had stayed. One surface sample from the faucet in patient B''s room was positive for SARS-CoV-2 RNA; the C t was 28.75 for the ORF1ab gene. We also detected SARS-CoV-2 RNA in the surface swab samples of the pillow cover, duvet cover, and sheet. SARS-CoV-2 RNA has been detected on environmental surfaces in isolation rooms where the symptomatic or paucisymptomatic patients stayed for several days (3) (4) (5) . abstract: We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. We detected SARS-CoV-2 RNA on 8 (36%) of 22 surfaces, as well as on the pillow cover, sheet, and duvet cover. url: https://doi.org/10.3201/eid2609.201435 doi: 10.3201/eid2609.201435 id: cord-304839-lesa5u2n author: Jiang, Fang title: Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19) date: 2020-03-04 words: 1896.0 sentences: 152.0 pages: flesch: 57.0 cache: ./cache/cord-304839-lesa5u2n.txt txt: ./txt/cord-304839-lesa5u2n.txt summary: In late December 2019, a cluster of cases with 2019 Novel Coronavirus pneumonia (SARS-CoV-2) in Wuhan, China, aroused worldwide concern. On January 7, 2020, researchers rapidly isolated a novel coronavirus (SARS-CoV-2, also referred to as 2019-nCoV) from confirmed infected pneumonia patients. 3 We reviewed the published clinical features, symptoms, complications, and treatments of patients with COVID-19 to help health workers around the world combat the current outbreak. Keywords used were "COVID-19," "2019 novel coronavirus," "SARS-CoV-2," "2019-nCoV," "Wuhan coronavirus," and "Wuhan seafood market pneumonia virus." After careful screening, six published articles with confirmed cases were identified and included in this review. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan abstract: In late December 2019, a cluster of cases with 2019 Novel Coronavirus pneumonia (SARS-CoV-2) in Wuhan, China, aroused worldwide concern. Previous studies have reported epidemiological and clinical characteristics of coronavirus disease 2019 (COVID-19). The purpose of this brief review is to summarize those published studies as of late February 2020 on the clinical features, symptoms, complications, and treatments of COVID-19 and help provide guidance for frontline medical staff in the clinical management of this outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32133578/ doi: 10.1007/s11606-020-05762-w id: cord-286217-3uklf2u2 author: Jiang, He-wei title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date: 2020-07-14 words: 6829.0 sentences: 423.0 pages: flesch: 54.0 cache: ./cache/cord-286217-3uklf2u2.txt txt: ./txt/cord-286217-3uklf2u2.txt summary: Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We detected the SARS-CoV-2-specific IgG and IgM proteins bound to the array using fluorescent-labeled anti-human antibodies, thereby generating a global assessment of each patient''s humoral antibody response. All of the samples and the controls were probed on the proteome microarray, and after data filtering and normalization, we constructed the IgG and IgM profile for each serum and performed clustering analysis to generate heatmaps (Figs. To statistically analyze the IgG responses against SARS-CoV-2 proteins, we calculated the p-values followed by multiple testing correction (or q-values), and applied significant analysis of microarray (SAM) to identify significant positive proteins (Supplementary Fig. 7 and Data 2). abstract: We still know very little about how the human immune system responds to SARS-CoV-2. Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We find that all these patients had IgG and IgM antibodies that specifically bind SARS-CoV-2 proteins, particularly the N protein and S1 protein. Besides these proteins, significant antibody responses to ORF9b and NSP5 are also identified. We show that the S1 specific IgG signal positively correlates with age and the level of lactate dehydrogenase (LDH) and negatively correlates with lymphocyte percentage. Overall, this study presents a systemic view of the SARS-CoV-2 specific IgG and IgM responses and provides insights to aid the development of effective diagnostic, therapeutic and vaccination strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32665645/ doi: 10.1038/s41467-020-17488-8 id: cord-285758-c18arb6s author: Jiang, Shibo title: SARS Vaccine Development date: 2005-07-17 words: 2305.0 sentences: 106.0 pages: flesch: 39.0 cache: ./cache/cord-285758-c18arb6s.txt txt: ./txt/cord-285758-c18arb6s.txt summary: The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. (30) reported that mucosal immunization of African green monkeys with an attenuated parainfluenza virus expressing S protein resulted in production of neutralizing antibodies and protected animals from infection by challenge with SARS-CoV. These findings suggest that RBD contains the major neutralizing epitopes in the S protein and is an ideal SARS vaccine candidate because RBD contains the receptor-binding site, which is critical for virus attachment to the target cell for infection (15, (17) (18) (19) . Epitope mapping and biological function analysis of antibodies produced by immunization of mice with an inactivated Chinese isolate of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine abstract: Developing effective and safe vaccines is urgently needed to prevent infection by severe acute respiratory syndrome (SARS)–associated coronavirus (SARS-CoV). The inactivated SARS-CoV vaccine may be the first one available for clinical use because it is easy to generate; however, safety is the main concern. The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. This suggests that recombinant proteins containing RBD and vectors encoding the RBD sequence can be used to develop safe and effective SARS vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/16022774/ doi: 10.3201/eid1107.050219 id: cord-290671-6p23qxb8 author: Jiang, Shibo title: An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies date: 2020-01-31 words: 1113.0 sentences: 55.0 pages: flesch: 45.0 cache: ./cache/cord-290671-6p23qxb8.txt txt: ./txt/cord-290671-6p23qxb8.txt summary: We have recently designed and engineered a pan-CoV fusion inhibitor, EK1 peptide, which could inhibit infection of five human coronaviruses, including SARS-CoV and MERS-CoV, and three bat-SL-CoVs [7] . Intranasal application of EK1 peptide before or after viral challenge, EK1 peptide can protect human DPP4-transgenic mice from MERS-CoV infection, suggesting its potential prophylactic and therapeutic effect against 2019-nCoV infection. The recently developed SARS-CoV and MERS-CoV neutralizing monoclonal antibodies (mAbs) and nanobodies with protective efficacy are specific to the S1 subunit of S protein, particularly the RBD [5, [8] [9] [10] . One of the rapid approaches is to evaluate the currently available SARS-CoV neutralizing antibodies with cross-neutralizing and protection activity against 2019-nCoV infection. The spike protein of SARS-CoV-a target for vaccine and therapeutic development A novel neutralizing monoclonal antibody targeting the N-terminal domain of the MERS-CoV spike protein abstract: nan url: https://doi.org/10.1080/22221751.2020.1723441 doi: 10.1080/22221751.2020.1723441 id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 words: 2465.0 sentences: 110.0 pages: flesch: 51.0 cache: ./cache/cord-349070-bqv03u2e.txt txt: ./txt/cord-349070-bqv03u2e.txt summary: title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. abstract: A quantitative, real-time, nested polymerase chain reaction (PCR) method, combining the high sensitivity of nested PCR with time-saving real-time instrumentation, was developed for large-scale screening for severe acute coronavirus (SARS) coronavirus. Forty-six clinical specimens were analyzed by this method, and results were compared with those obtained by conventional, single-round, real-time reverse-transcriptase PCR (RT-PCR) performed in parallel. Of the 17 positive results, 2 identified by our method were not detected by single-round, real-time RT-PCR, which suggests that real-time nested PCR has the potential for increased sensitivity, leading to earlier detection of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/14699465/ doi: 10.1086/380841 id: cord-267458-uofy7jyx author: Jiang, Xiao-Lin title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China date: 2020-04-22 words: 1622.0 sentences: 124.0 pages: flesch: 59.0 cache: ./cache/cord-267458-uofy7jyx.txt txt: ./txt/cord-267458-uofy7jyx.txt summary: title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China We report a three-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Herein, we report a 3-family cluster study of eight patients associated with asymptomatic and pauciasymptomatic (one mild symptom only) SARS-CoV-2 transmission in Shandong Province, China. The first positive SARS-CoV-2 patients in this cluster were identified on January 21, 2020 triggering an epidemiological investigation by the local center for disease control and prevention. Our findings show that the transmission of SARS-CoV-2 by individuals with asymptomatic or paucisymptomatic infections is possible. Patient 5 (asymptomatic) was identified to be infected with SARS-CoV-2 after frequent contact with Patients 3 and 4 during work and home visits. In this study, we detected SARS-CoV-2 in two environmental swabs from the household of Patient 3. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period abstract: Data concerning the transmission of SARS-CoV-2 in asymptomatic and paucisymptomatic patients are lacking. We report a three-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Eight (53%) of 15 members from three families were confirmed with SARS-CoV-2 infection. Of eight patients, three were asymptomatic and one was paucisymptomatic. An asymptomatic mother transmitted the virus to her son, and a paucisymptomatic father transmitted the virus to his three-month-old daughter. SARS-CoV-2 was detected in the environment of one household. The complete genomes of SARS-CoV-2 from the patients were >99.9% identical and were clustered with other SARS-CoV-2 sequences reported from China and other countries. url: https://doi.org/10.1093/infdis/jiaa206 doi: 10.1093/infdis/jiaa206 id: cord-292972-p7ifetgw author: Jiang, Xuan title: Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS? date: 2020-02-24 words: 1010.0 sentences: 64.0 pages: flesch: 54.0 cache: ./cache/cord-292972-p7ifetgw.txt txt: ./txt/cord-292972-p7ifetgw.txt summary: However, based on our analysis of a larger dataset available so far, we find there is no observable difference between the incubation time for SARS-CoV-2, severe acute respiratory syndrome coronavirus (SARS-CoV), and middle east respiratory syndrome coronavirus (MERS-CoV), highlighting the need for larger and well-annotated datasets. The symptom onset date of the first identified patient infected by SARS-CoV-2 was December 1st, 2019, which is about 14 days before the subsequent reported cases. 3 The first estimate of mean incubation time was based on the exposure information of 10 confirmed early SARS-CoV-2 infected cases in Wuhan, China and was predicted to be 5. The reported estimate of the SARS-CoV-2 incubation time was based on limited case data. For the MERS datasets, for example, we found only five reports published with accessible raw data, but one report had several patients with incubation times ranged from 0 to 21 days. abstract: The outbreak of a novel coronavirus (SARS‐CoV‐2) since December 2019 in Wuhan, the major transportation hub in central China, became an emergency of major international concern. While several etiological studies have begun to reveal the specific biological features of this virus, the epidemic characteristics need to be elucidated. Notably, a long incubation time was reported to be associated with SARS‐CoV‐2 infection, leading to adjustments in screening and control policies. To avoid the risk of virus spread, all potentially exposed subjects are required to be isolated for 14 days, which is the longest predicted incubation time. However, based on our analysis of a larger dataset available so far, we find there is no observable difference between the incubation time for SARS‐CoV‐2, severe acute respiratory syndrome coronavirus (SARS‐CoV), and middle east respiratory syndrome coronavirus (MERS‐CoV), highlighting the need for larger and well‐annotated datasets. url: https://www.ncbi.nlm.nih.gov/pubmed/32056235/ doi: 10.1002/jmv.25708 id: cord-258255-hzmcrenk author: Jiang, Xuejun title: Asymptomatic SARS‐CoV‐2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days date: 2020-04-24 words: 553.0 sentences: 35.0 pages: flesch: 49.0 cache: ./cache/cord-258255-hzmcrenk.txt txt: ./txt/cord-258255-hzmcrenk.txt summary: Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs([1]), but the presence of SARS‐CoV‐2 RNA in feces of COVID‐19 patients indicates the possibility of transmission via fecal‐oral route([2‐4]). Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs [1] , but the presence of SARS-CoV-2 RNA in feces of COVID-19 patients indicates the possibility of transmission via fecal-oral route [2] [3] [4] . Herein, we report the distinctive clinical characteristics of an asymptomatic case in which SARS-CoV-2 viral nucleotide detection was positive in anal swabs but negative in nasopharyngeal swabs for such a long period (42 days). This case will further provide the new information that, besides confirmed COVID-19 patients, the asymptomatic SARS-CoV-2 infected case can be persistently tested positive in the stool samples but negative in nasopharyngeal swabs for a long time. Detectable SARS-CoV-2 viral RNA in feces of three children during recovery period of COVID-19 pneumonia abstract: Coronavirus disease 2019 (COVID‐19), caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has spread rapidly around the world. Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs([1]), but the presence of SARS‐CoV‐2 RNA in feces of COVID‐19 patients indicates the possibility of transmission via fecal‐oral route([2‐4]). This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32330309/ doi: 10.1002/jmv.25941 id: cord-328373-cubp1cc1 author: Jiang, Yanfang title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 words: 3564.0 sentences: 217.0 pages: flesch: 50.0 cache: ./cache/cord-328373-cubp1cc1.txt txt: ./txt/cord-328373-cubp1cc1.txt summary: In the current study the use of a novel digital PCR assay to detect SARS-CoV-2 in both clinical patient-derived samples and environmentally derived samples was investigated, with the ultimate aim of reducing the rate of false negative results. Thirty-two patient samples including nasopharyngeal swabs, throat swabs, oropharyngeal swabs, phlegm, plasma/blood, and eye conjunctiva were collected at multiple timepoints during the disease course, and tested for the presence of SARS-CoV-2 via RT-PCR. SARS-CoV-2 nucleic acid sequences were detected in all clinical patient samples (respiratory tract samples including nasopharyngeal and oropharyngeal swabs). To prevent false-negative SARS-CoV-2 nucleic acid-based test results, and develop a new sensitive detection assay, we evaluated the performance of real-time RT-PCR and digital PCR for detecting SARS-CoV-2 nucleic acid in clinical patient-derived samples and environmentally derived samples. Strikingly, digital PCR detected SARS-CoV-2 nucleic acids in several samples that had previously tested negative via real-time RT-PCR, including 3 patient-derived samples and 5 environmentally derived samples. abstract: The global coronavirus disease 2019 (COVID-19) pandemic has posed great challenges in people’s daily lives. Highly sensitive laboratory techniques played a critical role in clinical COVID-19 diagnosis and management. In this study the feasibility of using a new digital PCR-based detection assay for clinical COVID-19 diagnosis was investigated by comparing its performance with that of RT-PCR. Clinical patient samples and samples obtained from potentially contaminated environments were analyzed. The study included 10 patients with confirmed COVID-19 diagnoses, 32 validated samples of various types derived from different clinical timepoints and sites, and 148 environmentally derived samples. SARS-CoV-2 nucleic acids were more readily detected in respiratory tract samples (35.0%). In analyses of environmentally derived samples, the positivity rate of air samples was higher than that of surface samples, probably due to differences in virus concentrations. Digital PCR detected SARS–CoV–2 in several samples that had previously been deemed negative, including 3 patient-derived samples and 5 environmentally derived samples. In this study digital PCR exhibited higher sensitivity than conventional RT-PCR, suggesting that it may be a useful new method for clinical SARS-CoV-2 detection. Improvement of SARS-CoV-2 detection would substantially reduce the rates of false-negative COVID-19 test results, in particular those pertaining to asymptomatic carriers. url: https://doi.org/10.1016/j.cca.2020.10.032 doi: 10.1016/j.cca.2020.10.032 id: cord-290218-dvyeg5fk author: Jiang, Yi title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 words: 2249.0 sentences: 143.0 pages: flesch: 53.0 cache: ./cache/cord-290218-dvyeg5fk.txt txt: ./txt/cord-290218-dvyeg5fk.txt summary: Interestingly, the structure of complexed nsp12 is almost identical to nsp12 in apo RdRp, with an RMSD of 0.5 Å [17] , coinciding with the high processivity of the viral RNA polymerase, which does not need to consume extra energy for conformation changes in the active site during the replication cycle (Fig. 3B ). These "sliding poles" are stabilized by interactions formed between the positively charged residues at the extended N-terminal of nsp8 and bases in RNA backbones ( Fig. 3E ) and reported to account for the known processivity of the RdRp, which is required for replicating the long coronavirus genomes [39] . Although the sequence identity of nsp12 across the RNA viruses is low, the polymerase active site is structurally highly conserved, suggesting that RdRp inhibitors may serve as a potential J o u r n a l P r e -p r o o f broad-spectrum antiviral drug against RNA viruses. abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global pandemic. Although great efforts have been made to develop effective therapeutic interventions, only the nucleotide analog remdesivir was approved for emergency use against COVID-19. Remdesivir targets the RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication and a promising drug target for COVID-19. Recently, several structures of RdRp in complex with substrate RNA and remdesivir were reported, providing insights into the mechanisms of RNA recognition by RdRp. These structures also reveal the mechanism of RdRp inhibition by nucleotide inhibitors and offer a molecular template for the development of RdRp-targeting drugs. This review discusses the recognition mechanism of RNA and nucleotide inhibitor by RdRp, and its implication in drug discovery. url: https://api.elsevier.com/content/article/pii/S0006291X20317216 doi: 10.1016/j.bbrc.2020.08.116 id: cord-323737-6ajqy0ch author: Jiang, Yuanyuan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 words: 6799.0 sentences: 399.0 pages: flesch: 51.0 cache: ./cache/cord-323737-6ajqy0ch.txt txt: ./txt/cord-323737-6ajqy0ch.txt summary: title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify potential inhibitors targeting 2 0 -O-MTase of SARS-CoV-2. To identify inhibitors targeting nsp16, we first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs. Supplementary Table 1 lists the detailed genome and protein information that were employed in this study. As seen from MM-PBSA results and docking studies, drugs including Hesperidin, Osi-027, Rimegepant, Sonedenoson, and Gs-9667 had higher binding affinities than SAM with the 2 0 -O-MTase of SARS-CoV-2. abstract: SARS-CoV-2, an emerging coronavirus, has spread rapidly around the world, resulting in over ten million cases and more than half a million deaths as of July 1, 2020. Effective treatments and vaccines for SARS-CoV-2 infection do not currently exist. Previous studies demonstrated that nonstructural protein 16 (nsp16) of coronavirus is an S-adenosyl methionine (SAM)-dependent 2’-O-methyltransferase (2’-O-MTase) that has an important role in viral replication and prevents recognition by the host innate immune system. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. Comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs defined the key residues for nsp16 2-O’-MTase functions. Virtual screening and docking analysis ranked the potential inhibitors of nsp16 from more than 4,500 clinically investigated and approved drugs. Furthermore, molecular dynamics simulations were carried out on eight top candidates, including Hesperidin, Rimegepant, Gs-9667, and Sonedenoson, to calculate various structural parameters and understand the dynamic behavior of the drug-protein complexes. Our studies provided the foundation to further test and repurpose these candidate drugs experimentally and/or clinically for COVID-19 treatment. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33016237/ doi: 10.1080/07391102.2020.1828172 id: cord-190207-en96o8zo author: Jim''enez-Avalos, Gabriel M. title: High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease date: 2020-08-30 words: 6206.0 sentences: 346.0 pages: flesch: 53.0 cache: ./cache/cord-190207-en96o8zo.txt txt: ./txt/cord-190207-en96o8zo.txt summary: title: High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease Here, a PAIN-filtered flavonoid database was screened against four sites of the protease: a free (normal) conformation of the Substrate Binding Site (NSBS), an induced-fit state of the SBS (ISBS), a Dimerization Site (DS) and a Cryptic Site (CS). In the case of SBS, the top 30 ligands with the lowest binding energies from NSBS and ISBS were contrasted and the ones present in both lists were selected as the final candidates. Each putative binding site had its respective solvent-accessible surface area (SASA) found in PyMol v.2.4 (44) , using as input the hydrogen-curated structure of M PRO obtained before. A previous study on SARS-CoV-1 3CL PRO reported two glycosylated flavonoids as inhibitors, whose sugar moieties interacted with the active sites''s S1 and S2 subsites through hydrogen bonds (31) . abstract: COVID-19 presents a great threat to public health worldwide and the infectious agent SARS-CoV-2 is currently the target of much research aiming at inhibition. The virus' main protease is a dimeric enzyme that has only recently begun to be thoroughly described, opening the door for virtual screening more broadly. Here, a PAIN-filtered flavonoid database was screened against four sites of the protease: a free (normal) conformation of the Substrate Binding Site (NSBS), an induced-fit state of the SBS (ISBS), a Dimerization Site (DS) and a Cryptic Site (CS). The mean binding energies of the top five ligands from each site were -9.52, -11.512, -7.042 and -10.348 kcal/mol for the NSBS, the ISBS, the DS and the CS, respectively. For the DS and CS, these top five compounds were selected as candidates to bind their respective site. In the case of SBS, the top 30 ligands with the lowest binding energies from NSBS and ISBS were contrasted and the ones present in both lists were selected as the final candidates. The final list was: Dorsilurin E (FL3FQUNP0001), Euchrenone a11 (FL2FALNP0014), Kurziflavolactone C (FL2FA9NC0016), Licorice glycoside E (FL2F1AGSN001) and Taxifolin 3'- (6"-phenyl- acetylglucoside) (FL4DACGS0020) for the SBS; Sanggenol O (FL2FALNP0020), CHEMBL2171573, Kanzonol E (FL3F1ANP0001), CHEMBL2171584 and Abyssynoflavanone VI (FL2FACNP0014) for DS and CHEMBL2171598, CHEMBL2171577, Denticulaflavanol (FL5FAANR0001), Kurzichalcolactone (FL1CA9NC0001) and CHEMBL2171578 for CS. Virtual screening integrated several confirmation methods, including cross-docking assays and positive and negative controls. All 15 compounds are currently subjected to molecular dynamics so as to theoretically validate their binding to the protease. url: https://arxiv.org/pdf/2008.13264v2.pdf doi: nan id: cord-334884-ig6n9cet author: Jiménez-Alberto, Alicia title: Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors date: 2020-06-25 words: 4071.0 sentences: 257.0 pages: flesch: 52.0 cache: ./cache/cord-334884-ig6n9cet.txt txt: ./txt/cord-334884-ig6n9cet.txt summary: The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. Taking this into consideration, we performed in silico evaluation of a set of approved drugs as potential inhibitors of Mpro from SARS-CoV-2; our findings show that several molecules warrant further analysis as treatment options against COVID-19. The SARS-CoV-2 Mpro structure and two of its main conformers, extracted from the molecular dynamics simulation trajectory file, were processed with AutoDockTools (Morris et al., 2009 ). Next, solvent-explicit molecular dynamics simulations were performed on Mpro; the resulting trajectory showed that the protein has a highly flexible active site as the amino acids surrounding the binding site had high RMSF (Root-Mean-Square Fluctuation) values. abstract: The global emergency caused by COVID-19 makes the discovery of drugs capable of inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease. Repurposing approved drugs can provide therapeutic alternatives that promise rapid and ample coverage because they have a documented safety record, as well as infrastructure for large-scale production. The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. A total of 4384 drugs, all approved for human use, were screened against three conformers of Mpro. The ligands were further studied through molecular dynamics simulations and binding free energy analysis. A total of nine currently approved molecules are proposed as potential inhibitors of SARS-CoV-2. These molecules can be further tested to speed the development of therapeutics against COVID-19. url: https://api.elsevier.com/content/article/pii/S1476927120304813 doi: 10.1016/j.compbiolchem.2020.107325 id: cord-316096-3fnwosst author: Jin, Huali title: Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice date: 2005-03-25 words: 4521.0 sentences: 222.0 pages: flesch: 54.0 cache: ./cache/cord-316096-3fnwosst.txt txt: ./txt/cord-316096-3fnwosst.txt summary: After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. All DNA vaccine constructs, encoding the E protein, the M glycoprotein, and the N protein of SARS-CoV, were obtained as follows: these genes were amplified from the cDNA by PCR amplifications using each set of specific primers, respectively. In the present study, it was consistent with their work that the N protein construct could induce the highest SARS-specific IgG, T cell proliferation, and in vivo CTL response (lysis rate of 50.6%) compared with M protein gene (lysis rate of 17%) and E protein gene (lysis rate of 5.6%) (Fig. 4) . In summary, the administrations with all three SARS-CoV DNA vaccines in our study were able to induce high levels of the antigen-specific IgG antibody, the T cell proliferation, IFN-c, DTH, and in vivo CTL responses. abstract: Abstract Vaccination against the SARS-CoV infection is an attractive means to control the spread of viruses in public. In this study, we employed a DNA vaccine technology with the levamisole, our newly discovered chemical adjuvant, to generate Th1 type of response. To avoid the enhancement antibody issue, genes encoding the nucleocapsid, membrane, and envelope protein of SARS-CoV were cloned and their expressions in mammalian cells were determined. After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. The highest immune responses were generated by the construct encoding the nucleocapsid protein. The results suggest that the N, M, and E genes could be used as the targets to prevent SARS-CoV infection in the DNA vaccine development. url: https://www.sciencedirect.com/science/article/pii/S0006291X05001026 doi: 10.1016/j.bbrc.2005.01.048 id: cord-334790-lav794w0 author: Jin, Huijuan title: Consensus for prevention and management of coronavirus disease 2019 (COVID-19) for neurologists date: 2020-04-01 words: 3557.0 sentences: 225.0 pages: flesch: 50.0 cache: ./cache/cord-334790-lav794w0.txt txt: ./txt/cord-334790-lav794w0.txt summary: 1 Clinical symptoms of 2019-nCoV have mostly resembled that of severe acute respiratory syndrome coronavirus (SARS-CoV) of 2003. The nervous system manifestations were significantly more common in patients with severe infection, manifested as ischaemic stroke and cerebral haemorrhage diagnosed by clinical symptoms and head CT, impaired consciousness and skeletal muscle injury. Symptoms related to the development of acute cerebrovascular diseases Among patients with SARS-CoV-2 infection, middle-aged and elderly people accounted for the majority of strokes, especially in critically ill patients. According to the ''Technical guidelines for prevention and control of new coronavirus infection in medical institutions (First Edition)'' 16 developed by General Office of the National Health Commission of the People''s Republic of China and clinical characteristics of these patients, we propose the following precautions for neurologists, especially for those who are working in high-risk areas. abstract: Coronavirus disease 2019 (COVID‐19) has become a pandemic disease globally. Although COVID-19 directly invades lungs, it also involves the nervous system. Therefore, patients with nervous system involvement as the presenting symptoms in the early stage of infection may easily be misdiagnosed and their treatment delayed. They become silent contagious sources or ‘virus spreaders’. In order to help neurologists to better understand the occurrence, development and prognosis, we have developed this consensus of prevention and management of COVID‐19. It can also assist other healthcare providers to be familiar with and recognise COVID-19 in their evaluation of patients in the clinic and hospital environment. url: https://www.ncbi.nlm.nih.gov/pubmed/32385132/ doi: 10.1136/svn-2020-000382 id: cord-325234-skshcrh1 author: Jin, Tingxu title: SARS-CoV-2 presented in the air of an intensive care unit (ICU) date: 2020-08-15 words: 4276.0 sentences: 205.0 pages: flesch: 54.0 cache: ./cache/cord-325234-skshcrh1.txt txt: ./txt/cord-325234-skshcrh1.txt summary: Therefore, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, it is necessary to 1) determine whether SARS-CoV-2 particles are present in the indoor air and 2) determine whether recovered patients are still shedding virus, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. To date, some studies have reported the presence of SARS-CoV-2 particles in the air in isolation rooms from hospitals treating COVID-19 patients (Yuanfang J,2020; Guo, Wang, Zhang, Li, & Chen,2020; Joshua L. Therefore, our study aims to 1) determine whether SARS-CoV-2 particles are present in the indoor air, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, and 2) determine whether recovered patients are still shedding SARS-CoV-2 particles, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. Our findings revealed the presence of SARS-CoV-2 in the indoor air of the ICU and indicate that the virus may be shed via aerosol for days, even after a patient has tested negative. abstract: As coronavirus disease 2019 (COVID-19) is spreading worldwide, there have been arguments regarding the aerosol transmission of its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Moreover, some re-detectable positive (RP) patients have been reported. However, little attention has been given to the follow-up of recovered patients, and there is no environmental evidence to determine whether these patients continue to shed the virus after they test negative. Therefore, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, it is necessary to 1) determine whether SARS-CoV-2 particles are present in the indoor air and 2) determine whether recovered patients are still shedding virus, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. In this study, surface and air samples were collected from an intensive care unit (ICU) containing one ready-for-discharge patient. All surface samples tested negative, but the air samples tested positive for SARS-CoV-2. This implies that SARS-CoV-2 particles may be shed in aerosol form for days after patients test negative. This finding may be one of the reasons for the observation of RP patients; therefore, there is a need for improved clinical and disease management guidelines for recovered COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S2210670720306661?v=s5 doi: 10.1016/j.scs.2020.102446 id: cord-286854-0s7oq0uv author: Jin, Xi title: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site date: 2020-07-03 words: 6012.0 sentences: 322.0 pages: flesch: 54.0 cache: ./cache/cord-286854-0s7oq0uv.txt txt: ./txt/cord-286854-0s7oq0uv.txt summary: title: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes. Sequence alignment analysis indicated 38 mutation sites for ZJ01 compared with other SARS-CoV-2 family members ( Figure 2(A) ). Further comparative alignment analysis of GZ02 (SARS viral strain), Wuhan-Hu-1 (the earliest sequenced SARS-CoV-2), RaTG13, HKU9-1 (the potential ancestor of SARS and SARS-CoV-2), HKU-1 and OC43 showed that the variation of FCS sequence had certain regularity in coronavirus evolution ( Figure 4(B) ). We speculated that, despite the gene similarity between ZJ01 and Wuhan-Hu-1, the mutation near the FCS changed the protein structure conformation and surface electrostatic potential of ZJ01, which further influenced its binding capacity with Furin. abstract: The mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified. Phylogenetic and relative synonymous codon usage analysis suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 global virus strains based on the base (C or T) at positions 8824 and 28247 while ZJ01 has T at both sites. The prediction of the Furin cleavage site (FCS) and sequence alignment indicated that the FCS may be an important site of coronavirus evolution. ZJ01 mutations identified near the FCS (F1-2) caused changes in the structure and electrostatic distribution of the S surface protein, further affecting the binding capacity of Furin. Single-cell sequencing and ACE2-Furin co-expression results confirmed that the Furin expression was especially higher in glands, liver, kidneys, and colon. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes. url: https://doi.org/10.1080/22221751.2020.1781551 doi: 10.1080/22221751.2020.1781551 id: cord-341804-rnj3wtg4 author: Jin, Zhe title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 words: 2048.0 sentences: 136.0 pages: flesch: 43.0 cache: ./cache/cord-341804-rnj3wtg4.txt txt: ./txt/cord-341804-rnj3wtg4.txt summary: This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. However, more evidence is needed either for 4 supporting or opposing the systemic therapeutic administration of glucocorticoids in 5 patients with SARS-CoV-2 infection (Qin et al., 2020 a variety of immune cells 20 and improves the immunity, while IFN-β takes effect by inhibiting the adsorption of certain 1 viruses, enhancing phagocytosis of natural killer cells and mononuclear macrophages Tocilizumab is a recombinant humanized anti-IL-6 receptor (IL-6R) monoclonal antibody, 21 13 which can specifically bind to soluble and membrane-bound IL-6 receptors and inhibit 1 signal transduction mediated by IL-6, thereby reducing inflammation and blocking cytokine 2 storm caused by COVID-19 (Scheinecker et al., 2009) . abstract: Since December 2019, the coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread throughout China as well as other countries. More than 8,700,000 confirmed COVID-19 cases have been recorded worldwide so far, with much more cases popping up overseas than those inside. As the initial epicenter in the world, China has been combating the epidemic for a relatively longer period and accumulated valuable experience in prevention and control of COVID-19. This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. Reviewing the progress in drug development for the treatment against COVID-19 in China may provide insight into the epidemic control in other countries. url: https://www.sciencedirect.com/science/article/pii/S0014299920304180?v=s5 doi: 10.1016/j.ejphar.2020.173326 id: cord-334976-53cd16w5 author: Jo, Seri title: Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro date: 2020-08-04 words: 3659.0 sentences: 222.0 pages: flesch: 55.0 cache: ./cache/cord-334976-53cd16w5.txt txt: ./txt/cord-334976-53cd16w5.txt summary: An in silico docking study showed that the binding modes of herbacetin and pectolinarin are similar to those obtained from the catalytic domain of SARS-CoV 3CLpro. Baicalin showed an effective inhibitory activity against SARS-CoV-2 3CLpro and its docking mode is different from those of herbacetin and pectolinarin. The proteolytic assay using SARS-CoV-2 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The compound showed the severely reduced fluorescent intensity and thus represented their SARS-CoV-2 3CLpro inhibitory activity. Among them, baicalin, herbacetin and pectolinarin revealed the prominent inhibitory activity against SARS-CoV-2 3CLpro. The binding modes of herbacetin and pectolinarin were similar to those obtained from the docking study of the catalytic domain of SARS-CoV 3CLpro 21 . In the previous results of SARS-CoV 3CLpro 21 , only the three effect flavonoids (herbacetin, pectolinarin, and rhoifolin) were mentioned. abstract: Coronavirus disease 2019 (COVID-19) has been a pandemic disease of which the termination is not yet predictable. Currently, researches to develop vaccines and treatments is going on globally to cope with this disastrous disease. Main protease (3CLpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the good targets to find antiviral agents before vaccines are available. Some flavonoids are known to inhibit 3CLpro from SARS-CoV which causes SARS. Since their sequence identity is 96%, a similar approach was performed with a flavonoid library. Baicalin, herbacetin, and pectolinarin have been discovered to block the proteolytic activity of SARS-CoV-2 3CLpro. An in silico docking study showed that the binding modes of herbacetin and pectolinarin are similar to those obtained from the catalytic domain of SARS-CoV 3CLpro. However, their binding affinities are different due to the usage of whole SARS-CoV-2 3CLpro in this study. Baicalin showed an effective inhibitory activity against SARS-CoV-2 3CLpro and its docking mode is different from those of herbacetin and pectolinarin. This study suggests important scaffolds to design 3CLpro inhibitors to develop antiviral agents or health-foods and dietary supplements to cope with SARS-CoV-2. url: https://doi.org/10.1080/14756366.2020.1801672 doi: 10.1080/14756366.2020.1801672 id: cord-348899-vynk8q8c author: Jo, Seri title: Inhibition of SARS-CoV 3CL protease by flavonoids date: 2019-11-14 words: 3989.0 sentences: 236.0 pages: flesch: 54.0 cache: ./cache/cord-348899-vynk8q8c.txt txt: ./txt/cord-348899-vynk8q8c.txt summary: A synthetic peptide labelled with an Edans-Dabcyl FRET (Fluorescence resonance energy transfer) pair 12 was used to search SARS-CoV 3CLpro inhibitory compounds against a flavonoid library. The proteolytic assay using the SARS-CoV 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The three compounds showed the severely reduced fluorescent intensity and thus represented their SARS-CoV 3CLpro inhibitory activity. The interactions between SARS-CoV 3CLpro and three inhibitory flavonoids were analysed to predict their binding affinities. We have created a library of flavonoids to systematically investigate SARS-CoV 3CLpro inhibitory compound by a FRET method. Herbacetin, rhoifolin and pectolinarin were the best inhibitory compounds against SARS-CoV 3CLpro in the flavonoid library. In order to predict the flavonoid scaffolds needed to interact with the catalytic site of SARS-CoV 3CLpro, an induced-fit docking study was performed and analysed. abstract: There were severe panics caused by Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome-Coronavirus. Therefore, researches targeting these viruses have been required. Coronaviruses (CoVs) have been rising targets of some flavonoids. The antiviral activity of some flavonoids against CoVs is presumed directly caused by inhibiting 3C-like protease (3CLpro). Here, we applied a flavonoid library to systematically probe inhibitory compounds against SARS-CoV 3CLpro. Herbacetin, rhoifolin and pectolinarin were found to efficiently block the enzymatic activity of SARS-CoV 3CLpro. The interaction of the three flavonoids was confirmed using a tryptophan-based fluorescence method, too. An induced-fit docking analysis indicated that S1, S2 and S3′ sites are involved in binding with flavonoids. The comparison with previous studies showed that Triton X-100 played a critical role in objecting false positive or overestimated inhibitory activity of flavonoids. With the systematic analysis, the three flavonoids are suggested to be templates to design functionally improved inhibitors. url: https://doi.org/10.1080/14756366.2019.1690480 doi: 10.1080/14756366.2019.1690480 id: cord-310631-ru5f69qg author: Joachim, Denner title: SARS-CoV-2 and enhancing antibodies date: 2020-05-07 words: 567.0 sentences: 40.0 pages: flesch: 50.0 cache: ./cache/cord-310631-ru5f69qg.txt txt: ./txt/cord-310631-ru5f69qg.txt summary: In contrast, other CoV infections including the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS) and the recent COVID-19 are characterised by a higher pathogenicity in certain human populations and may be lethal. In persons infected by SARS-CoV enhancing antibodies and neutralising antibodies may partly counteract each other''s function. In the case, cross-reactive enhancing antibodies exist, the infection with the new SARS-CoV-2 may be enhanced by these pre-existing antibodies against common CoV. Common CoV circulate every year in the human population [1] and it sounds logical that the amount of anti-CoV antibodies including potentially enhancing antibodies is higher in older persons. The assumption of ADE with pre-existing enhancing antibodies against common CoV may also explain why in some regions the infection rate with SARS-CoV-2 and its pathogenicity is higher compared with other regions. The possible existence of enhancing antibodies is also of importance for the development of a vaccine against SARS-CoV-2. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1386653220301669?v=s5 doi: 10.1016/j.jcv.2020.104424 id: cord-262184-uxyb4vih author: Jockusch, Steffen title: A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses that Cause SARS and COVID-19 date: 2020-06-18 words: 6488.0 sentences: 395.0 pages: flesch: 54.0 cache: ./cache/cord-262184-uxyb4vih.txt txt: ./txt/cord-262184-uxyb4vih.txt summary: We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. Using the criteria above, our study examines 11 nucleotide analogues with sugar or base modifications (structures shown in Fig. 1 ) for their ability to inhibit the SARS-CoV-2 or SARS-CoV RdRps: Ganciclovir 5''-triphosphate, Carbovir 5''-triphosphate, Cidofovir diphosphate, Stavudine 5''-triphosphate, Entecavir 5''-triphosphate, 2''-O-methyluridine-5''-triphosphate (2''-OMe-UTP), 3''-O-methyluridine-5''triphosphate (3''-OMe-UTP), 2''-fluoro-2''-deoxyuridine-5''-triphosphate (2''-F-dUTP), desthiobiotin-16aminoallyl-uridine-5''-triphosphate (Desthiobiotin-16-UTP), biotin-16-aminoallyl-2''-deoxyuridine-5''triphosphate (Biotin-16-dUTP) and 2''-amino-2''-deoxyuridine-5''-triphosphate (2''-NH 2 -dUTP). We then performed polymerase extension assays with the library of nucleoside triphosphate analogues (Fig. 1) either alone or in combination with natural nucleotides: 2''-OMe-UTP, 3''-OMe-UTP, 2''-F-dUTP, 2''-NH 2 -dUTP, Biotin-UTP, desthiobiotin-16-UTP, Sta-TP, Cid-DP + UTP + ATP, Car-TP + UTP + ATP + CTP, Gan-TP + UTP + ATP + CTP, or Ent-TP + UTP + ATP + CTP, following the addition of a pre-annealed RNA template and primer to a pre-assembled mixture of the SARS-CoV and/or SARS-CoV-2 RdRp (nsp12) and the two cofactor proteins (nsp7 and nsp8). abstract: SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2’ or 3’ modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses’ exonuclease activity. We examined these nucleotide analogues for their ability to be incorporated by the RdRps in the polymerase reaction and to prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (triphosphates of Carbovir, Ganciclovir, Stavudine and Entecavir; 3’-OMe-UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2’-OMe-UTP), and 3 did not terminate the polymerase reaction (2’-F-dUTP, 2’-NH(2)-dUTP and Desthiobiotin-16-UTP). The coronaviruses possess an exonuclease that apparently requires a 2’-OH at the 3’-terminus of the growing RNA strand for proofreading. In this study, all nucleoside triphosphate analogues evaluated form Watson-Crick-like base pairs. The nucleotide analogues demonstrating termination either lack a 2’-OH, have a blocked 2’-OH, or show delayed termination. Thus, these nucleotide analogues are of interest for further investigation to evaluate whether they can evade the viral exonuclease activity. Prodrugs of five of these nucleotide analogues (Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA-approved medications for treatment of other viral infections, and their safety profiles are well established. After demonstrating potency in inhibiting viral replication in cell culture, candidate molecules can be rapidly evaluated as potential therapies for COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0166354220302710?v=s5 doi: 10.1016/j.antiviral.2020.104857 id: cord-350211-vuxs5wtt author: Johanna, Barón‐Sánchez title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 words: 4028.0 sentences: 355.0 pages: flesch: 58.0 cache: ./cache/cord-350211-vuxs5wtt.txt txt: ./txt/cord-350211-vuxs5wtt.txt summary: Sin embargo, algunos autores sugieren que el virus puede infectar el sistema nervioso central (SNC), 17 donde el nivel de expresión de ECA2 es muy bajo, [18] [19] [20] [21] así, aunque la etiopatogenia de la anosmia por el virus SARS-CoV-2 no está todavía clara, esta podría estar medida por una infección directa la mucosa olfatoria, provocando destrucción de las neuronas sensoriales olfativas, por lo que la recuperación sería mas lenta y habría mayor probabilidad de que la perdida olfatoria permaneciera por mas tiempo, pudiendo incluso quedar un déficit permanente residual, 15 o por una afectación directa del lóbulo frontal como se ha reportado recientemente. abstract: Resumen Introducción: La enfermedad por coronavirus-2019 (Covid-19), se ha expandido con gran rapidez en todo el mundo. Las alteraciones del olfato y/o gusto han emergido como un síntoma muy frecuente a medida que la enfermedad se propagó en Europa. Uno de los países con mayor número de contagios en este continente ha sido España. Objetivo: Investigar la evolución clínica de los trastornos del olfato y el gusto en la enfermedad leve por COVID-19 en pacientes españoles. Métodos: Se realizó un estudio transversal a través de encuesta on‐line, en pacientes que presentaron afección súbita del olfato y/o el gusto, durante los dos meses de confinamiento total por COVID-19 en España. Resultados: El 91,18% de los sujetos con afectación del olfato y/o el gusto, que tuvieron a acceso a la realización de PCR, fueron positivos para COVID-19. El 6,5% presentó anosmia y ageusia de forma aislada. El 93,5% manifestó otros síntomas leves asociados: cefalea (51,6%), tos (51,6%), mialgias (45,2%), astenia (38,7%), congestión nasal o rinorrea (35,5%), fiebre (41,9%), febrícula (29,0%), odinofagia (25.8%) y diarrea (6,5%). La duración media de la anosmia fue de 8,33 días, posteriormente los pacientes manifestaron hiposmia, con resolución completa en 17,79 días de media. En el 22,6% de los pacientes el déficit olfatorio persistió. Todos los sujetos recuperaron el sentido del gusto. Conclusiones: Los trastornos olfativos y gustativos son síntomas prevalentes en la infección leve por COVID-19. Gran parte de los pacientes no presentan congestión nasal o rinorrea asociada y un grupo reducido de pacientes los presentan de forma aislada. Abstract Introduction: Coronavirus disease 2019 (COVID-19) has spread rapidly throughout the world. Smell and/or taste disorders have emerged as a very frequent symptom as the disease has spread in Europe. Spain is one of the European countries with the highest number of infections. Objective: This study aimed to investigate the clinical progression of smell and taste disorders in Spanish patients with mild COVID-19. Methods: An online survey was used to conduct a cross-sectional study of patients who presented sudden smell and/or taste disorders during the 2 months of total lockdown due to COVID-19 in Spain. Results: In our sample, 91.18% of respondents with impaired smell and/or taste and who were able to undergo PCR testing were positive for SARS-CoV-2 infection. Anosmia and ageusia presented in isolation in 6.5% of participants. The remaining 93.5% presented other mild symptoms: headache (51.6%), cough (51.6%), myalgia (45.2%), asthaenia (38.7%), nasal congestion or rhinorrhoea (35.5%), fever (41.9%), low-grade fever (29.0%), odynophagia (25.8%), or diarrhoea (6.5%). The mean duration of anosmia was 8.33 days, with patients subsequently manifesting hyposmia; complete resolution occurred after a mean of 17.79 days. In 22.6% of respondents, olfactory deficits persisted. All participants recovered their sense of taste. Conclusions: Olfactory and gustatory disorders are prevalent symptoms in mild COVID-19. Most patients do not present associated nasal congestion or rhinorrhoea and a small group of patients present these alterations in isolation. url: https://api.elsevier.com/content/article/pii/S0213485320302334 doi: 10.1016/j.nrl.2020.07.006 id: cord-265529-0n9xxa9h author: John Hann, Angus title: Controversies regarding shielding and susceptibility to COVID‐19 disease in liver transplant recipients in the United Kingdom date: 2020-06-17 words: 774.0 sentences: 46.0 pages: flesch: 49.0 cache: ./cache/cord-265529-0n9xxa9h.txt txt: ./txt/cord-265529-0n9xxa9h.txt summary: The objective of this case series is to report on SARS-CoV-2 infection in liver transplant recipients and discuss the role of immunosuppression, comorbidities and shielding. In the UK, transplant recipients were classified as individuals vulnerable to SARS-CoV-2 infection due to immunosuppression. A report from a high incidence area of northern Italy did not see fatalities in SARS-CoV-2-infected liver transplant patients, unless they were elderly and comorbid. 6 Therefore, these authors suggest that immunosuppression alone is not a risk factor for development of severe SARS-CoV-2 disease. We highlight three contrasting cases of SARS-CoV-2 infection in liver transplant recipients from the early stages of the pandemic in the UK (Table 1) . We suggest that liver transplant recipients are at high risk for severe SARS-CoV-2 infection and should continue to undergo strict isolation until the pandemic has passed, or robust evidence proves a lack of risk. abstract: December 2019 saw the emergence of a novel coronavirus, SARS-CoV-2, which rapidly escalated to a global pandemic 1 , with an unprecedented impact on healthcare systems worldwide. The objective of this case series is to report on SARS-CoV-2 infection in liver transplant recipients and discuss the role of immunosuppression, comorbidities and shielding. In the UK, transplant recipients were classified as individuals vulnerable to SARS-CoV-2 infection due to immunosuppression. They were advised in late March 2020 (Figure 1) by Public Health England to take additional social distancing precautions, a process referred to as 'shielding' 2 . This is a more rigorous form of isolation that requires the individual to not leave their place of residence or come into contact with others. In essence, completely isolate to minimise the risk of being exposed to SARS-CoV-2. url: https://doi.org/10.1111/tid.13352 doi: 10.1111/tid.13352 id: cord-305534-936peb1n author: Johnson, Kemmian D. title: Pulmonary and Extra-Pulmonary Clinical Manifestations of COVID-19 date: 2020-08-13 words: 6712.0 sentences: 346.0 pages: flesch: 43.0 cache: ./cache/cord-305534-936peb1n.txt txt: ./txt/cord-305534-936peb1n.txt summary: The severe acute respiratory syndrome coronavirus−2 (SARS-CoV-2) has been recently identified as the culprit of the highly infectious, outbreak named coronavirus disease 2019 (COVID-19) in China. While it is known that COVID-19 manifests similarly to the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2012 Middle East Respiratory Syndrome (MERS), primarily affecting the pulmonary system, the impact of the disease extends far beyond the respiratory system and affects other organs of the body. In the severe disease state, the patient''s clinical course is complicated by the development of pneumonia with ARDS, acute hypoxic respiratory failure, and/or death (7) . Several retrospective studies have consistently reported pulmonary manifestations in patients with COVID-19, which include cough, shortness of breath, sputum production, respiratory failure, and ARDS (Table 1) (5, 7, (9) (10) (11) (12) (13) (14) (15) (16) (17) . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: The severe acute respiratory syndrome coronavirus−2 (SARS-CoV-2) has been recently identified as the culprit of the highly infectious, outbreak named coronavirus disease 2019 (COVID-19) in China. Now declared a public health emergency, this pandemic is present in more than 200 countries with over 14 million cases and 600,000 deaths as of July 18, 2020. Primarily transmitted through the respiratory tract, the most common clinical presentations of symptomatic individuals infected with SARS-CoV-2 include fever, dyspnea, cough, fatigue, and sore throat. In advanced cases, patients may rapidly develop respiratory failure with acute respiratory distress syndrome, and even progress to death. While it is known that COVID-19 manifests similarly to the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2012 Middle East Respiratory Syndrome (MERS), primarily affecting the pulmonary system, the impact of the disease extends far beyond the respiratory system and affects other organs of the body. The literature regarding the extrapulmonary manifestations (cardiovascular, renal, hepatic, gastrointestinal, ocular, dermatologic, and neurological) of COVID-19 is scant. Herein, we provide a comprehensive review of the organ-specific clinical manifestations of COVID-19, to increase awareness about the various organs affected by SARS-CoV-2 and to provide a brief insight into the similarities and differences in the clinical manifestations of COVID-19 and the earlier SARS and MERS. url: https://doi.org/10.3389/fmed.2020.00526 doi: 10.3389/fmed.2020.00526 id: cord-309728-7vfotgrr author: Johnson, Kristen M. title: Managing COVID‐19 in Renal Transplant Recipients: A Review of Recent Literature and Case Supporting Corticosteroid‐sparing Immunosuppression date: 2020-05-26 words: 3202.0 sentences: 169.0 pages: flesch: 36.0 cache: ./cache/cord-309728-7vfotgrr.txt txt: ./txt/cord-309728-7vfotgrr.txt summary: PHARMACOTHERAPY Volume **, Number **, 2020 We present the case and outcomes of a renal transplant recipient with SAR-CoV-2 treated in our hospital whose immunosuppressive therapy was managed with only a modest reduction in calcineurin inhibitor target trough concentration and antiproliferative dose reduction. We have described the case of a renal transplant recipient who was successfully treated for COVID-19 with supportive care along with steroid-sparing immunosuppression regimen changes that included dose-reduced antiproliferative therapy and a modest decrease in tacrolimus target trough level. [22] [23] [24] Finally, currently published cases of SARS-CoV-2 in renal transplant recipients have demonstrated variable results in progression of respiratory disease and survival when substituting higher doses of corticosteroids for complete cessation of maintenance calcineurin inhibitor and antiproliferative therapy. 8, 11 Conclusion It is difficult to compare and draw conclusions regarding optimal immunosuppressant management in renal transplant recipients treated for SARS-CoV-2 from the limited data presented in currently published cases along with significant confounding variables. abstract: Novel coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome virus (SARS‐CoV‐2) has become a global health care crisis. The Centers for Disease Control and Prevention (CDC) lists immunocompromised patients, including those requiring immunosuppression following renal transplantation, as high risk for severe disease from SARS‐CoV‐2. Treatment for other viral infections in renal transplant recipients often includes a reduction in immunosuppression; however, no current guidelines are available recommending the optimal approach to managing immunosuppression in the patients who are infected with SARS‐CoV‐2. It is currently advised to avoid corticosteroids in the treatment of SARS‐CoV‐2 outside of critically ill patients. Recently published cases describing inpatient care of COVID‐19 in renal transplant recipients differ widely in disease severity, time from transplantation, baseline immunosuppressive therapy, and the modifications made to immunosuppression during COVID‐19 treatment. This review summarizes and compares inpatient immunosuppressant management strategies of recently published reports in the renal transplant population infected with SARS‐CoV‐2 and discusses the limitations of corticosteroids in managing immunosuppression in this patient population. url: https://www.ncbi.nlm.nih.gov/pubmed/32339304/ doi: 10.1002/phar.2410 id: cord-292578-co5essuw author: Johnson, Marina title: Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date: 2020-08-02 words: 2111.0 sentences: 121.0 pages: flesch: 52.0 cache: ./cache/cord-292578-co5essuw.txt txt: ./txt/cord-292578-co5essuw.txt summary: OBJECTIVES: The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS: A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). CONCLUSION: Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality. In summary, the MSD multiplexed coronavirus panel assay evaluated in this study is highly reproducible, specific and sensitive for the detection of anti-SARS-CoV-2 antibody over 14 days since the onset of COVID-19 symptoms. abstract: BACKGROUND: The emergence of SARS-CoV-2 has led to the development of serological assays that could aid in an understanding of the burden of COVID-19 disease. Many available tests lack rigorous evaluation and therefore results may be misleading. OBJECTIVES: The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS: A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). Sensitivity was evaluated with a total of 196 COVID-19 serum samples (169 confirmed PCR positive and 27 anti-nucleocapsid IgG positive) from individuals with mild symptomatic or asymptomatic disease. Specificity was evaluated with 194 control serum samples collected from adults prior to December 2019. RESULTS: The specificity and sensitivity of the binding IgG assay was highest for S protein with a specificity of 97.4 % and sensitivity of 96.2 % for samples taken 14 days and 97.9 % for samples taken 21 days following the onset of symptoms. IgG concentration to S and RBD correlated strongly with percentage inhibition measured by the pseudo-neutralisation assay. CONCLUSION: Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality. url: https://api.elsevier.com/content/article/pii/S1386653220303140 doi: 10.1016/j.jcv.2020.104572 id: cord-301622-mn59vszt author: Jomah, Shahamah title: Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review date: 2020-08-03 words: 6281.0 sentences: 405.0 pages: flesch: 50.0 cache: ./cache/cord-301622-mn59vszt.txt txt: ./txt/cord-301622-mn59vszt.txt summary: However, several agents are included in Infectious Diseases Society of America (IDSA) Management Guidelines for treatment of COVID-19 patients; including antimalaria (chloroquine, hydroxychloroquine), antivirals (lopinavir/ritonavir), antibacterial (azithromycin, and immunomodulators (Tocilizumab) based on their beneficial role reported by practicing physicians or small scale clinical trials. Additional keywords such as treatment", "antiviral", "protease inhibitors", "lopinavir ritonavir", "ribavirin", Remdesivir", "arbidol",Östalmovir", "Favipiravir", human studies, randomized controlled trials (RCT), prospective or retrospective cohort designs, case-control designs, case series and case report, with COVID-19 produced more than 300 trails. A randomized control trial including 199 severe COVID-19 patients revealed that lopinavir group had significantly shorter time for clinical improvement compared to standard therapy. Prospective, randomized, controlled, open-label multicenter trial [27] • 236 moderate/severe confirmed COVID-19 cases randomized; 116 to receive Favipiravir for 10 days and 120 to receive Umifenovir (Arbidol) for 10 days and all patients received conventional therapy. abstract: The unprecedented challenge faced by mankind due to emergence of coronavirus 2019 (COVID-19) pandemic has obligated researchers across the globe to develop effective medicine for prevention and treatment of this deadly infection. The aim of this review is to compile recently published research articles on anti-COVID 19 management with their benefits and risk to facilitate decision making of the practitioners and policy makers. Unfortunately, clinical outcomes reported for antivirals are not consistent. Initial favorable reports on lopinavir/ritonavir contradicted by recent studies. Ostalmovir has conflicting reports. Short term therapy of remdesivir claimed to be beneficial. Favipiravir demonstrated good recovery in some of the cases of COVID-19. Umifenovir (Arbidol) was associated with reduction in mortality in few studies. Overall, until now, U.S. Food and Drug administration issued only emergency use authorization to remdesivir for the treatment of suspected or laboratory-confirmed COVID-19 in adults and children hospitalized with severe disease. url: https://doi.org/10.1016/j.jiph.2020.07.013 doi: 10.1016/j.jiph.2020.07.013 id: cord-336837-rerp1g1w author: Jones, Nick K title: Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 date: 2020-06-19 words: 3082.0 sentences: 156.0 pages: flesch: 46.0 cache: ./cache/cord-336837-rerp1g1w.txt txt: ./txt/cord-336837-rerp1g1w.txt summary: These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent ''hubs'' of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely. Testing for SARS-CoV-2 RNA was performed with real-time RT-PCR using throat and nose swab samples of HCWs from Cambridge University Hospitals NHS Foundation Trust (CUHNFT) and their symptomatic household contacts. In the HCW symptomatic and HCW symptomatic household contact screening arms combined (reflecting all individuals with self-reported symptoms at the time of testing), 13/771 (1.7%) tests were positive, which was significantly lower than 30/221 (13%) in the original study period (Fisher''s exact test p<0.0001). In particular, during the last 2 weeks of the study period (11th to 24th May 2020), we identified only four positive SARS-CoV-2 samples from 2016 tests performed, two from the HCW asymptomatic and two from the HCW symptomatic/symptomatic household contact arms. abstract: Previously, we showed that 3% (31/1032)of asymptomatic healthcare workers (HCWs) from a large teaching hospital in Cambridge, UK, tested positive for SARS-CoV-2 in April 2020. About 15% (26/169) HCWs with symptoms of coronavirus disease 2019 (COVID-19) also tested positive for SARS-CoV-2 (Rivett et al., 2020). Here, we show that the proportion of both asymptomatic and symptomatic HCWs testing positive for SARS-CoV-2 rapidly declined to near-zero between 25th April and 24th May 2020, corresponding to a decline in patient admissions with COVID-19 during the ongoing UK ‘lockdown’. These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent ‘hubs’ of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely. url: https://www.ncbi.nlm.nih.gov/pubmed/32558644/ doi: 10.7554/elife.59391 id: cord-293938-40zyv1h8 author: Jonsdottir, Hulda R. title: Coronaviruses and the human airway: a universal system for virus-host interaction studies date: 2016-02-06 words: 5533.0 sentences: 288.0 pages: flesch: 41.0 cache: ./cache/cord-293938-40zyv1h8.txt txt: ./txt/cord-293938-40zyv1h8.txt summary: The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. Given the documented history of coronaviruses overcoming the species barrier and causing severe disease in humans, it is important to investigate the zoonotic potential of close evolutionary relatives of common HCoVs in a culture model that recapitulates the aspects of the human airway, e.g. morphology and receptor distribution. The establishment of transgenic animal models for human disease is attainable when either the virus receptor has been identified, which is not the case for all HCoVs, or when viruses can be adapted to a different host. abstract: Human coronaviruses (HCoVs) are large RNA viruses that infect the human respiratory tract. The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Various animal models have been established to investigate HCoV infection, including mice and non-human primates. To establish a link between the research conducted in animal models and humans, an organotypic human airway culture system, that recapitulates the human airway epithelium, has been developed. Currently, different cell culture systems are available to recapitulate the human airways, including the Air-Liquid Interface (ALI) human airway epithelium (HAE) model. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. These organotypic human airway cultures represent a universal platform to study respiratory virus-host interaction by offering more detailed insights compared to cell lines. Additionally, the epidemic potential of this virus family highlights the need for both vaccines and antivirals. No commercial vaccine is available but various effective antivirals have been identified, some with potential for human treatment. These morphological airway cultures are also well suited for the identification of antivirals, evaluation of compound toxicity and viral inhibition. url: https://doi.org/10.1186/s12985-016-0479-5 doi: 10.1186/s12985-016-0479-5 id: cord-324165-afdmsbw2 author: Joo, Heesoo title: The effects of past SARS experience and proximity on declines in numbers of travelers to the Republic of Korea during the 2015 MERS outbreak: A retrospective study date: 2019-08-31 words: 5124.0 sentences: 236.0 pages: flesch: 56.0 cache: ./cache/cord-324165-afdmsbw2.txt txt: ./txt/cord-324165-afdmsbw2.txt summary: The results from regression models and sensitivity analyses demonstrated that areas with ≥100 SARS cases and closer proximity to the ROK had significantly larger percentage decreases in traveler volumes during the outbreak. This evaluation estimates the changes in numbers of non-citizen short-term visitor arrivals from selected areas to the ROK during the 2015 MERS outbreak and examines the correlation between travel volume declines and previous experience of the most similar sizable outbreak, the 2003 severe acute respiratory syndrome (SARS) outbreak. Although WHO did not recommend any travel restrictions to the ROK during the 2015 MERS outbreak [17] , WHO noted that raising awareness about Table 4 Monthly marginal percentage change between actual (2015) and baseline projected (average of 2013 and 2014) non-citizen arrivals to the Republic of Korea (ROK) associated with areas that experienced ≥100 probable severe acute respiratory syndrome (SARS) cases and distance to the Republic of Korea. abstract: Abstract Background The experience of previous sizable outbreaks may affect travelers’ decisions to travel to an area with an ongoing outbreak. Methods We estimated changes in monthly numbers of visitors to the Republic of Korea (ROK) in 2015 compared to projected values by selected areas. We tested whether areas’ experience of a previous SARS outbreak of ≥100 cases or distance to the ROK had a significant effect on travel to the ROK during the MERS outbreak using t-tests and regression models. Results The percentage changes in visitors from areas with a previous SARS outbreak of ≥100 cases decreased more than the percentage changes in visitors from their counterparts in June (52.4% vs. 23.3%) and July (60.0% vs. 31.4%) during the 2015 MERS outbreak. The percentage changes in visitors from the close and intermediate categories decreased more than the far category. The results from regression models and sensitivity analyses demonstrated that areas with ≥100 SARS cases and closer proximity to the ROK had significantly larger percentage decreases in traveler volumes during the outbreak. Conclusions During the 2015 MERS outbreak, areas with a previous sizable SARS outbreak and areas near the ROK showed greater decreases in percentage changes in visitors to the ROK. url: https://doi.org/10.1016/j.tmaid.2019.05.009 doi: 10.1016/j.tmaid.2019.05.009 id: cord-346787-uo8k6qic author: Jorgensen, Sarah CJ title: Remdesivir: Review of pharmacology, pre‐clinical data and emerging clinical experience for COVID‐19 date: 2020-05-23 words: 5476.0 sentences: 367.0 pages: flesch: 51.0 cache: ./cache/cord-346787-uo8k6qic.txt txt: ./txt/cord-346787-uo8k6qic.txt summary: 3 The remdesivir dosing regimen being evaluated in clinical trials (200 mg IV on day 1, then 100 mg IV on days 2 through 5 or 10) was substantiated by in vitro data and bridging the PK with the rhesus monkey experience to humans. Prophylactic and therapeutic remdesivir treatment significantly reduced MERS-CoV-induced clinical signs, viral titers in respiratory specimens and the severity of lung lesions compared to control animals. 14 In the SARS-CoV-2 study, remdesivir was again initiated shortly before viral titers are expected to peak at 12 hours post-inoculation and a dosing regimen equivalent to the regimen being tested in human COVID-19 clinical trials was used (10 mg/kg load ~ 200 mg in humans, then 5 mg/kg daily ~ 100mg daily in humans x 6 days). In a summary of safety data reported by the FDA from the a remdesivir clinical trial comparing 5 and 10day treatment courses in patients with COVID-19, Grade 3 and 4 ALT and/or AST elevations occurred in 7% patients. abstract: The global pandemic of novel coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has created an urgent need for effective antivirals. Remdesivir (formerly GS‐5734) is a nucleoside analogue pro‐drug currently being evaluated in COVID‐19 clinical trials. Its unique structural features allow high concentrations of the active triphosphate metabolite to be delivered intracellularly and it evades proofreading to successfully inhibit viral RNA synthesis. In pre‐clinical models, remdesivir has demonstrated potent antiviral activity against diverse human and zoonotic β‐coronaviruses, including SARS‐CoV‐2. In this article we critically review available data on remdesivir with an emphasis on biochemistry, pharmacology, pharmacokinetics and in vitro activity against coronaviruses as well as clinical experience and current progress in COVID‐19 clinical trials. url: https://doi.org/10.1002/phar.2429 doi: 10.1002/phar.2429 id: cord-329904-e05ywn5e author: Jose, Merin title: Fatal Superimposed Bacterial Sepsis in a Healthy Coronavirus (COVID-19) Patient date: 2020-05-29 words: 2256.0 sentences: 118.0 pages: flesch: 46.0 cache: ./cache/cord-329904-e05ywn5e.txt txt: ./txt/cord-329904-e05ywn5e.txt summary: We present a case of a healthy COVID positive individual, with no underlying comorbidities, who rapidly deteriorated overnight on readmission to the hospital after initial discharge and succumbed to this disease due to a superimposed bacterial infection with COVID pneumonia. This case report highlights the importance of educating COVID-19 positive patients about the precautions, as well as signs and symptoms of a superimposed bacterial infection, when their plan of care is in a home setting. It also emphasizes the potential role of checking procalcitonin levels as a part of routine laboratory investigation at initial presentation in all suspected as well as confirmed COVID-19 cases to rule out an on-going bacterial infection that can prove fatal in the course of the disease. Our emphasis from this case report is to highlight the risk of superimposed bacterial infection in COVID-19 patients. abstract: Coronavirus disease 2019 (COVID-19) is a highly infectious disease caused by the newly discovered coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The novel coronavirus first emerged in Wuhan, China, in December 2019 and has led to a global pandemic. The virus mainly spreads through respiratory droplets from an infected person, but environmental contamination can also act as a source of infection, making social distancing an important key in containing the spread of infection. Those with underlying health conditions are more susceptible to complications such as acute respiratory distress syndrome, which can be fatal. However, healthy individuals experience a mild flu-like illness or may be asymptomatic, recuperating from the infection even without any particular intervention. We present a case of a healthy COVID positive individual, with no underlying comorbidities, who rapidly deteriorated overnight on readmission to the hospital after initial discharge and succumbed to this disease due to a superimposed bacterial infection with COVID pneumonia. This case report highlights the importance of educating COVID-19 positive patients about the precautions, as well as signs and symptoms of a superimposed bacterial infection, when their plan of care is in a home setting. It also emphasizes the potential role of checking procalcitonin levels as a part of routine laboratory investigation at initial presentation in all suspected as well as confirmed COVID-19 cases to rule out an on-going bacterial infection that can prove fatal in the course of the disease. url: https://doi.org/10.7759/cureus.8350 doi: 10.7759/cureus.8350 id: cord-344647-jr85915d author: Joseph, Adrien title: Acute kidney injury in patients with SARS-CoV-2 infection date: 2020-09-03 words: 3537.0 sentences: 193.0 pages: flesch: 51.0 cache: ./cache/cord-344647-jr85915d.txt txt: ./txt/cord-344647-jr85915d.txt summary: Acute Kidney Injury (AKI) is a frequent complication of severe SARS-CoV-2 infection but data are scarce in ICUs. AKI has been previously reported with an average incidence of 11% (8-17%) overall, with highest ranges in the critically ill (23%; 14-35%) [2] [3] [4] . Different applications of the Kidney Disease Improving Global Outcomes (KDIGO) criteria for AKI, in particular different methods to estimate missing baseline creatinine and handling urinary output, can cause important variations of estimated incidence [5, 6] and may contribute to the discrepancies among these studies. High levels of IL-6 have been associated with the development of severe disease [24, 25] and acute respiratory distress syndrome [8] during COVID-19 infection, but the role of inflammation markers in COVID-19-induced-AKI remains speculative [7] . Our study suggests a tremendously high incidence of AKI in our cohort of critically ill COVID-19 patients, along with an independent association between AKI and outcome. abstract: BACKGROUND: Acute Kidney Injury (AKI) is a frequent complication of severe SARS-CoV-2 infection. Multiple mechanisms are involved in COVID-19-associated AKI, from direct viral infection and secondary inflammation to complement activation and microthrombosis. However, data are limited in critically-ill patients. In this study, we sought to describe the prevalence, risk factors and prognostic impact of AKI in this setting. METHODS: Retrospective monocenter study including adult patients with laboratory confirmed SARS-CoV-2 infection admitted to the ICU of our university Hospital. AKI was defined according to both urinary output and creatinine KDIGO criteria. RESULTS: Overall, 100 COVID-19 patients were admitted. AKI occurred in 81 patients (81%), including 44, 10 and 27 patients with AKI stage 1, 2 and 3 respectively. The severity of AKI was associated with mortality at day 28 (p = 0.013). Before adjustment, the third fraction of complement (C3), interleukin-6 (IL-6) and ferritin levels were higher in AKI patients. After adjustment for confounders, both severity (modified SOFA score per point) and AKI were associated with outcome. When forced in the final model, C3 (OR per log 0.25; 95% CI 0.01–4.66), IL-6 (OR per log 0.83; 95% CI 0.51–1.34), or ferritin (OR per log 1.63; 95% CI 0.84–3.32) were not associated with AKI and did not change the model. CONCLUSION: In conclusion, we did not find any association between complement activation or inflammatory markers and AKI. Proportion of patients with AKI during severe SARS-CoV-2 infection is higher than previously reported and associated with outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/32880774/ doi: 10.1186/s13613-020-00734-z id: cord-271944-oxtus5vb author: Joseph, Rudman title: Seizure And COVID-19: Association and Review of Potential Mechanism date: 2020-10-13 words: 2360.0 sentences: 166.0 pages: flesch: 48.0 cache: ./cache/cord-271944-oxtus5vb.txt txt: ./txt/cord-271944-oxtus5vb.txt summary: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, this highly transmissible virus has since spread rapidly around the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a novel coronavirus that causes Coronavirus Disease of 2019 (COVID19) , a disease that can present with a variety of symptoms [1] . The most common symptoms at the onset of COVID-19 illness are fever, cough, and fatigue; in severe cases, patients may develop severe pneumonia, acute respiratory distress syndrome, and organ failure [4] . This article presents a review of the current literature on seizures linked with SARS-COV 2 infection and describes possible underlying mechanisms. describes the demographic data, time to onset of neurological symptoms, diagnostic criteria, intervention, and outcomes from 11 studies of seizures associated with SARS-COV-2 infection. abstract: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, this highly transmissible virus has since spread rapidly around the world. Though respiratory complication is the primarily reported manifestation though rare, yet serious neurological complications are being frequently reported in the literature. In selected coronavirus disease-2019 (COVID-19) cases neurologic complications may manifest as seizures. In this paper, we have reviewed current literature on seizures linked with SARS- COV 2 infection including published or pre-print original articles, review articles, and case reports. We have discussed the electroencephalogram (EEG), imaging, and Cerebrospinal fluid (CSF) findings in COVID-19 patients presenting with seizure. We will be concluding the paper by briefly discussing the three possible seizure development mechanisms in patients infected with SARS- COV 2, which includes - (a) Direct Mechanism (b) Indirect Mechanism and (c) Exacerbation of Seizure in Patients with Epilepsy (PWE). Our aim is to update the physicians working with COVID-19 patients about this potential complication and hope that understanding of these proposed mechanisms can provide an opportunity for the physicians for early diagnosis or even better, help prevent this complication. url: https://www.ncbi.nlm.nih.gov/pubmed/33071468/ doi: 10.1016/j.npbr.2020.10.001 id: cord-324251-wgtatr8v author: Joshi, Madhvi title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology date: 2020-07-13 words: 608.0 sentences: 46.0 pages: flesch: 57.0 cache: ./cache/cord-324251-wgtatr8v.txt txt: ./txt/cord-324251-wgtatr8v.txt summary: title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID. Positive selection of ORF3a and 477 ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic Full-genome sequences of the first two SARS-CoV-2 485 viruses from India abstract: Humanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and >18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID. url: https://doi.org/10.1101/2020.07.10.197095 doi: 10.1101/2020.07.10.197095 id: cord-353612-9ux181xg author: Josset, Laurence title: Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus date: 2013-04-30 words: 6299.0 sentences: 303.0 pages: flesch: 49.0 cache: ./cache/cord-353612-9ux181xg.txt txt: ./txt/cord-353612-9ux181xg.txt summary: Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. In addition, several kinase inhibitors (including SB203580, LY294002, and U0126) and a glucocorticoid (dexamethasone) were also predicted to be negative regulators of genes changed similarly after SARS-CoV and HCoV-EMC infection at late times postinfection (see Table S2 in the supplemental material). Importantly, this kinase inhibitor was predicted to regulate genes that were DE similarly by SARS-CoV and HCoV-EMC at late times postinfection (see Table S2 in the supplemental material) and could therefore inhibit both viruses'' replication. abstract: A novel human coronavirus (HCoV-EMC) was recently identified in the Middle East as the causative agent of a severe acute respiratory syndrome (SARS) resembling the illness caused by SARS coronavirus (SARS-CoV). Although derived from the CoV family, the two viruses are genetically distinct and do not use the same receptor. Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. HCoV-EMC was able to replicate as efficiently as SARS-CoV in Calu-3 cells and similarly induced minimal transcriptomic changes before 12 h postinfection. Later in infection, HCoV-EMC induced a massive dysregulation of the host transcriptome, to a much greater extent than SARS-CoV. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. This could have an important impact on the ability of the host to mount an adaptive host response. A unique set of 207 genes was dysregulated early and permanently throughout infection with HCoV-EMC, and was used in a computational screen to predict potential antiviral compounds, including kinase inhibitors and glucocorticoids. Overall, HCoV-EMC and SARS-CoV elicit distinct host gene expression responses, which might impact in vivo pathogenesis and could orient therapeutic strategies against that emergent virus. url: https://doi.org/10.1128/mbio.00165-13 doi: 10.1128/mbio.00165-13 id: cord-356195-5pcaxpp9 author: Jothimani, Dinesh title: COVID-19 and Liver. date: 2020-06-15 words: 3969.0 sentences: 267.0 pages: flesch: 47.0 cache: ./cache/cord-356195-5pcaxpp9.txt txt: ./txt/cord-356195-5pcaxpp9.txt summary: Similar to SARS Co-V, Angiotensin Converting Enzyme2 (ACE2) appears to be the susceptible receptor for COVID-19 and is expressed in more than 80% of alveolar cells in the lungs. Interestingly, the level of ACE2 expression in cholangiocytes was similar to type 2 alveolar cells of the lungs, indicating that the liver could be a potential target for SARS-CoV-2. Summary of recently published studies are in described in Table 2 With the knowledge of current evidence, it is clear that elevated liver enzymes are observed predominantly severe and critical cases of COVID-19 compared to mild infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection abstract: The current pandemic coronavirus labelled as Severe Acute Respiratory Distress Syndrome Coronavirus -2 (SARS -CoV-2) is a significant public health threat over for past few weeks. Overall case fatality rates range between 2-6%; however, the rates are higher in patients with severe disease, advanced age and underlying comorbidities like diabetes, hypertension and heart disease. Recent reports showed about 2-11% of patients with COVID-19 had underlying chronic liver disease. Experience from previous SARS epidemic suggest that 60% of patients developed various degrees of liver damage. In the current pandemic, hepatic dysfunction was seen in 14-53% of patients with COVID-19, particularly in those with severe disease. Cases of acute liver injury have been reported, associated with higher mortality. Hepatic involvement in COVID-19 could be multifactorial related to any of direct cytopathic effect of the virus, uncontrolled immune reaction, sepsis or drug induced liver injury. The postulated mechanism of viral entry is through the host ACE2 receptors that are abundantly present in type 2 alveolar cells. Interestingly, the expression of ACE2 receptors were identified in the gastrointestinal tract, vascular endothelium and cholangiocytes of the liver. Liver transplant recipients with COVID-19 have been reported recently. Effects of COVID-19 on underlying chronic liver disease requires a detailed evaluation and currently data is lacking and further research is warranted in this area. With lack of definitive therapy, patient education, hand hygiene and social distancing appears to be the cornerstone in minimising the disease spread. url: https://api.elsevier.com/content/article/pii/S0168827820303779 doi: 10.1016/j.jhep.2020.06.006 id: cord-265617-e91s6xo8 author: Jouali, Farah title: SARS-CoV-2 Genome Sequence from Morocco, Obtained Using Ion AmpliSeq Technology date: 2020-07-30 words: 933.0 sentences: 55.0 pages: flesch: 55.0 cache: ./cache/cord-265617-e91s6xo8.txt txt: ./txt/cord-265617-e91s6xo8.txt summary: This study describes a genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sampled from a male patient with SARS-CoV-2 who was likely infected in Casablanca, Morocco. As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here, we present the sequence of a SARS-CoV-2 genome that was obtained from a mildly symptomatic Moroccan patient. The five patients were found to be PCR positive for SARS-CoV-2 after a real-time reverse transcriptase PCR (RT-PCR) assay using a Da An gene kit (Sun Yat-sen University, China). The SARS-CoV-2 viral genome sequencing was performed manually using the Ion AmpliSeq technology and the Ion Torrent personal genome machine (PGM). The libraries were prepared using the Ion AmpliSeq library kit version 2.0 (Life Technologies) and Ion AmpliSeq SARS-CoV-2 research assay panel according to the manufacturer''s instructions. The genome sequence was compared to the complete genome of the SARS-CoV-2 Wuhan-Hu-1 isolate using the Betacoronavirus BLAST tool and showed 99.8% similarity. abstract: This study describes a genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sampled from a male patient with SARS-CoV-2 who was likely infected in Casablanca, Morocco. url: https://www.ncbi.nlm.nih.gov/pubmed/32732235/ doi: 10.1128/mra.00690-20 id: cord-325038-q7gxw1go author: Joyce, Andrew A title: Changes in Interventional Pain Physician Decision-Making, Practice Patterns, and Mental Health During the Early Phase of the SARS-CoV-2 Global Pandemic date: 2020-08-31 words: 4519.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-325038-q7gxw1go.txt txt: ./txt/cord-325038-q7gxw1go.txt summary: The survey consisted of a series of questions assessing prepandemic physician demographics and practice patterns, as well as new beliefs and behaviors following government-based medical policy changes resulting from the SARS-CoV-2 global pandemic (Supplementary Data). Multiple linear and logistic regression models were fit to continuous and dichotomous dependent variables, respectively, with independent variables consisting of the following: age, sex, training background (primary residency), number of years since completion of training, geographic region (Northeast, Midwest, South, Northwest, and international), regional density (rural, suburban, or urban) of practice location, practice setting (private practice, academic/university, hospital system employee, or other), prepandemic clinic/ procedure volumes, and personal relationship with someone who had tested positive for SARS-CoV-2 infection (defined as a positive test for the respondent, someone they live with, a personal patient, staff member they work with, or colleague in the group). abstract: BACKGROUND AND OBJECTIVES: The novel coronavirus outbreak (SARS-CoV-2) began in late 2019 and dramatically impacted health care systems. This study aimed to describe the impact of the early phase of the pandemic on physician decision-making, practice patterns, and mental health. METHODS: An anonymous survey was distributed to physician members of the Spine Intervention Society (SIS) on March 24 and April 7, 2020. Respondents provided information regarding changes in clinical volume, treatment, and mental health (Patient Health Questionnaire [PHQ-4]) before April 10, 2020. RESULTS: Of the 1,430 individuals who opened the survey, 260 completed it (18.2%). Overall clinical and procedural volume decreased to 69.6% and 13.0% of prepandemic volume, respectively. Mean in-person clinic visits were reduced to 17.7% of total prepandemic clinic volume. Ongoing clinical visits were predominantly completed via telemedicine (video) or telephone (74.5%), rather than in-person (25.5%). Telemedicine and telephone visits represented 24.6% and 27.3% of prepandemic clinical volume, respectively. Respondents decreased in-person visits of select groups of high-risk patients by 85.8–94.6%. Significantly more providers reported increasing rather than decreasing prescriptions of the following medications: opioids (28.8% vs 6.2% of providers, P < 0.001), muscle relaxants (22.3% vs 5.4%, P < 0.001), neuropathic pain medications (29.6% vs 3.8%, P < 0.001), and acetaminophen (26.2% vs 4.2%, P < 0.001). Respondents’ mean PHQ-4 score was 3.1, with 19% reporting moderate or severe psychological distress. Several demographic factors were significantly associated with practice changes. CONCLUSIONS: The novel coronavirus pandemic dramatically altered the practice and prescribing patterns of interventional pain physicians. url: https://www.ncbi.nlm.nih.gov/pubmed/32866247/ doi: 10.1093/pm/pnaa294 id: cord-351930-puhm3w42 author: Juan, J. title: Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies date: 2020-05-06 words: 4503.0 sentences: 285.0 pages: flesch: 53.0 cache: ./cache/cord-351930-puhm3w42.txt txt: ./txt/cord-351930-puhm3w42.txt summary: . https://doi.org/10.1101/2020.05.02.20088484 doi: medRxiv preprint are fever, cough, dyspnea/shortness of breath and fatigue; third, on admission, most cases have patchy shadowing or ground-glass opacity on CT of the chest, and that normal or low leukocyte, lymphocytopenia and raised CRP are the most common laboratory findings observed in COVID-19-infected pregnant patients; fourth, the rate of severe COVID-19 pneumonia is relatively low but there are two reported maternal deaths, as of April 23, 2020; fifth, COVID-19 does not appear to increase the risk of adverse pregnancy outcomes such as preeclampsia; sixth, only a few pregnancies have resulted in a spontaneous miscarriage or abortion; seventh, of those who have delivered, the gestational age at delivery ranged from 28 to 41 weeks and the majority of cases have had Cesarean delivery; and eighth, in the case-series there have been no reported cases of neonates tested positive for SARS-CoV-2, however, in the case-reports there has been one case each with positive SARS-CoV-2 in amniotic fluid and neonatal throat swab. abstract: Objective: To perform a systematic review of available published literature on pregnancies affected by COVID-19 to evaluate the effects of COVID-19 on maternal, perinatal and neonatal outcomes. Methods: We performed a systematic review to evaluate the effects of COVID-19 on pregnancy, perinatal and neonatal outcomes. We conducted a comprehensive literature search using PubMed, EMBASE, Cochrane library, China National Knowledge Infrastructure Database and Wan Fang Data until April 20, 2020 (studies were identified through PubMed alert after April 20, 2020). For the research strategy, combinations of the following keywords and MeSH terms were used: SARS-CoV-2, COVID-19, coronavirus disease 2019, pregnancy, gestation, maternal, mothers, vertical transmission, maternal-fetal transmission, intrauterine transmission, neonates, infant, delivery. Eligibility criteria included laboratory-confirmed and/or clinically diagnosed COVID-19, patient was pregnant on admission, availability of clinical characteristics, including maternal, perinatal or neonatal outcomes. Exclusion criteria were unpublished reports, unspecified date and location of the study or suspicion of duplicate reporting, and unreported maternal or perinatal outcomes. No language restrictions were applied. Results: We identified several case-reports and case-series but only 19 studies, including a total of 266 pregnant women with COVID-19, met eligibility criteria and were finally included in the review. In the combined data from seven case-series, the maternal age ranged from 20 to 41 years and the gestational age on admission ranged from 5 to 41 weeks. The most common symptoms at presentation were fever, cough, dyspnea/shortness of breath and fatigue. The rate of severe pneumonia was relatively low, with the majority of the cases requiring intensive care unit admission. Almost all cases from the case-series had positive computer tomography chest findings. There were six and 22 cases that had nucleic-acid testing in vaginal mucus and breast milk samples, respectively, which were negative for SARS-CoV-2. Only a few cases had spontaneous miscarriage or abortion. 177 cases had delivered, of which the majority by Cesarean section. The gestational age at delivery ranged from 28 to 41 weeks. Apgar scores at 1 and 5 minutes ranged from 7 to 10 and 8 to 10, respectively. A few neonates had birthweight less than 2500 grams and over one-third of cases were transferred to neonatal intensive care unit. There was one case each of neonatal asphyxia and neonatal death. There were 113 neonates that had nucleic-acid testing in throat swab, which was negative for SARS-CoV-2. From the case-reports, two maternal deaths among pregnant women with COVID-19 were reported. Conclusions: The clinical characteristics of pregnant women with COVID-19 are similar to those of nonpregnant adults with COVID-19. Currently, there is no evidence that pregnant women with COVID-19 are more prone to develop severe pneumonia, in comparison to nonpregnant patients. The subject of vertical transmission of SARS-CoV-2 remains controversial and more data is needed to investigate this possibility. Most importantly, in order to collect meaningful pregnancy and perinatal outcome data, we urge researchers and investigators to reference previously published cases in their publications and to record such reporting when the data of a case is being entered into a registry or several registries. url: https://doi.org/10.1101/2020.05.02.20088484 doi: 10.1101/2020.05.02.20088484 id: cord-291687-kwu0otpi author: Judson, Gregory L. title: Cardiovascular Implications and Therapeutic Considerations in COVID-19 Infection date: 2020-06-13 words: 5569.0 sentences: 273.0 pages: flesch: 40.0 cache: ./cache/cord-291687-kwu0otpi.txt txt: ./txt/cord-291687-kwu0otpi.txt summary: A review of 44,672 confirmed COVID-19 cases from Wuhan, China, demonstrated increased mortality in patients with cardiovascular disease (10.5%), diabetes (7.3%), and hypertension (6%), which was significantly higher than the overall case-fatality rate of 2.3% [22] . These initial cases series have shown a similar relationship between underlying cardiac comorbidities with a higher prevalence of hypertension, diabetes, coronary artery disease, and obesity in patients requiring mechanical ventilation [24] . Early studies reported a prevalence of acute cardiac injury of 12% in the entire cohort as defined by either high sensitivity troponin (Hs Tn) or the MB fraction of creatinine kinase (CK-MB) [ 99 th percentile or new echocardiographic or electrocardiographic abnormalities with greater elevations in cardiac biomarkers among patients requiring ICU care [1, 20] . Case cohort studies included data in patients for whom the outcome and illness course helped further elucidate the role of cardiac injury in COVID-19 disease. abstract: The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has profoundly impacted all fields of medicine. Infection with SARS-CoV-2 and the resulting coronavirus of 2019 (COVID-19) syndrome has multiorgan effects. The pandemic has united researchers from bench to bedside in attempts to understand the pathophysiology of the disease and define optimal treatment strategies. Cardiovascular disease is highly prevalent and a leading cause of death across gender, race, and ethnic groups. As the pandemic spreads, there is increasing concern about the cardiovascular effects of the viral infection and the interaction of infection with existing cardiovascular disease. Additionally, there are concerns about the cardiac effects of the numerous treatment agents under study. It will be essential for cardiologists to understand the interplay between underlying cardiac comorbidities, acute cardiovascular effects of COVID-19 disease, and adverse effects of new treatments. Here we describe emerging evidence of the epidemiology of SARS-CoV-2 infection and underlying cardiovascular disease, the evidence for direct myocardial injury in SARS-CoV-2 infection, the specific presentations of cardiovascular involvement by SARS-CoV-2, and the cardiac effects of emerging treatments. url: https://doi.org/10.1007/s40119-020-00184-5 doi: 10.1007/s40119-020-00184-5 id: cord-328587-vctvcyim author: Jun, Sun title: The hypothesis that SARS-CoV-2 affects male reproductive ability by regulating autophagy date: 2020-07-10 words: 2990.0 sentences: 143.0 pages: flesch: 47.0 cache: ./cache/cord-328587-vctvcyim.txt txt: ./txt/cord-328587-vctvcyim.txt summary: According to the existing clinical data, some patients not only suffer from respiratory diseases, but also have complications such as acute renal injury and even renal necrosis [2] [3] [4] , in addition, SARS-CoV-2 was also found in recent semen analysis of male patients [5] . Previous clinical data have shown that in addition to respiratory diseases, some male patients with COVID-19 are accompanied by kidney damage and even renal failure [2] [4], which suggest that SARS-CoV-2 may affect male fertility. Furthermore, clinical data also show that the receptor protein ACE2 that mediates the entry of SARS-CoV-2 into host cells is not only expressed in alveolar cells, but also highly expressed in male renal tubular cells [4] [21] [30] .All these suggest that SARS-CoV-2 not only causes damage to the respiratory system of patients, but also has a certain impact on the reproductive system of male patients. abstract: The outbreak of CoronaVirus Disease19 (COVID19) in December 2019 posed a serious threat to public safety, and its rapid spread caused a global health emergency. Clinical data show that in addition to respiratory system damage, some male patients with COVID-19 are also accompanied by abnormal renal function and even renal damage. As the main receptor of syndrome coronavirus 2 (SARS-CoV-2), angiotensin converting enzyme 2 (ACE2) is also found to be highly expressed not only in respiratory mucosa and alveolar epithelial cells, but also in renal tubule cells, testicular Leydig cells and seminiferous tubule cells. This suggests that SARS-CoV-2 has the possibility of infecting the male reproductive system, and the recent detection of SARS-CoV-2 in the patient's semen further confirms this theory. In previous studies, it has been found that ACE2 has the ability to regulate autophagy. Not only that, recent studies have also found that SARS-CoV-2 infection can also lead to a reduction in autophagy. All of these associate SARS-CoV-2 with autophagy. Furthermore, autophagy has been shown to have an effect on male reproduction in many studies. Based on these, we propose the hypothesis that SARS-CoV-2 affects male reproductive function by regulating autophagy. This hypothesis may provide a new idea for future treatment of COVID-19 male patients with reproductive function injury, and it can also prompt medical staff and patients to consciously check their reproductive function. url: https://doi.org/10.1016/j.mehy.2020.110083 doi: 10.1016/j.mehy.2020.110083 id: cord-014878-n6a9cq47 author: Jun-yi, Ma title: The characteristics and dynamic changes of X-ray chest film in 50 patients with severe acute respiratory syndrome date: 2003 words: 1386.0 sentences: 68.0 pages: flesch: 61.0 cache: ./cache/cord-014878-n6a9cq47.txt txt: ./txt/cord-014878-n6a9cq47.txt summary: The characteristics and dynamic changes of chest film in 50 SARS patients in Hebei Province were analysed by the authors and reported as follows. X-ray chest films of all the patients taken every 2--3 days in the hospitalized period were collected and those with significant changes were analysed. Because there lacks definite epidemiological contacting history in part of the patients, the disease shows no specificity in clinical manifestation and blood cell examination, and the therapeutic effect could give no help to diagnosis, it is of vital importance in clinical practice to decide whether there is lesion occurring in the lung through X-ray chest film examination for early diagnosis of SARS. The figure of chest film of SARS patients is characterized as follows: ( 1 ) Lesions often oc-curred at the lower field and outer zone of the lung; (2) Lesions are mostly multiply presented; Characteristics of X-ray chest film figure in patients with SARS abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089298/ doi: 10.1007/bf02838621 id: cord-285162-srkd3wh0 author: Jung, F. title: How we should respond to the Coronavirus SARS-CoV-2 outbreak: A German perspective date: 2020-06-05 words: 4634.0 sentences: 256.0 pages: flesch: 61.0 cache: ./cache/cord-285162-srkd3wh0.txt txt: ./txt/cord-285162-srkd3wh0.txt summary: Figure 1 shows that until March 20 (day 80), the daily cases of new confirmed infections increased with doubling times between 1-5 days, showing a strong exponential rise of positive tests for SARS-CoV-2 infections in Germany. Common elements of these Asian states were the immediate action of governments to implement certain social distancing strategies and the wearing of face masks in public to reduce the number of new cases, which has proven to be effective to prevent transmission from infected individuals [15] . This led to a longer phase of exponential growth of SARS-CoV-2 infections and deaths in Germany, France and Italy and caused cumulative case numbers to grow significantly higher in comparison to the East-Asian countries (Fig. 2) . Until the end of March (day 91), Japan, however, has managed to stabilize these at under 5,000 confirmed cases, while Germany had almost 71,000 and France almost 52,000 confirmed SARS-Cov-2 infections. abstract: BACKGROUND: In the early phase of the COVID-19 pandemic Germany missed to set up efficient containment measures. Consequently, the number of cases increased exponentially until a lockdown was implemented to suppress the spread of SARS-CoV-2. Fortunately, Germany has a high capability for coronavirus lab testing and more than 30,000 ICU beds. These capabilities and the lockdown turned out to be an advantage to combat the pandemic and to prevent a health-system overload. AIM: The aim was to predict the plateau day of SARS-CoV-2 infections or deaths. RESULTS: The effect on the viral spread of the German measures taken and the impact on the peak of new infection cases is shown. By normalizing daily case numbers, the plateau day of the current outbreak in Germany could be calculated to be reached at April 12, 2020 (day 103 of 2020). CONCLUSION: Normalized case number curves are helpful to predict the time point at which no further new infections will occur if the epidemic situation remains stable. Upon reaching the plateau day during a lockdown phase, a residual time-period of about 2-3 weeks can be utilized to prepare a safe unlocking period. As can be learned from Asian countries such as South Korea and Taiwan there must be strict rules to keep the risk of infection low. Those include social distancing, face mask wearing in combination with digital contact tracing and serosurveillance studies. Following those rules, a safe dance around the infection curve allows to keep the population at a reduced infection rate. url: https://www.ncbi.nlm.nih.gov/pubmed/32390611/ doi: 10.3233/ch-209004 id: cord-296319-fwn97wds author: Juno, J. A. title: Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19 date: 2020-05-21 words: 5331.0 sentences: 383.0 pages: flesch: 59.0 cache: ./cache/cord-296319-fwn97wds.txt txt: ./txt/cord-296319-fwn97wds.txt summary: In 139 summary, antibody responses against both S and the RBD are consistently elicited in 140 SARS-CoV-2 infected individuals, the endpoints titres of which correlate significantly 141 with neutralising activity (r=0.55 and r=0.61 respectively) and ACE2 binding 142 inhibition (r=0.72 and r=0.72 respectively) in the plasma ( Figure S2) . 143 144 B cell responses to S antigens following SARS-CoV-2 infection 145 We next examined the frequency and specificity of class-switched B cells in 146 convalescent subjects using SARS-CoV-2 spike or RBD proteins as flow cytometric 147 probes. Clear antigen-specific populations of CD19 + IgD -B cells (gating in Figure S3 ) 148 binding spike, spike and RBD or RBD alone could be resolved in our cohort of 149 recovered from SARS-CoV-2 subjects, with minimal background staining in 150 uninfected controls (Figure 2A ; Figure S4 ). abstract: The rapid global spread of SARS-CoV-2 and resultant mortality and social disruption have highlighted the need to better understand coronavirus immunity to expedite vaccine development efforts. Multiple candidate vaccines, designed to elicit protective neutralising antibodies targeting the viral spike glycoprotein, are rapidly advancing to clinical trial. However, the immunogenic properties of the spike protein in humans are unresolved. To address this, we undertook an in-depth characterisation of humoral and cellular immunity against SARS-CoV-2 spike in humans following mild to moderate SARS-CoV-2 infection. We find serological antibody responses against spike are routinely elicited by infection and correlate with plasma neutralising activity and capacity to block ACE2/RBD interaction. Expanded populations of spike-specific memory B cells and circulating T follicular helper cells (cTFH) were detected within convalescent donors, while responses to the receptor binding domain (RBD) constitute a minor fraction. Using regression analysis, we find high plasma neutralisation activity was associated with increased spike-specific antibody, but notably also with the relative distribution of spike-specific cTFH subsets. Thus both qualitative and quantitative features of B and T cell immunity to spike constitute informative biomarkers of the protective potential of novel SARS-CoV-2 vaccines. url: http://medrxiv.org/cgi/content/short/2020.05.17.20104869v1?rss=1 doi: 10.1101/2020.05.17.20104869 id: cord-258084-nkr3lrov author: Juthani, Prerak title: Coronavirus Disease 2019 (COVID-19) Manifestation as Acute Myocardial Infarction in a Young, Healthy Male date: 2020-07-11 words: 1753.0 sentences: 91.0 pages: flesch: 48.0 cache: ./cache/cord-258084-nkr3lrov.txt txt: ./txt/cord-258084-nkr3lrov.txt summary: In this case report, we describe a 29-year-old nonobese hospital food service associate who presented with diffuse abdominal and chest pain; he was found to be positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significantly elevated levels of troponin T and multiple acute phase reactants; his EKG demonstrated ST-elevations consistent with anterolateral infarction. In this case report, we discuss a young patient who tested positive for SARS-CoV-2 and subsequently developed significant cardiovascular complications. We believe that this case is unique because this was a young, athletic patient with minimal risk factors for coronary disease who tested positive for COVID-19 and developed an acute MI with STEMI and required stent placement. It is a reminder to us that cardiovascular complications must be considered in the COVID-19 population, even in those patients with minimal risk factors for heart disease. abstract: Although a large part of the symptomology of coronavirus disease 2019 (COVID-19) has been attributed to its effects in the lungs, the virus has also been shown to cause extensive cardiovascular complications in a small subset of patients. In this case report, we describe a 29-year-old nonobese hospital food service associate who presented with diffuse abdominal and chest pain; he was found to be positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significantly elevated levels of troponin T and multiple acute phase reactants; his EKG demonstrated ST-elevations consistent with anterolateral infarction. Despite having no significant past medical history or atherosclerotic risk factors, he was found to have a complete occlusion of his left anterior descending artery that required cardiac catheterization. This case demonstrates that cardiovascular complications must be considered in the COVID-19 population, even without the clear presence of other risk factors for heart disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32724685/ doi: 10.1155/2020/8864985 id: cord-338923-hc7gagnq author: Jääskeläinen, AJ title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation date: 2020-06-15 words: 2101.0 sentences: 131.0 pages: flesch: 53.0 cache: ./cache/cord-338923-hc7gagnq.txt txt: ./txt/cord-338923-hc7gagnq.txt summary: We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). In this study, we assessed the specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 antibodies, including two rapid lateral flow tests, in comparison with a neutralisation test. abstract: There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel (N=70) included sera from PCR confirmed COVID-19 patients, and the negative panel (N=81) included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS- CoV-2 serodiagnostics. url: https://www.sciencedirect.com/science/article/pii/S1386653220302547?v=s5 doi: 10.1016/j.jcv.2020.104512 id: cord-279132-florvm7z author: K., Branimir title: From apparent to true – from frequency to distributions (II) date: 2020-08-17 words: 2390.0 sentences: 113.0 pages: flesch: 45.0 cache: ./cache/cord-279132-florvm7z.txt txt: ./txt/cord-279132-florvm7z.txt summary: According to Roda et al (2) , one of the main reasons for the variability in predicting the COVID-19 epidemic is the lack of data on the actual dynamics of the infection spread, which results in so-called nonidentifiability in model calibration. The authors determined the model parameters using the Bayesian approach and Markov chain Monte Carlo, and concluded that the COVID-19 epidemics in Wuhan and Seattle had likely been spreading for several weeks before they became apparent and were far more extensive than initially reported. Feroze (7) used Bayesian structural time series models to investigate the pattern of SARS-CoV-2 spread in India, Brazil, USA, Russia, and the UK between March 1 and June 29, 2020 to assess the impact of mitigation measures and predict the dynamics of the epidemic over the next 30 days. Dehning et al (9) used the SIR epidemiological model framework in combination with Bayesian inference to analyze the effective growth rate of the number of new cases over time. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32881438/ doi: 10.3325/cmj.2020.61.381 id: cord-341524-zvic4xc9 author: KARAKURT, Hamza Umut title: Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks date: 2020-06-21 words: 3611.0 sentences: 192.0 pages: flesch: 45.0 cache: ./cache/cord-341524-zvic4xc9.txt txt: ./txt/cord-341524-zvic4xc9.txt summary: We analysed transcriptome of SARS-CoV-2 infected human lung epithelial cells, compared it with mock-infected cells, used network-based reporter metabolite approach and integrated the transcriptome data with protein-protein interaction network to elucidate the early cellular response. The response in signalling pathways, gene expression, protein levels and metabolic profiles are regulated as a result of interactions in multilayer biological networks, hence a holistic view of the cellular response can be elucidated by an integrated approach. Here, we provide an analysis of transcriptional response after 24 h of infection, further, we integrated transcriptome profile with metabolic and protein-protein interaction networks to reveal multilayer mechanistic details of the SARS-CoV-2 infection in NHBE cells. Significant upregulation in expression of matrix metalloproteinase 9 (MMP9) in NHBE cells indicates that drugs which target MMP9 have potential uses in SARS-CoV-2 infection. This complex network structure between signalling pathways indicated that RAGE receptor targeting drugs have the potential to be used in SARS-CoV-2 patients to suppress symptoms. abstract: A novel coronavirus (SARS-CoV-2, formerly known as nCoV-2019) that causes an acute respiratory disease has emerged in Wuhan, China and spread globally in early 2020. On January the 30th, the World Health Organization (WHO) declared spread of this virus as an epidemic and a public health emergency. With its highly contagious characteristic and long incubation time, confinement of SARS-CoV-2 requires drastic lock-down measures to be taken and therefore early diagnosis is crucial. We analysed transcriptome of SARS-CoV-2 infected human lung epithelial cells, compared it with mock-infected cells, used network-based reporter metabolite approach and integrated the transcriptome data with protein-protein interaction network to elucidate the early cellular response. Significantly affected metabolites have the potential to be used in diagnostics while pathways of protein clusters have the potential to be used as targets for supportive or novel therapeutic approaches. Our results are in accordance with the literature on response of IL6 family of cytokines and their importance, in addition, we find that matrix metalloproteinase 2 (MMP2) and matrix metalloproteinase 9 (MMP9) with keratan sulfate synthesis pathway may play a key role in the infection. We hypothesize that MMP9 inhibitors have potential to prevent "cytokine storm" in severely affected patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32595353/ doi: 10.3906/biy-2005-115 id: cord-291552-qv6koo6g author: KWAN, AMBROSE CHI‐PONG title: Severe acute respiratory syndrome‐related diarrhea date: 2005-02-23 words: 2840.0 sentences: 189.0 pages: flesch: 65.0 cache: ./cache/cord-291552-qv6koo6g.txt txt: ./txt/cord-291552-qv6koo6g.txt summary: Background: Severe acute respiratory syndrome (SARS) is an emerging infectious disease and diarrhea has been reported in up to 76% of cases. The purpose of the present paper was to carry out a retrospective study of the clinical and demographic data of SARS patients with diarrhea in Princess Margaret Hospital. Patient data, need of ventilatory care, survival, number of bowel movements per day, total potassium supplement, lowest serum potassium and lowest serum albumin level were retrieved from the records and entered into a database for further analysis. described the clinical course of 75 patients in United Christian Hospital in Hong Kong and reported that 73% had watery diarrhea 7.5 ± 2.3 days after the onset of symptoms. We noted that female patients and residents of Amoy Gardens Estate were associated with diarrhea, and loglinear analysis showed that there was no significant interaction between these two factors. Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens abstract: Background: Severe acute respiratory syndrome (SARS) is an emerging infectious disease and diarrhea has been reported in up to 76% of cases. The purpose of the present paper was to carry out a retrospective study of the clinical and demographic data of SARS patients with diarrhea in Princess Margaret Hospital. Methods: From 1 to 31 March 2003, hospital records from 240 patients with confirmed SARS were studied. Patients with watery stool of ≥3 times/day for at least 3 consecutive days were defined as the diarrhea group. Clinical and demographic data were compared between the diarrhea and non‐diarrhea groups. Chest X‐ray (CXR) scores during the peak of diarrhea period were recorded by a respiratory physician. These CXR scores were correlated with the peak frequency of diarrhea by Spearman's correlation coefficient. Results: Diarrhea occurred in 20.4% of patients after admission. Female patients were predominant with a female to male ratio of 6:1 (P < 0.001) and 69.4% of patients were living in Amoy Gardens Estate (P = 0.01). The proportions of patients requiring ventilatory care and mortality in the diarrhea group were 8.2% and 2%, respectively, which were significantly lower than those in the non‐diarrhea group (27.6% and 16.2%, P < 0.005). The CXR scores during the peak of diarrhea were not correlated with the maximum frequency of diarrhea (r = −0.09, P = 0.5). Conclusions: A total of 20.4% of SARS patients had the complication of diarrhea after hospital admission. Both female sex and being a resident of Amoy Gardens Estate were associated with diarrhea. The diarrhea group had a better prognosis. url: https://www.ncbi.nlm.nih.gov/pubmed/15836711/ doi: 10.1111/j.1440-1746.2005.03775.x id: cord-288017-f9b3t0ts author: Kabeerdoss, Jayakanthan title: Understanding immunopathological fallout of human coronavirus infections including COVID‐19: Will they cross the path of rheumatologists? date: 2020-08-10 words: 4281.0 sentences: 280.0 pages: flesch: 46.0 cache: ./cache/cord-288017-f9b3t0ts.txt txt: ./txt/cord-288017-f9b3t0ts.txt summary: High risks for fatal disease in COVID‐19 include older age, metabolic syndrome, male gender, and individuals who develop delayed type I IFN response. 54 In a macaque model of SARS-CoV infection too, aged macaques had more severe lung pathology, lower expression of type I IFN and higher expression of pro-inflammatory cytokines as compared to younger macaques. 80 to patients with COVID-19 that it is a mild immunomodulatory F I G U R E 2 Hydroxychloroquine (HCQ) inhibits SARS-CoV-2 entry and inhibits virus-induced type I interferon (IFN) signaling and proinflammatory cytokines production. While male gender, older age and people with metabolic syndrome seem to be at a higher risk of contracting more severe SARS-CoV-2 infection, younger females of African and Asian ancestry have higher risk for developing SLE; male gender among lupus patients, however, is an independent risk factor for severe disease. Evasion by stealth: inefficient immune activation underlies poor T cell response and severe disease in SARS-CoV-infected mice abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection causing coronavirus disease 2019 (COVID‐19) is the biggest pandemic of our lifetime to date. No effective treatment is yet in sight for this catastrophic illness. Several antiviral agents and vaccines are in clinical trials, and drug repurposings as immediate and alternative choices are also under consideration. Immunomodulatory agents like hydroxychloroquine (HCQ) as well as biological disease‐modifying anti‐rheumatic drugs (bDMARDs) such as tocilizumab and anakinra received worldwide attention for treatment of critical patients with COVID‐19. This is of interest to rheumatologists, who are well versed with rational use of these agents. This brief review addresses the understandings of some of the common immunopathogenetic mechanisms in the context of autoimmune rheumatic diseases like systemic lupus erythematosus (SLE) and COVID‐19. Apart from demographic comparisons, the role of type I interferons (IFN), presence of antiphospholipid antibodies and finally mechanism of action of HCQ in both the scenarios are discussed here. High risks for fatal disease in COVID‐19 include older age, metabolic syndrome, male gender, and individuals who develop delayed type I IFN response. HCQ acts by different mechanisms including prevention of cellular entry of SARS‐CoV‐2 and inhibition of type I IFN signaling. Recent controversies regarding efficacy of HCQ in management of COVID‐19 warrant more studies in that direction. Autoantibodies were also reported in severe acute respiratory syndrome (SARS) as well as in COVID‐19. Rheumatologists need to wait and see whether SARS‐CoV‐2 infection triggers development of autoimmunity in patients with COVID‐19 infection in the long run. url: https://doi.org/10.1111/1756-185x.13909 doi: 10.1111/1756-185x.13909 id: cord-294800-akr4f5p8 author: Kabir, Md. Tanvir title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 words: 14084.0 sentences: 700.0 pages: flesch: 44.0 cache: ./cache/cord-294800-akr4f5p8.txt txt: ./txt/cord-294800-akr4f5p8.txt summary: They also summarized that as viral load is quite high during the time of hospital admissions, use of potent antiviral agents at an early stage might prove Abbreviations: ACE2, angiotensin converting enzyme 2; AP, antigen presentation; APCs, antigen presentation cells; APN, aminopeptidase N, ARBs, angiotensin II receptor blockers; ARDS, acute respiratory distress syndrome; CDC, Centers for Disease Control; nCOVID-19, novel coronavirus disease 2019; CoVs, coronaviruses; DPP4, dipeptidyl peptidase 4; dsRNA, double-strand RNA; EC 50 , half maximal effective concentration; ED, emergency department; ELISA, enzymelinked immunosorbent assay; EUA, emergency use authorization; FDA, Food and Drug Administration; GGO, ground-glass opacity; HCV, hepatitis C virus; HIV, human immunodeficiency virus;, MHC, major histocompatibility complex; or HLA, human leukocyte antigen; ICU, intensive care unit; IL-6, interleukin 6; LPV/r, lopinavir/ritonavir; mAbs, monoclonal antibodies; MERS, Middle East respiratory syndrome; N7-MTase, N7-methyltransferase; NSAIDs, nonsteroidal anti-inflammatory drugs; PRRs, pattern recognition receptors; PUI, patient under investigation; RdRp, RNA-dependent RNA polymerase; RSV, respiratory syncytial virus; S protein, spike protein; SAM, S-adenosyl-methionine; SARS, severe acute respiratory syndrome; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; WHO, World Health Organization. abstract: In December 2019, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related epidemic was first observed in Wuhan, China. In 2020, owing to the highly infectious and deadly nature of the virus, this widespread novel coronavirus disease 2019 (nCOVID-19) became a worldwide pandemic. Studies have revealed that various environmental factors including temperature, humidity, and air pollution may also affect the transmission pattern of COVID-19. Unfortunately, still, there is no specific drug that has been validated in large-scale studies to treat patients with confirmed nCOVID-19. However, remdesivir, an inhibitor of RNA-dependent RNA polymerase (RdRp), has appeared as an auspicious antiviral drug. Currently, a large-scale study on remdesivir (i.e., 200 mg on first day, then 100 mg once/day) is ongoing to evaluate its clinical efficacy to treat nCOVID-19. Good antiviral activity against SARS-CoV-2 was not observed with the use of lopinavir/ritonavir (LPV/r). Nonetheless, the combination of umifenovir and LPV/r was found to have better antiviral activity. Furthermore, a combination of hydroxychloroquine (i.e., 200 mg 3 times/day) and azithromycin (i.e., 500 mg on first day, then 250 mg/day from day 2–5) also exhibited good activity. Currently, there are also ongoing studies to evaluate the efficacy of teicoplanin and monoclonal and polyclonal antibodies against SARS-CoV-2. Thus, in this article, we have analyzed the genetic diversity and molecular pathogenesis of nCOVID-19. We also present possible therapeutic options for nCOVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32754599/ doi: 10.3389/fcell.2020.00616 id: cord-353072-n92atcrx author: Kadkhoda, Kamran title: COVID-19: an Immunopathological View date: 2020-04-22 words: 2045.0 sentences: 107.0 pages: flesch: 45.0 cache: ./cache/cord-353072-n92atcrx.txt txt: ./txt/cord-353072-n92atcrx.txt summary: Unravelling these mechanisms can assist basic scientists, laboratory medicine practitioners, clinicians, public health practitioners, funding agencies, and health care policymakers in responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This is consistent with high-level surface expression of angiotensin-converting enzyme 2 (ACE2), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, on pneumocytes (2) . In the context of COVID-19, since ACE2 is highly expressed in the gastrointestinal (GI) tract (9), shedding the virus in the stool is prolonged (10); however, diarrhea is uncommon likely because virus-specific effector memory T cells typically home to the mucosal surfaces they had previously encountered with an infection with a common CoV, i.e., upper and lower respiratory tract. It has recently been shown that SARS-CoV and the Middle East respiratory syndrome (MERS)-CoV take advantage of non-or subneutralizing antibodies and enter cells via surface CD32a receptors (Trojan horse mechanism) (11, 12) . abstract: Since its emergence in December 2019, it took only a couple of months for an outbreak of the novel coronavirus disease 2019 (COVID-19) to be declared a pandemic by the World Health Organization (WHO). This along with the highly infectious nature of the disease and the associated mortality call for particular attention to the underlying (immuno)pathomechanism(s). The latter will inform case management and vaccine design. Unravelling these mechanisms can assist basic scientists, laboratory medicine practitioners, clinicians, public health practitioners, funding agencies, and health care policymakers in responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32321823/ doi: 10.1128/msphere.00344-20 id: cord-311905-4yu29b49 author: Kakoulidis, Ioannis title: SARS-CoV-2 infection and glucose homeostasis in pregnancy. What about antenatal corticosteroids? date: 2020-05-06 words: 1084.0 sentences: 69.0 pages: flesch: 40.0 cache: ./cache/cord-311905-4yu29b49.txt txt: ./txt/cord-311905-4yu29b49.txt summary: METHODS: We performed a literature search on PubMed, regarding the use of corticosteroids in patients with SARS-CoV-2 infection, in pregnancies complicated by SARS-CoV-2, as well as their impact on glycemia in pregnant women with or without diabetes. While the healthcare community worldwide struggles to manage the novel SARS-CoV-2 (Severe Acute Respiratory Coronavirus 2; Covid-19) pandemic, it is of great importance to ensure that optimal care continues to be given to special groups of patients such as pregnant women. Therefore, extreme caution should be given, regarding the use of antenatal corticosteroids, in case of pregnant women with SARS-CoV-2 requiring preterm delivery [1, 3, 4, 16] . Since there are few small studies in the 6 literature regarding the management of pregnant women with SARS-CoV-2 (and possibly lacking reliable conclusions), the decision about the use of antenatal corticosteroids should be carefully made in consultation with infectious disease specialists, obstetricians and neonatologists [4, 16] . Timedependent changes in insulin requirement for maternal glycemic control during antenatal corticosteroid therapy in women with gestational diabetes: a retrospective study abstract: BACKGROUND AND AIMS: Administration of corticosteroids is common in obstetric practice. In this concise review we queried on the effects of corticosteroids in pregnancies complicated by SARS-CoV-2. METHODS: We performed a literature search on PubMed, regarding the use of corticosteroids in patients with SARS-CoV-2 infection, in pregnancies complicated by SARS-CoV-2, as well as their impact on glycemia in pregnant women with or without diabetes. Furthermore, we searched for effects of SARS-CoV-2 and of other coronaviridae on insulin secretion and glycemia. RESULTS: SARS-CoV-2 infection appears to be a risk factor for complications in pregnancy. Corticosteroids may not be recommended for treating SARS-CoV-2 pneumonia but they may be needed for at-risk pregnancies. Corticosteroids in pregnancy have a diabetogenic potential. SARS-CoV-2 and other coronaviridae may have effects on glycemia. CONCLUSIONS: Caution should be exercised while using corticosteroids in pregnant women with COVID-19 requiring preterm delivery. url: https://doi.org/10.1016/j.dsx.2020.04.045 doi: 10.1016/j.dsx.2020.04.045 id: cord-350505-uh8r2vyz author: Kalantar-Zadeh, Kourosh title: Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles date: 2020-05-01 words: 2343.0 sentences: 145.0 pages: flesch: 38.0 cache: ./cache/cord-350505-uh8r2vyz.txt txt: ./txt/cord-350505-uh8r2vyz.txt summary: [Image: see text] The impact of dietary patterns and the commensal microbiome on susceptibility to and severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has been largely ignored to date. 2 Therefore, the elucidation of host cytokine molecular pathways and microbiota components 17 as well as bacterial reactions in association with cytokine responses may provide novel microbiome-based therapeutic approaches to SARS-CoV-2 infection. Considering the presented discussion, nutritional and dietary strategies directed at restoring the well-known beneficial microbiota, which can possibly suppress viral infection in the elderly and those with underlying health problems, may be an effective strategy to mitigate the harmful effects of this virus. One approach, as a whole and to be undertaken prior to any viral infection, could include strengthening the intestinal barrier against pathogens, increasing intestinal motility, and reducing an underlying pro-inflammatory state by adopting a Many different direct or indirect microbiome pathways could contribute to SARS-CoV-2-gut interactions. abstract: [Image: see text] The impact of dietary patterns and the commensal microbiome on susceptibility to and severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has been largely ignored to date. In this Perspective, we present a rationale for an urgent need to investigate this possible impact and therapeutic options for COVID-19 based on dietary and microbiome modifications. The mitigating role of nanotechnology with relation to the impact of SARS-CoV-2 virus is highlighted. url: https://www.ncbi.nlm.nih.gov/pubmed/32356654/ doi: 10.1021/acsnano.0c03402 id: cord-257611-z0sng9sx author: Kalantari, Hamidreza title: Determination of COVID-19 prevalence with regards to age range of patients referring to the hospitals located in western Tehran, Iran date: 2020-10-07 words: 2796.0 sentences: 148.0 pages: flesch: 61.0 cache: ./cache/cord-257611-z0sng9sx.txt txt: ./txt/cord-257611-z0sng9sx.txt summary: We decided to examine suspected samples of pneumonia outbreak caused by the new coronavirus SARS-CoV-2 and provide information about the mortality rate due to this infection in different age groups in Iran. In this descriptive-cross-sectional study, a total of 784 samples of naso/oropharyngeal swabs of suspected patients with COVID-19 symptoms who had referred to Imam Khomeini, Shahid Fayaz-Bakhsh and Modarres hospitals in Tehran from February 24, 2020 to March 24, 2020 were examined by RT-PCR method. Therefore, in this study, we aimed at targeting these three genes using real-time RT-PCR method to examine suspected samples of COVID-19 and to determine the mortality rate due to this infection in different age groups in Iran. This was in accordance with the results of the present study, in which the highest number of deaths and positive cases were reported in people in the age group of >70 years. abstract: We decided to examine suspected samples of pneumonia outbreak caused by the new coronavirus SARS-CoV-2 and provide information about the mortality rate due to this infection in different age groups in Iran. In this descriptive-cross-sectional study, a total of 784 samples of naso/oropharyngeal swabs of suspected patients with COVID-19 symptoms who had referred to Imam Khomeini, Shahid Fayaz-Bakhsh and Modarres hospitals in Tehran from February 24, 2020 to March 24, 2020 were examined by RT-PCR method. The highest incidence of the disease was within the age group of 50–59 years, while the lowest rate was in the 0–9 years age group. The highest rate of positive samples in terms of COVID-19 among suspected individuals was for patients >80 years of age (89%) and the highest mortality rate was in the age range of 70–79 years (31%) and >80 years (30), respectively. In terms of recovery, the highest rate was in the 30–39 years age group (65.2%). Statistical analysis showed that mortality significantly increased in the age group of >60 years old and in fact, mortality was significantly associated with older ages. According to the results of the current study, the prevalence of COVID-19 in lower age (0–9 years old) is lower and mortality rate is higher in older ages as significant increase in mortality was observed in those aged >60 years old. However, further epidemiological studies on a larger study population in different regions of Iran are needed to explain the prevalence, clinical features, and course of the disease. url: https://www.sciencedirect.com/science/article/pii/S2452014420303241?v=s5 doi: 10.1016/j.genrep.2020.100910 id: cord-306438-db2rqz4d author: Kalathiya, Umesh title: Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date: 2020-05-14 words: 6921.0 sentences: 354.0 pages: flesch: 49.0 cache: ./cache/cord-306438-db2rqz4d.txt txt: ./txt/cord-306438-db2rqz4d.txt summary: An important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. These findings identify a novel small molecule binding-site formed by the spike protein oligomer, that might assist in future drug discovery programs aimed at targeting the coronavirus (CoV) family of viruses. Our current study focuses on understanding the variability of the trimer spike glycoprotein in SARS-CoV-2 with respect to the genomes from other coronavirus strains, and identifying the changes in the molecular properties due to conformational flexibility in the spike protein. Our data suggest a mechanism whereby Chitosan (and possibly its derivatives), as well as macrolide type molecules, might bind to a pocket formed by the spike protein trimer and provide a novel domain to focus on for future drug discovery projects. abstract: An important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular dynamics (MD) simulation. The findings indicated that S2 subunit (heptad-repeat 1 (HR1), central helix (CH), and connector domain (CD) domains) showed low variability, low fluctuations in MD, and displayed a trimer cavity. By contrast, the receptor binding domain (RBD) domain, which is typically targeted in drug discovery programs, exhibits more sequence variability and flexibility. Interpretations from MD simulations suggest that the monomer form of spike protein is in constant motion showing transitions between an “up” and “down” state. In addition, the trimer cavity may function as a “bouncing spring” that may facilitate the homotrimer spike protein interactions with the ACE2 receptor. The feasibility of the trimer cavity as a potential drug target was examined by structure based virtual screening. Several hits were identified that have already been validated or suggested to inhibit the SARS-CoV-2 virus in published cell models. In particular, the data suggest an action mechanism for molecules including Chitosan and macrolides such as the mTOR (mammalian target of Rapamycin) pathway inhibitor Rapamycin. These findings identify a novel small molecule binding-site formed by the spike protein oligomer, that might assist in future drug discovery programs aimed at targeting the coronavirus (CoV) family of viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32422996/ doi: 10.3390/jcm9051473 id: cord-301876-d2j9wpqk author: Kalita, Parismita title: Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2 date: 2020-05-04 words: 3449.0 sentences: 212.0 pages: flesch: 49.0 cache: ./cache/cord-301876-d2j9wpqk.txt txt: ./txt/cord-301876-d2j9wpqk.txt summary: Few groups have designed subunit vaccines against SARS-CoV-2; however, their workflow involved either use of single protein for vaccine design [24, 25] or used only CTL epitopes without considering the importance of B-cell or HTL epitopes [26] . B-cell epitopes for the screened SARS-CoV-2 proteins were predicted using the ABCPred server (http://crdd.osdd.net/raghava/abcpred/). A total of 6 HTLs, 18 CTLs, and 9 B-cell epitopes derived from the three proteins were used to design the subunit vaccine (566 amino acid residues) against SARS-CoV-2 (Supplementary Figure 1) . Based on extensive bioinformatics analysis, we used three proteins to design a multi-epitope subunit vaccine against novel coronavirus SARS-CoV-2. Computational studies suggest that our multi-epitope based subunit vaccine has a probability of showing good protective efficacy and safety against SARS-CoV-2 infection in humans. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach abstract: Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan, China, and has subsequently spread worldwide. In the absence of any antiviral or immunomodulatory therapies, the disease is spreading at an alarming rate. A possibility of a resurgence of COVID-19 in places where lockdowns have already worked is also developing. Thus, for controlling COVID-19, vaccines may be a better option than drugs. An mRNA-based anti-COVID-19 candidate vaccine has entered a phase 1 clinical trial. However, its efficacy and potency have to be evaluated and validated. Since vaccines have high failure rates, as an alternative, we are presenting a new, designed multi-peptide subunit-based epitope vaccine against COVID-19. The recombinant vaccine construct comprises an adjuvant, cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes joined by linkers. The computational data suggest that the vaccine is non-toxic, non-allergenic, thermostable, with the capability to elicit a humoral and cell-mediated immune response. The stabilization of the vaccine construct is validated with molecular dynamics simulation studies. This unique vaccine is made up of 33 highly antigenic epitopes from three proteins that have a prominent role in host-receptor recognition, viral entry, and pathogenicity. We advocate this vaccine must be synthesized and tested urgently as a public health priority. url: https://doi.org/10.1016/j.micpath.2020.104236 doi: 10.1016/j.micpath.2020.104236 id: cord-341987-lsvifqyo author: Kalyanasundaram, Sridhar title: Novel Corona Virus Pandemic and Neonatal Care: It’s Too Early to Speculate on Impact! date: 2020-08-03 words: 3967.0 sentences: 206.0 pages: flesch: 50.0 cache: ./cache/cord-341987-lsvifqyo.txt txt: ./txt/cord-341987-lsvifqyo.txt summary: We discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 (COVID-19) in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. In this article, we discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. Another recent case study published in Nature Communication reported transplacental transmission of COVID-19 from a positive pregnant mother during the last trimester to her offspring which occurred due to maternal viremia, placental infection, and neonatal viremia following placental infection [34] . abstract: The entire world is reeling under the effects of the novel corona virus pandemic. As it is a new infection, our knowledge is evolving constantly. There is limited information about impact of corona virus on neonatal care in relation to newborns with confirmed or suspected COVID-19. In this article, we summarize the current approach to this infection in relation to newborn babies. We discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 (COVID-19) in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. Children are less susceptible to COVID-19 infection and generally have a mild course. There is a lower risk of severe disease among pregnant women and neonates. It was recommended to follow the current protocols for management of symptomatic newborn with isolation precautions, antibiotics, and respiratory support. url: https://doi.org/10.1007/s42399-020-00440-8 doi: 10.1007/s42399-020-00440-8 id: cord-292025-dr611nse author: Kam, Kai-qian title: Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children date: 2020-06-13 words: 1648.0 sentences: 104.0 pages: flesch: 52.0 cache: ./cache/cord-292025-dr611nse.txt txt: ./txt/cord-292025-dr611nse.txt summary: From 23 March 2020 to 3 April 2020, all inpatient pediatric confirmed COVID-19 cases diagnosed via positive SARS-CoV-2 polymerase chain reaction (PCR) from nasopharyngeal swabs using the real-time reverse transcription (rRT)-PCR assay for the E gene were included in this study. In the 9 infected children with detectable SARS-CoV-2 in buccal specimens, the mean difference of Ct values between buccal and nasopharyngeal specimens for all infected patients was 10.7 (range, 6.1-16.1), and this was statistically significant (P < .001). Our findings confirm that SARS-CoV-2 can be detected in buccal specimens of infected children and that the viral load is the highest in the first week of illness or diagnosis. In our study, the average viral loads of buccal SARS-CoV-2 were consistently lower than the respective nasopharyngeal specimens, with substantial differences between the average Ct values. Two COVID-19-infected children had negative buccal specimens despite detectable nasopharyngeal viral load. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected from at least 1 buccal specimen in 9 of 11 coronavirus disease 2019 (COVID-19)–infected children (81.8%). Viral loads in buccal specimens were substantially lower than those in nasopharyngeal specimens. Buccal swabs are not good as COVID-19 screening specimens in children. url: https://doi.org/10.1093/jpids/piaa068 doi: 10.1093/jpids/piaa068 id: cord-324307-2zbm4iwn author: Kam, Kai-qian title: A Well Infant With Coronavirus Disease 2019 With High Viral Load date: 2020-02-28 words: 1914.0 sentences: 123.0 pages: flesch: 62.0 cache: ./cache/cord-324307-2zbm4iwn.txt txt: ./txt/cord-324307-2zbm4iwn.txt summary: A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. abstract: A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. This case highlights the difficulties in establishing the true incidence of COVID-19, as asymptomatic individuals can excrete the virus. These patients may play important roles in human-to-human transmission in the community. url: https://doi.org/10.1093/cid/ciaa201 doi: 10.1093/cid/ciaa201 id: cord-334695-cjxlw1tu author: Kam, Yiu-Wing title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date: 2009-11-17 words: 6404.0 sentences: 315.0 pages: flesch: 43.0 cache: ./cache/cord-334695-cjxlw1tu.txt txt: ./txt/cord-334695-cjxlw1tu.txt summary: title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro We observed that SARS-CoV spike glycoprotein can be efficiently cleaved by several airway proteases and that this processing enhances entry of SARS-CoVpp. Furthermore, we have identified the putative cleavage sites of airway proteases and, by site-directed mutagenesis, have determined the role of specific amino acid residue for proteolytic processing of the envelope glycoprotein, and for SARS-CoVpp entry into human airway epithelial cells (16HBE) in vitro. In an effort to directly demonstrate that airway protease mediated virus entry enhancement is due to the presence of cleavage site on the SARS spike glycoprotein, 16HBE cells were pre-incubated with wild-type (SARS-CoVpp) or mutant (R667App) pseudotypes on ice, which allowed virus attachment but not entry. abstract: BACKGROUND: Entry of enveloped viruses into host cells requires the activation of viral envelope glycoproteins through cleavage by either intracellular or extracellular proteases. In order to gain insight into the molecular basis of protease cleavage and its impact on the efficiency of viral entry, we investigated the susceptibility of a recombinant native full-length S-protein trimer (triSpike) of the severe acute respiratory syndrome coronavirus (SARS-CoV) to cleavage by various airway proteases. METHODOLOGY/PRINCIPAL FINDINGS: Purified triSpike proteins were readily cleaved in vitro by three different airway proteases: trypsin, plasmin and TMPRSS11a. High Performance Liquid Chromatography (HPLC) and amino acid sequencing analyses identified two arginine residues (R667 and R797) as potential protease cleavage site(s). The effect of protease-dependent enhancement of SARS-CoV infection was demonstrated with ACE2 expressing human bronchial epithelial cells 16HBE. Airway proteases regulate the infectivity of SARS-CoV in a fashion dependent on previous receptor binding. The role of arginine residues was further shown with mutant constructs (R667A, R797A or R797AR667A). Mutation of R667 or R797 did not affect the expression of S-protein but resulted in a differential efficacy of pseudotyping into SARS-CoVpp. The R667A SARS-CoVpp mutant exhibited a lack of virus entry enhancement following protease treatment. CONCLUSIONS/SIGNIFICANCE: These results suggest that SARS S-protein is susceptible to airway protease cleavage and, furthermore, that protease mediated enhancement of virus entry depends on specific conformation of SARS S-protein upon ACE2 binding. These data have direct implications for the cell entry mechanism of SARS-CoV along the respiratory system and, furthermore expand the possibility of identifying potential therapeutic agents against SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/19924243/ doi: 10.1371/journal.pone.0007870 id: cord-275846-7onenxg7 author: Kamikubo, Yasuhiko title: Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2 date: 2020-03-27 words: 2302.0 sentences: 150.0 pages: flesch: 62.0 cache: ./cache/cord-275846-7onenxg7.txt txt: ./txt/cord-275846-7onenxg7.txt summary: Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here, we developed the world''s first influenza-based epidemiological method as a useful proxy to detect the spread of SARS-CoV-2 and the establishment of partial herd immunity in countries. These results prompted us to hypothesize that (i) S type SARS-CoV-2 exit Wuhan or other epicenter in China earlier than L type virus without recognition by infectious disease surveillance systems of China and other countries; (ii) the infection by S type induced herd immunity that provides at least partial protection against spread of SARS-CoV-2. abstract: The outbreak of SARS coronavirus 2 (SARS-CoV-2), which occurred in Wuhan, China in December 2019, has caused a worldwide pandemic of coronavirus disease 2019 (COVID-19). However, there is a lack of epidemiological tools to guide effective public policy development. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Analysis of regional disparities in incidence has revealed that a sharp decline in influenza epidemics is a useful surrogate indicator for the undocumented spread of SARS-CoV-2. The biggest concern in the world is knowing when herd immunity has been achieved and scheduling a time to regain the living activities of each country. This study provides a useful tool to guide the development of local policies to contain the virus. url: https://doi.org/10.1101/2020.03.25.20043679 doi: 10.1101/2020.03.25.20043679 id: cord-347351-emdj66vj author: Kampf, Günter title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 words: 10283.0 sentences: 592.0 pages: flesch: 50.0 cache: ./cache/cord-347351-emdj66vj.txt txt: ./txt/cord-347351-emdj66vj.txt summary: Originating from a single travel-associated primary case from China, the first documented chain of multiple human-to-human transmissions of SARS-CoV-2 outside of Asia allowed a detailed study of transmission events and identified several factors (e.g. cumulative face-toface contact, direct contact with secretions or body fluids of a patient, personal protective equipment) to classify contacts as low or high risk [32] . In the close surrounding of COVID-19 patients in hospitals SARS-CoV-2 RNA is detected more frequently compared to surfaces outside the patient rooms but samples were so far consistently negative for infectious virus. General disinfection of frequently touched surfaces in the public such as shopping carts or door handles is, however, unlikely to add any protective value because even in COVID-19 wards inanimate surfaces were mainly contaminated in the permanent and immediate surrounding of symptomatic patients (detection of viral RNA, not of infectious virus) and only rarely one room away [138] suggesting that the risk to find SARS-CoV-2 on frequently touched surfaces in the public is low. abstract: During the current SARS-CoV-2 pandemic new studies are emerging daily providing novel information about sources, transmission risks and possible prevention measures. In this review, we aimed to comprehensively summarize the current evidence on possible sources for SARS-CoV-2, including evaluation of transmission risks and effectiveness of applied prevention measures. Next to symptomatic patients, asymptomatic or pre-symptomatic carriers are a possible source with respiratory secretions as the most likely cause for viral transmission. Air and inanimate surfaces may be sources; however, viral RNA has been inconsistently detected. Similarly, even though SARS-CoV-2 RNA has been detected on or in personnel protective equipment, blood, urine, eyes, the gastrointestinal tract and pets, these sources are currently thought to play a negligible role for transmission. Finally, various prevention measures such as hand washing, hand disinfection, face masks, gloves, surface disinfection or physical distancing for the healthcare setting and public are analysed for their expected protective effect. url: https://doi.org/10.1016/j.jhin.2020.09.022 doi: 10.1016/j.jhin.2020.09.022 id: cord-338468-c0jv3i1t author: Kanduc, Darja title: From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date: 2020-07-16 words: 4143.0 sentences: 234.0 pages: flesch: 41.0 cache: ./cache/cord-338468-c0jv3i1t.txt txt: ./txt/cord-338468-c0jv3i1t.txt summary: Results: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. In the wake of such results, in order to validate (or, as well, invalidate) the cross-reactivity hypothesis, investigation was expanded here by analyzing the peptide sharing between the human host and immunoreactive epitopes that are also present in SARS-CoV-2. Table 2 documents that numerous immunoreactive SARS-CoV-2 epitopes are composed mostly or, in many instances, uniquely of peptide sequences shared with human proteins. This study shows that hexapeptides from immunoreactive epitopes present in SARS-CoV-2 are widespread among a high number of human proteins. Table S2 : Hexapeptide sharing between 233 epitopes present in SARS-CoV-2 and human proteins. Table S3 : List and short description of 460 human proteins that share hexapeptides with the 233 SARS-CoV-2 epitopes. abstract: Aim: To define the autoimmune potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Methods: Experimentally validated epitopes cataloged at the Immune Epitope DataBase (IEDB) and present in SARS-CoV-2 were analyzed for peptide sharing with the human proteome. Results: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. Conclusions: This study represents a starting point or hint for future scientific–clinical investigations and suggests a range of possible protein targets of autoimmunity in SARS-CoV-2 infection. From an experimental perspective, the results warrant the testing of patients’ sera for autoantibodies against these protein targets. Clinically, the results warrant a stringent surveillance on the future pathologic sequelae of the current SARS-CoV-2 pandemic. url: https://doi.org/10.3390/antib9030033 doi: 10.3390/antib9030033 id: cord-308400-8wihm63b author: Kanellopoulou, A. title: Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort date: 2020-11-13 words: 4420.0 sentences: 312.0 pages: flesch: 58.0 cache: ./cache/cord-308400-8wihm63b.txt txt: ./txt/cord-308400-8wihm63b.txt summary: Background: To assess the level of knowledge and trust in the policy decisions taken regarding the coronavirus disease (COVID-19) pandemic among Epirus Health Study (EHS) participants. Variables assessing knowledge and beliefs towards the pandemic were summarized overall and by gender, age group (25-39, 40-49, 50-59, 60+ years) and period of report (before the lifting of lockdown measures in Greece: March 30th to May 3rd, and two post-lockdown time periods: May 4th to June 31st, July 1st to August 31st). Therefore, the primary objective of this 123 study was to investigate the levels of knowledge and beliefs on the COVID-19 pandemic and the magnitude 124 of trust upon Greek authorities and how these measures differed according to age, gender and time period 125 among the participants of an ongoing Greek cohort study, the Epirus Health Study (EHS). abstract: Background: To assess the level of knowledge and trust in the policy decisions taken regarding the coronavirus disease (COVID-19) pandemic among Epirus Health Study (EHS) participants. Methods: The EHS is an ongoing and deeply-phenotyped prospective cohort study that has recruited 667 participants in northwest Greece until August 31st, 2020. Level of knowledge on coronavirus (SARS-CoV-2) transmission and COVID-19 severity was labeled as poor, moderate or good. Variables assessing knowledge and beliefs towards the pandemic were summarized overall and by gender, age group (25-39, 40-49, 50-59, 60+ years) and period of report (before the lifting of lockdown measures in Greece: March 30th to May 3rd, and two post-lockdown time periods: May 4th to June 31st, July 1st to August 31st). An exposure-wide association analysis was conducted to evaluate the associations between 153 explanatory variables and participants' knowledge. Correction for multiple comparisons was applied using a false discovery rate (FDR) threshold of 5%. Results: A total of 563 participants (49 years mean age; 60% women) had available information on the standard EHS questionnaire, the clinical and biochemical measurements, and the COVID-19-related questionnaire. Percentages of poor, moderate and good knowledge status regarding COVID-19 were 4.5%, 10.0% and 85.6%, respectively. The majority of participants showed absolute or moderate trust in the Greek health authorities for the management of the epidemic (90.1%), as well as in the Greek Government (84.7%) and the official national sources of information (87.4%). Trust in the authorities was weaker in younger participants and those who joined the study after the lifting of lockdown measures (p-value <= 0.001). None of the factors examined was associated with participants' level of knowledge after correction for multiple testing. Conclusions: High level of knowledge about the COVID-19 pandemic and trust in the Greek authorities was observed, possibly due to the plethora of good quality publicly available information and the timely management of the pandemic at its early stages in Greece. Information campaigns for the COVID-19 pandemic should be encouraged even after the lifting of lockdown measures to increase public awareness. url: http://medrxiv.org/cgi/content/short/2020.11.10.20229146v1?rss=1 doi: 10.1101/2020.11.10.20229146 id: cord-262029-zzn74cjr author: Kang, Chang Kyung title: In vitro activity of lopinavir/ritonavir and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2 at concentrations achievable by usual doses date: 2020-05-29 words: 2575.0 sentences: 151.0 pages: flesch: 52.0 cache: ./cache/cord-262029-zzn74cjr.txt txt: ./txt/cord-262029-zzn74cjr.txt summary: We examined the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2, at concentrations which can be used to treat coronavirus-19 patients with little concern of toxicity. Its in vitro antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19, has been recently suggested [4] . Therefore, the screening of poten-tial antivirals to fight COVID-19 is urgently needed and led us to assess the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2 at clinically administrable doses. We examined the in vitro activity of the oral antivirals lopinavir/ritonavir and hydroxychloroquine against SARS-CoV-2 at their patient administrable doses. In conclusion, this in vitro experimental study showed that lopinavir/ritonavir, at its clinically relevant concentration, showed significant anti-SARS-CoV-2 activity when it was administered following viral infection. 1. Lopinavir/ritonavir showed significant anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity both in terms of the prevention of cytotoxicity and reducing the viral load at plasma concentrations achievable by usual doses. abstract: BACKGROUND/AIMS: As the coronavirus disease-2019 global pandemic progresses, screening of antiviral agents effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed. In addition, considering the viral load kinetics of SARS-CoV-2, which peaks early in the illness, and the massive burden of the disease, which may increase in the near future, identifying well-tolerated oral antivirals becomes increasingly important. We examined the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2, at concentrations which can be used to treat coronavirus-19 patients with little concern of toxicity. METHODS: Lopinavir/ritonavir (7/1.75 μg/mL), hydroxychloroquine base (1 or 2 μg/mL), or a combination thereof were administered 1 hour after the inoculation of SARS-CoV-2 to Vero cells at a multiplicity of infection of 0.05. We examined cytopathic effects of virus 48 hours after administration of the respective treatments and measured viral loads at three time points (0, 24, and 48 hours post-treatment) by quantitative real-time reverse-transcription polymerase chain reaction, and compared the results obtained from the different antiviral regimens tested. RESULTS: The severity of cytopathic effects was lower in lopinavir/ritonavir-treated cells, and viral load was significantly reduced in this group compared with the control group (p < 0.001). However, hydroxychloroquine did not show significant inhibitory effects on anti-SARS-CoV-2-mediated cytotoxicity or on viral load at either concentration. CONCLUSIONS: Lopinavir/ritonavir showed significant inhibitory effects on SARS-CoV-2 in vitro at its usual plasma concentration. However, the in vitro antiviral activity of hydroxychloroquine at concentrations commonly used in humans was minimal, whether used alone or in combination with lopinavir/ritonavir. url: https://www.ncbi.nlm.nih.gov/pubmed/32460458/ doi: 10.3904/kjim.2020.157 id: cord-263594-jd9ako6c author: Kang, Sisi title: A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date: 2020-09-11 words: 2517.0 sentences: 181.0 pages: flesch: 56.0 cache: ./cache/cord-263594-jd9ako6c.txt txt: ./txt/cord-263594-jd9ako6c.txt summary: Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Severe acute 57 respiratory distress syndrome-associated coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein 58 is a highly immunopathogenic and multifunctional viral protein (14) (15) (16) (17) (18) (19) , which elicited high titers 59 of binding antibodies in humoral immune responses (20) (21) (22) . Herein, 66 we report a human mAb derived from COVID-19 convalescent, with specific targeting to SARS-67 CoV-2 N protein and functionally compromising complement hyper-activation ex vivo. Isolation of N protein-directed mAbs 69 To profile antibody response to SARS-CoV-2 N protein in early recovered patients, we collected 70 six convalescent blood samples at seven to 25 days after the onset of the disease symptoms. abstract: Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Herein, we isolated and profiled a panel of 32 N protein-specific monoclonal antibodies (mAb) from a quick recovery coronavirus disease-19 (COVID-19) convalescent, who had dominant antibody responses to SARS-CoV-2 N protein rather than to Spike protein. The complex structure of N protein RNA binding domain with the highest binding affinity mAb nCoV396 reveals the epitopes and antigen’s allosteric changes. Functionally, a virus-free complement hyper-activation analysis demonstrates that nCoV396 specifically compromises N protein-induced complement hyper-activation, a risk factor for morbidity and mortality in COVID-19, thus paving the way for functional anti-N mAbs identification. One Sentence Summary B cell profiling, structural determination, and protease activity assays identify a functional antibody to N protein. url: https://doi.org/10.1101/2020.09.10.292318 doi: 10.1101/2020.09.10.292318 id: cord-276487-8vkrh70j author: Kang, Sisi title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites date: 2020-04-20 words: 4092.0 sentences: 248.0 pages: flesch: 52.0 cache: ./cache/cord-276487-8vkrh70j.txt txt: ./txt/cord-276487-8vkrh70j.txt summary: title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2. In this study, we report the crystal structure of SARS-CoV-2 nucleocapsid N-terminal domain (termed as SARS-CoV-2 N-NTD) as a model for understanding the molecular interactions that govern SARS-CoV-2 N-NTD binding to ribonucleotides. Since full-length SARS-CoV-2 N protein aggregated status were found in our expression and purification studies (Supporting Information Fig. S2 ), as well as previously reported data on other coronavirus nucleocapsid protein, we next investigated the structural studies on N-terminal region of SARS-CoV-2 N protein (termed as SARS-CoV-2 N-NTD). abstract: The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually led to worldwide human infections and deaths. Currently, there is no specific viral protein-targeted therapeutics. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein remains unclear. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although the overall structure is similar as other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the β-sheet core. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S2211383520305505 doi: 10.1016/j.apsb.2020.04.009 id: cord-273035-sewfb3q8 author: Kang, Xixiong title: Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome date: 2005-01-01 words: 4128.0 sentences: 177.0 pages: flesch: 50.0 cache: ./cache/cord-273035-sewfb3q8.txt txt: ./txt/cord-273035-sewfb3q8.txt summary: Background: Definitive early-stage diagnosis of severe acute respiratory syndrome (SARS) is important despite the number of laboratory tests that have been developed to complement clinical features and epidemiologic data in case definition. Results: The discriminatory classifier with a panel of four biomarkers determined in the training set could precisely detect 36 of 37 (sensitivity, 97.3%) acute SARS and 987 of 993 (specificity, 99.4%) non-SARS samples. We established a decision tree algorithm consisting of four unique biomarkers for acute SARS in the training set and subsequently validated the accuracy of this classifier by use of a completely blinded test set. To identify the serum biomarkers that could distinguish SARS from non-SARS samples, we used a training set of specimens (37 SARS acute and 74 controls; Tables 1 and 2) and constructed the decision tree classification algorithm using 10 989 peaks [99 peaks ϫ (37 ϩ 74) spectra] of statistical significance identified in the low energy readings (see Materials and Methods). abstract: Background: Definitive early-stage diagnosis of severe acute respiratory syndrome (SARS) is important despite the number of laboratory tests that have been developed to complement clinical features and epidemiologic data in case definition. Pathologic changes in response to viral infection might be reflected in proteomic patterns in sera of SARS patients. Methods: We developed a mass spectrometric decision tree classification algorithm using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Serum samples were grouped into acute SARS (n = 74; <7 days after onset of fever) and non-SARS [n = 1067; fever and influenza A (n = 203), pneumonia (n = 176); lung cancer (n = 29); and healthy controls (n = 659)] cohorts. Diluted samples were applied to WCX-2 ProteinChip arrays (Ciphergen), and the bound proteins were assessed on a ProteinChip Reader (Model PBS II). Bioinformatic calculations were performed with Biomarker Wizard software 3.1.1 (Ciphergen). Results: The discriminatory classifier with a panel of four biomarkers determined in the training set could precisely detect 36 of 37 (sensitivity, 97.3%) acute SARS and 987 of 993 (specificity, 99.4%) non-SARS samples. More importantly, this classifier accurately distinguished acute SARS from fever and influenza with 100% specificity (187 of 187). Conclusions: This method is suitable for preliminary assessment of SARS and could potentially serve as a useful tool for early diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/15550479/ doi: 10.1373/clinchem.2004.032458 id: cord-267831-uu883ofc author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 words: 1257.0 sentences: 80.0 pages: flesch: 44.0 cache: ./cache/cord-267831-uu883ofc.txt txt: ./txt/cord-267831-uu883ofc.txt summary: We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry abstract: Virus entry is a multistep process. It initiates when the virus attaches to the host cell and ends when the viral contents reach the cytosol. Genetically unrelated viruses can subvert analogous subcellular mechanisms and use similar trafficking pathways for successful entry. Antiviral strategies targeting early steps of infection are therefore appealing, particularly when the probability for successful interference through a common step is highest. We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. We also describe potent inhibition of SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 by Apilimod. These results define new tools for studying the intracellular trafficking of pathogens elicited by inhibition of PIKfyve kinase and suggest the potential for targeting this kinase in developing small-molecule antivirals against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32511398/ doi: 10.1101/2020.04.21.053058 id: cord-291323-kbjyd5g3 author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-08-25 words: 5258.0 sentences: 266.0 pages: flesch: 49.0 cache: ./cache/cord-291323-kbjyd5g3.txt txt: ./txt/cord-291323-kbjyd5g3.txt summary: We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We have constructed chimeric forms of vesicular stomatitis virus (VSV) bearing the fusion proteins of Zaire ebolavirus (ZEBOV) or SARS coronavirus 2 (SARS-CoV-2) and shown that two small-molecule inhibitors of an endosomal lipid kinase (PIKfyve) inhibit viral infection by preventing release of the viral contents from endosomes. abstract: Virus entry is a multistep process. It initiates when the virus attaches to the host cell and ends when the viral contents reach the cytosol. Genetically unrelated viruses can subvert analogous subcellular mechanisms and use similar trafficking pathways for successful entry. Antiviral strategies targeting early steps of infection are therefore appealing, particularly when the probability for successful interference through a common step is highest. We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We also describe potent inhibition of SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 by Apilimod. These results define tools for studying the intracellular trafficking of pathogens elicited by inhibition of PIKfyve kinase and suggest the potential for targeting this kinase in developing small-molecule antivirals against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32764148/ doi: 10.1073/pnas.2007837117 id: cord-252234-3txk22yj author: Kaniyala Melanthota, Sindhoora title: Elucidating the microscopic and computational techniques to study the structure and pathology of SARS‐CoVs date: 2020-08-07 words: 3988.0 sentences: 226.0 pages: flesch: 50.0 cache: ./cache/cord-252234-3txk22yj.txt txt: ./txt/cord-252234-3txk22yj.txt summary: Coronavirus replication is initiated with the binding of virion particles to the receptors of the cells, further directing the translation of the viral genome in the cytoplasm and synthesis of membrane-bound proteins. Previous studies have shown the use of a scanning electron microscope (SEM) for obtaining surface information and TEM for revealing inner components of the SARS-CoV particle. Table 1 compares various microscopy techniques for understanding the structure of SARS-CoV and its effect in host cells. The E6 cell lines were subjected to thin-layer electron microscopy and the images revealed typical coronavirus particles within the rough endoplasmic reticulum, specifically in cisternae, as well as in vesicles and several large clusters of extracellular particles were found attached to the surface of the plasma membrane. Apart from studying how the virus enters the cell, immunofluorescence was also used to investigate antibody response to the SARS-CoV and use it as an efficient detection method. abstract: Severe Acute Respiratory Syndrome Coronaviruses (SARS‐CoVs), causative of major outbreaks in the past two decades, has claimed many lives all over the world. The virus effectively spreads through saliva aerosols or nasal discharge from an infected person. Currently, no specific vaccines or treatments exist for coronavirus; however, several attempts are being made to develop possible treatments. Hence, it is important to study the viral structure and life cycle to understand its functionality, activity, and infectious nature. Further, such studies can aid in the development of vaccinations against this virus. Microscopy plays an important role in examining the structure and topology of the virus as well as pathogenesis in infected host cells. This review deals with different microscopy techniques including electron microscopy, atomic force microscopy, fluorescence microscopy as well as computational methods to elucidate various prospects of this life‐threatening virus. url: https://doi.org/10.1002/jemt.23551 doi: 10.1002/jemt.23551 id: cord-254505-mjj8xrer author: Kannan, Saathvik R. title: Infectivity of SARS-CoV-2: there Is Something More than D614G? date: 2020-09-15 words: 1917.0 sentences: 130.0 pages: flesch: 65.0 cache: ./cache/cord-254505-mjj8xrer.txt txt: ./txt/cord-254505-mjj8xrer.txt summary: To gain insight into the distribution of mutations in SARS-CoV-2 nonstructural proteins (nsps) and structural proteins, we analyzed protein sequences (n = 7232) from the United States (n = 6302), Europe (n = 420), China (n = 104), and India (n = 406), and determined the mutations with respect to Wuhan-Hu-1 isolate (NCBI Reference Sequence: NC_045512.2). The results of the temporal analysis of the mutation frequency of P323L (nsp12), C241U (5''UTR) and D614G (S-protein) show that P323L was consistently present in the viruses that had D614G mutation and C241U started coevolving with D614G sometime late January 2020 (Fig. 1b) . A mutation of D614 to G614 should result in the loss of these interactions, which could alter the dynamics of S-protein conformational changes during SARS-CoV-2 infection. Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex cell doi The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity cell doi abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32930936/ doi: 10.1007/s11481-020-09954-3 id: cord-275348-jna496x7 author: Kapadia, Sagar U. title: SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date: 2008-06-20 words: 5982.0 sentences: 317.0 pages: flesch: 53.0 cache: ./cache/cord-275348-jna496x7.txt txt: ./txt/cord-275348-jna496x7.txt summary: A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells. abstract: A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. K., Lamirande, E., Vogel, L., Subbarao, K., Roberts, A., 2005. Long-term protection from SARS coronavirus infection conferred by a single immunization with an attenuated VSV-based vaccine. Virology 340(2), 174–82.). Because it is difficult to obtain regulatory approval of vaccine based on live viruses, we constructed a replication-defective single-cycle VSV vector in which we replaced the VSV glycoprotein (G) gene with the SARS-CoV S gene. The virus was only able to infect cells when pseudotyped with the VSV G protein. We measured the effectiveness of immunization with the single-cycle vaccine in mice. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. Our results, along with earlier studies showing potent induction of T-cell responses by single-cycle vectors, indicate that these vectors are excellent alternatives to live-attenuated VSV. url: https://api.elsevier.com/content/article/pii/S0042682208001736 doi: 10.1016/j.virol.2008.03.002 id: cord-304340-9mrtic2k author: Karacan, Ilker title: The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey date: 2020-05-15 words: 2988.0 sentences: 181.0 pages: flesch: 54.0 cache: ./cache/cord-304340-9mrtic2k.txt txt: ./txt/cord-304340-9mrtic2k.txt summary: Although SARS-CoV-2 has a lower mutation rate than expected [18] , real-time tracking of the virus isolates in populations may help epidemiological understanding of the disease and early detection of important mutational or recombination events. Herein, we analyzed full-length SARS-CoV-2 genomes from three patients in Istanbul together with their clinical findings. Sample Collection: Nasopharyngeal swabs were collected from unrelated patients and tested for SARS-CoV-2 presence as a standard care protocol for routine diagnosis in Umraniye Training and Research Hospital (UEAH), Istanbul. The physical examination in the emergency department revealed a body temperature of 36.8°C, blood pressure of 120/70 mm Hg, the pulse of 100 beats per minute, respiratory rate of 20 breaths per minute, and oxygen saturation of 97% while the patient was breathing ambient air. Herein, we report three virus genomes isolated in Istanbul for the first time together with patients'' clinical findings. abstract: OBJECTIVE: Turkey is one of the latest countries that COVID-19 disease was reported, with the first case on March 11, 2020, and since then, Istanbul became the epicenter of the pandemic in Turkey. Here, we reveal sequences of the virus isolated from three different patients with various clinical presentations. METHODS: Nasopharyngeal swab specimens of the patients were tested positive for the COVID-19 by qRT-PCR. Viral RNA extraction was performed from the same swab samples. Amplicon based libraries were prepared and sequenced using the Illumina NextSeq platform. Raw sequencing data were processed for variant calling and generating near-complete genome sequences. All three genomes were evaluated and compared with other worldwide isolates. RESULTS: The patients showed various clinics (an asymptomatic patient, patient with mild disease, and with severe pulmonary infiltration). Amplicon-based next-generation sequencing approach successfully applied to generate near-complete genomes with an average depth of 2.616. All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread first through China to Europe then to Istanbul. CONCLUSION: Here, we report the viral genomes circulating in Istanbul for the first time. Further sequencing of the virus isolates may enable us to understand variations in disease presentation and association with viral factors if there is any. In addition, the sequencing of more viral genomes will delineate the spread of disease and will guide and ease the necessary measures taken to stem the spread of the novel coronavirus. url: https://doi.org/10.14744/nci.2020.90532 doi: 10.14744/nci.2020.90532 id: cord-311105-8edwb59c author: Karamese, M. title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey date: 2020-06-26 words: 1386.0 sentences: 85.0 pages: flesch: 62.0 cache: ./cache/cord-311105-8edwb59c.txt txt: ./txt/cord-311105-8edwb59c.txt summary: title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world. In this study, we retrospectively analyzed RT-PCR results of 10,000 cases from April 2 to May 30, 2020 in Kars, Iğdır, and Ardahan cities that are located on the Eastern of Turkey. All the cases were suspected of SARS-CoV-2 infection because of the symptoms or close contact with a COVID-19 patient. . https://doi.org/10.1101/2020.06.25.20138131 doi: medRxiv preprint that are located on the Eastern of Turkey; however, 7853 cases were evaluated who had typical respiratory infection symptoms such as fever, cough and shortness of breath, or close contact with a COVID-19 patient. To our knowledge, this is one of the first epidemiologic study about the RT-PCR positivity of SARS-CoV-2 suspected cases in our country. abstract: COVID-19, is caused by SARS-CoV-2, has been started on December/2019 in Wuhan/China and spread all over the world. We analyzed RT-PCR results of 10,000 cases from April-2 to May-30, 2020 in three neighbor cities located on the Eastern of Turkey. The final study population was 7853 cases after excluded screening tests. RT-PCR were performed to detect the SARS-CoV-2-specific RdRp (RNA-dependent-RNA-polymerase) gene fragment. The number of total positive samples out of 7853 were 487; however, the number of non-repeating positive patient was 373 (4.8%). The cough and fever were the most common symptoms in positive cases. The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world. url: https://doi.org/10.1101/2020.06.25.20138131 doi: 10.1101/2020.06.25.20138131 id: cord-268339-jxm69ndw author: Karamitros, Timokratis title: SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date: 2020-03-28 words: 3755.0 sentences: 217.0 pages: flesch: 51.0 cache: ./cache/cord-268339-jxm69ndw.txt txt: ./txt/cord-268339-jxm69ndw.txt summary: We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify smalland large-scale intra-host variations in the viral genome. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays. Here, we explore intra-host genomic variants and low-frequency polymorphic quasispecies in Next Generation Sequencing (NGS) data derived from patients infected by SARS-CoV-2. The S1 subunit consists of a signal peptide and the NT and receptor binding (RB) domains, with the latter sharing only 40% amino acid identity with other SARS-related CoVs. Our analysis revealed that similarly to other genomic regions, the S1 subunit hosts many low-frequency SNVs, characterized by higher density compared to the rest of the S gene sequence (Figure 1-E) . abstract: In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 - COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, but also in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher-frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host but also strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays. url: https://doi.org/10.1101/2020.03.27.009480 doi: 10.1101/2020.03.27.009480 id: cord-353963-d3gk3519 author: Karampela, Irene title: Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19? date: 2020-06-06 words: 807.0 sentences: 48.0 pages: flesch: 29.0 cache: ./cache/cord-353963-d3gk3519.txt txt: ./txt/cord-353963-d3gk3519.txt summary: A recent in silico study has shown that the fluoroquinolones, ciprofloxacin and moxifloxacin, may inhibit SARS-CoV-2 replication by exhibiting stronger capacity for binding to its main protease than chloroquine and nelfinavir, a protease inhibitor antiretroviral drug. Based on their potential antiviral activity and immunomodulatory properties, the favorable pharmacokinetics and safety profile, we propose the use of respiratory fluoroquinolones as adjuncts in the treatment of SARS-CoV-2 associated pneumonia. However, preliminary clinical trials reported conflicting results regarding the use of the anti-malarial and anti-inflammatory chloroquine and the macrolide azithromycin, while the antiviral remdesivir has not been shown to significantly decrease COVID-19 mortality (1, 2) . Considering the potential antiviral activity of respiratory fluoroquinolones against SARS-CoV-2, along with their immunomodulatory properties, their favorable pharmacokinetics and the excellent safety profile, we propose their use as adjuncts in treating patients presenting COVID-19. Therefore, randomized clinical trials of respiratory fluoroquinolones are necessary to explore their potential Arch Med Res E20_832 3 therapeutic effect as an adjunct in the treatment of SARS-CoV-2 associated pneumonia. abstract: Since the beginning of the COVID-19 pandemic, researchers have focused on repurposing of existing antibiotics, antivirals and anti-inflammatory drugs to find an effective therapy. Fluoroquinolones are broad spectrum synthetic antimicrobial agents, being chemical derivatives of quinoline, the prodrome of chloroquine. Interestingly, fluoroquinolones may exert antiviral actions against vaccinia virus, papovavirus, CMV, VZV, HSV-1, HSV-2, HCV and HIV. A recent in silico study has shown that the fluoroquinolones, ciprofloxacin and moxifloxacin, may inhibit SARS-CoV-2 replication by exhibiting stronger capacity for binding to its main protease than chloroquine and nelfinavir, a protease inhibitor antiretroviral drug. Remarkably, fluoroquinolones have shown multiple immunomodulatory actions leading to an attenuation of the inflammatory response through the inhibition of pro-inflammatory cytokines. Noteworthy, respiratory fluoroquinolones, levofloxacin and moxifloxacin, constitute fist line therapeutic agents for the management of severe community-acquired pneumonia. They are characterized by advantageous pharmacokinetic properties; higher concentrations in the lungs; and an excellent safety profile comparable to other antibiotics used to treat respiratory infections, such as macrolides and b-lactams. Based on their potential antiviral activity and immunomodulatory properties, the favorable pharmacokinetics and safety profile, we propose the use of respiratory fluoroquinolones as adjuncts in the treatment of SARS-CoV-2 associated pneumonia. url: https://www.sciencedirect.com/science/article/pii/S0188440920309243?v=s5 doi: 10.1016/j.arcmed.2020.06.004 id: cord-253380-oymg1bba author: Karataş, Ayşe title: Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma date: 2020-07-03 words: 758.0 sentences: 52.0 pages: flesch: 51.0 cache: ./cache/cord-253380-oymg1bba.txt txt: ./txt/cord-253380-oymg1bba.txt summary: title: Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma Herein we report a patient with a history of autologous stem cell transplantation (ASCT) for lymphoma whose RT-PCR test remained positive for SARS-CoV-2 for 74 days. The prolonged RT-PCR positivity, despite convalescent plasma infusion, may suggest that the given antibodies may be ineffective in terms of viral clearance. In patients with hematological malignancies or immunosuppression, such as ASCT, may lead to prolonged viral shedding, and strict isolation is warranted for long-term SARS-CoV-2 infection control. A case whose viral shedding lasted 60 days is reported from China Our patient had also undergone bone ASCT thus, underlying immunosuppression might lead to prolonged shedding. In patients with hematological malignancies or immunosuppression such as ASCT may lead to J o u r n a l P r e -p r o o f prolonged viral shedding and strict medical precautions and isolation rules should be followed for SARS-CoV-2. abstract: Abstract Acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first identified in Wuhan, China; and spread all over the world. Reverse-transcription polymerase chain reaction (RT-PCR) test for SARS-CoV-2 usually returns to negative in 20 days post-infection, but prolonged positivity has been reported up to 63 days. A case whose viral shedding lasted 60 days is reported from China. Herein we report a patient with a history of autologous stem cell transplantation (ASCT) for lymphoma whose RT-PCR test remained positive for SARS-CoV-2 for 74 days. The prolonged RT-PCR positivity, despite convalescent plasma infusion, may suggest that the given antibodies may be ineffective in terms of viral clearance. In patients with hematological malignancies or immunosuppression, such as ASCT, may lead to prolonged viral shedding, and strict isolation is warranted for long-term SARS-CoV-2 infection control. url: https://www.sciencedirect.com/science/article/pii/S1473050220301762?v=s5 doi: 10.1016/j.transci.2020.102871 id: cord-261959-pvufajw4 author: Karathanou, Konstantina title: A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2 date: 2020-09-10 words: 9192.0 sentences: 455.0 pages: flesch: 59.0 cache: ./cache/cord-261959-pvufajw4.txt txt: ./txt/cord-261959-pvufajw4.txt summary: Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. The surface of the Severe Acute Respiratory Syndrome (SARS)-CoV-2 virion is decorated with large membrane-anchored spike proteins S (Figure 1 ) that bind to Angiotensin Converting Enzyme 2 (ACE2) receptor of the host cell (Briefing, 2020; Hoffmann et al., 2020; Li et al., 2003; Xiao et al., 2003; Zhou et al., 2020) . To derive clues about intra-molecular interactions with potential role in shaping structural dynamics of protein S, we computed two-dimensional graphs of all Hbonds of protein S in structures proposed for the closed, open, and pre-fusion conformation, and for ACE2 bound to an RBD fragment. abstract: Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding. url: https://api.elsevier.com/content/article/pii/S1047847720301908 doi: 10.1016/j.jsb.2020.107617 id: cord-303363-uu9hb1c9 author: Karimi, Mehran title: Implications of SARSr-CoV 2 infection in thalassemias: Do patients fall into the “high clinical risk” category? date: 2020-05-11 words: 3271.0 sentences: 174.0 pages: flesch: 42.0 cache: ./cache/cord-303363-uu9hb1c9.txt txt: ./txt/cord-303363-uu9hb1c9.txt summary: We''re all flying blind regarding coronavirus, but it''s fair to think if thalassemic patients are particularly vulnerable to SARS-COV-2 infection or are at potential higher risk of complications from COVID-19 than normal population, specially when they become older. Therefore, it is recommended that patients with diabetes maintain a good glycemic control, because it might help reduce the risk of infection itself and may also modulate the severity of the clinical expression of the disease (39) . Hemoglobin disorders including thalassemias are generally not associated with respiratory diseases but anemia and iron-overload involving the heart, lungs (pulmonary hypertension), liver disease, diabetes and even the immune system, can encounter these patients to have higher risk of complications from SARS-COV-2 infection than normal population, specially when they become older. The few reported cases of SARS-CoV-2 infection in people with thalassemias might reflect the efforts to minimise social contacts or other unclarified reasons, such as lower beta globin protein as a possible target of COVID-19 in these patients (51) . abstract: We’re all flying blind regarding coronavirus, but it’s fair to think if thalassemic patients are particularly vulnerable to SARS-COV-2 infection or are at potential higher risk of complications from COVID-19 than normal population, specially when they become older. The frustrating thing is that, right now, this virus is still new. It only came to the attention of the World Health Organization at the end of December. Very few cases in thalassemia have so far been reported; is this due to lack of testing or a true lack of infection/susceptibility? However, we believe that more data should be collected to better characterise the impact of SARS-CoV-2 infection in patients with thalassemias. Therefore, a multicenter registry and the collection of comprehensive data from both positive COVID-19 thalassemia major and non-transfusion dependent thalassemia are necessary to clarify debated issues. In the meantime an early and vigilant monitoring along with high quality supportive care are needed in thalassemic patients at high risk for SARS-CoV-2 infection. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420925/ doi: 10.23750/abm.v91i2.9592 id: cord-316186-254z62e4 author: Kario, Kazuomi title: COVID‐19 and hypertension—evidence and practical management: Guidance from the HOPE Asia Network date: 2020-07-09 words: 3315.0 sentences: 197.0 pages: flesch: 43.0 cache: ./cache/cord-316186-254z62e4.txt txt: ./txt/cord-316186-254z62e4.txt summary: 1 Early clinical experience suggested that older age and the presence of a number of comorbidities, including hypertension, cardiovascular disease, diabetes mellitus and chronic respiratory disease increased the risk of death in patients with 3 In addition, the renin-angiotensin aldosterone (RAS) system (specifically the angiotensin-converting enzyme 2 [ACE2] protein) has been identified as playing an important role in facilitating entry of coronaviruses, including SARS-CoV-2, into target cells, especially in the lungs. Despite the theoretical possibility that use of RAS inhibitors increases the risk of infection with SARS-CoV-2 and the severity of COVID-19 illness, analyses including patients from the current pandemic indicate that this does not seem to be the case ( Table 2 ). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China abstract: There are several risk factors for worse outcomes in patients with coronavirus 2019 disease (COVID‐19). Patients with hypertension appear to have a poor prognosis, but there is no direct evidence that hypertension increases the risk of new infection or adverse outcomes independent of age and other risk factors. There is also concern about use of renin‐angiotensin system (RAS) inhibitors due to a key role of angiotensin‐converting enzyme 2 receptors in the entry of the SARS‐CoV‐2 virus into cells. However, there is little evidence that use of RAS inhibitors increases the risk of SARS‐CoV‐2 virus infection or worsens the course of COVID‐19. Therefore, antihypertensive therapy with these agents should be continued. In addition to acute respiratory distress syndrome, patients with severe COVID‐19 can develop myocardial injury and cytokine storm, resulting in heart failure, arteriovenous thrombosis, and kidney injury. Troponin, N‐terminal pro‐B‐type natriuretic peptide, D‐dimer, and serum creatinine are biomarkers for these complications and can be used to monitor patients with COVID‐19 and for risk stratification. Other factors that need to be incorporated into patient management strategies during the pandemic include regular exercise to maintain good health status and monitoring of psychological well‐being. For the ongoing management of patients with hypertension, telemedicine‐based home blood pressure monitoring strategies can facilitate maintenance of good blood pressure control while social distancing is maintained. Overall, multidisciplinary management of COVID‐19 based on a rapidly growing body of evidence will help ensure the best possible outcomes for patients, including those with risk factors such as hypertension. url: https://www.ncbi.nlm.nih.gov/pubmed/32643874/ doi: 10.1111/jch.13917 id: cord-009573-ghv9uezx author: Karlberg, J title: Do sensational media reports about severe acute respiratory syndrome affect the mindset of healthcare workers? date: 2007-01-02 words: 1047.0 sentences: 66.0 pages: flesch: 68.0 cache: ./cache/cord-009573-ghv9uezx.txt txt: ./txt/cord-009573-ghv9uezx.txt summary: The doctor at Huddinge Hospital called the Karolinska Hospital, and told the mother that an isolation room would be available for them at the hospital. That afternoon, the mother and son arrived at the Astrid Lindgren''s Children''s Hospital of the Karolinska Hospital, and a doctor and nurse met them. Because the doctors and other hospital staff now regarded her son as a suspected SARS case, the mother was concerned about returning home to her daughter and mother. A few days later the mother called the hospital and was told that the laboratory results were negative for SARS. We are concerned because, at the time of writing, there has not been any report of this suspected SARS case to the Swedish Institute for Infectious Disease Control or to WHO. We believe that heightened anxiety about SARS, brought about by the popular media''s exaggerated reporting of the outbreak in Hong Kong, affected the way Swedish healthcare professionals reacted. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159675/ doi: 10.1111/j.1651-2227.2003.tb00508.x id: cord-338683-nzgnpi6f author: Karligkiotis, Apostolos title: Changing paradigms in sinus and skull base surgery as the COVID‐19 pandemic evolves: Preliminary experience from a single Italian tertiary care center date: 2020-06-08 words: 4301.0 sentences: 206.0 pages: flesch: 43.0 cache: ./cache/cord-338683-nzgnpi6f.txt txt: ./txt/cord-338683-nzgnpi6f.txt summary: The aim of the present paper is to report our preliminary experience with the management of urgent and nondeferrable endoscopic surgeries for sinus and skull base diseases, during the COVID-19 period, describing the evolving recommendations which have been implemented day by day, as new evidences emerged, until reaching the actual protocol of precautions. At the beginning, no specific protection was recommended during surgery and all health care workers in the operating room (OR) continued to wear standard surgical masks and gowns, leaving viral-filtering-PPE available to be used only in case of confirmed COVID-19 patients. 10 In order to investigate the health of the patients belonging to the PANDEMIC-group after their last postoperative medication, a telephone interview was carried out retrospectively, examining the following factors: fever, cough, dyspnoea, anosmia, dysgeusia, gastrointestinal signs/symptoms, myalgias, fatigue, headache, pharyngodynia, rhinorrhea, active pneumonia, need for hospitalization for any reason, potential swab or serological tests performed, and if they had been in contact with COVID-19 positive individuals. abstract: BACKGROUND: Italy was the first European country suffering from COVID‐19. Health care resources were redirected to manage the pandemic. We present our initial experience with the management of urgent and nondeferrable surgeries for sinus and skull base diseases during the COVID‐19 pandemic. METHODS: A retrospective review of patients treated in a single referral center during the first 2 months of the pandemic was performed. A comparison between the last 2‐month period and the same period of the previous year was carried out. RESULTS: Twenty‐four patients fulfilled the inclusion criteria. A reduction of surgical activity was observed (−60.7%). A statistically significant difference in pathologies treated was found (P = .016), with malignancies being the most frequent indication for surgery (45.8%). CONCLUSIONS: Although we feel optimistic for the future, we do not feel it is already time to restart elective surgeries. Our experience may serve for other centers who are facing the same challenges. url: https://www.ncbi.nlm.nih.gov/pubmed/32510716/ doi: 10.1002/hed.26320 id: cord-316498-f43apjul author: Karlsson, Jan Olof G title: May Mangafodipir or Other SOD Mimetics Contribute to Better Care in COVID-19 Patients? date: 2020-10-10 words: 1931.0 sentences: 102.0 pages: flesch: 42.0 cache: ./cache/cord-316498-f43apjul.txt txt: ./txt/cord-316498-f43apjul.txt summary: The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate—MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate-MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. Intravenously administration of mangafodipir will, in contrast to INO [1] : "Everyone will be exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and most people will become infected; the disease is known as COVID-19. When it comes to mangafodipir, its combined MnSOD mimetic and redox metal binding activity may be of particular importance when attacking the inflammatory storm in SARS-CoV-2 patients. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by massive inflammation of the arterial endothelium accompanied by vasoconstriction and widespread pulmonary micro thrombi. As a result, due to the destruction of nitric oxide ((•)NO) by inflammatory superoxide (O(2)(•−)), pulmonary (•)NO concentration ceases, resulting in uncontrolled platelet aggregation and massive thrombosis, which kills the patients. Introducing (•)NO by inhalation (INO) may replace the loss of endothelium-derived (•)NO. The first results from clinical trials with INO in SARS-CoV-2 patients show a rapid and sustained improvement in cardiopulmonary function and decreased inflammation. An ongoing phase III study is expected to confirm the method’s efficacy. INO may hence become a first line treatment in SARS-CoV-2 patients. However, due to the rapid inactivation of (•)NO by deoxyhemoglobin to nitrate, pulmonary administration of (•)NO will not protect remote organs. Another INO-related pharmacological approach to protect SARS-CoV-2 patients from developing life-threatening disease is to inhibit the O(2)(•−)-driven destruction of (•)NO by neutralizing inflammatory O(2)(•−). By making use of low molecular weight compounds that mimic the action of the enzyme manganese superoxide dismutase (MnSOD). The MnSOD mimetics of the so-called porphyrin type (e.g., AEOL 10150), salen type (e.g., EUK-8) and cyclic polyamine type (e.g., M40419, today known as GC4419 and avasopasem manganese) have all been shown to positively affect the inflammatory response in lung epithelial cells in preclinical models of chronic obstructive pulmonary disease. The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate—MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. Intravenously administration of mangafodipir will, in contrast to INO, reach remote organs and may hence become an important supplement to INO. From the authors’ viewpoint, it appears logical to test mangafodipr in COVID-19 patients at risk of developing life-threatening SARS-CoV-2. Five days after submission of the current manuscript, Galera Pharmaceuticals Inc. announced the dosing of the first patient in a randomized, double-blind pilot phase II clinical trial with GC4419 for COVID-19. The study was first posted on ClinicalTrials.gov (Identifier: NCT04555096) 18 September 2020. url: https://www.ncbi.nlm.nih.gov/pubmed/33050459/ doi: 10.3390/antiox9100971 id: cord-293710-f1tzt6jb author: Karolyi, M. title: Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients date: 2020-09-23 words: 1424.0 sentences: 85.0 pages: flesch: 49.0 cache: ./cache/cord-293710-f1tzt6jb.txt txt: ./txt/cord-293710-f1tzt6jb.txt summary: SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Studies showed reduced mortality in hospitalized COVID-19 patients treated vs not treated with anticoagulants in patients with a sepsis-induced-coagulopathy (SIC) score ≥ 4 or D-Dimer > 6 times upper limit of normal [4] . We describe a case series of four outpatients with proven SARS-CoV-2 infection who developed pulmonary embolism (PE) with a delay of 2-4 weeks after symptom onset with complete resolution of initial symptoms. The characteristics of outpatients who are suitable for anticoagulation have to be determined.In conclusion, new onset of dyspnea and tachycardia after initial resolution of COVID-19 symptoms ("disease trajectory characterised by two peaks") should raise suspicion of PE and a CT scan should be considered. abstract: SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Our case series consists of four male otherwise healthy patients between 32 and 50 years of age. Initial symptoms completely resolved but they developed new onset of dyspnea and thoracic pain at days 14 to 26. CT scan revealed pulmonary embolism in all patients which led to hospitalization. Standard anticoagulation practice needs to be re-evaluated and may be considered for certain outpatients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32965656/ doi: 10.1007/s10096-020-04044-x id: cord-268817-wx96wwpg author: Karp, Donna Grace title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 words: 3600.0 sentences: 182.0 pages: flesch: 47.0 cache: ./cache/cord-268817-wx96wwpg.txt txt: ./txt/cord-268817-wx96wwpg.txt summary: Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. 6 In this study, we report the development and validation of a highly sensitive and specific SARS-CoV-2 total antibody assay on a Hamilton MicroLab STAR liquid-handling platform (Fig. 1) , based on the ADAP STAR assay-ready workstation. The successful implementation of the automated high-throughput ADAP SARS-CoV-2 total antibody assay solution as described herein can help meet the surge in demand for COVID-19 infection testing. To evaluate the assay''s sensitivity, 57 serum specimens from COVID-19 patients were subjected to the ADAP SARS-CoV-2 total antibody analysis. abstract: As of July 22, 2020, more than 14.7 million infections of SARS-CoV-2, the virus responsible for Coronavirus Disease 2019 (COVID-19), have been confirmed globally. Serological assays are essential for community screening, assessing infection prevalence, aiding identification of infected patients, and enacting appropriate treatment and quarantine protocols in the battle against this rapidly expanding pandemic. Antibody detection by agglutination–PCR (ADAP) is a pure solution phase immunoassay that generates a PCR amplifiable signal when patient antibodies agglutinate DNA-barcoded antigen probes into a dense immune complex. Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. To assess the clinical performance of the ADAP assay, 57 PCR-confirmed COVID-19 patients and 223 control patients were tested. The assay showed a sensitivity of 98% (56/57) and a specificity of 99.55% (222/223). Notably, the SARS-CoV-2–negative control patients included individuals with other common coronaviral infections, such as CoV-NL63 and CoV-HKU, which did not cross-react. In addition to high performance, the hands-free automated workstation enabled high-throughput sample processing to reduce screening workload while helping to minimize analyst contact with biohazardous samples. Therefore, the ADAP STAR liquid-handling workstation can be used as a valuable tool to address the COVID-19 global pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32815769/ doi: 10.1177/2472630320950663 id: cord-260034-a1y0enrg author: Karsulovic, Claudio title: mTORC inhibitor Sirolimus deprograms monocytes in “cytokine storm” in SARS-CoV2 secondary hemophagocytic lymphohistiocytosis- like syndrome date: 2020-07-13 words: 930.0 sentences: 61.0 pages: flesch: 44.0 cache: ./cache/cord-260034-a1y0enrg.txt txt: ./txt/cord-260034-a1y0enrg.txt summary: title: mTORC inhibitor Sirolimus deprograms monocytes in "cytokine storm" in SARS-CoV2 secondary hemophagocytic lymphohistiocytosislike syndrome Human M1 monocytes in vitro were able to express higher levels of IL-6 and IL-1β after LPS stimulation (8) (Fig. 1) . When monocytes are treated in vitro with sirolimus, and mTORC blocker, they are unable to express M1 proteins even in presence of LPS. With this data and previous reports of its use in influenza pneumonia (13) , it seems reasonable to think that the SARS-CoV2 induced sHLH-Like syndrome could be successfully slowed or terminated by sirolimus, due to its action blocking the migration of monocytes to lung tissue. We propose at least compassionate use of sirolimus in SARS-CoV2 patients who are classified as high risk of ominous progression or are currently using tocilizumab, corticosteroids and/or J o u r n a l P r e -p r o o f protease inhibitors and Hscore shows high probability of sHLH. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32673711/ doi: 10.1016/j.clim.2020.108539 id: cord-025129-ry85kv9q author: Kashyap, Uddip title: Enhanced Design of PPE Based on Electrostatic Principle to Eliminate Viruses (SARS-CoV-2) date: 2020-05-23 words: 3094.0 sentences: 178.0 pages: flesch: 61.0 cache: ./cache/cord-025129-ry85kv9q.txt txt: ./txt/cord-025129-ry85kv9q.txt summary: In this work, we propose a sanitization procedure of the personal protective equipment (PPE), such as gloves and masks, before and after the use, by employing high voltage charge generator (30 kV) from a very low DC source of 5 V to eliminate the virus from the surface of PPE. The high electric field alters the induced dipole of the protein of the virus, causing permanent damage in terms of electroporation. The negative terminal of the high voltage output can be grounded, and the positive terminal is connected to a metallic layer with a coating of CNT or ablate nano-grooves with Lithography. However, in the current work, the step-up negative high voltage charge is grounded, and the positive charges are allowed to accumulate over the metallic surface. The high electric field alters the induced dipole of the protein of the virus (Sharp and Honig 1990) , causing permanent damage in terms of electroporation (Liu et al. abstract: The ongoing global pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is in the crucial stage. The vaccine is still at the developing stage. Currently, the only way to check the spreading of this virus is self-isolation. It is reported that a good number of health workers are infected while treating patients suffering from COVID 19. Therefore, an effort is made to develop a system that can enhance safety and check unwanted viruses. Although the complete specification of the SARS-CoV-2 is yet to be evaluated, the present work considers the characteristic of SARS-CoV-1, which closely relates to that of SARS-CoV-2. The proteins are one of the most important structural and functional molecules of the virus; therefore, few properties of a protein are considered. In this work, we propose a sanitization procedure of the personal protective equipment (PPE), such as gloves and masks, before and after the use, by employing high voltage charge generator (30 kV) from a very low DC source of 5 V to eliminate the virus from the surface of PPE. The positive output is connected to a metallic surface coated with carbon nanotubes (CNT) or a metallic surface ablated using lithography to achieve desired nano-grooves of 200 nm. At the tip of these nano-grooves, a very high electric field is generated which readily ionises the air in the vicinity of the tip. The high electric field alters the induced dipole of the protein of the virus, causing permanent damage in terms of electroporation. Further positive salt ions diffuse into the protein of the viruses, causing it inactive and disintegrate. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244939/ doi: 10.1007/s41403-020-00101-1 id: cord-261876-7rsc803x author: Kaslow, David C. title: Certainty of success: three critical parameters in coronavirus vaccine development date: 2020-05-25 words: 6462.0 sentences: 305.0 pages: flesch: 36.0 cache: ./cache/cord-261876-7rsc803x.txt txt: ./txt/cord-261876-7rsc803x.txt summary: In considering the "certainty of success" in development of human coronavirus vaccines, particularly SARS-CoV-2, a third, related critical parameter is proposed—infectious inoculum intensity, at an individual-level, and force of infection, at a population-level. Reducing the infectious inoculum intensity (and force of infection, at a population-level) is predicted to lengthen the incubation period, which in turn is predicted to reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. The one factor that emerges for consideration in SARS-CoV-2 vaccine development and implementation is reducing the infectious inoculum intensity (and force of infection, at a populationlevel) to lengthen the incubation period, reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. abstract: Vaccines for 17 viral pathogens have been licensed for use in humans. Previously, two critical biological parameters of the pathogen and the host–pathogen interaction—incubation period and broadly protective, relative immunogenicity—were proposed to account for much of the past successes in vaccine development, and to be useful in estimating the “certainty of success” of developing an effective vaccine for viral pathogens for which a vaccine currently does not exist. In considering the “certainty of success” in development of human coronavirus vaccines, particularly SARS-CoV-2, a third, related critical parameter is proposed—infectious inoculum intensity, at an individual-level, and force of infection, at a population-level. Reducing the infectious inoculum intensity (and force of infection, at a population-level) is predicted to lengthen the incubation period, which in turn is predicted to reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. Similarly, successfully implementing individual- and population-based behaviors that reduce the infectious inoculum intensity and force of infection, respectively, while testing and deploying COVID-19 vaccines is predicted to increase the “certainty of success” of demonstrating vaccine efficacy and controlling SARS-CoV-2 infection, disease, death, and the pandemic itself. url: https://www.ncbi.nlm.nih.gov/pubmed/32509338/ doi: 10.1038/s41541-020-0193-6 id: cord-289852-4uxb70rh author: Kassem, Dina H. title: Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis date: 2020-09-30 words: 6959.0 sentences: 342.0 pages: flesch: 44.0 cache: ./cache/cord-289852-4uxb70rh.txt txt: ./txt/cord-289852-4uxb70rh.txt summary: Thus, harnessing the immunomodulatory properties of mesenchymal stem cells (MSCs) to ameliorate that cytokine-storm can indeed provide a golden key for the treatment of COVID-19 patients, especially severe cases. In fact, MSCs transplantation can improve the overall outcome of COVID-19 patients via multiple mechanisms; first through their immunomodulatory effects which will help to regulate the infected patient inflammatory response, second via promoting tissue-repair and regeneration, and third through their antifibrotic effects. Similar studies are also warranted to compare the therapeutic benefit of a certain MSCs type, and its derived EVs. Antimicrobial activity of mesenchymal stem cells: current status and new perspectives of antimicrobial peptide-based therapies Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ILL COVID-19 patients: the case for compassionate use Human umbilical cord-derived mesenchymal stem cell therapy in patients with COVID-19: a phase 1 clinical trial abstract: Corona virus disease 2019 (COVID-19) is a global public health crisis. The high infectivity of the disease even from non-symptomatic infected patients, together with the lack of a definitive cure or preventive measures are all responsible for disease outbreak. The severity of COVID-19 seems to be mostly dependent on the patients’ own immune response. The over-activation of the immune system in an attempt to kill the virus, can cause a “cytokine storm” which in turn can induce acute respiratory distress syndrome (ARDS), as well as multi-organ damage, and ultimately may lead to death. Thus, harnessing the immunomodulatory properties of mesenchymal stem cells (MSCs) to ameliorate that cytokine-storm can indeed provide a golden key for the treatment of COVID-19 patients, especially severe cases. In fact, MSCs transplantation can improve the overall outcome of COVID-19 patients via multiple mechanisms; first through their immunomodulatory effects which will help to regulate the infected patient inflammatory response, second via promoting tissue-repair and regeneration, and third through their antifibrotic effects. All these mechanisms will interplay and intervene together to enhance lung-repair and protect various organs from any damage resulting from exaggerated immune-response. A therapeutic modality which provides all these mechanisms undoubtedly hold a strong potential to help COVID-19 patients even those with the worst condition to hopefully survive and recover. url: https://doi.org/10.3389/fcell.2020.587866 doi: 10.3389/fcell.2020.587866 id: cord-267307-kyh0xsrp author: Kasting, Monica L. title: Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date: 2020-11-04 words: 4343.0 sentences: 230.0 pages: flesch: 54.0 cache: ./cache/cord-267307-kyh0xsrp.txt txt: ./txt/cord-267307-kyh0xsrp.txt summary: Public health efforts should focus on increasing perceived severity and threat of SARS-CoV-2-related disease, while promoting NPI as effective in reducing threat. A six-item measure was used to assess participants'' perceptions of the effectiveness of NPIs to prevent SARS-CoV-2 infection and spread. Three of the six items measured the perceived effectiveness of preventing yourself from spreading COVID-19 to others and included: 1) wearing a mask anytime you leave the house to go out in public, 2) practicing social distancing by leaving at least six feet between you and other people (this does not include people you live with), and 3) covering your mouth when you cough. Any variable that was significant at p<0.01 in bivariate comparisons was included in an adjusted logistic regression model with the binary lower/ higher perceived effectiveness of COVID-19 prevention measures as the outcome. abstract: BACKGROUND: The COVID-19 pandemic is an unprecedented public health threat, both in scope and response. With no vaccine available, the public is advised to practice non-pharmaceutical interventions (NPI) including social distancing, mask-wearing, and washing hands. However, little is known about public perceptions of the effectiveness of these measures, and high perceived effectiveness is likely to be critical in order to achieve widespread adoption of NPI. METHODS: In May 2020, we conducted a cross-sectional survey among U.S. adults (N = 3,474). The primary outcome was a six-item measure assessing perceived effectiveness of recommended behaviors to prevent SARS-CoV-2 infection from 1 (not at all effective) to 5 (extremely effective). The sample was divided into “higher” and “lower” perceived effectiveness groups. Covariates included demographics, healthcare characteristics, and health beliefs. Variables that were significant at p<0.01 in bivariate analyses were entered into a multivariable logistic regression and a best-fit model was created using a cutoff of p<0.01 to stay in the model. RESULTS: Mean age was 45.5 years and most participants were non-Hispanic White (63%) and female (52.4%). The high perceived effectiveness group was slightly larger than the low perceived effectiveness group (52.7% vs. 47.3%). Almost all health belief variables were significant in the best-fit regression model. COVID-19-related worry (aOR = 1.82; 95% CI = 1.64–2.02), and perceived threat to physical health (aOR = 1.32; 95% CI = 1.20–1.45) were positively associated with perceived effectiveness while perceived severity of COVID-19 (0.84; 95% CI = 0.73–0.96) and perceived likelihood of infection (0.85; 95% CI = 0.77–0.94) switched directions in the adjusted model and were negatively associated with perceived effectiveness. CONCLUSIONS: This research indicates people generally believe NPI are effective, but there was variability based on health beliefs and there are mixed rates of engagement in these behaviors. Public health efforts should focus on increasing perceived severity and threat of SARS-CoV-2-related disease, while promoting NPI as effective in reducing threat. url: https://doi.org/10.1371/journal.pone.0241662 doi: 10.1371/journal.pone.0241662 id: cord-352969-rpt7xja6 author: Kataria, Ashish title: COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice date: 2020-07-15 words: 5975.0 sentences: 367.0 pages: flesch: 45.0 cache: ./cache/cord-352969-rpt7xja6.txt txt: ./txt/cord-352969-rpt7xja6.txt summary: 1, 4 Solid organ transplant (SOT) patients including kidney transplant recipients (KTRs) are at a uniquely increased risk of serious complications from COVID-19 because of immunosuppressive (IS) medication use, elderly age (>65 y), and preexisting comorbidities like diabetes, hypertension, and cardiovascular diseases. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. 71, 72 At this time, there is no evidence to suggest that kidney transplant patients are at an increased risk of thrombotic events compared with the general population for disease of similar severity. abstract: The novel severe acute respiratory syndrome coronavirus 2 was identified in the late 2019 as the cause of coronavirus disease 2019 (COVID-19), an acute respiratory viral illness. Patients with chronic underlying conditions may have an increased risk of morbidity and mortality from COVID-19. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. Early data suggest that the mortality of patients on dialysis may be comparable to those with kidney transplants, although more research is needed. This concise review aims to describe the epidemiology of COVID-19 in kidney transplant recipients, manifestations, appropriate management, and clinical outcomes based on the available literature. Current evidence on many of the specific antiviral measures against COVID-19 has not shown a clear-cut benefit in smaller studies and the results of several ongoing larger clinical trials are awaited. In addition, we also highlight the impact of COVID-19 on kidney transplant center practice and volumes; potential living or deceased donors, recipients; and induction immunosuppression and surgical strategies. url: https://doi.org/10.1097/txd.0000000000001031 doi: 10.1097/txd.0000000000001031 id: cord-322955-7dw32xby author: Kathwate, Gunderao H title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date: 2020-06-12 words: 5729.0 sentences: 392.0 pages: flesch: 47.0 cache: ./cache/cord-322955-7dw32xby.txt txt: ./txt/cord-322955-7dw32xby.txt summary: title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Those properties are calculated by different methods at IEDB server (http://tools.iedb.org/bcell/ )like Kolaskar-Tongaonkar antigenicity scale provide physiology of the amino acid residues(45), Emini Surface accessible score for accessible surface of the epitope(46), Secondary structure of epitopes also has role in antigenicity. High scored and common peptides predicted by various tools were selected for deriving sequence of potential vaccine candidate. We designed a multi-epitopes vaccine construct from S-protein of SARS-CoV2. From various epitopes predicted by the online server based on common sequence and high score three TCR and two BCR epitopes were selected as part of COVID19 vaccine. This vaccine codes epitopes form S protein of SARS-CoV2 virus for T and B cell receptors. abstract: COVID 19 is disease caused by novel corona virus, SARS-CoV2 originated in China most probably of Bat origin. Till date, no specific vaccine or drug has been discovered to tackle the infections caused by SARS-CoV2. In response to this pandemic, we utilized bioinformatics knowledge to develop efficient vaccine candidate against SARS-CoV2. Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes were antigenic in nature non-toxic and probably non-allergen. Modelled and refined tertiary structure was predicted as valid for further use. Protein-Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. Designed multiepitope vaccine has induced cell mediated and humoral immunity along with increased interferon gamma response. Macrophages and dendritic cells were also found increased over the vaccine exposure. In silico codon optimization and cloning in expression vector indicates that vaccine can be efficiently expressed in E. coli. In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity. url: https://doi.org/10.1101/2020.06.03.131755 doi: 10.1101/2020.06.03.131755 id: cord-319707-j8y9gt2o author: Kato, Verstrepen title: Neurological manifestations of COVID-19, SARS and MERS date: 2020-06-19 words: 3552.0 sentences: 188.0 pages: flesch: 43.0 cache: ./cache/cord-319707-j8y9gt2o.txt txt: ./txt/cord-319707-j8y9gt2o.txt summary: The novel coronavirus, SARS-CoV-2, is likewise a causative pathogen for severe viral pneumonia with the risk of progression to respiratory failure and systemic manifestations. Articles related to the topic were identified by following terms: "Severe Acute Respiratory Syndrome", "Middle East Respiratory Syndrome", Coronavirus disease 2019", "Neurology", "MERS", "SARS", "COVID-19", "Stroke", "Epilepsy", "Guillain-Barré Syndrome", "Encephalitis", "Myelitis", "Meningitis", "Neurological Sequels", "Polyneuropathy" and "Carotid Dissection". Several recent articles report associated cases of encephalitis, acute flaccid paralysis and other neurological symptoms, such as Guillain-Barré syndrome or ADEM, as possible complications of a HCoV infection [6] . Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Neurological complications of middle east respiratory syndrome coronavirus: a report of two cases and review of the literature abstract: Since December 2019, the world is affected by an outbreak of a new disease named COVID-19, which is an acronym of ‘coronavirus disease 2019’. Coronaviruses (CoV) were assumed to be associated with mild upper respiratory tract infections, such as common cold. This perception changed in time due to occurrence of the Severe Acute Respiratory Syndrome (SARS) caused by SARS-CoV in 2002 and the Middle East Respiratory Syndrome (MERS) caused by MERS-CoV in 2012, both inducing an epidemic severe viral pneumonia with potentially respiratory failure and numerous extra-pulmonary manifestations. The novel coronavirus, SARS-CoV-2, is likewise a causative pathogen for severe viral pneumonia with the risk of progression to respiratory failure and systemic manifestations. In this review, we will give a summary of the neurological manifestations due to SARS and MERS, as those might predict the neurological outcome in the novel COVID-19. Additionally, we provide an overview of the current knowledge concerning neurological manifestations associated with COVID-19, to the extent that literature is already available as the pandemic is still ongoing. url: https://www.ncbi.nlm.nih.gov/pubmed/32562214/ doi: 10.1007/s13760-020-01412-4 id: cord-314489-e5r5s5ee author: Katsidzira, Leolin title: The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date: 2020-05-11 words: 1948.0 sentences: 132.0 pages: flesch: 57.0 cache: ./cache/cord-314489-e5r5s5ee.txt txt: ./txt/cord-314489-e5r5s5ee.txt summary: The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . abstract: The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. We use the situation in Zimbabwe to build an argument that the epidemic is likely to be attenuated in some countries with similar socio-economic and cultural structures. However, even an attenuated epidemic may overwhelm weak health systems, emphasising the importance of prevention. These prevention strategies should be tailored to the unique social and cultural networks of individual countries which may facilitate the spread of SARS-CoV 2. It is also equally important to maintain services for the major infectious diseases in the region such as tuberculosis and malaria. A breakdown of treatment and prevention services for these conditions may even overshadow the projected morbidity and mortality from COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32392333/ doi: 10.1093/cid/ciaa552 id: cord-310064-p8u424ch author: Katz, Andrew P. title: False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date: 2020-06-12 words: 4503.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-310064-p8u424ch.txt txt: ./txt/cord-310064-p8u424ch.txt summary: [4] [5] [6] The virus responsible for COVID-19, SARS-CoV-2, poses a particular risk to providers involved in the care of otolaryngology patients due to examinations and surgeries involving the nasopharynx, oropharynx, and upper aerodigestive tract, which harbor high concentrations of viral particles. 6 In line with other institutions across the globe, these protocols call for preoperative testing of asymptomatic patients using reverse transcriptase polymerase chain reaction (RT-PCR) given reports of asymptomatic carriers of SARS-CoV-2 capable of transmission. Tahamtan and Ardebili discuss possible factors causing false negative results of SARS-CoV-2 RT-PCR, namely mismatches between the testing primers and viral genome or low viral loads in samples due to timing of disease or location of collection. In the most recent patient with positive preoperative testing without symptoms (patient #3), pathologists recommended immediate re-testing based on the borderline titers in her test results rather than delaying surgery for weeks for a potential COVID-19 infection. abstract: BACKGROUND: No reports describe falsepositive reverse transcriptase polymerase chain reaction (RT‐PCR) for novel coronavirus in preoperative screening. METHODS: Preoperative patients had one or two nasopharyngeal swabs, depending on low or high risk of viral transmission. Positive tests were repeated. RESULTS: Forty‐three of 52 patients required two or more preoperative tests. Four (9.3%) had discrepant results (positive/negative). One of these left the coronavirus disease (COVID) unit against medical advice despite an orbital abscess, with unknown true disease status. The remaining 3 of 42 (7.1%) had negative repeat RT‐PCR. Although ultimately considered falsepositives, one was sent to a COVID unit postoperatively and two had urgent surgery delayed. Assuming negative repeat RT‐PCR, clear chest imaging, and lack of subsequent symptoms represent the “gold standard,” RT‐PCR specificity was 0.97. CONCLUSIONS: If false positives are suspected, we recommend computed tomography (CT) of the chest and repeat RT‐PCR. Validated serum immunoglobulin testing may ultimately prove useful. url: https://www.ncbi.nlm.nih.gov/pubmed/32530131/ doi: 10.1002/hed.26317 id: cord-274097-11hvriqy author: Katz, Louis M. title: Is SARS‐CoV‐2 transfusion transmitted? date: 2020-06-16 words: 2023.0 sentences: 132.0 pages: flesch: 51.0 cache: ./cache/cord-274097-11hvriqy.txt txt: ./txt/cord-274097-11hvriqy.txt summary: The few studies of SARS-CoV-2 RNA in donors or of donors developing COVID-19 after giving blood are a mix of small series wherein prospectively test-positive units were quarantined and not transfused or involved units quarantined after donation to permit the donor time to get ill before units are distributed. In a lookback to recipients of 17 transfused components from seven South Korean donors who developed COVID-19 6 to 15 days after donation, there was no associated clinical morbidity in the recipients; however, archived samples tested by PCR after the donors reported their illnesses were negative. 21 Precise estimates of the prevalence of asymptomatic/presymptomatic infection and especially of whether RNA-emia or, more germane to this topic, viremia occur in the absence of illness (especially in healthy donors or the larger well population who might be qualified to donate) are among the key missing data needed to inform our debate about any risk of TTI and subsequent TTD. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations abstract: See article on page 1119–1122, in this issue url: https://doi.org/10.1111/trf.15831 doi: 10.1111/trf.15831 id: cord-327622-ezgufe24 author: Kaur, Ramandeep title: Practical strategies to reduce nosocomial transmission to healthcare professionals providing respiratory care to patients with COVID-19 date: 2020-09-23 words: 6333.0 sentences: 355.0 pages: flesch: 43.0 cache: ./cache/cord-327622-ezgufe24.txt txt: ./txt/cord-327622-ezgufe24.txt summary: • When removing the endotracheal tube, simultaneously turn off the ventilator • Avoid disconnecting ETT from the ventilator circuit before extubation to reduce spray of contaminated aerosols 9 Transport • Place a filter between the artificial airway and the transport ventilator circuit • Use HME that has filter function (HME-F) • Consider clamping the ETT before disconnection from ventilator circuit 10 Bronchoscopy assist* 2 in vivo [44, 45] • For spontaneously breathing patients, place a surgical mask on patient''s face (Fig. 7a, b) • Use NIV mask with examination port for patients on NIV (Fig. 7d) • Use swivel adapter to insert bronchoscope for intubated patient (Fig. 7c) Abbreviations: HFNC high-flow nasal cannula, IPPB intermittent positive pressure breathing, HME heat moisture exchanger, ETT endotracheal tube, NIV non-invasive ventilation *Based on CDC guidelines, these procedures should ideally be performed in airborne infection isolation rooms entrainment or nonrebreather mask [53] . abstract: Coronavirus disease (COVID-19) is an emerging viral infection that is rapidly spreading across the globe. SARS-CoV-2 belongs to the same coronavirus class that caused respiratory illnesses such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). During the SARS and MERS outbreaks, many frontline healthcare workers were infected when performing high-risk aerosol-generating medical procedures as well as when providing basic patient care. Similarly, COVID-19 disease has been reported to infect healthcare workers at a rate of ~ 3% of cases treated in the USA. In this review, we conducted an extensive literature search to develop practical strategies that can be implemented when providing respiratory treatments to COVID-19 patients, with the aim to help prevent nosocomial transmission to the frontline workers. url: https://doi.org/10.1186/s13054-020-03231-8 doi: 10.1186/s13054-020-03231-8 id: cord-300899-yi2mx91a author: Kaur, Satinder title: Understanding COVID-19 transmission, health impacts and mitigation: timely social distancing is the key date: 2020-07-18 words: 5347.0 sentences: 337.0 pages: flesch: 55.0 cache: ./cache/cord-300899-yi2mx91a.txt txt: ./txt/cord-300899-yi2mx91a.txt summary: COVID-19 is a highly infectious disease caused by SARS-CoV-2, first identified in China and spread globally, resulting into pandemic. Various measures are undertaken to prevent infection such as maintaining hygiene, using facemasks, isolation/quarantine, social/physical distancing, in extreme cases lockdown (restricted movement except essential services) in hot spot areas or throughout the country. Python programming is conducted for change point analysis (CPA) using Bayesian probability approach for understanding the impact of restrictions and mitigation methods in terms of either increase or stagnation in number of COVID-19 cases for eight countries. COVID-19 is caused by novel strain of virus SARS-CoV-2 emerged from China and now declared as pandemic due to its presence across the continents in more than 213 countries. Rise in number of cases in different weeks is presented in Table 1 where it can be observed that India, France and Japan had experienced increase in fifth week, that in USA and Spain in the fourth week, Italy in the third week except for Iran and China in second week. abstract: COVID-19 is a highly infectious disease caused by SARS-CoV-2, first identified in China and spread globally, resulting into pandemic. Transmission of virus takes place either directly through close contact with infected individual (symptomatic/asymptomatic) or indirectly by touching contaminated surfaces. Virus survives on the surfaces from few hours to days. It enters the human body through nose, eyes or mouth. Other sources of contamination are faeces, blood, food, water, semen etc. Parameters such as temperature/relative humidity also play an important role in transmission. As the disease is evolving, so are the number of cases. Proper planning and restriction are helping in influencing the trajectory of the transmission. Various measures are undertaken to prevent infection such as maintaining hygiene, using facemasks, isolation/quarantine, social/physical distancing, in extreme cases lockdown (restricted movement except essential services) in hot spot areas or throughout the country. Countries that introduced various mitigation measures had experienced control in transmission of COVID-19. Python programming is conducted for change point analysis (CPA) using Bayesian probability approach for understanding the impact of restrictions and mitigation methods in terms of either increase or stagnation in number of COVID-19 cases for eight countries. From analysis it is concluded that countries which acted late in bringing in the social distancing measures are suffering in terms of high number of cases with USA, leading among eight countries analysed. The CPA week in comparison with date of lockdown and first reported case strongly correlates (Pearson’s r = − 0.86 to − 0.97) to cases, cases per unit area and cases per unit population, indicating earlier the mitigation strategy, lesser the number of cases. The overall paper will help the decision makers in understanding the possible steps for mitigation, more so in developing countries where the fight against COVID-19 seems to have just begun. url: https://doi.org/10.1007/s10668-020-00884-x doi: 10.1007/s10668-020-00884-x id: cord-328396-p2gvpe8i author: Kaur, Savneet title: The Enigma of Endothelium in COVID-19 date: 2020-08-04 words: 4427.0 sentences: 246.0 pages: flesch: 39.0 cache: ./cache/cord-328396-p2gvpe8i.txt txt: ./txt/cord-328396-p2gvpe8i.txt summary: In the current perspective, we envisage a key role of mEC in the pathogenesis of coronavirus disease 2019 caused by the novel coronavirus, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV2). These studies along with the fact that the pulmonary epithelium is more resistant to injury than the endothelium signify that SARS-CoV-2-induced ARDS and associated coagulopathy may be caused by a direct endothelial infection by the virus in the lungs (Matthay et al., 2019) . A summary of such recent reviews and short reports is provided in Table 1 (Alvarado-Moreno and Majluf-Cruz, 2020; Amraei and Rahimi, 2020; Cure and Cure, 2020; Froldi and Dorigo, 2020; Guler et al., 2020; Gupta et al., 2020; Gustafson et al., 2020; Mangalmurti et al., 2020; Marchetti, 2020; Mondal et al., 2020; Panfoli, 2020; Pons et al., 2020; Sardu et al., 2020b; Teuwen et al., 2020) . abstract: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) has affected millions of people globally. Clinically, it presents with mild flu-like symptoms in most cases but can cause respiratory failure in high risk population. With the aim of unearthing newer treatments, scientists all over the globe are striving hard to comprehend the underlying mechanisms of COVID-19. Several studies till date have indicated a dysregulated host immune response as the major cause of COVID-19 induced mortality. In this Perspective, we propose a key role of endothelium, particularly pulmonary endothelium in the pathogenesis of COVID-19. We draw parallels and divergences between COVID-19-induced respiratory distress and bacterial sepsis-induced lung injury and recommend the road ahead with respect to identification of endothelium-based biomarkers and plausible treatments for COVID-19. url: https://doi.org/10.3389/fphys.2020.00989 doi: 10.3389/fphys.2020.00989 id: cord-258701-jyzxu9nk author: Kaushal, Darwin title: Endoscopy in Otorhinolaryngology During Corona Outbreak: A Proposal for Safe Practice date: 2020-08-13 words: 2464.0 sentences: 184.0 pages: flesch: 54.0 cache: ./cache/cord-258701-jyzxu9nk.txt txt: ./txt/cord-258701-jyzxu9nk.txt summary: In this article, we propose essential steps that can be implemented at the departmental and institutional levels to do endoscopic diagnostic procedures effectively during COVID-19 outbreak and to break the transmission chain. Coronavirus disease 2019 (COVID-19) is a type of viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Person-toperson transmission is thought to occur among close contacts mainly via respiratory droplets produced when an infected person coughs or sneezes, which is very common in endoscopic procedures in Otorhinolaryngology. • Deep cleaning and fumigation of the room should be performed when a reverse transcriptase-polymerase chain reaction COVID-19 positive patient undergoes a procedure. • When possible, procedures on COVID-19 suspect/positive patients should be performed as the last procedure, and the endoscopy room should be thoroughly ventilated for at least 1 h before the next procedure by using blowers or natural ventilation. abstract: Coronavirus disease 2019 (COVID-19) is a type of viral pneumonia that has paralysed the entire world both in terms of health and economy. It has been recently declared as a global pandemic. All the health care professionals must be aware of the disease entity and take precautionary measures to control its transmission from person to person, particularly in hospital settings. In this article, we propose essential steps that can be implemented at the departmental and institutional levels to do endoscopic diagnostic procedures effectively during COVID-19 outbreak and to break the transmission chain. url: https://doi.org/10.1007/s12070-020-02048-9 doi: 10.1007/s12070-020-02048-9 id: cord-288733-c51lfwd6 author: Kavanagh, Oisín title: Inhaled Hydroxychloroquine to Improve Efficacy and Reduce Harm in the Treatment of COVID-19 date: 2020-07-15 words: 769.0 sentences: 51.0 pages: flesch: 55.0 cache: ./cache/cord-288733-c51lfwd6.txt txt: ./txt/cord-288733-c51lfwd6.txt summary: An analysis of clinical trials registered on ClinicalTrials.gov revealed that this may continue as many studies combine HCQ with agents that prolong the QT interval. Here we describe an inhaled formulation of HCQ which has passed safety studies in clinical trials for the treatment of asthma and discuss how this approach may reduce side-effects and improve efficacy. Chloroquine and hydroxychloroquine (HCQ) were two of the earliest drugs to 33 receive attention as possible repurposable treatment options for COVID-19 3 . Concerns associated with severe side effects 41 are such that the FDA and EMA now formally recommend against taking HCQ for COVIDEffects of chloroquine on 178 viral infections: An old drug against today''s diseases? FDA Drug Safety Communication: FDA cautions 199 against use of hydroxychloroquine or chloroquine for COVID-19 outside of the 200 hospital setting or a clinical trial due to risk of heart rhythm problems Optimizing hydroxychloroquine 210 dosing for patients with COVID-19: An integrative modeling approach for effective 211 drug repurposing abstract: Current formulations and dose regimens of hydroxychloroquine (HCQ) put patients at risk of harm. An analysis of clinical trials registered on ClinicalTrials.gov revealed that this may continue as many studies combine HCQ with agents that prolong the QT interval. Further, almost all of the trials registered do not consider dosage adjustment in the elderly, a patient population most likely to require HCQ treatment. Here we describe an inhaled formulation of HCQ which has passed safety studies in clinical trials for the treatment of asthma and discuss how this approach may reduce side-effects and improve efficacy. As this simple formulation progressed to phase II studies, safety data can be used to immediately enable phase II trials in COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33017904/ doi: 10.1016/j.mehy.2020.110110 id: cord-331039-qgom2e3n author: Kavitha, Kuppuswamy title: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates date: 2020-09-22 words: 4929.0 sentences: 326.0 pages: flesch: 57.0 cache: ./cache/cord-331039-qgom2e3n.txt txt: ./txt/cord-331039-qgom2e3n.txt summary: A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 M(pro) and the top 2 lead compounds based on binding affinity were found to be 1,2,4 triazolo[1,5-a] pyrimidin-7-one compounds. The objectives of this study were i) to identify evolutionarily important active site amino acids by structure-based sequence alignment of SARS-CoV-2 and SARS-CoV M pro enzymes ii) to identify potential non-covalent M pro inhibitors by screening protease-inhibitor-like compounds available in the ZINC database by molecular docking studies iii) prediction of absorption, distribution metabolism, excretion and toxicity properties of the top-scoring inhibitors using in silico methods iv) to validate the stable binding of the lead compounds with SARS-CoV-2 M pro by molecular dynamics (MD) simulations and v) to calculate thermodynamic binding energies for each lead compound -SARS-CoV-2 M pro complex using Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) calculations. abstract: Discovery of a potent SARS-CoV-2 main protease (M(pro)) inhibitor is the need of the hour to combat COVID-19. A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 M(pro) and the top 2 lead compounds based on binding affinity were found to be 1,2,4 triazolo[1,5-a] pyrimidin-7-one compounds. We report these two compounds (ZINC000621278586 and ZINC000621285995) as potent SARS-CoV-2 M(pro) inhibitors with high affinity (<−9 kCal/mol) and less toxicity than Lopinavir and Nelfinavir positive controls. Both the lead compounds effectively interacted with the crucial active site amino acid residues His41, Cys145 and Glu166. The lead compounds satisfied all of the druglikeness rules and devoid of toxicity or mutagenicity. Molecular dynamics simulations showed that both lead 1 and lead 2 formed stable complexes with SARS-CoV-2 M(pro) as evidenced by the highly stable root mean square deviation (<0.23 nm), root mean square fluctuations (0.12 nm) and radius of gyration (2.2 nm) values. Molecular mechanics Poisson-Boltzmann surface area calculation revealed thermodynamically stable binding energies of −129.266 ± 2.428 kJ/mol and − 116.478 ± 3.502 kJ/mol for lead1 and lead2 with SARS-CoV-2 M(pro), respectively. url: https://www.sciencedirect.com/science/article/pii/S0301462220301861?v=s5 doi: 10.1016/j.bpc.2020.106478 id: cord-018101-zd4v222b author: Kawashima, Kent title: Disease Outbreaks: Critical Biological Factors and Control Strategies date: 2016-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Disease outbreaks remain a major threat to human health and welfare especially in urban areas in both developed and developing countries. A large body of theoretical work has been devoted to modeling disease emergence, and critical factors that predict outbreak occurrence and severity have been proposed. In this chapter, we focus on biological factors that underlie both theoretical models and urban planning. We describe the SARS 2002–2003 pandemic as a case study of epidemic control of a human infectious disease. We then describe theoretical analyses of disease dynamics and control strategies. An important conclusion is that epidemic control will be strongly dependent on particular aspects of pathogen biology including host breadth, virulence, incubation time, and/or mutation rate. The probability, and potential cost, of future outbreaks, may be high and lessons from both past cases and theoretical work should inform urban design and policy. Interdisciplinary collaboration in planning, swiftness of information dissemination and response, and willingness to forgo personal liberties during a crisis may be key factors in resilience to infectious disease outbreaks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122892/ doi: 10.1007/978-3-319-39812-9_10 id: cord-262412-bs7quwov author: Kaya, Gürkan title: Clinical and Histopathological Features and Potential Pathological Mechanisms of Skin Lesions in COVID-19: Review of the Literature date: 2020-06-30 words: 3358.0 sentences: 189.0 pages: flesch: 37.0 cache: ./cache/cord-262412-bs7quwov.txt txt: ./txt/cord-262412-bs7quwov.txt summary: Clinical manifestations are as follows (see Table 1 ): generalized or localized rash (erythematous, papulovesicular, maculopapular, petechial, morbilliform, symmetrical drug-related intertriginous and flexural exanthema (SDRIFE)-like, digitate papulosquamous pityriasis rosea-like), generalized urticaria, varicelliform rash, herpes lesions (zoster), purpuric lesions (retiform purpura), livedoid lesions (livedo reticularis, livedo racemosa), acro-ischemic lesions (dry gangrene, blisters, cyanosis), erythema multiforme-like, chilblain-like lesions (COVID toes) and other lesions such as urticarial vasculitis, acute generalized exanthematous pustulosis (AGEP)-like rash, eosinophilic panniculitis, COVID mask, periorbital dyschromia, oral ulcers and COVID red half-moon nail sign. In a recent report, the postmortem histology of COVID-19 patients revealed lymphocytic endotheliitis in lung, heart, kidney, liver and small intestine, a pathological picture reminiscent of what is seen in skin lesions, suggesting that SARS-CoV-2 infection facilitates the induction of endothelial inflammation in several organs as a direct consequence of viral involvement and of host inflammatory response [61] . abstract: In recent weeks, several reports have emerged of skin lesions with different clinical presentations in COVID-19 cases. All dermatologists should be aware of these cutaneous lesions, which may be early clinical symptoms of infection. We reviewed the literature on cutaneous manifestations in the PubMed database from December 2019 and June 2020. From the cases described as case reports or series in 57 recent articles, it appears that skin lesions (i) are highly varied, (ii) may not be related to the severity of the condition and (iii) resolve spontaneously in a few days. The frequency of these lesions in COVID-19 patients varies between 1.8% and 20.4%. The major clinical forms described were maculopapular eruptions, acral areas of erythema with vesicles or pustules (pseudochilblain), urticarial lesions, other vesicular eruptions and livedo or necrosis. The lesions were mainly localized in the trunk and extremities. The majority of patients were male, aged between 4.5 and 89 years. A minority of the patients were children presenting with acral, chilblain-like lesions, papulo-vesicular eruptions or Kawasaki disease-like pediatric inflammatory multisystem syndrome. The mean duration of the lesions was a few days, but some lasting as little as 20 min and others as long as four weeks have been reported. The mean latency time in the majority of cases was between 1 and 14 days; however, in some patients, lesions appeared 2 to 5 days before the onset of COVID-19 symptoms. The histopathological features of these lesions also vary, corresponding to the diversity of clinical manifestations. These features underline the nature of epidermal and dermal vascular lesions—and in severe cases, microvascular injury and thrombosis—associated with COVID-19, and provide important clues to their pathological mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/32608380/ doi: 10.3390/dermatopathology7010002 id: cord-302147-6r67g5zk author: Kayaaslan, Bircan title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact date: 2020-10-16 words: 370.0 sentences: 35.0 pages: flesch: 62.0 cache: ./cache/cord-302147-6r67g5zk.txt txt: ./txt/cord-302147-6r67g5zk.txt summary: title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact The author emphasizes that even if semen has a very low possibility for transmission of the virus, the disease can be transmitted by the respiratory route due to the very close contact between partners. We think that even if severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is detected in a patient''s semen sample, it is quite difficult to say that the transmission between partners has solely been through semen. However, sexual contact carries a high risk in terms of SARS-CoV-2 transmission between partners through the respiratory secretions, not semen. Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 No evidence of severe acute respiratory syndrome-coronavirus 2 in semen of males recovering from coronavirus disease 2019 Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection abstract: nan url: https://doi.org/10.1159/000511618 doi: 10.1159/000511618 id: cord-293692-t5rfvyvj author: Kazi, Sajida title: The delights and perils of publishing, knowledge-sharing and critique during a pandemic: Observations from COVID-19 coagulopathies date: 2020-05-16 words: 1958.0 sentences: 102.0 pages: flesch: 40.0 cache: ./cache/cord-293692-t5rfvyvj.txt txt: ./txt/cord-293692-t5rfvyvj.txt summary: Despite the limited data, the high-stakes milieu and risk of litigation have led several institutions to adopt a more aggressive approach of using intermediate or full-dose anticoagulation for most of their critically ill COVID-19 patients admitted to the Intensive Care Unit [22] . The dissemination of knowledge during times of international crisis is guided by the principles first set out in the World Health Organization''s 2016 statement on data-sharing during public health emergencies, which incorporated lessons from the Ebola and Zika outbreaks, and was undersigned by many notable foundations and journals [23] . These principles have been adopted for use in the current pandemic through a call to share "research data and findings relevant to the novel coronavirus (COVID19) outbreak" in the same fashion [24] . Sharing research data and findings relevant to the novel coronavirus (COVID-19) outbreak abstract: nan url: https://api.elsevier.com/content/article/pii/S004938482030195X doi: 10.1016/j.thromres.2020.05.023 id: cord-318029-xd7nuahh author: Ke, Chunjin title: 2019 novel coronavirus disease (COVID-19) in hemodialysis patients: a report of two cases date: 2020-04-30 words: 1097.0 sentences: 93.0 pages: flesch: 47.0 cache: ./cache/cord-318029-xd7nuahh.txt txt: ./txt/cord-318029-xd7nuahh.txt summary: authors: Ke, Chunjin; Wang, Yufeng; Zeng, Xing; Yang, Chunguang; Hu, Zhiquan OBJECTIVE: To analyze the diagnosis and treatment of patients with chronic renal failure complicated with novel coronavirus pneumonia, and to evaluate the effect of blood purification technology on the treatment and prognosis of such patients METHODS: Two COVID-19 cases undergoing hemodialysis with chronic renal failure were retrospectively analysed in our hospital. On January 8, 2020, the Chinese Center for Disease Control and Prevention officially announced the pneumonia was caused by a new type of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2] . Hyperviremia and cytokine storm are important causes for COVID-19''s evolution to severe pneumonia, even to multiple organ dysfunction in a few cases [6] . Blood purification technology seems to be helpful for preventing COVID-19 patients with chronic renal failure from severe pneumonia or even multiple organ dysfunction. Interferon and cytokine responses to SARS-coronavirus infection abstract: OBJECTIVE: To analyze the diagnosis and treatment of patients with chronic renal failure complicated with novel coronavirus pneumonia, and to evaluate the effect of blood purification technology on the treatment and prognosis of such patients METHODS: Two COVID-19 cases undergoing hemodialysis with chronic renal failure were retrospectively analysed in our hospital. RESULTS: Two COVID-19 patients were admitted to hospital due to cough, with or without fever. Laboratory tests showed decreased lymphocyte count, elevated PCT, IL-10, IL-6, TNF-α, IL-2R, high-sensitivity cardiac troponin I, NT-proBNP, creatinine, and urea nitrogen. Chest CT scan showed multiple blurred plaques and patchy shadows in both patients. Two patients received continuous venovenous hemodiafiltration (CVVHDF) every other day for 4-6 hours everytime, in addition to the standard treatment. After CVVHDF, not only cytokines were reduced, but also liver function and cardiac function significantly improved. Both patients did not develop severe pneumonia. They were discharged on March 1, 2020 when meeting the discharge criteria. CONCLUSION: Two COVID-19 patients on maintenance hemodialysis discharged after a month of hospitalization. The removal of cytokines through blood purification technology may be beneficial for the recovery of COVID-19 patients. url: https://api.elsevier.com/content/article/pii/S000991202030271X doi: 10.1016/j.clinbiochem.2020.04.008 id: cord-294073-65h2mkdy author: Ke, Jia title: Strategies and recommendations for the management of gastrointestinal surgery during the COVID-19 pandemic: experience shared by Chinese surgeons date: 2020-07-03 words: 4150.0 sentences: 234.0 pages: flesch: 43.0 cache: ./cache/cord-294073-65h2mkdy.txt txt: ./txt/cord-294073-65h2mkdy.txt summary: We also recommend that each hospital should establish a group of diagnostic experts with responsibilities for risk stratification, especially for patients under investigation who need urgent surgery. • It is known that fever is one of the most common symptoms of COVID-19 and that patients with certain GI diseases (e.g. acute appendicitis, gastric perforation, intestinal obstruction) who required urgent care with emergency GI surgery often present with high fever as well. COVID-19-positive patients with GI bleeding with hemodynamic stability should undergo conservative treatments first, including angioembolization, before endoscopic treatment due to the high risk of endoscopy being an aerosol-generating procedure. For confirmed/high-risk COVID-19 patients and PUIs, diagnostic and therapeutic GI endoscopies should be performed in a negative-pressure room with Level Three precautions. For all surgical personnel involved in GI surgery for confirmed/ high-risk COVID-19 patients or for PUIs for COVID-19, we recommend the following protective measures (Figure 1 ). abstract: Novel coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing public-health pandemic worldwide. Although SARS-CoV-2 has been known to spread primarily through respiratory droplets, recent evidence also supports fecal/oral as an additional route of transmission, raising concerns over gastrointestinal (GI) transmission of the infection. Herein, we, as the front-line Chinese GI surgeons, would like to share our experience and lessons in the combat against COVID-19. It is essential to create science-based, rational, and practical strategies during the outbreak of COVID-19. Here, we provide multi-institutional consensus on minimizing disease transmission while continuing to provide care from all aspects for patients in GI surgery, including outpatient clinics, inpatient units, gastrointestinal endoscopy centers, and adjustments in perioperative care. Our experiences and recommendations are worth sharing and may help to establish specific infection-control and outcome measures. url: https://www.ncbi.nlm.nih.gov/pubmed/32661490/ doi: 10.1093/gastro/goaa030 id: cord-287304-h6wj7m8u author: Keil, Roger title: Governing the Sick City: Urban Governance in the Age of Emerging Infectious Disease date: 2007-12-07 words: 11689.0 sentences: 450.0 pages: flesch: 45.0 cache: ./cache/cord-287304-h6wj7m8u.txt txt: ./txt/cord-287304-h6wj7m8u.txt summary: While there has been much attention in recent years on the significance of global city regions in the new world economy (Brenner and Keil 2006) and while the governance and regulation of these regions has captured the imagination of academics and policymakers alike (Buck et al 2005; Harding 2005; Heinelt and Kübler 2005; Kantor and Savitch 2005; Scott 2001) , little has been said specifically about the growing pressures posed by the potential threat of infectious disease through the global network on urban governance. 2 For the area of urban planning and governance a more or less critical literature has begun to explore the spaces that cities have to maneuver in the rather open field of infectious disease preparedness planning and public health since the onset of the "new normal" after the attacks of 9/11 Malizia 2006; Matthew and Macdonald 2006) . abstract: Abstract: Based on a case study of the 2003 severe acute respiratory syndrome (SARS) outbreak in Toronto, Canada, this article suggests that we may have to rethink our common perception of what urban governance entails. Rather than operating solely in the conceptual proximity of social cohesion and economic competitiveness, urban governance may soon prove to be more centrally concerned with questions of widespread disease, life and death and the construction of new internal boundaries and regulations just at the time that globalization seems to suggest the breakdown of some traditional scalar incisions such as national boundaries in a post‐Westphalian environment. We argue that urban governance must face the new (or reemerging) challenge of dealing with infectious disease in the context of the “new normal” and that global health governance may be better off by taking the possibilities that rest in metropolitan governance more seriously. url: https://www.ncbi.nlm.nih.gov/pubmed/32313325/ doi: 10.1111/j.1467-8330.2007.00555.x id: cord-305130-vz72ldbo author: Keil, Shawn D. title: Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment date: 2020-05-14 words: 3457.0 sentences: 173.0 pages: flesch: 52.0 cache: ./cache/cord-305130-vz72ldbo.txt txt: ./txt/cord-305130-vz72ldbo.txt summary: title: Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment CONCLUSION: Riboflavin and UV light effectively reduced the titre of SARS‐CoV‐2 in both plasma and platelet products to below the limit of detection in tissue culture. The author of MERS-CoV study also indicated that they were not able to recover infectious virus from those patient samples using cell culture, suggesting that transfusion transmission is a low risk [15] . As with the plasma study, the virus titre was reduced to the limit of detection (≤0Á25 log PFU/ml) in all three donor platelet units. Riboflavin and UV light effectively reduced the titre of SARS-CoV-2 in both human platelet and plasma products to below the limit of detection using an in vitro plaque assay. Inactivation of Middle East respiratory syndrome coronavirus (MERS-CoV) in plasma products using a riboflavinbased and ultraviolet light-based photochemical treatment abstract: BACKGROUND AND OBJECTIVE: Severe acute respiratory distress syndrome coronavirus‐2 (SARS‐CoV‐2), the causative agent of coronavirus disease 2019 (COVID‐19), is a member of the coronavirus family. Coronavirus infections in humans are typically associated with respiratory illnesses; however, viral RNA has been isolated in serum from infected patients. Coronaviruses have been identified as a potential low‐risk threat to blood safety. The Mirasol Pathogen Reduction Technology (PRT) System utilizes riboflavin and ultraviolet (UV) light to render blood‐borne pathogens noninfectious, while maintaining blood product quality. Here, we report on the efficacy of riboflavin and UV light against the pandemic virus SARS‐CoV‐2 when tested in both plasma and platelets units. MATERIALS AND METHODS: Stock SARS‐CoV‐2 was grown in Vero cells and inoculated into either plasma or platelet units. Those units were then treated with riboflavin and UV light. The infectious titres of SARS‐CoV‐2 were determined by plaque assay using Vero cells. A total of five (n = 5) plasma and three (n = 3) platelet products were evaluated in this study. RESULTS: In both experiments, the measured titre of SARS‐CoV‐2 was below the limit of detection following treatment with riboflavin and UV light. The mean log reductions in the viral titres were ≥3·40 and ≥4·53 for the plasma units and platelet units, respectively. CONCLUSION: Riboflavin and UV light effectively reduced the titre of SARS‐CoV‐2 in both plasma and platelet products to below the limit of detection in tissue culture. The data suggest that the process would be effective in reducing the theoretical risk of transfusion transmitted SARS‐CoV‐2. url: https://doi.org/10.1111/vox.12937 doi: 10.1111/vox.12937 id: cord-301744-rx7ywew5 author: Kelleni, Mina T. title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality date: 2020-08-15 words: 373.0 sentences: 30.0 pages: flesch: 59.0 cache: ./cache/cord-301744-rx7ywew5.txt txt: ./txt/cord-301744-rx7ywew5.txt summary: title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality have reported SARS-CoV-2 viral load at diagnosis as an independent predictor of mortality. In a trial to explain the apparent contradictory results found in different studies as well as the lack of a distinct boundary between the viral loads that might be associated with a higher mortality rate or a higher recover rate; the author would like to suggest that SARS CoV-2 viral load should be only considered as a personalized reflection to the immune response to COVID-19 as well as to the genetic polymorphisms in SARS CoV-2 receptors 3 . ACE2 polymorphisms might be a better field of study than SARS CoV-2 viral load wishing to develop a genetic test that might predict and exempt, if possible, from COVID-19 related duty those who are more vulnerable to complications and mortality 4 SARS-CoV-2 viral load predicts COVID-19 mortality abstract: nan url: https://doi.org/10.1016/j.jinf.2020.08.018 doi: 10.1016/j.jinf.2020.08.018 id: cord-353599-cw29edwr author: Kelleni, Mina T. title: Early use of Non-steroidal anti-inflammatory drugs in COVID-19 might reverse pathogenesis, prevent complications and improve clinical outcomes date: 2020-11-04 words: 2610.0 sentences: 116.0 pages: flesch: 39.0 cache: ./cache/cord-353599-cw29edwr.txt txt: ./txt/cord-353599-cw29edwr.txt summary: In this manuscript, we present a novel theory to explain the pathogenesis of COVID-19; lymphocyte distraction theory upon which the author has used, in a preprinted protocol, non-steroidal anti-inflammatory drugs (NSAIDs); diclofenac potassium, ibuprofen and ketoprofen, successfully to treat COVID-19 patients. It was previously suggested that SARS CoV induced lymphopenia is likely to be caused by indirect mechanisms such as an increase in cortisol levels that occurred as part of the body stress response to this severe respiratory viral infection or by an iatrogenic effect of glucocorticoids used to manage those patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: The pathogenesis of Coronavirus disease 2019 is still obscure and the need for exploration of possible mechanisms to suggest drugs based on knowledge should never be delayed. In this manuscript, we present a novel theory to explain the pathogenesis of COVID-19; lymphocyte distraction theory upon which the author has used, in a preprinted protocol, non-steroidal anti-inflammatory drugs (NSAIDs); diclofenac potassium, ibuprofen and ketoprofen, successfully to treat COVID-19 patients. Furthermore, we agree with a recommendation that glucocorticoids should not be used routinely for COVID-19 patients and suggested to be beneficial only for patients with late acute respiratory distress syndrome. A clinical proof of ibuprofen safety in COVID-19 has been published by other researchers and we suggest that early administration of NSAIDs, including ibuprofen, in COVID-19 is not only safe but it might also prevent COVID-19 complications and this manuscript explains some of the suggested associated protective mechanisms. url: https://api.elsevier.com/content/article/pii/S0753332220311744 doi: 10.1016/j.biopha.2020.110982 id: cord-337200-2qwty2jp author: Kempfle, J. S. title: Management von Patienten mit Tracheostoma während der COVID-19-Pandemie: Literaturüberblick und Demonstration date: 2020-06-08 words: 3529.0 sentences: 479.0 pages: flesch: 52.0 cache: ./cache/cord-337200-2qwty2jp.txt txt: ./txt/cord-337200-2qwty2jp.txt summary: Die durch das neue Coronavirus, auch Severe-Acute-Respiratory-Syndrome-Coronavirus 2, kurz SARS-CoV-2 genannt, ausgelöste Erkrankung (COVID19) , zeichnet sich durch eine hohe Variabilität an Symptomen aus. Während eine große Anzahl an SARS-CoV-2-positiven Patienten keine oder nur leichte Symptome einer oberen Atemwegsinfektion hat, gibt es eine Gruppe von Patienten, die eine deutliche Einschränkung ihrer Lungenfunktion mit Pneumonie bis hin zur lebensbedrohlichen Variante mit akutem Lungenversagen ("acute respiratory distress syndrome", ARDS) entwickelt [18, 37, 40] . Eine kürzlich in Nature Medicine erschienene Studie, welche sich mit den Erkältungs-Coronaviren beschäftigte, konnte diese sowohl in der ausgeatmeten Luft über einen Zeitraum von 30 min als auch in erhöhter Konzentration in Aerosolen und Tröpfchen von wiederholt hustenden Patienten nachweisen [19] . Während erste Leitlinien sowohl in Deutschland als auch international vorläufige Empfehlungen zu Vorsichtsmaßnahmen bei In-und Extubationen oder Tracheotomien von beatmungspflichtigen COVID-19-Patienten aussprechen [1, 4, 12, 20, 22, 30, 35] , ist vergleichsweise wenig Information zum weiteren Umgang mit einem tracheotomierten SARS-CoV-2-positiven Patienten auf Station, ambulant oder während der Rehabilitation zu finden [10] . abstract: BACKGROUND: Since emergence of the new coronavirus in China in December 2019, many countries have been struggling to control skyrocketing numbers of infections, including among healthcare personnel. It has now been clearly demonstrated that SARS-CoV‑2 resides in the upper airways and transmits easily via aerosols and droplets, which significantly increases the risk of infection when performing upper airway procedures. Ventilated COVID-19 patients in a critical condition in the intensive care unit may require tracheotomy for long-term ventilation and to improve weaning. However, the risk of secondary infection of medical personnel performing subsequent tracheostomy care remains unclear. OBJECTIVE: This study aimed to evaluate the risk of droplet dispersion during tracheostomy tube change and overview tracheostomy tube change in COVID-19 patients. MATERIALS AND METHODS: The current literature was reviewed, quantitative and qualitative analyses of droplet formation during tracheostomy tube change in n = 8 patients were performed, and an overview of and checklist for tracheostomy tube change were compiled. RESULTS: This study demonstrates that tracheostomy tube change, in particular insertion of the new tube, may cause significant droplet formation. The aerosolization of particles smaller than 5 µm was not analyzed. CONCLUSION: Our data, together with the current literature, clearly emphasize that tracheostomy care is associated with a high infection risk and should only be performed by a small group of well-trained, maximally protected healthcare personnel. url: https://www.ncbi.nlm.nih.gov/pubmed/32514605/ doi: 10.1007/s00106-020-00892-3 id: cord-329290-vqvujry3 author: Kempker, Russell R title: Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date: 2020-06-28 words: 1907.0 sentences: 90.0 pages: flesch: 55.0 cache: ./cache/cord-329290-vqvujry3.txt txt: ./txt/cord-329290-vqvujry3.txt summary: HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. abstract: Among 283 symptomatic healthcare personnel (HCP) tested for SARS-CoV-2, 51 (18%) were positive. Among those 51 HCP, self reported loss of smell and taste were present in 51% and 52.9%, respectively, with either present in 60.8%. These symptoms had high specificity (93% each, 96% for either) for a positive SARS-CoV-2 test. url: https://doi.org/10.1093/cid/ciaa877 doi: 10.1093/cid/ciaa877 id: cord-336488-opjjowcq author: Kenanidis, Eustathios title: Organizing an Orthopaedic Department During COVID-19 Pandemic to Mitigate In-Hospital Transmission: Experience From Greece date: 2020-06-17 words: 3384.0 sentences: 160.0 pages: flesch: 42.0 cache: ./cache/cord-336488-opjjowcq.txt txt: ./txt/cord-336488-opjjowcq.txt summary: The aim of this paper is to review the existing orthopaedic literature and to present the principles of management and care implemented in the orthopaedic departments of a tertiary academic hospital in Greece to operate during COVID-19 pandemic in order to mitigate the risk of in-hospital transmission of SARS-CoV-2 to the medical, nursing and administrative orthopaedic personnel. In addition, we presented the clinical indications to delineate orthopaedic patients who deserve emergency or urgent in-hospital care from those that can be treated in the outpatient setting, as well as from the day surgery clinics or could not be admitted in the hospital, in order to decrease the SARS-CoV-2 transmission load. The proposed principles of management and care are deployed below as (1) general management of the orthopaedic departments, (2) recommendations for the management of traumatic orthopaedic injuries, (3) hospital pathways for the admitted orthopaedic patients (4) workflow of the isolated and negative pressure COVID-19 operating theatre (COT) and (5) postoperative care of the COVID-19 infected patients. abstract: The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerging in Wuhan city of China, was the cause of a rare type of pneumonia evolving rapidly in pandemic early at the beginning of 2020. The rapid human-to-human transmission of SARS-CoV-2 increases the risk of in-hospital transmission, requiring re-definement of musculoskeletal trauma management and postoperative care. Following the review of the existing literature on COVID-19 and similar infectious diseases, National and Hospital Board instructions for Infectious Diseases, as well as the consensus for surgical care by the consortium of the Orthopaedic Department Directors, we present the outline of the implemented principles in the orthopaedic departments of a tertiary academic hospital in Greece to operate during COVID-19 pandemic. Our overall objectives were to decrease the admission load and mitigate the risk of in-hospital transmission of SARS-CoV-2. The principles involve the management of the Orthopaedic medical and nursing personnel, alterations of the workflow in the wards, operating rooms and outpatient clinics from the admission to the discharge of an orthopaedic patient. In addition, we present the recommended principles of management of traumatic orthopaedic injuries highlighting those deserving admission and in-hospital care and those that can be treated in the outpatient setting or day surgery clinics. url: https://doi.org/10.7759/cureus.8676 doi: 10.7759/cureus.8676 id: cord-023875-5mu5ra29 author: Keng, Choong-Tat title: Molecular and Biochemical Characterization of the SARS-CoV Accessory Proteins ORF8a, ORF8b and ORF8ab date: 2009-07-22 words: 5219.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-023875-5mu5ra29.txt txt: ./txt/cord-023875-5mu5ra29.txt summary: Epidemiological studies have revealed that the part of the viral genome that encodes for ORF8a and ORF8b showed major variations and the animal isolates contain an additional 29-nucleotide sequence which is absent in most of the human isolates. Although the mutations in the ORF8 region do not appear to have any adverse effect on the survival of the virus, it is conceivable that the ORF8a, ORF8b and ORF8ab proteins have different stabilities and/or functions, and hence would contribute differently to viral replication and/or pathogenesis in vivo. Since SARS-CoV grows well in cell culture, different groups also generated ORF8a and ORF8b specific antibodies in order to determine their expression during infection in vitro. As described above, the accessory proteins ORF8a and ORF8b are expressed during infection in vitro, but replacing them with ORF8ab does not affect SARS-CoV replication in cell culture or small animal models. abstract: A novel coronavirus was identified as the aetiological agent for the global outbreak of severe acute respiratory syndrome (SARS) at the beginning of the twenty-first century. The SARS coronavirus genome encodes for proteins that are common to all members of the coronavirus, i.e. replicase polyproteins (pp1a and pp1b) and structural proteins (spike, membrane, nucleocapsid and envelope), as well as eight accessory proteins. The accessory proteins have been designated as open reading frames (ORF) 3a, 3b, 6, 7a, 7b, 8a, 8b and 9b, and they do not show significant homology to viral proteins of other known coronaviruses. Epidemiological studies have revealed that the part of the viral genome that encodes for ORF8a and ORF8b showed major variations and the animal isolates contain an additional 29-nucleotide sequence which is absent in most of the human isolates. As a result, ORF8a and ORF8b in the human isolates become one ORF, termed ORF8ab. In this chapter, we will discuss the genetic variation in the ORF8 region, expression of ORF8a, ORF8b and ORF8ab during infection, cellular localization and posttranslational modification of ORF8a, ORF8b and ORF8ab, participation of ORF8a, ORF8b and ORF8ab in viral–viral interactions, their effects on other viral proteins and impact on viral replication and/or pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176222/ doi: 10.1007/978-3-642-03683-5_12 id: cord-332196-03cklmm3 author: Kennedy, Amy J. title: Retesting for severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Patterns of testing from a large US healthcare system date: 2020-08-10 words: 1056.0 sentences: 61.0 pages: flesch: 52.0 cache: ./cache/cord-332196-03cklmm3.txt txt: ./txt/cord-332196-03cklmm3.txt summary: Often decisions on who to test are left to individual clinicians, which leads to questions about when and who to retest for COVID-19, how often false positives or negatives might occur, and the duration of positivity. This report describes patterns of SARS-CoV-2 nucleic acid polymerase chain reaction (PCR) retesting in inpatients and outpatients within a large US healthcare system. We performed a retrospective chart review of all inpatients and outpatients aged ≥18 years receiving care within the University of Pittsburgh Medical Center (UPMC) with ≥2 SARS-CoV-2 PCR tests with an initial test between March 3 and May 3, 2020, and a subsequent test before May 21, 2020. In this retrospective study of a large US healthcare system, we found that retesting for SARS-CoV-2 was uncommon and often resulted in multiple negative tests. Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: impact of the interval between tests abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32772941/ doi: 10.1017/ice.2020.413 id: cord-260429-5wsj003j author: Kenyon, Chris title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study date: 2020-04-06 words: 2260.0 sentences: 160.0 pages: flesch: 61.0 cache: ./cache/cord-260429-5wsj003j.txt txt: ./txt/cord-260429-5wsj003j.txt summary: title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV1. Methods At a country level, linear regression was used to assess the association between COVID19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID19 epidemic and testing intensity. Conclusion Whilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections. /2020 In this ecological study we found that countries that promoted widespread face mask 185 usage had lower cumulative numbers of COVID-19 diagnosed after controlling for 186 testing intensity and age of the epidemic. abstract: Background The reasons for the large differences between countries in the sizes of their SARS CoV2 epidemics is unknown. Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV1. We hypothesized that population level usage of face masks may be negatively associated SARS CoV2 spread. Methods At a country level, linear regression was used to assess the association between COVID19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID19 epidemic and testing intensity. Results Eight of the 49 countries with available data advocated wearing face masks in public: China, Czechia, Hong Kong, Japan, Singapore, South Korea, Thailand and Malaysia. In multivariate analysis face mask use was negatively associated with number of COVID19 cases/inhabitant (coef. -326, 95% CI -601- -51, P=0.021). Testing intensity was positively associated with COVID-19 cases (coef. 0.07, 95% CI 0.05-0.08, P<0.001). Conclusion Whilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections. url: https://doi.org/10.1101/2020.03.31.20048652 doi: 10.1101/2020.03.31.20048652 id: cord-316970-n2dly3oa author: Kerbaj, Jad title: COVID-19: The New Caledonia experience date: 2020-05-16 words: 1444.0 sentences: 115.0 pages: flesch: 68.0 cache: ./cache/cord-316970-n2dly3oa.txt txt: ./txt/cord-316970-n2dly3oa.txt summary: Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island''s hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. abstract: New Caledonia is a French associated territory in the South Pacific Ocean. While COVID-19 is expanding over the world, we seem to be well preserved with a total of 18 documented cases. We report the measures implemented on our island that probably helped containing an epidemic spread. url: https://doi.org/10.1093/cid/ciaa600 doi: 10.1093/cid/ciaa600 id: cord-305610-v1hn934x author: Kerslake, Rachel title: Co-expression of peripheral olfactory receptors with SARS-CoV-2 infection mediators: Potential implications beyond loss of smell as a COVID-19 symptom date: 2020-06-17 words: 3002.0 sentences: 141.0 pages: flesch: 41.0 cache: ./cache/cord-305610-v1hn934x.txt txt: ./txt/cord-305610-v1hn934x.txt summary: Using Gene Expression Profiling Interactive Analysis, The Cancer Genome Atlas, Genotype-Tissue Expression, cBioPortal and Shiny Methylation Analysis Resource Tool, we highlight the expression of peripheral ORs in both healthy and malignant tissues, and describe their co-expression with key mediators of SARS-CoV-2 infection, such as ACE2 and TMPRSS2, as well as cathepsin L (CTSL; another cellular protease mediating SARS-CoV-2 infection of host cells). The present study aimed to identify, both in normal and cancer tissues, the co-expression profile of a number of ORs which are known to be expressed in peripheral tissues in relationship to key mediators of the SARS-coV-2 infection, namely AcE2, TMPRSS2 and cTSL. In conclusion, the present study offers new data regarding the expression of ORs in peripheral tissues and their co-expression pattern with key mediators of SARS-coV-2 cell entry and infection (i.e., AcE2, TMPRSS2, and cTSL). abstract: Severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) enters into human host cells via mechanisms facilitated mostly by angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2). New loss of smell (anosmia/hyposmia) is now recognized as a COVID-19 related symptom, which may be caused by SARS-CoV-2 infection and damage of the olfactory receptor (OR) cells in the nasal neuroepithelium and/or central involvement of the olfactory bulb. ORs are also expressed peripherally (e.g., in tissues of the gastrointestinal and respiratory systems) and it is possible that their local functions could also be impaired by SARS-CoV-2 infection of these tissues. Using Gene Expression Profiling Interactive Analysis, The Cancer Genome Atlas, Genotype-Tissue Expression, cBioPortal and Shiny Methylation Analysis Resource Tool, we highlight the expression of peripheral ORs in both healthy and malignant tissues, and describe their co-expression with key mediators of SARS-CoV-2 infection, such as ACE2 and TMPRSS2, as well as cathepsin L (CTSL; another cellular protease mediating SARS-CoV-2 infection of host cells). A wide expression profile of peripheral ORs was noted, particularly in tissues such as the prostate, testis, thyroid, brain, liver, kidney and bladder, as well as tissues with known involvement in cardio-metabolic disease (e.g., the adipose tissue, pancreas and heart). Among these, OR51E2, in particular, was significantly upregulated in prostate adenocarcinoma (PRAD) and co-expressed primarily with TMPRSS2. Functional networks of this OR were further analysed using the GeneMANIA interactive tool, showing that OR51E2 interacts with a plethora of genes related to the prostate. Further in vitro and clinical studies are clearly required to elucidate the role of ORs, both at the olfactory level and the periphery, in the context of COVID-19. url: https://doi.org/10.3892/ijmm.2020.4646 doi: 10.3892/ijmm.2020.4646 id: cord-287447-5lzzobl3 author: Keyaerts, Els title: In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date: 2004-10-08 words: 2159.0 sentences: 130.0 pages: flesch: 53.0 cache: ./cache/cord-287447-5lzzobl3.txt txt: ./txt/cord-287447-5lzzobl3.txt summary: Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Glycyrrhizin (an active component of liquorice roots), niclosamide (an antihelminthic drug), nelfinavir (a human immunodeficiency deficiency virus (HIV) protease inhibitor), and SNAP (a nitric oxide donor) were reported to have an antiviral effect against SARS-CoV [12] [13] [14] [15] . In this study we report the in vitro antiviral activity of chloroquine against SARS-CoV Frankfurt 1 strain infection. The IC 50 of chloroquine inhibition of SARS-CoV replication in Vero E6 cells, 8.8 lM, is below (1000-fold) the plasma concentrations of chloroquine that are reached in human plasma, following treatment with chloroquine (for acute malaria) at a dose of 25 mg/kg over three days [27] . Our results show that chloroquine inhibits the replication of SARS-CoV in Vero E6 cells. abstract: Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Chloroquine is a clinically approved drug effective against malaria. We tested chloroquine phosphate for its antiviral potential against SARS-CoV-induced cytopathicity in Vero E6 cell culture. Results indicate that the IC50 of chloroquine for antiviral activity (8.8±1.2μM) was significantly lower than its cytostatic activity; CC50 (261.3±14.5μM), yielding a selectivity index of 30. The IC50 of chloroquine for inhibition of SARS-CoV in vitro approximates the plasma concentrations of chloroquine reached during treatment of acute malaria. Addition of chloroquine to infected cultures could be delayed for up to 5h postinfection, without an important drop in antiviral activity. Chloroquine, an old antimalarial drug, may be considered for immediate use in the prevention and treatment of SARS-CoV infections. url: https://api.elsevier.com/content/article/pii/S0006291X0401839X doi: 10.1016/j.bbrc.2004.08.085 id: cord-284038-93s3ffoy author: Keyhanian, Kiandokht title: SARS-CoV-2 and nervous system: From pathogenesis to clinical manifestation date: 2020-11-07 words: 11701.0 sentences: 592.0 pages: flesch: 42.0 cache: ./cache/cord-284038-93s3ffoy.txt txt: ./txt/cord-284038-93s3ffoy.txt summary: Since the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a growing body of evidence indicates that besides common COVID-19 symptoms, patients may develop various neurological manifestations affecting both the central and peripheral nervous systems as well as skeletal muscles. Growing number of case reports and/or series indicate that a variety of neurological conditions and post-viral triggered autoimmune complications, as we discuss below, occur in association with SARS-CoV-2 infection which mainly include Guillain-Barré syndromes (GBSs) (table 2), myopathy and rhabdomyolysis (table 2) , encephalopathy, meningoencephalitis, encephalomyelitis, and myelitis (table 3) . Moreover, two cases of acute necrotizing encephalopathy (ANE) in patients with COVID-19 positivity from nasopharyngeal and oropharyngeal swab, but without CSF PCR for SARS-CoV-2 data, were reported in the literature (Poyiadji, Shahin, 2020 , Radmanesh et al. abstract: Since the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a growing body of evidence indicates that besides common COVID-19 symptoms, patients may develop various neurological manifestations affecting both the central and peripheral nervous systems as well as skeletal muscles. These manifestations can occur prior, during and even after the onset of COVID-19 general symptoms. In this Review, we discuss the possible neuroimmunological mechanisms underlying the nervous system and skeletal muscle involvement, and viral triggered neuroimmunological conditions associated with SARS-CoV-2, as well as therapeutic approaches that have been considered for these specific complications worldwide. url: https://www.sciencedirect.com/science/article/pii/S0165572820306974?v=s5 doi: 10.1016/j.jneuroim.2020.577436 id: cord-253862-jl1zhg13 author: Khalaf, Khalil title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 words: 14595.0 sentences: 760.0 pages: flesch: 45.0 cache: ./cache/cord-253862-jl1zhg13.txt txt: ./txt/cord-253862-jl1zhg13.txt summary: Although this novel virus is less severe than the first SARS-CoV outbreak, human-to-human transmission remains very high and the number of cases continues to rise exponentially in major urban areas, highlighting the urgent need to develop new containment, diagnostic, and treatment protocols. In the case of SARS-CoV-2, viral evasion of the innate immune system leads to an increase in cytokine production and late CD4+/CD8+ response, which then leads to pathogenic inflammation in patients with high viral loads. (ChiCTR2000029308), involving severe SARS-CoV-2 cases, compared lopinavir/ritonavir treatment with standard care alone, and they showed that the antivirals yielded no clinical benefits. In an open-label control study conducted by Cai et al., the antiviral activity of favipiravir + IFN-α was compared to that of lopinavir/ritonavir + IFN-α in patients with confirmed SARS-CoV-2 infection. abstract: The emergence and rapid spread of SARS-CoV-2 in December 2019 has brought the world to a standstill. While less pathogenic than the 2002–2003 SARS-CoV, this novel betacoronavirus presents a global threat due to its high transmission rate, ability to invade multiple tissues, and ability to trigger immunological hyperactivation. The identification of the animal reservoir and intermediate host were important steps toward slowing the spread of disease, and its genetic similarity to SARS-CoV has helped to determine pathogenesis and direct treatment strategies. The exponential increase in cases has necessitated fast and reliable testing procedures. Although RT-PCR remains the gold standard, it is a time-consuming procedure, paving the way for newer techniques such as serologic tests and enzyme immunoassays. Various clinical trials using broad antiviral agents in addition to novel medications have produced controversial results; however, the advancement of immunotherapy, particularly monoclonal antibodies and immune modulators is showing great promise in clinical trials. Non-orthodox medications such as anti-malarials have been tested in multiple institutions but definitive conclusions are yet to be made. Adjuvant therapies have also proven to be effective in decreasing mortality in the disease course. While no formal guidelines have been established, the multitude of ongoing clinical trials as a result of unprecedented access to research data brings us closer to halting the SARS-CoV-2 pandemic. url: https://doi.org/10.3389/fimmu.2020.570927 doi: 10.3389/fimmu.2020.570927 id: cord-301828-qux5hvcw author: Khalifa, Ibrahim title: Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date: 2020-08-11 words: 2519.0 sentences: 146.0 pages: flesch: 43.0 cache: ./cache/cord-301828-qux5hvcw.txt txt: ./txt/cord-301828-qux5hvcw.txt summary: We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS‐CoV‐2 by assembling with the catalytic dyad residues of its 3CL(pro) using molecular operating environment (MOE 09). Likewise, tannin-type compounds, such as epiacutissimins A and B, castalin, vescalin, chebulagic acid, and punicalagin showed anti-herpesvirus activity via targeting viral glycoprotein-glycosaminoglycan binding to inhibit access and cell-to-cell feast (Lin et al., 2011; Aires, 2020 The current study was designed to find out a potent inhibitor against COVID-19 from 19 structural different hydrolysable tannins which could target the main protease of SARS-CoV-2 using in silico approaches (molecular docking and drug-likeness scan). Among these hydrolysable tannins, pedunculagin, strongly interacted with the catalytic dyad residues (Cys-145 and His-41) of SARS-CoV-2-3CL pro , with sense binding affinity, docking score, and ADMET properties. Herein, we screened the structural relationship activity of 19 hydrolysable tannins as potential antiviral components and we chose the top three hits that may inhibit the main protease of SARS-CoV-2 and hence virus copying. abstract: Coronavirus epidemic 2019 (COVID‐19), instigated by SARS‐CoV‐2 virus, is recently raising worldwide and inspiring global health worries. The main 3‐chymotrypsin‐like cysteine protease (3CL(Pro)) enzyme of SARS‐CoV‐2, which operates its replication, could be used as a medication discovery point. We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS‐CoV‐2 by assembling with the catalytic dyad residues of its 3CL(pro) using molecular operating environment (MOE 09). Results discovered that pedunculagin, tercatain, and castalin intensely interacted with the receptor binding site and catalytic dyad (Cys145 and His41) of SARS‐CoV‐2. Our analyses estimated that the top three hits might serve as potential inhibitor of SARS‐CoV‐2 leading molecules for additional optimization and drug development process to combat COVID‐19. This study unleashed that tannins with specific structure could be utilized as natural inhibitors against COVID‐19. PRACTICAL APPLICATIONS: The 3CL(Pro) controls SARS‐CoV‐2 copying and manages its life series, which was targeted in case of SARS‐CoV and MERS‐CoV coronavirus. About 19 hydrolysable tannins were computed against 3CL(pro) of SARS‐CoV‐2. Pedunculagin, tercatain, and castalin interacted with Cys145 and His41 of SARS‐CoV‐2‐3CL(pro). Pedunculagin‐SARS‐CoV‐2‐3CL(pro) remain stable, with no obvious fluctuations. We predicted that the understandings gained in the current research may evidence valued for discovering and unindustrialized innovative natural inhibitors for COVID‐19 in the nearby future. url: https://www.ncbi.nlm.nih.gov/pubmed/32783247/ doi: 10.1111/jfbc.13432 id: cord-274459-781by93r author: Khalifa, Shaden A. M. title: Comprehensive Overview on Multiple Strategies Fighting COVID-19 date: 2020-08-11 words: 5466.0 sentences: 311.0 pages: flesch: 51.0 cache: ./cache/cord-274459-781by93r.txt txt: ./txt/cord-274459-781by93r.txt summary: Our review aims to evaluate strategies of the most affected countries from different continents all over the world (China, Italy, Germany, France, Spain, America, Canada, Brazil, UK, India, Japan, Singapore, Iran, Korea, and Australia) for confronting the epidemic as it explains the best practices that could help other countries to overcome current or any upcoming pandemic. Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . abstract: Lately, myriad of novel viruses have emerged causing epidemics such as SARS, MERS, and SARS-CoV-2, leading to high mortality rates worldwide. Thus, these viruses represented a challenging threat to mankind, especially considering the miniscule data available at our disposal regarding these novel viruses. The entire world established coordinative relations in research projects regarding drug and vaccine development on the external range, whereas on the internal range, all countries declared it an emergency case through imposing different restrictions related to their border control, large gatherings, school attendance, and most social activities. Pandemic combating plans prioritized all sectors including normal people, medical staff politicians, and scientists collectively shouldered the burden. Through planning and learning the previous lessons from SARS and MERS, healthcare systems could succeed in combating the viral spread and implications of these new pandemics. Different management strategies including social distance, social awareness and isolation represented successful ways to slow down the spread of the pandemic. Furthermore, pre-preparedness of some countries for emergencies is crucial to minimize the consequences of the crisis. url: https://doi.org/10.3390/ijerph17165813 doi: 10.3390/ijerph17165813 id: cord-322204-kc7dy2za author: Khalil, Asma title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date: 2020-08-08 words: 448.0 sentences: 50.0 pages: flesch: 60.0 cache: ./cache/cord-322204-kc7dy2za.txt txt: ./txt/cord-322204-kc7dy2za.txt summary: title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32770224/ doi: 10.1093/cid/ciaa893 id: cord-252725-e3pazjdi author: Khalil, Ayman title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 words: 8759.0 sentences: 338.0 pages: flesch: 30.0 cache: ./cache/cord-252725-e3pazjdi.txt txt: ./txt/cord-252725-e3pazjdi.txt summary: In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . abstract: Polyphenols are a large family of more than 10,000 naturally occurring compounds, which exert countless pharmacological, biological and physiological benefits for human health including several chronic diseases such as cancer, diabetes, cardiovascular, and neurological diseases. Their role in traditional medicine, such as the use of a wide range of remedial herbs (thyme, oregano, rosemary, sage, mint, basil), has been well and long known for treating common respiratory problems and cold infections. This review reports on the most highlighted polyphenolic compounds present in up to date literature and their specific antiviral perceptive properties that might enhance the body immunity facing COVID-19, and other viral infectious diseases. In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Thus, polyphenols ought to be considered as a potential and valuable source for designing new drugs that could be used effectively in the combat against COVID‐19 and other rigorous diseases. url: https://doi.org/10.1007/s13659-020-00271-z doi: 10.1007/s13659-020-00271-z id: cord-316129-mjg3un0l author: Khamar, Pooja title: Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases date: 2020-07-13 words: 3672.0 sentences: 228.0 pages: flesch: 59.0 cache: ./cache/cord-316129-mjg3un0l.txt txt: ./txt/cord-316129-mjg3un0l.txt summary: title: Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases METHOD: In an experimental setup, flap creation was performed on enucleated goat''s eyes (n = 8) mounted on a stand using One Use-Plus SBK Moria microkeratome (Moria SA) to assess the spread of aerosols and droplets using high-speed shadowgraphy. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. 13, 14 Therefore, we quantified the aerosol and droplet generation during flap creation using the Moria One Use-Plus SBK microkeratome (Moria SA) and assessed their trajectory using high-speed shadowgraphy and fluid mechanics principles. abstract: PURPOSE: To quantify the atomization of liquid over the cornea during flap creation using microkeratome using high-speed shadowgraphy. SETTING: Laboratory investigational study. DESIGN: Laboratory study. METHOD: In an experimental setup, flap creation was performed on enucleated goat's eyes (n = 8) mounted on a stand using One Use-Plus SBK Moria microkeratome (Moria SA) to assess the spread of aerosols and droplets using high-speed shadowgraphy. Two conditions were computed. A constant airflow assumed uniform air velocity throughout the room. A decaying jet assumed that local air velocity at the site of measurements was smaller than the exit velocity from the air duct. RESULTS: With the advancement of the microkeratome across the wet corneal surface, the atomization of a balanced salt solution was recorded on shadowgraphy. The minimum droplet size was ∼90 μm. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. CONCLUSIONS: The microkeratome-assisted LASIK flap creation does seem to cause spread of droplets. The droplet diameters and velocities did not permit the formation of aerosols. Therefore, the risk of transmission of the virus to the surgeon and surgical personnel due to the microkeratome procedure seems to be low. url: https://www.ncbi.nlm.nih.gov/pubmed/32675657/ doi: 10.1097/j.jcrs.0000000000000326 id: cord-352322-tsjwnvkk author: Khamassi Khbou, Médiha title: Coronaviruses in farm animals: Epidemiology and public health implications date: 2020-09-25 words: 8114.0 sentences: 453.0 pages: flesch: 49.0 cache: ./cache/cord-352322-tsjwnvkk.txt txt: ./txt/cord-352322-tsjwnvkk.txt summary: As consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (TGEV) of swine and the bovine CoV (BCoV) likely originated from the closely related canine coronavirus (CCoV) (Pratelli, 2011) . Coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean CoVs were also considered, as marine mammals are a food source in many countries around the world. Since the first case of human infected by the MERS-CoV was identified in September 2012 in Saudi Arabia (World Health Organization, 2019), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (Omrani, Al-Tawfiq, & Memish, 2015) . Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Infection with a new porcine respiratory coronavirus in Denmark: Serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies abstract: Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross‐species transmission easy. In fact, increasing contact between different animal species fosters cross‐species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human‐animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs. url: https://www.ncbi.nlm.nih.gov/pubmed/32976707/ doi: 10.1002/vms3.359 id: cord-278362-pwi48i20 author: Khan, Abbas title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) date: 2020-06-18 words: 5136.0 sentences: 287.0 pages: flesch: 55.0 cache: ./cache/cord-278362-pwi48i20.txt txt: ./txt/cord-278362-pwi48i20.txt summary: title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) Furthermore, results from molecular dynamics simulation and total binding free energy revealed that Saquinavir and TCM5280805 target the catalytic dyad (His41 and Cys145) and possess stable dynamics behavior. In this study, the protein of SARS-COV-2 (3CLpro, also named 3-chymotrypsin-like protease) was subjected to drug repurposing and virtual screening for potent drug identification followed by molecular dynamics simulation and binding free energy calculation. In the current study, the repurposing of anti-HIV drugs against the SARS-COV-2 main protease was carried out using structure-based screening methods. In this study, based on the results of bioinformatics analysis, we targeted 3CLpro from SARS-COV-2 using drugs repurposing (anti-HIV drugs) virtual drugs screening (TCM) approaches to shortlist the most potent compounds for the possible treatment. abstract: The current coronavirus (SARS-COV-2) pandemic and phenomenal spread to every nook and cranny of the world has raised major apprehensions about the modern public health care system. So far as a result of this epidemic, 4,434,653 confirmed cases and 302,169 deaths are reported. The growing infection rate and death toll demand the use of all possible approaches to design novel drugs and vaccines to curb this disease. In this study, we combined drugs repurposing and virtual drug screening strategies to target 3CLpro, which has an essential role in viral maturation and replication. A total of 31 FDA approved anti-HIV drugs, and Traditional Chinese medicines (TCM) database were screened to find potential inhibitors. As a result, Saquinavir, and five drugs (TCM5280805, TCM5280445, TCM5280343, TCM5280863, and TCM5458190) from the TCM database were found as promising hits. Furthermore, results from molecular dynamics simulation and total binding free energy revealed that Saquinavir and TCM5280805 target the catalytic dyad (His41 and Cys145) and possess stable dynamics behavior. Thus, we suggest that these compounds should be tested experimentally against the SARS-COV-2 as Saquinavir has been reported to inhibit HIV protease experimentally. Considering the intensity of coronavirus dissemination, the present research is in line with the idea of discovering the latest inhibitors against the coronavirus essential pathways to accelerate the drug development cycle. Communicated by Ramaswamy H. Sarma. url: https://doi.org/10.1080/07391102.2020.1779128 doi: 10.1080/07391102.2020.1779128 id: cord-300991-ipy24zxp author: Khan, Amira Sayed title: Obesity and COVID-19: Oro-Naso-Sensory Perception date: 2020-07-08 words: 5971.0 sentences: 314.0 pages: flesch: 47.0 cache: ./cache/cord-300991-ipy24zxp.txt txt: ./txt/cord-300991-ipy24zxp.txt summary: Through a recent upsurge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, the clinical assessment of most of the coronavirus disease 19 (COVID-19) patients clearly presents a health condition with the loss of oro-naso-sensory (ONS) perception, responsible for the detection of flavor and savor. Hence, obesity represents a great risk factor for SARS-CoV-2 infection, as it may hide the viral-associated altered ONS symptoms, thus leading to a high mortality rate in these subjects. Moreover, the number of immunosuppressive T-regulatory, Treg (CD4 + CD25 + Foxp3 + ) cells and concentrations of IL-6, IL-10, and C-reactive protein (CRP) were upregulated in patients with severe COVID-19 [18] , suggesting that SARS-CoV-2 infection may lead to "over-immunosuppression" in the case of obesity ( Figure 1 ). SARS-CoV-2 infection may further aggravate the ONS functions; mask the obesity-induced inflammation, including loss of taste and smell; and render the obese subjects more vulnerable and prone to severe pathophysiological consequences such as RTI, leading to death. abstract: Through a recent upsurge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, the clinical assessment of most of the coronavirus disease 19 (COVID-19) patients clearly presents a health condition with the loss of oro-naso-sensory (ONS) perception, responsible for the detection of flavor and savor. These changes include anosmia and dysgeusia. In some cases, these clinical manifestations appear even before the general flu-like symptoms, e.g., sore throat, thoracic oppression and fever. There is no direct report available on the loss of these chemical senses in obese COVID-19 patients. Interestingly, obesity has been shown to be associated with low ONS cues. These alterations in obese subjects are due to obesity-induced altered expression of olfacto-taste receptors. Besides, obesity may further aggravate the SARS-CoV-2 infection, as this pathology is associated with a high degree of inflammation/immunosuppression and reduced protection against viral infections. Hence, obesity represents a great risk factor for SARS-CoV-2 infection, as it may hide the viral-associated altered ONS symptoms, thus leading to a high mortality rate in these subjects. url: https://doi.org/10.3390/jcm9072158 doi: 10.3390/jcm9072158 id: cord-304792-8sdxqmkb author: Khan, Md. Abdullah-Al-Kamran title: SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date: 2020-05-08 words: 2983.0 sentences: 207.0 pages: flesch: 48.0 cache: ./cache/cord-304792-8sdxqmkb.txt txt: ./txt/cord-304792-8sdxqmkb.txt summary: title: SARS-CoV-2 proteins exploit host''s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. We have utilized KEGG mapper tool (Kanehisa and Sato, 2020) for the mapping of 197 deregulated genes SARS-CoV-2 interacting host proteins in different cellular pathways. abstract: The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization. Understanding of host-SARS-CoV-2 interaction in viral pathogenesis is still in its infancy. In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. We have utilized a blend of computational and knowledgebase approach to elucidate the interplay between host and SARS-CoV-2. Integrating the experimentally validated host interactome proteins and differentially expressed host genes due to SARS-CoV-2 infection, we have taken a blend of computational and knowledgebase approach to delineate the interplay between host and SARS-CoV-2 in various signaling pathways. Also, we have shown how host epigenetic factors are involved in the deregulation of gene expression. Strikingly, we have found that several transcription factors and other epigenetic factors can modulate some immune signaling pathways, helping both host and virus. We have identified miRNA hsa-miR-429 whose transcription factor was also upregulated and targets were downregulated and this miRNA can have pivotal role in suppression of host immune responses. While searching for the pathways in which viral proteins interact with host proteins, we have found pathways like-HIF-1 signaling, autophagy, RIG-I signaling, Toll-like receptor signaling, Fatty acid oxidation/degradation, Il-17 signaling etc significantly associated. We observed that these pathways can be either hijacked or suppressed by the viral proteins, leading to the improved viral survival and life-cycle. Moreover, pathways like-Relaxin signaling in lungs suggests aberration by the viral proteins might lead to the lung pathophysiology found in COVID-19. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. might suggest why patients with comorbidities are becoming more prone to SARS-CoV-2 infection. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. Our findings would help in designing more targeted therapeutic interventions against SARS-CoV-2. url: https://doi.org/10.1101/2020.05.06.050260 doi: 10.1101/2020.05.06.050260 id: cord-263874-q0egnzwf author: Khan, Md. Arif title: Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study date: 2020-07-22 words: 2991.0 sentences: 166.0 pages: flesch: 52.0 cache: ./cache/cord-263874-q0egnzwf.txt txt: ./txt/cord-263874-q0egnzwf.txt summary: Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. Also, researchers have currently reported using the drug repurposing approach based on the molecular docking and dynamics study where the key target proteins are 3CL protease, RNA dependent RNA polymerase (RdRp), and spike proteins (Elfiky, 2020b; Muralidharan et al., 2020; Smith & Smith, 2020; Tahir Ul Qamar et al., 2020; Yu et al., 2020) . In this ground, it is clearly seen that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions among the 23 potential inhibitors against SARS-CoV-19 main protease and those results pave the way in drug discovery although it has to be further validated by in vitro and in vivo investigations. abstract: Recent outbreak of novel coronavirus and its rapid pandemic escalation in all over the world has drawn the attention to urgent need for effective drug development. However, due to prolonged vaccine and drug development procedure against a newly emerged devastating SARS-CoV-2 virus pathogen, repurposing of existing potential pertinent drug molecules would be preferable strategy to reduce mortality immediately and further development of new drugs to combat overall global Covid-19 crisis in all over the world. Herein, we have filtered 23 prospective drug candidates through literature review. Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. However, 50 ns molecular dynamics simulation indicated the less mobile nature of the docked complex maintaining structural integrity. Our overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32696718/ doi: 10.1080/07391102.2020.1796813 id: cord-346819-11fkgzaa author: Khan, Mohd Imran title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 words: 4405.0 sentences: 291.0 pages: flesch: 57.0 cache: ./cache/cord-346819-11fkgzaa.txt txt: ./txt/cord-346819-11fkgzaa.txt summary: title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. The genome analysis of the SARS-CoV-2 strains from 13 different countries showed a large number of mutations within the major structural proteins. This study provides a deeper insight into the emergence of these mutations within the major structural as well as nsp encoded by the SARS-CoV-2 genome from different countries. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations backbone RMSD was also noticed (Fig 4A) . abstract: A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. This includes several important country-specific unique mutations in the major proteins of SARS-CoV-2 namely, replicase polyprotein, spike glycoprotein, envelope protein and nucleocapsid protein. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V,. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. Likewise, several important country specific mutations were analyzed. The effect of mutations of these major proteins were also investigated using various in silico approaches. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. The implications of mutation on structural characteristics were determined. The information provided in this manuscript holds great potential in further scientific research towards the design of potential vaccine candidates/small molecular inhibitor against COVID19. url: https://www.ncbi.nlm.nih.gov/pubmed/32881907/ doi: 10.1371/journal.pone.0238344 id: cord-304295-3mpymd8a author: Khan, Muhammad Muzamil title: Emergence of novel coronavirus and progress toward treatment and vaccine date: 2020-06-04 words: 2935.0 sentences: 210.0 pages: flesch: 48.0 cache: ./cache/cord-304295-3mpymd8a.txt txt: ./txt/cord-304295-3mpymd8a.txt summary: 10 Favipiravir was effectively used against influenza and has the potential to inhibit viral RNA synthesis and a new study also supports its activity against SARS-CoV-2. 15 In another recent study, Gao et al found that chloroquine phosphate reduced the symptoms of pneumonia in SARS-CoV-2 patients and shortening the duration of disease. 67 Different technologies are being utilized to F I G U R E 1 Mechanism of action of HCQ and CQ by blocking binding of virus with ACE-2 receptors and increasing endosomal pH and preventing fusion with the cell develop potential vaccine for SARS-CoV-2 including DNA and mRNAbased nanoparticles. Clinical study for safety and efficacy of favipiravir in the treatment of novel coronavirus pneumonia (COVID-19) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: In late December 2019, a group of patients was observed with pneumonia‐like symptoms that were linked with a wet market in Wuhan, China. The patients were found to have a novel coronavirus genetically related to a bat coronavirus that was termed SARS‐CoV‐2. The virus gradually spread worldwide and was declared a pandemic by WHO. Scientists have started trials on potential preventive and treatment options. Currently, there is no specific approved treatment for SARS‐CoV‐2, and various clinical trials are underway to explore better treatments. Some previously approved antiviral and other drugs have shown some in vitro activity. Here we summarize the fight against this novel coronavirus with particular focus on the different treatment options and clinical trials exploring treatment as well as work done toward development of vaccines. url: https://doi.org/10.1002/rmv.2116 doi: 10.1002/rmv.2116 id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 words: 8841.0 sentences: 603.0 pages: flesch: 50.0 cache: ./cache/cord-333524-a6p6ma8r.txt txt: ./txt/cord-333524-a6p6ma8r.txt summary: 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). abstract: [Image: see text] The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32966744/ doi: 10.1021/acssynbio.0c00359 id: cord-281501-ca9oxl7f author: Khan, Shumayila title: Neuropathogenesis of SARS-CoV-2 infection date: 2020-07-30 words: 3208.0 sentences: 163.0 pages: flesch: 43.0 cache: ./cache/cord-281501-ca9oxl7f.txt txt: ./txt/cord-281501-ca9oxl7f.txt summary: Emerging reports of encephalopathies and similar ailments with the detection of the virus in the CSF has elicited an urgent need for investigating the possibility of neuroinvasiveness of the virus, which cannot be ruled out given the expression of low levels of ACE2 receptors in the brain. One study from Japan which described the first case of COVID-19-associated encephalitis where the patient was admitted for convulsions accompanied by unconsciousness reported that although the patient tested negative for SARS-CoV-2 in a nasopharyngeal swab, the viral RNA was surprisingly detected in the CSF, and the patient MRI exhibited abnormalities of the medial temporal lobe and hippocampus (Moriguchi et al., 2020) . The preliminary reports which hint towards the involvement of the CNS imply an urgent need for more studies, and a systematic collection and preservation of CSF samples along with associated clinical data, at least in patients displaying extrapulmonary or neurological symptoms, to examine the neuronal aspect of COVID-19. abstract: The COVID-19 pandemic caused by the SARS-CoV-2 has recently emerged as a serious jolt to human life and economy. Initial knowledge established pulmonary complications as the chief symptom, however, the neurological aspect of the disease is also becoming increasingly evident. Emerging reports of encephalopathies and similar ailments with the detection of the virus in the CSF has elicited an urgent need for investigating the possibility of neuroinvasiveness of the virus, which cannot be ruled out given the expression of low levels of ACE2 receptors in the brain. Sensory impairments of the olfactory and gustatory systems have also been reported in a large proportion of the cases, indicating the involvement of the peripheral nervous system. Hence, the possibility of neurological damage caused by the virus demands immediate attention and investigation of the mechanisms involved, so as to customize the treatment of patients presenting with neurological complications. url: https://doi.org/10.7554/elife.59136 doi: 10.7554/elife.59136 id: cord-269553-d3hozs14 author: Khan, Suliman title: The spread of novel coronavirus has created an alarming situation worldwide date: 2020-04-30 words: 1491.0 sentences: 83.0 pages: flesch: 48.0 cache: ./cache/cord-269553-d3hozs14.txt txt: ./txt/cord-269553-d3hozs14.txt summary: The COVID-19 epidemic became a serious challenge for the healthcare authorities, scientific community, and the infections controlling agencies across China, in terms of spread, treatment, and prevention. In the current scenario of the outbreak in Wuhan, healthcare workers are at the highest risk of contracting an infection. This indicates that a large number of medical staffs is suspected to have contracted the infection and their confirmation may create an alarming situation for healthcare authorities. Therefore, the increasing numbers of infected and suspected doctors and nurses are creating an additional significant shortage of working medical staff, thus, increasing an additional working and mental pressure on the normal health workers [6] . The medical staff resisted to provide treatment services to the suspected individual, fearing the possible transmission of the infection. Beside this, hospitals in developing or underdeveloped countries should be equipped on urgent basis for providing effective services to the individuals infected by novel coronavirus. abstract: nan url: https://doi.org/10.1016/j.jiph.2020.03.005 doi: 10.1016/j.jiph.2020.03.005 id: cord-276769-th7iou21 author: Khan, Suliman title: Coronaviruses disease 2019 (COVID-19): causative agent, mental health concerns, and potential management options date: 2020-07-25 words: 3375.0 sentences: 173.0 pages: flesch: 45.0 cache: ./cache/cord-276769-th7iou21.txt txt: ./txt/cord-276769-th7iou21.txt summary: Despite physical health consequences, COVID-19 pandemic has created stress and anxiety, as result there is an increased risk of mental illnesses both in the infected and normal individuals. Although bats are thought to be the source of origin for SARS-CoV-2, the intermediate animal that caused the transmission of virus to humans, is still unknown [3] . The individuals at higher risk of developing severe disease after contracting the infection should be give the priority for treatment and providing the mangeemtn and health servicesConsidering the importance of COVID-19 in the aspects of the asymptomatic spread of the virus and adverse health impacts, it is deemed necessary to investigate the factors associated with the rate of infectiousness and severity of symptoms. After originating in bats, SARS-CoV-2 emerged in Wuhan, spread all over the world through human to human transmission, and infected millions of individuals. abstract: Coronavirus disease-2019 (COVID-19) pandemic started from Wuhan, China has infected more than 6.7 million individuals and killed more than 3,90000 individuals globally. Due to the higher transmissibility and infectiousness, asymptomatic infection, and lack of effective treatment options and vaccine, fatalities and morbidities are increasing day by day globally. Despite physical health consequences, COVID-19 pandemic has created stress and anxiety, as result there is an increased risk of mental illnesses both in the infected and normal individuals. To eradicate these risks, it is necessary to determine the COVID-19 zoonotic source of transmission to humans and clinical manifestations in infected individuals. Although, identification or development of the highly effective therapeutic agents is necessary, however, development of protective strategies against the COVID-19 by enhancing immune responses will be an asset in the current scenarios of the COVID-19 pandemic. In this paper, we discuss the transmission, health consequences, and potential management (therapeutic and preventive) options for COVID-19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32741731/ doi: 10.1016/j.jiph.2020.07.010 id: cord-279443-2e4gz2bo author: Khan, Suliman title: Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns date: 2020-06-09 words: 4939.0 sentences: 245.0 pages: flesch: 43.0 cache: ./cache/cord-279443-2e4gz2bo.txt txt: ./txt/cord-279443-2e4gz2bo.txt summary: To identify and select the papers in this review we searched the published research and review articles relevant to origin and outbreaks of three human coronaviruses, and features, transmission, spread, entry mechanisms, infectiousness, control strategies, and animals hosts for SARS-CoV-2. Although it is important to know about the symptoms'' appearance and severity, however, understanding the transmission of the infection to healthy individuals from COVID-19 patients and zoonotic sources can be of great importance in the aspects of developing strategies to prevent and control the spread of COVID-19. This outbreak was reported to be caused by SARS-CoV, originated from market civets before its transmission and infection in humans (17) . Early claims came FIGURE 2 | The SARS-CoV-2 transmission from bats via unknown intermediate to humans causes infectiousness known as COVID-19 disease. According to the CDC report on coronavirus disease, individuals with underlying chronic medical conditions are at higher risk for contracting COVID-19 infection. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rapidly spreading across the world to cause thousands of mortalities each day. Poor responses from the authorities to the spread of infection, lack of effective measures for prevention, unavailability of promising treatment options, and sufficient diagnostic options have created an alarming for the world. The transmission routes from human to human of SARS-CoV-2 can be the direct transmission, droplet inhalation transmission, contact transmission, transmission through saliva, and transmission via fecal–oral routes. Due to the asymptomatic spread of SARS-CoV-2's, developing control and prevention measures is challenging. Implementing proper strategies addressing the infection control and clinical supplies, understanding the mechanism associated with pathogenesis, advancing in preventive measures and effective treatment and diagnostic options are necessary to control the ongoing pandemic. In this article, we briefly discuss the features, entry mechanism, infectiousness, and health consequences related to the COVID-19 outbreak. url: https://doi.org/10.3389/fmed.2020.00310 doi: 10.3389/fmed.2020.00310 id: cord-312350-klxw65qa author: Khan, Zafran title: Diagnostic approaches and potential therapeutic options for coronavirus disease (COVID-19) date: 2020-09-30 words: 1017.0 sentences: 84.0 pages: flesch: 47.0 cache: ./cache/cord-312350-klxw65qa.txt txt: ./txt/cord-312350-klxw65qa.txt summary: To date, more than 300 clinical trials have been conducted on various antiviral drugs, and immunomodulators are being evaluated at various stages of COVID-19. This review is aimed to collect and summarize a list of drugs used to treat COVID-19 for instance, dexamethasone, chloroquine, hydroxychloroquine, lopinavir/ritonavir, favipiravir, remdesivir, tociluzimab, nitazoxanide, and ivermectin. WHO 154 launches the "Solidarity" clinical trial for COVID-19 treatment to further evaluate remdesivir, 155 hydroxychloroquine/chloroquine, and lopinavir-ritonavir with and without interferon-beta [64] . Recently in Singapore, the five COVID-19 patients were subjected to treatment with lopinavir 258 and ritonavir within 1 to 3 days of desaturation, but evidence of clinical use is ambiguous. Clinical and 708 microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-709 19 patients with at least a six-day follow up: A pilot observational study. Effective treatment of severe COVID-749 19 patients with tocilizumab Antigen Detection Tests for Respiratory Syncytial Virus Infection: Systematic Review and Meta-779 analysis abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan city of China in late December 2019 and identified as a novel coronavirus. Due to its contagious nature, the virus spreads rapidly and causes coronavirus disease 2019 (COVID-19). The global tally of COVID-19 spikes 28 million. The fears and stress associated with SARS- CoV-2 demolished the socio-economic status all over the world. Researchers are trying around the clock to find out the treatment especially antiviral drugs and/or vaccines that could potentially control the viral spread and manage the ongoing unprecedented global crises. To date, more than 300 clinical trials have been conducted on various antiviral drugs, and immunomodulators are being evaluated at various stages of COVID-19. This review is aimed to collect and summarize a list of drugs used to treat COVID-19 for instance, dexamethasone, chloroquine, hydroxychloroquine, lopinavir/ritonavir, favipiravir, remdesivir, tociluzimab, nitazoxanide, and ivermectin. However, some of these drugs are not effective and suspended by the WHO (World Health Organization). url: https://doi.org/10.1016/j.nmni.2020.100770 doi: 10.1016/j.nmni.2020.100770 id: cord-309138-44qpk2vf author: Khanna, Kanika title: Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date: 2020-10-03 words: 6385.0 sentences: 354.0 pages: flesch: 43.0 cache: ./cache/cord-309138-44qpk2vf.txt txt: ./txt/cord-309138-44qpk2vf.txt summary: Moreover, AYUSH has recommended certain preventive and medicinal plants for prevention and prophylactic of COVID-19 including warm extracts of Tinospora cordifolia (advised for chronic fever), Andrograhis paniculata (advised for fever and cold), Cydonia oblonga, Zizyphus jujube and Cordia myxa (enhancing antioxidant, immune-modulatory, anti-allergic, smooth muscle relaxant, anti-influenza activity) and Ever since, has been elucidated that, PAK1 tends to cause cancers, viral diseases like HIV, Hepatitis, pappiloma, influenza, ebola, SARS and corona virus along with immune system suppression of hosts, henceforth, propolis would be quintessential in blocking COVID/coronavirus curbed fibrosis in respiratory tract and boosting the immunity of an individual (Maruta, 2014) . Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study Molecular mechanism of action of repurposed drugs and traditional Chinese medicine used for the treatment of patients infected with COVID-19: A systematic review Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective abstract: Current scenario depicts that world has been clenched by COVID-19 pandemic. Inevitably, public health and safety measures could be undertaken in order to dwindle the infection threat and mortality. Moreover, to overcome the global menace and drawing out world from moribund stage, there is an exigency for social distancing and quarantines. Since December, 2019, coronavirus, SARS-CoV-2 (COVID-19) have came into existence and up till now world is still in the state of shock.At this point of time, COVID-19 has entered perilous phase, creating havoc among individuals, and this has been directly implied due to enhanced globalisation and ability of the virus to acclimatize at all conditions. The unabated transmission is due to lack of drugs, vaccines and therapeutics against this viral outbreak. But research is still underway to formulate the vaccines or drugs by this means, as scientific communities are continuously working to unravel the pharmacologically active compounds that might offer a new insight for curbing infections and pandemics. Therefore, the topical COVID-19 situation highlights an immediate need for effective therapeutics against SARS-CoV-2. Towards this effort, the present review discusses the vital concepts related to COVID-19, in terms of its origin, transmission, clinical aspects and diagnosis. However, here, we have formulated the novel concept hitherto, ancient means of traditional medicines or herbal plants to beat this pandemic. url: https://api.elsevier.com/content/article/pii/S0944711320301926 doi: 10.1016/j.phymed.2020.153361 id: cord-345999-iiw4cs8p author: Khare, Prashant title: Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date: 2020-09-24 words: 3283.0 sentences: 320.0 pages: flesch: 62.0 cache: ./cache/cord-345999-iiw4cs8p.txt txt: ./txt/cord-345999-iiw4cs8p.txt summary: Since it is a newly emerging viral disease and obviously there is a lack of anti-SARS-CoV-2 therapeutic agents, it is urgently required to develop an effective anti-SARS-CoV-2-agent.Through recent advancements in computational biology and biological assays, several natural compounds and their derivatives have been reported to confirm their target specific antiviral potential against Middle East respiratory syndrome coronavirus (MERS-CoV) or Severe Acute Respiratory Syndrome(SARS-CoV).These targets including an important host cell receptor, i.e., angiotensin-converting enzyme ACE2 and several viral proteins e.g. spike glycoprotein (S) containing S1 and S2 domains, SARS CoV Chymotrypsin-like cysteine protease (3CL(pro)), papain-like cysteine protease (PL(pro)), helicases and RNA-dependent RNA polymerase (RdRp). For the management J o u r n a l P r e -p r o o f of COVID-19 infection, various molecular targets playing important role in the SARS-CoV-2 life cycle including host cell receptor-Angiotensin-converting enzyme ACE2 (PDB ID 3D0G) and viral proteins such as S protein (containing S1 and S2 domains) (PDB ID 6XM0); various cysteine proteases such as papain-like cysteine protease (PL pro ) (PDB ID 6WX4) or Chymotrypsin like nprotease (3CL pro ) (PDB ID 1P9U), helicases and RNA-dependent RNA polymerase (RdRp) (PDB ID 6M71) could be evaluated . abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) recently caused a pandemic outbreak called coronavirus disease 2019 (COVID-19). This disease has initially been reported in China and also now it is expeditiously spreading around the globe directly among individuals through coughing and sneezing. Since it is a newly emerging viral disease and obviously there is a lack of anti-SARS-CoV-2 therapeutic agents, it is urgently required to develop an effective anti-SARS-CoV-2-agent.Through recent advancements in computational biology and biological assays, several natural compounds and their derivatives have been reported to confirm their target specific antiviral potential against Middle East respiratory syndrome coronavirus (MERS-CoV) or Severe Acute Respiratory Syndrome(SARS-CoV).These targets including an important host cell receptor, i.e., angiotensin-converting enzyme ACE2 and several viral proteins e.g. spike glycoprotein (S) containing S1 and S2 domains, SARS CoV Chymotrypsin-like cysteine protease (3CL(pro)), papain-like cysteine protease (PL(pro)), helicases and RNA-dependent RNA polymerase (RdRp). Due to physical, chemical, and some genetic similarities of SARS CoV-2 with SARS−COV and MERS−COV, repurposing various anti-SARS−COV or anti-MERS−COV natural therapeutic agents could be helpful for the development of anti−COVID-19 herbal medicine. Here we have summarized various drug targets in SARS−COV and MERS−COV using several natural products and their derivatives, which could guide researchers to design and develop a safe and cost-effective anti-SARS−COV-2 drugs. url: https://api.elsevier.com/content/article/pii/S0168170220310765 doi: 10.1016/j.virusres.2020.198169 id: cord-323061-0i5w7vm9 author: Kharel Sitaula, Ranju title: Unfolding COVID-19: Lessons-in-Learning in Ophthalmology date: 2020-09-28 words: 4845.0 sentences: 266.0 pages: flesch: 51.0 cache: ./cache/cord-323061-0i5w7vm9.txt txt: ./txt/cord-323061-0i5w7vm9.txt summary: 10 Epiphora and Conjunctival redness had been the first manifestation of SARS-CoV-2 infection in 3 reported cases till date which includes a member of National expert on pneumonia during his visit to endemic areas of Wuhan and an anesthesiologist contracting the virus from a known patient of novel coronavirus pneumonia during intubation in Italy; similarly, it was reported in a nurse working in the emergency department of ophthalmology who presented with viral conjunctivitis and watering as a first sign. Hence, our knowledge and understanding about the SARS-CoV-2 virus, modes of entry to the eye, hypothesis on the interaction with the Renin-Angiotensin System (RAS) system and ACE2 receptor and ocular pathogenesis and RT PCR analysis from the ocular secretions have been summarized below using text, tables, diagrams, and flowcharts. abstract: IMPORTANCE: An observant Chinese doctor Li Wenliang became the first physician to alert the world about COVID-19. Being an ophthalmologist himself, he has put the additional onus on us. The fact that the ocular manifestation could be the first presenting feature of novel coronavirus pneumonia should not be ignored and the possibility of spread of SARS-CoV-2 through the ocular secretions cannot be ruled out. However, with breakthroughs still evolving about this disease, the calls are now louder for closer examination on the pathogenesis of conjunctivitis associated with it. Hence, we conducted a scoping review of all available literature till date to fill in the “potential” gaps in currently available knowledge on ocular manifestations of SARS-CoV-2 infection in an attempt to establish continuity in the “chain of information” from December 2019 till April 2020. We also summarize a possible hypothesis on much less understood and highly debated topics on regard to the etiopathogenesis of ocular involvement in SARS-CoV-2 based on either presence or absence of ACE2 receptor in the ocular surface. METHODS: We conducted a scoping review search of published and unpublished SARS-CoV-2-related English language articles from December 2019 till mid of April 2020 from the online databases. The findings were summarized using text, tables, diagrams, and flowcharts. RESULTS: The commonest ocular manifestation in SARS-CoV-2 infection is follicular conjunctivitis and has been the first manifestation of SARS-CoV-2 infection in 3 reported cases till date. The ocular surface inoculated with the SARS-CoV-2 leads to the facilitation of the virus to the respiratory system via the lacrimal passage. RT-PCR analysis of the ocular secretions has shown the presence of the SARS-CoV-2 nucleotides indicating the possibility of infection of ocular secretions. ACE2 receptors and its expression on the ocular mucosal surface are linked behind the etiopathogenesis of conjunctivitis. CONCLUSION: Conjunctivitis can be the presenting manifestation but may go unnoticed due to its mild nature. The ocular surface could serve as the entry gateway for the virus and ocular secretions could play a role in virus shed. The eye care personnel, as well as the general people, need to be more vigilant and adopt protective eye measures. url: https://doi.org/10.2147/opth.s259857 doi: 10.2147/opth.s259857 id: cord-277679-sc9hugxr author: Khateb, Mohamed title: Coronaviruses and Central Nervous System Manifestations date: 2020-06-23 words: 4204.0 sentences: 245.0 pages: flesch: 41.0 cache: ./cache/cord-277679-sc9hugxr.txt txt: ./txt/cord-277679-sc9hugxr.txt summary: This minireview scans the literature regarding the involvement of the CNS in coronavirus infections in general, and in regard to the recent SARS-CoV-2, specifically. In December 2019, the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged in Wuhan, China. Accumulating evidence implies a possible link between infection with the novel SARS-CoV-2 and acute ischemic stroke (AIS). Accumulating evidence from the current SARS-CoV-2 pandemic, together with literature on other coronaviruses, suggest that infection with coronaviruses may be related to CNS manifestations or complications, including anosmia, acute ischemic strokes, viral meningoenchephalitis, acute necrotizing encephalopathy, acute flaccid paralysis, and other presumably post/para-infectious syndromes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome abstract: SARS-CoV-2 is a highly pathogenic coronavirus that has caused an ongoing worldwide pandemic. Emerging in Wuhan, China in December 2019, the virus has spread rapidly around the world. Corona virus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has resulted in significant morbidity and mortality. The most prominent symptoms of SARS-CoV-2 infection are respiratory. However, accumulating evidence highlights involvement of the central nervous system (CNS). This includes headache, anosmia, meningoencephalitis, acute ischemic stroke, and several presumably post/para-infectious syndromes and altered mental status not explained by respiratory etiologies. Interestingly, previous studies in animal models emphasized the neurotropism of coronaviruses; thus, these CNS manifestations of COVID-19 are not surprising. This minireview scans the literature regarding the involvement of the CNS in coronavirus infections in general, and in regard to the recent SARS-CoV-2, specifically. url: https://www.ncbi.nlm.nih.gov/pubmed/32655490/ doi: 10.3389/fneur.2020.00715 id: cord-349226-xzlc1pni author: Khatiwada, Saroj title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 words: 4312.0 sentences: 231.0 pages: flesch: 35.0 cache: ./cache/cord-349226-xzlc1pni.txt txt: ./txt/cord-349226-xzlc1pni.txt summary: To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease. abstract: Coronavirus disease 2019 (COVID-19) is a rapidly emerging disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease begins as an infection of lungs, which is self-limiting in the majority of infections; however, some develop severe respiratory distress and organ failures. Lung microbiome, though neglected previously have received interest recently because of its association with several respiratory diseases and immunity. Lung microbiome can modify the risk and consequences of COVID-19 disease by activating an innate and adaptive immune response. In this review, we examine the current evidence on COVID-19 disease and lung microbiome, and how lung microbiome can affect SARS-CoV-2 infection and the outcomes of this disease. To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. Future studies need to be undertaken to find the relationship between lung microbiome and COVID-19 disease. url: https://doi.org/10.1016/j.humic.2020.100073 doi: 10.1016/j.humic.2020.100073 id: cord-306581-g3d0lqxp author: Khattab, Mohamed H. title: Early detection of SARS-CoV-2 from staging PET-CT date: 2020-09-29 words: 1214.0 sentences: 78.0 pages: flesch: 45.0 cache: ./cache/cord-306581-g3d0lqxp.txt txt: ./txt/cord-306581-g3d0lqxp.txt summary: METHODS: Here, we present a case study of a mildly symptomatic patient with anal cancer diagnosed with SARS-CoV-2 from a staging PET-CT scan. Given the ongoing COVID-19 pandemic, a nasopharyngeal swab with polymerase chain reaction (PCR) was obtained and was confirmed positive for the potentially lethal SARS-CoV-2 viral infection. In geographic regions with a Fig. 1 Screening positron emission tomography fused with computed tomography demonstrating fluorodeoxyglucose-avid multifocal, rounded, peripheral ground-glass nodules, some demonstrating the reversed halo sign, within the right lower, right middle, and left lower lung lobes concerning for an infectious process significant and increasing COVID-19 case burden, routine PCR testing in the absence of clinical or radiologic findings may be indicated in patients undergoing chemoradiation or radiation, and it is our institutional practice to test all patients receiving any chemotherapy or greater than 10 days of radiation. In the setting of asymptomatic or mildly symptomatic patients with confirmed SARS-CoV-2 infection, multidisciplinary discussion with oncology and infectious disease teams is important to ascertain the risks and benefits of delaying cancer therapy. abstract: OBJECTIVE: SARS-CoV-2 infection may manifest with minimal or no clinical symptoms. However, signs of infection may appear on routine imaging obtained in the care of patients with cancer. The management of patients planned for chemoradiation with asymptomatic or mildly symptomatic SARS-CoV-2 infection is uncertain. METHODS: Here, we present a case study of a mildly symptomatic patient with anal cancer diagnosed with SARS-CoV-2 from a staging PET-CT scan. RESULTS: PET-CT scan for anal cancer staging demonstrated pulmonary avidity suspicious for an infectious, rather than malignant, process. In the setting of these imaging findings and new-onset anosmia, viral polymerase chain reaction was ordered and found to be positive for SARS-CoV-2. To avoid myelosuppression in the setting of active infection, planned chemoradiation was delayed until cessation of viral shedding. CONCLUSION: In the COVID-19 era, oncologists obtaining routine staging imaging should have high diagnostic suspicion for subclinical SARS-CoV-2 infection. To avoid precipitating severe pneumonia and hospitalization, multidisciplinary discussion with risk-benefit analysis is recommended before initiating immunosuppressive therapies such as chemoradiation. url: https://doi.org/10.1007/s13566-020-00436-w doi: 10.1007/s13566-020-00436-w id: cord-310803-iig414jg author: Khazeei Tabari, Mohammad Amin title: Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic date: 2020-10-17 words: 1337.0 sentences: 85.0 pages: flesch: 48.0 cache: ./cache/cord-310803-iig414jg.txt txt: ./txt/cord-310803-iig414jg.txt summary: COVID-19 is a disorder caused by SARS-CoV-2, which has CoV-2 genome sequencing demonstrated that ORF1a/b is closely similar to those from the bat, 4 civet, and other human SARS-CoVs, but the external sub-domain amino acid sequence of the 5 spike receptor-binding domain for this novel virus is only 40% similar to other SARS-related 6 coronaviruses. Nelfinavir was predicted to be a potential 5 inhibitor of 2019-nCov main protease by an integrative approach combining homology 6 modelling, molecular docking and binding free energy calculation Structural and molecular modelling studies 24 reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 25 infection Network-based drug repurposing 29 for novel coronavirus 2019-nCoV/SARS-CoV-2 Emodin blocks the SARS coronavirus 46 spike protein and angiotensin-converting enzyme 2 interaction Repurposing didanosine as a potential treatment for COVID-19 using scRNA-18 seq data Repurposing Didanosine as a Potential Treatment for COVID-19 Using Single-Cell 20 RNA Sequencing Data abstract: Coronavirus disease 2019 (COVID-19) has made many concerns for healthcare services especially, in finding useful therapeutic(s). Despite the scientists’ struggle to find and/or creating possible drugs, so far there is no treatment with high efficiency for the disease. During the pandemic, researchers have performed some molecular analyses to find potential therapeutics out of both the natural and synthetic available medicines. Computer simulations and related data have shown a significant role in drug discovery and development before. In this field, antiviral drugs, phytochemicals, anti-inflammatory agents, etc. were essential groups of compounds tested against COVID-19, using molecular modeling, molecular dynamics (MD), and docking tools. The results indicate promising effects of such compounds to be used in further experimental and clinical trials; Chloroquine, Chloroquine-OH, and Umifenovir as viral entry inhibitors, Remdesivir, Ribavirin, Lopinavir, Ritonavir, and Darunavir as viral replication inhibitors, and Sirolimus are the examples, which were tested clinically on patients after comprehensive assessments of the available data on molecular simulation. This review summarizes the outcomes of various computer simulations data in the battle against COVID-19 url: https://api.elsevier.com/content/article/pii/S2352914820306080 doi: 10.1016/j.imu.2020.100458 id: cord-337436-3xzgv370 author: Khider, Lina title: Curative anticoagulation prevents endothelial lesion in COVID‐19 patients date: 2020-06-18 words: 1774.0 sentences: 110.0 pages: flesch: 44.0 cache: ./cache/cord-337436-3xzgv370.txt txt: ./txt/cord-337436-3xzgv370.txt summary: METHODS: Study analyzed clinical and biological profiles of patients with suspected COVID‐19 infection at admission, including hemostasis tests and quantification of circulating endothelial cells (CECs). Circulating endothelial cells (CECs) are considered as relevant markers of Accepted Article 1 endothelial lesion or dysfunction (12) and were used to explore the potential vascular dysfunction 2 in COVID-19 patients. Among COVID-19 positive patients, 64% were above this threshold, suggesting a SARSThe originality of this study was to evidence an endothelial lesion during SARS-CoV-2 infection, 3 as witnessed by increased levels of CECs. Second, we show that this endothelial damage is 4 thwarted by curative anticoagulation. Interestingly, patients enrolled while they were treated with 6 curative anticoagulation had a significantly lower level of CECs, especially in the hypertensive 7 population treated with ACEi or ARBs. Increased mortality and/or morbidity of COVID-19 in 8 patients with hypertension has been described in China (3). abstract: BACKGROUND: Coronavirus disease‐2019 (COVID‐19) has been associated with cardiovascular complications and coagulation disorders. OBJECTIVES: To explore the coagulopathy and endothelial dysfunction in COVID‐19 patients. METHODS: Study analyzed clinical and biological profiles of patients with suspected COVID‐19 infection at admission, including hemostasis tests and quantification of circulating endothelial cells (CECs). RESULTS: Among 96 consecutive COVID‐19‐suspected patients fulfilling criteria for hospitalization, 66 were tested positive for SARS‐CoV‐2. COVID‐19 positive patients were more likely to present with fever (p=0.02), cough (p=0.03) and pneumonia at CT‐scan (p=0.002) at admission. Prevalence of D‐dimer >500 ng/mL was higher in COVID‐19 positive patients (74.2% vs. 43.3%; p=0.007). No sign of disseminated intravascular coagulation were identified. Adding D‐dimers >500 ng/mL to gender and pneumonia at CT scan in ROC curve analysis significantly increased AUC for COVID‐19 diagnosis. COVID‐19 positive patients had significantly more CECs at admission (p=0.008) than COVID‐19 negative ones. COVID‐19 positive patients treated with curative anticoagulant prior to admission had less CECs (p=0.02) than those without. Interestingly, patients treated with curative anticoagulation and ACEi or ARBs had even lesser CECs (p=0.007). CONCLUSION: Curative anticoagulation could prevent COVID‐19‐associated coagulopathy and endothelial lesion. url: https://doi.org/10.1111/jth.14968 doi: 10.1111/jth.14968 id: cord-031518-1w14wr0i author: Khodarahmi, Reza title: The ACE2 as a “rescue protein” or “suspect enzyme” in COVID-19: possible application of the “engineered inactive hrsACE2” as a safer therapeutic agent in the treatment of SARS-CoV-2 infection date: 2020-09-07 words: 4651.0 sentences: 190.0 pages: flesch: 42.0 cache: ./cache/cord-031518-1w14wr0i.txt txt: ./txt/cord-031518-1w14wr0i.txt summary: The authors expressed that hrsACE2 can block early entry of SARS-CoV-2 infections in various host cells, especially alveolar epithelial type II cells, as a viral reservoir and stated that they cannot make any predictions with respect to the effect of the recombinant protein on the later stages of COVID-19 and, also, honestly mentioned the study limitations. Moreover, since ACE2 is expressed in various tissues including the heart, kidney tubules, the luminal surface of the small intestine and blood vessels [2] and references therein), SARS-CoV-2could also infect these tissues, so that clinically, SARS-CoV-2 has been found in the urine, and cardiovascular and renal dysfunctions have been reported for many patients with COVID-19. As mentioned above, patients with COVID-19 have significantly elevated levels of plasma angiotensin II compared to that of healthy individual and membrane-bound ACE2 (in addition to protecting from lung injury, based on its catalytic domain) is the critical in vivo SARS-CoV spike glycoprotein receptor. abstract: COVID-19 is a devastating global pandemic around the world. While the majority of infected cases appear mild, in some cases, individuals present respiratory complications with possible serious lung damage. There are no specific treatments for COVID-19 as yet. Many repurposed antiviral drugs have had disappointing outcomes. Angiotensin-converting enzyme 2 (ACE2), an enzyme that physiologically counters renin–angiotensin–aldosterone system activation, functions as a receptor for both SARS viruses. The current study discusses on vague role of ACE2 under physiologic/pathologic conditions. The catalytically inactive hrsACE2 has been also proposed as an efficient treatment of SARS-CoV-2 infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13738-020-02049-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475728/ doi: 10.1007/s13738-020-02049-z id: cord-338680-wwlttymp author: Khonyongwa, K. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-07-30 words: 4839.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-338680-wwlttymp.txt txt: ./txt/cord-338680-wwlttymp.txt summary: Due to the high prevalence of infection during the peak of the outbreak, one of the suggested strategies to prevent healthcare transmission was to screen all patients on admission by a single combined nose and throat swab assessed for SARS-CoV-2 RNA to allow segregation into COVID-19 positive and non COVID-19 cohort wards. The latter included assessment of the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity, COVID-19 patients as sources of infection, self-reported COVID-19 sickness absence among hospital staff hospital bed occupancy, community incidence, and the incidence of other significant hospital-acquired infections. NHS England released its reporting criteria in May 2020 (written communication described in supplementary data) following which cases were also classified as per date of the SARS-CoV-2 RNA detection. Correlation between weekly incidence of HA-COVID-19 (including late indeterminate cases) and staff self-reported sickness absence, delayed RNA positive cases, community incidence and Trust COVID-19 bed occupancy is displayed in figure 3. abstract: Background: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions among vulnerable inpatients. Aims: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a London Teaching Hospital Trust. Methods: Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset >14d of admission. Test performance of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections (OHAI) was compared to previous years. Results: 58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years. Conclusion: Early diagnosis and isolation of COVID-19 would help reduce transmission. A single CTNS has limited value in segregating patients into positive and negative pathways. url: http://medrxiv.org/cgi/content/short/2020.07.24.20148262v1?rss=1 doi: 10.1101/2020.07.24.20148262 id: cord-269408-6qncy0nd author: Khonyongwa, Kirstin title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-10-13 words: 4131.0 sentences: 233.0 pages: flesch: 54.0 cache: ./cache/cord-269408-6qncy0nd.txt txt: ./txt/cord-269408-6qncy0nd.txt summary: AIMS: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a Teaching Hospital NHS Trust in London, England. Factors studied included the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity (DRP), selfreported COVID-19 sickness absence among hospital staff, total hospital bed occupancy, community incidence of COVID-19 (CIC19) and the change in incidence of other significant hospital-acquired bacterial infections (HAB). When a HA-COVID-19 case was identified, actions included staff refresher training for correct PPE usage, rapid transfer of patients to a COVID-19 positive cohort ward, deep cleaning (washing walls and carpets) followed by increasing the cleaning frequency until no further transmission was seen (defined as no new symptom onset within 2 weeks of last known case and in haematology and geriatrics a CNTS was tested for SARS-CoV-2 RNA twice weekly for all contacts up to 2 weeks from last positive case regardless of symptoms). abstract: BACKGROUND: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 led to onward transmissions among vulnerable inpatients. AIMS: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a Teaching Hospital NHS Trust in London, England. METHODS: Electronic laboratory, patient and staff self-reported sickness records were interrogated from 1(st) March to 18(th) April 2020. HA-COVID-19 was defined as COVID-19 with symptom onset >14 days of admission. Test performance of a single combined throat and nose swab (CTNS) for patient placement was calculated. The effect of delayed RNA positivity (DRP, defined as >48h delay), staff self-reported COVID-19 sickness absence, hospital bed occupancy, and community incidence of COVID-19 was compared for HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections (HAB) was compared to previous years. RESULTS: 58 HA-COVID-19 (7.1%) cases were identified. When compared to community-acquired admitted cases (CA-COVID-19), significant differences were observed in age (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30 d mortality. CTNS negative predictive value was 60.3%. DRP was associated with greater mortality (p=0.034) and incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). For the study period HAB rates were similar to previous 2 years. CONCLUSION: Early diagnosis and isolation of COVID-19 patients would help reduce transmission. A single CTNS has limited value in segregating patients into positive and negative pathways. url: https://www.sciencedirect.com/science/article/pii/S0195670120304667?v=s5 doi: 10.1016/j.jhin.2020.10.006 id: cord-282371-39qo9afy author: Khulood, Daulat title: Convalescent plasma appears efficacious and safe in COVID-19 date: 2020-09-28 words: 3095.0 sentences: 218.0 pages: flesch: 52.0 cache: ./cache/cord-282371-39qo9afy.txt txt: ./txt/cord-282371-39qo9afy.txt summary: Convalescent plasma (CP) therapy is a classic adaptive immunotherapy which has been in use for more a century to prevent and treat infections including SARS, Middle East respiratory syndrome (MERS), and H1N1 pandemic. Despite its promising beneficial effects in patients severely ill with COVID-19, CP therapy requires further evaluation in randomized clinical trials (RCTs) as a lack of satisfactory efficacy data from this area certainly enhances the hesitancy with regard to employing this treatment. Although CP therapy showed satisfactory efficacy in treating patients with severe COVID-19, 41 this approach requires evaluation in randomized clinical trials (RCTs) 38 as lack of data from this area certainly enhances the hesitation with regard to employing this treatment. 46 Recently, the FDA has approved use of CP to treat critically ill patients while a clinical trial of plasma therapy for COVID-19 has been approved in the UK. Treatment with convalescent plasma for critically ill patients with SARS-CoV-2 infection. abstract: A cluster of pneumonia cases of unknown etiology associated with pyrexia and acute respiratory distress was identified in Southern China. Links between the previous severe acute respiratory syndrome (SARS) cases and the region’s seafood market were noted with the possibility of a new zoonosis and SARS-CoV-2 was identified as the responsible agent. Currently, there are no effective prophylactic or therapeutic options to deal with coronavirus disease-19 (COVID-19) or any other human coronavirus (HCoV) infections. Convalescent plasma (CP) therapy is a classic adaptive immunotherapy which has been in use for more a century to prevent and treat infections including SARS, Middle East respiratory syndrome (MERS), and H1N1 pandemic. Moreover, the World Health Organization regarded CP transfusion as the most promising therapy to treat MERS-CoV. This review was undertaken to demonstrate the potential of CP in the treatment of the pandemic COVID-19 disease. A total of eight studies conducted on CP therapy in patients with COVID-19 were reviewed wherein 25,028 patients above 18 years of age were involved. The vast majority of patients reported favorable outcomes when treated with CP with <1% serious adverse events. Despite its promising beneficial effects in patients severely ill with COVID-19, CP therapy requires further evaluation in randomized clinical trials (RCTs) as a lack of satisfactory efficacy data from this area certainly enhances the hesitancy with regard to employing this treatment. In the present circumstances of unsatisfactory pharmacological therapy and the urgent need for a successful curative remedy, considering the use of CP therapy is reasonable provided RCTs confirm its safety, efficacy, and tolerability. url: https://www.ncbi.nlm.nih.gov/pubmed/33062267/ doi: 10.1177/2049936120957931 id: cord-315951-5gsbtfag author: Kiemer, Lars title: Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date: 2004-06-06 words: 3766.0 sentences: 200.0 pages: flesch: 51.0 cache: ./cache/cord-315951-5gsbtfag.txt txt: ./txt/cord-315951-5gsbtfag.txt summary: The general approach is still valid though, and we decided to apply this method to the problem of predicting the 3CL pro proteinase cleavage sites and identifying potential host cell target proteins. In this paper, we describe the development of a computational prediction method using artificial neural networks for predicting coronavirus 3CL pro proteinase cleavage sites. We discuss potential targets of 3CL pro proteinase, e.g. the cystic fibrosis transmembrane conductance regulator (CFTR) and translational and transcriptional factors, which may be involved in the molecular pathology of coronaviruses in general and SARS virus in particular. Another known target for viral infections is the microtubule-associated protein 4 (MAP-4) which is cleavable in HeLa cells by the poliovirus 3C pro proteinase [26, 27] . We have developed a neural network capable of identifying the cleavage site of the coronavirus proteinase 3CL pro and use this model to predict potential cleavage sites in host cell proteins. abstract: BACKGROUND: Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS), efficient counter-measures are still few and many believe that reappearance of SARS, or a similar disease caused by a coronavirus, is not unlikely. For other virus families like the picornaviruses it is known that pathology is related to proteolytic cleavage of host proteins by viral proteinases. Furthermore, several studies indicate that virus proliferation can be arrested using specific proteinase inhibitors supporting the belief that proteinases are indeed important during infection. Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods. RESULTS: We retrieved sequence data on seven fully sequenced coronaviruses and identified the main 3CL proteinase cleavage sites in polyproteins using alignments. A neural network was trained to recognise the cleavage sites in the genomes obtaining a sensitivity of 87.0% and a specificity of 99.0%. Several proteins known to be cleaved by other viruses were submitted to prediction as well as proteins suspected relevant in coronavirus pathology. Cleavage sites were predicted in proteins such as the cystic fibrosis transmembrane conductance regulator (CFTR), transcription factors CREB-RP and OCT-1, and components of the ubiquitin pathway. CONCLUSIONS: Our prediction method NetCorona predicts coronavirus cleavage sites with high specificity and several potential cleavage candidates were identified which might be important to elucidate coronavirus pathology. Furthermore, the method might assist in design of proteinase inhibitors for treatment of SARS and possible future diseases caused by coronaviruses. It is made available for public use at our website: . url: https://www.ncbi.nlm.nih.gov/pubmed/15180906/ doi: 10.1186/1471-2105-5-72 id: cord-342983-7o0slu0z author: Killeen, G. F. title: A simple arithmetic rationale for crushing the epidemic curve of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) instead of flattening it date: 2020-05-10 words: 2328.0 sentences: 103.0 pages: flesch: 43.0 cache: ./cache/cord-342983-7o0slu0z.txt txt: ./txt/cord-342983-7o0slu0z.txt summary: Here is presented a simple set of arithmetic modelling analyses that explain why preferable crush the "curve strategies", to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to "flatten the curve" strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. Here is presented a simple arithmetic rationale for why preferable crush the curve strategies, to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to flatten the curve strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. 2 From this assumed starting point, a country that contains its epidemic sufficiently to flatten the curve to a plateau, so that the rate of incidence of new infections remains constant, would have achieved a controlled reproductive number (Rc) of exactly 1.0 ( Figure 1A ). abstract: Countries with ambitious strategies to "crush the curve" of their epidemic trajectories, to promptly eliminate SARS-CoV-2 transmission at national level, include China, Korea, Japan, Taiwan, New Zealand and Australia. In stark contrast, many of the European countries hit hardest over the last two months, including Italy, Spain, France, Ireland and the United Kingdom, currently appear content to merely "flatten the curve" of their epidemic trajectories so that transmission persists at rates their critical care services can cope with. Here is presented a simple set of arithmetic modelling analyses that explain why preferable crush the "curve strategies", to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to "flatten the curve" strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. url: https://doi.org/10.1101/2020.05.06.20093112 doi: 10.1101/2020.05.06.20093112 id: cord-347128-6lyoz8nn author: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 words: 15413.0 sentences: 988.0 pages: flesch: 53.0 cache: ./cache/cord-347128-6lyoz8nn.txt txt: ./txt/cord-347128-6lyoz8nn.txt summary: O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. In RNA viruses, the S glycoprotein (PDB: 6VSB) is the biggest protein, heavily glycosylated and its N-terminal domain (NTD) sequence binds to the host receptor to enter the ER of host cells. However, MERS-CoV does not have a similar enzyme and thus MER-CoV binding to SA receptors is mediated by energetically reversible interactions of the lipid rafts with increased SA receptors [75] , thus enhancing dipeptidyl peptidase 4 (DPP4) or carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) recognition power and viral entry [76] and membrane-associated 78-kDa glucose-regulated protein (GRP78) [77] . Entry of host cells needs binding of S glycoproteins to the CEACAM receptor, forming S-protein-mediated membrane fusion. For example, impairment of ACE2 receptor glycosylation does not influence S-glycoprotein-ACE2 interaction, however, SARS-CoV-2 virus entry into respiratory epithelial host cells was downregulated [133] . abstract: The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA–specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA–ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein–glycan interaction and PCI stereochemistry potentiate the SA–ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future. url: https://doi.org/10.3390/ijms21124549 doi: 10.3390/ijms21124549 id: cord-346222-rzbzlnr4 author: Kim, Dae-Kyum title: A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions date: 2020-08-06 words: 1749.0 sentences: 110.0 pages: flesch: 48.0 cache: ./cache/cord-346222-rzbzlnr4.txt txt: ./txt/cord-346222-rzbzlnr4.txt summary: Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. SARS-CoV-2 coding sequence collection Gatewaycompatible TEV (tobacco etch virus) sequence A global pandemic of the coronavirus disease COVID-19, a severe respiratory illness caused by a novel virus from the family Coronaviridae (SARS-CoV-2), has infected millions and caused hundreds of thousands of deaths (World Health Organization 2020a). Broad availability of a collection of SARS-CoV-2 CDSs has the potential to enable many downstream biochemical and structural studies and thus a better understanding of processes within the viral life cycle, including scalable assays for screening drug candidates that could potentially disrupt these processes. However, to enable the subsequent removal of such N-terminal fusion tags, we generated an additional set of clones containing, at the N-terminus of the ORF, a recognition sequence for nuclear inclusion protease from tobacco etch virus (TEV). abstract: The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it. url: https://doi.org/10.1534/g3.120.401554 doi: 10.1534/g3.120.401554 id: cord-302020-ypsh3rjv author: Kim, Dongwan title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 words: 6092.0 sentences: 403.0 pages: flesch: 57.0 cache: ./cache/cord-302020-ypsh3rjv.txt txt: ./txt/cord-302020-ypsh3rjv.txt summary: In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. (A) Read counts from nanopore direct RNA sequencing of total RNA from Vero cells infected with SARS-CoV-2. We further discovered RNA modification sites and measured the poly(A) tail length of gRNAs and sgRNAs. To delineate the SARS-CoV-2 transcriptome, we first performed DRS runs on a MinION nanopore sequencer with total RNA extracted from Vero cells infected with SARS-CoV-2 (Be-taCoV/Korea/KCDC03/2020). To unambiguously investigate the modifications, we generated negative control RNAs by in vitro transcription of the viral sequences and performed a DRS run on these unmodified controls ( Figure S4A ). abstract: SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 genome was reported recently, its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous discontinuous transcription events. In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif, AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the modification and the 3′ tail. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32330414/ doi: 10.1016/j.cell.2020.04.011 id: cord-294698-mtfrbn87 author: Kim, H. K. title: Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date: 2016-05-23 words: 2682.0 sentences: 169.0 pages: flesch: 62.0 cache: ./cache/cord-294698-mtfrbn87.txt txt: ./txt/cord-294698-mtfrbn87.txt summary: In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential. abstract: Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), Nipah virus and Hendra virus. In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS‐CoV‐like and MERS‐CoV‐like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat. url: https://doi.org/10.1111/tbed.12515 doi: 10.1111/tbed.12515 id: cord-015235-lv8mll28 author: Kim, Hyun title: Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody date: 2014-04-16 words: 5855.0 sentences: 323.0 pages: flesch: 60.0 cache: ./cache/cord-015235-lv8mll28.txt txt: ./txt/cord-015235-lv8mll28.txt summary: The receptor-binding domain (RBD) positioned in S1 can specifically bind to angiotensin-converting enzyme 2 (ACE2) on target cells, and ACE2 regulates the balance between vasoconstrictors and vasodilators within the heart and kidneys. Infection of SARS-CoV is initiated by binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) functional receptor expressed on target cells (Li et al. Our cellular enzyme-linked immunosorbent assay (ELISA) and competitive binding assay using a polyclonal ACE2 antibody indicated that our prepared recombinant RBD fusion protein binds to various tissues as well as NIH3T3 and HEK293 cells through ACE2. After washing with PBS, the RBD fusion protein was incubated for 1 h at room temperature to bind with the ACE2 molecules on the cell membranes. Next, we examined whether RBD binding was blocked by the ACE2 antibody in a Western blot using mouse tissue cell lysates with a pair of membranes. abstract: Severe acute respiratory syndrome (SARS) is caused by the SARS coronavirus (CoV). The spike protein of SARS-CoV consists of S1 and S2 domains, which are responsible for virus binding and fusion, respectively. The receptor-binding domain (RBD) positioned in S1 can specifically bind to angiotensin-converting enzyme 2 (ACE2) on target cells, and ACE2 regulates the balance between vasoconstrictors and vasodilators within the heart and kidneys. Here, a recombinant fusion protein containing 193-amino acid RBD (residues 318–510) and glutathione S-transferase were prepared for binding to target cells. Additionally, monoclonal RBD antibodies were prepared to confirm RBD binding to target cells through ACE2. We first confirmed that ACE2 was expressed in various mouse cells such as heart, lungs, spleen, liver, intestine, and kidneys using a commercial ACE2 polyclonal antibody. We also confirmed that the mouse fibroblast (NIH3T3) and human embryonic kidney cell lines (HEK293) expressed ACE2. We finally demonstrated that recombinant RBD bound to ACE2 on these cells using a cellular enzyme-linked immunosorbent assay and immunoassay. These results can be applied for future research to treat ACE2-related diseases and SARS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097624/ doi: 10.1007/s13258-014-0186-9 id: cord-262107-qso8ewi9 author: Kim, In-Cheol title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned date: 2020-05-22 words: 429.0 sentences: 37.0 pages: flesch: 56.0 cache: ./cache/cord-262107-qso8ewi9.txt txt: ./txt/cord-262107-qso8ewi9.txt summary: title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned procurement team from the city (Daegu) where the COVID-19 outbreak was prevalent due to the concern of SARS-CoV-2 spread. Our procurement team decided to take a nasopharyngeal swab to prove negative of SARS-CoV-2 infection before the departure. Algorithm of the SARS-CoV-2 Test Strategy for the brain death donor and candidate for heart transplantation during COVID-19 outbreak. Brain death donors should be tested for SARS-CoV-2 infection (preferably rRT-PCR assay from upper and/or lower respiratory tract specimens). When the heart transplantation recipient has symptoms suggesting viral infection, unknown cause of fever, or close contact history with the SARS-CoV-2 infected patients prior 14 days, test for SARS-CoV-2 infection should be performed and proceed heart transplantation when the result is negative. Confirmation of the negative SARS-CoV-2 result need to be ensured according to the strategy of each hospital organ procurement organization. If the symptom of SARS-CoV-2 infection is highly suggested, repeated test need to be performed for the suspicious result. abstract: nan url: https://doi.org/10.4070/kcj.2020.0177 doi: 10.4070/kcj.2020.0177 id: cord-260310-0gkoanrg author: Kim, Jin Yong title: Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea date: 2020-02-20 words: 2171.0 sentences: 118.0 pages: flesch: 58.0 cache: ./cache/cord-260310-0gkoanrg.txt txt: ./txt/cord-260310-0gkoanrg.txt summary: In this patient, the initial test was performed on day 14 of symptom onset and SARS-CoV-2 was detected in both URT and LRT specimens. Although the viral load and CXR findings in these two patients may not represent the whole spectrum of SARS-CoV-2 illness, our report will provide many important findings and opportunity to understand this newly discovered virus infection in human. First, unlike SARS-CoV infection, 8 we found that viral load was highest during the early phase of the illness (3-5 days from first symptom onset, fever and myalgia were the only symptoms in Patient 1) and continued to decrease until the end of the second week. Second, even in a patient with mild disease, if visible infiltration on CXR is observed, virus is still detected in both URT and LRT specimens even at the end of second week after symptom onset. abstract: As of February 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started in China in December 2019 has been spreading in many countries in the world. With the numbers of confirmed cases are increasing, information on the epidemiologic investigation and clinical manifestation have been accumulated. However, data on viral load kinetics in confirmed cases are lacking. Here, we present the viral load kinetics of the first two confirmed patients with mild to moderate illnesses in Korea in whom distinct viral load kinetics are shown. This report suggests that viral load kinetics of SARS-CoV-2 may be different from that of previously reported other coronavirus infections such as SARS-CoV. url: https://doi.org/10.3346/jkms.2020.35.e86 doi: 10.3346/jkms.2020.35.e86 id: cord-281487-x0a9qgjs author: Kim, Min Young title: General Approach to the Clinical Care of Solid Organ Transplant Recipients with COVID-19 Infection: Management for Transplant Recipients date: 2020-10-29 words: 5908.0 sentences: 296.0 pages: flesch: 36.0 cache: ./cache/cord-281487-x0a9qgjs.txt txt: ./txt/cord-281487-x0a9qgjs.txt summary: The coronavirus disease 2019 (COVID19) pandemic has led to unique challenges in solid organ transplantation as centers balance the risk of caring for immunosuppressed patients with the best timing and urgency of transplantation. Patients hospitalized with COVID-19 pneumonia were included Abbreviations: CHF, congestive heart failure; Because renal abnormalities are associated with a high risk of in-hospital death and appear to be more prevalent in transplant recipients [36] , serum creatinine and urinalysis should be monitored closely. Figure 1 shows a model for the management of solid organ transplant recipients during COVID-19 pandemic, based on recommendations of the Centers for Disease Control and Prevention (CDC) and the American Society of Transplantation (AST) [52, 61] . Transplant recipients with direct contact (< 6 ft for ≥ 15 min) with a COVID-19 infected individual should be quarantined for 14 days and consider testing for SARS-CoV-2 after exposure or if they develop symptoms [49, 52] . abstract: PURPOSE OF REVIEW: Insufficient knowledge about COVID-19 and the potential risks of COVID-19 are limiting organ transplantation in wait-listed candidates and deferring essential health care in solid organ transplant recipients. In this review, we expand the understanding and present an overview of the optimized management of COVID-19 in solid organ transplant recipients. RECENT FINDINGS: Transplant recipients are at an increased risk of severe COVID-19. The unique characteristics of transplant recipients can make it more difficult to identify COVID-19. Based on the COVID-19 data to date and our experience, we present testing, management, and prevention methods for COVID-19. Comprehensive diagnostic tests should be performed to determine disease severity, phase of illness, and identify other comorbidities in transplant recipients diagnosed with COVID-19. Outpatients should receive education for preventative measures and optimal health care delivery minimizing potential infectious exposures. Multidisciplinary interventions should be provided to hospitalized transplant recipients for COVID-19 because of the complexity of caring for transplant recipients. SUMMARY: Transplant recipients should strictly adhere to infection prevention measures. Understanding of the transplant specific pathophysiology and development of effective treatment strategies for COVID-19 should be prioritized. url: https://www.ncbi.nlm.nih.gov/pubmed/33145146/ doi: 10.1007/s40472-020-00305-y id: cord-254825-c5d0wul9 author: Kim, Sei Won title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 words: 3554.0 sentences: 205.0 pages: flesch: 49.0 cache: ./cache/cord-254825-c5d0wul9.txt txt: ./txt/cord-254825-c5d0wul9.txt summary: In this study, we retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing, contact history, and presence of respiratory symptoms in a single center with a healthcare-associated COVID-19 outbreak. We reviewed the history of patients to assess whether they visited China or other high-risk countries within two weeks prior to the outbreak of healthcare-associated COVID-19, or if they came into contact with confirmed COVID-19 cases. After SARS-CoV-2 infection was confirmed, the Seoul city government announced the closure of the hospital on February 21, 2020, to prevent a healthcare-associated outbreak. After the hospital staff member responsible for transporting patients was confirmed as the first COVID-19 case, people with contact history, fever, or respiratory symptoms were tested for SARS-CoV-2 infection with RT-PCR (Fig 2) . After the first case was reported, epidemiologists from KCDC and the infection control unit of our hospital reviewed electronic medical charts, CCTV, and personal movements to identify individuals with potential contact with confirmed COVID-19 patients. abstract: BACKGROUND: Our hospital experienced the first healthcare-associated COVID-19 outbreak in Seoul at the time the first COVID-19 cases were confirmed in Korea. The first confirmed COVID-19 patient was a hospital personnel who was in charge of transferring patients inside our hospital. To contain the virus spread, we shutdown our hospital, and tested all inpatients, medical staff members, and employees. METHODS: We retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing according to the contact history, occupation, and presence of respiratory symptoms. Closed-circuit television (CCTV) was reviewed in the presence of an epidemiologist to identify individuals who came into contact with confirmed COVID-19 patients. RESULTS: A total of 3,091 respiratory samples from 2,924 individuals were obtained. Among 2,924 individuals, two inpatients, and one caregiver tested positive (positivity rate, 0.1%). Although all confirmed cases were linked to a general ward designated for pulmonology patients, no medical staff members, medical support personnel, or employees working at the same ward were infected. Contact with confirmed COVID-19 cases was frequent among inpatients and medical support personnel. The most common contact area was the general ward for pulmonology patients and medical support areas, including clinical and imaging examination rooms. Finally, the total number of hospital-associated infections was 14, consisting of four diagnosed at our hospital and ten diagnosed outside the hospital. CONCLUSIONS: The robust control of the COVID-19 outbreak further minimized the transmission of SARS-CoV-2 in the hospital and local communities. However, there was also a debate over the appropriate period of hospital shutdown and testing of all hospital staff and patients. Future studies are required to refine and establish the in-hospital quarantine and de-isolation guidelines based on the epidemiological and clinical settings. url: https://doi.org/10.1371/journal.pone.0237692 doi: 10.1371/journal.pone.0237692 id: cord-277564-x5qfxag3 author: Kim, Si-Hyun title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea date: 2020-10-24 words: 1310.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-277564-x5qfxag3.txt txt: ./txt/cord-277564-x5qfxag3.txt summary: title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea Patients with findings suggestive of COVID-19 should be placed in a negative-pressure isolation room in the ED until the results of the rRT-PCR test for SARS-CoV-2 are confirmed as negative. However, patients requiring emergency surgery before confirmed negative SARS-CoV-2 rRT-PCR test results are evaluated for the risk of transmission by infectious disease specialists and the infection control team based on 3 criteria: clinical signs or symptoms, epidemiological risk, and chest radiological findings (Fig. 1 ). Patients who still have unconfirmed SARS-CoV-2 rRT-PCR test at the end of the surgery are transferred to the cohort ward, a single room, or a negative-pressure isolation room according to their risk. abstract: • Proper risk assessment for COVID-19 should be implemented. • Appropriate infection prevention practices for perioperative management are important. -Hospitals should organize dedicated protocols considering its facilities and human resources. url: https://www.sciencedirect.com/science/article/pii/S2405857220300887?v=s5 doi: 10.1016/j.ijso.2020.10.007 id: cord-257058-wf6oxzrk author: Kim, Sinae title: The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene date: 2020-10-26 words: 3332.0 sentences: 237.0 pages: flesch: 61.0 cache: ./cache/cord-257058-wf6oxzrk.txt txt: ./txt/cord-257058-wf6oxzrk.txt summary: The S gene of SARS-CoV, which encodes for the spike glycoprotein on the viral envelope, recognizes a receptor on the membrane of specific host cells. The present study with novel mutations in critical RBD of S gene may explain the high pathogenicity of SARS-CoV2 through precise biochemistry result with recombinant spike proteins as well as cell infectivity experiment. The alignment of four SARS-CoV2 spike amino acid sequences compared to the wild type sequence revealed that there are two additional mutations in the critical RBD and another mutation in subdomain (SD) 2, which is very close to the known mutation residue D614G (Figs. A recent study reported a single point mutation in which amino acid residue aspartic acid 614 replaced by glycine (D614G) in S gene, resulting in enhanced infectivity of SARS-CoV2 (18) . However, two novel mutations in S gene of Korean COVID-19 in the Korean patients were present in RBD (Fig. 6 , green bar), a site that is important for binding to ACE2 receptor on the host cell membrane. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a positive-sense single-stranded RNA (+ssRNA) that causes coronavirus disease 2019 (COVID-19). The viral genome encodes twelve genes for viral replication and infection. The third open reading frame is the spike (S) gene that encodes for the spike glycoprotein interacting with specific cell surface receptor – angiotensin converting enzyme 2 (ACE2) – on the host cell membrane. Most recent studies identified a single point mutation in S gene. A single point mutation in S gene leading to an amino acid substitution at codon 614 from an aspartic acid 614 into glycine (D614G) resulted in greater infectivity compared to the wild type SARS-CoV2. We were interested in investigating the mutation region of S gene of SARS-CoV2 from Korean COVID-19 patients. New mutation sites were found in the critical receptor binding domain (RBD) of S gene, which is adjacent to the aforementioned D614G mutation residue. This specific sequence data demonstrated the active progression of SARS-CoV2 by mutations in the RBD of S gene. The sequence information of new mutations is critical to the development of recombinant SARS-CoV2 spike antigens, which may be required to improve and advance the strategy against a wide range of possible SARS-CoV2 mutations. url: https://www.ncbi.nlm.nih.gov/pubmed/33163249/ doi: 10.4110/in.2020.20.e41 id: cord-266869-fs8dn7ir author: Kim, So Young title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date: 2020-04-15 words: 3813.0 sentences: 217.0 pages: flesch: 54.0 cache: ./cache/cord-266869-fs8dn7ir.txt txt: ./txt/cord-266869-fs8dn7ir.txt summary: title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs might be involved in host cell entry of SARS-CoV-2. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. Using a modified version of Autodock Vina tuned for use with carbohydrates (Vina-Carb) [20, 21] , we performed blind docking on the trimeric SARS-CoV-2 SGP model to discover objectively the preferred binding GAG-binding sites on the SGP protein surface. abstract: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread around the globe at an unprecedented rate. To date, no effective therapeutic is available to fight its associated disease, COVID-19. Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs might be involved in host cell entry of SARS-CoV-2. Using a surface plasmon resonance direct binding assay, we found that both monomeric and trimeric SARS-CoV-2 spike more tightly bind to immobilized heparin (KD = 40 pM and 73 pM, respectively) than the SARS-CoV and MERS-CoV SGPs (500 nM and 1 nM, respectively). In competitive binding studies, the IC50 of heparin, tri-sulfated non-anticoagulant heparan sulfate, and non-anticoagulant low molecular weight heparin against SARS-CoV-2 SGP binding to immobilized heparin were 0.056 μM, 0.12 μM, and 26.4 μM, respectively. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. Our study augments our knowledge in SARS-CoV-2 pathogenesis and advances carbohydrate-based COVID-19 therapeutic development. url: https://doi.org/10.1101/2020.04.14.041459 doi: 10.1101/2020.04.14.041459 id: cord-295830-1sbnewog author: Kim, Sung-Jae title: A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? date: 2020-05-14 words: 2371.0 sentences: 133.0 pages: flesch: 50.0 cache: ./cache/cord-295830-1sbnewog.txt txt: ./txt/cord-295830-1sbnewog.txt summary: Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this study. The region containing this mutation point was confirmed as a B-cell epitope located in the S1 domain, and SARS-CoV-2b strains exhibited severe reduced antigenic indexes compared to SARS-CoV-2a in this area. Generally, several types of coronavirus are divided into subtypes depending on amino acid mutations in S gene sequences, and molecular analysis based on the S gene can provide insights into antigenicity, immunogenicity, or evolutionary trends [2, 4, 10, 12, 13] . Vaccines 2020, 8, 220 3 of 8 change alters the conformation of these immunogenic determinants; consequently, this region is expected to no longer act as a B-cell epitope in SARS-CoV-2b. The results of the antigenic index analysis showed severely reduced indexes of amino acids 615-617 in the SARS-CoV-2b strains compared to SARS-CoV-2a; it is predicted that the change of D614G affects the antigenicity of this region ( Figure 1F ). abstract: The S glycoprotein of coronaviruses is important for viral entry and pathogenesis with most variable sequences. Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this study. In phylogenetic analysis, two subtypes (SARS-CoV-2a and -b) were confirmed within SARS-CoV-2 strains. These two subtypes were divided by a novel synonymous mutation of D614G. This may play a crucial role in the evolution of SARS-CoV-2 to evade the host immune system. The region containing this mutation point was confirmed as a B-cell epitope located in the S1 domain, and SARS-CoV-2b strains exhibited severe reduced antigenic indexes compared to SARS-CoV-2a in this area. This may allow these two subtypes to have different antigenicity. If the two subtypes have different serological characteristics, a vaccine for both subtypes will be more effective to prevent COVID-19. Thus, further study is urgently required to confirm the antigenicity of these two subtypes. url: https://www.ncbi.nlm.nih.gov/pubmed/32422894/ doi: 10.3390/vaccines8020220 id: cord-323449-r1gyjxei author: Kim, Uh Jin title: Air and Environmental Contamination Caused by COVID-19 Patients: a Multi-Center Study date: 2020-09-08 words: 2012.0 sentences: 141.0 pages: flesch: 51.0 cache: ./cache/cord-323449-r1gyjxei.txt txt: ./txt/cord-323449-r1gyjxei.txt summary: BACKGROUND: The purpose of this study was to determine the extent of air and surface contamination of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in four health care facilities with hospitalized coronavirus disease 2019 (COVID-19) patients. CONCLUSION: Our data suggest that remote (> 2 m) airborne transmission of SARS-CoV-2 from hospitalized COVID-19 patients is uncommon when aerosol-generating procedures have not been performed. 10, 11 The objectives of the present study were 1) to investigate air and environmental contamination caused by COVID-19 patients in a variety of hospital settings; 2) to evaluate the effectiveness of environmental cleaning; and 3) to examine the potential for remote airborne transmission in the absence of aerosol-generating procedures. Despite extensive surface sampling, SARS-CoV-2 RNA was not detected in the room in Hospital B (AIIR with routine surface cleansing using disinfectant wipes the patient''s respiratory samples (Ct value 22.4-28.9) (Fig. 1B) . abstract: BACKGROUND: The purpose of this study was to determine the extent of air and surface contamination of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in four health care facilities with hospitalized coronavirus disease 2019 (COVID-19) patients. METHODS: We investigated air and environmental contamination in the rooms of eight COVID-19 patients in four hospitals. Some patients were in negative-pressure rooms, and others were not. None had undergone aerosol-generating procedures. On days 0, 3, 5, and 7 of hospitalization, the surfaces in the rooms and anterooms were swabbed, and air samples were collected 2 m from the patient and from the anterooms. RESULTS: All 52 air samples were negative for SARS-CoV-2 RNA. Widespread surface contamination of SARS-CoV-2 RNA was observed. In total, 89 of 320 (27%) environmental surface samples were positive for SARS-CoV-2 RNA. Surface contamination of SARS-CoV-2 RNA was common in rooms without surface disinfection and in rooms sprayed with disinfectant twice a day. However, SARS-CoV-2 RNA was not detected in a room cleaned with disinfectant wipes on a regular basis. CONCLUSION: Our data suggest that remote (> 2 m) airborne transmission of SARS-CoV-2 from hospitalized COVID-19 patients is uncommon when aerosol-generating procedures have not been performed. Surface contamination was widespread, except in a room routinely cleaned with disinfectant wipes. url: https://doi.org/10.3346/jkms.2020.35.e332 doi: 10.3346/jkms.2020.35.e332 id: cord-335443-iv2gs3kg author: Kim, Youngchang title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 words: 5464.0 sentences: 333.0 pages: flesch: 57.0 cache: ./cache/cord-335443-iv2gs3kg.txt txt: ./txt/cord-335443-iv2gs3kg.txt summary: Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme''s active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5''GAACU¯CAU¯GGACCU¯U¯GGCAG3'' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5''UMP, 3''UMP, 5''GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5''GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5''UMP complex. abstract: SARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (−) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme’s active site, providing basis for the uracil scaffold-based drug development. url: https://doi.org/10.1101/2020.06.26.173872 doi: 10.1101/2020.06.26.173872 id: cord-280621-tph5n7ak author: Kim, Yunjeong title: Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor date: 2016-03-30 words: 7417.0 sentences: 354.0 pages: flesch: 52.0 cache: ./cache/cord-280621-tph5n7ak.txt txt: ./txt/cord-280621-tph5n7ak.txt summary: Shifts in tissue or cell tropism and resulting changes in virulence have also been reported for coronaviruses; porcine respiratory coronavirus causes mild respiratory infection in pigs and presumably arose from transmissible gastroenteritis virus (TGEV), the etiologic agent of gastroenteritis in young pigs with a high fatality, by spontaneous mutations and/or deletions in its genome [9] . Effective treatment intervention for coronavirus infections with an immunopathological component, such as SARS, MERS and FIP, is speculated to involve the judicious use of immunomodulatory agents to enhance protective host immunity and decrease pathological immune responses and antiviral drugs to directly inhibit viral replication. These results on viral titers show that FIPV 3CLpro is a valid target for FIPV antiviral drugs and GC376 can effectively reduce the virus load in the macrophages from the ascites and the omentum of cats with FIP. abstract: Coronaviruses infect animals and humans causing a wide range of diseases. The diversity of coronaviruses in many mammalian species is contributed by relatively high mutation and recombination rates during replication. This dynamic nature of coronaviruses may facilitate cross-species transmission and shifts in tissue or cell tropism in a host, resulting in substantial change in virulence. Feline enteric coronavirus (FECV) causes inapparent or mild enteritis in cats, but a highly fatal disease, called feline infectious peritonitis (FIP), can arise through mutation of FECV to FIP virus (FIPV). The pathogenesis of FIP is intimately associated with immune responses and involves depletion of T cells, features shared by some other coronaviruses like Severe Acute Respiratory Syndrome Coronavirus. The increasing risks of highly virulent coronavirus infections in humans or animals call for effective antiviral drugs, but no such measures are yet available. Previously, we have reported the inhibitors that target 3C-like protease (3CLpro) with broad-spectrum activity against important human and animal coronaviruses. Here, we evaluated the therapeutic efficacy of our 3CLpro inhibitor in laboratory cats with FIP. Experimental FIP is 100% fatal once certain clinical and laboratory signs become apparent. We found that antiviral treatment led to full recovery of cats when treatment was started at a stage of disease that would be otherwise fatal if left untreated. Antiviral treatment was associated with a rapid improvement in fever, ascites, lymphopenia and gross signs of illness and cats returned to normal health within 20 days or less of treatment. Significant reduction in viral titers was also observed in cats. These results indicate that continuous virus replication is required for progression of immune-mediated inflammatory disease of FIP. These findings may provide important insights into devising therapeutic strategies and selection of antiviral compounds for further development for important coronaviruses in animals and humans. url: https://www.ncbi.nlm.nih.gov/pubmed/27027316/ doi: 10.1371/journal.ppat.1005531 id: cord-256537-axbyav1m author: Kimball, Ann Marie title: Emergence of Novel Human Infections: New Insights and New Challenges date: 2016-10-24 words: 4979.0 sentences: 283.0 pages: flesch: 50.0 cache: ./cache/cord-256537-axbyav1m.txt txt: ./txt/cord-256537-axbyav1m.txt summary: In reviewing the new challenges posed by these emergent events, new technologies promise some answers; however, global health security against pandemic threats, particularly given the uneven distribution of global resources for prevention, detection, and response, remains a critical area of challenge. Specifically: (1) it is now well appreciated that influenza can migrate directly from avian sources to humans, and the appreciation of the actual directness of ''species jumping'' has moved forward; (2) new infections have also introduced uncertainty in transmission dynamics with emphasis on super-spreader events as well as nosocomial transmission; (3) infectious particles are not confined to those organisms which contain genetic material; (4) a new paradigm such as ''Planetary Health'' may be necessary for defining these trends; and (5) global preparedness and response is not in place for the next pandemic. To summarize, the recent episodes of respiratory infectious diseases related to influenza, SARS-CoV, and MERS-CoV have demonstrated increasingly direct links between animal and human infections, agile intercontinental geographic spread, and complex transmission dynamics including ''superspreader'' events. abstract: Novel human infections have continued to emerge over the past decade. Their presentation, epidemiology, and microbiology have shifted the paradigms of traditional science. In particular insights into nongenetic or paragenetic mechanisms (plasmid mediated), modes of infection have challenged biology. In reviewing the new challenges posed by these emergent events, new technologies promise some answers; however, global health security against pandemic threats, particularly given the uneven distribution of global resources for prevention, detection, and response, remains a critical area of challenge. url: https://api.elsevier.com/content/article/pii/B9780128036785001533 doi: 10.1016/b978-0-12-803678-5.00153-3 id: cord-316632-rr9f88oi author: Kimura, Yurika title: Society of swallowing and dysphagia of Japan: Position statement on dysphagia management during the COVID-19 outbreak date: 2020-07-23 words: 3098.0 sentences: 188.0 pages: flesch: 52.0 cache: ./cache/cord-316632-rr9f88oi.txt txt: ./txt/cord-316632-rr9f88oi.txt summary: On April 14, the Society of Swallowing and Dysphagia of Japan (SSDJ) proposed its position statement on dysphagia treatment considering the ongoing spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This statement is arranged into separate sections providing information and advice in consideration of the COVID-19 outbreak, including "terminology", "clinical swallowing assessment and examination", "swallowing therapy", "oral care", "surgical procedure for dysphagia", "tracheotomy care", and "nursing care". The current set of statements on dysphagia management in the COVID-19 outbreak is not an evidence-based clinical practice guideline, but a guide for all healthcare workers involved in the treatment of dysphagia during the COVID-19 epidemic to prevent SARS-CoV-2 infection. 48 This statement is arranged into separate sections provid-49 ing information and advice considering the COVID-19 out-50 break, including "clinical swallowing assessment and ex-51 amination", "dysphagia rehabilitation", "oral care", "nursing 52 care", "surgical procedure for dysphagia", and "tracheotomy 53 care". abstract: On April 14, the Society of Swallowing and Dysphagia of Japan (SSDJ) proposed its position statement on dysphagia treatment considering the ongoing spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main routes of transmission of SARS-CoV-2 are physical contact with infected persons and exposure to respiratory droplets. In cases of infection, the nasal cavity and nasopharynx have the highest viral load in the body. Swallowing occurs in the oral cavity and pharynx, which correspond to the sites of viral proliferation. In addition, the possibility of infection by aerosol transmission is also concerning. Dysphagia treatment includes a broad range of clinical assessments and examinations, dysphagia rehabilitation, oral care, nursing care, and surgical treatments. Any of these can lead to the production of droplets and aerosols, as well as contact with viral particles. In terms of proper infection control measures, all healthcare professionals involved in dysphagia treatment must be fully briefed and must appropriately implement all measures. In addition, most patients with dysphagia should be considered to be at a higher risk for severe illness from COVID-19 because they are elderly and have complications including heart diseases, diabetes, respiratory diseases, and cerebrovascular diseases. This statement establishes three regional categories according to the status of SARS-CoV-2 infection. Accordingly, the SSDJ proposes specific infection countermeasures that should be implemented considering 1) the current status of SARS-CoV-2 infection in the region, 2) the patient status of SARS-CoV-2 infection, and 3) whether the examinations or procedures conducted correspond to aerosol-generating procedures, depending on the status of dysphagia treatment. This statement is arranged into separate sections providing information and advice in consideration of the COVID-19 outbreak, including “terminology”, “clinical swallowing assessment and examination“, “swallowing therapy”, “oral care”, “surgical procedure for dysphagia”, “tracheotomy care”, and “nursing care”. In areas where SARS-CoV-2 infection is widespread, sufficient personal protective equipment should be used when performing aerosol generation procedures. The current set of statements on dysphagia management in the COVID-19 outbreak is not an evidence-based clinical practice guideline, but a guide for all healthcare workers involved in the treatment of dysphagia during the COVID-19 epidemic to prevent SARS-CoV-2 infection. url: https://www.sciencedirect.com/science/article/pii/S0385814620301656 doi: 10.1016/j.anl.2020.07.009 id: cord-258019-njky7v5x author: Kinaret, Pia A.S. title: Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us date: 2020-08-10 words: 1359.0 sentences: 79.0 pages: flesch: 40.0 cache: ./cache/cord-258019-njky7v5x.txt txt: ./txt/cord-258019-njky7v5x.txt summary: However, similarities between the responses to SARS-CoV-2 and certain nanomaterials suggest fibrotic pulmonary disease as a concern for public health in the next future. Also rigid multi-walled carbon nanotubes (rMWCNT), among other nanomaterials, induce innate immune response by activation of NF-κB, STAT3 and HIF-1/2, and consequent cytokine cascade [15, 16] . As the Covid-19 disease progresses, massive damage of the pulmonary tissue occurs by induction of an uncontrolled innate immune response, mainly mediated by M1 pro-inflammatory macrophages and granulocytes. Moreover, up-regulation of antigen processing pathways, RIG-1 and several viral-induced human disease pathways have been reported consequently to carbon nanomaterial exposure, both in vitro [23] and in murine lung in vivo [19, 24] . On the other hand, certain nanoparticles might induce lung fibrosis by a combination of metabolic tissue damage and primary activation of the innate immune cells. Here we summarized noticeable cellular and molecular similarities between the acute responses to both SARS-CoV-2 infection and certain nanomaterials exposure. abstract: Long-term effects of Covid-19 disease are still poorly understood. However, similarities between the responses to SARS-CoV-2 and certain nanomaterials suggest fibrotic pulmonary disease as a concern for public health in the next future. Cross-talk between nanotoxicology and other relevant disciplines can help us to deploy more effective Covid-19 therapies and management strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32834832/ doi: 10.1016/j.nantod.2020.100945 id: cord-290744-m0vpizuh author: Kindler, E. title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date: 2016-09-09 words: 7229.0 sentences: 399.0 pages: flesch: 52.0 cache: ./cache/cord-290744-m0vpizuh.txt txt: ./txt/cord-290744-m0vpizuh.txt summary: Here, we will summarize the insights gathered so far on an important aspect of virulence and host adaptation, the interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells. The broad antiviral activity of IFNs occurs on several levels, namely virus entry, viral polymerase function, host cell translation, RNA availability, RNA stability, particle budding, apoptosis, or general boosting of innate and adaptive immune responses. Crystal structure of the middle east respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response abstract: Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells. url: https://api.elsevier.com/content/article/pii/S0065352716300458 doi: 10.1016/bs.aivir.2016.08.006 id: cord-285527-1mceq6v0 author: Kinloch, Natalie N title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date: 2020-06-28 words: 1910.0 sentences: 127.0 pages: flesch: 55.0 cache: ./cache/cord-285527-1mceq6v0.txt txt: ./txt/cord-285527-1mceq6v0.txt summary: To investigate suboptimal sample collection as a possible cause of false-negative test results, we quantified human DNA levels recovered on nasopharyngeal swabs submitted to a single laboratory for COVID-19 testing, hypothesizing that human DNA could serve as a stable molecular marker of specimen collection quality. Human DNA levels were quantified using droplet digital PCR (ddPCR), a technique where each sample is fractionated into 20,000 nanolitre-sized water-in-oil droplets prior to PCR amplification with sequence-specific primers and fluorescent probes, and where Poisson detection sensitivity compared to the original real-time RT-PCR assay, we re-tested the 40 suspected false-negative specimens by nested RT-PCR. Overall, we observed significantly lower human DNA levels in the suspected false-negative nasopharyngeal swab samples compared to a panel of consecutive samples submitted for testing during the same period, though overlap between groups was still substantial (Figure 1, p<0.001) . Our observations strongly support suboptimal biological sampling, but not PCR sensitivity for SARS-CoV-2 RNA detection, as a contributing cause of false-negative COVID-19 test results. abstract: False-negative SARS-CoV-2 test results can negatively impact the clinical and public health response to COVID-19. We used droplet digital PCR (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (i.e. suspected false-negative test results) compared to a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens. url: https://doi.org/10.1093/infdis/jiaa370 doi: 10.1093/infdis/jiaa370 id: cord-266996-knwpkyg6 author: Kipkorir, Vincent title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test date: 2020-05-13 words: 1050.0 sentences: 89.0 pages: flesch: 57.0 cache: ./cache/cord-266996-knwpkyg6.txt txt: ./txt/cord-266996-knwpkyg6.txt summary: title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test 2 Recently, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has also been isolated from anal/rectal swabs and stool specimens 3, 4 , raising concerns of potential alternative routes of viral transmission. Thereafter, a pooled analysis incorporating only cohort studies or case series with sample ≥10 patients was conducted to calculate pooled prevalence estimates (PPE) of prolonged SARS-CoV-2 RNA detection in anal/rectal swabs and stool samples after negative conversion in nasopharyngeal RT-PCR using the MetaXL (software Version 5.3, EpiGear International Pty Ltd., Sunrise Beach, Australia). In the pooled analysis of 8 cohort studies/ case series (n= 315), the pooled prevalence estimate (PPE) for prolonged rectal/anal/stool SARS-CoV-2 RNA was 32% (95% CI 22-44) (Figure 1 ). abstract: Coronavirus disease 2019 (COVID‐19) is a rapidly escalating pandemic that has spread to many parts of the world. Current data available on COVID‐19 would suggest that SARS‐CoV‐2 virus is shed through the gastrointestinal system via feces. Some reports further indicate that a subset of COVID‐19 patients may continue to have positive SARS‐CoV‐2 anal/rectal swab and stool test after negative conversion of nasopharyngeal test. This paper analyses current literature to so as to shed some light on this issue. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26007 doi: 10.1002/jmv.26007 id: cord-273891-7w334xgt author: Kirchdoerfer, Robert N. title: Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date: 2018-03-31 words: 3300.0 sentences: 170.0 pages: flesch: 55.0 cache: ./cache/cord-273891-7w334xgt.txt txt: ./txt/cord-273891-7w334xgt.txt summary: The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. Subsequent studies of the highly pathogenic human coronavirus S proteins of SARS-64 CoV 15,22 and MERS-CoV 17,22 showed that these viral S1 RBD do indeed sample an ''up'' 65 conformation where the receptor-binding site is accessible. 70 To examine the hypothesized conformational transitions induced by proteolysis and 71 receptor binding, we used single-particle cryo-EM to determine structures of S in uncleaved, 72 S1/S2 cleaved and ACE2-bound states. Three-dimensional classification of the S1 RBD 73 positions and corresponding atomic protein models revealed that neither ACE2-binding nor 74 trypsin cleavage at the S1/S2 boundary induced substantial conformational changes in the CoV may use a distinct mechanism of FP2 membrane insertion. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein 381 reveal a prerequisite conformational state for receptor binding abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as a highly transmissible pathogenic human betacoronavirus. The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. As SARS-CoV enters host cells, the viral S undergoes two proteolytic cleavages at S1/S2 and S2’ sites necessary for efficient membrane fusion. Here, we present a cryo-EM analysis of the trimeric SARS-CoV S interactions with ACE2 and of the trypsin-cleaved S. Surprisingly, neither binding to ACE2 nor cleavage by trypsin at the S1/S2 cleavage site impart large conformational changes within S or expose the secondary cleavage site, S2’. These observations suggest that S2’ cleavage does not occur in the S prefusion conformation and that additional triggers may be required. url: https://doi.org/10.1101/292672 doi: 10.1101/292672 id: cord-319100-3gdawhfn author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 words: 4624.0 sentences: 204.0 pages: flesch: 49.0 cache: ./cache/cord-319100-3gdawhfn.txt txt: ./txt/cord-319100-3gdawhfn.txt summary: authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). abstract: During the 2020 SARS-Cov-2 pandemic, there has been an acute shortage of viral transport medium. Many different products have been used to meet the demands of large-scale diagnostic and surveillance testing. The stability of SARS-Cov-2 RNA was assessed in several commercially produced transport media and an in-house solution. Coronavirus RNA was rapidly destroyed in the commercial transport media though the deleterious effects on intact virus were limited. Similar results were obtained for a Type A influenza virus. There was reduced detection of both virus and nucleic acid when a herpesvirus sample and purified DNA were tested. Collectively these data showed that the commercial viral transport media contained nucleases or similar substances and may seriously compromise diagnostic and epidemiological investigations. Recommendations to include foetal bovine serum as a source of protein to enhance the stabilising properties of viral transport media are contraindicated. Almost all commercial batches of foetal bovine serum contain pestiviruses and at times other bovine viruses. In addition to the potential for there to be nucleases in the transport medium, the presence of these viruses and other extraneous nucleic acid in samples may compromise the interpretation of sequence data. The inclusion of foetal bovine serum presents a biosecurity risk for the movement of animal pathogens and renders these transport media unsuitable for animal disease diagnostic applications. While these transport media may be suitable for virus culture purposes, there could be misleading results if used for nucleic acid-based tests. Therefore, these products should be evaluated to ensure fitness for purpose. url: https://doi.org/10.1101/2020.06.09.142323 doi: 10.1101/2020.06.09.142323 id: cord-336775-d4hi9myk author: Kirtipal, Nikhil title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 words: 8606.0 sentences: 442.0 pages: flesch: 46.0 cache: ./cache/cord-336775-d4hi9myk.txt txt: ./txt/cord-336775-d4hi9myk.txt summary: Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Hence, acute respiratory distress syndrome (ARDS) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of SARS-CoV-2 outbreak; similar observations were noted in case of SARS-CoV infection (Kumar et al., 2020) . When developing novel therapeutic strategies to check the immunoregulatory cytokines such as TNFβ and IL6, investigation should be considered on the viral strain and targeted organ specificity; for example, SARS-CoV-2 has more affinity to ACE2 which are scattering on different organs like lung and kidney while MERS-like CoV can even infect T-cells. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes repaid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this Review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutic against broad spectrum of coronaviruses. url: https://doi.org/10.1016/j.meegid.2020.104502 doi: 10.1016/j.meegid.2020.104502 id: cord-314960-f4hj35dr author: Kissler, Stephen M title: Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period date: 2020-03-06 words: 6253.0 sentences: 375.0 pages: flesch: 52.0 cache: ./cache/cord-314960-f4hj35dr.txt txt: ./txt/cord-314960-f4hj35dr.txt summary: To quantify the relative contribution of immunity versus seasonal forcing on the transmission dynamics of the betacoronaviruses, we adopted a regression model (22) that expressed the effective reproduction number for each strain (HKU1 and OC43) as the product of a baseline transmissibility constant (related to the basic reproduction number and the proportion of the population susceptible at the start of the season), the depletion of susceptibles due to infection with the same strain, the depletion of susceptibles due to infection with the other strain, and a spline to capture further unexplained seasonal variation in transmission strength (seasonal forcing). https://doi.org/10.1101/2020.03.04.20031112 doi: medRxiv preprint infection due to SARS-CoV-2, and autumn establishments and smaller seasonal fluctuations in transmissibility were associated with larger pandemic peak sizes. Peak simulated SARS-CoV-2 epidemic sizes, in units of percent influenza-like illness (ILI) x percent positive laboratory tests, by year for a representative set of cross immunities, immunity durations, and establishment times. abstract: There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission of human betacoronaviruses HCoV-OC43 and HCoV-HKU1. We then built a mathematical model to simulate transmission of SARS-CoV-2 through the year 2025. We project that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after an initial pandemic wave. We summarize the full range of plausible transmission scenarios and identify key data still needed to distinguish between them, most importantly longitudinal serological studies to determine the duration of immunity to SARS-CoV-2. url: https://doi.org/10.1101/2020.03.04.20031112 doi: 10.1101/2020.03.04.20031112 id: cord-331520-o9e4qqn4 author: Kistler, Christine E. title: The Winter Respiratory Viral Season During the COVID-19 Pandemic date: 2020-10-26 words: 2724.0 sentences: 168.0 pages: flesch: 44.0 cache: ./cache/cord-331520-o9e4qqn4.txt txt: ./txt/cord-331520-o9e4qqn4.txt summary: The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research. abstract: The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Specific topics include preventing the spread of respiratory viruses, promoting immunization, and the diagnosis and treatment of suspected respiratory infection. Policy-relevant issues are discussed, including whether to mandate influenza immunization for staff, the availability and use of personal protective equipment, supporting staff if they become ill, and the distribution of a COVID-19 vaccine when it becomes available. Research is applicable in all of these areas, including regarding the use of emerging electronic decision support tools. If there is a positive side to this year’s winter respiratory virus season, it is that staff, residents, family members, and clinicians will be especially vigilant about potential infection. url: https://api.elsevier.com/content/article/pii/S1525861020309221 doi: 10.1016/j.jamda.2020.10.030 id: cord-254957-jqp1gto6 author: Klann, Kevin title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date: 2020-08-11 words: 7002.0 sentences: 411.0 pages: flesch: 50.0 cache: ./cache/cord-254957-jqp1gto6.txt txt: ./txt/cord-254957-jqp1gto6.txt summary: We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. Additionally, we found carbon 160 metabolism among the pathways showing significantly increased phosphorylation upon SARS-CoV-2 infection (Table S4 ) in addition to previously described changes of total protein levels of enzymes part of glycolysis and carbon metabolism (Bojkova et al., 2020 )( Figure S3 ). We mapped identified members of GFR signaling and their respective phosphorylation differences upon SARS-CoV-2 infection ( Figure 3C ) revealing an extensive overall increase in phosphorylation of the whole pathway, including related components for cytoskeleton remodeling and receptor endocytosis. Growth factor receptor signaling was highly activated upon infection and its inhibition prevented SARS-CoV-2 replication in cells. abstract: Summary SARS-CoV-2 infections are rapidly spreading around the globe. The rapid development of therapies is of major importance. However, our lack of understanding of the molecular processes and host cell signaling events underlying SARS-CoV-2 infection hinder therapy development. We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. We identified viral protein phosphorylation and defined phosphorylation-driven host cell signaling changes upon infection. Growth factor receptor (GFR) signaling and downstream pathways were activated. Drug-protein network analyses revealed GFR signaling as key pathway targetable by approved drugs. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. This study describes host cell signaling events upon SARS-CoV-2 infection and reveals GFR signaling as central pathway essential for SARS-CoV-2 replication. It provides with novel strategies for COVID-19 treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32877642/ doi: 10.1016/j.molcel.2020.08.006 id: cord-338498-3238fz73 author: Kleen, Thomas-Oliver title: Mitigating Coronavirus Induced Dysfunctional Immunity for At-Risk Populations in COVID-19: Trained Immunity, BCG and “New Old Friends” date: 2020-09-04 words: 12523.0 sentences: 559.0 pages: flesch: 39.0 cache: ./cache/cord-338498-3238fz73.txt txt: ./txt/cord-338498-3238fz73.txt summary: Bacterial "new old friends" such as Bacille Calmette-Guérin (BCG) or Mycobacterium obuense have the ability to elevate basal systemic levels of type 1 cytokines and immune cells, correlating with increased protection against diverse and unrelated infectious agents, called "trained immunity." Here we describe dysfunctional immune responses induced by coronaviruses, representing potentially difficult to overcome obstacles to safe, effective vaccine development for COVID-19, and outline how trained immunity could help protect high risk populations through immunomodulation with BCG and other "new old friends." One recent example of the need for continued vigilance is a study using Chinese macaques indicating cause for concern by showing that vaccine-induced, S-specific immunity in the form of anti-spike IgG resulted in severe ALI by skewing macrophage responses during subsequent, acute infection with closely related SARS-CoV (139) . abstract: The novel, highly contagious coronavirus SARS-CoV-2 spreads rapidly throughout the world, leading to a deadly pandemic of a predominantly respiratory illness called COVID-19. Safe and effective anti-SARS-CoV-2 vaccines are urgently needed. However, emerging immunological observations show hallmarks of significant immunopathological characteristics and dysfunctional immune responses in patients with COVID-19. Combined with existing knowledge about immune responses to other closely related and highly pathogenic coronaviruses, this could forebode significant challenges for vaccine development, including the risk of vaccine failure. Animal data from earlier coronavirus vaccine efforts indicate that elderly people, most at risk from severe COVID-19 disease, could be especially at risk from immunopathologic responses to novel coronavirus vaccines. Bacterial “new old friends” such as Bacille Calmette-Guérin (BCG) or Mycobacterium obuense have the ability to elevate basal systemic levels of type 1 cytokines and immune cells, correlating with increased protection against diverse and unrelated infectious agents, called “trained immunity.” Here we describe dysfunctional immune responses induced by coronaviruses, representing potentially difficult to overcome obstacles to safe, effective vaccine development for COVID-19, and outline how trained immunity could help protect high risk populations through immunomodulation with BCG and other “new old friends.” url: https://doi.org/10.3389/fimmu.2020.02059 doi: 10.3389/fimmu.2020.02059 id: cord-328042-e1is656g author: Klein, Steffen title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date: 2020-08-07 words: 6328.0 sentences: 329.0 pages: flesch: 56.0 cache: ./cache/cord-328042-e1is656g.txt txt: ./txt/cord-328042-e1is656g.txt summary: The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] . abstract: Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and, alternatively, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot. url: https://doi.org/10.3390/v12080863 doi: 10.3390/v12080863 id: cord-315931-kc8gnj6z author: Klempt, Petr title: Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date: 2020-09-29 words: 4812.0 sentences: 224.0 pages: flesch: 49.0 cache: ./cache/cord-315931-kc8gnj6z.txt txt: ./txt/cord-315931-kc8gnj6z.txt summary: During the first attempt, thirty libraries (including 4 positive and 2 negative controls) were prepared in three plexes (10 samples each, see Supplementary Table S1 ) employing NEBNext ® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) followed by capture-based workflow utilizing the Twist SARS-CoV-2 Research Panel (Twist Bioscience). Compare to NEB+TWIST the capture-based Illumina approach data showed in average a lower percentage of mapped reads (Supplementary Table S1 ), this consequence could be related to the lower specificity of Respiratory Oligo Viral Panel designed next to the SARS-CoV-2 also for other pathogens (see https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/ngsenrichment-coronavirus-app-note-1270-2020-002.pdf). Also, the viral load in a sample (corresponding to sample Ct value ≤ 23.29 or positive control value ≤ 25.84) showed to be the limiting factor in case of each workflow, samples with higher Ct value resulted in either poor genome coverage (NEB+Twist workflow and Illumina workflow) or in absence of expected library preparation product (Paragon workflow). abstract: Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/33003465/ doi: 10.3390/diagnostics10100769 id: cord-300968-dtaasxk1 author: Kliger, Yossef title: From genome to antivirals: SARS as a test tube date: 2005-03-01 words: 5104.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-300968-dtaasxk1.txt txt: ./txt/cord-300968-dtaasxk1.txt summary: Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. This strategy seems promising in developing anti-viral therapeutic peptides to other viruses that possess type 1 viral fusion proteins [e.g. measles virus and respiratory syncytial virus (RSV)], which share some structural motifs with HIV. Similar to HIV, binding of the viral spike glycoprotein to some receptor(s) on host cells is the first step in SARS-CoV infection. HIV entry involves the binding of the viral envelope glycoproteins (comprising gp120 and gp41, which are the homologous of SARS-CoV S1 and S2, respectively) to CD4 on the host cell plasma membrane. Following the rule: formation of the 6-helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoproteinmediated viral entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeatderived peptides abstract: Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. Researchers have leveraged the 20-year battle against AIDS into a variety of possible treatments for SARS. Most prominently, based solely on viral genome information, silencers of viral genes, viral-enzyme blockers and viral-entry inhibitors were suggested as potential therapeutic agents for SARS. In particular, inhibitors of viral entry, comprising therapeutic peptides, were based on the recently launched anti-HIV drug enfuvirtide. This could represent one of the most direct routes from genome sequencing to the discovery of antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/15749283/ doi: 10.1016/s1359-6446(04)03320-3 id: cord-307248-8e34ndn4 author: Klimek, Ludger title: Handling of allergen immunotherapy in the COVID‐19 pandemic: An ARIA‐EAACI statement date: 2020-04-24 words: 2109.0 sentences: 128.0 pages: flesch: 36.0 cache: ./cache/cord-307248-8e34ndn4.txt txt: ./txt/cord-307248-8e34ndn4.txt summary: Allergen‐specific immunotherapy (AIT) is one of the most important treatment options for IgE‐mediated allergies and is based on immunological effects on the diseased patient Allergen-specific immunotherapy (AIT) is one of the most important treatment options for IgE-mediated allergies and is based on immunological effects on the diseased patient. The highest risk of healthcare-associated transmission occurs in the absence of standard precautions, when primary infection prevention and control measures for respiratory infections are not in place, and when handling patients whose COVID-19 diagnoses is yet to be confirmed. Eventhough it is well established that allergic airway diseases are associated with an Highly active antiretroviral treatment has improved the immune function and life expectancy in HIV-infected patients whose respiratory allergic incidence is similar to that of the general population (33) . In patients, who recovered from COVID-19 or who are found to have a sufficient SARS-CoV-2 antibody response after (asymptomatic) disease (14), AIT can be started or continued as planned. abstract: The current COVID‐19 pandemic influences many areas of social life, medical treatments and the way allergy is performed. Allergen‐specific immunotherapy (AIT) is one of the most important treatment options for IgE‐mediated allergies and is based on immunological effects on the diseased patient url: https://doi.org/10.1111/all.14336 doi: 10.1111/all.14336 id: cord-307605-8zgyar7e author: Klimek, Ludger title: Management von Anaphylaxie-gefährdeten Patienten während der Covid-19-Pandemie: Ein Positionspapier des Ärzteverbandes Deutscher Allergologen (AeDA)A, der Deutschen Gesellschaft für Allergologie und klinische Immunologie (DGAKI)B, der Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)C und des Deutschen Allergie- und Asthmabundes (DAAB)D date: 2020-11-09 words: 3716.0 sentences: 485.0 pages: flesch: 38.0 cache: ./cache/cord-307605-8zgyar7e.txt txt: ./txt/cord-307605-8zgyar7e.txt summary: Schlussfolgerung: Die Beratung, die Entwicklung von Strategien zur Expositionsprophylaxe und die Notfalltherapie von Patienten mit Anaphylaxie ist in der aktuellen Covid-19-Pandemie bei gefährdeten Patienten sehr wichtig. Die Selbstapplikation der Notfallmedikation ist gerade unter den Bedingungen einer möglichen Quarantäne oder Isolation zu bevorzugen und auch die Verordnung eines zweiten Adrenalin-Autoinjektors sollte großzügig Patientenindividuell geprüft werden. Der globale Ausbruch einer Pandemie von Infektionen mit dem neuartigen Coronavirus SARS-CoV-2 wurde als "Coronavirus-Krankheit 2019" ( Covid19) benannt und stellt die Gesundheitssysteme weltweit vor große Herausforderungen. Bei einer großen Zahl von Patienten führt die Infektion nach der Inkubationszeit zu einer Erkrankung der oberen und unteren Atemwege oder seltener anderer Organsysteme (NerAngiotensin-converting-enzyme-2 Fall zum Multiorganversagen und respiratorischer Insuffizienz führt, wie dies auch für andere Coronavirus-Infektionen (SARS-CoV-1, MERS-CoV) beschrieben wurde [4, 5, 6] . Unter Berücksichtigung der aktuellen Leitlinien zur Anaphylaxie-Behandlung wie auch der WHO-und RKI-Empfehlungen zu Covid-19 schlussfolgern wir, dass Anaphylaxie-Patienten mit vermuteter oder diagnostizierter SARS-CoV-2-Infektion weiterhin nach den aktuellen Richtlinien behandelt werden sollten. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33162681/ doi: 10.1007/s15007-020-2618-y id: cord-320831-owfnttqr author: Klimek, Ludger title: Allergen immunotherapy in the current COVID-19 pandemic: A position paper of AeDA, ARIA, EAACI, DGAKI and GPA: Position paper of the German ARIA Group(A) in cooperation with the Austrian ARIA Group(B), the Swiss ARIA Group(C), German Society for Applied Allergology (AEDA)(D), German Society for Allergology and Clinical Immunology (DGAKI)(E), Society for Pediatric Allergology (GPA)(F) in cooperation with AG Clinical Immunology, Allergology and Environmental Medicine of the DGHNO-KHC(G) and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-05-28 words: 3683.0 sentences: 195.0 pages: flesch: 41.0 cache: ./cache/cord-320831-owfnttqr.txt txt: ./txt/cord-320831-owfnttqr.txt summary: The highest risk of transmission for medical staff is present when standard precautions are missing, when primary infection prevention and control measures for respiratory infections are not undertaken, and when infected, potentially asymptomatic patients who are not yet tested positive for COVID-19 are treated without protective measures. The staff, including doctors, medical assistants, nutritional scientists, nursing and administrative staff, and all other staff at the facility with patient contact, should be made aware of: a) the current epidemiological situation of COVID-19 in Germany/Austria/ Switzerland and worldwide; b) known risk factors for infection; c) clinical signs and symptoms of COVID-19; d) recommended measures to prevent and contain infections in their region or country, including those mentioned in this document; e) procedures for reporting and transferring examined patients and probable/confirmed cases taking into account the appropriate regional regulations and specifications [36, 40] . abstract: No abstract available. url: https://doi.org/10.5414/alx02147e doi: 10.5414/alx02147e id: cord-345381-9cckppk2 author: Klimek, Ludger title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date: 2020-09-07 words: 6146.0 sentences: 332.0 pages: flesch: 43.0 cache: ./cache/cord-345381-9cckppk2.txt txt: ./txt/cord-345381-9cckppk2.txt summary: title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontaneous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontane-ous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. abstract: Background: Since the beginning of the COVID-19 pandemic, the treatment of patients with allergic and atopy-associated diseases has faced major challenges. Recommendations for “social distancing” and the fear of patients becoming infected during a visit to a medical facility have led to a drastic decrease in personal doctor-patient contacts. This affects both acute care and treatment of the chronically ill. The immune response after SARS-CoV-2 infection is so far only insufficiently understood and could be altered in a favorable or unfavorable way by therapy with monoclonal antibodies. There is currently no evidence for an increased risk of a severe COVID-19 course in allergic patients. Many patients are under ongoing therapy with biologicals that inhibit type 2 immune responses via various mechanisms. There is uncertainty about possible immunological interactions and potential risks of these biologicals in the case of an infection with SARS-CoV-2. Materials and methods: A selective literature search was carried out in PubMed, Livivo, and the internet to cover the past 10 years (May 2010 – April 2020). Additionally, the current German-language publications were analyzed. Based on these data, the present position paper provides recommendations for the biological treatment of patients with allergic and atopy-associated diseases during the COVID-19 pandemic. Results: In order to maintain in-office consultation services, a safe treatment environment must be created that is adapted to the pandemic situation. To date, there is a lack of reliable study data on the care for patients with complex respiratory, atopic, and allergic diseases in times of an imminent infection risk from SARS-CoV-2. Type-2-dominant immune reactions, as they are frequently seen in allergic patients, could influence various phases of COVID-19, e.g., by slowing down the immune reactions. Theoretically, this could have an unfavorable effect in the early phase of a SARS-Cov-2 infection, but also a positive effect during a cytokine storm in the later phase of severe courses. However, since there is currently no evidence for this, all data from patients treated with a biological directed against type 2 immune reactions who develop COVID-19 should be collected in registries, and their disease courses documented in order to be able to provide experience-based instructions in the future. Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontaneous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. If available, it is recommended to prefer a formulation for self-application and to offer telemedical monitoring. Treatment should aim at the best possible control of difficult-to-control allergic and atopic diseases using adequate rescue and add-on therapy and should avoid the need for systemic glucocorticosteroids. If SARS-CoV-2 infection is proven or reasonably suspected, the therapy should be determined by weighing the benefits and risks individually for the patient in question, and the patient should be involved in the decision-making. It should be kept in mind that the potential effects of biologicals on the immune response in COVID-19 are currently not known. Telemedical offers are particularly desirable for the acute consultation needs of suitable patients. url: https://doi.org/10.5414/alx02166e doi: 10.5414/alx02166e id: cord-286038-a62k3lma author: Klimke, A. title: Hydroxychloroquine as an aerosol might markedly reduce and even prevent severe clinical symptoms after SARS-CoV-2 infection date: 2020-04-27 words: 2336.0 sentences: 104.0 pages: flesch: 45.0 cache: ./cache/cord-286038-a62k3lma.txt txt: ./txt/cord-286038-a62k3lma.txt summary: The antimalarial drugs chloroquine phosphate (CQ) and hydroxychloroquine (HCQ) impair in vitro the terminal glycosylation of ACE2 without significant change of cell-surface ACE2 and, therefore, might be potent inhibitors of SARS-CoV-2 infections. We hypothesize that HCQ especially as an aerosol application will prevent or at least markedly reduce the replication rate of the SARS-CoV-2 virus in the early phase of the infection and subsequently substantially lower the number of severe pneumonias and casualties. This hypothesis is new since the major assumption in ongoing clinical studies and actual recommendations is that HCQ and CQ should be used in oral application form in patients with severe covid-19 pneumonia and only when other treatment strategies have failed. If our hypothesis is true, HCQ as an aerosol might not only reduce the side effect potential of the oral application form but can also be clinically used as an efficient antiviral agent in the early phase of COVID-19 and eventually lower the rate of severely ill patients and fatalities. abstract: Covid-19 is a new coronavirus disease first described in December 2019. This respiratory illness is severe and potentially fatal. Severe cases make up to 15%, lethality ranges between 1.5 and more than 10 %. What is urgently needed is an efficient pharmacological treatment for the treatment of severe cases. During the infection of alveolar epithelial cells of the lung, the ACE2 receptor has a central function. The antimalarial drugs chloroquine phosphate (CQ) and hydroxychloroquine (HCQ) impair in vitro the terminal glycosylation of ACE2 without significant change of cell-surface ACE2 and, therefore, might be potent inhibitors of SARS-CoV-2 infections. Starting inhibition at 0.1 µM, CQ completely prevented in vitro infections at 10 µM, suggesting a prophylactic effect and preventing the virus spread 5 hours after infection. In a first clinical trial, CQ was effective in inhibiting exacerbation of pneumonia, improving lung imaging findings, promotion of virus-negative conversion, and shortening the disease. In addition, HCQ, which is three times more potent than CQ in SARS-CoV-2 infected cells (EC50 0.72 µM), was significantly associated with viral load reduction/disappearance in COVID-19 patients compared to controls. Theoretically, CQ and HCQ could thus be effectively used in the treatment of SARS-CoV pneumonia. From a pharmacological standpoint, however, the major problems of oral treatment with these drugs are possible severe side effects and toxicity. Concretely, this relates to (a) the inconsistent individual bioavailability of these drugs at the alveolar target cells, depending on intestinal resorption, hepatic first-pass metabolism and accumulation in liver, spleen and lung, and (b) the need for a relatively high concentration of 1-5 µM at the alveolar surface. Therefore, we propose in a first dose estimation the use of HCQ as an aerosol in a dosage of 2-4 mg per inhalation in order to reach sufficient therapeutic levels at the alveolar epithelial cells. By using a low-dose non-systemic aerosol, adverse drug reactions will markedly be reduced compared with oral application. This increase in tolerability enables a broader use for prevention and after contact with an infected person, which would be an advantage especially for the high-risk, often multi-morbid and elderly patients. Empirical data on self-medication with a one-week aerosol application by two of the authors is presented. Inhalation was well tolerated without relevant side effects. url: https://doi.org/10.1016/j.mehy.2020.109783 doi: 10.1016/j.mehy.2020.109783 id: cord-312476-20ifwznd author: Kline, Jeffrey A. title: Crash Course in Decision Making date: 2008-01-08 words: 1089.0 sentences: 63.0 pages: flesch: 57.0 cache: ./cache/cord-312476-20ifwznd.txt txt: ./txt/cord-312476-20ifwznd.txt summary: in this month''s Academic Emergency Medicine shows how emergency physicians can use scientific method to ''''get it in gear'''' to produce a decision instrument, used in real time on huge numbers of patients, to render a major impact on public health. The Centers for Disease Control and Prevention (CDC) have issued specific recommendations for the diagnosis and evaluation of patients with suspected SARS. Curiously, at the time of this writing, no areas of the world are reporting ongoing SARS transmission, yet the CDC''s recommendation for infection control stated above were issued in September 2003, and are current and active. 2 Regardless of whether SARS returns to the public consciousness, the CDC''s recommendations for infection control of SARS have several major ramifications on the practice of emergency medicine. Numerous other contagious diseases that cause an ILI prodrome could emerge at any time and the CDC could issue similar infectious control recommendations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/14759962/ doi: 10.1111/j.1553-2712.2004.tb01431.x id: cord-321800-0h28pg3b author: Klingelhöfer, Doris title: Coronavirus: An insight into global research until outbreak of COVID-19 and its implications for the future date: 2020-09-23 words: 6119.0 sentences: 337.0 pages: flesch: 55.0 cache: ./cache/cord-321800-0h28pg3b.txt txt: ./txt/cord-321800-0h28pg3b.txt summary: RESULTS: The trend in publication and citation numbers shows the strong influence of the past pandemics SARS and MERS with an untypical decline afterward. The current extremely rapid global spread of SARS-CoV-2 has led to the highly dangerous outbreak of the pandemic CoVID-19 with daily increasing numbers of new infections and deaths around the world. Additionally, socio-economic, scientific and epidemiological parameters were related to the publication numbers to obtain an even more meaningful picture of the global landscape of CoV research. The resulting scientific interest and the possible in-si-VIEWPOINTS RESEARCH THEME 1: COVID-19 PANDEMIC tu investigation of the cases caused the publication figures to rise at the beginning of the SARS disease and to fall rapidly thereafter. Here, the USA and China are the highest-ranking countries, demonstrating their overall interest in CoV research and also focusing on the MERS pandemic, despite the relatively low case numbers. abstract: BACKGROUND: The currently prevailing global threat of COVID-19 caused the publication numbers on coronaviruses to explode. The awareness of the scientific and public community is enormous. But what about the sense of all these undertakings and what can be learned about the future for a better understanding? These questions were answered with established bibliometric analyses of the time until the avalanche of publications unfolded. METHODS: Chronological, geographical aspects of publication output on coronavirus were also evaluated under the influence of epidemiological and socio-economic parameters. RESULTS: The trend in publication and citation numbers shows the strong influence of the past pandemics SARS and MERS with an untypical decline afterward. Research is becoming increasingly multidisciplinary over time. The USA and China, as the countries with the highest number of publications, are being displaced by other countries in the consideration of socio-economic and epidemiological aspects, which shows the effect of regional interest in corona research. A significant correlation was found between the number of SARS cases per country and related publications, while no correlation was found for MERS cases and articles. CONCLUSIONS: The results underline the need for sustainable and forward-looking approaches that should not end with the containment of COVID-19. url: https://doi.org/10.7189/jogh.10.020508 doi: 10.7189/jogh.10.020508 id: cord-312560-onfabcfv author: Klingler, J. title: Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2 date: 2020-08-21 words: 5861.0 sentences: 353.0 pages: flesch: 55.0 cache: ./cache/cord-312560-onfabcfv.txt txt: ./txt/cord-312560-onfabcfv.txt summary: The data demonstrate high prevalence of spike-and RBD-specific IgM and IgA, similar to that of IgG1, in plasma/serum from COVID-19 patients and their significant contributions to virusneutralizing activities. In Fig. 3 , comparing levels of total Ig with the different Ig isotypes showed a highly significant correlation with IgG1 for both Abs specific for spike and RBD indicating that IgG1 is the major isotype induced by SARS-CoV-2 infection. To ask directly to what extent Abs of different isotypes mediate neutralization, we evaluated the neutralization activities of IgM, IgG, and IgA fractions purified from plasma from five COVID-19-convalescent individuals (RP#1-5). Several SARS-CoV-2 vaccine candidates tested in animal models and humans were shown to induce IgG responses against spike and RBD as well as virus neutralizing activities, but in many of these studies, the induction of other Ig isotypes was not evaluated 46-49 . abstract: SARS-CoV-2 has infected millions of people and is on a trajectory to kill more than one million globally. Virus entry depends on the receptor-binding domain (RBD) of the spike protein. Although previous studies demonstrated anti-spike and -RBD antibodies as essential for protection and convalescent plasma as a promising therapeutic option, little is known about the immunoglobulin (Ig) isotypes capable of blocking virus entry. Here, we studied spike- and RBD-specific Ig isotypes in plasma/sera from two acutely infected and 29 convalescent individuals. Spike- and RBD-specific IgM, IgG1, and IgA1 antibodies were produced by all or nearly all subjects at varying levels and detected at 7-8 days post-disease onset. IgG2, IgG3, IgG4, and IgA2 were also present but at much lower levels. All samples also displayed neutralizing activity. IgM, IgG, and IgA were capable of mediating neutralization, but neutralization titers correlated better with binding levels of IgM and IgA1 than IgG. url: http://medrxiv.org/cgi/content/short/2020.08.18.20177303v1?rss=1 doi: 10.1101/2020.08.18.20177303 id: cord-267723-loj718vd author: Kloc, Małgorzata title: Macrophages in diabetes mellitus (DM) and COVID-19: do they trigger DM? date: 2020-10-17 words: 2305.0 sentences: 128.0 pages: flesch: 47.0 cache: ./cache/cord-267723-loj718vd.txt txt: ./txt/cord-267723-loj718vd.txt summary: We also describe the DM-related changes in the monocyte/macrophages functions, how they could lead to the severe outcome of SARS-CoV-2 infection, and importantly, if and how they could initiate DM in DM-susceptible patients. Preclinical and clinical studies indicate that the increased numbers of innate immune cells, and produced by them inflammatory factors have causative and detrimental effects on the islets and β-cells in diabetes (Böni-Schnetzler and Meier 2019). As we wrote above, SARS-CoV-2 infects many types of cells expressing ACE2 receptors, including the macrophages and β-cell in the pancreas. One possibility is that, similar to the effect of SARS-CoV-2 in the lungs, the infection of pancreatic macrophages causes inflammatory cytokine and chemokines storm in the pancreas. Although, this scenario seemed the least likely because the direct damage to the pancreatic islets should result in higher than the reported incidence of COVID-19-induced diabetes, however, recent data presented in Nature News indicate that indead, the SARS-CoV-2 may cause direct damage to the insulin producing β-cells (Mallapaty 2020) . abstract: Diabetes mellitus (DM) augments the risk of hospitalization and mortality resulting from viral, bacterial, or fungal pathogen infection. This has been also true for the past SARS and MERS, and current SARS-CoV-2 coronavirus epidemics. Clinical data indicate that SARS-CoV-2 infection triggers a severe course of COVID-19 more frequently in diabetic than non-diabetic patients. Here we overview the cellular and molecular mechanisms associated with this phenomenon. We focus on alterations in the immune cells, especially monocytes and macrophages, involved in innate immune response and inflammatory processes, which differ in type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). We also describe the DM-related changes in the monocyte/macrophages functions, how they could lead to the severe outcome of SARS-CoV-2 infection, and importantly, if and how they could initiate DM in DM-susceptible patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33102261/ doi: 10.1007/s40200-020-00665-3 id: cord-336810-77wq9laa author: Klocperk, Adam title: Complex Immunometabolic Profiling Reveals the Activation of Cellular Immunity and Biliary Lesions in Patients with Severe COVID-19 date: 2020-09-17 words: 4679.0 sentences: 207.0 pages: flesch: 43.0 cache: ./cache/cord-336810-77wq9laa.txt txt: ./txt/cord-336810-77wq9laa.txt summary: Therefore, we observed a gradual increase of CRP, procalcitonin, ferritin, and serum IL-6 corresponding to the severity of the disease; however, these markers displayed a relative failure to upregulate in patients with a fatal course, who instead displayed high sIL2R and D-dimers ( Figure 1C ). Most markers of inflammation, the immune response, and liver damage presented in patients with a fatal course of COVID-19 so far seem mostly on par with those seen in patients with a moderate form of the disease, suggesting a weaker response to the infection compared to severely ill patients, which resulted in the patients'' deaths. In contrast, patients with fatal COVID-19 ( Figure 5B ) displayed a negative correlation between leukocytes and lymphocytes, and their inflammatory markers increased with markers of organ failure (liver enzymes, amylase, GGT, urea, and creatinine) and cytotoxic cellular immunity (activated CD38+ HLA-DR+ CD8 T cells) instead. abstract: This study aimed to assess the key laboratory features displayed by coronavirus disease 2019 (COVID-19) inpatients that are associated with mild, moderate, severe, and fatal courses of the disease, and through a longitudinal follow-up, to understand the dynamics of the COVID-19 pathophysiology. All severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive patients admitted to the University Hospital in Motol between March and June 2020 were included in this study. A severe course of COVID-19 was associated with an elevation of proinflammatory markers; an efflux of immature granulocytes into peripheral blood; the activation of CD8 T cells, which infiltrated the lungs; transient liver disease. In particular, the elevation of serum gamma-glutamyl transferase (GGT) and histological signs of cholestasis were highly specific for patients with a severe form of the disease. In contrast, patients with a fatal course of COVID-19 failed to upregulate markers of inflammation, showed discoordination of the immune response, and progressed toward acute kidney failure. COVID-19 is a disease with a multi-organ affinity that is characterized by the activation of innate and cellular adaptive immunity. Biliary lesions with an elevation of GGT and the organ infiltration of interleukin 6 (IL-6)-producing cells are the defining characteristics for patients with the fulminant disease. url: https://doi.org/10.3390/jcm9093000 doi: 10.3390/jcm9093000 id: cord-312005-9so3orib author: Klussmeier, Anja title: Etablierung der PCR-basierten SARS-CoV-2-Testung im Hochdurchsatz date: 2020-09-05 words: 414.0 sentences: 57.0 pages: flesch: 57.0 cache: ./cache/cord-312005-9so3orib.txt txt: ./txt/cord-312005-9so3orib.txt summary: Eine entscheidende Maßnahme zur Eindämmung des SARS-CoV-2-Infektionsgeschehens ist die rechtzeitige Diagnose von Einzelfällen. Ende März 2020 war daher abzusehen, dass bei einem stark steigendem Infektionsgeschehen, wie es zu diesem Zeitpunkt in Italien oder Spanien beobachtet werden konnte, hohe Laborkapazitäten für die Diagnostik von SARS-CoV-2 in Deutschland benötigt werden würden. Das DKMS Life Science Lab ist das weltweit größte Labor für die HLA-Genotypisierung von Personen, die sich für eine Stammzellspende registrieren möchten. Pro Werktag werden hier rund 5.000 Proben im Hochdurchsatz bearbeitet: von der Annahme der Abstrichtupfer, über die DNA-Isolation, PCR und Sequenzierung bis hin zur Datenanalyse [2, 3] Der hier beschriebene Laborprozess zur Diag nostik von akuten SARS-CoV-2-Infektionen wurde in einem Zeitraum von etwa drei Monaten geplant, umgesetzt und validiert. 2016-2019 Spezialist für Labortechnik und Automation und seit 2019 Business Development Manager bei DKMS Life Science Lab GmbH in Dresden. Abteilungsleiter Labortechnik und seit 2016 Geschäftsführer (CTO) der DKMS Life Science Lab GmbH in Dresden abstract: Timely identification and isolation of affected individuals is one of the most important factors to control spreading of the newly emerged SARS-CoV-2. Consequently, it is crucial to maintain sufficient sample capacities in diagnostic laboratories. Here, we present a high-through-put approach for PCR-based SARS-CoV-2 testing. The implementation of sample pooling reduces costs and workload, especially in times with low population prevalence. url: https://doi.org/10.1007/s12268-020-1431-1 doi: 10.1007/s12268-020-1431-1 id: cord-103837-iuvigqdx author: Knierman, Michael D. title: The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date: 2020-11-13 words: 8578.0 sentences: 439.0 pages: flesch: 54.0 cache: ./cache/cord-103837-iuvigqdx.txt txt: ./txt/cord-103837-iuvigqdx.txt summary: Mass spectrometry is used to identify 526 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The ability to automate and miniaturize the MAPPs assay enables facile identification of 1000''s of naturally processed and displayed HLA-II peptides from human DCs. Using this approach, we were able J o u r n a l P r e -p r o o f to determine the precise regions and sequences of peptides from SARS-CoV-2 spike glycoprotein ECD derived from a panel of healthy subjects presented for immune surveillance by T-cells. We observed a total of 526 unique peptide sequences contained within 73 clusters distributed across each segment of the SARS-CoV-2 spike glycoprotein ECD presented by human DCs (Figure 2 and Supplemental Table S2 ). abstract: The precise elucidation of the antigen sequences for T-cell immunosurveillance greatly enhances our ability to both understand and modulate humoral responses to viral infection or active immunization. Mass spectrometry is used to identify 526 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The identified sequences span the entire spike protein and several sequences are isolated from a majority of the donors sampled indicating promiscuous binding. Importantly, many peptides derived from the receptor binding domain used for cell entry are identified. This work represents a precise and comprehensive immunopeptidomic investigation with SARS-CoV-2 spike glycoprotein and allows detailed analysis of features which may aid vaccine development to end the current COVID-19 pandemic. url: https://api.elsevier.com/content/article/pii/S2211124720314431 doi: 10.1016/j.celrep.2020.108454 id: cord-331010-4phhz79k author: Knight, M. title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) date: 2020-05-12 words: 4582.0 sentences: 274.0 pages: flesch: 52.0 cache: ./cache/cord-331010-4phhz79k.txt txt: ./txt/cord-331010-4phhz79k.txt summary: title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) Objective: To describe a national cohort of pregnant women hospitalised with SARS-CoV-2 infection in the UK, identify factors associated with infection and describe outcomes, including transmission of infection, for mother and infant. Rates of maternal death, level 3 critical care unit admission, preterm birth, stillbirth, early neonatal death, perinatal death; odds ratios for infected versus comparison women. The incidence of hospitalisation with confirmed SARS-CoV-2 infection in pregnancy was calculated using denominator estimates based on the most recently available (2018) national maternity data for the constituent countries of the United Kingdom. The clinical data from this national surveillance study show black and minority ethnicity is significantly associated with admission with SARS-CoV-2 infection in pregnancy, along with preexisting co-morbidities, overweight and obesity and older maternal age. abstract: Objective: To describe a national cohort of pregnant women hospitalised with SARS-CoV-2 infection in the UK, identify factors associated with infection and describe outcomes, including transmission of infection, for mother and infant. Design: Prospective national population-based cohort study using the UK Obstetric Surveillance System (UKOSS). Setting: All 194 obstetric units in the UK Participants: 427 pregnant women admitted to hospital with confirmed Sars-CoV-2 infection between 01/03/2020 and 14/04/2020. 694 comparison women who gave birth between 01/11/2017 and 31/10/2018. Main outcome measures: Incidence of maternal hospitalisation, infant infection. Rates of maternal death, level 3 critical care unit admission, preterm birth, stillbirth, early neonatal death, perinatal death; odds ratios for infected versus comparison women. Results: Estimated incidence of hospitalisation with confirmed SARS-CoV-2 in pregnancy 4.9 per 1000 maternities (95%CI 4.5-5.4). The median gestation at symptom onset was 34 weeks (IQR 29-38). Black or other minority ethnicity (aOR 4.49, 95%CI 3.37-6.00), older maternal age (aOR 1.35, 95%CI 1.01-1.81 comparing women aged 35+ with those aged 30-34), overweight and obesity (aORs 1.91, 95%CI 1.37-2.68 and 2.20, 95%CI 1.56-3.10 respectively compared to women with a BMI<25kg/m2) and pre-existing comorbidities (aOR 1.52, 95%CI 1.12-2.06) were associated with admission with SARS-CoV-2 during pregnancy. 247 women (58%) gave birth or had a pregnancy loss; 180 (73%) gave birth at term. 40 (9%) hospitalised women required respiratory support. Twelve infants (5%) tested positive for SARS-CoV-2 RNA, six of these infants within the first 12 hours after birth. Conclusions: The majority of pregnant women hospitalised with SARS-CoV-2 were in the late second or third trimester, supporting guidance for continued social distancing measures in later pregnancy. Most had good outcomes and transmission of SARS-CoV-2 to infants was uncommon. The strong association between admission with infection and black or minority ethnicity requires urgent investigation and explanation. Study Registration: ISRCTN 40092247 url: https://doi.org/10.1101/2020.05.08.20089268 doi: 10.1101/2020.05.08.20089268 id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 words: 9930.0 sentences: 411.0 pages: flesch: 43.0 cache: ./cache/cord-339172-210dwhgj.txt txt: ./txt/cord-339172-210dwhgj.txt summary: Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''''inner vesicles,'''' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. abstract: Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs (diameter 200–300 nm), and “vesicle packets” apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this “replication network” will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/18798692/ doi: 10.1371/journal.pbio.0060226 id: cord-314546-fbddxbhd author: Ko, Meehyun title: Comparative analysis of antiviral efficacy of FDA‐approved drugs against SARS‐CoV‐2 in human lung cells date: 2020-08-16 words: 1345.0 sentences: 83.0 pages: flesch: 47.0 cache: ./cache/cord-314546-fbddxbhd.txt txt: ./txt/cord-314546-fbddxbhd.txt summary: Although nafamostat mesylate and camostat mesylate were not selected as potent antiviral drug candidates in our earlier study, we compared the antiviral efficacy of these drugs at this time in between Vero and Calu-3 cells following the discovery that TMPRSS2, a host protease necessary for priming viral spike glycoprotein, could be a target for COVID-19 antiviral development. 11 The discrepancy in IC 50 was specifically remarkable with nafamostat mesylate; the IC 50 decreased by approximately 6000 folds when the drug was used in the SARS-CoV-2-infected Calu-3 cells perhaps due to the dominant role of TMPRSS2-dependent viral entry in the Calu-3 human lung epithelial cells. In summary, we compared antiviral efficacy of the potential antiviral drug candidates against SARS-CoV-2 in between Vero and Calu-3 cells and found that nafamostat mesylate is the most potent antiviral drug candidate in vitro. Comparative analysis of antiviral efficacy of FDA-approved drugs against SARS-CoV-2 in human lung cells abstract: Drug repositioning represents an effective way to control the current COVID‐19 pandemic. Previously, we identified 24 FDA‐approved drugs which exhibited substantial antiviral effect against severe acute respiratory syndrome coronavirus 2 in Vero cells. Since antiviral efficacy could be altered in different cell lines, we developed an antiviral screening assay with human lung cells, which is more appropriate than Vero cell. The comparative analysis of antiviral activities revealed that nafamostat is the most potent drug in human lung cells (IC(50) = 0.0022 µM). url: https://www.ncbi.nlm.nih.gov/pubmed/32767684/ doi: 10.1002/jmv.26397 id: cord-306748-i9ndb71n author: Kobia, Francis title: COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness? date: 2020-04-17 words: 3218.0 sentences: 148.0 pages: flesch: 51.0 cache: ./cache/cord-306748-i9ndb71n.txt txt: ./txt/cord-306748-i9ndb71n.txt summary: In fact, this strategy is being used by Senegal, which together with UK collaborators, is developing an affordable COVID-19 RDT (expected to cost $1 per test) for home use in African countries (Financial Times, 2020b). The authors contend that most African countries lack the capacity to administer mass screening to ascertain the extent of the disease spread, and call for support toward the development of homegrown RDTs and POCTs as a strategy to achieve mass screening of COVID-19 in Africa The present review by the authors provides important information on diagnostic challenges facing African countries in their combat against the ongoing COVID-19 pandemic. Specific to the present COVID-19 case, would it be faster and cheaper importing the diagnostic tools, as is already being done by some countries?The authors may wish to put " " section before " COVID-19 point of care testing strategies " section, for consistency with the conclusion. abstract: Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19) has rapidly spread worldwide, achieving pandemic status on 11 (th) March, 2020. As of 1 (st) April 2020, COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had infected over 800,000 people and caused over 40,000 deaths in 205 countries and territories. COVID-19 has had its heaviest toll on Europe, United States and China. As of 1 (st) of April 2020, the number of confirmed COVID-19 cases in Africa was relatively low, with the highest number registered by South Africa, which had reported 1,380 confirmed cases. On the same date (also the date of this review), Africa had reported 5,999 confirmed cases, of which 3,838 (almost 65%) occurred in South Africa, Algeria, Egypt, Morocco and Tunisia, with the remaining 2,071 cases distributed unevenly across the other African countries. We speculate that while African nations are currently experiencing much lower rates of COVID-19 relative to other continents, their significantly lower testing rates may grossly underestimate incidence rates. Failure to grasp the true picture may mean crucial windows of opportunity shut unutilized, while limited resources are not deployed to maximum effect. In the absence of extensive testing data, an overestimation of spread may lead to disproportionate measures being taken, causing avoidable strain on livelihoods and economies. Here, based on the African situation, we discuss COVID-19 diagnostic challenges and how they may blunt responses. url: https://www.ncbi.nlm.nih.gov/pubmed/32399515/ doi: 10.12688/aasopenres.13061.1 id: cord-151024-qe7c2uks author: Koca, Caglar title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date: 2020-11-07 words: 5622.0 sentences: 353.0 pages: flesch: 56.0 cache: ./cache/cord-151024-qe7c2uks.txt txt: ./txt/cord-151024-qe7c2uks.txt summary: We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . abstract: Severe Acute Respiratory Syndrome-CoronaVirus 2 (SARS-CoV2) caused the ongoing pandemic. This pandemic devastated the world by killing more than a million people, as of October 2020. It is imperative to understand the transmission dynamics of SARS-CoV2 so that novel and interdisciplinary prevention, diagnostic, and therapeutic techniques could be developed. In this work, we model and analyze the transmission of SARS-CoV2 through the human respiratory tract from a molecular communication perspective. We consider that virus diffusion occurs in the mucus layer so that the shape of the tract does not have a significant effect on the transmission. Hence, this model reduces the inherent complexity of the human respiratory system. We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. Our findings confirm the results in the experimental literature on higher mucus flow rate causing virus migration to the lower respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. url: https://arxiv.org/pdf/2011.05154v1.pdf doi: nan id: cord-298372-4pw1y404 author: Koch, Lionel title: Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? date: 2020-08-18 words: 6206.0 sentences: 286.0 pages: flesch: 42.0 cache: ./cache/cord-298372-4pw1y404.txt txt: ./txt/cord-298372-4pw1y404.txt summary: The last Ebola outbreak in 2014 in West Africa was regarded as a paradigm of the issues caused by emerging infectious diseases nowadays: this extremely deadly pathogen has naturally emerged in a large new area, and its overwhelming spread has subsequently impacted Europe and the United States [3] . At the same time, some natural outbreaks were caused by naturally altered pathogens like the Escherichia coli O104:H4 in Europe in 2011, a strain that acquired and combined unusual virulence factor and drug resistance genes [25] or in 2003 the new human coronavirus (SARS-CoV) identified with surprise in front of severe acute respiratory syndrome cases [26] . Indeed, even if the substantial remaining risk in the case of an attack is the possibility of secondary actions aiming to maximise damages to the emergency infrastructure [38] , the real challenge for global safety remains the early detection, the accurate characterisation and the establishment of specific measures, whatever the outbreak origin [39, 40] . abstract: nan url: https://doi.org/10.7189/jogh.10.020317 doi: 10.7189/jogh.10.020317 id: cord-277539-xt2nt11e author: Kochhar, Anuraj Singh title: Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date: 2020 words: 4502.0 sentences: 296.0 pages: flesch: 50.0 cache: ./cache/cord-277539-xt2nt11e.txt txt: ./txt/cord-277539-xt2nt11e.txt summary: Despite the avalanche of information that has exploded in relation to this rapidly spreading disease, there is a lack of consolidated information to guide dentists regarding clinical management including precautions to take materials to use and postprocedure care, during and after the COVID-19 pandemic. This review aims to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan can be formulated and adapted to the circumstances of each dental practice during the pandemic and the times to follow. The purpose of this review is to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan of measures can be formulated and adapted according to the circumstances of each dental practice during the pandemic and the times to follow. abstract: This article is a rumination on the outbreak of the dreaded coronavirus disease-2019 (COVID-19) pandemic which has engulfed both the developed and the developing countries, thereby causing widespread global public health concerns and threats to human lives. Although countries have made varied efforts, the pestilence is escalating due to the high infectivity. It is highly likely that dental professionals in upcoming days will come across COVID-19 patients and SARS-CoV-2 carriers, and hence must ensure a tactful handling of such patients to prevent its nosocomial spread. Despite the avalanche of information that has exploded in relation to this rapidly spreading disease, there is a lack of consolidated information to guide dentists regarding clinical management including precautions to take materials to use and postprocedure care, during and after the COVID-19 pandemic. Available sources of information have been analyzed, while relying on peer-reviewed reports followed by information available from the most respected authoritative sources, such as WHO, Centers for Disease Control and Prevention (CDC), and ADA. This review aims to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan can be formulated and adapted to the circumstances of each dental practice during the pandemic and the times to follow. HOW TO CITE THIS ARTICLE: Kochhar AS, Bhasin R, Kochhar GK, et al. Dentistry during and after COVID-19 Pandemic: Pediatric Considerations. Int J Clin Pediatr Dent 2020;13(4):399–406. url: https://www.ncbi.nlm.nih.gov/pubmed/33149414/ doi: 10.5005/jp-journals-10005-1782 id: cord-321933-cq0fa3hs author: Koff, Alan G. title: Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy date: 2020-10-07 words: 1223.0 sentences: 77.0 pages: flesch: 50.0 cache: ./cache/cord-321933-cq0fa3hs.txt txt: ./txt/cord-321933-cq0fa3hs.txt summary: title: Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy The incubation period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rarely >14 days. We report a patient with hypogammaglobulinemia who developed coronavirus disease 2019 (COVID-19) with a confirmed incubation period of at least 21 days. [2] [3] [4] 6, 7 In the vast majority of cases, the incubation period is far less than 14 days, which has helped to inform the Centers for Disease Control and Prevention (CDC) recommendations for a 14-day quarantine period after a known coronavirus disease 2019 (COVID-19) exposure. This case demonstrates an objectively confirmed asymptomatic SARS-CoV-2 infection with symptom onset 21 days after her positive test. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application The difference in the incubation period of 2019 novel coronavirus (SARS-CoV-2) infection between travelers to Hubei and nontravelers: the need for a longer quarantine period abstract: The incubation period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rarely >14 days. We report a patient with hypogammaglobulinemia who developed coronavirus disease 2019 (COVID-19) with a confirmed incubation period of at least 21 days. These findings raise concern for a prolonged presymptomatic transmission phase, necessitating a longer quarantine duration in this patient population. url: https://doi.org/10.1017/ice.2020.1239 doi: 10.1017/ice.2020.1239 id: cord-253851-27nt0op8 author: Koh, David title: SARS: health care work can be hazardous to health date: 2003-06-17 words: 1451.0 sentences: 78.0 pages: flesch: 56.0 cache: ./cache/cord-253851-27nt0op8.txt txt: ./txt/cord-253851-27nt0op8.txt summary: Health care workers (HCWs) are a high-risk group for SARS-CoV infection. As at 4 May, 41% of 203 SARS patients in Singapore and 22% of 1629 cases in Hong Kong [7] were HCWs. The majority of cases in Canada (74.4%) have been attributed to exposure in a hospital or health care setting [8] . That the cluster of cases included housekeepers is also significant-preventive measures need to target much broader groups of HCWs than just the doctors and nurses in direct contact with patients. This was the case in a Singapore hospital [11] , where the experience was reported as: ''We did not see any further transmission from this index patient after we implemented strict infection control measures involving use of N95 masks, gown, gloves, and handwashing before and after patient contact''. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/12815118/ doi: 10.1093/occmed/kqg090 id: cord-276980-k8xi2zvh author: Koh, David title: Occupational Health Response to SARS date: 2005-01-17 words: 1120.0 sentences: 69.0 pages: flesch: 48.0 cache: ./cache/cord-276980-k8xi2zvh.txt txt: ./txt/cord-276980-k8xi2zvh.txt summary: detected severe acute respiratory syndrome-associated coronavirus (SARS-CoV) from throat wash and saliva specimens and suggested that these specimens have advantages over other specimens, including ease of procurement and safety for medical personnel (1) . To the Editor: Severe acute respiratory syndrome (SARS), an occupational disease risk for healthcare workers, warrants an occupational health response, as clearly described by Esswein et al. The occupational health audits included site inspections and reviews of work processes of those areas where actual transmission of SARS had occurred and where triage of febrile patients was taking place. Occupational health physicians subsequently served on hospital SARS debriefing committees that reviewed institutional shortcomings and recommended new measures for future outbreaks. Clinical specimens were retrieved, and RT-PCR was performed to specifically amplify a genomic segment of SARS-CoV encompassing the deletion site. Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15714660/ doi: 10.3201/eid1101.040637 id: cord-283116-ib5c3lbi author: Koh, David title: Occupational health responses to COVID‐19: What lessons can we learn from SARS? date: 2020-05-13 words: 3389.0 sentences: 204.0 pages: flesch: 58.0 cache: ./cache/cord-283116-ib5c3lbi.txt txt: ./txt/cord-283116-ib5c3lbi.txt summary: Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. coronavirus, COVID-19, health care, occupational health, outbreaks, public health, SARS-CoV-2 confirmed cases and over 62 000 deaths spread over 200 countries and territories. abstract: On 31 December 2019, the World Health Organization (WHO) received reports of pneumonia cases of unknown etiology in the city of Wuhan in Hubei Province, China. The agent responsible was subsequently identified as a coronavirus—SARS‐CoV‐2. The WHO declared this disease as a Public Health Emergency of International Concern at the end of January 2020. This event evoked a sense of déjà vu, as it has many similarities to the outbreak of severe acute respiratory syndrome (SARS) of 2002‐2003. Both illnesses were caused by a zoonotic novel coronavirus, both originated during winter in China and both spread rapidly all over the world. However, the case‐fatality rate of SARS (9.6%) is higher than that of COVID‐19 (<4%). Another zoonotic novel coronavirus, MERS‐CoV, was responsible for the Middle East respiratory syndrome, which had a case‐fatality rate of 34%. Our experiences in coping with the previous coronavirus outbreaks have better equipped us to face the challenges posed by COVID‐19, especially in the health care setting. Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. Given the perspectives gained and lessons learnt from these past events, we should be better prepared to face the current COVID‐19 outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32515882/ doi: 10.1002/1348-9585.12128 id: cord-278759-pykihnup author: Koh, Yiwen title: Nurses'' perceptions of risk from emerging respiratory infectious diseases: A Singapore study date: 2012-03-21 words: 4899.0 sentences: 277.0 pages: flesch: 53.0 cache: ./cache/cord-278759-pykihnup.txt txt: ./txt/cord-278759-pykihnup.txt summary: Another significant finding of this study is that the government''s, organizations'' and nurses'' perceptions of new emerging respiratory infectious diseases were influenced by their previous experience with SARS. 16 It can be seen from this discussion that there is a substantial amount of research examining how HCWs perceive the risks of Emerging Acute Respiratory Infectious Diseases such as H1N1 and SARS; 17, 25 however, few studies have focused specifically on nurses. 41, 42 With the resurgence of emerging acute respiratory infectious diseases such as SARS and pandemic influenza in the 21st century, research investigating nurses'' risk perceptions towards their exposure is more than ever pertinent. The data show that the nurses in this study have similar concerns to previous research on HCW''s perceptions of risk from SARS and other emerging acute respiratory infectious diseases in that these nurses were concerned about risks to their personal health (from patients, from colleagues and visitors to the organization). abstract: Koh Y, Hegney D, Drury V. International Journal of Nursing Practice 2012; 18: 195–204 Nurses' perceptions of risk from emerging respiratory infectious diseases: A Singapore study The recent emergence of virulent respiratory infectious diseases such as Severe Acute Respiratory Syndrome (SARS) and Influenza A/H1N1 viruses predisposes nurses to occupational risks. This qualitative study investigated how Chinese Singaporean nurses perceived the risks of exposure to these infectious diseases and the factors that influenced this risk perception. Data were collected through face‐to‐face interviews and were analyzed using Braun and Clarke's process of thematic analysis. Three themes emerged: living with risk; the experience of SARS; and acceptance of risk. The nature of nursing work was perceived to place participants at risk of infection. Another significant finding of this study is that the government's, organizations' and nurses' perceptions of new emerging respiratory infectious diseases were influenced by their previous experience with SARS. Similar to previous studies, nurses working at the ‘front line’ believed that infection from these diseases was an unavoidable occupational hazard. url: https://doi.org/10.1111/j.1440-172x.2012.02018.x doi: 10.1111/j.1440-172x.2012.02018.x id: cord-320560-yn3bbkdh author: Kohanski, Michael A. title: Review of indoor aerosol generation, transport, and control in the context of COVID‐19 date: 2020-07-24 words: 4514.0 sentences: 220.0 pages: flesch: 41.0 cache: ./cache/cord-320560-yn3bbkdh.txt txt: ./txt/cord-320560-yn3bbkdh.txt summary: [5] [6] [7] [8] [9] The lack of studies within the otorhinolaryngology field assessing the aerosol-generating potential of procedures involving mucosal surfaces pre-COVID-19 made it challenging to understand in an evidence-based fashion the potential risks of SARS-CoV-2 transmission associated with instrumentation of the upper airway; that is, whether these procedures may be infectious AGPs. At the early stages of the pandemic, based on the risks of exposure to high viral load mucosal surfaces, 10, 11 as well as on the lack of any immunity to SARS-CoV-2 and of any vaccines or effective treatments, an array of practice changes to protect health-care workers and patients were recommended and instituted for otorhinolaryngology procedures involving upper airway mucosal surfaces. abstract: The coronavirus disease‐2019 (COVID‐19) pandemic has heightened the awareness of aerosol generation by human expiratory events and their potential role in viral respiratory disease transmission. Concerns over high severe acute respiratory syndrome‒coronavirus‐2 (SARS‐CoV‐2) viral burden of mucosal surfaces has raised questions about the aerosol‐generating potential and dangers of many otorhinolaryngologic procedures. However, the risks of aerosol generation and associated viral transmission by droplet or airborne routes for many otorhinolaryngology procedures are largely unknown. Indoor aerosol and droplet viral respiratory transmission risk is influenced by 4 factors: (1) aerosol or droplet properties; (2) indoor airflow; (3) virus‐specific factors; and (4) host‐specific factors. Herein we elaborate on known aerosol vs droplet properties, indoor airflow, and aerosol‐generating events to provide context for risks of aerosol infectious transmission. We also provide simple but typically effective measures for mitigating the spread and inhalation of viral aerosols in indoor settings. Understanding principles of infectious transmission, aerosol and droplet generation, as well as concepts of indoor airflow, will assist in the integration of new data on SARS‐CoV‐2 transmission and activities that can generate aerosol to best inform on the need for escalation or de‐escalation from current societal and institutional guidelines for protection during aerosol‐generating procedures. url: https://doi.org/10.1002/alr.22661 doi: 10.1002/alr.22661 id: cord-327920-51s4figy author: Kohler, Philipp P. title: Prevalence of SARS-CoV-2 antibodies among Swiss hospital workers: Results of a prospective cohort study date: 2020-10-08 words: 1539.0 sentences: 92.0 pages: flesch: 50.0 cache: ./cache/cord-327920-51s4figy.txt txt: ./txt/cord-327920-51s4figy.txt summary: 5 The aims of this prospective cohort study were to assess seropositivity for SARS-CoV-2, to identify risk exposures, and to describe the spectrum of COVID-19 symptoms among hospital workers. Participants'' sera were analyzed for SARS-CoV-2 antibodies using 3 different tests: a lateral flow immunochromatographic assay (LFIA, Sugentech, Yuseong-gu, Daejeon, Republic of Korea), a chemiluminescence microparticle immunoassay (CMIA, Abbott Diagnostics, Lake Bluff, IL), and an electro-chemiluminescence immunoassay (ECLIA, Roche Diagnostics, Basel, Switzerland). At followup, 2 participants showed a positive LFIA (IgG) and ECLIA/ CMIA result in addition to the 8 samples confirmed at baseline, resulting in 10 of 1,012 true seropositives (1.0%) and 48 of 1,012 false seropositives (4.7%) (Fig. 1) . This finding is in line with data from the Infectious Diseases Society of America (IDSA) guideline on SARS-CoV serology testing showing a lower sensitivity of CMIA IgG compared to LFIA IgM early after infection. abstract: In this prospective cohort of 1,012 Swiss hospital employees, 3 different assays were used to screen serum for SARS-CoV-2 antibodies. Seropositivity was 1%; the positive predictive values of the lateral-flow immunoassay were 64% (IgG) and 13% (IgM). History of fever and myalgia most effectively differentiated seropositive and seronegative participants. url: https://doi.org/10.1017/ice.2020.1244 doi: 10.1017/ice.2020.1244 id: cord-351718-sf5zp5wg author: Kohli, Utkarsh title: COVID-19 pneumonia in an infant with a hemodynamically significant ventricular septal defect date: 2020-10-12 words: 1371.0 sentences: 77.0 pages: flesch: 42.0 cache: ./cache/cord-351718-sf5zp5wg.txt txt: ./txt/cord-351718-sf5zp5wg.txt summary: Reports thus far suggest a mild course for acute COVID-19 infection in children; however, its effects in vulnerable paediatric populations, including children with haemodynamically significant congenital heart disease, have rarely been reported. We therefore report on a 4-month-old Hispanic male with a moderate sized conoventricular ventricular septal defect and pulmonary overcirculation who presented with COVID-19-associated pneumonia. 6 Children with haemodynamically significant congenital heart disease are at an increased risk of decompensation and hospitalisation when concomitantly infected with other respiratory viruses such as respiratory syncytial virus and influenza, [12] [13] [14] lending credence to the notion that COVID-19 could run a more severe course in these children. Given the probable paucity of these patients at any single paediatric centre, there is a dire need for collaborative research efforts on a global scale to characterise the clinical features and outcomes of COVID-19 in children with haemodynamically significant congenital heart disease as well as other vulnerable paediatric populations. abstract: Reports thus far suggest a mild course for acute COVID-19 infection in children; however, its effects in vulnerable paediatric populations, including children with haemodynamically significant congenital heart disease, have rarely been reported. We therefore report on a 4-month-old Hispanic male with a moderate sized conoventricular ventricular septal defect and pulmonary overcirculation who presented with COVID-19-associated pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/33040743/ doi: 10.1017/s1047951120003303 id: cord-336535-r3a57m57 author: Kohmer, Niko title: Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays date: 2020-06-01 words: 1479.0 sentences: 91.0 pages: flesch: 52.0 cache: ./cache/cord-336535-r3a57m57.txt txt: ./txt/cord-336535-r3a57m57.txt summary: So far, there is limited data on how recently commercially available, high-throughput immunoassays, using different recombinant SARS-CoV-2 antigens, perform with clinical samples. Five follow-up samples of three individuals were only detected in either an S and/or N protein-based assay, indicating an individual different immune response to SARS-CoV-2 and the influence of the used assay in the detection of IgG antibodies. This study aims to provide a quick overview on some of these assays (two commercially available ELISA assays, four automated immunoassays and a plaque reduction neutralization test (PRNT)) focusing on the detection and neutralization capacity of IgG antibodies in follow up serum or plasma samples of individuals with PCR-diagnosed infections with SARS-CoV-2. The commercially available assays examined in our study, generated consistent results regarding the detection of SARS-CoV-2-IgG antibodies. Interestingly, in samples of three individuals with mild clinical course of COVID-19, examined in our study (1, 2, 3 in The automated immunoassays demonstrated a higher overall sensitivity than the ELISA based assays. abstract: Serological SARS-CoV-2 assays are urgently needed for diagnosis, contact tracing and for epidemiological studies. So far, there is limited data on how recently commercially available, high-throughput immunoassays, using different recombinant SARS-CoV-2 antigens, perform with clinical samples. Focusing on IgG and total antibodies, we demonstrate the performance of four automated immunoassays (Abbott Architect™ i2000 (N protein-based)), Roche cobas™ e 411 analyzer (N protein-based, not differentiating between IgA, IgM or IgG antibodies), LIAISON®XL platform (S1 and S2 protein-based), VIRCLIA® automation system (S1 and N protein-based) in comparison two ELISA assays (Euroimmun SARS-CoV-2 IgG (S1 protein-based) and Virotech SARS-CoV-2 IgG ELISA (N protein-based)) and an in-house developed plaque reduction neutralization test (PRNT). We tested follow up serum/plasma samples of individuals PCR-diagnosed with COVID-19. When calculating the overall sensitivity, in a time frame of 49 days after first PCR-positivity, the PRNT as gold standard, showed the highest sensitivity with 93.3% followed by the dual-target assay for the VIRCLIA® automation system with 89%. The overall sensitivity in the group of N protein-based assays ranged from 66.7 to 77.8% and in the S protein-based-assays from 71.1 to 75.6%. Five follow-up samples of three individuals were only detected in either an S and/or N protein-based assay, indicating an individual different immune response to SARS-CoV-2 and the influence of the used assay in the detection of IgG antibodies. This should be further analysed. The specificity of the examined assays was ≥ 97%. However, because of the low or unknown prevalence of SARS-CoV-2, the examined assays in this study are currently primarily eligible for epidemiological investigations, as they have limited information in individual testing. url: https://www.ncbi.nlm.nih.gov/pubmed/32505777/ doi: 10.1016/j.jcv.2020.104480 id: cord-340291-bah2ege0 author: Kohmer, Niko title: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date: 2020-05-10 words: 1001.0 sentences: 63.0 pages: flesch: 55.0 cache: ./cache/cord-340291-bah2ege0.txt txt: ./txt/cord-340291-bah2ege0.txt summary: With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. With exception of one sample, all positive tested samples in the analysed cohort, using the 37 commercially available assays examined (including the in-house developed IFA), demonstrated 38 neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-39 there is an increasing demand in the detection of antibodies -especially of IgG antibodies. Currently there are many S 57 protein based commercially or in-house developed assays available, but there is limited data on how 58 these tests perform with clinical samples and if the detected IgG antibodies provide protective 59 abstract: As the current SARS-CoV-2 pandemic continues, serological assays are urgently needed for rapid diagnosis, contact tracing and for epidemiological studies. So far, there is little data on how commercially available tests perform with real patient samples and if detected IgG antibodies provide protective immunity. Focusing on IgG antibodies, we demonstrate the performance of two ELISA assays (Euroimmun SARS-CoV-2 IgG & Vircell COVID-19 ELISA IgG) in comparison to one lateral flow assay ((LFA) FaStep COVID-19 IgG/IgM Rapid Test Device) and two in-house developed assays (immunofluorescence assay (IFA) and plaque reduction neutralization test (PRNT)). We tested follow up serum/plasma samples of individuals PCR-diagnosed with COVID-19. Most of the SARS-CoV-2 samples were from individuals with moderate to severe clinical course, who required an in-patient hospital stay. For all examined assays, the sensitivity ranged from 58.8 to 76.5% for the early phase of infection (days 5-9) and from 93.8 to 100% for the later period (days 10-18) after PCR-diagnosed with COVID-19. With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. Regarding specificity, there was evidence that samples of endemic coronavirus (HCoV-OC43, HCoV-229E) and Epstein Barr virus (EBV) infected individuals cross-reacted in the ELISA assays and IFA, in one case generating a false positive result (may giving a false sense of security). This need to be further investigated. url: https://doi.org/10.1101/2020.05.08.085506 doi: 10.1101/2020.05.08.085506 id: cord-308021-cnf4xljc author: Kohns Vasconcelos, Malte title: SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date: 2020-10-13 words: 1981.0 sentences: 99.0 pages: flesch: 47.0 cache: ./cache/cord-308021-cnf4xljc.txt txt: ./txt/cord-308021-cnf4xljc.txt summary: Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Paediatric departments of 23 mostly tertiary care hospitals in 12 European countries (Belgium, Germany, France, Italy, Poland, Portugal, the UK, the Netherlands, Greece, Spain, Lithuania and Switzerland) participated in the surveys (response rate 29%). This changed by April at all three sites, so that afterwards detection of another pathogen that could explain the respiratory symptoms no longer excluded a patient from being a suspect case and from undergoing SARS-CoV-2 testing. In the early stages of the COVID-19 pandemic, paediatric emergency departments implemented standardised case definitions, testing guidelines and infection control measures rapidly. abstract: Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Patient testing criteria initially focused on suspect cases and later began to include screening, mainly for hospital admissions. Long turnaround times for test results likely put additional strain on healthcare resources. Conclusion: Shortening turnaround times for SARS-CoV-2 tests should be a priority. Specific paediatric testing criteria are needed. url: https://www.ncbi.nlm.nih.gov/pubmed/33051714/ doi: 10.1007/s00431-020-03843-w id: cord-288146-xqxznv1r author: Kohyama, Shunsuke title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date: 2009-09-11 words: 6140.0 sentences: 347.0 pages: flesch: 59.0 cache: ./cache/cord-288146-xqxznv1r.txt txt: ./txt/cord-288146-xqxznv1r.txt summary: title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a As shown in Fig. 2 , significant numbers of IFN-␥-producing CD8 + T cells (p < 0.01) were detected in mice immunized with syngeneic cells pulsed with each of nine pp1aderived peptides including pp1a-2187, -2207, -2340, -2546, -2755, -2990, -3444, -3687, and -3709 , suggesting that these nine peptides may be HLA-A*0201-restricted CTL epitopes derived from SARS-CoV pp1a protein. After HHD mice were immunized once with one of the nine liposomal peptides, spleen cells of them were prepared, stimulated with a relevant synthetic peptide, and stained for their expression of surface CD8 and intracellular IFN-␥. In summary, we have identified seven HLA-A*0201-restricted CTL epitopes derived from pp1a protein of SARS-CoV using computational algorithms, HLA-A*0201 transgenic mice and the surface-linked liposomal peptide. abstract: Spike and nucleocapsid are structural proteins of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) and major targets for cytotoxic T lymphocytes (CTLs). In contrast, non-structural proteins encoded by two-thirds of viral genome are poorly characterized for cell-mediated immunity. We previously demonstrated that nucleocapsid-derived peptides chemically coupled to the surface of liposomes effectively elicited SARS-CoV-specific CTLs in mice. Here, we attempted to identify HLA-A*0201-restricted CTL epitopes derived from a non-structural polyprotein 1a (pp1a) of SARS-CoV, and investigated whether liposomal peptides derived from pp1a were effective for CTL induction. Out of 30 peptides predicted on computational algorithms, nine peptides could significantly induce interferon gamma (IFN-γ)-producing CD8(+) T cells in mice. These peptides were coupled to the surface of liposomes, and inoculated into mice. Six liposomal peptides effectively induced IFN-γ-producing CD8(+) T cells and seven liposomal peptides including the six peptides primed CTLs showing in vivo killing activities. Further, CTLs induced by the seven liposomal peptides lysed an HLA-A*0201 positive cell line expressing naturally processed, pp1a-derived peptides. Of note, one of the liposomal peptides induced high numbers of long-lasting memory CTLs. These data suggest that surface-linked liposomal peptides derived from pp1a might offer an efficient CTL-based vaccine against SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/19748524/ doi: 10.1016/j.antiviral.2009.09.004 id: cord-026099-97luq10a author: Kok, J title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus date: 2020-06-05 words: 761.0 sentences: 42.0 pages: flesch: 54.0 cache: ./cache/cord-026099-97luq10a.txt txt: ./txt/cord-026099-97luq10a.txt summary: title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus We reported that the sensitivity, specificity, positive predictive value (PPV) and negative predictive value of the AusDiagnostics RUO assay was 100%, 92.16%, 55.56% and 100%, respectively when compared to our RT-PCR assay. Even if the specificity of the AusDiagnostics RUO assay was 99% (i.e. a 1% false positive rate), given the current prevalence of COVID-19 infection in NSW of 0.84%, the calculated PPV of the assay would be 54.15%, which is concordant with our findings. Cohen et al also estimated false positive rates of up to 7% in commercial diagnostics assays detecting SARS-CoV-2 [Cohen] . Furthermore, false positive RT-PCR results have also been reported from commercial kits that have been contaminated with SARS-CoV-2 sequences [Bustin] . Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273136/ doi: 10.1016/j.jcv.2020.104484 id: cord-256458-3fyul3k2 author: Kolikonda, Murali Krishnan title: Association of Coronavirus Disease 2019 and Stroke: A Rising Concern date: 2020-08-13 words: 1167.0 sentences: 87.0 pages: flesch: 43.0 cache: ./cache/cord-256458-3fyul3k2.txt txt: ./txt/cord-256458-3fyul3k2.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) causes the coronavirus disease 2019 (COVID-19). Several chemical, mechanical, and/or inflammatory central nervous system pathologies are proposed to explain how this viral infection might induce acute cerebrovascular disease. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus 2019 (COVID19) disease, which quickly became a pandemic [1] . Beyond knowing that bacteria and viruses can be risk factors for cerebrovascular ischemia, the impact of this novel coronavirus on emergency medical issues like acute ischemic stroke remains to be clarified [2] . Although the exact mechanism of SARS-CoV-2 causing cerebrovascular pathology is unclear, there might be a neuroinvasive potential that increases the incidence of stroke, thromboses, and related neuropsychiatric conditions [10] [11] [12] . While coronavirus precautions are being relaxed, acknowledging COVID-19 associations to cerebrovascular disease helps plan health care services and should improve clinical outcomes. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) causes the coronavirus disease 2019 (COVID-19). It quickly became pandemic, and so did a new concern about COVID-19 infections increasing the risk for cerebrovascular diseases. There is an association between COVID-19 illness in people and acute stroke. Several chemical, mechanical, and/or inflammatory central nervous system pathologies are proposed to explain how this viral infection might induce acute cerebrovascular disease. Timely available evaluation and/or intervention is imperative for patients with concerns about acute cerebrovascular issues. url: https://www.ncbi.nlm.nih.gov/pubmed/32791504/ doi: 10.1159/000510134 id: cord-296619-uhhndp0a author: Kondo, Yuki title: Coinfection with SARS-CoV-2 and influenza A virus date: 2020-07-01 words: 1689.0 sentences: 118.0 pages: flesch: 53.0 cache: ./cache/cord-296619-uhhndp0a.txt txt: ./txt/cord-296619-uhhndp0a.txt summary: We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We report a case of coinfection with SARS-CoV-2 and influenza A virus in a patient with pneumonia in Japan. The patient with both COVID-19 and influenza virus infection presented similar clinical characteristics with COVID-19 only. Initial considerations for this patient who presented acutely with fever and cough include infection with a common virus (rhinoviruses, non-SARS-CoV-2 coronaviruses and influenza virus) and communityacquired pneumonia. 3 The clinical characteristics of patients with both COVID-19 and influenza virus infection were similar to those of COVID-19 cases. ► There was no significant difference in rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with and without other pathogens. The clinical characteristics of pneumonia patients coinfected with 2019 novel coronavirus and influenza virus in Wuhan abstract: Since December 2019, coronavirus disease 2019 (COVID-19) has been an international public health emergency. The possibility of COVID-19 should be considered primarily in patients with new-onset fever or respiratory tract symptoms. However, these symptoms can occur with other viral respiratory illnesses. We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. During the epidemic, the possibility of COVID-19 should be considered regardless of positive findings for other pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/32611659/ doi: 10.1136/bcr-2020-236812 id: cord-300466-sk9iilum author: Kong, Wen-Hua title: Serologic Response to SARS-CoV-2 in COVID-19 Patients with Different Severity date: 2020-07-23 words: 2461.0 sentences: 135.0 pages: flesch: 52.0 cache: ./cache/cord-300466-sk9iilum.txt txt: ./txt/cord-300466-sk9iilum.txt summary: According to the Chinese Centers for Disease Prevention and Control (CDC) report, among 72,314 COVID-19 cases in China''s mainland most of cases (81%) presented only mild illness or moderate pneumonia, yet 14% developed severe symptoms such as dyspnea, high respiratory frequency and low blood oxygen saturation, and another 5% were in critical conditions like respiratory failure, septic shock, and multiple organ dysfunction/failure (Epidemiology Working Group for NCIP Epidemic Response and Chinese CDC, 2020; Wu and McGoogan 2020) . In this study, we, compared the results of serologic tests and nucleic acid test (NAT) from a group of COVID-19 patients in Wuhan, and analyzed the serologic IgM and IgG antibody level of patients with different disease severity. In summary, this study supported the combination of serologic testing and NAT in routine COVID-19 diagnosis and provided evidence on the temporal profile of antibody response against SARS-CoV-2 in patients with different disease severity. abstract: The immense patient number caused by coronavirus disease 2019 (COVID-19) global pandemic brings the urge for more knowledge about its immunological features, including the profile of basic immune parameters. In this study, eighty-eight reported COVID-19 patients in Wuhan were recruited from January to February, 2020, including 32 severe/critical cases and 56 mild/moderate cases. Their mean age was 56.43 years (range 17–83) and gender ratio (male/female) was 43:45. We tested SARS-CoV-2 RNA with commercial kits, investigated the level of serologic IgM and IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using magnetic particle chemiluminescence immunoassays, and compared the results of serologic tests and nucleic acid test (NAT). Among 88 patients, 95.45% were confirmed as positive by the combination of NAT and antibody test, which was significantly higher (P < 0.001) than by single nucleic acid test (73.86%) or serologic test (65.91%). Then the correlation between temporal profile and the level of antibody response was analyzed. It showed that seroconversion started on day 5 after disease onset and IgG level was rose earlier than IgM. Comparison between patients with different disease severity suggested early seroconversion and high antibody titer were linked with less severe clinical symptoms. These results supported the combination of serologic testing and NAT in routine COVID-19 diagnosis and provided evidence on the temporal profile of antibody response in patients with different disease severity. url: https://www.ncbi.nlm.nih.gov/pubmed/32705575/ doi: 10.1007/s12250-020-00270-x id: cord-305093-og4k3fc7 author: Konno, Yoriyuki title: SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant date: 2020-09-04 words: 3192.0 sentences: 210.0 pages: flesch: 62.0 cache: ./cache/cord-305093-og4k3fc7.txt txt: ./txt/cord-305093-og4k3fc7.txt summary: Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Although 177 three additional ORF3b proteins of SARS-CoV-related viruses from bats (HKU3-2, 178 GX2013 and Yunnan2011) were shorter than 39 amino acids in length, they did not 179 exhibit anti-IFN-I activity, most likely because of their poor expression and/or 180 stability (Figures 2C and S2B) . mean values of three independent experiments with SEM are shown, 648 and statistically significant differences (P < 0.05) compared to the SeV-infected 649 empty vector-transfected cells (#) and the same amount of the SARS The mean values of three independent 753 experiments with SEM are shown, and statistically significant differences (P < 0.05) 754 compared to the SeV-infected empty vector-transfected cells (#) and the same 755 amount of the SARS-CoV-2 ORF3b WT abstract: One of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in its ORF3b gene. Here, we show that SARS-CoV-2 ORF3b is a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Furthermore, analyses of approximately 17,000 SARS-CoV-2 sequences identify a natural variant, in which a longer ORF3b reading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients, but also describe the emergence of natural SARS-CoV-2 quasispecies with an extended ORF3b gene that may potentially affect COVID-19 pathogenesis. url: https://api.elsevier.com/content/article/pii/S2211124720311748 doi: 10.1016/j.celrep.2020.108185 id: cord-316667-b1xabkzk author: Konopka, Kristine E. title: Diffuse Alveolar Damage (DAD) from Coronavirus Disease 2019 Infection is Morphologically Indistinguishable from Other Causes of DAD date: 2020-06-15 words: 2694.0 sentences: 157.0 pages: flesch: 45.0 cache: ./cache/cord-316667-b1xabkzk.txt txt: ./txt/cord-316667-b1xabkzk.txt summary: Additionally, to better understand if COVID-19 represents a histologic variant of DAD we systematically compare the pathologic findings of SARS-CoV-2-positive patients to uninfected controls. 11 Our autopsy databases were then searched from January 1, 2016 through December 31, 2019 for inpatient and nonhospitalized community cases diagnosed as "diffuse alveolar damage." Since these deaths occurred prior to the first reported case of COVID-19 in the United States, 12 they are considered SARS-CoV-2negative (further referred to as "control cohort"). To our knowledge, this is the first comparison of autopsy lung findings in SARS-CoV-2-positive medically managed inpatients and untreated, non-hospitalized decedents to uninfected historical control cases of DAD. Nonetheless, we think our SARS-CoV-2 positive cases are likely representative of the broader COVID-19 patient population, since both hospitalized and non-hospitalized decedents had underlying conditions previously identified as risk factors for severe disease, including diabetes, chronic lung disease, cardiovascular disease, 13 and obesity. abstract: AIMS: Diffuse alveolar damage (DAD) is a ubiquitous finding in inpatient coronavirus disease 2019 (COVID‐19)‐related deaths, but recent reports also describe additional atypical findings, including vascular changes. Here, we assess lung autopsy findings in COVID‐19 inpatients and untreated, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)‐positive individuals who died in the community to understand the relative impact of medical intervention on lung histology. Additionally, we investigate if COVID‐19 represents a unique histologic variant of DAD by comparing the pathologic findings to uninfected control patients. METHODS AND RESULTS: Lung sections from autopsy cases were reviewed by three pulmonary pathologists, including two who were blinded to patient cohort. The cohorts included 4 COVID‐19 inpatients, 4 cases with post‐mortem SARS‐CoV‐2 diagnoses who died in the community, and 8 SARS‐CoV‐2‐negative control cases. DAD was present in all but one SARS‐CoV‐2‐positive patient who was asymptomatic and died in the community. Although SARS‐CoV‐2‐positive patients were noted to have more focal perivascular inflammation/endothelialitis than control patients, there were no significant differences in the presence of hyaline membranes, fibrin thrombi, airspace organization, and “acute fibrinous and organizing pneumonia”‐like intraalveolar fibrin deposition between the cohorts. Fibrinoid vessel wall necrosis, hemorrhage, and capillaritis were not features of COVID‐19‐related DAD. CONCLUSIONS: DAD is the primary histologic manifestation of severe lung disease in COVID‐19 patients who die both in the hospital and in the community, suggesting no contribution of hyperoxemic mechanical ventilation to the histologic changes. There are no distinctive morphologic features to confidently differentiate COVID‐19‐related DAD from DAD due to other causes. url: https://doi.org/10.1111/his.14180 doi: 10.1111/his.14180 id: cord-349745-zlhu1jit author: Konrad, Regina title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 words: 2417.0 sentences: 137.0 pages: flesch: 55.0 cache: ./cache/cord-349745-zlhu1jit.txt txt: ./txt/cord-349745-zlhu1jit.txt summary: The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2 ), which complicated the evaluation of the qPCR result. The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. abstract: The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We describe our laboratory experiences during a large contact tracing investigation, comparing previously published real-time RT-PCR assays in different PCR systems and a commercial kit. We found that assay performance using the same primers and probes with different PCR systems varied and the commercial kit performed well. url: https://www.ncbi.nlm.nih.gov/pubmed/32156330/ doi: 10.2807/1560-7917.es.2020.25.9.2000173 id: cord-345101-h0i5o0do author: Koo, Bon-Sang title: Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date: 2020-08-03 words: 1808.0 sentences: 123.0 pages: flesch: 55.0 cache: ./cache/cord-345101-h0i5o0do.txt txt: ./txt/cord-345101-h0i5o0do.txt summary: Using a reliable primate model is critical for developing therapeutic advances to treat humans infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The absence of a reliable preclinical animal model that recapitulates patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection poses a major limitation to the development of improved diagnostics and therapeutics. Studies reported that SARS-CoV-2 developed no severe clinical signs, but pulmonary pneumonia in 50% of cynomolgus macaques, recapitulating mild symptoms in humans [6] . The viral RNA was highest in the upper respiratory swab samples and lung tissues at the earliest phase of infection, and the viral antigen was present in the lungs ( Figure 1C and D) , suggesting the predominant site of the virus. Using a high viral titre administered through combined routes, virus assays, and histopathological changes suggests that both cynomolgus and rhesus macaques are permissive to infection of SARS-CoV-2 and recapitulate COVID-19-like disease in human. abstract: Using a reliable primate model is critical for developing therapeutic advances to treat humans infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here, we exposed macaques to high titres of SARS-CoV-2 via combined transmission routes. We observed acute interstitial pneumonia with endotheliitis in the lungs of all infected macaques. All macaques had a significant loss of total lymphocytes during infection, which were restored over time. These data show that SARS-CoV-2 causes a coronavirus disease 2019 (COVID-19)-like disease in macaques. This new model could investigate the interaction between SARS-CoV-2 and the immune system to test therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32745172/ doi: 10.1093/infdis/jiaa486 id: cord-267770-ik1ib3zb author: Koo, Hyun Jung title: RadioGraphics Update: Radiographic and CT Features of Viral Pneumonia date: 2020-06-05 words: 2754.0 sentences: 145.0 pages: flesch: 46.0 cache: ./cache/cord-267770-ik1ib3zb.txt txt: ./txt/cord-267770-ik1ib3zb.txt summary: In this updated review, we expand on the information presented in our 2018 article (4) and focus on the clinical features and chest CT findings of SARS-CoV-2 pneumonia to help radiologists detect the disease at its early stage. A reverse transcription-polymerase chain reaction (RT-PCR) test of an upper respiratory tract specimen (obtained with nasopharyngeal swab and/or oropharyngeal swab) and/or sputum sample is the standard diagnostic tool for determining hospitalization and isolation of patients with SARS-CoV infection. After 13 days of conservative management, her respiratory symptoms ameliorated, and a negative RT-PCR test result for SARS-CoV-2 was obtained. On the basis of this suggestion and experience managing patients with COVID-19, we provide a brief clinical setting to show the use of chest CT to facilitate the diagnosis of SARS-CoV-2 pneumonia (Fig 5) . For the management of patients with respiratory symptoms in endemic areas, an RT-PCR test is the primary diagnostic tool used for discriminating SARS-CoV-2-positive cases. abstract: Editor’s Note.—Articles in the RadioGraphics Update section provide current knowledge to supplement or update information found in full-length articles previously published in RadioGraphics. Authors of the previously published article provide a brief synopsis that emphasizes important new information such as technological advances, revised imaging protocols, new clinical guidelines involving imaging, or updated classification schemes. Articles in this section are published solely online and are linked to the original article. url: https://www.ncbi.nlm.nih.gov/pubmed/32501740/ doi: 10.1148/rg.2020200097 id: cord-253238-ptmxkpae author: Kopel, Jonathan title: Clinical Insights into the Gastrointestinal Manifestations of COVID-19 date: 2020-05-23 words: 4148.0 sentences: 208.0 pages: flesch: 45.0 cache: ./cache/cord-253238-ptmxkpae.txt txt: ./txt/cord-253238-ptmxkpae.txt summary: Furthermore, testing stool after a patient has been infected with COVID-19 may be necessary to monitor any GI complications, and the potential for fecal-oral transmission after respiratory symptoms has resolved. Despite the limited information on COVID-19 and its GI symptoms, information from SARS-CoV and MERS-CoV provides some insights on the symptoms and disease severity from other CoVs. The MERS-CoV has shown to infect human primary intestinal epithelial cells, small intestine It is also found to transmit via the fecal-oral route [35] . Physicians should monitor for GI symptoms in COVID-19-infected patients and examine whether the virus continues to remain in their stools after their respiratory symptoms have resolved. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus abstract: The month of December 2019 became a critical part of the time of humanity when the first case of coronavirus disease 2019 (COVID-19) was reported in the Wuhan, Hubei Province in China. As of April 13th, 2020, there have been approximately 1.9 million cases and 199,000 deaths across the world, which were associated with COVID-19. The COVID-19 is the seventh coronavirus to be identified to infect humans. In the past, Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome were the two coronaviruses that infected humans with a high fatality, particularly among the elderly. Fatalities due to COVID-19 are higher in patients older than 50 years of age or those with multimorbid conditions. The COVID-19 is mainly transmitted through respiratory droplets, with the most common symptoms being high fever, cough, myalgia, atypical symptoms included sputum production, headache, hemoptysis and diarrhea. However, the incubation period can range from 2 to 14 days without any symptoms. It is particularly true with gastrointestinal (GI) symptoms in which patients can still shed the virus even after pulmonary symptoms have resolved. Given the high percentage of COVID-19 patients that present with GI symptoms (e.g., nausea and diarrhea), screening patients for GI symptoms remain essential. Recently, cases of fecal–oral transmission of COVID-19 have been confirmed in the USA and China, indicating that the virus can replicate in both the respiratory and digestive tract. Moreover, the epidemiology, clinical characteristics, diagnostic procedures, treatments and prevention of the gastrointestinal manifestations of COVID-19 remain to be elucidated. url: https://doi.org/10.1007/s10620-020-06362-8 doi: 10.1007/s10620-020-06362-8 id: cord-352577-h3652seb author: Kopić, Jasminka title: Expanding the Use of Noninvasive Ventilation During an Epidemic date: 2014-08-27 words: 3340.0 sentences: 183.0 pages: flesch: 39.0 cache: ./cache/cord-352577-h3652seb.txt txt: ./txt/cord-352577-h3652seb.txt summary: 4 When appropriately indicated and promptly administered, NIV offers an alternative to tracheal intubation, sedation, risk of infection, and myriad complications associated with invasive ventilation, and it can promote rapid respiratory recovery, and reduce a patient''s dependence on critical care facilities. Rello et al described NIV use at ICU admission in 1 of 3 patients with H1N1 virus and respiratory failure, but 75% of them had an unfavorable clinical course and required tracheal intubation and invasive mechanical ventilation. In a position statement, the Australian Society for Infectious Diseases recommends "reserving negative-pressure ventilation rooms (if available) for intensive care patients, especially those receiving non-invasive ventilation." 31 The UK Department of Health, in "Guidance for infection control in critical care for pandemic influenza," approved the use of NIV under strict infection control measures. abstract: Noninvasive ventilation (NIV) is a proved and effective therapeutic option for some patients with respiratory failure. During an epidemic, NIV can free up respirators and other intensive care unit equipment for patients with respiratory insufficiency whose survival depends exclusively on invasive ventilation. Some guidelines have indicated that NIV is potentially hazardous and should not be recommended for use during epidemics, given the perceived potential risk of transmission from aerosolized pathogen dispersion to other patients or medical staff. Conversely, some reports of previous epidemics describe NIV as a very efficient and safe modality of respiratory support, if strict infection control measures are implemented. We discuss NIV use during epidemics and indicate the need for prospective randomized clinical studies on the efficacy of NIV in epidemic conditions to provide important information to the current body of literature. Meanwhile, the use of NIV under strict infection control guidelines should be incorporated into epidemic preparedness planning. (Disaster Med Public Health Preparedness. 2014;8:1-5) url: https://doi.org/10.1017/dmp.2014.71 doi: 10.1017/dmp.2014.71 id: cord-277486-12uah5qi author: Kopp, Kristen title: Interdisciplinary Model for Scheduling Post-discharge Cardiopulmonary Care of Patients Following Severe and Critical SARS-CoV-2 (Coronavirus) Infection date: 2020-08-14 words: 3178.0 sentences: 146.0 pages: flesch: 32.0 cache: ./cache/cord-277486-12uah5qi.txt txt: ./txt/cord-277486-12uah5qi.txt summary: As Covid-19 can severely implicate the respiratory and cardiovascular systems, potential pulmonary, and/or cardiovascular sequelae may be anticipated in patients following severe and critical SARS-CoV-2 infection meriting coordinated post-discharge management to identify residual effects and to mitigate potential worsening of pre-existing conditions. The WHO report Interim Guidance: Clinical Management of Covid 19, released 27 May 2020 however anticipates potential sequelae in patients with severe and critical SARS-CoV-2 infection following treatment with mechanical ventilation, sedation, and/or prolonged bed rest based on evidence from general critical care populations. A coordinated post-discharge care concept for patients surviving Covid-19 is therefore warranted to identify any cardiopulmonary sequelae and to mitigate possible worsening of preexisting disease following severe and critical SARS-Cov-2 infection. Short, intermediate and long-term effects following severe and critical SARS-CoV-2 infection are unknown, and significant sequelae may be expected, especially in patient populations experiencing ARDS, sepsis, and/or multiple organ dysfunction, as well as patients with exacerbation or progression of preexisting pulmonary or cardiovascular disease. abstract: nan url: https://doi.org/10.3389/fcvm.2020.00157 doi: 10.3389/fcvm.2020.00157 id: cord-311535-ppkwd1kp author: Korakas, Emmanouil title: Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes date: 2020-07-01 words: 2778.0 sentences: 124.0 pages: flesch: 36.0 cache: ./cache/cord-311535-ppkwd1kp.txt txt: ./txt/cord-311535-ppkwd1kp.txt summary: The production of increased amounts of cytokines such as TNFα, IL-1, IL-6, and monocyte chemoattractant protein (MCP-1) lead to oxidative stress and defective function of innate and adaptive immunity, whereas the activation of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome seems to play a crucial role in the pathogenesis of the infection. Endothelial dysfunction and arterial stiffness could favor the recently discovered infection of the endothelium by SARS-CoV-2, whereas alterations in cardiac structure and function and the prothrombotic microenvironment in obesity could provide a link for the increased cardiovascular events in these patients. Chronic inflammation and oxidative stress, hypercytokinemia, immune dysregulation, endothelial dysfunction, and cardiovascular abnormalities are all possible mechanisms through which the excess in adipose tissue could lead to the acute hyperinflammatory state that characterizes severe SARS-CoV-2 infections and is responsible for its complications. abstract: Recent reports have shown a strong association between obesity and the severity of COVID-19 infection, even in the absence of other comorbidities. After infecting the host cells, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may cause a hyperinflammatory reaction through the excessive release of cytokines, a condition known as “cytokine storm,” while inducing lymphopenia and a disrupted immune response. Obesity is associated with chronic low-grade inflammation and immune dysregulation, but the exact mechanisms through which it exacerbates COVID-19 infection are not fully clarified. The production of increased amounts of cytokines such as TNFα, IL-1, IL-6, and monocyte chemoattractant protein (MCP-1) lead to oxidative stress and defective function of innate and adaptive immunity, whereas the activation of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome seems to play a crucial role in the pathogenesis of the infection. Endothelial dysfunction and arterial stiffness could favor the recently discovered infection of the endothelium by SARS-CoV-2, whereas alterations in cardiac structure and function and the prothrombotic microenvironment in obesity could provide a link for the increased cardiovascular events in these patients. The successful use of anti-inflammatory agents such as IL-1 and IL-6 blockers in similar hyperinflammatory settings, like that of rheumatoid arthritis, has triggered the discussion of whether such agents could be administrated in selected patients with COVID-19 disease. url: https://doi.org/10.1152/ajpendo.00198.2020 doi: 10.1152/ajpendo.00198.2020 id: cord-280025-4hmecfi0 author: Korber, B title: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date: 2020-05-05 words: 11173.0 sentences: 524.0 pages: flesch: 54.0 cache: ./cache/cord-280025-4hmecfi0.txt txt: ./txt/cord-280025-4hmecfi0.txt summary: We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. Over the past two months, the HIV database team at Los Alamos National Laboratory has turned to developing an analysis pipeline to track in real time the evolution of the SARS-CoV-2 Spike (S) protein in the COVID-19 pandemic, using the Global Initiative for Sharing All Influenza Data GISAID SARS-CoV-2 sequence database as our baseline (Sup. Item 1 is the GISAID acknowledgments table, listing all the groups who contribute sequences to this global effort) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) . GISAID is the primary SARS-CoV-2 sequence database resource, and our intent is to complement what they provide with visualizations and summary data specifically intended to support the immunology and vaccine communities, and to alert the broader community to changes in frequency of mutations that might signal positive selection and a change in either viral phenotype or antigenicity. abstract: We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions. url: https://doi.org/10.1101/2020.04.29.069054 doi: 10.1101/2020.04.29.069054 id: cord-337896-mct29erg author: Kornbluth, Asher title: Management of Inflammatory Bowel Disease and COVID-19 in New York City 2020: The Epicenter of IBD in the First Epicenter of the Global Pandemic date: 2020-09-03 words: 5111.0 sentences: 212.0 pages: flesch: 55.0 cache: ./cache/cord-337896-mct29erg.txt txt: ./txt/cord-337896-mct29erg.txt summary: A number of the major GI societies, the Crohn''s & Colitis Foundation, 3 British Society of Gastroenterology, 4 European Crohn''s and Colitis Organization, 5 The American Gastroenterology Association, 6 and the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) 7 have published guidelines regarding treating the IBD patient with SARS-CoV-2 and COVID-19. 8 The key features are that the patient without proven or suspected SARS-CoV-2 should continue on their current medications with aggressive attempts to reduce steroid usage because this is the only single agent that has been associated with increased poor outcomes with COVID-19, defined in the SECURE registry as a composite score of hospitalization, intubation, or death. 14 We are now participating in the development of a database that will follow patients after clearance of the SARS-CoV-2 virus to determine the courses and outcomes of the IBD and of any sequelae or recurrence of COVID-19 after any drug therapy has been suspended. abstract: nan url: https://doi.org/10.1093/ibd/izaa212 doi: 10.1093/ibd/izaa212 id: cord-323905-ayufx3wv author: Kort, N. P. title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members date: 2020-08-18 words: 3708.0 sentences: 225.0 pages: flesch: 53.0 cache: ./cache/cord-323905-ayufx3wv.txt txt: ./txt/cord-323905-ayufx3wv.txt summary: title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members The April 2020 SARS-CoV-2 survey completed by EHS and EKA members in Europe has confirmed the impact of SARS-CoV-2: this pandemic has resulted in a tremendous reduction in primary hip and knee arthroplasty procedures as shown in the survey. The benefits of hip and knee arthroplasty should be carefully weighed against the risks of viral transmission and infection, complications and mortality in the mostly elderly population requiring joint arthroplasty Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: pre-operative phase 1. Is there a need for -Modification or reorganization of hospital wards (patient density, bed density, medical and nursing stuff density, etc.)?417 (81) 70 (14) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase 1. abstract: PURPOSE: The COVID-19 pandemic has disrupted the health care system around the entire globe. A consensus is needed about resuming total hip and knee procedures. The European Hip Society (EHS) and the European Knee Association (EKA) formed a panel of experts that have produced a consensus statement on how the safe re-introduction of elective hip and knee arthroplasty should be undertaken. METHODS: A prospective online survey was done among members of EHS and EKA. The survey consisted of 27 questions. It includes basic information on demographics and details the participant’s agreement with each recommendation. The participant could choose among three options (agree, disagree, abstain). Recommendations focussed on pre-operative, peri-operative, and post-operative handling of patients and precautions. RESULTS: A total of 681 arthroplasty surgeons participated in the survey, with 479 fully completing the survey. The participants were from 44 countries and 6 continents. Apart from adhering to National and Local Guidelines, the recommendations concerned how to make elective arthroplasty safe for patients and staff. CONCLUSION: The survey has shown good-to-excellent agreement of the participants with regards to the statements made in the recommendations for the safe return to elective arthroplasty following the first wave of the COVID-19 pandemic. url: https://doi.org/10.1007/s00167-020-06212-0 doi: 10.1007/s00167-020-06212-0 id: cord-280544-1rhu478r author: Korte, Wolfgang title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on date: 2020-08-25 words: 822.0 sentences: 50.0 pages: flesch: 55.0 cache: ./cache/cord-280544-1rhu478r.txt txt: ./txt/cord-280544-1rhu478r.txt summary: title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on antibodies rapidly decline early on 1, 3 Wolfgang Korte*, 2,3 Marija Buljan, 2,3 Matthias Rösslein, 2,3 Peter Wick, 1 Valentina Golubov, 1 Jana Jentsch, 1 Michael Reut, 3, 4 Karen Peier, 3 Brigitte Nohynek, 3 Aldo Fischer, 3 Raphael Stolz, 3 This cohort study included patients with a history of a positive SARS-CoV-2 PCR test. Results of the antibody course in 159 participants (52·2% females, 47·8% males), effectively spanning the time frame of two to ten weeks after a positive SARS-CoV-2 PCR test, are provided. The decline is statistically significant for anti-SP and anti-NC IgG at weeks 8-10 ( Figure 1) ; this is remarkable, as a continued IgG response for more than 34 weeks was seen with the SARS-CoV(-1) outbreak 6 . Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32853597/ doi: 10.1016/j.jinf.2020.08.032 id: cord-289599-7vsynfgn author: Kostoff, Ronald N. title: COVID-19 vaccine safety date: 2020-09-18 words: 2715.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-289599-7vsynfgn.txt txt: ./txt/cord-289599-7vsynfgn.txt summary: The present article examines whether short-term, mid-term, and long-term vaccine safety can be achieved under such an accelerated schedule, given the myriad vaccine-induced mechanisms that have demonstrated adverse effects based on previous clinical trials and laboratory research. It is uncertain as to whether any of the drugs, vaccines, foods or radiation exposures of our predecessors, which were not tested for transgenerational effects, are adversely affecting human life at present. Of note, the question remains whether humanity is currently willing to pass on potential devastating diseases to future generations due to the present need for the speedy development of a vaccine, bypassing adequate long-term and transgenerational safety testing. The vaccine costs in this discussion are the potential adverse health effects from a cOVId-19 vaccine, particularly for the mid-and long-term. This least vulnerable demographic population would have to bear the brunt of any potential mid-and long-term adverse health impacts that may result from a vaccine inadequately tested for these effects. abstract: In response to the SARS-CoV-2 outbreak, and the resulting COVID-19 pandemic, a global competition to develop an anti-COVID-19 vaccine has ensued. The targeted time frame for initial vaccine deployment is late 2020. The present article examines whether short-term, mid-term, and long-term vaccine safety can be achieved under such an accelerated schedule, given the myriad vaccine-induced mechanisms that have demonstrated adverse effects based on previous clinical trials and laboratory research. It presents scientific evidence of potential pitfalls associated with eliminating critical phase II and III clinical trials, and concludes that there is no substitute currently available for long-term human clinical trials to ensure long-term human safety. url: https://www.ncbi.nlm.nih.gov/pubmed/33000193/ doi: 10.3892/ijmm.2020.4733 id: cord-311332-n8tvglif author: Kostoff, Ronald N. title: Literature-related discovery: Potential treatments and preventatives for SARS() date: 2011-04-20 words: 7191.0 sentences: 380.0 pages: flesch: 46.0 cache: ./cache/cord-311332-n8tvglif.txt txt: ./txt/cord-311332-n8tvglif.txt summary: The present paper presents a comprehensive approach to systematic acceleration of potential discovery and innovation, and demonstrates the generation of large amounts of potential discovery for prevention/treatment of an infectious disease: severe acute respiratory syndrome (SARS). Approximately four times as many records were retrieved from Medline when MeSH terms were included in the query compared to using only terms in the title or Abstract, due to the greater choice of potential discovery substances. To retrieve the directly related literature from which potential discovery would be extracted, this higher level functional query was applied to the search engines of three databases: SCI, Medline, and SD. This proximity form of the query (as contrasted to the Boolean form used in prior LRD studies) provided highly ''relevant'' retrievals, where ''relevant'' is defined as any article that contains a potential discovery or innovation candidate. abstract: Literature-related discovery (LRD) is the linking of two or more previously disjoint concepts in order to produce novel, interesting, plausible, and intelligible connections (i.e., potential discovery). LRD has been used to identify potential treatments or preventative actions for challenging medical problems, among myriad other applications. Severe acute respiratory syndrome (SARS) was the first pandemic of the 21st century. SARS was eventually controlled through increased hygienic measures (e.g., face mask protection, frequent hand washing, living quarter disinfection), travel restrictions, and quarantine. According to recent reviews of SARS, none of the drugs that were used during the pandemic worked. For the present paper, SARS was selected as the first application of LRD to an infectious disease. The main goal of this research was to identify non-drug non-surgical treatments that would 1) prevent the occurrence, or 2) reduce the progression rate, or 3) stop/reverse the progression of SARS. The MeSH taxonomy of Medline was used to restrict potential discoveries to selected semantic classes, and to identify potential discoveries efficiently. To enhance the volume of potential discovery, databases were used in addition to Medline. These included the Science Citation Index (SCI) and, in contrast to previous work, a full text database. Because of the richness of the full text, ‘surgical’ queries were developed that targeted the exact types of potential discovery of interest while eliminating clutter more efficiently. url: https://www.ncbi.nlm.nih.gov/pubmed/32287410/ doi: 10.1016/j.techfore.2011.03.022 id: cord-265022-p5cab562 author: Kotfis, Katarzyna title: COVID-19: ICU delirium management during SARS-CoV-2 pandemic date: 2020-04-28 words: 5426.0 sentences: 256.0 pages: flesch: 34.0 cache: ./cache/cord-265022-p5cab562.txt txt: ./txt/cord-265022-p5cab562.txt summary: Indeed, patients with COVID-19 are at accelerated risk for delirium due to at least seven factors including (1) direct central nervous system (CNS) invasion, (2) induction of CNS inflammatory mediators, (3) secondary effect of other organ system failure, (4) effect of sedative strategies, (5) prolonged mechanical ventilation time, (6) immobilization, and (7) other needed but unfortunate environmental factors including social isolation and quarantine without family. Given early insights into the pathobiology of the virus, as well as the emerging interventions utilized to treat the critically ill patients, delirium prevention and management will prove exceedingly challenging, especially in the intensive care unit (ICU). Many hospitalized patients with COVID-19 will develop delirium, and given early insights into the pathobiology of this virus indicating invasion into the brain stem, as well as the emerging interventions utilized to treat these critically ill patients, delirium prevention and management may prove exceedingly challenging, especially in the intensive care unit (ICU). abstract: The novel coronavirus, SARS-CoV-2-causing Coronavirus Disease 19 (COVID-19), emerged as a public health threat in December 2019 and was declared a pandemic by the World Health Organization in March 2020. Delirium, a dangerous untoward prognostic development, serves as a barometer of systemic injury in critical illness. The early reports of 25% encephalopathy from China are likely a gross underestimation, which we know occurs whenever delirium is not monitored with a valid tool. Indeed, patients with COVID-19 are at accelerated risk for delirium due to at least seven factors including (1) direct central nervous system (CNS) invasion, (2) induction of CNS inflammatory mediators, (3) secondary effect of other organ system failure, (4) effect of sedative strategies, (5) prolonged mechanical ventilation time, (6) immobilization, and (7) other needed but unfortunate environmental factors including social isolation and quarantine without family. Given early insights into the pathobiology of the virus, as well as the emerging interventions utilized to treat the critically ill patients, delirium prevention and management will prove exceedingly challenging, especially in the intensive care unit (ICU). The main focus during the COVID-19 pandemic lies within organizational issues, i.e., lack of ventilators, shortage of personal protection equipment, resource allocation, prioritization of limited mechanical ventilation options, and end-of-life care. However, the standard of care for ICU patients, including delirium management, must remain the highest quality possible with an eye towards long-term survival and minimization of issues related to post-intensive care syndrome (PICS). This article discusses how ICU professionals (e.g., physicians, nurses, physiotherapists, pharmacologists) can use our knowledge and resources to limit the burden of delirium on patients by reducing modifiable risk factors despite the imposed heavy workload and difficult clinical challenges posed by the pandemic. url: https://doi.org/10.1186/s13054-020-02882-x doi: 10.1186/s13054-020-02882-x id: cord-341819-emjg3dsw author: Kouznetsova, Valentina L. title: Potential COVID-19 papain-like protease PL(pro) inhibitors: repurposing FDA-approved drugs date: 2020-09-18 words: 3312.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-341819-emjg3dsw.txt txt: ./txt/cord-341819-emjg3dsw.txt summary: Using the crystal structure of SARS-CoV-2 papain-like protease (PL(pro)) as a template, we developed a pharmacophore model of functional centers of the PL(pro) inhibitor-binding pocket. In a previous report, we (Kouznetsova, Huang & Tsigelny, 2020 ) and others (Kandeel & Al-Nazawi, 2020; Arya et al., 2020; Plewczynski et al., 2007; Ton et al., 2020) have used molecular modeling studies to identify FDA-approved drugs and other compounds (Arya et al., 2020; Ton et al., 2020; Alamri, Tahir ul Qamar & Alqahtani, 2020) that are predicted to bind to 3CL pro . Based on the crystal structure of SARS-CoV-2 PL pro (PDB ID: 6W9C), we developed two pharmacophore models of the binding pocket of this protein. We developed a pharmacophore model of the binding pocket site S3/S4 of COVID-19 PL pro then conducted multi-conformational docking of these drug compounds to this site for ranging the potential inhibitors selected by pharmacophore-based search. Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs abstract: Using the crystal structure of SARS-CoV-2 papain-like protease (PL(pro)) as a template, we developed a pharmacophore model of functional centers of the PL(pro) inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PL(pro). The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PL(pro). Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19 url: https://doi.org/10.7717/peerj.9965 doi: 10.7717/peerj.9965 id: cord-334277-g3go3u02 author: Kovac, Marc title: EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA) date: 2020-08-14 words: 4725.0 sentences: 237.0 pages: flesch: 53.0 cache: ./cache/cord-334277-g3go3u02.txt txt: ./txt/cord-334277-g3go3u02.txt summary: While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). It can thus be concluded that the anti-SARS-CoV-2 antibody results in whole blood corrected for hematocrit with weakly and moderately positive findings are comparable to those obtained from serum. abstract: While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. CLIAs and ELISAs can be automated to a high degree but commonly require larger serum or plasma volumes for sample processing. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). Simultaneously drawn venous serum and EDTA-anticoagulated whole blood samples from 223 individuals were included. Correction of the whole blood results for hematocrit led to a good agreement with the serum results for weakly to moderately positive antibody signals. In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). In conclusion, our results suggest that the investigated assays can reliably detect antibodies against SARS-CoV-2 in hemolyzed whole blood anticoagulated with EDTA. Correction of these results for hematocrit is suggested. This study demonstrates that the automated processing of whole blood for identification of SARS-CoV-2 antibodies with common ECLIA and ELISA methods is accurate and feasible. url: https://www.ncbi.nlm.nih.gov/pubmed/32823852/ doi: 10.3390/diagnostics10080593 id: cord-261111-g1qxo01i author: Kowalewski, Joel title: Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space date: 2020-08-06 words: 6029.0 sentences: 349.0 pages: flesch: 58.0 cache: ./cache/cord-261111-g1qxo01i.txt txt: ./txt/cord-261111-g1qxo01i.txt summary: There are subsequently unmet needs in COVID-19 research, including identification of compounds that target the relevant SARS-CoV-2 human proteins from (1) approved drugs, (2) FDA registered chemicals or (3) a large repository of~14 million purchasable chemicals from the ZINC 15 database [18] , which we computed additional properties for such as mammalian toxicity, vapor pressure, and logP. For 65 human protein targets that SARS-CoV-2 interacts with that had publicly available bioassay and chemical data [6] , we first generated a database of predictions based on structural similarity to chemicals that interact with the targets and then machine learning models (34) . Accordingly, we used the machine learning models to predict activities of 100,000 FDA registered chemicals (UNII database) [19] as well as the DrugBank [20] and Therapeutic Targets [21, 22] databases, which include information on drug interactions, pathways, and approval status. abstract: There is an urgent need for the identification of effective therapeutics for COVID-19 and we have developed a machine learning drug discovery pipeline to identify several drug candidates. First, we collect assay data for 65 target human proteins known to interact with the SARS-CoV-2 proteins, including the ACE2 receptor. Next, we train machine learning models to predict inhibitory activity and use them to screen FDA registered chemicals and approved drugs (∼100,000) and ∼14 million purchasable chemicals. We filter predictions according to estimated mammalian toxicity and vapor pressure. Prospective volatile candidates are proposed as novel inhaled therapeutics since the nasal cavity and respiratory tracts are early bottlenecks for infection. We also identify candidates that act across multiple targets as promising for future analyses. We anticipate that this theoretical study can accelerate testing of two categories of therapeutics: repurposed drugs suited for short-term approval, and novel efficacious drugs suitable for a long-term follow up. url: https://doi.org/10.1016/j.heliyon.2020.e04639 doi: 10.1016/j.heliyon.2020.e04639 id: cord-355577-w1yhtbz8 author: Kowalski, Luiz Paulo title: Effect of the COVID-19 Pandemic on the Activity of Physicians Working in the Areas of Head and Neck Surgery and Otorhinolaryngology date: 2020-05-22 words: 4750.0 sentences: 253.0 pages: flesch: 50.0 cache: ./cache/cord-355577-w1yhtbz8.txt txt: ./txt/cord-355577-w1yhtbz8.txt summary: Conclusion The study demonstrated a direct impact of the COVID-19 pandemic on the clinical practice of specialties related to the treatment of patients with diseases of the head and neck region already in the beginning of the illness management in Brazil. Specifically, we collected data regarding the impact of de COVID-19 pandemic on: 1) the amount and type of outpatient appointments, surgeries and exams with the risk of generating aerosols; 2) availability of adequate PPE in different settings and practices; 3) the preparedness of the responder''s health institution in orienting their HCPs and developing strategies to manage COVID-19 suspected and confirmed patients. Although the pandemic is already in its 7 th week in Brazil, since the identification of the 1 st case, 45.3% and 48.8% of physicians in the private and public sectors, respectively, reported that they had not received face-to-face or distance training in the management of confirmed or suspected patients with COVID-19. abstract: Introduction Coronavirus disease 2019 (COVID-19) is an acute infection caused by the new coronavirus (SARS-CoV-2) and it is highly transmissible, especially through respiratory droplets. To prepare the health system for the care of these patients also led to a restriction in the activity of several medical specialties. Physicians who work with patients affected by diseases of the head and neck region constitute one of the populations most vulnerable to COVID-19 and also most affected by the interruption of their professional activities. Objective The aim of the present study was to assess the impact of the COVID-19 pandemic on the practice of head and neck surgeons and otorhinolaryngologists in Brazil. Methods An anonymous online survey of voluntary participation was applied, containing 30 questions regarding demographic aspects, availability of personal protective equipment (PPE), and impact on the routine of head and neck surgeons and otorhinolaryngologists, as well as clinical oncologists and radiation oncologists who work with head and neck diseases. Results Seven hundred and twenty-nine answers were received in a period of 4 days, ∼ 40 days after the 1 (st) confirmed case in Brazil. With professionals working in public and private services, there was a high level of concerns with the disease and its consequences, limited availability of PPE and a significant decrease in the volume of specialized medical care. Conclusion The study demonstrated a direct impact of the COVID-19 pandemic on the clinical practice of specialties related to the treatment of patients with diseases of the head and neck region already in the beginning of the illness management in Brazil. url: https://www.ncbi.nlm.nih.gov/pubmed/32754234/ doi: 10.1055/s-0040-1712169 id: cord-321624-z2mntwef author: Kowitdamrong, Ekasit title: Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date: 2020-10-09 words: 3382.0 sentences: 184.0 pages: flesch: 57.0 cache: ./cache/cord-321624-z2mntwef.txt txt: ./txt/cord-321624-z2mntwef.txt summary: AIM: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19. The objective of this study was to investigate the response of IgA and IgG antibodies to SARS--CoV-2 in serial blood samples collected from a population of Thai patients with confirmed COVID-19, and the association of these responses with the severity of the illness. The second subgroup included 49 plasma samples collected from May 1 to May 31, 2020, from patients under investigation (PUI) for COVID-19 with RT-PCR results that were negative for SARS-CoV-2. In the present study, 30% of COVID-19 patients developed positive IgA antibodies very early, within 3 days after the onset of symptoms. In the present study, 20% of the patients with mild symptoms did not develop any IgG antibodies specific to COVID-19, even after 2 weeks after the onset of symptoms. abstract: BACKGROUND: A greater understanding of the antibody response to SARS-CoV-2 in an infected population is important for the development of a vaccination. AIM: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19. METHODS: Plasma from the following patient groups was examined: 118 adult patients with confirmed SARS-CoV-2 infections, 49 patients under investigation (without confirmed infections), 20 patients with other respiratory infections, and 102 healthy control patients. Anti-SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA) from EUROIMMUN was performed to assess for IgA and IgG antibodies. The optical density (OD) ratio cutoff for a positive result was 1.1 for IgA and 0.8 for IgG. Additionally, the association of the antibody response with both the severity of disease and the date after onset of symptoms was analyzed. RESULTS: A total of 289 participants were enrolled and 384 samples analyzed from March 10 to May 31, 2020. Patients were categorized, based on their clinical manifestations, as mild (n = 59), moderate (n = 27), or severe (n = 32). The overall sensitivity of IgA and IgG from the samples collected after day 7 of the symptoms was 87.9% (95% CI: 79.8–93.6) and 84.8% (95% CI: 76.2–91.3), respectively. Compared to the mild group, the severe group had significantly higher levels of spike 1 (S1) antigen-specific IgA and IgG. All patients in the moderate and severe groups had S1-specific IgG, while 20% of the patients in the mild group did not have any IgG detected after two weeks after the onset of symptoms. Interestingly, in the severe group, the SARS-CoV-2 IgG level was significantly higher in males than females (p = 0.003). CONCLUSION: The serological test for SARS-CoV-2 has a high sensitivity more than two weeks after the onset of illness. Additionally, the serological response differs among patients based on sex as well as the severity of infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33035234/ doi: 10.1371/journal.pone.0240502 id: cord-269234-8twdx4g2 author: Koyama, Takahiko title: Variant analysis of SARS-CoV-2 genomes date: 2020-07-01 words: 4025.0 sentences: 321.0 pages: flesch: 66.0 cache: ./cache/cord-269234-8twdx4g2.txt txt: ./txt/cord-269234-8twdx4g2.txt summary: OBJECTIVE: To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here we analysed the SARS-CoV-2 genome from 10 022 samples to understand the variability in the viral genome landscape and to identify emerging clades. Finally, we carefully Objective To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Given the evolving nature of the SARS-CoV-2 genome, drug and vaccine developers should continue to be vigilant for emergence of new variants or sub-strains of the virus. Variant analysis of SARS-CoV-2 genomes [data repository abstract: OBJECTIVE: To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). METHODS: Between 1 February and 1 May 2020, we downloaded 10 022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For clade analysis, we used the open source software Bayesian evolutionary analysis by sampling trees, version 2.5. FINDINGS: We identified 5775 distinct genome variants, including 2969 missense mutations, 1965 synonymous mutations, 484 mutations in the non-coding regions, 142 non-coding deletions, 100 in-frame deletions, 66 non-coding insertions, 36 stop-gained variants, 11 frameshift deletions and two in-frame insertions. The most common variants were the synonymous 3037C > T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. Regarding the base changes, the C > T mutation was the most common with 1670 distinct variants. CONCLUSION: We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population. url: https://www.ncbi.nlm.nih.gov/pubmed/32742035/ doi: 10.2471/blt.20.253591 id: cord-322807-b24ujorz author: Koyama, Takahiko title: Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment date: 2020-04-26 words: 1869.0 sentences: 95.0 pages: flesch: 50.0 cache: ./cache/cord-322807-b24ujorz.txt txt: ./txt/cord-322807-b24ujorz.txt summary: The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. Typically, surface proteins outside of the viral virion are selected for antigens so that antibodies generated from a vaccine-trained B-cell can bind to the virus for neutralization. This study''s objective is to interrogate currently identified sub-strains of SARS-CoV-2 and identify genetic drifts and potential immune recognition escape sites that would be integral for the development of a successful vaccine. In these countries, the majority of infected patients possess the variant; therefore, vaccine design and convalescent plasma antibody treatment might require further considerations to accommodate the drift. A spike glycoprotein peptide encompassing residues 604-625 derived from a convalescent SARS-CoV-1 patient was successfully able to elicit humoral immune response and prevent infection in non-human primates, underscoring the immunogenic importance of this region [10] . abstract: New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China. url: https://www.ncbi.nlm.nih.gov/pubmed/32357545/ doi: 10.3390/pathogens9050324 id: cord-345730-bxwsup70 author: Kočar, Eva title: Cholesterol, lipoproteins, and COVID-19: basic concepts and clinical applications date: 2020-11-04 words: 4028.0 sentences: 221.0 pages: flesch: 40.0 cache: ./cache/cord-345730-bxwsup70.txt txt: ./txt/cord-345730-bxwsup70.txt summary: In vitro depletion of membrane-bound cholesterol from Angiotensin-Converting Enzyme 2 (ACE2)-expressing cells led to a reduced infectivity of CoVs, since the binding of the spike protein was reduced by half [44] . By participating in cholesterol outflow from the cell membrane to HDL particles, PON1 contributes to lowering the cholesterol levels within lipid rafts, thus modulating viral infection (Fig. 1c) . Therefore, it is intriguing to contemplate whether NAFLD patients without treatment are more J o u r n a l P r e -p r o o f susceptible for SARS-CoV-2 infection, or whether statin application may directly affect the entry of SARS-CoV-2 into the host cell by regulating cholesterol cell levels. As lipid lowering drugs, statins might thus significantly reduce the attachment and internalization of SARS-CoV-2 by lowering membrane cholesterol levels (Fig. 1c ) [37] . abstract: This review provides an overview of lipids and lipid metabolism in relation to COVID-19, with special attention on cholesterol. Cholesterol enriched lipid rafts represent a platform for viruses to enter the host cell by endocytosis. Generally, higher membrane cholesterol coincides with higher efficiency of COVID-19 entry. Inversely, patients with COVID-19 show lowered levels of blood cholesterol, high-density and low-density lipoproteins. The modulated efficiency of viral entry can be explained by availability of SR-B1 and LDL-receptors. Especially HDL seems to have a variety of roles, from being itself a scavenger for viruses, an immune modulator and mediator of viral entry. Due to inverse roles of membrane cholesterol and lipoprotein cholesterol in COVID-19 infected patients, treatment of these patients with cholesterol lowering statins remains controversial. In conclusion, cholesterol and lipoproteins are potential markers for monitoring the viral infection status where mechanistic inconsistencies warrant immediate further research. url: https://www.ncbi.nlm.nih.gov/pubmed/33157278/ doi: 10.1016/j.bbalip.2020.158849 id: cord-340799-1awmtj52 author: Krajewska, Joanna title: Review of practical recommendations for otolaryngologists and head and neck surgeons during the COVID-19 pandemic: Recommendations for otolaryngologists during the COVID-19 pandemic date: 2020-06-06 words: 7941.0 sentences: 395.0 pages: flesch: 42.0 cache: ./cache/cord-340799-1awmtj52.txt txt: ./txt/cord-340799-1awmtj52.txt summary: Laryngectomy patients and individuals after tracheotomy with COVID-19 carry a particularly high risk of infecting ENT specialists and other members of medical staff as the way of breathing is these individuals is modified and enables the easy spread of SARS-CoV-2 containing aerosolized tracheal secretions [11] . In accordance with such high risk of infection, only emergency consultations and procedures should be performed by ENT specialists in times of COVID-19 pandemic in areas with confirmed SARS-CoV-2 cases [23, 28] . American Head and Neck Society, AAO-HNS, and the American Colleges of Surgeons, recommended that preoperative testing for SARS-CoV-2 presence should be performed in all individuals undergoing high-risk procedures [22, 30] . Patients with acute airway obstruction requiring tracheotomy should be considered as COVID-19 positive, as there is no time for SARS-CoV-2 testing in case of such urgent surgery [29] . abstract: INTRODUCTION: Otolaryngologists are at very high risk of COVID-19 infection while performing examination or surgery. Strict guidelines for these specialists have not already been provided, while currently available recommendations could presumably change in course of COVID-19 pandemic as the new data increases. OBJECTIVES: This study aimed to synthesize evidence concerning otolaryngology during COVID‐19 pandemic. It presents a review of currently existing guidelines and recommendations concerning otolaryngological procedures and surgeries during COVID-19 pandemic, and provides a collective summary of all crucial information for otolaryngologists. It summarizes data concerning COVID-19 transmission, diagnosis, and clinical presentation highlighting the information significant for otolaryngologists. METHODS: The Medline and Web of Science databases were searched without time limit using terms ‘‘COVID-19”, “SARS-CoV-2” in conjunction with “head and neck surgery”, “otorhinolaryngological manifestations”. RESULTS: Patients in stable condition should be consulted using telemedicine options. Only emergency consultations and procedures should be performed during COVID-19 pandemic. Mucosa-involving otolaryngologic procedures are considered high risk procedures and should be performed using enhanced PPE (N95 respirator and full face shield or powered air-purifying respirator, disposable gloves, surgical cap, gown, shoe covers). Urgent surgeries for which there is not enough time for SARS-CoV-2 screening are also considered high risk procedures. These operations should be performed in a negative pressure operating room with high-efficiency particulate air filtration. Less urgent cases should be tested for COVID-19 twice, 48 hours preoperatively in 24 hours’ interval. CONCLUSIONS: This review serves as a collection of current recommendations for otolaryngologists for how to deal with their patients during COVID-19 pandemic. url: https://doi.org/10.1016/j.anl.2020.05.022 doi: 10.1016/j.anl.2020.05.022 id: cord-296483-x95lwwnm author: Kranke, Peter title: Geburtshilfliche Anästhesie während der SARS-CoV-2-Pandemie: Übersicht der Handlungsempfehlungen date: 2020-04-09 words: 1995.0 sentences: 241.0 pages: flesch: 43.0 cache: ./cache/cord-296483-x95lwwnm.txt txt: ./txt/cord-296483-x95lwwnm.txt summary: Diese Annahmen stützten sich möglicherweise auf den Umstand, dass die Morbidität Schwangerer bei saisonaler Influenza höher ist als in einem Vergleichskollektiv [4 -6] und im beschriebenen Kollektiv zu einer gegenüber einem Vergleichskollektiv überproportionalen Frühgeburtlichkeit von 24-25 % führte [7] . In Bezug auf die vertikale Übertragung (Übertragung von der Mutter auf das Kind prä-oder intrapartal) zeigen nahezu alle publizierten Fallberichte aus China keine Hinweise für eine Übertragung auf den Fetus [9, 15 -17] . Einschränkend sollte berücksichtigt werden, dass es sich bislang nur um einen einzigen Fallbericht handelt und es im Rahmen der systemischen Inflammation möglicherweise zu einem erhöhten Transfer von Antikörpern kommen könnte. Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 (23.03.2020). abstract: The most common human corona viruses cause common colds. But three of these viruses cause more serious, acute diseases; Middle East Respiratory Syndrome (MERS by MERS-CoV), Severe Acute Respiratory Syndrome (SARS) by SARS-CoV and COVID-19 by SARS-CoV-2. The current outbreak was classified by the WHO as a “global public health emergency”. Despite all efforts to reduce the surgical lists and to cancel or postpone non-time-critical surgical interventions, some surgical and anesthetic interventions outside of intensive care medicine are still necessary and must be performed. This is particularly true for obstetric interventions and neuraxial labor analgesia. Workload in the delivery room is presumably not going to decrease and planned cesarean sections cannot be postponed. In the meantime, the clinical course and outcome of some COVID-19 patients with an existing pregnancy or peripartum courses have been reported. There are already numerous recommendations from national and international bodies regarding the care of such patients. Some of these recommendations will be summarized in this manuscript. The selection of aspects should by no means be seen as a form of prioritization. The general treatment principles in dealing with COVID-19 patients and the recommendations for action in intensive care therapy also apply to pregnant and postpartum patients. In this respect, there are naturally considerable redundancies and only a few aspects apply strictly or exclusively to the cohort of obstetric patients. In summary, at present it must be stated that the general care recommendations that also apply to non-COVID-19 patients are initially valid with regard to obstetric anesthesia. Nevertheless, the special requirements on the part of hygiene and infection protection result in special circumstances that should be taken into account when caring for pregnant patients from an anesthetic point of view. These relate to both medical aspects, but also to a particular extent logistics issues with regard to spatial separation, staffing and material resources. url: https://www.ncbi.nlm.nih.gov/pubmed/32274774/ doi: 10.1055/a-1144-5562 id: cord-330031-c1n994j6 author: Kratzel, Annika title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date: 2020-03-17 words: 752.0 sentences: 51.0 pages: flesch: 50.0 cache: ./cache/cord-330031-c1n994j6.txt txt: ./txt/cord-330031-c1n994j6.txt summary: title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. We therefore determined the virucidal activity of two 5 alcohol-based hand rub solutions for hand disinfection recommended by the World 6 Hand Hygiene in Health Care'' suggests two alcohol-based formulations for hand 9 sanitization to reduce pathogen infectivity and spreading. abstract: The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 is a major burden for health care systems worldwide. It is important to address if the current infection control instructions based on active ingredients are sufficient. We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. Efficient SARS-CoV-2 inactivation was demonstrated for all tested alcohol-based disinfectants. These findings show the successful inactivation of SARS-CoV-2 for the first time and provide confidence in its use for the control of COVID-19. Importance The current COVID-19 outbreak puts a huge burden on the world’s health care systems. Without effective therapeutics or vaccines being available, effective hygiene measure are of utmost importance to prevent viral spreading. It is therefore crucial to evaluate current infection control strategies against SARS-CoV-2. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission. url: https://doi.org/10.1101/2020.03.10.986711 doi: 10.1101/2020.03.10.986711 id: cord-333703-1ku3jc9s author: Kraus, Aurora title: A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date: 2020-11-08 words: 8452.0 sentences: 605.0 pages: flesch: 57.0 cache: ./cache/cord-333703-1ku3jc9s.txt txt: ./txt/cord-333703-1ku3jc9s.txt summary: Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. In mice and humans, ace2 expression is detected in 121 sustentacular cells, olfactory stem cells known as horizontal and globose basal cells in the 122 olfactory epithelium, and vascular cells (pericytes) in the olfactory bulb (Brann et al., 2020 The present study reports for the first time that zebrafish larvae exposed to SARS-CoV-2 appear 134 to mount innate immune responses that resemble cytokine responses of mild COVID-19 patients. There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 abstract: The COVID-19 pandemic has prompted the search for animal models that recapitulate the pathophysiology observed in humans infected with SARS-CoV-2 and allow rapid and high throughput testing of drugs and vaccines. Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. Intranasal administration of SARS-CoV-2 S RBD in adult zebrafish recombinant protein caused severe olfactory and mild renal histopathology. Zebrafish intranasally treated with SARS-CoV-2 S RBD became hyposmic within minutes and completely anosmic by 1 day to a broad-spectrum of odorants including bile acids and food. Single cell RNA-Seq of the adult zebrafish olfactory organ indicated widespread loss of expression of olfactory receptors as well as inflammatory responses in sustentacular, endothelial, and myeloid cell clusters. Exposure of wildtype zebrafish larvae to SARS-CoV-2 in water did not support active viral replication but caused a sustained inhibition of ace2 expression, triggered type 1 cytokine responses and inhibited type 2 cytokine responses. Combined, our results establish adult and larval zebrafish as useful models to investigate pathophysiological effects of SARS-CoV-2 and perform pre-clinical drug testing and validation in an inexpensive, high throughput vertebrate model. url: https://doi.org/10.1101/2020.11.06.368191 doi: 10.1101/2020.11.06.368191 id: cord-319930-ymqnb54a author: Kremer, Stéphane title: Brain MRI Findings in Severe COVID-19: A Retrospective Observational Study date: 2020-06-16 words: 3185.0 sentences: 188.0 pages: flesch: 40.0 cache: ./cache/cord-319930-ymqnb54a.txt txt: ./txt/cord-319930-ymqnb54a.txt summary: Eight distinctive neuroradiologic patterns (excluding ischemic infarcts) were identified in patients with severe COVID-19 infection with abnormal brain MRIs. In patients with COVID-19, the most frequent neuroimaging features were: involvement of the medial temporal lobe, non-confluent multifocal white matter hyperintense lesions on FLAIR with variable enhancement and hemorrhagic lesions, and extensive and isolated white matter microhemorrhages. Inclusion criteria were: (i) diagnosis of COVID-19 based on possible exposure history or symptoms clinically compatible, validated with a detection of SARS-CoV-2 by reverse transcriptase-polymerase chain reaction (RT-PCR) assays on the nasopharyngeal, throat or lower respiratory tract swabs; (ii) severe COVID-19 infection defined as requirement for hospitalization and oxygen therapy; (iii) neurologic manifestations; (iv) abnormal brain MRI with acute/subacute abnormalities. Among the eight groups of brain MRI features classification, three main neuroradiological patterns appeared more frequently in patient with severe COVID-19: signal abnormalities located in the medial temporal lobe, non-confluent multifocal WM hyperintense lesions on FLAIR and diffusion with variable enhancement, associated with hemorrhagic lesions, and extensive and isolated WM microhemorrhages. abstract: BACKGROUND: Brain MRI parenchymal signal abnormalities have been in association with SARS-CoV-2. PURPOSE: Describe the neuroimaging findings (excluding ischemic infarcts) in patients with severe COVID-19 infection. METHODS: This was a retrospective study of patients evaluated from March 23th, 2020 to April 27th, 2020 at 16 hospitals. Inclusion criteria were: (i) positive nasopharyngeal or lower respiratory tract reverse transcriptase-polymerase chain reaction assays; (ii) severe COVID infection defined as requirement for hospitalization and oxygen therapy; (iii) neurologic manifestations; (iv) abnormal brain MRI. Exclusion criteria were patients with missing or non-contributory data regarding brain MRI or a brain MRI showing ischemic infarcts, cerebral venous thrombosis, or chronic lesions unrelated to the current event. Categorical data were compared using Fisher exact test. Quantitative data were compared using Student’s t-test or Wilcoxon test. A p-value lower than 0.05 was considered significant. RESULTS: Thirty men (81%) and 7 women (19%) met inclusion criteria, with a mean age of 61+/- 12 years (range: 8-78). The most common neurologic manifestations were alteration of consciousness (27/37, 73%), pathological wakefulness when the sedation was stopped (15/37, 41%), confusion (12/37, 32%), and agitation (7/37, 19%). The most frequent MRI findings were: signal abnormalities located in the medial temporal lobe in 16/37 (43%, 95% CI 27-59%) patients, non-confluent multifocal white matter hyperintense lesions on FLAIR and diffusion sequences, with variable enhancement, with associated hemorrhagic lesions in 11/37 patients (30%, 95% CI 15-45%), and extensive and isolated white matter microhemorrhages in 9/37 patients (24%, 95% CI 10-38%). A majority of patients (20/37, 54%) had intracerebral hemorrhagic lesions with a more severe clinical presentation: higher admission rate in intensive care units, 20/20 patients, 100% versus 12/17 patients, 71%, p=0.01; development of the acute respiratory distress syndrome in 20/20 patients, 100% versus 11/17 patients, 65%, p=0.005. Only one patient was positive for SARS-CoV-2 RNA in the cerebrospinal fluid. CONCLUSION: Patients with severe COVID-19 and without ischemic infarcts had a wide range of neurologic manifestations that were be associated with abnormal brain MRIs. Eight distinctive neuroradiological patterns were described. url: https://www.ncbi.nlm.nih.gov/pubmed/32544034/ doi: 10.1148/radiol.2020202222 id: cord-015552-pm9kdqdw author: Kreuder-Sonnen, Christian title: China vs the WHO: a behavioural norm conflict in the SARS crisis date: 2019-05-01 words: 8263.0 sentences: 390.0 pages: flesch: 46.0 cache: ./cache/cord-015552-pm9kdqdw.txt txt: ./txt/cord-015552-pm9kdqdw.txt summary: On the one hand, the established norm of sovereignty, particularly the principle of non-interference, had structured a regime for dealing with infectious disease outbreaks that provided ground rules of conduct but ascribed decision-making authority to member states alone. 33 This sediment of the unfinished IHR revision process reveals the limited degree to which the emerging norm of global health security had been accepted prior to the SARS outbreak: the powers conferred upon the WHO to deal with infectious disease outbreaks remained extremely limited and-apart from the outbreak information issue-mostly subject to member-state agreement. 35 This section of the article analyses the actions of China and the WHO during the SARS crisis as representing a behavioural norm conflict over the relative priority of sovereignty and global health security. abstract: This article studies a conflict over two competing norms in which the actors demonstrated incompatible positions not through arguments, but through actions. During the SARS crisis, China and the World Health Organization (WHO) entered a norm conflict over the precedence of sovereignty or global health security. Both resorted to behavioural, not discursive contestation: while the WHO practically but not rhetorically challenged the sovereignty norm by acting according to the norm of global health security, China—without openly acknowledging it—contravened the basic principles of global health security by acting according to the overlapping sovereignty norm. Why and with what consequences do actors choose to contest norms through actions rather than words? The article accounts for the resort to behavioural contestation by pointing to the strategic advantages it offers for furthering a contentious norm understanding without facing the social costs of making it explicit. It furthermore highlights that behavioural contestation may feed back into and change the odds of discursive contestation as its practical effects provide rhetorical resources to (de-)legitimate one or the other position. The propositions are illustrated in the interactions of China and the WHO during the SARS crisis and the subsequent norm development. This article forms part of the special section of the May 2019 issue of International Affairs on ‘The dynamics of dissent’, guest-edited by Anette Stimmer and Lea Wisken. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108605/ doi: 10.1093/ia/iiz022 id: cord-103576-g5de4fwj author: Kriegel, M. title: Predicted Infection Risk via Aerosols date: 2020-10-12 words: 4012.0 sentences: 284.0 pages: flesch: 62.0 cache: ./cache/cord-103576-g5de4fwj.txt txt: ./txt/cord-103576-g5de4fwj.txt summary: 34 In order to perform an infection risk assessment for the airborne transmission in the far field 35 and to introduce appropriate preventive measures, it would be necessary to know the amount The so-called aerosols (liquid or solid particles in a dispersed phase with a fluid) as well as 50 droplets differ by size. In equation (3), the number of infectious persons (I), the quanta emission rate depending on 74 the activity (q), the pulmonary ventilation rate of exposed susceptible persons (Qb), the 75 duration of stay (t) and the volume flow of pathogen free air (Q) was used. To calculate the predicted 156 infection risk via aerosols (PIRA) in the far field of a room the concentration of quanta (c(t)) 157 and the respiratory rate (Qb) has to be known. To reduce the risk of infection via aerosols the necessary volume flow of virus-free air 327 depending on the exposure time can be seen in Figure 5 . abstract: Currently, airborne transmission is seen as the most important transmission path for SARS-CoV-2. In this investigation, models of other researchers with the aim to predict an infection risk for exposed persons in a room through aerosols emitted by an infectious case-patient were extended. As a novelty parameters or boundary conditions, namely the non-stationarity of aerosol and the half life of aerosolized virus, were included and a new method for determining the quanta emission rate based on measurements of the particle emission rate and respiratory rate at different types of activities was implemented. As a second step, the model was applied to twelve outbreaks to compare the predicted infection risk with the observed attack rate. To estimate a 'credible interval' of the predicted infection risk the quanta emission rate, the respiratory rate as well as the air volume flow were varied. In nine out of twelve outbreaks, the calculated predicted infection risk via aerosols was found to be in the range the attack rate (with the variation of the boundary conditions) and reasons for the observed larger divergence were discussed. The validation was considered successful and therefore, the use of the model could be recommended to predict the risk of an infection via aerosols in given situations. Furthermore, appropriate preventive measures can be designed. url: http://medrxiv.org/cgi/content/short/2020.10.08.20209106v1?rss=1 doi: 10.1101/2020.10.08.20209106 id: cord-126015-zc7u3g34 author: Krieger, Elizabeth title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date: 2020-05-13 words: 6421.0 sentences: 348.0 pages: flesch: 42.0 cache: ./cache/cord-126015-zc7u3g34.txt txt: ./txt/cord-126015-zc7u3g34.txt summary: To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. The HLA genes exhibit extreme allelic polymorphisms and present viral peptides on host HLA molecules to T cells to trigger an adaptive immune response. A quantitative approach relating differences in cytokine levels and polymorphisms in the immune response pathways may help identify patients at risk of severe disease. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a variable clinical presentation that ranges from asymptomatic, to severe disease with cytokine storm. The mortality rates also differ across the globe, ranging from 0.5-13%. This variation is likely due to both pathogen and host factors. Host factors may include genetic differences in the immune response genes as well as variation in HLA and KIR allotypes. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. Based on this broad quantitative framework it may be posited that the spectrum of symptomatic to severely symptomatic presentations of COVID19 represents the balance between innate and adaptive immune responses. In asymptomatic patients, prompt and adequate adaptive immune response quells infection, whereas in those with severe symptoms a slower inadequate adaptive response leads to a runaway cytokine cascade fueled by ongoing viral replication. Polymorphisms in the various components of the innate and adaptive immune response may cause altered immune response kinetics that would result in variable severity of illness. Understanding how this genetic variation may alter the response to SARS-CoV-2 infection is critical to develop successful treatment strategies. url: https://arxiv.org/pdf/2005.06541v2.pdf doi: nan id: cord-318426-kv7aa0og author: Kritsotakis, Evangelos I. title: On the importance of population-based serological surveys of SARS-CoV-2 without overlooking their inherent uncertainties date: 2020-05-22 words: 1652.0 sentences: 101.0 pages: flesch: 53.0 cache: ./cache/cord-318426-kv7aa0og.txt txt: ./txt/cord-318426-kv7aa0og.txt summary: This brief note aims to explain the scope in conducting large-scale serological surveys of SARS-CoV-2 to define the landscape of population immunity, without overlooking the inherent uncertainty steaming from sampling design and diagnostic validity. The note completes with a succinct appendix of simple statistical methods for estimating prevalence from random population samples using imperfect diagnostic tests. They use serological tests to examine a large number of blood samples from people without a confirmed SARS-CoV-2 infection to detect signs that they were once infected with the virus. Available serological tests are not perfect but are acceptable for use in the context of surveying populations for SARS-CoV-2 antibodies, because survey estimates can be corrected for imperfect diagnostic performance. Large-scale seroprevalence surveys are an important tool in combating COVID-19 disease as they can provide much-needed estimates of the fraction of the population with antibodies against SARS-CoV-2. The quality of the antibody prevalence estimates depends on the sampling design and the diagnostic accuracy of serological tests. abstract: Abstract The SARS-CoV-2 epidemic has caused an unprecedented public health situation and more than ever it is important to be well informed on methods to monitor and analyse the progression of the epidemic. This brief note aims to explain the scope in conducting large-scale serological surveys of SARS-CoV-2 to define the landscape of population immunity, without overlooking the inherent uncertainty steaming from sampling design and diagnostic validity. The note completes with a succinct appendix of simple statistical methods for estimating prevalence from random population samples using imperfect diagnostic tests. url: https://api.elsevier.com/content/article/pii/S2666535220300124 doi: 10.1016/j.puhip.2020.100013 id: cord-284862-nhihxog0 author: Kroemer, Marie title: COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity date: 2020-08-25 words: 1043.0 sentences: 63.0 pages: flesch: 49.0 cache: ./cache/cord-284862-nhihxog0.txt txt: ./txt/cord-284862-nhihxog0.txt summary: Although the existence of SARS-CoV-2 specific T-cells has been described 2,3 , the frequency and the intensity of SARS-CoV-2 specific T-cell responses among mild illness and severe pneumonia convalescent COVID-19 patients remains to be investigated. In this prospective study, 60 patients who had COVID-19 were enrolled in a two cohorts study that were entitled mild illness (n=30) and severe pneumonia (n=30) at least 21 days after the first symptoms of ; Table 1 for CoV-N) might be explained by the sequence homology between structural proteins from various coronavirus suggesting the existence of cross reactive memory T-cells 5 . We observed that all patients with severe pneumonia had a positive serology index and most of them had at least one specific cellular response for SARS-CoV-2 proteins (28 out of 30). Specific T-cell responses for S, M and N proteins were simultaneously shown for 70.0% of severe pneumonia patients while only for 37.9% of mild illness patients (P=0.0191) (Fig. 1E) . abstract: Adaptive Immune responses generated by SARS-CoV-2 virus in convalescent patients according to disease severity remain poorly characterized. To this end, we designed a prospective study (NCT04365322) that included 60 COVID-19 convalescent patients (1-month post infection) in two cohorts respectively entitled mild illness and severe pneumonia. The monitoring of peripheral immune responses was performed using IFNᵧ ELISpot assay. The serology index of each patient was investigated at the same time. Patients with severe pneumonia were older and had more comorbidities than patients with mild illness. T-cell responses in term of frequency and intensity were clearly distinct between mild illness and severe pneumonia patients. Furthermore, our results demonstrated that recent history of COVID-19 did not hamper viral memory T-cell pool against common viruses (Cytomegalovirus, Epstein-Barr-virus and Flu-virus). The presence of potent adaptive immunity even in patients who underwent severe pneumonia sustain the rationale for the development of protective therapeutics against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32853599/ doi: 10.1016/j.jinf.2020.08.036 id: cord-252873-4tazhf40 author: Kruglikov, Ilja L. title: The role of adipocytes and adipocyte‐like cells in the severity of COVID‐19 infections date: 2020-04-27 words: 2295.0 sentences: 128.0 pages: flesch: 47.0 cache: ./cache/cord-252873-4tazhf40.txt txt: ./txt/cord-252873-4tazhf40.txt summary: Coronavirus disease‐2019 (COVID‐19), caused by the highly pathogenic virus SARS‐CoV‐2, demonstrates high morbidity and mortality caused by development of a severe acute respiratory syndrome connected with extensive pulmonary fibrosis (PF). Expression of angiotensin‐converting enzyme 2 (ACE2 ‐ the functional receptor for SARS‐CoV) ‐ is upregulated in adipocytes of obese and diabetic patients, which turns adipose tissue into a potential target and viral reservoir. Similar to the recently established adipocyte‐myofibroblast transition (AMT), pulmonary lipofibroblasts located in the alveolar interstitium and closely related to classical adipocytes, demonstrate the ability to transdifferentiate into myofibroblasts that play an integral part of PF. Recently it was shown that another anti-diabetic drug, metformin, accelerates resolution of pulmonary fibrosis by inducing trans-differentiation of myofibroblasts into lipofibroblasts (18) . Adipose tissue can serve as a viral reservoir, whereas transdifferentiation of pulmonary lipofibroblasts into myofibroblasts can contribute to the development of PF and thus is likely to influence the clinical severity of COVID-19. abstract: Coronavirus disease‐2019 (COVID‐19), caused by the highly pathogenic virus SARS‐CoV‐2, demonstrates high morbidity and mortality caused by development of a severe acute respiratory syndrome connected with extensive pulmonary fibrosis (PF). In this Perspective, we argue that adipocytes and adipocyte‐like cells, such as pulmonary lipofibroblasts, may play an important role in the pathogenic response to COVID‐19. Expression of angiotensin‐converting enzyme 2 (ACE2 ‐ the functional receptor for SARS‐CoV) ‐ is upregulated in adipocytes of obese and diabetic patients, which turns adipose tissue into a potential target and viral reservoir. This may explain why obesity and diabetes are potential comorbidities for COVID‐19 infections. Similar to the recently established adipocyte‐myofibroblast transition (AMT), pulmonary lipofibroblasts located in the alveolar interstitium and closely related to classical adipocytes, demonstrate the ability to transdifferentiate into myofibroblasts that play an integral part of PF. This may significantly increase the severity of the local response to COVID‐19 in the lung. To reduce the severity and mortality with COVID‐19, we propose to probe for the clinical response to thiazolidinediones (TZDs), PPARγ agonists, that are the well‐known anti‐diabetic drugs. TZDs are able to stabilize lipofibroblasts in their “inactive” state, preventing the transition to myofibroblasts and thereby reducing the development of pulmonary fibrosis and stimulating its resolution. url: https://doi.org/10.1002/oby.22856 doi: 10.1002/oby.22856 id: cord-350753-qbm145tr author: Krüttgen, Alexander title: Determination of SARS-CoV-2 antibodies with assays from Diasorin, Roche and IDvet date: 2020-09-23 words: 1826.0 sentences: 108.0 pages: flesch: 49.0 cache: ./cache/cord-350753-qbm145tr.txt txt: ./txt/cord-350753-qbm145tr.txt summary: Using 75 sera from patients tested positive or negative by SARS-CoV-2 PCR, we investigated the sensitivity and specificity of the Liaison SARS-CoV-2 S1/S2 IgG assay (DiaSorin), the Elecsys Anti-SARS-CoV-2 assay (Roche), and the ID Screen SARS-CoV-2-N IgG indirect kit (IDVet). We and others have published results of the assessment of the first commercially available serological assays, such as the Anti SARS-CoV-2 ELISA (IgG) from Euroimmun (Krüttgen et al., 2020; Okba et al., 2020) . We therefore compared these three new assays with respect to their sensitivity and specificity to detect SARS-CoV-2 specific antibodies using a collection of serum samples employed previously for the analysis of four other assays. Our comparative approach to test in total seven different SARS-CoV-2 antibody assays with an identical collection of serum samples allowed for the first time the direct comparison of performance indicators of such a large number of automated assays. abstract: There is an ongoing need for highly reliable serological assays to detect individuals with past SARS-CoV-2 infection. Using 75 sera from patients tested positive or negative by SARS-CoV-2 PCR, we investigated the sensitivity and specificity of the Liaison SARS-CoV-2 S1/S2 IgG assay (DiaSorin), the Elecsys Anti-SARS-CoV-2 assay (Roche), and the ID Screen SARS-CoV-2-N IgG indirect kit (IDVet). We determined a sensitivity of 95.5%, 95.5%, and 100% and a specificity of 90.5%, 96.2%, and 92,5% for the DiaSorin assay, the Roche assay, and the IDVet assay, respectively. We conclude that serologic assays combining very high sensitivity and specificity are still not commercially available for SARS-CoV-2. For maximizing sensitivity and specificity of SARS-CoV-2 serological diagnostics, the combination of two assays may be helpful. url: https://www.ncbi.nlm.nih.gov/pubmed/32979407/ doi: 10.1016/j.jviromet.2020.113978 id: cord-291655-l7mg5a0z author: Ku, C. W. title: Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19 date: 2020-10-05 words: 4332.0 sentences: 311.0 pages: flesch: 62.0 cache: ./cache/cord-291655-l7mg5a0z.txt txt: ./txt/cord-291655-l7mg5a0z.txt summary: Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods. In order to validate the use of buccal swabs and saliva specimen as alternative diagnostic tests for SARS-CoV-2, our group performed a cross-sectional study of NPS, self-collected buccal swabs and saliva specimens collected concurrently in order to determine the positive percent agreement (PPA), negative percent agreement (NPA), overall agreement (OA), positive and negative predictive values. In this study, we have shown that saliva tests and buccal swabs were comparable to each other and were in moderate agreement with NPS for the detection of SARS-CoV-2, with PPA between 56 and 66% and PPV 95 to 100%. abstract: Background: Effective management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) requires large-scale testing. Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods. Methods: A cross-sectional single centre study was conducted on 42 participants who were tested positive for SARS-CoV-2 via NPS within the past 7 days. A self-collected saliva and buccal swab and a HCW-collected NPS were obtained. Real-time polymerase chain reaction (RT-PCR) was performed and cycle threshold (CT) values were obtained. Positive percent agreement (PPA), negative percent agreement (NPA) and overall agreement (OA) were calculated for saliva and buccal swabs, as compared with NPS. Results: Among the 42 participants, 73.8% (31/42) tested positive via any one of the 3 tests. With reference to NPS, the saliva test had PPA 66.7%, NPA 91.7% and OA 69.0%. The buccal swab had PPA 56.7%, NPA 100% and OA 73.8%. Presence of symptoms improved diagnostic accuracy. There was no statistically significant association between CT values and duration of symptom onset within the first 12 days of symptoms for all three modalities. Conclusion: Self-collected saliva tests and buccal swabs have only moderate agreement with HCW-collected NPS swabs. Primary screening for SARS-CoV-2 may be performed with a saliva test or buccal swab, with a negative test warranting a confirmatory NPS to avoid false negatives. This combined strategy minimizes discomfort and reduces the risk of spread to the community and HCWs. url: http://medrxiv.org/cgi/content/short/2020.10.03.20205278v1?rss=1 doi: 10.1101/2020.10.03.20205278 id: cord-024317-w1ep0wq8 author: Ku, Zhiqiang title: Antibody therapies for the treatment of COVID-19 date: 2020-04-30 words: 2215.0 sentences: 152.0 pages: flesch: 47.0 cache: ./cache/cord-024317-w1ep0wq8.txt txt: ./txt/cord-024317-w1ep0wq8.txt summary: Here, we discuss some of the most active areas of developing strategies to treat COVID-19, focusing on approaches to generate neutralizing antibodies against SARS-CoV-2 for prophylactic and therapeutic treatment of COVID-19. SIGNIFICANCE: Development of SARS-CoV-2 neutralizing antibodies with the desired efficacy and safety profile is a critical part of the toolbox of therapies for the treatment of COVID-19. The spike protein of SARS-CoV-2 plays an essential role in virus entry into host cells and is a primary target of neutralizing antibodies 5, 9 (Figures 1C,D) . Two MERS-CoV neutralizing mAbs, G2 and 7D10, target the S1-NTD region and function by blocking spike protein interaction with the host receptor DPP4 47, 48 . In the monkey study, researchers found that rhesus macaques infected with SARS-CoV-2 through the intratracheal route had mild illness, and their lungs showed signs of pneumonia similar to those in humans with COVID-19 58 . abstract: An outbreak of COVID-19, the disease caused by infection of the coronavirus SARS-CoV-2, that began in December 2019 in Wuhan, China has caused more than 2,990,559 confirmed human infections and 207,446 deaths as of April 27, 2020 (Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University). Scientists are working quickly on multiple aspects of the pandemic. Genetic analyses are conducted to reveal the source and evolution of SARS-CoV-2, providing knowledge that can be used to contain it and to avoid future outbreaks. Epidemiological studies which incorporates lessons learned from outbreaks of previous related viral diseases can guide development of public health measures effective to contain the current and future outbreaks. Basic virology studies reveal viral structure and function. Pathology studies inform development of strategies to interfere with infection. COVID-19 prevention and treatment strategies are being developed in preclinical and clinical studies. Antibody-based therapy is one viable treatment option. Here, we discuss some of the most active areas of developing strategies to treat COVID-19, focusing on approaches to generate neutralizing antibodies against SARS-CoV-2 for prophylactic and therapeutic treatment of COVID-19. SIGNIFICANCE: Development of SARS-CoV-2 neutralizing antibodies with the desired efficacy and safety profile is a critical part of the toolbox of therapies for the treatment of COVID-19. We discuss in this review the current state of discovery and development of such antibodies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197606/ doi: 10.1093/abt/tbaa007 id: cord-337491-ztco6guw author: Kucharski, Adam J title: Using serological data to understand unobserved SARS-CoV-2 risk in health-care settings date: 2020-08-03 words: 929.0 sentences: 51.0 pages: flesch: 42.0 cache: ./cache/cord-337491-ztco6guw.txt txt: ./txt/cord-337491-ztco6guw.txt summary: 1 Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), growing evidence of nosocomial transmission has been observed, but tracking such outbreaks is challenging because a substantial proportion of infected individuals might exhibit mild or no symptoms. Staff working in dedicated COVID-19 wards showed substantially higher rates of seropositivity (1·65 [1·34-2·03]; p<0·001) than other frontline health-care workers working in hospitals, reflecting increased risk for this group, a pattern that has also been reported in neighbouring Sweden. The results highlight the risk that SARS-CoV-2 can pose to health-care workers, particularly those in regular contact with patients with COVID-19, and the importance of understanding possible routes of exposure in hospitals. However, the prevalence of asymptomatic SARS-CoV-2 infections and COVID-19-like symptoms among seronegative staff illustrates the limitations of relying on symptom-based surveillance alone. Risk of COVID-19 in health-care workers in Denmark: an observational cohort study SARS-CoV-2 exposure, symptoms and seroprevalence in health care workers abstract: nan url: https://api.elsevier.com/content/article/pii/S147330992030579X doi: 10.1016/s1473-3099(20)30579-x id: cord-290170-s6wjitfo author: Kuhrt, Katy title: Placental abruption in a twin pregnancy at 32 weeks’ gestation complicated by COVID-19, without vertical transmission to the babies. date: 2020-05-08 words: 304.0 sentences: 33.0 pages: flesch: 64.0 cache: ./cache/cord-290170-s6wjitfo.txt txt: ./txt/cord-290170-s6wjitfo.txt summary: key: cord-290170-s6wjitfo title: Placental abruption in a twin pregnancy at 32 weeks'' gestation complicated by COVID-19, without vertical transmission to the babies. cord_uid: s6wjitfo Other coronavirus spectrum infections have been 31 associated with miscarriage, preterm birth, preeclampsia, caesarean delivery, perinatal death, 32 fetal growth restriction, and placental abruption. She gave a one-day history of cough, fever and 100 5 mild shortness of breath. An echocardiogram performed the same day showed a mild pericardial 102 effusion, and NT-BNP was 28pg/ml (normal <100pg/ml) (done to rule out cardiac failure or 103 cardiomyopathy). Outcome 186 of Coronavirus spectrum infections (SARS, MERS, COVID 1 -19) during 187 pregnancy: a systematic review and meta-analysis MERS-CoV Infection in a Pregnant Woman in Korea Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in 198 Possible Vertical Transmission 202 of SARS-CoV-2 From an Infected Mother to Her Newborn Placental 210 abruption in twin pregnancies, risk factors and perinatal outcomes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32391520/ doi: 10.1016/j.ajogmf.2020.100135 id: cord-256146-d599uera author: Kuiken, Thijs title: Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date: 2003-07-26 words: 5686.0 sentences: 281.0 pages: flesch: 49.0 cache: ./cache/cord-256146-d599uera.txt txt: ./txt/cord-256146-d599uera.txt summary: METHODS: We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARSCoV, human metapneumovirus, and other respiratory pathogens. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. . Serial dilutions of the SARS-CoV virus stock and SARS-CoV-infected Vero cells from patient 5688 were made and tested with the NP and polymerase-specific RT-PCRs. Samples from the respiratory tract (nasal swabs, pharyngeal swabs, postmortem trachea, and lung samples) were also monitored for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E), and human metapneumovirus with use of essentially the same RT-PCR methods but with specific primers. Virological examinations of nasal and pharyngeal swabs, and tracheal and lung samples from all four macaques by RT-PCR for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E) and human metapneumovirus were negative. abstract: BACKGROUND: The worldwide outbreak of severe acute respiratory syndrome (SARS) is associated with a newly discovered coronavirus, SARS-associated coronavirus (SARSCoV). We did clinical and experimental studies to assess the role of this virus in the cause of SARS. METHODS: We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARSCoV, human metapneumovirus, and other respiratory pathogens. We infected four cynomolgus macaques (Macaca fascicularis) with SARS-CoV in an attempt to replicate SARS and did necropsies on day 6 after infection. FINDINGS: SARS-CoV infection was diagnosed in 329 (75%) of 436 patients fitting the case definition of SARS; human metapneumovirus was diagnosed in 41 (12%) of 335, and other respiratory pathogens were diagnosed only sporadically. SARS-CoV was, therefore, the most likely causal agent of SARS. The four SARS-CoV-infected macaques excreted SARS-CoV from nose, mouth, and pharynx from 2 days after infection. Three of four macaques developed diffuse alveolar damage, similar to that in SARS patients, and characterised by epithelial necrosis, serosanguineous exudate, formation of hyaline membranes, type 2 pneumocyte hyperplasia, and the presence of syncytia. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. INTERPRETATION: Replication in SARS-CoV-infected macaques of pneumonia similar to that in human beings with SARS, combined with the high prevalence of SARS-CoV infection in SARS patients, fulfill the criteria required to prove that SARS-CoV is the primary cause of SARS. Published online July 22, 2003 http://image.thelancet.com/extras/03art6318web.pdf url: https://www.ncbi.nlm.nih.gov/pubmed/12892955/ doi: 10.1016/s0140-6736(03)13967-0 id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 words: 4973.0 sentences: 241.0 pages: flesch: 51.0 cache: ./cache/cord-325113-sou8xyld.txt txt: ./txt/cord-325113-sou8xyld.txt summary: The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. abstract: SARS-CoV-2 is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a pre-requisite to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2 with the ability to detect as little as five viral genome equivalents. The approach delivers results without the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings. url: https://doi.org/10.1371/journal.pone.0241740 doi: 10.1371/journal.pone.0241740 id: cord-301292-yaii6e16 author: Kuk, Anthony Y. C. title: The estimation of SARS incubation distribution from serial interval data using a convolution likelihood date: 2005-07-12 words: 4354.0 sentences: 252.0 pages: flesch: 60.0 cache: ./cache/cord-301292-yaii6e16.txt txt: ./txt/cord-301292-yaii6e16.txt summary: By constructing a convolution likelihood based on the serial interval data, we are able to estimate the incubation distribution which is assumed to be Weibull, and justifications are given to support this choice over other distributions. The indirect estimate obtained using the method of convolution likelihood is validated by means of comparison with a direct estimate obtained directly from a subset of patients for whom the incubation time can be ascertained. Despite its name, the proposed indirect estimate is actually more precise than the direct estimate because serial interval data are recorded for almost all patients, whereas exact incubation times can be determined for only a small subset. By constructing a convolution likelihood based on the serial interval data in Singapore, we are able to estimate the incubation distribution parametrically. It is possible to obtain a combined estimate that makes use of the incubation times for the 50 patients in the ascertained subset and the serial intervals for the remaining 148 cases. abstract: The incubation period of SARS is the time between infection of disease and onset of symptoms. Knowledge about the distribution of incubation times is crucial in determining the length of quarantine period and is an important parameter in modelling the spread and control of SARS. As the exact time of infection is unknown for most patients, the incubation time cannot be determined. What is observable is the serial interval which is the time from the onset of symptoms in an index case to the onset of symptoms in a subsequent case infected by the index case. By constructing a convolution likelihood based on the serial interval data, we are able to estimate the incubation distribution which is assumed to be Weibull, and justifications are given to support this choice over other distributions. The method is applied to data provided by the Ministry of Health of Singapore and the results justify the choice of a ten‐day quarantine period. The indirect estimate obtained using the method of convolution likelihood is validated by means of comparison with a direct estimate obtained directly from a subset of patients for whom the incubation time can be ascertained. Despite its name, the proposed indirect estimate is actually more precise than the direct estimate because serial interval data are recorded for almost all patients, whereas exact incubation times can be determined for only a small subset. It is possible to obtain an even more efficient estimate by using the combined data but the improvement is not substantial. Copyright © 2005 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16013037/ doi: 10.1002/sim.2123 id: cord-269454-9gthf2jl author: Kulkarni, Rajesh title: Early-onset symptomatic neonatal COVID-19 infection with high probability of vertical transmission date: 2020-08-02 words: 1778.0 sentences: 109.0 pages: flesch: 59.0 cache: ./cache/cord-269454-9gthf2jl.txt txt: ./txt/cord-269454-9gthf2jl.txt summary: RESULTS: A COVID-19 suspected mother, who tested negative by RT-PCR for COVID, but tested positive for SARS-CoV-2 by serology, delivered a term baby. CONCLUSION: This report highlights a very strong possibility of vertical transmission of COVID-19 from a mildly symptomatic, RT-PCR negative but antibody-positive mother with significant symptomatic, early—onset neonatal infection. This report describes the clinical course and laboratory findings in a neonate born in Pune, India in whom infection with SARS-CoV-2 very likely occurred via vertical transmission. NPA from baby, cord stump, and placenta (which were collected as per national guidelines at birth) were reported as positive for SARS-CoV2 at 12 h of life. Two neonates with positive RT-PCR testing as early as 30 h after delivery have been reported; however, these cases lacked sufficient clinical data or precise information regarding isolation methods, and perinatal transmission could not be ruled out [7, 8] . abstract: BACKGROUND: There are few reports of COVID-19 in neonates and most are suspected to be due to postnatal transmission. Vertical transmission has been proven in only a couple of cases so far. METHODS: We describe early—onset, severe COVID-19 disease in a neonate with very strong evidence of vertical transmission of SARS-CoV-2. RESULTS: A COVID-19 suspected mother, who tested negative by RT-PCR for COVID, but tested positive for SARS-CoV-2 by serology, delivered a term baby. The neonate was kept in strict isolation. Molecular tests for SARS-CoV-2 on umbilical stump, placenta, and nasopharyngeal aspirate of the neonate, collected at birth were positive. On day 2, the neonate developed clinical features of COVID in the form of fever, poor feeding, and hyperbilirubenemia along with elevated inflammatory markers. Antibiotics were started empirically pending cultures. Blood, CSF, and urine cultures were sterile. Baby tested RT-PCR positive for SARS-CoV-2 on two more occasions before testing positive for antibodies and was discharged on day 21 of life. CONCLUSION: This report highlights a very strong possibility of vertical transmission of COVID-19 from a mildly symptomatic, RT-PCR negative but antibody-positive mother with significant symptomatic, early—onset neonatal infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32743723/ doi: 10.1007/s15010-020-01493-6 id: cord-346998-01i6zxv8 author: Kulkarni, Spoorthy title: COVID-19 and hypertension date: 2020-05-20 words: 2584.0 sentences: 163.0 pages: flesch: 48.0 cache: ./cache/cord-346998-01i6zxv8.txt txt: ./txt/cord-346998-01i6zxv8.txt summary: COVID-19 seems to follow a pattern seen with influenza and previous severe acute respiratory syndrome coronavirus (SARS-CoV) outbreaks: that the severity and mortality of the infection is higher in the elderly age group. The controversy regarding continuing or discontinuing angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) in COVID-19 patients arose after it became apparent that SARS-CoV uses angiotensin-converting enzyme 2 (ACE2) to gain entry in host cells. 12 Consequently, the increased expression of ACE2 would facilitate an increased rate or susceptibility to infection with SARS-CoV-2 and further hypothesis that this may increase the risk of developing severe and fatal COVID-19. The study tested the hypothesis of an increased risk of severe illness in COVID-19 with hypertension with ACEi use (on ACEi n=37; not on ACEi n=168) in admitted patients. Effect of angiotensin converting enzyme gene I/D polymorphism and its expression on clinical outcome in acute respiratory distress syndrome abstract: nan url: https://doi.org/10.1177/1470320320927851 doi: 10.1177/1470320320927851 id: cord-277443-mv7sk5aa author: Kumaki, Yohichi title: Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol(®) (Poly IC:LC), in a lethal SARS-CoV-infected BALB/c mouse model date: 2016-12-09 words: 10048.0 sentences: 686.0 pages: flesch: 62.0 cache: ./cache/cord-277443-mv7sk5aa.txt txt: ./txt/cord-277443-mv7sk5aa.txt summary: Hiltonol(®) at 5, 1, 0.5 or 0.25 mg/kg/day by intranasal (i.n.) route resulted in significant survival benefit when administered at selected times 24 h prior to challenge with a lethal dose of mouse-adapted severe acute respiratory syndrome coronavirus (SARS-CoV). In other studies, treatment with an interferon inducer, polyriboinosinicpolyribocytidylic acid stabilized with poly-L-lysine and carboxymethyl cellulose (poly IC:LC), given by the intranasal route, was effective in protecting mice against a lethal infection with mouseadapted SARS-CoV and reduced viral lung titers (Kumaki et al., 2010) . These treated, SARS-CoVinfected mice receiving the various Hiltonol ® dosing regimens were also significantly protected against weight loss due to virus infection (Table 1 , p < 0.05-p<0.001) from days 0e3 post virus exposure when the greatest weight loss occurred in this mouse model. abstract: Hiltonol(®), (Poly IC:LC), a potent immunomodulator, is a synthetic, double-stranded polyriboinosinic-polyribocytidylic acid (poly IC) stabilized with Poly-L-lysine and carboxymethyl cellulose (LC). Hiltonol(®) was tested for efficacy in a lethal SARS-CoV-infected BALB/c mouse model. Hiltonol(®) at 5, 1, 0.5 or 0.25 mg/kg/day by intranasal (i.n.) route resulted in significant survival benefit when administered at selected times 24 h prior to challenge with a lethal dose of mouse-adapted severe acute respiratory syndrome coronavirus (SARS-CoV). The infected BALB/c mice receiving the Hiltonol(®) treatments were also significantly effective in protecting mice against weight loss due to infection (p < 0.001). Groups of 20 mice were dosed with Hiltonol(®) at 2.5 or 0.75 mg/kg by intranasal instillation 7, 14, and 21 days before virus exposure and a second dose was given 24 h later, prophylactic Hiltonol(®) treatments (2.5 mg/kg/day) were completely protective in preventing death, and in causing significant reduction in lung hemorrhage scores, lung weights and lung virus titers. Hiltonol(®) was also effective as a therapeutic when give up to 8 h post virus exposure; 100% of the-infected mice were protected against death when Hiltonol(®) was administered at 5 mg/kg/day 8 h after infection. Our data suggest that Hiltonol(®) treatment of SARS-CoV infection in mice leads to substantial prophylactic and therapeutic effects and could be used for treatment of other virus disease such as those caused by MERS-CoV a related coronavirus. These properties might be therapeutically advantageous if Hiltonol(®) is considered for possible clinical use. url: https://www.ncbi.nlm.nih.gov/pubmed/27956136/ doi: 10.1016/j.antiviral.2016.12.007 id: cord-275111-38hgg0jz author: Kumar, Abhishek title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients date: 2020-10-06 words: 2300.0 sentences: 171.0 pages: flesch: 60.0 cache: ./cache/cord-275111-38hgg0jz.txt txt: ./txt/cord-275111-38hgg0jz.txt summary: title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients AIM: To analyse the liver function in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. 91 patients admitted with confirmed SARS-CoV-2 infection were included in this study and divided into asymptomatic, mild, moderate and severe groups. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. In this study, we aimed to analyse the liver function abnormalities in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. [16, 21, 22] In our study, the levels of AST and ALP between different groups of disease severity was highly significant which is consistent with a previous report. abstract: BACKGROUND: – COVID-19 caused by SARS-CoV-2 leads to myriad range of organ involvement including liver dysfunction. AIM: To analyse the liver function in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. MATERIALS AND METHODS: This study was a cross-sectional study done at Rajendra Institute of Medical Sciences, Ranchi. 91 patients admitted with confirmed SARS-CoV-2 infection were included in this study and divided into asymptomatic, mild, moderate and severe groups. Liver function tests were compared among different severity groups. RESULTS: Of 91 patients with COVID-19, 70 (76.9%) had abnormal liver function. Aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), total bilirubin levels was 1–2 × ULN in 33(36.3%), 34(37.3%), 12(13.2%), 6(6.6%) cases and >2 × ULN in 20(22%), 18(19.8%), 7(7.7%) and 2 (2.2%) cases respectively. Mean AST and ALP levels among different severity groups of COVID-19 was statistically significant (p < 0.05) whereas mean ALT and total bilirubin levels was statistically non-significant (p > 0.05). There was no statistical difference between males and females with regard to abnormal liver function. Liver injury was seen in 64.3% cases of hypertension and 73.3% cases of diabetes. Fever, myalgia, headache and breathlessness were found to be correlated significantly with severity of disease. CONCLUSION: Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. Aspartate transaminase and alkaline phosphatase are better indicators of covid-19 induced liver injury than alanine transaminase and total bilirubin. url: https://doi.org/10.1016/j.dsx.2020.10.001 doi: 10.1016/j.dsx.2020.10.001 id: cord-272241-2fwz8z8n author: Kumar, Amit title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date: 2020-09-09 words: 4608.0 sentences: 281.0 pages: flesch: 49.0 cache: ./cache/cord-272241-2fwz8z8n.txt txt: ./txt/cord-272241-2fwz8z8n.txt summary: title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach Hence, in this study, we have used immunoinformatic approaches to predict highly antigenic epitopes from SARS-CoV-2 structural proteins that would evoke a strong immune response in humans. For this purpose, we have used the structural proteins: Spike, Envelope, and nucleocapsid to predict B-cell, cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes for construction of vaccine. We have also performed the docking and molecular dynamic simulations (MDS) between the vaccine and human Toll-like Receptor-3 (TLR-3) to study their binding stability. The VaxiJen 2.0 server predicts the antigenicity of the multi-epitope vaccine peptide based on the physicochemical properties of the input protein. Whereas, ANTIGENpro server predicts the antigenicity of the multi-epitopic vaccine based on the protein microarray data analysis of the target organism. Three structural proteins (spike glycoprotein, nucleocapsid, and envelope) were selected to construct a multi-epitope vaccine, which is capable of eliciting the humoral and cell-mediated immune response. abstract: INTRODUCTION: The ongoing life-threatening pandemic of coronavirus disease 2019 (COVID-19) has extensively affected the world. During this global health crisis, it is fundamentally crucial to find strategies to combat SARS-CoV-2. Despite several efforts in this direction and continuing clinical trials, no vaccine has been approved for it yet. METHODS: To find a preventive measure, we have computationally designed a multi-epitopic subunit vaccine using immuno-informatic approaches. RESULTS: The structural proteins of SARS-CoV-2 involved in its survival and pathogenicity were used to predict antigenic epitopes. The antigenic epitopes were capable of eliciting a strong humoral as well as cell-mediated immune response, our predictions suggest. The final vaccine was constructed by joining the all epitopes with specific linkers and to enhance their stability and immunogenicity. The physicochemical property of the vaccine was assessed. The vaccine 3D structure prediction and validation were done and docked with the human TLR-3 receptor. Furthermore, molecular dynamics simulations of the vaccine-TLR-3 receptor complex are employed to assess its dynamic motions and binding stability in-silico. CONCLUSION: Based on this study, we strongly suggest synthesizing this vaccine, which further can be tested in-vitro and in-vivo to check its potency in a cure for COVID-19. url: https://doi.org/10.1080/14760584.2020.1813576 doi: 10.1080/14760584.2020.1813576 id: cord-287091-a3nieh5p author: Kumar, Anuj title: Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches date: 2020-06-04 words: 5544.0 sentences: 314.0 pages: flesch: 51.0 cache: ./cache/cord-287091-a3nieh5p.txt txt: ./txt/cord-287091-a3nieh5p.txt summary: In the current study, we report novel natural metabolites namely, ursolic acid, carvacrol and oleanolic acid as the potential inhibitors against main protease (M(pro)) of COVID-19 by using integrated molecular modeling approaches. Besides the uses of various FDA-approved antiviral compounds as mentioned above, there are many in-silico studies have been performed to screen the novel phytochemical molecules as a potential inhibitors of main protease of SARS-CoV-2 or develop new drugs against COVID-19 (Adem et al., 2020; Chandel et al., 2020; Gentile et al., 2020; Gonzalez-Paz et al., 2020; Khaerunnisa et al., 2020; Khan et al., 2020; Qamar et al., 2020; Sharma & Kaur, 2020; Sun et al., 2020) . In the present study, we have targeted the protease of SARS-CoV-2 virus using available molecular modelling based methods and studied the interactions with selected natural compounds (ursolic acid, carvacrol and oleanolic acid) by molecular docking and molecular dynamics simulations followed by molecular mechanic/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) validation. abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel corona virus that causes corona virus disease 2019 (COVID-19). The COVID-19 rapidly spread across the nations with high mortality rate even as very little is known to contain the virus at present. In the current study, we report novel natural metabolites namely, ursolic acid, carvacrol and oleanolic acid as the potential inhibitors against main protease (M(pro)) of COVID-19 by using integrated molecular modeling approaches. From a combination of molecular docking and molecular dynamic (MD) simulations, we found three ligands bound to protease during 50 ns of MD simulations. Furthermore, the molecular mechanic/generalized/Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energy calculations showed that these chemical molecules have stable and favourable energies causing strong binding with binding site of M(pro) protein. All these three molecules, namely, ursolic acid, carvacrol and oleanolic acid, have passed the ADME (Absorption, Distribution, Metabolism, and Excretion) property as well as Lipinski’s rule of five. The study provides a basic foundation and suggests that the three phytochemicals, viz. ursolic acid, carvacrol and oleanolic acid could serve as potential inhibitors in regulating the M(pro) protein’s function and controlling viral replication. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32448034/ doi: 10.1080/07391102.2020.1772112 id: cord-353716-gxgvhhv1 author: Kumar, Ashutosh title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients date: 2020-09-30 words: 2300.0 sentences: 136.0 pages: flesch: 40.0 cache: ./cache/cord-353716-gxgvhhv1.txt txt: ./txt/cord-353716-gxgvhhv1.txt summary: title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients Based on the circumstantial evidence present in the literature, we propose a SARS-CoV-2 cell entry receptor ACE2 based mechanism for vascular thrombosis in COVID-19 patients. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). SARS-CoV-2 binding to the cell entry receptor ACE2 downregulates receptor expression that in turn induces vascular endothelial dysfunction, which activates prothrombotic cascade and eventually leads to vascular thrombosis observed in COVID-19 patients. abstract: Several studies have described unusually high incidence of vascular thrombosis in coronavirus disease-2019 (COVID-19) patients. Pathogenesis of the vascular thrombosis in COVID-19 is least understood for now and presents a challenge to the treating physicians. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19, has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells which facilitates its entry in the organ and mediate tissue specific pathogenesis. For ACE2 mediated cell entry of the SARS-CoV-2, co-expression of one more protein—Transmembrane protease serine 2 (TMPRSS2) is essential. Existing studies suggested significant expression of ACE2 and TMPRSS2 in human vascular endothelium. Vascular endothelial dysfunction can potentially activate coagulation cascade eventually resulting in thrombosis. ACE2 has proven role in the maintenance of endothelial integrity inside the vessels. Existing in situ evidence for SARS-CoV-1 (the causative agent for SARS pandemic of 2002, which shared ACE2 as cell entry receptor) suggested that virus binding can downregulate ACE2, thus can induce endothelial dysfunction. Recently, in situ evidence has been presented that SARS-CoV-2 can infect cells in engineered human vascular endothelium, which can be effectively blocked by using clinical-grade recombinant human ACE2. Based on the circumstantial evidence present in the literature, we propose a SARS-CoV-2 cell entry receptor ACE2 based mechanism for vascular thrombosis in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33032170/ doi: 10.1016/j.mehy.2020.110320 id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 words: 9406.0 sentences: 511.0 pages: flesch: 37.0 cache: ./cache/cord-317037-1qydcc5e.txt txt: ./txt/cord-317037-1qydcc5e.txt summary: Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. abstract: Extracellular vesicles (EVs) have shown their potential as a carrier of molecular information, and they have been involved in physiological functions and diseases caused by viral infections. Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. They are released via a direct outward budding and fission of plasma membrane blebs into the extracellular space to either facilitate virus propagation or regulate the immune responses. Moreover, EVs generated by virus-infected cells can incorporate virulence factors including viral protein and viral genetic material, and thus can resemble noninfectious viruses. Interactions of EVs with recipient cells have been shown to activate signaling pathways that may contribute to a sustained cellular response towards viral infections. EVs, by utilizing a complex set of cargos, can play a regulatory role in viral infection, both by facilitating and suppressing the infection. EV-based antiviral and antiretroviral drug delivery approaches provide an opportunity for targeted drug delivery. In this review, we summarize the literature on EVs, their associated involvement in transmission in viral infections, and potential therapeutic implications. url: https://doi.org/10.3390/v12080887 doi: 10.3390/v12080887 id: cord-319797-455ldhiy author: Kumar, Deepali title: COVID‐19: A global transplant perspective on successfully navigating a pandemic date: 2020-04-12 words: 2058.0 sentences: 112.0 pages: flesch: 48.0 cache: ./cache/cord-319797-455ldhiy.txt txt: ./txt/cord-319797-455ldhiy.txt summary: The impact has not been just restricted to issues pertaining to donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. Here we provide a personal viewpoint representing different jurisdictions from around the world in order to outline the impact of the current COVID-19 pandemic on organ transplantation. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. The impact has not been just restricted to issues around donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. abstract: The COVID‐19 pandemic has rapidly evolved and changed our way of life in an unprecedented manner. The emergence of COVID‐19 has impacted transplantation worldwide. The impact has not been just restricted to issues pertaining to donors or recipients, but also health‐care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. Here we provide a personal viewpoint representing different jurisdictions from around the world in order to outline the impact of the current COVID‐19 pandemic on organ transplantation. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. We also discuss issues related to transplant‐related research during the pandemic, the role of transplant infectious diseases, and the influence of transplant societies for education and disseminating current information. url: https://doi.org/10.1111/ajt.15876 doi: 10.1111/ajt.15876 id: cord-301641-epr1sct6 author: Kumar, Durgesh title: Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures date: 2020-05-04 words: 4095.0 sentences: 204.0 pages: flesch: 49.0 cache: ./cache/cord-301641-epr1sct6.txt txt: ./txt/cord-301641-epr1sct6.txt summary: Herein, MM-GBSA method was to calculate the change in enthalpy and the change in free energy for the formation of complex, number of hydrogen bonds (HBs) are determined to study the binding of the hit molecule with the protease of SARS-CoV-2 for COVID-19. However, the designed molecules were filtered against the protease of SARS-CoV-2 for COVID-19 based on total energy or binding energy (kcal/mol) of drug-target complex using iGEMDOCK Singh et al., 2019; Zhao et al., 2019) . Herein, MM-GBSA method is used to determine the change in enthalpy and change in free energy for the formation of complex, number of HBs to understand the binding of screened noscapines with the protease of SARS-CoV-2 of COVID-19 (Al-Anazi et al., 2018; Chaudhari & Pahelkar, 2019; Chinnasamy et al., 2019; Du et al., 2011) . Further, the detailed analysis of newly formed drug-target complex through root-mean-square fluctuation (RMSF) versus the residue number of protease of coronavirus for COVID-19 for top hit molecule is represented in Figure 7 . abstract: The current outbreak of a novel coronavirus, named as SARS-CoV-2 causing COVID-19 occurred in 2019, is in dire need of finding potential therapeutic agents. Recently, ongoing viral epidemic due to coronavirus (SARS-CoV-2) primarily affected mainland China that now threatened to spread to populations in most countries of the world. In spite of this, there is currently no antiviral drug/ vaccine available against coronavirus infection, COVID-19. In the present study, computer-aided drug design-based screening to find out promising inhibitors against the coronavirus (SARS-CoV-2) leads to infection, COVID-19. The lead therapeutic molecule was investigated through docking and molecular dynamics simulations. In this, binding affinity of noscapines(23B)-protease of SARS-CoV-2 complex was evaluated through MD simulations at different temperatures. Our research group has established that noscapine is a chemotherapeutic agent for the treatment of drug resistant cancers; however, noscapine was also being used as anti-malarial, anti-stroke and cough-suppressant. This study suggests for the first time that noscapine exerts its antiviral effects by inhibiting viral protein synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/32362235/ doi: 10.1080/07391102.2020.1752310 id: cord-353392-rqeultbq author: Kumar, Govindarajan Venkat title: A short review on antibody therapy for COVID-19 date: 2020-04-20 words: 1944.0 sentences: 105.0 pages: flesch: 48.0 cache: ./cache/cord-353392-rqeultbq.txt txt: ./txt/cord-353392-rqeultbq.txt summary: Abstract The beginning of the novel SARS-CoV-2 human coronavirus in Wuhan, China, has triggered a worldwide respiratory disease outbreak (COVID-19). The third outbreak of severe illness caused by the novel SARS-CoV-2 coronavirus (COVID-19) that emerged in the Wuhan city, China, is pandemic and spread to more than 200 countries [5, 6, 7] . Based on the previous studies and reports in treating other coronaviruses such as SARS and MERS, the early administration of convalescent plasma from patients that contains raised antibodies can possibly reduce the spreading of infection and mortality [19, 20, 21, 22] . reported that the convalescent plasma transfusion may be beneficial in the treatment of critically ill patients with SARS-CoV-2 infections. After getting approval from the ethical committee, Shenzhen, Third People''s Hospital, they administrated convalescent plasma containing neutralizing antibodies to 5 critically ill patients with SARS-CoV-2. abstract: Abstract The beginning of the novel SARS-CoV-2 human coronavirus in Wuhan, China, has triggered a worldwide respiratory disease outbreak (COVID-19). By April 07, 2020, SARS-CoV-2 has affected more than 1.36 million people worldwide and caused more than 75,900 deaths. To date, the anti-malaria drug hydroxychloroquine found to be a treatment option for SARS-CoV-2. In addition to supportive treatment, such as oxygen supply in moderate cases and extracorporeal membrane oxygenation in critically ill patients, unique medications for this condition are also under investigation. Here we reviewed the antibody therapy might be an immediate strategy for emergency prophylaxis and SARS-CoV-2 therapy. url: https://doi.org/10.1016/j.nmni.2020.100682 doi: 10.1016/j.nmni.2020.100682 id: cord-329710-vqorb6j7 author: Kumar, Krishna title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 words: 2477.0 sentences: 147.0 pages: flesch: 49.0 cache: ./cache/cord-329710-vqorb6j7.txt txt: ./txt/cord-329710-vqorb6j7.txt summary: We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. abstract: [Image: see text] Discovery and development of COVID-19 prophylactics and treatments remains a global imperative. This perspective provides an overview of important molecular pathways involved in the viral life cycle of SARS-CoV-2, the infectious agent of COVID-19. We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. By discussing the current inventory of viral inhibitors, we identify molecular scaffolds that may be improved by medicinal chemistry efforts for effective therapeutics to treat current and future coronavirus-caused diseases. url: https://doi.org/10.1021/acsmedchemlett.0c00254 doi: 10.1021/acsmedchemlett.0c00254 id: cord-275565-xerr4vki author: Kumar, Manish title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date: 2020-09-15 words: 3456.0 sentences: 230.0 pages: flesch: 58.0 cache: ./cache/cord-275565-xerr4vki.txt txt: ./txt/cord-275565-xerr4vki.txt summary: For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. Thus, there still remains questions pertaining to: i) capability of conventional WWTPs to reduce the abundance of SARS-CoV-2 RNA, ii) better understanding of the protocol, virus J o u r n a l P r e -p r o o f Journal Pre-proof precipitation through PEG and filtration which one is better methods for concentrating the samples before RNA isolation. Appraising the genetic loading reduction through Upflow Anaerobic Sludge Blanket (UASB) systems, and iii) Comparing the performances between PEG and filtration as virus concentration methods in terms of SARS-CoV-2 RNA sensitivity and inhibition removal. abstract: For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. The objectives were achieved through tracking of SARS-CoV-2 genetic loadings i.e. ORF1ab, N and S protein genes on 8th and 27th May 2020 along the wastewater treatment plant (106 million liters per day) equipped with UASB system in Ahmedabad, India. PEG method performed better in removing materials inhibiting RT-qPCR for SARS-CoV-2 gene detection from the samples, as evident from constant and lower CT values of control (MS2). Using the PEG method, we found a reduction >1.3 log10 in SARS-CoV-2 RNA abundance during UASB treatment, and the RNA was not detected at all in the final effluent. The study implies that i) conventional wastewater treatment systems is effective in SARS-CoV-2 RNA removal, and ii) UASB system significantly reduces SARS-CoV-2 genetic loadings. Finally, PEG method is recommended for better sensitivity and inhibition removal during SARS-CoV-2 RNA quantification in wastewater. url: https://api.elsevier.com/content/article/pii/S0048969720358587 doi: 10.1016/j.scitotenv.2020.142329 id: cord-292045-pnid9dmq author: Kumar, Manish title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 words: 3037.0 sentences: 183.0 pages: flesch: 58.0 cache: ./cache/cord-292045-pnid9dmq.txt txt: ./txt/cord-292045-pnid9dmq.txt summary: While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. Consistency between abundance of SARS-CoV-2 genetic materials and number of confirmed cases was observed in the previous reports in Australia, France, Italy, Spain and Japan Further, referring to the limitations of the present study owing to lockdown scenario, we recommend that although based MPC analysis, the efficiency of RNA extraction and RT-PCR is considered high for all the wastewater samples collected for this study, the efficiency of PEG method could have been better established. The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 abstract: Abstract We made the first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India. Sampling was carried out on 8 and 27 May 2020 at the Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat that receives effluent from Civil Hospital treating COVID-19 patients. All three, i.e. ORF1ab, N and S genes of SARS-CoV-2, were found in the influent with no genes detected in effluent collected on 8 and 27 May 2020. Increase in SARS-CoV-2 genetic loading in the wastewater between 8 and 27 May 2020 samples concurred with corresponding increase in the number of active COVID-19 patients in the city. The number of gene copies was comparable to that reported in untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. However, temporal changes in SARS-CoV-2 RNA concentrations need to be substantiated further from the perspectives of daily and short-term changes of SARS-CoV-2 in wastewater through long-term monitoring. The study results SARS-CoV-2 will assist concerned authorities and policymakers to formulate and/or upgrade COVID-19 surveillance to have a more explicit picture of the pandemic curve. While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. url: https://doi.org/10.1016/j.scitotenv.2020.141326 doi: 10.1016/j.scitotenv.2020.141326 id: cord-296986-8fuj072z author: Kumar, Manish title: A chronicle of SARS-CoV-2: Part-I - Epidemiology, diagnosis, prognosis, transmission and treatment date: 2020-05-15 words: 4465.0 sentences: 308.0 pages: flesch: 52.0 cache: ./cache/cord-296986-8fuj072z.txt txt: ./txt/cord-296986-8fuj072z.txt summary: The review explicitly covers the aspects like genome and pedigree of SARS-CoV-2; epidemiology, prognosis, pathogenesis, symptoms and diagnosis of COVID-19 in order to catalog the right information on transmission route, and influence of environmental factors on virus transmissions, for the robust understanding of right strategical steps for proper COVID-19 management. We have explicitly highlighted several useful information and facts like: i) No established relationship between progression of SARS-CoV-2 with temperature, humidity and/or both, ii) The underlying mechanism of SARS-CoV-2 is not fully understood, iii) Respiratory droplet size determines drop and airborne-based transmission, iv) Prognosis of COVID-19 can be done by its effects on various body organs, v) Infection can be stopped by restricting the binding of S protein and AE2, vi) Hydroxychloroquine is believed to be better than chloroquine for COVID-19, vii) Ivermectin with Vero-hSLAM cells is able to reduce infection by ~5000 time within 2 days, and viii) Nafamostat mesylate can inhibit SARS-CoV-2 S protein-initiated membrane fusion. Outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): increased transmission beyond China-fourth update abstract: Abstract In order to benefit the public, community workers and scientific community, we hereby present a chronicle of SARS-CoV-2 that leads to the unseen precedent of social distancing and lockdown owing to coronavirus disease (COVID-19). Information on this life-threatening pandemic of COVID-19 is sparse and discrete; and the urgency is such that the dissemination of information is increasing with numerous daily publications on the topic. Therefore, we developed a comprehensive review on various aspects of SARS-CoV-2 and COVID-19. We scientifically compiled published research, news, and reports from various sources to comprehend and summarize the information and findings on Coronaviruses. The review explicitly covers the aspects like genome and pedigree of SARS-CoV-2; epidemiology, prognosis, pathogenesis, symptoms and diagnosis of COVID-19 in order to catalog the right information on transmission route, and influence of environmental factors on virus transmissions, for the robust understanding of right strategical steps for proper COVID-19 management. We have explicitly highlighted several useful information and facts like: i) No established relationship between progression of SARS-CoV-2 with temperature, humidity and/or both, ii) The underlying mechanism of SARS-CoV-2 is not fully understood, iii) Respiratory droplet size determines drop and airborne-based transmission, iv) Prognosis of COVID-19 can be done by its effects on various body organs, v) Infection can be stopped by restricting the binding of S protein and AE2, vi) Hydroxychloroquine is believed to be better than chloroquine for COVID-19, vii) Ivermectin with Vero-hSLAM cells is able to reduce infection by ~5000 time within 2 days, and viii) Nafamostat mesylate can inhibit SARS-CoV-2 S protein-initiated membrane fusion. We have also suggested future research perspectives, challenges and scope. url: https://www.sciencedirect.com/science/article/pii/S0048969720327959?v=s5 doi: 10.1016/j.scitotenv.2020.139278 id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 words: 6613.0 sentences: 346.0 pages: flesch: 44.0 cache: ./cache/cord-320935-3n157yl4.txt txt: ./txt/cord-320935-3n157yl4.txt summary: This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. abstract: Prevalence of SARS-CoV-2 in the aquatic environment pertaining to the COVID-19 pandemic has been a global concern. Though SARS-CoV-2 is known as a respiratory virus, its detection in faecal matter and wastewater demonstrates its enteric involvement resulting in vulnerable aquatic environment. Here, we provide the latest updates on wastewater-based epidemiology, which is gaining interest in the current situation as a unique tool of surveillance and monitoring of the disease. Transport pathways with its migration through wastewater to surface and subsurface waters, probability of infectivity and ways of inactivation of SARS-CoV-2 are discussed in detail. Epidemiological models, especially compartmental projections, have been explained with an emphasis on its limitation and the assumptions on which the future predictions of disease propagation are based. Besides, this review covers various predictive models to track and project disease spread in the future and gives an insight into the probability of a future outbreak of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32953402/ doi: 10.1007/s40726-020-00161-5 id: cord-252389-xrdbmosj author: Kumar, Mukesh title: Neurological manifestations and comorbidity associated with COVID-19: an overview date: 2020-10-14 words: 5447.0 sentences: 265.0 pages: flesch: 41.0 cache: ./cache/cord-252389-xrdbmosj.txt txt: ./txt/cord-252389-xrdbmosj.txt summary: In this article, we have reviewed the neurological characteristic features of COVID-19 patients, latent neurotropic mechanisms of SARS-CoV-2 involvement in the comorbidity associated with CNS disorders, and neurological manifestations associated with COVID-19. Therefore, exploring the neurologic manifestations associated with COVID-19 is urgently required for better understanding the SARS-CoV-2 brain infections, inhibiting the additional spread and treating patients affected by this pandemic. The neuronal cells infected with virus, immune systems (microphase, T cells, and monocytes) triggered, and inflammatory system activated leads to cytokine storm, oxidative stress, and associated neurological manifestations neuroinvasiveness of SARS-CoV-2 [11, 35] . In a recent review [51] , authors have categorized the reported neurological findings related to COVID-19 into three categories: a) Central (headache, dizziness, impaired consciousness, acute cerebrovascular disease, ataxia, seizures, and special senses) b) Peripheral (hypogeusia, hyposmia) c) Musculoskeletal (ischemic or hemorrhagic) Apart from the above, increasing evidence indicated that coronaviruses may invade the CNS, causing neurological disorders. abstract: First in 2002, severe acute respiratory syndrome coronavirus (SARS-CoV), second in 2012, Middle East respiratory syndrome coronavirus (MERS-CoV), and now the third in the December 2019, emergence of tremendously pathogenic and large-scale epidemic novel coronavirus (SARS-CoV-2) has brought the worst conditions into the human inhabitants of the twenty-first century. The SARS-CoV-2 uses the resembling receptor, angiotensin-converting enzyme 2 (ACE2) as that for SARS-CoV, and mainly feasts through the respiratory tract. The ACE2 receptor appearances have been also detected upon glial cells and neurons, which makes them a potential target of SARS-CoV-2 disease (COVID-19). Consequently, cells expressing ACE2, apart from lung and cardiovascular tissue, neurons and glial cells may act as targets and are thus vulnerable to SARS-CoV-2 systemic infection as well as its central nervous system (CNS) comorbidities. Investigation of the neurological manifestations of COVID-19 is a step towards better understanding the SARS-CoV-2 infections, inhibiting the additional spread and treating patients affected by this pandemic. In this concern, more clinical examinations for CNS involvement of SARS-CoV-2 are warranted. In this article, we have reviewed the neurological characteristic features of COVID-19 patients, latent neurotropic mechanisms of SARS-CoV-2 involvement in the comorbidity associated with CNS disorders, and neurological manifestations associated with COVID-19. Therefore, in the perspective of COVID-19 pandemic, clinicians and healthcare workers should be aware of a wide spectrum of neurological manifestations associated with COVID-19 along with their signs and symptoms for initial diagnosis and isolation of the patients. url: https://doi.org/10.1007/s10072-020-04823-6 doi: 10.1007/s10072-020-04823-6 id: cord-324166-6ydn2bvy author: Kumar, Neeraj title: Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis date: 2020-08-20 words: 5482.0 sentences: 284.0 pages: flesch: 45.0 cache: ./cache/cord-324166-6ydn2bvy.txt txt: ./txt/cord-324166-6ydn2bvy.txt summary: We found that Noscapine-Hydroxychloroquine (Nos-Hcq) conjugate has strong binding affinity for the main protease (Mpro) of SARS-CoV-2, which performs key biological function in virus infection and progression. Also, dynamical residue cross-correlation map with principal component analysis depicted the stable binding of Nos-Hcq conjugate to Mpro domains with optimal secondary structure statistics of complex dynamics. Similar binding sites were employed for performing the molecular docking of the noscapine conjugations with the target Mpro of coronavirus using the Hex 8.0 and SwissDock servers. With these significant results, it can be attributed that Nos-Hcq conjugate has a high potential to bind the target Mpro enzyme and further can be used as effective therapeutics for SARS-CoV-2. We report the efficient combinatorial therapy by conjugating the noscapine (antitussive drug) with potential hydroxychloroquine (Nos-Hcq) against the SARS-CoV-2, through the computational assays with insights into the experimental results. abstract: Coronavirus pandemic has caused a vast number of deaths worldwide. Thus creating an urgent need to develop effective counteragents against novel coronavirus disease (COVID-19). Many antiviral drugs have been repurposed for treatment but implicated minimal recovery, which further advanced the need for clearer insights and innovation to derive effective therapeutics. Strategically, Noscapine, an approved antitussive drug with positive effects on lung linings may show favorable outcomes synergistically with antiviral drugs in trials. Hence, we have theoretically examined the combinatorial drug therapy by culminating the existing experimental results with in silico analyses. We employed the antitussive noscapine in conjugation with antiviral drugs (Chloroquine, Umifenovir, Hydroxychloroquine, Favlplravir and Galidesivir). We found that Noscapine-Hydroxychloroquine (Nos-Hcq) conjugate has strong binding affinity for the main protease (Mpro) of SARS-CoV-2, which performs key biological function in virus infection and progression. Nos-Hcq was analyzed through molecular dynamics simulation. The MD simulation for 100 ns affirmed the stable binding of conjugation unprecedentedly through RMSD and radius of gyration plots along with critical reaction coordinate binding free energy profile. Also, dynamical residue cross-correlation map with principal component analysis depicted the stable binding of Nos-Hcq conjugate to Mpro domains with optimal secondary structure statistics of complex dynamics. Also, we reveal the drugs with stable binding to major domains of Mpro can significantly improve the work profile of reaction coordinates, drug accession and inhibitory regulation of Mpro. The designed combinatorial therapy paves way for further prioritized in vitro and in vivo investigations for drug with robust binding against Mpro of SARS-CoV-2. url: https://doi.org/10.1080/07391102.2020.1808072 doi: 10.1080/07391102.2020.1808072 id: cord-265418-yqe9vdj1 author: Kumar, Nilesh title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date: 2020-04-11 words: 5288.0 sentences: 363.0 pages: flesch: 54.0 cache: ./cache/cord-265418-yqe9vdj1.txt txt: ./txt/cord-265418-yqe9vdj1.txt summary: Integrated interactome-transcriptome analysis to generate Calu-3-specific humanIt is likely that the outcome of SARS-CoV-2 infection can largely be determined by the interaction patterns of host proteins and viral factors. By integrating this Calu-3 co-expression network with SIPs-derived PPI subnetwork, we generated Calu-3-specific human-SARS-CoV-2 Interactome (CSI) that contains 214 SIPs interacting with their first and second neighbors make a network of 4,123 nodes and 14,650 edges (Fig. 1c, Supplementary Data 1) . We showed that CSI follows a power law degree distribution with a few nodes harboring increased connectivity, and thus exhibits properties of a scale-free network (r 2 = 0.91; (Fig. 1d , Supplementary Data 1), similar to the previously generated other human-viral interactomes 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . In conclusion, we generated a human-SARS-CoV-2 interactome, integrated virusrelated transcriptome to interactome, discover COVID-19 pertinent structural and functional modules, identify high-value viral targets, and perform dynamic transcriptional modeling. abstract: COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrated multiomics data pertaining to lung epithelial cells-specific coexpression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity. url: https://doi.org/10.1101/2020.04.09.033910 doi: 10.1101/2020.04.09.033910 id: cord-336604-2auhkxce author: Kumar, Pramod title: Integrated genomic view of SARS-CoV-2 in India date: 2020-08-03 words: 4927.0 sentences: 324.0 pages: flesch: 58.0 cache: ./cache/cord-336604-2auhkxce.txt txt: ./txt/cord-336604-2auhkxce.txt summary: Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). A total of 127 laboratory-confirmed cases of COVID-19 from targeted testing and available samples at NCDC which represent different geographic locations or states and travel history from different countries during the early phase of the outbreak (Table 1 and Extended data, Supplementary figure S1 [Kumar et al., 2020b] ). We also compared SARS-CoV-2 mutation sites with other six coronavirus sequences (Extended data, Supplementary figure S5b [Kumar et al., 2020b] ). abstract: Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic. url: https://doi.org/10.12688/wellcomeopenres.16119.1 doi: 10.12688/wellcomeopenres.16119.1 id: cord-339329-8yvre7qc author: Kumar, Prashant title: Could fighting airborne transmission be the next line of defence against COVID-19 spread? date: 2020-05-23 words: 1011.0 sentences: 49.0 pages: flesch: 53.0 cache: ./cache/cord-339329-8yvre7qc.txt txt: ./txt/cord-339329-8yvre7qc.txt summary: Abstract The World Health Organization declared the infectious spread of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) an epidemic during its initial outbreak in Wuhan (China) and has since declared it a pandemic and, more recently, an endemic infection that may remain in our communities. While these measures have worked well under lockdowns, the potential of airborne transmission of COVID-19 under the eased restrictions has not been considered important enough. Social distancing, self-isolation, handwashing, provision of hand sanitisers in public buildings, frequent disinfection of high-touch surfaces and the use of face masks have been recommended as effective mitigation measures against the spread of COVID-19 by the SARS-CoV-2 virus. Another study has reported a high concentration of viral RNA peaks in sub-and super-micrometre particle ranges and highlighted the potential transmission of SARS-CoV-2 via aerosols inside two Wuhan hospitals [3] . This work highlighted the probability of a much higher COVID-19 infection rate in closed environments with re-circulated air, and substantiates our below point regarding airborne transmission. abstract: Abstract The World Health Organization declared the infectious spread of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) an epidemic during its initial outbreak in Wuhan (China) and has since declared it a pandemic and, more recently, an endemic infection that may remain in our communities. A vaccine for COVID-19 is expected to take several months, meaning that the spread may continue in future, in the absence of the most effective measures of social distancing and self-isolation. While these measures have worked well under lockdowns, the potential of airborne transmission of COVID-19 under the eased restrictions has not been considered important enough. We discuss the need to acknowledge the airborne spread of COVID-19 inside built spaces under eased movement restrictions and the potential steps that can be taken to control it. url: https://www.sciencedirect.com/science/article/pii/S2590252020300143?v=s5 doi: 10.1016/j.cacint.2020.100033 id: cord-311214-eqwxkwqa author: Kumar, Roshan title: Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date: 2020-04-16 words: 2724.0 sentences: 184.0 pages: flesch: 60.0 cache: ./cache/cord-311214-eqwxkwqa.txt txt: ./txt/cord-311214-eqwxkwqa.txt summary: Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-β, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. A manually annotated reference database was generated using the Genbank 128 file of Severe acute respiratory syndrome coronavirus 2 isolate-SARS-CoV-129 2/SH01/human/2020/CHN (Accession number: MT121215) and open reading frames (ORFs) 130 were predicted against the formatted database using prokka (-gcode 1) [22] . All these isolates 189 were found to harbor 9 open reading frames coding for ORF1a (13218 bp) and ORF1b (7788 190 bp) polyproteins, surface glycoprotein or S-protein (3822 bp), ORF3a protein (828 bp Our analysis revealed that strains of human infecting SARS-CoV-2 are novel and highly 201 identical (>99.9%). In this study, the analysis was 358 performed on the genomes of the novel SARS-CoV-2 isolates recently reported from different 359 countries to understand viral pathogenesis. abstract: The Coronavirus Disease-2019 (COVID-19) that started in Wuhan, China in December 2019 has spread worldwide emerging as a global pandemic. The severe respiratory pneumonia caused by the novel SARS-CoV-2 has so far claimed more than 60,000 lives and has impacted human lives worldwide. However, as the novel SARS-CoV-2 displays high transmission rates, their underlying genomic severity is required to be fully understood. We studied the complete genomes of 95 SARS-CoV-2 strains from different geographical regions worldwide to uncover the pattern of the spread of the virus. We show that there is no direct transmission pattern of the virus among neighboring countries suggesting that the outbreak is a result of travel of infected humans to different countries. We revealed unique single nucleotide polymorphisms (SNPs) in nsp13-16 (ORF1b polyprotein) and S-Protein within 10 viral isolates from the USA. These viral proteins are involved in RNA replication, indicating highly evolved viral strains circulating in the population of USA than other countries. Furthermore, we found an amino acid addition in nsp16 (mRNA cap-1 methyltransferase) of the USA isolate (MT188341) leading to shift in amino acid frame from position 2540 onwards. Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-β, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. Thus, the replicative machinery of SARS-CoV-2 is fast evolving to evade host challenges which need to be considered for developing effective treatment strategies. url: https://doi.org/10.1101/2020.03.25.006213 doi: 10.1101/2020.03.25.006213 id: cord-262550-oip5m9br author: Kumar, S. Udhaya title: The Rise and Impact of COVID-19 in India date: 2020-05-22 words: 2866.0 sentences: 179.0 pages: flesch: 58.0 cache: ./cache/cord-262550-oip5m9br.txt txt: ./txt/cord-262550-oip5m9br.txt summary: The coronavirus disease (COVID-19) pandemic, which originated in the city of Wuhan, China, has quickly spread to various countries, with many cases having been reported worldwide. The Ministry of Health and Family Welfare of India has raised awareness about the recent outbreak and has taken necessary actions to control the spread of COVID-19. The recent outbreak of COVID-19 in several countries is similar to the previous outbreaks of SARS and Middle East respiratory syndrome (MERS) that emerged in 2003 and 2012 in China and Saudi Arabia, respectively (8) (9) (10) . A recent study reported that affected family members had not visit the Wuhan market in China, suggesting that SARS-CoV-2 may spread without manifesting symptoms (21) . The Ministry of Health and Family Welfare (MOHFW), India, has raised awareness about the recent outbreak and taken necessary action to control COVID-19. The impacts on health, society, and economy of SARS and H7N9 outbreaks in China: a case comparison study abstract: The coronavirus disease (COVID-19) pandemic, which originated in the city of Wuhan, China, has quickly spread to various countries, with many cases having been reported worldwide. As of May 8th, 2020, in India, 56,342 positive cases have been reported. India, with a population of more than 1.34 billion—the second largest population in the world—will have difficulty in controlling the transmission of severe acute respiratory syndrome coronavirus 2 among its population. Multiple strategies would be highly necessary to handle the current outbreak; these include computational modeling, statistical tools, and quantitative analyses to control the spread as well as the rapid development of a new treatment. The Ministry of Health and Family Welfare of India has raised awareness about the recent outbreak and has taken necessary actions to control the spread of COVID-19. The central and state governments are taking several measures and formulating several wartime protocols to achieve this goal. Moreover, the Indian government implemented a 55-days lockdown throughout the country that started on March 25th, 2020, to reduce the transmission of the virus. This outbreak is inextricably linked to the economy of the nation, as it has dramatically impeded industrial sectors because people worldwide are currently cautious about engaging in business in the affected regions. url: https://www.ncbi.nlm.nih.gov/pubmed/32574338/ doi: 10.3389/fmed.2020.00250 id: cord-296917-yk574m99 author: Kumar, Sathish title: Aerosol‐mediated transmission of SARS‐Cov‐2 or COVID‐19 in the cardiac surgical operating room date: 2020-07-11 words: 738.0 sentences: 44.0 pages: flesch: 40.0 cache: ./cache/cord-296917-yk574m99.txt txt: ./txt/cord-296917-yk574m99.txt summary: The coronavirus disease-2019 (COVID-19) virus spreads predominantly through droplet and aerosol routes and blood-borne infection is not considered a major source of transmission. As a result, while contact is necessary for droplet infections and thereby handwashing and gloves are highly effective against contact transmission, viral particles transmitted though aerosol is absorbed via the respiratory mucosa and potentially across the conjunctivae, other measures are required to prevent transmission. However, because of the smaller size, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 as it is popularly known as, can spread across larger areas and has been shown to remain viable in aerosols even at 3 hours. 7 The highest viral load of the virus causing COVID-19 is in sputum and upper airway secretions and endotracheal intubation is the commonest and most relevant aerosol-generating procedure in cardiac surgery. Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review abstract: nan url: https://doi.org/10.1111/jocs.14728 doi: 10.1111/jocs.14728 id: cord-279180-xad53zht author: Kumaravel, Santhosh Kumar title: Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies date: 2020-08-17 words: 11396.0 sentences: 653.0 pages: flesch: 54.0 cache: ./cache/cord-279180-xad53zht.txt txt: ./txt/cord-279180-xad53zht.txt summary: The COVID-19 is a respiratory disease that spreads at a maximum rate through droplets of the infected people through the air (World Health Organisation 2020a). • In addition, the incorporation of lockdown with other treatment and prevention measures such as school closures, travel restrictions, and social distancing has had a greater impact on spread prevention, cases requiring critical care beds, and deaths compared with quarantine alone. Machine learning has the potential to support clinicians'' work processing and management of large amounts of medical data contained in electronic health records and used in clinical applications which includes recognizing high-risk patients in need of ICU, the identification of early signs of lung cancer, determination of patient''s respiratory status from X-rays in the chest, such deep learning approaches employ neural networks to predict the input-output data relationship. abstract: The present outbreak of the novel coronavirus SARS‐CoV‐2, epicentered in China in December 2019, has spread to many other countries. The entire humanity has a vital responsibility to tackle this pandemic and the technologies are being helpful to them to a greater extent. The purpose of the work is to precisely bring scientific and general awareness to the people all around the world who are currently fighting the war against COVID-19. It's visible that the number of people infected is increasing day by day and the medical community is tirelessly working to maintain the situation under control. Other than the negative effects caused by COVID-19, it is also equally important for the public to understand some of the positive impacts it has directly or indirectly given to society. This work emphasizes the various impacts that are created on society as well as the environment. As a special additive, some important key areas are highlighted namely, how the modernized technologies are aiding the people during the period of social distancing. Some effective technological implications carried out by both information technology and educational institutions are highlighted. There are also several steps taken by the state government and central government in each country in adopting the complete lockdown rule. These steps are taken primarily to prevent the people from COVID-19 impact. Moreover, the teachings we need to learn from the quarantine situation created to prevent further spread of this global pandemic is discussed in brief and the importance of carrying them to the future. Finally, the paper also elucidates the general preventive measures that have to be taken to prevent this deadly coronavirus, and the role of technology in this pandemic situation has also been discussed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02382-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32821645/ doi: 10.1007/s13205-020-02382-3 id: cord-277841-7sp8ftbc author: Kumari, Pratibha title: Potential diagnostics and therapeutic approaches in COVID-19 date: 2020-08-12 words: 4873.0 sentences: 279.0 pages: flesch: 45.0 cache: ./cache/cord-277841-7sp8ftbc.txt txt: ./txt/cord-277841-7sp8ftbc.txt summary: Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. COVID-19 is a contagious disease, caused by a novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2). In this article, we evaluated literature for reports informing various diagnostic methods, potential antiviral chemical therapeutics, and effective treatment strategies towards clinical management of COVID-19 patients. Molecular diagnostic methods target to detect either specific regions of the viral genome or RNA-dependent RNA polymerase (RdRP) and/or structural proteins of SARS-CoV-2 (Table 1) . Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2. Table 2: Primers and probes for targeting SARS-Cov-2 genes in an RT-PCR test for COVID-19 diagnosis. abstract: Abstract The most important aspect of controlling COVID-19 is its timely diagnosis. Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. This review highlights the underlying mechanisms, advancements, and clinical limitations for each of the diagnostic techniques authorized by the Food and Drug Administration (USA). Significance of diagnosis triaging, information on specimen collection, safety considerations while handling, transport, and storage of samples have been highlighted to make medical and research community more informed so that better clinical strategies are developed. We have discussed here the clinical manifestations and hospital outcomes along with the underlying mechanisms for several drugs administered to COVID-19 prophylaxis. In addition to favourable clinical outcomes, the challenges, and the future directions of management of COVOD-19 are highlighted. Having a comprehensive knowledge of the diagnostic approaches of SARS-CoV-2, and its pathogenesis will be of great value in designing a long-term strategy to tackle COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0009898120303958?v=s5 doi: 10.1016/j.cca.2020.08.013 id: cord-294696-pm6pfeeb author: Kunz, Y. title: Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag date: 2020-10-13 words: 3216.0 sentences: 392.0 pages: flesch: 43.0 cache: ./cache/cord-294696-pm6pfeeb.txt txt: ./txt/cord-294696-pm6pfeeb.txt summary: Ausgelöst wird diese Infektionskrankheit durch das Virus SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), das zur Familie der β-Coronaviridiae bzw. Das SARS-CoV-2 wird im Wesentlichen via Tröpfcheninfektion -und somit über Aerosole -von symptomatischen COVID-19-Patienten übertragen. Es wurde eine Literatursuche in PubMed, bioRxiv und medRxiv sowie den Datenbanken der WHO und des CDC über SARS-CoV-2 und chirurgisches Prozedere bei infizierten Patienten durchgeführt. Das Prostatagewebe scheint demgegenüber nicht von SARS-CoV-2 befallen zu werden, zumindest konnte eine chinesische Gruppe in einer kleinen Studie keine Virus-RNA im Prostatasekret nachweisen [29] . Da basierend auf der oben angesprochenen Studienlage eine SARS-CoV-2-Übertragung mittels Urin denkbar ist, muss bei COVID-19-Patienten und unklaren Verdachtsfällen zusätzlich zur gängigen Schutzkleidung im Operationssaal auf FFP-2-Masken und Schutzbrillen zurückgegriffen werden. Da Aerosole nicht nur während der Operation, sondern bereits zuvor im Rahmen einer OP-Einleitung entstehen können, sollte laut aktuellen Empfehlungen unbedingt auf FFP-2-Masken im Falle eines zu behandelnden Patienten mit Verdacht auf oder einer bestätigten COVID-19-Infektion zurückgegriffen werden. abstract: BACKGROUND: COVID-19 poses a challenge to healthcare systems worldwide. Due to the increasing number of cases, surgeons in urology have also been confronted with SARS-CoV‑2 infections. Thus, there is an urgent need for clinical guidance and recommendations. AIM: Our work aims to create a widespread assessment of a possible risk for infection with SARS-CoV‑2 during surgical procedures. Based on current data and current national and international guidelines, we try to assess the risk of infection when handling human tissue and the necessary hygienic measures that are needed. Finally, recommendations for daily urologic work are derived and explained. MATERIALS AND METHODS: The current literature in PubMed, bioRxiv and medRxiv and data available from the WHO and Robert-Koch-Institut on SARS-CoV‑2 and surgical procedures in (potentially) infected patients are reviewed. The endpoint of our research was 21 April 2020. CONCLUSION: Based on our research, general and specific recommendations for clinical urologic praxis can be derived. Although it remains unclear whether SARS-CoV‑2 is transmitted via the aerosols produced, current PPE in operating rooms probably does not offer sufficient protection during surgical interventions during the SARS-CoV‑2 pandemic. Use of FFP‑2 masks, safety goggles and full-body protective suits is crucial. To contain viral spread on surfaces and personnel, complex filter systems (HEPA) should be used as well as closed suction devices during surgery. Combined with consequent disinfection of surfaces and behavioral measures, a safe environment for healthcare workers in urology can be created. Thus, according to current knowledge, we believe that emergency and urgent surgical procedures are not contraindicated, provided that appropriate precautionary safety measures are followed. url: https://www.ncbi.nlm.nih.gov/pubmed/33048213/ doi: 10.1007/s00120-020-01264-z id: cord-343808-uqhiyj56 author: Kuo, Hsiao-I. title: Assessing impacts of SARS and Avian Flu on international tourism demand to Asia date: 2008-01-07 words: 7254.0 sentences: 328.0 pages: flesch: 53.0 cache: ./cache/cord-343808-uqhiyj56.txt txt: ./txt/cord-343808-uqhiyj56.txt summary: In order to estimate the impacts of epidemic diseases including SARS and Avian Flu on tourism demand in most Asian affected countries, the methodology of the ARMAX model is adopted in our study. The monthly data for international tourist arrivals are collected from statistical datasets for each country, and the probable numbers of SARS-infected patients and the confirmed human cases of Avian Flu are obtained from the World Health Organization (WHO, 2006 Furthermore, the ARMA and ARMAX models are estimated by using nonlinear least squares estimators, while dynamic panel models are implemented by using the panel GMM technique. Table 3 presents the results of the ADF tests for the three series, including tourism demand, namely, international tourist arrivals, the probable SARS-infected patients and the number of confirmed cases of Avian Flu. The ADF test statistics are compared with the critical values from the nonstandard Dickey-Fuller distribution at the 5% significance level. abstract: The purpose of this paper is to investigate the impacts of infectious diseases including Avian Flu and severe acute respiratory syndrome (hereafter SARS) on international tourist arrivals in Asian countries using both single datasets and panel data procedures. An autoregressive moving average model together with an exogenous variables (ARMAX) model are used to estimate the effects of these diseases in each SARS- and Avian Flu-infected country, while a dynamic panel model is adopted to estimate the overall impact on the region of these two diseases. The empirical results from both approaches are consistent and indicate that the numbers of affected cases have a significant impact on SARS-affected countries but not on Avian Flu-affected countries. However, since the potential damage arising from the Avian Flu and subsequent pandemic influenza is much greater than that resulting from the SARS, the need to take the necessary precautions in the event of an outbreak of Avian Flu and pandemic influenza warrants further attention and action. Therefore, the empirical findings of this study could add to the knowledge regarding the relationship between tourism and crisis management, especially in so far as the management of transmissible diseases is concerned. url: https://www.ncbi.nlm.nih.gov/pubmed/32287724/ doi: 10.1016/j.tourman.2007.10.006 id: cord-340240-dk48pdqa author: Kuo, Tsun-Yung title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date: 2020-08-11 words: 1240.0 sentences: 91.0 pages: flesch: 53.0 cache: ./cache/cord-340240-dk48pdqa.txt txt: ./txt/cord-340240-dk48pdqa.txt summary: title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 S-2P was combined with various adjuvants, including CpG 1018, and administered to mice to test its effectiveness in eliciting anti-SARS-CoV-2 neutralizing antibodies. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of spike-specific antibodies in sera of immunized mice. In this study, we present data from preclinical studies aimed at developing a COVID-19 candidate subunit 84 vaccine using CHO cell-expressed SARS-CoV-2 S-2P antigen combined with various adjuvants. We have 85 shown that S-2P, when mixed with CpG 1018 and aluminum hydroxide adjuvants, was most effective in 86 inducing antibodies that neutralized pseudovirus and wild-type live virus while minimizing Th2-biased 87 responses with no vaccine-related adverse effects. Previous studies showed that the lung-infiltrating eosinophils were a common 308 indication of Th2-biased immune responses seen in animal models testing SARS-CoV vaccine candidates [22] . abstract: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 is a worldwide health emergency. The immense damage done to public health and economies has prompted a global race for cures and vaccines. In developing a COVID-19 vaccine, we applied technology previously used for MERS-CoV to produce a prefusion-stabilized SARS-CoV-2 spike protein by adding two proline substitutions at the top of the central helix (S-2P). To enhance immunogenicity and mitigate the potential vaccine-induced immunopathology, CpG 1018, a Th1-biasing synthetic toll-like receptor 9 (TLR9) agonist was selected as an adjuvant candidate. S-2P was combined with various adjuvants, including CpG 1018, and administered to mice to test its effectiveness in eliciting anti-SARS-CoV-2 neutralizing antibodies. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of spike-specific antibodies in sera of immunized mice. The neutralizing abilities in pseudotyped lentivirus reporter or live wild-type SARS-CoV-2 were measured with reciprocal inhibiting dilution (ID50) titers of 5120 and 2560, respectively. In addition, the antibodies elicited were able to cross-neutralize pseudovirus containing the spike protein of the D614G variant, indicating the potential for broad spectrum protection. A marked Th-1 dominant response was noted from cytokines secreted by splenocytes of mice immunized with CpG 1018 and alum. No vaccine-related serious adverse effects were found in the dose-ranging study in rats administered single- or two-dose regimens with up to 50 μg of S-2P combined with CpG 1018 alone or CpG 1018 with alum. These data support continued development of CHO-derived S-2P formulated with CpG 1018/alum as a candidate vaccine to prevent COVID-19 disease. url: https://doi.org/10.1101/2020.08.11.245704 doi: 10.1101/2020.08.11.245704 id: cord-354685-oggtmum4 author: Kurup, Drishya title: Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2 date: 2020-10-16 words: 6509.0 sentences: 355.0 pages: flesch: 55.0 cache: ./cache/cord-354685-oggtmum4.txt txt: ./txt/cord-354685-oggtmum4.txt summary: This study reports that both a live and an inactivated rabies virus containing the SARS-CoV-2 spike S1 protein induces potent virus-neutralizing antibodies at much higher levels than seen in the sera of convalescent patients. To assess the correct confirmation of the chimeric S1 incorporated into CORAVAX, we first analyzed the binding of the recombinant human ACE-2 receptor-Fc chimera (human IgG) protein (Fig. 2a) and a SARS-COV-2 receptor binding domain (RBD) directed mouse monoclonal antibody (Fig. 2b) . After blocking, the membrane was incubated overnight with a human monoclonal 4C12 specific for the RABV glycoprotein (hybridoma kindly provided by Dr. Scott Dessain) or rabbit serum against the S1 subunit of SARS-CoV-2 Spike protein (Invitrogen, ThermoFisher Scientific, Cat# PA5-81798) at a dilution of 1:1000 in PBS containing 5% BSA. The cells were then stained for 2 h at RT with mouse polyclonal antiserum against the S1 subunit of SARS-CoV-2 Spike protein and a human monoclonal antibody 4C12 against RABV glycoprotein (2 µg/ ml). abstract: The recently emerged coronavirus SARS-CoV-2, the causative agent of COVID-19, is rapidly spreading in the world. The exponentially expanding threat of SARS-CoV-2 to global health highlights the urgent need for a vaccine. Herein we show the rapid development of a novel, highly efficient, and safe COVID-19 vaccine using a rabies virus-based vector that has proven to be an efficient vaccine against several emerging infectious diseases. This study reports that both a live and an inactivated rabies virus containing the SARS-CoV-2 spike S1 protein induces potent virus-neutralizing antibodies at much higher levels than seen in the sera of convalescent patients. In summary, the results provided here warrant further development of this safe and established vaccine platform against COVID-19. url: https://doi.org/10.1038/s41541-020-00248-6 doi: 10.1038/s41541-020-00248-6 id: cord-341543-gcnph9gf author: Kuryntseva, P. title: A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia date: 2020-09-23 words: 1831.0 sentences: 123.0 pages: flesch: 55.0 cache: ./cache/cord-341543-gcnph9gf.txt txt: ./txt/cord-341543-gcnph9gf.txt summary: The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of wastewater samples and their serial dilutions but the approach excludes usage of concentration techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. In the modelling experiment with the excreta of ten COVID-19 235 patients, it was demonstrated that the minimal rate of infected people in the community that can 236 be detected by this method is 10-2%. abstract: The number of registered cases of COVID-19 is increasing in the world, and some countries are reporting a second wave of the pandemic. Accurate and real time information about epidemiological situation is therefore urgently needed for managing decisions in the countries, regions and municipalities which are affected. Massive testing of viral presence in human saliva, a smear from the nose, nasopharynx and / or oropharynx, bronchial lavage water obtained by fibrobronchoscopy (bronchoalveolar lavage), as well as from (endo) tracheal, nasopharyngeal aspirate, sputum, biopsy or autopsy material of the lungs, whole blood, serum or antibodies presence in blood cannot give relevant information about the COVID-19 infection rate in the community since simultaneous testing of the whole community is not technically possible, the information obtained in testing of specific groups is retarded and, in addition, such testing is expensive. The alternative to mass testing of the population is the testing of wastewater that could contain SARS-CoV-2 particles originating from excreta. Such testing has several limitations connected with the particularities of the testing procedure. In the present study, a modified approach for detection of COVID-19 infection rate using wastewater analysis has been developed. The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of wastewater samples and their serial dilutions but the approach excludes usage of concentration techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. The minimum infection rate that can be detected using this approach is 0.01%. The approach developed was used to investigate wastewater from eleven sewage inspection chambers in the city of Kazan (Russia). It was demonstrated that the average infection rate of people using these sewers was over 0.4% in July 2020. url: https://doi.org/10.1101/2020.09.21.20197244 doi: 10.1101/2020.09.21.20197244 id: cord-293578-yu2i0u2h author: Kusadasi, Nuray title: A Pathophysiological Perspective on the SARS-CoV-2 Coagulopathy date: 2020-08-10 words: 3914.0 sentences: 259.0 pages: flesch: 38.0 cache: ./cache/cord-293578-yu2i0u2h.txt txt: ./txt/cord-293578-yu2i0u2h.txt summary: The potential role of plasma kallikrein in case of SARS-CoV-2 infection may be summarized as (1) the activation of FXII with the end-product thrombin (coagulation system) (2) the generation of bradykinin with subsequent vascular permeability and leakage (kallikrein-kinin system), (3) the activation of the renin-angiotensin system through conversion of renin from pre-renin leading to a pro-inflammatory state through increased angiotensin 1 receptor activation and (4) the activation of C5, in part through activation of C1 via FXII and in part through activation of C3 via plasmin (complement system). 54, 55 Since prekallikrein is seen as a potential regulator in the fibrin clot formation through FXII activation and is involved in the pathogenesis of thrombosis, there might be an important role for controlling the hypercoagulable state of the patients infected with SARS-CoV-2 as a therapeutic target. Taken together, all these mechanisms may contribute to the complex hypercoagulable state of the critically ill patients infected with SARS-CoV-2 having severe hypoxia and ongoing endothelial activation. abstract: Recent evidence is focusing on the presence of a hypercoagulable state with development of both venous and arterial thromboembolic complications in patients infected with SARS-CoV-2. The ongoing activation of coagulation related to the severity of the illness is further characterized by thrombotic microangiopathy and endotheliitis. These microangiopathic changes cannot be classified as classical disseminated intravascular coagulation (DIC). In this short review we describe the interaction between coagulation and inflammation with focus on the possible mechanisms that might be involved in SARS-CoV-2 infection associated coagulopathy in the critically ill. url: https://doi.org/10.1097/hs9.0000000000000457 doi: 10.1097/hs9.0000000000000457 id: cord-345689-5ns1onkw author: Kusters, Inca C. title: Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date: 2009-01-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The world was struck by surprise when a Severe Acute Respiratory Syndrome (SARS) epidemic started in 2003 in China. This disease had never been observed in man before; the SARS-Coronavirus causing the disease was unknown. With the uncertainty about the future impact of this epidemic, an important international collaboration started spontaneously sharing scientific knowledge and reagents. Resources became quickly available, and public and private efforts were undertaken to develop rapidly a vaccine. We will discuss here the importance of the international collaboration and the availability of funding. Moreover, we will review the most important and challenging steps during the industrial development of the SARS vaccine highlighting the difficulties in terms of safety working with such a highly pathogenic, unknown virus. We will emphasize the industrial perspectives on inactivation and decontamination experiments, the selection of the most promising vaccine candidate, the production process and the choice and use of animal models in such a pressing and difficult situation. Finally, we will briefly review the unique regulatory environment created during this period for the development of a SARS vaccine. url: https://www.sciencedirect.com/science/article/pii/B9780123694089000111 doi: 10.1016/b978-0-12-369408-9.00011-1 id: cord-263764-2ewz8ok4 author: Kutter, Jasmin S title: Transmission routes of respiratory viruses among humans date: 2018-01-17 words: 4392.0 sentences: 242.0 pages: flesch: 40.0 cache: ./cache/cord-263764-2ewz8ok4.txt txt: ./txt/cord-263764-2ewz8ok4.txt summary: We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . abstract: Respiratory tract infections can be caused by a wide variety of viruses. Airborne transmission via droplets and aerosols enables some of these viruses to spread efficiently among humans, causing outbreaks that are difficult to control. Many outbreaks have been investigated retrospectively to study the possible routes of inter-human virus transmission. The results of these studies are often inconclusive and at the same time data from controlled experiments is sparse. Therefore, fundamental knowledge on transmission routes that could be used to improve intervention strategies is still missing. We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. url: https://doi.org/10.1016/j.coviro.2018.01.001 doi: 10.1016/j.coviro.2018.01.001 id: cord-314937-jrxu65bl author: Kuwelker, K. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 words: 5868.0 sentences: 391.0 pages: flesch: 55.0 cache: ./cache/cord-314937-jrxu65bl.txt txt: ./txt/cord-314937-jrxu65bl.txt summary: The secondary attack rate of SARS-CoV-2 from index cases to household contacts reflects the natural spread of infection in immunologically naive populations with limited preventive measures to control transmission. Here, we estimated the secondary household attack rate of SARS-CoV-2 and identified the determinants of household transmission by measuring SARS-CoV-2-specific antibodies in household members of RT-PCR confirmed cases during the first month of the COVID-19 pandemic in Norway. Our study was specifically designed to assess household attack rates as measured by seropositivity in household members 6-8 weeks after onset of symptoms in the index case, with low prevalence of SARS-CoV-2 virus in the community. We calculated attack rates based on SARS-CoV-2-specific antibodies in household members, whereas the majority of previous studies have ascertained transmission based on RT-PCR, with estimates of 7·6% to 38% (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . abstract: Background: Household attack rates of SARS-CoV-2 ranging from 7% to 38% have been reported, using reverse transcription polymerase chain reaction (RT-PCR) of respiratory samples. Lower attack rates were described in children, but the importance of age in household transmission dynamics remains to be clarified. Methods: During the first month of the outbreak, we enrolled 112 households (291 participants) in a prospective case-ascertained study, collecting demographic and clinical data from index cases and household members. Sera were collected 6-8 weeks after index case symptom onset, to measure SARS-CoV-2-specific antibodies. Findings: The overall household attack rate was 45% assessed by seroconversion, and 47% when also including RT-PCR positives. Serology identified a significantly higher number of infected household members than RT-PCR. Attack rates were equally high in children (43%) and young adults (46%), but highest among household members aged [≥]60 years (72%). The attack rate was 16% in asymptomatic household members, and 42% in RT-PCR negative household members. Older adults generally had higher antibody titres than younger adults. The risk of household transmission was higher when the index case had fever or dyspnoea during acute illness but not associated with cough. Interpretation: Serological assays provide more accurate estimates of household secondary attack rate than RT-PCR, especially among children who have a lower RT-PCR positivity rate. Children are equally susceptible to infection as adults, but elderly show higher attack rates. Negative RT-PCR or lack of symptoms are not sufficient to rule out infection in household members. url: https://doi.org/10.1101/2020.11.02.20224485 doi: 10.1101/2020.11.02.20224485 id: cord-301946-erzh30mt author: Kwak-Kim, Joanne title: COVID-19 and immunomodulation treatment for women with reproductive failures date: 2020-06-12 words: 5604.0 sentences: 335.0 pages: flesch: 42.0 cache: ./cache/cord-301946-erzh30mt.txt txt: ./txt/cord-301946-erzh30mt.txt summary: With the Coronavirus Disease 2019 (COVID-19) pandemic, patient care has been significantly challenged not only for the COVID-19 cases but for the others, including pregnant women with a history of reproductive failures (RF), such as recurrent pregnancy losses (RPL), repeated implantation failures (RIF), with immune etiologies including autoimmune diseases, cellular immune dysfunction, and rheumatic conditions. SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus), which caused the SARS outbreak in 2003, infects macrophages and T cells (Perlman and Dandekar 2005) and induces various cytokines, such as type I IFN, TNF-α, IL-1, etc., and B cell-related antibodies (Prompetchara et al. With the currently available data, it is unlikely that the use of IVIg in patients with RFI will impact the chances of contracting the disease or negatively affect the clinical course in women with COVID-19 infection during pregnancy. abstract: COVID-19 pandemic is affecting various areas of health care, including human reproduction. Many women with reproductive failures, during the peri-implantation period and pregnancy, are on the immunotherapy using immune modulators and immunosuppressant due to underlying autoimmune diseases, cellular immune dysfunction, and rheumatic conditions. Many questions have been raised for women with immunotherapy during the COVID-19 pandemic, including infection susceptibility, how to manage women with an increased risk of and active COVID-19 infection. SARS-CoV-2 is a novel virus, and not enough information exists. Yet, we aim to review the data from previous coronavirus outbreaks and current COVID-19 and provide interim guidelines for immunotherapy in women with reproductive failures. url: https://www.ncbi.nlm.nih.gov/pubmed/32603991/ doi: 10.1016/j.jri.2020.103168 id: cord-284037-nj5jo1ev author: Kwee, Thomas C. title: Chest CT in COVID-19: What the Radiologist Needs to Know date: 2020-10-23 words: 7662.0 sentences: 363.0 pages: flesch: 41.0 cache: ./cache/cord-284037-nj5jo1ev.txt txt: ./txt/cord-284037-nj5jo1ev.txt summary: Chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available. According to the Fleischner Society consensus statement, chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available (59) . In cases of clinical worsening, chest imaging is advised to assess for COVID-19 progression or secondary cardiopulmonary complications such as acute respiratory distress syndrome (ARDS), PE, superimposed pneumonia, or heart failure that can potentially be secondary to COVID-19-induced cardiac injury (59) . abstract: Chest CT has a potential role in the diagnosis, detection of complications, and prognostication of coronavirus disease 2019 (COVID-19). Implementation of appropriate precautionary safety measures, chest CT protocol optimization, and a standardized reporting system based on the pulmonary findings in this disease will enhance the clinical utility of chest CT. However, chest CT examinations may lead to both false-negative and false-positive results. Furthermore, the added value of chest CT in diagnostic decision making is dependent on several dynamic variables, most notably available resources (real-time reverse transcription–polymerase chain reaction [RT-PCR] tests, personal protective equipment, CT scanners, hospital and radiology personnel availability, and isolation room capacity) and the prevalence of both COVID-19 and other diseases with overlapping manifestations at chest CT. Chest CT is valuable to detect both alternative diagnoses and complications of COVID-19 (acute respiratory distress syndrome, pulmonary embolism, and heart failure), while its role for prognostication requires further investigation. The authors describe imaging and managing care of patients with COVID-19, with topics including (a) chest CT protocol, (b) chest CT findings of COVID-19 and its complications, (c) the diagnostic accuracy of chest CT and its role in diagnostic decision making and prognostication, and (d) reporting and communicating chest CT findings. The authors also review other specific topics, including the pathophysiology and clinical manifestations of COVID-19, the World Health Organization case definition, the value of performing RT-PCR tests, and the radiology department and personnel impact related to performing chest CT in COVID-19. (©)RSNA, 2020 url: https://doi.org/10.1148/rg.2020200159 doi: 10.1148/rg.2020200159 id: cord-261750-6b1y7yxg author: Kwek, Seow-Khee title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge date: 2006-05-31 words: 2795.0 sentences: 179.0 pages: flesch: 58.0 cache: ./cache/cord-261750-6b1y7yxg.txt txt: ./txt/cord-261750-6b1y7yxg.txt summary: title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge Method Postal survey comprising Health-Related Quality of Life (HRQoL) questionnaires and anxiety and depression measures was sent to them at 3 months'' postdischarge. Hence, in this study, we undertook to ascertain systematically the quality of life and psychological well-being of SARS survivors 3 months'' postdischarge from the acute episode. The responders and the nonresponders were comparable on demographic parameters, duration of hospital stay, preillness health status, as well as the proportion of patients admitted to the intensive care unit ( Table 2 ). The health care workers appeared to be more adversely affected than nonstaff based on both the HRQol SF-36 scores (Fig. 1 , see staff-SARS) and the mean scores for IES, and the HADS Depression and Anxiety scores, although these were not significant. abstract: Abstract Background Little is known about the long-term consequence of severe acute respiratory syndrome (SARS). We carried out an assessment on SARS patients after their recovery from their acute illness. Method Postal survey comprising Health-Related Quality of Life (HRQoL) questionnaires and anxiety and depression measures was sent to them at 3 months' postdischarge. Results There was a significant impairment in both the HRQoL and mental functioning. Forty-one percent had scores indicative of a posttraumatic stress disorder (PTSD); about 30% had likely anxiety and depression. Conclusion SARS has significant impact on HRQoL and psychological status at 3 months. url: https://api.elsevier.com/content/article/pii/S0022399905004265 doi: 10.1016/j.jpsychores.2005.08.020 id: cord-333121-kt6t41ff author: Kwenandar, Felix title: Coronavirus Disease 2019 and Cardiovascular System: A Narrative Review date: 2020-06-03 words: 1923.0 sentences: 123.0 pages: flesch: 39.0 cache: ./cache/cord-333121-kt6t41ff.txt txt: ./txt/cord-333121-kt6t41ff.txt summary: At the end of 2019, a viral pneumonia disease called coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2), emerged in Wuhan, China. Although this infective disease is mostly characterized by respiratory tract symptoms, increasing numbers of evidence had shown considerable amounts of patients with cardiovascular involvements and these were associated with higher mortality among COVID-19 patients. Cardiovascular manifestation in COVID-19 patients include myocardial injury (MI), arrhythmias, cardiac arrests, heart failure and coagulation abnormality, ranging from 7.2% up to 33%. [2] With the increasing number of confirmed cases and the accumulating clinical data, in addition to the common clinical presentation of respiratory failure caused by COVID-19, the cardiovascular manifestations induced by this viral infection has generated considerable concern. Although the exact pathophysiological mechanism underlying myocardial injury caused by COVID-19 is not fully understood, a previous report showed that in 35% of the patients infected, the SARS-CoV genome was positively detected in the heart. abstract: At the end of 2019, a viral pneumonia disease called coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2), emerged in Wuhan, China. This novel disease rapidly spread at an alarming rate that as a result, it has now been declared pandemic by the World Health Organization. Although this infective disease is mostly characterized by respiratory tract symptoms, increasing numbers of evidence had shown considerable amounts of patients with cardiovascular involvements and these were associated with higher mortality among COVID-19 patients. Cardiac involvement as a possible late phenomenon of the viral respiratory infection is an issue that should be anticipated in patients with COVID-19. Cardiovascular manifestation in COVID-19 patients include myocardial injury (MI), arrhythmias, cardiac arrests, heart failure and coagulation abnormality, ranging from 7.2% up to 33%. The mechanism of cardiac involvement in COVID-19 patients involves direct injury to myocardial cells mediated by angiotensin-converting enzyme 2 (ACE2) receptors as suggested by some studies, while the other studies suggest that systemic inflammation causing indirect myocyte injury may also play a role. Combination of proper triage, close monitoring, and avoidance of some drugs that have cardiovascular toxicity are important in the management of cardiovascular system involvement in COVID-19 patients. The involvement of the cardiovascular system in COVID-19 patients is prevalent, variable, and debilitating. Therefore, it requires our attention and comprehensive management. url: https://api.elsevier.com/content/article/pii/S2352906720301949 doi: 10.1016/j.ijcha.2020.100557 id: cord-267566-gdjl0qmu author: Kweon, Oh Joo title: Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date: 2020-10-22 words: 3599.0 sentences: 232.0 pages: flesch: 51.0 cache: ./cache/cord-267566-gdjl0qmu.txt txt: ./txt/cord-267566-gdjl0qmu.txt summary: This study aims to assess the serologic profiles and time kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with COVID-19 using two immunoassays. METHODS: A total of 97 samples serially collected from 17 patients with COVID-19 and 137 negative control samples were analyzed for IgM and IgG against SARS-CoV-2 using the AFIAS COVID-19 Ab (Boditech Med Inc., Chuncheon, Republic of Korea) and the EDI(™) Novel Coronavirus COVID-19 ELISA Kit (Epitope Diagnostics, Inc., San Diego, CA). The diagnostic sensitivities of IgM/IgG for ≤14d PSO were 21.4%/35.7~57.1% and increased to 41.2~52.9%/88.2~94.1% at >14 d PSO with specificities of 98.5%/94.2% for AFIAS COVID-19 Ab and 100.0%/96.4% for EDI(™) Novel Coronavirus COVID-19 ELISA Kit. Among 137 negative controls, 12 samples (8.8%) showed positive or indeterminate results. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging threat worldwide. This study aims to assess the serologic profiles and time kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with COVID-19 using two immunoassays. METHODS: A total of 97 samples serially collected from 17 patients with COVID-19 and 137 negative control samples were analyzed for IgM and IgG against SARS-CoV-2 using the AFIAS COVID-19 Ab (Boditech Med Inc., Chuncheon, Republic of Korea) and the EDI(™) Novel Coronavirus COVID-19 ELISA Kit (Epitope Diagnostics, Inc., San Diego, CA). RESULTS: With both assays, IgM and IgG rapidly increased after 7 days post symptom onset (PSO). IgM antibody levels reached a peak at 15–35 d PSO and gradually decreased. IgG levels gradually increased and remained at similar levels after 22–35 d. The diagnostic sensitivities of IgM/IgG for ≤14d PSO were 21.4%/35.7~57.1% and increased to 41.2~52.9%/88.2~94.1% at >14 d PSO with specificities of 98.5%/94.2% for AFIAS COVID-19 Ab and 100.0%/96.4% for EDI(™) Novel Coronavirus COVID-19 ELISA Kit. Among 137 negative controls, 12 samples (8.8%) showed positive or indeterminate results. CONCLUSIONS: The antibody kinetics against SARS-CoV-2 are similar to common findings of acute viral infectious diseases. Antibody testing is useful for ruling out SARS-CoV-2 infection after 14 d PSO, detecting past infection, and epidemiologic surveys. url: https://www.ncbi.nlm.nih.gov/pubmed/33091042/ doi: 10.1371/journal.pone.0240395 id: cord-017995-azqjvxtu author: Kwong, Kim-hung title: Spatial Components in Disease Modelling date: 2010 words: 3117.0 sentences: 174.0 pages: flesch: 47.0 cache: ./cache/cord-017995-azqjvxtu.txt txt: ./txt/cord-017995-azqjvxtu.txt summary: Modelling of infectious diseases could help gain further understanding of their diffusion processes that provide knowledge on the detection of epidemics and decision making for future infection control measures. This research made an attempt to map different phases of the spatial diffusion of SARS in Hong Kong to identify the underlying spatial factors attributing to its transmission patterns. Socio-economic factors found statistically significant against SARS incidence included the following: c) percentage of population aged over 65, g) average number of rooms per household, and h) net residential density ( Table 1 ). Certain socio-economic factors (i.e., average number of rooms per household, percentage of elderly population, and net residential density) were found to correlate positively with the occurrence of SARS in Hong Kong, indicating their potential influence in the disease transmission. This research mapped different development phases of the SARS epidemic in Hong Kong and employed the Pearson''s correlation to isolate environmental factors and socio-economic factors of significant pertinence to the disease. abstract: Modelling of infectious diseases could help gain further understanding of their diffusion processes that provide knowledge on the detection of epidemics and decision making for future infection control measures. Conventional disease transmission models are inadequate in considering the diverse nature of a society and its location-specific factors. A new approach incorporating stochastic and spatial factors is necessary to better reflect the situation. However, research on risk factors in disease diffusion is limited in numbers. This paper mapped the different phases of spatial diffusion of SARS in Hong Kong to explore the underlying spatial factors that may have interfered and contributed to the transmission patterns of SARS. Results of the current study provide important bases to inform relevant environmental attributes that could potentially improve the spatial modelling of an infectious disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122710/ doi: 10.1007/978-3-642-12156-2_30 id: cord-104500-m0kfom0x author: Kyriakopoulos, Anthony M. title: The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review date: 2020-09-21 words: 6842.0 sentences: 357.0 pages: flesch: 40.0 cache: ./cache/cord-104500-m0kfom0x.txt txt: ./txt/cord-104500-m0kfom0x.txt summary: A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20(th) of August 2020. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. Following this initial selection stage, further screening was performed by all reviewers, using the previously described search items to identify parameters determining the global impact of COVID-19 due to SSEs. Identified parameters included the global impact of immunity and vaccination, the holy cup and religion transmission, and the austerity caused by COVID-19 and other coronavirus epidemics due to restrictions applied. abstract: Coronaviruses, members of Coronaviridae family, cause extensive epidemics of vast diseases like severe acute respiratory syndrome (SARS) and Coronavirus Disease-19 (COVID-19) in animals and humans. Super spread events (SSEs) potentiate early outbreak of the disease and its constant spread in later stages. Viral recombination events within species and across hosts lead to natural selection based on advanced infectivity and resistance. In this review, the importance of containment of SSEs was investigated with emphasis on stopping COVID-19 spread and its socio-economic consequences. A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the “potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic” and were published before 20(th) of August 2020. Overall, ninety-eight articles were found eligible and reviewed. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. The effect of SSEs on previous SARS epidemics has been documented in detail. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. This is crucial for SARS-COV-2 pandemic containment as the vaccine(s) development process will take considerable time to safely establish its potential usefulness for future clinical usage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587986/ doi: nan id: cord-298227-av1ev8ta author: Kähler, Christian J. title: Fundamental protective mechanisms of face masks against droplet infections date: 2020-06-28 words: 7149.0 sentences: 376.0 pages: flesch: 58.0 cache: ./cache/cord-298227-av1ev8ta.txt txt: ./txt/cord-298227-av1ev8ta.txt summary: Many governments have instructed the population to wear simple mouth-and-nose covers or surgical face masks to protect themselves from droplet infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in public. First of all, we show that the masks protect people in the surrounding area quite well, since the flow resistance of the face masks effectively prevents the spread of exhaled air, e.g. when breathing, speaking, singing, coughing and sneezing. Thirdly, we show that even simple mouth-and-nose covers made of good filter material cannot reliably protect against droplet infection in contaminated ambient air, since most of the air flows through gaps at the edge of the masks. However, if the distance rules cannot be observed and the risk of inhalation-based infection becomes high because many people in the vicinity are infectious and the air exchange rate is small, improved filtration efficiency masks are needed, to take full advantage of the three fundamental protective mechanisms these masks provide. abstract: Many governments have instructed the population to wear simple mouth-and-nose covers or surgical face masks to protect themselves from droplet infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in public. However, the basic protection mechanisms and benefits of these masks remain controversial. Therefore, the aim of this work is to show from a fluid physics point of view under which circumstances these masks can protect against droplet infection. First of all, we show that the masks protect people in the surrounding area quite well, since the flow resistance of the face masks effectively prevents the spread of exhaled air, e.g. when breathing, speaking, singing, coughing and sneezing. Secondly, we provide visual evidence that typical household materials used by the population to make masks do not provide highly efficient protection against respirable particles and droplets with a diameter of 0.3–2 μm as they pass through the materials largely unfiltered. According to our tests, only vacuum cleaner bags with fine dust filters show a comparable or even better filtering effect than commercial particle filtering FFP2/N95/KN95 half masks. Thirdly, we show that even simple mouth-and-nose covers made of good filter material cannot reliably protect against droplet infection in contaminated ambient air, since most of the air flows through gaps at the edge of the masks. Only a close-fitting, particle-filtering respirator without an outlet valve offers good self-protection and protection against droplet infection. Nevertheless, wearing simple homemade or surgical face masks in public is highly recommended if no particle filtrating respiratory mask is available. Firstly, because they protect against habitual contact of the face with the hands and thus serve as self-protection against contact infection. Secondly, because the flow resistance of the masks ensures that the air stays close to the head when breathing, speaking, singing, coughing and sneezing, thus protecting other people if they have sufficient distance from each other. However, if the distance rules cannot be observed and the risk of inhalation-based infection becomes high because many people in the vicinity are infectious and the air exchange rate is small, improved filtration efficiency masks are needed, to take full advantage of the three fundamental protective mechanisms these masks provide. url: https://www.sciencedirect.com/science/article/pii/S0021850220301063?v=s5 doi: 10.1016/j.jaerosci.2020.105617 id: cord-296605-p67twx7a author: LAU, Arthur Chun-Wing title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date: 2004-03-10 words: 4846.0 sentences: 247.0 pages: flesch: 38.0 cache: ./cache/cord-296605-p67twx7a.txt txt: ./txt/cord-296605-p67twx7a.txt summary: title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS) abstract: Severe acute respiratory syndrome (SARS) is frequently complicated with acute respiratory failure. In this article, we aim to focus on the management of the subgroup of SARS patients who are critically ill. Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). In some of these patients, the clinical course can progress relentlessly to septic shock and/or multiple organ dysfunction syndrome (MODS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). Superimposed bacterial and other opportunistic infections are common, especially in those treated with mechanical ventilation. Subcutaneous emphysema, pneumothoraces and pneumomediastinum may arise spontaneously or as a result of positive ventilatory assistance. Older age is a consistently a poor prognostic factor. Appropriate use of personal protection equipment and adherence to infection control measures is mandatory for effective infection control. Much of the knowledge about the clinical aspects of SARS is based on retrospective observational data and randomized-controlled trials are required for confirmation. Physicians and scientists all over the world should collaborate to study this condition which may potentially threaten human existence. url: https://www.ncbi.nlm.nih.gov/pubmed/15912185/ doi: nan id: cord-320787-dwyyjq6o author: La Rosa, Giuseppina title: First detection of SARS-CoV-2 in untreated wastewaters in Italy date: 2020-05-23 words: 2747.0 sentences: 141.0 pages: flesch: 54.0 cache: ./cache/cord-320787-dwyyjq6o.txt txt: ./txt/cord-320787-dwyyjq6o.txt summary: Italy is among the world''s worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Herein we report the results of the screening for SARS-CoV-2 presence in sewage samples collected between the end of February and the beginning of April 2020 from WWTPs in Milan (Northern Italy) and Rome (Central Italy). In the absence of a standardized method for SARS-CoV-2 detection in environmental samples, RNAs were tested for the presence of SARS-CoV-2 using three different nested RT-PCR assays and one real-time qPCR assay (Table 1 and Figure 1 b) a newly designed primer set specific for SARS-CoV-2. abstract: Abstract Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population. url: https://doi.org/10.1016/j.scitotenv.2020.139652 doi: 10.1016/j.scitotenv.2020.139652 id: cord-298321-8871aifz author: Laamarti, Meriem title: Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date: 2020-07-01 words: 2142.0 sentences: 123.0 pages: flesch: 58.0 cache: ./cache/cord-298321-8871aifz.txt txt: ./txt/cord-298321-8871aifz.txt summary: The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes. Our recent study (13) based on the analysis of 30,983 genomes of SARS-CoV-2 variants belonging to 80 countries, revealed 5.67% of total mutations with a frequency greater than 1% of all the sequences analyzed suggesting that this virus is not yet adapted to its host. In all Moroccan SARS-CoV-2 genomes, the analysis of genetic variants revealed 61 mutations compared to the reference sequence (Fig 1) , including 29 non-syn(Fig 2A) . abstract: In Morocco two waves of SARS-CoV-2 infections have been recorded. The first one occurred from March 02, 2020 with infections mostly imported from Europe and the second one dominated by local infections. At the time of writing, the genetic diversity of Moroccan isolates of SARS-CoV-2 has not yet been reported. The present study aimed to analyze first the genomic variation of the twenty-eight Moroccan strains of SARS-CoV-2 isolated from March 03, 2020 to May 15, 2020, to compare their distributions with twelve other viral genomes from North Africa as well as to identify their possible sources. Our finding revealed 61 mutations in the Moroccan genomes of SARS-CoV-2 compared to the reference sequence Wuhan-Hu-1/2019, of them 23 (37.7%) were present in two or more genomes. Focusing on non-synonymous mutations, 29 (47.54%) were distributed in five genes (ORF1ab, spike, membrane, nucleocapsid and ORF3a) with variable frequencies. The non-structural protein coding regions nsp3-Multi domain and nsp12-RdRp of the ORF1ab gene harbored more mutations, with six for each. The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes. Phylogenetic analysis showed that the Moroccan and Tunisian SARS-CoV-2 strains were closely related to those from different origins (Asia, Europe, North and South America) and distributed in different distinct subclades. This could indicate different sources of infection with no specific strain dominating yet in in these countries. These results have the potential to lead to new comprehensive investigations combining genomic data, epidemiological information and the clinical characteristics of patients with SARS-CoV-2. url: https://doi.org/10.1101/2020.06.30.181123 doi: 10.1101/2020.06.30.181123 id: cord-346331-d0s028wl author: Lackey, Kimberly A. title: SARS‐CoV‐2 and human milk: What is the evidence? date: 2020-05-30 words: 5628.0 sentences: 300.0 pages: flesch: 53.0 cache: ./cache/cord-346331-d0s028wl.txt txt: ./txt/cord-346331-d0s028wl.txt summary: Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. • Limited, weak evidence suggests that some coronaviruses (including SARS-CoV-2) may be present in human milk, but these studies do not report methods of sample collection and validation of reverse transcription polymerase chain reaction (RT-PCR) assays for human milk. Of particular interest in this context are (1) the potential role that breastfeeding could play in vertical transmission of SARS-CoV-2 from women to infants via human milk and (2) the potential protective effects of targeted antibodies and other immunoprotective components in human milk against COVID-19. Milk was submitted to the CDC, where it was analysed using reverse transcription polymerase chain reaction (RTSearch terms, databases and preprint servers used to identify existing literature reporting the possibility of vertical transmission of coronaviruses from mother to infant during breastfeeding as of 17 April 2020 The infant in this study was never tested for SARS-CoV infection. abstract: The novel coronavirus SARS‐CoV‐2 has emerged as one of the most compelling and concerning public health challenges of our time. To address the myriad issues generated by this pandemic, an interdisciplinary breadth of research, clinical and public health communities has rapidly engaged to collectively find answers and solutions. One area of active inquiry is understanding the mode(s) of SARS‐CoV‐2 transmission. Although respiratory droplets are a known mechanism of transmission, other mechanisms are likely. Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. However, there is limited published literature related to vertical transmission of any human coronaviruses (including SARS‐CoV‐2) via human milk and/or breastfeeding. Results of the literature search reported here (finalized on 17 April 2020) revealed a single study providing some evidence of vertical transmission of human coronavirus 229E; a single study evaluating presence of SARS‐CoV in human milk (it was negative); and no published data on MERS‐CoV and human milk. We identified 13 studies reporting human milk tested for SARS‐CoV‐2; one study (a non‐peer‐reviewed preprint) detected the virus in one milk sample, and another study detected SARS‐CoV‐2 specific IgG in milk. Importantly, none of the studies on coronaviruses and human milk report validation of their collection and analytical methods for use in human milk. These reports are evaluated here, and their implications related to the possibility of vertical transmission of coronaviruses (in particular, SARS‐CoV‐2) during breastfeeding are discussed. url: https://doi.org/10.1111/mcn.13032 doi: 10.1111/mcn.13032 id: cord-326965-xrnhkcsv author: Lacout, Carole title: A new diagnosis of systemic capillary leak syndrome in a patient with COVID-19 date: 2020-09-17 words: 968.0 sentences: 64.0 pages: flesch: 49.0 cache: ./cache/cord-326965-xrnhkcsv.txt txt: ./txt/cord-326965-xrnhkcsv.txt summary: SIR, With the coronavirus disease 2019 (COVID-19) pandemic, we are discovering that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has properties to induce a dysregulated immune response that exceed the simple respiratory infection [1] . Systemic capillary leak syndrome is a rare immune disorder that evolves with repeated episodes of pseudoshock that can occur spontaneously or can be triggered by viral infections. Systemic capillary leak syndrome is a rare disorder that can be secondary to blood malignancies, immune disorders, toxics, medication, infections or idiopathic (Clarkson''s disease) [4] . In conclusion, we think that it is not a coincidence that a first episode of systemic capillary leak syndrome, which is a very rare disease, occurred simultaneously with a respiratory infection caused by SARS-CoV-2. Idiopathic systemic capillary leak syndrome (Clarkson disease) SARS-CoV-2 induces acute and refractory relapse of systemic capillary leak syndrome (Clarkson''s disease) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32940700/ doi: 10.1093/rheumatology/keaa606 id: cord-287653-69nfi379 author: Lacy, J. Matthew title: COVID-19: POSTMORTEM DIAGNOSTIC AND BIOSAFETY CONSIDERATIONS date: 2020-04-24 words: 5202.0 sentences: 304.0 pages: flesch: 45.0 cache: ./cache/cord-287653-69nfi379.txt txt: ./txt/cord-287653-69nfi379.txt summary:  Prosect cases in negative pressure isolation suite with at least 6-12 air changes per hour  Doff contact and droplet precaution PPE, as well as N95 respirator or PAPR  Limit personnel in the isolation suite to the minimum necessary to perform the examination  Employ splash and aerosol reduction techniques during prosection; oscillating saws are discouraged but if used should have vacuum shroud attachment  Use caution when handling sharps; allow only one person to prosect at a given time  Ensure a technician is outside isolation room to monitor procedure and provide support as needed  Procure synthetic nasopharyngeal (+/-lung) respiratory swabs in sterile tubes of 2-3 ml of viral transport media for SARS-CoV-2 testing as needed  Carefully decontaminate morgue surfaces and outer body bag following autopsy  Ensure body is fully enclosed in a secure bag, tag as infectious and ensure funeral home is informed  Consider modifying release procedures to prevent bag being opened in morgue for identification  Perform hand hygiene after doffing PPE A C C E P T E D abstract: As a result of the 2019 novel human coronavirus (COVID-19) global spread, medical examiner/coroner offices will inevitably encounter increased numbers of COVID-19-infected decedents at autopsy. While in some cases a history of fever and/or respiratory distress (e.g. cough or shortness of breath) may suggest the diagnosis, epidemiologic studies indicate that the majority of individuals infected with COVID-19 develop mild to no symptoms. Those dying with—but not of—COVID-19 may still be infectious, however. While multiple guidelines have been issued regarding autopsy protocol in cases of suspected COVID-19 deaths, there is some variability in the recommendations. Additionally, limited recommendations to date have been issued regarding scene investigative protocol, and there are a paucity of publications characterizing COVID-19 postmortem gross and histologic findings. A case of sudden unexpected death due to COVID-19 is presented as a means of illustrating common autopsy findings, as well as diagnostic and biosafety considerations. We also review and summarize the current COVID-19 literature in an effort to provide practical evidence-based biosafety guidance for ME/C offices encountering COVID-19 at autopsy. url: https://www.ncbi.nlm.nih.gov/pubmed/32379077/ doi: 10.1097/paf.0000000000000567 id: cord-286919-fny060vk author: Lahfaoui, M title: Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson date: 2020-04-27 words: 1019.0 sentences: 78.0 pages: flesch: 64.0 cache: ./cache/cord-286919-fny060vk.txt txt: ./txt/cord-286919-fny060vk.txt summary: Les auteurs déclarent ne pas avoir de liens d''intérêts Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson L''émergence et la propagation d''un nouveau coronavirus (SARSCoV-2) à partir de Wuhan, en Chine, sont devenues une urgence de santé publique de portée internationale, désignée par l''Organisation mondiale de la santé [1]. Nous rapportons un cas d''un nourrisson, de sexe féminin âgée de 17 mois, de Berkan, Maroc, admis initialement pour prise en charge d''une anémie, puis un tableau de sepsis sévère, le body-scan a objectivé des lésions pulmonaire bilatérale d''allure virale, le RT-PCR a confirmé le diagnostic de SARS-COV-2, la patiente a été décédé après 24H suite à un syndrome de détresse respiratoire aigüe. A la date du 10 mars 2020, ce nouveau coronavirus (SRAS-CoV-2) est déjà responsable de plus de 110000 infections et de 4 000 décès dans le monde, mais les données concernant les caractéristiques épidémiologiques et cliniques des enfants abstract: Abstract The emergence and spread of a new coronavirus (SARSCoV-2) from Wuhan, China, has become a public health emergency of international concern, designated by the World Health Organization [1]. We report a case of an infant, female, 17 months old, from Berkan, Morocco, initially admitted for management of anemia, followed by a picture of severe sepsis, body scan showed bilateral viral-looking lung lesions, RT-PCR confirmed the diagnosis of SARS-COV-2, the patient died after 24H due to acute respiratory distress syndrome. url: https://doi.org/10.1016/j.rmr.2020.04.009 doi: 10.1016/j.rmr.2020.04.009 id: cord-253704-y0t30xw3 author: Lahiri, Durjoy title: COVID-19 Pandemic: A Neurological Perspective date: 2020-04-29 words: 4348.0 sentences: 210.0 pages: flesch: 40.0 cache: ./cache/cord-253704-y0t30xw3.txt txt: ./txt/cord-253704-y0t30xw3.txt summary: Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to principally affect the respiratory system, neurological involvements have already been reported in some published work. Neurological manifestations can further be subdivided into the central nervous system (headache, dizziness, alteration of the sensorium, ataxia encephalitis, stroke, and seizures) and peripheral nervous system (skeletal muscle injury and peripheral nerve involvement including hyposmia and hypogeusia) symptomatology. Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to mainly affect the respiratory system, neurological involvements have already been reported in some published work. In the present paper, we have reviewed the recently published or pre-print original articles, case reports, and existing open-source data-sets in order to delineate the spectrum of neurological disorders in SARS-CoV-2 positive cases. Another report from China describes a case of acute myelitis, possibly affecting the cervical spinal cord, as evidenced by the clinical features, in a known patient of SARS-CoV-2 infection [22] . abstract: Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to principally affect the respiratory system, neurological involvements have already been reported in some published work. We have reviewed original articles, case reports, and existing open-source data-sets to delineate the spectrum of neurological disorders potentially observed in SARS-CoV-2 positive cases. Neurological involvement in coronavirus disease 2019 (COVID-19) corresponds to three situations: (a) neurological manifestations of viral infection, (b) post-infective neurological complications, and (c) infection in patients with neurological co-morbidity. Neurological manifestations can further be subdivided into the central nervous system (headache, dizziness, alteration of the sensorium, ataxia encephalitis, stroke, and seizures) and peripheral nervous system (skeletal muscle injury and peripheral nerve involvement including hyposmia and hypogeusia) symptomatology. Post-infective neurological complications include demyelinating conditions. Reduced mobility and dementia as co-morbidities may predispose a patient to have a viral infection. It is concluded that the pandemic of COVID-19 presents for a neurologist some unique challenges. We observe that SARS-CoV-2 may have various neurological manifestations and in many cases, neurological features may precede typical respiratory symptoms. url: https://doi.org/10.7759/cureus.7889 doi: 10.7759/cureus.7889 id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 words: 5849.0 sentences: 329.0 pages: flesch: 48.0 cache: ./cache/cord-303665-l57e54hu.txt txt: ./txt/cord-303665-l57e54hu.txt summary: Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. abstract: Emerging viruses are a major public health problem. Most zoonotic pathogens originate in wildlife, including human immunodeficiency virus (HIV), influenza, Ebola, and coronavirus. Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV). Viruses are charged colloidal particles that have the ability to adsorb on surfaces depending on pH. Their sorptive interaction with solid particles has important implications for their behavior in aquatic environments, soils, sewage sludge, and other solid materials and their removal or concentration by water treatment processes. Current state of knowledge on the potential of wastewater surveillance to understand the COVID-19 pandemic is reviewed. This study also identified wastewater irrigation systems with a higher risk of COVID-19 transmission. Emphasis was placed on methodologies for the detection and quantification of SARS-CoV-2 in wastewater. url: https://doi.org/10.1016/j.scitotenv.2020.142325 doi: 10.1016/j.scitotenv.2020.142325 id: cord-016405-86kghmzf author: Lai, Allen Yu-Hung title: Impact of Disasters and Disaster Risk Management in Singapore: A Case Study of Singapore’s Experience in Fighting the SARS Epidemic date: 2014-06-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Singapore is vulnerable to both natural and man-made disasters alongside its remarkable economic growth. One of the most significant disasters in recent history was the Severe Acute Respiratory Syndrome (SARS) epidemic in 2003. The SARS outbreak was eventually contained through a series of risk mitigating measures introduced by the Singapore government. This would not be possible without the engagement and responsiveness of the general public. This chapter begins with a description of Singapore’s historical disaster profiles, the policy and legal framework in the all-hazard management approach. We use a case study to highlight the disaster impacts and insights drawn from Singapore’s risk management experience with specific references to the SARS epidemic. The implications from the SARS focus on four areas: staying vigilant at the community level, remaining flexible in a national command structure, the demand for surge capacity, and collaborative governance at regional level. This chapter concludes with a presence of the flexible command structure on both the way and the extent it was utilized. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120670/ doi: 10.1007/978-4-431-55022-8_15 id: cord-336066-n9yq8enz author: Lai, Chien‐Chen title: Proteomic analysis of up‐regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C‐like protease date: 2007-04-04 words: 4014.0 sentences: 213.0 pages: flesch: 45.0 cache: ./cache/cord-336066-n9yq8enz.txt txt: ./txt/cord-336066-n9yq8enz.txt summary: Functional classification of identified up-regulated proteins indicated that protein metabolism and modification, particularly in the ubiquitin proteasome pathway, was the main biological process occurring in SARS CoV 3CLpro-expressing cells. Interestingly, analysis of apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Table 3 ). Confocal imaging of the stained cells revealed that the release of apoptosis-inducing factor from mitochondria was found in the SARS CoV 3CLpro-expressing cells (Fig. 7A, right) , but not in mock cells (Fig. 7A, left) . Interestingly, analysis of the apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Figs. abstract: The pathogenesis of severe acute respiratory syndrome coronavirus (SARS CoV) is an important issue for treatment and prevention of SARS. Previously, SARS CoV 3C‐like protease (3CLpro) has been demonstrated to induce apoptosis via the activation of caspase‐3 and caspase‐9 (Lin, C. W., Lin, K. H., Hsieh, T. H., Shiu, S. Y. et al., FEMS Immunol. Med. Microbiol. 2006, 46, 375–380). In this study, proteome analysis of the human promonocyte HL‐CZ cells expressing SARS CoV 3CLpro was performed using 2‐DE and nanoscale capillary LC/ESI quadrupole‐TOF MS. Functional classification of identified up‐regulated proteins indicated that protein metabolism and modification, particularly in the ubiquitin proteasome pathway, was the main biological process occurring in SARS CoV 3CLpro‐expressing cells. Thirty‐six percent of identified up‐regulated proteins were located in the mitochondria, including apoptosis‐inducing factor, ATP synthase beta chain and cytochrome c oxidase. Interestingly, heat shock cognate 71‐kDa protein (HSP70), which antagonizes apoptosis‐inducing factor was shown to down‐regulate and had a 5.29‐fold decrease. In addition, confocal image analysis has shown release of mitochondrial apoptogenic apoptosis‐inducing factor and cytochrome c into the cytosol. Our results revealed that SARS CoV 3CLpro could be considered to induce mitochondrial‐mediated apoptosis. The study provides system‐level insights into the interaction of SARS CoV 3CLpro with host cells, which will be helpful in elucidating the molecular basis of SARS CoV pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/17407183/ doi: 10.1002/pmic.200600459 id: cord-304388-pth2d40p author: Lai, Chih-Cheng title: Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths date: 2020-03-04 words: 4374.0 sentences: 284.0 pages: flesch: 53.0 cache: ./cache/cord-304388-pth2d40p.txt txt: ./txt/cord-304388-pth2d40p.txt summary: Abstract Since the emergence of coronavirus disease 2019 (COVID-19) (formerly known as the 2019 novel coronavirus [2019-nCoV]) in Wuhan, China in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 75,000 cases have been reported in 32 countries/regions, resulting in more than 2000 deaths worldwide. 11, 15 Similarly, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team in China reported that 66.7% (n Z 29,798) of 44,672 cases of COVID-19 of varying degrees of severity were between 20 and 60 years of age. First, the clinical manifestation of COVID-19 ranges from the asymptomatic carrier state to severe pneumonia; however, most early reports only showed the findings of SARS-CoV-2 pneumonia, in which the ratio of male patients was much larger than that of female patients, there were no pediatric cases, and the mortality rate was high. abstract: Abstract Since the emergence of coronavirus disease 2019 (COVID-19) (formerly known as the 2019 novel coronavirus [2019-nCoV]) in Wuhan, China in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 75,000 cases have been reported in 32 countries/regions, resulting in more than 2000 deaths worldwide. Despite the fact that most COVID-19 cases and mortalities were reported in China, the WHO has declared this outbreak as the sixth public health emergency of international concern. The COVID-19 can present as an asymptomatic carrier state, acute respiratory disease, and pneumonia. Adults represent the population with the highest infection rate; however, neonates, children, and elderly patients can also be infected by SARS-CoV-2. In addition, nosocomial infection of hospitalized patients and healthcare workers, and viral transmission from asymptomatic carriers are possible. The most common finding on chest imaging among patients with pneumonia was ground-glass opacity with bilateral involvement. Severe cases are more likely to be older patients with underlying comorbidities compared to mild cases. Indeed, age and disease severity may be correlated with the outcomes of COVID-19. To date, effective treatment is lacking; however, clinical trials investigating the efficacy of several agents, including remdesivir and chloroquine, are underway in China. Currently, effective infection control intervention is the only way to prevent the spread of SARS-CoV-2. url: https://doi.org/10.1016/j.jmii.2020.02.012 doi: 10.1016/j.jmii.2020.02.012 id: cord-305763-160heazx author: Lai, Chih-Cheng title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 words: 4257.0 sentences: 264.0 pages: flesch: 61.0 cache: ./cache/cord-305763-160heazx.txt txt: ./txt/cord-305763-160heazx.txt summary: One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), has led to a global pandemic. However, the majority of currently available data are restricted to laboratory-confirmed cases for symptomatic patients, and the SARS-CoV-2 infection can manifest as an asymptomatic or mild disease; therefore, the true extent of the burden of COVID-19 can be underestimated. Improved serological detection of specific antibodies against SARS-CoV-2 can help estimate the true number of infections. This article comprehensively reviewed the associated literature and provides updated information regarding the seroprevalence of the anti-SARS-CoV-2 antibody. The seroprevalence can vary according to different sites and the seroprevalence can increase with time in the longitudinal follow-up. Although healthcare workers (HCWs), especially those caring for COVID-19 patients, are considered as a high-risk group, the seroprevalence of a HCW wearing adequate personal protective equipment is thought to not be higher than other groups. With regard to sex, no statistical difference has been found between male and female subjects. Some, but not all, studies have shown that children have a lower risk than other age groups. Finally, seroprevalence can vary according to different populations, such as pregnant women and hemodialysis patients; however, limited studies have examined these associations. Furthermore, continued seroprevalence surveillance is warranted to estimate and monitor the growing burden of COVID-19. url: https://doi.org/10.1016/j.ijid.2020.10.011 doi: 10.1016/j.ijid.2020.10.011 id: cord-332080-923jpec0 author: Lai, Chih-Cheng title: In vitro diagnostics of coronavirus disease 2019: technologies and application date: 2020-06-05 words: 1189.0 sentences: 92.0 pages: flesch: 58.0 cache: ./cache/cord-332080-923jpec0.txt txt: ./txt/cord-332080-923jpec0.txt summary: Abstract Laboratory-based diagnostic measures including virological and serological tests are essential for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, serological tests cannot confirm SARS-CoV-2, and results will be false-negative when antibody concentrations fall below detection limits. (Hangzhou Bigfish Bio-tech Co., Ltd., Zhejiang, China) was recently registered 127 as a CE-IVD for detecting SARS-CoV-2 ORF-1ab and N genes in 128 nasopharyngeal swabs, sputum, and BAL fluids. The 145 performance of the Xpress SARS-CoV-2 test was clinically evaluated in 146 patients with respiratory illnesses from whom contrived nasopharyngeal swab 147 samples were collected into viral transport media. Serological tests that can detect SARS-CoV-2 IgG-IgM antibodies are simpler 248 than rRT-PCR, and do not require complicated equipment and protocols 249 (Table 3) . During the previous SARS 251 epidemic, the IgM antibody was the first line of defense during viral infections 252 and was detectable in blood samples from patients after 3 -6 days. Dynamics of 617 anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients abstract: Abstract Laboratory-based diagnostic measures including virological and serological tests are essential for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Real-time reverse transcription-polymerase chain reactions (rRT-PCR) can detect SARS-COV-2 by targeting open reading frame-1 antibodies (ORF1ab), envelope protein, nucleocapsid protein, RNA-dependent RNA polymerase genes, and the N1, N2, and N3 (3N) target genes. Therefore, rRT-PCR remains the primary method of diagnosing SARS-CoV-2 despite being limited by false-negative results, long turnaround, complex protocols, and a need for skilled personnel. Serological diagnosis of coronavirus disease 2019 (COVID-19) is simple and does not require complex techniques and equipment, rendering it suitable for rapid detection and massive screening. However, serological tests cannot confirm SARS-CoV-2, and results will be false-negative when antibody concentrations fall below detection limits. Balancing the increased use of laboratory tests, risk of testing errors, need for tests, burden on healthcare systems, benefits of early diagnosis, and risk of unnecessary exposure is a significant and persistent challenge in diagnosing COVID-19. url: https://api.elsevier.com/content/article/pii/S1684118220301407 doi: 10.1016/j.jmii.2020.05.016 id: cord-269383-1tyorrb0 author: Lai, Christopher K C title: Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date: 2020-08-01 words: 2845.0 sentences: 186.0 pages: flesch: 57.0 cache: ./cache/cord-269383-1tyorrb0.txt txt: ./txt/cord-269383-1tyorrb0.txt summary: METHODS: We performed a prospective study in two regional hospitals in Hong Kong RESULTS: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep-throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. International authorities recommend laboratory diagnosis of SARS-CoV-2 infection should base on real-time PCR (RT-PCR) detection of viral RNA in respiratory specimens [2, 3] . In another study by the same research group [23] , they tested archived nasopharyngeal swabs and posterior oropharyngeal saliva specimens from 58 confirmed COVID-19 patients using Xpert® Xpress SARS-CoV-2 assay. To date, our current study provides the largest number of patients with prospectively collected saliva specimens throughout the clinical course and with head-to-head comparison of DTS to both upper and lower tract respiratory samples. DTS contains lower viral RNA concentration and is less sensitive in detecting SARS-CoV-2 infection than sputum and pooled NP and throat swabs. abstract: BACKGROUND: Self-collected specimens has been advocated to avoid infectious exposure to healthcare workers. Self-induced sputum in those with a productive cough, and saliva in those without a productive cough have been proposed, but sensitivity remains uncertain. METHODS: We performed a prospective study in two regional hospitals in Hong Kong RESULTS: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep-throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. DTS had the lowest overall RT-PCR positive rate (68.7% vs. 89.4% [sputum] and 80.9% [pooled NP and throat swabs]), and the lowest viral RNA concentration (mean log copy/mL 3.54 vs. 5.03 [sputum] and 4.63 [pooled NP and throat swabs]). Analyses with respect to time from symptom onset and severity also revealed similar results. Virus yield of DTS correlated with that of sputum (Pearson correlation index [95% CI]: 0.76 [0.62 – 0.86]). We estimated the overall false-negative rate of DTS could be 31.3%, and increased 2.7 times among patients without sputum. CONCLUSION: DTS produced the lowest viral RNA concentration and RT-PCR positive rate compared to conventional respiratory specimens in all phases of illness. Self-collect sputum should be the choice for patients with sputum. url: https://doi.org/10.1093/infdis/jiaa487 doi: 10.1093/infdis/jiaa487 id: cord-323038-hmi061vn author: Lai, Christopher K C title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy date: 2020-06-30 words: 4264.0 sentences: 257.0 pages: flesch: 53.0 cache: ./cache/cord-323038-hmi061vn.txt txt: ./txt/cord-323038-hmi061vn.txt summary: title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy METHODS: We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (R(t)), incubation period and time to containment. [8] [9] [10] The key measures included: (i) emergency arrangements according to a Preparedness and Response Plan that stipulated the Government''s actions against novel infectious diseases, (ii) mandatory quarantine for people at risk of carrying the infection, (iii) promoting ''social distancing'' including a work-from-home policy and school closure, (iv) implementing border control, (v) increasing the supply of surgical masks, and (vi) transparent communication with the public. We controlled for age (in four age strata: 0-24, 25-44, 45-64 and !65 years), gender, source of infection (local vs imported), case identification (self vs by others) and whether the patient had attended any healthcare services before admission to hospital. abstract: BACKGROUND: Hong Kong (HK) is a densely populated city near the epicentre of the coronavirus disease 2019 (COVID-19) outbreak. Stringent border control together with aggressive case finding, contact tracing, social distancing and quarantine measures were implemented to halt the importation and spread of the virus. METHODS: We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (R(t)), incubation period and time to containment. RESULTS: A total of 93 of the 100 cases were HK residents (6 infected in Mainland China, 10 on the Diamond Princess Cruise). Seven were visitors infected in Mainland China before entering HK. The majority (76%) were aged ≥45 years, and the incidence increased with age (P < 0.001). Escalation of border control measures correlated with a decrease in the proportion (62.5% to 0%) of cases imported from Mainland China, and a reduction in R(t) (1.07 to 0.75). The median incubation period was 4.2 days [95% confidence interval (CI), 4.0–4.5; 5th and 95th percentiles: 1.3 and 14.0). Most clusters with identifiable epidemiological links were households involving 2–4 people. Three medium-spreading events were identified: two from New Year gatherings (6–11 people), and another from environmental contamination of a worship hall (12 people). Despite intensified contact tracing, containment was delayed in 78.9% of cases (mean = 5.96 days, range = 0–24 days). An unusual transmission in a multi-storey building via faulty toilet plumbing was suspected with >100 residents evacuated overnight. Our analysis indicated that faulty plumbing was unlikely to be the source of this transmission. CONCLUSIONS: Timely stringent containment policies minimized the importation and transmission of COVID-19 in HK. url: https://www.ncbi.nlm.nih.gov/pubmed/32601677/ doi: 10.1093/ije/dyaa106 id: cord-314025-h9gj814e author: Lai, Mary Y. Y. title: Survival of Severe Acute Respiratory Syndrome Coronavirus date: 2005-10-01 words: 3089.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-314025-h9gj814e.txt txt: ./txt/cord-314025-h9gj814e.txt summary: SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. abstract: Background. The primary modes of transmission of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) appear to be direct mucus membrane contact with infectious droplets and through exposure to formites. Knowledge of the survival characteristics of the virus is essential for formulating appropriate infection-control measures. Methods. Survival of SARS-CoV strain GVU6109 was studied in stool and respiratory specimens. Survival of the virus on different environmental surfaces, including a laboratory request form, an impervious disposable gown, and a cotton nondisposable gown, was investigated. The virucidal effects of sodium hypochlorite, house detergent, and a peroxygen compound (Virkon S; Antec International) on the virus were also studied. Results. SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Even at a relatively high concentration (10(4) tissue culture infective doses/mL), the virus could not be recovered after drying of a paper request form, and its infectivity was shown to last longer on the disposable gown than on the cotton gown. All disinfectants tested were shown to be able to reduce the virus load by >3 log within 5 min. Conclusions. Fecal and respiratory samples can remain infectious for a long period of time at room temperature. The risk of infection via contact with droplet-contaminated paper is small. Absorbent material, such as cotton, is preferred to nonabsorptive material for personal protective clothing for routine patient care where risk of large spillage is unlikely. The virus is easily inactivated by commonly used disinfectants. url: https://www.ncbi.nlm.nih.gov/pubmed/16142653/ doi: 10.1086/433186 id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 words: 7004.0 sentences: 376.0 pages: flesch: 49.0 cache: ./cache/cord-352379-q5inrxcm.txt txt: ./txt/cord-352379-q5inrxcm.txt summary: Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern China. Its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. However, distinct patterns of several open reading frames in the SARS virus genome may contribute to its severe virulence. The potential mutability of the coronavirus genome may pose problems in the control of future SARS outbreaks. The mechanism of SARS pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. The life cycle of the SARS virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. Vaccines offer an important preventive measure for possible future recurrences of SARS, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in SARS virus pathogenesis. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus. url: https://www.ncbi.nlm.nih.gov/pubmed/14631105/ doi: 10.1007/bf02256318 id: cord-313415-5qrpucr4 author: Lai, Rongtao title: Sentinel surveillance strategies for early detection of coronavirus disease in fever clinics: experience from China date: 2020-08-25 words: 1902.0 sentences: 107.0 pages: flesch: 50.0 cache: ./cache/cord-313415-5qrpucr4.txt txt: ./txt/cord-313415-5qrpucr4.txt summary: During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. It is employed for discerning patients with suspected symptoms and signs, for timely isolation, for effectively blocking disease transmission during the early outbreak period before the pathogen has been identified, and for determining effective therapeutic methods; this strategy was used during the severe acute respiratory syndrome (SARS) epidemic in 2003 [2] . In the early outbreak period, the use of the sentinel surveillance strategy in fever clinics can provide benefits in terms of identifying patients with suspected symptoms, effectively blocking disease transmission, and protecting vulnerable populations. abstract: Sentinel surveillance system plays a key role in screening and monitoring emerging and acute infectious diseases in order to identify the suspected cases in time. During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. Shanghai city has reserved the fever clinics and the designated hospitals since then. Hence, clinicians in the front line are able to respond quickly to the emerging COVID-19 outbreak with their accumulated knowledge and experiences from the past. One hundred seventeen fever clinics distributed in various district areas in Shanghai have played a vital ‘sentinel’ role to fight against the COVID-19 epidemic. Most of suspected patients were identified in fever clinics and thereafter among these suspected patients the COVID-19 cases were confirmed and were isolated quickly to avoid the spread. We would like to share the sentinel roadmap for screening and diagnosis of COVID-19 to medical healthcare workers around the world, especially countries who are facing great challenges to cope with COVID-19 and meanwhile with limited medical resources. These sentinel surveillance strategies will certainly provide insight into the early detection and timely isolation of suspected cases from the others. url: https://www.ncbi.nlm.nih.gov/pubmed/32838815/ doi: 10.1017/s0950268820001892 id: cord-319273-ok2p1h9f author: Lai, Yu-Ju title: Severe acute respiratory syndrome coronavirus-2 and the deduction effect of angiotensin-converting enzyme 2 in pregnancy date: 2020-08-17 words: 2688.0 sentences: 214.0 pages: flesch: 53.0 cache: ./cache/cord-319273-ok2p1h9f.txt txt: ./txt/cord-319273-ok2p1h9f.txt summary: Angiotensin-converting enzyme 2 (ACE2) has transient overexpression and increased activity during pregnancy, which is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. The management strategy includes monitoring fetal heart rate and uterine contractions; early oxygenation if O(2) saturation is less than 95%; empiric antibiotics for prevention of secondary infection; corticosteroid to treat maternal SARS-CoV-2 disease routinely is not suggested, only for fetal lung maturation in selected cases; and consideration of delivery is according to the obstetric indication, gestational age, and severity of the disease. 40 But a study indicated that angiotensin-converting enzyme 2 (ACE2), which is the receptor of SARS-CoV-2, was highly expressed in maternal-fetal interface cells, suggesting the possibility of vertical transmission. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes abstract: The 2019 novel coronavirus (2019-nCoV, later named SARS-CoV-2) is a pandemic disease worldwide. The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is continuing at a rapid speed. Till May 4, 2020, there have been 3,407,747 confirmed cases and 238,198 deaths globally. The common symptoms in pregnant women are fever, cough, and dyspnea. Angiotensin-converting enzyme 2 (ACE2) has transient overexpression and increased activity during pregnancy, which is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. There is no evidence that pregnant women are more susceptible to SARS-CoV-2. To date, there is no valid medication or vaccination. The immune suppression or modulation during pregnancy increases the risk of severe pneumonia. Remdesivir is an antiviral medication targeting ribonucleic acid (RNA) synthesis that has clinical improvement in the treatment of SARS-CoV-2. Chloroquine is controversial in its effectiveness and safety to treat SARS-CoV-2. Remdesivir is safe in pregnancy. Chloroquine has not been formally assigned to a pregnancy category by the Food and Drug Administration (FDA). The management strategy includes monitoring fetal heart rate and uterine contractions; early oxygenation if O(2) saturation is less than 95%; empiric antibiotics for prevention of secondary infection; corticosteroid to treat maternal SARS-CoV-2 disease routinely is not suggested, only for fetal lung maturation in selected cases; and consideration of delivery is according to the obstetric indication, gestational age, and severity of the disease. During epidemics, delivery at 32–34 weeks is considered. The indication for the Cesarean section should be flexible to minimize the risk of infection during the delivery. The newborn should be in isolation ward immediately after birth; breastfeeding is not contraindicated but should avoid direct transmission infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32902940/ doi: 10.1097/jcma.0000000000000362 id: cord-342177-iqt3ghc0 author: Laine, Roger A title: The case for re-examining glycosylation inhibitors, mimetics, primers and glycosylation decoys as antivirals and anti-inflammatories in COVID19 date: 2020-08-21 words: 3060.0 sentences: 198.0 pages: flesch: 39.0 cache: ./cache/cord-342177-iqt3ghc0.txt txt: ./txt/cord-342177-iqt3ghc0.txt summary: 1974) and in 1976 showed that tunicamycin, which inhibits the formation of N-acetylglucosamine-lipid intermediates in N-linked glycan synthesis (Lennarz 1975) , suppressed glycoprotein synthesis in Semliki Forest, influenza and avian sarcoma virus (Schwarz et al. The "peplomeric glycoprotein E2 was not detectable upon tunicamycin treatment," indicating its synthesis was interdicted or its degradation was facilitated by lack of N-linked glycosylation and was improperly processed (Holmes et al. (1982) showed swainsonine, an α-mannosidase inhibitor, to inhibit processing of oligosaccharides on influenza viral hemagglutinin, and in 1983 showed its effect on vesicular stomatitis virus (Kang and Elbein 1983) . It seems a reasonable approach that interfering with host glycosylation systems hijacked by SARS COV2, plus interfering with the ACE2 receptor glycosylation may combine to 1) interdict infectivity and 2) glycosylation interference with Sialyl LeX can inhibit E-selectin-based inflammatory responses, mitigating the Covid19 ARDS pathology. Antiviral effect of alpha-glucosidase inhibitors on viral morphogenesis and binding properties of hepatitis C virus-like particles abstract: nan url: https://doi.org/10.1093/glycob/cwaa083 doi: 10.1093/glycob/cwaa083 id: cord-274508-nigru1o8 author: Lally, Michelle title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 date: 2020-10-26 words: 937.0 sentences: 64.0 pages: flesch: 41.0 cache: ./cache/cord-274508-nigru1o8.txt txt: ./txt/cord-274508-nigru1o8.txt summary: title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 Design Retrospective cohort study Setting and Participants: 775 nursing home residents infected with SARS-CoV-2 who resided in one of the 134 Community Living Centers (CLC) of the Veterans Health Administration (VHA) during March 1, 2020 to May 13, 2020 were included. Results Relative to those not receiving diabetes medications, residents taking metformin were at significantly reduced hazard of death (adjusted HR 0.48, 95%CI 0.28, 0.84) over the subsequent 30 days from COVID-19 diagnosis. Conclusions and Implications Our data suggests a reduction in 30-day mortality following SARS-CoV-2 infection in residents who were on metformin-containing diabetes regimens. These findings suggest a relative survival benefit in nursing home residents on metformin, potentially through its mTOR inhibition effects. A recent focus on potential treatment for SARS-CoV-2 42 infection includes a pathway not usually considered for its "antiviral" property, the mammalian 43 target of rapamycin (mTOR) pathway. abstract: Objectives The COVID-19 pandemic presents an urgent need to investigate whether existing drugs can enhance or even worsen prognosis; metformin, a known mammalian target of rapamycin (m-TOR) inhibitor, has been identified as a potential agent. We sought to evaluate mortality benefit among older persons infected with SARS-CoV-2 who were taking metformin as compared to those who were not. Design Retrospective cohort study Setting and Participants: 775 nursing home residents infected with SARS-CoV-2 who resided in one of the 134 Community Living Centers (CLC) of the Veterans Health Administration (VHA) during March 1, 2020 to May 13, 2020 were included. Methods Using a window of 14 days prior to SARS-CoV-2 testing, bar coded medication administration records were examined for dispensing of medications for diabetes. The COVID-19 infected residents were divided into groups: 1) residents administered metformin alone or in combination with other medications, 2) residents who used long acting or daily insulin, 3) residents administered other diabetes medications, and 4) residents not administered diabetes medication, including non-diabetics and untreated diabetics. Proportional hazard models adjusted for demographics, hemoglobin A1c, body mass index, and renal function. Results Relative to those not receiving diabetes medications, residents taking metformin were at significantly reduced hazard of death (adjusted HR 0.48, 95%CI 0.28, 0.84) over the subsequent 30 days from COVID-19 diagnosis. There was no association with insulin (adjusted HR 0.99, 95% 0.60, 1.64) or other diabetes medications (adjusted HR 0.71, 95% CI 0.38, 1.32). Conclusions and Implications Our data suggests a reduction in 30-day mortality following SARS-CoV-2 infection in residents who were on metformin-containing diabetes regimens. These findings suggest a relative survival benefit in nursing home residents on metformin, potentially through its mTOR inhibition effects. A prospective study should investigate the therapeutic benefits of metformin among persons with COVID-19. url: https://api.elsevier.com/content/article/pii/S1525861020309245 doi: 10.1016/j.jamda.2020.10.031 id: cord-316705-3wzurnfp author: Lalmuanawma, Samuel title: Applications of Machine Learning and Artificial Intelligence for Covid-19 (SARS-CoV-2) pandemic: A review date: 2020-06-25 words: 2939.0 sentences: 142.0 pages: flesch: 40.0 cache: ./cache/cord-316705-3wzurnfp.txt txt: ./txt/cord-316705-3wzurnfp.txt summary: A new novel model, that forecast and predicting 1-3 to 6 days ahead of total Covid-19 patient of 10 Brazilian states, using stacking-ensemble with support vector regression algorithm on the cumulative positive Covid-19 cases of Brazilian data was proposed, thus augmenting the short-term forecasting process to alert the healthcare expert and the government to tackle the pandemic [38] . A Canadian based forecasting model using time-series was developed employing Deep learning algorithm for the long-short-term-memory network, the studies found out a key factor intended for predicting the course with an ending point estimation of the current SARS-CoV-2 epidemic in Canada and all over the globe [40] . Since the outbreak of the novel SARS-CoV-2, scientists and medical industries around the globe ubiquitously urged to fight against the pandemic, searching alternative method of rapid screening and prediction process, contact tracing, forecasting, and development of vaccine or drugs with the more accurate and reliable operation. abstract: BACKGROUND AND OBJECTIVE: : During the recent global urgency, scientists, clinicians, and healthcare experts around the globe keep on searching for a new technology to support in tackling the Covid-19 pandemic. The evidence of Machine Learning (ML) and Artificial Intelligence (AI) application on the previous epidemic encourage researchers by giving a new angle to fight against the novel Coronavirus outbreak. This paper aims to comprehensively review the role of AI and ML as one significant method in the arena of screening, predicting, forecasting, contact tracing, and drug development for SARS-CoV-2 and its related epidemic. METHOD: A selective assessment of information on the research article was executed on the databases related to the application of ML and AI technology on Covid-19. Rapid and critical analysis of the three crucial parameters, i.e., abstract, methodology, and the conclusion was done to relate to the model's possibilities for tackling the SARS-CoV-2 epidemic. RESULT: This paper addresses on recent studies that apply ML and AI technology towards augmenting the researchers on multiple angles. It also addresses a few errors and challenges while using such algorithms in real-world problems. The paper also discusses suggestions conveying researchers on model design, medical experts, and policymakers in the current situation while tackling the Covid-19 pandemic and ahead. CONCLUSION: The ongoing development in AI and ML has significantly improved treatment, medication, screening, prediction, forecasting, contact tracing, and drug/vaccine development process for the Covid-19 pandemic and reduce the human intervention in medical practice. However, most of the models are not deployed enough to show their real-world operation, but they are still up to the mark to tackle the SARS-CoV-2 epidemic. url: https://www.sciencedirect.com/science/article/pii/S0960077920304562?v=s5 doi: 10.1016/j.chaos.2020.110059 id: cord-284925-vy2li9lz author: Lam, Dennis Shun Chiu title: COVID-19: Special Precautions in Ophthalmic Practice and FAQs on Personal Protection and Mask Selection date: 2020-04-29 words: 4717.0 sentences: 268.0 pages: flesch: 52.0 cache: ./cache/cord-284925-vy2li9lz.txt txt: ./txt/cord-284925-vy2li9lz.txt summary: We also endeavor to answer the key frequently asked questions in areas of the coronaviruses, COVID-19, disease transmission, personal protection, mask selection, and special measures in ophthalmic practices. Ophthalmologists are at risk of COVID-19 infection, since routine ophthalmic examinations are usually performed in a setting with close doctor-patient contact. We have also shared the precautions and strategies that we have implemented in our ophthalmic practice, based on our previous and current successful experiences in preventing severe acute respiratory syndrome (SARS) in 2003 and the current COVID-19 outbreaks in Hong Kong. For healthcare workers, surgical masks should be worn when performing sterile procedures, or as general protection against droplets infections. The close proximity of patients and doctors during eye examination, the presence of tears and liquids for anesthesia and dilation, or the potential aerosol or droplets from "air puff" tonometry, all pose a high risk for infective transmission. Interim infection prevention and control recommendations for patients with suspected or confirmed Coronavirus Disease 2019 (COVID-19) in healthcare settings abstract: The Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory coronavirus-2, was first reported in December 2019. The World Health Organization declared COVID-19 a pandemic on March 11, 2020 and as of April 17, 2020, 210 countries are affected with >2,000,000 infected and 140,000 deaths. The estimated case fatality rate is around 6.7%. We need to step up our infection control measures immediately or else it may be too late to contain or control the spread of COVID-19. In case of local outbreaks, the risk of infection to healthcare workers and patients is high. Ophthalmic practice carries some unique risks and therefore high vigilance and special precautions are needed. We share our protocols and experiences in the prevention of infection in the current COVID-19 outbreak and the previous severe acute respiratory syndrome epidemic in Hong Kong. We also endeavor to answer the key frequently asked questions in areas of the coronaviruses, COVID-19, disease transmission, personal protection, mask selection, and special measures in ophthalmic practices. COVID-19 is highly infectious and could be life-threatening. Using our protocol and measures, we have achieved zero infection in our ophthalmic practices in Hong Kong and China. Preventing spread of COVID-19 is possible and achievable. url: https://doi.org/10.1097/apo.0000000000000280 doi: 10.1097/apo.0000000000000280 id: cord-263471-u3su9loz author: Lam, Meylin Caballeros title: Cardiac magnetic resonance characterization of COVID-19 myocarditis date: 2020-07-04 words: 934.0 sentences: 67.0 pages: flesch: 49.0 cache: ./cache/cord-263471-u3su9loz.txt txt: ./txt/cord-263471-u3su9loz.txt summary: 1 Myocardial injury may occur at different phases of COVID-19 disease (ie, viral, pulmonary, inflammatory, and recovery phase), even late after the onset of symptoms. SARS-CoV-2 viral particles have been identified by real-time polymerase chain reaction (PCR) testing in cardiac tissue, providing evidence that direct cardiotoxicity might occur. Since more than 7.5% of myocardial cells have positive ACE2 expression, this could mediate SARS-CoV-2 entry into cardiomyocytes and cause direct cardiotoxicity. The CMR study performed on a 1.5T system (Magnetom Aera, Siemens Healthineers, Erlangen, Germany) showed normal biventricular function, no regional wall motion abnormalities, slightly increased T2 (54 ms, normal < 52 ms) and native T1 values (1110 ms, CMR allows targeting of several features of myocarditis, such as contractile dysfunction, inflammatory edema, and necrosis, and has become the gold standard for the noninvasive assessment of the disease. The role of cardiovascular imaging for myocardial injury in hospitalized COVID-19 patients abstract: nan url: https://api.elsevier.com/content/article/pii/S1885585720302875 doi: 10.1016/j.rec.2020.06.018 id: cord-288824-sygnmiun author: Lam, SD title: SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date: 2020-08-19 words: 7353.0 sentences: 412.0 pages: flesch: 54.0 cache: ./cache/cord-288824-sygnmiun.txt txt: ./txt/cord-288824-sygnmiun.txt summary: To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We correlated changes in the energy of the complex with changes in the structure of ACE2, chemical properties of residues in the binding interface, and experimental COVID-19 infection phenotypes from in vivo and in vitro animal studies. We used multiple methods to assess the relative change in binding energy (ΔΔG) of the SARS-CoV-2 S-protein:ACE2 complex following mutations in DC residues and DCEX residues that are likely to influence binding. Irrespective of host, the SARS-CoV-2 spike receptor binding domain is conserved (Fig. 4b) across tested human and animal associated SARS-CoV-2, suggesting mutations in the RBD are not required for infections observed in non-human species to date. abstract: SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance. url: https://doi.org/10.1101/2020.05.01.072371 doi: 10.1101/2020.05.01.072371 id: cord-342539-o004ggon author: Lam, Tommy Tsan-Yuk title: Tracking the genomic footprints of SARS-CoV-2 transmission date: 2020-05-28 words: 906.0 sentences: 47.0 pages: flesch: 43.0 cache: ./cache/cord-342539-o004ggon.txt txt: ./txt/cord-342539-o004ggon.txt summary: [1], conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains. Several studies using mathematical modelling of the COVID-19 incidence and other coronavirus infections have suggested the effectiveness of disease control such as social distancing and city lockdown [6, 7] , but these methods seldom assess individual transmission It is evident in literature that genomic information of pathogens provide valuable empirical information about their transmission histories [2] , such as the identification of transmission chains through phylogenetic analysis of the genome sequences as illustrated in the work done by Lu et al. In addition to revealing the evolutionary process of the pathogen and acting as a proxy of disease transmission history, phylogenetic trees also serve as versatile frameworks for comparative analysis of virus genetics and phenotypes, disease epidemiology and clinical manifestations, and population demography and environment, thus facilitating identification of a possible interplay between these various aspects in disease dynamics ( Figure 1 ). abstract: Abstract There is considerable public and scientific interest on the origin, spread and evolution of SARS-CoV-2. A recent study by Lu et al. [1], conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains. url: https://www.sciencedirect.com/science/article/pii/S0168952520301268?v=s5 doi: 10.1016/j.tig.2020.05.009 id: cord-355356-g7lvb8b4 author: Lamb, Yvette N. title: Remdesivir: First Approval date: 2020-09-01 words: 5025.0 sentences: 235.0 pages: flesch: 44.0 cache: ./cache/cord-355356-g7lvb8b4.txt txt: ./txt/cord-355356-g7lvb8b4.txt summary: Having demonstrated potent antiviral activity against coronaviruses in preclinical studies, remdesivir emerged as a candidate drug for the treatment of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, during the current global pandemic. Based on preliminary results from the randomized, double-blind, placebo-controlled, multinational phase III ACTT-1 trial (NCT04280705) in patients with COVID-19, remdesivir significantly reduced time to recovery relative to placebo (median 11 days vs 15 days; rate ratio for recovery 1.32; 95% CI 1.12-1.55; p < 0.001) [primary endpoint] [41] . Among pregnant women (n = 67) and postpartum women (n = 19) who received compassionate use remdesivir for severe COVID-19, rates of clinical improvement were 96% and 89%, respectively, at day 28 [45] . In paediatric patients (aged 0-17 years) with severe COVID-19 treated with compassionate use remdesivir (n = 77), the clinical improvement rate was 88% at day 28 [46] . abstract: The antiviral agent remdesivir (Veklury(®); Gilead Sciences), nucleotide analogue prodrug, has broad-spectrum activity against viruses from several families. Having demonstrated potent antiviral activity against coronaviruses in preclinical studies, remdesivir emerged as a candidate drug for the treatment of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, during the current global pandemic. Phase III evaluation of remdesivir in the treatment of COVID-19 commenced in early 2020 and has thus far yielded promising results. In late May 2020, Taiwan conditionally approved the use of remdesivir in patients with severe COVID-19. This was followed by a rapid succession of conditional approvals in various countries/regions including the EU and Canada. Preceding these conditional approvals, an emergency use authorization for remdesivir had been granted in the USA (on 1 May 2020) and a special approval for emergency use was granted in Japan (on 7 May 2020). This article summarizes the milestones in the development of remdesivir leading to its first conditional approval for the treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32870481/ doi: 10.1007/s40265-020-01378-w id: cord-350618-rtilfnzi author: Lambelet, Valentine title: Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date: 2020-05-26 words: 7287.0 sentences: 452.0 pages: flesch: 50.0 cache: ./cache/cord-350618-rtilfnzi.txt txt: ./txt/cord-350618-rtilfnzi.txt summary: College of Obstetricians and Gynaecologists (RCOG), pregnant women with moderate symptoms should self-isolate, unless they attend a maternity unit where patients in the 2 nd or 3 rd trimester meeting PHE criteria ( ≥ 1 of: (1) Clinical/radiological evidence of pneumonia, (2) Acute Respiratory Distress Syndrome (ARDS), (3) Fever ≥37.8 and at least one of acute persistent cough, hoarseness, nasal discharge/congestion, shortness of breath, sore throat, wheezing or sneezing) should be tested for COVID-19 and treated as infected until results are available. Past coronavirus epidemics were associated with adverse outcomes for the fetus and/or newborns including miscarriages (57%), preterm birth, fetal distress and FGR with SARS-CoV-1 infection during the 2 nd and 3 rd trimesters. In this review, we found that of 142 cases of SARS-CoV-2 infections in pregnancy, 28% experienced preterm birth and 14% had adverse fetal/neonata l outcomes (FGR, fetal/neonatal demise, severe symptoms at birth). abstract: Since December 2019, the novel SARS‐CoV‐2 outbreak has resulted in millions of cases and more than 200,000 deaths worldwide. The clinical course among non‐pregnant women has been described but data about potential risks for women and their fetus remain scarce. The SARS and MERS epidemics were responsible for miscarriages, adverse fetal and neonatal outcomes and maternal deaths. For COVID‐19 infection, only 9 cases of maternal death have been reported as of April 22, 2020 and pregnant women seem to develop the same clinical presentation as the general population. However, severe maternal cases, as well as prematurity, fetal distress and stillbirth among newborns have been reported. The SARS‐CoV‐2 pandemic greatly impacts prenatal management and surveillance and raise the need for clear unanimous guidelines. In this narrative review, we describe the current knowledge about coronaviruses (SARS, MERS and SARS‐CoV‐2) risks and consequences on pregnancies and we summarize available current candidate therapeutic options for pregnant women. Finally, we compare current guidance proposed by RCOG, ACOG and the WHO to give an overview of prenatal management which should be utilized until future data appear. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32453451/ doi: 10.1002/pd.5759 id: cord-294856-eeh2a0t8 author: Lambert, Paul-Henri title: Consensus Summary Report for CEPI/BC March 12-13, 2020 Meeting: Assessment of Risk of Disease Enhancement with COVID-19 Vaccines date: 2020-05-25 words: 5236.0 sentences: 251.0 pages: flesch: 40.0 cache: ./cache/cord-294856-eeh2a0t8.txt txt: ./txt/cord-294856-eeh2a0t8.txt summary: Therefore, CEPI and the Brighton Collaboration Safety Platform for Emergency vACcines (SPEAC) convened a scientific working meeting https://brightoncollaboration.us/brighton-collaboration-cepi-covid-19-web-conference/) on March 12 and 13, 2020 of experts in the field of vaccine immunology and coronaviruses to discuss current knowledge that could form the basis for the assessment of the risk of enhanced disease during SARS-CoV-2 vaccine development. Ferret models of SARS-CoV-1 also demonstrate virus replication in respiratory tracts with induction of a neutralizing antibody response but also demonstrated little evidence of clinical disease [13] . Efficacy of several SARS-CoV-1 vaccines was evaluated in these models with spike (S) protein based vaccines demonstrating neutralizing antibody and protection against pulmonary replication of the challenge virus in mice and hamsters [16] . There is evidence for disease enhancement in vaccinated animals after challenge with live virus in multiple studies with SARS-CoV-1 vaccine candidates as summarized in Table. Chinese macaques immunized with a modified vaccinia virus expressing S protein then challenged with SARS-CoV-1 did not develop clinical disease, but histopathology showed lung injury. abstract: A novel coronavirus (CoV), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in late 2019 in Wuhan, China and has since spread as a global pandemic. Safe and effective vaccines are thus urgently needed to reduce the significant morbidity and mortality of Coronavirus Disease 2019 (COVID-19) disease and ease the major economic impact. There has been an unprecedented rapid response by vaccine developers with now over one hundred vaccine candidates in development and at least six having reached clinical trials. However, a major challenge during rapid development is to avoid safety issues both by thoughtful vaccine design and by thorough evaluation in a timely manner. A syndrome of “disease enhancement” has been reported in the past for a few viral vaccines where those immunized suffered increased severity or death when they later encountered the virus or were found to have an increased frequency of infection. Animal models allowed scientists to determine the underlying mechanism for the former in the case of Respiratory Syncytial virus (RSV) vaccine and have been utilized to design and screen new RSV vaccine candidates. Because some Middle East respiratory syndrome (MERS) and SARS-CoV-1 vaccines have shown evidence of disease enhancement in some animal models, this is a particular concern for SARS-CoV-2 vaccines. To address this challenge, the Coalition for Epidemic Preparedness Innovations (CEPI) and the Brighton Collaboration (BC) Safety Platform for Emergency vACcines (SPEAC) convened a scientific working meeting on March 12 and 13, 2020 of experts in the field of vaccine immunology and coronaviruses to consider what vaccine designs could reduce safety concerns and how animal models and immunological assessments in early clinical trials can help to assess the risk. This report summarizes the evidence presented and provides considerations for safety assessment of COVID-19 vaccine candidates in accelerated vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/32507409/ doi: 10.1016/j.vaccine.2020.05.064 id: cord-320087-iu4ulxtu author: Lampe, Anne title: Guillain-Barré syndrome and SARS-CoV-2 date: 2020-07-08 words: 1748.0 sentences: 109.0 pages: flesch: 50.0 cache: ./cache/cord-320087-iu4ulxtu.txt txt: ./txt/cord-320087-iu4ulxtu.txt summary: Since January 2020, after Chinese health authorities identified a new type of coronavirus (SARS-CoV-2), the virus has spread throughout China and consecutively throughout the whole world. This article presents the case of a 65-years old man who was presumptively infected with SARS-CoV-2 during his ski vacation in Austria in March 2020 and acutely presented with typical symptoms of Guillain-Barré syndrome. We herein report about a COVID-19 patient who was admitted to the emergency department of our hospital with typical symptoms of Guillain-Barré syndrome (GBS). The interval between the onset of symptoms of SARS-CoV-2 infection and first symptoms of GBS was only 1 day in the case presented here. A case study of 5 patients with SARS-CoV-2 infection and GBS was published a few weeks ago [14] . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Guillain-Barre syndrome associated with SARS-CoV-2 infection: Causality or coincidence? abstract: Since January 2020, after Chinese health authorities identified a new type of coronavirus (SARS-CoV-2), the virus has spread throughout China and consecutively throughout the whole world. The most common symptoms include fever and respiratory tract symptoms. Nevertheless, some patients show less common symptoms such as gastrointestinal or neurological manifestations. This article presents the case of a 65-years old man who was presumptively infected with SARS-CoV-2 during his ski vacation in Austria in March 2020 and acutely presented with typical symptoms of Guillain-Barré syndrome. url: https://www.ncbi.nlm.nih.gov/pubmed/32835165/ doi: 10.1186/s42466-020-00066-0 id: cord-267782-4pjfnund author: Lan, Fan-Yun title: Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA date: 2020-10-30 words: 5048.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-267782-4pjfnund.txt txt: ./txt/cord-267782-4pjfnund.txt summary: Therefore, we conducted this study aiming to investigate: 1) SARS-CoV-2 infection rate, transmission and exposure risks among grocery retail employees, 2) their use of personal protective equipment (PPE) and perception on COVID-19 and 3) their mental health state during the COVID-19 pandemic. ► This is the first study to demonstrate the significant asymptomatic infection rate, exposure risks and associated psychological distress of grocery retail essential workers during the pandemic, which supports the policy recommendations that employers and government officials should take actions on implementing preventive strategies and administrative arrangements, such as methods to reduce interpersonal contact, repeat and routine SARS-CoV-2 employee testing, to ensure the health and safety of essential workers. 13 14 In fact, a pioneering study conducted in the Table 3 Characteristics of retail essential employees in a single grocery store in Massachusetts, USA presented for SARS-CoV-2, the virus causing COVID-19, RT-PCR assay testing by Patient Health Questionnaire-9 (PHQ-9) screening score for depression These are in contrast to positions mainly dealing with consumer goods or the environment, such as stocker, backroom, receiving and maintenance. abstract: OBJECTIVES: To investigate SARS-CoV-2 (the virus causing COVID-19) infection and exposure risks among grocery retail workers, and to investigate their mental health state during the pandemic. METHODS: This cross-sectional study was conducted in May 2020 in a single grocery retail store in Massachusetts, USA. We assessed workers’ personal/occupational history and perception of COVID-19 by questionnaire. The health outcomes were measured by nasopharyngeal SARS-CoV-2 reverse transcriptase PCR (RT-PCR) results, General Anxiety Disorder-7 (GAD-7) and Patient Health Questionnaire-9 (PHQ-9). RESULTS: Among 104 workers tested, 21 (20%) had positive viral assays. Seventy-six per cent positive cases were asymptomatic. Employees with direct customer exposure had an odds of 5.1 (95% CI 1.1 to 24.8) being tested positive for SARS-CoV-2 after adjustments. As to mental health, the prevalence of anxiety and depression (ie, GAD-7 score >4 or PHQ-9 score >4) was 24% and 8%, respectively. After adjusting for potential confounders, those able to practice social distancing consistently at work had odds of 0.3 (95% CI 0.1 to 0.9) and 0.2 (95% CI 0.03 to 0.99) screening positive for anxiety and depression, respectively. Workers commuting by foot, bike or private cars were less likely to screen positive for depression (OR 0.1, 95% CI 0.02 to 0.7). CONCLUSIONS: In this single store sample, we found a considerable asymptomatic SARS-CoV-2 infection rate among grocery workers. Employees with direct customer exposure were five times more likely to test positive for SARS-CoV-2. Those able to practice social distancing consistently at work had significantly lower risk of anxiety or depression. url: https://www.ncbi.nlm.nih.gov/pubmed/33127659/ doi: 10.1136/oemed-2020-106774 id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 words: 4339.0 sentences: 251.0 pages: flesch: 52.0 cache: ./cache/cord-291360-z19ri377.txt txt: ./txt/cord-291360-z19ri377.txt summary: Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system''s estimated total HCW population (n = 4600). abstract: BACKGROUND: Coronavirus 2019 disease (COVID-19) is caused by the virus SARS-CoV-2, transmissible both person-to-person and from contaminated surfaces. Early COVID-19 detection among healthcare workers (HCWs) is crucial for protecting patients and the healthcare workforce. Because of limited testing capacity, symptom-based screening may prioritize testing and increase diagnostic accuracy. METHODS AND FINDINGS: We performed a retrospective study of HCWs undergoing both COVID-19 telephonic symptom screening and nasopharyngeal SARS-CoV-2 assays during the period, March 9—April 15, 2020. HCWs with negative assays but progressive symptoms were re-tested for SARS-CoV-2. Among 592 HCWs tested, 83 (14%) had an initial positive SARS-CoV-2 assay. Fifty-nine of 61 HCWs (97%) who were asymptomatic or reported only sore throat/nasal congestion had negative SARS-CoV-2 assays (P = 0.006). HCWs reporting three or more symptoms had an increased multivariate-adjusted odds of having positive assays, 1.95 (95% CI: 1.10–3.64), which increased to 2.61 (95% CI: 1.50–4.45) for six or more symptoms. The multivariate-adjusted odds of a positive assay were also increased for HCWs reporting fever and a measured temperature ≥ 37.5°C (3.49 (95% CI: 1.95–6.21)), and those with myalgias (1.83 (95% CI: 1.04–3.23)). Anosmia/ageusia (i.e. loss of smell/loss of taste) was reported less frequently (16%) than other symptoms by HCWs with positive assays, but was associated with more than a seven-fold multivariate-adjusted odds of a positive test: OR = 7.21 (95% CI: 2.95–17.67). Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. The absence of symptoms or symptoms limited to nasal congestion/sore throat were associated with negative assays. url: https://doi.org/10.1371/journal.pone.0235460 doi: 10.1371/journal.pone.0235460 id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 words: 9315.0 sentences: 507.0 pages: flesch: 61.0 cache: ./cache/cord-329102-2y49kcwu.txt txt: ./txt/cord-329102-2y49kcwu.txt summary: We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. abstract: SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs or vaccines with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on predicted RNA structures in SARS-CoV-2 and most putative regulatory sequences are uncharacterized. Here we report the secondary structure of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq). Our results reveal previously undescribed structures within critical regulatory elements such as the genomic transcription-regulating sequences (TRSs). Contrary to previous studies, our in-cell data show that the structure of the frameshift element, which is a major drug target, is drastically different from prevailing in vitro models. The genomic structure detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics. url: https://doi.org/10.1101/2020.06.29.178343 doi: 10.1101/2020.06.29.178343 id: cord-267136-1abp6oom author: Lan, Yu-Ching title: Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan date: 2004-12-07 words: 3106.0 sentences: 173.0 pages: flesch: 63.0 cache: ./cache/cord-267136-1abp6oom.txt txt: ./txt/cord-267136-1abp6oom.txt summary: Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. To better understand evolutionary relationships between SCoVs isolated in Taiwan and those isolated in other parts of the world, we constructed phylogenetic trees with two different methods using full-length genomic sequences from 45 human (12 Taiwanese) and two civet SCoVs. Tree topologies were consistent for the NJ (Fig. 1a) and Pars (Fig. 1b) methods. Pairwise comparison methods were used to analyze nucleotide sequence variation within the full-length genomes of 20 human SCoVs (7 from early epidemic and 13 from late epidemic) (Fig. 2) . abstract: Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. This Taiwanese clade could be further divided into two epidemic waves. Taiwan SCoVs in the first wave clustered with three isolates from the Amoy Gardens housing complex in Hong Kong indicating their possible origin. Of the 45 human SCoVs, one isolate from Guangdong province, China, exhibited an extra 29-nucleotide fragment between Orf 10 and Orf 11—similar to the civet SCoV genome. Nucleotide and protein sequence comparisons suggested that all SCoVs of late epidemic came from human-to-human transmission, while certain SCoVs of early epidemic might have originated in animals. url: https://api.elsevier.com/content/article/pii/S1567134804001224 doi: 10.1016/j.meegid.2004.08.005 id: cord-322585-5gio6ruj author: Lanari, Marcello title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date: 2020-06-25 words: 441.0 sentences: 33.0 pages: flesch: 55.0 cache: ./cache/cord-322585-5gio6ruj.txt txt: ./txt/cord-322585-5gio6ruj.txt summary: The possible role of children in the COVID-19 viral disease pandemic is also commented. However, the current available data on severe acute respiratory syndrome 31 coronavirus 2 (SARS-CoV-2) show that, from the beginning of the outbreak until now, there is a 32 low attack rate in paediatrics worldwide. Particularly, in Madrid region (Spain), individuals <18 33 years-old accounted for 0.8% of the laboratory-confirmed cases during the first 2 weeks of the Finally, the lockdown imposed until recently by some governments, along with the growing fear of 103 going to hospitals, has led to a significant reduction in the circulation of the other respiratory pathogens and in the number of Paediatric ER visits. Screening 158 and severity of Coronavirus Disease 2019 (COVID-19) in children in Paediatric inflammatory multisystem 163 syndrome and SARS-CoV-2 infection in children -15 A Case Series of children with 2019 novel 180 coronavirus infection: clinical and epidemiological features abstract: In this commentary, we focus our attention on what is known about SARS-CoV-2 infection in the pediatric population. We report literature and National data. The possible and different explanations for understanding why the infection seems to be more benign and less frequent in children are discussed. The possible role of children in the COVID-19 viral disease pandemic is also commented. Finally, our work suggests to search for future evidence and containment strategies to manage virus spread. url: https://doi.org/10.1016/j.cmi.2020.06.017 doi: 10.1016/j.cmi.2020.06.017 id: cord-292733-dya40tln author: Lancman, Guido title: Severe COVID-19 virus reactivation following treatment for B cell acute lymphoblastic leukemia date: 2020-10-02 words: 1377.0 sentences: 84.0 pages: flesch: 51.0 cache: ./cache/cord-292733-dya40tln.txt txt: ./txt/cord-292733-dya40tln.txt summary: She was initially hospitalized with COVID-19 in April and developed a high antibody titer with two negative nasal polymerase chain reaction (PCR) swabs for SARS-CoV-2 on discharge. She developed a severe COVID-19 pneumonia with lymphopenia, high inflammatory markers, and characteristic bilateral ground-glass opacities on chest CT, requiring high-flow nasal cannula and transfer to the intensive care unit. Given the short time frame from leukemia treatment to PCR positivity and the low case rate in mid-June in New York City, reinfection appears to have been unlikely and SARS-CoV-2 reactivation is a possible explanation. This case illustrates the risks of treating recently recovered COVID-19 patients with immunosuppressive therapy, particularly lymphocyteand antibody-depleting therapy, and raises new questions about the potential of SARS-CoV-2 reactivation. Here, we report a case of severe COVID-19 virus reactivation following chemotherapy, including rituximab, cytarabine, and dasatinib for B cell acute lymphoblastic leukemia (B-ALL). abstract: SARS-CoV-2 has infected millions of people worldwide, but little is known at this time about second infections or reactivation. Here, we report a case of a 55-year-old female undergoing treatment for CD20+ B cell acute lymphoblastic leukemia who experienced a viral reactivation after receiving rituximab, cytarabine, and dasatinib. She was initially hospitalized with COVID-19 in April and developed a high antibody titer with two negative nasal polymerase chain reaction (PCR) swabs for SARS-CoV-2 on discharge. After recovery, she resumed treatment in June for her leukemia, which included rituximab, cytarabine, and dasatinib. She promptly lost her COVID-19 antibodies, and her nasal PCR turned positive in June. She developed a severe COVID-19 pneumonia with lymphopenia, high inflammatory markers, and characteristic bilateral ground-glass opacities on chest CT, requiring high-flow nasal cannula and transfer to the intensive care unit. She received steroids, anticoagulation, and convalescent plasma, and within 48 h she was off oxygen. She was discharged home in stable condition several days later. Given the short time frame from leukemia treatment to PCR positivity and the low case rate in mid-June in New York City, reinfection appears to have been unlikely and SARS-CoV-2 reactivation is a possible explanation. This case illustrates the risks of treating recently recovered COVID-19 patients with immunosuppressive therapy, particularly lymphocyte- and antibody-depleting therapy, and raises new questions about the potential of SARS-CoV-2 reactivation. url: https://www.ncbi.nlm.nih.gov/pubmed/33008453/ doi: 10.1186/s13045-020-00968-1 id: cord-332404-va3rxy5p author: Landeros, A. title: An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic date: 2020-08-06 words: 6144.0 sentences: 360.0 pages: flesch: 54.0 cache: ./cache/cord-332404-va3rxy5p.txt txt: ./txt/cord-332404-va3rxy5p.txt summary: Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence. Given transmission of SARS-CoV-2 occurs through respiratory droplets, any reopening policy must adequately reduce crowded environments at school to protect children, teachers, staff, and ultimately communities. A recent study on the effects of school closure in March in the U.S. suggests that it reduced COVID-19 cases in states with low cumulative incidence [2] , yet education researchers worry that teachers will face lagging educational development of children once schools reopen due to the extended period of remote learning [11] . Our simulations with a single cohort indicate that a 5% percent threshold policy can shift infections in children from 80% to 55% over a 6 month period when child-to-child transmission rates in school are high ( Figure 3C ). abstract: The SARS-CoV-2 pandemic led to the closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials also understand that risk reduction strategies and detection of cases must be in place to allow children to safely return to school. Furthermore, the consequences of reclosing recently reopened schools are substantial and impact teachers, parents, and ultimately the educational experience in children. Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence. Our model predicts that a combination of all three approaches will substantially reduce SARS-CoV-2 prevalence. The model also shows that reduction of class density and the implementation of rapid viral testing, even with imperfect detection, have greater impact than moderate measures for transmission mitigation. url: https://www.ncbi.nlm.nih.gov/pubmed/32793918/ doi: 10.1101/2020.08.05.20169086 id: cord-260402-9b1ltcf1 author: Lang, Adam Edward title: More Than Meets the Eye: The Similarities Between COVID-19 and Smoking date: 2020-08-11 words: 584.0 sentences: 42.0 pages: flesch: 54.0 cache: ./cache/cord-260402-9b1ltcf1.txt txt: ./txt/cord-260402-9b1ltcf1.txt summary: To the Editor: Research shows that cigarette smoking upregulates ACE2, the receptor by which SARS-CoV-2 gains entry to the host resulting in COVID-19, in the lungs and therefore potentially leads to increased morbidity [1] . As part of a tobacco treatment campaign implemented at the beginning of the pandemic at McDonald Army Health Center, the authors performed a literature search and found that SARS-CoV-2 and smoking both contribute to myocarditis, thrombosis, immune impairment, and increased inflammation. SARS-CoV-2 and smoking upregulate this cytokine release and lead to an increased risk of coagulopathy [4, 5] . The upregulation of ACE2 in smokers may predispose this population to an increased risk of SARS-CoV-2 infection. The host cell transmembrane protease, serine 2 (TMPSRSS2), which primes the SAR-CoV-2 S protein for entry, may also be upregulated in smokers [6] , which would further increase the odds of viral infectivity. Smoking-Mediated Upregulation of the Androgen Pathway Leads to Increased SARS-CoV-2 Susceptibility abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0025619620309095?v=s5 doi: 10.1016/j.mayocp.2020.08.008 id: cord-308071-1bk3xuwf author: Lang, Christian title: Lung transplantation for COVID-19-associated acute respiratory distress syndrome in a PCR-positive patient date: 2020-08-25 words: 2432.0 sentences: 128.0 pages: flesch: 46.0 cache: ./cache/cord-308071-1bk3xuwf.txt txt: ./txt/cord-308071-1bk3xuwf.txt summary: Herein, we report the first case of lung transplantation for a patient with a persistently positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR test result. This decision was based on the following considerations: (1) virus culture was negative and real-time RT-PCR Ct values were high; (2) it was more than 5 weeks since the start of the SARS-CoV-2 infection; (3) no alternative treatment options were available; (4) the case was a single-organ failure in a young patient; (5) it was a preseptic condition originating from the lungs; and (6) there were no other obvious barriers for long-term recovery. To our knowledge, available evidence for lung transplant ation in COVID-19 is limited to two preliminary reports from China, suggesting that this treatment might be an option for SARS-CoV-2 PCR-negative patients. 11, 12 The case we present here extends the reports from China by showing that lung transplantation can be done in patients with positive RT-PCR results, provided that Vero cell cultures confirm non-infectivity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32857987/ doi: 10.1016/s2213-2600(20)30361-1 id: cord-325958-1v1pg2z0 author: Lange, Clemens title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 words: 2672.0 sentences: 149.0 pages: flesch: 45.0 cache: ./cache/cord-325958-1v1pg2z0.txt txt: ./txt/cord-325958-1v1pg2z0.txt summary: In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. Since the outbreak, many studies described ACE2 expression across human tissues, including lung, stomach, ileum, colon, liver and kidney 8, 9 , supporting the clinical observation that SARS-CoV-2 can infect multiple organs. To obtain information on transcription of ACE2 and associated molecules required for cell entry by SARS-CoV-2, existing datasets of 38 conjunctival samples from 38 patients were included in this study. This study shows that ACE2, which is the main receptor for SARS-CoV-2 6 , is not significantly expressed in healthy and diseased human conjunctival samples. abstract: SARS‐CoV‐2 is assumed to use angiotensin‐converting enzyme 2 (ACE2) and other auxiliary proteins for cell entry. Recent studies have described conjunctival congestion in 0.8% of patients with laboratory‐confirmed SARS‐CoV‐2, and there has been speculation that SARS‐CoV‐2 can be transmitted through the conjunctiva. However, it is currently unclear whether conjunctival epithelial cells express ACE2 and its cofactors. In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. ACE2 protein expression was assessed in eight healthy conjunctival samples using immunohistochemistry. Our results show that the SARS‐CoV‐2 receptor ACE2 is not substantially expressed in conjunctival samples on the mRNA (median 0.0 transcripts per million (TPM), min 0.0 TPM, max 1.7 TPM) and protein levels. Similar results were obtained for the transcription of other auxiliary molecules. In conclusion, this study finds no evidence for a significant expression of ACE2 and its auxiliary mediators for cell entry in conjunctival samples, making conjunctival infection with SARS‐CoV‐2 via these mediators unlikely. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25981 doi: 10.1002/jmv.25981 id: cord-343836-daqrym0b author: Lange, Clemens title: Welche Bedeutung hat die Bindehaut als möglicher Übertragungsweg für eine SARS-CoV-2-Infektion? date: 2020-06-22 words: 985.0 sentences: 87.0 pages: flesch: 48.0 cache: ./cache/cord-343836-daqrym0b.txt txt: ./txt/cord-343836-daqrym0b.txt summary: Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV‑2 via these mediators unlikely. Es ist derzeit nicht eindeutig geklärt, ob Zellen der Augenoberfläche ACE2 oder TMPRSS2 exprimieren und damit für eine SARS-CoV-2-Infektion anfällig sind. The current body of evidence indicates that SARS-CoV-2 requires the membrane-bound angiotensinconverting enzyme 2 (ACE2) and the membrane-bound serine protease TMPRSS2 to enter cells. Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV-2 via these mediators unlikely. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection abstract: Recent studies have described conjunctivitis in approximately 1% of COVID-19 patients and speculated that SARS-CoV‑2 can be transmitted via the conjunctiva. In this article we recapitulate the molecular mechanisms of host cell entry of SARS-CoV‑2 and discuss the current evidence for a potential conjunctival transmission of SARS-CoV‑2. The current body of evidence indicates that SARS-CoV‑2 requires the membrane-bound angiotensin-converting enzyme 2 (ACE2) and the membrane-bound serine protease TMPRSS2 to enter cells. Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV‑2 via these mediators unlikely. Nevertheless, we consider the current evidence to be still too limited to provide a conclusive statement and recommend appropriate protective measures for healthcare personnel who are in close contact with suspected and confirmed COVID-19 patients. url: https://doi.org/10.1007/s00347-020-01150-1 doi: 10.1007/s00347-020-01150-1 id: cord-303692-py908dt8 author: Langley, Caroline title: Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement date: 2019-01-01 words: 6198.0 sentences: 316.0 pages: flesch: 55.0 cache: ./cache/cord-303692-py908dt8.txt txt: ./txt/cord-303692-py908dt8.txt summary: title: Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement davidii ISG15, we use this protease as a biochemical tool; specifically, as a tool to illuminate the importance of the hydrophobic interdomain interface of ISG15 and how residue variation in this region between different species of ISG15s leads to biochemical differences in ISG15-protein engagement. With the exception of Pro38, which is a histidine residue in hISG15, all of these positions are conserved between bISG15 and the ISG15s from mice and humans. Taking the ITC data as a whole, the impact of mutations at Phe40 in bISG15 and its counterparts highlights the importance of ISG15 interdomain interactions in the effective binding of ISG15 by a protein that engages more than one domain of ISG15. abstract: Bats have long been observed to be the hosts and the origin of numerous human diseases. Bats, like all mammals, rely on a number of innate immune mechanisms to combat invading pathogens, including the interferon type I, II and III responses. Ubiquitin-like interferon-stimulated gene product 15 (ISG15) is a key modulator of these interferon responses. Within these pathways, ISG15 can serve to stabilize host proteins modulating innate immune responses and act as a cytokine. Post-translational modifications of viral proteins introduced by ISG15 have also been observed to directly affect the function of numerous viral proteins. Unlike ubiquitin, which is virtually identical across all animals, comparison of ISG15s across species reveals that they are relatively divergent, with sequence identity dropping to as low as ∼58% among mammals. In addition to serving as an obstacle to the zoonotic transmission of influenza, these ISG15 species–species differences have also long been shown to have an impact on the function of viral deISGylases. Recently, the structure of the first nonhuman ISG15, originating from mouse, suggested that the structures of human ISG15 may not be reflective of other species. Here, the structure of ISG15 from the bat species Myotis davidii solved to 1.37 Å resolution is reported. Comparison of this ISG15 structure with those from human and mouse not only underscores the structural impact of ISG15 species–species differences, but also highlights a conserved hydrophobic motif formed between the two domains of ISG15. Using the papain-like deISGylase from Severe acute respiratory syndrome coronavirus as a probe, the biochemical importance of this motif in ISG15–protein engagements was illuminated. url: https://www.ncbi.nlm.nih.gov/pubmed/30644842/ doi: 10.1107/s2059798318015322 id: cord-331541-u0xm9a89 author: Lankes, Heather A title: Biospecimen Collection During the COVID-19 Pandemic: Considerations for Biobanking date: 2020-09-25 words: 3580.0 sentences: 250.0 pages: flesch: 40.0 cache: ./cache/cord-331541-u0xm9a89.txt txt: ./txt/cord-331541-u0xm9a89.txt summary: METHODS: Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Additional CDC SARS guidance recommended that laboratory personnel have a baseline serum sample collected prior to working with SARS-CoV biospecimens and stored for future reference. Testing of banked biospecimens collected in late 2019 may help define asymptomatic (or mildly symptomatic) circulation of SARS-CoV-2 prior to the presentation of severe cases in December; however, until a more accurate date is defined, use of October 1, 2019, as the start of the pandemic window is reasonable. Per CDC and WHO SARS-CoV-2 interim biosafety guidance 48, 49 and reported COVID-19 experience, 57 biobanks handling pandemic window biospecimens must: SARS-CoV-2 is the highly transmittable respiratory virus that causes COVID-19, a disease hallmarked by asymptomatic infection in some, and severe symptoms, including death, in others. abstract: OBJECTIVES: Millions of biospecimens will be collected during the coronavirus disease 2019 (COVID-19) pandemic. As learned from severe acute respiratory syndrome (SARS), proper biospecimen handling is necessary to prevent laboratory-related infections. METHODS: Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Presented here are additional considerations intended to complement the interim guidance. These considerations draw on prior SARS recommendations and recent COVID-19 reports. RESULTS: SARS-CoV-2 viral RNA has been detected in various biospecimen types; however, studies are needed to determine whether viral load indicates viable virus. Throughout the pandemic, biospecimens will be collected for various purposes from COVID-19 known and suspected cases, as well as presymptomatic and asymptomatic individuals. Current data suggest the pandemic start may be as early as October 2019; thus, all biospecimens collected since could be considered potentially infectious. CONCLUSIONS: All entities handling these biospecimens should do risk assessments in accordance with institutional policies and adhere to any guidance provided. The scientific community has a responsibility to safely handle and maintain all biospecimens collected during the COVID-19 pandemic. Soon, it will be imperative to convene expert working groups to address the current and long-term storage and use of these biospecimens. Ideally, worldwide guidelines will be established to protect the personnel handling these biospecimens and communities at large. url: https://www.ncbi.nlm.nih.gov/pubmed/32974640/ doi: 10.1093/ajcp/aqaa171 id: cord-323394-osx7llte author: Lanser, Lukas title: Evaluating the clinical utility and sensitivity of SARS-CoV-2 antigen testing in relation to RT-PCR Ct values date: 2020-11-13 words: 1214.0 sentences: 63.0 pages: flesch: 53.0 cache: ./cache/cord-323394-osx7llte.txt txt: ./txt/cord-323394-osx7llte.txt summary: We compared the SARS-CoV-2 antigen detection in nasopharyngeal swab samples by the Panbio™ COVID-19 Ag Rapid test (Abbott, Chicago, Illionis) with the simultaneous routinely conducted RT-PCR analysis of SARS-CoV-2 orf1 RNA detection with the cobas ® analyzer (Roche Diagnostics GmbH, Mannheim, Germany). Among 51 RT-PCR SARS-CoV-2 positive patients, the Pan-bio™ COVID-19 Ag Rapid test was positive in 31 subjects depicting a poor sensitivity of 60.8% (95% CI 46.1-74.2%), compared to 93.3% in the manufacturer''s information. In the 14 patients with a Ct-value ≤ 25, being indicative for higher viral loads, the sensitivity for the Panbio™ COVID-19 Ag Rapid test was at a level of 85.7% (95% CI 57.2-98.2%, Table 1 ). Although our results are quite encouraging regarding the use of antigen test as point-of-care diagnostic which may contribute to a better control of the pandemic, we need longitudinal studied which larger patient cohorts to corroborate our results and to develop algorithms or to identify those subjects who are contagious but not detected by that test. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33185807/ doi: 10.1007/s15010-020-01542-0 id: cord-329877-vish6v8e author: Lapinsky, Stephen E. title: ICU management of severe acute respiratory syndrome date: 2003-05-09 words: 2639.0 sentences: 149.0 pages: flesch: 45.0 cache: ./cache/cord-329877-vish6v8e.txt txt: ./txt/cord-329877-vish6v8e.txt summary: BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ). abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. It has now been documented in 26 countries worldwide, with significant outbreaks in China, Hong Kong, Singapore, and Toronto. Research into identifying the etiological agent, evaluating modes of disease transmission, and treatment options is currently ongoing. DISCUSSION: The disease can produce a severe bilateral pneumonia, with progressive hypoxemia. Up to 20% of patients require mechanical ventilatory support, with a fatal outcome occurring in about 5% of cases. CONCLUSIONS: We review the current knowledge about this disease, with particular emphasis on ICU management and infection control precautions to prevent disease transmission. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available if you access this article at http://dx.doi.org/10.1007/s00134-003-1821-0. On that page (frame on the left side) a link takes you directly to the supplementary material. url: https://doi.org/10.1007/s00134-003-1821-0 doi: 10.1007/s00134-003-1821-0 id: cord-309091-te15ahvw author: Larson, Derek title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 words: 498.0 sentences: 57.0 pages: flesch: 63.0 cache: ./cache/cord-309091-te15ahvw.txt txt: ./txt/cord-309091-te15ahvw.txt summary: A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32949240/ doi: 10.1093/cid/ciaa1436 id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 words: 14797.0 sentences: 760.0 pages: flesch: 42.0 cache: ./cache/cord-326017-qw4qynqv.txt txt: ./txt/cord-326017-qw4qynqv.txt summary: Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Overall, real-time RT-PCR based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against COVID-19 in clinical settings [39] . Another newly developed method, SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), was found to perform simultaneous reverse transcription and isothermal amplification by (i) RT-LAMP for RNA extracted (for nasopharyngeal or oropharyngeal swabs), (ii) Cas12 detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [56] . abstract: The outbreak of novel coronavirus disease (2019-nCoV or COVID-19) is responsible for severe health emergency throughout the world. The attack of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found to be responsible for COVID-19. The World Health Organization has declared the ongoing global public health emergency as a pandemic. The whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. Enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against COVID-19. Furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. Thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with COVID-19. In this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32781617/ doi: 10.3390/diseases8030030 id: cord-274409-4ugdxbmy author: Laskar, Rezwanuzzaman title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date: 2020-10-19 words: 3300.0 sentences: 190.0 pages: flesch: 57.0 cache: ./cache/cord-274409-4ugdxbmy.txt txt: ./txt/cord-274409-4ugdxbmy.txt summary: title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India Further, constitution of ''Disease'' mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. With a definitive possibility of India becoming the most affected country by SARS-CoV-2 in near future and the demographic burden involved, its pertinent to be analyze the accumulating variations in the genome accounting for possible changes in protein and their potential to alter the virus in any manner. Herein we extend our study using the same congregation of sequences to analyze the nature and composition of the observed mutations and their impact on proteins of SARS-CoV-2. The distribution of Disease and Neutral variants across the different genes of SARS-CoV-2 has been shown in Table 4 and Supplementary file 5. abstract: The ongoing global pandemic of SARS-CoV-2 implies a corresponding accumulation of mutations. Herein the mutational status of 611 genomes from India along with their impact on proteins was ascertained. After excluding gaps and ambiguous sequences, a total of 493 variable sites (152 parsimony informative and 341 singleton) were observed. The most prevalent reference nucleotide was C (209) and substituted one was T (293). NSP3 had the highest incidence of 101 sites followed by S protein (74 sites), NSP12b (43 sites) and ORF3a (31 sites). The average number of mutations per sample for males and females was 2.56 and 2.88 respectively suggesting a higher contribution of mutations from females. Non-uniform geographical distribution of mutations implied by Odisha (30 samples, 109 mutations) and Tamil Nadu (31 samples, 40 mutations) suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 ‘Neutral’ and 83 ‘Disease’) affecting amino acid sequence. NSP13 has a maximum of 14 ‘Disease’ variants followed by S protein and ORF3a with 13 each. Further, constitution of ‘Disease’ mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. url: https://doi.org/10.1101/2020.10.19.345066 doi: 10.1101/2020.10.19.345066 id: cord-287156-3plpi6i9 author: Lassandro, Giuseppe title: Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date: 2020-07-01 words: 8021.0 sentences: 535.0 pages: flesch: 43.0 cache: ./cache/cord-287156-3plpi6i9.txt txt: ./txt/cord-287156-3plpi6i9.txt summary: Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission abstract: Human coronaviruses (HCoVs) commonly cause mild upper-respiratory tract illnesses but can lead to more severe and diffusive diseases. A variety of signs and symptoms may be present, and infections can range in severity from the common cold and sore throat to more serious laryngeal or tracheal infections, bronchitis, and pneumonia. Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. In adults, they may cause severe pneumonia that evolves in respiratory distress syndrome and multiorgan failure with a high mortality rate. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. However, some children, such as infants, adolescents, or those with underlying diseases may be more at-risk categories and require greater caution from clinicians. Available data on pediatric coronavirus infections are rare and scattered in the literature. The purpose of this review is to provide to clinicians a complete and updated panel useful to recognize and characterize the broad spectrum of clinical manifestations of coronavirus infections in the pediatric age. url: https://www.ncbi.nlm.nih.gov/pubmed/32670520/ doi: 10.4084/mjhid.2020.042 id: cord-349744-8cg5yj20 author: Lassaunière, Ria title: Evaluation of nine commercial SARS-CoV-2 immunoassays date: 2020-04-10 words: 2649.0 sentences: 145.0 pages: flesch: 53.0 cache: ./cache/cord-349744-8cg5yj20.txt txt: ./txt/cord-349744-8cg5yj20.txt summary: The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. While the four POC tests evaluated according to illness duration were often weakly positive or detected only IgG or IgM during the early phase (data not shown), their sensitivities were comparable to the Wantai Total Ab ELISA and Euroimmun IgA ELISA in all three phases. In the present study, three SARS-CoV-2-specific commercial ELISA assays and six POC rapid tests were evaluated using sera from hospitalized adult patients with PCR-confirmed diagnoses for SARS-CoV-2 and a collection of control serum samples taken before the emergence of the virus in China in December 2019. Overall, the Wantai Total Ab ELISA had superior sensitivity and specificity compared to both Euroimmun IgA and IgG ELISAs. The POC tests varied notably, with the best performance observed for the test produced by AutoBio Diagnostics, followed by the tests produced by Dynamiker Biotechnology and CTK Biotech. abstract: Due to urgency and demand, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoassays are rapidly being developed and placed on the market with limited validation on clinical samples. Thorough validation of serological tests are required to facilitate their use in the accurate diagnosis of SARS-CoV-2 infection, confirmation of molecular results, contact tracing, and epidemiological studies. This study evaluated the sensitivity and specificity of nine commercially available serological tests. These included three enzyme-linked immunosorbent assays (ELISAs) and six point-of-care (POC) lateral flow tests. The assays were validated using serum samples from: i) SARS-CoV-2 PCR-positive patients with a documented first day of disease; ii) archived sera obtained from healthy individuals before the emergence of SARS-CoV-2 in China; iii) sera from patients with acute viral respiratory tract infections caused by other coronaviruses or non-coronaviruses; and iv) sera from patients positive for dengue virus, cytomegalovirus and Epstein Barr virus. The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. The overall performance of the POC tests according to manufacturer were in the rank order of AutoBio Diagnostics > Dynamiker Biotechnology = CTK Biotech > Artron Laboratories > Acro Biotech ≥ Hangzhou Alltest Biotech. Overall, these findings will facilitate selection of serological assays for the detection SARS-CoV-2-specific antibodies towards diagnosis as well as sero-epidemiological and vaccine development studies. url: https://doi.org/10.1101/2020.04.09.20056325 doi: 10.1101/2020.04.09.20056325 id: cord-294704-prizmksg author: Lateef, Fatimah title: New paradigm for protection:: The emergency ambulance services in the time of severe acute respiratory syndrome date: 2004-06-16 words: 2579.0 sentences: 144.0 pages: flesch: 56.0 cache: ./cache/cord-294704-prizmksg.txt txt: ./txt/cord-294704-prizmksg.txt summary: Severe acute respiratory syndrome (SARS) is a newly emerging and highly infectious form of atypical pneumonia with a high rate of transmission, especially among health care workers. With SARS, certain policies had to be implemented rapidly by the emergency ambulance services and the Ministry of Health to support and protect all personnel adequately. The authors hope to share their experience in the implementation of these strategies by the Singapore Civil Defence Force and stress the importance of the psychological preparedness of the paramedics and prehospital care providers worldwide in this era of SARS. To date, a total of seven probable and five suspected cases were conveyed by the EAS out of a total of 204 patients with SARS-like signs and symptoms. With the declaration of the SARS outbreak in Singapore, the Ministry of Health designated Tan Tock Seng Hospital (TTSH), one of the public hospitals, as the ''''SARS hospital.'''' All suspected and probable cases were sent and managed there. abstract: Severe acute respiratory syndrome (SARS) is a newly emerging and highly infectious form of atypical pneumonia with a high rate of transmission, especially among health care workers. With SARS, certain policies had to be implemented rapidly by the emergency ambulance services and the Ministry of Health to support and protect all personnel adequately. The authors discuss the changes in policies and personnel behavior, the training and education that had to be disseminated widely, and certain alternatives in policies such as transportation. The authors hope to share their experience in the implementation of these strategies by the Singapore Civil Defence Force and stress the importance of the psychological preparedness of the paramedics and prehospital care providers worldwide in this era of SARS. url: https://api.elsevier.com/content/article/pii/S1090312703004350 doi: 10.1016/j.prehos.2003.12.016 id: cord-257169-1lk737lw author: Lau, C. S. title: Performance of an automated chemiluminescence SARS-COV-2 IG-G Assay date: 2020-09-08 words: 4265.0 sentences: 230.0 pages: flesch: 53.0 cache: ./cache/cord-257169-1lk737lw.txt txt: ./txt/cord-257169-1lk737lw.txt summary: Methods We assessed assay precision, sensitivity, specificity, positive/negative predictive values (PPV/NPV), cross-reactivity (influenza/dengue/hepatitis B and C/rheumatoid factor/anti-nuclear/double-stranded DNA/syphilis) and sample throughput in samples from real-time polymerase chain reaction (RT-PCR) positive patients/healthcare workers (HCWs)/pre-pandemic samples. A lower COI limit for reactivity (≥0.55, using the 99th percentile COI of our controls and ROC analysis) improved diagnostic sensitivity, especially at 0-6 days POS (45.9% to 55.8%), with a small decrease in specificity (98.9%). We report on our evaluation of the Abbott Architect chemiluminescent immunoassay for SARS-CoV-2-IgG including deriving an optimised cut-off index that may be useful in testing early Covid-19 samples. An optimized COI limit for reactive samples (COI ≥0.55) (concordant values between 99th percentile of healthy controls and ROC analysis) improved the sensitivity of the assay in early infection (45.9% to 55.8% in subjects 0-6 days POS) but with a small decrease in specificity (99.8% to 98.9%). abstract: Introduction We describe our evaluation of the Abbott SARS-CoV-2 IgG assay on the Architect immunoassay analyser. Methods We assessed assay precision, sensitivity, specificity, positive/negative predictive values (PPV/NPV), cross-reactivity (influenza/dengue/hepatitis B and C/rheumatoid factor/anti-nuclear/double-stranded DNA/syphilis) and sample throughput in samples from real-time polymerase chain reaction (RT-PCR) positive patients/healthcare workers (HCWs)/pre-pandemic samples. We compared the cut-off indexes (COIs) between all control samples (HCWs and pre-pandemic) to generate an optimised COI limit for reactivity. Results The assay specificity was 99.8% (n=980) and sensitivity was 45.9-96.7% (n=279). When tested ≥14 days post-positive RT-PCR (POS), the PPV/NPV was 96.4%/99.8%. The difference between the COIs of HCWs/pre-pandemic samples was small (0.01, p<0.0001). There was minimal cross-reactivity with other antibodies. A lower COI limit for reactivity (≥0.55, using the 99th percentile COI of our controls and ROC analysis) improved diagnostic sensitivity, especially at 0-6 days POS (45.9% to 55.8%), with a small decrease in specificity (98.9%). The assay throughput was 100 samples in 70 min. Conclusion The Abbott SARS-CoV-2 IgG assay shows excellent performance in patients ≥14 days POS. The difference between the COIs of HCWs and pre-pandemic samples was numerically small. A lower COI limit improves assay sensitivity with a slight decrease in specificity. url: https://api.elsevier.com/content/article/pii/S000989812030437X doi: 10.1016/j.cca.2020.09.005 id: cord-338054-n2r4pzan author: Lau, Joseph TF title: Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date: 2007-03-15 words: 3846.0 sentences: 202.0 pages: flesch: 48.0 cache: ./cache/cord-338054-n2r4pzan.txt txt: ./txt/cord-338054-n2r4pzan.txt summary: Respondents were asked how likely they would be to adopt the following preventive behaviors if a local human-to-human H5N1 outbreak (defined as "if 2-3 new human-to-human transmission of H5N1 cases were to be reported in Hong Kong") were to occur: face mask use in public venues, increased frequency of handwashing, avoidance of eating poultry, declaration of influenzalike illness (ILI) symptoms at border health checkpoints, the seeking of medical consultation immediately with the onset of a fever, face mask use in public venues when having ILI symptoms and compliance with any quarantine policies. Respondents were asked about perceptions related to human-to-human H5N1 transmission, including perceived modes of transmission (whether human-to-human transmission of the H5N1 virus could occur via respiratory droplets, bodily contact, contaminated objects, eating well-cooked poultry), perceived susceptibility to H5N1 in different groups of people (self, family members, children, adults, older people, health care workers, food handlers, food vendors and the general public), perceived chance of having a major outbreak in Hong Kong in the next 12 months and perceived efficacy of various prevention measures (quarantine of infected people, face mask use in public venues, frequent handwashing, home disinfection, mass extermination of poultry). abstract: BACKGROUND: The prevalence of self-reported preventive behaviors in response to an anticipated local human-to-human H5N1 transmission outbreak and factors associated with such behaviors have not been examined. METHODS: A random, anonymous, cross-sectional telephone survey of 503 Hong Kong Chinese adults. RESULTS: The public in Hong Kong is likely to adopt self-protective behaviors (e.g., wearing face mask in public venues (73.8%), increasing the frequency of handwashing (86.7%)) and behaviors that protect others (e.g., wearing face masks when experiencing influenza-like illness (ILI, 92.4%), immediately seeking medical consultation (94.2%), making declarations when crossing the border with ILI (87.1%), complying to quarantine policies (88.3%)). Multivariate analyses indicated that factors related to age, full-time employment, perceived susceptibility, perceived efficacy of preventive measures, perceived higher fatality as compared to SARS, perceived chance of a major local outbreak, and being worried about self/family members contracting the virus were significantly associated with the inclination to adopt self-protective measures. Similar analyses showed that education level, variables related to perceived efficacy, perceived major local outbreak and such were significantly associated with various behaviors directed towards protecting others. CONCLUSION: In the event of a human-to-human H5N1 outbreak, the public in Hong Kong is likely to adopt preventive measures that may help contain the spread of the virus in the community. url: https://www.ncbi.nlm.nih.gov/pubmed/17359545/ doi: 10.1186/1471-2334-7-18 id: cord-270964-kxze0470 author: Lau, Kwok-Kwong title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 words: 1556.0 sentences: 93.0 pages: flesch: 57.0 cache: ./cache/cord-270964-kxze0470.txt txt: ./txt/cord-270964-kxze0470.txt summary: On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). In our patient, the occurrence of generalized convulsion with a positive RT-PCR for SARS-CoV in the CSF suggests possible infection of the central nervous system by SARS-CoV. The findings from our patient are not compatible with multiple sclerosis, and the PCR result suggests that the central nervous system (CNS) is affected by SARS-CoV. The possibility also remains that infection of the CNS never occurred, as suggested by the lack of focal neurologic deficit, normal CSF pressure, cell count, and biochemistry. Besides involvement of the lungs and possibly the CNS, no good alternative explanation exists for acute renal failure in this patient. Renal failure could possibly be caused by SARS-CoV involving the kidneys. Additionally, our patient had diarrhea from day 3 to day 20, with positive RT-PCR for SARS-CoV in stool specimens, suggesting involvement of the gastrointestinal tract as well. abstract: On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). Cerebrospinal fluid tested positive for SARS coronavirus (SARS-CoV) by reverse transcriptase–polymerase chain reaction. SARS-CoV may have caused an infection in the central nervous system in this patient. url: https://www.ncbi.nlm.nih.gov/pubmed/15030709/ doi: 10.3201/eid1002.030638 id: cord-284702-reu77suz author: Lau, Suet-Ting title: Tachycardia amongst subjects recovering from severe acute respiratory syndrome (SARS) date: 2005-04-08 words: 734.0 sentences: 51.0 pages: flesch: 46.0 cache: ./cache/cord-284702-reu77suz.txt txt: ./txt/cord-284702-reu77suz.txt summary: This study to identify the possible causes for the tachycardia excluded active disease, thyroid dysfunction, haematological, cardiac, autonomic and significant pulmonary defect at 2 months from onset of disease. Possible causes are deconditioning [2] , impaired pulmonary function, impaired cardiac function, cardiac arrhythmia, thyroid dysfunction, anaemia, autonomic dysfunction [3] and anxiety state. Chest radiography findings, haemoglobin level, length of hospital stay, time elapsed after discharge, presence of complications, WHO Quality of Life (QOL) score and Monitored Functional Task Evaluation (MFTE) score [4] are shown in Table 2 . Mild residual CXR changes, minor lung function impairment and normal blood gas makes pulmonary defect unlikely to be a significant cause of sinus tachycardia during normal activity. Deconditioning and anxiety state causes tachycardia in the daytime but not at night, and is compatible with the pattern observed in this cohort. In the absence of significant cardiac, pulmonary, thyroid and haematological dysfunction, we believe that sinus tachycardia is attributable to physical deconditioning and contributed by impaired psychological well-being. abstract: Abstract SARS is a new infection in human. Patients recovering from SARS had palpitation in the form of sinus tachycardia. This study to identify the possible causes for the tachycardia excluded active disease, thyroid dysfunction, haematological, cardiac, autonomic and significant pulmonary defect at 2 months from onset of disease. The symptomatology was attributed to physical deconditioning and anxiety state. Physical and psychological fitness should be restored with rehabilitation. url: https://www.sciencedirect.com/science/article/pii/S0167527305000665 doi: 10.1016/j.ijcard.2004.06.022 id: cord-267587-hag6qydb author: Lau, Susanna K.P. title: Engineering Coronaviruses to Evaluate Emergence and Pathogenic Potential date: 2016-04-16 words: 1977.0 sentences: 107.0 pages: flesch: 46.0 cache: ./cache/cord-267587-hag6qydb.txt txt: ./txt/cord-267587-hag6qydb.txt summary: A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. [1] and another similar study in Nature Medicine published in December 2015 by the same group [2] reported the use of existing sequence data with reverse genetics to engineer SARS-related CoVs and evaluate their potential of emergence and pathogenicity. In order to predict whether a SARS-related bat CoV, named WIV1-CoV, discovered in Chinese horseshoe bats in Yunnan [6] , had the potential to emerge in humans, Menachery et al. employed can be used for evaluating the emergence and pathogenic potential of other CoVs. Before the SARS epidemic, fewer than 10 CoVs with complete genome sequences were available. abstract: A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. Similar approaches could be used to assess the potential of human emergence and pathogenicity for other viruses. url: https://api.elsevier.com/content/article/pii/S0966842X16300038 doi: 10.1016/j.tim.2016.04.001 id: cord-332557-qm3qfvry author: Lau, Susanna K.P. title: SARS Coronavirus Detection Methods date: 2005-07-17 words: 1388.0 sentences: 67.0 pages: flesch: 54.0 cache: ./cache/cord-332557-qm3qfvry.txt txt: ./txt/cord-332557-qm3qfvry.txt summary: Using clinical samples from patients with severe acute respiratory syndrome, we showed that the sensitivities of a quantitative reverse transcription–polymerase chain reaction (80% for fecal samples and 25% for urine samples) were higher than those of the polyclonal (50% and 5%) and monoclonal (35% and 8%) antibody-based nucleocapsid antigen capture enzyme-linked immunosorbent assays. Specimens were tested with polyclonal and monoclonal antibody-based capture ELISAs for SARS-CoV nucleocapsid protein and realtime qRT-PCR. Among the 40 fecal samples from SARS patients, 32 (80%) were positive by qRT-PCR, which was significantly higher than that of the polyclonal (50%) and monoclonal (35%) antibody-based ELISAs (McNemar test, p<0.005 and p<0.001, respectively). Of the 133 urine samples from SARS patients, 33 (25%) were positive by qRT-PCR, which was also significantly higher than that of the polyclonal (5%) and monoclonal (8%) antibody-based ELISAs (McNemar test, p<0.001 for both comparisons). abstract: Using clinical samples from patients with severe acute respiratory syndrome, we showed that the sensitivities of a quantitative reverse transcription–polymerase chain reaction (80% for fecal samples and 25% for urine samples) were higher than those of the polyclonal (50% and 5%) and monoclonal (35% and 8%) antibody-based nucleocapsid antigen capture enzyme-linked immunosorbent assays. url: https://www.ncbi.nlm.nih.gov/pubmed/16022791/ doi: 10.3201/eid1107.041045 id: cord-270533-s2d3q4ob author: Lau, Yu-Lung title: SARS: future research and vaccine date: 2004-11-05 words: 3000.0 sentences: 167.0 pages: flesch: 47.0 cache: ./cache/cord-270533-s2d3q4ob.txt txt: ./txt/cord-270533-s2d3q4ob.txt summary: Severe acute respiratory syndrome (SARS), a newly emerged infectious disease of humans in the 21st century, appeared in Guangdong Province in Southern China in November 2002 and spread to 26 countries on five continents along international air travel routes, causing large scale outbreaks in Hong Kong, Singapore and Toronto in early 2003. This novel CoV has satisfied Koch''s postulates for causation by its consistent isolation from SARS patients, viral isolation, reproduction of disease in non-human primates after inoculation and the presence of specific antibody response against the virus in both patients and experimentally infected primates 8 . Indeed, sporadic reemergence of cases have been reported in Guangdong Province as well as from research laboratories Summary Severe acute respiratory syndrome (SARS) is a new infectious disease of the 21st century that has pandemic potential. The high morbidity and mortality of this potentially pandemic infection demands a rapid research response to develop effective antiviral treatment and vaccine. abstract: Severe acute respiratory syndrome (SARS) is a new infectious disease of the 21st century that has pandemic potential. A novel coronavirus (CoV) was identified as its aetiological agent and its genome was sequenced within months of the World Health Organisation issuing a global threat on SARS. The high morbidity and mortality of this potentially pandemic infection demands a rapid research response to develop effective antiviral treatment and vaccine. This will depend on understanding the pathogenesis and immune response to SARS CoV. Further understanding of the ecology of SARS CoV in human and animals will help prevent future cross species transmission. Likewise for the super-spreading events, clarification of the underlying reasons will be important to prevent a large scale outbreak of SARS. Lastly it is of utmost importance that international research collaboration should be strengthened to deal with SARS and any other emerging infectious disease that can seriously threaten our future. url: https://www.ncbi.nlm.nih.gov/pubmed/15531254/ doi: 10.1016/j.prrv.2004.07.005 id: cord-274707-mxh38hwd author: Laureano, Ana Flávia Santarine title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 words: 3736.0 sentences: 204.0 pages: flesch: 50.0 cache: ./cache/cord-274707-mxh38hwd.txt txt: ./txt/cord-274707-mxh38hwd.txt summary: The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor''s Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis abstract: SARS-CoV-2 is a novel virus from the coronavirus family that emerged in the end of December 2019 in Wuhan, China. The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Supportive care for patients is typically the standard protocol because no specific effective antiviral therapies have been identified so far. The current outbreak is challenging governments and health authorities all over the world. In here we present a comparison among the current diagnostic tools and kits being used to test Brazilian population. url: https://www.ncbi.nlm.nih.gov/pubmed/32491306/ doi: 10.5935/1518-0557.20200046 id: cord-283779-mudwcypl author: Lauretani, Fulvio title: Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date: 2020-05-11 words: 9727.0 sentences: 500.0 pages: flesch: 42.0 cache: ./cache/cord-283779-mudwcypl.txt txt: ./txt/cord-283779-mudwcypl.txt summary: The chronic increase in inflammatory cytokines, augmented by COVID-19 infection, may explain the higher tendency for "the cascade leading to pulmonary fibrosis and insufficiency and activation of clotting" and poorer clinical prognosis, especially in multimorbid older persons (4) . In case of persistent fever, higher than 37.5°C for a time longer than 3 days and peripheral oxygen level lower than 95% after starting therapy, we should consider and proceed to hospitalization especially in multimorbid older patients with cardiac, respiratory diseases and diabetes. First, patients at risk for poor outcomes and higher mortality following infection with SARS-CoV-2, namely older adults and multimorbid individuals, should be checked for malnutrition through screening and assessment. Older patients infected by COVID-19 often experience atypical and less severe symptoms in older persons, side-effects of the drugs and require specific nutritional and motor treatment for avoiding disability and death. abstract: Covid-19 infection is a multisystem disease more frequent in older individuals, especially in those with multiple chronic diseases. This multimorbid and frail population requires attention and a personalized comprehensive assessment in order to avoid the occurrence of adverse outcomes. As other diseases, the COVID-19 presentation in older patients is often atypical with less severe and unspecific symptoms. These subjects both at home and during hospitalization suffer isolation and the lack of support of caregivers. The geriatric care in COVID-19 wards is often missing. The application of additional instruments would be necessary to facilitate and personalize the clinical approach, not only based on diseases but also on functional status. This narrative review starts from diagnostic evaluation, continues with adapted pharmacologic treatment and ends with the recovery phase targeting the nutrition and physical exercise. We developed a check-list of respiratory, gastro-intestinal and other less-specific symptoms, summarized in a table and easily to be filled-up by patients, nurses and general practitioners. As second step, we reported the clinical phases of this disease. Far to be considered just viral infective and respiratory, this disease is also an inflammatory and thrombotic condition with frequent bacterial over-infection. We finally considered timing and selection of treatment, which depend on the disease phase, co-administration of other drugs and require the monitoring of renal, liver and cardiac function. This underlines the role of age not just as a limitation, but also an opportunity to increase the quality and the appropriateness of multidisciplinary and multidimensional intervention in this population. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420939/ doi: 10.23750/abm.v91i2.9629 id: cord-270510-z6qg48nz author: Lauro, A. title: Emergency Endoscopy During the SARS-CoV-2 Pandemic in the North of Italy: Experience from St. Orsola University Hospital—Bologna date: 2020-04-22 words: 1669.0 sentences: 87.0 pages: flesch: 42.0 cache: ./cache/cord-270510-z6qg48nz.txt txt: ./txt/cord-270510-z6qg48nz.txt summary: We report our experience with emergency endoscopies in the COVID-19 era; the goal was to sustain a full emergency endoscopic capability despite the hospital overload due to SARS-CoV-2-infected patients. Instead, emergency endoscopies were performed on SARS-CoV-2-negative and positive patients; a negative-pressure room outside the endoscopy department was planned, but, at the beginning of the pandemic, the only practical possibility was to create a separate suite for SARS-CoV-2-positive patients needing Editor''s Note: This report is one of a series documenting the impact of the pandemic caused by the SARS-CoV-2 virus with resultant morbidity and mortality due to COVID-19. In our hospital, trainees are essential to the management of the burden among patients infected by SARS-CoV-2, but, regarding endoscopy, our policy was to stop training in the urgent endoscopy suite in order to reduce the numbers of inside operators and their use of PPE. abstract: nan url: https://doi.org/10.1007/s10620-020-06270-x doi: 10.1007/s10620-020-06270-x id: cord-324752-t50bg7pq author: Lavery, Michael Joseph title: Cutaneous manifestations of COVID-19 in children (and adults): A virus that does not discriminate date: 2020-11-01 words: 2649.0 sentences: 185.0 pages: flesch: 49.0 cache: ./cache/cord-324752-t50bg7pq.txt txt: ./txt/cord-324752-t50bg7pq.txt summary: COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a beta coronavirus with a characteristic S-glycoprotein ''spike'' on the cell surface.(1) Initial reports did not include cutaneous manifestations as a feature of COVID-19; however, there is a growing repertoire of reports demonstrating an array of dermatologic manifestations on the skin in children and adults. Dermatologic afflictions have been summarized into different categories several times, with the most recent analysis identifying six clinical patterns: urticaria, maculopapular-morbilliform eruption, papulovesicular exanthem, chilblain-like acral pattern, livedo reticularis-livedo racemose pattern, and purpuric ''vasculitic'' pattern.(2) In children, the dermatologic features appear to occur before or concomitantly with other COVID-19 manifestations. 24 Recently, nail changes have been identified in patients with COVID-19 manifesting as a convex half-moon shaped erythematous band at the distal margin of the lunula and coined ''the red half-moon nail sign.'' 25, 26 In the United Kingdom (UK), researchers analyzed data from users of the COVID Symptom Study application and noted 8.8% of 336,847 users, with a positive SARS-CoV-2 viral swab, reported a skin eruption. abstract: COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a beta coronavirus with a characteristic S-glycoprotein ‘spike’ on the cell surface.(1) Initial reports did not include cutaneous manifestations as a feature of COVID-19; however, there is a growing repertoire of reports demonstrating an array of dermatologic manifestations on the skin in children and adults. Dermatologic afflictions have been summarized into different categories several times, with the most recent analysis identifying six clinical patterns: urticaria, maculopapular-morbilliform eruption, papulovesicular exanthem, chilblain-like acral pattern, livedo reticularis-livedo racemose pattern, and purpuric ‘vasculitic’ pattern.(2) In children, the dermatologic features appear to occur before or concomitantly with other COVID-19 manifestations. Dermatologists play a key role in diagnosing patients with COVID-19 who may present for the first time unwittingly exhibiting early signs of COVID-19. We have reviewed the current evidence on the dermatologic impact of COVID-19 in both the adult and pediatric population. url: https://www.sciencedirect.com/science/article/pii/S0738081X2030211X?v=s5 doi: 10.1016/j.clindermatol.2020.10.020 id: cord-302902-34vftqt9 author: Law, Brenda Hiu Yan title: Effect of COVID-19 Precautions on Neonatal Resuscitation Practice: A Balance Between Healthcare Provider Safety, Infection Control, and Effective Neonatal Care date: 2020-08-18 words: 2901.0 sentences: 157.0 pages: flesch: 33.0 cache: ./cache/cord-302902-34vftqt9.txt txt: ./txt/cord-302902-34vftqt9.txt summary: Adaptations have been proposed for resuscitation of infants born to women with COVID-19, to protect health care providers, maintain infection control, and limit post-natal transmission. Changes especially impact respiratory procedures, personal protective equipment (PPE) use, resuscitation environments, teamwork, and family involvement. Adaptations have been proposed for resuscitation of infants born to women with suspected or confirmed COVID-19, to protect health care providers (HCPs), limit post-natal transmission, and maintain infection control (7) . Neonatal resuscitation may be especially impacted by changes in (i) respiratory support, (ii) personal protective equipment (PPE), (iii) resuscitation environment, (iv) team-based activities, and (v) family involvement ( Table 1) . Modifications to ventilation practices during neonatal resuscitation have been proposed to protect HCPs during AGPs, based on limited evidence on vertical transmission and aerosolization of SARS-CoV-2 (7, 9) . General COVID-19 resuscitation guidelines recommend the use of viral filters on mask ventilation devices to decrease risks to HCPs (9) . abstract: Adaptations have been proposed for resuscitation of infants born to women with COVID-19, to protect health care providers, maintain infection control, and limit post-natal transmission. Changes especially impact respiratory procedures, personal protective equipment (PPE) use, resuscitation environments, teamwork, and family involvement. Adding viral filters to ventilation devices and modifications to intubation procedures might hinder effective ventilation. PPE could delay resuscitation, hinder task performance, and degrade communication. Changes to resuscitation locations and team composition alter workflow and teamwork. Physical distancing measures and PPE impede family-integrated care. These disruptions need to be considered given the uncertainty of vertical transmission of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33014919/ doi: 10.3389/fped.2020.00478 id: cord-296602-19noki6p author: Law, Helen KW title: Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells date: 2009-06-08 words: 4427.0 sentences: 230.0 pages: flesch: 53.0 cache: ./cache/cord-296602-19noki6p.txt txt: ./txt/cord-296602-19noki6p.txt summary: In this study, we focussed on the gene expression of toll-like receptors (TLRs), chemokine receptors (CCRs) and death receptor ligands in SARS-CoV infected DCs. We also compared adult and cord blood (CB) DCs to find a possible explanation for the age-dependent severity of SARS. There was also strong induction of TNF-related apoptosis-inducing ligand (TRAIL), but not Fas ligand gene expression in SARS-CoV infected DCs. Interestingly, the expressions of most genes studied were higher in CB DCs than adult DCs. CONCLUSION: The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. Interestingly, the SARS-CoV infected DCs showed low expression of antiviral cytokines (IFN-α, IFN-β, IFN-γ and IL-12p40), moderate upregulation of proinflammatory cytokines (TNF-α and IL-6) but significant upregulation of inflammatory chemokines (macrophage inflammatory protein (MIP)-1α/CCL3, regulated upon activation, normal T cell expressed and secreted (RANTES)/CCL-5, interferon-inducible protein of 10 kD (IP-10)/CXCL10 and monocyte chemotactic protein (MCP)-1/CCL2. abstract: BACKGROUND: The SARS outbreak in 2003 provides a unique opportunity for the study of human responses to a novel virus. We have previously reported that dendritic cells (DCs) might be involved in the immune escape mechanisms for SARS-CoV. In this study, we focussed on the gene expression of toll-like receptors (TLRs), chemokine receptors (CCRs) and death receptor ligands in SARS-CoV infected DCs. We also compared adult and cord blood (CB) DCs to find a possible explanation for the age-dependent severity of SARS. RESULTS: Our results demonstrates that SARS-CoV did not modulate TLR-1 to TLR-10 gene expression but significantly induced the expression of CCR-1, CCR-3, and CCR-5. There was also strong induction of TNF-related apoptosis-inducing ligand (TRAIL), but not Fas ligand gene expression in SARS-CoV infected DCs. Interestingly, the expressions of most genes studied were higher in CB DCs than adult DCs. CONCLUSION: The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. These findings may explain the increased lung infiltrations and lymphoid depletion in SARS patients. Further explorations of the biological significance of these findings are warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/19505311/ doi: 10.1186/1471-2172-10-35 id: cord-299308-gza1pwx6 author: Laxminarayan, Ramanan title: Is Gradual and Controlled Approach to Herd Protection a Valid Strategy to Curb the COVID-19 Pandemic? date: 2020-05-06 words: 1557.0 sentences: 80.0 pages: flesch: 52.0 cache: ./cache/cord-299308-gza1pwx6.txt txt: ./txt/cord-299308-gza1pwx6.txt summary: Most pandemics in the twentieth and twentyfirst centuries have been caused by virusesinfluenza, chikungunya, HIV/AIDS and now the coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients reportedly acquire COVID-19 either through close contact with infected family members (89%), exposure to endemic areas (33%), or both (22%); with the majority (53%) showing moderate symptoms and no severe or critical cases [2] . We do not endorse the idea of letting the epidemic a free hand in order to create sufficient herd immunity to end the epidemic;as it would entail an enormous burden on the healthcare system -United Kingdom, at first, considered a different approach -of unrestricted spread of disease without any brakes applied, but public health experts were able to convince the government to accept the more reasonable mitigation approach. The proportion of the population that should be exposed to the virus for herd immunity to be effective is calculated as 1-1/Ro. In the absence of serological studies, the true extent of spread of SARS-COV-2 in India is unknown. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32376793/ doi: 10.1007/s13312-020-1844-4 id: cord-316712-1ngcwdln author: Laxminarayan, Ramanan title: India’s Battle against COVID-19: Progress and Challenges date: 2020-08-24 words: 2592.0 sentences: 149.0 pages: flesch: 56.0 cache: ./cache/cord-316712-1ngcwdln.txt txt: ./txt/cord-316712-1ngcwdln.txt summary: The first reported case of infection with the SARS-CoV-2, the virus that causes COVID-19, in India was reported on January 30, 2020 in an Indian student evacuated from Wuhan, and the first death was reported on March 12, 2020. Model-based estimates 8 produced in March 2020 had indicated that a national lockdown could reduce the number of infections at the peak of the pandemic-expected in early May-by 70-80%, depending on the degree of public compliance with physical distancing. Mortality rates (based on reported cases and deaths) appear to be low in India, as they are in most countries in the region, perhaps indicative of both limited testing and other unexplained factors. 12 At the current time, India has conducted approximately 18,000 tests per million population, a rate that is a third that of South Africa, about 60% that of Nepal, and among the lowest of any large country. abstract: India's Battle against COVID-19: Progress and Challenges. url: https://doi.org/10.4269/ajtmh.20-0992 doi: 10.4269/ajtmh.20-0992 id: cord-308740-06jr58kz author: Lazaridis, Charalampos title: Involvement of Cardiovascular System As The Critical Point in Coronavirus Disease 2019 (COVID-19) Prognosis and Recovery date: 2020-06-10 words: 2536.0 sentences: 173.0 pages: flesch: 42.0 cache: ./cache/cord-308740-06jr58kz.txt txt: ./txt/cord-308740-06jr58kz.txt summary: All cases were linked to a seafood market in the same city 2 and were confirmed to be associated with a novel RNA betacoronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3,4 . A recent study in patients with heart failure found that circulating levels of ACE2 were higher in men than in women, suggesting increased ACE2 tissue expression which could contribute to susceptibility to SARS-CoV-2 infection and disease progress 49 . Remarkably, severe COVID-19 has been associated with hypokalemia and higher blood pressure, supporting suggestions of decreased ACE2 function and augmented levels of angiotensin II after SARS-CoV-2 infection 96 . The participation of ACE2 in the pathogenesis of COVID-19, acting as a cell receptor for SARS-CoV-2 13 has caused increasing concern about the role of antihypertensive therapy with angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II Chloroquine, an antimalarial agent with known anti-viral effects 141 Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan abstract: The novel coronavirus disease (COVID-19) pandemic has already caused more than 300,000 deaths worldwide. Several studies have elucidated the central role of cardiovascular complications in the disease course. Herein, we provide a concise review of current knowledge regarding the involvement of cardiovascular system in the pathogenesis and prognosis of COVID-19. We summarize data from 21 studies involving in total more than 21,000 patients from Asia, Europe and the USA indicating that severe disease is associated with the presence of myocardial injury, heart failure and arrhythmias. Additionally, we present the clinical and laboratory differences between recovered and deceased patients highlighting the importance of cardiac manifestations. For the infected patients, underlying cardiovascular comorbidities and especially existing cardiovascular disease seem to predispose to the development of cardiovascular complications, which are in turn associated with higher mortality rates. We provide mechanistic insights into the underlying mechanisms including direct myocardial damage by the virus and the consequences of the hyperinflammatory syndrome developed later in the disease course. Finally, we summarize current knowledge on therapeutic modalities and recommendations by scientific societies and experts regarding the cardiovascular management of COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S1109966620300932?v=s5 doi: 10.1016/j.hjc.2020.05.004 id: cord-023488-jf2xl3vl author: Le Duc, James W. title: Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date: 2016-02-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The emergence of a new viral disease is one of the most dramatic aspects of virology, which often receives widespread attention from the scientific community and the lay public. Considering that the discipline of animal virology was established over 100 years ago, it may seem surprising that new virus diseases are still being discovered. How this happens is the subject of this chapter. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170184/ doi: 10.1016/b978-0-12-800964-2.00016-1 id: cord-304418-k9owyolj author: Le Maréchal, M. title: COVID-19 in clinical practice: a narrative synthesis date: 2020-09-29 words: 6288.0 sentences: 367.0 pages: flesch: 49.0 cache: ./cache/cord-304418-k9owyolj.txt txt: ./txt/cord-304418-k9owyolj.txt summary: Plasmatic detection of SARS-CoV-2 has been reported but only with low viral titers, and mainly in clinically severe cases [44] ; bloodstream infectivity has yet to be demonstrated. The first large clinical trial published on LPV/RTV on SARS-CoV-2 compared 99 patients receiving the antiviral vs 100 receiving SoC alone [124] ; there was no difference between the 2 groups regarding the primary end point (time to improvement) (15 vs 16 days, p=0.09). Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China abstract: The coronavirus disease 2019 (COVID-19) was first reported in the city of Wuhan, China. The disease rapidly spread to the rest of China, to Southern-East Asia, then to Europe, America, and on to the rest of the world. COVID-19 is associated with a betacoronavirus named SARS-CoV-2. The virus penetrates the organism through the respiratory tract, conveyed by contaminated droplets. The main cell receptor targeted is the surface-bound ACE-2. As of the 26th July 2020, 15,200,000 COVID-19 cases and 650,000 deaths were reported worldwide. The mortality rate is estimated between 1.3 and 18.3%. The reproductive rate without any public health intervention is estimated around 4-5.1 in France. Most hospitalized patients for COVID-19 present respiratory symptoms, which in some cases is associated with fever. Up to 86% of admissions to ICU are related to acute respiratory failure. To date, no anti-viral therapy has proven its efficacy considering randomized trials. Only immunomodulatory treatments such as corticosteroids have shown to cause significant improvement in patient outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/33007400/ doi: 10.1016/j.medmal.2020.09.012 id: cord-349794-mhviub6e author: Le, Brian L. title: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date: 2020-10-23 words: 3810.0 sentences: 216.0 pages: flesch: 43.0 cache: ./cache/cord-349794-mhviub6e.txt txt: ./txt/cord-349794-mhviub6e.txt summary: We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. By infecting human adenocarcinomic alveolar basal epithelial cells with SARS-CoV-2 and comparing to controls, the authors generated a list of 120 differentially expressed genes. Here, we applied our existing computational drug repositioning pipeline to identify drug profiles with significantly reversed differential gene expression compared to predicted inhibitors (including one tested in Calu-3) were incubated with SARS-CoV-2 infected human embryonic kidney 293T cells overexpressing ACE2 (293T-ACE2) with viral replication determined using an immunofluorescence-based assay. In this study, we applied our drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available RNA-seq data ( Figure 1 ). Here, we used a transcriptomics-based drug repositioning pipeline to predict therapeutic drug hits for three different input SARS-CoV-2 signatures, each of which came from distinct human cell or tissue origins. abstract: The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated sixteen of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19. url: https://doi.org/10.1101/2020.10.23.352666 doi: 10.1101/2020.10.23.352666 id: cord-259558-remrzrq1 author: LeBlanc, Jason J. title: A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 date: 2020-05-16 words: 1458.0 sentences: 96.0 pages: flesch: 52.0 cache: ./cache/cord-259558-remrzrq1.txt txt: ./txt/cord-259558-remrzrq1.txt summary: Low viral loads are known to occur in the early and late stages of COVID-19 illness [4] [5] [6] [11] [12] [13] [14] [15] [16] [17] [18] [19] , and false negative results can arise from differences in analytical sensitivity between methods (Table S1 ) [20, 21] , the variability in specimen collection, or factors influencing specimen stability or recovery of SARS-CoV-2 RNA during specimen transport, storage or processing. [4, 13] For example, three different SARS-CoV-2 targets were detected between the various PCR methods used for testing of J o u r n a l P r e -p r o o f specimens from patient 1, yet high Ct values were observed for these targets (Table 1) . abstract: Given the global shortage of nasopharyngeal (NP) swabs typically used for respiratory virus detection, alternative collection methods were evaluated during the COVID-19 pandemic. This study showed that a combined oropharyngeal/nares swab is a suitable alternative to NP swabs for the detection of SARS-CoV-2, with sensitivities of 91.7% and 94.4%, respectively. url: https://www.ncbi.nlm.nih.gov/pubmed/32425660/ doi: 10.1016/j.jcv.2020.104442 id: cord-255069-9xueqdri author: Leary, Shay title: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date: 2020-04-11 words: 1821.0 sentences: 77.0 pages: flesch: 43.0 cache: ./cache/cord-255069-9xueqdri.txt txt: ./txt/cord-255069-9xueqdri.txt summary: The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . abstract: The COVID-19 pandemic is caused by the single-stranded RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus of zoonotic origin that was first detected in Wuhan, China in December 2019. There is evidence that homologous recombination contributed to this cross-species transmission. Since that time the virus has demonstrated a high propensity for human-to-human transmission. Here we report two newly identified adjacent amino acid polymorphisms in the nucleocapsid at positions 203 and 204 (R203K/G204R) due to three adjacent nucleotide changes across the two codons (i.e. AGG GGA to AAA CGA). This new strain within the LGG clade may have arisen by a form of homologous recombination from the core sequence (CS-B) of the transcription-regulating sequences of SAS-CoV-2 itself and has rapidly increased to approximately one third of reported sequences from Europe during the month of March 2020. We note that these polymorphisms are predicted to reduce the binding of an overlying putative HLA-C*07-restricted epitope and that HLA-C*07 is prevalent in Caucasians being carried by >40% of the population. The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. url: https://doi.org/10.1101/2020.04.10.029454 doi: 10.1101/2020.04.10.029454 id: cord-316646-rd3zl9qz author: Lebedin, Y. S. title: Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia date: 2020-09-25 words: 2531.0 sentences: 132.0 pages: flesch: 49.0 cache: ./cache/cord-316646-rd3zl9qz.txt txt: ./txt/cord-316646-rd3zl9qz.txt summary: The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia In this report, we evaluate the SARS-CoV-2 nucleocapsid antigen (N-Ag) and respective antibodies as diagnostic markers and demonstrate the total prevalence of N-Ag seroconversion in SARS-CoV-2-associated pneumonia patients. The immunoassay-based detection of serum N-Ag in combination with its respective antibodies confirmed COVID-19 in 280 patients (59%) of the studied cohort. The results indicate high relevance of combined serological tests for SARS-CoV-2 N-Ag and the antibodies to SARS-CoV-2 antigens as applied to the infectious pneumonia emergency patients at the admission, since: According to the results of the study, hospitalization of the patients with SARS-CoV-2associated pneumonia at the height of pandemic most frequently occurred before the onset of seroconversion (i.e. against the background of detectable serum N-Ag concentrations). abstract: The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia url: http://medrxiv.org/cgi/content/short/2020.09.24.20200303v1?rss=1 doi: 10.1101/2020.09.24.20200303 id: cord-324557-4u8dja0n author: Leblanc, Jean‐François title: Risk of Transmission of Severe Acute Respiratory Syndrome Coronavirus‐2 by Transfusion: A Literature Review date: 2020-08-15 words: 3044.0 sentences: 195.0 pages: flesch: 50.0 cache: ./cache/cord-324557-4u8dja0n.txt txt: ./txt/cord-324557-4u8dja0n.txt summary: Complementary searches have identified reports demonstrating that the correlation between the presence of viral RNA in a biological sample and infectivity requires a minimal RNA load, which is rarely, if at all observed, in blood components. More specifically, PubMed was interrogated with a series of queries aimed at identifying references that relate to COVID-19/SARS-CoV-2 and the detection of viral genomic material in blood, plasma, or serum. From this screen, 23 references reporting any data or stating any information on the detection of SARS-CoV-2 genomic material in human blood, plasma, or serum, were selected ( Table 2) . An exhaustive search strategy led to the identification of 23 references reporting data on the detection of SARS-CoV-2 genomic material in blood components (Table 2) . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a novel human coronavirus responsible for coronavirus disease 2019 (COVID‐19). The emergence of this virus in Wuhan (China) at the end of 2019, and its worldwide spread to reach the pandemic stage, has raised concerns about the possible risk that it might be transmissible by transfusion. This theoretical risk is further supported by reports of the detection of viral RNA in the blood of some infected individuals. To further address this risk, a thorough PubMed literature search was performed to systematically identify studies reporting data on the detection of SARS‐CoV‐2 RNA in blood or its components. Complementary searches were done to identify articles reporting data on the in vitro infectivity of blood components. At least 23 articles presenting data on the detection of SARS‐CoV‐2 RNA in blood, plasma, or serum were identified. Of these, three studies reported on blood donors with COVID‐19 infection identified post‐donation, and no cases of transfusion transmission were identified. A few studies mentioned results of in vitro infectivity assays of blood components in permissive cell lines, none of which were able to detect infectious virus in blood or its components. Complementary searches have identified reports demonstrating that the correlation between the presence of viral RNA in a biological sample and infectivity requires a minimal RNA load, which is rarely, if at all observed, in blood components. Overall, the available evidence suggests that the risk of transmission of SARS‐CoV‐2 by transfusion remains theoretical. url: https://doi.org/10.1111/trf.16056 doi: 10.1111/trf.16056 id: cord-304031-poh3te9j author: Leder, K. title: Respiratory infections during air travel date: 2005-01-13 words: 4521.0 sentences: 241.0 pages: flesch: 50.0 cache: ./cache/cord-304031-poh3te9j.txt txt: ./txt/cord-304031-poh3te9j.txt summary: Issues regarding cabin air quality and the potential risks of transmission of respiratory infections during flight have been investigated and debated previously, but, with the advent of severe acute respiratory syndrome and influenza outbreaks, these issues have recently taken on heightened importance. Confined space, limited ventilation, prolonged exposure times and recirculating air, all common to air travel, are demonstrated risk factors for the transmission of upper respiratory tract infections in other settings and create the potential for the spread of respiratory pathogens during flight. Aspects of the aircraft cabin environment that influence the potential transmission of respiratory pathogens on airplanes will be outlined here and then the Internal Medicine Journal 2005; 35: 50-55 evidence for the occurrence of outbreaks of respiratory illness among airline passengers will be reviewed. The majority of patients (68%) had recently completed a series of commercial aircraft flights, and the authors concluded that air travel played a role in the transmission of disease among the 60 infected persons. abstract: An increasing number of individuals undertake air travel annually. Issues regarding cabin air quality and the potential risks of transmission of respiratory infections during flight have been investigated and debated previously, but, with the advent of severe acute respiratory syndrome and influenza outbreaks, these issues have recently taken on heightened importance. Anecdotally, many people complain of respiratory symptoms following air travel. However, studies of ventilation systems and patient outcomes indicate the spread of pathogens during flight occurs rarely. In the present review, aspects of the aircraft cabin environment that affect the likelihood of transmission of respiratory pathogens on airplanes are outlined briefly and evidence for the occurrence of outbreaks of respiratory illness among airline passengers are reviewed. (Intern Med J 2005; 35: 50–55) url: https://www.ncbi.nlm.nih.gov/pubmed/15667469/ doi: 10.1111/j.1445-5994.2004.00696.x id: cord-263719-a9mnjr3s author: Lee, A. title: Wuhan novel coronavirus (COVID-19): why global control is challenging? date: 2020-02-29 words: 1276.0 sentences: 101.0 pages: flesch: 56.0 cache: ./cache/cord-263719-a9mnjr3s.txt txt: ./txt/cord-263719-a9mnjr3s.txt summary: At this stage, the global spread of COVID-19 acute respiratory disease continues to grow, and the full extent and severity of this outbreak remains to be seen. 7 Once the pathogen has landed in a new country, the likelihood of contagion and spread is dependent on local transmission pathways and the strength of local health protection systems. 8 High-income countries such as the United States and United Kingdom have well-developed health protection systems to detect and respond to communicable disease threats. The other component of well-developed health protection systems are strong infectious disease surveillance systems. The current concerns then regarding the 2019-nCoV outbreak must be for low-and middle-income countries where health protection systems tend to be weaker. In these settings, laboratory resources may be lacking, notification of infectious diseases are often not timely or complete, and their public health infrastructure is often weak. Global infectious disease surveillance and health intelligence abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32111295/ doi: 10.1016/j.puhe.2020.02.001 id: cord-274521-u8p5lz9o author: Lee, Abby C. title: Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation date: 2020-07-31 words: 5720.0 sentences: 308.0 pages: flesch: 51.0 cache: ./cache/cord-274521-u8p5lz9o.txt txt: ./txt/cord-274521-u8p5lz9o.txt summary: In this study, we mined three independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. Both smoking and use of nicotine and flavor-containing e-cigs led to upregulation of pro-inflammatory cytokines and inflammasome-related genes. Current data indicate that patients who have cardiovascular and chronic respiratory conditions, including those caused by tobacco use, are at higher risk of developing severe COVID-19 symptoms and have significantly increased fatality [1] . The GSE138326 dataset, from Song et al., details gene expression in the bronchial epithelial cells of patients who smoked flavor-less and nicotine-less e-cigs vs. The GSE112073 dataset, from Corbett et al., details gene expression in bronchial cells of patients who smoked nicotine-containing e-cigs of any flavor vs. The upregulation of a significant number of inflammatory cytokines in smokers and nicotine/flavor-containing e-cig users and the association of smoking with IL-1B prompted us to examine inflammasome activation in smokers and e-cig users ( Table 2 ). abstract: The COVID-19 pandemic caused by the SARS-CoV-2 virus, overlaps with the ongoing epidemics of cigarette smoking and electronic cigarette (e-cig) vaping. However, there is scarce data relating COVID-19 risks and outcome with cigarette or e-cig use. In this study, we mined three independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. We found that smoking, but not vaping, upregulates ACE2, the cellular receptor that SARS-CoV-2 requires for infection. Both smoking and use of nicotine and flavor-containing e-cigs led to upregulation of pro-inflammatory cytokines and inflammasome-related genes. Specifically, chemokines including CCL20 and CXCL8 are upregulated in smokers, and CCL5 and CCR1 are upregulated in flavor/nicotine-containing e-cig users. We also found genes implicated in inflammasomes, such as CXCL1, CXCL2, NOD2, and ASC, to be upregulated in smokers and these e-cig users. Vaping flavor and nicotine-less e-cigs, however, did not lead to significant cytokine dysregulation and inflammasome activation. Release of inflammasome products, such as IL-1B, and cytokine storms are hallmarks of COVID-19 infection, especially in severe cases. Therefore, our findings demonstrated that smoking or vaping may critically exacerbate COVID-19-related inflammation or increase susceptibility to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32752138/ doi: 10.3390/ijms21155513 id: cord-279105-e2zjxjox author: Lee, Cheryl Yi-Pin title: Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control date: 2020-04-24 words: 3872.0 sentences: 212.0 pages: flesch: 44.0 cache: ./cache/cord-279105-e2zjxjox.txt txt: ./txt/cord-279105-e2zjxjox.txt summary: With the limitations of qRT-PCR, immunoassays may offer another FIGURE 2 | Schematic illustration on the window period of detection for either viral RNA or antibodies in SARS-CoV-2-infected individuals. However, interestingly, one study demonstrated that longitudinal profiling of both antibodies in a population of 63 COVID-19 patients showed no specific chronological order in terms of IgM and IgG seroconversion (10) , which was also observed in patients infected with SARS-CoV and another human coronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV) (22, 23) . These findings on SARS-CoV-2-specific antibodies seroconversion against the S viral protein suggest the importance to test for both IgM and IgG antibodies to confirm a positive infection. With the availability of immunoassays utilizing various coronavirus structural proteins, the use of more than one different antigen-based serological approach may be essential to establish a true positive SARS-CoV-2 infection. abstract: Since December 2019, the novel coronavirus, SARS-CoV-2, has garnered global attention due to its rapid transmission, which has infected more than two million people worldwide. Early detection of SARS-CoV-2 is one of the crucial interventions to control virus spread and dissemination. Molecular assays have been the gold standard to directly detect for the presence of viral genetic material in infected individuals. However, insufficient viral RNA at the point of detection may lead to false negative results. As such, it is important to also employ immune-based assays to determine one's exposure to SARS-CoV-2, as well as to assist in the surveillance of individuals with prior exposure to SARS-CoV-2. Within a span of 4 months, extensive studies have been done to develop serological systems to characterize the antibody profiles, as well as to identify and generate potentially neutralizing antibodies during SARS-CoV-2 infection. The vast diversity of novel findings has added value to coronavirus research, and a strategic consolidation is crucial to encompass the latest advances and developments. This review aims to provide a concise yet extensive collation of current immunoassays for SARS-CoV-2, while discussing the strengths, limitations and applications of antibody detection in SARS-CoV-2 research and control. url: https://www.ncbi.nlm.nih.gov/pubmed/32391022/ doi: 10.3389/fimmu.2020.00879 id: cord-293826-2p7dqacd author: Lee, Cheryl Yi-Pin title: Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date: 2020-10-09 words: 1314.0 sentences: 84.0 pages: flesch: 54.0 cache: ./cache/cord-293826-2p7dqacd.txt txt: ./txt/cord-293826-2p7dqacd.txt summary: Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Overall, our study shows that the D614G mutation on the S protein does not 150 impact SARS-CoV-2 neutralization by the host antibody response, nor confer viral 151 resistance against the humoral immunity. abstract: The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralize against the G614 variant. In this report, profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralization profiles against both S protein variants, albeit waning neutralizing antibody capacity at the later phase of infection. These findings provide further insights towards the validity of current immune-based interventions. IMPORTANCE Random mutations in the viral genome is a naturally occurring event that may lead to enhanced viral fitness and immunological resistance, while heavily impacting the validity of licensed therapeutics. A single point mutation from aspartic acid (D) to glycine (G) at position 614 of the SARS-CoV-2 spike (S) protein, termed D614G, has garnered global attention due to the observed increase in transmissibility and infection rate. Given that a majority of the developing antibody-mediated therapies and serological assays are based on the S antigen of the original Wuhan reference sequence, it is crucial to determine if humoral immunity acquired from the original SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against the novel prevailing D614G variant. url: https://doi.org/10.1101/2020.10.08.332544 doi: 10.1101/2020.10.08.332544 id: cord-284028-l0r7f9sr author: Lee, Chi-Wei title: A loophole in international quarantine procedures disclosed during the SARS crisis date: 2004-12-30 words: 2797.0 sentences: 130.0 pages: flesch: 47.0 cache: ./cache/cord-284028-l0r7f9sr.txt txt: ./txt/cord-284028-l0r7f9sr.txt summary: This phenomenon revealed a loophole in the control mechanisms of international quarantine procedures, letting travelers carrying a highly contagious virus slip by undetected and causing possible multi-country outbreaks of communicable diseases. Reasons for its rapid global spread were the highly contagious nature of the virus with its air-borne route of infection, the busy links between affected countries, and probably inadequacies in international quarantine procedures. As shown in Tables 1 and 2, although none of the six patients were eventually diagnosed wild SARS, this observed phenomenon disclosed a very important loophole in the control aspect of international quarantine procedures: the inability to prevent persons with a highly contagious virus from slipping past undetected and thus preventing the further spread of epidemics like SARS on international travel routes. In this study, we identified that there were loopholes in the international quarantine system for controlling the international spread of contagious disease like SARS, especially when travelers lack a strong motivation to cooperate with national health authorities. abstract: This study describes a loophole in the international quarantine system during the recent Asian severe acute respiratory syndrome (SARS) outbreak. Specifically, that of travelers disguising symptoms of respiratory tract infection at international airports, in order to board aircraft to return to their home countries—notwithstanding the infection risks this involves to others. High medical fees for treatment to non-residents in epidemic areas were found to be the main cause for this behaviour. This phenomenon revealed a loophole in the control mechanisms of international quarantine procedures, letting travelers carrying a highly contagious virus slip by undetected and causing possible multi-country outbreaks of communicable diseases. Clinical evidence collected from medical records at medical centers can highlight this oversight. url: https://www.sciencedirect.com/science/article/pii/S1477893904001267 doi: 10.1016/j.tmaid.2004.10.002 id: cord-338723-3vm23fgy author: Lee, In-Hee title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date: 2020-08-26 words: 2784.0 sentences: 183.0 pages: flesch: 57.0 cache: ./cache/cord-338723-3vm23fgy.txt txt: ./txt/cord-338723-3vm23fgy.txt summary: title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. SARS-CoV-2 is an enveloped and positive single-stranded RNA (ssRNA) virus and initiates human cell entry by binding of spike (S) protein present on the viral envelope to angiotensin converting enzyme 2 (ACE2) receptor on the host cells (Zhou et al., 2020b) . Here we surveyed the genetic variants in functional residues of ACE2, TMPRSS2, CTSB/L (CatB/L), and TLR3/7/8 to investigate the difference in the genetic predisposition to the susceptibly of SARS-CoV-2 infection and the initiation of innate immune response. The list of reported genetic variants in the genes and their allele frequencies (AFs) were ACE2 is highly conserved with few nonsynonymous variants in the interacting domain with the SARS-CoV-2 RBM (Lan et al., 2020) . abstract: The COVID-19 pandemic highlighted healthcare disparities in multiple countries. As such morbidity and mortality vary significantly around the globe between populations and ethnic groups. Underlying medical conditions and environmental factors contribute higher incidence in some populations and a genetic predisposition may play a role for severe cases with respiratory failure. Here we investigated whether genetic variation in the key genes for viral entry to host cells—ACE2 and TMPRSS2—and sensing of viral genomic RNAs (i.e., TLR3/7/8) could explain the variation in incidence across diverse ethnic groups. Overall, these genes are under strong selection pressure and have very few nonsynonymous variants in all populations. Genetic determinant for the binding affinity between SARS-CoV-2 and ACE2 does not show significant difference between populations. Non-genetic factors are likely to contribute differential population characteristics affected by COVID-19. Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. url: https://doi.org/10.1016/j.meegid.2020.104507 doi: 10.1016/j.meegid.2020.104507 id: cord-332071-bqvn3ceq author: Lee, Jeong Seok title: Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 date: 2020-07-10 words: 7099.0 sentences: 412.0 pages: flesch: 53.0 cache: ./cache/cord-332071-bqvn3ceq.txt txt: ./txt/cord-332071-bqvn3ceq.txt summary: In a murine model of SARS-CoV infection, a delayed, but considerable type I IFN (IFN-I) response CORONAVIRUS Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 (Page numbers not final at time of first release) 2 promotes the accumulation of monocytes-macrophages and the production of pro-inflammatory cytokines, resulting in lethal pneumonia with vascular leakage and impaired virusspecific T-cell responses (10) . To examine the host immune responses in a cell type-specific manner, we subjected 59,572 cells to t-distributed stochastic neighbor embedding (tSNE) based on highly variable genes using the Seurat package (17) and identified 22 different clusters unbiased by patients or experimental batches of scRNA-seq (Fig. 1A, Fig. S1D ). First, we combined both mild and severe COVID-19 as a COVID-19 group and identified disease-specific changes in genes for each cell type compared to the healthy donor group using model-based analysis of single cell transcriptomics (MAST) (18) . abstract: Although most SARS-CoV-2-infected individuals experience mild coronavirus disease 2019 (COVID-19), some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly up-regulation of the TNF/IL-1β-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1β-driven inflammation, and this was not seen in patients with milder COVID-19. Interestingly, we documented type I IFN-driven inflammatory features in patients with severe influenza as well. Based on this, we propose that the type I IFN response plays a pivotal role in exacerbating inflammation in severe COVID-19. url: https://doi.org/10.1126/sciimmunol.abd1554 doi: 10.1126/sciimmunol.abd1554 id: cord-258360-fqrn02lr author: Lee, Jimmy title: No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date: 2020-06-19 words: 2833.0 sentences: 151.0 pages: flesch: 52.0 cache: ./cache/cord-258360-fqrn02lr.txt txt: ./txt/cord-258360-fqrn02lr.txt summary: In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ''upstream'' market chain samples suggests that these detections in ''downstream'' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. Our negative findings across five viral families associated with emerging and re-emerging zoonotic diseases in recent decades contrast with reports of the detection of parainfluenza virus (Wang et al., 2018) , coronaviruses and Sendai virus (Liu et al., 2019; Zhang et al., 2020) , and SARSr-CoVs (Lam et al., 2020; Xiao et al., 2020) in Sunda pangolins. We therefore conclude that the detections of SARS-CoV-2 related viruses in pangolins are more plausibly a result of their exposure to infected people, wildlife or other animals after they entered the trade network. abstract: The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (>50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families – Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ‘upstream’ market chain samples suggests that these detections in ‘downstream’ animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally. url: https://doi.org/10.1101/2020.06.19.158717 doi: 10.1101/2020.06.19.158717 id: cord-266903-lxtxqdst author: Lee, Jong-Hwan title: A novel rapid detection for SARS-CoV-2 spike 1 antigens using human angiotensin converting enzyme 2 (ACE2) date: 2020-10-15 words: 2514.0 sentences: 147.0 pages: flesch: 62.0 cache: ./cache/cord-266903-lxtxqdst.txt txt: ./txt/cord-266903-lxtxqdst.txt summary: In this study, we designed and developed a novel rapid detection method for SARS-CoV-2 spike 1 (S1) protein using the SARS-CoV-2 receptor ACE2, which can form matched pairs with commercially available antibodies. ACE2 and S1-mAb were paired with each other for capture and detection in a lateral flow immunoassay (LFIA) that did not cross-react with SARS-CoV Spike 1 or MERS-CoV Spike 1 protein. To decrease the non-specific interaction between capture probes in test lines and 20 detection probes, the nitrocellulose membrane was treated with the blocking solution (10 mM 2-21 amino-2-methyl-1-propanol (pH 9.0), 0.5% BSA, 0.5% β-Lactose, 0.05% Triton X-100, 0.05% 22 sodium azide) for 1 hour in a vacuum oven (37°C). -The human ACE2 and commercial antibody were paired with each other as capture and detection probes in a lateral flow immunoassay that was not cross-reactive with SARS-CoV S1 and MERS-CoV S1 proteins. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a newly emerging human infectious disease. Because no specific antiviral drugs or vaccines are available to treat COVID-19, early diagnostics, isolation, and prevention are crucial for containing the outbreak. Molecular diagnostics using reverse transcription polymerase chain reaction (RT-PCR) are the current gold standard for detection. However, viral RNAs are much less stable during transport and storage than proteins such as antigens and antibodies. Consequently, false-negative RT-PCR results can occur due to inadequate collection of clinical specimens or poor handling of a specimen during testing. Although antigen immunoassays are stable diagnostics for detection of past infection, infection progress, and transmission dynamics, no matched antibody pair for immunoassay of SARS-CoV-2 antigens has yet been reported. In this study, we designed and developed a novel rapid detection method for SARS-CoV-2 spike 1 (S1) protein using the SARS-CoV-2 receptor ACE2, which can form matched pairs with commercially available antibodies. ACE2 and S1-mAb were paired with each other for capture and detection in a lateral flow immunoassay (LFIA) that did not cross-react with SARS-CoV Spike 1 or MERS-CoV Spike 1 protein. The SARS-CoV-2 S1 (<5 ng of recombinant proteins/reaction) was detected by the ACE2-based LFIA. The limit of detection of our ACE2-LFIA was 1.86 × 10(5) copies/mL in the clinical specimen of COVID-19 Patients without no cross-reactivity for nasal swabs from healthy subjects. This is the first study to detect SARS-CoV-2 S1 antigen using an LFIA with matched pair consisting of ACE2 and antibody. Our findings will be helpful to detect the S1 antigen of SARS-CoV-2 from COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S095656632030703X?v=s5 doi: 10.1016/j.bios.2020.112715 id: cord-333929-oprpgcyr author: Lee, Justin title: Impact of Severe Acute Respiratory Syndrome on Patient Access to Palliative Radiation Therapy date: 2005-01-31 words: 2326.0 sentences: 130.0 pages: flesch: 56.0 cache: ./cache/cord-333929-oprpgcyr.txt txt: ./txt/cord-333929-oprpgcyr.txt summary: Abstract This study evaluated the impact of the severe acute respiratory syndrome (SARS) epidemic on access and utilization of palliative radiation therapy (RT) at a single institution using a retrospective chart review. 2, 3 Recent studies have demonstrated the negative impact of the SARS epidemic on access to health care services such as emergency room visits, cardiac surgery, lumpectomy/mastectomy, and chemotherapy procedures. The primary objective of the study was to identify any significant change in the number of patients seen and/or treated by the Rapid Response Radiotherapy Program (RRRP) at our center. A retrospective chart review was used to evaluate all patients who attended the RRRP at the Toronto Sunnybrook Regional Cancer Centre between January 1 and May 31, 2002, and the same time period in 2003. There was a significant decrease in the waiting times of patients seen during the SARS epidemic compared with the previous year ( Table 3 ). abstract: Abstract This study evaluated the impact of the severe acute respiratory syndrome (SARS) epidemic on access and utilization of palliative radiation therapy (RT) at a single institution using a retrospective chart review. A total of 649 patients seen between January and May 2002 and between January and May 2003 were evaluated. Treatment characteristics and waiting times were recorded. March 20 to May 30, 2003, was defined as the peak period of incidence and was compared with the same period in 2002. During the SARS epidemic, there was a 21% decrease in the number of patient consultations and a 15% reduction in the number of patients treated with RT. There was no significant change in the tumor type or reason for referral. Short fractionation schedules were employed for 35% of treated patients compared with 34% in 2002. Patient waiting times between referral and treatment decreased during the period of interest, from 16 days to 8 days (P = 0.021). This study demonstrates a reduction in palliative RT services that is similar in magnitude to decreases observed in other essential cancer services during the SARS epidemic. Use of single-fraction RT and delayed follow-up visits may help to minimize hospital transfers and visits in the event of future infectious disease outbreaks. url: https://www.sciencedirect.com/science/article/pii/S1543291213600454 doi: 10.3816/sct.2005.n.004 id: cord-287742-y1j9x5ne author: Lee, Kai Wei title: Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis date: 2020-10-06 words: 6545.0 sentences: 292.0 pages: flesch: 45.0 cache: ./cache/cord-287742-y1j9x5ne.txt txt: ./txt/cord-287742-y1j9x5ne.txt summary: Therefore, we performed a systematic review and meta-analysis of currently available epidemiological, clinical, and laboratory data related to both stroke and COVID-19 infection. We, therefore, performed a systematic review and metaanalysis involving the epidemiological, clinical presentation, imaging characteristics, and laboratory finding related to both stroke and COVID-19 infection. The following data were extracted from every study: the last name of the first author, year of publication, country, severity status, study design, patient characteristics (ethnicity composition, gender, and mean age), comorbidities (diabetes, hyperlipidemia, hypertension, ischemic heart disease, heart failure, previous stroke, chronic kidney disease/end-stage renal disease, number of stroke patients per overall participants, any information relevant to strokes such as the location of stroke [arterial or venous]), types of stroke (ischemic or haemorrhagic), classification of stroke, mortality rate, and blood parameters. The aim of this current study is to perform a systematic review and meta-analysis concerning the epidemiological, clinical presentation, imaging characteristics, and laboratory findings related to both stroke and COVID-19 infection. abstract: Background: As the world witnessed the devastation caused by the coronavirus disease 2019 (COVID-19) outbreak, a growing body of literature on COVID-19 is also becoming increasingly available. Stroke has increasingly been reported as a complication of COVID-19 infection. However, a systematic synthesis of the available data has not been conducted. Therefore, we performed a systematic review and meta-analysis of currently available epidemiological, clinical, and laboratory data related to both stroke and COVID-19 infection. Methods: We systematically searched Medline, Cinahl, and PubMed for studies related to stroke and COVID-19 from inception up to June 4, 2020. We selected cohort studies, case series, and case reports that reported the occurrence of stroke in COVID-19 patients. A fixed-effects model was used to estimate the pooled frequency of stroke in COVID-19 patients with a 95% confidence interval (CI). Results: Twenty-eight studies were included in the systematic review and seven studies for the meta-analysis. The pooled frequency of stroke in COVID-19 patients was 1.1% (95% CI: 0.8, 1.3). The heterogeneity was low (I(2) = 0.0%). Even though the frequency of stroke among patients having COVID-19 infection was low, those with concomitant COVID-19 infection and stroke suffered from a more severe infection and eventually had a poorer prognosis with a higher mortality rate (46.7%) than COVID-19 alone. Many COVID-19 patients shared the common traditional risk factors for stroke. We noted that ischemic stroke involving the anterior circulation with large vessels occlusion is the most common type of stroke with more strokes seen in multi-territorial regions, suggesting systemic thromboembolism. An elevated level of D-dimers, C-reactive protein, ferritin, lactic acid dehydrogenase, troponin, ESR, fibrinogen, and a positive antiphospholipid antibody were also noted in this review. Conclusions: The occurrence of stroke in patients with COVID-19 infection is uncommon, but it may pose as an important prognostic marker and indicator of severity of infection, by causing large vessels occlusion and exhibiting a thrombo-inflammatory vascular picture. Physicians should be made aware and remain vigilant on the possible two-way relationship between stroke and COVID-19 infection. The rate of stroke among patients with COVID-19 infection may increase in the future as they share the common risk factors. url: https://doi.org/10.3389/fneur.2020.579070 doi: 10.3389/fneur.2020.579070 id: cord-330583-ltkpt80u author: Lee, Kyu-Myoung title: Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date: 2019-04-22 words: 9200.0 sentences: 414.0 pages: flesch: 37.0 cache: ./cache/cord-330583-ltkpt80u.txt txt: ./txt/cord-330583-ltkpt80u.txt summary: Following the 2003 the severe acute respiratory syndrome (SARS) and the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to explore and examine the factors influencing the response to infectious diseases, which encompasses both communicable and non-communicable diseases. As the results conducted meta-analyses to comprehensively analyze the correlations of factors influencing disaster response from a Korean context, the findings show that the legislative factor had direct and indirect influence on the overall process of infectious disease response and that Leadership of the central government, establishment of an intergovernmental response system, the need for communication, information sharing and disclosure and onsite response were identified as key factors influencing effective infectious disease response. However, there is also need for comprehensive discussions that include the establishment of laws; regulations; resources; information on infectious disease response from administrative and policy perspectives; information sharing system; and the establishment of an international cooperation system and national response system involving the central government, the regional government, private organizations and the public for effective response when an actual infectious disease outbreak occurs. abstract: Following the 2003 the severe acute respiratory syndrome (SARS) and the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to explore and examine the factors influencing the response to infectious diseases, which encompasses both communicable and non-communicable diseases. Through a qualitative research method, this research categorizes the factors as inputs, processes and outputs and applies them into the 2003 SARS and MERS outbreak in South Korea. As the results conducted meta-analyses to comprehensively analyze the correlations of factors influencing disaster response from a Korean context, the findings show that the legislative factor had direct and indirect influence on the overall process of infectious disease response and that Leadership of the central government, establishment of an intergovernmental response system, the need for communication, information sharing and disclosure and onsite response were identified as key factors influencing effective infectious disease response. url: https://www.ncbi.nlm.nih.gov/pubmed/31013648/ doi: 10.3390/ijerph16081432 id: cord-325070-583innd7 author: Lee, Lennard Y.W. title: Utility of COVID-19 Screening in Cancer Patients date: 2020-07-24 words: 1121.0 sentences: 61.0 pages: flesch: 41.0 cache: ./cache/cord-325070-583innd7.txt txt: ./txt/cord-325070-583innd7.txt summary: We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care in the era of COVID-19. Patients with cancer are at increased risk of contracting SARS-CoV-2 and have a high mortality rate from COVID-19 (Lee et al., 2020) . A number of national and international cancer guidelines now advise the screening of every patient undergoing chemotherapy to enable early identification and isolation of patients with asymptomatic SARS-CoV-2 infections to prevent hospital transmission (https://www.idsociety.org/practice-guideline/covid-19-guidelinediagnostics/; https://www.rcr.ac.uk/sites/default/files/guidance-covid19-testing-asymptomatic-hcw-patientsoncology.pdf; https://www.asco.org/sites/new-www.asco.org/files/content-files/2020-ASCO-Guide-Cancer-COVID19.pdf). Our cohort demonstrates that uptake for screening of SARS-CoV-2 through nasopharyngeal testing is high in cancer patients. We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care; this will be monitored as the pandemic evolves. Screening for COVID-19 in asymptomatic patients with cancer in a hospital in the United Arab Emirates abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1535610820303706?v=s5 doi: 10.1016/j.ccell.2020.07.009 id: cord-308142-3x3n6cpt author: Lee, Nelson title: Chikungunya Fever, Hong Kong date: 2006-11-17 words: 1722.0 sentences: 85.0 pages: flesch: 46.0 cache: ./cache/cord-308142-3x3n6cpt.txt txt: ./txt/cord-308142-3x3n6cpt.txt summary: aureus isolated from active lesions were not available for testing, the recovery of identical PVL-positive organisms from nasal cultures strongly suggests the presence of a pathogenic clone that probably caused the recurrent infections in the 6 affected family members. Serum specimens taken on days 2 and 6 were positive for chikungunya virus RNA by in-house reverse transcription (RT)-PCR at the Public Health Laboratory Service (PHLS) (targeting the nonstructural protein-1 [NSP-1] gene) and PWH laboratory (targeting both NSP-1 and the envelope glycoprotein [E1] gene). The most striking finding from the cytokine analysis (Table) is the high level of interferon-γ (IFN-γ)-inducible protein-10 (IP-10/CXCL-10), up to 26 and 16 times the upper limit of the normal range at days 2 and 6 after disease onset, respectively. In severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (4, 5) and H5N1 influenza (6) infections, very high blood levels of CXCL10 and moderately high CCL2, CXCL9, and CXCL8 concentrations, or their enhanced expressions in vitro, have been reported. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17283640/ doi: 10.3201/eid1211.060574 id: cord-334628-axon4jdc author: Lee, Saemi title: Genetic Characteristics of Coronaviruses from Korean Bats in 2016 date: 2017-07-19 words: 3227.0 sentences: 205.0 pages: flesch: 66.0 cache: ./cache/cord-334628-axon4jdc.txt txt: ./txt/cord-334628-axon4jdc.txt summary: In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. Given the import of MERS into South Korea [14] and the presence of SARS in the relatively close geographic location of China [9] (Fig. 3) , together with the fact that bats are a reservoir for coronaviruses, the prevalence of coronavirus infection in Korean bat species should provide valuable information. Oral swabs and other samples (n = 60) were obtained from three species of bats, Rhinolophus ferrumequinum, Miniopterus schreibersii, and Myotis macrodactylus, but coronaviruses were only detected in samples from R. Thirteen sequences from oral swabs were clustered with Bat-CoV B15-21, which was detected in fecal bat samples collected from an abandoned mine in Gangwon province. abstract: Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1–95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs. url: https://www.ncbi.nlm.nih.gov/pubmed/28725945/ doi: 10.1007/s00248-017-1033-8 id: cord-333606-5z3kumu9 author: Lee, SangJoon title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines date: 2020-10-15 words: 1178.0 sentences: 69.0 pages: flesch: 44.0 cache: ./cache/cord-333606-5z3kumu9.txt txt: ./txt/cord-333606-5z3kumu9.txt summary: title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. Despite these limitations, significant work has been done to molecularly characterize the innate immune pathways involved in detecting and controlling CoV infections. patients with severe or critical COVID-19 also found that reduced amounts of type I IFNs in the blood during SARS-CoV-2 infection were associated with increased viral load in the blood, and exacerbation of the inflammatory response [38] . Pyroptosis and necroptosis are similar in that they are lytic forms of cell death driven by the GSDMD pore and MLKL channel, respectively, that release proinflammatory cytokines and other cellular factors to alert the surrounding cells of danger and to recruit innate and adaptive inflammatory cells [54, 55].  Specific CoV infections can activate inflammatory cell death (PANoptosis), thereby inducing cytokine release. abstract: The innate immune system acts as the first line of defense against pathogens, including coronaviruses. SARS-CoV and MERS-CoV are epidemic zoonotic coronaviruses that emerged at the beginning of the 21st century. The recently emerged virus SARS-CoV-2 is a novel strain of coronavirus that has caused the COVID-19 pandemic. Scientific advancements made by studying the SARS-CoV and MERS-CoV outbreaks have provided a foundation for understanding pathogenesis and innate immunity against SARS-CoV-2. In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. We also discuss how the pathogenesis of these viruses influences these biological processes. url: https://www.ncbi.nlm.nih.gov/pubmed/33153908/ doi: 10.1016/j.it.2020.10.005 id: cord-341502-jlzufa28 author: Lee, Sungyul title: The SARS-CoV-2 RNA interactome date: 2020-11-02 words: 5845.0 sentences: 362.0 pages: flesch: 51.0 cache: ./cache/cord-341502-jlzufa28.txt txt: ./txt/cord-341502-jlzufa28.txt summary: The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). abstract: SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its ability to repurpose host RNA-binding proteins (RBPs) to form its own RNA interactome. Here, we developed and applied a robust ribonucleoprotein capture protocol to uncover the SARS-CoV-2 RNA interactome. We report 109 host factors that directly bind to SARS-CoV-2 RNAs including general antiviral factors such as ZC3HAV1, TRIM25, and PARP12. Applying RNP capture on another coronavirus HCoV-OC43 revealed evolutionarily conserved interactions between viral RNAs and host proteins. Network and transcriptome analyses delineated antiviral RBPs stimulated by JAK-STAT signaling and proviral RBPs responsible for hijacking multiple steps of the mRNA life cycle. By knockdown experiments, we further found that these viral-RNA-interacting RBPs act against or in favor of SARS-CoV-2. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions. url: https://doi.org/10.1101/2020.11.02.364497 doi: 10.1101/2020.11.02.364497 id: cord-286537-7ri2p5b8 author: Lee, Ting-Wai title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide date: 2005-11-11 words: 7020.0 sentences: 365.0 pages: flesch: 61.0 cache: ./cache/cord-286537-7ri2p5b8.txt txt: ./txt/cord-286537-7ri2p5b8.txt summary: authors: Lee, Ting-Wai; Cherney, Maia M.; Huitema, Carly; Liu, Jie; James, Karen Ellis; Powers, James C.; Eltis, Lindsay D.; James, Michael N.G. title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. In contrast, in protomer A of the M pro CAðK1Þ :APE complex, the benzyl group of APE squeezes into and thereby widens the S4 specificity pocket of the peptidase, so that it is snugly accommodated in this enlarged pocket now formed by the residues 165 to 168, Phe185, Gln192 and the main-chain atoms of Val186 (Figures 3(b) and 4(c)). abstract: The main peptidase (Mpro) from the coronavirus (CoV) causing severe acute respiratory syndrome (SARS) is one of the most attractive molecular targets for the development of anti-SARS agents. We report the irreversible inhibition of SARS-CoV Mpro by an aza-peptide epoxide (APE; k inact/K i=1900(±400)M−1 s−1). The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. The aza-peptide component of APE binds in the substrate-binding regions of Mpro in a substrate-like manner, with excellent structural and chemical complementarity. In addition, the crystal structure of unbound Mpro in the space group C2 revealed that the “N-fingers” (N-terminal residues 1 to 7) of both protomers of Mpro are well defined and the substrate-binding regions of both protomers are in the catalytically competent conformation at the crystallization pH of 6.5, contrary to the previously determined crystal structures of unbound Mpro in the space group P21. url: https://www.ncbi.nlm.nih.gov/pubmed/16219322/ doi: 10.1016/j.jmb.2005.09.004 id: cord-339019-vgnxhksv author: Lee, Ting-Wai title: Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase date: 2007-02-23 words: 8447.0 sentences: 450.0 pages: flesch: 62.0 cache: ./cache/cord-339019-vgnxhksv.txt txt: ./txt/cord-339019-vgnxhksv.txt summary: We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M+A(-1) pro), both at a resolution of 2.00 Å, in space group P43212: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). 25 We have now grown crystals of M pro in the same space group (P2 1 with the same unit-cell constants) at pH 6.0 under slightly different conditions; the active sites and the S1 specificity pockets of both protomers are in the catalytically competent conformation (Figures 2(a) and (b), 3(a) and (b), 4(a) and (b)). Active sites and substrate-binding regions of the unbound SARS-CoV M +A(-1) pro We have reported the crystal structure of the SARS-CoV M +A (-1) pro :APE complex in space group P2 1 2 1 2 1 , whose asymmetric unit contains both protomers of the M +A(-1) pro dimer. abstract: Abstract The SARS coronavirus main peptidase (SARS-CoV Mpro) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of Mpro at a resolution of 1.82 Å, in space group P21 at pH 6.0. In contrast to the previously reported structure of Mpro in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of Mpro reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M+A(-1) pro), both at a resolution of 2.00 Å, in space group P43212: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M+A(-1) pro are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of Mpro exist in dynamic equilibrium. The structural data further suggest that the binding of APE to Mpro follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle. url: https://www.ncbi.nlm.nih.gov/pubmed/17196984/ doi: 10.1016/j.jmb.2006.11.078 id: cord-267744-asjvf123 author: Lee, Yu-Ching title: Chicken single-chain variable fragments against the SARS-CoV spike protein date: 2007-07-23 words: 4057.0 sentences: 212.0 pages: flesch: 52.0 cache: ./cache/cord-267744-asjvf123.txt txt: ./txt/cord-267744-asjvf123.txt summary: Following the immunization of chickens with these recombinant spike proteins, two single-chain variable fragment (scFv) antibody libraries were established with short or long linkers to contain 5 × 10(7) and 9 × 10(6) transformants, respectively. In a comparison of nucleotide sequences with the chicken germline gene, we found that all clones varied in the complementarity-determining regions, that two scFv antibodies reacted significantly with SARS-CoV-infected Vero cells, and that those two specific scFv antibodies recognized the same region of the spike protein spanning amino acid residues 750–1000. The current study aimed to show that monoclonal IgY scFv antibodies which bind specifically to the S protein and SARS-CoV-infected Vero cells can be isolated from chickens immunized with Escherichia coli-derived S proteins. Cellular lysates containing single-chain variable fragment (scFv) antibodies from various Ssc (A) and Lsc (B) library clones were examined for their binding to SARS-CoV-infected cell lysates using a commercially available kit. abstract: The major concern for severe acute respiratory syndrome (SARS), caused by the SARS-associated coronavirus (SARS-CoV), is the lack of diagnostic and therapeutic agents. Using a phage display technology in a chicken system, high-affinity monoclonal antibody fragments against the SARS-CoV spike protein were characterized. Ten truncated spike protein gene fragments were expressed in Escherichia coli cells. Following the immunization of chickens with these recombinant spike proteins, two single-chain variable fragment (scFv) antibody libraries were established with short or long linkers to contain 5 × 10(7) and 9 × 10(6) transformants, respectively. After four rounds of panning selection, the scFv antibodies of randomly chosen clones were demonstrated by Coomassie blue staining, and verified by western blot analysis. In a comparison of nucleotide sequences with the chicken germline gene, we found that all clones varied in the complementarity-determining regions, that two scFv antibodies reacted significantly with SARS-CoV-infected Vero cells, and that those two specific scFv antibodies recognized the same region of the spike protein spanning amino acid residues 750–1000. In conclusion, the results suggest that the chicken scFv phage display system can be a potential model for mass production of high-affinity antibodies against the SARS-CoV spike protein. url: https://api.elsevier.com/content/article/pii/S0166093407002236 doi: 10.1016/j.jviromet.2007.06.010 id: cord-308123-eu0azqfu author: Lee, Yun Young title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm date: 2020-10-23 words: 5002.0 sentences: 315.0 pages: flesch: 54.0 cache: ./cache/cord-308123-eu0azqfu.txt txt: ./txt/cord-308123-eu0azqfu.txt summary: title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm Our findings suggest that exogenously administered long-acting nanoparticulate DNase-1 can effectively reduce cfDNA levels and neutrophil activities and may be used as a potential therapeutic intervention for life-threatening SARS-CoV-2-mediated illnesses. We showed that an intravenous administration of DNase-1-coated polydopamine-poly (ethylene glycol) nanoparticulates, named long-acting DNase-1 (Scheme 1), effectively inhibited NETosis factors in blood samples of patients with COVID-19 and also improve survival in a sepsis model. We also observed markedly reduced NET levels, MPO activity, and NE levels in neutrophils of COVID-19 patients with sepsis upon treatment of the DNase-1 formulations (Fig. 4C-E) . patients with sepsis, the long-acting DNase-1 significantly reduced cfDNA levels and increased the activity of the DNase-1 ( Fig. S6A and B) . (C) NET ratio of SARS-CoV-2 Sepsis patient PBMCs was suppressed after free DNase-1 or long-acting DNase-1 treatment. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new strain of coronavirus not previously identified in humans. Globally, the number of confirmed cases and mortality rates of coronavirus disease 2019 (COVID-19) have risen dramatically. Currently, there are no FDA-approved antiviral drugs and there is an urgency to develop treatment strategies that can effectively suppress SARS-CoV-2-mediated cytokine storms, acute respiratory distress syndrome (ARDS), and sepsis. As symptoms progress in patients with SARS-CoV-2 sepsis, elevated amounts of cell-free DNA (cfDNA) are produced, which in turn induce multiple organ failure in these patients. Furthermore, plasma levels of DNase-1 are markedly reduced in SARS-CoV-2 sepsis patients. In this study, we generated recombinant DNase-1-coated polydopamine-poly(ethylene glycol) nanoparticulates (named long-acting DNase-1), and hypothesized that exogenous administration of long-acting DNase-1 may suppress SARS-CoV-2-mediated neutrophil activities and the cytokine storm. Our findings suggest that exogenously administered long-acting nanoparticulate DNase-1 can effectively reduce cfDNA levels and neutrophil activities and may be used as a potential therapeutic intervention for life-threatening SARS-CoV-2-mediated illnesses. url: https://doi.org/10.1016/j.biomaterials.2020.120389 doi: 10.1016/j.biomaterials.2020.120389 id: cord-321797-2xhusfth author: Lee‐Baggley, Dayna title: Coping with the threat of severe acute respiratory syndrome: Role of threat appraisals and coping responses in health behaviors date: 2004-03-11 words: 6358.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-321797-2xhusfth.txt txt: ./txt/cord-321797-2xhusfth.txt summary: Hierarchical linear regression indicated that the use of wishful thinking in response to the threat of SARS was related to both avoiding public places and avoiding people perceived to be possible carriers of the SARS virus, but was not associated with the use of more adaptive health behaviors, such as using disinfectants and hand washing. Perception of SARS threat was significantly related to reports of both coping (wishful thinking and support seeking) and health behaviors (avoidant behavior, avoiding people perceived to be at risk for SARS and taking precautions). In sum, multivariate analyses controlling for differences in perceived threat of SARS, state anxiety and other ways of coping indicated that both wishful thinking and empathic responding were significantly associated with specific SARS-related health behaviors. 4 Controlling for differences in perceived threat of SARS, state anxiety and other ways of coping, support seeking was not significantly related to the SARS-related health behaviors examined in the present study. abstract: The present study examines the psychological impact of severe acute respiratory syndrome (SARS) by exploring the coping strategies and health behaviors enacted in response to the SARS epidemic. Hierarchical linear regression indicated that the use of wishful thinking in response to the threat of SARS was related to both avoiding public places and avoiding people perceived to be possible carriers of the SARS virus, but was not associated with the use of more adaptive health behaviors, such as using disinfectants and hand washing. Conversely, those who reported engaging in empathic responding in response to the threat of SARS were both less likely to report avoiding people perceived as being at a high risk for SARS and more likely to report engaging in effective health behaviors. Support seeking was not a significant predictor of the health behaviors examined in the present study. Results are discussed in terms of coping with health threats and health promotion. url: https://www.ncbi.nlm.nih.gov/pubmed/32313437/ doi: 10.1111/j.1467-839x.2004.00131.x id: cord-311599-m400cal3 author: Lehmann, Christian title: A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses date: 2008-05-31 words: 5031.0 sentences: 289.0 pages: flesch: 50.0 cache: ./cache/cord-311599-m400cal3.txt txt: ./txt/cord-311599-m400cal3.txt summary: Here, we report the development of a serologic assay for detection of antibodies to human coronaviruses (HCoVs) based on recombinant nucleocapsid (N) proteins of all known pathogenic strains (229E, NL63, OC43, HKU1, SARS). Here, we describe the establishment of a line immunoassay for rapid and simultaneous detection of antibodies directed against the 5 known HCoVs (229E, NL63, OC43, HKU1, and SARS) in human sera based on recombinant viral N proteins. Table 2 Reactions of clinically defined sera with HCoV nucleocapsids In sera taken during acute phase of HCoV infection, no OC43-or 229E-specific antibodies could be detected, whereas samples collected after convalescence strongly reacted with the corresponding antigens. Consistently, all available human sera sampled from convalescent patients (tested positive for HCoVs 229E, OC43, or SARS-CoV by microneutralization experiments, Western blotting, ELISA, or IF) reacted with their respective antigens as expected, indicating an excellent sensitivity of our line immunoassay. abstract: Abstract Most coronaviruses infecting humans cause mild diseases, whereas severe acute respiratory syndrome (SARS)-associated coronavirus is an extremely dangerous pathogen. Here, we report the development of a serologic assay for detection of antibodies to human coronaviruses (HCoVs) based on recombinant nucleocapsid (N) proteins of all known pathogenic strains (229E, NL63, OC43, HKU1, SARS). The novel immunoassay is highly useful for epidemiologic surveys, where use of nucleic acid diagnostics often is limited. Purified recombinant antigens were immobilized on nitrocellulose membranes and applied in a line immunoassay, which allows rapid detection of antibodies to 5 different HCoVs in a single experiment. For assay evaluation, serum samples from persons infected with 229E or OC43 (acute/convalescent), recovered SARS patients and healthy donors were analyzed. Screening for nucleocapsid (N)-specific immunoglobulin G (IgG) in convalescent sera reached 100% sensitivity. With this new technique, we found that recently identified NL63 and HKU1 contribute significantly to the overall spectrum of coronavirus infections. Possibly, cross-reactive antibody responses were observed using 229E and OC43 serum pairs. However, the potential of this assay could clearly be demonstrated employing SARS-positive serum samples, where nonspecific binding to nucleocapsids of other HCoVs was not observed. This coronavirus strain-specific line immunoassay represents a powerful tool for serologic diagnostics. url: https://doi.org/10.1016/j.diagmicrobio.2007.12.002 doi: 10.1016/j.diagmicrobio.2007.12.002 id: cord-276316-7ot9ds34 author: Lei, Chunliang title: Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China date: 2020-10-14 words: 2375.0 sentences: 160.0 pages: flesch: 57.0 cache: ./cache/cord-276316-7ot9ds34.txt txt: ./txt/cord-276316-7ot9ds34.txt summary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in respiratory tract, blood samples and digestive tract was detected and lymphocyte subsets were tested periodically. 270 patients were detected for SARS-CoV-2 RNA in anal swabs and/or blood samples, and the overall positive rate was 23.0 % (62/270), higher in severe/critical cases than in mild/moderate cases (52.0 % vs. Detectable SARS-CoV-2 RNA in anal swabs and/or blood samples, as well as higher CD4/CD8 ratio were independent risk factors of respiratory failure and ICU admission. A total of 270 patients were detected for SARS-CoV-2 RNA in anal swabs J o u r n a l P r e -p r o o f 8 / 25 and/or blood samples, and the overall positive rate was 23.0% (62/270), higher in severe/critical cases than in mild/moderate cases (52.0% vs. abstract: BACKGROUND: Coronavirus Disease 2019 (COVID-19) is threatening billions of people. We described the clinical characteristics and explore virological and immunological factors associated with clinical outcomes. METHODS: 297 COVID-19 patients hospitalized in Guangzhou Eighth People's Hospital between January 20 and February 20, 2020 were included. Epidemiological, clinical and laboratory data were collected and analyzed. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in respiratory tract, blood samples and digestive tract was detected and lymphocyte subsets were tested periodically. RESULT: Among the 297 patients (median age of 48 years), 154 (51.9 %) were female, 245 (82.5 %) mild/moderate cases, and 52 (17.5 %) severe/critical cases. 270 patients were detected for SARS-CoV-2 RNA in anal swabs and/or blood samples, and the overall positive rate was 23.0 % (62/270), higher in severe/critical cases than in mild/moderate cases (52.0 % vs. 16.4 %, P < 0.001). The CD4/CD8 ratio on admission was significantly higher in severe/critical cases than in mild/moderate cases (1.84 vs. 1.50, P = 0.022). During a median follow-up period of 17 days, 36 (12.1 %) patients were admitted to intensive care unit (ICU), 16 (5.4 %) patients developed respiratory failure and underwent mechanical ventilation, four (1.3 %) patients needed extracorporeal membrane oxygenation (ECMO), only one (0.34 %) patients died of multiple organ failure. Detectable SARS-CoV-2 RNA in anal swabs and/or blood samples, as well as higher CD4/CD8 ratio were independent risk factors of respiratory failure and ICU admission. CONCLUSIONS: Most of COVID-19 patients in Guangzhou are mild/moderate, and presence of extrapulmonary virus and higher CD4/CD8 ratio are associated with higher risk of worse outcomes. url: https://api.elsevier.com/content/article/pii/S1386653220304030 doi: 10.1016/j.jcv.2020.104661 id: cord-329876-4cgrjnjo author: Lei, Jian title: Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin date: 2016-05-30 words: 6809.0 sentences: 421.0 pages: flesch: 69.0 cache: ./cache/cord-329876-4cgrjnjo.txt txt: ./txt/cord-329876-4cgrjnjo.txt summary: title: Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. The substrate-binding site of MERS-CoV PL pro features significant differences from those of the corresponding SARS-CoV enzyme and human ubiquitin-specific proteases (USPs, such as, USP14) (Hu et al., 2005; Chou et al., 2014; Ratia et al., 2014) . Hence, we crystallized the ubiquitin (Ub) complex of a MERS-CoV PL pro variant that had the active-site Cys111 replaced by serine (C111S) and determined the structure at 3.16 Å ( Figure 1A ). Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression abstract: The papain-like protease (PL(pro)) of Middle-East respiratory syndrome coronavirus (MERS-CoV) has proteolytic, deubiquitinating, and deISGylating activities. The latter two are involved in the suppression of the antiviral innate immune response of the host cell. To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. Five regions of the PL(pro) bind to two areas of the Ub. The C-terminal five residues of Ub, RLRGG, are similar to the P5–P1 residues of the polyprotein substrates of the PL(pro) and are responsible for the major part of the interaction between the two macromolecules. Through sitedirected mutagenesis, we demonstrate that conserved Asp165 and non-conserved Asp164 are important for the catalytic activities of MERS-CoV PL(pro). The enzyme appears not to be optimized for catalytic efficiency; thus, replacement of Phe269 by Tyr leads to increased peptidolytic and deubiquitinating activities. Ubiquitin binding by MERS-CoV PL(pro) involves remarkable differences compared to the corresponding complex with SARS-CoV PL(pro). The structure and the mutational study help understand common and unique features of the deubiquitinating activity of MERS-CoV PL(pro). ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at 10.1007/s12250-016-3742-4 and is accessible for authorized users. url: https://doi.org/10.1007/s12250-016-3742-4 doi: 10.1007/s12250-016-3742-4 id: cord-279569-289fu2yb author: Lei, Yu title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area date: 2020-03-13 words: 2291.0 sentences: 152.0 pages: flesch: 57.0 cache: ./cache/cord-279569-289fu2yb.txt txt: ./txt/cord-279569-289fu2yb.txt summary: title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area Abstract Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in Epidemiological, clinical laboratory and radiological characteristics, chronic medical histories, clinical symptoms, treatment and outcome data were obtained from electronic medical records and analysed by two independent researchers. With advancing time, the medical history associated with case exposure to SARS-CoV-2 infected patients from Wuhan has become less obvious. In conclusion, imported cases of SARS-CoV-2 infection in Tibetan patients were generally mild in this high-altitude area. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan abstract: Abstract Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. We aimed to investigate the epidemiological, clinical, laboratory and radiological characteristics of these patients. We included 67 Tibetan patients with confirmed SARS-CoV-2 infection. The patients were divided into two groups based on the presence of clinical symptoms at admission, with 31 and 36 patients in the symptomatic and asymptomatic groups, respectively. The epidemiological, clinical, laboratory and radiological characteristics were extracted and analysed. No patient had a history of exposure to COVID-19 patients from Wuhan or had travelled to Wuhan. The mean age of Tibetan patients was 39.3 years and 59% of the patients were male. Seven patients presented with fever on admission and lymphocytopenia was present in 20 patients. 47 patients had abnormal chest CTs at admission instead of stating that 20 were unchanged. Lactate dehydrogenase levels were increased in 31 patients. Seven patients progressed to severe COVID-19; however, after treatment, their condition was stable. No patients died. Of the 36 asymptomatic patients, the mean age was younger than the symptomatic group (34.4vs 44.9 years, P=0.02). Lymphocyte count and prealbumin levels were higher in the asymptomatic group than the group with clinical symptoms (1.6 vs 1.3 and 241.8 vs 191.9, respectively; P<0.05). Imported cases of COVID-19 in Tibetan patients were generally mild in this high-altitude area. Absence of fever or radiologic abnormalities on initial presentation were common url: https://doi.org/10.1101/2020.03.09.20033126 doi: 10.1101/2020.03.09.20033126 id: cord-310396-jitao9k0 author: Lei, Yu title: MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date: 2009-03-07 words: 6031.0 sentences: 325.0 pages: flesch: 46.0 cache: ./cache/cord-310396-jitao9k0.txt txt: ./txt/cord-310396-jitao9k0.txt summary: The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. Currently, there are no reports of viral proteins targeting MAVS for inhibition of virus-induced cell death responses. In this report, we describe a novel function of MAVS in mediating virus-induced apoptosis, and identify viral proteins as inhibitors of this response. In addition, the involvement of proteins on IFN axis in virusinduced host cell apoptosis has been implicated in another previous report, in which MAVS has been shown to be critical for reovirus-triggered caspase-3/7 activation in HEK293T cells [46] , however, the study did not evaluate whether MAVS mediates virus-induced apoptosis and what roles type 1 IFNs play in MAVS-mediated apoptosis. abstract: BACKGROUND: Host responses to viral infection include both immune activation and programmed cell death. The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. PRINCIPAL FINDINGS: We show that MAVS causes apoptosis independent of its function in initiating IFN-I production. MAVS-induced cell death requires mitochondrial localization, is caspase dependent, and displays hallmarks of apoptosis. Furthermore, MAVS(−/−) fibroblasts are resistant to Sendai virus-induced apoptosis. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. SIGNIFICANCE: This study describes a novel role for MAVS in controlling viral infections through the induction of apoptosis, and identifies viral proteins which inhibit this host response. url: https://doi.org/10.1371/journal.pone.0005466 doi: 10.1371/journal.pone.0005466 id: cord-265366-vmuqbpkk author: Leibowitz, Jill title: Comparison of Clinical and Epidemiologic Characteristics of Young Febrile Infants with and without SARS-CoV-2 Infection date: 2020-10-09 words: 2626.0 sentences: 142.0 pages: flesch: 54.0 cache: ./cache/cord-265366-vmuqbpkk.txt txt: ./txt/cord-265366-vmuqbpkk.txt summary: 7, 8, 9, 10, 11, 12, 13 The largest case series to date describes 18 infants younger than 90 days of age who tested positive for SARS-CoV-2, 14 of whom were febrile. 9 The objective of this study was to compare the clinical and demographic characteristics and hospital course of febrile infants who presented to Cohen Children''s Medical Center (CCMC) during March and April of 2020, the time period of peak COVID-19 incidence in our region, to febrile infants treated in CCMC during March and April of previous years. The key findings of our study are that during the peak of the COVID-19 pandemic in New York, SARS-CoV-2 was the predominant pathogen identified among febrile infants younger than 57 days of age, and the disease was self-limited in all infants with COVID-19. 26 Infants with COVID-19 presented with lethargy and feeding difficulty more with SARS-CoV-2 infection among infants younger than 90 days of age. abstract: OBJECTIVE: To determine features that distinguish febrile young infants with SARS-CoV-2 infection. STUDY DESIGN: Retrospective single-center study included febrile infants <57 days evaluated in the Emergency Department of Cohen Children’s Medical Center of Northwell Health, New Hyde Park, New York during March 1-April 30 of 2018, 2019, and 2020. Sociodemographic and clinical features were compared between those seen during the 2020 COVID-19 pandemic and previous years, as well as between SARS-CoV-2 infected infants and SARS-CoV-2 uninfected infants (SARS-CoV-2 negative or evaluated during 2018 and 2019). RESULTS: In all, 124 febrile infants <57 days of age were identified; 38 during the 2-month study period in 2018, 33 in 2019, and 53 in 2020. During 2020, fewer febrile infants had a serious bacterial infection (SBI) or a positive respiratory viral panel (RVP) than in prior years (6% versus 21%, P = .02; 15% versus 53%, p<.001, respectively). SARS-CoV-2 was the most frequent pathogen detected in 2020; of 30 infants tested, 20 tested positive. Infants with SARS-CoV-2 were more likely to identify as Hispanic (p=.004), have public insurance or were uninsured (p=.01), exhibited lethargy (p=.02), had feeding difficulties (p=.002), and had lower white blood cell (p=.001), neutrophil (p<.001), and lymphocyte counts (p=.005) than the 81 infants without SARS-CoV-2 infection. None of the infants with SARS-CoV-2 had concurrent SBI or detection of another virus. Overall, disease in infants with SARS-CoV-2 was mild. CONCLUSIONS: During the peak of the pandemic, SARS-CoV-2 was the predominant pathogen among febrile infants. Socioeconomic, historical, and laboratory features differed significantly between SARS-CoV-2 infected and uninfected infants. None of the 20 infants with SARS-CoV-2 infection had an identified co-viral or serious bacterial infection. url: https://www.sciencedirect.com/science/article/pii/S0022347620312646?v=s5 doi: 10.1016/j.jpeds.2020.10.002 id: cord-289476-8wh3hn0n author: Leiker, Brenna title: COVID - 19 BRIEF INTRODUCTION IN MENTAL HEALTH CONSIDERATIONS FOR HEALTH CARE WORKERS AND PATIENTS date: 2020-07-28 words: 3754.0 sentences: 208.0 pages: flesch: 48.0 cache: ./cache/cord-289476-8wh3hn0n.txt txt: ./txt/cord-289476-8wh3hn0n.txt summary: This document describes five categories of people for SARS-CoV-2 testing with viral tests (i.e., nucleic acid or antigen tests) [the following are hot links to CDC resources]:  Testing individuals with signs or symptoms consistent with COVID-19  Testing asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 to control transmission  Testing asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings  Testing to determine resolution of infection (i.e., test-based strategy for Discontinuation of Transmission-based Precautions, HCP Return to Work, and Discontinuation of Home Isolation)  Public health surveillance for SARS-CoV-2 Generally, viral testing for SARS-CoV-2 is considered to be diagnostic when conducted among individuals with symptoms consistent with COVID-19 or among asymptomatic individuals with known or suspected recent exposure to SARS-CoV-2 to control transmission, or to determine resolution of infection. Testing is considered to be surveillance when conducted among asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification, or to detect transmission hot spots or characterize disease trends. abstract: I.. COVID-19: TESTING: A.. Laboratory Testing - CDC Guidelines; url: https://doi.org/10.1016/j.disamonth.2020.101059 doi: 10.1016/j.disamonth.2020.101059 id: cord-307502-vuju89lc author: Leipe, J. title: SARS-CoV-2 & Rheuma: Konsequenzen der SARS-CoV-2-Pandemie für Patienten mit entzündlich rheumatischen Erkrankungen. Ein Vergleich der Handlungsempfehlungen rheumatologischer Fachgesellschaften und Risikobewertung verschiedener antirheumatischer Therapien date: 2020-08-26 words: 1854.0 sentences: 220.0 pages: flesch: 45.0 cache: ./cache/cord-307502-vuju89lc.txt txt: ./txt/cord-307502-vuju89lc.txt summary: V. (DGRh) bereits zu Beginn der COVID-19-Pandemie im März 2020 erste Handlungsempfehlungen zum Management von Patienten mit entzündlich rheumatischen Erkrankungen (ERE) unter dem Aspekt der SARS-CoV-2/COVID-19-Bedrohung herausgegeben hat [13] , wurden diese im Juli 2020 durch ein Update aktualisiert und erweitert (im Folgenden DGRh-Update) [14] . Bezüglich der Risikoeinschätzung für schwere COVID-19-Verläufe wurde in den Empfehlungen der DGRh, EULAR und ACR postuliert, dass Patienten mit ERE kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 oder eines schweren Verlaufes für COVID-19 aufweisen. a. basierend auf teilweise kurz davor publizierten Daten, davon aus, dass auch die medikamentöse antirheumatische Therapie kein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt, mit Ausnahme von Glukokortikoiden in einer Dosierung von 10 mg Prednisolonäquivalent/Tag und mehr [4] . Im DGRh-Update wurde, basierend auf aktuell publizierten Daten zu SARS-CoV-2 und Erkenntnissen aus früheren Studien zum allgemeinen Infektionsrisiko, von einem erhöhten Risiko für einen schweren COVID-19-Verlauf bei unzureichend eingestellten ERE ausgegangen [3] . abstract: The recommendations of the German Society of Rheumatology (DGRh) update, which update and expand the guidance on the management of patients with inflammatory rheumatic diseases in view of SARS-CoV‑2 created at the beginning of the COVID-19 pandemic, correspond in many points with the recommendations for action of the American (ACR) and European (EULAR) societies, but also differ in some points. Therefore, this article discusses the core recommendations of the DGRh update on the prevention of SARS-CoV-2/COVID-19, the risk assessment for inflammatory rheumatic diseases and the use of antirheumatic treatments in the context and in comparison to the ACR and EULAR recommendations, and provides an overview of the risk assessment of individual antirheumatic drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/32845393/ doi: 10.1007/s00393-020-00878-0 id: cord-310051-bl8l4bgo author: Leitner, Thomas title: Where did SARS-CoV-2 come from? date: 2020-07-06 words: 1185.0 sentences: 78.0 pages: flesch: 55.0 cache: ./cache/cord-310051-bl8l4bgo.txt txt: ./txt/cord-310051-bl8l4bgo.txt summary: Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastro-intestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. While it is possible that a bat coronavirus jumped directly to a human, the closest known bat virus, RaTG13 found in a Rhinolophus affinis bat , shows 96% genomic similarity to SARS-CoV-2. Canine coronaviruses were not the only viruses with CpG patterns similar to those observed in SARS-CoV-2. Therefore, reduced genomic CpG content alone cannot predict the zoonotic origin of SARS-CoV-2, even though Xia (2020) (Pollock et al. Identification of the zoonotic origin of SARS-CoV-2 may be particularly challenging, as coronaviruses frequently recombine and are found in many different host species in the wild (Graham and Baric 2010) . abstract: Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. While Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their genetic dissimilarity to SARS-CoV-2 is so high that they are highly unlikely to be its direct ancestors. Thus, an intermediary host is suspected to link bat to human coronaviruses. Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastro-intestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. Therefore, reduced genomic CpG alone is not a highly predictive biomarker, suggesting a need for additional biomarkers to reveal intermediate hosts or tissues. The hunt for the zoonotic origin of SARS-CoV-2 continues. url: https://www.ncbi.nlm.nih.gov/pubmed/32893295/ doi: 10.1093/molbev/msaa162 id: cord-348636-qqcb85uk author: Lekone, Phenyo E. title: Bayesian Analysis of Severe Acute Respiratory Syndrome: The 2003 Hong Kong Epidemic date: 2008-07-09 words: 4878.0 sentences: 286.0 pages: flesch: 62.0 cache: ./cache/cord-348636-qqcb85uk.txt txt: ./txt/cord-348636-qqcb85uk.txt summary: This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. These parameters were obtained using maximum likelihood estimation methods assuming a gamma distribution for each period with allowance for censoring due to incomplete observation. A simple model that captures the form of distributions of epidemiological determinants has been introduced to estimate the basic reproduction number and to assess the effect of control interventions introduced during the course of the epidemic. abstract: This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. A discrete time stochastic model that uses a back‐projection approach is proposed. Markov Chain Monte Carlo (MCMC) methods are developed for estimation of model parameters. The algorithm is further extended to integrate numerically over unobserved variables of the model. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. An estimate of the transmission parameter at the beginning of the epidemic was also obtained as 0.149 with a posterior standard deviation of 0.003. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. At the end of the epidemic, the effective reproduction number was as low as 0.001 suggesting that the epidemic was brought under control by the intervention measures introduced. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) url: https://doi.org/10.1002/bimj.200710431 doi: 10.1002/bimj.200710431 id: cord-309193-v8lphej4 author: Lemriss, Sanaâ title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco date: 2020-07-02 words: 544.0 sentences: 42.0 pages: flesch: 51.0 cache: ./cache/cord-309193-v8lphej4.txt txt: ./txt/cord-309193-v8lphej4.txt summary: title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19). Phylogenetic tree of the complete nucleotide sequence of hCoV-19_Morocco_OUA677_19_2020 and 54 other global strains obtained from the GISAID database, associated with a table representing single-nucleotide polymorphisms (SNPs). Phylogenetic analysis of this virus genome compared with 54 selected sequences showed that it was grouped in SARS-CoV-2 clade G, which includes strains from Asia, Europe, North America, Australia, and Africa (Fig. 1) . We are currently sequencing and analyzing more complete genomes from different regions of Morocco to understand the virus dispersion and to associate this information with epidemiological data. abstract: Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19). url: https://doi.org/10.1128/mra.00633-20 doi: 10.1128/mra.00633-20 id: cord-324888-oak27okj author: Leng, Ling title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date: 2020-04-18 words: 2814.0 sentences: 155.0 pages: flesch: 46.0 cache: ./cache/cord-324888-oak27okj.txt txt: ./txt/cord-324888-oak27okj.txt summary: title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. Therefore, we wonder whether there are some key local microenvironment proteins specifically expressed on the surface of airway EpC that makes the virus prefer airway EpCs. In some cases, additional cell surface molecules or co-receptors are required for sufficient viral entry into host cells. We used the human protein atlas (HPA) database [16] to extract the protein expression level of 65 receptors involved in "virus receptor activity" (GO:0001618) of EpCs and epithelial or epithelial-derived cells from 14 organs (16 cell types) ( Figure 1A and Supplementary Materials and Methods). abstract: The outbreak of COVID-19 has caused serious epidemic events in China and other countries. With the rapid spread of COVID-19, it is urgent to explore the pathogenesis of this novel coronavirus. However, the foundational research of COVID-19 is very weak. Although angiotensin converting enzyme 2 (ACE2) is the reported receptor of SARS-CoV-2, information about SARS-CoV-2 invading airway epithelial cells is very limited. Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. In addition, we found that these proteins were associated with virus reactive proteins in host airway epithelial cells, which may promote the activation of the immune system and the release of inflammatory factors. Our findings provide a new research direction for understanding the potential microenvironment required by SARS-CoV-2 infection in airway epithelial, which may assist in the discovery of potential drug targets against SARS-CoV-2 infection. url: https://doi.org/10.1101/2020.04.16.045799 doi: 10.1101/2020.04.16.045799 id: cord-280408-0ze1lfnf author: Leon, A. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 words: 147.0 sentences: 22.0 pages: flesch: 48.0 cache: ./cache/cord-280408-0ze1lfnf.txt txt: ./txt/cord-280408-0ze1lfnf.txt summary: key: cord-280408-0ze1lfnf authors: Leon, A.; Debry, C.; Renaud, M. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 journal: Eur Ann Otorhinolaryngol Head Neck Dis DOI: 10.1016/j.anorl.2020.05.005 sha: doc_id: 280408 cord_uid: 0ze1lfnf nan Brain CT, axial scan with bone window setting. Presence of a bone defect of the lateral wall of the left sphenoid sinus (arrow). MRI, gadolinium-enhanced T1-weighted sequence, coronal section through the cavernous sinus. Intense enhancement of the fluid-filled sphenoid sinus (solid arrow) and the walls of the lateral sellar compartment (*) with inflammatory stenosis of the intracavernous segment of the internal carotid arteries (dotted arrow). Neurological Complications of Acute and Chronic Sinusitis Neurologic Features in Severe SARS-CoV-2 Infection Incidence of thrombotic complications in critically ill ICU patients with COVID-19 European Position Paper on Rhinosinusitis and Nasal Polyps Intraoperative bacterial analysis in nasal polyposis: Clinical and functional impact abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32426076/ doi: 10.1016/j.anorl.2020.05.005 id: cord-338928-y5l7cf31 author: Leonardi, Matilde title: Neurological manifestations associated with COVID-19: a review and a call for action date: 2020-05-20 words: 2109.0 sentences: 110.0 pages: flesch: 36.0 cache: ./cache/cord-338928-y5l7cf31.txt txt: ./txt/cord-338928-y5l7cf31.txt summary: While the epidemic of Coronavirus disease 2019 (COVID-19) continues to spread globally, more and more evidences are collected about the presence of neurological manifestations and symptoms associated with it. The review shows that although more and more papers are reporting neurological manifestations associated with COVID-19; however, many items remain unclear and this uncertainty calls for a global action that requires close coordination and open-data sharing between hospitals, academic institutions and the fast establishment of harmonised research priorities and research consortia to face the NeuroCOVID-19 complications. Reports are emerging from China and Italy and increasingly from several countries of neurological symptoms associated with SARS-CoV-2, which may be worsening clinical pictures, respiratory outcomes and mortality rates in patients with COVID-19. Observations from Italy have confirmed Chinese data noting a high number of patients with hyposmia, anosmia and varying patterns of possibly centrally mediated symptoms including respiratory manifestations. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice abstract: While the epidemic of Coronavirus disease 2019 (COVID-19) continues to spread globally, more and more evidences are collected about the presence of neurological manifestations and symptoms associated with it. A systematic review has been performed of papers published until 5 April 2020. 29 papers related to neurological manifestations associated with COVID-19 were examined. The results show presence of central and peripheral nervous system manifestations related to coronavirus. Neurological manifestations, or NeuroCOVID, are part of the COVID-19 clinical picture, but questions remain regarding the frequency and severity of CNS symptoms, the mechanism of action underlying neurological symptoms, and the relationship of symptoms with the course and severity of COVID-19. Further clinical, epidemiological, and basic science research is urgently needed to understand and address neurological sequalae of COVID-19. Concomitant risk factors or determinants (e.g. demographic factors, comorbidities, or available biomarkers) that may predispose a person with COVID-19 to neurological manifestations also need to be identified. The review shows that although more and more papers are reporting neurological manifestations associated with COVID-19; however, many items remain unclear and this uncertainty calls for a global action that requires close coordination and open-data sharing between hospitals, academic institutions and the fast establishment of harmonised research priorities and research consortia to face the NeuroCOVID-19 complications. url: https://www.ncbi.nlm.nih.gov/pubmed/32436101/ doi: 10.1007/s00415-020-09896-z id: cord-324345-j43rpvwk author: Leong, Hoe Nam title: SARS – My personal battle date: 2010-11-19 words: 3111.0 sentences: 219.0 pages: flesch: 70.0 cache: ./cache/cord-324345-j43rpvwk.txt txt: ./txt/cord-324345-j43rpvwk.txt summary: I vividly remember the time when I first saw the index patient with Severe Acute Respiratory Syndrome (SARS) in Singapore. The index patient was admitted to Tan Tock Seng Hospital (TTSH) on Saturday, (1st March 2003), and an infectious disease consult was sought on the following Monday. It was an exceedingly busy day for me as I had to attend to new referrals, run an outpatient clinic, and subsequently draft a clinical summary of these two patients by the early evening. Eventually, the patient''s fever defervesced on day 14 of illness. I wasn''t scheduled to perform the ward round that day, but I returned to visit the patient that Sunday morning. My wife and I telephoned a colleague in Singapore and we concurred to have a full blood count test done at the clinic the next day. My wife eventually joined me when she developed fever at the end of the second day of arrival. With that news, my days as a patient in isolation continued. abstract: It isn’t every day that a doctor becomes a patient. It is more peculiar when it occurs with an unknown mysterious epidemic respiratory illness that kills. Severe acute respiratory syndrome (SARS) gripped the world in 2003, spreading via air-links and throwing the global economy into disarray. As a practicing physician in Singapore, one of the first countries affected, I describe my first-hand account of my battle with this illness, how I acquired this illness in Singapore, and eventually quarantine in Frankfurt am Main, Germany. url: https://doi.org/10.1016/j.tmaid.2010.10.007 doi: 10.1016/j.tmaid.2010.10.007 id: cord-355718-7dafsxp9 author: Leong, Hoe‐Nam title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 date: 2004-08-10 words: 2714.0 sentences: 172.0 pages: flesch: 60.0 cache: ./cache/cord-355718-7dafsxp9.txt txt: ./txt/cord-355718-7dafsxp9.txt summary: title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 We performed a retrospective cohort study assessing the effectiveness of ribavirin use in our patients with SARS. We compared the results of clinical and laboratory investigations at the start of ribavirin treatment with correspondent parameters of patients who did not receive ribavirin on day 6 of illness. * Parameters taken on start of treatment for those on ribavirin, and day 6 for the control group. Most patients received this combination therapy but no comparative efficacy data from treatment and control groups were available. After correcting for steroid use, the hazard ratio of death for patients treated with ribavirin was 1.03 (95% CI: 0.44-2.41, P ¼ 0.939). Our study was a retrospective analysis with two groups of patients being treated at different times of the epidemic. abstract: Objective Ribavirin is a broad spectrum nucleoside analogue efficacious in the treatment of several viral infections. In the recent severe acute respiratory syndrome (SARS) outbreak, ribavirin was used in various countries against this novel coronavirus. We conducted a retrospective analysis to assess the efficacy of ribavirin in the treatment of SARS in Singapore. Methods A total of 229 cases were analysed. Ninety‐seven (42.4%) patients received ribavirin at a mean of 6.4 days of illness. Clinical and laboratory parameters taken at the start of ribavirin treatment were compared with day 5, 6 or 7 parameters of those patients not on treatment. The two groups were compared using Fisher's exact test and Student's t‐test. Multivariate analysis was performed using Cox regression model with death as the outcome of interest. Results The treatment group had younger women with more symptoms of myalgia (P < 0.001). The crude death rate was 12.9% in the control and 10.3% (P = 0.679) in the treatment group. After correction for age, male sex, lactate dehydrogenase levels and steroid use, the hazard ratio was 1.03 (95% CI: 0.44–2.41, P = 0.939). Conclusion In this retrospective, uncontrolled cohort analysis, use of ribavirin did not appear to confer any benefit for patients with SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15303999/ doi: 10.1111/j.1365-3156.2004.01281.x id: cord-334210-lhadzo7o author: Lepak, Alexander J title: Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date: 2020-08-27 words: 3673.0 sentences: 227.0 pages: flesch: 55.0 cache: ./cache/cord-334210-lhadzo7o.txt txt: ./txt/cord-334210-lhadzo7o.txt summary: Key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible COVID-19 or for asymptomatic screening. CONCLUSIONS: In a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. In this paper we report the findings of a retrospective observational study to examine results of repeat SARS-CoV-2 RT-PCR testing for patients who were suspected of having COVID-19 (persons under investigation, or PUI) and asymptomatic patients and how the results may inform diagnostic stewardship within our academic medical center in Wisconsin. We believe the biggest lesson learned for our institution is that we found no cases of conversion from a negative to a positive result for inpatients undergoing a repeat PUI test or a repeat asymptomatic screen test. abstract: BACKGROUND: Multiple factors have led to an extremely high volume of SARS-CoV-2 RT-PCR testing. Concerns exist about sensitivity and false-negative SARS-CoV-2 RT-PCR testing results. We describe a retrospective observational study examining the utility of repeat nasopharyngeal (NP) SARS-CoV-2 RT-PCR testing at an academic center in a low prevalence setting. METHODS: All patients within our health system with >1 NP SARS-CoV-2 RT-PCR test result were included. SARS-CoV-2 RT-PCR testing was performed according to one of four validated assays. Key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible COVID-19 or for asymptomatic screening. RESULTS: A total of 660 patients had >1 NP SARS-CoV-2 PCR test performed. The initial test was negative in 638. There were only 6 negative-to-positive conversions (0.9%). All 6 were outpatients undergoing a PUI work-up 5-17 days after an initial negative result. In >260 inpatients with repeat testing, we found no instances of negative-to-positive conversion including those undergoing PUI or asymptomatic evaluation. CONCLUSIONS: In a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. The clinical sensitivity of NP RT-PCR testing may be higher than previously believed. These results have helped shape diagnostic stewardship guidelines, in particular guidance to decrease repeated testing in the inpatient setting to optimize test utilization and preserve resources. url: https://doi.org/10.1093/ofid/ofaa388 doi: 10.1093/ofid/ofaa388 id: cord-268935-4obwu75u author: Lepak, Alexander J. title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) date: 2020-10-12 words: 963.0 sentences: 57.0 pages: flesch: 45.0 cache: ./cache/cord-268935-4obwu75u.txt txt: ./txt/cord-268935-4obwu75u.txt summary: title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) Adoption of the infection control bundle described may be helpful to prevent SARS-CoV-2 spread within healthcare institutions. Notably, repeated inpatient testing of individuals was, in general, directed toward those undergoing procedures, those in whom signs or symptoms suggested possible COVID-19, those with acute changes in status requiring intensive care unit (ICU) or intermediate (IMC) care, and/or based on provider judgment. For the single positive inpatient without a prior history of SARS-CoV-2, chart review revealed that this adult patient lived in a community setting, had mild symptoms (sinus congestion, eye pain, and cough) that started 10 days prior to admission, and was self-isolating at home. We believe that infection was present from community exposure prior to admission; therefore, we did not find any laboratory-confirmed cases suggestive of possible nosocomially acquired SARS-CoV-2 infection despite a substantial inpatient population with and without COVID-19. abstract: Care of SARS-CoV-2-positive patients in healthcare institutions is challenging because of potential risk of transmission to other vulnerable patients. We describe infection control measures which were associated with no instances of hospital transmission. Adoption of the infection control bundle described may be helpful to prevent SARS-CoV-2 spread within healthcare institutions. url: https://doi.org/10.1017/ice.2020.1262 doi: 10.1017/ice.2020.1262 id: cord-310419-s3qkscw7 author: Lephart, Paul R. title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() date: 2020-09-03 words: 2049.0 sentences: 110.0 pages: flesch: 55.0 cache: ./cache/cord-310419-s3qkscw7.txt txt: ./txt/cord-310419-s3qkscw7.txt summary: title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. Within a few weeks, additional SARS-CoV-2 NAAT options emerged that were specifically designed for rapid testing of patients in the point of care setting: the Cepheid Xpert Xpress SARS-CoV-2 (Xpert) assay, which could provide results in 45 minutes, and the Abbott ID NOW COVID-19 (ID NOW) assay, ultimately approved for direct nasal, nasopharyngeal and throat swab testing only, with results in 5-15 minutes. This comparative analysis of SARS-CoV-2 NAATs utilizing the m2000, Simplexa, Xpert and ID NOW assays demonstrated that significant performance deficits were found in the ID NOW assay when tested in a mixed patient population using both NP and nasal specimens. abstract: The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. We compared the performance of four of these assays that were evaluated for use at our institution: Abbott RealTime m2000 SARS-CoV-2 Assay, DiaSorin Simplexa COVID-19 Direct, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID NOW COVID-19. Nasopharyngeal and nasal specimens were collected from 88 ED and hospital-admitted patients and tested by the four methods in parallel to compare performance. ID NOW performance stood out as significantly worse than the other three assays despite demonstrating comparable analytic sensitivity. Further study determined that the use of a nasal swab compared to a nylon flocked nasopharyngeal swab, as well as use in a population chronically vs. acutely positive for SARS-CoV-2, were substantial factors. url: https://api.elsevier.com/content/article/pii/S0732889320305770 doi: 10.1016/j.diagmicrobio.2020.115200 id: cord-355439-eqtk51q3 author: Lesko, Catherine R title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 words: 3288.0 sentences: 154.0 pages: flesch: 46.0 cache: ./cache/cord-355439-eqtk51q3.txt txt: ./txt/cord-355439-eqtk51q3.txt summary: Surveillance data, such as those available from South Africa or Wuhan, will provide the most complete picture of COVID-19 risk among PLWH (e.g., by not restricting to PLWH who are in care and who are more likely to have wellcontrolled HIV disease); however clinical data, such as those from Madrid, may provide the most depth (e.g., by allowing examination of the role of comorbidities, medications, and COVID-19 treatments) as long as potential selection bias is considered. Despite some good telehealth outcomes for some PLWH, telehealth has the potential to exacerbate disparities in care for people with lower socio-economic status: lack of necessary technology and services, technology literacy, and safe, confidential surroundings to participate fully in telehealth may be barriers to engagement in care (32 distancing restrictions if they need to go outside their homes to access alcohol or other drugs, or critically, medication assisted treatments (such as methadone or buprenorphine). abstract: As of July 2020, approximately 6 months into the pandemic of novel coronavirus disease 2019 (COVID-19), whether people living with HIV (PLWH) are disproportionately affected remains an unanswered question. Thus far, risk of COVID-19 in people with and without HIV appears similar but data are sometimes contradictory. Some uncertainty is due to the recency of the emergence of COVID-19 and sparsity of data; some is due to imprecision about what it means for HIV to be a “risk factor” for COVID-19. Forthcoming studies on the risk of COVID-19 to PLWH should differentiate between 1) the unadjusted, excess burden of disease among PLWH to inform surveillance efforts; and 2) any excess risk of COVID-19 among PLWH due to biological effects of HIV, independent of comorbidities that confound rather than mediate this effect. PLWH bear a disproportionate burden of alcohol, other drug use, mental health disorders, and other structural vulnerabilities, which may increase their risk of COVID-19. In addition to any direct effects of COVID-19 on the health of PLWH, we need to understand how physical distancing restrictions impact secondary health outcomes, and the need for, accessibility of, and impact of alternative modalities of providing ongoing medical, mental health, and substance use treatment that comply with physical distancing restrictions (e.g., telemedicine). url: https://www.ncbi.nlm.nih.gov/pubmed/32696057/ doi: 10.1093/aje/kwaa158 id: cord-298886-xidaim04 author: Leszczyński, Piotr title: COVID-19: a short message to rheumatologists date: 2020-06-29 words: 1571.0 sentences: 71.0 pages: flesch: 42.0 cache: ./cache/cord-298886-xidaim04.txt txt: ./txt/cord-298886-xidaim04.txt summary: In the treatment of cytokine storm in COVID-19, there is a possibility of using a TNF alpha inhibitor (adalimumab) or IL-6 receptor inhibitors (tocilizumab, sarilumab) [6] [7] [8] , which are currently being studied in randomized clinical trials in SARS-CoV-2 infected patients with signs and symptoms of rapidly progressing pneumonia. Our own experience with the combined use of chloroquine and azithromycin or ceftriaxone (n = 34) and tocilizumab (n = 1) in the treatment of severe pneumonia in the course of COVID-19 disease is very good, although it should only be considered as a series of cases (Figs. In accordance with some clinical concerns of rheumatologists, patients with rheumatic diseases treated with disease-modifying drugs (DMARDs) should have a higher risk of SARS-CoV-2 infection. Patient with pharmacologically treated rheumatic disease after close contact (staying at a distance of less than 2 m, for more than 15 minutes, in the last 7 days) with a person with confirmed SARS-CoV-2 infection without clinical symptoms of COVID-19: abstract: nan url: https://doi.org/10.5114/reum.2020.96685 doi: 10.5114/reum.2020.96685 id: cord-269465-3fdjqnhb author: Leth-Larsen, Rikke title: The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages date: 2007-05-15 words: 7168.0 sentences: 404.0 pages: flesch: 61.0 cache: ./cache/cord-269465-3fdjqnhb.txt txt: ./txt/cord-269465-3fdjqnhb.txt summary: The severe acute respiratory syndrome coronavirus (SARS-CoV) infects host cells with its surface glycosylated spike-protein (S-protein). Macrophages, DCs, 293T and Vero cells were harvested, incubated for 30 min with 20% (v/v) goat serum, and then stained for 45 min on ice with a mouse monoclonal anti-ACE2 antibody. Cells were washed twice with the binding buffer and then incubated with the myc antibody followed by goat anti-mouse IgG and analyzed by flow cytometry as above. To examine whether S-protein expressed in this study is recognized by ACE2, Vero cells were incubated with the purified S-protein and bound S-protein was detected by flow cytometry using a myc antibody. Blocking of Binding of S-protein to macrophages and DCs: (A) macrophages and DCs were cultured from monocytes and, upon washing, incubated with a mouse anti-human ACE2 monoclonal antibody (solid lines) or, as a control, isotype IgG (solid histograms). abstract: The severe acute respiratory syndrome coronavirus (SARS-CoV) infects host cells with its surface glycosylated spike-protein (S-protein). Here we expressed the SARS-CoV S-protein to investigate its interactions with innate immune mechanisms in the lung. The purified S-protein was detected as a 210 kDa glycosylated protein. It was not secreted in the presence of tunicamycin and was detected as a 130 kDa protein in the cell lysate. The purified S-protein bound to Vero but not 293T cells and was itself recognized by lung surfactant protein D (SP-D), a collectin found in the lung alveoli. The binding required Ca(2+) and was inhibited by maltose. The serum collectin, mannan-binding lectin (MBL), exhibited no detectable binding to the purified S-protein. S-protein binds and activates macrophages but not dendritic cells (DCs). It suggests that SARS-CoV interacts with innate immune mechanisms in the lung through its S-protein and regulates pulmonary inflammation. url: https://www.sciencedirect.com/science/article/pii/S0171298506001495 doi: 10.1016/j.imbio.2006.12.001 id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 words: 8625.0 sentences: 524.0 pages: flesch: 45.0 cache: ./cache/cord-253502-v2hh3w3r.txt txt: ./txt/cord-253502-v2hh3w3r.txt summary: authors: Leung, C.W.; Chiu, W.K. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children [5] [6] [7] [8] [9] [10] [11] Superspreading events including a major hospital outbreak, in-flight transmission on board commercial PAEDIATRIC RESPIRATORY REVIEWS (2004) Summary Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. abstract: Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. Teenagers resemble adults in presentation and disease progression and may develop severe illness requiring intensive care and assisted ventilation. Fever, malaise, cough, coryza, chills or rigor, sputum production, headache, myalgia, leucopaenia, lymphopaenia, thrombocytopaenia, mildly prolonged activated partial thromboplastin times and elevated lactate dehydrogenase levels are common presenting features. Radiographic findings are non-specific but high-resolution computed tomography of the thorax in clinically suspected cases may be an early diagnostic aid when initial chest radiographs appear normal. The improved reverse transcription-polymerase chain reaction (RT-PCR) assays are critical in the early diagnosis of SARS, with sensitivity approaching 80% in the first 3 days of illness when performed on nasopharyngeal aspirates, the preferred specimens. Absence of seroconversion to SARS-CoV beyond 28 days from disease onset generally excludes the diagnosis. The best treatment strategy for SARS among children remains to be determined. No case fatality has been reported in children and the short- to medium-term outcome appears to be good. The importance of continued monitoring for any long-term complications due to the disease or its empiric treatment, cannot be overemphasised. url: https://www.sciencedirect.com/science/article/pii/S152605420400079X doi: 10.1016/j.prrv.2004.07.010 id: cord-277735-a9gkath5 author: Leung, Danny Tze Ming title: Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date: 2004-07-15 words: 4010.0 sentences: 192.0 pages: flesch: 55.0 cache: ./cache/cord-277735-a9gkath5.txt txt: ./txt/cord-277735-a9gkath5.txt summary: We examined serum samples obtained from 46 patients with SARS, 40 patients with non-SARS pneumonia, and 38 healthy individuals, by use of Western blotting (WB), enzyme-linked immunoassay (ELISA), and immunofluorescence assay, using both native and bacterially produced antigens of the virus. Both the humoral and cellular arms of the adaptive immune response are presumed to be important in controlling 2 or preparation U reacted with a serum sample from a patient with SARS showing the highly reactive antigens-nucleocapsid (N) 1, N2, and N3-in the former. Second, we made a recombinant antigen of the N-terminal half of the N protein (rNa), and, when it was used in an IgG ELISA, we found results almost identical to those found with the crude viral extract (89% sensitivity and 94%-95% specificity), including 4 negative cases in common ( figure 2) . abstract: The recent outbreak of severe acute respiratory syndrome (SARS) provided an opportunity to study the antibody response of infected individuals to the causative virus, SARS coronavirus. We examined serum samples obtained from 46 patients with SARS, 40 patients with non-SARS pneumonia, and 38 healthy individuals, by use of Western blotting (WB), enzyme-linked immunoassay (ELISA), and immunofluorescence assay, using both native and bacterially produced antigens of the virus. We found a highly restricted, immunoglobulin G-dominated antibody response in patients with SARS, directed most frequently (89% by ELISA) and predominantly at the nucleocapsid. Almost all of the subjects without SARS had no antinucleocapsid antibodies. The spike protein was the next most frequently targeted, but only 63% of the patients (by ELISA) responded. Other targets of the response identified by use of WB included antigens of 80 and 60 kDa. Several nonstructural proteins cloned were not antigenic, and the culture-derived nucleocapsid appeared to be specifically degraded. url: https://www.ncbi.nlm.nih.gov/pubmed/15216476/ doi: 10.1086/422040 id: cord-310651-pxfwe67t author: Leung, Gabriel M. title: SARS-CoV Antibody Prevalence in All Hong Kong Patient Contacts date: 2004-09-17 words: 1927.0 sentences: 69.0 pages: flesch: 42.0 cache: ./cache/cord-310651-pxfwe67t.txt txt: ./txt/cord-310651-pxfwe67t.txt summary: A total of 1,068 asymptomatic close contacts of patients with severe acute respiratory (SARS) from the 2003 epidemic in Hong Kong were serologically tested, and 2 (0.19%) were positive for SARS coronavirus immunoglobulin G antibody. Serologic surveys can be based on a random sample from the total population with appropriate stratification, on serum collected for other reasons (e.g., blood donors, all hospital admissions), or on surveys of persons who resided in sites of superspreading events or who have had close contact with a confirmed SARS patient. During the epidemic, close contacts were prospectively identified by the Hong Kong Special Administrative Region Government Department of Health through standardized telephone interviews with all 1,755 confirmed SARS patients within 1 week of hospital admission (February 15-June 22, 2003). abstract: A total of 1,068 asymptomatic close contacts of patients with severe acute respiratory (SARS) from the 2003 epidemic in Hong Kong were serologically tested, and 2 (0.19%) were positive for SARS coronavirus immunoglobulin G antibody. SARS rarely manifests as a subclinical infection, and at present, wild animal species are the only important natural reservoirs of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/15498170/ doi: 10.3201/eid1009.040155 id: cord-275858-46jzw94p author: Leung, Janice M. title: COVID-19 and COPD date: 2020-08-13 words: 3024.0 sentences: 166.0 pages: flesch: 42.0 cache: ./cache/cord-275858-46jzw94p.txt txt: ./txt/cord-275858-46jzw94p.txt summary: Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study Risk factors associated with clinical outcomes in 323 COVID-19 hospitalized patients in Wuhan, China Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: a retrospective single center analysis A preliminary study on serological assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 238 admitted hospital patients Epidemiological, clinical, and virological characteristics of 465 hospitalized cases of coronavirus disease 2019 (COVID-19) from Zhejiang province in China. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China abstract: COPD patients have increased risk of severe pneumonia and poor outcomes when they develop COVID-19. This may be related to poor underlying lung reserves or increased expression of ACE-2 receptor in small airways. https://bit.ly/37dSB8l url: https://doi.org/10.1183/13993003.02108-2020 doi: 10.1183/13993003.02108-2020 id: cord-330093-asba80bi author: Leung, Janice M. title: Smoking, ACE-2 and COVID-19: ongoing controversies date: 2020-07-16 words: 2777.0 sentences: 145.0 pages: flesch: 48.0 cache: ./cache/cord-330093-asba80bi.txt txt: ./txt/cord-330093-asba80bi.txt summary: Both research teams are reporting increased angiotensin-converting enzyme 2 (ACE-2) expression in airways of current smokers and those with COPD, with important implications for coronavirus disease 2019 (COVID-19) patients. Since ACE-2 has been shown to be the main receptor utilised by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to enter the host cells [2] , the authors conclude that nicotine is a risk factor for COVID-19. Here, we bring to the discussion whether the increased susceptibility and virulence of SARS-CoV-2 via α7-nAChR and the upregulation of small airway ACE-2 expression may also be relevant for those who vape using nicotine-based e-cigarettes. While smoking may not necessarily increase one''s risk for contracting COVID-19, the biological and inflammatory cascade that occurs upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may be particularly devastating for a smoker. abstract: Smoking increases severity of COVID-19 https://bit.ly/2yWp3jb url: https://doi.org/10.1183/13993003.01759-2020 doi: 10.1183/13993003.01759-2020 id: cord-291149-j70b7kyi author: Leuzinger, K. title: Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures date: 2020-09-23 words: 5480.0 sentences: 369.0 pages: flesch: 55.0 cache: ./cache/cord-291149-j70b7kyi.txt txt: ./txt/cord-291149-j70b7kyi.txt summary: Aim: To cross-validate manual and automated high-throughput (Roche-cobas6800-Target1/Target2) testing for SARS-CoV-2-RNA, to describe detection rates following lockdown and relaxation, and to evaluate SARS-CoV-2-loads in different specimens. As comprehensive real-life data are scarce, we analyze the epidemiology of SARS-CoV-2detection following lockdown and relaxation measures and investigate the quantitative relationship of the different assays and explore SARS-CoV-2-loads in follow-up NOPS and in time-matched lower respiratory fluids, and in plasma samples. Basel-S-gene RT-QNAT was used for SARS-CoV-2 genome quantification in 936 follow-up NOPS from 261 patients with a positive Roche-Cobas-Target1/Target2 screening result, in 95 NOPS and time-matched lower respiratory fluids (tracheal aspirates, bronchial-alveolar lavage, or sputum) or in 259 NOPS and time-matched plasma samples from COVID-19 patients. To follow the SARS-CoV-2-detection rates after introducing more stringent lockdown measures in Switzerland in calendar week 12 (https://www.bag.admin.ch/bag/en/home/dasbag/aktuell/medienmitteilungen.msg-id-78454.html), we identified all NOPS from 12''363 symptomatic adults and children tested for SARS-CoV-2 from calendar week 14 to 24 (Follow-up cohort-1; Table 1 ) including 270 (2%) confirmed infections ( Figure 3A) . abstract: Introduction: SARS-CoV-2-detection is critical for clinical and epidemiological assessment of the ongoing CoVID-19 pandemic. Aim: To cross-validate manual and automated high-throughput (Roche-cobas6800-Target1/Target2) testing for SARS-CoV-2-RNA, to describe detection rates following lockdown and relaxation, and to evaluate SARS-CoV-2-loads in different specimens. Method: The validation cohort prospectively compared Basel-S-gene, Roche-E-gene, and Roche-cobas6800-Target1/Target2 in 1344 naso-oropharyngeal swabs (NOPS) taken in calendar week 13 using Basel-ORF8-gene-assay for confirmation. Follow-up-cohort-1 and -2 comprised 12363 and 10207 NOPS taken over 10 weeks until calendar week 24 and 34, respectively. SARS-CoV-2-loads were compared in follow-up NOPS, lower respiratory fluids, and plasma. Results: Concordant results were obtained in 1308 cases (97%) including 97 (9%) SARS-CoV-2-positives showing high quantitative correlations (Spearman r>0.95; p<0.001) for all assays. Discordant samples (N=36) had significantly lower SARS-CoV-2-loads (p<0.001). Following lockdown, weekly detection rates declined to <1% reducing single-test positive predictive values from 99.3% to 85.1%. Following relaxation, rates flared up to 4% with similarly high SARS-CoV-2-loads, but patients were significantly younger than during lockdown (34 vs 52 years, p<0.001). SARS-CoV-2-loads in follow-up NOPS declined by 3log10 copies/mL within 10 days post-diagnosis (p<0.001). SARS-CoV-2-loads in NOPS correlated weakly with those in time-matched lower respiratory fluids and plasma, but remained detectable in 14 and 7 cases of NOPS with undetectable SARS-CoV-2, respectively. Conclusion: Evaluated manual and automated assays are highly concordant and correlate quantitatively. Following successful lockdown, declining positive predictive values require dual-target-assays for clinical and epidemiologic assessment. Confirmatory and quantitative follow-up testing should be considered within <5 days, using lower respiratory fluids in symptomatic patients with SARS-CoV-2-negative NOPS. url: http://medrxiv.org/cgi/content/short/2020.09.22.20198697v1?rss=1 doi: 10.1101/2020.09.22.20198697 id: cord-018106-5giapmcf author: Levin, Jacqueline title: Mental Health Care for Survivors and Healthcare Workers in the Aftermath of an Outbreak date: 2019-05-16 words: 4253.0 sentences: 182.0 pages: flesch: 36.0 cache: ./cache/cord-018106-5giapmcf.txt txt: ./txt/cord-018106-5giapmcf.txt summary: Similar findings have been reported in multiple studies indicating acute and persistently elevated stress levels as well as other emotional sequelae of healthcare workers during and after pandemic disease outbreaks [10] [11] [12] . A study of the psychological impact of the 2003 SARS outbreak on healthcare workers in Singapore found that support from supervisors and colleagues was a significant negative predictor for psychiatric symptoms and PTSD, in addition to clear communication of directives and precautionary measures which also helped reduce psychiatric symptoms [15] . Providing psychiatric care to survivors and healthcare workers in the aftermath of a pandemic outbreak is a complicated, but crucial, imperative in the service of reducing the burden of human suffering. abstract: When pandemics sweep across communities, they leave behind tremendous suffering in their wake. It is not only the illness that becomes a pandemic, but the same can be inferred about fear, mourning, and despair. The reverberations of loss are felt in a multitude of ways by those left behind. Often times, the mental health issues of affected persons and entire communities do not receive the attention they deserve in the light of other competing, immediate needs imparted by the devastation of the pandemic. This chapter aims to develop strategies for providing psychiatric care to survivors and their families, in the aftermath of a pandemic outbreak. Lastly, special considerations in the application of psychopharmacological interventions are reviewed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122898/ doi: 10.1007/978-3-030-15346-5_11 id: cord-252005-3ld5e7f5 author: Lewis, Nathaniel M title: Household Transmission of SARS-CoV-2 in the United States date: 2020-08-16 words: 3039.0 sentences: 209.0 pages: flesch: 55.0 cache: ./cache/cord-252005-3ld5e7f5.txt txt: ./txt/cord-252005-3ld5e7f5.txt summary: The Centers for Disease Control and Prevention collaborated (CDC) with state and local health departments in the Milwaukee, Wisconsin, and Salt Lake City, Utah, metropolitan areas to identify persons with laboratory-confirmed SARS-CoV-2 infection captured by public health surveillance during March 22-April 25, 2020. The investigation team defined persons identified by local health departments as "index patients." Households were selected by convenience sampling and considered eligible if the index patient was not hospitalized at the time, lived with ≥1 additional person, and tested positive for SARS-CoV-2 rRT-PCR from a nasopharyngeal (NP) swab collected ≤10 days prior to enrollment. One study from China estimated a 28% SIR for spouses of primary patients and 4% for household contacts aged A c c e p t e d M a n u s c r i p t 10 <18 years by SARS-CoV-2 rRT-PCR testing [6] . abstract: BACKGROUND: Although many viral respiratory illnesses are transmitted within households, the evidence base for SARS-CoV-2 is nascent. We sought to characterize SARS-CoV-2 transmission within US households and estimate the household secondary infection rate (SIR) to inform strategies to reduce transmission. METHODS: We recruited laboratory-confirmed COVID-19 patients and their household contacts in Utah and Wisconsin during March 22–April 25, 2020. We interviewed patients and all household contacts to obtain demographics and medical histories. At the initial household visit, 14 days later, and when a household contact became newly symptomatic, we collected respiratory swabs from patients and household contacts for testing by SARS-CoV-2 rRT-PCR and sera for SARS-CoV-2 antibodies testing by enzyme-linked immunosorbent assay (ELISA). We estimated SIR and odds ratios (OR) to assess risk factors for secondary infection, defined by a positive rRT-PCR or ELISA test. RESULTS: Thirty-two (55%) of 58 households had evidence of secondary infection among household contacts. The SIR was 29% (n = 55/188; 95% confidence interval [CI]: 23–36%) overall, 42% among children (<18 years) of the COVID-19 patient and 33% among spouses/partners. Household contacts to COVID-19 patients with immunocompromised conditions had increased odds of infection (OR: 15.9, 95% CI: 2.4–106.9). Household contacts who themselves had diabetes mellitus had increased odds of infection (OR: 7.1, 95% CI: 1.2–42.5). CONCLUSIONS: We found substantial evidence of secondary infections among household contacts. People with COVID-19, particularly those with immunocompromising conditions or those with household contacts with diabetes, should take care to promptly self-isolate to prevent household transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/33185244/ doi: 10.1093/cid/ciaa1166 id: cord-256497-kyer0zjx author: Leyendecker, Pierre title: Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients date: 2020-08-27 words: 2776.0 sentences: 169.0 pages: flesch: 50.0 cache: ./cache/cord-256497-kyer0zjx.txt txt: ./txt/cord-256497-kyer0zjx.txt summary: title: Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients OBJECTIVES: To retrospectively investigate the incidence of acute adrenal infarction (AAI) in patients who underwent chest CT for severe SARS-CoV-2 infection and to correlate findings with prognosis. Consequently, the purpose of this study is to retrospectively investigate the incidence of AAI in patients with severe SARS-CoV-2 infection and to correlate findings to prognosis data. (a) Severe or critical lung parenchyma lesion characteristics of COVID-19, i.e., involving at least 50% of the total lung parenchyma [10] ; (b) Presence of both entire adrenal glands in the inferior part of the volume of acquisition; (c) Positive RT-PCR for SARS-CoV-2 at the time of chest CT. To conclude, our work demonstrated a high incidence of acute adrenal infarction on initial chest CT of severe COVID-19 (51/219, 23%), which might be a sign of a poorer prognosis. abstract: OBJECTIVES: To retrospectively investigate the incidence of acute adrenal infarction (AAI) in patients who underwent chest CT for severe SARS-CoV-2 infection and to correlate findings with prognosis. METHODS: The local ethics committee approved this retrospective study and waived the need of informed consent. From March 9 to April 10, 2020, all patients referred to our institution for a clinical suspicion of COVID-19 with moderate to severe symptoms underwent a chest CT for triage. Patients with a/parenchymal lesion characteristics of COVID-19 involving at least 50% of lung parenchyma and b/positive RT-PCR for SARS-CoV-2 were retrospectively included. Adrenal glands were reviewed by two independent readers to look for AAI. Additional demographics and potential biological markers of adrenal insufficiency were obtained. Correlations with ICU stay and mortality were sought. RESULTS: Out of the 219 patients with critical (n = 52) and severe lung (n = 167) parenchyma lesions, 51 (23%) had CT scan signs of AAI, which was bilateral in 45 patients (88%). Four patients had an acute biological adrenal gland insufficiency (8%). Univariate analysis in AAI+ patients demonstrated a higher rate of ICU stay (67% vs. 45%, p < 0.05) and a longer stay (more than 15 days for 31% for AAI+ vs. 19%, p < 0.05) compared with AAI− patients. Mortality rate was similar (27%, p = 0.92). CONCLUSIONS: Acute adrenal infarction on initial chest evaluation of severe COVID-19 is frequent (51/219, 23%) and might be a sign of poorer prognosis. KEY POINTS: • Acute adrenal infarction on initial chest CT evaluation of severe COVID-19 is frequent (51/219). • AAI might be a factor of poorer prognosis, with increased rate of ICU hospitalization and length of stay. url: https://doi.org/10.1007/s00330-020-07226-5 doi: 10.1007/s00330-020-07226-5 id: cord-320882-cr0ccsnp author: Li Volti, Giovanni title: Smoking and SARS-CoV-2 Disease (COVID-19): Dangerous Liaisons or Confusing Relationships? date: 2020-05-02 words: 1235.0 sentences: 69.0 pages: flesch: 47.0 cache: ./cache/cord-320882-cr0ccsnp.txt txt: ./txt/cord-320882-cr0ccsnp.txt summary: Keywords: COVID-19; SARS-Cov-2; smoking; angiotensin-converting enzyme-2 We read with great interest the article by Brake SJ and colleagues [1] investigating the relationship between smoking and angiotensin-converting enzyme-2 (ACE-2) and the potential implication for COVID-19. The authors present findings linking ACE-2 expression to smoking in a variety of experimental models together with observations of their own; immunohistochemistry data showing an increased expression of ACE-2 in a series of biopsies from a group of current smokers with chronic obstructive pulmonary disease when compared to a control group. The authors then venture into reporting existing Chinese case reports to support their hypothesis that smoking could increase the risk of COVID-19 via upregulation of ACE-2 expression, a known cellular entry gateway for SARS-CoV-2 [2] . Smoking upregulates angiotensin-converting enzyme-2 receptor: A potential adhesion site for novel coronavirus SARS-CoV-2 (Covid-19) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target abstract: We read with great interest the article by Brake SJ and colleagues [...]. url: https://www.ncbi.nlm.nih.gov/pubmed/32370269/ doi: 10.3390/jcm9051321 id: cord-338403-mfde6juv author: Li, Bo title: Prevalence and impact of cardiovascular metabolic diseases on COVID-19 in China date: 2020-03-11 words: 3419.0 sentences: 181.0 pages: flesch: 50.0 cache: ./cache/cord-338403-mfde6juv.txt txt: ./txt/cord-338403-mfde6juv.txt summary: METHODS: A meta-analysis of eligible studies that summarized the prevalence of cardiovascular metabolic diseases in COVID-19 and compared the incidences of the comorbidities in ICU/severe and non-ICU/severe patients was performed. Inclusion criteria are as follows: (1) comparative studies: randomised controlled trials RCTs or non-RCTs published in English; (2) study population: more than ten participants were included in the study; (3) study intervention: patients in the studies should be confirmed to have been infected by 2019 novel coronavirus; (4) parameters: the comorbidities of cardiovascular metabolic diseases and the outcome of cardiac injury should be given. Systematic analysis of studies that described the epidemiological and clinical features of COVID-19 cases and reported the prevalence of cardiovascular metabolic diseases as well as the impact on cardiac injury in the infectious disease, has identified six reports with 1527 patients ( Table 1 ). abstract: BACKGROUND: Studies have reminded that cardiovascular metabolic comorbidities made patients more susceptible to suffer 2019 novel corona virus (2019-nCoV) disease (COVID-19), and exacerbated the infection. The aim of this analysis is to determine the association of cardiovascular metabolic diseases with the development of COVID-19. METHODS: A meta-analysis of eligible studies that summarized the prevalence of cardiovascular metabolic diseases in COVID-19 and compared the incidences of the comorbidities in ICU/severe and non-ICU/severe patients was performed. Embase and PubMed were searched for relevant studies. RESULTS: A total of six studies with 1527 patients were included in this analysis. The proportions of hypertension, cardia-cerebrovascular disease and diabetes in patients with COVID-19 were 17.1%, 16.4% and 9.7%, respectively. The incidences of hypertension, cardia-cerebrovascular diseases and diabetes were about twofolds, threefolds and twofolds, respectively, higher in ICU/severe cases than in their non-ICU/severe counterparts. At least 8.0% patients with COVID-19 suffered the acute cardiac injury. The incidence of acute cardiac injury was about 13 folds higher in ICU/severe patients compared with the non-ICU/severe patients. CONCLUSION: Patients with previous cardiovascular metabolic diseases may face a greater risk of developing into the severe condition and the comorbidities can also greatly affect the prognosis of the COVID-19. On the other hand, COVID-19 can, in turn, aggravate the damage to the heart. url: https://doi.org/10.1007/s00392-020-01626-9 doi: 10.1007/s00392-020-01626-9 id: cord-338205-sy91rnse author: Li, Chenxi title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 words: 7515.0 sentences: 436.0 pages: flesch: 51.0 cache: ./cache/cord-338205-sy91rnse.txt txt: ./txt/cord-338205-sy91rnse.txt summary: With limited understanding of COVID-19, it is difficult to exclude SARS-CoV-2 infection based on a single negative PCR result, especially when testing was used for upper respiratory tract specimens. The study found that SARS-CoV-2 could be detected in all primer-probe sets applied in the qRT-PCR tests, but significant discrepancy was observed in the detection limit and the ability to identify negatives and positives with a lower viral load. Compared with the qRT-PCR kit, nested RT-PCR analysis showed higher sensitivity and specificity, indicating that it is more suitable for clinical application to detect SARS-CoV-2 in cases with low viral load. In cases where RT-PCR assays are negative and there is a strong epidemiological link to SARS-CoV-2 infection, paired serum samples (in the acute and convalescent-phase) could support diagnosis once validated serology tests are available with the initial samples collected in the first week of COVID-19 and the second collected after 2-4 weeks [28] . abstract: Abstract The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early laboratory diagnosis of COVID-19 is the main focus of treatment and control. Molecular tests are the basis for confirmation of COVID-19, but serological tests for SARS-CoV-2 are widely available and play an increasingly important role in understanding the epidemiology of the virus and in identifying populations at higher risk for infection. Point-of-care tests have the advantage of rapid, accurate, portable, low cost and non-specific device requirements, which provide great help for disease diagnosis and detection. This review will discuss the performance of different laboratory diagnostic tests and platforms, as well as suitable clinical samples for testing, and related biosafety protection. This review shall guide for the diagnosis of COVID-19 caused by SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32621814/ doi: 10.1016/j.cca.2020.06.045 id: cord-325124-0hxan9rw author: Li, Chenyu title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 words: 6119.0 sentences: 364.0 pages: flesch: 53.0 cache: ./cache/cord-325124-0hxan9rw.txt txt: ./txt/cord-325124-0hxan9rw.txt summary: However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. abstract: Many detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. Therefore, alternative and highly sensitive methods are imperative. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. url: https://doi.org/10.1101/2020.03.12.988246 doi: 10.1101/2020.03.12.988246 id: cord-334228-n69iewmx author: Li, Chunmei title: Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity date: 2016-02-16 words: 4643.0 sentences: 251.0 pages: flesch: 59.0 cache: ./cache/cord-334228-n69iewmx.txt txt: ./txt/cord-334228-n69iewmx.txt summary: Like other known CoV-3CLpro structures, such as TGEV, hCoV-229E, hCoV-HKU1, and IBV 2-5 , SARS-3CLpro has a highly conserved three-dimensional structure, dimer interface, catalysis dyad, and substrate binding site, but an extremely low homology with cellular proteases. Ser139 and Phe140 are two key residues that not only contribute to interactions between the two protomers in the parent dimer but also maintain the correct conformation of the S1 subsite in the substrate-binding pocket. Other residue mutations, which are neither on the dimer interface nor key to catalysis, can also influence enzyme activity and dimer association-dissociation of SARS-3CLpro via long-range interactions 15, 16 . Our molecular dynamics simulations showed that Ser139-Leu141 maintains a stable 3 10 -helix conformation in the inactive monomer structure and a well-defined loop conformation in the active protomer of the dimer structure. Although SARS-3CLpro uses the dimer structure to maintain its enzyme activity, our study shows that the monomer can also be evolved into an active enzyme via mutations. abstract: The SARS 3C-like proteinase (SARS-3CLpro), which is the main proteinase of the SARS coronavirus, is essential to the virus life cycle. This enzyme has been shown to be active as a dimer in which only one protomer is active. However, it remains unknown how the dimer structure maintains an active monomer conformation. It has been observed that the Ser139-Leu141 loop forms a short 3(10)-helix that disrupts the catalytic machinery in the inactive monomer structure. We have tried to disrupt this helical conformation by mutating L141 to T in the stable inactive monomer G11A/R298A/Q299A. The resulting tetra-mutant G11A/L141T/R298A/Q299A is indeed enzymatically active as a monomer. Molecular dynamics simulations revealed that the L141T mutation disrupts the 3(10)-helix and helps to stabilize the active conformation. The coil-3(10)-helix conformational transition of the Ser139-Leu141 loop serves as an enzyme activity switch. Our study therefore indicates that the dimer structure can stabilize the active conformation but is not a required structure in the evolution of the active enzyme, which can also arise through simple mutations. url: https://www.ncbi.nlm.nih.gov/pubmed/26879383/ doi: 10.1038/srep20918 id: cord-300322-koqm5yxq author: Li, Fang title: Interactions Between Sars Coronavirus and its Receptor date: 2006 words: 1711.0 sentences: 103.0 pages: flesch: 60.0 cache: ./cache/cord-300322-koqm5yxq.txt txt: ./txt/cord-300322-koqm5yxq.txt summary: The SARS-CoV RBD is sufficient for tight binding to ACE2, and thus it is the most important determinant of virus-receptor interactions, viral host range, and tropism. 8 The final model of the complex contains the N-terminal peptidase domain of human ACE2 (residues 19-615) and the spike RBD of human SARS-CoV (residues 323-502, missing residues 376-381). The structure reveals important residue changes at the binding interface that determine the species specificity of SARS-CoV. 6, 7 Detailed structural analysis sheds light on the significance of these residues in virus-receptor interactions (Figure 4 ). Rat ACE2 does not support SARS-CoV Leu472 on the RBD has a hydrophobic interaction with Met82 on ACE2. On rat ACE2, residue 82 is glycosylated, preventing the binding of SARS-CoV. In summary, the crystal structure of SARS-CoV spike RBD in complex with ACE2 has revealed detailed interactions between the virus and its receptor. Structure of SARS coronavirus spike receptor-binding abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037534/ doi: 10.1007/978-0-387-33012-9_38 id: cord-274528-mr81o9cu author: Li, Fei title: Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date: 2020-09-12 words: 6428.0 sentences: 416.0 pages: flesch: 53.0 cache: ./cache/cord-274528-mr81o9cu.txt txt: ./txt/cord-274528-mr81o9cu.txt summary: Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Notably, in addition to prostate, other essential 40 organs, including lung, kidney and liver, which are permissive for SARS-CoV-2 infection in human, were 41 characterized with Tmprss2-postive epithelial cells ( Fig. 1b and Extended Data Fig. 1c ). Consistently, 25 enzalutamide significantly decreased TMPRSS2 expression and inhibited SARS-CoV-2 infection in human 26 prostate cancer cells (Fig. 2) . abstract: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly become a global public health threat due to the lack of effective drugs or vaccines against SARS-CoV-2. The efficacy of several repurposed drugs has been evaluated in clinical trials. Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. However, definitive evidence for the therapeutic efficacy of enzalutamide in COVID-19 is lacking. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. TMPRSS2 knockout significantly inhibited SARS-CoV-2 infection in vivo. Enzalutamide effectively inhibited SARS-CoV-2 infection in human prostate cancer cells (LNCaP) but not in human lung cancer cells or patient-derived lung organoids. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Moreover, we observed distinct AR binding patterns between prostate cells and lung cells and a lack of direct binding of AR to TMPRSS2 in human lung cells. Thus, our findings do not support the postulated protective role of enzalutamide in treating COVID-19. url: https://doi.org/10.1101/2020.09.11.293035 doi: 10.1101/2020.09.11.293035 id: cord-251961-g0n85kxz author: Li, Guoming title: Safety and efficacy of Artemisinin-Piperaquine for treatment of COVID-19: an open-label, non-randomized, and controlled trial date: 2020-11-02 words: 3408.0 sentences: 190.0 pages: flesch: 53.0 cache: ./cache/cord-251961-g0n85kxz.txt txt: ./txt/cord-251961-g0n85kxz.txt summary: CONCLUSIONS: In patients with mild to moderate COVID-19, the time to reach undetectable SARS-CoV-2 was significantly shorter in the AP group than that in the control group. According to the "China''s Novel Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Seventh Edition) ", COVID-19 patients are usually categorized into mild, moderate, severe, and critical based on their symptoms. Initially, this trial was an open-label randomized parallel-group controlled trial intended to compare the efficacy and safety of AP tablets in comparison with hydroxychloroquine to treat patients with mild to moderate COVID-19. And the rate of patients to undetected SARS-CoV-2 by RT-PCR at day 7, 10, 14, 21, and 28 during drug administration, the CT images results within ten days, the abnormal laboratory index and adverse events would be compared between the two treatments. abstract: BACKGROUND: There are no effective therapies for patients with Coronavirus disease-2019 (COVID-19). METHODS: Forty-one patients with confirmed COVID-19 were enrolled in the study and divided into two groups: artemisinin-piperaquine (AP) group (n=23) and control group (n=18). The primary outcome was the time taken to reach undetectable levels of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and the percentage of participants with undetectable SARS-CoV-2 on day 7, 10, 14, and 28. The computed tomography (CT) imaging changes within ten days, the corrected QT interval changes, adverse events, and abnormal laboratory parameters were the secondary outcomes. RESULTS: The mean time to reach undetectable viral RNA (mean± standard deviation) was 10.6±1.1 days (95% confidence interval [CI]: 8.4-12.8) for AP group and 19.3±2.1 days (95% CI: 15.1-23.5) for the control group. The percentage of patients with undetectable viral RNA on day 7, 10, 14, 21, and 28 were 26.1%, 43.5%, 78.3%, 100%, and 100%, respectively, in the AP group and 5.6%, 16.7%, 44.4%, 55.6% and 72.2%, respectively, in the control group. The CT imaging within ten days post-treatment showed no significant differences between the two groups (p>0.05). Both groups had mild adverse events. CONCLUSIONS: In patients with mild to moderate COVID-19, the time to reach undetectable SARS-CoV-2 was significantly shorter in the AP group than that in the control group. However, physicians should consider the QT interval changes before using AP. url: https://api.elsevier.com/content/article/pii/S0924857920304271 doi: 10.1016/j.ijantimicag.2020.106216 id: cord-349645-6o8773c5 author: Li, He title: Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date: 2020-06-02 words: 3018.0 sentences: 177.0 pages: flesch: 50.0 cache: ./cache/cord-349645-6o8773c5.txt txt: ./txt/cord-349645-6o8773c5.txt summary: METHODS: A retrospective study is conducted to study whether air quality index (AQI), four ambient air pollutants (PM(2.5), PM(10), NO(2) and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26(th) to Feb 29(th) in 2020. In this retrospective study, we attempted to conduct an exploratory analysis looking at the association between environment conditions (including ambient pollutants and meteoroidal parameter) and COVID-19 incidence/mortality in Wuhan, given a city-wide lockdown and varying pollution/meteorological data throughout the entire study period. In the current study, although the NO 2 level was constantly lower than the US EPA standards (United States Environmental Protection Agency, 2016), our data revealed that COVID-19 incidence were highly correlated with the ambient NO 2 concentration. The correlation between the COVID-19 incidence and three ambient air pollution along with five meteorological parameters Jan 26 th to Feb 29 th in 2020 in Wuhan and XiaoGan, China. abstract: OBJECTIVES: Although the COVID-19 is known to cause by human-to-human transmission, it remains largely unclear whether ambient air pollutants and meteorological parameters could promote its transmission. METHODS: A retrospective study is conducted to study whether air quality index (AQI), four ambient air pollutants (PM(2.5), PM(10), NO(2) and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26(th) to Feb 29(th) in 2020. RESULTS: First, a significant correlation was found between COVID-19 incidence and AQI in both Wuhan (R(2) = 0.13, p < 0.05) and XiaoGan (R(2) = 0.223, p < 0.01). Specifically, among four pollutants, COVID-19 incidence was prominently correlated with PM(2.5) and NO(2) in both cities. In Wuhan, the tightest correlation was observed between NO(2) and COVID-19 incidence (R(2) = 0.329, p < 0.01). In XiaoGan, in addition to the PM(2.5) (R(2) = 0.117, p < 0.01) and NO(2) (R(2) = 0.015, p < 0.05), a notable correlation was also observed between the PM(10) and COVID-19 incidence (R(2) = 0.105, p < 0.05). Moreover, temperature is the only meteorological parameter that constantly correlated well with COVID-19 incidence in both Wuhan and XiaoGan, but in an inverse correlation (p < 0.05). CONCLUSIONS: AQI, PM(2.5), NO(2), and temperature are four variables that could promote the sustained transmission of COVID-19. url: https://api.elsevier.com/content/article/pii/S1201971220303830 doi: 10.1016/j.ijid.2020.05.076 id: cord-338901-1kzy7rts author: Li, Heng title: Overview of therapeutic drug research for COVID-19 in China date: 2020-06-17 words: 5098.0 sentences: 253.0 pages: flesch: 48.0 cache: ./cache/cord-338901-1kzy7rts.txt txt: ./txt/cord-338901-1kzy7rts.txt summary: According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. In these 155 pooled clinical trials, a number of approved chemical and biomacromolecule drugs have been used in COVID-19 treatment clinical trials for drug repurposing, most of which are nucleotide analogs and protease inhibitors against other viral pathogens, including influenza virus, HIV and HCV. In vitro studies have shown that lopinavir/ritonavir can inhibit the replication of MERS-CoV and SARS-CoV and exert antiviral effects [22] [23] [24] [25] . In the latest "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia", it is recommended to use ribavirin at a dose of 500 mg each time for adults and in combination with interferon or lopinavir/ritonavir, with 2-3 intravenous infusions daily. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) abstract: Since the outbreak of novel coronavirus pneumonia (COVID-19) in December 2019, more than 2,500,000 people worldwide have been diagnosed with SARS-CoV-2 as of April 22. In response to this epidemic, China has issued seven trial versions of diagnosis and treatment protocol for COVID-19. According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. Moreover, with further understanding of SARS-CoV-2 virus, new drugs targeting specific SARS-CoV-2 viral components arise and investigations on these novel anti-SARS-CoV-2 agents are also reviewed. url: https://doi.org/10.1038/s41401-020-0438-y doi: 10.1038/s41401-020-0438-y id: cord-316814-9fv9xrln author: Li, Hong-Ye title: Use of GFP to Investigate Expression of Plant-Derived Vaccines date: 2009 words: 2817.0 sentences: 204.0 pages: flesch: 53.0 cache: ./cache/cord-316814-9fv9xrln.txt txt: ./txt/cord-316814-9fv9xrln.txt summary: Agroinfiltration is a more recent technique that can be applied to investigate transient expression in plant cells by which an Agrobacterium liquid culture is infiltrated into intact plant leaves (7) . By simple infiltration of Agrobacterium cells carrying appropriate gene constructs into tobacco plants leaves, transient expression assays can be performed within 3 days without using expensive instruments or complicated procedures. Two days after agroinfiltration, expression and subcellular localization of the GFP fusion proteins in tobacco leaves can be determined by simple observation under fluorescence or confocal laser scanning microscopy. 7. Generate plasmid pCV12 (Fig. 1 ) or similar nuclear transformation vector for expression of a fusion protein consisting of the SARS-CoV S1 and GFP. Production of tobacco leaves transiently expressing a protein fusion consisting of the SARS-CoV S1 protein fused with the GFP was carried out using Agrobacterium-mediated transformation with plasmid pCV12. abstract: Plants are low-cost bioreactors for the production of various biopharmaceuticals including oral vaccines. Plant-derived oral vaccines are potentially useful in combating viral infections involving mucosal immunity. Transgenic plants have been generated to successfully produce mucosal vaccines against cholera, hepatitis B, foot-and-mouth disease, and Norwalk virus. As a first step toward the generation of oral vaccines against the severe acute respiratory syndrome coronavirus (SARS-CoV), we have expressed a recombinant S1 protein of the SARS-CoV in transformed tobacco. Since plant transformation and regeneration of stable transformants require considerable time, we initially used a green fluorescent protein (GFP) to tag the antigen in transient expression. GFP was fused to the carboxy-terminus of S1 for expression of S1-GFP to show expression of recombinant S1 by agroinfiltration of tobacco leaves. The GFP tag enables a relatively quick confirmation of antigen expression in plant cells by fluorescent microscopy. Such analysis using GFP that precedes stable plant transformation will enable the rapid screening of multiple constructs to attain optimal recombinant protein expression. Furthermore, this approach determines the subcellular localization of the recombinant protein in plant cells, providing information on optimal subcellular targeting for production in plant bioreactors. url: https://doi.org/10.1007/978-1-59745-559-6_19 doi: 10.1007/978-1-59745-559-6_19 id: cord-208426-wz3jan5d author: Li, Hongying title: Airborne dispersion of droplets during coughing: a physical model of viral transmission date: 2020-08-05 words: 4495.0 sentences: 245.0 pages: flesch: 57.0 cache: ./cache/cord-208426-wz3jan5d.txt txt: ./txt/cord-208426-wz3jan5d.txt summary: Using realistic air flow simulation, we model droplet dispersion from coughing and study the transmission risk related to SARS-CoV-2. Notably, numerical methods, such as Computational Fluid Dynamics (CFD) based on Reynolds Averaged Navier-Stokes (RANS) turbulence models 31 produce high resolution flow fields and concentration data, 32 which not only compensate for slow instrumental speeds of analytical techniques, 25 but are also adaptable to different environments and scenarios, such as passengers in an aircraft cabin, 33 and more recently, a cough dispersion study in an outdoor environment under significant wind speeds, 34 whose results are useful in integrated transmission modeling. As detailed in the Supplementary Information, the model cough is inclined downwards at an average of 27·5°, 37 follows a characteristic air flow pattern 33,37 at breath temperature of 36°C, and emits a cluster of droplets with a standard size distribution 11, 38 and viral loading 39 abstract: The Covid-19 pandemic has focused attention on airborne transmission of viruses. Using realistic air flow simulation, we model droplet dispersion from coughing and study the transmission risk related to SARS-CoV-2. Although most airborne droplets are 8-16 $mu$m in diameter, the droplets with the highest transmission potential are, in fact, 32-40 $mu$m. Use of face masks is therefore recommended for both personal and social protection. We found social distancing effective at reducing transmission potential across all droplet sizes. However, the presence of a human body 1 m away modifies the aerodynamics so that downstream droplet dispersion is enhanced, which has implications on safe distancing in queues. Based on median viral load, we found that an average of 0.55 viral copies is inhaled at 1 m distance per cough. Droplet evaporation results in significant reduction in droplet counts, but airborne transmission remains possible even under low humidity conditions. url: https://arxiv.org/pdf/2008.01912v1.pdf doi: nan id: cord-341254-xnj6slby author: Li, Hua title: A new and rapid approach for detecting COVID‐19 based on S1 protein fragments date: 2020-06-05 words: 1945.0 sentences: 120.0 pages: flesch: 46.0 cache: ./cache/cord-341254-xnj6slby.txt txt: ./txt/cord-341254-xnj6slby.txt summary: Based on it, the detection of IgM/IgG in blood became an optional approach to improve the diagnosis, especially for the COVID-19 patient with negative nucleic acid test result. 2. Colloidal gold-labeled mouse-antihuman lgM/lgG antibody was manufactured by SAIYA Hebei Biotechnology Co., Ltd. To obtain the well-performance antibody, the antibody was selected for functional test including the positive and negative coincidence rates, minimum test threshold, and accelerated stability. Due to only around 50% positive rate of SARS-CoV-2 nucleic acid test 8, 12 under various condition of sample collection and storage, viral infection regions, RNA extraction methods, the quality of nucleic acid detection kit, and so on, 13 detection of IgM/IgG became a powerful approach for the early diagnosis of COVID-19 and could help identify the patients with negative nucleic acid but with obvious clinical symptoms. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis abstract: The pandemic of novel coronavirus disease 2019 (COVID‐19) seriously threatened the public health all over the world. A colloidal gold immunochromatography assay for IgM/IgG antibodies against the receptor‐binding domain of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) S1 protein was established to assess its rapid diagnostic value. We first designed and manufactured all contents of the test cassette of SARS‐CoV‐2 rapid test kit: the colloidal gold‐labeled mouse‐antihuman lgM/lgG antibody, the recombinant SARS‐CoV‐2 antigen, the nitrocellulose membrane control line, and specimen diluents. Furthermore, reverse transcription‐polymerase chain reaction (RT‐PCR) assay, colloidal gold immunochromatography assay, serological validation of cross reaction with other common viruses, and clinical validation were performed. The kit was finally evaluated by 75 serum/plasma samples of SARS‐CoV‐2 infection cases and 139 healthy samples as control, with the result of that the sensitivity, specificity, and accuracy for IgM were 90.67%, 97.84%, and 95.33%, whereas for IgG were 69.33%, 99.28%, and 88.79%, respectively; the combination of IgM and IgG could improve the value: 92.00%, 97.12%, and 95.33%, respectively. Therefore, the rapid detection kit has high sensitivity and specificity, especially for IgM&IgG, showing a critical value in clinical application and epidemic control of COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32508026/ doi: 10.1002/ctm2.90 id: cord-295846-quhnesbr author: Li, Huan title: Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis date: 2020-05-05 words: 2788.0 sentences: 185.0 pages: flesch: 45.0 cache: ./cache/cord-295846-quhnesbr.txt txt: ./txt/cord-295846-quhnesbr.txt summary: In conclusion, corticosteroid use in subjects with SARS-CoV-2, SARS-CoV, and MERS-CoV infections delayed virus clearing and did not convincingly improve survival, reduce hospitalization duration or ICU admission rate and/or use of mechanical ventilation. Because of the overlapping genetic and clinical feature of SARS-CoV-2, SARS-CoV, and MERS-CoV, we performed a meta-analysis of safety and efficacy of corticosteroid use in these coronavirus infections. Our meta-analysis focus on the effects of corticosteroids on virus clearing and mortality in persons infected with SARS-CoV-2, SARS-CoV, or MERS-CoV. Inclusion criteria included: (1) research articles including observational studies and clinical trials but excluding reviews or case reports on the use of corticosteroids in persons with SARS-CoV-2, SARS-CoV, and MERS-CoV infections; (2) reported outcomes of virus clearance and/or death; and (3) published in English and/or Chinese. To test impact of corticosteroid use on duration of hospitalization we included 3 studies [12, 13, 16] involving 828 subjects (SARS, N = 519; MERS, N = 309). abstract: We performed a meta-analysis to determine safety and efficacy of corticosteroids in SARS-CoV-2, SARS-CoV, and MERS-CoV infections. We searched PubMed, Web of Science, Medline, WanFang Chinese database, and ZhiWang Chinese database using Boolean operators and search terms covering SARS-CoV-2, SARS-CoV, OR MERS-CoV AND corticosteroids to find appropriate studies. Review Manager 5.3 was used to analyze results of meta-analysis. Observational studies were analyzed for quality using the modified Newcastle–Ottawa scale and randomized clinical trials, using the Jadad scale. Subjects were divided into those with severe-only and other (severe and not severe) cohorts based on published criteria. Efficacy endpoints studied included mortality, hospitalization duration, rates of intensive care unit (ICU) admission, use of mechanical ventilation, and a composite endpoint (death, ICU admission, or mechanical ventilation). We included 11 reports including 10 cohort studies and 1 randomized clinical trial involving 5249 subjects (2003–2020). Two discussed the association of corticosteroids and virus clearing and 10 explored how corticosteroids impacted mortality, hospitalization duration, use of mechanical ventilation, and a composite endpoint. Corticosteroid use was associated with delayed virus clearing with a mean difference (MD) = 3.78 days (95% confidence Interval [CI] = 1.16, 6.41 days; I(2) = 0%). There was no significant reduction in deaths with relative Risk Ratio (RR) = 1.07 (90% CI = 0.81; 1.42; I(2) = 80%). Hospitalization duration was prolonged and use of mechanical ventilation increased. In conclusion, corticosteroid use in subjects with SARS-CoV-2, SARS-CoV, and MERS-CoV infections delayed virus clearing and did not convincingly improve survival, reduce hospitalization duration or ICU admission rate and/or use of mechanical ventilation. There were several adverse effects. Because of a preponderance of observational studies in the dataset and selection and publication biases our conclusions, especially regarding SARS-CoV-2, need confirmation in a randomized clinical trial. In the interim we suggest caution using corticosteroids in persons with COVID-19. url: https://doi.org/10.1038/s41375-020-0848-3 doi: 10.1038/s41375-020-0848-3 id: cord-298067-awo3smgp author: Li, Huanjie title: Transmission Routes Analysis of SARS-CoV-2: A Systematic Review and Case Report date: 2020-07-10 words: 4853.0 sentences: 268.0 pages: flesch: 51.0 cache: ./cache/cord-298067-awo3smgp.txt txt: ./txt/cord-298067-awo3smgp.txt summary: Through associating infection symptoms with the transmission routes of virus and the patient course of the disease, we expect to provide guidelines for clinical diagnosis and the basis for suppressing the spread of the virus and antiviral treatment. On February 1, 2020, respiratory samples of four patients were confirmed SARS-CoV-2 infections by real-time PCR in Jinan Central Hospital, Shandong province, China. Summarizing the published articles, including SARS-CoV and SARS-CoV-2, we combined with epidemiological and clinical data to analyze the possible routes of asymptomatic patients with virus infection in order to provide the basis for suppressing the spread of the virus, and antiviral treatment and advice for the protection of medical staff. The study found that the detection of SARS-CoV-2 nucleic acid positive in a few feces of patients with confirmed COVID-19 cases indicated the presence of a live virus. abstract: The global outbreak of SARS-CoV-2 spread rapidly throughout the world which transmitted among humans through various routes. Asymptomatic (carriers) and possible fecal-oral transmission, resulted into a large-scale spread. These issues pose great challenges to disease diagnosis and epidemic control. We obtained data on 29 cases of COVID-19 patients in Jinan, China, and reported the clinical data of asymptomatic patients confirmed with stool samples positive. Some patients with gastrointestinal infections are secondary to pulmonary infections, and during the patients' recovery period, the virus may still existin the patient's gastrointestinal tract over 7 days. We combined with epidemiological and clinical data of asymptomatic patients to analyze the possible routes of viral transmission and infection, including eyes-nose, hands-eyes, fecal-oral, and eyes-oral, et al., thus first presented the two-way transmission through eyes-oral. Through associating infection symptoms with the transmission routes of virus and the patient course of the disease, we expect to provide guidelines for clinical diagnosis and the basis for suppressing the spread of the virus and antiviral treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32754600/ doi: 10.3389/fcell.2020.00618 id: cord-274313-mrvk9r4w author: Li, Hui title: SARS-CoV-2 and viral sepsis: observations and hypotheses date: 2020-04-17 words: 2428.0 sentences: 138.0 pages: flesch: 44.0 cache: ./cache/cord-274313-mrvk9r4w.txt txt: ./txt/cord-274313-mrvk9r4w.txt summary: With evidence collected from autopsy studies on COVID-19 and basic science research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV, we have put forward several hypotheses about SARS-CoV-2 pathogenesis after multiple rounds of discussion among basic science researchers, pathologists, and clinicians working on COVID-19. Whether SARS-CoV-2 is able to directly attack vascular endothelial cells expressing high levels of ACE2, 13 and then lead to abnormal coagulation and sepsis, still needs to be explored. On the basis of observations from COVID-19 patients, we hypothesise that in mild cases, resident macrophages initiating lung inflammatory responses were able to contain the virus after SARS-CoV-2 infection; both innate and adaptive immune responses were efficiently established to curb the viral replication so that the patient would recover quickly. Meanwhile, the direct attack on other organs by disseminated SARS-CoV-2, the immune pathogenesis caused by the systemic cytokine storm, and the microcirculation dysfunctions together lead to viral sepsis (figure). abstract: Since the outbreak of coronavirus disease 2019 (COVID-19), clinicians have tried every effort to understand the disease, and a brief portrait of its clinical features have been identified. In clinical practice, we noticed that many severe or critically ill COVID-19 patients developed typical clinical manifestations of shock, including cold extremities and weak peripheral pulses, even in the absence of overt hypotension. Understanding the mechanism of viral sepsis in COVID-19 is warranted for exploring better clinical care for these patients. With evidence collected from autopsy studies on COVID-19 and basic science research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV, we have put forward several hypotheses about SARS-CoV-2 pathogenesis after multiple rounds of discussion among basic science researchers, pathologists, and clinicians working on COVID-19. We hypothesise that a process called viral sepsis is crucial to the disease mechanism of COVID-19. Although these ideas might be proven imperfect or even wrong later, we believe they can provide inputs and guide directions for basic research at this moment. url: https://doi.org/10.1016/s0140-6736(20)30920-x doi: 10.1016/s0140-6736(20)30920-x id: cord-264461-nzvuugls author: Li, Jing title: Puzzle of highly pathogenic human coronaviruses (2019-nCoV) date: 2020-02-22 words: 2048.0 sentences: 101.0 pages: flesch: 48.0 cache: ./cache/cord-264461-nzvuugls.txt txt: ./txt/cord-264461-nzvuugls.txt summary: The immunosuppressive drug CsA prevents the nucleocapsid protein of the virus from binding to cyclophilin A (CypA) of the host cell, which has a peptidyl prolyl cis/trans isomerase (PPIase) activity, and a combination of interferon and CsA has been shown previously to significantly inhibit the replication and tissue damage caused by coronavirus infection in bronchi and lungs of humans. reported a mathematical model for simulating the transmission of the novel Wuhan Coronavirus, which is a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source to the humans (Chen et al., 2020a) . They estimated the transmissibility of 2019-nCoV via the basic reproduction number based on only the data from the early stages of the outbreak (Zhao et al., 2020a) . From SARS-CoV to Wuhan 2019-nCoV outbreak: similarity of early epidemic and prediction of future trends Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin abstract: nan url: https://doi.org/10.1007/s13238-020-00693-y doi: 10.1007/s13238-020-00693-y id: cord-291361-2vn1o7ag author: Li, Jing title: Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China date: 2020-07-06 words: 3619.0 sentences: 185.0 pages: flesch: 53.0 cache: ./cache/cord-291361-2vn1o7ag.txt txt: ./txt/cord-291361-2vn1o7ag.txt summary: title: Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China The epidemiological and clinical characteristics of the family cluster patients were analysed and compared with those of 43 contemporaneous sporadic cases. In terms of epidemiological characters and clinical symptoms, no significant differences were observed between the family cluster and sporadic cases. In this study, we aimed to investigate the epidemiological and clinical characteristics of these three family clusters of COVID-19 cases by comparing them with sporadic cases, which would provide insights for epidemic control in the context of the current serious situation worldwide. This study revealed that sporadic cases had lower levels of albumin and lymphocyte counts than family cluster cases; otherwise, there were no significant differences in terms of other epidemiological characters and clinical features between the two groups. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: From 21 January 2020 to 9 February 2020, three family clusters involving 31 patients with coronavirus disease 2019 were identified in Wenzhou, China. The epidemiological and clinical characteristics of the family cluster patients were analysed and compared with those of 43 contemporaneous sporadic cases. The three index cases transmitted the infection to 28 family members 2–10 days before illness onset. Overall, 28 of the 41 sporadic cases and three of 31 patients in the family clusters came back from Wuhan (65.12 vs. 9.68%, P< 0.001). In terms of epidemiological characters and clinical symptoms, no significant differences were observed between the family cluster and sporadic cases. However, the lymphocyte counts of sporadic cases were significantly lower than those of family cluster cases ((1.32 ± 0.55) × 10(9)/l vs. (1.63 ± 0.70) × 10(9)/l, P = 0.037), and the proportion of hypoalbuminaemia was higher in sporadic cases (18/43, 41.86%) than in the family clusters (6/31, 19.35%) (P < 0.05). Within the family cluster, the second- and third-generation cases had milder clinical manifestations, without severe conditions, compared with the index and first-generation cases, indicating that the virulence gradually decreased following passage through generations within the family clusters. Close surveillance, timely recognition and isolation of the suspected or latent patient is crucial in preventing family cluster infection. url: https://doi.org/10.1017/s0950268820001491 doi: 10.1017/s0950268820001491 id: cord-294275-pp0vlaye author: Li, Jingjing title: Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date: 2020-06-03 words: 2367.0 sentences: 152.0 pages: flesch: 55.0 cache: ./cache/cord-294275-pp0vlaye.txt txt: ./txt/cord-294275-pp0vlaye.txt summary: Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. Here, we use nanopore Flongle workflow combined with LAMP reaction to propose a faster and more convenient method to detect SARS-CoV-2 and other respiratory viruses in two hours. This study presents a LAMP based method combined with nanopore Flongle rapid realtime sequencing workflow to detect COVID-19 as low as 3.25×10^2 copies/mL of SARS-CoV-2 in both laboratory and wild-caught environment. To test the limit of detection, the amplification products of dilution gradient 3.25×10^4, 3.25 × 10^3, 1.1 × 10^3, 6.5 × 10^2, 3.25 × 10^2 copies/mL and negative control total 12 samples were constructed another barcoding library (Oxford Nanopore, SQK-RBK004) as described above and sequenced using a PromethION flowcell to achieve more data. The study design ( Figure 2 ) for SARS-CoV-2 detection is based on LAMP rapid amplification of specific genes and sequenced by nanopore Flongle workflow. abstract: The ongoing novel coronavirus (COVID-19) outbreak as a global public health emergency infected by SARC-CoV-2 has caused devastating loss around the world. Currently, a lot of diagnosis methods have been used to detect the infection. The nucleic acid (NA) testing is reported to be the clinical standard for COVID-19 infection. Evidence shows that a faster and more convenient method to detect in the early phase will control the spreading of SARS-CoV-2. Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. In this approach, RNA reverse transcription and nucleic acid amplification reaction with one step in 30 minutes at 60-65°C constant temperature environment, nanopore Flongle rapidly adapter ligated within 10 minutes. Flongle flow cell sequencing and analysis in real-time. This method described here has the advantages of rapid amplification, convenient operation and real-time detection which is the most important for rapid and reliable clinical diagnosis of COVID-19. Moreover, this approach not only can be used for SARS-CoV-2 detection but also can be extended to other respiratory viruses and pathogens. url: https://doi.org/10.1101/2020.06.03.131474 doi: 10.1101/2020.06.03.131474 id: cord-029547-9ei1ram3 author: Li, Jingwei title: The epidemiology and therapeutic options for the COVID-19 date: 2020-05-28 words: 7841.0 sentences: 499.0 pages: flesch: 48.0 cache: ./cache/cord-029547-9ei1ram3.txt txt: ./txt/cord-029547-9ei1ram3.txt summary: According to the Diagnosis and Treatment Program of Novel Coronavirus Pneumonia, only a suspected case has one of the pieces of evidence of etiology or serology, such as positive nucleic acid, confirmation of gene sequencing, and virus specific antibody, to be confirmed to be COVID-19 patient, 55 and the suspected cases were identified by a comprehensive analysis of epidemiological history and clinical manifestations. 64 There have been tens of clinical trials to confirm the safety and efficiency of chloroquine in treating COVID-19 patients, and its mechanism can be described as interfering with the glycosylation of ACE2 or alkalizing the phagolysosome to inhibit viral replication, 65, 66 which prevents the SARS-Cov-2 entering the host cells. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial abstract: An outbreak of coronavirus disease 2019 (COVID-19), a disease caused by a novel pneumonia virus, has affected over 200 countries and regions worldwide. With the increasing number of patients and deaths, WHO have declared it as a global pandemic currently, indicating a third large-scale epidemic coronavirus has appeared since the emergence of severe acute respiratory syndrome coronavirus (SARS) and Middle-East respiratory syndrome (MERS) in the twenty-first century. Considering the great harm it has caused, researchers throughout the world have been chasing to exploit the pathophysiology, characteristics, and potential remedies for COVID-19 to better battle the outbreak. Therefore, the current study revisits advances of the virology, epidemiology, clinical features, therapeutic options, and prevention of COVID-19. The features of asymptomatic carriers are also been explored. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376264/ doi: 10.1093/pcmedi/pbaa017 id: cord-300604-xx2d1s41 author: Li, Juyi title: Association between ABO blood groups and risk of SARS‐CoV‐2 pneumonia date: 2020-05-26 words: 795.0 sentences: 47.0 pages: flesch: 58.0 cache: ./cache/cord-300604-xx2d1s41.txt txt: ./txt/cord-300604-xx2d1s41.txt summary: In December, 2019, a cluster of acute respiratory illness caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred in Wuhan, China.1,2 Epidemiological, clinical characteristics, risk factors for mortality of patients infected with SARS-CoV-2, and risk factors in the susceptibility to SARS-CoV-2 included age and chronic disease have been reported. 32Á2 %, P < 0Á01) in blood group A was much higher than that in the control group; however, there is currently no literature supporting that hypertension and hepatitis increase the risk of infection of SARS-CoV-2. 7 We still find that the proportion of blood group A in patients infected with SARS-CoV-2 was significantly higher than that in healthy controls (38Á0 % vs. 32Á2 %, P < 0Á001), while the proportion of blood group O in SARS-CoV-2 infected patients was significantly lower than in healthy controls (25Á7 % vs. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: In December, 2019, a cluster of acute respiratory illness caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred in Wuhan, China.1,2 Epidemiological, clinical characteristics, risk factors for mortality of patients infected with SARS-CoV-2, and risk factors in the susceptibility to SARS-CoV-2 included age and chronic disease have been reported. url: https://doi.org/10.1111/bjh.16797 doi: 10.1111/bjh.16797 id: cord-330887-q5i8lpan author: Li, K. title: The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19 date: 2020-05-21 words: 4021.0 sentences: 214.0 pages: flesch: 54.0 cache: ./cache/cord-330887-q5i8lpan.txt txt: ./txt/cord-330887-q5i8lpan.txt summary: By comprehensively analyzing the laboratory findings of 1,850 patients, we describe the dynamic changes of the total antibody, spike protein (S)-, receptor-binding domain (RBD)-, and nucleoprotein (N)specific IgM and IgG levels during SARS-CoV-2 infection and recovery. Our results indicate that the S-, RBD-, and Nspecific IgG generation of severe/critical COVID-19 patients is one week later than mild/moderate cases, while the levels of these antibodies are 1.5-fold higher in severe/critical patients during hospitalization (P<0.01). To explore the temporal dynamics of immune response after SARS-Cov-2 infection, we analyzed the antibody levels at different time points after symptoms onset, and the timing and level were compared between mild/moderate and severe/critical COVID-19 Results showed that total IgG, S-, RBD-, and N-specific IgG levels of the severe/critical COVID-19 patients were lower than that of the mild/moderate patients on admission, but these levels sharply increased during hospitalization and on discharge ( Figure 1 , Table 1 ). abstract: Deciphering the dynamic changes of antibodies against SARS-CoV-2 is essential for understanding the immune response in COVID-19 patients. By comprehensively analyzing the laboratory findings of 1,850 patients, we describe the dynamic changes of the total antibody, spike protein (S)-, receptor-binding domain (RBD)-, and nucleoprotein (N)- specific IgM and IgG levels during SARS-CoV-2 infection and recovery. Our results indicate that the S-, RBD-, and N- specific IgG generation of severe/critical COVID-19 patients is one week later than mild/moderate cases, while the levels of these antibodies are 1.5-fold higher in severe/critical patients during hospitalization (P<0.01). The decrease of these IgG levels indicates the poor outcome of severe/critical patients. The RBD- and S-specific IgG levels are 2-fold higher in virus-free patients (P<0.05). Notably, we found that the patients who got re-infected had a low level of protective antibody on discharge. Therefore, our evidence proves that the dynamic changes of antibodies could provide an important reference for diagnosis, monitoring, and treatment, and shed new light on the precise management of COVID-19. url: https://doi.org/10.1101/2020.05.18.20105155 doi: 10.1101/2020.05.18.20105155 id: cord-315046-ltmuw6f8 author: Li, Keying title: SARS‐CoV‐2 infection‐induced immune responses: friends or foes? date: 2020-05-23 words: 3390.0 sentences: 227.0 pages: flesch: 47.0 cache: ./cache/cord-315046-ltmuw6f8.txt txt: ./txt/cord-315046-ltmuw6f8.txt summary: 6-7 SARS-COV-2-infected patients were observed to have massive accumulation of inflammatory cytokines and aberrant T cell responses compared to healthy individuals, providing evidence that COVID-19 may be an immune interrelated disease. [12] [13] So, viral RNA and S protein of SARS-related coronaviruses may have evolved as major PAMPs which can mediate innate immune signaling cascades, initiating an antiviral state in infected-cells. All rights reserved SARS-CoV-2-induced respiratory distress syndrome may involve deranged innate immune effector molecule production, abnormal elevation of inflammatory immune cells and cytokine storms. Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice▿ Response of Memory CD8+ T Cells to Severe Acute Respiratory Syndrome (SARS) Coronavirus in Recovered SARS Patients and Healthy Individuals abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is an emerging coronavirus that belongs to the β genus, causing the outbreak of coronavirus disease 19 (COVID‐19). SARS‐CoV‐2 infection can stimulate a pronounced immune response in the host, which embodies in the decrease of lymphocytes and aberrant increase of cytokines in COVID‐19 patients. SARS‐CoV‐2 RNA and proteins interact with various pattern recognition receptors that switch on antiviral immune responses to regulate viral replication and spreading within the host in vivo. However, overactive and impaired immune responses also cause immune damage and subsequent tissue inflammation. This article focuses on the dual roles of immune system during SARS‐CoV‐2 infection, providing a theoretical basic for identifying therapeutic targets in a situation with an unfavorable immune reaction. url: https://www.ncbi.nlm.nih.gov/pubmed/32445403/ doi: 10.1111/sji.12895 id: cord-262841-nr42rs8f author: Li, Lanjuan title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 words: 2124.0 sentences: 107.0 pages: flesch: 58.0 cache: ./cache/cord-262841-nr42rs8f.txt txt: ./txt/cord-262841-nr42rs8f.txt summary: Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, "replicative intermediates") and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Although the virus has been identified Abbreviations: BNIBernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany; BSL3biosafety level 3; CoVcoronavirus; MHVmouse hepatitis virus; PCRpolymerase chain reaction; minus -RNAreplicative negative-stranded RNA; plus -RNApositive-stranded genomic RNA; RTreverse transcription; SARSsevere acute respiratory syndrome; SCAsodium citrate anticoagulant. In order to evaluate (i) whether SARS-CoV can infect peripheral blood mononuclear cells (PBMCs) of infected persons, (ii) whether the virus can replicate in their PBMCs, and (iii) to reveal any dynamic changes to the virus during the course of the disease, we carried out follow-up investigations on the plusand minus-RNA forms in SARS patients. abstract: Abstract Background: The etiologic agent of severe acute respiratory syndrome (SARS) is a recently identified, positive single-stranded RNA (ssRNA) coronavirus (SARS-CoV). Little is known about the dynamic changes of the viral replicative form in SARS cases. Objectives: Evaluate whether SARS-CoV can infect and replicate in peripheral blood mononuclear cells (PBMCs) of infected persons and reveal any dynamic changes to the virus during the course of the disease. Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, “replicative intermediates”) and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Results: SARS-CoV minus-RNA was detected in PBMCs from SARS patients. The viral replicative forms in PBMCs were detectable during a period of 6 days post-onset of the disease, while the plus-RNA were detectable for a longer period (8–12 days post-onset). Conclusions: SARS-coronavirus can infect and replicate within PBMCs of SARS patients, but viral replication in PBMCs seems subject to self-limitation. url: https://api.elsevier.com/content/article/pii/S1386653203001951 doi: 10.1016/s1386-6532(03)00195-1 id: cord-305582-3hmsknon author: Li, Lei title: Therapeutic strategies for critically ill patients with COVID-19 date: 2020-04-20 words: 6155.0 sentences: 310.0 pages: flesch: 39.0 cache: ./cache/cord-305582-3hmsknon.txt txt: ./txt/cord-305582-3hmsknon.txt summary: In the present article, we have summarized the promising drugs, adjunctive agents, respiratory supportive strategies, as well as circulation management, multiple organ function monitoring and appropriate nutritional strategies for the treatment of COVID-19 in the ICU based on the previous experience of treating other viral infections and influenza. According to the latest version of diagnosis and treatment guidelines, confirmed cases infected with 2019-nCoV are classified to have severe illness once complying with one of the following symptoms: (1) anhelation, respiratory rate ≥ 30 times/min; (2) oxygen saturation at rest ≤ 93%; (3) PaO2/FiO2 ≤ 300 mmHg; and classified to be the critical/life-threatening illness once complying with one of the following symptoms: (1) respiratory failure, mechanical ventilation needed; (2) shock; (3) other organ dysfunction syndrome and requirement of intensive care unit admission. abstract: Since the 2019 novel coronavirus disease (COVID-19) outbreak originated from Wuhan, Hubei Province, China, at the end of 2019, it has become a clinical threat to the general population worldwide. Among people infected with the novel coronavirus (2019-nCoV), the intensive management of the critically ill patients in intensive care unit (ICU) needs substantial medical resource. In the present article, we have summarized the promising drugs, adjunctive agents, respiratory supportive strategies, as well as circulation management, multiple organ function monitoring and appropriate nutritional strategies for the treatment of COVID-19 in the ICU based on the previous experience of treating other viral infections and influenza. These treatments are referable before the vaccine and specific drugs are available for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32307593/ doi: 10.1186/s13613-020-00661-z id: cord-262735-xj9md751 author: Li, Lian Yong title: Digestive system involvement of novel coronavirus infection: Prevention and control infection from a gastroenterology perspective date: 2020-05-12 words: 1280.0 sentences: 71.0 pages: flesch: 43.0 cache: ./cache/cord-262735-xj9md751.txt txt: ./txt/cord-262735-xj9md751.txt summary: In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. Gastrointestinal manifestation in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection above, by adopting single-cell RNA-sequencing technology from two cohort samples, a recent study has shown that ACE2 is highly expressed in cholangiocytes rather than the hepatocytes or other interstitial cells. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: An epidemic of an acute respiratory syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in Wuhan, China, now known as coronavirus disease 2019 (COVID‐19), beginning in December 2019, has attracted an intense amount of attention worldwide. As the natural history and variety of clinical presentations of this disease unfolds, extrapulmonary symptoms of COVID‐19 have emerged, especially in the digestive system. While the respiratory mode of transmission is well known and is probably the principal mode of transmission of this disease, a possibility of the fecal‐oral route of transmission has also emerged in various case series and clinical scenarios. In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. A timely understanding of the relationship between the disease and the digestive system and implementing effective preventive measures are of great importance for a favorable outcome of the disease and can help climnicians to mitigate further transmission by taking appropriate measures. url: https://doi.org/10.1111/1751-2980.12862 doi: 10.1111/1751-2980.12862 id: cord-348178-6bjimde4 author: Li, Ling title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 words: 3684.0 sentences: 205.0 pages: flesch: 52.0 cache: ./cache/cord-348178-6bjimde4.txt txt: ./txt/cord-348178-6bjimde4.txt summary: title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) abstract: Background. During the outbreak of the emergent severe acute respiratory syndrome (SARS) infection, >30% of the ∼8000 infected persons were health care workers. The highly infectious nature of SARS coronavirus (SARS-CoV) compelled our pathologists to consider biosafety issues in the autopsy room and for tissue processing procedures. Methods. A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. High-efficiency particulate air filters were placed in the air supply and exhaust systems. Laminar air flow was from the clean areas to the less clean areas. The negative pressures of the contaminated, semicontaminated, and clean areas were approximately -50 pa, -25 pa, and -5 pa, respectively. Personal protective equipment, including gas mask, impermeable protective clothing, and 3 layers of gloves worn during autopsies; the equipment was decontaminated before it was allowed to exit the facility. Strict BSL-3 practices were followed. Results. When a given concentration of particulate sarin simulant was introduced into the contaminated area, it could not be detected in either the semicontaminated area or clean area, and particles >0.3 μm in size were not detected in the exhaust air. A total of 16 complete postmortem examinations for probable and suspected SARS were performed during a 2-month period. Of these, 7 reported confirmed cases of SARS. None of the 23 pathologists and technicians who participated in these autopsies was infected with SARS-CoV. Conclusions. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. url: https://www.ncbi.nlm.nih.gov/pubmed/16107979/ doi: 10.1086/432720 id: cord-284008-vlwdtjbe author: Li, Na title: The Application of Corticosteroids in COVID-19: A Two-edged Sword date: 2020-06-25 words: 3092.0 sentences: 189.0 pages: flesch: 48.0 cache: ./cache/cord-284008-vlwdtjbe.txt txt: ./txt/cord-284008-vlwdtjbe.txt summary: Their study revealed that proper corticosteroid treatment resulted in lower mortality and shorter hospitalization stay in patients with critical SARS with an oxygenation index (OI) of <300 mm Hg, and it was not associated with significant secondary lower respiratory infection and other complications. [21] described the effect of different doses of adjuvant corticosteroid therapy on 30-or 60-day mortality of patients with influenza A (H1N1) pdm09 viral pneumonia through a retrospective analysis. The results of stratified analysis based on the doses of corticosteroids showed that only treatment with low-to moderate-dose corticosteroid could reduce 30-and 60-day mortality of patients with severe infection with PaO2/FiO2 <300 mm Hg. However, corticosteroids at any dose increased the 60-day mortality of patients with mild infection with PaO2/FiO2 >300 mm Hg. Cao et al. [25] reported the clinical characteristics and treatment of patients with COVID-19 with ARDS in a study available on the medRxiv preprint server. abstract: COVID-19 has become a global pandemic and requires the whole world to respond together. There is no specific antiviral treatment recommended at present for COVID-19. The patients must receive the supportive care to help relieve the symptoms and ensure appropriate infection control. Whether or not to use corticosteroids clinically caused controversy. This article has summarized previous researches about the using of corticosteroids in other viral pneumonia, related clinical data in COVID-19, and recommendations in Chinese guideline. url: https://www.ncbi.nlm.nih.gov/pubmed/32983928/ doi: 10.2478/jtim-2020-0011 id: cord-353862-7xe3fvd5 author: Li, Na title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 words: 3515.0 sentences: 199.0 pages: flesch: 52.0 cache: ./cache/cord-353862-7xe3fvd5.txt txt: ./txt/cord-353862-7xe3fvd5.txt summary: METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. abstract: BACKGROUND: The ongoing epidemics of coronavirus disease 2019 (COVID-19) have caused serious concerns about its potential adverse effects on pregnancy. There are limited data on maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia. METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. RESULTS: During January 24 to February 29, 2020, there were sixteen pregnant women with confirmed COVID-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. Two had vaginal delivery and the rest took cesarean section. Few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest CT images of COVID-19 pneumonia. Compared to the controls, COVID-19 pneumonia patients had lower counts of white blood cells (WBC), neutrophils, C-reactive protein (CRP), and alanine aminotransferase (ALT) on admission. Increased levels of WBC, neutrophils, eosinophils, and CRP were found in postpartum blood tests of pneumonia patients. There were three (18.8%) and three (16.7%) of the mothers with confirmed or suspected COVID-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. None experienced respiratory failure during hospital stay. COVID-19 infection was not found in the newborns and none developed severe neonatal complications. CONCLUSION: Severe maternal and neonatal complications were not observed in pregnant women with COVID-19 pneumonia who had vaginal delivery or caesarean section. Mild respiratory symptoms of pregnant women with COVID-19 pneumonia highlight the need of effective screening on admission. url: https://www.ncbi.nlm.nih.gov/pubmed/32249918/ doi: 10.1093/cid/ciaa352 id: cord-287054-zmxpuynv author: Li, Ning title: Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date: 2020-08-25 words: 6747.0 sentences: 356.0 pages: flesch: 37.0 cache: ./cache/cord-287054-zmxpuynv.txt txt: ./txt/cord-287054-zmxpuynv.txt summary: Since March 3, 2020, three methods have been used for the diagnosis of novel coronavirus pneumonia: i) Detection of positive 2019-nCoV nucleic acids by RT-PCR; ii) viral gene sequencing to detect known 2019-nCoV sequences; and iii) the identification of positive 2019-nCoV-specific IgM and IgG antibodies in serum (15) . The China National Medical Products Administration has approved a gene sequencing system (ultra-high-throughput sequencer DNBSEQ-T7), supporting analysis software and nucleic acid detection kits (Table Ⅲ ), which can identify and diagnose coronaviruses, including 2019-nCoV and other infectious respiratory pathogens and enable rapid detection of viral sequences (22) . The clinical application of the total antibody detection can improve limitations, including slow speed of nucleic acid detection in suspected patients, complex sampling, low sensitivity and the requirement for high-level biosafety measures for the control and prevention of the current 2019-nCoV epidemic (74) . abstract: COVID-19 is caused by a novel coronavirus (2019-nCoV or SARS-CoV-2) and has become a global public health emergency. Rapid and accurate molecular diagnostic technologies are crucial for the screening, isolation, treatment, prevention and control of COVID-19. Currently, nucleic acid detection-based techniques and rapid diagnostic tests that detect antigens or antibodies specific to 2019-nCoV infections are the primary diagnostic tools. China National Medical Products Administration has opened a special channel for approval of new pharmaceuticals owing to urgent clinical needs, with 18 nucleic acid detection kits, 11 protein detection kits and 1 sequencing-related equipment and supporting software having been approved until April 23, 2020. The current review summarizes the application situation, advantages, disadvantages and associated technology improvement trends of molecular diagnostics for COVID-19 in China, identifies knowledge gaps and indicates future priorities for research in this field. The most effective way to prevent and control COVID-19 is early detection, diagnosis, isolation and treatment. In the clinical application of molecular diagnosis technology, it is necessary to combine pathogenic microbiology, immunology and other associated detection technologies, advocate the combination of multiple technologies, determine how they complement each other, enhance practicability and improve the ability of rapid and accurate diagnosis and differential diagnosis of COVID-19. url: https://doi.org/10.3892/etm.2020.9142 doi: 10.3892/etm.2020.9142 id: cord-291790-z5rwznmv author: Li, Qianqian title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity date: 2020-07-17 words: 4884.0 sentences: 362.0 pages: flesch: 66.0 cache: ./cache/cord-291790-z5rwznmv.txt txt: ./txt/cord-291790-z5rwznmv.txt summary: We first tested the infectivity of 106 pseudotyped viruses (80 natural variants and 26 129 glycosylation mutants) in 293T-hACE2 cells, where a difference by 4 -fold in RLU compared 130 with the reference Wuhan-1 strain (GenBank: MN908947) was deemed as being significant 131 ( Figure S1 ). Notably, some RBD variants such as A475V 283 and F490L have been confirmed to have decreased sensitivity to both human sera and multiple 284 neutralizing mAbs. A475V reduced the sensitivity to 6 mAbs out of the 13 mAb used in this study, 285 while F490L reduced the sensitivity to neutralization by 3 mAbs. It is possible that antibodies in 286 14 convalescent sera are able to neutralize these critical epitopes targeted by these mAbs that are 287 known to disrupt the binding of the S protein to hACE2 receptor (Ju et Serial dilutions of mAb preparations were pre-incubated with the pseudotyped viruses at 37°C for 355 one hour before they were added to Huh-7 cells. abstract: Summary The spike protein of SARS-CoV-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here we investigated 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. Most variants with amino acid change at receptor binding domain were less infectious but variants including A475V, L452R, V483A and F490L became resistant to some neutralizing antibodies. Moreover, the majority of glycosylation deletions were less infectious whilst deletion of both N331 and N343 glycosylation drastically reduced infectivity, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in the development of vaccine and therapeutic antibodies. url: https://www.sciencedirect.com/science/article/pii/S0092867420308771?v=s5 doi: 10.1016/j.cell.2020.07.012 id: cord-310680-klywz85w author: Li, Qihan title: The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date: 2005-04-06 words: 4397.0 sentences: 210.0 pages: flesch: 53.0 cache: ./cache/cord-310680-klywz85w.txt txt: ./txt/cord-310680-klywz85w.txt summary: The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The pathological analysis of the lung tissue from the deceased patients revealed severe Abbreviations: SARS-CoV, severe acute respiratory syndrome coronavirus; BTF3, basic transcription factor-3; ATF5, activation transcription factor-5; NADH, nicotinamide adenine dinucleotide dehydrogenase; FBS, fetal bovine serum; DMEM, double minimal essential media; QDO, quartdrop-out; NC, nitrocellulose; HE, hematoxyline and eosin method; GFP, green fluorescence protein; GST, glutathione S-transferase * Corresponding author. To further investigate the contribution of this interaction to the cytopathic effect of SARS-CoV, a detection series of mitochondrial function and the activity of the oxido-reductase system in the human embryo lung fibroblast transfected with the nsp10 gene was performed. abstract: The pathological mechanism of SARS-CoV infection was investigated. The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The results indicated that apart from the two subunits of cellular RNA polymerase complex, BTF3 and ATF5, this nsp10 protein was also able to interact specifically with the NADH 4L subunit and cytochrome oxidase II. Further study revealed that the activity of the NADH-cytochrome was altered and the inner mitochondrial membrane was depolarized in the transfected human embryo lung fibroblast by the nsp10 protein gene. The cytopathic effect of the Coronavirus 229E strain appeared more extensive in these cells than in the control cells. url: https://www.ncbi.nlm.nih.gov/pubmed/16157265/ doi: 10.1016/j.jcv.2004.12.019 id: cord-024989-0o6agnrc author: Li, Qihao title: Prediction and analysis of key protein structures of 2019-nCoV date: 2020-05-12 words: 3244.0 sentences: 172.0 pages: flesch: 58.0 cache: ./cache/cord-024989-0o6agnrc.txt txt: ./txt/cord-024989-0o6agnrc.txt summary: Aim: The purpose of this study was to predict and analyze the structure and function of 2019-novel Coronavirus (nCoV) key proteins. Differential key protein structure analysis of 2019-nCoV Although some amino acids were inserted in two positions of nsp3 in orf1ab [23] , the insertion sites were in the nsp3b and nsp3c regions, which are mainly related to the binding reaction of nucleic acids. Back-mutating mutant amino acids to study the functional change of RBD of S protein In order to study the effect of interactional amino acid changes in 2019-nCoV-ACE2 binding region RBD, we mutated the changed three amino acid residues (Glu 470 , Gln 484 and Asn 487 ) within the RBD structure back to the original amino acids. • We elaborated the sequence and structure differences in each key protein of 2019-nCoV and other bat SARS coronaviruses (CoVs). abstract: Aim: The purpose of this study was to predict and analyze the structure and function of 2019-novel Coronavirus (nCoV) key proteins. Materials & methods: We obtained the structure and sequence of proteins from related databases and studied them through multiple sequence alignment, homology modeling, sequence analysis, virtual screening, reverse mutation, protein structure overlap and surface property analysis. Results & conclusion: We found no significant changes in envelope protein, membrane protein, nucleocapsid protein and key proteases in open reading frame 1ab, and predicted results of proteins and performed molecular dynamics simulations. Based on the surface properties of spike protein and docking results with angiotensin-converting enzyme 2, we believe that the binding ability of spike protein to angiotensin-converting enzyme 2 may be similar to SARS. These studies will help us in fighting 2019-nCoV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236793/ doi: 10.2217/fvl-2020-0020 id: cord-270622-aofva2ab author: Li, Qizhang title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 date: 2020-08-26 words: 2830.0 sentences: 165.0 pages: flesch: 55.0 cache: ./cache/cord-270622-aofva2ab.txt txt: ./txt/cord-270622-aofva2ab.txt summary: title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 Based on the "steric-clashes alleviating receptor (SCAR)" strategy developed in our lab recently, we screened the library of clinic and investigational drugs, and identified nine drugs that might be repurposed as covalent inhibitors of the priming proteases (cathepsin B, cathepsin L, and TMPRSS2) of the spike protein of SARS-CoV-2. After careful filtering and 79 evaluation, we identified five (trapoxin B, neratinib, HKI-357, domatinostat and (Z)-dacomitinib) 80 potential covalent inhibitors for CatB, three (neratinib, HKI-357 and (Z)-dacomitinib) for CatL Although the docked poses 160 were slightly different on these two proteins, the warheads of these drugs were also at the positions 161 suitable for covalent bonding (Figure 3F-H) Taken together, using our SCARdock protocol, we identified nine drugs that might be repurposed as 229 the covalent inhibitors of the priming proteases of the S protein of SARS-CoV-2. abstract: In less than eight months, the COVID-19 (coronavirus disease 2019) caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus has resulted in over 20,000,000 confirmed cases and over 700,000 deaths around the world. With the increasing worldwide spreading of this disease, the lack of effective drugs against SARS-CoV-2 infection makes the situation even more dangerous and unpredictable. Although many forces are speeding up to develop prevention and treatment therapeutics, it is unlikely that any de novo drugs will be available in months. Drug repurposing holds the promise to significantly save the time for drug development, since it could use existing clinic drugs to treat new diseases. Based on the “steric-clashes alleviating receptor (SCAR)” strategy developed in our lab recently, we screened the library of clinic and investigational drugs, and identified nine drugs that might be repurposed as covalent inhibitors of the priming proteases (cathepsin B, cathepsin L, and TMPRSS2) of the spike protein of SARS-CoV-2. Among these hits, five are known covalent inhibitors, and one is an anti-virus drug. Therefore, we hope our work would provide rational and timely help for developing anti-SARS-CoV-2 drugs. url: https://api.elsevier.com/content/article/pii/S200103702030369X doi: 10.1016/j.csbj.2020.08.016 id: cord-326882-bbn1tfq5 author: Li, Quan title: Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date: 2020-04-14 words: 1675.0 sentences: 104.0 pages: flesch: 55.0 cache: ./cache/cord-326882-bbn1tfq5.txt txt: ./txt/cord-326882-bbn1tfq5.txt summary: We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARSCoV-2. To explore the variability in genetic polymorphisms and expression in human ACE2 (hACE2), we set out to determine if there were any differences between the Asian and Caucasian populations for ACE2 polymorphisms and compare the variability of hACE2 expression in peripheral blood among eight different populations. In order to investigate whether differences in genetic variations exist between Caucasians and Asians and if these variants can influence the efficiency of cell entry of SARS-CoV-2, we retrieved the variants in the hACE2 from gnomAD v2.1 exomes13. Asians and Other Races Express Similar Levels of and Share the Same Genetic Polymorphisms of the SARS-CoV-2 Cell-Entry Receptor abstract: There appears to be large regional variations for susceptibility, severity and mortality for Covid-19 infections. We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARS- CoV-2. By comparing 56,885 Non-Finnish European and 9,197 East Asians (including 1,909 Koreans) four missense mutations were noted in the hACE2 gene. Molecular dynamic demonstrated that two of these variants (K26R and I468V) may affect binding characteristics between S protein of the virus and hACE2 receptor. We also examined hACE2 gene expression in eight global populations from the HapMap3 and noted marginal differences in expression for some populations as compared to the Chinese population. However, for both of our studies, the magnitude of the difference was small and the significance is not clear in the absence of further in vitro and functional studies. url: https://doi.org/10.1101/2020.04.14.041434 doi: 10.1101/2020.04.14.041434 id: cord-293180-f1ulk9ce author: Li, R W K title: Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs date: 2004-08-14 words: 4289.0 sentences: 295.0 pages: flesch: 51.0 cache: ./cache/cord-293180-f1ulk9ce.txt txt: ./txt/cord-293180-f1ulk9ce.txt summary: Special management protocols and modified measures that regulate droplet and aerosol contamination in a dental setting have to be introduced and may include the reduction or avoidance of droplet/aerosol generation, the disinfection of the treatment field, application of rubber dam, pre-procedural antiseptic mouthrinse and the dilution and efficient removal of contaminated ambient air. In the first part of this two-part article an account of the epidemiology, virology, pathology and management of Severe Acute Respiratory Syndrome (SARS) was provided together with public health issues and general aspects of infection control. On the other hand smaller droplets (or aerosols, generally under 10 µm in size) or small-particle residue of evaporated droplets are usually airborne and are entrained in the air for a lengthy period • SARS is a highly infectious disease and dental personnel are likely to be at risk because of the nature of their profession, working in close proximity to the patient. abstract: The transmission modes of SARS-coronavirus appear to be through droplet spread, close contact and fomites although air borne transmission has not been ruled out. This clearly places dental personnel at risks as they work in close proximity to their patients employing droplet and aerosol generating procedures. Although the principle of universal precautions is widely advocated and followed throughout the dental community, additional precautionary measures — termed standard precaution may be necessary to help control the spread of this highly contagious disease. Patient assessment should include questions on recent travel to SARS infected areas and, contacts of patients, fever and symptoms of respiratory infections. Special management protocols and modified measures that regulate droplet and aerosol contamination in a dental setting have to be introduced and may include the reduction or avoidance of droplet/aerosol generation, the disinfection of the treatment field, application of rubber dam, pre-procedural antiseptic mouthrinse and the dilution and efficient removal of contaminated ambient air. The gag, cough or vomiting reflexes that lead to the generation of aerosols should also be prevented. url: https://www.ncbi.nlm.nih.gov/pubmed/15311240/ doi: 10.1038/sj.bdj.4811522 id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 words: 11098.0 sentences: 688.0 pages: flesch: 48.0 cache: ./cache/cord-327000-oyg3oyx1.txt txt: ./txt/cord-327000-oyg3oyx1.txt summary: This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. abstract: Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus (CoV), is the causative agent of porcine epidemic diarrhea (PED). PED causes lethal watery diarrhea in piglets, which has led to substantial economic losses in many countries and is a great threat to the global swine industry. Interferons (IFNs) are major cytokines involved in host innate immune defense, which induce the expression of a broad range of antiviral effectors that help host to control and antagonize viral infections. PEDV infection does not elicit a robust IFN response, and some of the mechanisms used by the virus to counteract the host innate immune response have been unraveled. PEDV evades the host innate immune response by two main strategies including: 1) encoding IFN antagonists to disrupt innate immune pathway, and 2) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. url: https://doi.org/10.3390/pathogens9050367 doi: 10.3390/pathogens9050367 id: cord-301626-7ow1jja4 author: Li, Shih-Wen title: SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6 date: 2016-05-05 words: 3733.0 sentences: 183.0 pages: flesch: 47.0 cache: ./cache/cord-301626-7ow1jja4.txt txt: ./txt/cord-301626-7ow1jja4.txt summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) papain-like protease (PLPro) reportedly inhibits the production of type I interferons (IFNs) and pro-inflammatory cytokines in Toll-like receptor 3 (TLR3) and retinoic acid-inducible gene 1 (RIG-I) pathways. The decrease in the activated state of TRAF3 and TRAF6 correlated with the inactivation of TBK1 in response to IMQ by PLPro. The results revealed that the antagonism of SARS-CoV PLPro on TLR7-mediated innate immunity was associated with the negative regulation of TRAF3/6-TBK1-IRF3/NF-κB/AP1 signals. To examine whether SARS-CoV PLPro modulates the TLR7 signaling pathway, stable transfected promonocyte cells expressing PLPro and vector control cells were established, treated with TLR7 agonist (imiquimod (IMQ)), then further analyzed for activation of type I IFN production ( Figure 1 ). To examine the inhibitory mechanism of TLR7 antagonism by SARS-CoV PLPro, differential profiles of ubiquitin-conjugated proteins in the vector control and PLPro-expressing cells in the absence or presence of IMQ were analyzed using immune-precipitation ( Figure 5A,B) . abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) papain-like protease (PLPro) reportedly inhibits the production of type I interferons (IFNs) and pro-inflammatory cytokines in Toll-like receptor 3 (TLR3) and retinoic acid-inducible gene 1 (RIG-I) pathways. The study investigated the inhibitory effect and its antagonistic mechanism of SARS-CoV PLPro on TLR7-mediated cytokine production. TLR7 agonist (imiquimod (IMQ)) concentration-dependently induced activation of ISRE-, NF-κB- and AP-1-luciferase reporters, as well as the production of IFN-α, IFN-β, TNF-α, IL-6 and IL-8 in human promonocyte cells. However, SARS-CoV PLPro significantly inhibited IMQ-induced cytokine production through suppressing the activation of transcription factors IRF-3, NF-κB and AP-1. Western blot analysis with anti-Lys48 and anti-Lys63 ubiquitin antibodies indicated the SARS-CoV PLPro removed Lys63-linked ubiquitin chains of TRAF3 and TRAF6, but not Lys48-linked ubiquitin chains in un-treated and treated cells. The decrease in the activated state of TRAF3 and TRAF6 correlated with the inactivation of TBK1 in response to IMQ by PLPro. The results revealed that the antagonism of SARS-CoV PLPro on TLR7-mediated innate immunity was associated with the negative regulation of TRAF3/6-TBK1-IRF3/NF-κB/AP1 signals. url: https://doi.org/10.3390/ijms17050678 doi: 10.3390/ijms17050678 id: cord-273764-itu39mln author: Li, Taisheng title: Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date: 2006-12-20 words: 2660.0 sentences: 120.0 pages: flesch: 49.0 cache: ./cache/cord-273764-itu39mln.txt txt: ./txt/cord-273764-itu39mln.txt summary: In this report, we have sequentially monitored 30 recovered patients over a two-year period to characterize temporal changes in SARS-CoV-specific antibody responses as well as cytotoxic T cell (CTL) responses. As show in Fig. 1 , recovered patients clearly experienced two distinct phases of cell restoration in the peripheral blood; an initial rapid phase for all the cell populations studied in the first 3 months after the onset of symptoms followed by a significant slower phase during the subsequent months. To study the sequential changes in CTL responses against SARS-CoV, we used ELISPOT-based technique to quantify the number of INF-c releasing cells in the peripheral blood against peptide pools covering the entire N protein derived from the Urbani strain [3] . We have shown for the first time that recovered patients have persistent and robust binding as well as neutralizing antibody and CTL responses throughout the study period with a moderate decline one year after the onset of symptoms. abstract: Most of the individuals infected with SARS coronavirus (SARS-CoV) spontaneously recovered without clinical intervention. However, the immunological correlates associated with patients' recovery are currently unknown. In this report, we have sequentially monitored 30 recovered patients over a two-year period to characterize temporal changes in SARS-CoV-specific antibody responses as well as cytotoxic T cell (CTL) responses. We have found persistence of robust antibody and CTL responses in all of the study subjects throughout the study period, with a moderate decline one year after the onset of symptoms. We have also identified two potential major CTL epitopes in N proteins based on ELISPOT analysis of pooled peptides. However, despite the potent immune responses and clinical recovery, peripheral lymphocyte counts in the recovered patients have not yet been restored to normal levels. In summary, our study has, for the first time, characterized the temporal and dynamic changes of humoral and CTL responses in the natural history of SARS-recovered individuals, and strongly supports the notion that high and sustainable levels of immune responses correlate strongly with the disease outcome. Our findings have direct implications for future design and development of effective therapeutic agents and vaccines against SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/17183651/ doi: 10.1371/journal.pone.0000024 id: cord-297942-6wdwrttn author: Li, Taisheng title: Diagnosis and clinical management of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection: an operational recommendation of Peking Union Medical College Hospital (V2.0): Working Group of 2019 Novel Coronavirus, Peking Union Medical College Hospital date: 2020-03-14 words: 1825.0 sentences: 99.0 pages: flesch: 42.0 cache: ./cache/cord-297942-6wdwrttn.txt txt: ./txt/cord-297942-6wdwrttn.txt summary: To standardize the clinical diagnosis and treatment, Peking Union Medical College Hospital (PUMCH) has established a working group and formulated the following operational recommendation regarding "Diagnosis and Clinical Management of Severe Acute Respiratory Syndrome Coronavirus 2 Infection" (V2.0). According to the definition of the National Health Commission [1] , patients in accordance with one of the following standards should be hospitalized and transferred to Beijing designated medical institution as soon as possible; (1) respiratory rate increased (≥30 per min) or dyspnoea; (2) oxygen saturation ≤ 95% when breathing ambient air, or arterial oxygen tension (PaO₂) over inspiratory oxygen fraction (FIO₂) of less than 300 mm Hg (1 mm Hg equals to 0.133 kPa); (3) lung imaging indicating multilobular lesions or progression of lesions over 50% within 48 h; (4) quick sequential organ failure assessment (qSOFA) score ≥2; (5) community-acquired pneumonia-65 (CURB-65) score ≥ 1; (6) combined pneumothorax; (7) other clinical conditions that require hospitalization. abstract: Since December 2019, China has been experiencing an outbreak of a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The clinical features include fever, coughing, shortness of breath, and inflammatory lung infiltration. China rapidly listed SARS-CoV-2-related pneumonia as a statutory infectious disease. To standardize the diagnosis and treatment of this new infectious disease, an operational recommendation for the diagnosis and management of SARS-CoV-2 infection is developed by Peking Union Medical College Hospital. url: https://doi.org/10.1080/22221751.2020.1735265 doi: 10.1080/22221751.2020.1735265 id: cord-321455-ooouqna7 author: Li, Tao title: Characteristics of laboratory indexes in COVID-19 patients with non-severe symptoms in Hefei City, China: diagnostic value in organ injuries date: 2020-07-01 words: 2117.0 sentences: 119.0 pages: flesch: 52.0 cache: ./cache/cord-321455-ooouqna7.txt txt: ./txt/cord-321455-ooouqna7.txt summary: In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. In the process of continuous monitoring, the expression of CRE in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, and 7th days of admission, and showed an overall downward trend (Fig. 3a) . The expression of Ca 2+ in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, 7th and 10th days of admission, and showed an overall upward trend (Fig. 3d ). abstract: This study compared the laboratory indexes in 40 non-severe COVID-19 patients with those in 57 healthy controls. In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. SARS-CoV-2 infection can affect hematopoiesis, hemostasis, coagulation, fibrinolysis, bone metabolism, thyroid, parathyroid glands, the liver, and the reproductive system. url: https://doi.org/10.1007/s10096-020-03967-9 doi: 10.1007/s10096-020-03967-9 id: cord-328484-4iptwc3n author: Li, Tao title: Clinical Characteristics of 312 Hospitalized Older Patients with COVID-19 in Wuhan, China date: 2020-07-15 words: 3077.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-328484-4iptwc3n.txt txt: ./txt/cord-328484-4iptwc3n.txt summary: Although some case series have been published, no previous studies focused on older patients exclusively (Novel Coronavirus Pneumonia Emergency Response Epidemiology Team, 2020; Fu et al., 2020; . Further regression analysis suggested that age(OR 1.59, 95%CI 1.13-2.08), SOFA score(OR 5.89, 95%CI 3.48-7.96), APACHEⅡ score(OR 3.13, 95%CI 1.85-5.62), platelet count＜125×10 9 /L(OR 2.36, 95%CI 1.03-4.14), d-dimer(OR 4.37, 95%CI 2.58-7.16), creatinine＞133μmol/L(OR 1.85, 95%CI 1.12-3.04), interleukin-6(OR 4.32, 95%CI 2.07-7.13), and lung consolidation(OR 1.94, 95%CI 1.45-4.27) on admission were independent risk factors for severe COVID-19 (Table 3) . This study compared clinical characteristics between non-severe and severe COVID-19 cases among older patients, and identified several risk factors for severe cases. This study identified several risk factors for severe COVID-19 cases among older patients. Age, SOFA score, APACHEⅡ score, platelet count＜125×109/L, d-dimer, creatinine＞ 133μmol/L, interleukin-6, and lung consolidation on admission were independent risk factors for severe cases among older patients with COVID-19. abstract: OBJECTIVES: Much of the previous research on COVID-19 was based on all population. But substantial numbers of severe episodes occur in older patients. There is a lack of data about COVID-19 in older adults. The aims of this study were to analyze the clinical characteristics of older adult patients with COVID-19. METHODS: Retrospective study of older patients hospitalized with COVID-19 from February 1 st to March 31 st, 2020 was conducted in the Sino-French New City Branch of Tongjing Hospital in Wuhan, China. According to the degree of severity of COVID-19 during hospitalization, 312 older patients were divided into non-severe and severe cases. RESULTS: the mean age of the patients was 69.2 ± 7.3 years, and 47.4% of patients had exposure history. 77.2% of patients had a co-morbidity, with hypertension being the most common(57.1%), followed by diabetes(38.8%) and cardiovascular disease(29.8%). Multivariable regression showed increasing odds of severe COVID-19 associated with age(OR 1.59, 95%CI 1.13-2.08), SOFA score(OR 5.89, 95%CI 3.48-7.96), APACHEⅡ score(OR 3.13, 95%CI 1.85-5.62), platelet count＜125 × 10(9)/L(OR 2.36, 95%CI 1.03-4.14), d-dimer(OR 4.37, 95%CI 2.58-7.16), creatinine＞133 μmol/L(OR 1.85, 95%CI 1.12-3.04), interleukin-6(OR 4.32, 95%CI 2.07-7.13), and lung consolidation(OR 1.94, 95%CI 1.45-4.27) on admission. The most common complication was acute respiratory distress syndrome(35.6%), followed by acute cardiac injury(33.0%) and coagulation disorders(30.8%). 91.7% of patients were prescribed antiviral therapy, followed by immune globulin(52.9%) and systemic glucocorticoids(43.6%). 21.8% of patients received invasive ventilation, 1.92% for extracorporeal membrane oxygenation. The overall mortality was 6.73%, and mortality of severe patients was 17.1%, which was higher than non-severe patients(0.962%). CONCLUSIONS: Older patients with COVID-19 had much more co-morbidity, complications and mortality. More attention should be paid to older patients with COVID-19. url: https://doi.org/10.1016/j.archger.2020.104185 doi: 10.1016/j.archger.2020.104185 id: cord-012045-1cqqj84n author: Li, Tiao title: The Role of Deubiquitinating Enzymes in Acute Lung Injury and Acute Respiratory Distress Syndrome date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute lung injury and acute respiratory distress syndrome (ALI/ARDS) are characterized by an inflammatory response, alveolar edema, and hypoxemia. ARDS occurs most often in the settings of pneumonia, sepsis, aspiration of gastric contents, or severe trauma. The prevalence of ARDS is approximately 10% in patients of intensive care. There is no effective remedy with mortality high at 30–40%. Most functional proteins are dynamic and stringently governed by ubiquitin proteasomal degradation. Protein ubiquitination is reversible, the covalently attached monoubiquitin or polyubiquitin moieties within the targeted protein can be removed by a group of enzymes called deubiquitinating enzymes (DUBs). Deubiquitination plays an important role in the pathobiology of ALI/ARDS as it regulates proteins critical in engagement of the alveolo-capillary barrier and in the inflammatory response. In this review, we provide an overview of how DUBs emerge in pathogen-induced pulmonary inflammation and related aspects in ALI/ARDS. Better understanding of deubiquitination-relatedsignaling may lead to novel therapeutic approaches by targeting specific elements of the deubiquitination pathways. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402294/ doi: 10.3390/ijms21144842 id: cord-332134-88wfcc3y author: Li, Tingting title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date: 2020-09-24 words: 2051.0 sentences: 158.0 pages: flesch: 57.0 cache: ./cache/cord-332134-88wfcc3y.txt txt: ./txt/cord-332134-88wfcc3y.txt summary: title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection Molecular mechanism for neutralization 157 Structure alignment of SR4-, MR17-and ACE2-RBD 4 showed that both sybodies 158 engage with RBD at the receptor-binding motif (RBM) ( Fig. 2A, 2B) . Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. As LR5 showed 209 higher affinity and neutralization activity than LR1 (Fig. 1A) , we fused this non-210 competing sybody to the N-terminal of MR3 with various length of GS linkers ranging 211 from 13 to 34 amino acids (Extended Data Table S1 ). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with 803 abstract: SARS-CoV-2, the causative agent of COVID-191, recognizes host cells by attaching its receptor-binding domain (RBD) to the host receptor ACE22–7. Neutralizing antibodies that block RBD-ACE2 interaction have been a major focus for therapeutic development8–18. Llama-derived single-domain antibodies (nanobodies, ∼15 kDa) offer advantages including ease of production and possibility for direct delivery to the lungs by nebulization19, which are attractive features for bio-drugs against the global respiratory disease. Here, we generated 99 synthetic nanobodies (sybodies) by in vitro selection using three libraries. The best sybody, MR3 bound to RBD with high affinity (KD = 1.0 nM) and showed high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.40 μg mL−1). Structural, biochemical, and biological characterization of sybodies suggest a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency were generated by structure-based design, biparatopic construction, and divalent engineering. Among these, a divalent MR3 conjugated with the albumin-binding domain for prolonged half-life displayed highest potency (IC50 = 12 ng mL−1) and protected mice from live SARS-CoV-2 challenge. Our results pave the way to the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid responses for future outbreaks. url: https://doi.org/10.1101/2020.06.09.143438 doi: 10.1101/2020.06.09.143438 id: cord-264051-ps0x2es1 author: Li, Wei title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date: 2020-11-05 words: 8939.0 sentences: 450.0 pages: flesch: 51.0 cache: ./cache/cord-264051-ps0x2es1.txt txt: ./txt/cord-264051-ps0x2es1.txt summary: Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Besides, these virus fragments containing HIS can increase the H3K27 acetylation (H3K27ac) enrichment at their corresponding regions of the human genome in different mammalian cells and activate the expression of adjacent and distant genes associated with inflammation. Collectively, we identified HIS in SARS-CoV-2 genome, and the targeted human genome loci enriched with cytokines genes suggested that HIS may underly the clinical characteristics of COVID-19 patients and serve as a vital player in the pathological progression. abstract: The COVID-19 pandemic is a widespread and deadly public health crisis. The pathogen SARS-CoV-2 replicates in the lower respiratory tract and causes fatal pneumonia. Although tremendous efforts have been put into investigating the pathogeny of SARS-CoV-2, the underlying mechanism of how SARS-CoV-2 interacts with its host is largely unexplored. Here, by comparing the genomic sequences of SARS-CoV-2 and human, we identified five fully conserved elements in SARS-CoV-2 genome, which were termed as “human identical sequences (HIS)”. HIS are also recognized in both SARS-CoV and MERS-CoV genome. Meanwhile, HIS-SARS-CoV-2 are highly conserved in the primate. Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Noteworthily, hyaluronan level in plasma of COVID-19 patients is tightly correlated with severity and high risk for acute respiratory distress syndrome (ARDS) and may act as a predictor for the progression of COVID-19. HIS antagomirs, which downregulate hyaluronan level effectively, and 4-Methylumbelliferone (MU), an inhibitor of hyaluronan synthesis, are potential drugs to relieve the ARDS related ground-glass pattern in lung for COVID-19 treatment. Our results revealed that unprecedented HIS elements of SARS-CoV-2 contribute to the cytokine storm and ARDS in COVID-19 patients. Thus, blocking HIS-involved activating processes or hyaluronan synthesis directly by 4-MU may be effective strategies to alleviate COVID-19 progression. url: https://doi.org/10.1101/2020.11.04.361576 doi: 10.1101/2020.11.04.361576 id: cord-300847-ycuiso0g author: Li, Wei title: Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date: 2020-06-02 words: 2801.0 sentences: 172.0 pages: flesch: 55.0 cache: ./cache/cord-300847-ycuiso0g.txt txt: ./txt/cord-300847-ycuiso0g.txt summary: We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. By using phage display we have previously identified a number of potent fully human mAbs (m396, m336, m102.4) against emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV) (4) , Middle East respiratory syndrome coronavirus (MERS-CoV) (5) and henipaviruses (6, 7) , respectively, which are also highly effective in animal models of infection (8) (9) (10) (11) ; one of them was administered on a compassionate basis to humans exposed to henipaviruses and successfully evaluated in a clinical trial (12) . Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak. abstract: Effective therapies are urgently needed for the SARS-CoV-2/COVID19 pandemic. We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. One high affinity mAb, IgG1 ab1, specifically neutralized replication competent SARS-CoV-2 with exceptional potency as measured by two different assays. There was no enhancement of pseudovirus infection in cells expressing Fcγ receptors at any concentration. It competed with human angiotensin-converting enzyme 2 (hACE2) for binding to RBD suggesting a competitive mechanism of virus neutralization. IgG1 ab1 potently neutralized mouse ACE2 adapted SARS-CoV-2 in wild type BALB/c mice and native virus in hACE2 expressing transgenic mice. The ab1 sequence has relatively low number of somatic mutations indicating that ab1-like antibodies could be quickly elicited during natural SARS-CoV-2 infection or by RBD-based vaccines. IgG1 ab1 does not have developability liabilities, and thus has potential for therapy and prophylaxis of SARS-CoV-2 infections. The rapid identification (within 6 days) of potent mAbs shows the value of large antibody libraries for response to public health threats from emerging microbes. url: https://www.ncbi.nlm.nih.gov/pubmed/32511413/ doi: 10.1101/2020.05.13.093088 id: cord-332469-zegawla5 author: Li, Wei title: The characteristics of household transmission of COVID-19 date: 2020-04-17 words: 2513.0 sentences: 164.0 pages: flesch: 64.0 cache: ./cache/cord-332469-zegawla5.txt txt: ./txt/cord-332469-zegawla5.txt summary: Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. abstract: BACKGROUND: Since December 2019, SARS-CoV-2 virus has extended to most parts of China with more than 80 thousand cases and to at least 100 countries with more than 60 thousand international cases by March 15, 2020. Here we applied household cohort study to determine the features of household transmission of COVID-19. METHODS: Total 105 index patients and 392 household contacts were enrolled. Both index patients and household members were inspected by SARS-CoV-2 RT-PCR. The information of all recruited people was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. RESULTS: Secondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% comparing with 17.1% to adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% comparing with 16.9% to the contacts without index patients quarantined. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. CONCLUSION: The secondary attack rate of SARS-CoV-2 in household is 16.3%. Ages of household contacts and spouse relationship with index case are risk factors for transmission of SARS-CoV-2 within household. Quarantine of index patients at home since onset of symptom is useful to prevent the transmission of SARS-Co-2 within household. url: https://doi.org/10.1093/cid/ciaa450 doi: 10.1093/cid/ciaa450 id: cord-339093-mwxkvwaz author: Li, Wei title: High potency of a bivalent human VH domain in SARS-CoV-2 animal models date: 2020-09-04 words: 11419.0 sentences: 687.0 pages: flesch: 59.0 cache: ./cache/cord-339093-mwxkvwaz.txt txt: ./txt/cord-339093-mwxkvwaz.txt summary: It potently neutralized mouse adapted SARS-CoV-2 in wild type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. To identify potent neutralizing V H s against SARS-CoV-2, we panned our large (10 11 clones) and diverse phage-displayed human V H antibody library against recombinant RBD. One of those V H s, ab8, in an Fc (human IgG1, crystallizable fragment) fusion format, showed potent neutralization activity and specificity against SARS-CoV-2 both in vitro and in two animal models. They also suggest that the double mutations Q498T/P499Y on RBD did not influence V H -Fc ab8 binding and contribute to the validation of the mouse adapted SARS-CoV-2 model for evaluation of neutralizing antibody efficacy. In conclusion, we identified a fully human antibody V H domain that shows strong competition with ACE2 for binding to RBD and potent neutralization of SARS-CoV-2 in vitro and in two animal models. abstract: Novel COVID-19 therapeutics are urgently needed. We generated a phage-displayed human antibody VH domain library from which we identified a high-affinity VH binder ab8. Bivalent VH, VH-Fc ab8 bound with high avidity to membrane-associated S glycoprotein and to mutants found in patients. It potently neutralized mouse adapted SARS-CoV-2 in wild type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. Electron microscopy combined with scanning mutagenesis identified ab8 interactions with all three S protomers and showed how ab8 neutralized the virus by directly interfering with ACE2 binding. VH-Fc ab8 did not aggregate and did not bind to 5300 human membrane-associated proteins. The potent neutralization activity of VH-Fc ab8 combined with good developability properties and cross-reactivity to SARS-CoV-2 mutants provide a strong rationale for its evaluation as a COVID-19 therapeutic. url: https://api.elsevier.com/content/article/pii/S009286742031148X doi: 10.1016/j.cell.2020.09.007 id: cord-340472-9ijlj4so author: Li, Wenhui title: Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 date: 2005-03-24 words: 6610.0 sentences: 297.0 pages: flesch: 53.0 cache: ./cache/cord-340472-9ijlj4so.txt txt: ./txt/cord-340472-9ijlj4so.txt summary: Figure 3B -D shows three views of the crystal structure of human ACE2, in which residues that convert rat ACE2 to an efficient SARS-CoV receptor are shown in red, and additional residues whose alteration interferes with S1-Ig association are shown in yellow. (C) Murine leukemia viruses (MLV) expressing green fluorescent protein (GFP), lacking its endogenous envelope glycoprotein (MLV-GFP), and pseudotyped with the S protein of SARS-CoV (TOR2 isolate) were incubated with HEK293T cells transfected with plasmids encoding the indicated human or rat ACE2 variants. We have shown that entry is the primary barrier to SARS-CoV infection of murine Surface plasmon resonance experiments in which the indicated RBD-Ig TOR2 variants shown in Figure 6B bound to immobilized anti-human antibody were assayed for association with soluble human ACE2. S-protein alterations at residues 479 and 487 are important for high-affinity association with human ACE2, and for efficient infection of cells expressing this receptor. abstract: Human angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS coronavirus (SARS-CoV). Here we identify the SARS-CoV spike (S)-protein-binding site on ACE2. We also compare S proteins of SARS-CoV isolated during the 2002–2003 SARS outbreak and during the much less severe 2003–2004 outbreak, and from palm civets, a possible source of SARS-CoV found in humans. All three S proteins bound to and utilized palm-civet ACE2 efficiently, but the latter two S proteins utilized human ACE2 markedly less efficiently than did the S protein obtained during the earlier human outbreak. The lower affinity of these S proteins could be complemented by altering specific residues within the S-protein-binding site of human ACE2 to those of civet ACE2, or by altering S-protein residues 479 and 487 to residues conserved during the 2002–2003 outbreak. Collectively, these data describe molecular interactions important to the adaptation of SARS-CoV to human cells, and provide insight into the severity of the 2002–2003 SARS epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/15791205/ doi: 10.1038/sj.emboj.7600640 id: cord-269087-f9hyntvf author: Li, X. title: A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19 date: 2020-04-04 words: 4280.0 sentences: 236.0 pages: flesch: 49.0 cache: ./cache/cord-269087-f9hyntvf.txt txt: ./txt/cord-269087-f9hyntvf.txt summary: Results: We included 25 published literature references related to the epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. The risk factors which may suggest severe or critical progress for children are: Fast respiratory rate and/or; lethargy and drowsiness mental state and/or; lactate progressively increasing and/or; imaging showed bilateral or multi lobed infiltration, pleural effusion or rapidly expending of lesions in a short period of time and/or; less than 3 months old or those who underly diseases. To help better understand how it would affect children and what is the latest specific clinical and research finding on children with it, we provide a mini-review based on 25 literature references covering the fields of epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. According to the current literature on the pediatric cases, children confirmed with COVID-19 mostly had good prognosis, with considerably less severe to critical progress (5.9%) as compared to adult patients (18.5%). abstract: Background: As the novel coronavirus triggering COVID-19 has broken out in Wuhan, China and spread rapidly worldwide, it threatens the lives of thousands of people and poses a global threat on the economies of the entire world. However, infection with COVID-19 is currently rare in children. Objective To discuss the latest findings and research focus on the basis of characteristics of children confirmed with COVID-19, and provide an insight into the future treatment and research direction. Methods: We searched the terms "COVID-19 OR coronavirus OR SARS-CoV-2" AND "Pediatric OR children" on PubMed, Embase, Cochrane library, NIH, CDC, and CNKI. The authors also reviewed the guidelines published on Chinese CDC and Chinese NHC. Results: We included 25 published literature references related to the epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. Conclusion: The numbers of children with COVID-19 pneumonia infection are small, and most of them come from family aggregation. Symptoms are mainly mild or even asymptomatic, which allow children to be a risk factor for transmission. Thus, strict epidemiological history screening is needed for early diagnosis and segregation. This holds especially for infants, who are more susceptible to infection than other age groups in pediatric age, but have most likely subtle and unspecific symptoms. They need to be paid more attention to. CT examination is a necessity for screening the suspected cases, because most of the pediatric patients are mild cases, and plain chest X-ray do not usually show the lesions or the detailed features. Therefore, early chest CT examination combined with pathogenic detection is a recommended clinical diagnosis scheme in children. The risk factors which may suggest severe or critical progress for children are: Fast respiratory rate and/or; lethargy and drowsiness mental state and/or; lactate progressively increasing and/or; imaging showed bilateral or multi lobed infiltration, pleural effusion or rapidly expending of lesions in a short period of time and/or; less than 3 months old or those who underly diseases. For those critical pediatric patients with positive SARS-CoV-2 diagnosis, polypnea may be the most common symptom. For treatment, the elevated PCT seen in children in contrast to adults suggests that the underlying coinfection/secondary infection may be more common in pediatric patients and appropriate antibacterial treatment should be considered. Once cytokine storm is found in these patients, anti-autoimmune or blood-purifying therapy should be given in time. Furthermore, effective isolation measures and appropriate psychological comfort need to be provided timely. url: https://doi.org/10.1101/2020.03.30.20044545 doi: 10.1101/2020.03.30.20044545 id: cord-252910-7qvnj6c8 author: Li, Xin title: The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date: 2020-09-21 words: 4180.0 sentences: 223.0 pages: flesch: 54.0 cache: ./cache/cord-252910-7qvnj6c8.txt txt: ./txt/cord-252910-7qvnj6c8.txt summary: In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Different from these studies, we previously reported several other findings on SARS-CoV-2 for the first time, including the following in particular: (1) the alternative translation of Nankai coding sequence (CDS) that characterize the rapid mutation rate of betacoronavirus at the nucleotide level [2] ; (2) a furin cleavage site (FCS) "RRAR" in the junction region between S1 and S2 subunits (junction FCS) of SARS-CoV-2 that may increase the efficiency of viral entry into cells [3] ; and (3) the use of 5'' untranslated-region (UTR) barcoding for the detection, identification, classification and phylogenetic analysis of-though not limited to-CoVs [4] . Using the insertions and deletions (InDels) at six sites, we identified two recently detected betacoronavirus strains RmYN01 and RmYN02 from a bat [6] and discovered that RmYN02 was a recombinant SARS2-like CoV strain. abstract: In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Based on the analysis of these recombination events, we proposed that the Spike protein of SARS-CoV-2 may have more than one specific receptor for its function. In addition, we reported—for the first time—a recombination event of ORF8 at the whole-gene level in a bat and ultimately determined that ORF8 enhances the viral replication. In conjunction with our previous discoveries, we found that receptor binding abilities, junction furin cleavage sites (FCSs), strong first ribosome binding sites (RBSs) and enhanced ORF8s are main factors contributing to transmission, virulence and host adaptability of CoVs. Junction FCSs and enhanced ORF8s increase the efficiencies in viral entry into cells and replication, respectively while strong first RBSs enhance the translational initiation. The strong recombination ability of CoVs integrated these factors to generate multiple recombinant strains, two of which evolved into SARS-CoV and SARS-CoV-2 by nature selection, resulting in the SARS and COVID-19 pandemics. url: https://doi.org/10.1101/2020.07.22.213926 doi: 10.1101/2020.07.22.213926 id: cord-342947-dhe31r3a author: Li, Xin title: Preliminary recommendations for lung surgery during COVID‐19 epidemic period date: 2020-04-14 words: 2107.0 sentences: 103.0 pages: flesch: 51.0 cache: ./cache/cord-342947-dhe31r3a.txt txt: ./txt/cord-342947-dhe31r3a.txt summary: After SARS-CoV-2 infection has been excluded and space-occupying lesions in the lungs confirmed by computed tomography (CT) scan, they could be transferred to thoracic surgery for further diagnosis and treatment. • For peripheral solid nodules with a diameter of less than 3 cm considered as malignant lesions by PET-CT or percutaneous pulmonary puncture biopsy, short-term regular follow-up (once a month) can be recommended during the outbreak prevention and control period. 3 Therefore, we suggest that during the epidemic prevention and control period, whether the patient has pure GGNs, mixed GGNs or multiple GGNs (SARS-CoV-2 infection should be excluded for multiple GGNs), follow-up re-examination should be the main recommendation, and surgery should not be carried out. For patients undergoing emergency thoracic surgery, if the symptoms mentioned above occur, isolation measures should be taken during the operation, and the possibility of SARS-CoV-2 latent infection should be eliminated without delay. Preliminary recommendations for lung surgery during 2019 novel coronavirus disease (COVID-19) epidemic period abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32291939/ doi: 10.1111/1759-7714.13423 id: cord-253905-zknmfgsh author: Li, Xingguang title: Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 date: 2020-03-11 words: 3846.0 sentences: 194.0 pages: flesch: 49.0 cache: ./cache/cord-253905-zknmfgsh.txt txt: ./txt/cord-253905-zknmfgsh.txt summary: To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. Homology plot analysis of "dataset_6" also revealed that BetaCoV/bat/Yunnan/ RaTG13/2013 was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378), consistent with phylogenetic analysis ( Figure S5 ). 46, 47 Bayesian analyses with the tip-dating method using a strict clock as well as constant size coalescent tree prior indicated that SARS-CoV-2 is evolving at a rate of 1.24 × 10 −3 substitutions per site per year (Table 1 ), in accordance with our prior research 46, 47 and similar to that found for other human F I G U R E 4 Estimated maximum-clade-credibility tree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using tip-dating method. abstract: To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS‐CoV‐2 virus, we reanalyzed virome data sets from pangolins and representative SARS‐related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood‐mapping, and comparative analyses of the genomes. Based on Bayesian time‐scaled phylogenetic analysis using the tip‐dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS‐CoV‐2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10(−3) substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS‐CoV‐2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS‐CoV‐2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS‐CoV‐2 virus, which is responsible for the recent outbreak of COVID‐19, did not come directly from pangolins. url: https://doi.org/10.1002/jmv.25731 doi: 10.1002/jmv.25731 id: cord-298902-afek8kgr author: Li, Xingguang title: Transmission dynamics and evolutionary history of 2019‐nCoV date: 2020-02-14 words: 2020.0 sentences: 104.0 pages: flesch: 46.0 cache: ./cache/cord-298902-afek8kgr.txt txt: ./txt/cord-298902-afek8kgr.txt summary: To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019‐nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. 19 In the present study, we investigated the time origin and genetic diversity of 2019-nCoV in humans based on 32 genomes of virus strains sampled from China, Thailand, and the USA with known sampling dates between 24 December 2019 and 23 January 2020. Likelihood-mapping analysis of "dataset_14" revealed that 100% of the quartets were distributed in the center of the triangle, indicating a strong star-like topology signal reflecting a novel virus, which may be due to exponential epidemic spread ( Figure 1A) . Of note, the strong star-like signal (100% of quartets were distributed in the center of the triangle) from "dataset_14" at the beginning of the virus outbreak suggests that 2019-nCoV initially exhibited low genetic divergence, with recent and rapid human-tohuman transmission. abstract: To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019‐nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. Phylogenetic, transmission network, and likelihood‐mapping analyses of the genome sequences were performed. On the basis of the likelihood‐mapping analysis, the increasing tree‐like signals (from 0% to 8.2%, 18.2%, and 25.4%) over time may be indicative of increasing genetic diversity of 2019‐nCoV in human hosts. We identified three phylogenetic clusters using the Bayesian inference framework and three transmission clusters using transmission network analysis, with only one cluster identified by both methods using the above genome sequences of 2019‐nCoV strains. The estimated mean evolutionary rate for 2019‐nCoV ranged from 1.7926 × 10(−3) to 1.8266 × 10(−3) substitutions per site per year. On the basis of our study, undertaking epidemiological investigations and genomic data surveillance could positively impact public health in terms of guiding prevention efforts to reduce 2019‐nCOV transmission in real‐time. url: https://doi.org/10.1002/jmv.25701 doi: 10.1002/jmv.25701 id: cord-262000-k32cb9ym author: Li, Xue-Ting title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 date: 2020-09-07 words: 1911.0 sentences: 94.0 pages: flesch: 44.0 cache: ./cache/cord-262000-k32cb9ym.txt txt: ./txt/cord-262000-k32cb9ym.txt summary: title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 Angiotensin converting enzyme 2 (ACE2) has garnered widespread interest as the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19 pandemic, providing a critical link among COVID-19, inflammatory storm, ACE2 and cardiovascular disease 1,2 . Remarkably, recombinant human ACE2 (rhACE2), sACE2, ACE2-Fc, and ACE2-Ig are thought to be promising therapeutic approaches for COVID-19 patients with SARS-CoV-2 infection through competitive inhibiting the binding of viral Spike protein to mACE2 4 . Intriguingly, circulating Ang II level was obviously elevated in COVID-19 patients with lung injury (Table 1) 9 which further upregulates ADAM-17 activity by interacting with AT1 receptors, leading to more shedding of ACE2 and thereby accelerating renin-angiotensin-aldosterone system (RAAS)-mediated injury including severe cardiopulmonary damage (Fig. 1) (Table 1) 10 . abstract: nan url: https://doi.org/10.1016/j.apsb.2020.09.003 doi: 10.1016/j.apsb.2020.09.003 id: cord-355943-bezpprrk author: Li, Y. title: Urine Proteome of COVID-19 Patients date: 2020-05-06 words: 4439.0 sentences: 278.0 pages: flesch: 50.0 cache: ./cache/cord-355943-bezpprrk.txt txt: ./txt/cord-355943-bezpprrk.txt summary: In this study, we performed proteomic profiling of urine samples from 32 healthy control individuals and 6 COVID-19 positive patients (3 mild and 3 severe). We found that urine proteome samples from the mild and severe COVID-19 patients with comorbidities can be clearly differentiated from healthy proteome samples based on the clustering analysis. We identified and quantified 1380 and 1641 proteins in urine samples from COVID-19 and two recovery person in total, which was significantly lower than that of healthy controls ( Figure 2B and 2C , Tables S2 and S3 ). The molecular features used to distinguish the patient type (M and S) in our classifier ( Figure 5B and 5D, Tables S4-5) contain several potential biomarkers which were highly associated with the clinical characteristics of mild and severe COVID-19. . https://doi.org/10.1101/2020.05.02.20088666 doi: medRxiv preprint dysregulated proteins in the COVID-19 patients. abstract: The atypical pneumonia (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic and a serious threat to global public health. The COVID-19 patients with severe symptoms account for a majority of mortality of this disease. However, early detection and effective prediction of patients with mild to severe symptoms remains challenging. In this study, we performed proteomic profiling of urine samples from 32 healthy control individuals and 6 COVID-19 positive patients (3 mild and 3 severe). We found that urine proteome samples from the mild and severe COVID-19 patients with comorbidities can be clearly differentiated from healthy proteome samples based on the clustering analysis. Multiple pathways have been compromised after the COVID-19 infection, including the dysregulation of immune response, complement activation, platelet degranulation, lipoprotein metabolic process and response to hypoxia. We further validated our finding by directly comparing the same patients' urine proteome after recovery. This study demonstrates the COVID-19 pathophysiology related molecular alterations could be detected in the urine and the potential application of urinary proteome in auxiliary diagnosis, severity determination and therapy development of COVID-19. url: https://doi.org/10.1101/2020.05.02.20088666 doi: 10.1101/2020.05.02.20088666 id: cord-320717-wk4zxmz9 author: Li, Yang title: Lack of Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2, China date: 2020-06-17 words: 1073.0 sentences: 71.0 pages: flesch: 56.0 cache: ./cache/cord-320717-wk4zxmz9.txt txt: ./txt/cord-320717-wk4zxmz9.txt summary: We report a pregnant woman with confirmed SARS-CoV-2 infection who underwent cesarean section delivery of a SARS-CoV-2-negative infant in Zhejiang Province, China. On days 4 and 5 of hospitalization, the woman''s sputum tests were negative for SARS-CoV-2, and she remained afebrile. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. In conclusion, we report a pregnant woman with SARS-CoV-2 infection who delivered a healthy infant, suggesting that mother-to-child transmission is unlikely for this virus. Because our conclusions are limited by our sample size of 1, we cannot definitively state whether cesarean section is better than vaginal delivery for preventing transmission from a pregnant mother with SARS-CoV-2 infection. abstract: A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. The infant was negative for severe acute respiratory coronavirus 2. This case suggests that mother-to-child transmission is unlikely for this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32134381/ doi: 10.3201/eid2606.200287 id: cord-251986-ajlpb9li author: Li, Yan‐Chao title: The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date: 2020-03-11 words: 2250.0 sentences: 125.0 pages: flesch: 47.0 cache: ./cache/cord-251986-ajlpb9li.txt txt: ./txt/cord-251986-ajlpb9li.txt summary: This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients abstract: Following the severe acute respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV), another highly pathogenic coronavirus named SARS‐CoV‐2 (previously known as 2019‐nCoV) emerged in December 2019 in Wuhan, China, and rapidly spreads around the world. This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. The most characteristic symptom of patients with COVID‐19 is respiratory distress, and most of the patients admitted to the intensive care could not breathe spontaneously. Additionally, some patients with COVID‐19 also showed neurologic signs, such as headache, nausea, and vomiting. Increasing evidence shows that coronaviruses are not always confined to the respiratory tract and that they may also invade the central nervous system inducing neurological diseases. The infection of SARS‐CoV has been reported in the brains from both patients and experimental animals, where the brainstem was heavily infected. Furthermore, some coronaviruses have been demonstrated able to spread via a synapse‐connected route to the medullary cardiorespiratory center from the mechanoreceptors and chemoreceptors in the lung and lower respiratory airways. Considering the high similarity between SARS‐CoV and SARS‐CoV2, it remains to make clear whether the potential invasion of SARS‐CoV2 is partially responsible for the acute respiratory failure of patients with COVID‐19. Awareness of this may have a guiding significance for the prevention and treatment of the SARS‐CoV‐2‐induced respiratory failure. url: https://doi.org/10.1002/jmv.25728 doi: 10.1002/jmv.25728 id: cord-305640-tgowzrqo author: Li, Yong-Hua title: Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: Comparison with results of other viral markers date: 2005-07-15 words: 3688.0 sentences: 174.0 pages: flesch: 59.0 cache: ./cache/cord-305640-tgowzrqo.txt txt: ./txt/cord-305640-tgowzrqo.txt summary: A capture enzyme-enhanced chemiluminescence immunoassay (ECLIA) based on three specific monoclonal antibodies to detect the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in the serial serum samples from SARS patients was developed. The N protein is an extensively phosphorylated, highly basic protein, which interacts with viral RNA and makes up the viral core and nucleocapsid (Lai, 2003 the diagnosis of SARS depends basically upon detecting SARS-CoV RNA by RT-PCR and/or testing specific antibodies directed against SARS-CoV by assays based on cultured virus or recombinant viral antigens. In the present study, a capture ECLIA was developed based on three monoclonal antibodies directed against the N protein of SARS-CoV, and the N protein in the longitudinal serum samples from the SARS patients were detected with this method. The detection of the N protein of SARS-CoV in serum samples by ECLIA appears to be superior to the detection of the viral RNA by RT-PCR in rapid diagnosis of SARS patients. abstract: A capture enzyme-enhanced chemiluminescence immunoassay (ECLIA) based on three specific monoclonal antibodies to detect the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in the serial serum samples from SARS patients was developed. The anti-SARS-CoV IgG and the viral RNA were also detected in the sera by ELISA and RT-PCR, respectively. During the first 10 days after onset, anti-SARS-CoV IgG, SARS-CoV RNA and the N protein were detected in 21.4, 42.9, and 90% of the patients’ sera, respectively. The detection rate of the N protein during days 11–15 of the disease was still significantly higher than those of anti-SARS-CoV IgG and SARS-CoV RNA. The data demonstrated that detection of the N protein with the capture ECLIA appears to be more useful than detection of other viral makers for rapid diagnosis of SARS in patients. url: https://www.ncbi.nlm.nih.gov/pubmed/16024098/ doi: 10.1016/j.jviromet.2005.06.001 id: cord-336394-1xf2sxtv author: Li, Yu title: The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date: 2020-05-13 words: 1175.0 sentences: 76.0 pages: flesch: 57.0 cache: ./cache/cord-336394-1xf2sxtv.txt txt: ./txt/cord-336394-1xf2sxtv.txt summary: Here, bioinformatics approaches combining human-virus protein interaction prediction and protein docking based on crystal structures have revealed the high affinity between human dipeptidyl peptidase 4 (DPP4) and the spike (S) receptor-binding domain of SARS-CoV-2. The atomic interaction details of the 145 binding interface showed that almost all of the contacting residues of DPP4 with 146 SARS-CoV-2-S RBD were consistent with those for binding with MERS-CoV-S 147 RBD (Table S1 ) (Song et al., 2014) . In addition, the models evaluated the 228 binding potential, interface residues and structures that were consistent with those 229 Comparison of the key residues between human and pangolin DPP4 protein 471 Identification of residues on human receptor DPP4 critical for MERS-CoV binding 401 and entry Structure of MERS-CoV spike receptor-binding domain 417 complexed with human receptor DPP4 SARS-CoV-2 spike receptor-binding domain has a potentially high affinity with DPP4 abstract: SUMMARY The ongoing outbreak of the novel coronavirus pneumonia COVID-19 has caused great number of cases and deaths, but our understanding about the pathogen SARS-CoV-2 remains largely unclear. The attachment of the virus with the cell-surface receptor and a co-factor is the first step for the infection. Here, bioinformatics approaches combining human-virus protein interaction prediction and protein docking based on crystal structures have revealed the high affinity between human dipeptidyl peptidase 4 (DPP4) and the spike (S) receptor-binding domain of SARS-CoV-2. Intriguingly, the crucial binding residues of DPP4 are identical to those as bound to the MERS-CoV-S. Moreover, E484 insertion and adjacent substitutions should be most essential for this DPP4-binding ability acquirement of SARS-CoV-2-S compared with SARS-CoV-S. This potential utilization of DPP4 as a binding target for SARS-CoV-2 may offer novel insight into the viral pathogenesis, and help the surveillance and therapeutics strategy for meeting the challenge of COVID-19. url: https://doi.org/10.1016/j.isci.2020.101160 doi: 10.1016/j.isci.2020.101160 id: cord-348752-bbghqy1a author: Li, Yuguo title: Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant date: 2020-04-22 words: 4052.0 sentences: 252.0 pages: flesch: 60.0 cache: ./cache/cord-348752-bbghqy1a.txt txt: ./txt/cord-348752-bbghqy1a.txt summary: We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions. Methods: We collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Results: Three families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Year''s Eve (January 24, 2020) at three neighboring tables. healthy) of each person at non-A tables as the dependent variable and applied a binary logistic regression model to investigate the association between the measured concentrations of trace gas and infection probability. abstract: Background: The role of aerosols in the transmission of SARS-CoV-2 remains debated. We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions. Methods: We collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Computer simulations were performed to simulate the spread of fine exhaled droplets. We compared the in-room location of subsequently infected cases and spread of the simulated virus-laden aerosol tracer. The ventilation rate was measured using the tracer decay method. Results: Three families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Year's Eve (January 24, 2020) at three neighboring tables. Subsequently, three members of family B and two members of family C became infected with SARS-CoV-2, whereas none of the waiters or 68 patrons at the remaining 15 tables became infected. During this occasion, the ventilation rate was 0.75-1.04 L/s per person. No close contact or fomite contact was observed, aside from back-to-back sitting by some patrons. Our results show that the infection distribution is consistent with a spread pattern representative of exhaled virus-laden aerosols. Conclusions: Aerosol transmission of SARS-CoV-2 due to poor ventilation may explain the community spread of COVID-19. url: https://doi.org/10.1101/2020.04.16.20067728 doi: 10.1101/2020.04.16.20067728 id: cord-253438-k8iqv1jb author: Li, Yujun title: SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig date: 2020-10-27 words: 5339.0 sentences: 327.0 pages: flesch: 60.0 cache: ./cache/cord-253438-k8iqv1jb.txt txt: ./txt/cord-253438-k8iqv1jb.txt summary: We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. The RBD of Bat-CoV RaTG13 then showed a binding profile significantly different and narrower than the other three RBDs. Note that human ACE2 and ACE2 orthologs of some domestic animals, including camels, cattle, horses, goats, sheep, cats, and rabbits, support efficient binding to all the four tested RBDs, suggesting that these ACE2 orthologs might be generally functional for supporting cell entry of the four tested viruses. abstract: The ongoing coronavirus disease 2019 (COVID-19) pandemic has caused >20 million infections and >750,000 deaths. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, has been found closely related to the bat coronavirus strain RaTG13 (Bat-CoV RaTG13) and a recently identified pangolin coronavirus (Pangolin-CoV-2020). Here, we first investigated the ability of SARS-CoV-2 and three related coronaviruses to utilize animal orthologs of angiotensin-converting enzyme 2 (ACE2) for cell entry. We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In addition, the pangolin and bat coronaviruses, Pangolin-CoV-2020 and Bat-CoV RaTG13, were also found able to utilize human ACE2 and a number of animal-ACE2 orthologs for cell entry, indicating risks of spillover of these viruses into humans in the future. We then developed potently anticoronavirus ACE2-Ig proteins that are broadly effective against the four distinct coronaviruses. In particular, through truncating ACE2 at its residue 740 but not 615, introducing a D30E mutation, and adopting an antibody-like tetrameric-ACE2 configuration, we generated an ACE2-Ig variant that neutralizes SARS-CoV-2 at picomolar range. These data demonstrate that the improved ACE2-Ig variants developed in this study could potentially be developed to protect from SARS-CoV-2 and some other SARS-like viruses that might spillover into humans in the future. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the currently uncontrolled coronavirus disease 2019 (COVID-19) pandemic. It is important to study the host range of SARS-CoV-2, because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. We also developed recombinant ACE2-Ig proteins that are able to potently block these viral infections, providing a promising approach to developing antiviral proteins broadly effective against these distinct coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32847856/ doi: 10.1128/jvi.01283-20 id: cord-297989-4grwa4ab author: Li, Yunjin title: Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2 date: 2020-07-08 words: 1616.0 sentences: 89.0 pages: flesch: 46.0 cache: ./cache/cord-297989-4grwa4ab.txt txt: ./txt/cord-297989-4grwa4ab.txt summary: Since the expression profile of ACE2, a crucial cell entry receptor for SARS‐CoV‐2, could indicate the susceptibility to SARS‐CoV‐2 infection, here we systematically dissected ACE2 expression using large‐scale multi‐omics data from 30 organs/tissues, 33 cancer types and some common chronic diseases involving >28 000 samples. Furthermore, the patients with common chronic diseases regarding angiocardiopathy, type 2 diabetes, liver, pneumonia and hypertension were also with higher ACE2 expression compared to related controls, which were validated using independent data sets. Collectively, our study may reveal a novel important mechanism that the patients with certain cancers and chronic diseases may express higher ACE2 expression compared to the individuals without diseases, which could lead to their higher susceptibility to multi‐organ injury of SARS‐CoV‐2 infection. Here, we systematically analysed ACE2 expression using largescale multi-omics data from a variety of organs/tissues and cancer types, as well as the common chronic diseases of heart, liver, diabetes, pneumonia and hypertension involving a total of >28 000 samples. abstract: Recent retrospective studies of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) disease (COVID‐19) revealed that the patients with common comorbidities of cancers and chronic diseases face significantly poorer clinical outcomes than those without. Since the expression profile of ACE2, a crucial cell entry receptor for SARS‐CoV‐2, could indicate the susceptibility to SARS‐CoV‐2 infection, here we systematically dissected ACE2 expression using large‐scale multi‐omics data from 30 organs/tissues, 33 cancer types and some common chronic diseases involving >28 000 samples. It was found that sex and age could be correlated with the susceptibility of SARS‐CoV‐2 infection for certain tissues. Strikingly, ACE2 was up‐regulated in cervical squamous cell carcinoma and endocervical adenocarcinoma, colon adenocarcinoma, oesophageal carcinoma, kidney renal papillary cell carcinoma, lung adenocarcinoma and uterine corpus endometrial carcinoma compared to controls. Furthermore, the patients with common chronic diseases regarding angiocardiopathy, type 2 diabetes, liver, pneumonia and hypertension were also with higher ACE2 expression compared to related controls, which were validated using independent data sets. Collectively, our study may reveal a novel important mechanism that the patients with certain cancers and chronic diseases may express higher ACE2 expression compared to the individuals without diseases, which could lead to their higher susceptibility to multi‐organ injury of SARS‐CoV‐2 infection. url: https://doi.org/10.1111/jcmm.15607 doi: 10.1111/jcmm.15607 id: cord-257135-xt4w0baw author: Li, Zhengqian title: The brain, another potential target organ, needs early protection from SARS-CoV-2 neuroinvasion date: 2020-03-31 words: 1112.0 sentences: 61.0 pages: flesch: 44.0 cache: ./cache/cord-257135-xt4w0baw.txt txt: ./txt/cord-257135-xt4w0baw.txt summary: Based on the existing evidence and lessons from SARS outbreak in 2003, our attention should not be confined to the general organs whose dysfunctions were relatively easy to be observed or examined such as lung, kidney, and liver; at the same time, the brain should not be neglected due to the potential neuroinvasion of SARS-CoV-2, which prompts us to keep an alert on the onset of neurological symptoms, early diagnostics, and neuroprotection. So far, no direct evidence of entry of SARS-CoV-2 into the CNS has been reported in any international peer-reviewed journal, although some researchers have proposed that the neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients abstract: nan url: https://doi.org/10.1007/s11427-020-1690-y doi: 10.1007/s11427-020-1690-y id: cord-351031-e8suoeim author: Liang En Ian, Wee title: Containing COVID-19 outside the isolation ward: the impact of an infection control bundle on environmental contamination and transmission in a cohorted general ward date: 2020-06-26 words: 4123.0 sentences: 206.0 pages: flesch: 45.0 cache: ./cache/cord-351031-e8suoeim.txt txt: ./txt/cord-351031-e8suoeim.txt summary: In these general wards, termed as respiratory surveillance wards (RSWs), an infection control bundle was implemented comprising infrastructural enhancements, improved personal-protective-equipment (PPE), and social distancing between patients, in order to mitigate the risk of a potential COVID-19 case initially admitted outside of an AIIR. The main finding of our study was that an infection control bundle comprising infrastructural enhancements, improved PPE and social distancing mitigated the risk of environmental contamination and transmission in a cohorted general ward setting. In conclusion, over a 3-month period, our institution implemented a bundle of interventions to reduce risk of intra-hospital transmission of COVID-19 in a multi-bedded cohorted general ward setting, through the implementation of an infection control bundle comprising infrastructural enhancements, improved PPE, and social distancing between patients. abstract: BACKGROUND: During an ongoing outbreak of COVID-19, unsuspected cases may be housed outside of dedicated isolation wards. AIM: At a Singaporean tertiary hospital, individuals with clinical syndromes compatible with COVID-19 but no epidemiologic risk were placed in cohorted general wards for COVID-19 testing. To mitigate risk, an infection control bundle was implemented comprising infrastructural enhancements, improved personal-protective-equipment (PPE), and social distancing. We assessed the impact on environmental contamination and transmission. METHOD: Upon detection of a case of COVID-19 in the dedicated general ward, patients and healthcare workers (HCWs) contacts were identified. All patient and staff-close contacts were placed on 14-day phone surveillance and followed-up for 28 days; symptomatic contacts were tested. Environmental samples were also obtained. FINDINGS: Over a 3-month period, 28 unsuspected cases of COVID-19 were contained in the dedicated general ward. In 5 of the 28 cases, sampling of the patient's environment yielded SARS-CoV-2; index cases who required supplemental oxygen had higher odds of environmental contamination (p=0.01). A total of 253 staff close-contacts and 45 patient close-contacts were identified; only 3 HCWs (1.2%, 3/253) required quarantine. On 28-day follow-up, no patient-to-HCW transmission was documented; only one symptomatic patient close-contact tested positive. CONCLUSION: Our institution successfully implemented an intervention bundle to mitigate COVID-19 transmission in a multi-bedded cohorted general ward setting. url: https://api.elsevier.com/content/article/pii/S0196655320305691 doi: 10.1016/j.ajic.2020.06.188 id: cord-312664-tgpaidhp author: Liang, Julia title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex date: 2020-05-28 words: 3050.0 sentences: 189.0 pages: flesch: 52.0 cache: ./cache/cord-312664-tgpaidhp.txt txt: ./txt/cord-312664-tgpaidhp.txt summary: title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. Further, molecular dynamics simulations highlight the stability of the interaction of the α-ketoamide 13b ligand with the SARS-CoV-2 M(pro) (ΔG = -25.2 and -22.3 kcal/mol for protomers A and B). Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. In the absence of a vaccine, or an approved effective therapeutic, there is an intense interest in repositioning available drugs or designing small molecule antivirals. In this context, in silico modelling has proven to be an invaluable tool. An important target is the SARS-CoV-2 main protease (M(pro)), involved in processing translated viral proteins. Peptidomimetic α-ketoamides represent prototypical inhibitors of M(pro). A recent attempt at designing a compound with enhanced pharmacokinetic properties has resulted in the synthesis and evaluation of the α-ketoamide 13b analogue. Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M(pro). We included the widely used antibiotic, amoxicillin, for comparison. Our findings indicate that α-ketoamide 13b binds more tightly (predicted GlideScore = -8.7 and -9.2 kcal/mol for protomers A and B, respectively), to the protease active site compared to amoxicillin (-5.0 and -4.8 kcal/mol). Further, molecular dynamics simulations highlight the stability of the interaction of the α-ketoamide 13b ligand with the SARS-CoV-2 M(pro) (ΔG = -25.2 and -22.3 kcal/mol for protomers A and B). In contrast, amoxicillin interacts unfavourably with the protease (ΔG = +32.8 kcal/mol for protomer A), with unbinding events observed in several independent simulations. Overall, our findings are consistent with those previously observed, and highlight the need to further explore the α-ketoamides as potential antivirals for this ongoing COVID-19 pandemic. url: https://www.sciencedirect.com/science/article/pii/S1476927120304205?v=s5 doi: 10.1016/j.compbiolchem.2020.107292 id: cord-276394-s9y11oep author: Liang, W. title: Hindsight: A re-analysis of the severe acute respiratory syndrome outbreak in Beijing date: 2007-10-31 words: 2970.0 sentences: 140.0 pages: flesch: 54.0 cache: ./cache/cord-276394-s9y11oep.txt txt: ./txt/cord-276394-s9y11oep.txt summary: Summary Objective To review the severe acute respiratory syndrome (SARS) epidemic in Beijing using basic epidemiological principles omitted from the original analysis. Previously excluded cases were included for plotting on an epidemic curve, and basic spot mapping for distribution of cases was used from attack rates recalculated for age, gender, occupation, residential location, date of onset of illness and demographics. If a spot map of incidence density rates was used during the early phase of the outbreak, the inner city might have been identified as a major risk factor requiring rapid quarantining. 8 Re-analysis included an epidemic curve for ''probable'' SARS cases only and calculations of the Beijing population-based rate, stratified by age and sex, using the Fifth General Census of China (version 2000). The import phase of the Beijing epidemic occurred rapidly, between 1 and 10 March, with 14 cases admitted with an acute pneumonia of unknown cause without history taken for exposure to a case of respiratory illness or environmental contact. abstract: Summary Objective To review the severe acute respiratory syndrome (SARS) epidemic in Beijing using basic epidemiological principles omitted from the original analysis. Study design Analysis of Prospective surveillance data for Beijing collected during the outbreak. Methods Surveillance data were reclassified according to World Health Organization criteria. Cases previously excluded without date of onset of illness were included in the epidemic curve from estimates using the average time between date of onset and date of hospitalization for cases with both dates. Cases who failed to give a contact history were now included; 7% ( n = 5 ) of cases during the import phase and 61% ( n = 365 ) during the peak phase. Previously excluded cases were included for plotting on an epidemic curve, and basic spot mapping for distribution of cases was used from attack rates recalculated for age, gender, occupation, residential location, date of onset of illness and demographics. Results The spot map effectively illustrated clusters by residency, with the inner-city sustaining the highest attack rate (33.42 per 100,000), followed by an easterly distribution 5–30km away (21.62 per 10,000), and lowest in districts 60–160km away (9.21 per 100,000). The new epidemic curve shows the outbreak commencing 10 days earlier than initially reported, with a three-fold greater increase in cases during the escalation phase than previously estimated. Conclusion In hindsight, the investigation of the Beijing SARS would have benefited from the use of spot maping as an essential outbreak tool for early identification of specific geographical area(s) for quarantining. If a spot map of incidence density rates was used during the early phase of the outbreak, the inner city might have been identified as a major risk factor requiring rapid quarantining. Contact history became uncommon as the outbreak progressed, suggesting that hospitals were over-burdened or pathogenesis and environment risk factors changed, strengthening the usefulness of early spot mapping and the need to modify risk factors included as contact history as the epidemic progresses. url: https://api.elsevier.com/content/article/pii/S0033350607000819 doi: 10.1016/j.puhe.2007.02.023 id: cord-332348-yi85sfks author: Liang, Yujie title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 words: 2748.0 sentences: 172.0 pages: flesch: 56.0 cache: ./cache/cord-332348-yi85sfks.txt txt: ./txt/cord-332348-yi85sfks.txt summary: Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. abstract: Abstract Objectives To detailly described the neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, in patients with COVID-19. Methods Clinical characteristics and oropharyngeal swabs were obtained from 86 patients with COVID-19 hospitalized in Guangzhou Eighth People’s Hospital. Chronological analysis method was used to detailly clarify the neurosensory dysfunction. The cycle threshold (Ct) values were used to approximately indicate viral load. Results Forth-four (51.2%) patients had neurosensory dysfunction: hyposmia (34, 39.5%), hypogeusia (33, 38.4%), and tinnitus (3, 3.5%). Neurosensory dysfunction was significantly more common in patients under 40 years old (p = 0.001) or women (p = 0.006). Hyposmia and hypogeusia coexisted in 23 (26.7%) patients. The interval between onset of hyposmia and hypogeusia was 0.7 ± 1.46 days. The interval from onset of hyposmia and hypogeusia to typical symptoms was 0.22 ± 4.57 and 0.75 ± 6.77 days; the interval from onset of hyposmia and hypogeusia to admission was 6.06 ± 6.68 and 5.76 ± 7.68 days; and the duration of hyposmia and hypogeusia was 9.09 ± 5.74 and 7.12 ± 4.66 days, respectively. The viral load was high since symptoms onset, peaked within the first week, and then gradually declined. Conclusions The neurosensory dysfunction tends to occur in the early stage of COVID-19, and it could be used as a marker for early diagnosis of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305191?v=s5 doi: 10.1016/j.ijid.2020.06.086 id: cord-340746-icuzy3vp author: Liang, Yunfei title: Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date: 2005-08-01 words: 8408.0 sentences: 374.0 pages: flesch: 47.0 cache: ./cache/cord-340746-icuzy3vp.txt txt: ./txt/cord-340746-icuzy3vp.txt summary: We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display. The full-length SARS-CoV N protein (amino acids 1-422) was expressed on the yeast cell surface, as indicated by reactivity of the Xpress epitope tag with the anti-Xpress antibody (Fig. 2) . We used heat denaturation of the fusion proteins tethered to the EBY100 yeast cell surface to categorize the specific linear and conformational SARS-CoV N protein mAb epitopes (35, 36 ) . Our subsequent determination of the antigenic structures of the N protein responsible for antibodies in polyclonal antisera from immunized mice and sera from convalescent SARS patients demonstrated the immunogenic specificity of 3 conformational (amino acids 1-69, 68 -213, and 337-422) and 3 linear (amino acids 1-69, 121-213, and 337-422) epitopes (Fig. 1C) . abstract: Background: The epidemic outbreak of severe acute respiratory syndrome (SARS) posed a worldwide threat to public health and economic stability. Although the pandemic has been contained, concerns over its recurrence remain. It is essential to identify specific diagnostic agents and antiviral vaccine candidates to fight this highly contagious disease. Methods: We generated 14 monoclonal antibodies (mAbs) specific to the SARS coronavirus (SARS-CoV) nucleocapsid (N) protein and used these to thoroughly map the N protein antigenic determinants. We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display. Results: We identified 5 conformational and 3 linear epitopes within the entire N protein; 3 conformational and 3 linear epitopes were immunodominant. The antibody responses to the N protein fragments in mammalian sera revealed that 3 regions of the N protein are strong antigenic domains. We expanded the specificity of the N protein epitope and identified 4 novel conformational epitopes (amino acids 1–69, 68–213, 212–341, and 337–422). Conclusion: The antigenic structures identified for the SARS-CoV N protein, the epitope-specific mAbs, and the serum antibody profile in SARS patients have potential use in the clinical diagnosis and understanding of the protective immunity to SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/15976093/ doi: 10.1373/clinchem.2005.051045 id: cord-296227-dm1wkpnv author: Liao, L. title: Can N95 respirators be reused after disinfection? And for how many times? date: 2020-04-07 words: 5343.0 sentences: 272.0 pages: flesch: 56.0 cache: ./cache/cord-296227-dm1wkpnv.txt txt: ./txt/cord-296227-dm1wkpnv.txt summary: We found that heating (<100 {degrees}C) under various humidities (up to 100% RH at 75 {degrees}C) and ultraviolet (UV) irradiation were the most promising candidates for mask reuse in the modern hospital infrastructure (up to 20 cycles), when tested on a fabric with particle filtration efficiency [≥]95%. For dangerous airborne particulates, including viral aerosols during the current COVID-19 pandemic, the United States Centers for Disease Control and Prevention (CDC) recommends the usage of N95 filtering facepiece respirators (FFR) as personal protective equipment for healthcare professionals [18] [19] [20] . We applied these treatments (see methods for details) to a meltblown fabric (20 g/m 2 ) that has an initial efficiency of ≥95%, which may be integrated into N95 FFRs. We evaluated the filtration efficiency and pressure drop of these treated fabrics via industry standard equipment, Automated Filter Tester 8130A (TSI), with a flow rate of 32 L/min. abstract: The Coronavirus Disease 2019 (COVID-19) pandemic has led to a major shortage of N95 respirators, which protect healthcare professionals and the public who may come into contact with the virus. It is necessary to determine the conditions that would allow the safe reuse respirators and personal protection in this crisis. We found that heating (<100 {degrees}C) under various humidities (up to 100% RH at 75 {degrees}C) and ultraviolet (UV) irradiation were the most promising candidates for mask reuse in the modern hospital infrastructure (up to 20 cycles), when tested on a fabric with particle filtration efficiency [≥]95%. Treatments involving certain liquids and vapors may require caution, as steam, alcohol, and bleach all led to degradation in filtration efficiency, leaving the user vulnerable to viral aerosols. url: https://doi.org/10.1101/2020.04.01.20050443 doi: 10.1101/2020.04.01.20050443 id: cord-335446-8l1vfsbc author: Liao, M. title: The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing date: 2020-02-26 words: 4710.0 sentences: 311.0 pages: flesch: 55.0 cache: ./cache/cord-335446-8l1vfsbc.txt txt: ./txt/cord-335446-8l1vfsbc.txt summary: Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. To characterize the immune microenvironment of the SARS-CoV-2-infected lung, we performed scRNA-seq analysis of single cells in the lung BALF (37, 820 cells) using the 10X Genomics platform, from 3 of recovered mild cases and 3 of severe cases ( Figure 1A , Table 1 ). Our data indicated that the monocytes are recruited from circulation (FCN1 + ) to the lung to fuel the inflammation during severe diseases, and some monocytes may further go through the differentiation process into the SPP1 + populations and eventually the FABP4 + AMs. robust and early T cell response played crucial roles in viral clearance during acute respiratory infections [14] . abstract: The novel coronavirus SARS-CoV-2, etiological agent of recently named Coronavirus infected disease (COVID-19) by WHO, has caused more than 2, 000 deaths worldwide since its emergency in Wuhan City, Hubei province, China, in December, 2019. The symptoms of COVID-19 varied from modest, mild to acute respiratory distress syndrome (ARDS), and the latter of which is generally associated with deregulated immune cytokine production; however, we currently know little as to the interplay between the extent of clinical symptoms and the compositions of lung immune microenvironment. Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. Our data shows that monocyte-derived FCN1+ macrophages, whereas notFABP4+ alveolar macrophages that represent a predominant macrophage subset in BALF from patients with mild diseases, overwhelm in the severely damaged lungs from patients with ARDS. These cells are highly inflammatory and enormous chemokine producers implicated in cytokine storm. Furthermore, the formation of tissue resident, highly expanded clonal CD8+ T cells in the lung microenvironment of mild symptom patients suggests a robust adaptive immune response connected to a better control of COVID-19. This study first reported the cellular atlas of lung bronchoalveolar immune microenvironment in COVID-19 patients at the single-cell resolution, and unveiled the potential immune mechanisms underlying disease progression and protection in COVID-19. url: http://medrxiv.org/cgi/content/short/2020.02.23.20026690v1?rss=1 doi: 10.1101/2020.02.23.20026690 id: cord-271930-9a18h2tr author: Licari, Amelia title: Allergy and asthma in children and adolescents during the COVID outbreak: What we know and how we could prevent allergy and asthma flares date: 2020-05-28 words: 1177.0 sentences: 83.0 pages: flesch: 47.0 cache: ./cache/cord-271930-9a18h2tr.txt txt: ./txt/cord-271930-9a18h2tr.txt summary: The Center for Disease Control and Prevention (CDC) initially proposed that patients with chronic lung diseases, including moderate-severe asthma, and allergy may have a higher risk of developing severe COVID-19 than otherwise healthy people (https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/asthma.html). Allergic children had a significantly higher (P < .0001) eosinophil count than COVID-19 patients. However, it has been recently commented that chronic respiratory diseases, including COPD and asthma, seem to be underrepresented in the comorbidities of COVID-19 patients. On the other hand, children and adolescents with allergy and asthma should be adequately managed during this COVID-19 pandemic, also considering the restrictive rules released by governmental authorities that impose a strict limitation on movements. 10 In summary, the rapid spread of SARS-CoV-2 infection and the lack of specific antiviral therapies and vaccines currently require additional medical efforts to prevent COVID-19 and mostly protect patients with chronic diseases. Association of respiratory allergy, asthma, and expression of the SARS-CoV-2 receptor, ACE2 Do chronic respiratory diseases or their treatment affect the risk of SARS-CoV-2 infection? abstract: Coronavirus disease 2019 (COVID-19) pandemic is affecting people at any age with a more severe course in patients with chronic diseases or comorbidities, males and elderly patients. The Center for Disease Control and Prevention (CDC) initially proposed that patients with chronic lung diseases, including moderate-severe asthma, and allergy may have a higher risk of developing severe COVID-19 than otherwise healthy people (https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/asthma.html). url: https://www.ncbi.nlm.nih.gov/pubmed/32418233/ doi: 10.1111/all.14369 id: cord-298866-dzatps7b author: Licskai, Christopher title: Key highlights from the Canadian Thoracic Society’s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic date: 2020-05-28 words: 1545.0 sentences: 94.0 pages: flesch: 48.0 cache: ./cache/cord-298866-dzatps7b.txt txt: ./txt/cord-298866-dzatps7b.txt summary: title: Key highlights from the Canadian Thoracic Society''s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic In general, asthma maintenance and exacerbation management should continue according to national and international guidelines during the COVID-19 pandemic, however treatment decisions should be individualized based on patient characteristics. 6, 7, 8 Are patients with asthma at risk of having an exacerbation triggered by SARS-CoV-2 (COVID 19)? The Centers for Disease Control identify people with asthma as a group that may be at higher risk for severe illness from COVID-19. No. Asthma patients should restart or continue their prescribed inhaled corticosteroid or inhaled corticosteroid steroid plus long-acting beta 2 -agonist maintenance therapy to improve disease control and to reduce the severity of exacerbations, including exacerbations that may be caused by SARS-CoV-2. Yes. There is no evidence that inhaled corticosteroids increase the risk of acquiring COVID-19 or that inhaled corticosteroids increase the severity of infection. abstract: nan url: https://api.elsevier.com/content/article/pii/S0012369220316160 doi: 10.1016/j.chest.2020.05.551 id: cord-318909-h5b7mncf author: Liguori, Claudio title: Subjective neurological symptoms frequently occur in patients with SARS-CoV2 infection date: 2020-05-19 words: 3476.0 sentences: 203.0 pages: flesch: 45.0 cache: ./cache/cord-318909-h5b7mncf.txt txt: ./txt/cord-318909-h5b7mncf.txt summary: 7 A large retrospective analysis carried out in China on 214 patients affected by SARS-CoV2 infection confirmed that hospitalized patients complained of subjective neurological symptoms (sNS) in a 36 .4% of cases, including headache, disturbed consciousness, and paresthesia as the most frequent. This observational study, carried out in 103 patients affected by SARS-CoV2 infection, documented the high prevalence of sNS during the course of the disease, even immediately after admission to the Hospital. Although the involvement of nervous system during SARS-CoV2 infection has been extensively proposed, [10] [11] [12] few studies focused the investigation on neurological symptoms in patients with 7 The largest study examining the neurological manifestations of hospitalized patients with COVID-19 was a retrospective analysis achieved by reviewing patients'' clinical charts. 15 In the present study, we performed a prospective observation in patients with non-severe respiratory form of SARS-CoV2 by using an anamnestic interview designed to better determinate the occurrence and type of sNS over the course of the disease. abstract: OBJECTIVE: Coronavirus disease 2019 (COVID-19) represents a novel pneumonia leading to severe acute respiratory syndrome (SARS). Recent studies documented that SARS-Coronavirus2 (SARS-CoV2), responsible for COVID-19, can affect the nervous system. The aim of the present observational study was to prospectively assess subjective neurological symptoms (sNS) in patients with SARS-CoV2 infection. METHODS: We included patients hospitalized at the University Hospital of Rome Tor Vergata, medical center dedicated to the treatment of patients with COVID-19 diagnosis, who underwent an anamnestic interview about sNS consisting of 13 items, each related to a specific symptom, requiring a dichotomized answer. RESULTS: We included 103 patients with SARS-CoV2 infection. Ninety-four patients (91.3%) reported at least one sNS. Sleep impairment was the most frequent symptom, followed by dysgeusia, headache, hyposmia, and depression. Women more frequently complained hyposmia, dysgeusia, dizziness, numbeness/paresthesias, daytime sleepiness, and muscle ache. Moreover, muscle ache and daytime sleepiness were more frequent in the first 2 days after admission. Conversely, sleep impairment was more frequent in patients with more than 7 days of hospitalization. In these patients we also documented higher white blood cells and lower C-reactive protein levels. These laboratory findings correlated with the occurrence of hyposmia, dysgeusia, headache, daytime sleepiness, and depression. CONCLUSIONS: Patients with SARS-CoV2 infection frequently present with sNS. These symptoms were present from the early phases of the disease. The possibly intrinsic neurotropic properties of SARS-CoV2 may justify the very high frequency of sNS. Further studies targeted at investigating the consequences of SARS-CoV2 infection on the CNS should be planned. url: https://www.sciencedirect.com/science/article/pii/S088915912030876X?v=s5 doi: 10.1016/j.bbi.2020.05.037 id: cord-334012-b2akycst author: Liguori, Claudio title: Sleep and wake impairment in patients with SARS-CoV2 infection date: 2020-07-17 words: 474.0 sentences: 29.0 pages: flesch: 43.0 cache: ./cache/cord-334012-b2akycst.txt txt: ./txt/cord-334012-b2akycst.txt summary: Coronavirus Disease 2019 (COVID-19) is unquestionably a worldwide life-threatening condition causing severe acute respiratory distress; 1 however, pauci-symptomatic or non-severe forms of pneumonia currently represent the more frequent manifestations of the infection. [3] [4] Our NeuroCOVID-19 group performed a prospective observational study focused on the occurrence of subjective neurological symptoms in hospitalized patients with a non-severe respiratory form of COVID-19. 4 Here, we present data deriving from a secondary analysis of the previous study with the aims to emphasize and deepen the characteristics of sleep and wake impairment in patients with SARS-CoV2 infection and their relationships with the other neurological symptoms, white blood cells (WBC), C-reactive protein (CRP), and days of hospitalization. Considering patients with sleep impairment, they had higher CRP serum levels, more frequent dysgeusia, headache, and dizziness, and more concomitant neurological symptoms than patients without sleep alteration ( Table 1) . Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection abstract: nan url: https://api.elsevier.com/content/article/pii/S138994572030321X doi: 10.1016/j.sleep.2020.06.036 id: cord-336366-2y68n8s0 author: Liguori, Claudio title: Depressive and anxiety symptoms in patients with SARS-CoV2 infection date: 2020-09-14 words: 871.0 sentences: 52.0 pages: flesch: 40.0 cache: ./cache/cord-336366-2y68n8s0.txt txt: ./txt/cord-336366-2y68n8s0.txt summary: 5 Based on the study protocol, all patients underwent an anamnestic interview requiring a dichotomized answer (YES/NO) about 13 neurological symptoms (hyposmia, dysgeusia, auditory dysfunction, headache, confusion, dizziness, numbness/paresthesia, fatigue, daytime sleepiness, sleep impairment, muscle ache, depression, and anxiety). In this secondary analysis derived from this previous investigation, 5 we aimed at primarily focusing on the occurrence of depressive and anxiety symptoms in patients with COVID-19, also considering the possible correlation of these symptoms with the other neurological symptoms investigated and the demographic, clinical, and laboratory data achieved. 6 Depression, anxiety, and post-traumatic stress symptoms were more frequent in patients with COVID-19 compared to volunteers not affected by SARS-CoV2 infection. This result can be explained by a higher psychological burden in patients with several neurological symptoms, or by a more severe nervous system involvement also producing depression and anxiety. Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32987349/ doi: 10.1016/j.jad.2020.09.042 id: cord-281536-8y7yxcp4 author: Lim, Hocheol title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method date: 2020-10-08 words: 3527.0 sentences: 178.0 pages: flesch: 55.0 cache: ./cache/cord-281536-8y7yxcp4.txt txt: ./txt/cord-281536-8y7yxcp4.txt summary: title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method In this work, to find common hot spot amino acids on the interfaces between the RBD domain and hACE2 of the three complexes, RBD-SARS-CoV-2/hACE2 (twelve experimental structural data), RBD-SARS-CoV-1/ hACE2 (four experimental structural data), and RBD-HCoV-NL63/hACE2 (one experimental structural data), we performed FMO-DFTB3/D/PCM calculations. Consequently, we summarized the FMO-DFTB3/D/PCM/3D-SPIEs results as interaction maps and found the hot spot regions in RBD-SARS-CoV-2 and hACE2 at a QM level. In order to narrow down the hot spot regions between hACE2 and RBD-SARS-CoV-1, we performed FMO calculations on four RBD-SARS-CoV-1/antibody complexes (Supplementary Table S14-S19). In order to find common hot spot amino acids in RBD-SARS-CoV-1 against hACE2 and SARS-CoV-1 antibodies, we illustrated the FMO results with a 3D-SPIEs-based map. abstract: The prevalence of a novel β-coronavirus (SARS-CoV-2) was declared as a public health emergency of international concern on 30 January 2020 and a global pandemic on 11 March 2020 by WHO. The spike glycoprotein of SARS-CoV-2 is regarded as a key target for the development of vaccines and therapeutic antibodies. In order to develop anti-viral therapeutics for SARS-CoV-2, it is crucial to find amino acid pairs that strongly attract each other at the interface of the spike glycoprotein and the human angiotensin-converting enzyme 2 (hACE2) complex. In order to find hot spot residues, the strongly attracting amino acid pairs at the protein–protein interaction (PPI) interface, we introduce a reliable inter-residue interaction energy calculation method, FMO-DFTB3/D/PCM/3D-SPIEs. In addition to the SARS-CoV-2 spike glycoprotein/hACE2 complex, the hot spot residues of SARS-CoV-1 spike glycoprotein/hACE2 complex, SARS-CoV-1 spike glycoprotein/antibody complex, and HCoV-NL63 spike glycoprotein/hACE2 complex were obtained using the same FMO method. Following this, a 3D-SPIEs-based interaction map was constructed with hot spot residues for the hACE2/SARS-CoV-1 spike glycoprotein, hACE2/HCoV-NL63 spike glycoprotein, and hACE2/SARS-CoV-2 spike glycoprotein complexes. Finally, the three 3D-SPIEs-based interaction maps were combined and analyzed to find the consensus hot spots among the three complexes. As a result of the analysis, two hot spots were identified between hACE2 and the three spike proteins. In particular, E37, K353, G354, and D355 of the hACE2 receptor strongly interact with the spike proteins of coronaviruses. The 3D-SPIEs-based map would provide valuable information to develop anti-viral therapeutics that inhibit PPIs between the spike protein of SARS-CoV-2 and hACE2. url: https://www.ncbi.nlm.nih.gov/pubmed/33033344/ doi: 10.1038/s41598-020-73820-8 id: cord-352925-abry6oz3 author: Lim, Jia Yin title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic date: 2020-05-21 words: 716.0 sentences: 43.0 pages: flesch: 45.0 cache: ./cache/cord-352925-abry6oz3.txt txt: ./txt/cord-352925-abry6oz3.txt summary: title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic Months into the coronavirus disease (COVID-19) pandemic, healthcare workers continue the fight against an increasing disease burden worldwide. This requires mental resilience and perseverance to function under challenging working conditions, sometimes with limited resources and risking personal safety. [1] What often gets overlooked is the "heartware", such as addressing burnout, anxiety of perceived risks, moral injury [2] and the resultant long-term psychological impact that may impair performance and compromise staff and patient safety. [4] In this current pandemic, a considerable proportion of healthcare workers in China reported symptoms of depression, anxiety, insomnia, and distress, signifying the need for psychological support or interventions. [5] With these in mind, we recognized the need to prepare our anesthesia department staff for the threat and associated challenges when managing COVID-19 patients. Managing mental health challenges faced by healthcare workers during covid-19 pandemic abstract: nan url: https://doi.org/10.1016/j.jclinane.2020.109891 doi: 10.1016/j.jclinane.2020.109891 id: cord-298696-rsifxvtj author: Lim, Meng-Kin title: Global response to pandemic flu: more research needed on a critical front date: 2006-10-13 words: 2257.0 sentences: 100.0 pages: flesch: 50.0 cache: ./cache/cord-298696-rsifxvtj.txt txt: ./txt/cord-298696-rsifxvtj.txt summary: Given that air transportation is the one feature that most differentiates present day transmission scenarios from those in 1918, our present inability to prevent spread of influenza by international air travel, as reckoned by the World Health Organization, constitutes a major weakness in the current global preparedness plan against pandemic flu. Alas, the 2005 WHO report Avian influenza: assessing the pandemic has dismally concluded that "If only a few countries are affected, travel-related measures, such as exit screening for persons departing from affected areas, might delay international spread somewhat, but cannot stop it. Against a conservatively estimated US$800 billion a year that a human pandemic of avian influenza could cost the global economy [24] , not to mention the incalculable cost in terms of human lives [25] , it seems incredible that the aviation lessons of SARS have not led to an acceleration of scientific research and health policy evaluation aimed at strengthening public health defenses on the air transportation front. abstract: If and when sustained human-to-human transmission of H5N1 becomes a reality, the world will no longer be dealing with sporadic avian flu borne along migratory flight paths of birds, but aviation flu – winged at subsonic speed along commercial air conduits to every corner of planet Earth. Given that air transportation is the one feature that most differentiates present day transmission scenarios from those in 1918, our present inability to prevent spread of influenza by international air travel, as reckoned by the World Health Organization, constitutes a major weakness in the current global preparedness plan against pandemic flu. Despite the lessons of SARS, it is surprising that aviation-related health policy options have not been more rigorously evaluated, or scientific research aimed at strengthening public health measures on the air transportation front, more energetically pursued. url: https://www.ncbi.nlm.nih.gov/pubmed/17038194/ doi: 10.1186/1478-4505-4-8 id: cord-295514-vhymj0rw author: Lim, Peter A title: Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: Severe acute respiratory syndrome date: 2004-08-01 words: 5277.0 sentences: 244.0 pages: flesch: 43.0 cache: ./cache/cord-295514-vhymj0rw.txt txt: ./txt/cord-295514-vhymj0rw.txt summary: Severe acute respiratory syndrome (SARS) is a new respiratory viral epidemic that originated in China but has affected many parts of the world, with devastating impact on economies and the practice of medicine and rehabilitation. Rehabilitation was significantly affected by SARS, because strict infection control measures run counter to principles such as multidisciplinary interactions, patients encouraging and learning from each other, and close physical contact during therapy. Rehabilitation medicine was increasingly affected by everstricter infection control measures regarding close contacts and interactions between health care workers. Rehabilitation medicine was directly affected when the entire neurology ward, including patients and health care staff, were transferred out to TTSH for isolation and observation because of suspicious clusters of fevers that involved both patients and staff. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: Lim PA, Ng YS, Tay BK. Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: severe acute respiratory syndrome. Arch Phys Med Rehabil 2004;85:1365–70. Severe acute respiratory syndrome (SARS) is a new respiratory viral epidemic that originated in China but has affected many parts of the world, with devastating impact on economies and the practice of medicine and rehabilitation. A novel coronavirus has been implicated, with transmission through respiratory droplets. Rehabilitation was significantly affected by SARS, because strict infection control measures run counter to principles such as multidisciplinary interactions, patients encouraging and learning from each other, and close physical contact during therapy. Immunocompromised patients who may silently carry SARS are common in rehabilitation and include those with renal failure, diabetes, and cancer. Routine procedures such as management of feces and respiratory secretions (eg, airway suctioning, tracheotomy care) have been classified as high risk. Personal protection equipment presented not only a physical but also a psychologic barrier to therapeutic human contact. Visitor restriction to decrease chances of disease transmission are particularly difficult for long-staying rehabilitation patients. At the height of the epidemic, curtailment of patient movement stopped all transfers for rehabilitation, and physiatrists had to function as general internists. Our experiences strongly suggest that rehabilitation institutions should have emergency preparedness plans because such epidemics may recur, whether as a result of nature or of bioterrorism. url: https://www.ncbi.nlm.nih.gov/pubmed/15295768/ doi: 10.1016/j.apmr.2004.01.022 id: cord-329308-ipui7lo6 author: Lim, Soo title: Proper Management of People with Obesity during the COVID-19 Pandemic date: 2020-06-30 words: 4611.0 sentences: 281.0 pages: flesch: 43.0 cache: ./cache/cord-329308-ipui7lo6.txt txt: ./txt/cord-329308-ipui7lo6.txt summary: During the COVID-19 pandemic, people have tended to gain weight because of environmental factors imposed by quarantine policies, such as decreased physical activity and increased consumption of unhealthy food. The common medications used to treat people with obesity, such as glucagon-like peptide-1 analogues, statins, and antiplatelets agents, should be continued because these agents have anti-inflammatory properties and play protective roles against cardiovascular and all-cause mortality. 54 A cumulative effect of chronic inflammation and hypercytokinemia seems to bring about a hyperinflammatory response through macrophage active syndrome, especially in patients with severe COVID-19 (Fig. 2) . Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease abstract: Since December 2019, countries around the world have been struggling with a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Case series have reported that people with obesity experience more severe coronavirus disease 2019 (COVID-19). During the COVID-19 pandemic, people have tended to gain weight because of environmental factors imposed by quarantine policies, such as decreased physical activity and increased consumption of unhealthy food. Mechanisms have been postulated to explain the association between COVID-19 and obesity. COVID-19 aggravates inflammation and hypoxia in people with obesity, which can lead to severe illness and the need for intensive care. The immune system is compromised in people with obesity and COVID-19 affects the immune system, which can lead to complications. Interleukin-6 and other cytokines play an important role in the progression of COVID-19. The inflammatory response, critical illness, and underlying risk factors may all predispose to complications of obesity such as diabetes mellitus and cardiovascular diseases. The common medications used to treat people with obesity, such as glucagon-like peptide-1 analogues, statins, and antiplatelets agents, should be continued because these agents have anti-inflammatory properties and play protective roles against cardiovascular and all-cause mortality. It is also recommended that renin–angiotensin system blockers are not stopped during the COVID-19 pandemic because no definitive data about the harm or benefits of these agents have been reported. During the COVID-19 pandemic, social activities have been discouraged and exercise facilities have been closed. Under these restrictions, tailored lifestyle modifications such as home exercise training and cooking of healthy food are encouraged. url: https://www.ncbi.nlm.nih.gov/pubmed/32544885/ doi: 10.7570/jomes20056 id: cord-264012-q2quyijg author: Lim, Su Bin title: ACE2-expressing endothelial cells in aging mouse brain date: 2020-07-11 words: 2133.0 sentences: 106.0 pages: flesch: 48.0 cache: ./cache/cord-264012-q2quyijg.txt txt: ./txt/cord-264012-q2quyijg.txt summary: Further, scRNA-seq dataset specifically derived from brain vasculature in young adult and aged mice (T3) confirms the elevated ACE2 expression in subsets of the three identified cell types, which consist of 32.8% of the cell populations ( Fig. 1 C) . While our study provides a foundation for a more refined level of analysis of EC and vascular PC, a cell type that remains poorly understood despite its key roles in immune response and microvascular stability [17] , our analyses are limited only to the normal aging mouse and human brains, lacking the context of COVID-19 neuropathology. Despite the works that failed to identify direct signs of SARS-CoV-2 infection in the brains of COVID-19 patients [12, 13] , other lines of evidence support the neurotropism of the virus, as evidenced by experimental platforms leveraging human induced pluripotent stem cell (iPSC)derived dopaminergic neurons [22] and an organotypic brain model [23] . abstract: Angiotensin-converting enzyme 2 (ACE2) is a key receptor mediating the entry of SARS-CoV-2 into the host cell. Through a systematic analysis of publicly available mouse brain sc/snRNA-seq data, we found that ACE2 is specifically expressed in small sub-populations of endothelial cells and mural cells, namely pericytes and vascular smooth muscle cells. Further, functional changes in viral mRNA transcription and replication, and impaired blood-brain barrier regulation were most prominently implicated in the aged, ACE2-expressing endothelial cells, when compared to the young adult mouse brains. Concordant EC transcriptomic changes were further found in normal aged human brains. Overall, this work reveals an outline of ACE2 distribution in the mouse brain and identify putative brain host cells that may underlie the selective susceptibility of the aging brain to viral infection. url: https://doi.org/10.1101/2020.07.11.198770 doi: 10.1101/2020.07.11.198770 id: cord-256808-lxlerb13 author: Lim, W.S title: Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004 date: 2004-06-02 words: 2426.0 sentences: 167.0 pages: flesch: 55.0 cache: ./cache/cord-256808-lxlerb13.txt txt: ./txt/cord-256808-lxlerb13.txt summary: Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS. During 2003 Severe Acute Respiratory Syndrome caused by a novel coronavirus (SARS-CoV) emerged as an infectious disease with a significant inhospital mortality and posed a considerable occupational risk for healthcare workers. Please discuss the classification of SARS patients with the Health Protection Agency''s Communicable Disease Surveillance Centre (CDSC) Duty doctor (Tel.: 0208-200-6868) and complete a standard SARS report form and fax to your local Consultant in Communicable Disease Control (CCDC) and CDSC (details at: http://www.hpa.org.uk/infections/ topics_az/SARS/forms.htm). Inform the local Health Protection Team/CCDC regarding the hospital discharge of patients to ensure follow-up in the community. Severe acute respiratory syndrome (SARS): infection control abstract: Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS. url: https://api.elsevier.com/content/article/pii/S0163445304000830 doi: 10.1016/j.jinf.2004.04.001 id: cord-319864-t6ql9hz2 author: Lima, Amorce title: Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens date: 2020-11-11 words: 3048.0 sentences: 190.0 pages: flesch: 65.0 cache: ./cache/cord-319864-t6ql9hz2.txt txt: ./txt/cord-319864-t6ql9hz2.txt summary: In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. In this study, we sought to describe a modified CDC SARS-CoV-2 assay validation and compare its performance and workflow to that of the NeuMoDx SARS-CoV-2 and DiaSorin Simplexa Covid-19 Direct assays using respiratory specimens. The primer/probe sets used in this validation were selected from regions of the SARS-CoV-2 virus nucleocapsid (N) gene and were described in the CDC EUA protocol for COVID-19 diagnostic testing (7) . Of the 43 samples used for comparison between modified CDC SARS-CoV-2 assay and Simplexa Covid 19 Direct assay, 37 samples were run within 2 days and 6 were run within 5 days of first testing. The clinical performance comparison between NeuMoDx SARS-CoV-2 assay, Simplexa Covid-19 Direct assay, and the modified CDC SARS-CoV-2 assay showed an overall agreement of 100%. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has spread rapidly around the globe since it was first identified in December of 2019 in Wuhan, China. In a race to contain the infection, researchers and healthcare officials have developed several assays to help diagnose individuals with COVID-19. To help laboratories decide what assay to bring into testing lines, factors such as assay availability, cost, throughput, and TAT should be considered. Here we validated a modified version of the CDC assay and used it as a reference to evaluate the performance of the NeuMoDxTM SARS-CoV-2 and DiaSorin SimplexaTM Covid-19 Direct assays. In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. The performance of the three assays were analyzed using 159 nasopharyngeal swabs specimen tested within 1 to 5 days after routine testing. A 100% agreement was observed between the commercial assays and the modified CDC SARS-CoV-2 assay. A deeper look at the Ct values showed no significant difference between NeuMoDx and the modified CDC SARS-CoV-2 assay, whereas DiaSorin had lower overall Ct values than the modified CDC SARS-CoV-2 assay. NeuMoDx and DiaSorin workflows were much easier to perform. NeuMoDx has the highest throughput and shortest TAT, whereas although the modified CDC SARS-CoV-2 assay has comparable throughput to DiaSorin, it has the longest hands-on time and highest TAT. url: https://api.elsevier.com/content/article/pii/S1386653220304303 doi: 10.1016/j.jcv.2020.104688 id: cord-338734-laeocs3j author: Lima, Amorce title: Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date: 2020-06-30 words: 2533.0 sentences: 141.0 pages: flesch: 61.0 cache: ./cache/cord-338734-laeocs3j.txt txt: ./txt/cord-338734-laeocs3j.txt summary: In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. A 149 series of two-fold dilutions of SARS-CoV-2 strain USA_WA1/2020 RNA were spiked in pooled 150 sputum at concentrations of 800 copies/ml to 0.05 copy/ml in order to determine the limit of 151 detection (LoD) of the assay. On the other hand, the average Ct values difference between 235 samples run within 2 days between DiaSorin Simplexa Covid 19 Direct assay and the modified 236 CDC SARS-CoV-2 assay was -2.42, and -6.0 between samples run within 5 days. In this study, we validated a modified CDC SARS-CoV-2 assay and compared its 263 performance to two commercial automated sample-to-answer assays for the detection of SARS-264 The difference is even greater 286 in samples that were run 5 days after the routine testing on the modified CDC SARS-CoV-2 287 assay. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has spread rapidly around the globe since it was first identified in December of 2019 in Wuhan, China. In a race to contain the infection, researchers and healthcare officials have developed several assays to help diagnose individuals with COVID-19. To help laboratories in deciding what assay to bring into testing lines, factors such as assay availability, cost, throughput, and TAT should be considered. Here we validated a modified version of the CDC assay and used it as a reference to evaluate the performance of the NeuMoDx™ SARS-CoV-2 and DiaSorin Simplexa™ Covid-19 Direct assays. In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. The performance of the three assays were analyzed using 161 nasopharyngeal swabs specimen tested within 24 hours or 5 days from routine testing. A 100% agreement was observed between the commercial assays and the modified CDC SARS-CoV-2 assay. A deeper look at the Ct values showed no significant difference between NeuMoDx and the modified CDC SARS-CoV-2 assay, whereas DiaSorin had lower overall Ct values than the modified CDC SARS-CoV-2 assay. NeuMoDx and DiaSorin workflows were much easier to perform. NeuMoDx has the highest throughput and shortest TAT, whereas although the modified CDC SARS-CoV-2 assay has comparable throughput to DiaSorin, it has the longest hands-on time, and highest TAT. url: https://doi.org/10.1101/2020.06.29.179192 doi: 10.1101/2020.06.29.179192 id: cord-274834-24v2b509 author: Lima, Rosiane title: Establishment of a pediatric COVID-19 biorepository: unique considerations and opportunities for studying the impact of the COVID-19 pandemic on children date: 2020-09-11 words: 5588.0 sentences: 268.0 pages: flesch: 40.0 cache: ./cache/cord-274834-24v2b509.txt txt: ./txt/cord-274834-24v2b509.txt summary: Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. METHODS: A COVID-19 biospecimen collection study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. Specific questions that must be addressed revolve around the role children play in viral transmission, differences in pediatric viral susceptibility and immune responses, which could guide potential therapies for adults, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the development of severe hyperinflammatory shock and cardiac damage seen in Multisystem Inflammatory Syndrome in Children (MIS-C). In order to capture the full range of SARS-CoV-2 infection in the pediatric population, a COVID-19 biospecimen collection study was designed and implemented, including patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2-infected mothers, and asymptomatic children. abstract: BACKGROUND: COVID-19, the disease caused by the highly infectious and transmissible coronavirus SARS-CoV-2, has quickly become a morbid global pandemic. Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. This biorepository enables pediatric centers world-wide to collect samples uniformly to drive forward our understanding of COVID-19 by addressing specific pediatric and neonatal COVID-19-related questions. METHODS: A COVID-19 biospecimen collection study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. The methodology described here, details the importance of establishing collaborations between the clinical and research teams to harmonize protocols for patient recruitment and sample collection, processing and storage. It also details modifications required for biobanking during a surge of the COVID-19 pandemic. RESULTS: Considerations and challenges facing enrollment of neonatal and pediatric cohorts are described. A roadmap is laid out for successful collection, processing, storage and database management of multiple pediatric samples such as blood, nasopharyngeal and oropharyngeal swabs, sputum, saliva, tracheal aspirates, stool, and urine. Using this methodology, we enrolled 327 participants, who provided a total of 972 biospecimens. CONCLUSIONS: Pediatric biospecimens will be key in answering questions relating to viral transmission by children, differences between pediatric and adult viral susceptibility and immune responses, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the Multisystem Inflammatory Syndrome in Children. The specimens in this biorepository will allow necessary comparative studies between children and adults, help determine the accuracy of current pediatric viral testing techniques, in addition to, understanding neonatal exposure to SARS-CoV-2 infection and disease abnormalities. The successful establishment of a pediatric biorepository is critical to provide insight into disease pathogenesis, and subsequently, develop future treatment and vaccination strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32917141/ doi: 10.1186/s12874-020-01110-y id: cord-276630-qci7khki author: Lima, William Gustavo title: The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date: 2020-06-08 words: 3727.0 sentences: 214.0 pages: flesch: 49.0 cache: ./cache/cord-276630-qci7khki.txt txt: ./txt/cord-276630-qci7khki.txt summary: Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus. abstract: The novel human coronavirus (SARS-CoV-2), the causative agent of COVID-19, has quickly become a threat to the public health and economy worldwide. Despite the severity of some cases, there are no current pathogen-specific antivirals available to treat the disease. Therefore, many studies have focused on the evaluation of the anti-SARS-CoV-2 activity of clinically available drugs. Here, we conducted a systematic review to describe the drug repositioning strategy against SARS-CoV-2 and to discuss the clinical impact of this approach in the current pandemic context. The systematic review was performed on March 23, 2020, using PubMed/MEDLINE, Scopus, Cochrane Library, and Biblioteca Virtual de Saúde (BVS). The data were summarized in tables and critically analyzed. After the database search, 12 relevant studies were identified as eligible for the review. Among the drugs reported in these studies, 57 showed some evidence of antiviral activity. Antivirals, especially antiretrovirals, are the main class of therapeutic agents evaluated against COVID-19. Moreover, studies have reported the anti-SARS-CoV-2 activity of antitumor (16%; 9/57), antimalarial (7%, 4/57), and antibacterial (5%; 3/57) agents. Additionally, seven pharmacological agents (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, damageprevir, lopinavir/ritonavir) are in phase IV of clinical trials. Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04693-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04693-5 doi: 10.1007/s00705-020-04693-5 id: cord-350401-suefuurq author: Lima-Setta, Fernanda title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() date: 2020-11-09 words: 3943.0 sentences: 215.0 pages: flesch: 52.0 cache: ./cache/cord-350401-suefuurq.txt txt: ./txt/cord-350401-suefuurq.txt summary: title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() From March 25 to August 23, 2020, pediatric patients (age range: 1 month -19 years) were consecutively included if they met the CDC case definition[8] for MIS-C: 1) fever > 38.0°C for ≥ 24 hours (objective or subjective); 2) laboratory evidence of inflammation, including, but not limited to, one or more of the following: high values of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), fibrinogen, procalcitonin, d-dimer, ferritin, lactic acid dehydrogenase (LDH), or interleukin 6 (IL-6); elevated neutrophils, reduced lymphocytes, and low albumin; 3) no alternative plausible diagnosis; 4) current or recent SARS-CoV-2 infection diagnosed by a positive reverse transcription polymerase chain reaction (RT-PCR) or positive serological tests (IgM, IgG or IgA), or exposure to a suspected or confirmed COVID-19 case within the four weeks prior to the onset of symptoms. abstract: OBJECTIVE: To describe the clinical, laboratory, and radiological characteristics, as well as the outcomes of children with MIS-C. METHOD: Multicenter, prospective cohort study, conducted in 17 pediatric intensive care units in five states in Brazil, from March to July 2020. Patients from 1 month to 19 years who met the MIS-C diagnostic criteria were included consecutively. RESULTS: Fifty-six patients were included, with the following conditions: Kawasaki-like disease (n = 26), incomplete Kawasaki disease (n = 16), acute cardiac dysfunction (n = 10), toxic shock syndrome (n = 3), and macrophage activation syndrome (n = 1). Median age was 6.2 years (IQR 2.4-10.3), 70% were boys, 59% were non-whites, 20% had comorbidities, 48% reported a contact with COVID-19 cases, and 55% had a recent SARS-CoV-2 infection confirmed by RT-PCR and/or serology. Gastrointestinal symptoms were present in 71%, shock symptoms in 59%, and severe respiratory symptoms in less than 20%. D-dimer was increased in 80% and cardiac dysfunction markers in more than 75%. Treatment included immunoglobulin (89%); corticosteroids, antibiotics, and enoxaparin in about 50%; and oseltamivir and antifungal therapy in less than 10%. Only 11% needed invasive mechanical ventilation, with a median duration of five days (IQR 5-6.5). The median length of PICU stay was six days (IQR 5-11), and one death occurred (1.8%). CONCLUSIONS: Most characteristics of the present MIS-C patients were similar to that of other cohorts. The present results may contribute to a broader understanding of SARS-CoV-2 infection in children and its short-term consequences. Long-term multidisciplinary follow-up is needed, since it is not known whether these patients will have chronic cardiac impairment or other sequelae. url: https://api.elsevier.com/content/article/pii/S0021755720302254 doi: 10.1016/j.jped.2020.10.008 id: cord-328073-bqeffvzl author: Limonta, Daniel title: Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date: 2020-11-06 words: 1878.0 sentences: 113.0 pages: flesch: 55.0 cache: ./cache/cord-328073-bqeffvzl.txt txt: ./txt/cord-328073-bqeffvzl.txt summary: The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Next, we demonstrated that the NOD2 inhibitor GSK717 blocks infection by and 205 spread of ZIKV in human fetal brain and cell lines. Similarly, the work here which demonstrated the antiviral activity of NOD2 and RIPK2 inhibitors using tissue explants, 216 primary cells and cell lines, support the potential clinical use of these compounds in mono or co-217 infections by arboviruses as well as coronavirus infections at early and/or advanced stages. Calu-3 and Huh7 cells infected with SARS-CoV-2 (MOI=0.1) were also treated with GSK583 for 24 hours before collecting the cell supernatants for viral titer determination. abstract: In the present report, we describe two small molecules with broad-spectrum antiviral activity. These drugs block formation of the nodosome. The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Another drug that inhibits the receptor-interacting serine/threonine-protein kinase 2 (RIPK2) which functions downstream of NOD2, also decreased replication of these pathogenic RNA viruses. The broad-spectrum action of nodosome targeting drugs is mediated, at least in part, by enhancement of the interferon response. Together, these results suggest that further preclinical investigation of nodosome inhibitors as potential broad-spectrum antivirals is warranted. url: https://doi.org/10.1101/2020.11.05.370767 doi: 10.1101/2020.11.05.370767 id: cord-323105-gqqzekfk author: Lin, Chen-Si title: Enhancement of anti-murine colon cancer immunity by fusion of a SARS fragment to a low-immunogenic carcinoembryonic antigen date: 2012-02-03 words: 3208.0 sentences: 153.0 pages: flesch: 46.0 cache: ./cache/cord-323105-gqqzekfk.txt txt: ./txt/cord-323105-gqqzekfk.txt summary: Oral vaccination of an attenuated Salmonella typhimurium strain transformed with plasmids encoding CEA-SARS-CoV fusion gene into BALB/c mice elicited significant increases in TNF-α and IL-10 in the serum. For achieving simple administration of drugs and enhancement of host immunity, an oral DNA vaccine vector, Salmonella typhimurium (SL3261) [7] , was used as a carrier to deliver the SARS-CoV-CEA fusion genes. By combining SARS-CoV epitope, a tumor unrelated antigenic fragment, with CEA, we finally demonstrated this could be a promising anti-cancer strategy through effectively increasing both Th1 and Th2 cytokines and decreasing tumor volume. In comparison with the negative control group, no significant differences in tumor volume were observed in mice immunized with CEA alone, while the tumor volume was found to be smaller in the pCEA-SARS-CoV group in the protection and therapy assays (Figure 3 &4) . abstract: BACKGROUND: It is widely understood that tumor cells express tumor-associated antigens (TAAs), of which many are usually in low immunogenicity; for example, carcinoembryonic antigen (CEA) is specifically expressed on human colon cancer cells and is viewed as a low-immunogenic TAA. How to activate host immunity against specific TAAs and to suppress tumor growth therefore becomes important in cancer therapy development. RESULTS: To enhance the immune efficiency of CEA in mice that received, we fused a partial CEA gene with exogenous SARS-CoV fragments. Oral vaccination of an attenuated Salmonella typhimurium strain transformed with plasmids encoding CEA-SARS-CoV fusion gene into BALB/c mice elicited significant increases in TNF-α and IL-10 in the serum. In addition, a smaller tumor volume was observed in CT26/CEA-bearing mice who received CEA-SARS-CoV gene therapy in comparison with those administered CEA alone. CONCLUSION: The administration of fusing CEA-SARS-CoV fragments may provide a promising strategy for strengthening the anti-tumor efficacy against low-immunogenic endogenous tumor antigens. url: https://www.ncbi.nlm.nih.gov/pubmed/22304896/ doi: 10.1186/1480-9222-14-2 id: cord-354780-yzyixucr author: Lin, Chih-Yen title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date: 2020-06-13 words: 1757.0 sentences: 120.0 pages: flesch: 60.0 cache: ./cache/cord-354780-yzyixucr.txt txt: ./txt/cord-354780-yzyixucr.txt summary: title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan Conclusion This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This novel coronavirus was initially named 2019-novel coronavirus (2019-nCoV), however, currently the name has been established as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); with the disease being named as coronavirus disease 2019 (COVID-19) (Coronaviridae Study Group of the International Committee on Taxonomy of, 2020) Since the first reported case, there has been a rapid increase in the number of cases, with outbreaks being reported in countries all over the world. Accordingly, we suggest that the constant importation of SARS-CoV-2 infection is the major risk factor leading the COVID-19 epidemic in Taiwan. abstract: Abstract Objective COVID-19 has recently become a pandemic affecting many countries worldwide. This study aims to evaluate current status of COVID-19 in Taiwan and analyze the source of infection. Methods National data regarding SARS-CoV-2 infection were obtained from Taiwan CDC at the end of April, 2020. These data were subjected for analysis of the current status and correlation between indigenous and imported COVID-19 cases. Phylogenetic tree was performed to analyze the phylogeny of Taiwanese SARS-CoV-2 isolates. Results The initial case of SARS-CoV-2 infection in Taiwan was detected on January 21, 2020. Epidemiological data indicate that by April 30, there were a total of 429 COVID-19 confirmed cases with the death rate of 1.3%. Most of cases were identified as imported (79.9%; 343/429) with majority transmitted from United States of America (22.1%) and United Kingdom (17.6%). Results from phylogenetic tree analyses indicate that the Taiwanese SARS-CoV-2 isolates were clustered with the SARS-CoV-2 isolates from other countries (bootstrap value 98%) and sub-clustered with bat SARS-like coronaviruses (bootstrap value 99%). Conclusion This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. url: https://www.sciencedirect.com/science/article/pii/S1201971220304665?v=s5 doi: 10.1016/j.ijid.2020.06.031 id: cord-300950-ag0sql4i author: Lin, John title: Potential therapeutic options for coronavirus disease 2019: using knowledge of past outbreaks to guide future treatment date: 2020-06-05 words: 1899.0 sentences: 104.0 pages: flesch: 50.0 cache: ./cache/cord-300950-ag0sql4i.txt txt: ./txt/cord-300950-ag0sql4i.txt summary: Several case reports including the first report of SARS outbreak described the use of the anti-viral drug ribavirin and a corticosteroid in patients with contradictory clinical outcomes. In several studies, lopinavir/ritonavir was shown to have anti-CoV effects in vitro, in MERS-infected primate models, and in SARS-infected humans. Furthermore, in a single MERS patient, a triple-combination therapy of ribavirin, IFN and lopinavir/ ritonavir resolved viremia in 2 days following initiation of treatment. [7] [8] [9] In two reports from China and Korea, the use of lopinavir/ritonavir in patients with COVID-19 improved recovery and reduced viral load. [7, 8] However, Chen et al [9] showed that lopinavir/ ritonavir and the anti-influenza treatment Arbidol had no clinically significant improvement in 134 people with mild COVID-19. [17] In an effort to combat inflammation and improve clinical outcome, corticosteroid use has been described in SARS, MERS, and COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32209887/ doi: 10.1097/cm9.0000000000000816 id: cord-343850-p4bbb6vm author: Lin, Meng-Hsuan title: Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain date: 2020-09-18 words: 5149.0 sentences: 313.0 pages: flesch: 59.0 cache: ./cache/cord-343850-p4bbb6vm.txt txt: ./txt/cord-343850-p4bbb6vm.txt summary: SARS-CoV-2 encodes the conserved macro domain within nonstructural protein 3, which may reverse cellular ADP-ribosylation and potentially cut the signal of a viral infection in the cell. Herein, we report that the SARS-CoV-2 macro domain was examined as a poly-ADP-ribose (ADPR) binding module and possessed mono-ADPR cleavage enzyme activity. After confirming the ADPR binding ability via a biophysical approach, the X-ray crystal structure of the SARS-CoV-2 macro domain was determined and structurally compared with those of other viruses. This study provides structural, biophysical, and biochemical bases to further evaluate the role of the SARS-CoV-2 macro domain in the host response via ADP-ribose binding but also as a potential target for drug design against COVID-19. Virus macro domains were reported to have multiple functions, including a ADP-ribose (ADPR) 8−10 or poly-ADPR 9 interaction, adenine-rich RNA 11 binding, enzyme activities of ADPR-1″ phosphohydrolase, 7, 9 and the removal of mono(ADP-ribose) from protein. abstract: [Image: see text] The pandemic outbreak of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has threatened the global public health and economy since late December 2019. SARS-CoV-2 encodes the conserved macro domain within nonstructural protein 3, which may reverse cellular ADP-ribosylation and potentially cut the signal of a viral infection in the cell. Herein, we report that the SARS-CoV-2 macro domain was examined as a poly-ADP-ribose (ADPR) binding module and possessed mono-ADPR cleavage enzyme activity. After confirming the ADPR binding ability via a biophysical approach, the X-ray crystal structure of the SARS-CoV-2 macro domain was determined and structurally compared with those of other viruses. This study provides structural, biophysical, and biochemical bases to further evaluate the role of the SARS-CoV-2 macro domain in the host response via ADP-ribose binding but also as a potential target for drug design against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32946224/ doi: 10.1021/acsinfecdis.0c00441 id: cord-329959-4yecwdlo author: Lin, Min-Han title: Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes date: 2017-12-28 words: 5576.0 sentences: 319.0 pages: flesch: 58.0 cache: ./cache/cord-329959-4yecwdlo.txt txt: ./txt/cord-329959-4yecwdlo.txt summary: Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL(pro)s) of MERS-CoV and SARS-CoV. The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL(pro) by disulfiram, while synergistic inhibition of MERS-CoV PL(pro) by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. For the inactivation studies, SARS-CoV PL pro (0.05 μM in 20 mM phosphate buffer, pH 6.5) was incubated with different concentrations of disulfiram and peptide substrate, and enzymatic activity was traced for 5 min. On the other hand, the results of kinetic assays, continued inactivation after the removal of disulfiram, reactivation by reductant, and the phenomenon of slow-binding inhibition suggest that disulfiram may act at the active site of SARS-CoV PL pro , forming a covalent adduct with residue Cys112. abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in late 2002 and caused a global outbreak with a fatality rate around 10% in 2003. Ten years later, a second highly pathogenic human CoV, MERS-CoV, emerged in the Middle East and has spread to other countries in Europe, North Africa, North America and Asia. As of November 2017, MERS-CoV had infected at least 2102 people with a fatality rate of about 35% globally, and hence there is an urgent need to identify antiviral drugs that are active against MERS-CoV. Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL(pro)s) of MERS-CoV and SARS-CoV. Our findings suggest that disulfiram acts as an allosteric inhibitor of MERS-CoV PL(pro) but as a competitive (or mixed) inhibitor of SARS-CoV PL(pro). The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL(pro) by disulfiram, while synergistic inhibition of MERS-CoV PL(pro) by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. url: https://doi.org/10.1016/j.antiviral.2017.12.015 doi: 10.1016/j.antiviral.2017.12.015 id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 words: 14665.0 sentences: 840.0 pages: flesch: 42.0 cache: ./cache/cord-312741-0au4nctt.txt txt: ./txt/cord-312741-0au4nctt.txt summary: 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein abstract: Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single‐stranded RNA virus. Human coronavirus (HCoV) strains (HCoV‐229E, HCoV‐OC43, HCoV‐HKU1, HCoV‐NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID‐19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections. url: https://www.ncbi.nlm.nih.gov/pubmed/33173860/ doi: 10.1002/mco2.26 id: cord-272603-nbosceoz author: Lin, Qiuyuan title: Microfluidic Immunoassays for Sensitive and Simultaneous Detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min date: 2020-07-02 words: 1882.0 sentences: 98.0 pages: flesch: 42.0 cache: ./cache/cord-272603-nbosceoz.txt txt: ./txt/cord-272603-nbosceoz.txt summary: Facing the emergence of this pandemic, we established a portable microfluidic immunoassay system for easy-to-use, sensitive, rapid (<15 min), multiple, and on-site detection of IgG/IgM/Antigen of SARS-CoV-2 simultaneously. This integrated method was successfully applied for detecting SARS-CoV-2 IgM and IgG antibodies in clinical human serum as well as SARS-CoV-2 antigen in pharyngeal swabs from 26 patients with COVID-19 infection and 28 uninfected people. 26 To meet the challenge of the large epidemic, we describe the development of a point-of-care microfluidic platform integrating a homemade fluorescence detection analyzer ( Figure 1A ), SARS-CoV-2 diagnostic microchips ( Figure 1B) , and multiple immunoassays ( Figure 1C ) for detecting three biomarkers (IgG, IgM, and antigen). This robust microfluidic immunoassay system can provide a useful tool for SARS-CoV-2 diagnosis in public health laboratories as well as for timely screening potentially infected patients to monitor and prevent the epidemic owning to its capability of easy, fast, cost-effective, and point-of-care detection. abstract: [Image: see text] The outbreak of SARS-CoV-2 is posing serious global public health problems. Facing the emergence of this pandemic, we established a portable microfluidic immunoassay system for easy-to-use, sensitive, rapid (<15 min), multiple, and on-site detection of IgG/IgM/Antigen of SARS-CoV-2 simultaneously. This integrated method was successfully applied for detecting SARS-CoV-2 IgM and IgG antibodies in clinical human serum as well as SARS-CoV-2 antigen in pharyngeal swabs from 26 patients with COVID-19 infection and 28 uninfected people. The assay demonstrated high sensitivity and specificity, which is promising for the diagnosis and monitoring as well as control of SARS-CoV-2 worldwide. url: https://doi.org/10.1021/acs.analchem.0c01635 doi: 10.1021/acs.analchem.0c01635 id: cord-300300-jqi4ylrx author: Lin, Ray Junhao title: From SARS to COVID‐19: the Singapore journey date: 2020-05-31 words: 2611.0 sentences: 159.0 pages: flesch: 50.0 cache: ./cache/cord-300300-jqi4ylrx.txt txt: ./txt/cord-300300-jqi4ylrx.txt summary: The 2003 severe acute respiratory syndrome (SARS) outbreak challenged the nation''s public health system and now the coronavirus disease 2019 (COVID-19) pandemic is presenting a greater challenge. This framework serves as the foundation for the national responses to any outbreak and is divided into four levels of incremental severity (green, yellow, orange and red), based on risk assessment of the public health impact of the disease and the current disease situation in Singapore (Box 1). Workers who tested positive were transferred to community isolation facilities if they had mild symptoms, or to the NCID and public hospitals for further treatment and isolation. Health care workers in direct contact with COVID-19 patients who developed fever or symptoms of acute respiratory infection were encouraged to declare their symptoms to their superiors and present themselves to the screening centre, to be managed based on their exposure risk (Box 4). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32474940/ doi: 10.5694/mja2.50623 id: cord-339521-qfnu319w author: Lin, Shiming title: Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy date: 2005-08-08 words: 3647.0 sentences: 220.0 pages: flesch: 58.0 cache: ./cache/cord-339521-qfnu319w.txt txt: ./txt/cord-339521-qfnu319w.txt summary: Here, we used AFM to determine the surface ultra structure of each single SARS-CoV virion and observe the surface characteristics and their topography and phase changes after treatments with hydroxyoctanoic acid or protease. The higher-resolution image shows that many individual spherical protrusions exist on the surface and the corresponding cursor profile (Fig. 1 a ) clearly reveals the presence of SARS-CoV particles and each single particle is readily distinguishable. The corresponding cursor profile provides quantitative measurements of the heights for the SARS-CoV particles on the surface. It was found that from the contour map (Fig. 5C ) 15 spike proteins (arrowheads) surround the envelope of a single SARS-CoV virion. The phase image provides a measure of sample heterogeneity and also indicates that the small spherical particles (arrowheads) come from the SARS-CoV virion itself (Fig. 6B) . abstract: Atomic force microscopy has been used to probe the surface nanostructures of severe acute respiratory syndrome coronavirus (SARS‐CoV). Single crown‐like virion was directly visualized and quantitative measurements of the dimensions for the structural proteins were provided. A corona of large, distinctive spikes in the envelope was measured after treatment with hydroxyoctanoic acid. High‐resolution images revealed that the surface of each single SARS‐CoV was surrounded with at least 15 spherical spikes having a diameter of 7.29 ± 0.73 nm, which is in close agreement with that of S glycoproteins earlier predicted through the genomes of SARS‐CoV. This study represents the first direct characterization of the surface ultrastructures of SARS‐CoV particles at the nanometre scale and offers new prospects for mapping viral surface properties. url: https://www.ncbi.nlm.nih.gov/pubmed/16309462/ doi: 10.1111/j.1462-5822.2005.00593.x id: cord-314572-1pou702r author: Lin, Ya-Hui title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date: 2016-10-14 words: 7182.0 sentences: 337.0 pages: flesch: 47.0 cache: ./cache/cord-314572-1pou702r.txt txt: ./txt/cord-314572-1pou702r.txt summary: Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. In a first step to constructing a ligand-responsive −1 PRF stimulator, we designed Switch-0 RNA with a theophylline aptamer replacing the stem 3 of SARS-PK ( Figure 1A and C). We rationalized that such an engineered switch hairpin of reasonable stability (predicted free energy of −12.7 kcal/mole (37)) would be the dominant conformation that could interfere with the formation of pseudoknot stem 2 in the absence of theophylline (Supplementary Figure S2A) . To improve the dynamic range of ligand response and to see if theophylline aptamers can be functional while existing in both positive and negative regulators of −1 PRF, we fused previously designed theophylline-dependent upstream attenuator, theoOFF2 (24) with Switch-1 ( Figure 5A ) and examined theophylline-dependent −1 PRF activity in vitro. abstract: Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate −1 programmed ribosomal frameshifting (PRF), suggesting −1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by difficulty in identifying a specific ligand-responsive pseudoknot that also functions as a ligand-dependent -1 PRF stimulator. We addressed this problem by using the −1 PRF stimulation pseudoknot of SARS-CoV (SARS-PK) to build a ligand-dependent −1 PRF stimulator. In particular, the extra stem of SARS-PK was replaced by an RNA aptamer of theophylline and designed to couple theophylline binding with the stimulation of −1 PRF. Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. Thus, RNA–ligand interaction repertoire provided by in vitro selection becomes accessible to ligand-specific −1 PRF stimulator engineering using SARS-PK as the scaffold for synthetic biology application. url: https://www.ncbi.nlm.nih.gov/pubmed/27521370/ doi: 10.1093/nar/gkw718 id: cord-282177-8l7zukg4 author: Lin, Yi-Chun title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date: 2020-05-26 words: 370.0 sentences: 31.0 pages: flesch: 55.0 cache: ./cache/cord-282177-8l7zukg4.txt txt: ./txt/cord-282177-8l7zukg4.txt summary: title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 abstract: ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. There was transient existence of SARS-CoV-2 RNA in his oropharynx. The RNA was absent in the six respiratory specimens that were subsequently tested. Anti-SARS-CoV-2 antibody response in the acute and convalescent sera were absent. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. url: https://api.elsevier.com/content/article/pii/S1201971220303775 doi: 10.1016/j.ijid.2020.05.070 id: cord-352156-sa8cvyuw author: Lindeman, Robbert-Jan title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries date: 2020-05-06 words: 1834.0 sentences: 96.0 pages: flesch: 44.0 cache: ./cache/cord-352156-sa8cvyuw.txt txt: ./txt/cord-352156-sa8cvyuw.txt summary: title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries In both countries, the first weeks of preparation has seen a strong reduction in elective surgery, with several implemented principles to mitigate SARS-CoV-2 spread and prepare for surgical care for COVID-19 diseases as needed. Norway, that initially started with aggressive testing of subjects with symptoms or returning from high-endemic areas in order to get control over the spread pattern and asymptomatic COVID-19 patients, needed to restrict its activity later in March. An early effect of the initially suboptimal test routines for healthcare workers (HCW) was experienced in Norway, when one HCW returning from central Europe, was confirmed positive to SARS-CoV-2 only after having spent several days at work on the advice from the hospital. The acute threat of the COVID-19 epidemic to global healthcare has led to forced reorganization of surgical care in Norway and Sweden. abstract: A COVID-19 pandemic was declared on March 11 by the World Health Organization (WHO). The first cases of COVID-19 were confirmed on January 31 in Sweden and on February 26 in Norway. Despite being similar countries with universal healthcare systems, the governmental approaches to mitigation of the epidemic have varied considerably. Norway initiated a societal lockdown effective from March 12, the same day as the first confirmed death. Sweden has initiated a more laxed and gradual strategy based on the appeal for a strong personal sense of responsibility to mitigate the viral spread. In both countries, the first weeks of preparation has seen a strong reduction in elective surgery, with several implemented principles to mitigate SARS-CoV-2 spread and prepare for surgical care for COVID-19 diseases as needed. This invited leading article gives a brief overview of some of the early experiences of the outbreak in two Scandinavian countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32395226/ doi: 10.1093/jscr/rjaa131 id: cord-142389-t5swlp04 author: Linden, Matthias title: The foreshadow of a second wave: An analysis of current COVID-19 fatalities in Germany date: 2020-10-12 words: 3725.0 sentences: 272.0 pages: flesch: 65.0 cache: ./cache/cord-142389-t5swlp04.txt txt: ./txt/cord-142389-t5swlp04.txt summary: We investigated this apparent discrepancy using age-stratified case and death reports [3] , and an age-dependent infection fatality rate (IFR). From this age-dependent IFR we predict the temporal evolution of the COVID-19associated deaths by delaying each age group''s observed weekly cases by two weeks and multiplying by the IFR (see supplementary material). The observed number deaths (black) in each age group matches well the predicted deaths calculated from the case numbers (color) using an age-dependent infection-fatality rate from a metaanalysis [4] . b. IFR calculation The overall goal is to estimate death numbers from past reported cases per age group and compare them to the observed number of deaths. c. Estimating the number of deaths from the reported SARS-CoV-2 cases The number of deaths is estimated by multiplying the published weekly number of reported cases in 5-years-wide age groups by the associated IFR (equation (2)). abstract: A second wave of SARS-CoV-2 is unfolding in dozens of countries. However, this second wave manifests itself strongly in new reported cases, but less in death counts compared to the first wave. Over the past three months in Germany, the reported cases increased by a factor five or more, whereas the death counts hardly grew. This discrepancy fueled speculations that the rise of reported cases would not reflect a second wave but only wider testing. We find that this apparent discrepancy can be explained to a large extent by the age structure of the infected, and predict a pronounced increase of death counts in the near future, as the spread once again expands into older age groups. To re-establish control, and to avoid the tipping point when TTI capacity is exceeded, case numbers have to be lowered. Otherwise the control of the spread and the protection of vulnerable people will require more restrictive measures latest when the hospital capacity is reached. url: https://arxiv.org/pdf/2010.05850v2.pdf doi: nan id: cord-261619-31jk1vh6 author: Lindholm, David A title: Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date: 2020-07-17 words: 2176.0 sentences: 112.0 pages: flesch: 47.0 cache: ./cache/cord-261619-31jk1vh6.txt txt: ./txt/cord-261619-31jk1vh6.txt summary: Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. Mitigation of the coronavirus disease 2019 (COVID-19) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] . During the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (PPE) use [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . The electronic medical record was reviewed (1) for comorbid conditions in positive cases and (2) for additional SARS-CoV-2 testing and BAMC hospital admission within 14 days of screening for all patients. Nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. However, none of the screen-only patients later tested positive or were hospitalized for COVID-19 within 14 days. abstract: Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. We describe the characteristics of screened individuals as well as drive-through process and outcome measures. Optimal drive-through screening involves rapid turnaround of test results and linkage to follow-up care. url: https://doi.org/10.1093/ofid/ofaa306 doi: 10.1093/ofid/ofaa306 id: cord-261180-w62mynqb author: Ling, L. title: Infection control in non‐clinical areas during the COVID‐19 pandemic date: 2020-04-19 words: 482.0 sentences: 35.0 pages: flesch: 54.0 cache: ./cache/cord-261180-w62mynqb.txt txt: ./txt/cord-261180-w62mynqb.txt summary: SARS-CoV-2 is easily transmissible as each person with COVID-19 infects approximately 2.2 close contacts, and asymptomatic transmission has been reported [2,3]. Therefore, we believe non-clinical areas are potentially high-risk for transmission between healthcare workers, and often neglected by infection prevention and control protocols. To alert others to this risk and how it may be reduced, we describe our non-clinical workplace infection prevention and control measures that have been modified from those originally developed during the 2003 severe acute respiratory syndrome epidemic [5] . Infographics are displayed on walls as reminders to perform hand hygiene when entering offices, after contact with respiratory secretions, before and after eating or drinking, and donning and doffing of masks. Designated bins for mask disposal are placed in communal areas. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Transmission of SARS to healthcare workers. abstract: Large numbers of healthcare workers have acquired coronavirus disease (COVID-19) in the workplace [1]. SARS-CoV-2 is easily transmissible as each person with COVID-19 infects approximately 2.2 close contacts, and asymptomatic transmission has been reported [2,3]. SARS-CoV-2 survives in aerosols and on surfaces from hours to days, respectively [4]. Therefore, we believe non-clinical areas are potentially high-risk for transmission between healthcare workers, and often neglected by infection prevention and control protocols. To alert others to this risk and how it may be reduced, we describe our non-clinical workplace infection prevention and control measures that have been modified from those originally developed during the 2003 severe acute respiratory syndrome epidemic [5]. url: https://www.ncbi.nlm.nih.gov/pubmed/32267964/ doi: 10.1111/anae.15075 id: cord-007560-nck4f5ny author: Ling, Lowell title: COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics date: 2020-02-20 words: 2803.0 sentences: 135.0 pages: flesch: 40.0 cache: ./cache/cord-007560-nck4f5ny.txt txt: ./txt/cord-007560-nck4f5ny.txt summary: Infection control Outbreak SARS-CoV-2 strategies during mechanical ventilation and prevention of hospital acquired infections is likely to contribute to improved outcomes in critically ill patients. If full airborne precautions are not possible due to limited facilities or overwhelming numbers of cases, other measures that may decrease risk of nosocomial transmission include cohorting of patients in dedicated wards, or physical separation, supported by disciplined use of PPE, universal contact and droplet precautions and adequate ward ventilation [15, [19] [20] [21] . Within the ICU, and with HCW protected by high-level PPE (including an N95 mask), non-invasive ventilation (NIV) and HFNO use during SARS-CoV and 2009 influenza epidemic was not clearly associated with an increased risk in HCW [24, 25] . Anyone who develops symptoms that could suggest a coronavirus infection are encouraged to call a single emergency number and if COVID-19 is suspected, they are managed at their location by a specialised medical team equipped with PPE to prevent viral contamination, and when necessary, hospitalised in an intensive care unit. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119083/ doi: 10.1016/j.accpm.2020.02.002 id: cord-311585-h4holhit author: Ling, R. title: Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China date: 2020-06-19 words: 3784.0 sentences: 247.0 pages: flesch: 53.0 cache: ./cache/cord-311585-h4holhit.txt txt: ./txt/cord-311585-h4holhit.txt summary: Background The seroprevalence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. This retrospective study estimated the seroprevalence of IgM and IgG and compared the epidemiological characteristics of asymptomatic SARS-CoV-2-infected population. Hubei province including IgM and IgG tests for SARS-CoV-2 antibody, nucleic acid tests from March 26 to April 28, 2020 among people aged 16-64 years who went back to work. Clinical data were collected from March 26 to April 28, 2020, including serum IgG positivity and IgM positivity or negative results for SARS-CoV-2 antibodies, nucleic acid testing, clinical symptoms, previous medical history, and chest CT. . https://doi.org/10.1101/2020.06.16.20132423 doi: medRxiv preprint study, the IgG seroprevalence was higher in females than in males, indicating that women were more likely to have asymptomatic infections. abstract: Background The seroprevalence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. Few studies focus on the diagnosis of COVID-19 patients using serological tests. To detect and assess asymptomatic infections of COVID-19 among people in Wuhan, the epicenter of the COVID-19 pandemic in China, and provide evidence for planning adequate public health measures, we collected and analyzed the clinical data in the Wuhan General Hospital mandatory for 16- to 64-year-old asymptomatic people. This retrospective study estimated the seroprevalence of IgM and IgG and compared the epidemiological characteristics of asymptomatic SARS-CoV-2-infected population. Methods Demographical and radiological data were collected from the Wuhan General Hospital between March 26 and April 28, 2020. Serological tests for IgM and IgG antibodies against SARS-CoV-2 were conducted with a colloidal gold method. Nucleic acid sequences of viruses were detected with RT-PCR. Statistical analyses were carried out using SPSS 20.0 software. Findings Between March 26 and April 28, 2020, 18,391 asymptomatic back-to-work participants were enrolled. Among them, 89 had positivity for IgM (0.48%, 95% confidence interval (CI): 0.38-0.58%); 620 cases had IgG positivity (3.37%, 95% CI: 3.11-3.64%), and 650 cases had either IgG positivity or IgM positivity (3.53%, 95% CI: 3.26-3.80%). After standardizing for the genders and ages in the population of Wuhan, the overall standardized seroprevalence of IgG was 3.33% (95% CI: 3.07-3.59%) and the standardized seroprevalence of IgG was 3.01% (95% CI: 2.69-3.33%) among males and 3.66% (95 % CI: 3.23-4.09%) among females. The standardized seroprevalence of IgG was higher in women than in men with a significant difference ({chi}2 = 2,060.3, p < 0.01). By a detection method adjustment, the seroprevalence of IgG was 1.57% (95% CI: 1.39-1.75%) in all medical records, of which males were 1.96% (95% CI: 1.64-2.28%), and females were 1.19% (95% CI: 0.99-1.39%). The assay-adjusted seroprevalence of IgG was higher in women than in men, and the difference was significant ({chi}2 = 5,871.0, p < 0.01). The differences were significant for the seroprevalence of IgG among people who went back to work in different categories of workplace ({chi}2 = 198.44, p < 0.01). The differences in seroprevalence for IgG positivity or IgM positivity among people who went back to work in different urban and rural areas was also significant ({chi}2 = 45.110, p < 0.01). Calculated as IgG and/or IgM antibody positivity, the number of new infections was reduced by 64.8% from March 26 to April 28, 2020. Based on the census population aged 16-64 years in Wuhan in 2017, we estimated that 172,340 (95% CI: 157,568-187,112) asymptomatic people aged 16-64 years were infected with SARS-CoV-2 in Wuhan between March 25 and April 28, 2020. This estimate was 3.4-times higher than the officially reported 50,333 infections on April 28. Interpretation The seropositivity rate in Wuhan indicated that RT-PCR-confirmed patients only represented a small part of the total number of cases. Seropositivity progressively decreased in the Wuhan population from March 26 to April 28, 2020, comparable to Japan and Denmark, but well below the level reported in New York, Iran, Italy, and Germany. The prevalence of asymptomatic infection was higher in women than in men among people who went back to work in Wuhan. The low seroprevalence suggests that most of the population remains susceptible to COVID-19. Funding The Emergency Management Project of the National Natural Science Foundation of China (81842035) and Advisory Research Project of the Chinese Academy of Engineering in 2019 (2019-XZ-70). url: https://doi.org/10.1101/2020.06.16.20132423 doi: 10.1101/2020.06.16.20132423 id: cord-320428-sg3srt8r author: Ling, Zhoukun title: Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings date: 2020-03-12 words: 513.0 sentences: 39.0 pages: flesch: 52.0 cache: ./cache/cord-320428-sg3srt8r.txt txt: ./txt/cord-320428-sg3srt8r.txt summary: title: Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings In this family, a 10-year-old child had no clinical symptoms, but showed ground glass lung opacification on CT, subsequently, the patient presented positive for the SARS-CoV-2 nucleic acid by real time polymerase chain reaction (RT-PCR). Therefore, these findings indicated the clinical symptoms were not essential components of SARS-CoV-2 infection. In our observation, we found that four patients with SARS-CoV-2 infection, showed no clinical symptoms or abnormal chest CT images. It is worth noting that, the clinical symptoms and radiological abnormalities are not the essential components of SARS-CoV-2 infection. If some people have a history of exposure to infected areas or contact with patients, regardless of radiological manifestations or clinical symptoms, medical observation and home isolation or SARS-CoV-2 nucleic acid tests are quite important to rule out infection. SARS-CoV-2 viral load in upper respiratory specimens of infected patients abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0720048X20301455 doi: 10.1016/j.ejrad.2020.108956 id: cord-269130-zsem29ss author: Lingappan, K. title: Understanding the age divide in COVID-19: why are children overwhelmingly spared? date: 2020-07-01 words: 3121.0 sentences: 163.0 pages: flesch: 45.0 cache: ./cache/cord-269130-zsem29ss.txt txt: ./txt/cord-269130-zsem29ss.txt summary: The differences in the clinical course are highlighted by the lack of progression of the SARS-CoV-2 infection beyond mild symptoms in a majority of children, whereas in adults the disease progresses to acute lung injury and an acute respiratory distress syndrome (ARDS)-like phenotype with high mortality. The pathophysiological mechanisms leading to decreased lung injury in children may involve the decreased expression of the mediators necessary for viral entry into the respiratory epithelium and differences in the immune system responses in children. On the other hand, the heightened immune response to the virus in many adult patients can lead to the worsening of lung disease with SARS-CoV-2 infection (37) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice abstract: The rapid emergence and subsequent global dissemination of SARS-CoV-2 disease (COVID-19) has resulted in over 4 million cases worldwide. The disease has a marked predilection for adults, and children are relatively spared. Understanding the age-based differences in pathophysiological pathways and processes relevant to the onset and progression of disease both in the clinical course and in experimental disease models may hold the key to the identification of therapeutic targets. The differences in the clinical course are highlighted by the lack of progression of the SARS-CoV-2 infection beyond mild symptoms in a majority of children, whereas in adults the disease progresses to acute lung injury and an acute respiratory distress syndrome (ARDS)-like phenotype with high mortality. The pathophysiological mechanisms leading to decreased lung injury in children may involve the decreased expression of the mediators necessary for viral entry into the respiratory epithelium and differences in the immune system responses in children. Specifically, decreased expression of proteins, including angiotensin-converting enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2) in the airway epithelium in children may prevent viral entry. The immune system differences may include a relative preponderance of CD4(+) T cells, decreased neutrophil infiltration, decreased production of proinflammatory cytokines, and increased production of immunomodulatory cytokines in children compared with adults. Notably, the developing lung in children may have a greater capacity to recover and repair after viral infection. Understanding the relative contributions of the above processes to the protective phenotype in the developing lung can guide the trial of the appropriate therapies in adults. url: https://doi.org/10.1152/ajplung.00183.2020 doi: 10.1152/ajplung.00183.2020 id: cord-326341-egtnqlov author: Liotti, Flora Marzia title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 words: 514.0 sentences: 35.0 pages: flesch: 60.0 cache: ./cache/cord-326341-egtnqlov.txt txt: ./txt/cord-326341-egtnqlov.txt summary: title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus abstract: nan url: https://api.elsevier.com/content/article/pii/S1198743X20305838 doi: 10.1016/j.cmi.2020.09.030 id: cord-304013-nzigx0k0 author: Lipinski, Tom title: Review of ventilation strategies to reduce the risk of disease transmission in high occupancy buildings date: 2020-09-13 words: 12834.0 sentences: 557.0 pages: flesch: 47.0 cache: ./cache/cord-304013-nzigx0k0.txt txt: ./txt/cord-304013-nzigx0k0.txt summary: This paper will discuss the factors affecting air particle properties in-terms of flow dynamics and critically analyse current ventilation strategies and mechanisms and identify areas for improvement in the search for the reduction of indoor infections. The study by the University of Oregon [54, 58] observed that Natural Ventilation with a plentiful supply of fresh air dilutes and removes contaminated air much more effectively than fan driven, recirculated air movement, significantly reducing the risk of infection, as shown in Figure 17 . Displacement ventilation with a generously sized natural inlet is preferred as it can move stale, contaminated air directly to the exhaust of the room in a laminar fashion whilst the concentration of small droplets and airborne particles in the indoor air is significantly reduced. abstract: An unforeseen pandemic is facing the world caused by a corona virus known as SARS-CoV-2. Numerous measures are being put in place to try and reduce the spread of this deadly disease, with the most effective response to the outbreak being mass quarantines, a public health technique borrowed from the Middle Ages. The widely accepted main transmission mechanism is through droplet borne pathways. However, many researchers and studies are considering that this virus can also spread via the airborne route and remain for up to three hours in the air. This is leading to questions as to whether enough is being done regarding ventilation to reduce the risk of the spread of this or other diseases that may be air borne. Ventilation and air conditioning systems are the main focus when it comes to the transmission of such deadly pathogens and should be appropriately designed and operated. This paper reviews and critically evaluates the current ventilation strategies used in buildings to assess the state of the art and elaborates if there is room for further development, especially for high occupancy buildings, to reduce or eradicate the risk of pathogen transmission and adapt ventilation measures to new threats posed by pandemics. url: https://api.elsevier.com/content/article/pii/S266620272030032X doi: 10.1016/j.ijft.2020.100045 id: cord-319749-je0l22l5 author: Lippi, Alice title: SARS‐CoV‐2: At the Crossroad Between Aging and Neurodegeneration date: 2020-04-24 words: 3090.0 sentences: 190.0 pages: flesch: 43.0 cache: ./cache/cord-319749-je0l22l5.txt txt: ./txt/cord-319749-je0l22l5.txt summary: Here, we posit that severe acute respiratory distress syndrome coronavirus 2 infection may, in the long-term, lead to accelerated aging phenotypes in survivors, not only in affected tissues but also in other organs, including the brain. 1, 2 As the causative agent of coronavirus disease 2019 (COVID19) , the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) is now responsible for the third coronavirus-associated pandemic in recent human history. SARS-CoV-2 proteins with human proteins from several aging-related pathways, like vesicle trafficking (Nsp6, Nsp7, Nsp10, Nsp13, Nsp15, Orf3a, E, and Orf8), lipid modifications (Spike), RNA processing and regulation (Nsp8, N), ubiquitin ligases (Orf10), and mitochondrial activity (Nsp4, Nsp8, and Orf9c). Moreover, Hsp40-NP interaction plays a role at the late stages of infection by inhibiting protein kinase R (PKR) activation, essential in the antiviral response of the host. 25 The infection with SARS-CoV induces the unfolded protein response (UPR) in the host cell. abstract: The recent global severe acute respiratory distress syndrome coronavirus 2 pandemic is changing the world we live in. As we learn about the virus and the pandemic, it is becoming evident that it is an age-associated problem that affects the human population. Severe acute respiratory distress syndrome coronavirus 2 is one of seven coronaviruses known to infect humans. These are large enveloped non-segmented positive-sense RNA viruses. Our knowledge of severe acute respiratory distress syndrome coronavirus 2 is extremely recent but is growing daily. There are currently no antiviral treatments against the virus or vaccines for its prevention. The long term consequences of the infection on human health remain uncertain but extrapolations can be made about the potential effects of the virus on cellular lifespan as well as on organismal healthspan. Here, we posit that severe acute respiratory distress syndrome coronavirus 2 infection may, in the long-term, lead to accelerated aging phenotypes in survivors, not only in affected tissues but also in other organs, including the brain. Since some of the effects could manifest months or years after infection, it will be necessary to follow carefully people affected by coronavirus disease 2019. Keeping accurate registries may enable us to, in the future, establish connections with aging-associated disorders, such as Parkinson's disease and other neurodegenerative disorders. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32291797/ doi: 10.1002/mds.28084 id: cord-270116-r2rnnsfh author: Lippi, Giuseppe title: Current laboratory diagnostics of coronavirus disease 2019 (COVID-19) date: 2020-05-11 words: 4742.0 sentences: 192.0 pages: flesch: 37.0 cache: ./cache/cord-270116-r2rnnsfh.txt txt: ./txt/cord-270116-r2rnnsfh.txt summary: As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized especially by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. Recent studies have also been published on the possibility to use rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for SARS-CoV-2 detection, but additional evidence is needed at this point in time for validating their routine usage in COVID-19 diagnostics (38, 39) . As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. abstract: Laboratory medicine provides an almost irreplaceable contribution to the diagnostic reasoning and managed care of most human pathologies. The novel coronavirus disease 2019 (COVID-19) is not an exception to this paradigm. Although the relatively recent emergence does not allow to draw definitive conclusions on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics, some standpoints can be conveyed. First and foremost, it seems now clear that we will be living together with this virus for quite a long time, so that our vigilance and responsiveness against the emergence of new local outbreaks shall be maintained at the highest possible levels. The etiological diagnosis of COVID-19 is, and will remain for the foreseeable future, deeply based on direct identification of viral RNA by means of molecular biology techniques in biological materials, especially upper and lower respiratory tract specimens. Whether other materials, such as blood, urine, stools, saliva and throat washing, will become valid alternatives has not been unequivocally defined so far. As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized especially by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. Whether these antibodies will have persistent neutralizing activity against the virus is still to be elucidated on individual and general basis. The availability of rapid tests for detecting either viral antigens or anti-SARS-CoV-2 antibodies are a potentially viable opportunity for purposes of epidemiologic surveillance, though more information is needed on accuracy and reliability of these portable immunoassays. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420937/ doi: 10.23750/abm.v91i2.9548 id: cord-256233-k9hdq3z8 author: Lipsky, Martin S. title: Men and COVID-19: A Pathophysiologic Review date: 2020-09-16 words: 4620.0 sentences: 233.0 pages: flesch: 47.0 cache: ./cache/cord-256233-k9hdq3z8.txt txt: ./txt/cord-256233-k9hdq3z8.txt summary: The plausible theories underlying these observations include sex-related differences in angiotensin-converting enzyme 2 receptors, immune function, hormones, habits, and coinfection rates.In this review we examine these factors and explore the rationale as to how each may impact COVID-19. Epidemiological evidence from influenza outbreaks and pandemics also reveals a higher morbidity and mortality for menthan that for women in some age groups (Klein et al., 2012) .In animal studies, male animals have poorer immune responses when exposed to the coronavirus and experience more damage to their lungs (Vermillion et al., 2018) .For both SARS and the MERS coronavirus outbreaks, men fared worse than women did. A recent German study found that that critically ill male COVID-19 patients suffer from severe testosterone and dihydrotestosterone deficiencies and concluded that androgens are required to mount a strong antiviral immune response to combat infection in men (Schroeder et al., 2020) . abstract: Coronaviruses are single-stranded ribonucleic acid viruses that can cause illnesses in humans ranging from the common cold to severe respiratory disease and even death.In March 2020, the World Health Organization declared the 2019 novel coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the first pandemic. Compared to women, most countries with available data report that men with COVID-19 have greater disease severity and higher mortality. Lab and animal data indicate that men respond differently to the SARS-CoV-2 infection, offering possible explanations for the epidemiologic observations. The plausible theories underlying these observations include sex-related differences in angiotensin-converting enzyme 2 receptors, immune function, hormones, habits, and coinfection rates.In this review we examine these factors and explore the rationale as to how each may impact COVID-19. Understanding why men are more likely to experience severe disease can help in developing effective treatments, public health policies, and targeted strategies such as early recognition and aggressive testing in subgroups. url: https://doi.org/10.1177/1557988320954021 doi: 10.1177/1557988320954021 id: cord-271174-886xc1n3 author: Lipworth, Brian title: Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection date: 2020-04-18 words: 2344.0 sentences: 136.0 pages: flesch: 38.0 cache: ./cache/cord-271174-886xc1n3.txt txt: ./txt/cord-271174-886xc1n3.txt summary: High-risk patients requiring hospitalization for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are those over 60 years old, males, obese, smokers, and those with common comorbidities including hypertension, cardiovascular disease, diabetes, and chronic lung disease. The cytokine cascade resulting from acute severe SARS-CoV-2 infection, with downstream IL-6 activation considered to be a hallmark feature in terms of progression of COVID-19 pneumonia to hyperinflammation and ARDS. Also shown are the putative mechanisms of action for bromhexine and hydroxychloroquine in attenuating upstream SARS-CoV-2 tissue binding, the effect of antivirals on replication, azithromycin as an antiviral and immunomudulator, nonspecific cytokine suppression by corticosteroids, together with the selective downstream effect of IL-6 blockade with tocilizumab or sarilumab and effects of anti-TNF and interferon beta-1-a. Patients with eosinophilic asthma and COPD should continue to use ICS-containing therapy to maintain optimal control and protect against viral insults including SARS-CoV-2 infection. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2213219820303652 doi: 10.1016/j.jaip.2020.04.014 id: cord-334773-yw2qgv13 author: Lisco, Giuseppe title: Hypothesized mechanisms explaining poor prognosis in type 2 diabetes patients with COVID-19: a review date: 2020-08-10 words: 7901.0 sentences: 359.0 pages: flesch: 32.0 cache: ./cache/cord-334773-yw2qgv13.txt txt: ./txt/cord-334773-yw2qgv13.txt summary: This concern has been further confirmed by the results of a cohort study among 85 fatal cases of COVID-19 in Wuhan, hence defining DM as a potentially harmful comorbidity predisposing to worse clinical course or death once SARS-CoV-2 infection occurred [49] . Different hypothesis should be considered for explaining this clinical phenomenon, including glucose control at baseline and during the infection course, pathophysiology and immune system response in SARS-CoV-2 infected patients with T2D, diabetes-related comorbidities and concomitant medications. In conclusion, diabetic patients especially elderly individuals and those with worse baseline glucose control may exhibit immune system dysregulation that predispose them to a less effective response against SARS-CoV-2 and to a dysfunctional inflammation that requires to be carefully monitored in confirmed cases of COVID-19, for preventing or avoiding a harmful progression of the disease. Immune response and systemic inflammation play a crucial role in SARS-CoV-2 infection, particularly in case of severe clinical course of the disease. abstract: PURPOSE: Epidemiological data suggest that comorbid patients, mostly those with type 2 diabetes (T2D), are predisposed to poor prognosis in Coronavirus disease 2019 (COVID-19), leading to serious healthcare concerns. The aim of the present manuscript is to review the main relevant mechanisms possibly contributing to worsen the clinical course of COVID-19 in T2D. RESULTS: Poor glucose control, high glycaemic variability and diabetes-related comorbidities at baseline, particularly cardiovascular diseases and obesity, contribute in worsening the prognosis in the above-mentioned cluster of patients. Moreover, both a lower efficient innate immune system response and cytokine dysregulation predispose patients with T2D to impaired viral clearance and more serious pulmonary and systemic inflammation once the SARS-CoV-2 infection occurred. Inconclusive data are currently available for specifically indicate or contraindicate concurrent medications for managing T2D and its comorbidities in infected patients. CONCLUSIONS: T2D individuals should be considered as more vulnerable to COVID-19 than general population, and thus require adequate advices about hygienic tips to protect themselves during the pandemic. A careful management of glucose levels and diabetes-related comorbidities remains essential for avoiding further complications, and patient monitoring during the pandemic should be performed also at distance by means of telemedicine. Further studies are needed to clarify whether medications normally used for managing T2D and its associated comorbidities could have a protective or detrimental effect on COVID-19 clinical course. url: https://doi.org/10.1007/s12020-020-02444-9 doi: 10.1007/s12020-020-02444-9 id: cord-345371-pjbviagq author: Lisi, Lucia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 words: 10648.0 sentences: 512.0 pages: flesch: 37.0 cache: ./cache/cord-345371-pjbviagq.txt txt: ./txt/cord-345371-pjbviagq.txt summary: The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. Here, we review the recently published literature on the pharmacological treatments used so far and/or undergoing evaluation in clinical trials, with focus on the biochemical mechanisms of action of repurposed or investigational drugs, classified as agents directly targeting the virus ( Figure 1 and Table 1 ) and those used to treat the respiratory distress and inflammation associated with the cytokine release syndrome ( Figure 2 and Table 2 ). abstract: On March 11, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) a global pandemic. As of July 2020, SARS-CoV-2 has infected more than 14 million people and provoked more than 590,000 deaths, worldwide. From the beginning, a variety of pharmacological treatments has been empirically used to cope with the life-threatening complications associated with Corona Virus Disease 2019 (COVID-19). Thus far, only a couple of them and not consistently across reports have been shown to further decrease mortality, respect to what can be achieved with supportive care. In most cases, and due to the urgency imposed by the number and severity of the patients’ clinical conditions, the choice of treatment has been limited to repurposed drugs, approved for other indications, or investigational agents used for other viral infections often rendered available on a compassionate-use basis. The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. In several months, an exceptionally large number of clinical trials have been designed to evaluate the safety and efficacy of anti-COVID-19 therapies in different clinical settings (treatment or pre- and post-exposure prophylaxis) and levels of disease severity, but only few of them have been completed so far. This review focuses on the molecular mechanisms of action that have provided the scientific rationale for the empirical use and evaluation in clinical trials of structurally different and often functionally unrelated drugs during the SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32710969/ doi: 10.1016/j.bcp.2020.114169 id: cord-340201-ai4apr4w author: List, Wolfgang title: Occurrence of SARS-CoV-2 in the intraocular milieu date: 2020-09-28 words: 1439.0 sentences: 112.0 pages: flesch: 65.0 cache: ./cache/cord-340201-ai4apr4w.txt txt: ./txt/cord-340201-ai4apr4w.txt summary: All individuals were previously positive in nasopharyngeal swabbing and cause of death was respiratory failure due to SARS-CoV-2 infection. (Chen et al., 2020; Siedlecki et al., 2020; Wu et al., 2020; Xia et al., 2020; Zhang et al., 2020) In this study, we tested for SARS-CoV-2 in the aqueous humor and the vitreous representing the intraocular milieu. In sixteen individuals with confirmed SARS-CoV-2 infection samples from the vitreous and aqueous humor were taken during postmortem examinations. PCR was negative for all aqueous humor and vitreous samples for SARS-CoV-2. (Table 1) In this case series, SARS-CoV-2 could not be found in the aqueous humor and in the vitreous. In these patients, SARS-CoV-2 might be found in the aqueous humor and/or vitreous. In conclusion, this case series did not find SARS-CoV-2 in aqueous humor and vitreous samples during postmortem examinations of 16 patients with cause of death by SARS-CoV-2 infections. abstract: The purpose of this research is to study the intraocular occurrence of SARS-CoV-2. In postmortem examinations, aqueous humor and the vitreous samples were collected. All individuals were previously positive in nasopharyngeal swabbing and cause of death was respiratory failure due to SARS-CoV-2 infection. Testing was done using quantitative RT-PCR. We included 16 aqueous humor and 16 vitreous samples for PCR testing. None of the results was positive for SARS-CoV-2. Human GAPDH genes to verify the presence of RNA was present in all aqueous humor samples (16/16, 100%) and 15/16 (93.8%) vitreous samples. In conclusion, this case series found no evidence of SARS-CoV-2 in the intraocular milieu. url: https://doi.org/10.1016/j.exer.2020.108273 doi: 10.1016/j.exer.2020.108273 id: cord-282738-aqc9gxlw author: Liu, Anding title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 words: 179.0 sentences: 22.0 pages: flesch: 64.0 cache: ./cache/cord-282738-aqc9gxlw.txt txt: ./txt/cord-282738-aqc9gxlw.txt summary: key: cord-282738-aqc9gxlw authors: Liu, Anding; Li, Ying; Wan, Zhengce; Wang, Wenjie; Lei, Xiaomei; Lv, Yongman title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 cord_uid: aqc9gxlw This cross-sectional study examines the seropositive prevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, by sex and age group. Nasal swab specimens were obtained to test for SARS-CoV-2 by real-time RT-PCR. Total RNAs from nasal swab specimens was extracted by a viral nucleic acid kit The 95% CI of the seroprevalence was calculated from binomial probabilities using Wilson''s methods. Chisquare test was used for comparison of seroprevalence between groups, and logistic Association of Public Health Interventions With the Epidemiology of the COVID-19 Outbreak in Wuhan, China Antibody responses to SARS-CoV-2 in patients with COVID-19 Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely correlated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients abstract: This cross-sectional study examines the seropositive prevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, by sex and age group. url: https://www.ncbi.nlm.nih.gov/pubmed/33095246/ doi: 10.1001/jamanetworkopen.2020.25717 id: cord-327405-xgtqfwyn author: Liu, Bing title: Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients date: 2020-10-19 words: 3725.0 sentences: 199.0 pages: flesch: 52.0 cache: ./cache/cord-327405-xgtqfwyn.txt txt: ./txt/cord-327405-xgtqfwyn.txt summary: 37 non-severe patients with persistent SARS-CoV-2 presence that were transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to the PP (persistently positive) group, which was further allocated to PPP group (n = 19) and PPN group (n = 18), according to their testing results after 7 days (N = negative). Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. These results indicated that non-severe COVID-19 patients (PA group) have already dysregulated immune system at disease onset, and those with persistent SARS-CoV-2 shedding could restore this abnormality to certain level. Together, these results indicated that the abnormalities in adaptive immune cells, but not symptoms and laboratory indicators, were associated with SARS-CoV-2 viral RNA detection in non-severe COVID-19 patients. abstract: COVID-19 has been widely spreading. We aimed to examine adaptive immune cells in non-severe patients with persistent SARS-CoV-2 shedding. 37 non-severe patients with persistent SARS-CoV-2 presence that were transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to the PP (persistently positive) group, which was further allocated to PPP group (n = 19) and PPN group (n = 18), according to their testing results after 7 days (N = negative). Epidemiological, demographic, clinical and laboratory data were collected and analyzed. Data from age- and sex-matched non-severe patients at disease onset (PA [positive on admission] patients, n = 37), and lymphocyte subpopulation measurements from matched 54 healthy subjects were extracted for comparison (HC). Compared with PA patients, PP patients had much improved laboratory findings. The absolute numbers of CD3(+) T cells, CD4(+) T cells, and NK cells were significantly higher in PP group than that in PA group, and were comparable to that in healthy controls. PPP subgroup had markedly reduced B cells and T cells compared to PPN group and healthy subjects. Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Monitoring lymphocyte subpopulations could be clinically meaningful in identifying fully recovered COVID-19 patients. url: https://doi.org/10.1038/s41598-020-73955-8 doi: 10.1038/s41598-020-73955-8 id: cord-348065-0tkx7aas author: Liu, Bing title: Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients date: 2020-03-30 words: 2285.0 sentences: 124.0 pages: flesch: 54.0 cache: ./cache/cord-348065-0tkx7aas.txt txt: ./txt/cord-348065-0tkx7aas.txt summary: Methods 37 non-severe patients with persistent SARS-CoV-2 presence transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to PP (persistently positive) group, which was further allocated to PPP group (n=19) and PPN group (n=18), according to their testing results after 7 days (N=negative). Conclusion Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Next, we determined the abnormalities for each parameters Lymphopenia was observed at illness onset in 72.8% of non-severe COVID-19 patients (the PA group) in our study, which is similar to those reported by Zhang et al [15] (75.4%), Mo et al [17] (73.5%), Wang et al [27] (70.3%), and Guan et al [2] (83.2%), suggesting the involvement of lymphocytes in the early phase of SARS-CoV-2 infection. Together, these results suggest that measurement of these lymphocyte subpopulations could be used to distinguish non-severe patients with persistent viral presence from healthy subjects and those turned negative, and thus have clinical relevance for discharge management. abstract: Background: COVID-19 has been widely spreading. We aim to examine adaptive immune cells in non-severe patients with persistent SARS-CoV-2 shedding. Methods 37 non-severe patients with persistent SARS-CoV-2 presence transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to PP (persistently positive) group, which was further allocated to PPP group (n=19) and PPN group (n=18), according to their testing results after 7 days (N=negative). Epidemiological, demographic, clinical and laboratory data were collected and analyzed. Data from age- and sex-matched non-severe patients at disease onset (PA [positive on admission] patients, n=37), and lymphocyte subpopulation measurements from matched 54 healthy subjects were extracted for comparison. Results Compared with PA patients, PP patients had much improved laboratory findings, including WBCs, neutrophils, lymphocytes, neutrophil-to-lymphocyte ratio, albumin, AST, CRP, SAA, and IL-6. The absolute numbers of CD3+ T cells, CD4+ T cells, and NK cells were significantly higher in PP group than that in PA group, and were comparable to that in healthy controls. PPP subgroup had markedly reduced B cells and T cells compared to PPN group and healthy subjects. Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. Conclusion Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Monitoring lymphocyte subpopulations could be clinically meaningful in identifying fully recovered COVID-19 patients. Abbreviations COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; HC: Healthy controls. url: https://doi.org/10.1101/2020.03.26.20044768 doi: 10.1101/2020.03.26.20044768 id: cord-343818-pj1oludh author: Liu, Chan title: Children with COVID-19 behaving milder may challenge the public policies: a systematic review and meta-analysis date: 2020-09-01 words: 4850.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-343818-pj1oludh.txt txt: ./txt/cord-343818-pj1oludh.txt summary: We searched PubMed, Google Scholar, Web of Science, and several Chinese databases for studies presenting characteristics of children confirmed with Coronavirus Disease 2019 (COVID-19) from December 12, 2019 to May 10, 2020. The studies included in this meta-analysis should meet the following criteria: (1) all types of studies either retrospective or prospective (e.g. cohort, cross-sectional study, case report, case series); (2) studies reporting information regarding COVID-19; (3) studies describing clinical characteristics of pediatric patients (0-19 years) diagnosed by RT-PCR; (4) clinical data of more than five cases can be drawn from the articles. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha Clinical features of coronavirus disease 2019 in children aged <18 years in Jiangxi, China: an analysis of 23 cases abstract: BACKGROUND: The emerging virus is rampaging globally. A growing number of pediatric infected cases have been reported. Great efforts are needed to cut down the transmission. METHODS: A single-arm meta-analysis was conducted. We searched PubMed, Google Scholar, Web of Science, and several Chinese databases for studies presenting characteristics of children confirmed with Coronavirus Disease 2019 (COVID-19) from December 12, 2019 to May 10, 2020. Quality Appraisal of Case Series Studies Checklist was used to assess quality and publication bias was analyzed by Egger’s test. Random-effect model was used to calculate the pooled incidence rate (IR) or mean difference (MD) with 95% confidence intervals (CI), or a fixed model instead when I(2) < 50%. We conducted subgroup analysis according to geographic region. Additionally, we searched United Nations Educational Scientific and Cultural Organization to see how different countries act to the education disruption in COVID-19. RESULTS: 29 studies with 4300 pediatric patients were included. The mean age was 7.04 (95% CI: 5.06–9.08) years old. 18.9% of children were asymptomatic (95% CI: 0.121–0.266), 37.4% (95% CI: 0.280–0.474) had no radiographic abnormalities. Besides, a proportion of 0.1% patients were admitted to intensive care units (0, 95% CI: 0.000–0.013) and four deaths were reported (0, 95% CI: 0.000–0.000). Up to 159 countries have implemented nationwide school closures, affecting over 70% of the world’s students. CONCLUSION: Children were also susceptible to SARS-CoV-2, while critical cases or deaths were rare. Characterized by mild presentation, the dilemma that children may become a potential spreader in the pandemic, while strict managements like prolonged school closures, may undermine their well-beings. Thus, the public policies are facing challenge. url: https://doi.org/10.1186/s12887-020-02316-1 doi: 10.1186/s12887-020-02316-1 id: cord-294861-inlaz4od author: Liu, Chen title: Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series date: 2020-09-15 words: 3240.0 sentences: 167.0 pages: flesch: 51.0 cache: ./cache/cord-294861-inlaz4od.txt txt: ./txt/cord-294861-inlaz4od.txt summary: title: Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series METHODS: We retrospectively analyzed the diagnosis and treatment of six gynecological cancer patients infected with SARS-CoV-2 in Tongji Hospital in Wuhan from January 30 to March 25, 2020. RESULTS: We observed a high rate of nosocomial SARS-CoV-2 infection among these six gynecological cancer patients, who were in a low immune state. reported a case in which a lung cancer patient infected with SARS-CoV-2 recovered from pneumonia while continuing initial targeted therapy (10) . After antivirus and anti-infection treatment, combined with G-CSF (Recombinant Human Granulocytestimulating Factor) and immunity enhancing drugs, she was finally discharged from hospital after 35 days (Figure 1) . Moreover, cancer patients showed a state of low immunity after surgery or radio-/chemo-therapy treatment, so they became more susceptible to COVID-19 (12) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: OBJECTIVE: Recently, the number of gynecological cancer patients infected with SARS-CoV-2 has been increasing. This article was committed to studying the influence of gynecological tumor treatment history compared to the Coronavirus Disease 2019 (COVID-19), which was of great significance for the treatment of gynecological cancer patients during the outbreak of COVID-19. METHODS: We retrospectively analyzed the diagnosis and treatment of six gynecological cancer patients infected with SARS-CoV-2 in Tongji Hospital in Wuhan from January 30 to March 25, 2020. To better explain the treatment of gynecological cancer patients during the epidemic of COVID-19, we summarized the case characteristics, auxiliary examination, treatment plan, and outcome of these six patients. RESULTS: We observed a high rate of nosocomial SARS-CoV-2 infection among these six gynecological cancer patients, who were in a low immune state. Also, due to the influence of cancer treatment history, COVID-19-related atypical symptoms became the first symptom of COVID-19 in some cases, which increased the difficulty of diagnosis. Furthermore, in terms of treatment for these cases, immune boosters and reagents that raised white blood cells were applied, except for in symptomatic antiviral treatment. At present, all patients in this study were discharged from the hospital with a good prognosis. CONCLUSION: After cancer-related treatment, the gynecological cancer patients became more susceptible to COVID-19. Besides, the history of cancer treatment made the diagnosis of COVID-19 difficult, which also affected the treatment of COVID-19. Therefore, we put forward the corresponding therapy suggestions for gynecological cancer patients during the outbreak of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33042803/ doi: 10.3389/fonc.2020.01606 id: cord-322329-zqjiiy4l author: Liu, Chunyu title: Establishment of a reference panel for the detection of anti-SARS-CoV antibodies date: 2007-06-30 words: 4227.0 sentences: 200.0 pages: flesch: 56.0 cache: ./cache/cord-322329-zqjiiy4l.txt txt: ./txt/cord-322329-zqjiiy4l.txt summary: In this study, we have expressed and purified severe acute respiratory syndrome (SARS) structural proteins and their fragments and developed indirect enzyme-linked immunosorbent assays (ELISAs) that detect antibodies against the SARS N, N1, N2, S1, SC, S2, and M proteins as well as the human coronavirus OC43 and 229E N proteins. In this study, SARS N and S proteins and their fragments were expressed and purified, and samples from convalescent SARS patients and blood donors were screened with enzyme-linked immunosorbent assays (ELISAs) that were developed with these proteins. IgG and IgM immunoglobulin were detected in the 58 SARS convalescent plasma specimens using an indirect ELISA developed with entire virus antigens. In this study, the indirect ELISAs were developed with different fragments of SARS structure proteins and used to detect antibodies in 58 SARS plasma specimens donated by convalescent patients 3 months after onset of SARS. abstract: Abstract The immunological assays for detection of antibodies against SARS-CoV were developed in-house and some of them are available commercially. However, the antigens used in these assays differed. In order to validate the reliability of these assays, the standard panel should be established. In this study, we have expressed and purified severe acute respiratory syndrome (SARS) structural proteins and their fragments and developed indirect enzyme-linked immunosorbent assays (ELISAs) that detect antibodies against the SARS N, N1, N2, S1, SC, S2, and M proteins as well as the human coronavirus OC43 and 229E N proteins. These assays were used to screen 58 samples from SARS convalescent patients, 40 serial serum specimens from patients at different phases of SARS infection, and 88 plasma specimens from normal blood donors. The samples from normal blood donors were also tested for antibodies against other respiratory virus. The representative samples were chosen to comprise a reference panel of SARS antibodies that may be used for the detection of SARS. The panel is composed of 25 positive samples, 25 negative samples, 7 diluted samples for anti-N antibody, 6 diluted samples for anti-S antibody, and one sample for validating precision. Comparison of detection results with different SARS antibody assays indicated that our panel should differentiate the specificity and sensitivity of different assays. url: https://www.sciencedirect.com/science/article/pii/S1045105606001151 doi: 10.1016/j.biologicals.2006.11.001 id: cord-335916-fh28qrt7 author: Liu, Cuiwei title: COVID-19 in cancer patients: risk, clinical features, and management date: 2020-08-15 words: 3937.0 sentences: 189.0 pages: flesch: 40.0 cache: ./cache/cord-335916-fh28qrt7.txt txt: ./txt/cord-335916-fh28qrt7.txt summary: Cancer patients are regarded as a highly vulnerable population to SARS-CoV-2 infection and development of more severe COVID-19 symptoms, which is possibly due to the systemic immunosuppressive state caused directly by tumor growth and indirectly by effects of anticancer treatment. Another cohort study of 28 COVID-19 cancer patients reported that patients with Stage IV disease accounted for a higher percentage of infected patients (35.7%), suggesting that later stage cancer patients may be more susceptible to SARS-CoV-2 5 . Notably, a retrospective study of 28 COVID-19 cancer patients found that anti-cancer treatment within 14 days before COVID-19 diagnosis was more frequently associated with severe clinical events due to SARS-CoV-2 infection 5 . The higher proportion of COVID-19 patients with cancer requiring oxygen therapy and mechanical ventilation may be related to more severe disease and an immunosuppressive state in cancer patients, who are more susceptible to secondary lung infection with other pathogens. abstract: A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the world, prompting the World Health Organization to declare the coronavirus disease of 2019 (COVID-19) a public health emergency of international concern. Cancer patients are regarded as a highly vulnerable population to SARS-CoV-2 infection and development of more severe COVID-19 symptoms, which is possibly due to the systemic immunosuppressive state caused directly by tumor growth and indirectly by effects of anticancer treatment. Currently, much effort has been directed toward studying the pathogenesis and treatment of COVID-19, but the risk profiles, prognoses, and treatment outcomes in cancer patients remain unclear. Based on the current literature, we summarize the risk profiles, clinical and biochemical characteristics, and therapy outcomes of COVID-19 infections in cancer patients. The challenges in the clinical care of cancer patients with COVID-19 are discussed. The goal of this review is to stimulate research to better understand the biological impact and prognoses of COVID-19 infections in cancer patients, thus facilitating improvement of the clinical management of these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32944387/ doi: 10.20892/j.issn.2095-3941.2020.0289 id: cord-350309-j4oh1z8m author: Liu, D. X. title: Coronavirus envelope protein: A small membrane protein with multiple functions date: 2007-05-29 words: 3403.0 sentences: 167.0 pages: flesch: 48.0 cache: ./cache/cord-350309-j4oh1z8m.txt txt: ./txt/cord-350309-j4oh1z8m.txt summary: The E proteins from infectious bronchitis virus (IBV) and mouse hepatitis virus (MHV) are translated from the third and second ORFs of mRNA 3 and 5 of the respective viruses by a cap-independent, internal ribosomal entry mechanism [6] [7] [8] [9] [10] [11] [12] . This modification is unique to SARS-CoV E protein, and it is still unknown whether the modification can also be detected in virus-infected cells and in virions. However, the membrane topologies of SARS-CoV E protein in virions and in virusinfected cells are still unknown. Similar to other viroporins [46] , expression of SARS-CoV and MHV E protein enhanced the membrane permeability of bacterial and mammalian cells [47, 48] . These results indicate that the ion channel activity of coronavirus E protein is important for virus replication, especially in the case of some coronaviruses, such as MHV. Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells abstract: Coronavirus envelope protein is a small membrane protein and minor component of the virus particles. It plays important roles in virion assembly and morphogenesis, alteration of the membrane permeability of host cells and virus-host cell interaction. Here we review recent progress in characterization of the biochemical properties, membrane topology and functions of the protein. url: https://www.ncbi.nlm.nih.gov/pubmed/17530462/ doi: 10.1007/s00018-007-7103-1 id: cord-277253-vy0mvzeb author: Liu, Hongbo title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date: 2020-04-11 words: 2265.0 sentences: 154.0 pages: flesch: 52.0 cache: ./cache/cord-277253-vy0mvzeb.txt txt: ./txt/cord-277253-vy0mvzeb.txt summary: title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors. Inspired by the previous studies, several covalent inhibitors were experimentally identified to inhibit the 3CL pro activity and viral replication of SARS-CoV-2, and some of the complex crystal structures were solved [14, 15] . baicalensis inhibits SARS-CoV-2 3CL pro activity and the most active ingredient baicalein exhibits an IC50 of 0.39 M. We also identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CL pro activity at microM concentration. baicalensis and tested its inhibitory activity against SARS-CoV-2 3CL pro . baicalensis extract at different concentrations on SARS-CoV-2 3CL pro activity were 6 shown in Figure 1A . abstract: COVID-19 has become a global pandemic that threatens millions of people worldwide. There is an urgent call for developing effective drugs against the virus (SARS-CoV-2) causing this disease. The main protease of SARS-CoV-2, 3C-like protease (3CLpro), is highly conserved across coronaviruses and is essential for the maturation process of viral polyprotein. Scutellariae radix (Huangqin in Chinese), the root of Scutellaria baicalensis has been widely used in traditional Chinese medicine to treat viral infection related symptoms. The extracts of S. baicalensis have exhibited broad spectrum antiviral activities. We studied the anti-SARS-CoV-2 activity of S. baicalensis and its ingredient compounds. We found that the ethanol extract of S. baicalensis inhibits SARS-CoV-2 3CLpro activity in vitro and the replication of SARS-CoV-2 in Vero cells with an EC50 of 0.74 μg/ml. Among the major components of S. baicalensis, baicalein strongly inhibits SARS-CoV-2 3CLpro activity with an IC50 of 0.39 μM. We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. Our study demonstrates that the extract of S. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors. url: https://doi.org/10.1101/2020.04.10.035824 doi: 10.1101/2020.04.10.035824 id: cord-253513-zn87f1lk author: Liu, Jia title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro date: 2020-03-18 words: 2370.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-253513-zn87f1lk.txt txt: ./txt/cord-253513-zn87f1lk.txt summary: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Jia Liu 1 , Ruiyuan Cao 2 , Mingyue Xu 1,3 , Xi Wang 1 , Huanyu Zhang 1,3 , Hengrui Hu 1,3 , Yufeng Li 1,3 , Zhihong Hu 1 , Wu Zhong 2 and Manli Wang 1 Dear Editor, The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/2019-nCoV) poses a serious threat to global public health and local economies. To better compare the antiviral activity of CQ versus HCQ, the dose-response curves of the two compounds against SARS-CoV-2 were determined at four different multiplicities of infection (MOIs) by quantification of viral RNA copy numbers in the cell supernatant at 48 h post infection (p.i.). Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment (Supplementary Fig. S2 ). abstract: nan url: https://doi.org/10.1038/s41421-020-0156-0 doi: 10.1038/s41421-020-0156-0 id: cord-343362-4u2re1cu author: Liu, Jianjun title: SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis date: 2005-02-22 words: 5408.0 sentences: 234.0 pages: flesch: 49.0 cache: ./cache/cord-343362-4u2re1cu.txt txt: ./txt/cord-343362-4u2re1cu.txt summary: METHODS AND FINDINGS: The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. We present here a novel application of mass spectrometry (MS)-based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore. The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. A further application of MS-based viral sequence variation analysis in tracking the virus strain and thus the transmission of SARS-CoV was demonstrated by our confirmation of the Singapore origin of a SARS-CoV isolate from a German patient. abstract: BACKGROUND: Epidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation from clinical isolates. Direct sequence analysis of the pathogen, particularly at a population level, is generally thought to be too cumbersome, technically difficult, and expensive. We present here a novel application of mass spectrometry (MS)–based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore. METHODS AND FINDINGS: The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. Analysis of 13 SARS-CoV isolates from the different stages of the Singapore outbreak identified nine sequence variations that could define the molecular relationship between them and pointed to a new, previously unidentified, primary route of introduction of SARS-CoV into the Singapore population. Our direct determination of viral sequence variation from a clinical sample also clarified an unresolved epidemiological link regarding the acquisition of SARS in a German patient. We were also able to detect heterogeneous viral sequences in primary lung tissues, suggesting a possible coevolution of quasispecies of virus within a single host. CONCLUSION: This study has further demonstrated the importance of improving clinical and epidemiological studies of pathogen transmission through the use of genetic analysis and has revealed the MS-based analysis to be a sensitive and accurate method for characterizing SARS-CoV genetic variations in clinical samples. We suggest that this approach should be used routinely during outbreaks of a wide variety of agents, in order to allow the most effective control. url: https://www.ncbi.nlm.nih.gov/pubmed/15736999/ doi: 10.1371/journal.pmed.0020043 id: cord-307044-4czeehkq author: Liu, Jiaye title: Longitudinal Changes of Liver Function and Hepatitis B Reactivation in COVID‐19 Patients with Pre‐existing Chronic HBV Infection date: 2020-08-06 words: 3520.0 sentences: 178.0 pages: flesch: 50.0 cache: ./cache/cord-307044-4czeehkq.txt txt: ./txt/cord-307044-4czeehkq.txt summary: However, to the best of our knowledge, no studies had been carried out on the impact of chronic HBV infection on the disease progression and liver function changes of COVID-19 patients, and how the SARS-CoV-2 infection in turn affects the course of chronic HBV infection. 16 The factors for propensity score calculation include age, gender, body mass index (BMI), time intervals between COVID-19 onset to hospital admission, number of comorbidities except for CHB, liver biochemistries (ALT, AST, GGT, TBIL), PaO2/FIO2 ratio, chest CT score, CRP, lymphocyte count, and platelet count at baseline. As the median of testing/assessing time intervals and follow-up durations were 3 days and 14 days for liver biochemistries (ALT, AST, GGT, TBIL), we compared the dynamic levels of these indicators within/between the two groups at baseline, 3, 6, 9, 12, 15 days during hospitalization. The median levels of liver biochemistries over time were no significant difference between two groups ( Figure 3 ; Wilcoxon signed-rank test, ALT: p=0.56, AST: p=0.58, GGT: p=0.43, TBIL: p=0. abstract: AIM: With pandemic of COVID‐19 currently and high endemic of chronic HBV infection worldwide, it is quite urgent to investigate liver function changes of COVID‐19 patients with chronic HBV infection, and how SARS‐CoV‐2 infection in turn affects the course of chronic HBV infection. METHOD: We conducted a retrospective study based on 347 COVID‐19 patients (21 vs. 326 with vs. without chronic HBV infection). With the PSM method, we yielded 20 and 51 matched patients for HBV group and non‐HBV group, respectively. RESULTS: At the end of follow‐up, all these 71 patients achieved SARS‐CoV‐2 clearance (p=0.1). During the follow‐up, 30% vs. 31.4% in HBV group vs. non‐HBV group progressed to severe COVID‐19 (p=0.97). After PSM, the longitudinal changes of median values for liver biochemistries were no significant difference between two groups. In HBV group vs. non‐HBV‐group, 35% (7/20) vs. 37.25% (19/51) (p = 0.86) had abnormal ALT at least once during hospitalization, while 30% (6/20) vs. 31.37% (16/51) for abnormal AST (p = 0.91), 40% (8/20) vs. 37.25% (19/51) for abnormal GGT (p = 0.83), and 45% (9/20) vs. 39.22% (20/51) for abnormal TBIL (p = 0.91). Moreover, 3 patients in HBV group had hepatitis B reactivation. CONCLUSIONS: Liver dysfunction presented in COVID‐19 patients with/without chronic HBV. Moreover, those COVID‐19 patients coinfected with chronic HBV could had a risk of hepatitis B reactivation. It is necessary to monitor liver function of COVID‐19 patients, as well as HBV DNA levels for those coinfected with HBV during the whole disease course. url: https://doi.org/10.1111/hepr.13553 doi: 10.1111/hepr.13553 id: cord-352030-hnm54k4r author: Liu, Jie title: Epidemiological, Clinical Characteristics and Outcome of Medical Staff Infected with COVID-19 in Wuhan, China: A Retrospective Case Series Analysis date: 2020-03-13 words: 5263.0 sentences: 281.0 pages: flesch: 51.0 cache: ./cache/cord-352030-hnm54k4r.txt txt: ./txt/cord-352030-hnm54k4r.txt summary: These included age, sex, occupation (doctor, or nurse), body mass index (BMI ≥ 24, or <24 kg/m 2 ), current smoking status (yes, or no), disease severity (non-severe, or severe), date of symptom onset, symptoms before hospital admission (fever, cough, fatigue, sore throat, myalgia, sputum production, difficulty breathing or chest tightness, chill, loss of appetite, diarrhea, and chest pain), coexisting conditions (e.g. hypertension, diabetes, etc.), laboratory testing indicators on admission (leucocyte count, lymphocyte count, platelet count, D-dimer, creatinine, creatine kinase, lactose dehydrogenase, alanine aminotransferase, aspartate aminotransferase, hemoglobin, ferritin, C-reactive protein, Amyloid A, total bilirubin, procalcitonin, erythrocyte sedimentation rate, interleukin-6 (IL-6) and lymphocyte subsets, etc.), radiologic assessments of chest CT (lung involvement, lung lobe involvement, predominant CT changes, predominant distribution of opacities, etc.), treatment measures (antibiotics agents, antiviral agents, traditional Chinese medicine, immune globulin, thymosin, corticosteroids and oxygen therapy), and complications (e.g. pneumonia, acute respiratory distress syndrome, acute cardiac injury, acute kidney injury, shock, etc.). abstract: Backgrounds Since December 2019, a novel coronavirus epidemic has emerged in Wuhan city, China and then rapidly spread to other areas. As of 20 Feb 2020, a total of 2,055 medical staff confirmed with coronavirus disease 2019 (COVID-19) caused by SARS-Cov-2 in China had been reported. We sought to explore the epidemiological, clinical characteristics and prognosis of novel coronavirus-infected medical staff. Methods In this retrospective study, 64 confirmed cases of novel coronavirus-infected medical staff admitted to Union Hospital, Wuhan between 16 Jan, 2020 to 15 Feb, 2020 were included. Two groups concerned were extracted from the subjects based on duration of symptoms: group 1 (<= 10 days) and group 2 (>10 days). Epidemiological and clinical data were analyzed and compared across groups. The Kaplan-Meier plot was used to inspect the change in hospital discharge rate. The Cox regression model was utilized to identify factors associated with hospital discharge. Findings The median age of medical staff included was 35 years old. 64% were female and 67% were nurses. None had an exposure to Huanan seafood wholesale market or wildlife. A small proportion of the cohort had contact with specimens (5%) as well as patients in fever clinics (8%) and isolation wards (5%). Fever (67%) was the most common symptom, followed by cough (47%) and fatigue (34%). The median time interval between symptoms onset and admission was 8.5 days. On admission, 80% of medical staff showed abnormal IL-6 levels and 34% had lymphocytopenia. Chest CT mainly manifested as bilateral (61%), subpleural (80%) and ground-glass (52%) opacities. During the study period, no patients was transferred to intensive care unit or died, and 34 (53%) had been discharged. Higher body mass index (BMI) (HR 0.14; 95% CI 0.03-0.73), fever (HR 0.24; 95% CI 0.09-0.60) and higher levels of IL-6 on admission (HR 0.31; 95% CI 0.11-0.87) were unfavorable factors for discharge. Interpretation In this study, medical staff infected with COVID-19 have relatively milder symptoms and favorable clinical course, which may be partly due to their medical expertise, younger age and less underlying diseases. Smaller BMI, absence of fever symptoms and normal IL-6 levels on admission are favorable for discharge for medical staff. Further studies should be devoted to identifying the exact patterns of SARS-CoV-2 infection among medical staff. url: https://doi.org/10.1101/2020.03.09.20033118 doi: 10.1101/2020.03.09.20033118 id: cord-268254-1mg7a17c author: Liu, Li title: High neutralizing antibody titer in intensive care unit patients with COVID-19 date: 2020-07-20 words: 3475.0 sentences: 200.0 pages: flesch: 53.0 cache: ./cache/cord-268254-1mg7a17c.txt txt: ./txt/cord-268254-1mg7a17c.txt summary: This study determined the seroprevalence of 733 non-COVID-19 individuals from April 2018 to February 2020 in the Hong Kong Special Administrative Region and compared the neutralizing antibody (NAb) responses of eight COVID-19 patients admitted to the intensive care unit (ICU) with those of 42 patients not admitted to the ICU. In this study, the absence of NAb in the serum of over 733 HKSAR residents indicates that SARS-CoV-2 is unlikely to have spread silently in Hong Kong before its emergence in COVID-19 patients. During our manuscript revision, a preprint paper indicated that SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease [26] . Neutralizing antibodies responses to SARS-CoV-2 in COVID-19 inpatients and convalescent patients. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. abstract: Coronavirus disease 2019 (COVID-19) has a wide spectrum of disease severity from mild upper respiratory symptoms to respiratory failure. The role of neutralizing antibody (NAb) response in disease progression remains elusive. This study determined the seroprevalence of 733 non-COVID-19 individuals from April 2018 to February 2020 in the Hong Kong Special Administrative Region and compared the neutralizing antibody (NAb) responses of eight COVID-19 patients admitted to the intensive care unit (ICU) with those of 42 patients not admitted to the ICU. We found that NAb against SARS-CoV-2 was not detectable in any of the anonymous serum specimens from the 733 non-COVID-19 individuals. The peak serum geometric mean NAb titer was significantly higher among the eight ICU patients than the 42 non-ICU patients (7280 [95% confidence interval (CI) 1468-36099]) vs (671 [95% CI, 368-1223]). Furthermore, NAb titer increased significantly at earlier infection stages among ICU patients than among non-ICU patients. The median number of days to reach the peak Nab titers after symptoms onset was shorter among the ICU patients (17.6) than that of the non-ICU patients (20.1). Multivariate analysis showed that oxygen requirement and fever during admission were the only clinical factors independently associated with higher NAb titers. Our data suggested that SARS-CoV-2 was unlikely to have silently spread before the COVID-19 emergence in Hong Kong. ICU patients had an accelerated and augmented NAb response compared to non-ICU patients, which was associated with disease severity. Further studies are required to understand the relationship between high NAb response and disease severity. url: https://www.ncbi.nlm.nih.gov/pubmed/32618497/ doi: 10.1080/22221751.2020.1791738 id: cord-266052-rcuzi70u author: Liu, Lilong title: Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19 date: 2020-10-29 words: 5743.0 sentences: 275.0 pages: flesch: 53.0 cache: ./cache/cord-266052-rcuzi70u.txt txt: ./txt/cord-266052-rcuzi70u.txt summary: As pit latrines and the use of untreated excreta as fertilizer were common in rural China, we surveyed 27 villages of Jiangxi and Hubei provinces and found that pit latrines could be a potential source of SARS-CoV-2 water pollution. Another study showed that infectious SARS-CoV-2 virus were successfully isolated from 2 of 3 patients with viral RNA-positive, indicating that infectious virus in feces was a common manifestation of COVID-19 and confirmed the potential of fecal-oral or fecal-respiratory transmission (Xiao et al., 2020b) . Coupled with the fact that villagers usually use untreated excreta as agricultural fertilizer, we believe that the use of pit latrines in rural China and other low-income countries increases the possibility of SARS-CoV-2 contaminating the surrounding natural environment and ultimately harms human health. We proposed this hypothesis to illustrate the mechanism that SARS-COV-2 might spread from the excreta of infected humans in pit latrines to potential animal hosts and then become a sustainable source of infection in rural China and other low-income countries. abstract: According to the latest reports, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused coronavirus disease 2019 (COVID-19), was successfully isolated from the excreta (stool and urine) of COVID-19 patients, suggesting SARS-CoV-2 could be transmitted through excreta contaminated water. As pit latrines and the use of untreated excreta as fertilizer were common in rural China, we surveyed 27 villages of Jiangxi and Hubei provinces and found that pit latrines could be a potential source of SARS-CoV-2 water pollution. Recently, bats have been widely recognized as the source of SARS-CoV-2. There were many possible intermediate hosts of SARS-CoV-2, including pangolin, snake, bird and fish, but which one was still not clear exactly. Here, we proposed a hypothesis to illustrate the mechanism that SARS-CoV-2 might spread from the excreta of infected humans in pit latrines to potential animal hosts, thus becoming a sustainable source of infection in rural China. Therefore, we believe that abolishing pit latrines and banning the use of untreated excreta as fertilizer can improve the local living environment and effectively prevent COVID-19 and other potential waterborne diseases that could emanate from the excreta of infected persons. Although this study focused on rural areas in China, the results could also be applied to low-income countries, especially in Africa. url: https://api.elsevier.com/content/article/pii/S0048969720368145 doi: 10.1016/j.scitotenv.2020.143283 id: cord-030923-r0lfot3w author: Liu, Lixin title: Subunit Nanovaccine with Potent Cellular and Mucosal Immunity for COVID-19 date: 2020-08-18 words: 3704.0 sentences: 221.0 pages: flesch: 57.0 cache: ./cache/cord-030923-r0lfot3w.txt txt: ./txt/cord-030923-r0lfot3w.txt summary: [Image: see text] To combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we formulated the S1 subunit of the virus with two adjuvants, amphiphilic adjuvant monophosphoryl lipid A for Toll-like receptor 4 and CpG oligodeoxynucleotide for Toll-like receptor 9, into cationic liposomes to produce a potent, safer, and translatable nanovaccine. NANOVACCINE MPLA/CpG-loaded liposome particle, p(M+C), was produced via a thin-film hydration approach by using cationic 1,2dioleoyl-3-trimethylammonium-propane (DOTAP), helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and cholesterol as carrier materials. Previous research on vaccines using the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) as the subunit showed that the antibodies could effectively prevent the coronavirus from binding to the cell and undergoing membrane fusion, neutralizing the virus during infection. Moreover, MPLA/CpG-loaded liposomes alone can be used as nanoparticulate adjuvants of a coronavirus vaccine with different antigens to enhance an innate immunity and thus a cellular immune response. abstract: [Image: see text] To combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we formulated the S1 subunit of the virus with two adjuvants, amphiphilic adjuvant monophosphoryl lipid A for Toll-like receptor 4 and CpG oligodeoxynucleotide for Toll-like receptor 9, into cationic liposomes to produce a potent, safer, and translatable nanovaccine. The nanovaccine can efficiently elicit a humoral immune response and strong IgA antibodies in mice. The sera from the vaccinated mice significantly inhibit SARS-CoV-2 from infecting Vero cells. Moreover, relative to the free S1 with a traditional Alum adjuvant, the nanovaccine can elicit strong T-cell immunity by activating both CD4(+) and CD8(+) cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451068/ doi: 10.1021/acsabm.0c00668 id: cord-288357-3mqoexcr author: Liu, Pei title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds date: 2020-08-01 words: 1882.0 sentences: 148.0 pages: flesch: 61.0 cache: ./cache/cord-288357-3mqoexcr.txt txt: ./txt/cord-288357-3mqoexcr.txt summary: title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds We identified several N-substituted isatin compounds as potent SARS-CoV-2 3C-like protease inhibitors. [4, [9] [10] [11] [12] To date, several potential SARS-CoV-2 3CL pro inhibitors have been reported from compound library screening, [8] rational design [8, 13] , [14] and testing of ingredients from traditional Chinese medicine. Previously, we reported a series of N-substituted 5-carboxamide-isatin compounds as inhibitors of SARS CoV 3CL pro . [12] Apparently, the isatin scaffold with derivatization may also provide a good starting point for SARS CoV-2 3CL pro inhibitor development, because the two proteases share high sequence identity and the same active site. In conclusion, we have tested the inhibition activity of 29 N-substituted isatin derivatives against SARS-CoV-2 3CL pro . Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors substituted isatin compounds are potent SARS-CoV-2 3C-like protease inhibitors. abstract: SARS-CoV-2 3C-like protease is the main protease of SARS-CoV-2 and has been considered as one of the key targets for drug discovery against COVID-19. We identified several N-substituted isatin compounds as potent SARS-CoV-2 3C-like protease inhibitors. The three most potent compounds inhibit SARS-CoV-2 3C-like protease with IC(50)’s of 45 nM, 47 nM and 53 nM, respectively. Our study indicates that N-substituted isatin compounds have the potential to be developed as broad-spectrum anti-coronavirus drugs. url: https://api.elsevier.com/content/article/pii/S0223523420306747 doi: 10.1016/j.ejmech.2020.112702 id: cord-309970-jkmjiika author: Liu, Qin title: From SARS to COVID-19: What lessons have we learned? date: 2020-08-21 words: 3421.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-309970-jkmjiika.txt txt: ./txt/cord-309970-jkmjiika.txt summary: On December 1, 2019, the first case of coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), was reported in Wuhan, China, and CoVs returned to public view. In this review, we systematically compare COVID-19 and SARS in terms of epidemiology, pathogenesis and clinical characteristics and discuss the current treatment approaches, scientific advancements and Chinese experience in fighting the epidemic to combat the novel coronavirus pandemic. As the virus continued to spread, on March 11, 2020 , the WHO declared that COVID-19 is a pandemic disease, making this the first time that a coronavirus infection has been regarded as a global pandemic, in contrast to SARS in 2002, which did not reach this level. This paper summarizes the differences in the epidemiology, clinical manifestations, and treatment of SARS and COVID-19 during the two outbreaks, summarizes the lessons learned, and provides a comprehensive reference for the global epidemic prevention and treatment of reported in China and resulted in a large number of infections. abstract: Abstract After the outbreak of severe acute respiratory syndrome (SARS) in November 2002, coronaviruses (CoVs) received worldwide attention. On December 1, 2019, the first case of coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), was reported in Wuhan, China, and CoVs returned to public view. On December 30, 2019, the World Health Organization (WHO) declared that the COVID-19 epidemic is a public health emergency of international concern (PHEIC), and on March 11, 2020, the WHO classified COVID-19 as a pandemic disease. As of July 31, 2020, COVID-19 has affected 216 countries and regions, with 17,064,064 confirmed cases and 668,073 deaths, and the number of new cases has been increasing daily. Additionally, on March 19, 2020, there were no new confirmed cases in China, providing hope and valuable experience for the international community. In this review, we systematically compare COVID-19 and SARS in terms of epidemiology, pathogenesis and clinical characteristics and discuss the current treatment approaches, scientific advancements and Chinese experience in fighting the epidemic to combat the novel coronavirus pandemic. We also discuss the lessons that we have learned from COVID-19 and SARS. url: https://doi.org/10.1016/j.jiph.2020.08.001 doi: 10.1016/j.jiph.2020.08.001 id: cord-301167-101lnq4f author: Liu, Quanjun title: Microarray-in-a-Tube for Detection of Multiple Viruses date: 2007-02-01 words: 3248.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-301167-101lnq4f.txt txt: ./txt/cord-301167-101lnq4f.txt summary: Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube. abstract: Background: The detection of multiple viruses is important for pathogenic diagnosis and disease control. Microarray detection is a good method, but requires complex procedures for multiple virus detection. Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. Results: We were able to perform all detection processes in the encapsulated system without opening the cap. The 4 viruses were successfully amplified by one-step reverse transcription–PCR in the encapsulated tube. After the PCR process, the microarray-in-a-tube was inverted, and the fluorescence-labeled PCR products were directly hybridized on the microarray. Hybridization signals were obtained with an ordinary fluorescent microscope. The sensitivity of the system for virus detection reached 10(2) copies/μL. With the help of inner controls, the system provided reliable results without false negatives and false positives. Conclusions: The microarray-in-a-tube system is a rapid, labor-saving tool for multiple virus detection with several advantages, such as convenience, prevention of cross-contamination of the PCR products, and potential for multiple-gene detection. url: https://www.ncbi.nlm.nih.gov/pubmed/17158198/ doi: 10.1373/clinchem.2006.071720 id: cord-333381-wz70o9tt author: Liu, Shao title: Providing pharmacy services during the coronavirus pandemic date: 2020-03-28 words: 3195.0 sentences: 154.0 pages: flesch: 40.0 cache: ./cache/cord-333381-wz70o9tt.txt txt: ./txt/cord-333381-wz70o9tt.txt summary: Chinese pharmacists have acted swiftly in the public health response in China, such as drafting professional service guidance to pharmacists and pharmacies, establishing emergency drug formularies, monitoring and resolving drug shortages, establishing remote pharmacy services to prevent human-to-human infections, providing event-driven pharmaceutical care, educating the public on infection prevention and disease management, and participating in clinical trials and drug evaluation. Specifically, pharmacy needs to work with other healthcare organizations, professionals, and government agencies to address the following seven service needs: (1) drafting professional service guidances to pharmacists and pharmacies, (2) establishing emergency drug formularies based on treatment guidelines, (3) coordinating with drug companies and distributors to ensure adequate supply, storage and transport of identified formulary drugs, (4) providing event-driven pharmaceutical care, (5) establishing remote pharmacy services to reduce the incidence of human-to-human infections, (6) educating the public with a focus on infection prevention and disease management, and (7) involving in clinical trial research to screen, evaluate and develop antiviral medications in line with national and international guidelines [4] . abstract: The coronavirus disease 19 (COVID-19) is quickly spreading across China and globally. Pharmacy services are an important pillar in public health to prevent and contain the COVID-19 pandemic. Chinese pharmacists have acted swiftly in the public health response in China, such as drafting professional service guidance to pharmacists and pharmacies, establishing emergency drug formularies, monitoring and resolving drug shortages, establishing remote pharmacy services to prevent human-to-human infections, providing event-driven pharmaceutical care, educating the public on infection prevention and disease management, and participating in clinical trials and drug evaluation. This commentary reviews the unique needs of pharmacy services in the COVID-19 pandemic, and shares our experiences with the international pharmacy community in the response to these needs. url: https://doi.org/10.1007/s11096-020-01017-0 doi: 10.1007/s11096-020-01017-0 id: cord-272292-k0ugjb6f author: Liu, Shih-Jen title: Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates date: 2006-04-12 words: 4957.0 sentences: 261.0 pages: flesch: 57.0 cache: ./cache/cord-272292-k0ugjb6f.txt txt: ./txt/cord-272292-k0ugjb6f.txt summary: The recombinant nucleocapsid (rN) protein of the coronavirus (CoV) responsible for severe acute respiratory syndrome (SARS) was cloned and expressed in Escherichia coli, extracted from cell lysates containing 6 M urea, then purified by Ni(2+)-affinity chromatography. To identify the B-cell immunodominant epitopes of the rN protein in the mouse and monkey, the reactivities of antisera raised against purified rN proteins formulated in ISA-51/CpG were tested with a panel of overlapping synthetic peptides covering the entire N protein sequence. We also only observed that peptides corresponding to residues 336–350 were capable of stimulating IFN-γ production in T-cell cultures derived from peripheral blood mononuclear cells (PBMCs) of macaques immunized with the rN protein emulsified in ISA/CpG adjuvant. abstract: The recombinant nucleocapsid (rN) protein of the coronavirus (CoV) responsible for severe acute respiratory syndrome (SARS) was cloned and expressed in Escherichia coli, extracted from cell lysates containing 6 M urea, then purified by Ni(2+)-affinity chromatography. In animal immunogenicity studies, we found that most anti-rN protein antibodies were IgG2a in BALB/c mice vaccinated with rN emulsified in Montanide ISA-51 containing the synthetic oligodeoxynucleotide, CpG. In contrast, anti-rN protein antibodies of mice immunized with rN protein in PBS were found to mainly be IgG1. These results indicated that ISA-51/CpG-formulated rN protein was dramatically biased toward a Th1 immune response. To identify the B-cell immunodominant epitopes of the rN protein in the mouse and monkey, the reactivities of antisera raised against purified rN proteins formulated in ISA-51/CpG were tested with a panel of overlapping synthetic peptides covering the entire N protein sequence. Three immunodominant linear B-cell epitope regions were mapped to residues 166–180, 356–375, and 396–410 of the rN protein. When the reactivities of these peptides were screened with human sera from five SARS patients, peptides corresponding to residues 156–175 reacted strongly with sera from two of the SARS patients. These results indicated that the region around residues 156–175 of the N protein is immunogenic in the mouse, monkey, and human. We found that peptides corresponding to residues 1–30, 86–100, 306–320, and 351–365 contained murine immunodominant T-cell epitopes. To identify functional CTL epitopes of the N protein, BALB/c mice were immunized with peptides containing the H-2K(d) CTL motif emulsified in adjuvant ISA-51/CpG. Using an IFN-γ secretion cell assay and analysis by flow cytometry, peptides containing residues 81–95 were found to be capable of stimulating both CD4(+) and CD8(+) cell proliferation in vitro. We also only observed that peptides corresponding to residues 336–350 were capable of stimulating IFN-γ production in T-cell cultures derived from peripheral blood mononuclear cells (PBMCs) of macaques immunized with the rN protein emulsified in ISA/CpG adjuvant. Our current results together with those of others suggest that some immunodominant B-cell and T-cell epitopes are conserved in the mouse, monkey, and human. This information is very important for the development SARS diagnostic kits and a vaccine. url: https://api.elsevier.com/content/article/pii/S0264410X06000879 doi: 10.1016/j.vaccine.2006.01.058 id: cord-035307-r74ovkbd author: Liu, Shuchang title: Attitudes towards Wildlife Consumption inside and outside Hubei Province, China, in Relation to the SARS and COVID-19 Outbreaks date: 2020-11-11 words: 4133.0 sentences: 200.0 pages: flesch: 54.0 cache: ./cache/cord-035307-r74ovkbd.txt txt: ./txt/cord-035307-r74ovkbd.txt summary: Our study results indicate over the period between the SARS epidemic to the outbreak of the COVID-19 pandemic, attitudes towards the consumption of wildlife in China have changed significantly. Therefore, our aim in this study was to determine changes in attitudes towards wildlife consumption in Chinese adults in relation to the SARS and COVID-19 outbreaks with a particular focus on Hubei Province. abstract: We designed a self-administered 20-item questionnaire to determine changes in attitudes towards wildlife consumption in Chinese adults during the SARS epidemic in 2002–2003 and on-going COVID-19 pandemic that was first identified in December 2019. A total of 348 adults (177 males and 171 females) with a mean age of 29.4 ± 8.5 years participated, the majority (66.7%) from Hubei. The percentages of participants who had eaten wildlife significantly decreased from 27.0% during SARS to 17.8% during COVID-19 (P = 0.032). The most common reason participants provided for consuming wildlife was to try something novel (64.9% during SARS and 54.8% during COVID-19). More than half of participants (≥53.5%) reported that they had stopped eating wildlife meat because most species of wildlife are legally protected. Our study results indicate over the period between the SARS epidemic to the outbreak of the COVID-19 pandemic, attitudes towards the consumption of wildlife in China have changed significantly. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657065/ doi: 10.1007/s10745-020-00199-5 id: cord-284464-avriske3 author: Liu, Tao title: Recurrent positive SARS‐CoV‐2: Immune certificate may not be valid date: 2020-06-09 words: 295.0 sentences: 32.0 pages: flesch: 58.0 cache: ./cache/cord-284464-avriske3.txt txt: ./txt/cord-284464-avriske3.txt summary: key: cord-284464-avriske3 cord_uid: avriske3 The presence of SARS-CoV-2 in COVID-19 patients is usually confirmed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) method.2 This article is protected by copyright. Statistical analyses were conducted using SAS software version 9.4 (SAS Institute; Carey, NC). A two-sided P < .05 was considered statistically significant. Among 150 patients who were recovering from COVID-19, 11 (7.3%, 95% confidence interval: 3.1%-11.6%) tested positive again for SARS-CoV-2 in throat swabs. Positive rates for SARS-CoV-2 did not differ by sex or age. There were no differences in the prevalence of IgM or IgG to SARS-CoV-2 ( Figure S1 ) or serum levels of these antibodies (Table 1) Detection of SARS-CoV-2 in different types of clinical specimens Positive RT-PCR test results in patients recovered from COVID-19 Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis abstract: Currently, coronavirus disease in 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1 has become a global pandemic. The presence of SARS-CoV-2 in COVID-19 patients is usually confirmed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) method.2 This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26074 doi: 10.1002/jmv.26074 id: cord-258242-xblxjlb5 author: Liu, Tengwen title: Systems Pharmacology and Verification of ShenFuHuang Formula in Zebrafish Model Reveal Multi-Scale Treatment Strategy for Septic Syndrome in COVID-19 date: 2020-09-15 words: 5215.0 sentences: 310.0 pages: flesch: 44.0 cache: ./cache/cord-258242-xblxjlb5.txt txt: ./txt/cord-258242-xblxjlb5.txt summary: Recent studies reported that many critically ill COVID-19 patients developed typical septic syndrome, including inflammatory injury, immune dysfunction, coagulation disorder, and multiple organ failure (Bellinvia et al., 2020; Coronado et al., 2020; . Current studies reported that severe COVID-19 patients with septic syndrome mainly showed abnormal pathological features, including virus infection and tissue damage, excessive inflammation in early stage but immune suppression in late stage, and coagulation dysfunction . Since the data of systems pharmacology illustrated that SFH may regulate several key targets and biological processes of sepsis, such as PPARG in inflammatory response, GSK3b and MAPK14 in cell proliferation, and PTGS2 in coagulation, we hypothesized that SFH improves the condition of critically ill COVID-19 patients with septic syndrome by ameliorating lung injury, suppressing excessive inflammation but enhancing the capacity of pathogen phagocytosis and killing, and improving the function of blood coagulation. abstract: The outbreak of coronavirus disease 2019 (COVID-19) has affected millions of people worldwide. Critically ill COVID-19 patients develop viral septic syndrome, including inflammatory damage, immune dysfunction, and coagulation disorder. In this study, we investigated ShenFuHuang formula (SFH), a traditional Chinese medicine, which has been widely used as complementary therapy for clinical treatment of COVID-19 in Wuhan, to understand its pharmacological properties. Results of systems pharmacology identified 49 active compounds of SFH and their 69 potential targets, including GSK3β, ESR1, PPARG, PTGS2, AKR1B10, and MAPK14. Network analysis illustrated that the targets of SFH may be involved in viral disease, bacterial infection/mycosis, and metabolic disease. Moreover, signaling pathway analysis showed that Toll-like receptors, MAPK, PPAR, VEGF, NOD-like receptor, and NF-kappa B signaling pathways are highly connected with the potential targets of SFH. We further employed multiple zebrafish models to confirm the pharmacological effects of SFH. Results showed that SFH treatment significantly inhibited the inflammatory damage by reducing the generation of neutrophils in Poly (I:C)-induced viral infection model. Moreover, SFH treatment could improve the phagocytosis of macrophages and enhance the expression of immune genes in an immune deficiency model. Furthermore, SFH treatment exhibited promising anti-thrombosis effect in a thrombus model. This study provided additional evidence of SFH formula for treating COVID-19 patients with septic syndrome using multiple-scale estimation. url: https://doi.org/10.3389/fphar.2020.584057 doi: 10.3389/fphar.2020.584057 id: cord-258630-mvz2l3yj author: Liu, Tiantian title: A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date: 2020-11-10 words: 11041.0 sentences: 596.0 pages: flesch: 57.0 cache: ./cache/cord-258630-mvz2l3yj.txt txt: ./txt/cord-258630-mvz2l3yj.txt summary: We compared seven different library construction protocols and specifically evaluated the cross-protocol performance in sequencing read mappability, viral genome coverage percentage and uniformity, effect of sequence depth, SNV calling concordance (reproducibility), precision (positive predictive value), and sensitivity (proportion of consensus variants identified at different sequencing depths and viral copy number inputs) across protocols. Here, we compared seven WGS protocols for SARS-CoV-2 using clinical samples from infected patients, benchmarking the performances of these protocols in several aspects including the sequencing read mappability, genome coverage (percentage and uniformity, minimum sequences required); sample storage condition; effects of viral input, sequencing depth, length and platform; sensitivity, reproducibility and precision of SNV calling and related assay factors (e.g., amount of viral input, sequencing depth and bioinformatics pipeline). abstract: The COVID-19 pandemic is a once-in-a-lifetime event, exceeding mortality rates of the flu pandemics from the 1950’s and 1960’s. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions. We constructed multiple WGS libraries encompassing three different viral inputs: 1,000,000, 250,000 and 1,000 copies. Libraries were sequenced using two distinct platforms with varying sequencing depths and read lengths. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility and precision of single-nucleotide variant calling across different protocols. We ranked the performance of protocols based on six different metrics. Our results indicated that the most appropriate protocol depended on viral input amount and sequencing depth. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution. url: https://doi.org/10.1101/2020.11.10.375022 doi: 10.1101/2020.11.10.375022 id: cord-023463-vr6uaw3a author: Liu, Wei title: Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date: 2009-06-05 words: 3859.0 sentences: 180.0 pages: flesch: 47.0 cache: ./cache/cord-023463-vr6uaw3a.txt txt: ./txt/cord-023463-vr6uaw3a.txt summary: Objective To evaluate possible severe acute respiratory syndrome (SARS) infection associated risk factors in a SARS affected hospital in Beijing by means of a case control study. Results Multivariate analysis confirmed the strong role of performing chest compression (or intubation, which is highly correlated), contact with respiratory secretion, and emergency care experience as risk factors to acquire SARS infection. Measures to prevent nosocomial infection included establishing isolation wards for triage SARS patients; training and monitoring hospital staff in infection-control procedures; active and passive screening of HCWs; enforcement of droplet and contact precautions; and compliance with the use of PPE. In summary, this study identified exposure to high-risk procedures (such as chest compression), and contact with respiratory secretions to be significant risk factors for SARS infection among HCWs in a hospital in Beijing. abstract: Objective To evaluate possible severe acute respiratory syndrome (SARS) infection associated risk factors in a SARS affected hospital in Beijing by means of a case control study. Methods Fifty‐one infected and 426 uninfected staff members were asked about risk behaviours and protective measures when attending to SARS patients. Univariate and multivariate logistic regression analyses were performed to identify the major risk and protective factors. Results Multivariate analysis confirmed the strong role of performing chest compression (or intubation, which is highly correlated), contact with respiratory secretion, and emergency care experience as risk factors to acquire SARS infection. For the studied protective measures, wearing 16‐layer cotton surgical mask, wearing 12‐layer cotton surgical mask, wearing multiple layers of mask, taking prophylactic medicine, taking training and nose washing turned out to be protective against infection. Conclusions This study highlighted activities associated with increased and decreased risk for SARS infection during close contact with SARS patients. These findings may help to guide recommendations for the protection of high‐risk occupational groups. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169729/ doi: 10.1111/j.1365-3156.2009.02255.x id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 words: 4237.0 sentences: 245.0 pages: flesch: 42.0 cache: ./cache/cord-271188-ewlxy5po.txt txt: ./txt/cord-271188-ewlxy5po.txt summary: Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 abstract: PURPOSE OF THE REVIEW: The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) in China is lifting widespread concerns. Thus, therapeutic options are urgently needed, and will be discussed in this review. RECENT FINDINGS: Iron-containing enzymes are required for viruses most likely including coronaviruses (CoVs) to complete their replication process. Moreover, poor prognosis occurred in the conditions of iron overload for patients upon infections of viruses. Thus, limiting iron represents a promising adjuvant strategy in treating viral infection through oral uptake or venous injection of iron chelators, or through the manipulation of the key iron regulators. For example, treatment with iron chelator deferiprone has been shown to prolong the survival of acquired immunodeficiency syndrome (AIDS) patients. Increasing intracellular iron efflux via increasing iron exporter ferroportin expression also exhibits antiviral effect on human immunodeficiency virus (HIV). The implications of other metals besides iron are also briefly discussed. SUMMARY: For even though we know little about iron regulation in COVID-19 patients thus far, it could be deduced from other viral infections that iron chelation might be an alternative beneficial adjuvant in treating COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32318324/ doi: 10.1007/s40588-020-00140-w id: cord-343870-g2v7ihud author: Liu, Wei title: Virus-, host-, immune-based targets for COVID-19 therapy date: 2020-10-06 words: 1716.0 sentences: 102.0 pages: flesch: 46.0 cache: ./cache/cord-343870-g2v7ihud.txt txt: ./txt/cord-343870-g2v7ihud.txt summary: Anti-viral agents against different targets had exhibited profound therapeutic effect on SARS-CoV-2 through which the clinicians were able to control the COVID-19 outbreak. Clinicians worldwide have been voraciously seeking for a potential anti-COVID-19 drug of all modules such as vaccines; targetspecific monoclonal antibodies; viral oligonucleotide-based peptide drugs; interferons and other small bio-actives [2] . S protein being the crucial protein facilitating the SARS-CoV-2 entry into the host has been preferred as a potential therapeutic target of interests as it could be spliced into two individual peptides by the furin-like proteases [5] . The other novel drug-like K22 that inhibits the viral-dependent RNA synthesis exhibited strong anti-replicative activity against the coronaviruses in an in-vitro set-up. Stimulation of innate immune response is crucial for controlling the SARS-CoV-2 replication and its virulence on the infected hosts [8] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33035666/ doi: 10.1016/j.drudis.2020.10.001 id: cord-258902-h0wrs01h author: Liu, Xianglei title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date: 2020-09-22 words: 5015.0 sentences: 268.0 pages: flesch: 52.0 cache: ./cache/cord-258902-h0wrs01h.txt txt: ./txt/cord-258902-h0wrs01h.txt summary: title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice The cell-cell fusion assay results correlated well with the virus neutralization potency and could be used for high-throughput screening of large panels of anti-SARS-CoV-2 antibodies and vaccines without the requirement of live virus infection in BSL3 containment. Based on its highly homology to SARS-CoV, SARS-CoV-2 RBD is corroborated to contain immune dominant epitopes capable of eliciting antibodies that can neutralize viral infection and block viral entry by competing hACE2 Pseudovirus neutralization assay was then performed by incubation of SARS-CoV-2 pseudovirus with serially diluted mice serum for 1h at 37 °C, followed by addition of the mixture into pre-seeded 293T-ACE2 cells. On day 0 (pre-immunization), day 13 and day 27, mouse sera were collected and analyzed for RBD binding, pseudovirus and live virus neutralization, and cell-cell fusion inhibition. abstract: The development of an effective vaccine against SARS-CoV-2 is urgently needed. We generated SARS-CoV-2 RBD-Fc fusion protein and evaluated its potency to elicit neutralizing antibody response in mice. RBD-Fc elicited a higher neutralizing antibodies titer than RBD as evaluated by a pseudovirus neutralization assay and a live virus based microneutralization assay. Furthermore, RBD-Fc immunized sera better inhibited cell-cell fusion, as evaluated by a quantitative cell-cell fusion assay. The cell-cell fusion assay results correlated well with the virus neutralization potency and could be used for high-throughput screening of large panels of anti-SARS-CoV-2 antibodies and vaccines without the requirement of live virus infection in BSL3 containment. Moreover, the anti-RBD sera did not enhance the pseudotyped SARS-CoV-2 infection of K562 cells. These results demonstrate that Fc fusion can significantly improve the humoral immune response to recombinant RBD immunogen, and suggest that RBD-Fc could serve as a useful component of effective vaccines against SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S0264410X20312299?v=s5 doi: 10.1016/j.vaccine.2020.09.058 id: cord-273505-pcsw3vmx author: Liu, Xiaosheng title: High-Dose Intravenous Immunoglobulins in the Treatment of Severe Acute Viral Pneumonia: The Known Mechanisms and Clinical Effects date: 2020-07-14 words: 10764.0 sentences: 515.0 pages: flesch: 35.0 cache: ./cache/cord-273505-pcsw3vmx.txt txt: ./txt/cord-273505-pcsw3vmx.txt summary: Based on the previous clinical experience in China, it was proposed that early initiation of high-dose intravenous immunoglobulins (IVIg) and low-molecular-weight heparin might be effective in improving the prognosis of severe and critically ill COVID-19 patients (16, 17) . The substantial increase in IgG concentration may saturate FcRn and reduce the half-life of pathogenic antibodies, contributing to the anti-inflammatory mechanism of high-dose IVIg. A balance between activating and inhibitory FcγRs is critical for a well-regulated immune response, and a disbalance markedly influences immunopathology in autoimmune and infectious diseases. Based on these potential supportive F(ab) ′ 2 and Fc mediated mechanisms and the known clinical effects in treating severe virus pneumonia such as SARS, MERS, influenza, and RSV disease, the early application of high-dose IVIg therapy may be considered in the management of severe COVID-19 patients. abstract: The current outbreak of viral pneumonia, caused by novel coronavirus SARS-CoV-2, is the focus of worldwide attention. The WHO declared the COVID-19 outbreak a pandemic event on Mar 12, 2020, and the number of confirmed cases is still on the rise worldwide. While most infected individuals only experience mild symptoms or may even be asymptomatic, some patients rapidly progress to severe acute respiratory failure with substantial mortality, making it imperative to develop an efficient treatment for severe SARS-CoV-2 pneumonia alongside supportive care. So far, the optimal treatment strategy for severe COVID-19 remains unknown. Intravenous immunoglobulin (IVIg) is a blood product pooled from healthy donors with high concentrations of immunoglobulin G (IgG) and has been used in patients with autoimmune and inflammatory diseases for more than 30 years. In this review, we aim to highlight the known mechanisms of immunomodulatory effects of high-dose IVIg therapy, the immunopathological hypothesis of viral pneumonia, and the clinical evidence of IVIg therapy in viral pneumonia. We then make cautious therapeutic inferences about high-dose IVIg therapy in treating severe COVID-19. These inferences may provide relevant and useful insights in order to aid treatment for COVID-19. url: https://doi.org/10.3389/fimmu.2020.01660 doi: 10.3389/fimmu.2020.01660 id: cord-348729-kejlm425 author: Liu, Xiaoyu title: Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date: 2020-05-04 words: 3457.0 sentences: 178.0 pages: flesch: 50.0 cache: ./cache/cord-348729-kejlm425.txt txt: ./txt/cord-348729-kejlm425.txt summary: SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. These determined infection mechanisms indicated that blocking the interaction of SARS-CoV-2-RBD and ACE2 would cause a direct neutralizing effect against virus. This information suggests that the ACE2 interface of SARS-CoV-2-RBD might have high immunogenicity, which would be a suitable targeting epitope to develop SARS-CoV-2-specific antibodies with potent neutralizing function by in vitro screening. We performed site-directed antibody screening by phage display and finally obtained one IgG antibody and three single domain antibodies with potent neutralizing activities for SARS-CoV-2. Notably, the eluted phage exhibited a stronger binding signal on SARS-CoV-2-RBD compared to that on SARS-CoV-2-RBD mut, especially those from the domain antibody library ( Figure 2C ), indicating an expected precleaning effect during selection. abstract: Neutralizing antibody is one of the most effective interventions for acute pathogenic infection. Currently, over three million people have been identified for SARS-CoV-2 infection but SARS-CoV-2-specific vaccines and neutralizing antibodies are still lacking. SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Therefore, blocking the interaction of SARS-CoV-2-RBD and ACE2 by antibody would cause a directly neutralizing effect against virus. In the current study, we selected the ACE2 interface of SARS-CoV-2-RBD as the targeting epitope for neutralizing antibody screening. We performed site-directed screening by phage display and finally obtained one IgG antibody (4A3) and several domain antibodies. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. The domain antibody 4A12 was predicted to have the best accessibility to all three ACE2-interfaces on the spike homotrimer. Pseudovirus and authentic SARS-CoV-2 neutralization assays showed that all four antibodies could potently protect host cells from virus infection. Overall, we isolated multiple formats of SARS-CoV-2-neutralizing antibodies via site-directed antibody screening, which could be promising candidate drugs for the prevention and treatment of COVID-19. url: https://doi.org/10.1101/2020.05.03.074914 doi: 10.1101/2020.05.03.074914 id: cord-341976-yts6pzn3 author: Liu, Xintian title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China date: 2020-07-06 words: 3062.0 sentences: 213.0 pages: flesch: 57.0 cache: ./cache/cord-341976-yts6pzn3.txt txt: ./txt/cord-341976-yts6pzn3.txt summary: title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China We conducted a single-center, retrospective, cohort study to investigate the relationship between serum immunoglobulin G (IgG) and IgM and clinical outcomes in severe/critical patients with COVID-19. Specific serum immunoglobulin G (IgG) and IgM against SARS-CoV or Middle East Respiratory Syndrome-coronavirus (MERS-CoV) became detectable in patients as early as 11-15 days post illness onset [11, 12] . AGING Additionally, the titers of IgM and IgG were significantly correlated with viral load in patients infected by SARS-CoV-2 in a recent finding [14] , which promoted the hypothesis that specific antibody against virus might be associated with disease progression in COVID-19. In this retrospective cohort study, IgG and IgM against SARS-CoV-2 in severe/critical patients with COVID-19 were profiled, and relationship between antibody titers AGING and outcomes was also assessed. abstract: Severe/critical patients with coronavirus disease 2019 (COVID-19) have become the central issue in the current global pandemic due to their high mortality rate. However, the relationship between antibody response and clinical outcomes has not been well described in this group. We conducted a single-center, retrospective, cohort study to investigate the relationship between serum immunoglobulin G (IgG) and IgM and clinical outcomes in severe/critical patients with COVID-19. Seventy-nine severe/critical patients with COVID-19 admitted in Wuhan Asia General Hospital in Wuhan, China during January 22, 2020 to March 6, 2020 were included. Serum antibodies were measured at day 25 (SD, 7) post illness onset. The median IgG titer was 113 (IQR 81-167) AU/ml, and IgM titer was 50 (IQR, 23-105) AU/ml. Patients whose IgM titer ≥ 50 AU/ml had higher in-hospital mortality (p=0.026). IgM titer ≥ 50 AU/ml was also correlated with higher incidences of Acute Respiratory Distress Syndrome (ARDS) and sepsis shock. Antibody remeasurements were performed in 42 patients, where IgM titer declined significantly in survivors (p=0.031). Serum IgM titer changes according to the COVID-19 progression. The severe/critical patients with COVID-19 have a higher risk of clinical adverse events when IgM titer ≥ 50 AU/ml. Further decreasing of IgM could imply a better outcome in severe/critical cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32628642/ doi: 10.18632/aging.103417 id: cord-353484-q7d0ysbo author: Liu, Xue title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 words: 8557.0 sentences: 465.0 pages: flesch: 41.0 cache: ./cache/cord-353484-q7d0ysbo.txt txt: ./txt/cord-353484-q7d0ysbo.txt summary: Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] . abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently become a pandemic. As the sudden emergence and rapid spread of SARS-CoV-2 is endangering global health and the economy, the development of strategies to contain the virus's spread are urgently needed. At present, various diagnostic kits to test for SARS-CoV-2 are available for use to initiate appropriate treatment faster and to limit further spread of the virus. Several drugs have demonstrated in vitro activity against SARS-CoV-2 or potential clinical benefits. In addition, institutions and companies worldwide are working tirelessly to develop treatments and vaccines against COVID-19. However, no drug or vaccine has yet been specifically approved for COVID-19. Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. url: https://doi.org/10.7150/thno.47987 doi: 10.7150/thno.47987 id: cord-324902-18h0maxi author: Liu, Xuemei title: Patterns of IgG and IgM antibody response in COVID-19 patients date: 2020-06-09 words: 1117.0 sentences: 66.0 pages: flesch: 54.0 cache: ./cache/cord-324902-18h0maxi.txt txt: ./txt/cord-324902-18h0maxi.txt summary: As shown in Figure 1 , anti-SARS-CoV-2 S-specific IgG and IgM antibodies were not detectable in the very early days of infection (from day 0 to day 3). Anti-SARS-CoV-2 S-specific IgG antibodies were identifiable from day 7 onwards, peaking at approximately day 25, as shown in Figure 1(A) . Figure 1(B) shows a typical IgG and IgM antibody response in a 65-year-old woman with COVID-19 (supplementary materials, Table 1 ). As shown in Figure 1 (C), serum IgG antibody levels were not significantly correlated with clinical severity in the early stage of infection. Severe cases of COVID-19 tended to have a more vigorous IgG response against SARS-CoV-2 compared with mild cases. Our results also showed that mild cases tended to develop faster peak anti-SARS-CoV-2 S-specific IgM responses (approximately 17 days after symptom onset) compared with severe cases (approximately 21 days after symptom onset). abstract: nan url: https://doi.org/10.1080/22221751.2020.1773324 doi: 10.1080/22221751.2020.1773324 id: cord-266564-imj1lcy9 author: Liu, Yangli title: Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy date: 2020-03-05 words: 698.0 sentences: 47.0 pages: flesch: 52.0 cache: ./cache/cord-266564-imj1lcy9.txt txt: ./txt/cord-266564-imj1lcy9.txt summary: Given the maternal physiologic and immune function changes in pregnancy [2] , pregnant individuals might face greater risk of getting infected by SARS-CoV-2 and might have more complicated clinical events. We described epidemiological, clinical characteristics, pregnancy and perinatal outcomes of all hospitalized pregnant patients diagnosed with COVID-19 in China. We identified all hospitalized pregnant patients with laboratory-confirmed SARS-CoV-2 infection between December 8, 2019, and February 25, 2020 officially reported by the central government, in areas outside Wuhan, China. We reported 13 pregnant COVID-19 patients in China, indicating pregnant women also susceptible to SARS-CoV-2. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China abstract: nan url: https://doi.org/10.1016/j.jinf.2020.02.028 doi: 10.1016/j.jinf.2020.02.028 id: cord-320169-dtv7to3l author: Liu, Yen-Chin title: COVID-19: the First Documented Coronavirus Pandemic in History date: 2020-05-05 words: 1935.0 sentences: 127.0 pages: flesch: 51.0 cache: ./cache/cord-320169-dtv7to3l.txt txt: ./txt/cord-320169-dtv7to3l.txt summary: The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. The spike glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) in human and Chinese horseshoe bats, civet for cell entry, that is also dependent on S protein priming by the serine protease TMPRSS2. Domestic animals can suffer from disease as intermediate hosts that cause virus transmission from natural hosts to humans; for example, SARS-CoV and MERS-CoV crossed the species barriers into masked palm civets and camels, respectively [30, 31] [ Table 1 ]. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. abstract: The novel human coronavirus disease COVID-19 has become the fifth documented pandemic since the 1918 flu pandemic. COVID-19 was first reported in Wuhan, China, and subsequently spread worldwide. The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. SARS-CoV-2 is believed to be a spillover of an animal coronavirus and later adapted the ability of human-to-human transmission. Because the virus is highly contagious, it rapidly spreads and continuously evolves in the human population. In this review article, we discuss the basic properties, potential origin, and evolution of the novel human coronavirus. These factors may be critical for studies of pathogenicity, antiviral designs, and vaccine development against the virus. url: https://doi.org/10.1016/j.bj.2020.04.007 doi: 10.1016/j.bj.2020.04.007 id: cord-034481-zi9q96lj author: Liu, Yongjian title: Stability of SARS-CoV-2 on environmental surfaces and in human excreta date: 2020-11-01 words: 762.0 sentences: 54.0 pages: flesch: 66.0 cache: ./cache/cord-034481-zi9q96lj.txt txt: ./txt/cord-034481-zi9q96lj.txt summary: Although close exposure to respiratory droplets from an infected patient is the main transmission route of SARS-CoV-2, touching contaminated surfaces and objects might also contribute to transmission of this virus. Here, we provide a report of our study of the stability of SARS-CoV-2 on various environmental surfaces and in human excreta (feces and urine). SARS-CoV-2 was more stable in urine than in feces, and infectious virus was detected up to 3 days in two adult urine and 4 days in one child urine. Prior to our study, two research teams had just reported the stability of SARS-CoV-2 on different material surfaces [4, 5] . In comparison with the above two studies, our data displayed a prolonged survival time of this virus on environmental surfaces. In Chin''s study, a five microliters of virus stock with the infectious titer of 10 6.8 TCID 50 /ml was deposited on the surface. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603996/ doi: 10.1016/j.jhin.2020.10.021 id: cord-266616-boeb1xcp author: Liu, Yu title: Regulatory T cells: A potential weapon to combat COVID‐19? date: 2020-08-06 words: 4158.0 sentences: 233.0 pages: flesch: 49.0 cache: ./cache/cord-266616-boeb1xcp.txt txt: ./txt/cord-266616-boeb1xcp.txt summary: This review discusses the clinical and pathological features of COVID‐19, the roles of immune cells in pathological processes, and the possible avenues for induction of immunosuppressive T regulatory cells attenuating lung inflammation due to viral infection. 13, 19, 37, 38 In a mouse model study by Fulton et al, 38 evaluating the balance between virus clearance and immunopathology, Foxp3 + CD4 + regulatory T cells were shown to accumulate in mediastinal lymph nodes and the lungs of infected animals and to reduce immunopathology by regulating the responses of CD8 effector T cell during infection of respiratory syncytial virus. 38 IL-10 and TGF-β, antiinflammatory cytokines, could suppress the activity of NK cells, macrophage, cytotoxic CD8 T cells, and T helper cells 1 to reduce inflammatory storm caused by those during virus infection (Figure 1 ). Current pathology reports have revealed that the lung tissues in people infected with SARS-CoV-2 were prominently infiltrated with multinucleated giant cells and inflammatory cells. abstract: Since the end of December 2019, a novel coronavirus SARS‐CoV‐2 began to spread, an infection disease termed COVID‐19. The virus has spread throughout the world in a short period of time, resulting in a pandemic. The number of reported cases in global reached 5 695 596 including 352 460 deaths, as of May 27, 2020. Due to the lack of effective treatment options for COVID‐19, various strategies are being tested. Recently, pathologic studies conducted by two teams in China revealed immunopathologic abnormalities in lung tissue. These results have implications for immunotherapy that could offer a novel therapy strategy for combating lethal viral pneumonia. This review discusses the clinical and pathological features of COVID‐19, the roles of immune cells in pathological processes, and the possible avenues for induction of immunosuppressive T regulatory cells attenuating lung inflammation due to viral infection. It is our hope that these proposals may both be helpful in understanding the novel features of SARS‐CoV‐2 pneumonia as well as providing new immunological strategies for treating the severe sequelae of disease manifestations seen in people infected with SARS‐CoV‐2. url: https://doi.org/10.1002/mco2.12 doi: 10.1002/mco2.12 id: cord-305054-4d84b2g6 author: Liu, Yuan title: The selection of reference genome and the search for the origin of SARS-CoV-2 date: 2020-08-11 words: 2166.0 sentences: 140.0 pages: flesch: 60.0 cache: ./cache/cord-305054-4d84b2g6.txt txt: ./txt/cord-305054-4d84b2g6.txt summary: The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts. Zhang, Wu, and Zhang [13] re-analyzed the RNA-Seq reads from two pangolins carrying coronavirus using reference-guided de novo assembly method, with Wuhan-Hu-1 as the reference genome. They also performed RNA sequencing in five archived pangolins samples from Guangdong, and assembled the genomes using WIV04, another SARS-CoV-2 genome from human, as reference genome. Using de novo assembly method, they obtained viral genome that showed 90.32% and 90.24% of whole genome identify to Wuhan-Hu-1and Bat-CoV RaTG13, respectively. RaTG13, which is a bat CoV, had 1,287 reads mapped to it, and the resulting assembly has total length of 21,925 and N50 of 1,428. abstract: The pandemic caused by SARS-CoV-2 has a great impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins were considered a potential intermediate host. To assemble the coronavirus found in pangolins, SARS-CoV-2 were used a reference genome in most of studies, assuming that pangolins CoV and SARS-CoV-2 are the closest neighbors in the evolution. However, this assumption may not be true. We investigated how the selection of reference genome affect the resulting CoV genome assembly. We explored various representative CoV as reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts. url: https://doi.org/10.1101/2020.08.10.245290 doi: 10.1101/2020.08.10.245290 id: cord-349015-5oisrm5s author: Liu, Zhe title: Identification of a common deletion in the spike protein of SARS-CoV-2 date: 2020-04-02 words: 1182.0 sentences: 63.0 pages: flesch: 57.0 cache: ./cache/cord-349015-5oisrm5s.txt txt: ./txt/cord-349015-5oisrm5s.txt summary: In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. By sequencing the whole genome of SARS-CoV-2, we identified two variants having deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. To investigate whether these deletions described above are random mutations occasionally identified in a strain or would commonly occur after cell passages, we performed whole genome sequencing on the other 21 SARS-CoV-2 viral strains collected after 2 rounds of cell passage in Vero-E6 or Vero cells (Supplemental Table) . abstract: Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development. url: https://doi.org/10.1101/2020.03.31.015941 doi: 10.1101/2020.03.31.015941 id: cord-299480-mehwd0dk author: Liu, Zheng-Xue title: Identification of single-chain antibody fragments specific against SARS-associated coronavirus from phage-displayed antibody library date: 2005-04-08 words: 4261.0 sentences: 225.0 pages: flesch: 62.0 cache: ./cache/cord-299480-mehwd0dk.txt txt: ./txt/cord-299480-mehwd0dk.txt summary: Abstract To develop early diagnostic reagents, effective vaccines, and even drugs against SARS-associated coronavirus (SARS-CoV), the human single fold single-chain antibody fragments, (scFv) libraries I+J (Tomlinson I+J) were used to identify novel scFvs, which can specifically bind to SARS-CoV. Interestingly, two scFvs (B5 and B9) exhibited higher binding specificity to SARS-CoV with the OD450 value 0.608 and 0.545, respectively, and their coding sequences shared the identical sequence composed of VH gene (351bp) and VL gene (327bp), so the two scFvs were uniformly named as SA59B and chosen for further analysis. Hence, single-chain antibody fragments specific against SARS-CoV from phage-displayed antibody library have potential for exploitation as diagnostic or even antiviral therapeutic reagents. The ELISA plates coated with purified SARS-CoV lysate, positive and negative sera were provided by Military Medical Science Academic and HuaDa Gene Company (Beijing, China). The panning procedure was performed on a 96-well flexible assay plate coated with purified SARS-CoV lysate, which was blocked directly with MPBS (PBS containing 4% skimmed milk powder) at room temperature for 2 h. abstract: Abstract To develop early diagnostic reagents, effective vaccines, and even drugs against SARS-associated coronavirus (SARS-CoV), the human single fold single-chain antibody fragments, (scFv) libraries I+J (Tomlinson I+J) were used to identify novel scFvs, which can specifically bind to SARS-CoV. Interestingly, two scFvs (B5 and B9) exhibited higher binding specificity to SARS-CoV with the OD450 value 0.608 and 0.545, respectively, and their coding sequences shared the identical sequence composed of VH gene (351bp) and VL gene (327bp), so the two scFvs were uniformly named as SA59B and chosen for further analysis. SA59B scFv was expressed in soluble form in Escherichia coli HB2151 and purified by immobilized metal affinity chromatography. The soluble 30kDa SA59B scFv-antibody was verified in SDS–PAGE and Western-blot. The purified SA59B scFv-antibody was labeled with HRP by the glutaraldehyde method, and the concentration of HRP and SA59B scFv-antibody in the SA59B-HRP solution reached 2.4 and 2.28mg/ml, respectively. Then, the binding ability of SA59B-HRP to SARS-CoV was evaluated by ELISA with S/N of 11.6, indicating higher binding specificity between them. Finally, both the SA59B sequence specificity and its application for diagnosis, prophylaxis or therapy of SARS were discussed. url: https://api.elsevier.com/content/article/pii/S0006291X05002263 doi: 10.1016/j.bbrc.2005.02.003 id: cord-161674-nk0wie0w author: Liu, Zhi title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date: 2020-04-10 words: 5137.0 sentences: 304.0 pages: flesch: 54.0 cache: ./cache/cord-161674-nk0wie0w.txt txt: ./txt/cord-161674-nk0wie0w.txt summary: Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). abstract: The outbreak of COVID-19 caused by SARS-CoV-2 has rapidly spread worldwide and has caused over 1,400,000 infections and 80,000 deaths. There are currently no drugs or vaccines with proven efficacy for its prevention and little knowledge was known about the pathogenicity mechanism of SARS-CoV-2 infection. Previous studies showed both virus and host-derived MicroRNAs (miRNAs) played crucial roles in the pathology of virus infection. In this study, we use computational approaches to scan the SARS-CoV-2 genome for putative miRNAs and predict the virus miRNA targets on virus and human genome as well as the host miRNAs targets on virus genome. Furthermore, we explore miRNAs involved dysregulation caused by the virus infection. Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. The study may provide important clues for the mechisms of pathogenesis of SARS-CoV-2. url: https://arxiv.org/pdf/2004.04874v1.pdf doi: nan id: cord-103872-yzqic5vt author: Liu, Zhijin title: Global view on virus infection in non-human primates and implication for public health and wildlife conservation date: 2020-05-13 words: 1310.0 sentences: 81.0 pages: flesch: 51.0 cache: ./cache/cord-103872-yzqic5vt.txt txt: ./txt/cord-103872-yzqic5vt.txt summary: Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans and vice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission. First, we generated a summary statistics of worldwide reported VI-NHPs. We then 61 identified and predicted NHP species with a high risk of virus transmission from humans and 62 predicted geographic locations where disease outbreaks are likely to occur. Since centrality in primate-virus networks could assess the potential for the 72 circulation of viruses among NHPs and humans, we estimated the centrality using four metrics: 73 strength degree centrality, eigenvector centrality, betweenness centrality, and closeness centrality 74 implemented in the R package "igraph" and UCINET 6. Centrality in primate-parasite networks 225 reveals the potential for the transmission of emerging infectious diseases to humans abstract: The pandemic outbreak and rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not only a threat for humans, but potentially also for many animals. Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans and vice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. Non-human primates (NHPs), as our evolutionary closest relatives, are susceptible to human viruses, and a number of pathogens are known to circulate between humans and NHPs. Here we generated global statistics of virus infection in NHPs (VI-NHPs). In total, 121 NHP species from 14 families have been reported to be infected by 139 DNA and RNA viruses from 23 virus families; 74.8 percent of viruses in NHPs have also been found in humans, indicative of the high potential for cross species transmission of these viruses. The top ten NHP species with high centrality in the NHP-virus network are two apes (Pan troglodytes, Pongo pygmaeus), seven Old World monkeys (Macaca mulatta, M. fascicularis, Papio cynocephalus, Lophocebus albigena, Chlorocebus aethiops, Cercopithecus ascanius, C. nictitans) and a lemur (Propithecus diadema). Besides apes, there is a high risk of virus circulation between humans and Old World monkeys, given the wide distribution of many Old World monkey species and their frequent contact with humans. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission. url: https://doi.org/10.1101/2020.05.12.089961 doi: 10.1101/2020.05.12.089961 id: cord-351835-1s2zsqoq author: Liu, Zhixin title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 date: 2020-03-11 words: 1514.0 sentences: 101.0 pages: flesch: 54.0 cache: ./cache/cord-351835-1s2zsqoq.txt txt: ./txt/cord-351835-1s2zsqoq.txt summary: title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 In this study, we used systematic comparison and analysis to predict the interaction between the receptor‐binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin‐converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor-binding domain, contains core binding motif in the external subdomain; SP, signal peptide Phylogenetic reconstruction determines the evolutionary relationship and host selection between spike glycoproteins in the human-close beta coronaviruses. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2 abstract: From the beginning of 2002 and 2012, severe respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV) crossed the species barriers to infect humans, causing thousands of infections and hundreds of deaths, respectively. Currently, a novel coronavirus (SARS‐CoV‐2), which has become the cause of the outbreak of Coronavirus Disease 2019 (COVID‐19), was discovered. Until 18 February 2020, there were 72 533 confirmed COVID‐19 cases (including 10 644 severe cases) and 1872 deaths in China. SARS‐CoV‐2 is spreading among the public and causing substantial burden due to its human‐to‐human transmission. However, the intermediate host of SARS‐CoV‐2 is still unclear. Finding the possible intermediate host of SARS‐CoV‐2 is imperative to prevent further spread of the epidemic. In this study, we used systematic comparison and analysis to predict the interaction between the receptor‐binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin‐converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans. url: https://www.ncbi.nlm.nih.gov/pubmed/32100877/ doi: 10.1002/jmv.25726 id: cord-314072-av3r7it7 author: Liu, Zhuoming title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date: 2020-11-08 words: 1105.0 sentences: 74.0 pages: flesch: 54.0 cache: ./cache/cord-314072-av3r7it7.txt txt: ./txt/cord-314072-av3r7it7.txt summary: title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans. To select for SARS-CoV-2 S variants that escape neutralization, we used VSV-SARSas we isolated this mutation alone, and acquisition of the L517R substitution appeared to 141 increase viral fitness as judged by plaque morphology (Fig S2) . abstract: Although neutralizing antibodies against the SARS-CoV-2 spike (S) protein are a goal of most COVID-19 vaccines and being developed as therapeutics, escape mutations could compromise such countermeasures. To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. These variants were mapped onto the RBD structure and evaluated for cross-resistance by convalescent human plasma. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans. url: https://doi.org/10.1101/2020.11.06.372037 doi: 10.1101/2020.11.06.372037 id: cord-302912-aqutzlx4 author: Liu, Ziteng title: The Inhibitory Effect of Curcumin on Virus-Induced Cytokine Storm and Its Potential Use in the Associated Severe Pneumonia date: 2020-06-12 words: 5738.0 sentences: 286.0 pages: flesch: 42.0 cache: ./cache/cord-302912-aqutzlx4.txt txt: ./txt/cord-302912-aqutzlx4.txt summary: The development of coronavirus-evoked pneumonia is associated with excessive inflammatory responses in the lung, known as "cytokine storms," which results in pulmonary edema, atelectasis, and acute lung injury (ALI) or fatal acute respiratory distress syndrome (ARDS). Therefore, in this review, we summarize the mounting evidence obtained from preclinical studies using animal models of lethal pneumonia where curcumin exerts protective effects by regulating the expression of both proand anti-inflammatory factors such as IL-6, IL-8, IL-10, and COX-2, promoting the apoptosis of PMN cells, and scavenging the reactive oxygen species (ROS), which exacerbates the inflammatory response. As part of a robust immune response in severe cases, the virus triggers overaction of immune systems, producing a large number of inflammatory factors, which causes severe damage to the lung and manifests acute respiratory distress syndrome (ARDS), resulting in high mortality. Such an inflammatory response, including overproduction of immune cells and pro-inflammatory cytokines, is defined as the cytokine storm that usually occurs in viral infection and causes acute lung injury (ALI) and ARDS. abstract: Coronavirus infection, including SARS-CoV, MERS-CoV, and SARS-CoV2, causes daunting diseases that can be fatal because of lung failure and systemic cytokine storm. The development of coronavirus-evoked pneumonia is associated with excessive inflammatory responses in the lung, known as “cytokine storms,” which results in pulmonary edema, atelectasis, and acute lung injury (ALI) or fatal acute respiratory distress syndrome (ARDS). No drugs are available to suppress overly immune response-mediated lung injury effectively. In light of the low toxicity and its antioxidant, anti-inflammatory, and antiviral activity, it is plausible to speculate that curcumin could be used as a therapeutic drug for viral pneumonia and ALI/ARDS. Therefore, in this review, we summarize the mounting evidence obtained from preclinical studies using animal models of lethal pneumonia where curcumin exerts protective effects by regulating the expression of both pro- and anti-inflammatory factors such as IL-6, IL-8, IL-10, and COX-2, promoting the apoptosis of PMN cells, and scavenging the reactive oxygen species (ROS), which exacerbates the inflammatory response. These studies provide a rationale that curcumin can be used as a therapeutic agent against pneumonia and ALI/ARDS in humans resulting from coronaviral infection. url: https://doi.org/10.3389/fcell.2020.00479 doi: 10.3389/fcell.2020.00479 id: cord-297209-84gs67bn author: Livanos, A. E. title: Gastrointestinal involvement attenuates COVID-19 severity and mortality date: 2020-09-09 words: 7509.0 sentences: 496.0 pages: flesch: 54.0 cache: ./cache/cord-297209-84gs67bn.txt txt: ./txt/cord-297209-84gs67bn.txt summary: In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first time in vivo but failed to obtain culturable virus. . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint (nausea, vomiting and diarrhea) was associated with less severe disease (p<0.02 Fisher''s exact 188 test) and lower mortality (p<0.001 Fisher''s exact test) (Fig. 1a) . . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint CoV-2 nucleocapsid protein in small intestinal enterocytes of COVID-19 patients ( Fig. 4i,n, CD8 + T cells, the dominant IEL 388 population, showed an increase (2.6-fold) in COVID-19 cases compared to controls but the 389 difference did not reach statistical significance (p=0.4) ( Supplementary Table 12a ), likely owing 390 to inter-patient variability, also observed by light microscopy. abstract: Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated the impact of GI infection on disease pathogenesis in three large cohorts of patients in the United States and Europe. Unexpectedly, we observed that GI involvement was associated with a significant reduction in disease severity and mortality, with an accompanying reduction in key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation. In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first time in vivo but failed to obtain culturable virus. High dimensional analyses of GI tissues confirmed low levels of cellular inflammation in the GI lamina propria and an active downregulation of key inflammatory genes including IFNG, CXCL8, CXCL2 and IL1B among others. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit. url: http://medrxiv.org/cgi/content/short/2020.09.07.20187666v1?rss=1 doi: 10.1101/2020.09.07.20187666 id: cord-342139-t2tukk0z author: Livingston, Gill title: Prevalence, management, and outcomes of SARS-CoV-2 infections in older people and those with dementia in mental health wards in London, UK: a retrospective observational study date: 2020-10-05 words: 6631.0 sentences: 318.0 pages: flesch: 54.0 cache: ./cache/cord-342139-t2tukk0z.txt txt: ./txt/cord-342139-t2tukk0z.txt summary: For individuals, the following data were collected: demographic data (age, sex, ethnicity); mental health clinical details (ie, dementia or other diagnosis); Mental Health Act 1983 or Mental Capacity Act 2005 status 31 (these are legislative frameworks for those with mental illness, including an absence of decisional capacity, which in defined circumstances allow people to be detained in a hospital without giving consent); physical comorbidities; and COVID-19-related details, which were COVID-19 clinical diagnosis (date of clinical suspicion of COVID-19 and SARS-CoV-2 RT-PCR test result or results, if retested), possible COVID-19 symptoms (first symptom noted, presence of new persistent cough, shortness of breath [respiratory rate >20 breaths per min], temperature ≥37·8°C, new loss of smell or taste, sore throat, gastrointestinal symptoms, fatigue, loss of appetite, asymptomatic, duration of symptoms [days]), change to mental state related to COVID-19 (increased cognitive impairment or delirium, increased or new mood disturbance or psychosis); and manage ment (do not attempt resuscitation status; whether the patient was receiving vitamin D treatment; isolation of patients and duration [days] if applicable; whether venous thromboembolism [VTE] prophylaxis was given before the patient became symptomatic; whether VTE prophylaxis was given after symptoms developed; whether antipsychotic medication had been stopped, started, or increased during SARS-CoV-2 infection and treatment, and new antipsychotic sideeffects; whether prophylactic antibiotics were prescribed for community-acquired pneumonia or hospital-acquired pneumonia; whether oxygen therapy was administered on the ward; and whether the patient was transferred to a medical ward in a general hospital). abstract: BACKGROUND: People living in group situations or with dementia are more vulnerable to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Older people and those with multimorbidity have higher mortality if they become infected than the general population. However, no systematic study exists of COVID-19-related outcomes in older inpatients in psychiatric units, who comprise people from these high-risk groups. We aimed to describe the period prevalence, demographics, symptoms (and asymptomatic cases), management, and survival outcomes of COVID-19 in the older inpatient psychiatric population and people with young-onset dementia in five National Health Service Trusts in London, UK, from March 1 to April 30, 2020. METHODS: In this retrospective observational study, we collected demographic data, mental health diagnoses, clinical diagnosis of COVID-19, symptoms, management, and COVID-19-related outcome data of inpatients aged 65 years or older or with dementia who were already inpatients or admitted as inpatients to five London mental health Trusts between March 1 and April 30, 2020, and information about available COVID-19-related resources (ie, testing and personal protective equipment). Patients were determined to have COVID-19 if they had a positive SARS-CoV-2 PCR test, or had relevant symptoms indicative of COVID-19, as determined by their treating physician. We calculated period prevalence of COVID-19 and analysed patients’ characteristics, treatments, and outcomes. FINDINGS: Of 344 inpatients, 131 (38%) were diagnosed with COVID-19 during the study period (period prevalence 38% [95% CI 33–43]). The mean age of patients who had COVID-19 was 75·3 years (SD 8·2); 68 (52%) were women and 47 (36%) from ethnic minority groups. 16 (12%) of 131 patients were asymptomatic and 121 (92%) had one or more disease-related comorbidity. 108 (82%) patients were compulsorily detained. 74 (56%) patients had dementia, of whom 13 (18%) had young-onset dementia. On average, sites received COVID-19 testing kits 4·5 days after the first clinical COVID-19 presentation. 19 (15%) patients diagnosed with COVID-19 died during the study period, and their deaths were determined to be COVID-19 related. INTERPRETATION: Patients in psychiatric inpatient settings who were admitted without known SARS-CoV-2 infection had a high risk of infection with SARS-CoV-2 compared with those in the community and had a higher proportion of deaths from COVID-19 than in the community. Implementation of the long-standing policy of parity of esteem for mental health and planning for future COVID-19 waves in psychiatric hospitals is urgent. FUNDING: None. url: https://api.elsevier.com/content/article/pii/S221503662030434X doi: 10.1016/s2215-0366(20)30434-x id: cord-319194-ukuia48s author: Liò, Pietro title: Phylogenomics and bioinformatics of SARS-CoV date: 2004-02-04 words: 4488.0 sentences: 201.0 pages: flesch: 45.0 cache: ./cache/cord-319194-ukuia48s.txt txt: ./txt/cord-319194-ukuia48s.txt summary: Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Figure 1 shows the maximum likelihood tree produced using a set of homologous replicases from five SARS-CoV strains, 12 other coronaviruses representing both groups 1 and 2 of the genus [2, 3] , one torovirus (Breda virus) and one okavirus [yellow head (YH) virus], which were determined to most closely represent the consensus coronavirus sequence by a PSI-Blast search [12] . abstract: Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. The topology and branch lengths of the phylogenetic relationships among the family Coronaviridae, including SARS-CoV, have been estimated using the replicase polyprotein. The spike protein fragments S1 (involved in receptor-binding) and S2 (involved in membrane fusion) have been found to have different mutation rates. Fragment S1 can be further divided into two regions (S1A, which comprises approximately the first 400 nucleotides, and S1B, comprising the next 280) that also show different rates of mutation. The phylogeny presented on the basis of S1B shows that SARS-CoV is closely related to MHV (murine hepatitis virus), which is known to bind the murine receptor CEACAM1. The predicted structure, accessibility and mutation rate of the S1B region is also presented. Because anti-SARS drugs based on S2 heptads have short half-lives and are difficult to manufacture, our findings suggest that the S1B region might be of interest for anti-SARS drug discovery. url: https://api.elsevier.com/content/article/pii/S0966842X04000216 doi: 10.1016/j.tim.2004.01.005 id: cord-326643-obfvi3ms author: Lo Giudice, Roberto title: The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in Dentistry. Management of Biological Risk in Dental Practice date: 2020-04-28 words: 4574.0 sentences: 293.0 pages: flesch: 54.0 cache: ./cache/cord-326643-obfvi3ms.txt txt: ./txt/cord-326643-obfvi3ms.txt summary: Considering the virus'' route of transmission, a specific protocol should be applied to reduce the risk of infection in addition to measures that prevent the spread of infection from a patient to another person or medical tools and equipment (cross-infection). Due to the transmission route, in addition to measures that prevent diffusion of the infection from a patient to another person or medical tools and equipment (cross-infection), it is advisable to add further airborne and contact precautions to the routine standard hygienic procedures in order to reduce the risk of SARS-CoV-2 transmission. The use of personal protective equipment (PPE) such as gloves, masks, visors, goggles, dental uniform, and surgical gown and shoes (see section on PPEs below). To reduce the risk of SARS-CoV-2 infection, given how the disease spreads and the current health crisis, the following prevention measures are suggested in addition to what is already generally performed: abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in Wuhan, China, and the etiological agent of Coronavirus Disease-2019 (COVID-19). This infection spreads mainly through direct contact with Flügge micro droplets or core droplets that remain suspended as aerosol. Moreover, it has been reported that infected subjects, both with and without clinical signs of COVID-19, can transmit the virus. Since the infection typically enters through mouth, nose, and eyes, dentistry is one of the medical practices at highest risk of infection due to the frequent production of aerosol and the constant presence of saliva. The World Health Organization (WHO) has suggested that only emergency/urgent procedures should be performed during the coronavirus outbreak. Considering the virus’ route of transmission, a specific protocol should be applied to reduce the risk of infection in addition to measures that prevent the spread of infection from a patient to another person or medical tools and equipment (cross-infection). This protocol should be implemented by modifying both patient management and clinical practice, introducing particular devices and organizational practices. This paper aims to discuss and suggest the most appropriate procedures in every aspect of dental practice to reduce infection risk. url: https://doi.org/10.3390/ijerph17093067 doi: 10.3390/ijerph17093067 id: cord-337137-0ey40gzw author: Lo, Anthony WI title: How the SARS coronavirus causes disease: host or organism? date: 2005-12-17 words: 5201.0 sentences: 289.0 pages: flesch: 45.0 cache: ./cache/cord-337137-0ey40gzw.txt txt: ./txt/cord-337137-0ey40gzw.txt summary: Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection abstract: The previous epidemic of severe acute respiratory syndrome (SARS) has ended. However, many questions concerning how the aetiological agent, the novel SARS coronavirus (CoV), causes illness in humans remain unanswered. The pathology of fatal cases of SARS is dominated by diffuse alveolar damage. Specific histological changes are not detected in other organs. These contrast remarkably with the clinical picture, in which there are apparent manifestations in multiple organs. Both pathogen and host factors are important in the pathogenesis of SARS. The choice of specific receptors and the unique genome of the SARS‐CoV are important elements in understanding the biology of the pathogen. For the host cells, the outcome of SARS‐CoV infection, whether there are cytopathic effects or not, depends on the cell types that are infected. At the whole‐body level, immune‐mediated damage, due to activation of cytokines and/or chemokines and, perhaps, autoimmunity, may play key roles in the clinical and pathological features of SARS. Continued research is still required to determine the pathogenetic mechanisms involved and to combat this new emerging human infectious disease. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16362992/ doi: 10.1002/path.1897 id: cord-334849-8rblgq9b author: LoPresti, Marissa title: The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature date: 2020-08-12 words: 7290.0 sentences: 456.0 pages: flesch: 45.0 cache: ./cache/cord-334849-8rblgq9b.txt txt: ./txt/cord-334849-8rblgq9b.txt summary: 1 As with many complex diseases, the reality for most individuals likely involves a combination of genetic -including viral and host genetics -and non-genetic Relative to other coronaviruses, SARS-CoV-2 has unique biological properties and related clinical impact, but data regarding other coronaviruses may be relevant. This can help populate lists of genes that -along with data from related biological studies -may bear scrutiny in the developing and important large-scale host genetic 6 and porcine epidemic diarrhea virus (PEDV)in pigs. In various species, efforts have focused on genes encoding the relevant coronavirus receptor, including effects of viral and host genetic changes and how these may impact the disease process. 30 In humans (see Tables 1 and S2 and Figures 3 and 4 for details on human studies of these genes, including specific references), studies of specific ACE2 polymorphisms have not shown significant associations with SARS-CoV-1 susceptibility or outcome. abstract: Abstract The SARS-CoV-2 pandemic raises many scientific and clinical questions. These include how host genetic factors affect disease susceptibility and pathogenesis. New work is emerging related to SARS-CoV-2; previous work has been conducted on other coronaviruses that affect different species. We reviewed the literature on host genetic factors related to coronaviruses, with a systematic focus on human studies. We identified 1,832 articles of potential relevance. Seventy-five involved human host genetic factors, of which 35 involved analysis of specific genes or loci; aside from one meta-analysis, all were candidate-driven studies, typically investigating small numbers of research subjects and loci. Three additional case reports were described. Multiple significant loci were identified, including 16 related to susceptibility (of which 7 identified protective alleles), and 16 related to outcomes (of which 3 identified protective alleles). The types of cases and controls used varied considerably; four studies used traditional replication/validation cohorts. Among other studies, 30 involved both human and non-human host genetic factors related to coronavirus, 178 involved study of non-human (animal) host genetic factors related to coronavirus, and 984 involved study of non-genetic host factors related to coronavirus, including involving immunopathogenesis. Previous human studies have been limited by issues that may be less impactful now, including low numbers of eligible participants and limited availability of advanced genomic methods; however, these may raise additional considerations. We outline key genes and loci from animal and human host genetic studies that may bear investigation COVID-19. We also discuss how previous studies may direct current lines of inquiry. url: https://www.sciencedirect.com/science/article/pii/S0002929720302755?v=s5 doi: 10.1016/j.ajhg.2020.08.007 id: cord-334049-r3rlykli author: Lobo-Galo, Naún title: FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication date: 2020-05-14 words: 4132.0 sentences: 199.0 pages: flesch: 48.0 cache: ./cache/cord-334049-r3rlykli.txt txt: ./txt/cord-334049-r3rlykli.txt summary: Our inclusion criteria for the selection of drugs for potential COVID-19 therapy were: (1) The drug is a FDA-approved that can potentially be repurposed as an ready-to-use therapeutic antiviral; (2) Its use has been extensively studied, and there is sufficient literature on its pharmacology; (3) The drug has few side effects in long-term administration, with not known direct fatalities associated to it, and not additional extensive toxicological studies are needed; (4) Drug can interact with active site of SARS-CoV-2 main protease and reacts with thiol group of its catalytic cysteine, producing an irreversible covalent-inhibition; (5) Administered drug shows efficient distribution through multiple organs, as recent publications suggest the possibility that SARS-CoV-2 has tropism for multiple tissues, beyond the pneumocytes, including heart and blood vessels, liver, intestine, neural cortex and brain stem (Wadman et al., 2020); (6) Drug penetrates the cell membrane, as its antiviral target, the protease acts early during replication in the host cytoplasm; and (7) When administered, drug is metabolized and excreted slowly; and possible metabolites have also potential inhibitory activity. abstract: Emergent novel SARS-CoV-2 is responsible for the current pandemic outbreak of severe acute respiratory syndrome with high mortality among the symptomatic population worldwide. Given the absence of a current vaccine or specific antiviral treatment, it is urgent to search for FDA-approved drugs that can potentially inhibit essential viral enzymes. The inhibition of 3CL(pro) has potential medical application, due to the fact that it is required for processing of the first translated replicase polyproteins into a series of native proteins, which are essential for viral replication in the host cell. We employed an in silico approach to test if disulfiram, as well as its metabolites, and captopril could be used as potential antiviral drugs against COVID-19. We provide data on the potential covalent interaction of disulfiram and its metabolites with the substrate binding subsite of 3CL(pro) and propose a possible mechanism for the irreversible protease inactivation thought the reaction of the aforementioned compounds with the Cys145. Although, captopril is shown to be a potential ligand of 3CL(pro), it is not recommended anti-COVID-19 therapy, due to the fact that it can induce the expression of the viral cellular receptor such as, angiotensin-converting enzyme ACE-2, and thus, making the patient potentially more susceptible to infection. On the other hand, disulfiram, an alcoholism-averting drug, has been previously proposed as an antimicrobial and anti-SARS and MERS agent, safe to use even at higher doses with low side effects, it is recommended to be tested for control of SARS-CoV-2 infection. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1764393 doi: 10.1080/07391102.2020.1764393 id: cord-338317-ro041w5l author: Lockhart, Sam M. title: When two pandemics meet: Why is obesity associated with increased COVID-19 mortality? date: 2020-06-29 words: 4664.0 sentences: 247.0 pages: flesch: 47.0 cache: ./cache/cord-338317-ro041w5l.txt txt: ./txt/cord-338317-ro041w5l.txt summary: Thus, the association of obesity with worse 105 outcomes in acute lung infection or widespread alveolar damage of other types, appears to be 106 strongest and most consistent with COVID-19 and pandemic H1N1 influenza. In addition to being lower in obesity and most insulin 168 resistant states it is worth noting that adiponectin levels have been reported to be significantly 169 lower in many of the COVID-19 "at risk" groups e.g. Male < Females 20 and South Asians < White 170 is secreted from adipose tissue, associated with insulin resistance and likely contributes to 197 thrombotic risk in obesity by impairing fibrinolysis 23 . In summary, we have applied insights into the pathophysiology of the adverse consequences of 279 obesity and emerging evidence regarding the pathological mechanisms in COVID-19 to suggest 280 possible routes whereby obesity can exacerbate the tissue damage associated with infection by the 281 SARS-CoV-2 virus. abstract: Abstract A growing body of evidence indicates that obesity is strongly and independently associated with adverse outcomes of COVID-19 including death. By combining emerging knowledge of the pathological processes involved in COVID-19 with insights into the mechanisms underlying the adverse health consequences of obesity, we present some hypotheses regarding the deleterious impact of obesity on the course of COVID-19. These hypotheses are testable and could guide therapeutic and preventive interventions. As obesity is now almost ubiquitous and no vaccine for COVID-19 is currently available, even a modest reduction in the impact of obesity on mortality and morbidity from this viral infection could have profound consequences for public health. url: https://doi.org/10.1016/j.medj.2020.06.005 doi: 10.1016/j.medj.2020.06.005 id: cord-302228-n5o6jfs2 author: Lodise, Thomas P. title: COVID‐19: Important Therapy Considerations and Approaches in this Hour of Need date: 2020-05-05 words: 1935.0 sentences: 113.0 pages: flesch: 50.0 cache: ./cache/cord-302228-n5o6jfs2.txt txt: ./txt/cord-302228-n5o6jfs2.txt summary: A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients.1-3 However, optimal drug therapy decisions for those with moderate to severe COVID-19 infections are extremely challenging at this time as evidence is limited. A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified, and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients. If data are amassed on COVID-19 patients, it is important that detailed information is collected on the outcomes associated with the treatment strategies used at our respective institutions. Despite data suggesting that lopinavir-ritonavir was active against SARS-CoV-2 infection, no benefit was observed with lopinavir-ritonavir treatment versus standard care in a study of hospitalized adult patients with severe COVID-19. abstract: We are living in unprecedented times. While we had near pandemic events in the recent past with SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome), we have never experienced anything like coronavirus (COVID-19), also known as SARS-CoV-2 infection, since the Spanish flu. In contrast to the Spanish flu where medical care was limited, we are equipped to combat COVID-19 but there is considerable work ahead with many uncertainties. At this critical time, we must come together as one united country and world to stop the spread and provide the best care possible for individuals who contract the virus and develop infection. A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients.1-3 However, optimal drug therapy decisions for those with moderate to severe COVID-19 infections are extremely challenging at this time as evidence is limited. url: https://www.ncbi.nlm.nih.gov/pubmed/32267556/ doi: 10.1002/phar.2396 id: cord-266987-ikt8r2o1 author: Loeffelholz, Michael J. title: Laboratory diagnosis of emerging human coronavirus infections – the state of the art date: 2020-03-30 words: 4734.0 sentences: 269.0 pages: flesch: 46.0 cache: ./cache/cord-266987-ikt8r2o1.txt txt: ./txt/cord-266987-ikt8r2o1.txt summary: The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. It must be appreciated that no matter how accurate and fast laboratory testing methods are, the diagnosis of viral pneumonias such as caused by SARS-CoV-2 involves collecting the correct specimen from the patient at the right time. The authors recommended to use serology to facilitate the diagnosis of SARS-CoV-2 infections when an NP swab specimen was collected inappropriately and the molecular assays were performed unsatisfactorily [42] . Several RT-PCR protocols for detection of SARS-CoV-2 RNA have been posted by the World Health Organization at https://www.who.int/emergencies/ diseases/novel-coronavirus-2019/technical-guidance/ laboratory-guidance. Considering the increased levels of mortality and infectivity associated with three novel-coronavirus outbreaks, these random-access, safe and simple tests, which offer fast and accurate detection and identification, are likely to have an immediate impact on prompt clinical and epidemiological decisions [7, 63] . abstract: The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. Newer laboratory methods are fast, highly sensitive and specific, and are gradually replacing the conventional gold standards. This presentation reviews the current laboratory methods available for testing coronaviruses by focusing on the coronavirus disease 2019 (COVID-19) outbreak going on in Wuhan. Viral pneumonias typically do not result in the production of purulent sputum. Thus, a nasopharyngeal swab is usually the collection method used to obtain a specimen for testing. Nasopharyngeal specimens may miss some infections; a deeper specimen may need to be obtained by bronchoscopy. Alternatively, repeated testing can be used because over time, the likelihood of the SARS-CoV-2 being present in the nasopharynx increases. Several integrated, random-access, point-of-care molecular devices are currently under development for fast and accurate diagnosis of SARS-CoV-2 infections. These assays are simple, fast and safe and can be used in the local hospitals and clinics bearing the burden of identifying and treating patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32196430/ doi: 10.1080/22221751.2020.1745095 id: cord-291315-y40s45iv author: Logunov, Denis Y title: Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia date: 2020-09-04 words: 5697.0 sentences: 282.0 pages: flesch: 50.0 cache: ./cache/cord-291315-y40s45iv.txt txt: ./txt/cord-291315-y40s45iv.txt summary: title: Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). INTERPRETATION: The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong humoral and cellular immune responses in participants. These findings of two open, phase 1/2 non-randomised studies of a heterologous prime-boost COVID-19 vaccine based on recombinant adenoviral vectors rAd26-S and rAd5-S show that the vaccine is safe, well tolerated, and induces strong humoral and cellular immune responses in 100% of healthy participants. In our study, despite formation of neutralising antibodies to recombinant adenoviruses after vaccination with rAd26 and rAd5, formation of a humoral immune response to target antigen (SARS-CoV-2 glycoprotein S) in vaccinated volunteers was not affected. abstract: BACKGROUND: We developed a heterologous COVID-19 vaccine consisting of two components, a recombinant adenovirus type 26 (rAd26) vector and a recombinant adenovirus type 5 (rAd5) vector, both carrying the gene for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (rAd26-S and rAd5-S). We aimed to assess the safety and immunogenicity of two formulations (frozen and lyophilised) of this vaccine. METHODS: We did two open, non-randomised phase 1/2 studies at two hospitals in Russia. We enrolled healthy adult volunteers (men and women) aged 18–60 years to both studies. In phase 1 of each study, we administered intramuscularly on day 0 either one dose of rAd26-S or one dose of rAd5-S and assessed the safety of the two components for 28 days. In phase 2 of the study, which began no earlier than 5 days after phase 1 vaccination, we administered intramuscularly a prime-boost vaccination, with rAd26-S given on day 0 and rAd5-S on day 21. Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). Secondary outcome measures were antigen-specific cellular immunity (T-cell responses and interferon-γ concentration) and change in neutralising antibodies (detected with a SARS-CoV-2 neutralisation assay). These trials are registered with ClinicalTrials.gov, NCT04436471 and NCT04437875. FINDINGS: Between June 18 and Aug 3, 2020, we enrolled 76 participants to the two studies (38 in each study). In each study, nine volunteers received rAd26-S in phase 1, nine received rAd5-S in phase 1, and 20 received rAd26-S and rAd5-S in phase 2. Both vaccine formulations were safe and well tolerated. The most common adverse events were pain at injection site (44 [58%]), hyperthermia (38 [50%]), headache (32 [42%]), asthenia (21 [28%]), and muscle and joint pain (18 [24%]). Most adverse events were mild and no serious adverse events were detected. All participants produced antibodies to SARS-CoV-2 glycoprotein. At day 42, receptor binding domain-specific IgG titres were 14 703 with the frozen formulation and 11 143 with the lyophilised formulation, and neutralising antibodies were 49·25 with the frozen formulation and 45·95 with the lyophilised formulation, with a seroconversion rate of 100%. Cell-mediated responses were detected in all participants at day 28, with median cell proliferation of 2·5% CD4(+) and 1·3% CD8(+) with the frozen formulation, and a median cell proliferation of 1·3% CD4(+) and 1·1% CD8(+) with the lyophilised formulation. INTERPRETATION: The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong humoral and cellular immune responses in participants. Further investigation is needed of the effectiveness of this vaccine for prevention of COVID-19. FUNDING: Ministry of Health of the Russian Federation. url: https://api.elsevier.com/content/article/pii/S0140673620318663 doi: 10.1016/s0140-6736(20)31866-3 id: cord-283984-jch0ja1o author: Loizzo, Monica R. title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species date: 2008-03-20 words: 1495.0 sentences: 97.0 pages: flesch: 59.0 cache: ./cache/cord-283984-jch0ja1o.txt txt: ./txt/cord-283984-jch0ja1o.txt summary: title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species oxycedrus oil, in which α‐pinene and β‐myrcene were the major constituents, revealed antiviral activity against HSV‐1 with an IC (50) value of 200 μg/ml and a SI of 5. In this study, we report the antiviral activity of seven essential oils obtained from berry, fruits, and leaves of different species collected in Lebanon. nobilis berries oil exhibited an IC 50 value of 120 mg/ml against SARS-CoV with a selectivity index (SI; TC 50 /IC 50 ) of 4.2. oxycedrus oil exhibited the highest activity against HSV-1 with a IC 50 value of 200 mg/ml and a SI of 5. P. palaestina essential oil was inactive against SARS-CoV (IC 50 > 1000 mg/ml) and less active against HSV-1 (IC 50 500 mg/ml). nobilis oil against SARS-CoV, and we also reported the interesting anti-herpetic activity of J. abstract: The chemical composition of the essential oils of Laurus nobilis, Juniperus oxycedrus ssp. oxycedrus, Thuja orientalis, Cupressus sempervirens ssp. pyramidalis, Pistacia palaestina, Salvia officinalis, and Satureja thymbra was determined by GC/MS analysis. Essential oils have been evaluated for their inhibitory activity against SARS‐CoV and HSV‐1 replication in vitro by visually scoring of the virus‐induced cytopathogenic effect post‐infection. L. nobilis oil exerted an interesting activity against SARS‐CoV with an IC (50) value of 120 μg/ml and a selectivity index (SI) of 4.16. This oil was characterized by the presence of β‐ocimene, 1,8‐cineole, α‐pinene, and β‐pinene as the main constituents. J. oxycedrus ssp. oxycedrus oil, in which α‐pinene and β‐myrcene were the major constituents, revealed antiviral activity against HSV‐1 with an IC (50) value of 200 μg/ml and a SI of 5. url: https://doi.org/10.1002/cbdv.200890045 doi: 10.1002/cbdv.200890045 id: cord-270495-2u072mtp author: Lokida, Dewi title: Diagnosis of COVID-19 in a Dengue-Endemic Area date: 2020-08-05 words: 1750.0 sentences: 110.0 pages: flesch: 53.0 cache: ./cache/cord-270495-2u072mtp.txt txt: ./txt/cord-270495-2u072mtp.txt summary: When SARS-CoV-2 is negative and clinical indication is present (at least fever and thrombocytopenia), DENV NS1 antigen and/or IgM/IgG antibody testing may be performed. Clinicians from Singapore reported two COVID-19 cases that were misdiagnosed as dengue among patients who presented with clinical manifestations and hematology profiles, suggesting dengue infection and false-positive DENV IgM antibody using a rapid diagnostic test (RDT). COVID-19 cases were defined as inpatients who met the COVID-19 criteria based on a predetermined combination of symptoms, laboratory testing, imaging, and risk exposure at Tangerang District Hospital, Indonesia (see Supplemental Table 1 ), and had a positive nasopharyngeal or oropharyngeal real-time RT-PCR for SARS-CoV-2. None of the 42 subjects was positive for dengue NS1 or showed seroconversion or increasing DENV IgM and IgG index values, suggesting no acute DENV infection among these COVID-19 cases. The third patient did not recall having a fever before acute COVID-19 illness, suggesting asymptomatic or mild dengue, the most common presentation of DENV infection. abstract: Emergence of SARS-CoV-2 in dengue virus (DENV)–endemic areas complicates the diagnosis of both infections. COVID-19 cases may be misdiagnosed as dengue, particularly when relying on DENV IgM, which can remain positive months after infection. To estimate the extent of this problem, we evaluated sera from 42 confirmed COVID-19 patients for evidence of DENV infection. No cases of SARS-CoV-2 and DENV coinfection were identified. However, recent DENV infection, indicated by the presence of DENV IgM and/or high level of IgG antibodies, was found in seven patients. Dengue virus IgM and/or high IgG titer should not exclude COVID-19. SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) testing is appropriate when dengue nonstructural protein 1 (NS1) or RT-PCR is negative. Given the possibility of coinfection, testing for both DENV and SARS-CoV-2 is merited in the setting of the current pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32762798/ doi: 10.4269/ajtmh.20-0676 id: cord-263481-w5ytp1q7 author: Lokman, Syed Mohammad title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date: 2020-06-02 words: 3013.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-263481-w5ytp1q7.txt txt: ./txt/cord-263481-w5ytp1q7.txt summary: MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. abstract: The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected, 12 variations were located at the N-terminal domain and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin converting enzyme-2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure. url: https://www.sciencedirect.com/science/article/pii/S1567134820302203?v=s5 doi: 10.1016/j.meegid.2020.104389 id: cord-343517-vf32wxkx author: Lokman, Syed Mohammad title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date: 2020-04-11 words: 2745.0 sentences: 163.0 pages: flesch: 53.0 cache: ./cache/cord-343517-vf32wxkx.txt txt: ./txt/cord-343517-vf32wxkx.txt summary: However, SARS-CoV-2 has emerged with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. The evolutionary distances showed that all the SARS-CoV-2 spike proteins cluster in the same node of the phylogenetic tree confirming the sequences are similar to Refseq YP_009724390 (Fig. 2) . abstract: The newly identified SARS-CoV-2 has now been reported from around 183 countries with more than a million confirmed human cases including more than 68000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins have gotten substantial attention recently. Spike glycoprotein is widely considered as a possible target to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment tools. In this study, 483 unique variations have been identified among the genomes including 25 non-synonymous mutations and one deletion in the spike protein of SARS-CoV-2. Among the 26 variations detected, 12 variations were located at the N-terminal domain and 6 variations at the receptor-binding domain (RBD) which might alter the interaction with receptor molecules. In addition, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on our findings, potential inhibitors can be designed and tested targeting these proposed sites of variation. url: https://doi.org/10.1101/2020.04.07.030924 doi: 10.1101/2020.04.07.030924 id: cord-309737-u960ftdm author: Lolachi, Sanaz title: Macrophage activation syndrome as an unusual presentation of paucisymptomatic severe acute respiratory syndrome coronavirus 2 infection: A case report date: 2020-08-07 words: 1553.0 sentences: 108.0 pages: flesch: 42.0 cache: ./cache/cord-309737-u960ftdm.txt txt: ./txt/cord-309737-u960ftdm.txt summary: PATIENT CONCERNS: We describe the unique case of young man who developed MAS as the sole manifestation of an otherwise paucisymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. DIAGNOSES: Clinical and biological criteria led to the diagnosis of MAS; cytokine profile was highly suggestive reverse transcription polymerase chain reaction for SARS-CoV-2 in nasopharyngeal swabs was negative, but serum anti-SARS-CoV-2 immunoglobulin A and immunoglobulin G resulted positive leading to the diagnosis of SARS-CoV-2 infection. [2] Aims and scope of the report: to describe the unique case of a patient who developed MAS as the sole manifestation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and to highlight that even paucisymptomatic COVID-19 patients can develop life-threatening complications. Rapid clinical deterioration with high, sustained fever, cytopenias, rising transaminases and ferritin, and evolving coagulopathy prompted us to suspect a MAS (or secondary hemophagocytic lymphohistiocytosis, HLH) in the context of SARS-CoV-2 infection. abstract: RATIONALE: Macrophage activation syndrome (MAS) is a rare life-threatening condition characterized by cytokine-mediated tissue injury and multiorgan dysfunction. PATIENT CONCERNS: We describe the unique case of young man who developed MAS as the sole manifestation of an otherwise paucisymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. DIAGNOSES: Clinical and biological criteria led to the diagnosis of MAS; cytokine profile was highly suggestive reverse transcription polymerase chain reaction for SARS-CoV-2 in nasopharyngeal swabs was negative, but serum anti-SARS-CoV-2 immunoglobulin A and immunoglobulin G resulted positive leading to the diagnosis of SARS-CoV-2 infection. INTERVENTIONS: The patient was treated with empiric antibiotic and hydroxychloroquine. OUTCOMES: Clinical improvement ensued. At follow-up, the patient is well. LESSON: SARS-CoV-2 infection may trigger develop life-threatening complications, like MAS. This can be independent from coronavirus disease 2019 gravity. url: https://doi.org/10.1097/md.0000000000021570 doi: 10.1097/md.0000000000021570 id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 words: 1438.0 sentences: 67.0 pages: flesch: 52.0 cache: ./cache/cord-298441-77w86l8q.txt txt: ./txt/cord-298441-77w86l8q.txt summary: To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca'' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). abstract: OBJECTIVES: The management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. We aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with the infection. METHODS: Occupational and clinical characteristics of HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, to March 31, 2020, were collected. For those who tested positive and for the asymptomatic positives we checked laboratory and clinical data as of May 22 to calculate the time necessary to become test-negative and to verify whether symptoms developed thereafter. Frequencies of positive tests were compared according to selected variables using multivariable logistic regression models. RESULTS: Positive tests were 139 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.5-10.3), with a marked difference between symptomatic (122/503, 24.2%) and asymptomatic (17/1,070, 1.6%) workers (p<0.001). Physicians were the group with the highest frequency of positive tests (61/582, 10.5%), whereas clerical workers and technicians displayed the lowest frequency (5/137, 3.6%). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors were taste and smell alterations (odds ratio [OR]= 76.9) and fever (OR = 9.12). The median time from first positive test to a negative test was 27 days (95% CI: 24-30). CONCLUSIONS: A relevant number of HCWs can be infected by SARS-CoV-2 without displaying any symptom. Among symptomatic workers, the key symptoms to guide diagnosis are taste and smell alterations and fever. In median, almost four weeks are necessary to achieve negativity of nasopharyngeal swab. url: https://www.ncbi.nlm.nih.gov/pubmed/32569835/ doi: 10.1016/j.cmi.2020.06.013 id: cord-336026-x02f7byo author: Lommatzsch, Marek title: COVID‐19 in a patient with severe asthma treated with Omalizumab date: 2020-06-27 words: 650.0 sentences: 52.0 pages: flesch: 56.0 cache: ./cache/cord-336026-x02f7byo.txt txt: ./txt/cord-336026-x02f7byo.txt summary: 1, 3, 4 This is supwith asthma following Omalizumab treatment is primarily mediated by a downregulation of the high-affinity IgE receptor on pDCs. 8, 9 Thus, we hypothesize that the patient described in this case report might have been protected from an asthma exacerbation or pneumonia during COVID-19, either because of the underlying disease (allergic asthma) or because of the antibody used for treatment (Omalizumab), or both. Therefore, studies are needed to characterize the precise interaction of chronic airway diseases (such as asthma) and of biologics (such as Omalizumab) with SARS-CoV-2 infections in humans. We report a case of a 52-year-old man with severe allergic asthma treated with Omalizumab with no evidence of an asthma exacerbation, loss of asthma control or pneumonia during symptomatic COVID-19 disease. We hypothesize that the underlying disease (allergic asthma) or the antibody used for treatment (Omalizumab), or both, might have exerted protective effects. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32544254/ doi: 10.1111/all.14456 id: cord-262904-0b0ljjq1 author: Lon, Jerome Rumdon title: Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date: 2020-10-29 words: 5006.0 sentences: 263.0 pages: flesch: 53.0 cache: ./cache/cord-262904-0b0ljjq1.txt txt: ./txt/cord-262904-0b0ljjq1.txt summary: It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. On this basis, we predicted the linear and conformational B cell epitopes, analyzed the conservation of the epitopes, the adaptability and other evolutionary characteristics of the surface protein, which provided a theoretical basis for the vaccine development and prevention of SARS-CoV-2. With the amino acid sequences of the surface protein of SARS-CoV-2 of NC_045512.2 as templates, we predicted the 3D structure of E and M protein through the online server SWISS-MODEL [10] based on homology modeling method, selected the optimal structure based on the template identity and GMQE value [10] , and the rationality of the structure was evaluated by Ramachandran plot [11] with PDBsum server. abstract: BACKGROUND: In order to obtain antibodies that recognize natural proteins, it is possible to predict the antigenic determinants of natural proteins, which are eventually embodied as polypeptides. The polypeptides can be coupled with corresponding vectors to stimulate the immune system to produce corresponding antibodies, which is also a simple and effective vaccine development method. The discovery of epitopes is helpful to the development of SARS-CoV-2 vaccine. METHODS: The analyses were related to epitopes on 3 proteins, including spike (S), envelope (E) and membrane (M) proteins, which are located on the lipid envelope of the SARS-CoV-2. Based on the NCBI Reference Sequence: NC_045512.2, the conformational and linear B cell epitopes of the surface protein were predicted separately by various prediction methods. Furthermore, the conservation of the epitopes, the adaptability and other evolutionary characteristics were also analyzed, the sequences of the whole genome of SARS-CoV-2 were obtained from the GISAID. RESULTS: 7 epitopes were predicted, including 6 linear epitopes and 1 conformational epitope. One of the linear and one of the conformational consist of identical sequence, but represent different forms of epitopes. It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. CONCLUSION: The findings would facilitate the vaccine development, had the potential to be directly applied on the prevention in this disease, but also have the potential to prevent the possible threats caused by other types of coronavirus. url: https://doi.org/10.1186/s12985-020-01437-4 doi: 10.1186/s12985-020-01437-4 id: cord-353133-tsqb6pa8 author: Long, Dustin R. title: Considerations for Assessing Risk of Provider Exposure to SARS-CoV-2 after a Negative Test date: 2020-05-26 words: 1189.0 sentences: 66.0 pages: flesch: 39.0 cache: ./cache/cord-353133-tsqb6pa8.txt txt: ./txt/cord-353133-tsqb6pa8.txt summary: Recent publication of data suggesting imperfect clinical sensitivity of reverse transcription polymerase chain reaction assays for SARS-CoV-2 3 could lead healthcare providers to intuitively question the wisdom of a strategy that relies on a negative SARS-CoV-2 test, particularly when planning high-risk procedures such as endotracheal intubation. To help providers and clinical leaders grapple with this dynamic uncertainty, we have developed an online tool (https://covid-airway-npv.info) that enables the user to examine the impact of different assumptions regarding SARS-CoV-2 reverse transcription polymerase chain reaction test characteristics and disease prevalence on the potential risk of provider exposure during airway management. Uncertainty is modeled by asking the user to provide the most likely, minimum, and maximum value of the parameter (here, SARS-CoV-2 testing characteristics and COVID-19 community prevalence), using a Project Evaluation and Review Techniques distribution. abstract: nan url: https://doi.org/10.1097/aln.0000000000003392 doi: 10.1097/aln.0000000000003392 id: cord-334313-v2syspu6 author: Long, S. Wesley title: Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date: 2020-05-03 words: 4525.0 sentences: 251.0 pages: flesch: 48.0 cache: ./cache/cord-334313-v2syspu6.txt txt: ./txt/cord-334313-v2syspu6.txt summary: We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. Because in vitro resistance of SARS-CoV to remdesivir has been reported to be caused by either of two amino acid replacements in RdRp (Phe476Leu and Val553Leu), we interrogated our data for polymorphisms in the nsp12 gene. abstract: We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These genomes were from the viruses causing infections in the earliest recognized phase of the pandemic affecting Houston. Substantial viral genomic diversity was identified, which we interpret to mean that the virus was introduced into Houston many times independently by individuals who had traveled from different parts of the country and the world. The majority of viruses are apparent progeny of strains derived from Europe and Asia. We found no significant evidence of more virulent viral types, stressing the linkage between severe disease, underlying medical conditions, and perhaps host genetics. We discovered a signal of selection acting on the spike protein, the primary target of massive vaccine efforts worldwide. The data provide a critical resource for assessing virus evolution, the origin of new outbreaks, and the effect of host immune response. Significance COVID-19, the disease caused by the SARS-CoV-2 virus, is a global pandemic. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. We identified no evidence that a particular strain or its progeny causes more severe disease, underscoring the connection between severe disease, underlying health conditions, and host genetics. Some amino acid replacements in the spike protein suggest positive immune selection is at work in shaping variation in this protein. Our analysis traces the early molecular architecture of SARS-CoV-2 in Houston, and will help us to understand the origin and trajectory of future infection spikes. url: https://doi.org/10.1101/2020.05.01.072652 doi: 10.1101/2020.05.01.072652 id: cord-321670-f2d4bykp author: Longardt, Ann Carolin title: Perinatale Aspekte der SARS-CoV-2 Infektion date: 2020-08-24 words: 2927.0 sentences: 409.0 pages: flesch: 55.0 cache: ./cache/cord-321670-f2d4bykp.txt txt: ./txt/cord-321670-f2d4bykp.txt summary: In einer Studie aus den 50 Kliniken in Wuhan wurden 118 Frauen mit COVID-19 zwischen Dezember 2019 und März 2020 erfasst; 109 zeigten einen milden Verlauf und 9 (8 %) einen schweren Verlauf mit Hypoxämie, eine hiervon wurde beatmet. Abgesehen davon, dass das Virus selten im Blut detektiert wurde, stellt sich auch die Frage nach der Expres sion des SARS-CoV-2-Rezeptors ACE2 im Bereich der maternofetalen Grenzfläche beziehungsweise in der Plazenta. Gesichert ist der Infektionsweg durch eine SARS-CoV-2-Übertragung über die Muttermilch damit jedoch nicht. Anzunehmen ist aber auch die Weitergabe von SARSCoV2Antikörpern über die Muttermilch an das Kind, was den klinischen Verlauf einer kindlichen Infektion positiv beeinflussen könnte, ähnlich wie es bei der SARS-Epidemie 2002/2003 berichtet wurde [42] . Vertical Transmission of Coronavirus Disease 19 (COVID-19) from Infected Pregnant Mothers to Neonates: A Review An Analysis of 38 Pregnant Women with COVID19, Their Newborn Infants, and MaternalFetal Transmission of SARS CoV2: Maternal Coronavirus Infections and Pregnancy Outcomes abstract: The novel coronavirus SARS-CoV-2 has developed into a pandemic, yet still has many unknowns. The modalities of transmission, different symptoms and manifestations as well as concomitant circumstances of the disease are insufficiently characterized. Especially patient groups in special situations like pregnant women and newborns have to be considered separately. The current knowledge about pregnancy, labor and the first days of life is characterized by particular uncertainty due to the scarce data available. However, there is currently no evidence of significant unfavorable maternal and perinatal outcome. Many pregnant women with SARS-CoV-2 infection remain asymptomatic. The possibility of vertical transmission to the child cannot be excluded with certainty. However, indications of vertical transmission were detected only in individual cases. Newborn infections are also rather rare, unspecific and usually mild, with respiratory symptoms dominating. In this article, the data available to date are examined in order to provide better information, advice and treatment for pregnant women and newborns with SARS-CoV-2 and to provide suggestions for future research. url: https://www.ncbi.nlm.nih.gov/pubmed/32838447/ doi: 10.1055/a-1192-7437 id: cord-320673-4guarm0k author: Lopera, E. title: Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes date: 2020-04-25 words: 4180.0 sentences: 215.0 pages: flesch: 47.0 cache: ./cache/cord-320673-4guarm0k.txt txt: ./txt/cord-320673-4guarm0k.txt summary: title: Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes While large-scale genetic studies of COVID-19 patients are being assembled, such as those coordinated by the COVID host genetics consortium (https://www.covid19hg.com/), it is worthwhile to evaluate the effects of genetic variants in genes involved in SARS-CoV-2 infection on human phenotypes, including quantitative traits, taking advantage of already existing cohorts. Therefore, understanding the role of genetic variants at genes essential for SARS-CoV-2 infection in human quantitative phenotypes is important to explain the observed variability in infection susceptibility and severity of COVID-19 and this understanding may suggest potential treatments. In conclusion we carried out an extensive screening of potential genetic associations at common and low frequency variants in the ACE2 and TMPRSS2 genes, and found a lack of substantial effect in human quantitative phenotype variation in the general population. abstract: Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptomes, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection uses the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual's genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as 58 medications in 36,339 volunteers from the Lifelines population biobank, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed a suggestive association of polymorphisms within the ACE2 gene with (1) the use of ARBs combination therapies (p=5.7x10-4), an association that is significantly stronger in females (pdiff=0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p=5.5x10-4). While these associations need to be confirmed in larger sample sizes, they suggest that these variants play a role in diseases such as hypertension and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl. url: http://medrxiv.org/cgi/content/short/2020.04.22.20074963v1?rss=1 doi: 10.1101/2020.04.22.20074963 id: cord-335270-edga753o author: Lopez-Alvarez, Diana title: Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing date: 2020-06-25 words: 974.0 sentences: 70.0 pages: flesch: 50.0 cache: ./cache/cord-335270-edga753o.txt txt: ./txt/cord-335270-edga753o.txt summary: title: Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing We report the genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a patient with symptoms of coronavirus disease 2019 (COVID-19) who was infected in Cali, Colombia. We report the coding-complete genome sequence of SARS-CoV-2 isolate Cali-01, obtained from a Colombian patient with no recent record of international travel. First, for quality control and filtering of reads (fragments of 400 to 700 bp), we used the gupplyplex script of the ARTIC Network bioinformatics protocol (https://artic.network/ncov-2019/ncov2019-bioinformatics -sop.html), followed by a reference assembly with minimap2 (6) and Pilon (7), using the sequence of the Wuhan-Hu-1 isolate (GenBank accession number MN908947.3). The genome sequence of SARS-CoV-2 isolate Cali-01 was deposited in GISAID and GenBank under accession numbers EPI_ISL_445219 and MT470219, respectively. The sequencing work was carried out at the Virology Laboratory, Department of Microbiology, of the Universidad del Valle, in Cali. abstract: We report the genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a patient with symptoms of coronavirus disease 2019 (COVID-19) who was infected in Cali, Colombia. The patient had no recent travel record and did not require hospitalization. The virus genome was obtained using Oxford Nanopore MinION sequencing. url: https://doi.org/10.1128/mra.00573-20 doi: 10.1128/mra.00573-20 id: cord-314369-o4nis91y author: Lopez-Lopes, G. I. S. title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date: 2020-08-01 words: 3684.0 sentences: 211.0 pages: flesch: 55.0 cache: ./cache/cord-314369-o4nis91y.txt txt: ./txt/cord-314369-o4nis91y.txt summary: Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. During the initial months of the COVID-19 swabs and other collection methods were used by LHW in the institute to identify SARS-Cov-2 RNA in upper respiratory tract, but occasionally throat wash (TW) was alternatively used. We compared the CT obtained at this survey to results generated from contemporary swab collections, sent as routine testing at the institute, that provide SARS-CoV-2 rtPCR testing to clinical services. The study did not compare the rate of positivity in paired samples, and only one individual was documented that performed both a swab test (negative) and a positive throat wash collection at a same day. The study suggests that throat wash may be a valid alternative to the detection of SARS-CoV-2 RNA. abstract: Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease. url: http://medrxiv.org/cgi/content/short/2020.07.29.20163998v1?rss=1 doi: 10.1101/2020.07.29.20163998 id: cord-287658-c2lljdi7 author: Lopez-Rincon, Alejandro title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 words: 4766.0 sentences: 253.0 pages: flesch: 55.0 cache: ./cache/cord-287658-c2lljdi7.txt txt: ./txt/cord-287658-c2lljdi7.txt summary: The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets'' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. abstract: In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from available repositories, separating the genome of different virus strains from the Coronavirus family with considerable accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets on existing datasets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from NGDC, separating the genome of different virus strains from the Coronavirus family with accuracy 98.73%. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics. url: https://doi.org/10.1101/2020.03.13.990242 doi: 10.1101/2020.03.13.990242 id: cord-330536-q8zr0mkl author: Lopinto, Julien title: Severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection date: 2020-09-14 words: 1239.0 sentences: 82.0 pages: flesch: 45.0 cache: ./cache/cord-330536-q8zr0mkl.txt txt: ./txt/cord-330536-q8zr0mkl.txt summary: We report here a case of severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and managed in a referral center. CASE PRESENTATION: A 58-year-old man was admitted to our intensive care unit for severe hemoptysis with history of post-tuberculosis bronchiectasis. CONCLUSIONS: To our knowledge, this is the first case of acute exacerbation of bronchiectasis related to SARS-CoV-2 infection and complicated by severe hemoptysis. Since the beginning of SARS-CoV-2 outbreak in China, severe acute respiratory syndrome has been widely descripted [1] [2] [3] and hemoptysis has rarely been observed in this condition [1, 2, 4, 5] . We report here a case of acute exacerbation of posttuberculosis bronchiectasis precipitated by SARS-CoV-2 infection complicated by severe hemoptysis and managed in a referral center. To our knowledge, this is the first case reported of acute exacerbation of post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and complicated by severe hemoptysis. abstract: BACKGROUND: Since the beginning of SARS-CoV-2 outbreak in China, severe acute respiratory syndrome has been widely descripted. Hemoptysis has rarely been observed in SARS-CoV-2 infection. We report here a case of severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and managed in a referral center. CASE PRESENTATION: A 58-year-old man was admitted to our intensive care unit for severe hemoptysis with history of post-tuberculosis bronchiectasis. At ICU admission the patient had fever and severe acute respiratory failure requiring high flow oxygen therapy. Respiratory tract sampling was positive for SARS-CoV-2. Multi-detector computed tomography angiography pointed out localized bronchiectasis on the left lower lobe and enlarged left bronchial and phrenic arteries; bronchial arteriography with distal embolization was performed with favorable outcome and no bleeding recurrence. CONCLUSIONS: To our knowledge, this is the first case of acute exacerbation of bronchiectasis related to SARS-CoV-2 infection and complicated by severe hemoptysis. Whether the virus may play a role in the dysregulation of airway haemostasis, and contribute to episodes of hemoptysis in patients with chronic pulmonary diseases and predisposing factors might be investigated. url: https://doi.org/10.1186/s12890-020-01285-6 doi: 10.1186/s12890-020-01285-6 id: cord-317233-k3wuqwyu author: Lorenzo-Redondo, Ramon title: A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways date: 2020-11-11 words: 8170.0 sentences: 400.0 pages: flesch: 52.0 cache: ./cache/cord-317233-k3wuqwyu.txt txt: ./txt/cord-317233-k3wuqwyu.txt summary: INTERPRETATION: These results show that multiple variants of SARS-CoV-2 were circulating in the Chicago area in mid-March 2020 that differed in their relative viral loads in patient upper airways. While the predominant virus genotype in Washington state was most closely related to viruses in China in the early epidemic, the predominant virus genotype in New York was more closely related to viruses from Europe [12] .The latter viruses carry a mutation in their Spike protein (D614G) that has not only become more common worldwide over time, but that has also been associated with higher viral loads in COVID-19 patients. Furthermore, this study supports a correlation between SARS-CoV-2 clade and relative viral load in the upper airways of infected patients. In this study, we report the phylogenetic and phylodynamic analyses of 88 SARS-CoV-2 genomes from COVID-19 patients in Chicago, Illinois, US, which largely fall into three major clades. abstract: BACKGROUND: The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of distinct viral clades, though their clinical significance remains unclear. Here, we aimed to investigate the phylogenetic characteristics of SARS-CoV-2 infections in Chicago, Illinois, and assess their relationship to clinical parameters. METHODS: We performed whole-genome sequencing of SARS-CoV-2 isolates collected from COVID-19 patients in Chicago in mid-March, 2020. Using these and other publicly available sequences, we performed phylogenetic, phylogeographic, and phylodynamic analyses. Patient data was assessed for correlations between demographic or clinical characteristics and virologic features. FINDINGS: The 88 SARS-CoV-2 genome sequences in our study separated into three distinct phylogenetic clades. Clades 1 and 3 were most closely related to viral sequences from New York and Washington state, respectively, with relatively broad distributions across the US. Clade 2 was primarily found in the Chicago area with limited distribution elsewhere. At the time of diagnosis, patients infected with Clade 1 viruses had significantly higher average viral loads in their upper airways relative to patients infected with Clade 2 viruses, independent of disease severity. INTERPRETATION: These results show that multiple variants of SARS-CoV-2 were circulating in the Chicago area in mid-March 2020 that differed in their relative viral loads in patient upper airways. These data suggest that differences in virus genotype can impact viral load and may influence viral spread. FUNDING: Dixon Family Translational Research Award, Northwestern University Clinical and Translational Sciences Institute (NUCATS), National Institute of Allergy and Infectious Diseases (NIAID), Lurie Comprehensive Cancer Center, Northwestern University Emerging and Re-emerging Pathogens Program. url: https://api.elsevier.com/content/article/pii/S2352396420304886 doi: 10.1016/j.ebiom.2020.103112 id: cord-290209-gkx57lyq author: Losurdo, Pasquale title: Impact of lockdown for SARS-CoV-2 (COVID-19) on surgical site infection rates: a monocentric observational cohort study date: 2020-09-14 words: 4094.0 sentences: 207.0 pages: flesch: 45.0 cache: ./cache/cord-290209-gkx57lyq.txt txt: ./txt/cord-290209-gkx57lyq.txt summary: At multivariate analysis, the measures to reduce the SARS-CoV-2 spread (OR 0.368; p 0.05) were independently associated with the reduction for total, superficial and deep SSIs. Moreover, the presence of drains (OR 4.99; p 0.009) and a Type III–IV of SWC (OR 1.8; p 0.001) demonstrated a worse effect regarding the primary endpoint. The presence of a drain and a contaminated or dirty type of surgery (according to SWC) could increase the overall rate of SSIs, but the presence of a drain did not demonstrate an increased risk of superficial and/or deep SSIs. On the other hand, protection with surgical masks for both patient and surgeon during the post-operative period in the surgical unit and the absence of visitors, dramatically reduced superficial and deep SSIs. These two simple precautions emerged as independently associated with the reduction of both superficial and deep SSIs. Quality improvement initiatives aimed at reducing SSI rates are often hindered by limited or even conflicting evidence for proposed interventions to reduce SSI [33] . Surgery and the postoperative management of surgical wound carries a non-negligible risk of SSIs. In this study, we provided important insights into the superficial and deep surgical site infection risk assessment for patients who underwent surgery. abstract: Surgical site infections are the most common in-hospital acquired infections. The aim of this study and the primary endpoint is to evaluate how the measures to reduce the SARS-CoV-2 spreading affected the superficial and deep SSI rate. A total of 541 patients were included. Of those, 198 from March to April 2018, 220 from March till April 2019 and 123 in the COVID-19 era from March to April 2020. The primary endpoint occurred in 39 over 541 patients. In COVID-19 era, we reported a lower rate of global SSIs (3.3% vs. 8.4%; p 0.035), few patients developed a superficial SSIs (0.8% vs. 3.4%; p 0.018) and none experienced deep SSIs (0% vs. 3.4%; p 0.025). Comparing the previous two “COVID-19-free” years, no significative differences were reported. At multivariate analysis, the measures to reduce the SARS-CoV-2 spread (OR 0.368; p 0.05) were independently associated with the reduction for total, superficial and deep SSIs. Moreover, the presence of drains (OR 4.99; p 0.009) and a Type III–IV of SWC (OR 1.8; p 0.001) demonstrated a worse effect regarding the primary endpoint. Furthermore, the presence of the drain was not associated with an increased risk of superficial and deep SSIs. In this study, we provided important insights into the superficial and deep SSIs risk assessment for patients who underwent surgery. Simple and easily viable precautions such as wearing surgical masks and the restriction of visitors emerged as promising tools for the reduction of SSIs risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32926340/ doi: 10.1007/s13304-020-00884-6 id: cord-341176-83khavoh author: Lotfi, Melika title: CRISPR/Cas13: A potential therapeutic option of COVID-19 date: 2020-09-17 words: 5287.0 sentences: 274.0 pages: flesch: 49.0 cache: ./cache/cord-341176-83khavoh.txt txt: ./txt/cord-341176-83khavoh.txt summary: In contrast to traditional vaccines and therapies, which rely on priming the human immune system to identify viral proteins and components and reduce viral entrance into cells (12) , the CRISPR-based system has focused on identifying and degrading the intracellular viral genome and its resulting viral mRNAs. Thus, for using CRISPR as a therapeutic option, it is critical to identify the SARS-CoV-2 molecular characteristics. They found that the two highly-conserved regions in SARS-CoV-2 genome, which can be appropriate to be targeted by PAC-MAN as a potential pan-coronavirus inhibition strategy are respectively the RNA-dependent RNA polymerase (RdRP) gene in the open reading frame1a/b or ORF1a/b region, which maintains the proliferation of all coronaviruses, and the Nucleocapsid (N) gene at the 3'' end of the genome, which encodes the capsid protein for viral packaging (13) . abstract: The novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be considered as the most important current global issue, as it has caused the novel coronavirus disease (COVID-19) pandemic, which has resulted in high mortality and morbidity rates all around the world. Although scientists are trying to discover novel therapies and develop and evaluate various previous treatments, at the time of writing this paper, there was no definite therapy and vaccine for COVID-19. So, as COVID-19 has called ideas for treatment, controlling, and diagnosis, we discussed the application of Clustered Regularly Interspaced Short Palindromic Repeats/Cas13 (CRISPR/Cas13) as a treatment of COVID-19, which received less attention compared with other potential therapeutic options. url: https://doi.org/10.1016/j.biopha.2020.110738 doi: 10.1016/j.biopha.2020.110738 id: cord-314051-dr27bsvt author: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 words: 3121.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-314051-dr27bsvt.txt txt: ./txt/cord-314051-dr27bsvt.txt summary: If viral carriage is not detected by testing, patients may proceed with elective surgery whereby signs and symptoms of coronavirus disease (COVID-19) may arise in the postoperative period, leading to adverse outcomes. 3 While screening with RT-PCR may detect some presymptomatic preoperative patients, the window of diagnostic utility is small, and careful interpretation of negative and positive test results must be considered prior to altering the course of therapy. A positive RT-PCR result identifies a group of patients who may be infected with SARS-CoV-2 and should have elective surgeries delayed. Si la présence virale n''est pas dépistée par un test, les patients peuvent aller de l''avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d''une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32578049/ doi: 10.1007/s12630-020-01746-w id: cord-280003-ndpuezpo author: Lou, Bin title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date: 2020-03-27 words: 3024.0 sentences: 190.0 pages: flesch: 57.0 cache: ./cache/cord-280003-ndpuezpo.txt txt: ./txt/cord-280003-ndpuezpo.txt summary: Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. In order to answer some of the questions, we investigated the characteristics of antibody responses in 80 Covid-19 patients during their hospitalization periods, through detecting total antibody, IgM and IgG using immunoassays. A total of 80 Covid-19 patients and 100 to 300 healthy people were tested for antibodies against SARS-CoV-2 using different immunoassays. The present data showed that the sensitivity of total antibody detection was higher than that of IgM and IgG (p<0.001) while the specificities are overall comparable when the same testing technic (ELISA, CLMA or LFIA) is used. abstract: Background Timely diagnosis of SARS-CoV-2 infection is the prerequisite for treatment and preventive quarantine. The serology characteristics and complement diagnosis value of antibody test to RNA test needs to be demonstrated. Method A patient cohort study was conducted at the first affiliated hospital of Zhejiang University, China. Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The antibody dynamics during the infection were described. Results The seroconversion rate for Ab, IgM and IgG in COVID-19 patients was 98.8% (79/80), 93.8% (75/80) and 93.8% (75/80), respectively. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. The antibody levels increased rapidly since 6 d.p.o and accompanied with the decline of viral load. For patients in the early stage of illness (0-7d.p.o),Ab showed the highest sensitivity (64.1%) compared to the IgM and IgG (33.3% for both, p<0.001). The sensitivities of Ab, IgM and IgG detection increased to 100%, 96.7% and 93.3% two weeks later, respectively. Conclusions Typical acute antibody response is induced during the SARS-CoV-2 infection. The serology testing provides important complementation to RNA test for pathogenic specific diagnosis and helpful information to evaluate the adapted immunity status of patient. It should be strongly recommended to apply well-validated antibody tests in the clinical management and public health practice to improve the control of COVID-19 infection. url: https://doi.org/10.1101/2020.03.23.20041707 doi: 10.1101/2020.03.23.20041707 id: cord-256556-1zea3wa1 author: Lou, Yan title: Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial date: 2020-10-25 words: 4228.0 sentences: 225.0 pages: flesch: 50.0 cache: ./cache/cord-256556-1zea3wa1.txt txt: ./txt/cord-256556-1zea3wa1.txt summary: The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir marboxil, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. Then, an exploratory single center, open-label, randomized, controlled trial was conducted to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). This trial was an exploratory single center, open-label, randomized, controlled trial to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). The activity against SARS-CoV-2 was tested in vitro for the antiviral drugs used in this trial, including arbidol, ritonavir, lopinavir, darunavir, baloxavir acid, and favipiravir. abstract: Background: Effective antiviral drugs for COVID-19 are still lacking. This study aims to evaluate the clinical outcomes and plasma concentrations of baloxavir acid and favipiravir in COVID-19 patients. Methods: Favipiravir and baloxavir acid were evaluated for their antiviral activity against SARS-CoV-2 in vitro before the trial initiation. We conducted an exploratory trial with 3 arms involving hospitalized adult patients with COVID-19. Patients were randomized assigned in a 1:1:1 ratio into baloxavir marboxil group, favipiravir group, and control group. The primary outcome was the percentage of subjects with viral negative by Day 14 and the time from randomization to clinical improvement. Virus load reduction, blood drug concentration and clinical presentation were also observed. The trial was registered with Chinese Clinical Trial Registry (ChiCTR 2000029544). Results: Baloxavir acid showed antiviral activity in vitro with the half-maximal effective concentration (EC(50)) of 5.48 μM comparable to arbidol and lopinavir, but favipiravir didn't demonstrate significant antiviral activity up to 100 μM. Thirty patients were enrolled. The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir marboxil, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. One reason for the lack of virological effect and clinical benefits may be due to insufficient concentrations of these drugs relative to their antiviral activities. One of the limitations of this study is the time from symptom onset to randomization, especially in the baloxavir marboxil and control groups, which is higher than the favipiravir group. Conclusions: Our findings could not prove a benefit of addition of either baloxavir marboxil or favipiravir under the trial dosages to the existing standard treatment. url: https://www.sciencedirect.com/science/article/pii/S092809872030419X?v=s5 doi: 10.1016/j.ejps.2020.105631 id: cord-317468-pnxni1x5 author: Louie, Philip K. title: Early Peri-operative Outcomes Were Unchanged in Patients Undergoing Spine Surgery During the COVID-19 Pandemic in New York City date: 2020-09-15 words: 3474.0 sentences: 151.0 pages: flesch: 39.0 cache: ./cache/cord-317468-pnxni1x5.txt txt: ./txt/cord-317468-pnxni1x5.txt summary: The purpose of this study was to describe the peri-operative outcomes of patients undergoing spine surgery for spine pathology during the heights of the COVID-19 pandemic in New York City, including particular attention to the development of SARS-CoV-2 symptoms, post-operative complications, and patient monitoring following hospital discharge during the early post-operative period. The surgical dates also encompass a period of time in which the institution (1) followed state directives to suspend elective surgery and instead utilize strict criteria to define essential surgical cases (Table 1) , (2) dispensed personal protective equipment to medical personnel, (3) selectively performed post-admission SARS-CoV-2 testing (Cepheid Xpert Xpress SARS-CoV-2 RT-PCR, Sunnyvale, CA, USA) following patient assessment by a multidisciplinary team, (4) initiated a telehealth service for post-operative follow-up, and (5) began a progressively intensive patient screening process (Fig. 1) . abstract: BACKGROUND: Healthcare resources have been greatly limited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic halting non-essential surgical cases without clear service expansion protocols. QUESTIONS/PURPOSES: We sought to compare the peri-operative outcomes of patients undergoing spine surgery during the SARS-CoV-2 pandemic to a matched cohort prior to the pandemic. METHODS: We identified a consecutive sample of 127 adult patients undergoing spine surgery between March 9, 2020, and April 10, 2020, corresponding with the state of emergency declared in New York and the latest possible time for 1-month surgical follow-up. The study group was matched one-to-one based on age, gender, and body mass index with eligible control patients who underwent similar spine procedures prior to the SARS-CoV-2 outbreak. Surgeries performed for infectious or oncologic indications were excluded. Intra- and post-operative complication rates, re-operations, hospital length of stay, re-admissions, post-operative visit format, development of post-operative fever and/or respiratory symptoms, and SAR-CoV2 testing. RESULTS: A total of 254 patients (127 SARS-CoV-2 pandemic, 127 matched controls) were included. One hundred fifty-eight were male (62%), and 96 were female (38%). The mean age in the pandemic group was 59.8 ± 13.4 years; that of the matched controls was 60.3 ± 12.3. All patients underwent general anesthesia and did not require re-intubation. There were no significant differences in 1-month post-operative complication rates (16.5% pandemic vs. 12.6% control). There was one death in the pandemic group. No patients tested positive for the virus. CONCLUSION: This study represents the first report of post-operative outcomes in a large group of spine surgical patients in an area heavily affected by the SARS-CoV-2 pandemic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11420-020-09797-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11420-020-09797-x doi: 10.1007/s11420-020-09797-x id: cord-334858-wxexl0qy author: Lozada-Nur, Francina title: Dysgeusia in COVID-19: possible mechanisms and implications date: 2020-06-27 words: 1839.0 sentences: 113.0 pages: flesch: 50.0 cache: ./cache/cord-334858-wxexl0qy.txt txt: ./txt/cord-334858-wxexl0qy.txt summary: A European multi-center epidemiological study 6 analyzing the prevalence of olfactory and gustatory dysfunctions as a clinical presentation in a cohort of 417 laboratory-confirmed cases of COVID-19 with mild-to-moderate disease presentation reported that 88.8% of patients population had gustatory disorders. 18, 19 It may be quite plausible that SARS-Cov-2 binds to ACE2 receptors present in oral mucosa, triggering an inflammatory response that leads to cellular and genetic changes which could alter taste. It is possible that zinc chelation through immune mechanisms and molecules known to increase in concentration with inflammatory processes may result in acute hypozincemia 27 or a more localized change in cellular zinc homeostasis of oral gustatory cells due to infection with SARS-Cov-2. We hypothesize that changes in localized cellular zinc homeostasis in oral gustatory cells due to immune responses to SARS-Cov-2 viral replication, may result in dysgeusia which may or may not be accompanied by hypozincemia. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2212440320310750?v=s5 doi: 10.1016/j.oooo.2020.06.016 id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 words: 2679.0 sentences: 172.0 pages: flesch: 61.0 cache: ./cache/cord-329794-msxrdhb3.txt txt: ./txt/cord-329794-msxrdhb3.txt summary: Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. abstract: Abstract Severe acute respiratory syndrome (SARS) is a highly contagious and sometimes a lethal disease, which spread over five continents in 2002–2003. Laboratory analysis showed that the etiologic agent for SARS is a new type of coronavirus. Currently, there is no specific treatment for this disease. RNA interference (RNAi) is a recently discovered antiviral mechanism in plant and animal cells that induces a specific degradation of double-stranded RNA. Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Moreover, this construct significantly reduced the plaque formation of SARS coronaviruses in Vero-E6 cells. The data may suggest a new approach for treatment of SARS patients. url: https://www.sciencedirect.com/science/article/pii/S0042682204002181 doi: 10.1016/j.virol.2004.03.031 id: cord-296661-6ndn2qxc author: Lu, Dingnan title: Primary concentration – The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review date: 2020-07-25 words: 6214.0 sentences: 304.0 pages: flesch: 42.0 cache: ./cache/cord-296661-6ndn2qxc.txt txt: ./txt/cord-296661-6ndn2qxc.txt summary: This review provides new insights into the primary concentration methods that have been adopted by the eighteen recently reported COVID-19 wastewater detection studies, along with a brief discussion of the mechanisms of the most commonly used virus concentration methods, including the PEG-based separation, electrostatically charged membrane filtration, and ultrafiltration. The PEG-based separation is the most used technique (7 out of 18) among all concentration methods, and all four studies that adopted this concentration method showed positive results regarding the SARS-CoV-2 detection in wastewater samples (Bar Or et al., 2020; Hata et al., 2020; La Rosa et al., 2020b; Wu et al., 2020) . As previously mentioned, using electrostatically charged membranes filtration to concentrate viruses from turbid water, such as raw wastewater, can be subject to a significant reduction of virus recovery efficiency due to the presence of organic matter and high turbidity, which can lead to a preferential attachment to the charged filters and raise the risk of detrimental clogging. abstract: Abstract The recent outbreak of a novel coronavirus SARS-CoV-2 has posed a significant global public health threat and caused dramatic social and economic disruptions. A new research direction is attracting a significant amount of attention in the academic community of environmental sciences and engineering, in which rapid community-level monitoring could be achieved by applying the methodology of wastewater based epidemiology (WBE). Given the fact that the development of a mass balance on the total number of viral RNA copies in wastewater samples and the infected stool specimens is the heart of WBE, the result of the quantitative RNA detection in wastewater has to be highly sensitive, accurate, and reliable. Thus, applying effective concentration methods before the subsequent RNA extraction and RT-qPCR detection is a must-have procedure for the WBE. This review provides new insights into the primary concentration methods that have been adopted by the eighteen recently reported COVID-19 wastewater detection studies, along with a brief discussion of the mechanisms of the most commonly used virus concentration methods, including the PEG-based separation, electrostatically charged membrane filtration, and ultrafiltration. In the end, two easy and well-proven concentration strategies are recommended as below, aiming to maximize the practical significance and operational effectiveness of the SARS-CoV-2 virus concentration from wastewater samples. Strategy1: Prefiltration-Salt addition-Electronegative membrane filtration (for initial volume ≤ 50 mL). Strategy2: Prefiltration-PEG-based separation-Overnight standing (for initial volume from 50 to 1000 mL). url: https://api.elsevier.com/content/article/pii/S0048969720347744 doi: 10.1016/j.scitotenv.2020.141245 id: cord-273893-3nd6ptrg author: Lu, Guangwen title: Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 date: 2013-07-07 words: 4674.0 sentences: 260.0 pages: flesch: 56.0 cache: ./cache/cord-273893-3nd6ptrg.txt txt: ./txt/cord-273893-3nd6ptrg.txt summary: Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. abstract: The newly emergent Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe pulmonary disease in humans(1,2), representing the second example of a highly pathogenic coronavirus, the first being SARS-CoV(3). CD26 (also known as dipeptidyl peptidase 4, DPP4) was recently identified as the cellular receptor for MERS-CoV(4). The engagement of the MERS-CoV spike protein with CD26 mediates viral attachment to host cells and virus–cell fusion, thereby initiating infection. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Furthermore, binding between the RBD and CD26 is measured using real-time surface plasmon resonance with a dissociation constant of 16.7 nM. The viral RBD is composed of a core subdomain homologous to that of the SARS-CoV spike protein, and a unique strand-dominated external receptor binding motif that recognizes blades IV and V of the CD26 β-propeller. The atomic details at the interface between the two binding entities reveal a surprising protein–protein contact mediated mainly by hydrophilic residues. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature12328) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nature12328 doi: 10.1038/nature12328 id: cord-275357-yx8lsfdv author: Lu, J. title: Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting date: 2020-05-15 words: 2348.0 sentences: 130.0 pages: flesch: 56.0 cache: ./cache/cord-275357-yx8lsfdv.txt txt: ./txt/cord-275357-yx8lsfdv.txt summary: The Limits of Detection of two sets of RT-PCR assays, the TaqPath Multiplex RT-PCR COVID-19 Kit (Thermo) and the PrimerDesign COVID-19 assay, were determined using different viral RNA and reaction volumes ( Supplementary Table 1 ). In the Helix lab, a miniaturized 5 uL input RNA (10 uL total reaction volume) TaqPath assay was performed on a Quantstudio 7 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 6.25 viral copies. In the UCSD lab, a miniaturized 2 uL input RNA (3 uL total reaction volume) TaqPath assay was performed on a Quantstudio 5 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 3.125 viral copies. RNA was extracted from the NPS VTM and Saliva samples and analyzed using the PrimerDesign and TaqPath assays at the sites shown in Table 2 (full dataset with Ct values for each viral target sequence and internal control sequences are shown in Supplementary Table 2 ). abstract: The use of saliva collection for SARS-CoV-2 diagnostics in the ambulatory setting provides several advantages when compared to nasopharyngeal swabs (NPS), including ease of self-collection and reduced use of personal protective equipment (PPE). In addition saliva collection could be advantageous in advising if a convalescent patient is able to return to work after a period of self-quarantine. We investigated the utility of saliva collection in the community setting at Renown Health in a prospective Diagnostic Cohort of 88 patients and in a Convalescent Cohort of 24 patients. In the Diagnostic Cohort, we find that saliva collection has reduced sensitivity (~15% less) relative than NPS. And in our convalescent cohort of patients greater than 8 days and less than 21 days from first symptom, we find that saliva has ~ 50% sensitivity relative to NPS. Our results suggest that rigorous studies in the intended populations should be performed before large-scale screening using saliva as the test matrix is initiated. url: http://medrxiv.org/cgi/content/short/2020.05.11.20092338v1?rss=1 doi: 10.1101/2020.05.11.20092338 id: cord-342361-eu3rry7p author: Lu, Jiatao title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China date: 2020-02-23 words: 3782.0 sentences: 232.0 pages: flesch: 55.0 cache: ./cache/cord-342361-eu3rry7p.txt txt: ./txt/cord-342361-eu3rry7p.txt summary: title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China Our current study was conducted aiming to characterize the clinical features of either confirmed or suspected COVID-19 patients who were hospitalized in a COVID-19-designated hospital in Wuhan, and to develop a mortality risk index, as an evaluation tool used for establishing a COVID-19 hierarchical management system in highly endemic areas. To our knowledge, this is the first-ever study to compare the clinical characteristics of pneumonia patients who were either positive or negative for SARS-CoV-2 by RT-PCR assay, and to develop a first-ever COVID-19 mortality risk index derived from patients in highly endemic areas during early stage of outbreak. abstract: Background: Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) outbreaks in Wuhan, China, healthcare systems capacities in highly endemic areas have been overwhelmed. Approaches to efficient management are urgently needed and key to a quicker control of the outbreaks and casualties. We aimed to characterize the clinical features of hospitalized patients with confirmed or suspected COVID-19, and develop a mortality risk index for COVID-19 patients. Methods: In this retrospective one-centre cohort study, we included all the confirmed or suspected COVID-19 patients hospitalized in a COVID-19-designated hospital from January 21 to February 5, 2020. Demographic, clinical, laboratory, radiological and clinical outcome data were collected from the hospital information system, nursing records and laboratory reports. Results: Of 577 patients with at least one post-admission evaluation, the median age was 55 years (interquartile range [IQR], 39 - 66); 254 (44.0%) were men; 22.8% (100/438) were severe pneumonia on admission, and 37.7% (75/199) patients were SARS-CoV-2 positive. The clinical, laboratory and radiological data were comparable between positive and negative SARS-CoV-2 patients. During a median follow-up of 8.4 days (IQR, 5.8 - 12.0), 39 patients died with a 12-day cumulative mortality of 8.7% (95% CI, 5.9% to 11.5%). A simple mortality risk index (called ACP index), composed of Age and C-reactive Protein, was developed. By applying the ACP index, patients were categorized into three grades. The 12-day cumulative mortality in grade three (age ≥ 60 years and CRP ≥ 34 mg/L) was 33.2% (95% CI, 19.8% to 44.3%), which was significantly higher than those of grade two (age ≥ 60 years and CRP < 34 mg/L; age < 60 years and CRP ≥ 34 mg/L; 5.6% [95% CI, 0 to 11.3%]) and grade one (age < 60 years and CRP < 34 mg/L, 0%) (P <0.001), respectively. Conclusion: The ACP index can predict COVID-19 related short-term mortality, which may be a useful and convenient tool for quickly establishing a COVID-19 hierarchical management system that can greatly reduce the medical burden and therefore mortality in highly endemic areas. url: https://doi.org/10.1101/2020.02.20.20025510 doi: 10.1101/2020.02.20.20025510 id: cord-319964-ju9japd8 author: Lu, Jing title: Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China date: 2020-04-04 words: 4100.0 sentences: 250.0 pages: flesch: 53.0 cache: ./cache/cord-319964-ju9japd8.txt txt: ./txt/cord-319964-ju9japd8.txt summary: Highlights: 1) 1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020; 2) Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint To understand the genetic diversity of the SARS-CoV-2 epidemic in Guangdong we performed phylogenetic analyses using maximum likelihood and Bayesian molecular clock approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint Our analyses of the genomic epidemiology of SARS-CoV-2 in Guangdong province indicate that, following the first COVID-19 case detected in early January, most infections were the result of virus importation from elsewhere, and that chains of local transmission were limited in size and duration. abstract: Highlights: 1) 1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020; 2) Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples. 3) Genomic analyses reveal multiple virus importations into Guangdong Province, resulting in genetically distinct clusters that require careful interpretation. 4) Large-scale epidemiological surveillance and intervention measures were effective in interrupting community transmission in Guangdong Summary: COVID-19 is caused by the SARS-CoV-2 coronavirus and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain due to low virus genetic variation early in the pandemic. Our results illustrate how the timing, size and duration of putative local transmission chains were constrained by national travel restrictions and by the province's large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required as the number of cases imported from other countries is increasing. url: https://doi.org/10.1101/2020.04.01.20047076 doi: 10.1101/2020.04.01.20047076 id: cord-326282-uxn64olw author: Lu, Maolin title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 words: 3264.0 sentences: 207.0 pages: flesch: 55.0 cache: ./cache/cord-326282-uxn64olw.txt txt: ./txt/cord-326282-uxn64olw.txt summary: To measure conformational dynamics of the SARS-CoV-2 S trimer on the surface of virus particles, we established two types of particles, lentiviral pseudoparticles carrying S, as well as coronaviruslike particles generated by expression of S, membrane (M), envelope (E) and nucleocapsid (N) 15 protein (S-MEN)(24, 25) (Fig. 1, A and B ). Analyses of smFRET data from ligand-free S protein on lentiviral particles revealed that the SARS-CoV-2 S protein is dynamic, sampling at least four distinct conformational states To identify the receptor-bound conformation of the SARS-CoV-2 S protein by smFRET, we measured the conformational consequences of soluble, monomeric hACE2 binding. Addition of 5 the monomeric hACE2 receptor to surface-immobilized virus particles lead to increased occupancy of the low-(~0.1) FRET S protein conformation (Fig. 2E) , which was observed at both the single-molecule and population level (Fig. 2F ). Relative state-occupancy and fitting parameters in each of four FRET-defined conformational states of SARS-CoV-2 spike protein on the surface of virus particles. abstract: SARS-CoV-2 spike (S) mediates entry into cells and is critical for vaccine development against COVID-19. Structural studies have revealed distinct conformations of S, but real-time information that connects these structures, is lacking. Here we apply single-molecule Förster Resonance Energy Transfer (smFRET) imaging to observe conformational dynamics of S on virus particles. Virus-associated S dynamically samples at least four distinct conformational states. In response to hACE2, S opens sequentially into the hACE2-bound S conformation through at least one on-path intermediate. Conformational preferences of convalescent plasma and antibodies suggest mechanisms of neutralization involving either competition with hACE2 for binding to RBD or allosteric interference with conformational changes required for entry. Our findings inform on mechanisms of S recognition and conformations for immunogen design. url: https://doi.org/10.1101/2020.09.10.286948 doi: 10.1101/2020.09.10.286948 id: cord-016312-u47mb2h0 author: Lu, Pu-Xuan title: Introduction of Emerging Infectious Diseases date: 2015-07-25 words: 1780.0 sentences: 115.0 pages: flesch: 51.0 cache: ./cache/cord-016312-u47mb2h0.txt txt: ./txt/cord-016312-u47mb2h0.txt summary: Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specific preventive or control measures. Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specifi c preventive or control measures. Cases in point are the epidemics of SARS in 2003 and H7N9 avian infl uenza around 2006, which have eloquently demonstrated their great threats to human health, society, and economy. Such contagious diseases did not exist in the past and newly emerge due to new pathogens such as AIDS, severe acute respiratory syndrome (SARS), human infection with highly pathogenic avian infl uenza H5N1, infl uenza A (HlN1), and human infection with avian infl uenza H7N9. revealed that 60.3 % EIDs were zoonotic, with 71.8 % caused by wild animals, such as human avian infl uenza and Ebola virus. abstract: Emerging infectious diseases (EIDs) refer to contagious diseases newly appeared, or with drug resistance, whose incidences have been rapidly increasing and are likely to further rise in the future. EIDs are usually discovered in three ways. Firstly, some existing diseases are ascertained as EIDs due to the recent discovery of pathogens. Secondly, previously considered noninfectious diseases are identified contagious as a result of new etiological findings. Thirdly, new infectious diseases are incurred by various complicated reasons such as evolution of pathogens. Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specific preventive or control measures. Therefore, EIDs have become a major public health problem worldwide. Cases in point are the epidemics of SARS in 2003 and H7N9 avian influenza around 2006, which have eloquently demonstrated their great threats to human health, society, and economy. In the coming twenty-first century, contagious diseases are expected to remain as a crucial public health concern for countries around the world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120557/ doi: 10.1007/978-94-017-7363-8_1 id: cord-310657-04pp0o74 author: Lu, Renfei title: A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date: 2020-04-18 words: 4064.0 sentences: 206.0 pages: flesch: 51.0 cache: ./cache/cord-310657-04pp0o74.txt txt: ./txt/cord-310657-04pp0o74.txt summary: Using a mismatch-tolerant amplification technique, we developed a simple, rapid, sensitive and visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection based on its N gene. In this study, we applied the mismatch-tolerant technique to develop novel real-time fluorescent and visual RT-LAMP assays for the rapid and sensitive detection of SARS-CoV-2 RNA, and evaluated the novel assays using clinical samples. The novel RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies per reaction, and shows no cross-reactivity with 17 common human respiratory viruses, including four other human coronaviruses (OC43, 229E, HKU-1 and NL63). In view of a mean viral load of 1.4 × 10 6 copies/mL in nasal swabs of COVID-19 patients, the novel assay is sufficiently sensitive for the detection of SARS-CoV-2 at an early stage of infection using nasal swab specimens. The RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies of SARS-CoV-2 RNA per 25 µL reaction, and good specificity regarding common respiratory viruses. abstract: COVID-19 has become a major global public health burden, currently causing a rapidly growing number of infections and significant morbidity and mortality around the world. Early detection with fast and sensitive assays and timely intervention are crucial for interrupting the spread of the COVID-19 virus (SARS-CoV-2). Using a mismatch-tolerant amplification technique, we developed a simple, rapid, sensitive and visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection based on its N gene. The assay has a high specificity and sensitivity, and robust reproducibility, and its results can be monitored using a real-time PCR machine or visualized via colorimetric change from red to yellow. The limit of detection (LOD) of the assay is 118.6 copies of SARS-CoV-2 RNA per 25 μL reaction. The reaction can be completed within 30 min for real-time fluorescence monitoring, or 40 min for visual detection when the template input is more than 200 copies per 25 μL reaction. To evaluate the viability of the assay, a comparison between the RT-LAMP and a commercial RT-qPCR assay was made using 56 clinical samples. The SARS-CoV-2 RT-LAMP assay showed perfect agreement in detection with the RT-qPCR assay. The newly-developed SARS-CoV-2 RT-LAMP assay is a simple and rapid method for COVID-19 surveillance. url: https://www.ncbi.nlm.nih.gov/pubmed/32325642/ doi: 10.3390/ijms21082826 id: cord-333195-m4gvpsf8 author: Lu, Renfei title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date: 2020-04-01 words: 1894.0 sentences: 102.0 pages: flesch: 54.0 cache: ./cache/cord-333195-m4gvpsf8.txt txt: ./txt/cord-333195-m4gvpsf8.txt summary: title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Here, we present a novel visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid and sensitive detection of SARS-CoV-2 using mismatch-tolerant technique. The RdRp primers showed higher amplification efficiency, and were selected to establish the SARS-CoV-2 detection assay using the mismatch-tolerant RT-LAMP method Zhou et al. For the POCT diagnosis of SARS-CoV-2 infection in the resource-poor settings, we developed the assay into a visual detection using WarmStart Colorimetric LAMP 2 9 Master Mix (New England Biolabs, Beverly, MA, United States). The sensitivity of the colorimetric RT-LAMP assay for SARS-CoV-2 was 30 copies per reaction, slightly lower than the real-time monitoring (Fig. 1E) . The evaluation with 24 clinical samples showed that all 17 COVID-19 patients in Nantong city were positive for SARS-CoV-2 by both the RT-LAMP and the RT-qPCR assays, showing a full consistence. abstract: nan url: https://doi.org/10.1007/s12250-020-00218-1 doi: 10.1007/s12250-020-00218-1 id: cord-256961-935r7w01 author: Lu, S. title: Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis date: 2020-04-22 words: 5136.0 sentences: 465.0 pages: flesch: 57.0 cache: ./cache/cord-256961-935r7w01.txt txt: ./txt/cord-256961-935r7w01.txt summary: We included RCTs and cohort studies evaluating the effectiveness and safety of glucocorticoids in children and adults with COVID-19, SARS and MERS, and conducted meta-analyses of the main indicators that were identified in the studies. We used the following search: ("COVID-19" OR "SARS-CoV-2" OR "2019 novel coronavirus" OR "2019-nCoV" OR "Wuhan coronavirus" OR "novel coronavirus" OR "Wuhan seafood market pneumonia virus" OR "Wuhan virus" OR "MERS" OR "SARS" OR "Severe Acute Respiratory Syndrome" OR "Middle East Respiratory Syndrome Coronavirus" OR "Influenza") AND ("adrenal cortex hormones" OR " betamethasone valerate " OR " glucocorticoids" OR " methylprednisolone" OR "Cortisone" OR "Dexamethasone" OR "Cortodoxone" OR "Hydrocortisone"). Five cohort studies (one on COVID-19, three on SARS, one on severe MERS) with a total of 5872 patients assessed the duration of hospital stay (29, 31, 35, 37, 41 Figure 9 ). abstract: Background: Glucocorticoids are widely used in the treatment of various pulmonary inflammatory diseases, but they are also often accompanied by significant adverse reactions. Published guidelines point out that low dose and short duration systemic glucocorticoid therapy may be considered for patients with rapidly progressing COVID-19 while the evidence is still limited. Methods: We comprehensively searched electronic databases and supplemented the screening by conducting a manual search. We included RCTs and cohort studies evaluating the effectiveness and safety of glucocorticoids in children and adults with COVID-19, SARS and MERS, and conducted meta-analyses of the main indicators that were identified in the studies. Results: Our search retrieved 23 studies, including one RCT and 22 cohort studies, with a total of 13,815 patients. In adults with COVID-19, the use of systemic glucocorticoid did not reduce mortality (RR=2.00, 95% CI: 0.69 to 5.75, I 2=90.9%) or the duration of lung inflammation (WMD=-1 days, 95% CI: -2.91 to 0.91), while a significant reduction was found in the duration of fever (WMD=-3.23 days, 95% CI: -3.56 to -2.90). In patients with SARS, glucocorticoids also did not reduce the mortality (RR=1.52, 95% CI: 0.89 to 2.60, I2=84.6%), duration of fever (WMD=0.82 days, 95% CI: -2.88 to 4.52, I2=97.9%) or duration of lung inflammation absorption (WMD=0.95 days, 95% CI: -7.57 to 9.48, I2=94.6%). The use of systemic glucocorticoid therapy prolonged the duration of hospital stay in all patients (COVID-19, SARS and MERS). Conclusions: Glucocorticoid therapy was found to reduce the duration of fever, but not mortality, duration of hospitalization or lung inflammation absorption. Long-term use of high-dose glucocorticoids increased the risk of adverse reactions such as coinfections, so routine use of systemic glucocorticoids for patients with COVID-19 cannot be recommend. Keywords: COVID-19; glucocorticoids; meta-analysis; rapid review url: http://medrxiv.org/cgi/content/short/2020.04.17.20064469v1?rss=1 doi: 10.1101/2020.04.17.20064469 id: cord-328585-1rkrrx8a author: Lu, Shuai title: The immunodominant and neutralization linear epitopes for SARS-CoV-2 date: 2020-08-27 words: 2954.0 sentences: 254.0 pages: flesch: 69.0 cache: ./cache/cord-328585-1rkrrx8a.txt txt: ./txt/cord-328585-1rkrrx8a.txt summary: To investigate the spectrum of antibodies in COVID-19 patients, we detected the binding of the 155 early convalescent sera of 8 imported (Europe) cases which infected SARS-CoV-2 in early April, 156 2020 and 12 domestic (China) cases in early February, 2020 to various epitopes ( Table 1) K203R204/G189R203G204/R203G204/R203G204S344 in N protein, respectively (Table 1) , 172 resulting in different immunodominant epitopes of different virus sub-strains which provide the 173 bases for the differential diagnosis. The predicted epitopes induce neutralization antibody production 175 SARS-CoV-2 pseudo-virus neutralization assay is a well-accepted method to detect the ability of 176 vaccine to inhibit SARS-CoV-2 infection . To assess 8 neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with 178 D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT 179 cells which stably expressed ACE2. abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses. url: https://doi.org/10.1101/2020.08.27.267716 doi: 10.1101/2020.08.27.267716 id: cord-273645-czh3zfb3 author: Lu, Shuaiyao title: Comparison of SARS-CoV-2 infections among 3 species of non-human primates date: 2020-07-17 words: 2197.0 sentences: 171.0 pages: flesch: 65.0 cache: ./cache/cord-273645-czh3zfb3.txt txt: ./txt/cord-273645-czh3zfb3.txt summary: In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Here, to establish the COVID-19 model, two families including 3 species of non-human primates, which are widely used for animal models with their own advantages and disadvantages, were experimentally infected with SARS-CoV-2, followed by comparisons of clinical symptoms, hematology, biochemical indexes, immunology and histopathology among 3 species. Given that host factors may be involved in viral pathogenesis, we designed an experiment in the present study to investigate whether host genetics, age and gender affect SARS-CoV-2 infection in non-human primates ( Figure 1 ). To know dynamics of viral replication and virus shedding, samples of nasal swabs, throat swabs, anal swabs, feces, blood and tissues were collected at the indicated time points, and SARS-CoV-2 genomes were quantitated by RT-qPCR. abstract: COVID-19, caused by SARS-CoV-2 infection, has recently been announced as a pandemic all over the world. Plenty of diagnostic, preventive and therapeutic knowledges have been enriched from clinical studies since December 2019. However, animal models, particularly non-human primate models, are urgently needed for critical questions that could not be answered in clinical patients, evaluations of anti-viral drugs and vaccines. In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Clinical signs were recorded. Samples were collected for analysis of viral shedding, viremia and histopathological examination. Increased body temperature was observed in 100% (12/12) M. mulatta, 33.3% (2/6) M. fascicularis and none (0/6) of C. jacchus post inoculation of SARS-CoV-2. All of M. mulatta and M. fascicularis showed chest radiographic abnormality. Viral genomes were detected in nasal swabs, throat swabs, anal swabs and blood from all 3 species of monkeys. Viral shedding from upper respiratory samples reached the peak between day 6 and day 8 post inoculation. From necropsied M. mulatta and M. fascicularis, the tissues showing virus positive were mainly lung, weasand, bronchus and spleen. No viral genome was seen in any of tissues from 2 necropsied C. jacchus. Severe gross lesions and histopathological changes were observed in lung, heart and stomach of SARS-CoV-2 infected animals. In summary, we have established a NHP model for COVID-19, which could be used to evaluate drugs and vaccines, and investigate viral pathogenesis. M. mulatta is the most susceptible to SARS-CoV-2 infection, followed by M. fascicularis and C. jacchus. One Sentence Summary M. mulatta is the most susceptible to SARS-CoV-2 infection as compared to M. fascicularis and C. jacchus. url: https://doi.org/10.1101/2020.04.08.031807 doi: 10.1101/2020.04.08.031807 id: cord-303027-r2jgu2be author: Lu, Yen-Ta title: Viral load and outcome in SARS infection: The role of personal protective equipment in the emergency department date: 2006-01-24 words: 4579.0 sentences: 234.0 pages: flesch: 57.0 cache: ./cache/cord-303027-r2jgu2be.txt txt: ./txt/cord-303027-r2jgu2be.txt summary: Both specific droplet and rigorous universal precautions were thus recommended for healthcare workers (HCWs) taking care of patients with severe acute respiratory syndrome (SARS) (4) . We designed this study to explore the relationship between personal protective equipment (PPE) used by HCWs and the clinical course, outcome, and viral load in both HCWs and non-HCWs involved in a SARS cluster stemming from exposure to a single index case in our Emergency Department. Differences between the quantitative RT-PCR values for SARS-CoV in nasopharyngeal swab and HRCT scores in HCWs and non-HCWs were tested for significance using the Mann-Whitney U test. We have described a better clinical outcome after SARS in 4 HCWs compared with 12 non-HCWs; despite all having been involved in a cluster related to one index patient, with 13 apparently directly infected by that patient and 3 others by secondary transmission. abstract: This study was conducted to evaluate the effectiveness of personal protective equipment (PPE) against severe acute respiratory syndrome (SARS). Sixteen patients in a SARS cluster, including 4 health care workers (HCWs) and 12 non-HCWs were studied. We compared the initial viral load by nasopharyngeal swabs, clinical progression, and outcome of this cluster. The HCWs had a lower viral load. The non-HCWs had a higher mean C-reactive protein, lower oxygen saturation, and a higher incidence of intubation and death. Secondary household transmission developed in three of the non-HCWs’ families. One month after discharge, non-HCWs had more signs of fibrosis on high resolution computed tomography (HRCT) scan and an impaired pulmonary function test. Although most of the PPE do not confer absolute protection against SARS, it seems that they may lower exposure to the virus, leading to a lower risk of secondary transmission, and be associated with relatively mild disease and a better early outcome. url: https://api.elsevier.com/content/article/pii/S0736467905003513 doi: 10.1016/j.jemermed.2005.03.011 id: cord-326956-oz047qmf author: Lu, Yiping title: Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study date: 2020-08-03 words: 5822.0 sentences: 287.0 pages: flesch: 48.0 cache: ./cache/cord-326956-oz047qmf.txt txt: ./txt/cord-326956-oz047qmf.txt summary: COVID-19 patients had statistically significantly higher bilateral gray matter volumes (GMV) in olfactory cortices, hippocampi, insulas, left Rolandic operculum, left Heschl''s gyrus and right cingulate gyrus and a general decline of MD, AD, RD accompanied with an increase of FA in white matter, especially AD in the right CR, EC and SFF, and MD in SFF compared with non-COVID-19 volunteers (corrected p value <0.05). We found that these recovered COVID-19 patients were more likely to have enlarged olfactory cortices, hippocampi, insulas, Heschl''s gyrus, Rolandic operculum and cingulate gyrus, and a general decline of Mean Diffusivity (MD), Axial Diffusivity (AD), Radial Diffusivity (RD) accompanied with an increase of Fractional Anisotropy (FA) in white matter, especially AD in the right Coronal Radiata (CR), External Capsule (EC) and Superior Frontal-occipital Fasciculus (SFF), and MD in SFF compared with non-COVID-19 volunteers. abstract: BACKGROUND: Increasing evidence supported the possible neuro-invasion potential of SARS-CoV-2. However, no studies were conducted to explore the existence of the micro-structural changes in the central nervous system after infection. We aimed to identify the existence of potential brain micro-structural changes related to SARS-CoV-2. METHODS: In this prospective study, diffusion tensor imaging (DTI) and 3D high-resolution T1WI sequences were acquired in 60 recovered COVID-19 patients (56.67% male; age: 44.10 ± 16.00) and 39 age- and sex-matched non-COVID-19 controls (56.41% male; age: 45.88 ± 13.90). Registered fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were quantified for DTI, and an index score system was introduced. Regional volumes derived from Voxel-based Morphometry (VBM) and DTI metrics were compared using analysis of covariance (ANCOVA). Two sample t-test and Spearman correlation were conducted to assess the relationships among imaging indices, index scores and clinical information. FINDINGS: In this follow-up stage, neurological symptoms were presented in 55% COVID-19 patients. COVID-19 patients had statistically significantly higher bilateral gray matter volumes (GMV) in olfactory cortices, hippocampi, insulas, left Rolandic operculum, left Heschl's gyrus and right cingulate gyrus and a general decline of MD, AD, RD accompanied with an increase of FA in white matter, especially AD in the right CR, EC and SFF, and MD in SFF compared with non-COVID-19 volunteers (corrected p value <0.05). Global GMV, GMVs in left Rolandic operculum, right cingulate, bilateral hippocampi, left Heschl's gyrus, and Global MD of WM were found to correlate with memory loss (p value <0.05). GMVs in the right cingulate gyrus and left hippocampus were related to smell loss (p value <0.05). MD-GM score, global GMV, and GMV in right cingulate gyrus were correlated with LDH level (p value <0.05). INTERPRETATION: Study findings revealed possible disruption to micro-structural and functional brain integrity in the recovery stages of COVID-19, suggesting the long-term consequences of SARS-CoV-2. FUNDING: Shanghai Natural Science Foundation, Youth Program of National Natural Science Foundation of China, Shanghai Sailing Program, Shanghai Science and Technology Development, Shanghai Municipal Science and Technology Major Project and ZJ Lab. url: https://www.sciencedirect.com/science/article/pii/S2589537020302285 doi: 10.1016/j.eclinm.2020.100484 id: cord-277705-6lgt2i7f author: Luan, Junwen title: A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2 date: 2020-04-10 words: 1149.0 sentences: 89.0 pages: flesch: 64.0 cache: ./cache/cord-277705-6lgt2i7f.txt txt: ./txt/cord-277705-6lgt2i7f.txt summary: An RGD motif (403-405) was identified in SARS-CoV-2 S protein ( Figure 1A ). These results suggested that RGD/KGD integrin-binding motif is conserved in several coronaviruses including SARS-CoV-2 and SARS-CoV. To investigate whether RGD/KGD motif in S proteins from SARS-CoV-2 We identified a KGD motif in 353-355 of ACE2 (BAB40370.1), which is a key region for binding S protein ( Figure 1F ). Integrin associates with ACE2 through its KGD motif including K353, which is one of key AAs for S protein recognition. Integrin associates with S protein by its RGD/KGD motif, which would shield the space of RBM for contacting with ACE2. Because RGD recognized a broader spectrum of integrins than KGD, more integrins could block receptor binding of SARS-CoV-2 S than that of SARS-CoV S. In conclusion, we identified an RGD/KGD integrin-binding motif in S proteins from SARS-CoV-2 and SARS-CoV. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S016344532030181X?v=s5 doi: 10.1016/j.jinf.2020.03.046 id: cord-344949-9zyz4hll author: Luban, Jeremy title: The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date: 2020-08-05 words: 5552.0 sentences: 277.0 pages: flesch: 47.0 cache: ./cache/cord-344949-9zyz4hll.txt txt: ./txt/cord-344949-9zyz4hll.txt summary: a Selectivity index is the ratio of CC50 to EC50 b values are mean ± standard deviation (SD) Abbreviations: CC50, compound concentration at which cell number is reduced by 50%; EC50, compound concentration at which viral replication on a linear scale is inhibited by 50%; GFP, green fluorescent protein; HCV, hepatitis C virus replicon genotype 1b; PIV-3, Parainfluenza type 3; RSV, respiratory syncytial virus; RT-qPCR, quantitative reverse transcription PCR; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TCID50, tissue culture infectious dose 50%. In the BT co-cell culture system, which models chronic inflammatory conditions driven by B cell activation and antibody production, incubation of cells with 10 nM PTC299 resulted in a significant reduction in the levels of soluble (s)IgG, sIL-17A, sIL-17F, sIL-6, and sTNFα released from the cells after 72 hours of stimulation (range, 49% to 68%) (all p values <0.01) ( Figure 4 and Table 2 ). abstract: The coronavirus disease 2019 (COVID-19) pandemic has created an urgent need for therapeutics that inhibit the SARS-CoV-2 virus and suppress the fulminant inflammation characteristic of advanced illness. Here, we describe the anti-COVID-19 potential of PTC299, an orally available compound that is a potent inhibitor of dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme of the de novo pyrimidine biosynthesis pathway. In tissue culture, PTC299 manifests robust, dose-dependent, and DHODH-dependent inhibition of SARS CoV-2 replication (EC50 range, 2.0 to 31.6 nM) with a selectivity index >3,800. PTC299 also blocked replication of other RNA viruses, including Ebola virus. Consistent with known DHODH requirements for immunomodulatory cytokine production, PTC299 inhibited the production of interleukin (IL)-6, IL-17A (also called IL-17), IL-17F, and vascular endothelial growth factor (VEGF) in tissue culture models. The combination of anti-SARS-CoV-2 activity, cytokine inhibitory activity, and previously established favorable pharmacokinetic and human safety profiles render PTC299 a promising therapeutic for COVID-19. url: https://doi.org/10.1101/2020.08.05.238394 doi: 10.1101/2020.08.05.238394 id: cord-269521-vq2m4c8q author: Lucchese, Guglielmo title: Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons date: 2020-05-01 words: 815.0 sentences: 59.0 pages: flesch: 43.0 cache: ./cache/cord-269521-vq2m4c8q.txt txt: ./txt/cord-269521-vq2m4c8q.txt summary: Brainstem involvement has been proposed as a possible cause of respiratory failure in SARS-CoV-2 infection, given that the virus appears to have potential for inducing neurological damage, a number of neurological symptoms have been described, and SARS-CoV has been reported to massively infect the brainstem in both patients and experimental animals [3] . Indeed, the proteome of the virus (https://www.ncbi.nlm.nih.gov/nuccore/ MN908947) shares three sequences of six amino acids (GSQASS, LNEVAK, and SAAEAS) with three proteins, namely DAB1, AIFM, and SURF1 (as catalogued at www.uniprot.org) that are present in the human brainstem preBötC (Table 1 ) and are part of experimentally validated epitopes [10] . In the context of this peptide sharing between the preBötc, and SARS-CoV-2, it appears possible that immunological targeting of DAB1, AIFM1, and SURF1 might contribute to brainstem-related respiratory failure in COVID-19 patients and that a therapeutic benefit might come from immunomodulatory agents. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32361194/ doi: 10.1016/j.autrev.2020.102556 id: cord-319728-d0kf9gme author: Lucchini, Matteo title: Is serological response to SARS-CoV-2 preserved in MS patients on ocrelizumab treatment? A case report date: 2020-06-22 words: 1382.0 sentences: 85.0 pages: flesch: 50.0 cache: ./cache/cord-319728-d0kf9gme.txt txt: ./txt/cord-319728-d0kf9gme.txt summary: We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. Few case reports of multiple sclerosis (MS) patients receiving ocrelizumab who contracted COVID-19 with a benign course have recently been published (Novi et al., 2020; Suwanwongse and Shabarek, 2020) . Forty days before COVID-19 onset, the patient performed routine blood tests including cell blood count (CBC), lymphocyte subtypes, immunoglobulin dosage and liver and kidney function showing CD19+ complete depletion (normal CD4+ and CD8+) and IgG at lower limit (700 mg/dl, normal range 700-1600). Despite an optimal recovery from COVID-19, our patient did not develop a full serological response against SARS-CoV-2 as demonstrated by the absence of specific IgG production. abstract: The emergency represented by the COVID-19 pandemic represents a new challenge for clinicians who deal with autoimmune diseases because of patients undergoing immunosuppressive therapy. Few cases of Multiple Sclerosis (MS) patients receiving ocrelizumab who contracted COVID-19 with a benign course have recently been published. We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. Patients on B-cell depleting drugs have a reduced antibody immune response to viral neoantigens. A relative sparing of mucosal-associated lymphoid tissues (MALT) could be responsible for IgA response in our patient. url: https://doi.org/10.1016/j.msard.2020.102323 doi: 10.1016/j.msard.2020.102323 id: cord-304574-03s404s5 author: Luciani, Lorenzo G. title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. Urinary Frequency as a Possible Overlooked Symptom in COVID-19 Patients: Does SARS-CoV-2 Cause Viral Cystitis? Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection date: 2020-06-12 words: 174.0 sentences: 25.0 pages: flesch: 67.0 cache: ./cache/cord-304574-03s404s5.txt txt: ./txt/cord-304574-03s404s5.txt summary: key: cord-304574-03s404s5 authors: Luciani, Lorenzo G.; Gallo, Fabrizio; Malossini, Gianni title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection journal: Eur Urol DOI: 10.1016/j.eururo.2020.06.006 cord_uid: 03s404s5 Mumm et al [1] reported that urinary frequency might be a symptom of SARS-CoV-2. This assumption is based on the finding that the bladder urothelium, as well as the kidney, harbors cells expressing ACE2, the receptor for the viral spike protein [2,3]. Our experience appears to confirm their suspicion, further suggesting that the urinary tract may become the target of life-threatening involvement by SARS-CoV-2. We report three cases of gross hematuria admitted to two hospitals in Northern Italy between The authors have nothing to disclose. Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Eur Urol Eur Urol abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32591102/ doi: 10.1016/j.eururo.2020.06.006 id: cord-259619-sco0d5cc author: Ludvigsson, Johnny title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society date: 2020-09-30 words: 2498.0 sentences: 129.0 pages: flesch: 51.0 cache: ./cache/cord-259619-sco0d5cc.txt txt: ./txt/cord-259619-sco0d5cc.txt summary: title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society We suggest here that more selective assisted isolation of vulnerable populations would reduce the predictable increase in hospital admissions and more rapidly alleviate the fallout from total lockdown measures. Even though COVID19 sometimes leads to need for treatment at intensive care units (ICU) also for younger individuals, the virus appears most dangerous for a selected group of the most vulnerable people. We must consider diverting our major efforts to protect the vulnerable-elderly and patients with preexisting comorbidities-by providing safe and assisted isolation and care; not least now that lockdown rules start to be relaxed. However, these measures have isolated subjects at risk, but have not increased immunization of the population with so called herd immunity through the transient infection of the less vulnerable. abstract: nan url: https://doi.org/10.3389/fpubh.2020.562901 doi: 10.3389/fpubh.2020.562901 id: cord-337572-kx5hihnr author: Ludwig, Stephan title: Coronaviruses and SARS-CoV-2: A Brief Overview date: 2020-04-20 words: 2668.0 sentences: 167.0 pages: flesch: 54.0 cache: ./cache/cord-337572-kx5hihnr.txt txt: ./txt/cord-337572-kx5hihnr.txt summary: The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 . Here we provide a short background on coronaviruses and their origin, and we describe in more detail the novel SARS-CoV-2 and the efforts thus far to identify effective therapies against COVID-19. The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). 19 SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 At the end of December 2019, China reported the increasing occurrence of pneumonia in the city of Wuhan, Hubei province. Identification of a novel coronavirus in patients with severe acute respiratory syndrome abstract: In late December 2019, several cases of pneumonia of unknown origin were reported from China, which in early January 2020 were announced to be caused by a novel coronavirus. The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). Despite massive attempts to contain the disease in China, the virus has spread globally, and COVID-19 was declared a pandemic by the World Health Organization (WHO) in March 2020. Here we provide a short background on coronaviruses, and describe in more detail the novel SARS-CoV-2 and attempts to identify effective therapies against COVID-19. url: https://doi.org/10.1213/ane.0000000000004845 doi: 10.1213/ane.0000000000004845 id: cord-319164-wbrnhpgs author: Luellen, E. title: A Machine Learning Explanation of Incidence Inequalities of SARS-CoV-2 Across 88 Days in 157 Countries date: 2020-06-08 words: 1911.0 sentences: 114.0 pages: flesch: 49.0 cache: ./cache/cord-319164-wbrnhpgs.txt txt: ./txt/cord-319164-wbrnhpgs.txt summary: Because the SARS-CoV-2 (COVID-19) pandemic viral outbreaks will likely continue until effective vaccines are widely administered, (1) new capabilities to accurately predict incidence rates by location and time to know in advance the disease burden and specific needs for any given population are valuable to minimize morbidity and mortality. In this study, a random forest of 9,250 regression trees was applied to 6,941 observations of 13 statistically significant predictor variables targeting SARS-CoV-2 incidence rates per 100,000 across 88 days in 157 countries. One key finding is an algorithm that can predict the incidence rate per day of a SARS-CoV-2 epidemic cycle with a pseudo-R2 accuracy of 98.5% and explain 97.4% of the variances. In this study, machine learning -a robust statistical version of artificial intelligence -was applied to a data set of 6,941 observations to identify the relative importance of 13 demographic, economic, environmental, and public health factors in modulating the incidence rate per 100,000 population of SARS-CoV-2 across 88 days in 157 countries. abstract: Because the SARS-CoV-2 (COVID-19) pandemic viral outbreaks will likely continue until effective vaccines are widely administered, (1) new capabilities to accurately predict incidence rates by location and time to know in advance the disease burden and specific needs for any given population are valuable to minimize morbidity and mortality. In this study, a random forest of 9,250 regression trees was applied to 6,941 observations of 13 statistically significant predictor variables targeting SARS-CoV-2 incidence rates per 100,000 across 88 days in 157 countries. One key finding is an algorithm that can predict the incidence rate per day of a SARS-CoV-2 epidemic cycle with a pseudo-R2 accuracy of 98.5% and explain 97.4% of the variances. Another key finding is the relative importance of 13 demographic, economic, environmental, and public health modulators to the SARS-CoV-2 incidence rate. Four factors proposed in earlier research as potential modulators have no statistically significant relationship with incidence rates (2)(3). These findings give leaders new capabilities for improved capacity planning and targeting stay-at-home interventions and prioritizing programming by knowing the atypical social determinants that are the root causes of SARS-CoV-2 incidence variance. This work also proves that machine learning can accurately and quickly explain disease dynamics for zoonoses with pandemic potential. url: http://medrxiv.org/cgi/content/short/2020.06.06.20124529v1?rss=1 doi: 10.1101/2020.06.06.20124529 id: cord-261405-n05wjimk author: Lui, Grace title: Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19 date: 2020-04-18 words: 1157.0 sentences: 81.0 pages: flesch: 56.0 cache: ./cache/cord-261405-n05wjimk.txt txt: ./txt/cord-261405-n05wjimk.txt summary: reported in this journal that viral shedding of SARS-CoV-2 in nasal swabs was longer in intensive care unit (ICU) patients compared with non-ICU patients with Coronavirus Disease 2019 (COVID-19). 3 We collected serial upper (pooled nasopharyngeal and throat swabs, N=75) and lower respiratory tract samples (sputum and tracheal aspirate, N=43), peripheral blood plasma (N=50), urine (N=43) and stool (N=43) samples from all participants, and monitored SARS-CoV-2 viral loads in these samples. In all five participants with severe/critical and three with moderate disease, viral loads in respiratory tract samples continued to rise and peaked in the second week of illness (range 5.57-9.66 log copies/mL). In this study of patients with COVID-19 across a wide spectrum of severity, we observed that viral shedding in the respiratory tract lasting longer than 14 days was common. In more severe disease, viral load appeared to peak in the second week of illness in both upper and lower respiratory tract. abstract: nan url: https://doi.org/10.1016/j.jinf.2020.04.014 doi: 10.1016/j.jinf.2020.04.014 id: cord-273859-tr4s5i7h author: Luis García Garmendia, José title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 words: 1379.0 sentences: 139.0 pages: flesch: 61.0 cache: ./cache/cord-273859-tr4s5i7h.txt txt: ./txt/cord-273859-tr4s5i7h.txt summary: En las formas clínicas menos graves, la detección de ARN viral es máxima durante las dos primeras semanas desde el inicio de los síntomas(4), y a partir de los 7-10 días se produce respuesta inmunológica de IgM y después de IgG (5) . El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). A estos pacientes se les hicieron 2 determinaciones de rRT-PCR de Coronavirus a partir de 21 días del inicio de síntomas, separadas por 24 h, para comprobar si persistía eliminación del virus. La detección del ARN viral mediante técnicas de rRT-PCR parece ser una forma adecuada de determinar la necesidad de aislamiento de los pacientes con SARS-CoV-2(8, 12). Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. abstract: nan url: https://api.elsevier.com/content/article/pii/S0210569120301534 doi: 10.1016/j.medin.2020.04.014 id: cord-289490-u0f0zyad author: Lumba, Rishi title: Neonate Born to a Mother with a Diagnosis of Suspected Intra-Amniotic Infection versus COVID-19 or Both date: 2020-07-18 words: 1444.0 sentences: 73.0 pages: flesch: 44.0 cache: ./cache/cord-289490-u0f0zyad.txt txt: ./txt/cord-289490-u0f0zyad.txt summary: In this report, we detail a case of a newborn born to a mother with a clinical diagnosis of intra-amniotic infection with maternal fever and fetal tachycardia, who was then found to be SARS-CoV-2 positive on testing. Due to the varying presentation of COVID-19, this case illustrates the low threshold needed to test mothers for SARS-CoV-2 in order to prevent horizontal transmission to neonates and to healthcare providers. e current recommendations made by the American College of Obstetricians and Gynecologists (ACOG) are that the diagnosis of suspected intraamniotic infection be made on clinical criteria, which include maternal intrapartum fever and one or more of the following: maternal leukocytosis, purulent cervical drainage, or fetal tachycardia. Although a clinical diagnosis of Triple I was made by the obstetrics team, given maternal fever, testing for SARS-CoV-2 was included as well. abstract: A diagnosis of intra-amniotic infection is typically made based on clinical criteria, including maternal intrapartum fever and one or more of the following: maternal leukocytosis, purulent cervical drainage, or fetal tachycardia. The diagnosis can also be made in patients with an isolated fever of 39°C, or greater, without any other clinical risk factors present. Coronavirus disease 2019 (COVID-19), caused by the virus SARS-CoV-2, has been noted to have varying signs and symptoms over the course of the disease including fever, cough, fatigue, anorexia, shortness of breath, sputum production, and myalgia. In this report, we detail a case of a newborn born to a mother with a clinical diagnosis of intra-amniotic infection with maternal fever and fetal tachycardia, who was then found to be SARS-CoV-2 positive on testing. Due to the varying presentation of COVID-19, this case illustrates the low threshold needed to test mothers for SARS-CoV-2 in order to prevent horizontal transmission to neonates and to healthcare providers. url: https://doi.org/10.1155/2020/8886800 doi: 10.1155/2020/8886800 id: cord-277669-uujny2dm author: Lumpuy-Castillo, Jairo title: Cardiovascular Damage in COVID-19: Therapeutic Approaches Targeting the Renin-Angiotensin-Aldosterone System date: 2020-09-04 words: 7443.0 sentences: 476.0 pages: flesch: 40.0 cache: ./cache/cord-277669-uujny2dm.txt txt: ./txt/cord-277669-uujny2dm.txt summary: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can differentially infect multiple tissues (i.e., lung, vessel, heart, liver) in different stages of disease, and in an ageand sex-dependent manner. In particular, treatments with angiotensin-converting enzyme inhibitors (ACEi) and angiotensin-receptor blockers (ARB) may help to reduce hyperinflammation and viral propagation, while infusion of soluble ACE2 may trap plasma viral particles and increase cardioprotective Ang-(1–9) and Ang-(1–7) peptides. SARS-CoV-2 infection initiates in the respiratory system, when the S protein of its external layer binds the angiotensin-converting enzyme-2 (ACE2) at the plasma membrane of host cells [5] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . abstract: Coronavirus disease 2019 (COVID-19) is usually more severe and associated with worst outcomes in individuals with pre-existing cardiovascular pathologies, including hypertension or atherothrombosis. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can differentially infect multiple tissues (i.e., lung, vessel, heart, liver) in different stages of disease, and in an age- and sex-dependent manner. In particular, cardiovascular (CV) cells (e.g., endothelial cells, cardiomyocytes) could be directly infected and indirectly disturbed by systemic alterations, leading to hyperinflammatory, apoptotic, thrombotic, and vasoconstrictive responses. Until now, hundreds of clinical trials are testing antivirals and immunomodulators to decrease SARS-CoV-2 infection or related systemic anomalies. However, new therapies targeting the CV system might reduce the severity and lethality of disease. In this line, activation of the non-canonical pathway of the renin-angiotensin-aldosterone system (RAAS) could improve CV homeostasis under COVID-19. In particular, treatments with angiotensin-converting enzyme inhibitors (ACEi) and angiotensin-receptor blockers (ARB) may help to reduce hyperinflammation and viral propagation, while infusion of soluble ACE2 may trap plasma viral particles and increase cardioprotective Ang-(1–9) and Ang-(1–7) peptides. The association of specific ACE2 polymorphisms with increased susceptibility of infection and related CV pathologies suggests potential genetic therapies. Moreover, specific agonists of Ang-(1–7) receptor could counter-regulate the hypertensive, hyperinflammatory, and hypercoagulable responses. Interestingly, sex hormones could also regulate all these RAAS components. Therefore, while waiting for an efficient vaccine, we suggest further investigations on the non-canonical RAAS pathway to reduce cardiovascular damage and mortality in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32899833/ doi: 10.3390/ijms21186471 id: cord-323383-dmzhywb9 author: Lundon, DJ title: Early Mortality Risk Stratification after SARS-CoV-2 Infection date: 2020-07-04 words: 899.0 sentences: 50.0 pages: flesch: 50.0 cache: ./cache/cord-323383-dmzhywb9.txt txt: ./txt/cord-323383-dmzhywb9.txt summary: While the majority of those who test positive for SARS-CoV-2 will not require hospital admission, intensive care or mechanical ventilation, some will (data from our institution suggest ~13% of those hospitalized due to COVID-19 underwent mechanical ventilation). Using the Mount Sinai Health Systems'' database of all SARS-Co-V-2 positive patients with an encounter in New York City, we developed a prediction model to identify those patients most likely to succumb to the disease thin 7 days (the median time to death of those who died) from the onset of COVID-19 symptoms. The risk probability of death within 7 days for patients was calculated from a model developed in 80% of this cohort, using the 3 demographic and 4 clinical variables listed above. This model demonstrates the significant role that both clinical and social determinants play in predicting the clinical outcome for patients infected with SARS-CoV-2 and tested positive for COVID-19. abstract: nan url: https://doi.org/10.1016/j.medin.2020.06.011 doi: 10.1016/j.medin.2020.06.011 id: cord-310062-mmlh9i1o author: Luo, Haibin title: In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS date: 2004-12-01 words: 5161.0 sentences: 269.0 pages: flesch: 54.0 cache: ./cache/cord-310062-mmlh9i1o.txt txt: ./txt/cord-310062-mmlh9i1o.txt summary: Both the thermal and chemical denaturant-induced denaturation analyses showed that oligomeric SARS_NP unfolds and refolds through a two-state model, and the electrostatic interactions among the charge groups of SARS_NP made a significant contribution to its conformational stability. In addition, the unfolding and refolding characterizations of SARS _ NP dimer caused by thermaland chemical denaturant-induced denaturations were also inspected by fluorescent and CD spectral investigation, it is found that SARS _ NP exhibits its most stable conformation near pH 9.0, and its oligomer dissociation and protein unfolding seem to be of coinstantaneous occurring events. The fluorescent intensity was found to decrease with increase of temperature accompanied by a shift in emission k max from 333 to 343 nm ( Fig. 4A and C) , whereas far-UV CD spectral information suggested the loss of secondary structure for SARS _ NP during its thermal-induced denaturation (Fig. 4B and D) . abstract: The major biochemical and thermodynamic features of nucelocapsid protein of SARS coronavirus (SARS_NP) were characterized by use of non-denatured gel electrophoresis, size-exclusion chromatographic and surface plasmon resonance (SPR) techniques. The results showed that SARS_NP existed in vitro as oligomer, more probably dimer, as the basic functional unit. This protein shows its maximum conformational stability near pH 9.0, and it seems that its oligomer dissociation and protein unfolding occur simultaneously. Thermal-induced unfolding for SARS_NP was totally irreversible. Both the thermal and chemical denaturant-induced denaturation analyses showed that oligomeric SARS_NP unfolds and refolds through a two-state model, and the electrostatic interactions among the charge groups of SARS_NP made a significant contribution to its conformational stability. url: https://www.sciencedirect.com/science/article/pii/S0301462204001607 doi: 10.1016/j.bpc.2004.06.008 id: cord-297599-y4lu8m4k author: Luo, Hua title: Anti-COVID-19 drug screening: Frontier concepts and core technologies date: 2020-10-28 words: 7665.0 sentences: 373.0 pages: flesch: 44.0 cache: ./cache/cord-297599-y4lu8m4k.txt txt: ./txt/cord-297599-y4lu8m4k.txt summary: This paper thoroughly summarizes interdisciplinary notions and techniques, including disease model, biochip, network pharmacology, and molecular docking technology, etc., providing a reference for researchers in the screening of drugs for COVID-19 prevention and treatment. Some researchers are currently using mice as an animal model to test drugs and vaccines and to investigate the nature of the infection of SARS-CoV-2 [49] [50] [51] . In fact, in a study led by Qin Chuan on SARS, engineered mice that could express human ACE2 protein was successfully established, leading this Chinese team pioneered the establishment of a SARS-CoV-2 infected hACE2 transgenic mouse model [54] . For example, an effective and convenient novel mouse model in evaluating in vivo protective capacity of the SARS-CoV-2 vaccines was developed through stitching the human gene for ACE2 into an adenovirus by Perlman et al. abstract: The outbreak of COVID-19 has recently evolved into a global pandemic. Up to July 2020, almost every country has confirmed COVID-19 cases reported worldwide. Many leading experts have predicted that the epidemic will persist for relatively a long period of time. Thus far, there have been no remedies proven effective against the disease. As the nation where COVID-19 broke out first, China has adopted a combination of traditional Chinese medicine and western medicine to fight against the disease, and has achieved significant clinical result. Up to now, the COVID-19 pandemic has been effectively controlled in China. However, the rest of the world (except for a limited number of countries and regions) is still in deep water. This paper thoroughly summarizes interdisciplinary notions and techniques, including disease model, biochip, network pharmacology, and molecular docking technology, etc., providing a reference for researchers in the screening of drugs for COVID-19 prevention and treatment. These methodologies may facilitate researchers to screen out more potential drugs for treating COVID-19 pneumonia and to tackle this global crisis. url: https://www.ncbi.nlm.nih.gov/pubmed/33133232/ doi: 10.1186/s13020-020-00393-z id: cord-313215-diqfmitr author: Luo, Lei title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date: 2020-07-09 words: 1593.0 sentences: 90.0 pages: flesch: 52.0 cache: ./cache/cord-313215-diqfmitr.txt txt: ./txt/cord-313215-diqfmitr.txt summary: title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. To address this question, in this study, we sampled total of 641 surfaces 63 environmental and air specimens among 39 cases in Guangzhou, China, to explore the 64 surrounding environmental surfaces and air contamination by SARS-CoV-2 in non-65 health care settings. A total of 641 157 environmental surfaces and air specimens were collected among 39 COVID-19 cases, 158 and 20 specimens (20/641, 3.1%) were positive by RT-PCR testing from 9 COVID-19 159 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic 160 cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases 161 ( of SARS-CoV-2 (Table 2) . abstract: Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. Methods and findings We explored the SARS-CoV-2 contamination of environmental surfaces and air by collecting air and swabbing environmental surfaces among 39 COVID-19 cases in Guangzhou, China. The specimens were tested by RT-PCR testing. The information collected for COVID-19 cases included basic demographic, clinical severity, onset of symptoms, radiological testing, laboratory testing and hospital admission. A total of 641 environmental surfaces and air specimens were collected among 39 COVID-19 cases before disinfection. Among them, 20 specimens (20/641, 3.1%) were tested positive from 9 COVID-19 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases. All positive specimens were collected within 3 days after diagnosis, and 10 (10/42, 23.8%) were found in toilet (5 on toilet bowl, 4 on sink/faucet/shower, 1 on floor drain), 4 (4/21, 19.0%) in anteroom (2 on water dispenser/cup/bottle, 1 on chair/table, 1 on TV remote), 1 (1/8, 12.5%) in kitchen (1 on dining-table), 1 (1/18, 5.6%) in bedroom (1 on bed/sheet pillow/bedside table), 1 (1/5, 20.0%) in car (1 on steering wheel/seat/handlebar) and 3 (3/20, 21.4%) on door knobs. Air specimens in room (0/10, 0.0%) and car (0/1, 0.0%) were all negative. Conclusions SARS-CoV-2 was found on environmental surfaces especially in toilet, and could survive for several days. We provided evidence of potential for SARS-CoV-2 transmission through contamination of environmental surfaces. url: https://doi.org/10.1101/2020.07.09.195008 doi: 10.1101/2020.07.09.195008 id: cord-347804-kxhasabe author: Luo, Ruibang title: Tracking cytosine depletion in SARS-CoV-2 date: 2020-10-26 words: 1084.0 sentences: 69.0 pages: flesch: 63.0 cache: ./cache/cord-347804-kxhasabe.txt txt: ./txt/cord-347804-kxhasabe.txt summary: Results We built a website to track the composition change of mono-, di-, and tri-nucleotide of SARS-CoV-2 over time. Using 137,315 SARS-CoV-2 strains collected in ten months, we observed cytosine depletion at a rate of about one cytosine loss per month from the whole genome. We built an interactive website at http://www.bio8.cs.hku.hk/sarscov2 to show the mono-, di-, and tri-nucleotide composition trends of the whole genome and single genes. In Table 1 , we first compared the composition of nucleotides in multiple coronaviruses, including SARS-CoV-2 (an average of 76 strands collected from Dec 20, 2019 to Feb 15, 2020), SARS, MERS, and four that causes a common cold. Compared to SARS-CoV-2, which we assumed a relative mortality level of 3, the percentage of cytosine is lower in almost all of the eleven genes in the four common cold coronaviruses with a lower mortality level 1. The results are available on an interactive website at http://www.bio8.cs.hku.hk/sarscov2. abstract: Motivation Danchin et al. have pointed out that cytosine drives the evolution of SARS-CoV-2. A depletion of cytosine might lead to the attenuation of SARS-CoV-2. Results We built a website to track the composition change of mono-, di-, and tri-nucleotide of SARS-CoV-2 over time. The website downloads new strains available from GISAID and updates its results daily. Our analysis suggests that the composition of cytosine in coronaviruses is related to their reported mortality. Using 137,315 SARS-CoV-2 strains collected in ten months, we observed cytosine depletion at a rate of about one cytosine loss per month from the whole genome. Availability The website is available at http://www.bio8.cs.hku.hk/sarscov2/. Contact rbluo@cs.hku.hk Supplementary information Supplementary data are available at Bioinformatics online. url: https://doi.org/10.1101/2020.10.26.354787 doi: 10.1101/2020.10.26.354787 id: cord-279158-dsnniuo6 author: Luo, Y. title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study date: 2020-05-22 words: 3903.0 sentences: 200.0 pages: flesch: 47.0 cache: ./cache/cord-279158-dsnniuo6.txt txt: ./txt/cord-279158-dsnniuo6.txt summary: title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study Through a systematic review, meta-analysis and retrospective cohort study, we found that the low blood sodium population may significantly increase the risk and severity of SARS-CoV-2 infection. In this study, we aimed to find a key risk factor for SARS-CoV-2 epidemic by investigating the relationship between the blood sodium concentration and the severity of patients with COVID-19 through a systematic reviews, meta-analysis and retrospective cohort study. For the systematic review and meta-analysis, median or mean values of serum sodium, chloride and potassium concentrations from each report were considered as an independent variable for statistical analysis, and an unpaired t-test was used to compare the differences between the groups related to the severity of disease. In this study, we found that the patients infected by SARS-CoV-2 on admission have presented the low blood sodium levels (hyponatremia) that were related to the disease severity. abstract: Background Novel coronavirus (SARS-CoV-2) infects human lung tissue cells through angiotensin-converting enzyme-2 (ACE2), and the body sodium is an important factor for regulating the expression of ACE2. Through a systematic review, meta-analysis and retrospective cohort study, we found that the low blood sodium population may significantly increase the risk and severity of SARS-CoV-2 infection. Methods We extracted the data of serum sodium concentrations of patients with COVID-19 on admission from the articles published between Jan 1 and April 28, 2020, and analyzed the relationship between the serum sodium concentrations and the illness severity of patients. Then we used a cohort of 244 patients with COVID-19 for a retrospective analysis. Results We identified 36 studies, one of which comprised 2736 patients.The mean serum sodium concentration in patients with COVID-19 was 138.6 mmol/L, which was much lower than the median level in population (142.0). The mean serum sodium concentration in severe/critical patients (137.0) was significantly lower than those in mild and moderate patients (140.8 and 138.7, respectively). Such findings were confirmed in a retrospective cohort study, of which the mean serum sodium concentration in all patients was 137.5 mmol/L, and the significant differences were found between the mild (139.2) and moderate (137.2) patients, and the mild and severe/critical (136.6) patients. Interestingly, such changes were not obvious in the serum chlorine and potassium concentrations. Conclusions The low sodium state of patients with COVID-19 may not be the consequence of virus infection, but could be a physiological state possibly caused by living habits such as low salt diet and during aging process, which may result in ACE2 overexpression, and increase the risk and severity of COVID-19. These findings may provide a new idea for the prevention and treatment of COVID-19. url: http://medrxiv.org/cgi/content/short/2020.05.18.20102509v1?rss=1 doi: 10.1101/2020.05.18.20102509 id: cord-318006-9op556q2 author: Luo, Y. R. title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-08-02 words: 1063.0 sentences: 67.0 pages: flesch: 51.0 cache: ./cache/cord-318006-9op556q2.txt txt: ./txt/cord-318006-9op556q2.txt summary: Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. . https://doi.org/10.1101/2020.07.30.20165522 doi: medRxiv preprint Further studies are needed to determine if the antibody response, both IgG concentration and avidity, correlate with virus neutralization and persist over time. abstract: The kinetics of immunoglobulin G (IgG) avidity maturation during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was studied. The IgG avidity assay used a novel label-free immunoassay technology to test IgG against the virus spike protein receptor-binding domain (RBD). The technology, thin-film interferometry (TFI), is able to sense the formation of immune complex on a sensing probe without attaching a reporter (enzyme, fluorophore, etc.). It was found that there was a strong correlation between IgG antibody avidity and days since symptom onset (p < 0.0001). In addition, peak readings were significantly higher for specimens from ICU than non-ICU patients for the first month after symptom onset (1-4 weeks) and thereafter (p<0.0001). The findings are consistent for what has been reported for SARS-CoV. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. url: https://doi.org/10.1101/2020.07.30.20165522 doi: 10.1101/2020.07.30.20165522 id: cord-334945-lxowaacg author: Luo, Yi title: Asymptomatic SARS-CoV-2 Infection in Household Contacts of a Healthcare Provider, Wuhan, China date: 2020-08-17 words: 1796.0 sentences: 95.0 pages: flesch: 48.0 cache: ./cache/cord-334945-lxowaacg.txt txt: ./txt/cord-334945-lxowaacg.txt summary: We describe the case of a physician in Wuhan, China, who had mildly symptomatic COVID-19 and the subsequent asymptomatic SARS-CoV-2 infection in all 5 of his household contacts. All 5 household contacts of patient 1 had laboratory evidence of SARS-CoV-2 infection but remained asymptomatic throughout the period of observation (February 11-March 1) (Figure, panel A) . An early report from China on 72,314 COVID-19 cases found that only 1% of SARS-CoV-2 infections were asymptomatic; however, asymptomatic close contacts were not routinely tested in that study (7) . In summary, this single-household study found a high attack rate for asymptomatic SARS-CoV-2 infection among the immediate family members of a symptomatic COVID-19 case-patient. Moreover, our experience indicates that screening symptomatic contacts with a single throat swab test for SARS-CoV-2 might lead to an underestimate of the rate of infection and that asymptomatic persons can repeatedly revert between positive and negative PCR results on throat specimens. abstract: We found that all 5 asymptomatic household contacts of a Wuhan, China, physician with coronavirus disease had severe acute respiratory syndrome coronavirus 2 detected by PCR. The index patient and 2 contacts also had abnormal chest computed tomography scans. Asymptomatic infected household contacts of healthcare workers with coronavirus disease might be underrecognized. url: https://www.ncbi.nlm.nih.gov/pubmed/32330112/ doi: 10.3201/eid2608.201016 id: cord-327862-zcg3baym author: Luo, Yiqi Ruben title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-09-14 words: 1141.0 sentences: 93.0 pages: flesch: 59.0 cache: ./cache/cord-327862-zcg3baym.txt txt: ./txt/cord-327862-zcg3baym.txt summary: The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity abstract: The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. The IgG avidity assay used a novel label-free immunoassay technology. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. url: https://doi.org/10.1093/cid/ciaa1389 doi: 10.1093/cid/ciaa1389 id: cord-276013-8dhqa2gj author: Luo, Yung-Hung title: Overview of coronavirus disease 2019: Treatment updates and advances date: 2020-08-17 words: 3764.0 sentences: 232.0 pages: flesch: 47.0 cache: ./cache/cord-276013-8dhqa2gj.txt txt: ./txt/cord-276013-8dhqa2gj.txt summary: 7, 11 Patients with severe symptoms may have unfavorable disease Abstract: In late December 2019, several cases of pneumonia with unknown cause were reported in Wuhan, China, and this new type of pneumonia spread rapidly to across provinces during the subsequent weeks. Clinical trials on baricitinib demonstrated at least some effects in selective patient populations with COVID-19 acute respiratory disease. On March 17, 2020, the National Medical Products Administration of China approved favipiravir as the first coronavirus drug with evidence from clinical trials showing efficacy for the treatment of COVID-19 infection. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: In late December 2019, several cases of pneumonia with unknown cause were reported in Wuhan, China, and this new type of pneumonia spread rapidly to across provinces during the subsequent weeks. The pathogen was identified quickly and was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infectious disease caused by this virus is referred to as coronavirus disease 2019 (COVID-19). Within months, it has caused a global pandemic and posed a major threat to public health worldwide. As of May 23, 2020, 5 252 452 patients have been confirmed to have the disease, and 339 026 deaths have been reported. Multiple therapeutic trials are ongoing, and some promising results have been released. A vaccine would provide the most effective approach to fight the virus by preventing infection, but none are currently available. To control the COVID-19 outbreak, large-scale measures have been applied to reduce human-to-human transmission of SARS-CoV-2. Susceptible populations, including older adults, children, and healthcare providers, warrant particular attention to avoid transmission and infection. This review introduces current understanding of SARS-CoV-2 infection and treatment strategies, emphasizing the relevant challenges associated with prevention, diagnosis, and management. url: https://doi.org/10.1097/jcma.0000000000000367 doi: 10.1097/jcma.0000000000000367 id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 words: 14361.0 sentences: 795.0 pages: flesch: 42.0 cache: ./cache/cord-271504-t3y1w9ef.txt txt: ./txt/cord-271504-t3y1w9ef.txt summary: A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . abstract: The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression. url: https://www.ncbi.nlm.nih.gov/pubmed/32607499/ doi: 10.34133/2020/6925296 id: cord-297747-kifqgskc author: Lupala, Cecylia S. title: Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date: 2020-03-27 words: 4522.0 sentences: 231.0 pages: flesch: 57.0 cache: ./cache/cord-297747-kifqgskc.txt txt: ./txt/cord-297747-kifqgskc.txt summary: Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. When this study was started, neither the crystal structure of the SARS-CoV-2 spike protein nor the RBD segment were determined, so the homology modeling approach was applied to construct the model of the SARS-CoV-2 spike RBD in complex with the human ACE2 binding domain (denoted as CoV2-RBD/ACE2 in the following). Although the crystal structure and the predicted model of the CoV2-RBD/ACE2 complex provide important information about the binding interactions at the molecular interfaces, MD simulations can extend the knowledge to a dynamics regime in a fully solvated environment. abstract: A novel coronavirus (the SARS-CoV-2) has been identified in January 2020 as the causal pathogen for COVID-19 pneumonia, an outbreak started near the end of 2019 in Wuhan, China. The SARS-CoV-2 was found to be closely related to the SARS-CoV, based on the genomic analysis. The Angiotensin converting enzyme 2 protein (ACE2) utilized by the SARS-CoV as a receptor was found to facilitate the infection of SARS-CoV-2 as well, initiated by the binding of the spike protein to the human ACE2. Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The predicted model is highly consistent with the experimentally determined complex structures. Plausible binding modes between human ACE2 and the RBD were revealed from all-atom MD simulations. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. Two mutants mimicking rat ACE2 were modeled to study the mutation effects on RBD binding to ACE2. The simulations showed that the N-terminal helix and the K353 of the human ACE2 alter the binding modes of the CoV2-RBD to the ACE2. url: https://doi.org/10.1101/2020.03.24.005561 doi: 10.1101/2020.03.24.005561 id: cord-285852-ocu69od2 author: Luqman, Zubair title: Disinfection of corona virus in histopathology laboratories date: 2020-06-25 words: 599.0 sentences: 40.0 pages: flesch: 46.0 cache: ./cache/cord-285852-ocu69od2.txt txt: ./txt/cord-285852-ocu69od2.txt summary: Severe acute respiratory syndrome (SARS CoV‐2/COVID‐19) is a highly contagious and deadly disease caused by a virus belonging to the coronaviridae family. Researchers working in histopathology laboratories, dealing with morbid samples, are particularly vulnerable to infection unless they have very strong immunity. The current review highlights the biological and physical agents that can be used to inactivate the virus and disinfect the surrounding environment in the laboratory. Severe acute respiratory syndrome, also termed SARS-CoV, was first (Lim et al., 2004; Rachael, 2004; World Health Organization [WHO], 2003 , 2006 . Severe acute respiratory syndrome (SARS CoV-2/COVID-19) is a highly communicable and lethal virus (WHO, 2020). Scientists working in histopathology laboratories, handling morbid samples, can be infected with this dangerous virus and are more likely to be susceptible to it regardless of well-functioning immune systems. Severe Acute Respiratory Syndrome (SARS) Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Laboratory-acquired severe acute respiratory syndrome abstract: Severe acute respiratory syndrome (SARS CoV‐2/COVID‐19) is a highly contagious and deadly disease caused by a virus belonging to the coronaviridae family. Researchers working in histopathology laboratories, dealing with morbid samples, are particularly vulnerable to infection unless they have very strong immunity. Hence, a proper precautionary protocol is required for the safety of the laboratory staff. The current review highlights the biological and physical agents that can be used to inactivate the virus and disinfect the surrounding environment in the laboratory. url: https://doi.org/10.1002/ca.23636 doi: 10.1002/ca.23636 id: cord-297451-p5rlquym author: Luz María Trujillo, G title: Relación Entre Covid-19 Y Síndrome De Guillain-Barre En Adultos.Revisión Sistemática date: 2020-07-24 words: 1737.0 sentences: 141.0 pages: flesch: 52.0 cache: ./cache/cord-297451-p5rlquym.txt txt: ./txt/cord-297451-p5rlquym.txt summary: Se han reportado varios casos en distintos centros de salud, de ingreso de pacientes que presentan Síndrome de Guillain-Barré (SGB) y son COVID-19 positivo activos o cursaron con la enfermedad, por lo que se ha planteado la asociación entre ambas patologías. Encefalopatía infecciosa Aguda/tóxica, descrita como síndrome de disfunción cerebral reversible causado por cuadros tóxicos sistémicos, trastornos metabólicos e hipoxia durante un período de infección aguda; y por último, la Enfermedad cerebrovascular aguda (Ataque cerebrovascular) que en los últimos meses ha sido ampliamente atribuida al SARS-CoV-2, debido a que este virus causa una cascada de citoquinas proinflamatorias, encontrándose también niveles elevados de Dímero-D y bajos niveles de plaquetas, pudiendo presentarse un Ataque cerebrovascular 4 . Los estudios analizados demuestran una clara tendencia de asociación entre ambas patologías, donde el virus SARS-CoV-2, sería el potencial gatillador del SGB. Guillain-Barré Syndrome associated with SARS-CoV-2 infection Guillain-Barré Syndrome associated with SARS-CoV-2 infection abstract: ABSTRACT Introduction: Numerous cases have been reported of patients with symptoms of Guillain-Barré syndrome associated with COVID-19, but much information is still lacking on this association and its implications. The objective of this review is to analyse the available evidence on this topic in the adult population. Material and methods: A systematic review was conducted of studies published on scientific databases: PubMed, Cochrane, Science Direct, MEDLINE, and WHO COVID-19 database. Results: We identified 45 studies, which were analysed and completed using the Covidence platform; the final analysis included 24 articles, with a total of 30 patients. Conclusions: We found a strong association between both conditions; furthermore, the studies analysed highlight differences in the presentation of the disease, with greater severity of symptoms in Guillain-Barre syndrome associated with COVID-19. url: https://doi.org/10.1016/j.nrl.2020.07.004 doi: 10.1016/j.nrl.2020.07.004 id: cord-279260-tdvb0fhv author: Lv, Huibin title: COVID‐19 vaccines: knowing the unknown date: 2020-05-21 words: 1476.0 sentences: 98.0 pages: flesch: 46.0 cache: ./cache/cord-279260-tdvb0fhv.txt txt: ./txt/cord-279260-tdvb0fhv.txt summary: It is also important to note that T-cell immunity was found to be elicited by SARS-CoV or MERS-CoV DNA vaccines (both express trimeric spike protein) [7, 9] . Determining which adjuvants can enhance protective vaccine response to SARS-CoV-2 will be important. For example, the MF59-adjuvanted influenza vaccine, Fluad, is only licensed and approved for adults aged 65 years and older, to elicit a higher protective immune response in the elderly This article is protected by copyright. To accelerate vaccine development, animal infection models for SARS-CoV-2 are needed. Although macaques show COVID-19-like disease upon SARS-CoV-2 infection, the non-human primate model is usually not readily accessible to most laboratories [27] . Expressing hACE2 through adenoviral transduction may provide another possible approach to generate a mouse model for SARs-CoV-2 infection. For example, a conserved CD4 T-cell epitope can mediate cross-reactive protection between SARS-CoV and MERS-CoV [38] . abstract: Vaccine development against SARS‐CoV‐2 has drawn attention around the globe due to the exploding pandemic. Although COVID‐19 is caused by a new coronavirus, SARS‐CoV‐2, previous research on other coronavirus vaccines, such as FIPV, SARS and MERS, has provided valuable information for the rapid development of COVID‐19 vaccine. However, important knowledge gaps remain – some are specific to SARS‐CoV‐2, others are fundamental to immunology and vaccinology. Here we discuss areas that need to be addressed for COVID‐19 vaccine development, and what can be learned from examples of vaccine development in the past. Since the beginning of the outbreak, the research progress on COVID‐19 has been remarkable. We are therefore optimistic about the rapid development of COVID‐19 vaccine. This article is protected by copyright. All rights reserved url: https://www.ncbi.nlm.nih.gov/pubmed/32437587/ doi: 10.1002/eji.202048663 id: cord-317042-dll3qt4g author: Lv, Jun title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date: 2020-06-19 words: 2710.0 sentences: 153.0 pages: flesch: 54.0 cache: ./cache/cord-317042-dll3qt4g.txt txt: ./txt/cord-317042-dll3qt4g.txt summary: title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. In this study, we aimed to 1) determine the concentration of SARS-Cov-2 present on the object surfaces and personal protective equipment after the nucleic acid test, 2) identify the risk areas and operation behaviors that may cause contamination, and 3) provide reference basis for the targeted formulation of laboratory disinfection programs and personal operating specifications. The SARS-CoV-2 test results of object surface samples from nucleic acid detection laboratory were shown in Table 1 . In this study, all objects in nucleic acid detection laboratory that tested positive for SARS-CoV-2 were directly or indirectly contacted by the operator''s gloved hands. abstract: Abstract The rapid development of global COVID-19 pandemic poses an unprecedented challenge to the safety and quality of laboratory diagnostic testing. Little is known about the laboratory surface areas and operation behaviors that may cause potential contamination in SARS-CoV-2 nucleic acid testing. This study aims to provide reference basis for the improvement of laboratory disinfection programs and personal operating protocols. In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. All samples were negative by qRT-PCR, in contrast, 13 of 61 samples were positive for SARS-CoV-2 by ddPCR. The areas with highest density of SARS-CoV-2 nucleic acid were the outer gloves of operator A (37.4 copies/cm2), followed by door handle of 4 °C refrigerator (26.25 copies/cm2), goggles of operator A (22.16 copies/cm2), outer cover of high speed centrifuge (19.95 copies/cm2), inner wall of high speed centrifuge (14.70 copies/cm2) and others. We found that all the positive objects were directly or indirectly contacted by the operator's gloved hands, suggesting that hands contact was the main transmission pathway that led to laboratory environmental contamination. In summary, ddPCR has an advantage over qRT-PCR in tracing laboratory contamination. We evaluated the risk areas and operation behaviors that may easily cause contamination, and provided recommendation for improving the laboratory disinfection programs and personal operating specifications. url: https://api.elsevier.com/content/article/pii/S0048969720338924 doi: 10.1016/j.scitotenv.2020.140370 id: cord-346957-bmajkabp author: Lv, Yanbo title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 words: 4933.0 sentences: 261.0 pages: flesch: 57.0 cache: ./cache/cord-346957-bmajkabp.txt txt: ./txt/cord-346957-bmajkabp.txt summary: RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. abstract: BACKGROUND: The spike (S) protein is a major structural glycoprotein of coronavirus (CoV), the causal agent of severe acute respiratory syndrome (SARS). The S protein is a potent target for SARS-specific cell-mediated immune responses. However, the mechanism CoV pathogenesis in SARS and the role of special CTLs in virus clearance are still largely uncharacterized. Here, we describe a study that leads to the identification of a novel HLA-A*0201-restricted epitope from conserved regions of S protein. RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. Four of eight candidate peptides were tested by HLA-A*0201 binding assays. Among the four candidate peptides, Sp8 (S(958-966), VLNDILSRL) induced specific CTLs both ex vivo in PBLs of healthy HLA-A2(+ )donors and in HLA-A2.1/K(b )transgenic mice immunized with a plasmid encoding full-length S protein. The immunized mice released IFN-γ and lysed target cells upon stimulation with Sp8 peptide-pulsed autologous dendritic cells in comparison to other candidates. CONCLUSION: These results suggest that Sp8 is a naturally processed epitope. We propose that Sp8 epitope should help in the characterization of mechanisms of virus control and immunopathology in SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/19958537/ doi: 10.1186/1471-2172-10-61 id: cord-336057-tj9qcuf8 author: Lv, Yantian title: No intrauterine vertical transmission in pregnancy with COVID-19: a case report date: 2020-08-05 words: 1338.0 sentences: 88.0 pages: flesch: 59.0 cache: ./cache/cord-336057-tj9qcuf8.txt txt: ./txt/cord-336057-tj9qcuf8.txt summary: The data of status of pregnant women and neonates after infection of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is limited. We report a case of pregnant woman in her third trimester with critical COVID-19, and amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were retained during cesarean section. Amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were collected during the operation and tested for the SARS-COV-2 nucleic acid, and the mother and infant were separated after the operation. In addition, not only SARS-COV-2 nucleic acid test results were negative in 4 times pharyngeal swabs, but also the anal swab, amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were negative. Li 9 also reported a 35-week pregnant woman with COVID-19, whose amniotic fluid, cord blood and placenta, breast milk samples as well as neonates swab SARS-COV-2 nucleic acid were all negative. abstract: Abstract The coronavirus disease 2019(COVID-19)has been a worldwide pandemic diseases, nearly 400,000 people died at now. The data of status of pregnant women and neonates after infection of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is limited. We report a case of pregnant woman in her third trimester with critical COVID-19, and amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were retained during cesarean section. The SARS-COV-2 nucleic acid test results of these specimens were negative. there is no evidence of intrauterine vertical transmission during delivery in the third trimester, but the data are limited and need to be further explored. url: https://api.elsevier.com/content/article/pii/S1341321X2030266X doi: 10.1016/j.jiac.2020.07.015 id: cord-298327-j04nyg5y author: Lv, Zhihua title: Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study date: 2020-05-18 words: 1892.0 sentences: 118.0 pages: flesch: 51.0 cache: ./cache/cord-298327-j04nyg5y.txt txt: ./txt/cord-298327-j04nyg5y.txt summary: Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Preliminary analysis indicated that higher white blood cell and 129 neutrophil counts, as well as higher levels of D-dimer, IL-6, IL-10, CRP and PCT were found 130 in male patients compared to those of females, which was similar to patients in critical and 131 severe groups compared with those of mild groups (Table 2) . Higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, IL-6, 155 IL-10, CRP and PCT were observed in patients co-infected with other respiratory pathogens 156 than those of infected with SARS-CoV-2 homogeneously (Table 2) . abstract: From December 2019, a novel coronavirus, SARS-CoV-2, caused an outbreak of pneumonia in Wuhan city and rapidly spread throughout China and globally. However, the clinical characteristics and co-infection with other respiratory pathogens of patients with COVID-19 and the factors associated with severity of COVID-19 are still limited. In this retrospective cohort study, we included 354 inpatients with COVID-19 admitted to Renmin Hospital of Wuhan University from February 4, 2020 to February 28, 2020. We found levels of interleukin-6, interleukin-10, C-reactive protein, D-dimer, white blood cell count and neutrophil count were clearly elevated in males and critical cases compared with females and severe and mild cases, respectively. However, lymphopenia was more severe in males than females and levels of tumor necrosis factor alpha were reduced significantly in critical cases than severe and mild cases. 23.5% of severe cases and 24.4% of critical cases were co-infected with other respiratory pathogens. Additionally, stepwise multivariable regression analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated with severity of COVID-19.These findings provide crucial clues for further identification of the mechanisms, characteristics and treatments of patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32425649/ doi: 10.1016/j.micinf.2020.05.007 id: cord-292600-mgvrbfzd author: Ly, T. D. A. title: Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020. date: 2020-05-11 words: 2220.0 sentences: 125.0 pages: flesch: 52.0 cache: ./cache/cord-292600-mgvrbfzd.txt txt: ./txt/cord-292600-mgvrbfzd.txt summary: In March-April, we enrolled 411 homeless individuals, 77 asylum-seekers, 58 people living in precarious conditions, and 152 employees working in these accommodation centres and collected nasal samples. In this study, we present the results of SARS-CoV-2 screening campaigns conducted among sheltered homeless individuals, in comparison with asylum-seekers, other persons living in precarious conditions, and employees working in the accommodation centres. . https://doi.org/10.1101/2020.05.05.20091934 doi: medRxiv preprint Table 3 shows SARS-CoV-2 positivity rates among homeless people according to the time of screening, demographics and housing facility, using univariate analysis. We found an overall 7.0% SARS-CoV-2 positivity rate, with most infected individuals among homeless people and employees working in homeless facilities, while no cases were found in asylum-seekers and in other people also living in precarious conditions. Grey cells: four groups in study : Homeless people (N=411); other specific population living in precarious conditions (N=58), asylum seekers (N=77), and employees (N=152) and SARS-CoV-2 prevalence in each group. abstract: Surveillance of SARS-CoV-2 infection among sheltered homeless and other vulnerable people might provide the information needed to prevent its spread within accommodation centres. In March-April, we enrolled 411 homeless individuals, 77 asylum-seekers, 58 people living in precarious conditions, and 152 employees working in these accommodation centres and collected nasal samples. SARS-CoV-2 carriage was assessed by quantitative PCR. Overall, 49 (7.0%) people were positive for SARS-CoV-2, including 37 homeless individuals (of 411, 9.0%), 12 employees (of 152, 7.9%). SARS-CoV-2 positivity correlated with symptoms, although 51% of positive patients did not report respiratory symptoms or fever. Among homeless people, being young (18-34 years) (OR: 3.83 [1.47-10.0], p=0.006) and being housed in one specific shelter (OR: 9.13 [4.09-20.37], p<0.0001) were independent factors associated with the SARS-CoV-2 positivity rates (11.4% and 20.6%, respectively). The survey reveals the role of collective housing in relation to viral transmission within centres. url: https://doi.org/10.1101/2020.05.05.20091934 doi: 10.1101/2020.05.05.20091934 id: cord-325598-gy809ee0 author: Lyne, Cloutier title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study date: 2020-08-21 words: 1483.0 sentences: 102.0 pages: flesch: 53.0 cache: ./cache/cord-325598-gy809ee0.txt txt: ./txt/cord-325598-gy809ee0.txt summary: title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study In our cross-sectional study, 1.82% of 330 asymptomatic confined individuals living in the community carried SARS-CoV-2 despite no contact with declared cases, raising concerns about unnoticed transmission. Cloutier, Lyne 1 ; Merindol, Natacha 2,3 ; Pépin, Geneviève 4 ; Marcoux-Huard, Caroline 5 ; Vasil, Pier-Alexandre 5 ; Houle, Claudia 6, 7 ; Todkar, Shweta 1 ; Lehoux, Marie-Claude 3 ; Houle, Nathalie 1 ; Germain, Hugo 2,3 ; Danylo, Alexis 6  SARS-CoV-2 may spread asymptomatically in a population under social distancing restrictions. Studies conducted on individuals from the same households have convincingly shown that pre-symptomatic or asymptomatic SARS-CoV-2 carriers might transmit to their family members [8] [9] [10] . Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China. abstract: Several countries have undertaken social distancing measures to stop SARS-CoV-2’ spread. Asymptomatic carriers’ prevalence is unknown and would provide essential information on hidden viral circulation. In our cross-sectional study, 1.82% of 330 asymptomatic confined individuals living in the community carried SARS-CoV-2 despite no contact with declared cases, raising concerns about unnoticed transmission. url: https://api.elsevier.com/content/article/pii/S0196655320307811 doi: 10.1016/j.ajic.2020.08.015 id: cord-310008-hwpn7ti1 author: Lyons-Weiler, James title: Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity date: 2020-04-09 words: 2090.0 sentences: 122.0 pages: flesch: 45.0 cache: ./cache/cord-310008-hwpn7ti1.txt txt: ./txt/cord-310008-hwpn7ti1.txt summary: Failure of SARS and MERS vaccines in animal trials involved pathogenesis consistent with an immunological priming that could involve autoimmunity in lung tissues due to previous exposure to the SARS and MERS spike protein. In this study, I present the likely human epitopic targets of biomimicry-induced autoimmunological components of morbidity and mortality caused by SARS-CoV-2 infection. This is achieved via bioinformatics analysis of the homology between highly immunogenic SARS-CoV-2 epitopes and human proteins to promote comprehension of the etiologies of pathogenesis of SARS-CoV-2 in COVID-19. A list of human peptides with high local homology was compiled and their roles in the pathogenesis of COVID-19 from SARS-CoV-2 infection noted. Remarkably, over 1/3 (11/27) of the immunogenic proteins in SARS-CoV-2 have potentially problematic homology to proteins that are key to the human adaptive immune system (emboldened in Table 1 ). abstract: Homology between human and viral proteins is an established factor in viral- or vaccine-induced autoimmunity. Failure of SARS and MERS vaccines in animal trials involved pathogenesis consistent with an immunological priming that could involve autoimmunity in lung tissues due to previous exposure to the SARS and MERS spike protein. Exposure pathogenesis to SARS-CoV-2 in COVID-19 likely will lead to similar outcomes. Immunogenic peptides in viruses or bacteria that match human proteins are good candidates for pathogenic priming peptides (similar to the more diffuse idea of “immune enhancement”). Here I provide an assessment of potential for human pathogenesis via autoimmunity via exposure, via infection or injection. SAR-CoV-2 spike proteins, and all other SARS-CoV-2 proteins, immunogenic epitopes in each SARS-CoV-2 protein were compared to human proteins in search of high local homologous matching. Only one immunogenic epitope in a SARS-CoV-2 had no homology to human proteins. If all of the parts of the epitopes that are homologous to human proteins are excluded from consideration due to risk of pathogenic priming, the remaining immunogenic parts of the epitopes may be still immunogenic and remain as potentially viable candidates for vaccine development. Mapping of the genes encoding human protein matches to pathways point to targets that could explain the observed presentation of symptoms in COVID-19 disease. It also strongly points to a large number of opportunities for expected disturbances in the immune system itself, targeting elements of MHC Class I and Class II antigen presentation, PD-1 signaling, cross-presentation of soluble exogenous antigens and the ER-Phagosome pathway. Translational consequences of these findings are explored. url: https://api.elsevier.com/content/article/pii/S2589909020300186 doi: 10.1016/j.jtauto.2020.100051 id: cord-258533-gds7sdc9 author: Lytras, Theodore title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries date: 2020-04-16 words: 357.0 sentences: 28.0 pages: flesch: 50.0 cache: ./cache/cord-258533-gds7sdc9.txt txt: ./txt/cord-258533-gds7sdc9.txt summary: title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries Passengers on repatriation flights to Greece from the UK, Spain and Turkey were screened with oropharyngeal swabs on arrival for SARS-CoV-2 infection. Despite almost all passengers being asymptomatic, many tested positive (3.6% from UK, 6.3% from Spain and 6.3% from Turkey), indicating widespread transmission of SARS-CoV-2 in these countries. Even more remarkably, the infection prevalence in these passengers was much higher than in the repatriation flights from Wuhan during the peak of the epidemic there, which was reported as <1%. Estimating infection prevalence in Wuhan City from repatriation flights Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries Estimating the ascertainment rate of SARS-CoV-2 infection in Wuhan, China: implications for management of the global outbreak abstract: Passengers on repatriation flights to Greece from the UK, Spain and Turkey were screened with oropharyngeal swabs on arrival for SARS-CoV-2 infection. Despite almost all passengers being asymptomatic, many tested positive (3.6% from UK, 6.3% from Spain and 6.3% from Turkey), indicating widespread transmission of SARS-CoV-2 in these countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32297940/ doi: 10.1093/jtm/taaa054 id: cord-278271-rpq62xhl author: Lyu, Jinglu title: Reflection on lower rates of COVID-19 in children: does childhood immunizations offer unexpected protection? date: 2020-05-15 words: 4641.0 sentences: 230.0 pages: flesch: 46.0 cache: ./cache/cord-278271-rpq62xhl.txt txt: ./txt/cord-278271-rpq62xhl.txt summary: The frequent childhood vaccinations and repeated pathogens infections might be resulting in trained immunity of innate immune cells, immune fitness of adaptive immune cells or cross-protection of antibodies in the children. Candida isolated from 4 airway specimens in a case report of patients with new coronavirus pneumonia Compared with adult cases, children tend to have milder symptoms, shorter disease course and generally better prognosis. found that memory lymphocytes can also mediate longer-term cross-protection as a byproduct of adaptive immunity: CD8 + memory T cells can be activated by cytokines (IL-12 and IL-18) in early stages of infection in an antigen-independent manner, leading to the production of IFN-γ and enhanced response to subsequent infectious agents (45) . Equipping confirmed COVID-19 patients with these vaccinations as emergent prophylaxis may prevent severe illness caused by secondary infection, in the meantime, it may mobilize the host''s lymphocyte response to the opposite direction in response to SARS-CoV-2. abstract: The incidence of COVID-19 in children and teenagers is only about 2% in China. Children had mild symptoms and hardly infected other children or adults. It is worth considering that children are the most vulnerable to respiratory pathogens, but fatal SARS-like virus had not caused severe cases among them. According to the pathological studies of COVID-19 and SARS, a sharp decrease in T lymphocytes leads to the breakdown of the immune system. The cellular immune system of children differs from that of adults may be the keystone of atypical clinical manifestations or even covert infection. The frequent childhood vaccinations and repeated pathogens infections might be resulting in trained immunity of innate immune cells, immune fitness of adaptive immune cells or cross-protection of antibodies in the children. Therefore, due to lack of specific vaccine, some vaccines for tuberculosis, influenza and pneumonia may have certain application potential for the front-line health workers in the prevention and control of COVID-19. However, for high-risk susceptible populations, such as the elderly with basic diseases such as hypertension and diabetes, it is necessary to explore the acclimatization effect of the planned immune process on their immunity to achieve the trained immunity or immune fitness, so as to improve their own antiviral ability. url: https://www.sciencedirect.com/science/article/pii/S0306987720305090?v=s5 doi: 10.1016/j.mehy.2020.109842 id: cord-253968-jtr0p930 author: López, Verónica title: Recomendaciones en el manejo de la pandemia por coronavirus SARS-CoV-2 (Covid-19) en pacientes con trasplante renal date: 2020-04-03 words: 3627.0 sentences: 405.0 pages: flesch: 56.0 cache: ./cache/cord-253968-jtr0p930.txt txt: ./txt/cord-253968-jtr0p930.txt summary: Manejo clínico del COVID-19: tratamiento médico, del 19 de marzo de 2020), los pacientes receptores de un trasplante renal en los que haya sospecha de infección por SARS-CoV-2 tienen indicación de test diagnóstico y valoración de ingreso si el resultado es positivo, así como de inicio de tratamiento específico. Por tanto, dada la escasa experiencia acumulada y la alta probabilidad de evolución tórpida del cuadro clínico en un breve periodo de tiempo, con desarrollo de fracaso multiorgánico y necesidad de soporte ventilatorio, la estrategia inmunosupresora recomendada a priori, al menos en los casos más graves de pacientes trasplantados renales con neumonía por COVID-19, debe consistir en la interrupción temporal de los inmunosupresores e inicio de metilprednisolona a dosis bajas entre 20 y 40 mg/día, para conferir la adquisición en un corto periodo de tiempo de la inmunidad celular necesaria para controlar la infección y evitar así la progresión de la misma y sus complicaciones vitales. abstract: Resumen La pandemia por coronavirus SARS-CoV-2 (Covid-19) está evolucionando de manera muy rápida y representa un riesgo especial en pacientes inmunodeprimidos y con comorbilidades añadidas. El conocimiento sobre esta infección emergente va también en aumento, si bien, aún sigue habiendo muchas incógnitas, sobre todo en la población con trasplante renal. Este manuscrito presenta una propuesta de actuación con recomendaciones generales y específicas para proteger y prevenir de la infección a esta población tan vulnerable como son los receptores de un trasplante renal. Abstract The SARS-CoV-2 (Covid-19) coronavirus pandemic is evolving very quickly and means a special risk for both immunosuppressed and comorbid patients. Knowledge about this growing infection is also increasing although many uncertainties remain, especially in the kidney transplant population. This manuscript presents a proposal for action with general and specific recommendations to protect and prevent infection in this vulnerable population such as kidney transplant recipients. url: https://doi.org/10.1016/j.nefro.2020.03.002 doi: 10.1016/j.nefro.2020.03.002 id: cord-330369-75cotmn2 author: López, Verónica title: Recommendations on management of the SARS-CoV-2 coronavirus pandemic (Covid-19) in kidney transplant patients date: 2020-04-06 words: 3483.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-330369-75cotmn2.txt txt: ./txt/cord-330369-75cotmn2.txt summary: In kidney transplant recipients, due to their status of immunosuppression, the clinical manifestations, treatment, and prognosis of COVID-19 pneumonia may differ from the general population, hence the importance of early diagnosis by SARS-CoV-2 screening, in those cases where the infection is suspected. Currently there is no evidence from controlled clinical trials to recommend a specific treatment for the SARS-CoV-2 coronavirus in the general population in patients with suspected or confirmed COVID19. 7 Therefore, given the limited experience accumulated and the high probability of torpid evolution in a short period of time, with the development of multi-organ failure and the need for respiratory support, the immunosuppressive strategy recommended a priori, at least in the most severe cases of kidney transplant patients with COVID-19 pneumonia, should involve the temporary interruption of immunosuppressants and the start of methylprednisolone at low doses between 20 and 40 mg/day, to confer the rapid acquisition of the necessary cellular immunity to control the infection and thus prevent vital complications. abstract: Abstract The SARS-CoV-2 (Covid-19) coronavirus pandemic is evolving very quickly and means a special risk for both immunosuppressed and comorbid patients. Knowledge about this growing infection is also increasing although many uncertainties remain, especially in the kidney transplant population. This manuscript presents a proposal for action with general and specific recommendations to protect and prevent infection in this vulnerable population such as kidney transplant recipients. url: https://api.elsevier.com/content/article/pii/S2013251420300481 doi: 10.1016/j.nefroe.2020.03.017 id: cord-287100-xkp8a9b9 author: López-Díaz, Álvaro title: COVID-19 Infection During Pregnancy and Risk of Neurodevelopmental Disorders in Offspring: Time for Collaborative Research date: 2020-10-31 words: 1390.0 sentences: 68.0 pages: flesch: 28.0 cache: ./cache/cord-287100-xkp8a9b9.txt txt: ./txt/cord-287100-xkp8a9b9.txt summary: Cohorts of COVID-19-infected pregnant women may currently provide biological (e.g., umbilical cord and placenta samples) and clinical (e.g., maternal serum samples and neonatal filter paper blood samples) data that would enable the acquisition of very valuable genetic, metabolic, and immunological information. Such information would help determine the extent to which maternal infection, in addition to genetic vulnerability, contributes to an increased risk of neuropsychiatric disturbance in the offspring, and would improve our understanding of the role of immune-inflammatory mechanisms during pregnancy in the etiology of neurodevelopmental disorders (10). Such populationbased birth cohort studies of SARS-CoV-2-infected pregnant women should involve detailed systematic clinical and biological examinations during pregnancy and delivery along with an extended follow-up of the offspring, including neurocognitive, neuroimaging, and electrophysiological examination. Large-scale and long-term prospective population-based birth cohort studies of COVID-19-infected and unaffected pregnant women are needed to unravel the complex interactions between maternal infection and risk of neurodevelopmental disorders in offspring. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33131716/ doi: 10.1016/j.biopsych.2020.09.011 id: cord-344979-ngujhhp6 author: Lübke, Nadine title: Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials date: 2020-08-05 words: 3242.0 sentences: 217.0 pages: flesch: 59.0 cache: ./cache/cord-344979-ngujhhp6.txt txt: ./txt/cord-344979-ngujhhp6.txt summary: OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. Ct values of 91 SARS-CoV-2 positive samples analyzed in direct comparison by RT-qPCR using different primary materials and extracted RNA showed a significant correlation. abstract: BACKGROUND: Fast and reliable detection of SARS-CoV-2 is crucial for efficient control of the COVID-19 pandemic. Due to the high demand for SARS-CoV-2 testing there is a worldwide shortage of RNA extraction reagents. Therefore, extraction-free RT-qPCR protocols are urgently needed. OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). SARS-CoV-2 was detected using novel primers targeted to the E-gene. RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. For validation, 91 respiratory samples were analyzed in direct comparison to classical RNA-based RT-qPCR. Overall 81.3% of the samples were detected in both assays with a strong correlation between both Ct values (r = 0.8492, p < 0.0001). The SARS-CoV-2 detection rate by direct RT-qPCR was 95.8% for Ct values <35. All negative samples were characterized by low viral loads (Ct >35) and/or long storage times before sample processing. CONCLUSION: Direct RT-qPCR is a suitable alternative to classical RNA RT-qPCR, provided that only fresh samples (storage <1 week) are used. RNA extraction should be considered if samples have longer storage times or if PCR inhibition is observed. In summary, this protocol is fast, inexpensive and suitable for all respiratory materials. url: https://www.sciencedirect.com/science/article/pii/S1386653220303218?v=s5 doi: 10.1016/j.jcv.2020.104579 id: cord-196265-mvnkkcow author: M''esz''aros, B''alint title: Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date: 2020-04-21 words: 12653.0 sentences: 666.0 pages: flesch: 47.0 cache: ./cache/cord-196265-mvnkkcow.txt txt: ./txt/cord-196265-mvnkkcow.txt summary: We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. Proximity-based mass spectrometry on the MHV replication complex further revealed that the RTC environment repurposes components from the host autophagy, vesicular trafficking and translation machineries (V''kovski et al., 2019) In the present work, we identify a set of conserved SLiM candidates in the ACE2 and integrin proteins, which are likely to act in the cell entry system of SARS-CoV-2. The C-terminal tail of both subunits share a high degree of sequence similarity, and similarly to ACE2, contain several known and candidate SLiMs (see Table 1 and Figure 6 ) that propagate signals in the cytoplasm and regulate integrin activity not just through intracellular pathways, but also changing the structural state of the ectodomains determining ligand binding capacity (Anthis and Campbell, 2011) . abstract: The primary cell surface receptor for SARS-CoV-2 is the angiotensin-converting enzyme 2 (ACE2). Recently it has been noticed that the viral Spike protein has an RGD motif, suggesting that cell surface integrins may be co-receptors. We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. These SLiM candidates are highly conserved in vertebrates. They suggest potential interactions with the AP2 mu2 subunit as well as I-BAR, LC3, PDZ, PTB and SH2 domains found in signalling and regulatory proteins present in epithelial lung cells. Several motifs overlap in the tail sequences, suggesting that they may act as molecular switches, often involving tyrosine phosphorylation status. Candidate LIR motifs are present in the tails of ACE2 and integrin beta3, suggesting that these proteins can directly recruit autophagy components. We also noticed that the extracellular part of ACE2 has a conserved MIDAS structural motif, which are commonly used by beta integrins for ligand binding, potentially supporting the proposal that integrins and ACE2 share common ligands. The findings presented here identify several molecular links and testable hypotheses that might help uncover the mechanisms of SARS-CoV-2 attachment, entry and replication, and strengthen the possibility that it might be possible to develop host-directed therapies to dampen the efficiency of viral entry and hamper disease progression. The strong sequence conservation means that these putative SLiMs are good candidates: Nevertheless, SLiMs must always be validated by experimentation before they can be stated to be functional. url: https://arxiv.org/pdf/2004.10274v1.pdf doi: nan id: cord-301484-y9l2hmqf author: MASSAROTTI, Claudia title: Asymptomatic SARS‐CoV‐2 infections in pregnant patients in an Italian city during complete lockdown date: 2020-08-25 words: 1102.0 sentences: 64.0 pages: flesch: 47.0 cache: ./cache/cord-301484-y9l2hmqf.txt txt: ./txt/cord-301484-y9l2hmqf.txt summary: Data from both New York and London report a high prevalence of the asymptomatic SARS‐CoV‐2 infection in pregnant patients admitted for delivery, raising questions on the possible correlated dangers (i.e. contacts with healthcare workers; the possible creation of an intra‐hospital outbreak at birth; conflicting evidences on vertical transmission). For this study, results from SARS‐CoV‐2 screening via nasopharyngeal swab from maternity wards of the four hospitals of Genoa, Italy were collected during a month of complete lockdown, from April 1 to April 30, 2020. Early detection and isolation of asymptomatic SARS-CoV-2 positive patients is a crucial public safety action [1] , but a screening of the entire population is difficult to be This article is protected by copyright. The incidence of positive SARS-CoV-2 nasopharyngeal swabs in asymptomatic pregnant women were 13.5 and 6.2% in two reported screened cohort in New York and London [2, 3] . Since the implementation of the universal screening, all pregnant women admitted for delivery were tested for SARS-CoV-2. abstract: Data from both New York and London report a high prevalence of the asymptomatic SARS‐CoV‐2 infection in pregnant patients admitted for delivery, raising questions on the possible correlated dangers (i.e. contacts with healthcare workers; the possible creation of an intra‐hospital outbreak at birth; conflicting evidences on vertical transmission). For this study, results from SARS‐CoV‐2 screening via nasopharyngeal swab from maternity wards of the four hospitals of Genoa, Italy were collected during a month of complete lockdown, from April 1 to April 30, 2020. Out of 333 tested women, only nine were symptomatic. Only one symptomatic patient (0.3%) and six asymptomatic ones (1.8%) tested positive. Out of the six positive asymptomatic patients, five were from the most disadvantaged neighbourhood of the city (assessed by postal code). In conclusion, even if Italy was badly affected by COVID19 in the studied month, the reported prevalence of SARS‐CoV‐2 infections in asymptomatic pregnant patients at term was lower than the ones reported in literature. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26458 doi: 10.1002/jmv.26458 id: cord-279316-xz7aawem author: MIZUTANI, T. title: Signal Transduction in SARS‐CoV‐Infected Cells date: 2007-04-23 words: 3156.0 sentences: 171.0 pages: flesch: 45.0 cache: ./cache/cord-279316-xz7aawem.txt txt: ./txt/cord-279316-xz7aawem.txt summary: Recent studies regarding SARS and SARS‐CoV have clarified that activation of mitogen‐activated protein kinases (MAPKs) plays important roles in upregulation of cytokine expression and apoptosis both in vitro and in vivo. For example, mitogen-activated protein kinases (MAPKs) are well-known signal transducers that respond to extracellular stimulation by cytokines, growth factors, viral infection, and stress, and in turn regulate cell differentiation, proliferation, survival, and apoptosis. Extracellular signal-regulated kinase (ERK) 1/2 was phosphorylated in SARS-CoV-infected Vero E6 cells, 27 whereas ERK1/2 was downregulated in N protein-expressing COS-1 cells as described below. Activation of the p38 MAPK signaling pathway and dephosphorylation of STAT3 via p38 MAPK induced by SARS-CoV infection have partially proapoptotic roles in Vero E6 cells. Importance of Akt signaling pathway for apoptosis in SARS-CoV-infected Vero E6 cells abstract: abstract: Severe acute respiratory syndrome (SARS) is a newly found infectious disease that is caused by a novel human coronavirus, SARS coronavirus (SARS‐CoV). Because the mortality rate of SARS patients is very high, understanding the pathological mechanisms of SARS not only in vivo but in vitro is important for the prevention of SARS. Activation of signaling pathways caused by SARS‐CoV infection leads to the phosphorylation and activation of downstream molecules. Two conflicting cellular programs, apoptosis to eliminate virus‐infected cells and survival to delay apoptosis by producing antiviral cytokines, occur in SARS patients. Recent studies regarding SARS and SARS‐CoV have clarified that activation of mitogen‐activated protein kinases (MAPKs) plays important roles in upregulation of cytokine expression and apoptosis both in vitro and in vivo. Both Akt and p38 MAPK are keys for determination of cell survival or death in SARS‐CoV‐infected cells in vitro. Agents being developed to target these signaling cascades may be important for the design of anti‐SARS‐CoV drugs. This review highlights recent progress regarding SARS‐CoV biology, especially signal transduction in SARS‐CoV‐infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/17470913/ doi: 10.1196/annals.1408.006 id: cord-033951-77tfhm5b author: Ma, Chunlong title: Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors date: 2020-10-09 words: 6998.0 sentences: 428.0 pages: flesch: 60.0 cache: ./cache/cord-033951-77tfhm5b.txt txt: ./txt/cord-033951-77tfhm5b.txt summary: In this study, we investigated the mechanism of action of six previously reported M(pro) inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. 31 Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin were recently reported as SARS-CoV-2 M pro inhibitors with IC 50 values ranging from 0.67 to 21.39 μM in the FRET-based enzymatic assay. Collectively, our results showed that in the absence of DTT, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 nonspecifically inhibit all six viral cysteine proteases including SARS-CoV-2 M pro . Collectively, the enzymatic assay results suggest that ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are promiscuous cysteine protease inhibitors that inhibit not only M pro but also five other related and unrelated viral cysteine proteases including SARS-CoV-2 PL pro and EV-A71 and EV-D68 2A pro and 3C pro in the absence of DTT, and the abstract: [Image: see text] Among the drug targets being investigated for SARS-CoV-2, the viral main protease (M(pro)) is one of the most extensively studied. M(pro) is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites. It is highly conserved and has a unique substrate preference for glutamine in the P1 position. Therefore, M(pro) inhibitors are expected to have broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compounds have been reported as M(pro) inhibitors. In this study, we investigated the mechanism of action of six previously reported M(pro) inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of M(pro) by these six compounds is nonspecific and that the inhibition is abolished or greatly reduced with the addition of reducing reagent 1,4-dithiothreitol (DTT). Without DTT, these six compounds inhibit not only M(pro) but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease and 2A(pro) and 3C(pro) from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC(50) values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that these six compounds are nonspecific SARS-CoV-2 M(pro) inhibitors and urge the scientific community to be stringent with hit validation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571300/ doi: 10.1021/acsptsci.0c00130 id: cord-305587-xtqvtleb author: Ma, Cuiqing title: From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development date: 2020-05-11 words: 2310.0 sentences: 122.0 pages: flesch: 40.0 cache: ./cache/cord-305587-xtqvtleb.txt txt: ./txt/cord-305587-xtqvtleb.txt summary: Identification and characterization of novel neutralizing epitopes in the 506 receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic determinants in inactivated 507 SARS-CoV vaccine Intranasal vaccination of recombinant adeno-associated virus 533 encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces 534 strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of SARS-CoV spike protein induces highly 556 potent neutralizing antibodies: implication for developing subunit vaccine Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies 613 primarily targeting the receptor binding region Receptor-binding domain of severe acute respiratory syndrome coronavirus 621 spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies. Cross-neutralization of human and palm civet severe acute 636 respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein abstract: The global pandemic of COVID-19 caused by SARS-CoV-2 (also known as 2019-nCoV and HCoV-19) has posed serious threats to public health and economic stability worldwide, thus calling for development of vaccines against SARS-CoV-2 and other emerging and reemerging coronaviruses. Since SARS-CoV-2 and SARS-CoV have high similarity of their genomic sequences and share the same cellular receptor (ACE2), it is essential to learn the lessons and experiences from the development of SARS-CoV vaccines for the development of SARS-CoV-2 vaccines. In this review, we summarized the current knowledge on the advantages and disadvantages of the SARS-CoV vaccine candidates and prospected the strategies for the development of safe, effective and broad-spectrum coronavirus vaccines for prevention of infection by currently circulating SARS-CoV-2 and other emerging and reemerging coronaviruses that may cause future epidemics or pandemics. url: https://api.elsevier.com/content/article/pii/S1286457920300824 doi: 10.1016/j.micinf.2020.05.004 id: cord-324970-yty7aajj author: Ma, Di title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea date: 2020-05-07 words: 3734.0 sentences: 194.0 pages: flesch: 51.0 cache: ./cache/cord-324970-yty7aajj.txt txt: ./txt/cord-324970-yty7aajj.txt summary: title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea PURPOSE: To determine the expressions of SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS2) genes in human and mouse ocular cells and comparison to other tissue cells. The expression of ACE2 and TMPRSS2 genes was determined in human primary conjunctival and pterygium cells, human ocular and other tissue cell lines, mesenchymal stem cells as well as mouse ocular and other tissues by reverse transcription-polymerase chain reaction (RT-PCR) and SYBR green PCR. Herein, this study aimed to determine the expressions of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human and mouse ocular cells and tissues. In summary, this study revealed the expression of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human conjunctival and pterygium cells as well as mouse cornea tissue. abstract: PURPOSE: To determine the expressions of SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS2) genes in human and mouse ocular cells and comparison to other tissue cells. METHODS: Human conjunctiva and primary pterygium tissues were collected from pterygium patients who underwent surgery. The expression of ACE2 and TMPRSS2 genes was determined in human primary conjunctival and pterygium cells, human ocular and other tissue cell lines, mesenchymal stem cells as well as mouse ocular and other tissues by reverse transcription-polymerase chain reaction (RT-PCR) and SYBR green PCR. RESULTS: RT-PCR analysis showed consistent expression by 2 ACE2 gene primers in 2 out of 3 human conjunctival cells and pterygium cell lines. Expression by 2 TMPRSS2 gene primers could only be found in 1 out of 3 pterygium cell lines, but not in any conjunctival cells. Compared with the lung A549 cells, similar expression was noted in conjunctival and pterygium cells. In addition, mouse cornea had comparable expression of Tmprss2 gene and lower but prominent Ace2 gene expression compared with the lung tissue. CONCLUSION: Considering the necessity of both ACE2 and TMPRSS2 for SARS-CoV-2 infection, our results suggest that conjunctiva would be less likely to be infected by SARS-CoV-2, whereas pterygium possesses some possibility of SARS-CoV-2 infection. With high and consistent expression of Ace2 and Tmprss2 in cornea, cornea rather than conjunctiva has higher potential to be infected by SARS-CoV-2. Precaution is necessary to prevent possible SARS-CoV-2 infection through ocular surface in clinical practice. url: https://doi.org/10.1038/s41433-020-0939-4 doi: 10.1038/s41433-020-0939-4 id: cord-333754-copxoyqu author: Ma, Hsin-Chieh title: Expression and membrane integration of SARS-CoV M protein date: 2008-04-09 words: 3930.0 sentences: 191.0 pages: flesch: 60.0 cache: ./cache/cord-333754-copxoyqu.txt txt: ./txt/cord-333754-copxoyqu.txt summary: Full-length SARS-CoV M gene fragment was cloned and expressed as a recombinant protein (221 a.a.) with a C-terminal V5-His tag (29 a.a.) in Vero E6 cells (Fig. 1a) . In addition to the glycosylated and un-glycosylated SARS-CoV M proteins, two smaller protein products (marked by thick line and thin line, respectively) were also detected when M gene was expressed in Vero E6 cells ( Fig. 1a and b) . The protein translated in-frame from the third Met (amino acid 83) could still be detected when the authentic 5 0 -untranslated region of SARS-CoV M gene was included in the expression vector (lane 3 in supplement Fig. 2 ). In this study, SARS-CoV M gene fragment was cloned and expressed as a recombinant protein fused with a C-terminal V5 tag in Vero E6 cells (Fig. 1) . Two other expressed SARS-CoV M protein products with smaller size than the full-length one were also detected in Vero E6 cells (Figs. abstract: SARS-CoV M gene fragment was cloned and expressed as a recombinant protein fused with a V5 tag at the C-terminus in Vero E6 cells. In addition to un-glycosylated and glycosylated proteins, one product with smaller size initiated in-frame from the third Met residues probably through ribosomal re-initiation was also detected. Translation initiated in-frame from the third Met is unusual since the sequence around the first Met of SARS-CoV M protein contains the optimal consensus Kozak sequence. The function of this smaller translated product awaits further investigation. Similar to other N-glycosylated proteins, glycosylation of SARS-CoV M protein was occurred co-translationally in the presence of microsomes. The SARS-CoV M protein is predicted as a triple-spanning membrane protein lack of a conventional signal peptide. The second and third trans-membrane regions (a.a. 46–68 and 78–100) are predicted to be the primary type helices, which will be able to penetrate into membrane by themselves, while the first trans-membrane region (a.a. 14–36) is predicted to be the secondary type helix, which is considered to be stabilized by the interaction with other trans-membrane segments. As expected, the second and third trans-membrane regions were able to insert a cytoplasmic protein into the endoplasmic reticulum membrane more efficiently than the first one. These results should be important for the study of SARS-CoV morphogenesis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11373-008-9235-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/18398701/ doi: 10.1007/s11373-008-9235-1 id: cord-300784-4jeaqqn9 author: Ma, Huan title: COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay date: 2020-04-22 words: 3493.0 sentences: 203.0 pages: flesch: 56.0 cache: ./cache/cord-300784-4jeaqqn9.txt txt: ./txt/cord-300784-4jeaqqn9.txt summary: Here, we aimed to develop a more quantitative and sensitive serological test for COVID-19 diagnosis, monitoring and clinical investigation, based on the detection of antigen-specific IgA as well as IgM and IgG in blood in response to SARS-CoV-2 infection. Methods In this investigation, we report the development of a set of validated diagnostic kits for detecting serum IgA, IgM, and IgG specific to SARS-CoV-2 nucleocapsid protein (NP) and receptor-binding domain (RBD) of the spike protein by chemi-luminescence immuno-analysis. . https://doi.org/10.1101/2020.04.17.20064907 doi: medRxiv preprint Based on the clinical RT-qPCR diagnosis results of SARS-CoV-2 infection, receiver operating 208 characteristic (ROC) analysis was conducted using MedCalc software to determine the optimal cut-off 209 value (criterion) and evaluate the diagnostic value of NP-or RBD-specific IgA, IgM, and IgG kits. Nonetheless, we showed that our serological kits based on SARS-CoV-2 spike 322 protein RBD as an immobilized antigen provide a high sensitivity and specificity for detecting IgA, IgM, 323 and IgG in a quantitative manner. abstract: Background The current pandemic of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a great loss in lives and economy. Detecting viral RNAs on nasopharyngeal and throat swabs is the standard approach for SARS-CoV-2 diagnosis with variable success. Currently, there are only a few studies describing the serological diagnostic methods that involve the detection of SARS-CoV-2-specific IgM and IgG. Here, we aimed to develop a more quantitative and sensitive serological test for COVID-19 diagnosis, monitoring and clinical investigation, based on the detection of antigen-specific IgA as well as IgM and IgG in blood in response to SARS-CoV-2 infection. Methods In this investigation, we report the development of a set of validated diagnostic kits for detecting serum IgA, IgM, and IgG specific to SARS-CoV-2 nucleocapsid protein (NP) and receptor-binding domain (RBD) of the spike protein by chemi-luminescence immuno-analysis. The kits were tested with a cohort of 216 sera from 87 laboratory-confirmed COVID-19 patients, and 483 sera from SARS-CoV-2 negative or healthy individuals as negative controls. A standard receiver operating characteristic (ROC) analysis was conducted to evaluate the diagnostic accuracy. Using the kits, serum levels of IgA, IgM, and IgG were analyzed, in response to SARS-CoV-2 infection and COVID-19 pathogenesis. Findings The diagnostic kits based on the RBD antigen outperformed those based on the NP. RBD-specific IgA, IgM, and IgG detection kits showed sensitivities of 98.6%, 96.8%, and 96.8%, and specificities of 98.1%, 92.3%, and 99.8%, respectively. In addition, using purified RBD-specific immunoglobulins from a serum pool of COVID-19 patients as standards, the serum concentrations of RBD-specific IgA, IgM, and IgG proteins were determined. The concentrations varied widely among different patients. Median concentration of IgA and IgM reached peaks at 16-20 days after illness onset at 8.84 μg/mL and 7.25 μg/mL, respectively, while median concentration of IgG peaked during 21-25 days after illness onset at 16.47 μg/mL. Furthermore, the serum IgA level positively correlates with COVID-19 severity. Interpretation Our immunoassay of measuring SARS-CoV-2 specific antibodies IgA, IgM, and IgG in serum provides a better serological testing with improved sensitivity and specificity. Data of IgA, IgM, and IgG responses in blood of COVID-19 patients may provide novel insight for the monitoring and treatments of COVID-19. The kits are also suitable for epidemiological studies and vaccine validations. url: https://doi.org/10.1101/2020.04.17.20064907 doi: 10.1101/2020.04.17.20064907 id: cord-298343-nvuc1j7t author: Ma, J. title: Exhaled breath is a significant source of SARS-CoV-2 emission date: 2020-06-02 words: 2791.0 sentences: 170.0 pages: flesch: 64.0 cache: ./cache/cord-298343-nvuc1j7t.txt txt: ./txt/cord-298343-nvuc1j7t.txt summary: Here, 35 COVID-19 subjects were recruited; exhaled breath condensate (EBC), air samples and surface swabs were collected and analyzed for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). COVID-19 patients were shown to exhale SARS-CoV-2 into the air at an estimated rate of 103-105 RNA copies/min; while toilet and floor surfaces represented two important SARS-CoV-2 reservoirs. Surface swabs from the cell phone and hands of one patient(ITA-YL1) tested negative for the virus, but the SARS-CoV-2 was present on the toilet pit surface in that patient''s hotel room (Fig. 1C ). Although EBC samples from two patients (ITA-YW2 and UK-YJ1) were shown to 20 contain SARS-CoV-2, surface swabs from their cell phones, hands, and toilet surfaces were negative for the virus. . https://doi.org/10.1101/2020.05.31.20115154 doi: medRxiv preprint Out of 242 surface swab samples, 13 were positive for SARS-CoV-2 ( Fig. 3 and Table S4 ). abstract: Despite notable efforts in airborne SARS-CoV-2 detection, no clear evidence has emerged to show how SARS-CoV-2 is emitted into the environments. Here, 35 COVID-19 subjects were recruited; exhaled breath condensate (EBC), air samples and surface swabs were collected and analyzed for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). EBC samples had the highest positive rate (16.7%, n=30), followed by surface swabs (5.4%, n=242), and air samples (3.8%, n=26). COVID-19 patients were shown to exhale SARS-CoV-2 into the air at an estimated rate of 103-105 RNA copies/min; while toilet and floor surfaces represented two important SARS-CoV-2 reservoirs. Our results imply that airborne transmission of SARS-CoV-2 plays a major role in COVID-19 spread, especially during the early stages of the disease. url: http://medrxiv.org/cgi/content/short/2020.05.31.20115154v1?rss=1 doi: 10.1101/2020.05.31.20115154 id: cord-284449-z7r4n0w7 author: Ma, L. title: Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study date: 2020-03-24 words: 2847.0 sentences: 181.0 pages: flesch: 53.0 cache: ./cache/cord-284449-z7r4n0w7.txt txt: ./txt/cord-284449-z7r4n0w7.txt summary: This study provides the first direct evidence about the influence of medical condition of COVID-19 on male sex hormones, alerting more attention to gonadal function evaluation among patients recovered from SARS-CoV-2 infection, especially the reproductive-aged men. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. abstract: Since SARS-CoV-2 infection was first identified in December 2019, it spread rapidly and a global pandemic of COVID-19 has occurred. ACE2, the receptor for entry into the target cells by SARS-CoV-2, was found to abundantly express in testes, including spermatogonia, Leydig and Sertoli cells. However, there is no clinical evidence about whether SARS-CoV-2 infection can affect male gonadal function so far. In this study, we compared the sex-related hormones between 81 reproductive-aged men with SARS-CoV-2 infection and 100 age-matched healthy men, and found that serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in males with COVID-19. Besides, multivariable regression analysis indicated that c-reactive protein (CRP) level was significantly associated with serum T:LH ratio in COVID-19 patients. This study provides the first direct evidence about the influence of medical condition of COVID-19 on male sex hormones, alerting more attention to gonadal function evaluation among patients recovered from SARS-CoV-2 infection, especially the reproductive-aged men. url: http://medrxiv.org/cgi/content/short/2020.03.21.20037267v1?rss=1 doi: 10.1101/2020.03.21.20037267 id: cord-310027-846vp7ii author: Ma, Lin-Lu title: Coronavirus Disease 2019 Related Clinical Studies: A Cross-Sectional Analysis date: 2020-09-02 words: 4246.0 sentences: 245.0 pages: flesch: 49.0 cache: ./cache/cord-310027-846vp7ii.txt txt: ./txt/cord-310027-846vp7ii.txt summary: METHODS: We did an electronic search of COVID-19 related clinical studies registered between December 1, 2019 and February 21, 2020 (updated to May 28, 2020) from the ClinicalTrials.gov, and collected registration information, study details, recruitment status, characteristics of the subjects, and relevant information about the trial implementation process. We extracted the following information from registered studies: registration number, registration date, registration title, primary sponsor, funding source, study type, study phase, study objectives, study design, length of the study, intervention, countries of recruitment and research settings, recruiting status, allocation, sample size, participant age, gender, masking, the time and method of sharing individual participant data (IPD), data management committee. Among the 943 interventional studies, 416 studies (44.1%) explored the effectiveness and/or safety of drugs commonly used in preventing and treating COVID-19, such as hydroxychloroquine (HCQ), chloroquine (CQ), immunotherapy (including stem cell therapy, monoclonal antibody, immunoregulation), lopinavir/ritonavir, glucocorticoids, interferon, targeted therapy (Baricitinib, Ruxolitinib, Imatinib), favipiravir, and Remdesivir. abstract: OBJECTIVE: The quality and rationality of many recently registered clinical studies related to coronavirus disease 2019 (COVID-19) needs to be assessed. Hence, this study aims to evaluate the current status of COVID-19 related registered clinical trial. METHODS: We did an electronic search of COVID-19 related clinical studies registered between December 1, 2019 and February 21, 2020 (updated to May 28, 2020) from the ClinicalTrials.gov, and collected registration information, study details, recruitment status, characteristics of the subjects, and relevant information about the trial implementation process. RESULTS: A total of 1,706 studies were included 10.0% of which (n=171) were from France, 943 (55.3%) used an interventional design, and 600 (35.2%) used an observational design. Most of studies (73.6%) aimed to recruit fewer than 500 people. Interferon was the main prevention program, and antiviral drugs were the main treatment program. Hydroxychloroquine and chloroquine (230/943, 24.4%) were widely studied. Some registered clinical trials are incomplete in content, and 37.4% of the 1,706 studies may have had insufficient sample size. CONCLUSION: The quality of COVID-19 related studies needs to be improved by strengthening the registration process and improving the quality of clinical study protocols so that these clinical studies can provide high-quality clinical evidence related to COVID-19. url: https://doi.org/10.3389/fphar.2020.540187 doi: 10.3389/fphar.2020.540187 id: cord-322009-0cwljo0c author: Ma, Ling title: Coinfection of SARS-CoV-2 and Other Respiratory Pathogens date: 2020-08-26 words: 3793.0 sentences: 170.0 pages: flesch: 42.0 cache: ./cache/cord-322009-0cwljo0c.txt txt: ./txt/cord-322009-0cwljo0c.txt summary: Although the number of confirmed global cases of COVID-19 now exceeds 16 million, as of July 29, and several retrospective observational studies have noted that coinfection with other respiratory pathogens is relatively common, [1] [2] [3] [4] the clinical features of coinfection and its impact on patient outcomes, is yet to be clarified. All these patients were tested for SARS-CoV-2, respiratory syncytial virus, influenza A virus, influenza B virus, adenovirus, Chlamydia pneumoniae, and Mycoplasma pneumoniae, using sputum or nasopharyngeal swab specimens collected in the interval between the onset of symptoms, and up to seven days after their hospital admission. Routine laboratory tests, including tests for SARS-CoV-2 and other common respiratory viral and atypical bacterial pathogens, routine blood investigations, coagulation studies, organ function tests and inflammatory biomarkers, such as c-reactive protein (CRP) and procalcitonin (PCT), were taken at the time of patient presentation, while the serum interleukin (IL)-2, IL-4, IL-6, IL-10, TNF-α and IFN-γ levels were obtained on the 2nd day of admission. abstract: PURPOSE: To differentiate between respiratory infections caused by SARS-CoV-2 and other respiratory pathogens during the COVID-19 outbreak in Wuhan, we simultaneously tested for SARS-CoV-2 and pathogens associated with CAP to determine the incidence and impact of respiratory coinfections in COVID-19 patients. PATIENTS AND METHODS: We included 250 patients who were diagnosed with COVID-19. RT-PCR was used to detect influenza A, influenza B and respiratory syncytial viruses. Chemiluminescence immunoassays were used to detect IgM antibodies for adenovirus, Chlamydia pneumoniae and Mycoplasma pneumoniae in the serum of patients. Based on these results, we divided the patients into two groups, the simple SARS-CoV-2-infected group and the coinfected SARS-COV-2 group. Coinfected patients were then further categorized as having a coinfection of viral pathogen (CoIV) or coinfection of atypical bacterial pathogen (CoIaB). RESULTS: No statistically significant differences were found in age, gender, the time taken to return negative SARS-CoV-2 nucleic acid test results, length of hospital stays, and mortality between the simple SARS-CoV-2 infection group and the coinfection group. Of the 250 hospitalized COVID-19 patients, 39 (15.6%) tested positive for at least one respiratory pathogen in addition to SARS-CoV-2. A third of these pathogens were detected as early as the 1st week after symptom onset and another third were identified after more than three weeks. The most detected CAP pathogen was C. pneumoniae (5.2%), followed by the respiratory syncytial virus (4.8%), M. pneumoniae (4.4%) and adenovirus (2.8%). Patients coinfected with viral pathogens (CoIV) (n=18) had longer hospital stays when compared to patients coinfected with atypical bacterial pathogens (CoIaB) (n=21). Except for one fatality, the remaining 38 coinfected patients all recovered with favourable outcomes. CONCLUSION: Coinfections in COVID-19 patients are common. The coinfecting pathogens can be detected at variable intervals during COVID-19 disease course and remain an important consideration in targeted treatment strategies for COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32922049/ doi: 10.2147/idr.s267238 id: cord-310691-6danlh8h author: Ma, Simin title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date: 2020-05-26 words: 2297.0 sentences: 149.0 pages: flesch: 57.0 cache: ./cache/cord-310691-6danlh8h.txt txt: ./txt/cord-310691-6danlh8h.txt summary: title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. abstract: OBJECTIVE: To delineate the clinical characteristics of critically ill COVID-19 patients co-infected with influenza. METHODS: In this study, we included adult patients with laboratory-confirmed COVID-19 form Tongji Hospital (Wuhan, China), with or without influenza, and compared their clinical characteristics. RESULTS: Among 93 patients, 44 died and 49 were discharged. Forty-four (47.3%) were infected with influenza virus A and 2 (2.2%) with influenza virus B. Twenty-two (50.0%) of the non-survivors and 24 (49.0%) of the survivors were infected with the influenza virus. Critically ill COVID-19 patients with influenza were more prone to cardiac injury than those without influenza. For the laboratory indicators at admission, white blood cell counts, neutrophil counts, levels of tumor necrosis factor-α, D-dimer value, and proportion of elevated creatinine were higher in non-survivors with influenza than in those without influenza. CONCLUSION: The results showed a high proportion of COVID-19 patients were co-infected with influenza in Tongji Hospital, with no significant difference in the proportion of co-infection between survivors and non-survivors. The critically ill COVID-19 patients with influenza exhibited more severe inflammation and organ injury, indicating that co-infection with the influenza virus may induce an earlier and more frequently occurring cytokine storm. url: https://www.ncbi.nlm.nih.gov/pubmed/32470606/ doi: 10.1016/j.ijid.2020.05.068 id: cord-193893-rzurz5bj author: Ma, Zhanshan title: Spatiotemporal fluctuation scaling law and metapopulation modeling of the novel coronavirus (COVID-19) and SARS outbreaks date: 2020-03-08 words: 3683.0 sentences: 200.0 pages: flesch: 48.0 cache: ./cache/cord-193893-rzurz5bj.txt txt: ./txt/cord-193893-rzurz5bj.txt summary: Another TPL parameter (M0) (i.e., infection critical threshold) depends on virus kinds (COVID-19/SARS), time (disease-stages), space (regions) and public-health interventions (e.g., quarantines and mobility control). While TPL can be harnessed to investigate the spatiotemporal fluctuations of coronaviruses, specifically, the scaling (changes) law of coronaviruses infections over space and time, we also aim to understand the spread of the virus infections from both local contagion (endemic) and external migration (epidemic and pandemic) perspectives. Overall, this study sets two primary objectives: (i) to investigate the spatiotemporal fluctuation scaling law and (ii) to obtain an educated guess for the local contagion spread and global migration parameters of the COVID-19 infections. At the community level, the four Taylor''s power law extensions (TPLE), can be used to measure the community spatial (temporal) heterogeneity ( on both the general principle of TPL (explained above) and system-or data-specific information (such as the biology of COVID or SARS). abstract: We comparatively analyzed the spatiotemporal fluctuations of the 2019-novel coronavirus (COVID-19) and SARS outbreaks to understand their epidemiological characteristics. Methodologically, we introduced TPL (Taylor power law) to characterize their spatiotemporal heterogeneity/stability and Hubbell (2001) unified neutral theory of biodiversity (UNTB) [specifically Harris et al. (2015) HDP-MSN model (hierarchical Dirichlet process multi-site neutral model)] to approximate the metapopulation of coronavirus infections. First, TPL analysis suggested that the coronaviruses appear to have a specific heterogeneity/stability scaling parameter (TPL-b) slightly exceeding 2 for cumulative infections or exceeding 1 for daily incremental infections, suggesting their potentially chaotic, unstable outbreaks. Another TPL parameter (M0) (i.e., infection critical threshold) depends on virus kinds (COVID-19/SARS), time (disease-stages), space (regions) and public-health interventions (e.g., quarantines and mobility control). M0 measures the infection level, at which infections are random (Poisson distribution) and below which infections follow uniform distribution and may die off if M0 coincides or below the level of Allee effects. It was found that COVID-19 outbreak seems nearly twice more risky than SARS, and the lower infection threshold may be due to its lower lethality than SARS since lower fatality rates can facilitate the survival and spread of pathogen. Second, metacommunity UNTB neutrality testing seems appropriate for approximating metapopulation of coronavirus infections. Specifically, two parameters {theta} and M, borrowed from neutral theory, may be used to assess the relative significance of infection through local contagion vs. infection through migration, both of which may depend on time, space, virus kinds, and particularly public-health interventions. url: https://arxiv.org/pdf/2003.03714v1.pdf doi: nan id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 words: 8373.0 sentences: 423.0 pages: flesch: 44.0 cache: ./cache/cord-354582-fniymnmf.txt txt: ./txt/cord-354582-fniymnmf.txt summary: In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . abstract: Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine. url: https://doi.org/10.1016/bs.aivir.2020.06.003 doi: 10.1016/bs.aivir.2020.06.003 id: cord-308996-tf0v2ojk author: Maas, Angela HEM title: The Coronavirus Disease 2019 Outbreak Highlights the Importance of Sex-sensitive Medicine date: 2020-08-24 words: 2188.0 sentences: 138.0 pages: flesch: 45.0 cache: ./cache/cord-308996-tf0v2ojk.txt txt: ./txt/cord-308996-tf0v2ojk.txt summary: The novel coronavirus disease 2019 (COVID-19) pandemic has revealed important differences between the sexes in epidemiology, risk factors, clinical course, mortality and socioeconomic dimensions of the disease in all populations worldwide. The role of the TMPRSS2 protease in SARS-CoV-2 needs to be further investigated, but information on other diseases points towards sexspecific differences. 34 Sex differences in the binding of SARS-CoV-2 to the ACE2 receptor have been identified as an important contributor to the initiation and course of the disease. 27, 35, 36 Sex differences regarding potential protective effects of renin-angiotensin-aldosterone system inhibitors in SARS-CoV-2 infections are as yet unknown. Sex-specific SARS-CoV-2 mortality: among hormone-modulated ACE2 expression, risk of venous thromboembolism and hypovitaminosis D The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Gender differences in patients with COVID-19: focus on severity and mortality abstract: The novel coronavirus disease 2019 (COVID-19) pandemic has revealed important differences between the sexes in epidemiology, risk factors, clinical course, mortality and socioeconomic dimensions of the disease in all populations worldwide. This has emphasised the need for a better understanding of diversity aspects in healthcare to improve prevention, treatment and long-term consequences. In this article, the authors describe the most relevant knowledge thus far on sex differences regarding COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32944091/ doi: 10.15420/ecr.2020.28 id: cord-269289-6uog10j4 author: Mabillard, Holly title: Electrolyte Disturbances in SARS-CoV-2 Infection date: 2020-07-22 words: 5684.0 sentences: 289.0 pages: flesch: 44.0 cache: ./cache/cord-269289-6uog10j4.txt txt: ./txt/cord-269289-6uog10j4.txt summary: These include additional respiratory complications (pulmonary fibrosis -reported in 21% of those hospitalised with SARS-CoV-2 9 months post-discharge in one study 3 ) 7 , cardiovascular complications (acute cardiac injury (7% 8 ), cardiomyopathy (1/3 patients 9 ), cardiac tamponade, heart failure, dysrhythmias (17% 8 ) and venous thromboembolic events (20% 10 )) 11 , neurological complications (myopathy, acute stroke (5.7% of those with severe infection 12 ), Guillain-Barre syndrome (0.4% hospitalised patients 11 ) and encephalopathy) 13 , acute liver and/or pancreatic injury (29% and 17% respectively in one cohort) 14 , cytokine storm syndrome, septic shock, DIC, diarrhoea, Kawasaki-like disease 14 and renal complications (acute tubular injury, rhabdomyolysis, proteinuria, secondary focal segmental glomerulosclerosis and possible renin-angiotensinaldosterone system activation) 15 . The study reported that the degree of hypokalaemia correlated with severity of SARS-CoV-2 symptoms and they suggested that hypokalaemia can be difficult to correct as seen in two patients because the renal potassium wasting persists until clinical recovery from the virus. abstract: The global pandemic secondary to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading to unprecedented global morbidity and mortality. With a bewildering array of complications, renal involvement in various forms is common, including serum electrolyte derangements. Hypokalaemia secondary to SARS-CoV-2 was common in a reported Chinese cohort. Here we review the emerging evidence on hypokalaemia and SARS-CoV-2 infection, the potential pathophysiological mechanisms based on early clinical and histopathological data and important clinical implications. Mechanisms of hypokalaemia are multifactorial and so the electrolyte disturbance can be difficult to avoid. We provide further support to the theory of renin-angiotensin-aldosterone (RAS) activation, discuss the strengths and weaknesses of implicating RAS involvement and highlight the importance of calculating the transtubular potassium gradient to identify those at risk of hypokalaemia and its complications. url: https://www.ncbi.nlm.nih.gov/pubmed/33093945/ doi: 10.12688/f1000research.24441.2 id: cord-336142-jmetfa6x author: MacDougall, Heather title: Toronto’s Health Department in Action: Influenza in 1918 and SARS in 2003 date: 2006-10-11 words: 10366.0 sentences: 520.0 pages: flesch: 55.0 cache: ./cache/cord-336142-jmetfa6x.txt txt: ./txt/cord-336142-jmetfa6x.txt summary: This article compares the Toronto Health Department''s role in controlling the 1918 influenza epidemic with its activities during the SARS outbreak in 2003 and concludes that local health departments are the foundation for successful disease containment, provided that there is effective coordination, communication, and capacity. 3 By comparing and contrasting the way in which public health authorities in Toronto managed the 1918 influenza pandemic and SARS in 2003, we can see how a century of medical advances had conditioned the public and health care professionals to expect prompt control of communicable diseases, speedy development of a prophylactic vaccine, and effective exchange of information at the provincial, national, and international levels. For Toronto''s medical officer and its Local Board of Health (LBH), this presented a challenge, because influenza was not a reportable disease under the 1912 Ontario Public Health Act, and most doctors were hoping that the outbreak would be similar to the one in 1889-90 that had attacked primarily the elderly and apparently provided some immunity to those who survived. abstract: This article compares the Toronto Health Department’s role in controlling the 1918 influenza epidemic with its activities during the SARS outbreak in 2003 and concludes that local health departments are the foundation for successful disease containment, provided that there is effective coordination, communication, and capacity. In 1918, Toronto’s MOH Charles Hastings was the acknowledged leader of efforts to contain the disease, care for the sick, and develop an effective vaccine, because neither a federal health department nor an international body like WHO existed. During the SARS outbreak, Hastings’s successor, Sheela Basrur, discovered that nearly a decade of underfunding and new policy foci such as health promotion had left the department vulnerable when faced with a potential epidemic. Lack of cooperation by provincial and federal authorities added further difficulties to the challenge of organizing contact tracing, quarantine, and isolation for suspected and probable cases and providing information and reassurance to the multi-ethnic population. With growing concern about a flu pandemic, the lessons of the past provide a foundation for future communicable disease control activities. url: https://www.ncbi.nlm.nih.gov/pubmed/17035296/ doi: 10.1093/jhmas/jrl042 id: cord-343476-0chuwvg6 author: MacLean, Oscar A. title: Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date: 2020-05-29 words: 1386.0 sentences: 73.0 pages: flesch: 51.0 cache: ./cache/cord-343476-0chuwvg6.txt txt: ./txt/cord-343476-0chuwvg6.txt summary: Here we contrast the role of positive selection and recombination in the Sarbecoviruses in horseshoe bats to SARS-CoV-2 evolution in humans. While methods can detect some evidence for positive selection in SARS-CoV-2, we demonstrate these are mostly due to recombination and sequencing artefacts. For all but two of the ten positive selected codons, this signal was being driven by apparent convergent evolution (or homoplasy) in the tree, with the same mutation occurring in parallel across the phylogeny. To investigate whether this observation was truly due to independent events or because of recombination signatures in the SARS-CoV-2 outbreak tree, we firstly determined if the samples with these convergent mutations were geographically correlated. The Spike V367F signal was driven by apparent convergent evolution between four french samples sequenced in January and a Hong Kong sample 412028, which shows shared variation either side of the homoplasy suggesting it is not a recombinant (Supplementary figure 3C) . abstract: RNA viruses are proficient at switching to novel host species due to their fast mutation rates. Implicit in this assumption is the need to evolve adaptations in the new host species to exploit their cells efficiently. However, SARS-CoV-2 has required no significant adaptation to humans since the pandemic began, with no observed selective sweeps to date. Here we contrast the role of positive selection and recombination in the Sarbecoviruses in horseshoe bats to SARS-CoV-2 evolution in humans. While methods can detect some evidence for positive selection in SARS-CoV-2, we demonstrate these are mostly due to recombination and sequencing artefacts. Purifying selection is also substantially weaker in SARS-CoV-2 than in the related bat Sarbecoviruses. In comparison, our results show evidence for positive, specifically episodic selection, acting on the bat virus lineage SARS-CoV-2 emerged from. This signature of selection can also be observed among synonymous substitutions, for example, linked to ancestral CpG depletion on this bat lineage. We show the bat virus RmYN02 has recombinant CpG content in Spike pointing to coinfection and evolution in bats without involvement of other species. Our results suggest the non-human progenitor of SARS-CoV-2 was capable of human-human transmission as a consequence of its natural evolution in bats. url: https://www.ncbi.nlm.nih.gov/pubmed/32577659/ doi: 10.1101/2020.05.28.122366 id: cord-278406-n5e3a09i author: Macauley, Precious title: CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date: 2020-08-21 words: 1492.0 sentences: 79.0 pages: flesch: 39.0 cache: ./cache/cord-278406-n5e3a09i.txt txt: ./txt/cord-278406-n5e3a09i.txt summary: Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). abstract: The SARS-CoV-2 pandemic has introduced the medical community to a lung disease heretofore unknown to most clinicians. In much of the discourse about COVID-19 lung disease, the more familiar clinical entity of ARDS has been used as the guiding paradigm. Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. The voice of the pulmonology community—the community of lung experts—has continued to be among the quietest in this conversation. Herein we offer our perspective as academic pulmonologists who encountered COVID-19 in its first United States epicenter of New York City. We encourage a conceptual separation between early COVID-19 lung involvement and ARDS. We draw on history with other immune cell-mediated lung diseases, on insights from the SARS-CoV experience, and on frontline observations in an attempt to allay the skepticism towards corticosteroids in COVID-19 lung disease that is likely to persist even as favorable study results emerge. url: https://doi.org/10.1016/j.ijid.2020.08.051 doi: 10.1016/j.ijid.2020.08.051 id: cord-015613-ls9qus8y author: Macdonald, David W. title: Infectious disease: Inextricable linkages between human and ecosystem health date: 2006-06-06 words: 6157.0 sentences: 300.0 pages: flesch: 47.0 cache: ./cache/cord-015613-ls9qus8y.txt txt: ./txt/cord-015613-ls9qus8y.txt summary: Several papers, including those on rabies in Ethiopian wolves, Canis simensis (Randall et al., 2006) , and African wild dogs, Lycaon pictus (Vial et al., 2006) , disease in Island foxes, Urocyon littoralis (Clifford et al., 2006) , squirrel parapox virus (SQPV) in red squirrels, Sciurus vulgaris (Gurnell et al., 2006) , and devil facial tumour disease (DFTD) in Tasmanian devils, Sarcophilus harrisii (Hawkins et al., 2006) examine this theme. The importance of reservoir identification is classically illustrated by a range of papers in this Special Issue, for example the ongoing dilemma facing bovine tuberculosis control , the diseases emerging from bats (Breed et al., 2006) , phocine distemper virus (PDV) in northern seal population (Hall et al., 2006) and the canid pathogens threatening Island foxes (Clifford et al., 2006) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111083/ doi: 10.1016/j.biocon.2006.05.007 id: cord-319158-n8e2n30b author: Mackenzie, John S title: COVID-19: a novel zoonotic disease caused by a coronavirus from China: what we know and what we don’t date: 2020-03-17 words: 1862.0 sentences: 113.0 pages: flesch: 51.0 cache: ./cache/cord-319158-n8e2n30b.txt txt: ./txt/cord-319158-n8e2n30b.txt summary: Based on established practice, the new virus was named SARS-CoV-2 by the Coronavirus Study Group of the International Committee for the Taxonomy of Viruses 10 , and the disease it causes as COVID-19 by WHO 11 . Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven modelling analysis of the early outbreak Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China SARS-CoV-2 viral load in upper respiratory specimens of infected patients A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan (2020) The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) -China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32226946/ doi: 10.1071/ma20013 id: cord-339459-z22a5yzo author: Mackey, Katherine title: Risks and Impact of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers on SARS-CoV-2 Infection in Adults: A Living Systematic Review date: 2020-05-15 words: 4132.0 sentences: 202.0 pages: flesch: 44.0 cache: ./cache/cord-339459-z22a5yzo.txt txt: ./txt/cord-339459-z22a5yzo.txt summary: PURPOSE: To evaluate, on an ongoing basis, whether use of ACEIs or ARBs either increases risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or is associated with worse COVID-19 disease outcomes, and to assess the efficacy of these medications for COVID-19 treatment. STUDY SELECTION: Observational studies and trials in adults that examined associations and effects of ACEIs or ARBs on risk for SARS-CoV-2 infection and COVID-19 disease severity and mortality. Three studies (33, 36, 37) , which included a total of 8766 patients with COVID-19 and presented analyses adjusted for important confounding factors, had consistent results and provide moderate-certainty evidence that ACEIs or ARBs are not associated with a higher likelihood of positive SARS-CoV-2 test results among symptomatic patients ( Table 1) . Risks and Impact of ACEIs or ARBs in Adults With SARS-CoV-2 Infection REVIEW Annals.org Annals of Internal Medicine other U.S. study included patients with COVID-19 in the New York University health system and examined ICU admission, assisted ventilation, and death as outcomes (37) . abstract: BACKGROUND: The role of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin-receptor blockers (ARBs) in COVID-19 disease susceptibility, severity, and treatment is unclear. PURPOSE: To evaluate, on an ongoing basis, whether use of ACEIs or ARBs either increases risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or is associated with worse COVID-19 disease outcomes, and to assess the efficacy of these medications for COVID-19 treatment. DATA SOURCES: MEDLINE (Ovid) and Cochrane Database of Systematic Reviews from 2003 to 4 May 2020, with planned ongoing surveillance for 1 year; the World Health Organization database of COVID-19 publications and medRxiv.org through 17 April 2020; and ClinicalTrials.gov to 24 April 2020, with planned ongoing surveillance. STUDY SELECTION: Observational studies and trials in adults that examined associations and effects of ACEIs or ARBs on risk for SARS-CoV-2 infection and COVID-19 disease severity and mortality. DATA EXTRACTION: Single-reviewer abstraction confirmed by another reviewer, independent evaluation by 2 reviewers of study quality, and collective assessment of certainty of evidence. DATA SYNTHESIS: Two retrospective cohort studies found that ACEI and ARB use was not associated with a higher likelihood of receiving a positive SARS-CoV-2 test result, and 1 case–control study found no association with COVID-19 illness in a large community (moderate-certainty evidence). Fourteen observational studies, involving a total of 23 565 adults with COVID-19, showed consistent evidence that neither medication was associated with more severe COVID-19 illness (high-certainty evidence). Four registered randomized trials plan to evaluate ACEIs and ARBs for treatment of COVID-19. LIMITATION: Half the studies were small and did not adjust for important confounding variables. CONCLUSION: High-certainty evidence suggests that ACEI or ARB use is not associated with more severe COVID-19 disease, and moderate-certainty evidence suggests no association between use of these medications and positive SARS-CoV-2 test results among symptomatic patients. Whether these medications increase the risk for mild or asymptomatic disease or are beneficial in COVID-19 treatment remains uncertain. PRIMARY FUNDING SOURCE: None. (PROSPERO: registration number pending) url: https://doi.org/10.7326/m20-1515 doi: 10.7326/m20-1515 id: cord-256374-l492w2i2 author: Mackler, Niklas title: Will First-Responders Show Up for Work During a Pandemic? Lessons From a Smallpox Vaccination Survey of Paramedics date: 2007-05-22 words: 2368.0 sentences: 144.0 pages: flesch: 58.0 cache: ./cache/cord-256374-l492w2i2.txt txt: ./txt/cord-256374-l492w2i2.txt summary: Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. The results of this survey indicate that in the event of an outbreak of a contagious disease like smallpox or pandemic influenza, a significant number of paramedics might be unwilling to remain on duty to care for patients without adequate protection against infection. 2, 5 Several recent studies have addressed public health worker and basic and paramedic emergency medical technician (EMT) perceptions about coming to work during a contagious outbreak. abstract: BACKGROUND: The presence of H5N1 influenza in Southeast Asia has reawakened fears of a worldwide influenza pandemic of the sort that occurred in 1918. It is estimated that up to 1.9 million people in the United States could die if such an outbreak occurs. It is unlikely that a vaccine for a pandemic strain will be available quickly enough to protect first-responders. Similar concerns existed in 2002 when the United States attempted to vaccinate first-responders against smallpox, a potential biologic weapon. METHOD: We conducted a survey of one group of first-responders, paramedics, to determine if fear of infection would compromise their ability to care for persons potentially infected with smallpox. RESULTS: Three hundred paramedics were given the survey, and 95 (32%) responded. More than 80% of paramedics polled would not remain on duty if there were no vaccine and no protective gear. Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. Finally, although 91% of paramedics would remain on duty if they were fully protected, this number falls to 38% if the respondent believed that his or her immediate family was not protected. The results of this survey are relevant to current concerns about an influenza pandemic. Every effort must be made to protect first-responders from pandemic influenza and educate them about it. url: https://api.elsevier.com/content/article/pii/S1540248707000272 doi: 10.1016/j.dmr.2007.02.002 id: cord-305134-s7h6bpof author: Mackman, Nigel title: Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses date: 2020-07-13 words: 6412.0 sentences: 443.0 pages: flesch: 41.0 cache: ./cache/cord-305134-s7h6bpof.txt txt: ./txt/cord-305134-s7h6bpof.txt summary: It is likely that multiple systems contribute to thrombosis in COVID-19 patients, such as activation of coagulation, platelet activation, hypofibrinolysis, endothelial cell dysfunction, inflammation, neutrophil extracellular traps, and complement. 60, 82 Taken together, these results indicate that most COVID-19 patients have an activated coagulation system that is associated with increased levels of d-dimer; however, it is unlike classic DIC since there is little change in PT and the thrombocytopenia is generally mild. [95] [96] [97] [98] [99] There is clear evidence for activation of different cell types, such as lung epithelial cells, macrophages, neutrophils, endothelial cells, and platelets, as well as different systems, such as coagulation, inflammation, and complement, in the lungs of COVID-19 patients (Figure) . We found that plasma levels of extracellular vesicle TF activity were increased in severe influenza virus patients and were associated with mortality. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infects lung epithelial cells and endothelial cells (ECs), which leads to the recruitment of a variety of immune cells, such as macrophages and neutrophils. abstract: The world is amid a pandemic caused by severe acute respiratory syndrome-coronavirus 2. Severe acute respiratory syndrome-coronavirus causes serious respiratory tract infections that can lead to viral pneumonia, acute respiratory distress syndrome, and death. Some patients with coronavirus disease 2019 (COVID-19) have an activated coagulation system characterized by elevated plasma levels of d-dimer—a biomarker of fibrin degradation. Importantly, high levels of D-dimer on hospital admission are associated with increased risk of mortality. Venous thromboembolism is more common than arterial thromboembolism in hospitalized COVID-19 patients. Pulmonary thrombosis and microvascular thrombosis are observed in autopsy studies, and this may contribute to the severe hypoxia observed in COVID-19 patients. It is likely that multiple systems contribute to thrombosis in COVID-19 patients, such as activation of coagulation, platelet activation, hypofibrinolysis, endothelial cell dysfunction, inflammation, neutrophil extracellular traps, and complement. Targeting these different pathways may reduce thrombosis and improve lung function in COVID-19 patients. url: https://doi.org/10.1161/atvbaha.120.314514 doi: 10.1161/atvbaha.120.314514 id: cord-303022-9hqoq7tf author: Madapusi Balaji, Thodur title: Oral cancer and periodontal disease increase the risk of COVID 19? A mechanism mediated through furin and cathepsin overexpression date: 2020-06-01 words: 888.0 sentences: 54.0 pages: flesch: 47.0 cache: ./cache/cord-303022-9hqoq7tf.txt txt: ./txt/cord-303022-9hqoq7tf.txt summary: In addition to furin, another protease cathepsin L is also elevated in chronic periodontitis and oral cancer, which in turn could be a result of the interleukin 6 mediated activation of the caveolin -1 mediated JNK-AP-1 signaling pathway [8] [9] [10] . 3) Following binding of the S1 subunit to the ACE-2 receptors, the virus fuses with the host cell in two mechanisms: (a) endosomal fusion which is mediated by cysteine proteases cathepsin B/L and (b) plasma membrane fusion mediated by the serine protease TMPRSS2. Based on the above-mentioned data, it can be hypothesized that the increased protease levels in chronic periodontitis and oral cancer could potentially increase the risk of an oral mucosa mediated SARS-corona virus-2 infection (figure 1). In addition to increasing proteases, chronic periodontitis, and oral cancer patients have also reported having a low melatonin level [14, 15] . abstract: nan url: https://doi.org/10.1016/j.mehy.2020.109936 doi: 10.1016/j.mehy.2020.109936 id: cord-026803-p1o4qc1h author: Maddury, Jyotsna title: Need of the Hour— COVID-19 for Cardiologists date: 2020-04-16 words: 1671.0 sentences: 111.0 pages: flesch: 46.0 cache: ./cache/cord-026803-p1o4qc1h.txt txt: ./txt/cord-026803-p1o4qc1h.txt summary: The most distressing pandemic at present is coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial studies showed low association of chronic cardiac diseases (10%) in COVID-19 patients along with the acute cardiac injury accounting to 23%. These reports with new information urge cardiologists to warn patients about the potential risk and encourage them to practice "additional, reasonable precautions" for those with underlying heart disease. As SARS-CoV-2 and MERS-CoV have similar pathogenicity, myocardial injury caused due to SARS-CoV-2 infection may be immune mediated through the ACE2 receptor or cytokine storm and/or hypoxia due to acute respiratory distress syndrome (ARDS). As there is an increased risk of secondary infections with COVID-19, patients are advised to remain current with vaccinations, including the pneumococcal vaccine and influenza vaccine in accordance with current ACC/American Heart Association (AHA) guidelines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295288/ doi: 10.1055/s-0040-1709950 id: cord-274648-e0daf8w6 author: Madeddu, Paolo title: Cardiovascular complications of COVID-19: evidence, misconceptions, and new opportunities date: 2020-06-08 words: 1940.0 sentences: 95.0 pages: flesch: 41.0 cache: ./cache/cord-274648-e0daf8w6.txt txt: ./txt/cord-274648-e0daf8w6.txt summary: The virus binds with its spike protein to the surface receptor angiotensin converting enzyme 2 (ACE2) to unlock human cells and begin infection. Likewise, it remains to be established whether repeated exposures or a single contact with massive doses of the virus, like in the case of clinical staff caring patients who are not known to be infected, can increase the risk of developing severe forms of the disease. The binding of SARS-CoV-2 to ACE2 is stronger than previous coronaviruses, due to difference in key amino acid residues allowing for enhanced interactions between the virus and human cells. Therefore, when considering severity of COVID-19, the low ACE2 levels observed in elderly people and those with cardiovascular disease seem to facilitate rather than protect from the disease (9) . The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32923968/ doi: 10.1530/vb-20-0008 id: cord-340942-oatf59k0 author: Magalhães, Jurandy Júnior Ferraz de title: Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil date: 2020-09-21 words: 3949.0 sentences: 225.0 pages: flesch: 59.0 cache: ./cache/cord-340942-oatf59k0.txt txt: ./txt/cord-340942-oatf59k0.txt summary: METHODS: In this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for SARS-CoV-2 living in Pernambuco state, Northeast Brazil. Here, we describe for the first time the clinical, epidemiological and demographic features of the first 557 laboratory-confirmed COVID-19 cases in Pernambuco state, Northeast Brazil, who were diagnosed between March 12 and April 22, 2020. Patient epidemiological information, demographic and clinical characteristics, including medical history, signs and symptoms, laboratory findings, underlying co-morbidities, and date of disease onset were obtained from electronic medical records of the Pernambuco Central Public Health Laboratory (LACEN) and analyzed. Regarding the distribution of COVID-19 cases in the different household income ranges (Fig. 1B) , we found that SARS-CoV-2 infections occurred in neighborhoods with greater purchasing power. Here, we described for the first time the epidemiological and clinical characteristics of the first 557 consecutive patients diagnosed with SARS-CoV-2 in the state of Pernambuco between 12 March and April 22, 2020. abstract: BACKGROUND: South America is the current epicenter of COVID-19 pandemic. Yet, the epidemiological and clinical features of the disease have not been described in Brazil, the third most affected country in the world. METHODS: In this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for SARS-CoV-2 living in Pernambuco state, Northeast Brazil. RESULTS: The first COVID-19 cases occurred in the high income population. The age of infected patients ranged from 27 days to 97 years with a median of 47 years. The ratio of males to female in the SARS-CoV-2-infected group was 0.83:1. The most common symptom was cough (74.51%), followed by fever (66.79%), dyspnea (56.01%), sore throat (28.19%) and O(2) saturation <95% (24.42%). 86.44% of the lethal cases were patients older than 51 years. The median time from illness onset to diagnosis was 4.0 days (range 0–39 days) Severe patients diagnosed after 14 days of symptoms onset had higher viral load than patients with mild disease. CONCLUSIONS: Our study provides important information about COVID-19 in the tropics and will assist physicians and health officials to face the current pandemics as SARS-CoV-2 continues to spread in the human population. url: https://www.ncbi.nlm.nih.gov/pubmed/32971239/ doi: 10.1016/j.tmaid.2020.101884 id: cord-270635-l8380adr author: Maggi, Enrico title: COVID-19: unanswered questions on immune response and pathogenesis date: 2020-05-08 words: 880.0 sentences: 64.0 pages: flesch: 60.0 cache: ./cache/cord-270635-l8380adr.txt txt: ./txt/cord-270635-l8380adr.txt summary: It is generally accepted that only achieving a better understanding of the interactions between the virus and host immune response and of the pathogenesis of infection is crucial to identify valid therapeutic tools to control virus entry, replication and spread as well as to impair its lethal effects. On this basis, we also touch important aspects regarding the immune response in asymptomatic subjects, the immune-evasion of SARS-CoV-2 in severe patients and differences in disease severity by age and gender. This implies to be able to answer many questions on the virus itself, on the pathogenesis of infection, on the 81 host immune response and to identify therapeutic tools to control virus entry into the cells, its replication and 82 spread as well as its lethal effects. Humoral Immune Responses SARS-CoV 3 -Seroconversion few days after the disease onset and specific IgG detectable in most patients by 14 days. abstract: Abstract The novel coronavirus disease 2019 (COVID-19) has rapidly increased in pandemic scale since it first appeared in Wuhan, China, in December 2019. In these troubled days the scientific community is asking rapid replies to prevent and combat the emergency. It is generally accepted that only achieving a better understanding of the interactions between the virus and host immune response and of the pathogenesis of infection is crucial to identify valid therapeutic tools to control virus entry, replication and spread as well as to impair its lethal effects. Based on the recent research progress of SARS-CoV-2 and the results on previous coronaviruses, in this contribution we underscore some of the main unsolved problems, mostly focusing on pathogenetic aspects and host immunity to the virus. On this basis, we also touch important aspects regarding the immune response in asymptomatic subjects, the immune-evasion of SARS-CoV-2 in severe patients and differences in disease severity by age and gender. url: https://www.sciencedirect.com/science/article/pii/S009167492030631X?v=s5 doi: 10.1016/j.jaci.2020.05.001 id: cord-342391-arp07mck author: Magiorkinis, G. title: Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions date: 2004-09-14 words: 1901.0 sentences: 81.0 pages: flesch: 49.0 cache: ./cache/cord-342391-arp07mck.txt txt: ./txt/cord-342391-arp07mck.txt summary: Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. Bayesian scanning and subsequent phylogenetic analysis revealed that the SARS-CoV sequence was related more closely to Group II than the other two groups in most of its genome (e.g., at the region spanning amino acid positions 4309-5612 in reference to the murine hepatitis virus ORF1ab gene) (Fig. 1) . This clustering was supported by high quartet puzzling support values and high posterior probabilities under various substitution models, thus suggesting that 80% of the SARS-CoV genomic sequence is related more closely to coronaviruses Group II than any other members of this family. abstract: The origin of the severe acute respiratory syndrome‐coronavirus (SARS‐CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS‐CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both. J. Med. Virol. 74:369–372, 2004. © 2004 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/15368527/ doi: 10.1002/jmv.20187 id: cord-303330-zh8wzza5 author: Magleby, Reed title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 words: 3557.0 sentences: 204.0 pages: flesch: 51.0 cache: ./cache/cord-303330-zh8wzza5.txt txt: ./txt/cord-303330-zh8wzza5.txt summary: In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. abstract: BACKGROUND: Patients hospitalized with coronavirus disease 2019 (COVID-19) frequently require mechanical ventilation and have high mortality rates, but the impact of viral burden on these outcomes is unknown. METHODS: We conducted a retrospective cohort study of patients hospitalized with COVID-19 from March 30 to April 30, 2020 at two hospitals in New York City. SARS-CoV-2 viral load was assessed using cycle threshold (Ct) values from a reverse transcription-polymerase chain reaction assay applied to nasopharyngeal swab samples. We compared patient characteristics and outcomes among patients with high, medium, and low admission viral loads and assessed whether viral load was independently associated with risk of intubation and in-hospital mortality. RESULTS: We evaluated 678 patients with COVID-19. Higher viral load was associated with increased age, comorbidities, smoking status, and recent chemotherapy. In-hospital mortality was 35.0% with a high viral load (Ct<25; n=220), 17.6% with a medium viral load (Ct 25-30; n=216), and 6.2% with a low viral load (Ct>30; n=242; P<0.001). The risk of intubation was also higher in patients with a high viral load (29.1%), compared to those with a medium (20.8%) or low viral load (14.9%; P<0.001). High viral load was independently associated with mortality (adjusted odds ratio [aOR] 6.05; 95% confidence interval [CI]: 2.92-12.52; P<0.001) and intubation (aOR 2.73; 95% CI: 1.68-4.44; P<0.001) in multivariate models. CONCLUSIONS: Admission SARS-CoV-2 viral load among hospitalized patients with COVID-19 independently correlates with the risk of intubation and in-hospital mortality. Providing this information to clinicians could potentially be used to guide patient care. url: https://doi.org/10.1093/cid/ciaa851 doi: 10.1093/cid/ciaa851 id: cord-285806-363ivs67 author: Magro, Giuseppe title: SARS-CoV-2 and COVID-19: is interleukin-6 (IL-6) the ''culprit lesion'' of ARDS onset? What is there besides Tocilizumab? SGP130Fc date: 2020-05-14 words: 5157.0 sentences: 257.0 pages: flesch: 41.0 cache: ./cache/cord-285806-363ivs67.txt txt: ./txt/cord-285806-363ivs67.txt summary: In a humanized transgenic mouse MERS-CoV infection model, Remdesivir (a drug already being used against SARS-CoV-2 in patients with severe and moderate disease, GS-US-540-5773/4 Studies) showed more activity and efficacy in prophylactic and therapeutic use then the combination of Lopinavir/Ritonavir and Interferon beta 9 , this points towards the necessity to explore other options regarding immune system modulation and how control of viraemia is also essential. More evidence suggests that critically ill patients with severe respiratory failure and SARS-CoV-2 have either immune dysregulation or macrophage-activation syndrome, both of which are characterized by pro-inflammatory cytokines. This is another evidence of the pro-inflammatory role of the trans-signaling pathway and it could also be the explanation as to why some patients show a higher inflammatory response mediated by IL-6, similarly to what is happening with SARS-CoV-2 infection. abstract: Since the outbreak of COVID-19 many studies have been published showing possible therapies, here the author discusses the end of stage disease related drugs, like Tocilizumab which is currently being used in ARDS patients. In some patients, disease progression leads to an enormous secretion of cytokines, known as cytokine storm, among those cytokines IL-6 plays an important role. Here the author shows how IL-6 has both pro and anti-inflammatory properties, depending on the pathway of transduction: soluble (trans-signaling) or membrane-related (classic signaling), and suggests how targeting only the pro-inflammatory pathway, with SGP130Fc, could be a better option then targeting them both. Other possible IL-6 pathway inhibitors such as Ruxolitinib and Baricinitib are then analyzed, underlying how they lack the benefit of targeting only the pro-inflammatory pathway. url: https://api.elsevier.com/content/article/pii/S2590153220300094 doi: 10.1016/j.cytox.2020.100029 id: cord-287256-hgqz1bcs author: Magurano, Fabio title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date: 2020-11-05 words: 1177.0 sentences: 76.0 pages: flesch: 60.0 cache: ./cache/cord-287256-hgqz1bcs.txt txt: ./txt/cord-287256-hgqz1bcs.txt summary: title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID 50 viral titre of 0,67 and 0,25 log10 respectively. abstract: Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Methods The virus was inoculated on plastic surface and harvested at predefined time-points in parallel at 20-25°C (RT) and at 28°C (JT). Samples collections were tested by TCID50 titers on Vero cells. Samples collections were tested by TCID50 titers on Vero cells. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. At RT, an important reduction in the viral titre, from 4 log10 to 3 log10 TCID50 was observed during the first 24-36 hours. At JT the same decay was observed more rapidly (between 8 and 12 hours), The rate of viral inactivation by D-value was 24.74 at RT and 12,21 hours at JT. Conclusions This remarkable difference between the two temperatures suggests that virus vitality can be influenced by the environmental temperature and that the hot season could reduce the probability of COVID-19 transmission. url: https://www.sciencedirect.com/science/article/pii/S1198743X20306881?v=s5 doi: 10.1016/j.cmi.2020.10.034 id: cord-281141-ouno4jpl author: Mahajan, Swapnil title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 words: 6208.0 sentences: 307.0 pages: flesch: 52.0 cache: ./cache/cord-281141-ouno4jpl.txt txt: ./txt/cord-281141-ouno4jpl.txt summary: A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . abstract: The COVID-19 pandemic has revealed a range of disease phenotypes in infected patients with asymptomatic, mild or severe clinical outcomes, but the mechanisms that determine such variable outcomes remain unresolved. In this study, we identified immunodominant CD8 T-cell epitopes in the RBD and the non-RBD domain of the spike antigen using a novel TCR-binding algorithm. A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. The T-cell reactivity to the predicted epitopes was higher than the Spike-S1 and S2 peptide pools containing 157 and 158 peptides both in unexposed donors and in convalescent patients suggesting that strong T-cell epitopes are likely to be missed when larger peptide pools are used in assays. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. This finding is in contrast to multiple published studies in which pre-existing T-cell immunity is suggested to arise from shared epitopes between SARS-CoV-2 and other common cold-causing coronaviruses. Whether the presence of pre-existing T-cell immunity provides protection against COVID-19 or contributes to severe disease phenotype remains to be determined in a larger cohort. However, our findings raise the expectation that a significant majority of the global population is likely to have SARS-CoV-2 reactive T-cells because of prior exposure to flu and CMV viruses, in addition to common cold-causing coronaviruses. url: https://doi.org/10.1101/2020.11.03.367375 doi: 10.1101/2020.11.03.367375 id: cord-025623-1v9614f8 author: Mahapatra, Pallab Sinha title: Surface Treatments to Enhance the Functionality of PPEs date: 2020-05-29 words: 2039.0 sentences: 131.0 pages: flesch: 48.0 cache: ./cache/cord-025623-1v9614f8.txt txt: ./txt/cord-025623-1v9614f8.txt summary: This paper focuses on improving PPE functionality in a scalable manner by surface treatment and coating with appropriate materials and other functional enhancements, such as exposure to UV rays or other sterilizing agents (e.g., hydrogen peroxide). Surface treatments to enhance resistance against diseasecausing microbes, i.e., antimicrobial coatings, have the potential to improve PPE functionalities dramatically. Hydrophobic coatings make it difficult for droplets/particles to adhere on surfaces and are known to provide antimicrobial characteristics, which are retained after multiple washes; antibacterial and antifungal properties were demonstrated by Mukherjee et al. Klibanov''s group at MIT has shown extended functionality of hydrophobic coating characteristics against influenza viruses, which get transmitted through respiratory droplets, like SARS-CoV-2; Halder et al. Scalable surface treatment strategies that combine antiviral action with liquid-repelling properties are one of many possible approaches to enhance the functionality of PPEs, thereby serving to satisfy their high demand in the healthcare industry and other fronts where the COVID-19 pandemic is being fought. abstract: The outbreak of unknown viral pneumonia in Wuhan China in December 2019 led to a new coronavirus (SARS-CoV-2), which attracted worldwide attention, with the related COVID-19 disease quickly becoming a global pandemic. In about 5 months, this disease has led to ~ 4 million cases and claimed more than 200 k deaths as a result of its highly contagious nature. The present understanding is that SARS-CoV-2 is a type of influenza virus that can be transmitted through respiratory droplets and aerosols; Lewis (Nature 580:175, 2020). The primary methodology to prevent the spreading of this disease has been “social distancing” and usage of personal protective equipment (PPE) at the front lines of healthcare and other critical operations. The scale of the disease has led to unprecedented demand for PPEs and increased functionality of the same. This paper focuses on improving PPE functionality in a scalable manner by surface treatment and coating with appropriate materials and other functional enhancements, such as exposure to UV rays or other sterilizing agents (e.g., hydrogen peroxide). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7257351/ doi: 10.1007/s41403-020-00110-0 id: cord-344934-m0q7rm6z author: Mahapatra, Sovesh title: Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking date: 2020-04-07 words: 3876.0 sentences: 228.0 pages: flesch: 56.0 cache: ./cache/cord-344934-m0q7rm6z.txt txt: ./txt/cord-344934-m0q7rm6z.txt summary: Here, we report the ML model based on the Naive Bayes algorithm, which has an accuracy of around 73% to predict the drugs that could be used for the treatment of COVID-19. Bioactivity datasets which are available from the numerous high throughput screens deliver useful means for machine learning classifiers as they contain binary information (active/inactive) as well as numerical values to classify different compounds under consideration 22, 23 . These drugs were downloaded in the form of SDFs and after processing, the descriptions generated were taken as the test model for developing the train model which was made on the basis of a database containing the inhibitors of the SARS coronavirus. Around 178 drugs were predicted by our ML model which can be effective for the treatment of diseases caused by SARS-Cov-2. abstract: Background The outbreak of the novel coronavirus disease COVID 19, caused by the SARS-CoV-2 virus has spread rapidly around the globe during the past 3 months. As the virus infected cases and mortality rate of this disease is increasing exponentially, scientists and researchers all over the world are relentlessly working to understand this new virus along with possible treatment regimens by discovering active therapeutic agents and vaccines. So, there is an urgent requirement of new and effective medications that can treat the disease caused by SARS CoV 2. Methods and findings We perform the study of drugs that are already available in the market and being used for other diseases to accelerate clinical recovery, in other words repurposing of existing drugs. The vast complexity in drug design and protocols regarding clinical trials often prohibit developing various new drug combinations for this epidemic disease in a limited time. Recently, remarkable improvements in computational power coupled with advancements in Machine Learning (ML) technology have been utilized to revolutionize the drug development process. Consequently, a detailed study using ML for the repurposing of therapeutic agents is urgently required. Here, we report the ML model based on the Naive Bayes algorithm, which has an accuracy of around 73% to predict the drugs that could be used for the treatment of COVID-19. Our study predicts around ten FDA approved commercial drugs that can be used for repurposing. Among all, we suggest that the antiretroviral drug Atazanavir (DrugBank ID DB01072) would probably be one of the most effective drugs based on the selected criterions. Conclusions Our study can help clinical scientists in being more selective in identifying and testing the therapeutic agents for COVID 19 treatment. The ML based approach for drug discovery as reported here can be a futuristic smart drug designing strategy for community applications. url: https://doi.org/10.1101/2020.04.05.20054254 doi: 10.1101/2020.04.05.20054254 id: cord-297859-p57pl45i author: Mahlke, Lutz title: Chirurgie in der SARS-CoV-2-Pandemie: Empfehlungen zum operativen Vorgehen date: 2020-06-02 words: 2374.0 sentences: 329.0 pages: flesch: 49.0 cache: ./cache/cord-297859-p57pl45i.txt txt: ./txt/cord-297859-p57pl45i.txt summary: authors: Mahlke, Lutz; Flohé, Sascha; Matthes, Gerrit; Paffrath, Thomas; Wagner, Frithjof; Wölfl, Christoph Die Virusinfektion mit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ist hochkontagiös, daher besteht auch für die Mitarbeiter des Krankenhauses ein hohes Risiko [1] . Über die persönliche Schutzausrüstung (PSA) für Mitarbeiter der Anästhesie sind in einer kürzlich erschienenen Publikation sehr detailliert das Vorgehen und das notwendige Equipment beschrieben worden [2] , sodass hier v. Sofern es Personalschlüssel und Ausbildungsstand der Abteilung erlauben, ist die Schaffung von speziell geschulten "COVID-19"-OP-Teams sinnvoll. Auch die bisherigen Virusnachweise im Darm und im Stuhl lassen keine hohe Viruslast erkennen [13] , zumal unklar ist, ob es sich hierbei noch um ein infektiöses Virus handelt [14] . Even patients infected by SARS-CoV-2 or COVID-19 may need operative procedures. Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 abstract: BACKGROUND: In February 2020 Germany was also hit by the SARS-CoV‑2 pandemic. Even patients infected by SARS-CoV‑2 or COVID-19 may need operative procedures. Currently, no uniform recommendations exist on precautions to be taken when operating on these patients. Furthermore, they may differ from one hospital to another. METHODS: The task force COVID-19 of the emergency, intensive and severely injured section of the German Trauma Society (DGU e. V.) has developed consensus-based recommendations on surgical treatment of patients with SARS-CoV‑2 infections. Great importance is placed on the implementation in hospitals at all levels of care. RESULTS: The indications for surgical interventions in patients with COVID-19 infections require an extremely critical evaluation. When indicated these surgical intervention should ideally be performed in a separate operating theater. All personnel involved should wear personal protective equipment with FFP2 masks, face shields and double gloves. The emergency team in the resuscitation bay should generally wear the same personal protective equipment. Special training is mandatory and the exposure of team members should be minimized. CONCLUSION: The recommendations are principally used for all kinds of surgery and comply with the currently available knowledge. Nevertheless, all recommendations represent a compromise between maximum safety of all medical staff and practicability in the routine hospital workflow. url: https://doi.org/10.1007/s00113-020-00830-6 doi: 10.1007/s00113-020-00830-6 id: cord-270015-5gtxfkoz author: Mahmood Shah, Sayed Mustafa title: Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health date: 2020-08-20 words: 1003.0 sentences: 70.0 pages: flesch: 49.0 cache: ./cache/cord-270015-5gtxfkoz.txt txt: ./txt/cord-270015-5gtxfkoz.txt summary: title: Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health 6 This comes at a time when many Muslim majority countries are stilling struggling with the public health crisis posed by COVID-19, with variable success in controlling the transmission of the virus. 7 A structural analysis of ACE-2 receptor in vertebrates has shown artiodactyl mammals (which include domesticated cattle, sheep and goats) express ACE-2 receptors and were classified as medium score for binding to SARS-CoV-2 Spike protein. 7 This finding has been reiterated in a comparative x-ray structural analysis of SARS-CoV-2 spike protein receptor binding domain to ACE-2 receptors in humans and putative intermediate hosts. Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts SARS-CoV-2: structural diversity, phylogeny, and potential animal host identification of spike glycoprotein abstract: nan url: https://doi.org/10.1002/hpm.3040 doi: 10.1002/hpm.3040 id: cord-291595-8241pjpe author: Mahmudpour, Mehdi title: COVID-19 cytokine storm: The anger of inflammation date: 2020-05-30 words: 5842.0 sentences: 351.0 pages: flesch: 43.0 cache: ./cache/cord-291595-8241pjpe.txt txt: ./txt/cord-291595-8241pjpe.txt summary: The virus-mediated down-regulation of ACE2 causes a burst of inflammatory cytokine release through dysregulation of the renin-angiotensin-aldosterone system (ACE/angiotensin II/AT1R axis), attenuation of Mas receptor (ACE2/MasR axis), increased activation of [des-Arg9]-bradykinin (ACE2/bradykinin B1R/DABK axis), and activation of the complement system including C5a and C5b-9 components. Because Ang-(1-7) exerts a critical role in counteracting the pro-inflammatory effect of RAAS, protecting from endothelial cell activation and resulting lung damage from inflammatory mediators in the cytokine storm, the administration of Ang-(1-7) or one of its similar agents to patients with COVID-19 pneumonitis has been suggested [35, 66] . We suggested ACE2/Bradykinin/DABK may be involved in the inflammatory response of SARS CoV-2; therefore, blockade of this axis by inhibiting BKB1R may ameliorate a part of the cytokine storm which occurs in COVID-19 infection. abstract: Patients with COVID-19 who require ICU admission might have the cytokine storm. It is a state of out-of-control release of a variety of inflammatory cytokines. The molecular mechanism of the cytokine storm has not been explored extensively yet. The attachment of SARS-CoV-2 spike glycoprotein with angiotensin-converting enzyme 2 (ACE2), as its cellular receptor, triggers complex molecular events that leads to hyperinflammation. Four molecular axes that may be involved in SARS-CoV-2 driven inflammatory cytokine overproduction are addressed in this work. The virus-mediated down-regulation of ACE2 causes a burst of inflammatory cytokine release through dysregulation of the renin-angiotensin-aldosterone system (ACE/angiotensin II/AT1R axis), attenuation of Mas receptor (ACE2/MasR axis), increased activation of [des-Arg9]-bradykinin (ACE2/bradykinin B1R/DABK axis), and activation of the complement system including C5a and C5b-9 components. The molecular clarification of these axes will elucidate an array of therapeutic strategies to confront the cytokine storm in order to prevent and treat COVID-19 associated acute respiratory distress syndrome. url: https://api.elsevier.com/content/article/pii/S1043466620301678 doi: 10.1016/j.cyto.2020.155151 id: cord-335302-6wsx0jby author: Mahy, Brian W.J. title: The diversity of viruses infecting humans date: 2011-12-12 words: 2865.0 sentences: 123.0 pages: flesch: 48.0 cache: ./cache/cord-335302-6wsx0jby.txt txt: ./txt/cord-335302-6wsx0jby.txt summary: Other new viruses have been recognized because of a new disease they caused in humans, such as the severe acute respiratory syndrome (SARS) coronavirus . Studies on the origin of the SARS coronavirus are still ongoing: there is recent evidence of a zoonotic origin of the human disease, perhaps from palm civets, but the true natural reservoir of the virus seems most likely to be in a bat species, probably Chinese horseshoe bats (Lau et al. This was the only known human parvovirus until very recently, when a new parvovirus was discovered to be the cause of lower respiratory tract infections in children. 2006 ) and elsewhere (unpublished) have revealed a significant number of children whose lower respiratory tract disease appears to be caused by human bocavirus infection. New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children abstract: Most human viruses have been discovered through the diseases they cause in animals, plants, bacteria or fungi. Recent finds include human bocaviruses, which now seem to have a global distribution, and cause respiratory tract disease in infants, and several new pathogenic human coronaviruses. The SARS coronavirus, genetically distinct from all previously known coronaviruses, caused a disease which was highly transmissible and very severe, eventually leading to 8000 cases worldwide with over 800 deaths. Many viruses which are transmitted to humans by invertebrates, such as insects or ticks, have the ability to infect and replicate in cells of both vertebrate and invertebrate origin. However human virology is a rapidly expanding field and recent technologies such as the polymerase chain reaction (PCR) amplification system have made it possible to look for previously unrecognized viruses which may or may not be involved in pathogenesis. For example viruses in the genus Anellovirus are found in 80% of human blood samples yet do not seem to cause any disease. This paper overviews known human vertebrate viruses, more recent discoveries, and recommends a systematic search for viruses which may already infect the human population but have so far remained undetected. url: https://www.ncbi.nlm.nih.gov/pubmed/32309018/ doi: 10.1080/14888386.2006.9712792 id: cord-272573-wxqly479 author: Maia Chagas, Andre title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date: 2020-04-24 words: 5074.0 sentences: 317.0 pages: flesch: 55.0 cache: ./cache/cord-272573-wxqly479.txt txt: ./txt/cord-272573-wxqly479.txt summary: Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. Community and commercial open source efforts in diagnostic technology to date have focused on four areas: i) open platforms for scaling reactions as exemplified by Opentrons ( Fig 3A) [28] , an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona; ii) trying to fill gaps where less attention is being paid by clinical diagnostics companies, such as Chia Bio''s Open qPCR (Fig 3B) environmental test kit for surveillance via surface swabs [111] ; iii) distributed reproduction of rapidly-published, lab-scale protocols, seen within the OpenCOVID initiative hosted by Just One Giant Lab [39] which involves many community labs worldwide; iv) initiatives such as the Open Enzyme Collection [93] , Free Genes [94] and Biomaker Challenge [112] which are investigating new approaches to foundational technologies such as reagents and instrumentation, with a view to building capacity and resources or global science and medicine to face a future pandemic. abstract: With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/32330124/ doi: 10.1371/journal.pbio.3000730 id: cord-257310-wqu7t44n author: Maideniuc, Catalina title: Acute necrotizing myelitis and acute motor axonal neuropathy in a COVID-19 patient date: 2020-08-09 words: 1091.0 sentences: 78.0 pages: flesch: 51.0 cache: ./cache/cord-257310-wqu7t44n.txt txt: ./txt/cord-257310-wqu7t44n.txt summary: A 61-year-old woman with COVID 19 infection developed acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. Here we present a unique case of COVID 19 patients with acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. However, MRI Cervical spine showed patchy T2 hyperintensities within the central cord extending from below the foreman magnum, proximal Electronic supplementary material The online version of this article (https ://doi.org/10.1007/s0041 5-020-10145 -6) contains supplementary material, which is available to authorized users. The patient had a spinal fluid analysis that showed a hemorrhagic tap (red blood cells 312/mm 3 ) with normal white blood cells (3/mm 3) elevated protein (87 mg/ dl) and glucose (73 mg/dl). Acute necrotizing encephalitis, myelitis and variants of GBS such as axonal, demyelinating, and Miller Fisher Syndrome have been reported with the COVID 19 [2] [3] [4] [5] . abstract: A 61-year-old woman with COVID 19 infection developed acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. MRI of the cervical spine demonstrated longitudinally extensive transverse myelitis, and EMG was consistent with the diagnosis of AMAN. CSF testing was negative for SARS-CoV-2. High dose steroids followed by plasma exchange were administered, and the patient made a clinical recovery. Immunotherapy has some role in fastening the improvement of immune-mediated neurological conditions associated with COVID-19. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00415-020-10145-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00415-020-10145-6 doi: 10.1007/s00415-020-10145-6 id: cord-314109-wb45naw2 author: Maiese, Kenneth title: The Mechanistic Target of Rapamycin (mTOR): Novel Considerations as an Antiviral Treatment date: 2020-06-17 words: 4134.0 sentences: 226.0 pages: flesch: 35.0 cache: ./cache/cord-314109-wb45naw2.txt txt: ./txt/cord-314109-wb45naw2.txt summary: One such avenue that may prove to be exceedingly fruitful and offer exciting potential as new antiviral therapy involves the mechanistic target of rapamycin (mTOR) and its associated pathways of mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK). Recent work has shown that mTOR pathways in conjunction with AMPK may offer valuable targets to control cell injury, oxidative stress, mitochondrial dysfunction, and the onset of hyperinflammation, a significant disability associated with COVID-19. Considering that one of the mechanisms that can lead to severe disability and death during infection with SARS-CoV-2 is an exaggerated activation of the host''s immune system that results in systemic hyperinflammation with the elevation of multiple pro-inflammatory cytokines, it is interesting to note that mTOR pathways have been tied to immune system modulation [40, 54, 55] . • The mechanistic target of rapamycin (mTOR) and its associated pathways with mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK) offer new avenues of opportunity for the development of innovative antiviral treatment strategies. abstract: Multiple viral pathogens can pose a significant health risk to individuals. As a recent example, the β-coronavirus family virion, SARS-CoV-2, has quickly evolved as a pandemic leading to coronavirus disease 2019 (COVID-19) and has been declared by the World Health Organization as a Public Health Emergency of International Concern. To date, no definitive treatment or vaccine application exists for COVID-19. Although new investigations seek to repurpose existing antiviral treatments for COVID-19, innovative treatment strategies not normally considered to have antiviral capabilities may be critical to address this global concern. One such avenue that may prove to be exceedingly fruitful and offer exciting potential as new antiviral therapy involves the mechanistic target of rapamycin (mTOR) and its associated pathways of mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK). Recent work has shown that mTOR pathways in conjunction with AMPK may offer valuable targets to control cell injury, oxidative stress, mitochondrial dysfunction, and the onset of hyperinflammation, a significant disability associated with COVID-19. Furthermore, pathways that can activate mTOR may be necessary for anti-hepatitis C activity, reduction of influenza A virus replication, and vital for type-1 interferon responses with influenza vaccination. Yet, important considerations for the development of safe and effective antiviral therapy with mTOR pathways exist. Under some conditions, mTOR can act as a double edge sword and participate in virion replication and virion release from cells. Future work with mTOR as a potential antiviral target is highly warranted and with a greater understanding of this novel pathway, new treatments against several viral pathogens may successfully emerge. url: https://www.ncbi.nlm.nih.gov/pubmed/32334502/ doi: 10.2174/1567202617666200425205122 id: cord-342996-honeavwj author: Mair-Jenkins, John title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 words: 5306.0 sentences: 284.0 pages: flesch: 45.0 cache: ./cache/cord-342996-honeavwj.txt txt: ./txt/cord-342996-honeavwj.txt summary: title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . abstract: Background. Administration of convalescent plasma, serum, or hyperimmune immunoglobulin may be of clinical benefit for treatment of severe acute respiratory infections (SARIs) of viral etiology. We conducted a systematic review and exploratory meta-analysis to assess the overall evidence. Methods. Healthcare databases and sources of grey literature were searched in July 2013. All records were screened against the protocol eligibility criteria, using a 3-stage process. Data extraction and risk of bias assessments were undertaken. Results. We identified 32 studies of SARS coronavirus infection and severe influenza. Narrative analyses revealed consistent evidence for a reduction in mortality, especially when convalescent plasma is administered early after symptom onset. Exploratory post hoc meta-analysis showed a statistically significant reduction in the pooled odds of mortality following treatment, compared with placebo or no therapy (odds ratio, 0.25; 95% confidence interval, .14–.45; I(2) = 0%). Studies were commonly of low or very low quality, lacked control groups, and at moderate or high risk of bias. Sources of clinical and methodological heterogeneity were identified. Conclusions. Convalescent plasma may reduce mortality and appears safe. This therapy should be studied within the context of a well-designed clinical trial or other formal evaluation, including for treatment of Middle East respiratory syndrome coronavirus CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/25030060/ doi: 10.1093/infdis/jiu396 id: cord-296147-yfcp0xf2 author: Mairesse, Antoine title: High clinical performance and quantitative assessment of antibody kinetics using a dual recognition assay for the detection of SARS-CoV-2 IgM and IgG antibodies date: 2020-08-25 words: 3217.0 sentences: 226.0 pages: flesch: 56.0 cache: ./cache/cord-296147-yfcp0xf2.txt txt: ./txt/cord-296147-yfcp0xf2.txt summary: This study aims at assessing the analytical and clinical performances of the iFlash® anti-SARS-CoV-2 chemiluminescence assay for the detection of both IgM and IgG antibodies. The determination of anti-SARS-CoV-2 IgG antibodies from 28 days since symptom onset was associated with high sensitivity, especially using optimized cut-offs (i.e. 100%). The aim of this study was to evaluate the analytical and clinical performances of the iFlash ® SARS-CoV-2 antibodies (IgM and IgG) chemiluminescence assay (CLIA). Clinical sensitivity for SARS-Cov-2 serological test depending on the onset of COVID-19 symptoms was carried out with the manufacturer''s cut-off (>10 AU/mL for both IgM and IgG) and with ROC curve adapted cut-offs (2.81 AU/mL for IgM; 4.86 AU/mL for IgG). The aims of the present study were to evaluate the analytical and clinical performances of the iFlash ® anti-SARS-CoV-2 CLIA assay for IgM and IgG antibodies with a large cohort of COVID-19 patients, to provide an external validation of this test and to evaluate the antibody kinetics since symptom onset. abstract: Abstract Objectives Several serological SARS-CoV-2 immunoassays have been developed recently but require external validation before widespread use. This study aims at assessing the analytical and clinical performances of the iFlash® anti-SARS-CoV-2 chemiluminescence assay for the detection of both IgM and IgG antibodies. The kinetics of the antibody response was also evaluated. Design & Methods The precision, carry-over, linearity, limit of blank, detection and quantification were assessed. Sensitivity analysis was performed by using 178 sera collected from 154 RT-PCR confirmed patients COVID-19 samples. The specificity analysis was performed from 75 selected non-SARS-CoV-2 sera with a potential cross-reaction to the SARS-CoV-2 immunoassay. Results This iFlash® SARS-CoV-2 assay showed excellent analytical performances. After 2 weeks since symptom onset, the sensitivities for IgM and IgG were 62.2% (95% CI: 52.3-71.2%) and 92.9%% (95% CI: 85.7-96.7%), respectively by using the cut-off provided by the manufacturer. After cut-off optimization (i.e. >2.81 for IgM and >4.86 for IgG), the sensitivity for IgM and IgG were 81.6 (95% CI: 72.7-88.1%) and 95.9% (95% CI: 89.4-98.7%), respectively. Optimized cut-off for IgG improved the sensitivity to reach 100% (95%CI: 87.6-100) from 28 days since symptom onset. Conclusions This study shows that the iFlash® SARS-CoV-2 assay from YHLO biotechnology, has satisfactory analytical performances. Nevertheless, the sensitivity of the IgM is limited for a proper clinical use compared to IgG. The determination of anti-SARS-CoV-2 IgG antibodies from 28 days since symptom onset was associated with high sensitivity, especially using optimized cut-offs (i.e. 100%). url: https://doi.org/10.1016/j.clinbiochem.2020.08.009 doi: 10.1016/j.clinbiochem.2020.08.009 id: cord-300458-jeuwaj50 author: Maisch, Bernhard title: COVID-19—What we know and what we need to know: There are more questions than answers date: 2020-04-23 words: 1156.0 sentences: 73.0 pages: flesch: 57.0 cache: ./cache/cord-300458-jeuwaj50.txt txt: ./txt/cord-300458-jeuwaj50.txt summary: COVID-19-What we know and what we need to know: There are more questions than answers This collection of short statements from the editors of HERZ/Cardiovascular Diseases is a strong signal to the readers of our journal in critical times. But we also fear that with a low herd immunity a second wave of infection might follow, since no proven antiviral treatment for COVID-19 exists and vaccination is not yet available [3] . Pulmonology demonstrates with every ventilated patient that COVID-19 is a potentially lethal lung disease. The first reported Chinese patient with suspected myocarditis from SARS-CoV-2 was treated with ventilation, methylprednisolone, i.v. immunoglobulins and inotropics and survived [4] . A total of 55 authors (!) have described in an observational study with 66 COVID-19 patients without a control group a beneficial effect in the New England Journal of Medicine [5] . 2020) compassionate use of remdesivir for patients with severe Covid-19 abstract: nan url: https://doi.org/10.1007/s00059-020-04929-9 doi: 10.1007/s00059-020-04929-9 id: cord-025948-6dsx7pey author: Maitra, Arindam title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date: 2020-06-04 words: 7218.0 sentences: 382.0 pages: flesch: 56.0 cache: ./cache/cord-025948-6dsx7pey.txt txt: ./txt/cord-025948-6dsx7pey.txt summary: Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. We have initiated a study on sequencing of SARS-CoV-2 genome from swab samples obtained from infected individuals from different regions of West Bengal in Eastern India and report here the first nine sequences and the results of analysis of the sequence data with respect to other sequences reported from the country until date. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. We have also detected emergence of mutations in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. abstract: Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a clade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S(2) domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, the possible implications of mutation D614G (in S(D) domain) and G1124V (in S(2) subunit) on the structural stability of S protein have also been discussed. Results report for the first time a bird’s eye view on the accumulation of mutations in SARS-CoV-2 genome in Eastern India. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12038-020-00046-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269891/ doi: 10.1007/s12038-020-00046-1 id: cord-258312-3v5t4k8d author: Majachani, Nicole title: A Case of a Newborn Baby Girl Infected with SARS-CoV-2 Due to Transplacental Viral Transmission date: 2020-10-25 words: 1962.0 sentences: 131.0 pages: flesch: 51.0 cache: ./cache/cord-258312-3v5t4k8d.txt txt: ./txt/cord-258312-3v5t4k8d.txt summary: Patient: Female, 31-year-old Final Diagnosis: COVID-19 • SARS-CoV-2 Symptoms: Asymptomatic Medication:— Clinical Procedure: — Specialty: Pediatrics and Neonatology OBJECTIVE: Unusual clinical course BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious virus and is responsible for the current pandemic. CASE REPORT: 31-year-old Hispanic woman in the final week of pregnancy developed mild respiratory symptoms of COVID-19 pneumonia and tested positive for SARS-CoV-2 infection. In response to the potential risks to both the mother and fetus, the American College of Obstetricians and Gynecologists, the American Academy of Pediatrics, and the Centers for Disease Control have developed guidelines which provide a framework for detecting infections early and preventing potential transmission of SARS-CoV-2. Although similar viruses like severe acute respiratory syndrome coronavirus 1 have not demonstrated the ability to cause fetal infection, SARS-CoV-2 is able to bind ACE2 with much higher affinity [11] , thus increasing the probability of transplacental transmission. abstract: Patient: Female, 31-year-old Final Diagnosis: COVID-19 • SARS-CoV-2 Symptoms: Asymptomatic Medication:— Clinical Procedure: — Specialty: Pediatrics and Neonatology OBJECTIVE: Unusual clinical course BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious virus and is responsible for the current pandemic. It mainly infects cells of the lower respiratory tract and has been linked to severe respiratory complications. Although multiple routes of transmission have been reported in the literature, there is no definitive evidence for transplacental transmission. We present a case of neonatal SARS-CoV-2 likely due to transplacental transmission. CASE REPORT: 31-year-old Hispanic woman in the final week of pregnancy developed mild respiratory symptoms of COVID-19 pneumonia and tested positive for SARS-CoV-2 infection. She had a history of Human immunodeficiency virus (HIV) infection and gestational diabetes. Two days later, she gave birth to a baby girl who tested positive for SARS-CoV-2 on the first day after birth. She was delivered via elective cesarean section adhering to a strict infection control protocol. CONCLUSIONS: This report presents a case of a 31-year-old mother with mild symptoms of COVID-19 pneumonia who was positive for SARS-CoV-2 infection and who gave birth to a baby girl who was also positive for SARS-CoV-2. This case supports the possibility of transplacental transmission of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33099570/ doi: 10.12659/ajcr.925766 id: cord-263844-ixgejst2 author: Majdic, Gregor title: Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? date: 2020-06-09 words: 1702.0 sentences: 87.0 pages: flesch: 49.0 cache: ./cache/cord-263844-ixgejst2.txt txt: ./txt/cord-263844-ixgejst2.txt summary: title: Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? If there is a sex difference in the expression of ACE2 in the lung, this could theoretically explain the gender disparity in COVID-19 disease. Epidemiological data show that a much larger number of men are severely affected by the disease, and there is an even more substantial gender difference in the mortality of patients with COVID-19. Here, I propose a novel hypothesis that not only addresses the significant gender differences in morbidity and mortality due to COVID-19 but also potentially tackles the low morbidity and especially the low mortality in children infected by the SARS-CoV-2 virus. Therefore, I propose the hypothesis that the expression of ACE2 protein is different between males and females and that this sex difference contributes to the gender disparity in morbidity and mortality from the COVID-19 disease. abstract: COVID-19 morbidity and mortality have significant gender disparities, with higher prevalence and mortality in men. SARS-CoV-2 enters the lungs through the ACE2 enzyme, a member of the renin-angiotensin system (RAS). Although there are no data for the lung, the expressions of RAS components in other tissues are modulated by sex hormones, androgens, and estrogens. However, there are no data on sex-specific differences in ACE2 expression. If there is a sex difference in the expression of ACE2 in the lung, this could theoretically explain the gender disparity in COVID-19 disease. More importantly, although modulation of ACE2 will certainly not provide a cure for the COVID-19 disease, modulation of ACE2 by sex hormone modulators, if they affect the expression of ACE2, could potentially be developed into a supportive therapy for COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32582576/ doi: 10.3389/fcimb.2020.00327 id: cord-344217-kci4uw7u author: Majid, Sabhiya title: Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses date: 2020-08-25 words: 5645.0 sentences: 316.0 pages: flesch: 46.0 cache: ./cache/cord-344217-kci4uw7u.txt txt: ./txt/cord-344217-kci4uw7u.txt summary: Coronavirus disease 2019 (COVID-19), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses (CoVs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-CoV (SARS-CoV) in 2002–2003, Middle East respiratory syndrome-CoV (MERS-CoV) in 2012, and currently this devastating COVID-19. Beta coronaviruses are a subgroup of the coronavirus family, large enveloped positive-sense singlestranded RNA (+ssRNA) viruses able to infect a wide variety of mammals and avian species, causing mainly respiratory or enteric diseases [2] . The disease caused by SARS-CoV-2 has been named COVID-19, a highly transmittable and pathogenic respiratory infection, which has become a public health emergency of international concern as no clinically approved antiviral drug or vaccine is available-though few broad spectrum antiviral drugs and drug combinations in clinical trials have resulted in clinical recovery [23] [24] [25] [26] [27] . abstract: Coronavirus disease 2019 (COVID-19), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging in Wuhan, China, in December 2019, it spread widely across the world causing panic—worst ever economic depression is visibly predictable. Coronaviruses (CoVs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-CoV (SARS-CoV) in 2002–2003, Middle East respiratory syndrome-CoV (MERS-CoV) in 2012, and currently this devastating COVID-19. Research strategies focused on understanding the evolutionary origin, transmission, and molecular basis of SARS-CoV-2 and its pathogenesis need to be urgently formulated to manage the current and possible future coronaviral outbreaks. Current response to the COVID-19 outbreak has been largely limited to monitoring/containment. Although frantic global efforts for developing safe and effective prophylactic and therapeutic agents are on, no licensed antiviral treatment or vaccine exists till date. In this review, research strategies for coping with COVID-19 based on evolutionary and molecular aspects of coronaviruses have been proposed. url: https://doi.org/10.1007/s42399-020-00457-z doi: 10.1007/s42399-020-00457-z id: cord-274474-u2fdicgz author: Majumder, Joydeb title: Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus date: 2020-10-13 words: 10098.0 sentences: 634.0 pages: flesch: 46.0 cache: ./cache/cord-274474-u2fdicgz.txt txt: ./txt/cord-274474-u2fdicgz.txt summary: The present review summarizes recent advances in the development of nanocarrier based therapeutics for local and targeted delivery of drugs, nucleic acids and imaging agents for diagnostics and treatment of various diseases such as cancer, cystic fibrosis, and coronavirus. [1, 2] Therefore, methods of developing new therapeutic solutions as well as improving the current therapies for the common lung diseases such as asthma, cystic fibrosis, chronic obstructive pulmonary disease, lung cancer, and coronavirus infections remain the main focus in the fields of targeted drug delivery. In this review, we will summarize recent reports on the development of lipid and polymer based nanocarriers for targeted delivery of drugs and nucleic acids for the treatment of lung cancer. In a similar study, we used a complex liposomal drug delivery system containing anticancer drug doxorubicin and both MRP1 and BCL2 targeting antisense oligonucleotides for inhalation treatment in lung cancer cells. abstract: Systemic delivery of therapeutics for treatment of lung diseases has several limitations including poor organ distribution of delivered payload with relatively low accumulation of active substances in the lungs and severe adverse side effects. In contrast, nanocarrier based therapeutics provide a broad range of opportunities due to their ability to encapsulate substances with different aqueous solubility, transport distinct types of cargo, target therapeutics specifically to the deceased organ, cell, or cellular organelle limiting adverse side effects and increasing the efficacy of therapy. Moreover, many nanotherapeutics can be delivered by inhalation locally to the lungs avoiding systemic circulation. In addition, nanoscale based delivery systems can be multifunctional, simultaneously carrying out several tasks including diagnostics, treatment and suppression of cellular resistance to the treatment. Nanoscale delivery systems improve the clinical efficacy of conventional therapeutics allowing new approaches for the treatment of respiratory diseases which are difficult to treat or possess intrinsic or acquired resistance to treatment. The present review summarizes recent advances in the development of nanocarrier based therapeutics for local and targeted delivery of drugs, nucleic acids and imaging agents for diagnostics and treatment of various diseases such as cancer, cystic fibrosis, and coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/33173809/ doi: 10.1002/adtp.202000203 id: cord-307853-m1q1sjr4 author: Majumder, Satyabrata title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model date: 2020-10-16 words: 3048.0 sentences: 176.0 pages: flesch: 57.0 cache: ./cache/cord-307853-m1q1sjr4.txt txt: ./txt/cord-307853-m1q1sjr4.txt summary: title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model In this study we have examined the intrinsic dynamics of the prefusion, lying state of trimeric S protein of these viruses through Normal Mode Analysis using Anisotropic Network Model. MERS-CoV spike shows unique dynamical motion compared to the other two S protein indicated by low RMSIP, spectral overlap and cosine correlation value. A detailed study to explore the intrinsic dynamical motion of the prefusion lying state spike protein trimer is needed for proper understanding of its function from conformation perspective. RMSIP computes quantitative comparison value between the sets of normal modes and expressed as: Structural alignments of the models were done using PyMol. We have computed the eigenvalues of first hundred non-zero normal modes of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike (S) proteins in the lying state ( Fig. 1 ). abstract: COVID-19 caused by SARS-CoV-2 have become a global pandemic with serious rate of fatalities. SARS-CoV and MERS-CoV have also caused serious outbreak previously but the intensity was much lower than the ongoing SARS-CoV-2. The main infectivity factor of all the three viruses is the spike glycoprotein. In this study we have examined the intrinsic dynamics of the prefusion, lying state of trimeric S protein of these viruses through Normal Mode Analysis using Anisotropic Network Model. The dynamic modes of the S proteins of the aforementioned viruses were compared by root mean square inner product (RMSIP), spectral overlap and cosine correlation matrix. S proteins show homogenous correlated or anticorrelated motions among their domains but direction of C(α) atom among the spike proteins show less similarity. SARS-CoV-2 spike shows high vertically upward motion of the receptor binding motif implying its propensity for binding with the receptor even in the lying state. MERS-CoV spike shows unique dynamical motion compared to the other two S protein indicated by low RMSIP, spectral overlap and cosine correlation value. This study will guide in developing common potential inhibitor molecules against closed state of spike protein of these viruses to prevent conformational switching from lying to standing state. url: https://doi.org/10.1016/j.jmgm.2020.107778 doi: 10.1016/j.jmgm.2020.107778 id: cord-300018-3uzau7if author: Mak, Gannon C.K. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date: 2020-07-24 words: 649.0 sentences: 54.0 pages: flesch: 61.0 cache: ./cache/cord-300018-3uzau7if.txt txt: ./txt/cord-300018-3uzau7if.txt summary: authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong In an attempt to understand the relevance of D614G substitution among COVID-19 patients in Hong Kong, full length S gene sequences from severe and non-severe cases were examined. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 The SARS-CoV-2 Spike Protein D614G abstract: nan url: https://doi.org/10.1016/j.jcv.2020.104550 doi: 10.1016/j.jcv.2020.104550 id: cord-337799-mc1oqhf4 author: Mak, Gannon CK title: Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus date: 2020-10-29 words: 2329.0 sentences: 153.0 pages: flesch: 60.0 cache: ./cache/cord-337799-mc1oqhf4.txt txt: ./txt/cord-337799-mc1oqhf4.txt summary: STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using PCR as a reference method. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. Besides RT-PCR, rapid antigen detection (RAD) kits for qualitative determination of SARS-CoV-2 antigen are available. The purpose of this evaluation is to assess analytical sensitivity of the three SARS-CoV-2 RAD kits by means of limit of detection (LOD) using a set of serial tenfold dilution samples; and It means that if we set a cut off by means of ≤day X after symptom onset for performing RAD kits, we will miss another group of specimens having a similar high viral load. abstract: BACKGROUND: Numerous rapid antigen detection (RAD) kits for diagnosing COVID-19 patients are available in the market recently. OBJECTIVE: To compare analytical sensitivity and clinical sensitivity for the three commercially available RAD kits. STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the three RAD kits varied 102 to 105 fold less sensitive than RT-PCR. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. The likelihood of positive results for RAD kits will be higher. url: https://doi.org/10.1016/j.jcv.2020.104684 doi: 10.1016/j.jcv.2020.104684 id: cord-325213-e6i6buow author: Mak, Ivan Wing Chit title: Risk factors for chronic post-traumatic stress disorder (PTSD) in SARS survivors date: 2010-09-15 words: 4871.0 sentences: 254.0 pages: flesch: 46.0 cache: ./cache/cord-325213-e6i6buow.txt txt: ./txt/cord-325213-e6i6buow.txt summary: BACKGROUND: Post-traumatic stress disorder (PTSD) is one of the most prevalent long-term psychiatric diagnoses among survivors of severe acute respiratory syndrome (SARS). Previous reported predictors of acute psychiatric complications include sociodemographic variables [e.g., being a health care worker (HCW)] [11] [12] [13] ; illness-related variables [e.g., the severity of disease and the administration of high-dose corticosteroids [11] , lowest level of arterial oxygen saturation (SaO 2 ) during hospitalisation] [14] ; and psychosocial variables including social support, cognitive appraisal and coping style [13, 15] . In the univariate analysis, variables significantly associated with current PTSD in the predictor block included female gender (P=.019), being a HCW(P=.031), pre-SARS chronic medical illness (P=.044) and having AVN as a complication (P=.035) ( Table 1) . Logistic regression of predictor and association factor block Multivariate logistic regression analysis showed that being of the female gender (P=.003), the presence of chronic medical illness before SARS (P=.014) and having AVN as a physical complication (P=.01) were predictors of PTSD at 30 months post-SARS (Table 3) . abstract: BACKGROUND: Post-traumatic stress disorder (PTSD) is one of the most prevalent long-term psychiatric diagnoses among survivors of severe acute respiratory syndrome (SARS). OBJECTIVES: The objective of this study was to identify the predictors of chronic PTSD in SARS survivors. DESIGN: PTSD at 30 months after the SARS outbreak was assessed by the Structured Clinical Interview for the DSM-IV. Survivors' demographic data, medical information and psychosocial variables were collected for risk factor analysis. RESULTS: Multivariate logistic regression analysis showed that female gender as well as the presence of chronic medical illnesses diagnosed before the onset of SARS and avascular necrosis were independent predictors of PTSD at 30 months post-SARS. Associated factors included higher-chance external locus of control, higher functional disability and higher average pain intensity. CONCLUSION: The study of PTSD at 30 months post-SARS showed that the predictive value of acute medical variables may fade out. Our findings do not support some prior hypotheses that the use of high dose corticosteroids is protective against the development of PTSD. On the contrary, the adversity both before and after the SARS outbreak may be more important in hindering recovery from PTSD. The risk factor analysis can not only improve the detection of hidden psychiatric complications but also provide insight for the possible model of care delivery for the SARS survivors. With the complex interaction of the biopsychosocial challenges of SARS, an integrated multidisciplinary clinic setting may be a superior approach in the long-term management of complicated PTSD cases. url: https://www.sciencedirect.com/science/article/pii/S0163834310001453 doi: 10.1016/j.genhosppsych.2010.07.007 id: cord-278649-ge9ike2c author: Makaronidis, Janine title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study date: 2020-10-01 words: 4278.0 sentences: 232.0 pages: flesch: 58.0 cache: ./cache/cord-278649-ge9ike2c.txt txt: ./txt/cord-278649-ge9ike2c.txt summary: title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study The study aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a community-based population with acute loss of smell and/or taste and to compare the frequency of COVID-19 associated symptoms in participants with and without SARS-CoV-2 antibodies. • Recruited participants completed online questionnaires regarding demographics, their loss of smell and/or taste, and other COVID-19 symptoms, before they had a telemedicine consultation with a healthcare professional who confirmed the history of their symptoms and supervised a test to find out if they had SARS-CoV-2 antibodies. In this community-based cohort study, undertaken during the peak of the COVID-19 outbreak in London, the seroprevalence of SARS-CoV-2 antibodies in participants with new onset loss of sense of smell and/or taste, was 77.6%. abstract: BACKGROUND: Loss of smell and taste are commonly reported symptoms associated with coronavirus disease 2019 (COVID-19); however, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in people with acute loss of smell and/or taste is unknown. The study aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a community-based population with acute loss of smell and/or taste and to compare the frequency of COVID-19 associated symptoms in participants with and without SARS-CoV-2 antibodies. It also evaluated whether smell or taste loss are indicative of COVID-19 infection. METHODS AND FINDINGS: Text messages, sent via primary care centers in London, United Kingdom, invited people with loss of smell and/or taste in the preceding month, to participate. Recruitment took place between 23 April 2020 and 14 May 2020. A total of 590 participants enrolled via a web-based platform and responded to questions about loss of smell and taste and other COVID-19–related symptoms. Mean age was 39.4 years (SD ± 12.0) and 69.1% (n = 392) of participants were female. A total of 567 (96.1%) had a telemedicine consultation during which their COVID-19–related symptoms were verified and a lateral flow immunoassay test that detected SARS-CoV-2 immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies was undertaken under medical supervision. A total of 77.6% of 567 participants with acute smell and/or taste loss had SARS-CoV-2 antibodies; of these, 39.8% (n = 175) had neither cough nor fever. New loss of smell was more prevalent in participants with SARS-CoV-2 antibodies, compared with those without antibodies (93.4% versus 78.7%, p < 0.001), whereas taste loss was equally prevalent (90.2% versus 89.0%, p = 0.738). Seropositivity for SARS-CoV-2 was 3 times more likely in participants with smell loss (OR 2.86; 95% CI 1.27–6.36; p < 0.001) compared with those with taste loss. The limitations of this study are the lack of a general population control group, the self-reported nature of the smell and taste changes, and the fact our methodology does not take into account the possibility that a population subset may not seroconvert to develop SARS-CoV-2 antibodies post-COVID-19. CONCLUSIONS: Our findings suggest that recent loss of smell is a highly specific COVID-19 symptom and should be considered more generally in guiding case isolation, testing, and treatment of COVID-19. TRIALS REGISTRATION: ClinicalTrials.gov NCT04377815 url: https://www.ncbi.nlm.nih.gov/pubmed/33001967/ doi: 10.1371/journal.pmed.1003358 id: cord-258307-nsdhvc8w author: Maki, Dennis G. title: SARS Revisited: The Challenge of Controlling Emerging Infectious Diseases at the Local, Regional, Federal, and Global Levels date: 2011-10-20 words: 5019.0 sentences: 252.0 pages: flesch: 48.0 cache: ./cache/cord-258307-nsdhvc8w.txt txt: ./txt/cord-258307-nsdhvc8w.txt summary: The most recent and perhaps most fearsome emerging infections are the appearance of West Nile virus encephalitis in New York City in 1999 and its rapid spread westward 6 ; inhalation anthrax, deriving from use of Bacillus anthracis spores as a biologic weapon against the US civilian population in 2001 7 ; the global outbreak of severe acute respiratory syndrome (SARS) in 2003 8 ; and the looming threat of pandemic influenza, especially global disease caused by the highly virulent avian subtype A (H5N1). If it is not, the effort will not have been wasted because it is likely that all the planning and resource allocation will prove invaluable for controlling the spread of natural emerging pathogens, such as SARS-CoV or a new strain of influenza virus, which are probably far more likely to pose a serious threat to human and animal health in the United States and worldwide. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0025619611621812 doi: 10.4065/79.11.1359 id: cord-292152-gmru83ac author: Makrinioti, Heidi title: Intussusception in two children with SARS-CoV-2 infection in children date: 2020-08-08 words: 1752.0 sentences: 109.0 pages: flesch: 45.0 cache: ./cache/cord-292152-gmru83ac.txt txt: ./txt/cord-292152-gmru83ac.txt summary: This report compares intussusception as likely associated with SARS-CoV-2 infection in infants that presented in Wuhan and London. Based on the data so far, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in children is shown to run a milder course with lower reported mortality rates (1, 2) . However, as the definition of suspected cases does not include presentations with gastrointestinal symptoms only, there is still no clear answer to the question "should we screen for SARS-CoV-2 infection in children who require admission to hospital with gastrointestinal symptoms?". In addition to the fact that most of the presentations of the infection in children are atypical, there is very recent evidence showing that the highest viral shedding is taking place 2 to 3 days before onset of symptoms (https://www.nature.com/articles/s41591-020-0869-5). This brief report describes two cases of intussusception in infants found to be positive with SARS-CoV-2. This report describes two infants with intussusception and SARS-CoV-2 infection. abstract: This report compares intussusception as likely associated with SARS-CoV-2 infection in infants that presented in Wuhan and London. While the intussusception was reduced by enemas in Wuhan, the outcome was fatal. Whereas the intussusception was not reduced by enemas in London and required surgery, the outcome was favourable. url: https://doi.org/10.1093/jpids/piaa096 doi: 10.1093/jpids/piaa096 id: cord-277585-evw3pu87 author: Malavolta, Marco title: Exploring the Relevance of Senotherapeutics for the Current SARS-CoV-2 Emergency and Similar Future Global Health Threats date: 2020-04-08 words: 4183.0 sentences: 211.0 pages: flesch: 36.0 cache: ./cache/cord-277585-evw3pu87.txt txt: ./txt/cord-277585-evw3pu87.txt summary: Drugs targeting IL-6 have been included among the potential strategies to inhibit the deleterious consequences of the senescence-associated secretory phenotype (SASP), the secretome produced by senescent cells [31, 32] . The evidence that patients with cancer, hypertension or with smoking habits (conditions associated with a pathological role of cellular senescence) experienced worse outcomes from COVID-19 [71] , further supports the hypothesis that an accumulation of senescent cells may favor the development of severe events during SARS-CoV-2 infection. In the case of dengue virus infection, cellular senescence seems to exert an anti-viral function [64] but other viruses, such as IFV, have evolved mechanisms to increase replication in senescent cells [68] . Clarifying the role of cellular senescence in SARS-CoV infection may additionally provide a strong rationale for the use of senotherapeutics, such as SASP inhibitors, in the management of elderly patients affected by COVID-19. abstract: The higher death rate caused by COVID-19 in older people, especially those with comorbidities, is a challenge for biomedical aging research. Here we explore the idea that an exacerbated inflammatory response, in particular that mediated by IL-6, may drive the deleterious consequences of the infection. Data shows that other RNA viruses, such as influenza virus, can display enhanced replication efficiency in senescent cells, suggesting that the accumulation of senescent cells with aging and age-related diseases may play a role in this phenomenon. However, at present, we are completely unaware of the response to SARS-CoV and SARS-COV-2 occurring in senescent cells. We deem that this is a priority area of research because it could lead to the development of several therapeutic strategies based on senotherapeutics or prevent unsuccessful attempts. Two of these senotherapeutics, azithromycin and ruxolitinib, are currently undergoing testing for their efficacy in treating COVID-19. The potential of these strategies is not only for ameliorating the consequences of the current emergence of SARS-CoV-2, but also for the future emergence of new viruses or mutated ones for which we are completely unprepared and for which no vaccines are available. url: https://doi.org/10.3390/cells9040909 doi: 10.3390/cells9040909 id: cord-346281-sma6e891 author: Maldonado, Valente title: Repositioning of pentoxifylline as an immunomodulator and regulator of the renin-angiotensin system in the treatment of COVID-19 date: 2020-06-09 words: 5711.0 sentences: 260.0 pages: flesch: 35.0 cache: ./cache/cord-346281-sma6e891.txt txt: ./txt/cord-346281-sma6e891.txt summary: Pentoxifylline (PTX) is a phosphodiesterase inhibitor that increases cyclic adenosine monophosphate levels, which in turn activate protein kinase, leading to a reduction in the synthesis of proinflammatory cytokines to ultimately influence the renin-angiotensin system (RAS) in vitro by inhibiting angiotensin 1 receptor (AT1R) expression. The rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19 by helping reduce the production of the inflammatory cytokines without deleterious effects on the immune system to delay viral clearance. 5 Overall, the rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19, which can help reduce the production of the inflammatory cytokines TNF-α, IL-6, IFN-γ, and IL-17 and increase the anti-inflammatory cytokine IL-10. abstract: Pentoxifylline (PTX) is a phosphodiesterase inhibitor that increases cyclic adenosine monophosphate levels, which in turn activate protein kinase, leading to a reduction in the synthesis of proinflammatory cytokines to ultimately influence the renin-angiotensin system (RAS) in vitro by inhibiting angiotensin 1 receptor (AT1R) expression. The rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19 by helping reduce the production of the inflammatory cytokines without deleterious effects on the immune system to delay viral clearance. Moreover, PTX can restore the balance of the immune response, reduce damage to the endothelium and alveolar epithelial cells, improve circulation, and prevent microvascular thrombosis. There is further evidence that PTX can improve ventilatory parameters. Therefore, we propose repositioning PTX in the treatment of COVID-19. The main advantage of repositioning PTX is that it is an affordable drug that is already available worldwide with an established safety profile, further offering the possibility of immediately analysing the result of its use and associated success rates. Another advantage is that PTX selectively reduces the concentration of TNF-α mRNA in cells, which, in the case of an acute infectious state such as COVID-19, would seem to offer a more strategic approach. url: https://www.ncbi.nlm.nih.gov/pubmed/32540603/ doi: 10.1016/j.mehy.2020.109988 id: cord-289216-g4kqi560 author: Malecki, M. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 words: 1927.0 sentences: 127.0 pages: flesch: 51.0 cache: ./cache/cord-289216-g4kqi560.txt txt: ./txt/cord-289216-g4kqi560.txt summary: title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. In this study, two diagnostic laboratories of a tertiary care hospital equipped with different PCR systems validated the available kits on the respective systems for SARS-CoV-2 testing. In order to evaluate the performance of analytical components used for SARS-CoV-2 diagnostic we compared three commercially available RT-PCR kits, six extraction kits and four PCR cyclers in all possible combinations using predefined EQA samples. abstract: In limelight of the ongoing pandemic SARS-CoV-2 testing is critical for the diagnosis of infected patients, contact-tracing and mitigating the transmission. Diagnostic laboratories are expected to provide appropriate testing with maximum accuracy. Real-time reverse transcriptase PCR (RT-PCR) is the diagnostic standard yet many commercial diagnostic kits have become available. However, only a handful of studies have reviewed their performance in clinical settings. The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. The greatest difference of the Ct values between the matrices was 9 cycles. One borderline sample could not be detected by 3 out of 12 analytical matrices and yielded a false negative result. We therefore conclude that diagnostic laboratories should take the complete analytical matrix in addition to the performance values published by the manufacturer for a respective RT-PCR kit into account. With limited resources laboratories have to validate a wide range of kits to determine appropriate analytical matrices for detecting SARS-CoV-2 reliably. The interpretation of clinical results has to be adapted accordingly. url: http://medrxiv.org/cgi/content/short/2020.09.18.20185744v1?rss=1 doi: 10.1101/2020.09.18.20185744 id: cord-344003-oul2hdyq author: Maleki Dana, Parisa title: An Insight into the Sex Differences in COVID-19 Patients: What are the Possible Causes? date: 2020-06-18 words: 2761.0 sentences: 168.0 pages: flesch: 51.0 cache: ./cache/cord-344003-oul2hdyq.txt txt: ./txt/cord-344003-oul2hdyq.txt summary: Moreover, it is observed that men have a higher risk of developing a severe form of the disease compared to women, highlighting the importance of disaggregated data of male and female COVID-19 patients. ACE2: angiotensin converting enzyme-2 ADAM-17: ADAM metallopeptidase domain-17 AR: androgen receptor CCL: chemokine (C-C motif) ligand cFT: calculated free testosterone CRP: C-reactive protein CXCL: chemokine (C-X-C motif) ligand E2: estradiol ESR: estrogen receptor ICU: intensive care unit IL: interleukin mACE2: myocardial angiotensin converting enzyme-2 NHBE: normal human bronchial epithelial RICU: respiratory intensive care unit sACE2: soluble angiotensin converting enzyme-2 SARS: Severe Acute Respiratory Syndrome SARS-CoV: Severe Acute Respiratory Syndrome Coronavirus TMPRSS2: transmembrane serine protease-2 TT: total testosterone with the virus will die in comparison with men (1.7%/2.8%). Studies of COVID-19 patients have shown that men have a higher risk of developing to the severe form of the disease compared to women. abstract: Studies have reported a sex bias in case fatalities of COVID-19 patients. Moreover, it is observed that men have a higher risk of developing a severe form of the disease compared to women, highlighting the importance of disaggregated data of male and female COVID-19 patients. On the other hand, other factors (eg, hormonal levels and immune functions) also need to be addressed due to the effects of sex differences on the outcomes of COVID-19 patients. An insight into the underlying causes of sex differences in COVID-19 patients may provide an opportunity for better care of the patients or prevention of the disease. The current study reviews the reports concerning with the sex differences in COVID-19 patients. It is explained how sex can affect angiotensin converting enzyme-2 (ACE2), that is a key component for the pathogenesis of COVID-19, and summarized the gender differences in immune responses and how sex hormones are involved in immune processes. Furthermore, the available data about the impact of sex hormones on the immune functions of COVID-19 cases are looked into. url: https://www.ncbi.nlm.nih.gov/pubmed/32600476/ doi: 10.1017/s1049023x20000837 id: cord-328704-m2seavg6 author: Malfertheiner, Peter title: COVID-19: Don''t Neglect the Gastrointestinal Tract! date: 2020-04-29 words: 1206.0 sentences: 63.0 pages: flesch: 45.0 cache: ./cache/cord-328704-m2seavg6.txt txt: ./txt/cord-328704-m2seavg6.txt summary: There are 2 main aspects of concern: one being related to gastrointestinal symptoms (GIS) and their influence on the course of disease; the other being related to excretion of the virus (or its RNA fragments) in the patient''s faeces and a possible role for faecal-oral transmission. To prevent faecal SARS-CoV-2 transmission, a group of experts proposed assessing potential donors for the presence of typical COVID-19 symptoms within 30 days prior to donation. It certainly demands for studies on (a) the pathogenesis and impact of direct viral damage of the whole digestive system; and (b) factors contributing to COVID-19-associated diarrhoea with special emphasis on the gut microbiome and anti-diarrhoea management.A special focus should be directed on the role of the digestive system in transmitting the infection, on how to reduce the length of infectiousness, and on which precautions to be taken with regard to this matter. Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms abstract: n/a. url: https://doi.org/10.1159/000508289 doi: 10.1159/000508289 id: cord-263179-uvq3hzga author: Malik, Zohra R title: A Case of a COVID-19-positive Patient date: 2020-04-09 words: 1558.0 sentences: 106.0 pages: flesch: 60.0 cache: ./cache/cord-263179-uvq3hzga.txt txt: ./txt/cord-263179-uvq3hzga.txt summary: Virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) or the 2019 novel coronavirus (2019-nCoV) belong to the broad family of coronaviruses (subgenus Sarbecovirus). The HCoV (human coronavirus) is responsible for up to 10% -30% of the upper respiratory tract infections globally [2] . Historically, HCoV''s were only responsible for mild infections until 2002, with the emergence of the severe acute respiratory syndrome (SARS) that started in the Guangdong province of China. Based on available data of SARS and MERS, the Centers for Disease Control and Prevention (CDC) has estimated an incubation period for the COVID-19 to be between two and 14 days [6] . There have been reported cases involving large populations showing people with varying incubation periods and the severity of symptoms based on age and immune status. The patient was placed on airborne, droplet, and contact isolation because of the high suspicion of coronavirus infection. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease abstract: The coronavirus (COVID-19), discovered in 2019, has been creating havoc since it first emerged in China and is now spreading worldwide. Its presentation is somewhat similar to influenza. We hereby discuss the salient features of the coronavirus and present the case of a 33-year-old male who was tested positive for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32399342/ doi: 10.7759/cureus.7608 id: cord-293481-bmfj50fb author: Malin, Jakob J. title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 words: 9097.0 sentences: 428.0 pages: flesch: 42.0 cache: ./cache/cord-293481-bmfj50fb.txt txt: ./txt/cord-293481-bmfj50fb.txt summary: Remdesivir or GS-5734 is a prodrug of a nucleoside analog with direct antiviral activity against several single-stranded RNA viruses, including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, preliminary data from a randomized placebo-controlled clinical trial showed that remdesivir reduces the time to recovery in patients with COVID-19 (5) , leading to an emergency-use authorization (EUA) by the U.S. Food and Drug Administration (FDA) only 2 days after the first press release from the National Institute of Allergy and Infectious Diseases (NIAID) (6) . There were strong arguments for the antiviral effect of remdesivir against coronaviruses emerging from multiple cell-based in vitro models, including primary human airway epithelial (HAE) cell cultures (25) , and, for MERS-CoV, from a mouse model of pulmonary infection (28) . After the outbreak of SARS-CoV-2 in January 2020, remdesivir was rapidly tested in a Vero E6 cell-based model that made use of direct viral quantification by rtPCR along with the antimalaria and immune-modulating drug chloroquine and known antivirals such as ribavirin and penciclovir. abstract: Patients and physicians worldwide are facing tremendous health care hazards that are caused by the ongoing severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) pandemic. Remdesivir (GS-5734) is the first approved treatment for severe coronavirus disease 2019 (COVID-19). It is a novel nucleoside analog with a broad antiviral activity spectrum among RNA viruses, including ebolavirus (EBOV) and the respiratory pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2. First described in 2016, the drug was derived from an antiviral library of small molecules intended to target emerging pathogenic RNA viruses. In vivo, remdesivir showed therapeutic and prophylactic effects in animal models of EBOV, MERS-CoV, SARS-CoV, and SARS-CoV-2 infection. However, the substance failed in a clinical trial on ebolavirus disease (EVD), where it was inferior to investigational monoclonal antibodies in an interim analysis. As there was no placebo control in this study, no conclusions on its efficacy in EVD can be made. In contrast, data from a placebo-controlled trial show beneficial effects for patients with COVID-19. Remdesivir reduces the time to recovery of hospitalized patients who require supplemental oxygen and may have a positive impact on mortality outcomes while having a favorable safety profile. Although this is an important milestone in the fight against COVID-19, approval of this drug will not be sufficient to solve the public health issues caused by the ongoing pandemic. Further scientific efforts are needed to evaluate the full potential of nucleoside analogs as treatment or prophylaxis of viral respiratory infections and to develop effective antivirals that are orally bioavailable. url: https://doi.org/10.1128/cmr.00162-20 doi: 10.1128/cmr.00162-20 id: cord-270866-olc5r2yx author: Mallet, Jasmina title: Addictions in the COVID-19 era: Current evidence, future perspectives a comprehensive review date: 2020-08-12 words: 6839.0 sentences: 392.0 pages: flesch: 53.0 cache: ./cache/cord-270866-olc5r2yx.txt txt: ./txt/cord-270866-olc5r2yx.txt summary: RESULTS: Overall, pathophysiological data showed an increased risk of infections for individuals with Substance Use Disorders (SUD) and a possible protective role of nicotine. An electronic search was conducted in Medline (PubMed interface), using the MESH (Medical Subject Headings) search terms ("coronavirus 2019" OR "COVID-19" OR "2019-nCoV" OR "SARS-CoV-2") AND "substance use" OR "SUD" OR "tobacco smoking" OR "cigarette "OR "smoking" OR "nicotine" / "alcohol" / "cannabis" OR "THC" /"opiates" OR "opioid"; between 2019 and the present time (i.e., June 4, 2020), with language restriction (English or French). Heavy alcohol use (assessed several years before) was not associated with an increased risk of COVID-19 infection or COVID-19 related hospitalization (OR=1.12 (0.93-1.35)). Finally, as all past economic crises were associated with increased long-term alcohol-related problems (especially for men and low socio-economic strata) (de Goeij et al., 2015) , we might expect important effects of the COVID-19 pandemic in the next decade. Prevalence, Severity and Mortality associated with COPD and Smoking in patients with COVID-19: A Rapid Systematic Review and Meta-Analysis abstract: BACKGROUND: In the context of the COVID-19 worldwide pandemic, an up-to-date review of current challenges in addictions is necessary. While large scale disasters may have an impact on substance use and addictions, the use of some substances is also likely to modify the risk of COVID-19 infection or course. Many countries have imposed lockdowns. Whether this quarantine or the end of lockdown measures will have an impact on substance use is discussed. The aim of this review is to gather knowledge for clinicians and to guide public health policies during/after lockdown. METHODS: PubMed was reviewed in August 6th (2020), to determine the current evidences and observations concerning the addictions and SARS-CoV2. We used all the names of the severe acute respiratory syndrome of coronavirus 2 (SARS-CoV2 previously 2019 nCoV), the name of the coronavirus disease 2019 (COVID-19), and common substances of abuse. For the physiopathological parts, searches were conducted using key words such as “infection” or “pneumonia”. For the lockdown effects, key words such as “quarantine”, “disaster” or “outbreak” were used. RESULTS: Overall, pathophysiological data showed an increased risk of infections for individuals with Substance Use Disorders (SUD) and a possible protective role of nicotine. During lockdown, there is a substantial risk of increasing SUDs. Individuals with opioid use disorder are particularly at risk of relapse or of involuntary withdrawal. After lockdown, increase of use may be observed as far as years after. Individuals with addictions are at higher risk of multimorbidity and mortality during COVID outbreak. CONCLUSION: This review describes useful strategies in clinical practice, including a systematic assessment of addiction comorbidity during this almost worldwide lockdown/pandemic. This review also highlights important areas for future research. url: https://www.ncbi.nlm.nih.gov/pubmed/32800868/ doi: 10.1016/j.pnpbp.2020.110070 id: cord-346859-r1v6ir8u author: Mallett, Sue title: At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date: 2020-11-04 words: 5020.0 sentences: 277.0 pages: flesch: 52.0 cache: ./cache/cord-346859-r1v6ir8u.txt txt: ./txt/cord-346859-r1v6ir8u.txt summary: BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. Because testing is pivotal to management and containment of COVID-19, we performed an individual participant data (IPD) systematic review of emerging evidence about test accuracy by anatomical sampling site to inform optimal sampling strategies for SARS-CoV-2. Previous studies have established that in COVID-19 infection, viral loads typically peak just before symptoms and at symptom onset [4] and estimated false negative test results over time since exposure from upper respiratory tract samples [2] . • Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). abstract: BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. RESULTS: Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from − 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset. CONCLUSIONS: RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated. url: https://doi.org/10.1186/s12916-020-01810-8 doi: 10.1186/s12916-020-01810-8 id: cord-266983-hpwebkbi author: Mallhi, Tauqeer Hussain title: Risks of Zoonotic Transmission of COVID-19 During Eid-Ul-Adha in Pakistan date: 2020-07-27 words: 946.0 sentences: 54.0 pages: flesch: 53.0 cache: ./cache/cord-266983-hpwebkbi.txt txt: ./txt/cord-266983-hpwebkbi.txt summary: P akistan is expected to celebrate Eid-ul-Adha, an annual religious festival during which millions of farm animals, including sheep, goats, cows, buffalo, and camels are sacrificed, in the end of July or early August this year. 2 Since a recent investigation found the potential of zoonotic transmission of coronavirus disease (COVID-19) by farm animals, 3 we felt inclined to underscore the risks of virus transmission from humans to animals due to various activities surrounded by the festive celebration in Pakistan. It is pertinent to mention that ACE2s in animals, which are abundantly sacrificed during the Eid-Ul-Adha, have the ability to contract SARS-CoV-2, like humans. We believe that risks of zoonotic transmission of COVID-19 should be considered during the preparation of festive celebrations, and immediate measures must be taken to avoid any possible surge in COVID-19 cases during the Eid-Ul-Adha. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32713407/ doi: 10.1017/dmp.2020.278 id: cord-291624-fod0eyuj author: Malone, Robert W. title: COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms date: 2020-06-22 words: 6496.0 sentences: 354.0 pages: flesch: 43.0 cache: ./cache/cord-291624-fod0eyuj.txt txt: ./txt/cord-291624-fod0eyuj.txt summary: We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H (2) activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. Patients with COVID-19 disease can present with a range of mild to severe non-speci c clinical signs and symptoms which develop two to fourteen days after exposure to SARS-CoV-2. The most likely mechanisms of actions include: via antiviral activity, via novel human targets, or via the on-target mechanism described in the current FDA market authorization-famotidine is a histamine receptor H 2 antagonist (and inverse agonist). To assess the possibility that famotidine may inhibit SARS-CoV-2 infection by other routes, a Vero E6 cell-based assay was performed to compare median tissue culture infectious doses (TCID50/mL) of famotidine, remdesivir, and hydroxychloroquine ( Figure 2 ). In both of these studies, the observed non-in ammatory edema in early-stage COVID-19 pulmonary disease is consistent with histamine release by mast cells. abstract: SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. Currently, there are no pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We explore several plausible avenues of activity including antiviral and host-mediated actions. We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H (2) activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. url: https://doi.org/10.21203/rs.3.rs-30934/v2 doi: 10.21203/rs.3.rs-30934/v2 id: cord-130351-w9mij6c6 author: Mamidala, Estari title: In silico identification of clinically approved medicines against the main protease of SARS-CoV-2, causative agent of covid-19 date: 2020-04-25 words: 2676.0 sentences: 155.0 pages: flesch: 50.0 cache: ./cache/cord-130351-w9mij6c6.txt txt: ./txt/cord-130351-w9mij6c6.txt summary: In the present study, we report the potential inhibitory activity of some FDA approved drugs against SARS-CoV-2 main protease by molecular docking study to investigate their binding affinity in protease active site. Docking studies revealed that drug Oseltamivir (anti-H1N1 drug), Rifampin (anti-TB drug), Maraviroc, Etravirine, Indinavir, Rilpivirine (anti-HIV drugs) and Atovaquone, Quinidine, Halofantrine, Amodiaquine, Tetracylcine, Azithromycin, hydroxycholoroquine (anti-malarial drugs) among others binds in the active site of the protease with similar or higher affinity. 11 The free energy (DG) binding of SARS-CoV-2 viral protease with the selected FDA approved drugs was created by means of this molecular docking package. Oseltamivir and Zanamivir, two FDA approved drugs docked with SARS-CoV-2 main protease and obtained binding energy is −7.39 kcal/mol and -3.88 kcal/mol respectively (Table-2 Figure 2 ). abstract: The COVID-19 pandemic triggered by SARS-CoV-2 is a worldwide health disaster. Main protease is an attractive drug target among coronaviruses, due to its vital role in processing the polyproteins that are translated from the viral RNA. There is presently no exact drug or treatment for this diseases caused by SARS-CoV-2. In the present study, we report the potential inhibitory activity of some FDA approved drugs against SARS-CoV-2 main protease by molecular docking study to investigate their binding affinity in protease active site. Docking studies revealed that drug Oseltamivir (anti-H1N1 drug), Rifampin (anti-TB drug), Maraviroc, Etravirine, Indinavir, Rilpivirine (anti-HIV drugs) and Atovaquone, Quinidine, Halofantrine, Amodiaquine, Tetracylcine, Azithromycin, hydroxycholoroquine (anti-malarial drugs) among others binds in the active site of the protease with similar or higher affinity. However, the in-silico abilities of the drug molecules tested in this study, further needs to be validated by carrying out in vitro and in vivo studies. Moreover, this study spreads the potential use of current drugs to be considered and used to comprise the fast expanding SARS-CoV-2 infection. url: https://arxiv.org/pdf/2004.12055v1.pdf doi: nan id: cord-319664-gyktrd36 author: Mancini, Fabiola title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date: 2020-06-18 words: 2082.0 sentences: 112.0 pages: flesch: 54.0 cache: ./cache/cord-319664-gyktrd36.txt txt: ./txt/cord-319664-gyktrd36.txt summary: Finally, to evaluate the performance of molecular assays a standard curve was generated by 10-fold dilutions of SARS-CoV-2 RNA, isolated and extracted at Istituto Superiore di Sanità in Rome, Italy, and quantified by a well-established copy number of RNA synthetic E gene (Wuhan coronavirus, EVAg, www. All specimens were also manually extracted and tested for the presence of SARS-CoV-2 by in-house rt-Realtime PCR and the 2019-nCoV TaqMan RT-PCR Kit. In particular, we investigated the RNA availability and virus detection using both the purified and thermal/non-extractive procedures also with this commercial kit because it is based on the same primers, probes and assays developed by the CDC and used in the inhouse molecular method. This study corroborates our results for in-house rt-Real Time PCR, showing a lower sensitivity of the heat treatment (range ΔCT value of 0.5-1.0) when compared with purified samples, but, dissimilar to our findings, a total inhibition was found by the commercial kit RealStar SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), where all positive samples failed in the detection of Sars-CoV-2 [14] . abstract: The RNA purification is the gold standard for the detection of SARS-CoV-2 in swab samples, but it is dependent on the availability of chemical reagents. In this study, we evaluated the heat treatment method without RNA extraction as a reliable option to nucleic acid purification. url: https://www.ncbi.nlm.nih.gov/pubmed/32552549/ doi: 10.1080/22221751.2020.1775500 id: cord-312971-r9sggqh8 author: Mancino, Enrica title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 date: 2020-04-29 words: 1306.0 sentences: 83.0 pages: flesch: 46.0 cache: ./cache/cord-312971-r9sggqh8.txt txt: ./txt/cord-312971-r9sggqh8.txt summary: title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Key words: Community Acquired Pneumonia, SARS-CoV-2, COVID-19, virus Community Acquired Pneumonia (CAP) remains the leading cause of mortality and morbidity in children worldwide [1] . Surprisingly, only a small number of cases of COVID-19 has been described in children, suggesting that SARS-CoV-2 infection in the paediatric population is unusual [6] . Our aim was to describe viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children under 14 years of age. However, the clinical severity score was higher in RSV patients and hRV was found in 9/17 cases (53%) in coinfection, consistent with the notion that hRV is very frequently detected in respiratory infections J o u r n a l P r e -p r o o f during childhood. abstract: Pneumonia is an important cause of morbidity and mortality in children. We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Human rhinovirus was the most frequently detected agent. No children tested positive for SARS-CoV-2. Our findings suggest that SARS-CoV-2 infection is rare in children and it was not circulating in Rome before COVID-19 outbreak. url: https://doi.org/10.1016/j.jcv.2020.104385 doi: 10.1016/j.jcv.2020.104385 id: cord-268085-vpzrk8u7 author: Mandal, Amrendra title: Gastrointestinal Manifestations in COVID-19 Infection and Its Practical Applications date: 2020-06-21 words: 3106.0 sentences: 163.0 pages: flesch: 43.0 cache: ./cache/cord-268085-vpzrk8u7.txt txt: ./txt/cord-268085-vpzrk8u7.txt summary: This outbreak is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is also commonly known as COVID-19. We reviewed the mechanisms, clinical manifestation, impact on pre-existing liver diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. This article aims to review the mechanisms, clinical manifestation, impact on pre-existing digestive diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. Clinical characteristics of hospitalized patients with SARS-CoV-2 and hepatitis B virus co-infection Exploring the mechanism of liver enzyme Abnormalities in patients with novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. abstract: The latest novel coronavirus (COVID-19) outbreak, which emerged in December 2019 in Wuhan, Hubei, China, is a significant cause of the pandemic. This outbreak is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is also commonly known as COVID-19. A typical symptom includes cough and fever, but a considerable number of patients can manifest gastrointestinal (GI) symptoms, including diarrhea, which can be the initial presentations and may or may not present with respiratory symptoms or fever. COVID-19 virus may be present in stool samples of patients infected with COVID-19, and angiotensin-converting enzyme 2 (ACE2) is a receptor for this virus, which is substantially present in GI epithelial cells. The wide availability of this receptor facilitates COVID-19 infection to be proactive and multiply in the GI tract. Although no antiviral treatments have been approved, several approaches have been proposed, and at present, optimized supportive care remains the mainstay of therapy. Elective endoscopic procedures should be delayed, but the urgent procedures should be performed as indicated. Due to the rapidly evolving data on COVID-19, it is difficult to keep up with the outpouring of information. We reviewed the mechanisms, clinical manifestation, impact on pre-existing liver diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/32714688/ doi: 10.7759/cureus.8750 id: cord-293655-2ab7wdsk author: Mandic-Rajcevic, S. title: Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy) date: 2020-05-08 words: 6602.0 sentences: 327.0 pages: flesch: 56.0 cache: ./cache/cord-293655-2ab7wdsk.txt txt: ./txt/cord-293655-2ab7wdsk.txt summary: Objective To study the source, symptoms, and duration of infection, preventive measures, contact tracing and their effects on SARS-CoV-2 epidemic among healthcare workers (HCW) in 2 large hospitals and 40 external healthcare services in Milan (Italy) to propose effective measures to control the COVID-19 epidemic among healthcare workers. Most prominent symptoms include fever, dry cough, headache, sore throat and sneezing, although a growing number of reports underline asymptomatic and patients with mild symptoms having the same viral load as symptomatic patients and spreading the infection in the general population and among healthcare workers (HCW) (2) (3) (4) (5) . A much smaller sample of workers (N=10), commonly found among close contacts but absent from the hospital for other reasons, reported their daily symptoms even in the days leading to the positive NF swab. abstract: Objective To study the source, symptoms, and duration of infection, preventive measures, contact tracing and their effects on SARS-CoV-2 epidemic among healthcare workers (HCW) in 2 large hospitals and 40 external healthcare services in Milan (Italy) to propose effective measures to control the COVID-19 epidemic among healthcare workers. Design Epidemiological observational study. Setting Two large hospitals and 40 territorial healthcare units, with a total of 5700 workers. Participants 143 HCWs with a SARS-CoV-2 positive nasopharyngeal (NF) swab in a population made of 5,700 HCWs. Main outcome measures Clinical data on the history of exposure, contacts inside and outside of the hospital, NF swab dates and results. A daily online self-reported case report form consisting of the morning and evening body temperature and 11 other symptoms (cough, dyspnoea, discomfort, muscle pain, headache, sore throat, vomiting, diarrhoea, anosmia, dysgeusia, conjunctival hyperaemia). Results Most workers were tested and found positive due to a close contact with a positive colleague (49%), followed by worker-initiated testing due to symptoms (and unknown contact, 28%), and a SARS-CoV-2 positive member of the family (9.8%). 10% of NF swabs performed in the framework of contact tracing resulted positive, compared to only 2.6% through random testing. The first (index) case caused a cluster of 7 positive HCWs discovered through contact tracing and testing of 250 asymptomatic HCWs. HCWs rarely reported symptoms of a respiratory infection, and up to 90% were asymptomatic or with mild symptoms in the days surrounding the positive NF swab. During the 15-day follow-up period, up to 40% of HCWs reported anosmia and dysgeusia/ageusia as moderate or heavy, more frequently than any other symptom. The time necessary for 95% of HCWs to be considered cured (between the positive and two negative NF swabs) was 30 days. Conclusion HCWs represent the main source of infection in healthcare institutions, 90% are asymptomatic or with symptoms not common in a respiratory infection. The time needed to overcome the infection in 95% of workers was 30 days. Contact tracing allows identifying asymptomatic workers which would spread SARS-CoV-2 in the hospital and is a more successful strategy than random testing. url: https://doi.org/10.1101/2020.05.03.20082818 doi: 10.1101/2020.05.03.20082818 id: cord-297630-eabtzfd0 author: Manganaro, Marco title: First considerations on the SARS-CoV-2 epidemic in the Dialysis Units of Piedmont and Aosta Valley, Northern Italy date: 2020-04-10 words: 1285.0 sentences: 70.0 pages: flesch: 53.0 cache: ./cache/cord-297630-eabtzfd0.txt txt: ./txt/cord-297630-eabtzfd0.txt summary: No SARS-COV-2 cases were observed in the only Paediatric Nephrology Unit in the Region (having in charge 4 hemodialysis, 4 peritoneal dialysis, and 35 transplanted The members of the Working group of the Piedmont and Aosta Valley Section of the SIN are listed in "Acknowledgements" section. In adults, 156 SARS-COV-2 cases were recorded: 130 RRT patients including 98 in hemodialysis, 4 in peritoneal dialysis, 26 transplanted, and 2 waiting for transplantation, and 26 health care workers (6 physicians, 18 nurses and 2 members of auxiliary staff). This is much higher than the rates for the general population in Piedmont and Aosta Valley (7782 subjects affected by SARS-CoV-2, i.e., 0.17% of the population), with an odds ratio of 13.43, 95% CI 11.27 to 16.00; z score p < 0.0001 for RRT patients, and of 12.80 (95% CI 8.67 to 18.89; z score p < 0.0001) for staff. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32277423/ doi: 10.1007/s40620-020-00732-1 id: cord-299024-jkqdzt87 author: Mangner, Norman title: Paraneoplastic syndrome and SARS-CoV-2 – incremental effect of two thrombogenic conditions? date: 2020-10-21 words: 1071.0 sentences: 65.0 pages: flesch: 40.0 cache: ./cache/cord-299024-jkqdzt87.txt txt: ./txt/cord-299024-jkqdzt87.txt summary: We present the case of a patient with a non-bacterial thrombotic aortic valve endocarditis experiencing severe thromboembolic complications and an acute right internal carotid artery occlusion in the context of a paraneoplastic syndrome and an asymptomatic SARS-CoV-2 infection, despite treatment with different and overlapping anticoagulant medication. This case describes a patient with non-bacterial thrombotic aortic valve endocarditis that developed despite treatment with a factor-Xa-inhibitor and who subsequently suffered a myocardial infarction and two strokes within a short period of time in the context of a paraneoplastic syndrome and asymptomatic SARS-CoV-2 infection. Paraneoplastic syndromes are often linked to increased thrombogenicity; however, non-bacterial thrombotic aortic valve endocarditis is rare even in the situation of cancer. 3 This case highlights the many-sided effects of paraneoplastic syndromes and SARS-CoV-2 infection in patients being already at increased risk for thrombotic complications due to underlying disease. abstract: We present the case of a patient with a non-bacterial thrombotic aortic valve endocarditis experiencing severe thromboembolic complications and an acute right internal carotid artery occlusion in the context of a paraneoplastic syndrome and an asymptomatic SARS-CoV-2 infection, despite treatment with different and overlapping anticoagulant medication. Patients with increased thrombogenicity due to an underlying disease might be at increased risk for thrombotic events during a SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33106785/ doi: 10.1016/j.cjco.2020.10.010 id: cord-274715-dcs1rgd0 author: Mani Mishra, Pushpendra title: Serum albumin-mediated strategy for the effective targeting of SARS-CoV-2 date: 2020-04-24 words: 2145.0 sentences: 121.0 pages: flesch: 45.0 cache: ./cache/cord-274715-dcs1rgd0.txt txt: ./txt/cord-274715-dcs1rgd0.txt summary: Novel coronavirus (NCoV-19), also known as SARS CoV-2, is a pathogen causing an emerging infection that rapidly increases in incidence and geographic range, is associated with the ever-increasing morbidity and mortality rates, and shows sever economic impact worldwide. We are suggesting here a strategy for the COVID-19 treatment that could be effective in curing the patients in the current scenario when no efficient medicine or Vaccine is currently available, and Clinicians solely depend upon the performing trials with drugs with known antiviral activities. If the albumin is used to stabilize and deliver the EGCG and Curcumin for targeting the intracellular virus components in combination with the drug that could block the virus fusion and/or entry to a cell, this strategy might represent an effective way of treating the SARS CoV-2 infection. abstract: Novel coronavirus (NCoV-19), also known as SARS CoV-2, is a pathogen causing an emerging infection that rapidly increases in incidence and geographic range, is associated with the ever-increasing morbidity and mortality rates, and shows sever economic impact worldwide. The WHO declares the NCoV-19 infection disease (COVID-19) a Public Health Emergency of International Concern on 30 January 2020 and subsequently, on March 11, 2020, declared it a Global Pandemic. Although some people infected with SARS CoV-2 have no symptoms, the spectrum of symptomatic infection ranges from mild to critical, with most COVID-19 infections being not severe. The common mild symptoms include body aches, dry cough, fatigue, low-grade fever, nasal congestion, and sore throat. More severe COVID-19 symptoms are typical of pneumonia, and upon progression, the patient’s condition can worsen with severe respiratory and cardiac problems. Currently, there is no drug or vaccine for curing patients. It has been observed that people with challenged immunity are highly prone to SARS CoV-2 infection and least likely to recover. Also, older adults and people of any age with serious underlying medical conditions might be at higher risk for severe forms of COVID-19. We are suggesting here a strategy for the COVID-19 treatment that could be effective in curing the patients in the current scenario when no efficient medicine or Vaccine is currently available, and Clinicians solely depend upon the performing trials with drugs with known antiviral activities. Our proposed strategy is based on the compilation of published scientific research and concepts. The different published research indicates the success of a similar strategy in different physiological conditions, and such a strategy is widely studied at the cellular level and in animal models. url: https://www.ncbi.nlm.nih.gov/pubmed/32353740/ doi: 10.1016/j.mehy.2020.109790 id: cord-278939-z6kiee09 author: Mani, Janice S. title: Natural product-derived phytochemicals as potential agents against coronaviruses: a review date: 2020-04-30 words: 8148.0 sentences: 435.0 pages: flesch: 46.0 cache: ./cache/cord-278939-z6kiee09.txt txt: ./txt/cord-278939-z6kiee09.txt summary: As previous work has highlighted the potential of traditional Chinese medicines as a source of potential novel drugs (Ling, 2020) , we have not included details on such studies investigating the antiviral activity of remedies comprising portions of numerous plant species in this review. (2020) virtually screened 83 compounds found in Chinese traditional medicines for activity against the RNA-dependent RNA polymerase of SARS-CoV-2, identifying theaflavin, an antioxidant polyphenol, as a potential inhibitor. Several authors have utilised virtual computer docking models to screen for potential compounds that could bind to and inhibit key proteins present in SARS-CoV (Liu and Zhou, 2005; Toney et al., 2004; Wang et al., 2007) , highlighting the potential antiviral activity of compounds such as sabadinine and aurantiamide acetate. Several large in vitro screening studies searching for inhibitory activity of naturally occurring compounds against SARS-CoV have been performed, mainly on Chinese medicinal herbs (Li et al., 2005; Wang et al., 2003) . abstract: Coronaviruses are responsible for a growing economic, social and mortality burden, as the causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), avian infectious bronchitis virus (IBV) and COVID-19. However, there is a lack of effective antiviral agents for many coronavirus strains. Naturally existing compounds provide a wealth of chemical diversity, including antiviral activity, and thus may have utility as therapeutic agents against coronaviral infections. The PubMed database was searched for papers including the keywords coronavirus, SARS or MERS, as well as traditional medicine, herbal, remedy or plants, with 55 primary research articles identified. The overwhelming majority of publications focussed on polar compounds. Compounds that show promise for the inhibition of coronavirus in humans include scutellarein, silvestrol, tryptanthrin, saikosaponin B(2), quercetin, myricetin, caffeic acid, psoralidin, isobavachalcone, and lectins such as griffithsin. Other compounds such as lycorine may be suitable if a therapeutic level of antiviral activity can be achieved without exceeding toxic plasma concentrations. It was noted that the most promising small molecules identified as coronavirus inhibitors contained a conjugated fused ring structure with the majority being classified as being polyphenols. url: https://www.ncbi.nlm.nih.gov/pubmed/32360300/ doi: 10.1016/j.virusres.2020.197989 id: cord-313427-6y4zvrmn author: Mani, Nandita S title: Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date: 2020-06-16 words: 3433.0 sentences: 226.0 pages: flesch: 57.0 cache: ./cache/cord-313427-6y4zvrmn.txt txt: ./txt/cord-313427-6y4zvrmn.txt summary: Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. abstract: BACKGROUND: Healthcare workers (HCW) serving on the front lines of the coronavirus disease 2019 (COVID-19) pandemic have been at increased risk for infection due to SARS-CoV-2 in some settings. Healthcare-acquired infection has been reported in similar epidemics, but there are limited data on the prevalence of COVID-19 among HCWs and their associated clinical outcomes in the United States. METHODS: We established two high-throughput employee testing centers in Seattle, Washington with drive-through and walk-through options for symptomatic employees in the University of Washington Medicine system and its affiliated organizations. Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. RESULTS: Between March 12 and April 23, a total of 3,477 symptomatic employees were tested for COVID-19 at two employee testing centers; 185 (5.3%) employees tested positive for COVID-19. The prevalence of SARS-CoV-2 was similar when comparing frontline HCWs (5.2%) to non-frontline staff (5.5%). Among 174 positive employees reached for follow-up at least 14 days after diagnosis, 6 reported COVID-related hospitalization; all recovered. CONCLUSIONS: During the study period, we observed that the prevalence of positive SARS-CoV-2 tests among symptomatic HCWs was comparable to that of symptomatic non-frontline staff. Reliable and rapid access to testing for employees is essential to preserve the health, safety, and availability of the healthcare workforce during this pandemic and to facilitate the rapid return of SARS-CoV-2 negative employees to work. url: https://www.ncbi.nlm.nih.gov/pubmed/32548613/ doi: 10.1093/cid/ciaa761 id: cord-278509-k62bsk9b author: Manikandan, Natesan title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? date: 2020-09-12 words: 589.0 sentences: 50.0 pages: flesch: 48.0 cache: ./cache/cord-278509-k62bsk9b.txt txt: ./txt/cord-278509-k62bsk9b.txt summary: title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? 7 In a new modeling study in Singapore, Joel R Koo and colleagues found that the combined approach of physical distancing interventions, quarantine, school closure, and workplace distancing, is the most effective at reducing the transmission of SARS-CoV-2. 8 A report from the United States suggested that social distancing interventions can give communities vital time to mitigate the spread of COVID-19 pandemic. Nevertheless, to overcome this global threat, combination of preventive measures like social distancing, hand washing and wearing face masks are the important key practices to mitigate the transmission of COVID-19 in the community. The role of community-wide wearing of face mask for control of Coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2 Impact of self-imposed prevention measures and short-term governmentimposed social distancing on mitigating and delaying a COVID-19 epidemic: A modelling study abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1576988720300443?v=s5 doi: 10.1016/j.vacun.2020.09.001 id: cord-274008-p3st70u3 author: Mann, E. R. title: Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis date: 2020-06-16 words: 6004.0 sentences: 359.0 pages: flesch: 49.0 cache: ./cache/cord-274008-p3st70u3.txt txt: ./txt/cord-274008-p3st70u3.txt summary: Here we report the outcome of a longitudinal immune profiling study in hospitalised patients during the peak of the COVID-19 pandemic in the UK and show the relationship between immune responses and severity of the clinical presentation. Although, as reported previously 4 , a higher neutrophil to lymphocyte ratio (NLR) on hospital admission was observed in those patients whose disease trajectory was ultimately severe, whereas there were no appreciable differences observed in monocytes (figure 1A, 1B and table 1). Longitudinal analysis revealed that in the majority of patients (70%) (irrespective of severity) T cell frequencies in whole blood increased prior to hospital discharge, while neutrophil frequencies reciprocally decreased (figure 1E). Severe COVID-19, on the other hand, was associated with monocytes displaying increased expression of the cell cycle marker, Ki67 (normally <5% in healthy peripheral blood), irrespective of whether monocytes were stimulated or not (figure 3C and appendix 6C), which strongly correlated with hospital data for CRP (figure 3C). abstract: Background The pathogenesis of COVID-19, caused by a novel strain of coronavirus (SARS-CoV-2), involves a complex host-virus interaction and is characterised by an exaggerated immune response, the specific components of which are poorly understood. Here we report the outcome of a longitudinal immune profiling study in hospitalised patients during the peak of the COVID-19 pandemic in the UK and show the relationship between immune responses and severity of the clinical presentation. Methods The Coronavirus Immune Response and Clinical Outcomes (CIRCO) study was conducted at four hospitals in Greater Manchester. Patients with SARS-CoV-2 infection, recruited as close to admission as possible, provided peripheral blood samples at enrolment and sequentially thereafter. Fresh samples were assessed for immune cells and proteins in whole blood and serum. Some samples were also stimulated for 3 hours with LPS and analysed for intracellular proteins. Results were stratified based on patient-level data including severity of symptoms and date of reported symptom onset. Findings Longitudinal analysis showed a very high neutrophil to T cell ratio and abnormal activation of monocytes in the blood, which displayed high levels of the cell cycle marker, Ki67 and low COX-2. These properties all reverted in patient with good outcome. Unexpectedly, multiple aspects of inflammation were diminished as patients progressed in severity and time, even in ITU patients not recovering. Interpretation This is the first detailed longitudinal analysis of COVID-19 patients of varying severity and outcome, revealing common features and aspects that track with severity. Patients destined for a severe outcome can be identified at admission when still displaying mild-moderate symptoms. We provide clues concerning pathogenesis that should influence clinical trials and therapeutics. Targeting pathways involved in neutrophil and monocyte release from the bone marrow should be tested in patients with COVID-19. Funding: The Kennedy Trust for Rheumatology Research, The Wellcome Trust, The Royal Society, The BBSRC, National Institute for Health Research (NIHR) Biomedical Research Centres (BRC). url: https://doi.org/10.1101/2020.06.13.20127605 doi: 10.1101/2020.06.13.20127605 id: cord-033334-p7szd86k author: Mann, Jaclyn Kelly title: The potential of lactoferrin, ovotransferrin and lysozyme as antiviral and immune-modulating agents in COVID-19 date: 2020-10-08 words: 7284.0 sentences: 366.0 pages: flesch: 33.0 cache: ./cache/cord-033334-p7szd86k.txt txt: ./txt/cord-033334-p7szd86k.txt summary: Enhanced phagocytic activity as well as cytokine production of macrophages Enhanced intestinal immune responses: dendritic cell maturation, Th1/Th2 balance restored and humoral immunity promoted [77, 78] Peptides Anti-inflammatory Downregulates IL-6 and TNF-␣ and myeloperoxidase activity in peritonitis Binds to angiotensin II receptor type 1 to inhibit angiotensin II pro-inflammatory activity ACE inhibitory activity (antihypertensive) [79] [80] [81] [82] Intact Iron-binding activity* Sequestering free iron [83] Intact and peptides Antioxidant* Sequestering free iron Free radical scavenging [79, 84] Lysozyme Intact and peptides Antiviral Inhibits viral entry by binding to cell receptors or virus -cationic and hydrophobic nature is required rather than enzymatic activity Binds nucleic acids Inhibits virus-induced cell fusion Affects cell signaling, including NF-B pathway, to influence susceptibility to infection [85] [86] [87] [88] Intact and/or peptides Antibacterial Hydrolyzes cell wall of gram-positive bacteria (enzyme activity) Insert into and form pores in negatively charged bacterial membranes [40] † Specific anticoronavirus activity has been demonstrated: inhibits SARS-CoV cell entry by binding to HSPGs; inhibits entry and postentry steps of SARS-CoV-2 replication and elevates interferon-stimulated genes in SARS-CoV-2-infected cells. abstract: Coronavirus disease 2019 (COVID-19), caused by SARS coronavirus 2 (SARS-CoV-2), is spreading rapidly with no established effective treatments. While most cases are mild, others experience uncontrolled inflammatory responses with oxidative stress, dysregulation of iron and coagulation as features. Lactoferrin, ovotransferrin and lysozyme are abundant, safe antimicrobials that have wide antiviral as well as immunomodulatory properties. In particular, lactoferrin restores iron homeostasis and inhibits replication of SARS-CoV, which is closely related to SARS-CoV-2. Ovotransferrin has antiviral peptides and activities that are shared with lactoferrin. Both lactoferrin and lysozyme are ‘immune sensing’ as they may stimulate immune responses or resolve inflammation. Mechanisms by which these antimicrobials may treat or prevent COVID-19, as well as sources and forms of these, are reviewed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543043/ doi: 10.2217/fvl-2020-0170 id: cord-293732-rxd1lyi7 author: Manoj, M.G. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 words: 4180.0 sentences: 210.0 pages: flesch: 49.0 cache: ./cache/cord-293732-rxd1lyi7.txt txt: ./txt/cord-293732-rxd1lyi7.txt summary: Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. abstract: The emergence of a novel human corona virus disease (COVID-19) has been declared as a pandemic by the World Health Organization. One of the mechanisms of airborne transmission of the severe acute respiratory syndrome - corona virus (SARS-CoV-2) amid humans is through direct ejection of droplets via sneezing, coughing and vocalizing. Nevertheless, there are ample evidences of the persistence of infectious viruses on inanimate surfaces for several hours to a few days. Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. This mechanism partially explains the role of polluted air besides the exacerbation of chronic respiratory diseases in the rapid transmission of the virus amongst the public. Hence, it is stressed that more ambitious policies towards a cleaner environment are required globally to nip in the bud what could be the seeds of a fatal outbreak such as COVID-19. url: https://doi.org/10.1016/j.envres.2020.110001 doi: 10.1016/j.envres.2020.110001 id: cord-322388-c2nymio9 author: Manopo, Ivanus title: Evaluation of a safe and sensitive Spike protein-based immunofluorescence assay for the detection of antibody responses to SARS-CoV date: 2005-01-31 words: 3546.0 sentences: 185.0 pages: flesch: 52.0 cache: ./cache/cord-322388-c2nymio9.txt txt: ./txt/cord-322388-c2nymio9.txt summary: To study the diagnostic potential of our Spike protein-based immunoassay based on protein C expressed by recombinant baculovirus in Sf-9 cell, a panel of sera containing 21 SARS-positive samples collected 7-76 days after the onset of SARS symptom, 42 non-SARS serum samples, and 100 normal serum samples were subjected to our Spike protein-based IFA test. The immunoblot showed a 32-kDa band, indicating that protein C expressed in a baculovirus system is antigenic for antibody detection of SARS-CoV infection (represented by Fig. 1a) . Fig. 2 shows representative IFA results in the detection of positive serum samples using our Spike protein-based IFA, compared to the conventional IFA performed by SGH and the commercial SARS IFA kit (EUROIMMUN). In this study, we are the first to show that the immunogenic protein C-based IFA is a sensitive and specific method for detecting SARS-CoV infection. abstract: Abstract Previously, we have identified a truncated antigenic fragment named protein C [441 to 700 amino acids (a.a.)] as the immunodominant fragment of Spike (S) protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV). We have now successfully expressed protein C using the baculovirus system in S. frugiperda (Sf-9) cells. This recombinant baculovirus expressing protein C was first characterized using five SARS convalescent human sera and five normal human sera. The results showed that protein C is an authentic antigen against SARS-CoV antibody. Our Spike protein-based immunoflourescence assay (IFA) based on this recombinant baculovirus-Sf-9 system was further assessed with a panel of 163 clinical samples collected during the SARS epidemic in Singapore, which include samples from 21 clinically confirmed SARS, 42 non-SARS patient sera, and 100 normal sera. The results were compared to a commercial SARS IFA kit (EUROIMMUN, Germany) and a conventional IFA test performed in Singapore General Hospital. All of the 21 SARS-positive serum samples could be recognized by our IFA, giving a specificity and sensitivity of 100%, which was compatible with both whole virus-based IFA assays. No cross-reactivity with serum samples against infectious bronchitis virus (IBV) and transmissible gastroenteritis virus (TGEV) were detected in our assays. Thus, our Spike protein-based IFA could offer a safer procedure which can be performed in a BSL-2 laboratory as it could mimic the whole virus based-IFA without any loss of sensitivity and specificity. It is also more user-friendly and cost-effective than the whole virus-based IFA. url: https://www.ncbi.nlm.nih.gov/pubmed/15680149/ doi: 10.1016/j.jim.2004.10.012 id: cord-258548-1u7v1nlr author: Mansueto, Gelsomina title: Can COVID 2019 disease induces a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? date: 2020-06-26 words: 5924.0 sentences: 280.0 pages: flesch: 35.0 cache: ./cache/cord-258548-1u7v1nlr.txt txt: ./txt/cord-258548-1u7v1nlr.txt summary: Only one case of cardiac tamponade in a 47-year-old man SARS-CoV-2 infected without cardiovascular risk is reported in the literature as a complication of myocarditis and pericarditis (29) . Large and more recent studies have reported that previous myocardial infarction, diabetes, J o u r n a l P r e -p r o o f dyslipidaemias, hypertension, and other cardiovascular risk factors can predispose to an acute ischemic event in respiratory virus infections such as recently reported during the pandemic COVID-19 disease (34, 35, 36) . It is known that patients with cardiovascular disease have a higher risk of a thrombo-embolic event as it is known that all viral infections have a potential role in disseminated intravascular coagulation J o u r n a l P r e -p r o o f (DIC) The endothelial damage, the blood flow turbulence, and hypercoagulability are the basis of the mechanism. There is no substantial data to say that anti-RAAS, ACE inhibitors, statins increase the risk of cardiovascular damage in COVID patients. abstract: A novel coronavirus SARS-CoV-2 causes acute respiratory distress syndrome (ARDS) with cardiovascular and multiple organ failure till death. The main mechanisms of virus internalization and interaction with the host are down-regulation or upregulation of the ACE2 receptor, the surface glycoprotein competition mechanism for the binding of porphyrin to iron in heme formation as well as interference with the immune system. The interference on renin–angiotensin–aldosterone system (RAAS) activation, heme formation, and the immune response is responsible for infection diffusion, endothelial dysfunction, vasoconstriction, oxidative damage and releasing of inflammatory mediators. The main pathological findings are bilateral interstitial pneumonia with diffuse alveolar damage (DAD). Because ACE receptor is also present in the endothelium of other districts as well as in different cell types, and as porphyrins are transporters in the blood and other biological liquids of iron forming heme, which is important in the assembly of the hemoglobin, myoglobin and the cytochromes, multiorgan damage occurs both primitive and secondary to lung damage. More relevantly, myocarditis, acute myocardial infarction, thromboembolism, and disseminated intravasal coagulation (DIC) are described as complications in patients with poor outcome. Here, we investigated the role of SARSCoV-2 on the cardiovascular system and in patients with cardiovascular comorbidities, and possible drug interference on the heart. url: https://api.elsevier.com/content/article/pii/S0344033820314795 doi: 10.1016/j.prp.2020.153086 id: cord-318492-uu1p1rgi author: Mansueto, Gelsomina title: COVID-19: Brief Check Point Through The Pathologist''s Eye (autopsy archive) date: 2020-08-28 words: 1971.0 sentences: 100.0 pages: flesch: 41.0 cache: ./cache/cord-318492-uu1p1rgi.txt txt: ./txt/cord-318492-uu1p1rgi.txt summary: The autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (DAD), myocarditis, acute myocardial infarction (AMI), and disseminated intravascular coagulation (DIC); these aspects are not only in COVID-19 but also in other viral infections and associated sepsis. In this brief summary, I would like to induce the reader''s reflection to the fact that coronavirus appears already before the pandemic in many texts of medical doctrine and that the pathological findings related to lung and multi-organ damage are described similar to those induced by other viral pathogens both from the same or different family. The autopsy pathologists can confirm that many deaths are due to complications from viral infections especially in subjects with comorbidities and they can also confirm that the aspects often observed are diffuse alveolar damage (DAD), cardiac damage from myocarditis or acute myocardial infarction (AMI), or even disseminated intra-vascular coagulation (DIC); these findings are also present in sepsis associated with various viral infections. abstract: During the COVID-19 pandemic many deaths have been caused, especially of patients with cardiovascular comorbidities and old age. Many questions have been asked and few simple answers have been given. The autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (DAD), myocarditis, acute myocardial infarction (AMI), and disseminated intravascular coagulation (DIC); these aspects are not only in COVID-19 but also in other viral infections and associated sepsis. We must not lose sight of the fact that coronavirus with its pathological organ changes have already been described in the years preceding the pandemic. url: https://www.sciencedirect.com/science/article/pii/S0344033820320501?v=s5 doi: 10.1016/j.prp.2020.153195 id: cord-298075-lzuxlzb0 author: Mao, Kang title: Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology? date: 2020-03-23 words: 1095.0 sentences: 52.0 pages: flesch: 46.0 cache: ./cache/cord-298075-lzuxlzb0.txt txt: ./txt/cord-298075-lzuxlzb0.txt summary: However, an alternative method utilizing wastewater-based epidemiology (WBE), may provide an effective approach to predict the potential spread of the infection by testing for infectious agents in wastewater, which has been approved as an effective way to trace illicit drugs, and obtain information on health, disease, and pathogens. Therefore, it is critical to develop efficient transportable and robust analytical tools to accurately and quickly trace low-level SARS-CoV-2 sources through WBE to confirm these suspected cases and screen asymptomatic infected cases without centralized laboratories. We believe that in the case of asymptomatic infections in the community or people are not sure whether they are infected or not, rapid and real-time community sewage detection through paper analytical devices can determine whether there are SARS-CoV-2 carriers in the area in a timely manner to enable rapid screening, quarantine, and prevention. The potentially infected patient will also benefit from paper analytical device tracing SARS-CoV-2 sources with WBE, providing information for the correct and timely treatment of COVID-19. abstract: nan url: https://doi.org/10.1021/acs.est.0c01174 doi: 10.1021/acs.est.0c01174 id: cord-272423-o5yinjcz author: Mao, Xiao-Yuan title: iPSCs-Derived Platform: A Feasible Tool for Probing the Neurotropism of SARS-CoV-2 date: 2020-08-25 words: 1219.0 sentences: 76.0 pages: flesch: 46.0 cache: ./cache/cord-272423-o5yinjcz.txt txt: ./txt/cord-272423-o5yinjcz.txt summary: In a recent article, Yuen and colleagues present the first experimental evidence of SARS-CoV-2 infection in the human central nervous system using induced pluripotent stem cells (iPSCs)-derived platform including human neural progenitor cells, neurospheres, and three-dimensional brain organoids (Yuen, K.Y., and Huang, J.D. et al. Recently, Yuen and colleagues used induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and three-dimensional (3D) brain organoids for evaluation of SARS-CoV-2 infection in the brain. provided the first experimental evidence showing that SARS-CoV-2 could replicate in hNPCs and neurospheres and also the novel virus could productively infect cortical neurons and NPCs in 3D brain organoids ( Figure 1 ). In summary, the data provided by Yuen and colleagues offer useful experimental evidence supporting that SARS-CoV-2 can infect the human brain using an iPSCs-derived platform including hNPCs, neurospheres, and 3D human organoids. abstract: Coronavirus Disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a severe public health problem with a high rate of morbidity and mortality. A mounting number of clinical investigations illustrate that COVID-19 patients suffer from neurologic conditions in addition to respiratory symptoms. In a recent article, Yuen and colleagues present the first experimental evidence of SARS-CoV-2 infection in the human central nervous system using induced pluripotent stem cells (iPSCs)-derived platform including human neural progenitor cells, neurospheres, and three-dimensional brain organoids (Yuen, K.Y., and Huang, J.D. et al. (2020) Cell Res. DOI: 10.1038/s41422-020-0390-x). url: https://doi.org/10.1021/acschemneuro.0c00512 doi: 10.1021/acschemneuro.0c00512 id: cord-292650-i95upz10 author: Marafini, Irene title: LOW FREQUENCY OF COVID-19 IN INFLAMMATORY BOWEL DISEASES date: 2020-06-13 words: 1053.0 sentences: 56.0 pages: flesch: 53.0 cache: ./cache/cord-292650-i95upz10.txt txt: ./txt/cord-292650-i95upz10.txt summary: The risk of infection or death due to Covid-19 in patients with inflammatory bowel diseases (IBD) is unknown at this stage. We here examined the frequency of symptoms/signs suggestive of Covid-19 in IBD patients and assessed the risk of SARS-CoV-2 infection in IBD. Cumulative incidence of SARS-CoV-2 infection in IBD was calculated dividing the positive cases by the overall population of IBD patients enrolled for the study. Although, we need more robust epidemiological data to draw a conclusion regarding the incidence rate of Covid-19 in IBD, our findings suggest that IBD patients are not at increased risk of Covid-19 as compared with the general population. It is likely that the incidence of SARS-CoV-2 infection in our IBD population is underestimated as the majority of the patients did not underwent rhino-pharyngeal swab. published recently by Norsa and colleagues, who reported no case of SARS-CoV-2 infection in a cohort of IBD patients living in a high-risk area of Northern Italy (7). abstract: nan url: https://api.elsevier.com/content/article/pii/S1590865820302668 doi: 10.1016/j.dld.2020.06.007 id: cord-340085-ywg4rhnn author: Maras, J. S. title: Multi-Omics integration analysis of respiratory specimen characterizes baseline molecular determinants associated with COVID-19 diagnosis. date: 2020-07-07 words: 7383.0 sentences: 476.0 pages: flesch: 42.0 cache: ./cache/cord-340085-ywg4rhnn.txt txt: ./txt/cord-340085-ywg4rhnn.txt summary: Quantitative proteomics identified significant increase in 6 SARS-CoV-2 proteins along with ACE2 in the respiratory specimen of COVID-19 positive patients compared to negative patients (p<0.05, Figure 1C , H1N1 samples did not enrich any or associated proteins). /2020 Diagnostic accuracy: Amongst the identified DEP''s, mean decrease in the accuracy (calculated by random forest; 1000 trees) was highest for MX1 (MX Dynamin like GTPase 1) and WARS (Tryptophan--tRNA ligase) making them the most important proteins for segregating COVID-19 positive patients from negative or H1N1 patients ( Figure Together these findings showed that COVID-19 positive patients have virus mediated hyper immune activation involving monocytes and neutrophils, deregulated oxygen transport, increased fluid shear stress, bacterial invasion of the epithelial cells and glucose metabolism. Viral infection are also known for metabolic reprograming of host (Thaker et al., 2019) and proteome analysis of the respiratory specimen showed that there is significant increase in proteins associated to glucose metabolism suggesting that SARS-CoV-2 induces energy metabolism (Supplementary Figure 18 ). abstract: Abstract: Rapid diagnosis and precise prognostication of SARS-CoV-2 infection remains a major challenge. A multi-omic approach was adopted, and in the discovery phase, global proteome/metaproteome/metabolome were analysed in the respiratory specimens of SARS-CoV-2 positive [n=20], negative [n=20], and H1N1 positive [n=5] cases. We identified MX1 (MX Dynamin Like GTPase 1) and WARS (Tryptophan--tRNA ligase) as clues to viral diagnosis and validated in 200 SARS-CoV-2 suspects. MX1 >30pg/ml and WARS >25ng/ml segregated virus positives patients [(AUC=94%CI(0.91-0.97)]. Distinct increase in SARS-CoV-2 induced immune activation, metabolic reprograming and a decrease in oxygen transport, wound healing, fluid regulation, vitamin and steroid metabolism was seen (p<0.05). Multi-omics profiling correlated with viraemia and segregated asymptomatic COVID-19 patients. Additionally, the multiomics approach identified increased respiratory pathogens [Burkholderiales, Klebsiella pneumonia] and decreased lactobacillus salivarius (FDR<0.05, p<0.05) in COVID-19 specimens. Conclusion: Novel proteins [MX1 and WARS] can rapidly and reliably diagnose SARS-CoV-2 infection and identify asymptomatic and mild disease. url: https://doi.org/10.1101/2020.07.06.20147082 doi: 10.1101/2020.07.06.20147082 id: cord-352365-b9cmviny author: Marchetti, Monia title: COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure date: 2020-06-24 words: 3887.0 sentences: 176.0 pages: flesch: 29.0 cache: ./cache/cord-352365-b9cmviny.txt txt: ./txt/cord-352365-b9cmviny.txt summary: This review also highlights potential targets for prevention and therapy of COVID-19-related organ damage and discusses the role of marketed drugs, such as eculizumab and imatinib, as suitable candidates for clinical trials. Also, C3a complement fraction plays a relevant role in the pathogenesis of infection-related lung injury: high serum C3a predicts evolution to ARDS [9, 10] , while both C3a and C5a increase endothelial permeability and activate endothelial cells, thereby increasing the expression of adhesion molecules and cytokines [11, 12] , and the distal complement activation product C5 b-9 triggers intracellular fluxes of calcium in epithelial and endothelial cells. Apoptosis of human pulmonary microvascular endothelial cell may be chronically triggered by inflammation, such as in COPD, or acutely induced by ARDS; the latter is mediated by Bruton kinase (BTK), IL-17, and macrophage stimulating-1, while IL-35 seems protective [41] [42] [43] [44] . abstract: COVID-19 pandemia is a major health emergency causing hundreds of deaths worldwide. The high reported morbidity has been related to hypoxia and inflammation leading to endothelial dysfunction and aberrant coagulation in small and large vessels. This review addresses some of the pathways leading to endothelial derangement, such as complement, HIF-1α, and ABL tyrosine kinases. This review also highlights potential targets for prevention and therapy of COVID-19-related organ damage and discusses the role of marketed drugs, such as eculizumab and imatinib, as suitable candidates for clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32583086/ doi: 10.1007/s00277-020-04138-8 id: cord-330465-16j5vm7h author: Marciniec, Krzysztof title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 words: 6908.0 sentences: 396.0 pages: flesch: 48.0 cache: ./cache/cord-330465-16j5vm7h.txt txt: ./txt/cord-330465-16j5vm7h.txt summary: The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. In order to check the potential toxic properties of the compounds 3-5, docking study of phosphate betulin derivatives to cellular proteins was carried out. According to the results of docking (Table S1 ) obtained from AutoDock Vina, four potential SARS-CoV-2 inhibitors (BVM, betulinic acid, and compounds 4 and 6) were selected based on a lower negative dock energy value. abstract: Lupane-type pentacyclic triterpenes such as betulin and betulinic acid play an important role in the search for new therapies that would be effective in controlling viral infections. The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. Compound 3 inhibits viral replication at a level comparable to bevirimat and is also more selective (selectivity indices = 1250 and 967, respectively). Molecular docking was used to examine the probable interaction between the phosphate derivatives of 3-carboxyacylbetulin and C-terminal domain (CTD) of the HIV-1 capsid (CA)–spacer peptide 1 (SP1) fragment of Gag protein, designated as CTD-SP1. Compared with interactions between bevirimat (BVM) and the protein, an increased number of strong interactions between ligand 3 and the protein, generated by the phosphate group, were observed. These compounds might have the potential to also inhibit SARS-CoV2 proteins, in as far as the intrinsically imprecise docking scores suggest. url: https://www.ncbi.nlm.nih.gov/pubmed/32764519/ doi: 10.3390/biom10081148 id: cord-354972-nc496v6s author: Margolin, Emmanuel title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 words: 10919.0 sentences: 464.0 pages: flesch: 37.0 cache: ./cache/cord-354972-nc496v6s.txt txt: ./txt/cord-354972-nc496v6s.txt summary: As of 8 August 2020, there have been over 1.2 million confirmed cases of COVID-19 in Africa, with 29,833 deaths reported (Africa CDC) There is concern that the pandemic may pose an even greater risk to countries in Africa owing to their weak health-care infrastructure, large burden of co-infections, including HIV-1 and tuberculosis, and ongoing outbreaks of emerging and re-emerging infections such as Ebola virus (Democratic Republic of Congo) and Lassa haemorrhagic fever (Nigeria) that will divert much-needed resources away from the fight against COVID-19 (ref. Given the optimistic development timeline of 12-18 months before any vaccines could be available for widespread use, it is clear that these efforts will not Box 1 | Potential impact of climate on SArS-coV-2 dissemination the comparatively low incidence of coronavirus disease-2019 (COviD19) in africa has raised the possibility that climate could influence the spread of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2). abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic, prompting unprecedented efforts to contain the virus. Many developed countries have implemented widespread testing and have rapidly mobilized research programmes to develop vaccines and therapeutics. However, these approaches may be impractical in Africa, where the infrastructure for testing is poorly developed and owing to the limited manufacturing capacity to produce pharmaceuticals. Furthermore, a large burden of HIV-1 and tuberculosis in Africa could exacerbate the severity of infection and may affect vaccine immunogenicity. This Review discusses global efforts to develop diagnostics, therapeutics and vaccines, with these considerations in mind. We also highlight vaccine and diagnostic production platforms that are being developed in Africa and that could be translated into clinical development through appropriate partnerships for manufacture. url: https://www.ncbi.nlm.nih.gov/pubmed/32913297/ doi: 10.1038/s41579-020-00441-3 id: cord-353551-un4jw7aw author: Margoni, Monica title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic date: 2020-10-12 words: 836.0 sentences: 49.0 pages: flesch: 56.0 cache: ./cache/cord-353551-un4jw7aw.txt txt: ./txt/cord-353551-un4jw7aw.txt summary: title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic The authors, considering the impact of MS on brain atrophy and the high risk POMS have to develop cognitive impairment and evolve in the secondary progressive disease phase, recommend to keep in mind that MS in children/teens is a severe, highly active form of disease, and suggest the early use of highly effective second-line disease modifying drugs rather than the first-line injectable ones. May these drugs expose POMS to a greater risk of SARS-Cov-2 infection as well as to a symptomatic and potentially more severe COVID-19 or to longterm autoimmune severe adverse events? NTZ treatment does not seem not to expose POMS to a higher risk of SARS-Cov-2 infection. No evidence of disease activity including cognition (NEDA-3 plus) in naive pediatric multiple sclerosis patients treated with natalizumab Disease Modifying Therapies and COVID-19 Severity in Multiple Sclerosis abstract: nan url: https://doi.org/10.1177/2055217320966346 doi: 10.1177/2055217320966346 id: cord-353576-f29kmtot author: Maricic, T. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 words: 3499.0 sentences: 200.0 pages: flesch: 60.0 cache: ./cache/cord-353576-f29kmtot.txt txt: ./txt/cord-353576-f29kmtot.txt summary: We then tested 1 l of mouthwash from each of the 20 individuals using two RT-qPCR kits advertised to allow direct detection of SARS-CoV-2 from nasopharyngeal swabs: Luna Universal Probe (NEB, Ipswich, USA) and PrimeDirect (Takara, Kyoto, Japan) as well as another kit, SuperScript III with Platinum Taq (Invitrogen, Waltham, USA). To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations. In the first scheme, the samples were tested individually using the direct RT-qPCR protocol and the results were evaluated and reported back to the facility by 7 p.m. To detect any inhibition that the mouthwash samples may introduce into the RT-qPCR reactions, we added a synthesized control RNA that was quantified in parallel with SARS-CoV-2 by a probe . abstract: SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARS-CoV-2 in single or pooled gargle lavages ('mouthwashes'). With this approach, we test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches could be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics. url: https://doi.org/10.1101/2020.06.24.20139501 doi: 10.1101/2020.06.24.20139501 id: cord-324265-j3v3i8vm author: Marietta, Marco title: COVID-19, coagulopathy and venous thromboembolism: more questions than answers date: 2020-07-11 words: 5031.0 sentences: 242.0 pages: flesch: 37.0 cache: ./cache/cord-324265-j3v3i8vm.txt txt: ./txt/cord-324265-j3v3i8vm.txt summary: The severity of the derangement of coagulation parameters in COVID-19 patients has been associated with a poor prognosis, and the use of low molecular weight heparin (LMWH) at doses registered for prevention of venous thromboembolism (VTE) has been endorsed by the World Health Organization and by Several Scientific societies. In these patients, low molecular weight heparin (LMWH) or unfractionated heparin (UFH) at doses registered for prevention of venous thromboembolism (VTE) seemed to be associated with a lower risk of death [10] and is currently recommended by the World Health Organization [11] and by several scientific societies [12] [13] [14] [15] [16] [17] [18] (Table 1) . abstract: The acute respiratory illnesses caused by severe acquired respiratory syndrome corona Virus-2 (SARS-CoV-2) is a global health emergency, involving more than 8.6 million people worldwide with more than 450,000 deaths. Among the clinical manifestations of COVID-19, the disease that results from SARS-CoV-2 infection in humans, a prominent feature is a pro-thrombotic derangement of the hemostatic system, possibly representing a peculiar clinicopathologic manifestation of viral sepsis. The severity of the derangement of coagulation parameters in COVID-19 patients has been associated with a poor prognosis, and the use of low molecular weight heparin (LMWH) at doses registered for prevention of venous thromboembolism (VTE) has been endorsed by the World Health Organization and by Several Scientific societies. However, some relevant issues on the relationships between COVID-19, coagulopathy and VTE have yet to be fully elucidated. This review is particularly focused on four clinical questions: What is the incidence of VTE in COVID-19 patients? How do we frame the COVID-19 associated coagulopathy? Which role, if any, do antiphospolipid antibodies have? How do we tackle COVID-19 coagulopathy? In the complex scenario of an overwhelming pandemic, most everyday clinical decisions have to be taken without delay, although not yet supported by a sound scientific evidence. This review discusses the most recent findings of basic and clinical research about the COVID-associated coagulopathy, to foster a more thorough knowledge of the mechanisms underlying this compelling disease. url: https://doi.org/10.1007/s11739-020-02432-x doi: 10.1007/s11739-020-02432-x id: cord-326833-boxgt4kb author: Marimuthu, Janakiram title: HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date: 2020-07-07 words: 1364.0 sentences: 103.0 pages: flesch: 65.0 cache: ./cache/cord-326833-boxgt4kb.txt txt: ./txt/cord-326833-boxgt4kb.txt summary: We conducted a retrospective, record based case series including three males, 2 females and 1 transgender PLHA co‐infected with SARS CoV‐2 in the Indian state of Tamil Nadu. Through literature search in PubMed and World Health organization'' (WHO) database on COVID-19, we obtained 5 case reports, and 5 case series on PLHA infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). Hence, we conducted a retrospective, record based case series on the PLHA who were infected with SARS CoV-2, in the Indian state of Tamil Nadu. 5 Our study reports that the clinical features of COVID-19 co-infection among PLHA in South India is mild, and the clinical outcomes are favorable. Further studies including greater number of patients should be done, to better understand the epidemiology, clinical outcomes and appropriate treatment modalities in the HIV-COVID 19 co-infection. COVID-19 in patients with HIV: clinical case series abstract: HIV prevalence in India is about 0.22%, with the total number of people living with HIV/AIDS (PLHA) is estimated at 21.40 lakhs, constituting third largest epidemic in world. However, no study on HIV‐COVID‐19 co‐infection has been reported from India. We conducted a retrospective, record based case series including three males, 2 females and 1 transgender PLHA co‐infected with SARS CoV‐2 in the Indian state of Tamil Nadu. Fever (5), followed by cough (2) and sore throat (1), were the presenting symptoms. Latest Median CD4 count among our patients was 535 cells/ mm3. One of the patients was not under clinical HIV control, with an opportunistic infection Two among our patients were having hypertension. The mainstay of treatment given for the patients consisted of multi‐vitamins in addition to the ARV drugs, anti‐pyretics and anti‐tussives. One of the patient was on low dose Ritonavir boosted HAART regimen. All patients had stable vitals at room conditions, did not have any complications during their entire stay in health care facility for COVID‐19, treated and discharged. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32633846/ doi: 10.1002/jmv.26271 id: cord-315696-43wmazxa author: Marinaki, Smaragdi title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients’ Lives and Allografts date: 2020-09-16 words: 6015.0 sentences: 368.0 pages: flesch: 46.0 cache: ./cache/cord-315696-43wmazxa.txt txt: ./txt/cord-315696-43wmazxa.txt summary: title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients'' Lives and Allografts Kidney transplant (KTx) recipients have been recently classified by the Center for Disease Control and Prevention (CDC) as a high-risk group for severe COVID-19 [2] . All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. A Case Report of Oligosymptomatic Kidney Transplant Patients with COVID-19: Do They Pose a Risk to Other Recipients? abstract: The coronavirus disease 2019 (COVID-19) pandemic has posed a significant challenge to physicians and healthcare systems worldwide. Evidence about kidney transplant (KTx) recipients is still limited. A systematic literature review was performed. We included 63 articles published from 1 January until 7 July 2020, reporting on 420 adult KTx recipients with confirmed COVID-19. The mean age of patients was 55 ± 15 years. There was a male predominance (67%). The majority (74%) were deceased donor recipients, and 23% were recently transplanted (<1 year). Most patients (88%) had at least one comorbidity, 29% had two, and 18% three. Ninety-three percent of cases were hospitalized. Among them, 30% were admitted to the intensive care unit, 45% developed acute respiratory distress syndrome, and 44% had acute kidney injury with 23% needing renal replacement therapy. From the hospitalized patients a total of 22% died, 59% were discharged, and 19% were still in hospital at the time of publication. Immunosuppression was reduced in 27%, discontinued in 31%, and remained unchanged in 5%. Hydroxychloroquine was administered to 78% of patients, antibiotics to 73%, and antivirals to 30% while 25% received corticosteroid boluses, 28% received anti-interleukin agents, and 8% were given immunoglobulin. The main finding of our analysis was that the incidence of COVID-19 among kidney transplant patients is not particularly high, but when they do get infected, this is related to significant morbidity and mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/32947798/ doi: 10.3390/jcm9092986 id: cord-254079-pvl44u4d author: Marinella, Mark A. title: COVID-19 pandemic and the stethoscope: don''t forget to sanitize date: 2020-04-11 words: 739.0 sentences: 46.0 pages: flesch: 45.0 cache: ./cache/cord-254079-pvl44u4d.txt txt: ./txt/cord-254079-pvl44u4d.txt summary: Indirect pathogen transmission from inanimate objects is of potential concern not only for the general public, but also for healthcare professionals whose hands come into frequent contact with hard surfaces. Viral pathogens have also been isolated on hard surfaces in the healthcare setting, 3,4 but have not received as much attention as a risk for nosocomial and person-to-person transmission until very recently with the COVID-19 pandemic. 4 The severe fever with thrombocytopenia syndrome (SFTS) virus, an emerging fatal viral hemorrhagic fever in East Asia, has been recovered from stethoscopes and other hard surfaces in patient rooms who were diagnosed with SFTS, also raising concern for nosocomial transmission of highly pathogenic viruses. Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32402598/ doi: 10.1016/j.hrtlng.2020.03.017 id: cord-275336-lnhkux0m author: Marino Gammazza, Antonella title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 date: 2020-08-04 words: 1935.0 sentences: 104.0 pages: flesch: 41.0 cache: ./cache/cord-275336-lnhkux0m.txt txt: ./txt/cord-275336-lnhkux0m.txt summary: title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the cause of COVID-19 disease, has the potential to elicit autoimmunity because mimicry of human molecular chaperones by viral proteins. We compared viral proteins with human molecular chaperones, many of which are heat shock proteins, to determine if they share amino acid-sequence segments with immunogenic-antigenic potential, which can elicit cross-reactive antibodies and effector immune cells with the capacity to damage-destroy human cells by a mechanism of autoimmunity. We identified the chaperones that can putatively participate in molecular mimicry phenomena after SARS-CoV-2 infection, focusing on those for which endothelial cell plasma-cell membrane localization has already been demonstrated. We compared the amino acid sequences of all the SARS-CoV-2 proteins with the sequences of human chaperones to determine if they share segments with immunogenic-antigenic potential that might be causing autoimmunity. abstract: Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the cause of COVID-19 disease, has the potential to elicit autoimmunity because mimicry of human molecular chaperones by viral proteins. We compared viral proteins with human molecular chaperones, many of which are heat shock proteins, to determine if they share amino acid-sequence segments with immunogenic-antigenic potential, which can elicit cross-reactive antibodies and effector immune cells with the capacity to damage-destroy human cells by a mechanism of autoimmunity. We identified the chaperones that can putatively participate in molecular mimicry phenomena after SARS-CoV-2 infection, focusing on those for which endothelial cell plasma-cell membrane localization has already been demonstrated. We also postulate that post-translational modifications, induced by physical (shear) and chemical (metabolic) stress caused respectively by the risk factors hypertension and diabetes, might have a role in determining plasma-cell membrane localization and, in turn, autoimmune-induced endothelial damage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12192-020-01148-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12192-020-01148-3 doi: 10.1007/s12192-020-01148-3 id: cord-289076-8iymevqm author: Marjanovic, Zdravko title: The relevance of psychosocial variables and working conditions in predicting nurses’ coping strategies during the SARS crisis: An online questionnaire survey date: 2007-08-31 words: 4581.0 sentences: 210.0 pages: flesch: 42.0 cache: ./cache/cord-289076-8iymevqm.txt txt: ./txt/cord-289076-8iymevqm.txt summary: Three multiple regression analysis revealed that the model we evolved—including higher levels of vigor, organizational support, and trust in equipment/infection control initiative; and lower levels of contact with SARS patients, and time spent in quarantine—predicted to lower levels of avoidance behavior, emotional exhaustion, and state anger. We hypothesized that greater vigor, organizational support, and trust in equipment/infection control, and less contact with SARS patients and time spent in quarantine, would predict to lower levels of emotional exhaustion, state anger, and avoidance behavior. The five independent measures (predictors) were three psychosocial variables, vigor, organizational support, and trust in equipment/ infection control initiatives; and two working conditions variables, contact with SARS patients, and time spent in quarantine. State anger was positively correlated to avoidance behavior, contact with SARS patients, and greater time in quarantine; and negatively related to vigor, organizational support, and trust in equipment/ infection control initiatives. abstract: Abstract Objectives The purpose of this investigation was to examine the relationship between psychosocial variables and working conditions, and nurses’ coping methods and distress in response to the severe acute respiratory syndrome (SARS) crisis in Canada. Participants and procedure The sample consisted of 333 nurses (315 women, 18 men) who completed an Internet-mediated questionnaire that was posted on the Registered Nurses’ Association of Ontario (RNAO) website between March and May 2004. The questionnaire was restricted to respondents who had to authenticate their RNAO membership with a valid username and password before accessing the questionnaire. This served a dual purpose: to ensure that only RNAO nurses completed the questionnaire and thereby safeguarding the generalizability of the findings; and second, to prevent any one nurse from contributing more than once to the overall sample. Results Correlational analysis yielded several significant relationships between psychosocial variables and working conditions, and the traditional correlates of burnout and stress. Three multiple regression analysis revealed that the model we evolved—including higher levels of vigor, organizational support, and trust in equipment/infection control initiative; and lower levels of contact with SARS patients, and time spent in quarantine—predicted to lower levels of avoidance behavior, emotional exhaustion, and state anger. Conclusions By employing models of stress and burnout that combine psychosocial variables and working conditions, researchers can account for significant amounts of variance in outcomes related to burnout. These findings highlight the importance of vigor and perceived organizational support in predicting nurses’ symptoms of burnout. For healthcare administrators, this means that a likely strategy for assuaging the negative outcomes of stress should address nurses’ psychosocial concerns and the working conditions that they face during novel times of crisis. url: https://api.elsevier.com/content/article/pii/S0020748906000745 doi: 10.1016/j.ijnurstu.2006.02.012 id: cord-255170-bp3irxlh author: Mark, John title: SARS coronavirus: Unusual lability of the nucleocapsid protein date: 2008-12-12 words: 5274.0 sentences: 355.0 pages: flesch: 95.0 cache: ./cache/cord-255170-bp3irxlh.txt txt: ./txt/cord-255170-bp3irxlh.txt summary: The exper i ments used prep a ra tions of recombinant N-pro tein from which the His-tag had not been enzy mat i cally removed; thus, cal cu la tion of the resul tant pro tein/ pep tide masses must take into con sid er ation the pres ence of the His-tag (an addi tional 11 amino acid sequence). A spe cific pro te ol y sis assay was then devel oped using pep tides con tain ing the SR-rich region cor re spond ing to the SARS N-pro tein cleav age site. Taken together, the results from the FITC-labelled casein, the refold ing, and the FRET (EDANS/DAB CYL) detec tion exper i ments strongly sug gest that the SR-spe cific cleav age of N-pro tein is not the result of a con tam i nat ing pro te ase activ ity. Cell type-spe cific cleav age of nucle o cap sid pro tein by effec tor casp as es dur ing SARS coro na vi rus infec tion abstract: Abstract The severe acute respiratory syndrome (SARS) is a contagious disease that killed hundreds and sickened thousands of people worldwide between November 2002 and July 2003. The nucleocapsid (N) protein of the coronavirus responsible for this disease plays a critical role in viral assembly and maturation and is of particular interest because of its potential as an antiviral target or vaccine candidate. Refolding of SARS N-protein during production and purification showed the presence of two additional protein bands by SDS–PAGE. Mass spectroscopy (MALDI, SELDI, and LC/MS) confirmed that the bands are proteolytic products of N-protein and the cleavage sites are four SR motifs in the serine–arginine-rich region—sites not suggestive of any known protease. Furthermore, results of subsequent testing for contaminating protease(s) were negative: cleavage appears to be due to inherent instability and/or autolysis. The importance of N-protein proteolysis to viral life cycle and thus to possible treatment directions are discussed. url: https://doi.org/10.1016/j.bbrc.2008.09.153 doi: 10.1016/j.bbrc.2008.09.153 id: cord-320663-xypg6evo author: Market, Marisa title: Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies date: 2020-06-23 words: 14038.0 sentences: 659.0 pages: flesch: 42.0 cache: ./cache/cord-320663-xypg6evo.txt txt: ./txt/cord-320663-xypg6evo.txt summary: A common feature of coronavirus infections is that significant morbidity and mortality is associated with lung injury and acute respiratory distress syndrome resulting from an exaggerated immune response, of which NK cells are an important component. Natural Killer (NK) cells are a key component of the innate immune system and are critical in the response to many viral infections in humans and animal models (1) (2) (3) . Altogether these studies show that during acute CoV infection, inflammatory monocyte-macrophages and neutrophils accumulate in the lungs and produce cytokines and chemokines that induce the activation and migration of lymphocytes, including NK cells, to the lungs, where they could be one of the main producers of IFN-γ (148). Studies have reported that patients infected with SARS-CoV-2 have lower levels of circulating NK cells and these express a greater level of inhibitory receptors (e.g., NKG2A) while producing less IFN-γ (127, 129, 130) . abstract: Natural Killer (NK) cells are innate immune responders critical for viral clearance and immunomodulation. Despite their vital role in viral infection, the contribution of NK cells in fighting SARS-CoV-2 has not yet been directly investigated. Insights into pathophysiology and therapeutic opportunities can therefore be inferred from studies assessing NK cell phenotype and function during SARS, MERS, and COVID-19. These studies suggest a reduction in circulating NK cell numbers and/or an exhausted phenotype following infection and hint toward the dampening of NK cell responses by coronaviruses. Reduced circulating NK cell levels and exhaustion may be directly responsible for the progression and severity of COVID-19. Conversely, in light of data linking inflammation with coronavirus disease severity, it is necessary to examine NK cell potential in mediating immunopathology. A common feature of coronavirus infections is that significant morbidity and mortality is associated with lung injury and acute respiratory distress syndrome resulting from an exaggerated immune response, of which NK cells are an important component. In this review, we summarize the current understanding of how NK cells respond in both early and late coronavirus infections, and the implication for ongoing COVID-19 clinical trials. Using this immunological lens, we outline recommendations for therapeutic strategies against COVID-19 in clearing the virus while preventing the harm of immunopathological responses. url: https://doi.org/10.3389/fimmu.2020.01512 doi: 10.3389/fimmu.2020.01512 id: cord-310753-sv88b0dt author: Marks, M. title: Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study date: 2020-10-27 words: 3585.0 sentences: 210.0 pages: flesch: 56.0 cache: ./cache/cord-310753-sv88b0dt.txt txt: ./txt/cord-310753-sv88b0dt.txt summary: By the time of performing this search, various 57 authors had reported on retrospective analyses of clusters of index cases and their corresponding contacts, 58 as well as series of patients who developed symptomatic Covid-19 disease after PCR positive result. The objective of this study was to evaluate transmission dynamics of SARS-CoV-2 in the context of a trial 109 of post-exposure prophylaxis and evaluate the influence of baseline variables-including viral load of the 110 index cases and exposed contacts-to transmission, development of symptomatic disease, and the 111 incubation period. Also, after excluding 215 contacts who were PCR positive at the first study visit, we found no association between the viral load of 216 the index case and the time to onset of incident SARS-CoV-2 infection (HR 1.01 95% CI 0.83-1.23). abstract: Background There remains limited data on what variables affect the risk of transmission of SARS-CoV-2 and developing symptomatic Covid-19 and in particular the relationship to viral load (VL). Methods We analysed data collected in a trial of hydroxychloroquine post-exposure prophylaxis. Covid-19 cases and their contacts were identified through the local epidemiological surveillance system. VL, estimated by quantitative PCR, was assessed at enrollment, at day 14, and whenever the participant reported Covid-19-like symptoms. Risk of transmission, risk of developing symptomatic disease and incubation dynamics were evaluated using random-effects regression analysis. Findings We identified 314 cases, 282 of which had at least one contact (753 contacts in total). Ninety (33%) of 282 clusters had at least one transmission event. The secondary attack rate was 16% (125/753), with a variation from 12% to 24% for VL of the index case of <106, and >109 copies/mL, respectively (OR per log10 increase in VL 1.3 95%CI 1.1 to 1.6). Increased risk of transmission was also associated with household contact (OR 2.7; 1.4 to 5.06) and age of the contact (OR 1.02; 1.01 to 1.04). The proportion of PCR positive contacts who developed symptomatic Covid-19 was 40.3% (181/449), with a variation from 25% to 60% for VL of the contact <107, and >109 copies/mL (HR log10 increase in VL 1.12; 95% CI 1.05 to 1.2). Time to onset of symptomatic disease decreased from a median of 7 days (IQR 5 to 10) for individuals with an initial viral load <107 to 6 days (4 to 8) and 5 days (3 to 8) for individuals with an initial viral load of 107 to 109 and >109, respectively. Interpretation We show that the viral load of the index case is a leading driver of SARS-CoV-2 transmission. The risk of symptomatic Covid-19 is strongly associated with viral load of the contact at baseline, which shortens the incubation time in a dose-dependent manner. url: http://medrxiv.org/cgi/content/short/2020.10.27.20220277v1?rss=1 doi: 10.1101/2020.10.27.20220277 id: cord-263970-9w6ciglv author: Marquez-Miranda, Valeria title: Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date: 2020-10-22 words: 2882.0 sentences: 166.0 pages: flesch: 53.0 cache: ./cache/cord-263970-9w6ciglv.txt txt: ./txt/cord-263970-9w6ciglv.txt summary: SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. Here we used this dimeric structure to perform full atom molecular dynamic simulations and electrostatic potential calculations to ask questions concerning the dimers'' stability and whether ions could be populating specific regions of the channel. To assess the impact of the ion occupancies described above, we obtained the electrostatic potential maps for the ORF3a channel for the initial configuration, and the last frame, at the end of a trajectory of 500 ns of the molecular dynamics simulations, by employing the Poison-Boltzmann approach implemented in the APBS package [12] . This analysis shows that the entry of Cl-ions through the inter-subunit tunnel into the central polar cavity and the accumulation of K+ ions at the cytosolic domain''s surface changed the channel''s electrostatic profile. abstract: SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. ORF3a assemblies as homotetramers, which are stabilized by residue C133. A recent cryoEM structure of a homodimeric complex of ORF3a has been released. A lower-resolution cryoEM map of the tetramer suggests two dimers form it, arranged side by side. The dimer’s cryoEM structure revealed that each protomer contains three transmembrane helices arranged in a clockwise configuration forming a six helices transmembrane domain. This domain’s potential permeation pathway has six constrictions narrowing to about 1 Å in radius, suggesting the structure solved is in a closed or inactivated state. At the cytosol end, the permeation pathway encounters a large and polar cavity formed by multiple beta strands from both protomers, which opens to the cytosolic milieu. We modeled the tetramer following the arrangement suggested by the low-resolution tetramer cryoEM map. Molecular dynamics simulations of the tetramer embedded in a membrane and solvated with 0.5 M of KCl were performed. Our simulations show the cytosolic cavity is quickly populated by both K+ and Cl-, yet with different dynamics. K+ ions moved relatively free inside the cavity without forming proper coordination sites. In contrast, Cl- ions enter the cavity, and three of them can become stably coordinated near the intracellular entrance of the potential permeation pathway by an inter-subunit network of positively charged amino acids. Consequently, the central cavity’s electrostatic potential changed from being entirely positive at the beginning of the simulation to more electronegative at the end. url: https://www.ncbi.nlm.nih.gov/pubmed/33106803/ doi: 10.1101/2020.10.22.349522 id: cord-273913-xem3alih author: Marraha, Farah title: A Review of the Dermatological Manifestations of Coronavirus Disease 2019 (COVID-19) date: 2020-08-11 words: 4225.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-273913-xem3alih.txt txt: ./txt/cord-273913-xem3alih.txt summary: In this review, we discuss these various cutaneous manifestations and skin problems related to personal protective equipment, as well as different cutaneous anti-COVID-19 drug-associated reactions. e first case infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was reported in Wuhan, China, in late November 2019. ese skin lesions can guide clinicians for diagnosis if the patients present other COVID-19 symptoms; however, viral infection cannot be the only cause; mediated inflammatory responses and drug reactions can also be suspected. e aim of our literature review is to report the various cutaneous manifestations described to date associated with COVID-19, the skin problems related to personal protective equipment, and the different cutaneous anti-COVID-19 drug reactions [6, 7] . e frequency of the skin lesions associated with COVID-19 infection varies according to the series; in a Chinese study of 1099 positive cases, the incidence was only 0.2%, while in an Italian series of 88 patients it was 20.4% [42] . abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has affected 210 countries and territories around the world. The virus has spread rapidly, and the disease is still extending up to now. The pathophysiology for SARS-CoV-2 has not been well elucidated, and diverse hypotheses to date have been proposed. Initially, no skin manifestations were observed among patients with COVID-19, but recently a few cases have been described. In this review, we discuss these various cutaneous manifestations and skin problems related to personal protective equipment, as well as different cutaneous anti-COVID-19 drug-associated reactions. We also focus on the currently proposed managements of these rare manifestations. url: https://doi.org/10.1155/2020/9360476 doi: 10.1155/2020/9360476 id: cord-252761-ro5tj0tx author: Marriott, Deborah title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date: 2020-08-25 words: 1228.0 sentences: 92.0 pages: flesch: 60.0 cache: ./cache/cord-252761-ro5tj0tx.txt txt: ./txt/cord-252761-ro5tj0tx.txt summary: title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent''s Hospital and associated screening clinics, Sydney, NSW. Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. We report the prevalence of SARS-CoV-2 and other respiratory pathogens including co-infection, and evaluate the A c c e p t e d M a n u s c r i p t 4 temporal pattern of respiratory infections alongside the introduction, and subsequent relaxation, of physical distancing measures. Limited data have been reported on co-infection between SARS-CoV-2 and other respiratory viruses. In conclusion, the introduction of multiple public health measures to minimise SARS-CoV-2 transmission in Australia from mid to late-March 2020 had a major impact on the prevalence of all respiratory viral infections highlighting the effectiveness of this approach. abstract: Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of COVID-19 resurgence url: https://doi.org/10.1093/cid/ciaa1256 doi: 10.1093/cid/ciaa1256 id: cord-335122-8s3bcyo8 author: Marshall, Steve title: COVID-19: What do we know? date: 2020-09-21 words: 5249.0 sentences: 375.0 pages: flesch: 41.0 cache: ./cache/cord-335122-8s3bcyo8.txt txt: ./txt/cord-335122-8s3bcyo8.txt summary: 44, 45, [47] [48] [49] The amount of viable SARS-CoV-2 in droplet nuclei remains unclear, but in subjects infected with other respiratory viruses, such as influenza, experiments comparing coughing and breathing suggest an equivalent production of viral RNA and replication-competent virus, detected at close range (< 12 inches). 78 In situations where healthcare workers wearing personal protective equipment (PPE) attend to patients with COVID-19 and do not perform medical AGPs, direct airborne transmission of replicationcompetent SARS-CoV-2 has not been confirmed. 79 The results of hospital studies evaluating aerosolization of body fluids and respiratory droplets of SARS-CoV-1 infected patients generated during certain medical AGPs (tracheal intubation, non-invasive ventilation, bronchoscopy, etc.), suggest that airborne transmission of SARS-CoV-2 may be possible during these procedures. Currently there are no studies reporting airborne viable (replication-competent) SARS-CoV-2 virus J o u r n a l P r e -p r o o f in hospital settings where infected patients are cared for, but not subjected to medical AGPs, by healthcare workers wearing surgical masks. abstract: Evidence regarding provision of orthodontic care during COVID-19 pandemic is examined. url: https://www.sciencedirect.com/science/article/pii/S0889540620305758?v=s5 doi: 10.1016/j.ajodo.2020.08.010 id: cord-266536-4frv2vb7 author: Martel, Jan title: Could nitric oxide help to prevent or treat COVID-19? date: 2020-05-06 words: 2067.0 sentences: 110.0 pages: flesch: 44.0 cache: ./cache/cord-266536-4frv2vb7.txt txt: ./txt/cord-266536-4frv2vb7.txt summary: In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. During the 2002-2003 severe acute respiratory syndrome (SARS) epidemic, also caused by a coronavirus, inhaled NO was tested in six SARS patients, producing beneficial effects that include decreased pulmonary hypertension, improved arterial oxygenation, and reduced spread and density of lung infiltrates [5] . In addition, limiting the lifestyle factors that reduce endogenous NO levels in the airways-such as mouth breathing and smoking-may also help to reduce SARS-CoV-2 viral load and symptoms of COVID-19 pneumonia by promoting more efficient antiviral defense mechanisms in the respiratory tract. abstract: The nasal cavity and turbinates play important physiological functions by filtering, warming and humidifying inhaled air. Paranasal sinuses continually produce nitric oxide (NO), a reactive oxygen species that diffuses to the bronchi and lungs to produce bronchodilatory and vasodilatory effects. Studies indicate that NO may also help to reduce respiratory tract infection by inactivating viruses and inhibiting their replication in epithelial cells cultured in vitro. In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. We discuss here additional lifestyle factors such as mouth breathing which may affect the antiviral response against SARS-CoV-2 by bypassing the filtering effect of the nose and by decreasing NO levels in the airways. Simple devices that promote nasal breathing during sleep may help prevent the common cold, suggesting potential benefits against coronavirus infection. In the absence of effective treatments against COVID-19, the alternative strategies proposed here should be considered and studied in more detail. url: https://doi.org/10.1016/j.micinf.2020.05.002 doi: 10.1016/j.micinf.2020.05.002 id: cord-270645-tzctvs9q author: Martelletti, Luigi title: Air Pollution and the Novel Covid-19 Disease: a Putative Disease Risk Factor date: 2020-04-15 words: 946.0 sentences: 58.0 pages: flesch: 50.0 cache: ./cache/cord-270645-tzctvs9q.txt txt: ./txt/cord-270645-tzctvs9q.txt summary: This study analyzed the correlation between the increment of the API (Air Pollution Index) and the rate of fatality due to SARS across 5 regions in China. In 2017, Ciencewicki and Jaspers conducted an epidemiological analysis regarding air pollution and respiratory viral infections which noted positive correlation between the high level of particulate matter (PM) in some urban areas and mortality due to cardiovascular and respiratory conditions. A recent study from the SIMA (Società Italiana di Medicina Ambientale) reported that the specificity of the high spread of the contagious virus in some areas of Northern Italy is likely to be linked to air pollution conditions. The above studies show that air pollutants, such as particulate matter, nitrogen dioxide, and carbon monoxide, are most likely direct to facilitate the longevity of virus particles in favorable climate conditions. Air pollution and case fatality of SARS in the People''s Republic of China: an ecologic study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32296757/ doi: 10.1007/s42399-020-00274-4 id: cord-299810-e57pwgnx author: Martelloni, Gabriele title: Modelling the downhill of the Sars-Cov-2 in Italy and a universal forecast of the epidemic in the world date: 2020-07-01 words: 3022.0 sentences: 180.0 pages: flesch: 62.0 cache: ./cache/cord-299810-e57pwgnx.txt txt: ./txt/cord-299810-e57pwgnx.txt summary: Finally we study the behavior of the ratio infected over swabs for Italy, Germany and USA, and we show as studying this parameter we recover the generalized Logistic model used in [1] for these three countries. The parameters r 0 represents the rates of growth of epidemic, K is the carrying capacity for the classical logistic model, α is a constant in order to have a power low initial growth before LD, β is the exponent of the second term of equation 1 that represents the influence of asymptomatic; δ,a correction of the quadratic term of logistic, and γ are the constant parameters considering the influence of the government measures 1 , K f is a proportionality constant between deaths and total number of infected, while t d and t r are the delays of deaths and recoveries respect to infected respectively; the constant A represents the contribution of asymptomatic people as introduced in [1] and finally t 0 is the time of LD start. abstract: In a previous article [1] we have described the temporal evolution of the Sars-Cov-2 in Italy in the time window February 24-April 1. As we can see in [1] a generalized logistic equation captures both the peaks of the total infected and the deaths. In this article our goal is to study the missing peak, i.e. the currently infected one (or total currently positive). After the April 7 the large increase in the number of swabs meant that the logistical behavior of the infected curve no longer worked. So we decided to generalize the model, introducing new parameters. Moreover, we adopt a similar approach used in [1] (for the estimation of deaths) in order to evaluate the recoveries. In this way, introducing a simple conservation law, we define a model with 4 populations: total infected, currently positives, recoveries and deaths. Therefore, we propose an alternative method to a classical SIRD model for the evaluation of the Sars-Cov-2 epidemic. However, the method is general and thus applicable to other diseases. Finally we study the behavior of the ratio infected over swabs for Italy, Germany and USA, and we show as studying this parameter we recover the generalized Logistic model used in [1] for these three countries. We think that this trend could be useful for a future epidemic of this coronavirus. url: https://doi.org/10.1016/j.chaos.2020.110064 doi: 10.1016/j.chaos.2020.110064 id: cord-342013-k54u2q0d author: Martenot, Antoine title: Favorable outcomes among neonates not separated from their symptomatic SARS-CoV-2-infected mothers date: 2020-11-03 words: 1944.0 sentences: 124.0 pages: flesch: 55.0 cache: ./cache/cord-342013-k54u2q0d.txt txt: ./txt/cord-342013-k54u2q0d.txt summary: 1, 2 Although neonates born of mothers infected with SARS-CoV-2 during pregnancy are seemingly vulnerable to infection, studies have found that they were not at a high risk for severe infection and were very rarely affected by COVID-19. This strategy involved preservation of continuous mother-infant proximity with specific hygienic measures, breast milk as the main source of feeding, early discharge with home isolation, and a structured follow-up with hospital-assisted home care. Breastfeeding may protect against the horizontal transmission of SARS-CoV-2, as specific antibodies against this virus have been found in the breast milk of a COVID-19-infected mother. 19 Our results support early postnatal proximity, despite many mothers worldwide being separated from their newborn infants during the COVID-19 pandemic. Even during the COVID-19 pandemic, safely maintaining familycentered perinatal care and continuing the promotion of bonding between neonates and their SARS-CoV-2-positive mothers appear possible, as these newborns are very rarely infected and, if infected, show only mild symptoms. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33144706/ doi: 10.1038/s41390-020-01226-3 id: cord-140318-xtx8hl14 author: Martin, Alexandra title: High-sensitivity COVID-19 group testing by digital PCR date: 2020-06-03 words: 4252.0 sentences: 213.0 pages: flesch: 58.0 cache: ./cache/cord-140318-xtx8hl14.txt txt: ./txt/cord-140318-xtx8hl14.txt summary: Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. The results for SARS-CoV-2 detection by RT-dPCR in groups of 8 samples, detailed in Tables 1 and 2 , are in concordance with the reference individual RT-PCR testing for 52 groups (corresponding for 416 samples), out of which 32 were RT-PCR negative groups and 20 groups contained at least one RT-PCR+ sample. In this work, we assessed the sensitivity and specificity of group testing combined with digital PCR for SARS-CoV-2 detection. abstract: Background: Worldwide demand for SARS-CoV-2 RT-PCR testing is increasing as more countries are impacted by COVID-19 and as testing remains central to contain the spread of the disease, both in countries where the disease is emerging and in countries that are past the first wave but exposed to re-emergence. Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns have limited its impact on the management of the pandemic. Digital PCR (RT-dPCR) has been shown to be more sensitive than RT-PCR and could help in this context. Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. We tested the protocol in a direct comparison with reference RT-PCR testing on 448 samples split into groups of 3 sizes for RT-dPCR analysis: 56 groups of 8 samples, 28 groups of 16 samples and 14 groups of 32 samples. Results: Individual RT-PCR testing identified 25 positive samples. Using groups of 8, testing by RT-dPCR identified 23 groups as positive, corresponding to 26 true positive samples including 2 samples not initially detected by individual RT-PCR but confirmed positive by further RT-PCR and RT-dPCR investigation. For groups of 16, 15 groups tested positive, corresponding to 25 true positive samples identified. 100% concordance is found for groups of 32 but with limited data points. url: https://arxiv.org/pdf/2006.02908v1.pdf doi: nan id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 words: 5925.0 sentences: 340.0 pages: flesch: 53.0 cache: ./cache/cord-286343-s8n1ldol.txt txt: ./txt/cord-286343-s8n1ldol.txt summary: We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory (data not shown). abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. url: https://www.ncbi.nlm.nih.gov/pubmed/33050264/ doi: 10.3390/v12101144 id: cord-307227-x6xketcn author: Martin, William R. title: Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date: 2020-09-10 words: 3999.0 sentences: 219.0 pages: flesch: 52.0 cache: ./cache/cord-307227-x6xketcn.txt txt: ./txt/cord-307227-x6xketcn.txt summary: Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19. 2, 3 In our initial network-based drug repurposing study, 4 we identified toremifene, another selective estrogen receptor modulator (SERM), as a strong candidate for the potential treatment of COVID-19. A drug repurposing study for SARS-CoV-1 5 indicated a low 50% effective concentration (EC 50 ) for toremifene, and noted that estrogen signaling may not be involved in the inhibitory pathway, similar to that of inhibition of Ebola. Future work will be needed to confirm these results; optimally, the determination of a cocrystal structure with Journal of Proteome Research pubs.acs.org/jpr Article NSP14 and/or the spike glycoprotein from SARS-CoV-2 with toremifene would be solved. abstract: [Image: see text] The global pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to the death of more than 675,000 worldwide and over 150,000 in the United States alone. However, there are currently no approved effective pharmacotherapies for COVID-19. Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. Our results indicate the possibility of inhibition of the spike glycoprotein by toremifene, responsible for aiding in fusion of the viral membrane with the cell membrane, via a perturbation to the fusion core. An interaction between the dimethylamine end of toremifene and residues Q954 and N955 in heptad repeat 1 (HR1) perturbs the structure, causing a shift from what is normally a long, helical region to short helices connected by unstructured regions. Additionally, we found a strong interaction between toremifene and the methyltransferase nonstructural protein (NSP) 14, which could be inhibitory to viral replication via its active site. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32907334/ doi: 10.1021/acs.jproteome.0c00397 id: cord-307109-nz8qvuw6 author: Martinez, Miguel Angel title: Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus date: 2020-04-21 words: 3758.0 sentences: 201.0 pages: flesch: 42.0 cache: ./cache/cord-307109-nz8qvuw6.txt txt: ./txt/cord-307109-nz8qvuw6.txt summary: The previous epidemics of infections by high-morbidity human coronaviruses, such as SARS-CoV in 2003 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, prompted the characterization of compounds that could be potentially active against the currently emerging novel coronavirus, SARS-CoV-2. In addition, a combination of the human immunodeficiency virus type 1 (HIV-1) protease inhibitors lopinavir/ritonavir and interferon beta (LPV/RTV–IFN-β) was shown to be effective in patients infected with SARS-CoV. To predict new zoonotic coronavirus jumps across species and to understand the rate of virus spread among people, it is crucial to determine whether SARS-CoV-2 is mutating to improve its binding to human receptors for infection. Clinical observations in animals and humans showed that MERS-CoV infections were mediated by both virus replication and host inflammatory responses. However, therapeutic treatment with human monoclonal antibodies did not protect against the severe disease or the loss of lung function induced by MERS-CoV in animal models (20) . abstract: Currently, the expansion of the novel human respiratory coronavirus (known as SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2], COVID-2019 [coronavirus disease 2019], or 2019-nCoV [2019 novel coronavirus]) has stressed the need for therapeutic alternatives to alleviate and stop this new epidemic. The previous epidemics of infections by high-morbidity human coronaviruses, such as SARS-CoV in 2003 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, prompted the characterization of compounds that could be potentially active against the currently emerging novel coronavirus, SARS-CoV-2. The most promising compound is remdesivir (GS-5734), a nucleotide analog prodrug currently in clinical trials for treating Ebola virus infections. Remdesivir inhibited the replication of SARS-CoV and MERS-CoV in tissue cultures, and it displayed efficacy in nonhuman animal models. In addition, a combination of the human immunodeficiency virus type 1 (HIV-1) protease inhibitors lopinavir/ritonavir and interferon beta (LPV/RTV–IFN-β) was shown to be effective in patients infected with SARS-CoV. LPV/RTV–IFN-β also improved clinical parameters in marmosets and mice infected with MERS-CoV. Remarkably, the therapeutic efficacy of remdesivir appeared to be superior to that of LPV/RTV–IFN-β against MERS-CoV in a transgenic humanized mouse model. The relatively high mortality rates associated with these three novel human coronavirus infections, SARS-CoV, MERS-CoV, and SARS-CoV-2, have suggested that proinflammatory responses might play a role in the pathogenesis. It remains unknown whether the generated inflammatory state should be targeted. Therapeutics that target the coronavirus alone might not be able to reverse highly pathogenic infections. This minireview aims to provide a summary of therapeutic compounds that have shown potential in fighting SARS-CoV-2 infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32152082/ doi: 10.1128/aac.00399-20 id: cord-303745-wx3udkee author: Martinez-Fleta, P. title: SARS-Cov-2 cysteine-like protease (Mpro) is immunogenic and can be detected in serum and saliva of COVID-19-seropositive individuals date: 2020-07-18 words: 5031.0 sentences: 328.0 pages: flesch: 57.0 cache: ./cache/cord-303745-wx3udkee.txt txt: ./txt/cord-303745-wx3udkee.txt summary: Using ELISA tests, coating several SARS-CoV-2 proteins produced in vitro, we describe that COVID-19 patients make high titre IgG, IgM and IgA antibody responses to the Cys-like protease from SARS-CoV-2, also known as 3CLpro or Mpro, and it can be used to identify individuals with positive serology against the coronavirus. Since this study evaluated, for the first time, whether coronavirus-infected individuals could 121 generate an antibody response against the Cys-like protease, MPro, other SARS-CoV-2 122 proteins, commonly used in serology tests, were produced, for comparison. 1101 individuals with high specificity and sensitivity 153 A cohort of 36 COVID-19 patients (PCR+) and 33 healthy donors was recruited at La Princesa 154 University Hospital, Madrid (Table 1 ) and ELISA assays were performed to detect Mpro-, as 155 well as RBD-and NP-, specific antibodies of the IgG, IgA and IgM subclasses in sera ( Figure 156 3). abstract: Currently, there is a need for reliable tests that allow identification of individuals that have been infected with SARS-CoV-2 even if the infection was asymptomatic. To date, the vast majority of the serological tests for SARS-CoV-2 specific antibodies are based on serum detection of antibodies to either the viral spike glycoprotein (the major target for neutralising antibodies) or the viral nucleocapsid protein that are known to be highly immunogenic in other coronaviruses. Conceivably, exposure of antigens released from infected cells could stimulate antibody responses that might correlate with tissue damage and, hence, they may have some value as a prognostic indicator. We addressed whether other non-structural viral proteins, not incorporated into the infectious viral particle, specifically the viral cysteine-like protease, might also be potent immunogens. Using ELISA tests, coating several SARS-CoV-2 proteins produced in vitro, we describe that COVID-19 patients make high titre IgG, IgM and IgA antibody responses to the Cys-like protease from SARS-CoV-2, also known as 3CLpro or Mpro, and it can be used to identify individuals with positive serology against the coronavirus. Higher antibody titres in these assays associated with more severe disease and no cross-reactive antibodies against prior betacoronavirus were found. Remarkably, IgG antibodies specific for Mpro and other SARS-CoV-2 antigens can also be detected in saliva. In conclusion, Mpro is a potent antigen in infected patients that can be used in serological tests and its detection in saliva could be the basis for a rapid, non-invasive test for COVID-19 seropositivity. url: https://doi.org/10.1101/2020.07.16.20155853 doi: 10.1101/2020.07.16.20155853 id: cord-349313-2gupfqnl author: Martinez-Perez, Clara title: Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19) date: 2020-10-21 words: 7148.0 sentences: 437.0 pages: flesch: 53.0 cache: ./cache/cord-349313-2gupfqnl.txt txt: ./txt/cord-349313-2gupfqnl.txt summary: This study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. Methods: The search for publications was carried out through the Web of Science database using terms such as "COVID-19" and "SARS-CoV-2" for the period between January and July 2020. The search of publications was carried out using the Web of Science (WOS) database with the following search terms: "COVID-19", "SARS-CoV-2", "The Coronavirus Disease 2019" and "Corona Virus Disease 2019". Moreover, the most common keywords used in Chinese journals were "COVID-19", "SARS-CoV-2", "Prevention and control", "Traditional Chinese Medicine", "Computed tomography", "Epidemic", "Public health", "MERS", "Pneumonia" and "Male". In this group, the different articles analyze the viral transmission of SARS-CoV-2, the most frequent symptoms (fever, cough, diarrhea, etc.) and experimental treatment methods such as chloroquine phosphate (Figure 7 ). abstract: Background: The first outbreaks of the new coronavirus disease, named COVID-19, occurred at the end of December 2019. This disease spread quickly around the world, with the United States, Brazil and Mexico being the countries the most severely affected. This study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. Methods: The search for publications was carried out through the Web of Science database using terms such as “COVID-19” and “SARS-CoV-2” for the period between January and July 2020. The Citation Network Explorer software was used for publication analysis. Results: A total of 14,335 publications were found with 42,374 citations generated in the network, with June being the month with the largest number of publications. The most cited publication was “Clinical Characteristics of Coronavirus Disease 2019 in China” by Guan et al., published in April 2020. Nine groups comprising different research areas in this field, including clinical course, psychology, treatment and epidemiology, were found using the clustering functionality. Conclusions: The citation network offers an objective and comprehensive analysis of the main papers on COVID-19 and SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33096796/ doi: 10.3390/ijerph17207690 id: cord-326393-gxy1w0qk author: Martino, Marcello Di title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD date: 2020-04-29 words: 4243.0 sentences: 399.0 pages: flesch: 52.0 cache: ./cache/cord-326393-gxy1w0qk.txt txt: ./txt/cord-326393-gxy1w0qk.txt summary: title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD Desde que se produjeron los primeros casos de infección por SARS-CoV-2 (COVID-19) a finales de diciembre de 2019 en Wuhan (China), el crecimiento exponencial de esta enfermedad ha llevado a una pandemia, declarada como tal por la Organización Mundial de la Sanidad (OMS) el 11 de marzo J o u r n a l P r e -p r o o f 2020 (1, 2) . Se analizaron la edad, sexo, estado funcional definido según la escala ECOG (21), antecedentes personales, diagnóstico, tipo de intervención quirúrgica, momento en que se confirmó la infección por SARS-CoV-2, el tratamiento requerido para la misma (Tabla 1), la gravedad de la infección respiratoria según la BRCSS (20) y las complicaciones postoperatorias según la clasificación de Dindo-Clavien (19) . abstract: Resume Introducción: La expansión de la infección por SARS-CoV-2 (COVID-19) ha requerido la adaptación de los hospitales afectados por la pandemia, causando una reducción de la actividad quirúrgica electiva. Material y método: Estudio retrospectivo de pacientes operados durante el mes previo y el pico de la pandemia. Se analizó la tasa de contagio por COVID-19, la gravedad de la infección respiratoria según la Brescia Respiratory COVID-19 Severity Scale, las medidas terapéuticas adoptadas y las complicaciones postoperatorias globales. Resultados: Desde el 17 de febrero hasta el 31 de marzo de 2020 se produjo una reducción progresiva de la actividad quirúrgica, interviniéndose únicamente 213 pacientes: 59 (27,8%) de forma programada por patología tumoral, 97 (45,5%) por patología benigna y 57 (26,7%) de forma urgente. Se produjo un aumento progresivo de la tasa de contagio por COVID-19 con un total de 15 (7%) casos. De los pacientes oncológicos, 10 (16,9%) resultaron afectos; en el grupo de cirugía electiva 1 (1%) y en el grupo de cirugía urgente 4 (7%) (p<0,001). Cinco pacientes presentaron una infección respiratoria grave de los cuales 4 estaban afectos por enfermedad oncológica. Hubo 3 (1,4%) exitus, todos debidos a progresión de la infección respiratoria. Conclusiones: Los pacientes sometidos a cirugía presentaron una elevada tasa de infección por COVID-19 y de complicaciones postoperatorias, sobre todo en los pacientes oncológicos. La puesta en marcha de la de la actividad quirúrgica debe basarse en una priorización de los casos a operar, respetando unas premisas de seguridad y optimización de los recursos disponibles. Abstract Introduction: The spread of the SARS-CoV-2 infection (COVID-19) has required adaptation by hospitals affected by the pandemic, which has caused a reduction in elective surgical activity. Material and method: Retrospective study of patients operated on in the previous month and during the peak of the pandemic. We analysed the COVID-19 infection rate, the severity of respiratory infection according to the Brescia respiratory COVID-19 severity scale (BRCSS), the adopted therapeutic measures and the overall postoperative complications. Results: From 17th February to 31st March 2020, there was a progressive decrease in surgical activity, with only 213 patients operated on. This comprised 59 (27.8%) elective operations for oncological diseases, 97 (45.5%) elective operations for benign diseases and 57 (26.7%) as urgent procedures. There was a progressive increase in the rate of infection by COVID-19, with a total of 15 cases (7%). This included 10 patients (16.9%) in the elective group for oncological disease, 1 (1%) in the elective surgery group for benign disease and 4 (7%) in the urgent surgery group (p <0.001). Five patients presented with a severe respiratory infection, of which 4 were affected by oncological disease. There were 3 deaths (1.4%), which were all due to the worsening of a respiratory infection. Conclusions: The patients undergoing the surgical procedures showed high rates of COVID-19 infection and postoperative complications, especially the patients with oncological diseases. Local resumption of surgical activity must be based on the prioritisation of the cases to be operated on, respecting certain premises of security and optimisation of the available resources. url: https://www.ncbi.nlm.nih.gov/pubmed/32408995/ doi: 10.1016/j.ciresp.2020.04.029 id: cord-334688-0i1pu8wc author: Martos Pérez, F. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 words: 3445.0 sentences: 208.0 pages: flesch: 57.0 cache: ./cache/cord-334688-0i1pu8wc.txt txt: ./txt/cord-334688-0i1pu8wc.txt summary: Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. In this study, we describe the first cases of COVID-19 in patients hospitalized in a general hospital and analyze the characteristics upon admission associated with in-hospital death. Our model shows that a medical history of cardiopathy, LDH levels ≥345 IU/L upon admission, and age ≥65 years are associated with greater in-hospital mortality due to COVID-19. Predictors of Mortality for Patients with COVID-19 Pneumonia Caused by SARS-CoV-2: A Prospective Cohort Study Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. abstract: Abstract Antecedents and objective To describe clinical features, comorbidity, and prognostic factors associated with in-hospital mortality in a cohort of COVID-19 admitted to a general hospital. Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. A descriptive study and an analysis of factors associated with intrahospital mortality were performed. Results Out of the 101 patients, 96 were analysed. Of these, 79 (82%) recovered and were discharged, and 17 (18%) died in the hospital. Diagnosis of COVID-19 was confirmed by polymerase chain reaction to SARS-CoV2 in 92 (92.5%). The mean age was 63 years, and 66% were male. The most frequent comorbidities were hypertension (40%), diabetes mellitus (16%) y cardiopathy (14%). Patients who died were older (mean 77 vs 60 years), had higher prevalence of hypertension (71% vs 33%), and cardiopathy (47% vs 6%), and higher levels of lactate dehydrogenase (LDH) and reactive C protein (mean 662 vs 335 UI/L, and 193 vs 121 mg/L respectively) on admission. In a multivariant analysis the variables significantly associated to mortality were the presence of cardiopathy (CI 95% OR 2,58-67,07), levels of LDH ≥ 345 IU/L (CI 95% OR 1,52-46,00), and age ≥ 65 years (CI 95% OR 1,23-44,62). Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. This model should be validated in prospective cohorts. url: https://www.sciencedirect.com/science/article/pii/S2254887420300928?v=s5 doi: 10.1016/j.rceng.2020.05.010 id: cord-343845-suoy3ojr author: Martín, Vicente title: Prevalencia de la Infección por SARS-CoV-2 en médicos y enfermeras de Atención Primaria y Residencias de Ancianos del Área de Salud de León y Factores asociados date: 2020-06-06 words: 2712.0 sentences: 194.0 pages: flesch: 56.0 cache: ./cache/cord-343845-suoy3ojr.txt txt: ./txt/cord-343845-suoy3ojr.txt summary: ABSTRACT Objective: To evaluate the prevalence and associated factors with SARS-CoV-2 infection in general practitioners and nurses of primary care centers and nursing homes in the health area of León (Spain). The aim of this study is to evaluate the prevalence and factors associated with SARS-CoV-2 infection in General Practitioners and Nurses of primary care centers and nursing homes in the health area of León. The most relevant results of this study indicate that the observed prevalence of SARS-CoV-2 infection in the health workers analyzed is 5.9% (CI95% 4.4%-8.0%), being higher in nursing home workers compared to primary care centers (9.5% vs. Our results indicate that a high number of professionals remain susceptible to SARS-CoV-2 infection and therefore protective measures should be taken, not only in primary care, as the main contact with the health system, but also in nursing homes. abstract: ABSTRACT Objective: To evaluate the prevalence and associated factors with SARS-CoV-2 infection in general practitioners and nurses of primary care centers and nursing homes in the health area of León (Spain). Materials and methods: Cross-sectional study in a convenience sample of professionals from 30 health centers and 30 nursing homes from the primary care management division of the Healthcare Area of Leon. The work center, type of profession, COVID-19 infection, level of exposure, compliance with preventive measures, isolation (if required) and diagnostic tests carried out were collected. The determination of infection was made by differentiated rapid diagnostic test (dRDT), using a finger-stick whole-blood sample. The association of variables with infection was assessed by multivariable non-conditional logistic regression. The true prevalence of SARS-CoV-2 infection was calculated according to two scenarios for RDT (Sensitivity=0.6 and Specificity=0.985; Sensitivity=0.8 and Specificity=1). Results: The true prevalence of SARS-CoV-2 infection was between 4.9% - 11.0%. The observed prevalence was 5.9%, being higher in nursing home compared to primary care centers (9.5% vs. 5.5%). No statistically significant differences were observed by sex, type of professional, level of exposure or compliance with preventive measures. Conclusions: The prevalence of SARS-CoV-2 infection in this group is low. A high number of professionals remain susceptible to SARS-CoV-2 infection and therefore protective measures should be taken, especially in nursing home professionals. RESUMEN Objetivo: Evaluar la prevalencia y los factores asociados a la infección por SARS-CoV-2 en médicos y enfermeras de centros de atención primaria y residencias de ancianos del área de salud de León (España). Material y métodos: Estudio observacional realizado en una muestra de conveniencia de profesionales de 30 centros de salud y 30 residencias de ancianos, de la Gerencia de Atención Primaria del área de salud de León. Se recogió información del centro de trabajo, tipo de profesión, infección por COVID-19, nivel de exposición, cumplimiento de medidas preventivas, aislamiento (si fue requerido) y test diagnósticos realizados. La determinación de infección fue llevada a cabo mediante prueba de diagnóstico rápido diferenciado (PDRd), usando muestra de sangre capilar. La asociación de las variables con la infección se evaluó mediante regresión logística multivariable no condicional. La prevalencia real de infección por SARS-CoV-2 fue calculada de acuerdo a dos escenarios para el PDRd (Sensibilidad=0,6 y Especificidad=0,985; Sensibilidad=0,8 y Especificidad=1). Resultados: La prevalencia real de infección por SARS-CoV-2 se encontró entre 4,9%-11,0%. La prevalencia observada fue de 5,9%, siendo mayor en trabajadores de residencias de ancianos que de centros de salud de atención primaria (9,5% vs 5,5%). No hubo diferencias estadísticamente significativas por sexo, tipo de profesional, nivel de exposición o cumplimiento de medidas preventivas. Conclusiones: La prevalencia de la infección por el SARS-CoV-2 en este grupo es baja. Un gran número de profesionales siguen siendo susceptibles a la infección por el SARS-CoV-2 y, por lo tanto, medidas de protección deben ser adoptadas, especialmente en los profesionales de las residencias de ancianos. url: https://www.ncbi.nlm.nih.gov/pubmed/32646731/ doi: 10.1016/j.semerg.2020.05.014 id: cord-291436-cu5o8ipw author: Martínez-Hernández, Fernando title: Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals date: 2020-10-05 words: 2947.0 sentences: 176.0 pages: flesch: 57.0 cache: ./cache/cord-291436-cu5o8ipw.txt txt: ./txt/cord-291436-cu5o8ipw.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect animals, however, the whole range of potential hosts is still unknown. This work makes an assessment of wildlife susceptibility to SARS-CoV-2 by analyzing the similarities of Angiotensin Converting Enzyme 2 (ACE2) and Transmembrane Protease, Serine 2 (TMPRSS2) —both recognized as receptors and protease for coronavirus spike protein— and the genetic variation of the viral protein spike in the recognition sites. Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is causing the biggest pandemic 52 of this century, and could potentially infect between 30 to 40% of the world''s populations (De 53 Soto et al., 2020) . Due to its high transmission rate and mortality, researches around the world 54 are trying to get some insight about its origin through the analysis of related-virus genes 55 sequences in humans and animals (Lu R et al., 2020) , and looking for Angiotensin-Converting 56 abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect animals, however, the whole range of potential hosts is still unknown. This work makes an assessment of wildlife susceptibility to SARS-CoV-2 by analyzing the similarities of Angiotensin Converting Enzyme 2 (ACE2) and Transmembrane Protease, Serine 2 (TMPRSS2) —both recognized as receptors and protease for coronavirus spike protein— and the genetic variation of the viral protein spike in the recognition sites. The sequences from different mammals, birds, reptiles, and amphibians, and the sequence from SARS-CoV-2 S protein were obtained from the GenBank. Comparisons of aligned sequences were made by selecting amino acids residues of ACE2, TMPRSS2 and S protein; phylogenetic trees were reconstructed using the same sequences. The species susceptibility was ranked by substituting the values of amino acid residues for both proteins. Our results ranked primates at the top, but surprisingly, just below are carnivores, cetaceans and wild rodents, showing a relatively high potential risk, as opposed to lab rodents that are typically mammals at lower risk. Most of the sequences from birds, reptiles and amphibians occupied the lowest ranges in the analyses. Models and phylogenetic trees outputs showed the species that are more prone to getting infected with SARS-CoV-2. Interestingly, during this short pandemic period, a high haplotypic variation was observed in the RBD of the viral S protein, suggesting new risks for other hosts. Our findings are consistent with other published results reporting laboratory and natural infections in different species. Finally, urgent measures of wildlife monitoring are needed regarding SARS-CoV-2, as well as measures for avoiding or limiting human contact with wildlife, and precautionary measures to protect wildlife workers and researchers; monitoring disposal of waste and sewage than can potentially affect the environment, and designing protocols for dealing with the outbreak. url: https://api.elsevier.com/content/article/pii/S2530064420300596 doi: 10.1016/j.pecon.2020.09.008 id: cord-313571-umcbulcw author: Martínez-Murcia, Antonio title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date: 2020-05-05 words: 1189.0 sentences: 85.0 pages: flesch: 54.0 cache: ./cache/cord-313571-umcbulcw.txt txt: ./txt/cord-313571-umcbulcw.txt summary: title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. As the number of genomes available rapidly expanded during last January, the GPS™ CoVID-19 230 dtec-RT-qPCR Test was based on a more specific target for SARS-CoV-2 detection, being this 231 company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. abstract: Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, several RT-qPCR were designed by using only the first SARS-CoV-2 genome sequence. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. The kit was validated following criteria recommended by the UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Methods The present study approached the in silico specificity of the GPS™ CoVID-19 dtec-RT-qPCR Test and RT-qPCR designs currently published. The empirical validation parameters specificity (inclusivity/exclusivity), quantitative phase analysis (10-106 copies), reliability (repeatability/reproducibility) and sensitivity (detection/quantification limits) were evaluated for a minimum of 10-15 assays. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III (ISCIII), (Madrid, Spain) and the Public Health England (PHE; Colindale, London, UK). Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. The kits passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by suing reference methods and received an evaluation with 100% of diagnostic sensitivity and specificity. Conclusions The GPS™ CoVID-19 dtec-RT-qPCR Test, available with full analytical and diagnostic validation, represents a case of efficient transfer of technology being successfully used since the pandemic was declared. The analysis suggested the GPS™ CoVID-19 dtec-RT-qPCR Test is the more exclusive by far. url: https://doi.org/10.1101/2020.04.27.065383 doi: 10.1101/2020.04.27.065383 id: cord-269045-i7vijtol author: Martínez‐Murcia, A. title: Comparative in silico design and validation of GPS™ CoVID‐19 dtec‐RT‐qPCR test date: 2020-07-29 words: 3889.0 sentences: 239.0 pages: flesch: 59.0 cache: ./cache/cord-269045-i7vijtol.txt txt: ./txt/cord-269045-i7vijtol.txt summary: An illustration of the mismatching of primers/probe sequences of the GPS CoVID-19 dtec-RT-qPCR Test, respect of the SARS-CoV-2, Bat SARS-like-CoV, SARS-CoV, Bat-CoV, and Pangolin-CoV groups is shown in Fig. 2 . Finally, the results obtained in the diagnostic validation of the GPS TM CoVID-19 dtec-RT-qPCR Test, carried out by the Instituto de Salud Carlos III (ISCIII), are shown in Table 3 . As the number of genomes available rapidly expanded during last January, the GPS TM CoVID-19 dtec-RT-qPCR test was based on a more specific target for SARS-CoV-2 detection, being this company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. Finally, the kit GPS TM COVID-19 dtec-RT-qPCR Test showed the highest number of mismatches (i.e. 19-48) for all coronavirus sequences described so far, including these of Pangolin-CoV, which showed a range of 19-31 mismatches. abstract: AIMS: Providing a ready‐to‐use reverse transcriptase qPCR (RT‐qPCR) method fully validated to detect the SARS‐CoV‐2 with a higher exclusivity than this shown by early published RT‐qPCR designs. METHODS AND RESULTS: The specificity of the GPS™ CoVID‐19 dtec‐RT‐qPCR test by analysis of sequence alignments was approached and compared with other RT‐qPCR designs. The GPS™ CoVID‐19 dtec‐RT‐qPCR test was validated following criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III, (Madrid, Spain), the Public Health England (Colindale, London, UK), and received the label CE‐IVD. The GPS design showed the highest exclusivity and passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by using reference methods and showed 100% of diagnostic sensitivity and specificity. CONCLUSIONS: The CE‐IVD GPS™ CoVID‐19 dtec‐RT‐qPCR test, available worldwide with full analytical and diagnostic validation, is the more exclusive for SARS‐CoV‐2 by far. SIGNIFICANCE AND IMPACT OF THE STUDY: Considering the CoVID‐19 pandemic status, the exclusivity of RT‐qPCR tests is crucial to avoid false positives due to related coronaviruses. This work provides of a highly specific and validated RT‐qPCR method for detection of SARS‐CoV‐2, which represents a case of efficient transfer of technology successfully used since the pandemic was declared. url: https://www.ncbi.nlm.nih.gov/pubmed/32652813/ doi: 10.1111/jam.14781 id: cord-308424-crvnzr44 author: Mascarenhas, Victor Hugo Alves title: Care recommendations for parturient and postpartum women and newborns during the COVID-19 pandemic: a scoping review date: 2020-08-10 words: 4494.0 sentences: 276.0 pages: flesch: 49.0 cache: ./cache/cord-308424-crvnzr44.txt txt: ./txt/cord-308424-crvnzr44.txt summary: Normal childbirth: • Mild clinical conditions; • There are no contraindications, especially due to a lack of evidence on vertical transmissions; • If pregnant women infected with SARS-CoV-2* present spontaneous labor and good cervical conditions, normal childbirth is advised, provided that the health service has the apparatus necessary to promote appropriate precautions; • To shorten the duration of the second stage of labor, directed pushing is recommended and parturient women are supposed to wear a surgical mask. This decision should be taken together with the mother and health workers involved in care delivery; • There is a risk of mothers transmitting SARS-CoV-2* to their NB † through respiratory droplets at the time of breastfeeding, even when wearing a surgical mask; • Women who opt not to breastfeed during the period of the disease should be encouraged to express breast milk to feed their NB † ; abstract: OBJECTIVE: to map the current knowledge on recommendations for labor, childbirth, and newborn (NB) care in the context of the novel coronavirus. METHOD: scoping review of papers identified in databases, repositories, and reference lists of papers included in the study. Two researchers independently read the papers’ full texts, extracted and analyzed data, and synthesized content. RESULTS: 19 papers were included, the content of which was synthesized and organized into two conceptual categories: 1) Recommendations concerning childbirth with three subcategories – Indications to anticipate delivery, Route of delivery, and Preparation of the staff and birth room, and 2) Recommendations concerning postpartum care with four categories – Breastfeeding, NB care, Hospital discharge, and Care provided to NB at home. CONCLUSION: prevent the transmission of the virus in the pregnancy-postpartum cycle, assess whether there is a need to interrupt pregnancies, decrease the circulation of people, avoid skin-to-skin contact and water births, prefer epidural over general anesthesia, keep mothers who tested positive or are symptomatic isolated from NB, and encourage breastfeeding. Future studies are needed to address directed pushing, instrumental delivery, delayed umbilical cord clamping, and bathing NB immediately after birth. url: https://www.ncbi.nlm.nih.gov/pubmed/32785566/ doi: 10.1590/1518-8345.4596.3359 id: cord-304280-2a84u4tm author: Masic, Izet title: Public Health Aspects of COVID-19 Infection with Focus on Cardiovascular Diseases date: 2020-03-17 words: 4693.0 sentences: 196.0 pages: flesch: 43.0 cache: ./cache/cord-304280-2a84u4tm.txt txt: ./txt/cord-304280-2a84u4tm.txt summary: METHODS: We used method of descriptive analysis of the published papers with described studies about Corona virus connected with CVD, and, also, Guidelines proposed by World Health Organization (WHO) and European Society of Cardiology (ESC), and some other international associations which are included in global fighting against COVID-19 infection. Early COVID-19 case reports suggest that patients with underlying conditions are at higher risk for complications or mortality -up to 50% of hospitalized patients have a chronic medical illness (40% cardiovascular or cerebrovascular disease). The clinical effects of pneumonia have been linked to increased risk of CVD up to 10-year follow-up (11) and it is likely that cases infected via respiratory virus outbreaks will experience similar adverse outcomes. The European Medicines Agency (EMA) has issued a statement advising that patients continue treatment with angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs), despite widely circulated reports that the agents could worsen coronavirus disease (20) . abstract: INTRODUCTION: COVID-19 is the disease caused by an infection of the SARS-CoV-2 virus, first identified in the city of Wuhan, in China’s Hubei province in December 2019. COVID-19 was previously known as 2019 Novel Coronavirus (2019-nCoV) respiratory disease before the World Health Organization (WHO) declared the official name as COVID-19 in February 2020. AIM: The aim of this study is to search scientific literature in the biomedicine and analyzed current results of investigations regarding morbidity and mortality rates as consequences of COVID-19 infection of Cardiovascular diseases (CVD), and other most common chronic diseases which are on the top mortality and morbidity rates in almost all countries in the world. Also, to propose most useful measures how to prevent patients to keep themselves against COVID-19 infection. METHODS: We used method of descriptive analysis of the published papers with described studies about Corona virus connected with CVD, and, also, Guidelines proposed by World Health Organization (WHO) and European Society of Cardiology (ESC), and some other international associations which are included in global fighting against COVID-19 infection. RESULTS: After searching current scientific literature we have acknowledged that not any Evidence Based Medicine (EBM) study in the world during last 5 months from the time when first cases of COVID-10 infection was detected. Also, there is no unique proposed ways of treatments and drugs to protect patients, especially people over 65 years old, who are very risk group to be affected with COVID-19. Expectations that vaccine against COVID-19 will be produced optimal during at least 10 months to 2 years, and in all current Guidelines most important proposed preventive measures are the same like which one described in Strategic documents of WHO, in statements of Declaration of Primary Health Care in Alma Ata in 1978. CONCLUSION: WHO proposed preventive measures can be helpful to everybody. Physicians who work at every level of Health Care Systems, but especially at primary health care level, must follow those recommendations and teach their patients about it. But, the fact is that current focus of COVID-19 epidemic has targeted on protection of physical health of population in global, however, the influence on mental health which will be one of the important consequences of COVID-19 pandemic in the future, and which could be declared as «Post-coronavirus Stress Syndrome„ (PCSS) could be bigger challenge for Global Public Health. url: https://www.ncbi.nlm.nih.gov/pubmed/32410896/ doi: 10.5455/msm.2020.32.71-76 id: cord-282853-l0c69uul author: Massad, Eduardo title: Forecasting versus projection models in epidemiology: The case of the SARS epidemics date: 2005-03-30 words: 3085.0 sentences: 173.0 pages: flesch: 56.0 cache: ./cache/cord-282853-l0c69uul.txt txt: ./txt/cord-282853-l0c69uul.txt summary: In this work we propose a simple mathematical model for the analysis of the impact of control measures against an emerging infection, namely, the severe acute respiratory syndrome (SARS). The model provides a testable hypothesis by considering a dynamical equation for the contact parameter, which drops exponentially with time, simulating control measures. In contrast, with control measures, which reduce the contact rate to about 25% of its initial value, the expected final number of cases is reduced to 1778 in Hong Kong and 226 in Toronto (Canada). The aim of this work is to provide a projection of what would have happened with the course of severe acute respiratory syndrome (SARS) epidemic if the universal procedures to reduce contact were not implemented in the affected areas. The model projects that, in the absence of control, the final number of cases would be 320,000 in Hong Kong and 36,900 in Toronto (Canada). abstract: In this work we propose a simple mathematical model for the analysis of the impact of control measures against an emerging infection, namely, the severe acute respiratory syndrome (SARS). The model provides a testable hypothesis by considering a dynamical equation for the contact parameter, which drops exponentially with time, simulating control measures. We discuss the role of modelling in public health and we analyse the distinction between forecasting and projection models as assessing tools for the estimation of the impact of intervention strategies. The model is applied to the communities of Hong Kong and Toronto (Canada) and it mimics those epidemics with fairly good accuracy. The estimated values for the basic reproduction number, R(0), were 1.2 for Hong Kong and 1.32 for Toronto (Canada). The model projects that, in the absence of control, the final number of cases would be 320,000 in Hong Kong and 36,900 in Toronto (Canada). In contrast, with control measures, which reduce the contact rate to about 25% of its initial value, the expected final number of cases is reduced to 1778 in Hong Kong and 226 in Toronto (Canada). Although SARS can be a devastating infection, early recognition, prompt isolation, and appropriate precaution measures, can be very effective to limit its spread. url: https://www.sciencedirect.com/science/article/pii/S0306987705000800 doi: 10.1016/j.mehy.2004.09.029 id: cord-345033-guisyj11 author: Massarotti, Claudia title: SARS‐CoV‐2 in the semen: where does it come from? date: 2020-06-13 words: 694.0 sentences: 49.0 pages: flesch: 55.0 cache: ./cache/cord-345033-guisyj11.txt txt: ./txt/cord-345033-guisyj11.txt summary: This finding re‐opened the discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and safety of fertility treatments during the pandemic period [1]. 2 A recent report by Li et al., described the presence of SARS-CoV-2 in semen samples of six patients, 3 including two subjects who were recovering from the clinical disease. This finding re-opened the 4 discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and 5 safety of fertility treatments during the pandemic period [1] . Regarding Coronaviruses, there is evidence that 35 MERS-CoV binds to the host cell receptor dipeptidyl peptidase 4 (DPP4), which is broadly expressed 36 on prostate cells [12] . The ACE2 Expression in Sertoli cells and Germ cells may cause male reproductive disorder after SARS-CoV-2 Infection. Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues abstract: A recent report by Li et al., described the presence of SARS‐CoV‐2 in semen samples of six patients, including two subjects who were recovering from the clinical disease. This finding re‐opened the discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and safety of fertility treatments during the pandemic period [1]. As stated by the Authors themselves, the small sample size and short follow up dictate caution in the interpretation of their results. url: https://doi.org/10.1111/andr.12839 doi: 10.1111/andr.12839 id: cord-340590-7jql1ftj author: Massullo, Domenico title: Mountain Rescue During the COVID-19 Outbreak: Considerations and Practical Implications date: 2020-09-23 words: 889.0 sentences: 62.0 pages: flesch: 52.0 cache: ./cache/cord-340590-7jql1ftj.txt txt: ./txt/cord-340590-7jql1ftj.txt summary: The COVID-19 pandemic causes several issues during rescue 48 operations in the wilderness environment due to concern for viral contagiousness during prolonged 49 close interaction between rescuers and victims. The key points during rescues are the protection of operators and patients from 59 infection and disinfection of materials and vehicles used during outdoor operations. In addition, each rescuer, before giving their availability to participate in 65 rescue operations, should perform a self-check through a COVID-19 screening questionnaire 66 ( Figure 1 ). In conclusion, during the COVID-19 pandemic, protocols for mountain rescue services should be 85 reassessed in order to protect both rescuers and victims from possible contagion. Characteristics of and important lessons from the coronavirus disease 144 2019 (COVID-19) outbreak in China: summary of a report of 72 SARS-CoV-2 in patients with COVID-19 Protection 155 and disinfection policies against SARS-CoV-2 (COVID-19) abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1080603220301666?v=s5 doi: 10.1016/j.wem.2020.09.003 id: cord-313957-hviv5zar author: Masucci, Maria Grazia title: Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection date: 2020-08-01 words: 11747.0 sentences: 541.0 pages: flesch: 37.0 cache: ./cache/cord-313957-hviv5zar.txt txt: ./txt/cord-313957-hviv5zar.txt summary: UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. abstract: Posttranslational modifications of cellular proteins by covalent conjugation of ubiquitin and ubiquitin-like polypeptides regulate numerous cellular processes that are captured by viruses to promote infection, replication, and spreading. The importance of these protein modifications for the viral life cycle is underscored by the discovery that many viruses encode deconjugases that reverse their functions. The structural and functional characterization of these viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infections and the host’s antiviral defense. Given the growing body of evidence demonstrating their key contribution to pathogenesis, the viral deconjugases are now recognized as attractive targets for the design of novel antiviral therapeutics. url: https://doi.org/10.3390/biom10081137 doi: 10.3390/biom10081137 id: cord-255290-p64apuk1 author: Matheeussen, Veerle title: International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 date: 2020-07-09 words: 2121.0 sentences: 102.0 pages: flesch: 41.0 cache: ./cache/cord-255290-p64apuk1.txt txt: ./txt/cord-255290-p64apuk1.txt summary: title: International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. Between 6 April and 20 May 2020, each participating laboratory received a blinded panel of eight samples, with five samples containing serial 10-fold dilutions (2.30-5.30 dPCR log10 RNA copies/mL, one duplicated) of non-infectious SARS-CoV-2-positive supernatant obtained from Vero cell culture, two samples with cell culture-derived common human coronavirus (HCoV-NL63, HCoV-OC43) and one negative control with transport medium only. In parallel with the EQA study, laboratories were surveyed to assess their challenges in implementing and executing molecular testing capacity and throughput for SARS-CoV-2 detection, also in April and May 2020. abstract: Laboratory preparedness with quality-assured diagnostic assays is essential for controlling the current coronavirus disease (COVID-19) outbreak. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. To analyse SARS-CoV-2 testing performance, we used an online questionnaire developed for the European Union project RECOVER to assess molecular testing capacities in clinical diagnostic laboratories. url: https://www.ncbi.nlm.nih.gov/pubmed/32672149/ doi: 10.2807/1560-7917.es.2020.25.27.2001223 id: cord-274708-w6gmscv4 author: Mathewson, Alison C. title: Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 date: 2008-11-17 words: 2800.0 sentences: 135.0 pages: flesch: 60.0 cache: ./cache/cord-274708-w6gmscv4.txt txt: ./txt/cord-274708-w6gmscv4.txt summary: Although in different groups, the coronaviruses severe acute respiratory syndrome-coronavirus (SARS-CoV) and NL63 use the same receptor, angiotensin converting enzyme (ACE)-2, for entry into the host cell. (2007) showed that incubation of a tagged form of the RBD with cell lines expressing a number of natural and synthetic ACE-2 variants indicated that the ACE-2 contact residues critical for binding both SARS-CoV and NL63 S overlap (Li et al., 2007) . To investigate CoV S protein binding to ACE-2 in a unified format, we produced soluble and cell-bound versions of the two S proteins through the use of baculovirus expression vectors designed for secretion of proteins as Fc-tagged fusion proteins (Chen et al., 2007) or, separately, displayed on the insect cell surface following tagging with the VSV G protein transmembrane (TM) domain (Chapple & Jones, 2002 ) (see Supplementary Fig. S1 , available in JGV Online). Identification of residues in the receptor-binding domain (RBD) of the spike protein of human coronavirus NL63 that are critical for the RBD-ACE2 receptor interaction abstract: Although in different groups, the coronaviruses severe acute respiratory syndrome-coronavirus (SARS-CoV) and NL63 use the same receptor, angiotensin converting enzyme (ACE)-2, for entry into the host cell. Despite this common receptor, the consequence of entry is very different; severe respiratory distress in the case of SARS-CoV but frequently only a mild respiratory infection for NL63. Using a wholly recombinant system, we have investigated the ability of each virus receptor-binding protein, spike or S protein, to bind to ACE-2 in solution and on the cell surface. In both assays, we find that the NL63 S protein has a weaker interaction with ACE-2 than the SARS-CoV S protein, particularly in solution binding, but the residues required for contact are similar. We also confirm that the ACE-2-binding site of NL63 S lies between residues 190 and 739. A lower-affinity interaction with ACE-2 might partly explain the different pathological consequences of infection by SARS-CoV and NL63. url: https://doi.org/10.1099/vir.0.2008/003962-0 doi: 10.1099/vir.0.2008/003962-0 id: cord-288271-p074ffpt author: Mathies, D. title: A Case of SARS‐CoV‐2‐pneumonia with successful antiviral therapy in a 77‐year‐old male with heart transplant date: 2020-04-21 words: 2473.0 sentences: 155.0 pages: flesch: 52.0 cache: ./cache/cord-288271-p074ffpt.txt txt: ./txt/cord-288271-p074ffpt.txt summary: In this report, we present a 77‐year old patient with a heart transplant under relevant immunosuppressive therapy who was tested positive for SARS‐CoV‐2 after several days of dyspnoea, dry cough and light general symptoms. All rights reserved Diagnosis: SARS-CoV-2-Infection with viral pneumonia in a patient with heart transplant due to coronary artery disease with ischemic cardiomyopathy In this case the combination of radiologic signs of viral pneumonia and the supposed high-risk state of severe immunosuppression led to the decision to start an antiviral therapy immediately after receiving the positive rtPCR-results although the patient presented only mild symptoms. [13] A second question is whether patients with a solid organ transplant who receive immunosuppressive medication are at greater risk for a severe manifestation of a SARS-CoV 2-Infection or might even benefit from a reduced immunologic reaction. For SARS-CoV 2 we found two cases of patients with a heart transplant of which one had only mild manifestations and one required mechanical ventilation but survived [9] . abstract: The SARS‐CoV‐2‐infection can be seen as a single disease but also affects patients with relevant comorbidities who may have an increased risk of a severe course of infection. In this report, we present a 77‐year old patient with a heart transplant under relevant immunosuppressive therapy who was tested positive for SARS‐CoV‐2 after several days of dyspnoea, dry cough and light general symptoms. The CT‐scan confirmed an interstitial pneumonia. The patient received an antiviral therapy with hydroxychloroquine showing no further deterioration of the clinical state. After 12 days of hospitalisation the patient was released SARS‐CoV‐2 negative and completely asymptomatic. url: https://doi.org/10.1111/ajt.15932 doi: 10.1111/ajt.15932 id: cord-269377-ylgyvxtd author: Matos, Ana R. title: COVID-19 Associated Central Nervous System Vasculopathy date: 2020-06-02 words: 939.0 sentences: 57.0 pages: flesch: 38.0 cache: ./cache/cord-269377-ylgyvxtd.txt txt: ./txt/cord-269377-ylgyvxtd.txt summary: Stroke in the setting of viral vasculopathy has been described with other viruses, such as varicella zoster virus (VZV) or 1 ; more recently, it has also been associated with other coronavirus, namely, Middle East respiratory syndrome coronavirus, during the outbreak in Saudi Arabia in 2012. The imaging presentation of multiple lesions involving deep and subcortical white matter, as well as deep gray nuclei, with marked restricted diffusion of some, has been described in the setting of VZV vasculopathy. Primary angiitis of the central nervous system was also considered, but the absence of obvious large vessel irregularities, normal CSF cellular count, and concomitant SARS-CoV-2 infection led us consider a COVID-19-related vasculopathy as the most probable diagnosis, potentially induced by misdirected immune mediated-vasoconstriction of medium-/ small-sized arteries; we believe this represents a new imaging presentation of a SARS-CoV-2-related complication. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32484130/ doi: 10.1017/cjn.2020.109 id: cord-302115-r39ser2c author: Matricardi, Paolo Maria title: The first, holistic immunological model of COVID‐19: implications for prevention, diagnosis, and public health measures date: 2020-05-02 words: 3738.0 sentences: 237.0 pages: flesch: 46.0 cache: ./cache/cord-302115-r39ser2c.txt txt: ./txt/cord-302115-r39ser2c.txt summary: We propose here the first model, explaining how the outcome of first, crucial 10‐15 days after infection, hangs on the balance between the cumulative dose of viral exposure and the efficacy of the local innate immune response (natural IgA and IgM antibodies, Mannose Binding Lectin ). The delayed and strong adaptive immune response (high affinity IgM and IgG antibodies) that follows, causes severe inflammation and triggers mediator cascades (complement, coagulation, and cytokine storm) leading to complications often requiring intensive therapy and being, in some patients, fatal. All rights reserved We focused on humoral components and, in particular on natural antibodies and MBL, to ascertain whether these players of the innate immunity fit all the epidemiological and clinical pre-conditions presented in the last three months by SARS-CoV-2. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for Accepted Article This article is protected by copyright. abstract: The natural history of COVID‐19 caused by SARS‐CoV‐2 is extremely variable, ranging from asymptomatic or mild infection, mainly in children, to multi‐organ failure, eventually fatal, mainly in the eldest. We propose here the first model, explaining how the outcome of first, crucial 10‐15 days after infection, hangs on the balance between the cumulative dose of viral exposure and the efficacy of the local innate immune response (natural IgA and IgM antibodies, Mannose Binding Lectin ). If SARS‐CoV‐2 runs the blockade of this innate immunity and spreads from the upper airways to the alveoli in the early phases of the infections, it can replicate with no local resistance, causing pneumonia and releasing high amounts of antigens. The delayed and strong adaptive immune response (high affinity IgM and IgG antibodies) that follows, causes severe inflammation and triggers mediator cascades (complement, coagulation, and cytokine storm) leading to complications often requiring intensive therapy and being, in some patients, fatal. Low‐moderate physical activity can still be recommended. However, extreme physical activity and hyperventilation during the incubation days and early stages of COVID‐19, facilitates early direct penetration of high numbers of virus particles in the lower airways and the alveoli, without impacting on the airway’s mucosae covered by neutralizing antibodies. This allows the virus bypassing the efficient immune barrier of the upper airways mucosa in already infected, young and otherwise healthy athletes. In conclusion, whether the virus or the adaptative immune response reach the lungs first, is a crucial factor deciding the fate of the patient. This “quantitative and time‐sequence dependent” model has several implications for prevention, diagnosis, and therapy of COVID‐19 at all ages. url: https://doi.org/10.1111/pai.13271 doi: 10.1111/pai.13271 id: cord-277873-4819g00y author: Matson, M. Jeremiah title: Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum date: 2020-09-17 words: 1418.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-277873-4819g00y.txt txt: ./txt/cord-277873-4819g00y.txt summary: We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. We describe SARS-CoV-2 stability in human nasal mucus and sputum under different environmental conditions. The t 1/2 we report here for SARS-CoV-2 in surface nasal mucus and sputum at 21°C/40% (Table) is considerably shorter than what we found in culture media under similar conditions (t 1/2 6.8 [95% CI 5.6-8.2] hours) (3). Nevertheless, with our experimental protocol and initial titer, we predicted that SARS-CoV-2 would remain infectious in nasal mucus and sputum on surfaces for >10-12 hours even in warm, humid conditions. In addition, reduced surface stability of SARS-CoV-2 in human nasal mucus and sputum in warmer and more humid conditions might result in decreased virus transmission, and climatic influence on SARS-CoV-2 transmission rates might eventually drive seasonal outbreak dynamics in a postpandemic period (7) , similar to other respiratory viruses (e.g., influenza A virus or human coronavirus OC43). abstract: We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. The virus is more stable at low-temperature and low-humidity conditions, whereas warmer temperature and higher humidity shortened half-life. Although infectious virus was undetectable after 48 hours, viral RNA remained detectable for 7 days. url: https://www.ncbi.nlm.nih.gov/pubmed/32511089/ doi: 10.3201/eid2609.202267 id: cord-318934-dxipu00r author: Matsuyama, Shutoku title: Enhancement of SARS-CoV Infection by Proteases date: 2006 words: 1861.0 sentences: 109.0 pages: flesch: 56.0 cache: ./cache/cord-318934-dxipu00r.txt txt: ./txt/cord-318934-dxipu00r.txt summary: Moreover, SARS-CoV entry from the cell surface mediated by proteases was a 100-fold more efficient infection than entry through endosomes. However, no S2 band was detected in SARS-CoV infected cells treated with proteases that failed to induce fusion. 3 stated that SARS-CoV is able to enter cells directly from their surface, if receptor-bound virus is treated with trypsin and other proteases that induce fusion. Treatment of VeroE6 cells with bafilomycin was shown to suppress SARS-CoV infection via the endosomal pathway to less than 1/100 (Fig. 2) . Pseudotype VSV bearing SARS-CoV S protein infection was also facilitated in bafilomycin-treated VeroE6 cells after treatment with proteases that induce fusion of SARS-CoV infected cells. These observations suggest that proteases that facilitate SARS-CoV entry from the cell surface support efficient SARS-CoV infection. Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037538/ doi: 10.1007/978-0-387-33012-9_42 id: cord-336793-9bbyu1qx author: Matsuyama, Shutoku title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date: 2020-08-24 words: 709.0 sentences: 48.0 pages: flesch: 62.0 cache: ./cache/cord-336793-9bbyu1qx.txt txt: ./txt/cord-336793-9bbyu1qx.txt summary: title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells We screened steroid compounds to obtain a drug expected to block host inflammatory responses and MERS-CoV replication. Ciclesonide, an inhaled corticosteroid, suppressed replication of MERS-CoV and other coronaviruses, including SARS-CoV-2, the cause of COVID-19, in cultured cells. Eight consecutive passages of 43 SARS-CoV-2 isolates in the presence of ciclesonide generated 15 resistant mutants harboring single amino acid substitutions in non-structural protein 3 (nsp3) or nsp4. These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. In the present study, we found that an inhaled corticosteroid, ciclesonide suppresses replication of coronaviruses, including beta-coronaviruses (MHV-2, MERS-CoV, SARS-CoV, and SARS-CoV-2) and an alpha-coronavirus (HCoV-229E) in cultured cells. The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral abstract: We screened steroid compounds to obtain a drug expected to block host inflammatory responses and MERS-CoV replication. Ciclesonide, an inhaled corticosteroid, suppressed replication of MERS-CoV and other coronaviruses, including SARS-CoV-2, the cause of COVID-19, in cultured cells. The effective concentration (EC90) of ciclesonide for SARS-CoV-2 in differentiated human bronchial tracheal epithelial cells was 0.55 μM. Ciclesonide inhibited formation of double membrane vesicles, which anchor the viral replication-transcription complex in cells. Eight consecutive passages of 43 SARS-CoV-2 isolates in the presence of ciclesonide generated 15 resistant mutants harboring single amino acid substitutions in non-structural protein 3 (nsp3) or nsp4. Of note, ciclesonide still suppressed replication of all these mutants by 90% or more, suggesting that these mutants cannot completely overcome ciclesonide blockade. These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. Importance The outbreak of SARS-CoV-2, the cause of COVID-19, is ongoing. To identify the effective antiviral agents to combat the disease is urgently needed. In the present study, we found that an inhaled corticosteroid, ciclesonide suppresses replication of coronaviruses, including beta-coronaviruses (MHV-2, MERS-CoV, SARS-CoV, and SARS-CoV-2) and an alpha-coronavirus (HCoV-229E) in cultured cells. The inhaled ciclesonide is safe; indeed, it can be administered to infants at high concentrations. Thus, ciclesonide is expected to be a broad-spectrum antiviral drug that is effective against many members of the coronavirus family. It could be prescribed for the treatment of MERS, and COVID-19. url: https://doi.org/10.1101/2020.08.22.258459 doi: 10.1101/2020.08.22.258459 id: cord-319248-ynoxec7k author: Matsuyama, Toshifumi title: An aberrant STAT pathway is central to COVID-19 date: 2020-10-09 words: 9962.0 sentences: 619.0 pages: flesch: 45.0 cache: ./cache/cord-319248-ynoxec7k.txt txt: ./txt/cord-319248-ynoxec7k.txt summary: In SARS-CoV-2-infected cells, a positive feedback loop established between STAT3 and plasminogen activator inhibitor-1 (PAI-1) may lead to an escalating cycle of activation in common with the interdependent signaling networks affected in COVID-19. After a careful review of the scientific literature, we realized that the SARS-CoV-2-mediated inhibition of IFN and STAT1, and the subsequent shift to a STAT3dominant signaling network (see below), could result in almost all of the clinical features of COVID-19. Molecular patterns derived from SARS-CoV-2-associated molecules, such as ssRNA, dsRNA, and viral proteins, bind to host PRRs and trigger the activation of signal transducers and transcription factors that drive the production of IFN-I and proinflammatory cytokines and chemokines. Therefore, in COVID-19, EGFR signaling may become an alternative pathway that activates STAT3 specifically when the lung is damaged while the production of IFN-I is severely impaired by SARS-CoV-2 infection [12] . abstract: COVID-19 is caused by SARS-CoV-2 infection and characterized by diverse clinical symptoms. Type I interferon (IFN-I) production is impaired and severe cases lead to ARDS and widespread coagulopathy. We propose that COVID-19 pathophysiology is initiated by SARS-CoV-2 gene products, the NSP1 and ORF6 proteins, leading to a catastrophic cascade of failures. These viral components induce signal transducer and activator of transcription 1 (STAT1) dysfunction and compensatory hyperactivation of STAT3. In SARS-CoV-2-infected cells, a positive feedback loop established between STAT3 and plasminogen activator inhibitor-1 (PAI-1) may lead to an escalating cycle of activation in common with the interdependent signaling networks affected in COVID-19. Specifically, PAI-1 upregulation leads to coagulopathy characterized by intravascular thrombi. Overproduced PAI-1 binds to TLR4 on macrophages, inducing the secretion of proinflammatory cytokines and chemokines. The recruitment and subsequent activation of innate immune cells within an infected lung drives the destruction of lung architecture, which leads to the infection of regional endothelial cells and produces a hypoxic environment that further stimulates PAI-1 production. Acute lung injury also activates EGFR and leads to the phosphorylation of STAT3. COVID-19 patients’ autopsies frequently exhibit diffuse alveolar damage (DAD) and increased hyaluronan (HA) production which also leads to higher levels of PAI-1. COVID-19 risk factors are consistent with this scenario, as PAI-1 levels are increased in hypertension, obesity, diabetes, cardiovascular diseases, and old age. We discuss the possibility of using various approved drugs, or drugs currently in clinical development, to treat COVID-19. This perspective suggests to enhance STAT1 activity and/or inhibit STAT3 functions for COVID-19 treatment. This might derail the escalating STAT3/PAI-1 cycle central to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33037393/ doi: 10.1038/s41418-020-00633-7 id: cord-281113-t450ccnq author: Mattar, Rejane title: Breath tests for gastrointestinal diseases - will it be safe to conduct breath tests after the COVID-19 pandemic? date: 2020-06-16 words: 756.0 sentences: 53.0 pages: flesch: 55.0 cache: ./cache/cord-281113-t450ccnq.txt txt: ./txt/cord-281113-t450ccnq.txt summary: Viral RNA was detected in respiratory droplets and aerosols from coronavirus-, influenza virus-, and rhinovirus-infected patients (9) . The test carries risks of contamination to the healthcare worker collecting the breath samples and to the patients, as the ultrafine aerosol droplets may also carry SARS-CoV-2 and remain airborne for long periods, and could be inhaled (5) . pylori infection diagnosis, the patient blows into a plastic mouthpiece attached to an aluminized bag. Although the test lasts 20 minutes, it carries the risk of contamination by SARS-CoV-2 in the aerosol droplets generated by the exhaled air (5) . Other analytical assays for SARS-CoV-2 diagnosis include antigen detection by lateral flow assays that are fast and low cost; nonetheless, these tests lack good sensitivity early in the infection stage (11) . Digestive Symptoms in COVID-19 Patients With Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32578832/ doi: 10.6061/clinics/2020/e2092 id: cord-346246-2phtdgh4 author: Mattar, Shaikh Abdul Matin title: Subacute thyroiditis associated with COVID-19 date: 2020-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We report a case of a hospitalised patient with COVID-19 who developed subacute thyroiditis in association with SARS-COV-2 infection. The patient presented with tachycardia, anterior neck pain and thyroid function tests revealing hyperthyroidism together with consistent ultrasonographic evidence suggesting subacute thyroiditis. Treatment with corticosteroids resulted in rapid clinical resolution. This case illustrates that subacute thyroiditis associated with viruses such as SARS-CoV-2 should be recognised as a complication of COVID-19 and considered as a differential diagnosis when infected patients present with tachycardia without evidence of progression of COVID-19 illness. url: https://doi.org/10.1136/bcr-2020-237336 doi: 10.1136/bcr-2020-237336 id: cord-302983-3v5bc80z author: Matterne, Uwe title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review date: 2020-10-10 words: 5446.0 sentences: 296.0 pages: flesch: 46.0 cache: ./cache/cord-302983-3v5bc80z.txt txt: ./txt/cord-302983-3v5bc80z.txt summary: title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review OBJECTIVE: The aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). METHODS: We searched major databases and included publications of quantitative and qualitative studies in English and German on any type of research on the functional, critical and communicative domains of HL conducted in the context of the three outbreaks in the general population. Therefore, the aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). abstract: OBJECTIVE: The aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). METHODS: We searched major databases and included publications of quantitative and qualitative studies in English and German on any type of research on the functional, critical and communicative domains of HL conducted in the context of the three outbreaks in the general population. We extracted and tabulated relevant data and narratively reported where and when the study was conducted, the design and method used, and how HL was measured. RESULTS: 72 studies were included. Three investigated HL or explicitly referred to the concept of HL, 14 were guided by health behaviour theory. We did not find any study designed to develop or psychometrically evaluate pandemic/epidemic HL instruments, or relate pandemic/epidemic or general HL to a pandemic/epidemic outcome, or any controlled intervention study. Type of assessment of the domains of HL varied widely. CONCLUSION: Theory-driven observational studies and interventions, examining whether pandemic-related HL can be improved are needed. PRACTICE IMPLICATIONS: The development and validation of instruments that measure pandemic-related HL is desirable. url: https://www.sciencedirect.com/science/article/pii/S0738399120305474?v=s5 doi: 10.1016/j.pec.2020.10.012 id: cord-029419-b0w9nomq author: Matthews, Adam title: Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date: 2020-07-20 words: 3955.0 sentences: 186.0 pages: flesch: 54.0 cache: ./cache/cord-029419-b0w9nomq.txt txt: ./txt/cord-029419-b0w9nomq.txt summary: Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to ''fix'' ourselves and the planet, including new viral outbreaks. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369538/ doi: 10.1007/s42438-020-00170-z id: cord-308093-m40czdsr author: Matthews, M. M. title: COVID-19 serological survey using micro blood sampling date: 2020-10-13 words: 3542.0 sentences: 249.0 pages: flesch: 60.0 cache: ./cache/cord-308093-m40czdsr.txt txt: ./txt/cord-308093-m40czdsr.txt summary: During August 2020, we carried out a serological survey among students and employees at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, testing for the presence of antibodies against SARS-CoV-2, the causative agent of COVID-19. We used a FDA-authorized 2-step ELISA protocol developed by the Krammer Lab in combination with at-home self-collection of blood samples using a custom low-cost finger prick-based capillary blood collection kit. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. . https://doi.org/10.1101/2020.10.09.20209858 doi: medRxiv preprint 48 Serological surveys which detect the presence of antibodies against SARS-CoV-2 49 antigens can provide important information to the government for issuing health care 50 guidelines. abstract: During August 2020, we carried out a serological survey among students and employees at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, testing for the presence of antibodies against SARS-CoV-2, the causative agent of COVID-19. We used a FDA-authorized 2-step ELISA protocol developed by the Krammer Lab in combination with at-home self-collection of blood samples using a custom low-cost finger prick-based capillary blood collection kit. Although our survey did not find any COVID-19 seropositive individuals among the OIST cohort, it reliably detected all positive control samples obtained from a local hospital and excluded all negatives controls. Among our controls, we found strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in the anti-SARS-CoV-2-S ELISA. Here we show that a centralized ELISA in combination with patient-based capillary blood collection using as little as one drop of blood can reliably assess the seroprevalence among communities. Anonymous sample tracking and an integrated website created a stream-lined procedure. Major parts of the workflow were automated on a liquid handler, demonstrating scalability. We anticipate this concept to serve as a prototype for reliable serological testing among larger populations. url: http://medrxiv.org/cgi/content/short/2020.10.09.20209858v1?rss=1 doi: 10.1101/2020.10.09.20209858 id: cord-266022-aco5kpaj author: Matusiak, Magdalena title: Expression of SARS-CoV-2 entry receptors in the respiratory tract of healthy individuals, smokers and asthmatics date: 2020-09-29 words: 1837.0 sentences: 122.0 pages: flesch: 48.0 cache: ./cache/cord-266022-aco5kpaj.txt txt: ./txt/cord-266022-aco5kpaj.txt summary: We analyzed publicly available RNA microarray datasets for SARS-CoV-2 entry receptors and cofactors ACE2, TMPRSS2, BSG (CD147) and FURIN. Furthermore, respiratory epithelia were negative for ACE-2 and TMPRSS2 protein expression while positive for BSG and furin, suggesting a possible alternative entry route for SARS-CoV-2. First, by plotting the first 2 principal components computed on ACE2, TMPRSS2, BSG and FURIN expression across smokers'' and asthmatics'' datasets, we verified that there were no detectable batch effects within each of the six microarray datasets we sought to analyze (Figs. We next examined four RNA microarray datasets for ACE2, TMPRSS2, BSG and FURIN expression in airway epithelia from patients with a common respiratory disease, asthma. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; COVID-19: Coronavirus disease 2019; ACE-2: Angiotensin I converting enzyme 2; TMPRSS2: Transmembrane serine protease 2; BSG: Basigin; XIST: X inactive specific transcript; RPS4Y1: Ribosomal protein S4 Y-linked 1 SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues abstract: SARS-CoV-2 is causing a pandemic with currently > 29 million confirmed cases and > 900,000 deaths worldwide. The locations and mechanisms of virus entry into the human respiratory tract are incompletely characterized. We analyzed publicly available RNA microarray datasets for SARS-CoV-2 entry receptors and cofactors ACE2, TMPRSS2, BSG (CD147) and FURIN. We found that ACE2 and TMPRSS2 are upregulated in the airways of smokers. In asthmatics, ACE2 tended to be downregulated in nasal epithelium, and TMPRSS2 was upregulated in the bronchi. Furthermore, respiratory epithelia were negative for ACE-2 and TMPRSS2 protein expression while positive for BSG and furin, suggesting a possible alternative entry route for SARS-CoV-2. url: https://doi.org/10.1186/s12931-020-01521-x doi: 10.1186/s12931-020-01521-x id: cord-328499-d6cvaxm9 author: Matzkies, Lucie-Marie title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date: 2020-07-08 words: 569.0 sentences: 50.0 pages: flesch: 62.0 cache: ./cache/cord-328499-d6cvaxm9.txt txt: ./txt/cord-328499-d6cvaxm9.txt summary: RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. Clinical Evaluation of 179 the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the VIASURE SARS-CoV-2 S-gene Real Time PCR Detection Kit abstract: OBJECTIVES: New molecular tests for SARS-CoV-2 are rapidly launched in response to the COVID-19 pandemic. The aim of this study was to evaluate the analytical and the clinical performance of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. METHODS: For testing the analytical performance, reference material was used. Clinical samples (n=101) obtained from patients with symptoms compatible to COVID-19 were studied. Oro- and nasopharyngeal swabs were collected by using either ESwab™ or UTM™ collection systems. RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. Six out of the 101 clinical samples (5.9%) showed an inhibition with the VIASURE test. When analyzing the remaining 95 clinical samples, 27 were found to be negative with both assays. Of 68 samples positive with the cobas® test, the VIASURE test missed 21 (30.9 %) samples. All of those 21 samples had shown Ct values ≥ 31 with the cobas® 6800 system. None of the samples tested positive with the VIASURE test and negative with the cobas® test. CONCLUSIONS: The VIASURE test was impaired by a lack of sensitivity and a relatively high number of invalid results. When using the VIASURE test for routine testing, a significant number of COVID-19 positive samples would have been missed. url: https://doi.org/10.1016/j.cmi.2020.06.036 doi: 10.1016/j.cmi.2020.06.036 id: cord-103914-ppgx7mci author: Maughan, Elizabeth F. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 words: 8186.0 sentences: 419.0 pages: flesch: 47.0 cache: ./cache/cord-103914-ppgx7mci.txt txt: ./txt/cord-103914-ppgx7mci.txt summary: Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). abstract: The airway epithelium is a key protective barrier whose integrity is preserved by the self-renewal and differentiation of basal progenitor cells. Epithelial cells are central to the pathogenesis of multiple lung diseases. In chronic diseases, increasing age is a principle risk factor. In acute diseases, such as COVID-19, children suffer less severe symptoms than adults and have a lower rate of mortality. Few studies have explored differences between airway epithelial cells in children and adults to explain this age dependent variation in diseases. Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We find that, while the cellular composition of the paediatric and adult tracheobronchial epithelium is broadly similar, in cell culture, paediatric airway epithelial cells displayed higher colony forming ability, better in vitro growth and outcompeted adult cells in competitive proliferation assays. In RNA sequencing experiments, we observed potentially important differences in airway epithelial gene expression between samples from children and adults. However, genes known to be associated with SARS-CoV-2 infection were not differentially expressed between children and adults. Our results chart cell-intrinsic differences in transcriptional profile and regenerative capacity between proximal airway epithelial cells of children and adults. url: https://doi.org/10.1101/2020.04.20.027144 doi: 10.1101/2020.04.20.027144 id: cord-263224-osf0tkzr author: Maunder, Robert G. title: Long-term Psychological and Occupational Effects of Providing Hospital Healthcare during SARS Outbreak date: 2006-12-17 words: 4091.0 sentences: 171.0 pages: flesch: 42.0 cache: ./cache/cord-263224-osf0tkzr.txt txt: ./txt/cord-263224-osf0tkzr.txt summary: To identify factors that might explain variance in adverse outcome, between-group differences in traumatic stress symptoms, psychological distress, and burnout were tested for the following categories: gender; duration of healthcare experience; job type; regular work during the SARS outbreak in emergency department, intensive care unit, or SARS isolation unit; indicators of the frequency and intensity of contact with SARS patients; and exposure to quarantine. For this analysis, the functional impact of SARS experience was operationalized as the number of adverse outcomes experienced by a person (from 0 to 7) of the following 7 outcomes: posttraumatic stress (IES >26); psychological distress (K10 >16); burnout (MBI-EE >27); decrease in face-to-face patient contact since SARS; decrease in work hours since SARS; increase in smoking, alcohol, or other problematic behavior since SARS; and >4 shifts missed because of stress or illness in the 4 months before the survey. abstract: Healthcare workers (HCWs) found the 2003 outbreak of severe acute respiratory syndrome (SARS) to be stressful, but the long-term impact is not known. From 13 to 26 months after the SARS outbreak, 769 HCWs at 9 Toronto hospitals that treated SARS patients and 4 Hamilton hospitals that did not treat SARS patients completed a survey of several adverse outcomes. Toronto HCWs reported significantly higher levels of burnout (p = 0.019), psychological distress (p<0.001), and posttraumatic stress (p<0.001). Toronto workers were more likely to have reduced patient contact and work hours and to report behavioral consequences of stress. Variance in adverse outcomes was explained by a protective effect of the perceived adequacy of training and support and by a provocative effect of maladaptive coping style and other individual factors. The results reinforce the value of effective staff support and training in preparation for future outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/17326946/ doi: 10.3201/eid1212.060584 id: cord-318786-qd0k8174 author: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 words: 9868.0 sentences: 516.0 pages: flesch: 35.0 cache: ./cache/cord-318786-qd0k8174.txt txt: ./txt/cord-318786-qd0k8174.txt summary: Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. abstract: The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics’ platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses (e.g., hepatitis virus, influenza virus, norovirus, dengue virus, Ebola virus, Zika virus) with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches. url: https://www.ncbi.nlm.nih.gov/pubmed/32842601/ doi: 10.3390/s20174745 id: cord-315604-a6fvsd45 author: Maurya, Santosh K. title: Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 date: 2020-06-01 words: 3219.0 sentences: 198.0 pages: flesch: 55.0 cache: ./cache/cord-315604-a6fvsd45.txt txt: ./txt/cord-315604-a6fvsd45.txt summary: title: Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. HIGHLIGHTS: NSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs. Hydrophobic interaction successfully delineates specific functional groups that may be responsible for the hydrophobic generating effect of these compounds with strong binding affinity against target proteins and may play a highly influencing against SARS-CoV-2 infection All the compounds showed good binding free energy with their respective proteins of SARS-CoV-2. In this study, it has been shown that selected screened compounds have good docking score, high DG binding free energy as well as strong hydrophobic interactions, and follows the Lipinski rule of five. abstract: Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The uncontrolled release of cytokines is seen from the primary stages of symptoms to last acute respiratory distress syndrome (ARDS). Thus, it is necessary to find out safe and effective drugs against this deadly coronavirus as soon as possible. Here, we downloaded the three-dimensional model of NSP10/NSP16 methyltransferase (PDB-ID: 6w6l) and main protease (PDB-ID: 6lu7) of COVID-19. Using these molecular models, we performed virtual screening with our anti-viral, inti-infectious, and anti-protease compounds, which are attractive therapeutics to prevent infection of the COVID-19. We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. We observed that protease complexed with Cyclocytidine hydrochloride (anti-viral and anti-cancer), Trifluridine (anti-viral), Adonitol, and Meropenem (anti-bacterial), and Penciclovir (anti-viral) bound with a good docking score ranging from −6.8 to −5.1 (Kcal/mol). Further, NSP10/NSP16 methyltransferase complexed with Telbivudine, Oxytetracycline dihydrate (anti-viral), Methylgallate (anti-malarial), 2-deoxyglucose and Daphnetin (anti-cancer) from the docking score of −7.0 to −5.7 (Kcal/mol). In conclusion, the selected compounds may be used as a novel therapeutic agent to combat this deadly pandemic disease, SARS-CoV-2 infection, but needs further experimental research. HIGHLIGHTS: NSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs. NSP10/NSP16 methyltransferase and protease interacted with drugs by hydrophobic interactions. Compounds show good DG binging free energy with protein complexes. Ligands were found to follow the Lipinski rule of five. url: https://doi.org/10.1080/10799893.2020.1772298 doi: 10.1080/10799893.2020.1772298 id: cord-317413-w2xfdwea author: Maurya, Vimal K. title: Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection date: 2020-10-19 words: 5654.0 sentences: 285.0 pages: flesch: 30.0 cache: ./cache/cord-317413-w2xfdwea.txt txt: ./txt/cord-317413-w2xfdwea.txt summary: Therefore, we have planned to investigate the active constituents present in these medicinal plants for possible antiviral activity against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor using structure-based drug design method. Besides these active constituents, molecules such as 6-gingerol, glycyrrhetic acid, piperine, sawertiamarine, magnoflorine, scopolamine, atropine, eupafolin, and hyoscyamine also have strong binding affinity towards spike glycoprotein and may be developed potential candidates against SARS-CoV-2 infection (supplementary Figures 1 and 2 ). The active constituents present in selected plants were evaluated for the prediction of potential attachment inhibitors against SARS-CoV-2 via targeting spike glycoprotein as well as its host receptor ACE2. Structure-based drug designing for potential antiviral activity of selected natural products from Ayurveda against SARS-CoV-2 spike glycoprotein and its cellular receptor abstract: SARS-CoV-2 is the etiological agent of COVID-19 and responsible for more than 6 million cases globally, for which no vaccine or antiviral is available. Therefore, this study was planned to investigate the antiviral role of the active constituents against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor. Structure-based drug design approach has been used to elucidate the antiviral activity of active constituents present in traditional medicinal plants from Ayurveda. Further, parameters like drug-likeness, pharmacokinetics, and toxicity were determined to ensure the safety and efficacy of active constituents. Gene network analysis was performed to investigate the pathways altered during COVID-19. The prediction of drug–target interactions was performed to discover novel targets for active constituents. The results suggested that amarogentin, eufoliatorin, α-amyrin, caesalpinins, kutkin, β-sitosterol, and belladonnine are the top-ranked molecules have the highest affinity towards both the spike glycoprotein and ACE2. Most active constituents have passed the criteria of drug-likeness and demonstrated good pharmacokinetic profile with minimum predicted toxicity level. Gene network analysis confirmed that G-protein coupled receptor, protein kinase B signaling, protein secretion, peptidyl-serine phosphorylation, nuclear transport, apoptotic pathway, tumor necrosis factor, regulation of angiotensin level, positive regulation of ion transport, and membrane protein proteolysis were altered during COVID-19. The target prediction analysis revealed that most active constituents target the same pathways which are found to be altered during COVID-19. Collectively, our data encourages the use of active constituents as a potential therapy for COVID-19. However, further studies are ongoing to confirm its efficacy against disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33073699/ doi: 10.1080/07391102.2020.1832577 id: cord-327086-u3l8nr73 author: Mauvais-Jarvis, Franck title: Estradiol, Progesterone, Immunomodulation, and COVID-19 Outcomes date: 2020-07-30 words: 4712.0 sentences: 214.0 pages: flesch: 34.0 cache: ./cache/cord-327086-u3l8nr73.txt txt: ./txt/cord-327086-u3l8nr73.txt summary: Abbreviations: COVID-19, coronavirus disease-2019; E2, 17β-estradiol; ER, estrogen receptor; HCC, hepatocellular carcinoma; IL-1β, interleukin-1β; IL-6, interleukin-6; ISARIC, International Severe Acute Respiratory and Emerging Infections Consortium; MERS-CoV, Middle East respiratory syndrome coronavirus; MHT, menopausal hormone therapy; P4, progesterone; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SERM, selective estrogen receptor modulator; TNF-α, tumor necrosis factor α; Tregs, regulatory T cells. In most experimental human or rodent models, the anti-inflammatory actions of E2 on innate immunity includes the suppression of the production of proinflammatory cytokines, for example, IL-6, IL-1β, and TNF-α, by monocytes and macrophages (a major factor in the COVID-19 cytokine storm) and a strong inhibition of CCL2, thus preventing innate immune cells migration into inflamed areas, particularly neutrophils and monocytes. Taken together, these findings suggest that E2 and related SERMs have 2 potential protective mechanisms of action against SARS-CoV-mediated pneumonias in mice: 1) an estrogen-dependent decrease in the deadly innate immune response and cytokine storm in the lungs, thus preventing respiratory failure, and 2) specific to SERMs, an off-target direct inhibition of SARS-CoV replication and cytopathic effects. abstract: Severe outcomes and death from the novel coronavirus disease 2019 (COVID-19) appear to be characterized by an exaggerated immune response with hypercytokinemia leading to inflammatory infiltration of the lungs and acute respiratory distress syndrome. Risk of severe COVID-19 outcomes is consistently lower in women than men worldwide, suggesting that female biological sex is instrumental in protection. This mini-review discusses the immunomodulatory and anti-inflammatory actions of high physiological concentrations of the steroids 17β-estradiol (E2) and progesterone (P4). We review how E2 and P4 favor a state of decreased innate immune inflammatory response while enhancing immune tolerance and antibody production. We discuss how the combination of E2 and P4 may improve the immune dysregulation that leads to the COVID-19 cytokine storm. It is intended to stimulate novel consideration of the biological forces that are protective in women compared to men, and to therapeutically harness these factors to mitigate COVID-19 morbidity and mortality. url: https://doi.org/10.1210/endocr/bqaa127 doi: 10.1210/endocr/bqaa127 id: cord-331193-33cyvidx author: Mawhinney, Jamie A title: Neurotropism of SARS-CoV-2: COVID-19 presenting with an acute manic episode date: 2020-06-14 words: 2512.0 sentences: 161.0 pages: flesch: 50.0 cache: ./cache/cord-331193-33cyvidx.txt txt: ./txt/cord-331193-33cyvidx.txt summary: Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. [9] [10] [11] [12] This article outlines a case of COVID-19 presenting with an acute manic episode necessitating emergency intubation and discusses potential mechanisms for the development of neuropsychiatric disease. ► The neuroinvasive potential of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (neurotropism) has been reported, but the pathophysiology remains unclear with uncertainty over its long-term consequences. abstract: A 41-year-old man with no significant medical history presented with acute behavioural disruption on the background of a 1-day history of severe headache and a 10-day history of dry cough and fever. He was sexually disinhibited with pressured speech and grandiose ideas. His behaviour worsened, necessitating heavy sedation and transfer to intensive care for mechanical ventilation despite no respiratory indication. Investigations confirmed that he was positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neuroimaging and a lumbar puncture were normal. Initial screening for SARS-CoV-2 in the cerebrospinal fluid was negative although no validated assay was available. The patient’s mental state remained abnormal following stepdown from intensive care. Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. url: https://doi.org/10.1136/bcr-2020-236123 doi: 10.1136/bcr-2020-236123 id: cord-259907-yqmi0cqy author: Maxwell, Cynthia title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 date: 2009-10-31 words: 3419.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-259907-yqmi0cqy.txt txt: ./txt/cord-259907-yqmi0cqy.txt summary: title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 Labour triage and antenatal hospital admission Actions • Assessment is made as to whether the patient has suspected or probable SARS [1, 14] • Upon arrival in the labour and delivery triage unit, pregnant patients presenting with fever N38°C and respiratory symptoms and one of the associated symptoms (cough, unexplained hypoxia, shortness of breath, or dyspnea) and history of an exposure to an individual with probable SARS are immediately transferred to the designated isolation room, which is equipped with negative pressure ventilation. • Parents and family are counselled to look for symptoms and signs of SARS in the mother and newborn, especially in the first 10 days following delivery, and to report to any findings to the health care team Summary SARS, a life-threatening respiratory illness caused by a novel coronavirus, was responsible for a worldwide outbreak in 2003. abstract: Abstract Objective This document summarizes the limited experience of SARS in pregnancy and suggests guidelines for management. Outcomes Cases reported from Asia suggest that maternal and fetal outcomes are worsened by SARS during pregnancy. Evidence Medline was searched for relevant articles published in English from 2000 to 2007. Case reports were reviewed and expert opinion sought. Values Recommendations were made according to the guidelines developed by the Canadian Task Force on Preventive Health Care. url: https://www.ncbi.nlm.nih.gov/pubmed/19780222/ doi: 10.1016/j.ijgo.2009.05.006 id: cord-332610-t99l3zii author: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 words: 9596.0 sentences: 469.0 pages: flesch: 52.0 cache: ./cache/cord-332610-t99l3zii.txt txt: ./txt/cord-332610-t99l3zii.txt summary: The potential for new diseases to emerge in the United States was there, and it took just a few years until this happened, catching the medical and public health communities by surprise. The issue at the time was whether legionnaires disease and toxic shock syndrome were anomalies, whether the assumption of the conquest of infectious diseases had clearly been erroneous, or whether these two outbreaks were harbingers of a new stage in ''epidemiologic history''a historical period during which emerging infections would become common and would catch the attention of the public, the public health community, the medical community, and government agencies. Severe acute respiratory syndrome (SARS) proved to be of great import in both the public awareness of emerging infectious diseases and in the testing and real-time construction of both domestic and international systems of public health surveillance and response. abstract: Emerging infectious diseases are diseases that are either new, are newly recognized, or are increasing in prevalence in new areas. Resurgent diseases are also usually grouped in this category, as is antimicrobial resistance. These diseases have been given formal recognition in the past two decades, although a historical outlook demonstrates that the phenomenon has probably been persistent, although largely undetected, through recorded history. Emergence has accelerated recently, driven by factors such as demographic change, land use change, increased rapidity and frequency of intercontinental transportation, and other mostly social trends. Continued infectious disease emergence poses, and will continue to pose, significant challenges for public health and for basic science. url: https://api.elsevier.com/content/article/pii/B9780123739605004536 doi: 10.1016/b978-012373960-5.00453-6 id: cord-265855-zf52vl11 author: Mayor-Ibarguren, Ander title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 words: 5324.0 sentences: 283.0 pages: flesch: 47.0 cache: ./cache/cord-265855-zf52vl11.txt txt: ./txt/cord-265855-zf52vl11.txt summary: Zinc deficiency may increase ACE-2 receptor activity on type 2 pneumocytes and other cells that are infected by SARS-COV-2, mainly in the lower respiratory tract. Although there are no specific data regarding zinc in this pathway for SARS-CoV-2, zinc may limit infection through upregulation of IFN-alpha production and an increase in its antiviral activity (77, 78) . Thus, patients with IL-6-174 GG polymorphism (C-carriers) may be susceptible to developing a severe infection due to SARS-CoV-2, leading to an increase in IL-6 levels that produce a cytokine storm related to impaired zinc homeostasis. We believe there is enough evidence to further investigate how zinc status or homeostasis is involved in the pathogenesis of severe illness produced by SARS-CoV-2 infection, and its potential role as an active treatment should be assessed in clinical trials. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32754165/ doi: 10.3389/fimmu.2020.01736 id: cord-254094-ed1epul1 author: Mayoral, Eduardo Pérez-Campos title: Factors related to asymptomatic or severe COVID-19 infection date: 2020-09-24 words: 1665.0 sentences: 98.0 pages: flesch: 48.0 cache: ./cache/cord-254094-ed1epul1.txt txt: ./txt/cord-254094-ed1epul1.txt summary: In particular, we refer to the TMPRSS2 expression profile, balance of androgen and estrogen, blood group-A and/or B, nonsynonymous mutations in ORF3, and proteins NS7b and NS8 in SARS-CoV-2. In the first months of the COVID-19 pandemic, most authors focused their attention on features such as the high expression of ACE2 in the salivary glands in asymptomatic infection [4] , and the maturity and binding capacity of ACE2 [5, 6] . A higher 2D:4D ratio is associated with COVID-19 severity in men [14] , this means that sex hormones play a role in protection, thus, causing women to develop less serious complications or an asymptomatic COVID-19 Infection [12] . An in-depth study of the factors associated with asymptomatic subjects can provide information to limit severe COVID-19 as much as possible. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated abstract: The factors that may contribute to a COVID-19 patient remaining in the asymptomatic stage, or to the infection evolving into the more serious stages are examined. In particular, we refer to the TMPRSS2 expression profile, balance of androgen and estrogen, blood group-A and/or B, nonsynonymous mutations in ORF3, and proteins NS7b and NS8 in SARS-CoV-2. Also, we review other factors related to the susceptibility and pathogenicity of SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0306987720327328 doi: 10.1016/j.mehy.2020.110296 id: cord-296388-ayfdsn07 author: Maziarz, Mariusz title: Agent‐based modelling for SARS‐CoV‐2 epidemic prediction and intervention assessment: A methodological appraisal date: 2020-08-21 words: 4560.0 sentences: 240.0 pages: flesch: 41.0 cache: ./cache/cord-296388-ayfdsn07.txt txt: ./txt/cord-296388-ayfdsn07.txt summary: CONCLUSIONS: Given this, we claim that the best epidemiological ABMs are models of actual mechanisms and deliver both mechanistic and difference‐making evidence. While the 2009 swine flu pandemic was the motivation for constructing AceMod, the model was not intended to accurately represent the outbreak of the H1N1 strain, but rather as a generalized framework for studying how an infectious disease spreads through the social interactions of Australians. In cases like the current pandemic, effective interventions may best be aimed at the societal level and therefore mechanistic models that integrate social factors, human behaviour and biological aspects (something that the ABM discussed here attempts to do) are arguably best suited for providing understanding and suggesting policy decisions. 10 Our claim that AceMod calibrated for SARS-CoV-2 bears similarity to the actual mechanism of the epidemic depends on the accuracy of the empirical results used as an input for this model. Agent-based modelling for SARS-CoV-2 epidemic prediction and intervention assessment: A methodological appraisal abstract: BACKGROUND: Our purpose is to assess epidemiological agent‐based models—or ABMs—of the SARS‐CoV‐2 pandemic methodologically. The rapid spread of the outbreak requires fast‐paced decision‐making regarding mitigation measures. However, the evidence for the efficacy of non‐pharmaceutical interventions such as imposed social distancing and school or workplace closures is scarce: few observational studies use quasi‐experimental research designs, and conducting randomized controlled trials seems infeasible. Additionally, evidence from the previous coronavirus outbreaks of SARS and MERS lacks external validity, given the significant differences in contagiousness of those pathogens relative to SARS‐CoV‐2. To address the pressing policy questions that have emerged as a result of COVID‐19, epidemiologists have produced numerous models that range from simple compartmental models to highly advanced agent‐based models. These models have been criticized for involving simplifications and lacking empirical support for their assumptions. METHODS: To address these voices and methodologically appraise epidemiological ABMs, we consider AceMod (the model of the COVID‐19 epidemic in Australia) as a case study of the modelling practice. RESULTS: Our example shows that, although epidemiological ABMs involve simplifications of various sorts, the key characteristics of social interactions and the spread of SARS‐CoV‐2 are represented sufficiently accurately. This is the case because these modellers treat empirical results as inputs for constructing modelling assumptions and rules that the agents follow; and they use calibration to assert the adequacy to benchmark variables. CONCLUSIONS: Given this, we claim that the best epidemiological ABMs are models of actual mechanisms and deliver both mechanistic and difference‐making evidence. Consequently, they may also adequately describe the effects of possible interventions. Finally, we discuss the limitations of ABMs and put forward policy recommendations. url: https://www.ncbi.nlm.nih.gov/pubmed/32820573/ doi: 10.1111/jep.13459 id: cord-320127-55h4hhm3 author: Mazingi, Dennis title: Mitigating the impact of COVID-19 on children''s surgery in Africa date: 2020-06-10 words: 2671.0 sentences: 159.0 pages: flesch: 46.0 cache: ./cache/cord-320127-55h4hhm3.txt txt: ./txt/cord-320127-55h4hhm3.txt summary: 13 The COVID-19 pandemic has placed unprecedented strain on health services around the world, and paediatric surgical services are no exception. During the 2003 severe acute respiratory syndrome-related coronavirus (SARS-CoV)-1 outbreak in Toronto, stringent restrictions on non-essential surgical services were thought to have aggravated precipitous declines in surgical volume, with only small increases in surge capacity for the outbreak. 42 Paediatric care in Africa is typically characterised by significant involvement by guardians and other family members who support the child during hospital admission, assist the overburdened healthcare workforce and act as care advocates. A recent global review of paediatric surgical workforce density showed that a minimum of four paediatric surgeons per million children under 15 years of age would be required to achieve a survival of >80% for a group of four bellwether paediatric surgical conditions. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review abstract: nan url: https://doi.org/10.1136/bmjgh-2020-003016 doi: 10.1136/bmjgh-2020-003016 id: cord-256109-dkp0fwe3 author: Mazzulli, Tony title: Severe Acute Respiratory Syndrome–associated Coronavirus in Lung Tissue date: 2004-01-17 words: 2554.0 sentences: 115.0 pages: flesch: 53.0 cache: ./cache/cord-256109-dkp0fwe3.txt txt: ./txt/cord-256109-dkp0fwe3.txt summary: Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). All patients who met the current World Health Organization case definition of probable SARS and who underwent a postmortem examination in Canada during the March-April 2003 outbreak were included in this study. The clinical description and RT-PCR results for the 11 patients with probable SARS from whom postmortem lung tissue samples were examined are summarized in Table 1 . By using a standardized RT-PCR assay, SARS-CoV has been unequivocally identified in the lung tissue of all patients who died with probable SARS but not in any of the controls. abstract: Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). We used a standardized reverse transcription-polymerase chain reaction assay to detect SARS-CoV in lung samples obtained from well-characterized patients who died of SARS and from those who died of other reasons. SARS-CoV was detected in all 22 postmortem lung tissues (to 10(9) viral copies/g) from 11 patients with probable SARS but was not detected in any of the 23 lung control samples (sample analysis was blinded). The sensitivity and specificity (95% confidence interval) were 100% (84.6% to 100%) and 100% (85.1% to 100%), respectively. Viral loads were significantly associated with a shorter course of illness but not with the use of ribavirin or steroids. CoV was consistently identified in the lungs of all patients who died of SARS but not in control patients, supporting a primary role for CoV in deaths. url: https://www.ncbi.nlm.nih.gov/pubmed/15078592/ doi: 10.3201/eid1001.030404 id: cord-261952-xq6qney7 author: Mazzulli, Tony title: Proteomics and Severe Acute Respiratory Syndrome (SARS): Emerging Technology Meets Emerging Pathogen date: 2005-01-01 words: 1471.0 sentences: 75.0 pages: flesch: 49.0 cache: ./cache/cord-261952-xq6qney7.txt txt: ./txt/cord-261952-xq6qney7.txt summary: This approach was hampered, however, by the fact that clinical and laboratory features did not distinguish patients with SARS from those with other respiratory illnesses and that there was no reliable rapid diagnostic test (1) (2) (3) . Characterizing the proteins that make up SELDI-TOF profiles in this manner not only provides insight into the pathophysiology of the disease, but may also lead to the development of more direct diagnostic tools and novel therapeutic targets relevant to SARS-CoV. In addition, in both studies (7, 8 ) , the patients with SARS were well characterized in terms of timing of specimen collection and severity of disease. (8 ) chose to apply SELDI-TOF to the diagnosis of SARS, there are many other, more common infectious diseases, such as influenza, that would also benefit from more rapid and reliable diagnostic and prognostic tests. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15613703/ doi: 10.1373/clinchem.2004.041574 id: cord-292742-mio4przi author: McAloose, Denise title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 words: 6364.0 sentences: 309.0 pages: flesch: 47.0 cache: ./cache/cord-292742-mio4przi.txt txt: ./txt/cord-292742-mio4przi.txt summary: KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4). abstract: Despite numerous barriers to transmission, zoonoses are the major cause of emerging infectious diseases in humans. Among these, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and ebolaviruses have killed thousands; the human immunodeficiency virus (HIV) has killed millions. Zoonoses and human-to-animal cross-species transmission are driven by human actions and have important management, conservation, and public health implications. The current SARS-CoV-2 pandemic, which presumably originated from an animal reservoir, has killed more than half a million people around the world and cases continue to rise. In March 2020, New York City was a global epicenter for SARS-CoV-2 infections. During this time, four tigers and three lions at the Bronx Zoo, NY, developed mild, abnormal respiratory signs. We detected SARS-CoV-2 RNA in respiratory secretions and/or feces from all seven animals, live virus in three, and colocalized viral RNA with cellular damage in one. We produced nine whole SARS-CoV-2 genomes from the animals and keepers and identified different SARS-CoV-2 genotypes in the tigers and lions. Epidemiologic and genomic data indicated human-to-tiger transmission. These were the first confirmed cases of natural SARS-CoV-2 animal infections in the United States and the first in nondomestic species in the world. We highlight disease transmission at a nontraditional interface and provide information that contributes to understanding SARS-CoV-2 transmission across species. url: https://doi.org/10.1128/mbio.02220-20 doi: 10.1128/mbio.02220-20 id: cord-313795-jr3n3uo9 author: McAuley, Julie L. title: Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date: 2020-11-02 words: 1411.0 sentences: 85.0 pages: flesch: 56.0 cache: ./cache/cord-313795-jr3n3uo9.txt txt: ./txt/cord-313795-jr3n3uo9.txt summary: We investigated whether liquid chalk is an antiseptic against highly pathogenic human viruses including, SARS-CoV-2, influenza virus and noroviruses. We observed that addition of chalk before or after virus contact lead to a significant reduction on recovery of infectious SARS-CoV-2 and influenza but had little impact on norovirus. To further our study, we also tested the antiviral effect of Liquid Chalk against another 155 highly infectious and pathogenic respiratory viral pathogen IAV. 157 As can be observed in Figure 2 , all four Liquid Chalk products were effective in restricting the 158 recovery of IAV compared to SARS-CoV-2. transmission of SARS-CoV-2 (the 52 causative agent of the COVID-19 pandemic), influenza A virus (H1N1) (IAV) and norovirus, 53 using the surrogate model of mouse norovirus As a comparator, we also investigated the ability of Liquid Chalk to inactivate another 178 highly infectious viral pathogen, norovirus. abstract: The COVID-19 pandemic has impacted and enforced significant restrictions within our societies, including the attendance of the public and professional athletes in gyms. Liquid chalk is a commonly used accessories in gyms and is comprised of magnesium carbonate and alcohol that quickly evaporates on the hands to leave a layer of dry chalk. We investigated whether liquid chalk is an antiseptic against highly pathogenic human viruses including, SARS-CoV-2, influenza virus and noroviruses. Chalk was applied before or after virus inoculum and recovery of infectious virus was determined to mimic the use in the gym. We observed that addition of chalk before or after virus contact lead to a significant reduction on recovery of infectious SARS-CoV-2 and influenza but had little impact on norovirus. These observations suggest that the use and application of liquid chalk can be an effective and suitable antiseptic for major sporting events, such as the Olympic Games. url: https://doi.org/10.1101/2020.11.02.364661 doi: 10.1101/2020.11.02.364661 id: cord-290993-bsnja161 author: McAuliffe, Josephine title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 words: 4548.0 sentences: 203.0 pages: flesch: 52.0 cache: ./cache/cord-290993-bsnja161.txt txt: ./txt/cord-290993-bsnja161.txt summary: Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. abstract: SARS coronavirus (SARS-CoV) administered intranasally and intratracheally to rhesus, cynomolgus and African Green monkeys (AGM) replicated in the respiratory tract but did not induce illness. The titer of serum neutralizing antibodies correlated with the level of virus replication in the respiratory tract (AGM>cynomolgus>rhesus). Moderate to high titers of SARS-CoV with associated interstitial pneumonitis were detected in the lungs of AGMs on day 2 and were resolving by day 4 post-infection. Following challenge of AGMs 2 months later, virus replication was highly restricted and there was no evidence of enhanced disease. These species will be useful for the evaluation of the immunogenicity of candidate vaccines, but the lack of apparent clinical illness in all three species, variability from animal to animal in level of viral replication, and rapid clearance of virus and pneumonitis in AGMs must be taken into account by investigators considering the use of these species in efficacy and challenge studies. url: https://www.ncbi.nlm.nih.gov/pubmed/15527829/ doi: 10.1016/j.virol.2004.09.030 id: cord-256737-ptjng78b author: McBride, Corrin E. title: Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date: 2010-09-01 words: 8233.0 sentences: 414.0 pages: flesch: 58.0 cache: ./cache/cord-256737-ptjng78b.txt txt: ./txt/cord-256737-ptjng78b.txt summary: The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step. abstract: Coronaviruses are enveloped RNA viruses that generally cause mild disease in humans. However, the recently emerged coronavirus that caused severe acute respiratory syndrome (SARS-CoV) is the most pathogenic human coronavirus discovered to date. The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Coronavirus S proteins are palmitoylated, which may affect function. Here, we created a non-palmitoylated SARS-CoV S protein by mutating all nine cytoplasmic cysteine residues. Palmitoylation of SARS-CoV S was required for partitioning into detergent-resistant membranes and for cell-cell fusion. Surprisingly, however, palmitoylation of S was not required for interaction with SARS-CoV M protein. This contrasts with the requirement for palmitoylation of mouse hepatitis virus S protein for interaction with M protein, and may point to important differences in assembly and infectivity of these two coronaviruses. url: https://doi.org/10.1016/j.virol.2010.05.031 doi: 10.1016/j.virol.2010.05.031 id: cord-321013-8pkrg0mx author: McBride, Ruth title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 words: 10761.0 sentences: 476.0 pages: flesch: 44.0 cache: ./cache/cord-321013-8pkrg0mx.txt txt: ./txt/cord-321013-8pkrg0mx.txt summary: The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. Recent studies have confirmed that N is a multifunctional protein. The aim of this review is to highlight the properties and functions of the N protein, with specific reference to (i) the topology; (ii) the intracellular localization and (iii) the functions of the protein. url: https://doi.org/10.3390/v6082991 doi: 10.3390/v6082991 id: cord-319580-awtp0mpg author: McCartney, Stephen A. title: Obesity as a contributor to immunopathology in pregnant and non‐pregnant adults with COVID‐19 date: 2020-08-11 words: 3709.0 sentences: 221.0 pages: flesch: 46.0 cache: ./cache/cord-319580-awtp0mpg.txt txt: ./txt/cord-319580-awtp0mpg.txt summary: The synergistic effects of obesity‐associated delays in immune control of COVID‐19 with mechanical stress of increased adipose tissue may contribute to a greater risk of pulmonary compromise in obese pregnant women. The expression of ACE2 by adipocytes and immune cells also suggests the possibility that adipose tissue may represent a potential reservoir for viral infection and may lead to increased viral burden or persistence; however, no studies to date have demonstrated that adipocytes can be directly infected with SARS-CoV-2. Maternal obesity has emerged as a key risk factor increasing susceptibility of pregnant women to severe COVID-19 disease. There is also an urgent need to focus research on how risk factors, like obesity, alter the immune response to SARS-CoV-2 and influence disease pathogenesis of COVID-19 (Box 1). What is the mechanism of increased risk for severe COVID-19 disease in obese nonpregnant and pregnant women? abstract: The ongoing coronavirus disease 2019 (COVID‐19) pandemic has led to a global public health emergency with the need to identify vulnerable populations who may benefit from increased screening and healthcare resources. Initial data suggests that overall, pregnancy is not a significant risk factor for severe coronavirus disease 2019 (COVID‐19). However, case series have suggested that maternal obesity is one of the most important co‐morbidities associated with more severe disease. In obese individuals, suppressors of cytokine signaling are upregulated and type I and III interferon responses are delayed and blunted leading to ineffective viral clearance. Obesity is also associated with changes in systemic immunity involving a wide range of immune cells and mechanisms that lead to low‐grade chronic inflammation, which can compromise antiviral immunity. Macrophage activation in adipose tissue can produce low levels of pro‐inflammatory cytokines (TNF‐α, IL‐1β, IL‐6). Further, adipocyte secretion of leptin is pro‐inflammatory and high circulating levels of leptin have been associated with mortality in patients with acute respiratory distress syndrome. The synergistic effects of obesity‐associated delays in immune control of COVID‐19 with mechanical stress of increased adipose tissue may contribute to a greater risk of pulmonary compromise in obese pregnant women. In this review, we bring together data regarding obesity as a key co‐morbidity for COVID‐19 in pregnancy with known changes in the antiviral immune response associated with obesity. We also describe how the global burden of obesity among reproductive age women has serious public health implications for COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32779790/ doi: 10.1111/aji.13320 id: cord-280062-1qrav1d5 author: McClenaghan, Elliot title: The global impact of SARS-CoV-2 in 181 people with cystic fibrosis date: 2020-11-04 words: 1707.0 sentences: 95.0 pages: flesch: 62.0 cache: ./cache/cord-280062-1qrav1d5.txt txt: ./txt/cord-280062-1qrav1d5.txt summary: Whilst outcomes in this large cohort are better than initially feared overall, possibly due to a protective effect of the relatively younger age of the CF population compared to other chronic conditions, SARS-CoV-2 is not a benign disease for all people in this patient group. The characteristics of the 149 people in the non-transplant cohort were; median age 24 years (range 0-74 years), 48% male, 36% were homozygous and 37% were heterozygous for F508del, 24% had CFrelated diabetes (CFRD), 43% were taking CFTR modulator therapy, and median best FEV 1 prior to infection was 73% predicted, (range 18-123%) ( Table 1) . One of the seven deaths, in a non-transplant patient, was reported by the clinical team as being related to advanced cystic fibrosis, not SARS-CoV-2. In the non-transplant cohort, 4 deaths were recorded, 2 of which had a best FEV1 the year prior to infection of <40% predicted and 2 with 40-70% predicted. abstract: With the growing SARS-CoV-2 pandemic, we need to better understand its impact in specific patient groups like those with Cystic Fibrosis (CF). We report on 181 people with CF (32 post-transplant) from 19 countries diagnosed with SARS-CoV-2 prior to 13 June 2020. Infection with SARS-CoV-2 appears to exhibit a similar spectrum of outcomes to that seen in the general population, with 11 people admitted to intensive care (7 post-transplant), and 7 deaths (3 post-transplant). A more severe clinical course may be associated with older age, CF-related diabetes, lower lung function in the year prior to infection, and having received an organ transplant. Whilst outcomes in this large cohort are better than initially feared overall, possibly due to a protective effect of the relatively younger age of the CF population compared to other chronic conditions, SARS-CoV-2 is not a benign disease for all people in this patient group. url: https://doi.org/10.1016/j.jcf.2020.10.003 doi: 10.1016/j.jcf.2020.10.003 id: cord-354453-uze6ze8o author: McCloskey, Brian title: SARS to novel coronavirus – old lessons and new lessons date: 2020-02-05 words: 3153.0 sentences: 116.0 pages: flesch: 47.0 cache: ./cache/cord-354453-uze6ze8o.txt txt: ./txt/cord-354453-uze6ze8o.txt summary: By 26 January also, almost 50 million people in Wuhan and neighbouring cities had effectively been placed in quarantine while the WHO had determined that the event should not yet be declared as a Public Health Emergency of International Concern (PHEIC) [2] and had recommended no specific travel restrictions. There was extensive criticism of China for its perceived failure to share information about the emerging SARS infection early enough in the outbreak to allow countries to prepare and respond. The rapid sharing of information in this outbreak and the speed of the coordinated response both in the country and internationally suggest that lessons have been learned from SARS that improve global capacity. The global media response to the unfolding events has been relatively balanced and informed but the nuances of the evolving situation have not been critically examined in partnership with the media and as a result the public perception of the risk may be exaggeratedalthough it of course remains possible that the outbreak will develop in a way that matches up to the perceived risk. abstract: The response to the novel coronavirus outbreak in China suggests that many of the lessons from the 2003 SARS epidemic have been implemented and the response improved as a consequence. Nevertheless some questions remain and not all lessons have been successful. The national and international response demonstrates the complex link between public health, science and politics when an outbreak threatens to impact on global economies and reputations. The unprecedented measures implemented in China are a bold attempt to control the outbreak – we need to understand their effectiveness to balance costs and benefits for similar events in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32019614/ doi: 10.1017/s0950268820000254 id: cord-279334-j0i9ozsz author: McCreary, Erin K title: Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date: 2020-03-23 words: 8269.0 sentences: 363.0 pages: flesch: 44.0 cache: ./cache/cord-279334-j0i9ozsz.txt txt: ./txt/cord-279334-j0i9ozsz.txt summary: Most existing preclinical and clinical data on antiviral therapy are derived from other viruses, including SARS-CoV-1 (first reported in 2003), Middle East respiratory syndrome coronavirus ([MERS-CoV] first reported in 2012), and non-coronaviruses (eg, Ebola virus disease). The use of 500 mg of chloroquine by mouth twice daily as the reference for efficacy is rational given initial reports from China [16] , but it is important to note that this dosing still requires validation, and the improved R LTEC values reported are largely driven by the finding that hydroxychloroquine was 7.6 times more potent than chloroquine in vitro. Given this finding, the small numbers in this study, the lack of clinical outcomes presented, the potential for additive toxicity with hydroxychloroquine and azithromycin, and the desperate need to practice good antimicrobial stewardship during the COVID-19 pandemic, we would caution clinicians against using these data to support combination therapy. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread across the globe resulting in a pandemic. At the time of this review, COVID-19 has been diagnosed in more than 200 000 patients and associated with over 8000 deaths (Centers for Disease Control and Prevention, World Health Organization). On behalf of the Society of Infectious Diseases Pharmacists, we herein summarize the current evidence as of March 18, 2020 to provide guidance on potential COVID-19 treatment options. It is important to caution readers that new data emerges daily regarding clinical characteristics, treatment options, and outcomes for COVID-19. Optimized supportive care remains the mainstay of therapy, and the clinical efficacy for the subsequent agents is still under investigation. Antimicrobial stewardship programs, including infectious diseases pharmacists and physicians, are at the forefront of COVID-19 emergency preparedness. We encourage all readers to continue to assess clinical data as it emerges and share their experience within our community in a well-controlled, adequately powered fashion. url: https://doi.org/10.1093/ofid/ofaa105 doi: 10.1093/ofid/ofaa105 id: cord-342857-vj6sw2ne author: McCullough, Peter A. title: Pathophysiological Basis and Rationale for Early Outpatient Treatment of SARS-CoV-2 (COVID-19) Infection date: 2020-08-07 words: 2215.0 sentences: 120.0 pages: flesch: 39.0 cache: ./cache/cord-342857-vj6sw2ne.txt txt: ./txt/cord-342857-vj6sw2ne.txt summary: In the absence of clinical trial results, physicians must use what has been learned about the pathophysiology of SARS-CoV-2 infection in determining early outpatient treatment of the illness with the aim of preventing hospitalization or death. Thus, in the context of present knowledge, given the severity of the outcomes and the relative availability, cost, and toxicity of the therapy, each physician and patient must make a choice: watchful waiting in self-quarantine or empiric treatment with the aim of reducing hospitalization and death. (10) For the ambulatory patient with recognized early signs and symptoms of COVID-19, often with nasal real-time reverse transcription or oral antigen testing pending, the following four principles could be deployed in a layered and escalating manner depending on clinical manifestations of COVID-19 like illness(11) and confirmed infection: 1) reduction of reinoculation, 2) combination antiviral therapy, 3) immunomodulation, 4) antiplatelet/antithrombotic therapy. abstract: Approximately 9 months of the SARS-CoV-2 virus spreading across the globe has led to widespread COVID-19 acute hospitalizations and death. The rapidity and highly communicable nature of the SARS-CoV-2 outbreak has hampered the design and execution of definitive randomized, controlled trials of therapy outside of the clinic or hospital. In the absence of clinical trial results, physicians must use what has been learned about the pathophysiology of SARS-CoV-2 infection in determining early outpatient treatment of the illness with the aim of preventing hospitalization or death. This paper outlines key pathophysiological principles that relate to the patient with early infection treated at home. Therapeutic approaches based on these principles include: 1) reduction of reinoculation, 2) combination antiviral therapy, 3) immunomodulation, 4) antiplatelet/antithrombotic therapy 5) administration of oxygen, monitoring, and telemedicine. Future randomized trials testing the principles and agents discussed in this paper will undoubtedly refine and clarify their individual roles, however we emphasize the immediate need for management guidance in the setting of widespread hospital resource consumption, morbidity, and mortality. url: https://doi.org/10.1016/j.amjmed.2020.07.003 doi: 10.1016/j.amjmed.2020.07.003 id: cord-255446-wddj6hrv author: McDade, T. W. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-06-02 words: 3121.0 sentences: 234.0 pages: flesch: 59.0 cache: ./cache/cord-255446-wddj6hrv.txt txt: ./txt/cord-255446-wddj6hrv.txt summary: To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. 7 We adapted this ELISA to measure IgG antibodies to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in DBS samples. . https://doi.org/10.1101/2020.06.01.20119602 doi: medRxiv preprint Participants who previously tested positive for SARS-CoV-2 virus were recruited from the community through direct contact. Seroprevalence in 202 samples collected from the community, which includes health care workers and first responders, none of which were confirmed SARS-CoV-2 viral positive. abstract: Objective: Serological testing is needed to investigate the extent of transmission of SARS-CoV-2 from front-line essential workers to their household members. However, the requirement for serum/plasma limits serological testing to clinical settings where it is feasible to collect and process venous blood. To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Methods: An ELISA to the receptor binding domain of the SARS-CoV-2 spike protein was optimized to quantify IgG antibodies in DBS. Samples were self-collected from a community sample of 232 participants enriched with health care workers, including 30 known COVID-19 cases and their household members. Results: Among 30 individuals sharing a household with a virus-confirmed case of COVID-19, 80% were seropositive. Of 202 community individuals without prior confirmed acute COVID-19 diagnoses, 36% were seropositive. Of documented convalescent COVID-19 cases from the community, 29 of 30 (97%) were seropositive for IgG antibodies to the receptor binding domain. Conclusion: DBS ELISA provides a minimally-invasive alternative to venous blood collection. Early analysis suggests a high rate of transmission among household members. High rates of seroconversion were also noted following recovery from infection. Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. url: https://doi.org/10.1101/2020.06.01.20119602 doi: 10.1101/2020.06.01.20119602 id: cord-346089-u31n0qxa author: McDade, Thomas W. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-08-14 words: 2232.0 sentences: 140.0 pages: flesch: 52.0 cache: ./cache/cord-346089-u31n0qxa.txt txt: ./txt/cord-346089-u31n0qxa.txt summary: title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. In addition, we demonstrate the feasibility and utility of quantifying SARS-CoV-2 antibodies in self-collected DBS with results from a community-based sample enriched with health care workers. We have validated a DBS assay to facilitate large-scale serological testing of SARS-CoV-2 IgG antibodies, and results from our feasibility study document a high rate of household transmission. abstract: OBJECTIVE: Serological testing is needed to investigate the extent of transmission of SARS-CoV-2 from front-line essential workers to their household members. However, the requirement for serum/plasma limits serological testing to clinical settings where it is feasible to collect and process venous blood. To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). We describe assay performance and demonstrate its utility for remote sampling with results from a community-based study. METHODS: An ELISA to the receptor binding domain of the SARS-CoV-2 spike protein was optimized to quantify IgG antibodies in DBS. Samples were self-collected from a community sample of 232 participants enriched with health care workers, including 30 known COVID-19 cases and their household members. RESULTS: Among 30 individuals sharing a household with a virus-confirmed case of COVID-19, 80% were seropositive. Of 202 community individuals without prior confirmed acute COVID-19 diagnoses, 36% were seropositive. Of documented convalescent COVID-19 cases from the community, 29 of 30 (97%) were seropositive for IgG antibodies to the receptor binding domain. CONCLUSION: DBS ELISA provides a minimally-invasive alternative to venous blood collection. Early analysis suggests a high rate of transmission among household members. High rates of seroconversion were also noted following recovery from infection. Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. url: https://doi.org/10.1371/journal.pone.0237833 doi: 10.1371/journal.pone.0237833 id: cord-350029-1y5ex4d5 author: McDade, Thomas W. title: Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date: 2020-08-09 words: 2690.0 sentences: 129.0 pages: flesch: 43.0 cache: ./cache/cord-350029-1y5ex4d5.txt txt: ./txt/cord-350029-1y5ex4d5.txt summary: Serological testing is a complementary approach that detects the presence of antibodies against SARS-CoV-2 in blood samples from exposed individuals (World Health Organization, 2020). If sufficient time has passed since the initial infection, the presence of IgM antibodies against SARS-CoV-2 antigens can be used to confirm a clinical case of COVID-19. In developing a low-cost ELISA for SARS-CoV-2 antibodies, our hope is that others can draw on the longstanding tradition of methodological innovation in human biology to promote community-based research on COVID-19. Human biologists are also well-positioned to consider a life course perspective on variation in outcomes in response to SARS-CoV-2 infection. Human biologists are uniquely positioned to make important contributions to our understanding of COVID-19, and methods that facilitate research in community-based settings globally will be central to that effort. Enzyme immunoassay for SARS-CoV-2 antibodies in dried blood spot samples: A minimally-invasive approach to facilitate community-and population-based screening abstract: nan url: https://doi.org/10.1002/ajhb.23483 doi: 10.1002/ajhb.23483 id: cord-262020-ygl8xlhk author: McDermott, Aoibhinn title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection date: 2020-05-16 words: 300.0 sentences: 30.0 pages: flesch: 55.0 cache: ./cache/cord-262020-ygl8xlhk.txt txt: ./txt/cord-262020-ygl8xlhk.txt summary: authors: McDermott, Aoibhinn; O''Kelly, John; de Barra, Eoghan; Fitzpatrick, Fidelma; Little, Dilly M.; Davis, Niall F. title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection To date, many urological centres have prioritised their patients for urgent surgical intervention because of a reduction in operating theatre availability and the risk of hospital-acquired SARS-CoV-2 infection [1, 2] . Here we present our perioperative outcomes for patients undergoing urological surgery during the initial stage of the SARS-CoV-2 pandemic in Ireland (between March 16 and May 1, 2020, inclusive). Our hospital has an onsite microbiology laboratory that performs daily SARS-CoV-2 realJ o u r n a l P r e -p r o o f Elective surgery was prioritised according to recent European guidelines and patients were then placed on a centralised departmental theatre waiting list [1] . abstract: nan url: https://doi.org/10.1016/j.eururo.2020.05.012 doi: 10.1016/j.eururo.2020.05.012 id: cord-286472-pqtem19t author: McFee, R.B. title: MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date: 2020-07-28 words: 5364.0 sentences: 291.0 pages: flesch: 47.0 cache: ./cache/cord-286472-pqtem19t.txt txt: ./txt/cord-286472-pqtem19t.txt summary: This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol abstract: nan url: https://api.elsevier.com/content/article/pii/S0011502920301152 doi: 10.1016/j.disamonth.2020.101053 id: cord-007049-02p8ug67 author: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 words: 1613.0 sentences: 92.0 pages: flesch: 48.0 cache: ./cache/cord-007049-02p8ug67.txt txt: ./txt/cord-007049-02p8ug67.txt summary: In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107923/ doi: 10.1086/421784 id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 words: 8499.0 sentences: 482.0 pages: flesch: 49.0 cache: ./cache/cord-339386-sxyeuiw1.txt txt: ./txt/cord-339386-sxyeuiw1.txt summary: The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. abstract: nan url: https://api.elsevier.com/content/article/pii/B9781455748013001570 doi: 10.1016/b978-1-4557-4801-3.00157-0 id: cord-329010-n0mz098o author: McKee, Dwight L. title: Candidate drugs against SARS-CoV-2 and COVID-19 date: 2020-04-29 words: 5193.0 sentences: 260.0 pages: flesch: 41.0 cache: ./cache/cord-329010-n0mz098o.txt txt: ./txt/cord-329010-n0mz098o.txt summary: Further, chloroquine and hydroxychloroquine, and off-label antiviral drugs, such as the nucleotide analogue remdesivir, HIV protease inhibitors lopinavir and ritonavir, broad-spectrum antiviral drugs arbidol and favipiravir as well as antiviral phytochemicals available to date may prevent spread of SARS-CoV-2 and morbidity and mortality of COVID-19 pandemic. Drugs that have recently been shown to target MERS-CoV in mice [15] , and to inhibit Ebola virus RdRP and SARS-CoV-2 proteases in humans, such as remdesivir and ritonavir/lopinavir, also constitute candidate drugs against SARS-CoV-2 and are now investigated for their therapeutic efficacy in COVID-19 patients in 2 international clinical trials (SOLIDARITY Trial and DisCoVeRy Trial). The emergence of the novel beta coronavirus SARS-CoV-2 from Wuhan, Hubei province, China in December 2019 rapidly led to a pandemic involving more than 2,500,000 infected persons and more proven drugs such as camostat mesilate which prevents virus host cell entry by inhibiting TMPRSS2 [8] , and chloroquine phosphate which inhibits terminal phosphorylation of ACE2, or hydroxychloroquine which is metabolized in vivo to chloroquine [44] . abstract: Outbreak and pandemic of coronavirus SARS-CoV-2 in 2019/2020 will challenge global health for the future. Because a vaccine against the virus will not be available in the near future, we herein try to offer a pharmacological strategy to combat the virus. There exists a number of candidate drugs that may inhibit infection with and replication of SARS-CoV-2. Such drugs comprise inhibitors of TMPRSS2 serine protease and inhibitors of angiotensin-converting enzyme 2 (ACE2). Blockade of ACE2, the host cell receptor for the S protein of SARS-CoV-2 and inhibition of TMPRSS2, which is required for S protein priming may prevent cell entry of SARS-CoV-2. Further, chloroquine and hydroxychloroquine, and off-label antiviral drugs, such as the nucleotide analogue remdesivir, HIV protease inhibitors lopinavir and ritonavir, broad-spectrum antiviral drugs arbidol and favipiravir as well as antiviral phytochemicals available to date may prevent spread of SARS-CoV-2 and morbidity and mortality of COVID-19 pandemic. url: https://www.sciencedirect.com/science/article/pii/S1043661820311671?v=s5 doi: 10.1016/j.phrs.2020.104859 id: cord-282732-qym6wji7 author: McLaughlin, Katie-May title: COVID-19-Related Coagulopathy—Is Transferrin a Missing Link? date: 2020-07-30 words: 2895.0 sentences: 164.0 pages: flesch: 46.0 cache: ./cache/cord-282732-qym6wji7.txt txt: ./txt/cord-282732-qym6wji7.txt summary: To identify gene products that may contribute to COVID-19-related coagulopathy, we analyzed the expression of genes associated with the Gene Ontology (GO) term "blood coagulation" in the Genotype-Tissue Expression (GTEx) database and identified four procoagulants, whose expression is higher in males and increases with age (ADAMTS13, F11, HGFAC, KLKB1), and two anticoagulants, whose expression is higher in females and decreases with age (C1QTNF1, SERPINA5). Thus, gene products that (1) are involved in coagulation, (2) change with age, (3) differ in their levels between females and males, and (4) are regulated in response to SARS-CoV-2 infection represent candidate factors that may contribute to COVID-19-related coagulopathy and disease severity. To identify such candidate factors that may be involved in COVID-19-related coagulopathy, we here performed a combined analysis of a proteomics dataset derived from SARS-CoV-2-infected cells [10] , of a dataset of host cell proteins found to bind to SARS-CoV-2 proteins [11] , and of human gene expression data from the Genotype-Tissue Expression (GTEx) database [12] . abstract: SARS-CoV-2 is the causative agent of COVID-19. Severe COVID-19 disease has been associated with disseminated intravascular coagulation and thrombosis, but the mechanisms underlying COVID-19-related coagulopathy remain unknown. The risk of severe COVID-19 disease is higher in males than in females and increases with age. To identify gene products that may contribute to COVID-19-related coagulopathy, we analyzed the expression of genes associated with the Gene Ontology (GO) term “blood coagulation” in the Genotype-Tissue Expression (GTEx) database and identified four procoagulants, whose expression is higher in males and increases with age (ADAMTS13, F11, HGFAC, KLKB1), and two anticoagulants, whose expression is higher in females and decreases with age (C1QTNF1, SERPINA5). However, the expression of none of these genes was regulated in a proteomics dataset of SARS-CoV-2-infected cells and none of the proteins have been identified as a binding partner of SARS-CoV-2 proteins. Hence, they may rather generally predispose individuals to thrombosis without directly contributing to COVID-19-related coagulopathy. In contrast, the expression of the procoagulant transferrin (not associated to the GO term “blood coagulation”) was higher in males, increased with age, and was upregulated upon SARS-CoV-2 infection. Hence, transferrin warrants further examination in ongoing clinic-pathological investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/32751741/ doi: 10.3390/diagnostics10080539 id: cord-017224-naromr0a author: McLeish, Caitriona title: Evolving Biosecurity Frameworks date: 2016-12-06 words: 6005.0 sentences: 257.0 pages: flesch: 44.0 cache: ./cache/cord-017224-naromr0a.txt txt: ./txt/cord-017224-naromr0a.txt summary: The relationship between infectious disease and security concerns has undergone an evolution since the end of the Cold War. What was previously seen as two separate domains – public health and national security – have, through various events and disease outbreaks in the last 15 years, become intertwined and as a result biosecurity policies now need to address a spectrum of disease threats that encompass natural outbreaks, accidental releases and the deliberate use of disease as weapons. Calling it niche is not to say that bioterrorism had not been considered a security threat prior to 2001many commentators had noted the potential (see for example Stern, 1993; Tucker, 1996 Tucker, , 2000 Moodie and Roberts, 1997; Smithson and Levy, 2000) ; table top exercises had been conducted, domestic preparedness programmes initiated (Guillemin, 2011, p7) , and in countries such as the US, policy directives had been crafted that gave the highest priority to "developing effective capabilities to detect, prevent, defeat and manage the consequences of nuclear, biological or chemical materials or weapons use by terrorists" (United States, 1995) . abstract: The relationship between infectious disease and security concerns has undergone an evolution since the end of the Cold War. What was previously seen as two separate domains – public health and national security – have, through various events and disease outbreaks in the last 15 years, become intertwined and as a result biosecurity policies now need to address a spectrum of disease threats that encompass natural outbreaks, accidental releases and the deliberate use of disease as weapons. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121729/ doi: 10.1057/978-1-137-53675-4_4 id: cord-260048-yis26g81 author: McNamara, Ryan P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-10-20 words: 2272.0 sentences: 156.0 pages: flesch: 55.0 cache: ./cache/cord-260048-yis26g81.txt txt: ./txt/cord-260048-yis26g81.txt summary: The 154 number of reads aligned varied depending on the viral load, as determined by real-time qPCR using 155 CDC primer N1, but not total RNA, as determined using RNAse P, of the samples ( Figure 1B) . At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 158 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 159 and coverage was more variable. This data is consistent with the 187 astonishingly high reported genome copy numbers of SARS-CoV-2 in some cases 188 and demonstrates the principal suitability of "testing by sequencing" as a diagnostic option for SARSCoV-2 and other rapidly evolving viruses. In sum, this study generated exhaustive SNV information representing the introduction and 276 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 277 from symptomatic cases and the majority of genomes clustered with variants that predominate the 278 outbreak in the U.S., rather than Europe or China. abstract: SARS-CoV-2 is constantly evolving. Prior studies focused on high case-density locations, such as the U.S. Northern and Western metropolitan areas. This study demonstrates continued SARS-CoV-2 evolution in a suburban Southern U.S. region by high-density amplicon sequencing of symptomatic cases. 57% of strains carried the spike D614G variant, which was associated with higher genome copy numbers and its prevalence expanded with time. Four strains carried a deletion in a predicted stem loop of the 3’ untranslated region. The data are consistent with community spread within local populations and the larger continental U.S. The data instill confidence in current testing sensitivity and validate “testing by sequencing” as an option to uncover cases, particularly non-standard COVID-19 clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. url: https://www.ncbi.nlm.nih.gov/pubmed/33113345/ doi: 10.1016/j.celrep.2020.108352 id: cord-314445-4cb4a9r5 author: McNamara, Ryan P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-06-19 words: 1960.0 sentences: 131.0 pages: flesch: 53.0 cache: ./cache/cord-314445-4cb4a9r5.txt txt: ./txt/cord-314445-4cb4a9r5.txt summary: This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. The current COVID-19 pandemic is an urgent public health emergency with over 112,000 deaths in the United States (U.S.) alone. At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 227 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 228 and coverage was more variable. In sum, this study generated exhaustive SNV information representing the introduction and 325 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 326 from symptomatic cases and the majority of genomes clustered with variants that predominate the 327 outbreak in the U.S., rather than Europe or China. abstract: SARS-CoV-2 is constantly evolving. Prior studies have focused on high case-density locations, such as the Northern and Western metropolitan areas in the U.S. This study demonstrates continued SARS-CoV-2 evolution in a suburban Southern U.S. region by high-density amplicon sequencing of symptomatic cases. 57% of strains carried the spike D614G variant. The presence of D614G was associated with a higher genome copy number and its prevalence expanded with time. Four strains carried a deletion in a predicted stem loop of the 3’ untranslated region. The data are consistent with community spread within the local population and the larger continental U.S. No strain had mutations in the target sites used in common diagnostic assays. The data instill confidence in the sensitivity of current tests and validate “testing by sequencing” as a new option to uncover cases, particularly those not conforming to the standard clinical presentation of COVID-19. This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. url: https://doi.org/10.1101/2020.06.19.161141 doi: 10.1101/2020.06.19.161141 id: cord-331283-bfyoavon author: Meca-Lallana, Dra. Virginia title: COVID-19 IN 7 MULTIPLE SCLEROSIS PATIENTS IN TREATMENT WITH ANTI-CD20 THERAPIES date: 2020-06-15 words: 1223.0 sentences: 85.0 pages: flesch: 53.0 cache: ./cache/cord-331283-bfyoavon.txt txt: ./txt/cord-331283-bfyoavon.txt summary: We describe our experience in seven cases of patients with multiple sclerosis who have been affected by SARS-COV-2 (with a clinical/serological diagnosis or PCR diagnosis) and who were being treated with anti-CD20+ monoclonal antibodies. CONCLUSIONS: Patients treated with anti-CD20+ have adequate resolution of COVID-19 despite the fact that the presence of antibodies against SARS-CoV-2 was not detected in all cases. Ocrelizumab is associated with decreased levels of IgM (and to a lesser degree for IgA and IgG), and serious infections occurred, but their incidence was low in clinical trials and extended phases 4 In this work, we report our experience in MS patients with anti-CD20+ antibodies who have 2. We have found antibodies against SARS-CoV-2 in patients treated with ocrelizumab, but in patients who previously used rituximab this immunity is not achieved or we are not able to detect it. abstract: BACKGROUND AND AIM: In December 2019, the first cases of SARS-CoV-2 infection were detected in Wuhan. Within two months, it had begun to spread around the world in what became an unprecedented pandemic. Patients with Multiple Sclerosis (MS) in a state of immunosuppression may be considered at risk for complications in the COVID-19 pandemic, although there is increasing evidence postulating a possible protective role of selective immunosuppression. One group of such immunosuppressants used in MS comprises the anti-CD20 monoclonal antibodies (mAbs) ocrelizumab and rituximab. Anti-CD20 mAbs bind to the surface of B cells, causing their depletion. We describe our experience in seven cases of patients with multiple sclerosis who have been affected by SARS-COV-2 (with a clinical/serological diagnosis or PCR diagnosis) and who were being treated with anti-CD20+ monoclonal antibodies. MATERIAL AND METHODS: We review the development of patients during infection as well as the resolution of their clinical picture. We also analyze the serology status against SARS-CoV-2 after resolution of the infection. RESULTS: Although the severity of the clinical pictures was variable, patients' development was good. Not all patients, however, developed antibodies against SARS-CoV-2. CONCLUSIONS: Patients treated with anti-CD20+ have adequate resolution of COVID-19 despite the fact that the presence of antibodies against SARS-CoV-2 was not detected in all cases. It is possible that the presence of humoral immunity is not always necessary fora good clinical course of SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S2211034820303825 doi: 10.1016/j.msard.2020.102306 id: cord-295274-gzkfy70s author: Mecham, Jeffrey C. title: Utility of Tracheostomy in Patients With COVID‐19 and Other Special Considerations date: 2020-05-12 words: 2901.0 sentences: 160.0 pages: flesch: 37.0 cache: ./cache/cord-295274-gzkfy70s.txt txt: ./txt/cord-295274-gzkfy70s.txt summary: METHODS: We explore current literature and recommendations for tracheostomy in patients with COVID‐19 and look back at previous data from severe acute respiratory syndrome coronavirus 1 (SARS‐CoV‐1), the virus responsible for the SARS outbreak of 2003. RESULTS: Given the severity and clinical uncertainty of patients with COVID‐19 and the increased risk of transmission to clinicians, careful consideration should be taken prior to performing tracheostomy. One concern for healthcare professionals managing the airways of COVID-19 patients is the risk of viral exposure during aerosol-generating procedures, including intubation and tracheostomy. There is a plausible risk for increased intraprocedural viral exposure via secretions and aerosolized particles when tracheostomy is performed percutaneously because this technique requires additional manipulation of the airway with multiple, repetitive dilations. Given the severity and uncertain clinical outcome of patients with COVID-19, in addition to the increased risk of transmission to clinicians during aerosol generating procedures, careful consideration should be taken prior to performing tracheostomy. abstract: INTRODUCTION: Patients who become severely ill from coronavirus disease 2019 (COVID‐19) have a high likelihood of needing prolonged intubation, making tracheostomy a likely consideration. The infectious nature of COVID‐19 poses an additional risk of transmission to healthcare workers that should be taken into consideration. METHODS: We explore current literature and recommendations for tracheostomy in patients with COVID‐19 and look back at previous data from severe acute respiratory syndrome coronavirus 1 (SARS‐CoV‐1), the virus responsible for the SARS outbreak of 2003. RESULTS: Given the severity and clinical uncertainty of patients with COVID‐19 and the increased risk of transmission to clinicians, careful consideration should be taken prior to performing tracheostomy. If tracheostomy is performed, we recommend a bedside approach to limit exposure time and number of exposed personnel. Bronchoscopy use with a percutaneous approach should be limited in order to decrease viral exposure. CONCLUSION: Thorough preprocedural planning, use of experienced personnel, enhanced personal protective equipment where available, and a thoughtful anesthesia approach are instrumental in maximizing positive patient outcomes while successfully protecting the safety of healthcare personnel. Laryngoscope, 2020 url: https://doi.org/10.1002/lary.28734 doi: 10.1002/lary.28734 id: cord-281679-xmbnpawj author: Meekins, David A. title: Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date: 2020-08-16 words: 3402.0 sentences: 191.0 pages: flesch: 46.0 cache: ./cache/cord-281679-xmbnpawj.txt txt: ./txt/cord-281679-xmbnpawj.txt summary: In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Cats, hamsters, and ferrets are highly susceptible to SARS-CoV-2 infection, demonstrate varying clinical and pathological disease manifestations, readily transmit the virus to naïve animals, and mount a virusspecific immune response [22] [23] [24] [25] [26] [27] [28] . Pigs are therefore unlikely to play an important role in the COVID-19 pandemic as a virus reservoir or as a pre-clinical animal model to study SARS-CoV-2 pathogenesis or develop novel countermeasures. abstract: The emergence of SARS-CoV-2 has resulted in an ongoing global pandemic with significant morbidity, mortality, and economic consequences. The susceptibility of different animal species to SARS-CoV-2 is of concern due to the potential for interspecies transmission, and the requirement for pre-clinical animal models to develop effective countermeasures. In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. SARS-CoV-2 was able to replicate in two different porcine cell lines with cytopathic effects. Interestingly, none of the SARS-CoV-2-inoculated pigs showed evidence of clinical signs, viral replication or SARS-CoV-2-specific antibody responses. Moreover, none of the sentinel pigs displayed markers of SARS-CoV-2 infection. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Pigs are therefore unlikely to be significant carriers of SARS-CoV-2 and are not a suitable pre-clinical animal model to study SARS-CoV-2 pathogenesis or efficacy of respective vaccines or therapeutics. url: https://doi.org/10.1101/2020.08.15.252395 doi: 10.1101/2020.08.15.252395 id: cord-342380-lihz7h1k author: Meguid Kassem, Abdel title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 words: 3044.0 sentences: 164.0 pages: flesch: 51.0 cache: ./cache/cord-342380-lihz7h1k.txt txt: ./txt/cord-342380-lihz7h1k.txt summary: BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). This work has been conducted to determine the extent of infection by realtime reverse transcription polymerase chain reaction (RT-PCR) and rapid serological test (RST) for SARS-CoV-2 among frontline HCWs providing gastrointestinal services. Previous studies in developed countries reported variable infection rates in HCWs. In a study on 957 employees in a German university hospital, 52 of them (5.4%) tested positive for SARS-CoV-2 by PCR [13] . abstract: BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. This study aimed to assess SARS-CoV-2 infection among HCWs providing gastroenterological services. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). A questionnaire was used to collect demographic, occupational and clinical data. RESULTS: Of the 74 HCWs, 10 tested positive by RT-PCR (13.5%). In 9/74 (12.2 %) HCWs, antibodies could be detected by RST: three with both IgM and IgG lines; six with IgM line only and none with IgG line only. Frequency of positive tests was more among subjects with minor symptoms compared to completely asymptomatic HCWs (50% vs 16.1%, respectively). Neither age, gender or occupation was a risk factor for SARS-CoV-2 infection. CONCLUSIONS: Point prevalence of COVID-19 in gastroenterology HCWs is 13.5% by RT-PCR. Continued measures are warranted to assure HCWs safety and reduce transmission from healthcare settings to the community during COVID-19 pandemic. Presence of positive test results among asymptomatic HCWs illustrates the importance of screening all HCWs irrespective of symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/32732168/ doi: 10.1016/j.ajg.2020.07.005 id: cord-030254-eevqclsy author: Mehta, Chitra title: Management of Coronavirus 2019 date: 2020-04-24 words: 4032.0 sentences: 287.0 pages: flesch: 56.0 cache: ./cache/cord-030254-eevqclsy.txt txt: ./txt/cord-030254-eevqclsy.txt summary: A suspected case has been defined as a patient with acute onset respiratory infection with fever, cough, sore throat, and an epidemiological link in the form of a history of travel 14 days prior to the onset of symptoms to countries afflicted with COVID-19, or a close contact with a confirmed or probable case of COVID-19 14 days prior to symptom onset, or some acute respiratory infection requiring hospitalization with no other etiology fully explaining the clinical presentation, as per WHO guidelines. • In patients with severe COVID-19 infection requiring supplemental oxygen, lopinavir/ritonavir combination plus hydroxychloroquine plus favipiravir 1,600 mg (eight tablets) twice daily as a loading dose followed by 600 mg (three tablets) every 8 hours for 14 days is being used. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical management of severe acute respiratory infection when COVID-19 disease is suspected. abstract: Coronavirus 2019 (COVID-19) disease is the most recent global public health problem. It is caused by SARS-CoV-2 (severe acute respiratory syndrome related coronavirus 2), which is a RNA virus with a high mutation rate, belonging to the genus Coronavirus . The objective of this communication is to provide an initial understanding regarding pathophysiology, clinical manifestations, management, and prevention of this devastating disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416204/ doi: 10.1055/s-0040-1710401 id: cord-257805-pcp3qgn0 author: Mehta, Harsh title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date: 2020-05-16 words: 2222.0 sentences: 148.0 pages: flesch: 50.0 cache: ./cache/cord-257805-pcp3qgn0.txt txt: ./txt/cord-257805-pcp3qgn0.txt summary: title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Since its first reported case in China, more than 4 Coronaviruses are known pathogens and have previously been responsible for epidemics caused by severe acute respiratory syndrome coronavirus (SARS-CoV1) and We report a case of a high-risk pregnant woman who developed respiratory failure associated with COVID-19, and had a favorable outcome postdelivery. A repeat chest X-ray showed worsening bilateral pulmonary infiltrates, raising concern for development of acute respiratory distress syndrome (ARDS). In the data available in pregnant patients from the previous coronavirus outbreaks, no vertical transmission was reported [4] . abstract: We present the case of a 39-year-old woman, G1P0, who had conceived twins via in-vitro fertilization, who presented at 27 weeks of gestation with nasal congestion and dry cough for 7 days. On presentation, her physical examination was benign, except for sinus tachycardia, and she was oxygenating adequately on room air. Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. A fetal non-stress test was reassuring. She was treated with intravenous fluids, ceftriaxone, azithromycin, and hydroxychloroquine. During her hospital stay, she developed progressively worsening respiratory failure, initially requiring non-invasive ventilation, and subsequently progressed to acute respiratory distress syndrome requiring mechanical ventilation. She then suffered from sudden hypoxemia and hemodynamic collapse, on maximal ventilatory support, prompting an emergency cesarean section at bedside. This led to rapid stabilization of hemodynamic parameters, and of her overall respiratory status. Both the twins were born prematurely, and one of them tested positive for SARS-COV2. url: https://www.sciencedirect.com/science/article/pii/S2214911220300503?v=s5 doi: 10.1016/j.crwh.2020.e00220 id: cord-300848-0igfcixy author: Meijers, Björn title: The clinical characteristics of coronavirus-associated nephropathy date: 2020-09-02 words: 1687.0 sentences: 109.0 pages: flesch: 52.0 cache: ./cache/cord-300848-0igfcixy.txt txt: ./txt/cord-300848-0igfcixy.txt summary: While a minority of SARS-CoV patients did develop acute kidney injury (AKI), this was attributed to critical illness with acute tubular necrosis in post-mortem kidney tissue. In kidney tissue obtained at autopsy of 26 critically ill patients with COVID-19, diffuse proximal tubule injury also was the main finding on light microscopy [9] . This puts SARS-CoV-2 in an expanding list of other viruses with proven kidney tropism, including hantavirus [14] , the Middle East respiratory syndrome coronavirus [15] , polyomavirus (polyomavirus-associated nephropathy) [16] and the human immunodeficiency virus (HIV-associated nephropathy) [17] . To date, kidney histology of COVID-19 patients with a less severe clinical course has not been reported. In this issue of Nephrology Dialysis Transplantation, data from a large European cohort study of patients with COVID-19 are reported [3] . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: nan url: https://doi.org/10.1093/ndt/gfaa197 doi: 10.1093/ndt/gfaa197 id: cord-314880-0cfq52hn author: Meireles, Pedro Antunes title: Acalculous Acute Pancreatitis in a COVID-19 Patient date: 2020-05-13 words: 803.0 sentences: 53.0 pages: flesch: 43.0 cache: ./cache/cord-314880-0cfq52hn.txt txt: ./txt/cord-314880-0cfq52hn.txt summary: An increase in pancreatic enzymes has been increasingly recognized in patients with COVID-19, but little is known about the real prevalence of acute pancreatitis in this population. We report a case of acute pancreatitis in a patient with SARS-CoV-2 infection. Liu et al [1] showed an increase in amylase and lipase in a series of 121 patients admitted with COVID-19 pneumonia, suggesting some degree of pancreatic injury in these patients. Similarly, Anand et al [3] have reported the case of a 59-year-old female patient who was diagnosed with acute pancreatitis based on typical abdominal pain and imaging findings 10 days after positive PCR-confirmed SARS-CoV-2 infection. The authors report a case of acute pancreatitis in a COVID-19 patient, highlighting the importance of considering SARS-CoV-2 as a new aetiological agent of acute viral pancreatitis. We suggest that pancreatic enzymes should be evaluated in COVID-19 in-patients presenting with gastrointestinal symptoms, since it could reveal unrecognized pancreatic involvement in this population. abstract: Coronavirus disease 2019 (COVID-19) is a multisystemic condition caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with manifestations ranging from mild upper respiratory symptoms to cytokine storm causing acute respiratory distress syndrome. Pancreatic exocrine tissue and endocrine islets both express angiotensin-converting enzyme 2 (ACE2), the proven receptor for SARS-CoV-2 cell internalization. An increase in pancreatic enzymes has been increasingly recognized in patients with COVID-19, but little is known about the real prevalence of acute pancreatitis in this population. We report a case of acute acalculous pancreatitis in a COVID-19 patient. LEARNING POINTS: Acute pancreatitis may be a manifestation of SARS-CoV-2 infection. Future studies must address the real impact of pancreatic involvement in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32523925/ doi: 10.12890/2020_001710 id: cord-354315-yfn9vaan author: Meirson, Tomer title: Structural basis of SARS-CoV-2 spike protein induced by ACE2 date: 2020-05-24 words: 5190.0 sentences: 253.0 pages: flesch: 49.0 cache: ./cache/cord-354315-yfn9vaan.txt txt: ./txt/cord-354315-yfn9vaan.txt summary: This conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The critical step in SARS-CoV-2 infection which involves the transition between a metastable prefusion state to a stable post-fusion state is triggered by binding to ACE2 which induces conformational changes in the RBD and the hinge region (Gui, et al., 2017; Pallesen, et al., 2017; Song, et al., 2018; Walls, et al., 2020) . To gain insights into the effects of ACE2 interaction on the S protein of SARS-COV-2, we analyzed the intramolecular structural variations in the bound versus the unbound-closed Numerous structures of the prefusion human CoV S proteins were determined at different states, and the key regions responsible for the interaction with the receptor were previously reported (Lan, et al., 2020; Shang, et al., 2020; Walls, et al., 2020; Wan, et al., 2020; Wrapp, et al., 2020; Yan, et al., 2020) . abstract: Motivation The recent emergence of the novel SARS-coronavirus 2 (SARS-CoV-2) and its international spread pose a global health emergency. The viral spike (S) glycoprotein binds the receptor (angiotensin-converting enzyme 2) ACE2 and promotes SARS-CoV-2 entry into host cells. The trimeric S protein binds the receptor using the distal receptor-binding domain (RBD) causing conformational changes in S protein that allow priming by host cell proteases. Unravelling the dynamic structural features used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal novel therapeutic targets. Using structures determined by X-ray crystallography and cryo-EM, we performed structural analysis and atomic comparisons of the different conformational states adopted by the SARS-CoV-2-RBD. Results Here, we determined the key structural components induced by the receptor and characterized their intramolecular interactions. We show that κ-helix (also known as polyproline II) is a predominant structure in the binding interface and in facilitating the conversion to the active form of the S protein. We demonstrate a series of conversions between switch-like κ-helix and β-strand, and conformational variations in a set of short α-helices which affect the proximal hinge region. This conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The structural information presented herein enables us to inspect and understand the important dynamic features of SARS-CoV-2-RBD and propose a novel potential therapeutic strategy to block viral entry. Overall, this study provides guidance for the design and optimization of structure-based intervention strategies that target SARS-CoV-2. url: https://doi.org/10.1101/2020.05.24.113175 doi: 10.1101/2020.05.24.113175 id: cord-322129-uyswj4ow author: Melin, Amanda D. title: Comparative ACE2 variation and primate COVID-19 risk date: 2020-10-27 words: 6310.0 sentences: 305.0 pages: flesch: 47.0 cache: ./cache/cord-322129-uyswj4ow.txt txt: ./txt/cord-322129-uyswj4ow.txt summary: Infection studies of rhesus monkeys, long-tailed macaques, and vervets as biomedical models have made it clear that at least some nonhuman primate species are permissive to SARS-CoV-2 infection and develop symptoms in response to infection that resemble those of humans following the development of COVID-19, including similar age-related effects [11] [12] [13] [14] [15] [16] . We assessed the variation at amino acid residues identified as critical for ACE2 recognition by the SARS-CoV-2 RBD and undertook an analysis of positive selection and protein modeling to gauge the potential for adaptive differences and the likely effects of protein variation. In particular, the twelve sites in the ACE2 protein that are critical for binding of the SARS-CoV-2 virus are invariant across the Catarrhini, which includes great apes, gibbons, and monkeys of Africa and Asia (Fig. 1) . abstract: The emergence of SARS-CoV-2 has caused over a million human deaths and massive global disruption. The viral infection may also represent a threat to our closest living relatives, nonhuman primates. The contact surface of the host cell receptor, ACE2, displays amino acid residues that are critical for virus recognition, and variations at these critical residues modulate infection susceptibility. Infection studies have shown that some primate species develop COVID-19-like symptoms; however, the susceptibility of most primates is unknown. Here, we show that all apes and African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at critical contact residues, and protein modeling predicts that these differences should greatly reduce SARS-CoV-2 binding affinity. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, and some lemurs, are likely to be highly susceptible to SARS-CoV-2. Urgent actions have been undertaken to limit the exposure of great apes to humans, and similar efforts may be necessary for many other primate species. url: https://www.ncbi.nlm.nih.gov/pubmed/33110195/ doi: 10.1038/s42003-020-01370-w id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 words: 3122.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-342344-jjnf4yje.txt txt: ./txt/cord-342344-jjnf4yje.txt summary: Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. abstract: Quantifying SARS-CoV-2 infectivity, formulating well-calibrated public-health policy, and managing the safety of workplaces would all be facilitated by precise measurement of the extent to which SARS-CoV-2 RNA is present in an intact form in biological specimens and human environments. We describe assays that use digital PCR in nanoliter droplets (droplet digital PCR) to measure these properties. Such assays could be broadly deployed to inform COVID-19 epidemiology, measure symptomatic and asymptomatic infectivity, and help manage the safety of environments in which people live, move, and work. url: http://medrxiv.org/cgi/content/short/2020.06.24.20139584v1?rss=1 doi: 10.1101/2020.06.24.20139584 id: cord-304626-ffao7vka author: Mellors, Jack title: Viral Evasion of the Complement System and Its Importance for Vaccines and Therapeutics date: 2020-07-09 words: 11744.0 sentences: 539.0 pages: flesch: 34.0 cache: ./cache/cord-304626-ffao7vka.txt txt: ./txt/cord-304626-ffao7vka.txt summary: A better understanding of this virus-host interplay and its contribution to pathogenesis has previously led to: the identification of genetic factors which influence viral infection and disease outcome, the development of novel antivirals, and the production of safer, more effective vaccines. Infected host cells which present viral antigens on the cell surface membrane can activate the classical pathway, as the antigens bind IgM/IgG to induce complement dependent cytotoxicity (CDC). Non-neutralizing antibodies can still bind the viral target with the potential to cross-link with Fc receptors, or activate complement and interact with complement receptors, to enhance viral infection of host cells (241) . Use of the non-neutralizing influenza virus M2 extracellular vaccine in mice required functional C3 to confer protection and induce effective humoral and cell-mediated immune responses (245) . abstract: The complement system is a key component of innate immunity which readily responds to invading microorganisms. Activation of the complement system typically occurs via three main pathways and can induce various antimicrobial effects, including: neutralization of pathogens, regulation of inflammatory responses, promotion of chemotaxis, and enhancement of the adaptive immune response. These can be vital host responses to protect against acute, chronic, and recurrent viral infections. Consequently, many viruses (including dengue virus, West Nile virus and Nipah virus) have evolved mechanisms for evasion or dysregulation of the complement system to enhance viral infectivity and even exacerbate disease symptoms. The complement system has multifaceted roles in both innate and adaptive immunity, with both intracellular and extracellular functions, that can be relevant to all stages of viral infection. A better understanding of this virus-host interplay and its contribution to pathogenesis has previously led to: the identification of genetic factors which influence viral infection and disease outcome, the development of novel antivirals, and the production of safer, more effective vaccines. This review will discuss the antiviral effects of the complement system against numerous viruses, the mechanisms employed by these viruses to then evade or manipulate this system, and how these interactions have informed vaccine/therapeutic development. Where relevant, conflicting findings and current research gaps are highlighted to aid future developments in virology and immunology, with potential applications to the current COVID-19 pandemic. url: https://doi.org/10.3389/fimmu.2020.01450 doi: 10.3389/fimmu.2020.01450 id: cord-268755-13xmmin1 author: Meltzer, Martin I. title: Multiple Contact Dates and SARS Incubation Periods date: 2004-02-17 words: 1522.0 sentences: 85.0 pages: flesch: 50.0 cache: ./cache/cord-268755-13xmmin1.txt txt: ./txt/cord-268755-13xmmin1.txt summary: Many severe acute respiratory syndrome (SARS) patients have multiple possible incubation periods due to multiple contact dates. I present a simple spreadsheet-based method that uses multiple contact dates to calculate the possible incubation periods of SARS. I present a simple method that allows a simulation of the frequency distribution, including confidence intervals, of the possible incubation periods (in days) for SARS. The method can also be used to calculate when infectious persons are most likely to have transmitted SARS to susceptible persons, even when multiple days of possible transmission exist. Simulation of frequency distribution of incubation period of severe acute respiratory syndrome. Many of the patients included in the database had multiple possible incubation periods (see Table) , resulting in the confidence intervals displayed for each day. The method readily "accepts" data in which patients have multiple possible incubation periods. abstract: Many severe acute respiratory syndrome (SARS) patients have multiple possible incubation periods due to multiple contact dates. Multiple contact dates cannot be used in standard statistical analytic techniques, however. I present a simple spreadsheet-based method that uses multiple contact dates to calculate the possible incubation periods of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15030684/ doi: 10.3201/eid1002.030426 id: cord-321552-lsz1onrj author: Membrilla, Javier A. title: Headache as a Cardinal Symptom of Coronavirus Disease 2019: A Cross‐Sectional Study date: 2020-09-28 words: 4335.0 sentences: 256.0 pages: flesch: 46.0 cache: ./cache/cord-321552-lsz1onrj.txt txt: ./txt/cord-321552-lsz1onrj.txt summary: OBJECTIVE: To describe the semiology of pain and its associated features in patients with coronavirus disease 2019 (COVID‐19) and headache presenting to the emergency department who do not require urgent services. 27 We hypothesized that COVID-19-related headache might be one of the most frequent symptoms of the infection and can have a more severe presentation in patients with migraine. We aimed to describe the semiology of pain and associated symptoms in patients with COVID-19-related headache in a clinical setting who visit the emergency department but do not require urgent services. Study Population and Eligibility.-Patients attending the emergency department of our hospital were included if they met all of the following inclusion criteria: (1) patients classified by the Manchester Triage System 29 as priority levels 5 (non-urgent) and 4 (standard); (2) fulfilled the criteria for a "probable COVID-19 case" or "confirmed COVID-19 case" according to the WHO guidance on global surveillance for COVID-19; 30 (3) and presented with headache alongside other COVID-19-related symptoms. abstract: OBJECTIVE: To describe the semiology of pain and its associated features in patients with coronavirus disease 2019 (COVID‐19) and headache presenting to the emergency department who do not require urgent services. BACKGROUND: Headache is one of the most frequent neurological symptoms reported in case series, epidemiological studies, and meta‐analyses of COVID‐19, with a prevalence ranging from 8 to 71.1%. Studies addressing the semiology of these headaches are lacking. METHODS: We conducted a cross‐sectional study in the emergency department of a tertiary hospital. Patients classified according to the Manchester Triage System as standard and non‐urgent and those fulfilling the criteria for probable or confirmed COVID‐19 according to World Health Organization guidelines who presented with headache were included. A standardized questionnaire was used for data collection. RESULTS: Of the 145 confirmed and probable COVID‐19 patients, 99 (68.3%) reported headache. A total of 54/99 (54.5%) were classified with probable COVID‐19 and 45/99 (45.5%) with confirmed COVID‐19. The mean age (44.7 ± 11.8 vs 40.4 ± 10.7, P = .061), sex distribution (35/54 [64.8%] vs 28/45 [62.2%] female, P = .768), and headache comorbidity (19/54 [35.2%] vs 17/45 [37.8%], P = .789) were similar between the probable and confirmed COVID‐19 groups, along with other medical comorbidities and laboratory data. Patients with confirmed COVID‐19 showed a higher incidence of anosmia (21/54 [38.9%] vs 28/45 [62.2%], P = .021) and pneumonia (10/54 [18.5%] vs 18/45 [40%], P = .018), headache at onset (32/54 [59.3%] vs 39/45 [86.7%], P = .002), and hospital admission (0/54 [0%] vs 2/45 [11.1%], P = .017). In most cases, the headache appeared simultaneously with other COVID‐19 symptoms (57/99, 57.6%). It was bilateral (86/99, 86.9%), frontal or holocranial (34/99, 34.3% each) in location and intense (60/99, 60.6%, reported a visual analog scale [VAS] score ≥7). A total of 39/99 (39.4%) identified triggers, most commonly fever. The most frequent aggravating factors were physical activity (45/99, 45.5%) and coughing (43/99, 43.4%). Patients showed a propensity toward prostration (41/99, 41.4%), photophobia (29/99, 29.3%), and phonophobia (27/99, 27.3%). Partial (53/99, 53.5%) or total (26/99, 26.3%) responses to first‐step analgesics were reported. A total of 25/99 (25.3%) patients had a prior history of migraine, presenting with headache different from the usual in 23/25 (92.0%) patients. Individuals with migraine were more likely to have earlier (headache at onset of the respiratory symptoms in 24/25 [96.0%] vs 57/74 [77.0%], P = .023 [95% CI: 0.067, 0.313]), longer (>24 hours of pain in 20/25 [80%] vs 25/74 [33.8%], P < .001 [95% CI: 0.272, 0.652]), and more intense (VAS score ≥5 in 25/25 [100%] vs 63/74 [85.1%], P = .043 [95% CI: 0.057, 0.213]) headaches than patients without migraine. CONCLUSIONS: Headache is a very prevalent COVID‐19 symptom among patients presenting to the emergency room, most frequently presenting as holocranial or bifrontal moderate to severe, and pressing quality headache. Individuals with migraine tend to present with earlier, longer, and more intense headaches. url: https://doi.org/10.1111/head.13967 doi: 10.1111/head.13967 id: cord-278648-hkvurb2k author: Menachery, Vineet D. title: Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis date: 2017-11-15 words: 5195.0 sentences: 263.0 pages: flesch: 47.0 cache: ./cache/cord-278648-hkvurb2k.txt txt: ./txt/cord-278648-hkvurb2k.txt summary: While the absence of 2′O-MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Generation of mutants with changes in the NSP16 KDKE active site resulted in IFN-mediated in vitro and in vivo attenuation of both mouse hepatitis virus (MHV) and SARS-CoV (9, 10) . While a more rapid CPE following both WT and dNSP16 mutant MERS-CoV infections precluded an equivalent finding at late time points, the SARS-CoV results suggest that the absence of NSP16 activity eventually initiates host response changes that contribute to attenuation at late time points. abstract: Coronaviruses (CoVs) encode a mixture of highly conserved and novel genes, as well as genetic elements necessary for infection and pathogenesis, raising the possibility of common targets for attenuation and therapeutic design. In this study, we focused on highly conserved nonstructural protein 16 (NSP16), a viral 2′O-methyltransferase (2′O-MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of Middle East respiratory syndrome CoV (MERS-CoV) NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2′O-MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo. Further examination indicated that dNSP16 mutant MERS-CoV had a type I interferon (IFN)-based attenuation and was partially restored in the absence of molecules of IFN-induced proteins with tetratricopeptide repeats. Importantly, the robust attenuation permitted the use of dNSP16 mutant MERS-CoV as a live attenuated vaccine platform protecting from a challenge with a mouse-adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2′O-MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting. IMPORTANCE Coronavirus (CoV) emergence in both humans and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of severe acute respiratory syndrome CoV (SARS-CoV), MERS-CoV, porcine epidemic diarrhea virus, and swine delta CoV in the 21st century. These studies describe an approach that effectively targets the highly conserved 2′O-MTase activity of CoVs for attenuation. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-CoV functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2′O-MTase function across CoVs. url: https://doi.org/10.1128/msphere.00346-17 doi: 10.1128/msphere.00346-17 id: cord-277039-yo5ojr0s author: Mendenhall, Ian H. title: Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date: 2019-04-17 words: 2419.0 sentences: 133.0 pages: flesch: 55.0 cache: ./cache/cord-277039-yo5ojr0s.txt txt: ./txt/cord-277039-yo5ojr0s.txt summary: In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. The zoonotic SARS-coronavirus (SARS-CoV) outbreak originated in southern China from horseshoe bats, where wet markets permitted atypical contact between species, including subsequent spillover to humans [9] . On the other hand, camels are the putative natural reservoir for MERS-coronavirus, although recent phylogenetic analysis indicated that bats harbor coronaviruses that are ancestral to the MERS-CoV lineage [11] . In this study, we collected fresh bat guano from three caves at different locations in Kazakhstan and conducted molecular screening for coronaviruses. To further understand the evolutionary relationships of these viruses, we analyzed novel bat coronavirus sequences in combination with 2811 RdRp sequences of coronavirus from different host species worldwide, representing the three genera: Alpha-, Beta-, and Gamma-coronaviruses. The Alpha-CoV genus comprises a large number of coronaviruses from diverse hosts, including bats, shrews, dogs, cats, ferrets, pigs, and humans. abstract: Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world’s ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases. url: https://doi.org/10.3390/v11040356 doi: 10.3390/v11040356 id: cord-296268-kb7fgfaq author: Mendonça, Luiza title: SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date: 2020-11-05 words: 2647.0 sentences: 161.0 pages: flesch: 57.0 cache: ./cache/cord-296268-kb7fgfaq.txt txt: ./txt/cord-296268-kb7fgfaq.txt summary: Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Understanding the genome 27 replication, assembly and egress of SARS-CoV-2, a multistage process that involves different 28 cellular compartments and the activity of many viral and cellular proteins, is critically Krios to identify each individual infected cell (39.2 % for MOI of 0.1 and 45.4% for MOI 124 0.5) where cryoET tilt series were collected at the cell periphery. The grids were then 125 transferred to a FIB/SEM dualbeam instrument and the same infected cells were subjected to 126 either serial cryoFIB/SEM volume imaging (Zhu et al., 2021) or cryoFIB milling of cellular 127 lamellae where additional cryoET tilt series were collected (Sutton et al., 2020) . abstract: Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, investigation of the SARS-CoV-2 infection in the native cellular context is scarce, and there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Our results reveal at the whole cell level profound cytopathic effects of SARS-CoV-2 infection, exemplified by a large amount of heterogeneous vesicles in the cytoplasm for RNA synthesis and virus assembly, formation of membrane tunnels through which viruses exit, and drastic cytoplasm invasion into nucleus. Furthermore, cryoET of cell lamellae reveals how viral RNAs are transported from double-membrane vesicles where they are synthesized to viral assembly sites; how viral spikes and RNPs assist in virus assembly and budding; and how fully assembled virus particles exit the cell, thus stablishing a model of SARS-CoV-2 genome replication, virus assembly and egress pathways. url: https://doi.org/10.1101/2020.11.05.370239 doi: 10.1101/2020.11.05.370239 id: cord-353953-83d0g8ix author: Mendoza, Emelissa J. title: Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2 date: 2020-05-31 words: 4265.0 sentences: 281.0 pages: flesch: 57.0 cache: ./cache/cord-353953-83d0g8ix.txt txt: ./txt/cord-353953-83d0g8ix.txt summary: Plaque assays are a quantitative method of measuring infectious SARS‐CoV‐2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen. Plaque assays are a quantitative method of measuring infectious SARS-CoV-2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen (Harcourt et al., 2020) . The first plaque assay method that we describe (Basic Protocol) uses Noble agar as the matrix in a solid overlay and neutral red as the stain to enhance plaque visualization. This protocol outlines a plaque assay method that can be used for the quantification of SARS-CoV-2 plaque-forming units (PFUs) in virus specimens, including viral stocks prepared from infected cell culture supernatants, and with further optimization, bodily fluids from animals infected with SARS-CoV-2. Use Formula 8 (see Basic Protocol) to calculate the titer of SARS-CoV-2 in the specimen using the identified dilution factor and the inoculum volume of 0.1 ml. abstract: Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) has been identified as the causal agent of COronaVIrus Disease‐19 (COVID‐19), an atypical pneumonia‐like syndrome that emerged in December 2019. While SARS‐CoV‐2 titers can be measured by detection of viral nucleic acid, this method is unable to quantitate infectious virions. Measurement of infectious SARS‐CoV‐2 can be achieved by tissue culture infectious dose−50 (TCID(50)), which detects the presence or absence of cytopathic effect in cells infected with serial dilutions of a virus specimen. However, this method only provides a qualitative infectious virus titer. Plaque assays are a quantitative method of measuring infectious SARS‐CoV‐2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen. As such, plaque assays remain the gold standard in quantifying concentrations of replication‐competent lytic virions. Here, we describe two detailed plaque assay protocols to quantify infectious SARS‐CoV‐2 using different overlay and staining methods. Both methods have several advantages and disadvantages, which can be considered when choosing the procedure best suited for each laboratory. These assays can be used for several research purposes, including titration of virus stocks produced from infected cell supernatant and, with further optimization, quantification of SARS‐CoV‐2 in specimens collected from infected animals. © 2019 The Authors. Basic Protocol: SARS‐CoV‐2 plaque assay using a solid double overlay method Alternate Protocol: SARS‐CoV‐2 plaque assay using a liquid overlay and fixation‐staining method url: https://www.ncbi.nlm.nih.gov/pubmed/32475066/ doi: 10.1002/cpmc.105 id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 words: 69640.0 sentences: 6489.0 pages: flesch: 54.0 cache: ./cache/cord-315598-qwh72inx.txt txt: ./txt/cord-315598-qwh72inx.txt summary: De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). abstract: Antecedentes y objetivos: La enfermedad por coronavirus de 2019 (COVID-19) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (SARS-CoV-2). Se identificó por primera vez en diciembre de 2019 en la ciudad de Wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la Organización Mundial de la Salud (OMS), la reconoció como una pandemia global el 11 de marzo de 2020. La mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. Este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la Asociación Colombiana de Medicina Crítica (AMCI) para el manejo del paciente críticamente enfermo con COVID-19 dentro de las áreas críticas de las instituciones de salud. Métodos: Este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: Delphi modificada y grupos nominales. Se construyeron preguntas por la estrategia PICO. 10 grupos nominales desarrollaron recomendaciones para cada unidad temática. El producto del consenso fue evaluado y calificado en una ronda Delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con COID-19. Resultados: 80 expertos nacionales participaron en la actualización del consenso AMCI, especialistas en Medicina Critica y Cuidados Intensivos, Nefrología, Neurología, Neumología, bioeticistas, Medicina interna, Anestesia, Cirugía General, Cirugía de cabeza y cuello, Cuidados Paliativos, Enfermeras Especialistas en Medicina crítica, Terapeutas respiratorias especialistas en medicina crítica y Fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. La declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de COVID-19 al interior de las unidades de cuidados intensivos en el contexto nacional de Colombia. Conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con COVID-19. Las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. Background and objectives: The 2019 coronavirus disease (COVID-19) is caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2). It was first identified in December 2019 in Wuhan, China. In the following months it spread quickly to all continents and was recognised as a global pandemic by the World Health Organization (WHO) on March 11th, 2020. Most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. This consensus aims to update the initial statement issued by the Colombian Association of Critical Medicine (AMCI) for the management of the critically ill patient with COVID-19 within the critical areas of health institutions. Methods: This study used two formal consensus techniques to construct the final recommendations: modified Delphi and nominal groups. Questions were constructed using the PICO strategy. Recommendations for each thematic unit were developed by 10 nominal groups. The consensus product was evaluated and qualified in a Delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with COVID-19. Results: A total of 80 national experts participated in the update of the AMCI consensus, all specialists in Critical and Intensive Care Medicine, Nephrologists, Neurologists, Chest physician, bioethicists, Internal medicine specialists, Anaesthetists, General Surgeons, head and neck surgery, palliative care, Nurses Specialised in Critical Medicine, Respiratory therapists specialised in critical medicine and Physiotherapy, with clinical experience in the care of critically ill patients. This update issues recommendations in the most relevant areas for health care of COVID-19 patients within the intensive care units, contextualised for Colombia. Conclusions: A significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with COVID-19 through formal consensus techniques. Recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country. url: https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5 doi: 10.1016/j.acci.2020.09.004 id: cord-264709-p835wf4f author: Menezes, A. M. B. title: High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey date: 2020-08-12 words: 3169.0 sentences: 174.0 pages: flesch: 55.0 cache: ./cache/cord-264709-p835wf4f.txt txt: ./txt/cord-264709-p835wf4f.txt summary: Using data from the most recent wave of the EPICOVID19 study, a nationwide household-based survey including 133 cities from all states of Brazil, we estimated the proportion of people with and without antibodies for SARS-CoV-2 who were asymptomatic, which symptoms were most frequently reported, the number of symptoms reported and the association between symptomatology and socio-demographic characteristics. Symptoms change in smell or taste, fever and myalgia were most likely to predict positive test results as suggested by recursive partitioning tree analysis. 62 63 Using data from the most recent wave of the EPICOVID19 study, a nationwide 64 household-based survey including 133 cities from all states of Brazil, 7 we estimate the 65 proportion of people with and without antibodies for SARS-CoV-2 who were 66 asymptomatic. The above results from the third wave of the study confirmed a high prevalence of 232 symptoms using a 4-month recall period; only 12.1% positive subjects were 233 asymptomatic, compared to 42.2% of those without antibodies. abstract: Since the beginning of the pandemic of COVID-19, there has been a widespread assumption that most infected persons are asymptomatic. A frequently-cited early study from China suggested that 86% of all infections were undocumented, which was used as indirect evidence that patients were asymptomatic. Using data from the most recent wave of the EPICOVID19 study, a nationwide household-based survey including 133 cities from all states of Brazil, we estimated the proportion of people with and without antibodies for SARS-CoV-2 who were asymptomatic, which symptoms were most frequently reported, the number of symptoms reported and the association between symptomatology and socio-demographic characteristics. We were able to test 33,205 subjects using a rapid antibody test that was previously validated. Information on symptoms was collected before participants received the test result. Out of 849 (2.7%) participants who tested positive for SARS-CoV-2 antibodies, only 12.1% (95%CI 10.1-14.5) reported no symptoms since the start of the pandemic, compared to 42.2% (95%CI 41.7-42.8) among those who tested negative. The largest difference between the two groups was observed for changes in smell or taste (56.5% versus 9.1%, a 6.2-fold difference). Symptoms change in smell or taste, fever and myalgia were most likely to predict positive test results as suggested by recursive partitioning tree analysis. Among individuals without any of these three symptoms (74.2% of the sample), only 0.8% tested positive, compared to 18.3% of those with both fever and changes in smell or taste. Most subjects with antibodies against SARS-CoV-2 in Brazil are symptomatic, even though most present only mild symptoms. url: https://doi.org/10.1101/2020.08.10.20171942 doi: 10.1101/2020.08.10.20171942 id: cord-257398-fmkfo5ju author: Meng, Qing-Bin title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 words: 3231.0 sentences: 190.0 pages: flesch: 49.0 cache: ./cache/cord-257398-fmkfo5ju.txt txt: ./txt/cord-257398-fmkfo5ju.txt summary: In the present study, we collected clinical data from 652 suspected COVID-19 patients and 206 non-COVID-19 patients to investigate the diagnostic value of SARS-CoV-2 IgM/IgG antibody test kits with colloidal gold immunoassays and nucleic acid RT-PCR test kits. As recently reported, a rapid IgM/IgG October 6, 2020 Volume 8 Issue 19 combined antibody test was used for the diagnosis of SARS-CoV-2 infection, showing 88.66% sensitivity and 90.63% specificity [15] . Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. abstract: BACKGROUND: The global outbreak of human severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection represents an urgent need for readily available, accurate and rapid diagnostic tests. Nucleic acid testing of respiratory tract specimens for SARS-CoV-2 is the current gold standard for diagnosis of coronavirus disease 2019 (COVID-19). However, the diagnostic accuracy of reverse transcription polymerase chain reaction (RT-PCR) tests for detecting SARS-CoV-2 nucleic acid may be lower than optimal. The detection of SARS-CoV-2-specific antibodies should be used as a serological non-invasive tool for the diagnosis and management of SARS-CoV-2 infection. AIM: To investigate the diagnostic value of SARS-CoV-2 IgM/IgG and nucleic acid detection in COVID-19. METHODS: We retrospectively analyzed 652 suspected COVID-19 patients, and 206 non-COVID-19 patients in Wuhan Integrated TCM and Western Medicine Hospital. Data on SARS-CoV-2 nucleic acid tests and serum antibody tests were collected to investigate the diagnostic value of nucleic acid RT-PCR test kits and immunoglobulin (Ig)M/IgG antibody test kits. The χ2 test was used to compare differences between categorical variables. A 95% confidence interval (CI) was provided by the Wilson score method. All analyses were performed with IBM SPSS Statistics version 22.0 (IBM Corp., Armonk, NY, United States). RESULTS: Of the 652 suspected COVID-19 patients, 237 (36.3%) had positive nucleic acid tests, 311 (47.7%) were positive for IgM, and 592 (90.8%) were positive for IgG. There was a significant difference in the positive detection rate between the IgM and IgG test groups (P < 0.001). Using the RT-PCR results as a reference, the specificity, sensitivity, and accuracy of IgM/IgG combined tests for SARS-CoV-2 infection were 98.5%, 95.8%, and 97.1%, respectively. Of the 415 suspected COVID-19 patients with negative nucleic acid test results, 366 had positive IgM/IgG tests with a positive detection rate of 88.2%. CONCLUSION: Our data indicate that serological IgM/IgG antibody combined test had high sensitivity and specificity for the diagnosis of SARS-CoV-2 infection, and can be used in combination with RT-PCR for the diagnosis of SARS-CoV-2 infection. url: https://doi.org/10.12998/wjcc.v8.i19.4360 doi: 10.12998/wjcc.v8.i19.4360 id: cord-349912-em1abdrg author: Meng, Xiangming title: COVID-19 and anosmia: A review based on up-to-date knowledge date: 2020-06-02 words: 1517.0 sentences: 111.0 pages: flesch: 57.0 cache: ./cache/cord-349912-em1abdrg.txt txt: ./txt/cord-349912-em1abdrg.txt summary: Multiple cross-sectional studies have demonstrated that the incidence rate of Olfactory dysfunction in COVID-19 patients varies from 33.9–68% with female dominance. Clinical evidence has shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted by person-to-person [1] . Furthermore, SARS-CoV-2 was detected in the tears of COVID-19 patient and can cause nasal infection via the nasolacrimal duct [17, 18] . performed the olfactory function test (OFT)of 60 SARS-CoV-2 positive patients and took 60 subjects from previous studies as a control group matching the age and gender of the patient''s group [35] . Another investigation, using a self-reported questionnaire, analyzed the prevalence of smell and/or taste disorders in J o u r n a l P r e -p r o o f 8 OFT has been the mainstay for diagnosis of OD; however, the patients in most studies were untested by OFT. abstract: The pandemic of Coronavirus Disease 2019 (COVID-19) has caused a vast disaster throughout the world. There is increasing evidence that Olfactory dysfunction can present in COVID-19 patients. Anosmia can occur alone or can be accompanied by other symptoms of COVID-19, such as a dry cough. However, the pathogenic mechanism of olfactory dysfunction and its clinical characteristics in patients with COVID-19 remains unclear. Multiple cross-sectional studies have demonstrated that the incidence rate of Olfactory dysfunction in COVID-19 patients varies from 33.9–68% with female dominance. Anosmia and dysgeusia are often comorbid in COVID-19 patients. Otolaryngologists should be mindful of the symptom of anosmia in outpatients so as not to delay the diagnosis of COVID-19. In this paper, we have reviewed the relevant knowledge based on up-to-date literature. url: https://www.ncbi.nlm.nih.gov/pubmed/32563019/ doi: 10.1016/j.amjoto.2020.102581 id: cord-297641-bgmib6xb author: Meng, Xiujuan title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China date: 2020-04-07 words: 638.0 sentences: 47.0 pages: flesch: 56.0 cache: ./cache/cord-297641-bgmib6xb.txt txt: ./txt/cord-297641-bgmib6xb.txt summary: title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China 1 The virus causing COVID-19, designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is closely related to SARS-CoV. 2 In 2003, a SARS-CoV outbreak at Amoy Gardens in Hong Kong led to 329 confirmed cases of infection and 42 deaths. 3 Subsequent studies suggested that the plumbing and ventilation systems at Amoy Gardens interacted to allow transmission of the SARS virus and that high concentrations of viral aerosols in the plumbing were the primary mode of transmission in this outbreak. Based on these characteristics, SARS-CoV-2 is prone to cause outbreaks in the community, particularly in rural areas. In concentrated areas, residents mainly use flush toilets, which can generate huge quantities of aerosols; the ventilation and plumbing systems in these places are not effective for maximal hygiene. The feces may form high concentrations of viral aerosols that travel through the air to cause infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32252855/ doi: 10.1017/ice.2020.114 id: cord-278225-d0gxb6bx author: Meng, Yifan title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients date: 2020-04-30 words: 900.0 sentences: 68.0 pages: flesch: 56.0 cache: ./cache/cord-278225-d0gxb6bx.txt txt: ./txt/cord-278225-d0gxb6bx.txt summary: title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients It has been emphasized that diagnostic testing for SARS-CoV-2 was an especially important tool in the diagnosis and management of patients with COVID-19. All patients included in the present study were verified as positive for SARS-CoV-2 infection by reverse transcriptase polymerase chain reaction (RT-PCR). At present clinical practice, patients with improved respiratory symptoms, improved pulmonary imaging, and nucleic acid tests negative twice consecutively (sampling interval ≥ 24 hours) can be discharged. reported that potential false-negative nucleic acid testing results for SARS-CoV-2 could be caused by thermal inactivation of samples with low viral loads. Value of Diagnostic Testing for SARS-CoV-2/COVID-19 Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19 Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads abstract: nan url: https://doi.org/10.1016/j.jinf.2020.04.036 doi: 10.1016/j.jinf.2020.04.036 id: cord-340619-3tjquzx8 author: Menghua, Wu title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 words: 1601.0 sentences: 119.0 pages: flesch: 63.0 cache: ./cache/cord-340619-3tjquzx8.txt txt: ./txt/cord-340619-3tjquzx8.txt summary: title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. Here we reported a case of HIV and SARS-CoV-2 coinfection who had a prolonged viral shedding duration about 28 days. [11] reported a patient with kidney transplantation who had a prolonged viral shedding duration for 63 days. This is the first report of a patient co-infected with HIV and SARS-CoV-2 who showed a prolonged viral shedding duration. The lymphocyte count of our case was also less than 2.0 × 10 9 /L, which might be a co-factor for the prolonged viral shedding duration. Viral shedding prolongation in a kidney transplant patient with COVID-19 pneumonia abstract: BACKGROUND: The COVID-19 has been a severe pandemic all around the world. Nowadays the patient with co-infection of HIV and SARS-CoV-2 was rarely reported. Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. CASE PRESENTATION: The patient was infected with HIV 8 years ago through sexual transmission and had the normal CD4(+)T cell count. She was found SARS-CoV-2 positive using real-time Polymerase Chain Reaction (RT-PCR) during the epidemic. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. CONCLUSION: The viral shedding duration may be prolonged in people living with HIV. The 14 days isolation strategy might not be long enough for them. The isolation or discharge of these patients needs further confirmation for preventing epidemics. url: https://doi.org/10.1186/s12981-020-00301-3 doi: 10.1186/s12981-020-00301-3 id: cord-316117-o29773cz author: Menzella, Francesco title: Pharmacologicaltreatment of COVID-19: lights and shadows date: 2020-05-19 words: 4459.0 sentences: 265.0 pages: flesch: 45.0 cache: ./cache/cord-316117-o29773cz.txt txt: ./txt/cord-316117-o29773cz.txt summary: At the end of December 2019, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China and then the entire world, forcing the World Health Organization (WHO) to make the assessment that the coronavirus disease (COVID19) can be characterized as a pandemic, the first ever caused by a coronavirus. The search strategy was based on the following keywords: coronavirus, SARS-CoV-2 pneumonia, COVID-19, severe acute respiratory syndrome, antivirals, corticosteroids, biologics, and anticoagulants. Current antiviral treatments are mainly based on previous experiences (favipiravir) or on experimental drugs (remdesivir) used for the treatment of viral infections due to different viruses, such as influenza virus (InfV), Ebolavirus (EBOV), human immunodeficiency virus (HIV), MERS, and SARS. 38 On the contrary, in a study with a small cohort of patients hospitalized for severe SARS-CoV-2 infection, no strong antiviral activity or clinical efficacy of the combination of hydroxychloroquine and azithromycin was found. abstract: At the end of December 2019, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2, caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China and then the entire world, forcing the World Health Organization to make the assessment that the coronavirus disease (COVID-19) can be characterized as a pandemic, the first ever caused by a coronavirus. To date, clinical evidence and guidelines based on reliable data and randomized clinical trials for the treatment of COVID-19 are lacking. In the absence of definitive management protocols, many treatments for COVID-19 are currently being evaluated and tested worldwide. Some of these options were soon abandoned due to ineffectiveness, while others showed promising results. The basic treatments are mainly represented by antiviral drugs, even if the evidence is not satisfactory. Among the antivirals, the most promising appears to be remdesivir. Corticosteroids and tocilizumab seem to guarantee positive results in selected patients so far, although the timing of starting therapy and the most appropriate therapeutic schemes remain to be clarified. Efficacy of the other drugs is still uncertain, and they are currently used as a cocktail of treatments in the absence of definitive guidelines. What will represent the real solution to the enormous problem taking place worldwide is the identification of a safe and effective vaccine, for which enormous efforts and investments are underway. url: https://doi.org/10.7573/dic.2020-4-6 doi: 10.7573/dic.2020-4-6 id: cord-269470-emzr3dzb author: Menéndez, Cintia A. title: Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease date: 2020-09-11 words: 4729.0 sentences: 252.0 pages: flesch: 56.0 cache: ./cache/cord-269470-emzr3dzb.txt txt: ./txt/cord-269470-emzr3dzb.txt summary: In addition, the authors considered the potential mutability of residues belonging to the M pro catalytic site and explained that the development of drug resistance associated with the natural evolution of M pro could wipe out efforts that target this protein for COVID-19 treatment. Apart from these residues, ebselen bound at both sites shows the lowest  factor values; however, at this specific point, this system exhibits as high flexibility as M pro -apo protein (Fig. 3A , green line). A total of more than 6 s of classical MD simulations of SARS-CoV-2 M pro -apo state and M pro -ebselen complex were run using the AMBER18 (29) simulation package (3 s, ebselen as a molecular probe; 2.4 s, shear strain analysis; 100 ns, water structure and flux analysis; 990 ns, free energy analysis). abstract: There is an urgent need to repurpose drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent computational-experimental screenings have identified several existing drugs that could serve as effective inhibitors of the virus’ main protease, M(pro), which is involved in gene expression and replication. Among these, ebselen (2-phenyl-1,2-benzoselenazol-3-one) appears to be particularly promising. Here, we examine, at a molecular level, the potential of ebselen to decrease M(pro) activity. We find that it exhibits a distinct affinity for the catalytic region. Our results reveal a higher-affinity, previously unknown binding site localized between the II and III domains of the protein. A detailed strain analysis indicates that, on such a site, ebselen exerts a pronounced allosteric effect that regulates catalytic site access through surface-loop interactions, thereby inducing a reconfiguration of water hotspots. Together, these findings highlight the promise of ebselen as a repurposed drug against SARS-CoV-2. url: https://doi.org/10.1126/sciadv.abd0345 doi: 10.1126/sciadv.abd0345 id: cord-027582-ygforvya author: Mermel, Leonard A. title: Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) date: 2020-06-10 words: 1420.0 sentences: 92.0 pages: flesch: 47.0 cache: ./cache/cord-027582-ygforvya.txt txt: ./txt/cord-027582-ygforvya.txt summary: title: Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) Patients with coronavirus disease 2019 (COVID-19) infection may respiratory tract specimens positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) for several days while in isolation precautions or for several weeks after removal from isolation precautions. Thus, decisions regarding discontinuing isolation precautions for severely immunocompromised patients, or possibly those who are otherwise critically ill with COVID-19 infection, should be based on a high SARS-CoV-2 PCR cycle threshold. Are patients infectious if they previously had a COVID-19 infection, met criteria for removal from isolation precautions, and they have SARS-CoV-2 PCR-positive respiratory tract specimens over the next several weeks? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7308630/ doi: 10.1017/ice.2020.286 id: cord-350172-w3yoxhsg author: Mertens, Pascal title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 words: 7563.0 sentences: 336.0 pages: flesch: 47.0 cache: ./cache/cord-350172-w3yoxhsg.txt txt: ./txt/cord-350172-w3yoxhsg.txt summary: Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. Regarding the COVID-19 pandemic and the urgency of sharing relevant data, in this original research article we describe the analytical performance of the COVID-19 Ag Respi-Strip according to the requirements of the current European Directive 98/79/EC (9) , the future European Regulation 2017/746 on in vitro diagnostic (IVD) medical devices (10) , the Scandinavian SKUP-protocol (11) used for the validation of qualitative tests and the clinical performance obtained with a multi-centric retrospective study. Overall, 328 nasopharyngeal samples from symptomatic patients suspected of SARS-CoV-2 infections attending from 19th to 30th March 2020 in three university laboratories located in Belgium were tested following the manufacturer''s instructions to assess the clinical sensitivity, clinical specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy in order to propose a diagnostic algorithm adapted to the current situation. abstract: Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. In this original research article, we describe the conception, the analytical and clinical performances as well as the risk management of implementing the COVID-19 Ag Respi-Strip in a diagnostic decision algorithm. Materials and Methods: Development of the COVID-19 Ag Respi-Strip resulted in a ready-to-use ICT assay based on a membrane technology with colloidal gold nanoparticles using monoclonal antibodies directed against the SARS-CoV and SARS-CoV-2 highly conserved nucleoprotein antigen. Four hundred observations were recorded for the analytical performance study and thirty tests were analyzed for the cross-reactivity study. The clinical performance study was performed in a retrospective multi-centric evaluation on aliquots of 328 nasopharyngeal samples. COVID-19 Ag Respi-Strip results were compared with qRT-PCR as golden standard for COVID-19 diagnostics. Results: In the analytical performance study, the reproducibility showed a between-observer disagreement of 1.7%, a robustness of 98%, an overall satisfying user friendliness and no cross-reactivity with other virus-infected nasopharyngeal samples. In the clinical performance study performed in three different clinical laboratories during the ascendant phase of the epidemiological curve, we found an overall sensitivity and specificity of 57.6 and 99.5%, respectively with an accuracy of 82.6%. The cut-off of the ICT was found at CT <22. User-friendliness analysis and risk management assessment through Ishikawa diagram demonstrate that COVID-19 Ag Respi-Strip may be implemented in clinical laboratories according to biosafety recommendations. Conclusion: The COVID-19 Ag Respi-Strip represents a promising rapid SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 in 15 min at the peak of the pandemic. Its role in the proposed diagnostic algorithm is complementary to the currently-used molecular techniques. url: https://doi.org/10.3389/fmed.2020.00225 doi: 10.3389/fmed.2020.00225 id: cord-334220-sqvfr31q author: Messina, Francesco title: Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date: 2020-11-03 words: 4218.0 sentences: 237.0 pages: flesch: 44.0 cache: ./cache/cord-334220-sqvfr31q.txt txt: ./txt/cord-334220-sqvfr31q.txt summary: The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. In SFigure For KEGG database the gene enrichment analysis on interactomes of NS7b, ORF1a, ORF3a and ORF8 showed pathway clusters highly significant and consistent with possible pathogenic mechanisms, such as the activation of the complement and of the coagulative cascade, (29) and the TGF-β-dominated immune response (30) . We identified different host response induced by specific proteins of SARS-CoV-2, underlining the important role of ORF3a and ORF8 in phenotypes of severe COVID-19 patients. abstract: In the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level. Host conditions and comorbidities were identified as risk factors for severe and fatal disease courses, but the mechanisms of interaction between host and SARS-CoV-2 determining the grade of COVID- 19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred on published PPI, using an explorative algorithm (Random Walk with Restart) triggered by all the 28 proteins of SARS-CoV-2, or each single viral protein one-by-one. The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, an explorative network-based approach was applied to Bradykinin Storm, highlighting a possible direct action of ORF3a and NS7b to enhancing this condition. This network-based model for SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific clinical outcomes. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. url: https://doi.org/10.1101/2020.11.03.366666 doi: 10.1101/2020.11.03.366666 id: cord-311012-wyglrpqh author: Meyers, Craig title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 words: 3271.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-311012-wyglrpqh.txt txt: ./txt/cord-311012-wyglrpqh.txt summary: AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. abstract: BACKGROUND: The COVID-19 pandemic has greatly increased the frequency of disinfecting surfaces in public places causing a strain on the ability to obtain disinfectant solutions. An alternative is to supply plain alcohols (EtOH and IPA) or sodium hypochlorite (SH). AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. METHODS: Multiple concentrations of EtOH, IPA, and SH to inactivate high numbers of HCoV under real-life conditions were tested. High concentrations of infectious HCoV were dried on porcelain and ceramic tiles, then treated with multiple concentrations of the alcohols for contact times of 15 sec, 30 sec, and 1 min. Center for Disease Control (CDC) recommended three concentrations of SH were also tested. Reductions in titres were measured by using the tissue culture infectious dose 50 (TCID(50)) assay. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. Concentrations of 95% dehydrated the virus, allowing infectious virus to survive. The CDC recommended 1/10 and 1/50 dilutions of SH were efficient at inactivating high numbers of HCoV dried on tile surfaces, whereas, a 1/100 dilution had substantially lower activity. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Often no remaining infectious HCoV could be detected. url: https://api.elsevier.com/content/article/pii/S0195670120304515 doi: 10.1016/j.jhin.2020.09.026 id: cord-291920-gtzc69lc author: Meyers, Kristin J. title: A cross‐sectional community‐based observational study of asymptomatic SARS‐CoV‐2 prevalence in the greater Indianapolis area date: 2020-06-16 words: 1466.0 sentences: 91.0 pages: flesch: 45.0 cache: ./cache/cord-291920-gtzc69lc.txt txt: ./txt/cord-291920-gtzc69lc.txt summary: The Asymptomatic novel CORonavirus iNfection (ACORN) study was designed to investigate the prevalence of SARS‐CoV‐2 infection in the asymptomatic adult population of the Indianapolis metropolitan area, to follow individuals testing positive for the development of symptoms, and to understand duration of positive test results. A nested longitudinal study for participants who test positive for SARS-CoV-2 is ongoing to investigate symptom development at approximately 2 weeks post-index testing. Further, participants who test positive are invited to return for repeat testing at approximately 2-week intervals until the nasopharyngeal swab result is negative for SARS-CoV-2 infection (for a maximum of 3 additional tests). Baseline characteristics, medical history, and overall infection risk factors were generally consistent between SARS-CoV-2 positive and negative participants (Table I) . The identified prevalence of asymptomatic SARS-CoV-2 infection in the community from the ACORN study, the high This article is protected by copyright. abstract: The Asymptomatic novel CORonavirus iNfection (ACORN) study was designed to investigate the prevalence of SARS‐CoV‐2 infection in the asymptomatic adult population of the Indianapolis metropolitan area, to follow individuals testing positive for the development of symptoms, and to understand duration of positive test results. ACORN is a cross‐sectional community‐based observational study of adult residents presenting asymptomatic for COVID‐like illness, defined as the self‐reported absence of the following 3‐symptoms in the last 7‐days: fever (≥100°F), new onset or worsening cough, and new onset or worsening shortness of breath. SARS‐CoV‐2 infection was determined by RT‐PCR in nasopharyngeal swab samples. SARS‐CoV‐2 infection prevalence was expressed as a point estimate with 95%‐CI. Test results are reported for 2953 participants who enrolled and underwent nasopharyngeal swab testing between April 7, 2020 and May 16, 2020. Among tested participants, 91 (3.1%; 95%‐CI; 2.5%‐3.7%) were positive for SARS‐CoV‐2. Overall, baseline characteristics, medical history, and infection risk factors were comparable between SARS‐CoV‐2 positive and negative participants. Within the ongoing 14‐day follow‐up period for positive participants, 58 (71.6%) of 81‐assessed participants remained asymptomatic while others (n=23, 28.4%) reported one or more symptoms. Indiana had “Stay‐at‐Home” orders in place during nearly the entire test period reported here, yet 3.1% of asymptomatic participants tested positive for SARS‐CoV‐2. These results indicate screening questions had limited predictive utility for testing in an asymptomatic population and suggest broader testing strategies are needed. Importantly, these findings underscore that more research is needed to understand the viral transmission and the role asymptomatic and pre‐symptomatic individuals play in this global pandemic. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26182 doi: 10.1002/jmv.26182 id: cord-271849-wxmr8eki author: Meysman, Pieter title: Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date: 2020-09-09 words: 2924.0 sentences: 166.0 pages: flesch: 58.0 cache: ./cache/cord-271849-wxmr8eki.txt txt: ./txt/cord-271849-wxmr8eki.txt summary: In this paper, we demonstrate the use of machine learning to classify SARS-CoV-2 epitope specific T-cell clonotypes in T-cell receptor (TCR) sequencing data. We apply these models to public TCR data and show how they can be used to study T-cell longitudinal profiles in COVID-19 patients to characterize how the adaptive immune system reacts to the SARS-CoV-2 virus. No other epitopes present in TCRex (including the 49 non-SARS-CoV-2 models) were predicted to have a single TCR target within this data set. Once established, these models can be applied to any TCR repertoire data and thus can be used to study putative SARS-CoV-2 reactive T cells in the currently available COVID-19 data. In addition, using such models on longitudinal data reveals a potential difference in temporal dynamics between T cells predicted to react against epitopes that are unique to SARS-CoV-2 and those that are shared among other coronaviruses. abstract: Much is still not understood about the human adaptive immune response to SARS-CoV-2, the causative agent of COVID-19. In this paper, we demonstrate the use of machine learning to classify SARS-CoV-2 epitope specific T-cell clonotypes in T-cell receptor (TCR) sequencing data. We apply these models to public TCR data and show how they can be used to study T-cell longitudinal profiles in COVID-19 patients to characterize how the adaptive immune system reacts to the SARS-CoV-2 virus. Our findings confirm prior knowledge that SARS-CoV-2 reactive T-cell diversity increases over the course of disease progression. However our results show a difference between those T cells that react to epitope unique to SARS-CoV-2, which show a more prominent increase, and those T cells that react to epitopes common to other coronaviruses, which begin at a higher baseline. url: https://doi.org/10.1101/2020.09.09.289355 doi: 10.1101/2020.09.09.289355 id: cord-354113-j8odxs1h author: Miao, Congliang title: A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19 date: 2020-03-24 words: 3129.0 sentences: 200.0 pages: flesch: 52.0 cache: ./cache/cord-354113-j8odxs1h.txt txt: ./txt/cord-354113-j8odxs1h.txt summary: Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group. Methods We retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in We retrospectively collected demographic data, medical history, epidemiological, clinical, laboratory, and CT imaging characteristics of all suspected patients on admission from medical records. 22.20040782 doi: medRxiv preprint This report demonstrated that the incidence of dry cough in confirmed group was significantly higher than that in unconfirmed group, but the clinical symptoms of patients with COVID-19 were nonspecific. abstract: Background Previous studies had described the differences in clinical characteristics between ICU and non-ICU patients. However, seldom study focused on confirmed and unconfirmed groups. Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group. Methods We retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared. Results This study enrolled 163 patients with 62 confirmed cases and 101 unconfirmed cases. Most confirmed patients were clustered (31, 50.0%) and with definite epidemiological exposure. Symptoms of COVID-19 were nonspecific, largely fever and dry cough. Laboratory findings in confirmed group were characterized by normal or reduced white blood cell count, reduced the absolute value of lymphocytes, and elevated levels of C-reactive protein (CRP) and accelerated Erythrocyte sedimentation rate (ESR). The typical chest CT imaging features of patients with confirmed COVID-19 were peripherally distributed multifocal GGO with predominance in the lower lung lobe. Compared with unconfirmed patients, confirmed patients had significantly higher proportion of dry cough, leucopenia, lymphopenia and accelerated ESR (P<0.05); but not with alanine aminotransferase, aspartate aminotransferase, D-dimer, lactic dehydrogenase, and myoglobin (P>0.05). Proportion of peripheral, bilateral or lower lung distribution and multi-lobe involvement, GGO, crazy-paving pattern, air bronchogram and pleural thickening in the confirmed group were also higher (P<0.05). Conclusions Symptoms of COVID-19 were nonspecific. Leukopenia, lymphopenia and ESR, as well as chest CT could be used as a clue for clinical diagnosis of COVID-19. url: https://doi.org/10.1101/2020.03.22.20040782 doi: 10.1101/2020.03.22.20040782 id: cord-308752-uylvtqlu author: Miao, Y. title: First case of acute pancreatitis related to SARS‐CoV‐2 infection date: 2020-06-03 words: 401.0 sentences: 38.0 pages: flesch: 55.0 cache: ./cache/cord-308752-uylvtqlu.txt txt: ./txt/cord-308752-uylvtqlu.txt summary: title: First case of acute pancreatitis related to SARS‐CoV‐2 infection Indeed, we have made similar observations: abdominal pain mimicking surgical disease is frequent during the first days of COVID-19, specifically pancreatitis-like presentation. We report the first case of symptomatic acute pancreatitis associated with SARS-CoV-2 without pulmonary symptoms. Blood tests revealed leucocytes 5960/mm 3 , haemoglobin 13⋅7 g/dl, neutrophils 3650/mm 3 , lymphocytes 1580/mm 3 , eosinophils 30/mm 3 , platelets 242 000/mm 3 , lipase at 211 U/l (3⋅5 N), gamma-glutamyl transferase 65 UI/l, alcaline phosphatase level 83 U/l, lactate dehydrogenase 170 U/l and C-reactive protein at 13⋅8 mg/l. Lipase level peaked on day 4 (430 U/l = 7 N). 4 reported elevated lipase or amylase in 17 per cent of a Chinese cohort without mentioning abdominal pain. Covid-19-related pancreatic injury Pancreatic injury patterns in patients with COVID-19 pneumonia Binding of SARS coronavirus to its receptor damages islets and causes acute diabetes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32492174/ doi: 10.1002/bjs.11741 id: cord-305521-lkou3ycu author: Michel, W. title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay date: 2020-09-27 words: 1072.0 sentences: 104.0 pages: flesch: 65.0 cache: ./cache/cord-305521-lkou3ycu.txt txt: ./txt/cord-305521-lkou3ycu.txt summary: title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay Conclusions: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. A meta-53 analysis of different SARS-CoV-2 studies showed the highest detection rates in Expected shortages of swabs led us to assess alternative diagnostic specimens. In 59 this study, we compared test performance when using mouthwash or a combined oro-60 nasopharyngeal swab. This may limit its use in patients 144 to minimize exposure of health-care personel.In conclusion, SARS-CoV2 detection 145 with mouthwash showed a low sensitivity compared to oro-nasopharyngeal swabs. abstract: Objectives: The optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance. Methods: We tested asymptomatic persons with a previous diagnosis of COVID-19 and their household contacts. First, a mouthwash (gargling for at least 5 sec) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800 system with the Roche SARS-CoV-2 test. Results: Of 76 persons, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 (17%) of these infections but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs. Conclusions: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection. url: https://doi.org/10.1101/2020.09.25.20201541 doi: 10.1101/2020.09.25.20201541 id: cord-287101-k3zq75zc author: Micheli, V. title: Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase date: 2020-07-24 words: 2400.0 sentences: 149.0 pages: flesch: 51.0 cache: ./cache/cord-287101-k3zq75zc.txt txt: ./txt/cord-287101-k3zq75zc.txt summary: The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. A dataset of 41 genome assemblies of Sars-Cov-2 strains isolated in Italy between 20 February 2020 and 30 March 2020 were retrieved from GISAID database 12 , (see Supplementary Table 1 for details). All patients were resident in Lombardy Region, distributed in different provinces, as reported in table X: in particular, the category ''Milano'' contains also patients hospitalized for non-COVID-19 disease, for whom SARS-CoV-2 hospital acquisition was supposed; in addition, HSacco-20, in ''Other'' category, was a nurse living in Bergamo and working at Lodi Hospital. abstract: The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The aim of the study was to expand understanding on the circulation of SARS-CoV-2 in the affected Lombardy areas. To this purpose, twenty full length genomes were collected from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020. The obtained genome assemblies, available on the GISAD database and performed at the Referral Center for COVID-19 diagnosis, identified 2 main monophyletic clades, containing 9 and 52 isolates, respectively. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, the epidemiological reconstruction carried out by this work highlights multiple inputs of the virus into its initial circulation in Lombardy Region. However, a phylogenetic reconstruction robustness will be improved when other genomic sequences will be available, in order to guarantee a complete epidemiological surveillance. url: https://doi.org/10.1101/2020.07.23.20159871 doi: 10.1101/2020.07.23.20159871 id: cord-306770-hjzlj8k3 author: Mick, Paul title: Aerosol-generating otolaryngology procedures and the need for enhanced PPE during the COVID-19 pandemic: a literature review date: 2020-05-11 words: 6318.0 sentences: 332.0 pages: flesch: 43.0 cache: ./cache/cord-306770-hjzlj8k3.txt txt: ./txt/cord-306770-hjzlj8k3.txt summary: During the coronavirus disease 2019 (COVID-19) pandemic, personal protective equipment (PPE) worn by health care workers is critical for reducing transmission of the infection in health care settings, particularly when aerosol-generating medical procedures (AGMP) are being performed. For example, Givi et al and the Canadian Society of Otolaryngology-Head and Neck Surgery [2] call for airborne precautions when performing AGMP on patients for whom the index of suspicion for COVID-19 infection is not high, whereas the World Health Organization, the U.S. Centers for Disease Control, and the Public Health Agency of Canada do not [3, 14, 15] . Measuring the level of aerosolized viral particles in rooms where AGMPs are being performed on patients with COVID-19 would provide indirect evidence of the degree to which these procedures put health care workers at risk of aerosolized transmission, and whether exposure concentration affects risk of infection and/or severity of disease. abstract: BACKGROUND: Adequate personal protective equipment is needed to reduce the rate of transmission of COVID-19 to health care workers. Otolaryngology groups are recommending a higher level of personal protective equipment for aerosol-generating procedures than public health agencies. The objective of the review was to provide evidence that a.) demonstrates which otolaryngology procedures are aerosol-generating, and that b.) clarifies whether the higher level of PPE advocated by otolaryngology groups is justified. MAIN BODY: Health care workers in China who performed tracheotomy during the SARS-CoV-1 epidemic had 4.15 times greater odds of contracting the virus than controls who did not perform tracheotomy (95% CI 2.75–7.54). No other studies provide direct epidemiological evidence of increased aerosolized transmission of viruses during otolaryngology procedures. Experimental evidence has shown that electrocautery, advanced energy devices, open suctioning, and drilling can create aerosolized biological particles. The viral load of COVID-19 is highest in the upper aerodigestive tract, increasing the likelihood that aerosols generated during procedures of the upper aerodigestive tract of infected patients would carry viral material. Cough and normal breathing create aerosols which may increase the risk of transmission during outpatient procedures. A significant proportion of individuals infected with COVID-19 may not have symptoms, raising the likelihood of transmission of the disease to inadequately protected health care workers from patients who do not have probable or confirmed infection. Powered air purifying respirators, if used properly, provide a greater level of filtration than N95 masks and thus may reduce the risk of transmission. CONCLUSION: Direct and indirect evidence suggests that a large number of otolaryngology-head and neck surgery procedures are aerosol generating. Otolaryngologists are likely at high risk of contracting COVID-19 during aerosol generating procedures because they are likely exposed to high viral loads in patients infected with the virus. Based on the precautionary principle, even though the evidence is not definitive, adopting enhanced personal protective equipment protocols is reasonable based on the evidence. Further research is needed to clarify the risk associated with performing various procedures during the COVID-19 pandemic, and the degree to which various personal protective equipment reduces the risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32393346/ doi: 10.1186/s40463-020-00424-7 id: cord-274122-n9jnu2ah author: Mielech, Anna M. title: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date: 2014-02-01 words: 4845.0 sentences: 242.0 pages: flesch: 51.0 cache: ./cache/cord-274122-n9jnu2ah.txt txt: ./txt/cord-274122-n9jnu2ah.txt summary: Coronaviruses encode papain-like proteases (PLpro) that are often multifunctional enzymes with protease activity to process the viral replicase polyprotein and deubiquitinating (DUB)/deISGylating activity, which is hypothesized to modify the innate immune response to infection. Further, we compared the ability of MERS-CoV PLpro and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) PLpro to block innate immune signaling of proinflammatory cytokines. In this study, we demonstrate the deISGylating and deubiquitinating (DUB) activities of the papain-like protease from MERS-CoV, and provide new information on the potential role of coronavirus protease/DUBs to inhibit the innate immune response. Our results suggest that PLpro might contribute to the modulation of innate immune responses upon SARS-CoV and MERS-CoV infection, however, the exact mechanism and the role of coronavirus PLPs and their associated DUB and deISGylating activities in these processes remains to be determined. abstract: Coronaviruses encode papain-like proteases (PLpro) that are often multifunctional enzymes with protease activity to process the viral replicase polyprotein and deubiquitinating (DUB)/deISGylating activity, which is hypothesized to modify the innate immune response to infection. Here, we investigate the predicted DUB activity of the PLpro domain of the recently described Middle East Respiratory Syndrome Coronavirus (MERS-CoV). We found that expression of MERS-CoV PLpro reduces the levels of ubiquitinated and ISGylated host cell proteins; consistent with multifunctional PLpro activity. Further, we compared the ability of MERS-CoV PLpro and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) PLpro to block innate immune signaling of proinflammatory cytokines. We show that expression of SARS-CoV and MERS-CoV PLpros blocks upregulation of cytokines CCL5, IFN-β and CXCL10 in stimulated cells. Overall these results indicate that the PLpro domains of MERS-CoV and SARS-CoV have the potential to modify the innate immune response to viral infection and contribute to viral pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0042682213006624 doi: 10.1016/j.virol.2013.11.040 id: cord-323967-2mo915u1 author: Miersch, Shane title: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date: 2020-11-01 words: 3231.0 sentences: 173.0 pages: flesch: 57.0 cache: ./cache/cord-323967-2mo915u1.txt txt: ./txt/cord-323967-2mo915u1.txt summary: Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Moreover, the use of a highly stable framework 77 enabled facile and modular design of ultra-high affinity nAbs in tetravalent formats that retained 78 favorable drug-like properties and exhibited neutralization potencies that greatly exceeded those 79 of the bivalent IgG format. Fab-phage were screened by ELISA and those that exhibited >50% loss in binding 92 to RBD in the presence of 200 nM ACE2 were sequenced, revealing 34 unique clones (Fig. 1A) , 93 deemed to be potential nAbs and converted into the full-length human IgG1 format for 94 purification and functional characterization. abstract: Recombinant neutralizing antibodies (nAbs) derived from recovered patients have proven to be effective therapeutics for COVID-19. Here, we describe the use of advanced protein engineering and modular design principles to develop tetravalent synthetic nAbs that mimic the multi-valency exhibited by IgA molecules, which are especially effective natural inhibitors of viral disease. At the same time, these nAbs display high affinity and modularity typical of IgG molecules, which are the preferred format for drugs. We show that highly specific tetravalent nAbs can be produced at large scale and possess stability and specificity comparable to approved antibody drugs. Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Design principles defined here can be readily applied to any antibody drug, including IgGs that are showing efficacy in clinical trials. Thus, our results present a general framework to develop potent antiviral therapies against COVID-19, and the strategy can be readily deployed in response to future pathogenic threats. url: https://doi.org/10.1101/2020.10.31.362848 doi: 10.1101/2020.10.31.362848 id: cord-292561-iy06b9h9 author: Miesbach, Wolfgang title: COVID-19: Coagulopathy, Risk of Thrombosis, and the Rationale for Anticoagulation date: 2020-07-17 words: 4889.0 sentences: 262.0 pages: flesch: 45.0 cache: ./cache/cord-292561-iy06b9h9.txt txt: ./txt/cord-292561-iy06b9h9.txt summary: The novel coronavirus infection (COVID-19) is caused by the new coronavirus SARS-CoV-2 and is characterized by an exaggerated inflammatory response that can lead to severe manifestations such as adult respiratory syndrome, sepsis, coagulopathy, and death in a proportion of patients. 5 While most patients show only mild symptoms, 6 a characteristic feature of COVID-19 is that a proportion of patients develop severe complications within a short time after infection, such as adult respiratory syndrome (ARDS) or disseminated intravascular coagulation (DIC), sepsis followed by organ failure, and death. 15 These laboratory changes are consistent with previous studies which showed that hypoalbuminemia, lymphopenia, and C-reactive protein 4 mg/dL were the predictive factors for the progression of pneumonia to respiratory failure in MERS-CoV-infected patients and that elevated lactate dehydrogenase (LDH) levels were associated with hospital-acquired infection with SARS-CoV. abstract: The novel coronavirus infection (COVID-19) is caused by the new coronavirus SARS-CoV-2 and is characterized by an exaggerated inflammatory response that can lead to severe manifestations such as adult respiratory syndrome, sepsis, coagulopathy, and death in a proportion of patients. Among other factors and direct viral effects, the increase in the vasoconstrictor angiotensin II, the decrease in the vasodilator angiotensin, and the sepsis-induced release of cytokines can trigger a coagulopathy in COVID-19. A coagulopathy has been reported in up to 50% of patients with severe COVID-19 manifestations. An increase in d-dimer is the most significant change in coagulation parameters in severe COVID-19 patients, and progressively increasing values can be used as a prognostic parameter indicating a worse outcome. Limited data suggest a high incidence of deep vein thrombosis and pulmonary embolism in up to 40% of patients, despite the use of a standard dose of low-molecular-weight heparin (LMWH) in most cases. In addition, pulmonary microvascular thrombosis has been reported and may play a role in progressive lung failure. Prophylactic LMWH has been recommended by the International Society on Thrombosis and Haemostasis (ISTH) and the American Society of Hematology (ASH), but the best effective dosage is uncertain. Adapted to the individual risk of thrombosis and the d-dimer value, higher doses can be considered, especially since bleeding events in COVID-19 are rare. Besides the anticoagulant effect of LMWH, nonanticoagulant properties such as the reduction in interleukin 6 release have been shown to improve the complex picture of coagulopathy in patients with COVID-19. url: https://doi.org/10.1177/1076029620938149 doi: 10.1177/1076029620938149 id: cord-339701-j0sr3ifq author: Mikami, Takahisa title: Risk Factors for Mortality in Patients with COVID-19 in New York City date: 2020-06-30 words: 3406.0 sentences: 183.0 pages: flesch: 44.0 cache: ./cache/cord-339701-j0sr3ifq.txt txt: ./txt/cord-339701-j0sr3ifq.txt summary: PARTICIPANTS: 6493 patients who had laboratory-confirmed COVID-19 with clinical outcomes between March 13 and April 17, 2020, who were seen in one of the 8 hospitals and/or over 400 ambulatory practices in the New York City metropolitan area MAIN MEASURES: Clinical characteristics and risk factors associated with in-hospital mortality. Cox proportional hazard regression modeling showed an increased risk of in-hospital mortality associated with age older than 50 years (hazard ratio [HR] 2.34, CI 1.47–3.71), systolic blood pressure less than 90 mmHg (HR 1.38, CI 1.06–1.80), a respiratory rate greater than 24 per min (HR 1.43, CI 1.13–1.83), peripheral oxygen saturation less than 92% (HR 2.12, CI 1.56–2.88), estimated glomerular filtration rate less than 60 mL/min/1.73m(2) (HR 1.80, CI 1.60–2.02), IL-6 greater than 100 pg/mL (HR 1.50, CI 1.12–2.03), D-dimer greater than 2 mcg/mL (HR 1.19, CI 1.02–1.39), and troponin greater than 0.03 ng/mL (HR 1.40, CI 1.23–1.62). In this study, we describe the clinical characteristics of COVID-19 in ambulatory and inpatient settings and identify risk factors associated with mortality in hospitalized patients. abstract: BACKGROUND: New York City emerged as an epicenter of the coronavirus disease 2019 (COVID-19) pandemic. OBJECTIVE: To describe the clinical characteristics and risk factors associated with mortality in a large patient population in the USA. DESIGN: Retrospective cohort study. PARTICIPANTS: 6493 patients who had laboratory-confirmed COVID-19 with clinical outcomes between March 13 and April 17, 2020, who were seen in one of the 8 hospitals and/or over 400 ambulatory practices in the New York City metropolitan area MAIN MEASURES: Clinical characteristics and risk factors associated with in-hospital mortality. KEY RESULTS: A total of 858 of 6493 (13.2%) patients in our total cohort died: 52/2785 (1.9%) ambulatory patients and 806/3708 (21.7%) hospitalized patients. Cox proportional hazard regression modeling showed an increased risk of in-hospital mortality associated with age older than 50 years (hazard ratio [HR] 2.34, CI 1.47–3.71), systolic blood pressure less than 90 mmHg (HR 1.38, CI 1.06–1.80), a respiratory rate greater than 24 per min (HR 1.43, CI 1.13–1.83), peripheral oxygen saturation less than 92% (HR 2.12, CI 1.56–2.88), estimated glomerular filtration rate less than 60 mL/min/1.73m(2) (HR 1.80, CI 1.60–2.02), IL-6 greater than 100 pg/mL (HR 1.50, CI 1.12–2.03), D-dimer greater than 2 mcg/mL (HR 1.19, CI 1.02–1.39), and troponin greater than 0.03 ng/mL (HR 1.40, CI 1.23–1.62). Decreased risk of in-hospital mortality was associated with female sex (HR 0.84, CI 0.77–0.90), African American race (HR 0.78 CI 0.65–0.95), and hydroxychloroquine use (HR 0.53, CI 0.41–0.67). CONCLUSIONS: Among patients with COVID-19, older age, male sex, hypotension, tachypnea, hypoxia, impaired renal function, elevated D-dimer, and elevated troponin were associated with increased in-hospital mortality and hydroxychloroquine use was associated with decreased in-hospital mortality. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11606-020-05983-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32607928/ doi: 10.1007/s11606-020-05983-z id: cord-330213-reb9vo7x author: Miladi, Milad title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 words: 3213.0 sentences: 210.0 pages: flesch: 55.0 cache: ./cache/cord-330213-reb9vo7x.txt txt: ./txt/cord-330213-reb9vo7x.txt summary: From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). abstract: In 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions. url: https://doi.org/10.1101/2020.07.18.204362 doi: 10.1101/2020.07.18.204362 id: cord-287847-rmhvc5n5 author: Miles, Brett A. title: Tracheostomy during SARS‐CoV‐2 pandemic: Recommendations from the New York Head and Neck Society date: 2020-04-20 words: 3458.0 sentences: 166.0 pages: flesch: 38.0 cache: ./cache/cord-287847-rmhvc5n5.txt txt: ./txt/cord-287847-rmhvc5n5.txt summary: Patients with significant medical comorbidities, acute respiratory distress syndrome/severe respiratory failure and a low chance of recovery who are infected with SARS-CoV-2 should be carefully evaluated, and discussions with family members, consultants, institutional ethics committees and the treating team should focus on overall prognosis and goals of care prior to performing tracheostomy as a routine matter of care. Although there are limited data on the current pandemic to fully inform personal protective equipment (PPE) recommendations, performing tracheostomy in an actively infected SARS-CoV-2 patient is certainly a high-risk procedure for health care workers. Techniques to manage the acute airway with endotracheal intubation, video laryngoscope for example, should be utilized if possible to avoid emergent tracheostomy in SARS-CoV-2 patients due to the high risk of unsafe conditions and health care worker contaminations. • When clinically appropriate, delay of tracheostomy procedures is recommended to allow for reduced viral load and to decrease the risk of nosocomial infection to critical health care providers. abstract: The rapid spread of SARS‐CoV‐2 in 2019 and 2020 has resulted in a worldwide pandemic characterized by severe pulmonary inflammation, effusions, and rapid respiratory compromise. The result of this pandemic is a large and increasing number of patients requiring endotracheal intubation and prolonged ventilator support. The rapid rise in endotracheal intubations coupled with prolonged ventilation requirements will certainly lead to an increase in tracheostomy procedures in the coming weeks and months. Performing tracheostomy in the setting of active SARS‐CoV‐2, when necessary, poses a unique situation, with unique risks and benefits for both the patient and the health care providers. The New York Head and Neck Society has collaborated on this document to provide guidance on the performance of tracheostomies during the SARS‐CoV‐2 pandemic. url: https://doi.org/10.1002/hed.26166 doi: 10.1002/hed.26166 id: cord-350182-s10nong7 author: Milionis, Charalampos title: A brief analysis and hypotheses about the risk of COVID-19 for people with type 1 and type 2 diabetes mellitus date: 2020-07-20 words: 2733.0 sentences: 164.0 pages: flesch: 42.0 cache: ./cache/cord-350182-s10nong7.txt txt: ./txt/cord-350182-s10nong7.txt summary: Coronavirus disease 2019 (COVID-19) is a respiratory infection which is caused by a novel virus belonging to the Coronaviridae family [1] and is officially named SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The existence of diabetes is strongly associated with an increased risk of developing severe COVID-19 in case of infection with SARS-CoV-2 [24, 25] . The present article supports that heightened inflammatory processes constitute the main pathophysiologic factor for the severity of COVID-19 among patients with diabetes mellitus, whilst impairments in immune response and diabetic comorbidities contribute to the aggravated pathogenesis. Yet it remains unclear whether the innate immune response is vitally impaired in both types of diabetes mellitus and whether hyperglycaemia favours the initial virulence of SARS-CoV-2. Furthermore, patients with diabetes mellitus may present dysfunctional type IV (delayed) hypersensitivity reaction and abnormal complement activation [35] which may hinder the immune response. Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? abstract: COVID-19 is an infectious respiratory disease which firstly occurred in Wuhan, China and evolved rapidly around the globe. The causative pathogen is a novel coronavirus called SARS-CoV-2 with genomic similarities with SARS-CoV and MERS-CoV. The disease is transmitted among humans either through direct contact or via droplets from sneeze or cough. Most infected persons remain asymptomatic or mildly symptomatic, but some patients may develop severe clinical features, including pneumonia, respiratory failure, sepsis and even death. People of advanced age and/or with underlying diseases (including diabetes mellitus) are at greater risk. The innate and adaptive immune system are responsible for protecting the body against viral infection. Nevertheless, it is assumed that SARS-CoV-2 interferes with the immune system through immunomodulating mechanisms which intensify its pathogenesis. A delayed or reduced response of the innate immune system is critical for the development of pathogenesis of the virus. People with diabetes are more likely to develop severe symptoms of COVID-19. The present article speculates that special aspects of the immune dysfunction caused by chronic hyperglycaemia is the main reason for this susceptibility. url: https://doi.org/10.1007/s40200-020-00592-3 doi: 10.1007/s40200-020-00592-3 id: cord-330287-bkqjkhwu author: Miller, Danielle title: Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel date: 2020-11-02 words: 6758.0 sentences: 329.0 pages: flesch: 49.0 cache: ./cache/cord-330287-bkqjkhwu.txt txt: ./txt/cord-330287-bkqjkhwu.txt summary: So-called genomic epidemiology allows for effective reconstruction of viral geographical spread as well as estimation of key epidemiological quantities such as the basic reproduction number of a virus, its growth rate and doubling time, and patterns of disease incidence and prevalence. Here, we set out to sequence SARS-CoV-2 from samples across the state of Israel, with the aim of gaining a better understanding of introductions of the virus into Israel, spread of the virus inside the country, and the epidemiology of the disease, including (a) the basic reproduction number of the virus before and after social distancing measures were implemented, and (b) the extent of viral superspreading within Israel. To estimate the basic reproduction number of SARS-CoV-2 in Israel initially and then following the implementation of social distancing measures, we performed coalescent-based phylodynamic inference using the PhyDyn program implemented in BEAST2 (Methods). Our phylodynamic analysis assumes an underlying susceptibleexposed-infected-recovered (SEIR)-type epidemiological model for SARS-CoV-2 transmission dynamics and explicitly incorporates transmission heterogeneity ( Supplementary Fig. 4 , Methods). abstract: Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread. url: https://doi.org/10.1038/s41467-020-19248-0 doi: 10.1038/s41467-020-19248-0 id: cord-266156-xmf4emln author: Miller, Tyler E. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 words: 4329.0 sentences: 221.0 pages: flesch: 45.0 cache: ./cache/cord-266156-xmf4emln.txt txt: ./txt/cord-266156-xmf4emln.txt summary: Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. The goal of this study is to examine the clinical sensitivity and provide insights into the interpretation of the two most common SARS-CoV-2 diagnostic test modalities: polymerase chain reaction (PCR) and serology. Serologic analysis of IgM, IgA and IgG status was performed in a subset of the above SARS-CoV-2 PCR-positive patients for which we had excess material in the MGH core laboratories for clinical validation studies. To assess the sensitivity of our serology assay over time, we tested for IgM, IgG, and IgA antibodies against the RBD of SARS-CoV-2 spike protein in 157 SARS-CoV-2 PCR-positive patients using an in-house ELISA (Table 1) . abstract: The diagnosis of COVID‐19 requires integration of clinical and laboratory data. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) diagnostic assays play a central role in diagnosis and have fixed technical performance metrics. Interpretation becomes challenging because the clinical sensitivity changes as the virus clears and the immune response emerges. Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. We conducted a single‐center, retrospective study. To derive clinical sensitivity of PCR, we identified 209 PCR‐positive SARS‐CoV‐2 patients with multiple PCR test results (624 total PCR tests) and calculated daily sensitivity from date of symptom onset or first positive test. Clinical sensitivity of PCR decreased with days post symptom onset with >90% clinical sensitivity during the first 5 days after symptom onset, 70%‐71% from Days 9 to 11, and 30% at Day 21. To calculate daily clinical sensitivity by serology, we utilized 157 PCR‐positive patients with a total of 197 specimens tested by enzyme‐linked immunosorbent assay for IgM, IgG, and IgA anti‐SARS‐CoV‐2 antibodies. In contrast to PCR, serological sensitivity increased with days post symptom onset with >50% of patients seropositive by at least one antibody isotype after Day 7, >80% after Day 12, and 100% by Day 21. Taken together, PCR and serology are complimentary modalities that require time‐dependent interpretation. Superimposition of sensitivities over time indicate that serology can function as a reliable diagnostic aid indicating recent or prior infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32856766/ doi: 10.1096/fj.202001700rr id: cord-281391-0qkku2jd author: Miller-Handley, Hilary title: Treatment Options for COVID-19 in Patients with Reduced or Absent Kidney Function date: 2020-09-17 words: 4720.0 sentences: 276.0 pages: flesch: 47.0 cache: ./cache/cord-281391-0qkku2jd.txt txt: ./txt/cord-281391-0qkku2jd.txt summary: COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, was first identified in the Hubei Province of China in late 2019. Because of these findings, chloroquine and hydroxychloroquine were used as early therapies in the treatment of COVID-19, and its use was further propagated by a small, retrospective, biased study from France with 36 patients which showed decrease in viral burden, and improved outcomes in patients treated with hydroxychloroquine [17] . A retrospective study from the Veterans Affairs, looked at hospitalized patients who received hydroxychloroquine and showed no evidence that use of hydroxychloroquine reduced the risk of progression of disease including mechanical ventilation and death [20] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, was first identified in the Hubei Province of China in late 2019. Currently the only role for therapy is treatment of the disease, as opposed to post-exposure prophylaxis, however multiple clinical trials are currently ongoing for both treatment and prophylaxis. Treating COVID-19 relies on two components; the first is inhibition of the viral entrance and replication within the body and the second is inhibition of an exacerbated immune response which can be seen in patients with severe disease. Many drugs have shown in vitro antiviral activity, however clinical trials have not been as promising. Remdesivir has shown a shortening in the time to recovery in hospitalized adults, however currently no mortality benefit demonstrated. Dexamethasone has shown improved mortality in patients requiring respiratory support, but not otherwise. Current research is ongoing in immunomodulation with monoclonal antibodies including interleukin (IL)-6 receptor antagonists and Janus Kinase (JAK) inhibitors. This review summarizes the current data for the most commonly used drugs for COVID-19, and will cover the unique factors that may affect the dosing of these medications in patients with chronic kidney disease (CKD). While clinical trials are ongoing, most are in patients with normal kidney function. During a pandemic when patients with CKD are at higher risk of both infection and death, it is imperative to include patients these patients in the clinical trials. url: https://www.sciencedirect.com/science/article/pii/S1548559520301336?v=s5 doi: 10.1053/j.ackd.2020.09.001 id: cord-301947-b6nwaost author: Millán-Oñate, José title: Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin date: 2020-04-24 words: 3699.0 sentences: 205.0 pages: flesch: 48.0 cache: ./cache/cord-301947-b6nwaost.txt txt: ./txt/cord-301947-b6nwaost.txt summary: We report here the clinical features and therapeutic course of the first reported patient with confirmed COVID-19 pneumonia that recovered in Colombia, after the use of chloroquine and clarithromycin. It is essential to acknowledge that no good controlled data are supporting the use of any of these agents, except for a recent randomized, controlled, open-label trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection, that showed no benefit with lopinavir-ritonavir (LPV/RTV) treatment beyond standard care [13] . We present a confirmed case of COVID-19 from Buga, Valle del Cauca, Colombia, that successful recovered of SARS-CoV-2 infection after receiving chloroquine. Although that just based in one case, we cannot recommend the use of these drugs, our patient improved significantly, and his clinical manifestations ceased, including becoming negative for the SARS-CoV-2 infection, as observed in the rRT-PCR test. abstract: BACKGROUND: COVID-19 pandemics is a challenge for public health and infectious diseases clinicians, especially for the therapeutical approach that is not yet adequately defined. Amid this situation, investigational agents are being used, including chloroquine. We report here the clinical features and therapeutic course of the first reported patient with confirmed COVID-19 pneumonia that recovered in Colombia, after the use of chloroquine and clarithromycin. CASE PRESENTATION: A 34-year-old male, returning from Spain, presented with complaints of fever, and cough, and class-II obesity, being hospitalized. The respiratory viruses and bacteria tested by FilmArray(®) PCR were negative. Two days later, clarithromycin was started because the patient was suspected as community-acquired pneumonia. At the third day, the rRT-PCR confirmed the SARS-CoV-2 infection. A day later, chloroquine was started because of that. His chest computed tomography was performed and showed bilateral multifocal ground-glass opacities with consolidation, which suggested viral pneumonia as a differential diagnosis. Progressively his clinical condition improved and at day 9, patient rRT-PCR for SARS-CoV-2 became negative. The patient was discharged and isolated at home per 14 days. CONCLUSIONS: Our patient improved significantly. This and other COVID-19 cases are urgently demanding results from clinical trials that support evidence-based therapeutical approaches to this pandemic and the clinical management of patients, especially those at critical care. url: https://doi.org/10.1186/s12941-020-00358-y doi: 10.1186/s12941-020-00358-y id: cord-284302-odvv2yn3 author: Minagorre, Pedro J. Alcalá title: CAMBIOS A PARTIR DE LA COVID-19. UNA PERSPECTIVA DESDE LA PEDIATRÍA INTERNA HOSPITALARIA date: 2020-06-19 words: 3134.0 sentences: 297.0 pages: flesch: 49.0 cache: ./cache/cord-284302-odvv2yn3.txt txt: ./txt/cord-284302-odvv2yn3.txt summary: Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Pero ante el impacto anual del VRS y la gripe en las unidades de críticos (15, 16) y los posibles rebrotes de COVID-19, se ha de proveer una adecuada disponibilidad de recursos para el conjunto de pacientes afectados. El notable incremento del número de niños con patología crónica compleja en los últimos años obliga a todos los centros a disponer de planes asistenciales específicos para este grupo de pacientes, también en situaciones excepcionales como esta pandemia por COVID-19. abstract: Resumen La dimensión de la pandemia por SARS-CoV2 ha afectado a la organización asistencial de la Pediatría Hospitalaria de nuestro país. Los nuevos retos generados por la COVID-19 exigen una serie de medidas proactivas basadas en los conocimientos científicos existentes y las normas de buena práctica, que permitan la preparación y la mayor operatividad de los servicios pediátricos hospitalarios. La Pediatría Interna Hospitalaria, como responsable de la atención integral del niño hospitalizado, tiene un papel principal en el nuevo modelo de hospital surgido de esta epidemia. En la presente revisión se analiza la repercusión pediátrica que ha tenido la epidemia por SARS-CoV2 y la preparación ante futuros rebrotes, en posible coexistencia con otras infecciones virales. Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. La Sociedad Española de Pediatría Hospitalaria (SEPHO) pretende con este documento ofrecer a los pediatras internistas hospitalarios una serie de reflexiones y recursos de utilidad en un escenario con muchas incertidumbres. Abstract SARS-CoV2 pandemic dimension has affected the Hospital Pediatrics Medicine assistance in our country. New challenges generated by COVID-19 require a series of proactive measures, based on existing scientific knowledge and standards of good practice, that allow the Pediatric Hospital services readiness and operability. Hospital Internal Pediatrics, as responsible of integral care of the hospitalized child, plays a leading role in the new hospital model emerging from this crisis. This review analyzes the impact of the current SARS-CoV2 epidemic on pediatric care, and perspective of new COVID-19 outbreaks in coexistence with other viral infections. Changes secondary to pandemic involved in Hospital Pediatric units must be analyzed, and how to prepare for future epidemics, also the involvement of pediatric units in adult care and the possible opportunities for improvement. Assistance of patients with chronic complex conditions in epidemic circumstances, safety aspects, opportunities for teaching and ethical considerations are reviewed. The Spanish Society of Hospital Pediatrics Medicine offers with this article a series of resources for Internal Pediatric Medicine practitioners responsible to face next challenges in pediatric hospitalization units. url: https://api.elsevier.com/content/article/pii/S1695403320302071 doi: 10.1016/j.anpedi.2020.06.004 id: cord-274114-fglyfz8p author: Minervina, Anastasia A. title: Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date: 2020-10-01 words: 5557.0 sentences: 297.0 pages: flesch: 56.0 cache: ./cache/cord-274114-fglyfz8p.txt txt: ./txt/cord-274114-fglyfz8p.txt summary: In this study we use longitudinal TCRalpha and TCRbeta repertoire sequencing to quantitatively track T cell clones that significantly expand and contract after recovery from a mild COVID-19 infection, and determine their phenotype. We reveal the dynamics and the phenotype of the memory cells formed after infection, identify pre-existing T cell memory clones participating in the response, and describe public TCR sequence motifs of SARS-CoV-2-reactive clones, suggesting a response to immunodominant epitopes. At the time of writing, no data on TCR sequences specific to MHC-II class epitopes exist to map specificities of CD4+ T-cells in a similar way as we did with MIRA-specific TCRs. However, a recently published database of 1414 bulk TCRbeta repertoires from COVID-19 patients allowed us to confirm the SARS-CoV-2 specificity of contracting clones indirectly. Public TCRbeta sequences that can recognize SARS-CoV-2 epitopes are expected to be clonally expanded and thus sampled more frequently in the repertoires of COVID-19 patients than in control donors. abstract: COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T cell response nor the diversity of resulting immune memory are well understood. In this study we use longitudinal high-throughput T cell receptor (TCR) sequencing to track changes in the T cell repertoire following two mild cases of COVID-19. In both donors we identified CD4+ and CD8+ T cell clones with transient clonal expansion after infection. The antigen specificity of CD8+ TCR sequences to SARS-CoV-2 epitopes was confirmed by both MHC tetramer binding and presence in large database of SARS-CoV-2 epitope-specific TCRs. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T cell clones were detected in the memory fraction at the pre-infection timepoint, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2. url: https://doi.org/10.1101/2020.05.18.100545 doi: 10.1101/2020.05.18.100545 id: cord-322596-vfmzk2el author: Ming, Yi title: Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications date: 2020-07-11 words: 3595.0 sentences: 193.0 pages: flesch: 43.0 cache: ./cache/cord-322596-vfmzk2el.txt txt: ./txt/cord-322596-vfmzk2el.txt summary: Current clinical reports indicate that SARS-CoV-2 is associated with significant morbidity of cardiovascular diseases and complications, such as hypertension (HTN), myocarditis, acute myocardial infarction, and increased heart failure [5, 6] . Based on these theoretical assumptions, it can be concluded that the S protein/host furin/ACE2 signal axis exists in the pathological process of SARS-Cov-S2 infection and mediates the occurrence of adverse cardiovascular prognosis events. Furthermore, a unique furin-like cleavage site exists in the S protein of SARS-Cov-S2 [16] ; thus, the theoretical advantage inferred from this cleavage site in disease infection models can be deduced to prevent and combat COVID-19 caused by SARS-CoV-2. However, in the process of infection, the S protein plays a direct damaging role by recognizing and binding to the ACE2 receptor and invading the host cell [10] . Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein abstract: The novel coronavirus disease 2019 (COVID-19) is a global epidemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 has a similar structure to severe acute respiratory syndrome coronavirus-1(SARS-CoV-1). The S protein on the surface of the virus is cleaved by host proprotein convertases (PCs) to expose the active N-terminal S1 extracellular domain. Its receptors are angiotensin-converting enzyme 2 (ACE2), and the C-terminal S2 membrane anchoring protein is responsible for translocating the virus into the cell. Among patients with COVID-19, there is a higher prevalence of cardiovascular disease, and more than 7% of patients have suffered myocardial damage due to the infection, but the internal mechanism is still poorly understood. There is currently no specific and effective targeted treatment. Reduction of the patient’s morbidity and mortality is an urgent problem that needs to be solved clinically. By exploring the theoretical analysis of PCs and ACE2 in COVID-19 cardiovascular susceptibility, some insights on how to prevent and alleviate adverse cardiovascular prognosis have been provided in this study. url: https://www.ncbi.nlm.nih.gov/pubmed/32838164/ doi: 10.1007/s42399-020-00400-2 id: cord-291513-vpehn6nx author: Minich, Jeremiah title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date: 2020-08-18 words: 6429.0 sentences: 326.0 pages: flesch: 55.0 cache: ./cache/cord-291513-vpehn6nx.txt txt: ./txt/cord-291513-vpehn6nx.txt summary: Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. Here we characterize the suitability of detecting SARS-CoV-2 RNA in experimental conditions as well as COVID-19 patient and built-environment samples using viral-inactivating storage solutions and alternative medical-grade and consumer-grade swabs. In a subset of seven COVID-19 patient nares samples stored in 95% EtOH, we also detected signi cantly higher SARS-CoV-2 viral load in RNA extracted from the swab head versus eluent ( Fig. 1b ; one-tailed paired Student''s t-test p = 0.03). Based on the results from these initial experiments, we conducted a proof-of-concept study in the clinical setting by performing RT-qPCR for the SARS-CoV-2 N1 amplicon and human RNase P gene on RNA extracted from the swab head of nasal samples collected using TMI and/or CGp swabs alongside the recommended SYN swabs. abstract: Background: Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. Results: Compared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while SYN and CGp were both between 725–1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal). Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis. url: https://doi.org/10.21203/rs.3.rs-56028/v1 doi: 10.21203/rs.3.rs-56028/v1 id: cord-294115-7t7kubf6 author: Miralles, Oriol title: Unmet needs, health policies, and actions during the COVID-19 pandemic: a report from six European countries date: 2020-10-15 words: 7255.0 sentences: 343.0 pages: flesch: 48.0 cache: ./cache/cord-294115-7t7kubf6.txt txt: ./txt/cord-294115-7t7kubf6.txt summary: The information collected from the six national reports was pulled together and discussed following the key priorities for action outlined in the UN Policy Brief: (1) Right to health and the participation in the decision-making process; (2) Social inclusion and solidarity under conditions of physical distancing; (3) Necessity of adequate, correctly funded care and support services for older adults; and (4) Need to expand participation by older adults, share good practice and harness knowledge and data [4] . In the Frenchspeaking region, the "Plan d''Urgence Hospitalier" was launched on 14th March and focused on ensuring distribution of hospital equipment, including personal protective equipment (PPE), and human resources (e.g., by reduction/ Impact of COVID-19 on health inequity: On 25th May, Belgium had reported 5734 people with confirmed SARS-CoV-2 infection in long-term care facilities (LTCF). abstract: PURPOSE: The United Nations (UN) has published a Policy Brief on the impact of the Coronavirus Disease 2019 (COVID-19) that identifies policies and responses to protect older adults. Our objective was to summarize actions, health policies and clinical guidelines adopted by six European countries (Belgium, France, Italy, Poland, Spain and United Kingdom) during the pandemic, and to assess the impact of national policies on reducing adverse effects of the COVID-19 pandemic in older populations. METHODS: Reports by geriatricians on the measures and actions undertaken by governmental institutions in each country between March and July 2020, as well as the role of primary care during the pandemic, covered three areas: (a) general health strategies related to the pandemic; (b) impact of COVID-19 on health inequity; and (c) initiatives and challenges for the COVID-19 pandemic and beyond. RESULTS: In the six countries, COVID-19 mortality in nursing homes ranged from 26 to 66%. Although all countries endorsed the World Health Organization general recommendations, the reports identified the lack of harmonized European guidelines and policies for nursing homes, with competencies transferred to national (or regional) governments. All countries restricted visits in nursing homes, but no specific action plans were provided. The role of primary care was limited by the centralization of the crisis in hospital settings. CONCLUSIONS: The older population has been greatly affected by COVID-19 and by the policies initiated to control its spread. The right to health and dignity are transgenerational; chronological age should not be the sole criterion in policy decisions. url: https://www.ncbi.nlm.nih.gov/pubmed/33057981/ doi: 10.1007/s41999-020-00415-x id: cord-349623-dw5o9i59 author: Miranda, José P. title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 words: 3813.0 sentences: 174.0 pages: flesch: 48.0 cache: ./cache/cord-349623-dw5o9i59.txt txt: ./txt/cord-349623-dw5o9i59.txt summary: Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise''s buffer pH 7.2. For the standard protocol, routinely used in the laboratory for the detection of SARS-CoV-2, an aliquot of 180 ul of the sample from the nasopharyngeal swab, including 10 ul of extraction control, was used to extract RNA with the MagNA Pure 96 DNA and Viral NA LV Kit (Roche Diagnostics, Cat. No. For the standardization of the direct SARS-CoV-2 detection protocol without RNA extraction steps, 50 ul aliquots from the primary sample (nasopharyngeal swabs) of 5 anonymized patients were subjected to heat shock (65, 70, or 95 • C) during different incubation times (5, 10, or 30 min), and then were quickly placed at 4 • C until the moment of amplification. abstract: Background: The recent COVID-19 pandemic has posed an unprecedented challenge to laboratory diagnosis, based on the amplification of SARS-CoV-2 RNA. With global contagion figures exceeding 4 million persons, the shortage of reagents for RNA extraction represents a bottleneck for testing globally. We present the validation results for an RT-qPCR protocol without prior RNA extraction. Due to its simplicity, this protocol is suitable for widespread application in resource-limited settings. Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise's buffer pH 7.2. The selected protocol was evaluated for classification concordance with a standard protocol (automated RNA extraction) in 130 routine samples and 50 historical samples with Cq values near to the clinical decision limit. Results: Optimal selected conditions for direct protocol were: thermal shock at 70°C for 10 min, loading 3.5 ul in the RT-qPCR. Prospective evaluation in 130 routine samples showed a 100% classification concordance with the standard protocol. The evaluation in historical samples, selected because their Cqs were at the clinical decision limit, showed 94% concordance with our confirmatory standard, which includes manual RNA extraction. Conclusions : Our results validate the use of this direct RT-qPCR protocol as a safe alternative for SARS-CoV-2 diagnosis in the case of a shortage of reagents for RNA extraction, with minimal clinical impact. url: https://www.ncbi.nlm.nih.gov/pubmed/33178714/ doi: 10.3389/fmed.2020.567572 id: cord-346894-iy35298o author: Miranda-Schaeubinger, Monica title: A primer for pediatric radiologists on infection control in an era of COVID-19 date: 2020-07-07 words: 7262.0 sentences: 372.0 pages: flesch: 42.0 cache: ./cache/cord-346894-iy35298o.txt txt: ./txt/cord-346894-iy35298o.txt summary: In pediatric radiology departments, the risk involved ranges from low (e.g., office workers, remote workers, telemedicine) to very high (e.g., workers performing aerosol-generating procedures on known or suspected COVID-19 patients), depending on the job task assigned [28, 29] . Standard precautions to minimize the spread of infection within health care facilities from direct contact with contaminations include hand hygiene, use of PPE based on anticipated contact with contaminated material, respiratory hygiene/ cough etiquette, cleaning and disinfection of the environment, and proper handling of patient care equipment and waste [10] . Appropriate personal protective equipment usage stratified by COVID-19 status (Table 3) Because of the possibility of airborne transmission of the virus, the CDC recommends respirators for care of all patients with COVID-19 if adequate supplies are available. For all aerosol-generating procedures in children who have either unknown or confirmed positive COVID-19 status, radiologists should adhere to the highest level of respiratory protection available: a respirator, an eye shield, a disposable gown and gloves. abstract: Pediatric radiology departments across the globe face unique challenges in the midst of the current COVID-19 pandemic that have not been addressed in professional guidelines. Providing a safe environment for personnel while continuing to deliver optimal care to patients is feasible when abiding by fundamental recommendations. In this article, we review current infection control practices across the multiple pediatric institutions represented on the Society for Pediatric Radiology (SPR) Quality and Safety committee. We discuss the routes of infectious transmission and appropriate transmission-based precautions, in addition to exploring strategies to optimize personal protective equipment (PPE) supplies. This work serves as a summary of current evidence-based recommendations for infection control, and current best practices specific to pediatric radiologists. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00247-020-04713-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00247-020-04713-1 doi: 10.1007/s00247-020-04713-1 id: cord-352341-dhc748pn author: Miranda-Zazueta, G. title: Manejo farmacológico de pacientes con enfermedades hepáticas y pancreáticas que involucran terapias inmunosupresoras. Posicionamiento en el marco de la pandemia de SARS-COV-2 (COVID-19) date: 2020-06-17 words: 4118.0 sentences: 422.0 pages: flesch: 54.0 cache: ./cache/cord-352341-dhc748pn.txt txt: ./txt/cord-352341-dhc748pn.txt summary: 5 Hasta este momento se han emitido las siguientes recomendaciones en pacientes infectados por COVID-19 que tienen una enfermedad hepática autoinmune de base y usan inmunosupresores: [5] [6] [7] [8]  El presentar alteraciones en las pruebas de función hepática no limita iniciar el tratamiento para COVID-19. Las recomendaciones generales para el manejo de pacientes con trasplante hepático y diagnóstico de COVID-19 se realizan de acuerdo con los diferentes escenarios posibles que nos podemos enfrentar en la práctica clínica. No existe hasta el momento de esta publicación información sobre el riesgo de infecciones en pacientes con inmunosupresión y Pancreatitis Autoinmune (PAI), muchos menos en el contexto del nuevo coronavirus SARS-CoV-2, Sin embargo, teóricamente este riesgo no debería ser mayor al observado para otro tipo de infecciones. abstract: Resumen La enfermedad por coronavirus 2019 (COVID-19) es causada por el virus de Síndrome Respiratorio Agudo Grave - Coronavirus 2 (SARS-CoV-2). COVID 19 ha afectado cerca de 2 millones de personas en todo el mundo en menos de 4 meses posterior al reporte de los primeros casos en China en diciembre 2019. La relación que guarda la enfermedad por SARS-Cov-2 con el tratamiento inmunosupresor utilizado en diversos trastornos gastrointestinales es incierta, esto genera el debate sobre suspender el tratamiento inmunosupresor para mejorar el pronóstico de la infección, lo cual incluye el riesgo inherente de rechazo de injerto o agudización de enfermedades autoinmunes que potencialmente pudieran agravar el curso de la infección. En base a la evidencia disponible se logra establecer una postura de tratamiento en pacientes con enfermedades gastrointestinales que requieren terapia inmunosupresora. Abstract The coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. COVID-19 affected close to 2 million persons worldwide in fewer than 4 months, after the report of the first cases in China in December 2019. The relation of the disease caused by SARS-Cov-2 to immunosuppressive treatment used in different gastrointestinal disorders is uncertain, resulting in debate with regard to suspending immunosuppressive therapy to improve infection outcome. Said suspension implies the inherent risk for graft rejection or autoimmune disease exacerbation that can potentially worsen the course of the infection. Based on the presently available evidence, a treatment stance has been established for patients with gastrointestinal diseases that require immunosuppressive therapy. url: https://www.sciencedirect.com/science/article/pii/S0375090620300653?v=s5 doi: 10.1016/j.rgmx.2020.06.001 id: cord-258128-qtmjgrml author: Mirjalili, Mahtabalsadat title: Coronavirus Disease 2019 (COVID-19) and Transplantation: Pharmacotherapeutic Management of Immunosuppression Regimen date: 2020-07-03 words: 6450.0 sentences: 369.0 pages: flesch: 38.0 cache: ./cache/cord-258128-qtmjgrml.txt txt: ./txt/cord-258128-qtmjgrml.txt summary: 12 In one case report regarding the successful treatment of a kidney transplant recipient with pneumonia caused by SARS-CoV-2 in China, all the immunosuppressants were stopped and the patient received 5 g intravenous immunoglobulin (IVIG) on the first day and then 10 g/day for the next 11 days, with 40 mg/day methylprednisolone for 12 days and 5 million units/day interferon as atomization inhalation. 17, 18 Considering that adverse clinical outcomes and increased mortality and morbidity following the administration of corticosteroids in patients with respiratory infections caused by respiratory syncytial virus (RSV), influenza, SARS-CoV-1, or MERS-CoV may be due to an increased risk of secondary bacterial infections, their use for the prevention of disease progression or its treatment remains under discussion. So far, few studies have been conducted regarding the use of this drug in liver and kidney transplant patients, but if it is administered to this population, its adverse effects and interactions with immunosuppressants and other medications used in transplant patients, such as fluoroquinolones for the treatment of Gram-negative infections, should be considered. abstract: The 2019 novel coronavirus disease (COVID-19) was first detected in Wuhan, Hubei Province, China, in late 2019. Since then, COVID-19 has spread to more than 200 countries in the world, and a global pandemic has been declared by the World Health Organization (WHO). At present, no vaccines or therapeutic regimens with proven efficacy are available for the management of COVID-19. Hydroxychloroquine/chloroquine, lopinavir/ritonavir, ribavirin, interferons, umifenovir, remdesivir, and interleukin antagonists, such as tocilizumab, have been recommended as potential treatment options in COVID-19. Transplant patients receiving immunosuppressant medications are at the highest risk of severe illness from COVID-19. At the same time, with regard to receiving polypharmacy and immunosuppressants, treatment options should be chosen with more attention in this population. Considering drug–drug interactions and adverse effects of medications used for the treatment of COVID-19, such as QT prolongation, the dose reduction of some immunosuppressants or avoidance is recommended in transplant recipients with COVID-19. Thus, this narrative review describes clinically important considerations about the treatment of COVID-19 and immunosuppressive regimens regarding modifications, side effects, and interactions in adult kidney or liver allograft recipients. url: https://doi.org/10.2147/tcrm.s256246 doi: 10.2147/tcrm.s256246 id: cord-103899-6tqm99g1 author: Mirzaei, Rasoul title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date: 2020-11-13 words: 9756.0 sentences: 554.0 pages: flesch: 47.0 cache: ./cache/cord-103899-6tqm99g1.txt txt: ./txt/cord-103899-6tqm99g1.txt summary: Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. This review will summarize the recent discoveries associated with miRNAs in various respiratory infections caused by viruses, especially coronavirus, and address all feasible therapeutic options to mitigate the burden of VRIs. The humoral immunity is immunologically categorized as an acquired immune response in which T helper cells collaborate with B cells to differentiate these types of cells to plasma cells [17] [18] [19] . The immune responses against VRIs, such as IV, hRV, human coronavirus (HcoV), hMPV, and RSV, are correlated with the aberrant expression of several miRNAs in epithelial cells and participate in the pathogenesis of chronic and acute forms of respiratory disorders (Table 1 ) [16] . abstract: The novel coronavirus disease 2019 (COVID-19) pandemic has imposed significant public health problems for the human populations worldwide after the 1918 influenza A virus (IVA) (H1N1) pandemic. Although numerous efforts have been made to unravel the mechanisms underlying the coronavirus, a notable gap remains in our perception of the COVID-19 pathogenesis. The innate and adaptive immune systems have a pivotal role in the fate of viral infections, such as COVID-19 pandemic. MicroRNAs (miRNAs) are known as short noncoding RNA molecules and appear as indispensable governors of almost any cellular means. Several lines of evidence demonstrate that miRNAs participate in essential mechanisms of cell biology, regulation of the immune system, and the onset and progression of numerous types of disorders. The immune responses to viral respiratory infections (VRIs), including influenza virus (IV), respiratory syncytial virus (RSV), and rhinovirus (RV), are correlated with the ectopic expression of miRNAs. Alterations of the miRNA expression in epithelial cells may contribute to the pathogenesis of chronic and acute airway infections. Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. In this article, we present a general review of current studies concerning the function of miRNAs in different VRIs, particularly in coronavirus infection, and address all available therapeutic prospects to mitigate the burden of viral infections. url: https://api.elsevier.com/content/article/pii/S1567576920336717 doi: 10.1016/j.intimp.2020.107204 id: cord-328659-miujzgtd author: Mishra, Akhilesh title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 words: 6064.0 sentences: 361.0 pages: flesch: 55.0 cache: ./cache/cord-328659-miujzgtd.txt txt: ./txt/cord-328659-miujzgtd.txt summary: title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. abstract: The COVID-19 pandemic has spread across the globe at an alarming rate. However, unlike any of the previous global outbreaks the availability of a large number of SARS-CoV-2 sequences provides us with a unique opportunity to understand viral evolution in real time. We analysed 1448 full-length (>29000 nt) sequences available and identified 40 single-nucleotide substitutions occurring in >1% of the genomes. Majority of the substitutions were C to T or G to A. We identify C/Gs with an upstream TTT trinucleotide motif as hotspots for mutations in the SARS-CoV-2 genome. Interestingly, three of the 40 substitutions occur within highly conserved secondary structures in the 5’ and 3’ regions of the genomic RNA that are critical for the virus life cycle. Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. Of note, we observed several co-occurring mutations that almost never occur individually. We define five mutually exclusive lineages (A1, B1, C1, D1 and E1) of SARS-CoV-2 which account for about three quarters of the genomes analysed. We identify lineage-defining leading mutations in the SARS-CoV-2 genome which precede the occurrence of sub-lineage defining trailing mutations. The identification of mutually exclusive lineage-defining mutations with geographically restricted patterns of distribution has potential implications for diagnosis, pathogenesis and vaccine design. Our work provides novel insights on the temporal evolution of SARS-CoV-2. Importance The SARS-CoV-2 / COVID-19 pandemic has spread far and wide with high infectivity. However, the severeness of the infection as well as the mortality rates differ greatly across different geographic areas. Here we report high frequency mutations in the SARS-CoV-2 genomes which show the presence of linage-defining, leading and trailing mutations. Moreover, we propose for the first time, five mutually exclusive clusters of SARS-CoV-2 which account for 75% of the genomes analysed. This will have implications in diagnosis, pathogenesis and vaccine design url: https://doi.org/10.1101/2020.05.07.082768 doi: 10.1101/2020.05.07.082768 id: cord-321146-dd8z5c6d author: Mishra, Rakesh title: SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem date: 2020-07-30 words: 530.0 sentences: 43.0 pages: flesch: 50.0 cache: ./cache/cord-321146-dd8z5c6d.txt txt: ./txt/cord-321146-dd8z5c6d.txt summary: title: SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem It is prudent to identify if SARS CoV-2 affects the respiratory control mechanisms at the brainstem and lead to complications in addition to primary respiratory damage. 5 There are reports which suggest that involvement of pontine and medullary centres by SARS-CoV-2 is a mechanism implicated in potential central respiratory failure complicating primary pulmonary injury. Recently a case report published illustrated brainstem dysfunction due to rhombencephalitis in a patient with acute COVID-19. 7 Therefore, patients with SARS-CoV-2 with neurological symptoms must be followed up closely as they can have further deterioration in their respiratory function. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Does SARS-Cov-2 invade the brain? Neurologic features in severe SARS-CoV-2 infection Neurological manifestations of patients with COVID-19: potential routes of SARS-CoV-2 neuroinvasion from the periphery to the brain abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0929664620303478?v=s5 doi: 10.1016/j.jfma.2020.07.035 id: cord-323832-w19ump0o author: Mishra, Vijaya Nath title: Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection date: 2020-09-19 words: 2881.0 sentences: 183.0 pages: flesch: 52.0 cache: ./cache/cord-323832-w19ump0o.txt txt: ./txt/cord-323832-w19ump0o.txt summary: It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. Since currently available antiviral drugs attack influenza and coronavirus after they have already infected the lung cells, it is important to target the virus and prevent infection in the first stage of viral infection. Phages in the body compete with the other highly infective eukaryotic viruses for cellular receptors and thereby restrict their harmful actions on the host cell [23] . A study of staphylococcal phages on the expression of genes which are involved in antimicrobial immunity in the A549 cell line showed that there is an increased translation of interleukin-2 (IL-2) [25] . e in vitro studies on bacteriophage influence on the ability of human viruses to infect epithelial cells abstract: An outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan City, China, in December 2019. Since then, the outbreak has grown into a global pandemic, and neither a vaccine nor a treatment for the disease, termed coronavirus disease 2019 (COVID-19), is currently available. The slow translational progress in the field of research suggests that a large number of studies are urgently required. In this context, this review explores the impact of bacteriophages on SARS-CoV-2, especially concerning phage therapy (PT). Bacteriophages are viruses that infect and kill bacterial cells. Several studies have confirmed that in addition to their antibacterial abilities, bacteriophages also show antiviral and antifungal properties. It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. The Ganges river in India, which originates from the Himalayan range, is known to harbor a large number of bacteriophages, which are released into the river gradually by the melting permafrost. Water from this river has traditionally been considered a therapeutic agent for several diseases. In this review, we hypothesize that the Ganges river may play a therapeutic role in the treatment of COVID-19. url: https://doi.org/10.1155/2020/8844963 doi: 10.1155/2020/8844963 id: cord-154844-nuqx3tv6 author: Misirli, Goksel title: A comparative analysis for SARS-CoV-2 date: 2020-04-08 words: 1660.0 sentences: 112.0 pages: flesch: 58.0 cache: ./cache/cord-154844-nuqx3tv6.txt txt: ./txt/cord-154844-nuqx3tv6.txt summary: Comparative analyses particularly can play a key role to reveal structural changes in proteins due to mutations, which can lead to behavioural changes, such as the increased binding of the SARS-CoV-2 surface glycoprotein to human ACE2 receptors. Starting with a SARS-CoV-2 genome sequence, the report shows visualising DNA sequence features, deriving amino acid sequences, and aligning different genomes to analyse mutations and differences. The report provides further insights into how the SARS-CoV-2 surface glycoprotein mutated for higher binding affinity to human ACE2 receptors, compared to the SARS-CoV protein, by integrating existing 3D protein models. Here, we integrated secondary structure predictions and realigned the sequences in order to show how these five mutations may affect the binding of the SARS-CoV-2 protein ( Figure 6 ). Compared to the SARS-CoV secondary structures, both the CLC Genomics Workbench predictions and the SARS-CoV-2 ''6W41'' model reveal additional beta strands in the mutated region (shown using the dashed box in Figure 6 ) of the surface glycoprotein. abstract: COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key role to reveal structural changes in proteins due to mutations, which can lead to behavioural changes, such as the increased binding of the SARS-CoV-2 surface glycoprotein to human ACE2 receptors. The aim of this report is to provide an easy to follow tutorial for biologists and others without delving into different bioinformatics tools. More complex analyses such as the use of large-scale computational methods can then be utilised. Starting with a SARS-CoV-2 genome sequence, the report shows visualising DNA sequence features, deriving amino acid sequences, and aligning different genomes to analyse mutations and differences. The report provides further insights into how the SARS-CoV-2 surface glycoprotein mutated for higher binding affinity to human ACE2 receptors, compared to the SARS-CoV protein, by integrating existing 3D protein models. url: https://arxiv.org/pdf/2004.04281v1.pdf doi: nan id: cord-253833-0lajhqn5 author: Misra-Hebert, Anita D title: Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system. date: 2020-08-19 words: 2860.0 sentences: 133.0 pages: flesch: 50.0 cache: ./cache/cord-253833-0lajhqn5.txt txt: ./txt/cord-253833-0lajhqn5.txt summary: [7] [8] [9] 11 A recent prospective study in the United Kingdom and US suggested a ve-fold increased risk for HCW caring for patients with COVID-19 compared to HCW not caring for patients with COVID-19, even with the use of PPE 12 while another study of HCW in a large healthcare system showed a decrease in positive tests for SARS-CoV-2 associated with a universal masking recommendation. In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19 related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. [7] [8] [9] [10] 12 The fact that HCW identi ed as patient-facing had a signi cantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. abstract: Background: Understanding the impact of the COVID-19 pandemic on healthcare workers (HCW) is crucial. Objective: Utilizing a health system COVID-19 research registry, we assessed HCW risk for COVID-19 infection, hospitalization and intensive care unit (ICU) admission. Design: Retrospective cohort study with overlap propensity score weighting. Participants: Individuals tested for SARS-CoV-2 infection in a large academic healthcare system (N=72,909) from March 8-June 9 2020 stratified by HCW and patient-facing status. Main Measures: SARS-CoV-2 test result, hospitalization, and ICU admission for COVID-19 infection. Key Results: Of 72,909 individuals tested, 9.0% (551) of 6,145 HCW tested positive for SARS-CoV-2 compared to 6.5% (4353) of 66,764 non-HCW. The HCW were younger than non-HCW (median age 39.7 vs. 57.5, p<0.001) with more females (proportion of males 21.5 vs. 44.9%, p<0.001), higher reporting of COVID-19 exposure (72 vs. 17 %, p<0.001) and fewer comorbidities. However, the overlap propensity score weighted proportions were 8.9 vs. 7.7 for HCW vs. non-HCW having a positive test with weighted odds ratio (OR) 1.17, 95% confidence interval (CI) 0.99-1.38. Among those testing positive, weighted proportions for hospitalization were 7.4 vs.15.9 for HCW vs. non-HCW with OR of 0.42 (CI 0.26-0.66) and for ICU admission: 2.2 vs.4.5 for HCW vs. non-HCW with OR of 0.48 (CI 0.20 -1.04). Those HCW identified as patient-facing compared to not had increased odds of a positive SARS-CoV-2 test (OR 1.60, CI 1.08-2.39, proportions 8.6 vs. 5.5), but no statistically significant increase in hospitalization (OR 0.88, CI 0.20-3.66, proportions 10.2 vs. 11.4) and ICU admission (OR 0.34, CI 0.01-3.97, proportions 1.8 vs. 5.2). Conclusions: In a large healthcare system, HCW had similar odds for testing SARS-CoV-2 positive, but lower odds of hospitalization compared to non-HCW. Patient-facing HCW had higher odds of a positive test. These results are key to understanding HCW risk mitigation during the COVID-19 pandemic. url: https://doi.org/10.21203/rs.3.rs-61235/v1 doi: 10.21203/rs.3.rs-61235/v1 id: cord-261173-lnjh56ts author: Misra-Hebert, Anita D. title: Impact of the COVID-19 Pandemic on Healthcare Workers’ Risk of Infection and Outcomes in a Large, Integrated Health System date: 2020-09-01 words: 3574.0 sentences: 166.0 pages: flesch: 47.0 cache: ./cache/cord-261173-lnjh56ts.txt txt: ./txt/cord-261173-lnjh56ts.txt summary: In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19-related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. 23 For the outcomes of hospital and intensive care unit (ICU) admission of COVID-19 testpositive patients, the propensity score covariates are those that were found associated with COVID-19 hospitalization outcome in our previous work including age, race, ethnicity, gender, smoking history, body mass index, median income, population per housing unit, presenting symptoms (including fever, fatigue, shortness of breath, diarrhea, vomiting), comorbidities (including asthma, hypertension, diabetes, immunosuppressive disease), medications (including immunosuppressive treatment, nonsteroidal anti-inflammatory drugs [NSAIDs]), and laboratory values (including pre-testing platelets, aspartate aminotransferase, blood urea nitrogen, chloride, and potassium). [7] [8] [9] [10] 12 The fact that HCW identified as patient facing had a significantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. abstract: BACKGROUND: Understanding the impact of the COVID-19 pandemic on healthcare workers (HCW) is crucial. OBJECTIVE: Utilizing a health system COVID-19 research registry, we assessed HCW risk for COVID-19 infection, hospitalization, and intensive care unit (ICU) admission. DESIGN: Retrospective cohort study with overlap propensity score weighting. PARTICIPANTS: Individuals tested for SARS-CoV-2 infection in a large academic healthcare system (N = 72,909) from March 8–June 9, 2020, stratified by HCW and patient-facing status. MAIN MEASURES: SARS-CoV-2 test result, hospitalization, and ICU admission for COVID-19 infection. KEY RESULTS: Of 72,909 individuals tested, 9.0% (551) of 6145 HCW tested positive for SARS-CoV-2 compared to 6.5% (4353) of 66,764 non-HCW. The HCW were younger than the non-HCW (median age 39.7 vs. 57.5, p < 0.001) with more females (proportion of males 21.5 vs. 44.9%, p < 0.001), higher reporting of COVID-19 exposure (72 vs. 17%, p < 0.001), and fewer comorbidities. However, the overlap propensity score weighted proportions were 8.9 vs. 7.7 for HCW vs. non-HCW having a positive test with weighted odds ratio (OR) 1.17, 95% confidence interval (CI) 0.99–1.38. Among those testing positive, weighted proportions for hospitalization were 7.4 vs. 15.9 for HCW vs. non-HCW with OR of 0.42 (CI 0.26–0.66) and for ICU admission: 2.2 vs. 4.5 for HCW vs. non-HCW with OR of 0.48 (CI 0.20–1.04). Those HCW identified as patient facing compared to not had increased odds of a positive SARS-CoV-2 test (OR 1.60, CI 1.08–2.39, proportions 8.6 vs. 5.5), but no statistically significant increase in hospitalization (OR 0.88, CI 0.20–3.66, proportions 10.2 vs. 11.4) and ICU admission (OR 0.34, CI 0.01–3.97, proportions 1.8 vs. 5.2). CONCLUSIONS: In a large healthcare system, HCW had similar odds for testing SARS-CoV-2 positive, but lower odds of hospitalization compared to non-HCW. Patient-facing HCW had higher odds of a positive test. These results are key to understanding HCW risk mitigation during the COVID-19 pandemic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11606-020-06171-9) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11606-020-06171-9 doi: 10.1007/s11606-020-06171-9 id: cord-340821-kelq45dw author: Misrahi, James J. title: HHS/CDC Legal Response to SARS Outbreak date: 2004-02-17 words: 1856.0 sentences: 65.0 pages: flesch: 35.0 cache: ./cache/cord-340821-kelq45dw.txt txt: ./txt/cord-340821-kelq45dw.txt summary: Before the severe acute respiratory syndrome (SARS) outbreak, the Centers for Disease Control and Prevention''s (CDC) legal authority to apprehend, detain, or conditionally release persons was limited to seven listed diseases, not including SARS, and could only be changed using a two-step process: 1) executive order of the President of the United States on recommendation by the Secretary, U.S. Department of Health and Human Services (HHS), and 2) amendment to CDC quarantine regulations (42 CFR Parts 70 and 71). Recognizing the cross border nature of some communicable diseases and in light of this nation''s constitutional structure, section 361 of the Public Health Service Act (42 United States Code section 264) authorizes the Health and Human Services (HHS) Secretary to make and enforce regulations necessary to prevent the introduction, transmission, and spread of communicable diseases from foreign countries into the United States and from one state or possession into another. abstract: Before the severe acute respiratory syndrome (SARS) outbreak, the Centers for Disease Control and Prevention’s (CDC) legal authority to apprehend, detain, or conditionally release persons was limited to seven listed diseases, not including SARS, and could only be changed using a two-step process: 1) executive order of the President of the United States on recommendation by the Secretary, U.S. Department of Health and Human Services (HHS), and 2) amendment to CDC quarantine regulations (42 CFR Parts 70 and 71). In April 2003, in response to the SARS outbreak, the federal executive branch acted rapidly to add SARS to the list of quarantinable communicable diseases. At the same time, HHS amended the regulations to streamline the process of adding future emerging infectious diseases. Since the emergence of SARS, CDC has increased legal preparedness for future public health emergencies by establishing a multistate teleconference program for public health lawyers and a Web-based clearinghouse of legal documents. url: https://www.ncbi.nlm.nih.gov/pubmed/15030712/ doi: 10.3201/eid1002.030721 id: cord-292004-9rpoll7y author: Mitchell, Hugh D. title: The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections date: 2019-09-20 words: 8357.0 sentences: 373.0 pages: flesch: 43.0 cache: ./cache/cord-292004-9rpoll7y.txt txt: ./txt/cord-292004-9rpoll7y.txt summary: The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The same relationships between network topology, viral pathogenicity, and gene expression that were observed for influenza virus were also noted when we used a similar dataset of SARS-CoV infections, thus further validating our analysis and demonstrating that these relationships appear to apply to respiratory viruses in general. abstract: Despite high sequence similarity between pandemic and seasonal influenza viruses, there is extreme variation in host pathogenicity from one viral strain to the next. Identifying the underlying mechanisms of variability in pathogenicity is a critical task for understanding influenza virus infection and effective management of highly pathogenic influenza virus disease. We applied a network-based modeling approach to identify critical functions related to influenza virus pathogenicity using large transcriptomic and proteomic datasets from mice infected with six influenza virus strains or mutants. Our analysis revealed two pathogenicity-related gene expression clusters; these results were corroborated by matching proteomics data. We also identified parallel downstream processes that were altered during influenza pathogenesis. We found that network bottlenecks (nodes that bridge different network regions) were highly enriched in pathogenicity-related genes, while network hubs (highly connected network nodes) were significantly depleted in these genes. We confirmed that this trend persisted in a distinct virus: Severe Acute Respiratory Syndrome Coronavirus (SARS). The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. We demonstrate that EGFR is important during influenza infection, but the role it plays changes for lethal versus non-lethal infections. Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene’s involvement in influenza virus pathogenicity. We also demonstrate the utility of employing multiple network approaches for analyzing host response data from viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/31616667/ doi: 10.3389/fcell.2019.00200 id: cord-324707-9ld73wv1 author: Mitjà, Oriol title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date: 2020-07-16 words: 4268.0 sentences: 263.0 pages: flesch: 54.0 cache: ./cache/cord-324707-9ld73wv1.txt txt: ./txt/cord-324707-9ld73wv1.txt summary: Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . abstract: BACKGROUND: No therapeutics have yet been proven effective for the treatment of mild-illness caused by SARS-CoV-2. We aimed to determine whether early treatment with hydroxychloroquine (HCQ) would be more efficacious than no-treatment for outpatients with mild Covid-19. METHODS: We conducted a multicenter, open label, randomized controlled trial in Catalonia (Spain) between March 17, and May 26, 2020. Eligible Covid-19 cases were non-hospitalized adult patients with recently confirmed SARS-CoV-2 infection and less than five days of symptoms. Patients were assigned to receive HCQ (800 mg on day 1, followed by 400 mg once daily for 6 days) or no antiviral treatment (not-placebo controlled). Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adverse events were assessed up to 28 days. RESULTS: A total of 293 patients were eligible for intention-to-treat analysis: 157 in the control arm and 136 in the intervention arm. The mean age was 41.6 years (SD 12.6), mean viral load at baseline was 7.90 (SD 1.82) Log(10) copies/mL, and median time from symptom onset to randomization was 3 days. No significant differences were found in the mean reduction of viral load at day 3 (-1.41 vs. -1.41 Log(10) copies/mL in the control and intervention arm, respectively; difference 0.01 [95% CI -0.28;0.29]) or at day 7 (-3.37 vs. -3.44; d –0.07 [-0.44;0.29]). This treatment regimen did not reduce risk of hospitalization (7.1%, control vs. 5.9%, intervention; RR 0.75 [0.32;1.77]) nor shortened the time to complete resolution of symptoms (12 days, control vs. 10 days, intervention; p = 0.38). No relevant treatment-related AEs were reported. CONCLUSIONS: In patients with mild Covid-19, no benefit was observed with HCQ beyond the usual care. url: https://doi.org/10.1093/cid/ciaa1009 doi: 10.1093/cid/ciaa1009 id: cord-313755-y7regza1 author: Mitra, Kartik title: Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads date: 2020-07-22 words: 5226.0 sentences: 285.0 pages: flesch: 50.0 cache: ./cache/cord-313755-y7regza1.txt txt: ./txt/cord-313755-y7regza1.txt summary: Further, docking of these candidates against SARS-CoV-2 3CLp and PLp indicated that nelfinavir, tipranavir, novobiocin and ofloxacin, possessed better binding potential when compared to lopinavir (binding energy ¼ -7.3 kcal/mol). Our study suggests that nelfinavir and tipranavir (existing anti-HIV protease inhibitors) which bears the desired pharmacophoric features could be considered as potential candidates for inhibiting SARS-CoV-2 proteases. It is heartening to note that these natural products identified in the study have also shown in vitro anti-viral activity against several viruses and hence can be considered as potential lead candidates for designing SARS-CoV-2 inhibitors. The top two candidates with best docking binding energy were selected from the final shortlisted candidates, namely nelfinavir and tipranavir from FDA-approved drugs and licochalcone-D and wedelolactone from natural product database for molecular dynamics simulations studies with both the proteases. abstract: SARS-related coronaviruses poses continual threat to humanity by rapidly mutating and emerging as severe pandemic outbreaks, including the current nCoV-19 pandemic. Hence a rapid drug repositioning and lead identification strategy are required to mitigate these outbreaks. We report a pharmacophore and molecular dynamics-based approach for drug repositioning and lead identification against dual targets (3CLp and PLp) of SARS-CoV-2. The pharmacophore model of 3CLp inhibitors was apolar with two aromatic and two H-bond acceptors, whereas that of PLp was relatively polar, bearing one aromatic and three H-bond acceptors. Pharmacophore-based virtual screening yielded six existing FDA-approved drugs and twelve natural products with both the pharmacophoric features. Among them are nelfinavir, tipranavir and licochalcone-D, which has shown better binding characteristics with both the proteases compared to lopinavir. The molecular dynamics revealed that the connecting loop (residues 176–199) of 3CLp is highly flexible, and hence, inhibitors should avoid high-affinity interactions with it. Lopinavir, due to its high affinity with the loop region, exhibited unstable binding. Further, the van der Waals size of the 3CLp inhibitors positively correlated with their binding affinity with 3CLp. However, the van der Waals size of a ligand should not cross a threshold of 572Å(3), beyond which the ligands are likely to make high-affinity interaction with the loop and suffer unstable binding as observed in the case of lopinavir. Similarly, the total polar surface area of the ligands were found to be negatively correlated with their binding affinity with PLp. url: https://www.ncbi.nlm.nih.gov/pubmed/32698693/ doi: 10.1080/07391102.2020.1796802 id: cord-356166-fpno9zg5 author: Miyakawa, Kei title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles date: 2020-09-15 words: 1548.0 sentences: 94.0 pages: flesch: 52.0 cache: ./cache/cord-356166-fpno9zg5.txt txt: ./txt/cord-356166-fpno9zg5.txt summary: title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles However, a simple, convenient, rapid, and high-throughput test capable of directly detecting nAbs with high specificity, which could act as an ideal alternative to the neutralization assay, is yet to be developed (Ozcurumez et al., 2020) . In this report, we have developed a HiBiT-VLP-based neutralization test (hiVNT) that can readily detect SARS-CoV-2 nAbs ( Figure 1A ). We noticed a robust increase in NanoLuc activity when the LgBiT-expressing We next tested whether our newly developed hiVLP-SARS2 system could detect nAbs in the serum of COVID-19 patients. In this study, we established the hiVNT, a simple, high-throughput assay system for the quantitative and rapid determination of SARS-CoV-2 nAbs in the sera of individuals after recovery from symptomatic or subclinical COVID-19. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients'' B Cells abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32931563/ doi: 10.1093/jmcb/mjaa047 id: cord-023871-9vi0m378 author: Mizutani, Tetsuya title: Signaling Pathways of SARS-CoV In Vitro and In Vivo date: 2009-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe acute respiratory syndrome (SARS) is a respiratory illness with variable symptoms that was recognized as the first near-pandemic infectious disease of the twenty-first century. A novel human coronavirus, named SARS coronavirus (SARS-CoV), derived from SARS patients was reported as the etiologic agent of SARS. Studying the signaling pathways of SARS-infected cells is key to understanding the molecular mechanism of SARS viral infection. Cell death is observed in cultured Vero E6 cells after SARS-CoV infection. From SARS-CoV infection to cell death, p38 mitogen-activated protein kinase (MAPK) is a key participant in the determination of cell death and survival. Two signaling pathways comprising signal transducer and activator of transcription 3 (STAT3) and p90 ribosomal S6 kinase (p90RSK) are downstream of p38 MAPK. AKT and JNK (Jun NH(2)-terminal kinase) signaling pathways are important to establish persistent infection of SARS-CoV in Vero E6 cells. Expression studies of SARS-CoV proteins indicate that the viral proteins are able to activate signaling pathways of host cells. The study of signaling pathways in SARS-CoV patients is difficult to perform compared with in vitro studies due to the effects of the human immune system. This review highlights recent progress in characterizing signal transduction pathways in SARS-CoV-infected cells in vitro and in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176218/ doi: 10.1007/978-3-642-03683-5_19 id: cord-315337-vgi91uzg author: Mizutani, Tetsuya title: Characterization of Persistent SARS-CoV Infection in Vero E6 Cells date: 2006 words: 912.0 sentences: 63.0 pages: flesch: 54.0 cache: ./cache/cord-315337-vgi91uzg.txt txt: ./txt/cord-315337-vgi91uzg.txt summary: A human intestinal cell line, LoVo, was shown to permit SARS-CoV infection, resulting in the establishment of persistent infection. This cell line expresses the viral receptor ACE-2 4 at high levels, and SARS-CoV infection of Vero E6 causes cytopathic effects within 24 h. In the present study, we established a persistently SARS-CoV-infected cell line after passage 6. Here, we reported a possible mechanism of the establishment of persistent SARS-CoV infection in Vero E6 cells (Fig. 2) . Although the majority of cells died due to apoptosis after SARS-CoV infection, activation of JNK and PI3K/Akt signaling pathways aided a minor population of cells with the potential to support persistent infection to establish persistence. pathways are required for establishing persistent SARS-CoV-infection in Vero E6 cells abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037553/ doi: 10.1007/978-0-387-33012-9_57 id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 words: 4920.0 sentences: 281.0 pages: flesch: 52.0 cache: ./cache/cord-312477-2y88gzji.txt txt: ./txt/cord-312477-2y88gzji.txt summary: title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. abstract: Abstract Background Rapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis is complicated by 30-50% of COVID-19 hospital admissions with negative nose/throat swabs negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We tested two promising candidate lateral flow rapid fingerprick test with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralization, ELISA and the candidate POC antibody tests. We determined the sensitivity and specificity of the individual and combined rapid POC diagnostic tests against a composite gold standard of neutralisation and the standard laboratory RT-PCR. Results 45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Serum neutralisation assay, SARS-CoV-2 Spike IgG ELISA and the POC antibody test results were concordant. Using the composite gold standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our gold standard and 63.0 (IQR 41.0-72.0) years in those without disease. Median duration of symptoms was 7 days (IQR 1-8) in those with infection. The overall sensitivity of rapid NAAT diagnosis was 79.2% (95CI 57.8-92.9%) and 50.0% (11.8-88.2) at days 8-28. Sensitivity and specificity of the combined rapid POC diagnostic tests reached 100% (95CI 85.8-100) and 94.7% (95CI 74.0-99.0) overall. Conclusions Dual point of care SARS-CoV-2 testing can significantly improve diagnostic sensitivity, whilst maintaining high specificity. Rapid combined tests have the potential to transform our management of COVID-19, including inflammatory manifestations where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used. url: http://medrxiv.org/cgi/content/short/2020.06.16.20133157v1?rss=1 doi: 10.1101/2020.06.16.20133157 id: cord-315278-iv2zj67t author: Moazzam, Zorays title: Intussusception in an infant as a manifestation of COVID-19 date: 2020-06-20 words: 2166.0 sentences: 137.0 pages: flesch: 51.0 cache: ./cache/cord-315278-iv2zj67t.txt txt: ./txt/cord-315278-iv2zj67t.txt summary: This is the first documented case of survival in a SARS-CoV-2 positive patient presenting with intussusception as the primary manifestation. A case series from the UK documented 8 COVID-19 patients presenting with fever, abdominal pain and diarrhea with a working diagnosis of systemic sepsis secondary to suspected appendicitis [6] . According to our literature review, this is only the second such instance of a SARS-CoV-2 positive patient presenting to a healthcare center with intussusception as the primary manifestation, and the first documented case in which the patient survived. This would be the first such reported incidence of intussusception as a manifestation of SARS-CoV-2 infection, with no respiratory symptoms. We report, to the best of our knowledge, the first documented instance of survival in a case of intussusception in a SARS-CoV-2 positive pediatric patient. Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children abstract: Gastrointestinal manifestations of COVID-19 are rare and have primarily been limited to diarrhea or vomiting. Intussusception is the most common cause of bowel obstruction in infants, with up to 30% of pediatric intussusception cases having a preceding viral illness. We present the rare case of intussusception in a SARS-CoV-2 positive infant. This is the first documented case of survival in a SARS-CoV-2 positive patient presenting with intussusception as the primary manifestation. As our knowledge of this disease evolves, surgeons need to remain suspicious for possible gastrointestinal manifestations of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32834997/ doi: 10.1016/j.epsc.2020.101533 id: cord-260062-qajk0ov4 author: Mocchegiani, Federico title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area date: 2020-09-10 words: 667.0 sentences: 40.0 pages: flesch: 54.0 cache: ./cache/cord-260062-qajk0ov4.txt txt: ./txt/cord-260062-qajk0ov4.txt summary: title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area reported 200 LTRs with 3 tested positive patients for SARS-CoV-2, none developed a clinical pulmonary disease [3] . reported three deaths among 111 long-term adult liver transplant survivors (transplanted more than 10 years ago) following severe COVID-19 while 3 of 40 recently transplanted (ie, within the past 2 years) patients who were found SARS-CoV-2 positive experienced an uneventful course of the disease [4] . reported an incidence of confirmed COVID-19 infection of 1.25% in the population of LTRs of one Milan transplant centre of whom none developed such a severe disease to require invasive ventilation [5] . During the outbreak of COVID-19, in Marche region the infection rate of SARS-Cov-2 has been of 0.44% [1], similar to that observed in our LTRs population. abstract: nan url: https://doi.org/10.1007/s13304-020-00881-9 doi: 10.1007/s13304-020-00881-9 id: cord-274520-c674wkmt author: Moelling, Karin title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection date: 2020-05-28 words: 6725.0 sentences: 370.0 pages: flesch: 47.0 cache: ./cache/cord-274520-c674wkmt.txt txt: ./txt/cord-274520-c674wkmt.txt summary: title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection e authors concluded that there was likely no risk for contracting infectious diseases from pollutant-associated microbes, but they recommended fixing soil by vegetation to reduce the amount of airborne microbes originating from fecal and terrestrial sources, including potential allergens [31] . As observed in the New York City subway, bacterial communities showed significant similarities with those of outdoor air samples, with some human skin-associated bacteria also being present. ere is evidence that people exposed to severe air pollution are more susceptible to infection with the present SARS-CoV-2 pandemic virus and experience stronger symptoms, not only in large cities of China but also in other parts of the world [46] [47] [48] [49] [50] [51] . Potential human pathogens are typically below the detection limit in air samples even from closed environments such as subway systems, which means that there is not likely a significant risk for infection [31, 32, [34] [35] [36] [37] . abstract: Polluted air poses a significant threat to human health. Exposure to particulate matter (PM) and harmful gases contributes to cardiovascular and respiratory diseases, including allergies and obstructive lung disease. Air pollution may also be linked to cancer and reduced life expectancy. Uptake of PM has been shown to cause pathological changes in the intestinal microbiota in mice and humans. Less is known about the effects of pollution-associated microbiota on human health. Several recent studies described the microbiomes of urban and rural air samples, of the stratosphere and sand particles, which can be transported over long distances, as well as the air of indoor environments. Here, we summarize the current knowledge on airborne bacterial, viral, and fungal communities and discuss their potential consequences on human health. The current data suggest that bacterial pathogens are typically too sparse and short-lived in air to pose a significant risk for infecting healthy people. However, airborne fungal spores may exacerbate allergies and asthma. Little information is available on viruses including phages, and future studies are likely to detect known and novel viruses with a yet unknown impact on human health. Furthermore, varying experimental protocols have been employed in the recent microbiome and virome studies. Therefore, standardized methodologies will be required to allow for better comparisons between studies. Air pollution has been linked to more severe outcomes of SARS (severe acute respiratory syndrome) coronavirus (SARS-CoV) infections. This may have contributed to severe SARS-CoV-2 outbreaks, especially those in China, Northern Italy, Iran, and New York City. url: https://doi.org/10.1155/2020/1646943 doi: 10.1155/2020/1646943 id: cord-262420-vw7fnguu author: Moey, Melissa Y.Y. title: Electrocardiographic Changes and Arrhythmias in Hospitalized Patients With COVID-19 date: 2020-09-15 words: 733.0 sentences: 53.0 pages: flesch: 37.0 cache: ./cache/cord-262420-vw7fnguu.txt txt: ./txt/cord-262420-vw7fnguu.txt summary: Subgroup analysis was performed by gender, race, intensive care unit (ICU) admission, troponin-I levels, and SARS-CoV-2 specific therapy (hydroxychloroquine, azithromycin, tocilizumab). Patients had significant lengthening of their QTc intervals during hospitalization regardless of whether they received SARS-CoV-2 specific therapy. Ours is the first report of electrocardiographic changes in patients hospitalized with SARS-CoV-2 showing significant prolongation of PR, QRS, and QTc intervals. PR interval prolonged significantly in all patients admitted with SARS-CoV-2 infection regardless of medication status or troponin elevation. Critically ill patients with SARS-CoV-2 admitted to ICU and those with elevated troponin-I levels had a significantly wider QRS at the time of admission and during the hospital course. Interestingly, we observed significant QTc lengthening during hospitalization in the small subgroup of patients (n=25) not receiving hydroxychloroquine or azithromycin, suggesting an additional unknown mechanism responsible for QTc prolongation in patients with SARS-CoV-2. Observational study of hydroxychloroquine in hospitalized patients with COVID-19 abstract: nan url: https://doi.org/10.1161/circep.120.009023 doi: 10.1161/circep.120.009023 id: cord-259660-x9sobzyw author: Mohakud, Nirmal K title: An Assumed Vertical Transmission of SARS-CoV-2 During Pregnancy: A Case Report and Review of Literature date: 2020-09-26 words: 1435.0 sentences: 90.0 pages: flesch: 56.0 cache: ./cache/cord-259660-x9sobzyw.txt txt: ./txt/cord-259660-x9sobzyw.txt summary: In the present report, we describe a premature newborn, who was born to a primigravida mother with HELLP (hemolysis, elevated liver enzymes, and low platelet count) syndrome and moderate COVID-19 pneumonia. The newborn tested positive at 12 hours of life for COVID-19 by real-time polymerase chain reaction (RT-PCR) of the tracheal aspirate sample [9] . The authors in one review reported 179 cases of newborns tested positive at birth, whose mothers were infected in the third trimester of pregnancy [5] . The authors of one study described that three newborns born to mothers with COVID-19 infection had positive antibodies (IgM and IgG) at birth [7, 8] . In the present report, the index newborn was tested positive at 12 hours of life without any features of symptomatic COVID-19 infection [9] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn A neonate born to mother with COVID-19 during pregnancy & HELLP syndrome: a possible vertical transmission abstract: The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected persons of all ages, including the newborns. Few published case reports and case series have described the possibility of vertical transmission of COVID-19. In the present report, we describe a young primigravida at 33 weeks of gestation, who presented with a four-day history of low-grade fever, malaise, and breathing difficulty. She underwent testing of nasopharyngeal swab sample by real-time polymerase chain reaction (RT-PCR), which was positive for COVID-19. Cesarean section was done, and a preterm low birthweight baby was delivered. The baby required resuscitation at birth and was mechanically ventilated for a shorter duration. A tracheal aspirate that was taken at 12 hours of life tested positive for COVID-19. The course and outcome of the newborn are described here along with the possibility of vertical transmission. url: https://doi.org/10.7759/cureus.10659 doi: 10.7759/cureus.10659 id: cord-288066-sh6n2c3n author: Mohamed, Mohamed S. title: Sex differences in COVID-19: the role of androgens in disease severity and progression date: 2020-11-11 words: 2489.0 sentences: 155.0 pages: flesch: 41.0 cache: ./cache/cord-288066-sh6n2c3n.txt txt: ./txt/cord-288066-sh6n2c3n.txt summary: Variants in the androgen receptor gene correlate with androgen sensitivity and are implicated in diseases like androgenetic alopecia and prostate cancer, conditions that have been associated with worse COVID-19 outcomes and hospitalization. The proposed mechanism behind this effect is based on the idea that androgen receptor and, subsequently, TMPPRSS2 expression affects the SARS-COV2 virus ability to enter host cells and its spike proteins affinity to bind ACE2 receptors (Fig. 1 ). SARS-CoV2 spike proteins are then primed by TMPRSS2, allowing the interaction with ACE2 receptors to enter host cells Fig. 2 Theoretical mechanisms suggesting CAG repeats length and associated androgen sensitivity as a predictor for COVID-19 disease severity lack of control groups or testosterone levels prior to infection, the results warrant consideration. Increased androgen receptor expression might lead to a higher risk of acquiring a severe COVID-19 disease by promoting TMPRSS2 transcription (Fig. 2) . Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men abstract: PURPOSE: Throughout the SARS-CoV2 pandemic, multiple reports show higher percentages of hospitalization, morbidity, and mortality among men than women, indicating that men are more affected by COVID-19. The pathophysiology of this difference is yet not established, but recent studies suggest that sex hormones may influence the viral infectivity process. Here, we review the current evidence of androgen sensitivity as a decisive factor for COVID-19 disease severity. METHODS: Relevant literature investigating the role of androgens in COVID-19 was assessed. Further, we describe several drugs suggested as beneficial for COVID-19 treatment related to androgen pathways. Lastly, we looked at androgen sensitivity as a predictor for COVID-19 progression and ongoing clinical trials on androgen suppression therapies as a line of treatment. RESULTS: SARS-COV2 virus spike proteins utilize Transmembrane protease serine 2 (TMPRSS2) for host entry. Androgen receptors are transcription promoters for TMPRSS2 and can, therefore, facilitate SARS-COV2 entry. Variants in the androgen receptor gene correlate with androgen sensitivity and are implicated in diseases like androgenetic alopecia and prostate cancer, conditions that have been associated with worse COVID-19 outcomes and hospitalization. CONCLUSION: Androgen’s TMPRSS2-mediated actions might explain both the low fatalities observed in prepubertal children and the differences between sexes regarding SARS-COV2 infection. Androgen sensitivity may be a critical factor in determining COVID-19 disease severity, and sensitivity tests can, therefore, help in predicting patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/33179220/ doi: 10.1007/s12020-020-02536-6 id: cord-262786-otxpc46a author: Mohammadi, Soheil title: Understanding the Immunologic Characteristics of Neurologic Manifestations of SARS-CoV-2 and Potential Immunological Mechanisms date: 2020-09-01 words: 6290.0 sentences: 334.0 pages: flesch: 38.0 cache: ./cache/cord-262786-otxpc46a.txt txt: ./txt/cord-262786-otxpc46a.txt summary: Here, we review the currently available evidence to discuss the plausible immunologic pathways that may contribute to the development of COVID-19 neurological complications, namely Alzheimer''s disease, Parkinson''s disease, stroke, multiple sclerosis, Guillain-Barre syndrome, seizure, and brainstem involvement. Although the virus, also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mainly manifests as an acute respiratory infection [2] , recent evidence suggests that 36% of affected patients exhibit neurological sequelae [3] . Systemic inflammatory response syndrome (SIRS) is defined as excessive host immune response against noxious stimuli (e.g., viral infection), through which the primary protective role of cytokine release turns into a detrimental response against host tissues, leading to impaired integrity of capillary walls and end-organ dysfunction [22] . We hypothesize that not only the persistent systemic inflammation caused by SARS-CoV-2 may act as a trigger for microglial activation but also large amounts of pro-inflammatory cytokines secreted in response to this viral infection may aggravate neurodegeneration leading to AD. abstract: Similar to its predecessors, coronavirus disease 2019 (COVID-19) exhibits neurotrophic properties, which lead to progression of neurologic sequelae. Besides direct viral invasion to the central nervous system (CNS), indirect CNS involvement through viral-mediated immune response is plausible. Aberrant immune pathways such as extreme release of cytokines (cytokine storm), autoimmunity mediated by cross-reactivity between CNS components and viral particles, and microglial activation propagate CNS damage in these patients. Here, we review the currently available evidence to discuss the plausible immunologic pathways that may contribute to the development of COVID-19 neurological complications, namely Alzheimer’s disease, Parkinson’s disease, stroke, multiple sclerosis, Guillain-Barre syndrome, seizure, and brainstem involvement. url: https://www.ncbi.nlm.nih.gov/pubmed/32869183/ doi: 10.1007/s12035-020-02094-y id: cord-349445-yh6ndtgm author: Mohammed El Tabaa, Manar title: Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost date: 2020-05-27 words: 11840.0 sentences: 618.0 pages: flesch: 39.0 cache: ./cache/cord-349445-yh6ndtgm.txt txt: ./txt/cord-349445-yh6ndtgm.txt summary: Therefore, researchers suggested that the use of angiotensin converting enzyme inhibitors (ACEIs) and/or angiotensin receptor blockers (ARBs), may show a positive trend towards the severe inflammatory reactions and endothelial dysfunction caused by stimulating the function of ACE/Ang II/AT-1 axis and thereby, towards the bad pulmonary effects associated with the COVID-19 infection [29, 30] . Since IL-6 would inactivate endothelial nitric oxide synthase (eNOS), it could disrupt NO production [90] , decreasing its level and inducing a state of oxidative stress that may lead to Ang II-induced impairment in endothelial responses [91] Postulating impaired endothelium functions as a principal factor in the pathogenesis of heart failure, hypertension and diabetes, it will be expected to classify the patients of such diseases as high risk groups for COVID-19 development [92] [93] [94] . Taken into consideration the numerous harmful effects possibly induced by Ang II during COVID-19 pathogenesis, we found that most novel studies aim to use the anti-hypertensive drugs which act either by inhibiting the ACE activity or by blocking AT1 receptor, suggesting that action may mitigate the disease severity in COVID-19 patients. abstract: COVID-19 is an ongoing viral pandemic disease that is caused by SARS-CoV2, inducing severe pneumonia in humans. However, several classes of repurposed drugs have been recommended, no specific vaccines or effective therapeutic interventions for COVID-19 are developed till now. Viral dependence on ACE-2, as entry receptors, drove the researchers into RAS impact on COVID-19 pathogenesis. Several evidences have pointed at Neprilysin (NEP) as one of pulmonary RAS components. Considering the protective effect of NEP against pulmonary inflammatory reactions and fibrosis, it is suggested to direct the future efforts towards its potential role in COVID-19 pathophysiology. Thus, the review aimed to shed light on the potential beneficial effects of NEP pathways as a novel target for COVID-19 therapy by summarizing its possible molecular mechanisms. Additional experimental and clinical studies explaining more the relationships between NEP and COVID-19 will greatly benefit in designing the future treatment approaches. url: https://api.elsevier.com/content/article/pii/S0006295220302914 doi: 10.1016/j.bcp.2020.114057 id: cord-343136-kftffes0 author: Mohon, Abu Naser title: Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2 date: 2020-09-15 words: 2591.0 sentences: 164.0 pages: flesch: 54.0 cache: ./cache/cord-343136-kftffes0.txt txt: ./txt/cord-343136-kftffes0.txt summary: A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. Limit of detection of the LAMP assay was evaluated by using a nasopharyngeal (NP) swab sample infected with SARS-CoV-2 for which the viral load was quantified using digital droplet PCR (see Supplementary Methods). Twenty four replicates from a serial dilution containing 25-50 copies of SARS-CoV-2 which equates to 1X LOD (patient sample NP swab in VTM viral load confirmed by digital droplet PCR) per reaction were tested using dual-target RT-LAMP (Table 3) . The dual-target RT-LAMP test for SARS-CoV-2 developed in this study has comparable analytical sensitivity and specificity, limit of detection, precision, and achieved excellent agreement compared to the reference RT-PCR methods used internationally. abstract: A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. The LAMP assay achieves a comparable limit of detection (25 copies per reaction) as commonly used RT-PCR protocols using clinical samples quantified by digital droplet PCR. Precision, cross-reactivity, inclusivity, and limit of detection studies were performed according to regulatory standards. Clinical validation of dual-target RT-LAMP (S and RdRP gene) achieved a PPA of 98.48% (95% CI 91.84% to 99.96%) and NPA 100.00% (95% CI 93.84% to 100.00%) based on the E gene and N2 gene reference RT-PCR methods. The method has implications for development of point of care technology using isothermal amplification. url: https://www.ncbi.nlm.nih.gov/pubmed/32941977/ doi: 10.1016/j.jviromet.2020.113972 id: cord-296007-1gsgd22t author: Mohseni, Amir Hossein title: Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date: 2020-09-12 words: 2327.0 sentences: 110.0 pages: flesch: 64.0 cache: ./cache/cord-296007-1gsgd22t.txt txt: ./txt/cord-296007-1gsgd22t.txt summary: Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV N proteins prefers the 2 2 1 hydrophobic amino acid residues (e.g. Ile, Leu, Met, and Phe), and the second position of these hit peptides 2 2 2 is an hydrophobic amino acid residue Pro forming five strong VDW forces with residues Y99, V67, M45, 2 2 3 Y7, and F9 and two H-bonds with residues K66 and E63 on MHC molecule ( Figure S2A , left). Visualization of interactions in the atomic level structure of a TCR-pMHC complex in the hit peptide of 2 4 9 SARS-CoV-2 N protein for HLA-E ( Figure S3C ) within 20 and 8 Å was generated on-the-fly using of the homologous peptide antigens of all queries has no detectable binding to both MHC and TCR. abstract: The coronavirus disease 2019 (COVID-19) is triggered by severe acute respiratory syndrome mediated by coronavirus 2 (SARS-CoV-2) infection and was declared by WHO as a major international public health concern. While worldwide efforts are being advanced towards vaccine development, the structural modeling of TCR-pMHC (T Cell Receptor-peptide-bound Major Histocompatibility Complex) regarding SARS-CoV-2 epitopes and the design of effective T cell vaccine based on these antigens are still unresolved. Here, we present both pMHC and TCR-pMHC interfaces to infer peptide epitopes of the SARS-CoV-2 proteins. Accordingly, significant TCR-pMHC templates (Z-value cutoff > 4) along with interatomic interactions within the SARS-CoV-2-derived hit peptides were clarified. Also, we applied the structural analysis of the hit peptides from different coronaviruses to highlight a feature of evolution in SARS-CoV-2, SARS-CoV, bat-CoV, and MERS-CoV. Peptide-protein flexible docking between each of the hit peptides and their corresponding MHC molecules were performed, and a multi-hit peptides vaccine against the S and N glycoprotein of SARS-CoV-2 was designed. Filtering pipelines including antigenicity, and also physiochemical properties of designed vaccine were then evaluated by different immunoinformatics tools. Finally, vaccine-structure modeling and immune simulation of the desired vaccine were performed aiming to create robust T cell immune responses. We anticipate that our design based on the T cell antigen epitopes and the frame of the immunoinformatics analysis could serve as valuable supports for the development of COVID-19 vaccine. url: https://doi.org/10.1101/2020.09.12.294413 doi: 10.1101/2020.09.12.294413 id: cord-305330-mklkugj5 author: Moiseev, Sergey title: Cancer in intensive care unit patients with COVID-19 date: 2020-05-28 words: 489.0 sentences: 35.0 pages: flesch: 49.0 cache: ./cache/cord-305330-mklkugj5.txt txt: ./txt/cord-305330-mklkugj5.txt summary: susceptible to severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection and complications, although data on COVID-19 and malignancies remain limited. noted that patients with cancer were more likely to experience severe sequelae of SARS-CoV-2 infection, such as intensive care admission, invasive ventilation or death. 2 However, Wang and Zhang argued that the most important morbidity factor is exposure to an infection source, whereas worse outcomes from SARS-CoV-2 infection could be associated (at least partly) with older age of patients with cancer 3 . In a nationwide study, we evaluated the prevalence of malignancies among 1307 intensive care unit (ICU) patients with SARS-CoV-2 pneumonia who required respiratory support. However, our data suggest that other factors, such as older age and comorbidities, contribute significantly to the more severe course of SARS-CoV-2 infection in cancer patients. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320303273?v=s5 doi: 10.1016/j.jinf.2020.05.053 id: cord-284068-sbon3aes author: Mok, Chee Keng title: Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date: 2020-06-22 words: 1798.0 sentences: 104.0 pages: flesch: 49.0 cache: ./cache/cord-284068-sbon3aes.txt txt: ./txt/cord-284068-sbon3aes.txt summary: Validation assays to determine changes in infectious virus titres upon treatment was carried out by testing selected hit compounds in dose-dependent assays in Vero E6 to confirm the primary screen observation and also in the human hepatocarcinoma HuH7 cell line as the latter cell line expresses high levels of the ACE2 receptor (10) and supports replication of coronaviruses (11) . While recent data has shown that vitamin D levels are negatively associated with morbidity and mortality of COVID-19 cases (13, 14) , this is the first report of a direct inhibitory effect of calcitriol on SARS-CoV-2. The authors speculated that vitamin D supplementation could protect against SARS-CoV-2 infection and improve patient disease outcomes (16) , and our finding certainly provides credence to this hypothesis. Given the high transmissibility of SARS-CoV-2 globally (23), if these findings can be replicated in clinical trials, calcitriol may certainly prove to be an effective tool in the effort to control the pandemic while waiting for an effective vaccine to be rolled out globally. abstract: COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients. url: https://doi.org/10.1101/2020.06.21.162396 doi: 10.1101/2020.06.21.162396 id: cord-296339-23yi8so0 author: Mok, Wendy title: Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens date: 2007-09-26 words: 1395.0 sentences: 75.0 pages: flesch: 43.0 cache: ./cache/cord-296339-23yi8so0.txt txt: ./txt/cord-296339-23yi8so0.txt summary: We used computational methods to examine the extent to which this practice can result in inaccurate ''retrodiction.'' Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance. Herein, we show that adopting molecular clock assumptions can yield inaccurate estimated origin times, considering as an example data from the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) infection in humans. Recognizing that this change in substitution rate would violate a molecular clock assumption and could cause pairwise genetic distances to yield inaccurate evolutionary divergence estimates (especially if genetic distance calculations were performed with respect to a reference sequence representing an hypothetical common ancestor), we quantifi ed the extent to which failing to account for dynamic SARS-CoV evolution might affect estimating an origin time. abstract: Researchers routinely adopt molecular clock assumptions in conducting sequence analyses to estimate dates for viral origins in humans. We used computational methods to examine the extent to which this practice can result in inaccurate ‘retrodiction.’ Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance. url: https://www.ncbi.nlm.nih.gov/pubmed/19461973/ doi: nan id: cord-345717-ktajrf7d author: Monagin, Corina title: Serologic and behavioral risk survey of workers with wildlife contact in China date: 2018-04-03 words: 4585.0 sentences: 241.0 pages: flesch: 45.0 cache: ./cache/cord-345717-ktajrf7d.txt txt: ./txt/cord-345717-ktajrf7d.txt summary: We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. The present study focuses on the potential for zoonotic viral transfer through contact with wildlife in Guangdong prefectures in China, and seeks to augment our understanding and identification of risky populations, occupations, and behaviors, as well as the perceptions of risk at these interfaces. We performed a serological survey and concurrent behavioral questionnaire of individuals with wildlife contact in Guangdong Province, China, in order to better characterize occupations and community-level behavioral risks that contribute to zoonotic transmission of various wildlife pathogens with pandemic potential. We targeted high-risk individuals, defined as individuals with high levels of exposure to wildlife (wild animal blood or bodily fluids)-primarily hunters, persons working in wet markets and restaurants that butcher wild game, who could be followed over a period of time. abstract: We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. A risk factor/exposure survey was administered to individuals with high levels of exposure to wildlife. Serological testing was performed to evaluate prior infection with several wildlife viral pathogens. Follow up serology was performed on a subset of the cohort as well as close contacts of individuals. 1,312 individuals were enrolled in the study. Contact with a wide range of wildlife species was reported in both occupational and occasional contexts. The overall proportion of individuals seropositive to any of the tested wildlife pathogens was approximately 4.0%. However, persons employed as butchers demonstrated a seropositivity of 9.0% to at least one pathogen of interest. By contrast, individuals working as hunters had lower rates of seropositivity. Among the study population, a number of other behaviors showed correlation with seropositivity, including contact with particular wildlife species such as field rats. These results demonstrate the need to further explore zoonotic risks of particular activities regarding wildlife contact, and to better understand risks of persons working as butchers with wildlife species. url: https://doi.org/10.1371/journal.pone.0194647 doi: 10.1371/journal.pone.0194647 id: cord-272419-y3ebt4jm author: Monari, Caterina title: A Focus on the Nowadays Potential Antiviral Strategies in Early Phase of Coronavirus Disease 2019 (Covid-19): A Narrative Review date: 2020-08-09 words: 6476.0 sentences: 318.0 pages: flesch: 46.0 cache: ./cache/cord-272419-y3ebt4jm.txt txt: ./txt/cord-272419-y3ebt4jm.txt summary: Possible inhibition of SARS-CoV-2 3-chymotrisyn-like (3CL)-protease and papain-like protease Lopinavir is excreted in the gastrointestinal (GI) tract, and thus coronavirus-infected enterocytes might be exposed to higher concentrations of the drug LPV/r tab 200/50 mg: 2 tab BID LPV/r oral sol 80/20 mg: 5 mL BID DRV/cobi tab 800/150 mg: 1 tab QD Gastrointestinal: diarrhea, nausea, vomiting, increased amylase, lipase, total cholesterol and triglycerides (risk factor for pancreatitis) Hepatotoxicity: increasing in GGT, AST, ALT, total bilirubin, hepatitis Cardiological: QT-and PR-interval prolongation, hypertension, bradyarrhytmias; torsade de pointes have been reported in patients treated with LPV/r Metabolical: hyperglycemia and diabetes mellitus, increased uric acid Recently, a randomized, controlled, open-label trial comparing the efficacy of LPV/r versus standard of care was conducted in 199 hospitalized adult patients with severe COVID-19: no significant difference between the two groups neither in the time of clinical improvement (hazard ratio [HR] 1.31; 95% CI 0.95-1.80; p 0.09), nor in the 28-day mortality rate (19.2% versus 25.0%; 95% CI −17.3 to 5.7) was observed [40] . abstract: Background: The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the related disease (COVID-19) has rapidly spread to a pandemic proportion, increasing the demands on health systems for the containment and management of COVID-19. Nowadays, one of the critical issues still to be pointed out regards COVID-19 treatment regimens and timing: which drug, in which phase, for how long? Methods: Our narrative review, developed using MEDLINE and EMBASE, summarizes the main evidences in favor or against the current proposed treatment regimens for COVID-19, with a particular focus on antiviral agents. Results: Although many agents have been proposed as possible treatment, to date, any of the potential drugs against SARS-CoV-2 has shown to be safe and effective for treating COVID-19. Despite the lack of definitive evidence, remdesivir remains the only antiviral with encouraging effects in hospitalized patients with COVID-19. Conclusions: In such a complex moment of global health emergency, it is hard to demand scientific evidence. Nevertheless, randomized clinical trials aiming to identify effective and safe drugs against SARS-CoV-2 infection are urgently needed in order to confirm or reject the currently available evidence. url: https://www.ncbi.nlm.nih.gov/pubmed/32784922/ doi: 10.3390/life10080146 id: cord-297879-6xb25uhx author: Moncunill, G. title: SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up date: 2020-08-25 words: 5546.0 sentences: 320.0 pages: flesch: 56.0 cache: ./cache/cord-297879-6xb25uhx.txt txt: ./txt/cord-297879-6xb25uhx.txt summary: A follow-up survey one month after the baseline (April-May 2020) measured SARS-CoV-2 infection by real time reverse-transcriptase polymerase chain reaction (rRT-PCR) and IgM, IgA, IgG and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein by Luminex. We found that 9.3% (95% CI: 7.1-12.0) of the participants were seropositive and the cumulative prevalence of SARS-CoV-2 infection (considering a past or current positive result to either antibody testing or rRT-PCR) was 11.2% (95% CI: 8.8-14.1). We measured IgM, IgG, and IgA isotypes and subclasses, and assessed the factors associated with new infections as well as levels and kinetics of antibodies. Levels (median fluorescence intensity, MFI) of IgM, IgG, and IgA against receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein stratified by asymptomatic participants and participants who reported COVID-19 compatible symptoms at recruitment (month 0, M0), month 1 (M1) or at both visits (M0&M1). abstract: Background. At the peak of the COVID-19 pandemic in Spain, cumulative prevalence of SARS-CoV-2 infection in a cohort of 578 randomly selected health care workers (HCW) from Hospital Clinic de Barcelona was 11.2%. Methods. A follow-up survey one month after the baseline (April-May 2020) measured SARS-CoV-2 infection by real time reverse-transcriptase polymerase chain reaction (rRT-PCR) and IgM, IgA, IgG and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein by Luminex. Prevalence of infection was defined by a positive SARS-CoV-2 rRT-PCR and/or antibody seropositivity. Results. The cumulative prevalence of infection at month 1 was 14.9% (84/565) and the seroprevalence 14.5% (82/565) for IgM and/or IgG and/or IgA. We found 25 (5%) new infections in participants without previous evidence of infection at baseline (501) and two participants seroreverted for IgM and/or IgG and/or IgA. Among seropositive participants at baseline, IgM and IgA levels generally declined at month 1 (antibody decay rates of 0.49 (95% CI, 0.40-0.60) and 0.34 (95% CI, 0.26-0.44)), respectively. Eight percent of the participants seroreverted for IgM and 11% for IgA. Subjects reporting COVID-19-like symptoms and laboratory and other technicians had higher risk of infection. The most frequent subclass responses were IgG1 and IgG2, followed by IgG3, with higher levels of IgG1, and only IgA1 but no IgA2 was detected. Conclusions. Our findings highlight the importance of a continuous and improved surveillance of SARS-CoV-2 infections in HCW, particularly in high risk groups. The decay of IgA and IgM levels have implications for seroprevalence studies using these isotypes. url: http://medrxiv.org/cgi/content/short/2020.08.23.20180125v1?rss=1 doi: 10.1101/2020.08.23.20180125 id: cord-266308-fjpq1ljp author: Mondal, Priya title: Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation date: 2020-11-05 words: 6882.0 sentences: 383.0 pages: flesch: 50.0 cache: ./cache/cord-266308-fjpq1ljp.txt txt: ./txt/cord-266308-fjpq1ljp.txt summary: Binding energies (BEs; kcal/mol) of selected bioactives from medicinal plants with SARS-CoV-2 M pro , S-protein and human ACE2 and their chemical interactions with the binding site. Among the standard drugs, nelfinavir, an anti-retroviral and protease inhibitor, has shown a stronger affinity towards all three targets of SARS-CoV-2 with the BE of À8.3 kcal/mol for M pro , À6.6 kcal/mol for S-protein and À6.4 kcal/mol for ACE2 (Supporting Information Table S1 ). In our current study, the selected bioactives from medicinal plants as well as standard drugs have shown interaction towards the key residues of the S-protein receptor-binding motif, as shown in Supporting Information Fig. S4 and S5 . The interactions of the standard drugs and medicinal plant bioactives were also similar towards hotspot residues of the ACE2 receptor as shown in Supporting Information Fig. S7 and S8. abstract: COVID-19 is an infectious pandemic caused by the SARS-CoV-2 virus. The critical components of SARS-CoV-2 are the spike protein (S-protein) and the main protease (M(pro)). M(pro) is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the host cells through the angiotensin-converting enzyme 2 (ACE2). Since ACE2 is required for the binding of SARS-CoV-2 on the host cells, ACE2 inhibitors and blockers have got wider attention, in addition to S-protein and M(pro) modulators as potential therapeutics for COVID-19. So far, no specific drugs have shown promising therapeutic potential against COVID-19. The current study was undertaken to evaluate the therapeutic potential of traditional medicinal plants against COVID-19. The bioactives from the medicinal plants, along with standard drugs, were screened for their binding against S-protein, M(pro) and ACE2 targets using molecular docking followed by molecular dynamics. Based on the higher binding affinity compared with standard drugs, bioactives were selected and further analyzed for their pharmacological properties such as drug-likeness, ADME/T-test, biological activities using in silico tools. The binding energies of several bioactives analyzed with target proteins were relatively comparable and even better than the standard drugs. Based on Lipinski factors and lower binding energies, seven bioactives were further analyzed for their pharmacological and biological characteristics. The selected bioactives were found to have lower toxicity with a higher GI absorption rate and potent anti-inflammatory and anti-viral activities against targets of COVID-19. Therefore, the bioactives from these medicinal plants can be further developed as phytopharmaceuticals for the effective treatment of COVID-19. url: https://doi.org/10.1080/07391102.2020.1842246 doi: 10.1080/07391102.2020.1842246 id: cord-292350-cmrtg91a author: Mondal, Samhati title: Thromboembolic disease in COVID-19 patients: A brief narrative review date: 2020-09-14 words: 4000.0 sentences: 207.0 pages: flesch: 29.0 cache: ./cache/cord-292350-cmrtg91a.txt txt: ./txt/cord-292350-cmrtg91a.txt summary: Table 1 & 2 summarize the various thrombotic complications noted in COVID-19 patients as published as of June 6 th , 2020 obtained by a literature search on PubMed and EMBASE using combinations of the following MeSH terms: COVID-19, SARS-COV2, novel corona virus, thrombosis, thromboembolic complications, pulmonary embolism. Clinical signs and symptoms of thrombosis such as cutaneous manifestations ("COVID toe") [84] , overt line thrombosis, arterial or venous clots, unexplained increase in oxygen requirement, or organ dysfunction should raise suspicion and prompt further investigation and/or discussion about therapeutic intervention [7] As new information becomes available, it appears increasingly important to routinely monitor platelet count, PT/aPTT, d-dimer, and fibrinogen to assist in anticipating and managing thrombotic complications. ICU patients positive for COVID-19 with elevated d-dimer levels and/or clinico-radiological suspicion for thrombosis as noted above should be considered for therapeutic anticoagulation only after careful assessment of their bleeding risk. abstract: Corona virus 2 (SARS-CoV2/ Severe Acute Respiratory Syndrome Corona Virus 2) infection has emerged as a global health crisis. Incidence of thromboembolic disease is reported to be high in SARS-CoV2 disease and is seen in a multitude of organ systems ranging from cutaneous thrombosis to pulmonary embolism, stroke or coronary thrombosis sometimes with catastrophic outcomes. Evidence points towards a key role of thromboembolism, hypercoagulability and over production of proinflammatory cytokines mimicking a “cytokine storm” which leads to multiorgan failure. This brief narrative review highlights the pathophysiology and risk factors of thromboembolic disease and provides a framework for management of anticoagulation based on the current evidence. url: https://doi.org/10.1186/s40560-020-00483-y doi: 10.1186/s40560-020-00483-y id: cord-327169-sz4ildnd author: Mondoni, Michele title: Utility and safety of bronchoscopy during SARS-CoV-2 outbreak in Italy: a retrospective, multicenter study date: 2020-08-28 words: 1346.0 sentences: 86.0 pages: flesch: 42.0 cache: ./cache/cord-327169-sz4ildnd.txt txt: ./txt/cord-327169-sz4ildnd.txt summary: The primary aim of the present study was to describe the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swab(s) and a clinical and radiological suspicion of COVID-19 pneumonia. The indications of bronchoscopy were: -diagnosis of SARS-CoV-2 pneumonia in patients with previously negative nasopharyngeal swab (clinical and radiological suspicion of pneumonia); -need for undelayable procedures in COVID-19 patients (e.g., massive hemoptysis, post-obstructive atelectasis). The diagnostic yield of bronchoscopy was calculated dividing the number of patients with a molecular diagnosis of SARS-CoV-2 infection following the collection of bronchoscopic specimens by the number of patients with a suspected diagnosis of COVID-19 pneumonia. This is to our knowledge the largest study on the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swabs and a clinical/radiological suspicion of SARS-CoV-2 infection. Urgent/life-saving bronchoscopies were performed in 31 patients with a confirmed COVID-19 diagnosis for obstructive atelectasis, suspected concomitant lower respiratory tract infections, severe hemoptysis, suspected tracheal lacerations in patients mechanically ventilated, tracheostomy complications, and suspected concomitant pulmonary tuberculosis. abstract: Utility and safety of bronchoscopy during SARS-CoV-2 outbreak url: https://www.ncbi.nlm.nih.gov/pubmed/32859682/ doi: 10.1183/13993003.02767-2020 id: cord-232446-vvb2ffhv author: Mongia, Aanchal title: A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date: 2020-07-03 words: 7123.0 sentences: 382.0 pages: flesch: 47.0 cache: ./cache/cord-232446-vvb2ffhv.txt txt: ./txt/cord-232446-vvb2ffhv.txt summary: In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. abstract: COVID-19 has fast-paced drug re-positioning for its treatment. This work builds computational models for the same. The aim is to assist clinicians with a tool for selecting prospective antiviral treatments. Since the virus is known to mutate fast, the tool is likely to help clinicians in selecting the right set of antivirals for the mutated isolate. The main contribution of this work is a manually curated database publicly shared, comprising of existing associations between viruses and their corresponding antivirals. The database gathers similarity information using the chemical structure of drugs and the genomic structure of viruses. Along with this database, we make available a set of state-of-the-art computational drug re-positioning tools based on matrix completion. The tools are first analysed on a standard set of experimental protocols for drug target interactions. The best performing ones are applied for the task of re-positioning antivirals for COVID-19. These tools select six drugs out of which four are currently under various stages of trial, namely Remdesivir (as a cure), Ribavarin (in combination with others for cure), Umifenovir (as a prophylactic and cure) and Sofosbuvir (as a cure). Another unanimous prediction is Tenofovir alafenamide, which is a novel tenofovir prodrug developed in order to improve renal safety when compared to the counterpart tenofovir disoproxil. Both are under trail, the former as a cure and the latter as a prophylactic. These results establish that the computational methods are in sync with the state-of-practice. We also demonstrate how the selected drugs change as the SARS-Cov-2 mutates over time, suggesting the importance of such a tool in drug prediction. The dataset and software is available publicly at https://github.com/aanchalMongia/DVA and the prediction tool with a user-friendly interface is available at http://dva.salsa.iiitd.edu.in. url: https://arxiv.org/pdf/2007.01902v2.pdf doi: nan id: cord-328287-3qgzulgj author: Moni, Mohammad Ali title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 words: 10643.0 sentences: 547.0 pages: flesch: 43.0 cache: ./cache/cord-328287-3qgzulgj.txt txt: ./txt/cord-328287-3qgzulgj.txt summary: Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . abstract: BACKGROUND: Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I’d rather have HIV than diabetes" as life expectancy among diabetes patients is lower than that of HIV. However, HIV has a comorbidity impact on the diabetes. RESULTS: We present a quantitative framework to compare and explore comorbidity between diseases. By using neighbourhood based benchmark and topological methods, we have built comorbidity relationships network based on the OMIM and our identified significant genes. Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). Phenotypic association is measured by calculating both the Relative Risk as the quantified measures of comorbidity tendency of two disease pairs and the ϕ-correlation to measure the robustness of the comorbidity associations. The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). HIV-1 induces comorbidities relationship with many other diseases, particularly strong correlation with the neurological, cancer, metabolic and immunological diseases. Similar comorbidities risk is observed from the clinical information. Moreover, SARS and HIV infections dysregulate 4 genes (ANXA3, GNS, HIST1H1C, RASA3) and 3 genes (HBA1, TFRC, GHITM) respectively that affect the ageing process. It is notable that HIV and SARS similarly dysregulated 11 genes and 3 pathways. Only 4 significantly dysregulated genes are common between SARS-CoV and MERS-CoV, including NFKBIA that is a key regulator of immune responsiveness implicated in susceptibility to infectious and inflammatory diseases. CONCLUSIONS: Our method presents a ripe opportunity to use data-driven approaches for advancing our current knowledge on disease mechanism and predicting disease comorbidities in a quantitative way. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-333) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/1471-2105-15-333 doi: 10.1186/1471-2105-15-333 id: cord-021152-6znmkvy9 author: Montecino-Latorre, Diego title: Reproduction of East-African bats may guide risk mitigation for coronavirus spillover date: 2020-02-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the Coronaviridae family. If bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the Severe Acute Respiratory Syndrome virus, spillover may occur. Therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. Past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. We assessed, via Bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. RESULTS: We found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. CONCLUSIONS: These findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. In these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). Our proposed strategy provides an alternative to culling – an ethically questionable practice that may result in higher pathogen levels – and supports the conservation of bats and the delivery of their key ecosystem services. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149079/ doi: 10.1186/s42522-019-0008-8 id: cord-293127-c27qh5y7 author: Monteleone, Pedro AA title: A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments date: 2020 words: 4508.0 sentences: 224.0 pages: flesch: 47.0 cache: ./cache/cord-293127-c27qh5y7.txt txt: ./txt/cord-293127-c27qh5y7.txt summary: In this review, we summarize the latest research progress related to COVID-19 epidemiology and the reported data of pregnant women, and discuss the current evidence of COVID-19 infections during pregnancy and its potential consequences for assisted reproductive treatments. The current outbreak of the novel 2019 coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China in December 2019 and subsequently spread to many other countries. Coronaviruses are a large family of viruses known to cause symptoms ranging from a common cold to more severe diseases, such as the severe acute respiratory syn A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments Pedro AA Monteleone 1,2 , Mayra Nakano 1,2 , Victor Lazar 1 , Alecsandra P Gomes 1 , (Drosten et al., 2003; Ksiazek et al., 2003) , and MERS coronavirus (MERS-CoV) was the pathogen responsible for severe respiratory disease outbreaks in the Middle East in 2012 (Zaki et al., 2012) . abstract: The current outbreak of the novel 2019 coronavirus disease (COVID-19) started in China in December 2019 and has since spread to several other countries. On March 25, 2020, a total of 375,498 cases had been confirmed globally with 2,201 cases in Brazil, showing the urgency of reacting to this international public health emergency. While in most cases, mild symptoms are observed, in some cases the infection leads to serious pulmonary disease. As a result, the possible consequences of the COVID-19 outbreak for pregnant women and its potential effects on the management of assisted reproductive treatments, demand attention. In this review, we summarize the latest research progress related to COVID-19 epidemiology and the reported data of pregnant women, and discuss the current evidence of COVID-19 infections during pregnancy and its potential consequences for assisted reproductive treatments. Reported data suggest that symptoms in pregnant women are similar to those in other people, and that there is no evidence for higher maternal or fetal risks. However, considering the initial data and lack of comprehensive knowledge on the pathogenesis of SARS-CoV-2 during pregnancy, human reproduction societies have recommended postponing the embryo transfers and do not initiate new treatment cycles. New evidence must be considered carefully in order to adjust these recommendations accordingly at any time and to guide assisted reproductive treatments. url: https://doi.org/10.5935/1518-0557.20200030 doi: 10.5935/1518-0557.20200030 id: cord-291028-ejidqmpm author: Montero Feijoo, A. title: Recomendaciones prácticas para el manejo perioperatorio del paciente con sospecha o infección grave por coronavirus SARS-CoV-2 date: 2020-03-17 words: 4603.0 sentences: 443.0 pages: flesch: 51.0 cache: ./cache/cord-291028-ejidqmpm.txt txt: ./txt/cord-291028-ejidqmpm.txt summary: Debe de estar compuesto por: mascarilla N95 o preferiblemente FFP3, protección ocular ajustada de montura integral o facial completa, bata impermeable, doble guante, gorro y calzas impermeables La higiene de manos debe ser realizada por el personal antes y después de todo contacto con el paciente, particularmente antes de ponerse y después de quitarse el EPI Se deben minimizar los procesos que generen aerosoles y en el caso de ser necesarios usar siempre las medidas de protección recomendadas En el caso de ser necesaria la intubación traqueal se recomienda debe ser realizada por el profesional más experimentado disponible, realizar una inducción de secuencia rápida, evitar la ventilación manual, usar videolaringoscopio y preferiblemente tubo endotraqueal con aspiración subglótica Iniciar de forma precoz el tratamiento de soporte a los pacientes con compromiso respiratorio (taquipnea, hipoxemia) o shock séptico El uso de gafas nasales de alto flujo o ventilación mecánica no invasiva debe ser evitado en la medida de lo posible y reservado para pacientes muy concretos, puesto que son dispositivos que generan aerosoles La administración de antimicrobianos no está recomendada inicialmente, tan solo si existe sospecha de sepsis asociada o sobreinfección bacteriana. abstract: Resumen En diciembre del 2019, la Comisión Municipal de Salud y Sanidad de Wuhan (provincia de Hubei, China) informó de una serie de casos de neumonía de etiología desconocida. El 7 de enero del 2020, las autoridades chinas identificaron como agente causante del brote un nuevo tipo de virus de la familia Coronaviridae, denominado SARS-CoV-2. Desde entonces, se han notificado miles de casos con una diseminación global. Las infecciones en humanos provocan un amplio espectro clínico que va desde infección leve del tracto respiratorio superior, hasta síndrome de distrés respiratorio agudo grave y sepsis. No existe un tratamiento específico para SARS-CoV-2, motivo por lo que los aspectos fundamentales son establecer medidas adecuadas de prevención y el tratamiento de soporte y manejo de las complicaciones. Abstract In December 2019, the Wuhan Municipal Health and health Commission (Hubei Province, China) reported a series of cases of pneumonia of unknown etiology. On January 7, 2020, the Chinese authorities identified as a causative agent of the outbreak a new type of virus of the Coronaviridiae family, called SARS-CoV-2. Since then, thounsands of cases have been reported with global dissemination. Infections in humans cause a broad clinical spectrum ranging from mild upper respiratory tract infection, to severe acute respiratory distress syndrome and sepsis. There is not specific treatment for SARS-CoV-2, which is why the fundamental aspects are to establish adequate prevention measures and support treatment and management of complications. url: https://www.sciencedirect.com/science/article/pii/S0034935620300530 doi: 10.1016/j.redar.2020.03.003 id: cord-341531-w788qwya author: Montero Feijoo, A. title: Practical recommendations for the perioperative management of patients with suspicion or serious infection by coronavirus SARS-CoV date: 2020-05-04 words: 3716.0 sentences: 202.0 pages: flesch: 44.0 cache: ./cache/cord-341531-w788qwya.txt txt: ./txt/cord-341531-w788qwya.txt summary: Protective measures should be maximised when caring for patients with confirmed infection, in critically ill patients with a high viral load, and in patients that require invasive aerosol-generating procedures and manoeuvres such as aerosol therapy and nebulisation, aspiration of respiratory secretions, bag-mask ventilation, non-invasive ventilation, intubation, respiratory sampling, bronchoalveolar lavage, tracheostomy or cardiopulmonary resuscitation. If postoperative surveillance is necessary, it will be carried out in adequately monitored isolation units, preferably with negative pressure Avoid using aerosols, high-flow nasal oxygen or non-invasive ventilation as far as possible in patients requiring postoperative oxygen therapy Healthcare personnel who care for patients during postoperative surveillance must wear appropriate personal protective equipment at all times and must be taught donning and doffing techniques The same recommendations for transferring patients to the operating room apply to postoperative transfer abstract: Abstract In December 2019, the Wuhan Municipal Health and health Commission (Hubei Province, China) reported a series of cases of pneumonia of unknown aetiology. On January 7, 2020, the Chinese authorities identified as a causative agent of the outbreak a new type of virus of the Coronaviridiae family, called SARS-CoV-2. Since then, thounsands of cases have been reported with global dissemination. Infections in humans cause a broad clinical spectrum ranging from mild upper respiratory tract infection, to severe acute respiratory distress syndrome and sepsis. There is not specific treatment for SARS-CoV-2, which is why the fundamental aspects are to establish adequate prevention measures and support treatment and management of complications. url: https://www.sciencedirect.com/science/article/pii/S2341192920300597 doi: 10.1016/j.redare.2020.03.002 id: cord-305616-2obemy16 author: Montes, Maria Teresa title: Neonatal nursing in the COVID-19 pandemic: can we improve the future? date: 2020-07-10 words: 3520.0 sentences: 162.0 pages: flesch: 46.0 cache: ./cache/cord-305616-2obemy16.txt txt: ./txt/cord-305616-2obemy16.txt summary: Contingency plans due to the covid-19 pandemic have impacted on three key areas: 1) the organization and workflow of neonatal units, 2) perinatal and neonatal care, including breastfeeding, and 3) communicationcollaboration with parents. Many centres have adopted very restrictive policies to care for pregnant women who are positive for SARS-CoV-2 in the maternal area, as well as in the NUs, in order to control the spread of the virus and protect health professionals. Initial recommendations to the management regarding the SARS-CoV-2-positive puerperant supported changes to delivery plans by introducing restrictions, both in vaginal deliveries and caesarean sections on the presence of the other parent at childbirth and postpartum unit, early skin-to-skin contact, and late-cord clamping . In addition to frequent hand-washing, cleaning of the breast before breastfeeding and skin-to-skin contact, and wearing face masks, the risk to others can be reduced, for example, by testing parents and health professionals for SARS-CoV-2 and restricting their access to where their child is placed. abstract: The current 2019 coronavirus disease (COVID-19) is the world's largest and most pervasive public health emergency in more than one hundred years. Although neonatal units have not been at the epicentre of the current health crisis, they have also been forced to adopt contingency plans with the aim of protecting hospitalised neonates, their families, and professionals. Neonatal units have been forced to alter the neonatal care framework based on promoting neurodevelopment and family-centred care. The peak of the pandemic is falling in most countries, but COVID-19 infection is not eradicated and there is uncertainty about new outbreaks. It is time to reflect about better strategies to preserve the rights and excellence of care for newborns and their families. This column will highlight the changes that have occurred in neonatal units, and their impact on neonatal care and families. It is a time for critical reflection on nursing practice. url: https://api.elsevier.com/content/article/pii/S1355184120301010 doi: 10.1016/j.jnn.2020.07.005 id: cord-325595-y9ae6zbr author: Montopoli, M. title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality date: 2020-10-23 words: 1251.0 sentences: 72.0 pages: flesch: 46.0 cache: ./cache/cord-325595-y9ae6zbr.txt txt: ./txt/cord-325595-y9ae6zbr.txt summary: title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality in the Annals of Oncology reported findings congruent with the prevailing notion that high SARS-CoV-2 infection rates and disease severity in men may be the result of high androgen-driven TMPRSS2 expression in the lungs. The authors posit that since TMPRSS2 is under positive transcriptional control by the androgen receptor (AR), reduction of TMPRSS2 expression following androgen deprivation therapy (ADT) in prostate cancer patients would be expected to correlate with reduced SARS-CoV-2 incidence, and in case of infection, with lesser disease severity. In particular, disease stage and the type of treatment that may affect AR or TMPRSS2 expression and/or patients'' The current thinking posits that under ADT, expression of TMPRSS2 (a co-factor for SARS-CoV-2 activation and virulence) would be reduced in the lungs, leading to less severe disease, hospitalizations, ICU admissions, and deaths. abstract: nan url: https://api.elsevier.com/content/article/pii/S0923753420421015 doi: 10.1016/j.annonc.2020.07.022 id: cord-268049-7xqln70d author: Montrief, Tim title: COVID-19 respiratory support in the emergency department setting date: 2020-08-08 words: 5197.0 sentences: 337.0 pages: flesch: 45.0 cache: ./cache/cord-268049-7xqln70d.txt txt: ./txt/cord-268049-7xqln70d.txt summary: DISCUSSION: Patients presenting with SARS-CoV-2 infection are at high risk for acute respiratory failure requiring airway management. [29] [30] [31] [32] Based on currently available evidence, the WHO states that "HFNC and NIV systems with good interface fitting do not create widespread dispersion of exhaled air and therefore should be associated with [a] low risk of airborne transmission." 15 The risk of respiratory pathogen transmission when using HFNC is subject to a variety of factors, including the duration of support, maximal flow rate, patient sneezing or coughing, cannula fit, and patient cooperation. 35 Many guidelines, including those by Australian and New Zealand Intensive Care Society (ANZICS), the WHO, and the Surviving Sepsis Campaign recommend the use of HFNC in COVID-19 patients presenting with acute hypoxemic respiratory failure unresponsive to conventional oxygen therapy. 20 Notably, the SCCM guidelines on the management of critically ill patients with COVID-19 recommend "a trial of NIV with close monitoring and shortinterval assessment for worsening of respiratory failure" if HFNC is not available and there is no urgent indication for intubation. abstract: INTRODUCTION: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), may result in severe complications, multiorgan dysfunction, acute respiratory failure, and death. SARS-CoV-2 is highly contagious and places healthcare workers at significant risk, especially during aerosol-generating procedures, including airway management. OBJECTIVE: This narrative review outlines the underlying respiratory pathophysiology of patients with COVID-19 and discusses approaches to airway management in the emergency department (ED) based on current literature. DISCUSSION: Patients presenting with SARS-CoV-2 infection are at high risk for acute respiratory failure requiring airway management. Among hospitalized patients, 10–20% require intensive care unit admission, and 3–10% require intubation and mechanical ventilation. While providing respiratory support for these patients, proper infection control measures, including adherence to personal protective equipment policies, are necessary to prevent nosocomial transmission to healthcare workers. A structured approach to respiratory failure in these patients includes the use of exogenous oxygen via nasal cannula or non-rebreather, as well as titrated high-flow nasal cannula and non-invasive ventilation. This review offers several guiding principles and resources designed to be adapted in conjunction with local workplace policies for patients requiring endotracheal intubation. CONCLUSIONS: While the fundamental principles of acute respiratory failure management are similar between COVID-19 and non-COVID-19 patients, there are some notable differences, including a focus on provider safety. This review provides an approach to airway management and respiratory support in the patient with COVID-19. url: https://doi.org/10.1016/j.ajem.2020.08.001 doi: 10.1016/j.ajem.2020.08.001 id: cord-339669-p61j2caf author: Monzani, Alice title: QTc evaluation in COVID‐19 patients treated with chloroquine/hydroxychloroquine date: 2020-05-18 words: 1244.0 sentences: 63.0 pages: flesch: 44.0 cache: ./cache/cord-339669-p61j2caf.txt txt: ./txt/cord-339669-p61j2caf.txt summary: In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China and has spread rapidly initially throughout Europe and later USA (1). In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China, and has spread rapidly initially throughout Europe and later in the United States. Despite poor real clinical evidence of unequivocal beneficial effect of chloroquine/hydroxychloroquine (CQ/HCQ), the absence of an effective COVID-19 treatment and the social pressure raised the demand of these drugs for its compassionate use, both in hospital and outpatient settings. 10 High-dosed HCQ showed promising potential effect in reducing SARS-CoV-2 viral load in COVID-19 patients with enhanced effects in combination with azithromycin or several antiviral drugs. In so forth, we believe that is probably time to have prospective clinical trials that will evaluate the safety and efficacy of HCQ during treatment of COVID-infected patients. abstract: In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China and has spread rapidly initially throughout Europe and later USA (1). The pathogen was originally called 2019 novel coronavirus (2019-nCoV) and later named severe acute respiratory syndrome coronavirus 2 (SARS-nCoV-2) by the World Health Organization (WHO). url: https://www.ncbi.nlm.nih.gov/pubmed/32356580/ doi: 10.1111/eci.13258 id: cord-340516-9dfaqsv7 author: Moore, Anne C. title: Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date: 2020-09-06 words: 6679.0 sentences: 335.0 pages: flesch: 48.0 cache: ./cache/cord-340516-9dfaqsv7.txt txt: ./txt/cord-340516-9dfaqsv7.txt summary: We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Here, we report the induction of neutralizing antibody (Nab), IgG and IgA antibody responses, and T cell responses in mice following immunization of rAd vectors expressing one or more SARS-CoV-2 antigens. We have previously demonstrated that an oral, tableted rAd-based vaccine can induce protection against respiratory infection and shedding following influenza virus challenge 15 as well as intestinal immunity to norovirus antigens in humans 12 . In summary, these studies in mice represent our first step in creating a vaccine candidate, demonstrating the immunogenicity of the construct at even low vaccine doses and the elucidation of the full-length spike protein as a leading candidate antigen to induce T cell responses and superior systemic and mucosal neutralizing antibody. abstract: There is an urgent need to develop efficacious vaccines against SARS-CoV-2 that also address the issues of deployment, equitable access, and vaccine acceptance. Ideally, the vaccine would prevent virus infection and transmission as well as preventing COVID-19 disease. We previously developed an oral adenovirus-based vaccine technology that induces both mucosal and systemic immunity in humans. Here we investigate the immunogenicity of a range of candidate adenovirusbased vaccines, expressing full or partial sequences of the spike and nucleocapsid proteins, in mice. We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Antigen-specific CD4+ and CD8+ T cells were induced by this leading vaccine candidate at low and high doses. This fulllength spike antigen plus nucleocapsid adenovirus construct has been prioritized for further clinical development. url: https://doi.org/10.1101/2020.09.04.283853 doi: 10.1101/2020.09.04.283853 id: cord-289407-8fje16z1 author: Moore, G. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 words: 4720.0 sentences: 328.0 pages: flesch: 59.0 cache: ./cache/cord-289407-8fje16z1.txt txt: ./txt/cord-289407-8fje16z1.txt summary: Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. 6 Air samples taken during tracheostomy procedures, high flow nasal oxygen treatment, non-invasive ventilation and nebulisation have not contained SARS-CoV-2 RNA 7 and HCWs exposed to unrecognised COVID-19 patients undergoing similar high-risk AGPs have not become infected. . https://doi.org/10.1101/2020.09.24.20191411 doi: medRxiv preprint Several studies, utilising a range of air and surface sampling methods, have been carried out to determine the presence and prevalence of SARS-CoV-2 in the healthcare environment. [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients abstract: Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalised patients, with and without respiratory symptoms, was investigated. Environmental sampling was carried out within eight hospitals in England during the first wave of the COVID-19 outbreak. Samples were analysed using reverse transcription polymerase chain reaction (RT-PCR) and virus isolation assays. SARS-CoV-2 RNA was detected on 30 (8.9%) of 336 environmental surfaces. Ct values ranged from 28.8 to 39.1 equating to 2.2 x 105 to 59 genomic copies/swab. Concomitant bacterial counts were low, suggesting the cleaning performed by nursing and domestic staff across all eight hospitals was effective. SARS-CoV-2 RNA was detected in four of 55 air samples taken < 1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from < 10 to 460 genomic copies per m3 of air. Infectious virus was not recovered from any of the PCR positive samples analysed. Effective cleaning can reduce the risk of fomite (contact) transmission but some surface types may facilitate the survival, persistence and/or dispersal of SARS-CoV-2. The presence of low or undetectable concentrations of viral RNA in the air supports current guidance on the use of specific PPE ensembles for aerosol and non-aerosol generating procedures. url: http://medrxiv.org/cgi/content/short/2020.09.24.20191411v1?rss=1 doi: 10.1101/2020.09.24.20191411 id: cord-282724-zzkqb0u2 author: Moore, Jason H. title: Ideas for how informaticians can get involved with COVID-19 research date: 2020-05-12 words: 7588.0 sentences: 315.0 pages: flesch: 33.0 cache: ./cache/cord-282724-zzkqb0u2.txt txt: ./txt/cord-282724-zzkqb0u2.txt summary: Some key considerations and targets of research include: (1) feature engineering, transforming raw data into features (i.e. variables) that ML can better utilize to represent the problem/target outcome, (2) feature selection, applying expert domain knowledge, statistical methods, and/or ML methods to remove ''irrelevant'' features from consideration and improve downstream modeling, (3) data harmonization, allowing for the integration of data collected at different sites/institutions, (4) handling different outcomes and related challenges, e.g. binary classification, multi-class, quantitative phenotypes, class imbalance, temporal data, multi-labeled data, censored data, and the use of appropriate evaluation metrics, (5) ML algorithm selection for a given problem can be a challenge in itself, thus strategies to integrate the predictions of multiple machine learners as an ensemble are likely to be important, (6) ML modeling pipeline assembly, including critical considerations such as hyper-parameter optimization, accounting for overfitting, and clinical interpretability of trained models, and (7) considering and accounting for covariates as well as sources of bias in data collection, study design, and application of ML tools in order to avoid drawing conclusions based on spurious correlations. abstract: The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on population health and wellbeing. Biomedical informatics is central to COVID-19 research efforts and for the delivery of healthcare for COVID-19 patients. Critical to this effort is the participation of informaticians who typically work on other basic science or clinical problems. The goal of this editorial is to highlight some examples of COVID-19 research areas that could benefit from informatics expertise. Each research idea summarizes the COVID-19 application area, followed by an informatics methodology, approach, or technology that could make a contribution. It is our hope that this piece will motivate and make it easy for some informaticians to adopt COVID-19 research projects. url: https://www.ncbi.nlm.nih.gov/pubmed/32419848/ doi: 10.1186/s13040-020-00213-y id: cord-331831-gw42e6ce author: Moore, Luke S P title: Near-patient SARS-CoV-2 molecular platforms: new-old tools for new-old problems date: 2020-10-08 words: 1101.0 sentences: 53.0 pages: flesch: 48.0 cache: ./cache/cord-331831-gw42e6ce.txt txt: ./txt/cord-331831-gw42e6ce.txt summary: In their prospective, interventional, non-randomised, controlled trial published in The Lancet Respiratory Medicine, Nathan Brendish and colleagues 1 move COVID-19 diagnostics forward, both by expanding the repertoire of in-situ evaluated molecular platforms, and also methodologically, with a diagnostic controlled trial using clinical impact as a primary outcome measure, analogous to their previous work on other respiratory viruses. 1 Nevertheless, this level of accuracy is attractive in the context of the recently published (yet perhaps already outdated) Cochrane review 3 of early-tomarket, rapid, point-of-care molecular tests for SARS-CoV-2, which looked at 13 evaluations of four platforms, finding a mean sensitivity of 95·2% (86·7-98·3) with a specificity of 98·9% (97·3-99·5). Brendish and colleagues also showed that the fast turnaround time of the QIAstat-Dx Respiratory SARS-CoV-2 Panel decreased the time taken for patients to be placed in an appropriate care area, and led to fewer bed moves and faster time to enrolment into other COVID-19 clinical trials-all significant advantages. Clinical impact of molecular point-ofcare testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33038973/ doi: 10.1016/s2213-2600(20)30451-3 id: cord-328712-7q9mg2tu author: Moore, Nicholas title: Chloroquine for COVID-19 Infection date: 2020-04-07 words: 794.0 sentences: 55.0 pages: flesch: 60.0 cache: ./cache/cord-328712-7q9mg2tu.txt txt: ./txt/cord-328712-7q9mg2tu.txt summary: Caused by a new virus, SARS-CoV2, COVID-19 is related to the common cold and the SARS-CoV1 virus that was responsible for the 2003 Severe Acute Respiratory Syndrome (SARS) infection in Asia, causing about 8000 cases and 774 deaths (https ://www. Raoult was based on theory [5] , on the effects of the drug on coronavirus replication in vitro [1, 4, [6] [7] [8] , and on experimental data [2] showing SARS-CoV inhibition [3] , concluding to a hypothetical effect of hydroxychloroquine on COVID-19 [9] without clinical proof other than a non-randomized open study of 20 patients, purported to show extraordinary results on virus washout (notwithstanding a slew of typical biases) [10] . In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) abstract: nan url: https://doi.org/10.1007/s40264-020-00933-4 doi: 10.1007/s40264-020-00933-4 id: cord-345183-80rflm7u author: Moore, Nicholas M. title: Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2 date: 2020-07-23 words: 3635.0 sentences: 228.0 pages: flesch: 58.0 cache: ./cache/cord-345183-80rflm7u.txt txt: ./txt/cord-345183-80rflm7u.txt summary: We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. In this study, we compared the performance of the ACOV and IDNOW assays and a laboratory developed test that is a modification of the CDC 2019-nCoV assay (CDC COV) for the detection of SARS-CoV-2 RNA from upper respiratory tract specimens. abstract: We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. Discrepant results were adjudicated by medical record review. A total of 200 nasopharyngeal swab specimens in viral transport medium (VTM) were collected from symptomatic patients between 27 March and 9 April 2020. Results were concordant for 167 specimens (83.5% overall agreement), including 94 positive and 73 negative specimens. The ACOV assay yielded 33 additional positive results, 25 of which were also positive by the CDC COV assay but not by the IDNOW assay. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. Medical record review deemed all discrepant results to be true positives. The IDNOW test was the easiest to perform and provided a result in the shortest time but detected fewer cases of COVID-19. The ACOV assay detected more cases of COVID-19 than the CDC COV or IDNOW assays. url: https://doi.org/10.1128/jcm.00938-20 doi: 10.1128/jcm.00938-20 id: cord-307160-1vz0gw1w author: Morais-Almeida, Mário title: COVID-19, asthma, and biologic therapies: What we need to know date: 2020-05-16 words: 3561.0 sentences: 160.0 pages: flesch: 41.0 cache: ./cache/cord-307160-1vz0gw1w.txt txt: ./txt/cord-307160-1vz0gw1w.txt summary: Ongoing prospective cohort studies (SARP, NHLBI and others) provide a unique opportunity to examine the effects of COVID-19 on severe asthma and potential interactions with therapy, including inhaled and oral corticosteroids, as well as targeted treatment with biologics. It was believed that low eosinophil counts in peripheral blood would be related to the infection with the SARS-CoV-2 virus itself, and not necessarily an indicator that treatments which reduce eosinophil counts in patients with asthma would be associated with more severe COVID-19 disease. As in the placebo controlled trials with omalizumab, mepolizumab, benralizumab, reslizumab and dupilumab in asthmatic patients, no risk of increased infection susceptibility or immunosuppressive effect was reported to date and, in the case of omalizumab, there is a possible anti-infectious effect; hence we do not need to discontinue these treatments during the current pandemic. abstract: Abstract Managing patients with severe asthma during the coronavirus pandemic COVID-19 is a challenge. Authorities and physicians are still learning how COVID-19 affects people with underlying diseases, and severe asthma is not an exception. Unless relevant data emerges that changes our understanding of the relative safety of medications indicated in patients with asthma during this pandemic, clinicians must follow the recommendations of current evidence-based guidelines, preventing loss of control and exacerbations. Also, with the absence of data that would indicate any potential harm, current advice is to continue the administration of biologic agents during the COVID-19 pandemic in patients with asthma for whom such agents are clearly indicated and have been effective. For the patients with severe asthma infected by SARS-CoV-2, the decision to maintain or postpone biologic therapy until the patient recovers should be a case-by-case based decision supported by a multidisciplinary team. A registry of cases of COVID-19 in patients with severe asthma, including those treated with biologics, will help to address a clinical challenge where we have more questions than answers. url: https://www.sciencedirect.com/science/article/pii/S1939455120300296?v=s5 doi: 10.1016/j.waojou.2020.100126 id: cord-348392-e35cd9sg author: Moraleda, Cinta title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date: 2020-07-25 words: 1759.0 sentences: 165.0 pages: flesch: 66.0 cache: ./cache/cord-348392-e35cd9sg.txt txt: ./txt/cord-348392-e35cd9sg.txt summary: Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. abstract: Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. We describe the epidemiological and clinical features of children with MIS-C in Spain. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32710613/ doi: 10.1093/cid/ciaa1042 id: cord-283432-od5nnxvg author: Morawska, Lidia title: How can airborne transmission of COVID-19 indoors be minimised? date: 2020-05-27 words: 5052.0 sentences: 246.0 pages: flesch: 41.0 cache: ./cache/cord-283432-od5nnxvg.txt txt: ./txt/cord-283432-od5nnxvg.txt summary: We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. While evidence for airborne transmission of COVID-19 is currently incomplete, several hospital-based studies have performed air-sampling for SARS-COV-2, including one published paper (Ong et al. abstract: Abstract During the rapid rise in COVID-19 illnesses and deaths globally, and notwithstanding recommended precautions, questions are voiced about routes of transmission for this pandemic disease. Inhaling small airborne droplets is probable as a third route of infection, in addition to more widely recognized transmission via larger respiratory droplets and direct contact with infected people or contaminated surfaces. While uncertainties remain regarding the relative contributions of the different transmission pathways, we argue that existing evidence is sufficiently strong to warrant engineering controls targeting airborne transmission as part of an overall strategy to limit infection risk indoors. Appropriate building engineering controls include sufficient and effective ventilation, possibly enhanced by particle filtration and air disinfection, avoiding air recirculation and avoiding overcrowding. Often, such measures can be easily implemented and without much cost, but if only they are recognised as significant in contributing to infection control goals. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. url: https://www.ncbi.nlm.nih.gov/pubmed/32521345/ doi: 10.1016/j.envint.2020.105832 id: cord-253459-tcn10pho author: Moreau, Gregory Brett title: Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection date: 2020-07-28 words: 2377.0 sentences: 154.0 pages: flesch: 58.0 cache: ./cache/cord-253459-tcn10pho.txt txt: ./txt/cord-253459-tcn10pho.txt summary: 4 A transgenic mouse model to study SARS-CoV-1 infection was developed that expresses the hACE2 gene under the control of the human cytokeratin 18 promoter. To investigate the potential of this transgenic mouse strain as a model for COVID-19 infection, five K18-hACE2 mice were intranasally inoculated with 8 × 10 4 Median Tissue Culture Infectious Dose (TCID50) of SARS-CoV-2, and five mice were mock-infected with sterile Dulbecco''s Modified Eagle''s Medium (DMEM). In the mouse model expressing hACE2 under the mouse ACE2 promoter, infected mice did not exhibit any clinical symptoms other than maximal weight loss on day 3 postinfection, and those mice recovered. 10 In contrast to these models, in which mice exhibited mild symptoms and recovered, only 60% of the mice survived past day 5 in the mouse strain expressing hACE2 under the lung ciliated epithelial cell HFH4 promoter. abstract: Murine models of SARS-CoV-2 infection are critical for elucidating the biological pathways underlying COVID-19. Because human angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2, mice expressing the human ACE2 gene have shown promise as a potential model for COVID-19. Five mice from the transgenic mouse strain K18-hACE2 were intranasally inoculated with SARS-CoV-2 Hong Kong/VM20001061/2020. Mice were followed twice daily for 5 days and scored for weight loss and clinical symptoms. Infected mice did not exhibit any signs of infection until day 4, when no other obvious clinical symptoms other than weight loss were observed. By day 5, all infected mice had lost around 10% of their original body weight but exhibited variable clinical symptoms. All infected mice showed high viral titers in the lungs as well as altered lung histology associated with proteinaceous debris in the alveolar space, interstitial inflammatory cell infiltration, and alveolar septal thickening. Overall, these results show that the K18-hACE2 transgenic background can be used to establish symptomatic SARS-CoV-2 infection and can be a useful mouse model for COVID-19. url: https://doi.org/10.4269/ajtmh.20-0762 doi: 10.4269/ajtmh.20-0762 id: cord-337636-3yc0ribg author: Morehouse, Zachary P. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 words: 2980.0 sentences: 169.0 pages: flesch: 52.0 cache: ./cache/cord-337636-3yc0ribg.txt txt: ./txt/cord-337636-3yc0ribg.txt summary: Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. Using human coronavirus 229E (HCoV-229E) as our model organism, we developed a novel two-step methodology of optimized shaker-mill homogenization parameters that allowed for direct-to-PCR viral detection. abstract: BACKGROUND: Currently, one of the most reliable methods for viral infection detection are polymerase chain reaction (PCR) based assays. This process is time and resource heavy, requiring multiple steps of lysis, extraction, purification, and amplification procedures. Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. METHODS: Using Human Coronavirus 229E (HCoV-229E) as a model system, we spiked swabs in vitro for proof-of-concept testing. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. After homogenization, 1 μL of lysate was processed using RT-qPCR for amplification of the nucleocapsid (N) gene, qualifying viral detection. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. After running 54 swabs, we confidently determined our limit of detection to be 1.2 × 10(3) viral copies/mL with 96.30% sensitivity. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. This finding allows for reductions in the time and resources required for PCR based virus detection in comparison to the traditional extraction-to-PCR methodology. url: https://doi.org/10.1186/s12985-020-01405-y doi: 10.1186/s12985-020-01405-y id: cord-322348-8opy5z9h author: Morelli, Mara title: Parents and Children During the COVID-19 Lockdown: The Influence of Parenting Distress and Parenting Self-Efficacy on Children’s Emotional Well-Being date: 2020-10-06 words: 7098.0 sentences: 309.0 pages: flesch: 46.0 cache: ./cache/cord-322348-8opy5z9h.txt txt: ./txt/cord-322348-8opy5z9h.txt summary: Within the Social Cognitive Theory framework, a path model in which parenting self-efficacy and parental regulatory emotional self-efficacy mediated the relationship between parents'' psychological distress and both children''s emotional regulation, and children''s lability/negativity, was investigated. (2020) in Italy showed that it was the parenting stress related to the health emergency, the pandemic, and the lockdown that increased children''s psychological, emotional, and behavioral problems. For this reason, this study focused on identifying which parental psychological variables can mediate the relationship between parents'' psychological distress during the pandemic and the lockdown and their children''s emotional regulation, in order to understand which possible intervention should be implemented to ameliorate families'' well-being. A SEM was employed to test the hypothesized mediation model in which parenting self-efficacy and parents'' regulatory emotional self-efficacy (related to the COVID-19 lockdown) mediated the relationship between parents'' psychological distress and both children''s emotional regulation and children''s lability/negativity. abstract: On March 10, 2020, Italy went into lockdown due to the Coronavirus Disease-19 (COVID-19) pandemic. The World Health Organization highlighted how the lockdown had negative consequences on psychological well-being, especially for children. The present study aimed to investigate parental correlates of children’s emotion regulation during the COVID-19 lockdown. Within the Social Cognitive Theory framework, a path model in which parenting self-efficacy and parental regulatory emotional self-efficacy mediated the relationship between parents’ psychological distress and both children’s emotional regulation, and children’s lability/negativity, was investigated. A total of 277 parents of children aged from 6 to 13 years completed an online survey that assessed their psychological distress, regulatory emotional self-efficacy, and parenting self-efficacy. Parents reported also children’s emotional regulation and lability/negativity. A structural equation model (SEM) using MPLUS 8.3 was tested. Results showed that the hypothesized model exhibited excellent fit, chi-square (83) = 140.40, p < 0.01, RMSEA = 0.05, CFI = 0.97, TLI = 0.96, SRMR = 0.04. The influences of parents’ psychological distress and parents’ regulatory emotional self-efficacy on children’s emotional regulation and lability/negativity were mediated by parenting self-efficacy. The mediation model was invariant across children’s biological sex and age, and geographical residence area (high risk vs. low risk for COVID-19). Results suggested how parents’ beliefs to be competent in managing parental tasks might be a protective factor for their children’s emotional well-being. Implications for intervention programs are discussed. url: https://doi.org/10.3389/fpsyg.2020.584645 doi: 10.3389/fpsyg.2020.584645 id: cord-102411-0mo1198e author: Moreno Borraz, LA title: PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date: 2020-11-13 words: 3432.0 sentences: 268.0 pages: flesch: 55.0 cache: ./cache/cord-102411-0mo1198e.txt txt: ./txt/cord-102411-0mo1198e.txt summary: Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. El objetivo principal del estudio fue conocer la prevalencia de infección por Coronavirus SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia de Zaragoza en el pico de la pandemia en España, entre el 20 de marzo y el 21 de abril de 2020. abstract: Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. Material y Métodos: A finales de febrero de 2020, se diseñó en el hospital una estrategia para el diagnóstico de la infección por SARS-CoV-2 consistente en complementar la realización de PCR a tiempo real con una técnica rápida de inmunocromatografía de flujo lateral para la detección de anticuerpos IgG e IgM frente al virus. Se protocolizó la realización de dichas pruebas diagnósticas y se consideró como infección (actual o pasada) un resultado positivo de alguna de ellas. Se incluyeron en el estudio 524 participantes (230 pacientes y 294 profesionales). Los pacientes se agruparon en ingresados y en ambulatorios para terapia de hemodiálisis. Los trabajadores se agruparon en asistenciales y no asistenciales. El periodo de tiempo que se documenta, es el comprendido entre el 20 de marzo y el 21 de abril de 2020. Resultados: En 26 de los 230 pacientes el resultado fue positivo en alguna de las técnicas, con una prevalencia del 11,30%. Por grupos, en ingresados fue del 14,38% frente al 5,95% de los ambulatorios (p=0,055), siendo significativamente superior el riesgo en pacientes ingresados tras ajustar por sexo y edad (OR=3,309 (IC95%:1,154-9,495). En 24 de los 294 profesionales el resultado fue positivo en alguna de las técnicas, con una prevalencia del 8,16%. Por grupos, en asistenciales fue del 8,91% frente al 4,26% de los no asistenciales (p=0,391), OR ajustado=2,502 (IC95%: 0,559-11,202) Conclusiones: Se ha encontrado una tasa de prevalencia baja frente a SARS-CoV-2 tanto en pacientes como en profesionales. La prevalencia en pacientes hospitalizados es mayor que en ambulatorios, también es superior la prevalencia de sanitarios asistenciales respecto a los no asistenciales. Background and goals: The aim of the study is to know the prevalence of SARS-CoV-2 infection in patients and professional staff of a medium or long-stay hospital during the peak period of the pandemic in Spain, spring 2020. Equipment and methods: At the end of February 2020, we developed at the hospital a strategy to diagnose the SARS-CoV-2 infection consisting of complementing the realization of PCR tests at real time with a quick technique of lateral flow immunochromatography to detect IgG and IgM antibodies against the virus. We also developed a protocol to realize those diagnostic tests and considered an infection (current or past) a positive result in any of the above tests. We included 524 participants in the study (230 patients and 294 hospital staff), and divided them into hospital patients and Hemodialysis outpatients. Furthermore, we divided the hospital staff into healthcare and non-healthcare staff. The documented period was from March, 20th to April, 21st, 2020. Results: 26 out of 230 patients tested positive in any of the diagnostic techniques (PCR, antibodies IgG, IgM) with a 11.30% prevalence. According to patients groups, we got a 14.38% prevalence in hospital patients vs. 5.95% in outpatients, with a significantly higher risk in admitted patients after adjustment for age and gender (OR=3,309 (IC95%:1,154-9,495). 24 out of 294 hospital staff tested positive in any of the diagnostic techniques, with a 8.16% prevalence. According to the groups, we got a 8.91% prevalence in healthcare staff vs. 4.26% in non-healthcare staff. Thus, we do not see any statistically significant differences between hospital staff and patients as far as prevalence is concerned (p=0,391), (OR=2,200 IC95 %: 0,500-9,689). Conclusions: The result of the study was a quite low prevalence rate of SARS-CoV-2 infection, in both patients and hospital staff, being the hospital patients’ prevalence rate higher than the outpatients’, and the healthcare staff higher than the non-healthcare’s. Combining PCR tests (gold standard) with antibodies tests proved useful as a diagnostic strategy. url: https://api.elsevier.com/content/article/pii/S0211139X20301803 doi: 10.1016/j.regg.2020.10.005 id: cord-304734-r0k1rfmt author: Moreno-Casbas, María Teresa title: Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI date: 2020-05-25 words: 3237.0 sentences: 343.0 pages: flesch: 60.0 cache: ./cache/cord-304734-r0k1rfmt.txt txt: ./txt/cord-304734-r0k1rfmt.txt summary: La población diana está constituida por profesionales de la salud de todas las Comunidades Autónomas de España, con actividad en cualquier centro que atienda a pacientes con COVID-19 y que sean un caso confirmado de infección por SARS-CoV-2 por laboratorio. Laborales y epidemiológicas: lugar y unidad de trabajo, tiempo trabajado en los últimos 10 años, elementos de protección (disponibilidad, utilización y percepción del uso correcto), métodos y frecuencia de la higiene de manos y de otras medidas higiénicas en el trabajo, carga de trabajo en la última jornada, existencia de protocolos de protección, motivo de realización del test y responsable de indicarlo, fechas de inicio de síntomas, de test positivo y test negativo, contactos previos al test, aislamiento y sus características y reincorporación al trabajo. En relación a la percepción de los profesionales, en las primeras semanas de la pandemia, de la disponibilidad de medidas de protección en la categoría "siempre/frecuentemente" fue: para mascarilla FPP1 57,3%, guantes 89,5%, jabón 95% y solución hidroalcohólica 91,5%. abstract: ABSTRACT Objective: To describe the factors related to the situation of SARS-CoV-2 transmission identified by health professionals in Spain and to propose prevention strategies. Method: Cross-sectional descriptive study. The population were healthcare professionals working in institutions caring for COVID-19 patients and also confirmed cases of SARS-CoV-2 infection. A questionnaire with sociodemographic, occupational and epidemiological variables was used. Descriptive and bivariate analysis was performed according to the nature of the variables. Results: Twenty-two hundred and thirty questionnaires were analysed on a potential population of 41,239 (5.47%). The diagnosis was made based on a suspicious case (63.4%) and a probable case (12.3%). A study of contacts was carried out at 50.3%. The perception about the availability of protective measures as "always/frequently" were: FPP1 mask 57.3%, gloves 89.5%, soap 95% and hydroalcoholic solution 91.5%. In PPE, FPP2, FPP3 mask, goggles and disposable gowns at around 50%. The availability of protective measures, by field of work, presented significant differences. The average number of patients attended related to the performance of hand hygiene at moment 4 and the perception of performing it correctly at moments 4 and 5. Conclusions: Preliminary data are presented, with variability in the response rate by Autonomous Region. Healthcare professionals infected by SARS-CoV-2 identified the management of the chain of infection transmission, the use and adequacy of protective equipment, as well as the effectiveness of handwashing as factors related to the transmission of the virus among professionals. url: https://www.ncbi.nlm.nih.gov/pubmed/32571661/ doi: 10.1016/j.enfcli.2020.05.021 id: cord-295130-e7j7kac0 author: Moreno-Contreras, Joaquín title: Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date: 2020-09-22 words: 2906.0 sentences: 122.0 pages: flesch: 58.0 cache: ./cache/cord-295130-e7j7kac0.txt txt: ./txt/cord-295130-e7j7kac0.txt summary: In this study, we compared the RT-qPCR results from 253 paired samples obtained from saliva and swabs of ambulatory patients; the RNA in the swab samples was extracted using a commercial RNA purification kit, and the saliva samples were directly mixed with a lysis buffer, boiled, and used for the RT-qPCR protocol. To evaluate if saliva is a good source of viral RNA for the RT-qPCR, we determined the presence of the SARS-CoV-2 genome in paired saliva and swab samples from 253 ambulatory patients. Direct lysis of nasopharyngeal or oropharyngeal swab samples in viral transport medium using the QE buffer has been reported as a suitable method for direct RT-qPCR for SARS-CoV-2 detection, with rates similar to those of methods based on column purification (11, 15) . abstract: As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is less expensive and can be as efficient as the classical protocol, which involves column purification of the viral RNA. In addition, it bypasses the need for swab sampling, decreases the risk of the health care personnel involved in the testing process, and accelerates the diagnostic procedure. url: https://doi.org/10.1128/jcm.01659-20 doi: 10.1128/jcm.01659-20 id: cord-282839-3ii79g6j author: Moreno-Fernández Ayala, Daniel J. title: Age-related mitochondrial dysfunction as a key factor in COVID-19 disease date: 2020-11-07 words: 10245.0 sentences: 560.0 pages: flesch: 37.0 cache: ./cache/cord-282839-3ii79g6j.txt txt: ./txt/cord-282839-3ii79g6j.txt summary: Thus, it seems clear that mitochondrial dysfunction is an important factor in the proinflammatory profile caused by the release of inflammatory cytokines produced by activation of NLRP3 inflammasome and other mechanisms over-activated in aging and in metabolic diseases. It seems clear that, mitochondrial dysfunction in diabetic patients contributes importantly to the low-grade inflammatory profile associated with this disease that is aggravated during aging and has been associated with higher severity in COVID-19 infection. Mediterranean diet, rich in plant foods, is associated with reduced risk of developing age-J o u r n a l P r e -p r o o f related chronic diseases by inducing protection against oxidative stress and improving mitochondrial activity that could be the cause of a reduced inflammation level (Tosti et al., 2018) . Mitochondrial dysfunction releases many damage signals to cytosol that end in the activation of inflammasome and the release of inflammatory cytokines that cause the chronic inflammation associated with aging and age-related diseases. abstract: SARS-CoV-2 causes a severe pneumonia (COVID-19) that affects essentially elderly people. In COVID-19, macrophage infiltration into the lung causes a rapid and intense cytokine storm leading finally to a multi-organ failure and death. Comorbidities such as metabolic syndrome, obesity, type 2 diabetes, lung and cardiovascular diseases, all of them age-associated diseases, increase the severity and lethality of COVID-19. Mitochondrial dysfunction is one of the hallmarks of aging and COVID-19 risk factors. Dysfunctional mitochondria is associated with defective immunological response to viral infections and chronic inflammation. This review discuss how mitochondrial dysfunction is associated with defective immune response in aging and different age-related diseases, and with many of the comorbidities associated with poor prognosis in the progression of COVID-19. We suggest here that chronic inflammation caused by mitochondrial dysfunction is responsible of the explosive release of inflammatory cytokines causing severe pneumonia, multi-organ failure and finally death in COVID-19 patients. Preventive treatments based on therapies improving mitochondrial turnover, dynamics and activity would be essential to protect against COVID-19 severity. url: https://api.elsevier.com/content/article/pii/S0531556520304952 doi: 10.1016/j.exger.2020.111147 id: cord-278050-wl83d6gs author: Morgenstern, Birgit title: Ribavirin and interferon-β synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines date: 2005-01-28 words: 2390.0 sentences: 127.0 pages: flesch: 50.0 cache: ./cache/cord-278050-wl83d6gs.txt txt: ./txt/cord-278050-wl83d6gs.txt summary: Abstract Initial in vitro investigations demonstrated type I interferons (IFNs: IFN-α, IFN-β) to inhibit replication of SARS coronavirus (SARS-CoV), but found the nucleoside analogue ribavirin ineffective in Vero cells. In this report, ribavirin was shown to inhibit SARS-CoV replication in five different cell types of animal or human origin at therapeutically achievable concentrations. The influence of the infectious dose on the anti-SARS-CoV activity of ribavirin was investigated in Caco2 cells infected at different MOIs by measurement of virus titre. For example, in Caco2 cells infected with SARS-CoV FFM1 strain (MOI 0.01), ribavirin concentrations inhibiting virus production in combination with IFN-b were at least 10-fold lower when compared with cultures receiving single treatment with ribavirin. These clinical findings together with the observation of antiviral activity in different SARS-CoV-infected cell lines encourage the testing of treatment strategies using ribavirin in combination with other antiviral agents such as IFNs to increase inhibitory effects on virus replication and subsequently minimised immunopathological damages. abstract: Abstract Initial in vitro investigations demonstrated type I interferons (IFNs: IFN-α, IFN-β) to inhibit replication of SARS coronavirus (SARS-CoV), but found the nucleoside analogue ribavirin ineffective in Vero cells. In this report, ribavirin was shown to inhibit SARS-CoV replication in five different cell types of animal or human origin at therapeutically achievable concentrations. Since clinical anti-SARS-CoV activity of type I interferons or ribavirin is limited, we investigated the combination of IFN-β and ribavirin. Determination of the virus yield indicated highly synergistic anti-SARS-CoV action of the combination suggesting the consideration of ribavirin plus IFN-β for the treatment of SARS. url: https://www.sciencedirect.com/science/article/pii/S0006291X04027299 doi: 10.1016/j.bbrc.2004.11.128 id: cord-344614-5zcylf6k author: Moriconi, Diego title: Obesity prolongs the hospital stay in patients affected by COVID-19, and may impact on SARS-COV-2 shedding date: 2020-06-04 words: 3225.0 sentences: 168.0 pages: flesch: 49.0 cache: ./cache/cord-344614-5zcylf6k.txt txt: ./txt/cord-344614-5zcylf6k.txt summary: Partial least square regression analysis showed that BMI, age and CRP at admission were related to longer length of hospital stay, and time for negative swab. Our study shows that obesity is associated with a severer respiratory presentation of COVID-19 and severer elevation of inflammatory markers, likely leading to higher oxygen demands at admission, prolonged oxygen requirement during hospitalization, delayed viral clearance and extended hospital stay. For this reason, beyond the potential impact on the lung mechanics, obesity might influence the clinical presentation and evolution of SARS-COV-2 infection through J o u r n a l P r e -p r o o f exacerbation of the immune-inflammatory response related to the disease, as confirmed by the increased levels of several inflammatory markers detected in the peripheral blood of patients with obesity in our population. abstract: INTRODUCTION: On the last three months the new SARS-COV-2 coronavirus has created a pandemic, rapidly spreading all around the world. The aim of the study is to investigate whether obesity impacts on COVID-19 morbidity. METHODS: One hundred consecutive patients with COVID-19 pneumonia admitted in our Medical Unit were evaluated. Anthropometric parameters and past medical history were registered. Nasopharyngeal swab samples and biochemical analysis were obtained at admission and during hospital stay. RESULTS: Patients with (OB, 29) and without obesity (N-OB, 71) were similar in age, gender and comorbidities, with the exception of hypertension that was more frequent in OB group. At admission, inflammatory markers were higher in OB than N-OB group. OB group showed a worse pulmonary clinical picture, with lower PaO2 (57 ± 15 vs. 68 ± 14 mmHg, p = 0.042), and SaO2 (88 ± 6 vs. 92 ± 5 %, p = 0.049) at admission consequently requiring higher volumes of oxygen (Fi02: 38 ± 15 vs. 29 ± 19%, p = 0.047) and a longer period to achieve oxygen weaning (10 ± 6 vs. 15 ± 7 days, p = 0.03). OB group also had positive swabs for longer time (19 ± 8 vs. 13 ± 7, days, p = 0.002), and required longer hospital stay (21 ± 8 vs. 13 ± 8, days, p = 0.0008). Partial least square regression analysis showed that BMI, age and CRP at admission were related to longer length of hospital stay, and time for negative swab. On the contrary, in this cohort, obesity did not predict higher mortality. CONCLUSIONS: Subjects with obesity affected by COVID-19 require longer hospitalization, more intensive and longer oxygen treatment, and they may have longer SARS-COV-2 shedding. url: https://doi.org/10.1016/j.orcp.2020.05.009 doi: 10.1016/j.orcp.2020.05.009 id: cord-329262-ybr1auo2 author: Moriel‐Carretero, María title: The hypothetical role of Phosphatidic Acid in subverting ER membranes during SARS‐CoV infection date: 2020-05-18 words: 3957.0 sentences: 203.0 pages: flesch: 44.0 cache: ./cache/cord-329262-ybr1auo2.txt txt: ./txt/cord-329262-ybr1auo2.txt summary: Subsequently, a major path for viral internalization relies on the endocytic pathway and culminates with the release of the viral RNA genome into the cytoplasm of the infected cell (reviewed in 3 After this, +RNA viruses need to establish a complex capable of amplifying and further expressing their genome, the "replication/transcription complex", as well as additional (termed "non-structural") proteins capable of coordinating accessory functions. A relevant point when analyzing the morphological particularities of DMVs induced during SARS-CoV infection is that, in contrast to those triggered by other +RNA viruses, the inner layer indeed constitutes a closed circle, but the outer one is continuous all along with that of the other DMVs, giving the impression that the whole is disconnected from the cytoplasm ( Figure 1A , right panel) 11 . abstract: Positive sense (+) RNA viruses exploit membranes from a variety of cellular organelles to support the amplification of their genomes. This association concurs with the formation of vesicles whose main morphological feature is that of being wrapped by a double membrane. In the case of the SARS‐CoV virus, the outer membrane is not discrete for each vesicle, but seems to be continuous and shared between many individual vesicles, a difference with other +RNA viruses whose nature has remained elusive. I present morphological, biochemical and pharmacological arguments defending the striking analogy of this arrangement and that of entangled, nascent Lipid Droplets whose birth has been aborted by an excess of Phosphatidic Acid. Since Phosphatidic Acid can be targeted with therapeutical purposes, considering this working hypothesis may prove important in tackling SARS‐CoV infection. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/tra.12738 doi: 10.1111/tra.12738 id: cord-292256-jp80u828 author: Moriguchi, Takeshi title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 words: 1742.0 sentences: 121.0 pages: flesch: 53.0 cache: ./cache/cord-292256-jp80u828.txt txt: ./txt/cord-292256-jp80u828.txt summary: We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient''s nasopharyngeal specimen is negative. abstract: Novel coronavirus (SARS-Coronavirus-2:SARS-CoV-2) which emerged in Wuhan, China, has spread to multiple countries rapidly. We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. He had never been to any foreign countries. He felt generalized fatigue and fever (day 1). He saw doctors nearby twice (day 2 and 5) and was prescribed Laninamivir and antipyretic agents, His family visited his home and found that he was unconsciousness and lying on the floor in his vomit. He was immediately transported to this hospital by ambulance (day 9). Under emergency transport, he had transient generalized seizures that lasted about a minute. He had obvious neck stiffness. The specific SARS-CoV-2 RNA was not detected in the nasopharyngeal swab but was detected in a CSF. Anti- HSV 1 and varicella-zoster IgM antibodies were not detected in serum samples. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. This case warns the physicians of patients who have CNS symptoms. url: https://doi.org/10.1016/j.ijid.2020.03.062 doi: 10.1016/j.ijid.2020.03.062 id: cord-326503-ljle4vq3 author: Morioka, Shinichiro title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study date: 2020-07-30 words: 447.0 sentences: 39.0 pages: flesch: 61.0 cache: ./cache/cord-326503-ljle4vq3.txt txt: ./txt/cord-326503-ljle4vq3.txt summary: key: cord-326503-ljle4vq3 authors: Morioka, Shinichiro; Nakamura, Keiji; Iida, Shun; Kutsuna, Satoshi; Kinoshita, Noriko; Suzuki, Tetsuya; Suzuki, Tadaki; Yamamoto, Kei; Hayakawa, Kayoko; Saito, Sho; Ohmagari, Norio title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study Summary This report aimed to investigate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a hospital setting. A 63-year-old man with pneumonia and an asymptomatic 70-year-old man were admitted to a tertiary hospital with SARS-CoV-2 infection. He was admitted to a general ward of our hospital due to SARS-CoV-2 63 pneumonia on Day 7, and was intubated on Day 10 from diagnosis. of Novel Coronavirus-Infected Pneumonia Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient Evidence of airborne 226 transmission of the severe acute respiratory syndrome virus abstract: Summary This report aimed to investigate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a hospital setting. A 63-year-old man with pneumonia and an asymptomatic 70-year-old man were admitted to a tertiary hospital with SARS-CoV-2 infection. Both men were accompanied by their wives, who stayed with their husbands during their hospitalisation. The wives of Patient 1 and Patient 2 tested positive and negative for SARS-CoV-2, respectively. Of the environmental samples tested, 1/21 and 0/25 from the rooms of Patient 1 and Patient 2, respectively, tested positive for SARS-CoV-2. Route of transmission from Patient 1 to his wife was unclear. url: https://api.elsevier.com/content/article/pii/S2590088920300433 doi: 10.1016/j.infpip.2020.100079 id: cord-320845-imxby1b1 author: Morley, G. L. title: Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples date: 2020-07-02 words: 1711.0 sentences: 106.0 pages: flesch: 52.0 cache: ./cache/cord-320845-imxby1b1.txt txt: ./txt/cord-320845-imxby1b1.txt summary: title: Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples Objective: To validate the use of dried blood spot sampling for the detection of SARS-CoV-2-specific antibodies. Results: Specific anti-SARS-Cov-2 spike glycoprotein antibodies were detectable in both serum and DBS eluate and there was a significant correlation between the antibody levels detected in matched samples (r = 0.96, p<0.0001). Using serum as the gold standard in the assay, matched DBS samples achieved a Cohens kappa coefficient of 0.975 (near-perfect agreement), a sensitivity of 98.1% and specificity of 100%, for detecting anti-spike glycoprotein antibodies. . https://doi.org/10.1101/2020.07.01.20144295 doi: medRxiv preprint against matched serum in a highly sensitive and specific SARS-CoV-2 Enzyme Linked Immunosorbent Assay (ELISA). To detect antibodies to SARS-CoV-2-anti-spike (S) glycoprotein, matched serum and DBS titration curves were generated. We show that DBS samples can be used for the detection of SARS-CoV-2-specific antibodies with high levels of sensitivity and specificity and compared well with matched serum samples. abstract: Abstract Importance: Population-wide serological testing is an essential component in understanding the COVID-19 pandemic. The logistical challenges of undertaking widespread serological testing could be eased through use of a reliable dried blood spot (DBS) sampling method. Objective: To validate the use of dried blood spot sampling for the detection of SARS-CoV-2-specific antibodies. Design, setting and participants: Eighty-seven matched DBS and serum samples were obtained from eighty individuals, including thirty-one who were previously PCR-positive for SARS-CoV-2. DBS eluates and sera were used in an ELISA to detect antibodies to the viral spike protein. Results: Specific anti-SARS-Cov-2 spike glycoprotein antibodies were detectable in both serum and DBS eluate and there was a significant correlation between the antibody levels detected in matched samples (r = 0.96, p<0.0001). Using serum as the gold standard in the assay, matched DBS samples achieved a Cohens kappa coefficient of 0.975 (near-perfect agreement), a sensitivity of 98.1% and specificity of 100%, for detecting anti-spike glycoprotein antibodies. Conclusions and relevance: Eluates from DBS samples are a reliable and reproducible source of antibodies to be used for the detection of SARS-CoV-2-specific antibodies. The use of DBS sampling could complement the use of venepuncture in the immunosurveillance of COVID-19 in both low and high income settings. url: https://doi.org/10.1101/2020.07.01.20144295 doi: 10.1101/2020.07.01.20144295 id: cord-327575-5pcnuqgy author: Morrisette, Taylor title: The Pharmacokinetic and Pharmacodynamic Properties of Hydroxychloroquine and Dose Selection for COVID-19: Putting the Cart Before the Horse date: 2020-08-01 words: 5447.0 sentences: 233.0 pages: flesch: 45.0 cache: ./cache/cord-327575-5pcnuqgy.txt txt: ./txt/cord-327575-5pcnuqgy.txt summary: The objective of this review was to describe the current understanding of the PK/PD and dose selection of HCQ against SARS-CoV-2, discuss knowledge gaps, and identify future studies that are needed to optimize the efficacy and safety of treatments against COVID-19. Although studies completed thus far show variable results, Arshad and colleagues performed a large multicenter, retrospective, observational analysis that evaluated patients hospitalized because of a COVID-19-related admission receiving HCQ 400 mg twice daily on day 1, followed by HCQ 200 mg twice daily on days 2 to 5 [14] [15] [16] [17] . Furthermore, the World Health Organization discontinued the HCQ arm in the Solidarity trial because it showed ''''little or no reduction in the mortality of hospitalized COVID-19 patients when compared to standard of care'''' (HCQ dosed 800 mg twice daily on day 1, followed by HCQ 400 mg twice daily for a total of 10 days), and the Food and Drug Administration revoked the emergency use authorization to utilize HCQ for the treatment of COVID-19 [16] [17] [18] . abstract: Coronavirus disease 2019 (COVID-19), caused by the 2019 novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently responsible for a global pandemic. To date, only remdesivir and dexamethasone have demonstrated a positive response in a prospective, randomized trial for the treatment of patients with COVID-19. Hydroxychloroquine (HCQ) is an agent available in an oral formulation with in vitro activity against SARS-CoV-2 that has been suggested as a potential agent. Unfortunately, results of randomized trials evaluating HCQ as treatment against a control group are lacking, and little is known about its pharmacokinetic/pharmacodynamic (PK/PD) profile against SARS-CoV-2. The objective of this review was to describe the current understanding of the PK/PD and dose selection of HCQ against SARS-CoV-2, discuss knowledge gaps, and identify future studies that are needed to optimize the efficacy and safety of treatments against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32740858/ doi: 10.1007/s40121-020-00325-2 id: cord-255602-3pzh5ur9 author: Moscadelli, Andrea title: Fake News and Covid-19 in Italy: Results of a Quantitative Observational Study date: 2020-08-12 words: 4590.0 sentences: 213.0 pages: flesch: 51.0 cache: ./cache/cord-255602-3pzh5ur9.txt txt: ./txt/cord-255602-3pzh5ur9.txt summary: We used the BuzzSumo application to gather the most shared links on the Internet related to the pandemic in Italy, using keywords chosen according to the most frequent "fake news" during that period. We used the BuzzSumo pplication [38] in order to gather the most shared links or posts on the Internet and social media related to SARS-CoV-2 and the Covid-19 pandemic. The 9 keywords were chosen in a consensus meeting of the research group, since they were the most likely to uncover health-related false information using the BuzzSumo search engine, and specifically fake news that would not meet our exclusion criteria. An article was immediately excluded when the content did not deal specifically with health or science, i.e., the focus may have been on the socioeconomic consequences of the pandemic, which was a topic we excluded from our fake news review. abstract: During the Covid-19 pandemic, risk communication has often been ineffective, and from this perspective “fake news” has found fertile ground, both as a cause and a consequence of it. The aim of this study is to measure how much “fake news” and corresponding verified news have circulated in Italy in the period between 31 December 2019 and 30 April 2020, and to estimate the quality of informal and formal communication. We used the BuzzSumo application to gather the most shared links on the Internet related to the pandemic in Italy, using keywords chosen according to the most frequent “fake news” during that period. For each research we noted the numbers of “fake news” articles and science-based news articles, as well as the number of engagements. We reviewed 2102 articles. Links that contained fake news were shared 2,352,585 times, accounting for 23.1% of the total shares of all the articles reviewed. Our study throws light on the “fake news” phenomenon in the SARS-CoV-2 pandemic. A quantitative assessment is fundamental in order to understand the impact of false information and to define political and technical interventions in health communication. Starting from this evaluation, health literacy should be improved by means of specific interventions in order to improve informal and formal communication. url: https://www.ncbi.nlm.nih.gov/pubmed/32806772/ doi: 10.3390/ijerph17165850 id: cord-311240-o0zyt2vb author: Motayo, Babatunde Olarenwaju title: Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date: 2020-07-27 words: 3091.0 sentences: 167.0 pages: flesch: 50.0 cache: ./cache/cord-311240-o0zyt2vb.txt txt: ./txt/cord-311240-o0zyt2vb.txt summary: Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa. The pathogen was later identified to be a novel coronavirus closely related to the severe acute respiratory syndrome virus (SARS), with a possible bat origin (Zhou et al, 2020) . This study was designed to determine to the genetic diversity and evolutionary history of genome sequences of SARSCoV-2 isolated in Africa. Results of recombination analysis of the African SARSCoV-2 (AfrSARSCoV-2) sequences against references whole genome sequences of SARS, Recombination signals were observed between the African SARSCoV-2 sequences and reference sequence (Major recombinant hCoV-19 Pangolin/Guangu P4L/2017; Minor parent hCoV-19 B batYunan/RaTG13) between the RdRP and S gene regions (Figure 2 ). abstract: The ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 × 10−4 high posterior density HPD (4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa. url: https://doi.org/10.1101/2020.07.27.222901 doi: 10.1101/2020.07.27.222901 id: cord-272501-byfxqsbu author: Motta, Juan Camilo title: Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report date: 2020-08-22 words: 1507.0 sentences: 92.0 pages: flesch: 48.0 cache: ./cache/cord-272501-byfxqsbu.txt txt: ./txt/cord-272501-byfxqsbu.txt summary: title: Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report We report a case of SARS-Cov2 and adenovirus coinfection, which further developed into acute respiratory distress syndrome. The exact time of coinfection could not be established, and additional poor prognostic factor to the development of severe disease added to patient''s comorbidities and reported tests [1, 6] . Although coinfection is not common, in cases with severe disease or CT findings that are not explained by COVID-19 infection [11, 14, 15] , additional studies such as nested PCR for respiratory germs are required to detect potentially treatable pathogens, such as mycoplasma or influenza virus [14] . Larger and better designed prospective analytical studies are required to determine further risk factors, clinical impact, prognosis, and the prevalence of SARS-Cov2 and another respiratory pathogen coinfection. Coinfection with SARS-CoV-2 and other respiratory pathogens in COVID-19 patients in Guangzhou abstract: SARS-Cov2 coinfection with other respiratory viruses is very rare. Adenovirus coinfection is even more unusual. We report the case of a patient with poorly controlled diabetes, and he was admitted to the emergency department because of severe COVID-19 infection. He had unfavorable prognostic factors such as moderate oxygen impairment, positive D-dimer, increased lactate dehydrogenase and ferritin. Adenovirus was isolated in a respiratory viral panel. He developed acute respiratory distress syndrome and required pronation and neuromuscular relaxation in the intensive care unit. Hydroxychloroquine was administered as suggested by the national guidelines. The symptoms resolved, and hospital discharge was indicated. COVID-19 association with another respiratory virus is related with adverse clinical outcomes, such as shock, ventilatory support requirement and greater lymphopenia and thrombocytopenia. url: https://doi.org/10.1016/j.idcr.2020.e00936 doi: 10.1016/j.idcr.2020.e00936 id: cord-336053-cjq7szcn author: Mottola, Filiberto Fausto title: Cardiovascular System in COVID-19: Simply a Viewer or a Leading Actor? date: 2020-08-27 words: 5639.0 sentences: 268.0 pages: flesch: 41.0 cache: ./cache/cord-336053-cjq7szcn.txt txt: ./txt/cord-336053-cjq7szcn.txt summary: Several studies have observed a relationship between coronavirus disease (COVID-19) infection and the cardiovascular system with the appearance of myocardial damage, myocarditis, pericarditis, heart failure and various arrhythmic manifestations, as well as an increase in thromboembolic risk. Compared to those without an increase in TnT, these patients were more likely to require invasive or non-invasive ventilation (22% versus 4%, and 46% versus 4%, respectively) and to develop acute respiratory distress syndrome (59% versus 15%) or acute kidney injury (9% versus 0%; p < 0.001 for all); in addition, the mortality rate was higher (51.2% vs. A recent meta-analysis showed that cardiac troponin I (cTnI) values were significantly higher in patients with severe SARS-CoV-2 infection compared to those observed with mild forms [14] . However, myocardial damage alone is not enough and there are other factors involved in enhancing the arrhythmic risk in COVID-19: in fact, in these patients, only half showed acute cardiac injury despite the high frequency of arrhythmias [32] . abstract: As of January 2020, a new pandemic has spread from Wuhan and caused thousands of deaths worldwide. Several studies have observed a relationship between coronavirus disease (COVID-19) infection and the cardiovascular system with the appearance of myocardial damage, myocarditis, pericarditis, heart failure and various arrhythmic manifestations, as well as an increase in thromboembolic risk. Cardiovascular manifestations have been highlighted especially in older and more fragile patients and in those with multiple cardiovascular risk factors such as cancer, diabetes, obesity and hypertension. In this review, we will examine the cardiac involvement associated with SARS-CoV-2 infection, focusing on the pathophysiological mechanism underlying manifestations and their clinical implication, taking into account the main scientific papers published to date. url: https://www.ncbi.nlm.nih.gov/pubmed/32867137/ doi: 10.3390/life10090165 id: cord-312524-ee5xw1r8 author: Moustafa, Ahmed M. title: Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date: 2020-06-08 words: 2058.0 sentences: 129.0 pages: flesch: 61.0 cache: ./cache/cord-312524-ee5xw1r8.txt txt: ./txt/cord-312524-ee5xw1r8.txt summary: Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. Rapid sequencing of the SARS-CoV-2 pandemic virus has presented an 40 unprecedented opportunity to track the evolution of the virus and to understand the 41 emergence of a new pathogen in near-real time. Our panallelome approach to developing a whole genome (wgMLST) scheme for 58 SARS-CoV-2 uses a modified version of our recently developed tool, WhatsGNU [10], 59 to rapidly assign an allele number to each gene nucleotide sequence in the virus''s 60 genome creating a sequence type (ST). We developed the GNU-based Virus IDentification (GNUVID) system as a tool 71 that automatically assigns a number to each unique allele of the 10 open reading 72 frames (ORFs) of SARS-CoV-2 ( Figure 1A) information. When the global region of origin for each genome sequence was mapped to 102 each CC there was a strong association of some CCs with certain geographical 103 locations. abstract: As the pandemic SARS-CoV-2 virus has spread globally its genome has diversified to an extent that distinct clones can now be recognized, tracked, and traced. Identifying clonal groups allows for assessment of geographic spread, transmission events, and identification of new or emerging strains that may be more virulent or more transmissible. Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. This sequence typing scheme can be updated with new genomic information extremely rapidly, making our technique continually adaptable as databases grow. We show that our method is consistent with phylogeny and recovers waves of expansion and replacement of sequence types/clonal complexes in different geographical locations. GNUVID is available as a command line application (https://github.com/ahmedmagds/GNUVID). url: https://doi.org/10.1101/2020.06.08.139055 doi: 10.1101/2020.06.08.139055 id: cord-280454-etf32afd author: Moustaqil, Mehdi title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date: 2020-06-05 words: 10152.0 sentences: 562.0 pages: flesch: 56.0 cache: ./cache/cord-280454-etf32afd.txt txt: ./txt/cord-280454-etf32afd.txt summary: title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts Direct cleavage of IRF3 by NSP3 could explain the blunted TypeI IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. In this report, we show that the viral proteases PLpro and 3CLpro of SARS-CoV2 lead to the in-vitro proteolytic cleavage of three important proteins of the host immune response: IRF3, TAB1 and NLRP12 (Fig. 1B) . The presence of the five human-like cleavage sites for IRF3, TAB1 and NLRP12 in a single species shows that it is possible that the SARS viruses could have gained the new functionality of cleaving these Human Innate Immune Proteins in a single reservoir host, potentially in Myotis Davidii. abstract: The genome of SARS-CoV-2 (SARS2) encodes for two viral proteases (NSP3/ papain-like protease and NSP5/ 3C-like protease or major protease) that are responsible for cleaving viral polyproteins for successful replication. NSP3 and NSP5 of SARS-CoV (SARS1) are known interferon antagonists. Here, we examined whether the protease function of SARS2 NSP3 and NSP5 target proteins involved in the host innate immune response. We designed a fluorescent based cleavage assay to rapidly screen the protease activity of NSP3 and NSP5 on a library of 71 human innate immune proteins (HIIPs), covering most pathways involved in human innate immunity. By expressing each of these HIIPs with a genetically encoded fluorophore in a cell-free system and titrating in the recombinant protease domain of NSP3 or NSP5, we could readily detect cleavage of cognate HIIPs on SDS-page gels. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type- I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. Surprisingly, both NLRP12 and TAB1 have each two distinct cleavage sites. We demonstrate that in mice, the second cleavage site of NLRP12 is absent. We pushed this comparative alignment of IRF-3 and NLRP12 homologs and show that the lack or presence of cognate cleavage motifs in IRF-3 and NLRP12 could contribute to the presentation of disease in cats and tigers, for example. Our findings provide an explanatory framework for in-depth studies into the pathophysiology of COVID-19 and should facilitate the search or development of more effective animal models for severe COVID-19. Finally, we discovered that one particular species of bats, David’s Myotis, possesses the five cleavage sites found in humans for NLRP12, TAB1 and IRF3. These bats are endemic from the Hubei province in China and we discuss its potential role as reservoir for the evolution of SARS1 and SASR2. url: https://doi.org/10.1101/2020.06.05.135699 doi: 10.1101/2020.06.05.135699 id: cord-277763-ihg3te63 author: Moynan, David title: The role of healthcare staff COVID-19 screening in infection prevention & control date: 2020-06-25 words: 654.0 sentences: 51.0 pages: flesch: 51.0 cache: ./cache/cord-277763-ihg3te63.txt txt: ./txt/cord-277763-ihg3te63.txt summary: While HCW can acquire infections and contribute to cross-transmission during hospital outbreaks such as influenza or norovirus, asymptomatic staff are usually not routinely screened as part of the outbreak control measures. In March and April 2020, on three wards with two or more positive COVID-19 patients after three days of admission (designated as potential nosocomial infection), we implemented universal staff SARS-CoV-2 testing on that ward as part of outbreak management. As asymptomatic (or indeed, pre-symptomatic) HCW may have similar viral loads and may be capable of transmission as much as symptomatic individuals 9 , their detection and subsequent exclusion from work is an important aspect of a hospital''s COVID-19 strategy. In conclusion, as hospitals begin to reopen to routine non-COVID-19 services, HCW SARS-CoV-2 testing irrespective of symptoms should be considered, particularly as part of outbreak management to rapidly prevent onward transmission to patients and other staff. COVID-19: PCR Screening of Asymptomatic Health-Care Workers at London Hospital abstract: nan url: https://api.elsevier.com/content/article/pii/S0163445320304382 doi: 10.1016/j.jinf.2020.06.057 id: cord-266104-xqvwht7c author: Mu, Chenglin title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology date: 2020-08-14 words: 2149.0 sentences: 137.0 pages: flesch: 52.0 cache: ./cache/cord-266104-xqvwht7c.txt txt: ./txt/cord-266104-xqvwht7c.txt summary: title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology Here using TCMSP and Swiss Target Prediction databases to sort out the potential targets of the main chemical components and GenCLiP3, NCBI, and GeneCard databases to search for COVID-19 related targets, the chemical compound-target-pathway network was analyzed. Moreover, modern and ancient pharmacological records showed that Rhizoma Polygonati has a wide pharmacological function in antibacterial, antiviral, immunity enhancement, anti-ageing, anti-cancer, anti-diabetes, anti-fatigue, and anti-heart Network pharmacology in TCM combines with multidisciplinary technologies, such as systems biology, and computational biology in order to build a complex network between drug-target-diseases, and elucidate the mechanism of drugs in treatment (Luo et al., 2020) . Therefore, to explore the active ingredients and mechanism of different species of Rhizoma Polygonati based on their active compounds concentration in the treatment of pulmonary symptoms caused by the new coronavirus will help to precisely apply TCM for anti-virus. abstract: Abstract Rhizoma Polygonati (huangjing in Chinese, 黄精) is an herb-homology-food used as a component of alternative medicine treating COVID-19 in the current pandemic emergency in China but the mechanisms remain elusive. Here using TCMSP and Swiss Target Prediction databases to sort out the potential targets of the main chemical components and GenCLiP3, NCBI, and GeneCard databases to search for COVID-19 related targets, the chemical compound-target-pathway network was analyzed. Each component was molecularly docked with host cell target angiotensin converting enzyme II, SARS-CoV-2 targets Spike protein, RNA-dependent RNA polymerase, or 3CL hydrolase. Our results showed a higher affinity of the compound diosgenin and (+)-Syringaresinol-O-beta-D-glucoside binding to the three SARS-CoV-2 proteins compared to the other compounds tested. Thus, our data suggest that potential compounds in Rhizoma Polygonati may act on different targets and have a great potential in treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32837538/ doi: 10.1016/j.jff.2020.104149 id: cord-316859-h8lfmr3e author: Mu, Jingfang title: SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells date: 2020-04-10 words: 2063.0 sentences: 132.0 pages: flesch: 59.0 cache: ./cache/cord-316859-h8lfmr3e.txt txt: ./txt/cord-316859-h8lfmr3e.txt summary: Previous study has reported that severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N) protein displayed a VSR activity in mammalian cells via a cellular reversal-of-silencing assay (Cui et al., 2015) . We first examined whether SARS-CoV-2 N possessed VSR activity via a classic reversal-of-silencing assay, in which enhanced green fluorescent protein (EGFP)-specific shRNA was transfected into EGFP-expressing 293T cells, together with a plasmid encoding SARS-CoV-2 N protein with Flag tag. Our data showed that expression of SARS-CoV-2 N markedly restored the protein level of EGFP ( Figure 1A Because RNAi directly results in the cleavage and degradation of target mRNAs, we further examined the VSR activity of SARS-CoV-2 N using the reversal-of-silencing system via Northern blotting with a digoxin (DIG)-labeled RNA probe targeting EGFP ORF 1-400 nt. Our findings showed that SARS-CoV-2 N can antagonize RNAi in both initiation (i.e., siRNA biogenesis) and effector (i.e., RISC assembly and target RNA cleavage) steps. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32291557/ doi: 10.1007/s11427-020-1692-1 id: cord-261566-fn08b0y2 author: Mudgal, Rajat title: Prospects for mucosal vaccine: shutting the door on SARS-CoV-2 date: 2020-09-15 words: 7060.0 sentences: 413.0 pages: flesch: 38.0 cache: ./cache/cord-261566-fn08b0y2.txt txt: ./txt/cord-261566-fn08b0y2.txt summary: 15 The disease severity and lung damage in the case of SARS-CoV-2 infection can be directly correlated with the dysregulated immune response at 7-10 days after symptom onset and is characterized by exuberant production of cytokines including IL-2, IL-7, IL-10, MIP-1A, IP-10, and TNF-α. 53, [98] [99] [100] [101] [102] Ferrets are a suitable animal model for SARS-CoV vaccine evaluation as they support viral replication in the respiratory tract, develop similar disease symptoms, and display severe lung pathology. Potential ADE and waning of vaccine-induced immune response represent other obstacles in the development of a mucosal vaccine against SARS-CoV-2. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Effect of mucosal and systemic immunization with virus-like particles of severe acute respiratory syndrome coronavirus in mice abstract: The sudden emergence of a highly transmissible and pathogenic coronavirus SARS-CoV-2 in December 2019 from China and its rapid global spread has posed an international health emergency. The rapid development of an effective vaccine is imperative to control the spread of SARS-CoV-2. A number of concurrent efforts to find an effective therapeutic agent or vaccine for COVID-19 (coronavirus disease 2019) are being undertaken globally. Oral and nasal mucosal surfaces serve as the primary portal of entry for pathogens like coronaviruses in the human body. As evidenced by studies on similar coronaviruses (SARS-CoV and MERS-CoV), mucosal vaccination can provide a safe and effective means for the induction of long-lasting systemic and mucosal immunity to confer protection against SARS-CoV-2. This article summarizes the approaches to an effective mucosal vaccine formulation which can be a rewarding approach to combat the unprecedented threat posed by this emerging global pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32931361/ doi: 10.1080/21645515.2020.1805992 id: cord-267690-g0kesgjm author: Mueller, Sarina K. title: Considerations for Continuing Semielective and Emergency Otolaryngological Procedures During the COVID-19 Pandemic date: 2020-09-07 words: 2802.0 sentences: 154.0 pages: flesch: 51.0 cache: ./cache/cord-267690-g0kesgjm.txt txt: ./txt/cord-267690-g0kesgjm.txt summary: The objective of this study was to analyze procedures and outcomes of continuing semielective and emergency surgeries during the COVID-19 pandemic. CONCLUSIONS: Continuing selected otorhinolaryngological surgeries is crucial for patients'' health, survival, and long-time quality of life, yet, the protection of the medical personnel has to be granted. In case of a negative SARS-CoV-2 test, the scheduled surgery was performed the following day without special protective equipment ( Figure 1A) . If the SARS-CoV-2 test result could not be awaited due to the condition of the patient, the surgery was performed with full protective equipment consisting of a FFP2 or FFP3 (filtering face piece mask), a gown, a face shield, and double gloves. If the SARS-CoV-2 test result was positive, surgery was also performed with the full protective equipment. If the SARS-CoV-2 test was negative, surgery was performed as in the semi-elective cases without the above named protective equipment ( Figure 1B ). abstract: INTRODUCTION: During the COVID-19 pandemic, worldwide over 600,000 human beings died due to the cause of the disease. In order to deescalate the transmission rate and to avoid crush loading the countries medical health systems social distancing, face masks, and lockdowns have been considered essential by the majority of governments. Whereas some countries have highly reduced or completely stopped otorhinolaryngological procedures, other countries have continued selected surgeries. The objective of this study was to analyze procedures and outcomes of continuing semielective and emergency surgeries during the COVID-19 pandemic. METHODS: Retrospective analysis of n = 750 patients who received semi-elective or emergency surgery between March 26 and June 16, 2020, in the Otolaryngology Department of the Friedrich-Alexander-University of Erlangen-Nürnberg. All patients were screened for COVID symptoms and swabbed for SARS-CoV-2 prior to surgery. RESULTS: Of the n = 750 patients, n = 699 patients received semielective surgery and n = 51 emergency surgery. For 27 patients, the swab result could not be awaited due to a life-threatening condition. In these cases, surgery was performed in full protective equipment. No patient was tested positive during or after the surgery (follow-up 45 to 127 days). No member of the medical personnel showed symptoms or was tested positive after contact with patients. Due to the continuation of surgeries, patients’ lives were saved and improvement of long-term quality-of-life and outcomes is anticipated. CONCLUSIONS: Continuing selected otorhinolaryngological surgeries is crucial for patients’ health, survival, and long-time quality of life, yet, the protection of the medical personnel has to be granted. url: https://www.ncbi.nlm.nih.gov/pubmed/32894699/ doi: 10.1177/0145561320952506 id: cord-320567-7je1i8qd author: Muenchhoff, Maximilian title: Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020 date: 2020-06-18 words: 1759.0 sentences: 91.0 pages: flesch: 52.0 cache: ./cache/cord-320567-7je1i8qd.txt txt: ./txt/cord-320567-7je1i8qd.txt summary: The aim of this study was to compare the inter-laboratory and inter-method sensitivity of different RT-PCR assays by providing a blinded, frozen dilution series of a nucleic acid extract of a highly positive biosample to seven different diagnostic laboratories in Germany in March 2020. Digital droplet PCR quantification of the distributed dilution series of nucleic acid eluate of SARS-CoV-2-positive clinical material, Germany, March 2020 The undiluted sample showed between 4,325 and 5,015 SARS-CoV-2 RNA copies per reaction using 5 µL of eluate for the CDC N1, N2, N3 and Charité E protocols, but only 850 and 1,951 RNA copies for the Charité N and P primer/probe combinations ( Figure 1A) , respectively, indicating a lower sensitivity of the latter. Driven by false-negative results for samples with low PCR-positivity using the original Charité RdRp reaction (see below and others [8, 9] ), we compared the primer/ probe sequences with currently available SARS-CoV-2 genomes. abstract: Containment strategies and clinical management of coronavirus disease (COVID-19) patients during the current pandemic depend on reliable diagnostic PCR assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we compare 11 different RT-PCR test systems used in seven diagnostic laboratories in Germany in March 2020. While most assays performed well, we identified detection problems in a commonly used assay that may have resulted in false-negative test results during the first weeks of the pandemic. url: https://doi.org/10.2807/1560-7917.es.2020.25.24.2001057 doi: 10.2807/1560-7917.es.2020.25.24.2001057 id: cord-342254-vdovpfu1 author: Mugheddu, C. title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management date: 2020-06-04 words: 766.0 sentences: 54.0 pages: flesch: 45.0 cache: ./cache/cord-342254-vdovpfu1.txt txt: ./txt/cord-342254-vdovpfu1.txt summary: title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management Novel coronavirus 2019 (SARS-CoV2) pandemic has particularly affected Italy, with a profound impact on the therapeutic strategy for complex disorder such as psoriasis, whose extensive skin damage might expose to an increased infective risk compared to the general population. Psoriasis treatment relies on immunosuppression, and although most experts agree that the benefit-to risk-ratio is in favor of maintaining selective biologic therapies, and small molecules such as apremilast, they recommend dismission if severe COVID-19 symptoms occur. The fact that patient with a severe form of psoriasis contracted the COVID-19 pneumonia, while on treatment with apremilast is worth of some considerations. 11 Recently, another Italian psoriasis patient contracting COVID-19 under IL-23 inhibitor treatment (guselkumab) has been reported, and completely recovered from the infection. 12 From our experience, apremilast confirms its safety in very critical patients with severe infections, including COVID-19. abstract: Novel coronavirus 2019 (SARS-CoV2) pandemic has particularly affected Italy, with a profound impact on the therapeutic strategy for complex disorder such as psoriasis, whose extensive skin damage might expose to an increased infective risk compared to the general population. Psoriasis treatment relies on immunosuppression, and although most experts agree that the benefit-to risk-ratio is in favor of maintaining selective biologic therapies, and small molecules such as apremilast, they recommend dismission if severe COVID-19 symptoms occur. url: https://doi.org/10.1111/jdv.16625 doi: 10.1111/jdv.16625 id: cord-257809-bq9ha4d0 author: Mukaino, Masahiko title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-04-08 words: 708.0 sentences: 46.0 pages: flesch: 45.0 cache: ./cache/cord-257809-bq9ha4d0.txt txt: ./txt/cord-257809-bq9ha4d0.txt summary: title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection T he recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a pandemic. Here, therefore, we introduce a preliminary attempt to use a telerehabilitation system to deliver exercise opportunities to individuals isolated because of SARS-CoV-2 infection. Four hospitalized individuals (aged 19-66 yrs, median age = 53 yrs, 2 male individuals), who were infected with SARS-CoV-2 during the outbreak on the Diamond Princess cruise ship, participated in the program. Using videoconferencing (Zoom by Zoom Video Communications Inc, San Jose, CA) and remote control software (TeamViewer; TeamViewer GmbH, Göppingen, Germany), a physical therapist guided each individual in a 20-min exercise program (Fig. 1) . With the pandemic spread of SARS-CoV-2, the number of isolated individuals is expected to increase. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32282339/ doi: 10.1097/phm.0000000000001441 id: cord-294592-zwvr57a0 author: Mukherjee, Moumita title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 words: 6099.0 sentences: 371.0 pages: flesch: 57.0 cache: ./cache/cord-294592-zwvr57a0.txt txt: ./txt/cord-294592-zwvr57a0.txt summary: title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. There are experimentally validated evidences of human RBPs binding to the regulated signals within the untranslated region of SARS-CoV RNA in order to control the viral RNA synthesis and turnover. abstract: BACKGROUND: The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5’ and 3’ untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. METHODS: To have an idea of the global changes in 5’ and 3’-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. RESULTS: We identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5’-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3’UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future. url: https://www.ncbi.nlm.nih.gov/pubmed/32780783/ doi: 10.1371/journal.pone.0237559 id: cord-327134-egp4t82x author: Mukherjee, Prasenjit title: Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits date: 2008-04-01 words: 6100.0 sentences: 286.0 pages: flesch: 54.0 cache: ./cache/cord-327134-egp4t82x.txt txt: ./txt/cord-327134-egp4t82x.txt summary: A series of phthalhydrazide based peptidic analogues 45 (Supplementary information, Fig. S1 ) with inhibitory activity against the SARS-3CL pro had been reported and was utilized in a validation study using Gold 2.2 to select the binding site definition and scoring function utilized for binding pose calculation. The group of top-ranking structurally diverse molecules obtained through the clustering analysis were visually inspected based on their (1) ability to occupy the key substrate specificity sites S1 0 , S1, S2, and S4, (2) geometric quality of the ligand binding pose, (3) hydrophilic/ lipophilic mismatches, and (4) complementarity of the key interacting features. The final docking parameters (binding site definition, scoring function for pose generation) selected through this study were identical to those used in the first phase of screening except for the addition of a constraint set. abstract: Abstract Severe acute respiratory syndrome is a highly infectious upper respiratory tract disease caused by SARS-CoV, a previously unidentified human coronavirus. SARS-3CLpro is a viral cysteine protease critical to the pathogen’s life cycle and hence a therapeutic target of importance. The recently elucidated crystal structures of this enzyme provide an opportunity for the discovery of inhibitors through rational drug design. In the current study, Gold docking program was utilized to conduct extensive docking studies against the target crystal structure to develop a robust and predictive docking protocol. The validated docking protocol was used to conduct a structure-based virtual screening of the Asinex Platinum collection. Biological evaluation of a screened selection of compounds was carried out to identify novel inhibitors of the viral protease. url: https://api.elsevier.com/content/article/pii/S0968089608000163 doi: 10.1016/j.bmc.2008.01.011 id: cord-265887-g5zhoyo9 author: Mukherjee, Shruti title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 words: 9085.0 sentences: 538.0 pages: flesch: 41.0 cache: ./cache/cord-265887-g5zhoyo9.txt txt: ./txt/cord-265887-g5zhoyo9.txt summary: (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. abstract: The Envelope (E) protein in SARS Coronavirus (CoV) is a small structural protein, incorporated as part of the envelope. A major fraction of the protein has been known to be associated with the host membranes, particularly organelles related to intracellular trafficking, prompting CoV packaging and propagation. Studies have elucidated the central hydrophobic transmembrane domain of the E protein being responsible for much of the viroporin activity in favor of the virus. However, newer insights into the organizational principles at the membranous compartments within the host cells suggest further complexity of the system. The lesser hydrophobic Carboxylic-terminal of the protein harbors interesting amino acid sequences- suggesting at the prevalence of membrane-directed amyloidogenic properties that remains mostly elusive. These highly conserved segments indicate at several potential membrane-associated functional roles that can redefine our comprehensive understanding of the protein. This should prompt further studies in designing and characterizing of effective targeted therapeutic measures. url: https://api.elsevier.com/content/article/pii/S0301462220301605 doi: 10.1016/j.bpc.2020.106452 id: cord-296187-nnv2e7gr author: Mulgaonkar, Nirmitee title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 words: 4943.0 sentences: 306.0 pages: flesch: 57.0 cache: ./cache/cord-296187-nnv2e7gr.txt txt: ./txt/cord-296187-nnv2e7gr.txt summary: The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. This study utilizes in silico methodology followed by in vitro experimental validation to screen existing FDA-approved small molecule drugs specific to the RBD of the spike protein of SARS-CoV-2 to identify repurposable drugs targeting further clinical validation. abstract: The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. Enveloped viruses infect the host cell by cellular membrane fusion, a crucial mechanism required for virus replication. The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. We also show that imatinib inhibits other coronaviruses, SARS-CoV, and MERS-CoV via fusion inhibition. Based on promising in vitro results, we propose the Abl tyrosine kinase inhibitor (ATKI), imatinib, to be a viable repurposable drug against COVID-19. url: https://doi.org/10.1101/2020.06.18.158196 doi: 10.1101/2020.06.18.158196 id: cord-294551-s3nsiano author: Muller, M. P. title: Early diagnosis of SARS: lessons from the Toronto SARS outbreak date: 2006-04-04 words: 3638.0 sentences: 160.0 pages: flesch: 47.0 cache: ./cache/cord-294551-s3nsiano.txt txt: ./txt/cord-294551-s3nsiano.txt summary: To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Patients were classified as confirmed SARS if they had a compatible clinical illness (fever or nonproductive cough or dyspnea), an exposure to SARS (direct contact with a known SARS case or travel to a SARS-endemic area or time spent at an institution where SARS transmission was occurring, within 12 days of symptom onset), and a positive microbiological test (positive acute or convalescent serology, or positive PCR from clinical or pathological specimens). Findings associated with a confirmed diagnosis included direct exposure to a known case (OR, 2.34; 95%CI, 1.01-5.40), symptomatic fever as an initial symptom (OR, 5.07; 95%CI, 2.24-11.50), a documented temperature of 38.0°C on admission to hospital (OR, 2.6; 95%CI, 1.14-5.92), and the presence of a pulmonary infiltrate by the time of admission (OR, 2.46; 95%CI, 1.09-5.56). abstract: The clinical presentation of SARS is nonspecific and diagnostic tests do not provide accurate results early in the disease course. Initial diagnosis remains reliant on clinical assessment. To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Findings were compared between patients with laboratory-confirmed SARS and those in whom SARS was excluded by laboratory or public health investigation. Of 364 cases, 273 (75%) had confirmed SARS, 30 (8%) were excluded, and 61 (17%) remained indeterminate. Among confirmed cases, exposure occurred in the healthcare environment (80%) or in the households of affected patients (17%); community or travel-related cases were rare (<3%). Fever occurred in 97% of patients by the time of admission. Respiratory findings including cough, dyspnea and pulmonary infiltrates evolved later and were present in only 59, 37 and 68% of patients, respectively, at admission. Direct exposure, fever on the first day of illness, and elevated temperature, pulmonary infiltrates, lymphopenia and thrombocytopenia at admission were associated with confirmed cases. Rhinorrhea, sore throat, and an elevated neutrophil count at admission were associated with excluded cases. In the absence of fever or significant exposure, SARS is unlikely. Other clinical, laboratory and radiographic findings further raise or lower the likelihood of SARS and provide a rational basis for estimating the likelihood of SARS and directing initial management. url: https://www.ncbi.nlm.nih.gov/pubmed/16586072/ doi: 10.1007/s10096-006-0127-x id: cord-327240-nohxk3y6 author: Muller, Matthew P. title: Adverse Events Associated with High‐Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome date: 2012-01-06 words: 4551.0 sentences: 254.0 pages: flesch: 48.0 cache: ./cache/cord-327240-nohxk3y6.txt txt: ./txt/cord-327240-nohxk3y6.txt summary: Logistic regression was used to evaluate the association between ribavirin use and each adverse event (progressive anemia, hypomagnesemia, hypocalcemia, bradycardia, transaminitis, and hyperamylasemia) after adjusting for SARS‐related prognostic factors and corticosteroid use. 11, 12 In Toronto, Ontario, Canada, most patients seen during the initial phase of the outbreak were treated with high-dose intravenous ribavirin, based on a protocol recommended for the treatment of hemorrhagic fever. [13] [14] [15] [16] Studies of the clinical efficacy of ribavirin in patients with SARS were inconclusive, 11, [17] [18] [19] [20] and significant adverse events were reported, including severe hemolysis. 27, 28 We report the frequency of adverse events in 183 patients treated with high-dose ribavirin during the Toronto SARS outbreak. Our finding that 57% of patients developed progressive anemia (largely associated with hemolysis) is substantially higher than the 9-19% rate seen in ribavirin-treated patients with hepatitis C but is consistent with the 49-73% reported in previous noncontrolled studies of ribavirin-related adverse events in patients with SARS. abstract: Study Objectives. To distinguish adverse events related to ribavirin therapy from those attributable to severe acute respiratory syndrome (SARS), and to determine the rate of potential ribavirin‐related adverse events. Design. Retrospective cohort study. Setting. Hospitals in Toronto, Ontario, Canada. Patients. A cohort of 306 patients with confirmed or probable SARS, 183 of whom received ribavirin and 123 of whom did not, between February 23, 2003, and July 1, 2003. Of the 183 treated patients, 155 (85%) received very high‐dose ribavirin; the other 28 treated patients received lower‐dose regimens. Measurements and Main Results. Data on all patients with SARS admitted to hospitals in Toronto were abstracted from charts and electronic databases onto a standardized form by trained research nurses. Logistic regression was used to evaluate the association between ribavirin use and each adverse event (progressive anemia, hypomagnesemia, hypocalcemia, bradycardia, transaminitis, and hyperamylasemia) after adjusting for SARS‐related prognostic factors and corticosteroid use. In the primary logistic regression analysis, ribavirin use was strongly associated with anemia (odds ratio [OR] 3.0, 99% confidence interval [CI] 1.5–6.1, p<0.0001), hypomagnesemia (OR 21, 99% CI 5.8–73, p<0.0001), and bradycardia (OR 2.3, 99% CI 1.0–5.1, p=0.007). Hypocalcemia, transaminitis, and hyperamylasemia were not associated with ribavirin use. The risk of anemia, hypomagnesemia, and bradycardia attributable to ribavirin use was 27%, 45%, and 17%, respectively. Conclusions. High‐dose ribavirin is associated with a high rate of adverse events. The use of high‐dose ribavirin is appropriate only for the treatment of infectious diseases for which ribavirin has proven clinical efficacy, or in the context of a clinical trial. Ribavirin should not be used empirically for the treatment of viral syndromes of unknown origin. url: https://www.ncbi.nlm.nih.gov/pubmed/17381375/ doi: 10.1592/phco.27.4.494 id: cord-304073-f3iwclkm author: Mullick, Jhinuk Basu title: Animal Models to Study Emerging Technologies Against SARS-CoV-2 date: 2020-07-27 words: 5315.0 sentences: 322.0 pages: flesch: 50.0 cache: ./cache/cord-304073-f3iwclkm.txt txt: ./txt/cord-304073-f3iwclkm.txt summary: Animal models are indispensable to understand these processes and develop and test emerging technologies; however, the mechanism of infection for SARS-CoV-2 requires certain similarities to humans that do not exist in common laboratory rodents. Here, we review important elements of viral infection, transmission, and clinical presentation reflected by various animal models readily available or being developed and studied for SARS-CoV-2 to help bioengineers evaluate appropriate preclinical models for their emerging technologies. Non-human primates, Syrian hamsters, ferrets, cats, and engineered chimeras mimic the human infection more closely and hold strong potential as animal models of SARS-CoV-2 infection and progression of resulting human disease. Overall, the studies show that the Syrian hamster is a useful animal model for SARS-CoV-2 infection especially to study viral replication, shedding, and transmission through the respiratory tract. In all studies, animals developed NAbs. Overall, the rhesus macaque model has been similar in many aspects to the human COVID-19 pathogenesis. abstract: New technologies are being developed toward the novel coronavirus SARS-CoV-2 to understand its pathogenesis and transmission, to develop therapeutics and vaccines, and to formulate preventive strategies. Animal models are indispensable to understand these processes and develop and test emerging technologies; however, the mechanism of infection for SARS-CoV-2 requires certain similarities to humans that do not exist in common laboratory rodents. Here, we review important elements of viral infection, transmission, and clinical presentation reflected by various animal models readily available or being developed and studied for SARS-CoV-2 to help bioengineers evaluate appropriate preclinical models for their emerging technologies. Importantly, applications of traditional mice and rat models are limited for studying SARS-CoV-2 and development of COVID-19. Non-human primates, Syrian hamsters, ferrets, cats, and engineered chimeras mimic the human infection more closely and hold strong potential as animal models of SARS-CoV-2 infection and progression of resulting human disease. url: https://doi.org/10.1007/s12195-020-00638-9 doi: 10.1007/s12195-020-00638-9 id: cord-289064-435bp4rt author: Muniangi-Muhitu, Hermine title: Covid-19 and Diabetes: A Complex Bidirectional Relationship date: 2020-10-08 words: 5744.0 sentences: 290.0 pages: flesch: 43.0 cache: ./cache/cord-289064-435bp4rt.txt txt: ./txt/cord-289064-435bp4rt.txt summary: Identified risk factors for disease severity and death from SARS-Cov2 infection include older age, male sex, diabetes, obesity and hypertension. We consider roles for the immune system, the observed phenomenon of microangiopathy in severe Covid-19 infection and the potential for direct viral toxicity on metabolically-relevant tissues including pancreatic beta cells and targets of insulin action. (18) , patients with diabetes and hypertension who had been treated with ACE inhibitors or angiotensin receptor blockers (ARB) had a high number of ACE2 receptors in the lung, and could therefore be at higher risk of developing severe symptoms, if infected with Covid-19. With respect to the glycemic deterioration seen in patients with preexisting T2D during Covid-19, a very recent report (63) provides the intriguing observation that ACE2 expression at both the mRNA and protein is increased substantially in human beta cells in response to response to inflammatory cytokines, presumably rendering these cells more susceptible to infection. abstract: Covid-19 is a recently-emerged infectious disease caused by the novel severe acute respiratory syndrome coronavirus SARS-CoV2. SARS-CoV2 differs from previous coronavirus infections (SARS and MERS) due to its high infectivity (reproduction value, R(0), typically 2–4) and pre- or asymptomatic transmission, properties that have contributed to the current global Covid-19 pandemic. Identified risk factors for disease severity and death from SARS-Cov2 infection include older age, male sex, diabetes, obesity and hypertension. The reasons for these associations are still largely obscure. Evidence is also emerging that SARS-CoV2 infection exacerbates the underlying pathophysiology of hyperglycemia in people with diabetes. Here, we discuss potential mechanisms through which diabetes may affect the risk of more severe outcomes in Covid-19 and, additionally, how diabetic emergencies and longer term pathology may be aggravated by infection with the virus. We consider roles for the immune system, the observed phenomenon of microangiopathy in severe Covid-19 infection and the potential for direct viral toxicity on metabolically-relevant tissues including pancreatic beta cells and targets of insulin action. url: https://www.ncbi.nlm.nih.gov/pubmed/33133024/ doi: 10.3389/fendo.2020.582936 id: cord-355841-m6dl8a0w author: Munz, Maike title: Acute transverse myelitis after COVID-19 pneumonia date: 2020-05-26 words: 858.0 sentences: 72.0 pages: flesch: 47.0 cache: ./cache/cord-355841-m6dl8a0w.txt txt: ./txt/cord-355841-m6dl8a0w.txt summary: A repeated throat swab showed a negative SARS-CoV2 PCR. Magnetic resonance imaging (MRI) of the spine revealed T2 signal hyperintensity of the thoracic spinal cord at Th9 level suggestive of acute transverse myelitis rather than multiple sclerosis [3] (Fig. 1a) . SARS-CoV2-PCR in the CSF and oligoclonal bands were negative. Follow-up MRI on day 6 further showed a patchy hyperintensity of the thoracic myelon at Th9-10 and at Th3-5 level (Fig. 1d) , suggestive of transverse myelitis. Follow-up CSF on day 12 showed normalization of cell count (3/µl) and regressing protein levels (734 mg/l), no Maike Munz and Swen Weßendorf authors contributed equally. Cases of Guillain-Barré Syndrome in association with severe COVID-19 infections were reported [6] . In a series of 58 severely affected COVID-19 patients, 67% showed clinical corticospinal tract signs but received no spinal MRI [7] . Preprint) Acute myelitis after SARS-CoV-2 infection: A case report https abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32458198/ doi: 10.1007/s00415-020-09934-w id: cord-310928-g553afo9 author: Murch, Simon H title: Common determinants of severe Covid-19 infection are explicable by SARS-CoV-2 secreted glycoprotein interaction with the CD33-related Siglecs, Siglec-3 and Siglec-5/14 date: 2020-08-07 words: 3724.0 sentences: 224.0 pages: flesch: 46.0 cache: ./cache/cord-310928-g553afo9.txt txt: ./txt/cord-310928-g553afo9.txt summary: In contrast to the SARS secreted glycoprotein (SGP), SARS-CoV-2 SGP are thus potential ligands for Sialic acid-binding Siglecs on host immune cells, known to regulate immune function. CD33 + MDSC populations release Arginase-1 to cause arginine depletion, inducing decreased T cell receptor (TCR)- chain expression and impaired adaptive immune responses 20, 21 . There is so far no clear consensus on their eventual phenotype but these new marrow derived cells are initially characterised as Early stage MDSC (eMDSC), which do not initially express lineage markers but do express CD33 and would thus be susceptible to SARS-CoV-2 SGP manipulation until the virus was cleared ( Figure 3 ). In due course, this might allow persons who fail to respond to immunisation to be pre-treated to block Siglec binding sites, allowing them to be exposed to small infecting doses of SARS-Cov-2 in clinically controlled circumstances and thus generate a broad immune response, including to the pathogenic glycan determinants abstract: SARS-CoV-2 interaction with the ACE-2 receptor cannot alone explain the demography and remarkable variation in clinical progression of Covid-19 infection. Unlike SARS-CoV, the cause of SARS, several SARS-CoV-2 spike glycans contain sialic acid residues. In contrast to the SARS secreted glycoprotein (SGP), SARS-CoV-2 SGP are thus potential ligands for Sialic acid-binding Siglecs on host immune cells, known to regulate immune function. Such SARS-CoV-2 glycoproteins would contribute to immune deviation. CD33-related Siglecs are important immune regulators. Siglec-5 and -14 are paired receptors with opposed actions on the NLRP3 inflammasome, which is critical in early viral clearance. SGP binding in persons of Siglec-14 null genotype (30-70% in Black, Asian and Minority Ethnic (BAME) persons, 10% in North Europeans) would induce unopposed inhibitory signalling, causing viral persistence through inflammasome inhibition. Siglec-3 (CD33) and Siglec-5 are expressed on CD33 myeloid derived suppressor cells (CD33 MDSC). Immunosuppressive CD33 MDSC populations are increased in all groups at risk of severe Covid-19 infection. CD33 expression is increased in persons with the CD33 rs3865444 CC allele, associated with Alzheimer’s disease, who would thus show enhanced susceptibility. Viral SGP ligation of CD33, potentially in conjunction with Siglec-5, would promote expansion of CD33 MDSC cells, as occurs in cancers but at much greater scale. CD33 is expressed on CNS microglia, potentially activated by SGP penetration through the porous cribriform plate to cause anosmia. Genotyping of severe or fatal Covid-19 cases can confirm or refute this pathophysiological mechanism. Early data have confirmed extremely high-level increase of CD33 MDSC numbers in severe Covid-19 infection, consistent with the proposed mechanism. url: https://api.elsevier.com/content/article/pii/S0306987720313347 doi: 10.1016/j.mehy.2020.110168 id: cord-286441-nl3kuqw3 author: Murray, D. D. title: Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative date: 2020-11-12 words: 5560.0 sentences: 303.0 pages: flesch: 48.0 cache: ./cache/cord-286441-nl3kuqw3.txt txt: ./txt/cord-286441-nl3kuqw3.txt summary: Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. abstract: Background: The SARS-CoV-2 pandemic is a public health emergency. Safe and effective therapies are urgently needed. Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. The protocol design allows multiple therapeutic agents to be evaluated in an efficient and scientifically rigorous manner, with efficiencies delivered by the MAMS design, and began by studying neutralizing monoclonal antibodies. TICO employs an agile and robust approach to futility and safety evaluation at 300 patients enrolled (Stage 1), with subsequent expansion to full sample size and an expanded target population (Stage 2) if the agent shows an acceptable safety profile and evidence of efficacy. Two ordinal outcomes applied early (Day 5) determine the efficacy signals of the investigational agents(s) and progression to Stage 2. These ordinal outcomes assess both respiratory and other organ failure events, recognizing the broad range of COVID-19 morbidity. In Stage 2, overall efficacy is assessed using the primary outcome of time to sustained recovery, assessed over 90 days. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. The implementation of TICO across a global network allows for continued enrollment despite variations in geographic epidemiology. Study Status: The TICO master protocol moved from conception to first patient enrolled in approximately 9 weeks, a testament to the expedited regulatory and ethics review, coupled with flexible and responsive study operations. The first agent to be tested using this protocol, LY-CoV-555, enrolled N=326 participants before undergoing Stage 1 futility and safety assessment. Two additional agents will enter the study in November 2020, with other agents planned. Conclusion: The TICO MAMS platform trial has been implemented efficiently across a global network of sites and several trial networks. It will generate results rapidly for multiple novel neutralizing monoclonal antibodies and other therapeutics agents. url: https://doi.org/10.1101/2020.11.08.20227876 doi: 10.1101/2020.11.08.20227876 id: cord-333909-uco4c946 author: Murray, Meghan T. title: Mitigating a COVID-19 Outbreak Among Major League Baseball Players — United States, 2020 date: 2020-10-23 words: 2988.0 sentences: 149.0 pages: flesch: 52.0 cache: ./cache/cord-333909-uco4c946.txt txt: ./txt/cord-333909-uco4c946.txt summary: Certain MLB health and safety protocols, which include frequent diagnostic testing for rapid case identification, isolation of persons with positive test results, quarantine for close contacts, mask wearing, and social distancing, might have limited COVID-19 transmission between teams. The health and safety protocols established tiered, risk-based testing for MLB teams, which called for persons who received a positive SARS-CoV-2 test result to be placed in isolation and for close contacts to be quarantined separately. Before game play on day 4, the index team A player (an asymptomatic tier 1 risk group member who received every other day testing, per protocol) received a positive SARS-CoV-2 real-time reverse transcription-polymerase chain reaction (RT-PCR) test result from collection on day 2. Investigators received from MLB a deidentified line list of team members with diagnosed COVID-19, a timeline of the outbreak response, the duration of on-field play by potentially infectious persons (within 24 hours before the date of collection of the test-positive specimen), contact tracing procedures, and the MLB health and safety protocols. abstract: Mass gatherings have been implicated in higher rates of transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), and many sporting events have been restricted or canceled to limit disease spread (1). Based on current CDC COVID-19 mitigation recommendations related to events and gatherings (2), Major League Baseball (MLB) developed new health and safety protocols before the July 24 start of the 2020 season. In addition, MLB made the decision that games would be played without spectators. Before a three-game series between teams A and B, the Philadelphia Department of Public Health was notified of a team A player with laboratory-confirmed COVID-19; the player was isolated as recommended (2). During the series and the week after, laboratory-confirmed COVID-19 was diagnosed among 19 additional team A players and staff members and one team B staff member. Throughout their potentially infectious periods, some asymptomatic team A players and coaches, who subsequently received positive SARS-CoV-2 test results, engaged in on-field play with teams B and C. No on-field team B or team C players or staff members subsequently received a clinical diagnosis of COVID-19. Certain MLB health and safety protocols, which include frequent diagnostic testing for rapid case identification, isolation of persons with positive test results, quarantine for close contacts, mask wearing, and social distancing, might have limited COVID-19 transmission between teams. url: https://www.ncbi.nlm.nih.gov/pubmed/33090983/ doi: 10.15585/mmwr.mm6942a4 id: cord-320740-npoje09j author: Musa, Arif title: Remdesivir for the Treatment of COVID-19: A Systematic Review of the Literature date: 2020-05-20 words: 2292.0 sentences: 153.0 pages: flesch: 54.0 cache: ./cache/cord-320740-npoje09j.txt txt: ./txt/cord-320740-npoje09j.txt summary: To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Given the worldwide urgency for an effective and safe treatment for COVID-19 and the therapeutic potential of remdesivir, this systematic review was performed to determine the outcomes and adverse events associated with this investigational, anti-viral medication. abstract: In March 2020, the World Health Organization declared the spread of SARS-CoV-2 a global pandemic. To date, coronavirus disease-2019 (COVID-19) has spread to over 200 countries, leading to over 1.6 million cases and over 99,000 deaths. Given that there is neither a vaccine nor proven treatment for COVID-19, there is currently an urgent need for effective pharmacotherapy. To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. Remdesivir, an anti-viral prodrug originally developed to treat Ebola virus disease, has shown broad spectrum activity against the Coronavirus family. A recent case report reported improvement of clinical symptoms with remdesivir in a patient with COVID-19. After conducting a systematic search of 18 clinical trial registries and three large scientific databases, we identified 86 potentially eligible items. Following removal of duplicates (n = 21), eligible studies were reviewed independently by two authors. After the first round of screening, inter-rater agreement was 98.5% (κ = 0.925). After the second round of full-text screening, inter-rater agreement was 100%. A total of seven ongoing and recruiting clinical trials of remdesivir (100–200 milligrams, intravenous [IV]) were included. We identified the following primary outcomes: patients discharged (n = 2); time to clinical status improvement (n = 2); improved O2 saturation (n = 2); body temperature normalization (n = 2); and clinical status (n = 1). Secondary outcomes in all identified studies included documentation of adverse events. Phase 3 trials are expected to be completed between April 2020–2023. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. url: https://www.ncbi.nlm.nih.gov/pubmed/32726230/ doi: 10.5811/westjem.2020.5.47658 id: cord-305816-06lddk87 author: Musarrat, Farhana title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections date: 2020-05-17 words: 3227.0 sentences: 189.0 pages: flesch: 52.0 cache: ./cache/cord-305816-06lddk87.txt txt: ./txt/cord-305816-06lddk87.txt summary: title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections A systematic screening of several drugs including cardiac glycosides and kinase inhibitors and inhibitors of human immunodeficiency virus (HIV) entry revealed that only the FDA‐approved HIV protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S‐n‐ and S‐o‐mediated cell fusion with complete inhibition at a 10‐μM concentration. 26 In addition to its potent activity against the HIV protease, nelfinavir mesylate was found to produce multiple effects on cellular processes including the induction of apoptosis and necrosis as well as induction of cell-protective mechanisms, including cell cycle retardation and the unfolded protein response. HRP, horseradish peroxidase; SARS CoV, severe acute respiratory syndrome coronavirus; Sn, S-new Recently, it was shown that a peptide that targeted the S-n HR1 domain S inhibited SARS-CoV-2 virus replication, virus entry, and virus-induced cell fusion. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides abstract: Severe acute respiratory syndrome coronavirus‐2 (SARS CoV‐2) is the causative agent of the coronavirus disease‐2019 (COVID‐19) pandemic. Coronaviruses enter cells via fusion of the viral envelope with the plasma membrane and/or via fusion of the viral envelope with endosomal membranes after virion endocytosis. The spike (S) glycoprotein is a major determinant of virus infectivity. Herein, we show that the transient expression of the SARS CoV‐2 S glycoprotein in Vero cells caused extensive cell fusion (formation of syncytia) in comparison to limited cell fusion caused by the SARS S glycoprotein. Both S glycoproteins were detected intracellularly and on transfected Vero cell surfaces. These results are in agreement with published pathology observations of extensive syncytia formation in lung tissues of patients with COVID‐19. These results suggest that SARS CoV‐2 is able to spread from cell‐to‐cell much more efficiently than SARS effectively avoiding extracellular neutralizing antibodies. A systematic screening of several drugs including cardiac glycosides and kinase inhibitors and inhibitors of human immunodeficiency virus (HIV) entry revealed that only the FDA‐approved HIV protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S‐n‐ and S‐o‐mediated cell fusion with complete inhibition at a 10‐μM concentration. In‐silico docking experiments suggested the possibility that nelfinavir may bind inside the S trimer structure, proximal to the S2 amino terminus directly inhibiting S‐n‐ and S‐o‐mediated membrane fusion. Also, it is possible that nelfinavir may act to inhibit S proteolytic processing within cells. These results warrant further investigations of the potential of nelfinavir mesylate to inhibit virus spread at early times after SARS CoV‐2 symptoms appear. url: https://doi.org/10.1002/jmv.25985 doi: 10.1002/jmv.25985 id: cord-301025-cf2jcw6x author: Musca, Serban C. title: A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine''s Prophylactic Effect Against Infection With SARS-CoV-2 date: 2020-08-13 words: 4364.0 sentences: 190.0 pages: flesch: 54.0 cache: ./cache/cord-301025-cf2jcw6x.txt txt: ./txt/cord-301025-cf2jcw6x.txt summary: title: A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine''s Prophylactic Effect Against Infection With SARS-CoV-2 We propose to use data from patients with rheumatic diseases (RA, SLR) who have been chronically taking HCQ medication since before the COVID-19 outbreak (hereafter: HCQpa), in order to evaluate the potential of HCQ for preventing infection with SARS-CoV-2. If HCQ has no prophylactic effect against infection with SARS-CoV-2, COVID-19 prevalence in HCQpa will not be statistically different from that in the general population (all comers who do not take HCQ medication; hereafter: pop gen ). HCQ having a prophylactic effect against SARS-CoV-2 infection would manifest itself by a COVID-19 prevalence in HCQpa that is lower than the COVID-19 prevalence in the general population. abstract: No vaccine against infection by SARS-CoV-2 yet exists. Treatment by hydroxychloroquine (HCQ) medication, among others, has been proposed. However, prophylactic HCQ medication has been little evaluated. We propose to use data from patients with rheumatic diseases (RA, SLR) who have been chronically taking HCQ medication since before the COVID-19 outbreak (hereafter: HCQpa), in order to evaluate the potential of HCQ for preventing infection with SARS-CoV-2. This can be achieved with relative ease by considering whether COVID-19 prevalence is significantly lower in HCQpa than in the general population (i.e., all people that are not HCQpa). Even if COVID-19 prevalence is truly significantly lower in HCQpa, some HCQpa may still present with COVID-19 (lower prevalence does not mean a prevalence of zero). However, given a value for COVID-19 prevalence in the general population and a number of available HCQpa, one may compute the maximum number of HCQpa for that total number of HCQpa considered that can have COVID-19 in order to still be able to conclude a lower COVID-19 prevalence in HCQpa (i.e., if there is one more case of COVID-19 than that maximum number, the COVID-19 prevalence in the HCQpa cannot be said to be lower than in the general population). Because the COVID-19 prevalence in the general population is not known with precision, we will consider different general population prevalence values. Among these contemplated prevalence values, one is derived from the official total number of confirmed cases, others by computing the total number of cases from the number of fatal COVID-19 cases so far and considering different case fatality rates per total cases. Our analyses show that systematic testing for COVID-19 in as few as 5,000 HCQpa is all that is needed for a test of whether HCQ has a prophylactic action against COVID-19, even for a COVID-19 prevalence value as low as 250 per 100,000, provided that test sensitivity is at least equal to its specificity. For higher COVID-19 prevalence values, the number of HCQpa needed is even lower. url: https://www.ncbi.nlm.nih.gov/pubmed/32903552/ doi: 10.3389/fmed.2020.00490 id: cord-293988-f5gvwjyh author: Musso, Nicolò title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 words: 3223.0 sentences: 186.0 pages: flesch: 54.0 cache: ./cache/cord-293988-f5gvwjyh.txt txt: ./txt/cord-293988-f5gvwjyh.txt summary: The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat''s pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2. abstract: The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. Despite close pet–human contact, little is known about the predisposition of pets to SARS-CoV-2. Among these, felines are the most susceptible. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. This is the first Italian study responding to the request of the scientific community to focus attention on the possible role of pets as a viral reservoir. An important question remains unanswered: did the cat actually die due to SARS-CoV-2 infection? url: https://www.ncbi.nlm.nih.gov/pubmed/32932800/ doi: 10.3390/pathogens9090746 id: cord-290123-scd9u8ix author: Mustafa, Mujahed I. title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors date: 2020-09-23 words: 3551.0 sentences: 202.0 pages: flesch: 47.0 cache: ./cache/cord-290123-scd9u8ix.txt txt: ./txt/cord-290123-scd9u8ix.txt summary: title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors In this review, we will focus on cytokine storm in COVID-19 patients, their impact on the body organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. However, novel coronavirus still gains entry into humans by targeting ACE2 receptor that is found on lung cells, which destroy human lungs through cytokine storms, and this leads to hyperinflammation, forcing the immune cells to destroy healthy cells, which could be the reason behind COVID-19 patients'' frequent intensive care admission [28] . This review deals with cytokine storm in COVID-19 patients, their impact on the organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. COVID-19 triggers cytokine storm in many stages of its pathological course that causes lung fibrosis, acute respiratory distress syndrome, and eventually leads to multiorgan failure [34, 54, 61] . abstract: The novel coronavirus is not only causing respiratory problems, but it may also damage the heart, kidneys, liver, and other organs; in Wuhan, 14 to 30% of COVID-19 patients have lost their kidney function and now require either dialysis or kidney transplants. The novel coronavirus gains entry into humans by targeting the ACE2 receptor that found on lung cells, which destroy human lungs through cytokine storms, and this leads to hyperinflammation, forcing the immune cells to destroy healthy cells. This is why some COVID-19 patients need intensive care. The inflammatory chemicals released during COVID-19 infection cause the liver to produce proteins that defend the body from infections. However, these proteins can cause blood clotting, which can clog blood vessels in the heart and other organs; as a result, the organs are deprived of oxygen and nutrients which could ultimately lead to multiorgan failure and consequent progression to acute lung injury, acute respiratory distress syndrome, and often death. However, there are novel protein modification tools called the QTY code, which are similar in their structure to antibodies, which could provide a solution to excess cytokines. These synthetic proteins can be injected into the body to bind the excess cytokines created by the cytokine storm; this will eventually remove the excessive cytokines and inhibit the severe symptoms caused by the COVID-19 infection. In this review, we will focus on cytokine storm in COVID-19 patients, their impact on the body organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. url: https://doi.org/10.1155/2020/8198963 doi: 10.1155/2020/8198963 id: cord-332448-5fz8ef4f author: Mutnal, M. B. title: Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date: 2020-05-02 words: 2583.0 sentences: 159.0 pages: flesch: 55.0 cache: ./cache/cord-332448-5fz8ef4f.txt txt: ./txt/cord-332448-5fz8ef4f.txt summary: Testing for SARS-CoV-2 was performed by real-time RT-PCR assay and results were shared with State public health officials for immediate interventions. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint of this study is to encourage other laboratories to consider an early start to testing during pandemics, share 74 initial trends in this part of the world and possible impact of SARS-CoV-2 on other seasonal respiratory 75 This report describes the early trends of SARS-CoV-2 infections in the central and north Texas, 76 USA and impact of epidemiological interventions that may have led to the decrease in the incidence of was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. BSWH laboratory provided test results data on both ambulatory and inpatient 275 population, and shared patient demographics with local public health officials. abstract: Introduction: Rapid diagnosis and isolation are key to containing the rapid spread of a pandemic agent like SARS-CoV-2, which has spread globally since its initial outbreak in Wuhan province in China. SARS-CoV-2 is novel to most parts of the world including USA and the effect on normally prevalent viruses is just becoming apparent. We present our initial data on the prevalence of respiratory viruses in the month of March, 2020. Methods: This is a retrospective cohort study post launching of SARS-CoV-2 testing at BSWH, Temple TX. Testing for SARS-CoV-2 was performed by real-time RT-PCR assay and results were shared with State public health officials for immediate interventions. Results: More than 3500 tests were performed during the first two weeks of testing for SARS-CoV-2 and identified 168 (4.7%) positive patients. Sixty-two (3.2%) of the 1,912 ambulatory patients and 106 (6.3%) of the 1,659 ED/inpatients were tested positive. Higher rate of infection (6.9%) were noted in the patients belonging to age group 25-34 years and least number of positive cases were noted in <25 years old (2%) group. The TX State county specific patient demographic information was shared with respective public health departments for epidemiological interventions. Incidentally, this study showed that there was a sudden decrease in the occurrence of other infections due to seasonal viruses, perhaps due to increased epidemiological awareness, about SARS-CoV-2, among general public. Authors would also like to share a small study on SARS-CoV-2 serological assay for the detection of IgG antibodies. Conclusions: This study was intended to provide an initial experience of dealing with a pandemic and the role of laboratories in crisis management. Epidemiological interventions depend on timely availability of accurate diagnostic tests and throughput capacity of such systems during large outbreaks like SARS-CoV-2. url: http://medrxiv.org/cgi/content/short/2020.04.30.20086116v1?rss=1 doi: 10.1101/2020.04.30.20086116 id: cord-333670-qv1orlv5 author: Mutti, Luciano title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 words: 2500.0 sentences: 123.0 pages: flesch: 40.0 cache: ./cache/cord-333670-qv1orlv5.txt txt: ./txt/cord-333670-qv1orlv5.txt summary: In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32574270/ doi: 10.3389/fimmu.2020.01208 id: cord-262470-nkql7h9x author: Muus, Christoph title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date: 2020-04-20 words: 17577.0 sentences: 869.0 pages: flesch: 50.0 cache: ./cache/cord-262470-nkql7h9x.txt txt: ./txt/cord-262470-nkql7h9x.txt summary: title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. To assess the association of age, sex, and smoking status with the expression of ACE2, TMPRSS2, and CTSL, we aggregated 22 scRNA-seq datasets of healthy human nasal and lung cells, as well as fetal samples. abstract: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis. url: https://doi.org/10.1101/2020.04.19.049254 doi: 10.1101/2020.04.19.049254 id: cord-253606-o8a0jhx2 author: Mégarbane, Bruno title: Comment on: Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial date: 2020-08-07 words: 844.0 sentences: 58.0 pages: flesch: 44.0 cache: ./cache/cord-253606-o8a0jhx2.txt txt: ./txt/cord-253606-o8a0jhx2.txt summary: 4 Thirdly, using in vitro anti-SARS-CoV-2 activity and drug exposure at the putative target site of action to determine the effective regimen in vivo is misleading. 4 Interestingly, one mechanistic PK/virological/QTc model developed to predict SARS-CoV-2 decline rate and QTc prolongation suggested that only elevated hydroxychloroquine regimens (>400 mg twice daily for 5 days) are predicted to rapidly decrease viral loads, reduce the infected patient proportion and shorten the treatment course, compared with routine regimens (400 mg daily). To conclude, prediction of the effective hydroxychloroquine regimen to treat the SARS-CoV-2-infected patient is doomed due to uncertainties related to the lack of in vitro model reliability and EC 50 pertinence and to the weakness of used PBPK models that did not mirror hydroxychloroquine PK complexity at the intracellular target level. Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32766679/ doi: 10.1093/jac/dkaa327 id: cord-293736-nyvwv31m author: Méry, Geoffroy title: COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella date: 2020-07-21 words: 5746.0 sentences: 268.0 pages: flesch: 39.0 cache: ./cache/cord-293736-nyvwv31m.txt txt: ./txt/cord-293736-nyvwv31m.txt summary: Here we seek to explore what underlies the link between immune response and respiratory failure in CoV infections on the one hand, and the current observation of obesity as a risk factor for severe outcome in COVID-19 on the other. Indeed, during COVID-19 infection, most patients exhibit a specific cytokine profile, associating innate immunity chemokines (such as monocyte chemoattractant protein 3 and interferon gamma-induced protein 10 (IP-10), which are suggestive of macrophage activation and epithelial suffering), and pro-inflammatory macrophage-produced cytokines such as IL-6 (45). We suggest that the tampering with such pathways could also lead to abnormalities in the inflammatory response observed in severe CoV infections through their influence on immune regulation and cytokine production. Besides suffering from a pro-inflammatory environment, which favors macrophage activation and neutrophil production, obese patients exhibit abnormal responses to viral infection. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third coronavirus leading to a global health outbreak. Despite the high mortality rates from SARS-CoV-1 and Middle-East respiratory syndrome (MERS)-CoV infections, which both sparked the interest of the scientific community, the underlying physiopathology of the SARS-CoV-2 infection, remains partially unclear. SARS-CoV-2 shares similar features with SARS-CoV-1, notably the use of the angiotensin conversion enzyme 2 (ACE2) as a receptor to enter the host cells. However, some features of the SARS-CoV-2 pandemic are unique. In this work, we focus on the association between obesity, metabolic syndrome, and type 2 diabetes on the one hand, and the severity of COVID-19 infection on the other, as it seems greater in these patients. We discuss how adipocyte dysfunction leads to a specific immune environment that predisposes obese patients to respiratory failure during COVID-19. We also hypothesize that an ACE2-cleaved protein, angiotensin 1-7, has a beneficial action on immune deregulation and that its low expression during the SARS-CoV-2 infection could explain the severity of infection. This introduces angiotensin 1-7 as a potential candidate of interest in therapeutic research on CoV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32793244/ doi: 10.3389/fimmu.2020.01714 id: cord-287758-da11ypiy author: Mônica Vitalino de Almeida, Sinara title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 words: 17412.0 sentences: 1034.0 pages: flesch: 45.0 cache: ./cache/cord-287758-da11ypiy.txt txt: ./txt/cord-287758-da11ypiy.txt summary: The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. abstract: Urgent treatments, in any modality, to fight SARS-CoV-2 infections are desired by society in general, by health professionals, by Estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding COVID-19: knowledge is the means to discover or to produce an effective treatment against this global disease. Scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of 2020 with over 25,000 published articles related to the new coronavirus. Three great lines of publications related to COVID-19 were identified for building this article: The first refers to knowledge production concerning the virus and pathophysiology of COVID-19; the second regards efforts to produce vaccines against SARS-CoV-2 at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat COVID-19 by drug repurposing. In this review, the drugs that have been repurposed so far are grouped according to their chemical class. Their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. This can help identifying anti-SARS-CoV-2 promising therapeutic agents. url: https://doi.org/10.1016/j.bmc.2020.115757 doi: 10.1016/j.bmc.2020.115757 id: cord-253615-qylm0koe author: Müller, Marcel A title: Human Coronavirus NL63 Open Reading Frame 3 encodes a virion-incorporated N-glycosylated membrane protein date: 2010-01-15 words: 5810.0 sentences: 305.0 pages: flesch: 51.0 cache: ./cache/cord-253615-qylm0koe.txt txt: ./txt/cord-253615-qylm0koe.txt summary: In-silico analysis of potential glycosylation sites and membrane topology suggest properties similar to SARS-CoV ORF 3a protein ( Figure 1B and Table 1 ). To analyze the expression of ORF 3 protein during viral replication, colon carcinoma cells (CaCo-2) and Rhesus monkey kidney cells (LLC-MK2) cells were infected with hCoV-NL63 and an immunofluorescence assay (IFA) was done after two and four days, respectively. In contrast to virus-infected cells, cells overexpressing ORF 3 protein from plasmid with an N-terminal FLAG epitope showed only a single band in Western blot whose migration was consistent with the hypothetical unglycosylated form ( Figure 5B, left panel) . Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice Severe acute respiratory syndrome coronavirus 3a protein is released in membranous structures from 3a protein-expressing cells and infected cells abstract: BACKGROUND: Human pathogenic coronavirus NL63 (hCoV-NL63) is a group 1 (alpha) coronavirus commonly associated with respiratory tract infections. In addition to known non-structural and structural proteins all coronaviruses have one or more accessory proteins whose functions are mostly unknown. Our study focuses on hCoV-NL63 open reading frame 3 (ORF 3) which is a highly conserved accessory protein among coronaviruses. RESULTS: In-silico analysis of the 225 amino acid sequence of hCoV-NL63 ORF 3 predicted a triple membrane-spanning protein. Expression in infected CaCo-2 and LLC-MK2 cells was confirmed by immunofluorescence and Western blot analysis. The protein was detected within the endoplasmatic reticulum/Golgi intermediate compartment (ERGIC) where coronavirus assembly and budding takes place. Subcellular localization studies using recombinant ORF 3 protein transfected in Huh-7 cells revealed occurrence in ERGIC, Golgi- and lysosomal compartments. By fluorescence microscopy of differently tagged envelope (E), membrane (M) and nucleocapsid (N) proteins it was shown that ORF 3 protein colocalizes extensively with E and M within the ERGIC. Using N-terminally FLAG-tagged ORF 3 protein and an antiserum specific to the C-terminus we verified the proposed topology of an extracellular N-terminus and a cytosolic C-terminus. By in-vitro translation analysis and subsequent endoglycosidase H digestion we showed that ORF 3 protein is N-glycosylated at the N-terminus. Analysis of purified viral particles revealed that ORF 3 protein is incorporated into virions and is therefore an additional structural protein. CONCLUSIONS: This study is the first extensive expression analysis of a group 1 hCoV-ORF 3 protein. We give evidence that ORF 3 protein is a structural N-glycosylated and virion-incorporated protein. url: https://www.ncbi.nlm.nih.gov/pubmed/20078868/ doi: 10.1186/1743-422x-7-6 id: cord-340063-nmx91h0a author: Müller, Olaf title: Epidemiologie und Kontrollmaßnahmen bei COVID-19 date: 2020-04-28 words: 3011.0 sentences: 349.0 pages: flesch: 53.0 cache: ./cache/cord-340063-nmx91h0a.txt txt: ./txt/cord-340063-nmx91h0a.txt summary: The Coronavirus Disease Pandemic 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), started in December 2019 in China. Es gibt bisher weder wirksame Medikamente noch eine Impfung, somit stehen nur Public-Health-Interventionen wie einerseits physisches Abstandhalten und Hygienemaßnahmen sowie andererseits gezieltes Testen gefolgt von Isolations-und Quarantänemaßnahmen zur Verfügung. Der Erreger des Coronavirus Disease 2019 (COVID19) , das Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), gehört zu einer RNA-Virusfamilie, die sowohl bei Tieren als auch beim Menschen Erkrankungen hervorrufen kann. Der Verlauf nationaler Epidemien sowie der Pandemie wird von Faktoren bestimmt, die bisher für COVID-19 noch nicht vollständig verstanden sind. Prinzipiell unterscheidet man hierbei Isolationsmaßnahmen (SARS-CoV-2-Infizierte und COVID-19-Patienten) und Quarantänemaßnahmen (Kontaktpersonen von Infizierten und Erkrankten, stark betroffene Gemeinden); diese Maßnahmen sind besonders wirksam zum Beginn einer Epidemie, wenn Infektionsketten noch nachvollziehbar sind [35] . Es ist momentan auch noch offen, welche Ausmaße die Pandemie in den Industrieländern erlangen wird; dies hängt primär von der Intensität und Dauer der durchgeführten Public-Health-Maßnahmen ab. abstract: The Coronavirus Disease Pandemic 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), started in December 2019 in China. SARS-CoV-2 is easily transmitted by droplet infection. After an incubation period of 1–14 days, COVID-19 shows a mild course in 80 % of observed cases and a severe course in 20 %, with a lethality rate of 0.3–5.8 %. Elderly people and people with underlying diseases have a higher risk of severe courses with mandatory ventilation. So far there are neither effective drugs nor vaccinations available, so only public health interventions such as physical distancing and hygiene measures on the one hand and targeted testing followed by isolation and quarantine measures on the other hand are available. China has shown that maximum use of these measures can control the epidemic. The further course and also the consequences for the global economy cannot be clearly predicted at present. url: https://doi.org/10.1055/a-1162-1987 doi: 10.1055/a-1162-1987 id: cord-314515-p40x3cxr author: NGAI, Jenny C. title: The long‐term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status date: 2010-03-19 words: 3506.0 sentences: 209.0 pages: flesch: 57.0 cache: ./cache/cord-314515-p40x3cxr.txt txt: ./txt/cord-314515-p40x3cxr.txt summary: Methods: A prospective cohort study of SARS patients at the Prince of Wales Hospital, Hong Kong was conducted, with serial assessments of lung function, 6MWD and 36 item Short Form General Health Survey at 3, 6, 12, 18 and 24 months after disease onset. 1 3 Previous studies of survivors of acute lung injury and ARDS unrelated to SARS have shown variable degrees of residual abnormalities in pulmonary function, exercise capacity and impairment in health-related quality of life. 20, 21 The objectives of the present study were to evaluate the 2-year outcome of lung function, exercise capacity, health and work status of SARS survivors based on updated normative lung function data collected in Hong Kong (HK) from 2001-2003. This prospective cohort study has shown that 52% of SARS survivors had persistent impairment in DLCO and that exercise capacity and health status were significantly lower than the normal controls of the same age groups at 24 months post-illness. abstract: Background and objective: Severe acute respiratory syndrome (SARS) emerged in 2003 and its long‐term sequelae remain largely unclear. This study examined the long‐term outcome of pulmonary function, exercise capacity, health and work status among SARS survivors. Methods: A prospective cohort study of SARS patients at the Prince of Wales Hospital, Hong Kong was conducted, with serial assessments of lung function, 6MWD and 36 item Short Form General Health Survey at 3, 6, 12, 18 and 24 months after disease onset. The work status was also recorded. Results: Serial assessments were completed by 55 of the 123 (39.9%) subjects, of whom 27 were health‐care workers (HCW). The mean age of the group was 44.4 (SD 13.2) years and 19 (34.5%) were males. At 24 months, 10 (18.2%), 9 (16.4%), 6 (10.9%) and 29 (52.7%) subjects had FEV(1), FVC, TLC and DL(CO) < 80% of predicted values, respectively. The mean (SD) 6MWD increased significantly from 439.0 (89.1) m at 3 months to 460.1 (102.8) m at 6 months (P 0.016) and became steady after 6 months. However, 6MWD and 36 item Short Form General Health Survey scores were lower than the normal population throughout the study. Moreover, 29.6% of HCW and 7.1% of non‐HCW had not returned to work 2 years after illness onset. Conclusions: This 2‐year study of a selected population of SARS survivors, showed significant impairment of DL(CO), exercise capacity and health status persisted, with a more marked adverse impact among HCW. url: https://www.ncbi.nlm.nih.gov/pubmed/20337995/ doi: 10.1111/j.1440-1843.2010.01720.x id: cord-297681-m0cckidw author: Na, Joo-Young title: [Secondary Publication] Standard Operating Procedure for Post-mortem Inspection in a Focus on Coronavirus Disease-19: the Korean Society for Legal Medicine date: 2020-08-13 words: 2813.0 sentences: 139.0 pages: flesch: 48.0 cache: ./cache/cord-297681-m0cckidw.txt txt: ./txt/cord-297681-m0cckidw.txt summary: The Korean Society for Legal Medicine, a highly specialized organization responsible for post-mortem examination and death investigation, aims to protect multiple staff-related post-mortem examinations and prevent the spread of COVID-19 in medical institutions and communities to improve social stability through this guideline for COVID-19 post-mortem inspections. The risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during post-mortem inspection of a dead body is relatively lower than that in the case of medical procedures or treatments because dead bodies do not cough and spread droplets. Due to the nature of postmortem inspection, in most cases, there is no or insufficient ante-mortem information, so collaboration with investigative agencies, local governments, and relevant public health centers is essential to determine the possibility of SARS-CoV-2 infection. 1) After confirming the identity of the deceased, if it is necessary to confirm whether he or she has the possibility of infection with COVID-19, request confirmation to the public health center through the police in charge, and proceed with the post-mortem inspection. abstract: Coronavirus disease 2019 (COVID-19) is a respiratory syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerged in Wuhan, China, in late 2019. It resulted in a worldwide pandemic, and spread through community transmission in the Republic of Korea (ROK). In the ROK, SARS-CoV-2 is categorized as a first-degree infectious disease of the legal communicable disease present. The Korean Society for Legal Medicine (KSLM) is the sole official academic association of forensic professionals in the ROK. As such, this society has played an important role in forensic medicine and science in the ROK. Therefore, KSLM suggests a standard operating procedure for the postmortem inspection in a focus on COVID-19. This article includes the background of this suggested standard operation procedure, basic principles for postmortem inspections of individuals suggested of having an infectious disease, and specific procedures according to the probability level of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32830469/ doi: 10.3346/jkms.2020.35.e302 id: cord-283512-qly8iclf author: Na, Ki Ryang title: Acute Kidney Injury and Kidney Damage in COVID-19 Patients date: 2020-07-07 words: 3170.0 sentences: 206.0 pages: flesch: 60.0 cache: ./cache/cord-283512-qly8iclf.txt txt: ./txt/cord-283512-qly8iclf.txt summary: METHODS: From February 21 to April 24, 2020, 66 patients diagnosed with COVID-19 at Chungnam National University Hospital were analyzed; all patients underwent routine urinalysis and were tested for serum creatinine, urine protein to creatinine ratio (PCR), and urine albumin to creatinine ratio (ACR). In this study, the clinical data of 66 patients diagnosed with COVID-19 were analyzed, and the effects of SARS-CoV-2 infection on renal function and its complications were explored. Data were collected, including age, gender, initial and follow-up SCr and eGFR (chronic kidney disease [CKD]-epidemiology collaboration), routine urinalysis with microscopy, urine PCR, urine ACR, underlying disease (diabetes mellitus [DM], hypertension, CKD, and cardiovascular disease), and whether mechanical ventilation, extracorporeal membrane oxygenation (ECMO), or renal replacement therapy was implemented. In our study, there was a lower percentage of patients with AKI (4.5%) and moderately to severely increased proteinuria (30.3%) than in previous human coronavirus infections. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This disease, which is quickly spreading worldwide, has high potential for infection and causes rapid progression of lung lesions, resulting in a high mortality rate. This study aimed to investigate the effects of SARS-CoV-2 infection on renal function in patients with COVID-19. METHODS: From February 21 to April 24, 2020, 66 patients diagnosed with COVID-19 at Chungnam National University Hospital were analyzed; all patients underwent routine urinalysis and were tested for serum creatinine, urine protein to creatinine ratio (PCR), and urine albumin to creatinine ratio (ACR). RESULTS: Acute kidney injury (AKI) occurred in 3 (4.5%) of the 66 patients, and 1 patient with AKI stage 3 underwent hemodialysis. Upon follow-up, all 3 patients recovered normal renal function. Compared with patients with mild COVID-19, AKI (n = 3) occurred in patients with severe COVID-19, of whom both urine PCR and ACR were markedly increased. CONCLUSION: The incidence of AKI was not high in COVID-19 patients. The lower mortality rate in SARS-CoV-2 infection compared with previous Middle East respiratory syndrome and SARS-CoV infections is thought to be associated with a low incidence of dysfunction in organs other than the lungs. url: https://www.ncbi.nlm.nih.gov/pubmed/32686373/ doi: 10.3346/jkms.2020.35.e257 id: cord-272445-0xauff51 author: Naaber, Paul title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date: 2020-10-27 words: 2751.0 sentences: 150.0 pages: flesch: 50.0 cache: ./cache/cord-272445-0xauff51.txt txt: ./txt/cord-272445-0xauff51.txt summary: title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients'' clinical data and the time-point the test was performed. Our study aimed to compare the performance characteristics of seven commercial and two in-house IgG/total Ab tests, which analyze the reactivity to several target proteins, and to correlate the results with the patients'' clinical data (with different symptoms score and age), and time from disease onset. abstract: SARS-CoV-2 antibody tests are available in various formats, detecting different viral target proteins and antibody subclasses. The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients’ clinical data and the time-point the test was performed. We found a remarkable variation in the sensitivity of antibody tests with the following performance: LIPS N (91.8%), Epitope (85.6%), Abbott and in-house LIPS S-RBD (both 84.5%), Roche (83.5%), Euroimmun (82.5%), DiaSorin (81.4%), SNIBE (70.1%), and Biosensor (64.9%). The overall agreement between the tests was between 71–95%, whereas the specificity of all tests was within 98–100%. The correlation with patients’ clinical symptoms score ranged from strongest in LIPS N (ρ = 0.41; p<0.001) to nonsignificant in LIPS S-RBD. Furthermore, the time of testing since symptom onset had an impact on the sensitivity of some tests. Our study highlights the importance to consider clinical symptoms, time of testing, and using more than one viral antigen in SARS-CoV-2 antibody testing. Our results suggest that some antibody tests are more sensitive for the detection of antibodies in early stage and asymptomatic patients, which may explain the contradictory results of previous studies and should be taken into consideration in clinical practice and epidemiological studies. url: https://www.ncbi.nlm.nih.gov/pubmed/33108380/ doi: 10.1371/journal.pone.0237548 id: cord-296881-2g81sjnl author: Nabil, Ahmed title: Current coronavirus (SARS-CoV-2) epidemiological, diagnostic and therapeutic approaches: An updated review until June 2020 date: 2020-07-20 words: 4802.0 sentences: 253.0 pages: flesch: 43.0 cache: ./cache/cord-296881-2g81sjnl.txt txt: ./txt/cord-296881-2g81sjnl.txt summary: On May 7, 2020, Gilead Sciences, announced that the Japanese Ministry of Health, Labour and Welfare (MHLW) has granted regulatory approval of Veklury® (Remdesivir) as a treatment for SARS-CoV-2 infection, the virus that causes COVID-19 acute respiratory syndrome, under an exceptional approval pathway. In COVID-19 infection, a massive number of T-lymphocytes and mononuclear macrophages are activated, emitting different cytokines such as interleukin-6 (IL-6), which binds to the IL-6 receptor on its target cells, causing the cytokine storm and severe inflammatory responses in most organs including lungs, liver, kidney and other tissues and organs. Moreover, in July 2020 the WHO discontinued clinical trials with hydroxychloroquine and lopinavir/ritonavir treatment arms for COVID-19 (WHO, 2020b), where both therapies produced little and no reduction in the mortality of hospitalized SARS-CoV-2 cases when compared to standard of care. COVID-19 infection and treatment with hydroxychloroquine cause severe haemolysis crisis in a patient with glucose-6-phosphate dehydrogenase deficiency abstract: Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in Wuhan City, China. The World Health Organization (WHO) declared the coronavirus outbreak as a global pandemic in March 2020. Fever, dry cough and fatigue are found in the vast majority of all COVID-19 cases. Early diagnosis, treatment and future prevention are keys to COVID-19 management. Currently, the unmet need to develop cost-effective point-of-contact test kits and efficient laboratory techniques for confirmation of COVID-19 infection has powered a new frontier of diagnostic innovation. No proven effective therapies or vaccines for SARS-CoV-2 currently exist. The rapidly increasing research regarding COVID-19 virology provides a significant number of potential drug targets. Remdesivir may be the most promising therapy up till now. On May 1, 2020, Gilead Sciences, announced that the U.S. Food and Drug Administration (FDA) has granted emergency use authorization (EUA) for the investigational Remdesivir as a potential antiviral for COVID-19 treatment. On May 7, 2020, Gilead Sciences, announced that the Japanese Ministry of Health, Labour and Welfare (MHLW) has granted regulatory approval of Veklury® (Remdesivir) as a treatment for SARS-CoV-2 infection, the virus that causes COVID-19 acute respiratory syndrome, under an exceptional approval pathway. Also, Corticosteroids are recommended for severe cases only to suppress the immune response and reduce symptoms, but not for mild and moderate patients where they are associated with a high-risk side effect. Based on the currently published evidence, we tried to highlight different diagnostic approaches, side effects and therapeutic agents that could help physicians in the frontlines. url: https://www.ncbi.nlm.nih.gov/pubmed/32788913/ doi: 10.17179/excli2020-2554 id: cord-268661-a56u5e2o author: Nadeau, S. A. title: The origin and early spread of SARS-CoV-2 in Europe date: 2020-06-12 words: 5407.0 sentences: 289.0 pages: flesch: 55.0 cache: ./cache/cord-268661-a56u5e2o.txt txt: ./txt/cord-268661-a56u5e2o.txt summary: Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions. Here, we fit a phylodynamic model with geographic structure to full-length SARS-CoV-2 genomes to (i) estimate the early patterns of SARS-CoV-2 spread into and across Europe, (ii) weigh genomic evidence for competing hypotheses about the geographic origin of the predominant A2a lineage in Europe, (iii) report on the epidemiological parameters, and (iv) compare the rate of new cases arising from within-region transmission versus migration during the early epidemic. abstract: The investigation of migratory patterns of the SARS-CoV-2 pandemic before border closures in Europe is a crucial first step towards an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions. We find that the predominant lineage spreading in Europe has a most recent common ancestor in Italy and was probably seeded by a transmission event in either Hubei or Germany. We do not find evidence for preferential migration paths from Hubei into different European regions or from each European region to the others. Sustained local transmission is first evident in Italy and then shortly thereafter in the other European regions considered. Before the first border closures in Europe, we estimate that the rate of occurrence of new cases from within-country transmission was within the bounds of the estimated rate of new cases from migration. In summary, our analysis offers a view on the early state of the epidemic in Europe and on migration patterns of the virus before border closures. This information will enable further study of the necessity and timeliness of border closures. url: https://doi.org/10.1101/2020.06.10.20127738 doi: 10.1101/2020.06.10.20127738 id: cord-309147-c3ikb81g author: Nadeem, Muhammad Shahid title: Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19) date: 2020-04-22 words: 4984.0 sentences: 315.0 pages: flesch: 51.0 cache: ./cache/cord-309147-c3ikb81g.txt txt: ./txt/cord-309147-c3ikb81g.txt summary: According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The recent reports have suggested that SARS-CoV-2 is a modified coronavirus of bat origin [22, 32] , which came to humans as a result of zoonotic transmission [33, 34] . The receptor-binding domain (RBD) of pangolin-CoV has only a one amino acid difference with that of SARS-CoV-2; the infected pangolins exhibit pathological symptoms similar to humans suffering from COVID-19, and their blood circulating antibodies can react with the spike protein of SARS-CoV-2 [35, 36] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): The epidemic and the challenges abstract: The ongoing episode of coronavirus disease 19 (COVID-19) has imposed a serious threat to global health and the world economy. The disease has rapidly acquired a pandemic status affecting almost all populated areas of the planet. The causative agent of COVID-19 is a novel coronavirus known as SARS-CoV-2. The virus has an approximate 30 kb single-stranded positive-sense RNA genome, which is 74.5% to 99% identical to that of SARS-CoV, CoV-pangolin, and the coronavirus the from horseshoe bat. According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The serine protease inhibitors, spike protein-based vaccines, or ACE2 blockers may have therapeutic potential in the near future. At present, no vaccine is available against COVID-19. The disease is being treated with antiviral, antimalarial, anti-inflammatory, herbal medicines, and active plasma antibodies. In this context, the present review article provides a cumulative account of the recent information regarding the viral characteristics, potential therapeutic targets, treatment options, and prospective research questions. url: https://www.ncbi.nlm.nih.gov/pubmed/32331255/ doi: 10.3390/pathogens9040307 id: cord-027253-wfmm7naa author: Nag, Pooja title: Optical Fiber Sensors for Rapid Screening of COVID-19 date: 2020-06-19 words: 1710.0 sentences: 94.0 pages: flesch: 45.0 cache: ./cache/cord-027253-wfmm7naa.txt txt: ./txt/cord-027253-wfmm7naa.txt summary: The article provides an overview of evanescent wave absorbance and localized surface plasmon resonance-based optic fiber platform for potential screening of COVID-19. Two alternative approaches for viral infection diagnostics are possible and practiced: the first involves serological investigations for measurement of elevated biomarker levels, for example, measurement of immunoglobin M (IgM) and immunoglobin G (IgG), while the second involves direct determination of the virus itself, utilizing its unique cellular proteins. This report explores the possible approaches of development of a point of care, low-cost evanescent wave absorbance (EWA)-based optical fiber sensor for quick and specific diagnosis of SARS-CoV-2. The wave is very sensitive to changes in refractive index at the interface and this property is utilized to develop EWA-based fiber optic sensors. While Fig. 3b has specific surface proteins (of the virus) immobilized on the optical fiber for detection of IgG and/or IgM (produced as an immune response). abstract: Rapid diagnosis of coronavirus disease COVID-19 is challenging in developing countries due to diverse clinical presentations and limited healthcare infrastructure. Biosensors hold immense prospects for diagnosis of the disease. Two approaches are proposed: the first involves measurement of host immune response and second, the detection of viruses or viral cell surface proteins using suitable bioreceptors. The article provides an overview of evanescent wave absorbance and localized surface plasmon resonance-based optic fiber platform for potential screening of COVID-19. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303588/ doi: 10.1007/s41403-020-00128-4 id: cord-335292-x2vjzp18 author: Nagashima, S. title: The Endothelial Dysfunction and Pyroptosis Driving the SARS-CoV-2 Immune-Thrombosis date: 2020-06-19 words: 3502.0 sentences: 221.0 pages: flesch: 43.0 cache: ./cache/cord-335292-x2vjzp18.txt txt: ./txt/cord-335292-x2vjzp18.txt summary: Approach and Results: Post-mortem lung (6 cases of COVID-19 group; 10 cases of H1N1 group and 11 cases of Control group) and myocardial samples (2 cases of COVID-19 and one control) were analyzed by conventional immunohistochemistry by using antibodies to identify molecules involving with endothelial activation (CD163, Interleukin-6 (IL-6), Tumor Necrosis Factor alpha (TNF-alpha), Intercellular Adhesion Molecule 1 (ICAM-1)) and pyroptosis (Caspase-1). In addition to COVID-19 endothelial activation, the probable higher significant involvement of pyroptosis, in this pandemic disease, but not in H1N1pdm09, may drive the massive endothelial cell death contributing to thrombogenic mechanism. The presence of the same pattern of tissue expression (COVID-19 patients with higher CD163, IL-6, ICAM-1, TNF-alpha, and Caspase-1 tissue expression than control patient) in the myocardial samples might suggest that endothelial dysfunction and pyroptosis mechanism could be more than a local lung process, but a systemic event. abstract: Objective: Endothelial activation after viral infection could contribute to changes in the vascular glycocalyx associated with programmed inflammatory cell death called pyroptosis. Thus, our goal is to recognize endothelial activation and pyroptosis in lung and myocardial samples of Coronavirus disease (COVID-19) cases and compare to H1N1pdm09 and control cases. Approach and Results: Post-mortem lung (6 cases of COVID-19 group; 10 cases of H1N1 group and 11 cases of Control group) and myocardial samples (2 cases of COVID-19 and one control) were analyzed by conventional immunohistochemistry by using antibodies to identify molecules involving with endothelial activation (CD163, Interleukin-6 (IL-6), Tumor Necrosis Factor alpha (TNF-alpha), Intercellular Adhesion Molecule 1 (ICAM-1)) and pyroptosis (Caspase-1). As a result, IL-6, TNF-alpha, ICAM-1, and Caspase-1 show higher tissue expression in the COVID-19 group compared to H1N1 and Control groups. Conclusion: Our results indicate that the vascular endothelium has been activated and the presence of pyroptosis and endothelial dysfunction in lung and myocardial samples. These conditions could lead to a systemic immune-thrombotic process that may impair the clinical staff's efforts to prevent fatal outcomes. One aim of the health professionals is to avoid COVID-19 systemic vascular injury and immune-thrombosis by blocking the endothelial dysfunction and its consequences. url: https://doi.org/10.1101/2020.06.17.20133124 doi: 10.1101/2020.06.17.20133124 id: cord-263350-i02z0hgx author: Nagata, Noriyo title: Pathological and Virological Analyses of Severe Acute Respiratory Syndrome–Associated Coronavirus Infections in Experimantal Animals date: 2006 words: 982.0 sentences: 56.0 pages: flesch: 52.0 cache: ./cache/cord-263350-i02z0hgx.txt txt: ./txt/cord-263350-i02z0hgx.txt summary: To determine the pathological features of SARS-CoV infection in experimental animals, its clinical, pathological, and virological features were investigated in cynomolgus monkeys, BALB/c mice, and F344 rats. In monkeys, following intranasal inoculation with 10 6 TCID 50 of SARS-CoV, the virus was isolated from throat and nasal swabs, and the viral genome was detected in rectal swabs collected between 2 and 7 days postinoculation (p.i.). Angiotensin-converting enzyme 2 (ACE2, a receptor for SARS-CoV 2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium in the lung of monkeys ( Figure 1A , B, and C). In BALB/c mice, the virus was detected in nasal and lung washes on days 3 and 5 after intranasal inoculation with 10 6 TCID 50 of SARS-CoV. In these experimental animals, ACE2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium (Table 1 ). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037588/ doi: 10.1007/978-0-387-33012-9_92 id: cord-314333-hkyiy1gm author: Nagata, Noriyo title: Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice date: 2008-06-30 words: 6908.0 sentences: 334.0 pages: flesch: 52.0 cache: ./cache/cord-314333-hkyiy1gm.txt txt: ./txt/cord-314333-hkyiy1gm.txt summary: title: Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice Adult mice showed early and acute excessive proinflammatory responses (ie, cytokine storm) in the lungs after SARS-CoV infection, which led to severe pulmonary edema and diffuse alveolar damage. Because advanced age is associated with higher mortality in human SARS patients and SARS-CoV replicates better in aged mice, 6 -10,29 we experimentally infected 6-month-old (adult) female BALB/c mice with F-musX-VeroE6 or the Frankfurt 1 isolate. With regard to the cytokine responses of the mice, the lung homogenates of adult mice on day 1 after inoculation had significantly higher levels of monocyterelated chemokines [ie, MCP-1, macrophage inflammatory protein 1 (MIP-1), and IFN-␥-inducible protein 10 (IP-10)] than those from young mice ( Figure 5 ). abstract: Advanced age is a risk factor of severe acute respiratory syndrome (SARS) in humans. To understand its pathogenesis, we developed an animal model using BALB/c mice and the mouse-passaged Frankfurt 1 isolate of SARS coronavirus (SARS-CoV). We examined the immune responses to SARS-CoV in both young and adult mice. SARS-CoV induced severe respiratory illness in all adult, but not young, mice on day 2 after inoculation with a mortality rate of 30 to 50%. Moribund adult mice showed severe pulmonary edema and diffuse alveolar damage accompanied by virus replication. Adult murine lungs, which had significantly higher interleukin (IL)-4 and lower IL-10 and IL-13 levels before infection than young murine lungs, rapidly produced high levels of proinflammatory chemokines and cytokines known to induce macrophage and neutrophil infiltration and activation (eg, tumor necrosis factor-α). On day 2 after inoculation, young murine lungs produced not only proinflammatory cytokines but also IL-2, interferon-γ, IL-10, and IL-13. Adult mice showed early and acute excessive proinflammatory responses (ie, cytokine storm) in the lungs after SARS-CoV infection, which led to severe pulmonary edema and diffuse alveolar damage. Intravenous injection with anti-tumor necrosis factor-α antibody 3 hours after infection had no effect on SARS-CoV infection. However, intraperitoneal interferon-γ injection protected adult mice from the lethal respiratory illness. The experimental model described here may be useful for elucidating the pathophysiology of SARS and for evaluating therapies to treat SARS-CoV infection. url: https://api.elsevier.com/content/article/pii/S0002944010619219 doi: 10.2353/ajpath.2008.071060 id: cord-272902-kdkyzfjv author: Naghibzadeh, Mahmoud title: Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19 date: 2020-05-21 words: 5406.0 sentences: 322.0 pages: flesch: 61.0 cache: ./cache/cord-272902-kdkyzfjv.txt txt: ./txt/cord-272902-kdkyzfjv.txt summary: An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. Therefore, this research follows two objectives, development of a general microsatellite discoverer which can be used for different genomes, and analysis of the structures of both SARS-CoV-1 and that of Coronavirus-Covid-19 using this tool and revealing their differences. The properties and novelties of the presented method, which is named Fast MicroSatellite Discoverer (FMSD), for finding all microsatellites of a given gene, DNA, RNA, or other genome sequences including the Novel Coronavirus (GenBabk 2019) and SARS (Rota et al. Section 5 details the evaluation, reports the comparison results, and highlights the structural differences with respect to microsatellites between SARS and Coronavirus-Covid-19 as a case study. A software tool called mreps is develop to detect all tandem repeats, including microsatellites, in DNA as well as whole genome. abstract: MOTIVATION: Recently, the outbreak of Coronavirus-Covid-19 has forced the World Health Organization to declare a pandemic status. A genome sequence is the core of this virus which interferes with the normal activities of its counterparts within humans. Analysis of its genome may provide clues toward the proper treatment of patients and the design of new drugs and vaccines. Microsatellites are composed of short genome subsequences which are successively repeated many times in the same direction. They are highly variable in terms of their building blocks, number of repeats, and their locations in the genome sequences. This mutability property has been the source of many diseases. Usually the host genome is analyzed to diagnose possible diseases in the victim. In this research, the focus is concentrated on the attacker's genome for discovery of its malicious properties. RESULTS: The focus of this research is the microsatellites of both SARS and Covid-19. An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. The Microsatellite discovery is based on an efficient indexing technique called K-Mer Hash Indexing. The method is called Fast Microsatellite Discovery (FMSD) and it is used for both SARS and Covid-19. A table composed of all microsatellites is reported. There are many differences between SARS and Covid-19, but there is an outstanding difference which requires further investigation. AVAILABILITY: FMSD is freely available at https://gitlab.com/FUM_HPCLab/fmsd_project, implemented in C on Linux-Ubuntu system. Software related contact: hossein_savari@mail.um.ac.ir. url: https://doi.org/10.1016/j.imu.2020.100356 doi: 10.1016/j.imu.2020.100356 id: cord-352943-ztonp62x author: Nagpal, Sunil title: What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date: 2020-08-20 words: 2776.0 sentences: 174.0 pages: flesch: 47.0 cache: ./cache/cord-352943-ztonp62x.txt txt: ./txt/cord-352943-ztonp62x.txt summary: Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a ''Bag of Words'' to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes). In fact, Latent Dirichlet Allocation (LDA), an unsupervised machine learning approach, is particularly known for identifying latent topics in large document collections and deciphering the words that define the inferred topics using a generative statistical model. Classical LDA was employed to generate topic models leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through rigorous hyper-parameter tuning for coherence optimization (Figure 2) . abstract: Topic modeling is frequently employed for discovering structures (or patterns) in a corpus of documents. Its utility in text-mining and document retrieval tasks in various fields of scientific research is rather well known. An unsupervised machine learning approach, Latent Dirichlet Allocation (LDA) has particularly been utilized for identifying latent (or hidden) topics in document collections and for deciphering the words that define one or more topics using a generative statistical model. Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a ‘Bag of Words’ to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Topic models were generated using ~47000 novel corona virus genomes (considered as documents), leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through coherence optimization. The document assumption for genomes also helped in identification of contextual nucleotide mutation signatures in the form of conventional N-grams (e.g. bi-grams and tri-grams). We validated the signatures obtained using LDA driven method against the previously reported recurrent mutations and phylogenetic clades for genomes. Additionally, we report the geographical distribution of the identified mutation signatures in SARS-CoV-2 genomes on the global map. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes). url: https://doi.org/10.1101/2020.08.20.258772 doi: 10.1101/2020.08.20.258772 id: cord-349762-f5no10eq author: Nagura-Ikeda, Mayu title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 words: 4270.0 sentences: 233.0 pages: flesch: 54.0 cache: ./cache/cord-349762-f5no10eq.txt txt: ./txt/cord-349762-f5no10eq.txt summary: The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). Here, we describe the clinical performance of various molecular diagnostic methods, including the RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, 3 direct RT-qPCR kits, and RT-LAMP, and a commercial SARS-CoV-2 RAT used on self-collected saliva specimens in diagnosing COVID-19. The RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed different sensitivities for detecting viral RNA in saliva specimens, but each can be selectively used according to the clinical setting and facilities if close attention is paid to any false-negative results. abstract: The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity. url: https://www.ncbi.nlm.nih.gov/pubmed/32636214/ doi: 10.1128/jcm.01438-20 id: cord-273961-ja8xggnd author: Nakagawara, Kensuke title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date: 2020-07-26 words: 784.0 sentences: 54.0 pages: flesch: 58.0 cache: ./cache/cord-273961-ja8xggnd.txt txt: ./txt/cord-273961-ja8xggnd.txt summary: title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . abstract: We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. url: https://doi.org/10.1016/j.ijid.2020.07.034 doi: 10.1016/j.ijid.2020.07.034 id: cord-343691-sjz5og78 author: Nakajima, Kei title: Serious Conditions in COVID-19 Accompanied With a Feature of Metabolic Syndrome date: 2020-05-08 words: 1224.0 sentences: 75.0 pages: flesch: 47.0 cache: ./cache/cord-343691-sjz5og78.txt txt: ./txt/cord-343691-sjz5og78.txt summary: Retrospective research has shown that COVID-19 is frequently observed in people with obesity, diabetes, and hypertension [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] , which are pivotal components of metabolic syndrome (MetS), a cluster of cardiometabolic risks based on excess visceral fat. In recent decades, many investigators have convincingly shown that people with obesity, prediabetes, diabetes and MetS are at increased risk for impaired lung function, and especially impaired restrictive lung pattern [16] [17] [18] [19] [20] [21] [22] , which is primarily determined by reduced predicted forced vital capacity. In patients with any of the specific metabolic abnormalities of MetS, pre-existing impaired lung function can predispose them to SARS-CoV-2 infection and even accelerate it, potentially worsening the condition. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32489501/ doi: 10.14740/jocmr4187 id: cord-324328-olnwynfu author: Nakamichi, K. title: Outcomes associated with SARS-CoV-2 viral clades in COVID-19 date: 2020-09-25 words: 4633.0 sentences: 305.0 pages: flesch: 49.0 cache: ./cache/cord-324328-olnwynfu.txt txt: ./txt/cord-324328-olnwynfu.txt summary: This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Even though we found several baseline clinical factors to be significantly associated with clade 2 in univariate analyses and history of malignancy in the multivariate model, rates of hospitalization were not significantly different between patients infected with the two major clades of virus in our study (p=0.063), nor were mortality rates (p=0.58). Patient demographics and clinical history were strongly predictive of hospitalization, and viral clade information did not substantially improve predictions, suggesting that it contributes minimally to determination of outcome. abstract: Background The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Methods Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Findings Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. Conclusion SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/32995827/ doi: 10.1101/2020.09.24.20201228 id: cord-331155-jkm4fuw4 author: Nakashima, Akiko title: Virus database annotations assist in tracing information on patients infected with emerging pathogens date: 2020-10-08 words: 3868.0 sentences: 238.0 pages: flesch: 48.0 cache: ./cache/cord-331155-jkm4fuw4.txt txt: ./txt/cord-331155-jkm4fuw4.txt summary: Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. COVID-19 presents varied symptomatic features [2] , [3] , [4] , [5] , [6] , [7] with a wide range of incubation periods and epidemic curves J o u r n a l P r e -p r o o f 4 are occurring [21] , [22] , the pathogenicity and origins of the mutated substrains of SARS-CoV-2 should be available in real time to adopt early measures by authorities at the onset of emergence. We examined the nucleotide mutations and visualized the transmission trajectories of SARS-CoV-2 by consulting the world specimens registered in the virus data bank of the National Center for Biotechnology Information (NCBI) [32] . Collectively, the annotations in the virus genome database are of fundamental use to hypothesize the pathogenicity and to trace the transmission route at the early phase of emergence of the new substrains. abstract: The global pandemic of SARS-CoV-2 has disrupted human social activities. In restarting economic activities, successive outbreaks by new variants are concerning. Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. Among the detectable multiple mutations, we retraced the mutation in the spike protein. With the aid of the protein database, structural modelling yielded a testable scientific hypothesis on viral entry to host cells. Simultaneously, annotations for locations and collection dates suggested that the variant virus emerged somewhere in the world in approximately February 2020, entered the USA and propagated nationwide with periodic sampling fluctuation likely due to an approximately 5-day incubation delay. Thus, public database annotations are useful for automated elucidation of the early spreading patterns in relation to human behaviours, which should provide objective reference for local governments for social decision making to contain emerging substrains. We propose that additional annotations for past paths and symptoms of the patients should further assist in characterizing the exact virulence and origins of emerging pathogens. url: https://www.sciencedirect.com/science/article/pii/S235291482030592X?v=s5 doi: 10.1016/j.imu.2020.100442 id: cord-339516-xfwxtjry author: Nakashima, Tsutomu title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses date: 2020-05-05 words: 692.0 sentences: 52.0 pages: flesch: 47.0 cache: ./cache/cord-339516-xfwxtjry.txt txt: ./txt/cord-339516-xfwxtjry.txt summary: title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses Two nurses working in the National Cancer Center Hospital underwent the viral PCR test because they had similar symptoms, and they were both SARS-CoV-2 positive, although they had neither fever nor cough (Asahi Shimbun newspaper [digital], March 28, 2020). [2] [3] [4] The influenza and parainfluenza type 3 viruses were reported to be causative of olfactory loss most frequently. However, the adverse effect of olfactory dysfunction due to influenza vaccination was also reported. Suzuki et al 8 confirmed the presence of various viruses in the nasal discharge of patients with postviral infection olfactory dysfunction, such as rhinovirus, parainfluenza virus, Epstein-Barr virus, and coronavirus. However, only short-term follow-up investigation has been conducted regarding the effect of SARS-CoV-2 infection on the chemosensory function. We believe that epidemiological investigation is required regarding the effect of SARS-CoV-2 on the olfactory and gustatory functions in terms of the frequency, time course, and relationship with other symptoms. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32366336/ doi: 10.1017/ice.2020.196 id: cord-346413-2njl0fd3 author: Nakazawa, Daigo title: Immunothrombosis in severe COVID-19 date: 2020-08-15 words: 836.0 sentences: 52.0 pages: flesch: 39.0 cache: ./cache/cord-346413-2njl0fd3.txt txt: ./txt/cord-346413-2njl0fd3.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread all over the world immediately after the first patient infected with this virus was discovered in Wuhan, China, in December 2019. It has been demonstrated that SARS-CoV-2 infection induces vascular endothelial injury, resulting from coagulation [3] . Because these are degradation products of fibrin or neutrophil extracellular traps (NETs), an enhanced turnover of coagulation and NET formation appears to characterize severe COVID-19. Based on the loss of CD31 + cells in the endothelium that were close to the aggregated NETs, Leppkes and coworkers suggested that the injury of vascular endothelial cells infected with SARS-CoV-2 could trigger neutrophil attraction and NET formation (Fig. 1) . Leppkes and coworkers suggested that the prevention of excessive NET formation and aggregation could provide an approach to inhibit vascular occlusion and the development of severe COVID-19. When SARS-CoV-2 injures vascular endothelial cells, coagulation is invoked, and simultaneously, DAMPs are secreted from the damaged cells. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32810824/ doi: 10.1016/j.ebiom.2020.102942 id: cord-314662-nem6dw34 author: Nakra, Natasha A. title: Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management date: 2020-07-01 words: 5543.0 sentences: 299.0 pages: flesch: 40.0 cache: ./cache/cord-314662-nem6dw34.txt txt: ./txt/cord-314662-nem6dw34.txt summary: Initial reports surfaced in the UK [3] and Italy [4] , followed by New York and other parts of the U.S. Preliminary accounts of the features of this syndrome resemble those of known entities such as Kawasaki Disease (KD), toxic shock syndrome (TSS), and secondary hemophagocytic lymphohistiocytosis (SHLH)/macrophage activation syndrome (MAS). Early consultation of specialists to assist in management, such as intensive care, cardiology, rheumatology, infectious diseases, allergy/immunology, neurology Abbreviations: ALT, alanine transaminase; AST, aspartate transaminase; pro-BNP, pro-B-type natriuretic peptide; BUN, blood urea nitrogen; CRP, C-reactive protein; CT, computed tomography; ESR, erythrocyte sedimentation rate; GI, gastrointestinal; HLH, hemophagocytic lymphohistiocytosis; IL, interleukin; MIS-C, multisystem inflammatory syndrome in children; NK, natural killer; NP, nasopharyngeal; PT, prothrombin time; PTT, partial thromboplastin time; RT-PCR, reverse transcriptase polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may result in the multisystem inflammatory syndrome in children (MIS-C). The clinical presentation of MIS-C includes fever, severe illness, and the involvement of two or more organ systems, in combination with laboratory evidence of inflammation and laboratory or epidemiologic evidence of SARS-CoV-2 infection. Some features of MIS-C resemble Kawasaki Disease, toxic shock syndrome, and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome. The relationship of MIS-C to SARS-CoV-2 infection suggests that the pathogenesis involves post-infectious immune dysregulation. Patients with MIS-C should ideally be managed in a pediatric intensive care environment since rapid clinical deterioration may occur. Specific immunomodulatory therapy depends on the clinical presentation. The relationship between the immune response to SARS-CoV-2 vaccines in development and MIS-C requires further study. url: https://doi.org/10.3390/children7070069 doi: 10.3390/children7070069 id: cord-292423-jupcit75 author: Narkhede, Rohan R. title: Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences date: 2020-06-17 words: 2709.0 sentences: 134.0 pages: flesch: 47.0 cache: ./cache/cord-292423-jupcit75.txt txt: ./txt/cord-292423-jupcit75.txt summary: With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. We proposed some natural products including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene as potential candidate for exerting the antiviral activity against SARS-CoV-2 infection using molecular docking study. The results acquired after docking analysis in terms of ligand binding affinity (kcal/mol), the interaction of natural products with the COVID-19 main protease, and the drug-like properties were shown in (Table 1 ). A promising binding to the COVID-19 main protease was observed in the case of rhein and berberine where both natural products were found to exhibit an affinity of − 8.9 and − 8.1 kcal/mol respectively. abstract: ABSTRACT: SARS-CoV-2 (2019-nCoV) emerged in the back of December 2019 and proliferated rapidly across the globe. Scientists are attempting to investigate antivirals specific to COVID-19 treatment. The 2019-nCoV and SARS-CoV utilize the same receptor of the host which is COVID-19 of the main protease (Mpro).COVID-19 caused by SARS-CoV-2 is burdensome to overcome by presently acquired antiviral candidates. So the objective and purpose of this work was to investigate the plants with reported potential antiviral activity. With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. Promising docking outcomes have been executed which evidenced the worthy of these selected herbal remedies for future drug development to combat coronavirus disease. GRAPHIC ABSTRACT: [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32557405/ doi: 10.1007/s13659-020-00253-1 id: cord-269474-94c1mudi author: Nasef, Nehad title: Lessons from SARS: A retrospective study of outpatient care during an infectious disease outbreak date: 2010-07-20 words: 3171.0 sentences: 154.0 pages: flesch: 52.0 cache: ./cache/cord-269474-94c1mudi.txt txt: ./txt/cord-269474-94c1mudi.txt summary: In response, a decision was made by the neonatal neuro-developmental follow up (NNFU) clinic staff to select patients with scheduled appointments to have a mail/telephone assessment using Ages and Stages Questionnaire (ASQ) or to postpone/skip their visit. The objective of this study was to compare the developmental assessment and its outcome in two groups of NNFU clinic patients, SARS versus non-SARS, over three standard clinic appointments. The objective of this retrospective study was to compare the developmental assessment and its'' outcome in two groups of NNFU clinic patients, SARS versus non-SARS over an assessment trajectory of 3 booked clinic appointments (labeled before, during and after according to the time of clinic closure during SARS). Of 30 patients diagnosed with developmental delay at the before visit in the SARS group, 8 were contacted by mail or telephone and 22 were never contacted during the period of clinic closure. abstract: BACKGROUND: During severe acute respiratory syndrome (SARS) outbreak in Toronto, outpatient clinics at SickKids Hospital were closed to prevent further disease transmission. In response, a decision was made by the neonatal neuro-developmental follow up (NNFU) clinic staff to select patients with scheduled appointments to have a mail/telephone assessment using Ages and Stages Questionnaire (ASQ) or to postpone/skip their visit. The objective of this study was to compare the developmental assessment and its outcome in two groups of NNFU clinic patients, SARS versus non-SARS, over three standard clinic appointments. METHODS: We compared the diagnostic accuracy (identification of developmental delay), and patient management (referral for therapy or communication of a new diagnosis) of the strategies used during SARS, April/May 2003, to the standard assessment methods used for patients seen in April/May 2005 (non-SARS). In all cases data were obtained for 3 patient visits: before, during and after these 2 months and were compared using descriptive statistics. RESULTS: There were 95 patients in the SARS group and 99 non-SARS patients. The gestational age, sex, entry diagnosis and age at the clinic visit was not different between the groups. The NNFU clinic staff mailed ASQ to 27 families during SARS, 17 (63%) were returned, and 8 of the 17 were then contacted by telephone. Criteria used to identify infants at risk selected for either mailed ASQ or phone interviews were not clearly defined in the patients' charts. There was a significant under identification of developmental delay during SARS (18% versus 45%). Of those who responded to the mailed questionnaire, referrals for therapy rates were similar to non-SARS group. The lost to follow up rate was 24% for the SARS group compared with 7% for non-SARS. There was no difference in the overall rate of developmental delay in the two groups as identified at the 'after' visit. CONCLUSIONS: Poor advanced planning led to a haphazard assessment of patients during this infectious disease outbreak. Future pandemic plans should consider planning for outpatient care as well as in hospital management of patients. url: https://doi.org/10.1186/1471-2431-10-51 doi: 10.1186/1471-2431-10-51 id: cord-291190-f6km3c7z author: Nasi, Aikaterini title: Reactive oxygen species as an initiator of toxic innate immune responses in retort to SARS-CoV-2 in an ageing population, consider N-acetylcysteine as early therapeutic intervention date: 2020-06-18 words: 2999.0 sentences: 155.0 pages: flesch: 42.0 cache: ./cache/cord-291190-f6km3c7z.txt txt: ./txt/cord-291190-f6km3c7z.txt summary:  SARS-CoV has been reported to modulate PARP function and thereby NAD+ biosynthesis  Cellular homeostasis and redox imbalances by SARS-CoV2 can cause stress responses  Antioxidants such as NAC could limit ROS mediated tissue damage during COVID-19 Hereby, based on literature review from the current pandemic and previous outbreaks with corona viruses we analyze the impact of the virus infection on cell stress responses and redox balance. PLA2G2D expression was shown to be increased in the lungs of middle aged mice, resulting in decreased survival and impaired T cell responses upon infection with SARS-CoV1 [20] . Interestingly, NAC administration to aged mice, diminished PLAG2D expression in both lung cells and CD11c+ DCs. In addition, increased levels of oxidized phospholipidsare a common feature associated with acute respiratory distress syndrome (ARDS) caused by viruses including SARS and H5N1. abstract: During the current COVID-19 pandemic, a need for evaluation of already available drugs for treatment of the disease is crucial. Hereby, based on literature review from the current pandemic and previous outbreaks with corona viruses we analyze the impact of the virus infection on cell stress responses and redox balance. High levels of mortality are noticed in elderly individuals infected with SARS-CoV2 and during the previous SARS-CoV1 outbreak. Elderly individuals maintain a chronic low level of inflammation which is associated with oxidative stress and inflammatory cytokine production, a condition that increases the severity of viral infections in this population. SARS-CoV2 infection can lead to alterations of redox balance in infected cells through modulation of NAD + biosynthesis, PARP function along with altering proteasome and mitochondrial function in the cell thereby leading to enhanced cell stress responses which further exacerbate inflammation. ROS production can increase IL-6 production and lipid peroxidation resulting in cell damage. Therefore, early treatment with anti-oxidants such as NAC during COVID-19 can be a way to bypass the excessive inflammation and cell damage that lead to severe infection. url: https://www.sciencedirect.com/science/article/pii/S221475002030336X?v=s5 doi: 10.1016/j.toxrep.2020.06.003 id: cord-320909-p93gxjm2 author: Natoli, S. title: Does SARS‐Cov‐2 invade the brain? Translational lessons from animal models date: 2020-05-22 words: 4718.0 sentences: 246.0 pages: flesch: 39.0 cache: ./cache/cord-320909-p93gxjm2.txt txt: ./txt/cord-320909-p93gxjm2.txt summary: Animal models of SARS and Middle East respiratory syndrome, caused by structurally similar CoVs during the 2002 and 2012 epidemics, have provided valuable data on nervous system involvement by CoVs and the potential for central nervous system spread of SARS‐CoV‐2. The expression of this receptor in neurons and endothelial cells hints that SARS‐CoV‐2 may have higher neuroinvasive potential compared with previous CoVs. However, it remains to be determined how such invasiveness might contribute to respiratory failure or cause direct neurological damage. Highly pathogenic coronavirus (CoV) infections are well-established sources of previous epidemics in humans, i.e. severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice abstract: The current coronavirus disease (COVID‐19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has raised the possibility of potential neurotropic properties of this virus. Indeed, neurological sequelae of SARS‐CoV‐2 infection have already been reported and highlight the relevance of considering the neurological impact of coronavirus (CoV) from a translational perspective. Animal models of SARS and Middle East respiratory syndrome, caused by structurally similar CoVs during the 2002 and 2012 epidemics, have provided valuable data on nervous system involvement by CoVs and the potential for central nervous system spread of SARS‐CoV‐2. One key finding that may unify these pathogens is that all require angiotensin‐converting enzyme 2 as a cell entry receptor. The CoV spike glycoprotein, by which SARS‐CoV‐2 binds to cell membranes, binds angiotensin‐converting enzyme 2 with a higher affinity compared with SARS‐CoV. The expression of this receptor in neurons and endothelial cells hints that SARS‐CoV‐2 may have higher neuroinvasive potential compared with previous CoVs. However, it remains to be determined how such invasiveness might contribute to respiratory failure or cause direct neurological damage. Both direct and indirect mechanisms may be of relevance. Clinical heterogeneity potentially driven by differential host immune‐mediated responses will require extensive investigation. Development of disease models to anticipate emerging neurological complications and to explore mechanisms of direct or immune‐mediated pathogenicity in the short and medium term is therefore of great importance. In this brief review, we describe the current knowledge from models of previous CoV infections and discuss their potential relevance to COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32333487/ doi: 10.1111/ene.14277 id: cord-344446-5d7yuoz1 author: Naughton, Sean X. title: The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection date: 2020-05-12 words: 754.0 sentences: 45.0 pages: flesch: 46.0 cache: ./cache/cord-344446-5d7yuoz1.txt txt: ./txt/cord-344446-5d7yuoz1.txt summary: One of the more perplexing aspects of the recent SARS-CoV-2 pandemic is the high level of variability among patients in terms of disease severity. Exposure to environmental toxins as well as lifestyle choices can affect ACE2 expression, and may possibly increase the severity of infection. For example, exposure to ultrafine particulate matter from air pollution (PM 2.5) has previously been shown to increase the expression of ACE2 [4] . In line with these findings, a recent report indicates that higher levels of air pollution may be a contributing factor to the increased fatality rate among COVID-19 patients in northern Italy [5] . Dietary/lifestyle factors may also play a role in determining resilience or susceptibility to severe outcomes after SARS-CoV-2 infection. Thus, it is possible that multiple independent variables may affect ACE2 expression and thereby confer resilience or susceptibility towards severe life-threatening conditions after SARS-Cov-2 infection. abstract: nan url: https://doi.org/10.1038/s41370-020-0232-4 doi: 10.1038/s41370-020-0232-4 id: cord-027499-mvqoarsh author: Navel, Valentin title: Coronavirus: good or bad news for ocular diseases? date: 2020-06-09 words: 1395.0 sentences: 81.0 pages: flesch: 44.0 cache: ./cache/cord-027499-mvqoarsh.txt txt: ./txt/cord-027499-mvqoarsh.txt summary: Even if SARS-CoV-2 involves conjunctivitis and external ocular infections, 12 there are not yet published data describing the effects of a reduction of air pollutants on the ocular surface during the quarantine period, and a putative decrease in some ocular complaints-individuals being at home and less exposed to pollens and atmospheric pollutants. 16 17 SARS-CoV-2 patients without any ocular symptoms could Open access Figure 1 The decrease of global air pollution following the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic (satellite images from NASA and European Space Agency). 22 In conclusion, even if individuals are less exposed to air pollutants and environmental allergens during quarantine weeks, SARS-CoV-2 seems to be a foe both for ophthalmologists-with a risk of infection through contact with eye secretions of patients-and for patients-with a delay in their medical management. SARS-CoV-2 in the ocular surface of COVID-19 patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306266/ doi: 10.1136/bmjophth-2020-000495 id: cord-301233-nenw0f81 author: Naydenova, Katerina title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 words: 4059.0 sentences: 217.0 pages: flesch: 51.0 cache: ./cache/cord-301233-nenw0f81.txt txt: ./txt/cord-301233-nenw0f81.txt summary: Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. abstract: The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses. url: https://doi.org/10.1101/2020.10.21.347690 doi: 10.1101/2020.10.21.347690 id: cord-346176-w6uaet7l author: Nayeri, Shadi title: Conducting Translational Gastrointestinal Research in the Era of COVID-19 date: 2020-08-26 words: 3097.0 sentences: 213.0 pages: flesch: 49.0 cache: ./cache/cord-346176-w6uaet7l.txt txt: ./txt/cord-346176-w6uaet7l.txt summary: In this document we provide a suggested roadmap for resuming gastrointestinal translational research activities, emphasising physical distancing and use of personal protective equipment. We discuss modes of virus transmission in enclosed environments [including clinical workplaces and laboratories] and potential risks of exposure in the endoscopy environment for research staff. Efforts focus primarily on physical distancing, use of PHASE personal protective equipment [PPE] , and addressing capacity needs of health care systems to deal with the outbreak. Local and institutional guidance is required to resume translational research activities, including patient interactions. • Invitation of persons currently infected with SARS-CoV-2 from the community into the research environment would cause unnecessary and inappropriate risk of viral transmission. These guidelines address safety precautions in relevant workspaces [including laboratory and endoscopy environments] as well as in specific research activities such as sample collection, handling, and transportation. abstract: Abstract Spread of the novel coronavirus SARS-CoV-2 has resulted in a global pandemic that is affecting the health and economy of all World Health Organization [WHO] regions. Clinical and translational research activities have been affected drastically by this global catastrophe. In this document we provide a suggested roadmap for resuming gastrointestinal translational research activities, emphasising physical distancing and use of personal protective equipment. We discuss modes of virus transmission in enclosed environments [including clinical workplaces and laboratories] and potential risks of exposure in the endoscopy environment for research staff. The proposed guidelines should be considered in conjunction with local institutional and government guidelines so that translational research can be resumed as safely as possible. url: https://doi.org/10.1093/ecco-jcc/jjaa171 doi: 10.1093/ecco-jcc/jjaa171 id: cord-348283-7xorq5ce author: Naz, Anam title: Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date: 2020-07-10 words: 8183.0 sentences: 482.0 pages: flesch: 56.0 cache: ./cache/cord-348283-7xorq5ce.txt txt: ./txt/cord-348283-7xorq5ce.txt summary: The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. abstract: A recent pandemic caused by a single-stranded RNA virus, COVID-19, initially discovered in China, is now spreading globally. This poses a serious threat that needs to be addressed immediately. Genome analysis of SARS-CoV-2 has revealed its close relation to SARS-coronavirus along with few changes in its spike protein. The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. The S1 and S2 domains of spike proteins were analyzed, and two vaccine constructs were prioritized with T-cell and B-cell epitopes. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Prioritized epitopes were then modeled using linkers and adjuvants, and respective 3D models were constructed to evaluate their physiochemical properties and their possible interactions with ACE2, HLA Superfamily alleles, TLR2, and TLR4. url: https://www.ncbi.nlm.nih.gov/pubmed/32754160/ doi: 10.3389/fimmu.2020.01663 id: cord-253201-r6vsa0pw author: Nazari, S. title: Central Nervous System Manifestations in COVID-19 Patients: A Systematic Review and Meta-analysis date: 2020-07-22 words: 3950.0 sentences: 281.0 pages: flesch: 49.0 cache: ./cache/cord-253201-r6vsa0pw.txt txt: ./txt/cord-253201-r6vsa0pw.txt summary: Despite many studies reporting respiratory infections as the primary manifestations of this illness, an increasing number of investigations have focused on the central nervous system (CNS) manifestations in COVID-19. Based on the results shown in (Table 3 and The highest incidence rate among CNS symptoms of COVID-19 patients was for headache (8.69% with 95% CI: 6.76%-10.82%), followed by Dizziness (5.94%, 95%CI: 3.66%-8.22%), and Impaired consciousness (1.9% with 95% CI: 1%-2.79%). . https://doi.org/10.1101/2020.07.21.20158691 doi: medRxiv preprint CNS: Central nervous system; COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; PHEIC: Public health emergency of international concern; WHO: World health organization; PRISMA: Preferred reporting items for systematic reviews and meta-analyses; PNS: Peripheral nervous system; BBB: Blood brain barrier; ACE2: Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms abstract: Background: At the end of December 2019, a novel respiratory infection, initially reported in China, known as COVID-19 initially reported in China, and later known as COVID-19, led to a global pandemic. Despite many studies reporting respiratory infections as the primary manifestations of this illness, an increasing number of investigations have focused on the central nervous system (CNS) manifestations in COVID-19. In this study, we aimed to evaluate the CNS presentations in COVID-19 patients in an attempt to identify the common CNS features and provide a better overview to tackle this new pandemic. Methods: In this systematic review and meta-analysis, we searched PubMed, Web of Science, Ovid, Embase, Scopus, and Google Scholar. Included studies were publications that reported the CNS features between January 1st, 2020, to April 20th, 2020. The data of selected studies were screened and extracted independently by four reviewers. Extracted data analyzed by using STATA statistical software. The study protocol registered with PROSPERO (CRD42020184456). Results: Of 2353 retrieved studies, we selected 64 studies with 11282 patients after screening. Most of the studies were conducted in China (58 studies). The most common CNS symptom of COVID-19 were Headache (8.69%, 95%CI: 6.76%-10.82%), Dizziness (5.94%, 95%CI: 3.66%-8.22%), and Impaired consciousness (1.9%, 95%CI: 1%-2.79%). Conclusions: The growing number of studies have reported COVID-19, CNS presentations as remarkable manifestations that happen. Hence, understanding the CNS characteristics of COVID-19 can help us for better diagnosis and ultimately prevention of worse outcomes. url: https://doi.org/10.1101/2020.07.21.20158691 doi: 10.1101/2020.07.21.20158691 id: cord-279629-t1xjy12y author: Nazneen Akhand, Mst Rubaiat title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date: 2020-04-15 words: 6717.0 sentences: 379.0 pages: flesch: 47.0 cache: ./cache/cord-279629-t1xjy12y.txt txt: ./txt/cord-279629-t1xjy12y.txt summary: The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Hence, the study was designed to develop a chimeric recombinant vaccine against COVID-19 by targeting four major structural proteins of the pathogen, while revealing the evolutionary history of different species of coronavirus based on whole genome and protein domain-based phylogeny. Apart from the human coronaviruses, we introduced other coronaviruses which choose different species of bats, whale, turkey, rat, mink, ferret, swine, camel, rabbit, cow and others as host (Supplementary TableDomain analysis of spike protein of coronaviruses reveals that they contain mainly one signature domains namely, coronavirus S2 glycoprotein (IPR002552), which is present in all the candidates. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. abstract: SARS-CoV-2 is known to infect the neurological, respiratory, enteric, and hepatic systems of human and has already become an unprecedented threat to global healthcare system. COVID-19, the most serious public condition caused by SARS-CoV-2 leads the world to an uncertainty alongside thousands of regular death scenes. Unavailability of specific therapeutics or approved vaccine has made the recovery of COVI-19 more troublesome and challenging. The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins (S, E, M and N) reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and Normal Mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. The development of preventive measures to combat COVID-19 infections might be aided the present study. However, the in vivo and in vitro validation might be ensured with wet lab trials using model animals for the implementation of the presented data. url: https://doi.org/10.1101/2020.04.15.036285 doi: 10.1101/2020.04.15.036285 id: cord-277874-cr53ycrm author: Neault, N. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 words: 7079.0 sentences: 372.0 pages: flesch: 49.0 cache: ./cache/cord-277874-cr53ycrm.txt txt: ./txt/cord-277874-cr53ycrm.txt summary: We believe MPAD based SARS-CoV-2 protein quantitation represents a promising epidemiological tool with a sensitivity sufficiently superior to viral RNA measurement that, in addition to enabling early detection and population tracking of COVID-19 load, will also open the way to effective infection surveillance of specific facilities, schools and residences. Primary sludge and PEG precipitated influent fractions, collected from the contiguous cities of Ottawa and Gatineau in April through June 2020, were analysed for the presence of four SARS-CoV-2 structural proteins, N (nucleocapsid), M (membrane), S (spike), and E (envelope), by western blot. Next, in order to assure specificity for detection of SARS-CoV-2 proteins, we used MPAD with an expanded panel to simultaneously measure three viral proteins, N, S and M, along with six fecal content control proteins in PEG precipitated "influent solids" samples drawn from the Ottawa WRRF during the study period ( Fig 5) . abstract: The COVID-19 pandemic has given rise to diverse approaches to track infections. The causative agent, SARS-CoV-2 is a fecally-shed RNA virus, and many groups have assayed wastewater for viral RNA fragments by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as a proxy of COVID-19 prevalence in the community. Most groups report low levels of viral RNA that often skirt the methods theoretical limits of detection and quantitation. Here, we demonstrate the presence of SARS-CoV-2 structural proteins in wastewater using traditional immunoblotting and quantitate them from wastewater solids using an immuno-linked PCR method called Multiplex Paired-antibody Amplified Detection (MPAD). In this longitudinal study, we corrected for stochastic variability inherent to wastewater-based epidemiology using multiple fecal content protein biomarkers. These normalized SARS-CoV-2 protein data correlated well with public health metrics. Our method of assaying SARS-CoV-2 protein from wastewater represents a promising and sensitive epidemiological tool to assess prevalence of fecally-shed pathogens in the community. url: http://medrxiv.org/cgi/content/short/2020.09.01.20185280v1?rss=1 doi: 10.1101/2020.09.01.20185280 id: cord-328853-0iqdqcp6 author: Neidleman, Jason title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential date: 2020-08-19 words: 2431.0 sentences: 133.0 pages: flesch: 52.0 cache: ./cache/cord-328853-0iqdqcp6.txt txt: ./txt/cord-328853-0iqdqcp6.txt summary: title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential SUMMARY Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19. Furthermore, the clonality of T cell receptor (TCR) sequences 54 5 is higher in patients with mild rather than severe COVID-19, suggesting a role for antigen-55 specific T cell responses in symptom resolution. We report here that SARS-CoV-2-specific CD4+ and CD8+ T cells from convalescent 86 individuals are diverse, exhibit features different from antigen-specific T cells against CMV, 87 include cells with both lymphoid and tissue homing potential, harbor phenotypic features of 88 functional effector cells, and are long-lived and capable of homeostatic proliferation. abstract: SUMMARY Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. To date, the phenotypes of SARS-CoV-2-specific T cells remain poorly defined. Using 38-parameter CyTOF, we phenotyped longitudinal specimens of SARS-CoV-2-specific CD4+ and CD8+ T cells from nine individuals who recovered from mild COVID-19. SARS-CoV-2-specific CD4+ T cells were exclusively Th1 cells, and predominantly Tcm with phenotypic features of robust helper function. SARS-CoV-2-specific CD8+ T cells were predominantly Temra cells in a state of less terminal differentiation than most Temra cells. Subsets of SARS-CoV-2-specific T cells express CD127, can homeostatically proliferate, and can persist for over two months. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19. url: https://api.elsevier.com/content/article/pii/S2666379120301026 doi: 10.1016/j.xcrm.2020.100081 id: cord-282272-wy8do2z6 author: Nelson, Atiba title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks date: 2020-07-06 words: 952.0 sentences: 56.0 pages: flesch: 48.0 cache: ./cache/cord-282272-wy8do2z6.txt txt: ./txt/cord-282272-wy8do2z6.txt summary: title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. 2, 3 We conducted environmental sampling to assess the extent of surface contamination with SARS-CoV-2 virus within long-term care facilities with declared COVID-19 outbreaks. Environmental contamination with SARS-CoV-2 virus was detected at each of three COVID-19 outbreak facilities sampled in this study, including surfaces of five frequently used medical devices transferred between patient rooms, and one high-touch surface used by care staff This study contains limitations. Our findings suggest medical equipment is a potential environmental route for transmission of SARS-CoV-2 virus in long-term care facilities. abstract: We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. Medical equipment used throughout the facility was determined to be contaminated. url: https://api.elsevier.com/content/article/pii/S019665532030643X doi: 10.1016/j.ajic.2020.07.001 id: cord-325830-mrtpihc7 author: Nelson, Philipp P. title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 words: 4974.0 sentences: 273.0 pages: flesch: 46.0 cache: ./cache/cord-325830-mrtpihc7.txt txt: ./txt/cord-325830-mrtpihc7.txt summary: In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. abstract: The availability of pathogen-specific treatment options for respiratory tract infections (RTIs) increased the need for rapid diagnostic tests. Besides, retrospective studies, improved lab-based detection methods and the intensified search for new viruses since the beginning of the twenty-first century led to the discovery of several novel respiratory viruses. Among them are human bocavirus (HBoV), human coronaviruses (HCoV-HKU1, -NL63), human metapneumovirus (HMPV), rhinovirus type C (RV-C), and human polyomaviruses (KIPyV, WUPyV). Additionally, new viruses like SARS coronavirus (SARS-CoV), MERS coronavirus (MERS-CoV), novel strains of influenza virus A and B, and (most recently) SARS coronavirus 2 (SARS-CoV-2) have emerged. Although clinical presentation may be similar among different viruses, associated symptoms may range from a mild cold to a severe respiratory illness, and thus require a fast and reliable diagnosis. The increasing number of commercially available rapid point-of-care tests (POCTs) for respiratory viruses illustrates both the need for this kind of tests but also the problem, i.e., that the majority of such assays has significant limitations. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. While prototypes for some methods already exist, other ideas are still experimental, but all of them give an outlook of what can be expected as the next generation of POCTs. url: https://www.ncbi.nlm.nih.gov/pubmed/32411619/ doi: 10.3389/fcimb.2020.00181 id: cord-291420-40xsypzt author: Nelson-Sathi, Shijulal title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date: 2020-10-01 words: 2274.0 sentences: 145.0 pages: flesch: 54.0 cache: ./cache/cord-291420-40xsypzt.txt txt: ./txt/cord-291420-40xsypzt.txt summary: title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. The structural analysis of the mutated spike glycoprotein of SARS-CoV-2 RBD domain was done to assess the impact of interface amino acid residue mutations on binding affinity towards the human ACE2 (hACE2) receptor. Comparative analysis of structures showed key differences in all three binding clusters of SARS-CoV-2 RBD wild type and mutant interfaces with human or mouse ACE2 (Figure 2C, 2D and Table S1 ). abstract: Protein-protein interactions between virus and host are crucial for infection. SARS-CoV-2, the causative agent of COVID-19 pandemic is an RNA virus prone to mutations. Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. Yet, how this binding interface evolves as virus acquires mutations during pandemic remains elusive. Here, using a high fidelity bioinformatics pipeline, we analysed 31,403 SARS-CoV-2 genomes across the globe, and identified 444 non-synonymous mutations that cause 49 distinct amino acid substitutions in the RBD. Molecular phylogenetic analysis suggested independent emergence of these RBD mutants during pandemic. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. Comparative structure analysis using binding interface from mouse that prevents SARS-CoV-2 entry uncovered minimal molecular determinants in RBD necessary for the formation of stable interface. We identified that interfacial interaction involving amino acid residues N487 and G496 on either ends of the binding scaffold are indispensable to anchor RBD and are well conserved in all SARS-like corona viruses. All other interactions appear to be required to locally remodel binding interface with varying affinities and thus may decide extent of viral transmission and disease outcome. Together, our findings propose the modalities and variations in RBD-ACE2 interface formation exploited by SARS-CoV-2 for endurance. Importance COVID-19, so far the worst hit pandemic to mankind, started in January 2020 and is still prevailing globally. Our study identified key molecular arrangements in RBD-ACE2 interface that help virus to tolerate mutations and prevail. In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. The minimal molecular requirements for the formation of RBD-ACE2 interface predicted using in silico structure models may help precisely design neutralizing antibodies, vaccines and therapeutics. Our study also proposes the significance of understanding evolution of protein interfaces during pandemic. url: https://doi.org/10.1101/2020.05.02.071811 doi: 10.1101/2020.05.02.071811 id: cord-025251-evnfvc0l author: Nemunaitis, John title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection: let the virus be its own demise date: 2020-05-26 words: 7308.0 sentences: 397.0 pages: flesch: 38.0 cache: ./cache/cord-025251-evnfvc0l.txt txt: ./txt/cord-025251-evnfvc0l.txt summary: Herein we describe the rationale and potential of repurposing a dual plasmid, Vigil (pbi-shRNA(furin)-GM-CSF), now in Phase III cancer trials, for the treatment of and, in certain circumstances, enhancement of the immune response to SARS-CoV-2. A recent publication from Nankai University (Tianjin, China) on SARS-CoV-2 reported that genome sequence analysis revealed a section of genes that was not present in SARS-CoV that had a cleavage site similar to HIV and Ebola which carry viral proteins necessary for fusogenic activity of viral species to the human cell membrane. Another immunotherapeutic intervention would be to increase the pulmonary expression of GM-CSF, which, in vivo, redirects macrophages from an M1 state of activation to an M2 activation state and enhances expression of anti-inflammatory mediators and perhaps allow more time for patients to mount an effective immune response against SARS-CoV-2 [25] . Similar to SARS-CoV-2, alveolar epithelial cells are the primary target of influenza virus (IV) and are the first site of entry and support for viral propagation and replication. abstract: There has been a collaborative global effort to construct novel therapeutic and prophylactic approaches to SARS-CoV-2 management. Although vaccine development is crucial, acute management of newly infected patients, especially those with severe acute respiratory distress syndrome, is a priority. Herein we describe the rationale and potential of repurposing a dual plasmid, Vigil (pbi-shRNA(furin)-GM-CSF), now in Phase III cancer trials, for the treatment of and, in certain circumstances, enhancement of the immune response to SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7249572/ doi: 10.2217/fvl-2020-0068 id: cord-293167-3bd3adip author: Nepal, Gaurav title: Neurological manifestations of COVID-19: a systematic review date: 2020-07-13 words: 5534.0 sentences: 311.0 pages: flesch: 44.0 cache: ./cache/cord-293167-3bd3adip.txt txt: ./txt/cord-293167-3bd3adip.txt summary: Most patients infected by SARS-CoV-2 have presented with a mild clinical course: beginning with fever and dry cough, progressing to a form of mild or moderate respiratory disease, and resolving without specific treatment [2] . A retrospective observational study from Wuhan, China, reported that six (2.8%) patients, out of the 214 reviewed COVID-19 cases, developed ischemic stroke. A retrospective observational study from a different center in Wuhan, China, found eleven (5.0%) patients, out of 221 reviewed COVID-19 cases, developed acute ischemic stroke. Those who had COVID-19 infection with new onset of ischemic stroke were more likely to have a severe SARS-CoV-2 presentation, an advanced age (71.6 ± 15.7 years versus 52.1 ± 15.3 years), and preexisting cardiovascular risk factors including hypertension, diabetes, and previous cerebrovascular disease. A retrospective observational study from Wuhan, China, reported one (0.45%) patient, out of 221 reviewed COVID-19 cases, who developed intracerebral hemorrhage. abstract: INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the global spread of coronavirus disease (COVID-19). Our understanding of the impact this virus has on the nervous system is limited. Our review aims to inform and improve decision-making among the physicians treating COVID-19 by presenting a systematic analysis of the neurological manifestations experienced within these patients. METHODS: Any study, released prior to May 20, 2020, that reported neurological manifestations in patients infected by SARS-CoV-2 was systematically reviewed using the PRISMA (Preferred Reporting Items for Systemic review and Meta-Analysis) statement. RESULTS: Our systematic review included data from 37 articles: twelve retrospective studies, two prospective studies, and the rest case reports/series. The most commonly reported neurological manifestations of COVID-19 were myalgia, headache, altered sensorium, hyposmia, and hypogeusia. Uncommonly, COVID-19 can also present with central nervous system manifestations such as ischemic stroke, intracerebral hemorrhage, encephalo-myelitis, and acute myelitis, peripheral nervous manifestations such as Guillain-Barré syndrome and Bell’s palsy, and skeletal muscle manifestations such as rhabdomyolysis. CONCLUSION: While COVID-19 typically presents as a self-limiting respiratory disease, it has been reported in up to 20% of patients to progress to severe illness with multi-organ involvement. The neurological manifestations of COVID-19 are not uncommon, but our study found most resolve with treatment of the underlying infection. Although the timeliness of this review engages current challenges posed by the COVID-19 pandemic, readers must not ignore the limitations and biases intrinsic to an early investigation. url: https://www.ncbi.nlm.nih.gov/pubmed/32660520/ doi: 10.1186/s13054-020-03121-z id: cord-256217-fnjer0e0 author: Neri, Piergiorgio title: COVID-19 and the eye immunity: lesson learned from the past and possible new therapeutic insights date: 2020-04-20 words: 1928.0 sentences: 88.0 pages: flesch: 43.0 cache: ./cache/cord-256217-fnjer0e0.txt txt: ./txt/cord-256217-fnjer0e0.txt summary: Corona virus represents nowadays the hot topic in the scientific world due to the outbreak of a novel serotype formerly named coronavirus disease (COVID)-19 and now identified as severe acute respiratory syndrome (SARS)-COV-2 [1] . Although ECOR was used to study retinal degeneration specifically, it might represent a possible experimental model for interesting speculations on how to approach severe SARS-COV-2 pulmonary complications. Looking at the ECOR model, it gives the impression that coronavirus creates two different phases: the first is represented by the primary infection which induces the triggering of the immune system, while the second phase is likely to be an autoimmune disease where the role of the severe postviral inflammation represents a severe occurrence worth of prompt intervention. Albeit it is true that anti-IL-6 receptor monoclonal antibody has given promising results for the control of severe SARS-COV-2 pneumonia, it is interesting to notice that retinal degeneration in ECOR is associated with an evident increase in TNF-alpha, as well as soluble TNFR2, inducing an anomaly of TNF-alpha signaling [12] . abstract: nan url: https://doi.org/10.1007/s10792-020-01389-2 doi: 10.1007/s10792-020-01389-2 id: cord-336628-0evl3wnd author: Neufeldt, Christopher J. title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 words: 5880.0 sentences: 362.0 pages: flesch: 49.0 cache: ./cache/cord-336628-0evl3wnd.txt txt: ./txt/cord-336628-0evl3wnd.txt summary: Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. abstract: SARS-CoV-2 is a novel virus that has rapidly spread, causing a global pandemic. In the majority of infected patients, SARS-CoV-2 leads to mild disease; however, in a significant proportion of infections, individuals develop severe symptoms that can lead to permanent lung damage or death. These severe cases are often associated with high levels of pro-inflammatory cytokines and low antiviral responses which can lead to systemic complications. We have evaluated transcriptional and cytokine secretion profiles from infected cell cultures and detected a distinct upregulation of inflammatory cytokines that parallels samples taken from infected patients. Building on these observations, we found a specific activation of NF-κB and a block of IRF3 nuclear translocation in SARS-CoV-2 infected cells. This NF-κB response is mediated by cGAS-STING activation and could be attenuated through STING targeting drugs. Our results show that SARS-CoV-2 curates a cGAS-STING mediated NF-κB driven inflammatory immune response in epithelial cells that likely contributes to inflammatory responses seen in patients and might be a target to suppress severe disease symptoms. url: https://doi.org/10.1101/2020.07.21.212639 doi: 10.1101/2020.07.21.212639 id: cord-253178-c41xejo3 author: Neuman, B.W. title: Supramolecular Architecture of the Coronavirus Particle date: 2016-09-15 words: 7814.0 sentences: 390.0 pages: flesch: 46.0 cache: ./cache/cord-253178-c41xejo3.txt txt: ./txt/cord-253178-c41xejo3.txt summary: M proteins in SARS-CoV, FCoV, and MHV virions and virus-like particles (VLPs) form homodimers (Neuman et al., 2011) , which appear to be functionally analogous to the M-GP5 heterodimers of Arteriviridae (de Vries et al., 1995; Faaberg et al., 1995; Snijder et al., 2003) . However, a recent study found that a chimeric MHV with SARS-CoV M and S transmembrane and endodomain was severely deficient in incorporating S into virions, suggesting that cellular localization signals or more complex interactions among the structural proteins may help support S incorporation (Kuo et al., 2016) . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles abstract: Coronavirus particles serve three fundamentally important functions in infection. The virion provides the means to deliver the viral genome across the plasma membrane of a host cell. The virion is also a means of escape for newly synthesized genomes. Lastly, the virion is a durable vessel that protects the genome on its journey between cells. This review summarizes the available X-ray crystallography, NMR, and cryoelectron microscopy structural data for coronavirus structural proteins, and looks at the role of each of the major structural proteins in virus entry and assembly. The potential wider conservation of the nucleoprotein fold identified in the Arteriviridae and Coronaviridae families and a speculative model for the evolution of corona-like virus architecture are discussed. url: https://doi.org/10.1016/bs.aivir.2016.08.005 doi: 10.1016/bs.aivir.2016.08.005 id: cord-301942-ppa7gb95 author: Neuman, Benjamin W. title: Ultrastructure of SARS-CoV, FIPV, and MHV Revealed by Electron Cryomicroscopy date: 2006 words: 1189.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-301942-ppa7gb95.txt txt: ./txt/cord-301942-ppa7gb95.txt summary: The current understanding of coronavirus ultrastructure relies heavily on transmission electron microscopy of negatively stained images. Each virus appeared approximately round in cryo-EM images, with a fringe of spikes protruding from the viral membrane and a region of lower density near the virion center ( Fig. 1A-B) . Spike-depleted SARS-CoV particles appeared similar to spike-depleted MHV particles in negative stain, but were produced in lower yield, not suitable for effective cryo-EM imaging. The arrangement of spike densities near the center of some particles approximates a rhombus, which would not be inconsistent with a paracrystalline organization of spikes as observed in the virions of pleomorphic arenavirus particles, 17 or a local hexagonal close-packing of structural proteins as observed in retroviral particles. Fine structure of influenza A virus observed by electron cryo-microscopy Cryo-electron microscopy reveals ordered domains in the immature HIV-1 particle Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: implications for retroviral assembly mechanisms abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037527/ doi: 10.1007/978-0-387-33012-9_31 id: cord-325971-volbaipv author: Neupane, Karun title: Potential Treatment Options for COVID-19: A Comprehensive Review of Global Pharmacological Development Efforts date: 2020-06-26 words: 3017.0 sentences: 141.0 pages: flesch: 45.0 cache: ./cache/cord-325971-volbaipv.txt txt: ./txt/cord-325971-volbaipv.txt summary: Several drugs are being tested in the trials, and the United States Food and Drugs Administration (FDA) has given Emergency Use Authorization (EUA) for remdesivir to treat COVID-19 patients on May 1, 2020 [5] . Therapeutic remdesivir treatment in MERS-CoV inoculated rhesus macaques resulted in the reduction in clinical signs, virus replication, and the absence of lung lesions in 2/6 remdesivirtreated animals along with the reduction in lesion severity in three additional animals. In a randomized controlled clinical trial of 1063 patients conducted by the National Institute of Allergy and Infectious Disease (NIAID), remdesivir has shown the efficacy in the early results against advanced COVID-19 (NCT04280705). In a retrospective observational study involving twenty patients with severe or critical COVID-19, treatment with tocilizumab in addition to lopinavir, methylprednisolone, other symptom relievers, and oxygen therapy, resulted in body temperature of all the patients returning to normal on the first day of receiving tocilizumab and significant relief of clinical symptoms synchronously in the following days. abstract: Coronavirus disease-2019 (COVID-19), first reported in China during December of 2019, is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection later spread very rapidly around the globe with over 8,708,008 cases reported, including more than 461,715 deaths reported across at least 216 countries by June 20, 2020. It was declared as a global pandemic by the World Health Organization (WHO) on March 11, 2020. With the rapidly increasing number of positive cases and deaths, there is a dire need for effective treatment. An urgent unmet need led to the planning and opening of multiple drug development trials for treatment and vaccine development. In this article, we have compiled comprehensive data on many candidate drugs such as remdesivir, favipiravir, ribavirin, umifenovir, arbidol, lopinavir, ritonavir, baricitinib, hydroxychloroquine, nitazoxanide, azithromycin, baloxavir, oseltamivir, losartan, and tocilizumab. We have tabulated available data on various clinical trials testing various aspects of COVID-19 therapeutics. url: https://doi.org/10.7759/cureus.8845 doi: 10.7759/cureus.8845 id: cord-349500-603v8lfb author: Neurath, Markus F title: Covid-19 and immunomodulation in IBD date: 2020-04-16 words: 6548.0 sentences: 386.0 pages: flesch: 45.0 cache: ./cache/cord-349500-603v8lfb.txt txt: ./txt/cord-349500-603v8lfb.txt summary: Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infects ACE2 expressing epithelial cells in the lung and/or the intestine. The covid-19 receptor ACE2 is particularly highly expressed in intestinal epithelial cells from the terminal ileum and to a lesser extent in the colon, where mucosal inflammation in patients with IBD (Crohn''s disease (CD); UC) is frequently detected. abstract: The current coronavirus pandemic is an ongoing global health crisis due to covid-19, caused by severe acute respiratory syndrome coronavirus 2. Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. This situation causes various major challenges for gastroenterology. In the context of IBD, several key questions arise. For instance, it is an important question to understand whether patients with IBD (eg, due to intestinal ACE2 expression) might be particularly susceptible to covid-19 and the cytokine release syndrome associated with lung injury and fatal outcomes. Another highly relevant question is how to deal with immunosuppression and immunomodulation during the current pandemic in patients with IBD and whether immunosuppression affects the progress of covid-19. Here, the current understanding of the pathophysiology of covid-19 is reviewed with special reference to immune cell activation. Moreover, the potential implications of these new insights for immunomodulation and biological therapy in IBD are discussed. url: https://doi.org/10.1136/gutjnl-2020-321269 doi: 10.1136/gutjnl-2020-321269 id: cord-302707-cap2rgf7 author: Ng, Dianna L. title: SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood date: 2020-09-17 words: 4364.0 sentences: 224.0 pages: flesch: 50.0 cache: ./cache/cord-302707-cap2rgf7.txt txt: ./txt/cord-302707-cap2rgf7.txt summary: Here, we present data validating the use of the EUA authorized Abbott Architect SARS-CoV-2 IgG test for antibody detection in two populations in March 2020, a hospitalized COVID-19 patient cohort at a tertiary care hospital in San Francisco and a cohort of blood donors from the San Francisco Bay Area. These studies demonstrate that SARS-CoV-2 seroprevalence in the San Francisco Bay Area was very low, suggesting limited circulation of the virus in the community as of early March, and that IgG and IgM titers are predictive of neutralizing activity, with high positive percent agreement. To evaluate assay sensitivity, we assembled a cohort of 38 hospitalized patients and 5 outpatients at University of California, San Francisco (UCSF) Medical Center and the San Francisco Veterans Affairs (SFVA) Health Care System, all of whom received care at adult inpatient units or clinics and were real-time polymerase chain reaction (RT-PCR) positive for SARS-CoV-2 from nasopharyngeal and/or oropharyngeal swab testing ( Fig. 1a and Supplementary Table 1 ). abstract: Given the limited availability of serological testing to date, the seroprevalence of SARS-CoV-2-specific antibodies in different populations has remained unclear. Here, we report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seroreactivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors in early April 2020. We additionally describe the longitudinal dynamics of immunoglobulin-G (IgG), immunoglobulin-M (IgM), and in vitro neutralizing antibody titers in COVID-19 patients. The median time to seroconversion ranged from 10.3–11.0 days for these 3 assays. Neutralizing antibodies rose in tandem with immunoglobulin titers following symptom onset, and positive percent agreement between detection of IgG and neutralizing titers was >93%. These findings emphasize the importance of using highly accurate tests for surveillance studies in low-prevalence populations, and provide evidence that seroreactivity using SARS-CoV-2 anti-nucleocapsid protein IgG and anti-spike IgM assays are generally predictive of in vitro neutralizing capacity. url: https://www.ncbi.nlm.nih.gov/pubmed/32943630/ doi: 10.1038/s41467-020-18468-8 id: cord-339762-lh8czr0a author: Ng, Dianna L. title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 date: 2016-03-31 words: 3207.0 sentences: 162.0 pages: flesch: 38.0 cache: ./cache/cord-339762-lh8czr0a.txt txt: ./txt/cord-339762-lh8czr0a.txt summary: title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) was initially isolated from a sputum specimen of a patient who died of respiratory and renal failure in Saudi Arabia in 2012. Although the pathogenesis of severe and fatal MERS-CoV infection is unknown, these postmortem findings provide critical insights, including evidence that pneumocytes are important targets, suggesting that direct cytopathic effects contribute to MERS-CoV respiratory symptoms. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. We describe the histopathologic, immunohistochemical, and ultrastructural findings from the first autopsy performed on a fatal case of MERS-CoV in the world, which was related to a hospital outbreak in the United Arab Emirates in April 2014. The main histopathologic finding in the lungs was diffuse alveolar damage. Evidence of chronic disease, including severe peripheral vascular disease, patchy cardiac fibrosis, and hepatic steatosis, was noted in the other organs. Double staining immunoassays that used anti–MERS-CoV antibodies paired with immunohistochemistry for cytokeratin and surfactant identified pneumocytes and epithelial syncytial cells as important targets of MERS-CoV antigen; double immunostaining with dipeptidyl peptidase 4 showed colocalization in scattered pneumocytes and syncytial cells. No evidence of extrapulmonary MERS-CoV antigens were detected, including the kidney. These results provide critical insights into the pathogenesis of MERS-CoV in humans. url: https://www.sciencedirect.com/science/article/pii/S0002944015006471 doi: 10.1016/j.ajpath.2015.10.024 id: cord-290813-6ylwj5je author: Ng, Enders K. O. title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 words: 3125.0 sentences: 179.0 pages: flesch: 53.0 cache: ./cache/cord-290813-6ylwj5je.txt txt: ./txt/cord-290813-6ylwj5je.txt summary: To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Subsequently, together with the improvement of viral RNA extraction in which plasma or serum requires no ultracentrifugation, two real-time quantitative RT-PCR assays, one aimed toward the polymerase region and the other toward the nucleocapsid region of the virus genome ( Fig. 1) , were developed for measuring the concentration of SARS-CoV RNA in serum/plasma samples from SARS patients (13, 14) . With the use of the real-time quantitative RT-PCR assay, SARS-CoV RNA has recently been shown to be detectable in the plasma samples of pediatric patients during different stages of SARS (Fig. 4) (14) . Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome abstract: The etiologic agent of severe acute respiratory syndrome (SARS) has been identified as a new type of coronavirus, known as SARS-coronavirus (SARS-CoV). Although the SARS epidemic has subsided, many authorities, including the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC), have warned of the possible re-emergence of this highly infectious disease. Although antibody-based diagnosis of SARS has been demonstrated to be a reliable proof of SARS infection, it is not sensitive enough for detection during the early phase of the disease. To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Although most of the assays have initially been focused on RNA extracted from nasopharyngeal aspirates, urine, and stools, several of the more recently developed assays have been based on the analysis of RNA extracted from plasma and serum. Such assays allow the more standardized quantitative expression of viral loads and are potentially useful for early SARS diagnosis. In this chapter, two real-time quantitative RT-PCR systems for the quantification of SARS-CoV RNA in serum are discussed. The two RT-PCR systems, one aimed toward the nucleocapsid region and the other toward the polymerase region of the virus genome, have a detection rate of up to 80% during the first week of illness. These quantitative systems are potentially useful for the early diagnosis of SARS and can also provide viral load information that might assist clinicians in making a prognostic evaluation of an infected individual. url: https://www.ncbi.nlm.nih.gov/pubmed/16916262/ doi: 10.1385/1-59745-074-x:163 id: cord-276874-9rjbmsvb author: Ng, M.L. title: Topographic Changes in SARS Coronavirus–infected Cells at Late Stages of Infection date: 2004-11-17 words: 3172.0 sentences: 188.0 pages: flesch: 52.0 cache: ./cache/cord-276874-9rjbmsvb.txt txt: ./txt/cord-276874-9rjbmsvb.txt summary: Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome–associated coronavirus at the cell surface. Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome-associated coronavirus at the cell surface. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. The aim of this study was to use scanning electron and atomic force microscopes to investigate changes in the surface topography of SARS-CoV-infected cells at late infection. Scanning electron microscopy of Vero E6 cells infected with severe acute respiratory syndrome-associated coronavirus at 24 h after infection. abstract: Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome–associated coronavirus at the cell surface. The surface form of the cells at advanced infection displayed prolific pseudopodia that, in addition to the rest of the plasma membrane, were also active sites of virus release. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. The final expulsion step of the maturing virus particles seemed to result in some disruptions to the plasma membrane. The cytoskeletal network along the edge of the infected cells was enhanced and could be involved in transporting and expelling the progeny virus particles. Thickening of the actin filaments at the cell edge provided the bending force to extrude the virus particles. url: https://www.ncbi.nlm.nih.gov/pubmed/15550199/ doi: 10.3201/eid1011.040195 id: cord-260550-ld9eieik author: Ng, Man Wai title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date: 2007-06-01 words: 2839.0 sentences: 164.0 pages: flesch: 63.0 cache: ./cache/cord-260550-ld9eieik.txt txt: ./txt/cord-260550-ld9eieik.txt summary: title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese In this study, we investigated the single nucleotide polymorphisms (SNPs) of inflammatory chemokine genes, i.e. RANTES, IP-10 and monokine induced by gamma interferon gene (Mig) in two Chinese cohorts from Hong Kong and Beijing and found that the RANTES -28 G allele was associated with disease susceptibility and severity of SARS. Among them, 20 patients were classified as severe group, which were identified by their admissions to intensive care units or deaths from SARS (mean ± SD age = 39.45 ± 12.8, 11 male and 9 female). After correction by Bonferroni method, the significant P value should be less than 0.007 This study showed that RANTES -28 G allele was a risk factor that associated with severe clinical outcomes in both Hong Kong and Beijing Chinese SARS patients. abstract: BACKGROUND: Chemokines play important roles in inflammation and antiviral action. We examined whether polymorphisms of RANTES, IP-10 and Mig affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: We tested the polymorphisms of RANTES, IP-10 and Mig for their associations with SARS in 495 Hong Kong Chinese SARS patients and 578 controls. Then we tried to confirm the results in 356 Beijing Chinese SARS patients and 367 controls. RESULTS: RANTES -28 G allele was associated with SARS susceptibility in Hong Kong Chinese (P < 0.0001, OR = 2.80, 95%CI:2.11–3.71). Individuals with RANTES -28 CG and GG genotypes had a 3.28-fold (95%CI:2.32–4.64) and 3.06-fold (95%CI:1.47–6.39) increased risk of developing SARS respectively (P < 0.0001). This -28 G allele conferred risk of death in a gene-dosage dependent manner (P = 0.014) with CG and GG individuals having a 2.12-fold (95% CI: 1.11–4.06) and 4.01-fold (95% CI: 1.30–12.4) increased risk. For the replication of RANTES data in Beijing Chinese, the -28 G allele was not associated with susceptibility to SARS. However, -28 CG (OR = 4.27, 95%CI:1.64–11.1) and GG (OR = 3.34, 95%CI:0.37–30.7) were associated with admission to intensive care units or death due to SARS (P = 0.011). CONCLUSION: RANTES -28 G allele plays a role in the pathogenesis of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/17540042/ doi: 10.1186/1471-2334-7-50 id: cord-257792-m7nij17v author: Ng, Oi-Wing title: Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection date: 2016-04-12 words: 4237.0 sentences: 203.0 pages: flesch: 56.0 cache: ./cache/cord-257792-m7nij17v.txt txt: ./txt/cord-257792-m7nij17v.txt summary: In this study, the screening for the presence of SARS-specific T cells in a cohort of three SARS-recovered individuals at 9 and 11 years post-infection was carried out, and all memory T cell responses detected target the SARS-CoV structural proteins. As shown in Fig. 1 , higher frequencies of IFN␥producing SFUs were observed for in vitro-expanded PBMCs from SARS subject 1 compared to the healthy individual, suggesting the presence of SARS-specific memory T cells at 9 years post-infection. In another study looking at SARSspecific memory T cell responses in SARS-recovered individuals at 4 years post-infection, 28.75% of them presented T cell responses to M peptides [22] , further supporting the role of M protein in eliciting dominant cellular immunity during SARS-CoV infection. In SARS subject 1 at 6 years post-infection, a HLA-B*1525-restricted memory CD8 + T cell response targeting the N53 peptide, corresponding to residues 261-275 of N protein, was detected. abstract: Severe acute respiratory syndrome (SARS) is a highly contagious infectious disease which first emerged in late 2002, caused by a then novel human coronavirus, SARS coronavirus (SARS-CoV). The virus is believed to have originated from bats and transmitted to human through intermediate animals such as civet cats. The re-emergence of SARS-CoV remains a valid concern due to the continual persistence of zoonotic SARS-CoVs and SARS-like CoVs (SL-CoVs) in bat reservoirs. In this study, the screening for the presence of SARS-specific T cells in a cohort of three SARS-recovered individuals at 9 and 11 years post-infection was carried out, and all memory T cell responses detected target the SARS-CoV structural proteins. Two CD8(+) T cell responses targeting the SARS-CoV membrane (M) and nucleocapsid (N) proteins were characterized by determining their HLA restriction and minimal T cell epitope regions. Furthermore, these responses were found to persist up to 11 years post-infection. An absence of cross-reactivity of these CD8(+) T cell responses against the newly-emerged Middle East respiratory syndrome coronavirus (MERS-CoV) was also demonstrated. The knowledge of the persistence of SARS-specific celullar immunity targeting the viral structural proteins in SARS-recovered individuals is important in the design and development of SARS vaccines, which are currently unavailable. url: https://api.elsevier.com/content/article/pii/S0264410X16002589 doi: 10.1016/j.vaccine.2016.02.063 id: cord-307036-n44yml79 author: Ng, Oi-Wing title: Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date: 2014-07-14 words: 8528.0 sentences: 392.0 pages: flesch: 57.0 cache: ./cache/cord-307036-n44yml79.txt txt: ./txt/cord-307036-n44yml79.txt summary: Next, to determine if mAb 1A9 exhibits cross-neutralizing activity, S-pseudotyped virus particles, or S-pps, carrying the human SARS-CoV S or the various RBD-modified chimeric S of civet SARS-CoV SZ3 strain and bat SL-CoV Rp3 and Rf1 strains were generated and used to infect CHO-ACE2 cells in the absence or presence of different concentrations (100, 150 and 200 mg/ml) of mAb 1A9. Wild-type S, substitution S mutants, namely D1128A, N1056K, and that containing both D1128A and N1056K, were then expressed in 293 FT cells and Western Blot analysis was performed to determine the effects of these mutations on the binding of the S protein to mAb 1A9. (A) S-pp expressing S protein of humans SARS-CoV HKU39849, civet SARS-CoV SZ3, bat SL-CoV Rp3 and Rf1 and (B) S-pp containing wild-type or mutant D1128A, N1056K or D1128A/ N1056K S were generated and used to infect CHO-ACE2 cells at equal amount (as quantitated using P24 ELISA). abstract: The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) is the etiological agent for the infectious disease, SARS, which first emerged 10 years ago. SARS-CoV is a zoonotic virus that has crossed the species barriers to infect humans. Bats, which harbour a diverse pool of SARS-like CoVs (SL-CoVs), are believed to be the natural reservoir. The SARS-CoV surface Spike (S) protein is a major antigenic determinant in eliciting neutralizing antibody production during SARS-CoV infection. In our previous work, we showed that a panel of murine monoclonal antibodies (mAbs) that target the S2 subunit of the S protein are capable of neutralizing SARS-CoV infection in vitro (Lip KM et al, J Virol. 2006 Jan; 80(2): 941–50). In this study, we report our findings on the characterization of one of these mAbs, known as 1A9, which binds to the S protein at a novel epitope within the S2 subunit at amino acids 1111–1130. MAb 1A9 is a broadly neutralizing mAb that prevents viral entry mediated by the S proteins of human and civet SARS-CoVs as well as bat SL-CoVs. By generating mutant SARS-CoV that escapes the neutralization by mAb 1A9, the residue D1128 in S was found to be crucial for its interaction with mAb 1A9. S protein containing the substitution of D1128 with alanine (D1128A) exhibited a significant decrease in binding capability to mAb 1A9 compared to wild-type S protein. By using a pseudotyped viral entry assay, it was shown that the D1128A substitution in the escape virus allows it to overcome the viral entry blockage by mAb 1A9. In addition, the D1128A mutation was found to exert no effects on the S protein cell surface expression and incorporation into virion particles, suggesting that the escape virus retains the same viral entry property as the wild-type virus. url: https://www.ncbi.nlm.nih.gov/pubmed/25019613/ doi: 10.1371/journal.pone.0102415 id: cord-254884-5rmnwcfd author: Ng, S. M. title: Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) date: 2006-01-21 words: 2218.0 sentences: 130.0 pages: flesch: 52.0 cache: ./cache/cord-254884-5rmnwcfd.txt txt: ./txt/cord-254884-5rmnwcfd.txt summary: title: Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) The SMART debriefing (1) aimed at boosting resilience and catalyzing transformation among persons undergoing stressful events, (2) adopted a growth-oriented and holistic approach of health promotion, and (3) employed methods drawn from various indigenous sources (e.g. Asian philosophies and Traditional Chinese Medicine). Participants (N=51) were people with chronic diseases recruited about 1 month (August 2003) after the Severe Acute Respiratory Syndrome (SARS) outbreak was eventually under control, after causing widespread panic in Hong Kong. After the one-day group debriefing, participants showed significant decrease in depression level, as measured by Brief Symptom Inventory (Derogatis & Melisaratos, 1983, Psychological Medicine, 13(3), 595–605) and changes in cognitive appraisal towards SARS. We hypothesize the SMART debriefing can promote positive growth among people with chronic diseases and reduce their distress levels at the same time. abstract: This study presented preliminary results on the efficacy of a novel group debriefing model called Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART). The SMART debriefing (1) aimed at boosting resilience and catalyzing transformation among persons undergoing stressful events, (2) adopted a growth-oriented and holistic approach of health promotion, and (3) employed methods drawn from various indigenous sources (e.g. Asian philosophies and Traditional Chinese Medicine). Participants (N=51) were people with chronic diseases recruited about 1 month (August 2003) after the Severe Acute Respiratory Syndrome (SARS) outbreak was eventually under control, after causing widespread panic in Hong Kong. After the one-day group debriefing, participants showed significant decrease in depression level, as measured by Brief Symptom Inventory (Derogatis & Melisaratos, 1983, Psychological Medicine, 13(3), 595–605) and changes in cognitive appraisal towards SARS. Such changes were sustained in a 1-month follow-up. Clinical implications and directions for further study were discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/16429250/ doi: 10.1007/s10597-005-9002-y id: cord-275760-hi9sj0d7 author: Ng, Siew C title: Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification date: 2020-04-22 words: 644.0 sentences: 39.0 pages: flesch: 59.0 cache: ./cache/cord-275760-hi9sj0d7.txt txt: ./txt/cord-275760-hi9sj0d7.txt summary: title: Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification We read with interest the Correspondence by Christopher Green and colleagues 1 suggesting the need for a molecular test to screen faecal microbiota transplant (FMT ) donors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to prevent the potential risk of transmission. 5 As described by Green and colleagues, 1 the University of Birmingham Microbiota Treatment Centre (Birmingham, UK) is not actively processing new donors until a validated SARS-CoV-2 stool test is available. As per the diagnostic protocol of our local health authority, all COVID-19 cases had been confirmed by two RT-PCR tests targeting different regions of the RdRp gene in respiratory specimens. Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2468125320301242 doi: 10.1016/s2468-1253(20)30124-2 id: cord-303018-3ka72y3p author: Ng, Siew C title: COVID-19 and the gastrointestinal tract: more than meets the eye date: 2020-04-09 words: 1646.0 sentences: 98.0 pages: flesch: 54.0 cache: ./cache/cord-303018-3ka72y3p.txt txt: ./txt/cord-303018-3ka72y3p.txt summary: COVID-19 and the gastrointestinal tract: more than meets the eye Siew C Ng , 1 Herbert Tilg 2 An outbreak of coronavirus disease 2019 , caused by severe acute respiratory syndrome (SARS-CoV-2), has rapidly spread from China to almost all over the world affecting over 800,000 people across 199 countries. 5 In GUT several articles report on GI symptoms, detection of the virus in faeces and potential pathophysiological aspects including viral receptor expression in the GI tract. In about 50% of COVID-19 cases, the presence of SARS-CoV-2 in faecal samples and detection of SARS-CoV-2 in intestinal mucosa of infected patients suggest that enteric symptoms could be caused by invasion of ACE2 expressing enterocytes and the GI tract may be an alternative route of infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms abstract: nan url: https://doi.org/10.1136/gutjnl-2020-321195 doi: 10.1136/gutjnl-2020-321195 id: cord-300627-7x4me5lx author: Ng, W. F. title: The placentas of patients with severe acute respiratory syndrome: a pathophysiological evaluation date: 2006-06-30 words: 4396.0 sentences: 293.0 pages: flesch: 57.0 cache: ./cache/cord-300627-7x4me5lx.txt txt: ./txt/cord-300627-7x4me5lx.txt summary: Summary Aims The pathology of the placentas delivered from pregnant women who had severe acute respiratory syndrome (SARS) in Hong Kong was studied. In three placentas delivered in the acute stage of SARS, there were increases in intervillous or subchorionic fibrin which might be related to disturbances in maternal placental blood flow due to the hypoxic respiratory disease. Extensive fetal thrombotic vasculopathy (FTV) with sharply demarcated zones of avascular fibrotic villi was noted in the placentas of two patients convalescent from SARS in the third trimester. Wong also showed that pregnant SARS patients had a higher rate of respiratory failure and drew an analogy with the more severe clinical course of epidemic influenza in pregnant women. This study was undertaken to examine the pathology of the placentas delivered from women who contracted SARS during pregnancy and to correlate the findings with the clinical and obstetric course and the neonatal outcome. abstract: Summary Aims The pathology of the placentas delivered from pregnant women who had severe acute respiratory syndrome (SARS) in Hong Kong was studied. Methods The pathology of the placentas was retrospectively studied in detail and compared with control sets. The clinical data of the women and neonates were also reviewed. Results A total of seven placentas were studied. The placentas from two women convalescent from SARS in the first trimester were normal. In three placentas delivered in the acute stage of SARS, there were increases in intervillous or subchorionic fibrin which might be related to disturbances in maternal placental blood flow due to the hypoxic respiratory disease. Extensive fetal thrombotic vasculopathy (FTV) with sharply demarcated zones of avascular fibrotic villi was noted in the placentas of two patients convalescent from SARS in the third trimester. Both pregnancies had intrauterine growth retardation, oligohydramnios and newborns small for gestation. The aetiology of the FTV might be related to thrombotic tendency due to SARS or placental hypoxia. Conclusions This report highlights placental pathology that was probably the result of pathophysiological alteration of the maternal fetal unit during SARS. Further studies are required to delineate the relationship between severe maternal respiratory disease, placental pathology and pregnancy outcome. url: https://www.sciencedirect.com/science/article/pii/S003130251633937X doi: 10.1080/00313020600696280 id: cord-262640-4vr4cm1s author: Nguyen, N. N. title: Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2 date: 2020-07-08 words: 2744.0 sentences: 208.0 pages: flesch: 54.0 cache: ./cache/cord-262640-4vr4cm1s.txt txt: ./txt/cord-262640-4vr4cm1s.txt summary: This paper highlights the analytical characteristic of an ELISA based assay by AnshLabs and three random access immunoassay (RAIA) by DiaSorin, Roche, and Abbott that have been approved for emergency use authorization (EUA), at a tertiary academic center in a low disease-prevalence area. All discrepant samples that were positive by AnshLabs and negative by RAIA tested positive by all-in-one step SARS-CoV-2 Total (COV2T) assay performed on the automated Siemens Advia Centaur XPT analyzer. The Elecsys Anti-SARS-CoV-2 assay is performed on the Roche cobas e601 analyzer for total antibodies 126 specific for IgG, IgM and IgA which target nucleocapsid protein, in human serum or plasma. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint Table 4 shows the concordance between ELISA and RAIA results for samples that were confirmed 174 positive for SARS-CoV-2 by rtPCR. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint non-specific binding in AnshLabs ELISA assay 320 All rights reserved. abstract: Public health emergency of SARS-CoV-2 has facilitated diagnostic testing as a related medical countermeasure against COVID-19 outbreak. Numerous serologic antibody tests have become available through an expedited federal emergency use only process. This paper highlights the analytical characteristic of an ELISA based assay by AnshLabs and three random access immunoassay (RAIA) by DiaSorin, Roche, and Abbott that have been approved for emergency use authorization (EUA), at a tertiary academic center in a low disease-prevalence area. The AnshLabs gave higher estimates of sero-prevalence, over the three RAIA methods. For positive results, AnshLabs had 93.3% and 100% concordance with DiaSorin or Abbott and Roche respectively. For negative results, AnshLabs had 69.7% and 73.0% concordance with DiaSorin and Roche or Abbott respectively. All discrepant samples that were positive by AnshLabs and negative by RAIA tested positive by all-in-one step SARS-CoV-2 Total (COV2T) assay performed on the automated Siemens Advia Centaur XPT analyzer. None of these methods, however, are useful in early diagnosis of SARSCoV- 2. url: https://doi.org/10.1101/2020.07.06.20145938 doi: 10.1101/2020.07.06.20145938 id: cord-255371-o9oxchq6 author: Nguyen, Thanh Thi title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date: 2020-07-10 words: 5640.0 sentences: 365.0 pages: flesch: 59.0 cache: ./cache/cord-255371-o9oxchq6.txt txt: ./txt/cord-255371-o9oxchq6.txt summary: title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. We use 6,324 SARS-CoV-2 genome sequences collected in 45 countries and deposited to the NCBI GenBank so far and create a spreadsheet dataset of all mutations occurred across different genes. In this paper, to evaluate the possible impacts of genomic mutations on the virus functions, we propose the use of the SSpro/ACCpro 5 methods to predict protein secondary structure and relative solvent accessibility [13] . By comparing the prediction results obtained on the reference genome and mutated genomes, we are able to assess whether the detected mutations have the potential to change the protein structure and solvent accessibility, and thus lead to possible changes of the virus characteristics. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6,324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development. url: https://doi.org/10.1101/2020.07.10.171769 doi: 10.1101/2020.07.10.171769 id: cord-291523-4dtk1kyh author: Nguyen, Thanh Thi title: Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date: 2020-07-01 words: 5361.0 sentences: 313.0 pages: flesch: 62.0 cache: ./cache/cord-291523-4dtk1kyh.txt txt: ./txt/cord-291523-4dtk1kyh.txt summary: Outcomes of a phylogenetic analysis suggest that the virus belongs to the genus Betacoronavirus, sub-genus Sarbecovirus, which includes many bat SARS-like CoVs and SARS CoVs. Another study in [5] confirms this finding by analysing genomes obtained from three adult patients admitted to a hospital in Wuhan on December 27, 2019. With the cut-off parameter C is set equal to 0.7, the hierarchical clustering algorithm separates the reference sequences into 6 clusters in which cluster "5" comprises all examined viruses of the Sarbecovirus sub-genus, including many SARS CoVs, bat SARS-like CoVs and pangolin CoVs (Fig. 7A) . With the results obtained in Fig. 7D (and also in the experiments with the DBSCAN method presented next), we support a hypothesis that bats or pangolins are the probable origin of SARS-CoV-2. In this Appendix, we first present results of the hierarchical clustering method applied to the dataset that combines Set 1 of reference sequences (Table 1 ) with all 334 SARS-CoV-2 sequences (see Fig. 9 ). abstract: Origin of the COVID-19 virus has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the original hosts for the virus based on comparative studies using its genomic sequences. This paper investigates the COVID-19 virus origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined COVID-19 virus genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidences strongly supporting scientific hypotheses that bats and pangolins are probable hosts for the COVID-19 virus. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins. url: https://doi.org/10.1101/2020.05.12.091397 doi: 10.1101/2020.05.12.091397 id: cord-268894-amfv3z2y author: Nguyen-Contant, Phuong title: S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date: 2020-07-21 words: 4632.0 sentences: 269.0 pages: flesch: 56.0 cache: ./cache/cord-268894-amfv3z2y.txt txt: ./txt/cord-268894-amfv3z2y.txt summary: Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Approximately one-third of non-SARS-CoV-140 2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N 141 proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs ( Figure 1A ). In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E 192 and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-193 exposed subjects, consistent with the higher levels of serum IgG against these antigens ( Figure 2E -194 2H) . abstract: The high susceptibility of humans to SARS-CoV-2 infection, the cause of COVID-19, reflects the novelty of the virus and limited preexisting B cell immunity. IgG against the SARS-CoV-2 spike (S) protein, which carries the novel receptor binding domain (RBD), is absent or at low levels in unexposed individuals. To better understand the B cell response to SARS-CoV-2 infection, we asked whether virus-reactive memory B cells (MBCs) were present in unexposed subjects and whether MBC generation accompanied virus-specific IgG production in infected subjects. We analyzed sera and PBMCs from non-SARS-CoV-2-exposed healthy donors and COVID-19 convalescent subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD and S2 subunit, and nucleocapsid [N]) and non-SARS-CoV-2 proteins were related to measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Most unexposed subjects had anti-S2 IgG and a minority had anti-N IgG, but IgG MBCs with these specificities were not detected, perhaps reflecting low frequencies. Convalescent subjects had high levels of IgG against the RBD, S2, and N, together with large populations of RBD- and S2-reactive IgG MBCs. Notably, IgG titers against the S protein of the human coronavirus OC43 in convalescent subjects were higher than in unexposed subjects and correlated strongly with anti-S2 titers. Our findings indicate cross-reactive B cell responses against the S2 subunit that might enhance broad coronavirus protection. Importantly, our demonstration of MBC induction by SARS-CoV-2 infection suggests that a durable form of B cell immunity is maintained even if circulating antibody levels wane. IMPORTANCE Recent rapid worldwide spread of SARS-CoV-2 has established a pandemic of potentially serious disease in the highly susceptible human population. Key questions are whether humans have preexisting immune memory that provides some protection against SARS-CoV-2 and whether SARS-CoV-2 infection generates lasting immune protection against reinfection. Our analysis focused on pre- and post-infection IgG and IgG memory B cells (MBCs) reactive to SARS-CoV-2 proteins. Most importantly, we demonstrate that infection generates both IgG and IgG MBCs against the novel receptor binding domain and the conserved S2 subunit of the SARS-CoV-2 spike protein. Thus, even if antibody levels wane, long-lived MBCs remain to mediate rapid antibody production. Our study also suggests that SARS-CoV-2 infection strengthens preexisting broad coronavirus protection through S2-reactive antibody and MBC formation. url: https://doi.org/10.1101/2020.07.20.213298 doi: 10.1101/2020.07.20.213298 id: cord-292883-7hvq9qaj author: Nguyen-Contant, Phuong title: S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date: 2020-09-25 words: 5334.0 sentences: 264.0 pages: flesch: 51.0 cache: ./cache/cord-292883-7hvq9qaj.txt txt: ./txt/cord-292883-7hvq9qaj.txt summary: RBD-binding MBCs sampled in the convalescent phase of SARS-CoV-2 infection expressed Abs with relatively low numbers of V gene mutations, suggesting that this component of the response largely reflected naive B cell activation by novel epitopes (20) . Approximately one-third of non-SARS-CoV-2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs (Fig. 1A) . Since the healthy donor samples in our analysis were collected 6 to 10 years before the emergence of SARS-CoV-2, we considered the possibility that a recently circulating HCoV was responsible for the higher anti-OC43 S IgG titers in the convalescent subjects. In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-exposed subjects, consistent with the higher levels of serum IgG against these antigens (Fig. 2E to H) . abstract: The high susceptibility of humans to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the cause of coronavirus disease 2019 (COVID-19), reflects the novelty of the virus and limited preexisting B cell immunity. IgG against the SARS-CoV-2 spike (S) protein, which carries the novel receptor binding domain (RBD), is absent or at low levels in unexposed individuals. To better understand the B cell response to SARS-CoV-2 infection, we asked whether virus-reactive memory B cells (MBCs) were present in unexposed subjects and whether MBC generation accompanied virus-specific IgG production in infected subjects. We analyzed sera and peripheral blood mononuclear cells (PBMCs) from non-SARS-CoV-2-exposed healthy donors and COVID-19 convalescent subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD and S2 subunit, and nucleocapsid [N]) and non-SARS-CoV-2 proteins were related to measurements of circulating IgG MBC levels. Anti-RBD IgG was absent in unexposed subjects. Most unexposed subjects had anti-S2 IgG, and a minority had anti-N IgG, but IgG MBCs with these specificities were not detected, perhaps reflecting low frequencies. Convalescent subjects had high levels of IgG against the RBD, S2, and N, together with large populations of RBD- and S2-reactive IgG MBCs. Notably, IgG titers against the S protein of the human coronavirus OC43 were higher in convalescent subjects than in unexposed subjects and correlated strongly with anti-S2 titers. Our findings indicate cross-reactive B cell responses against the S2 subunit that might enhance broad coronavirus protection. Importantly, our demonstration of MBC induction by SARS-CoV-2 infection suggests that a durable form of B cell immunity is maintained even if circulating antibody levels wane. url: https://www.ncbi.nlm.nih.gov/pubmed/32978311/ doi: 10.1128/mbio.01991-20 id: cord-300324-95fty9yi author: Ni Lochlainn, M. title: Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals date: 2020-04-29 words: 4271.0 sentences: 247.0 pages: flesch: 51.0 cache: ./cache/cord-300324-95fty9yi.txt txt: ./txt/cord-300324-95fty9yi.txt summary: Conclusions: Being older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. Visit to hospital as outcome were fit to test for association between i) self-reported obesity and ii) chronic lung disease and asthma, heart disease, diabetes and kidney disease in the following groups: 1) self-reported COVID-19 infection with classical symptoms (SR-COVID19); 2) self-reported positive COVID-19 test results (T-COVID19); 3) imputed/predicted COVID-19 infection based on symptomatology (I-COVID19) Imputation for testing positive for COVID was performed using the data at day of maximum sum of symptoms and applying a logistic regression using coefficients defined previously (2) . In this study we found that age, obesity, diabetes and pre-existing lung, renal and cardiac disease, were risk factors for a hospital visit with COVID-19 amongst a large but relatively young, community-based population of app users. abstract: Objectives: We aimed to identify key demographic risk factors for hospital attendance with COVID-19 infection. Design: Community survey Setting: The COVID Symptom Tracker mobile application co-developed by physicians and scientists at Kings College London, Massachusetts General Hospital, Boston and Zoe Global Limited was launched in the UK and US on 24th and 29th March 2020 respectively. It captured self-reported information related to COVID-19 symptoms and testing. Participants: 2,618,948 users of the COVID Symptom Tracker App. UK (95.7%) and US (4.3%) population. Data cut-off for this analysis was 21st April 2020. Main outcome measures: Visit to hospital and for those who attended hospital, the need for respiratory support in three subgroups (i) self-reported COVID-19 infection with classical symptoms (SR-COVID-19), (ii) self-reported positive COVID-19 test results (T-COVID-19), and (iii) imputed/predicted COVID-19 infection based on symptomatology (I-COVID-19). Multivariate logistic regressions for each outcome and each subgroup were adjusted for age and gender, with sensitivity analyses adjusted for comorbidities. Classical symptoms were defined as high fever and persistent cough for several days. Results: Older age and all comorbidities tested were found to be associated with increased odds of requiring hospital care for COVID-19. Obesity (BMI >30) predicted hospital care in all models, with odds ratios (OR) varying from 1.20 [1.11; 1.31] to 1.40 [1.23; 1.60] across population groups. Pre-existing lung disease and diabetes were consistently found to be associated with hospital visit with a maximum OR of 1.79 [1.64,1.95] and 1.72 [1.27; 2.31]) respectively. Findings were similar when assessing the need for respiratory support, for which age and male gender played an additional role. Conclusions: Being older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. It is of utmost importance for governments and the scientific and medical communities to work together to find evidence-based means of protecting those deemed most vulnerable from COVID-19. Trial registration: The App Ethics have been approved by KCL ethics Committee REMAS ID 18210, review reference LRS-19/20-18210 url: http://medrxiv.org/cgi/content/short/2020.04.25.20079251v1?rss=1 doi: 10.1101/2020.04.25.20079251 id: cord-323828-ug2duzw1 author: Ni, Dongchun title: Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date: 2020-10-12 words: 3408.0 sentences: 234.0 pages: flesch: 65.0 cache: ./cache/cord-323828-ug2duzw1.txt txt: ./txt/cord-323828-ug2duzw1.txt summary: Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. The clinical-grade soluble form of hACE2 has been reported to be a 74 potential novel therapeutic approach for reducing the infection of SARS-CoV-2 (Monteil et al., 2020) by preventing the viral Spike from interacting with other hACE2 present on human cells. The final 3D 115 reconstruction from 72''446 particles at 5.1Å overall resolution showed a density map corresponding to a single, 116 monomeric Spike protein in complex with hACE2 (Fig. 1a) . Figure 1 Cryo-EM maps of SARS-CoV-2 Spike-hACE2 complexes and fitted models. Cryo-EM structure of the SARS coronavirus spike glycoprotein in 352 complex with its host cell receptor ACE2 abstract: The human membrane protein Angiotensin-converting enzyme 2 (hACE2) acts as the main receptor for host cells invasion of the new coronavirus SARS-CoV-2. The viral surface glycoprotein Spike binds to hACE2, which triggers virus entry into cells. As of today, the role of hACE2 for virus fusion is not well understood. Blocking the transition of Spike from its prefusion to post-fusion state might be a strategy to prevent or treat COVID-19. Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. This observed hACE2 dependent dissociation of the Spike trimer suggests a mechanism for the therapeutic role of recombinant soluble hACE2 for treatment of COVID-19. url: https://doi.org/10.1101/2020.10.12.336016 doi: 10.1101/2020.10.12.336016 id: cord-341396-0tn06al2 author: Ni, Ling title: Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals date: 2020-05-03 words: 2100.0 sentences: 128.0 pages: flesch: 64.0 cache: ./cache/cord-341396-0tn06al2.txt txt: ./txt/cord-341396-0tn06al2.txt summary: In this study, we collected blood from COVID-19 patients who have recently become 5 virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody 6 and T cell responses. NP-and S-RBD-specific 9 IgM and IgG antibodies were both detected in the sera of newly discharged patients, 10 compared with healthy donor groups. Anti-SARS-CoV-2 IgG antibodies were also more 11 obviously observed than IgM in the follow-up patients (#9-14), when compared with healthy 12 donors ( Figure 1B ). As shown in Figure 3C , compared with healthy donors, 25 the numbers of IFN-γ-secreting NP-specific T cells in patients #1, 2, 4, 5 and 8 were much 26 higher than other patients, suggesting that they had developed SARS-CoV-2-specific T cell responses. More interestingly, when combining all 14 patients in our analysis, there 9 was a significant correlation between the neutralizing antibody titers and the numbers of NPIn this study, we characterized SARS-CoV-2-specific humoral and cellular immunity in 2 recovered patients. abstract: Summary The World Health Organization has declared SARS-CoV-2 virus outbreak a world-wide pandemic. However, there is very limited understanding on the immune responses, especially adaptive immune responses to SARS-CoV-2 infection. Here, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and detected SARS-CoV-2-specific humoral and cellular immunity in 8 newly discharged patients. Follow-up analysis on another cohort of 6 patients 2 weeks post discharge also revealed high titers of IgG antibodies. In all 14 patients tested, 13 displayed serum neutralizing activities in a pseudotype entry assay. Notably, there was a strong correlation between neutralization antibody titers and the numbers of virus-specific T cells. Our work provides a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases. It has also implications in developing an effective vaccine to SARS-CoV-2 infection. url: https://www.sciencedirect.com/science/article/pii/S1074761320301813?v=s5 doi: 10.1016/j.immuni.2020.04.023 id: cord-282571-ilf73g71 author: Ni, Wentao title: Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19 date: 2020-07-13 words: 5424.0 sentences: 287.0 pages: flesch: 46.0 cache: ./cache/cord-282571-ilf73g71.txt txt: ./txt/cord-282571-ilf73g71.txt summary: Both SARS-CoV-2 and SARS-CoV enter host cells via the angiotensin-converting enzyme 2 (ACE2) receptor, which is expressed in various human organs. In addition to the direct viral effects and inflammatory and immune factors associated with COVID-19 pathogenesis, ACE2 downregulation and the imbalance between the RAS and ACE2/angiotensin-(1–7)/MAS after infection may also contribute to multiple organ injury in COVID-19. Autopsies of SARS patients showed that SARS-CoV infection can cause injury to multiple organs, such as the heart, kidney, liver, skeletal muscle, central nervous system, and adrenal and thyroid glands, besides the lungs [30, 31] . Several studies have shown that SARS-CoV infection can downregulate ACE2 expression on cells, thereby disrupting the physiological balance between ACE/ACE2 and Ang-II/angiotensin-(1-7) and subsequently causing severe organ injury [44] [45] [46] [47] . Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS abstract: ABSTRACT: An outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that started in Wuhan, China, at the end of 2019 has become a global pandemic. Both SARS-CoV-2 and SARS-CoV enter host cells via the angiotensin-converting enzyme 2 (ACE2) receptor, which is expressed in various human organs. We have reviewed previously published studies on SARS and recent studies on SARS-CoV-2 infection, named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO), confirming that many other organs besides the lungs are vulnerable to the virus. ACE2 catalyzes angiotensin II conversion to angiotensin-(1–7), and the ACE2/angiotensin-(1–7)/MAS axis counteracts the negative effects of the renin-angiotensin system (RAS), which plays important roles in maintaining the physiological and pathophysiological balance of the body. In addition to the direct viral effects and inflammatory and immune factors associated with COVID-19 pathogenesis, ACE2 downregulation and the imbalance between the RAS and ACE2/angiotensin-(1–7)/MAS after infection may also contribute to multiple organ injury in COVID-19. The SARS-CoV-2 spike glycoprotein, which binds to ACE2, is a potential target for developing specific drugs, antibodies, and vaccines. Restoring the balance between the RAS and ACE2/angiotensin-(1–7)/MAS may help attenuate organ injuries. GRAPHICAL ABSTRACT: SARS-CoV-2 enters lung cells via the ACE2 receptor. The cell-free and macrophage-phagocytosed virus can spread to other organs and infect ACE2-expressing cells at local sites, causing multi-organ injury. [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32660650/ doi: 10.1186/s13054-020-03120-0 id: cord-309120-05bg7rfa author: Niazi, Sadegh title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 words: 2717.0 sentences: 180.0 pages: flesch: 38.0 cache: ./cache/cord-309120-05bg7rfa.txt txt: ./txt/cord-309120-05bg7rfa.txt summary: title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses'' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs abstract: Whether virulent human pathogenic coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) are effectively transmitted by aerosols remains contentious. Transmission modes of the novel coronavirus have become a hot topic of research with the importance of airborne transmission controversial due to the many factors that can influence virus transmission. Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. Infectious virus-laden aerosols can be produced by natural human respiratory activities, and their features are vital determinants for virus carriage and transmission. Physicochemical characteristics of infectious respiratory aerosols can influence the efficiency of virus transmission by droplets. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses’ viability. We also review studies evaluating these viruses in the air, field studies and available evidence about seasonality patterns. Ultimately the literature suggests that a proportion of virulent human coronaviruses can plausibly be transmitted via the air, even though this might vary in different conditions. Evidence exists for respirable-sized airborne droplet nuclei containing viral RNA, although this does not necessarily imply that the virus is transmittable, capable of replicating in a recipient host, or that inoculum is sufficient to initiate infection. However, evidence suggests that coronaviruses can survive in simulated droplet nuclei for a significant time (>24 h). Nevertheless, laboratory nebulized virus-laden aerosols might not accurately model the complexity of human carrier aerosols in studying airborne viral transport. In summary, there is disagreement on whether wild coronaviruses can be transmitted via an airborne path and display seasonal patterns. Further studies are therefore required to provide supporting evidence for the role of airborne transmission and assumed mechanisms underlying seasonality. url: https://api.elsevier.com/content/article/pii/S0269749120364563 doi: 10.1016/j.envpol.2020.115767 id: cord-252574-7oh0k139 author: Nicastro, Emanuele title: A Pediatric Emergency Department Protocol to Avoid Intra-Hospital Dispersal of SARS-CoV-2 during the Outbreak in Bergamo, Italy date: 2020-04-21 words: 1594.0 sentences: 88.0 pages: flesch: 41.0 cache: ./cache/cord-252574-7oh0k139.txt txt: ./txt/cord-252574-7oh0k139.txt summary: In Lombardy, the main outbreak of the infection was located in a community hospital in the Bergamo province, suggesting that the community spread of the infection probably arose from a large cohort of subjects who were in contact with SARS-CoV-2 infected patients attending health care facilities, and who were probably unrecognized at that time., so far pediatric services have not experienced the COVID-19 To address these issues, we developed a protocol addressing reception, risk-management and hospitalization of suspected SARS-CoV-2 cases at the pediatric emergency department and medical-surgical units aimed at containing intra-hospital transmission of the infection, considering that currently our hospital is the largest referral site in the primary outbreak area in Italy. Suspected COVID-19 patients requiring hospitalization are managed by health care personnel (HCP) using personal protective equipment (PPE) (FFP2/N95 respirator + eye protection goggles or face shield + 5 isolation gowns + face mask + gloves), who perform the acquisition of an NP/OP swab for SARS-CoV-2 real time-PCR testing. abstract: The pandemic of coronavirus SARS-CoV-2 disease affected Northern Italy, spreading from the Bergamo province to the entire country. During reorganization of our emergency department to support patients presenting with coronavirus SARS-CoV-2 disease, we aimed to evaluate whether children play a role in intrahospital spread of the infection. url: https://doi.org/10.1016/j.jpeds.2020.04.026 doi: 10.1016/j.jpeds.2020.04.026 id: cord-286006-t5gj0k54 author: Nicholas, David B. title: Pediatric epidemic crisis: Lessons for policy and practice development date: 2008-12-31 words: 5026.0 sentences: 283.0 pages: flesch: 44.0 cache: ./cache/cord-286006-t5gj0k54.txt txt: ./txt/cord-286006-t5gj0k54.txt summary: Methods Qualitative interviews were conducted with 23 participants representing key stakeholder groups: (a) pediatric patients with probable or suspected SARS, (b) their parents, and (c) health care professionals providing direct care to SARS patients. Semi-structured, qualitative interviews were conducted with 23 participants from key stakeholder groups affected by pediatric SARS as follows: pediatric patients between the ages of 5 and 17 years (n = 5), their parents (n = 10), and frontline pediatric health care providers (n = 8). The majority of health care providers (88%) recognized the importance of their work, yet grappled with concerns related to personal vulnerability and the impact of SARS policies on patients and families. Accordingly findings speak clearly to the need for: systematic and well-orchestrated information flow; communication strategies in responding and disseminating relevant information; means to ease vulnerability among stakeholders; strategies for ensuring effective and responsive leadership; and the development of practice and policy guidelines for treatment and contingency planning for an unknown patient care path. abstract: Abstract Objectives This research study addresses health policy and patient care considerations, and outlines policy and practice implications resulting from a crisis in a pediatric setting. This crisis, an epidemic outbreak of Severe Acute Respiratory Syndrome (SARS), dramatically impacted the delivery of health care in Canada. Despite the passage of time since the last diagnosed case of SARS in April 2004, researchers have warned the global community to be prepared for future outbreaks of SARS or other infectious diseases. Methods Qualitative interviews were conducted with 23 participants representing key stakeholder groups: (a) pediatric patients with probable or suspected SARS, (b) their parents, and (c) health care professionals providing direct care to SARS patients. Results Participants conveyed key areas in which health policy and practice were affected. These included the development of communication strategies for responding to SARS; easing vulnerability among all stakeholders; and the rapid development of practice guidelines. Conclusion Given the continuing threat of current and future airborne viruses with potential for epidemic spread and devastating outcomes, preparedness strategies are certainly needed. Effective strategies in pediatrics include practices that provide family centered care while minimizing disease transmission. Toward this end, lessons learned from previous outbreaks merit consideration and may inform future epidemics. url: https://www.ncbi.nlm.nih.gov/pubmed/18456367/ doi: 10.1016/j.healthpol.2007.11.006 id: cord-325783-pqonn0as author: Nicholls, John M title: Lung pathology of fatal severe acute respiratory syndrome date: 2003-05-24 words: 4022.0 sentences: 250.0 pages: flesch: 49.0 cache: ./cache/cord-325783-pqonn0as.txt txt: ./txt/cord-325783-pqonn0as.txt summary: Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines). abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a novel infectious disease with global impact. A virus from the family Coronaviridae has been identified as the cause, but the pathogenesis is still unclear. METHODS: Post-mortem tissue samples from six patients who died from SARS in February and March, 2003, and an open lung biopsy from one of these patients were studied by histology and virology. Only one full autopsy was done. Evidence of infection with the SARS-associated coronavirus (SARS-CoV) and human metapneumovirus was sought by reverse-transcriptase PCR and serology. Pathological samples were examined by light and electron microscopy and immunohistochemistry. FINDINGS: All six patients had serological evidence of recent infection with SARS-CoV. Diffuse alveolar damage was common but not universal. Morphological changes identified were bronchial epithelial denudation, loss of cilia, and squamous metaplasia. Secondary bacterial pneumonia was present in one case. A giant-cell infiltrate was seen in four patients, with a pronounced increase in macrophages in the alveoli and the interstitium of the lung. Haemophagocytosis was present in two patients. The alveolar pneumocytes also showed cytomegaly with granular amphophilic cytoplasm. The patient for whom full autopsy was done had atrophy of the white pulp of the spleen. Electron microscopy revealed viral particles in the cytoplasm of epithelial cells corresponding to coronavirus. INTERPRETATION: SARS is associated with epithelial-cell proliferation and an increase in macrophages in the lung. The presence of haemophagocytosis supports the contention that cytokine dysregulation may account, at least partly, for the severity of the clinical disease. The case definition of SARS should acknowledge the range of lung pathology associated with this disease. Published online May 16, 2003 http://image.thelancet.com/extras/03art4347web.pdf url: https://www.sciencedirect.com/science/article/pii/S0140673603134137 doi: 10.1016/s0140-6736(03)13413-7 id: cord-284841-flhfagp3 author: Nicol, Thomas title: Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech) date: 2020-06-15 words: 2806.0 sentences: 214.0 pages: flesch: 58.0 cache: ./cache/cord-284841-flhfagp3.txt txt: ./txt/cord-284841-flhfagp3.txt summary: METHODS: Two automated immunoassays (Abbott SARS-CoV-2 CLIA IgG and Euroimmun Anti-SARS-CoV-2 ELISA IgG/IgA assays) and one lateral flow immunoassay (LFIA NG-Test® IgG-IgM COVID-19) were tested. The aim of the study was to assess the clinical performance of CE marked assays available in Europe to detect SARS-CoV-2 antibodies: two automated immunoassays (Euroimmun and Abbott assays) targeting two different proteins and also one lateral flow immunoassay (NG Biotech). On May, 2020, the French Health Authority (Haute Autorité de Santé) and Infectious Diseases Society of America recommended that patients with symptoms consistent with COVID-19 but having a positive result for SARS-CoV-2 by RT-PCR may be diagnosed by serological tests [22, 23] . Here, we did not observe any significant difference between sensitivity of IgA ELISA and IgM LFIA In conclusion, our study showed equivalent clinical performance for IgG of three immunoassays (ELISA, CLIA and LFIA) >14 days after symptoms onset. abstract: BACKGROUND: The emergence of new SARS-CoV-2 has promoted the development of new serological tests that could be complementary to RT-PCR. Nevertheless, the assessment of clinical performances of available tests is urgently required as their use has just been initiated for diagnose. OBJECTIVES: The aim of this study was to assess the performance of three immunoassays for the detection of SARS-CoV-2 antibodies. METHODS: Two automated immunoassays (Abbott SARS-CoV-2 CLIA IgG and Euroimmun Anti-SARS-CoV-2 ELISA IgG/IgA assays) and one lateral flow immunoassay (LFIA NG-Test® IgG-IgM COVID-19) were tested. 293 specimens were analyzed from patients with a positive RT-PCR response, from patients with symptoms consistent with COVID-19 but exhibiting a negative response to the RT-PCR detection test, and from control group specimens. Days since symptoms onset were collected from clinical information sheet associated with respiratory tract samples. RESULTS: Overall sensitivity for IgG was equivalent (around 80%) for CLIA, ELISA and LFIA. Sensitivity for IgG detection, >14 days after onset of symptoms, was 100.0% for all assays. Overall specificity for IgG was greater for CLIA and LFIA (more than 98%) compared to ELISA (95.8%). Specificity was significantly different between IgA ELISA (78.9%) and IgM LFIA (95.8%) (p < 0.05). The best agreement was observed between CLIA and LFIA assays (97%; k = 0.936). CONCLUSION: Excellent sensitivity for IgG detection was obtained >14 days after onset of symptoms for all immunoassays. Specificity was also excellent for IgG CLIA and IgG LFIA. Our study shows that NG-Test® is reliable and accurate for routine use in clinical laboratories. url: https://doi.org/10.1016/j.jcv.2020.104511 doi: 10.1016/j.jcv.2020.104511 id: cord-343618-jjb8da4a author: Nie, Kai title: Gastrointestinal insights during the COVID-19 epidemic date: 2020-09-26 words: 2046.0 sentences: 129.0 pages: flesch: 40.0 cache: ./cache/cord-343618-jjb8da4a.txt txt: ./txt/cord-343618-jjb8da4a.txt summary: Thus, cancer and inflammatory bowel disease (IBD) management, stool viral tests, and virus exposure are major concerns in the context of COVID-19 epidemic. Patients with digestive disease bear a relatively high risk of SARS-CoV-2 infection. This finding suggests that gastrointestinal cancer patients may be more susceptible to SARS-CoV-2 infection [47] . To date, several cases of SARS-CoV-2 infection in IBD patients have been reported. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China abstract: Coronavirus disease-2019 (COVID-19) has so far caused hundreds of mortalities worldwide. Although respiratory symptoms are the main complication in COVID-19 patients, the disease is also associated with gastrointestinal problems, with diarrhea, nausea, and vomiting being primary COVID-19 symptoms. Thus, cancer and inflammatory bowel disease (IBD) management, stool viral tests, and virus exposure are major concerns in the context of COVID-19 epidemic. In patients with colorectal cancer and IBD, the colonic mucosa exhibits elevated angiotensin-converting enzyme 2 receptor levels, enhancing COVID-19 susceptibility. In some cases, positive viral stool tests may be the only indicator of infection at admission or after leaving quarantine. Without supplemental stool tests, the risk of undetected COVID-19 transmission is high. Moreover, viral exposure during the regular or emergency endoscopic examination should be avoided. We carefully discuss key gastrointestinal concerns with regard to COVID-19 and call for more attention to such problems. url: https://www.ncbi.nlm.nih.gov/pubmed/33024750/ doi: 10.12998/wjcc.v8.i18.3934 id: cord-344419-3wcfpw2z author: Niedzwiedz, C. L. title: Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study date: 2020-04-27 words: 5025.0 sentences: 271.0 pages: flesch: 48.0 cache: ./cache/cord-344419-3wcfpw2z.txt txt: ./txt/cord-344419-3wcfpw2z.txt summary: Interpretation Some minority ethnic groups have a higher risk of confirmed SARS-CoV-2 infection in the UK Biobank study which was not accounted for by differences in socioeconomic conditions, measured baseline health or behavioural risk factors. In a large population-based cohort study in the UK, we found an increased risk of developing confirmed SARS-CoV-2 infection in Black, South Asian and White Irish ethnic groups. The ideal approach to estimating infection risk across different social groups is to analyse data from a cohort study, but most existing cohort studies which include detailed information about ethnicity and socioeconomic position are subject to long delays in data being available for analysis and are too small to provide useful estimates of infection risk. We therefore aimed to investigate the relationship between ethnicity, socioeconomic position and the risk of having confirmed SARS-CoV-2 infection in the population-based UK Biobank study. Several ethnic minority groups had a higher risk of both being diagnosed and testing positive as an inpatient with laboratory-confirmed SARS-CoV-2 infection in the UK Biobank study. abstract: Background Understanding of the role of ethnicity and socioeconomic position in the risk of developing SARS-CoV-2 infection is limited. We investigated this in the UK Biobank study. Methods The UK Biobank study recruited 40-70 year olds in 2006-2010 from the general population, collecting information about self-defined ethnicity and socioeconomic variables (including Townsend deprivation index and educational attainment). SARS-CoV-2 test results from Public Health England were linked to baseline UK Biobank data. Poisson regression with robust standard errors was used to assess risk ratios (RRs) between the exposures and dichotomous variables for: being tested, having a positive test and testing positive in hospital. We also investigated whether ethnicity and socioeconomic position were associated with having a positive test amongst those tested. We adjusted for covariates including age, sex, social variables (including healthcare work and household size), behavioural risk factors and baseline health. Findings Among 428,225 participants, 1,474 had been tested and 669 had tested positive between 16 March and 13 April 2020. Black, south Asian and white Irish people were more likely to have confirmed infection (RR 4.01 (95%CI 2.92-5.12); RR 2.11 (95%CI 1.43-3.10); and RR 1.60 (95% CI 1.08-2.38) respectively) and were more likely to be hospitalised compared to White British. While they were more likely to be tested, they were also more likely to test positive. Adjustment for baseline health and behavioural risk factors led to little change, with only modest attenuation when accounting for socioeconomic variables. Area socioeconomic deprivation and having no qualifications were consistently associated with a higher risk of confirmed infection (RR 1.91 (95%CI 1.53-2.38); and RR 2.26 (95%CI 1.76-2.90) respectively). Interpretation Some minority ethnic groups have a higher risk of confirmed SARS-CoV-2 infection in the UK Biobank study which was not accounted for by differences in socioeconomic conditions, measured baseline health or behavioural risk factors. An urgent response to addressing these elevated risks is required. Funding Medical Research Council, Chief Scientist Office. url: https://doi.org/10.1101/2020.04.22.20075663 doi: 10.1101/2020.04.22.20075663 id: cord-328325-yonbkrwe author: Nielsen, Sandra C. A. title: B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date: 2020-05-06 words: 3377.0 sentences: 180.0 pages: flesch: 57.0 cache: ./cache/cord-328325-yonbkrwe.txt txt: ./txt/cord-328325-yonbkrwe.txt summary: Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of V genes, and extensive activation of IgG and IgA subclasses without significant somatic mutation. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Sequences convergent to known SARS-CoV-speci c antibody IGH sequences13 were identi ed in one COVID-19 patient (7453-D2) but were not detected in the HHC samples (Fig. 4c) . abstract: During virus infection B cells are critical for the production of antibodies and protective immunity. Establishment of a diverse antibody repertoire occurs by rearrangement of germline DNA at the immunoglobulin heavy and light chain loci to encode the membrane-bound form of antibodies, the B cell antigen receptor. Little is known about the B cells and antigen receptors stimulated by the novel human coronavirus SARS-CoV-2. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of V genes, and extensive activation of IgG and IgA subclasses without significant somatic mutation. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. A shared convergent B cell clonotype in SARS-CoV-2 infected patients was previously seen in patients with SARS. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32702737/ doi: 10.21203/rs.3.rs-27220/v1 id: cord-312275-plqturzi author: Nielsen, Sandra C.A. title: Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date: 2020-09-03 words: 2624.0 sentences: 219.0 pages: flesch: 65.0 cache: ./cache/cord-312275-plqturzi.txt txt: ./txt/cord-312275-plqturzi.txt summary: To directly test the 154 antigen specificity of these convergent clones, we expressed human IgG1 monoclonal antibodies 155 (mAbs 2A and 4A, Table S2 ) from two COVID-19 convergence groups in two patients 156 following paired immunoglobulin heavy and light chain sequencing of single B cells with the immunosorbent assay (ELISA) testing, both mAbs bound SARS-CoV-2 spike and S1 domain, 160 but not the RBD or nucleocapsid ( Figure 3C ). To evaluate whether such in silico IGH 185 sequence comparisons could predict the serological responses of patients, we tested the plasma 186 samples from COVID-19 patients in SARS-CoV RBD ELISAs and detected cross-reactivity in 187 five of the 13 patients ( Figure 3F) or RBD antigens will also stimulate B cells expressing these common antibody types in a 214 significant fraction of the human population. abstract: B cells are critical for the production of antibodies and protective immunity to viruses. Here we show that patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) display early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify convergence of antibody sequences across SARS-CoV-2 infected patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain (RBD). These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses. url: https://www.sciencedirect.com/science/article/pii/S1931312820305035?v=s5 doi: 10.1016/j.chom.2020.09.002 id: cord-276358-so390gp4 author: Nieto-Torres, Jose L. title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome date: 2015-11-30 words: 7169.0 sentences: 396.0 pages: flesch: 49.0 cache: ./cache/cord-276358-so390gp4.txt txt: ./txt/cord-276358-so390gp4.txt summary: title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome In this report, we demonstrate that SARS-CoV E protein forms protein–lipid channels in ERGIC/Golgi membranes that are permeable to calcium ions, a highly relevant feature never reported before. Previously, we reported that SARS-CoV E protein showed mild selectivity for cations (Na þ and K þ ) when reconstituted in ERGIC/ Golgi membranes, mostly conferred by the negative charges of the lipids (Verdia-Baguena et al., 2012 . Synthetic peptides representing the full-length SARS-CoV E protein, or its transmembrane domain (amino acids 7-38) containing point mutations that inhibited ion channel activity (N15A and V25F), were generated by standard phase synthesis and purified by HPLC, as previously described (Verdia-Baguena et al., 2012) . Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis abstract: Abstract Severe acute respiratory syndrome coronavirus (SARS-CoV) envelope (E) protein is a viroporin involved in virulence. E protein ion channel (IC) activity is specifically correlated with enhanced pulmonary damage, edema accumulation and death. IL-1β driven proinflammation is associated with those pathological signatures, however its link to IC activity remains unknown. In this report, we demonstrate that SARS-CoV E protein forms protein–lipid channels in ERGIC/Golgi membranes that are permeable to calcium ions, a highly relevant feature never reported before. Calcium ions together with pH modulated E protein pore charge and selectivity. Interestingly, E protein IC activity boosted the activation of the NLRP3 inflammasome, leading to IL-1β overproduction. Calcium transport through the E protein IC was the main trigger of this process. These findings strikingly link SARS-CoV E protein IC induced ionic disturbances at the cell level to immunopathological consequences and disease worsening in the infected organism. url: https://doi.org/10.1016/j.virol.2015.08.010 doi: 10.1016/j.virol.2015.08.010 id: cord-321673-v5o49ees author: Nieto-Torres, Jose L. title: Relevance of Viroporin Ion Channel Activity on Viral Replication and Pathogenesis date: 2015-07-03 words: 8398.0 sentences: 451.0 pages: flesch: 38.0 cache: ./cache/cord-321673-v5o49ees.txt txt: ./txt/cord-321673-v5o49ees.txt summary: Modification of host-cell ionic content is a significant issue for viruses, as several viral proteins displaying ion channel activity, named viroporins, have been identified. Noticeably, these proteins oligomerize in cell membranes to form ion conductive pores, which generally display mild ion selectivity, indicating that viroporins do not show preference for particular ionic species. Influenza viruses lacking M2 ion conductivity, presented either a 15-fold reduction of viral titer in tissue culture [74] , or showed a standard production in cell culture but a restricted growth in the nasal turbinates of infected mice [75] . Several compounds inhibit viroporin ion conductivity in artificial lipid membranes, and some of them efficiently reduce viral growth when administered to infected cells. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells abstract: Modification of host-cell ionic content is a significant issue for viruses, as several viral proteins displaying ion channel activity, named viroporins, have been identified. Viroporins interact with different cellular membranes and self-assemble forming ion conductive pores. In general, these channels display mild ion selectivity, and, eventually, membrane lipids play key structural and functional roles in the pore. Viroporins stimulate virus production through different mechanisms, and ion channel conductivity has been proved particularly relevant in several cases. Key stages of the viral cycle such as virus uncoating, transport and maturation are ion-influenced processes in many viral species. Besides boosting virus propagation, viroporins have also been associated with pathogenesis. Linking pathogenesis either to the ion conductivity or to other functions of viroporins has been elusive for a long time. This article summarizes novel pathways leading to disease stimulated by viroporin ion conduction, such as inflammasome driven immunopathology. url: https://www.ncbi.nlm.nih.gov/pubmed/26151305/ doi: 10.3390/v7072786 id: cord-266896-unb9yvjr author: Nihei, Yoshihito title: Continuous extracorporeal treatments in a dialysis patient with COVID-19 date: 2020-10-04 words: 2821.0 sentences: 127.0 pages: flesch: 44.0 cache: ./cache/cord-266896-unb9yvjr.txt txt: ./txt/cord-266896-unb9yvjr.txt summary: Inflammatory cytokine storm caused by SARS-CoV-2 infection has been reported to play a central role in COVID-19; therefore, treatments for suppressing cytokines, including extracorporeal treatments, are considered to be beneficial. The cytokine storm caused by SARS-CoV-2 infection, primarily characterised by elevated plasma concentrations of interleukin 6 (IL-6), plays a central role in COVID-19 [2] ; therefore, its suppression is considered a key treatment approach in patients with COVID-19. Especially, CHDF is reported to continually suppress inflammatory cytokines and has been used in critically ill patients, including those with septic shock, ARDS and infections with viruses such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus [5] . We herein present a patient on PD who became critically ill due to COVID-19 and was treated with several extracorporeal treatments including PE, PMX-DHP and CHDF to suppress the cytokine storm. abstract: The coronavirus disease 2019 (COVID-19) pandemic is now a major global health threat. More than half a year have passed since the first discovery of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2), no effective treatment has been established especially in intensive care unit. Inflammatory cytokine storm caused by SARS-CoV-2 infection has been reported to play a central role in COVID-19; therefore, treatments for suppressing cytokines, including extracorporeal treatments, are considered to be beneficial. However, until today the efficacy of removing cytokines by extracorporeal treatments in patients with COVID-19 is unclear. Herein, we report our experience with a 66-year-old male patient undergoing maintenance peritoneal dialysis who became critically ill with COVID-19 and underwent several extracorporeal treatment approaches including plasma exchange, direct hemoperfusion using a polymyxin B-immobilized fiber column and continuous hemodiafiltration. Though the patient developed acute respiratory distress syndrome (ARDS) repeatedly and subacute cerebral infarction and finally died for respiratory failure on day 30 after admission, these attempts appeared to dampen the cytokine storm based on the observed decline in serum IL-6 levels and were effective against ARDS and secondary haemophagocytic lymphohistiocytosis. This case suggests the significance of timely initiation of extracorporeal treatment approaches in critically ill patients with COVID-19. url: https://doi.org/10.1007/s13730-020-00538-x doi: 10.1007/s13730-020-00538-x id: cord-335293-pac6wbgz author: Nijman, Ruud G. title: Pediatric Inflammatory Multisystem Syndrome: Statement by the Pediatric Section of the European Society for Emergency Medicine and European Academy of Pediatrics date: 2020-08-28 words: 3516.0 sentences: 175.0 pages: flesch: 45.0 cache: ./cache/cord-335293-pac6wbgz.txt txt: ./txt/cord-335293-pac6wbgz.txt summary: A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome—temporally associated with SARS-CoV-2 (PIMS-TS). A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS). This statement aims to -provide information about the Pediatric Inflammatory Multisystem Syndrome temporally associated with SARS-CoV-2 (PIMS-TS); -give initial guidance on the clinical assessment and management of children suspected of this new condition for health care professionals dealing with acutely unwell children; -point out useful resources on the recognition and management of these children. The initial guidance from the Royal College of Pediatrics and Child Health in the United Kingdom provided a case definition and called this emerging disease entity the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS) (28) . abstract: A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome—temporally associated with SARS-CoV-2 (PIMS-TS). There appears to be a wide spectrum of signs and symptoms with varying degrees of severity, including a toxic shock like presentation with hypovolaemia and shock, and a Kawasaki-like presentation with involvement of the coronary arteries. Most of these children have evidence of a previous infection with SARS-CoV-2, or a history of significant exposure, but not all. Limited data exist on the incidence of PIMS-TS, but it remains a rare condition. Early recognition and escalation of care is important to prevent the development of serious sequelae, such as coronary artery aneurysms. Clinicians assessing febrile children in primary and secondary care should include PIMS-TS in their differential diagnoses. In children fulfilling the case definition, additional investigations should be undertaken to look for evidence of inflammation and multiorgan involvement. Suspected cases should be discussed with experts in pediatric infectious diseases at an early stage, and advice should be sought from critical care in more severe cases early. There is limited consensus on treatment; but most children have been treated with immunoglobulins or steroids, and with early consideration of biologicals such anti-TNF and anti-IL1 agents. Treatment should ideally be within the context of controlled treatment trials. Clinicians are encouraged to document and share their cases using research registries. url: https://doi.org/10.3389/fped.2020.00490 doi: 10.3389/fped.2020.00490 id: cord-297691-w4cdfwv0 author: Nikaeen, Ghazal title: Application of nanomaterials in treatment, anti-infection and detection of coronaviruses date: 2020-05-07 words: 4537.0 sentences: 228.0 pages: flesch: 39.0 cache: ./cache/cord-297691-w4cdfwv0.txt txt: ./txt/cord-297691-w4cdfwv0.txt summary: In this special report, different strategies of using nanoparticles in dealing with coronaviruses are discussed in three parts: applications in nano-based vaccines, antiviral activity and development of diagnostic sensors. Meanwhile, as nanoparticles have been proven to have immunostimulatory effects [28] , a great deal of attention has been given to development of nano-based therapeutic agent or vaccines against different types of coronaviruses. evaluated the protective immune response stimulated by the administration of gold nanoparticles (Au NPs) conjugated with a type of coronavirus known as swine transmissible gastroenteritis virus (TGEV) in immunized mice and rabbits [29] . Recent applications of nanoparticles in developing coronaviruses sensors based on different analytical techniques and related limit of detections. The above studies on the recent applications of NPs in developing sensors based on different analytical techniques for coronaviruses and their related limit of detections are compared in Table 3 . abstract: Nanotechnology and nanomedicine have excellent potential in dealing with a range of different health problems, including viruses, which are considered to be a serious challenge in the medical field. Application of nanobiotechnology could represent a new avenue for the treatment or disinfection of viruses. There is increasing concern regarding the control of coronaviruses, among these, Middle East respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus-2 are well known and dangerous examples. This article aims to provide an overview of recent studies on the effectiveness of nanoparticles as diagnostic or antiviral tools against coronaviruses. The possibilities of effectively using nanomaterials as vaccines and nanosensors in this field are also presented. url: https://www.ncbi.nlm.nih.gov/pubmed/32378459/ doi: 10.2217/nnm-2020-0117 id: cord-282604-xp71rkxc author: Nikolaev, EN title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date: 2020-05-25 words: 2181.0 sentences: 114.0 pages: flesch: 53.0 cache: ./cache/cord-282604-xp71rkxc.txt txt: ./txt/cord-282604-xp71rkxc.txt summary: title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. We have performed a pilot study on nasopharynx epithelial swabs already collected from patients with CODIV-19 for RT-qPCR and showed confident identification of the N protein of the SARS CoV-2 virus by mass-spectrometry with the use of a very basic sample preparation procedure. Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients abstract: Detection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids. url: https://doi.org/10.1101/2020.05.24.113043 doi: 10.1101/2020.05.24.113043 id: cord-340992-88t1c0zs author: Nikolai, Lea A title: Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date: 2020-09-03 words: 3092.0 sentences: 193.0 pages: flesch: 44.0 cache: ./cache/cord-340992-88t1c0zs.txt txt: ./txt/cord-340992-88t1c0zs.txt summary: Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection abstract: While successful containment measures of COVID-19 in China and many European countries have led to flattened curves, case numbers are rising dramatically in other countries, with the emergence of a second wave expected. Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The data addressed here show that characteristics of asymptomatic and presymptomatic infection are not identical. Younger age correlates strongly with asymptomatic and mild infections, and children as hidden drivers. The estimated proportion of asymptomatic infections ranges from 18% to 81%. The current perception of asymptomatic infections does not provide clear guidance for public-health measures. Asymptomatic infections will be a key contributor in COVID-19 spread. Asymptomatic cases should be reported in official COVID-19 statistics. url: https://www.sciencedirect.com/science/article/pii/S1201971220307062?v=s5 doi: 10.1016/j.ijid.2020.08.076 id: cord-336119-8g37xsys author: Nimgampalle, Mallikarjuna title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 words: 5464.0 sentences: 283.0 pages: flesch: 50.0 cache: ./cache/cord-336119-8g37xsys.txt txt: ./txt/cord-336119-8g37xsys.txt summary: Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . abstract: Recently Chloroquine and its derivative Hydroxychloroquine have garnered enormous interest amongst the clinicians and health authorities’ world over as a potential treatment to contain COVID-19 pandemic. The present research aims at investigating the therapeutic potential of Chloroquine and its potent derivative Hydroxychloroquine against SARS-CoV-2 viral proteins. At the same time screening was performed for some chemically synthesized derivatives of Chloroquine and compared their binding efficacy with chemically synthesized Chloroquine derivatives through in silico approaches. For the purpose of the study, some essential viral proteins and enzymes were selected that are implicated in SARS-CoV-2 replication and multiplication as putative drug targets. Chloroquine, Hydroxychloroquine, and some of their chemically synthesized derivatives, taken from earlier published studies were selected as drug molecules. We have conducted molecular docking and related studies between Chloroquine and its derivatives and SARS-CoV-2 viral proteins, and the findings show that both Chloroquine and Hydroxychloroquine can bind to specific structural and non-structural proteins implicated in the pathogenesis of SARS-CoV-2 infection with different efficiencies. Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. These findings bring into light another possible mechanism of action of Chloroquine and Hydroxychloroquine and also pave the way for further drug repurposing and remodeling. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1782265 doi: 10.1080/07391102.2020.1782265 id: cord-355655-l684uy4h author: Ning, Ling title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report date: 2020-05-08 words: 1426.0 sentences: 99.0 pages: flesch: 49.0 cache: ./cache/cord-355655-l684uy4h.txt txt: ./txt/cord-355655-l684uy4h.txt summary: title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report This case states the importance of close monitoring of the concentration of cyclosporine in patients treated with lopinavir/ritonavir; the routine treatment of corticosteroid can be continued. Further data are needed to achieve better understanding of the impact of immunosuppressive therapy on the clinical presentation, severity, and outcome of SARS‐CoV‐2 infections in solid organ transplant recipients. Laboratory results on day 6 of hospitalization showed improved creatinine level and hyponatremia; again, the sputum and oropharyngeal swab specimens tested negative on RT-PCR for SARS-CoV-2. Methylprednisolone was routinely used as baseline immunosuppression in this case, although its use for the treatment of SARS-CoV-2 infection remains controversial. 15 No clinical data exist to indicate that net benefit is derived from corticosteroids in the treatment of respiratory infection due to coronavirus included SARS-CoV and MERS-CoV. Novel coronavirus (SARS-CoV-2) infection in a renal transplant recipient: Case report abstract: An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (SARS‐CoV‐2) started in Wuhan, China, with cases now confirmed in multiple countries. The clinical course of patients remains to be fully characterized, clinical presentation ranges from asymptomatic infection to acute respiratory distress syndrome and acute renal failure, and no pharmacological therapies of proven efficacy yet exist. We report a case of SARS‐CoV‐2 infection in a renal transplant recipient with excellent outcome. This case states the importance of close monitoring of the concentration of cyclosporine in patients treated with lopinavir/ritonavir; the routine treatment of corticosteroid can be continued. This is a rare report of SARS‐CoV‐2 infection in a renal transplant recipient. Further data are needed to achieve better understanding of the impact of immunosuppressive therapy on the clinical presentation, severity, and outcome of SARS‐CoV‐2 infections in solid organ transplant recipients. url: https://doi.org/10.1111/ajt.15897 doi: 10.1111/ajt.15897 id: cord-320350-zeeozmm9 author: Nisoli, Enzo title: COVID-19 and Hartnup disease: an affair of intestinal amino acid malabsorption date: 2020-07-20 words: 2496.0 sentences: 140.0 pages: flesch: 44.0 cache: ./cache/cord-320350-zeeozmm9.txt txt: ./txt/cord-320350-zeeozmm9.txt summary: We hypothesize that SARS-CoV-2 spike protein, binding to intestinal angiotensin-converting enzyme 2, negatively regulates the absorption of neutral amino acids, and this could explain not only the GI, but also systemic disturbances in COVID-19. Altered composition of the gut microbiota (as a consequence of impaired amino acid transport and reduced secretion of antimicrobial peptides by Paneth cells in the small intestine) and changes in innate immunity contribute to the colitis phenotype observed in ACE2 knockout mice [17] . Based on clinical observations and basic research, we hypothesise that, in response to the SARS-CoV-2 binding to intestinal ACE2, the absorption of neutral amino acids is negatively regulated in COVID-19 patients. In malnourished patients or conditions of intestinal amino acid malabsorption, as in the COVID-19 or Hartnup patients, the adaptive immune response cannot be effectively initiated because the absorption of essential energy substrates is impaired by SARS-CoV-2 binding to ACE2. abstract: Since the outbreak of COVID-19, clinicians have tried every effort to fight the disease, and multiple drugs have been proposed. However, no proven effective therapies currently exist, and different clinical phenotypes complicate the situation. In clinical practice, many severe or critically ill COVID-19 patients developed gastrointestinal (GI) disturbances, including vomiting, diarrhoea, or abdominal pain, even in the absence of cough and dyspnea. Understanding the mechanism of GI disturbances is warranted for exploring better clinical care for COVID-19 patients. With evidence collected from clinical studies on COVID-19 and basic research on a rare genetic disease (i.e., Hartnup disorder), we put forward a novel hypothesis to elaborate an effective nutritional therapy. We hypothesize that SARS-CoV-2 spike protein, binding to intestinal angiotensin-converting enzyme 2, negatively regulates the absorption of neutral amino acids, and this could explain not only the GI, but also systemic disturbances in COVID-19. Amino acid supplements could be recommended. Level of evidence No level of evidence: Hypothesis article. url: https://doi.org/10.1007/s40519-020-00963-y doi: 10.1007/s40519-020-00963-y id: cord-314386-cxq9v218 author: Nitsche, Andreas title: SARS Coronavirus Detection date: 2004-07-17 words: 1904.0 sentences: 96.0 pages: flesch: 55.0 cache: ./cache/cord-314386-cxq9v218.txt txt: ./txt/cord-314386-cxq9v218.txt summary: We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. To improve the ability to detect SARS-CoV safely and reduce the risk of eliciting false-negative results caused by genome sequence variations, we established three individual real-time RT-PCR assays. Target sequences were chosen by using the following criteria: 1) the regions are distributed over the whole genome, including the nonstructural polyprotein 1a and 1ab genes and the spike glycoprotein gene (Table 1) ; 2) the regions are highly conserved among the 89, 90, and 100 respective sequences available in public sequence databases; 3) the regions are suitable for the design of a real-time RT-PCR assay; and 4) the designed primers, 5′-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from http://www.ncbi.nlm.nih.gov/BLAST/). abstract: We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. The assays consider all currently available SARS-CoV sequences and are optimized for two prominent real-time PCR platforms. url: https://www.ncbi.nlm.nih.gov/pubmed/15324554/ doi: 10.3201/eid1007.030678 id: cord-252015-9oiwcn8q author: Niu, Alex title: COVID-19 in allogeneic stem cell transplant: high false-negative probability and role of CRISPR and convalescent plasma date: 2020-06-15 words: 1278.0 sentences: 82.0 pages: flesch: 49.0 cache: ./cache/cord-252015-9oiwcn8q.txt txt: ./txt/cord-252015-9oiwcn8q.txt summary: Shortly thereafter, RT-PCR/CRISPR was performed on a blood sample collected on hospital day 36 for clinical purposes and demonstrated strong detection of SARS-CoV-2 RNA (Fig. 1c) . Here, we present two cases of ASCT recipients who presented with respiratory illnesses, initially testing negative for SARS-CoV-2 with conventional RT-PCR, then positive with the more sensitive RT-PCR/CRISPR technique. Our findings suggest that ASCT recipients with negative nasopharyngeal SARS-CoV-2 RT-PCR, but evidence of lower respiratory tract disease, might indeed have COVID-19 that can be detected using a CRISPR-based platform. While safety concerns with performing bronchoscopy remain high with this infection, and COVID-19specific treatments depend on securing a positive test, it may be beneficial to pursue diagnosis with other tissue sources, such as whole blood or plasma. In conclusion, early diagnosis and treatment of COVID-19 is crucial in ASCT recipients, and evaluation regarding the use of other tissue sources for detection of SARS-CoV-2 along with multimodality therapy is required in the continual evolution of this pandemic. abstract: nan url: https://doi.org/10.1038/s41409-020-0972-8 doi: 10.1038/s41409-020-0972-8 id: cord-306508-xpwluph5 author: Nkengasong, John title: China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response date: 2020-01-27 words: 1452.0 sentences: 68.0 pages: flesch: 56.0 cache: ./cache/cord-306508-xpwluph5.txt txt: ./txt/cord-306508-xpwluph5.txt summary: It shows a marked departure from public health policies that, during the SARS outbreak in 2002, contributed to the deaths of 774 people, spread of the disease to 37 countries and an economic loss of over US$40 billion over a period of 6 months 6, 7 . As of 20 January 2020, the Chinese government reported 136 new cases of infection with this virus over the weekend that were spreading to other cities in the country, bringing the total cumulative cases worldwide to over 200 (ref. There is also a need for closer coordination of efforts between the Africa Centres for Disease Control and Prevention, based in Addis Ababa, Ethiopia, and China CDC for sharing information on potential people suspected of being infected who are traveling from China to Africa. China''s political openness to reporting in a timely manner and the emergence of the novel virus 2019-nCoV, coupled with the rapid sequencing and public sharing of the sequences, represents a new dawn for global health security and international health diplomacy. abstract: The strengthening of the Chinese Center for Disease Control and Prevention has been a turning point in outbreak responses in the area. This represents very welcome progress and development for global health security and diplomacy. url: https://www.ncbi.nlm.nih.gov/pubmed/31988464/ doi: 10.1038/s41591-020-0771-1 id: cord-356217-igm2t7md author: Noda, Sakura title: Severe COVID-19 initially presenting as mesenteric adenopathy date: 2020-10-10 words: 1597.0 sentences: 87.0 pages: flesch: 40.0 cache: ./cache/cord-356217-igm2t7md.txt txt: ./txt/cord-356217-igm2t7md.txt summary: We report a case of COVID-19 in a healthy teenager who initially presented with isolated mesenteric adenopathy, typically a self-limited illness, which progressed to severe illness requiring intensive care before complete recovery. A generally healthy, immunized, non-obese White 17-yearold boy presented to an outside emergency department (ED) with 3 days of initially moderate progressing to severe abdominal pain focused in the right lower quadrant, fever as high as 103°F, and vomiting without diarrhea. Although we did not obtain tissue sampling to prove that the mesenteric adenopathy was secondary to COVID-19, the boy eventually developed chest CT findings and severe hyperinflammatory response consistent with COVID-19, tested positive for SARS-CoV-2 by PCR from sputum, and recovered with primarily supportive care. This case report describes a severe case of COVID-19 in a previously healthy teenage patient who initially presented with gastrointestinal symptoms and isolated acute mesenteric adenopathy on imaging. abstract: Coronavirus disease 2019 (COVID-19) can present with abdominal pain in children and adults. Most imaging findings have been limited to characteristic lung findings, as well as one report of bowel-ischemia-related findings in adults. We report a case of COVID-19 in a healthy teenager who initially presented with isolated mesenteric adenopathy, typically a self-limited illness, which progressed to severe illness requiring intensive care before complete recovery. The boy tested negative for COVID-19 twice by polymerase chain reaction (PCR) from upper respiratory swabs before sputum PCR resulted positive. A high index of suspicion should be maintained for COVID-19 given the continued emergence of new manifestations of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33037889/ doi: 10.1007/s00247-020-04789-9 id: cord-348209-rkkhv4mw author: Noerz, Dominik title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 words: 1643.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-348209-rkkhv4mw.txt txt: ./txt/cord-348209-rkkhv4mw.txt summary: title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 30 system, a fully automated device performing extraction and real-time PCR. Due to its random-access workflow concept and rapid time-to-39 result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 40 diagnostics for urgent clinical samples in the hospital setting. For the assay presented in this study, we used a fully automated random-access platform for molecular 56 diagnostics, handling everything from extraction, amplification, signal detection to reporting of results 57 (10). Evaluation of a quantitative RT-PCR assay for 180 the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system abstract: The ongoing SARS-CoV-2 pandemic presents a unique challenge for diagnostic laboratories around the world. Automation of workflows in molecular diagnostics is instrumental for coping with the large number of tests ordered by clinicians, as well as providing fast-tracked rapid testing for urgent cases. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. url: https://doi.org/10.1101/2020.04.07.20056234 doi: 10.1101/2020.04.07.20056234 id: cord-257994-i6hut28h author: Nogee, Daniel title: Covid-19 and the N95 respirator shortage: Closing the gap date: 2020-04-13 words: 592.0 sentences: 36.0 pages: flesch: 35.0 cache: ./cache/cord-257994-i6hut28h.txt txt: ./txt/cord-257994-i6hut28h.txt summary: Due to extreme shortages of personal protective equipment caused by the COVID-19 pandemic, many healthcare workers will be forced to recycle protective masks intended for disposal after a single use. We propose investigating the use of ultraviolet germicidal irradiation to sterilize masks of SARS-CoV-2 for safer reuse. The Centers for Disease Control and Prevention has published guidelines for optimizing supply to extend stocks through limiting use, reuse at the patient and provider levels, and alternative personal protective equipment recommendations. Although further work will be needed to determine dosages of UVGI to effectively sterilize SARS-CoV-2 contaminated FFRs, UVGI provides a potential avenue for greatly extending the limited FFR supply in the face of the ongoing COVID-19 pandemic in a simple, cost-effective, and rapidly deployable manner. A pandemic influenza preparedness study: use of energetic methods to decontaminate filtering facepiece respirators contaminated with H1N1 aerosols and droplets Ultraviolet germicidal irradiation of influenza-contaminated N95 filtering facepiece respirators No financial support was provided relevant to this article. abstract: Due to extreme shortages of personal protective equipment caused by the COVID-19 pandemic, many healthcare workers will be forced to recycle protective masks intended for disposal after a single use. We propose investigating the use of ultraviolet germicidal irradiation to sterilize masks of SARS-CoV-2 for safer reuse. url: https://doi.org/10.1017/ice.2020.124 doi: 10.1017/ice.2020.124 id: cord-294910-gnc04ax1 author: Nogueira, Paulo Jorge title: The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases date: 2020-07-24 words: 4935.0 sentences: 251.0 pages: flesch: 42.0 cache: ./cache/cord-294910-gnc04ax1.txt txt: ./txt/cord-294910-gnc04ax1.txt summary: The risk factors for increased odds of death by COVID-19 were: sex (male: OR = 1.47, ref = female), age ((56–60) years, OR = 6.01; (61–65) years, OR = 10.5; (66–70) years, OR = 20.4; (71–75) years, OR = 34; (76–80) years, OR = 50.9; (81–85) years, OR = 70.7; (86–90) years, OR = 83.2; (91–95) years, OR = 91.8; (96–104) years, OR = 140.2, ref = (0–55)), Cardiac disease (OR = 2.86), Kidney disorder (OR = 2.95), and Neuromuscular disorder (OR = 1.58), while condition (None (absence of precondition); OR = 0.49) was associated with a reduced chance of dying after adjusting for other variables of interest. The data retrieved include individuals'' demographic characteristics (age, sex, region), COVID-19 disease information (death, recovery, still in treatment, hospitalization, intensive care, respiratory support), and preconditions (Asthma, Cancer, Cardiac disease, Hematological disorder, Diabetes, HIV and other immune deficiency, Kidney disorder, Liver disorder, Neuromuscular disorder, Other precondition and None (absence of precondition)). abstract: Background: It is essential to study the effect of potential co-factors on the risk of death in patients infected by COVID-19. The identification of risk factors is important to allow more efficient public health and health services strategic interventions with a significant impact on deaths by COVID-19. This study aimed to identify factors associated with COVID-19 deaths in Portugal. Methods: A national dataset with the first 20,293 patients infected with COVID-19 between 1 January and 21 April 2020 was analyzed. The primary outcome measure was mortality by COVID-19, measured (registered and confirmed) by Medical Doctors serving as health delegates on the daily death registry. A logistic regression model using a generalized linear model was used for estimating Odds Ratio (OR) with 95% confidence intervals (95% CI) for each potential risk indicator. Results: A total of 502 infected patients died of COVID-19. The risk factors for increased odds of death by COVID-19 were: sex (male: OR = 1.47, ref = female), age ((56–60) years, OR = 6.01; (61–65) years, OR = 10.5; (66–70) years, OR = 20.4; (71–75) years, OR = 34; (76–80) years, OR = 50.9; (81–85) years, OR = 70.7; (86–90) years, OR = 83.2; (91–95) years, OR = 91.8; (96–104) years, OR = 140.2, ref = (0–55)), Cardiac disease (OR = 2.86), Kidney disorder (OR = 2.95), and Neuromuscular disorder (OR = 1.58), while condition (None (absence of precondition); OR = 0.49) was associated with a reduced chance of dying after adjusting for other variables of interest. Conclusions: Besides age and sex, preconditions justify the risk difference in mortality by COVID-19. url: https://doi.org/10.3390/jcm9082368 doi: 10.3390/jcm9082368 id: cord-316260-1t3ifsfi author: Nogueira-de-Almeida, Carlos Alberto title: COVID-19 and obesity in childhood and adolescence: A clinical review()() date: 2020-08-04 words: 7974.0 sentences: 450.0 pages: flesch: 43.0 cache: ./cache/cord-316260-1t3ifsfi.txt txt: ./txt/cord-316260-1t3ifsfi.txt summary: In severe acute respiratory syndrome coronavirus 2 infection, these organic changes from obesity may increase the need for ventilatory assistance, risk of thromboembolism, reduced glomerular filtration rate, changes in the innate and adaptive immune response, and perpetuation of the chronic inflammatory response. 3--6 The present review aims to identify the factors that contribute to the increase in the susceptibility and severity of COVID-19 in obese children and adolescents, and its health consequences, to collaborate for better clinical care of these patients. The three main risk factors that link obesity to COVID-19 demonstrated for adults 52 are also present among children and adolescents: chronic subclinical inflammation, impaired immune response, and underlying cardiorespiratory diseases. In conclusion, obesity in childhood and adolescence can be considered a risk factor for greater susceptibility and severity of COVID-19 and is associated with nutritional, cardiac, respiratory, renal, and immunological alterations, which may potentiate the complications of SARS-CoV-2 infection. abstract: OBJECTIVE: To identify factors that contribute to the increased susceptibility and severity of COVID-19 in obese children and adolescents, and its health consequences. SOURCES: Studies published between 2000 and 2020 in the PubMed, MEDLINE, Scopus, SciELO, and Cochrane databases. SUMMARY OF FINDINGS: Obesity is a highly prevalent comorbidity in severe cases of COVID-19 in children and adolescents; social isolation may lead to increase fat accumulation. Excessive adipose tissue, deficit in lean mass, insulin resistance, dyslipidemia, hypertension, high levels of proinflammatory cytokines, and low intake of essential nutrients are factors that compromise the functioning of organs and systems in obese individuals. These factors are associated with damage to immune, cardiovascular, respiratory, and urinary systems, along with modification of the intestinal microbiota (dysbiosis). In severe acute respiratory syndrome coronavirus 2 infection, these organic changes from obesity may increase the need for ventilatory assistance, risk of thromboembolism, reduced glomerular filtration rate, changes in the innate and adaptive immune response, and perpetuation of the chronic inflammatory response. CONCLUSIONS: The need for social isolation can have the effect of causing or worsening obesity and its comorbidities, and pediatricians need to be aware of this issue. Facing children with suspected or confirmed COVID-19, health professionals should 1) diagnose excess weight; 2) advise on health care in times of isolation; 3) screen for comorbidities, ensuring that treatment is not interrupted; 4) measure levels of immunonutrients; 5) guide the family in understanding the specifics of the situation; and 6) refer to units qualified to care for obese children and adolescents when necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/32768388/ doi: 10.1016/j.jped.2020.07.001 id: cord-349907-dwhyx97y author: Noh, Ji Yeong title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 words: 3274.0 sentences: 138.0 pages: flesch: 62.0 cache: ./cache/cord-349907-dwhyx97y.txt txt: ./txt/cord-349907-dwhyx97y.txt summary: Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] . abstract: Since severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) share similar characteristics with respect to clinical signs, etiology, and transmission, methods for a rapid and accurate differential diagnosis are important. Therefore, the aim of this study was to develop a duplex real-time reverse transcription (RT)-PCR method for the simultaneous detection of these viruses. Primers and probes that target the conserved spike S2 region of human SARS-CoV, MERS-CoV, and their related bat CoVs were designed. The results of real-time RT-PCR showed specific reactions for each virus with adequate detection limits of 50–100 copies/mL and 5–100 copies/mL using pUC57-SARS-pS2 (a template for SARS-CoV) and pGEM-MERS-S2 (a template for MERS-CoV), respectively. In addition, this real-time RT-PCR system was able to detect the target viruses SARS-like bat CoV and MERS-CoV in bat fecal samples and sputum of MERS patients, respectively. Therefore, this newly developed real-time RT-PCR method is expected to detect not only SARS-CoV and MERS-CoV in humans but also several bat CoVs that are closely related to these viruses in bats. url: https://doi.org/10.1007/s00705-017-3281-9 doi: 10.1007/s00705-017-3281-9 id: cord-325134-z9n17z72 author: Nolan, Brodie title: Recommendations for emergency departments receiving patients with vital signs absent from paramedics during COVID-19 date: 2020-05-05 words: 1693.0 sentences: 86.0 pages: flesch: 49.0 cache: ./cache/cord-325134-z9n17z72.txt txt: ./txt/cord-325134-z9n17z72.txt summary: Due to their small size and potential to be suspended in the air for prolonged periods, additional precautions are required for health care workers who are exposed to AGMPs. Obtaining an accurate history and COVID-19 risk factors for patients in cardiac arrest is difficult; therefore, we suggest presuming all patients presenting vital signs absent (VSA) to be infectious with COVID-19. The purpose of this study is to provide recommendations to enhance staff and patient safety during COVID-19 by reducing unnecessary exposure to AGMPs for ED staff, paramedics, and other ED patients when receiving patients with VSA. 3 To aid in justification of our recommendations, we present a brief summary of available evidence regarding common AGMPs that occur during cardiopulmonary resuscitation (CPR) and the risks of transmission to health care workers ( Figure 1 ). abstract: nan url: https://doi.org/10.1017/cem.2020.389 doi: 10.1017/cem.2020.389 id: cord-304943-thg4fqi2 author: Noor, Aziz Ullah title: Epidemiology of CoViD-19 Pandemic: Recovery and mortality ratio around the globe date: 2020-05-17 words: 3237.0 sentences: 217.0 pages: flesch: 57.0 cache: ./cache/cord-304943-thg4fqi2.txt txt: ./txt/cord-304943-thg4fqi2.txt summary: SARS-CoV-1 disease was originated in Guangzhou city of China and the start of 2020 was again a challenging year for this country because of extremely contagion 2019-novel coronavirus (2019-nCoV) disease outbreak. Chinese health ministry took immediate action to investigate and control the disease, including quarantine measures, continuous observation of contacts, clinical and epidemiological data collection from infected people and development of diagnostic tools and efficient treatment protocols. 9 Previous study revealed that wet markets of southern China including Wuhan and Guangzhou cities have the greater risk of spreading novel corona viruses, because of wild animal trading and the absence of biosecurity measures. In-vitro studies indicated that Remdesivir has been successful in the termination of viral RNA replication, 30, 32 and showed effectiveness against the MERS-CoV, SARS-CoV and other bat originated coronaviruses. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: Coronavirus Disease 2019 (CoViD-19) is the third type of coronavirus disease after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) that appears in human population from the past two decades. It is highly contagious and rapidly spread in the human population and compelled global public health institutions on high alert. Due to genetic similarity of this novel coronavirus 2019 with bat virus its emergence from bat to humans is possible. The virus survive in the droplets of coughing and sneezing and spread around the large areas through infected person resulting in its rapid spread among people. Clinical symptoms of CoViD-19 include fever, dry cough, dyspnea, loose stool, nausea and vomiting. The present review discuss the origin of CoViD-19, its rapid spread, mortality rate and recoveries ratio around the world. Since its origin from Wuhan, the CoViD-19 spread very rapidly all across the countries, on April 17, 2020 this disease has affected 210 countries of the globe. The data obtained showed over 2.4 million confirmed cases of CoViD-19. Higher mortality rate was found in Algeria and Belgium as 15% and 13.95%, respectively. Lower mortality rate was found in Qatar 0.17% and Singapore 0.2%. Recovery versus deceased ratio showed that recovery was 68, 59 and 35 times higher than the death in Singapore, Qatar and Thailand respectively. It is concluded that 2019-novel corona virus is a zoonotic pathogen similar to MERS and SARS. Therefore, a barrier should be maintained between and across the human, household and wild animals to avoid such pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32582319/ doi: 10.12669/pjms.36.covid19-s4.2660 id: cord-253869-1ouai07v author: Noorimotlagh, Zahra title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies date: 2020-10-02 words: 4151.0 sentences: 204.0 pages: flesch: 44.0 cache: ./cache/cord-253869-1ouai07v.txt txt: ./txt/cord-253869-1ouai07v.txt summary: title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies In the current SARS-CoV-2 pandemic, identification of the chemical and/or physical disinfectant that interrupts the virus transmission routes including human-to-human, spreads via respiratory droplets, and contaminated hands or surfaces are of utmost importance. According to finding of the included studies, the SARS-CoV-2 can be easily spread via two main ways in human-tohuman transmission: (1) respiratory droplet and (2) direct and indirect contact with aerosol infected surfaces. In addition to chemical disinfectant, in the present SR, the reviewed studies reported that the efficiency of physical disinfectant including temperature (56°C, 60°C), gamma irradiation using a cobalt-60 source at 1 Mrad, and disinfection of virus in human plasma by amotosalen and ultraviolet A were in effective for inactivating coronavirus in a short contact time. abstract: Recently, an outbreak of a novel human coronavirus which is referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19) by the World Health Organization (WHO) was identified in Wuhan, China. To help combat the pandemic, a systematic review (SR) was performed to collect all available studies concerning inactivation methods, environmental survival, and control and prevention strategies. A comprehensive literature survey yielded 42 eligible studies which included in the SR. The results confirmed that the WHO recommended two alcohol-based hand rub formulations (ethanol 70–95% and 2-propanol 70–100%) had an efficient virucidal activity in less than 60 s by more and equal 4 log(10) (≥ 99.99) approximately and could be used for disinfection in public health and health-care facilities. The findings indicated that SARS-CoV-1 and SARS-CoV-2 can survive under different environmental conditions between 4 and 72 h approximately. The results also demonstrate that temperature and relative humidity are important factors in the survival of SARS-CoV-2. The main strategies recommended by the WHO to avoid contracting SARS-CoV-2 are hand washing several times in the day and maintaining social distancing with others. It is important to note that the more studies require addressing, the more possible airborne transmission due to the survival of SARS-CoV-2 in aerosols for 3 h approximately. We hope that the results of the present SR can help researchers, health decision-makers, policy-makers, and people for understanding and taking the proper behavior to control and prevent further spread of SARS-CoV-2. url: https://doi.org/10.1007/s11356-020-11060-z doi: 10.1007/s11356-020-11060-z id: cord-293688-g6kag5ij author: Nora, Holtmann title: Assessment of SARS-CoV-2 in human semen - a cohort study date: 2020-05-29 words: 2231.0 sentences: 146.0 pages: flesch: 57.0 cache: ./cache/cord-293688-g6kag5ij.txt txt: ./txt/cord-293688-g6kag5ij.txt summary: OBJECTIVE: To investigate the presence of viral RNA in human semen of severe-acute-respiratory syndrome coronavirus 2 (SARS-CoV-2) recovered and positive patients and to evaluate its presence and relevance on semen parameters. SARS-CoV-2 RNA could not be detected in semen of recovered and acute COVID-19 positive males. SARS-CoV-2 RNA could neither be detected in semen samples from recovered nor from acute infected subjects. On another note, it is of interest, that although it was described before in the literature that viral infections have a negative impact on semen parameters like 306 volume, number of spermatozoa and motility we could not detect a negative influence of the SARS-CoV-2 infection in respect of the aforementioned sperm count parameters in recovered subjects with mild symptoms. We found no evidence of SARS-CoV-2 shedding in semen of recovered males or patients with an acute COVID-19 infection after a recovery time of 32,7 days on average. abstract: OBJECTIVE: To investigate the presence of viral RNA in human semen of severe-acute-respiratory syndrome coronavirus 2 (SARS-CoV-2) recovered and positive patients and to evaluate its presence and relevance on semen parameters. DESIGN: Pilot cohort study SETTING: University hospital PATIENTS: 34 adult males were distributed into a) patients in convalescence (patients with confirmed SARS-CoV-2 infection in pharyngeal swab by RT-PCR and/or antibodies), b) negative control group (no antibodies) and c) patients with an acute infection (detection of SARS-CoV-2 in pharyngeal swab). INTERVENTION: Semen and a blood sample were collected from each individual. MAIN OUTCOME MEASURES: Analysis of semen quality according to the WHO standards. Detection of SARS-CoV-2 by RT-PCR in the native semen sample and after density gradient preparation. Confirmation of Immunoglobulin (Ig)-A und Ig-G antibodies in the blood. RESULTS: 18 semen samples from recovered males were obtained 8 to 54 days after absence of symptoms, 14 samples from controls and 2 samples from patients with an active COVID-19 infection. No RNA was detected by RT-PCR in the semen including semen samples from two patients with an acute COVID-19 infection. Subjects with a moderate infection showed an impairment of sperm quality. CONCLUSION: A mild COVID-19 infection is not likely to affect testis and epididymis function, whereas semen parameters did seem impaired after a moderate infection . SARS-CoV-2 RNA could not be detected in semen of recovered and acute COVID-19 positive males. This suggests no viral transmission during sexual contact and assisted reproductive techniques (ART), however, further data need to be obtained. url: https://doi.org/10.1016/j.fertnstert.2020.05.028 doi: 10.1016/j.fertnstert.2020.05.028 id: cord-346291-qqy9ld94 author: Noroozi, Rezvan title: Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions date: 2020-05-21 words: 1464.0 sentences: 88.0 pages: flesch: 42.0 cache: ./cache/cord-346291-qqy9ld94.txt txt: ./txt/cord-346291-qqy9ld94.txt summary: In the current review, we summarize the results of studies which reported alterations in cytokine levels and immune cell functions in patients affected with SARS-CoV-2 and related viruses. Alternatively named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus has been shown to induce various clinical manifestation in hosts ranging from asymptomatic conditions to severe symptoms including respiratory failure, shock, or multiorgan system dysfunction (1) Notably, this condition has been accompanied by a significant increase in the proportion of naïve helper T cells while reduction in memory helper T cells and regulatory T cells (5) . Notably, author reported significant over-production of IL-2, IL-7, IL-10, GCSF, IP-10, MCP1, MIP1A, and TNF-α in ICU patients compared with other group of SARS-CoV-2 infected persons (6) . Notably, T cell counts and cytokine concentrations in severe SARS-CoV-2 infected patients who stayed alive gradually returned to their levels in the mild cases. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in early 2020. The infection has been associated with a wide range of clinical symptoms. In the severely affected patients, it has caused dysregulation of immune responses including over-secretion of inflammatory cytokines and imbalances in the proportion of naïve helper T cells, memory helper T cells and regulatory T cells. Identification of the underlying mechanism of such aberrant function of immune system would help in the prediction of disease course and selection of susceptible patients for more intensive cares. In the current review, we summarize the results of studies which reported alterations in cytokine levels and immune cell functions in patients affected with SARS-CoV-2 and related viruses. url: https://api.elsevier.com/content/article/pii/S1043466620301599 doi: 10.1016/j.cyto.2020.155143 id: cord-297178-moxhk2e0 author: Novaes Rocha, Vinicius title: Viral replication of SARS-CoV-2 could be self-limitative - the role of the renin-angiotensin system on COVID-19 pathophysiology date: 2020-10-01 words: 3272.0 sentences: 184.0 pages: flesch: 46.0 cache: ./cache/cord-297178-moxhk2e0.txt txt: ./txt/cord-297178-moxhk2e0.txt summary: Caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus disease 2019 (COVID-19) is provoking devastating consequences on economic and social fields throughout all continents. Amongst the components of rennin-angiotensin system (RAS), the angiotensin-converting enzyme 2 (ACE2) has gained great prominence for being directly associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the coronavirus related to COVID-19 [4, 5] . ACE2 is a fundamental piece in the pathophysiology of COVID-19, since the high replication capacity of SAR-CoV-2 is directly related to the coupling to ACE2 and cell infection. The ACE2 level reduction caused by SARS-CoV-2 infection may be directly related to the pathogenesis of COVID-19 [26] . The reduction in ACE2 expression may be related to pulmonary inflammation and subsequent cytokine storm seen in patients with severe COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severeacute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensinconverting enzyme-2 (ACE2) abstract: Currently, the world is suffering with one of the biggest pandemics of recent history. Caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus disease 2019 (COVID-19) is provoking devastating consequences on economic and social fields throughout all continents. Therefore, pathophysiological knowledge about COVID-19 is imperative for better planning of preventive measures, diagnosis, and therapeutics of the disease. Based on previous studies, this work proposes new hypothesis related to the role of the renin-angiotensin system on the pathophysiology of COVID-19, and its purpose is to enrich the discussion and to offer alternative ways for experimental and clinical studies aiming at the formulation of new diagnosis and / or treatment methods. url: https://www.sciencedirect.com/science/article/pii/S0306987720320818?v=s5 doi: 10.1016/j.mehy.2020.110330 id: cord-270377-lfcoy8n1 author: Novazzi, Federica title: SARS-CoV-2 positivity in rectal swabs implication for possible transmission date: 2020-07-02 words: 422.0 sentences: 37.0 pages: flesch: 62.0 cache: ./cache/cord-270377-lfcoy8n1.txt txt: ./txt/cord-270377-lfcoy8n1.txt summary: Currently, the diagnosis is based on molecular detection of SARS-CoV-2 RNA in respiratory samples such as nasal swab (NS) [1] . However, the evidence that NS in patients with pneumoniae were sometimes negative highlight the needed to collect alternative clinical specimens in whom SARS-CoV-2 RNA could be detected. From the past coronavirus epidemics (SARS-CoV and MERS-CoV) we learned that viral RNA could be also detected in several clinical specimens such as rectal swab (RS) other than respiratory samples [2] . In this perspective, we explored the potential diagnostic role of SARS-CoV-2 real-time RT-PCR performed in biological specimens different from respiratory samples. However, the very low rate of SARS-CoV-2 positivity in samples different from respiratory specimens suggest a limited J o u r n a l P r e -p r o o f Detection of SARS-CoV-2 in Different Types of Clinical Specimens abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32623000/ doi: 10.1016/j.jgar.2020.06.011 id: cord-264421-799n9wqj author: Novelli, Antonio title: Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients date: 2020-09-11 words: 3316.0 sentences: 197.0 pages: flesch: 52.0 cache: ./cache/cord-264421-799n9wqj.txt txt: ./txt/cord-264421-799n9wqj.txt summary: Several studies suggested that genetic variants in the ACE2 gene may influence the host susceptibility or resistance to SARS-CoV-2 infection according to the functional role of ACE2 in human pathophysiology. We therefore investigated the occurrence of ACE2 variants in a cohort of 131 Italian unrelated individuals clinically diagnosed with COVID-19 and in an Italian control population, to evaluate a possible allelic association with COVID-19, by direct DNA analysis. METHODS: As a pilot study, we analyzed, by whole-exome sequencing, genetic variants of ACE2 gene in 131 DNA samples of COVID-19 patients hospitalized at Tor Vergata University Hospital and at Bambino Gesù Children''s Hospital, Rome. Indeed, several studies inferred that genetic variants in ACE2 gene may influence the individual susceptibility or resistance to SARS-CoV-2 according to the functional role of ACE2 in human pathophysiology [12] . In this study, we, therefore, investigated the occurrence of ACE2 variants in a cohort of 131 Italian SARS-CoV-2-positive patients, extracting data on ACE2 variants by direct DNA analysis. abstract: BACKGROUND: Coronaviruses (CoV) are a large family of viruses that are common in humans and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East respiratory syndrome (MERS-CoV), the severe acute respiratory syndrome corona virus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Several studies suggested that genetic variants in the ACE2 gene may influence the host susceptibility or resistance to SARS-CoV-2 infection according to the functional role of ACE2 in human pathophysiology. However, many of these studies have been conducted in silico based on epidemiological and population data. We therefore investigated the occurrence of ACE2 variants in a cohort of 131 Italian unrelated individuals clinically diagnosed with COVID-19 and in an Italian control population, to evaluate a possible allelic association with COVID-19, by direct DNA analysis. METHODS: As a pilot study, we analyzed, by whole-exome sequencing, genetic variants of ACE2 gene in 131 DNA samples of COVID-19 patients hospitalized at Tor Vergata University Hospital and at Bambino Gesù Children’s Hospital, Rome. We used a large control group consisting of 1000 individuals (500 males and 500 females). RESULTS: We identified three different germline variants: one intronic c.439+4G>A and two missense c.1888G>C p.(Asp630His) and c.2158A>G p.(Asn720Asp) in a total of 131 patients with a similar frequency in male and female. Thus far, only the c.1888G>C p.(Asp630His) variant shows a statistically different frequency compared to the ethnically matched populations. Therefore, further studies are needed in larger cohorts, since it was found only in one heterozygous COVID-19 patient. CONCLUSIONS: Our results suggest that there is no strong evidence, in our cohort, of consistent association of ACE2 variants with COVID-19 severity. We might speculate that rare susceptibility/resistant alleles could be located in the non-coding regions of the ACE2 gene, known to play a role in regulation of the gene activity. url: https://doi.org/10.1186/s40246-020-00279-z doi: 10.1186/s40246-020-00279-z id: cord-353509-yfkiaq80 author: Nugraha, Rhea Veda title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 words: 7433.0 sentences: 413.0 pages: flesch: 48.0 cache: ./cache/cord-353509-yfkiaq80.txt txt: ./txt/cord-353509-yfkiaq80.txt summary: This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. abstract: Coronavirus disease 2019 (COVID-19) is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that belongs to the coronavirus family. The first case was reported in December 2019, and the disease has become a pandemic. Impaired immune regulation is one of the factors that play a role in its pathogenesis and results in poor outcomes of COVID-19 patients. There have been many studies with drug candidates used as antivirals or immunomodulators. However, the results of these investigations showed that the drug candidates were not significantly effective against the disease. Meanwhile, people believe that consuming herbal immunomodulators can prevent or even cure COVID-19. Unfortunately, specific preclinical and clinical trials to evaluate the effects of herbal immunoregulators have not been conducted. Certain natural compounds might be effective for the treatment of COVID-19 based on general concepts from previous experiments. This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. In addition, we discuss the pros and cons of utilising herbal medicine during the COVID-19 pandemic, draw some conclusions, and make recommendations at the end of the session. url: https://doi.org/10.1155/2020/2560645 doi: 10.1155/2020/2560645 id: cord-323603-99d0wv1h author: Nunez Garcia, B. title: Real-world data: Cancer and SARS-CoV-2 infection date: 2020-09-30 words: 1537.0 sentences: 106.0 pages: flesch: 56.0 cache: ./cache/cord-323603-99d0wv1h.txt txt: ./txt/cord-323603-99d0wv1h.txt summary: Methods: EGFR, KRAS, BRAF, BRCA1/2 mutation testing of advanced lung adenocarcinoma, metastatic colorectal, metastatic melanoma and ovarian cancer patients were performed by qPCR and NGS. Methods: During the period 11 th March to 15 th May 2020, patients diagnosed with COVID-19 infection who were attending Beaumont Hospital for systemic anti-cancer therapy were included. Those with an ECOG performance status (PS) 3 were more likely to die than those with PS 2 (p<0.001).Compared to those who recovered, patients who died from COVID-19 had higher mean number of organs affected by cancer (3.7 vs. Conclusions: Patients with cancer who contracted COVID-19 and died had more sites of metastatic disease, a poorer performance status, and a higher Palliative Prognostic Score. Results: Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0923753420417934 doi: 10.1016/j.annonc.2020.08.1797 id: cord-035015-slgywe0c author: Nunn, Alistair V. W. title: SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date: 2020-11-09 words: 14660.0 sentences: 715.0 pages: flesch: 36.0 cache: ./cache/cord-035015-slgywe0c.txt txt: ./txt/cord-035015-slgywe0c.txt summary: Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. abstract: Infection with SARs-COV-2 displays increasing fatality with age and underlying co-morbidity, in particular, with markers of the metabolic syndrome and diabetes, which seems to be associated with a “cytokine storm” and an altered immune response. This suggests that a key contributory factor could be immunosenescence that is both age-related and lifestyle-induced. As the immune system itself is heavily reliant on mitochondrial function, then maintaining a healthy mitochondrial system may play a key role in resisting the virus, both directly, and indirectly by ensuring a good vaccine response. Furthermore, as viruses in general, and quite possibly this new virus, have also evolved to modulate immunometabolism and thus mitochondrial function to ensure their replication, this could further stress cellular bioenergetics. Unlike most sedentary modern humans, one of the natural hosts for the virus, the bat, has to “exercise” regularly to find food, which continually provides a powerful adaptive stimulus to maintain functional muscle and mitochondria. In effect the bat is exposed to regular hormetic stimuli, which could provide clues on how to resist this virus. In this paper we review the data that might support the idea that mitochondrial health, induced by a healthy lifestyle, could be a key factor in resisting the virus, and for those people who are perhaps not in optimal health, treatments that could support mitochondrial function might be pivotal to their long-term recovery. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649575/ doi: 10.1186/s12979-020-00204-x id: cord-319023-ucm8frol author: Nuzzo, Andrea title: Universal Shelter-in-Place vs. Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics date: 2020-06-22 words: 3141.0 sentences: 190.0 pages: flesch: 45.0 cache: ./cache/cord-319023-ucm8frol.txt txt: ./txt/cord-319023-ucm8frol.txt summary: Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Conclusion Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated. Such Advanced Automated Contact Tracing (AACT) systems -which could infer exposure risk and propagate warnings to people at risk -may help curb disease spread by facilitating targeted self-isolation rather than universal mandates such as shelter-inplace. In AACT, an additional compartment Sq (Traced contacts that are exposed and under selfisolation) was used while for shelter-in-place, the compartment Q (Individuals isolated through universal enforcement measures) was used. The basic difference between the models is that isolation/quarantine is based solely on exposure history in AACT, while isolation orders apply to the entire population in universal shelter-in-place. Contact tracing can mitigate disease spread through a curated approach of identifying and isolating exposed individuals, as opposed to shelter-in-place orders. abstract: Abstract Objective To model and compare effect of digital contact tracing versus shelter-in-place on SARS-CoV-2 spread. Methods Using a classical epidemiologic framework, and parameters estimated from literature published between February 1, 2020 and May 25, 2020, we modeled two non-pharmacologic interventions- shelter-in-place and digital contact tracing- to curb spread of SARS-CoV-2. For contact tracing, we assumed an advanced, automated contact tracing (AACT) application that sends alerts to individuals advising self-isolation based on individual exposure profile. Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Under influence of these variables, number of individuals infected, exposed, and isolated were estimated. Results Without any intervention, a high rate of infection (>10 million) with early peak is predicted. Shelter-in-place results in rapid decline in infection rate at the expense of impacting a large population segment. The AACT model achieves reduction in infected and exposed individuals similar to shelter-in-place without impacting a large number of individuals. For example, a 50% AACT adoption rate mimics a shelter-in-place order for 40% of the population and results in >90% decrease in peak number of infections. However, as compared to shelter-in-place, with AACT significantly fewer individuals would be isolated. Conclusion Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated. url: https://www.ncbi.nlm.nih.gov/pubmed/32861334/ doi: 10.1016/j.mayocp.2020.06.027 id: cord-342204-9tgxijvn author: Nuzzo, Domenico title: Potential neurological effects of severe COVID-19 infection date: 2020-07-03 words: 3227.0 sentences: 183.0 pages: flesch: 44.0 cache: ./cache/cord-342204-9tgxijvn.txt txt: ./txt/cord-342204-9tgxijvn.txt summary: In this axis, virus-induced inflammation and oxidative stress could be the common mechanisms responsible for CoV neurological symptoms. People with COVID-19 generally develop respiratory symptoms but the increasing evidence shows that some patients with a severe infection also develop neurological ailments like confusion, stroke, seizure, or loss of smell and taste. Recent studies discussed the neuroinvasive potential of SARS-CoV-2; in fact, some infected subjects did show neurological effects. In fact, detection of some RNA of human-coronavirus in human brain samples clearly demonstrates that these respiratory pathogens are naturally neuroinvasive in J o u r n a l P r e -p r o o f humans and suggests that they establish a persistent infection in human CNS (Arbour et al., 2000) . Therefore, inflammation and oxidative stress systemic, induced by SARS-CoV-2 lung injury, could has effect in CNS causing neuronal dysfunction. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients abstract: Coronaviruses (CoVs) are large positive stranded enveloped RNA viruses that generally cause enteric and respiratory diseases in humans and in animals. Most human CoVs have recently attracted global attention to their lethal potential and great infectious capacity. A highly pathogenic CoV, called COVID-19 or SARS‐CoV2, dramatically emerged in December 2019 in Wuhan, China. This new CoV has caused severe pneumonia in China and rapidly spreads around the world, the COVID-19 pandemic. Growing evidence pieces show that viruses, such as CoVs, can enter the central nervous system from different pathways and inducing neurotoxicity. Therefore, it is urgent to make clear whether SARS-CoV-2 has access to the central nervous system and can cause direct neuronal effects. Moreover, a brain–lung–brain axis is been proposed from the scientific community where severe neurological dysfunction and injury are associated with lung injury, and vice versa. In this axis, virus-induced inflammation and oxidative stress could be the common mechanisms responsible for CoV neurological symptoms. Therefore, is important to make clear whether SARS-CoV-2 lung damage can cause indirect or indirect neuronal effects. url: https://www.sciencedirect.com/science/article/pii/S0168010220303990?v=s5 doi: 10.1016/j.neures.2020.06.009 id: cord-328242-afof417h author: Nuñez, M. A. title: Invasion Science and the Global Spread of SARS-CoV-2 date: 2020-05-19 words: 1363.0 sentences: 67.0 pages: flesch: 28.0 cache: ./cache/cord-328242-afof417h.txt txt: ./txt/cord-328242-afof417h.txt summary: Invasion science inherently examines the connectedness between natural and anthropogenic systems by integrating perspectives of, inter alia, ecology, biogeography, population dynamics, evolutionary biology, risk analysis, human history, and environmental management to understand the spread and impact of introduced organisms in non-native contexts. Biomedical research on emergent infectious diseases would benefit from what invasion science can offer in terms of, for example, 1) a consolidated array of frameworks for studying the consequences of eco-evolutionary novelty, and specifically the release of organisms lacking ecological analogues in their recipient environments [4] ; 2) expanding knowledge of the eco-evolutionary factors that determine the success of transitions between stages of invasion (Figure 1 ), which are influenced by a combination of human activities, environmental conditions, and their feedbacks [4, 11, 12] ; and 3) a rich literature on the context-dependent dynamics and predictive modeling of organismal spread and their effects. abstract: Abstract Emerging infectious diseases like COVID19 are driven by ecological and socioeconomic factors, and their rapid spread and devastating impacts mirror those of invasive species. Collaborations between biomedical researchers and ecologists, heretofore rare, are vital to limiting future outbreaks. Enhancing the cross-disciplinary framework offered by invasion science could achieve this goal. url: https://api.elsevier.com/content/article/pii/S0169534720301348 doi: 10.1016/j.tree.2020.05.004 id: cord-351116-jwy6k0ih author: O''Reilly, GM title: Epidemiology and clinical features of emergency department patients with suspected and confirmed COVID‐19: A multisite report from the COVED Quality Improvement Project for July 2020 (COVED‐3) date: 2020-09-21 words: 3598.0 sentences: 222.0 pages: flesch: 49.0 cache: ./cache/cord-351116-jwy6k0ih.txt txt: ./txt/cord-351116-jwy6k0ih.txt summary: METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study in Australian EDs. This analysis presents data from eight sites across Victoria and Tasmania for July 2020 (during Australia''s ''second wave''). 3 The objectives of this analysis (COVED-3), undertaken during the ‗second wave'', were to explore the association between SARS-CoV-2 test result and mechanical ventilation and death in hospital and to identify clinical and epidemiological variables predictive of SARS-CoV-2 positivity. 12 These include history (age, sex, symptoms and duration of presenting complaint, epidemiological features, co-morbidities), findings on clinical examination, radiological and blood investigations, care provided in the ED and hospital (including commencement of invasive mechanical ventilation and ED disposition destination) and patient outcomes (including survival to discharge). In terms of clinical and epidemiological risk factors, SARS-CoV-2 positive patients were more likely to report close contact with a confirmed case of COVID-19 or a positive SARS-CoV-2 PCR swab result in the 14 days prior to their ED presentation. abstract: OBJECTIVE: The aim of this study was to describe the epidemiology and clinical features of patients presenting to the emergency department (ED) with suspected and confirmed COVID‐19. METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study in Australian EDs. This analysis presents data from eight sites across Victoria and Tasmania for July 2020 (during Australia's ‘second wave’). All adult patients who met criteria for ‘suspected COVID‐19’ and underwent testing for SARS‐CoV‐2 in the ED were eligible for inclusion. Study outcomes included a positive SARS‐CoV‐2 test result and mechanical ventilation. RESULTS: In the period 1 to 31 July 2020, there were 30 378 presentations to the participating EDs and 2917 (9.6%; 95% CI: 9.3–9.9) underwent testing for SARS‐CoV‐2. Of these, 50 (2%) patients returned a positive result. Among positive cases, two (4%) received mechanical ventilation during their hospital admission compared to 45 (2%) of the SARS‐CoV‐2 negative patients (OR 1.7 [95% CI: 0.4–7.3], p = 0.47). Two (4%) SARS‐CoV‐2 positive patients died in hospital compared to 46 (2%) of the SARS‐CoV‐2 negative patients (OR 1.7 [0.4–7.1] p = 0.49). Strong clinical predictors of a positive result included self‐reported fever, non‐smoking status, bilateral infiltrates on CXR, and absence of a leucocytosis on first ED blood tests (p < 0.05). CONCLUSIONS: In this prospective multi‐site study from July 2020, a substantial proportion of ED patients required SARS‐CoV‐2 testing, isolation and enhanced infection prevention and control precautions. Presence of SARS‐CoV‐2 on nasopharyngeal swab was not associated with death or mechanical ventilation. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/1742-6723.13651 doi: 10.1111/1742-6723.13651 id: cord-301313-9595vm0k author: OKBA, NISREEN M.A. title: SARS-CoV-2 specific antibody responses in COVID-19 patients date: 2020-03-20 words: 4271.0 sentences: 248.0 pages: flesch: 55.0 cache: ./cache/cord-301313-9595vm0k.txt txt: ./txt/cord-301313-9595vm0k.txt summary: Here, we describe development of serological assays for the detection of virus neutralizing antibodies and antibodies to the nucleocapsid (N) protein and various spike (S) domains including the S1 subunit, and receptor binding domain (RBD) of SARS-CoV-2 in ELISA format. Using a wellcharacterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house as well as a commercial platform. We evaluated SARS-CoV-2 specific antibody responses in severe and mild cases using serum samples collected at different times post-disease onset from three French PCR-confirmed CoVID-19 patients. We tested sera for SARS-CoV-2 specific antibodies using different ELISAs. Following infections, all three patients seroconverted between days 13 and 21 post onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S and S1 subunit including the N-terminal (S1 A ) domain and the receptor binding domain (RBD). abstract: A new coronavirus, SARS-CoV-2, has recently emerged to cause a human pandemic. Whereas molecular diagnostic tests were rapidly developed, serologic assays are still lacking, yet urgently needed. Validated serologic assays are important for contact tracing, identifying the viral reservoir and epidemiological studies. Here, we developed serological assays for the detection of SARS-CoV-2 neutralizing, spike- and nucleocapsid-specific antibodies. Using serum samples from patients with PCR-confirmed infections of SARS-CoV-2, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrate that most PCR-confirmed SARS-CoV-2 infected individuals seroconverted, as revealed by sensitive and specific in-house ELISAs. We found that commercial S1 IgG or IgA ELISAs were of lower specificity while sensitivity varied between the two, with IgA showing higher sensitivity. Overall, the validated assays described here can be instrumental for the detection of SARS-CoV-2-specific antibodies for diagnostic, seroepidemiological and vaccine evaluation studies. url: https://doi.org/10.1101/2020.03.18.20038059 doi: 10.1101/2020.03.18.20038059 id: cord-338023-gb5jgqcg author: Obara, Shinju title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission date: 2020-08-27 words: 2820.0 sentences: 123.0 pages: flesch: 39.0 cache: ./cache/cord-338023-gb5jgqcg.txt txt: ./txt/cord-338023-gb5jgqcg.txt summary: title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission Because SARS-CoV-2 can be transmitted via aerosols and surface contaminations of the environment, appropriate use of anesthesia machines and appropriate behavior in the operation room (OR) are required specifically in relation to this disease. For patients with confirmed or suspected COVID-19 infection, recommendations are use of (1) a high-performance hydrophobic filter (artificial nose) with a high rate of virus rejection (viral filtration efficiency > 99.99% [12] ), and (2) use of a viral filter at the expiratory gas inlet of the anesthesia machine from the expiratory circuit to protect the machine from viruses passing through the artificial nose [12, 13] . Recommendations for anesthesia in patients suspected of COVID-19 Coronavirus infection abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease [coronavirus disease 2019 (COVID-19) infection] first appeared in December 2019 in China and is now spreading worldwide. Because SARS-CoV-2 can be transmitted via aerosols and surface contaminations of the environment, appropriate use of anesthesia machines and appropriate behavior in the operation room (OR) are required specifically in relation to this disease. The use of high-performance hydrophobic filters with a high rate of virus rejection is recommended as the type of viral filter, and surgical team behaviors that result in aerosol splashes should be avoided. Appropriate hand hygiene by the anesthesiologist is crucial to prevent unexpected environmental contamination. When the anesthesia machine is used instead of an intensive care unit ventilator, it is important to keep the fresh gas flow at least equal to the minute ventilation to prevent excessive humidity in the circuit and to monitor condensation in the circuit and inspiratory carbon dioxide pressure. In addition, both the surgical smoke inherent in thermal tissue destruction and the surgical team’s shoe soles may be factors for the presence of SARS-CoV-2 in the operating room. Ensuring social distancing—even with a mask in the OR—may be beneficial because healthcare providers may be asymptomatic carriers. After the acute crisis period of COVID-19, the number of cases of essential but nonurgent surgeries for waiting patients is likely to increase; therefore, optimization of OR scheduling will be an important topic. Anesthesiologists will benefit from new standard practices focusing on the prevention of COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32856167/ doi: 10.1007/s00540-020-02846-z id: cord-320270-lduhhdld author: Obek, Can title: Management of prostate cancer patients during COVID-19 pandemic date: 2020-07-20 words: 5550.0 sentences: 322.0 pages: flesch: 43.0 cache: ./cache/cord-320270-lduhhdld.txt txt: ./txt/cord-320270-lduhhdld.txt summary: National Comprehensive Cancer Network (NCCN), European Association of Urology (EAU), and the Canadian Framework advise against routine PC screening, including prostate specific antigen (PSA) testing and digital rectal examination (DRE), for all asymptomatic individuals until the pandemic subsides [11, 14, 17] . Although authors recognize that neoadjuvant ADT prior to surgery is normally not recommended outside of clinical trials, they state that upfront ADT may be an option in patients with UIR, HR, and VHR disease during COVID-19 crisis, if prolonged surgical delays are expected [11] . Likewise, Royal College of Surgeons'' Updated Intercollegiate General Surgery Guidance on COVID-19 initial statement of "laparoscopy should generally not be used during the pandemic" was later changed to "consider laparoscopy only in selected individual cases, where clinical benefit to the patient substantially exceeds the risk of viral transmission to surgical and theater teams" [27, 28] . abstract: Prostate cancer patients’ management demands prioritization, adjustments, and a tailored approach during the unprecedented SARS-CoV-2 pandemic. Benefit of care from treatment must be carefully weighed against the potential of infection and morbidity from COVID-19. Furthermore, urologists need to be cognizant of their obligation for wise consumption of restricted healthcare resources and protection of the safety of their coworkers. Nonurgent in-person clinic visits should be postponed or conducted remotely via phone or teleconference. Prostate cancer screening, imaging, and biopsies may be suspended in general. Treatment may be safely deferred in low and intermediate risk patients. Surgery may be delayed in most high-risk patients and neoadjuvant ADT is generally not advocated prior to surgery. Initiation of long-term ADT coupled with EBRT subsequent to the pandemic may be favored as a feasible alternative in high-risk and very high-risk disease. In patients with cN1 disease, treatment within 6 weeks is advocated. Presurgery assessment should include testing for COVID-19 and preferably a chest imaging. In the presence of SARS-CoV-2 infection, surgery should be postponed whenever possible. All protective measurements suggested by national/international authorities must to be diligently followed during perioperative period. Strict precautions specific to laparoscopic/robotic surgery are required, considering the unproven but potential risk of aerosolization of SARS-CoV-2 virus and spillage with pneumoperitoneum. Regarding radiotherapy, shortest safe EBRT regimen should be favored and prophylactic whole pelvic RT and brachytherapy avoided. Chemotherapy should be avoided whenever possible. url: https://doi.org/10.1038/s41391-020-0258-7 doi: 10.1038/s41391-020-0258-7 id: cord-303297-fiievwy7 author: Oberemok, Volodymyr V. title: SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date: 2020-04-30 words: 4082.0 sentences: 174.0 pages: flesch: 49.0 cache: ./cache/cord-303297-fiievwy7.txt txt: ./txt/cord-303297-fiievwy7.txt summary: In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. abstract: At the population level, the virus-host relationship is not set up to end with the complete elimination of either or both. Pathogen-resistant individuals will always remain in the host population. In turn, the virus can never completely eliminate the host population, because evolutionarily such an event is a dead end for the virus as an obligate intracellular parasite. A certain existential balance exists in the virus-host relationship. Against this backdrop, viral epidemics and pandemics only become manifest and egregious to human beings when tens and hundreds of thousands of people die and the question emerges what caused the high mortality peaks on the death chart. The answer seems clear; the emerging strain of the virus is new to the host population, and new mutations of the virus and natural selection will lead to a survival of only genetically resistant individuals in a host population. The dangers inherent to a novel virus are due to new features generally inthe molecular structure of proteins, which enable the virus to infect the cells of the host organism more intensively, dramatically challenging host immunity, and thus be transmitted more readily in the host population. In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In fact, only two scenarios will occur simultaneously in the very near future: people who are genetically resistant to the virus will get sick, recover, and develop immunity, while people who are sensitive to the virus will need drugs and vaccines, which will have to be researched and developed if they are to recover. If the pandemic does not stop, in a few decades it is anticipated that SARS-CoV-2 will become as safe as the four non-severe acute respiratory syndrome human coronaviruses (HCoV-NL63, HCoV-HKU1, HCoV-OC43, and HCoV-229E) currently circulating but causing low mortality in the human population. url: https://www.ncbi.nlm.nih.gov/pubmed/32350571/ doi: 10.1007/s00011-020-01352-y id: cord-336696-c3rbmysh author: Oberfeld, Blake title: SnapShot: COVID-19 date: 2020-04-30 words: 1228.0 sentences: 75.0 pages: flesch: 44.0 cache: ./cache/cord-336696-c3rbmysh.txt txt: ./txt/cord-336696-c3rbmysh.txt summary: authors: Oberfeld, Blake; Achanta, Aditya; Carpenter, Kendall; Chen, Pamela; Gilette, Nicole M.; Langat, Pinky; Said, Jordan Taylor; Schiff, Abigail E.; Zhou, Allen S.; Barczak, Amy K.; Pillai, Shiv Abstract Coronavirus disease 2019 (COVID-19) is a novel respiratory illness caused by SARS-CoV-2. The causative agent was characterized as a novel coronavirus, initially referred to as 2019-nCoV and renamed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (Zhou et al., 2020b) . This respiratory illness, coronavirus disease 2019 (COVID-19), has spread rapidly by human-to-human transmission, caused major outbreaks worldwide, and resulted in considerable morbidity and mortality. Based on our understanding of SARS and MERS, and their similarity to COVID-19, the human immune response in mild cases is likely characterized by a robust type I interferon antiviral response and CD4+ Th1 and CD8+ T cell response, resulting in viral clearance. abstract: Abstract Coronavirus disease 2019 (COVID-19) is a novel respiratory illness caused by SARS-CoV-2. Viral entry is mediated through viral spike protein and host ACE2 enzyme interaction. Most cases are mild; severe disease often involves cytokine storm and organ failure. Therapeutics including antivirals, immunomodulators, and vaccines are in development. To view this SnapShot, open or download the PDF. url: https://doi.org/10.1016/j.cell.2020.04.013 doi: 10.1016/j.cell.2020.04.013 id: cord-259852-skhoro95 author: Oboh, Mary Aigbiremo title: Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics date: 2020-08-18 words: 1661.0 sentences: 69.0 pages: flesch: 42.0 cache: ./cache/cord-259852-skhoro95.txt txt: ./txt/cord-259852-skhoro95.txt summary: In addition to the Regional Disease Surveillance Systems Enhancement fund (US$600 million) provided by the World Bank for strengthening health systems and disease surveillance, each country should further establish an epidemic emergency fund for epidemic preparedness and response. Given the various epidemic events that have previously oc-curred in Africa, from Ebola virus disease (EVD) [4] to yellow fever, cholera, measles and Lassa fever [5] , it would almost be safe to assume that African governments have prepared proactive measures against possible future epidemics. A measure could have been applied to restrict travel even from countries with fewer than 100 confirmed SARS-CoV-2 cases given that the virus is highly transmissible, with a high reproductive number [3] . In addition to the REDISSE fund (US$600 million) created by the World Bank for strengthening health systems and disease surveillance, each country should further map out an epidemic emergency fund that will be used to address situations such as this in the future. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has placed unprecedented pressure on healthcare systems, even in advanced economies. While the number of cases of SARS-CoV-2 in Africa compared to other continents has so far been low, there are concerns about under-reporting, inadequate diagnostic tools, and insufficient treatment facilities. Moreover, proactiveness on the part of African governments has been under scrutiny. For instance, issues have emerged regarding the responsiveness of African countries in closing international borders to limit trans-continental transmission of the virus. Overdependence on imported products and outsourced services could have contributed to African governments’ hesitation to shut down international air and seaports. In this era of emerging and re-emerging pathogens, we recommend that African nations should consider self-sufficiency in the health sector as an urgent priority, as this will not be the last outbreak to occur. In addition to the Regional Disease Surveillance Systems Enhancement fund (US$600 million) provided by the World Bank for strengthening health systems and disease surveillance, each country should further establish an epidemic emergency fund for epidemic preparedness and response. We also recommend that epidemic surveillance units should create a secure database of previous and ongoing pandemics in terms of aetiology, spread, and treatment, as well as financial management records. Strategic collection and analysis of data should also be a central focus of these units to facilitate studies of disease trends and to estimate the scale of requirements in preparation and response to any future pandemic or epidemic. url: https://doi.org/10.3961/jpmph.20.259 doi: 10.3961/jpmph.20.259 id: cord-298490-p1msabl5 author: Obukhov, Alexander G. title: SARS-CoV-2 Infections and ACE2: Clinical Outcomes Linked With Increased Morbidity and Mortality in Individuals With Diabetes date: 2020-07-15 words: 6493.0 sentences: 319.0 pages: flesch: 41.0 cache: ./cache/cord-298490-p1msabl5.txt txt: ./txt/cord-298490-p1msabl5.txt summary: As suggested by the recent reports regarding the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), upon entry into the host, this virus binds to the extracellular domain of ACE2 in nasal, lung, and gut epithelial cells through its spike glycoprotein subunit S1. In this Perspective, we bring attention to specific factors that may complicate COVID-19 in individuals with diabetes including 1) the presence of bone marrow changes (myeloidosis) that predispose those with diabetes to an excessive proinflammatory response (cytokine storm) and contribute to insulin resistance and reduced vascular repair, and worsening function of the heart, kidney, and systemic vasculature as a whole; 2) increased circulating furin levels that could cleave the spike protein and increase infectivity of SARS-CoV-2; 3) dysregulated autophagy that may promote replication and/or reduce viral clearance; and 4) gut dysbiosis that leads to widespread systemic inflammation, increased gut glucose and sodium absorption, and reduced tryptophan and other key amino acid absorption needed for incretin secretion and glucose homeostasis. abstract: Individuals with diabetes suffering from coronavirus disease 2019 (COVID-19) exhibit increased morbidity and mortality compared with individuals without diabetes. In this Perspective, we critically evaluate and argue that this is due to a dysregulated renin-angiotensin system (RAS). Previously, we have shown that loss of angiotensin-I converting enzyme 2 (ACE2) promotes the ACE/angiotensin-II (Ang-II)/angiotensin type 1 receptor (AT1R) axis, a deleterious arm of RAS, unleashing its detrimental effects in diabetes. As suggested by the recent reports regarding the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), upon entry into the host, this virus binds to the extracellular domain of ACE2 in nasal, lung, and gut epithelial cells through its spike glycoprotein subunit S1. We put forth the hypothesis that during this process, reduced ACE2 could result in clinical deterioration in COVID-19 patients with diabetes via aggravating Ang-II–dependent pathways and partly driving not only lung but also bone marrow and gastrointestinal pathology. In addition to systemic RAS, the pathophysiological response of the local RAS within the intestinal epithelium involves mechanisms distinct from that of RAS in the lung; however, both lung and gut are impacted by diabetes-induced bone marrow dysfunction. Careful targeting of the systemic and tissue RAS may optimize clinical outcomes in subjects with diabetes infected with SARS-CoV-2. url: https://doi.org/10.2337/dbi20-0019 doi: 10.2337/dbi20-0019 id: cord-259585-mjtxiu0t author: Occhipinti, Vincenzo title: Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date: 2020-04-21 words: 2803.0 sentences: 122.0 pages: flesch: 46.0 cache: ./cache/cord-259585-mjtxiu0t.txt txt: ./txt/cord-259585-mjtxiu0t.txt summary: Every possible effort was made to quickly increase the capacity of intensive care units (ICUs) to accommodate the alarming numbers of very sick CoViD-19 patients, including constructing new units in unused areas of the hospital or converting surgical rooms into ICUs. These drastic measures were implemented in a very short period of time, and although necessary to counteract the devastation brought about by the outbreak, they also posed tremendous challenges to the care of patients with GI conditions, including those with inflammatory bowel diseases (IBD). However, for patients on biologic therapies, we have implemented a mandatory phone call-in the day before any planned hospital visit to screen for possible CoViD-19 symptoms or contact with infected individuals and to reassure patients that all possible precautions are being taken by the IBD center to reduce the risk of infection. abstract: nan url: https://doi.org/10.1093/ibd/izaa084 doi: 10.1093/ibd/izaa084 id: cord-348192-ibohbjfb author: Odih, Erkison E. title: Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks? date: 2020-06-09 words: 2676.0 sentences: 163.0 pages: flesch: 49.0 cache: ./cache/cord-348192-ibohbjfb.txt txt: ./txt/cord-348192-ibohbjfb.txt summary: Endemic and epidemic transmission of multiple feco-oral pathogens via this route continues to be documented in areas without safely managed sanitation, and, therefore, the risk of SARS-CoV-2 transmission needs to be evaluated, tracked, and forestalled in such settings. Furthermore, environmental surveillance of SARS-CoV-2 in wastewater and accumulated human waste, as well as efforts to mitigate the virus'' entry into unprotected household water sources, should be a priority part of the COVID-19 response in settings without safely managed sanitation for the duration of the pandemic. 3, 5, 6 Considerable concern has been expressed in the literature that the feco-oral transmission potential for SARS-CoV-2 places endoscopists, caregivers of diapered children who shed the virus, 7 and fecal transplant recipients 8 at high risk of contracting the infection. 20, 21 Although there are as yet no reports of transmission of SARS-CoV-2 via sewage or fecal matter in settings without safely managed sanitation, or recovery from household water, these examples demonstrate that feco-oral transmission by endemic pathogenic organisms is commonplace in these settings. abstract: SARS-CoV-2, the etiologic agent of COVID-19, is shed in stool. SARS coronaviruses have been detected in wastewater during outbreaks in China, Europe, and the United States. In this perspective, we outline the risk fecal shedding poses at locations without safely managed sanitation, as in most of Nigeria where we work. We believe that feco-oral transmission could occur if community transmission becomes high and sustained in densely populated cities without proper sanitation in Nigeria and many other African and Asian settings. In the absence of basic sanitation, or where existing sanitation is not safely managed, groundwater, which is often drawn up from wells and boreholes for drinking and household use, can become contaminated with enteric bacteria and viruses from fecal matter. Endemic and epidemic transmission of multiple feco-oral pathogens via this route continues to be documented in areas without safely managed sanitation, and, therefore, the risk of SARS-CoV-2 transmission needs to be evaluated, tracked, and forestalled in such settings. We suggest that fecal matter from treatment facilities and recovered patients should be carefully and properly disposed. Furthermore, environmental surveillance of SARS-CoV-2 in wastewater and accumulated human waste, as well as efforts to mitigate the virus’ entry into unprotected household water sources, should be a priority part of the COVID-19 response in settings without safely managed sanitation for the duration of the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32524953/ doi: 10.4269/ajtmh.20-0462 id: cord-254916-y1rw9q11 author: Ogando, Natacha S. title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date: 2020-06-22 words: 8571.0 sentences: 423.0 pages: flesch: 50.0 cache: ./cache/cord-254916-y1rw9q11.txt txt: ./txt/cord-254916-y1rw9q11.txt summary: The overall level of amino acid sequence identity of viral proteins ranges from about 65 % in the least conserved parts of the S protein to about 95 % in the most conserved replicative enzyme domains, prompting the coronavirus study group of the International Committee on the Taxonomy of Viruses to classify the new agent within the species Severe acute respiratory syndrome-related coronavirus, which also includes the 2003 SARS-CoV [1] . In this report, we describe a comparative study of the basic replication features of SARS-CoV and SARS-CoV-2 in Vero E6 cells, including growth kinetics, virus titres, plaque phenotype and an analysis of intracellular viral RNA and protein synthesis. One of them is the rapid evolution -during virus passaging in Vero cells -of a specific region of the SARS-CoV-2 S protein that contains the so-called furin-like cleavage site. abstract: The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of non-structural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (remdesivir, alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that – upon passaging in Vero E6 cells – SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32568027/ doi: 10.1099/jgv.0.001453 id: cord-291590-24psoaer author: Ogando, Natacha S. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 words: 4299.0 sentences: 228.0 pages: flesch: 52.0 cache: ./cache/cord-291590-24psoaer.txt txt: ./txt/cord-291590-24psoaer.txt summary: In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. abstract: Coronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains an N-terminal 3’-to-5’ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase) domain. While the latter presumably operates during viral mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. This is in agreement with observations previously made for alpha- and gammacoronaviruses. Only a single MERS-CoV ExoN active site mutant could be recovered, likely because the introduced D191E substitution is highly conservative in nature. For 11 other MERS-CoV ExoN active site mutants, not a trace of RNA synthesis could be detected, unless – in some cases – reversion had first occurred. Subsequently, we expressed and purified recombinant MERS-CoV nsp14 and established in vitro assays for both its ExoN and N7-MTase activities. All ExoN knockout mutations that were lethal when tested via reverse genetics were found to severely decrease ExoN activity, while not affecting N7-MTase activity. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Importance The bifunctional nsp14 subunit of the coronavirus replicase contains 3’-to-5’ exoribonuclease (ExoN) and N7-methyltransferase (N7-MTase) domains. For the betacoronaviruses MHV and SARS-CoV, the ExoN domain was reported to promote the fidelity of genome replication, presumably by mediating some form of proofreading. For these viruses, ExoN knockout mutants are alive while displaying an increased mutation frequency. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. Both enzymatic activities of (recombinant) MERS-CoV nsp14 were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development. url: https://doi.org/10.1101/2020.06.19.162529 doi: 10.1101/2020.06.19.162529 id: cord-337396-g69bb60d author: Ogawa, Yoshihiko title: Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date: 2020-11-07 words: 1785.0 sentences: 121.0 pages: flesch: 56.0 cache: ./cache/cord-337396-g69bb60d.txt txt: ./txt/cord-337396-g69bb60d.txt summary: A follow-up survey was conducted with healthcare personnel (HCP) who were exposed to a patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative PCR results. No apparent infection was found in any of the HCP who had contact exposure with and/or aerosol exposure to the patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative results of PCR tests for SARS-CoV-2. Thus, we created a policy that for patients whose sputum and/or nasopharyngeal PCR test results for SARS-CoV-2 were negative when measured twice separately over 24 h, we stopped the precautions against aerosol transmission. We did not perform PCR tests for SARS-CoV-2 until the 63rd day of illness, and the result of this test was re-negative. In conclusion, no HCP were infected by contact with and aerosol exposures to SARS-CoV-2 re-positive patients in our hospital. abstract: OBJECTIVE: To evaluate whether patients with COVID-19 who have tested re-positive with the PCR test for the SARS-CoV-2 virus are infectious is a challenge in the current circumstances. A follow-up survey was conducted with healthcare personnel (HCP) who were exposed to a patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative PCR results. RESULTS: We studied a total of 15 HCP who had contact exposures (15/15) and aerosol exposures (7/15). None of them tested positive for IgG against SARS-CoV-2 on blood examination. None of them had any symptoms during 10 days of active isolation. All PCR tests conducted using the nasopharyngeal swabs collected from the HCP on day 10 were negative. No apparent infection was found in any of the HCP who had contact exposure with and/or aerosol exposure to the patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative results of PCR tests for SARS-CoV-2. Clinical trial: Trial Registration: No. 170, approved June 10th, 2020 by the ethics committee of Sakai City Medical Center. url: https://doi.org/10.1186/s13104-020-05365-y doi: 10.1186/s13104-020-05365-y id: cord-258614-7unadw41 author: Ogidigo, Joyce Oloaigbe title: Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach date: 2020-10-25 words: 8459.0 sentences: 416.0 pages: flesch: 47.0 cache: ./cache/cord-258614-7unadw41.txt txt: ./txt/cord-258614-7unadw41.txt summary: Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M(pro)) SARS-CoV-2. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; −41.1 and −43.4 kcal/mol) against the M(pro) of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Thus, among the 86 phytocompounds and 3 antiviral drugs screened (Supplementary material Table S1 ), 6 phyto ligands exhibited appreciable binding energies against the SARS-CoV-2 M pro and strong interactions within the binding pocket. Analysis of the per-residue additional showed that studied compounds interact with these key amino acid residues in the active site of the main protease, suggesting that these phytocompounds could emerge as ideal candidate''s inhibitors against SARS-CoV-2 M pro and another virus protease. abstract: At present, there is no cure or vaccine for the devastating new highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has affected people globally. Herein, we identified potent phytocompounds from two antiviral plants Momordica charantia L. and Azadirachta indica used locally for the treatment of viral and parasitic infections. Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M(pro)) SARS-CoV-2. A total of 86 compounds from M. charantia L. and A. indica were identified. The top six phytocompounds; momordicine, deacetylnimninene, margolonone, momordiciode F2, nimbandiol, 17-hydroxyazadiradione were examined and when compared with three FDA reference drugs (remdesivir, hydroxychloroquine and ribavirin). The top six ranked compounds and FDA drugs were then subjected to MD simulation and pharmacokinetic studies. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; −41.1 and −43.4 kcal/mol) against the M(pro) of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Per-residue analysis, root mean square deviation and solvent-accessible surface area revealed that compounds interacted with key amino acid residues at the active site of the enzyme and showed good system stability. The results obtained in this study show that these phytocompounds could emerge as promising therapeutic inhibitors for the M(pro) of SARS-CoV-2. However, urgent trials should be conducted to validate this outcome. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33103616/ doi: 10.1080/07391102.2020.1837681 id: cord-292836-1o2ynvy3 author: Ogimi, Chikara title: What’s New With the Old Coronaviruses? date: 2020-04-21 words: 5194.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-292836-1o2ynvy3.txt txt: ./txt/cord-292836-1o2ynvy3.txt summary: In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] . abstract: Coronaviruses contribute to the burden of respiratory diseases in children, frequently manifesting in upper respiratory symptoms considered to be part of the “common cold.” Recent epidemics of novel coronaviruses recognized in the 21st century have highlighted issues of zoonotic origins of transmissible respiratory viruses and potential transmission, disease, and mortality related to these viruses. In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. url: https://doi.org/10.1093/jpids/piaa037 doi: 10.1093/jpids/piaa037 id: cord-335591-r0x8yaqj author: Ohnishi, Kazuo title: Establishment and Characterization of Monoclonal Antibodies Against SARS Coronavirus date: 2007-11-28 words: 3126.0 sentences: 242.0 pages: flesch: 67.0 cache: ./cache/cord-335591-r0x8yaqj.txt txt: ./txt/cord-335591-r0x8yaqj.txt summary: The hybridomas produce monoclonal antibodies that recognize viral component molecules, including the spike protein (S) and the nucleocapsid protein (N), enabling the immunological detection of SARS-CoV by immunofluorescence staining, immunoblot, or an antigen-capture ELISA system. Based on clinical experience, several options have been considered in the quest to develop the capacity to accurately diagnose SARS-CoV infection, including molecular biology techniques and serological tests such as antigen-capture ELISA assay and immunofluorescence assay to detect virus-infected cells in respiratory swabs (3-7) . These mAbs enable the general immunological detection of SARS-CoV by methods such as immunofluorescent staining, immunoblotting, and immunohistology, in addition to the construction of a highly sensitive antigen-capture sandwich ELISA (6). The UV-inactivated purified SARS-CoV samples (see Note 1), which are serially diluted with 1% OVA/PBS-Tween, are added to the wells and incubated for 1 h at room temperature abstract: Immunological detection of viruses and their components by monoclonal antibodies is a powerful method for studying the structure and function of viral molecules. Here we describe detailed methods for establishing monoclonal antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV). B cell hybridomas are generated from mice that are hyperimmunized with inactivated SARS-CoV virions. The hybridomas produce monoclonal antibodies that recognize viral component molecules, including the spike protein (S) and the nucleocapsid protein (N), enabling the immunological detection of SARS-CoV by immunofluorescence staining, immunoblot, or an antigen-capture ELISA system. In addition, several S protein-specific antibodies are shown to have in vitro neutralization activity. Thus the monoclonal antibody approach provides useful tools for rapid and specific diagnosis of SARS, as well as for possible antibody-based treatment of the disease. url: https://doi.org/10.1007/978-1-59745-181-9_15 doi: 10.1007/978-1-59745-181-9_15 id: cord-261193-960th627 author: Ohnishi, Kouji title: Evaluation of a non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold as a SARS 3CL protease inhibitor date: 2019-01-15 words: 6061.0 sentences: 348.0 pages: flesch: 70.0 cache: ./cache/cord-261193-960th627.txt txt: ./txt/cord-261193-960th627.txt summary: A non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold was evaluated as a novel inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)). The synthesized decahydroisoquinolin inhibitors showed about 2.4 times potent inhibitory activities for SARS 3CL(pro) when combined with a non-prime site substituent. The residue was purified by silica gel column chromatography (hexane/EtOAc = 5:1) to give a title alcohol ( TPAP (tetra-n-propyl ammonium perrutenate, 316 mg, 0.9 mmol) was added to a solution of above alcohol (10.5 g, 47.5 mmol) and NMO (N-methylmorphline-N-oxide, 21.1 g, 180 mmol) in CH 2 Cl 2 (180 mL) at 0°C. After being stirred for 30 min, the reaction mixture was filtered through a silica gel layer and the filtrate was concentrated. The filtrate was concentrated and resulting residue was purified by silica gel column chromatography (hexane/ EtOAc = 10:1) to afford 15 (640 mg, 50%). abstract: A non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold was evaluated as a novel inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)). The decahydroisoquinolin scaffold has been demonstrated to be an effective hydrophobic center to interact with S2 site of SARS 3CL(pro), but the lack of interactions at S3 to S4 site is thought to be a major reason for the moderate inhibitory activity. In this study, the effects of an additional non-prime site substituent on the scaffold as well as effects of several warheads are evaluated. For the introduction of a desired non-prime site substituent, amino functionality was introduced on the decahydroisoquinolin scaffold, and the scaffold was constructed by Pd(II) catalyzed diastereoselective ring formation. The synthesized decahydroisoquinolin inhibitors showed about 2.4 times potent inhibitory activities for SARS 3CL(pro) when combined with a non-prime site substituent. The present results indicated not only the expected additional interactions with the SARS 3CL(pro) but also the possibility of new inhibitors containing a fused-ring system as a hydrophobic scaffold and a new warhead such as thioacetal. url: https://api.elsevier.com/content/article/pii/S0968089618319163 doi: 10.1016/j.bmc.2018.12.019 id: cord-349682-kpg0vley author: Ojha, Probir Kumar title: Therapeutics for COVID-19: from computation to practices—where we are, where we are heading to date: 2020-09-02 words: 7923.0 sentences: 416.0 pages: flesch: 49.0 cache: ./cache/cord-349682-kpg0vley.txt txt: ./txt/cord-349682-kpg0vley.txt summary: For example, the broad-spectrum antiviral drug Arbidol recently entered the clinical trial for the treatment of SARS-CoV-2 which may act by inhibiting virus-host cell fusion, thus preventing the viral entry into host cells against influenza virus [37] [38] [39] . Smith and Smith [22] analyzed 8000 small drug molecules and natural products (SWEETLEAD library database) employing restrained temperature replica-exchange MD simulations combining virtual screening through the ensemble docking to identify the effective drug for COVID-19 which might stop the virus by two ways: (a) disrupting S protein and ACE2 receptor interface stability; or (b) by troubling the capability of the S protein to recognize Table 2 Pharmacological safety data of selected potential drug candidates [11, 12, 14, 34, 38, 39, 43-45, 57-59, 64, 69, 70, 89] Drug Dose Drug-drug interaction Toxicity Chloroquine phosphate (Aralen) [11, 12, 14, 43, 89] This is a genetically engineered vaccine candidate with the replicationdefective adenovirus type 5 as the vector to express SARS-CoV-2 spike protein. abstract: ABSTRACT: After the 1918 Spanish Flu pandemic caused by the H1N1 virus, the recent coronavirus disease 2019 (COVID-19) brought us to the time of serious global health catastrophe. Although no proven therapies are identified yet which can offer a definitive treatment of the COVID-19, a series of antiviral, antibacterial, antiparasitic, immunosuppressant drugs have shown clinical benefits based on repurposing theory. However, these studies are made on small number of patients, and, in majority of the cases, have been carried out as nonrandomized trials. As society is running against the time to combat the COVID-19, we present here a comprehensive review dealing with up-to-date information of therapeutics or drug regimens being utilized by physicians to treat COVID-19 patients along with in-depth discussion of mechanism of action of these drugs and their targets. Ongoing vaccine trials, monoclonal antibodies therapy and convalescent plasma treatment are also discussed. Keeping in mind that computational approaches can offer a significant insight to repurposing based drug discovery, an exhaustive discussion of computational modeling studies is performed which can assist target-specific drug discovery. GRAPHIC ABSTRACT: [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32880078/ doi: 10.1007/s11030-020-10134-x id: cord-303056-bdse9o26 author: Okada, Masaji title: Development of vaccines and passive immunotherapy against SARS corona virus using SCID-PBL/hu mouse models date: 2007-04-20 words: 1290.0 sentences: 81.0 pages: flesch: 56.0 cache: ./cache/cord-303056-bdse9o26.txt txt: ./txt/cord-303056-bdse9o26.txt summary: The production of neutralizing antibodies against SARS CoV was observed in the serum from mice immunized with S DNA vaccine SARS (M) DNA vaccine and N DNA vaccine induced murine T cell responses against SARS [4] . Human neutralizing antibodies were induced from SCID-PBL/hu mice vaccines with SARSS [6] and M DNA vaccines (Fig. 2) . Titer of neutralizing antibody in the serum from SCID-PBL/hu mice immunized with SARS (M) DNA vaccine was 1:10. SARS S DNA vaccine which elicits effective neutralizing antibody responses that generate protective immunity in a mouse model [9] . Furthermore, SARS M DNA as well as SARSS DNA vaccine induce human neutralizing antibodies against SARS CoV by the SCID-PBL/hu model. Therefore, the effect of combination immunization with such SARS vaccines (M vaccine and S vaccine) and the specificity of human monoclonal neutralizing antibodies are now being studied. A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice abstract: We have investigated novel vaccine strategies against severe acute respiratory syndrome (SARS) CoV using cDNA constructs encoding the structural antigens: (S), (M), (E), or (N) protein, derived from SARS CoV. PBL from healthy human volunteers were administered i.p. into IL-2 receptor γ-chain disrupted SCID mice, and SCID-PBL/hu mice were constructed. These mice can be used to analyze the human immune response in vivo. SARS M DNA vaccine and N DNA vaccine induced human CTL specific for SARS CoV antigens. Alternatively, SARS M DNA vaccines inducing human neutralizing antibodies and human monoclonal antibodies against SARS CoV are now being developed. These results show that these vaccines can induce virus-specific immune responses and should provide a useful tool for development of protective and therapeutic vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/17289225/ doi: 10.1016/j.vaccine.2007.01.032 id: cord-308110-cco3aq4n author: Okamoto, Mika title: The chemokine receptor antagonist cenicriviroc inhibits the replication of SARS-CoV-2 in vitro date: 2020-07-30 words: 2689.0 sentences: 148.0 pages: flesch: 51.0 cache: ./cache/cord-308110-cco3aq4n.txt txt: ./txt/cord-308110-cco3aq4n.txt summary: In this study, CVC was examined for its inhibitory effect on the replication of SARS-CoV-2, the causative agent of COVID-19, in cell cultures and found to be a selective inhibitor of the virus. The 50% effective concentrations of CVC were 19.0 and 2.9 μM in the assays based on the inhibition of virus-induced cell destruction and viral RNA levels in culture supernatants of the infected cells, respectively. Considering the fact that the regulation of excessive immune activation is required to treat COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. Since not only the inhibition of viral replication but also the control of excessive immune activation is mandatory to save COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. abstract: Cenicriviroc (CVC) is a small-molecule chemokine receptor antagonist with highly potent and selective anti-human immunodeficiency virus type 1 (HIV-1) activity through antagonizing C-C chemokine receptor type 5 (CCR5) as a coreceptor of HIV-1. CVC also strongly antagonizes C-C chemokine receptor type 2b (CCR2b), thereby it has potent anti-inflammatory and immunomodulatory effects. CVC is currently under clinical trials in the patients for treatment of nonalcoholic steatohepatitis, in which immune cell activation and dysregulation of proinflammatory cytokines play an important role in its pathogenesis. In this study, CVC was examined for its inhibitory effect on the replication of SARS-CoV-2, the causative agent of COVID-19, in cell cultures and found to be a selective inhibitor of the virus. The 50% effective concentrations of CVC were 19.0 and 2.9 μM in the assays based on the inhibition of virus-induced cell destruction and viral RNA levels in culture supernatants of the infected cells, respectively. Interestingly, the CCR5-specific antagonist maraviroc did not show any anti-SARS-CoV-2 activity. Although the mechanism of SARS-CoV-2 inhibition by CVC remains to be elucidated, CCR2b does not seem to be its target molecule. Considering the fact that the regulation of excessive immune activation is required to treat COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. url: https://doi.org/10.1016/j.antiviral.2020.104902 doi: 10.1016/j.antiviral.2020.104902 id: cord-347374-mryazbnq author: Okba, Nisreen M.A. title: Severe Acute Respiratory Syndrome Coronavirus 2−Specific Antibody Responses in Coronavirus Disease Patients date: 2020-07-17 words: 3565.0 sentences: 186.0 pages: flesch: 51.0 cache: ./cache/cord-347374-mryazbnq.txt txt: ./txt/cord-347374-mryazbnq.txt summary: Using serum samples from patients with PCR-confirmed SARS-CoV-2 infections, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrated that most PCR-confirmed SARS-CoV-2–infected persons seroconverted by 2 weeks after disease onset. Using a well-characterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house, as well as a commercial platform. We evaluated SARS-CoV-2-specific antibody responses in severe and mild cases by using serum samples collected at different times postonset of disease from 3 PCR-confirmed COVID-19 patients from France. We tested serum samples for SARS-CoV-2specific antibodies by using different ELISAs. After infection, all 3 patients seroconverted between days 13 and 21 after onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S, S1 subunit, and RBD, but only 2/3 patients had detectable antibodies to the N-terminal (S1 A ) domain. abstract: A new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently emerged to cause a human pandemic. Although molecular diagnostic tests were rapidly developed, serologic assays are still lacking, yet urgently needed. Validated serologic assays are needed for contact tracing, identifying the viral reservoir, and epidemiologic studies. We developed serologic assays for detection of SARS-CoV-2 neutralizing, spike protein–specific, and nucleocapsid-specific antibodies. Using serum samples from patients with PCR-confirmed SARS-CoV-2 infections, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrated that most PCR-confirmed SARS-CoV-2–infected persons seroconverted by 2 weeks after disease onset. We found that commercial S1 IgG or IgA ELISAs were of lower specificity, and sensitivity varied between the 2 assays; the IgA ELISA showed higher sensitivity. Overall, the validated assays described can be instrumental for detection of SARS-CoV-2–specific antibodies for diagnostic, seroepidemiologic, and vaccine evaluation studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32267220/ doi: 10.3201/eid2607.200841 id: cord-278238-w1l8h8g8 author: Okba, Nisreen MA title: Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches date: 2017-04-13 words: 5086.0 sentences: 226.0 pages: flesch: 39.0 cache: ./cache/cord-278238-w1l8h8g8.txt txt: ./txt/cord-278238-w1l8h8g8.txt summary: Nisreen MA Okba, V Stalin Raj and Bart L Haagmans Middle East respiratory syndrome coronavirus (MERS-CoV) is a cause of severe respiratory infection in humans, specifically the elderly and people with comorbidities. The other candidate MVA-S, a viral-vector-based vaccine, induced systemic neutralizing antibodies and mucosal immunity which conferred protection against MERS-CoV challenge and reduced virus shedding in vaccinated camels [52 ] Therefore, this vaccine candidate may provide a means to prevent zoonotic transmission of the virus to the human population. Prophylaxis with a Middle East respiratory syndrome coronavirus (MERS-CoV)-specific human monoclonal antibody protects rabbits from MERS-CoV infection T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice The recombinant Nterminal domain of spike proteins is a potential vaccine against Middle East respiratory syndrome coronavirus (MERS-CoV) infection abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a cause of severe respiratory infection in humans, specifically the elderly and people with comorbidities. The re-emergence of lethal coronaviruses calls for international collaboration to produce coronavirus vaccines, which are still lacking to date. Ongoing efforts to develop MERS-CoV vaccines should consider the different target populations (dromedary camels and humans) and the correlates of protection. Extending on our current knowledge of MERS, vaccination of dromedary camels to induce mucosal immunity could be a promising approach to diminish MERS-CoV transmission to humans. In addition, it is equally important to develop vaccines for humans that induce broader reactivity against various coronaviruses to be prepared for a potential next CoV outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/28412285/ doi: 10.1016/j.coviro.2017.03.007 id: cord-298725-da71febn author: Okuhama, Ayako title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan date: 2020-11-17 words: 1433.0 sentences: 100.0 pages: flesch: 46.0 cache: ./cache/cord-298725-da71febn.txt txt: ./txt/cord-298725-da71febn.txt summary: title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Reports have been published on COVID-19 among patients receiving hemodialysis (2), but none have evaluated whether HD effluent is infectious. We report detection of SARS-CoV-2 RNA in hemodialysis effluent from a patient with COVID-19 pneumonia and prolonged inflammation. PCR results showed SARS-CoV-2 RNA of 157.9 copies/μL with cycle threshold (C t ) values of 38.3 at 1 hour after starting hemodialysis but were negative on effluent collected at 2 hours. In conclusion, we report positive qRT-PCR results for SARS-CoV-2 RNA from hemodialysis effluent in a patient receiving renal dialysis. abstract: We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Healthcare workers should observe strict standard and contact precautions and use appropriate personal protective equipment when handling hemodialysis circuitry from patients with diagnosed coronavirus disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32730734/ doi: 10.3201/eid2611.201956 id: cord-334175-x10bbv7y author: Okur, Hacer Kuzu title: Preliminary report of In vitro and In vivo Effectiveness of Dornase alfa on SARS-CoV-2 infection date: 2020-09-07 words: 4026.0 sentences: 251.0 pages: flesch: 55.0 cache: ./cache/cord-334175-x10bbv7y.txt txt: ./txt/cord-334175-x10bbv7y.txt summary: Dornase alfa, the recombinant form of the human DNase I enzyme, breaks down neutrophil extracellular traps (NET) that include a vast amount of DNA fragments, histones, microbicidal proteins and oxidant enzymes released from necrotic neutrophils in the highly viscous mucus of cystic fibrosis patients. We followed clinical improvement in the radiological analysis (2-of-3 cases), oxygen saturation (SpO2), respiratory rate, disappearing of dyspnea, coughing and a decrease in NET formation and SARS-CoV-2 viral load after the treatment. Also here, we share our preliminary results suggesting that Dornase alfa has an anti-viral effect against SARS-CoV-2 infection in a green monkey kidney cell line, Vero, and a bovine kidney cell line, MDBK without determined cytotoxicity on healthy peripheral blood mononuclear cells. In this study, preliminary data is presented about in-vitro and in-vivo anti-viral and nuclease activity of Dornase alfa for the clearance of SARS-CoV-2 viral load and NETs in the lungs of COVID-19 patients. abstract: Dornase alfa, the recombinant form of the human DNase I enzyme, breaks down neutrophil extracellular traps (NET) that include a vast amount of DNA fragments, histones, microbicidal proteins and oxidant enzymes released from necrotic neutrophils in the highly viscous mucus of cystic fibrosis patients. Dornase alfa has been used for decades in patients with cystic fibrosis to reduce the viscoelasticity of respiratory tract secretions, to decrease the severity of respiratory tract infections, and to improve lung function. Previous studies have linked abnormal NET formations to lung diseases, especially to acute respiratory distress syndrome (ARDS). It is well known that novel Coronavirus disease 2019 (COVID-19) pneumonia progresses to ARDS and even multiple organ failure. High blood neutrophil levels are an early indicator of COVID-19 and predict severe respiratory diseases. Also it is reported that mucus structure of COVID-19 is very similar to cystic fibrosis due to the accumulation of excessive NET in the lungs. In this study, we showed the recovery of three COVID-19 patients after including Dornase alfa in their treatment. We followed clinical improvement in the radiological analysis (2-of-3 cases), oxygen saturation (SpO2), respiratory rate, disappearing of dyspnea, coughing and a decrease in NET formation and SARS-CoV-2 viral load after the treatment. Also here, we share our preliminary results suggesting that Dornase alfa has an anti-viral effect against SARS-CoV-2 infection in a green monkey kidney cell line, Vero, and a bovine kidney cell line, MDBK without determined cytotoxicity on healthy peripheral blood mononuclear cells. url: https://doi.org/10.1016/j.nmni.2020.100756 doi: 10.1016/j.nmni.2020.100756 id: cord-322942-y4zd2oui author: Olagnier, David title: Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date: 2020-07-17 words: 3756.0 sentences: 203.0 pages: flesch: 50.0 cache: ./cache/cord-322942-y4zd2oui.txt txt: ./txt/cord-322942-y4zd2oui.txt summary: Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. Here we demonstrate that expression of NRF2-dependent genes is suppressed in biopsies from 104 COVID-19 patients and that treatment of cells with NRF2 agonists 4-OI and DMF induces a 105 strong anti-viral program that limits SARS-CoV2 replication. Interestingly, when 176 treating Calu3 cells with DMF, another known NRF2 inducer and a clinically approved drug in 177 the first-line-of treatment of multiple sclerosis, we could also observe an anti-viral effect toward 178 SARS-CoV2 replication similar in magnitude as what we had observed with 4-OI (Fig 2p-q) as 179 well as a reduced but significant effect when using Vero cells (Fig. 2r) . abstract: Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here we demonstrate that the NRF2 anti-oxidant gene expression pathway is suppressed in biopsies obtained from COVID-19 patients. Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. The anti-viral program extended to inhibit the replication of several other pathogenic viruses including Herpes Simplex Virus-1 and-2, Vaccinia virus, and Zika virus through a type I interferon (IFN)-independent mechanism. In addition, induction of NRF2 by 4-OI and DMF limited host inflammatory responses to SARS-CoV2 infection associated with airway COVID-19 pathology. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. One Sentence Summary NRF2 agonists 4-octyl-itaconate (4-OI) and dimethyl fumarate inhibited SARS-CoV2 replication and virus-induced inflammatory responses, as well as replication of other human pathogenic viruses. url: https://doi.org/10.1101/2020.07.16.206458 doi: 10.1101/2020.07.16.206458 id: cord-351719-xqmir1ca author: Olaimat, Amin N. title: Food Safety During and After the Era of COVID-19 Pandemic date: 2020-08-04 words: 3906.0 sentences: 208.0 pages: flesch: 51.0 cache: ./cache/cord-351719-xqmir1ca.txt txt: ./txt/cord-351719-xqmir1ca.txt summary: The coronavirus disease 2019 (COVID-19) is a clinical syndrome caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). COVID-19 is the clinical syndrome caused by SARS-CoV-2 infection which is characterized by a respiratory disease with symptoms ranging from mild influenza (flu-like) to severe pneumonia and acute respiratory distress syndrome (Petrosillo et al., 2020) . A previous study reported that food products were a plausible transmission route for respiratory viruses including SARS-CoV-1 and influenza (Klein, 2004) . The proper use of gloves, sanitizers, and disinfectants can minimize the risk of virus spread and disease transmission (Food and Agriculture Organization of the United Nations [FAO] and World Health Organization [WHO], 2020; Food and Drug Administration [FDA], 2020a). The current guidelines issued by public health authorities are based on the disease patterns of previously encountered coronaviruses and they need to be updated according to the novel coronavirus SARS-CoV-2 as this virus is likely to persist and people will have to modify their "normal behavior" to a "new normal." abstract: The coronavirus disease 2019 (COVID-19) is a clinical syndrome caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). COVID-19 was declared a pandemic by the World Health Organization (WHO) on March 11, 2020 due to its rapid and extensive spread among many countries through its very contagious nature and its high mortality among the elderly and infirm. Recently, data on the survival of SARS-CoV-2 on contact surfaces has been reported, but there is none on the survival of COVID-19 on food surfaces and packages. The potential survival and transmission of SARS-CoV-2 on/via food and packages are discussed based on data available for other respiratory viruses such as SARS-CoV and MERS-CoV. However, studies are needed to explore its transmission via food and survival on food packaging materials. The implementation of food safety management systems such as Hazard Analysis and Critical Control Points (HACCP), and Good Manufacturing Practices (GMP) are important to reduce the risk of COVID-19 infection. Cleaning, sanitation, good hygienic practices, and active packaging are also needed from farm to fork. url: https://www.ncbi.nlm.nih.gov/pubmed/32849446/ doi: 10.3389/fmicb.2020.01854 id: cord-280198-bhjw6xc5 author: Olaleye, Omonike A. title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date: 2020-08-14 words: 1814.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-280198-bhjw6xc5.txt txt: ./txt/cord-280198-bhjw6xc5.txt summary: title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 Spike Protein Interaction In Vitro Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effect in vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. Therefore, targeting 106 the interaction between human ACE2 receptor and the RBD in S protein of SARS-CoV-2 could 107 serve as a promising approach for the development of effective entry inhibitors for potential 108 prevention and/or treatment of COVID-19. Activity of Clioquinol (CLQ) and Analogues against ACE2 Exopeptidase Activity and 725 ACE2 and SARS-CoV-2 Spike (RBD) Protein Interaction abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent for coronavirus disease 2019 (COVID-19), has emerged as an ongoing global pandemic. Presently, there are no clinically approved vaccines nor drugs for COVID-19. Hence, there is an urgent need to accelerate the development of effective antivirals. Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effect in vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. CLQ displayed the highest potency in the low micromolar range, with its antiviral activity showing strong correlation with inhibition of rhACE2 and rhACE2-RBD interaction. Altogether, our findings provide a new mode of action and molecular target for CLQ and validates this pharmacophore as a promising lead series for clinical development of potential therapeutics for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32817951/ doi: 10.1101/2020.08.14.250480 id: cord-340252-9gr2iw15 author: Olalla, J. title: Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience date: 2020-05-20 words: 2398.0 sentences: 140.0 pages: flesch: 54.0 cache: ./cache/cord-340252-9gr2iw15.txt txt: ./txt/cord-340252-9gr2iw15.txt summary: Conclusions: the prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This identification, together with the appropriate measures, could result in less spread of the virus from the healthcare center and, therefore, in fewer healthcare providers and patients affected by In this article, we present the results of an active search study of asymptomatic and seroprevalence carriers of SARS-CoV-2 among high-risk healthcare workers in a hospital in southern Spain. The main objective was to determine the prevalence of asymptomatic carriers of SARS-CoV-2 in healthcare professionals, defined as those individuals with PCR of a positive respiratory sample without presenting symptoms suggestive of CoVID-19 on the day of sampling. . https://doi.org/10.1101/2020.05.18.20103283 doi: medRxiv preprint workers in the total workforce presented positive PCR, although in this study it was performed testing only symptomatic workers (6) . abstract: Objective: determine the percentage of healthcare workers (HCW) carrying SARS-CoV-2 in high exposure areas of the hospital. Design: cross- sectional study during April 15-24th in Hospital Costa del Sol (Marbella, Spain), excluding HCW with previous COVID19. Setting: hospital based, focused on patient care areas COVID19. Participants: 498 subjects, 80% women. Participation was offered to all the HCW of Emergencies, Intensive Care and Anesthesia, Internal Medicine and Pneumology. Other units not directly involved in the care of these patients were offered to participate. Intervention: naso and oropharyngeal PCR determination was performed together with IgG and IgM antibody determination by immunochromatography. On the day of sampling, a health questionnaire was answered, reporting symptoms on the same day and in the previous fourteen days. Main outcome measures: percentage of HCW with positive PCR for SARS-CoV-2, percentage of HCW with positive IgG for SARS-CoV-2. Results: Two individuals were detected with PCR for SARS-CoV-2 positive (0.4%). Both were asymptomatic on the day of sampling, but one of them had had a CoVID-19 compatible picture in the previous two weeks and had positive IgG and IgM; therefore, only one subject was truly asymptomatic carrier (0.2%). 9 workers with positive IgG (1.8%) were detected. Conclusions: the prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This type of strategy can be one more tool in controlling the pandemic. url: https://doi.org/10.1101/2020.05.18.20103283 doi: 10.1101/2020.05.18.20103283 id: cord-330433-y5dvlcda author: Olivieri, Emily R. title: Analysis of SARS-CoV Receptor Activity of ACE2 Orthologs date: 2006 words: 1730.0 sentences: 102.0 pages: flesch: 60.0 cache: ./cache/cord-330433-y5dvlcda.txt txt: ./txt/cord-330433-y5dvlcda.txt summary: 2 Coronavirus spike-receptor interactions are major determinants of species specificity, and transfection of viral genomic RNA or expression of receptors in nonpermissive cell lines usually results in productive infection. The goals of this study were to determine whether ACE2 transcript is produced by permissive and nonpermissive cells derived from diverse species and to use speciesspecific differences in ACE2 to identify amino acids or other post-translational modifications critical for SARS-CoV binding and/or fusion. Cell lines derived from monkey (VeroE6, pRhMk, and pCMK), human (HRT-18, HEK293T, and Huh-7), mink (Mv1Lu), dog (MDCK), cat (CRFK), hamster (BHK-21), and chicken (CEF) were analyzed for susceptibility to SARS-CoV. This data suggests that dog ACE2 and chicken ACE2 may have amino acid or other differences, which inhibit their function as SARS-CoV receptors. 13 We used multiple sequence alignment of efficient and poor receptors, combined with difference mapping on the hACE2 structure, to identify specific residues or post-translational modifications within ACE2 that may be critical for SARS-CoV entry. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037542/ doi: 10.1007/978-0-387-33012-9_46 id: cord-323468-xn7anxj6 author: Olloquequi, Jordi title: COVID‐19 Susceptibility in chronic obstructive pulmonary disease date: 2020-08-11 words: 4155.0 sentences: 220.0 pages: flesch: 45.0 cache: ./cache/cord-323468-xn7anxj6.txt txt: ./txt/cord-323468-xn7anxj6.txt summary: Chronic obstructive pulmonary disease (COPD) is a leading cause of death and disability globally, characterized by persistent respiratory symptoms and airflow limitation due to airway inflammation and/or alveolar abnormalities 10 . All rights reserved are associated to impaired lung function and risk of developing COPD 42-44 , it has also been demonstrated that people born with a diminished airway function are more likely to suffer COPD symptoms and subsequent viral infections [45] [46] [47] . In any case, there is no doubt that subjects who develop COPD are at an increased risk of suffering respiratory infections, a matter of importance in the context of COVID-19 pandemics. Increased cytokine response of rhinovirus-infected airway epithelial cells in chronic obstructive pulmonary disease DPP4, the Middle East Respiratory Syndrome Coronavirus Receptor, is Upregulated in Lungs of Smokers and Chronic Obstructive Pulmonary Disease Patients abstract: In the middle of December 2019, Chinese health authorities detected a series of pneumonia cases caused by an unknown agent in Wuhan, the capital of Hubei province. The causative agent was soon identified as a new strain of human‐infecting coronavirus(1), firstly named 2019 novel coronavirus (2019‐nCoV) and later renamed as severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The infection disease caused by SARS‐CoV‐2, known as coronavirus disease 2019 (COVID‐19), varied from asymptomatic or common cold‐like symptoms such as dry cough, fever and tiredness to severe dyspnea and respiratory failure(2). url: https://doi.org/10.1111/eci.13382 doi: 10.1111/eci.13382 id: cord-332948-h297ukuu author: Olotu, Fisayo A. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date: 2020-10-16 words: 5176.0 sentences: 315.0 pages: flesch: 51.0 cache: ./cache/cord-332948-h297ukuu.txt txt: ./txt/cord-332948-h297ukuu.txt summary: authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. 30 Identification of other functional (allosteric) sites on the prefusion S protein could present another dynamic and effective approach of preventing SARS-CoV-2 infectivity relative to its interaction with the host cell ACE2 and proteases. 53 Relatively, this study was implemented to (i) identify potential druggable sites across the S1 and S2 domains of the SARS-CoV-2 S protein other than the RBD-hACE2 interface (ii) perform high-throughput (virtual) screening of ~1500 FDA approved drugs against the most druggable site(s) (iii) investigate the binding dynamics and interaction mechanisms of the compounds and their consequential effects on the S-protein RBD-ACE2 complex. We believe this systematic study will be able to provide structural and molecular insights into possible allosteric sites on SARS-CoV-2 S protein suitable for selective targeting and structureComputational methodologies abstract: The systematic entry of SARS-CoV-2 into host cells, as mediated by its Spike (S) protein, is highly essential for pathogenicity in humans. Hence, targeting the viral entry mechanisms remains a major strategy for COVID-19 treatment. Although recent efforts have focused on the direct inhibition of S-protein receptor-binding domain (RBD) interactions with human angiotensin-converting enzyme 2 (hACE2), allosteric targeting remains an unexplored possibility. Therefore, in this study, for the first time, we employed an integrative meta-analytical approach to investigate the allosteric inhibitory mechanisms of SARS-CoV-2 S-protein and its association with hACE2. Findings revealed two druggable sites (Sites 1 and 2) located at the N-terminal domain (NTD) and S2 regions of the protein. Two high-affinity binders; ZINC3939013 (Fosaprepitant – Site 1) and ZINC27990463 (Lomitapide – Site 2) were discovered via site-directed high-throughput screening against a library of ∼1500 FDA approved drugs. Interestingly, we observed that allosteric binding of both compounds perturbed the prefusion S-protein conformations, which in turn, resulted in unprecedented hACE2 displacement from the RBD. Estimated ΔG(binds) for both compounds were highly favorable due to high-affinity interactions at the target sites. In addition, Site 1 residues; R190, H207, K206 and K187, I101, R102, I119, F192, L226, V126 and W104 were identified for their crucial involvement in the binding and stability of ZINC3939013. Likewise, energy contributions of Q957, N953, Q954, L303, Y313, Q314, L858, V952, N953, and A956 corroborated their importance to ZINC27990463 binding at the predicted Site 2. We believe these findings would pave way for the structure-based discovery of allosteric SARS-CoV-2 S-protein inhibitors for COVID-19 treatment. url: https://api.elsevier.com/content/article/pii/S2352914820306018 doi: 10.1016/j.imu.2020.100451 id: cord-338972-uq2ha8xs author: Olson, Michael T. title: Resumption of elective surgery during the COVID-19 pandemic: what lessons can we apply? date: 2020-06-05 words: 1688.0 sentences: 84.0 pages: flesch: 37.0 cache: ./cache/cord-338972-uq2ha8xs.txt txt: ./txt/cord-338972-uq2ha8xs.txt summary: authors: Olson, Michael T.; Triantafyllou, Tania; Singhal, Saurabh Ensure quality and quantity assessment of local PPE availability, and closely follow PPE recommendations for COVID-19+ patients, patients under investigations, and non-COVID-19 patients Re-evaluate health care facility capacity, including resources (e.g., beds, ICUs, ventilators), and expansion strategies Operating rooms should take inventory of existing surgical and cleaning supplies before re-activating elective surgeries Ensure coordination among surgery, anesthesia, nursing, engineering, housekeeping, and other hospital staff or specialties involved in multidisciplinary care; assure adequate staff volume Assign a governance committee to clarify, interpret, and iterate policies, make real-time decisions, and initiate and communicate messaging Although leading surgical societies have guided surgeons in terms of appropriate surgical practice amid the ongoing viral pandemic, certain questions remain, particularly pertaining to the safety of performing minimally invasive surgery in the setting of COVID-19. It remains to be determined how these infection-control measures, albeit contributing to the safety of the patient and staff, impact surgical care when elective surgeries are again performed. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32837512/ doi: 10.1007/s10353-020-00645-0 id: cord-303061-vvzkpetn author: Olyaee, Mohammad Hossein title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation date: 2020-08-07 words: 1343.0 sentences: 110.0 pages: flesch: 59.0 cache: ./cache/cord-303061-vvzkpetn.txt txt: ./txt/cord-303061-vvzkpetn.txt summary: title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation Utilizing chaos game representation (CGR) as well as recurrence quantification analysis (RQA) as a powerful nonlinear analysis technique, we proposed an effective process to extract several valuable features from genomic sequences of SARS-CoV-2.  The dataset involves features that enable us to compare genomic sequences with different lengths. In this work, according to the diagram represented in Fig. 1 , several recurrencequantification-based features are extracted from the nucleotide sequences. In this paper, we introduce a new dataset which involves efficient nonlinear features related to genomic sequences of SARS-CoV-2. In the final step, by applying recurrence quantification analysis (RQA), from each extracted coordinate series, 9 features are provided and totally 18 ( ) features will be extracted. • Extract features from coordinate series by applying recurrence quantification analysis measure gives the probability that two neighbors of any state are also neighbors and is obtained as below: abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. It was first detected in China and was rapidly spread to other countries. Several thousands of whole genome sequences of SARS-CoV-2 have been reported and it is important to compare them and identify distinctive evolutionary/mutant markers. Utilizing chaos game representation (CGR) as well as recurrence quantification analysis (RQA) as a powerful nonlinear analysis technique, we proposed an effective process to extract several valuable features from genomic sequences of SARS-CoV-2. The represented features enable us to compare genomic sequences with different lengths. The provided dataset involves totally 18 RQA-based features for 4496 instances of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S2352340920310386?v=s5 doi: 10.1016/j.dib.2020.106144 id: cord-273723-srfypn7j author: Omar, Sarah title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 words: 2932.0 sentences: 135.0 pages: flesch: 46.0 cache: ./cache/cord-273723-srfypn7j.txt txt: ./txt/cord-273723-srfypn7j.txt summary: title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis As far as we are aware, there are currently no published data on the duration of RNA positivity in the upper respiratory of patients with mild COVID-19 that could inform a public health assessment of RT-qPCR as a tool for monitoring home isolation. At 14 days after onset, the earliest moment to discontinue home isolation currently recommended in Germany [18] , 53.5% of COVID-19 patients still had detectable SARS-CoV-2 RNA (Figure 2) . Duration of SARS-CoV-2-RNA positivity in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 (n = 537) For cases where laboratory monitoring is indispensable, knowledge of the RT-qPCR threshold cycle may improve our judgement on whether a positive result indicates infectiousness or not [20] . abstract: We analysed consecutive RT-qPCR results of 537 symptomatic coronavirus disease (COVID-19) patients in home quarantine. Respectively 2, 3, and 4 weeks after symptom onset, 50%, 25% and 10% of patients had detectable RNA from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In patients with mild COVID-19, RNA detection is likely to outlast currently known periods of infectiousness by far and fixed time periods seem more appropriate in determining the length of home isolation than laboratory-based approaches. url: https://doi.org/10.2807/1560-7917.es.2020.25.30.2001292 doi: 10.2807/1560-7917.es.2020.25.30.2001292 id: cord-330129-izr62c68 author: Omer, Sumaira title: Preventive measures and management of COVID-19 in pregnancy date: 2020-04-09 words: 1950.0 sentences: 124.0 pages: flesch: 51.0 cache: ./cache/cord-330129-izr62c68.txt txt: ./txt/cord-330129-izr62c68.txt summary: As of 17 March 2020, there are 153 countries who have reported cases of infection caused by this virus [i.e., coronavirus disease-2019 (COVID19) ], with Italy becoming the new epicentre [1] . Importantly, viral respiratory illnesses, such as influenza, can easily develop during pregnancy, which means pregnant women may be more vulnerable to COVID-19 and require prioritized medical care. Interim COVID-19 guidelines for the effective counselling and education of pregnant women are currently available from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) [5, 6] . For effective management, pregnant women with suspected COVID-19 should be isolated and then transferred to a hospital equipped with sufficient health facilities and fully trained clinicians to take proper care of critically ill obstetric patients. Interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease 2019 (COVID-19) in healthcare settings abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32292265/ doi: 10.1007/s40267-020-00725-x id: cord-302393-hrz3bypr author: Omrani, Ali S. title: The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date: 2020-10-19 words: 4533.0 sentences: 269.0 pages: flesch: 52.0 cache: ./cache/cord-302393-hrz3bypr.txt txt: ./txt/cord-302393-hrz3bypr.txt summary: Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. In this study, we describe 60-day outcomes of a nationwide COVID-19 cohort from Qatar, and explore patient characteristics associated with the need for admission to an intensive care unit (ICU). In the multivariable logistic regression, we found that older age, male sex, co-existing diabetes or chronic kidney disease, and higher BMI were all independently associated with increased risk of need for ICU admission ( Table 2) . abstract: BACKGROUND: There are limited data on Coronavirus Disease 2019 (COVID-19) outcomes at a national level, and none after 60 days of follow up. The aim of this study was to describe national, 60-day all-cause mortality associated with COVID-19, and to identify risk factors associated with admission to an intensive care unit (ICU). METHODS: This was a retrospective cohort study including the first consecutive 5000 patients with COVID-19 in Qatar who completed 60 days of follow up by June 17, 2020. The primary outcome was all-cause mortality at 60 days after COVID-19 diagnosis. In addition, we explored risk factors for admission to ICU. RESULTS: Included patients were diagnosed with COVID-19 between February 28 and April 17, 2020. The majority (4436, 88.7%) were males and the median age was 35 years [interquartile range (IQR) 28–43]. By 60 days after COVID-19 diagnosis, 14 patients (0.28%) had died, 10 (0.2%) were still in hospital, and two (0.04%) were still in ICU. Fatal COVID-19 cases had a median age of 59.5 years (IQR 55.8–68), and were mostly males (13, 92.9%). All included pregnant women (26, 0.5%), children (131, 2.6%), and healthcare workers (135, 2.7%) were alive and not hospitalized at the end of follow up. A total of 1424 patients (28.5%) required hospitalization, out of which 108 (7.6%) were admitted to ICU. Most frequent co-morbidities in hospitalized adults were diabetes (23.2%), and hypertension (20.7%). Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. CONCLUSIONS: In a relatively younger national cohort with a low co-morbidity burden, COVID-19 was associated with low all-cause mortality. Independent risk factors for ICU admission included older age, male sex, higher BMI, and co-existing diabetes or chronic kidney disease. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12879-020-05511-8. url: https://doi.org/10.1186/s12879-020-05511-8 doi: 10.1186/s12879-020-05511-8 id: cord-285018-l26px1bc author: Ong, David S.Y. title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date: 2020-09-07 words: 1492.0 sentences: 90.0 pages: flesch: 55.0 cache: ./cache/cord-285018-l26px1bc.txt txt: ./txt/cord-285018-l26px1bc.txt summary: title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? OBJECTIVES: The aim of this study was to assess the diagnostic performance of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2. RealAmp Kit on the sample-to-result InGenius® platform in comparison to the national reference standard in the Netherlands, and to determine the added value of nucleoprotein (N) gene detection to establish the diagnosis of COVID-19. Patients were sampled from the oral cavity and subsequently from the nasal cavity using the same nasopharyngeal swab, which was tested by a validated in-house NAT assay on the presence of COVID-19 envelope protein (E) gene and RNA dependent RNA polymerase (RdRp) gene according to a reference method that was established after international collaboration [5] . abstract: BACKGROUND: Due to the emergence of the coronavirus disease 2019 (COVID-19) pandemic there is an urgent need for rapid and accurate testing on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). OBJECTIVES: The aim of this study was to assess the diagnostic performance of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2. STUDY DESIGN: Patients were eligible between March 18 and May 27, 2020, when they had respiratory symptoms that were suspected for COVID-19. The InGenius platform was compared to routine in-house NAT that was validated according to the national reference. RESULTS: Of 128 randomly selected patients, 58 (45%) tested positive and 55 (43%) tested negative in both platforms. Sensitivity of the InGenius platform was 100% (95% confidence interval 94-100). In the remaining 15 (12%) cases E and RdRp genes were not detected in both platforms but the nucleoprotein (N) gene was tested positive by the InGenius platform. All solitary N gene positive cases were confirmed by a N-gene specific in-house validated NAT, and most of these patients could also be considered positive based on other recently available COVID-19 positive respiratory samples or highly suspected radiological findings. CONCLUSION: The InGenius platform for SARS-CoV-2 detection has excellent sensitivity, is easy to use and provides fast results. The inclusion of the N gene as a third gene target may further increase sensitivity for the diagnosis of COVID-19 in comparison to the national reference method. url: https://api.elsevier.com/content/article/pii/S1386653220303747 doi: 10.1016/j.jcv.2020.104632 id: cord-338001-jig46hsk author: Ong, Jacqueline S. M. title: Coronavirus Disease 2019 in Critically Ill Children: A Narrative Review of the Literature date: 2020-04-21 words: 3418.0 sentences: 178.0 pages: flesch: 50.0 cache: ./cache/cord-338001-jig46hsk.txt txt: ./txt/cord-338001-jig46hsk.txt summary: In the small cohort from Tongji Hospital (6), Wuhan, one out of the six children with COVID-19 was admitted to intensive care. Given that children appear to have mild disease and may have a clinical picture similar to that of viral bronchiolitis, the use of noninvasive ventilation (NIV), and/or high-flow nasal cannula (HFNC) for respiratory support would likely be preferred amongst PICU clinicians. Caregivers are close contacts of the infected patient, although they may be asymptomatic at the time-in the Wuhan Children''s Hospital series with active case finding of close contacts, 90% of confirmed cases had family members who were either confirmed or suspect disease (5) . Given the low rates of critical illness due to COVID-19, this process will likely exert more impact on day-to-day processes in PICUs than sick patients with confirmed infection. Paediatric Intensive Care Society UK: PICS Guidance on Management of Critically Ill Children With COVID-19 Infection abstract: Coronavirus disease 2019 has spread around the world. In the 3 months since its emergence, we have learned a great deal about its clinical management and its relevance to the pediatric critical care provider. In this article, we review the available literature and provide valuable insight into the clinical management of this disease, as well as information on preparedness activities that every PICU should perform. url: https://doi.org/10.1097/pcc.0000000000002376 doi: 10.1097/pcc.0000000000002376 id: cord-252557-f89m6xv5 author: Ong, John title: Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard date: 2020-04-02 words: 1300.0 sentences: 97.0 pages: flesch: 47.0 cache: ./cache/cord-252557-f89m6xv5.txt txt: ./txt/cord-252557-f89m6xv5.txt summary: title: Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Over 3000 healthcare workers (HCW) in China are suspected of having coronavirus disease 2019 (COVID-19) and over 1700 tested positive. PPE recommendation (general staff): ► All patients to be offered surgical face masks Contingency plan for high-risk patients detected in endoscopy: ► Not stated. PPE recommendation (general staff): ► None stated Contingency plan for high-risk patients detected in endoscopy: ► Not stated. 4 Patient screening undoubtedly is the foremost step at preventing nosocomial transmission; timely detection allows postponement of non-urgent procedures until the infection has resolved, significantly reducing transmission risk to patients and staff. Detecting ''false negatives'' that slip through processes allows for the identification of HCWs and patients with infection risk after exposure to asymptomatic or subclinical carriers in the viral incubation period at the time of endoscopy. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32241901/ doi: 10.1136/gutjnl-2020-321154 id: cord-255997-oer5lxxr author: Onodi, Fanny title: SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date: 2020-07-10 words: 4209.0 sentences: 254.0 pages: flesch: 53.0 cache: ./cache/cord-255997-oer5lxxr.txt txt: ./txt/cord-255997-oer5lxxr.txt summary: Here, we have studied the interaction of isolated primary SARS-CoV-2 viral strains with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. Importantly, all major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine, including P2and P3-pDC differentiation, the expression of maturation markers, and the production of interferon-α and inflammatory cytokines. Interestingly, pDC responded to SARS-CoV-2 by a complete activation program, including diversification into effector subsets, production of type I and type III IFN, as well as inflammatory cytokines. We also showed that hydroxychloroquine, an antimalarial drug proposed for treatment of COVID-19 patients (Das et al., 2020; Mahévas et al., 2020) , inhibits SARS-CoV-2-induced pDC activation and IFN production in a dose-dependent manner. Following 24 hours of culture, we found that HCQ inhibited pDC diversification in response to SARS-CoV-2, which is similar to the decrease observed with Flu, used as a positive control ( Fig 4A) . abstract: Several studies have analyzed antiviral immune pathways in severe COVID-19 patients. However, the initial steps of antiviral immunity are not known. Here, we have studied the interaction of isolated primary SARS-CoV-2 viral strains with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. We show that pDC are not permissive to SARS-CoV-2 infection. However, they efficiently diversified into activated P1-, P2-, and P3-pDC effector subsets in response to viral stimulation. They expressed checkpoint molecules at levels similar to influenza virus-induced activation. They rapidly produced high levels of interferon-α, interferon-λ1, IL-6, IP-10, and IL-8. Importantly, all major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine, including P2- and P3-pDC differentiation, the expression of maturation markers, and the production of interferon-α and inflammatory cytokines. Our results indicate that pDC may represent a major player in the first line of defense against SARS-CoV-2 infection, and call for caution in the use of hydroxychloroquine in the early treatment of the disease. url: https://doi.org/10.1101/2020.07.10.197343 doi: 10.1101/2020.07.10.197343 id: cord-315283-xwan2t1u author: Ooi, Setthasorn Zhi Yang title: Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching date: 2020-09-15 words: 797.0 sentences: 56.0 pages: flesch: 50.0 cache: ./cache/cord-315283-xwan2t1u.txt txt: ./txt/cord-315283-xwan2t1u.txt summary: title: Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. The Human Tissue Authority has also released a statement that medical schools in the UK (UK) are not allowed to receive body donations due to the SARS-CoV-2 virus outbreak [3] . In the upcoming academic years, incoming students of medical schools who practice cadaveric dissection teaching will miss out on the opportunity to learn anatomy through dissections. This letter aims to explore the implications of the cancellation of cadaveric dissection in anatomy teaching as a result of the SARS-CoV-2 virus pandemic. What does this mean for medical students at schools who traditionally teach anatomy through cadaveric dissections? abstract: The SARS-CoV-2 virus pandemic has left a huge impact on medical education globally. An area that has not been discussed in medical education is the potential implications of the cessation of body and organ donations on medical education. We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. url: https://doi.org/10.1080/10872981.2020.1823089 doi: 10.1080/10872981.2020.1823089 id: cord-317971-kuwargnp author: Opatz, Till title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 words: 2881.0 sentences: 176.0 pages: flesch: 53.0 cache: ./cache/cord-317971-kuwargnp.txt txt: ./txt/cord-317971-kuwargnp.txt summary: [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. abstract: The SARS‐CoV‐2 outbreak causing the respiratory disease COVID‐19 has left many chemists in academia without an obvious option to contribute to fighting the pandemic. Some of our recent experiences indicate that there are ways to overcome this dilemma. A three‐pronged approach is proposed. url: https://www.ncbi.nlm.nih.gov/pubmed/32329159/ doi: 10.1002/anie.202004721 id: cord-346153-9162w7il author: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 words: 1716.0 sentences: 90.0 pages: flesch: 43.0 cache: ./cache/cord-346153-9162w7il.txt txt: ./txt/cord-346153-9162w7il.txt summary: Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. However, the coronavirus copy number in some studies showed an increase between day 5 and day 10, so that maximal infectivity followed the fever, 7 leading perhaps to a false sense of security amongst those caring for SARS patients. e reason for these interactions are incompletely understood, but intriguing recent study show that in uenza and respiratory syndrome virus are both capable of causing a persistent inhibition of the innate response to bacterial superinfection, and therefore to increased bacterial replication and disease. Highly pathogenic strains of in uenza also cause intense systemic symptoms, sometimes associated with gastrointestinal disease. Microbial translocation is a cause of systemic immune activation in chronic HIV infection abstract: Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. In addition, other classically non-enteric viruses (such as HIV and influenza) may also have enteric effects that are crucial in their pathogeneses. These effects can be due to direct infection of the gut mucosa, but can also be because of decreased antibacterial defenses, increased mucosal permeability, bacterial translocation, and systemic leak of endotoxin. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/mi.2008.79) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/19129753/ doi: 10.1038/mi.2008.79 id: cord-283824-c7y9zf7o author: Opitz, Sven title: Regulating epidemic space: the nomos of global circulation date: 2015-02-20 words: 8618.0 sentences: 492.0 pages: flesch: 46.0 cache: ./cache/cord-283824-c7y9zf7o.txt txt: ./txt/cord-283824-c7y9zf7o.txt summary: The first concerns the referent object of governmental practice: the regulatory effort to secure global public health does not focus on human life so much as it does on post-human materialities of global traffic. Most importantly, the key passages of the IHR read like a clear-cut manifestation of the liberal government of circulation: ''The purpose and scope of these Regulations are to prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which avoid unnecessary interference with international traffic and trade.'' (IHR, Article 2) The mobility of disease and the mobility of goods and people are conjoined in this problem space. These bodies of transmission belong to a governmental vision that pictures the world as a space of universal traffic and that focuses on routes and material means of global circulation. abstract: After the Severe Acute Respiratory Syndrome (SARS) outbreak in 2002, legal theorist David Fidler diagnosed the arrival of the ‘first post-Westphalian pathogen’. The coinage indicates that the spread of infectious disease transforms the spatial coordinates of the modern political environment. This article analyses this transformation by asking how the legal regime, designed to prepare for the pandemic, envisions the globe as an object of government. It demonstrates that the WHO’s International Health Regulations (IHR) articulate a space of global circulation that exhibits two features. First, the infrastructures of microbial traffic become the primary matters of concern. The IHR do not focus on human life so much as they aim at securing transnational mobilities. Second, the IHR circumscribe a space that is fragmented by zones of intensified governmental control at transportational nodal points, such as airports and harbours. In these zones, technologies of screening and quarantine are applied to modulate the connectivity of people, organic matter and things. As a whole, the article investigates how processes of de- and re-territorialisation interact in the context of global health security. In analysing forms of legal worldmaking, it unearths a nomos of global circulation which applies its regulatory force to the post-human materialities of microbial traffic. url: https://doi.org/10.1057/jird.2014.30 doi: 10.1057/jird.2014.30 id: cord-304232-c0cpx2q3 author: Opriessnig, Tanja title: Update on possible animal sources for COVID‐19 in humans date: 2020-06-17 words: 988.0 sentences: 75.0 pages: flesch: 54.0 cache: ./cache/cord-304232-c0cpx2q3.txt txt: ./txt/cord-304232-c0cpx2q3.txt summary: 7 In support of these early results, an ongoing study conducted at the Friedrich Loeffler Institute in Germany further confirmed that pigs and chickens are not susceptible to intranasal infection with SARS-CoV-2 (https://prome dmail.org/prome d-post/?id=7196506). 7 Natural infection, as evidenced by the presence of antibodies, SARS-CoV-2 RNA or both, has been identified in selected dogs in close contact with COVID-19 patients (Table 3) . A recent French study, which investigated nine cats and 12 dogs in close contact with a cluster of COVID-19 patients, was unable to detect evidence of SARS-CoV-2 infection in any of the animals. Moreover, animal-to-human SARS-CoV-2 infection as well as natural animal-to-animal transmission has yet to be confirmed and none of the species considered to be susceptible to the virus at this point are presently used for xenotransplantation. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32557711/ doi: 10.1111/xen.12621 id: cord-337789-pabaoiqs author: Oprinca, George-Călin title: Postmortem examination of three SARS-CoV-2-positive autopsies including histopathologic and immunohistochemical analysis date: 2020-08-27 words: 4995.0 sentences: 282.0 pages: flesch: 47.0 cache: ./cache/cord-337789-pabaoiqs.txt txt: ./txt/cord-337789-pabaoiqs.txt summary: This paper describes three autopsy cases with postmortem diagnosis of SARS-CoV-2 infection, with detailed macroscopic examination as well as advanced microscopic studies of organ tissues collected using hematoxylin-eosin stains and immunohistochemical markers. Microscopic evaluation revealed viral cytopathic effect of type II pneumocytes with a couple of cells that presented cytoplasmic and nuclear inclusions and who tend to form clusters mimicking multinucleated giant cells. This paper describes three autopsy cases with unknown cause of death, with full macroscopic examination as well as histopathologic and immunohistochemical analysis of collected organ tissues, including the lung from which reverse transcription polymerase chain reaction (rt-PCR) tests were made to determine SARS-CoV-2 infection. Microscopic examination of the pulmonary tissue revealed large areas of alveolar damage with destruction of the alveolar wall lining and intra-alveolar septa, marked vascular congestion, accompanied by intra-alveolar hemorrhage. abstract: This paper describes three autopsy cases with postmortem diagnosis of SARS-CoV-2 infection, with detailed macroscopic examination as well as advanced microscopic studies of organ tissues collected using hematoxylin-eosin stains and immunohistochemical markers. Two of the cases were admitted briefly in the County Clinical Emergency Hospital of Sibiu, and one was found deceased at his home address. All three autopsies were completed at the County morgue, in the COVID-19 restricted area, using complete protective equipment. The lungs of the patients seemed to be the center organ of invasion and pathogenesis of the novel coronavirus with diffuse areas of condensation, subpleural retraction zones but with different aspect of the classic bacterial bronchopneumonia. Microscopic evaluation revealed viral cytopathic effect of type II pneumocytes with a couple of cells that presented cytoplasmic and nuclear inclusions and who tend to form clusters mimicking multinucleated giant cells. Hyaline membranes and destruction of the alveolar wall as well as microthrombi formation within the small blood vessels were constantly found in almost all our three cases. The spleen had sustained white pulp atrophy with absence of lymphoid follicles. There were no microscopic signs of viral infection on the myocardium or the other organs. url: https://www.ncbi.nlm.nih.gov/pubmed/32851474/ doi: 10.1007/s00414-020-02406-w id: cord-338351-y1t9emu1 author: Ora, Josuel title: Does bronchoscopy help the diagnosis in Covid-19 infection? date: 2020-06-11 words: 968.0 sentences: 59.0 pages: flesch: 46.0 cache: ./cache/cord-338351-y1t9emu1.txt txt: ./txt/cord-338351-y1t9emu1.txt summary: The diagnosis of COVID-19 is mainly based on typical symptoms, history of exposure to an infected person and bilateral involvement on chest radiographs, and it is confirmed by a positive nucleic acid test for SARS-CoV-2 from numerous types of specimens including Oropharyngeal (OP) and nasopharyngeal (NP) swabs, anal swabs, stool, urine and bronchoalveoalr lavage fluid (BALF) 1,2 . Here we report our experience from a COVID-19 hospital in Rome, Italy, where patients with typical symptoms of the disease, suggestive CT scans and three NP/OP negative swabs performed on consecutive days and IgG and IgM serology negative for SARS-CoV-2 underwent bronchoscopy with BAL to define the diagnostic issue. In conclusion, our findings demonstrate that three negative swabs along with negative antibodies, despite a suggestive CT scan, can safely rule out the SARS-CoV-2 infection in suspected patients, hence to proceed in alternative diagnosis process. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent responsible for the recent Coronavirus Disease 2019 (COVID-19) pandemic. This virus is predominantly spread through large droplets. The clinical features of COVID-19 are varied, ranging from asymptomatic to acute respiratory distress syndrome and multi-organ dysfunction [1]. url: https://www.ncbi.nlm.nih.gov/pubmed/32527742/ doi: 10.1183/13993003.01619-2020 id: cord-318069-logh6rnu author: Ordás, Carlos M. title: Concurrent tonic pupil and trochlear nerve palsy in COVID-19 date: 2020-09-10 words: 1334.0 sentences: 85.0 pages: flesch: 50.0 cache: ./cache/cord-318069-logh6rnu.txt txt: ./txt/cord-318069-logh6rnu.txt summary: We report a case of concurrent tonic pupil and trochlear nerve palsy in this context. A 62-year-old man reported a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. Clinical exam showed a right trochlear nerve palsy and a left mydriatic pupil. This is the first case reporting Adie''s pupil as a postinfectious manifestation of COVID-19. Here, we report a case of a fourth cranial mononeuropathy coexisting with a contralateral tonic pupil developing 2 weeks after a SARS-CoV-2 infection. A 62-year-old man with an antecedent of hypertension attended our hospital reporting a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. In conclusion, we report an exceptional case of trochlear mononeuropathy and tonic pupil occurring shortly after a SARS-CoV-2 infection, with a presumable immunemediated mechanism. abstract: Since COVID-19 was first reported, different neurological complications have been acknowledged, but their description is constantly evolving. We report a case of concurrent tonic pupil and trochlear nerve palsy in this context. A 62-year-old man reported a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. He had suffered a flu-like syndrome 2 weeks before. Clinical exam showed a right trochlear nerve palsy and a left mydriatic pupil. MRI, X chest ray, and analytical results were normal. Antibodies for SARS-CoV-2 were positive (low IgM and high IgG titers). Antiganglioside antibodies were negative. A 0.125% pilocarpine test confirmed Adie’s pupil diagnosis. The patient was treated with a tapered prednisone dose with resolution of his diplopia but no change in Adie’s pupil. This is the first case reporting Adie’s pupil as a postinfectious manifestation of COVID-19. An immune-mediated mechanism is presumed. url: https://doi.org/10.1007/s13365-020-00909-1 doi: 10.1007/s13365-020-00909-1 id: cord-292041-a65kfw80 author: Orienti, Isabella title: Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19 date: 2020-05-27 words: 6110.0 sentences: 334.0 pages: flesch: 34.0 cache: ./cache/cord-292041-a65kfw80.txt txt: ./txt/cord-292041-a65kfw80.txt summary: At present, there is no vaccine or effective standard treatment for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (or coronavirus disease-19 (COVID-19)), which frequently leads to lethal pulmonary inflammatory responses. Therefore, due to its poly-pharmacology, fenretinide administration by pulmonary formulations may be expected to be protective against acute lung injury (ALI)/ acute respiratory distress syndrome (ARDS) caused by SARS-CoV infection and could represent a useful tool in a multimodal therapy aimed at establishing a rapid anti-inflammatory and antiviral effect. Pulmonary delivery of fenretinide could be a valuable tool in COVID-19 due to the possibility of obtaining a very high drug concentration in the airway and alveolar epithelia, thus triggering a rapid onset of local anti-inflammatory response. Moreover, the pulmonary administration of fenretinide, in combination with the drugs that are currently used in SARS-CoV-2 infection, could represent a new, effective tool in COVID-19 treatment. abstract: At present, there is no vaccine or effective standard treatment for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (or coronavirus disease-19 (COVID-19)), which frequently leads to lethal pulmonary inflammatory responses. COVID-19 pathology is characterized by extreme inflammation and amplified immune response with activation of a cytokine storm. A subsequent progression to acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) can take place, which is often followed by death. The causes of these strong inflammatory responses in SARS-CoV-2 infection are still unknown. As uncontrolled pulmonary inflammation is likely the main cause of death in SARS-CoV-2 infection, anti-inflammatory therapeutic interventions are particularly important. Fenretinide N-(4-hydroxyphenyl) retinamide is a bioactive molecule characterized by poly-pharmacological properties and a low toxicity profile. Fenretinide is endowed with antitumor, anti-inflammatory, antiviral, and immunomodulating properties other than efficacy in obesity/diabetic pathologies. Its anti-inflammatory and antiviral activities, in particular, could likely have utility in multimodal therapies for the treatment of ALI/ARDS in COVID-19 patients. Moreover, fenretinide administration by pulmonary delivery systems could further increase its therapeutic value by carrying high drug concentrations to the lungs and triggering a rapid onset of activity. This is particularly important in SARS-CoV-2 infection, where only a narrow time window exists for therapeutic intervention. url: https://doi.org/10.3390/ijms21113812 doi: 10.3390/ijms21113812 id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 words: 3804.0 sentences: 228.0 pages: flesch: 51.0 cache: ./cache/cord-340627-xyvzgkxl.txt txt: ./txt/cord-340627-xyvzgkxl.txt summary: title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening abstract: OBJECTIVES: 1. To assess the performance of an extended questionnaire in identifying cases of SARS-CoV-2 infection among obstetric patients. 2. To evaluate the rate of infection among healthcare workers involved in women’s care. STUDY DESIGN: A prospective cohort study of obstetric patients admitted to MBBM Foundation and Buzzi Hospital (Lombardy, Northern Italy) from March 16(th) to May 22(nd), 2020. Women were screened on admission by a questionnaire investigating major and minor symptoms of infection and high-risk contacts in the last 14 days. SARS-CoV-2 assessment was performed by RT-PCR on nasopharyngeal swabs. Till April 7(th), a targeted SARS-CoV-2 testing triggered by a positive questionnaire was used; from April 8(th), a universal testing approach was implemented. RESULTS: There were 1,177 women screened by the questionnaire, which yielded a positive result in 130 (11.0%) cases. SARS-CoV-2 RT-PCR was performed in 865 (73.5%) patients, identifying 51 (5.9%) infections. During the first period, there were 29 infected mothers, 4 (13.8%) of whom had a negative questionnaire. After universal testing implementation, there were 22 (3%, 95% CI 1.94% - 4.04%) infected mothers, 13 (59.1%) of whom had a negative questionnaire; rate of infection among asymptomatic women was 1.9%. Six of the 17 SARS-CoV-2-positive women with a negative questionnaire reported symptoms more than 14 but within 30 days before admission. Isolated olfactory or taste disorders were identified in 15.7% of infected patients. Rate of infection among healthcare workers was 5.8%. CONCLUSIONS: An exhaustive triage questionnaire can effectively discriminate women at low risk of SARS-CoV-2 infection in the context of a targeted and a universal viral testing approach. In 15.7% of infected women, correct classification as a suspected case of infection was due to investigation of olfactory and taste disorders. Extension of the assessed time-frame to 30 days may be worth considering to increase the questionnaire’s performance. url: https://www.ncbi.nlm.nih.gov/pubmed/32931524/ doi: 10.1371/journal.pone.0239173 id: cord-285603-f4572w5m author: Ortega, Joseph T. title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 words: 5994.0 sentences: 348.0 pages: flesch: 47.0 cache: ./cache/cord-285603-f4572w5m.txt txt: ./txt/cord-285603-f4572w5m.txt summary: In order to gain a deeper understanding if the pharmacokinetic parameters of the SARS-CoV2 protease inhibitors could be related to positive outcomes in the therapy, we analyzed the ADME parameters of famotidine and compared with several known antiviral drugs such as ribavirin, lopinavir, and nafamostat, which were evaluated against SARS-CoV2. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Altogether, in this study, we showed that famotidine could be used as an antiviral agent against SARS-CoV2, targeting proteases involved in the virus replication, mostly the main protease, as well as the viral PLpro and human host Tmprss2. abstract: The pandemic associated with Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV2) and its disease named COVID-19 challenged the scientific community to discover effective therapeutic solutions in a short period. Repurposing existing drugs is one viable approach that emphasizes speed during these urgent times. Famotidine, a class A G protein-coupled receptor antagonist used for the treatment of gastroesophageal reflux was recently identified in an in silico screening. Additionally, a recent retrospective clinical report showed that the treatment with famotidine provided a good outcome in patients infected with SARS-CoV2. A clinical trial testing effectiveness of famotidine in combination with hydroxychloroquine is currently ongoing in the United States (US). In the 1990s, famotidine was described as an antiviral agent against human immunodeficiency virus (HIV). Interestingly, some HIV protease inhibitors are presently being used against SARS-CoV2. However, it is not clear if famotidine could be effective against SARS-CoV2. Thus, by using a computational analysis, we aimed to examine if the antiviral effect of famotidine could be related to the inhibition of proteases involved in the virus replication. Our results showed that famotidine could interact within the catalytic site of the three proteases associated with SARS-CoV2 replication. However, weak binding affinity of famotidine to these proteases suggests that a successful famotidine therapy could likely be achieved only in combination with other antiviral drugs. Finally, analysis of famotidine’s pharmacokinetic parameters indicated that its effect against SARS-CoV2 infection could be reached only upon intravenous administration. This work will contribute to the pharmacological knowledge of famotidine as an antiviral agent against SARS-CoV2. url: https://www.ncbi.nlm.nih.gov/pubmed/32599963/ doi: 10.3390/biom10060954 id: cord-318316-9unfl966 author: Ortega, Joseph T. title: Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies date: 2020-10-23 words: 4022.0 sentences: 236.0 pages: flesch: 46.0 cache: ./cache/cord-318316-9unfl966.txt txt: ./txt/cord-318316-9unfl966.txt summary: SUMMARY: This review focused on the basic principles of virology and pharmacology to understand the importance of early stages of virus-cell interaction as therapeutic targets and other main processes vital for SARS-CoV-2 replication. Furthermore, we focused on describing the main targets associated with SARS-CoV-2 antiviral therapy and the rationale of drug combinations for efficiently suppressing viral replication. Another early target evaluated against SARS-CoV-2 is a cellular protease related to the priming of the spike protein (S), which exposes the fusion motive and allows the release of viral RNA into the cytosol. HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; ORF, open reading frame. Favipiravir, another antiviral agent with broad activity against other RNA viruses by inhibiting the RdRp, halting viral replication, was evaluated against SARS-CoV-2, showing effects in vitro and in vivo [43] [44] [45] . abstract: BACKGROUND: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its disease CO­VID-19 has strongly encouraged the search for antiviral compounds. Most of the evaluated drugs against SARS-CoV-2 derive from drug repurposing of Food and Drug Administration-approved molecules. These drugs have as target three major processes: (1) early stages of virus-cell interaction, (2) viral proteases, and (3) the viral RNA-dependent RNA polymerase. SUMMARY: This review focused on the basic principles of virology and pharmacology to understand the importance of early stages of virus-cell interaction as therapeutic targets and other main processes vital for SARS-CoV-2 replication. Furthermore, we focused on describing the main targets associated with SARS-CoV-2 antiviral therapy and the rationale of drug combinations for efficiently suppressing viral replication. KEY MESSAGES: We hypothesized that blocking of both entry mechanisms could allow a more effective antiviral effect compared to the partial results obtained with chloroquine or its derivatives alone. This approach, already used to achieve an antiviral effect higher than that offered by every single drug administered separately, has been successfully applied in several viral infections such as HIV and HCV. This review will contribute to expanding the perception of the possible therapeutic targets in SARS-CoV-2 infection and highlight the benefits of using combination therapies. url: https://doi.org/10.1159/000512141 doi: 10.1159/000512141 id: cord-294692-qfz6a1kc author: Ortega, Karem L. title: SARS-CoV-2 and dentistry date: 2020-06-05 words: 1014.0 sentences: 56.0 pages: flesch: 49.0 cache: ./cache/cord-294692-qfz6a1kc.txt txt: ./txt/cord-294692-qfz6a1kc.txt summary: The identification that the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a virus transmitted through airways or by direct contact with the mucosas [2] has prompted the dental community to become alert. They concluded that human coronavirus on inanimate surfaces could be inactivated by using ethanol (62-71%), hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%) for 1 min, whereas other substances such as benzalkonium chloride (0.05% and 0.2%) and chlorhexidine digluconate (0.02%) were less effective. The authors also pointed out that although no study had tested the virucidal capacity of those agents against SARS-CoV-2, they expected a similar effect against this virus [5] . However, the suggestion to use mouthwash with 1% hydrogen peroxide or 0.2% povidone in order to decrease the viral load in saliva, based on the idea that SARS-CoV-2 would be vulnerable to oxidation, does not seem to be based on scientific evidence to date. abstract: nan url: https://doi.org/10.1007/s00784-020-03381-7 doi: 10.1007/s00784-020-03381-7 id: cord-259668-nwezszhj author: Ortiz, Alberto title: Complement and protection from tissue injury in COVID-19 date: 2020-10-04 words: 2618.0 sentences: 129.0 pages: flesch: 37.0 cache: ./cache/cord-259668-nwezszhj.txt txt: ./txt/cord-259668-nwezszhj.txt summary: Finally, preclinical studies in endotoxaemia, another hyperinflammation syndrome characterized by lung and kidney injury, suggest that cilastatin, an inexpensive drug already in clinical use, may provide tissue protection against hyperinflammation in COVID-19. In any case, this report suggests that assessing complement peptides may eventually contribute to define clusters of COVID-19 patients, as has been done for C3 glomerulopathies/immune complex-mediated membranoproliferative glomerulonephritis [11, 12] . In non-controlled case series and case reports, relatively positive results have been reported for the anti-C5 monoclonal antibody eculizumab, for C3 inhibitor AMY-101, for the mannan-binding lectin-associated serine protease 2 blocker narsoplimab (OMS721), for aliskiren and for nafamostat mesylate, a US Food and Drug Administration-approved anticoagulant agent that has broad-spectrum serine protease inhibitory activity, including for C1 esterase [2, [19] [20] [21] [22] [23] [24] [25] [26] . [3] emphasize, the fact that the SARS-CoV-2 cellular receptor ACE2 is expressed in lipid rafts may provide two mechanisms by which cilastatin may protect from severe COVID-19: (i) stabilizing ACE2 at the cell surface lipid rafts and preventing virus/ACE2 internalization and (ii) preventing hyperinflammation-induced tissue injury as observed in rat endotoxemia. abstract: As the second wave of coronavirus disease 2019 (COVID-19) is well under way around the world, the optimal therapeutic approach that addresses virus replication and hyperinflammation leading to tissue injury remains elusive. This issue of Clinical Kidney Journal provides further evidence of complement activation involvement in COVID-19. Taking advantage of the unique repeat access to chronic haemodialysis patients, the differential time course of C3 and C5 activation in relation to inflammation and severity of disease have been characterized. This further points to complement as a therapeutic target. Indeed, clinical trials targeting diverse components of complement are ongoing. However, a unique case of COVID-19 in a patient with pre-existent atypical haemolytic syndrome on chronic eculizumab therapy suggests that even early eculizumab may fail to prevent disease progression to a severe stage. Finally, preclinical studies in endotoxaemia, another hyperinflammation syndrome characterized by lung and kidney injury, suggest that cilastatin, an inexpensive drug already in clinical use, may provide tissue protection against hyperinflammation in COVID-19. url: https://doi.org/10.1093/ckj/sfaa196 doi: 10.1093/ckj/sfaa196 id: cord-286683-mettlmhz author: Ortiz-Prado, Esteban title: Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date: 2020-05-30 words: 13299.0 sentences: 726.0 pages: flesch: 45.0 cache: ./cache/cord-286683-mettlmhz.txt txt: ./txt/cord-286683-mettlmhz.txt summary: Interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in SARS [59] and MERS diseases [60] were also reported in the early study of 41 patients with COVID-19 in Wuhan [41] . A recently published case report of a patient with mild-to-moderate COVID-19 revealed the presence of an increased activated CD4+ T cells and CD8+ T cells, antibody-secreting cells (ASCs), follicular helper T cells (TFH cells), and anti-SARS-CoV-2 IgM and IgG antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [82] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series abstract: Abstract Coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. The current classification of coronaviruses recognizes 39 species in 27 subgenera that belong to the family Coronaviridae. From those, at least seven coronaviruses are known to cause respiratory infections in humans. Four of these viruses can cause common cold-like symptoms. Those that infect animals can evolve and become infectious to humans. Three recent examples of these viral jumps include SARS CoV, MERS-CoV and SARS CoV-2 virus. They are responsible for causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the most recently discovered coronavirus disease during 2019 (COVID-19). COVID-19, a respiratory disease caused by the SARS-CoV-2 virus, was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. The rapid spread of the disease has taken the scientific and medical community by surprise. Latest figures from 20th May 2020 show more than 5 million people had been infected with the virus, causing more than 330,000 deaths in over 210 countries worldwide. The large amount of information received daily relating to COVID-19 is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. In order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the SARS CoV-2 Virus and the Coronavirus Diseases 2019 (COVID-19). url: https://doi.org/10.1016/j.diagmicrobio.2020.115094 doi: 10.1016/j.diagmicrobio.2020.115094 id: cord-312918-iof45k1r author: Ortolani, Claudio title: Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost? date: 2020-09-09 words: 4637.0 sentences: 213.0 pages: flesch: 45.0 cache: ./cache/cord-312918-iof45k1r.txt txt: ./txt/cord-312918-iof45k1r.txt summary: Recently, four large Randomized Controlled Trials (RCTs) have been performed in record time delivering reliable data: (1) the National Institutes of Health (NIH) RCT included 60 hospitals participating all over the world and showed the efficacy of remdesivir in reducing the recovery time in hospitalized adults with COVID-19 pneumonia; (2) three large RCTs already completed, for hydroxychloroquine, dexamethasone and Lopinavir and Ritonavir respectively. In 2019, at the beginning of the SARS-CoV-2 pandemic, at least 4 anti-inflammatory and antiviral drugs were available and in use, with possible efficacy for COVID-19: hydroxychloroquine, corticosteroids, remdesivir and Lopinavir / Ritonavir. Remark 1 cited a number of systematic reviews, which however had selected only observational clinical studies that addressed the efficacy and side effects of the corticosteroid treatment of viral pneumonia from SARS, H1N1 influenza virus and MERS virus, but not from SARS-CoV-2 virus [31] [32] [33] [34] . abstract: BACKGROUND: On June 30, 2020, the WHO reported over 10 millions of COVID-19 cases worldwide with over half a million deaths. In severe cases the disease progresses into an Acute Respiratory Distress Syndrome (ARDS), which in turn depends on an overproduction of cytokines (IL-6, TNFα, IL-12, IL-8, CCL-2 and IL1) that causes alveolar and vascular lung damage. Clearly, it is essential to find an immunological treatment that controls the “cytokine storm”. In the meantime, however, it is essential to have effective antiviral and anti-inflammatory drugs available immediately. PHARMACOLOGIC THERAPY FOR COVID-19: Hydroxychloroquine or chloroquine have been widely adopted worldwide for the treatment of SARS-CoV-2 pneumonia. However, the choice of this treatment was based on low quality of evidence, i.e. retrospective, non-randomized controlled studies. Recently, four large Randomized Controlled Trials (RCTs) have been performed in record time delivering reliable data: (1) the National Institutes of Health (NIH) RCT included 60 hospitals participating all over the world and showed the efficacy of remdesivir in reducing the recovery time in hospitalized adults with COVID-19 pneumonia; (2) three large RCTs already completed, for hydroxychloroquine, dexamethasone and Lopinavir and Ritonavir respectively. These trials were done under the umbrella of the 'Recovery' project, headed by the University of Oxford. The project includes 176 participating hospitals in the UK and was set up to verify the efficacy of some of the treatments used for COVID-19. These three ‘Recovery’ RCTs concluded definitely: (a) that treatment with hydroxychloroquine provides no benefits in patients hospitalized with COVID-19; (b) that treatment with dexamethasone reduced deaths by one-third in COVID-19 patients that were mechanically ventilated, and by one-fifth in patients receiving oxygen only; (c) that the combination of Lopinavir and Ritonavir is not effective in reducing mortality in COVID-19 hospitalized patients. CONCLUSIONS: The results of these four large RCTs have provided sound indications to doctors for the treatment of patients with COVID-19 and prompted the correction of many institutional provisions and guidelines on COVID-19 treatments (i.e. FDA, NIH, UK Health Service, etc.). Even though a definitive treatment for COVID-19 has not yet been found, large RCTs stand as the Gold Standards for COVID-19 therapy and offer a solid scientific base on which to base treatment decisions. url: https://doi.org/10.1186/s12948-020-00132-7 doi: 10.1186/s12948-020-00132-7 id: cord-339968-s1kmipir author: Osier, Faith title: The global response to the COVID-19 pandemic: how have immunology societies contributed? date: 2020-09-10 words: 6123.0 sentences: 290.0 pages: flesch: 36.0 cache: ./cache/cord-339968-s1kmipir.txt txt: ./txt/cord-339968-s1kmipir.txt summary: Y.; Fraser, John; Lambrecht, Bart N.; Romano, Marta; Gazzinelli, Ricardo T.; Bortoluci, Karina R.; Zamboni, Dario S.; Akbar, Arne N.; Evans, Jennie; Brown, Doug E.; Patel, Kamala D.; Wu, Yuzhang; Perez, Ana B.; Pérez, Oliver; Kamradt, Thomas; Falk, Christine; Barda-Saad, Mira; Ariel, Amiram; Santoni, Angela; Annunziato, Francesco; Cassatella, Marco A.; Kiyono, Hiroshi; Chereshnev, Valeriy; Dieye, Alioune; Mbow, Moustapha; Mbengue, Babacar; Niang, Maguette D. Efforts included writing to President Donald Trump and Congressional leaders urging that they heed the advice of scientific/public health leaders, including AAI member Anthony Fauci 3 ; writing to National Institutes of Health (NIH) Director Francis Collins requesting justification for terminating an NIH-funded grant focusing on understanding the risk of bat coronavirus emergence 4 ; advocating supplemental funding for federal science agencies, including the NIH, for pandemic-related research losses and additional trainee support; and issuing a statement opposing actions taken by the Trump administration that will damage international scientific collaboration 5 . abstract: The COVID-19 pandemic is shining a spotlight on the field of immunology like never before. To appreciate the diverse ways in which immunologists have contributed, Nature Reviews Immunology invited the president of the International Union of Immunological Societies and the presidents of 15 other national immunology societies to discuss how they and their members responded following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). url: https://doi.org/10.1038/s41577-020-00428-4 doi: 10.1038/s41577-020-00428-4 id: cord-262119-s6hc7fxs author: Ostaszewski, Marek title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date: 2020-10-27 words: 12332.0 sentences: 742.0 pages: flesch: 38.0 cache: ./cache/cord-262119-s6hc7fxs.txt txt: ./txt/cord-262119-s6hc7fxs.txt summary: title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms abstract: We hereby describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied to the contents of the COVID-19 Disease Map for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases. url: https://doi.org/10.1101/2020.10.26.356014 doi: 10.1101/2020.10.26.356014 id: cord-337339-0vkigjv2 author: Osterrieder, Nikolaus title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 words: 4327.0 sentences: 220.0 pages: flesch: 47.0 cache: ./cache/cord-337339-0vkigjv2.txt txt: ./txt/cord-337339-0vkigjv2.txt summary: We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Moreover, transgenic mice expressing human ACE2 represent a lethal SARS-CoV-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . In contrast to SARS-CoV-2 titers, histopathological changes differed markedly between young and aged Syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. Based on the data presented here, we propose that comparative preclinical assessments of SARS-CoV-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. abstract: In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals. Since age-dependent differences of COVID-19 were identified in humans, we compared the course of SARS-CoV-2 infection in young and aged Syrian hamsters. We show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. However, older hamsters exhibited more pronounced and consistent weight loss. In situ hybridization in the lungs identified viral RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. The latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32698441/ doi: 10.3390/v12070779 id: cord-268970-uz7q6z2f author: Ott, Isabel M. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 words: 2790.0 sentences: 181.0 pages: flesch: 58.0 cache: ./cache/cord-268970-uz7q6z2f.txt txt: ./txt/cord-268970-uz7q6z2f.txt summary: Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes. Following RNA extraction 9 and RT-qPCR 10 testing for SARS-CoV-2 on the day of saliva collection 2 , the remaining sample volumes (n=20) were aliquoted and stored at -80°C, room temperature (recorded as ~19°C) and 30°C. Moreover, SARS-CoV-2 RNA remained relatively stable in saliva samples left for up to 25 days at room temperature (~19°C; Ct increase of 0.027, 95% CI: -0.019, 0.071) ( Figure 1B) . abstract: Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies. url: https://doi.org/10.1101/2020.08.03.20165233 doi: 10.1101/2020.08.03.20165233 id: cord-253671-g3ypisig author: Otte, Martin Sylvester title: Riechstörungen bei COVID-19 – aktueller Wissensstand date: 2020-06-10 words: 2511.0 sentences: 290.0 pages: flesch: 53.0 cache: ./cache/cord-253671-g3ypisig.txt txt: ./txt/cord-253671-g3ypisig.txt summary: Bislang existiert keine Studie, die mittels validierter Riechtests die tatsächliche Prävalenz von Riechstörungen bei COVID-19-Patienten zu ermitteln versucht hat. In einer retrospektiven Datenauswertung aus San Diego (USA) zeigte sich, dass Riech-und Schmeckstörungen vor allem von SARS-CoV-2-positiven Personen angegeben werden, deren Krankheit eher milde bis moderat verläuft und die ambulant mittels häuslicher Quarantäne behandelt werden können. Dies konnte auch in einer Fragebogenstudie aus Spanien bestätigt werden, in der 35,3 % von 79 Patienten mit PCR-bestätigter COVID-19-Erkrankung die Riechstörung als initiales Symptom angaben. Dies könnte jedoch auch der Tatsache geschuldet sein, dass es sich wie bei den meisten Studien zum Thema bislang um fragebogenbasierte Erhebungen handelt, die vor allem von Patienten mit geringerer Symptomatik beantwortet werden. Nachdem anfängliche Berichte über die SARS-CoV-2-Infektion Riech-und Schmeckstörungen kaum erwähnten, haben mittlerweile mehrere Studien, insbesondere aus Europa und den USA, Wahrnehmungsschwelle, Erkennungsschwelle diese Symptome als Merkmal von COVID-19 bestätigt. abstract: Early reports of SARS-CoV-2 infections only rarely mentioned smell and taste disorders. Several studies, particularly from Europe and the USA, have now confirmed these symptoms as an early key feature of COVID-19. About 70 % of patients seem to experience a reduction of smell and taste in the course of the disease, with most of the studies published to date based on questionnaires and anamnestic data. Validated smell tests have so far only been used in a few studies. A distinction between taste and taste disorders, i. e. a distinction between retronasal aroma taste and the olfactory system from the dysfunction of taste capsules and the further cranial nerves, was mostly not made in the studies available to date. Some reports associate olfactory disorders with a milder clinical course. At the same time, the olfactory system via the olfactory bulb represents an entry point into the central nervous system, and an olfactory disorder could be a predisposing factor for central neurological symptoms. The clinical significance of smell and taste disorders in COVID-19 patients is currently still unclear. Further open questions concern the exact prevalence and the prognosis, so that overall higher quality studies with validated smell tests and larger numbers of patients are required. url: https://www.ncbi.nlm.nih.gov/pubmed/32521557/ doi: 10.1055/a-1183-4835 id: cord-323622-229kub7c author: Ou, Xueting title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens date: 2020-04-16 words: 663.0 sentences: 50.0 pages: flesch: 62.0 cache: ./cache/cord-323622-229kub7c.txt txt: ./txt/cord-323622-229kub7c.txt summary: title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens To the Editor Since December, 2019, corona virus disease 2019 (COVID-19) caused by SARS-CoV-2, has spread to the majority of countries worldwide [1, 2] . Here, we reported the clinical characteristics of a severe case with co-infection of SARS-CoV-2 and common respiratory pathogens. However, sputum samples collected on the same day were positive for SARS-CoV-2 by NGS. The patient was diagnosed as severe COVID-19, and was transferred to the First Affiliated Hospital of Guangzhou Medical University for isolation and treatment where are designed to treat severe COVID-19 cases by local health authorities. In the present study, the cause that resulted in severe condition of the patient could be the co-infection of SARS-CoV-2, Haemophilus parainfluenzae and Moraxella catarrhalis. Older patients, having diabetes, hypertension are causes of severe COVID-19 cases [3, 4] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32305630/ doi: 10.1016/j.tmaid.2020.101672 id: cord-351002-msjurww1 author: Ouanes, Y. title: Does BCG protect against SARS-CoV-2 infection ?: elements of proof. date: 2020-05-06 words: 2997.0 sentences: 185.0 pages: flesch: 53.0 cache: ./cache/cord-351002-msjurww1.txt txt: ./txt/cord-351002-msjurww1.txt summary: Results : Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). Based on these observations, we hypothesized that countries which have an early start of universal BCG vaccination policy would have a reduced morbidity and mortality attributed to SARS-CoV-2 infection. Or results revealed that countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection. abstract: Background : There are several factors explaining the difference in the spread of SARS-CoV-2 infection including the BCG vaccination. This fact is supported by the concept of beneficial non specific effect of this live vaccine associated to its interaction with the immune system. Our study aims to identify the correlation between the universal BCG vaccination policy and the mortality attributed to COVID-19. Methods : We conducted an epidemiological study in which we collected COVID-19 pandemic data of April 11th, 2020 from the web site worldometers.info . The exclusion criteria for our study were a number of inhabitants less than one million, low-income countries according to the World Bank classification, a total number of infection cases less than 500 and countries that have performed less than one hundred tests per million inhabitants. Results : Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). We found that the year of introduction of vaccination influenced significantly the mortality. Countries that started immunization policy before 1960 had more favorable results (p=0.049). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). Conclusions : Countries that have a BCG vaccination policy have a lower mortality attributed to SARS-CoV-2 infection. The populations of countries that applied this immunization before 1960 are more protected even if this universal policy has been interrupted. url: https://doi.org/10.1101/2020.05.01.20087437 doi: 10.1101/2020.05.01.20087437 id: cord-301771-43fl2gwp author: Ouassou, Hayat title: The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention date: 2020-07-10 words: 3866.0 sentences: 179.0 pages: flesch: 45.0 cache: ./cache/cord-301771-43fl2gwp.txt txt: ./txt/cord-301771-43fl2gwp.txt summary: The causative virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the World Health Organization (WHO) named the new epidemic disease Coronavirus Disease (COVID-19). Several coronaviruses can infect humans, like the globally endemic human coronaviruses HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43 that tend to cause mild respiratory disease, and the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that have a higher case fatality rate [2] . After the diagnosis of SARS-Cov2 infection was made, the prevention and quarantine are considered as the most way to stop the fast spreading of the virus, because there is no effective vaccine, drugs, or antiviral to prevent and treat this disease despite the great efforts made by the scientists and researchers around the world to develop vaccines and treatments of coronavirus. abstract: Coronavirus Disease 2019 (COVID-19) has become a major health problem causing severe acute respiratory illness in humans. It has spread rapidly around the globe since its first identification in Wuhan, China, in December 2019. The causative virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the World Health Organization (WHO) named the new epidemic disease Coronavirus Disease (COVID-19). The incidence of COVID-19 continues to increase with more than three million confirmed cases and over 244,000 deaths worldwide. There is currently no specific treatment or vaccine against COVID-19. Therefore, in the absence of pharmaceutical interventions, the implementation of precautions and hygienic measures will be essential to control and to minimize human transmission of the virus. In this review, we highlight the epidemiology, transmission, symptoms, and treatment of this disease, as well as future strategies to manage the spread of this fatal coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/32671115/ doi: 10.1155/2020/1357983 id: cord-296259-4kdblf4z author: Oudit, Gavin Y title: Plasma angiotensin-converting enzyme 2: novel biomarker in heart failure with implications for COVID-19 date: 2020-05-14 words: 1811.0 sentences: 102.0 pages: flesch: 44.0 cache: ./cache/cord-296259-4kdblf4z.txt txt: ./txt/cord-296259-4kdblf4z.txt summary: This editorial refers to ''Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors'' † , by I.E. Sama et al., on page 1810. Angiotensin-converting enzyme 2 (ACE2) has emerged as the negative regulator of the renin-angiotensin system (RAS) and was more recently identified as the SARS-CoV-2 receptor responsible for the current COVID-19 pandemic. [3] [4] [5] Direct clinical evidence came from SARS and the current COVID-19 pandemic, where there is down-regulation of tissue ACE2 through endocytosis and proteolytic processing which leads to a corresponding increase in plasma angiotensin II (Ang II) levels as seen in COVID-19 patients (linearly correlated with SARS-CoV-2 viral load), thus providing a direct link between the tissue and systemic RAS. obtained in heart failure patients in the pre-COVID-19 period offer supporting evidence to continue ACE inhibitors or ARBs in patients at risk for SARS-CoV-2 infection. abstract: nan url: https://doi.org/10.1093/eurheartj/ehaa414 doi: 10.1093/eurheartj/ehaa414 id: cord-330315-upcf15q5 author: Oudshoorn, Diede title: Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication date: 2017-11-21 words: 7718.0 sentences: 349.0 pages: flesch: 50.0 cache: ./cache/cord-330315-upcf15q5.txt txt: ./txt/cord-330315-upcf15q5.txt summary: Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. To study whether the transmembrane nsp''s of MERS-CoV are able to induce DMV formation, we expressed nsp3 and nsp4 from a CAG promoter (43) either by cotransfection of cells with plasmids encoding individual proteins or by transfection with a single plasmid encoding a self-cleaving nsp3-4 polyprotein fragment ( Fig. 1A ; Table S1 ). The observation of maze-like bodies and circular double-membrane profiles, which were interpreted to represent tubular structures, led these authors to conclude that coexpression of SARS-CoV nsp3 and nsp4 was not sufficient for DMV formation. abstract: Betacoronaviruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV), are important pathogens causing potentially lethal infections in humans and animals. Coronavirus RNA synthesis is thought to be associated with replication organelles (ROs) consisting of modified endoplasmic reticulum (ER) membranes. These are transformed into double-membrane vesicles (DMVs) containing viral double-stranded RNA and into other membranous elements such as convoluted membranes, together forming a reticulovesicular network. Previous evidence suggested that the nonstructural proteins (nsp’s) 3, 4, and 6 of the severe acute respiratory syndrome coronavirus (SARS-CoV), which contain transmembrane domains, would all be required for DMV formation. We have now expressed MERS-CoV replicase self-cleaving polyprotein fragments encompassing nsp3-4 or nsp3-6, as well as coexpressed nsp3 and nsp4 of either MERS-CoV or SARS-CoV, to characterize the membrane structures induced. Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. Addition of the third MERS-CoV transmembrane protein, nsp6, did not noticeably affect DMV formation. These findings provide important insight into the biogenesis of coronavirus DMVs, establish strong similarities with other nidoviruses (specifically, the arteriviruses), and highlight possible general principles in viral DMV formation. url: https://doi.org/10.1128/mbio.01658-17 doi: 10.1128/mbio.01658-17 id: cord-302382-eifh95zm author: Owji, Hajar title: Immunotherapeutic approaches to curtail COVID-19 date: 2020-08-21 words: 11312.0 sentences: 606.0 pages: flesch: 40.0 cache: ./cache/cord-302382-eifh95zm.txt txt: ./txt/cord-302382-eifh95zm.txt summary: Active immunization through vaccines, interferon administration, passive immunotherapy by convalescent plasma or synthesized monoclonal and polyclonal antibodies, as well as immunomodulatory drugs, are different immunotherapeutic approaches that will be mentioned in this review. Nevertheless, the similarity of severe respiratory failure induced by SARS-CoV-2 to acute respiratory distress syndrome (ARDS) and the deterioration of patients'' conditions in around a week following the first symptoms implicate the role of immunity dysregulation in COVID-19 profile [6] . Subsequently, plasma transfusion was recommended as a safe and effective way for the prevention or treatment of the Ebola virus in 2014 and also several other severe viral infections, including MERS, SARS-CoV, and avian influenza A [35, 36] . CP extracted from the SARS-COV-2 survivors may be a promising approach for the protection of COVID-19 patients with antibody deficiency before the development of an effective vaccine [44] . abstract: COVID-19, the disease induced by the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has imposed an unpredictable burden on the world. Drug repurposing has been employed to rapidly find a cure; but despite great efforts, no drug or vaccine is presently available for treating or prevention of COVID-19. Apart from antivirals, immunotherapeutic strategies are suggested considering the role of the immune response as the host defense again the virus, and the fact that SARS-CoV-2 suppresses interferon induction as an immune evasion strategy. Active immunization through vaccines, interferon administration, passive immunotherapy by convalescent plasma or synthesized monoclonal and polyclonal antibodies, as well as immunomodulatory drugs, are different immunotherapeutic approaches that will be mentioned in this review. The focus would be on passive immunotherapeutic interventions. Interferons might be helpful in some stages. Vaccine development has been followed with unprecedented speed. Some of these vaccines have been advanced to human clinical trials. Convalescent plasma therapy is already practiced in many countries to help save the lives of severely ill patients. Different antibodies that target various steps of SARS-CoV-2 pathogenesis or the associated immune responses are also proposed. For treating the cytokine storm induced at a late stage of the disease in some patients, immune modulation through JAK inhibitors, corticosteroids, and some other cognate classes are evaluated. Given the changing pattern of cytokine induction and immune responses throughout the COVID-19 disease course, different adapted approaches are needed to help patients. Gaining more knowledge about the detailed pathogenesis of SARS-CoV-2, its interplay with the immune system, and viral-mediated responses are crucial to identify efficient preventive and therapeutic approaches. A systemic approach seems essential in this regard. url: https://www.sciencedirect.com/science/article/pii/S1567576920324309?v=s5 doi: 10.1016/j.intimp.2020.106924 id: cord-328395-2cakgmsj author: Oxford, Alexandra E. title: Endothelial Cell Contributions to COVID-19 date: 2020-09-25 words: 6707.0 sentences: 353.0 pages: flesch: 39.0 cache: ./cache/cord-328395-2cakgmsj.txt txt: ./txt/cord-328395-2cakgmsj.txt summary: Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. This review will focus on the concept of endothelial cell infection and dysfunction as an active driver of COVID-19, which begins as a respiratory illness, with vascular pathology contributing significantly to the most negative patient outcomes. Endothelial cell infection that proceeds via ACE2 shows how SARS-CoV-2 can replicate into a wide range of cells, which may explain some of the clinical symptoms found in COVID-19 patients. Thus far, we have discussed the viral mechanisms of SARS-CoV-2 and resultant COVID-19 sequelae as they relate to endotheliitis and endothelial cell infection mediated by viral spike protein-ACE2 interaction. The successful use of anti-interleukin drugs to treat the inflammatory symptoms seen in severe COVID-19 would have marked effects on endothelial pathology as these cells are highly responsive to cytokine signaling [59] . abstract: Understanding of the clinical, histological and molecular features of the novel coronavirus 2019 (Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)) has remained elusive. Coronavirus disease 2019 (COVID-19) caused by this virus has unusual clinical presentation with regard to other related coronaviruses. Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. Likewise, mounting evidence associates vascular and endothelial cell dysfunction with increased mortality. This review focuses on understanding how endothelial cell pathology is caused by SARS-CoV-2 at the molecular and cellular levels and how these events relate to COVID-19. A detailed examination of current knowledge regarding canonical inflammatory reaction pathways as well as alteration of endothelial cell-derived exosomes and transdifferentiation by SARS-CoV-2 is included in this assessment. Additionally, given an understanding of endothelial contributions to COVID-19, potential therapeutic aims are discussed, particularly as would affect endothelial function and pathology. url: https://doi.org/10.3390/pathogens9100785 doi: 10.3390/pathogens9100785 id: cord-268340-xwj8ge5t author: Ozaki, Masayuki title: Reducing Aerosol Generation During Ventilator Weaning in a Coronavirus Disease 2019 Patient Using a Supraglottic Airway: A Case Report date: 2020-05-21 words: 1034.0 sentences: 79.0 pages: flesch: 47.0 cache: ./cache/cord-268340-xwj8ge5t.txt txt: ./txt/cord-268340-xwj8ge5t.txt summary: Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. We conducted a weaning procedure from mechanical ventilation in advance of emergence from sedation in a patient with COVID-19 by exchanging the tracheal tube to a supraglottic airway (SGA), which is associated with fewer coughs. Reducing patients'' coughing cases-anesthesia-analgesia.org a & a pRaCtICe and avoiding this aerosol-generating procedure during tracheal extubation may reduce occupational infection. To reduce the risk of occupational infection with SARS-CoV-2 at the time of weaning from mechanical ventilation, we propose replacing the tracheal tube with an SGA such as i-gel before emergence from sedation to reduce environmental distribution of the virus. abstract: We report weaning from mechanical ventilation with no coughing in a patient with coronavirus disease 2019 (COVID-19). Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. Personal protective equipment is in short supply worldwide. Reducing spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is beneficial in terms of occupational health of health care workers. url: https://doi.org/10.1213/xaa.0000000000001247 doi: 10.1213/xaa.0000000000001247 id: cord-268939-ws74xprt author: Ozoner, Baris title: Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic date: 2020-05-28 words: 5138.0 sentences: 391.0 pages: flesch: 46.0 cache: ./cache/cord-268939-ws74xprt.txt txt: ./txt/cord-268939-ws74xprt.txt summary: The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. [5] [6] [7] In neurosurgery practice, intensive modifications were required in surgical scheduling, administration of inpatient and outpatient clinics, management of emergency cases, and even academic & educational activities. 26 A recent study from Wuhan City, China reported that some severe COVID-19 patients developed neurologic manifestations, such as acute cerebrovascular diseases (5.7%), and impaired consciousness (14.8%). 76, 80 Also, a patient with a mass lesion in the sellar region that underwent endonasal endoscopic surgery in Neurosurgery Department, Tongji Medical College, Wuhan City, China was diagnosed with COVID-19 after surgery, and disease was confirmed in 14 healthcare professionals in the same clinic afterwards. abstract: Abstract Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly contagious, life-threatening condition with unprecedented impacts for worldwide societies and healthcare systems. Since the first detection in China, it has spread rapidly worldwide. The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. In some systems, non-overlapping teams were created to minimize transmission among healthcare workers. In case of a massive burden, neurosurgeons may be needed to reassign to the COVID-19 wards, or teams from other regions may be needed to send to severely affected areas. In outpatient practice, if possible, appointments should be turned into telemedicine. All staff assigned in the non-COVID treatment unit should be clothed in level 1 personal protective equipment. If possible, postponement is recommended for operations that do not require urgent or emergent intervention. All patients indicated for surgery must receive a COVID-19 screening, including nasopharyngeal swab, and thorax computed tomography. Level 2 protection measures would be appropriate during COVID-19 negative patients' operations. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. During surgery, the use of high-speed drills and electrocautery should be reduced to minimize aerosol production. Screening is crucial in all patients since the surgical outcome is highly mortal in COVID-19 patients. All educational and academic conferences can be turned into virtual webinars. url: https://api.elsevier.com/content/article/pii/S1878875020311669 doi: 10.1016/j.wneu.2020.05.195 id: cord-294441-nehorqhi author: O’Brien, Stephen J. title: Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS date: 2006-08-31 words: 6767.0 sentences: 390.0 pages: flesch: 50.0 cache: ./cache/cord-294441-nehorqhi.txt txt: ./txt/cord-294441-nehorqhi.txt summary: A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach. Representing carnivores, the cat family Felidae offers numerous examples of reduced genetic var-iation in natural populations common to endangered species including Asian lion (Panthera leo persica) (Gilbert et al., 1991) , cheetah (Acinonyx jubatus) (Menotti-Raymond and O''Brien, 1993) , tiger (P. Our ongoing research into host-pathogen interactions in the cat family Felidae offers additional insights on how the application of molecular genomic technologies to non-human animal species not traditionally studied in research laboratories holds real promise in conservation. abstract: Abstract Research studies of infectious disease outbreaks in wild species of the cat family Felidae have revealed unusual details regarding forces that shape population survival and genetic resistance in these species. A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. Widespread prevalence of species specific feline immunodeficiency virus (FIV), a relative of HIV–AIDS, occurs with little pathogenesis in felid species, except in domestic cats, suggesting immunological adaptation in species where FIV is endemic. Resolving the interaction of host and pathogen genomes can shed new light on the process of disease outbreak in wildlife and in humankind. The role of disease in endangered populations and species is difficult to access as opportunities to monitor outbreaks in natural populations are limited. Conservation management may benefit greatly from advances in molecular genetic tools developed for human biomedical research to assay the biodiversity of both host species and emerging pathogen. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach. url: https://www.ncbi.nlm.nih.gov/pubmed/32226081/ doi: 10.1016/j.biocon.2006.05.001 id: cord-282965-xguotf4m author: O’Callaghan-Gordo, Cristina title: COVID-19: The Disease of the Anthropocene date: 2020-05-15 words: 1585.0 sentences: 66.0 pages: flesch: 47.0 cache: ./cache/cord-282965-xguotf4m.txt txt: ./txt/cord-282965-xguotf4m.txt summary: Since the emergence of AIDS, many other epidemic infectious diseases, such as Ebola, SARS and MERS to name the most recent, have been caused by the transmission of viruses from wild animal species to humans as shown in 2008 by Jones et al. The complete causal sequences and impacts of these ecological changes are still poorly understood, but frequently these emerging zoonosis appear and spread in circumstances that denote the effects of an economic and commercial practices that destroys natural habitats and animal populations, including those of humans living there, in the absence of effective protection and regulatory policies. The destruction of natural habitats and the extinction of species, the poorly regulated capture, marketing and consumption of non-human animals, the influence of lobbies to nullify or delay measures to protect natural and social systems, the limitation of current scientific knowledge and the contempt by governments and companies of the available evidence, have all worked in an orchestrated sequence to facilitate the current COVID-19 pandemic. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0013935120305764?v=s5 doi: 10.1016/j.envres.2020.109683 id: cord-328262-hw8swbt5 author: O’Neill, Luke A. J. title: BCG-induced trained immunity: can it offer protection against COVID-19? date: 2020-05-11 words: 2177.0 sentences: 102.0 pages: flesch: 42.0 cache: ./cache/cord-328262-hw8swbt5.txt txt: ./txt/cord-328262-hw8swbt5.txt summary: Bacillus Calmette–Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. This effect was mediated by peritoneal macrophages 10 Bacillus Calmette-Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity abstract: Bacillus Calmette–Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. url: https://doi.org/10.1038/s41577-020-0337-y doi: 10.1038/s41577-020-0337-y id: cord-338203-le5lbw5y author: O’Reilly, GM title: Epidemiology and clinical features of emergency department patients with suspected COVID‐19: Results from the first month of the COVED Quality Improvement Project (COVED‐2). date: 2020-06-13 words: 2848.0 sentences: 151.0 pages: flesch: 50.0 cache: ./cache/cord-338203-le5lbw5y.txt txt: ./txt/cord-338203-le5lbw5y.txt summary: METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study that includes all adult patients presenting to The Alfred Hospital ED who undergo testing for SARS‐CoV‐2. As cases accumulate, the COVED Project aims to determine and report the clinical and epidemiological predictors of a positive SARS-CoV-2 test result and the requirement for intensive respiratory support among patients presenting to the ED with suspected COVID-19. In the first full month of the COVED Project, the daily number and proportion of patients with a positive SARS-CoV-2 test remained relatively low, but the rate of patients presenting to the ED with suspected COVID-19 increased significantly. The low incidence of SARS-CoV-2 positive results over the first full month of the COVED Project has precluded valid inferential analyses regarding how COVID-19 patients differ in terms of their demographic features, clinical presentation, severity risk factors, need for intensive respiratory support and key outcomes. abstract: OBJECTIVE: The aim of this study was to describe the epidemiological and clinical features of emergency department (ED) patients with suspected and confirmed COVID‐19. METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study that includes all adult patients presenting to The Alfred Hospital ED who undergo testing for SARS‐CoV‐2. Current guidelines recommend testing for patients with fevers or chills, acute respiratory symptoms or a high‐risk exposure history, as well as implementation of infection control and prevention (IPC) precautions for all suspected and confirmed cases. Study outcomes include a positive SARS‐CoV‐2 test result and intensive respiratory support. RESULTS: In the period 1‐30 April 2020, 702 of 3453 ED patients (20%; 95%CI: 19‐22) were tested, with a significant increase during the study period (IRR 1.019; 95%CI: 1.017‐1.021, p<0.001). The primary outcome of a positive SARS‐CoV‐2 test was recorded in 14 patients (2%; 95%CI: 1‐3). Shortness of breath (77%), fatigue (100%), myalgia (67%) and diarrhoea (67%) were common among positive cases, while close contact (9%), fever (0%) and healthcare occupation (0%) were not. No positive cases required intensive respiratory support in the ED. CONCLUSIONS: The volume of ED patients with suspected COVID‐19 is increasing. Low numbers of positive cases precluded development of accurate predictive tools, but the COVED Project is fulfilling an important role in monitoring the burden of IPC requirements on the ED. The increasing number of patients meeting isolation criteria has the potential to impact on patient flow and may lead to ED overcrowding. url: https://doi.org/10.1111/1742-6723.13573 doi: 10.1111/1742-6723.13573 id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 words: 9409.0 sentences: 500.0 pages: flesch: 46.0 cache: ./cache/cord-340629-1fle5fpz.txt txt: ./txt/cord-340629-1fle5fpz.txt summary: In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. abstract: Foodborne pathogens cause acute and chronic health outcomes of very different durations, severity and mortality, resulting in high costs and burdens to society. The issues of food safety and food poisoning are being increasingly emphasised, particularly in developed countries. Infection/contamination with many agents i.e., bacterial, parasitic and viral entities can result in foodborne illness. This article will focus mainly on viral agents of infection. A range of different viruses can cause food poisoning/foodborne infection, and infection can result in a myriad of symptoms, ranging from mild, acute disease to chronic, debilitating disease and even death. Due to the inherent differences between bacteria and viruses, namely the fact that viruses do not replicate in food, while bacteria do, viruses are frequently difficult to detect. This is compounded by the fact that many of the viruses associated with enteric disease do not replicate in cell culture. These factors can lead to a lag between reporting, detection and analysis of foodborne viruses versus bacterial agents. Despite these constraints, it is now evident that there are both well-established and emerging viruses implicated in foodborne infections, and the role of molecular detection and characterisation is becoming increasingly important. url: https://www.sciencedirect.com/science/article/pii/B9780128096338902735 doi: 10.1016/b978-0-12-809633-8.90273-5 id: cord-345841-pq5f82gf author: PATBERG, Elizabeth T. title: COVID-19 Infection and Placental Histopathology in Women Delivering at Term date: 2020-10-19 words: 5903.0 sentences: 282.0 pages: flesch: 46.0 cache: ./cache/cord-345841-pq5f82gf.txt txt: ./txt/cord-345841-pq5f82gf.txt summary: Conclusions – Despite the fact that all neonates born to mothers with COVID-19 were negative for SARS-CoV-2 by PCR, we found that COVID-19 in term patients admitted to Labor and Delivery is associated with increased rates of placental histopathologic abnormalities, particularly fetal vascular malperfusion and villitis of unknown etiology. In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . abstract: Background – There is a paucity of data describing the effects of COVID-19, especially in asymptomatic patients, on placental pathology. Although the pathophysiology of COVID-19 is not completely understood, there is emerging evidence that it causes a severe systemic inflammatory response and results in a hypercoagulable state with widespread microthrombi. We hypothesized that it is plausible that a similar disease process may occur in the fetal-maternal unit. Objective – The aim of this study was to determine whether COVID-19 in term patients admitted to Labor and Delivery, including women without COVID-19 symptomatology, is associated with increased placental injury compared to a cohort of COVID-19 negative controls. Study Design – This was a retrospective cohort study performed at NYU Winthrop Hospital between 3/31/2020 and 6/17/2020. During the study period all women admitted to Labor and Delivery were routinely tested for SARS-CoV-2 regardless of symptomatology. The placental histopathological findings of COVID-19 patients (n=77) who delivered a singleton gestation at term were compared to a control group of term patients without COVID-19 (n=56). Controls were excluded if they had obstetric or medical complications including fetal growth restriction, oligohydramnios, hypertension, diabetes, coagulopathy or thrombophilia. Multivariable logistic regression models were performed for variables that were significant in univariable analyses. A subgroup analysis was also performed comparing asymptomatic COVID-19 cases to negative controls. Results – In univariable analyses, COVID-19 cases were more likely to have evidence of fetal vascular malperfusion, i.e. presence of avascular villi and/or mural fibrin deposition (32.5% (25/77) vs. 3.6% (2/56), p<0.0001) and villitis of unknown etiology (20.8% (16/77) vs. 7.1% (4/56), p=0.030). These findings persisted in a subgroup analysis of asymptomatic COVID-19 cases compared to COVID-19 negative controls. In a multivariable model adjusting for maternal age, race/ethnicity, mode of delivery, preeclampsia, fetal growth restriction and oligohydramnios, the frequency of fetal vascular malperfusion abnormalities remained significantly higher in the COVID-19 group (OR= 12.63, 95% CI [2.40, 66.40]). While the frequency of villitis of unknown etiology was more than double in COVID-19 cases compared to controls, this did not reach statistical significance in a similar multivariable model (OR=2.11, 95% CI [0.50, 8.97]). All neonates of mothers with COVID-19 tested negative for SARS-CoV-2 by PCR. Conclusions – Despite the fact that all neonates born to mothers with COVID-19 were negative for SARS-CoV-2 by PCR, we found that COVID-19 in term patients admitted to Labor and Delivery is associated with increased rates of placental histopathologic abnormalities, particularly fetal vascular malperfusion and villitis of unknown etiology. These findings appear to occur even among asymptomatic term patients. url: https://api.elsevier.com/content/article/pii/S0002937820311947 doi: 10.1016/j.ajog.2020.10.020 id: cord-339772-q814d6l7 author: Pach, Szymon title: ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date: 2020-05-14 words: 3735.0 sentences: 229.0 pages: flesch: 60.0 cache: ./cache/cord-339772-q814d6l7.txt txt: ./txt/cord-339772-q814d6l7.txt summary: To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Moreover, we compared ACE2 sequences from rodents (mouse, rat, hamster, and red squirrel) to sample additional binding pockets in the ACE2-RBD interface and predict susceptibility to SARS-CoV-2 of the red squirrel (Sciurus vulgaris). To compare three-dimensional binding interfaces of animal ACE2-RBD complexes, we developed homology models of dog, cat, ferret, hamster, mouse, rat, and red squirrel proteins. Both outlier residues are located on flexible loops of ACE2 distal to the S binding site and represent polymorphic mutations from glycine in human crystal structure to serine in homology models. Based on known susceptibility of animal species to SARS-CoV-2 and the comparison of MD trajectories, we were able to develop models for prediction of RBD binding to ACE2. abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) emerged in late 2019 and since evolved into a global threat with nearly 4.4 million infected people and over 290,000 confirmed deaths worldwide.1 SARS-CoV-2 is an enveloped virus presenting spike (S) glycoproteins on its outer surface. Binding of S to host cell angiotensin converting enzyme 2 (ACE2) is thought to be critical for cellular entry. The host range of the virus extends far beyond humans and non-human primates. Natural and experimental infections have confirmed high susceptibility of cats, ferrets, and hamsters, whereas dogs, mice, rats, pigs, and chickens seem refractory to SARS-CoV-2 infection. To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Based on our analyses we predict that: (i) the red squirrel is likely susceptible to SARS-CoV-2 infection and (ii) specific mutations in ACE2 of dogs, rats, and mice render them susceptible to SARS-CoV-2 infection. url: https://doi.org/10.1101/2020.05.14.092767 doi: 10.1101/2020.05.14.092767 id: cord-268071-ow2aijmj author: Pachetti, Maria title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 words: 4449.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-268071-ow2aijmj.txt txt: ./txt/cord-268071-ow2aijmj.txt summary: Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. Naturally occurring mutations in critical residues for drug efficacy can lead to drug resistance phenomena, with a significant loss in the binding affinity of these molecules to the RdRp. We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. Among all mutation sites analyzed, RdRp mutant is particularly interesting given that the enzyme is directly involved in viral replication and its fidelity determines the mutagenic capabilities of SARS-CoV-2. In the present work we have compared the SARS-CoV-2 reference genome to those exported from the GISAID database with the aim of gaining important insights into virus mutations, their occurrence over time and within different geographic areas. abstract: BACKGROUND: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS: We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann–Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS: We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5], otherwise they have a median of 1 mutation [range: 0–3] (p value < 0.001). CONCLUSIONS: These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates. url: https://www.ncbi.nlm.nih.gov/pubmed/32321524/ doi: 10.1186/s12967-020-02344-6 id: cord-304724-luql6159 author: Paderno, Alberto title: Smell and taste alterations in Covid‐19: a cross‐sectional analysis of different cohorts date: 2020-05-14 words: 3347.0 sentences: 207.0 pages: flesch: 50.0 cache: ./cache/cord-304724-luql6159.txt txt: ./txt/cord-304724-luql6159.txt summary: The study aims to estimate the different characteristics of OD and GD in hospitalized patients and home-quarantined subjects with a nasal/pharyngeal swab positive for SARS-CoV-2 in an epidemic area. All subjects with positive nasal/pharyngeal swab for SARS-CoV-2 were home-quarantined or Patients were not informed about the specific study aim to minimize confirmation bias. The study describes a sample of more than 500 cases with confirmed SARS-CoV-2 infection, distinguishing between hospitalized patients and home-quarantined subjects. All cases with OD and GD reported an acute onset and a significant degree of dysfunction, without solid connection with other symptoms suggestive of upper airway infection (i.e., pharyngodynia and nasal congestion). # Patients affected by olfactory and gustatory dysfunction reported these complains as delayed symptom of presentation of the infection with SARS-CoV-2 in 231 (81.6%) and 264 (82.2%) cases, respectively. abstract: BACKGROUND: : Olfactory (OD) and gustatory (GD) dysfunction have been proven to be a typical symptom of SARS‐CoV‐2 infection. However, their prevalence in different patient populations still needs to be clarified. METHODS: : A cross‐sectional study was performed from March 27 to April 1 2020 in Northern Italy. Physicians administered a survey‐based questionnaire to SARS‐CoV‐2 positive patients with the aim of assessing symptoms, focusing on OD and GD. Two groups were studied: patients hospitalized at ASST Spedali Civili University Hospital of Brescia (A); home‐quarantined subjects (B). RESULTS: : A total of 508 patients were enrolled: 295 in Group A and 213 in Group B. Mean age (±SD) was 55±15 years; 56% were men. Overall, OD and GD were present in 56% (95% CI 51‐60%) and 63% (59‐67%) of cases, respectively. In Group A, the prevalence of OD and GD was 44% (38‐50%) and 52% (46‐58%). In Group B, the prevalence of OD and GD was 72% (65‐79%) and 79% (73‐84%). In the entire cohort, total loss of olfaction and taste was reported in 64% and 60% of cases, respectively. OD and GD occurred as the first symptom in 10% and 11% of cases; in the remaining cases, they occurred after a mean of 4±3 days following the first symptom. At the time of the questionnaire, complete resolution of OD and GD was reported in 52% and 55% of cases (mean duration: 9±5 in both). CONCLUSIONS: : OD and GD are more prevalent in home‐quarantined subjects, and they are independently associated with younger age and female gender. This article is protected by copyright. All rights reserved url: https://doi.org/10.1002/alr.22610 doi: 10.1002/alr.22610 id: cord-324288-qgxswltx author: Padhi, Sunali title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study date: 2020-09-14 words: 3332.0 sentences: 179.0 pages: flesch: 37.0 cache: ./cache/cord-324288-qgxswltx.txt txt: ./txt/cord-324288-qgxswltx.txt summary: title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study In the present study, we hypothesized that vitamin D deficiency would be associated with the SARS-CoV-2 infection rate and mortality in the Indian population. Further, a recent report highlighted a higher chance of SARS-CoV-2 infected patients being admitted to an intensive care unit compared to those with insufficient or sufficient levels of vitamin D in the UK population [9] . Low plasma 25(OH) vitamin D level is associated with increased risk of COVID-19 infection: an Israeli population-based study Current Scenario of Prevalence of Vitamin D Deficiency in Ostensibly Healthy Indian Population: A Hospital Based Retrospective Study Serum Vitamin D Levels and Alopecia Areata-A Hospital Based Case-Control Study from North-India Low levels of serum Vitamin D in chronic periodontitis patients with type 2 diabetes mellitus: A hospital-based crosssectional clinical study abstract: BACKGROUND: The role of vitamin D in the susceptibility and severity of various viral diseases has been well documented. Recently, some reports highlighted the possible importance of vitamin D in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although India receives adequate sunlight throughout the year, the majority of Indians are deficient in vitamin D levels. In the present study, we hypothesized that vitamin D deficiency would be associated with the SARS-CoV-2 infection rate and mortality in the Indian population. MATERIALS AND METHODS: SARS-CoV-2 infection and mortality data were obtained from the Government of India's official website (accessed on 16(th) August 2020). Various literature databases like PubMed and Google Scholar were searched to find the mean of 25-hydroxyvitamin D [25(OH)D] levels in different states and union territories of India, Pearson correlation was carried out to investigate the possible link between mean 25(OH)D levels and SARS-CoV-2 infection and mortality per million of the population. RESULTS: An inverse correlation was observed between the mean level of 25(OH)D and SARS-CoV-2 infection rate (r= -0.43, p= 0.02) and mortality rate (r= -0.42, p= 0.02). CONCLUSIONS: The present observational study revealed an association of vitamin D with SARS-CoV-2 infection and related mortality. Further studies are required to validate our observations. url: https://www.ncbi.nlm.nih.gov/pubmed/33182040/ doi: 10.1016/j.intimp.2020.107001 id: cord-291738-nak5357h author: Padoan, Andrea title: Clinical performances of an ELISA for SARS-CoV-2 antibody assay and correlation with neutralization activity date: 2020-08-18 words: 1111.0 sentences: 66.0 pages: flesch: 49.0 cache: ./cache/cord-291738-nak5357h.txt txt: ./txt/cord-291738-nak5357h.txt summary: Here we describe the clinical performances of an ELISA (Novalisa NovaTec Immunodiagnostica, Dietzenbach, Germany) for the detection of SARS-CoV-2 IgA, IgM and IgG and the comparison of results with the neutralization activity. A total of 171 leftover serum samples from 41 SARS-CoV-2 negative subjects (20 healthcare workers, 13 autoimmune patients, 8 pregnant women) and 130 COVID-19 patients (9 asymptomatic/mildly symptomatic recovered at home with supportive care and isolation, and 121 hospitalized, classified with moderate or severe disease following WHO interim guidance [5] ) were included in the study. As expected, when the time frame < 12 days was considered, the diagnostic sensitivity of the three assays was very limited and the best performances were found for IgA with a sensitivity equal to 65%, thus confirming our previously reported findings, as in most patients increased antibody levels should be detected only after 6-7 days post symptom onset (PSO) [7] [8] [9] . Evaluation of an ELISA for SARS-CoV-2 antibody testing: clinical performances and correlation with plaque reduction neutralization titer abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0009898120304174?v=s5 doi: 10.1016/j.cca.2020.08.024 id: cord-266923-hd1tjj6b author: Padroni, Marina title: Guillain-Barré syndrome following COVID-19: new infection, old complication? date: 2020-04-24 words: 1146.0 sentences: 70.0 pages: flesch: 38.0 cache: ./cache/cord-266923-hd1tjj6b.txt txt: ./txt/cord-266923-hd1tjj6b.txt summary: Taking together all these findings, the causal association between GBS and COVID-19 remains speculative, but more probable, given that GBS and Bickerstaff''s encephalitis have been already described as postinfectious complications of other coronavirus, sharing similarities with SARS-CoV-2 (Middle East respiratory syndrome, MERS-CoV) [11] . If our hypothesis will be confirmed in larger case series, neurologists and other clinicians should be aware of the important early recognition and treatment of the potential neuromuscular and autonomic worsening leading to cardio-respiratory failure in patients with GBS and mild or controlled pulmonary COVID-19 Notwithstanding the causative relationship remains unproved, we believe that our case description provide further evidence to the heterogenous and multi-systemic complications associated with SARS-CoV-2. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS CoV-2 infection: causality or coincidence Toscana virus associated with Guillain-Barré syndrome: a case-control study abstract: nan url: https://doi.org/10.1007/s00415-020-09849-6 doi: 10.1007/s00415-020-09849-6 id: cord-355935-psnqrdo2 author: Paez, Antonio title: A Spatio‐Temporal Analysis of the Environmental Correlates of COVID‐19 Incidence in Spain date: 2020-06-08 words: 8984.0 sentences: 487.0 pages: flesch: 54.0 cache: ./cache/cord-355935-psnqrdo2.txt txt: ./txt/cord-355935-psnqrdo2.txt summary: Use of spatial Seemingly Unrelated Regressions (SUR) allows us to model the incidence of reported cases of the disease per 100,000 population as an interregional contagion process, in addition to a function of temperature, humidity, and sunshine. We adopt a population health approach, and report results from a spatio-temporal model of the incidence of COVID-19 in the coterminous provinces in Spain, one of the countries hardest hit by the pandemic. Higher incidence is associated with higher GDP per capita and presence of mass transit systems in the province; in contrast, population density and percentage of older adults display negative associations with incidence of COVID-19. The coefficients of the spatially lagged variable are estimated for each time period ρ t and identify the intensity and the sign of the contagion effect. Fig. 3 includes three maps that display the spatial variation of our control variables, namely GDP per capita, percentage of older adults in province, population density, and presence of mass transit systems. abstract: The novel SARS‐CoV2 has disrupted health systems and the economy, and public health interventions to slow its spread have been costly. How and when to ease restrictions to movement hinges in part on whether SARS‐CoV2 will display seasonality due to variations in temperature, humidity, and hours of sunshine. Here, we address this question by means of a spatio‐temporal analysis in Spain of the incidence of COVID‐19, the disease caused by the virus. Use of spatial Seemingly Unrelated Regressions (SUR) allows us to model the incidence of reported cases of the disease per 100,000 population as an interregional contagion process, in addition to a function of temperature, humidity, and sunshine. In the analysis we also control for GDP per capita, percentage of older adults in the population, population density, and presence of mass transit systems. The results support the hypothesis that incidence of the disease is lower at higher temperatures and higher levels of humidity. Sunshine, in contrast, displays a positive association with incidence of the disease. Our control variables also yield interesting insights. Higher incidence is associated with higher GDP per capita and presence of mass transit systems in the province; in contrast, population density and percentage of older adults display negative associations with incidence of COVID‐19. url: https://doi.org/10.1111/gean.12241 doi: 10.1111/gean.12241 id: cord-332312-od3vjuw5 author: Pagani, G. title: Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA). date: 2020-06-24 words: 1030.0 sentences: 73.0 pages: flesch: 59.0 cache: ./cache/cord-332312-od3vjuw5.txt txt: ./txt/cord-332312-od3vjuw5.txt summary: In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. Results were reported in terms of 54 estimated probabilities of being positive to IgG test as a function of age, with respective 95% 55 confidence intervals. Estimates of probabilities of 64 being positive to IgG test, from a model including only age as independent variable, are reported in 65 susceptibility to the infection. In conclusion, our findings suggest that IgG seroprevalence for SARS-CoV-2 increases with 83 increasing age and these data suggest a lower susceptibility to infection in the lower age groups. abstract: Castiglione D'Adda is one of the towns earlier and more severely affected by the SARS-CoV-2 epidemic in Lombardy. In a mass screening involving 4174 out of about 4550 total inhabits, significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the lowest prevalence in the youngest inhabitants. url: http://medrxiv.org/cgi/content/short/2020.06.24.20138875v1?rss=1 doi: 10.1101/2020.06.24.20138875 id: cord-259471-lsdodl0a author: Pagliano, Pasquale title: Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date: 2020-03-24 words: 626.0 sentences: 29.0 pages: flesch: 39.0 cache: ./cache/cord-259471-lsdodl0a.txt txt: ./txt/cord-259471-lsdodl0a.txt summary: In contrast, no similar effect on early phases of coronavirus infection has been reported for other drugs proposed for SARS-CoV-2 treatment, which are able to interfere only after cell infection, affecting protease cleavage (protease inhibitors) or viral genome replication (remdesivir or ribavirin). Hydroxychloroquine, the HIV protease inhibitors (particularly lopinavir), ribavirin, and remdesivir are the most promising drugs proposed for coronavirus disease 2019 (COVID-19) treatment, but currently no drug has been proposed for postexposure or preexposure prophylaxis for those accidently exposed to SARS-CoV-2 [6] . Hydroxychloroquine''s effectiveness profile, its ability to inhibit lung viral replication for a 10-day period after only a 5-day cycle of therapy, and the large amounts of knowledge in term of safety deriving from its use for malaria prophylaxis and rheumatologic diseases lead us to recommend its preexposure or postexposure use for those performing procedures at high risk of viral diffusion in patients with COVID-19 pneumonia. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32211764/ doi: 10.1093/cid/ciaa320 id: cord-355854-hksq8gy4 author: Pagliaro, Pasquale title: ACE/ACE2 Ratio: A Key Also in 2019 Coronavirus Disease (Covid-19)? date: 2020-06-18 words: 3027.0 sentences: 171.0 pages: flesch: 46.0 cache: ./cache/cord-355854-hksq8gy4.txt txt: ./txt/cord-355854-hksq8gy4.txt summary: Therefore, we wonder whether the invasion by SARS-CoV-2 and the downregulation of ACE2 are jointly responsible for a high incidence of dramatic acute respiratory distress syndrome (ARDS), cardiovascular complications, and high lethality of Covid-19. Moreover, estrogen shifts the system toward the ACE2/Ang 1-7 formation and ACE2 activity is higher in female than that in the male serum (18) ; however, the worst and most lethal Covid-19 infections occur predominantly in males [the Italian ISS (https://www.epicentro.iss.it/coronavirus/ sars-cov-2-decessi-italia, accessed on April 26th 2020) reports that among 23,188 SARS-CoV-2 patients dying in Italy, women are 8,500 (36.7%)]. It has also been suggested that the increased concentration of ACE2 receptors in in the lungs of children may have a protective effect on severe clinical manifestations due to SARS-CoV-2 invasion (36) . ACE/ACE2 ratio is increased in many pathologies (especially dis-metabolisms and cardiovascular diseases) and conditions (obesity and aging) that exacerbate Covid-19 symptomatology and worsen outcomes. abstract: nan url: https://doi.org/10.3389/fmed.2020.00335 doi: 10.3389/fmed.2020.00335 id: cord-273083-xrydkiu4 author: Pahmeier, Felix title: A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date: 2020-09-01 words: 999.0 sentences: 64.0 pages: flesch: 49.0 cache: ./cache/cord-273083-xrydkiu4.txt txt: ./txt/cord-273083-xrydkiu4.txt summary: Here, we describe the generation and characterization of a reporter system to visualize dengue virus and SARS-CoV-2 replication in live cells. The system is based on viral protease activity causing cleavage and nuclear translocation of an engineered fluorescent protein that is expressed in the infected cells. Here we describe a reporter system that takes advantage of virus-encoded proteases that are expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. In order to generate a reporter system that can specifically indicate virus infection, we 219 designed a construct expressing a GFP fusion protein that could selectively be cleaved 220 by viral proteases. However, since no fluorescent 304 protein coding sequence is incorporated into the construct, expression of the DENV 305 polyprotein cannot be followed by live cell imaging. abstract: Positive-strand RNA viruses have been the etiological agents in several major disease outbreaks over the last few decades. Examples of that are flaviviruses, such as dengue virus and Zika virus that cause millions of yearly infections and spread around the globe, and coronaviruses, such as SARS-CoV-2, which is the cause of the current pandemic. The severity of outbreaks caused by these viruses stresses the importance of virology research in determining mechanisms to limit virus spread and to curb disease severity. Such studies require molecular tools to decipher virus-host interactions and to develop effective interventions. Here, we describe the generation and characterization of a reporter system to visualize dengue virus and SARS-CoV-2 replication in live cells. The system is based on viral protease activity causing cleavage and nuclear translocation of an engineered fluorescent protein that is expressed in the infected cells. We show the suitability of the system for live cell imaging and visualization of single infected cells as well as for screening and testing of antiviral compounds. Given the modular building blocks, the system is easy to manipulate and can be adapted to any virus encoding a protease, thus offering a high degree of flexibility. IMPORTANCE Reporter systems are useful tools for fast and quantitative visualization of viral replication and spread within a host cell population. Here we describe a reporter system that takes advantage of virus-encoded proteases that are expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Upon cleavage, the fluorescent protein translocates to the nucleus, allowing for rapid detection of the infected cells. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. We apply this reporter system to live cell imaging and use it for proof-of-concept to validate antiviral activity of a nucleoside analogue. This reporter system is not only an invaluable tool for the characterization of viral replication, but also for the discovery and development of antivirals that are urgently needed to halt the spread of these viruses. url: https://doi.org/10.1101/2020.08.31.276683 doi: 10.1101/2020.08.31.276683 id: cord-252279-0gozdv43 author: Pal, Amit title: Hydroxychloroquine and Covid-19: A Cellular and Molecular Biology Based Update date: 2020-06-10 words: 3858.0 sentences: 207.0 pages: flesch: 39.0 cache: ./cache/cord-252279-0gozdv43.txt txt: ./txt/cord-252279-0gozdv43.txt summary: Without a therapeutic vaccine or specific antiviral drugs, and with a desperate attempt to find a cure against novel Corona Virus Disease 2019 (Covid-19) [1] , the limelight was shifted to hydoxychloroquine (derivative of chloroquine that has antimalarial, antiinflammatory, immunosuppressive and antiautophagy activities [2, 3] ; upon a tweet by US president Mr. Donald J. The main aim of this review is to discuss the mode of action of hydroxychloroquine at cellular and molecular levels, that potentially support the clinical efficacy and few adverse side effects observed in Covid-19 patients treated with hydroxychloroquine, which may further help in improving the clinical outcomes by modifying or altering the drug itself or its restricted use in certain individuals by enforcing strict inclusion and exclusion criteria. Due to its cellular and molecular effects as discussed in previous sections, quite a few clinical trials are studying the effectiveness and safety of hydroxychloroquine (also chloroquine) for Covid-19 (https://clinicaltrials.gov/ct2/ results?cond=%22wuhan?coronavirus%22). abstract: As the time for finding a definitive and safe cure as a vaccine for novel Corona Virus Disease 2019 (Covid-19) is still far, there is need to study in depth about the other potential drugs, which can save millions of lives due to Covid-19 pandemic. Right at the center of the debate is the use of drug “Hydroxychloroquine” as a prophylaxis as well as a treatment strategy against Covid-19 in conjunction with azithromycin. In this review, we will study the cellular and molecular aspects of hydroxychloroquine, which had driven its use in Covid-19 patients, as well as its chemistry and pharmacokinetics along with clinical trials going on worldwide using hydroxychloroquine against Covid-19. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12291-020-00900-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12291-020-00900-x doi: 10.1007/s12291-020-00900-x id: cord-333041-69n2wwn3 author: Pal, Anandita title: Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection date: 2020-08-11 words: 4394.0 sentences: 227.0 pages: flesch: 43.0 cache: ./cache/cord-333041-69n2wwn3.txt txt: ./txt/cord-333041-69n2wwn3.txt summary: Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Obesity is an independent risk factor for increased morbidity and mortality upon infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic. The SPM precursor 17-hydroxydocosahexaenoic acid (17-HDHA) increased antibody levels and improved survival upon pH1N1 influenza vaccination and infection in lean mice by promoting B cell differentiation toward the formation of CD138 + long-lived antibody secreting cells (18) . Taken together, these data suggest that the susceptibility of obese individuals to environmental lung diseases may drive an altered pulmonary immune response and a state of SPM deficiency that increases the morbidity and mortality to respiratory infections, including COVID-19. abstract: Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). Therefore, there is a critical need to identify underlying metabolic factors associated with obesity that could be contributing toward increased susceptibility to SARS-CoV-2 in this vulnerable population. Here, we focus on the critical role of potent endogenous lipid metabolites known as specialized pro-resolving mediators (SPMs) that are synthesized from polyunsaturated fatty acids. SPMs are generated during the transition of inflammation to resolution and have a vital role in directing damaged tissues to homeostasis; furthermore, SPMs display anti-viral activity in the context of influenza infection without being immunosuppressive. We cover evidence from rodent and human studies to show that obesity, and its co-morbidities, induce a signature of SPM deficiency across immunometabolic tissues. We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Finally, we highlight potential approaches to overcome the loss of SPMs using dietary and pharmacological interventions. Collectively, this mini-review underscores the need for mechanistic studies on how SPM deficiencies driven by obesity and environmental exposures may exacerbate the response to SARS-CoV-2. url: https://doi.org/10.3389/fimmu.2020.01997 doi: 10.3389/fimmu.2020.01997 id: cord-281346-bjhdy8mg author: Palacios Cruz, M. title: COVID-19, a worldwide public health emergency() date: 2020-04-21 words: 3481.0 sentences: 190.0 pages: flesch: 51.0 cache: ./cache/cord-281346-bjhdy8mg.txt txt: ./txt/cord-281346-bjhdy8mg.txt summary: This new species of coronavirus has been termed 2019-nCoV and has caused a considerable number of cases of infection and deaths in China and, to a growing degree, beyond China, becoming a worldwide public health emergency. 2019-nCoV has high homology to other pathogenic coronaviruses, such as those originating from bat-related zoonosis (SARS-CoV), which caused approximately 646 deaths in China at the start of the decade. 17 Moreover, a recently published study estimated that 95% of the cases of 2019-nCoV infections in Wuhan showed symptoms before the 12th of January 2020, 18,19 a fact that, combined with the virus'' incubation period, suggests a high possibility of the disease''s travelrelated propagation. According to the WHO, a suspected case involves a patient with severe acute respiratory infection (fever, cough, requiring hospitalization) and with no other etiology that completely explains the clinical presentation, as well as a history of travel or residence in China during the 14 days before symptom onset. abstract: A new coronavirus outbreak emerged on the 31st of December 2019 in Wuhan, China, causing commotion among the medical community and the rest of the world. This new species of coronavirus has been termed 2019-nCoV and has caused a considerable number of cases of infection and deaths in China and, to a growing degree, beyond China, becoming a worldwide public health emergency. 2019-nCoV has high homology to other pathogenic coronaviruses, such as those originating from bat-related zoonosis (SARS-CoV), which caused approximately 646 deaths in China at the start of the decade. The mortality rate for 2019-nCoV is not as high (approximately 2–3%), but its rapid propagation has resulted in the activation of protocols to stop its spread. This pathogen has the potential to become a pandemic. It is therefore vital to follow the personal care recommendations issued by the World Health Organization. url: https://api.elsevier.com/content/article/pii/S2254887420300333 doi: 10.1016/j.rceng.2020.03.001 id: cord-278370-fuu20ae7 author: Palao, M. title: Multiple Sclerosis following SARS-CoV-2 infection date: 2020-07-07 words: 1544.0 sentences: 93.0 pages: flesch: 44.0 cache: ./cache/cord-278370-fuu20ae7.txt txt: ./txt/cord-278370-fuu20ae7.txt summary: However, available information about demyelinating complications of the central nervous system (CNS) is limited with only one report of acute disseminated encephalomyelitis (ADEM) in a severe COVID-19 patient being published to date 5 and a single case of meningo-encephalitis 6 , the latter with the presence of SARS-CoV-2 in the cerebrospinal fluid (CSF) confirmed by PCR. As viral infections have been linked to the development of demyelinating diseases 7 it would be interesting to know if this relationship also exists in the case of SARS-CoV-2. We present a case of first presentation of demyelinating disease in the form of optic neuritis following SARS-CoV-2 infection. In our case, the patient presented symptoms attributed to COVID-19 infection (anosmia and dysgeusia) prior to the visual manifestations. In this case, SARS-CoV-2 may have acted as a precipitating factor rather than multiple sclerosis being a direct consequence of the infection. abstract: SARS-CoV-2 infection can produce neurological features. The most common are headache, anosmia and dysgeusia but patients may also develop other central nervous system (CNS) injuries. We present a patient affected by Covid-19 who initially consulted for decreased visual acuity. The MRI showed inflammation in the right optic nerve and demyelinating lesions in the CNS. We speculate that an immune mechanism induced by SARS-CoV-2, which can activate lymphocytes and an inflammatory response, plays a role in the clinical onset of the disease. This pathogen may be associated with either the triggering or the exacerbation of inflammatory/demyelinating disease. url: https://api.elsevier.com/content/article/pii/S2211034820304521 doi: 10.1016/j.msard.2020.102377 id: cord-268501-z4oztgi0 author: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 words: 6331.0 sentences: 280.0 pages: flesch: 46.0 cache: ./cache/cord-268501-z4oztgi0.txt txt: ./txt/cord-268501-z4oztgi0.txt summary: In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32983183/ doi: 10.3389/fimmu.2020.02173 id: cord-311029-x0lk4110 author: Palermo, Sara title: Covid-19 Pandemic: Maximizing Future Vaccination Treatments Considering Aging and Frailty date: 2020-09-18 words: 6411.0 sentences: 353.0 pages: flesch: 40.0 cache: ./cache/cord-311029-x0lk4110.txt txt: ./txt/cord-311029-x0lk4110.txt summary: For that reason, the Clinical Trials Regulation (EC) No. 536/2014 states that "in order to improve treatments available for vulnerable groups such as frail or older people, people suffering from multiple chronic conditions, and people affected by mental health disorders, medicinal products which are likely to be of significant clinical value should be fully and appropriately studied for their effects in these specific groups, including as regards requirements related to their specific characteristics and the protection of the health and well-being of subjects belonging to these groups." Indeed, EMA develops scientific guidelines to help medicine developers address the specific requirements of older people in their medicine development programs, including in the design and conduct of clinical trials. EMA disclosed a reflection paper on "Physical frailty: instruments for baseline characterization of older populations in clinical trials" (7), actively recognizing the importance of considering the various types of aging when experimenting and developing new pharmacological treatments. abstract: The COVID-19 pandemic is proving to be a multiplier of inequalities. Especially toward the elderly population. A voiceless scream that comes from geriatrics, nursing homes, hospices from all over Italy. They call it the silent massacre: from North to South, the bulletin of coronavirus positive—or already deceased—elderly people continues to grow exponentially without a chance to counter it. Population aging and chronicity are a question that needs to be addressed. Frailty is the most challenging expression of population aging, with major consequences for public health and clinical practice. It is a geriatric syndrome which consists in a state of higher vulnerability to stressors attributed to a lower homeostatic reserve due to an age-related multisystem physiological change. People over 60, and especially over 80, are particularly vulnerable to severe or fatal infection. Moreover, the age-related dysregulation of the immune system in the elderly (i.e., immunosenescence and inflammaging) results in poorer responses to vaccination. Physical frailty is an effective health indicator and it has previously shown to predict the response to the seasonal flu vaccine. These findings suggest that assessing frailty in the elderly may identify those who are less likely to respond to immunization and be at higher risk for COVID-19 and its complications. Moreover, cognitive frailty and neurocognitive disorders, mental health and reduced awareness of illness negatively impact on adherence to complex medication regimens among elderly patients. A worldwide research and development blueprint have been initiated to accelerate the development of vaccines and therapeutics for the COVID-19 outbreak. Considered the above, I suggest the importance to consider aging in thinking about future Civud-19 vaccination and treatment, focusing on the possible impact of physical and cognitive frailty. url: https://doi.org/10.3389/fmed.2020.558835 doi: 10.3389/fmed.2020.558835 id: cord-350622-8tgxdbyi author: Palit, Partha title: Phytopharmaceuticals mediated Furin and TMPRSS2 receptor blocking: can it be a potential therapeutic option for Covid-19? date: 2020-10-28 words: 5083.0 sentences: 206.0 pages: flesch: 37.0 cache: ./cache/cord-350622-8tgxdbyi.txt txt: ./txt/cord-350622-8tgxdbyi.txt summary: Hence, this strategy may limit life-threatening Covid-19 infection and its mortality rate through nano-suspension based intra-nasal or oral nebulizer spray, to treat mild to moderate SARS-COV-2 infection, when Furin and TMPRSS2 receptor may initiate to express and activate for processing the virus to cause cellular infection by replication within the host cell. Drug particle formulated as a harmonious combination of cocktail receptor inhibitors at optimal and pharmacologically relevant dose could block the host cell receptor Furin, and TMPRSS2 receptor located in the target organs like esophagus, lungs, as well as in colon, liver, heart, kidneys, intestine and pancreas to prevent the entry of the SARS-CoV-2. Hence, some selected lead phytopharmaceuticals can primarily be focused on anti-COVID-19 drug discovery and development as mentioned in Table 1 and Table 2 based on their anti-viral activity reported against influenza, HIV, and other RNA viruses through host cell surface receptors ACE2, Furin and TMPRSS2 blocking action. abstract: Currently, novel coronavirus disease (Covid-19) outbreak creates global panic across the continents, as people from almost all countries and territories have been affected by this highly contagious viral disease. The scenario is deteriorating due to lack of proper & specific target-oriented pharmacologically safe prophylactic agents or drugs, and or any effective vaccine. drug development is urgently required to back in the normalcy in the community and to combat this pandemic. Thus, we have proposed two novel drug targets, Furin and TMPRSS2, as Covid-19 treatment strategy. We have highlighted this target-oriented novel drug delivery strategy, based on their pathophysiological implication on SARS-CoV-2 infection, as evident from earlier SARS-CoV-1, MERS, and influenza virus infection via host cell entry, priming, fusion, and endocytosis. An earlier study suggested that Furin and TMPRSS2 knockout mice had reduced level of viral load and a lower degree of organ damage such as the lung. The present study thus highlights the promise of some selected novel and potential anti-viral Phytopharmaceutical that bind to Furin and TMPRSS2 as target. As, few of them had shown promising anti-viral response in both preclinical and clinical study with acceptable therapeutic safety-index. Hence, this strategy may limit life-threatening Covid-19 infection and its mortality rate through nano-suspension based intra-nasal or oral nebulizer spray, to treat mild to moderate SARS-COV-2 infection, when Furin and TMPRSS2 receptor may initiate to express and activate for processing the virus to cause cellular infection by replication within the host cell. url: https://www.sciencedirect.com/science/article/pii/S0944711320302270?v=s5 doi: 10.1016/j.phymed.2020.153396 id: cord-340103-dc3wye9s author: Pallanti, Stefano title: Importance of SARs-Cov-2 anosmia: From phenomenology to neurobiology date: 2020-05-11 words: 2348.0 sentences: 99.0 pages: flesch: 42.0 cache: ./cache/cord-340103-dc3wye9s.txt txt: ./txt/cord-340103-dc3wye9s.txt summary: All clinicians should be aware that the presentation of SARS-CoV-2''s symptoms goes far beyond respiratory and sensorial dimensions and involves psychosensorial and neurological dimensions; these clinical observations could shed light on the neurobiological substrates involved in COVID-19 disease. In the long list of clinical symptoms of COVID-19, ENT-UK (The British Association of Otorhinolaryngology) has recently identified anosmia-hyposmia and hypogeusia, respectively, the sudden loss of sense of smell and taste, as "significant symptoms" which were found even in the absence of other symptoms, so that they could identify otherwise hidden carriers of this highly contagious disease. In the present report, anticipation of anosmia and hypogeusia to respiratory symptoms seems consistent with the ENT UK hypothesis that loss of sense of smell (and taste) could be considered as a symptom of COVID-19 infection; and, if confirmed, these symptoms may represent markers or early signs of SARS-CoV-2 sufficient to trigger quarantine. abstract: Anosmia and hypogeusia, the inability or decreased ability to smell and taste, have been reported as common complaints in SARS-CoV-2 patients who were still in an asymptomatic phase. These impairments affect the ability to sense odors in foods and the environment, obviously affecting quality of life, related to social interactions and general well-being. The British Association of Otorhinolaryngology (ENT-UK) considers loss of sense of smell in their list of COVID-19's markers of infection. Here we present two cases in which early manifestations of anosmia and hypogeusia were experienced with psycho-sensorial and atmospheric phenomena. Psychiatrists, neurologists and physicians in general should be aware of this symptom presentation in order to avoid mistreatment, given that persistent olfactory dysfunction might increase the risks of nutritional deficit and lead to development of adjustment disorders. All clinicians should be aware that the presentation of SARS-CoV-2's symptoms goes far beyond respiratory and sensorial dimensions and involves psychosensorial and neurological dimensions; these clinical observations could shed light on the neurobiological substrates involved in COVID-19 disease. url: https://www.sciencedirect.com/science/article/pii/S0010440X20300262?v=s5 doi: 10.1016/j.comppsych.2020.152184 id: cord-264045-h0vt3r9j author: Pallett, Scott J C title: Serological assays for delayed SARS-CoV-2 case identification – Author''s reply date: 2020-09-14 words: 644.0 sentences: 34.0 pages: flesch: 46.0 cache: ./cache/cord-264045-h0vt3r9j.txt txt: ./txt/cord-264045-h0vt3r9j.txt summary: We read with interest the insightful comments put forward by Kay Weng Choy, raising important considerations for clinicians planning to use pointof-care serological assays for delayed case identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in response to those presented in our Article. Our study was designed specifically to evaluate the use of point-ofcare assays for frontline health-care workers directly involved in the clinical care of patients with SARS-CoV-2 infection; therefore, it was not possible to evaluate any difference in detection of SARS-CoV-2 IgG in young or older people. 4 An evaluation of the potential effect of immunodeficiency on assay performance was beyond the scope of our study; however, we strongly agree that this is an important issue for future studies where consideration can be given to testing in different populations. Pointof-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study abstract: nan url: https://api.elsevier.com/content/article/pii/S2213260020304069 doi: 10.1016/s2213-2600(20)30406-9 id: cord-327890-ocisq7e4 author: Pallett, Scott J C title: Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study date: 2020-07-24 words: 5947.0 sentences: 271.0 pages: flesch: 42.0 cache: ./cache/cord-327890-ocisq7e4.txt txt: ./txt/cord-327890-ocisq7e4.txt summary: In phase 1, two point-of-care lateral flow serological assays, the Onsite CTK Biotech COVID-19 split IgG/IgM Rapid Test (CTK Bitotech, Poway, CA, USA) and the Encode SARS-CoV-2 split IgM/IgG One Step Rapid Test Device (Zhuhai Encode Medical Engineering, Zhuhai, China), were evaluated for performance against a laboratory immunoassay (EDI Novel Coronavirus COVID-19 IgG ELISA kit [Epitope Diagnostics, San Diego, CA, USA]) in 300 samples from health-care workers and 100 pre-COVID-19 negative control samples. These include point-of-care molecular platforms for acute phase testing, and laboratory ELISA or lateral flow serological assays for antibodies specific to SARS-CoV-2 for delayed case identification. To derive a measure of sensitivity, the results of lateral flow serological assays and ELISA were compared in 300 health-care workers who had previously received PCR testing (AusDiagnostics, Sydney, Australia) at initial presentation with COVID-19 symptoms. abstract: BACKGROUND: Health-care workers constitute a high-risk population for acquisition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Capacity for acute diagnosis via PCR testing was limited for individuals with mild to moderate SARS-CoV-2 infection in the early phase of the COVID-19 pandemic and a substantial proportion of health-care workers with suspected infection were not tested. We aimed to investigate the performance of point-of-care and laboratory serology assays and their utility in late case identification, and to estimate SARS-CoV-2 seroprevalence. METHODS: We did a prospective multicentre cohort study between April 8 and June 12, 2020, in two phases. Symptomatic health-care workers with mild to moderate symptoms were eligible to participate 14 days after onset of COVID-19 symptoms, as per the Public Health England (PHE) case definition. Health-care workers were recruited to the asymptomatic cohort if they had not developed PHE-defined COVID-19 symptoms since Dec 1, 2019. In phase 1, two point-of-care lateral flow serological assays, the Onsite CTK Biotech COVID-19 split IgG/IgM Rapid Test (CTK Bitotech, Poway, CA, USA) and the Encode SARS-CoV-2 split IgM/IgG One Step Rapid Test Device (Zhuhai Encode Medical Engineering, Zhuhai, China), were evaluated for performance against a laboratory immunoassay (EDI Novel Coronavirus COVID-19 IgG ELISA kit [Epitope Diagnostics, San Diego, CA, USA]) in 300 samples from health-care workers and 100 pre-COVID-19 negative control samples. In phase 2 (n=6440), serosurveillance was done among 1299 (93·4%) of 1391 health-care workers reporting symptoms, and in a subset of asymptomatic health-care workers (405 [8·0%] of 5049). FINDINGS: There was variation in test performance between the lateral flow serological assays; however, the Encode assay displayed reasonable IgG sensitivity (127 of 136; 93·4% [95% CI 87·8–96·9]) and specificity (99 of 100; 99·0% [94·6–100·0]) among PCR-proven cases and good agreement (282 of 300; 94·0% [91·3–96·7]) with the laboratory immunoassay. By contrast, the Onsite assay had reduced sensitivity (120 of 136; 88·2% [95% CI 81·6–93·1]) and specificity (94 of 100; 94·0% [87·4–97·8]) and agreement (254 of 300; 84·7% [80·6–88·7]). Five (7%) of 70 PCR-positive cases were negative across all assays. Late changes in lateral flow serological assay bands were recorded in 74 (9·3%) of 800 cassettes (35 [8·8%] of 400 Encode assays; 39 [9·8%] of 400 Onsite assays), but only seven (all Onsite assays) of these changes were concordant with the laboratory immunoassay. In phase 2, seroprevalence among the workforce was estimated to be 10·6% (95% CI 7·6–13·6) in asymptomatic health-care workers and 44·7% (42·0–47·4) in symptomatic health-care workers. Seroprevalence across the entire workforce was estimated at 18·0% (95% CI 17·0–18·9). INTERPRETATION: Although a good positive predictive value was observed with both lateral flow serological assays and ELISA, this agreement only occurred if the pre-test probability was modified by a strict clinical case definition. Late development of lateral flow serological assay bands would preclude postal strategies and potentially home testing. Identification of false-negative results among health-care workers across all assays suggest caution in interpretation of IgG results at this stage; for now, testing is perhaps best delivered in a clinical setting, supported by government advice about physical distancing. FUNDING: None. url: https://www.ncbi.nlm.nih.gov/pubmed/32717210/ doi: 10.1016/s2213-2600(20)30315-5 id: cord-307653-nyr6mtj1 author: Palmeira, Patricia title: Why is SARS-CoV-2 infection milder among children? date: 2020-05-11 words: 3455.0 sentences: 163.0 pages: flesch: 40.0 cache: ./cache/cord-307653-nyr6mtj1.txt txt: ./txt/cord-307653-nyr6mtj1.txt summary: As with SARS-CoV, COVID-19 is believed to be initiated by the binding of the SARS-CoV-2 envelope-anchored spike protein to the outer surface of the angiotensin-converting enzyme 2 (ACE2) catalytic domain (13) , promoting endocytosis where viral and host membranes fuse and consequent entry of the virus into the host cell. (16) reported that ACE2 pulmonary expression is concentrated mainly in type II alveolar cells, which express many other genes that could favor viral replication, thus offering an explanation for the severe alveolar damage associated with SARS-CoV-2 infection. In agreement with the hypothesis that ACE2 expression levels have a significant role in acute respiratory distress syndrome (ARDS), which also occurs in COVID-19, an experimental mouse model of H5N1 virus-induced lung injury and death showed ACE2 downregulation following infection (25) . abstract: nan url: https://doi.org/10.6061/clinics/2020/e1947 doi: 10.6061/clinics/2020/e1947 id: cord-277345-bbgerem6 author: Pan, A. title: Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area date: 2020-08-22 words: 4219.0 sentences: 271.0 pages: flesch: 44.0 cache: ./cache/cord-277345-bbgerem6.txt txt: ./txt/cord-277345-bbgerem6.txt summary: Disparate racial and ethnic burdens of the Coronavirus Disease 2019 (COVID-19) pandemic may be attributable to higher susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or to factors such as differences in hospitalization and care provision. In our cross-sectional analysis of lab-confirmed COVID-19 cases from a tertiary, eight-hospital healthcare system (Houston Methodist) across greater Houston, multivariable logistic regression models were fitted to evaluate the odds of hospitalization and mortality for non-Hispanic Blacks (NHBs) vs. Models adjusted for demographics, vital signs, laboratory parameters, hospital complications, and ICU admission demonstrated non-significantly lower likelihoods of in-hospital mortality among NHBs and Hispanics, aOR (CI): 0.65 (0.40-1.03) and 0.89 (0.59-1.31), respectively. Given our prior data, we hypothesized that Black race and Hispanic ethnicity will be independently associated with a higher hospitalization rate and in-hospital mortality in the population of COVID-19 patients across HM. abstract: Disparate racial and ethnic burdens of the Coronavirus Disease 2019 (COVID-19) pandemic may be attributable to higher susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or to factors such as differences in hospitalization and care provision. In our cross-sectional analysis of lab-confirmed COVID-19 cases from a tertiary, eight-hospital healthcare system (Houston Methodist) across greater Houston, multivariable logistic regression models were fitted to evaluate the odds of hospitalization and mortality for non-Hispanic Blacks (NHBs) vs. non-Hispanic Whites (NHWs) and Hispanics vs. non-Hispanics. Between March 3rd and July 18th, 2020, 70,496 individuals were tested for SARS-CoV-2; 12,084 (17.1%) tested positive, of whom 3,536 (29.3%) were hospitalized. Among positive cases, NHBs and Hispanics were significantly younger than NHWs and Hispanics, respectively (mean age NHBs vs. NHWs: 46.0 vs. 51.7 year and Hispanic vs. non-Hispanic: 44.0 vs. 48.7 years). Despite younger age, NHBs (vs. NHWs) had a higher prevalence of diabetes (25.2%), hypertension (47.7%), and chronic kidney disease (5.0%). Both minority groups resided in lower median income and higher population density areas. In fully adjusted models, NHBs and Hispanics had higher likelihoods of hospitalization, aOR (CI): 1.42 (1.24-1.63) and 1.61 (1.46-1.78), respectively. No differences were observed in intensive care unit (ICU) utilization or treatment parameters. Models adjusted for demographics, vital signs, laboratory parameters, hospital complications, and ICU admission demonstrated non-significantly lower likelihoods of in-hospital mortality among NHBs and Hispanics, aOR (CI): 0.65 (0.40-1.03) and 0.89 (0.59-1.31), respectively. Our data did not demonstrate racial and ethnic differences in care provision and hospital outcomes. Higher susceptibility of racial and ethnic minorities to SARS-CoV-2 and subsequent hospitalization may be driven primarily by social determinants. url: http://medrxiv.org/cgi/content/short/2020.08.19.20177956v1?rss=1 doi: 10.1101/2020.08.19.20177956 id: cord-304355-y3fagw3t author: Pan, Boyu title: Chinese herbal compounds against SARS-CoV-2: puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor date: 2020-11-11 words: 4390.0 sentences: 212.0 pages: flesch: 45.0 cache: ./cache/cord-304355-y3fagw3t.txt txt: ./txt/cord-304355-y3fagw3t.txt summary: Here, we identified puerarin (PubChem CID: 5281807), quercetin (PubChem CID: 5280343) and kaempferol (PubChem CID: 5280863) as potential compounds with binding activity to ACE2 by using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). In this study, we first screened out puerarin as the candidate compound targeting human ACE2 from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and identified the potential effective herbs containing puerarin through TCMSP analysis platform. The possible interaction of these compounds with ACE2 was further investigated by molecular docking and surface plasmon resonance assays, and the results support the view that puerarin and quercetin could significantly impair the binding of viral S-protein to its human ACE2 receptor, shedding light on CHM-based new drug discovery against COVID-19 (See workflow scheme in Figure 1 ). To screen the potential CHM compounds targeting human ACE2 receptor, Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was employed. abstract: The outbreak of COVID-19 raises an urgent need for the therapeutics to contain the emerging pandemic. However, no effective treatment has been found for SARS-CoV-2 infection to date. Here, we identified puerarin (PubChem CID: 5281807), quercetin (PubChem CID: 5280343) and kaempferol (PubChem CID: 5280863) as potential compounds with binding activity to ACE2 by using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Molecular docking analysis showed that puerarin and quercetin exhibit good binding affinity to ACE2, which was validated by surface plasmon resonance (SPR) assay. Furthermore, SPR-based competition assay revealed that puerarin and quercetin could significantly affect the binding of viral S-protein to ACE2 receptor. Notably, quercetin could also bind to the RBD domain of S-protein, suggesting not only a receptor blocking, but also a virus neutralizing effect of quercetin on SARS-CoV-2. The results from network pharmacology and bioinformatics analysis support a view that quercetin is involved in host immunomodulation, which further renders it a promising candidate against COVID-19. Moreover, given that puerarin is already an existing drug, results from this study not only provide insight into its action mechanism, but also propose a prompt application of it on COVID-19 patients for assessing its clinical feasibility. url: https://api.elsevier.com/content/article/pii/S2001037020304773 doi: 10.1016/j.csbj.2020.11.010 id: cord-312984-rzryn3on author: Pan, Daniel title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity date: 2020-09-19 words: 946.0 sentences: 63.0 pages: flesch: 59.0 cache: ./cache/cord-312984-rzryn3on.txt txt: ./txt/cord-312984-rzryn3on.txt summary: title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity 8 From this small longitudinal cohort study on serially collected samples in acute COVID-19 cases of differing severity, we conclude that for symptomatic patients, it is difficult to obtain a ''false negative'' result on NPS, OPS, NS or CS samples, if sampled early (within 5 days) post-symptom onset, even if the swab was ''poorly'' taken. Despite a previous meta-analysis showing that sputum testing is possibly more sensitive for SARS-CoV-2 PCR testing, 9 other studies have shown that self-sampling from various URT sites performed satisfactorily for the diagnosis of acute COVID-19. Therefore, we further confirm that early (within 5 days of symptom onset), self-swabbed NPS, OPS, NS or CS samples for SARS-CoV-2 diagnostic testing in acute COVID-19 cases is a sensitive, practical approach, which reduces patient discomfort (as self-swabbing can be controlled) and minimises virus exposure to healthcare workers. abstract: nan url: https://api.elsevier.com/content/article/pii/S016344532030623X doi: 10.1016/j.jinf.2020.09.016 id: cord-330022-n3d130t8 author: Pan, Daniel title: The impact of ethnicity on clinical outcomes in COVID-19: A systematic review date: 2020-06-03 words: 5069.0 sentences: 254.0 pages: flesch: 44.0 cache: ./cache/cord-330022-n3d130t8.txt txt: ./txt/cord-330022-n3d130t8.txt summary: However, emerging data from the grey literature and preprint articles suggest BAME individuals are at an increased risk of acquiring SARS-CoV-2 infection compared to White individuals and also worse clinical outcomes from COVID-19. We found 17 published studies of patients with COVID-19 which reported data on ethnicity; 1 reported an increased risk of acquiring SARS-CoV-2 in Black compared to White patients and 5 reported no association between ethnicity and clinical outcomes. 34 preprint articles on MedRxiv reported ethnicity; 13 reported an increased risk of acquiring infection with SARS-CoV-2 and 12 reported adverse clinical outcomes with COVID-19 in BAME compared to White patients. Increasing numbers of articles from the UK and USA in the grey literature and in preprint suggest that individuals from BAME communities are at increased risk of infection from SARS-CoV-2 and worse clinical outcomes including hospitalization, ITU admission and mortality, compared to White patients. abstract: BACKGROUND: The relationship between ethnicity and COVID-19 is uncertain. We performed a systematic review to assess whether ethnicity has been reported in patients with COVID-19 and its relation to clinical outcomes. METHODS: We searched EMBASE, MEDLINE, Cochrane Library and PROSPERO for English-language citations on ethnicity and COVID-19 (1(st) December 2019-15(th) May 2020). We also reviewed: COVID-19 articles in NEJM, Lancet, BMJ, JAMA, clinical trial protocols, grey literature, surveillance data and preprint articles on COVID-19 in MedRxiv to evaluate if the association between ethnicity and clinical outcomes were reported and what they showed. PROSPERO:180654. FINDINGS: Of 207 articles in the database search, five reported ethnicity; two reported no association between ethnicity and mortality. Of 690 articles identified from medical journals, 12 reported ethnicity; three reported no association between ethnicity and mortality. Of 209 preprints, 34 reported ethnicity – 13 found Black, Asian and Minority Ethnic (BAME) individuals had an increased risk of infection with SARS-CoV-2 and 12 reported worse clinical outcomes, including ITU admission and mortality, in BAME patients compared to White patients. Of 12 grey literature reports, seven with original data reported poorer clinical outcomes in BAME groups compared to White groups. INTERPRETATION: Data on ethnicity in patients with COVID-19 in the published medical literature remains limited. However, emerging data from the grey literature and preprint articles suggest BAME individuals are at an increased risk of acquiring SARS-CoV-2 infection compared to White individuals and also worse clinical outcomes from COVID-19. Further work on the role of ethnicity in the current pandemic is of urgent public health importance. FUNDING: NIHR url: https://www.ncbi.nlm.nih.gov/pubmed/32632416/ doi: 10.1016/j.eclinm.2020.100404 id: cord-310947-aqau2n7q author: Pan, Ji''An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 words: 6821.0 sentences: 302.0 pages: flesch: 43.0 cache: ./cache/cord-310947-aqau2n7q.txt txt: ./txt/cord-310947-aqau2n7q.txt summary: In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . abstract: Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp) 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/18827877/ doi: 10.1371/journal.pone.0003299 id: cord-345529-f12v6bp0 author: Pan, Q. title: Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China date: 2020-06-18 words: 1588.0 sentences: 109.0 pages: flesch: 57.0 cache: ./cache/cord-345529-f12v6bp0.txt txt: ./txt/cord-345529-f12v6bp0.txt summary: In order to better treat these patients and provide basis for further control measures, we analyze the epidemiological outcomes and clinical features of patients with residual Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) in Linyi city. Gender, age, exposure history to Hubei Province or contact with confirmed patients, onsets of symptoms, data of diagnosis, date of testing first negative, date of re-positive testing , severity of disease and other information were included for further analysis. The reason maybe that serious illness resulted from more virus infections, and more residual SARS-Cov-2 remained in the body of these patients, which makes the positive testing appear easier and more likely. The analysis also indicates that even discharge from hospital with negative testing at least two times, some patients still carry residual SARS-Cov-2 and show repeatedly positive testing outcome for 22.44±13.61 days. abstract: Patients with 2019 novel Coronavirus infection are probably showing positive testing results again. In order to better treat these patients and provide basis for further control measures, we analyze the epidemiological outcomes and clinical features of patients with residual Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) in Linyi city. From January 23 to March 31 in 2020, epidemiological and clinical information of confirmed patients are collected for analysis. Stool and pharyngeal swab samples are collected for RT-PCR testing. 64 confirmed patients are included and 17 patients present re-positive testing after discharge. For these 17 patients, 70.59% are family aggregated, the interval between first time of negative testing and first time of re-positive testing is 11.82{+/-}3.42 days. There is no difference between patients with continued negative testing results and re-positive testing. After discharge, the interval between first time of negative testing and first time of re-positive testing is associated with severity of disease (p=0.013). Besides, the duration from first time to last time of re-positive testing is associated with exposure or contact history (p=0.049) and severity of disease (p=0.001). The analysis reveals epidemiological characteristics of patients with residual SARS-Cov-2 and provide basis for further control measures. url: https://doi.org/10.1101/2020.06.16.20133199 doi: 10.1101/2020.06.16.20133199 id: cord-254017-4a6fs57r author: Pan, Xiu-wu title: Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis date: 2020-03-31 words: 870.0 sentences: 52.0 pages: flesch: 54.0 cache: ./cache/cord-254017-4a6fs57r.txt txt: ./txt/cord-254017-4a6fs57r.txt summary: Colocalization analysis of ACE2 and TMPRSS genes showed relatively high coexpression in podocytes and proximal straight tubule cells, which were identified as candidate host cells (Fig. 1a, b) . Second, although there was no significant difference in the expression of TMPRSS genes, the expression of the receptor ACE2 in podocytes and proximal straight tubule cells in Occidental donors was more pronounced than that in Asian donors (Fig. S2B) , suggesting that Occidental populations might be at higher risk for developing AKI in COVID-19. In addition, comparative analysis showed that the coexpression of the receptor ACE2 and TMPRSS genes in kidney cells was no less than that in the lung, oesophagus, small intestine and colon (Fig. S2C) , suggesting that the kidney might also be an important target organ for SARS-CoV-2. Based on our findings, we conclude that the cytopathic effects of SARS-CoV-2 on podocytes and proximal straight tubule cells may cause AKI in patients with COVID-19, especially in patients with SARS-CoV-2 infection in blood samples. abstract: nan url: https://doi.org/10.1007/s00134-020-06026-1 doi: 10.1007/s00134-020-06026-1 id: cord-339271-t7cxqkp1 author: Pan, Yanfeng title: Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date: 2020-04-22 words: 3277.0 sentences: 230.0 pages: flesch: 55.0 cache: ./cache/cord-339271-t7cxqkp1.txt txt: ./txt/cord-339271-t7cxqkp1.txt summary: The median period from diagnosis to negative nucleic acid test was significantly different between patients with normal or atypical chest computed tomography (CT) findings (n=16, 61.5%; 7.5 days [2–20 days]) and patients with typical ground-glass or patchy opacities on CT(n=10, 38.5%; 12.5 days[8–22 days]; P<0.01). Here, we identified a total of 26 persistently asymptomatic patients with positive test results for SARS-CoV-2 nucleic acid to determine the clinical characteristics and asymptomatic carrier transmission of COVID-19 infection. A total of 26 hospitalized patients with a SARS-CoV-2 epidemiological history and positive SARS-CoV-2 nucleic acid test results were identified to analyze the epidemiological and clinical characteristics of COVID-19infected asymptomatic carriers. Discharge criteria for COVID-19 were as follows: 1) normal body temperature for more than 3 days; 2) significantly improved respiratory symptoms; 3) significantly improved chest radiography; and 4) two consecutive negative SARS-CoV-2 nucleic acid test results (sampling interval at least 1 day). abstract: BACKGROUND: We retrospectively analysed 26 persistently asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carriers. METHODS: Epidemiological and clinical characteristics from the 26 asymptomatic patients with positive results for SARS-CoV-2 RNA testing were obtained. RESULTS: Twenty-two patients (84.6%) correlated with clustering occurrence. The median period from contact to diagnosis and the last positive nucleic acid test was 19 (8–24 days) and 21.5 days (10–36 days), respectively. The median period from diagnosis to negative nucleic acid test was significantly different between patients with normal or atypical chest computed tomography (CT) findings (n=16, 61.5%; 7.5 days [2–20 days]) and patients with typical ground-glass or patchy opacities on CT(n=10, 38.5%; 12.5 days[8–22 days]; P<0.01). Seven patients (70.0%) with initial positive nucleic acid test results had a negative result simultaneously with improved CT findings. Obvious improvement in CT findings was observed in three patients (30.0%) despite positive nucleic acid test results. CONCLUSION: In asymptomatic patients, changes in biochemical and inflammatory variables are small and changes on chest CT can occur. It is worth noting the long existence of SARS-CoV-2 in some asymptomatic patients and false-negative results need to be considered in SARS-CoV-2nucleic acid test. url: https://doi.org/10.1093/infdis/jiaa205 doi: 10.1093/infdis/jiaa205 id: cord-297470-lx3xwg92 author: Pan, Yunbao title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date: 2020-10-07 words: 1600.0 sentences: 97.0 pages: flesch: 51.0 cache: ./cache/cord-297470-lx3xwg92.txt txt: ./txt/cord-297470-lx3xwg92.txt summary: title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Hence, Wuhan launched a population-scale, massive SARS-CoV-2 testing campaign for detecting viral nucleic acid and antibodies in residents to further prevent viral transmission, screen out infected patients who were in the incubation period or were asymptomatic virus carriers, and map the epidemiological sero-distribution of this infectious disease in the epicenter. The present study described the screening results of 61,437 community members in Wuchang District, Wuhan. Most of the recent studies showed detectable SARS-CoV-2 anti-IgM antibodies after one to two months (10, 11) . Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China abstract: OBJECTIVES: The outbreak of 2019 coronavirus disease (COVID-19) pandemic in Wuhan, China, has subsided after a hard hit by the disease and subsequent city lockdown. Information on the number of people involved in Wuhan is still inadequate. This study aimed to describe the screening results of 61,437 community members in Wuchang District, Wuhan. METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Here we show the screening results of cluster sampled 61,437 residents in Wuchang District, Wuhan, China. RESULTS: A total of 1470 (2.39%, 95% CI: 2.27-2.52) individuals were detected positive for at least one antiviral antibody. Among the positive individuals, 324 (0.53%, 95% CI: 0.47-0.59) and 1200 (1.95%, 95% CI: 1.85-2.07) were positive for immunoglobulin IgM and IgG, respectively, and 54 (0.08%, 95% CI: 0.07-0.12) were positive for both antibodies. The positive rate of female carriers of antibodies were higher than those of male counterparts (male-to-female ratio of 0.75), especially in elderly citizens (ratio of 0.18 in 90+ age subgroup), indicating a sexual discrepancy in seroprevalence. In addition, viral nucleic acid detection using real-time PCR had showed 8 (0.013%, 95% CI: 0.006-0.026) asymptomatic virus carriers. CONCLUSIONS: The seroprevalence of SARS-CoV-2 in Wuhan was low. Most of Wuhan residents are still susceptible to this virus. Precautions, such as wearing mask, frequent hand hygiene, and proper social distance, are necessary before an effective vaccine or antiviral treatments are available. url: https://www.ncbi.nlm.nih.gov/pubmed/33035672/ doi: 10.1016/j.cmi.2020.09.044 id: cord-341284-jmqdnart author: Panagopoulos, Periklis title: Lopinavir/ritonavir as a third agent in the antiviral regimen for SARS-CoV-2 infection date: 2020-06-12 words: 1548.0 sentences: 106.0 pages: flesch: 53.0 cache: ./cache/cord-341284-jmqdnart.txt txt: ./txt/cord-341284-jmqdnart.txt summary: Further studies are needed in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection. 9 The aim of the present study was to assess the impact of lopinavir/ritonavir as a third agent for the treatment of SARS COV 2 infection especially for patients with severe pneumonia emphasizing in the number of days needed for reduction of viral load. However, the number of days needed for the first negative result of RT-PCR for SARS-CoV-2 was significantly lower for patients of group A. The present study suggests that lopinavir/ritonavir could be a potential effective choice in treatment of patients with CoVID-19. 12 However, a retrospective study conducted in China including 134 patients with CoVID-19 showed no effect on accelerating the clearance of SARS-CoV-2. Further studies are needed with larger patient series in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection and confirm the findings of the present study. abstract: Corona Virus Disease (CoVID-19) is an emerging public health problem rapidly spread globally. New treatment options for patients with severe symptoms and ways of reducing transmission in the community are taken into consideration. A retrospective study was conducted in the Department of Infectious Diseases of Alexandroupolis (Greece) including 16 patients with CoVID-19. They were classified into two groups, A and B. Group A received lopinavir/ritonavir as a third agent in the antiviral regimen, while group B did not. Lymphocytes were more significantly increased in patients of group A. Ferritin serum levels were also decreased significantly in these patients. Number of days needed for a first negative result of Real Time- Polymerase Chain Reaction (RT-PCR) was lower for Group A. The present study suggests that lopinavir/ritonavir may reduce the viral carriage in a shorter period of time compared with other antiviral regimens. Further studies are needed in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection. url: https://doi.org/10.1080/1120009x.2020.1775424 doi: 10.1080/1120009x.2020.1775424 id: cord-303173-q88zdf03 author: Panchaud, Alice title: An international registry for emergent pathogens and pregnancy date: 2020-04-27 words: 530.0 sentences: 29.0 pages: flesch: 43.0 cache: ./cache/cord-303173-q88zdf03.txt txt: ./txt/cord-303173-q88zdf03.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) pandemic is no exception. 3 To tweak resources, we have adjusted the Zika virus international web registry 9 to create COVI-Preg, a structured data collection tool available to any facility assessing pregnant patients for SARS-CoV-2 infection. For the ongoing SARS-CoV-2 pandemic, we hypothesise that the collected data will allow researchers and health-care professionals to better characterise the disease course and spectrum, quantitatively estimate associated risks, and identify specific risk factors that can be used to define screening strategies in pregnant women and adequate prevention meas ures, and to direct specific and early clinical management of women and fetuses at risk. Clinical analysis of pregnancy in second and third trimesters complicated severe acute respiratory syndrome An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes abstract: nan url: https://doi.org/10.1016/s0140-6736(20)30981-8 doi: 10.1016/s0140-6736(20)30981-8 id: cord-035157-97tfcgvq author: Panchin, Alexander Y. title: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes date: 2020-07-28 words: 2803.0 sentences: 196.0 pages: flesch: 57.0 cache: ./cache/cord-035157-97tfcgvq.txt txt: ./txt/cord-035157-97tfcgvq.txt summary: RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). SARS-CoV-2 is closely related to the bat coronavirus RaTG13 with around 96% whole genome nucleotide sequence identity . We compared the relative frequencies of single nucleotide variations (which we will refer to as mutations) in SARS-CoV-2 with the relative frequencies of substitutions that it acquired since the divergence with its last common ancestor with a closely related coronavirus from bats RaTG13. On the other hand, the substitution profile of SARS-CoV-2 turned out to be quite similar to that of the other coronaviruses, lending further support to existing scenarios of its natural origin (Andersen et al., 2020) and suggesting that the changes in SARS-CoV-2 mutation frequencies have accompanied its transition to human hosts. abstract: BACKGROUND: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. METHODS: We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394058/ doi: 10.7717/peerj.9648 id: cord-286895-i3g4ad4z author: Panciani, Pier Paolo title: SARS-CoV-2: “Three-steps” infection model and CSF diagnostic implication date: 2020-05-05 words: 772.0 sentences: 61.0 pages: flesch: 52.0 cache: ./cache/cord-286895-i3g4ad4z.txt txt: ./txt/cord-286895-i3g4ad4z.txt summary: Dear Editor, An increasing number of Coronavirus Disease 2019 (COVID-19) patients shows neurological symptoms, but currently few studies have systematically analyzed the impact of SARS-CoV-2 on the Central Nervous System (CNS). (Bertran Recasens et al., 2020) In our Department we observed 3 different clinical pictures in SARS-CoV-2 infection with neurological impairment: cerebral thrombosis (CTh) with hemorrhagic infarction, demyelinating lesions and encephalopathy. SARS-CoV-2 may lead to Neuro-COVID through three phases ( Fig.1) : neuroinvasion, CNS clearance and immune response. Negative results could also be explained by the lack of apoptosis and/or necrosis as observed in pre-clinical models (Netland et al., 2008) , the lowsensitivity of the method and the CSF clearance of SARS-CoV-2 that lead to a low viral below the sensitivity of currently available instrumentation. In the last phase, the respiratory system is severely affected leading to potential hypoxia with subsequent brain damage. abstract: nan url: https://doi.org/10.1016/j.bbi.2020.05.002 doi: 10.1016/j.bbi.2020.05.002 id: cord-301730-flv5lnv8 author: Pandey, Anamika title: Natural Plant Products: A Less Focused Aspect for the COVID-19 Viral Outbreak date: 2020-10-15 words: 7101.0 sentences: 346.0 pages: flesch: 50.0 cache: ./cache/cord-301730-flv5lnv8.txt txt: ./txt/cord-301730-flv5lnv8.txt summary: Despite the previous positive reports of plant-based medications, no successful clinical trials of phyto-anti-COVID drugs could be conducted to date. Medicinal plant extracts have been reported to impede the replication of several viruses including human immunodeficiency virus (HIV), hepatitis B virus (HBV), poxvirus, severe acute respiratory syndrome (SARS) virus, and herpes simplex virus type 2 (HSV-2) (Vermani and Garg, 2002; Kotwal et al., 2005; Huang et al., 2006) . Different researchers are investigating diverse plant forms based on ethnopharmacological data to find effective anti-CoV drugs with novel action mechanisms especially targeting viral replication. Moreover, creating an effective phyto-anti-COVID drug during this pandemic may provide an idea on the duration and the strategy required for the development of potent plant-based therapeutics in case of such random viral outbreaks (Figure 1) . abstract: The sudden emergence of COVID-19 caused by a novel coronavirus (nCoV) led the entire world to search for relevant solutions to fight the pandemic. Although continuous trials are being conducted to develop precise vaccines and therapeutic antibodies, a potential remedy is yet to be developed. Plants have largely contributed to the treatment of several human diseases and different phytoconstituents have been previously described to impede the replication of numerous viruses. Despite the previous positive reports of plant-based medications, no successful clinical trials of phyto-anti-COVID drugs could be conducted to date. In this article, we discuss varying perspectives on why phyto-anti-viral drug clinical trials were not successful in the case of COVID-19. The issue has been discussed in light of the usage of plant-based therapeutics in previous coronavirus outbreaks. Through this article, we aim to identify the disadvantages in this research area and suggest some measures to ensure that phytoconstituents can efficiently contribute to future random viral outbreaks. It is emphasized that if used strategically phyto-inhibitors with pre-established clinical data for other diseases can save the time required for long clinical trials. The scientific community should competently tap into phytoconstituents and take their research up to the final stage of clinical trials so that potential phyto-anti-COVID drugs can be developed. url: https://www.ncbi.nlm.nih.gov/pubmed/33178237/ doi: 10.3389/fpls.2020.568890 id: cord-260057-2m6jdvtc author: Pandey, Preeti title: Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date: 2020-09-23 words: 7756.0 sentences: 409.0 pages: flesch: 51.0 cache: ./cache/cord-260057-2m6jdvtc.txt txt: ./txt/cord-260057-2m6jdvtc.txt summary: To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking–based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. The selected docking conformations of NSP6 in complex with haloperidol and dextromethorphan were sampled by 100-ns MD simulation, and the dynamic stability of the complex was elucidated by calculating the Cα-RMSD values of the protein as the function of simulation time ( Figure S3A ). In conclusion, the study elucidated the detailed interaction mechanism of dextromethorphan and haloperidol to NSP6 protein and the associated structural and dynamical changes upon drug binding. abstract: ABSTRACT: The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus continually led to infect a large population worldwide. SARS-CoV-2 utilizes its NSP6 and Orf9c proteins to interact with sigma receptors that are implicated in lipid remodeling and ER stress response, to infect cells. The drugs targeting the sigma receptors, sigma-1 and sigma-2, have emerged as effective candidates to reduce viral infectivity, and some of them are in clinical trials against COVID-19. The antipsychotic drug, haloperidol, exerts remarkable antiviral activity, but, at the same time, the sigma-1 benzomorphan agonist, dextromethorphan, showed pro-viral activity. To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking–based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. On the other hand, the strong binding of haloperidol leads to minimal structural and dynamical perturbations to NSP6. Thus, the structural insights of stronger binding affinity and favorable molecular interactions of haloperidol towards viral NSP6 suggests that haloperidol can be potentially explored as a candidate drug against COVID-19. KEY MESSAGES: •Inhibitors of sigma receptors are considered as potent drugs against COVID-19. •Antipsychotic drug, haloperidol, binds strongly to NSP6 and induces the minimal changes in structure and dynamics of NSP6. •Dextromethorphan, agonist of sigma receptors, binding leads to overall destabilization of NSP6. •These two drugs bind with NSP6 differently and also induce differences in the structural and conformational changes that explain their different mechanisms of action. •Haloperidol can be explored as a candidate drug against COVID-19. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00109-020-01980-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32965508/ doi: 10.1007/s00109-020-01980-1 id: cord-308408-aciaj30k author: Paneesha, S. title: Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia date: 2020-04-30 words: 2069.0 sentences: 129.0 pages: flesch: 60.0 cache: ./cache/cord-308408-aciaj30k.txt txt: ./txt/cord-308408-aciaj30k.txt summary: It is likely that patients who undergo immuno-chemotherapy as part of disease management will be at increased risk of clinical complications following SARS-CoV-2 infection. As such, the clinical outcome of SARS-CoV-2 infection in patients with therapy-naive CLL is an area of considerable importance. These findings suggest that SARS-CoV-2 infection in patients with therapy-naive CLL may be associated with considerably greater clinical risk than seen in the general population and argue for strict enforcement of quarantine conditions. At clinic one month prior to final admission the blood count showed Hb 85 g/l, WBC 274 x10 9 /l and platelets 127 x10 9 /l. Clinically, it is important to recognise that this is a feature of acute SARS-CoV-2 infection in patients with CLL and that the lymphocytosis can resolve quickly. Covid-induced lymphocytosis The peripheral lymphocyte count is shown for each patient at the most recent outpatient clinic prior to onset of SAR-CoV-2 infection and also the peak value during Covid-19 infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32388230/ doi: 10.1016/j.leukres.2020.106366 id: cord-277683-9cg90zbo author: Panettieri, Reynold A. title: Asthma and COVID: What are the Important Questions? date: 2020-06-22 words: 946.0 sentences: 60.0 pages: flesch: 49.0 cache: ./cache/cord-277683-9cg90zbo.txt txt: ./txt/cord-277683-9cg90zbo.txt summary: However, critical questions remain about the biologic and 40 clinical features that predispose to CSS and critical illness, including underlying comorbidities 41 such as asthma and the medications used to treat them. Older age and comorbidities, especially heart disease, hypertension, chronic obstructive 43 pulmonary disease (COPD), diabetes and obesity, are reported risk factors for the development 44 and progression of COVID-19 (3). However, controversy exists as to whether patients with 45 asthma manifest high or elevated rates of COVID-19 incidence. Inhaled steroids 62 have also been associated with decreased expression of angiotensin-converting enzyme 2 63 (ACE2), the co-receptor for SARS-CoV-2 raising the question of whether these drugs could Future studies should address whether inhaled steroids in patient with asthma and/or allergic 68 rhinitis increase or decrease risks of SARS-CoV-2 infection, and whether these effects different 69 across inhaled steroid types. Changes in medication 115 adherence among patients with asthma and COPD during the COVID-19 pandemic abstract: nan url: https://api.elsevier.com/content/article/pii/S2213219820306061 doi: 10.1016/j.jaip.2020.06.008 id: cord-348567-rvwxysvc author: Panfili, F. M. title: Possible role of vitamin D in Covid-19 infection in pediatric population date: 2020-06-15 words: 5375.0 sentences: 229.0 pages: flesch: 36.0 cache: ./cache/cord-348567-rvwxysvc.txt txt: ./txt/cord-348567-rvwxysvc.txt summary: CONCLUSIONS: In this review, we suggest that vitamin D supplementation might play a role in the prevention and/or treatment to SARS-CoV-2 infection disease, by modulating the immune response to the virus both in the adult and pediatric population. Although the effect of normal to high levels of vitamin D on increasing CD4+ count is still unclear, a recent review proved that vitamin D plays an important role in reducing the immune activation of HIV-infected patients. In this autoimmune disease using calcitriol supplementation reduces serum levels of antibodies and slows the progression of β cell destruction down in the early stages of the disease [38] , Interestingly, it has also been demonstrated that in Systemic Sclerosis (SSc) [39] the VDR could act as a negative regulator of TGF-β/ Hydroxyproline, col1a1, col3a1 and alfa-SMA mRNAs ↓ Prevention of bleomycin-induced lung fibrosis in a murine model [48] Smad signaling, thus making vitamin D a putative antifibrotic treatment in the early stages of the disease. abstract: PURPOSE: Covid-19 is a pandemic of unprecedented proportion, whose understanding and management is still under way. In the emergency setting new or available therapies to contrast the spread of COVID-19 are urgently needed. Elderly males, especially those affected by previous diseases or with comorbidities, are more prone to develop interstitial pneumonia that can deteriorate evolving to ARDS (acute respiratory distress syndrome) that require hospitalization in Intensive Care Units (ICUs). Even children and young patients are not spared by SARS-CoV 2 infection, yet they seem to develop a milder form of disease. In this setting the immunomodulatory role of Vitamin D, should be further investigated. Methods: We reviewed the literature about the immunomodulatory role of Vitamin D collecting data from the databases Medline and Embase. RESULTS: Vitamin D proved to interact both with the innate immune system, by activating Toll-like receptors (TLRs) or increasing the levels of cathelicidins and β-defensins, and adaptive immune system, by reducing immunoglobulin secretion by plasma cells and pro-inflammatory cytokines production, thus modulating T cells function. Promising results have been extensively described as regards the supplementation of vitamin D in respiratory tract infections, autoimmune diseases and even pulmonary fibrosis. CONCLUSIONS: In this review, we suggest that vitamin D supplementation might play a role in the prevention and/or treatment to SARS-CoV-2 infection disease, by modulating the immune response to the virus both in the adult and pediatric population. url: https://doi.org/10.1007/s40618-020-01327-0 doi: 10.1007/s40618-020-01327-0 id: cord-274284-mi4n7xty author: Pang, Khang Wen title: Frequency and Clinical Utility of Olfactory Dysfunction in COVID-19: a Systematic Review and Meta-analysis date: 2020-10-13 words: 4402.0 sentences: 254.0 pages: flesch: 50.0 cache: ./cache/cord-274284-mi4n7xty.txt txt: ./txt/cord-274284-mi4n7xty.txt summary: Meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if OD symptoms were explicitly asked in questionnaires or interviews or if smell tests were performed. RESULTS: The pooled frequency of OD in COVID-19 positive patients (17,401 patients, 60 studies) was 0.56 (0.47–0.64) but differs between detection via smell testing (0.76 [0.51–0.91]) and survey/questionnaire report (0.53 [0.45–0.62]), although not reaching statistical significance (p = 0.089). To investigate the estimated frequency of OD amongst COVID-19 patients, meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if smell tests were performed or if OD symptoms were explicitly asked in questionnaires or interviews. Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Self-reported olfactory and taste disorders in patients With severe acute respiratory coronavirus 2 infection: a cross-sectional study abstract: BACKGROUND: Olfactory dysfunction (OD) has been gaining recognition as a symptom of COVID-19, but its clinical utility has not been well defined. OBJECTIVES: To quantify the clinical utility of identifying OD in the diagnosis of COVID-19 and determine an estimate of the frequency of OD amongst these patients. METHODS: PubMed was searched up to 1 August 2020. Meta-analysis A included studies if they compared the frequency of OD in COVID-19 positive patients (proven by reverse transcription polymerase chain reaction) to COVID-19 negative controls. Meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if OD symptoms were explicitly asked in questionnaires or interviews or if smell tests were performed. RESULTS: The pooled frequency of OD in COVID-19 positive patients (17,401 patients, 60 studies) was 0.56 (0.47–0.64) but differs between detection via smell testing (0.76 [0.51–0.91]) and survey/questionnaire report (0.53 [0.45–0.62]), although not reaching statistical significance (p = 0.089). Patients with reported OD were more likely to test positive for COVID-19 (diagnostic odds ratio 11.5 [8.01–16.5], sensitivity 0.48 (0.40 to 0.56), specificity 0.93 (0.90 to 0.96), positive likelihood ratio 6.10 (4.47–8.32) and negative likelihood ratio 0.58 (0.52–0.64)). There was significant heterogeneity amongst studies with possible publication bias. CONCLUSION: Frequency of OD in COVID-19 differs greatly across studies. Nevertheless, patients with reported OD were significantly more likely to test positive for COVID-19. Patient-reported OD is a highly specific symptom of COVID-19 which should be included as part of the pre-test screening of suspect patients. url: https://doi.org/10.1007/s11882-020-00972-y doi: 10.1007/s11882-020-00972-y id: cord-309554-ctc84tfy author: Pang, Ronald TK title: Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome date: 2006-03-01 words: 5189.0 sentences: 273.0 pages: flesch: 52.0 cache: ./cache/cord-309554-ctc84tfy.txt txt: ./txt/cord-309554-ctc84tfy.txt summary: To identify proteomic features associated only with disease, we used 2 criteria: (a) the normalized peak intensities had to be significantly higher/lower in SARS patients than in non-SARS individuals; and (b) the normalized peak intensities had to correlate with 2 or more clinical/ biochemical variables, indicating their biological meaningfulness. These potential biomarkers were found to be significantly associated with SARS-CoV viral load (2 correlated with SARS-CoV RNA), acute-phase reaction [ differentiation of sars by two-way hierarchical clustering analysis of serum proteomic fingerprints We successfully identified potential biomarkers reflecting various physiologic or pathologic responses of the body to SARS infection, including acute-phase reaction (7, 17 ) , lung damage (18 -20 ) , impairment of liver function (21) (22) (23) , neutrophil activation (24 -26 ) , and viral load (5, 10, 27, 28 ) . Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia abstract: Background: Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a new coronavirus strain, SARS-CoV. Specific proteomic patterns might be present in serum in response to the infection and could be useful for early detection of the disease. Methods: Using surface-enhanced laser desorption/ionization (SELDI) ProteinChip technology, we profiled and compared serum proteins of 39 patients with early-stage SARS infection and 39 non-SARS patients who were suspected cases during the SARS outbreak period. Proteomic patterns associated with SARS were identified by bioinformatic and biostatistical analyses. Features of interest were then purified and identified by tandem mass spectrometry. Results: Twenty proteomic features were significantly different between the 2 groups. Fifteen were increased in the SARS group, and 5 were decreased. Their concentrations were correlated with 2 or more clinical and/or biochemical variables. Two were correlated with the SARS-CoV viral load. Hierarchical clustering analysis showed that a majority of the SARS patients (95%) had similar serum proteomic profiles and identified 2 subgroups with poor prognosis. ROC curve analysis identified individual features as potential biomarkers for SARS diagnosis (areas under ROC curves, 0.733–0.995). ROC curve areas were largest for an N-terminal fragment of complement C3c α chain (m/z 28 119) and an internal fragment of fibrinogen α-E chain (m/z 5908). Immunoglobulin κ light chain (m/z 24 505) positively correlated with viral load. Conclusions: Specific proteomic fingerprints in the sera of adult SARS patients could be used to identify SARS cases early during onset with high specificity and sensitivity. url: https://www.ncbi.nlm.nih.gov/pubmed/16423906/ doi: 10.1373/clinchem.2005.061689 id: cord-314714-ehxxvenb author: Pang, Xiaocong title: Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication date: 2020-06-24 words: 1219.0 sentences: 74.0 pages: flesch: 44.0 cache: ./cache/cord-314714-ehxxvenb.txt txt: ./txt/cord-314714-ehxxvenb.txt summary: title: Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication However, the addition of exogenous ACE2 could be a potential treatment for SARS-CoV-2 infection, which might not only restrain the spread of SARS-CoV-2 by blocking its interaction with ACE2 on the host cell, but also modulate RAS to treat SARS-CoV-2-related underlying comorbidities and protect the lung from developing ARDS. Although Ang II receptor and ACE blockage were also effective in lung failure in animal models, this treatment could cause potential adverse effects, causing systemic hypotension in humans [22] . Currently, phase I (NCT00886353) and phase II (NCT01597635) clinical studies with a recombinant version of the catalytic ectodomain of human ACE2 (GSK2586881) have been successfully completed, providing safety and efficacy for ARDS treatment [25, 26] . Recombinant human ACE2 and the angiotensin 1-7 axis as potential new therapies for heart failure A pilot clinical trial of recombinant human angiotensin-converting enzyme 2 in acute respiratory distress syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32581256/ doi: 10.1038/s41401-020-0430-6 id: cord-332654-nav15g8k author: Paniri, Alireza title: Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations date: 2020-08-04 words: 5712.0 sentences: 341.0 pages: flesch: 47.0 cache: ./cache/cord-332654-nav15g8k.txt txt: ./txt/cord-332654-nav15g8k.txt summary: The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy. Furthermore, growing body of evidence demonstrated that several factors including CYP450 single nucleotide polymorphisms (SNPs), and epigenetic molecules such as non-coding RNAs (ncRNAs), DNA methylation and histone acetylation influenced the expression levels of CYP450, and consequently might influence HCQ metabolism. The major purpose of this review is to discuss the pharmacokinetic and pharmacodynamic characteristics of CQ and HCQ that may be influenced by epigenetic mechanisms including ncRNAs and CYP2D6 SNPs, and thereby cause several side effects such as cardiotoxicity, prolonged QT interval, gastrointestinal problems (like dyspepsia and abdominal cramps), central nervous system or skin disorders, and especially retinopathy. abstract: Antimalaria drugs such as chloroquine (CQ) and hydroxychloroquine (HCQ) have been administered to several inflammatory diseases including rheumatoid arthritis and systemic lupus erythematosus, and infectious diseases such as acquired immune deficiency syndrome and influenza. Recently, several patients infected with novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were given HCQ, and showed a discrepant response. HCQ inhibits SARS-CoV-2 cell entry, and inflammatory cascade by interfering with lysosomal and endosomal activities, and autophagy, impeding virus-membrane fusion, and inhibiting cytokine production resulted from inflammatory pathways activation. Despite ongoing administration of HCQ in a wide spectrum of disorders, there are some reports about several side effects, especially retinopathy in some patients treated with HCQ. Cytochrome P450 (CYP450) and its isoforms are the main metabolizers of HCQ and CQ. Pharmacokinetic properties of CYP enzymes are influenced by CYP polymorphism, non-coding RNAs, and epigenetic mechanisms such as DNA methylation, and histone acetylation. Accumulating evidence about side effects of HCQ in some patients raise the possibility that different response of patients to HCQ might be due to difference in their genome. Therefore, CYP450 genotyping especially for CYP2D6 might be helpful to refine HCQ dosage. Also, regular control of retina should be considered for patients under HCQ treatment. The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy. url: https://api.elsevier.com/content/article/pii/S001429992030546X doi: 10.1016/j.ejphar.2020.173454 id: cord-337026-osgi06o4 author: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 words: 3174.0 sentences: 171.0 pages: flesch: 48.0 cache: ./cache/cord-337026-osgi06o4.txt txt: ./txt/cord-337026-osgi06o4.txt summary: Given the uprising number of publications and case reports of COVID-19 patients showing conjunctivitis [61, 62] and the history of other coronaviruses that are found in tears, we have to consider the possibility of a separate, alternative viral mechanism through which the virus can enter the patient''s organism through epithelial cells of the eye [63] . The growing evidence on COVID-19 and its ocular implications and manifestations, in both animals and humans, is covered by many interesting reviews, all published 5 to 6 months after the novel coronavirus'' outbreak [64] [65] [66] [67] [68] , something that reveals the need to understand the virus from different perspectiveswhich at first may have seemed secondary in priority-in order to be able to reach a treatment. abstract: COVID-19 has been declared a pandemic by the World Health Organization on March 11, and since then, more than 3 million cases and a quarter million deaths have occurred due to it. Lately, there is a growing evidence for an ophthalmologic symptom (conjunctivitis) to be connected with the disease. This seems to happen in early stages of the infection by SARS-CoV-2, and thus, it is of major importance to understand the mechanism through which the virus can facilitate such a symptom. Here, we are proposing a molecular mechanism through which the novel coronavirus could act in order to affect the eye and use it as another, secondary but alternative, point of entry to the host organism. url: https://www.ncbi.nlm.nih.gov/pubmed/32838145/ doi: 10.1007/s42399-020-00360-7 id: cord-318164-6rqi17oz author: Paoli, D. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 words: 3258.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-318164-6rqi17oz.txt txt: ./txt/cord-318164-6rqi17oz.txt summary: This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. This study thus aimed to evaluate the safety of sperm cryopreservation of cancer patients referred to our sperm bank after the onset of the pandemic in Italy through the assessment of the risk of SARS-CoV-2 exposure and, in selected volunteers, viral RNA testing of semen samples. This was further confirmed by testing seminal fluid samples from 10 asymptomatic cancer patients for SARS-CoV-2 RNA. abstract: PURPOSE: Sperm cryopreservation is fundamental in the management of patients undergoing gonadotoxic treatments. Concerns have risen in relation to SARS-CoV-2 and its potential for testicular involvement, since SARS-CoV-2-positive cryopreserved samples may have unknown effects on fertilization and embryo safety. This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. METHODS: We recruited 10 cancer patients (mean age 30.5 ± 9.6 years) referred to our Sperm Bank during the Italian lockdown (from March 11th to May 4th 2020) who had not undergone a nasopharyngeal swab for SARS-CoV-2 testing. Patients were administered a questionnaire on their exposure to COVID-19, and semen samples were taken. Before cryopreservation, SARS-CoV-2 RNA was extracted from a 150 µl aliquot of seminal fluid in toto using QIAamp viral RNA kit (Qiagen) and amplified by a real time RT PCR system (RealStar SARS-CoV2 RT PCR, Altona Diagnostics) targeting the E and S genes. RESULTS: The questionnaire and medical interview revealed that all patients were asymptomatic and had had no previous contact with COVID-19 infected patients. All semen samples were negative for SARS-CoV-2 RNA. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. url: https://doi.org/10.1007/s40618-020-01438-8 doi: 10.1007/s40618-020-01438-8 id: cord-323695-jkik03lb author: Paolo, Gisondi title: Incidence rates of hospitalization and death from COVID-19 in patients with psoriasis receiving biological treatment: a Northern Italy experience date: 2020-11-05 words: 1745.0 sentences: 88.0 pages: flesch: 46.0 cache: ./cache/cord-323695-jkik03lb.txt txt: ./txt/cord-323695-jkik03lb.txt summary: Objective investigating the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. Materials and methods This is a retrospective multicenter cohort study including patients with chronic plaque psoriasis (n=6,501) being treated with biologic therapy and regularly followed up at the Divisions of Dermatology of several main hospitals in the Northern Italian cities of Verona, Padua, Vicenza, Modena, Bologna, Piacenza, Turin, and Milan. Incidence rates (IR) of hospitalization and death per 10,000 person-months with exact mid-p 95% confidence intervals (CI) and standardized incidence ratios (SIR) were estimated in the psoriasis patients and compared with the general population in the same geographic areas. We would not advise biologic discontinuation in patients on treatment since more than 6 months and not infected with SARS-CoV-2 to prevent hospitalization and death from COVID-19. In this study, we evaluated the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. abstract: Introduction Whether biologic therapies enhance the risk of COVID-19 or affect the disease outcome in patients with chronic plaque psoriasis remains to be ascertained. Objective investigating the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. Materials and methods This is a retrospective multicenter cohort study including patients with chronic plaque psoriasis (n=6,501) being treated with biologic therapy and regularly followed up at the Divisions of Dermatology of several main hospitals in the Northern Italian cities of Verona, Padua, Vicenza, Modena, Bologna, Piacenza, Turin, and Milan. Incidence rates (IR) of hospitalization and death per 10,000 person-months with exact mid-p 95% confidence intervals (CI) and standardized incidence ratios (SIR) were estimated in the psoriasis patients and compared with the general population in the same geographic areas. Results The IR of hospitalization for COVID-19 was 11.7 (95% CI: 7.2-18.1) per 10,000 person-months in psoriasis patients and 14.4 (95% CI: 14.3-14.5) in the general population; the IR of death from COVID-19 was 1.3 (95% CI: 0.2-4.3) and 4.7 (95% CI: 4.6-4.7) in psoriasis patients and the general population, respectively. The SIR of hospitalization and death in psoriasis patients compared with the general population was 0.94 (95% CI: 0.57-1.45; p=0.82) and 0.42 (95% CI: 0.07-1.38; p=0.19) respectively. Conclusions Our data did not show any adverse impact of biologics on COVID-19 outcome in psoriasis patients. We would not advise biologic discontinuation in patients on treatment since more than 6 months and not infected with SARS-CoV-2 to prevent hospitalization and death from COVID-19. url: https://www.sciencedirect.com/science/article/pii/S009167492031558X?v=s5 doi: 10.1016/j.jaci.2020.10.032 id: cord-317151-cxx5pcln author: Papa, Alfredo title: Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date: 2020-10-24 words: 5030.0 sentences: 254.0 pages: flesch: 44.0 cache: ./cache/cord-317151-cxx5pcln.txt txt: ./txt/cord-317151-cxx5pcln.txt summary: 14 Since the beginning of the pandemic, the World Health Organization has provided general recommendations for the prevention of They include: to wash hands frequently and properly with soap or alcohol-based sanitizer, to maintain social distancing (at least 1 m of distance), to avoid touching eyes, nose and mouth, to cover mouth and nose when coughing or sneezing, to seek medical care early when fever, cough or difficulty in breathing are recorded, to wear personal protective equipment (PPE), in particular the facial mask when social distancing is not possible to maintain or in closed places, to stay informed and follow any advice provided by own healthcare providers. This may require further changes in the planning of healthcare activities, both by using different prioritization criteria for outpatient visits, diagnostic tests and surgical interventions and by continuing to use treatment strategies that have worked well during the pandemic such as telemedicine, psychological support to patients and the educational function of patient associations (Table 1) . abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised several concerns for patients with chronic immune-mediated diseases, including inflammatory bowel disease (IBD). As the outbreak appears to be in the descending phase, at least in some part of the world, as in most European countries, guidance is urgently needed to provide optimal care for our IBD patients in order to gradually and safely reduce the gap in care that has been accumulated in the months of lockdown and to face all the backlogs. Therefore, we have provided a decalogue of practical recommendations for gastroenterologists to manage patients with IBD in the post-peak phase of the COVID-19 pandemic. They include all the aspects of IBD care, not only pharmacological ones but also endoscopy, surgery, psychological treatment, telemedicine, diagnostics and educational tasks provided by doctors and patient associations. url: https://doi.org/10.1177/1756284820968747 doi: 10.1177/1756284820968747 id: cord-308667-6jr3z9wx author: Papachristodoulou, Eleni title: Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge date: 2020-06-08 words: 1768.0 sentences: 82.0 pages: flesch: 51.0 cache: ./cache/cord-308667-6jr3z9wx.txt txt: ./txt/cord-308667-6jr3z9wx.txt summary: Furthermore, data from SARS-CoV suggest that the duration of immunity may not be sufficiently significant, while the immunity response against SARS-CoV-2 may not be efficiently effective in all patients, as relapses have already been reported. In conclusion, the development of an effective vaccine is an urgent necessity, as long-term natural immunity to SARS-CoV-2 may not be sufficient for the control of the current and future outbreaks. Information from follow-up studies of patients recovered from other coronaviruses may provide a background regarding the possible long-term immune response of SARS-CoV-2 infection. (2011) reported that antibody titers were undetectable in 21/23 patients at six years post-infection, while SARS-CoV antigen-specific memory B-cell response was undetectable in all 23 patients. As a consequence, the increasing number of individuals recovered from COVID-19 may not be able to provide effective herd immunity during subsequent post-pandemic waves of infection by mutant variants (Biswas et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered 1 patient cohort and their implications abstract: Effective herd immunity against SARS-CoV-2 will be determined on many factors: the percentage of the immune population, the length and effectiveness of the immune response and the stability of the viral epitopes. The required percentage of immune individuals has been estimated to be 50–66% of the population which, given the current infection rates, will take long to be achieved. Furthermore, data from SARS-CoV suggest that the duration of immunity may not be sufficiently significant, while the immunity response against SARS-CoV-2 may not be efficiently effective in all patients, as relapses have already been reported. In addition, the development of mutant strains, which has already been documented, can cause the reemergence of the epidemic. In conclusion, the development of an effective vaccine is an urgent necessity, as long-term natural immunity to SARS-CoV-2 may not be sufficient for the control of the current and future outbreaks. url: https://doi.org/10.1093/femspd/ftaa025 doi: 10.1093/femspd/ftaa025 id: cord-284045-scd3f8vk author: Pape, Constantin title: Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date: 2020-10-07 words: 5627.0 sentences: 300.0 pages: flesch: 53.0 cache: ./cache/cord-284045-scd3f8vk.txt txt: ./txt/cord-284045-scd3f8vk.txt summary: Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay which complements the portfolio of SARS-CoV-2 serological assays. The dsRNA co-localizing pattern 213 observed for sera from the negative control cohort is by definition non-specific for SARS-CoV-2, 214 but would be classified as a positive hit based on staining intensity alone. The high information content of the IF data (differential staining patterns) 363 together with a machine learning-based approach [45] and the implementation of stable cell lines 364 expressing selected viral antigens in the IF assay will provide additional parameters for 365 classification of patient sera and further improve sensitivity and specificity of the presented IF 366 assay. abstract: Emergence of the novel pathogenic coronavirus SARS-CoV-2 and its rapid pandemic spread presents numerous questions and challenges that demand immediate attention. Among these is the urgent need for a better understanding of humoral immune response against the virus as a basis for developing public health strategies to control viral spread. For this, sensitive, specific and quantitative serological assays are required. Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay which complements the portfolio of SARS-CoV-2 serological assays. The procedure described here has been used for clinical studies and provides a general framework for the application of quantitative high-throughput microscopy to rapidly develop serological assays for emerging virus infections. url: https://doi.org/10.1101/2020.06.15.152587 doi: 10.1101/2020.06.15.152587 id: cord-352799-qmzh976f author: Paquin, Leo J. title: Was WHO SARS-related Travel Advisory for Toronto Ethical? date: 2007-05-01 words: 2302.0 sentences: 183.0 pages: flesch: 68.0 cache: ./cache/cord-352799-qmzh976f.txt txt: ./txt/cord-352799-qmzh976f.txt summary: Guénaël R.M. Rodier thinks WHO''s decision to impose a SARS-related travel advisory was justifiable, even reasonable, though it caused a loss of over $1.1 billion in the Greater Toronto Area. However, as suggested in the Naylor report, issuing a travel advisory does not keep infected individuals from leaving Toronto and such individuals account for 5 of 6 cases where SARS was spread from Canada. "…a decision to lift the travel advisory, effective April 30, was made based on consideration of 3 criteria: a decrease to below 5 new SARS cases per day, a period of 20 days since the last case of community transmission occurred, and no new confirmed cases of exportation." 4 There are some data that suggest that Rodier is justified in his views. Why was Toronto included in the World Health Organization''s SARS-related travel advisory abstract: Freedom of movement is undoubtedly a fundamental international right. However, circumstances may arise where that right must be curtailed. Was the 2003 SARS outbreak in Toronto one such circumstance? Guénaël R.M. Rodier thinks WHO’s decision to impose a SARS-related travel advisory was justifiable, even reasonable, though it caused a loss of over $1.1 billion in the Greater Toronto Area. That travel to an infected area was the most common epidemiological link with SARS infections supports Rodier’s position. However, as suggested in the Naylor report, issuing a travel advisory does not keep infected individuals from leaving Toronto and such individuals account for 5 of 6 cases where SARS was spread from Canada. That alone would discount Rodier’s argument and the WHO decision on purely logistical grounds. But there is an ethical question as well. Was the travel advisory implemented fairly? This question is best judged using Nancy E. Kass’s framework for public health. From that framework, two points are placed in immediate relief. First, the Toronto authorities were not given an opportunity to state their case to WHO before the travel advisory was implemented. Second, the framework requires that burdens be distributed fairly and the travel advisory did not do that, or even attempt to do so. url: https://www.ncbi.nlm.nih.gov/pubmed/17626386/ doi: 10.1007/bf03403714 id: cord-300640-9pvhaz8q author: Parackova, Zuzana title: Disharmonic Inflammatory Signatures in COVID-19: Augmented Neutrophils’ but Impaired Monocytes’ and Dendritic Cells’ Responsiveness date: 2020-09-29 words: 5975.0 sentences: 344.0 pages: flesch: 47.0 cache: ./cache/cord-300640-9pvhaz8q.txt txt: ./txt/cord-300640-9pvhaz8q.txt summary: We demonstrate the impaired functionality of COVID-19 dendritic cells and monocytes, particularly their low expression of maturation markers, increased PD-L1 levels, and their inability to upregulate phenotype upon stimulation. Ex vivo stimulation of peripheral whole blood with lipopolysaccharide (LPS) led to a rapid increase in surface degranulation markers CD11b and CD66b, and decrease in CD62L, a lectin involved in granulocyte trafficking, on both patient and healthy donor neutrophils ( Figure 1C and Figure S1C ). Only the COVID-19, but not the healthy neutrophils, were able to increase the production of IL-1β and TNFα upon ssRNA stimulation in comparison with untreated cells ( Figure 2B ) indicating a pro-inflammatory bias, possibly due to priming with SARS-CoV-2 or excessive cytokine/chemokine stimulation. In contrast to monocytes and DCs, COVID-19 neutrophils expressed significantly decreased levels of PD-L1 and their stimulation with ssRNA led to elevated production of proinflammatory cytokines. abstract: COVID-19, caused by SARS-CoV-2 virus, emerged as a pandemic disease posing a severe threat to global health. To date, sporadic studies have demonstrated that innate immune mechanisms, specifically neutrophilia, NETosis, and neutrophil-associated cytokine responses, are involved in COVID-19 pathogenesis; however, our understanding of the exact nature of this aspect of host–pathogen interaction is limited. Here, we present a detailed dissection of the features and functional profiles of neutrophils, dendritic cells, and monocytes in COVID-19. We portray the crucial role of neutrophils as drivers of hyperinflammation associated with COVID-19 disease via the shift towards their immature forms, enhanced degranulation, cytokine production, and augmented interferon responses. We demonstrate the impaired functionality of COVID-19 dendritic cells and monocytes, particularly their low expression of maturation markers, increased PD-L1 levels, and their inability to upregulate phenotype upon stimulation. In summary, our work highlights important data that prompt further research, as therapeutic targeting of neutrophils and their associated products may hold the potential to reduce the severity of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33003471/ doi: 10.3390/cells9102206 id: cord-285203-ilxd0ih9 author: Paradiso, Angelo Virgilio title: Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date: 2020-04-06 words: 3073.0 sentences: 174.0 pages: flesch: 49.0 cache: ./cache/cord-285203-ilxd0ih9.txt txt: ./txt/cord-285203-ilxd0ih9.txt summary: Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint All the 191 subjects enrolled in the study had a SARS-CoV-2 RT-PCR test and RapidIgG/IgM test performed. The design of our study allowed us to specifically analyze two aspects of the open issue: the concordance of the rapid serological test with standard molecular testing; the trend of immunoglobulinsIgG/IgMexpression with respect to the onset of clinical symptoms. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint symptom appearance is accompanied by an improvement in serological test sensitivity compared to standard molecular testing Our study has some important limitations. Our study analyzed theclinical performance of the rapid serological test, Viva-Diag TM and confirmedthe test''s limited applicability for the diagnosis of SARS-CoV-2 infection when compared to standard molecular testing. abstract: Background RT-PCR test for identifiction of viral nucleic acid is the current standard diagnostic method for the diagnosis of COVID-19 disease but technical reasons limit the utilization of this assay on large scale screenings. Method We verified in a consecutive series of 191 symptomatic patients the clinical information that new rapid serological colorimetric test qualitatively analyzing IgM/IgG expression can provide with respect to standard assay and with respect to clinical outcome of patients. Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. After 10 days of symptoms the predictive value of rapid serological test is higher than that of standard assay. When the behaviour of the two immunoglobulins was evaluated with respect to time length of symptoms appearance, no significant difference in immunoglobulins behaviour was shown. Conclusions The rapid serological test analyzed in the present study is candidate to provide information on immunoreaction of the subject to COVID-19 exposure. url: https://doi.org/10.1101/2020.04.03.20052183 doi: 10.1101/2020.04.03.20052183 id: cord-278440-vti6xp9v author: Paraiso, Ines L title: Potential use of polyphenols in the battle against COVID-19 date: 2020-09-09 words: 2338.0 sentences: 124.0 pages: flesch: 45.0 cache: ./cache/cord-278440-vti6xp9v.txt txt: ./txt/cord-278440-vti6xp9v.txt summary: The present mini-review aims to report in silico and in vitro evidence of the potential of polyphenols as anti-SARS-CoV-2 agents. Screening by molecular docking of 33 molecules including natural products, antivirals, antifungals and antiprotozoal agents revealed that rutin (a citrus flavonoid) could bind to the active site of the SARS-CoV-2 3CL pro (PDB: 6Y84) with the highest affinity among the molecules screened [44] . •This study demonstrates that SARS-CoV-2 uses ACE2 as receptor for host-cell entry and the S protein needs the serine protease TMPRSS2 for priming. A: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: An in-silico analysis abstract: The coronavirus disease 2019 (COVID-19) is a public health emergency of international concern. The rising number of cases of this highly transmissible infection have stressed the urgent need to find a potent drug. Although repurposing of known drugs currently provides an accelerated route to approval, there is no satisfactory treatment. Polyphenols, a major class of bioactive compounds in nature, are known for their antiviral activity and pleiotropic effects. The aim of this review is to assess the effects of polyphenols on COVID-19 drug targets as well as to provide a perspective on the possibility to use polyphenols in the development of natural approaches against this viral disease. url: https://doi.org/10.1016/j.cofs.2020.08.004 doi: 10.1016/j.cofs.2020.08.004 id: cord-352891-ljmkqdzx author: Parang, Keykavous title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 words: 3165.0 sentences: 182.0 pages: flesch: 52.0 cache: ./cache/cord-352891-ljmkqdzx.txt txt: ./txt/cord-352891-ljmkqdzx.txt summary: title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells. abstract: Remdesivir is a nucleotide prodrug that is currently undergoing extensive clinical trials for the treatment of COVID-19. The prodrug is metabolized to its active triphosphate form and interferes with the action of RNA-dependent RNA polymerase of SARS-COV-2. Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. The anti-HIV nucleosides interfere with HIV RNA-dependent DNA polymerase and/or act as chain terminators. Normal human fibroblast lung cells (MRC-5) were used to determine the cytotoxicity of the compounds. The study revealed that remdesivir exhibited an EC(50) value of 0.07 µM against HCoV-229E with TC(50) of > 2.00 µM against MRC-5 cells. Parent NRTIs were found to be inactive against (HCoV-229E) at tested concentrations. Among all the NRTIs and 5′-O-fatty acyl conjugates of NRTIs, 5′-O-tetradecanoyl ester conjugate of FTC showed modest activity with EC(50) and TC(50) values of 72.8 µM and 87.5 µM, respectively. These data can be used for the design of potential compounds against other coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32429580/ doi: 10.3390/molecules25102343 id: cord-353308-e4s8el0s author: Parashar, Umesh D title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 words: 4499.0 sentences: 224.0 pages: flesch: 45.0 cache: ./cache/cord-353308-e4s8el0s.txt txt: ./txt/cord-353308-e4s8el0s.txt summary: This dramatic chain of transmission brought to the world''s attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15155694/ doi: 10.1093/ije/dyh198 id: cord-273898-i7icvsg1 author: Parcell, B. title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland date: 2020-05-11 words: 1755.0 sentences: 99.0 pages: flesch: 60.0 cache: ./cache/cord-273898-i7icvsg1.txt txt: ./txt/cord-273898-i7icvsg1.txt summary: title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland Scotland recently began reporting staff absence rates in the health and social care sector showing that at the time of writing 1 in 20 staff were absent as a direct result of Current UK guidance for social distancing and self-isolation requires that HSCWs experiencing symptoms of a respiratory infection, such as cough or fever, should be absent from work for 7 days, while if a household contact is unwell, the staff member should be absent from work for 14 days to account for the incubation period of the virus. The results show a striking save of over 8000 lost working days for health and social care staff over a period of just 3 weeks which is likely to have a significant impact on the ability of health systems to respond to the SARS-CoV-2 pandemic. abstract: It has been recognised that health and social care workers (HSCW) experience higher rates of infection with SARS-CoV-2. Widespread testing of HSCWs and their symptomatic household contacts (SHCs) has not been fully implemented in the United Kingdom. We describe the results of a testing programme for HSCWs and SHCs in a single UK region (Tayside, Scotland). The testing service was established 17 th March 2020 as the first in the country, and samples were collected at a drive-through testing hub based at a local community hospital. HSCWs with mild symptoms who were self-isolating and the SHCs of HSCWs who would therefore be absent from work attended for testing. From 17 th March 2020 to 11 th April, 1887 HSCWs and SHCs underwent testing. Clinical information was available for 1727 HSCWs and SHCs. 4/155 (2.6%) child contacts, 73/374 (19.5%) adult contacts and 325/1173 (27.7%) HSCWs tested positive for SARS-CoV-2. 15 of 188 undetermined cases were positive (8.0%). We estimate that testing prevented up to 3634 lost work days from HSCW testing, 2795 from adult SHC testing and 1402 lost work days from child SHC testing. The establishment of this testing programme has assisted the infection prevention and control team in their investigation of transmission and supported adequate staffing in health and social care sectors. url: http://medrxiv.org/cgi/content/short/2020.05.08.20078386v1?rss=1 doi: 10.1101/2020.05.08.20078386 id: cord-339859-anatn295 author: Paret, Michal title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date: 2020-04-17 words: 1286.0 sentences: 105.0 pages: flesch: 59.0 cache: ./cache/cord-339859-anatn295.txt txt: ./txt/cord-339859-anatn295.txt summary: title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient''s NP sample. abstract: We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. url: https://doi.org/10.1093/cid/ciaa452 doi: 10.1093/cid/ciaa452 id: cord-307596-0bbxyyea author: Parhar, Harman S. title: Topical preparations to reduce SARS‐CoV‐2 aerosolization in head and neck mucosal surgery date: 2020-04-25 words: 2377.0 sentences: 129.0 pages: flesch: 42.0 cache: ./cache/cord-307596-0bbxyyea.txt txt: ./txt/cord-307596-0bbxyyea.txt summary: AIM: The COVID‐19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has put health care workers at risk when exposed to aerosolized viral particles during upper airway mucosal surgery. 12, 13 There has been very little published, however, regarding whether there exist any topical agents that could be utilized preoperatively to potentially lower the viral load in the upper aerodigestive tract thereby mitigating any risk of viral aerosolization in persons undergoing head and neck mucosal surgery. 14 While studies on virucidal activity of PVP-I have not yet been performed specifically on SARS-CoV-2, there have been numerous in vitro studies demonstrating its effectiveness against multiple viruses including related coronaviruses. Though no topical therapies have been studied to specifically reduce the viral load and potential aerosolization of SARS-CoV-2 during upper airway mucosal surgery, PVP-I solutions have demonstrated effective virucidal activity against related coronaviruses in numerous studies. abstract: AIM: The COVID‐19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has put health care workers at risk when exposed to aerosolized viral particles during upper airway mucosal surgery. The objective of this review was to discuss topical preparations that could be utilized preoperatively to help to decrease viral load and potentially reduce the risks of viral transmission. METHODS: A PubMed/MEDLINE database review of articles was performed querying topical preparations with virucidal activity against coronaviruses. RESULTS: Povidone‐iodine (PVP‐I) solutions ranging from 0.23% to 7% have been found to demonstrate highly effective virucidal activity against a broad range of viruses including several coronaviruses responsible for recent epidemics including SARS‐CoV‐1 and MERS‐CoV. CONCLUSIONS: While specific evidence regarding SARS‐CoV‐2 is lacking, PVP‐I‐based preparations have been successfully demonstrated to reduce viral loads of coronaviruses. They are relatively safe to use in the upper airway and may reduce risk of SARS‐CoV‐2 aerosolization during upper airway mucosal surgery. url: https://doi.org/10.1002/hed.26200 doi: 10.1002/hed.26200 id: cord-283823-8n1cy0hj author: Parikh, Bijal A. title: The Brief Case: “Not Positive” or “Not Sure”—COVID-19-Negative Results in a Symptomatic Patient date: 2020-07-23 words: 1618.0 sentences: 84.0 pages: flesch: 49.0 cache: ./cache/cord-283823-8n1cy0hj.txt txt: ./txt/cord-283823-8n1cy0hj.txt summary: The diagnosis of SARS-CoV-2 has relied almost exclusively on molecular testing of upper and lower respiratory specimens. As of 7 April 2020 (when the BAL fluid sample for this patient was sent to a reference laboratory for testing), 28 of the 29 commercially available assays approved by the FDA for emergency use were for testing on nasopharyngeal swabs (Table 1 ). Case reports of SARS-CoV-2 detection in sputum, tracheal aspirate, and BAL fluid specimens suggest that these specimens may be positive when NP swabs are negative, though large-scale studies have yet to be published (5) . It has become clear that negative NP swabs alone do not rule out SARS-CoV-2 infection, and as of now, there is no single "ideal" specimen for the diagnosis of COVID-19 (5) . Updated IDSA (Infectious Diseases Society of America) guidelines for COVID-19 diagnosis describe an algorithmic approach based on patient symptomatology, suspicion for infection, hospitalization status, and availability of lower respiratory specimens (6) . SARS-CoV-2 viral load in upper respiratory specimens of infected patients abstract: nan url: https://doi.org/10.1128/jcm.01195-20 doi: 10.1128/jcm.01195-20 id: cord-330814-7incf20e author: Parikh, Priyanka A title: COVID-19 Pandemic: Knowledge and Perceptions of the Public and Healthcare Professionals date: 2020-05-15 words: 3804.0 sentences: 184.0 pages: flesch: 51.0 cache: ./cache/cord-330814-7incf20e.txt txt: ./txt/cord-330814-7incf20e.txt summary: Background and objective The recent pandemic due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major concern for the people and governments across the world due to its impact on individuals as well as on public health. Conclusion Most healthcare professionals and the general public that we surveyed were well informed about SARS-CoV-2 and have been taking adequate measures in preventing the spread of the same. Social media platforms arguably support the conditions necessary for attitude change by exposing individuals to correct, accurate, health-promoting messages from healthcare professionals In order to investigate community responses to SARS-CoV-2, we conducted this online survey among the general public and healthcare professionals to identify awareness of SARS-CoV-2 (perceived burden and risk), trusted sources of information, awareness of preventative measures and support for governmental policies and trust in authority to handle SARS-CoV-2 outbreak and put forward policy recommendations in case of similar future conditions. abstract: Background and objective The recent pandemic due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major concern for the people and governments across the world due to its impact on individuals as well as on public health. The infectiousness and the quick spread across the world make it an important event in everyone’s life, often evoking fear. Our study aims at assessing the overall knowledge and perceptions, and identifying the trusted sources of information for both the general public and healthcare personnel. Materials and methods This is a questionnaire-based survey taken by a total of 1,246 respondents, out of which 744 belonged to the healthcare personnel and 502 were laypersons/general public. There were two different questionnaires for both groups. The questions were framed using information from the World Health Organization (WHO), UpToDate, Indian Council of Medical Research (ICMR), Center for Disease Control (CDC), National Institute of Health (NIH), and New England Journal of Medicine (NEJM) website resources. The questions assessed awareness, attitude, and possible practices towards ensuring safety for themselves as well as breaking the chain of transmission. A convenient sampling method was used for data collection. Descriptive statistics [mean(SD), frequency(%)] were used to portray the characteristics of the participants as well as their awareness, sources of information, attitudes, and practices related to SARS-CoV-2. Results The majority (94.3%) of the respondents were Indians. About 80% of the healthcare professionals and 82% of the general public were worried about being infected. Various websites such as ICMR, WHO, CDC, etc., were a major source of information for the healthcare professional while the general public relied on television. Almost 98% of healthcare professionals and 97% of the general public, respectively, identified ‘Difficulty in breathing” as the main symptom. More than 90% of the respondents in both groups knew and practiced different precautionary measures. A minority of the respondents (28.9% of healthcare professionals and 26.5% of the general public) knew that there was no known cure yet. Almost all respondents from both the groups agreed on seeking medical help if breathing difficulty is involved and self-quarantine if required. Conclusion Most healthcare professionals and the general public that we surveyed were well informed about SARS-CoV-2 and have been taking adequate measures in preventing the spread of the same. There is a high trust of the public in the government. There are common trusted sources of information and these need to be optimally utilized to spread accurate information. url: https://www.ncbi.nlm.nih.gov/pubmed/32550063/ doi: 10.7759/cureus.8144 id: cord-309411-2dfiwo65 author: Paris, Kristina A. title: Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date: 2020-06-23 words: 4728.0 sentences: 256.0 pages: flesch: 58.0 cache: ./cache/cord-309411-2dfiwo65.txt txt: ./txt/cord-309411-2dfiwo65.txt summary: On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. Work on SARS-CoV (CoV1) has already determined that the virus enters cells via receptormediated endocytosis in a pH-dependent manner (Wang et al., 2008) that is characterized by cotranslocation of the viral spike glycoprotein and its specific functional receptor, the angiotensinconverting enzyme 2 (ACE2), from the cell surface to early endosomes. This newly discovered difference in protein sequence in the receptor binding domain of the spike glycoprotein and its impact on receptor binding reveals a mechanism that allows SARS-CoV2 internalization to take advantage of the high expression of ACE2 in the nasal epithelium¾resulting in increased retention times in the upper respiratory tract and augmented infectivity. abstract: Cell surface receptor engagement is a critical aspect of viral infection. This paper compares the dynamics of virus-receptor interactions for SARS-CoV (CoV1) and CoV2. At low (endosomal) pH, the binding free energy landscape of CoV1 and CoV2 interactions with the angiotensin-converting enzyme 2 (ACE2) receptor is almost the same. However, at neutral pH the landscape is different due to the loss of a pH-switch (His445Lys) in the receptor binding domain (RBD) of CoV2 relative to CoV1. Namely, CoV1 stabilizes a transition state above the bound state. In situations where small external strains are applied by, say, shear flow in the respiratory system, the off rate of the viral particle is enhanced. As a result, CoV1 virions are expected to detach from cell surfaces in time scales that are much faster than the time needed for other receptors to reach out and stabilize virus attachment. On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. This has important implications for viral infection and its pathology. CoV1 does not trigger high infectivity in the nasal area because it either rapidly drifts down the respiratory tract or is exhaled. By contrast, this novel mutation in CoV2 should not only retain the infection in the nasal cavity until ACE2-rich cells are sufficiently depleted, but also require fewer particles for infection. This mechanism explains observed longer incubation times, extended period of viral shedding, and higher rate of transmission. These considerations governing viral entry suggest that number of ACE2-rich cells in human nasal mucosa, which should be significantly smaller for children (and females relative to males), should also correlate with onset of viral load that could be a determinant of higher virus susceptibility. Critical implications for the development of new vaccines to combat current and future pandemics that, like SARS-CoV2, export evolutionarily successful strains via higher transmission rates by viral retention in nasal epithelium are also discussed. url: https://doi.org/10.1101/2020.06.16.155457 doi: 10.1101/2020.06.16.155457 id: cord-318253-vp22xd8p author: Parisi, Ortensia Ilaria title: “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date: 2020-05-28 words: 1858.0 sentences: 96.0 pages: flesch: 38.0 cache: ./cache/cord-318253-vp22xd8p.txt txt: ./txt/cord-318253-vp22xd8p.txt summary: Our idea is focused on the development of "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. In this context, our idea is to develop "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) for the selective recognition and binding of the RBD of the novel coronavirus SARS-CoV-2 in the aim to block the function of its spike protein (Figure 1.) . abstract: Our idea is focused on the development of “monoclonal-type” plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. Molecular Imprinting, indeed, represents a very promising and attractive technology for the synthesis of MIPs characterized by specific recognition abilities for a target molecule. Given these characteristics, MIPs can be considered tailor-made synthetic antibodies obtained by a templating process. In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. Finally, the hemocompatibility of the prepared MIP-based plastic antibodies was also evaluated. url: https://doi.org/10.1101/2020.05.28.120709 doi: 10.1101/2020.05.28.120709 id: cord-291222-n8kgsz2e author: Park, Benjamin J. title: Lack of SARS Transmission among Healthcare Workers, United States date: 2004-02-17 words: 2399.0 sentences: 125.0 pages: flesch: 45.0 cache: ./cache/cord-291222-n8kgsz2e.txt txt: ./txt/cord-291222-n8kgsz2e.txt summary: We conducted an investigation of healthcare workers exposed to laboratory-confirmed SARS patients in the United States to evaluate infection-control practices and possible SARS-associated coronavirus (SARS-CoV) transmission. Due to the importance of healthcare facilities in transmission of SARS worldwide, state and local health departments, together with the Centers for Disease Control and Prevention (CDC), conducted a review of U.S. healthcare workers exposed to patients positive for SARS-associated coronavirus (SARS-CoV). In the United States, potential droplet-and aerosol-generating procedures were infrequent: only one patient required mechanical ventilation, and few healthcare workers reported administering aerosolized medication or performing 1 0 (0) 0 (0) a SARS, severe acute respiratory syndrome; HCWs, healthcare workers; NA, not available due to incomplete reporting. Unprotected exposures in healthcare workers exposed to laboratory-confirmed SARS patients after full infection-control procedures were initiated (n = 43) a Exposure type n (%) Any unprotected exposure 21 (49) Without eye protection 18 (42) Without N95 or higher respirator 6 (14) Direct contact without gloves 6 (14) a SARS, severe acute respiratory syndrome. abstract: Healthcare workers accounted for a large proportion of persons with severe acute respiratory syndrome (SARS) during the worldwide epidemic of early 2003. We conducted an investigation of healthcare workers exposed to laboratory-confirmed SARS patients in the United States to evaluate infection-control practices and possible SARS-associated coronavirus (SARS-CoV) transmission. We identified 110 healthcare workers with exposure within droplet range (i.e., 3 feet) to six SARS-CoV–positive patients. Forty-five healthcare workers had exposure without any mask use, 72 had exposure without eye protection, and 40 reported direct skin-to-skin contact. Potential droplet- and aerosol-generating procedures were infrequent: 5% of healthcare workers manipulated a patient’s airway, and 4% administered aerosolized medication. Despite numerous unprotected exposures, there was no serologic evidence of healthcare-related SARS-CoV transmission. Lack of transmission in the United States may be related to the relative absence of high-risk procedures or patients, factors that may place healthcare workers at higher risk for infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15030686/ doi: 10.3201/eid1002.030793 id: cord-256750-5m7psxri author: Park, Hye Yoon title: Posttraumatic stress disorder and depression of survivors 12 months after the outbreak of Middle East respiratory syndrome in South Korea date: 2020-05-15 words: 4564.0 sentences: 196.0 pages: flesch: 48.0 cache: ./cache/cord-256750-5m7psxri.txt txt: ./txt/cord-256750-5m7psxri.txt summary: Acute infectious outbreaks of Emerging Infectious Diseases (EIDs) are known to influence the physical as well as the mental health of affected patients, as observed during similar events such as the Severe Acute Respiratory Syndrome (SARS) outbreak [3] , which was associated with such issues during the acute phase [4] and the long-term follow-up phase [5, 6] . Thus, the present study explored mental health issues and related factors in MERS survivors 12 months after the outbreak to determine the long-term psychological outcomes of this population. The univariate analysis revealed that several factors were significantly associated with PTSD, including previous psychiatry history, having a family member who died from MERS, depression and anxiety during the MERSaffected period, greater perceived stigma currently and during the illness, and negative coping strategies (Table S2) . Our study showed that nearly half the assessed MERS survivors experienced significant mental health problems, including PTSD and depression, at 12 months post-MERS. abstract: BACKGROUND: The 2015 outbreak of Middle East Respiratory Syndrome (MERS) in the Republic of Korea is a recent and representative occurrence of nationwide outbreaks of Emerging Infectious Diseases (EIDs). In addition to physical symptoms, posttraumatic stress disorder (PTSD) and depression are common following outbreaks of EID. METHODS: The present study investigated the long-term mental health outcomes and related risk factors in survivors of MERS. A prospective nationwide cohort study was conducted 12 months after the MERS outbreak at multi-centers throughout Korea. PTSD and depression as the main mental health outcomes were assessed with the Impact of Event Scale-Revised Korean version (IES-R-K) and the Patient Health Questionnaire-9 (PHQ-9) respectively. RESULTS: 42.9% of survivors reported PTSD (IES-R-K ≥ 25) and 27.0% reported depression (PHQ-9 ≥ 10) at 12 months post-MERS. A multivariate analysis revealed that anxiety (adjusted odds ratio [aOR], 5.76; 95%CI, 1.29–25.58; P = 0.021), and a greater recognition of stigma (aOR, 11.09, 95%CI, 2.28–53.90; P = 0.003) during the MERS-affected period were independent predictors of PTSD at 12 months after the MERS outbreak. Having a family member who died from MERS predicted the development of depression (aOR, 12.08, 95%CI, 1.47–99.19; P = 0.020). CONCLUSION: This finding implies that psychosocial factors, particularly during the outbreak phase, influenced the mental health of patients over a long-term period. Mental health support among the infected subjects and efforts to reduce stigma may improve recovery from psychological distress in an EID outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32410603/ doi: 10.1186/s12889-020-08726-1 id: cord-278522-e4qa19o6 author: Park, Se Yoon title: Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs date: 2020-06-19 words: 1605.0 sentences: 106.0 pages: flesch: 56.0 cache: ./cache/cord-278522-e4qa19o6.txt txt: ./txt/cord-278522-e4qa19o6.txt summary: There are limited data on the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory specimens after resolution of coronavirus disease 2019 (COVID-19)-associated symptoms/signs. Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs Se Yoon Park 1 , Soon Gyu Yun 2 , Jeong Won Shin 2 , Bo Young Lee 3 , Hyo-Ju Son 1 , Seungjae Lee 1 , Eunjung Lee 1 , and Tae Hyong Kim 1 Since the first case of coronavirus disease 2019 (COVID-19) was reported in Wuhan, China in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than three million people in 211 countries. Few studies have investigated the duration of SARS-CoV-2 detection during the patients'' recovery phase after resolution of COVID-19-associated symptoms/signs. SARS-CoV-2 shedding continued for about 4 weeks after resolution of COVID-19-associated symptoms/signs, with the longest period being 48 days. In conclusion, we found that SARS-CoV-2 virus shedding can persist for more than three weeks after resolution of COVID-19-associated symptoms/signs. abstract: There are limited data on the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory specimens after resolution of coronavirus disease 2019 (COVID-19)-associated symptoms/signs. We determined duration of SARS-CoV-2 virus shedding in symptomatic patients after remission of symptoms. We investigated the duration of SARS-CoV-2 RNA detection using real-time reverse transcriptase polymerase chain reaction for SARS-CoV-2 in nasopharyngeal/oropharyngeal swabs or sputum or saliva. Six patients were included in the final analysis. The median (range) duration of SARS-CoV-2 viral detection after hospitalization was 34 days (22 to 67). After resolution of symptoms/signs, SARS-CoV-2 RNA was detected for median (range) of 26 days (9 to 48). Among the six patients, one had persistent detection of SARS-CoV-2 RNA until day 67 of hospitalization, which was 30 days after symptom resolution. This case represents the longest duration of SARS-CoV-2 detection, and highlights the need for long-term follow up of COVID-19 patients despite resolution of symptoms to confirm SARS-CoV-2 clearance. url: https://doi.org/10.3904/kjim.2020.203 doi: 10.3904/kjim.2020.203 id: cord-329193-xuxbqbsf author: Park, Soo-kyung title: Detection of SARS-CoV-2 in Fecal Samples from Patients with Asymptomatic and Mild COVID-19 in Korea date: 2020-06-10 words: 3532.0 sentences: 184.0 pages: flesch: 53.0 cache: ./cache/cord-329193-xuxbqbsf.txt txt: ./txt/cord-329193-xuxbqbsf.txt summary: Methods We collected data from 46 patients (median age, 26 years; 46% men) with asymptomatic or mild COVID-19 (without fever and pneumonia) and prolonged respiratory shedding of SARS-CoV-2, quarantined from April 4, 2020 through April 24, 2020 in Korea. Conclusions In an analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea, we found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. abstract: Abstract: Background & Aims Although COVID-19 is characterized by fever and respiratory symptoms, some patients have no or mild symptoms. SARS-CoV-2 has been detected in feces of patients. We investigated gastrointestinal symptoms and shedding of virus into feces of patients with asymptomatic or mild COVID-19. Methods We collected data from 46 patients (median age, 26 years; 46% men) with asymptomatic or mild COVID-19 (without fever and pneumonia) and prolonged respiratory shedding of SARS-CoV-2, quarantined from April 4, 2020 through April 24, 2020 in Korea. Respiratory specimens included upper respiratory specimens (nasopharyngeal and oropharyngeal swabs) and lower respiratory specimens (sputum) and were collected twice per week. The median interval between COVID-19 diagnosis to the start of fecal sample collection was 37 days (range, 29–41); 213 stool specimens were collected from 46 patients. We used real-time reverse transcription PCR to detect SARS-CoV-2 in the respiratory and fecal specimens. Results Gastrointestinal manifestations were observed in 16 of the 46 patients (35%); diarrhea was the most common (15%), followed by abdominal pain (11%), dyspepsia (11%), and nausea (2%). Virus RNA was detected in feces from 2 patients without gastrointestinal symptoms (4%). Mean cycle threshold values from the time of quarantine to the time of fecal collection tended to be lower in patients with virus detected in fecal samples than patients without virus in fecal samples (29.91 vs 33.67 in the first week; 29.47 vs 35.71 in the fifth week, respectively). Shedding of virus into feces persisted until day 50 after diagnosis; fecal samples began to test negative before or at approximately the time that respiratory specimens also began to test negative. Conclusions In an analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea, we found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. The viral load of the respiratory specimens appears be related to shedding of the virus into feces in this group of patients. url: https://www.sciencedirect.com/science/article/pii/S1542356520307771?v=s5 doi: 10.1016/j.cgh.2020.06.005 id: cord-334960-l5q5wc06 author: Park, Su Eun title: Epidemiology, virology, and clinical features of severe acute respiratory syndrome -coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19) date: 2020-04-02 words: 3757.0 sentences: 258.0 pages: flesch: 58.0 cache: ./cache/cord-334960-l5q5wc06.txt txt: ./txt/cord-334960-l5q5wc06.txt summary: 9) Two novel strains of coronavirus have jumped species from animal to human, spread by human-to-human transmission, and caused severe acute respiratory syndrome leading to high fatality rate in the past 2 decades. 10) Severe acute respiratory syndrome-associated virus (SARS-CoV), previously unknown coronavirus traced to horseshoe bats in southern China, caused 8,096 confirmed cases and 774 deaths (9.6% fatality rate) in 29 countries from November 2002 to July 2003. 19, 20) The virus was initially called 2019-novel coronavirus (2019-nCoV) upon its emergence, until the Coronaviridae Study Group of International Committee on Taxonomy of Viruses named the virus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the phylogenetic analysis, on February 11, 2020. 10) Conclusion Within 3 months since the discovery of a novel coronavirus in patients with pneumonia of unknown origin in Wuhan City, China, COVID-19 has spread rapidly throughout the world and is beating SARS-CoV and MERS-CoV in the number of confirmed cases and deaths. abstract: A cluster of severe pneumonia of unknown etiology in Wuhan City, Hubei province in China emerged in December 2019. A novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was isolated from lower respiratory tract sample as the causative agent. The current outbreak of infections with SARS-CoV-2 is termed Coronavirus Disease 2019 (COVID-19) by the World Health Organization (WHO). COVID-19 rapidly spread into at least 114 countries and killed more than 4,000 people by March 11 2020. WHO officially declared COVID-19 a pandemic on March 11, 2020. There have been 2 novel coronavirus outbreaks in the past 2 decades. The outbreak of severe acute respiratory syndrome (SARS) in 2002–2003 caused by SARS-CoV had a case fatality rate of around 10% (8,098 confirmed cases and 774 deaths), while Middle East respiratory syndrome (MERS) caused by MERS-CoV killed 861 people out of a total 2,502 confirmed cases between 2012 and 2019. The purpose of this review is to summarize known-to-date information about SARS-CoV-2, transmission of SARS-CoV-2, and clinical features. url: https://doi.org/10.3345/cep.2020.00493 doi: 10.3345/cep.2020.00493 id: cord-274396-l611eisi author: Park, Su-Jin title: Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets date: 2020-05-22 words: 4355.0 sentences: 208.0 pages: flesch: 46.0 cache: ./cache/cord-274396-l611eisi.txt txt: ./txt/cord-274396-l611eisi.txt summary: While the lopinavir-ritonavir-, hydroxychloroquine sulfate-, or emtricitabine-tenofovir-treated group exhibited lower overall clinical scores than the phosphate-buffered saline (PBS)-treated control group, the virus titers in nasal washes, stool specimens, and respiratory tissues were similar between all three antiviral-candidate-treated groups and the PBS-treated control group. Compared to the PBS-treated control group, azathioprine-immunosuppressed ferrets exhibited a longer period of clinical illness, higher virus titers in nasal turbinate, delayed virus clearance, and significantly lower serum neutralization (SN) antibody titers. In order to determine the antiviral efficacies of lopinavir-ritonavir, hydroxychloroquine (HCQ) sulfate, or emtricitabine-tenofovir for treatment of SARS-CoV-2 infection, SARS-CoV-2 antibody-free ferrets (10/group) were inoculated with 10 5.8 50% tissue culture infective doses (TCID 50 )/ml of an NMC-nCoV02 strain through the intranasal (i.n.) route ( Fig. 1 ). Therefore, although clinical symptoms were attenuated in ferret groups treated with antiviral candidates, we also evaluated virus titers in respiratory and gastrointestinal tracts using nasal washes and stool samples, respectively, from SARS-CoV-2-infected ferrets. abstract: Due to the urgent need of a therapeutic treatment for coronavirus (CoV) disease 2019 (COVID-19) patients, a number of FDA-approved/repurposed drugs have been suggested as antiviral candidates at clinics, without sufficient information. Furthermore, there have been extensive debates over antiviral candidates for their effectiveness and safety against severe acute respiratory syndrome CoV 2 (SARS-CoV-2), suggesting that rapid preclinical animal studies are required to identify potential antiviral candidates for human trials. To this end, the antiviral efficacies of lopinavir-ritonavir, hydroxychloroquine sulfate, and emtricitabine-tenofovir for SARS-CoV-2 infection were assessed in the ferret infection model. While the lopinavir-ritonavir-, hydroxychloroquine sulfate-, or emtricitabine-tenofovir-treated group exhibited lower overall clinical scores than the phosphate-buffered saline (PBS)-treated control group, the virus titers in nasal washes, stool specimens, and respiratory tissues were similar between all three antiviral-candidate-treated groups and the PBS-treated control group. Only the emtricitabine-tenofovir-treated group showed lower virus titers in nasal washes at 8 days postinfection (dpi) than the PBS-treated control group. To further explore the effect of immune suppression on viral infection and clinical outcome, ferrets were treated with azathioprine, an immunosuppressive drug. Compared to the PBS-treated control group, azathioprine-immunosuppressed ferrets exhibited a longer period of clinical illness, higher virus titers in nasal turbinate, delayed virus clearance, and significantly lower serum neutralization (SN) antibody titers. Taken together, all antiviral drugs tested marginally reduced the overall clinical scores of infected ferrets but did not significantly affect in vivo virus titers. Despite the potential discrepancy of drug efficacies between animals and humans, these preclinical ferret data should be highly informative to future therapeutic treatment of COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32444382/ doi: 10.1128/mbio.01114-20 id: cord-268874-ldja6aa4 author: Park, Sun Hee title: Personal Protective Equipment for Healthcare Workers during the COVID-19 Pandemic date: 2020-06-24 words: 6754.0 sentences: 330.0 pages: flesch: 44.0 cache: ./cache/cord-268874-ldja6aa4.txt txt: ./txt/cord-268874-ldja6aa4.txt summary: Although no study has conclusively linked SARS-CoV-2 transmission to contaminated environmental surfaces, indirect contact with fomites is considered a possible route based on the evidence of heavy environmental contamination in healthcare settings, objects used by COVID-19 patients [26, 27] , and the finding that the virus remains viable on plastic surfaces for as long as 3 days [28] . Initially, the Korea Center for Disease Control and Prevention (KCDC) guidelines recommended coveralls with shoe covers for contact precautions, goggles/face shields for eye protection, N95 or equivalent respirators for respiratory protection, and powered airpurifying respirators (PAPRs) when AGPs are performed [46] . PPE for droplet and contact precautions, such as surgical masks with eye protection, gowns, and gloves, are recommended for HCWs in contact with suspected or confirmed COVID-19 patients, and N95 or equivalent respirators should to be worn by HCWs whenever AGPs are performed. abstract: The coronavirus disease (COVID-19) pandemic has posed a challenge for healthcare systems, and healthcare workers (HCWs) are at high risk of exposure. Protecting HCWs is of paramount importance to maintain continuous patient care and keep healthcare systems functioning. Used alongside administrative and engineering control measures, personal protective equipment (PPE) is the last line of defense and the core component of protection. Current data suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is mainly transmitted through respiratory droplets and close contact. Airborne transmission may occur during aerosol-generating procedures. However, the modes of transmission still remain uncertain, especially regarding the possibility of airborne transmission when aerosol-generating procedures are not performed. Thus, there are some inconsistencies in the respiratory protective equipment recommended by international and national organizations. In Korea, there have been several modifications to PPE recommendations offering options in choosing PPE for respiratory and body protection, which confuses HCWs; they are often unsure what to wear and when to wear it. The choice of PPE is based on the risk of exposure and possible modes of transmission. The level of protection provided by PPE differs based on standards and test methods. Thus, understanding them is the key in selecting the proper PPE. This article reviews evidence on the mode of SARS-CoV-2 transmission, compares the current PPE recommendations of the World Health Organization with those in Korea, and discusses standard requirements and the proper selection of PPE. url: https://doi.org/10.3947/ic.2020.52.2.165 doi: 10.3947/ic.2020.52.2.165 id: cord-297023-0qlo0mun author: Park, Sung‐Soo title: Mass screening of healthcare personnel for SARS-CoV-2 in the northern emirates date: 2020-10-17 words: 753.0 sentences: 57.0 pages: flesch: 66.0 cache: ./cache/cord-297023-0qlo0mun.txt txt: ./txt/cord-297023-0qlo0mun.txt summary: While healthcare personnel (HCP) potentially has an increased risk of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the era of the pandemic [1] , the approach to testing HCP for the virus has not been uniform [2] . Given the significant percentage of asymptomatic coronavirus disease 2019 (COVID-19) infection [3] , universal testing of HCP could allow infected workers to be identified and isolated early, reduce in-hospital transmission, mitigate potential workforce depletion, and enhance healthcare workers'' safety [4] . This study aimed to evaluate the effectiveness of the universal staff screening for COVID-19 and identify any risk factor for viral infection. The staff were encouraged to notify the occupational health nurse for SARS-CoV-2 test any time if they had any suspicious symptoms of COVID-19 or close contact with COVID-19 patients. Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 COVID-19: the case for healthcare worker screening to prevent hospital transmission abstract: nan url: https://doi.org/10.1016/j.jhin.2020.10.008 doi: 10.1016/j.jhin.2020.10.008 id: cord-268540-wrjzr3ws author: Park, You Jeong title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 words: 16363.0 sentences: 868.0 pages: flesch: 45.0 cache: ./cache/cord-268540-wrjzr3ws.txt txt: ./txt/cord-268540-wrjzr3ws.txt summary: A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells'' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . abstract: The human population is in the midst of battling a rapidly-spreading virus— Severe Acute Respiratory Syndrome Coronavirus 2, responsible for Coronavirus disease 2019 or COVID-19. Despite the resurgences in positive cases after reopening businesses in May, the country is seeing a shift in mindset surrounding the pandemic as people have been eagerly trickling out from federally-mandated quarantine into restaurants, bars, and gyms across America. History can teach us about the past, and today’s pandemic is no exception. Without a vaccine available, three lessons from the 1918 Spanish flu pandemic may arm us in our fight against COVID-19. First, those who survived the first wave developed immunity to the second wave, highlighting the potential of passive immunity-based treatments like convalescent plasma and cell-based therapy. Second, the long-term consequences of COVID-19 are unknown. Slow-progressive cases of the Spanish flu have been linked to bacterial pneumonia and neurological disorders later in life, emphasizing the need to reduce COVID-19 transmission. Third, the Spanish flu killed approximately 17 to 50 million people, and the lack of human response, overcrowding, and poor hygiene were key in promoting the spread and high mortality. Human behavior is the most important strategy for preventing the virus spread and we must adhere to proper precautions. This review will cover our current understanding of the pathology and treatment for COVID-19 and highlight similarities between past pandemics. By revisiting history, we hope to emphasize the importance of human behavior and innovative therapies as we wait for the development of a vaccine. [Figure: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32789802/ doi: 10.1007/s12015-020-10026-5 id: cord-315498-gpzee1f2 author: Parkinson, N. title: Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date: 2020-09-01 words: 4964.0 sentences: 296.0 pages: flesch: 46.0 cache: ./cache/cord-315498-gpzee1f2.txt txt: ./txt/cord-315498-gpzee1f2.txt summary: 2, 6, 7, 8, 9, 10 In this analysis we systematically identify and combine existing data from human betacoronavirus research to generate a comprehensive ranked list of host genes as a resource to inform further work on COVID-19. To identify existing literature which could provide informative datasets for host gene prioritisation, we conducted a systematic review of published studies and preprint manuscripts pertaining to host gene involvement in human betacoronavirus infection and associated disease. Results from identified studies, in the form of lists of implicated host factor genes, were combined using meta-analysis by information content (MAIC), 3 an approach we previously developed to identify host genes necessary for Influenza A virus (IAV) replication. Table 2 Candidate-gene human genetic studies < 5 hosts in virus group or control group in patient studies Meta-analyses, in silico anayses, re-analysis of data published elsewhere Potentially relevant pre-print manuscripts were identified by screening all papers categorised as COVID-19-related in the bioRxiv and medRxiv servers. abstract: An increasing body of literature describes the role of host factors in COVID-19 pathogenesis. There is a need to combine diverse, multi-omic data in order to evaluate and substantiate the most robust evidence and inform development of future therapies. We conducted a systematic review of experiments identifying host factors involved in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). Gene lists from these diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes. 5,418 genes implicated in human betacoronavirus infection were identified from 32 datasets. The top ranked gene was *PPIA*, encoding cyclophilin A. Pharmacological inhibition with cyclosporine in vitro exerts antiviral activity against several coronaviruses including SARS-CoV. Other highly-ranked genes included proposed prognostic factors (*CXCL10*, *CD4*, *CD3E*) and investigational therapeutic targets (*IL1A*) for COVID-19, but also previously overlooked genes with potential as therapeutic targets. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating *FYCO1* over other nearby genes in a disease-associated locus on chromosome 3. Pathways enriched in gene rankings included T-cell receptor signalling, protein processing, and viral infections. We identified limited overlap of our gene list with host genes implicated in ARDS (innate immune and inflammation genes) and Influenza A virus infection (RNA-binding and ribosome-associated genes). We will continue to update this dynamic ranked list of host genes as the field develops, as a resource to inform and prioritise future studies. Updated results are available at https://baillielab.net/maic/covid19. url: https://doi.org/10.1101/2020.08.27.20182238 doi: 10.1101/2020.08.27.20182238 id: cord-318205-qxkel0ww author: Parkulo, Mark A. title: Risk of SARS-CoV-2 Transmission Among Coworkers in a Surgical Environment date: 2020-10-22 words: 1266.0 sentences: 75.0 pages: flesch: 60.0 cache: ./cache/cord-318205-qxkel0ww.txt txt: ./txt/cord-318205-qxkel0ww.txt summary: This was an observational study of 394 health care workers in a surgical environment who were exposed to 2 known SARS-CoV-2–positive coworkers. Infections of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) among health care workers is a serious consequence of the coronavirus disease 2019 (COVID-19) pandemic. Of the COVID-19 cases reported to the US Centers for Disease Control and Prevention (CDC) between February 12 and April 9, 2020, that contained information about workers, 19% were identified as health care personnel. 2, 3 Here we report the outcome of a widespread surveillance program in a surgical area which was implemented as a result of health care workers testing positive for SARS-CoV-2 at Mayo Clinic, Jacksonville, Florida. Employee Health determined that 394 other employees worked in the surgical area at the same time as the index cases, and all were recommended to undergo SARS-CoV-2 PCR testing as surveillance. abstract: Health care workers are at high risk for contracting coronavirus disease 2019 (COVID-19). However, little is known about the risk of transmission between coworkers. The objective of this study was to determine the risk of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between coworkers in a surgical environment. This was an observational study of 394 health care workers in a surgical environment who were exposed to 2 known SARS-CoV-2–positive coworkers. Standard infection precautions were in place at the time of the exposure. All 394 exposed workers initially underwent nasopharyngeal swab testing for SARS-CoV-2 using the polymerase chain reaction technique. Of the original group, 387 were tested again with the same technique 1 week later. Of 394 SARS-CoV-2–exposed health care workers initially tested, 1 was positive. No new positive cases were found on repeated testing of 387 participants 1 week later. The risk of transmission of SARS-CoV-2 in a health care unit with universal masking and appropriate hand hygiene is low. This should provide some reassurance to surgical practices as they reopen. url: https://api.elsevier.com/content/article/pii/S0025619620312027 doi: 10.1016/j.mayocp.2020.10.016 id: cord-285254-8a1cia8s author: Parry, Nicola M.A. title: COVID-19 and pets: When pandemic meets panic date: 2020-12-31 words: 3624.0 sentences: 206.0 pages: flesch: 57.0 cache: ./cache/cord-285254-8a1cia8s.txt txt: ./txt/cord-285254-8a1cia8s.txt summary: Concern also rapidly emerged among pet owners and the general public in late February 2020, when a dog in Hong Kong tested positive for the novel coronavirus. Although the dog had no clinical signs, he was taken to a nearby animal quarantine facility where oral, nasal, and rectal swab specimens were collected from him for SARS-CoV-2 testing. In late March 2020, health officials in Belgium reported that a cat from Liège province had also tested positive for SARS-CoV-2, about 1 week after its owner was diagnosed with COVID-19. Thus, the positive RT-PCR results in these pets do not necessarily indicate the presence of viable virus that was infectious and could potentially have put other people (or animals) at risk of SARS-CoV-2 infection. abstract: Abstract As the novel coronavirus outbreak spreads globally with devastating effects on human health, pets are also becoming unnecessary victims amidst the pandemic panic. Many have been reluctantly left home alone by owners who have been forced to temporarily evacuate their homes. And, although no evidence exists to indicate that they can either transmit the virus or develop its associated coronavirus disease 2019 (COVID-19), fear among the public that pets might play a role in spreading COVID-19 has resulted in pets being abandoned or even killed. This article outlines some of the ways in which the current pandemic has negatively impacted the welfare of pets. It also highlights the relationships between animal, human, and environmental health, as well as the importance of taking a collaborative transdisciplinary One Health approach to help prevent future COVID-19 outbreaks. url: https://www.sciencedirect.com/science/article/pii/S2665910720300396 doi: 10.1016/j.fsir.2020.100090 id: cord-309829-3dlfcy31 author: Parupudi, Tejasvi title: Evidence-based point-of-care technology development during the COVID-19 pandemic date: 2020-11-09 words: 4774.0 sentences: 223.0 pages: flesch: 44.0 cache: ./cache/cord-309829-3dlfcy31.txt txt: ./txt/cord-309829-3dlfcy31.txt summary: As learnt from previous viral epidemicsfor example, influenza (H1N1) in 2009, Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 and the SARS outbreak during 2003 -rapid and accurate diagnostic testing with point-of-care technologies (POCTs) is beneficial in early identification [2, 3] . The need for rapid screening, triage and isolation of affected populations, the ability to monitor and stratify patients at home, in the clinic and in intensive care units (ICUs), and the associated decisions caregivers must take based on the test results underline the significance of POCTs. The WHO forum responsible for identifying immediate research needs and research gaps for COVID-19 recognized mobilizing research on rapid POC diagnostics for use at the community level and ensuring access to accurate and standardized diagnostics as one of the eight immediate research actions [4] . abstract: Since December 2019, the SARS-CoV-2 outbreak that began in Wuhan, China has spread to nearly every continent and become a global health concern. Although much has been discovered about COVID-19 and its pathogenesis, the WHO has identified an immediate need to increase the levels of testing for COVID-19 and identify the stages of the disease accurately for appropriate action to be taken by clinicians and emergency care units. Harnessing technology for accurate diagnosis and staging will improve patient outcomes and minimize serious consequences of false-positive test results. Point-of-care technologies aim to intervene at every stage of the disease to quickly identify infected patients and asymptomatic carriers and stratify them for timely treatment. This requires the tests to be rapid, accurate, sensitive, simple to use and compatible with many body fluids. Mobile platforms are optimal for remote, small-scale deployment, whereas facility-based platforms at hospital centers and laboratory settings offer higher throughput. Here we review evidence-based point-of-care technologies in the context of the entire continuum of COVID-19, from early screening to treatment, and discuss their impact on improving patient outcomes. url: https://doi.org/10.2144/btn-2020-0096 doi: 10.2144/btn-2020-0096 id: cord-184744-oyc2djxk author: Parvez, Md Sorwer Alam title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date: 2020-05-22 words: 3653.0 sentences: 224.0 pages: flesch: 49.0 cache: ./cache/cord-184744-oyc2djxk.txt txt: ./txt/cord-184744-oyc2djxk.txt summary: The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. The main protease proteins, RNA-dependent RNA polymerase and spike protein of SARS-CoV-2 were employed to molecular docking study with the repurposed drug candidates from plant origin for find out the better drug option towards the COVID-19 pandemic. In the present study, five plantr based therapeutics such as Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were suggested for potential inhibitors for the Main Protease protein, RNA dependent RNA polymerase and Spike protein of SARS-CoV-2 by using molecular docking based virtual screening study. abstract: Covid-19, a serious respiratory complications caused by SARS-CoV-2 has become one of the global threat to human healthcare system. The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. After the comparative analysis of all docking results, Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were exhibited as the most potential inhibitory plant compounds for targeting the key proteins of SARS-CoV-2. However, amino acid positions; H41, C145, and M165 of MPP played crucial roles for the drug surface interaction where F368, L371, L372, A375, W509, L514, Y515 were pivotal for RdRP. In addition, the drug interaction surface of S proteins also showed similar patterns with all of its maximum inhibitors. ADME analysis also strengthened the possibility of screened plant therapeutics as the potent drug candidates against SARS-C with the highest drug friendliness. url: https://arxiv.org/pdf/2005.11254v1.pdf doi: nan id: cord-347441-8ow952d8 author: Parvez, Md Sorwer Alam title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date: 2020-06-07 words: 1027.0 sentences: 75.0 pages: flesch: 62.0 cache: ./cache/cord-347441-8ow952d8.txt txt: ./txt/cord-347441-8ow952d8.txt summary: title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh. As many of the Bangladeshi people return during the COVID-19 39 outbreak mainly from China, India, Saudi Arabia, Spain, Italy, Japan, Qatar, Canada, Kuwait, USA, 40 France, Sweden, and Switzerland, the first deposited genome sequence of those countries were also 41 retrieved. In total, three models were generated using the template PDB ID: 6VSB; one model for the spike protein 118 of reference strain, and the two others were for two different mutant isolates from Bangladesh (Fig 3) . abstract: As the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), rages across the world, killing hundreds of thousands and infecting millions, researchers are racing against time to elucidate the viral genome. Some Bangladeshi institutes are also in this race, sequenced a few isolates of the virus collected from Bangladesh. Here, we present a genomic analysis of 14 isolates. The analysis revealed that SARS-CoV-2 isolates sequenced from Dhaka and Chittagong were the lineage of Europe and the Middle East, respectively. Our analysis identified a total of 42 mutations, including three large deletions, half of which were synonymous. Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh. url: https://doi.org/10.1101/2020.06.07.138800 doi: 10.1101/2020.06.07.138800 id: cord-272405-jmwn8pdn author: Parvez, Mohammad K. title: Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date: 2017-08-04 words: 4192.0 sentences: 210.0 pages: flesch: 43.0 cache: ./cache/cord-272405-jmwn8pdn.txt txt: ./txt/cord-272405-jmwn8pdn.txt summary: Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. abstract: Incidences of emerging/re-emerging deadly viral infections have significantly affected human health despite extraordinary progress in the area of biomedical knowledge. The best examples are the recurring outbreaks of dengue and chikungunya fever in tropical and sub-tropical regions, the recent epidemic of Zika in the Americas and the Caribbean, and the SARS, MERS, and influenza A outbreaks across the globe. The established natural reservoirs of human viruses are mainly farm animals, and, to a lesser extent, wild animals and arthropods. The intricate “host-pathogen-environment” relationship remains the key to understanding the emergence/re-emergence of pathogenic viruses. High population density, rampant constructions, poor sanitation, changing climate, and the introduction of anthropophilic vectors create selective pressure on host-pathogen reservoirs. Nevertheless, the knowledge and understanding of such zoonoses and pathogen diversity in their known non-human reservoirs are very limited. Prevention of arboviral infections using vector control methods has not been very successful. Currently, new approaches to protect against food-borne infections, such as consuming only properly cooked meats and animal products, are the most effective control measures. Though significant progress in controlling human immunodeficiency virus and hepatitis viruses has been achieved, the unpredictable nature of evolving viruses and the rare occasions of outbreaks severely hamper control and preventive modalities. url: https://doi.org/10.1159/000478729 doi: 10.1159/000478729 id: cord-282862-kve6fa49 author: Pastick, Katelyn A title: A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date: 2020-08-13 words: 3313.0 sentences: 206.0 pages: flesch: 47.0 cache: ./cache/cord-282862-kve6fa49.txt txt: ./txt/cord-282862-kve6fa49.txt summary: Clinicaltrials.gov was searched for relevant studies, using the preprogrammed search terms "COVID-19," "SARS-CoV-2," "2019-nCoV," "2019 novel coronavirus," and "severe acute respiratory syndrome coronavirus 2." Inclusion and exclusion criteria were examined to determine whether pregnant and/or breastfeeding patients were excluded from the study. Of the actively ongoing interventional clinical trials investigating the use of a drug (including dietary supplements and biologic agents) that did not report the exclusion of pregnant or breastfeeding women, the first author contacted study personnel for each of these studies by email to discern whether or not pregnant or breastfeeding women were eligible to be enrolled. Despite available safety data in pregnancy for hydroxychloroquine and lopinavir/ritonavir, we were surprised to find 68% and 80% of the respective clinical trials had excluded pregnant or breastfeeding persons. Our review of the literature was timely and is the first study (to our knowledge) to systematically examine and compile the available data related to treatment and outcomes of COVID-19 in pregnancy and related clinical trials. abstract: BACKGROUND: Data pertaining to COVID-19 in pregnancy are limited; to better inform clinicians, we collated data from COVID-19 cases in pregnancy and summarized clinical trials enrolling this population. METHODS: We performed a systematic literature review of PubMed/MEDLINE to identify cases of COVID-19 in pregnancy or the postpartum period and associated outcomes. We then evaluated the proportion of COVID-19 clinical trials (from Clinicaltrials.gov) excluding pregnant or breastfeeding persons (both through June 29(th), 2020). RESULTS: We identified 11,308 published cases of COVID-19 in pregnancy. Of those reporting disease severity, 21% (416/1999) were severe/critical. Maternal and neonatal survival were reassuring (98% [10437/10597] and 99% [1155/1163], respectively). Neonatal disease was rare with only 41 possible cases of infection reported in the literature. Of 2351 ongoing COVID-19 therapeutic clinical trials, 1282 were enrolling persons of reproductive age and 65% (829/1282) excluded pregnant persons. Pregnancy was an exclusion criterion for 69% (75/109) of chloroquine/hydroxychloroquine, 80% (28/35) of lopinavir/ritonavir, and 48% (44/91) of convalescent plasma studies. We identified 48 actively recruiting or completed drug trials reporting inclusion of this population. CONCLUSIONS: There are limited published reports of COVID-19 in pregnancy despite more than 14 million cases worldwide. To date, clinical outcomes appear reassuring, but data related to important long-term outcomes are missing or not yet reported. The large number of clinical trials excluding pregnant persons, despite interventions with safety data in pregnancy, is concerning. In addition to observational cohort studies, pregnancy specific adaptive clinical trials could be designed to identify safe and effective treatments. url: https://www.ncbi.nlm.nih.gov/pubmed/32929403/ doi: 10.1093/ofid/ofaa350 id: cord-345288-qyz83xx2 author: Pata, Francesco title: Enteral stoma care during COVID‐19 pandemic: practical advice date: 2020-07-21 words: 2700.0 sentences: 158.0 pages: flesch: 48.0 cache: ./cache/cord-345288-qyz83xx2.txt txt: ./txt/cord-345288-qyz83xx2.txt summary: To face the COVID-19 pandemic, metamorphosis of surgical services is required to prevent in-hospital transmission, optimize allocation of scarce resources, establish new intensive care units (ICUs) and redeploy healthcare workers to emergency departments or COVID-19 dedicated wards [8] [9] [10] . Furthermore, although many recommendations suggest to consider performing stoma surgery instead of primary anastomosis in high-risk emergency surgery 14,20-23 none of those consider the potential problems related to reduced availability of stoma care services and reduced access in the hospital to caregivers for stoma training which may represent a problem for elderly and frail patients after discharge. Second, in-hospital stoma training pathways should be implemented to allow patients to confidently manage their own stomas independently prior to discharge and reduce the need for home nursing care 37 . In addition to standard precautions for infection prevention and control (i.e. correct use of PPE, keeping appropriate interpersonal distance, proper hand washing) indoor air quality should be preserved to limit the SARS-CoV-2 spread, and to protect patients and healthcare workers. abstract: The COVID‐19 pandemic represents an enormous challenge for global health systems. Stoma care represents a potentially neglected component during the outbreak and no specific recommendations on stoma care have been published up till now. In this manuscript, MISSTO (Multidisciplinary Italian Study group for STOmas) provides practical advice on optimal enteral stoma care in adults during the COVID‐19 pandemic. Translations in four other languages (Spanish, Italian, Traditional Chinese, Simplified Chinese) are attached in the appendix to enable dissemination of the document worldwide. url: https://doi.org/10.1111/codi.15279 doi: 10.1111/codi.15279 id: cord-317863-xf0bn3cv author: Pata, Ramakanth title: Probability of COVID-19 Being the Culprit in Neurocognitive Deception: A Case Series of Incidental Strokes in ICU Patients With COVID-19 date: 2020-08-18 words: 2201.0 sentences: 113.0 pages: flesch: 48.0 cache: ./cache/cord-317863-xf0bn3cv.txt txt: ./txt/cord-317863-xf0bn3cv.txt summary: The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, originated in Wuhan, China, and spread rapidly throughout the world, infecting millions and killing thousands. Additionally, it has a high incubation period (average 6.4 and range of 0-24 days) [2] , reproductive number (R0 ranged from 1.4 to 6.49, with a mean of 3.28) [3] , and reports have shown that the majority of patients are asymptomatic or have a mild response to the SARS-CoV-2 virus but release large amounts of viruses [2] . Furthermore, a chest X-ray showed no acute pathologies (Figure 3) , and the COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCT) was performed due to the recent outbreak of the SARS-CoV-2 virus, which came back positive. Other reports suggest a higher rate of cerebrovascular disease (mainly ischemic stroke) in severe COVID-19 patients as compared to non-severe cases [5] . abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, originated in Wuhan, China, and spread rapidly throughout the world, infecting millions and killing thousands. Although some patients have mild or even asymptomatic responses to this infection, hospitalized patients present with symptoms such as fever, cough, and difficulty breathing. Some patients have a severe response to the insult and experience rapid progression to acute respiratory distress and multiorgan failure. Furthermore, many patients developed complications due to this infection. Here, we present three patients who had strokes during their hospitalization for COVID-19 pneumonia. url: https://doi.org/10.7759/cureus.9857 doi: 10.7759/cureus.9857 id: cord-339665-nwwutduy author: Patel, Ami title: Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date: 2020-07-29 words: 5258.0 sentences: 286.0 pages: flesch: 52.0 cache: ./cache/cord-339665-nwwutduy.txt txt: ./txt/cord-339665-nwwutduy.txt summary: Prior work with the related coronaviruses, SARS-CoV and MERS-CoV, delineated that the Spike protein of these viruses was an important target for development of neutralizing antibodies, and in animal viral challenges vaccine targeted immunity (reviewed in (Du et al., 2009; Roper and Rehm, 2009; Thanh Le et al., 2020) (Liu et al., 2018; Muthumani et al., 2015; van Doremalen et al., 2020a) . These memory titers were comparable to those observed in other reported protection studies in macaques performed at the acute phase of the vaccine-induced immune response (Gao et al., 2020; van Doremalen et al., 2020b; Yu et al., 2020) and those reported in the sera of convalescent patients (Ni et al., 2020; Robbiani et al., 2020) . Our study and other published reports show that DNA vaccination with candidates targeting the full-length SARS-CoV-2 spike protein likely increase the availability of T cell immunodominant epitopes leading to a broader and more potent immune response, compared to partial domains and truncated immunogens. abstract: Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has had a dramatic global impact on public health, social, and economic infrastructures. Here, we assess immunogenicity and anamnestic protective efficacy in rhesus macaques of the intradermal (ID)-delivered SARS-CoV-2 spike DNA vaccine, INO-4800. INO-4800 is an ID-delivered DNA vaccine currently being evaluated in clinical trials. Vaccination with INO-4800 induced T cell responses and neutralizing antibody responses against both the D614 and G614 SARS-CoV-2 spike proteins. Several months after vaccination, animals were challenged with SARS-CoV-2 resulting in rapid recall of anti-SARS-CoV-2 spike protein T and B cell responses. These responses were associated with lower viral loads in the lung and with faster nasal clearance of virus. These studies support the immune impact of INO-4800 for inducing both humoral and cellular arms of the adaptive immune system which are likely important for providing durable protection against COVID-19 disease. url: https://doi.org/10.1101/2020.07.28.225649 doi: 10.1101/2020.07.28.225649 id: cord-285459-fph03r22 author: Patel, Ami B title: SARS-CoV-2 Point Prevalence among Asymptomatic Hospitalized Children and Subsequent Healthcare Worker Evaluation date: 2020-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Asymptomatic SARS-CoV-2 carriage among hospitalized children and the risk of transmission to healthcare workers (HCW) was evaluated through a point prevalence survey. We estimated a low, 1-2%, prevalence of SARS-CoV-2 among children without symptoms of COVID-19 and there were no secondary transmission events among HCW exposed to these patients url: https://doi.org/10.1093/jpids/piaa102 doi: 10.1093/jpids/piaa102 id: cord-287604-w0ktwl8q author: Patel, Chirag N. title: Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation date: 2020-09-29 words: 4840.0 sentences: 259.0 pages: flesch: 46.0 cache: ./cache/cord-287604-w0ktwl8q.txt txt: ./txt/cord-287604-w0ktwl8q.txt summary: We selected HE as a target in this study to identify potential inhibitors using a combination of various computational approaches such as molecular docking, ADMET analysis, dynamics simulations and binding free energy calculations. Virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin as potential HE inhibitors with better binding energy. In this study, we employed virtual screening approach to screen NPACT (Naturally occurring Plant-based Anti-cancer Compound activity-Target database) compounds against HE target [32, 35] and the best-scoring molecules were validated using molecular dynamics simulations analysis to better understand the interactions and conformational changes to inhibit HE target [36, 37] . Different molecular modeling techniques were employed in this study viz, molecular docking, Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) prediction, molecular dynamics simulations, and binding free energy calculations to obtain new leads from NPACT compounds [38] . abstract: ABSTRACT: The pandemic outbreak of the Corona viral infection has become a critical global health issue. Biophysical and structural evidence shows that spike protein possesses a high binding affinity towards host angiotensin-converting enzyme 2 and viral hemagglutinin-acetylesterase (HE) glycoprotein receptor. We selected HE as a target in this study to identify potential inhibitors using a combination of various computational approaches such as molecular docking, ADMET analysis, dynamics simulations and binding free energy calculations. Virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin as potential HE inhibitors with better binding energy. Furthermore, molecular dynamics simulations for 100 ns time scale revealed that most of the key HE contacts were retained throughout the simulations trajectories. Binding free energy calculations using MM/PBSA approach ranked the top-five potential NPACT compounds which can act as effective HE inhibitors. GRAPHIC ABSTRACT: [Image: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11030-020-10135-w) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32996011/ doi: 10.1007/s11030-020-10135-w id: cord-276090-n8c2jpr6 author: Patel, Hiren N. title: Cerebellar Infarction Requiring Surgical Decompression in patient with COVID 19 Pathological Analysis, Brief Review date: 2020-07-29 words: 2871.0 sentences: 162.0 pages: flesch: 41.0 cache: ./cache/cord-276090-n8c2jpr6.txt txt: ./txt/cord-276090-n8c2jpr6.txt summary: CONCLUSION: A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. angiography, CXR denotes chest X-ray, FiO2 denotes fraction of inspired oxygen, SARS-COV-2 denotes severe acute respiratory syndrome coronavirus 2, STAT denotes statum which is Latin meaning immediately, t-PA denotes tissue plasminogen activator, WHO denotes World Health Organization. A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. COVID-19 complicated with cerebral and large vessel vasculitis and its treatment will require a need for randomized clinical trials showing benefit in outcomes and mortality. This is a report of a patient with COVID-19 immune dysregulation who developed an acute cerebellar ischemic stroke secondary to vertebral artery thrombosis. abstract: BACKGROUND: This report and literature review describes a case of a COVID-19 patient who suffered a cerebellar stroke requiring neurosurgical decompression. This is the first reported case of a sub-occipital craniectomy with brain biopsy in a COVID-19 patient showing leptomeningeal venous intimal inflammation. CLINICAL DESCRIPTION: The patient is a 48-year-old SARS-COV-2 positive male with multiple comorbidities, who presented with fevers and respiratory symptoms, and imaging consistent with multifocal pneumonia. On day 5 of admission, the patient had sudden change in mental status, increased C-Reactive Protein, ferritin and elevated Interleukin-6 levels. Head CT showed cerebral infarction from vertebral artery occlusion. Given subsequent rapid neurologic decline from cerebellar swelling and mass effect on his brainstem emergent neurosurgical intervention was performed. Brain biopsy found a vein with small organizing thrombus adjacent to focally proliferative intima with focal intimal neutrophils. CONCLUSION: A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. Brain biopsy was suggestive of inflammation from thrombosed vessel, and neutrophilic infiltration of cerebellar tissue. url: https://www.sciencedirect.com/science/article/pii/S2214751920304114?v=s5 doi: 10.1016/j.inat.2020.100850 id: cord-331300-u5fltc10 author: Patel, Jay title: Viability of SARS‐CoV‐2 in faecal bio‐aerosols date: 2020-06-09 words: 469.0 sentences: 33.0 pages: flesch: 53.0 cache: ./cache/cord-331300-u5fltc10.txt txt: ./txt/cord-331300-u5fltc10.txt summary: I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) positive faecal samples in patients with coronavirus disease 2019 (COVID‐19). The authors acknowledge insufficient evidence in support of transmission via faeco‐oral route and identify the need for further research regarding the viability of SARS‐CoV‐2 in the context of human faeces. Dear Editor, I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive faecal samples in patients with coronavirus disease 2019 (COVID-19). The authors acknowledge insufficient evidence in support of transmission via faeco-oral route and identify the need for further Accepted Article research regarding the viability of SARS-CoV-2 in the context of human faeces. Put a lid on it: Are faecal bio-aerosols a route of transmission for SARS-CoV-2? abstract: I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) positive faecal samples in patients with coronavirus disease 2019 (COVID‐19). The authors acknowledge insufficient evidence in support of transmission via faeco‐oral route and identify the need for further research regarding the viability of SARS‐CoV‐2 in the context of human faeces. However, it is equally pertinent to consider the viability of the virus in faecal bio‐aerosols generated by toilet plumes [2]. url: https://www.ncbi.nlm.nih.gov/pubmed/32515130/ doi: 10.1111/codi.15181 id: cord-338578-e0aiknb6 author: Patel, Kajal title: Applying the WHO ICF Framework to the Outcome Measures Used in the Evaluation of Long-Term Clinical Outcomes in Coronavirus Outbreaks date: 2020-09-05 words: 3937.0 sentences: 201.0 pages: flesch: 46.0 cache: ./cache/cord-338578-e0aiknb6.txt txt: ./txt/cord-338578-e0aiknb6.txt summary: (2) Methods: EMBASE, MEDLINE, CINAHL and PsycINFO were systematically searched for original studies assessing clinical outcomes in adult survivors of severe acute respiratory distress syndrome (SARS), middle east respiratory syndrome (MERS) and coronavirus disease-19 (COVID-19) after hospital discharge. (4) Conclusions: We recommend future COVID-19 follow-up studies to use the ICF framework to select a combination of outcome measures that capture all the components for a better understanding of the impact on survivors and planning interventions to maximize functional return. The aim of this systematic review is to identify outcome measures which have been used in follow-up studies in the coronavirus outbreaks, including SARS in 2002 and MERS in 2012 [21] , and to classify them using the ICF model. In conclusion, we are proposing an ICF-based framework to assist researchers in selecting outcome measures for future follow-up studies of COVID-19 survivors. abstract: (1) Objective: The World Health Organization’s (WHO) International Classification of Functioning, Disability and Health (ICF) classification is a unified framework for the description of health and health-related states. This study aimed to use the ICF framework to classify outcome measures used in follow-up studies of coronavirus outbreaks and make recommendations for future studies. (2) Methods: EMBASE, MEDLINE, CINAHL and PsycINFO were systematically searched for original studies assessing clinical outcomes in adult survivors of severe acute respiratory distress syndrome (SARS), middle east respiratory syndrome (MERS) and coronavirus disease-19 (COVID-19) after hospital discharge. Individual items of the identified outcome measures were linked to ICF second-level and third-level categories using ICF linking rules and categorized according to an ICF component. (3) Results: In total, 33 outcome measures were identified from 36 studies. Commonly used (a) ICF body function measures were Pulmonary Function Tests (PFT), Impact of event scale (IES-R) and Hospital Anxiety and Depression Scale (HADS); (b) ICF activity was 6-Minute Walking Distance (6MWD); (c) ICF participation measures included Short Form-36 (SF-36) and St George’s Respiratory Questionnaire (SGRQ). ICF environmental factors and personal factors were rarely measured. (4) Conclusions: We recommend future COVID-19 follow-up studies to use the ICF framework to select a combination of outcome measures that capture all the components for a better understanding of the impact on survivors and planning interventions to maximize functional return. url: https://www.ncbi.nlm.nih.gov/pubmed/32899534/ doi: 10.3390/ijerph17186476 id: cord-271781-cfv0ta10 author: Patel, Kishan P. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 words: 4469.0 sentences: 232.0 pages: flesch: 47.0 cache: ./cache/cord-271781-cfv0ta10.txt txt: ./txt/cord-271781-cfv0ta10.txt summary: To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent for the 2019 coronavirus disease (COVID-19) pandemic, has caused a public health emergency. The need for additional research in viral pathogenesis is essential as the number of cases and deaths rise. Understanding the virus and its ability to cause disease has been the main focus of current literature; however, there is much unknown. Studies have revealed new findings related to the full transmission potential of SARS-CoV-2 and its subsequent ability to cause infection by different means. The virus is hypothesized to be of increased virulence compared with previous coronavirus that caused epidemics, in part due to its overall structural integrity and resilience to inactivation. To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. Additionally, the receptor by which the virus gains cellular entry, ACE2, has been found to be expressed in different human body systems, thereby potentiating its infection in those locations. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Understanding these different routes is important as they pertain to clinical practice, especially in taking preventative measures to mitigate the spread of SARS-CoV-2. url: https://doi.org/10.1007/s10096-020-03961-1 doi: 10.1007/s10096-020-03961-1 id: cord-333532-vrfduv5a author: Patel, Kishan Pravin title: COVID-19 Patients: Are Current Isolation Guidelines Effective Enough? date: 2020-05-11 words: 862.0 sentences: 49.0 pages: flesch: 48.0 cache: ./cache/cord-333532-vrfduv5a.txt txt: ./txt/cord-333532-vrfduv5a.txt summary: We believe the current isolation guidelines need to be revisited and clinicians should counsel COVID-19 patients to practice contact precautions for longer durations given new evidence suggesting the possibility of a fecaloral route of transmission. Furthermore, a recent case reported an asymptomatic COVID-19 patient who retested positive for SARS-CoV-2 despite being discharged after two negative consecutive respiratory nucleic acid tests at least 24 hours apart, raising concern for inadequate discharge protocol. With consideration of its high virulence, high infectivity, and the concern for a fecal-oral route of transmission, we suggest modifying guidelines to extend isolation and/or contact precautions in the best interest of patients, healthcare workers, and the global community as a whole. Key words: COVID 19; SARS CoV-2; Gastrointestinal; Isolation; Fecal-oral; transmission; precautions abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32417566/ doi: 10.1016/j.puhe.2020.04.048 id: cord-280001-y7pvj2l1 author: Patel, Robin title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 words: 1785.0 sentences: 77.0 pages: flesch: 46.0 cache: ./cache/cord-280001-y7pvj2l1.txt txt: ./txt/cord-280001-y7pvj2l1.txt summary: If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness. abstract: nan url: https://doi.org/10.1128/mbio.00722-20 doi: 10.1128/mbio.00722-20 id: cord-283152-wav0d0ws author: Patel, Sanjay K. S. title: Deploying Biomolecules as Anti-COVID-19 Agents date: 2020-06-09 words: 3094.0 sentences: 166.0 pages: flesch: 50.0 cache: ./cache/cord-283152-wav0d0ws.txt txt: ./txt/cord-283152-wav0d0ws.txt summary: Severe acute respiratory syndrome coronavirus (SARS-CoV-2) known as COVID-19 has emerged as a major threat to human existence. The emergence of a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, renamed as COVID19) in 2019 from Wuhan, China has led to a global crisis and it has been declared as a pandemic emergency by World Health Organization (WHO) due to its fast rate of transmission among human beings [1, 2] . Coronaviruses (CoVs) are a group of genetically distinct viruses, which originated from broad ranges of hosts, including animal and bird species, and primarily cause respiratory and intestinal infections to humans and animals [1, [5] [6] [7] [8] . Transmission of COVID-19 possibly involved an adaptive evolution through an intermediate host (bat) before infecting humans. Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV-2) known as COVID-19 has emerged as a major threat to human existence. COVID-19 seems to have undergone adaptive evolution through an intermediate host, most likely bats. The flu leads to severe pneumonia that causes respiratory and multi-organ failure. The absence of any known treatment procedures, drugs, or vaccines has created panic around the World. The need is to develop rapid testing kits, drugs and vaccines. However, these proposals are time-consuming processes. At present social distancing along with previously known traditional medicines can act as quick and short-term alternatives for treating this viral flu. url: https://doi.org/10.1007/s12088-020-00893-4 doi: 10.1007/s12088-020-00893-4 id: cord-029965-bt87kai8 author: Patel, Shailesh Kumar title: The kidney and COVID-19 patients – important considerations date: 2020-08-01 words: 1049.0 sentences: 78.0 pages: flesch: 48.0 cache: ./cache/cord-029965-bt87kai8.txt txt: ./txt/cord-029965-bt87kai8.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily affects the lungs, however, this virus can also affect other organs such as intestine, kidney, heart, and brain [1] [2] [3] . Studies reporting albuminuria and haematuria in the COVID-19 patients along with the detection of viral RNA from the urine samples further support the potential tropism of the SARS-CoV-2 for the renal tissues [4, 12] . Therefore, along with clinical management for pneumonia, potential intervention to protect the kidneys from the virus tropism and cytokine storm must be considered to minimize the mortalities associated with acute renal failure (Figure 1 ). Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395611/ doi: 10.1016/j.tmaid.2020.101831 id: cord-330074-5iqqgy65 author: Patel, Smit D. title: Malignant Cerebral Ischemia in A COVID-19 Infected Patient: Case Review and Histopathological Findings date: 2020-08-05 words: 1451.0 sentences: 89.0 pages: flesch: 38.0 cache: ./cache/cord-330074-5iqqgy65.txt txt: ./txt/cord-330074-5iqqgy65.txt summary: However, this data is limited and comes from recent small case series and observational studies on stroke types, mechanisms, and outcomes.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Furthermore, evidence on the role of therapeutic anticoagulation in SARS-CoV-2 infected patients with elevated inflammatory markers, such as D-dimer, is also limited. We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection (COVID-19). We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection . Ischemic stroke, Inflammatory conditions, COVID-19, Corona virus, SARS-CoV-2 RNA, cerebrovascular disease, hemorrhagic stroke, cerebral sinus thrombosis, vasculitis, anticoagulation, thrombotic conditions, thromboembolic conditions Introduction: abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is responsible for an unprecedented worldwide pandemic that has severely impacted the United States. As the pandemic continues, a growing body of evidence suggests that infected patients may develop significant coagulopathy with resultant thromboembolic complications including deep vein thrombosis, pulmonary embolism, myocardial infarction, and ischemic stroke. However, this data is limited and comes from recent small case series and observational studies on stroke types, mechanisms, and outcomes.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Furthermore, evidence on the role of therapeutic anticoagulation in SARS-CoV-2 infected patients with elevated inflammatory markers, such as D-dimer, is also limited. We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection (COVID-19). Histopathologic analysis of the patient's ischemic brain tissue revealed hypoxic neurons and significant edema from the underlying ischemic insult, fibrin thrombi in small vessels, and fibroid necrosis of the vascular wall without any signs of vasculature inflammation. Brain biopsy was negative for the presence of SARS-CoV-2 RNA (RT-PCR assay). Along with a growing body of literature, our case suggests that cerebrovascular thromboembolic events in COVID-19 infection may be related to acquired hypercoagulability and coagulation cascade activation due to the release of inflammatory markers and cytokines, rather than virus-induced vasculitis. Further studies to investigate the mechanism of cerebrovascular thromboembolic events and their prevention is warranted. url: https://doi.org/10.1016/j.jstrokecerebrovasdis.2020.105231 doi: 10.1016/j.jstrokecerebrovasdis.2020.105231 id: cord-303506-rqerh2u3 author: Patel, V. title: A call for governments to pause Twitter censorship: a cross-sectional study using Twitter data as social-spatial sensors of COVID-19/SARS-CoV-2 research diffusion date: 2020-05-29 words: 2933.0 sentences: 187.0 pages: flesch: 56.0 cache: ./cache/cord-303506-rqerh2u3.txt txt: ./txt/cord-303506-rqerh2u3.txt summary: Objectives: To determine whether Twitter data can be used as social-spatial sensors to show how research on COVID-19/SARS-CoV-2 diffuses through the population to reach the people that are especially affected by the disease. Mapping of worldwide data illustrated that high Twitter activity was related to high numbers of COVID-19/SARS-CoV-2 deaths, with tweets inversely weighted with number of publications. • Using Twitter data used as social-spatial sensors, we demonstrated that Twitter activity was significantly positively correlated to the numbers of COVID-19/SARS-CoV-2 deaths, when holding the country''s number of publications constant. Mapping of worldwide data illustrated that high Twitter activity was related to high Conclusions: This study shows that Twitter can play a crucial role in the rapid research response during the COVID-19/SARS-CoV-2 global pandemic, especially to spread research with prompt public scrutiny. abstract: Objectives: To determine whether Twitter data can be used as social-spatial sensors to show how research on COVID-19/SARS-CoV-2 diffuses through the population to reach the people that are especially affected by the disease. Design: Cross-sectional bibliometric analysis conducted between 23rd March and 14th April 2020. Setting: Three sources of data were used in the analysis: (1) deaths per number of population for COVID-19/SARS-CoV-2 retrieved from Coronavirus Resource Center at John Hopkins University and Worldometer, (2) publications related to COVID-19/SARS-CoV-2 retrieved from WHO COVID-19 database of global publications, and (3) tweets of these publications retrieved from Altmetric.com and Twitter. Main Outcome(s) and Measure(s): To map Twitter activity against number of publications and deaths per number of population worldwide and in the USA states. To determine the relationship between number of tweets as dependent variable and deaths per number of population and number of publications as independent variables. Results: Deaths per one hundred thousand population for countries ranged from 0 to 104, and deaths per one million population for USA states ranged from 2 to 513. Total number of publications used in the analysis was 1761, and total number of tweets used in the analysis was 751,068. Mapping of worldwide data illustrated that high Twitter activity was related to high numbers of COVID-19/SARS-CoV-2 deaths, with tweets inversely weighted with number of publications. Poisson regression models of worldwide data showed a positive correlation between the national deaths per number of population and tweets when holding the country's number of publications constant (coefficient 0.0285, S.E. 0.0003, p<0.001). Conversely, this relationship was negatively correlated in USA states (coefficient -0.0013, S.E. 0.0001, p<0.001). Conclusions: This study shows that Twitter can play a crucial role in the rapid research response during the COVID-19/SARS-CoV-2 global pandemic, especially to spread research with prompt public scrutiny. Governments are urged to pause censorship of social media platforms during these unprecedented times to support the scientific community's fight against COVID-19/SARS-CoV-2. url: https://doi.org/10.1101/2020.05.27.20114983 doi: 10.1101/2020.05.27.20114983 id: cord-328069-a9fi9ssg author: Pathan, Refat Khan title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model date: 2020-06-13 words: 3402.0 sentences: 202.0 pages: flesch: 64.0 cache: ./cache/cord-328069-a9fi9ssg.txt txt: ./txt/cord-328069-a9fi9ssg.txt summary: title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model This study explores the mutation rate of the whole genomic sequence gathered from the patient''s dataset of different countries. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, The United States, and the rest of the World. Using this train and testing process, the nucleotide mutation rate of 400(th) patient in future time has been predicted. The complete genomic sequence (Wuhan-HU1) of this large RNA virus (SARS-CoV-2) was first discovered in the laboratory of China on 10th January [10] and placed in the NCBI GenBank. al have performed Phylogenetic analysis of SARS-CoV-2 virus based on the spike gene of the genomic sequence [17] . An adequate amount of gene dataset is currently available in the NCBI GenBank which has the complete genome sequence of SARS-CoV-2. abstract: SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. As of May 18, already more than 4.8 million people have been infected and 316k people died. This RNA virus has the ability to do the mutation in the human body. Accurate determination of mutation rates is essential to comprehend the evolution of this virus and to determine the risk of emergent infectious disease. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, The United States, and the rest of the World. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. A recurrent neural network-based Long Short Term Memory (LSTM) model has been applied to predict the future mutation rate of this virus. The LSTM model gives Root Mean Square Error (RMSE) of 0.06 in testing and 0.04 in training, which is an optimized value. Using this train and testing process, the nucleotide mutation rate of 400(th) patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time. url: https://api.elsevier.com/content/article/pii/S0960077920304161 doi: 10.1016/j.chaos.2020.110018 id: cord-017210-5nc8f3a4 author: Pathegama, Mahinda P. title: Interactive Real-time Image Analysis System for Distant Operation date: 2005 words: 2415.0 sentences: 129.0 pages: flesch: 43.0 cache: ./cache/cord-017210-5nc8f3a4.txt txt: ./txt/cord-017210-5nc8f3a4.txt summary: This paper reports on the development and implementation of an integrated and interactive system for cell analysis featuring remote operation and real-time analysis for generating analytical data from microscopic images. Advancement of image processing techniques is a welcome adjunct in electronmicroscopic cell analysis and is the object of increasing interest in research for the enhancement of accuracy in disease diagnosis. The emergence and rapid spread of SARS (Severe Acute Respiratory Syndrome) has dramatically emphasised the need for both collaborative international networks [4] and linking of personnel from distant locations with laboratories monitoring and analysing test samples of the causative agent by electron microscopy. Remote users would derive considerable benefit from a system endowed with facilities enabling image acquisition, camera control, real-time monitoring, automated pattern recognition for cell feature extraction and quantitative result generation. The techniques used aid in image enhancement and provide feature highlighting needed for quantitative report generation on each cell object detected in the microscopic image. abstract: This paper reports on the development and implementation of an integrated and interactive system for cell analysis featuring remote operation and real-time analysis for generating analytical data from microscopic images. The system consists of a number of image processing modules implemented in a virtual instrumentation environment, combined with novel techniques developed for thinning and local edge-gap filling in the cell image segmentation process. These approaches, integrated with advances in networking, have been initially applied to viral feature analysis in SARS-CoV microscopy. Real-time operation through the user-interface of the proposed system generates quantitative results for remote clients. The rapidity and viability of operation permit the investigation of mutant viral agents on the basis of their morphological cell features. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121714/ doi: 10.1007/0-387-26325-x_3 id: cord-299853-pvugij9l author: Patil, Uday P. title: Newborns of COVID-19 mothers: short-term outcomes of colocating and breastfeeding from the pandemic’s epicenter date: 2020-08-10 words: 1217.0 sentences: 67.0 pages: flesch: 54.0 cache: ./cache/cord-299853-pvugij9l.txt txt: ./txt/cord-299853-pvugij9l.txt summary: Newborns are at high risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from their infected mothers who delivered during this period; however, data remains limited [3] . Data regarding demographic and clinical characteristics, SARS-CoV-2 test results, symptoms and signs of COVID-19, colocation (rooming-in), breastfeeding, and newborn follow-up were obtained from review of electronic medical records. During the early period of the pandemic, our center tested only symptomatic pregnant women for SARS-CoV-2 and newborns of infected mothers were placed in isolation rooms based on the available literature at that time [6] . However, due to the dramatic surge in the number of SARS-CoV-2 positive mothers delivering at our center after initiation of universal screening of all pregnant women admitted for delivery, the limited isolation spaces for the newborns, early postpartum discharges, the crowded housing conditions in our community and the desire to promote breastfeeding, we utilized shared decision-making and offered rooming-in of mothers with their newborns [7] . abstract: nan url: https://doi.org/10.1038/s41372-020-0765-3 doi: 10.1038/s41372-020-0765-3 id: cord-296020-kje1wiah author: Patoulias, Dimitrios title: Diabetes mellitus and SARS-CoV-2-related mortality: the impact of acute hyperglycemic crises and some further considerations date: 2020-08-20 words: 604.0 sentences: 27.0 pages: flesch: 42.0 cache: ./cache/cord-296020-kje1wiah.txt txt: ./txt/cord-296020-kje1wiah.txt summary: We would like to emphasize on another aspect of SARS-CoV-2 infection among patients with DM, the triggering of acute hyperglycemic crises, either diabetic ketoacidosis (DKA) or hyperosmolar hyperglycemic state (HHS). described the presentation and clinical course of 6 patients with DM who developed DKA and HHS in the context of SARS-CoV-2 infection [2] . However, according to a recent retrospective analysis from the UK, patients with DM who develop DKA due to disease are more likely to survive compared to those patients that are not complicated by an acute hyperglycemic crisis [5] . Therefore, it would be interesting to know in future, large, observational studies the proportion of patients that developed DKA/HHS in the context of SARS-CoV-2 infection, the underlying treatment and the outcome of disease. Clinical characteristics and outcome in patients with combined diabetic ketoacidosis and hyperosmolar hyperglycemic state associated with COVID-19 :a retrospective, hospital-based observational case series abstract: nan url: https://doi.org/10.1007/s00592-020-01593-7 doi: 10.1007/s00592-020-01593-7 id: cord-352642-u513wnu1 author: Patrocínio de Jesus, Rita title: Reactivation of SARS-CoV-2 after Asymptomatic Infection while on High-Dose Corticosteroids. Case Report date: 2020-10-02 words: 2211.0 sentences: 113.0 pages: flesch: 46.0 cache: ./cache/cord-352642-u513wnu1.txt txt: ./txt/cord-352642-u513wnu1.txt summary: After reviewing this case in light of current evidence and debates surrounding SARS-CoV-2 RT-PCR results, we hypothesize that patients on corticosteroids may have particular viral shedding dynamics and should prompt a more conservative approach in regard to isolation discontinuation and monitoring. Since the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the cause of the disease which was later named COVID-19, and as it progressed to the current worldwide pandemic, much investigation has been made regarding its clinical presentation, transmission route, and immunity. This could point either to a reactivation of the disease in a patient who first presented as asymptomatic or to a long incubation period (18 days from risk contact until developing symptoms, with a CT performed 3 days prior to the onset of symptoms showing an evolving disease, which is consistent with previous studies reporting typical radiological findings of COVID-19 in asymptomatic or presymptomatic patients [2] ). abstract: As SARS-CoV-2 and its related clinical syndrome (COVID-19) became a pandemic worldwide, questions regarding its clinical presentation, infectivity, and immune response have been the subject of investigation. We present a case of a patient previously considered recovered from nosocomially transmitted asymptomatic COVID-19 illness, who presented with new respiratory, radiological, and RT-PCR findings consistent with COVID-19, while on high-dose prednisolone due to a suspected secondary demyelinating disease. Importantly, it led to three subsequent cases within patient’s household after discharge from the hospital. After reviewing this case in light of current evidence and debates surrounding SARS-CoV-2 RT-PCR results, we hypothesize that patients on corticosteroids may have particular viral shedding dynamics and should prompt a more conservative approach in regard to isolation discontinuation and monitoring. url: https://www.ncbi.nlm.nih.gov/pubmed/33043249/ doi: 10.1007/s42399-020-00548-x id: cord-323241-1twnqr4k author: Patrì, Angela title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? date: 2020-04-09 words: 633.0 sentences: 50.0 pages: flesch: 51.0 cache: ./cache/cord-323241-1twnqr4k.txt txt: ./txt/cord-323241-1twnqr4k.txt summary: title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? 2, 3 In addition, SARS-CoV-2 RNA identification and intracellular staining of viral nucleocapsid protein in rectal epithelia demonstrated that the virus infects such epithelial cells. [2] [3] [4] Moreover, SARS-CoV-2 can also be transmitted through the saliva, and ACE2 has been detected on the mucosa of oral cavity, which is rich in epithelial cells. 4 Therefore, if saliva and feces are both capable of carrying the virus and ACE2 is expressed both in the glandular cells of rectal epithelia and oral mucosa, how can we be sure that sexual intercourse does not represent another way of contagion? 5 This means that the gastrointestinal tract may continue shedding the virus and that fecal-oral, or eventually sexual, transmission may be possible despite the apparent recovery. abstract: nan url: https://api.elsevier.com/content/article/pii/S0190962220305211 doi: 10.1016/j.jaad.2020.03.098 id: cord-338365-9sd62a2w author: Patrício Silva, Ana L. title: Increased plastic pollution due to Covid-19 pandemic: challenges and recommendations date: 2020-08-17 words: 7418.0 sentences: 354.0 pages: flesch: 42.0 cache: ./cache/cord-338365-9sd62a2w.txt txt: ./txt/cord-338365-9sd62a2w.txt summary: This paper provides a comprehensive review on the potential impact of COVID-19 pandemic precautionary measures in the environment while considering the shift on public behaviour and policies towards single-use items and waste management. At first glance COVID-19 pandemic seems to be indirectly contributing towards the UN 2030 Sustainable Development Goals (namely 11, 12, 13, 15 SGDs) by increasing overall health and safety of cities by reducing the greenhouse gas emissions (GHG), outdoor air pollution, environmental noise level (including underwater noise due to reduced marine transportation activities), land and wildlife pressure. While the positive impacts of COVID-19 in the environment are resulting from a "postponed" anthropogenic activity that soon will entail after the pandemic scenario; the negative short-term effects (that are mostly related with plastic use, consumption and waste mismanagement as discussed below) will shortly add-up to the current environmental issues, aggravating their impact in the natural ecosystems and compromising potential mitigation/remediation measures. abstract: Plastics have become a severe transboundary threat to natural ecosystems and human health, with studies predicting a twofold increase in the number of plastic debris (including micro and nano-sized plastics) by 2030. However, such predictions will likely be aggravated by the excessive use and consumption of single-use plastics (including personal protective equipment such as masks and gloves) due to COVID-19 pandemic. This review aimed to provide a comprehensive overview on the effects of COVID-19 on macroplastic pollution and its potential implications on the environment and human health considering short- and long-term scenarios; addressing the main challenges and discussing potential strategies to overcome them. It emphasises that future measures, involved in an emergent health crisis or not, should reflect a balance between public health and environmental safety as they are both undoubtedly connected. Although the use and consumption of plastics significantly improved our quality of life, it is crucial to shift towards sustainable alternatives, such as bio-based plastics. Plastics should remain in the top of the political agenda in Europe and across the world, not only to minimise plastic leakage and pollution, but to promote sustainable growth and to stimulate both green and blue- economies. Discussions on this topic, particularly considering the excessive use of plastic, should start soon with the involvement of the scientific community, plastic producers and politicians in order to be prepared for the near future. url: https://www.sciencedirect.com/science/article/pii/S1385894720328114?v=s5 doi: 10.1016/j.cej.2020.126683 id: cord-269114-mdsiv6tr author: Pattabiraman, C. title: Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka date: 2020-07-11 words: 3141.0 sentences: 203.0 pages: flesch: 62.0 cache: ./cache/cord-269114-mdsiv6tr.txt txt: ./txt/cord-269114-mdsiv6tr.txt summary: A comprehensive study of circulating variants of the virus in Iceland, which included over 580 complete genomes in combination with epidemiological information (travel history and contact tracing) revealed that while the initial importation of the virus was from China and Southeast Asia subsequent importations were from different parts of Europe 8 . While these studies have added valuable information on circulating lineages of SARS-CoV-2 in India, they have not comprehensively linked genomic data with epidemiological information. Here we report 47 full-length SARS-CoV-2 genome sequences obtained from individuals who tested positive for the virus by RT-PCR and present an analysis of epidemiological information combined with genomic data to elucidate the introduction and spread of the virus in the state. The data from this study using a combination of genomic epidemiology and contact tracing provides evidence for multiple introductions of the virus into the state, with sustained local transmission. abstract: Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 47 full genomes of SARS-CoV-2 which clustered into six lineages (Pangolin lineages-A, B, B.1, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 12 contact clusters and 11 cases with no known contacts. We found nine of the 12 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (8/12) were contained within a single district, consistent with local spread. In most of the twelve clusters, the index case (9/12) and spreaders (8/12) were symptomatic. Of the 47 sequences, 31 belonged to the B/B.6 lineage, including seven of eleven cases with no known contact, this is consistent with the ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka is consistent with multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response. url: https://doi.org/10.1101/2020.07.10.20150045 doi: 10.1101/2020.07.10.20150045 id: cord-274542-fpzk5k79 author: Patti, Giuseppe title: Questions and Answers on Practical Thrombotic Issues in SARS-CoV-2 Infection: A Guidance Document from the Italian Working Group on Atherosclerosis, Thrombosis and Vascular Biology date: 2020-11-03 words: 5628.0 sentences: 239.0 pages: flesch: 32.0 cache: ./cache/cord-274542-fpzk5k79.txt txt: ./txt/cord-274542-fpzk5k79.txt summary: UFH should be limited to patients with CrCl < 30 mL/min An invasive "catheter"-based therapy for PE is indicated in selected cases with contraindication to anticoagulant drugs, recurrent events despite adequate anticoagulation, or when systemic fibrinolysis cannot be performed For the risk stratification of patients with VTE, monitoring of the following parameters is useful: troponin, BNP, D-dimer, blood cell count, fibrinogen, prothrombin time, activated partial thromboplastin time, and degradation products of fibrin After the initial approach, DOACs may represent an option for in-hospital treatment of a VTE episode in patients with clinical stability and decreasing inflammation After a VTE episode, DOACs should represent the therapy of choice at discharge The use of imaging techniques in diagnosing a VTE episode is complex, because of the risk of viral transmission to other patients and to healthcare workers, and must be regulated by specific in-hospital protocols aimed at limiting such risk. abstract: In patients with coronavirus disease 2019 (COVID-19), the prevalence of pre-existing cardiovascular diseases is elevated. Moreover, various features, also including pro-thrombotic status, further predispose these patients to increased risk of ischemic cardiovascular events. Thus, the identification of optimal antithrombotic strategies in terms of the risk–benefit ratio and outcome improvement in this setting is crucial. However, debated issues on antithrombotic therapies in patients with COVID-19 are multiple and relevant. In this article, we provide ten questions and answers on risk stratification and antiplatelet/anticoagulant treatments in patients at risk of/with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection based on the scientific evidence gathered during the pandemic. url: https://doi.org/10.1007/s40256-020-00446-6 doi: 10.1007/s40256-020-00446-6 id: cord-352779-zdtpnip0 author: Patti, Ravi Karan title: Subacute Aspergillosis “Fungal Balls” Complicating COVID-19 date: 2020-10-15 words: 1548.0 sentences: 108.0 pages: flesch: 39.0 cache: ./cache/cord-352779-zdtpnip0.txt txt: ./txt/cord-352779-zdtpnip0.txt summary: Severe acute respiratory syndrome coronavirus-2 infection (SARS-CoV-2), commonly known as COVID-19 (coronavirus disease-2019), began in the Wuhan District of Hubei Province, China. We report the case of a 73-year-old male who presented with progressive dyspnea; diagnosed with SARS-CoV-2–related severe acute respiratory distress syndrome and complicated with lung cavitations growing Aspergillus sp. Due to persistence of the SARS-CoV-2 and severe acute respiratory distress syndrome complicated by pulmonary aspergillosis, the patient further underwent tracheostomy and was discharged to a subacute rehabilitation facility. 11 We report this case of subacute invasive pulmonary aspergillosis in a patient with SARS-CoV-2 infection, who did not have any history of pulmonary tuberculosis, sarcoidosis, or preformed cavities to predispose for aspergillus infection. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. abstract: Severe acute respiratory syndrome coronavirus-2 infection (SARS-CoV-2), commonly known as COVID-19 (coronavirus disease-2019), began in the Wuhan District of Hubei Province, China. It is regarded as one of the worst pandemics, which has consumed both human lives and the world economy. COVID-19 infection mainly affects the lungs triggering severe hypoxemic respiratory failure, also providing a nidus for superimposed bacterial and fungal infections. We report the case of a 73-year-old male who presented with progressive dyspnea; diagnosed with SARS-CoV-2–related severe acute respiratory distress syndrome and complicated with lung cavitations growing Aspergillus sp. COVID-19, to our knowledge, has rarely been associated with subacute invasive pulmonary aspergillosis with aspergillomas. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. By reporting this case, we would like to make the readers aware of this association. url: https://doi.org/10.1177/2324709620966475 doi: 10.1177/2324709620966475 id: cord-355475-kdubhh73 author: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 words: 2161.0 sentences: 104.0 pages: flesch: 45.0 cache: ./cache/cord-355475-kdubhh73.txt txt: ./txt/cord-355475-kdubhh73.txt summary: An early survey in May and June 2020 of practicing dentists in private practice and public health settings in the United States (U.S.), a short 2 months after the first COVID-19 wave and national shortages of personal protective equipment caused offices to move to emergency only dental care, showed that 99.7% of offices had implemented enhanced infection control procedures. While hope for a COVID-19 vaccine to quell transmission is widespread, we must not lose sight of the fact that diverse vaccine development technologies and novel drug discovery efforts made today will benefit our response to the next pandemic. 14 When the diversity of oral mucosal and salivary gland disorders were observed in HIV/AIDS patients, international collaborative groups such as the European Community We learned from HIV disease management that the antiretroviral drugs can have acute and long-term toxicities including ulcers, xerostomia/parotid lipomatosis, taste disturbances, perioral paresthesia, erythema multiforme and facial fat wasting. abstract: nan url: https://api.elsevier.com/content/article/pii/S2212440320313146 doi: 10.1016/j.oooo.2020.10.022 id: cord-027309-8siz9rb8 author: Paul, Debjani title: Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2 date: 2020-06-19 words: 2269.0 sentences: 136.0 pages: flesch: 51.0 cache: ./cache/cord-027309-8siz9rb8.txt txt: ./txt/cord-027309-8siz9rb8.txt summary: The recent pandemic of COVID-19 caused by the novel coronavirus (SARS-CoV-2) has drawn attention to the need for developing rapid and accurate diagnostic tests. The widespread use of these immunodiagnostic tests in clinical settings, in spite of their shortcomings, emphasizes the need for developing rapid and point-of-care (POC) tests that are based on molecular diagnostics (i.e., tests that detect the viral RNA directly in a manner similar to RT-PCR). We believe we can build on our past experience with isothermal DNA amplification techniques and paperfluidic devices to develop an isothermal amplification-based molecular diagnostic test for COVID-19 that can be deployed more easily. The ID NOW COVID-19 assay from Abbott, which recently got an emergency use authorization (EUA) from the US government for clinical use, detects SARS-CoV-2 RNA using an isothermal amplification test and can enable a clinical decision in as early as 13 min (ID NOWTM Covid-19 2020). abstract: There is a need for widespread testing in India to stop the spread of the novel coronavirus in the population. While RT-PCR is the recommended diagnostic technique, its use is limited to well-equipped laboratories due to the need for specialized instrumentation, reagents and trained personnel. Immunodiagnostic tests are not yet recommended by the WHO for diagnosing active infections. There is a strong need for developing point-of-care molecular tests. Based on our past experience with paperfluidic devices for diagnosing bacterial infections by molecular tests, we propose the development of a diagnostic test for COVID-19. As a platform technology, it could be adapted to other viral outbreaks in future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303936/ doi: 10.1007/s41403-020-00127-5 id: cord-030870-ao5p3ra3 author: Paul, Suman title: Dynamics and risk assessment of SARS-CoV-2 in urban areas: a geographical assessment on Kolkata Municipal Corporation, India date: 2020-08-25 words: 6496.0 sentences: 323.0 pages: flesch: 60.0 cache: ./cache/cord-030870-ao5p3ra3.txt txt: ./txt/cord-030870-ao5p3ra3.txt summary: Nearly 85% cases are reported from major cities of India and most interestingly, Mumbai, Delhi, Ahmedabad, Chennai, Thane, Pune, Kolkata become the most contributing urban centres to SARS-CoV-2 cases (as on 19 May, 2020). Further an attempt has also been made to quantify and assess the hotspot zones along with risks of the concentrated areas of Kolkata (one of the Metro city) for proper understanding of transmission of diseases in the congested and unhealthy places as a case study [9, 15, 16] . Based on socio-economic data of slum of Kolkata Municipal Corporation and containment zone data and containment zone data from different web sources we have selected the following indicators for quantity exposure, sensitivity and resilience for assessing the risk [22] infector disease like SARS-CoV-2 (see Table 1 ). As Kolkata has experienced 1st case of SARS-CoV-2, here we have taken ward wise containment zone to find out the nature of hot spots located in the Municipal area. abstract: SARS-CoV-2 has been transmitted and outbreak took place in India during the last week before nationwide 1st lockdown took place. Urban areas found more vulnerable and reported nearly 65% of cases during every phase of lockdown. Mumbai, among four metropolitan cities found huge number of containment zones with nearly 30% of SARS-CoV-2 cases indicating clustering of cases. Most of the containment zones of SARS-CoV-2 cases in Kolkata Municipal Corporation found a significant relation with slum areas. The study primarily tries considering the nature of SARS-CoV-2 cases in different urban centres with the help of cartographic techniques. AHP method has been used to determine the factors responsible for such concentration of SARS-CoV-2 cases with vulnerability assessment (exposure, sensitivity and resilience) and risks. Before nationwide lockdown starts, the share of urban centres found 25% which has been transformed into nearly 60% at the end of 3(rd) phase of lockdown. Growth rate of SARS-CoV-2 cases found very high for Chennai and Thane with less number of doubling time to nation. Slum concentration and containment density shows a higher degree of correlation in Kolkata Municipal Corporation. Risk map also shows the concentration of cases in central and north Kolkata with higher degree of diseases exposure and sensitivity. Control measures must be taken by the central and state Government to minimise the transmission rate of SARS-CoV-2 mainly urban areas. As urban area contributing a higher share of SARS-CoV-2 cases, a proper management plan must be enforce. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s41324-020-00354-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445076/ doi: 10.1007/s41324-020-00354-6 id: cord-270683-982eqtog author: Pavel, Shaikh Terkis Islam title: Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date: 2020-09-16 words: 5515.0 sentences: 318.0 pages: flesch: 61.0 cache: ./cache/cord-270683-982eqtog.txt txt: ./txt/cord-270683-982eqtog.txt summary: We determined that the Vero E6 and MA-104 cell lines are suitable for supporting SARS-CoV-2 that supports viral replication, development of cytopathic effect (CPE) and subsequent cell death. Phylogenetic analyses of the whole genome sequences showed that the hCoV-19/Turkey/ERAGEM-001/2020 strain clustered with the strains primarily from Australia, Canada, England, Iran and Kuwait and that the cases in the nearby clusters were reported to have travel history to Iran and to share the common unique nucleotide substitutions. For whole genome sequencing of hCoV-19/Turkey/ERAGEM-001/2020, Vero E6 cells infected with the virus were used for RNA extraction. The growth kinetics study showed that SARS-CoV-2 replicated rapidly and efficiently and could be detected within 6 h post-infection in Vero E6 and MA-104 cells (Fig 6A and 6B ). Immunoblotting analysis also confirmed that only Vero E6 and MA-104 cell lines infected with SARS-CoV-2 showed the expression of the virus specific proteins expression (Fig 5) . abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and associated with severe respiratory illness emerged in Wuhan, China, in late 2019. The virus has been able to spread promptly across all continents in the world. The current pandemic has posed a great threat to public health concern and safety. Currently, there are no specific treatments or licensed vaccines available for COVID-19. We isolated SARS-CoV-2 from the nasopharyngeal sample of a patient in Turkey with confirmed COVID-19. We determined that the Vero E6 and MA-104 cell lines are suitable for supporting SARS-CoV-2 that supports viral replication, development of cytopathic effect (CPE) and subsequent cell death. Phylogenetic analyses of the whole genome sequences showed that the hCoV-19/Turkey/ERAGEM-001/2020 strain clustered with the strains primarily from Australia, Canada, England, Iran and Kuwait and that the cases in the nearby clusters were reported to have travel history to Iran and to share the common unique nucleotide substitutions. url: https://doi.org/10.1371/journal.pone.0238614 doi: 10.1371/journal.pone.0238614 id: cord-348478-ho89o8mj author: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 words: 2100.0 sentences: 138.0 pages: flesch: 48.0 cache: ./cache/cord-348478-ho89o8mj.txt txt: ./txt/cord-348478-ho89o8mj.txt summary: This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) abstract: December 2019 saw the emergence of a new epidemic of pneumonia of varying severity, called COVID-19, caused by a newly identified coronavirus, SARS-CoV-2. No therapeutic option is available to treat this infection that has already killed more than 235,000 people worldwide. This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. Alisporivir should be tested without delay on both virological and clinical endpoints in patients with or at-risk of severe forms of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32409832/ doi: 10.1093/cid/ciaa587 id: cord-342383-ckswlo9o author: Pawlowski, C. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 words: 5479.0 sentences: 273.0 pages: flesch: 51.0 cache: ./cache/cord-342383-ckswlo9o.txt txt: ./txt/cord-342383-ckswlo9o.txt summary: Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). Given this study population, we assess the rates of SARS-CoV-2 infection among individuals who did and did not receive one of 18 vaccines in the past 1, 2, and 5 years relative to the date of PCR testing. In Figure 6 , we present the results from the tipping point analysis on the statistically significant associations between vaccination and reduced rates of SARS-CoV-2 infection in the overall study population. For example, for the polio vaccine at the 1 year time horizon, an unobserved confounder with a relative risk of 2.78 which is prevalent in 17.8% of the vaccinated cohort and 0% of the unvaccinated cohort could explain the differences in SARS-CoV-2 infection rates that we observe in the data. abstract: Multiple clinical studies are ongoing to assess whether existing vaccines may afford protection against SARS-CoV-2 infection through trained immunity. In this exploratory study, we analyze immunization records from 137,037 individuals who received SARS-CoV-2 PCR tests. We find that polio, Hemophilus influenzae type-B (HIB), measles-mumps-rubella (MMR), varicella, pneumococcal conjugate (PCV13), geriatric flu, and hepatitis A / hepatitis B (HepA-HepB) vaccines administered in the past 1, 2, and 5 years are associated with decreased SARS-CoV-2 infection rates, even after adjusting for geographic SARS-CoV-2 incidence and testing rates, demographics, comorbidities, and number of other vaccinations. Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). These findings suggest that additional pre-clinical and clinical studies are warranted to assess the protective effects of existing non-COVID-19 vaccines and explore underlying immunologic mechanisms. We note that the findings in this study are preliminary and are subject to change as more data becomes available and as further analysis is conducted. url: https://doi.org/10.1101/2020.07.27.20161976 doi: 10.1101/2020.07.27.20161976 id: cord-336769-5x6xjuew author: Payne, Daniel C. title: SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020 date: 2020-06-12 words: 2567.0 sentences: 112.0 pages: flesch: 42.0 cache: ./cache/cord-336769-5x6xjuew.txt txt: ./txt/cord-336769-5x6xjuew.txt summary: In April, the U.S. Navy and CDC investigated this outbreak, and the demographic, epidemiologic, and laboratory findings among a convenience sample of 382 service members serving aboard the aircraft carrier are reported in this study. At the time of specimen collection, participants completed a questionnaire eliciting information on demographic characteristics, exposure, COVID-19 protective behaviors, health history, and symptoms; participants also reported whether they had had a previous positive COVID-19 test since deployment but before this investigation. Among a convenience sample of 382 young adult U.S. service members aboard an aircraft carrier experiencing a COVID-19 outbreak, 60% had reactive antibodies, and 59% of those also had neutralizing antibodies at the time of specimen collection. In this convenience sample of young, healthy U.S. service members experiencing close contact aboard an aircraft carrier, those with previous or current SARS-CoV-2 infection experienced mild illness overall, and nearly 20% were asymptomatic. abstract: Compared with the volume of data on coronavirus disease 2019 (COVID-19) outbreaks among older adults, relatively few data are available concerning COVID-19 in younger, healthy persons in the United States (1,2). In late March 2020, the aircraft carrier USS Theodore Roosevelt arrived at port in Guam after numerous U.S. service members onboard developed COVID-19. In April, the U.S. Navy and CDC investigated this outbreak, and the demographic, epidemiologic, and laboratory findings among a convenience sample of 382 service members serving aboard the aircraft carrier are reported in this study. The outbreak was characterized by widespread transmission with relatively mild symptoms and asymptomatic infection among this sample of mostly young, healthy adults with close, congregate exposures. Service members who reported taking preventive measures had a lower infection rate than did those who did not report taking these measures (e.g., wearing a face covering, 55.8% versus 80.8%; avoiding common areas, 53.8% versus 67.5%; and observing social distancing, 54.7% versus 70.0%, respectively). The presence of neutralizing antibodies, which represent antibodies that inhibit SARS-CoV-2, among the majority (59.2%) of those with antibody responses is a promising indicator of at least short-term immunity. This report improves the understanding of COVID-19 in the U.S. military and among young adults in congregate settings and reinforces the importance of preventive measures to lower risk for infection in similar environments. url: https://www.ncbi.nlm.nih.gov/pubmed/32525850/ doi: 10.15585/mmwr.mm6923e4 id: cord-319781-6thdg2up author: Payne, Kelly title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date: 2020-07-24 words: 8233.0 sentences: 454.0 pages: flesch: 51.0 cache: ./cache/cord-319781-6thdg2up.txt txt: ./txt/cord-319781-6thdg2up.txt summary: To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). Then, we present the state of current research regarding presence in semen, sexual transmission, and fertility effects for the Zika virus (ZIKV), Ebola virus (EBOV), West Nile virus (WNV), pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-coronavirus-2 (SARS-CoV-2) ( Table 1) . In this article, we have reviewed the presence in semen, possibility of sexual transmission, and fertility implications of each of the major recent viral pandemics: Zika, Ebola, West Nile, pandemic influenza, SARS, and SARS-CoV-2. abstract: INTRODUCTION: The 21st century has seen a series of viral pandemics that have collectively infected millions of individuals. To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. AIM: To review the current literature regarding the sexual transmissibility of recent viral pandemics and their effects on semen parameters and fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). METHODS: A literature search was conducted to identify relevant studies. Titles and abstracts were reviewed for relevance. References from identified articles were searched and included, if appropriate. MAIN OUTCOME MEASURES: The main outcome measure of this study was reviewing of peer-reviewed literature. RESULTS: Both the Ebola virus and Zika virus are present in semen, but only the Zika virus shows consistent evidence of sexual transmission. Current evidence does not support the presence of the West Nile virus, pandemic influenza, SARS, and SARS-CoV-2 in semen. The Zika virus appears to alter semen parameters in a way that diminishes fertility, but the effect is likely time limited. The West Nile virus and SARS have been associated with orchitis in a small number of case reports. Viruses that cause febrile illness, such as pandemic influenza, SARS, and SARS-CoV-2, are associated with decreased sperm count and motility and abnormal morphology. SARS and SARS-CoV-2 may interact with angiotensin-converting enzyme 2 receptors present in the testes, which could impact spermatogenesis. CONCLUSIONS: We have reported the presence in semen, sexual transmission potential, and fertility side effects of recent viral pandemics. Overall, semen studies and fertility effects are highly understudied in viral pandemics, and rigorous study on these topics should be undertaken as novel pandemics emerge. Payne K, Kenny P, Scovell JM, et al. Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications for Men. Sex Med Rev 2020;XX:XXX–XXX. url: https://doi.org/10.1016/j.sxmr.2020.06.003 doi: 10.1016/j.sxmr.2020.06.003 id: cord-281508-zl2url8z author: Pearce, N. title: Is death from Covid-19 a multistep process? date: 2020-06-03 words: 4997.0 sentences: 245.0 pages: flesch: 53.0 cache: ./cache/cord-281508-zl2url8z.txt txt: ./txt/cord-281508-zl2url8z.txt summary: The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope (indicating a smaller number of steps); in contrast, seasonal and pandemic influenza showed quite different agepatterns. These findings are consistent with a multistep model of disease involving a six-step process that in the case of SARS-COV-2 is probably defined by comorbidities and age producing immune-related susceptibility. abstract: Covid-19 death has a different relationship with age than is the case for other severe respiratory pathogens. The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Furthermore, the almost complete lack of deaths in children suggests that infection alone is not sufficient to cause death; rather, one must have gone through a number of changes, either as a result of undefined aspects of aging, or as a result of chronic disease. These characteristics of Covid-19 death are consistent with the multistep model of disease, a model which has primarily been used for cancer, and more recently for amyotrophic lateral sclerosis (ALS). We applied the multi-step model to data on Covid-19 case fatality rates (CFRs) from China, South Korea, Italy, Spain and Japan. In all countries we found that a plot of ln (CFR) against ln (age) was approximately linear with a slope of about 5. As a comparison, we also conducted similar analyses for selected other respiratory diseases. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope, whereas seasonal and pandemic influenza showed quite different age-patterns. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. Identification of these steps would be potentially important for prevention and therapy for SARS-COV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.06.01.20116608v1?rss=1 doi: 10.1101/2020.06.01.20116608 id: cord-252103-lsaa1nx0 author: Pearks Wilkerson, Alison J title: Coronavirus outbreak in cheetahs: Lessons for SARS date: 2004-03-23 words: 956.0 sentences: 52.0 pages: flesch: 54.0 cache: ./cache/cord-252103-lsaa1nx0.txt txt: ./txt/cord-252103-lsaa1nx0.txt summary: To characterize the genomic disposition of the cheetahs'' Aju-CoV strain, PCR primers based on alignment of seven coronavirus gene segments (pol1a, pol1b, S, M, N, 7a/7b, and 3′ ′UTR), were used to amplify cDNA from archived cheetah liver and kidney tissues collected during the Winston outbreak. The phylogenetic analyses indicate a close similarity of the Aju-CoV and the FCoV strains, suggesting the cheetah virus is closely related to, if not indistinguishable from, domestic cat isolates. Fourth, while mortality among humans with SARS symptoms and house cats with FCoV is low, around 5-10%, cheetahs with Aju-CoV exhibited the opposite extreme, showing 90% morbidity and over 60% mortality. If this hypothesis is correct, the greater genetic diversity of domestic cats and humans may reduce the severity of the epidemic, and also contribute to the occurrence of rare genetically determined SARS-CoV super-spreaders who can infect with high virulence. abstract: nan url: https://api.elsevier.com/content/article/pii/S0960982204001435 doi: 10.1016/j.cub.2004.02.051 id: cord-354051-ro3o27pv author: Peccia, J. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 words: 1244.0 sentences: 101.0 pages: flesch: 57.0 cache: ./cache/cord-354051-ro3o27pv.txt txt: ./txt/cord-354051-ro3o27pv.txt summary: title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant. SARS-CoV-2 viral RNA concentrations were quantitatively compared with local hospital admission data and community COVID-19 compiled testing data. SARS-CoV-2 RNA sludge concentrations were quantitatively compared with data that are commonly used to track the community progression of COVID-19 including hospital admissions (Figure 2A This study uniquely utilized primary sewage sludge instead of raw wastewater for virus RNA measurements. abstract: We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples and, when adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99). SARS-CoV-2 RNA concentrations were a seven-day leading indicator ahead of compiled COVID-19 testing data and led local hospital admissions data by three days. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community. url: http://medrxiv.org/cgi/content/short/2020.05.19.20105999v1?rss=1 doi: 10.1101/2020.05.19.20105999 id: cord-327894-b0bsseui author: Pecellín, Lidia Gestoso title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 words: 4897.0 sentences: 446.0 pages: flesch: 56.0 cache: ./cache/cord-327894-b0bsseui.txt txt: ./txt/cord-327894-b0bsseui.txt summary: En respuesta a la COVID-19, el gobierno español inicialmente instó a limitar el contacto social como medida general, sin embargo, otros países, además, implementaron pruebas generalizadas para la infección por SARS-COV-2 desde el principio de la pandemia. Son test sencillos de hacer, pero deben ser interpretados con prudencia, en relación con el curso de la infección, sobre todo por la tasa de falsos negativos en la detección de IgM ya que la respuesta de IgM en un enfermo COVID-19 puede tardar en aparecer desde varios días a dos semanas 21 Algunos estudios han mostrado que durante los primeros 7 días desde el inicio de síntomas, menos de un 40% de pacientes presentan anticuerpos IgM detectables. abstract: En la actual crisis provocada por el SARS-CoV-2, surge la necesidad global de conocer y combatir el virus. Una de las estrategias es rastrear y diagnosticar los casos con el fin de aislar e interrumpir la cadena epidemiológica. Por ello, el objetivo de este artículo es describir las distintas pruebas diagnósticas más utilizadas y analizar su validez y recomendaciones de uso según la evidencia científica y las principales recomendaciones nacionales e internacionales de sociedades científicas y organismos de referencia. Desde el inicio de la pandemia la disponibilidad de test ha estado supeditada a las condiciones del propio mercado de fabricación y a las directrices marcadas en cada país. Entre los tipos de test más utilizados cabe destacar la PCR, los Tests de detección de anticuerpos (IgG e IGM) y anticuerpos totales (Ab), también conocidos como tests rápidos, y los tests de detección de antígenos en exudado naso-faríngeo u otras muestras respiratorias de vías altas/bajas. Para cada uno de estos tests, es necesario conocer sus recomendaciones de uso y el procedimiento para la toma de muestras, siendo fundamental para minimizar las alteraciones en los resultados debido a una manipulación deficitaria. Asimismo, se recomienda determinar el momento más adecuado para la toma de muestras y su adecuada interpretación de los resultados obtenidos, que siempre ha de ser considerada junto con la sintomatología del paciente para la toma de decisiones clínicas. In the current crisis caused by SARS-CoV-2, there is a global need to know and combat the virus. One of the strategies is to track and diagnose cases in order to isolate and interrupt the epidemiological chain. Therefore, the aim of this article is to describe the different most used diagnostic tests and analyze their validity and recommendations for use according to scientific evidence and the main national and international recommendations of scientific societies and reference organizations. Since the beginning of the pandemic, the availability of tests has been subject to the conditions of the manufacturing market itself and to the guidelines set in each country. Among the most used types of tests, it is worth highlighting PCR, antibody detection tests (IgG and IGM) and total antibodies (Ab), also known as rapid tests, and tests for the detection of antigens in nasopharyngeal exudate or other upper / lower respiratory samples. For each of these tests, it is necessary to know their recommendations for use and the procedure for taking samples, which is essential to minimize alterations in the results due to poor handling. Likewise, it is recommended to determine the most appropriate moment for taking samples and their adequate interpretation of the results obtained, which must always be considered together with the patient's symptoms for clinical decision-making. url: https://api.elsevier.com/content/article/pii/S1130862120304952 doi: 10.1016/j.enfcli.2020.10.001 id: cord-262266-m0fjt483 author: Peddu, Vikas title: Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization date: 2020-05-07 words: 1847.0 sentences: 110.0 pages: flesch: 53.0 cache: ./cache/cord-262266-m0fjt483.txt txt: ./txt/cord-262266-m0fjt483.txt summary: METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Eight unique patient samples consisting of six positive and two negative cases of suspected SARS-CoV-2 were sequenced using RNA extracted for a qRT-PCR diagnostic assay. Despite our reference database not containing any SARS-CoV-2 genomes, the six samples that were positive for SARS-CoV-2 by qRT-PCR had reads classified to Table 2) . Phylogenetic analysis revealed that the six SARS-CoV-2 sequences found cluster within two clades representing the Washington state and European outbreaks. abstract: BACKGROUND: More than two months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. RESULTS: Within 36 hours our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients’ respiratory symptoms. CONCLUSION: Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics. url: https://doi.org/10.1093/clinchem/hvaa106 doi: 10.1093/clinchem/hvaa106 id: cord-320970-ru2iw0py author: Peeling, Rosanna W title: Serology testing in the COVID-19 pandemic response date: 2020-07-17 words: 3669.0 sentences: 186.0 pages: flesch: 49.0 cache: ./cache/cord-320970-ru2iw0py.txt txt: ./txt/cord-320970-ru2iw0py.txt summary: On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. Point-of-care molecular assays for SARS-CoV-2 detection are now available to enable community-based testing for COVID-19 in LMICs. Unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving LMICs struggling for access. On the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. abstract: The collapse of global cooperation and a failure of international solidarity have led to many low-income and middle-income countries being denied access to molecular diagnostics in the COVID-19 pandemic response. Yet the scarcity of knowledge on the dynamics of the immune response to infection has led to hesitation on recommending the use of rapid immunodiagnostic tests, even though rapid serology tests are commercially available and scalable. On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. The WHO R&D Blue Print expert group identified eight priorities for research and development, of which the highest is to mobilise research on rapid point-of-care diagnostics for use at the community level. This research should inform control programmes of the required performance and utility of rapid serology tests, which, when applied specifically for appropriate public health measures to then be put in place, can make a huge difference. url: https://www.sciencedirect.com/science/article/pii/S147330992030517X doi: 10.1016/s1473-3099(20)30517-x id: cord-311207-qkkn0297 author: Pegoraro, Manuela title: Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness date: 2020-10-20 words: 1664.0 sentences: 92.0 pages: flesch: 46.0 cache: ./cache/cord-311207-qkkn0297.txt txt: ./txt/cord-311207-qkkn0297.txt summary: Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. In COVID-19 confirmed cases (symptomatic patient with SARS-CoV-2 positive molecular detection), date of symptoms onset was used to timing infection at the moment of specimens'' collection. Three stages were identified: early (0-7 days from symptoms onset), intermediate (8China), COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co., Ltd Huzhou, Zhejiang, China), and PRIMA Professional (PRIMA Lab SA, Balerbna, Switzerland) are lateral flow immunochromatographic assays. Sensitivities were assessed on confirmed COVID-19 cases, combining IgG and IgM/IgA positive results, while specificities were estimated on the group of healthy volunteer''s. Compared with the automated immunoassays, the ability of ICTs to detect anti-SARS-CoV-2 IgG was equivalent to that of CLIA-MAGLUMI and better than ELISA-Euroimmun, whose IgG positive rates ranged between 0 and 86% at 14 days after symptoms onset. abstract: Results of three rapid immunochromatographic tests (ICTs) were compared with those obtained with two automated immunoassays for evaluation of their usefulness. One hundred fifty-nine patients and 67 healthy volunteers were included. Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. ICTs could have a role as screening approach due to their easy usability. Subjective interpretation, significant rate of uncertain results, uncertainty on viral antigens source are undoubtedly drawbacks. url: https://www.ncbi.nlm.nih.gov/pubmed/33078222/ doi: 10.1007/s10096-020-04040-1 id: cord-260238-2p209g2p author: Peiris, J S M title: Severe acute respiratory syndrome date: 2004-11-30 words: 6296.0 sentences: 317.0 pages: flesch: 40.0 cache: ./cache/cord-260238-2p209g2p.txt txt: ./txt/cord-260238-2p209g2p.txt summary: Severe acute respiratory syndrome (SARS) was caused by a previously unrecognized animal coronavirus that exploited opportunities provided by ''wet markets'' in southern China to adapt to become a virus readily transmissible between humans. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Characterization of severe acute respiratory syndrome-associated coronavirus (SARS CoV) spike glycoprotein-mediated viral entry Severe acute respiratory syndrome associated coronavirus (SARS CoV) infection inhibition using spike protein heptad repeat-derived peptides Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAB to S1 protein that blocks receptor association abstract: Severe acute respiratory syndrome (SARS) was caused by a previously unrecognized animal coronavirus that exploited opportunities provided by 'wet markets' in southern China to adapt to become a virus readily transmissible between humans. Hospitals and international travel proved to be 'amplifiers' that permitted a local outbreak to achieve global dimensions. In this review we will discuss the substantial scientific progress that has been made towards understanding the virus—SARS coronavirus (SARS-CoV)—and the disease. We will also highlight the progress that has been made towards developing vaccines and therapies The concerted and coordinated response that contained SARS is a triumph for global public health and provides a new paradigm for the detection and control of future emerging infectious disease threats. url: https://www.ncbi.nlm.nih.gov/pubmed/15577937/ doi: 10.1038/nm1143 id: cord-260559-n8i52e8q author: Peiris, Malik title: What can we expect from first-generation COVID-19 vaccines? date: 2020-09-21 words: 1355.0 sentences: 87.0 pages: flesch: 41.0 cache: ./cache/cord-260559-n8i52e8q.txt txt: ./txt/cord-260559-n8i52e8q.txt summary: A popular assumption is that these vaccines will provide population immunity that can reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and lead to a resumption of pre-COVID-19 "normalcy". The immunological correlates of protection from SARS-CoV-2 infection and COVID-19 have yet to be elucidated. Pre-existing neutralising antibody seemed to have afforded protection against re-infection in people on board a fishing vessel where there was an outbreak of SARS-CoV-2 with a high infection attack rate. 20 Alongside the risks of severe morbidity and mortality and of disease transmission, this framework stipulates two additional criteria for equitable vaccine allocation-namely, risks of acquiring infection and of negative societal impact. If COVID-19 vaccines have acceptable effectiveness in reducing morbidity and mortality in high-risk groups, they would have an important role, irrespective of impact on transmission and population immunity. abstract: nan url: https://doi.org/10.1016/s0140-6736(20)31976-0 doi: 10.1016/s0140-6736(20)31976-0 id: cord-332827-gll4nqdd author: Peixe, Paula title: Hepatology in the COVID Era: Another C Virus, again Challenging the Liver date: 2020-04-30 words: 3989.0 sentences: 221.0 pages: flesch: 52.0 cache: ./cache/cord-332827-gll4nqdd.txt txt: ./txt/cord-332827-gll4nqdd.txt summary: In published series, liver disease was not identified as a risk factor for SARS-Cov2 infection [11] [12] [13] [14] [15] . The authors state that NAFLD patients also had a higher risk of progression to severe COVID-19 and present an increased viral clearance time. Immune-mediated liver diseases, particularly autoimmune hepatitis, have not been mentioned as risk factors for COVID-19, but the immunosuppressive treatment required has triggered fears about the risk of infection in patients. Extensive records and targeted studies are needed to explore multiple open-ended questions such as the severity and mortality of COVID-19 and episodes of acute-on-chronic or decompensation associated with the presence of this disease (ascites, hepatic encephalopathy, digestive bleeding, kidney dysfunction, and the risk of infection) or the response to treatment [25, 26] . However, it is not yet possible to say whether transplantation-associated immunosuppression can alter the predisposition for the acquisition of SARS-Cov2 infection or how COVID-19 evolves in these patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32775544/ doi: 10.1159/000508116 id: cord-331423-5wpx0bd0 author: Pelea, Teodor title: SARS-CoV-2 associated Guillain–Barré syndrome date: 2020-08-08 words: 2174.0 sentences: 126.0 pages: flesch: 50.0 cache: ./cache/cord-331423-5wpx0bd0.txt txt: ./txt/cord-331423-5wpx0bd0.txt summary: Presented herein is a severe case of SARS-CoV-2 associated Guillain–Barré syndrome (GBS), showing only slight improvement despite adequate therapy. Therefore patients with SARS-CoV-2 infection are at risk of being affected by coincident immune-mediated neurological diseases such as GBS. Severe course of GBS-associated SARS-CoV-2 infections occur also in patients with mild respiratory symptoms, but must be taken into account with seriously ill cases. To date, the previously described courses of the SARS-CoV-2 infection-associated GBS do not describe a special clinical pattern. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. abstract: Presented herein is a severe case of SARS-CoV-2 associated Guillain–Barré syndrome (GBS), showing only slight improvement despite adequate therapy. To date, only few cases of GBS associated with this infection have been described. This case report summarizes the insights gain so far to GBS with this antecedent trigger. So far, attention has mostly focused on complications of the CNS involvement. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should pay attention to symptoms of the peripheral nervous system. As far as we know from this reported case and the review of the current literature, there seems to be no association with antiganglioside antibodies or a positive SARS-CoV-2 RT-PCR in CSF. An obvious frequent occurrence of a bilateral facial weakness or bilateral peripheral facial diplegia should be emphasized. url: https://doi.org/10.1007/s00415-020-10133-w doi: 10.1007/s00415-020-10133-w id: cord-311696-ccbc1k1m author: Pelisser, Michel title: Sports balls as potential SARS-CoV-2 transmission vectors date: 2020-07-10 words: 2295.0 sentences: 111.0 pages: flesch: 55.0 cache: ./cache/cord-311696-ccbc1k1m.txt txt: ./txt/cord-311696-ccbc1k1m.txt summary: Sports objects can only harbour inactivated SARS-CoV-2 under specific, directly transferred conditions, but wiping with a dry tissue or moist ''baby wipe'' or dropping and rolling the balls removes all detectable viral traces. The transmission potential of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) includes exposure duration of the virus, the number of viral particles one is exposed to and the route of exposure such as inhalation or skin contact [1, 2] . When SARS-CoV-2 positive control materials at 1,000 and 5,000 dC/mL concentrations are applied onto the whole surface of sport balls using BD polyester swabs, there was no detectable levels of the virus when observing the variables imposed in the experiment, including very short term testing after 30 seconds. On the other hand, when positive control at 5,000 copies/mL and 10,000 copies/mL concentrations are directly applied to the surface of cricket ball there are detectable levels of the virus at 30 seconds, 5 minutes and 1 hour (experiment 3). abstract: Abstract Objects passed from one player to another have not been assessed for their ability to transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that the surface of sport balls, notably a football, tennis ball, golf ball, and cricket ball could not harbour inactivated virus when it was swabbed onto the surface, even for 30 seconds. However, when high concentrations of 5,000 dC/mL and 10,000 dC/mL are directly pipetted onto the balls, it could be detected after for short time periods. Sports objects can only harbour inactivated SARS-CoV-2 under specific, directly transferred conditions, but wiping with a dry tissue or moist ‘baby wipe’ or dropping and rolling the balls removes all detectable viral traces. This has helpful implications to sporting events. url: https://api.elsevier.com/content/article/pii/S2666535220300288 doi: 10.1016/j.puhip.2020.100029 id: cord-271411-h3k7r2ia author: Pelletier, Jesse S. title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination date: 2020-08-26 words: 1330.0 sentences: 82.0 pages: flesch: 46.0 cache: ./cache/cord-271411-h3k7r2ia.txt txt: ./txt/cord-271411-h3k7r2ia.txt summary: title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination We believe that, additionally, nasal and oral decontamination measures may be implemented to reduce viral aerosolization before it reaches barriers, surfaces, and fomites. Nasal and oral decontamination is currently a routine step used to reduce postoperative infectious contamination across many surgical subspecialties. Povidone-iodine (PVP-I) is nearly universally virucidal and has recently shown rapid in vitro inactivation of SARS-CoV-2. Clinical studies of PVP-I in vivo support a durable, protective effect against bacteria and possibly SARS-CoV-2. 12 Nasal and oral decontamination strategy should be effective and convenient for use in outpatient ophthalmic clinics and ambulatory surgery centers (ASCs) in both developed and developing countries alike. Rapid in-vitro inactivation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using povidone-iodine oral antiseptic rinse Is povidone iodine mouthwash effective against SARS-CoV-2? abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32923943/ doi: 10.1177/2515841420951392 id: cord-346512-y5d8q5b9 author: Pellicciaro, Marco title: Breast cancer patients with hormone neoadjuvant bridging therapy due to asymptomatic Corona virus infection. Case report, clinical and histopathologic findings date: 2020-10-08 words: 2050.0 sentences: 145.0 pages: flesch: 45.0 cache: ./cache/cord-346512-y5d8q5b9.txt txt: ./txt/cord-346512-y5d8q5b9.txt summary: INTRODUCTION: Breast cancer management during COVID-19 pandemic has changed and in case of COVID-19 patients with simultaneous neoplasia, it has been strongly recommended to treat Sars-CoV-2 infection firstly. According to COVID-19 breast cancer recommendations she underwent hormone neoadjuvant treatment as a bridging therapy for surgery. We report a case of woman with COVID-19 and simultaneous early breast cancer treated with neoadjuvant endocrine therapy in lieu of upfront surgery and with lymph node micrometastases at pathological examination. Immunohistochemical staining revealed strongly and diffusely ER and PR positive in tumor cells: <95% and 40% respectively ( Figure 1B Before COVID-19 pandemic, patient such as this, with clinical stage T1N0, hormone receptors positive HER2-negative breast cancer, would have been a candidate for upfront surgery [11] . Therefore, the use of bridging therapy in patients with early breast cancer, during pandemic, that could benefit from upfront surgery should be evaluated in large sample studies. abstract: INTRODUCTION: Breast cancer management during COVID-19 pandemic has changed and in case of COVID-19 patients with simultaneous neoplasia, it has been strongly recommended to treat Sars-CoV-2 infection firstly. Presentation of case: We reported a case of a 53-years-old women with early breast cancer and simultaneous asymptomatic SARS-CoV-2 infection. According to COVID-19 breast cancer recommendations she underwent hormone neoadjuvant treatment as a bridging therapy for surgery. Six months from the diagnosis, after virus eradication, patient underwent breast surgery. No SARS-CoV-2 RNA was found both in the surgical specimen and sentinel lymph node but micrometastasis were reported. During the last follow-up, the patient was in good clinical condition and started the adjuvant chemotherapy. DISCUSSION: COVID-19 outbreak determined the publication of temporary recommendation leading to an extensive use of neoadjuvant chemotherapy in breast cancer patients. Although endocrine therapy is a mainstay in the adjuvant treatment, its role in the neoadjuvant schedule is unclear. CONCLUSION: Upfront awake surgery should be preferred especially in asymptomatic COVID-19 patient with early breast cancer when monitoring of tumor response is not feasible. url: https://doi.org/10.1016/j.ijscr.2020.10.020 doi: 10.1016/j.ijscr.2020.10.020 id: cord-295029-zki5ac2g author: Pena, Robert C.F. title: In Reply to the Letter to the Editor Regarding “Coronavirus Neurosurgical/Head and Neck Drape to Prevent Aerosolization of Coronavirus Disease 2019 (COVID-19): The Lenox Hill Hospital/Northwell Health Solution” date: 2020-11-03 words: 1647.0 sentences: 93.0 pages: flesch: 38.0 cache: ./cache/cord-295029-zki5ac2g.txt txt: ./txt/cord-295029-zki5ac2g.txt summary: 1 This simple, cost-effective method can be easily assembled and is flexible with minimal disruption of the surgery being performed, while offering the ability to shield essential personnel in the operating room during procedures involving drilling of air-cells potentially harboring SARS-CoV-2 virions. 1,10 This draping method may therefore provide additional protection to surgeons against multiple viruses aerosolized by a wide range of drill settings, although further research should be conducted regarding COVID-19 aerosol generation in relation to drill speed in neurosurgical and otolaryngology-based procedures. Finally, whereas other researchers have proposed various methods of mask modification or alternate materials to provide barrier protection against COVID-19 aerosol transmission, 9 this and prior draping techniques may offer additional simple, easy to assemble, and cost-effective intraoperative protection. Specifically, this method provides protection to neurosurgical staff during high-speed drilling in the posterior fossa, whereas previously described drapes focus more on the restricted dissemination of COVID-19-laden aerosols during intubation, extubation, positive pressure ventilation, and endonasal endoscopic procedures. abstract: nan url: https://api.elsevier.com/content/article/pii/S1878875020318854 doi: 10.1016/j.wneu.2020.08.116 id: cord-280970-gy0kfhy6 author: Peng, Fujun title: Management and Treatment of COVID-19: The Chinese Experience date: 2020-04-17 words: 2618.0 sentences: 188.0 pages: flesch: 48.0 cache: ./cache/cord-280970-gy0kfhy6.txt txt: ./txt/cord-280970-gy0kfhy6.txt summary: Since mid-December 2019, there has been a worldwide outbreak of COronaVIrus Disease 90 (COVID)-19, caused by SARS-CoV-2 (formerly 2019-nCoV or and first detected in 91 Wuhan, China. 52 However, 421 a single-center in Wuhan shared that early, low-dose and short-term (1-2mg/kg/d for 5-7 days) 422 corticosteroids was associated with a faster improvement of clinical symptoms and absorption of 423 focal lung lesions in severe cases of COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Early, low-dose and short-term application of corticosteroid treatment in patients with severe COVID-19 pneumonia: single-center experience from Wuhan, China. abstract: With over 1,800,000 cases and 110,000 deaths globally, COVID-19 is one of worst infectious disease outbreaks in history. The objective of this paper is to critically review the available evidence regarding the lessons learned from the Chinese experience regarding COVID-19 prevention and management. The steps that have led to a near disappearance of new cases in China included rapid sequencing of the virus to establish testing kits which allowed tracking of infected persons in and out of Wuhan. In addition, aggressive quarantine measures included the complete isolation of Wuhan and then later Hebei and the rest of the country, as well as closure of all schools and non-essential businesses. Other measures included the rapid construction of two new hospitals and the establishment of Fangcang shelter hospitals. In the absence of a vaccine, the management of COVID-19 included antivirals, high flow oxygen, mechanical ventilation, corticosteroids, hydroxychloroquine, tocilizumab, interferons, intravenous immunoglobulin and convalescent plasma infusions. These measures appeared to provide only moderate success. While some measures have been supported by weak descriptive data, their effectiveness is still unclear pending well-controlled clinical trials. In the end, it was the enforcement of drastic quarantine measures that stopped SARS-CoV-2 from spreading. The earlier the implementation, the less likely resources will be depleted. The most critical factors in stopping a pandemic are early recognition of infected individuals, carriers and contacts, and early implementation of quarantine measures with an organized, proactive and unified strategy at a national level. Delays result in significantly higher death tolls. url: https://doi.org/10.1016/j.cjca.2020.04.010 doi: 10.1016/j.cjca.2020.04.010 id: cord-264260-8p6pvjkn author: Peng, Hongbing title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report date: 2020-07-16 words: 3163.0 sentences: 161.0 pages: flesch: 49.0 cache: ./cache/cord-264260-8p6pvjkn.txt txt: ./txt/cord-264260-8p6pvjkn.txt summary: title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report We note that the intravenous infusion of CP and MSCs for the treatment of severe COVID-19 patients may have synergistic characteristics in inhibiting cytokine storm, promoting the repair of lung injury, and recovering pulmonary function. We reviewed a case of severe COVID-19 cured successfully with convalescent plasma-umbilical cord mesenchymal stem cells and observed and analyzed the change of clinical symptoms and laboratory data before and after treatment. From admission to discharge, the researchers continue to observe and evaluate patients'' dynamic changes in clinical symptoms and laboratory results, especially after receiving plasma and stem cell therapy. Intravenous infusion of human umbilical cord Wharton''s jelly-derived mesenchymal stem cells as a potential treatment for patients with COVID-19 pneumonia abstract: Acute respiratory distress syndrome virus-2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) infection, which causes global public health emergencies, has sped widely for more than 5 months and has the risk of long-term transmission. No effective treatment has been discovered to date. In the cases we report, the patient continued to deteriorate even after administration of antiviral drugs such as lopinavir/ritonavir, interferon-α, and ribavirin, as well as intravenous injection of meropenem, methylprednisolone, and immunoglobulin. So, we infused the patient with convalescent plasma (CP), and the absolute lymphocyte count increased the next day and returned to normal on the fourth day. Followed by intravenous infusion of mesenchymal stem cells (MSCs), bilateral infiltrates were absorbed and the pulmonary function was significantly improved. We note that the intravenous infusion of CP and MSCs for the treatment of severe COVID-19 patients may have synergistic characteristics in inhibiting cytokine storm, promoting the repair of lung injury, and recovering pulmonary function. We hope to provide a reference for the research direction of COVID-19 clinical strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32678017/ doi: 10.1186/s13287-020-01802-8 id: cord-297365-11es4w0u author: Peng, Hui title: Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes date: 2020-05-07 words: 1697.0 sentences: 113.0 pages: flesch: 56.0 cache: ./cache/cord-297365-11es4w0u.txt txt: ./txt/cord-297365-11es4w0u.txt summary: METHODS: We retrospectively summarized the characteristics, treatment and outcomes of pediatric cases in Wuhan children''s hospital which was the only designated hospital for children with COVID-19 in Hubei Province. In December 2019, a cluster of cases caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Wuhan, Hubei The observed cases were pediatric patients who were discharged from the Wuhan Children''s Hospital from December 8, 2019 to February 29, 2020 and diagnosed with COVID-19. Chinese Center for Disease Control and Prevention has analyzed the illness severity of 44415 adult and pediatric patients, and found that severe and critical cases accounted for nearly 20% [9] . A epidemiological study in Chinese children with COVID-19 (n=2143) showed that severe and critical illness accounted for J o u r n a l P r e -p r o o f 5.8% [10, 11] . Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study abstract: BACKGROUND: At present, coronavirus disease 2019 (COVID-19) has spread in many countries. We conducted this study to help paediatricians To help pediatricians understand the conditions of COVID-19 in children, we conducted this study. METHODS: We retrospectively summarized the characteristics, treatment and outcomes of pediatric cases in Wuhan children's hospital which was the only designated hospital for children with COVID-19 in Hubei Province. A Cox proportional hazards regression analysis was used to evaluate factors associated with clinical outcomes. RESULTS: As of February 29, 75 children had been discharged, of which only one was has severe pneumonia and one was critical cases. Children younger than 2 years were more susceptible to COVID-19. All patients have received interferon-α nebulization, and eight cases including the severe and critical cases were co-administrated ribavirin. Five patients with mild pneumonia were given arbidol. Twenty-three patients were given traditional Chinese medicine (TCM). The average length of stay (LOS) and the time of SARS-CoV-2 clearance were 10.57 and 6.39 days, respectively. None of the factors was associated with LOS or time of SARS-CoV-2 clearance. CONCLUSIONS: The severity of COVID-19 in pediatric cases were milder than adults. The efficacy of the antiviral therapy in children with COVID-19 remains to be evaluated. url: https://www.ncbi.nlm.nih.gov/pubmed/32446167/ doi: 10.1016/j.jcv.2020.104425 id: cord-317573-wp2wr3b5 author: Peng, Hui title: Human memory T cell responses to SARS-CoV E protein date: 2006-06-30 words: 4124.0 sentences: 197.0 pages: flesch: 60.0 cache: ./cache/cord-317573-wp2wr3b5.txt txt: ./txt/cord-317573-wp2wr3b5.txt summary: In this study, we found that peripheral blood mononuclear cells (PBMCs) from fully recovered SARS individuals rapidly produced IFN-γ and IL-2 following stimulation with a pool of 9 peptides overlapping the entire E protein sequence. To assess memory T cell response specific for E protein after SARS-CoV infection in humans, PBMCs from individuals who had fully recovered from SARS two years after infection were stimulated with a pool of 9 peptides spanning the entire amino acid sequence of the SARS-CoV E protein, or the cells were stimulated with anti-CD3 and anti-CD28 antibodies under the same culture conditions as positive controls. Similarly, the frequency of SARS-CoV E antigen-specific IFN-g-producing cells determined by IFN-g ELISPOT assay in PBMCs from 8 fully recovered SARS individuals was significantly higher than that of the cells from the normal donor controls in response to E peptides (Fig. 1B) . abstract: E protein is a membrane component of severe acute respiratory syndrome coronavirus (SARS-CoV). Disruption of E protein may reduce viral infectivity. Thus, the SARS-CoV E protein is considered a potential target for the development of antiviral drugs. However, the cellular immune responses to E protein remain unclear in humans. In this study, we found that peripheral blood mononuclear cells (PBMCs) from fully recovered SARS individuals rapidly produced IFN-γ and IL-2 following stimulation with a pool of 9 peptides overlapping the entire E protein sequence. Analysis of the immune responses by flow cytometry showed that both CD4(+) and CD8(+)T cells were involved in the SARS-CoV E-specific immune responses after stimulation with SARS-CoV E peptides. Moreover, the majority of IFN-γ(+)CD4(+)T cells were central memory cells expressing CD45RO(+)CCR7(+)CD62L(−); whereas IFN-γ(+)CD8(+) memory T cells were mostly effector memory cells expressing CD45RO(−)CCR7(−)CD62L(−). The results of T-cell responses to 9 individual peptides indicated that the E protein contained at least two major T cell epitopes (E2 amino acid [aa] 9–26 and E5–6: aa 33–57) which were important in eliciting cellular immune response to SARS-CoV E protein in humans. url: https://www.ncbi.nlm.nih.gov/pubmed/16844400/ doi: 10.1016/j.micinf.2006.05.008 id: cord-281860-zjvrohgg author: Peng, Jing title: Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2 date: 2020-09-18 words: 2493.0 sentences: 122.0 pages: flesch: 51.0 cache: ./cache/cord-281860-zjvrohgg.txt txt: ./txt/cord-281860-zjvrohgg.txt summary: Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. To address this, we treated clinical sputum specimens with four commonly used reagents-saline, NALC, PK, and DTT, prior to NA extraction, and compared their performance in diagnosing COVID-19 in real practice. With the sputum samples collected from the 47 patients having non-COVID-19 diseases, no amplification curves were observed for either the ORF1ab or N gene under any treatment conditions (saline, NALC, PK, and DTT), suggesting no SARS-CoV-2 in these samples. According to the positive criteria described in the methods section, pretreatment of sputum samples with NALC, PK, and DTT increased the detection of SARS-CoV-2 + cases to 85.7% (18/21), 95.2% (20/21), and 95.2% (20/21), respectively, as compared to the 52.4% (11/21) obtained with saline pretreated sputum (see Table 1 ). abstract: One of the primary tools for diagnosing COVID-19 is the nucleic acid-based real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test performed on respiratory specimens. The detection rate of SARS-CoV-2 in lower respiratory specimens (such as sputum) is higher than that for upper respiratory specimens (such as nasal and pharyngeal swabs). However, sputum specimens are usually quite viscous, requiring a homogenization process prior to nucleic acid (NA) extraction for RT-PCR. Sputum specimens from COVID-19 and non-COVID-19 patients were treated with four commonly used reagents—saline, N-acetyl-L-cysteine (NALC), proteinase K (PK), and dithiothreitol (DTT), prior to NA extraction. These reagents were then compared for their performance in diagnosing COVID-19 in real clinical practice. The detection rate of SARS-CoV-2 in PK- or DTT-treated sputum was comparable, and higher than that in sputum treated with NALC or saline. While there was a 4.8% (1/21) false negative rate for the PK- and DTT-treated sputum, neither treatment showed any false positive cases among patients with non-COVID diseases. Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. Taken together, we provide direct evidence recommending the use of PK or DTT to pretreat sputum samples to facilitate SARS-CoV-2 detection by clinical laboratories. Moreover, our methods should help to standardize the procedure of processing sputum specimens and improve the ability to detect SARS-CoV-2 in these samples. url: https://www.ncbi.nlm.nih.gov/pubmed/33043036/ doi: 10.3389/fmed.2020.549860 id: cord-318036-t05ummop author: Peng, Liang title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples date: 2020-02-25 words: 1000.0 sentences: 84.0 pages: flesch: 60.0 cache: ./cache/cord-318036-t05ummop.txt txt: ./txt/cord-318036-t05ummop.txt summary: title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples We aim to detect SARS-CoV-2 nucleic acid from urine, blood, anal swab and oropharyngeal swab samples. Nine patients confirmed diagnosed with SARS-CoV-2 infection(2) were included in this prospective study. https://doi.org/10.1101/2020.02.21.20026179 doi: medRxiv preprint enrolled patients were obtained and detected SARS-CoV-2 RNA level by quantitative real-time polymerase chain reaction (qRT-PCR). Patient 7, a 31 years old female without any urinary irritation, had positive results of SARS-CoV-2 in both urine and oropharyngeal swab on the 7 th day after symptom onset. Patient 8 had three positive results in blood, anal swab and oropharyngeal swab on the 3 rd day after onset. In our study, urine, blood, anal swab and oropharyngeal swab from 9 patients were retested by qRT-PCR. Nevertheless, the relative symptoms, including diarrhea and urinary irritation did not happen to every patient with virus in anal swab and urine specimens. abstract: We tested samples collected from nine patients diagnosed with coronavirus disease 2019 (COVID-19). The virus was found in urine, blood, anal swabs and oropharyngeal swabs. It is the first time for SARS-CoV-2 found in urine, though no urinary irritation was found. url: https://doi.org/10.1101/2020.02.21.20026179 doi: 10.1101/2020.02.21.20026179 id: cord-286573-k4khwvt7 author: Peng, Michael title: The Role of the Ocular Tissue in SARS-CoV-2 Transmission date: 2020-10-02 words: 4362.0 sentences: 305.0 pages: flesch: 54.0 cache: ./cache/cord-286573-k4khwvt7.txt txt: ./txt/cord-286573-k4khwvt7.txt summary: Here, we reviewed both clinical and research evidence on the ocular manifestations associated with COVID-19, the presence of SARS-CoV-2 in ocular surface tissues and tears, and the potential role of the eye in contracting SARS-CoV-2. For this review, relevant studies that emphasized ocular manifestations of COVID-19 or SARS-CoV-2, viral detection of SARS-CoV-2 in ocular surface secretions or tears, and ACE2 presence in ocular tissues were included. 29 Zhang et al also reported that one of the two COVID-19 patients with conjunctivitis was SARS-CoV-2 RNA positive in the tear sample. Similarly, in a cross sectional study of 33 COVID-19 patients, most of the ocular samples were collected more than 7 days of symptom onset, and Xie et al found only 2 cases with positive ocular SARS-CoV-2 RNA results. 44 Recent studies have attempted to determine ACE2 in ocular surface tissues, such as the conjunctiva and cornea, which are exposed to the external environment and are potential entry points for SARS-CoV-2 infection. abstract: The current global pandemic of coronavirus disease 2019 (COVID-19) has affected over 21 million people and caused over half a million deaths within a few months. COVID-19 has become one of the most severe public health crises in recent years. Compared to other pathogenic coronaviruses, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly infectious. Due to the lack of specific and effective treatment or vaccines, disease prevention and early detection are essential for establishing guidelines to mitigate further spread. The potential role of the ocular system in COVID-19 is still not clear but it has gained increasing attention. Here, we reviewed both clinical and research evidence on the ocular manifestations associated with COVID-19, the presence of SARS-CoV-2 in ocular surface tissues and tears, and the potential role of the eye in contracting SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33061288/ doi: 10.2147/opth.s269868 id: cord-312065-nqy7m38f author: Peng, Philip W. H. title: Infection control and anesthesia: Lessons learned from the Toronto SARS outbreak date: 2003 words: 4582.0 sentences: 384.0 pages: flesch: 66.0 cache: ./cache/cord-312065-nqy7m38f.txt txt: ./txt/cord-312065-nqy7m38f.txt summary: PURPOSE: To describe the outbreak of severe acute respiratory syndrome (SARS) in Toronto, its impact on anesthesia practice and the infection control guidelines adopted to manage patients in the operating room (OR) and to provide emergency intubation outside the OR. S of July 10, 2003, 438 cases (250 probable, 188 suspect) of severe acute respiratory syndrome (SARS) were reported in Canada, 375 (85.3%) of which occurred in Ontario. Because of early reports of clusters of cases in community settings such as apartment buildings and the high infection rates among health care workers in Hong Kong, Taiwan, Hanoi and Toronto, the etiological agent of SARS was thought to be highly contagious. Time should be allowed for the anesthesiologist and assistant to remove contaminated gloves, gowns, face shields or masks and head cover and renew protective precautions at the end of the case. abstract: PURPOSE: To describe the outbreak of severe acute respiratory syndrome (SARS) in Toronto, its impact on anesthesia practice and the infection control guidelines adopted to manage patients in the operating room (OR) and to provide emergency intubation outside the OR. CLINICAL FEATURES: The SARS outbreak in Toronto was the result of a single index patient. The causative virus, SARS-CoV, is moderately contagious, and is spread by droplets and contact. The virus gains access to host through the mucosa of the respiratory tract and the eyes. It can affect both healthy and compromised patients. The use of several precautionary measures such as goggles, gloves, gowns and facemasks and the application of various infection control strategies designed to minimize the spread of the virus are discussed. CONCLUSION: In containing the spread of SARS, vigilance and strict infection control are important. This results in the rediscovery of standards of infection control measures in daily anesthesia practice. url: https://www.ncbi.nlm.nih.gov/pubmed/14656775/ doi: 10.1007/bf03018361 id: cord-280994-w8dtfjel author: Peng, Qi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 words: 2105.0 sentences: 135.0 pages: flesch: 55.0 cache: ./cache/cord-280994-w8dtfjel.txt txt: ./txt/cord-280994-w8dtfjel.txt summary: Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus. The viral polymerase is a promising antiviral target. However, the structure of COVID-19 virus polymerase is yet unknown. Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate a well adaptation of COVID-19 virus towards humans with relatively lower body temperatures than the natural bat hosts. url: https://doi.org/10.1101/2020.04.23.057265 doi: 10.1101/2020.04.23.057265 id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 words: 7697.0 sentences: 348.0 pages: flesch: 49.0 cache: ./cache/cord-351482-hzh5tyoo.txt txt: ./txt/cord-351482-hzh5tyoo.txt summary: The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). abstract: We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22086488/ doi: 10.1128/mbio.00198-11 id: cord-311358-nrj4aysh author: Peng, Yuzhu title: Is novel coronavirus disease (COVID‐19) transmitted through conjunctiva? date: 2020-03-16 words: 346.0 sentences: 35.0 pages: flesch: 58.0 cache: ./cache/cord-311358-nrj4aysh.txt txt: ./txt/cord-311358-nrj4aysh.txt summary: In theory, the premise for transmission through conjunctiva is that SARS-CoV-2 can replicate in conjunctival epithelia. 7 Currently it is unknown whether conjunctival epithelia can express ACE2. However, oral, nasal, and nasopharyngeal epithelia do not express ACE2, 8 which can explain that most of the COVID-19 patients did not have upper respiratory symptoms. It has been proposed that ''''2019-nCoV transmission through the ocular surface must not be ignored'''' based on the nosocomial infection of some ophthalmologists and an expert who wore an N95 mask but did not wear anything to protect his eyes was infected with SARS-CoV-2. Moreover, the inEvaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical characteristics of 50466 hospitalized patients with 2019-nCoV infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32176356/ doi: 10.1002/jmv.25753 id: cord-288758-onis9xmo author: Peng, Z. title: Exhaled CO2 as COVID-19 infection risk proxy for different indoor environments and activities date: 2020-09-10 words: 3167.0 sentences: 191.0 pages: flesch: 58.0 cache: ./cache/cord-288758-onis9xmo.txt txt: ./txt/cord-288758-onis9xmo.txt summary: Contrary to some earlier recommendations setting a single indoor CO2 threshold, we show that the CO2 level corresponding to a given infection risk varies by over 2 orders of magnitude for different environments and activities. Although large uncertainties, mainly from virus exhalation rates, are still associated with our infection risk estimates, our study provides more specific and practical recommendations for low-cost CO2-based indoor infection risk monitoring. In this study, we derive the analytical expressions of the probability of indoor COVID-19 infection through room-level aerosol transmission only (i.e., assuming social distance is kept so that close proximity aerosol and droplet pathways are eliminated; fomite transmission is not included), human-exhaled CO2 concentration, and subsequently a few CO2-based quantities as infection risk proxies. where N is number of occupants, Ep is the SARS-CoV-2 exhalation rate by an infector (quanta h -1 ), mex mask filtration efficiency for exhalation, V indoor environment volume (m 3 ), and λ firstorder virus loss rate coefficient (h -1 ) that includes the ventilation with outdoor air and all other virus removal and deactivation processes. abstract: CO2 is co-exhaled with aerosols containing SARS-CoV-2 by COVID-19 infected people and can be used as a proxy of SARS-CoV-2 concentrations indoors. Indoor CO2 measurements by low-cost sensors hold promise for mass monitoring of indoor aerosol transmission risk for COVID-19 and other respiratory diseases. We derive analytical expressions of CO2-based risk proxies and apply them to various typical indoor environments. Contrary to some earlier recommendations setting a single indoor CO2 threshold, we show that the CO2 level corresponding to a given infection risk varies by over 2 orders of magnitude for different environments and activities. Although large uncertainties, mainly from virus exhalation rates, are still associated with our infection risk estimates, our study provides more specific and practical recommendations for low-cost CO2-based indoor infection risk monitoring. url: https://doi.org/10.1101/2020.09.09.20191676 doi: 10.1101/2020.09.09.20191676 id: cord-315730-fzgxuak7 author: Penman, Sophie L. title: Safety perspectives on presently considered drugs for the treatment of COVID‐19 date: 2020-07-17 words: 12067.0 sentences: 627.0 pages: flesch: 42.0 cache: ./cache/cord-315730-fzgxuak7.txt txt: ./txt/cord-315730-fzgxuak7.txt summary: Owing to their efficacy against viruses (mostly demonstrated in vitro) including influenza, HIV, coronavirus OC43, and SARS-CoV, a large number of clinical trials (>230) have been registered worldwide using chloroquine/hydroxychloroquine alone, or in combination with other drugs (e.g. azithromycin) for the treatment of COVID-19. At the time of writing, the RECOVERY trial (clinical trial identifier NCT04381936) which is the largest randomised control trial so far conducted for the treatment of COVID, has stopped recruiting to the hydroxychloroquine arm (1542 patients compared with 3132 on standard care) because of no beneficial effect either in terms of mortality or hospital stay (P. Assessment of QT Intervals in a Case Series of Patients With Coronavirus Disease 2019 (COVID-19) Infection Treated With Hydroxychloroquine Alone or in Combination With Azithromycin in an Intensive Care Unit Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: Intense effort is underway to evaluate potential therapeutic agents for the treatment of COVID‐19. In order to respond quickly to the crisis, the repurposing of existing drugs is the primary pharmacological strategy. Despite the urgent clinical need for these therapies, it is imperative to consider potential safety issues. This is important due to the harm‐benefit ratios that may be encountered when treating COVID‐19, which can depend on the stage of the disease, when therapy is administered and underlying clinical factors in individual patients. Treatments are currently being trialled for a range of scenarios from prophylaxis (where benefit must greatly exceed risk) to severe life‐threatening disease (where a degree of potential risk may be tolerated if it is exceeded by the potential benefit). In this perspective, we have reviewed some of the most widely‐researched repurposed agents in order to identify potential safety considerations using existing information in the context of COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32681537/ doi: 10.1111/bph.15204 id: cord-269612-pmzdovna author: Pennington, Hugh title: Politics, media and microbiologists date: 2004 words: 3821.0 sentences: 177.0 pages: flesch: 52.0 cache: ./cache/cord-269612-pmzdovna.txt txt: ./txt/cord-269612-pmzdovna.txt summary: Studies on the SARS outbreak in Hong Kong 1 -after the exclusion of two ''superspread'' events where special circumstances allowed index cases to infect many individuals (at the Prince of Wales Hospital and at the Amoy Gardens estate) -gave an estimated R 0 value of 2.7. From analyses of samples taken from Vietnam, Singapore and Hong Kong, laboratories in the network ruled out the possibility of infection by any of the known influenza virus strains or other established causes of pneumonia, and concluded that SARS was new. It meant that the Hong Kong Department of Health, Hospital Authority and laboratory surveillance facility 11 , and the WHO, were particularly well prepared to respond to the SARS outbreak. In March 1997, an outbreak of avian influenza caused by the A virus subtype H5N1 killed several thousand chickens in three rural Hong Kong chicken farms. abstract: Severe acute respiratory syndrome (SARS) took everybody by surprise. Its emergence was one of the most significant microbiological events of 2003. It challenged microbiologists to identify the aetiological agent and satisfy Koch's postulates — in so far as they ever can be met for a virus — in real time. Not only were the patients' respiratory secretions and the agents grown in cultured cells put under the microscope, but so were the actions of politicians. What lessons can we learn from SARS? url: https://www.ncbi.nlm.nih.gov/pubmed/15083161/ doi: 10.1038/nrmicro846 id: cord-311847-2czqs84q author: Pennisi, Manuela title: SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms date: 2020-07-31 words: 9002.0 sentences: 433.0 pages: flesch: 40.0 cache: ./cache/cord-311847-2czqs84q.txt txt: ./txt/cord-311847-2czqs84q.txt summary: Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). Although there are limitations in the epidemiological studies carried on COVID-19, as well as limited case records for determining the actual incidence of these complications, some patients reported neurological symptoms, but clinical findings and pathogenic features have not yet systematically addressed. The aims of this review are i) to summarize the available information on the relationship between CoVs and the nervous system, ii) to identify the potential targets and routes of entry of SARS-CoV-2 into the nervous system, and iii) to describe the range of the neurological features reported to date in patients with COVID-19 and the proposed pathogenic mechanisms. Indeed, no axonal transport of SARS-CoV-2 to the brain has been demonstrated in the hamster model during the first two weeks after infection [89] , and no viral accumulation or persistence has been reported in cerebral olfactory regions of autopsy material from patients with COVID-19 [90] . abstract: Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). However, findings available on its neurological manifestations and their pathogenic mechanisms have not yet been systematically addressed. A literature search on neurological complications reported in patients with COVID-19 until June 2020 produced a total of 23 studies. Overall, these papers report that patients may exhibit a wide range of neurological manifestations, including encephalopathy, encephalitis, seizures, cerebrovascular events, acute polyneuropathy, headache, hypogeusia, and hyposmia, as well as some non-specific symptoms. Whether these features can be an indirect and unspecific consequence of the pulmonary disease or a generalized inflammatory state on the CNS remains to be determined; also, they may rather reflect direct SARS-CoV-2-related neuronal damage. Hematogenous versus transsynaptic propagation, the role of the angiotensin II converting enzyme receptor-2, the spread across the blood-brain barrier, the impact of the hyperimmune response (the so-called “cytokine storm”), and the possibility of virus persistence within some CNS resident cells are still debated. The different levels and severity of neurotropism and neurovirulence in patients with COVID-19 might be explained by a combination of viral and host factors and by their interaction. url: https://www.ncbi.nlm.nih.gov/pubmed/32751841/ doi: 10.3390/ijms21155475 id: cord-351430-bpv7p7zo author: Pequeno, Pedro title: Air transportation, population density and temperature predict the spread of COVID-19 in Brazil date: 2020-06-03 words: 4780.0 sentences: 222.0 pages: flesch: 47.0 cache: ./cache/cord-351430-bpv7p7zo.txt txt: ./txt/cord-351430-bpv7p7zo.txt summary: Further, we considered the following predictors: (1) time in days, to account for the exponential growth in case numbers during this period (Fig. 2) ; (2) number of arriving flights in the city''s metropolitan area in 2020, as airline connections can facilitate the spread of the virus (Ribeiro et al., 2020) ; (3) city population density, to account for facilitation of transmission under higher densities (Poole, 2020) ; (4) proportion of elderly people (≥60 years old) in the population, assuming that the elderly may be more likely to show severe symptoms of SARS-CoV-2 and, thus, to be diagnosed with COVID-19; (5) citizen mean income, which may affect the likelihood of people being infected by the virus, for example, due to limited access to basic sanitation or limited social isolation capabilities; (6) and the following meteorological variables: mean daily temperature ( C), mean daily solar radiation (kJ/m 2 ), mean daily relative humidity (%) and mean daily precipitation (mm). abstract: There is evidence that COVID-19, the disease caused by the betacoronavirus SARS-CoV-2, is sensitive to environmental conditions. However, such conditions often correlate with demographic and socioeconomic factors at larger spatial extents, which could confound this inference. We evaluated the effect of meteorological conditions (temperature, solar radiation, air humidity and precipitation) on 292 daily records of cumulative number of confirmed COVID-19 cases across the 27 Brazilian capital cities during the 1st month of the outbreak, while controlling for an indicator of the number of tests, the number of arriving flights, population density, proportion of elderly people and average income. Apart from increasing with time, the number of confirmed cases was mainly related to the number of arriving flights and population density, increasing with both factors. However, after accounting for these effects, the disease was shown to be temperature sensitive: there were more cases in colder cities and days, and cases accumulated faster at lower temperatures. Our best estimate indicates that a 1 °C increase in temperature has been associated with a decrease in confirmed cases of 8%. The quality of the data and unknowns limit the analysis, but the study reveals an urgent need to understand more about the environmental sensitivity of the disease to predict demands on health services in different regions and seasons. url: https://doi.org/10.7717/peerj.9322 doi: 10.7717/peerj.9322 id: cord-263039-uoxaem82 author: Perchetti, Garrett A. title: Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection date: 2020-07-23 words: 664.0 sentences: 42.0 pages: flesch: 58.0 cache: ./cache/cord-263039-uoxaem82.txt txt: ./txt/cord-263039-uoxaem82.txt summary: Nucleic acid degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can compromise the accuracy of molecular detection methods. It has been demonstrated that nasopharyngeal specimens containing SARS-CoV-2 can be stored in phosphate-buffered saline (PBS) as a substitute for viral transport medium (VTM) for up to 7 days (3). Here, we evaluate the stability of differing viral loads of SARS-CoV-2 over 28 days stored at room temperature, 4°C, -20°C, or -80°C. For the high concentration of SARS-CoV-2, regardless of storage conditions, 100% of samples were detected by qRT-PCR through day 28. For lower concentrations of virus, storage at room temperature was associated with reductions of positivity beginning at day 7, and by day 28, 0% of samples were detected for N1. At viral loads of Ͼ5,000 copies/ ml-corresponding to Ͼ75% of positive samples recovered in our clinical lab to date-different storage temperatures did not have a substantial impact on our ability to detect SARS-CoV-2 when stored in PBS. abstract: RNA viruses often require "cold-chains" of transportation to prevent the breakdown of genetic material.…. url: https://doi.org/10.1128/jcm.01094-20 doi: 10.1128/jcm.01094-20 id: cord-340336-u59l0taa author: Perchetti, Garrett A. title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date: 2020-06-08 words: 1390.0 sentences: 99.0 pages: flesch: 50.0 cache: ./cache/cord-340336-u59l0taa.txt txt: ./txt/cord-340336-u59l0taa.txt summary:  -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control. abstract: BACKGROUND: The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. The pandemic's initial challenges include broad diagnostic testing, consistent reagent supply lines, and access to laboratory instruments and equipment. In early 2020, primer/probe sets distributed by the CDC utilized the same fluorophore for molecular detection - requiring multiple assays to be run in parallel - consuming valuable and limited resources. METHODS: Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) - a CDC-based quantitative reverse transcriptase PCR reaction - and analyzed for agreement between the multiplexed assay. Laboratory- confirmed respiratory infection samples were included to evaluate assay cross-reaction specificity. RESULTS: Triplexing correctly identified SARS-CoV-2 in 98.4% of confirmed positive or inconclusive patient samples by single-plex LDT (n = 183/186). All 170 SARS-CoV-2 negative samples tested by single-plex LDT were negative by triplexing. Other laboratory-confirmed respiratory infections did not amplify for SARS-CoV-2 in the triplex reaction. CONCLUSIONS: Multiplexing two virus-specific gene targets and an extraction control was found to be comparable to running parallel assays independently, while significantly improving assay throughput. url: https://www.sciencedirect.com/science/article/pii/S1386653220302419?v=s5 doi: 10.1016/j.jcv.2020.104499 id: cord-318483-il5aq8py author: Perez Gaxiola, G. title: Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa date: 2020-07-11 words: 1758.0 sentences: 125.0 pages: flesch: 54.0 cache: ./cache/cord-318483-il5aq8py.txt txt: ./txt/cord-318483-il5aq8py.txt summary: Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children admitted with COVID-19 to a secondary hospital. Although the prevalence of COVID-19 in childhood represents a low percentage of the totality of reported cases, varying between 0.8% and 2.7% (9) (10) (11) , the number of children that may become affected and the different clinical presentation of the disease compared to the adult population (4, 12) may be a challenge for pediatricians and general practitioners. The objectives of this study were to describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic in the region, and of a subset of those children admitted with COVID-19 to Sinaloa Pediatric Hospital (Hospital Pediátrico de Sinaloa "Dr. Rigoberto Aguilar Pico", HPS). This case series describes the clinical and epidemiological characteristics of children infected by SARS-CoV-2 during the first three months of the pandemic in the state of Sinaloa. abstract: Background: The SARS-CoV-2 virus may affect both adults and children. Although the disease, named COVID-19, has a lower prevalence in infancy and has been described as mild, the clinical characteristics may vary and there is a possibility of complications. Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children admitted with COVID-19 to a secondary hospital. Methods: This case series includes all patients with SARS-CoV-2 infection confirmed by PCR testing, identified in the state epidemiological surveillance system between March 1 and May 31, 2020. Confirmed patients admitted to the Sinaloa Pediatric Hospital (HPS) during the same dates are also described. Results: Fifty one children with SARS-CoV-2 were included, 10 of the admitted to HPS. The median age was 10 years. The more frequent symptoms were fever (78%), cough (67%) and headache (57%). Most cases were mild or asymptomatic. Three patients with comorbidities died. Only 4 of 10 patients identified in HPS had been admitted with the diagnosis of possible COVID-19. Conclusions: SARS-CoV-2 infection in children was mostly mild or asymptomatic, but with a wide range of clinical presentations. url: https://doi.org/10.1101/2020.07.07.20146332 doi: 10.1101/2020.07.07.20146332 id: cord-301216-a0rkpez7 author: Perez, Adriana title: Presentation of SARS-CoV-2 Infection As Cholestatic Jaundice in Two Healthy Adolescents date: 2020-07-23 words: 1667.0 sentences: 117.0 pages: flesch: 49.0 cache: ./cache/cord-301216-a0rkpez7.txt txt: ./txt/cord-301216-a0rkpez7.txt summary: Liver abnormalities in severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, including hepatitis and cholestasis, have been observed in adults and is associated with worse outcomes. As of June 25, 2020, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) resulted in >9.4 million confirmed cases worldwide and > 482,000 deaths worldwide, including > 2.3 million cases and > 121,000 deaths reported in the US, among which were 84 pediatric deaths in persons < 24 years of age by June 13 2020. The incidence of liver injury in adult patients with COVID-19 has been ranges from 14.8% -53%(, being more significant in severe cases and ranging up to 78% among fatal cases.(10) Liver abnormalities described included elevation of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST), mildly elevated bilirubin levels, high gamma-glutamyl transferase (GGT) and low albumin levels (2.6-3.3 g/L) (10, 11) . We present two cases of acute hepatitis with clinically apparent jaundice and cholestasis without biliary obstruction associated with SARS-CoV-2 infection. abstract: nan url: https://doi.org/10.1016/j.jpeds.2020.07.054 doi: 10.1016/j.jpeds.2020.07.054 id: cord-309915-isw1arrp author: Perez-Jurado, L. A. title: Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men? date: 2020-04-24 words: 3328.0 sentences: 200.0 pages: flesch: 49.0 cache: ./cache/cord-309915-isw1arrp.txt txt: ./txt/cord-309915-isw1arrp.txt summary: The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has an estimated overall case fatality ratio of 1.38% in China, being 53% higher in males and increasing exponentially with age. Using comparative transcriptomic data, we have defined that XCM/LOY is associated with abnormal peripheral blood cell counts with decreased progenitor cells and multiple biomarkers of immune system dysfunction, pro-coagulation activity and increased cardiovascular risk. 8 Individuals with XCM have an increased risk for autoimmune disease, recurrent viral infections and earlier cardiovascular mortality, 9 which has been attributed to X-chromosome haploinsufficiency for multiple genes, and is associated with excessive production of proinflammatory cytokines (IL-6), decrease in anti-inflammatory cytokines (IL-10, TGF-β) and a lower CD4:CD8 ratio. 19.20071357 doi: medRxiv preprint Association analysis between LOY status and clinical data, including blood cell counts and biochemical parameters, was assessed using linear models adjusted by age. abstract: The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has an estimated overall case fatality ratio of 1.38% in China, being 53% higher in males and increasing exponentially with age. Mosaicism for X chromosome monosomy (XCM) shows a similar increase in aging population mostly driven by loss of chromosome Y in males (LOY), and is associated with a raise in all-cause mortality. Using comparative transcriptomic data, we have defined that XCM/LOY is associated with abnormal peripheral blood cell counts with decreased progenitor cells and multiple biomarkers of immune system dysfunction, pro-coagulation activity and increased cardiovascular risk. Several differentially down-regulated genes in XCM/LOY individuals are involved in the initial immune response to SARS-CoV-2 (OR of enrichment=7.23, p=1.5x10-7), mainly interferon-induced genes that code for inhibitors of viral processes. Thus, our data suggest that XCM mosaicism underlies at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential relevance for modulating prognosis and therapeutic response, we propose that evaluation of LOY and XCM by currently established methods should be implemented as biomarkers in infected patients, including currently ongoing clinical trials with different medications and vaccines for COVID-19. Testing for LOY/XCM at large scale among elderly people may also be helpful to identify still unexposed people who may be especially vulnerable to severe Covid-19 disease. url: https://doi.org/10.1101/2020.04.19.20071357 doi: 10.1101/2020.04.19.20071357 id: cord-293274-ysr1l557 author: Perisé-Barrios, Ana Judith title: Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date: 2020-09-22 words: 4140.0 sentences: 267.0 pages: flesch: 54.0 cache: ./cache/cord-293274-ysr1l557.txt txt: ./txt/cord-293274-ysr1l557.txt summary: Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. abstract: COVID-19 is a zoonotic disease originated by SARS-CoV-2. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Therefore it is necessary to describe the pathological processes in those animals that show symptoms similar to those described in humans affected by COVID-19. The potential for companion animals contributing to the continued human-to-human disease, infectivity, and community spread is an urgent issue to be considered. Forty animals with pulmonary pathologies were studied by chest X-ray, ultrasound study, and computed tomography. Nasopharyngeal and rectal swab were analyzed to detect canine pathogens, including SARS-CoV-2. Twenty healthy dogs living in SARS-CoV-2 positive households were included. Immunoglobulin detection by different immunoassays was performed. Our findings show that sick dogs presented severe alveolar or interstitial pattern, with pulmonary opacity, parenchymal abnormalities, and bilateral lesions. Forty dogs were negative for SARS-CoV-2 but Mycoplasma spp. was detected in 26 of 33 dogs. Five healthy and one pathological dog presented IgG against SARS-CoV-2. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Moreover, dogs living in COVID-19 positive households could have been more exposed to be infected during outbreaks. url: https://doi.org/10.1101/2020.09.22.308023 doi: 10.1101/2020.09.22.308023 id: cord-259396-vmc2q1bi author: Periyasamy, Petrick title: Aerosolized SARS-CoV-2 transmission risk: Surgical or N95 masks? date: 2020-09-15 words: 1527.0 sentences: 96.0 pages: flesch: 51.0 cache: ./cache/cord-259396-vmc2q1bi.txt txt: ./txt/cord-259396-vmc2q1bi.txt summary: WHO underlines the use of N95 respirators or equivalent as part of personal protective equipment (PPE) for healthcare workers (HCW) managing COVID-19 positive patients when aerosolised-generating-procedures (AGP) are being conducted.This retrospective observational study describes the result of COVID-19 reverse transcriptase polymerase chain reaction (RT-PCR) in health care workers (HCW) wearing different form of personal protective equipment (PPE) who had had close contact with a confirmed COVID-19 patient during performing such procedures. Little is known about the effectiveness of different types of personal protective equipment (PPE) for preventing SARS-CoV-2 in HCWs. We describe the clinical outcome of HCWs exposed to sudden acute respiratory infection patient before the diagnosis of COVID-19 was known. This retrospective observational study describes the result of reverse-transcriptase polymerase chain reaction (RT-PCR) testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in HCWs wearing different form of PPE who had close contact with a confirmed COVID-19 patient during performing AGPs. All HCWs were quarantined for 14 days after the exposure. abstract: Based on available evidence, the COVID-19 virus is thought to spread through close contact and droplet transmission. However, some have debated that it could be airborne. Airborne transmission occurs when particles of less than 0.5 μm within droplets spread through exhaled air via a process called aerosolisation. These particles can remain in the air for long periods and can disseminate over distances further than 1 meter. In the context of COVID-19, airborne particles can occur during certain aerosolised-generating-procedures (AGP). WHO underlines the use of N95 respirators or equivalent as part of personal protective equipment (PPE) for healthcare workers (HCW) managing COVID-19 positive patients when aerosolised-generating-procedures (AGP) are being conducted.This retrospective observational study describes the result of COVID-19 reverse transcriptase polymerase chain reaction (RT-PCR) in health care workers (HCW) wearing different form of personal protective equipment (PPE) who had had close contact with a confirmed COVID-19 patient during performing such procedures. All HCWs were quarantined for 14 days after the exposure. COVID-19 RT-PCR nasopharyngeal swabs were performed at different intervals. Little is known about the effectiveness of different types of personal protective equipment (PPE) for preventing SARS-CoV-2 in HCWs. We describe the clinical outcome of HCWs exposed to sudden acute respiratory infection patient before the diagnosis of COVID-19 was known. url: https://doi.org/10.1017/ice.2020.465 doi: 10.1017/ice.2020.465 id: cord-257140-ge15qrqg author: Perkmann, T. title: Increasing both specificity and sensitivity of SARS-CoV-2 antibody tests by using an adaptive orthogonal testing approach date: 2020-11-07 words: 3949.0 sentences: 255.0 pages: flesch: 51.0 cache: ./cache/cord-257140-ge15qrqg.txt txt: ./txt/cord-257140-ge15qrqg.txt summary: Methods To increase sensitivity, cut-offs of three commercially available SARS-CoV-2 automated assays (Roche, Abbott, and DiaSorin) were reduced according to published values in a pre-pandemic specificity cohort (n=1117) and a SARS-CoV-2 positive cohort (n=64). In our cohort, regardless of whether the assays were used for screening or confirmation, combining Roche and Abbott delivered the best overall performance (+~10% sensitivity compared to the single tests and 100% specificity). The disadvantage of this test strategy, which was recently shown in a study for the SARS-CoV-2 antibody tests from Abbott, Roche, and DiaSorin (19) , is that the gain in specificity usually comes at the expense of sensitivity and therefore increases the number of false negatives of individual tests. The Abbott Anti-SARS-CoV-2 IgG test, in contrast, reached 100.0% specificity only when followed by the Roche assay; in the other combinations, it remained slightly below, as a few false-positives persisted (99.8-99.9%). abstract: Background SARS-CoV-2 antibody tests have undergone a remarkable improvement in performance. However, due to the low seroprevalence in several areas, very high demands are made on their specificity. Furthermore, the low antibody-response in some individuals requires high test sensitivity to avoid underestimating true seroprevalence. Optimization of testing has been reported through lowering manufacturer cut-offs to improve SARS-CoV-2 assay sensitivity or by combining two tests to improve specificity at the cost of sensitivity. However, these strategies have thus far been used in isolation of each other. Methods To increase sensitivity, cut-offs of three commercially available SARS-CoV-2 automated assays (Roche, Abbott, and DiaSorin) were reduced according to published values in a pre-pandemic specificity cohort (n=1117) and a SARS-CoV-2 positive cohort (n=64). All three testing systems were combined in an orthogonal approach with a confirmatory test, which was one of the remaining automated assays or one of two commercial ELISAs directed against the spike protein receptor binding-domain (RBD) or the nucleocapsid antigen (NP). Results The modified orthogonal test strategy resulted in an improved specificity of at least 99.8%, often even 100%, in all 12 tested combinations with no significant decline in sensitivity. In our cohort, regardless of whether the assays were used for screening or confirmation, combining Roche and Abbott delivered the best overall performance (+~10% sensitivity compared to the single tests and 100% specificity). Conclusion Here we propose a novel orthogonal assay strategy that approaches 100% specificity while maintaining or even significantly improving the screening test's sensitivity. url: https://doi.org/10.1101/2020.11.05.20226449 doi: 10.1101/2020.11.05.20226449 id: cord-326730-aprb819p author: Perkmann, T. title: Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity date: 2020-06-05 words: 3232.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-326730-aprb819p.txt txt: ./txt/cord-326730-aprb819p.txt summary: Methods: We included a total of 1,154 specimens from pre-COVID-19 times and 65 samples from COVID-19 patients ([≥]14 days after symptom onset) to evaluate the test performance of SARS-CoV-2 serological assays by Abbott, Roche, and DiaSorin. Conclusion: We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. The present evaluation aims to compare three of these test systems manufactured by Abbott (11), DiaSorin (12), and Roche (13) , with particular emphasis on specificity, which is crucial for an adequate positive predictive value given the current low seroprevalence worldwide. We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. abstract: Background: In the context of the COVID-19 pandemic, numerous new serological test systems for the detection of anti-SARS-CoV-2 antibodies have become available quickly. However, the clinical performance of many of them is still insufficiently described. Therefore we compared three commercial, CE-marked, SARS-CoV-2 antibody assays side by side. Methods: We included a total of 1,154 specimens from pre-COVID-19 times and 65 samples from COVID-19 patients ([≥]14 days after symptom onset) to evaluate the test performance of SARS-CoV-2 serological assays by Abbott, Roche, and DiaSorin. Results: All three assays presented with high specificities: 99.2% (98.6-99.7) for Abbott, 99.7% (99.2-100.0) for Roche, and 98.3% (97.3-98.9) for DiaSorin. In contrast to the manufacturers' specifications, sensitivities only ranged from 83.1% to 89.2%. Although the three methods were in good agreement (Cohen's Kappa 0.71-0.87), McNemar's test revealed significant differences between results obtained from Roche and DiaSorin. However, at low seroprevalences, the minor differences in specificity resulted in profound discrepancies of positive predictability at 1% seroprevalence: 52.3% (36.2-67.9), 77.6% (52.8-91.5), and 32.6% (23.6-43.1) for Roche, Abbott, and DiaSorin, respectively. Conclusion: We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. url: https://doi.org/10.1101/2020.06.04.20117911 doi: 10.1101/2020.06.04.20117911 id: cord-291374-1bpcj9dw author: Pernazza, Angelina title: Early histologic findings of pulmonary SARS-CoV-2 infection detected in a surgical specimen date: 2020-04-30 words: 1652.0 sentences: 83.0 pages: flesch: 41.0 cache: ./cache/cord-291374-1bpcj9dw.txt txt: ./txt/cord-291374-1bpcj9dw.txt summary: Here we describe the pathologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who developed SARS-CoV-2 infection soon after surgery. The main histologic findings observed were pneumocyte damage, alveolar hemorrhages with clustering of macrophages, prominent and diffuse neutrophilic margination within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T lymphocytes. Here we describe the histologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who later developed SARS-CoV-2 infection. A recent autopsy report highlights the finding of diffuse alveolar damage as the major lung feature also in severe SARS-CoV-2 infection [4] . Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore abstract: Despite the current pandemic season, reports on pathologic features of coronavirus disease 19 (Covid-19) are exceedingly rare at the present time. Here we describe the pathologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who developed SARS-CoV-2 infection soon after surgery. The main histologic findings observed were pneumocyte damage, alveolar hemorrhages with clustering of macrophages, prominent and diffuse neutrophilic margination within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T lymphocytes. These features are similar to those previously described in SARS-CoV-2 infection. Subtle histologic changes suggestive pulmonary involvement by Covid-19 may be accidentally encountered in routine pathology practice, especially when extensive sampling is performed for histology. These findings should be carefully interpreted in light of the clinical context of the patient and could prompt a pharyngeal swab PCR test to rule out the possibility of SARS-CoV-2 infection in asymptomatic patients. url: https://doi.org/10.1007/s00428-020-02829-1 doi: 10.1007/s00428-020-02829-1 id: cord-300850-59j1m2tm author: Peron, Jean Pierre Schatzmann title: Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE) date: 2020-05-11 words: 3267.0 sentences: 171.0 pages: flesch: 44.0 cache: ./cache/cord-300850-59j1m2tm.txt txt: ./txt/cord-300850-59j1m2tm.txt summary: Toward this, we raise two main points, i) increased ACE-2 expression in pulmonary and heart tissues in users of chronic angiotensin 1 receptor (AT1R) blockers; and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. Toward this, we raise two main points of discussion, i) the increased angiotensin-converting enzyme-2 (ACE-2) expression in pulmonary and heart tissues of hypertensive patients with chronic use of AT1R blockers and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. SARS-CoV-2 spike proteins bind to angiotensin-converting enzyme-2 (ACE-2), which is expressed in the epithelial cells of the lungs (8, 9) . We believe that i) increased expression of ACE-2 in hypertensive patients being treated with ACE inhibitors and AT1R blockers and ii) previous exposure to circulating coronaviruses with low neutralizing capacity to SARS-CoV-2 may greatly contribute to the increased susceptibility of the elderly patients to COVID-19. abstract: The world is currently facing a serious SARS-CoV-2 infection pandemic. This virus is a new isolate of coronavirus, and the current infection crisis has surpassed the SARS and MERS epidemics that occurred in 2002 and 2013, respectively. SARS-CoV-2 has currently infected more than 142,000 people, causing 5,000 deaths and spreading across more than 130 countries worldwide. The spreading capacity of the virus clearly demonstrates the potential threat of respiratory viruses to human health, thereby reiterating to the governments around the world that preventive health policies and scientific research are pivotal to overcoming the crisis. Coronavirus disease (COVID-19) causes flu-like symptoms in most cases. However, approximately 15% of the patients need hospitalization, and 5% require assisted ventilation, depending on the cohorts studied. What is intriguing, however, is the higher susceptibility of the elderly, especially individuals who are older than 60 years of age, and have comorbidities, including hypertension, diabetes, and heart disease. In fact, the death rate in this group may be up to 10-12%. Interestingly, children are somehow less susceptible and are not considered as a risk group. Therefore, in this review, we discuss some possible molecular and cellular mechanisms by virtue of which the elderly subjects may be more susceptible to severe COVID-19. Toward this, we raise two main points, i) increased ACE-2 expression in pulmonary and heart tissues in users of chronic angiotensin 1 receptor (AT1R) blockers; and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. We believe that these points are pivotal for a better understanding of the pathogenesis of severe COVID-19, and must be carefully addressed by physicians and scientists in the field. url: https://doi.org/10.6061/clinics/2020/e1912 doi: 10.6061/clinics/2020/e1912 id: cord-273114-eanwxkvt author: Perrone, Serafina title: Report of a series of healthy term newborns from convalescent mothers with COVID-19 date: 2020-05-11 words: 1666.0 sentences: 106.0 pages: flesch: 53.0 cache: ./cache/cord-273114-eanwxkvt.txt txt: ./txt/cord-273114-eanwxkvt.txt summary: A further case series described 7 women with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), all of whom required oxygen therapy and received Caesarean section at term; only 3 neonates were tested, of whom one was positive. Here we report a series of cases of healthy term newborns whose mother developed COVID-19 infection during the third trimester of pregnancy and were convalescent with negative test at the time of delivery. Moreover, birth date, mode of delivery, gestational age, birth weight (g), anthropometric data, Apgar score 1''-5'', amniotic fluid, mother-child contact, clinical signs or symptoms and swab results was collected by newborns. Her husband suffered from COVID-19 infection and RT-PCR assay on her nasopharyngeal swab was positive for SARS-CoV-2. We reported four cases of healthy neonates born from mothers with previous SARS-CoV-2 pneumonia in the third trimester of pregnancy. abstract: BACKGROUND: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmittable virus associated with a significantly increased risk of complications among the infected population. Few data are available for the outcome of pregnancy complicated by serious respiratory disease due to SARS-CoV-2 infection. AIM: We herein report a series of four neonates whose mothers had recovered from new coronavirus 2019 disease (COVID-19) diagnosed in the third trimester of pregnancy. METHODS: pregnant women with documented COVID-19 infection during their pregnancy, who gave birth in Parma Hospital, University of Parma, Italy, in March and April 2020, during the peak of incidence of COVID-19 in Italy. Clinical records and laboratory tests were retrospectively reviewed. RESULTS: All neonates were delivered at term in good conditions without congenital COVID-19 infection. CONCLUSIONS: Findings from our series of cases indicated that adverse effects on foetuses from pregnancies complicated by COVID-19 infection in late pregnancy are unlikely. url: https://www.ncbi.nlm.nih.gov/pubmed/32420961/ doi: 10.23750/abm.v91i2.9743 id: cord-276619-6ndkz1da author: Perrone, Serafina title: Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum date: 2020-06-02 words: 912.0 sentences: 68.0 pages: flesch: 56.0 cache: ./cache/cord-276619-6ndkz1da.txt txt: ./txt/cord-276619-6ndkz1da.txt summary: title: Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum Lack of viral transmission to preterm newborn from a COVID-19 positive breastfeeding mother at 11 days postpartum In this paper, we reported the case of a mother who presented clinical symptoms of respiratory tract infection 10 days after the spontaneous delivery of a preterm newborn. Since birth, the newborn was fed with both breastfeeding and expressed maternal milk, and received Kangaroo Mother Care sessions. Postnatal horizontal COVID-19 infection occurred in newborns but expressed breast milk analysis did not reveal traces of the virus, so breastfeeding continued and the dyad was not separate. 9, 10 Here we describe a case of preterm baby breastfeeding mother at 11 days postpartum COVID-19 affected, in a NICU setting. Clinical characteristics of novel coronavirus disease 2019 (COVID-19) in newborns, infants and children abstract: In December 2019, novel coronavirus 2019 has appeared in China. On 11 February 2020, the World Health Organization officially names the disease as COVID-19.1 The new coronavirus is highly contagious. The rapid spread of SARS-CoV-2 lead to declare the pandemic on the 11th March 2020. On 10 May 2020 the number of infected people is 4,132,373 worldwide.2 This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32436998/ doi: 10.1002/jmv.26037 id: cord-354209-g1zynbul author: Person, Bobbie title: Fear and Stigma: The Epidemic within the SARS Outbreak date: 2004-02-17 words: 3913.0 sentences: 160.0 pages: flesch: 35.0 cache: ./cache/cord-354209-g1zynbul.txt txt: ./txt/cord-354209-g1zynbul.txt summary: While other NCID/CDC response teams dealt with laboratory investigations, surveillance, communica-tion, and clinical infection control practices, the Community Outreach Team worked to implement rapid public health strategies to document, monitor, and assist in ameliorating specific problems associated with fear, stigmatization, and discrimination attributed to the SARS outbreak in the United States. The team carried out the following activities: 1) facilitated group discussions with key opinion leaders within the Asian community in the United States; 2) collected and monitored the CDC Public Response Service data; 3) collected and monitored Asian-language newspapers, Internet sites, and other information sources; 4) reviewed polling data and other communication information; 5) conducted community visits, panel discussions, and media interviews; 6) solicited information from state and regional minority health liaisons nationwide; 7) developed ongoing relationships with the Asian-American communities; particularly in major metropolitan areas throughout the United States; and 8) determined new datagathering strategies as needed. abstract: Because of their evolving nature and inherent scientific uncertainties, outbreaks of emerging infectious diseases can be associated with considerable fear in the general public or in specific communities, especially when illness and deaths are substantial. Mitigating fear and discrimination directed toward persons infected with, and affected by, infectious disease can be important in controlling transmission. Persons who are feared and stigmatized may delay seeking care and remain in the community undetected. This article outlines efforts to rapidly assess, monitor, and address fears associated with the 2003 severe acute respiratory syndrome (SARS) epidemic in the United States. Although fear, stigmatization, and discrimination were not widespread in the general public, Asian-American communities were particularly affected. url: https://www.ncbi.nlm.nih.gov/pubmed/15030713/ doi: 10.3201/eid1002.030750 id: cord-278093-0twnkv93 author: Perveen, Shagufta title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 words: 3149.0 sentences: 162.0 pages: flesch: 56.0 cache: ./cache/cord-278093-0twnkv93.txt txt: ./txt/cord-278093-0twnkv93.txt summary: Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. abstract: Now nCOVID-19 has a foothold in many countries, and the threat of a pandemic situation has risen. Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). The nCOVID-19 has reported in Wuhan city of China has recently infected over six million people and at least 0.4 million confirmed deaths all over the world, while 2.8 million people has recovered from this deadly virus. Many instances of this respiratory syndrome coronavirus infection have already reported in more than 216 countries and territories. In contrast, the majority of cases reported in the USA, Brazil, Russia, Spain, UK, Italy, France and many more countries. In today's context, the coronavirus is one of the significant issues faced by the world with plenty of cases. In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). This review article describes the possible modes of transmission so that proper preventive actions should be taking. Importantly, this work mentioned the animal reservoir through which may infect humans, and it must be identified to break the transmission chain. In additions, this review paper briefly discussed the spread of the coronavirus in the Arabian Peninsula and what precaution measures are in place by each country to limit the spreading of this virus. Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. url: https://doi.org/10.1016/j.jsps.2020.06.006 doi: 10.1016/j.jsps.2020.06.006 id: cord-267917-belkwihy author: Peters, Alexandra title: Putting some context to the aerosolization debate around SARS-CoV-2 date: 2020-04-30 words: 887.0 sentences: 54.0 pages: flesch: 60.0 cache: ./cache/cord-267917-belkwihy.txt txt: ./txt/cord-267917-belkwihy.txt summary: 1 The experiments reported in this letter compared the stability of SARS-CoV-2 and SARS-CoV-1 in aerosols and on a number of different surfaces. The work showed that "SARS-CoV-2 remained viable in aerosols throughout the duration of (the) experiment (3 hours), with a reduction in infectious titer from 10 3.5 to 10 2.7 TCID50 per liter of air. [2] [3] [4] These media articles'' assertions include that SARS-Co V-2 can last "three hours after being coughed out into the air", 4 and that the van Doremalen et al. 2 The media even went as far as suggesting that the aerosols generated by the three-jet Collison nebulizer "duplicated the microscopic droplets created in a cough or a sneeze". It is for these reasons that the WHO and infection prevention specialists continue to support assertion that transmission of SARS-CoV-2 is primarily through droplets and contact (including indirect contact with contaminated surfaces). abstract: nan url: https://api.elsevier.com/content/article/pii/S0195670120302255 doi: 10.1016/j.jhin.2020.04.040 id: cord-311026-mpr3xb2a author: Petersen, Eskild title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 words: 5624.0 sentences: 339.0 pages: flesch: 56.0 cache: ./cache/cord-311026-mpr3xb2a.txt txt: ./txt/cord-311026-mpr3xb2a.txt summary: Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state''s strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. abstract: Abstract Aim The purpose of this perspective is to review the options countries have to exit the draconian “lock downs” in a carefully staged manner. Methods Experts from different countries experiencing Corona Virus Infectious Disease 2019 (COVID-19) review evidence and country specific approaches and results of their interventions. Results Three key factors are important: 1. Reintroduction from countries with ongoing community transmission; 2. The need for extensive testing capacity and widespread community testing, and 3. Adequate supply of personal protective equipment, PPE, to protect health care workers. Lifting social distancing is discussed at length. How to open manufacturing, construction and logistics. The opening og higher educational institutions and schools. The use of electronic surveillance is discussed. Conclusion Each country has to decide what is the best path forward. However, we can learn from each other and the approach is in reality very similar. url: https://www.ncbi.nlm.nih.gov/pubmed/32360552/ doi: 10.1016/j.ijid.2020.04.035 id: cord-274343-y9zqbefu author: Petersen, Irene title: Three Quarters of People with SARS-CoV-2 Infection are Asymptomatic: Analysis of English Household Survey Data date: 2020-10-08 words: 2197.0 sentences: 151.0 pages: flesch: 57.0 cache: ./cache/cord-274343-y9zqbefu.txt txt: ./txt/cord-274343-y9zqbefu.txt summary: We estimated sensitivity, specificity, the proportion of asymptomatic cases (1 – sensitivity), positive predictive value (PPV) and negative predictive value (NPV) of COVID-19 symptoms as a marker of infection using results of the SARS-CoV-2 test as the "gold standard". 8 In this analysis of data from a large representative study by the English Office for National Statistics we aimed to understand the value of COVID-19 symptoms as a marker for SARS-CoV-2 infection. We estimated the sensitivity, specificity, positive and negative predictive values of COVID-19 symptoms for SARS-CoV-2 infections as well as the proportion of asymptomatic cases (1 -sensitivity). We estimated the sensitivity, specificity, and positive and negative predictive values of COVID-19 symptoms as a marker of infection by using the results of the SARS-CoV-2 test as the "gold standard". To our knowledge, the Office for National Statistics Coronavirus (COVID-19) Infection Survey pilot is the largest population survey carried out to date including information on the association between COVID-19 symptoms and SARS-CoV-2 test results. abstract: BACKGROUND: To reduce transmission of SARS-CoV-2, it is important to identify those who are infectious. However, little is known about what proportion of infectious people are asymptomatic and potential “silent” transmitters. We evaluated the value of COVID-19 symptoms as a marker for SARS-CoV-2 infection from a representative English survey. METHODS: We used data from the Office for National Statistics Coronavirus (COVID-19) Infection Survey pilot study. We estimated sensitivity, specificity, the proportion of asymptomatic cases (1 – sensitivity), positive predictive value (PPV) and negative predictive value (NPV) of COVID-19 symptoms as a marker of infection using results of the SARS-CoV-2 test as the “gold standard”. RESULTS: In total, there were 36,061 individuals with a SARS-CoV-2 test between 26 April and 27 June 2020. Of these, 625 (1.7%) reported symptoms on the day of the test. There were 115 (0.32%) with a positive SARS-CoV-2 test result. Of the 115, there were 27 (23.5%) who were symptomatic and 88 (76.5%) who were asymptomatic on the day of the test. Focusing on those with specific symptoms (cough, and/or fever, and/or loss of taste/smell), there were 158 (0.43%) with such symptoms on the day of the test. Of the 115 with a positive SARS-CoV-2, there were 16 (13.9%) reporting symptoms. In contrast, 99 (86.1%) did not report specific symptoms on the day of the test. The PPV for all symptoms was 4.3% and for the specific symptoms 10.1%. The specificity and NPV of symptoms were above 98%. CONCLUSION: COVID-19 symptoms are poor markers of SARS-CoV-2. Thus, 76.5% of this random sample who tested positive reported no symptoms, and 86.1% reported none of those specific to COVID-19. A more widespread testing programme is necessary to capture “silent” transmission and potentially prevent and reduce future outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/33116898/ doi: 10.2147/clep.s276825 id: cord-274750-fynxciwg author: Peterson, Danielle title: Calm before the storm: understanding the role of JAK inhibitors in COVID-19 date: 2020-04-25 words: 462.0 sentences: 40.0 pages: flesch: 51.0 cache: ./cache/cord-274750-fynxciwg.txt txt: ./txt/cord-274750-fynxciwg.txt summary: Based on these 51 considerations, we believe there is insufficient evidence to recommend continuing JAK inhibitors in 52 patients who are acutely infected with SARS-CoV-2. 53 54 Napolitano et al suggest that baricitinib and upadacitinib might be useful in treating the cytokine 55 release syndrome (CRS) that can occur in SARS-CoV-2 infection. Furthermore, there is 58 evidence in both rhesus macaques and mice infected with the original SARS virus, SARS-CoV, that a 59 suboptimal early anti-viral type I interferon response may predispose to this late manifestation. In summary, we believe there is insufficient evidence to recommend that JAK inhibitors be continued in 70 all patients taking these medications who are acutely infected with SARS-CoV-2. While JAK inhibitors 71 may prove useful in the treatment of SARS-CoV-2-associated CRS, this is a separate consideration of a 72 relatively uncommon manifestation of this viral infection that occurs late in disease course. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0190962220307131?v=s5 doi: 10.1016/j.jaad.2020.04.097 id: cord-309914-1lpl26eo author: Peterson, Danielle title: The use of Janus kinase inhibitors in the time of SARS-CoV-2 date: 2020-04-09 words: 503.0 sentences: 40.0 pages: flesch: 60.0 cache: ./cache/cord-309914-1lpl26eo.txt txt: ./txt/cord-309914-1lpl26eo.txt summary: During the time of the SARS-CoV-2 pandemic, questions arise regarding patients being treated with 37 immunomodulatory therapies. In particular, is there an increased risk of acquiring the infection or 38 experiencing a worse outcome from SARS-CoV-2? we can look at safety data from clinical trials to try to understand patient susceptibility to different 40 infections. In light of the 42 growing off-label use of JAKi in dermatology in addition to pharmaceutical industry sponsored clinical 43 trials of JAKi for alopecia areata, atopic dermatitis, vitiligo, etc, dermatologists need data to better 44 understand the risks of JAKi treatment in order to best manage and counsel our patients during this 45 unique time. We analyzed and collated Adverse Events data from JAKi clinical trials. We also collated pulmonary 53 toxicities of JAKi to identify potential risks of worsening severe respiratory disease from SARS-CoV-2, and 54 such toxicities are all but absent. abstract: nan url: https://api.elsevier.com/content/article/pii/S0190962220305223 doi: 10.1016/j.jaad.2020.03.099 id: cord-312488-uzhj4i1q author: Petrosillo, Nicola title: SARS-CoV-2, “common cold” coronaviruses’ cross-reactivity and “herd immunity”: The razor of Ockham (1285-1347)? date: 2020-05-29 words: 1033.0 sentences: 69.0 pages: flesch: 59.0 cache: ./cache/cord-312488-uzhj4i1q.txt txt: ./txt/cord-312488-uzhj4i1q.txt summary: After the rapid spread of coronavirus-19 infectious disease (COVID-19) worldwide between February and April 2020, with a total of 5,267,419 confirmed cases and 341,155 deaths as of May 25, 2020, 1 in the last weeks we are observing a decrease in new infections in European countries, and the confirmed cases are not as severe as in the past, so much so that the number of patients transferred to intensive care for the worsening of the systemic and pulmonary disease is dramatically decreasing. 8 Virologists are claiming that there is no evidence of SARS-CoV-2 mutations causing less virulence and change of pathogenicity, 9 therefore, bending the epidemic curve could be simply the effect of progressive exhaustion of people susceptible to infection either due to a COVID-19 infection or for previous/recent "common cold" coronaviruses'' infections. abstract: nan url: https://doi.org/10.4081/idr.2020.8647 doi: 10.4081/idr.2020.8647 id: cord-286555-rz88g3ze author: Petrovan, Vlad title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 words: 3527.0 sentences: 156.0 pages: flesch: 55.0 cache: ./cache/cord-286555-rz88g3ze.txt txt: ./txt/cord-286555-rz88g3ze.txt summary: The most widely used molecular method approved by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) to detect SARS-CoV-2 is the real-time reverse transcription polymerase chain reaction (qRT-PCR) [4] . The protocol for the COVID-19 PCR Diatheva Detection Kit used with Fast Gene Probe One Step Mix uses 5 µL of mix 1 mixed with 0.625 µL of mix 2, 9.375 µL of primer/probe mix, and 5 µL of RNA template, with a total volume of 20 µL. An initial interlaboratory validation was performed by the Molecular Pathology Laboratory from the University Emergency Hospital Bucharest, using the PowerCheck 2019-nCoV Real-Time PCR Kit. This study was conducted as part of a surveillance program for COVID-19 implemented by the Romanian government. To determine the analytical sensitivity of the COVID-19 commercial assays used in Romanian hospitals (PowerCheck Kogene 2019-nCoV, COVID-19 PCR Diatheva Detection Kit, and 2019-nCoV CDC EUA), we first evaluated their limit of detection (LOD) by performing 10-fold serial dilutions of the controls provided by the kits. abstract: Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their sensitivity and feasibility for use in pooling. In this preliminary study, we showed that pooling of up to 80 samples did not affect the efficacy of the kits. Additionally, the RNA-dependent RNA polymerase (RdRp) gene is a more suitable target in pooled samples than the envelope (E) gene. This approach could provide an easy method of screening a large number of samples and help adjust different governmental regulations. url: https://doi.org/10.3390/diagnostics10070472 doi: 10.3390/diagnostics10070472 id: cord-353911-hp6s6ebh author: Petráš, Marek title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date: 2020-11-03 words: 2119.0 sentences: 134.0 pages: flesch: 54.0 cache: ./cache/cord-353911-hp6s6ebh.txt txt: ./txt/cord-353911-hp6s6ebh.txt summary: title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. The above laboratory procedure generated a semi-split inactivated vaccine, i.e., a vaccine with 307 the S protein separated from the viral particle exhibiting an early, both humoral and cellular, 308 immune response. Safety and immunogenicity of the ChAdOx1 nCoV-386 19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, 387 randomised controlled trial An in-depth investigation of the safety and immunogenicity of an 468 inactivated SARS-CoV-2 vaccine A double-inactivated 499 whole virus candidate SARS coronavirus vaccine stimulates neutralising and 500 protective antibody responses. Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity 526 abstract: The development of a vaccine against COVID-19 is a hot topic for many research laboratories all over the world. Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. We designed a semi-split vaccine prototype consisting of S protein-depleted viral particles and free S protein. Next, we investigated its immunogenic potential in BALB/c mice. The animals were immunized intradermally or intramuscularly with the dose adjusted with buffer or addition of aluminum hydroxide, respectively. The antibody response was evaluated by plasma analysis at 7 days after the first or second dose. The immune cell response was studied by flow cytometry analysis of splenocytes. The data showed a very early onset of both S protein-specific antibodies and virus-neutralizing antibodies at 90% inhibition regardless of the route of vaccine administration. However, significantly higher levels of neutralizing antibodies were detected in the intradermally (geometric mean titer - GMT of 7.8 ± 1.4) than in the intramuscularly immunized mice (GMT of 6.2 ± 1.5). In accordance with this, stimulation of cellular immunity by the semi-split vaccine was suggested by elevated levels of B and T lymphocyte subpopulations in the murine spleens. These responses were more predominant in the intradermally immunized mice compared with the intramuscular route of administration. The upward trend in the levels of plasmablasts, memory B cells, Th1 and Th2 lymphocytes, including follicular helper T cells, was confirmed even in mice receiving the vaccine intradermally at a dose of 0.5 μg. We demonstrated that the semi-split vaccine is capable of eliciting both humoral and cellular immunity early after vaccination. Our prototype thus represents a promising step toward the development of an efficient anti-COVID-19 vaccine for human use. url: https://doi.org/10.1101/2020.11.03.366641 doi: 10.1101/2020.11.03.366641 id: cord-337692-b89ow1mf author: Petti, S. title: Ecologic association between influenza and COVID-19 mortality rates in European countries date: 2020-09-11 words: 5103.0 sentences: 251.0 pages: flesch: 41.0 cache: ./cache/cord-337692-b89ow1mf.txt txt: ./txt/cord-337692-b89ow1mf.txt summary: Ecologic studies investigating COVID-19 mortality determinants, used to make predictions and design public health control measures, generally focused on population-based variable counterparts of individual-based risk factors. We considered the 3-year average influenza (2014–2016) and COVID-19 (31 May 2020) crude mortality rates in 34 countries using EUROSTAT and ECDC databases and performed correlation and regression analyses. An apparently perplexing characteristic of the reported association between the two mortality rates was that while influenza virus circulation during the seasons considered in the present analysis was uncontrolled, SARS-CoV-2 circulation was probably limited by the widespread exceptional public health measures implemented in Europe [32] . This study reported an inverse association between number of hospital beds and mortality rates (Table 2) , thus showing that high influenza and COVID-19 mortality was also due to inefficiencies of the healthcare systems, and corroborated by data from several European countries [45] . abstract: Ecologic studies investigating COVID-19 mortality determinants, used to make predictions and design public health control measures, generally focused on population-based variable counterparts of individual-based risk factors. Influenza is not causally associated with COVID-19, but shares population-based determinants, such as similar incidence/mortality trends, transmission patterns, efficacy of non-pharmaceutical interventions, comorbidities and underdiagnosis. We investigated the ecologic association between influenza mortality rates and COVID-19 mortality rates in the European context. We considered the 3-year average influenza (2014–2016) and COVID-19 (31 May 2020) crude mortality rates in 34 countries using EUROSTAT and ECDC databases and performed correlation and regression analyses. The two variables – log transformed, showed significant Spearman's correlation ρ = 0.439 (P = 0.01), and regression coefficients, b = 0.743 (95% confidence interval, 0.272–1.214; R(2) = 0.244; P = 0.003), b = 0.472 (95% confidence interval, 0.067–0.878; R(2) = 0.549; P = 0.02), unadjusted and adjusted for confounders (population size and cardiovascular disease mortality), respectively. Common significant determinants of both COVID-19 and influenza mortality rates were life expectancy, influenza vaccination in the elderly (direct associations), number of hospital beds per population unit and crude cardiovascular disease mortality rate (inverse associations). This analysis suggests that influenza mortality rates were independently associated with COVID-19 mortality rates in Europe, with implications for public health preparedness, and implies preliminary undetected SARS-CoV-2 spread in Europe. url: https://www.ncbi.nlm.nih.gov/pubmed/32912363/ doi: 10.1017/s0950268820002125 id: cord-346146-yal0ctpq author: Peyronnet, Violaine title: Infection par le SARS-CoV-2 chez les femmes enceintes. Actualisation de l’état des connaissances et de la proposition de prise en charge. CNGOF date: 2020-10-05 words: 9027.0 sentences: 922.0 pages: flesch: 67.0 cache: ./cache/cord-346146-yal0ctpq.txt txt: ./txt/cord-346146-yal0ctpq.txt summary: L''objectif de la rédaction de ce document est d''actualiser les connaissances des professionnels de santé sur le SARS-Covid-2, ses symptômes, la connaissance actuelle sur la transmission inter individuelle et pendant la grossesse et de proposer un protocole de prise en charge pour les femmes enceintes en France modifiant celui proposé précédemment (1) . Cependant, des symptômes plus graves ont également été décrits dans ce contexte (16 à 32%) comme la pneumonie ou le syndrome de détresse respiratoire aiguë (SDRA) qui sont présents majoritairement chez les personnes âgées, les patients présentant une immunodépression ou des comorbidités telles que le diabète, un cancer ou une maladie respiratoire chronique et les femmes enceintes (4; 8; 12-17) Les caractéristiques épidémiologiques, cliniques, biologiques et radiologiques ont été décrites dans la population générale en premier par Huang et al. Enfin une autre série française multicentrique portant sur 100 femmes enceintes avec une infection certaine rapporte 5 cas de césariennes avant 32 SA pour cause de COVID chez des patientes hospitalisées en réanimation. abstract: Objectifs: Le coronavirus SARS-CoV-2 mis en évidence en fin d’année 2019 en Chine a atteint tous les continents, avec plus de 28 millions de cas déclarés dont plus de 920 000 décès au 17/9/2020. Le plus souvent à l’origine d’un syndrome infectieux bénin, associant à différents degrés des symptômes (fièvre, toux, myalgies, céphalées et éventuels troubles digestifs), voire totalement asymptomatique, le SARS-CoV-2 peut être à l’origine de pathologies pulmonaires graves et parfois de décès. Méthode: Au vu de l’évolution de l’épidémie, le Collège National Des Gynécologues Obstétriciens Français a décidé de mettre à jours les avis émis précédemment. Pour cela, le même groupe d’experts, a été sollicité avec réalisation d’une revue de la littérature et prise en compte des avis de la Direction Générale de la Santé, la Haute Autorité de Santé, du Haut Conseil de Santé Publique. Résultats: Les données pendant la grossesse sont plus nombreuses et plus précises. Les données publiées semblent montrer que les symptômes chez la femmes enceintes sont les mêmes que ceux de la population générale et qu’un sur risque existe chez la femme enceinte particulièrement au troisième trimestre. Un cas de transmission materno-fœtale intra utérine a été formellement identifié. Une prématurité induite et des cas de détresses respiratoires chez les nouveau-nés de mères infectées ont été décrits. Conclusion: A la lumière des nouvelles données, nous proposons une actualisation des recommandations de prise en charge. Ces propositions peuvent encore évoluer avec l’avancée de la pandémie et de potentielles nouvelles connaissances chez la femme enceinte. Objectives: The coronavirus SARS-CoV-2 identified late 2019 in China had spread across all continents. In the majority of cases, patients have mild symptoms (fever, cough, myalgia, headache, some digestive disorders) or are asymptomatic, however it can cause serious lung diseases and lead to death. On September 2020, over 28 million people have been infected with over 920,000 deaths. Methods: In view of the evolution of the epidemic the French National College of Obstetricians and Gynecologists has decided to update the recommendations previously issued. To do this, the same group of experts was called upon to carry out a review of the literature and take into account the opinions of the General Directorate of Health (DGS), the “Haute Autorité de Santé” (HAS) and the “Haut Conseil de santé Publique” (HCSP). Results: The data on consequences during pregnancy have accumulated. The symptoms in pregnant women appear to be similar to those of the general population, but an increased risk of respiratory distress exists in pregnant women especially in the third trimester. A case of intrauterine maternal-fetal transmission has been clearly identified. Induced prematurity and cases of respiratory distress in newborns of infected mothers have been described. Conclusion: In light of the new data, we propose updated recommendations. These proposals may continue to evolve in view of the pandemic and of advances in studies in pregnant women. url: https://www.sciencedirect.com/science/article/pii/S2468718920302798?v=s5 doi: 10.1016/j.gofs.2020.10.001 id: cord-290950-v28kilvn author: Peyrony, Olivier title: Surfaces and equipment contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Emergency Department at a university hospital date: 2020-08-07 words: 3158.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-290950-v28kilvn.txt txt: ./txt/cord-290950-v28kilvn.txt summary: METHODS: We performed multiple samples from different sites in ED patients care and non-patient care areas with sterile premoistened swabs and used real-time reverse transcriptase polymerase chain reaction (RT-PCR) to detect the presence of SARS-CoV-2 ribonucleic acid (RNA). CONCLUSIONS: Our findings suggest that surfaces and equipment contamination by SARS-CoV-2 RNA in an ED during the COVID-19 outbreak is low and concerns exclusively patients'' examination and monitoring rooms, preserving non-patient care areas. In this study, we aimed to assess the surface and equipment contamination by SARS-CoV-2 of an ED during the COVID-19 outbreak depending on patient care and non-patient care areas. In our study, a sample was considered positive if either both ORF1a/b and E genes were Also, we did not detect any presence of SARS-CoV-2 RNA on the different surfaces of the patients'' registration desk or COVID-19 patients'' waiting room. abstract: OBJECTIVES: Environmental contamination by patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through respiratory droplets suggests that surfaces and equipment could be a medium of transmission. We aimed to assess the surface and equipment contamination by SARS-COV-2 of an emergency department (ED) during the coronavirus infectious disease-2019 (COVID-19) outbreak. METHODS: We performed multiple samples from different sites in ED patients care and non-patient care areas with sterile premoistened swabs and used real-time reverse transcriptase polymerase chain reaction (RT-PCR) to detect the presence of SARS-CoV-2 ribonucleic acid (RNA). We also sampled the personal protective equipment (PPE) from health care workers (HCWs). RESULTS: Among the 192 total samples, 10 (5.2%) were positive. In patient care areas, 5/46 (10.9%) of the surfaces directly in contact with COVID-19 patients revealed the presence of SARS-CoV-2 RNA, and 4/56 (7.1%) of the surfaces that were not directly in contact with COVID-19 patients were positive. SARS-CoV-2 RNA was present only in the patients’ examination and monitoring rooms. Before decontamination SARS-CoV-2 RNA was present on the saturation clip, the scuff for blood pressure measurement, the stretcher, the plastic screens between patients and the floor. After decontamination, SARS-CoV-2 RNA remained on the scuff, the stretcher and the trolleys. All samples from non-patient care areas or staff working rooms were negative. Only one sample from the PPE of the HCWs was positive. CONCLUSIONS: Our findings suggest that surfaces and equipment contamination by SARS-CoV-2 RNA in an ED during the COVID-19 outbreak is low and concerns exclusively patients’ examination and monitoring rooms, preserving non-patient care areas. url: https://www.sciencedirect.com/science/article/pii/S1438463920305460?v=s5 doi: 10.1016/j.ijheh.2020.113600 id: cord-305139-851v2qr3 author: Peys, Elise title: Haemoptysis as the first presentation of COVID-19: a case report date: 2020-10-22 words: 2555.0 sentences: 172.0 pages: flesch: 53.0 cache: ./cache/cord-305139-851v2qr3.txt txt: ./txt/cord-305139-851v2qr3.txt summary: This case emphasises the added value of bronchoscopy with BAL in the diagnostic work-up in case of high clinical suspicion and negative serial NPS in patients presenting with severe symptoms. Here, we report an unusual case of a man who presented with life-threatening haemoptysis as the first and unique symptom of COVID-19. According to the institutional guidelines during the current COVID-19 pandemic, nasopharyngeal swab (NPS) samples on two consecutive days were obtained and tested for SARS-CoV-2 using real-time polymerase chain reaction (RT-PCR), which repeatedly returned negative. Unusually, in this case, haemoptysis was the initial and unique symptom of SARS-CoV-2 infection in a patient with underlying emphysema. [7] , haemoptysis was the only clinical symptom during the first ten days of the disease course, whereas Casey and co-workers presented a case of COVID-19 associated with acute segmental pulmonary emboli which eventually caused haemoptysis [8] . abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing pandemic that profoundly challenges healthcare systems all over the world. Fever, cough and fatigue are the most commonly reported clinical symptoms. CASE PRESENTATION: A 58-year-old man presented at the emergency department with acute onset haemoptysis. On the fifth day after admission, he developed massive haemoptysis. Computed tomography (CT) angiography of the chest revealed alveolar haemorrhage, more prominent in the left lung. Flexible bronchoscopy confirmed bleeding from the left upper lobe, confirmed by a bronchial arteriography, which was successfully embolized. Nasopharyngeal swabs (NPS) tested for SARS-CoV-2 using real-time polymerase chain reaction (RT-PCR) repeatedly returned negative. Surprisingly, SARS-CoV-2 was eventually detected in bronchoalveolar lavage (BAL) fluid. CONCLUSIONS: Life-threatening haemoptysis is an unusual presentation of COVID-19, reflecting alveolar bleeding as a rare but possible complication. This case emphasises the added value of bronchoscopy with BAL in the diagnostic work-up in case of high clinical suspicion and negative serial NPS in patients presenting with severe symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/33092563/ doi: 10.1186/s12890-020-01312-6 id: cord-349684-2tioh80m author: Pezzotti, Giuseppe title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 words: 5388.0 sentences: 338.0 pages: flesch: 51.0 cache: ./cache/cord-349684-2tioh80m.txt txt: ./txt/cord-349684-2tioh80m.txt summary: The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. abstract: Introduction Viral disease spread by contaminated commonly touched surfaces is a global concern. Silicon nitride, an industrial ceramic that is also used as an implant in spine surgery, has known antibacterial activity. The mechanism of antibacterial action relates to the hydrolytic release of surface disinfectants. It is hypothesized that silicon nitride can also inactivate the coronavirus SARS-CoV-2. Methods SARS-CoV-2 virions were exposed to 15 wt.% aqueous suspensions of silicon nitride, aluminum nitride, and copper particles. The virus was titrated by the TCD50 method using VeroE6/TMPRSS2 cells, while viral RNA was evaluated by real-time RT-PCR. Immunostaining and Raman spectroscopy were used as additional probes to investigate the cellular responses to virions exposed to the respective materials. Results All three tested materials showed >99% viral inactivation at one and ten minutes of exposure. Degradation of viral RNA was also observed with all materials. Immunofluorescence testing showed that silicon nitride-treated virus failed to infect VeroE6/TMPRSS2 cells without damaging them. In contrast, the copper-treated virus suspension severely damaged the cells due to copper ion toxicity. Raman spectroscopy indicated differential biochemical cellular changes due to infection and metal toxicity for two of the three materials tested. Conclusions Silicon nitride successfully inactivated the SARS-CoV-2 in this study. The mechanism of action was the hydrolysis-mediated surface release of nitrogen-containing disinfectants. Both aluminum nitride and copper were also effective in the inactivation of the virus. However, while the former compound affected the cells, the latter compound had a cytopathic effect. Further studies are needed to validate these findings and investigate whether silicon nitride can be incorporated into personal protective equipment and commonly touched surfaces, as a strategy to discourage viral persistence and disease spread. url: https://doi.org/10.1101/2020.06.19.159970 doi: 10.1101/2020.06.19.159970 id: cord-267815-4fw7xgnt author: Peña, Juan A. title: A Survey of Labor and Delivery Practices in New York City during the COVID-19 Pandemic date: 2020-06-09 words: 2888.0 sentences: 170.0 pages: flesch: 54.0 cache: ./cache/cord-267815-4fw7xgnt.txt txt: ./txt/cord-267815-4fw7xgnt.txt summary: We therefore developed an internet-based survey to elucidate the practices put into place to guide the care of obstetrical patients during the COVID-19 pandemic. We found that all sites made changes to their practices, and that there appeared to be agreement with screening and testing for COVID-19, as well as labor and delivery protocols, for SARS-CoV-2-positive patients. One center performed SARS-CoV-2 PCR testing for all support persons either on admission to labor and delivery (L&D), or 24 to 48 hours prior to a scheduled admission. For half of the sites, after 34 weeks, the risks of continued expectant management of a patient with COVID-19 seemed to outweigh the risks of prematurity, and these centers would forgo testing and recommend delivery. Here we report on the obstetrical practices and protocols from four academic medical centers in NYC at the height of the COVID-19 pandemic. abstract: Recently, a novel coronavirus, precisely severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), that causes the disease novel coronavirus disease 2019 (COVID-19) has been declared a worldwide pandemic. Over a million cases have been confirmed in the United States. As of May 5, 2020, New York State has had over 300,000 cases and 24,000 deaths with more than half of the cases and deaths occurring in New York City (NYC). Little is known, however, of how this virus impacts pregnancy. Given this lack of data and the risk for severe disease in this relatively immunocompromised population, further understanding of the obstetrical management of COVID-19, as well as hospital level preparation for its control, is crucial. Guidance has come from expert opinion, professional societies and public health agencies, but to date, there is no report on how obstetrical practices have adapted these recommendations to their local situations. We therefore developed an internet-based survey to elucidate the practices put into place to guide the care of obstetrical patients during the COVID-19 pandemic. We surveyed obstetrical leaders in four academic medical centers in NYC who were implementing and testing protocols at the height of the pandemic. We found that all sites made changes to their practices, and that there appeared to be agreement with screening and testing for COVID-19, as well as labor and delivery protocols, for SARS-CoV-2-positive patients. We found less consensus with respect to inpatient antepartum fetal surveillance. We hope that this experience is useful to other centers as they formulate their plans to face this pandemic. Key Points: Practices changed to accommodate public health needs. Most practices are screened for novel COVID-19 on admission. Fetal testing in COVID-19 patients varied. url: https://www.ncbi.nlm.nih.gov/pubmed/32516817/ doi: 10.1055/s-0040-1713120 id: cord-293547-29i3u83s author: Pfaar, O title: COVID‐19 pandemic: Practical considerations on the organization of an allergy clinic – an EAACI/ARIA Position Paper date: 2020-06-12 words: 8811.0 sentences: 512.0 pages: flesch: 42.0 cache: ./cache/cord-293547-29i3u83s.txt txt: ./txt/cord-293547-29i3u83s.txt summary: RESULTS: Based on diagnostic and treatment standards developed by EAACI, on international information regarding COVID‐19, on guidelines of the World Health Organization (WHO) and other international organizations as well as on previous experience, a panel of experts including clinicians, psychologists, IT experts and basic scientists along with EAACI and the "Allergic Rhinitis and its Impact on Asthma (ARIA)" inititiative have developed recommendations for the optimal management of allergy clinics during the current COVID‐19 pandemic. CONCLUSIONS: This international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients whilst ensuring necessary safety in the current COVID‐19 pandemic. In the current SARS-CoV-2 pandemic, the European Task Force on Atopic Dermatitis (ETFAD) recommends to continue all immune-modulating treatment since exacerbations of underlying diseases can have a large negative impact on the patient''s immunity [30] . abstract: BACKGROUND: The Coronavirus disease 2019 (COVID‐19) has evolved as a pandemic infectious disease transmitted by the severe acute respiratory syndrome coronavirus (SARS‐CoV‐)2. Allergists and other health care providers (HCPs) in the field of allergies and associated airway diseases are in the front line, taking care of patients potentially infected with SARS‐CoV‐2. Hence, strategies and practices to minimize risks of infection for both HCPs and treated patients have to be developed and followed by allergy clinics. METHOD: The scientific information on COVID‐19 was analyzed by a literature search in Medline, Pubmed, national and international guidelines from the European Academy of Allergy and Clinical Immunology (EAACI), the Cochrane Library and the Internet. RESULTS: Based on diagnostic and treatment standards developed by EAACI, on international information regarding COVID‐19, on guidelines of the World Health Organization (WHO) and other international organizations as well as on previous experience, a panel of experts including clinicians, psychologists, IT experts and basic scientists along with EAACI and the “Allergic Rhinitis and its Impact on Asthma (ARIA)” inititiative have developed recommendations for the optimal management of allergy clinics during the current COVID‐19 pandemic. These recommendations are grouped into nine sections on different relevant aspects for the care of patients with allergies. CONCLUSIONS: This international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients whilst ensuring necessary safety in the current COVID‐19 pandemic. url: https://doi.org/10.1111/all.14453 doi: 10.1111/all.14453 id: cord-277025-gmy51dx4 author: Pfefferle, Susanne title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date: 2020-06-04 words: 949.0 sentences: 59.0 pages: flesch: 56.0 cache: ./cache/cord-277025-gmy51dx4.txt txt: ./txt/cord-277025-gmy51dx4.txt summary: title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany. A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China, as the alleged cause of a cluster of severe pneumonia cases (1) . Here, we describe the full-genome sequence of a SARS-CoV-2 strain (SARS-CoV-2/ human/DEU/HH-1/2020) isolated from a female patient with COVID-19. The isolate was obtained from an upper respiratory tract specimen (oropharyngeal swab) from a 62-year-old woman who was part of a small local cluster of COVID-19 cases, originating from a household contact who likely acquired the virus while traveling in Italy. The samples after trimming contained 18,369,904 high-quality paired-end reads, with 61,312 ϫ 2 reads (e.g., 122,624 reads) mapping to the reference Wuhan-Hu-1 sequence (GenBank accession number NC_045512.2) (6). abstract: Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany. url: https://www.ncbi.nlm.nih.gov/pubmed/32499358/ doi: 10.1128/mra.00520-20 id: cord-291965-9r9ll83m author: Pfefferle, Susanne title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date: 2009-09-17 words: 4306.0 sentences: 245.0 pages: flesch: 56.0 cache: ./cache/cord-291965-9r9ll83m.txt txt: ./txt/cord-291965-9r9ll83m.txt summary: Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc. abstract: We tested 12 bat species in Ghana for coronavirus (CoV) RNA. The virus prevalence in insectivorous bats (n = 123) was 9.76%. CoV was not detected in 212 fecal samples from Eidolon helvum fruit bats. Leaf-nosed bats pertaining to Hipposideros ruber by morphology had group 1 and group 2 CoVs. Virus concentrations were <45,000 copies/100 mg of bat feces. The diversified group 1 CoV shared a common ancestor with the human common cold virus hCoV-229E but not with hCoV-NL63, disputing hypotheses of common human descent. The most recent common ancestor of hCoV-229E and GhanaBt-CoVGrp1 existed in ≈1686–1800 ad. The GhanaBt-CoVGrp2 shared an old ancestor (≈2,400 years) with the severe acute respiratory syndrome–like group of CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/19788804/ doi: 10.3201/eid1509.090224 id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 words: 9548.0 sentences: 514.0 pages: flesch: 53.0 cache: ./cache/cord-304058-i8cywew0.txt txt: ./txt/cord-304058-i8cywew0.txt summary: title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). abstract: During the outbreak of SARS in 2002/3, a prototype virus was isolated from a patient in Frankfurt/Germany (strain Frankfurt-1). As opposed to all other SARS-Coronavirus strains, Frankfurt-1 has a 45-nucleotide deletion in the transmembrane domain of its ORF 7b protein. When over-expressed in HEK 293 cells, the full-length protein but not the variant with the deletion caused interferon beta induction and cleavage of procaspase 3. To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. Transfection of capped RNA transcribed from this construct yielded infectious virus that was indistinguishable from the original virus isolate. The presumed Frankfurt-1 ancestor with an intact ORF 7b was reconstructed. In CaCo-2 and HUH7 cells, but not in Vero cells, the variant carrying the ORF 7b deletion had a replicative advantage against the parental virus (4- and 6-fold increase of virus RNA in supernatant, respectively). This effect was neither associated with changes in the induction or secretion of type I interferon, nor with altered induction of apoptosis in cell culture. However, pretreatment of cells with interferon beta caused the deleted virus to replicate to higher titers than the parental strain (3.4-fold in Vero cells, 7.9-fold in CaCo-2 cells). In Syrian Golden Hamsters inoculated intranasally with 10e4 plaque forming units of either virus, mean titers of infectious virus and viral RNA in the lungs after 24 h were increased 23- and 94.8-fold, respectively, with the deleted virus. This difference could explain earlier observations of enhanced virulence of Frankfurt-1 in Hamsters as compared to other SARS-Coronavirus reference strains and identifies the SARS-CoV 7b protein as an attenuating factor with the SARS-Coronavirus genome. Because attenuation was focused on the early phase of infection in-vivo, ORF 7b might have contributed to the delayed accumulation of virus in patients that was suggested to have limited the spread of the SARS epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/19698190/ doi: 10.1186/1743-422x-6-131 id: cord-320085-n9i54wzh author: Pfefferle, Susanne title: Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date: 2020-03-05 words: 2032.0 sentences: 116.0 pages: flesch: 52.0 cache: ./cache/cord-320085-n9i54wzh.txt txt: ./txt/cord-320085-n9i54wzh.txt summary: We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus. In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. abstract: Facing the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), high-volume respiratory testing is demanded in laboratories worldwide. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ‘open channel’ for integration of a laboratory-developed assay. We observed good analytical performance in clinical specimens. The fully automated workflow enables high-throughput testing with minimal hands-on time, while offering fast and reliable results. url: https://doi.org/10.2807/1560-7917.es.2020.25.9.2000152 doi: 10.2807/1560-7917.es.2020.25.9.2000152 id: cord-298773-vnmc6nqd author: Pfeiffer, Julie K. title: Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? date: 2015-01-20 words: 1713.0 sentences: 87.0 pages: flesch: 50.0 cache: ./cache/cord-298773-vnmc6nqd.txt txt: ./txt/cord-298773-vnmc6nqd.txt summary: title: Is the Debate and "Pause" on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? This letter is about the potential impact of the debate and pause on graduate students and postdoctoral fellows and how their future plans may be affected. To gain initial insight into how the debate and research pause have affected trainees, I created an informal survey 2 days before the National Academy of Sciences meeting. These projects involve a subset of "gain of function" experiments designed to create mouse adapted viral strains, generate drug resistant viruses to understand drug mechanisms of action, understand host immunity by analyzing viruses with resistance to certain host immune pathways, and to study factors that influence transmission by the respiratory route (which was made famous by work from the Kawaoka and Fouchier labs in 2012). Third, the debate and research pause are influencing future plans of virology trainees. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25604793/ doi: 10.1128/mbio.02525-14 id: cord-312646-hfv7ce3f author: Pfützner, Andreas title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV- 2 in a community screening setting shows low sensitivity date: 2020-06-02 words: 485.0 sentences: 30.0 pages: flesch: 58.0 cache: ./cache/cord-312646-hfv7ce3f.txt txt: ./txt/cord-312646-hfv7ce3f.txt summary: title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV2 in a community screening setting shows low sensitivity In this manuscript, a point-of-care rapid test for assessment of anti-SARS-CoV-2 virus antibodies (IgG/IgM) is evaluated for sensitivity and specificity to detect the viral infection. They found that the antibody rapid test only detects 36.4 % of the samples identified as positive by means of RT-PCR, and conclude that this POCT is not recommendable for community screenings. In case that recent reports are confirmed that people with past infections may become asymptomatic carriers of the SARS-CoV-2 virus [3] , the antibody tests may be the only way to differentiate PCR-positive subjects into two groups: i.) patients who are freshly infected and may soon develop clinical symptoms (negative IgG result) and ii.) patients who have developed antibodies and may now be asymptomatic virus spreaders (positive IgG result). Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity abstract: nan url: https://doi.org/10.1016/j.puhe.2020.05.048 doi: 10.1016/j.puhe.2020.05.048 id: cord-255293-8necodtw author: Phakthanakanok, Krongsakda title: A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism date: 2009-01-30 words: 3958.0 sentences: 222.0 pages: flesch: 63.0 cache: ./cache/cord-255293-8necodtw.txt txt: ./txt/cord-255293-8necodtw.txt summary: The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. In order to perform molecular dynamics simulations, three structures of the SARS CoVMpro complexed with the octapeptides obtained from the docking, were prepared. However, one atom of the Na+ was also added in each system of the enzyme-substrate complexed of the octapeptide P3Lys and P3Arg due to it neutralized the amino acid, Lys and Arg. In the simulation, each time step was set to 2 fs and the simulation of the whole system performed for 2,000 ps (2 ns). The structure of the enzyme-substrate complex (SARS CoVMpro-octapeptide) obtained from molecular docking was then subjected to MD simulation. abstract: BACKGROUND: SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to structural-based drug design. The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. RESULTS: The one turn α-helix chain (residues 47–54) of the SARS CoVMpro was directly involved in the induced-fit model of the enzyme-substrate complex. The S3 subsite of the enzyme had a negatively charged region due to the presence of Glu47. During MD simulations, Glu47 of the enzyme was shown to play a key role in electrostatic bonding with the P3Lys of the octapeptide. CONCLUSION: MD simulations were carried out on the SARS CoVMpro-octapeptide complex. The hypothesis proposed that Glu47 of SARS CoVMpro is an important residue in the S3 subsite and is involved in binding with P3Lys of the octapeptide. url: https://doi.org/10.1186/1471-2105-10-s1-s48 doi: 10.1186/1471-2105-10-s1-s48 id: cord-310160-55yltan1 author: Pham, Jimmykim title: Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection date: 2020-09-22 words: 2745.0 sentences: 147.0 pages: flesch: 48.0 cache: ./cache/cord-310160-55yltan1.txt txt: ./txt/cord-310160-55yltan1.txt summary: In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. The analytical sensitivity of the SARS-CoV-2 TMA assay was assessed using 2 lots of reagents to test 60 replicates each of dilution panels containing cultured SARS-CoV-2 virus strain USA-WA1/2020 (BEI Resources, Manassas, VA) and diluted in Aptima specimen transport medium (STM) matrix to a range of 0.03 to 0.0003 50% tissue culture infectious dose (TCID 50 )/ml. This analysis resulted in positive, negative, and overall agreements of 100% (95% CI, 94.3% to 100%), Clinical performance of the SARS-CoV-2 TMA assay was also assessed by testing sets of NP swab, OP swab, and nasal swab specimens co-collected from 35 symptomatic patients suspected of being infected with SARS-CoV-2. abstract: The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID(50))/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32727828/ doi: 10.1128/jcm.01669-20 id: cord-325136-oyizfh2z author: Pham, Quang Thai title: The first 100 days of SARS-CoV-2 control in Vietnam date: 2020-08-01 words: 2655.0 sentences: 164.0 pages: flesch: 53.0 cache: ./cache/cord-325136-oyizfh2z.txt txt: ./txt/cord-325136-oyizfh2z.txt summary: METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). abstract: BACKGROUND: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23(rd), 270 cases were confirmed, with no deaths. We describe the control measures used by the Government and their relationship with imported and domestically-acquired case numbers, with the aim of identifying the measures associated with successful SARS-CoV-2 control. METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Apple and Google mobility data provided proxies for population movement. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. RESULTS: A national lockdown was implemented between April 1(st) and 22(nd). Around 200 000 people were quarantined and 266 122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections remained asymptomatic for the duration of infection. The serial interval was 3·24 days, and 27·5% (95% confidence interval, 15·7%-40·0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1·15 (95% confidence interval, 0·37-2·36). No community transmission has been detected since April 15(th). CONCLUSIONS: Vietnam has controlled SARS-CoV-2 spread through the early introduction of mass communication, meticulous contact-tracing with strict quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic and imported cases, and evidence for substantial pre-symptomatic transmission. url: https://doi.org/10.1093/cid/ciaa1130 doi: 10.1093/cid/ciaa1130 id: cord-301183-k39e12cq author: Pham, Tho D. title: SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution date: 2020-07-17 words: 289.0 sentences: 26.0 pages: flesch: 55.0 cache: ./cache/cord-301183-k39e12cq.txt txt: ./txt/cord-301183-k39e12cq.txt summary: title: SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution than 1 month after symptom resolution is concerning in light of current guidelines, which do not recommend SARS-CoV-2 screening in the general allogeneic donor population (5) . In this case, plasma viral RNA was reproducibly detected at a time point that exceeded recommendations for deferral based on time since symptom resolution (14 days). Of importance, these results are unlikely to be false-positive given that 2 different regions of the SARS-CoV-2 genome were detected in separate specimens collected on the day of donation and that quality control passed on all runs, including the absence of amplification in the negative controls. Of note, however, the infectivity of SARS-CoV-2 from blood remains unknown and, to date, we are not aware of cases of transfusion-transmitted COVID-19. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations abstract: nan url: https://doi.org/10.7326/l20-0725 doi: 10.7326/l20-0725 id: cord-318239-2sraqm6e author: Phan, Lan T. title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam date: 2020-05-28 words: 1591.0 sentences: 100.0 pages: flesch: 54.0 cache: ./cache/cord-318239-2sraqm6e.txt txt: ./txt/cord-318239-2sraqm6e.txt summary: title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent In this report, we describe clinical features, virus isolation, and complete genome sequences from the first two SARS-CoV-2 infections in Vietnam. A suspected case was defined as a person with an acute respiratory tract illness, who reported that he/she had fever and cough (with and without difficulty in breathing) and that within 14 days before the onset of disease, he/she had returned or came from areas where SARS-CoV-2 was spreading or had exposed to a laboratory-confirmed case of Covid-19. NP and OP swab specimens of the patients were collected in a single tube containing 3mL virus transport media and tested for SARS-CoV-2 by real-time RT-PCR assays described previously. Once the CPE was observed under the microscope, cell culture supernatants were harvested, divided into aliquots, tested for the presence of SARS-CoV-2 by real-time RT-PCR assays, and stored at -70°C until virus titration and sequencing were performed. abstract: In January 2020, we identified two SARS‐CoV‐2 infections in a familial cluster with one person coming from Wuhan, China. The complete genome sequences of two SARS‐CoV‐2 strains isolated from these patients were identical and 99.98% similar to strains isolated in Wuhan. This is genetically suggestive of human‐to‐human transmission of SARS‐CoV‐2 and indicates Wuhan as the most plausible origin of the early outbreak in Vietnam. The younger patient with a mild upper respiratory illness and a brief viral shedding, while the elderly with multi‐morbidity had pneumonia, prolonged viral shedding, and residual lung damage. Evidence of nonsynonymous substitutions in the ORF1ab region of the viral sequence warrants further studies. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32462705/ doi: 10.1002/jmv.26075 id: cord-351169-y91fdf66 author: Phillips, Lia title: Successful management of SARS-CoV-2 acute respiratory distress syndrome and newly diagnosed acute lymphoblastic leukemia date: 2020-09-14 words: 1732.0 sentences: 105.0 pages: flesch: 37.0 cache: ./cache/cord-351169-y91fdf66.txt txt: ./txt/cord-351169-y91fdf66.txt summary: Corticosteroid can be given safely to patients with SARS-CoV-2 presenting with acute respiratory distress syndrome and ALL. Although recommendations are emerging for the general management of oncology patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 1,2 there is little experience in patients with newly diagnosed acute lymphoblastic leukemia (ALL). Providers may have concern about initiating multiagent chemotherapy in patients with SARS-CoV-2, particularly corticosteroids, which are an essential part of induction regimens, but raise the theoretical possibility of delayed viral clearance. We describe our experience of successfully initiating therapy for an adolescent diagnosed with ALL, while managing severe SARS-CoV-2 infection marked by respiratory failure, systemic inflammation, and autoimmune hemolytic anemia (AIHA). 1, 2 In this case, intensive remission induction chemotherapy was initially delayed due to concern for potential worsening of SARS-CoV-2 disease by exacerbating the patient''s already immunocompromised state in the setting of ALL. abstract: Standard chemotherapy can still be used for new diagnosis of acute lymphoblastic leukemia in patients with SARS-CoV-2. Corticosteroid can be given safely to patients with SARS-CoV-2 presenting with acute respiratory distress syndrome and ALL. url: https://doi.org/10.1182/bloodadvances.2020002745 doi: 10.1182/bloodadvances.2020002745 id: cord-288632-2aliqy8p author: Phillips, Nicole title: The Perfect Storm: COVID-19 Health Disparities in US Blacks date: 2020-09-23 words: 4575.0 sentences: 210.0 pages: flesch: 36.0 cache: ./cache/cord-288632-2aliqy8p.txt txt: ./txt/cord-288632-2aliqy8p.txt summary: Specifically, Fig. 1 illustrates a conceptual model through which psychological influences (stress, anxiety, depression), pre-existing/comorbid disease (e.g., HTN, T2DM), and COVID-19 interconnect on the basis of known and unknown genetic variations that translate into human health outcomes and molecular modes of viral pathogenesis. Importantly, it is the interplay between key environmental exposures (stress; social determinants of health, SDH) and genetic predisposition for aspects of viral pathogenesis and/or comorbid disease (e.g., type 2 diabetes mellitus, T2DM; hypertension, HTN) that ultimately converges on COVID-19 manifestation and affects mortality . While there is conflicting data regarding the effects of variants in all three of the candidate genes discussed here, the remarkable relevance of associated phenotypes to COVID-19 pathophysiology together implies that genetic polymorphisms which regulate immune and stress responses may interact to affect underlying disease risk and, simultaneously, SARS-CoV-2 pathogenicity. abstract: Coronavirus disease 2019 (COVID-19) accounts for over 180,000 deaths in the USA. Although COVID-19 affects all racial ethnicities, non-Hispanic Blacks have the highest mortality rates. Evidence continues to emerge, linking the disproportion of contagion and mortality from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a result of adverse social determinants of health. Yet, genetic predisposition may also play a credible role in disease transmission. SARS-CoV-2 enters cells by interaction between SARS-CoV-2 spike protein and the receptor molecule angiotensin converting enzyme 2 (ACE2) expressed on the surface of the target cells, such that polymorphisms and the expression level of ACE2 influence infectivity and consequent pathogenesis of SARS-CoV-2. Genetic polymorphisms in other multiple genes, such as acetylcholinesterase (AChE) and interleukin-6, are also closely associated with underlying diseases, such as hypertension and type 2 diabetes mellitus, which substantially raise SARS-CoV-2 mortality. However, it is unknown how these genetic polymorphisms contribute to the disparate mortality rates, with or without underlying diseases. Of particular interest is the potential that genetic polymorphisms in these genes may be influencing the disparity of COVID-19 mortality rates in Black communities. Here, we review the evidence that biological predisposition for high-risk comorbid conditions may be relevant to our ability to fully understand and therefore address health disparities of COVID-19 deaths in Blacks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40615-020-00871-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s40615-020-00871-y doi: 10.1007/s40615-020-00871-y id: cord-273251-k3ltbpnb author: Phipps, Meaghan M. title: Acute Liver Injury in COVID‐19: Prevalence and Association with Clinical Outcomes in a Large US Cohort date: 2020-05-30 words: 4025.0 sentences: 204.0 pages: flesch: 50.0 cache: ./cache/cord-273251-k3ltbpnb.txt txt: ./txt/cord-273251-k3ltbpnb.txt summary: In multivariable analysis, peak ALT was significantly associated with death or discharge to hospice (OR 1.14, p=0.044), controlling for age, body mass index, diabetes, hypertension, intubation, and renal replacement therapy. (18) Patients with a positive test for SARS-CoV-2 were evaluated in subsequent analyses, categorized into those with peak ALT consistent with no/mild liver injury (<2 times ULN), moderate liver injury (2) (3) (4) (5) times ULN) and severe liver injury (>5 times ULN). Although initial alkaline phosphatase levels were similar across all categories of ALT, median peak value was higher in patients with severe liver injury (p<0.001), however it was only mildly elevated. In this cohort with 2273 cases and 1108 controls, we demonstrate that initial and peak ALT are higher in those who test positive for SARS-CoV-2 compared to those who test negative with a similar clinical presentation. Higher peak ALT values were also significantly associated with overall disease severity and measured clinical outcomes. abstract: BACKGROUND & AIMS: Coronavirus disease 2019 (COVID‐19) has been associated with acute liver injury manifested by increased liver enzymes in reports worldwide. Prevalence of liver injury and associated clinical characteristics are not well‐defined. We aim to identify the prevalence of and risk factors for development of COVID‐19 associated acute liver injury in a large cohort in the United States. APPROACH & RESULTS: In this retrospective cohort study, all patients who underwent SARS‐CoV‐2 testing at three hospitals in the NewYork‐Presbyterian network were assessed. Of 3381 patients, 2273 tested positive and had higher initial and peak ALT than those who tested negative. Acute liver injury was categorized as mild if alanine aminotransferase (ALT) was > upper limit of normal (ULN) but < two times ULN, moderate if ALT was between two and five times ULN, and severe if ALT was > five times ULN. Among patients who tested positive, 45% had mild, 21% moderate, and 6.4% severe liver injury. In multivariable analysis, severe acute liver injury was significantly associated with elevated inflammatory markers including ferritin (OR 2.40, p<0.001) and IL‐6 (OR 1.45, p=0.009). Patients with severe liver injury had a more severe clinical course, including higher rates of ICU admission (69%), intubation (65%), renal replacement therapy (33%), and mortality (42%). In multivariable analysis, peak ALT was significantly associated with death or discharge to hospice (OR 1.14, p=0.044), controlling for age, body mass index, diabetes, hypertension, intubation, and renal replacement therapy. CONCLUSION: Acute liver injury is common in patients who test positive for SARS‐CoV‐2, but is most often mild. However, among the 6.4% of patients with severe liver injury, a severe disease course should be anticipated. url: https://www.ncbi.nlm.nih.gov/pubmed/32473607/ doi: 10.1002/hep.31404 id: cord-308945-i2agpvhk author: Phipps, William S title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 words: 3167.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-308945-i2agpvhk.txt txt: ./txt/cord-308945-i2agpvhk.txt summary: METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. Long et al 8 have described a variable antiviral IgM and IgG immune response to SARS-CoV-2 infection in a Chinese population in which seroconversion in a group of 285 patients from 3 hospitals showed IgG positivity for all cases beyond 17 to 19 days. The goals of this study were to ascertain key performance metrics of analytical specificity and cross-reactivity for a SARS-CoV-2 IgG serologic assay, perform a detailed cross-sectional and serial assessment of IgG and IgM antibody responses in suspected COVID-19 patients, and determine their relation to disease severity. SARS-CoV-2 IgG antibody results agreed with the PCR-negative samples for 96 of 97 (99%) of cases, including 55 instances of patients with new or acute-on-chronic symptoms suspicious for COVID-19 and with known time of onset. abstract: OBJECTIVES: Initial reports indicate adequate performance of some serology-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assays. However, additional studies are required to facilitate interpretation of results, including how antibody levels impact immunity and disease course. METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. A subgroup of SARS-CoV-2 PCR-positive cases was tested for IgM antibodies by proteome array method. RESULTS: All specificity and cross-reactivity specimens were negative for SARS-CoV-2 IgG antibodies (0/795, 0%). Positive agreement of IgG with PCR was 83% of samples confirmed to be more than 14 days from symptom onset, with less than 100% sensitivity attributable to a case with severe immunosuppression. Virus-specific IgM was positive in a higher proportion of cases less than 3 days from symptom onset. No association was observed between mild and severe disease course with respect to IgG and IgM levels. CONCLUSIONS: The studied SARS-CoV-2 IgG assay had 100% specificity and no adverse cross-reactivity. Measures of IgG and IgM antibodies did not predict disease severity in our patient population. url: https://www.ncbi.nlm.nih.gov/pubmed/32666092/ doi: 10.1093/ajcp/aqaa123 id: cord-351107-a5bx74ao author: Phua, Ghee-Chee title: Mechanical Ventilation in an Airborne Epidemic date: 2008-06-30 words: 2981.0 sentences: 145.0 pages: flesch: 40.0 cache: ./cache/cord-351107-a5bx74ao.txt txt: ./txt/cord-351107-a5bx74ao.txt summary: The severe acute respiratory syndrome outbreak exposed the vulnerability of health care workers and highlighted the importance of establishing stringent infection control and crisis management protocols. Approximately 20% to 30% of SARS patients required intensive care and mechanical ventilation for acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) [9] . Adjuvant strategies shown to decrease morbidity and mortality in critically ill patients on mechanical ventilation include deep venous thrombosis prophylaxis, stress ulcer prophylaxis, sedation protocols, and avoidance of neuromuscular blockage, if possible; semirecumbent position should also be employed during airborne epidemics causing hypoxemic respiratory failure [18] . With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. abstract: With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. The severe acute respiratory syndrome outbreak exposed the vulnerability of health care workers and highlighted the importance of establishing stringent infection control and crisis management protocols. Patients who have acute lung injury and acute respiratory distress syndrome who require mechanical ventilation should receive a lung protective, low tidal volume strategy. Controversy remains regarding the use of high-frequency oscillatory ventilation and noninvasive positive pressure ventilation. Standard, contact, and airborne precautions should be instituted in intensive care units, with special care taken when aerosol-generating procedures are performed. url: https://doi.org/10.1016/j.ccm.2008.01.001 doi: 10.1016/j.ccm.2008.01.001 id: cord-301454-ayf42grs author: Phyu Khin, Phyu title: A potential therapeutic combination for treatment of COVID-19: synergistic effect of DPP4 and RAAS suppression date: 2020-08-14 words: 1762.0 sentences: 105.0 pages: flesch: 45.0 cache: ./cache/cord-301454-ayf42grs.txt txt: ./txt/cord-301454-ayf42grs.txt summary: A recent study proved that coronavirus SARS-CoV-2 also uses dipeptidyl peptidase-4 (DPP4, also known as adenosine deaminase complexing protein 2, CD26) as a co-receptor when entering cells. In particular, SARS-CoV-2 is able to infect T lymphocytes despite their very low expression level of ACE-2, implying an alternate receptor for viral entry [5, 6] . Among elderly patients (average age: 80 years) infected with SARS-CoV-2 in Italy in early 2020, the mortality rate was highest in patients with hypertension (69%), followed by those with type 2 diabetes (31%), and those with ischemic heart diseases (27%) [5] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients With Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China abstract: Abstract COVID-19, caused by the novel coronavirus SARS-CoV-2, is an abbreviated name for coronavirus disease 2019. COVID-19 became a global pandemic in early 2020. It predominantly affects not only the upper and lower respiratory tract, but also multiple organs, including the kidney, heart, and brain. The mortality of COVID-19 patients is high in men and in elderly patients with age-related diseases such as hypertension and diabetes. The angiotensin converting enzyme-2 (ACE-2), a component in the renin–angiotensin–aldosterone system (RAAS), plays as cell surface receptors for SARS-CoV-2. A recent study proved that coronavirus SARS-CoV-2 also uses dipeptidyl peptidase-4 (DPP4, also known as adenosine deaminase complexing protein 2, CD26) as a co-receptor when entering cells. In addition, DPP4 is also implicated in the regulation of the immune response. Thus, the combination of DPP4 inhibition and suppression of ACE-2/RAAS may be a novel therapeutic strategy for combating this pandemic. url: https://api.elsevier.com/content/article/pii/S0306987720323756 doi: 10.1016/j.mehy.2020.110186 id: cord-263308-q0iriid8 author: Piano, Carla title: An Italian Neurology Outpatient Clinic Facing SARS-CoV-2 Pandemic: Data From 2,167 Patients date: 2020-05-29 words: 3561.0 sentences: 169.0 pages: flesch: 36.0 cache: ./cache/cord-263308-q0iriid8.txt txt: ./txt/cord-263308-q0iriid8.txt summary: Methods: Patients with chronic neurologic diseases routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for symptoms suggestive of SARS-CoV-2 infection in the pandemic period, consequences of social restrictions, and neurological disease features, concomitant medical conditions, current medical and disease-specific treatments. Specifically, the survey assessed: (1) Demographic and clinical characteristics, including age at onset, duration of illness, and disability measures (ADL/IADL) (8); (2) COVID-19 related questions, including history of recent travel in endemic areas, direct contacts with COVID-19 confirmed cases (COVID-19+), symptoms suggestive of COVID-19 infection started or worsened in the last 3 months (fever, cough/sore throat, asthenia, dyspnea, myalgia, and hyposmia/hypogeusia), and confirmatory testing for COVID-19 (nasal/pharyngeal swab test results); (3) information related to the impact of COVID-19 on disease burden, including subjective worsening of neurological symptoms, compliance with restrictions and specific effects of restriction measures on the perception of illness (need of urgent neurological care, discontinuation of pharmacological treatment or physiotherapy, difficulties in finding drugs). abstract: Objective: Neurological sequelae of SARS-CoV-2 infection have already been reported, but there is insufficient data about the impact of the pandemic on the management of the patients with chronic neurological diseases. We aim to analyze the effect of COVID-19 pandemic and social restriction rules on these fragile patients. Methods: Patients with chronic neurologic diseases routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for symptoms suggestive of SARS-CoV-2 infection in the pandemic period, consequences of social restrictions, and neurological disease features, concomitant medical conditions, current medical and disease-specific treatments. Data source: a dedicated telephone survey designed to encompass questions on COVID-19 symptoms and on pandemic effects in chronic neurologic conditions. Results: Overall, 2,167 individuals were analyzed: 63 patients reported contact with COVID-19 positive cases, 41 performed the swab, and 2 symptomatic patients tested positive for COVID-19 (0.09%). One hundred fifty-eight individuals (7%) needed urgent neurological care, deferred due to the pandemic; 641 patients (30%) suspended hospital treatments, physiotherapy or other support interventions; 405 individuals (19%) reported a subjective worsening of neurological symptoms. Conclusions: In our population, the presence of neurological chronic diseases did not increase the prevalence of COVID-19 infection. Nevertheless, the burden of neurological disorders has been worsened by the lockdown. url: https://www.ncbi.nlm.nih.gov/pubmed/32574249/ doi: 10.3389/fneur.2020.00564 id: cord-295523-5pv7kw6i author: Picchianti Diamanti, Andrea title: Cytokine Release Syndrome in COVID-19 Patients, A New Scenario for an Old Concern: The Fragile Balance between Infections and Autoimmunity date: 2020-05-08 words: 7905.0 sentences: 390.0 pages: flesch: 39.0 cache: ./cache/cord-295523-5pv7kw6i.txt txt: ./txt/cord-295523-5pv7kw6i.txt summary: However, in about 20% of patients, the infection progresses to severe interstitial pneumonia and can induce an uncontrolled host-immune response, leading to a life-threatening condition called cytokine release syndrome (CRS). We critically review the rationale for the adoption of immunosuppressive agents, commonly used in autoimmune diseases, in the treatment of SARS-CoV-2 infection and report current knowledge of ongoing studies. The exacerbated reaction to infections or to biological therapy is caused by the rapid recruitment of macrophages and neutrophils, which produce pro-inflammatory cytokines and alter the fragile balance between a controlled immune response and a host-damaging reaction. As of now, four clinical trials are recruiting patients with COVID-19, severe acute respiratory failure, and CRS, aiming at evaluating the safety and effectiveness of anakinra alone or in combination with anti-IL-6 agents (NCT04330638, NCT0432402, NCT04357366, NCT04339712). High disease activity is associated with an increased risk of infection in patients with rheumatoid arthritis abstract: On 7 January 2020, researchers isolated and sequenced in China from patients with severe pneumonitis a novel coronavirus, then called SARS-CoV-2, which rapidly spread worldwide, becoming a global health emergency. Typical manifestations consist of flu-like symptoms such as fever, cough, fatigue, and dyspnea. However, in about 20% of patients, the infection progresses to severe interstitial pneumonia and can induce an uncontrolled host-immune response, leading to a life-threatening condition called cytokine release syndrome (CRS). CRS represents an emergency scenario of a frequent challenge, which is the complex and interwoven link between infections and autoimmunity. Indeed, treatment of CRS involves the use of both antivirals to control the underlying infection and immunosuppressive agents to dampen the aberrant pro-inflammatory response of the host. Several trials, evaluating the safety and effectiveness of immunosuppressants commonly used in rheumatic diseases, are ongoing in patients with COVID-19 and CRS, some of which are achieving promising results. However, such a use should follow a multidisciplinary approach, be accompanied by close monitoring, be tailored to patient’s clinical and serological features, and be initiated at the right time to reach the best results. Autoimmune patients receiving immunosuppressants could be prone to SARS-CoV-2 infections; however, suspension of the ongoing therapy is contraindicated to avoid disease flares and a consequent increase in the infection risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32397174/ doi: 10.3390/ijms21093330 id: cord-275173-ely3aen3 author: Pickering, Brad S. title: Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date: 2020-09-10 words: 1917.0 sentences: 107.0 pages: flesch: 52.0 cache: ./cache/cord-275173-ely3aen3.txt txt: ./txt/cord-275173-ely3aen3.txt summary: The work reported here aims to determine whether domestic swine are susceptible to 63 SARS-CoV-2 infection, providing critical information to aid public health risk assessments. The data presented in 66 this study provides evidence live SARS-CoV-2 virus can persist in swine for at least 13 days 67 following experimental inoculation. Two pigs (20-10, 20-11) displayed low 237 levels of viral RNA by RT-qPCR at 3 DPI (Table 2, Detection of SARS-CoV-2 was also attempted from whole blood by RT-qPCR, following 253 the sampling schedule outlined in Table 1 . To identify potential target tissues or gross lesions consistent with SARS-CoV-2 disease, 261 necropsy was performed on two animals starting at 3 DPI and every other day up to day 15; with 262 an additional two pigs necropsied at both 22 and 29 DPI (Table 1) (Table 2) . The results presented in this study define domestic swine as a susceptible species albeit at 293 low levels to SARS-CoV-2 viral infection. abstract: SARS-CoV-2, the agent responsible for COVID-19 has been shown to infect a number of species. The role of domestic livestock and the risk associated for humans in close contact remains unknown for many production animals. Determination of the susceptibility of pigs to SARS-CoV-2 is critical towards a One Health approach to manage the potential risk of zoonotic transmission. Here, pigs undergoing experimental inoculation are susceptible to SARS-CoV-2 at low levels. Viral RNA was detected in group oral fluids and nasal wash from at least two animals while live virus was isolated from a pig. Further, antibodies could be detected in two animals at 11 and 13 days post infection, while oral fluid samples at 6 days post inoculation indicated the presence of secreted antibodies. These data highlight the need for additional livestock assessment to better determine the potential role domestic animals may contribute towards the SARS-CoV-2 pandemic. url: https://doi.org/10.1101/2020.09.10.288548 doi: 10.1101/2020.09.10.288548 id: cord-317057-c2bwky6e author: Pickering, S. title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date: 2020-06-04 words: 5304.0 sentences: 269.0 pages: flesch: 53.0 cache: ./cache/cord-317057-c2bwky6e.txt txt: ./txt/cord-317057-c2bwky6e.txt summary: A highly specific in-house ELISA was developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs) on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative 4 ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing gold standard for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the best performing configuration of the in-house ELISA (detection of anti-S IgM and IgG antibodies), which was also most likely to represent antibodies detected by the commercial tests. abstract: There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential as diagnostic tools. A highly specific in-house ELISA was developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays - a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs) - on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. There was a wide variation in the performance of the different platforms, with specificity ranging from 82% to 100%, and overall sensitivity from 60.9% to 87.3%. However, the head to head comparison of multiple serodiagnostic assays on identical sample sets revealed that performance is highly dependent on the time of sampling, with sensitivities of over 95% seen in several tests when assessing samples from more than 20 days post onset of symptoms. Furthermore, these analyses identified clear outlying samples that were negative in all tests, but were later shown to be from individuals with mildest disease presentation. Rigorous comparison of antibody testing platforms will inform the deployment of point of care technologies in healthcare settings and their use in the monitoring of SARS-CoV-2 infections. url: http://medrxiv.org/cgi/content/short/2020.06.02.20120345v1?rss=1 doi: 10.1101/2020.06.02.20120345 id: cord-351952-lhhjax3s author: Pickering, Suzanne title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date: 2020-09-24 words: 5310.0 sentences: 247.0 pages: flesch: 48.0 cache: ./cache/cord-351952-lhhjax3s.txt txt: ./txt/cord-351952-lhhjax3s.txt summary: Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays—a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)—on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing standardised diagnostic test for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the configuration of the in-house ELISA most likely to represent antibodies detected by the commercial tests (detection of anti-S IgM and IgG antibodies), and that had high specificity and sensitivity (S1 Table) . abstract: There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential use as diagnostic tools. Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays—a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)—on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. There was a wide variation in the performance of the different platforms, with specificity ranging from 82% to 100%, and overall sensitivity from 60.9% to 87.3%. However, the head-to-head comparison of multiple sero-diagnostic assays on identical sample sets revealed that performance is highly dependent on the time of sampling, with sensitivities of over 95% seen in several tests when assessing samples from more than 20 days post onset of symptoms. Furthermore, these analyses identified clear outlying samples that were negative in all tests, but were later shown to be from individuals with mildest disease presentation. Rigorous comparison of antibody testing platforms will inform the deployment of point-of-care technologies in healthcare settings and their use in the monitoring of SARS-CoV-2 infections. url: https://doi.org/10.1371/journal.ppat.1008817 doi: 10.1371/journal.ppat.1008817 id: cord-285580-gq7400tq author: Pieretti, Joana C. title: Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date: 2020-10-18 words: 4877.0 sentences: 281.0 pages: flesch: 49.0 cache: ./cache/cord-285580-gq7400tq.txt txt: ./txt/cord-285580-gq7400tq.txt summary: In this mini-review, we discuss recent progress concerning the antivirus activity of NO in clinical, pre-clinical and research settings, and its beneficial effects in the treatment of clinical complications in patients infected with coronaviruses and other respiratory viral diseases, including COVID-19. Although positive biological effects have been reported for the administration of NO donors, further studies are required to better evaluate the levels of inflammatory mediators and the activity of important heme-containing enzymes, such as indoleamine 2,3-dioxygenase (IDO), directly involved in the inflammatory responses in respiratory viral infections (Anderson and Russel, 2020) . In other words, NO demonstrates potential for the treatment of patients infected with COVID-19 both in severe and nonsevere conditions, improving oxygenation and antiviral mechanisms, and preventing aggravation of the disease (Ferrari et al., 2020; Parikh et al., 2020) . Protocol of a randomized controlled trial testing inhaled nitric oxide in mechanically ventilated patients with severe acute respiratory syndrome in COVID-19 (SARS-CoV-2) abstract: The endogenous free radical nitric oxide (NO) plays a pivotal role in the immunological system. NO has already been reported as a potential candidate for use in the treatment of human coronavirus infections, including COVID-19. In fact, inhaled NO has been used in clinical settings for its antiviral respiratory action, and in the regulation of blood pressure to avoid clot formation. In this mini-review, we discuss recent progress concerning the antivirus activity of NO in clinical, pre-clinical and research settings, and its beneficial effects in the treatment of clinical complications in patients infected with coronaviruses and other respiratory viral diseases, including COVID-19. We also highlight promising therapeutic effects of NO donors allied to nanomaterials to combat COVID-19 and other human coronavirus infections. Nanomaterials can be designed to deliver sustained, localized NO release directly at the desired application site, enhancing the beneficial effects of NO and minimizing the side effects. Challenges and perspectives are presented to open new fields of research. url: https://doi.org/10.1016/j.virusres.2020.198202 doi: 10.1016/j.virusres.2020.198202 id: cord-316979-uadlclsv author: Pierri, Ciro Leonardo title: SARS-CoV-2 spike protein: flexibility as a new target for fighting infection date: 2020-10-30 words: 1456.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-316979-uadlclsv.txt txt: ./txt/cord-316979-uadlclsv.txt summary: The recent study of Turoňová et al., is the first to combine cryoelectron tomography, subtomogram averaging, and molecular dynamics simulations for analyzing the structure of the SARS-CoV-2 spike protein in situ, 1 i.e. while the virus interacts with tissue cultured cells. Notably, in a recent analysis of conformational changes determining the post-fusion conformation observed for a similar coronavirus spike cryo-EM structure 5 and the related SARS-CoV-2 spike 3D comparative model 2 ( Fig. 1) , it was proposed that the loss of the N-terminal domain (residues 1-703, black cartoon) causes the reorientation of the 704-715 peptide, which was involved in maintaining the tight packing of the central helix (CH) and the heptad repeat 1 (HR1) domain, together with the N-terminal domain. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies abstract: nan url: https://doi.org/10.1038/s41392-020-00369-3 doi: 10.1038/s41392-020-00369-3 id: cord-261718-zqoggwnk author: Pietschmann, Jan title: Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date: 2020-06-03 words: 1188.0 sentences: 76.0 pages: flesch: 45.0 cache: ./cache/cord-261718-zqoggwnk.txt txt: ./txt/cord-261718-zqoggwnk.txt summary: Available point-of-care diagnostic systems as lateral flow assays have high potential for fast and easy on-site antibody testing but are lacking specificity, sensitivity or possibility for quantitative measurements. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. For magnetic immuno-detection, immunofiltration columns were coated with a SARS-CoV-2 spike protein peptide. After addition of 176 biotinylated GaR and subsequent labelling with streptavidin-AP, the ELISA plate was read out at 177 405 nm and obtained measuring values were used to generate calibration curves for SARS-CoV-2 178 specific antibody concentrations in PBS (Fig 1, black curve) and in human serum samples (Fig 1, red 179 curve). Same calibration measurements employing dilutions of SARS-CoV-2 specific antibody were 211 done with our PoC MInD-based setup (Fig 2 and 3) . Comparable to laboratory-based ELISA, the same 212 dilutions of SARS-CoV-2 spike protein peptide specific antibody in PBS-buffer (Fig 3, black abstract: SARS-CoV-2 causes ongoing infections worldwide, and identifying people with immunity is becoming increasingly important. Available point-of-care diagnostic systems as lateral flow assays have high potential for fast and easy on-site antibody testing but are lacking specificity, sensitivity or possibility for quantitative measurements. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. For magnetic immuno-detection, immunofiltration columns were coated with a SARS-CoV-2 spike protein peptide. SARS-CoV-2 peptide reactive antibodies, spiked at different concentrations into PBS and human serum, were rinsed through immunofiltration columns. Specific antibodies were retained within the IFC and labelled with an isotype specific biotinylated antibody. Streptavidin-functionalized magnetic nanoparticles were applied to label the secondary antibodies. Enriched magnetic nanoparticles were then detected by means of frequency magnetic mixing detection technology, using a portable magnetic read-out device. Measuring signals corresponded to the amount of SARS-CoV-2 specific antibodies in the sample. Our preliminary magnetic immuno-detection setup resulted in a higher sensitivity and broader detection range and was four times faster than ELISA. Further optimizations could reduce assay times to that of a typical lateral flow assay, enabling a fast and easy approach, well suited for point-of-care measurements without expensive lab equipment. url: https://doi.org/10.1101/2020.06.02.131102 doi: 10.1101/2020.06.02.131102 id: cord-333654-8rg99di5 author: Pillai, Presaad title: COVID-19 AND MAJOR ORGAN THROMBOEMBOLISM: MANIFESTATIONS IN NEUROVASCULAR AND CARDIOVASCULAR SYSTEMS. date: 2020-10-24 words: 4128.0 sentences: 210.0 pages: flesch: 39.0 cache: ./cache/cord-333654-8rg99di5.txt txt: ./txt/cord-333654-8rg99di5.txt summary: The disease, caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2), has to date been responsible for more than 800,000 deaths globally, economic upheaval and significant lifestyle changes. 5, 6, 7 However, more recently immune mediated thrombosis has been a consistent finding in a significant number of patients with of Covid-19 and understanding its pathophysiological mechanisms and impact on morbidity and mortality in COVID-19 may open new avenues in disease prognostication and management. Thus, D-dimer level could potentially be an early and helpful marker to improve the management of COVID-19 and point clinicians to the possibility of silent thrombosis occurring in the pre-symptomatic stage which might dictate the natural history, progression and severity of the disease in a manner that has not been seen in previous coronavirus infections. Other significant risk factors, excluding raised D-dimer and CRP, that were associated with a high mortality rate for these patients with NVD, were comorbidities, age and increased severity of COVID-19 infection. abstract: COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to cause multisystemic damage. We undertook a systematic literature review and comprehensive analysis of a total of 55 articles on arterial and venous thromboembolism in COVID-19 and articles on previous pandemics with respect to thromboembolism and compared the similarities and differences between them. The presence of thrombosis in multiple organ systems points to thromboembolism being an integral component in the pathogenesis of this disease. Thromboembolism is likely to be the main player in the morbidity and mortality of COVID -19 in which the pulmonary system is most severely affected. We also hypothesize that D-dimer values could be used as an early marker for prognostication of disease as it has been seen to be raised even in the pre-symptomatic stage. This further strengthens the notion that thromboembolism prevention is necessary. We also examined literature on the cerebrovascular and cardiovascular systems, as the manifestation of thromboembolic phenomenon in these two systems varied, suggesting different pathophysiology of damage. Further research into the role of thromboembolism in COVID-19 is important to advance the understanding of the virus, its effects and to tailor treatment accordingly to prevent further casualties from this pandemic. url: https://doi.org/10.1016/j.jstrokecerebrovasdis.2020.105427 doi: 10.1016/j.jstrokecerebrovasdis.2020.105427 id: cord-346145-hnfeauow author: Pillay, Sureshnee title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic date: 2020-08-17 words: 7281.0 sentences: 371.0 pages: flesch: 56.0 cache: ./cache/cord-346145-hnfeauow.txt txt: ./txt/cord-346145-hnfeauow.txt summary: title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic In our SARS-CoV-2 assembly workflow, the initial assembly obtained from Genome Detective was polished by aligning mapped reads to the reference (NC_045512) and filtering out mutations with low genotype likelihoods, using bcftools 1.7-2 mpileup method. Furthermore, reagents for only 24 samples were available, as the order of Illumina TruSeq DNA Library preparation kit (x 96 sample libraries), which was placed in February and was enough to produce 480 genomes, had not arrived, due to the restrictions on international flights. The Nextera Flex library preparation kit was suggested by their technical team as a potentially better and quicker solution to produce SARS-CoV-2 genomes, which we found to be true. The Nextera Flex DNA library preparation kit was also evaluated, and we found it saved up to nine hours of hands-on time, when compared with the original ARTIC protocol that uses TruSeq. All three library preparation methods produced high-quality genomes. abstract: The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium. url: https://doi.org/10.3390/genes11080949 doi: 10.3390/genes11080949 id: cord-315556-84rgd2s9 author: Pilotto, A. title: Steroid-responsive severe encephalopathy in SARS-CoV-2 infection date: 2020-04-17 words: 2335.0 sentences: 176.0 pages: flesch: 46.0 cache: ./cache/cord-315556-84rgd2s9.txt txt: ./txt/cord-315556-84rgd2s9.txt summary: SARS-CoV-2 infection has the potential for targeting central nervous system and several neurological symptoms have been described in patients with severe respiratory distress. Here we described the case of an otherwise healthy 60-year old subject with SARS-CoV-2 infection but only mild respiratory abnormalities who developed severe progressive encephalopathy associated with mild pleocytosis and hyperproteinorrachia. The patient dramatically improved after high-doses steroid treatment suggesting an inflammatory-mediated brain involvement related to SARS-CoV-2 infection Recently, a study posted in medRxiv4 and still unpublished has reported neurological manifestations in COVID-19 in the outbreak in China in up to 36.4% of patients hospitalized, including alteration of consciousness, headache, dizziness and delirium 6 . The here described COVID-19 case is of particular interest, as the patients presented with severe encephalopathy with only mild respiratory alterations. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. abstract: SARS-CoV-2 infection has the potential for targeting central nervous system and several neurological symptoms have been described in patients with severe respiratory distress. Here we described the case of an otherwise healthy 60-year old subject with SARS-CoV-2 infection but only mild respiratory abnormalities who developed severe progressive encephalopathy associated with mild pleocytosis and hyperproteinorrachia. MRI was negative whereas EEG showed theta waves on the anterior brain regions. Serum and CSF analyses excluded other known infectious or autoimmune disorders. The patient dramatically improved after high-doses steroid treatment suggesting an inflammatory-mediated brain involvement related to SARS-CoV-2 infection url: https://doi.org/10.1101/2020.04.12.20062646 doi: 10.1101/2020.04.12.20062646 id: cord-290001-603qy8ml author: Pimentel, Lígia L. title: Cholesterol, inflammation, and phospholipids: COVID-19 share traits with cardiovascular disease date: 2020-10-17 words: 1836.0 sentences: 92.0 pages: flesch: 44.0 cache: ./cache/cord-290001-603qy8ml.txt txt: ./txt/cord-290001-603qy8ml.txt summary: COVID-19, the severe acute respiratory syndrome produced by the coronavirus SARS-CoV-2, has resulted to date in more than 27 million infected cases and 900000 deaths worldwide since the first reported cases in December 2019 at the Chinese city of Wuhan (for updated information readers can consult https://covid19.who.int/). Moreover, total counts of white blood cells (WBC) were significantly higher in patients in critical condition [1] and those with severe respiratory failure showed macrophage activation syndrome [4], confirmed by the presence of monocyte recruiting chemokines in bronchoalveolar fluid [2] . Furthermore, plasma lipidomic analyses have revealed a close relationship between the severity of COVID-19 and circulating lipids: a combination of larger levels of atherogenic diglycerides (DG 16:0/20:2/20:0) and triglycerides (TG 14:0/22:1/22:3), alterations of the phosphatidylinositol (PI) signalling system with decreased concentrations of phosphatidylcholine (PC) [7] and sphingosine-1-phosphate (S1P) [8] . Thus, it was observed in SARS-CoV-2 positive subjects that anticardiolipin antibodies (aCL IgG) profile (>15 U/mL) was associated to disease severity (i.e.respiratory distress) while those patients have not a previous record history of thrombosis [11] . abstract: nan url: https://doi.org/10.1016/j.bbalip.2020.158839 doi: 10.1016/j.bbalip.2020.158839 id: cord-345887-ymo4mxx7 author: Pinky title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 date: 2020-07-13 words: 5713.0 sentences: 306.0 pages: flesch: 42.0 cache: ./cache/cord-345887-ymo4mxx7.txt txt: ./txt/cord-345887-ymo4mxx7.txt summary: title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 With an urgent need for the development of potential strategies, two recent studies from China using Mesenchymal Stem Cells (MSCs) to treat COVID-19 pneumonia have shed some light on a potential cure for the COVID-19 infected patients. Also, attractive features like cell targeting, low-immunogenicity, safety, and high biocompatibility distinguish these exosomes from other synthetic nano-vesicles and thus potentiate their role as a drug delivery nano-platform. However, this study is first of its kind evaluating MSCs derived exosomes therapeutic potential for COVID-19 [45] . Some of the pre-clinical studies evaluating the effect of MSC derived exosomes on lung macrophages in various lung injury models have provided insights into the exosome derived approach as a new strategy for treating nCOV associated pathogenicity. Exosomes derived from bone marrow mesenchymal stem cells as treatment for severe COVID-19 abstract: The recent pandemic situation transpired due to coronavirus novel strain SARS-CoV-2 has become a global concern. This human coronavirus (HCov-19) has put the world on high alert as the numbers of confirmed cases are continuously increasing. The world is now fighting against this deadly virus and is leaving no stone unturned to find effective treatments through testing of various available drugs, including those effective against flu, malaria, etc. With an urgent need for the development of potential strategies, two recent studies from China using Mesenchymal Stem Cells (MSCs) to treat COVID-19 pneumonia have shed some light on a potential cure for the COVID-19 infected patients. However, MSCs, despite being used in various other clinical trials have always been questioned for their tendency to aggregate or form clumps in the injured or disease microenvironment. It has also been reported in various studies that exosomes secreted by these MSCs, contribute towards the cell’s biological and therapeutic efficacy. There have been reports evaluating the safety and feasibility of these exosomes in various lung diseases, thereby proposing them as a cell-free therapeutic agent. Also, attractive features like cell targeting, low-immunogenicity, safety, and high biocompatibility distinguish these exosomes from other synthetic nano-vesicles and thus potentiate their role as a drug delivery nano-platform. Building upon these observations, herein, efforts are made to give an overview of stem cell-derived exosomes as an appealing therapeutic agent and drug delivery nano-carrier. In this review, we briefly recapitulate the recent evidence and developments in understanding exosomes as a promising candidate for novel nano-intervention in the current pandemic scenario. Furthermore, this review will highlight and discuss mechanistic role of exosomes to combat severe lung pathological conditions. We have also attempted to dwell into the nano-formulation of exosomes for its better applicability, storage, and stability thereby conferring them as off the shelf therapeutic. url: https://www.ncbi.nlm.nih.gov/pubmed/32661867/ doi: 10.1007/s12015-020-10002-z id: cord-352526-t8odetzw author: Pinto, Bruna G G title: ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date: 2020-06-11 words: 3032.0 sentences: 199.0 pages: flesch: 50.0 cache: ./cache/cord-352526-t8odetzw.txt txt: ./txt/cord-352526-t8odetzw.txt summary: Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. The molecular mechanism responsible for the increased disease severity in patients with these comorbidities is not fully understood, but previous studies suggest a role for angiotensin-converting enzyme 2 (ACE2) (5) . Here, we showed that the expression of the gene encoding the ACE2 receptor in lung tissue is upregulated by diseases representing comorbidities along with COVID-19. abstract: Patients who died from COVID-19 often had comorbidities, such as hypertension, diabetes, and chronic obstructive lung disease. Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. This finding suggests that patients with such comorbidities may have higher chances of developing severe COVID-19. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. Our systems biology approach offers a possible explanation for increase of COVID-19 severity in patients with certain comorbidities. url: https://www.ncbi.nlm.nih.gov/pubmed/32526012/ doi: 10.1093/infdis/jiaa332 id: cord-262958-tmp6yxlv author: Pinto, Dora title: Structural and functional analysis of a potent sarbecovirus neutralizing antibody date: 2020-04-09 words: 2241.0 sentences: 147.0 pages: flesch: 55.0 cache: ./cache/cord-262958-tmp6yxlv.txt txt: ./txt/cord-262958-tmp6yxlv.txt summary: The SARS-CoV-2 spike (S) glycoprotein 26 promotes entry into host cells and is the main target of neutralizing antibodies. None of the mAbs studied bound to 97 prefusion OC43 S or MERS-CoV S ectodomain trimers, indicating a lack of cross-98 reactivity outside the sarbecovirus subgenus (Extended Data Fig.1) . The structural data explain the S309 cross-reactivity between SARS-CoV-2 and 148 SARS-CoV as 19 out of 24 residues of the epitope are strictly conserved ( Fig. 2f and 149 Extended Data Fig. 6a To further investigate the mechanism of S309-mediated neutralization, we 175 compared side-by-side transduction of SARS-CoV-2-MLV in the presence of either 176 S309 Fab or S309 IgG. This analysis 208 identified at least four antigenic sites within the S B domain of SARS-CoV targeted by 209 our panel of mAbs. The receptor-binding motif, which is targeted by S230, S227 and 210 S110, is termed site I. abstract: SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths1,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32511354/ doi: 10.1101/2020.04.07.023903 id: cord-313247-55loucvc author: Pipes, Lenore title: Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date: 2020-10-07 words: 2546.0 sentences: 209.0 pages: flesch: 64.0 cache: ./cache/cord-313247-55loucvc.txt txt: ./txt/cord-313247-55loucvc.txt summary: We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. There are many different methods for inferring the root of a phylogenetic tree, but they largely depend on three possible sources of information: outgroups, the molecular clock, and non-reversibility. To investigate the possible rootings of the SARS-CoV-2 phylogeny we used six different methods and quantified the uncertainty in the placement of the root for each method on the inferred maximum likelihood topology. We note that while interpretation of bootstrap proportions in phylogenetics can be problematic (see Efron et al., 1996) we performed 1,000 parametric simulations using pyvolve (Spielman and Wilke, 2015) using maximum likelihood estimates, from the original data set, of the model of molecular evolution and the phylogenetic tree, including branch lengths (see Table S2 ). abstract: The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, while methods based on outgroup rooting tend to place the root in the A clade. The results from the two approaches are statistically incompatible, possibly as a consequence of deviations from a molecular clock or excess back-mutations. We also show that none of the methods provide strong statistical support for the placement of the root in any particular edge of the tree. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. url: https://doi.org/10.1101/2020.06.19.160630 doi: 10.1101/2020.06.19.160630 id: cord-193133-puqcbf8t author: Piplani, Sakshi title: In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date: 2020-05-13 words: 3815.0 sentences: 215.0 pages: flesch: 51.0 cache: ./cache/cord-193133-puqcbf8t.txt txt: ./txt/cord-193133-puqcbf8t.txt summary: The devastating impact of the COVID19 pandemic caused by SARS coronavirus 2 (SARSCoV2) has raised important questions on the origins of this virus, the mechanisms of any zoonotic transfer from exotic animals to humans, whether companion animals or those used for commercial purposes can act as reservoirs for infection, and the reasons for the large variations in susceptibilities across animal species. Here we show how computational chemistry methods from structure-based drug design can be used to determine the relative binding affinities of the SARS-CoV-2 spike protein for its receptor, angiotensin converting enzyme (ACE)-2, a critical initiating event for SARS-CoV-2 infection, across multiple common and exotic animal species. 31, 32 Molecular docking was performed on the homology modelled SARS-CoV-2 spike protein with human and animal ACE2 proteins. The molecular dynamics simulation of complexes of SARS-CoV-2 spike protein and ACE2 receptors of various species were performed for 100ns. abstract: The devastating impact of the COVID19 pandemic caused by SARS coronavirus 2 (SARSCoV2) has raised important questions on the origins of this virus, the mechanisms of any zoonotic transfer from exotic animals to humans, whether companion animals or those used for commercial purposes can act as reservoirs for infection, and the reasons for the large variations in susceptibilities across animal species. Traditional lab-based methods will ultimately answer many of these questions but take considerable time. In silico modeling methods provide the opportunity to rapidly generate information on newly emerged pathogens to aid countermeasure development and also to predict potential future behaviors. We used a structural homology modeling approach to characterize the SARSCoV2 spike protein and predict its binding strength to the human ACE2 receptor. We then explored the possible transmission path by which SARSCoV2 might have crossed to humans by constructing models of ACE2 receptors of relevant species, and calculating the binding energy of SARSCoV2 spike protein to each. Notably, SARSCoV2 spike protein had the highest overall binding energy for human ACE2, greater than all the other tested species including bat, the postulated source of the virus. This indicates that SARSCoV2 is a highly adapted human pathogen. Of the species studied, the next highest binding affinity after human was pangolin, which is most likely explained by a process of convergent evolution. Binding of SARSCoV2 for dog and cat ACE2 was similar to affinity for bat ACE2, all being lower than for human ACE2, and is consistent with only occasional observations of infections of these domestic animals. Overall, the data indicates that SARSCoV2 is uniquely adapted to infect humans, raising questions as to whether it arose in nature by a rare chance event or whether its origins lie elsewhere. url: https://arxiv.org/pdf/2005.06199v1.pdf doi: nan id: cord-353365-ujz5nkk3 author: Pirnay, Jean-Paul title: Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger date: 2020-08-27 words: 4773.0 sentences: 246.0 pages: flesch: 53.0 cache: ./cache/cord-353365-ujz5nkk3.txt txt: ./txt/cord-353365-ujz5nkk3.txt summary: The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compromises the ability of military forces to fulfill missions. At the beginning of May 2020, 22 out of 70 Belgian soldiers deployed to a military education and training center in Maradi, Niger, developed mild COVID-19 compatible symptoms. Immediately upon their return to Belgium, and two weeks later, all seventy soldiers were tested for SARS-CoV-2 RNA (RT-qPCR) and antibodies (two immunoassays). Nine soldiers had at least one positive COVID-19 diagnostic test result. Five of them exhibited COVID-19 symptoms (mainly anosmia, ageusia, and fever), while four were asymptomatic. In four soldiers, SARS-CoV-2 viral load was detected and the genomes were sequenced. Conventional and genomic epidemiological data suggest that these genomes have an African most recent common ancestor and that the Belgian military service men were infected through contact with locals. The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. Some military operational settings (e.g., training camps in austere environments and ships) were also equipped with mobile infectious disease (COVID-19) testing capacity. url: https://www.ncbi.nlm.nih.gov/pubmed/32867108/ doi: 10.3390/v12090949 id: cord-297208-f4ob3ox6 author: Pisano, Antonio title: Cardiothoracic surgery at the time of COVID-19 pandemic: lessons from the East (and from a previous epidemic) for western battlefields date: 2020-05-06 words: 1376.0 sentences: 62.0 pages: flesch: 39.0 cache: ./cache/cord-297208-f4ob3ox6.txt txt: ./txt/cord-297208-f4ob3ox6.txt summary: 1 Evidently, countries which faced the severe acute respiratory syndrome (SARS) outbreak, the first coronavirus pandemic of the current century which affected more than 8000 people (mainly in China, Vietnam, Singapore and Canada) in 2003 7 , were much more prepared, both culturally and in terms of facilities and equipment, as compared with western countries (many of which had to face, in the initial stages of the emergency, the shortage of even simple and cheap devices such as surgical masks). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32482506/ doi: 10.1053/j.jvca.2020.04.051 id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 words: 6148.0 sentences: 396.0 pages: flesch: 49.0 cache: ./cache/cord-336447-hpnkou41.txt txt: ./txt/cord-336447-hpnkou41.txt summary: Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. abstract: In December 2019, the first cases of a new contagious disease were diagnosed in the city of Wuhan, the capital of Hubei province in China. Within a short period of time the outbreak developed exponentially into a pandemic that infected millions of people, with a global death toll of more than 500,000 during its first 6 months. Eventually, the novel disease was named coronavirus disease 2019 (COVID-19), and the new virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Similar to all known pandemics throughout history, COVID-19 has been accompanied by a large degree of fear, anxiety, uncertainty, and economic disaster worldwide. Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. Past pandemics were caused by a wide range of microbes, primarily viruses, but also bacteria. Characteristically, a significant proportion of them originated in different animal species (zoonoses). Since an understanding of the microbial cause of these diseases was unveiled relatively late in human history, past pandemics were often attributed to strange causes including punishment from God, demonic activity, or volatile unspecified substances. Although a high case fatality ratio was common to all pandemic diseases, some striking clinical characteristics of each disease allowed contemporaneous people to clinically diagnose the infection despite null microbiological information. In comparison to past pandemics, SARS-CoV-2 has tricky and complex mechanisms that have facilitated its rapid and catastrophic spread worldwide. url: https://doi.org/10.5041/rmmj.10418 doi: 10.5041/rmmj.10418 id: cord-253876-2dc9jq79 author: Pitocco, Dario title: Lack of type 1 diabetes involvement in SARS-COV-2 population: Only a particular coincidence? date: 2020-05-19 words: 477.0 sentences: 36.0 pages: flesch: 56.0 cache: ./cache/cord-253876-2dc9jq79.txt txt: ./txt/cord-253876-2dc9jq79.txt summary: In 1591 Italian subjects affected by SARS-COV-2, there was a prevalence of 17% of type 2 diabetes. This observation needs to be confirmed and further evaluated, for example in regions with high prevalence of the disease (Scandinavian, Finland or Sardinian), but there could be a number of reasons that justify a low incidence of SARS-COV-2 in subjects with type 1 diabetes. Indeed, we cannot rule out that there are some asymptomatic subjects with SARS-COV-2 infection in type 1 diabetic population. Finally, while the infected population has a high prevalence of hypertension, type 1 diabetes is often characterized by hyperglycemia in the absence of the other cardiovascular risk factors. Prevalence and impact of diabetes among people infected with SARS-CoV-2 All the authors have made substantive contributions to the article and assume full responsibility for its content abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32442557/ doi: 10.1016/j.diabres.2020.108220 id: cord-347221-g98q9cga author: Piyush, Ravikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 words: 4217.0 sentences: 246.0 pages: flesch: 50.0 cache: ./cache/cord-347221-g98q9cga.txt txt: ./txt/cord-347221-g98q9cga.txt summary: This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen. abstract: The coronavirus disease 2019 (COVID-19), the pandemic that originated in China has already spread into more than 190 countries, resulting in huge loss of human life and many more are at the stake of losing it; if not intervened with the best therapeutics to contain the disease. For that aspect, various scientific groups are continuously involved in the development of an effective line of treatment to control the novel coronavirus from spreading rapidly. Worldwide scientists are evaluating various biomolecules and synthetic inhibitors against COVID-19; where the nucleic acid-based molecules may be considered as potential drug candidates. These molecules have been proved potentially effective against SARS-CoV, which shares high sequence similarity with SARS-CoV-2. Recent advancements in nucleic acid-based therapeutics are helpful in targeted drug delivery, safely and effectively. The use of nucleic acid-based molecules also known to regulate the level of gene expression inside the target cells. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. url: https://doi.org/10.1016/j.heliyon.2020.e05007 doi: 10.1016/j.heliyon.2020.e05007 id: cord-272626-bw9lbzvt author: Pizzorno, Andrés title: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date: 2020-04-02 words: 2051.0 sentences: 116.0 pages: flesch: 40.0 cache: ./cache/cord-272626-bw9lbzvt.txt txt: ./txt/cord-272626-bw9lbzvt.txt summary: Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Developed from biopsies of nasal or bronchial cells differentiated in the air/liquid interphase, these models reproduce with high fidelity most of the main structural, functional and innate immune features of the human respiratory epithelium that play a central role 70 in the early stages of infection and constitute robust surrogates to study airway disease mechanisms and for drug discovery (10) . Comparably, daily treatment with 20 µM remdesivir resulted in 7.3 log10 and 7.9 log10 reductions of intracellular SARS-CoV-2 viral titers at 48 hpi in nasal and bronchial HAE, respectively (Fig. 4D, upper panel) . abstract: In the current COVID-19 pandemic context, proposing and validating effective treatments represents a major challenge. However, the lack of biologically relevant pre-clinical experimental models of SARS-CoV-2 infection as a complement of classic cell lines represents a major barrier for scientific and medical progress. Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Our results underline the relevance of this model for the preclinical evaluation of antiviral candidates. Foremost, we provide evidence on the antiviral efficacy of remdesivir and the therapeutic potential of the remdesivir-diltiazem combination as a rapidly available option to respond to the current unmet medical need imposed by COVID-19. One Sentence Summary New insights on SARS-CoV-2 biology and drug combination therapies against COVID-19. url: https://doi.org/10.1101/2020.03.31.017889 doi: 10.1101/2020.03.31.017889 id: cord-277860-vzyrcmu4 author: Pizzorno, Andrés title: In vitro evaluation of antiviral activity of single and combined repurposable drugs against SARS-CoV-2 date: 2020-07-15 words: 960.0 sentences: 71.0 pages: flesch: 45.0 cache: ./cache/cord-277860-vzyrcmu4.txt txt: ./txt/cord-277860-vzyrcmu4.txt summary: In vitro evaluation of antiviral activity of single and combined repurposable drugs 1 against SARS-CoV-2 2 3 Authors: Andrés Pizzorno a , Blandine Padey a,b , Julia Dubois a , Thomas Julien a,c , Aurélien 4 Traversier a , Victoria Dulière a,c , Pauline Brun a,c , Bruno Lina a,d , Manuel Rosa-Calatrava a,c* † , 5 Olivier Terrier a* † 6 7 Author affiliations: Abstract: 27 In response to the current pandemic caused by the novel SARS-CoV-2, identifying and 28 validating effective therapeutic strategies is more than ever necessary. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. abstract: In response to the current pandemic caused by the novel SARS-CoV-2, identifying and validating effective therapeutic strategies is more than ever necessary. We evaluated the in vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum activities, together with drugs that are currently under evaluation in clinical trials for COVID-19 patients. We report the antiviral effect of remdesivir, lopinavir, chloroquine, umifenovir, berberine and cyclosporine A in Vero E6 cells model of SARS-CoV-2 infection, with estimated 50% inhibitory concentrations of 0.99, 5.2, 1.38, 3.5, 10.6 and 3 μM, respectively. Virus-directed plus host-directed drug combinations were also investigated. We report a strong antagonism between remdesivir and berberine, in contrast with remdesivir/diltiazem, for which we describe high levels of synergy, with mean Loewe synergy scores of 12 and peak values above 50. Combination of host-directed drugs with direct acting antivirals underscore further validation in more physiological models, yet they open up interesting avenues for the treatment of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0166354220302928?v=s5 doi: 10.1016/j.antiviral.2020.104878 id: cord-253282-zwl0safn author: Plant, Ewan P. title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date: 2013-01-18 words: 5007.0 sentences: 266.0 pages: flesch: 55.0 cache: ./cache/cord-253282-zwl0safn.txt txt: ./txt/cord-253282-zwl0safn.txt summary: In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. Here, analyses using synonymous protein coding mutations demonstrate that the region of the genome that harbors the frameshift signal affects the regulation of genomic and subgenomic RNA production without altering protein sequence. Here we describe deletion and mutagenesis experiments with a dual luciferase reporter to show that the effect the sequence between stems 1 and 2 has on frameshifting efficiency is due to structural changes those mutations cause in the pseudoknot. Similar to previously described viruses containing mutations in the slippery site of the frameshift signal [7] , here we show that mutations to the SARS-CoV frameshift stimulating mRNA pseudoknot can also affect the production of viral genomic RNA. abstract: In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. It was not clear if these differences were due to changes in genomic sequence, the protein sequence or the frequency of frameshifting. Here, viruses with synonymous codon changes are shown to produce different ratios of genomic and subgenomic RNA. These findings demonstrate that the protein sequence is not the primary cause of altered genomic and subgenomic RNA production. The synonymous codon changes affect both the structure of the frameshift signal and frameshifting efficiency. Small differences in frameshifting efficiency result in dramatic differences in genomic RNA production and TCID(50) suggesting that the frameshifting frequency must stay above a certain threshold for optimal virus production. The data suggest that either the RNA sequence or the ratio of viral proteins resulting from different levels of frameshifting affects viral replication. url: https://doi.org/10.3390/v5010279 doi: 10.3390/v5010279 id: cord-329914-3b233vxl author: Plantier, L. title: Pratique des explorations fonctionnelles respiratoires pendant l’épidémie COVID-19 date: 2020-06-05 words: 2169.0 sentences: 239.0 pages: flesch: 61.0 cache: ./cache/cord-329914-3b233vxl.txt txt: ./txt/cord-329914-3b233vxl.txt summary: Préambule et mise en garde L''objectif de ces propositions est de prévenir la transmission du virus SARS-Cov2 lors de la pratique des explorations fonctionnelles respiratoires au repos et à l''exercice, dans le contexte général de l''assouplissement progressif des mesures de distanciation sociale débuté le 11 mai 2020. On peut rappeler que la persistance dans le poumon profond de l''ARN viral au-delà du 50 e jour avait été observée chez des patients infectés par SARS-Cov1 [7] . Proposition 3 : Bien que la structure d''EFR réponde à la définition d''un secteur à faible densité virale, nous considérons que des précautions complémentaires visant à protéger les personnels et les patients sont indispensables du fait 1) de la contagiosité des sujets asymptomatiques et 2) des particularités de l''EFR et notamment de la génération de gouttelettes et/ou d''aérosols potentiellement infectants lors des manoeuvres expiratoires [12] et la toux [13, 14] , du risque de déconnexion accidentelle du filtre antimicrobien et de la possibilité d''une toux induite par l''examen. abstract: Due to proven risks of hospital-acquired transmission and contamination of healthcare personnel, the COVID-19 outbreak significantly disrupts lung function and exercise testing facilities. This document reports proposals made by the "Respiratory Function" and "Alvéole" working groups of the French language respiratory society with regard to the completion of lung function testing at rest, cardiopulmonary exercise testing and the 6-minute walking test, in the current period of activity resumption following the lifting of the strict lockdown in force from March 17 to May 11, 2020. url: https://doi.org/10.1016/j.rmr.2020.06.002 doi: 10.1016/j.rmr.2020.06.002 id: cord-323943-9916y6x0 author: Platt, Daniel E title: Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails date: 2020-04-21 words: 4149.0 sentences: 230.0 pages: flesch: 46.0 cache: ./cache/cord-323943-9916y6x0.txt txt: ./txt/cord-323943-9916y6x0.txt summary: Therefore, we sought to understand whether the parameters of epidemic models could be determined from the trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the quality and comparability of data between jurisdictions reporting their statistics necessary for the analysis of model parameters across populations. Beside host and viral genetic impacts, other aspects driving SARS-COV-2 rates are population specific and demic, such as the impact of age on both asymptomatic and mild cases, as well as the proportion of severe and critical cases. In this paper, we seek to identify the limitations of using compartmental models to estimate or test hypotheses concerning parameters governing the growth of SARS-COV-2 epidemics. Therefore, infected population growth may be more closely reflected in the fraction of positive results normalized by total number of tests applied, in spite of very highly biased sampling selection. The rate of growth and doubling time may reflect availability and levels of testing more than the actual disease in the population. abstract: An opportunity exists in exploring epidemic modeling as a novel way to determine physiological and demic parameters for genetic association studies on a population/environmental (quasi) epidemiological study level. First, the spread of SARS-COV-2 has produced population specific lineages; second, epidemic spread model parameters are tied directly to these physiological and demic rates (e. g. incubation time, recovery time, transmission rate); and third, these parameters may serve as novel phenotypes to associate with region-specific genetic mutations as well as demic characteristics (e. g. age structure, cultural observance of personal space, crowdedness). Therefore, we sought to understand whether the parameters of epidemic models could be determined from the trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the quality and comparability of data between jurisdictions reporting their statistics necessary for the analysis of model parameters across populations. We found that, analytically, the pre-peak growth of an epidemic is limited by a subset of the model variates, and that the rate limiting variables are dominated by the expanding eigenmode of their equations. The variates quickly converge to the ratio of eigenvector components of the positive growth rate, which determines the doubling time. There are 9 parameters and 4 independent components in the eigenmode, leaving 5 undetermined parameters. Those parameters can be strikingly population dependent, and can have significant impact on estimates of hospital loads downstream. Without a sound framework, measurements of infection rates and other parameters are highly corrupted by uneven testing rates to uneven counting and reporting of relevant values. From the standpoint of phenotype parameters, this means that structured experiments must be performed to estimate these parameters in order to perform genetic association studies, or to construct viable models that accurately predict critical quantities such as hospitalization loads. url: https://doi.org/10.1101/2020.04.20.20071928 doi: 10.1101/2020.04.20.20071928 id: cord-346960-3empldlo author: Plebani, M. title: Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity date: 2020-08-04 words: 2282.0 sentences: 134.0 pages: flesch: 46.0 cache: ./cache/cord-346960-3empldlo.txt txt: ./txt/cord-346960-3empldlo.txt summary: In 184 serum samples from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). On limiting the analysis to samples collected 12 days after onset of symptoms, the sensitivity of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. 54 SARS-CoV-2 negative subjects (33 healthcare workers, 21 autoimmune patients, 8 pregnant women) were included in the study ( Moreover, Liaison SARS-CoV-2 S1/S2 IgG (Diasorin, Sallugia-VC, Italy), ENZY-Well SARS-CoV-2 IgA and IgM were evaluated for the correlation with the neutralization results. . To provide insight on neutralization activity compared with immunoassays results, PRNT assay was performed on 52 samples from SARS-CoV-2 positive subjects. abstract: Background. Reliable high-throughput serological assays for SARS-CoV-2 antibodies (Abs) are urgently needed for the effective containment of the COVID-19 pandemic, as it is of crucial importance to understand the strength and duration of immunity after infection, and to make informed decisions concerning the activation or discontinuation of physical distancing restrictions. Methods. In 184 serum samples from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). Findings. Precision results ranged from 0.9% to 11.8% for all assays. Elecsys anti-SARS-CoV-2 demonstrated linearity of results at concentrations within the cut-off value. Overall, sensitivity ranged from 78.5 to 87.8%, and specificity, from 97.6 to 100%. On limiting the analysis to samples collected 12 days after onset of symptoms, the sensitivity of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. The strongest PRNT50 correlation with antibody levels was obtained with ENZY-Well SARS-CoV-2 IgG (rho = 0.541, p < 0.001). Interpretation. The results confirmed that all immunoassays had an excellent specificity, whereas sensitivity varied across immunoassays, depending strongly on the time interval between symptoms onset and sample collection. Further studies should be conducted to achieve a stronger correlation between antibody measurement and PRNT50 in order to obtain useful information for providing effective passive antibody therapy, and developing a vaccine against the SARS-CoV-2 virus. url: http://medrxiv.org/cgi/content/short/2020.08.01.20166546v1?rss=1 doi: 10.1101/2020.08.01.20166546 id: cord-252033-43fbfglt author: Plebani, Mario title: Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays? date: 2020-05-30 words: 2999.0 sentences: 152.0 pages: flesch: 44.0 cache: ./cache/cord-252033-43fbfglt.txt txt: ./txt/cord-252033-43fbfglt.txt summary: METHODS: Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Aim of this study was to evaluate different chemiluminescent (CLIA) and enzyme-linked immunosorbent (ELISA) assays for SARS-CoV-2 antibodies in COVID-19 patients and healthcare operators, to identify appropriate cut-offs and evaluate diagnostic accuracy. Donors (only for CLIA assays) and negative autoimmune patients results were included to verify possible analytical interferences and differences with respect to healthcare workers who repeatedly tested negative to nasopharyngeal swab. Rigorous comparative performance data are crucial to understanding the potential clinical usefulness of serological assays, starting from the evaluation of analytical performance characteristics to improve the definition of diagnostic accuracy not only in terms of specificity and sensitivity but also as positive and negative likelihood ratios, in order to provide reliable clinical information in different disease prevalence settings. abstract: BACKGROUND: The evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibody (Ab) assay performances is of the utmost importance in establishing and monitoring virus spread in the community. In this study focusing on IgG antibodies, we compare reliability of three chemiluminescent (CLIA) and two enzyme linked immunosorbent (ELISA) assays. METHODS: Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Diagnostic sensitivity and specificity, positive and negative likelihood ratios were evaluated using manufacturers’ and optimized thresholds. RESULTS: Optimized thresholds (Maglumi 2 kAU/L, Liaison 6.2 kAU/L and iFlash 15.0 kAU/L) allowed us to achieve a negative likelihood ratio and an accuracy of: 0.06 and 93.5% for Maglumi; 0.03 and 93.1% for Liaison; 0.03 and 91% for iFlash. Diagnostic sensitivities and specificities were above 93.8% and 85.9%, respectively for all CLIA assays. Overall agreement was 90.3% (Cohen’s kappa = 0.805 and SE = 0.041) for CLIA, and 98.4% (Cohen’s kappa = 0.962 and SE = 0.126) for ELISA. CONCLUSIONS: The results obtained indicate that, for CLIA assays, it might be possible to define thresholds that improve the negative likelihood ratio. Thus, a negative test result enables the identification of subjects at risk of being infected, who should then be closely monitored over time with a view to preventing further viral spread. Redefined thresholds, in addition, improved the overall inter-assay agreement, paving the way to a better harmonization of serologic tests. url: https://doi.org/10.1016/j.cca.2020.05.050 doi: 10.1016/j.cca.2020.05.050 id: cord-284954-uuqchon4 author: Plebani, Mario title: SARS-CoV-2 antibody-based SURVEILLANCE: New light in the SHADOW date: 2020-11-05 words: 963.0 sentences: 48.0 pages: flesch: 44.0 cache: ./cache/cord-284954-uuqchon4.txt txt: ./txt/cord-284954-uuqchon4.txt summary: The paper by Perico and coworkers, published in this issue of EBioMedicine, is a comprehensive analysis of the prevalence of SARS-CoV-2 infection in the Bergamo province, an area of Italy that experienced a massive COVID-19 outbreak, with its epicenter in the whole Lombardy region. Furthermore, in a study performed in Iceland on the measurement of SARS-CoV-2 antibodies, it is estimated that 44% of individuals infected with the virus were not diagnosed by quantitative polymerase-chain-reaction (qPCR) thus confirming the risk of under-diagnosis on using molecular testing alone [2] . The paper by Perico and colleagues is welcome for several reasons: first, it confirms the usefulness of SARS-CoV-2 antibody assay for a better knowledge of the spread of the infection in a specific population or subpopulation, and for avoiding the risk of under-diagnosis when using rRT-PCR testing alone. abstract: nan url: https://api.elsevier.com/content/article/pii/S2352396420304631 doi: 10.1016/j.ebiom.2020.103087 id: cord-024100-lk67yfrp author: Plewczynski, Dariusz title: In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening date: 2007-04-24 words: 2398.0 sentences: 135.0 pages: flesch: 47.0 cache: ./cache/cord-024100-lk67yfrp.txt txt: ./txt/cord-024100-lk67yfrp.txt summary: Selected molecules having close structural relationship to a 2‐methyl‐2,4‐pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors. In this study, we exploited structural homologs of SARS-CoV protease co-crystallized with small molecules to explore opportunities for drug design of potential inhibitors for this therapeutic target enzyme. We have explored the use of structural information contained in PDB database for an in silico virtual drug discovery campaign using, as a case study, the main protease of SARS-CoV. Using this method, plausible inhibitors were generated as based only on the set of ligands from crystallized complexes of a protein Figure 1 : Two dimensional chemical structures presented in Table II: Plewczynski et al. The docking was performed on small molecules and short peptides extracted from protein-ligand complexes of the viral cysteine proteases of trypsin-fold. Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease abstract: A structure‐based in silico virtual drug discovery procedure was assessed with severe acute respiratory syndrome coronavirus main protease serving as a case study. First, potential compounds were extracted from protein–ligand complexes selected from Protein Data Bank database based on structural similarity to the target protein. Later, the set of compounds was ranked by docking scores using a Electronic High‐Throughput Screening flexible docking procedure to select the most promising molecules. The set of best performing compounds was then used for similarity search over the 1 million entries in the Ligand.Info Meta‐Database. Selected molecules having close structural relationship to a 2‐methyl‐2,4‐pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188353/ doi: 10.1111/j.1747-0285.2007.00475.x id: cord-279932-bilr71ay author: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 words: 1119.0 sentences: 61.0 pages: flesch: 52.0 cache: ./cache/cord-279932-bilr71ay.txt txt: ./txt/cord-279932-bilr71ay.txt summary: A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32674139/ doi: 10.1093/cid/ciaa1013 id: cord-294999-a5x8bmfr author: Plotkin, Stanley A title: The New Coronavirus, the Current King of China date: 2020-02-21 words: 1185.0 sentences: 82.0 pages: flesch: 54.0 cache: ./cache/cord-294999-a5x8bmfr.txt txt: ./txt/cord-294999-a5x8bmfr.txt summary: There are several candidate vaccines against MERS being developed by an international organization, the Coalition for Epidemic Preparedness (CEPI; see below) [13] . Although yet to be confirmed at this writing, it is likely that SARS-CoV-2 originated from infections transferred from small mammals in the Wuhan market to humans. Aside from the development of vaccines against SARS-CoV-2, a step the Chinese government should take is to ban the sale of small mammals in their markets to prevent the introduction of other coronaviruses or, for that matter, pathogens in general that could adapt to humans. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study A synthetic consensus anti-spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates A double-inactivated whole virus candidate SARS coronavirus vaccine stimulates neutralising and protective antibody responses abstract: nan url: https://doi.org/10.1093/jpids/piaa018 doi: 10.1093/jpids/piaa018 id: cord-323216-rgj8vs9z author: Plotkin, Stanley A title: Vaccination Against Severe Acute Respiratory Syndrome Coronavirus 2 date: 2020-08-03 words: 970.0 sentences: 63.0 pages: flesch: 51.0 cache: ./cache/cord-323216-rgj8vs9z.txt txt: ./txt/cord-323216-rgj8vs9z.txt summary: There is a universal and widely acknowledged need for a vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because of its widespread circulation and high mortality and morbidity. Although some vaccine efforts use the whole inactivated or attenuated virus, the great majority concentrate on the Spike protein, which contains 2 parts: S1 and S2. Table 1 summarizes the current approaches to development of vaccines against SARS-CoV-2. Vaccine developers have experimented with many different ways to present the S protein or, in some cases, the RBD domain to the immune system. There are many important issues that must be answered in these trials, including: Can vaccination prevent infection as well as disease? Will evolution of the SARS-CoV-2 virus require changes in vaccine antigens? Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry The challenges of vaccine development against a new virus during a pandemic abstract: Over 100 attempts are being made to develop a vaccine for use in the epidemic of COVID-19. Many different technologies are being used in an effort to prevent the infection or at least the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32744616/ doi: 10.1093/jpids/piaa093 id: cord-324949-sqy03dks author: Poe, Francis L. title: N-Acetylcysteine: a potential therapeutic agent for SARS-CoV-2 date: 2020-05-30 words: 3485.0 sentences: 208.0 pages: flesch: 47.0 cache: ./cache/cord-324949-sqy03dks.txt txt: ./txt/cord-324949-sqy03dks.txt summary: In vivo, in vitro, and human clinical trials have demonstrated N-acetylcysteine (NAC) as an effective method of improving redox status, especially when under oxidative stress. Mediation of the viral load could occur through NAC''s ability to increase cellular redox status via maximizing the rate limiting step of glutathione synthesis, and thereby potentially decreasing the effects of virally induced oxidative stress and cell death. The pathogenic factors of SARS-CoV-2 that could possibly be mediated by NAC are (1) T cell exhaustion, which manifests as lower counts and decreased functional capacity of CD4+ and CD8+ cells; (2) pro-inflammatory state via increase in TNF-ɑ, IL1β, IL18; and (3) modulation of viral activity through increased glutathione. Mediation of the viral load could occur through the ability of NAC to increase cellular redox status by maximizing the rate limiting step of glutathione synthesis, and thereby decreasing the effects of virally induced oxidative stress and cell death. abstract: COVID-19, a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread across the globe. Predisposing factors such as age, diabetes, cardiovascular disease, and lowered immune function increase the risk of disease severity. T cell exhaustion, high viral load, and high levels of TNF-ɑ, IL1β, IL6, IL10 have been associated with severe SARS-CoV-2. Cytokine and antigen overstimulation are potentially responsible for poor humoral response to the virus. Lower cellular redox status, which leads to pro-inflammatory states mediated by TNF-ɑ is also potentially implicated. In vivo, in vitro, and human clinical trials have demonstrated N-acetylcysteine (NAC) as an effective method of improving redox status, especially when under oxidative stress. In human clinical trials, NAC can be used to replenish glutathione stores and increase the proliferative response of T cells. NAC has also been shown to inhibit the NLRP3 inflammasome pathway (IL1β and IL18) in vitro, and decrease plasma TNF-ɑ in human clinical trials. Mediation of the viral load could occur through NAC’s ability to increase cellular redox status via maximizing the rate limiting step of glutathione synthesis, and thereby potentially decreasing the effects of virally induced oxidative stress and cell death. We hypothesize that NAC could act as a potential therapeutic agent in the treatment of COVID-19 through a variety of potential mechanisms, including increasing glutathione, improving T cell response, and modulating inflammation. In this article, we present evidence to support the use of NAC as a potential therapeutic agent in the treatment of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0306987720308811?v=s5 doi: 10.1016/j.mehy.2020.109862 id: cord-355181-affuyn8z author: Poggio, Claudio title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 words: 5793.0 sentences: 304.0 pages: flesch: 43.0 cache: ./cache/cord-355181-affuyn8z.txt txt: ./txt/cord-355181-affuyn8z.txt summary: SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . abstract: The latest diffusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease (COVID-19), has involved the whole world population. Even if huge efforts to control the pandemic have been done, the viral spread is still continuing. COVID-19 is reported as a zoonosis jumped from bats and pangolins to humans. After infection in humans, SARS-CoV-2 is found in the nasopharyngeal and salivary secretions. The virus has also been detected in the blood plasma of infected patients. The viral spread occurs through droplets exhaled from the nose and mouth of the infected people when they breath or talk, or through droplets propelled as a dense cloud by chough or sneeze. The virus can also be delivered as an aerosol from blood plasma, through surgical procedures. Following these ways, the virus can disperse in the air, then reaching and settling on the exposed surfaces. How long the virus will survive on a surface depends on the material the surface is made from. Infection via high-touch surfaces should be prevented. Copper alloy coatings, combined with efficient hygienic/disinfectant procedures and careful surgical practice, could be helpful to health protection in dental practice and can also be adopted in orthopedic traumatology. url: https://www.ncbi.nlm.nih.gov/pubmed/32707757/ doi: 10.3390/ma13153244 id: cord-257719-5s6acr7m author: Poh Ng, Lisa Fong title: The Virus That Changed My World date: 2003-12-22 words: 1510.0 sentences: 74.0 pages: flesch: 61.0 cache: ./cache/cord-257719-5s6acr7m.txt txt: ./txt/cord-257719-5s6acr7m.txt summary: In the three months that Singapore was labelled as a "SARS country" by the World Health Organization (WHO), over 200 cases of SARS were reported, and 33 people died. Referring to the high standards of medical care and the societal measures put in place, Dr David Mansoor of WHO said that if not even Singapore could contain the outbreak, it was going to be very hard for other countries to prevent SARS from spreading (Chua 2003 I was to be part of the diagnostic team, and work began almost immediately. Data obtained from this work were significant for further understanding of coronavirus replication and pathogenesis, but never had I imagined that I would be able to use this knowledge in designing the SARS-CoV diagnostic kit with Roche. The months working on SARS opened my mind, as it did my heart, about the importance of research and of keeping our faith and motivation even in the toughest times. abstract: Personal account of a young virologist working in Singapore at the height of the 2003 SARS pandemic url: https://www.ncbi.nlm.nih.gov/pubmed/14691538/ doi: 10.1371/journal.pbio.0000066 id: cord-276335-e1xlwcvc author: Poh, W.P. title: Characterization of cytotoxic T‐lymphocyte epitopes and immune responses to SARS coronavirus spike DNA vaccine expressing the RGD‐integrin‐binding motif date: 2009-05-27 words: 6046.0 sentences: 326.0 pages: flesch: 52.0 cache: ./cache/cord-276335-e1xlwcvc.txt txt: ./txt/cord-276335-e1xlwcvc.txt summary: Significant cell‐mediated immune responses were characterized by cytotoxic T‐lymphocyte (51)Cr release assay and interferon‐gamma secretion ELISPOT assay against RMA‐S target cells presenting predicted MHC class I H2‐Kb epitopes, including those spanning residues 884–891 and 1116–1123 within the S2 subunit of SARS‐CoV spike protein. The production of antigen-specific antibody induced by the SARS-CoV spike DNA vaccinations was assessed For the MHC-peptide binding assay, the mean fluorescence increase (MFI) was calculated as the ratio of the fluorescence of peptide-loaded RMA-S cells to the fluorescence of unloaded RMA-S cells. Mouse IFN-g ELISPOT for splenocytes of C57BL/6 mice immunized with selected S-His and S-RGD/His DNA vaccines to confirm T-cell epitopes of spike protein. This study demonstrated that prime-boost immunization of mice with SARS-CoV spike DNA vaccine constructs S-His and S-RGD/His induced significant antigen-specific cellular immune responses, IFN-g stimulation, and CTL activation. abstract: Integrins are critical for initiating T‐cell activation events. The integrin‐binding motif Arg‐Gly‐Asp (RGD) was incorporated into the pcDNA 3.1 mammalian expression vector expressing the codon‐optimized extracellular domain of SARS coronavirus (SARS‐CoV) spike protein, and tested by immunizing C57BL/6 mice. Significant cell‐mediated immune responses were characterized by cytotoxic T‐lymphocyte (51)Cr release assay and interferon‐gamma secretion ELISPOT assay against RMA‐S target cells presenting predicted MHC class I H2‐Kb epitopes, including those spanning residues 884–891 and 1116–1123 within the S2 subunit of SARS‐CoV spike protein. DNA vaccines incorporating the Spike‐RGD/His motif or the Spike‐His construct generated robust cell‐mediated immune responses. Moreover, the Spike‐His DNA vaccine construct generated a significant antibody response. Immunization with these DNA vaccine constructs elicited significant cellular and humoral immune responses. Additional T‐cell epitopes within the SARS‐CoV spike protein that may contribute to cell‐mediated immunity in vivo were also identified. J. Med. Virol. 81:1131–1139, 2009. © 2009 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/19475608/ doi: 10.1002/jmv.21571 id: cord-276209-5999g9gp author: Poland, Gregory A. title: Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine development date: 2020-06-02 words: 1607.0 sentences: 105.0 pages: flesch: 55.0 cache: ./cache/cord-276209-5999g9gp.txt txt: ./txt/cord-276209-5999g9gp.txt summary: Very soon thereafter, the causative agent was identified as the now-named SARS-CoV-2 virus-a betacoronavirus that had crossed the species barrier to infect humans. There is no question that a vaccine against this virus, and other as-yet-to-come coronaviruses, is imperative to protect human health and to quickly respond to future viral introductions, epidemics, and pandemics. These pathways, informed by science and the past history of successes and failures, are designed to maximize the chances of efficacy and safety. Further mutations could conceivably lead to issues of original antigenic sin with resultant disease enhancement after exposure or to vaccines that simply are not effective into the future. In addition to safety issues, I raise concern over ''''S-only" vaccine approaches for the mid-to long-term control of this RNA virus. We need a vaccine-and we need it as quickly as one can be developed-that demonstrates safety and efficacy in adequately powered studies. abstract: nan url: https://doi.org/10.1016/j.vaccine.2020.04.073 doi: 10.1016/j.vaccine.2020.04.073 id: cord-287205-k64svq6n author: Pollet, Jeroen title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date: 2020-11-05 words: 4245.0 sentences: 282.0 pages: flesch: 56.0 cache: ./cache/cord-287205-k64svq6n.txt txt: ./txt/cord-287205-k64svq6n.txt summary: title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. The modified SARS-CoV-2 antigen, 264 RBD219-N1C1, when formulated on Alhydrogel ® , was shown to induce virus-neutralizing antibodies 265 in mice, equivalent to those levels elicited by the wild-type (RBD219-WT) recombinant protein 266 counterpart. Here we report on a yeast-expressed SARS-CoV-2 RBD219-N1C1 protein and its potential as a 397 vaccine candidate antigen for preventing COVID-19. In a mouse virus challenge model for the SARS CoV RBD recombinant protein vaccine, we 422 found that Alhydrogel ® formulations induced high levels of protective immunity but did not 423 stimulate eosinophilic immune enhancement, suggesting that Alhydrogel ® may even reduce immune The selection of the P. abstract: There is an urgent need for an accessible and low-cost COVID-19 vaccine suitable for low- and middle-income countries. Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. After introducing two modifications into the wild-type RBD gene to reduce yeast-derived hyperglycosylation and improve stability during protein expression, we show that the recombinant protein, RBD219-N1C1, is equivalent to the wild-type RBD recombinant protein (RBD219-WT) in an in vitro ACE-2 binding assay. Immunogenicity studies of RBD219-N1C1 and RBD219-WT proteins formulated with Alhydrogel® were conducted in mice, and, after two doses, both the RBD219-WT and RBD219-N1C1 vaccines induced high levels of binding IgG antibodies. Using a SARS-CoV-2 pseudovirus, we further showed that sera obtained after a two-dose immunization schedule of the vaccines were sufficient to elicit strong neutralizing antibody titers in the 1:1,000 to 1:10,000 range, for both antigens tested. The vaccines induced IFN-γ, IL-6, and IL-10 secretion, among other cytokines. Overall, these data suggest that the RBD219-N1C1 recombinant protein, produced in yeast, is suitable for further evaluation as a human COVID-19 vaccine, in particular, in an Alhydrogel® containing formulation and possibly in combination with other immunostimulants. url: https://doi.org/10.1101/2020.11.04.367359 doi: 10.1101/2020.11.04.367359 id: cord-298669-g2up0cfi author: Pollock, David D title: Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2 date: 2020-07-13 words: 3261.0 sentences: 158.0 pages: flesch: 52.0 cache: ./cache/cord-298669-g2up0cfi.txt txt: ./txt/cord-298669-g2up0cfi.txt summary: Nevertheless, the evolutionary reasons for low GC content are still debated in even exceptionally well-studied systems with unquestioned animal origins (2020) points out, the mammalian zinc finger antiviral protein (ZAP) binds to CpG dinucleotides in viral RNA genomes and inhibits viral replication and mediates viral degradation (Ficarelli et al., 2020; Ficarelli et al., 2019; Meagher et al., 2019; Takata et al., 2017) . Despite this, Xia (2020) speculated that low viral genomic CpG levels in SARS-CoV-2 required evolutionary time in a previous host species and tissue that more actively selected for CpG depletion than do bats. In addition to being unsupported by positive evidence, Xia''s (2020) hypothesis for dogs as intermediate hosts of ancestral viruses giving rise to SARS-CoV-2 requires an unlikely history of cross-species viral transmission (see Fig. 2 for potential hypotheses) for which there is no evidence. abstract: Due to the scope and impact of the COVID-19 pandemic there exists a strong desire to understand where the SARS-CoV-2 virus came from and how it jumped species boundaries to humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness and divergence times of viruses and identifying past selective pressures. However, we must uphold rigorous standards of inference and interpretation on this topic because of the ramifications of being wrong. Here, we dispute the conclusions of Xia (2020) that dogs are a likely intermediate host of a SARS-CoV-2 ancestor. We highlight major flaws in Xia’s inference process and his analysis of CpG deficiencies, and conclude that there is no direct evidence for the role of dogs as intermediate hosts. Bats and pangolins currently have the greatest support as ancestral hosts of SARS-CoV-2, with the strong caveat that sampling of wildlife species for coronaviruses has been limited. url: https://www.ncbi.nlm.nih.gov/pubmed/32658964/ doi: 10.1093/molbev/msaa178 id: cord-346441-b1r6i0wq author: Polverino, Francesca title: Cigarette Smoking and COVID-19: A Complex Interaction date: 2020-08-01 words: 895.0 sentences: 53.0 pages: flesch: 48.0 cache: ./cache/cord-346441-b1r6i0wq.txt txt: ./txt/cord-346441-b1r6i0wq.txt summary: These findings have putatively important implications for patients with COVID-19 because ACE2 has been shown to be the receptor used by SARS-CoV-2 to enter the host cells (3) and yet seem in contrast with the consolidated epidemiological data worldwide indicating a low prevalence of active smokers among patients with COVID-19. Last, though it is possible that cigarette smoke increases the ACE2 expression by the bronchial epithelium, thus facilitating the entry of SARS-CoV-2, this does not necessarily translate into a higher risk for developing COVID-19 pneumonia. To conclude, what is unchallengeable is that cigarette smoke is detrimental for the lungs in several ways, and further studies are needed to clarify the reasons behind the reported low prevalence of current smokers among hospitalized patients with COVID-19. Tobacco smoking increases the lung gene expression of ACE2, the receptor of SARS-CoV-2 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32530714/ doi: 10.1164/rccm.202005-1646le id: cord-154170-7pnz98o6 author: Ponciano, Jos''e Miguel title: Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America date: 2020-05-22 words: 3253.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-154170-7pnz98o6.txt txt: ./txt/cord-154170-7pnz98o6.txt summary: Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. Here we show that a multi-model, multi-stages modeling approach helps elucidate i) early epidemic growth in fourteen Latin-American countries ii) the role of poverty in shaping the growth rate of the number of cases and iii) the probability that the number of cases of SARS-CoV-2 exceeds any given amount within arbitrarily defined small windows of time, starting from the present. We draw on prior work in conservation biology, population dynamics and epidemiological theory to complement the current suite of deterministic epidemiological models, characterize the role of urban poverty in shaping the region''s SARS-CoV-2 epidemics, and develop a methodology to generate short (5-15 days), sequentially updatable, process-based forecasts. abstract: Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. We present an alternative approach that draws on advances in statistical ecology and conservation biology to enhance the value of sparse data in projecting and ameliorating epidemics. Our approach, leading to what we call a Stochastic Epidemic Gompertz model, with few parameters can flexibly incorporate heterogeneity in transmission within populations and across time. We demonstrate that poverty has a large impact on the course of the pandemic, across fourteen Latin American countries, and show how our approach provides flexible, time-varying projections of disease risk that can be used to refine public health strategies. url: https://arxiv.org/pdf/2005.11201v1.pdf doi: nan id: cord-342681-pqzcy9wu author: Pongpirul, Wannarat A. title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 words: 1740.0 sentences: 117.0 pages: flesch: 41.0 cache: ./cache/cord-342681-pqzcy9wu.txt txt: ./txt/cord-342681-pqzcy9wu.txt summary: Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. During the study period, Thailand''s discharge criteria for hospitalized COV-ID-19 patients required resolution of clinical signs and symptoms and 2 respiratory specimens without detectable SARS-CoV-2 RNA collected >24 hours apart. Clinical resolution occurred a median of 12 (9-13.5 ) days after illness onset, and these patients had detectable SARS-CoV-2 RNA in upper respiratory tract specimens for a median of 14 (9-26) days after illness onset (Table 2) . However, patients became afebrile 6 days after illness onset, with a median of 9 (3-19.75 ) additional days of detectable SARS-CoV-2 RNA in respiratory specimens after resolution of fever ( Table 2 ). Other studies have described asymptomatic patients with upper respiratory specimens positive for SARS-CoV-2 (9), and evidence suggests such cases pose a risk for transmission (10) (11) (12) . abstract: Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. We identified viral co-infections and an asymptomatic person with detectable virus RNA in serial tests. We describe implications for surveillance. url: https://www.ncbi.nlm.nih.gov/pubmed/32267826/ doi: 10.3201/eid2607.200598 id: cord-335308-5kh7wgvx author: Ponnusamy, Rajesh title: Variable Oligomerization Modes in Coronavirus Non-structural Protein 9 date: 2008-11-28 words: 10725.0 sentences: 580.0 pages: flesch: 62.0 cache: ./cache/cord-335308-5kh7wgvx.txt txt: ./txt/cord-335308-5kh7wgvx.txt summary: In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Although the residue responsible for disulfide formation in HCoV-229E Nsp9, Cys69, is conserved in SARS-CoV Nsp9, and the sequence identity is as high as 45% between the two proteins (see Supplementary Data Fig. S3 ), the mode of dimerization in the latter is very different from what we observe in our structure. Wild-type SARS-CoV Nsp9 and the HCoV-229E Nsp9 Cys69Ala mutant form higher oligomers at a protein concentration of 100 μM, presumably involving interactions similar to those seen in the crystal structure. On the other hand, the HCoV-229E Cys69Ala mutant has a dimerization mode similar to that of the wild-type SARS-CoV Nsp9 but it does not show binding with the nucleic acid in the gel mobility-shift experiment (except for the small shift seen for the 55-mer, the longest oligonucleotide tested). abstract: Abstract Non-structural protein 9 (Nsp9) of coronaviruses is believed to bind single-stranded RNA in the viral replication complex. The crystal structure of Nsp9 of human coronavirus (HCoV) 229E reveals a novel disulfide-linked homodimer, which is very different from the previously reported Nsp9 dimer of SARS coronavirus. In contrast, the structure of the Cys69Ala mutant of HCoV-229E Nsp9 shows the same dimer organization as the SARS-CoV protein. In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Chemical cross-linking suggests similar modes of aggregation in solution. In zone-interference gel electrophoresis assays and surface plasmon resonance experiments, the HCoV-229E wild-type protein is found to bind oligonucleotides with relatively high affinity, whereas binding by the Cys69Ala and Cys69Ser mutants is observed only for the longest oligonucleotides. The corresponding mutations in SARS-CoV Nsp9 do not hamper nucleic acid binding. From the crystal structures, a model for single-stranded RNA binding by Nsp9 is deduced. We propose that both forms of the Nsp9 dimer are biologically relevant; the occurrence of the disulfide-bonded form may be correlated with oxidative stress induced in the host cell by the viral infection. url: https://www.sciencedirect.com/science/article/pii/S0022283608009406 doi: 10.1016/j.jmb.2008.07.071 id: cord-310477-vniokol0 author: Pontes, Camila title: Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date: 2020-08-21 words: 4371.0 sentences: 197.0 pages: flesch: 46.0 cache: ./cache/cord-310477-vniokol0.txt txt: ./txt/cord-310477-vniokol0.txt summary: More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). In summary, the SDPs found within these β-CoV subgenera define a specific region of the receptor binding domains: they are part of, or in direct contact with, the ACE2 interacting surface ( A second S3Det analysis was performed on the full β-CoV MSA. On the other hand, the analysis performed on individual β-CoV subgenera, i.e. Sarbecovirus, Merbecovirus and Embecovirus subgroups, allowed a fine-grained classification into subfamily clusters that clearly reflect the functional diversification of the spike protein family, that is, the specificity to different host-cell receptors (Figure 2-3) . abstract: The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the β-CoV spike protein family, using sequence information alone, can provide rich information on the molecular basis of the specificity of β-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptors adaptation of circulating and future novel β-CoVs. Significance Unraveling the molecular basis for host cell receptor usage among β-CoVs is crucial to our understanding of cross-species transmission, adaptation and for molecular-guided epidemiological monitoring of potential outbreaks. In the present study, we survey the sequence conservation patterns of the β-CoV spike protein family to identify the evolutionary constraints shaping the functional specificity of the protein across the β-CoV lineage. We show that the unsupervised analysis of statistical patterns in a MSA of the spike protein family can help tracing the amino acid space encoding the specificity of β-CoVs to their cognate host cell receptors. We argue that the results obtained in this work can provide a framework for monitoring the evolution of SARS-CoV-2 specificity to the hACE2 receptor, as the virus continues spreading in the human population and differential virulence starts to arise. url: https://doi.org/10.1101/2020.08.21.260745 doi: 10.1101/2020.08.21.260745 id: cord-279519-4ad8ubrt author: Poochi, Saravana Prabha title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein date: 2020-07-06 words: 2363.0 sentences: 146.0 pages: flesch: 50.0 cache: ./cache/cord-279519-4ad8ubrt.txt txt: ./txt/cord-279519-4ad8ubrt.txt summary: title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein Angiotensin converting enzyme 2 (ACE2) and main protease (M(Pro)) are significant target proteins, mainly involved in the attachment of viral genome to host cells and aid in replication of severe acute respiratory syndrome‐coronaviruses or SARS‐CoV genome. In the present study, we identified 11 potent bioactive compounds from ethanolic leaf extract of Ipomoea obscura (L.) by using GC‐MS analysis. These potential bioactive compounds were considered for molecular docking studies against ACE2 and M(Pro) target proteins to determine the antiviral effects against SARS‐COV. In this investigation we performed in silico docking by applying Glide 5.5 (Dik-Lung, Daniel, & Chung, 2011; Glide, 2009 ), against respiratory therapeutic target ACE2 exhibited in human and M Pro in SARS-CoV-2. Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS-CoV-2 main protease and ACE2 protein abstract: Angiotensin converting enzyme 2 (ACE2) and main protease (M(Pro)) are significant target proteins, mainly involved in the attachment of viral genome to host cells and aid in replication of severe acute respiratory syndrome‐coronaviruses or SARS‐CoV genome. In the present study, we identified 11 potent bioactive compounds from ethanolic leaf extract of Ipomoea obscura (L.) by using GC‐MS analysis. These potential bioactive compounds were considered for molecular docking studies against ACE2 and M(Pro) target proteins to determine the antiviral effects against SARS‐COV. Results exhibits that among 11 compounds from I. obscura (L.), urso‐deoxycholic acid, demeclocycline, tetracycline, chlorotetracycline, and ethyl iso‐allocholate had potential viral inhibitory activity. Hence, the present findings suggested that chemical constitution present in I. obscura (L.) will address inhibition of corona viral replication in host cells. url: https://www.ncbi.nlm.nih.gov/pubmed/32838301/ doi: 10.1002/fft2.29 id: cord-347289-3yi5tz04 author: Poon, L. . C. title: ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update date: 2020-06-01 words: 8036.0 sentences: 413.0 pages: flesch: 42.0 cache: ./cache/cord-347289-3yi5tz04.txt txt: ./txt/cord-347289-3yi5tz04.txt summary: American College of Obstetricians and Gynecologists (ACOG): https://www.acog.org/clinical-information/phys ician-faqs/covid-19-faqs-for-ob-gyns-obstetrics Centers for Disease Control , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health emergency. A case series of 12 pregnant women with SARS-CoV in Hong Kong, China, reported three maternal deaths, that four of seven patients who presented in the first trimester had spontaneous miscarriage, four of five patients who presented after 24 weeks had preterm birth and two mothers recovered without delivery but their ongoing pregnancies were complicated by FGR 8 . In two studies, with a combined total of 10 pregnant women with COVID-19 in the third trimester, amniotic fluid, cord blood and neonatal throat swab samples tested negative for SARS-CoV-2, suggesting there was no evidence of vertical transmission in women who developed COVID-19 pneumonia in late pregnancy 26, 76 . An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32356590/ doi: 10.1002/uog.22061 id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 words: 2425.0 sentences: 115.0 pages: flesch: 54.0 cache: ./cache/cord-300685-bcjnujlj.txt txt: ./txt/cord-300685-bcjnujlj.txt summary: The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/12765993/ doi: 10.1373/49.6.953 id: cord-270613-vnjuubt4 author: Poon, Terence C.W. title: Proteomic analysis reveals platelet factor 4 and beta‐thromboglobulin as prognostic markers in severe acute respiratory syndrome date: 2012-06-28 words: 3358.0 sentences: 176.0 pages: flesch: 49.0 cache: ./cache/cord-270613-vnjuubt4.txt txt: ./txt/cord-270613-vnjuubt4.txt summary: The data on 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count) from 38 SARS patients before treatment were subjected to forward stepwise multiple logistic regression (SPSS, v18, IBM) for prediction of the ICU admission and/or supplemental oxygen administration in the later period. Among the 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count), multiple logistic regress analyses identified four proteomic features (m/z 6634, m/z 7769, m/z 8635, m/z 8865) as statistically significant prognostic markers for supplemental oxygen administration or ICU admission in the later period. To confirm the differential patterns and the identities of the m/z 7769 and m/z 8865 proteomic features, serum samples were subjected to Western blot analysis using specific antibodies against PF4 and beta-TG. abstract: Previously, we reported that proteomic fingerprints were present in sera of patients with severe acute respiratory syndrome (SARS), and could separate patients into subgroups with different prognoses. In the present study, we examined the prognostic values of the SARS‐associated proteomic features by biostatistical analysis, and deciphered the identities of those with prognostic values. Data of 20 SARS‐associated serum proteomic features and ten serological variables from 38 SARS adult patients before treatment were subjected to multivariate logistic regression. Proteomic features of m/z 6634, m/z 7769, m/z 8635, and m/z 8865 were identified as independent prognostic markers. After purification by cation‐exchange chromatography and gel electrophoresis, proteomic features of m/z 7769 and m/z 8865 were found to be platelet factor 4 (PF4) and beta‐thromboglobulin (beta‐TG) by tandem mass spectrometry, respectively. The associations of decreased serum PF4 and increased serum beta‐TG levels with poor prognosis were confirmed by Western blot. Previous studies suggest that PF4 and beta‐TG are involved in the pathogenesis of acute respiratory distress syndrome (ARDS) in a negative and positive way, respectively. Our results suggest that PF4 and beta‐TG may also play similar roles in the development of ARDS in SARS patients. url: https://doi.org/10.1002/elps.201200002 doi: 10.1002/elps.201200002 id: cord-310017-c8rd714a author: Popa, Alexandra title: Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date: 2020-07-17 words: 5572.0 sentences: 330.0 pages: flesch: 49.0 cache: ./cache/cord-310017-c8rd714a.txt txt: ./txt/cord-310017-c8rd714a.txt summary: Moreover, we combined our deep viral genome sequencing data with epidemiologically identified chains of transmissions and family clusters together with biomathematical analyses to study genetic bottlenecks and the dynamics of genome evolution of SARS-CoV-2. We assembled SARS-CoV-2 genome sequences, constructed phylogenies and identified low 15 frequency mutations based on high-quality sequencing results with >5 million reads per sample and >80% of mapped viral reads (Fig. S2A-B) . Our pipeline was validated by experimental controls involving sample titration and technical sample replicates ( Fig. S2CTo investigate the link between local outbreaks in Austria and the global pandemic, we 20 performed phylogenetic analysis of 305 SARS-CoV-2 genomes from the Austrian cases (>96% genome coverage, >80% aligned viral reads) and 7,695 global genomes from the GISAID database (Fig. 1B, Table S1 ). 7 Dynamics of low frequency and fixed mutations in clusters Next, we sought to gain insights into the fundamental processes of SARS-CoV-2 infection by integrative analysis of viral genomes. abstract: Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations. Graphical Abstract url: https://doi.org/10.1101/2020.07.15.204339 doi: 10.1101/2020.07.15.204339 id: cord-319831-e07vt846 author: Popescu, Saskia title: Roadblocks to Infection Prevention Efforts in Health Care: SARS-CoV-2/COVID-19 Response date: 2020-03-30 words: 1827.0 sentences: 86.0 pages: flesch: 44.0 cache: ./cache/cord-319831-e07vt846.txt txt: ./txt/cord-319831-e07vt846.txt summary: T he emergence of a novel coronavirus (SARS-CoV-2) causing the disease, COVID-19, in Wuhan, China, in late 2019 is currently testing international public health and preparedness efforts. 1 These IPC outbreak efforts include education, reinforcement of infection prevention standards like isolation and proper usage of personal protective equipment (PPE), and established processes to ensure that the i3 strategy (identify, isolate, and inform) is used and that the health care facilities meet the guidance of the Centers for Disease Control and Prevention and World Health Organization. Unfortunately, to truly use IPC programs for COVID-19 response, it is important to understand why health-care-associated outbreaks and infection prevention failures occur all too often. A 2018 Report by the Office Inspector General of the US Department of Health and Human Services assessed hospital readiness to emerging infectious disease threats following the 2013-2016 Ebola outbreak. abstract: The outbreak of a novel coronavirus, SARS-CoV-2, is challenging international public health and health care efforts. As hospitals work to acquire enough personal protective equipment and brace for potential cases, the role of infection prevention efforts and programs has become increasingly important. Lessons from the 2003 SARS-CoV outbreak in Toronto and 2015 MERS-CoV outbreak in South Korea have unveiled the critical role that hospitals play in outbreaks, especially of novel coronaviruses. Their ability to amplify the spread of disease can rapidly fuel transmission of the disease, and often those failures in infection prevention and general hospital practices contribute to such events. While efforts to enhance infection prevention measures and hospital readiness are underway in the United States, it is important to understand why these programs were not able to maintain continued, sustainable levels of readiness. History has shown that infection prevention programs are primarily responsible for preparing hospitals and responding to biological events but face understaffing and focused efforts defined by administrators. The current US health care system, though, is built upon a series of priorities that often view biopreparedness as a costly endeavor. Awareness of these competing priorities and the challenges that infection prevention programs face when working to maintain biopreparedness is critical in adequately addressing this critical infrastructure in the face of an international outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32223774/ doi: 10.1017/dmp.2020.55 id: cord-303407-n7j56sci author: Popofsky, Stephanie title: Impact of Maternal SARS-CoV-2 Detection on Breastfeeding Due to Infant Separation at Birth date: 2020-08-10 words: 4364.0 sentences: 204.0 pages: flesch: 45.0 cache: ./cache/cord-303407-n7j56sci.txt txt: ./txt/cord-303407-n7j56sci.txt summary: CONCLUSION: In the setting of COVID-19, separation of mother–newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following discharge compared with unseparated mothers and infants. In the setting of COVID-19, separation of mother-newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following J o u r n a l P r e -p r o o f 3 discharge compared with unseparated mothers and infants. The Centers for Disease Control and Prevention (CDC) [4] and American Academy of Pediatrics (AAP) [5] each published interim guidelines for management of neonates born to mothers with confirmed or suspected COVID-19, including recommendations for temporary separation of these dyads. To assess the impact of our policy change surrounding mother-newborn dyad separation on breastfeeding rates, we evaluated mothers'' pre-delivery plans for feeding, and compared these with actual outcomes of breastfeeding during perinatal admission and following discharge. abstract: OBJECTIVE: To assess the impact of separation of SARS-CoV-2 PCR-positive mother–newborn dyads on breastfeeding outcomes. STUDY DESIGN: This is an observational longitudinal cohort study of SARS-CoV-2 PCR-positive mothers and their infants at three NYU Langone Health hospitals from March 25, 2020 through May 30, 2020. Mothers were surveyed by telephone regarding pre-delivery feeding plans, in-hospital feeding, and home feeding of their neonates. Any change prompted an additional question to determine whether this change was due to COVID-19. RESULTS: Of the 160 mother–newborn dyads, 103 mothers were reached by telephone, and 85 consented to participate. No significant difference was observed in pre-delivery feeding plan between the separated and unseparated dyads (P = .268). Higher rates of breastfeeding were observed in the unseparated dyads compared with the separated dyads in the hospital (p<0.001), and at home (p=0.012). Only two mothers in each group reported expressed breast milk as the hospital feeding source (5.6% of unseparated vs 4.1% of separated). COVID-19 was more commonly cited as the reason for change among the separated compared with the unseparated group (49.0% vs 16.7%, p<0.001). When dyads were further stratified by symptom status into four groups (asymptomatic separated, asymptomatic unseparated, symptomatic separated, and symptomatic unseparated), results remained unchanged. CONCLUSION: In the setting of COVID-19, separation of mother–newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following discharge compared with unseparated mothers and infants. No evidence of vertical transmission was observed; one case of postnatal transmission occurred from an unmasked symptomatic mother who held her infant at birth. url: https://doi.org/10.1016/j.jpeds.2020.08.004 doi: 10.1016/j.jpeds.2020.08.004 id: cord-286631-3fmg3scx author: Pormohammad, Ali title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis date: 2020-06-05 words: 3669.0 sentences: 212.0 pages: flesch: 47.0 cache: ./cache/cord-286631-3fmg3scx.txt txt: ./txt/cord-286631-3fmg3scx.txt summary: title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis The trigger for rapid screening and treatment of COVID-19 patients is based on clinical symptoms, laboratory, and radiographic findings that are similar to SARS and MERS infections. In this study, we attempted to distinguish the clinical symptoms, laboratory findings, radiographic signs, and outcomes of confirmed COVID-19, SARS, and MERS patients. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Clinical aspects and outcomes of 70 patients with Middle East respiratory syndrome coronavirus infection: a single-center experience in Saudi Arabia Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection Middle East respiratory syndrome coronavirus: a case-control study of hospitalized patients abstract: INTRODUCTION: Within this large‐scale study, we compared clinical symptoms, laboratory findings, radiographic signs, and outcomes of COVID‐19, SARS, and MERS to find unique features. METHOD: We searched all relevant literature published up to February 28, 2020. Depending on the heterogeneity test, we used either random or fixed‐effect models to analyze the appropriateness of the pooled results. Study has been registered in the PROSPERO database (ID 176106). RESULT: Overall 114 articles included in this study; 52 251 COVID‐19 confirmed patients (20 studies), 10 037 SARS (51 studies), and 8139 MERS patients (43 studies) were included. The most common symptom was fever; COVID‐19 (85.6%, P < .001), SARS (96%, P < .001), and MERS (74%, P < .001), respectively. Analysis showed that 84% of Covid‐19 patients, 86% of SARS patients, and 74.7% of MERS patients had an abnormal chest X‐ray. The mortality rate in COVID‐19 (5.6%, P < .001) was lower than SARS (13%, P < .001) and MERS (35%, P < .001) between all confirmed patients. CONCLUSIONS: At the time of submission, the mortality rate in COVID‐19 confirmed cases is lower than in SARS‐ and MERS‐infected patients. Clinical outcomes and findings would be biased by reporting only confirmed cases, and this should be considered when interpreting the data. url: https://www.ncbi.nlm.nih.gov/pubmed/32502331/ doi: 10.1002/rmv.2112 id: cord-271544-i20105lq author: Poston, Daniel title: Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection date: 2020-10-11 words: 1366.0 sentences: 87.0 pages: flesch: 53.0 cache: ./cache/cord-271544-i20105lq.txt txt: ./txt/cord-271544-i20105lq.txt summary: Cross-reactive immune responses elicited by seasonal coronaviruses might impact SARS-CoV-2 susceptibility and disease outcomes. We measured neutralizing activity against SARS-CoV-2 in pre-pandemic sera from patients with prior PCR-confirmed seasonal coronavirus infection. One hypothesis is that cross reactive immune responses, elicited by prior 46 infection with seasonal coronaviruses impacts the course of SARS-CoV-2 infection, perhaps 47 providing a degree of protection against severe COVID-19 disease. The numbers of rVSV/SARS-2/GFP was assessed by flow cytometric detection of 92 GFP expression as described previously To assess whether prior infection by seasonal coronaviruses could elicit antibodies with 104 neutralization activity against SARS-CoV-2, we identified 37 serum samples collected prior to 105 the COVID19 pandemic from patients who were diagnosed using PCR with a seasonal 106 coronavirus 11-291 days (median 80 = days) prior to serum sample collection. . https://doi.org/10.1101/2020.10.08.20209650 doi: medRxiv preprint neutralize rVSV/SARS-CoV-2/GFP with NT50 values ranging from 96 to 5400. abstract: Cross-reactive immune responses elicited by seasonal coronaviruses might impact SARS-CoV-2 susceptibility and disease outcomes. We measured neutralizing activity against SARS-CoV-2 in pre-pandemic sera from patients with prior PCR-confirmed seasonal coronavirus infection. While neutralizing activity against seasonal coronaviruses was detected in nearly all sera, cross-reactive neutralizing activity against SARS-CoV-2 was undetectable. url: https://www.ncbi.nlm.nih.gov/pubmed/33052353/ doi: 10.1101/2020.10.08.20209650 id: cord-349541-7g50vg14 author: Poulikakos, Dimitrios title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date: 2020-07-07 words: 427.0 sentences: 39.0 pages: flesch: 66.0 cache: ./cache/cord-349541-7g50vg14.txt txt: ./txt/cord-349541-7g50vg14.txt summary: key: cord-349541-7g50vg14 title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England cord_uid: 7g50vg14 Please cite this article as: Poulikakos D, Sinha S, Kalra PA, SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104545 Amongst the 22 (7·8%) HCW with previous SARS-Cov-2 PCR nasopharyngeal swabs, 2 were positive, 12 were negative, and 7 did not disclose the result. Positive SARS-Cov-2 IgG was detected in 17 (6%) HCW and 6 (35·3%) had been asymptomatic. All IgG positive cases were in DIPC HCW (17 out of 195; 8·7%). One IgG positive HCW did not disclose ethnicity. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients Hospital-Wide SARS-CoV-2 Antibody Screening Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics First experience of COVID-19 screening of health-care workers in England abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1386653220302870?v=s5 doi: 10.1016/j.jcv.2020.104545 id: cord-307287-zpq6byml author: Poulsen, Nadia Nicholine title: Cyclosporine and COVID‐19: Risk or Favorable? date: 2020-08-10 words: 4455.0 sentences: 235.0 pages: flesch: 39.0 cache: ./cache/cord-307287-zpq6byml.txt txt: ./txt/cord-307287-zpq6byml.txt summary: A letter by Russel et al suggests that there is tantalizing in vitro evidence for cyclosporine as an anti-coronavirus agent as well as a potential disease-modifying role through inhibition of Severe Acute Respiratory Syndrome (SARS) coronavirus-mediated IL-2 induction and authors advocate that a trial of cyclosporine should be considered in the event of a future SARS epidemic 22 . The Immunonephrology Working Group of the European Renal Association-European Dialysis and Transplant Association has published recommendations for the management of patients with immune-mediated kidney disease during this current pandemic, and authors point out that patients with mild COVID-19 might continue low dose of cyclosporine due to the in vitro evidence of inhibition of coronavirus replication 84 . We are still awaiting robust data from COVID-19 patients actively treated with calcineurin inhibitors due to transplantation or autoimmune diseases but so far there is no evidence that use of cyclosporine possess an additional risk for severe COVID-19 in addition to the co-morbidities such as diabetes, smoking, hypertension and obesity that often co-exist in these patients. abstract: The coronavirus disease 2019 (COVID‐19) pandemic is declared a global health emergency. COVID‐19 is triggered by a novel coronavirus: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV2). Baseline characteristics of admitted patients with COVID‐19 show that adiposity, diabetes and hypertension are risk factors for developing severe disease, but so far immunosuppressed patients that are listed as high‐risk patients have not been more susceptible to severe COVID‐19 than the rest of the population. Multiple clinical trials are currently being conducted, which hopefully can identify more drugs that can lower mortality, morbidity and burden on the society. Several independent studies have convincingly shown that cyclosporine inhibit replication of several different coronaviruses in vitro. The cyclosporine‐analog Alisporivir has recently been shown to inhibit SARS‐CoV2 in vitro. These findings are intriguing, although there is no clinical evidence for a protective effect to reduce the likelihood of severe COVID‐19 or to treat the immune storm or adult respiratory distress syndrome (ARDS) that often causes severe morbidity. Here, we review the putative link between COVID‐19 and cyclosporine, while we await more robust clinical data. url: https://doi.org/10.1111/ajt.16250 doi: 10.1111/ajt.16250 id: cord-284734-qioy7eso author: Pourahmad, Ramtin title: Efficacy of Plasmapheresis and Immunoglobulin Replacement Therapy (IVIG) on Patients with COVID-19 date: 2020-07-31 words: 3073.0 sentences: 168.0 pages: flesch: 45.0 cache: ./cache/cord-284734-qioy7eso.txt txt: ./txt/cord-284734-qioy7eso.txt summary: According to recent observations about different modalities in treatment of patients infected with COVID-19, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection. According to the medical experiences in the treatment of patients infected with other members of coronavirus family such as SARS-CoV and MERS-CoV, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection [1] [2] [3] [4] [5] [6] [7] . As the world confronting a pandemic due to SARS-CoV-2, immunoglobulin replacement therapy (IVIG) could be an ideal option for prevention and treatment of COVID-19 disease. According to the reports, China has used immunoglobulin replacement therapy on several COVID-19 patients during the outbreak of this novel coronavirus which showed promising results [46] . The use of convalescent plasma therapy and remdesivir in the successful management of a critically ill obstetric patient with novel coronavirus 2019 infection: a case report. abstract: Since the rapidly evolving outbreak of COVID-19, several empirical therapeutic options have been recommended including the use of antivirals, steroids, and vaccines. According to recent observations about different modalities in treatment of patients infected with COVID-19, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection. In this review, we aimed to provide an overview on the possible application of plasmapheresis and intravenous immunoglobulin in patients with COVID-19. url: https://doi.org/10.1007/s42399-020-00438-2 doi: 10.1007/s42399-020-00438-2 id: cord-343127-n3fs8ph8 author: Pousa, Pedro A. title: Extrapulmonary manifestations of COVID-19 in children: a comprehensive review and pathophysiological considerations date: 2020-09-22 words: 5503.0 sentences: 318.0 pages: flesch: 46.0 cache: ./cache/cord-343127-n3fs8ph8.txt txt: ./txt/cord-343127-n3fs8ph8.txt summary: OBJECTIVE: The aim of this review was to summarize the most common extrapulmonary manifestations in pediatric patients with COVID-19, as well as to discuss clinical, epidemiological, and pathophysiological aspects of these clinical presentations in children. In addition, epithelial cells of the small intestine is another tissue that highly express ACE2 in cell membrane, [42] creating another potential region for SARS-CoV-2 infection and enteric manifestations of COVID-19. Hence, the present authors speculate that, although children and adults have similar rates of GI symptoms, children GI symptoms are usually associated as a primary response of SARS-CoV-2 infection, due to this minor expression of ACE2, and represent milder symptoms. Children are susceptible to liver injury, as shown by a meta-analysis of 551 laboratory-confirmed pediatric COVID-19 patients reporting that 9% (35/290) presented increased ALT and 18% (58/280), high levels of AST. Therefore, children might present less severe cases of kidney injury associated with COVID-19 due to this greater expression of AT2R than adults. abstract: OBJECTIVE: The aim of this review was to summarize the most common extrapulmonary manifestations in pediatric patients with COVID-19, as well as to discuss clinical, epidemiological, and pathophysiological aspects of these clinical presentations in children. SOURCE OF DATA: An extensive search of literature was performed in order to identify pediatric cases with extrapulmonary manifestations between January 1, 2020 and June 21, 2020. Generic keywords, such as “Novel coronavirus” or “Novel coronavirus 2019” or “2019 nCoV” or “COVID-19” or “SARS-CoV-2” were searched on PubMed database, associated either with age filters or generic pediatric terms. SUMMARY OF FINDINGS: A total of 28 articles, including 199 patients, were considered suitable to review and data extraction. The main findings were summarized in tables. The main non-pulmonary manifestations in pediatric patients, in decreasing order of frequency, were gastrointestinal, renal, cardiovascular, neurological, hematological and lymphatic, cutaneous, hepatic, ocular, olfactory, and gustatory. Multisystem impairment and Kawasaki-like disease were also described. CONCLUSIONS: Differences in immune response of children and variations of tissue expression of angiotensin converting enzyme 2, the virus receptor, are likely to influence clinical, epidemiological, and pathophysiological patterns of the disease. url: https://doi.org/10.1016/j.jped.2020.08.007 doi: 10.1016/j.jped.2020.08.007 id: cord-351225-dq0xu85c author: Poutanen, Susan M. title: Transmission and control of SARS date: 2004 words: 5584.0 sentences: 229.0 pages: flesch: 45.0 cache: ./cache/cord-351225-dq0xu85c.txt txt: ./txt/cord-351225-dq0xu85c.txt summary: During the outbreak, it was evident that SARS was readily transmissible from person to person, especially in health Severe acute respiratory syndrome (SARS) was first recognized in China in November 2002 and was subsequently associated with a worldwide outbreak involving 8098 people, 774 of whom died. Evidence for this includes studies in Hong Kong and Toronto, Canada that show an increased risk for SARS in health care workers who entered the room of a patient with SARS, with increasing risk in those with closer proximity to the patient and those remaining in the room for a longer duration, suggesting that transmission is enhanced by close, prolonged contact [19•,20 •] In addition, an increased risk in household members of patients with SARS has been shown in those who had close, prolonged contact with the index person, and in particular, in those who shared a bed, reported being within 1 meter of the index person, and dined together [21•] . abstract: Severe acute respiratory syndrome (SARS) was first recognized in China in November 2002 and was subsequently associated with a worldwide outbreak involving 8098 people, 774 of whom died. The outbreak was declared contained on July 5, 2003, after the last human chain of transmission of SARS had been broken. Whether outbreaks of SARS will return is debatable, but no one disagrees that it is important to be prepared for this possibility. This article presents an overview of the transmission and control of SARS based on the current state of knowledge derived from published studies of the outbreak and on our own personal experience. url: https://www.ncbi.nlm.nih.gov/pubmed/15142486/ doi: 10.1007/s11908-004-0012-7 id: cord-352678-8f2ygul2 author: Prasad, Ashish title: Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading? date: 2020-08-05 words: 3488.0 sentences: 191.0 pages: flesch: 48.0 cache: ./cache/cord-352678-8f2ygul2.txt txt: ./txt/cord-352678-8f2ygul2.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causal agent of Coronavirus disease 2019 (COVID19) , is a single-stranded RNA virus with a non-segmented genome. In another study with COVID-19 patients in China, an early response of IgA instead of IgG was observed in the humoral immune response against SARS-CoV-2 (11) . It has been observed that 5% of COVID-19 patients become critically ill with severe pneumonia and multiple-organ damage and cytokine storm might be a possible explanation for such an observation. A case study on 214 COVID-19 patients from three special care centers of Union Hospital, Wuhan, revealed that 36.4% of the infected people had neurologic symptoms (46) . The adverse effects of antiviral drugs like hydroxychloroquine, which is reported to cause acute toxic hepatitis (54) and cytokine burst, might be responsible for such high percentage of hepatic damage cases in severely ill patients. abstract: COVID-19 caused by SARS-CoV-2 has already infected more than 6. 3 million people worldwide as of 1st June 2020 and caused a global medical emergency. Healthcare professionals have been struggling to devise appropriate therapeutic strategies against the virus mainly due to the diverse range of symptoms and multiple-organ failure in infected patients. Several broad-spectrum antiviral drugs are being used for treatment; however, there is yet no specific drug or vaccine against the virus. Multiple-organ failure due to hyperactivity of the immune system resulting in cytokine storms is a major reason for death among the 5% critically ill patients. In this article, we have discussed the damage caused by COVID-19 on different organs of the human body. url: https://www.ncbi.nlm.nih.gov/pubmed/32850890/ doi: 10.3389/fmed.2020.00370 id: cord-351845-bli3qm8w author: Prasad, Kartikay title: Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date: 2020-06-26 words: 4626.0 sentences: 293.0 pages: flesch: 46.0 cache: ./cache/cord-351845-bli3qm8w.txt txt: ./txt/cord-351845-bli3qm8w.txt summary: Towards this goal, in this study, we have generated a human-SARS-CoV-2 interactome based on recently published RNA-Seq analysis of human adenocarcinomic alveolar basal epithelial (A549) cells infected with SARS-CoV-2, and identified disease-related functional genes that will provide the insights into the patho-J o u r n a l P r e -p r o o f 4 mechanisms of COVID-19. Overall, the analysis demonstrated that the upregulated genes are mainly linked to the host response to SARS-CoV-2 infection, type I interferon signaling and the cytokine-mediated signaling pathway. The PPI network analysis indicates that the pathways are enriched in host response to virus infection, type I interferons signaling, and cytokine activation. [74] reported high SARS-CoV-2 loads very early during infection, suggesting that the virus may have developed arsenals that is able to delay the IFN response by inhibiting innate immune signaling. abstract: The current pandemic of 2019 novel coronavirus disease (COVID-19) caused by a novel virus strain, 2019-nCoV/SARS-CoV-2 have posed a serious threat to global public health and economy. It is largely unknown how the human immune system responds to this infection. A better understanding of the immune response to SARS-CoV-2 will be important to develop therapeutics against COVID-19. Here, we have used transcriptomic profile of human alveolar adenocarcinoma cells (A549) infected with SARS-CoV-2 and employed a network biology approach to generate human-virus interactome. Network topological analysis discovers 15 SARS-CoV-2 targets, which belongs to a subset of interferon (IFN) stimulated genes (ISGs). These ISGs (IFIT1, IFITM1, IRF7, ISG15, MX1, and OAS2) can be considered as potential candidates for drug targets in the treatments of COVID-19. We have identified significant interaction between ISGs and TLR3 agonists, like poly I: C, and imiquimod, and suggests that TLR3 agonists can be considered as a potential drug for drug repurposing in COVID-19. Our network centric analysis suggests that moderating the innate immune response is a valuable approach to target COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0141813020336837?v=s5 doi: 10.1016/j.ijbiomac.2020.06.228 id: cord-335610-3v8140b6 author: Prasanth, D. S. N. B. K. title: In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2 date: 2020-06-22 words: 5031.0 sentences: 310.0 pages: flesch: 49.0 cache: ./cache/cord-335610-3v8140b6.txt txt: ./txt/cord-335610-3v8140b6.txt summary: Our research study is intended to recognize the phyto-derived antiviral substances from Cinnamon against COVID-19 main protease enzyme and to understand the in silico molecular basis of its activity. Based on the above properties of Cinnamon, this research aimed to show a variety of active compounds across all Cinnamon varities and decide whether and how they interact with proteins i.e. main protease (Joshi et al., 2020) and spike protein, that are essential in the management of SARS-CoV-2. The crystal structure of Main protease (6LU7) and Spike receptor-binding domain complexed with its receptor ACE2 (6LZG) with selected top ligands identified from docking analysis such as Tenufolin (TEN) and Pavetannin C1 (PAV) were subjected to molecular dynamics using gromacs GPU enabled package. The main protease with tenufolin Spike protein (6LZG), associated with SARS was found to exhibit the best possible interaction with Pavetannin C1 (À11.1 kcal/mol) among the phytochemicals ( Table 2) . abstract: Cinnamon has been utilized to remedy a lot of afflictions of humans. Literary works illustrate that it possesses numerous biological activities. Our research study is intended to recognize the phyto-derived antiviral substances from Cinnamon against COVID-19 main protease enzyme and to understand the in silico molecular basis of its activity. In the present study, 48 isolates compounds from Cinnamon retrieved from the PubMed database, are subjected to docking analysis. Docking study was performed using Autodock vina and PyRx software. Afterwards, admetSAR, as well as DruLiTo servers, were used to investigate drug-likeness prophecy. Our study shows that the nine phytochemicals of Cinnamon are very likely against the main protease enzyme of COVID-19. Further MD simulations could identify Tenufolin (TEN) and Pavetannin C1 (PAV) as hit compounds. Utilizing contemporary strategies, these phyto-compounds from a natural origin might establish a reliable medication or support lead identification. Identified hit compounds can be further taken for in vitro and in vivo studies to examine their effectiveness versus COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32567989/ doi: 10.1080/07391102.2020.1779129 id: cord-294677-l1b4mw9d author: Prashantha, C.N. title: Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date: 2020-10-13 words: 2409.0 sentences: 147.0 pages: flesch: 48.0 cache: ./cache/cord-294677-l1b4mw9d.txt txt: ./txt/cord-294677-l1b4mw9d.txt summary: (2) Coronavirus S2 glycoprotein (662-1270) is translated as a large polypeptide that is subsequently cleaved to S1 and S2 domains from Molecular docking plays vital role in computer-aided drug discovery to predict best active molecules to the target protein. Using AutoDock 4.2 and AutoDock Vina to predict the best drug binding sites towards the affinity of active site amino acids are screened based on binding energy and number of hydrogen bonds formed to the target amino acids. • Computational Approaches to build the 3D structure of protein • Drug selection for preclinical trials to study the efficacy and disease treatment • Molecular docking approaches to screen the compounds based on binding energy abstract: The Target spike protein docking with antimalarial, antimicrobial, anti-inflammatory and HIV-Protease inhibitors. The docking processed using AutoDock Vina and the binding affinity score is noted based on kcal/mol and estimated inhibitory constant (KI). [Figure: see text] url: https://www.sciencedirect.com/science/article/pii/S1093326320305581?v=s5 doi: 10.1016/j.jmgm.2020.107769 id: cord-269025-2j37561h author: Pratelli, Annamaria title: Canine coronavirus inactivation with physical and chemical agents date: 2007-05-21 words: 6155.0 sentences: 325.0 pages: flesch: 53.0 cache: ./cache/cord-269025-2j37561h.txt txt: ./txt/cord-269025-2j37561h.txt summary: The methods for CCoV inactivation could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure of researchers to pathogens during routine laboratory procedures. To examine the ability of heat to inactivate CCoV, 500 lL aliquots of virus samples were incubated in duplicate in a 15 mL polypropylene conical tube (Falcon, Becton Dickinson Labware) for increasing periods of time at three different temperatures: +56°C, +65°C and +75°C. To examine formaldehyde and glutaraldehyde inactivation of CCoV, aliquots of virus and aldehyde samples, each at two different dilutions, were incubated at +4°C, +25°C and +37°C, respectively, for up to 3 days. Despite the differences in stability during heat treatment at 56°C between SARS-CoV and CCoV, the several methods of CCoV inactivation, including inhibition of viral entry, could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure to the virus through unsafe laboratory practices. abstract: Canine coronavirus (CCoV) is responsible for mild or moderate enteritis in puppies. The virus is highly contagious and avoiding contact with infected dogs and their excretions is the only way to ensure disease prevention. Since no studies have yet focused on the sensitivity of CCoV to chemical biocides the present investigation examined the efficiency of physical and chemical methods of viral inactivation. CCoV infectivity was stable at +56 °C for up to 30 min, but tended to decrease rapidly at +65 °C and +75 °C. Germicidal ultra-violet (UV–C) light exposure demonstrated no significant effects on virus inactivation for up to 3 days. CCoV was observed to be more stable at pH 6.0–6.5 while extreme acidic conditions inactivated the virus. Two tested aldehydes inactivated the virus but their action was temperature- and time-dependent. The methods for CCoV inactivation could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure of researchers to pathogens during routine laboratory procedures. url: https://www.ncbi.nlm.nih.gov/pubmed/17513145/ doi: 10.1016/j.tvjl.2007.03.019 id: cord-273882-tqdcb3oo author: Pratibha, title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date: 2020-08-21 words: 1958.0 sentences: 122.0 pages: flesch: 62.0 cache: ./cache/cord-273882-tqdcb3oo.txt txt: ./txt/cord-273882-tqdcb3oo.txt summary: title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. These ubiquitous forbidden orders (UFO) are unique structures of the viruses that may provide an insight into viruses'' chemical behavior and the folding patterns of the proteins. Next, we analyzed protein sequences of 26 viruses (Figures 2, 3 , and Supplementary Figures 1 -4) to search for a ubiquitous forbidden order in each one of them. Among the 26 viruses studied, we noted that the forbidden order BPAB is unique to SARS CoV-2, Rubella, and Avian IB (Figure 3) . We found that at R-group classified sequences of N, B, A, and P in these two samples are identical up to level 4 of the amino acid ordering in the protein structures (Figures 4a, d, g) . abstract: Each amino acid in a polypeptide chain has a distinctive R-group associated with it. We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. In an otherwise pseudo-random sequence, we search for forbidden combinations of kth order. We applied this method to analyze the available protein sequences of various viruses including SARS-CoV-2. We found that these ubiquitous forbidden orders (UFO) are unique to each of the viruses we analyzed. This unique structure of the viruses may provide an insight into viruses’ chemical behavior and the folding patterns of the proteins. This finding may have a broad significance for the analysis of coding sequences of species in general. url: https://doi.org/10.1101/2020.08.21.261289 doi: 10.1101/2020.08.21.261289 id: cord-029450-4rnrq78l author: Prattichizzo, Francesco title: Response to: Letter to the Editor on “Bonafè M, Prattichizzo F, Giuliani A, Storci G, Sabbatinelli J, Olivieri F. Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes. Cytokine Growth Factor Rev” by Eugenia Quiros-Roldan, Giorgio Biasiotto and Isabella Zanella date: 2020-07-18 words: 1570.0 sentences: 73.0 pages: flesch: 45.0 cache: ./cache/cord-029450-4rnrq78l.txt txt: ./txt/cord-029450-4rnrq78l.txt summary: Preliminary data on an Italian cohort suggest that only a minor portion of HIV-positive patients with probable SARS-CoV-2 infection died, which yields a low case-fatality rate if compared to other highrisk populations [3] . Of note, the mean age of all the four HIV-positive cohorts was lower compared to other reports showing data of SARS-CoV-2 infection in the general population [7] . On the basis of the literature above, we posit that testing for T-cell senescence markers (e.g. PD-1, Tim-3, CTLA-4, and TIGIT) [9] and measuring major inflammatory markers in HIV-SARS-CoV-2 co-infected patients is mandatory to disentangle the relevance of immune senescence and inflamm-aging in the COVID-19 outcome in this specific population. A randomized controlled trial evaluating the efficacy of a triple antiviral therapy with combined interferon beta-1b, ribavirin, and lopinavir-ritonavir on COVID-19 patients proved the superiority of the triple antiviral therapy compared to lopinavirritonavir alone in terms of improved clinical recovery and faster rate of viral clearance, with a striking suppression of IL-6 levels in the interferon arm of the study after 48 hours of treatment [17] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368416/ doi: 10.1016/j.cytogfr.2020.07.013 id: cord-342783-85b4lwh3 author: Prazuck, T. title: Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date: 2020-05-27 words: 2640.0 sentences: 174.0 pages: flesch: 61.0 cache: ./cache/cord-342783-85b4lwh3.txt txt: ./txt/cord-342783-85b4lwh3.txt summary: In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. Methods RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orleans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated. The SARS-CoV-2 IgG/IgM antibody test kits, COVID-PRESTO ® and COVID-DUO ® , are 137 RDT test, the IgM were the first antibodies to be detected and were systematically present in 209 the few positive patients with an onset of symptoms from 0 to 5 days ago (n=2 in COVID-210 PRESTO ® population; n=5 in COVID-DUO ® ). Development and Clinical Application of A 371 Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis abstract: Background The SARS-CoV-2 virus is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease). In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a real-life study to evaluate the performance of two RDTs, COVID-PRESTO and COVID-DUO, compared to the gold standard, RT-PCR. Methods RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orleans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated. Results Among 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with RDTs were all negative for these patients, indicating a specificity of 100% for both RDTs. In the RT-PCR positive subgroup (n=238), 133 patients were tested with COVID-PRESTO and 129 patients were tested with COVID-DUO (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days). Conclusion COVID-PRESTO and DUO RDTs turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with capillary blood sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings. url: https://doi.org/10.1101/2020.05.27.20112888 doi: 10.1101/2020.05.27.20112888 id: cord-304787-fohgekp4 author: Prazuck, Thierry title: Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission date: 2020-06-29 words: 1126.0 sentences: 75.0 pages: flesch: 62.0 cache: ./cache/cord-304787-fohgekp4.txt txt: ./txt/cord-304787-fohgekp4.txt summary: 1 Herein, we describe the epidemiological, clinical and biological characteristics of 30 households in close contact with SARS-CoV-2-infected members, living in a confined environment during the French national lockdown. During the 5 days before the French national lockdown, both families moved from their usual Parisian residence to a closed property in the countryside, composed by 3 neighboring houses (A, B and C) in a park. House A was inhabited by 8 persons from a single family, including 3 couples who shared their bed for at least 4 days after the onset of symptoms. The first diagnosed case was a 67-year-old man (resident #1) living in the house A and referring to the Infectious Diseases outpatient clinic on March 17 for cough, fever and asthenia for 4 days. No transmission occurred between husbands and wives in house A although couples moved to separated rooms only 4 days after the onset of symptoms of the index case. abstract: nan url: https://api.elsevier.com/content/article/pii/S0163445320304485 doi: 10.1016/j.jinf.2020.06.066 id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 words: 1454.0 sentences: 111.0 pages: flesch: 61.0 cache: ./cache/cord-329311-p68kr4ga.txt txt: ./txt/cord-329311-p68kr4ga.txt summary: title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . abstract: The clinical significance of SARS-CoV-2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58/123 (47%) patients hospitalized with COVID-19. RNA was detected more frequently, and levels were higher, in patients who were admitted to the ICU and/or died. url: https://www.ncbi.nlm.nih.gov/pubmed/32888003/ doi: 10.1093/cid/ciaa1338 id: cord-309182-t9ywnshj author: Premkumar, Lakshmanane title: The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date: 2020-06-11 words: 6068.0 sentences: 319.0 pages: flesch: 52.0 cache: ./cache/cord-309182-t9ywnshj.txt txt: ./txt/cord-309182-t9ywnshj.txt summary: These results establish that most individuals, including people who have been recently exposed to acute common HCoV infections, do not have detectable levels of cross-reactive antibodies to the recombinant RBD of SARS-CoVs. To evaluate the sensitivity of the RBD of SARS-CoV-2 for identifying infected individuals, we obtained a total of 77 serum samples from 63 patients with laboratory-confirmed (i.e., PCR positive) SARS-CoV-2 infections collected at different times after the onset of symptoms. All the samples were tested for binding of total immunoglobulin (Ig) and IgM antibodies to recombinant RBD antigens from SARS-CoVs and common-cold HCoVs. The sensitivity of the assay was high (98% and 81% respectively for Ig and IgM) for specimens collected 9 days or more after onset of symptoms (Fig. 4A ). A total of 50 serum samples collected between 1 and 39 days after onset of symptoms from PCR-confirmed SARS-CoV-2 subjects were measured for Ig and IgM binding to spike RBD antigen and SARS-CoV-2 neutralization assay. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that first emerged in late 2019 is responsible for a pandemic of severe respiratory illness. People infected with this highly contagious virus can present with clinically inapparent, mild, or severe disease. Currently, the virus infection in individuals and at the population level is being monitored by PCR testing of symptomatic patients for the presence of viral RNA. There is an urgent need for SARS-CoV-2 serologic tests to identify all infected individuals, irrespective of clinical symptoms, to conduct surveillance and implement strategies to contain spread. As the receptor binding domain (RBD) of the spike protein is poorly conserved between SARS-CoVs and other pathogenic human coronaviruses, the RBD represents a promising antigen for detecting CoV-specific antibodies in people. Here we use a large panel of human sera (63 SARS-CoV-2 patients and 71 control subjects) and hyperimmune sera from animals exposed to zoonotic CoVs to evaluate RBD's performance as an antigen for reliable detection of SARS-CoV-2-specific antibodies. By day 9 after the onset of symptoms, the recombinant SARS-CoV-2 RBD antigen was highly sensitive (98%) and specific (100%) for antibodies induced by SARS-CoVs. We observed a strong correlation between levels of RBD binding antibodies and SARS-CoV-2 neutralizing antibodies in patients. Our results, which reveal the early kinetics of SARS-CoV-2 antibody responses, support using the RBD antigen in serological diagnostic assays and RBD-specific antibody levels as a correlate of SARS-CoV-2 neutralizing antibodies in people. url: https://www.ncbi.nlm.nih.gov/pubmed/32527802/ doi: 10.1126/sciimmunol.abc8413 id: cord-287819-qzg4bhoy author: Priftis, Konstantinos title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke date: 2020-09-28 words: 1164.0 sentences: 81.0 pages: flesch: 47.0 cache: ./cache/cord-287819-qzg4bhoy.txt txt: ./txt/cord-287819-qzg4bhoy.txt summary: title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke COVID-19 following infection by SARS-CoV-2 can affect the brain causing confusion, depression, and dementia-like signs. We report on LA, a patient who was affected by a left-hemisphere ischemic stroke, probably because of SARS-CoV-2. The patient showed a highly specific neuropsychological profile characterized by severe agraphia and some signs of conduction aphasia. Therefore, in the present study, we aimed to investigate, more in depth, the specific and focal neuropsychological consequences of SARS-CoV-2, in a patient affected by lefthemisphere stroke. LA had a largely intact neuropsychological profile, except for the presence of severe agraphia and some signs of conduction aphasia. We suggest that patients affected by SARS-CoV-2 and stroke might not only show diffuse neurocognitive and neurobehavioural signs (e.g. confusion, agitation, psychosis), but they can also present with highly focal neuropsychological disorders, such as agraphia and conduction aphasia. abstract: COVID-19 following infection by SARS-CoV-2 can affect the brain causing confusion, depression, and dementia-like signs. Nonetheless, the presence of more specific neuropsychological signs because of COVID-19 remains unexplored. We report on LA, a patient who was affected by a left-hemisphere ischemic stroke, probably because of SARS-CoV-2. The patient showed a highly specific neuropsychological profile characterized by severe agraphia and some signs of conduction aphasia. All other cognitive and sensorimotor functions remained intact. We sustain that specific neuropsychological signs can be observed in patients with COVID-19. Therefore, in-depth and comprehensive neuropsychological assessment should be included to better explore and qualify the neuropsychological consequences of COVID-19. This is a new challenge for diagnosis and rehabilitation, with important consequences for the involved neuropsychological services. url: https://doi.org/10.1007/s10072-020-04768-w doi: 10.1007/s10072-020-04768-w id: cord-266135-jbc9nml0 author: Princiotta Cariddi, Lucia title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient date: 2020-06-24 words: 1141.0 sentences: 78.0 pages: flesch: 41.0 cache: ./cache/cord-266135-jbc9nml0.txt txt: ./txt/cord-266135-jbc9nml0.txt summary: title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient Besides pneumonia, it has been demonstrated that SARS-CoV-2 infection affects multiple organs, including brain tissues, causing different neurological manifestations, especially acute cerebrovascular disease (ischemic and hemorrhagic stroke), impaired consciousness and skeletal muscle injury. To our knowledge, among neurological disorders associated with SARS-CoV2 infection, no Posterior Reversible Encephalopathy Syndrome (PRES) has been described yet. Herein, we report a case of a 64-year old woman with COVID19 infection who developed a PRES, and we suggest that it could be explained by the disruption of the blood brain barrier induced by the cerebrovascular endothelial dysfunction caused by SARS-CoV-2. Brain CT and CTA were consistent with hemorrhagic Posterior Reversible Encephalopathy Syndrome (PRES; Fig. 1a, b) . Posterior reversible encephalopathy syndrome in infection, sepsis, and shock Posterior reversible encephalopathy syndrome (PRES) and infection: a systematic review of the literature Hemorrhagic posterior reversible encephalopathy syndrome as a manifestation of COVID-19 infection abstract: Recently WHO has declared novel coronavirus disease 2019 (COVID-19) outbreak a pandemic. Acute respiratory syndrome seems to be the most common manifestation of COVID-19. Besides pneumonia, it has been demonstrated that SARS-CoV-2 infection affects multiple organs, including brain tissues, causing different neurological manifestations, especially acute cerebrovascular disease (ischemic and hemorrhagic stroke), impaired consciousness and skeletal muscle injury. To our knowledge, among neurological disorders associated with SARS-CoV2 infection, no Posterior Reversible Encephalopathy Syndrome (PRES) has been described yet. Herein, we report a case of a 64-year old woman with COVID19 infection who developed a PRES, and we suggest that it could be explained by the disruption of the blood brain barrier induced by the cerebrovascular endothelial dysfunction caused by SARS-CoV-2. url: https://doi.org/10.1007/s00415-020-10001-7 doi: 10.1007/s00415-020-10001-7 id: cord-257663-i7wrqh2g author: Principi, Nicola title: Effects of Coronavirus Infections in Children date: 2010-02-17 words: 4205.0 sentences: 176.0 pages: flesch: 49.0 cache: ./cache/cord-257663-i7wrqh2g.txt txt: ./txt/cord-257663-i7wrqh2g.txt summary: The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The identifi cation of SARS-CoV and the isolation of 2 novel HCoVs in humans (HCoV-NL63 and HCoV-HKU1) (5,6) have led to several studies of the epidemiology and clinical and socioeconomic effects of HCoV infections, which were greatly facilitated by the availability of modern molecular biology methods that enable direct viral identifi cation in respiratory secretions (7) (8) (9) (10) (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) . abstract: The isolation of the coronavirus (CoV) identified as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). HCoV infections can be associated with respiratory and extrarespiratory manifestations, including central nervous system involvement. Furthermore, unlike other RNA viruses, HCoVs can easily mutate and recombine when different strains infect the same cells and give rise to a novel virus with unpredictable host ranges and pathogenicity. Thus, circulating HCoVs should be closely monitored to detect the spread of particularly virulent strains in the community at an early stage and to facilitate the development of adequate preventive and therapeutic measures. url: https://doi.org/10.3201/eid1602.090469 doi: 10.3201/eid1602.090469 id: cord-302735-zal2gr28 author: Priyanka title: Aerosol transmission of SARS-CoV-2: The unresolved paradox date: 2020-09-04 words: 218.0 sentences: 25.0 pages: flesch: 59.0 cache: ./cache/cord-302735-zal2gr28.txt txt: ./txt/cord-302735-zal2gr28.txt summary: key: cord-302735-zal2gr28 title: Aerosol transmission of SARS-CoV-2: The unresolved paradox cord_uid: zal2gr28 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the aetiological agent 18 of coronavirus disease 2019 , has led to a global pandemic defying the 19 geographical borders and putting the lives of billions at risk. The commonly evident 20 symptoms include fever, altered sense of smell and/or taste, cough, sputum expectoration, 21 sore throat, dyspnoea, fatigue and myalgia; whereas the uncommon symptoms include 22 confusion, dizziness, headache, conjunctivitis, rhinorrhoea, nasal congestion, hemoptysis, 23 chest pain, bronchial breath sounds, tachypnoea, crackles/rales on auscultation, cutaneous The transmission of respiratory pathogens have been associated with three primary modes 30 known as "contact," "droplet," and "airborne" transmission. These modes are also being 31 speculated in the context of SARS-CoV-2, but the existing research-based literature and the 32 consequent guidance from the leading public health agencies are still paradoxical. Viable 117 SARS-CoV-2 in the air of a hospital room 1 with COVID-19 patients. Aerosol transmission of SARS-CoV-2? abstract: nan url: https://api.elsevier.com/content/article/pii/S1477893920303653 doi: 10.1016/j.tmaid.2020.101869 id: cord-311035-s3tkbh9r author: Procko, Erik title: Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community date: 2020-10-21 words: 4033.0 sentences: 210.0 pages: flesch: 45.0 cache: ./cache/cord-311035-s3tkbh9r.txt txt: ./txt/cord-311035-s3tkbh9r.txt summary: A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. • The experimental mutational landscape of ACE2 for binding the RBD of SARS-CoV-2 provides a blueprint for engineering high affinity decoy receptors. Following FACS selection of the human culture to enrich a cell population with high binding activity for SARS-CoV-2 protein S, RNA transcripts were isolated and Illumina sequenced. The deep mutational scan of ACE2 revealed that mutations can indeed be found to enhance binding toward SARS-CoV-2 RBD (Figure 2) , suitable for engineering high affinity soluble decoy receptors [15] . A soluble ACE2 variant that combines three mutations, called sACE2 2 .v2.4, was found to be highly expressed, is a stable monodisperse dimer, binds SARS-CoV-2 S with picomolar affinity and potently neutralizes infection of a susceptible cell line by authentic virus. abstract: Introduction The spike (S) of SARS coronavirus 2 (SARS-CoV-2) engages angiotensin-converting enzyme 2 (ACE2) on a host cell to trigger viral-cell membrane fusion and infection. The extracellular region of ACE2 can be administered as a soluble decoy to compete for binding sites on the receptor-binding domain (RBD) of S, but it has only moderate affinity and efficacy. The RBD, which is targeted by neutralizing antibodies, may also change and adapt through mutation as SARS-CoV-2 becomes endemic, posing challenges for therapeutic and vaccine development. Areas Covered Deep mutagenesis is a Big Data approach to characterizing sequence variants. A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. A deep mutational scan of the RBD displayed on the surface of yeast has revealed residues tolerant of mutational changes that may act as a source for drug resistance and antigenic drift. Expert Opinion Deep mutagenesis requires a selection of diverse sequence variants; an in vitro evolution experiment that is tracked with next-generation sequencing. The choice of expression system, diversity of the variant library and selection strategy have important consequences for data quality and interpretation. url: https://doi.org/10.1080/14789450.2020.1833721 doi: 10.1080/14789450.2020.1833721 id: cord-258914-g6pv8zz9 author: Proud, Pamela C. title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date: 2020-09-25 words: 1191.0 sentences: 90.0 pages: flesch: 51.0 cache: ./cache/cord-258914-g6pv8zz9.txt txt: ./txt/cord-258914-g6pv8zz9.txt summary: title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19. The TLRs are key microbe-recognition receptors with a crucial role in 97 activation of host defence and protection from infections and therefore attractive drug 98 targets against infectious diseases [12] [13] [14] To determine whether TLR2/6 agonists are also active against SARS-CoV-2, we used In life samples were taken at days 1, 3, 5, 7, 10 and 12, with scheduled culls at days 137 3 (n=6) and end of study days 12-14 (n=18) (Fig 1A) . abstract: Respiratory viruses such as coronaviruses represent major ongoing global threats, causing epidemics and pandemics with huge economic burden. Rapid spread of virus through populations poses an enormous challenge for outbreak control. Like all respiratory viruses, the most recent novel human coronavirus SARS-CoV-2, initiates infection in the upper respiratory tract (URT). Infected individuals are often asymptomatic, yet highly infectious and readily transmit virus. A therapy that restricts initial replication in the URT has the potential to prevent progression of severe lower respiratory tract disease as well as limiting person-to-person transmission. We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19. url: https://doi.org/10.1101/2020.09.25.309914 doi: 10.1101/2020.09.25.309914 id: cord-350045-85jug39x author: Pruc, Michal title: Risk of coronavirus infections among medical personnel date: 2020-05-08 words: 632.0 sentences: 40.0 pages: flesch: 65.0 cache: ./cache/cord-350045-85jug39x.txt txt: ./txt/cord-350045-85jug39x.txt summary: Due to the current situation of the COVID-19 pandemic, we can predict how the morbidity of health care workers will develop based on data on other viruses from the coronavirus group. In global research on SARS-CoV-1, MERS-CoV and SARS-CoV-2, it can be seen that a very large percentage of the number of infected people are health professionals struggling with them in various medical facilities. In the Netherlands a survey was conducted from 6-8 March 2020 on 1097 health care workers, among whom the percentage of infected was 4.1%. 4 Currently, the total number of infected healthcare workers on SARS-CoV-2 is unknown due to the steadily increasing number of infections and the lack of global data on the problem. The data on SARS-CoV-1 and MERS-CoV can predict how much health care workers may be infected despite the lack of up-to-date data on SARS-CoV-2. Risks to healthcare workers with emerging diseases: lessons from MERS-CoV, Ebola, SARS, and avian flu abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32414525/ doi: 10.1016/j.ajem.2020.05.017 id: cord-255791-ghrlj6b2 author: Pruijssers, Andrea J. title: Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date: 2020-04-27 words: 3444.0 sentences: 219.0 pages: flesch: 57.0 cache: ./cache/cord-255791-ghrlj6b2.txt txt: ./txt/cord-255791-ghrlj6b2.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 μM). These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19. RDV and GS-441524 potently inhibited 110 SARS-CoV-2 replication in a dose-dependent manner in both cell types ( Fig. 2; Table 1 ). Together, these data demonstrate that RDV is potently antiviral 131 against SARS-CoV-2 in primary human lung cultures with a selectivity index of >1000. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 μM). Weaker activity was observed in Vero E6 cells (EC50 = 1.65 μM) due to their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase, of SARS-CoV-2. In mice infected with chimeric virus, therapeutic RDV administration diminished lung viral load and improved pulmonary function as compared to vehicle treated animals. These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19. url: https://doi.org/10.1101/2020.04.27.064279 doi: 10.1101/2020.04.27.064279 id: cord-265899-skpkuzyu author: Pryzdial, Edward L. G. title: Antiviral anticoagulation date: 2020-07-06 words: 5658.0 sentences: 354.0 pages: flesch: 36.0 cache: ./cache/cord-265899-skpkuzyu.txt txt: ./txt/cord-265899-skpkuzyu.txt summary: 129 Although known as the cold sore virus and typically not life threatening, there are numerous correlations between HSV1 and other members of the herpesvirus family to cardiovascular disease, 130, 131 suggesting links to TF: (i) HSV1 seropositivity is associated with a 2-fold increase in myocardial infarction incidence and death due to coronary heart disease 113 ; (ii) fibrin deposits in the microvasculature are linked to HSV1 infection 132, 133 ; (iii) DIC in neonates may occur during severe HSV1 infection 134 ; (iv) HSV2 is linked to ischemic and hemorrhagic stroke due to DIC 107, 135 ; (v) a history of CMV infection is linked to subclinical and clinical arterial thickening [136] [137] [138] ; (vi) CMV is strongly correlated to accelerated atherosclerosis in immunosuppressed organ transplant recipients [139] [140] [141] [142] ; and (vii) CMV infection is a strong risk factor for restenosis after angioplasty. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a novel envelope virus that causes coronavirus disease 2019 (COVID‐19). Hallmarks of COVID‐19 are a puzzling form of thrombophilia that has elevated D‐dimer but only modest effects on other parameters of coagulopathy. This is combined with severe inflammation, often leading to acute respiratory distress and possible lethality. Coagulopathy and inflammation are interconnected by the transmembrane receptor, tissue factor (TF), which initiates blood clotting as a cofactor for factor VIIa (FVIIa)‐mediated factor Xa (FXa) generation. TF also functions from within the nascent TF/FVIIa/FXa complex to trigger profound changes via protease‐activated receptors (PARs) in many cell types, including SARS‐CoV‐2–trophic cells. Therefore, aberrant expression of TF may be the underlying basis of COVID‐19 symptoms. Evidence suggests a correlation between infection with many virus types and development of clotting‐related symptoms, ranging from heart disease to bleeding, depending on the virus. Since numerous cell types express TF and can act as sites for virus replication, a model envelope virus, herpes simplex virus type 1 (HSV1), has been used to investigate the uptake of TF into the envelope. Indeed, HSV1 and other viruses harbor surface TF antigen, which retains clotting and PAR signaling function. Strikingly, envelope TF is essential for HSV1 infection in mice, and the FXa‐directed oral anticoagulant apixaban had remarkable antiviral efficacy. SARS‐CoV‐2 replicates in TF‐bearing epithelial and endothelial cells and may stimulate and integrate host cell TF, like HSV1 and other known coagulopathic viruses. Combined with this possibility, the features of COVID‐19 suggest that it is a TFopathy, and the TF/FVIIa/FXa complex is a feasible therapeutic target. url: https://doi.org/10.1002/rth2.12406 doi: 10.1002/rth2.12406 id: cord-264497-7xz97awb author: Przedlacki, Jerzy title: Patients’ and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic date: 2020-07-27 words: 1000.0 sentences: 58.0 pages: flesch: 56.0 cache: ./cache/cord-264497-7xz97awb.txt txt: ./txt/cord-264497-7xz97awb.txt summary: title: Patients'' and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic One mandatory swab test in all patients and dialysis unit HCP taken at a "time zero", followed by swabs taken in the presence of clinical indications only (as in answer 1) 3. The members of the healthcare team had an additional option: (4) as in answer 1 plus testing "on demand", in the case of even weak clinical suspicion of SARS-CoV-2 infection. Eventually, all patients were asked to report their sense of safety related to the risk of contracting SARS-CoV-2 while attending the dialysis unit during the COVID-19 pandemic. All participants were informed that an increased frequency of screening tests is not an alternative to self-isolation or to the use of personal protective equipment during dialysis. In summary, the perception of safety in the context of the COVID-19 pandemic can be related to the availability of the SARS-CoV-2 screening test. abstract: nan url: https://doi.org/10.1007/s40620-020-00811-3 doi: 10.1007/s40620-020-00811-3 id: cord-273604-0w5shxmf author: Psevdos, George title: Halting a SARS-CoV-2 Outbreak in a U.S. Veterans Affairs Nursing Home date: 2020-11-03 words: 1241.0 sentences: 76.0 pages: flesch: 51.0 cache: ./cache/cord-273604-0w5shxmf.txt txt: ./txt/cord-273604-0w5shxmf.txt summary: Faced with a dwindling supply of PPE, the Infection Control team distributed supplies saved for a possible Ebola outbreak; A COVID unit was created within the nursing home facilitating the geographic isolation of cases; universal testing of residents and employees allowed for the implementation of proper quarantine measures. 7 Although nationally the virus spreads like wildfire in nursing homes (among residents and working staff), the Department of Veterans Affairs (VA) reported lower COVID-19 rates in their affiliated nursing homes in a U.S. Congressional hearing. Swift detection by rapid RT-PCR testing of all asymptomatic carriers (residents and employees via universal testing) and implementation of strict infection control and isolation measures are pivotal in containing and thus eliminating a COVID-19 outbreak. Universal and Serial Laboratory Testing for SARS-CoV-2 at a Long-Term Care Skilled Nursing Facility for Veterans Hospital affiliated long term care facility COVID-19 containment strategy by using prevalence testing and infection control practices abstract: A Veterans Affairs long term care facility on Long Island New York was confronted with a COVID-19 outbreak in late March to Mid-April 2020. Faced with a dwindling supply of PPE, the Infection Control team distributed supplies saved for a possible Ebola outbreak; A COVID unit was created within the nursing home facilitating the geographic isolation of cases; universal testing of residents and employees allowed for the implementation of proper quarantine measures. It was a multidisciplinary team approach led by the Infection Control team that successfully contained this outbreak. url: https://api.elsevier.com/content/article/pii/S0196655320309640 doi: 10.1016/j.ajic.2020.10.022 id: cord-351503-2f0sk24j author: Pua, Uei title: What Is Needed to Make Interventional Radiology Ready for COVID-19? Lessons from SARS-CoV Epidemic date: 2020-03-13 words: 1276.0 sentences: 76.0 pages: flesch: 53.0 cache: ./cache/cord-351503-2f0sk24j.txt txt: ./txt/cord-351503-2f0sk24j.txt summary: During the initial stage, Singapore recorded one of the highest number of infections outside of China (3), reminiscence of the SARS-CoV epidemic 17 years ago (4). In 2003, the authors were deployed to perform IR as well as critical care procedures in critically ill SARS-CoV patients, and today, providing IR support to the COVID-19 patients. Save for the critically ill, the vast majority of patients with viral pneumonia will not require any IR procedure (28 IR procedures in 27 patients out of the cohort of 206 during SARS-CoV epidemic) (4) . Similarly during the SARS-CoV epidemic in Singapore, among the 206 cases, there were 84 healthcare workers infection resulting in 5 deaths. To assume that the COVID-19 outbreak would be the same as the SARS-CoV epidemic, would be overly simplistic and to ignore our prior experience. abstract: nan url: https://doi.org/10.3348/kjr.2020.0163 doi: 10.3348/kjr.2020.0163 id: cord-288731-x2cwyvb7 author: Puenpa, Jiratchaya title: Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020 date: 2020-10-06 words: 4207.0 sentences: 275.0 pages: flesch: 57.0 cache: ./cache/cord-288731-x2cwyvb7.txt txt: ./txt/cord-288731-x2cwyvb7.txt summary: In the current study associations between SARS-CoV-2 gene variation and exposure history during the first wave of the outbreak in Thailand between January and May 2020 were investigated. In Thailand the Ministry of Public Health reported the first laboratory-confirmed case of SARS-CoV-2 in a 61-year-old Chinese traveller who had arrived from Wuhan on 12 January 2020. Based on the genome sequences available in GIASID, nucleotide variation in four regions of the SARS-CoV-2 genome was used to conduct viral tracking and identify sites of origin of outbreaks in Thailand. One sample in the current study collected in January 2020 was closely related to the SARS-CoV-2 strain circulating in China at that time identified as type L. A new cohort of imported cases identified in May 2020 included a group of migrant workers in the southern part of Thailand 24 with type G2 SARS-CoV-2. abstract: The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global concern. Several SARS-CoV-2 gene mutations have been reported. In the current study associations between SARS-CoV-2 gene variation and exposure history during the first wave of the outbreak in Thailand between January and May 2020 were investigated. Forty samples were collected at different time points during the outbreak, and parts of the SARS-CoV-2 genome sequence were used to assess genomic variation patterns. The phylogenetics of the 40 samples were clustered into L, GH, GR, O and T types. T types were predominant in Bangkok during the first local outbreak centered at a boxing stadium and entertainment venues in March 2020. Imported cases were infected with various types, including L, GH, GR and O. In southern Thailand introductions of different genotypes were identified at different times. No clinical parameters were significantly associated with differences in genotype. The results indicated local transmission (type T, Spike protein (A829T)) and imported cases (types L, GH, GR and O) during the first wave in Thailand. Genetic and epidemiological data may contribute to national policy formulation, transmission tracking and the implementation of measures to control viral spread. url: https://www.ncbi.nlm.nih.gov/pubmed/33024144/ doi: 10.1038/s41598-020-73554-7 id: cord-271338-v2k9zn87 author: Pujadas, E. title: SARS-CoV-2 Viral Load Predicts COVID-19 Mortality date: 2020-06-12 words: 1007.0 sentences: 72.0 pages: flesch: 57.0 cache: ./cache/cord-271338-v2k9zn87.txt txt: ./txt/cord-271338-v2k9zn87.txt summary: We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). To date, few studies have reported on SARS-CoV-2 viral loads, and no studies have assessed viral load and mortality in large patient cohorts. 2, 3, 4, 5 This letter is the first to report SARS-CoV-2 viral load at the time of diagnosis as an independent predictor of COVID-19 mortality in a large hospitalized cohort (n=1,145) within the Mount Sinai Health System in New York City. . https://doi.org/10.1101/2020.06.11.20128934 doi: medRxiv preprint Transforming front-line qualitative testing into a quantitative viral load will assist clinicians in risk-stratifying patients who should be admitted and closely monitored versus those who may safely convalesce at home. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients abstract: The need for reliable and widely available SARS-CoV-2 testing is well recognized, but it will be equally necessary to develop quantitative methods that determine viral load in order to guide patient triage and medical decision making. We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). Viral loads should be used to identify higher-risk patients that may require more aggressive care and should be included as a key biomarker in the development of predictive algorithms. url: https://doi.org/10.1101/2020.06.11.20128934 doi: 10.1101/2020.06.11.20128934 id: cord-259523-92hz534s author: Pullen, Lara C. title: COVID‐19: transplant works toward adaptation date: 2020-09-29 words: 1642.0 sentences: 93.0 pages: flesch: 52.0 cache: ./cache/cord-259523-92hz534s.txt txt: ./txt/cord-259523-92hz534s.txt summary: These recommendations state that during the COVID-19 pandemic, deceased donor kidney transplantations should be performed only if it is possible to transplant a SARS-CoV-2 negative organ into a SARS-CoV-2 negative patient, and that renal transplantation should be prioritized for recipients facing urgent clinical conditions "because frequent healthcare contact due to the severity of their underlying disease means that these patients will remain at high risk for acquiring SARS-CoV-2, a risk that might be greater than the risk of SARS-CoV-2 acquisition through successful transplantation," says Dr. Remuzzi. Currently, the American Society of Transplantation and the ISOT do not recommend the use of organs from living donors who are SARS-CoV-2 positive or classifi ed as high risk after screening. Recently, colleagues at Dr. Remuzzi''s institution reported the presence of SARS-CoV-2 in the kidney, and the potential for donor-derived COVID-19 infection remains unknown. Dr. Potena estimates that in a typical winter, 20 to 25% of the transplant center''s patients have COVID-like symptoms. abstract: This month's installment of “The AJT Report” explores some remaining questions about how the transplant community should adapt to the changing landscape created by the COVID‐19 pandemic. We also look at how xenotransplantation may soon be viewed in a different light. url: https://www.ncbi.nlm.nih.gov/pubmed/32996294/ doi: 10.1111/ajt.16298 id: cord-282009-a83mun7u author: Pundir, Hemlata title: Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors date: 2020-10-20 words: 6213.0 sentences: 360.0 pages: flesch: 53.0 cache: ./cache/cord-282009-a83mun7u.txt txt: ./txt/cord-282009-a83mun7u.txt summary: To identify possible inhibitors against SARS-CoV-2, we applied the Pharmacophore-based virtual screening method following Chou''s 5-step rule [16] , molecular docking, drug-like analysis, and toxicity prediction (Fig. 1) . After the pharmacophore-based screening using Chou''s 5-steps rule, we performed the molecular docking of all screened compounds with crystal structure of SARS-CoV-2 Mpro. After successful completion of MDS, the MD trajectories were used to calculate root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R g ), hydrogen bonds, solvent accessible surface area (SASA) [28] , principal component analysis (PCA) [29] , and distance to analyze the stability of Mpro and Mpro-ligand complex. Pharmacophore-based screening by Chou''s 5-steps rule X77 binds to the active site of SARS-CoV-2 Mpro with binding energy − 8.4 kcal/mol as shown in Fig. 2 . abstract: ABSTRACT: Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across the world. Control of this pandemic disease is challenging because there is no effective drug or vaccine available against this virus and this situation demands an urgent need for the development of anti-SARS-CoV-2 potential medicines. In this regard, the main protease (Mpro) has emerged as an essential drug target as it plays a vital role in virus replication and transcription. In this research, we have identified two novel potent inhibitors of the Mpro (PubChem3408741 and PubChem4167619) from PubChem database by pharmacophore-based high-throughput virtual screening. The molecular docking, toxicity, and pharmacophore analysis indicate that these compounds may act as potential anti-viral candidates. The molecular dynamic simulation along with the binding free energy calculation by MMPBSA showed that these compounds bind to Mpro enzyme with high stability over 50 ns. Our results showed that two compounds: PubChem3408741 and PubChem4167619 had the binding free energy of − 94.02 kJ mol(−1) and − 122.75 kJ mol(−1), respectively, as compared to reference X77 (− 76.48 kJ mol(−1)). Based on our work’s findings, we propose that these compounds can be considered as lead molecules for targeting Mpro enzyme and they can be potential SARS-CoV-2 inhibitors. These inhibitors could be tested in vitro and explored for effective drug development against COVID-19. GRAPHIC ABSTRACT: [Image: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11030-020-10148-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11030-020-10148-5 doi: 10.1007/s11030-020-10148-5 id: cord-228152-k4bw8w5g author: Pyzer-Knapp, Edward O. title: Using Bayesian Optimization to Accelerate Virtual Screening for the Discovery of Therapeutics Appropriate for Repurposing for COVID-19 date: 2020-05-11 words: 2981.0 sentences: 140.0 pages: flesch: 49.0 cache: ./cache/cord-228152-k4bw8w5g.txt txt: ./txt/cord-228152-k4bw8w5g.txt summary: The novel Wuhan coronavirus known as SARS-CoV-2 has brought almost unprecedented effects for a non-wartime setting, hitting social, economic and health systems hard.~ Being able to bring to bear pharmaceutical interventions to counteract its effects will represent a major turning point in the fight to turn the tides in this ongoing battle.~ Recently, the World''s most powerful supercomputer, SUMMIT, was used to identify existing small molecule pharmaceuticals which may have the desired activity against SARS-CoV-2 through a high throughput virtual screening approach. In this communication, we demonstrate how the use of Bayesian optimization can provide a valuable service for the prioritisation of these calculations, leading to the accelerated identification of high-performing candidates, and thus expanding the scope of the utility of HPC systems for time critical screening It can be seen than on every task the PDTS method of Bayesian optimization outperforms random sampling and thus shows great potential for the efficient prioritisation of HTVS testing of pharmaceuticals for activity against SARS-CoV-2. abstract: The novel Wuhan coronavirus known as SARS-CoV-2 has brought almost unprecedented effects for a non-wartime setting, hitting social, economic and health systems hard.~ Being able to bring to bear pharmaceutical interventions to counteract its effects will represent a major turning point in the fight to turn the tides in this ongoing battle.~ Recently, the World's most powerful supercomputer, SUMMIT, was used to identify existing small molecule pharmaceuticals which may have the desired activity against SARS-CoV-2 through a high throughput virtual screening approach. In this communication, we demonstrate how the use of Bayesian optimization can provide a valuable service for the prioritisation of these calculations, leading to the accelerated identification of high-performing candidates, and thus expanding the scope of the utility of HPC systems for time critical screening url: https://arxiv.org/pdf/2005.07121v1.pdf doi: nan id: cord-352871-0xgjpd80 author: Pérez Bartolomé, Francisco title: Manifestaciones oftalmológicas del SARS-Cov-2: Revisión de la literatura date: 2020-08-08 words: 4221.0 sentences: 371.0 pages: flesch: 54.0 cache: ./cache/cord-352871-0xgjpd80.txt txt: ./txt/cord-352871-0xgjpd80.txt summary: En Diciembre de 2019 se identificaron a los primeros pacientes diagnosticados con la enfermedad causada por el nuevo coronavirus (SARS-CoV2), denominada COVID-19, en Wuhan, China 1,2 . Se procedió a la combinación de diferentes palabras clave, tales como "SARS-Cov-2", "COVID 19", "2019-nCoV", "Coronavirus 2019", y (término "AND" en el proceso de búsqueda avanzada) "Ophthalmology", "Eye disease", "Conjunctivitis", "Ocular Surface", "Glaucoma", "Orbit", "Tears", "Uveitis", "Retina", "Vasculitis", "ophthalmoparesis", "palsy", "optic nerve", "anterior ischemic optic neuropathy" (AION), "retinal venous occlusion" (RVO), "retinal artery occlusion" (RAO). La primera referencia de conjuntivitis por SARS-CoV-2 figura en una carta al editor, publicada en la revista "The Lancet" 28 , en la que describe el cuadro de enrojecimiento ocular unilateral en un experto neumólogo (ataviado con su equipo de protección y una mascarilla N95, pero sin gafas protectoras), días después de haber visitado un hospital de Wuhan. abstract: Resumen En esta revisión resumimos las principales publicaciones que informan sobre las potenciales manifestaciones oculares de la enfermedad por el nuevo coronavirus (COVID-19). La evidencia científica se basa en cartas al editor, casos clínicos aislados y series de casos, principalmente de corte transversal. Hasta la fecha, incluimos la conjuntivitis viral, una conjuntivitis inmunomediada y parálisis oculomotoras (POM). Se discute la posibilidad de retinopatía pero no se ha publicado ningún caso. La conjuntivitis viral puede aparecer aislada o asociada al cuadro sistémico, principalmente pulmonar, antes o después del inicio de los síntomas respiratorios. Puede ser tanto unilateral como bilateral, es típica la presencia de folículos, y presenta una duración variable entre 5 y 20 días. La conjuntivitis inmunomediada consiste en un enrojecimiento ocular acompañada de eritrodermia y febrícula. Aparece más frecuentemente en los niños y se ha asociado a un cuadro “Kawasaki-like” y síndrome del shock tóxico. Las POM pueden presentarse de forma aislada, o formando parte de un síndrome de Miller- Fisher, junto con ataxia e hiporreflexia. Los oftalmólogos presentamos un riesgo considerable de contraer la COVID-19 debido a un contacto estrecho con el paciente, exposición a las lágrimas y a las secreciones oculares y al uso de multitud de equipos y aparatos susceptibles de contaminarse. Abstract In this review, a summary is presented of the main reports regarding the potential ocular manifestations of the new coronavirus disease (COVID-19). Scientific evidence is based on letters to the editor, clinical cases and case series, cross-sectional, and a few longitudinal studies. To date, it includes viral conjunctivitis, immune conjunctivitis, and oculomotor palsies (OCP) due to the novel coronavirus. Retinopathy is discussed, but no cases have been published yet. A viral conjunctivitis outbreak can be isolated or associated with the systemic picture, mainly pulmonary, before or after the onset of respiratory symptoms. It can be both unilateral and bilateral, follicles are typical, and duration is variable between 5 and 21 days. Immune-mediated conjunctivitis consists of eye redness, together with erythroderma and fever. It appears more frequently in children, and has been associated with a "Kawasaki-like" disease and toxic shock syndrome. OCP can present on its own, or as part of Miller-Fisher syndrome, along with ataxia, and hyporeflexia. Ophthalmologists have a considerable risk of developing COVID-19 due to close contact with the patient, exposure to tears and eye secretions, and the use of various pieces of equipment and devices susceptible to contamination. url: https://www.ncbi.nlm.nih.gov/pubmed/32873480/ doi: 10.1016/j.oftal.2020.07.020 id: cord-340070-de7sfccy author: Pérez-Martinez, Antonio title: Clinical outcome of SARS-CoV-2 infection in immunosuppressed children in Spain date: 2020-08-29 words: 2306.0 sentences: 119.0 pages: flesch: 45.0 cache: ./cache/cord-340070-de7sfccy.txt txt: ./txt/cord-340070-de7sfccy.txt summary: In this series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. A retrospective study (1st to 31st of March, 2020) of children less than 15 years old with primary or secondary immunosuppression infected with SARS-CoV-2 and treated at the University Hospital La Paz, Madrid, Spain, was performed. Hydroxychloroquine was initiated upon diagnosis (positive PCR for SARS-CoV-2) when there were signs/ symptoms of moderate-severe disease (respiratory signs, pneumonia on chest X ray, blood parameters of severity such as lymphopenia or elevated CRP, D-dimer or Il-6). In this small series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. Based on our experience, monitoring of children with immunosuppression and COVID-19 disease can be performed as outpatients, if close monitoring is possible with radiological and blood test controls if necessary, and carefully selecting the patients depending on their individual risk. abstract: Limited information is available regarding SARS-CoV-2 infections in children with underlying diseases. A retrospective study of children less than 15 years old with primary or secondary immunosuppression infected with SARS-CoV-2 during March 2020 was performed. In this series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. The severity of the symptoms was mild-moderate in the majority with a predominance of febrile syndrome, with mild radiological involvement and in some cases with mild respiratory distress that required oxygen therapy. The rational and prudent management of these patients is discussed, evaluating possible treatments and options for hospitalization or outpatient follow-up. Conclusion: In our experience, monitoring of children with immunosuppression and COVID-19 disease can be performed as outpatients if close monitoring is possible. Hospitalization should be assessed when high fever, radiological involvement, and/or respiratory distress are present. url: https://doi.org/10.1007/s00431-020-03793-3 doi: 10.1007/s00431-020-03793-3 id: cord-302125-96w0nh9q author: Péré, Hélène title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date: 2020-09-03 words: 370.0 sentences: 27.0 pages: flesch: 58.0 cache: ./cache/cord-302125-96w0nh9q.txt txt: ./txt/cord-302125-96w0nh9q.txt summary: title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Running title: Sequential SARS-CoV-2 serology testing in health-workers Hélène Péré 1,2,3 , Maxime Wack 4 , Benoit Védie 5 , Nathalie Demory Guinet 6 , Kassis Chikani Najiby 7 , Laurence Janot 6 , Laurent Bélec 1,2,3 , David Veyer 1, 8 surface protein, with the high-throughput UniCel DxI 800 Access Immunoassay System (Beckman Coulter), to increase hospital productivity in SARS-CoV-2 IgG serology testing. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients The authors are also grateful to Beckman Coulter, France, for providing the ACCESS SARS-CoV-2 IgG kits for the study.J o u r n a l P r e -p r o o f abstract: nan url: https://api.elsevier.com/content/article/pii/S1386653220303590 doi: 10.1016/j.jcv.2020.104617 id: cord-311633-i9ret7bw author: Péré, Hélène title: Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology date: 2020-08-04 words: 1673.0 sentences: 103.0 pages: flesch: 52.0 cache: ./cache/cord-311633-i9ret7bw.txt txt: ./txt/cord-311633-i9ret7bw.txt summary: We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. To analytically and clinically validate the Abbott SARS-CoV-2 IgG assay, we tested pre-epidemic sera, sera from pauci-symptomatic health-worker with SARS-CoV-2 positive RT-PCR and sera from hospitalized patients from both the COVID-positive area and the COVID-free area. abstract: Facing the ongoing pandemic caused by SARS-CoV-2, there is an urgent need for serological assays identifying individuals with on-going infection as well as past coronavirus infectious disease 2019 (COVID-19). We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. The Abbott SARS-CoV-2 IgG assay showed sensitivity of 94% and specificity of 100%, demonstrating high analytical performances allowing convenient management of suspected on-going and past-infections. In addition, the SARS-CoV-2 IgG positivity rates were compared in COVID-19 positive and COVID-19 free areas from our hospital. Thus, the frequency of SARS-CoV-2-specific IgG was around 10-fold higher in COVID-19 areas than COVID-19 free areas (75% versus 8%; P < 0.001). Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. Taken together, these observations highlight the potential interest of SARS-CoV-2-specific serology in the context of COVID-19 epidemic, especially to assess past SARS-CoV-2 infection as well as possible unexpected COVID-19-associated disorders. url: https://doi.org/10.1016/j.jcv.2020.104568 doi: 10.1016/j.jcv.2020.104568 id: cord-292675-tkyngspy author: Qi, Furong title: Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses date: 2020-03-19 words: 3513.0 sentences: 217.0 pages: flesch: 50.0 cache: ./cache/cord-292675-tkyngspy.txt txt: ./txt/cord-292675-tkyngspy.txt summary: For this purpose, we collected single cell gene expression matrices from 13 relatively normal human tissues, consisting of lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] from published literatures. We analyzed the single cell co-expression profiles of 51 known ssRNA viral receptors and 400 membrane proteins, including ACE2, in the identified 119 cell types across the 13 human tissues. Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] (Table S1) . abstract: Abstract The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted “CellPhoneDB” analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0006291X20305234 doi: 10.1016/j.bbrc.2020.03.044 id: cord-335155-x9az3twa author: Qi, Zhen title: Phylogeny of SARS-CoV as inferred from complete genome comparison date: 2003 words: 1616.0 sentences: 97.0 pages: flesch: 59.0 cache: ./cache/cord-335155-x9az3twa.txt txt: ./txt/cord-335155-x9az3twa.txt summary: SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. To date, genomes from 12 SARS-CoV isolates and 12 previously identified coronaviruses have been completely sequenced. The unrooted phylogenetic tree was constructed for genomes from 12 SARS-CoV isolates and that from 12 previously identified coronviruses (Fig. 1) . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJOI) abstract: SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS. url: https://doi.org/10.1007/bf03183930 doi: 10.1007/bf03183930 id: cord-337324-jxtch47t author: Qian, Guo-Qing title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series date: 2020-02-25 words: 3331.0 sentences: 207.0 pages: flesch: 59.0 cache: ./cache/cord-337324-jxtch47t.txt txt: ./txt/cord-337324-jxtch47t.txt summary: title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series 8 Three further cases were reported in Ningbo cohort as clinical-diagnosed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to National Health Commission of the People''s Republic of China guidance, though they tested negative for the SARS-CoV-2. This report, to our knowledge, is the largest case study to date of hospitalized patients with COVID-19 in Zhejiang province, which is outwith of Wuhan and Hubei. Our study provided three cases as clinical-confirmed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to guidance, though they tested negative for the SARS-CoV-2. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: Background Recent studies have focused initial clinical and Epidemiologic characteristics on the COVID-19, mainly revealing situation in Wuhan, Hubei. Aim To reveal more data on the epidemiologic and clinical characteristics of COVID-19 patients outside of Wuhan, in Zhejiang, China. Design Retrospective case series. Methods 88 cases of laboratory-confirmed and 3 cases of clinical-confirmed COVID-19 were admitted to five hospitals in Zhejiang province, China. Data were collected from 20 January 2020 to 11 February 2020. Results Of all 91 patients, 88 (96.70%) were laboratory-confirmed COVID-19 with throat swab samples that tested positive for SARS-Cov-2 while 3 (3.30%) were clinical-diagnosed COVID-19 cases. The median age of the patients was 50 (36.5-57) years, and female accounted for 59.34%. In this sample 40 (43.96%) patients had contracted the diseases from local cases, 31 (34.07%) patients had been to Wuhan/Hubei, 8 (8.79%) cases had contacted with people from Wuhan, 11 (12.09%) cases were confirmed aircraft transmission. In particular within the city of Ningbo, 60.52% cases can be traced back to an event held in a temple. The most common symptoms were fever (71.43%), cough (60.44%) and fatigue (43.96%). The median of incubation period was 6 (IQR, 3-8) days and the median time from first visit to a doctor to confirmed diagnosis was 1 (1-2) days. According to the Chest computed tomography scans, 67.03% cases had bilateral pneumonia. Conclusions Social activity cluster, family cluster and travel by airplane were how COVID-19 patients get transmitted and could be rapidly diagnosed COVID-19 in Zhejiang. url: https://doi.org/10.1101/2020.02.23.20026856 doi: 10.1101/2020.02.23.20026856 id: cord-263738-8g5ujfaf author: Qian, Jing-Yi title: Acute Kidney Injury in the 2019 Novel Coronavirus Disease date: 2020-06-18 words: 3509.0 sentences: 189.0 pages: flesch: 49.0 cache: ./cache/cord-263738-8g5ujfaf.txt txt: ./txt/cord-263738-8g5ujfaf.txt summary: COVID-19 is characterized by acute respiratory disease, with 80% of patients presenting mild like flu-like symptoms; however, 20% of patients may have a severe or critical clinical presentation, which likely causes multiple organ injuries (e.g., kidney, heart, blood, and nervous system). Novel coronavirus disease (COVID-19) is a newly discovered acute infectious disease caused by the SARS-CoV-2 virus, which is mainly manifested as acute respiratory diseases characterized by acute interstitial and alveolar pneumonia and can affect multiple organs such as the kidneys, the heart, the digestive tract, and blood [1] . In another study of 99 patients with COVID-19, seven cases developed various degrees of kidney injury with elevated serum creatinine (Scr) and/or blood urea nitrogen (BUN) levels, and 3 of them were diagnosed with AKI [4] . These results provide direct evidence that the SARS-CoV-2 virus can directly infect the renal tubular epithelium and podocytes, which may induce AKI in COVID-19 patients [17] . abstract: BACKGROUND: The 2019 novel coronavirus disease (CO­VID-19) is a newly defined serious infectious disease caused by the SARS-CoV-2 virus. The epidemic started in Wuhan, China, in December of 2019 and quickly spread to over 200 countries. It has affected 4,258,666 people, with 294,190 deaths worldwide by May 15, 2020. COVID-19 is characterized by acute respiratory disease, with 80% of patients presenting mild like flu-like symptoms; however, 20% of patients may have a severe or critical clinical presentation, which likely causes multiple organ injuries (e.g., kidney, heart, blood, and nervous system). Among them, acute kidney injury (AKI) is a critical complication due to its high incidence and mortality rate. Here we present a review of the current understanding of AKI in COVID-19. SUMMARY: CO­VID-19 is a catastrophic contagious disease caused by the coronavirus, and the AKI induced by COVID-19 significantly increases the mortality rate. In this review, we summarize the clinical characteristics of COVID-19 induced AKI by focusing on its epidemiology, pathogenesis, clinical diagnosis, and treatment. KEY MESSAGES: Multiple studies have shown that COVID-19 may involve the kidneys and cause AKI. This article reviews the characteristics of COVID-19-induced AKI largely based on up-to-date studies in the hope that it will be helpful in the current global fight against and treatment of COVID-19. url: https://doi.org/10.1159/000509086 doi: 10.1159/000509086 id: cord-293831-28ddm9um author: Qian, Mengcen title: Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey date: 2020-02-20 words: 4851.0 sentences: 304.0 pages: flesch: 51.0 cache: ./cache/cord-293831-28ddm9um.txt txt: ./txt/cord-293831-28ddm9um.txt summary: Objective: To investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China Design: Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020 Setting: Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan) Participants: Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18 Main outcome measures: Anxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). 18.20024448 doi: medRxiv preprint We found that higher perceived risk and severity of contracting the novel coronavirus, higher perceived relative transmissibility and harm to body to SARS, and more confusion about information reliability were all significantly and positively associated with reported moderate or severe anxiety during the outbreak (Table 3 ). abstract: Objective: To investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China Design: Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020 Setting: Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan) Participants: Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18 Main outcome measures: Anxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). Results: The prevalence rates of moderate or severe anxiety (score ≥10 on GAD-7) were 32.7% (n=167) among Wuhan participants and 20.4% (n=102) among Shanghai participants. 78.6% (n=401) of Wuhan participants and 63.9% (n=320) of Shanghai participants had carried out all six precautionary behaviors. For both measures, Wuhan participants were more responsive to the outbreak (p<0.001). Controlling for personal characteristics, logistic regression results suggested that risks of moderate or severe anxiety were positively associated with perceived susceptibility (odds ratio 1.6, 95% confidence interval 1.3-1.8) and severity of the disease (1.6, 1.4-1.9) and confusion about information reliability (1.6, 1.5-1.9). Having confidence in taking measures to protect oneself against the disease was associated with a lower risk (0.6, 0.5-0.7). The strongest predictor of behavioral change was perceived severity (1.2, 1.1-1.4), followed by confusion about information reliability (1.1, 1.0-1.3). Conclusions: Psychological and behavioral responses to COVID-19 have been dramatic during the rising phase of the outbreak. Our results support efforts for timely dissemination of accurate and reliable information to address the high anxiety level. url: https://doi.org/10.1101/2020.02.18.20024448 doi: 10.1101/2020.02.18.20024448 id: cord-343827-jo61t3m0 author: Qian, Qun title: Direct evidence of active SARS-CoV-2 replication in the intestine date: 2020-07-08 words: 1314.0 sentences: 98.0 pages: flesch: 53.0 cache: ./cache/cord-343827-jo61t3m0.txt txt: ./txt/cord-343827-jo61t3m0.txt summary: We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. abstract: BACKGROUND: Currently, there is no direct evidence to prove the active SARS-CoV-2 replication in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. METHODS: Here, the clinical data were collected during hospitalization and follow-up of this patient. Quantitative RT-PCR was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen, and immune cell infiltrations. RESULTS: The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some are SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage. CONCLUSIONS: We firstly reported that direct evidence of the active SARS-CoV-2 replication in the patient's rectum during the incubation period, which might explain SARS-CoV-2 fecal-oral transmission. url: https://doi.org/10.1093/cid/ciaa925 doi: 10.1093/cid/ciaa925 id: cord-295559-yc8q62z8 author: Qian, Zhaohui title: Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date: 2013-10-03 words: 7303.0 sentences: 303.0 pages: flesch: 50.0 cache: ./cache/cord-295559-yc8q62z8.txt txt: ./txt/cord-295559-yc8q62z8.txt summary: Coronavirus S proteins are Class I viral fusion proteins like the HIV envelope (env), influenza hemagglutinin (HA) and paramyxovirus fusion (F) glycoproteins [17] , which typically require protease cleavage between the S1 and S2 domains ( Figure 1A ) to permit conformational changes in S2, activated by receptor binding and/or low pH, that mediate membrane fusion leading to virus entry and syncytia formation [3, 17, 18] . In addition to entry by endocytosis, we showed that, like SARS-CoV [21, 22] , MERS pseudovirions could enter susceptible Vero E6 cells at the plasma membrane if virions were first bound to cell surface receptors at 4°C at neutral pH in the presence of NH 4 Cl to inhibit acidification of endosomes, and also treated briefly at room temperature with trypsin to cleave the viral S protein. abstract: Little is known about the biology of the emerging human group c betacoronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV). Because coronavirus spike glycoproteins (S) mediate virus entry, affect viral host range, and elicit neutralizing antibodies, analyzing the functions of MERS-CoV S protein is a high research priority. MERS-CoV S on lentivirus pseudovirions mediated entry into a variety of cell types including embryo cells from New World Eptesicus fuscus bats. Surprisingly, a polyclonal antibody to the S protein of MHV, a group a murine betacoronavirus, cross-reacted in immunoblots with the S2 domain of group c MERS-CoV spike protein. MERS pseudovirions released from 293T cells contained only uncleaved S, and pseudovirus entry was blocked by lysosomotropic reagents NH(4)Cl and bafilomycin and inhibitors of cathepsin L. However, when MERS pseudovirions with uncleaved S protein were adsorbed at 4°C to Vero E6 cells, brief trypsin treatment at neutral pH triggered virus entry at the plasma membrane and syncytia formation. When 293T cells producing MERS pseudotypes co-expressed serine proteases TMPRSS-2 or -4, large syncytia formed at neutral pH, and the pseudovirions produced were non-infectious and deficient in S protein. These experiments show that if S protein on MERS pseudovirions is uncleaved, then viruses enter by endocytosis in a cathepsin L-dependent manner, but if MERS-CoV S is cleaved, either during virus maturation by serine proteases or on pseudovirions by trypsin in extracellular fluids, then viruses enter at the plasma membrane at neutral pH and cause massive syncytia formation even in cells that express little or no MERS-CoV receptor. Thus, whether MERS-CoV enters cells within endosomes or at the plasma membrane depends upon the host cell type and tissue, and is determined by the location of host proteases that cleave the viral spike glycoprotein and activate membrane fusion. url: https://doi.org/10.1371/journal.pone.0076469 doi: 10.1371/journal.pone.0076469 id: cord-309999-izdl0f2i author: Qin, Ede title: Immunogenicity and protective efficacy in monkeys of purified inactivated Vero-cell SARS vaccine date: 2006-02-13 words: 3944.0 sentences: 205.0 pages: flesch: 46.0 cache: ./cache/cord-309999-izdl0f2i.txt txt: ./txt/cord-309999-izdl0f2i.txt summary: Additionally, three groups of rhesus monkeys were immunized with different doses of the purified inactivated SARS vaccine (0.5, 1 and 2 μg/time/monkey) on days 0 and 7, and the monkeys were challenged with SARS-CoV GZ-01 strain. INTERPRETATION: The purified inactivated SARS vaccine could induce high levels of neutralizing antibody, and protect the monkeys from the challenge of SARS-CoV. The results showed that both the purified and the unpurified SARS vaccines can induce high levels of SARS-CoV specific neutralizing antibodies in monkeys, thus demonstrating high immunogenicity. Our observations of immunogenicity in monkeys showed that the unpurified inactivated SARS vaccine induced almost the same level of neutralizing antibody as the purified vaccine. The results indicated that the purified inactivated SARS vaccine we developed could induce high levels of neutralizing antibody, protect monkeys after a SARS-CoV challenge, and be administered safely in monkeys. abstract: BACKGROUND: In 2003, severe acute respiratory syndrome (SARS) resulted in hundreds of infections and deaths globally. We aim to assess immunogenicity and protective efficacy of purified inactivated Vero-cell SARS vaccine in monkeys. METHODS: The cultures of SARS coronavirus (SARS-CoV) BJ-01 strain infected Vero cells were inactivated with β-propiolactone. Sequential procedures, including ultrafiltration, gel filtration and ion exchange chromatography, were performed to obtain purified inactivated SARS vaccine. The purified SARS vaccine was analyzed with electron microscope, HPLC and Western blotting. We immunized three groups of cynomolgus macaques fascicularis with adjuvant-containing purified vaccine, purified vaccine and unpurified vaccine, respectively, and a fourth group served as a control. Antibody titers were measured by plaque reduction neutralization test. The vaccinated monkeys were challenged with SARS-CoV BJ-01 strain to observe protective efficacy. Additionally, three groups of rhesus monkeys were immunized with different doses of the purified inactivated SARS vaccine (0.5, 1 and 2 μg/time/monkey) on days 0 and 7, and the monkeys were challenged with SARS-CoV GZ-01 strain. We assessed the safety of the SARS vaccine and observed whether the antibody dependent enhancement (ADE) occurred under low levels of neutralizing antibody in rhesus. FINDINGS: The purity of SARS vaccine was 97.6% by HPLC identification and reacted with convalescent sera of SARS patients. The purified SARS vaccine induced high levels of neutralizing antibodies and prevented the replication of SARS-CoV in monkeys. Under low levels of neutralizing antibody, no exacerbation of clinical symptoms was observed when the immunized monkeys were challenged with SARS-CoV. In this preliminary animal trial, no side effects were detected when monkeys were immunized with purified SARS vaccine either at normal or large doses. INTERPRETATION: The purified inactivated SARS vaccine could induce high levels of neutralizing antibody, and protect the monkeys from the challenge of SARS-CoV. The SARS vaccine prepared in the study appeared to be safe in monkeys. url: https://api.elsevier.com/content/article/pii/S0264410X05008960 doi: 10.1016/j.vaccine.2005.06.038 id: cord-334430-1udn20wo author: Qin, Li title: The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice date: 2007 words: 1890.0 sentences: 107.0 pages: flesch: 58.0 cache: ./cache/cord-334430-1udn20wo.txt txt: ./txt/cord-334430-1udn20wo.txt summary: title: The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice The immune effect of two recombinant protein fragments of spike protein in severe acute respiratory syndrome coronavirus (SARS CoV) was investigated in Balb/c mice. Two partial spike gene fragments S1 (322 1464 bp) and S2 (2170 2814 bp) of SARS coronavirus were amplified by RT-PCR, and cloned into pET-23a prokaryotic expression vector, then transformed into competent Escherichia E. The results showed that recombinant proteins of SARS coronavirus spike protein induced hormonal and cellular immune response in Balb/c mice. Spike protein is also the main protective antigen inducing the generation of neutralizing antibodies, and it can be detected in infected cell culture supernatants with antisera from SARS patients [7, 8] . An exposed domain in the severe acute respiratory syndrome coronavirus spike protein induces neutralizing antibodies abstract: The immune effect of two recombinant protein fragments of spike protein in severe acute respiratory syndrome coronavirus (SARS CoV) was investigated in Balb/c mice. Two partial spike gene fragments S1 (322 1464 bp) and S2 (2170 2814 bp) of SARS coronavirus were amplified by RT-PCR, and cloned into pET-23a prokaryotic expression vector, then transformed into competent Escherichia E. coli BL21 (DE3)(pLysS) respectively. Recombinant proteins were expressed and purified by Ni(2+) immobilized metal ion affinity chromatography. The purified proteins mixed with complete Freund adjuvant were injected into Balb/c mice three times at a two-week interval. High titer antibody was detected in the serum of immunized Balb/c mice, and mice immunized with S1 protein produced high titer IgG1, IgG2a, IgG2b and IgG3, while those immunized with S2 protein produced high titer IgG1, IgG2a, but lower titer IgG2b and IgG3. Serum IFN-concentration was increased significantly but the concentrations of Il-2, IL-4 and IL-10 had no significant change. And a marked increase was observed in the number of spleen CD8+ T cells. The results showed that recombinant proteins of SARS coronavirus spike protein induced hormonal and cellular immune response in Balb/c mice. url: https://www.ncbi.nlm.nih.gov/pubmed/17641827/ doi: 10.1007/s11596-007-0301-0 id: cord-304271-vyayyk50 author: Qin, Yuan-Yuan title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial date: 2020-03-05 words: 3984.0 sentences: 228.0 pages: flesch: 42.0 cache: ./cache/cord-304271-vyayyk50.txt txt: ./txt/cord-304271-vyayyk50.txt summary: title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial [9] During the SARS epidemic of 2003, therapeutic systemic glucocorticoids were widely administered in patients who were infected with the severe acute respiratory syndrome coronavirus (SARS-COV), and who subsequently developed severe respiratory disease. [12] In addition, a further retrospective observational study found that glucocorticoid therapy in patients with MERS was associated with delayed Middle East respiratory syndrome coronavirus (MERS-CoV) RNA clearance. [13, 20, 21] Glucocorticoid therapy was used in the treatment of severe SARS because early anecdotal experience supported it, and radiologic findings and histologic features of critically ill patients with SARS were similar to those of patients with acute respiratory distress syndrome (ARDS). Factors associated with psychosis among patients with severe acute respiratory syndrome: a case-control study Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial abstract: BACKGROUND: At the end of 2019, a novel coronavirus outbreak emerged in Wuhan, China, and its causative organism has been subsequently designated the 2019 novel coronavirus (2019-nCoV). The effectiveness of adjunctive glucocorticoid therapy in the management of 2019-nCoV-infected patients with severe lower respiratory tract infections is not clear, and warrants further investigation. METHODS: The present study will be conducted as an open-labeled, randomized, controlled trial. We will enrol 48 subjects from Chongqing Public Health Medical Center. Each eligible subject will be assigned to an intervention group (methylprednisolone via intravenous injection at a dose of 1–2 mg/kg/day for 3 days) or a control group (no glucocorticoid use) randomly, at a 1:1 ratio. Subjects in both groups will be invited for 28 days of follow-up which will be scheduled at four consecutive visit points. We will use the clinical improvement rate as our primary endpoint. Secondary endpoints include the timing of clinical improvement after intervention, duration of mechanical ventilation, duration of hospitalization, overall incidence of adverse events, as well as rate of adverse events at each visit, and mortality at 2 and 4 weeks. DISCUSSION: The present coronavirus outbreak is the third serious global coronavirus outbreak in the past two decades. Oral and parenteral glucocorticoids have been used in the management of severe respiratory symptoms in coronavirus-infected patients in the past. However, there remains no definitive evidence in the literature for or against the utilization of systemic glucocorticoids in seriously ill patients with coronavirus-related severe respiratory disease, or indeed in other types of severe respiratory disease. In this study, we hope to discover evidence either supporting or opposing the systemic therapeutic administration of glucocorticoids in patients with severe coronavirus disease 2019. TRIAL REGISTRATION: ClinicalTrials.gov, ChiCTR2000029386, http://www.chictr.org.cn/showproj.aspx?proj=48777. url: https://doi.org/10.1097/cm9.0000000000000791 doi: 10.1097/cm9.0000000000000791 id: cord-259593-shrd1s7r author: Qin, Zhao-ling title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 words: 4603.0 sentences: 255.0 pages: flesch: 56.0 cache: ./cache/cord-259593-shrd1s7r.txt txt: ./txt/cord-259593-shrd1s7r.txt summary: title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. abstract: SARS-associated coronavirus (SCoV) M protein plays a key role in viral assembly and budding. Recent studies revealed that M protein could interact with N protein in the Golgi complex. In this study, we showed that SCoV M protein co-localized in the Golgi apparatus with a Golgi vector marker. To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The plasmid, pEGFP-M, encoding SCoV M protein as a fusion protein with EGFP, was used for silencing and for reporter gene detection in HEK 293T cells transfected with siRNA constructs. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. url: https://www.sciencedirect.com/science/article/pii/S016609340700198X doi: 10.1016/j.jviromet.2007.05.017 id: cord-291467-vv2lrx2p author: Qing, Huiling title: The possibility of COVID‐19 transmission from eye to nose date: 2020-03-18 words: 526.0 sentences: 41.0 pages: flesch: 62.0 cache: ./cache/cord-291467-vv2lrx2p.txt txt: ./txt/cord-291467-vv2lrx2p.txt summary: T he Coronavirus Disease 2019 , caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not only spreading throughout China but has reached more than 20 countries and has already posed threats to global health and economy. The reason is that although a small number of COVID-19 patients have conjunctivitis, not all of them show positive test of SARS-CoV-2 nucleic acid in conjunctival sac swabs. In addition, some patients did not have conjunctivitis despite positive test results for the SARS-CoV-2 nucleic acid in their conjunctiva sac swabs (Dr. Yanping Song from Wuhan City, China, the outbreak area in China, unpublished paper). Studies show that, like the severe acute respiratory syndrome coronavirus (SARS-CoV) that caused SARS, SARS-CoV-2 binds to human angiotensin-enzyme II (ACE2), using it as a cell entry receptor to invade respiratory and lung epithelium through the spike (S) protein (Zhou et al., 2020a (Zhou et al., ,2020b . abstract: nan url: https://doi.org/10.1111/aos.14412 doi: 10.1111/aos.14412 id: cord-292030-cjz4nuag author: Qiu, Guangyu title: Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection date: 2020-04-13 words: 5689.0 sentences: 305.0 pages: flesch: 48.0 cache: ./cache/cord-292030-cjz4nuag.txt txt: ./txt/cord-292030-cjz4nuag.txt summary: In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. 26−29 In this work, we developed a dual-functional LSPR biosensor through combining the photothermal effect and plasmonic sensing transduction for SARS-CoV-2 viral nucleic acid detection. The plasmonic chip with the twodimensional distribution of nanoabsorbers (AuNIs) is capable to generate the local PPT heat and transduce the in situ hybridization for highly sensitive and accurate SARS-CoV-2 detection. According to the phase-sensing diagram in Figure 4b and S6a, the LSPR response of the dual-functional AuNI biosensor started to increase when the RdRp-COVID genes were injected into the microfluidic chamber at about 200 s and attained the maximum phase value after about 800 s hybridization. abstract: [Image: see text] The ongoing outbreak of the novel coronavirus disease (COVID-19) has spread globally and poses a threat to public health in more than 200 countries. Reliable laboratory diagnosis of the disease has been one of the foremost priorities for promoting public health interventions. The routinely used reverse transcription polymerase chain reaction (RT-PCR) is currently the reference method for COVID-19 diagnosis. However, it also reported a number of false-positive or -negative cases, especially in the early stages of the novel virus outbreak. In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. For better sensing performance, the thermoplasmonic heat is generated on the same AuNIs chip when illuminated at their plasmonic resonance frequency. The localized PPT heat is capable to elevate the in situ hybridization temperature and facilitate the accurate discrimination of two similar gene sequences. Our dual-functional LSPR biosensor exhibits a high sensitivity toward the selected SARS-CoV-2 sequences with a lower detection limit down to the concentration of 0.22 pM and allows precise detection of the specific target in a multigene mixture. This study gains insight into the thermoplasmonic enhancement and its applicability in the nucleic acid tests and viral disease diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/32281785/ doi: 10.1021/acsnano.0c02439 id: cord-278256-dmrtsxik author: Qiu, Haiyan title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study date: 2020-03-25 words: 3458.0 sentences: 199.0 pages: flesch: 50.0 cache: ./cache/cord-278256-dmrtsxik.txt txt: ./txt/cord-278256-dmrtsxik.txt summary: title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study INTERPRETATION: Although all paediatric patients in our cohort had mild or moderate type of COVID-19, the large proportion of asymptomatic children indicates the difficulty in identifying paediatric patients who do not have clear epidemiological information, leading to a dangerous situation in community-acquired infections. All children with COVID-19 had been infected either by close contact with adults infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or by exposure to the epidemic area. By contrast with findings in adults, children with COVID-19 had milder clinical manifestations; nearly half of paediatric patients were asymptomatic (ie, no fever and no cough). When compared with children with SARS, paediatric patients with COVID-19 had much milder disease in terms of the prevalence of fever, cough, pneumonia, and severe case type. abstract: BACKGROUND: Since December, 2019, an outbreak of coronavirus disease 2019 (COVID-19) has spread globally. Little is known about the epidemiological and clinical features of paediatric patients with COVID-19. METHODS: We retrospectively retrieved data for paediatric patients (aged 0–16 years) with confirmed COVID-19 from electronic medical records in three hospitals in Zhejiang, China. We recorded patients' epidemiological and clinical features. FINDINGS: From Jan 17 to March 1, 2020, 36 children (mean age 8·3 [SD 3·5] years) were identified to be infected with severe acute respiratory syndrome coronavirus 2. The route of transmission was by close contact with family members (32 [89%]) or a history of exposure to the epidemic area (12 [33%]); eight (22%) patients had both exposures. 19 (53%) patients had moderate clinical type with pneumonia; 17 (47%) had mild clinical type and either were asymptomatic (ten [28%]) or had acute upper respiratory symptoms (seven [19%]). Common symptoms on admission were fever (13 [36%]) and dry cough (seven [19%]). Of those with fever, four (11%) had a body temperature of 38·5°C or higher, and nine (25%) had a body temperature of 37·5–38·5°C. Typical abnormal laboratory findings were elevated creatine kinase MB (11 [31%]), decreased lymphocytes (11 [31%]), leucopenia (seven [19%]), and elevated procalcitonin (six [17%]). Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB. All children received interferon alfa by aerosolisation twice a day, 14 (39%) received lopinavir–ritonavir syrup twice a day, and six (17%) needed oxygen inhalation. Mean time in hospital was 14 (SD 3) days. By Feb 28, 2020, all patients were cured. INTERPRETATION: Although all paediatric patients in our cohort had mild or moderate type of COVID-19, the large proportion of asymptomatic children indicates the difficulty in identifying paediatric patients who do not have clear epidemiological information, leading to a dangerous situation in community-acquired infections. FUNDING: Ningbo Clinical Research Center for Children's Health and Diseases, Ningbo Reproductive Medicine Centre, and Key Scientific and Technological Innovation Projects of Wenzhou. url: https://api.elsevier.com/content/article/pii/S1473309920301985 doi: 10.1016/s1473-3099(20)30198-5 id: cord-296492-knofua00 author: Qiu, L. title: Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province date: 2020-07-07 words: 2889.0 sentences: 201.0 pages: flesch: 54.0 cache: ./cache/cord-296492-knofua00.txt txt: ./txt/cord-296492-knofua00.txt summary: Lung transplantation recipients (LTx) were susceptible to severe acute respiratory syndrome-corona virus-2 (SARS-Cov-2) and suffered a higher mortality risk than healthy subjects. In this study, the clinical characteristics, laboratory testing and epidemiology survey results of 10 LTx recipients undergoing allograft lung transplantation surgeries in the First Affiliated Hospital of Zhengzhou University during the COVID-19 pandemic were collected. In this work, we collected characteristics of these LTx recipients and designed an epidemiology questionnaire to obtain the information of SARS-CoV-2 infection condition and after-discharge preventive measures of LTx recipients who underwent surgeries in the hospital accepting COVID-19 patients during the COVID-19 pandemic. Consistent with previous reports [12, 13] , the key reasons for the zero SARS-CoV-2 infective rate of LTx recipients in our study may be due to the good performance of hand hygiene, wearing masks and indoor disinfection, and even isolation from family members. abstract: Lung transplantation recipients (LTx) were susceptible to severe acute respiratory syndrome-corona virus-2 (SARS-Cov-2) and suffered a higher mortality risk than healthy subjects. Here we aim to analyze whether it was appropriate or and valuable to maintain lung transplant programs in medical institutions accepting coronavirus disease 2019 (COVID-19) patients. In this study, the clinical characteristics, laboratory testing and epidemiology survey results of 10 LTx recipients undergoing allograft lung transplantation surgeries in the First Affiliated Hospital of Zhengzhou University during the COVID-19 pandemic were collected. A web-based epidemiology questionnaire was used to collect the information of LTx recipients after discharge. Up to now, none of the LTx recipients or their family members get infected with SARS-CoV-2 during the novel coronavirus pandemic. In conclusion, under the premise of taking appropriate preventive measures during hospitalization and after discharge, the lung transplant program can be maintained in the medical institution that accepts patients with COVID-19. url: http://medrxiv.org/cgi/content/short/2020.07.06.20147264v1?rss=1 doi: 10.1101/2020.07.06.20147264 id: cord-289349-imkgpwn0 author: Qiu, Li title: Strong immunity in the early two years of age links to frequent immunization of routine vaccines date: 2020-08-08 words: 2040.0 sentences: 121.0 pages: flesch: 52.0 cache: ./cache/cord-289349-imkgpwn0.txt txt: ./txt/cord-289349-imkgpwn0.txt summary: In this retrospective study, 25 patients under 10 years old were selected from a total of 186 laboratory-confirmed COVID-19 patients (Materials and methods, Fig. S1 , and Table S1 online). The patient age distribution revealed that children of all ages are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (Fig. 1a) . Because pediatric COVID-19 patients aged under 2 years were found to have shorter recovery times, we next further analyzed the clinical differences between children under and over 2 years old; several variables were compared between these two groups (Table S7 online). However, a previous epidemiological study revealed that the incidence of seasonal coronavirus infection in children under one year old is not significantly different from that in older children [15] . Pre-existing cross-reactive T-cell immunity to infections or vaccinations alters subsequent T-cell responses to antigens of unrelated pathogens [18] [19] [20] , thus frequently contributing to a protective or pathogenic role in infectious diseases [18, 20] . abstract: nan url: https://api.elsevier.com/content/article/pii/S2095927320305338 doi: 10.1016/j.scib.2020.08.012 id: cord-310909-nc82a70n author: Qiu, Maofeng title: Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date: 2005-04-13 words: 4520.0 sentences: 196.0 pages: flesch: 48.0 cache: ./cache/cord-310909-nc82a70n.txt txt: ./txt/cord-310909-nc82a70n.txt summary: In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. In the present study, to understand the profile of antibodies to individual proteins of the SARS-CoV, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of this virus were prepared and used to screen and monitor their specific IgG antibodies in SARS patient sera using protein microarray, and the rabbit antisera to recombi-nant proteins S3 (aa 241-591), N (full length), 3a (aa 125-274) and 9b (full length) were prepared and used to investigate their neutralizing activity to the SARS-CoV infection in Vero E6 cells. abstract: A novel coronavirus, the severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), was identified as the causative agent of SARS. The profile of specific antibodies to individual proteins of the virus is critical to the development of vaccine and diagnostic tools. In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. Antibodies to proteins S, 3a, N and 9b were detected in the sera from convalescent-phase SARS patients, whereas those to proteins E, M, 3b, 6 and 7a were undetected. In the detectable specific antibodies, anti-S and anti-N were dominant and could persist in the sera of SARS patients until week 30. Among the rabbit antisera to recombinant proteins S3, N, 3a and 9b, only anti-S3 serum showed significant neutralizing activity to the SARS-CoV infection in Vero E6 cells. The results suggest (1) that anti-S and anti-N antibodies are diagnostic markers and in particular that S3 is immunogenic and therefore is a good candidate as a subunit vaccine antigen; and (2) that, from a virus structure viewpoint, the presence in some human sera of antibodies reacting with two recombinant polypeptides, 3a and 9b, supports the hypothesis that they are synthesized during the virus cycle. url: https://www.ncbi.nlm.nih.gov/pubmed/15878679/ doi: 10.1016/j.micinf.2005.02.006 id: cord-334194-28ygsbo1 author: Qiu, Tianyi title: Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus date: 2020-02-20 words: 1727.0 sentences: 98.0 pages: flesch: 53.0 cache: ./cache/cord-334194-28ygsbo1.txt txt: ./txt/cord-334194-28ygsbo1.txt summary: title: Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Letter to the editor Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Recently, a new type of unknown virus causing severe acute respiratory infection was reported in Wuhan city, Hubei province, China (WHO, 2020b) . Recently, the binding sites of S protein to human ACE2 were identified as residues 455, 486, 493, 501, and 505 (numbered according to the 2019-nCoV S protein sequence), which are located near the potential CRE positions (Fig. 1E) . Possibility of an additional CRE may also exist in other regions of S protein or other antigens between 2019-nCoV and SARS-CoV. In summary, a highly similar epitope was identified computationally between the 2019-nCoV and SARS virus, in the region of the binding site of the S proteins to the human ACE2 receptor. abstract: nan url: https://api.elsevier.com/content/article/pii/S1673852720300138 doi: 10.1016/j.jgg.2020.01.003 id: cord-259993-hlsvu1cg author: Qiu, Wuqi title: The Impacts on Health, Society, and Economy of SARS and H7N9 Outbreaks in China: A Case Comparison Study date: 2018-06-28 words: 3417.0 sentences: 178.0 pages: flesch: 56.0 cache: ./cache/cord-259993-hlsvu1cg.txt txt: ./txt/cord-259993-hlsvu1cg.txt summary: AIMS: This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country''s economy, its society, and its place in the global community. In the past 15 years China has experienced numerous public health crises caused by disease outbreaks including Severe Acute Respiratory Syndromes (SARS) in 2003 and Influenza A Virus Subtype H7N9 (H7N9) in 2013. This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country''s economy, its society, and its place in the global community. abstract: BACKGROUND: Epidemics such as SARS and H7N9 have caused huge negative impacts on population health and the economy in China. AIMS: This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country's economy, its society, and its place in the global community. METHODS: To provide the results of an analysis of impacts of SARS and H7N9 based on feedback from documents, informants, and focus groups on events during the SARS and H7N9 outbreaks. RESULTS: Both outbreaks of SARS and H7N9 have had an impact on China, causing significant negative impacts on health, the economy, and even national and even international security. CONCLUSIONS: Both SARS coronavirus and H7N9 viruses presented a global epidemic threat, but the social and economic impacts of H7N9 were not as serious as in the case of SARS because the response to H7N9 was more effective. url: https://www.ncbi.nlm.nih.gov/pubmed/30050581/ doi: 10.1155/2018/2710185 id: cord-339625-ucfjo73c author: Qiu, Xiang title: Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus date: 2012-07-26 words: 3586.0 sentences: 178.0 pages: flesch: 55.0 cache: ./cache/cord-339625-ucfjo73c.txt txt: ./txt/cord-339625-ucfjo73c.txt summary: Given that rCRT/39–272 can drive the maturation of bone‐marrow‐derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39–272 of CRT is an effective molecular adjuvant capable of enhancing target Ag‐specific humoral responses in both a T cell‐dependent and independent manner. By using DNA vaccines encoding fusion proteins between CRT and target antigens such as tumor antigen E7, N protein of SARS-CoV and Bacillus anthracis protective antigen domain IV, previous investigators have also observed that CRT can function as a molecular adjuvant (13) (14) (15) (16) . Cheng and colleagues found that intradermal immunization with a DNA vaccine encoding a fusion protein between CRT, or CRT fragments, and the E7 tumor antigen was more efficient at eliciting E7-specific CD8 + T cells and protecting against E7-expressing tumors in C57BL/6 mice (13, 14) . abstract: Fragment 450–650 of the spike (S) protein (S450–650) of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) contains epitopes capable of being recognized by convalescent sera of SARS patients. Vaccination of mice with recombinant S450–650 (rS450–650) can induce Abs against SARS‐CoV, although the titer is relatively low. In the present study, a fusion protein linking a fragment (residues 39–272) of murine calreticulin (CRT) to S450–650 in a prokaryotic expression system was created. Compared with target antigen alone, the recombinant fusion product (rS450–650‐CRT) has much improved hydrophilicity and immunogenicity. The S450–650‐specific IgG Abs of BALB/c mice subcutaneously immunized with rS450–650‐CRT were in substantially higher titer (approximately fivefold more). Furthermore, the fusion protein, but not rS450–650 alone, was able to elicit S450–650‐specific IgG responses in T cell deficient nude mice. Given that rCRT/39–272 can drive the maturation of bone‐marrow‐derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39–272 of CRT is an effective molecular adjuvant capable of enhancing target Ag‐specific humoral responses in both a T cell‐dependent and independent manner. Fusion protein rS450–650‐CRT is a potential candidate vaccine against SARS‐CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22530918/ doi: 10.1111/j.1348-0421.2012.00467.x id: cord-305059-8z54lw2d author: Qu, Jie-Ming title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 words: 5054.0 sentences: 271.0 pages: flesch: 45.0 cache: ./cache/cord-305059-8z54lw2d.txt txt: ./txt/cord-305059-8z54lw2d.txt summary: If any one of the following pathogenic or serological tests is positive, the patient is confirmed as COVID-19: (1) positive RT-PCR results for SARS-CoV-2 nucleic acid; (2) viral gene sequencing highly homologous to the known SARS-CoV-2; or (3) serum samples positive for SARS-CoV-2-specific IgM and IgG antibodies. The fifth edition of the program was specially designed for Hubei to establish the diagnostic criteria of "clinical diagnosis cases," which include clinical compliance with the characteristics of viral pneumonia, such as corresponding clinical symptoms and imaging CT findings, especially the multiple lobes exudative ground-glass shadow and intermittent consolidation, normal or decreased total count of white blood cells in laboratory examination, and reduced lymphocyte count. The methods are: (1) real-time fluorescence RT-PCR detection of SARS-CoV-2 nucleic acid positive and (2) viral gene sequencing, highly homologous with the known novel coronavirus. abstract: The diagnosis of COVID-19 is based on epidemiological history, clinical manifestations, and pathogenic confirmation. url: https://www.sciencedirect.com/science/article/pii/B9780128240038000048 doi: 10.1016/b978-0-12-824003-8.00004-8 id: cord-356084-621qzpqd author: Qu, Jiuxin title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 words: 1578.0 sentences: 98.0 pages: flesch: 61.0 cache: ./cache/cord-356084-621qzpqd.txt txt: ./txt/cord-356084-621qzpqd.txt summary: title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus abstract: We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. The majority of the patients developed robust antibody responses between 17 and 23 days after illness onset. Delayed, but stronger antibody responses were observed in critical patients. url: https://doi.org/10.1093/cid/ciaa489 doi: 10.1093/cid/ciaa489 id: cord-337663-ow1l18li author: Qu, Liang G. title: Scoping review: hotspots for COVID-19 urological research: what is being published and from where? date: 2020-09-09 words: 4694.0 sentences: 306.0 pages: flesch: 45.0 cache: ./cache/cord-337663-ow1l18li.txt txt: ./txt/cord-337663-ow1l18li.txt summary: This comprehensive review aimed to: identify all up-to-date original publications relating to urology and COVID-19, characterise where publications were from, and outline what topics were investigated. Topics of the study included pathophysiological, administrative, and clinical fields: translational (n = 14), COVID-19-related outcomes (n = 5), urology training (n = 4), telemedicine (n = 7), equipment and safety (n = 2), urology in general (n = 4), uro-oncology (n = 3), urolithiasis (n = 1), and kidney transplantation (n = 8). A registered study in France (NCT04341714) is similarly assessing the efficiency and satisfaction of telemedicine consults, aiming to recruit 400 patients from a neuro-urology clinic. 48 studies were included, investigating pathophysiological, administrative, and clinical outcomes relating to COVID-19 and urology. Clinical fields of COVID-19-related urological research seem to focus on uro-oncology, urolithiasis, and kidney transplant recipients. Nevertheless, our review is the first to provide a comprehensive country-level analysis of current original urological research related to COVID-19. abstract: PURPOSE: Contemporary, original research should be utilised to inform guidelines in urology relating to the COVID-19 pandemic. This comprehensive review aimed to: identify all up-to-date original publications relating to urology and COVID-19, characterise where publications were from, and outline what topics were investigated. METHODS: This review utilised a search strategy that assessed five electronic databases, additional grey literature, and global trial registries. All current published, in-press, and pre-print manuscripts were included. Eligible studies were required to be original research articles of any study design, reporting on COVID-19 or urology, in any of study population, intervention, comparison, or outcomes. Included studies were reported in a narrative synthesis format. Data were summarised according to primary reported outcome topic. A world heatmap was generated to represent where included studies originated from. RESULTS: Of the 6617 search results, 48 studies met final inclusion criteria, including 8 pre-prints and 7 ongoing studies from online registries. These studies originated from ten countries according to first author affiliation. Most studies originated from China (n = 13), followed by Italy (n = 12) and USA (n = 11). Topics of the study included pathophysiological, administrative, and clinical fields: translational (n = 14), COVID-19-related outcomes (n = 5), urology training (n = 4), telemedicine (n = 7), equipment and safety (n = 2), urology in general (n = 4), uro-oncology (n = 3), urolithiasis (n = 1), and kidney transplantation (n = 8). CONCLUSION: This review has outlined available original research relevant to COVID-19 and urology from the international community. This summary may serve as a guide for future research priorities in this area. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00345-020-03434-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00345-020-03434-2 doi: 10.1007/s00345-020-03434-2 id: cord-270886-m9na7cbm author: Quadeer, Ahmed Abdul title: Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges date: 2020-08-15 words: 1216.0 sentences: 60.0 pages: flesch: 37.0 cache: ./cache/cord-270886-m9na7cbm.txt txt: ./txt/cord-270886-m9na7cbm.txt summary: Serological assays can also assist in detecting a large number of subclinical infections in the community arising largely due to the high proportion of asymptomatic COVID-19 cases, and in identifying donors with highly reactive antibodies for convalescent plasma therapy. In the current issue of EBioMedicine, Ng and colleagues attempt to address the above limitations of current serological assays by presenting a novel linear B cell immunodominant epitopes based assay for detecting exposure to SARS-CoV-2 [5] . Specifically, they identified a set of five immunodominant linear B cell epitopes from a peptide library of SARS-CoV-2 structural proteins by performing IgG reactivity test on pooled plasma samples of COVID-19 infected patients from Singapore. Consistent with multiple recent reports (e.g., [7, 8] ), the authors also found that the magnitude of IgG responses in COVID-19 patients against the identified epitopes correlated with disease severity. Second, the usefulness of serological assays in detecting prior exposure relies on the stimulation and persistence of SARS-CoV-2-specific antibody responses in infected patients. abstract: nan url: http://www.thelancet.com/article/S2352396420303236/pdf doi: 10.1016/j.ebiom.2020.102947 id: cord-329890-wg23sa1u author: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 words: 9734.0 sentences: 423.0 pages: flesch: 49.0 cache: ./cache/cord-329890-wg23sa1u.txt txt: ./txt/cord-329890-wg23sa1u.txt summary: Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people''s lifestyles and approaches to the control and prevention of epidemics. The second assumption is that in contrast to SARS, the overall negative public ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. The second assumption to be explored here is that in contrast to SARS, the overall negative social ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. abstract: Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people's lifestyles and approaches to the control and prevention of epidemics. The main research question is: what can we learn from the SARS experience about effective prevention of HIV/AIDS? The sources of data include population figures on the development of these epidemics and findings from two sociological studies of representative samples of Singapore's multi-ethnic population. The comparative study illustrates the impact of cultural beliefs and attitudes in shaping the public image of these two different infectious diseases; the relevance of public image of the disease for effective prevention and control of epidemics. url: https://www.ncbi.nlm.nih.gov/pubmed/16632071/ doi: 10.1016/j.healthpol.2006.03.002 id: cord-260132-lqpk3ig7 author: Quartuccio, Luca title: Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome date: 2020-04-19 words: 2463.0 sentences: 116.0 pages: flesch: 39.0 cache: ./cache/cord-260132-lqpk3ig7.txt txt: ./txt/cord-260132-lqpk3ig7.txt summary: Currently, the humanized monoclonal antibody anti-interleukin-6 receptor (anti-IL-6R), namely tocilizumab, appears as a promising tool to turn off the cytokine storm, which dramatically complicates the course of the infection in some patients, causing a rapidly fatal acute respiratory distress syndrome. Importantly, SARS-CoV patients admitted to the Intensive Care Unit showed higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, creatine kinase, and creatine, emphasizing the role of the systemic inflammation downstream the virus infection, and the transformation of the infectious disease into a systemic immunological and inflammatory disease. Lung pathology in 2003 SARS-CoV patients showed epithelial cell proliferation and desquamation, hyaline membranes formation along alveolar walls and cells infiltration (lymphocytes, neutrophils, and monocytes) during the early stage of the disease, while, of note, increased fibrosis and multinucleated epithelial giant cells formation at a later stage, highlighting the existence of a two-phase lung injury. abstract: nan url: https://api.elsevier.com/content/article/pii/S1297319X20300476 doi: 10.1016/j.jbspin.2020.03.011 id: cord-349954-bozgrzvf author: Quintaliani, Giuseppe title: Exposure to novel coronavirus in patients on renal replacement therapy during the exponential phase of COVID-19 pandemic: survey of the Italian Society of Nephrology date: 2020-07-03 words: 3454.0 sentences: 206.0 pages: flesch: 50.0 cache: ./cache/cord-349954-bozgrzvf.txt txt: ./txt/cord-349954-bozgrzvf.txt summary: During the COVID-19 pandemic, among SARS-Cov-2 positive RRT patients the fatality rate was 32.8%, as compared to 13.3% observed in the Italian population as of April 23rd. CONCLUSIONS: A substantial proportion of the 60,441 surveyed RRT patients in Italy were SARS-Cov-2 positive and subsequently died during the exponential phase of COVID-19 pandemic. The urgent need for a better understanding of the epidemic in RRT patients was immediately evident, and therefore we designed a survey of the Nephrology centers in Italy, aimed to capture the main features, impact and geographical distribution of SARS-CoV-2 spread in over 60,000 prevalent RRT patients during the exponential phase of the COVID-19 pandemic in Italy. The Italian Society of Nephrology COVID-19 survey confirms and extends previous preliminary observations suggesting that RRT patients, especially those on HD, are at increased risk of developing severe SARS-Cov-2 infections. abstract: BACKGROUND: Between February and April 2020, Italy experienced an overwhelming growth of the COVID-19 pandemic. Little is known, at the country level, where and how patients on renal replacement therapy (RRT) have been mostly affected. METHODS: Survey of the network of Nephrology centers using a simplified 17 items electronic questionnaire designed by Italian Society of Nephrology COVID-19 Research Group. We used spatial epidemiology and geographical information systems to map SARS-CoV-2 spread among RRT patients in Italy. RESULTS: On April 9th 2020, all nephrology centers (n = 454) listed in the DialMap database were invited to complete the electronic questionnaire. Within 11 days on average, 365 centers responded (80.4% response rate; 2.3% margin of error) totaling 60,441 RRT patients. The surveyed RRT population included 30,821 hemodialysis (HD), 4139 peritoneal dialysis (PD), and 25,481 transplanted (Tx) patients respectively. The proportion of SARS-CoV-2 positive RRT patients in Italy was 2.26% (95% CI 2.14–2.39) with significant differences according to treatment modality (p < 0.001). The proportion of patients positive for SARS-CoV-2 was significantly higher in HD (3.55% [95% CI 3.34–3.76]) than PD (1.38% [95% CI 1.04–1.78] and Tx (0.86% [95% CI 0.75–0.98]) (p < 0.001), with substantial heterogeneity across regions and along the latitude gradient (p < 0.001). In RRT patients the highest rate was in the north-west (4.39% [95% CI 4.11–4.68], followed by the north-east (IR 2.06% [1.79–2.36]), the center (0.91% [0.75–1.09]), the main islands (0.67% [0.47–0.93]), and the south (0.59% [0.45–0.75]. During the COVID-19 pandemic, among SARS-Cov-2 positive RRT patients the fatality rate was 32.8%, as compared to 13.3% observed in the Italian population as of April 23rd. CONCLUSIONS: A substantial proportion of the 60,441 surveyed RRT patients in Italy were SARS-Cov-2 positive and subsequently died during the exponential phase of COVID-19 pandemic. Infection risk and rates seems to differ substantially across regions, along geographical latitude, and by treatment modality. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40620-020-00794-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32621109/ doi: 10.1007/s40620-020-00794-1 id: cord-293860-6kz0iws6 author: Qutayba Almerie, Muhammad title: The Association between Obesity and Poor Outcome after COVID-19 Indicates a Potential Therapeutic Role for Montelukast date: 2020-05-27 words: 2801.0 sentences: 139.0 pages: flesch: 41.0 cache: ./cache/cord-293860-6kz0iws6.txt txt: ./txt/cord-293860-6kz0iws6.txt summary: HYPOTHESIS: Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. With its prominent effect in reducing leukotriene-mediated cytokine release montelukast would have the potential to moderate the background inflammation associated with obesity and the body''s inflammatory response to SARS-CoV2. The strong association between the pro-inflammatory state found in metabolic syndrome and obesity and a more aggressive clinical course in COVID-19 suggests a potential treatment role for drugs that inhibit cytokine release and macrophage activation. abstract: It is widely believed that infection with the SARS-CoV2 virus triggers a disproportionate immune response which causes a devastating systemic injury, particularly in individuals with obesity, itself a chronic, multi-organ inflammatory disease. Immune cells accumulate in visceral adipose tissue and together with paracrine adipocytes release a wide range of biologically active cytokines (including IL-1β, IL5, IL6 and IL8) that can result in both local, pulmonary and systemic inflammation. A more intense ‘cytokine storm’ is postulated as the mechanism behind the extreme immune response seen in severe COVID-19. It is striking how dangerous the combination of obesity and COVID-19 is, resulting in a greater risk of ICU admission and a higher mortality. Furthermore, patients from a BAME background appear to have increased mortality after SARS-CoV2 infection; they also have a higher prevalence of central obesity and its metabolic complications. In the absence of an effective vaccine, the therapeutic potential of immune-modulating drugs is a priority, but the development of new drugs is expensive and time-consuming. A more pragmatic solution would be to seek to repurpose existing drugs, particularly those that might suppress the heightened cytokine activity seen in obesity, the major risk factor for a poor prognosis in COVID-19. Montelukast is a cysteinyl leukotriene receptor antagonist licensed to treat asthma and allergic rhinitis. It has been shown to diminish pulmonary response to antigen, tissue eosinophilia and IL-5 expression in inflammatory cells. It has also been shown to decrease elevated levels of IL-1β and IL8 in humans with viral upper respiratory tract infections compared with placebo-treated patients. In addition, in silico studies have demonstrated a high binding affinity of the montelukast molecule to the terminal site of the virus’s main protease enzyme which is needed for virus RNA synthesis and replication. Montelukast, which is cheap, safe and widely available would appear to have the potential to be an ideal candidate drug for clinical trials, particularly in early stage disease before irreparable tissue damage has already occurred. HYPOTHESIS: Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. url: https://www.sciencedirect.com/science/article/pii/S0306987720311488?v=s5 doi: 10.1016/j.mehy.2020.109883 id: cord-290792-ggcz1zfw author: Qutob, N. title: Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study date: 2020-09-01 words: 2051.0 sentences: 129.0 pages: flesch: 54.0 cache: ./cache/cord-290792-ggcz1zfw.txt txt: ./txt/cord-290792-ggcz1zfw.txt summary: Serological tests for the 2455 serum samples were done using an Immunoassay for the qualitative detection of antibodies against SARS-CoV-2 .The random sample of Palestinians living in the West Bank yielded 0% seroprevalence with 95% CI [0,0.0036], while the lab referrals sample yielded 4 positive cases. Most authorities rely on PCR testing results to estimate number of COVID-19 cases and make up-to-date decisions 6 . The proportion of the population who have overcome the infection without being noticed can probably be approximated by testing for antibodies against SARS-CoV-2. The study included 2491 individuals (1355 from randomly selected households and 1136 from laboratory referrals; was designed to be representative by cities and used Elecsys ® Anti-SARS-CoV-2 testing. We estimated seroprevalence as the proportion of individuals who had a positive result in the total SARS-CoV-2 antibodies in the immunoassay. Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from abstract: Seroprevalence rates are important indicators to the epidemiology of Covid-19 and the rates vary according to the population. In Palestine, there is lack of data on the the percentage of undiagnosed population with previous mild or asymptomatic COVID-19. The purpose of this study is to assess the seroprevalence rate in the Palestinian population residing in the West Bank. Blood samples were collected from1319 adults from Palestinian households in the West Bank and 1136 individuals visiting laboratories for a routine checkup. Serological tests for the 2455 serum samples were done using an Immunoassay for the qualitative detection of antibodies against SARS-CoV-2 .The random sample of Palestinians living in the West Bank yielded 0% seroprevalence with 95% CI [0,0.0036], while the lab referrals sample yielded 4 positive cases. Hence the estimated seroprevalence in this sample is 0.354% with 95% CI [0.0011,0096]. Our results indicate that seroprevalence persist low and is inadequate to provide herd immunity and emphasize the need to maintain health measures to keep the outbreak under control. url: http://medrxiv.org/cgi/content/short/2020.08.28.20180083v1?rss=1 doi: 10.1101/2020.08.28.20180083 id: cord-329190-kv9n2qj3 author: Rabaan, Ali A. title: A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective date: 2017-09-01 words: 8886.0 sentences: 433.0 pages: flesch: 44.0 cache: ./cache/cord-329190-kv9n2qj3.txt txt: ./txt/cord-329190-kv9n2qj3.txt summary: The current therapies have mainly been adapted from severe acute respiratory syndrome (SARS-CoV) treatments, including broad-spectrum antibiotics, corticosteroids, interferons, ribavirin, lopinavir–ritonavir or mycophenolate mofetil, and have not been subject to well-organized clinical trials. The Medline database was searched using combinations and variations of terms, including ''Middle East respiratory syndrome coronavirus'', ''MERS-CoV'', ''SARS'', ''therapy'', ''molecular'', ''vaccine'', ''prophylactic'', ''S protein'', ''DPP4'', ''heptad repeat'', ''protease'', ''inhibitor'', ''anti-viral'', ''broad-spectrum'', ''interferon'', ''convalescent plasma'', ''lopinavir ritonavir'', ''antibodies'', ''antiviral peptides'' and ''live attenuated viruses''. A position paper on the evidence base for specific MERS-CoV therapies, published by Public Health England (PHE) and the World Health Organization-International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC-WHO), suggested that benefit was likely to exceed risk for convalescent plasma, lopinavir-ritonavir, IFNs and monoclonal/polyclonal antibodies, while, by contrast, for ribavirin monotherapy and corticosteroids it was considered that the risks would outweigh the benefits [42] . abstract: There have been 2040 laboratory-confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) in 27 countries, with a mortality rate of 34.9 %. There is no specific therapy. The current therapies have mainly been adapted from severe acute respiratory syndrome (SARS-CoV) treatments, including broad-spectrum antibiotics, corticosteroids, interferons, ribavirin, lopinavir–ritonavir or mycophenolate mofetil, and have not been subject to well-organized clinical trials. The development of specific therapies and vaccines is therefore urgently required. We examine existing and potential therapies and vaccines from a molecular perspective. These include viral S protein targeting; inhibitors of host proteases, including TMPRSS2, cathepsin L and furin protease, and of viral M(pro) and the PL(pro) proteases; convalescent plasma; and vaccine candidates. The Medline database was searched using combinations and variations of terms, including ‘Middle East respiratory syndrome coronavirus’, ‘MERS-CoV’, ‘SARS’, ‘therapy’, ‘molecular’, ‘vaccine’, ‘prophylactic’, ‘S protein’, ‘DPP4’, ‘heptad repeat’, ‘protease’, ‘inhibitor’, ‘anti-viral’, ‘broad-spectrum’, ‘interferon’, ‘convalescent plasma’, ‘lopinavir ritonavir’, ‘antibodies’, ‘antiviral peptides’ and ‘live attenuated viruses’. There are many options for the development of MERS-CoV-specific therapies. Currently, MERS-CoV is not considered to have pandemic potential. However, the high mortality rate and potential for mutations that could increase transmissibility give urgency to the search for direct, effective therapies. Well-designed and controlled clinical trials are needed, both for existing therapies and for prospective direct therapies. url: https://doi.org/10.1099/jmm.0.000565 doi: 10.1099/jmm.0.000565 id: cord-271998-hdkmwihu author: Rabenau, H. F. title: SARS-coronavirus (SARS-CoV) and the safety of a solvent/detergent (S/D) treated immunoglobulin preparation date: 2005-06-30 words: 3071.0 sentences: 170.0 pages: flesch: 49.0 cache: ./cache/cord-271998-hdkmwihu.txt txt: ./txt/cord-271998-hdkmwihu.txt summary: SARS-CoV viraemia does not seem to reach high titres, however, it has to be excluded that virus transmission may occur via blood transfusion or application of therapeutic plasma products, e.g. fresh-frozen plasma or single components derived thereof. On the basis of existing validation data for enveloped viruses, it can be anticipated that the inactivation/ removal steps incorporated into manufacturing processes for plasma-derived medicinal products will also be effective for SARS-CoV. Therefore, the inactivation of SARS-CoV by SD treatment was investigated in the laboratory scale at lowered concentration of solvent and detergent (75% of standard SD concentration) and at a shortened process time (30 min). In conclusion, the results obtained in our investigation demonstrated that the process conditions specified for the SD treatment of OCTAGAM are very sufficient to inactivate enveloped viruses such as SARS-CoV to below the limit of detection. abstract: Abstract SARS-coronavirus (SARS-CoV) is a newly emerged, highly pathogenic agent that caused over 8000 human infections with nearly 800 deaths between November 2002 and September 2003. While direct person-to-person transmission via respiratory droplets accounted for most cases, other modes have not been ruled out. SARS-CoV viraemia does not seem to reach high titres, however, it has to be excluded that virus transmission may occur via blood transfusion or application of therapeutic plasma products, e.g. fresh-frozen plasma or single components derived thereof. Manufacturing processes of all plasma derivatives are required to comprise dedicated virus inactivation/removal steps. Treatment with a mixture of solvent and detergent (SD) has successfully been applied to inactivate the most members of the transfusion-relevant viruses without affecting therapeutic properties of the products. The SD treatment irreversibly disrupts the lipid envelope of viruses such as HIV, HBV, HCV, HGV and CMV. In this study we evaluated the manufacturing process of an immunoglobulin preparation (OCTAGAM, manufactured by Octapharma Pharmazeutika Produktionsges.m.b.H., Vienna, Austria) for its capacity to inactivate the SARS-CoV. Our results demonstrate that SARS-CoV was completely inactivated below the limit of detection. This was found to occur within 1min of SD treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/15939287/ doi: 10.1016/j.biologicals.2005.01.003 id: cord-333738-3xtb8gye author: Rabets, A. title: Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients date: 2020-08-22 words: 2486.0 sentences: 146.0 pages: flesch: 49.0 cache: ./cache/cord-333738-3xtb8gye.txt txt: ./txt/cord-333738-3xtb8gye.txt summary: Investigating patient serum samples after SARS-CoV-2 infection in cross-reactivity studies of immunogenic peptides from Middle East respiratory syndrome coronavirus (MERS-CoV), we were able to detect the production of antibodies also recognizing MERS virus antigens. Indeed, the peptide of the HR2 domain of the MERS spike protein, previously proven to induce antibodies against MERS-CoV is sharing 74% homology with the corresponding sequence of SARS-CoV-19 virus. If used as an antigen, the peptide of the HR2 domain of the MERS spike protein allows discrimination between post-Covid populations from non-infected ones by the presence of antibodies in blood samples. The high homology of the spike protein domain suggests in addition that the opposite effect can also be true: coronaviral infections producing cross-reactive antibodies affective against SARS-CoV-19. SARS-CoV-2 infections results in the generation of antibodies with significantly strong cross-reactive towards a MERS specific peptide with 76% homology. Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein abstract: Coronaviruses are sharing several protein regions notable the spike protein (S) on their enveloped membrane surface, with the S1 subunit recognizing and binding to the cellular receptor, while the S2 subunit mediates viral and cellular membrane fusion. This similarity opens the question whether infection with one coronavirus will confer resistance to other coronaviruses? Investigating patient serum samples after SARS-CoV-2 infection in cross-reactivity studies of immunogenic peptides from Middle East respiratory syndrome coronavirus (MERS-CoV), we were able to detect the production of antibodies also recognizing MERS virus antigens. The cross-reactive peptide comes from the heptad repeat 2 (HR2) domain of the MERS virus spike protein. Indeed, the peptide of the HR2 domain of the MERS spike protein, previously proven to induce antibodies against MERS-CoV is sharing 74% homology with the corresponding sequence of SARS-CoV-19 virus. Sera samples of 47 convalescent SARS-CoV-2 patients, validated by RT-PCR-negative testes 30 days post-infection, and samples of 40 sera of control patients (not infected with SARS-CoV-2 previously) were used to establish eventual cross-bind reactivity with the MERS peptide antigen. Significantly stronger binding (p<0.0001) was observed for IgG antibodies in convalescent SARS-CoV-2 patients compared to the control group. If used as an antigen, the peptide of the HR2 domain of the MERS spike protein allows discrimination between post-Covid populations from non-infected ones by the presence of antibodies in blood samples. This suggests that polyclonal antibodies established during SARS-CoV-2 infection has the ability to recognize and probably decrease infectiveness of MERS-CoV infections as well as other coronaviruses. The high homology of the spike protein domain suggests in addition that the opposite effect can also be true: coronaviral infections producing cross-reactive antibodies affective against SARS-CoV-19. The collected data prove in addition that despite the core HR2 region being hidden in the native viral conformation, its exposure during cell entry makes it highly immunogenic. Since inhibitory peptides to this region were previously described, this opens new possibilities in fighting coronaviral infections. url: https://doi.org/10.1101/2020.08.20.20178566 doi: 10.1101/2020.08.20.20178566 id: cord-351567-ifoe8x28 author: Rabi, Firas A. title: SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far date: 2020-03-20 words: 5745.0 sentences: 315.0 pages: flesch: 54.0 cache: ./cache/cord-351567-ifoe8x28.txt txt: ./txt/cord-351567-ifoe8x28.txt summary: However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. To assess the magnitude of the risk posed by the SARS-CoV-2, we review four parameters that we believe important: the transmission rate, the incubation period, the case fatality rate (CFR), and the determination of whether asymptomatic transmission can occur. A small study of 17 patients showed that nasal viral load peaks within days of symptom onset, suggesting that transmission of disease is more likely to occur early in the course of infection [40] . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19)-China 2020 Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia abstract: In December 2019, a cluster of fatal pneumonia cases presented in Wuhan, China. They were caused by a previously unknown coronavirus. All patients had been associated with the Wuhan Wholefood market, where seafood and live animals are sold. The virus spread rapidly and public health authorities in China initiated a containment effort. However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. Based on clinical criteria and available serological and molecular information, the new disease was called coronavirus disease of 2019 (COVID-19), and the novel coronavirus was called SARS Coronavirus-2 (SARS-CoV-2), emphasizing its close relationship to the 2002 SARS virus (SARS-CoV). The scientific community raced to uncover the origin of the virus, understand the pathogenesis of the disease, develop treatment options, define the risk factors, and work on vaccine development. Here we present a summary of current knowledge regarding the novel coronavirus and the disease it causes. url: https://doi.org/10.3390/pathogens9030231 doi: 10.3390/pathogens9030231 id: cord-354608-1me3nopu author: Rabinowicz, Shira title: COVID-19 in the Pediatric Population—Review and Current Evidence date: 2020-09-19 words: 5426.0 sentences: 298.0 pages: flesch: 42.0 cache: ./cache/cord-354608-1me3nopu.txt txt: ./txt/cord-354608-1me3nopu.txt summary: By mid-August 2020, the World Health Organization reported over 23 million confirmed cases of infection with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), resulting in more than 710,000 death worldwide [1] . We review the current evidence of epidemiology, clinical presentation, treatment, and indirect health consequences of SARS-CoV-2 on children. In reports from countries that were severely affected early in course of the pandemic, children comprise 1-2% the diagnosed COVID-19 cases, underrepresented compared with other age groups [3, [13] [14] [15] . In summary, children at any age may be infected with SARS-CoV-2, with reduced frequency and severity compared with adults, although clear epidemiologic data is still missing. Characteristics and outcomes of children with coronavirus disease 2019 (COVID-19) infection admitted to US and Canadian Pediatric Intensive Care Units American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS-C) associated with SARS-CoV-2 and hyperinflammation in COVID-19. abstract: PURPOSE OF REVIEW: Coronavirus disease 2019 (COVID-19) pandemic has major health and economic impacts. We review disease characteristics in children. RECENT FINDINGS: Children comprise 1–2% of the diagnosed cases, and typically suffer mild disease. The median age of infected children is 3.3–11 years, and male/female ratio is 1.15–1.55. Common symptoms in children include upper respiratory symptoms (26–54%), cough (44–54%), fever (32–65%), and gastrointestinal (15–30%) symptoms. Substantial proportion (4–23%) are asymptomatic. Death rates are up to 0.7%. Risk factors associated with severe disease are neonatal age group, male gender, lower respiratory tract disease, and pre-existing medical conditions. Vertical transmission was reported. Multisystem inflammatory syndrome (MIS), characterized by fever, multisystem organ involvement, and laboratory markers of inflammation, causes critical illness in > 50% of cases and is increasingly reported from endemic countries. Indirect effects of the coronavirus epidemic include higher rates of psychiatric morbidities, education loss, unhealthy lifestyle changes, and increased child neglect. Vaccines are in clinical trials and immunogenicity has not yet been shown in children. SUMMARY: Overall, COVID-19 has lower incidence and causes milder disease in children compared with adult patients. MIS is a rare severe complication more common in children. More data on the efficacy and safety of antivirals in children are needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32982599/ doi: 10.1007/s11908-020-00739-6 id: cord-021847-wea0qpq2 author: Race, Jeffrey D. title: Chemical, Biological, Radiological, and Nuclear Quarantine date: 2015-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152103/ doi: 10.1016/b978-0-323-28665-7.00082-0 id: cord-275252-4e3cn50u author: Rad SM, Ali Hosseini title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 words: 4368.0 sentences: 302.0 pages: flesch: 53.0 cache: ./cache/cord-275252-4e3cn50u.txt txt: ./txt/cord-275252-4e3cn50u.txt summary: In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. abstract: The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. url: https://doi.org/10.1101/2020.05.15.098947 doi: 10.1101/2020.05.15.098947 id: cord-265740-wjdeps3h author: Radbel, Jared title: Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media date: 2020-05-13 words: 2250.0 sentences: 121.0 pages: flesch: 51.0 cache: ./cache/cord-265740-wjdeps3h.txt txt: ./txt/cord-265740-wjdeps3h.txt summary: Given that SARS-CoV-2 viral RNA has demonstrated stability, we posited that phosphate buffered saline (PBS) may be a viable transport medium, as an alternative to VTM), for clinical qPCR testing. We assessed the intraand inter-individual reliability of SARS-CoV-2 qPCR in clinical endotracheal secretion samples transported in VTM or PBS, evaluating the stability of the RT-qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that using PBS as a transport medium has high intra-and inter-individual reliability, maintains viral stability, and is comparable to VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. SARS-CoV-2 detection using standard testing of upper airway secretions requires a nasopharyngeal (NP) or oropharyngeal (OP) swab that is transported to a clinical laboratory using viral transport media (VTM) (https://www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testingsars-cov-2#offeringtests, last accessed April 29 2020). abstract: As the COVID-19 pandemic sweeps across the world, the availability of viral transport media (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that SARS-CoV-2 viral RNA has demonstrated stability, we posited that phosphate buffered saline (PBS) may be a viable transport medium, as an alternative to VTM), for clinical qPCR testing. We assessed the intra- and inter-individual reliability of SARS-CoV-2 qPCR in clinical endotracheal secretion samples transported in VTM or PBS, evaluating the stability of the RT-qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that using PBS as a transport medium has high intra-and inter-individual reliability, maintains viral stability, and is comparable to VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. Our study establishes PBS as a clinically useful medium that can be readily deployed for transporting and short-term preservation of specimens containing SARS-CoV-2. Use of PBS as a transport medium has the potential to increase testing capacity for SARS-CoV-2, aiding more widespread screening and early diagnosis of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1525157820303238?v=s5 doi: 10.1016/j.jmoldx.2020.04.209 id: cord-311114-ggcpsjk8 author: Radhakrishnan, Chandni title: Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date: 2020-09-09 words: 4383.0 sentences: 274.0 pages: flesch: 52.0 cache: ./cache/cord-311114-ggcpsjk8.txt txt: ./txt/cord-311114-ggcpsjk8.txt summary: The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. In our analysis, we mapped the SARS-CoV-2 genetic variants obtained from Kerala genomes to the 132 primer or probes sequence and calculated the melting temperature (Tm) of the mutant with the wild type sequence. abstract: Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala. url: https://doi.org/10.1101/2020.09.09.289892 doi: 10.1101/2020.09.09.289892 id: cord-344270-874i31h8 author: Radke, Robert M title: Adult congenital heart disease and the COVID-19 pandemic date: 2020-06-10 words: 4677.0 sentences: 273.0 pages: flesch: 39.0 cache: ./cache/cord-344270-874i31h8.txt txt: ./txt/cord-344270-874i31h8.txt summary: Based on anatomy and additional physiological factors including symptoms, exercise capacity, heart failure, pulmonary hypertension and cyanosis, we propose a pragmatic approach to categorising patients into low-risk, intermediate-risk and high-risk groups. Patients with right heart dilatation or dysfunction are potentially at increased risk of right heart failure as mechanical ventilation and acute respiratory distress syndrome can lead to increase in pulmonary arterial pressures. While this may have ample indirect implications for the regular care of adults with congenital heart disease (ACHD) due to postponement of diagnostic and therapeutic procedures, the focus of the current review is on the direct impact of SARS-CoV-2 on congenital patients. 31 Infection with SARS-CoV-2 should be suspected in ACHD patients presenting with fever, onset or worsening of dyspnoea, lower than usual peripheral oxygen saturation but also in case of unexplained worsening of ventricular function or new arrhythmia. Patients with Down syndrome (commonly associated with congenital heart disease and immune defects) are at higher risk for pulmonary infections and ARDS. abstract: Adults with congenital heart disease (ACHD) may be at high risk in the case of COVID-19. Due to the heterogeneity of ACHD and secondary complications, risk profiles are, however, not uniform. This document aims to give an overview of relevant data and outline our pragmatic approach to disease prevention and management. Based on anatomy and additional physiological factors including symptoms, exercise capacity, heart failure, pulmonary hypertension and cyanosis, we propose a pragmatic approach to categorising patients into low-risk, intermediate-risk and high-risk groups. We regard especially patients with complex cyanotic conditions, those with palliated univentricular hearts, heart failure, severe valvular disease or pulmonary hypertension as high-risk patients. To avoid infection, we recommend self-isolation and exemption from work for these cohorts. Infected ACHD patients with low or moderate risk and without signs of deterioration may be remotely followed and cared for at home while in self isolation. High-risk patients or those with signs of respiratory or cardiovascular impairment require admission ideally at a tertiary ACHD centre. Especially patients with complex, cyanotic disease, heart failure and arrhythmias require particular attention. Treatment in patients with cyanotic heart disease should be guided by the relative degree of desaturation compared with baseline and lactate levels rather than absolute oxygen saturation levels. Patients with right heart dilatation or dysfunction are potentially at increased risk of right heart failure as mechanical ventilation and acute respiratory distress syndrome can lead to increase in pulmonary arterial pressures. url: https://www.ncbi.nlm.nih.gov/pubmed/32522822/ doi: 10.1136/heartjnl-2020-317258 id: cord-319333-jwbgytwd author: Radmard, Sara title: Inpatient Neurology Consultations During the Onset of the SARS-CoV-2 New York City Pandemic: A Single Center Case Series date: 2020-07-10 words: 3401.0 sentences: 214.0 pages: flesch: 46.0 cache: ./cache/cord-319333-jwbgytwd.txt txt: ./txt/cord-319333-jwbgytwd.txt summary: The encountered neurological problems associated with SARS-CoV-2 infection were encephalopathy (12 patients, 36.4%), seizure (9 patients, 27.2%), stroke (5 patients, 15.2%), recrudescence of prior neurological disease symptoms (4 patients, 12.1%), and neuromuscular (3 patients, 9.1%). Adult inpatients diagnosed with COVID-19 infection by nasopharyngeal swab reverse transcription polymerase chain reaction (RT-PCR) and required neurological evaluation by consultation or admission for primary neurological care were included in this single-center retrospective case-series study at Columbia University Irving Medical Center (CUIMC)-New York Presbyterian Hospital. Most of the patients in our case series developed neurological symptoms several days after COVID-19 symptom-onset and demonstrated elevated inflammatory markers. As in prior literature reviewing neurological manifestations of COVID-19 infection, our case series included instances of both ischemic stroke and intracranial hemorrhage, although our patients also had other cardiovascular risk factors for stroke. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study abstract: Objective: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily causes respiratory illness. However, neurological sequelae from novel coronavirus disease 2019 (COVID-19) can occur. Patients with neurological conditions may be at higher risk of developing worsening of their underlying problem. Here we document our initial experiences as neurologic consultants at a single center quaternary hospital at the epicenter of the COVID-19 pandemic. Methods: This was a retrospective case series of adult patients diagnosed with SARS-CoV-2 who required neurological evaluation in the form of a consultation or primary neurological care from March 13, 2020 to April 1, 2020. Results: Thirty-three patients (ages 17–88 years) with COVID-19 infection who required neurological or admission to a primary neurology team were included in this study. The encountered neurological problems associated with SARS-CoV-2 infection were encephalopathy (12 patients, 36.4%), seizure (9 patients, 27.2%), stroke (5 patients, 15.2%), recrudescence of prior neurological disease symptoms (4 patients, 12.1%), and neuromuscular (3 patients, 9.1%). The majority of patients who required evaluation by neurology had elevated inflammatory markers. Twenty-one (63.6%) patients were discharged from the hospital and 12 (36.4%) died from COVID-19 related complications. Conclusion: This small case series of our initial encounters with COVID-19 infection describes a range of neurological complications which are similar to presentations seen with other critical illnesses. COVID-19 infection did not change the overall management of neurological problems. url: https://www.ncbi.nlm.nih.gov/pubmed/32754113/ doi: 10.3389/fneur.2020.00805 id: cord-316232-7w1vrx96 author: Radon, K. title: Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19) date: 2020-05-02 words: 6356.0 sentences: 392.0 pages: flesch: 54.0 cache: ./cache/cord-316232-7w1vrx96.txt txt: ./txt/cord-316232-7w1vrx96.txt summary: For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children <14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. 28.20082743 doi: medRxiv preprint 3 a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. With the community-based household study presented in this paper, we therefore aim to study the sero-prevalence and -incidence of SARS-CoV-2 antibodies in a representative household sample of the Munich population. 28.20082743 doi: medRxiv preprint • The temporal course of SARS-CoV-2 sero-positivity in the Munich general population (point prevalence and incidence) stratified for symptomatic and asymptomatic subjects and reported cases • The daily prevalence and incidence of possible COVID-19 symptoms in the study population abstract: Background: The SARS-CoV-2 pandemic is leading to the global introduction of public health interventions to prevent the spread of the virus and avoid the overload of health care systems, especially for the most severely affected patients. Scientific studies to date have focused primarily on describing the clinical course of patients, identifying treatment options and developing vaccines. In Germany, as in many other regions, current tests for SARS-CoV2 are not being conducted on a representative basis and in a longitudinal design. Furthermore, knowledge about the immune status of the population is lacking. Yet these data are needed to understand the dynamics of the pandemic and to thus appropriately design and evaluate interventions. For this purpose, we recently started a prospective population-based cohort in Munich, Germany, with the aim to better understand the state and dynamics of the pandemic. Methods: In 100, randomly selected constituencies out of 755, 3,000 Munich households are identified via random route and offered enrollment into the study. All household members are asked to complete a baseline questionnaire and subjects [≥]14 years of age are asked to provide a venous blood sample of [≤]3 ml for the determination of SARS-CoV-2 IgG/IgA status. The residual plasma and the blood pellet are preserved for later genetic and molecular biological investigations. For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children <14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. In case of severe symptoms, participants will be transferred to a Munich hospital. For one year, the study teams re-visits the households for blood sampling every six weeks. Discussion: With the planned study we will establish a reliable epidemiological tool to improve the understanding of the spread of SARS-CoV-2 and to better assess the effectiveness of public health measures as well as their socio-economic effects. This will support policy makers in managing the epidemic based on scientific evidence. url: http://medrxiv.org/cgi/content/short/2020.04.28.20082743v1?rss=1 doi: 10.1101/2020.04.28.20082743 id: cord-283486-ji0e8yoo author: Radulesco, Thomas title: Safety and Impact of Nasal Lavages During Viral Infections Such as SARS-CoV-2 date: 2020-08-27 words: 1600.0 sentences: 122.0 pages: flesch: 46.0 cache: ./cache/cord-283486-ji0e8yoo.txt txt: ./txt/cord-283486-ji0e8yoo.txt summary: 8 Regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Carrouel et al found the use of a mouth rinses with local nasal applications that contain b-cyclodextrins combined with flavonoids agents reduce the viral load of saliva and nasopharyngeal microbiota, including potential SARS-CoV-2 carriage. Nasal mucosa have high viral loads and include cells expressing proteases responsible for virus entry (such as angiotensinconverting enzyme 2 and TMPRSS2 for SARS-CoV-2), 19, 20 The upper airway has shown to be a reservoir for descending bacterial or viral infection to the lung. 3, 23, 24 Given the potential benefits summarized above, nasal saline irrigation may enhance recovery in patients known to be infected with COVID-19. 26 The potential direct antiviral actions and reduction in viral load have led to proposals that use in patients with COVID-19 may reduce risk of nosocomial transmission. Copper enhanced nasal saline irrigations: a safe potential treatment and protective factor for COVID-19 infection? abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32853040/ doi: 10.1177/0145561320950491 id: cord-257556-lmws8eed author: Rafiq, Danish title: Three months of COVID‐19: A systematic review and meta‐analysis date: 2020-05-18 words: 3195.0 sentences: 223.0 pages: flesch: 50.0 cache: ./cache/cord-257556-lmws8eed.txt txt: ./txt/cord-257556-lmws8eed.txt summary: 2 While several other human coronaviruses such as HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1 cause mild respiratory disease, others like the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV tend to have a higher fatality rate 6 (summarized in Table 1 ). Typical of respiratory viruses like influenza virus, SARS-CoV-2019 can spread through large droplets (with a transmission risk restricted tõ 6 ft from the patient). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: a data-driven Modelling analysis of the early outbreak Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: a data driven analysis in the early phase of the outbreak abstract: The pandemic of 2019 novel coronavirus (SARS‐CoV‐2019), reminiscent of the 2002‐SARS‐CoV outbreak, has completely isolated countries, disrupted health systems and partially paralyzed international trade and travel. In order to be better equipped to anticipate transmission of this virus to new regions, it is imperative to track the progress of the virus over time. This review analyses information on progression of the pandemic in the past 3 months and systematically discusses the characteristics of SARS‐CoV‐2019 virus including its epidemiologic, pathophysiologic, and clinical manifestations. Furthermore, the review also encompasses some recently proposed conceptual models that estimate the spread of this disease based on the basic reproductive number for better prevention and control procedures. Finally, we shed light on how the virus has endangered the global economy, impacting it both from the supply and demand side. url: https://www.ncbi.nlm.nih.gov/pubmed/32420674/ doi: 10.1002/rmv.2113 id: cord-285467-uxfk6k3c author: Ragni, Enrico title: Management of osteoarthritis during COVID‐19 pandemic date: 2020-05-21 words: 7077.0 sentences: 353.0 pages: flesch: 37.0 cache: ./cache/cord-285467-uxfk6k3c.txt txt: ./txt/cord-285467-uxfk6k3c.txt summary: Since an effective immune response against viral infections depends on cytotoxic T cells activation (25) , experimental evidence supports the observation that overexpression of inflammatory cytokines like IL-6 during the viral immune response might be associated with a decreased viral clearance by impairing the polarization and functionality of Th1 and CD8 cells (26), contributing to the worsening of the COVID-19 symptoms, and their management may appear an intriguing therapeutical approach. Overall, the administration of drugs for the control of inflammation, inhibiting the response of the immune system, may be detrimental in the initial phases of the viral infection, reducing the ability of the body to react to the presence of SARS-CoV-2, as observed in patients chronically treated for rheumatoid arthritis (27) . All rights reserved This shall prompt orthopaedics and clinicians in general to evaluate with extreme care the clinical conditions of OA patients not only under the perspective of OA symptoms management but also for undercurrent comorbidities, naturally occurring or OA-treatment-related, that, in the era of COVID-19 pandemic, may strongly affect patients outcomes more than the net combination of SARS-CoV-2 infection and OA. abstract: The pandemic spread of the new COVID‐19 coronavirus infection in China first, and all over the world at present, has become a global health emergency due to the rapidly increasing number of affected patients. Currently, a clear relationship between COVID‐19 infection incidence and/or complications due to chronic or occasional treatments for other pathologies is still not clear, albeit COVID‐19 pandemic may condition the treatment strategy of complex disorders, as osteoarthritis (OA). Importantly, OA is the most common age‐related joint disease affecting more than 80% of people older than the age of 55, an age burden also shared with the highest severity in COVID‐19 patients. OA patients often show a large array of concomitant pathologies such as diabetes, inflammation and cardiovascular diseases that are again shared with COVID‐19 patients and may therefore increase complications. Moreover, different OA treatments such as NSAIDs, paracetamol, corticosteroids, opioids or other molecules have a wide array of iatrogenic effects, potentially increasing COVID‐19 secondary infection incidence or complications. In this review we critically analyse the evidences on either negative or positive effect of drugs commonly used to manage OA in this particular scenario. This would provide orthopaedic surgeons at first, and physicians, pharmacologists and clinicians at general, a comprehensive description about the safety of the current pharmacological approaches and a decision making tool to treat their OA patients as the coronavirus pandemic continues. url: https://www.ncbi.nlm.nih.gov/pubmed/32438454/ doi: 10.1002/cpt.1910 id: cord-338980-pygykil7 author: Rahaman, Jordon title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date: 2016-11-09 words: 5801.0 sentences: 308.0 pages: flesch: 52.0 cache: ./cache/cord-338980-pygykil7.txt txt: ./txt/cord-338980-pygykil7.txt summary: Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. For the DISOPRED2 predictions that were inferred using the nr database, the continuous disorder propensities for every site in a protein were mapped onto their corresponding position in the multiple sequence alignment as raw disorder propensities and as binary states, order or disorder, using a cutoff of 5. For regions with five or more consecutive sites that were 100% conserved in sequence across 1) all CoV or 2) across the MERS and SARS clades, the information of structural disorder prediction from IUPred and DISOPRED2 was used to identify all ungapped sites that were consistently predicted to have 100% conserved order. abstract: Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals. url: https://doi.org/10.1093/gbe/evw246 doi: 10.1093/gbe/evw246 id: cord-303960-86mukxg1 author: Rahimi, Farid title: Tackling the COVID-19 Pandemic date: 2020-04-24 words: 1754.0 sentences: 111.0 pages: flesch: 54.0 cache: ./cache/cord-303960-86mukxg1.txt txt: ./txt/cord-303960-86mukxg1.txt summary: Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. abstract: Abstract After the initial breakout of the SARS-CoV-2 epidemic (now called COVID-19)—in Wuhan, China—and its subsequent fast dispersion throughout the world, many questions regarding its pathogenesis, genetic evolution, prevention, and transmission routes remain unanswered but fast explored. More than 100,000 confirmed, infected cases within a relatively short period of time globally corroborated the presumption that a pandemic will develop; such a pandemic will require a suite of global intervention measures. Consequently, different countries have reacted differently to the COVID-19 outbreak, but a uniform global response is necessary for tackling the pandemic. Managing the present or future COVID-19 outbreaks is not impossible but surely difficult. Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. Increasing numbers of infected cases had heightened concerns about the public health and welfare. Thus, preparing for the next probable pandemic of COVID-19 demands scrutinization of the lessons we have learnt so far. url: https://api.elsevier.com/content/article/pii/S0188440920305257 doi: 10.1016/j.arcmed.2020.04.012 id: cord-316425-fnlgeubu author: Rahimi, Farid title: Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 date: 2020-04-15 words: 811.0 sentences: 51.0 pages: flesch: 54.0 cache: ./cache/cord-316425-fnlgeubu.txt txt: ./txt/cord-316425-fnlgeubu.txt summary: title: Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 We were delighted to read the enlightening letter titled, The Global Threat of SARS-CoV-2/COVID-19 and the Need for More and Better Diagnostic Tools submitted to the Archives of Medical Research (1). The main rationale behind the recent advances in developing diagnostics for COVID-19 is achieving fast and cheap initial detection and confirmation of SARS-CoV-2 infection in different biological samples, including fecal samples, nasopharyngeal or oropharyngeal swabs, and environmental samples. Thus, providing a rapid, accurate and cheap diagnostic kit will efficiently help the health authorities in the developing countries to expedite case-finding within the population. Global threat of SARS-CoV-2/ COVID-19 and the need for more and better diagnostic tools Mesa biotech receives emergency use authorization from FDA for a 30 minute point of care molecular COVID-19 test: Mesa Biotech abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0188440920304847 doi: 10.1016/j.arcmed.2020.04.008 id: cord-283367-azzy2t1a author: Rahman, Asma title: Neurological manifestations in COVID-19: A narrative review date: 2020-09-10 words: 4426.0 sentences: 364.0 pages: flesch: 54.0 cache: ./cache/cord-283367-azzy2t1a.txt txt: ./txt/cord-283367-azzy2t1a.txt summary: Some patients show neurological manifestations such as headache, dizziness, cerebrovascular disease, peripheral nerve and muscle symptoms and smell and taste impairment. Sarma and Bilello 41 1 Acute transverse myelitis A 28-year-old female patient with SARS-CoV-2 presenting lower back pain, bilateral symmetric upper, and lower extremity numbness. 50 None of the patients with post-COVID-19 GBS tested positive for SARS-CoV-2 in the CSF, 51 points to an immune mechanism such as inflammation secondary to a cytokine storm as a possible cause. During the COVID-19 pandemic, if a patient has neurological symptoms such as loss of the sense of smell and taste or delirium, testing for SARS-CoV-2 should be considered irrespective of them not having the other typical symptoms. Stroke in patients with SARS-CoV-2 infection: case series Acute myelitis after SARS-CoV-2 infection: a case report. Self-reported olfactory and taste disorders in patients with severe acute respiratory coronavirus 2 infection: a cross-sectional study abstract: COVID-19, a respiratory viral infection, has affected more than 10 million individuals worldwide. Common symptoms include fever, dry cough, fatigue and shortness of breath. Some patients show neurological manifestations such as headache, dizziness, cerebrovascular disease, peripheral nerve and muscle symptoms and smell and taste impairment. In previous studies, SARS-CoV-1 and MERS-CoV were found to affect the nervous system. Given the high similarity between SARS-CoV-1 and SARS-CoV-2, effects on the nervous system by SARS-CoV-2 are a possibility. We have outlined the common neurological manifestations in COVID-19 (information are up-to-date as of June 2020) and discussed the possible pathogenetic mechanisms and management options. url: https://doi.org/10.1177/2050312120957925 doi: 10.1177/2050312120957925 id: cord-328705-024y5k72 author: Rahman, Md. Mahbubur title: Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment date: 2020-07-21 words: 4487.0 sentences: 246.0 pages: flesch: 51.0 cache: ./cache/cord-328705-024y5k72.txt txt: ./txt/cord-328705-024y5k72.txt summary: In this study, computational screening is performed by molecular docking of 1615 Food and Drug Administration (FDA) approved drugs against the main protease (Mpro) of SARS-CoV-2. Several promising approved drugs, including Simeprevir, Ergotamine, Bromocriptine and Tadalafil, stand out as the best candidates based on their binding energy, fitting score and noncovalent interactions at the binding sites of the receptor. The MD simulations for the main protease were conducted (6LU7) in apo-form (protein without ligand) and in holo-form (protein-drug complex) to assess any probable conformational changes to and interactions with their structures over the 100 nanoseconds (ns). The selected four drug-main protease complexes may have dissimilarities with the apo-Mpro during MD simulation regarding the energy profile. Identification of potential binders of the SARS-Cov-2 spike protein via molecular docking, dynamics simulation and binding free energy calculation abstract: Computer-aided drug screening by molecular docking, molecular dynamics (MD) and structural–activity relationship (SAR) can offer an efficient approach to identify promising drug repurposing candidates for COVID-19 treatment. In this study, computational screening is performed by molecular docking of 1615 Food and Drug Administration (FDA) approved drugs against the main protease (Mpro) of SARS-CoV-2. Several promising approved drugs, including Simeprevir, Ergotamine, Bromocriptine and Tadalafil, stand out as the best candidates based on their binding energy, fitting score and noncovalent interactions at the binding sites of the receptor. All selected drugs interact with the key active site residues, including His41 and Cys145. Various noncovalent interactions including hydrogen bonding, hydrophobic interactions, pi–sulfur and pi–pi interactions appear to be dominant in drug–Mpro complexes. MD simulations are applied for the most promising drugs. Structural stability and compactness are observed for the drug–Mpro complexes. The protein shows low flexibility in both apo and holo form during MD simulations. The MM/PBSA binding free energies are also measured for the selected drugs. For pattern recognition, structural similarity and binding energy prediction, multiple linear regression (MLR) models are used for the quantitative structural–activity relationship. The binding energy predicted by MLR model shows an 82% accuracy with the binding energy determined by molecular docking. Our details results can facilitate rational drug design targeting the SARS-CoV-2 main protease. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1794974 doi: 10.1080/07391102.2020.1794974 id: cord-315411-11mq8wll author: Rahman, Mohammad Azizur title: Neurobiochemical Cross-talk Between COVID-19 and Alzheimer’s Disease date: 2020-10-19 words: 4116.0 sentences: 224.0 pages: flesch: 41.0 cache: ./cache/cord-315411-11mq8wll.txt txt: ./txt/cord-315411-11mq8wll.txt summary: COVID-19 and AD share common links with respect to angiotensin-converting enzyme 2 (ACE2) receptors and pro-inflammatory markers such as interleukin-1 (IL-1), IL-6, cytoskeleton-associated protein 4 (CKAP4), galectin-9 (GAL-9 or Gal-9), and APOE4 allele. Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that attacks predominantly the human respiratory system and has also central nervous system (CNS) targeting and neuroinvasive capabilities [1, 2] . Among inflammatory markers, interleukin 6 (IL-6), interleukin 1 (IL-1), cytoskeleton-associated protein 4 (CKAP4), and galectin-9 (GAL-9 or Gal-9) had received most attention as the common links between COVID-19 and AD manifestations [18] (Fig. 1 ). Among its three alleles (ε2, ε3, and ε4), individuals carrying the ε4 allele are at a heightened risk of developing AD as the ApoE ɛ4/ɛ4 genotype increases fibrinogenesis in the brains of Alzheimer''s disease patients [41] . abstract: COVID-19, the global threat to humanity, shares etiological cofactors with multiple diseases including Alzheimer’s disease (AD). Understanding the common links between COVID-19 and AD would harness strategizing therapeutic approaches against both. Considering the urgency of formulating COVID-19 medication, its AD association and manifestations have been reviewed here, putting emphasis on memory and learning disruption. COVID-19 and AD share common links with respect to angiotensin-converting enzyme 2 (ACE2) receptors and pro-inflammatory markers such as interleukin-1 (IL-1), IL-6, cytoskeleton-associated protein 4 (CKAP4), galectin-9 (GAL-9 or Gal-9), and APOE4 allele. Common etiological factors and common manifestations described in this review would aid in developing therapeutic strategies for both COVID-19 and AD and thus impact on eradicating the ongoing global threat. Thus, people suffering from COVID-19 or who have come round of it as well as people at risk of developing AD or already suffering from AD, would be benefitted. url: https://doi.org/10.1007/s12035-020-02177-w doi: 10.1007/s12035-020-02177-w id: cord-283439-hqdq2qrh author: Rahman, Mohammad Tariqur title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 words: 5248.0 sentences: 315.0 pages: flesch: 50.0 cache: ./cache/cord-283439-hqdq2qrh.txt txt: ./txt/cord-283439-hqdq2qrh.txt summary: The suggested treatments for COVID-19 are, but not limited to, the use of (i) convalescent plasma for COVID-19 treatment [63] [64] [65] ; (ii) ribavirin, a nucleoside analogue in combination with recombinant interferon showed inhibition of MERS-CoV replication [66] ; (iii) lopinavir/ritonavir-a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus infection [67] ; (iv) remdesivir, a nucleotide analogue that inhibit RNA polymerase with a broad spectrum of anti-viral activities; in inhibition of human and zoonotic coronavirus [15, 68, 69] ; (v) favipiravir (also known as T-705, Avigan or favilavir) is a pyrazinecarboxamide derivative known to inhibit RNA polymerase [70] . In the current pandemic of SARS-CoV-2, Zn supplement could play an important role to treat COVID-19 patients such as (i) added immune boosting effects with anti-viral drugs and (ii) stopping SARS-CoV-2 replication in infected cells, if combined with chloroquine. abstract: The current COVID-19 pandemic caused by SARS-CoV-2 has prompted investigators worldwide to search for an effective anti-viral treatment. A number of anti-viral drugs such as ribavirin, remdesivir, lopinavir/ritonavir, antibiotics such as azithromycin and doxycycline, and anti-parasite such as ivermectin have been recommended for COVID-19 treatment. In addition, sufficient pre-clinical rationale and evidence have been presented to use chloroquine for the treatment of COVID-19. Furthermore, Zn has the ability to enhance innate and adaptive immunity in the course of a viral infection. Besides, Zn supplement can favour COVID-19 treatment using those suggested and/or recommended drugs. Again, the effectiveness of Zn can be enhanced by using chloroquine as an ionophore while Zn inside the infected cell can stop SARS-CoV-2 replication. Given those benefits, this perspective paper describes how and why Zn could be given due consideration as a complement to the prescribed treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32458149/ doi: 10.1007/s12011-020-02194-9 id: cord-316536-jpbfgwhl author: Raj, V. Stalin title: Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC date: 2013-03-13 words: 4501.0 sentences: 221.0 pages: flesch: 48.0 cache: ./cache/cord-316536-jpbfgwhl.txt txt: ./txt/cord-316536-jpbfgwhl.txt summary: Moreover, transient expression of human DPP4 in the non-susceptible COS-7 cells rendered these cells susceptible to binding the hCoV-EMC S1-Fc protein to their surface ( Supplementary Fig. 4) . e, Double-stranded viral RNA (cyan) was detected in hCoV-EMC-infected primary human bronchiolar epithelial cell cultures and appeared to be localized to nonciliated cells that express DPP4 (red). In addition, hCoV-EMC infection of human bronchiolar epithelial cell cultures appeared to be localized to the non-ciliated cells that express DPP4 (Fig. 3e) . COS-7 cells transfected with the human DPP4 expression plasmid, but not with the empty plasmid, were efficiently infected by hCoV-EMC as demonstrated by the presence of viral non-structural proteins in the cells (Fig. 4c) and of viral RNA (Fig. 4d) and infectious virus in the cell supernatants (not shown). S1 receptor-binding domains of hCoV-EMC, SARS-CoV and FIPV fused to the Fc region of human IgG, and soluble versions of DPP4 and ACE2 were expressed and purified as described in the Methods. abstract: Most human coronaviruses cause mild upper respiratory tract disease but may be associated with more severe pulmonary disease in immunocompromised individuals(1). However, SARS coronavirus caused severe lower respiratory disease with nearly 10% mortality and evidence of systemic spread(2). Recently, another coronavirus (human coronavirus-Erasmus Medical Center (hCoV-EMC)) was identified in patients with severe and sometimes lethal lower respiratory tract infection(3,4). Viral genome analysis revealed close relatedness to coronaviruses found in bats(5). Here we identify dipeptidyl peptidase 4 (DPP4; also known as CD26) as a functional receptor for hCoV-EMC. DPP4 specifically co-purified with the receptor-binding S1 domain of the hCoV-EMC spike protein from lysates of susceptible Huh-7 cells. Antibodies directed against DPP4 inhibited hCoV-EMC infection of primary human bronchial epithelial cells and Huh-7 cells. Expression of human and bat (Pipistrellus pipistrellus) DPP4 in non-susceptible COS-7 cells enabled infection by hCoV-EMC. The use of the evolutionarily conserved DPP4 protein from different species as a functional receptor provides clues about the host range potential of hCoV-EMC. In addition, it will contribute critically to our understanding of the pathogenesis and epidemiology of this emerging human coronavirus, and may facilitate the development of intervention strategies. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature12005) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/23486063/ doi: 10.1038/nature12005 id: cord-340114-ycgc6yyc author: Rajagopal, Kalirajan title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies date: 2020-07-28 words: 3640.0 sentences: 225.0 pages: flesch: 52.0 cache: ./cache/cord-340114-ycgc6yyc.txt txt: ./txt/cord-340114-ycgc6yyc.txt summary: title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies In this article, some oxazine substituted 9-anilinoacridines (A1–A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1–A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Using different modules (Glide, QikProp, Prime and Desmond) of Schr€ odinger suite LLC, various computational methods such as molecular docking, ADMET screening, binding free energy calculations and molecular dynamics (MD) simulations were performed to find the interactions responsible for COVID-19 inhibition. abstract: Coronavirus disease (COVID-19), a life-threatening disease, is caused by SARS-CoV-2. The targeted therapeutics of small molecules helps the scientific community to fight against SARS-CoV-2. In this article, some oxazine substituted 9-anilinoacridines (A1–A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1–A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Compound A38 has the highest G-score (−7.83) when compared to all the standard compounds which are proposed for COVID-19 treatment such as ritonavir (−7.48), lopinavir (−6.94), nelfinavir (−5.93), hydroxychloroquine (−5.47) and mataquine (−5.37). Compounds A13, A23, A18, A7, A48, A46, A32, A20, A1 and A47 are significantly active against SARS-CoV-2 main protease when compared with hydroxychloroquine and mataquine. The residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN119, ASN142, HIE164, MET165, ASP187, ARG188 and GLN189 of SARS-CoV-2 main protease play a crucial role in binding with ligands. The in silico ADMET properties of the molecules are within the recommended values. The binding free energy was calculated using PRIME MM-GB/SA studies. From the ligands A38, A13, A23, A18, A7, A48 and A46 with significant Glide scores may produce significant COVID-19 activity for further development. Compound A38 was subjected to MD simulation at 100 ns to study the dynamic behaviour of protein–ligand complex. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32720578/ doi: 10.1080/07391102.2020.1798285 id: cord-354658-v451z3jq author: Rajagopal, Keshava title: Advanced Pulmonary and Cardiac Support of COVID-19 Patients: Emerging Recommendations From ASAIO—A “Living Working Document” date: 2020-05-11 words: 8876.0 sentences: 483.0 pages: flesch: 41.0 cache: ./cache/cord-354658-v451z3jq.txt txt: ./txt/cord-354658-v451z3jq.txt summary: The severe acute respiratory syndrome (SARS)-CoV-2 is an emerging viral pathogen responsible for the global coronavirus disease 2019 (COVID)-19 pandemic resulting in significant human morbidity and mortality. We review the rapidly changing epidemiology, pathophysiology, emerging therapy, and clinical outcomes of COVID-19; and based on these data and previous experience with artificial cardiopulmonary support strategies, particularly in the setting of infectious diseases, provide consensus recommendations from ASAIO. It is the specific goal of the present paper to provide a resource document to the clinical community regarding evolving best practice strategies for advanced pulmonary and cardiac support in patients with severe progressive COVID-19. Although central cannulation is hemodynamically advantageous (with respect to higher flow rates; hemodynamic support is not relevant in pure V-V ECMO), in light of its invasiveness, bleeding risks, and specialized training required, it is more reasonable to propose peripheral cannulation as the initial approach of choice for COVID-19-related respiratory failure. abstract: The severe acute respiratory syndrome (SARS)-CoV-2 is an emerging viral pathogen responsible for the global coronavirus disease 2019 (COVID)-19 pandemic resulting in significant human morbidity and mortality. Based on preliminary clinical reports, hypoxic respiratory failure complicated by acute respiratory distress syndrome is the leading cause of death. Further, septic shock, late-onset cardiac dysfunction, and multiorgan system failure are also described as contributors to overall mortality. Although extracorporeal membrane oxygenation and other modalities of mechanical cardiopulmonary support are increasingly being utilized in the treatment of respiratory and circulatory failure refractory to conventional management, their role and efficacy as support modalities in the present pandemic are unclear. We review the rapidly changing epidemiology, pathophysiology, emerging therapy, and clinical outcomes of COVID-19; and based on these data and previous experience with artificial cardiopulmonary support strategies, particularly in the setting of infectious diseases, provide consensus recommendations from ASAIO. Of note, this is a “living document,” which will be updated periodically, as additional information and understanding emerges. url: https://www.ncbi.nlm.nih.gov/pubmed/32358232/ doi: 10.1097/mat.0000000000001180 id: cord-295075-cqbayzat author: Rajnarayanan, Rajendram V. title: “Teaching old drugs to kill new bugs”: structure-based discovery of anti-SARS drugs date: 2004-08-20 words: 3675.0 sentences: 208.0 pages: flesch: 50.0 cache: ./cache/cord-295075-cqbayzat.txt txt: ./txt/cord-295075-cqbayzat.txt summary: Several old drugs that bind to SARS 3CLpro active site were selected and in silico derivatized to generate covalent irreversible inhibitors with enhanced affinity. Structural conclusions from active site similarity within the coronavirus family and virtual screening on homology models have provided some clues regarding the class of compounds that could interact with SARS protease. The present study employs in silico derivatization as a method to ''''teach old drugs to kill new bugs.'''' We have designed irreversible covalent inhibitors by selective derivatization of top non-covalent leads, which includes several old drugs especially a class of HIV inhibitors identified from virtual screening. The side chains of His163 and Phe140 and the main-chain atoms of Met165, Glu166, and His172 form the S1 subsite, which confers specificity towards Gln. Thus, specific covalent inhibitors of SARS 3CLpro could be designed by substituting the amino acid at the P1 0 position with a thiol specific reactive organic moiety like chloromethyl ketone. abstract: Abstract Severe acute respiratory syndrome (SARS) main protease or 3C-like protease (3CLpro) is essential for the propagation of the coronaviral life cycle and is regarded as one of the main targets for structure-based anti-SARS drug design. It is an attractive approach to find new uses for old drugs as they have already been through extensive clinical testing and could easily be accelerated for clinical approval. Briefly, we performed virtual screening of a database of small molecules against SARS 3CLpro, analyzed inhibitor–protease complexes, and identified several covalent and non-covalent inhibitors. Several old drugs that bind to SARS 3CLpro active site were selected and in silico derivatized to generate covalent irreversible inhibitors with enhanced affinity. Furthermore, we show that pharmacophores derived from clusters of compounds resulting out of virtual screening could be useful probes for future structure–activity relationship studies (SARs) and fine-tune the lead molecules identified. url: https://www.ncbi.nlm.nih.gov/pubmed/15358186/ doi: 10.1016/j.bbrc.2004.06.155 id: cord-291923-jvbehgb7 author: Rajoli, R. K. title: Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis date: 2020-05-06 words: 4442.0 sentences: 286.0 pages: flesch: 55.0 cache: ./cache/cord-291923-jvbehgb7.txt txt: ./txt/cord-291923-jvbehgb7.txt summary: The present study used physiologically-based pharmacokinetic (PBPK) modelling to inform optimal doses of nitazoxanide capable of maintaining plasma and lung tizoxanide exposures above the reported nitazoxanide 90% effective concentration (EC90) against SARS-CoV-2. Methods: A whole-body PBPK model was constructed for oral administration of nitazoxanide and validated against available tizoxanide pharmacokinetic data for healthy individuals receiving single doses between 500 mg SARS-CoV-2 4000 mg with and without food. The model predicted optimal doses of 1200 mg QID, 1600 mg TID, 2900 mg BID in the fasted state and 700 mg QID, 900 mg TID and 1400 mg BID when given with food, to provide tizoxanide plasma and lung concentrations over the reported in vitro EC90 of nitazoxanide against SARS-CoV-2. The model and the reported dosing strategies provide a rational basis for the design (optimising plasma and lung exposures) of future clinical trials of nitazoxanide in the treatment or prevention of SARS-CoV-2 infection. abstract: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a global pandemic by the World Health Organisation and urgent treatment and prevention strategies are needed. Many clinical trials have been initiated with existing medications, but assessments of the expected plasma and lung exposures at the selected doses have not featured in the prioritisation process. Although no antiviral data is currently available for the major phenolic circulating metabolite of nitazoxanide (known as tizoxanide), the parent ester drug has been shown to exhibit in vitro activity against SARS-CoV-2. Nitazoxanide is an anthelmintic drug and its metabolite tizoxanide has been described to have broad antiviral activity against influenza and other coronaviruses. The present study used physiologically-based pharmacokinetic (PBPK) modelling to inform optimal doses of nitazoxanide capable of maintaining plasma and lung tizoxanide exposures above the reported nitazoxanide 90% effective concentration (EC90) against SARS-CoV-2. Methods: A whole-body PBPK model was constructed for oral administration of nitazoxanide and validated against available tizoxanide pharmacokinetic data for healthy individuals receiving single doses between 500 mg SARS-CoV-2 4000 mg with and without food. Additional validation against multiple-dose pharmacokinetic data when given with food was conducted. The validated model was then used to predict alternative doses expected to maintain tizoxanide plasma and lung concentrations over the reported nitazoxanide EC90 in >90% of the simulated population. Optimal design software PopDes was used to estimate an optimal sparse sampling strategy for future clinical trials. Results: The PBPK model was validated with AAFE values between 1.01 SARS-CoV-2 1.58 and a difference less than 2-fold between observed and simulated values for all the reported clinical doses. The model predicted optimal doses of 1200 mg QID, 1600 mg TID, 2900 mg BID in the fasted state and 700 mg QID, 900 mg TID and 1400 mg BID when given with food, to provide tizoxanide plasma and lung concentrations over the reported in vitro EC90 of nitazoxanide against SARS-CoV-2. For BID regimens an optimal sparse sampling strategy of 0.25, 1, 3 and 12h post dose was estimated. Conclusion: The PBPK model predicted that it was possible to achieve plasma and lung tizoxanide concentrations, using proven safe doses of nitazoxanide, that exceed the EC90 for SARS-CoV-2. The PBPK model describing tizoxanide plasma pharmacokinetics after oral administration of nitazoxanide was successfully validated against clinical data. This dose prediction assumes that the tizoxanide metabolite has activity against SARS-CoV-2 similar to that reported for nitazoxanide, as has been reported for other viruses. The model and the reported dosing strategies provide a rational basis for the design (optimising plasma and lung exposures) of future clinical trials of nitazoxanide in the treatment or prevention of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32511548/ doi: 10.1101/2020.05.01.20087130 id: cord-190540-zf5ksac2 author: Rakshit, Kausik title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date: 2020-06-18 words: 2065.0 sentences: 104.0 pages: flesch: 46.0 cache: ./cache/cord-190540-zf5ksac2.txt txt: ./txt/cord-190540-zf5ksac2.txt summary: title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. The electrostatic charges accumulated in the layers between the Gr IV Ge is sufficient enough to either fuse or repel the charges of the spike proteins of the RNA, DNA viruses including SARS-Cov-2 (RNA virus) or the aerosols. abstract: The objective of this paper is to provide a mathematical model to construct a barrier that may be useful to prevent the penetration of different viruses (Eg. SARS-COV-2) as well as charged aerosols through the concept of electrostatic charge negotiation. (Fusion for the opposite types of charges and repulsion for the similar types of charges). Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. Based upon the above transport properties of electrons of different particles having different dimensions, a mathematical model has been established to find out the penetration potential of those particles under different electrostatic fields. An intensive study have been carried out to find out the generation of electrostatic charges due to the surface emission of electrons (SEE), when a conducting material like silk, nylon or wool makes a friction with the Gr IV elements like Germanium or Silicon, it creates an opposite layer of charges in the outer conducting surface and the inner semiconducting surface separated by a dielectric materials. This opposite charge barriers may be considered as Inversion layers (IL). The electrostatic charges accumulated in the layers between the Gr IV Ge is sufficient enough to either fuse or repel the charges of the spike proteins of the RNA, DNA viruses including SARS-Cov-2 (RNA virus) or the aerosols. url: https://arxiv.org/pdf/2006.10603v1.pdf doi: nan id: cord-315632-29x6l5yh author: Rali, Aniket S title: High-flow Nasal Cannula Oxygenation Revisited in COVID-19 date: 2020-04-21 words: 1098.0 sentences: 60.0 pages: flesch: 48.0 cache: ./cache/cord-315632-29x6l5yh.txt txt: ./txt/cord-315632-29x6l5yh.txt summary: A case series of 138 COVID-19 patients from Wuhan, China showed that a total of 36 (26%) patients required ICU level care, of whom 22 (61%) developed ARDS and 17 (47.2%) required invasive mechanical ventilation. 1 Other retrospective analyses have reported similarly that 20-31% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients develop ARDS and require ICU care. [2] [3] [4] Therefore, it is critical that we explore the utility and safety of other forms of respiratory support devices, including high-flow nasal cannula oxygenation (HFNCO) in the treatment of acute respiratory failure. 4 We present a case of a SARS-CoV-2-positive patient with acute respiratory failure who was successfully treated with HFNCO. On day 3, his hypoxic respiratory failure worsened, requiring high-flow nasal cannula at 40 l/min and 90% fractional inspired oxygen, (FiO 2 ) and he was transferred to the medical ICU. Beneficial effects of humidified high flow nasal oxygen in critical care patients: a prospective pilot study abstract: nan url: https://doi.org/10.15420/cfr.2020.06 doi: 10.15420/cfr.2020.06 id: cord-273553-xp4nfnq3 author: Ramatillah, D. L. title: TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA date: 2020-10-16 words: 3967.0 sentences: 217.0 pages: flesch: 54.0 cache: ./cache/cord-273553-xp4nfnq3.txt txt: ./txt/cord-273553-xp4nfnq3.txt summary: Conclusion: The most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine.The higher the patient''s average treatment duration, the lower the average survival rate for COVID-19 patients. Samples used in this study were patients with confirmed COVID-19 who were undergoing treatment and receiving antiviral agent therapy. Patients receiving the combination Oseltamivir + Chloroquine therapy had an average survival rate of about 17% after about 23 days of treatment. Meanwhile, patients who received combination therapy Favipiravir + Oseltamivir + Chloroquine had an average survival rate of about 10% after undergoing treatment for about 39 days. Based on the Chi-Square test, it was found that there was a significant relationship between COVID-19 antiviral agent therapy and the clinical outcome of COVID-19 patients (p = 0.025). Based on the Chi-Square test, there was no significant effect between gender (p = 0.174) and age (p = 0.065) on the clinical outcome of COVID-19 patients. abstract: Background: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a virus that causes COVID-19, which has become a worldwide pandemic. However, until now, there is no vaccine or specific drug to prevent or treat COVID-19. Objectives: To find out the effective treatment as an antiviral agent for COVID-19, to determine the correlation between sociodemography with clinical outcomes and duration of treatment, and to determine the relationship between comorbidities with clinical outcomes and duration of treatment for COVID-19 patients. Methods: A prospective cohort study was conducted in this study. This study included only confirmed COVID-19 patients who were admitted to the hospital during April-May 2020. Convenience sampling was used to select 103 patients, but only 72 patients were suitable for inclusion. Results: The survival analysis for COVID-19 patients using the Kaplan Meier method showed that patients receiving Oseltamivir + Hydroxychloroquine had an average survival rate of about 83% after undergoing treatment for about ten days. Gender (p = 0.450) and age (p = 0.226) did not have a significant correlation with the duration of treatment for COVID-19 patients. Gender (p = 0.174) and age (p = 0.065) also did not have a significant correlation with clinical outcome of COVID-19 patients. Comorbidities showed a significant correlation with duration of treatment (p = 0.002) and clinical outcome (p = 0.014) of COVID-19 patients. Conclusion: The most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine.The higher the patient's average treatment duration, the lower the average survival rate for COVID-19 patients. url: http://medrxiv.org/cgi/content/short/2020.10.14.20212449v1?rss=1 doi: 10.1101/2020.10.14.20212449 id: cord-252597-ea78sjcs author: Ramazzotti, Daniele title: VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date: 2020-10-19 words: 10701.0 sentences: 502.0 pages: flesch: 45.0 cache: ./cache/cord-252597-ea78sjcs.txt txt: ./txt/cord-252597-ea78sjcs.txt summary: Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. The outbreak of coronavirus disease 2019 (COVID19) , which started in late 2019 in Wuhan (China) [1, 2] and was declared pandemic by the World Health Organization, is fueling the publication of an increasing number of studies aimed at exploiting the information provided by the viral genome of SARS-CoV-2 virus to identify its proximal origin, characterize the mode and timing of its evolution, as well as to define descriptive and predictive models of geographical spread and evaluate the related clinical impact [3, 4, 5] . abstract: A global cross-discipline effort is ongoing to characterize the evolution of SARS-CoV-2 virus and generate reliable epidemiological models of its diffusion. To this end, phylogenomic approaches leverage accumulating genomic mutations to track the evolutionary history of the virus and benefit from the surge of sequences deposited in public databases. Yet, such methods typically rely on consensus sequences representing the dominant virus lineage, whereas a complex intra-host genomic composition is often observed within single hosts. Furthermore, most approaches might produce inaccurate results with noisy data and sampling limitations, as witnessed in most countries affected by the epidemics. We introduce VERSO (Viral Evolution ReconStructiOn), a new comprehensive framework for the characterization of viral evolution and transmission from sequencing data of viral genomes. Our probabilistic approach first delivers robust phylogenetic models from clonal variant profiles and then exploits variant frequency patterns to characterize and visualize the intra-host genomic diversity of samples, which may reveal uncovered infection events. We prove via extensive simulations that VERSO outperforms the state-of-the-art tools for phylogenetic inference, also in condition of noisy observations and sampling limitations. The application of our approach to 3960 SARS-CoV-2 samples from Amplicon sequencing and to 2766 samples from RNA-sequencing unravels robust phylogenomic models, improving the current knowledge on SARS-CoV-2 evolution and spread. Importantly, by exploiting co-occurrence patterns of minor variants, VERSO allows us to reveal uncovered infection paths, which are validated with contact tracing data. Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. Overall, the results show that the joint application of our framework and data-driven epidemiological models might improve currently available strategies for pathogen surveillance and analysis. VERSO is released as an open source tool at https://github.com/BIMIB-DISCo/VERSO. url: https://doi.org/10.1101/2020.04.22.044404 doi: 10.1101/2020.04.22.044404 id: cord-260315-uau554jj author: Ramirez, Santseharay title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date: 2020-10-04 words: 2269.0 sentences: 122.0 pages: flesch: 54.0 cache: ./cache/cord-260315-uau554jj.txt txt: ./txt/cord-260315-uau554jj.txt summary: title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. Importance The cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. 137 We performed a comparative titration in various cells of the P2 VeroE6 and the P5 Huh7.5 viruses ( Figure 138 1b) and found that the infectivity titers in Huh7.5 cells after culture adaptation had increased by more 139 than 3 logs (mean of 4.7 and 8.0 Log 10 TCID 50 /mL, respectively). abstract: Efforts to mitigate COVID-19 include screening of existing antiviral molecules that could be re-purposed to treat SARS-CoV-2 infections. Although SARS-CoV-2 propagates efficiently in African green monkey kidney (Vero) cells, antivirals such as nucleos(t)ide analogs (nucs) often exhibit decreased activity in these cells due to inefficient metabolization. Limited SARS-CoV-2 replication and propagation occurs in human cells, which are the most relevant testing platforms. By performing serial passages of a SARS-CoV-2 isolate in the human hepatoma cell line clone Huh7.5, we selected viral populations with improved viability in human cells. Culture adaptation led to the emergence of a significant number of high frequency changes (>90% of the viral population) in the region coding for the spike glycoprotein, including a deletion of nine amino acids in the N-terminal domain and 3 amino acid changes (E484D, P812R, and Q954H). We demonstrated that the Huh7.5-adapted virus exhibited a >3-Log10 increase in infectivity titers (TCID50) in Huh7.5 cells, with titers of ~8 Log10TCID50/mL, and >2-Log10 increase in the human lung cancer cell line Calu-1, with titers of ~6 Log10TCID50/mL. Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. The enhanced ability of the virus to replicate and propagate in human cells permitted screening of a panel of nine nucs, including broad-spectrum compounds. Remdesivir, EIDD-2801 and to a limited extent galidesivir showed antiviral effect across these human cell lines, whereas sofosbuvir, uprifosbuvir, valopicitabine, mericitabine, ribavirin, and favipiravir had no apparent activity. Importance The cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. This SARS-CoV-2 variant will be a valuable tool permitting investigations across human cell types, and studies of identified mutations could contribute to our understanding of viral pathogenesis. In particular, the adapted virus can be a good model for investigations of viral entry and cell tropism for SARS-CoV-2, in which the spike glycoprotein plays a central role. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. Thus, it is essential to select the most relevant target cells for pre-clinical screenings of antiviral compounds, facilitated by using a virus with broader tropism. url: https://doi.org/10.1101/2020.10.04.325316 doi: 10.1101/2020.10.04.325316 id: cord-276548-bh3w7oas author: Ramkumar, K. title: Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer date: 2020-09-30 words: 1114.0 sentences: 81.0 pages: flesch: 51.0 cache: ./cache/cord-276548-bh3w7oas.txt txt: ./txt/cord-276548-bh3w7oas.txt summary: title: Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. Furthermore, SARS-CoV-2 infection reduces ACE2 expression and shifts cells to a more mesenchymal phenotype with loss of EPCAM and upregulation of ZEB1 and other EMT-associated genes. Methods: We analyzed mRNA expression of AXL and other TAM family members as well as angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor, in treatment-naïve (n¼1016) and previously treated (n¼239) NSCLC tumors and in a panel of NSCLC cell lines (n¼70). Notably, expression of ACE2 was downregulated while that of AXL and ZEB1, an EMT transcription factor, were upregulated in NSCLC cells infected with SARS-CoV-2 as compared to mock infected cells, suggesting a shift to a more mesenchymal phenotype. D. Gibbons: Advisory/Consultancy, Research grant/Funding (self Advisory/Consultancy: Synta; Research grant/Funding (self): Bayer. L.A. Byers: Advisory/Consultancy, Research grant/Funding (self abstract: nan url: https://api.elsevier.com/content/article/pii/S092375342041796X doi: 10.1016/j.annonc.2020.08.1800 id: cord-343330-wuzts3mt author: Ramos da Silva, S. title: Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19 date: 2020-09-29 words: 3447.0 sentences: 229.0 pages: flesch: 56.0 cache: ./cache/cord-343330-wuzts3mt.txt txt: ./txt/cord-343330-wuzts3mt.txt summary: Background Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection in patients with Coronavirus Disease 2019 (COVID-19) prominently manifests with pulmonary symptoms histologically reflected by diffuse alveolar damage (DAD), excess inflammation, pneumocyte hyperplasia and proliferation, and formation of platelet aggregates or thromboemboli. Methods We performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections. Single cell RNA sequencing (scRNA-seq) analysis of lung tissues from healthy 120 subjects have revealed that many cell types express SARS-CoV-2 entry receptor and 121 cofactors including angiotensin-converting enzyme-2 (ACE2), transmembrane serine 122 protease 2 (TMPRSS2), and furin, that are involved in viral entry, suggesting 123 susceptibility of these cells to infection. 7-10 Furthermore, scRNA-seq analysis of 124 bronchoalveolar lavage fluid (BALF), blood, oropharyngeal or lung tissues from COVID-125 19 patients has identified different types of SARS-CoV-2-infected cells, including 126 macrophages, neutrophils, type II pneumocytes (AT2), and ciliated and endothelial 127 cells. abstract: Background Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection in patients with Coronavirus Disease 2019 (COVID-19) prominently manifests with pulmonary symptoms histologically reflected by diffuse alveolar damage (DAD), excess inflammation, pneumocyte hyperplasia and proliferation, and formation of platelet aggregates or thromboemboli. However, the mechanisms mediating these processes remain unclear. Methods We performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections. Findings The lung parenchyma showed severe DAD with thromboemboli in all cases. SARS-CoV-2 infection was found in an extensive range of cells including alveolar epithelial type II/pneumocyte type II (AT2) cells (HT2-280), ciliated cells (tyr--tubulin), goblet cells (MUC5AC), club-like cells (MUC5B) and endothelial cells (CD31 and CD34). Greater than 90% of infiltrating immune cells were positive for viral proteins including macrophages and monocytes (CD68 and CD163), neutrophils (ELA-2), natural killer (NK) cells (CD56), B-cells (CD19 and CD20), and T-cells (CD3{varepsilon}). Most but not all infected cells were positive for the viral entry receptor angiotensin-converting enzyme-2 (ACE2). The numbers of infected and ACE2-positive cells correlated with the extent of tissue damage. The infected tissues exhibited low numbers of B-cells and abundant CD3{varepsilon}+ T-cells consisting of mainly T helper cells (CD4), few cytotoxic T cells (CTL, CD8), and no T regulatory cell (FOXP3). Antigen presenting molecule HLA-DR of B and T cells was abundant in all cases. Robust interleukin-6 (IL-6) expression was present in most uninfected and infected cells, with higher expression levels observed in cases with more tissue damage. Interpretation In lung tissues from severely affected COVID-19 patients, there is evidence for broad SARS-CoV-2 cell tropisms, activation of immune cells, and clearance of immunosuppressive cells, which could contribute to severe tissue damage, thromboemboli, excess inflammation and compromised adaptive immune responses. url: https://doi.org/10.1101/2020.09.25.20195818 doi: 10.1101/2020.09.25.20195818 id: cord-316330-55nd3pwe author: Ramos-Lopez, Omar title: Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date: 2020-10-19 words: 3499.0 sentences: 193.0 pages: flesch: 37.0 cache: ./cache/cord-316330-55nd3pwe.txt txt: ./txt/cord-316330-55nd3pwe.txt summary: RESULTS: Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. CONCLUSIONS: Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments. Observational (cross-sectional, cohort, or case-control) studies exploring the role of host genetic polymorphisms in SARS-CoV disease (infection susceptibility, disease progression, and clinical outcomes) in adult subjects were included. The present systematic review revealed that 29 polymorphisms located in 21 genes were associated with SARS-CoV susceptibility/resistance, disease severity, and clinical manifestations/outcomes (Table 1) . abstract: OBJECTIVE: To systematically explore genetic polymorphisms associated with the clinical outcomes in SARS-CoV infection in humans. METHODS: This comprehensive literature search comprised available English papers published in PubMed/Medline and SCOPUS databases following the PRISMA-P guidelines and PICO/AXIS criteria. RESULTS: Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. Thus, genes implicated in key pathophysiological processes such as the mechanisms related to the entry of the virus into the cell and the antiviral immune/inflammatory responses were identified. CONCLUSIONS: Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments. url: https://www.ncbi.nlm.nih.gov/pubmed/33110916/ doi: 10.1155/2020/6901217 id: cord-326911-va3x6au2 author: Ramos-Mandujano, G. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 words: 4424.0 sentences: 288.0 pages: flesch: 55.0 cache: ./cache/cord-326911-va3x6au2.txt txt: ./txt/cord-326911-va3x6au2.txt summary: We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. To date, molecular diagnosis of COVID-19 predominantly relies on detection of SARS-CoV-2 RNA using real-time reverse transcription polymerase chain reaction (rRT-PCR) assays, such as those approved by the US Centers for Disease Control and Prevention (US CDC) 1 . MAVRICS performed on par or better than commercial RNA extraction kits in rRT-PCR detection of SARS-CoV-2, influenza viruses and respiratory syncytial virus in various clinical and environmental samples. . https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint Next, we aimed to develop an efficient SiMNP-based RNA extraction protocol using the contrived SARS-CoV-2 samples and US CDC 2019-nCoV_N1 and N3 rRT-PCR assays. abstract: Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magnetic- nanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics. url: https://doi.org/10.1101/2020.06.28.20141945 doi: 10.1101/2020.06.28.20141945 id: cord-253618-bosb7e63 author: Ramteke, Shobhana title: Novel coronavirus disease 2019 (COVID-19) pandemic: considerations for the biomedical waste sector in India date: 2020-08-01 words: 2732.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-253618-bosb7e63.txt txt: ./txt/cord-253618-bosb7e63.txt summary: During this epidemic condition, expulsion of biomedical waste created from crisis facilities treating COVID-19 patients in like manner demands unprecedented thought as they can be potential bearers of the disease SARS-CoV-2. During December 2019, a novel Beta-coronavirus temporarily named 2019 novel coronavirus (2019-nCoV), and along these lines authoritatively renamed extreme intense respiratory disorder coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV), causing coronavirus ailment 2019 (or COVID19) , was related with a group of respiratory tract diseases in Wuhan, Hubei Province, China and has quickly spread across main land''s [3] . From that point forward, the whole world has been found napping by the clueless increment in the number of new cases because of the exponential increment in the pace of transmission of 2019-nCoV, presently formally alluded to as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) by the International Committee on Taxonomy of Viruses, the causative operator of COVID-19 [5] . abstract: Abstract In late December 2019, the world woke to a truth of a pandemic of Coronavirus Disease (COVID-19), inspired by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which has a place with a gathering of beta-coronavirus. As of July 21 India is still fighting to survive against the SARS-CoV-2 as called coronavirus disease. The contaminations, first constrained in the Kerala state, have inevitably spread to every single other area. The possibility to cause dangerous respiratory disappointment and quick transmission puts COVID-19 in the rundown of the Public Health Emergency of International Concern (PHEIC). There is a flow overall break out of the novel coronavirus Covid-19, which started from Wuhan in China and has now spread to more than 212 countries including 14,753,034 cases, as of 12:20 AM on July 21, 2020. Governments are feeling the squeeze to prevent the outbreak from spiralling into a worldwide wellbeing crisis. At this stage, readiness, straightforwardness, and sharing of data are vital to hazard evaluations and starting explosion control exercises. Since the episode of serious intense respiratory disorder (SARS) 18 years back, an enormous number of SARS-related coronaviruses (SARSr-CoVs) have been found in their regular repository have, bats. During this epidemic condition, expulsion of biomedical waste created from crisis facilities treating COVID-19 patients in like manner demands unprecedented thought as they can be potential bearers of the disease SARS-CoV-2. This article discusses the potential consequences of the COVID-19 pandemic on biomedical waste administrations, concentrating on basic focuses where option working methodology or extra moderation measures might be fitting. url: https://api.elsevier.com/content/article/pii/S266601642030027X doi: 10.1016/j.cscee.2020.100029 id: cord-265353-xwpdq8wo author: Ramzy, Danny title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. date: 2020-09-15 words: 174.0 sentences: 21.0 pages: flesch: 54.0 cache: ./cache/cord-265353-xwpdq8wo.txt txt: ./txt/cord-265353-xwpdq8wo.txt summary: key: cord-265353-xwpdq8wo title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. cord_uid: xwpdq8wo In December 2019, an outbreak of pneumonia traced to a wet market in Wuhan, China, proliferated into a global pandemic with seemingly exponential vehemence and in just eight months spread globally with over 800, 000 deaths 1,2 . Coronavirus Disease 2019 (COVID 19), is caused by the novel betacoronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which is characterized by extreme virulence and a complex spectrum of pathologies ranging in severity from mild constitutional symptoms to multi-organ failure 3 A Novel Coronavirus from Patients with Pneumonia in China The outbreak of COVID-19: An overview COVID-19 Illness in Native and Immunosuppressed States: A Clinical-Therapeutic Staging Proposal Pneumatocele and cysts in a patient with SARS-CoV-2 infection Spontaneous tension pneumothorax and acute pulmonary emboli in a patient with COVID-19 infection COVID-19 Complicated by Spontaneous Pneumothorax abstract: nan url: https://doi.org/10.1016/j.xjtc.2020.09.012 doi: 10.1016/j.xjtc.2020.09.012 id: cord-339558-li65qvq9 author: Rana, Rashmi title: A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date: 2020-11-02 words: 5934.0 sentences: 334.0 pages: flesch: 44.0 cache: ./cache/cord-339558-li65qvq9.txt txt: ./txt/cord-339558-li65qvq9.txt summary: Structural proteome analysis of earlier SARS epidemic in 2003 revealed a large array of proteins that could be targeted for this pandemic too. They used affinity purification followed by mass spectrometry analysis and statistical modeling of the MS1level quantitative data which allowed the identification of 1484 interactions between 1086 cellular proteins and 24 SARS-CoV bait proteins. 2013 ) A recently published study involves the development of an Opto-microfluidic sensing platform to rapidly detect antibodies against SARS-CoV2 spike protein in diluted human plasma with high sensitivity. It is the first study to detect the SARS-CoV-2 antigens in the blood plasma of COVID-19-positive patients. Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry abstract: World Health Organisation declared COVID-19 a pandemic on March 11, 2020. It was temporarily named as 2019-nCoV then subsequently named as COVID-19 virus. A coronavirus is a group of viruses, known to be zoonotic, causing illness ranging from acute to mild respiratory infections. These are spherical or pleomorphic enveloped particles containing positive sense RNA. The virus enters host cells, its uncoated genetic material transcribes, and translates. Since it has started spreading rapidly, protective measures have been taken all over the world. However, its transmission has been proved to be unstoppable and the absence of an effective drug makes the situation worse. The scientific community has gone all-out to discover and develop a possible vaccine or a competent antiviral drug. Other domains of biological sciences that promise effective results and target somewhat stable entities that are proteins, could be very useful in this time of crisis. Proteomics and metabolomics are the vast fields that are equipped with sufficient technologies to face this challenge. Various protein separation and identification techniques are available which facilitates the analysis of various types of interactions among proteins and their evolutionary lineages. The presented review aims at confronting the question: ‘how proteomics can help in tackling SARS-CoV-2?’ It deals with the role of upcoming proteome technology in these pandemic situations and discusses the proteomics approach towards the COVID-19 dilemma. url: https://www.ncbi.nlm.nih.gov/pubmed/33162722/ doi: 10.1007/s42485-020-00052-9 id: cord-301226-hmc2wmst author: Randazzo, Walter title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 words: 2158.0 sentences: 127.0 pages: flesch: 52.0 cache: ./cache/cord-301226-hmc2wmst.txt txt: ./txt/cord-301226-hmc2wmst.txt summary: Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Here, we show that SARS-CoV-2 can be reproducibly detected by RT-qPCR in longitudinal samples from sewage treatment plants that receive wastewaters from over one million inhabitants in the metropolitan area of Valencia, Spain. Following concentration of viral content by flocculation, a standard RT-qPCR procedure allowed us to detect SARS-CoV-2 RNA in 12/12 samples collected from March 9 to April 14, 2020, with Ct values ranging between 34•00 and 37•84, correspondingly revealing between 5•22 and 5•99 log 10 genomic copies (gc)/L (Table 1) . Interestingly, we consistently detected SARS-CoV-2 RNA in samples collected on March 9 and March 11, when only 50 and 76 cumulative cases were declared in the entire Region of Valencia. abstract: Background: The COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly emerging pandemic which has enforced extreme containment measures worldwide. In the absence of a vaccine or efficient treatment, cost-effective epidemiological surveillance strategies are urgently needed. Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Results: We were able to consistently detect SARS-CoV-2 RNA in samples taken when communicated cases in that region were only incipient. We also find that the wastewater viral RNA context increased rapidly and anticipated the subsequent ascent in the number of declared cases. Interpretation: Our results strongly suggest that the virus was undergoing community transmission earlier than previously believed, and show that wastewater analysis is a sensitive and cost-effective strategy for COVID-19 epidemiological surveillance. Routine implementation of this surveillance tool would significantly improve our preparedness against new or re-occurring viral outbreaks. url: http://medrxiv.org/cgi/content/short/2020.04.23.20076679v1?rss=1 doi: 10.1101/2020.04.23.20076679 id: cord-300063-5jemq8nm author: Rane, Jitendra Subhash title: Targeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19 date: 2020-07-20 words: 5786.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-300063-5jemq8nm.txt txt: ./txt/cord-300063-5jemq8nm.txt summary: Because of the enormous therapeutic importance, we selected some well-characterized pyrimidine substituted phenols (Kumar & Rao, 2018; Table S1 , supplementary material) to investigate their efficiency in binding to the interface of the hACE2-S protein complex and modulate the pattern of infectivity of the SARS-CoV-2 virus. In this study, we aim to identify diaryl pyrimidine derivatives as a potential lead molecule which may bind at the interface of the hACE2-S protein complex with high affinity. The study presented here, using molecular docking tool, revealed significant binding interaction of diaryl pyrimidines with the interface of the hACE2-S receptor complex (hACE2-spike protein complex: PDB ID 6VW1) (Table 1) . To examine the spatial stability and mechanistic aspects of conformational dynamics underlying the molecular interaction of diaryl pyrimidine derivatives, AP-NP, AP-3-OMe-Ph and AP-4-Me-Ph with hACE2-S protein complex, we performed MD simulation in an aqueous environment for the period of 100 ns, at physiological temperature (300 K). abstract: The entire human population over the globe is currently facing appalling conditions due to the spread of infection from coronavirus disease-2019 (COVID-19). The spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present on the surface of the virion mediates the virus entry into the host cells and therefore is targeted by several scientific groups as a novel drug target site. The spike glycoprotein binds to the human angiotensin-converting enzyme-2 (hACE2) cell surface receptor abundantly expressed in lung tissues, and this binding phenomenon is a primary determinant of cell tropism and pathogenesis. The binding and internalization of the virus is the primary and most crucial step in the process of infection, and therefore the molecules targeting the inhibition of this process certainly hold a significant therapeutic value. Thus, we systematically applied the computational techniques to identify the plausible inhibitor from a chosen set of well characterized diaryl pyrimidine analogues which may disrupt interfacial interaction of spike glycoprotein (S) at the surface of hACE2. Using molecular docking, molecular dynamics (MD) simulation and binding free energy calculation, we have identified AP-NP (2-(2-amino-5-(naphthalen-2-yl)pyrimidin-4-yl)phenol), AP-3-OMe-Ph (2-(2-amino-5-(3-methoxyphenyl)pyrimidin-4-yl)phenol) and AP-4-Me-Ph (2-(2-amino-5-(p-tolyl) pyrimidin-4-yl)phenol) from a group of diaryl pyrimidine derivatives which appears to bind at the interface of the hACE2-S complex with low binding free energy. Thus, pyrimidine derivative AP-NP may be explored as an effective inhibitor for hACE2-S complex. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-COV-2. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1794969 doi: 10.1080/07391102.2020.1794969 id: cord-273906-s7l0yxc0 author: Ranga, Vipin title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 words: 7046.0 sentences: 354.0 pages: flesch: 53.0 cache: ./cache/cord-273906-s7l0yxc0.txt txt: ./txt/cord-273906-s7l0yxc0.txt summary: Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] . abstract: The emergence of the COVID-19 outbreak at the end of 2019, caused by the novel coronavirus SARS-CoV-2, has, to date, led to over 13.6 million infections and nearly 600,000 deaths. Consequently, there is an urgent need to better understand the molecular factors triggering immune defense against the virus and to develop countermeasures to hinder its spread. Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. The identified epitopes, each one of nine amino acids, have high sequence similarity to the equivalent epitopes of SARS-CoV virus, which are known to elicit an effective T cell response in vitro. Moreover, we give a structural explanation for the binding of SARS-CoV-2-epitopes to MHC molecules. Our data can help us to better understand the differences in outcomes of COVID-19 patients and may aid the development of vaccines against SARS-CoV-2 and possible future outbreaks of novel coronaviruses. url: https://doi.org/10.3390/vaccines8030408 doi: 10.3390/vaccines8030408 id: cord-302381-oujsmf8d author: Rankin, John title: Godzilla in the corridor: The Ontario SARS crisis in historical perspective date: 2006-06-30 words: 5098.0 sentences: 252.0 pages: flesch: 61.0 cache: ./cache/cord-302381-oujsmf8d.txt txt: ./txt/cord-302381-oujsmf8d.txt summary: The following evaluation of yellow fever, cholera and the Spanish influenza will illustrate a continuity in epidemic nurses'' feelings of fear and isolation from the mid-19th to the early 20th century. The five submissions studied were: the Canadian Nursing Association Brief to the National Advisory Committee on SARS and Public Health On 5 March 2003, SARS claimed its first Ontario victim when Sui-chu Kwan, a 78-year-old woman who had returned from a trip to Hong Kong, died of the disease. Instead, the silencing of nurses proved deadly as the SARS virus continued to spread placing both the public and health care workers at heightened risk. It is evident that nurses had little knowledge of previous public health crises and no context in which to place the SARS epidemic. That is they reacted to health care crisis of unknown epidemiology with much fear and, due to the nature of nursing during these crises, are prone to feelings of isolation. abstract: Summary Ontario nurses were employed as the front-line workers when SARS descended upon Toronto in March 2003. Once the crisis had subsided, many nurses remarked that SARS had forever altered their chosen profession; employment, which they once viewed as relatively safe, had been transformed into potentially life-threatening. This discussion provides descriptions of these expressions through nurses who experienced the crisis and chose to go on the public record. Secondly, it compares the subjective perceptions of those nurses to those held by nurses who worked through historical epidemics of unknown or contested epidemiology. The historical literature on nursing in yellow fever, cholera and influenza epidemics has been employed to offer insight. The goal is to determine whether the SARS outbreak was a unique experience for nurses or whether similar experiences were shared by nurses in the past? In summary, the reactions of nurses when confronted with the possibility of contracting a deadly disease remain altogether human, not dissimilar in past or present. Nurses’ responses to SARS can be usefully studied within a larger historical vision of crisis nursing, and information or impressions from earlier crises are potentially of interest to the nursing profession. url: https://www.sciencedirect.com/science/article/pii/S0964339705001333 doi: 10.1016/j.iccn.2005.10.001 id: cord-346978-ubkqny8j author: Ranoa, Diana Rose E. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 words: 6476.0 sentences: 325.0 pages: flesch: 54.0 cache: ./cache/cord-346978-ubkqny8j.txt txt: ./txt/cord-346978-ubkqny8j.txt summary: 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) . Similar results were observed with heat-inactivated SARS-CoV-2, whereby the LOD was measured to be 5000 viral copies/mL for both RNA extraction of saliva samples and direct saliva-to-RT-qPCR, with greater detection if the virus was directly analyzed in water (Supporting Limit of Detection (LOD) for assessment of SARS-CoV-2 from saliva, comparing a process utilizing RNA isolation/purification to one that bypasses RNA isolation/purification. Altogether, these findings indicate that the optimized protocol (heat treatment of saliva samples at 95°C for 30 min / addition of TBE buffer and Tween 20) yields a LOD that is comparable to reported clinical viral shedding concentrations in oral fluid, thus emphasizing the translatability of the protocol to detecting SARS-CoV-2 in patient samples. abstract: Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract url: https://doi.org/10.1101/2020.06.18.159434 doi: 10.1101/2020.06.18.159434 id: cord-351340-7y19ystp author: Rao, Gundu H. R. title: Coronavirus Disease and Acute Vascular Events date: 2020-07-31 words: 2557.0 sentences: 140.0 pages: flesch: 43.0 cache: ./cache/cord-351340-7y19ystp.txt txt: ./txt/cord-351340-7y19ystp.txt summary: 3 On the other hand, in a study performed in COVID-19 patients in New York, with observed ST-segment elevated myocardial infraction, 64% had normal D-dimer levels according to Dr Bangalore and associates from the New York University Grossman School of Medicine. At the time of admission, COVID-19 patients reported as having at least 1 acute comorbidity: diabetes (10%-20%), hypertension (10%-15%), or other CVD and cerebrovascular diseases (7%-40%). 12 In a seminal article by Bikdeli et al, endorsed by multiple specialty societies, the authors summarize their findings in the following way: "Coronavirus disease 2019 (COVID-19) , a viral respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), may predispose patients to thrombotic disease, both in the venous and arterial circulations, due to excessive inflammation, platelet activation, endothelial dysfunction, and stasis. Elevated plasmin(ogen) seems to be a common biomarker in people with hypertension, diabetes, CVD, and cerebrovascular diseases, who are susceptible to SARS-CoV-2 infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32735130/ doi: 10.1177/1076029620929091 id: cord-321603-lbbsnriv author: Rao, Mohan title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date: 2020-08-06 words: 2186.0 sentences: 172.0 pages: flesch: 59.0 cache: ./cache/cord-321603-lbbsnriv.txt txt: ./txt/cord-321603-lbbsnriv.txt summary: The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. abstract: BACKGROUND: The ideal SARs-CoV-2 testing method would be accurate and also be patient-performed to reduce exposure to healthcare workers. The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. Paired NPS and saliva specimens were collected and processed within 5 hours of sample collection. Real time reverse transcriptase polymerase chain reaction (RT-PCR) targeting Envelope (E) and RNA-dependent RNA polymerase (RdRp) genes was performed and the results were compared. RESULTS: Overall, 160 of the 217 (74%) participants tested positive for Covid-19 based on saliva, NPS, or both testing methods. The detection rate for SARS-CoV-2 was higher in saliva compared to NPS testing (93.1%, 149/160 vs 52.5%, 84/160, p<0.001). The concordance between the two tests was 45.6% (virus was detected in both saliva and NPS in 73/160), while 47.5% were discordant (87/160 tested positive for one while negative for the other). The Ct values for E and RdRp genes were significantly lower in saliva specimens compared to NP swab specimens. CONCLUSIONS: Our findings demonstrate that saliva is a better alternative specimen for detection of SARS-CoV-2. Taking into consideration, the simplicity of specimen collection, shortage of PPE and the transmissibility of the virus, saliva could enable self-collection for an accurate SARS-CoV-2 surveillance testing. url: https://doi.org/10.1093/cid/ciaa1156 doi: 10.1093/cid/ciaa1156 id: cord-334612-lxqcvqca author: Rao, Nirmala title: Sars, preschool routines and children’s behaviour: Observations from preschools in Hong Kong date: 2006 words: 4265.0 sentences: 239.0 pages: flesch: 62.0 cache: ./cache/cord-334612-lxqcvqca.txt txt: ./txt/cord-334612-lxqcvqca.txt summary: This paper considers the influence of the SARS epidemic on children''s routines and behaviour when preschools re-opened, after a six-week closure. Items on the survey fell into 6 categories including: Information about the preschool and children (21 questions); Routines before the SARS outbreak (4 questions); Learning during School Closure (2 questions); Preparing the kindergarten for re-opening (2 questions); Students return to kindergartens (18 questions); Lessons from SARS (4 questions); and Demographic information about the observers. The 18 items on Students'' return to kindergartens included questions on Daily routines (3 questions); Health issues (2 questions); Social Interaction among children (6 questions); Preschool Management (3 questions); and School Holidays (4 questions). During the SARS outbreak, the Education and Manpower Bureau of the Hong Kong Government issued a curriculum for children ranging in age from 3-6 years. As mentioned earlier the Education and Manpower Bureau of the Hong Kong Government developed a programme for preschool children on SARS. abstract: All schools in Hong Kong were closed in April 2003 to prevent the spread of SARS. This paper considers the influence of the SARS epidemic on children’s routines and behaviour when preschools re-opened, after a six-week closure. Observations were made in 20 kindergartens and principals of another 10 kindergartens completed questionnaires. The influence of SARS was evident in all preschools, be it through teachers and students wearing masks, notices on hand washing or the provision of alcohol dispensers for hand disinfection. The outbreak impacted noticeably upon children’s routines and social exchanges. In all schools, physical contact among children and sharing of food were not allowed. Children were also prohibited from talking to their peers when they had removed their masks. The SARS outbreak provided us a “natural experiment” to consider the influence of epidemics on preschools. url: https://doi.org/10.1007/bf03168205 doi: 10.1007/bf03168205 id: cord-334564-bqh9jkds author: Raony, Ícaro title: Psycho-Neuroendocrine-Immune Interactions in COVID-19: Potential Impacts on Mental Health date: 2020-05-27 words: 9893.0 sentences: 464.0 pages: flesch: 41.0 cache: ./cache/cord-334564-bqh9jkds.txt txt: ./txt/cord-334564-bqh9jkds.txt summary: Since COVID-19 is associated with increased levels of pro-inflammatory cytokines (8) , an immune signature shared with several psychiatric disorders, we propose how the relationship between SARS-CoV-2/host can possibly impair interactions between the immune, nervous and endocrine systems, leading to psychiatric symptoms. Several studies have demonstrated psychiatric manifestations in patients with MERS or SARS during the acute phase, such as increased stress levels, impaired memory, symptoms of depression, anxiety, PTSD, psychoses, and suicidal behavior (28) (29) (30) (31) (32) (33) . If the increase in cytokine levels and the manifestation of psychiatric symptoms are related to the severity of the symptoms of SARS-CoV infection, the "cytokine storm" might also be related to the "mental health thunderstorms" seen in patients with COVID-19? Similar to possible mechanisms involved in the impacts of SARS-CoV-2 infection on mental health, social isolation may also be associated with dysfunctional psycho-neuroendocrine-immune interactions, which in turn can contribute to the development or the worsening of psychiatric disturbances (Figure 2) . abstract: Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The impacts of the disease may be beyond the respiratory system, also affecting mental health. Several factors may be involved in the association between COVID-19 and psychiatric outcomes, such as fear inherent in the pandemic, adverse effects of treatments, as well as financial stress, and social isolation. Herein we discuss the growing evidence suggesting that the relationship between SARS-CoV-2 and host may also trigger changes in brain and behavior. Based on the similarity of SARS-CoV-2 with other coronaviruses, it is conceivable that changes in endocrine and immune response in the periphery or in the central nervous system may be involved in the association between SARS-CoV-2 infection and impaired mental health. This is likely to be further enhanced, since millions of people worldwide are isolated in quarantine to minimize the transmission of SARS-CoV-2 and social isolation can also lead to neuroendocrine-immune changes. Accordingly, we highlight here the hypothesis that neuroendocrine-immune interactions may be involved in negative impacts of SARS-CoV-2 infection and social isolation on psychiatric issues. url: https://doi.org/10.3389/fimmu.2020.01170 doi: 10.3389/fimmu.2020.01170 id: cord-335599-98ovzui5 author: Raony, Ícaro title: Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus date: 2020-06-25 words: 1198.0 sentences: 54.0 pages: flesch: 42.0 cache: ./cache/cord-335599-98ovzui5.txt txt: ./txt/cord-335599-98ovzui5.txt summary: title: Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus Notwithstanding this, it was not discussed whether the patients already presenting changes in the retina before infection with COVID-19, or even if there was any systemic disease (e.g. type 2 diabetes mellitus) that could also be associated with retinal lesions. Thus, it is possible that CD147, by mediating the breakdown of the blood-retinal barrier in a hyperglycemic context, may facilitate the invasion of retinal cells by SARS-CoV-2 in people with DM, which deserves to be investigated by future studies with animal models and humans. The reverse is also possible, with COVID-19 being able to precipitate or worsen retinal lesions present in patients with DM in the short or long term, either by direct effects of retinal SARS-CoV-2 infection, or by the indirect effects of the cytokine storm associated with COVID-19. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0168822720305325?v=s5 doi: 10.1016/j.diabres.2020.108280 id: cord-298440-0pb8ssj2 author: Rascón-Ramírez, Fernando J title: Supra and infratentorial massive strokes in previously healthy young patients with SARS-CoV-2. The role of neurosurgery date: 2020-09-06 words: 1428.0 sentences: 94.0 pages: flesch: 50.0 cache: ./cache/cord-298440-0pb8ssj2.txt txt: ./txt/cord-298440-0pb8ssj2.txt summary: COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). Keywords: Cerebrovascular disease; COVID-19; Coronavirus; stroke; decompressive craniectomy; Cerebellar; SARS-CoV-2. We present two massive supra and infratentorial strokes in people of young age with no known risk factors and with the severe acute respiratory syndrome (SARS-CoV-2), requiring Endotracheal Intubation (ETI). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. abstract: The coronavirus disease 2019 (COVID-19) has amazed by its distinct forms of presentation and severity. COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). We hypothesize that ischemic events are usually the result of the combined process of a pro-inflammatory and pro-coagulant state plus vascular endothelial dysfunction probably potentiated by hypoxia, hemodynamic instability, and immobilization, as reported in other cases. To the best of our knowledge, we report the first case of partial obstruction of a vertebral artery in a patient with COVID-19. Decompressive surgery remains a life-saving maneuver in these patients (as in other non-COVID-19 strokes) and requires further investigation. url: https://www.sciencedirect.com/science/article/pii/S1130147320300981?v=s5 doi: 10.1016/j.neucir.2020.08.001 id: cord-270606-r46pbaf0 author: Rashed, Mohamed Z. title: Rapid detection of SARS-CoV-2 antibodies using electrochemical impedance-based detector date: 2020-10-07 words: 3135.0 sentences: 152.0 pages: flesch: 42.0 cache: ./cache/cord-270606-r46pbaf0.txt txt: ./txt/cord-270606-r46pbaf0.txt summary: Here, we demonstrate rapid label-free electrochemical detection of SARS-CoV-2 antibodies using a commercially available impedance sensing platform. A 16-well plate containing sensing electrodes was pre-coated with receptor binding domain (RBD) of SARS-CoV-2 spike protein, and subsequently tested with samples of anti-SARS-CoV-2 monoclonal antibody CR3022 (0.1 [Formula: see text] g/ml, 1.0 [Formula: see text] g/ml, 10 [Formula: see text] g/ml). In this study, we report a non-faradic capacitive immunosensing assay using a commercially-available impedance detection system that uses specialized well-plates that have integrated sensing electrodes from ACEA Biosciences ( Figure 1 ). Coating the wells with anti-SARS-CoV-2 antibodies instead of spike RBD antigen may enable rapid EIS detection of viral particles in patient samples, although further testing is needed to determine the limit of detection for that approach. An alternative medical Rapid Detection of SARS-CoV-2 Antibodies Figure S1 : Measurements with greater time resolution were acquired with a different impedance analyzer (Agilent 4294A, 10 kHz, 0.5 V), demonstrating improved resolution. abstract: Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was classified as a pandemic by the World Health Organization and has caused over 550,000 deaths worldwide as of July 2020. Accurate and scalable point-of-care devices would increase screening, diagnosis, and monitoringof COVID-19 patients. Here, we demonstrate rapid label-free electrochemical detection of SARS-CoV-2 antibodies using a commercially available impedance sensing platform. A 16-well plate containing sensing electrodes was pre-coated with receptor binding domain (RBD) of SARS-CoV-2 spike protein, and subsequently tested with samples of anti-SARS-CoV-2 monoclonal antibody CR3022 (0.1 [Formula: see text] g/ml, 1.0 [Formula: see text] g/ml, 10 [Formula: see text] g/ml). Subsequent blinded testing was performed on six serum specimens taken from COVID-19 and non-COVID-19 patients (1:100 dilution factor). The platform was able to differentiate spikes in impedance measurements from a negative control (1% milk solution) for all CR3022 samples. Further, successful differentiation and detection of all positive clinical samples from negative control was achieved. Measured impedance values were consistent when compared to standard ELISA test results showing a strong correlation between them (R [Formula: see text]). Detection occurs in less than five minutes and the well-based platform provides a simplified and familiar testing interface that can be readily adaptable for use in clinical settings. url: https://www.sciencedirect.com/science/article/pii/S095656632030693X?v=s5 doi: 10.1016/j.bios.2020.112709 id: cord-274007-zndtddty author: Rasmussen, Sonja A. title: Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date: 2020-02-24 words: 5912.0 sentences: 330.0 pages: flesch: 50.0 cache: ./cache/cord-274007-zndtddty.txt txt: ./txt/cord-274007-zndtddty.txt summary: For Middle East respiratory syndrome, there were 13 case reports in pregnant women, of which 2 were asymptomatic, identified as part of a contact investigation; 3 patients (23%) died. Principles of management of coronavirus disease 2019 in pregnancy include early isolation, aggressive infection control procedures, oxygen therapy, avoidance of fluid overload, consideration of empiric antibiotics (secondary to bacterial infection risk), laboratory testing for the virus and coinfection, fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations. General principles regarding management of COVID-10 during pregnancy include early isolation, aggressive infection control procedures, testing for SARS-CoV-2 and coinfection, oxygen therapy as needed, avoidance of fluid overload, empiric antibiotics (because of secondary bacterial infection risk), fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations (Box 2). abstract: Coronavirus disease 2019 is an emerging disease with a rapid increase in cases and deaths since its first identification in Wuhan, China, in December 2019. Limited data are available about coronavirus disease 2019 during pregnancy; however, information on illnesses associated with other highly pathogenic coronaviruses (ie, severe acute respiratory syndrome and the Middle East respiratory syndrome) might provide insights into coronavirus disease 2019’s effects during pregnancy. Coronaviruses cause illness ranging in severity from the common cold to severe respiratory illness and death. Currently the primary epidemiologic risk factors for coronavirus disease 2019 include travel from mainland China (especially Hubei Province) or close contact with infected individuals within 14 days of symptom onset. Data suggest an incubation period of ∼5 days (range, 2–14 days). Average age of hospitalized patients has been 49–56 years, with a third to half with an underlying illness. Children have been rarely reported. Men were more frequent among hospitalized cases (54–73%). Frequent manifestations include fever, cough, myalgia, headache, and diarrhea. Abnormal testing includes abnormalities on chest radiographic imaging, lymphopenia, leukopenia, and thrombocytopenia. Initial reports suggest that acute respiratory distress syndrome develops in 17–29% of hospitalized patients. Overall case fatality rate appears to be ∼1%; however, early data may overestimate this rate. In 2 reports describing 18 pregnancies with coronavirus disease 2019, all were infected in the third trimester, and clinical findings were similar to those in nonpregnant adults. Fetal distress and preterm delivery were seen in some cases. All but 2 pregnancies were cesarean deliveries and no evidence of in utero transmission was seen. Data on severe acute respiratory syndrome and Middle East respiratory syndrome in pregnancy are sparse. For severe acute respiratory syndrome, the largest series of 12 pregnancies had a case-fatality rate of 25%. Complications included acute respiratory distress syndrome in 4, disseminated intravascular coagulopathy in 3, renal failure in 3, secondary bacterial pneumonia in 2, and sepsis in 2 patients. Mechanical ventilation was 3 times more likely among pregnant compared with nonpregnant women. Among 7 first-trimester infections, 4 ended in spontaneous abortion. Four of 5 women with severe acute respiratory syndrome after 24 weeks’ gestation delivered preterm. For Middle East respiratory syndrome, there were 13 case reports in pregnant women, of which 2 were asymptomatic, identified as part of a contact investigation; 3 patients (23%) died. Two pregnancies ended in fetal demise and 2 were born preterm. No evidence of in utero transmission was seen in severe acute respiratory syndrome or Middle East respiratory syndrome. Currently no coronavirus-specific treatments have been approved by the US Food and Drug Administration. Because coronavirus disease 2019 might increase the risk for pregnancy complications, management should optimally be in a health care facility with close maternal and fetal monitoring. Principles of management of coronavirus disease 2019 in pregnancy include early isolation, aggressive infection control procedures, oxygen therapy, avoidance of fluid overload, consideration of empiric antibiotics (secondary to bacterial infection risk), laboratory testing for the virus and coinfection, fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations. Information on coronavirus disease 2019 is increasing rapidly. Clinicians should continue to follow the Centers for Disease Control and Prevention website to stay up to date with the latest information (https://www.cdc.gov/coronavirus/2019-nCoV/hcp/index.html). url: https://www.sciencedirect.com/science/article/pii/S0002937820301976 doi: 10.1016/j.ajog.2020.02.017 id: cord-009891-gqrhbhbn author: Rassool, G. Hussein title: Current issues and forthcoming events date: 2003-09-03 words: 3466.0 sentences: 168.0 pages: flesch: 49.0 cache: ./cache/cord-009891-gqrhbhbn.txt txt: ./txt/cord-009891-gqrhbhbn.txt summary: The Centers for Disease Control and Prevention (CDC), USA, reports that ''transmission to health care workers appears to have occurred after close contact with symptomatic individuals (e.g. persons with fever or respiratory symptoms) before recommended infection control precautions for SARS were implemented (i.e. unprotected exposures).'' There is also a possibility that the causative agent can remain viable for extended periods of time after drying on environmental surfaces. Preliminary results of a large-scale trial of a candidate AIDS vaccine announced by the US-based biotechnology company VaxGen suggest that it is possible to protect some individuals from HIV infection. The result is that poor diagnosis of pain in cancer patients remains a significant problem, with many physicians finding it difficult to differentiate between the various pain types; and, many underestimating its severity. Poor diagnosis, poor assessment, the choice of less appropriate treatments, plus patients and physicians fears about controlled drugs such as morphine all contribute to under treatment of cancer pain. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166755/ doi: 10.1046/j.1365-2648.2003.02701.x-i2 id: cord-299940-nvlcwcz8 author: Rastrelli, Giulia title: Low testosterone levels predict clinical adverse outcomes in SARS‐CoV‐2 pneumonia patients date: 2020-06-03 words: 3458.0 sentences: 187.0 pages: flesch: 47.0 cache: ./cache/cord-299940-nvlcwcz8.txt txt: ./txt/cord-299940-nvlcwcz8.txt summary: OBJECTIVES: To estimate the association between T level and SARS‐CoV‐2 clinical outcomes (defined as conditions requiring transfer to higher or lower intensity of care or death) in a cohort of patients admitted in the respiratory intensive care unit (RICU). 16, 17 Thereof, we sought to estimate the association between the T levels and the SARS-CoV-2 infection clinical outcomes (defined as conditions requiring to transfer to a higher or lower intensity of care units or even death) as well as the biochemical prognostic predictors of severe and fatal SARS-CoV-2 infection in a cohort of patients admitted in the respiratory intensive care unit (RICU) of a single Hospital in Mantua, one of the epicenter of the global SARS-CoV-2 pandemic in Italy. Discussion and conclusion: Our study demonstrates for the first time that lower baseline levels of TT and cFT levels predict poor prognosis and mortality in SARS-CoV-2-infected men admitted to RICU. abstract: BACKGROUND: The pandemic of new severe acute respiratory syndrome (SARS) due to coronavirus (CoV) 2 (SARS‐CoV‐2) has stressed the importance of effective diagnostic and prognostic biomarkers of clinical worsening and mortality. Epidemiological data showing a differential impact of SARS‐CoV‐2 infection on women and men have suggested a potential role for testosterone (T) in determining gender disparity in the SARS‐CoV‐2 clinical outcomes. OBJECTIVES: To estimate the association between T level and SARS‐CoV‐2 clinical outcomes (defined as conditions requiring transfer to higher or lower intensity of care or death) in a cohort of patients admitted in the respiratory intensive care unit (RICU). MATERIALS AND METHODS: A consecutive series of 31 male patients affected by SARS‐CoV‐2 pneumonia and recovered in the respiratory intensive care unit (RICU) of the “Carlo Poma” Hospital in Mantua were analyzed. Several biochemical risk factors (ie, blood count and leukocyte formula, C‐reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), ferritin, D‐dimer, fibrinogen, interleukin 6 (IL‐6)) as well as total testosterone (TT), calculated free T (cFT), sex hormone–binding globulin (SHBG), and luteinizing hormone (LH) were determined. RESULTS: Lower TT and cFT were found in the transferred to ICU/deceased in RICU group vs groups of patients transferred to IM or maintained in the RICU in stable condition. Both TT and cFT showed a negative significant correlation with biochemical risk factors (ie, the neutrophil count, LDH, and PCT) but a positive association with the lymphocyte count. Likewise, TT was also negatively associated with CRP and ferritin levels. A steep increase in both ICU transfer and mortality risk was observed in men with TT < 5 nmol/L or cFT < 100 pmol/L. DISCUSSION AND CONCLUSION: Our study demonstrates for the first time that lower baseline levels of TT and cFT levels predict poor prognosis and mortality in SARS‐CoV‐2‐infected men admitted to RICU. url: https://www.ncbi.nlm.nih.gov/pubmed/32436355/ doi: 10.1111/andr.12821 id: cord-310124-3bc8zeww author: Ratajczak, Mariusz Z. title: SARS-CoV-2 Entry Receptor ACE2 Is Expressed on Very Small CD45(−) Precursors of Hematopoietic and Endothelial Cells and in Response to Virus Spike Protein Activates the Nlrp3 Inflammasome date: 2020-07-20 words: 5165.0 sentences: 281.0 pages: flesch: 52.0 cache: ./cache/cord-310124-3bc8zeww.txt txt: ./txt/cord-310124-3bc8zeww.txt summary: We demonstrate for the first time that ACE2 and the entry-facilitating transmembrane protease TMPRSS2 are expressed on very small CD133(+)CD34(+)Lin(−)CD45(−) cells in human umbilical cord blood (UCB), which can be specified into functional HSCs and EPCs. The existence of these cells known as very small embryonic-like stem cells (VSELs) has been confirmed by several laboratories, and some of them may correspond to putative postnatal hemangioblasts. Moreover, we demonstrate for the first time that, in human VSELs and HSCs, the interaction of the ACE2 receptor with the SARS-CoV-2 spike protein activates the Nlrp3 inflammasome, which if hyperactivated may lead to cell death by pyroptosis. We sorted very small CD34 + Lin − CD45 − cells (VSELs) and CD34 + Lin − CD45 + cells (HSCs) from UCB by FACS (Fig. 1) and phenotyped them by real-time PCR for expression of mRNAs for the ACE2 entry receptor for SARS-CoV-2, the spike protein-processing enzyme TIMPRSS2, the receptors for Ang II (AT 1 R and AT 2 R), and the Ang (1-7) receptor (MasR, Fig. 2) . abstract: Angiotensin-converting enzyme 2 (ACE2) plays an important role as a member of the renin–angiotensin–aldosterone system (RAAS) in regulating the conversion of angiotensin II (Ang II) into angiotensin (1–7) (Ang [1–7]). But at the same time, while expressed on the surface of human cells, ACE2 is the entry receptor for SARS-CoV-2. Expression of this receptor has been described in several types of cells, including hematopoietic stem cells (HSCs) and endothelial progenitor cells (EPCs), which raises a concern that the virus may infect and damage the stem cell compartment. We demonstrate for the first time that ACE2 and the entry-facilitating transmembrane protease TMPRSS2 are expressed on very small CD133(+)CD34(+)Lin(−)CD45(−) cells in human umbilical cord blood (UCB), which can be specified into functional HSCs and EPCs. The existence of these cells known as very small embryonic-like stem cells (VSELs) has been confirmed by several laboratories, and some of them may correspond to putative postnatal hemangioblasts. Moreover, we demonstrate for the first time that, in human VSELs and HSCs, the interaction of the ACE2 receptor with the SARS-CoV-2 spike protein activates the Nlrp3 inflammasome, which if hyperactivated may lead to cell death by pyroptosis. Based on this finding, there is a possibility that human VSELs residing in adult tissues could be damaged by SARS-CoV-2, with remote effects on tissue/organ regeneration. We also report that ACE2 is expressed on the surface of murine bone marrow-derived VSELs and HSCs, although it is known that murine cells are not infected by SARS-CoV-2. Finally, human and murine VSELs express several RAAS genes, which sheds new light on the role of these genes in the specification of early-development stem cells. [Figure: see text] url: https://doi.org/10.1007/s12015-020-10010-z doi: 10.1007/s12015-020-10010-z id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 words: 1662.0 sentences: 124.0 pages: flesch: 55.0 cache: ./cache/cord-329395-4k8js9v2.txt txt: ./txt/cord-329395-4k8js9v2.txt summary: Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 abstract: Accurate identification of individuals infected with SARS-CoV-2 is crucial for efforts to control the ongoing COVID-19 pandemic. Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. Most currently used quantitative PCR (RT-qPCRs) rely upon real-time detection of PCR product using specialized laboratory equipment. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. Samples and transcripts were further evaluated in an additional N protein real-time quantitative PCR assay. As determined by 50% endpoint detection, the sensitivities of three RT-qPCRs and nested PCR methods varied substantially depending on the transcript target with no method approaching single copy detection. Overall, these findings highlight the need for assay validation and optimization and demonstrate the inability to precisely compare viral quantification from different PCR methodologies without calibration. url: https://doi.org/10.1101/2020.06.24.168013 doi: 10.1101/2020.06.24.168013 id: cord-300194-nsp53lv6 author: Rath, Soumya Lipsa title: Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date: 2020-06-19 words: 4302.0 sentences: 226.0 pages: flesch: 54.0 cache: ./cache/cord-300194-nsp53lv6.txt txt: ./txt/cord-300194-nsp53lv6.txt summary: Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. and S2 domains individually, with respect to the starting structure, to understand the ause for higher R S values o served at and igure The R S values of S1 domain at and were found to e around nm nearly nm more than simulations at 1 and respe tively similar trend was o served in the R S of S domain ut the differen e in values was only 1 nm lthough in this study we haven''t considered the bilayer lipid membrane of the SARS-COV-2 envelope inside which the Spike 9 glycoprotein resides, the S2 domain shows remarkable stability in its RMSD values ( Figure 2 ). abstract: Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV-2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10-30 °C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40 °C and attains a completely closed conformation at 50 °C. The closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics. Graphical Abstract Highlights Statistical and epidemiological evidence show that external climatic conditions influence the SARS-CoV infectivity, but we still lack a molecular level understanding of the same. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. Results show that the Spike’s S1 domain is very sensitive to external atmospheric conditions compared to the S2 transmembrane domain. The N-terminal domain comprises of several solvent exposed charged residues that are capable of binding to human proteins. The region is specifically stable at temperatures ranging around 10-30° C. The Receptor Binding Motif adopts a closed conformation at 40°C and completely closes at higher temperatures making it unsuitable of binding to human receptors url: https://doi.org/10.1101/2020.06.10.145086 doi: 10.1101/2020.06.10.145086 id: cord-323093-u3ozc9ry author: Rathnayake, Athri D. title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice date: 2020-08-19 words: 7158.0 sentences: 362.0 pages: flesch: 56.0 cache: ./cache/cord-323093-u3ozc9ry.txt txt: ./txt/cord-323093-u3ozc9ry.txt summary: After we observed that treatment with compound 6j resulted in the survival of MERS MA -CoV-infected hDPP4-KI mice, we conducted another study by delaying treatment initiation until 3 dpi. This nucleoside analog was originally developed as an antiviral drug against Ebola virus and has been shown to be effective against both MERS-CoV and SARS-CoV in cell culture assays and in animal models of coronavirus infection (23) (24) (25) (26) . Prophylactic treatment or early therapeutic treatment of infected mice with remdesivir reduced MERS-CoV-or SARS-CoV-mediated weight loss and decreased lung virus titers and lung injury scores compared to those of vehicle-treated animals (23, 26) . The goal of this study was to evaluate the efficacy of 3CLpro inhibitors against human coronaviruses, including SARS-CoV-2, in a FRET enzyme assay and cell culture assays, as well as in a mouse model of MERS-CoV infection. abstract: Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32747425/ doi: 10.1126/scitranslmed.abc5332 id: cord-336150-l8w7xk0b author: Rathore, Jitendra Singh title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview date: 2020-08-25 words: 7362.0 sentences: 399.0 pages: flesch: 54.0 cache: ./cache/cord-336150-l8w7xk0b.txt txt: ./txt/cord-336150-l8w7xk0b.txt summary: The essential surface glycoprotein of SARS-CoV-2 known as spike (S) protein, essential for host cell receptor binding, showed only 72% similarity with SARS-CoV at the nucleotide level. Comparative genome analysis of RaTG13, a virus from a Rhinolophusaffinis (i.e. horseshoe) bat sampled from Yunnan province in China in 2013, with SARS-CoV-2, showed that SARS-CoV-2 has 96% similarity at the nucleotide sequence level . Later, it was found that the disease was caused by a virus designated as a novel human coronavirus, MERS-CoV, phylogenetic data showed that it belonged to lineage C of the Betacoronavirusgenus and was highly similar to bat coronaviruses HKU4 (Tylonycterispachypus) and HKU5 (Pipistrelluspipistrellus; Lau et al. When cell lines over-expressed the transmembrane protein ''angiotensin-converting enzyme 2'' (ACE2) from humans, bats, pig or civet cats and were infected with SARS-CoV-2, results showed that they became hypersensitized to infection, thus indicating that ACE2 is a SARS-CoV-2 receptor . Recently, neutralizing monoclonal antibodies and nanobodies against the RBD domain of S protein showed protection against SARS-CoV and MERS-CoV (Du et al. abstract: Coronavirus disease 2019 (COVID-19) is a viral pneumonia, responsible for the recent pandemic, and originated from Wuhan, China, in December 2019. The causative agent of the outbreak was identified as coronavirus and designated as severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2). Few years back, the severe acute respiratory syndrome coronavirus (SARS- CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) were reported to be highly pathogenic and caused severe infections in humans. In the current situation SARS-CoV-2 has become the third highly pathogenic coronavirus that is responsible for the present outbreak in human population. At the time of this review, there were more than 14 007 791 confirmed COVID-19 patients which associated with over 597 105 deaths in more then 216 countries across the globe (as reported by World Health Organization). In this review we have discussed about SARS-CoV, MERS-CoV and SARC-CoV-2, their reservoirs, role of spike proteins and immunogenicity. We have also covered the diagnosis, therapeutics and vaccine status of SARS-CoV-2. url: https://doi.org/10.1093/femspd/ftaa042 doi: 10.1093/femspd/ftaa042 id: cord-349501-p1fttfpr author: Ratia, Kiira title: Chapter 494 Coronavirus Papain-like Peptidases date: 2013-12-31 words: 1322.0 sentences: 77.0 pages: flesch: 45.0 cache: ./cache/cord-349501-p1fttfpr.txt txt: ./txt/cord-349501-p1fttfpr.txt summary: Keywords: Coronavirus, Severe acute respiratory syndrome, SARS-CoV, polyprotein processing, ubiquitin-like domain, noncovalent protease inhibitors, de-ubiquitination, DUB, ISG-15, de-ISGylation. For coronaviruses, a family of positive-stranded RNA viruses with large genomes (28À32 kb), the gene encoding the viral non-structural proteins (nsp''s), including the RNA-dependent RNA-polymerase, is translated into a large precursor polyprotein, which must be proteolytically processed to mediate viral transcription and replication [1] . Cloning and expression of the N-terminal region of the murine coronavirus replicase polyprotein revealed that a predicted papain-family protease (papain-like protease, PLP) domain was responsible for processing the aminoterminal non-structural protein (nsp) from the replicase polyprotein [2À3] . Analysis of the N-terminal region of the replicase polyprotein of SARS-CoV revealed only one PLP domain, termed PLpro, which was shown to process the nsp1/2, nsp2/3 and nsp3/4 cleavage sites using the LXGG recognition motif [18] . Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme abstract: The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 494 is Coronavirus papain-like endopeptidases. Keywords: Coronavirus, Severe acute respiratory syndrome, SARS-CoV, polyprotein processing, ubiquitin-like domain, noncovalent protease inhibitors, de-ubiquitination, DUB, ISG-15, de-ISGylation. url: https://api.elsevier.com/content/article/pii/B9780123822192004932 doi: 10.1016/b978-0-12-382219-2.00493-2 id: cord-313076-531wksez author: Rauch, J. N. title: CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population date: 2020-08-07 words: 5576.0 sentences: 313.0 pages: flesch: 54.0 cache: ./cache/cord-313076-531wksez.txt txt: ./txt/cord-313076-531wksez.txt summary: Our results substantiate that large, population-level asymptomatic screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPRand PCR-based assays indicate expanded options for surveillance testing The objectives of our study were to: (i) establish the prevalence of asymptomatic SARS-CoV2 infection in a university population, (ii) assess for any dynamic change associated with the changing community conditions related to NPIs, and (iii) systematically compare the performance of our newly developed CRISPR-based test alongside that of the established, CDC-recommended reference testing by RT-qPCR. We used two assays to detect SARS-CoV-2 genomes in the collected OP swab samples: a CRISPR-based method we recently developed at UCSB known as CREST 23 , and the RT-qPCR test recommended by the CDC 24 (Sup. Fig. abstract: Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission of SARS-CoV-2 by asymptomatic people is thought to be the underlying cause of a large proportion of new infections. However, the local prevalence of asymptomatic and pre-symptomatic carriers of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence of asymptomatic SARS-CoV-2 infection on a university campus in California. Second, we sought to assess the changes in viral prevalence associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic persons. Methods: We enrolled 1,808 asymptomatic persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence of the virus, calculated using the confirmed cases, was 0.74%. The average age of our sample population was 28.33 (18-75) years, and the average age of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence, in a young and asymptomatic population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing url: http://medrxiv.org/cgi/content/short/2020.08.06.20169771v1?rss=1 doi: 10.1101/2020.08.06.20169771 id: cord-340523-wujzihbn author: Ravelli, Angelo title: Kawasaki disease or Kawasaki syndrome? date: 2020-06-22 words: 2158.0 sentences: 115.0 pages: flesch: 43.0 cache: ./cache/cord-340523-wujzihbn.txt txt: ./txt/cord-340523-wujzihbn.txt summary: 3 4 However, between April and May 2020, a rise in the number of children and adolescents with an acute multisystem hyperinflammatory state fulfilling full or partial criteria for Kawasaki disease (KD), 5 although frequently accompanied by unusual or less common symptoms, such as abdominal pain, diarrhoea and myocardial failure, was noticed in European and North American countries or regions mostly hit by the COVID-19 pandemic. One month later, Riphagen et al 6 described the features of eight children with the aforementioned hyperinflammatory syndrome, which presented with clinical manifestations similar to atypical KD, together with prominent gastrointestinal symptoms, and progressed towards multiorgan involvement and severe shock, requiring admission to the Intensive Care Unit (ICU) and haemodynamic support. Interim guidance on Kawasaki disease and acute multisystem inflammatory syndrome in children and adolescents in the current emergency scenario of SARS-CoV-2 infection Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort abstract: nan url: https://doi.org/10.1136/annrheumdis-2020-218110 doi: 10.1136/annrheumdis-2020-218110 id: cord-350557-7i7122zi author: Rawlings, Stephen A title: No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date: 2020-08-07 words: 1750.0 sentences: 115.0 pages: flesch: 57.0 cache: ./cache/cord-350557-7i7122zi.txt txt: ./txt/cord-350557-7i7122zi.txt summary: We evaluated the presence and level of SARS-CoV-2 RNA in semen, nasal secretion, and saliva collected after confirmed infection. SARS-CoV-2 RNA was not detected in semen 6–17 days after the onset of symptoms despite concomitant shedding in oral secretions. Here, we evaluated the presence and level of SARS-CoV-2 in paired semen, nasal secretion, and saliva samples collected in the short and medium term after confirmed SARS-CoV-2 symptomatic infections. Before enrollment, 5/6 participants tested positive for SARS-CoV-2 RNA on NP swab samples collected within 1-3 days following the onset of symptoms. Upon enrollment in the study, the diagnosis of active SARS-CoV-2 infection was confirmed by positive PCR on NP swab on day 6 post-symptom onset. We found no evidence of SARS-CoV-2 in semen collected 6-17 days after the onset of symptoms despite all men having concomitant shedding of virus in oral secretions up to 792 copies/µL. abstract: RNA viruses (eg, Zika, Ebola, HIV) are often shed in male genital secretions. We evaluated the presence and level of SARS-CoV-2 RNA in semen, nasal secretion, and saliva collected after confirmed infection. SARS-CoV-2 RNA was not detected in semen 6–17 days after the onset of symptoms despite concomitant shedding in oral secretions. url: https://www.ncbi.nlm.nih.gov/pubmed/32875005/ doi: 10.1093/ofid/ofaa325 id: cord-307770-1igydu3y author: Rawson, Timothy M title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date: 2020-05-02 words: 2998.0 sentences: 266.0 pages: flesch: 45.0 cache: ./cache/cord-307770-1igydu3y.txt txt: ./txt/cord-307770-1igydu3y.txt summary: title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. abstract: BACKGROUND: To explore and describe the current literature surrounding bacterial/fungal co-infection in patients with coronavirus infection. METHODS: MEDLINE, EMBASE, and Web of Science were searched using broad based search criteria relating to coronavirus and bacterial co-infection. Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. Data describing bacterial/fungal co-infections, treatments, and outcomes were extracted. Secondary analysis of studies reporting antimicrobial prescribing in SARS-COV-2 even in the absence of co-infection was performed. RESULTS: 1007 abstracts were identified. Eighteen full texts reported bacterial/fungal co-infection were included. Most studies did not identify or report bacterial/fungal coinfection (85/140;61%). 9/18 (50%) studies reported on COVID-19, 5/18 (28%) SARS-1, 1/18 (6%) MERS, and 3/18 (17%) other coronavirus. For COVID-19, 62/806 (8%) patients were reported as experiencing bacterial/fungal co-infection during hospital admission. Secondary analysis demonstrated wide use of broad-spectrum antibacterials, despite a paucity of evidence for bacterial coinfection. On secondary analysis, 1450/2010 (72%) of patients reported received antimicrobial therapy. No antimicrobial stewardship interventions were described. For non-COVID-19 cases bacterial/fungal co-infection was reported in 89/815 (11%) of patients. Broad-spectrum antibiotic use was reported. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. Generation of prospective evidence to support development of antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic are urgently required. url: https://www.ncbi.nlm.nih.gov/pubmed/32358954/ doi: 10.1093/cid/ciaa530 id: cord-319469-fkuqs3ie author: Ray, A. title: Seroprevalence of anti-SARS-CoV-2 IgG antibody in hospitalized patients in a tertiary referral center in North India date: 2020-08-25 words: 2937.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-319469-fkuqs3ie.txt txt: ./txt/cord-319469-fkuqs3ie.txt summary: While there was no significant difference in the different age groups and socio-economic classes; residence in Delhi was associated with increased risk (relative risk of 3.62, 95% CI 1.59-8.21) Key Words: SARS-CoV-2 IgG Antibody, Seroprevalence, Hospitalized patient, COVID-19 Seroprevalence studies for SARS-CoV-2 have been conducted in different settings, including community(4)(5)(6)(7), special populations like parturients (8) , liver disease patients (9) , hemodialysis patients (10) , blood donors (11) , health care workers (12) (13) as well in hospitals (14) . In this study, the seroprevalence of SARS-CoV-2 IgG antibody in patients admitted to a major tertiary hospital in Delhi was estimated as well as characteristics of the seropositive patients vis-à-vis the seronegative patients were determined. . https://doi.org/10.1101/2020.08.22.20179937 doi: medRxiv preprint statistically significant difference in seroprevalence of anti-SARS-CoV-2 IgG antibodies were observed between patients admitted with or without comorbidities. abstract: Background: Seroprevalence of IgG antibodies against SARS-CoV-2 is an important tool to estimate the true extent of infection in a population. However, seroprevalence studies have been scarce in South East Asia including India, which, as of now, carries the third largest burden of confirmed cases in the world. The present study aimed to estimate the seroprevalence of the anti-SARS-CoV-2 IgG antibody among hospitalized patients at one of the largest government hospital in India. Method: This cross-sectional study, conducted at a tertiary care hospital in North India, recruited consecutive patients who were negative for SARS-CoV-2 by RT-PCR or CB-NAAT. Anti-SARS-CoV-2 IgG antibody levels targeting recombinant spike receptor-binding domain (RBD) protein of SARS CoV-2 were estimated in serum samples by the ELISA method. Results: A total of 212 hospitalized patients were recruited in the study with mean age (+/-SD) of 41.2 (+/-15.4) years and 55% male population. Positive serology against SARS CoV-2 was detected in 19.8% patients(95% CI 14.7-25.8). Residency in Delhi conferred a higher frequency of seropositivity 26.5% (95% CI 19.3-34.7) as compared to that of other states 8% (95% CI 3.0-16.4) with p-value 0.001. No particular age groups or socio-economic strata showed a higher proportion of seropositivity. Conclusion: Around, one-fifth of hospitalized patients, who were not diagnosed with COVID-19 before, demonstrated seropositivity against SARS-CoV-2. While there was no significant difference in the different age groups and socio-economic classes; residence in Delhi was associated with increased risk (relative risk of 3.62, 95% CI 1.59-8.21) Key Words: SARS-CoV-2 IgG Antibody, Seroprevalence, Hospitalized patient, COVID-19 url: https://doi.org/10.1101/2020.08.22.20179937 doi: 10.1101/2020.08.22.20179937 id: cord-290687-kc7t1y5o author: Ray, Soumi title: Susceptibility and Sustainability of India against CoVid19: a multivariate approach date: 2020-04-21 words: 4768.0 sentences: 303.0 pages: flesch: 60.0 cache: ./cache/cord-290687-kc7t1y5o.txt txt: ./txt/cord-290687-kc7t1y5o.txt summary: Materials and Methods: Data of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. Conclusions: Though depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation. We have considered life expectancy also to inspect its impact on the number of infected cases and deaths. In This article, the data of Bacillus Calmette-Guérin (BCG) vaccination has been compared with present death rate of different countries. These diseases have shown an impact on death rate in many countries which are badly affected by coronavirus. Negative minimum temperature, a specific range of maximum temperature, lack of BCG vaccination and tendency of other lungs diseases have shown some positive impact in increasing the number of CoVid19 cases and death. abstract: Purpose: We are currently in the middle of a global crisis. Covid19 pandemic has suddenly threatened the existence of human life. Till date, as no medicine or vaccine is discovered, the best way to fight against this pandemic is prevention. The impact of different environmental, social, economic and health parameters is unknown and under research. It is important to identify the factors which can weaken the virus, and the nations which are more vulnerable to this virus. Materials and Methods: Data of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. These are extracted from authentic online resources and published reports. Analysis is done to find the possible impact of each parameter on CoVid19. Results: CoVid19 has no linear correlation with any of the selected parameters, though few parameters have depicted non-linear relationship in the graphs. Further investigations have shown better result for some parameters. A combination of the parameters results in a better correlation with infection rate. Conclusions: Though depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation. url: http://medrxiv.org/cgi/content/short/2020.04.16.20066159v1?rss=1 doi: 10.1101/2020.04.16.20066159 id: cord-199630-2lmwnfda author: Ray, Sumanta title: Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date: 2020-07-05 words: 6389.0 sentences: 379.0 pages: flesch: 53.0 cache: ./cache/cord-199630-2lmwnfda.txt txt: ./txt/cord-199630-2lmwnfda.txt summary: Therefore, host-(1) We link existing high-quality, long-term curated and refined, large scale drug/protein -protein interaction data with (2) molecular interaction data on SARS-CoV-2 itself, raised only a handful of weeks ago, (3) exploit the resulting overarching network using most advanced, AI boosted techniques (4) for repurposing drugs in the fight against SARS-CoV-2 (5) in the frame of HDT based strategies. As for (3)-(5), we will highlight interactions between SARS-Cov-2-host protein and human proteins important for the virus to persist using most advanced deep learning techniques that cater to exploiting network data. As per our simulation study, a large fraction, if not the vast majority of the predictions establish true, hence actionable interactions between drugs on the one hand and SARS-CoV-2 associated human proteins (hence of use in HDT) on the other hand. abstract: Coronavirus Disease 2019 (COVID-19) has been creating a worldwide pandemic situation. Repurposing drugs, already shown to be free of harmful side effects, for the treatment of COVID-19 patients is an important option in launching novel therapeutic strategies. Therefore, reliable molecule interaction data are a crucial basis, where drug-/protein-protein interaction networks establish invaluable, year-long carefully curated data resources. However, these resources have not yet been systematically exploited using high-performance artificial intelligence approaches. Here, we combine three networks, two of which are year-long curated, and one of which, on SARS-CoV-2-human host-virus protein interactions, was published only most recently (30th of April 2020), raising a novel network that puts drugs, human and virus proteins into mutual context. We apply Variational Graph AutoEncoders (VGAEs), representing most advanced deep learning based methodology for the analysis of data that are subject to network constraints. Reliable simulations confirm that we operate at utmost accuracy in terms of predicting missing links. We then predict hitherto unknown links between drugs and human proteins against which virus proteins preferably bind. The corresponding therapeutic agents present splendid starting points for exploring novel host-directed therapy (HDT) options. url: https://arxiv.org/pdf/2007.02338v1.pdf doi: nan id: cord-276132-tv5y1eqc author: Ray, Upasana title: COVID-19: The Impact in Oncology Care date: 2020-10-23 words: 5696.0 sentences: 243.0 pages: flesch: 39.0 cache: ./cache/cord-276132-tv5y1eqc.txt txt: ./txt/cord-276132-tv5y1eqc.txt summary: The COVID-19 pandemic has imposed a critical challenge to the current oncology care and practices including late diagnoses, delayed anti-cancer treatment, and static clinical trials. Delaying anti-cancer treatment in the ongoing pandemic cannot be recommended as a sensible choice to reduce the associated infection risk in patients. The American Society of Clinical Oncology (ASCO) recommends that in cancer patients diagnosed with the infection, the immunosuppressive therapies should be withheld until the symptoms resolve like complete remission of fever without use of antipyretics along with a negative COVID-19 test. Nevertheless, contact limitation and physical distancing guidelines continue to be an important part of the cancer treatment strategies during the pandemic in order to protect the patients, health-care personnel and non-COVID-19 patients being treated in the same organization. A practical approach to the management of cancer patients during the novel coronavirus disease 2019 (COVID-19) pandemic: an international collaborative group Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan abstract: The COVID-19 pandemic has imposed a critical challenge to the current oncology care and practices including late diagnoses, delayed anti-cancer treatment, and static clinical trials. With the increasing risk of cancer patients acquiring infection during receiving the essential care, the debate ensues on how to balance the risk factors and benefits out of the oncologic emergencies in cancer patients. In this review article, we have focused on the current global re-organization of the integrity and effectiveness of the treatment modalities depending on the patient and cancer-specific urgencies while minimizing exposure to the infection. In this review, we addressed how the worldwide oncology community is united to share therapy schemes and the best possible guidelines to help cancer patients, and to strategize and execute therapy/trial protocols. This review provides collective knowledge on the current re-structuring of the general framework that prioritizes cancer care with the available exploitation of the reduced resources and most importantly the unparalleled levels of companionship as a large health care community towards the need to offer the best possible care to the patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33134842/ doi: 10.1007/s42399-020-00592-7 id: cord-310464-lkdkdque author: Rayko, Mikhail title: Quality control of low-frequency variants in SARS-CoV-2 genomes date: 2020-05-07 words: 1702.0 sentences: 109.0 pages: flesch: 58.0 cache: ./cache/cord-310464-lkdkdque.txt txt: ./txt/cord-310464-lkdkdque.txt summary: During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. As a result of the collaborative efforts of the researchers worldwide, on April 14, 2020 it contained over 8,000 SARS-nCoV-2 genomes from different countries, sequenced and assembled using various technologies and approaches. GISAID database curators do a tremendous job of filtering submitted sequences, but sometimes it is difficult to distinguish real variants from errors, especially at the lack of information about coverage. Dataset 8,053 full-length (>29,000 bp) sequences of the SARS-CoV-2 were downloaded from the GISAID database ( www.epicov.org ) on April 14, 2020, including 5,556 genomes marked as "high coverage". Full table with percentage of singleton-containing genomes depending on sequencing and assembly method. abstract: During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. We explored the variations in the submitted genomes and found a significant number of variants that can be seen only in one submission (singletons). While it is not completely clear whether these variants are erroneous or not, these variants show lower transition/transversion ratio. These singleton variants may influence the estimations of the viral mutation rate and tree topology. We suggest that genomes with multiple singletons even marked as high-covered should be considered with caution. We also provide a simple script for checking variant frequency against the database before submission. url: https://doi.org/10.1101/2020.04.26.062422 doi: 10.1101/2020.04.26.062422 id: cord-264646-d7qexyav author: Raza, Syed Shadab title: Mesenchymal Stem Cells: A new front emerge in COVID19 treatment: Mesenchymal Stem Cells therapy for SARS-CoV2 viral infection date: 2020-07-15 words: 2773.0 sentences: 143.0 pages: flesch: 43.0 cache: ./cache/cord-264646-d7qexyav.txt txt: ./txt/cord-264646-d7qexyav.txt summary: Currently, treating coronavirus disease 2019 (COVID19) patients, particularly those afflicted with severe pneumonia, is challenging, as no effective pharmacotherapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exists. Based on results from preliminary clinical investigations, one predicts that MSCs therapy for SARS-CoV-2 infected patients is safe and effective although multiple clinical trials with a protracted follow-up will be necessary to determine the long term effects of the treatment on COVID19 patients. Further, MSCs exhibit broad immune regulatory function, which makes them suitable for anti-viral therapy as safety and effectiveness of these cells have been documented in clinical trials of severe lung infections [9, 10, 11] . The first study was a case report [12] , in which a critically ill 65-year-old female with severe pneumonia, respiratory failure, moderate anemia, hypertension, and multiple organ failure received three infusions of umbilical cord MSCs (UCMSCs, 5X10 7 cells/infusion), three days apart. abstract: Currently, treating coronavirus disease 2019 (COVID19) patients, particularly those afflicted with severe pneumonia, is challenging, as no effective pharmacotherapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exists. Severe pneumonia is recognized as a clinical syndrome, characterized by hyper induction of proinflammatory cytokine production, which can induce organ damage followed by edema, dysfunction of air exchange, acute respiratory distress syndrome, acute cardiac injury, secondary infection, and increased mortality. Owing to the immunoregulatory and differentiation potential of mesenchymal stem cells (MSCs), we aimed to outline current insights into the clinical application of MSCs in the patients of COVID19. Based on results from preliminary clinical investigations, one predicts that MSCs therapy for SARS-CoV-2 infected patients is safe and effective although multiple clinical trials with a protracted follow-up will be necessary to determine the long term effects of the treatment on COVID19 patients. url: https://www.sciencedirect.com/science/article/pii/S1465324920307891?v=s5 doi: 10.1016/j.jcyt.2020.07.002 id: cord-312677-rwznqiib author: Razmi, Mahdieh title: Immunomodulatory-Based Therapy as a Potential Promising Treatment Strategy against Severe COVID-19 Patients: A Systematic Review date: 2020-08-29 words: 6545.0 sentences: 306.0 pages: flesch: 39.0 cache: ./cache/cord-312677-rwznqiib.txt txt: ./txt/cord-312677-rwznqiib.txt summary: Sixty-six publications and 111 clinical trials were recognized as eligible, reporting the efficacy of the immunomodulatory agents, including corticosteroids, hydroxychloroquine, passive and cytokine-targeted therapies, mesenchymal stem cells, and blood-purification therapy, in COVID-19 patients. Various studies have focused on the efficacy of the immunomodulatory agents including corticosteroids, hydroxychloroquine or chloroquine, cytokine-targeted therapies (e.g., anakinra, siltuximab, or tocilizumab), passive immunotherapy (convalescent plasma and intravenous immunoglobulin), mesenchymal stem cells, and bloodpurification therapy, mostly as adjuvant therapy for treatment of the patients with severe COVID-19 and partly have reported promising outcomes. Included clinical studies with 1-63 participants have shown that both antagonists, specially TCZ, are effective in reducing the mortality rate specially in the severely ill patients, improving the symptoms including fever resolution, oxygenation and resolved CT scans, reducing the inflammation markers (ferritin, CRP, and D-dimer), weaning from the ICU hospitalization and ventilation, and dampening the risk of disease progression to ARDS by mitigating the cytokine storm in the NCP patients [60, 62] , as applied for CRS controlling in the CAR-T therapy [90] . abstract: The global panic of the novel coronavirus disease 2019 (COVID-19) triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an urgent requirement for effective therapy. COVID-19 infection, especially in severely ill patients, is likely to be associated with immune dysregulation, prompting the development of novel treatment approaches. Therefore, this systematic review was designed to assess the available data regarding the efficacy of the immunomodulatory drugs used to manage COVID-19. A systematic literature search was carried out up to May 27, 2020, in four databases (PubMed, Scopus, Web of Science, and Embase) and also Clinicaltrials.gov. Sixty-six publications and 111 clinical trials were recognized as eligible, reporting the efficacy of the immunomodulatory agents, including corticosteroids, hydroxychloroquine, passive and cytokine-targeted therapies, mesenchymal stem cells, and blood-purification therapy, in COVID-19 patients. The data were found to be heterogeneous, and the clinical trials were yet to post any findings. Medicines were found to regulate the immune system by boosting the innate responses or suppressing the inflammatory reactions. Passive and cytokine-targeted therapies and mesenchymal stem cells were mostly safe and could regulate the disease much better. These studies underscored the significance of severity profiling in COVID-19 patients, along with appropriate timing, duration, and dosage of the therapies. Therefore, this review indicates that immunomodulatory therapies are potentially effective for COVID-19 and provides comprehensive information for clinicians to fight this outbreak. However, there is no consensus on the optimal therapy for COVID-19, reflecting that the immunomodulatory therapies still warrant further investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/32896750/ doi: 10.1016/j.intimp.2020.106942 id: cord-350437-dq1il88y author: Reale, Maria Lucia title: SARS-CoV-2 Infection in Cancer Patients: A Picture of an Italian Onco-Covid Unit date: 2020-08-19 words: 4177.0 sentences: 216.0 pages: flesch: 47.0 cache: ./cache/cord-350437-dq1il88y.txt txt: ./txt/cord-350437-dq1il88y.txt summary: This retrospective study aims to collect epidemiological, clinical, laboratory, and therapeutic data from SARS-CoV-2 positive cancer patients hospitalized at the Onco-Covid unit in San Luigi Gonzaga Hospital, Italy, one of the few oncological wards for cancer patients with SARS-Cov-2 infection, in order to provide a deeper insight into the clinical evolution of infection in cancer patients, particularly in lung cancer patients. This retrospective study included all SARS-CoV-2 oncological patients accepted at the Onco-Covid Unit at San Luigi Gonzaga Hospital, Orbassano, between March 27th and April 19th 2020. The mean length of hospitalization at data cut-off was 30 days ±14 (0-53), while it resulted 16 ± 9 days (0-37) when calculated from COVID 19 positivity (characteristics and outcomes of individual patients included in the analysis are reported in Supplementary Table 2) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: Background: The world, and Italy on the front lines, has experienced a major medical emergency due to the novel coronavirus outbreak. Cancer patients are one of the potentially most vulnerable cohorts of people, but data about their management are still few. Patients and Methods: In this monocentric retrospective study we included all SARS-CoV-2 oncological patients accepted, between March 27th and April 19th 2020, at the Onco-COVID Unit at San Luigi Gonzaga Hospital, one of the few Italian oncological-COVID wards. Data were obtained from medical records. Results: Eighteen cancer patients with COVID-19 were included. The mean (±SD) age of patients was 67 ± 14 years, 89% were men. Seven (39%) developed infection in communities and 11 (61%) during hospitalization. Lung cancer was the most frequent type of cancer (10, 56%). Seven patients (39%) were symptomatic for COVID-19 at the time of diagnosis and symptoms began 2 (±2) days before. The most common were shortness of breath and diarrhea. Fever was present in 5 patients (28%). Among the 11 asymptomatic patients, 8 (73%) became symptomatic during the hospitalization (mean time of symptoms onset 4 days ±4). Six patients (33%) were on active anti-tumor treatment: 2 (33%) received anti-tumor therapy within 2 weeks before the infection diagnosis and 2 (33%) continued oncological treatment after SARS-CoV-2 positivity. Eight (44%) patients died within a mean of 12 days (±8) from the infection diagnosis. Conclusions: Our series confirms the high mortality among cancer patients with COVID-19. The presence of asymptomatic cases evidences that typical symptoms and fever are not the only parameters to suspect the infection. The Onco-Covid unit suggests the importance of a tailored and holistic approach, even in this difficult situation. url: https://doi.org/10.3389/fonc.2020.01722 doi: 10.3389/fonc.2020.01722 id: cord-293557-jcgc93it author: Recalde, Borja title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients date: 2020-08-23 words: 1412.0 sentences: 93.0 pages: flesch: 47.0 cache: ./cache/cord-293557-jcgc93it.txt txt: ./txt/cord-293557-jcgc93it.txt summary: title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients In December 2019, an outbreak of severe acute respiratory syndrome associated to SARS-CoV2 was reported in Wuhan, China. To date, little is known on histopathological findings in patients infected with the new SARS-CoV2. Postmortem multiorgan biopsies in 10 patients who died with SARS COV-2 infection were performed after oral authorisation of a first-degree relative. In this report, we describe the histopathology of lung damage in COVID-19 with DAD in all lung samples, associated with medium size arterial thrombosis in four cases, and the presence of viral RNA in all organs. It is remarkable that 9 out of the 10 patients had at least one organ with significant amount of SARS-CoV2 RNA, being most prevalent in lung tissue. Pathological findings of COVID-19 associated with acute respiratory distress syndrome abstract: In December 2019, an outbreak of severe acute respiratory syndrome associated to SARS-CoV2 was reported in Wuhan, China. To date, little is known on histopathological findings in patients infected with the new SARS-CoV2. Lung histopathology shows features of acute and organising diffuse alveolar damage. Subtle cellular inflammatory infiltrate has been found in line with the cytokine storm theory. Medium-size vessel thrombi were frequent, but capillary thrombi were not present. Despite the elevation of biochemical markers of cardiac injury, little histopathological damage could be confirmed. Viral RNA from paraffin sections was detected at least in one organ in 90% patients. url: https://doi.org/10.1136/thoraxjnl-2020-215577 doi: 10.1136/thoraxjnl-2020-215577 id: cord-299333-qu0bmov5 author: Reddy, Gireesh B. title: Clinical Characteristics and Multisystem Imaging Findings of COVID-19: An Overview for Orthopedic Surgeons date: 2020-08-17 words: 4412.0 sentences: 235.0 pages: flesch: 37.0 cache: ./cache/cord-299333-qu0bmov5.txt txt: ./txt/cord-299333-qu0bmov5.txt summary: Since December 2019, infections with severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), a novel betacoronavirus strain responsible for coronavirus disease 2019 (COVID19) , rapidly progressed from an isolated cluster of cases in the Hubei province of east central China to a pandemic, with significant global health and economic repercussions [4, 5, 10, 24, 25, 27, 28, 44, 58, 80, 91] . Early reports from Italy and China indicated that although pulmonary diseases including ARDS and diffuse pneumonia comprise the predominant lethal complications of COVID-19, patients have also presented with or developed significant cardiac signs and symptoms [50] . COVID-19 musculoskeletal and neurologic manifestations are being reported with increased frequency, particularly in patients with more severe respiratory disease, indicating coronavirus neurotropism possibly directly related with higher viral loads, which are now detectable in cerebrospinal fluid [20] . abstract: The COVID-19 pandemic holds widespread implications for global public health, economies, societies, and the practice of orthopedic surgery. As our knowledge of the transmissibility of SARS-CoV-2 and the symptomatology and management of COVID-19 expands, orthopedic surgeons must remain up to date on the latest medical evidence and surgical perspectives. While COVID-19 primarily manifests with pulmonary symptoms, cardiovascular, neurologic, and other major organ systems may also be affected and present with hallmark imaging findings. This article reviews initial and emerging literature on clinical characteristics and imaging findings of COVID-19. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11420-020-09775-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11420-020-09775-3 doi: 10.1007/s11420-020-09775-3 id: cord-272318-8yfg1j0o author: Reddy, Sujan T. title: Cerebrovascular Disease in Patients with COVID-19: A Review of the Literature and Case Series date: 2020-06-11 words: 3392.0 sentences: 197.0 pages: flesch: 41.0 cache: ./cache/cord-272318-8yfg1j0o.txt txt: ./txt/cord-272318-8yfg1j0o.txt summary: To further characterize cerebrovascular disease (CVD) in COVID-19, we review the current literature of published cases and additionally report the clinical presentation, laboratory and diagnostic testing results of 12 cases with COVID-19 infection and concurrent CVD from two academic medical centers in Houston, TX, USA, between March 1 and May 10, 2020. To date, few studies have reported cerebrovascular complications in COVID-19 [3, 4] and 4 small case series have described the clinical and laboratory findings in patients with COVID-19 and concurrent stroke [5] [6] [7] [8] . We review the current literature of published cases and describe our experience of 12 cases with COVID-19 infection and concurrent cerebrovascular disease (CVD) to highlight the clinical presentation and proposed mechanisms of central nervous system (CNS) involvement by SARS-CoV-2. Additionally, we performed a retrospective chart review of all hospitalized cases with confirmed COVID-19 infection (SARS-CoV-2 RT-PCR positive) and CVD (ischemic and hemorrhagic stroke) between March 1 and May 10, 2020 seen at two comprehensive stroke centers in Houston, TX, USA. abstract: COVID-19 has been associated with a hypercoagulable state causing cardiovascular and neurovascular complications. To further characterize cerebrovascular disease (CVD) in COVID-19, we review the current literature of published cases and additionally report the clinical presentation, laboratory and diagnostic testing results of 12 cases with COVID-19 infection and concurrent CVD from two academic medical centers in Houston, TX, USA, between March 1 and May 10, 2020. To date, there are 12 case studies reporting 47 cases of CVD in COVID-19. However, only 4 small case series have described the clinical and laboratory findings in patients with COVID-19 and concurrent stroke. Viral neurotropism, endothelial dysfunction, coagulopathy and inflammation are plausible proposed mechanisms of CVD in COVID-19 patients. In our case series of 12 patients, 10 patients had an ischemic stroke, of which 1 suffered hemorrhagic transformation and two had intracerebral hemorrhage. Etiology was determined to be embolic without a clear cause identified in 6 ischemic stroke patients, while the remaining had an identifiable source of stroke. The majority of the patients had elevated inflammatory markers such as D-dimer and interleukin-6. In patients with embolic stroke of unclear etiology, COVID-19 may have played a direct or indirect role in the processes that eventually led to the strokes while in the remaining cases, it is unclear if infection contributed partially or was an incidental finding. url: https://www.ncbi.nlm.nih.gov/pubmed/32647526/ doi: 10.1159/000508958 id: cord-293559-c78wcr8m author: Rego, Gabriel N. A. title: Current Clinical Trials Protocols and the Global Effort for Immunization against SARS-CoV-2 date: 2020-08-25 words: 9752.0 sentences: 506.0 pages: flesch: 53.0 cache: ./cache/cord-293559-c78wcr8m.txt txt: ./txt/cord-293559-c78wcr8m.txt summary: Two purified inactivated SARS-CoV-2 vaccine candidates, an mRNA-based vaccine mRNA1273, and the chimpanzee adenoviral vaccine ChAdOx1 are currently in phase III clinical trials in the respective countries Brazil, the United Arab Emirates, the USA, and the United Kingdom. Thus, during the pandemic caused by COVID-19, several vaccine candidates with attenuated virus, encoding, or presenting SARS-CoV-2 antigens have been developed globally, reaching clinical trial phases I or II for the evaluation of their safety and immunogenicity. Six protocols are developing phase II and/or III clinical trials using the chimpanzee adenoviral vector ChAdOx1 [50] [51] [52] , purified inactivated SARS-CoV-2 vaccine [53, 54] , and mRNA-1273 vaccine [55] . A Phase I Clinical Trial to Evaluate the Safety, Tolerance and Preliminary Immunogenicity of Different Doses of a SARS-CoV-2 mRNA Vaccine in Population Aged 18-59 Years and 60 Years and Above abstract: Coronavirus disease 2019 (COVID-19) is the biggest health challenge of the 21st century, affecting millions of people globally. The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has ignited an unprecedented effort from the scientific community in the development of new vaccines on different platforms due to the absence of a broad and effective treatment for COVID-19 or prevention strategy for SARS-CoV-2 dissemination. Based on 50 current studies selected from the main clinical trial databases, this systematic review summarizes the global race for vaccine development against COVID-19. For each study, the main intervention characteristics, the design used, and the local or global center partnerships created are highlighted. Most vaccine developments have taken place in Asia, using a viral vector method. Two purified inactivated SARS-CoV-2 vaccine candidates, an mRNA-based vaccine mRNA1273, and the chimpanzee adenoviral vaccine ChAdOx1 are currently in phase III clinical trials in the respective countries Brazil, the United Arab Emirates, the USA, and the United Kingdom. These vaccines are being developed based on a quickly formed network of collaboration. url: https://doi.org/10.3390/vaccines8030474 doi: 10.3390/vaccines8030474 id: cord-268390-npuvodd4 author: Rehman, Aziz ul title: The role of primary and secondary bio-molecules in optical diagnosis of pandemic COVID-19 outbreak date: 2020-08-17 words: 1277.0 sentences: 64.0 pages: flesch: 42.0 cache: ./cache/cord-268390-npuvodd4.txt txt: ./txt/cord-268390-npuvodd4.txt summary: • Raman and fluorescence signature of ACE-2 specific proteins is the basis for real time detection of COVID-19. This letter to the editor aims to introduce primary and secondary biomarkers whose reflectance, transmittance and fluorescence signals can be used for optical diagnosis of COVID-19 to the scientific community and persuade to build portable, cost effective, label free and real time optical devices for its detection. Keeping in view the epidemic nature of COVID-19, we need early stage, cost effective, real time diagnosis and portable devices to detect this disease so that treatment can be started to save the vulnerable population. Similarly, nucleic acid and protein bound coenzymes molecules like NADH, FAD have their own specific fluorescence biomarkers when excited with UV-A light [13] and can be used for label free detection of COVID-19 on early stages employing portable optical detection systems. abstract: • Primary and secondary biomarkers for optical diagnosis in of COVID-19 infected patients for early diagnosis of disease. • Raman and fluorescence signature of ACE-2 specific proteins is the basis for real time detection of COVID-19. • Label free detection. • Portable optical devices for fast screening of COVID-19 patients. url: https://api.elsevier.com/content/article/pii/S1572100020303070 doi: 10.1016/j.pdpdt.2020.101953 id: cord-324644-sz5n7a5z author: Rehman, Mahin title: Atypical Manifestation of COVID-19-Induced Myocarditis date: 2020-06-18 words: 1906.0 sentences: 91.0 pages: flesch: 45.0 cache: ./cache/cord-324644-sz5n7a5z.txt txt: ./txt/cord-324644-sz5n7a5z.txt summary: There was a case report that described a patient with COVID-19 with regional wall motion abnormalities who had a biopsy consistent with lymphocytic myocarditis but histopathological and viral genomic polymerase chain reaction (PCR) analysis of the biopsy did not reveal the SARS-CoV-2 viral genome to be present within the myocytes [3] . With this report, we aim to highlight an atypical presentation of COVID-19 (SARS-CoV-2)induced myocarditis as this patient was completely afebrile and had no respiratory symptoms, both of which are typical characteristics. Current consensus around COVID-19-induced myocardial injury is to maintain conservative management especially in those without suspected acute coronary syndrome (ACS) who have mild troponin elevation, as in our young patient. COVID-19-induced myocardial injury can present as a STEMI or non-STEMI (given the evidence of troponin leak) and without concurrent febrile illness or respiratory symptoms of the disease. abstract: We present a case of a 39-year-old male who presented with chest pain without fever or respiratory symptoms. Troponins were elevated and electrocardiogram (ECG) was inconclusive for ST-elevation myocardial infarction (STEMI). Angiography revealed normal coronaries and the patient was found to be coronavirus disease 2019 (COVID-19) positive; he was diagnosed with COVID-19 myocarditis. With the global pandemic, more cases are emerging regarding myocardial injury induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although COVID-19 manifests primarily as respiratory disease, few cases of cardiac injury without respiratory involvement or febrile illness have been reported. This case illustrates that COVID-19 can present atypically and affect an isolated non-respiratory organ system. url: https://www.ncbi.nlm.nih.gov/pubmed/32577331/ doi: 10.7759/cureus.8685 id: cord-340666-zl9pp2h3 author: Reifer, Josh title: SARS-CoV-2 IgG antibody responses in New York City date: 2020-07-21 words: 764.0 sentences: 56.0 pages: flesch: 60.0 cache: ./cache/cord-340666-zl9pp2h3.txt txt: ./txt/cord-340666-zl9pp2h3.txt summary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a strain of coronavirus that causes coronavirus disease 2019 (Covid-19) and has been declared a global pandemic by the World Health Organization. Additionally, for a subset of patients, we report on the correlation between SARS-CoV-2 patient symptom severity and level of SARS-CoV-2 IgG antibody found in the patient sample. We next sought to evaluate whether semi-quantitative SARS-CoV-2 IgG antibody levels were correlated to severity of symptoms as measured by the SSI. Levels of SARS-CoV-2 IgG antibody are plotted against SSI in Figure 2A . A linear regression analysis of the data indicates that SARS-CoV-2 IgG antibody levels are positively correlated with SSI (p-value < 0.01). In addition, we tested 28,523 patient specimens for SARS-CoV-2 IgG antibody levels for whom we did not obtain a SSI. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease Antibody responses to SARS-CoV-2 in patients with COVID-19 abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a strain of coronavirus that causes coronavirus disease 2019 (Covid-19) and has been declared a global pandemic by the World Health Organization. Total cases of SARS-CoV-2 worldwide exceed 10.2 million, with over 503,000 deaths recorded. Little is known about the body's immune response to SARS-CoV-2 infection. In this paper, we describe SARS-CoV-2 IgG antibody responses in 28,523 patients from the New York City metropolitan area and report a SARS-CoV-2 IgG positivity rate of 44%, indicating the widespread nature of the pandemic in the city and state of New York. Additionally, for a subset of patients, we report on the correlation between SARS-CoV-2 patient symptom severity and level of SARS-CoV-2 IgG antibody found in the patient sample. url: https://www.ncbi.nlm.nih.gov/pubmed/32777699/ doi: 10.1016/j.diagmicrobio.2020.115128 id: cord-346325-grt67p73 author: Reilev, M. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 words: 4655.0 sentences: 258.0 pages: flesch: 48.0 cache: ./cache/cord-346325-grt67p73.txt txt: ./txt/cord-346325-grt67p73.txt summary: Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. In this population-based study of a Danish COVID-19 cohort capturing all individuals with a positive PCR test for SARS-CoV-2 in Denmark, we provide nationwide data on clinical characteristics and predictors of hospitalization and death for all SARS-CoV-2 PCR-positive cases identified from February 27 th , 2020 to April 30 th , 2020. In this nationwide cohort of SARS-CoV-2 PCR positive cases and test-negative individuals from the general population in Denmark, we found that older age (e.g., >70 years), male sex, and number of comorbidities were risk factors for hospitalization and death. In this first nationwide population-based study, increasing age, sex, and number and type of comorbidities were closely associated with hospitalization requirement and death in SARS-CoV-2 PCR positive cases. abstract: Objective To provide population-level knowledge on individuals at high risk of severe and fatal coronavirus disease 2019 (COVID-19) in order to inform targeted protection strategies in the general population and appropriate triage of hospital contacts. Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. Main Outcomes and Measures We examined characteristics and predictors of inpatient hospitalization versus community-management, and death versus survival, adjusted for age-, sex- and number of comorbidities. Results We identified 9,519 SARS-CoV-2 PCR-positive cases of whom 78% were community-managed, 22% were hospitalized (3.2% at an intensive care unit) and 5.5% had died within 30 days. Median age varied from 45 years (interquartile range (IQR) 31-57) among community-managed cases to 82 years (IQR 75-89) among those who died. Age was a strong predictor of fatal disease (odds ratio (OR) 14 for 70-79-year old, OR 26 for 80-89-year old, and OR 82 for cases older than 90 years, when compared to 50-59-year old and adjusted for sex and number of comorbidities). Similarly, the number of comorbidities was strongly associated with fatal disease (OR 5.2, for cases with [≥]4 comorbidities versus no comorbidities), and 82% of fatal cases had at least 2 comorbidities. A wide range of major chronic diseases were associated with hospitalization with ORs ranging from 1.3-1.4 (e.g. stroke, ischemic heart disease) to 2.2-2.7 (e.g. heart failure, hospital-diagnosed kidney disease, chronic liver disease). Similarly, chronic diseases were associated with mortality with ORs ranging from 1.2-1.3 (e.g. ischemic heart disease, hypertension) to 2.4-2.7 (e.g. major psychiatric disorder, organ transplantation). In the absence of comorbidities, mortality was relatively low (5% or less) in persons aged up to 80 years. Conclusions and Relevance In this first nationwide population-based study, increasing age and number of comorbidities were strongly associated with hospitalization requirement and death in COVID-19. In the absence of comorbidities, the mortality was, however, lowest until the age of 80 years. These results may help in accurate identification, triage and protection of high-risk groups in general populations, i.e. when reopening societies. url: https://doi.org/10.1101/2020.05.24.20111823 doi: 10.1101/2020.05.24.20111823 id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 words: 15712.0 sentences: 976.0 pages: flesch: 44.0 cache: ./cache/cord-331673-xv1tcugl.txt txt: ./txt/cord-331673-xv1tcugl.txt summary: For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). abstract: [Image: see text] The SARS-Cov-2 pandemic has spread worldwide during 2020, setting up an uncertain start of this decade. The measures to contain infection taken by many governments have been extremely severe by imposing home lockdown and industrial production shutdown, making this the biggest crisis since the second world war. Additionally, the continuous colonization of wild natural lands may touch unknown virus reservoirs, causing the spread of epidemics. Apart from SARS-Cov-2, the recent history has seen the spread of several viral pandemics such as H2N2 and H3N3 flu, HIV, and SARS, while MERS and Ebola viruses are considered still in a prepandemic phase. Hard nanomaterials (HNMs) have been recently used as antimicrobial agents, potentially being next-generation drugs to fight viral infections. HNMs can block infection at early (disinfection, entrance inhibition) and middle (inside the host cells) stages and are also able to mitigate the immune response. This review is focused on the application of HNMs as antiviral agents. In particular, mechanisms of actions, biological outputs, and limitations for each HNM will be systematically presented and analyzed from a material chemistry point-of-view. The antiviral activity will be discussed in the context of the different pandemic viruses. We acknowledge that HNM antiviral research is still at its early stage, however, we believe that this field will rapidly blossom in the next period. url: https://doi.org/10.1021/acsnano.0c04117 doi: 10.1021/acsnano.0c04117 id: cord-321208-zemex8bf author: Reina, Jordi title: Evaluación de diferentes genes en la detección por RT-PCR del SARS-CoV-2 en muestras respiratorias y su evolución en la infección date: 2020-05-27 words: 999.0 sentences: 135.0 pages: flesch: 70.0 cache: ./cache/cord-321208-zemex8bf.txt txt: ./txt/cord-321208-zemex8bf.txt summary: En nuestro estudio el 96,5% de las primeras muestras positivas presentaron positividad en este gen y el 94% con el gen E, a pesar que su capacidad de detección es de unas 100 genomas-copias/reacción. Sin embargo, al analizar las segundas muestras se observa como la detección del gen E ha mostrado una disminución significativa, a pesar de que todavía el 42% de todos los pacientes seguían siendo positivos a los tres genes, frente al 84% de la primoinfección. Por ello podría afirmarse que para el primer diagnóstico de infección por SARS-CoV-2 debería utilizarse de forma preferentemente el gen E o el gen RpRd. Este mismo dato lo confirma el estudio comparativo de Nalla et al. Por ello se presenta un estudio prospectivo que evalúa la capacidad de amplificación de los tres genes del SARS-CoV-2 (E, RpRd y N) en el diagnóstico de infección por este virus. abstract: nan url: https://doi.org/10.37201/req/045.2020 doi: 10.37201/req/045.2020 id: cord-306390-pzzev8hd author: Reisinger, Emil C. title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest date: 2020-06-22 words: 1531.0 sentences: 180.0 pages: flesch: 57.0 cache: ./cache/cord-306390-pzzev8hd.txt txt: ./txt/cord-306390-pzzev8hd.txt summary: title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest Somit kann die Bestimmung der Antikörper gegen SARS-CoV-2 bei Müttern indirekt Auskunft über den Infektionsstatus bei deren Kindern geben. Für den in dieser Studie verwendeten ELISA-Test zum Nachweis von SARS-CoV-2-Antikörpern (Euroimmun) wird in der Literatur eine hohe Sensitivität und Spezifität angegeben [6] . In dieser Pilotstudie wurden 401 Mütter von Kindern im Alter von 1-10 Jahren als Sentinel untersucht, um die Prävalenz der Infektion mit SARS-CoV-2 auch bei Kindern abzuschätzen. Die Aussagekraft dieser Studie zur Prävalenz der Infektion mit SARS-CoV-2 bei Müttern ist durch die relativ geringe Fallzahl (5 % der Mütter mit schulpflichtigen Kindern in Rostock) limitiert. Da in dieser Studie durch die indirekte Immunfluoreszenz weder das positive Ergebnis des ELISA für IgG, noch die 11 positiven und 3 grenzwertigen Ergebnisse des ELISA für IgA bestätigt wurden, empfehlen wir, positive SARS-CoV-2-Antikörperbefunde in den hier verwendeten ELISA-Tests mittels Bestätigungstests (z. abstract: Background In children, the infection with SARS-CoV-2, the cause of COVID-19, tends to be clinically inapparent more often or less severe than in adults. The spread of this infection from children poses a danger to vulnerable adults. Therefore, child care institutions and schools currently are widely closed. Methods Since the status of infection tends to be congruent in mothers and their children, we tested 401 mothers of children between 1 and 10 years in the city of Rostock (State of Mecklenburg-Westpomerania, northeast of Germany), for the presence of RNA of SARS-CoV-2 in throat swabs, and of antibodies against SARS-CoV-2 in serum. Results In none of the mothers tested, RNA of this virus was detected in the throat swab. In the ELISA test, IgG antibodies were positive in one serum sample, IgA antibodies were positive in 11, and borderline in 3 serum samples. All 401 sera were negative in the indirect immunofluorescence test (IIFT) with FITC-labeled IgG, IgA, und IgM antibodies. Conclusion At the time of this study, neither SARS-CoV-2 RNA, nor specific antibodies against SARS-CoV-2 were detectable in the mothers tested in Rostock. url: https://www.ncbi.nlm.nih.gov/pubmed/32572869/ doi: 10.1055/a-1197-4293 id: cord-252857-vaq0kwln author: Rejdak, Konrad title: Adamantanes might be protective from COVID-19 in patients with neurological diseases: multiple sclerosis, parkinsonism and cognitive impairment date: 2020-04-30 words: 1227.0 sentences: 74.0 pages: flesch: 47.0 cache: ./cache/cord-252857-vaq0kwln.txt txt: ./txt/cord-252857-vaq0kwln.txt summary: We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson''s disease (n=5) or cognitive impairment (n=7). We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson''s disease (n=5) or cognitive impairment (n=7). Hereby we report on the result of a questionaire-based study performed to assess whether adamantanes could exert protective antiviral effect against COVID-19 among different neurological disease patients including multiple sclerosis, parkinsonism and cognitive impairment. In this study, twenty-two patients (10 with multiple sclerosis, 5 with Parkinson''s disease and 7 with cognitive impairment) who were tested positive for SARS-CoV-2 and were receiving treatment with either amantadine or memantine on stable registered doses (100mg q.d. and 10mg b.i.d, respectively) for at least 3 months prior to the infection exposure, were surveyed on their laboratory results and clinical status (remote contact with verbally received information). abstract: Facing the outbreak of coronavirus disease 2019 (COVID-19) pandemic, there is an urgent need to find protective or curable drugs to prevent or to stop the course of the coronavirus SARS-CoV-2 infection. Recent evidence accumulates that adamantanes, widely used in different neurological diseases, could be repurposed for COVID-19. We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson's disease (n=5) or cognitive impairment (n=7). In all patients infection with SARS-CoV-2 was confirmed by rtPCR of nasopharyngeal swabs. They were receiving treatment with either amantadine (n=15) or memantine (n=7) in stable registered doses. All of them had two-week quarantine since documented exposure and none of them developed clinical manifestations of infectious disease. They also did not report any significant changes in neurological status in the course of primary nervous system disease. Above results warrant further studies on protective effects of adamantanes against COVID-19 manifestation, especially in subjects suffering from neurological disease. url: https://www.sciencedirect.com/science/article/pii/S221103482030239X?v=s5 doi: 10.1016/j.msard.2020.102163 id: cord-263965-i8yutik6 author: Relf, Michael V. title: What''s Old is New! Similarities Between SARS-CoV-2 and HIV date: 2020-04-09 words: 1787.0 sentences: 97.0 pages: flesch: 61.0 cache: ./cache/cord-263965-i8yutik6.txt txt: ./txt/cord-263965-i8yutik6.txt summary: In time, I anticipate analysts examining the domestic and global response to this pandemic will evaluate if the use of Covid-19, in an effort to reduce global anxiety and fear associated with SARS, helped or hindered governmental responses and the initial public awareness about the emerging threat. As I witness the unfolding of the Covid-19 pandemic, I continue to think back to the early years of the HIV epidemic. Today, the SARS-CoV-2 pandemic, like the HIV epidemic of the 1980s and 1990s, is a metamorphosis described as "invading the society, and efforts to reduce mortality … are called a fight, a struggle, a war" (Sontag, 1989, p. The U.S. Centers for Disease Control and Prevention (CDC) has published a great resource document, entitled COVID-19: What people with HIV should know (CDC, 18 March 2020), which is available at https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/hiv.html. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32282428/ doi: 10.1097/jnc.0000000000000174 id: cord-299679-6z9e5gi6 author: Rello, Jordi title: Clinical phenotypes of SARS-CoV-2: implications for clinicians and researchers date: 2020-05-21 words: 1961.0 sentences: 112.0 pages: flesch: 37.0 cache: ./cache/cord-299679-6z9e5gi6.txt txt: ./txt/cord-299679-6z9e5gi6.txt summary: Many intubated patients present with phenotype 4, characterised by pulmonary hypoxic vasoconstriction, being associated with severe hypoxaemia with "normal" (>40 mL·cmH(2)O(−1)) lung compliance and likely representing pulmonary microvascular thrombosis. Phenotype 5 is often associated with high plasma procalcitonin and has low pulmonary compliance, Which is a result of co-infection or acute lung injury after noninvasive ventilation. The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad, ranging from asymptomatic infection to flu-like illness (sometimes with digestive disturbances) to viral pneumonia. Phenotype 2 represents 80% of hospitalisations and is characterised by the presence of hypoxaemia or small opacities on chest radiographs and these patients should be referred for close respiratory monitoring ( particularly respiratory rate and oxygen saturation measure by pulse oximetry) because they are at risk of rapid deterioration progressing to death if intubation is not timely instituted. abstract: Patients with COVID-19 present a broad spectrum of clinical presentation. Whereas hypoxaemia is the marker of severity, different strategies of management should be customised to five specific individual phenotypes. Many intubated patients present with phenotype 4, characterised by pulmonary hypoxic vasoconstriction, being associated with severe hypoxaemia with “normal” (>40 mL·cmH(2)O(−1)) lung compliance and likely representing pulmonary microvascular thrombosis. Phenotype 5 is often associated with high plasma procalcitonin and has low pulmonary compliance, Which is a result of co-infection or acute lung injury after noninvasive ventilation. Identifying these clinical phenotypes and applying a personalised approach would benefit the optimisation of therapies and improve outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/32341111/ doi: 10.1183/13993003.01028-2020 id: cord-352065-960xqft4 author: Rello, Jordi title: Update in COVID-19 in the Intensive Care Unit from the 2020 HELLENIC Athens International Symposium date: 2020-10-22 words: 4976.0 sentences: 264.0 pages: flesch: 41.0 cache: ./cache/cord-352065-960xqft4.txt txt: ./txt/cord-352065-960xqft4.txt summary: Experts reviewed the latest literature relating to the COVID-19 pandemic in critically ill patients, such as epidemiology, pathophysiology, phenotypes of infection, COVID-19 as a systematic infection, molecular diagnosis, mechanical ventilation, thromboprophylaxis, COVID-19 associated co-infections, immunotherapy, plasma treatment, Catheter-Related bloodstream infections, artificial intelligence for COVID-19, and vaccination. A major problem of the coronavirus pandemic is the considerable burden imposed on National Health Systems worldwide due to the hyperacute outbreak and the proportional increase of patients requiring intensive care unit (ICU) support in an extremely limited period of time, while outcomes vary according to the burden of the disease in each country. Acute respiratory distress syndrome (ARDS) is the primary cause of death in COVID-19 [7] and a recent scope review found that for COVID-19, < 5% of patients were reported as experiencing bacterial/fungal coinfection at admission, but development of secondary infections during ICU admission is common [8, 9] . abstract: The 2020 International Web Scientific Event in COVID-19 pandemic in critically ill patients aimed at updating the information and knowledge on the COVID-19 pandemic in the intensive care unit. Experts reviewed the latest literature relating to the COVID-19 pandemic in critically ill patients, such as epidemiology, pathophysiology, phenotypes of infection, COVID-19 as a systematic infection, molecular diagnosis, mechanical ventilation, thromboprophylaxis, COVID-19 associated co-infections, immunotherapy, plasma treatment, Catheter-Related bloodstream infections, artificial intelligence for COVID-19, and vaccination. Antiviral therapy and co-infections are out of the scope of this review. In this review, each of these issues is discussed with key messages regarding management and further research being presented after a brief review of available evidence. url: https://www.ncbi.nlm.nih.gov/pubmed/33172592/ doi: 10.1016/j.accpm.2020.10.008 id: cord-306718-7wp5jmxe author: Remaeus, Katarina title: Characteristics and short‐term obstetric outcomes in a case series of 67 women tested positive for SARS‐CoV‐2 in Stockholm, Sweden date: 2020-09-27 words: 2558.0 sentences: 154.0 pages: flesch: 57.0 cache: ./cache/cord-306718-7wp5jmxe.txt txt: ./txt/cord-306718-7wp5jmxe.txt summary: For the care of pregnant women positive for SARS-CoV-2, National Swedish guidelines were published early in the pandemic and recommended individualized antenatal care, mode of delivery based on obstetric considerations, and no routine separation of the mother and newborn after birth. Here, we want to report a case series of 67 women with a positive test for SARS-CoV-2, who gave birth from March 19 until April 26, 2020 in the Stockholm region, Sweden. In this case series of 67 SARS-CoV-2 test-positive delivered women with varying clinical presentation ranging from asymptomatic to manifest COVID19 disease, the majority had a vaginal, term birth and delivered a healthy normal weight neonate that did not test positive for SARS-CoV-2. In this case series of 67 test-positive women few women presented with severe COVID-19 illness, a majority had a vaginal birth at term with a healthy neonate that were test-negative for SARS-CoV-2. abstract: INTRODUCTION: The Stockholm region was the first area in Sweden to be hit by the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Our national guidelines regarding care of women with positive test for SARS‐CoV‐2 (detection with polymerase chain reaction) recommend individualized antenatal care, mode of delivery based on obstetric considerations, and no routine separation of the mother and newborn after birth. Breastfeeding is encouraged, and although there is no specific recommendation on wearing a face mask to prevent viral transmission to the newborn while nursing, instructions are given to keep high hygiene standards. All studies based on cases tested due to hospital admittance, including our, will capture more women with pregnancy complications than in the general population. Our aim was to describe the clinical characteristics in 67 SARS‐CoV‐2 positive women and their 68 neonates, and to report short‐term maternal and neonate outcomes. MATERIAL AND METHODS: A retrospective case series with data from medical records including all test‐positive women (n=67) who gave birth from March 19 to April 26, 2020 in Stockholm, Sweden. Means, proportions and percentages were calculated for characteristics and outcomes. RESULTS: The mean age was 32 years, 40% were nulliparous, and 61% were overweight or obese. Further, 15% had diabetes and 21% a hypertensive disease. 70% of the women had a vaginal birth. Preterm delivery occurred in 19% of the women. The preterm deliveries were mostly medically indicated, including two women who were delivered preterm due to severe coronavirus disease 19 (COVID‐19) illness, corresponding to 15% of the preterm births. Four women (6%) were admitted to intensive care unit postpartum. Three neonates were PCR‐positive for SARS‐CoV‐2 after birth. CONCLUSIONS: In this case series of 67 test‐positive women with clinical presentation ranging from asymptomatic to manifest COVID‐19 disease few women presented with severe COVID‐19 illness, a majority had a vaginal birth at term with a healthy neonate that were test‐negative for SARS‐CoV‐2. url: https://doi.org/10.1111/aogs.14006 doi: 10.1111/aogs.14006 id: cord-320864-k9zksbyt author: Remes-Troche, J. M. title: Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date: 2020-11-01 words: 4669.0 sentences: 256.0 pages: flesch: 46.0 cache: ./cache/cord-320864-k9zksbyt.txt txt: ./txt/cord-320864-k9zksbyt.txt summary: When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. Positions have already been established on how to work and/or resume activities at those units (e.g., those issued by the American Neurogastroenterology and Motility Society [ANMS] 4 and the Grupo Español de Motilidad Digestiva [GEMD]) 5 but due to the fact that the epidemiologic behavior, protective equipment avail-ability, serologic diagnostic test performance capacity for corroborating immunity, and socioeconomic context are different throughout Latin America, a group of experts that are members of the Sociedad Latinoamericana de Neurogastroenterología (SLNG) had a virtual meeting to formulate a consensus document with recommendations for the performance of gastrointestinal motility tests. abstract: The COVID 19 pandemic has forced the establishment of measures to avoid contagion during diagnostic and therapeutic tests in gastroenterology. Gastrointestinal motility studies involve a high and intermediate risk of transmission of infection by this virus. Given its elective or non-urgent indication in most cases, we recommend deferring the performance of these tests until there is a significant control of the infection rate in each country, during the pandemic. When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. url: https://api.elsevier.com/content/article/pii/S2255534X2030092X doi: 10.1016/j.rgmxen.2020.07.004 id: cord-259747-sl9q63oc author: Remmelink, Myriam title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 words: 4541.0 sentences: 244.0 pages: flesch: 48.0 cache: ./cache/cord-259747-sl9q63oc.txt txt: ./txt/cord-259747-sl9q63oc.txt summary: BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). In this post-mortem study, we included the first 17 adult patients (> 18 years) who died in our hospital (either in a COVID-19 unit or an intensive care unit) from March 13, 2020, with confirmed SARS-CoV-2 infection (i.e., positive RT-PCR assay on nasopharyngeal swab and/or bronchoalveolar lavage specimen). This post-mortem study showed several histopathological abnormalities in COVID-19 non-survivors; however, none of the findings was specific for direct viral injury, even though SARS-CoV-2 was detected in all examined organs using RT-PCR. abstract: BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. METHODS: We evaluated whether some specific post-mortem features are observed in these patients and if these changes are related to the presence of the virus in different organs. Complete macroscopic and microscopic autopsies were performed on different organs in 17 COVID-19 non-survivors. Presence of SARS-CoV-2 was evaluated with immunohistochemistry (IHC) in lung samples and with real-time reverse-transcription polymerase chain reaction (RT-PCR) test in the lung and other organs. RESULTS: Pulmonary findings revealed early-stage diffuse alveolar damage (DAD) in 15 out of 17 patients and microthrombi in small lung arteries in 11 patients. Late-stage DAD, atypical pneumocytes, and/or acute pneumonia were also observed. Four lung infarcts, two acute myocardial infarctions, and one ischemic enteritis were observed. There was no evidence of myocarditis, hepatitis, or encephalitis. Kidney evaluation revealed the presence of hemosiderin in tubules or pigmented casts in most patients. Spongiosis and vascular congestion were the most frequently encountered brain lesions. No specific SARS-CoV-2 lesions were observed in any organ. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). CONCLUSIONS: In conclusion, autopsies revealed a great heterogeneity of COVID-19-associated organ injury and the remarkable absence of any specific viral lesions, even when RT-PCR identified the presence of the virus in many organs. url: https://www.ncbi.nlm.nih.gov/pubmed/32787909/ doi: 10.1186/s13054-020-03218-5 id: cord-313984-7wvfnag1 author: Remy, Kenneth E title: Immunotherapies for COVID-19: lessons learned from sepsis date: 2020-04-28 words: 2174.0 sentences: 108.0 pages: flesch: 39.0 cache: ./cache/cord-313984-7wvfnag1.txt txt: ./txt/cord-313984-7wvfnag1.txt summary: Although more recent controlled studies indicate that plasma IL-6 concentrations can be in the range seen in bacterial infections, the time course of change is very different; in some cases, concentrations in patients with coronavirus disease 2019 (COVID-19) seem to increase over time with illness severity and worsening lung function. Indeed, when measured in patients infected with SARS-CoV-2, IL-10 concentrations (the most immunosuppressant cytokine in the body) are also elevated, which might lead to a different conclusion for therapeutic approaches and in understanding the disease pathophysiology. In particular, the modest inflammatory response and the progressive and profound suppression of adaptive immunity in COVID-19 relative to sepsis argues for perhaps a different therapeutic approach. However, if SARS-CoV-2 infection is similar to other chronic inflammatory and immune suppressive diseases, such as sepsis, we argue that immune stimulants, and not anti-inflammatory agents, should be considered as the first-line treatment option. abstract: nan url: https://api.elsevier.com/content/article/pii/S2213260020302174 doi: 10.1016/s2213-2600(20)30217-4 id: cord-327138-l2m2g0v8 author: Ren, Chao title: Comparison of clinical laboratory tests between bacterial sepsis and SARS-CoV-2-associated viral sepsis date: 2020-08-04 words: 870.0 sentences: 59.0 pages: flesch: 54.0 cache: ./cache/cord-327138-l2m2g0v8.txt txt: ./txt/cord-327138-l2m2g0v8.txt summary: Twenty-one patients with SARS-CoV-2-induced sepsis and 46 patients with bacterial sepsis were finally recruited (Additional file 2). The median age was 64.0 years (IQR, 60.5-68.0) and 65.5 years (IQR, 49.3-77.3) for patients of SARS-CoV-2-induced sepsis and bacterial sepsis, respectively (Additional file 1). 8.0 (IQR, 6.5-9.5), P < 0.001] were consistently higher among patients with bacterial sepsis than those with SARS-CoV-2-induced sepsis. In this study, ICU patients with SARS-CoV-2-induced sepsis and those with bacterial sepsis revealed comparable demographic characteristics, like age, gender distribution, and comorbidities, after rigorous screening processes. However, patients with bacterial sepsis were found with more severe organ dysfunction and poor outcomes when compared with those caused by SARS-CoV-2-induced sepsis, including higher values in SOFA and APACHE II, as well as more ICU deaths. This is the first report that compared clinical features and host responses between bacterial and SARS-CoV-2-induced viral sepsis. Baseline characteristics of critically ill patients with SARS-CoV-2-and bacteria-induced sepsis. abstract: Sepsis is a life-threatening condition that is characterized by multiple organ dysfunction due to abnormal host response to various pathogens, like bacteria, fungi and virus. The differences between viral and bacterial sepsis are indeed of great significance to deepen the understanding of the pathogenesis of sepsis, especially under pandemics of SARS-CoV-2 infection. url: https://doi.org/10.1186/s40779-020-00267-3 doi: 10.1186/s40779-020-00267-3 id: cord-353923-ou7w3zkv author: Ren, Shi-Yan title: Stability and infectivity of coronaviruses in inanimate environments date: 2020-04-26 words: 4946.0 sentences: 267.0 pages: flesch: 58.0 cache: ./cache/cord-353923-ou7w3zkv.txt txt: ./txt/cord-353923-ou7w3zkv.txt summary: Most viruses from the respiratory tract, such as coronaviruses, influenza, SARS-CoV, or rhinovirus, can persist on surfaces for a few days. The SARS-CoV-2 is presumed to be transmitted by respiratory droplets, viral aerosols, close contacts, and self-inoculation to nose, mouth, or eyes after touching a contaminated surface [16] . We therefore reviewed the persistence and infectivity of viruses on inanimate surfaces to provide clear information for containing the epidemic of SARS-CoV-2. One COVID-19 patient had upper respiratory tract infection with no pneumonia or diarrhea, and his two stool samples were positive for SARS-CoV-2 on RT-PCR. Persistence of most bacteria, fungi, and viruses (e.g., SARS-CoV) on surfaces depends on environmental conditions [37] , such as air temperature and RH [39] , inoculums, and the materials that they stayed on. Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious virus that can transmit through respiratory droplets, aerosols, or contacts. Frequent touching of contaminated surfaces in public areas is therefore a potential route of SARS-CoV-2 transmission. The inanimate surfaces have often been described as a source of nosocomial infections. However, summaries on the transmissibility of coronaviruses from contaminated surfaces to induce the coronavirus disease 2019 are rare at present. This review aims to summarize data on the persistence of different coronaviruses on inanimate surfaces. The literature was systematically searched on Medline without language restrictions. All reports with experimental evidence on the duration persistence of coronaviruses on any type of surface were included. Most viruses from the respiratory tract, such as coronaviruses, influenza, SARS-CoV, or rhinovirus, can persist on surfaces for a few days. Persistence time on inanimate surfaces varied from minutes to up to one month, depending on the environmental conditions. SARS-CoV-2 can be sustained in air in closed unventilated buses for at least 30 min without losing infectivity. The most common coronaviruses may well survive or persist on surfaces for up to one month. Viruses in respiratory or fecal specimens can maintain infectivity for quite a long time at room temperature. Absorbent materials like cotton are safer than unabsorbent materials for protection from virus infection. The risk of transmission via touching contaminated paper is low. Preventive strategies such as washing hands and wearing masks are critical to the control of coronavirus disease 2019. url: https://www.ncbi.nlm.nih.gov/pubmed/32368532/ doi: 10.12998/wjcc.v8.i8.1391 id: cord-253656-2x4y403o author: Ren, Wenlin title: Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates date: 2020-06-24 words: 3645.0 sentences: 202.0 pages: flesch: 60.0 cache: ./cache/cord-253656-2x4y403o.txt txt: ./txt/cord-253656-2x4y403o.txt summary: In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. The sera were collected on Day 38 and evaluated by ELISA against SARS-CoV-2 S1-6His protein using HRP-conjugated goat anti-mouse IgG Fc-specific secondary antibodies. As shown in Table 1 and Fig. 5A , immunization of SARS-CoV-2 S1-Fc fusion protein with AD20Gold + as adjuvant also induced very high neutralizing activities with IC50 titers >3000 and IC90 titers around 440-501 in both rabbits on Day 27 after immunizations. Beside high levels of the anti-S1 antibodies elicited, higher neutralizing activities against live SARS-CoV-2 virus and/or pseudovirus from the anti-sera of macaques and rabbits. abstract: Abstract The COVID-19 outbreak has become a global pandemic responsible for over 2,000,000 confirmed cases and over 126,000 deaths worldwide. In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. We demonstrate that the S1-Fc fusion protein is extremely immunogenic, as evidenced by strong antibody titers observed by day 7. Strong virus neutralizing activity was observed on day 14 in rabbits immunized with the S1-Fc fusion protein using a pseudovirus neutralization assay. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. Our data strongly suggests that the CHO-expressed SARS-CoV-2 S1-Fc recombinant protein could be a strong candidate for vaccine development against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32651113/ doi: 10.1016/j.vaccine.2020.06.066 id: cord-261435-wcn4bjnw author: Ren, Xianwen title: Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date: 2020-10-29 words: 8495.0 sentences: 468.0 pages: flesch: 57.0 cache: ./cache/cord-261435-wcn4bjnw.txt txt: ./txt/cord-261435-wcn4bjnw.txt summary: Notably, the percentages of megakaryocytes 207 and monocytes in PBMCs were elevated, particularly in severe COVID-19 patients during 208 the disease progression stage (Figure 2A) The increased plasma B cells in peripheral blood appeared to be derived from active 231 proliferation of plasmablasts and transitions from memory B cells based on the paired BCR 232 sequencing analyses. Similarly, the clonal expansion of 398 a central memory CD4+ T cell cluster highly expressing AQP3 (T_CD4_c02-AQP3) was 399 also associated with the triad interaction by disease severity, age, and sex ( SARS-CoV-2 detected in multiple epithelial and immune cell types with 414 interferon response phenotypes 415 The enrichment of plasma B and proliferative T cells in BALF and the elevation of these 416 cells in PBMCs of COVID-19 patients highlighted the roles of these cells in combating 417 SARS-CoV-2 infection. abstract: Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19. HIGHLIGHTS Large-scale scRNA-seq analysis depicts the immune landscape of COVID-19 Lymphopenia and active T and B cell responses coexist and are shaped by age and sex SARS-CoV-2 infects diverse epithelial and immune cells, inducing distinct responses Cytokine storms with systemic S100A8/A9 are associated with COVID-19 severity url: https://doi.org/10.1101/2020.10.29.360479 doi: 10.1101/2020.10.29.360479 id: cord-274326-msbdrp3e author: Ren, Xiaohan title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 date: 2020-11-04 words: 4897.0 sentences: 291.0 pages: flesch: 46.0 cache: ./cache/cord-274326-msbdrp3e.txt txt: ./txt/cord-274326-msbdrp3e.txt summary: title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 We hypothesized that in critically ill patients, an inflammatory cytokine storm could directly attack specific cells in the kidney and testis due to their high expression of ACE2 and cytokine receptors, leading to injury of the urinary tract. Compared with the control group, patients with pulmonary arterial hypertension, chronic kidney disease, and diabetic Infection and Drug Resistance 2020:13 submit your manuscript | www.dovepress.com DovePress 3979 nephropathy, as well as smokers, exhibited higher expression levels of ACE2 in their affected tissues (kidneys or lungs) ( Figure 3A -D). 48 Considering the high level of IL6 in severe COVID-19 patients and the enrichment of the IL6 receptor in various testicular cells, this might be a reason for the potential orchitis caused by SARS-CoV-2 infection. abstract: BACKGROUND: Since December 2019, the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first spread quickly in Wuhan, China, then globally. Based on previously published evidence, ACE2 and TMPRSS2 are both pivotal entry molecules that enable cellular infection by SARS-CoV-2. Also, increased expression of pro-inflammatory cytokines, or a “cytokine storm,” is associated with multiple organ dysfunction syndrome often observed in critically ill patients. METHODS: We investigated the expression pattern of ACE2 and TMPRSS2 in major organs in the human body, especially in specific disease conditions. Multiple sequence alignment of ACE2 in different species was used to explain animal susceptibility. Moreover, the cell-specific expression patterns of ACE2 and cytokine receptors in the urinary tract were assessed using single-cell RNA sequencing (scRNA-seq). Additional biological relevance was determined through Gene Set Enrichment Analysis (GSEA) using an ACE2-specific signature. RESULTS: Our results revealed that ACE2 and TMPRSS2 were highly expressed in genitourinary organs. ACE2 was highly and significantly expressed in the kidney among individuals with chronic kidney diseases or diabetic nephropathy. In single cells, ACE2 was primarily enriched in gametocytes in the testis and renal proximal tubules. The receptors for pro-inflammatory cytokines, especially IL6ST, were notably concentrated in endothelial cells, macrophages, spermatogonial stem cells in the testis, and renal endothelial cells, which suggested the occurrence of alternative damaging autoimmune mechanisms. CONCLUSION: This study provided new insights into the pathogenic mechanisms of SARS-CoV-2 that underlie the clinical manifestations observed in the human testis and kidney. These observations might substantially facilitate the development of effective treatments for this rapidly spreading disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33177848/ doi: 10.2147/idr.s270543 id: cord-334268-n2hon61o author: Ren, Yanfang title: Risk for dental healthcare professionals during the COVID-19 global pandemic: an evidence-based assessment date: 2020-07-18 words: 6861.0 sentences: 300.0 pages: flesch: 48.0 cache: ./cache/cord-334268-n2hon61o.txt txt: ./txt/cord-334268-n2hon61o.txt summary: Considering that the primary route of transmission for COVID-19 is from respiratory droplets, and potentially from spatters or aerosols generated during dental treatments, risks of COVID-19 J o u r n a l P r e -p r o o f transmission from asymptomatic patients to DHPs are dependent on several factors: effectiveness of PPE, specifically the N95 masks in preventing virus transmission, prevalence of asymptomatic cases in the local community, rate of transmission from asymptomatic patients to healthcare providers in close contact, probability for an infection acquired from an asymptomatic patient become symptomatic, and age-adjusted infection fatality rate of symptomatic COVID-19 patients. To understand the potential impact of COVID-19 on dental care and oral health and assess the risks to DHPs from the disease while providing essential services to the community, we periodically searched and reviewed published literature in PubMed and Google Scholar using various combinations of keywords, including SARS CoV-2, COVID-19, Dental, Dentist, Dentistry, Droplets, Aerosols, Healthcare Workers, Symptomatic, Asymptomatic, Saliva, PPE, N95 Masks, Face Shields, and Infection Fatality Rate. abstract: Abstract Objectives Heightened anxiety among dental healthcare professionals (DHPs) during the COVID-19 pandemic stems from uncertainties about the effectiveness of personal protective equipment (PPE) against dental aerosols and risk levels of asymptomatic patients. Our objective was to assess the risks for DHPs providing dental care during the pandemic based on available scientific evidence. Methods We reviewed the best available evidence and estimated the annualized risk (p=d a s(1-1-p 0 p 1(1-e)y n ) for a DHP during the COVID-19 pandemic based on the following basic parameters: p 0, the prevalence of asymptomatic patients in the local population; p 1, the probability that a DHP gets infected by an asymptomatic patient; e, the effectiveness of the PPE; s, the probability of becoming symptomatic after getting infected from asymptomatic patient; d a, the probability of dying from the disease in age group a; n, number of patients seen per day; and y, number of days worked per year. Results With the assumption that DHPs work fulltime and wear a N95 mask, the annualized probability for a DHP to acquire COVID-19 infection in a dental office, become symptomatic, and die from the infection is estimated at 1:13,000 (0.008%). Conclusions Risk of COVID-19 transmission in dental office is very low based on available evidence on effectiveness of PPE and prevalence of asymptomatic patients. Face shields and pre-procedure oral rinses may further reduce the risks. Clinical significance DHPs should follow guidelines on pre-appointment protocols and on PPE use during dental treatments to keep the risk low. url: https://api.elsevier.com/content/article/pii/S0300571220301809 doi: 10.1016/j.jdent.2020.103434 id: cord-254446-yxqbe1dj author: Ren, Yunzhao R. title: A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19 date: 2020-05-29 words: 6723.0 sentences: 426.0 pages: flesch: 49.0 cache: ./cache/cord-254446-yxqbe1dj.txt txt: ./txt/cord-254446-yxqbe1dj.txt summary: The disease name -COVID-19‖ and the associated virus name -SARS-CoV-2‖ were coined by the World Health Organization (WHO) and the Coronavirus Study Group of the International Committee on Virus Taxonomy, respectively, on February 11 1, 2 . Interestingly, pharyngeal swab viral nucleic acid screening results of 2,510 patients between January 23 and February 25 from a hospital fever clinic in Hunan Province (a neighboring province of Hubei) demonstrated that the positive rate of SARS-CoV-2 (1.3%) was lower than that of Influenza A (2.3%) and Influenza B (3.3%) 42 . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: This literature review aims to provide a comprehensive current summary of the pathogenesis, clinical features, disease course, host immune responses, and current investigational antiviral and immunomodulatory pharmacotherapies, in order to facilitate the development of future therapies and measures for prevention and control. This article is protected by copyright. All rights reserved url: https://www.ncbi.nlm.nih.gov/pubmed/32469437/ doi: 10.1002/jcph.1673 id: cord-324270-8rgkop42 author: Renaud-Picard, Benjamin title: Delayed pulmonary abscess following COVID-19 pneumonia: a case report date: 2020-06-18 words: 1184.0 sentences: 80.0 pages: flesch: 43.0 cache: ./cache/cord-324270-8rgkop42.txt txt: ./txt/cord-324270-8rgkop42.txt summary: The chest radiography showed bilateral diffuse ground-glass opacities that were consistent with a COVID-19 infection ( Figure 1A) . A nasopharyngeal swab, using RT-PCR, tested positive for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between Days 8 and 25 of hospitalization, three specific serologies for SARS-CoV-2 were performed, all of which strongly demonstrated positive IgM and IgG levels (BIOSYNEX COVID-19 BSS rapid test, Strasbourg, France). We believe that patients that present with a severe form of COVID-19 pneumonia would benefit from a well-defined and specific followup after hospital discharge, including early clinical examination, chest CT, and pulmonary-function tests. Figure 1 : A: Chest radiography showing bilateral diffuse ground-glass opacities, which are consistent with a COVID-19 infection, four days after symptom onset. B: Axial chest CT, one month after symptom onset, revealing one pulmonary abscess in the right lower lobe, which is associated with sub-pleural bilateral ground-glass opacities that are consistent with partially resolved moderate-to-severe COVID-19 pneumonia. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32623310/ doi: 10.1016/j.resmer.2020.100776 id: cord-270475-mkpn9tz6 author: Requena, Manuel title: COVID-19 and Stroke: incidence and etiological description in a high-volume center. date: 2020-08-05 words: 2426.0 sentences: 137.0 pages: flesch: 49.0 cache: ./cache/cord-270475-mkpn9tz6.txt txt: ./txt/cord-270475-mkpn9tz6.txt summary: Although COVID-19 pandemic has produced an enormous collateral damage over stroke systems of care leading to a drop of mild strokes admissions and late arrival of severe strokes, only incidental cases of large vessel occlusion (LVO) in young adults infected by SARS-CoV-2 have been reported without a clear causative relationship (4) . The presence of SARS-CoV-2 infection has been associated with worse functional outcome and higher mortality among patients with acute stroke (11) ; in parallel, history of stroke has also been associated with more severe clinical symptoms and poorer outcomes in patients with COVID-19 (12) . From March 2 nd to April 30 th , 2050 patients were admitted to our center with RT-PCR confirmed SARS-CoV-2 infection; of them 21 (1.02%) presented an acute ischemic stroke 21 and 4 (0.2%) suffered an ICH. Our study shows that the frequency of acute stroke in patients with COVID-19 requiring hospital admission is low (1%) and in most cases a usual cause of stroke was identified. abstract: BACKGROUND: An increased rate of thrombotic events has been associated to Coronavirus Disease 19 (COVID-19) with a variable rate of acute stroke. Our aim is to uncover the rate of acute stroke in COVID-19 patients and identify those cases in which a possible causative relationship could exist. METHODS: We performed a single-center analysis of a prospective mandatory database. We studied all patients with confirmed COVID-19 and stroke diagnoses from March 2(nd) to April 30(th). Demographic, clinical, and imaging data were prospectively collected. Final diagnosis was determined after full diagnostic work-up unless impossible due to death. RESULTS: Of 2050 patients with confirmed SARS-CoV-2 infection, 21 (1.02%) presented an acute ischemic stroke 21 and 4 (0.2%) suffered an intracranial hemorrhage. After the diagnostic work-up, in 60.0% ischemic and all hemorrhagic strokes patients an etiology non-related with COVID-19 was identified. Only in 6 patients the stroke cause was considered possibly related to COVID-19, all of them required mechanical ventilation before stroke onset. Ten patients underwent endovascular treatment; compared with patients who underwent EVT in the same period, COVID-19 was an independent predictor of in-hospital mortality (50% versus 15%; Odds Ratio, 6.67; 95% CI, 1.1-40.4; p 0.04). CONCLUSIONS: The presence of acute stroke in patients with COVID-19 was below 2% and most of them previously presented established stroke risk factors. Without other potential cause, stroke was an uncommon complication and exclusive of patients with a severe pulmonary injury. The presence of COVID-19 in patients who underwent EVT was an independent predictor of in-hospital mortality. url: https://doi.org/10.1016/j.jstrokecerebrovasdis.2020.105225 doi: 10.1016/j.jstrokecerebrovasdis.2020.105225 id: cord-267845-18hb5ndr author: Resende, Paola Cristina title: SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date: 2020-05-01 words: 1616.0 sentences: 89.0 pages: flesch: 48.0 cache: ./cache/cord-267845-18hb5ndr.txt txt: ./txt/cord-267845-18hb5ndr.txt summary: Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. Despite those limitations, we developed a sequencing protocol that successfully obtained whole genomes from SARS-CoV-2 positive samples referred to the National Reference laboratory at FIOCRUZ in Brazil. The tiling amplicon multiplex PCR method has been previously used for virus sequencing directly from clinical samples to obtain consensus genome sequences (3). Here, we describe three protocols using a primer set designed to sequence SARS-CoV-2 directly from total RNA extracted from clinical samples, which were initially diagnosed using real-time RT-PCR (7, 8) . Here we introduce a versatile sequencing protocol to recover the complete SARS-CoV-2 genome based on reverse transcription plus an overlapping long amplicon multiplex PCR strategy, and associated with pipelines to report the data, and recover the consensus files. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples abstract: Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger. url: https://doi.org/10.1101/2020.04.30.069039 doi: 10.1101/2020.04.30.069039 id: cord-313505-2lr4xara author: Resende, Paola Cristina title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date: 2020-06-18 words: 1145.0 sentences: 99.0 pages: flesch: 55.0 cache: ./cache/cord-313505-2lr4xara.txt txt: ./txt/cord-313505-2lr4xara.txt summary: title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. Introduction 59 COVID-19, the disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 60 (SARS-CoV-2), is leading to high rates of acute respiratory syndrome, hospitalization, and death 61 genomes (> 10% of ambiguous positions), we obtained a final dataset of 7,674 sequences. The prevalence of the sub-clade 211 B.1.1 in our sample (92%) was much higher than that observed in other Brazilian sequences 212 available in GISAID (36%) (Fig. 1C) phylogenetic tree, consistent with the hypothesis of multiple independent introductions (Fig. 2) (Fig. 2) . Revealing COVID-19 Transmission by SARS-CoV-2 Genome 410 Sequencing and Agent Based Modelling. abstract: Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil. url: https://doi.org/10.1101/2020.06.17.158006 doi: 10.1101/2020.06.17.158006 id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 words: 10548.0 sentences: 574.0 pages: flesch: 43.0 cache: ./cache/cord-330800-s91zfzfi.txt txt: ./txt/cord-330800-s91zfzfi.txt summary: e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. abstract: Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32908530/ doi: 10.1155/2020/8832728 id: cord-311635-hf6vrbyx author: Reuken, Philipp Alexander title: Between Fear and Courage: Attitudes, Beliefs, and Behavior of Liver Transplantation Recipients and Waiting List Candidates during the COVID‐19 Pandemic date: 2020-06-08 words: 3481.0 sentences: 209.0 pages: flesch: 47.0 cache: ./cache/cord-311635-hf6vrbyx.txt txt: ./txt/cord-311635-hf6vrbyx.txt summary: We evaluated fears, attitudes, and opinions associated with COVID‐19 in 365 SOT recipients (95% liver, 5% pancreas/kidney), 112 SOT candidates, and 394 immediate household contacts in two German transplant centers. Thus, we assessed COVID-19 prevalence/exposure, perception, compliance and behavior of transplant recipients and candidates on the waiting list in two German liver transplant centers in April 2020 using a crosssectional anonymous survey in patients and their household members. Responding to the item "I am afraid to become infected with the Coronavirus", SOT recipients reported a significantly greater fear of being infected with SARS-CoV-2 than their household controls ( Figure 1A and Supplementary Table S1). Here we demonstrate that fears associated with the SARS-CoV-2 pandemic are frequently expressed by liver transplantation recipients and candidates as well as by their household members. While fears and concerns associated with the SARS-CoV-2 pandemic are frequently expressed by SOT recipients and candidates, measures to prevent infection were frequently followed in the vast majority of patients. abstract: Patients with chronic liver disease and patients after solid organ transplantation (SOT) are vulnerable to severe Coronavirus Disease 2019 (COVID‐19). We evaluated fears, attitudes, and opinions associated with COVID‐19 in 365 SOT recipients (95% liver, 5% pancreas/kidney), 112 SOT candidates, and 394 immediate household contacts in two German transplant centers. Seven (1.5%) patients and 10 (2.5%) controls had contact to confirmed COVID‐19 cases. Fear of infection with SARS‐CoV‐2 was expressed by 65% SOT recipients and by 55% SOT candidates. SOT recipients had higher levels of fear of infection and more often wore personal protective gear than household controls. Female gender, steroid treatment, and using the local newspaper as a primary source of information were independently associated with expressed fear of infection in SOT recipients. Younger age and more recent transplantation correlated with concerns of severe COVID‐19 expressed by patients and with concerns of worse medical care expressed by household controls. One third of the patients expressed fear that immunosuppression could worsen COVID‐19 but only 15% used the transplantation center as a source of information. These data show that fears associated with the SARS‐CoV‐2 pandemic are frequently expressed but measures to prevent infection are frequently followed patients before and after SOT. url: https://doi.org/10.1111/ajt.16118 doi: 10.1111/ajt.16118 id: cord-256051-87alqfkd author: Revzin, Margarita V. title: Multisystem Imaging Manifestations of COVID-19, Part 1: Viral Pathogenesis and Pulmonary and Vascular System Complications date: 2020-10-01 words: 8850.0 sentences: 448.0 pages: flesch: 39.0 cache: ./cache/cord-256051-87alqfkd.txt txt: ./txt/cord-256051-87alqfkd.txt summary: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in coronavirus disease 2019 (COVID-19), which was declared an official pandemic by the World Health Organization on March 11, 2020. Although SARS-CoV-2 disease (or coronavirus disease 2019 ) primarily manifests as a lung infection, with symptoms ranging from those of a mild upper respiratory infection to severe pneumonia and acute respiratory distress syndrome (ARDS), other multisystemic manifestations of this disease and related complications are becoming more commonly recognized (3) . Thromboembolic complications, including pulmonary embolism (PE), peripheral venous and arterial thrombosis, and acute stroke (seen also in patients older than 50 years without risk factors) have all been reported (50-57). On the basis of the pattern and distribution of the opacities and the presence or absence of certain clinical signs (such as obesity), the authors developed a chest radiography severity scoring system that could be used as a prognostic factor of outcomes in young adult patients with COVID-19 (Fig 3) . abstract: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in coronavirus disease 2019 (COVID-19), which was declared an official pandemic by the World Health Organization on March 11, 2020. The infection has been reported in most countries around the world. As of August 2020, there have been over 21 million cases of COVID-19 reported worldwide, with over 800 000 COVID-19–associated deaths. It has become apparent that although COVID-19 predominantly affects the respiratory system, many other organ systems can also be involved. Imaging plays an essential role in the diagnosis of all manifestations of the disease, as well as its related complications, and proper utilization and interpretation of imaging examinations is crucial. With the growing global COVID-19 outbreak, a comprehensive understanding of the diagnostic imaging hallmarks, imaging features, multisystemic involvement, and evolution of imaging findings is essential for effective patient management and treatment. To date, only a few articles have been published that comprehensively describe the multisystemic imaging manifestations of COVID-19. The authors provide an inclusive system-by-system image-based review of this life-threatening and rapidly spreading infection. In part 1 of this article, the authors discuss general aspects of the disease, with an emphasis on virology, the pathophysiology of the virus, and clinical presentation of the disease. The key imaging features of the varied pathologic manifestations of this infection that involve the pulmonary and peripheral and central vascular systems are also described. Part 2 will focus on key imaging features of COVID-19 that involve the cardiac, neurologic, abdominal, dermatologic and ocular, and musculoskeletal systems, as well as pediatric and pregnancy-related manifestations of the virus. Vascular complications pertinent to each system will be also be discussed in part 2. Online supplemental material is available for this article. (©)RSNA, 2020 url: https://www.ncbi.nlm.nih.gov/pubmed/33001783/ doi: 10.1148/rg.2020200149 id: cord-284444-mgxxbm0u author: Reychler, G. title: Nebulization: A potential source of SARS-CoV-2 transmission date: 2020-08-04 words: 1122.0 sentences: 68.0 pages: flesch: 54.0 cache: ./cache/cord-284444-mgxxbm0u.txt txt: ./txt/cord-284444-mgxxbm0u.txt summary: authors: Reychler, G.; Vecellio, L.; Dubus, J.C. title: Nebulization: A potential source of SARS-CoV-2 transmission However, the Aerosoltherapy workgroup (GAT) of the Société de Pneumologie de Langue Franç aise decided at SARS-CoV2 pandemic preparedness to suggest avoiding a drug delivery via nebulization to reduce the risk of spreading the virus by this way. Indeed, some arguments suggested that the aerosol generated from the patient during the nebulization or from the nebulizer can directly exposes mucosae and eyes of the health care workers and contaminate surfaces with potentially infective droplets. One can suppose that the particles generated by the nebulizer and those exhaled by the patient will have optimal sizes to transmit the SARS-CoV2 to the healthcare workers. Based on these three elements, we think reasonable to avoid delivery of drugs via nebulization to SARS CoV2 patients for reducing the risk of exposure of the healthcare workers. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32763845/ doi: 10.1016/j.resmer.2020.100778 id: cord-329328-c6svx4qa author: Reydon, Thomas A. C. title: How can science be well-ordered in times of crisis? Learning from the SARS-CoV-2 pandemic date: 2020-11-03 words: 1740.0 sentences: 67.0 pages: flesch: 49.0 cache: ./cache/cord-329328-c6svx4qa.txt txt: ./txt/cord-329328-c6svx4qa.txt summary: Kitcher''s ideal should play a role in assessing the allocation of research resources in future crisis situations, as it provides a way to balance highly divergent interests and incorporate the common good into decision-making processes on research. I want to suggest that one way of doing better is to explicitly pose the question what the common good in a crisis such as the SARS-CoV-2 pandemic encompasses, and how during such a crisis and its aftermath research can be directed toward accommodating the needs of all. While this cannot and should not replace an ongoing global dialogue about how research can serve the common good in times of crisis, making Kitcher''s ideal more concrete and familiarizing researchers, policy makers and other stakeholders with it (which both are tasks for philosophers of science) will be a first step in the right direction. abstract: The SARS-CoV-2 pandemic constituted a crisis situation in which science was very far from Kitcher’s ideal of well-ordered science. I suggest that this could and should have been different. Kitcher’s ideal should play a role in assessing the allocation of research resources in future crisis situations, as it provides a way to balance highly divergent interests and incorporate the common good into decision-making processes on research. url: https://www.ncbi.nlm.nih.gov/pubmed/33141370/ doi: 10.1007/s40656-020-00348-5 id: cord-287043-53oy5w34 author: Reyes‐Bueno, José Antonio title: Miller‐Fisher syndrome after SARS‐CoV‐2 infection date: 2020-06-05 words: 1423.0 sentences: 91.0 pages: flesch: 49.0 cache: ./cache/cord-287043-53oy5w34.txt txt: ./txt/cord-287043-53oy5w34.txt summary: The neurophysiological study carried out on April 14 th showed F-wave anomalies such as asymmetric latency for the lower limbs and low A-wave amplitude on the left leg, alteration of bilateral R1 responses in the Blink-Reflex and in the intermediary standard electromyography poor activity in right rectus-anterior femoral muscle and little spontaneous denervation activity in left rectus-anterior femoral (RAF) muscle; all of this was compatible with an acute Guillain-Barre type demyelinating polyneuropathy in a very early stage. In the papers reviewed, the presence of anosmia and/or ageusia was only present in one case of Guillain-Barré syndrome (11) and in the two patients described with Miller-Fisher syndrome (5) . Our case would be the 3rd patient with MFS associated with COVID-19 as far as we know. Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré Syndrome Associated with SARS-CoV-2 Guillain Barre syndrome associated with COVID-19 infection: A case report abstract: On March 11th, 2020, the WHO declared the SARS‐Cov‐2 pandemic. Syndromes have been detected in relation to COVID‐19 such as encephalitis, acute necrotizing hemorrhagic encephalopathy and cerebrovascular complications. There are also cases of peripheral nervous system involvement. Our case would be the 3rd patient with MFS associated with COVID‐19 as far as we know. We present a 51 years old female diagnosed with MFS two weeks after COVID‐19. RT‐PCR to SARS‐CoV‐2 was negative but IgG was positive. Most of the cases were mild or moderate with typical signs and symptoms. All were treated with IV immunoglobulin with good response in most cases. Despite the short evolution time of the cases surviving the current pandemic, the description of cases of post‐infectious neurological syndromes suggests that this is probably not an infrequent complication in the subacute stage of Covid‐19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32503084/ doi: 10.1111/ene.14383 id: cord-281887-b511bjdy author: Ribeiro, Reitan title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 words: 4739.0 sentences: 234.0 pages: flesch: 45.0 cache: ./cache/cord-281887-b511bjdy.txt txt: ./txt/cord-281887-b511bjdy.txt summary: DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. CONCLUSIONS: We present a protocol, focused on the patients'' outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Our objective was to present the Brazilian Society of Surgical Oncology (BSSO) protocol for rational use of resources and for reducing the risk of surgical cancer patients being operated on during the coronavirus incubation period, in the context of areas with limited resources, and focused on patient outcomes. In light of all the previous considerations, Table 3 presents our suggested protocol for the rational use of resources to reduce the risk of surgical cancer patients from being operated on during the COVID-19 incubation period, in the context of areas with limited resources. abstract: BACKGROUND: As the COVID-19 pandemic moves from rich to poor nations, the healthcare systems of developing countries have to deal with this extra burden. As cancer care cannot stop and surgery is the main mechanism for cure and palliation, it is important to provide safe and rational access to cancer surgery during the COVID-19 pandemic. METHODS: From April 1st to May 1st, the committee of the Brazilian Society of Surgical Oncology (BSSO) was responsible for reviewing the literature and writing recommendations for perioperative cancer care in the context of limited resources during the pandemic. The recommendations were submitted to the BSSO board of directors. The orientations that were not consensual were removed and the suggestions were added to the text. From May 15 to 30th, the committee revised the recommendations, aligned them with the objectives of the work and standardize the text. DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. Prevalence of corona virus in the region, the need for surgery, surgical complexity, patient age and comorbidities, and availability of corona virus testing are central aspects in this matter and are discussed. CONCLUSIONS: We present a protocol, focused on the patients’ outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. url: https://doi.org/10.1245/s10434-020-09098-x doi: 10.1245/s10434-020-09098-x id: cord-337421-4v48kkus author: Ribeiro, Servio Pontes title: Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil date: 2020-03-27 words: 3488.0 sentences: 178.0 pages: flesch: 56.0 cache: ./cache/cord-337421-4v48kkus.txt txt: ./txt/cord-337421-4v48kkus.txt summary: After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. We developed a SIR (Susceptible-Infected-Recovered) model divided in 9 a metapopulation structure, where cities with airports were demes connected by the 10 number of flights. 142 143 Results 144 The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to 145 the airport closeness centrality within the Brazilian air transportation network. abstract: Background. We investigated a likely scenario of COVID-19 spreading in Brazil through the complex airport network of the country, for the 90 days after the first national occurrence of the disease. After the confirmation of the first imported cases, the lack of a proper airport entrance control resulted in the infection spreading in a manner directly proportional to the amount of flights reaching each city, following first occurrence of the virus coming from abroad. Methodology. We developed a SIR (Susceptible-Infected-Recovered) model divided in a metapopulation structure, where cities with airports were demes connected by the number of flights. Subsequently, we further explored the role of Manaus airport for a rapid entrance of the pandemic into indigenous territories situated in remote places of the Amazon region. Results. The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to the airport closeness centrality within the Brazilian air transportation network. There was a clear pattern in the expansion of the pandemic, with a stiff exponential expansion of cases for all cities. The more an airport showed closeness centrality, the greater was its vulnerability to SARS-CoV-2. Conclusions. We discussed the weak pandemic control performance of Brazil in comparison with other tropical, developing countries, namely India and Nigeria. Finally, we proposed measures for containing virus spreading taking into consideration the scenario of high poverty. url: https://doi.org/10.1101/2020.03.26.20044370 doi: 10.1101/2020.03.26.20044370 id: cord-275978-pezm1tnw author: Riccardo, Flavia title: Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic date: 2020-04-11 words: 5549.0 sentences: 310.0 pages: flesch: 55.0 cache: ./cache/cord-275978-pezm1tnw.txt txt: ./txt/cord-275978-pezm1tnw.txt summary: Methods We analysed data from the national case-based integrated surveillance system of all RT-PCR confirmed COVID-19 infections as of March 24th 2020, collected from all Italian regions and autonomous provinces. However, once interventions are introduced or the susceptibility in the population decreases, the transmission potential at a given time t is measured as the net reproduction number Rt. In this paper, we estimated both R0 and Rt for Italian regions in different epidemiological situations (high, intermediate and low age-adjusted attack rates), selected among those with highest data robustness. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. abstract: Background In February 2020, a locally-acquired COVID-19 case was detected in Lombardia, Italy. This was the first signal of ongoing transmission of SARS-CoV-2 in the country. The outbreak rapidly escalated to a national level epidemic, amid the WHO declaration of a pandemic. Methods We analysed data from the national case-based integrated surveillance system of all RT-PCR confirmed COVID-19 infections as of March 24th 2020, collected from all Italian regions and autonomous provinces. Here we provide a descriptive epidemiological summary on the first 62,843 COVID-19 cases in Italy as well as estimates of the basic and net reproductive numbers by region. Findings Of the 62,843 cases of COVID-19 analysed, 71.6% were reported from three Regions (Lombardia, Veneto and Emilia-Romagna). All cases reported after February 20th were locally acquired. Estimates of R0 varied between 2.5 (95%CI: 2.18-2.83) in Toscana and 3 (95%CI: 2.68-3.33) in Lazio, with epidemic doubling time of 3.2 days (95%CI: 2.3-5.2) and 2.9 days (95%CI: 2.2-4.3), respectively. The net reproduction number showed a decreasing trend starting around February 20-25, 2020 in northern regions. Notably, 5,760 cases were reported among health care workers. Of the 5,541 reported COVID-19 associated deaths, 49% occurred in people aged 80 years or above with an overall crude CFR of 8.8%. Male sex and age were independent risk factors for COVID-19 death. Interpretation The COVID-19 infection in Italy emerged with a clustering onset similar to the one described in Wuhan, China and likewise showed worse outcomes in older males with comorbidities. Initial R0 at 2.96 in Lombardia, explains the high case-load and rapid geographical spread observed. Overall Rt in Italian regions is currently decreasing albeit with large diversities across the country, supporting the importance of combined non-pharmacological control measures. url: https://doi.org/10.1101/2020.04.08.20056861 doi: 10.1101/2020.04.08.20056861 id: cord-031818-lawd185l author: Rich, Robert Soler title: Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case() date: 2020-09-12 words: 973.0 sentences: 58.0 pages: flesch: 48.0 cache: ./cache/cord-031818-lawd185l.txt txt: ./txt/cord-031818-lawd185l.txt summary: title: Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Letter to the Editor Expanded Mesenchymal Stem Cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case in Spain To the Editor: When the natural immune response does not control the replication of the SARS-CoV-2 coronavirus, it induces the production of macrophages and granulocytes with the consequent massive release of CD4 + T cells that produce IL-6 and other proinflammatory cytokines, resulting in lung tissue damage 1,2 . This challenge was faced by researchers from the University of Shanghai, intravenously infusing a suspension of mesenchymal cells (MSC), reporting rapid clinical, radiological and laboratory improvements, comparing them with those of the untreated control group 5 ; effects attributable to the massive release of anti-inflammatory and pro-regenerative cytokines from these cells that are trapped in the pulmonary capillaries. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486814/ doi: 10.1016/j.medcle.2020.06.011 id: cord-282318-890mltl8 author: Richard, Mathilde title: Factors determining human-to-human transmissibility of zoonotic pathogens via contact date: 2017-02-28 words: 3647.0 sentences: 173.0 pages: flesch: 44.0 cache: ./cache/cord-282318-890mltl8.txt txt: ./txt/cord-282318-890mltl8.txt summary: We used the following examples to illustrate these four modes of contact transmission: Treponema pallidum pertenue (TPE) for skin contact transmission, human immunodeficiency virus type 1 (HIV-1) for sexual contact transmission, coronaviruses (CoV) for respiratory contact transmission and Ebola virus for contact transmission via multiple routes. Other pathogen factors that have contributed to the ''success'' of HIV-1 M strain as a human pathogen, despite its relatively low infectivity (risk estimate of 1 in 1000 exposures for heterosexual transmission; [9] ), include its extraordinary propensity to evolve its genome through recombination and low-fidelity replication, allowing immune and therapeutic escape [20] , the nature of its long, ''latent'', often sub-clinical infection, during which patients can transmit the virus [21] , and high viral load. Amongst the pathogen factors that promote H2H transmission of Ebola virus is the high virus load in secreted bodily fluids combined with a very low infectious dose, as low as 10 plaque forming units as measured in experimental infection studies in nonhuman primates [56] . abstract: The pandemic potential of zoonotic pathogens lies in their ability to become efficiently transmissible amongst humans. Here, we focus on contact-transmitted pathogens and discuss the factors, at the pathogen, host and environmental levels that promote or hinder their human-to-human transmissibility via the following modes of contact transmission: skin contact, sexual contact, respiratory contact and multiple route contact. Factors common to several modes of transmission were immune evasion, high viral load, low infectious dose, crowding, promiscuity, and co-infections; other factors were specific for a pathogen or mode of contact transmission. The identification of such factors will lead to a better understanding of the requirements for human-to-human spread of pathogens, as well as improving risk assessment of newly emerging pathogens. url: https://www.sciencedirect.com/science/article/pii/S1879625716301845 doi: 10.1016/j.coviro.2016.11.004 id: cord-017489-ftz9190a author: Richards, Guy A. title: Viruses in the Intensive Care Unit (ICU) date: 2005 words: 5792.0 sentences: 330.0 pages: flesch: 44.0 cache: ./cache/cord-017489-ftz9190a.txt txt: ./txt/cord-017489-ftz9190a.txt summary: Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. abstract: Whereas viruses are not usually considered to be important causes of ICU admission this review has demonstrated this perception to be incorrect. Viruses and their manifestations differ from continent to continent and hemisphere to hemisphere and it is essential that the intensivist be familiar with diagnosis and management of these ubiquitous organisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122063/ doi: 10.1007/0-387-23380-6_3 id: cord-352096-cc3dzycl author: Richman, Douglas D. title: Antiviral Drug Discovery To Address the COVID-19 Pandemic date: 2020-09-25 words: 1520.0 sentences: 70.0 pages: flesch: 35.0 cache: ./cache/cord-352096-cc3dzycl.txt txt: ./txt/cord-352096-cc3dzycl.txt summary: Regardless of whether or when a vaccine becomes available, antivirals for SARS-CoV-2 will still be needed for several reasons: the unlikelihood that a vaccine will be 100% effective, the incompleteness of vaccine coverage because of both vaccine hesitancy and the numerous logistical challenges to accomplishing prompt large-scale immunization of the majority of the population, the possibility of limited durability of vaccine protection, the need for additional prophylaxis for high-risk subjects and poor vaccine responders, and the future value of effective antiviral treatment for Middle East respiratory syndrome (MERS) and new coronaviruses that will likely emerge from zoonoses. suggest that the purported activity against SARS-CoV-2 of the two HIV protease inhibitors, lopinavir and nelfinavir, is probably attributable to cellular toxicity. Structurebased design of antiviral drug candidates targeting the SARS-CoV-2 main protease AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic abstract: The magnitude of the morbidity and mortality inflicted upon the global population in less than 1 year has driven the inescapable conclusion that the discovery and development of effective antiviral drugs for COVID-19 are urgent and should be prioritized. The antiviral drug discovery programs that emerged for HIV and hepatitis C virus have enabled technology and expertise to accelerate this process for SARS-CoV-2. The description of candidate lead inhibitors for the viral main protease (M(pro)) exemplifies this accelerated approach and reminds us of the needs and opportunities for addressing this pandemic. url: https://doi.org/10.1128/mbio.02134-20 doi: 10.1128/mbio.02134-20 id: cord-261634-vfe1lawl author: Riddell, Shane title: The effect of temperature on persistence of SARS-CoV-2 on common surfaces date: 2020-10-07 words: 4210.0 sentences: 224.0 pages: flesch: 55.0 cache: ./cache/cord-261634-vfe1lawl.txt txt: ./txt/cord-261634-vfe1lawl.txt summary: Currently, there are conflicting reports on the survivability of SARS-CoV-2, with data ranging from 3 to 14 days at room temperature for a single surface type, stainless steel Open Access *Correspondence: Shane.Riddell@csiro.au Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia [5, 11] . At 20 °C, infectious SARS-CoV-2 virus was still detectable after 28 days post inoculation, for all non-porous surfaces tested (glass, polymer note, stainless steel, vinyl and paper notes). The present study has demonstrated that in controlled conditions, SARS-CoV-2 at a starting viral load and in a fluid matrix equivalent to that typically excreted by infected patients, remains viable for at least 28 days when dried onto non-porous surfaces at 20 °C and 50% relative humidity. It is important to note that after 28 days, infectious SARS-CoV-2 was also recovered from stainless steel, vinyl and glass, suggesting survivability on paper or polymer banknotes was not very different from the other non-porous surfaces studied. abstract: BACKGROUND: The rate at which COVID-19 has spread throughout the globe has been alarming. While the role of fomite transmission is not yet fully understood, precise data on the environmental stability of SARS-CoV-2 is required to determine the risks of fomite transmission from contaminated surfaces. METHODS: This study measured the survival rates of infectious SARS-CoV-2, suspended in a standard ASTM E2197 matrix, on several common surface types. All experiments were carried out in the dark, to negate any effects of UV light. Inoculated surfaces were incubated at 20 °C, 30 °C and 40 °C and sampled at various time points. RESULTS: Survival rates of SARS-CoV-2 were determined at different temperatures and D-values, Z-values and half-life were calculated. We obtained half lives of between 1.7 and 2.7 days at 20 °C, reducing to a few hours when temperature was elevated to 40 °C. With initial viral loads broadly equivalent to the highest titres excreted by infectious patients, viable virus was isolated for up to 28 days at 20 °C from common surfaces such as glass, stainless steel and both paper and polymer banknotes. Conversely, infectious virus survived less than 24 h at 40 °C on some surfaces. CONCLUSION: These findings demonstrate SARS-CoV-2 can remain infectious for significantly longer time periods than generally considered possible. These results could be used to inform improved risk mitigation procedures to prevent the fomite spread of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33028356/ doi: 10.1186/s12985-020-01418-7 id: cord-028711-zlj48aq7 author: Ridgway, Jessica P. title: Prolonged shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA among patients with coronavirus disease 2019 (COVID-19) date: 2020-06-24 words: 1005.0 sentences: 88.0 pages: flesch: 61.0 cache: ./cache/cord-028711-zlj48aq7.txt txt: ./txt/cord-028711-zlj48aq7.txt summary: Early reports from China indicate that severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA may persist in the respiratory tracts of patients with coronavirus disease 2019 (COVID-19) for several weeks after symptom onset. To estimate the duration of SARS-CoV-2 RNA shedding, we conducted a multisite study among patients who had nasopharyngeal specimens tested for SARS-CoV-2 RNA via real-time polymerase chain reaction (PCR) assay at Providence St Joseph Health (a 51-hospital healthcare organization based in Renton, Washington), University of Chicago Medicine in Chicago, Illinois, and NorthShore University HealthSystem (a 5-hospital healthcare system based in Evanston, Illinois). 4 Our findings that SARS-CoV-2 PCR tests remain positive for >3 weeks in most patients suggest that patients following the test-based strategy may remain on precautions for prolonged periods. It was a retrospective cohort study among patients with COVID-19 who underwent SARS-CoV-2 PCR testing at the discretion of their medical providers. Duration of SARS-CoV-2 RNA Detection No. of Days After 1 st Positive SARS-CoV-2 PCR Test abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338434/ doi: 10.1017/ice.2020.307 id: cord-298894-t5hyfum3 author: Rifino, Nicola title: Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital, Bergamo, Italy date: 2020-10-07 words: 4682.0 sentences: 247.0 pages: flesch: 44.0 cache: ./cache/cord-298894-t5hyfum3.txt txt: ./txt/cord-298894-t5hyfum3.txt summary: Neurological manifestations were classified as: (a) cerebrovascular disease [53 pts (38.7%)] including 37 ischemic and 11 haemorrhagic strokes, 4 transient ischemic attacks, 1 cerebral venous thrombosis; (b) peripheral nervous system diseases [31 (22.6%)] including 17 Guillain–Barrè syndromes; (c) altered mental status [49 (35.8%)] including one necrotizing encephalitis and 2 cases with RT-PCR detection of SARS-Cov-2 RNA in CSF; (d) miscellaneous disorders, among whom 2 patients with myelopathy associated with Ab anti-SARS-CoV-2 in CSF. COVID-19 diagnosis was confirmed: (1) by real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) on nasopharyngeal specimens [13] ; or (2) by RT-PCR on bronchoalveolar lavage (BAL) obtained by bronchoscopy in case of high clinical suspicion of SARS-CoV-2 infection and negative test results on at least two nasopharyngeal swabs performed at least 24 h apart; or (3) in the presence of characteristic radiological interstitial pneumonia associated with typical symptoms (fever, dry cough, dyspnea), even with negative RT-PCR, with no other possible aetiologic explanation. abstract: OBJECTIVES: Evidences from either small series or spontaneous reporting are accumulating that SARS-CoV-2 involves the Nervous Systems. The aim of this study is to provide an extensive overview on the major neurological complications in a large cohort of COVID-19 patients. METHODS: Retrospective, observational analysis on all COVID-19 patients admitted from February 23rd to April 30th, 2020 to ASST Papa Giovanni XXIII, Bergamo, Italy for whom a neurological consultation/neurophysiological assessment/neuroradiologic investigation was requested. Each identified neurologic complication was then classified into main neurologic categories. RESULTS: Of 1760 COVID-19 patients, 137 presented neurologic manifestations that manifested after COVID-19 symptoms in 98 pts and was the presenting symptom in 39. Neurological manifestations were classified as: (a) cerebrovascular disease [53 pts (38.7%)] including 37 ischemic and 11 haemorrhagic strokes, 4 transient ischemic attacks, 1 cerebral venous thrombosis; (b) peripheral nervous system diseases [31 (22.6%)] including 17 Guillain–Barrè syndromes; (c) altered mental status [49 (35.8%)] including one necrotizing encephalitis and 2 cases with RT-PCR detection of SARS-Cov-2 RNA in CSF; (d) miscellaneous disorders, among whom 2 patients with myelopathy associated with Ab anti-SARS-CoV-2 in CSF. Patients with peripheral nervous system involvement had more frequently severe ARDS compared to patients with cerebrovascular disease (87.1% vs 42%; difference = 45.1% 95% CI 42.0–48.2; χ(2)= 14.306; p < 0.0002) and with altered mental status (87.1% vs 55.6%; difference = 31.5% 95% CI 27.5–37.5%; χ(2)= 7.055; p < 0.01). CONCLUSION: This study confirms that involvement of nervous system is common in SARS-CoV-2 infection and offers clinicians useful information for prevention and prompt identification in order to set the adequate therapeutic strategies. url: https://doi.org/10.1007/s00415-020-10251-5 doi: 10.1007/s00415-020-10251-5 id: cord-266930-a1mzxmsb author: Rigatti, S. J. title: SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population date: 2020-09-11 words: 2620.0 sentences: 167.0 pages: flesch: 52.0 cache: ./cache/cord-266930-a1mzxmsb.txt txt: ./txt/cord-266930-a1mzxmsb.txt summary: Using state population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. Conclusions: The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. abstract: Objectives: The prevalence of SARS-CoV-2 antibodies in the general population is largely unknown. Since many infections, even among the elderly and other vulnerable populations, are asymptomatic, the prevalence of antibodies could help determine how far along the path to herd immunity the general population has progressed. Also, in order to clarify the clinical manifestations of current or recent past COVID-19 illness, it may be useful to determine if there are any common alterations in routine clinical laboratory values. Methods: We performed SARS-CoV-2 antibody tests on 50,130 consecutive life insurance applicants who were having blood drawn for the purpose of underwriting (life risk assessment). Subjects were also tested for lipids, liver function tests, renal function studies, as well as serum proteins. Other variables included height, weight, blood pressure at the time of the blood draw, and history of common chronic diseases (hypertension, heart disease, diabetes, and cancer). Results: The overall prevalence of SARS-CoV-2 was 3.0%, and was fairly consistent across the age range and similar in males and females. Several of the routine laboratory tests obtained were significantly different in antibody-positive vs. antibody-negative subjects, including albumin, globulins, bilirubin, and the urine albumin:creatinine ratio. The BMI was also significantly higher in the antibody-positive group. Geographical distribution revealed a very high level of positivity in the state of New York compared to all other areas (17.1%). Using state population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. Conclusions: The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. Certain laboratory values, particularly serum protein levels, are associated with positive serology, though these associations are not likely to be clinically meaningful. url: http://medrxiv.org/cgi/content/short/2020.09.09.20191296v1?rss=1 doi: 10.1101/2020.09.09.20191296 id: cord-346539-kxnrf5g5 author: Riggioni, Carmen title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 words: 15760.0 sentences: 1112.0 pages: flesch: 48.0 cache: ./cache/cord-346539-kxnrf5g5.txt txt: ./txt/cord-346539-kxnrf5g5.txt summary: This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: In December 2019, China reported the first cases of the coronavirus disease 2019 (COVID‐19). This disease, caused by the severe acute respiratory syndrome‐related coronavirus 2 (SARS‐CoV‐2), has developed into a pandemic. To date it has resulted in ~6.5 million confirmed cases and caused almost 400,000 related deaths worldwide. Unequivocally, the COVID‐19 pandemic is the gravest health and socio‐economic crisis of our time. In this context, numerous questions have emerged in demand of basic scientific information and evidence‐based medical advice on SARS‐CoV‐2 and COVID‐19. Although the majority of the patients show a very mild, self‐limiting viral respiratory disease, many clinical manifestations in severe patients are unique to COVID‐19, such as severe lymphopenia and eosinopenia, extensive pneumonia, a “cytokine storm” leading to acute respiratory distress syndrome, endothelitis, thrombo‐embolic complications and multiorgan failure. The epidemiologic features of COVID‐19 are distinctive and have changed throughout the pandemic. Vaccine and drug development studies and clinical trials are rapidly growing at an unprecedented speed. However, basic and clinical research on COVID‐19‐related topics should be based on more coordinated high‐quality studies. This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. Over 140 questions were answered by experts in the field providing a comprehensive and practical overview of COVID‐19 and allergic disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32535955/ doi: 10.1111/all.14449 id: cord-342599-558yn6pu author: Rinchai, Darawan title: A modular framework for the development of targeted Covid-19 blood transcript profiling panels date: 2020-05-22 words: 5230.0 sentences: 298.0 pages: flesch: 42.0 cache: ./cache/cord-342599-558yn6pu.txt txt: ./txt/cord-342599-558yn6pu.txt summary: Here we aimed to develop an approach to support the design of focused blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: therapeutic development relevance, SARS biology relevance and immunological relevance. In this proof of principle study, we used the available transcript profiling data from two separate studies to select Covid-19 relevant sets of modules (8, 9) . One of these applications provides access to module-level transcript abundance profiles for available Covid-19 blood transcriptome profiling datasets. Despite large differences between the two studies in terms of design, range of clinical severity, technology platforms and module coverage, the combined overall changes (detected at a high-level perspective) are consistent with those observed in known acute infections, such as those caused by influenza, respiratory syncytial virus (RSV) or S. abstract: Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of focused blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates. As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: therapeutic development relevance, SARS biology relevance and immunological relevance. Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients. url: https://doi.org/10.1101/2020.05.20.107243 doi: 10.1101/2020.05.20.107243 id: cord-321854-cy8vyb6j author: Ripperger, Tyler J. title: Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date: 2020-10-14 words: 3289.0 sentences: 193.0 pages: flesch: 51.0 cache: ./cache/cord-321854-cy8vyb6j.txt txt: ./txt/cord-321854-cy8vyb6j.txt summary: Relative to mild COVID-19 cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against nucleocapsid (N) and the receptor binding domain (RBD) of spike protein. However, 6.5% of the expanded negative control 149 group displayed RBD reactivity that overlapped with PCR+ individuals (Figure 1B, blue shade) , 150 some of whom may have been early into disease and had not yet generated high levels of 151 antibodies. To quantify the sensitivity of the assay relative to time of diagnosis, we measured 152 antibody levels to RBD and plotted these values against time following SARS-CoV-2 PCR+ 153 confirmation. For 308 both memory and plasma cells, there appears to be a ''sweet spot'' of antigen avidity that Taken together, we have reported a highly specific serological assay for SARS-CoV-2 323 exposure that is usable in very low seroprevalence communities, and that returns positive 324 results that are highly co-incident with virus neutralization. abstract: We conducted a serological study to define correlates of immunity against SARS-CoV-2. Relative to mild COVID-19 cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against nucleocapsid (N) and the receptor binding domain (RBD) of spike protein. Age and sex played lesser roles. All cases, including asymptomatic individuals, seroconverted by 2 weeks post-PCR confirmation. Spike RBD and S2 and neutralizing antibodies remained detectable through 5-7 months post-onset, whereas α-N titers diminished. Testing of 5882 members of the local community revealed only 1 sample with seroreactivity to both RBD and S2 that lacked neutralizing antibodies. This fidelity could not be achieved with either RBD or S2 alone. Thus, inclusion of multiple independent assays improved the accuracy of antibody tests in low seroprevalence communities and revealed differences in antibody kinetics depending on the antigen. We conclude that neutralizing antibodies are stably produced for at least 5-7 months after SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33129373/ doi: 10.1016/j.immuni.2020.10.004 id: cord-293389-3h9vsc1a author: Risitano, Antonio M. title: Complement as a target in COVID-19? date: 2020-04-23 words: 1069.0 sentences: 53.0 pages: flesch: 34.0 cache: ./cache/cord-293389-3h9vsc1a.txt txt: ./txt/cord-293389-3h9vsc1a.txt summary: Most patients who become critically ill following infection with SARS-CoV-2, the causative agent of COVID-19, develop acute respiratory distress syndrome (ARDS) 1 . The prominent decrease in lung-infiltrating neutrophils and the reduced levels of both intrapulmonary and plasma IL-6 seen in SARS-CoV-infected C3-deficient mice suggests the potential of combining C3 inhibitors with anti-IL-6 regimens. A recent preprint study reported that lung biopsy samples from patients with severe COVID-19 showed widespread complement activation, characterized by C3a generation and C3-fragment deposition 6 . Proximal complement inhibitors (which target C3 or its upstream activators) could be more effective, but these are still in clinical development, and none has yet been approved, although limited data from phase II clinical trials are available. However, the combination of clinical indicators of ARDS progression with known biomarkers of inflammation (C-reactive protein, plasma IL-6 levels and ferritin) would allow identification of patients that could benefit from complement inhibition. abstract: There is an urgent need to develop effective therapies for COVID-19. Here, we urge immunologists and clinicians to consider the potential of targeting the complement system in these patients. url: https://doi.org/10.1038/s41577-020-0320-7 doi: 10.1038/s41577-020-0320-7 id: cord-264360-eroqjkoh author: Risku, Minna title: Detection of human coronaviruses in children with acute gastroenteritis date: 2010-03-15 words: 2364.0 sentences: 154.0 pages: flesch: 60.0 cache: ./cache/cord-264360-eroqjkoh.txt txt: ./txt/cord-264360-eroqjkoh.txt summary: STUDY DESIGN: 878 stool specimens from children with acute gastroenteritis and 112 from control children were tested by RT-PCR to detect HCoV groups 1B, 2A and SARS. On the basis of this study, the significance of coronaviruses as gastrointestinal pathogens in children appears minor, since most of the coronavirus findings were co-infections with known gastroenteritis viruses. Our study shows that human coronaviruses OC43, HKU1, 229E and NL63 can be found in stool samples of children with acute gastroenteritis. 10 In our study one of the 36 healthy control patients had coronavirus detected in stool specimen and thus, there was no difference in the HCoV detection rate between the cases of acute gastroenteritis and control children. Future studies should investigate such mild cases for HCoVs. In conclusion, non-SARS human coronaviruses can be found in stool samples of children with acute gastroenteritis. abstract: BACKGROUND: Human coronaviruses (HCoVs) are known respiratory pathogens. Moreover, coronavirus-like particles have been seen by electron microscope in stools, and SARS-HCoV has been isolated from intestinal tissue and detected in stool samples. OBJECTIVES: To find out if HCoVs can be found in stools of children with acute gastroenteritis and to assess the significance of HCoVs in the etiology of acute gastroenteritis in children. STUDY DESIGN: 878 stool specimens from children with acute gastroenteritis and 112 from control children were tested by RT-PCR to detect HCoV groups 1B, 2A and SARS. HCoVs were typed by sequencing all PCR positive samples. RESULTS: Twenty-two (2.5%) of the 878 stool specimens of children with acute gastroenteritis were positive for HCoVs. The following HCoV types were detected: OC43 (10 cases, 45.5%), HKU1 (6 cases, 27.3%), 229E (2 cases, 9.1%) and NL63 (4 cases, 18.2%). In 4 of the cases a HCoV was the only detected virus; in the remaining cases rotavirus or norovirus was found in the same sample. In control groups there were two HCoV positive samples of 112 tested. CONCLUSIONS: This study shows that all known non-SARS HCoVs can be found in stools of children with acute gastroenteritis. On the basis of this study, the significance of coronaviruses as gastrointestinal pathogens in children appears minor, since most of the coronavirus findings were co-infections with known gastroenteritis viruses. url: https://www.sciencedirect.com/science/article/pii/S1386653210000855 doi: 10.1016/j.jcv.2010.02.013 id: cord-294537-wpq1492g author: Ritschl, Paul V. title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach date: 2020-05-10 words: 2530.0 sentences: 176.0 pages: flesch: 46.0 cache: ./cache/cord-294537-wpq1492g.txt txt: ./txt/cord-294537-wpq1492g.txt summary: title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach 6 As no consensus guidelines or international recommendations have been published on coronavirus disease 2019 (COVID19) and organ transplant, the aim of this study was to offer a consensus-based approach to manage transplant programs until reliable data on risk and benefits of conducting organ transplants in times of a viral pandemic are available. the United Kingdom recommend a low threshold for SARS-CoV-2testing in transplant patients after contact with a positively tested person or subject to a broader spectrum of COVID-19-associated symptoms. Although SARS-CoV-2 nasopharyngeal PCR shows reasonable sensitivity, a recently published study demonstrates that of 51 COVID-19 patients only 36 were initially positive in NAT. Until now, no solid organ transplant procedure has reportedly been performed on a SARS-CoV-2-infected patient. Solid organ transplantation programs facing lack of empiric evidence in the COVID-19 pandemic: A By-proxy Society Recommendation Consensus approach abstract: The ongoing severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic has a drastic impact on national health care systems. Given the overwhelming demand on facility capacity, the impact on all health care sectors has to be addressed. Solid organ transplantation represents a field with a high demand on staff, intensive care units, and follow‐up facilities. The great therapeutic value of organ transplantation has to be weighed against mandatory constraints of health care capacities. In addition, the management of immunosuppressed recipients has to be reassessed during the ongoing coronavirus disease 2019 (COVID‐19) pandemic. In addressing these crucial questions, transplant physicians are facing a total lack of scientific evidence. Therefore, the aim of this study was to offer an approach of consensus‐based guidance, derived from individual information of 22 transplant societies. Key recommendations were extracted and the degree of consensus among different organizations was calculated. A high degree of consensus was found for temporarily suspending nonurgent transplant procedures and living donation programs. Systematic polymerase chain reaction‐based testing of donors and recipients was broadly recommended. Additionally, more specific aspects (eg, screening of surgical explant teams and restricted use of marginal donor organs) were included in our analysis. This study offers a novel approach to informed guidance for health care management when a priori no scientific evidence is available. url: https://www.ncbi.nlm.nih.gov/pubmed/32323460/ doi: 10.1111/ajt.15933 id: cord-313058-nrrl4kjc author: Rivas, Magali Noval title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis date: 2020-10-16 words: 1054.0 sentences: 68.0 pages: flesch: 51.0 cache: ./cache/cord-313058-nrrl4kjc.txt txt: ./txt/cord-313058-nrrl4kjc.txt summary: title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. As of mid-September, the novel severe acute respiratory syndrome coronavirus 2 26 (SARS-CoV-2) has infected more than 30 million people, resulting in approximately one 27 million deaths worldwide, including over 200,000 deaths in the USA alone. Exacerbation of the COVID-19 immune response manifested by extensive cytokines 33 release, called cytokine storm, may lead to multisystem inflammatory syndrome that is 34 fatal in 28% of cases 1 . Interestingly, SAg-induced TSS has been associated with long-term 94 neuropsychologic deficits in adults, including cognitive decline 10 , and we identified a 95 homology between the SAg motif of SARS-CoV-2 and neurotoxin-like sequences which 96 are able to bind the TCR 5 . Clinical 131 Characteristics of 58 Children With a Pediatric Inflammatory Multisystem Syndrome 132 Temporally Associated With SARS-CoV-2 abstract: nan url: https://api.elsevier.com/content/article/pii/S0091674920314147 doi: 10.1016/j.jaci.2020.10.008 id: cord-305798-7b8rua4z author: Rivas-García, S title: Rhabdomyolysis as the main manifestation of coronavirus disease 2019 date: 2020-06-25 words: 1133.0 sentences: 76.0 pages: flesch: 53.0 cache: ./cache/cord-305798-7b8rua4z.txt txt: ./txt/cord-305798-7b8rua4z.txt summary: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China in the late December 2019. Recent patient case series published in the setting of COVID-19 infection in China have described myalgia and elevated CK as frequent findings. High levels of CK-MB (muscle and brain isoform) were found in 4.5% of a 201 patient case series in Wuhan, [3] showing a significant association with acute respiratory syndrome distress development. Muscle weakness and elevated serum CK levels were also commonly found in coronavirus case series reported in the 2003 outbreak of SARS and the 2012 outbreak of Middle East respiratory syndrome (MERS) [4] . Even if myalgia and CK elevation are relatively frequent, rhabdomyolysis symptoms have been rarely reported in SARS-CoV-2 outbreaks. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32584414/ doi: 10.1093/rheumatology/keaa351 id: cord-266820-exl36jt3 author: Rivera, Frida title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 words: 873.0 sentences: 76.0 pages: flesch: 61.0 cache: ./cache/cord-266820-exl36jt3.txt txt: ./txt/cord-266820-exl36jt3.txt summary: title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. abstract: SARS-CoV-2 asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of COVID-19 in Milwaukee county url: https://doi.org/10.1093/cid/ciaa1225 doi: 10.1093/cid/ciaa1225 id: cord-263509-wi0um8cm author: Rivera, Victor M title: Actitudes Terapéuticas Hacia La Esclerosis Múltiple En Centroamérica Y El Caribe Frente A La Pandemia De Sars-Cov-2 date: 2020-07-28 words: 921.0 sentences: 96.0 pages: flesch: 53.0 cache: ./cache/cord-263509-wi0um8cm.txt txt: ./txt/cord-263509-wi0um8cm.txt summary: Esclerosis Múltiple (EM) en Centroamérica y el Caribe (CAC) mantiene una baja prevalencia¹ mientras que el impacto socioeconómico ejercido por esta enfermedad en los sistemas de salud de la región es severo considerando el nivel de crecimiento económico de estos países. A pesar de esta limitación, en años recientes la mayoría de los sistemas de seguridad social y algunos de atención pública en esta zona, han dedicado una gran porción de sus presupuestos a la adquisición de las variadas y onerosas terapias aprobadas por agencias internacionales para el manejo de EM². La teórica posibilidad que pacientes con EM pudieran ser especialmente vulnerables a la infección con SARS-CoV-2 considerando presencia de discapacidad neurológica y uso de tratamientos que afectan al sistema inmune, varios medicamentos de hecho causando persistente depleción linfocitaria, conllevó al Foro Centroamericano y del Caribe de Esclerosis Múltiple (FOCEM) a explorar actitudes terapéuticas en la región hispanoparlante encarando la pandemia. abstract: nan url: https://api.elsevier.com/content/article/pii/S0213485320302371 doi: 10.1016/j.nrl.2020.07.009 id: cord-288584-wql253d8 author: Rivera-Oyola, Ryan title: Dermatologic findings in two patients with COVID-19 date: 2020-04-28 words: 362.0 sentences: 28.0 pages: flesch: 46.0 cache: ./cache/cord-288584-wql253d8.txt txt: ./txt/cord-288584-wql253d8.txt summary: Cutaneous involvement was observed both at symptom onset (8 patients) and after hospitalization (10 patients).(4) A study from Thailand described a dengue-like rash in a COVID-19 patient who was initially misdiagnosed with dengue.(5) Additionally, a recent letter reported a COVID-19 patient who simultaneously developed a non-pruritic, diffuse body rash, myalgia and cephalgia. (6) It is worth noting the variability in clinical presentation of cutaneous findings following SARS-CoV-2 infection. Similarly, we observed a diversity of morphological presentations and variability in time to onset of cutaneous manifestations in the literature (4) (5) (6) . It is unlikely that our patients'' rashes were due to a medication reaction as there had been no changes to their medication regimen, the rashes had an acute onset following COVID-19 symptom onset, and, in Case 1, the biopsy did not illustrate tissue eosinophilia. At present, there is limited data regarding the cutaneous manifestations following SARS-CoV-2 infection. COVID-19 should be considered in the initial differential diagnosis for a patient with acute skin changes following flu-like symptoms. abstract: nan url: https://api.elsevier.com/content/article/pii/S2352512620303106 doi: 10.1016/j.jdcr.2020.04.027 id: cord-296306-xcomjvaa author: Rivett, Lucy title: Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date: 2020-05-11 words: 6500.0 sentences: 350.0 pages: flesch: 48.0 cache: ./cache/cord-296306-xcomjvaa.txt txt: ./txt/cord-296306-xcomjvaa.txt summary: Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Table 3 outlines the total number of SARS-CoV-2 tests performed in each screening group (HCW asymptomatic, HCW symptomatic, and HCW symptomatic household contact) categorised according to the ward with the highest anticipated risk of exposure to high; ''amber'', medium; ''green'', low; . Three subgroups of SARS-CoV-2 positive asymptomatic HCW Each individual in the HCW asymptomatic screening group was contacted by telephone to establish a clinical history, and COVID-19 probability criteria ( Table 1) were retrospectively applied to categorise any symptoms in the month prior to testing ( Figure 2 ). 12/30 (40%) individuals from the HCW asymptomatic screening group reported symptoms > 7 days prior to testing, and the majority experiencing symptoms consistent with a high probability of COVID-19 had appropriately self-isolated during that period. abstract: Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff. url: https://www.ncbi.nlm.nih.gov/pubmed/32392129/ doi: 10.7554/elife.58728 id: cord-322141-4a81mapc author: Rizzo, Emanuele title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government date: 2020-09-09 words: 722.0 sentences: 41.0 pages: flesch: 44.0 cache: ./cache/cord-322141-4a81mapc.txt txt: ./txt/cord-322141-4a81mapc.txt summary: title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government For these reasons, the territorial medicine and the operators of the Apulian prevention services have decided to propose to the regional government the possibility of adopting a specific exemption code for COVID-19, taking on the economic burden deriving from treatments and diagnostic investigations once the acute phase of the disease has been overcome. Moreover, a similar procedure would also have the comfort of numbers: the sum of confirmed cases remains limited to date (as reported by the latest epidemiological bulletin -01/08/2020 h :14:00 CEST -, there are 4631 total cases of COVID-19 syndrome in Apulia, including 112 currently positive, 3967 healed subjects and 552 deaths [6] ), which makes the operation sustainable and not expensive for the regional finances. abstract: nan url: https://api.elsevier.com/content/article/pii/S2589537020302601 doi: 10.1016/j.eclinm.2020.100516 id: cord-291397-look6ddt author: Roberto, Palumbo title: Current treatment of COVID-19 in renal patients: hope or hype? date: 2020-09-28 words: 5827.0 sentences: 326.0 pages: flesch: 46.0 cache: ./cache/cord-291397-look6ddt.txt txt: ./txt/cord-291397-look6ddt.txt summary: Given the lack of specific therapy about the ongoing SARS-CoV-2 infection, we conducted a brief review to summarize the mechanism of action and the potentially side effects of the treatment currently available, focusing on the effects of the drugs on renal disease at different stages in terms of therapeutic management and survival. A randomized clinical trial, handled by a Chinese group, suggested that in hospitalized adult patients with severe infection, no benefit was observed with lopinavir/ritonavir beyond standard care in terms of time to clinical improvement, reduction of mortality and safety (side effects and discontinuation of treatment) [29, 30] . Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial abstract: To date the severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2), known as COVID-19, is for clinicians the most difficult global therapeutic problem. In this landscape, the management of patients with chronic kidney disease, acute kidney injury or patients undergoing immunosuppressant therapies for kidney transplant or glomerular diseases, represent a clinical challenge for nephrologists, especially in patients with severe acute lung involvement. Therefore in this setting, due to the lack of anti-COVID treatment schedules, tailored management is mandatory to reduce the side effects, as consequence of impaired renal function and drugs interactions. We report the main treatment actually used against SARS-CoV-2, underlining its possible use in the nephropatic patients and the central role of nephrologists to improve the clinical outcome. url: https://doi.org/10.1007/s11739-020-02510-0 doi: 10.1007/s11739-020-02510-0 id: cord-314451-mqnqjn0c author: Roberts, Anjeanette title: A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice date: 2007-01-12 words: 9794.0 sentences: 433.0 pages: flesch: 48.0 cache: ./cache/cord-314451-mqnqjn0c.txt txt: ./txt/cord-314451-mqnqjn0c.txt summary: To generate a model that satisfies these criteria, we have serially passaged SARS-CoV in the respiratory tract of young BALB/c mice, resulting in a lethal virus that causes dosedependent weight loss and mortality associated with higher viral titers in the respiratory tract than are seen with the wildtype virus and with histopathologic findings of severe pulmonary disease. Northern blot analysis of RNA from infected Vero E6 cells indicated that genomic vRNA and viral mRNA and all eight sub-genomic mRNAs were present in similar ratios for the recombinant viruses and MA15 virus as for SARS-CoV (Urbani) ( Figure 2A ). In order to evaluate whether changes in tissue tropism or levels of viral replication could contribute to the lethal phenotype of the MA15 virus, viral titers in lungs, spleen, liver, and brain of BALB/c mice were determined at various time points following intranasal inoculation with SARS-CoV (Urbani) or MA15. abstract: No single animal model for severe acute respiratory syndrome (SARS) reproduces all aspects of the human disease. Young inbred mice support SARS-coronavirus (SARS-CoV) replication in the respiratory tract and are available in sufficient numbers for statistical evaluation. They are relatively inexpensive and easily accessible, but their use in SARS research is limited because they do not develop illness following infection. Older (12- to 14-mo-old) BALB/c mice develop clinical illness and pneumonitis, but they can be hard to procure, and immune senescence complicates pathogenesis studies. We adapted the SARS-CoV (Urbani strain) by serial passage in the respiratory tract of young BALB/c mice. Fifteen passages resulted in a virus (MA15) that is lethal for mice following intranasal inoculation. Lethality is preceded by rapid and high titer viral replication in lungs, viremia, and dissemination of virus to extrapulmonary sites accompanied by lymphopenia, neutrophilia, and pathological changes in the lungs. Abundant viral antigen is extensively distributed in bronchial epithelial cells and alveolar pneumocytes, and necrotic cellular debris is present in airways and alveoli, with only mild and focal pneumonitis. These observations suggest that mice infected with MA15 die from an overwhelming viral infection with extensive, virally mediated destruction of pneumocytes and ciliated epithelial cells. The MA15 virus has six coding mutations associated with adaptation and increased virulence; when introduced into a recombinant SARS-CoV, these mutations result in a highly virulent and lethal virus (rMA15), duplicating the phenotype of the biologically derived MA15 virus. Intranasal inoculation with MA15 reproduces many aspects of disease seen in severe human cases of SARS. The availability of the MA15 virus will enhance the use of the mouse model for SARS because infection with MA15 causes morbidity, mortality, and pulmonary pathology. This virus will be of value as a stringent challenge in evaluation of the efficacy of vaccines and antivirals. url: https://www.ncbi.nlm.nih.gov/pubmed/17222058/ doi: 10.1371/journal.ppat.0030005 id: cord-321901-zpi7uis1 author: Roberts, Anjeanette title: Animal models and antibody assays for evaluating candidate SARS vaccines: Summary of a technical meeting 25–26 August 2005, London, UK date: 2006-11-30 words: 6600.0 sentences: 311.0 pages: flesch: 40.0 cache: ./cache/cord-321901-zpi7uis1.txt txt: ./txt/cord-321901-zpi7uis1.txt summary: Scientists at the WHO Technical Meeting on Animal Models and Antibody Assays for Evaluating Candidate SARS Vaccines held on 25-26 August 2005 in South Mimms, UK, discussed many aspects of research pertaining to the use of animal models in vaccine development including available animal models, suitability of the various models, correlates of protection, critical components of potential vaccines, and the potential for disease enhancement in vaccinated animals following exposure to SARS-CoV. It may actually be worthwhile to enhance the virulence of a SARS-CoV isolate by serial passages in an animal model to produce a challenge virus stock for vaccine studies that would elicit more reproducible disease in the animals. Although none of the studies to date have shown enhanced respiratory disease following SARS-CoV challenge in previously immunized animals, further studies in this area are warranted in view of some of the available in vitro data. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice abstract: Abstract Severe acute respiratory syndrome (SARS) emerged in the Guangdong province of China in late 2002 and spread to 29 countries. By the end of the outbreak in July 2003, the CDC and WHO reported 8437 cases with a 9.6% case fatality rate. The disease was caused by a previously unrecognized coronavirus, SARS-CoV. Drawing on experience with animal coronavirus vaccines, several vaccine candidates have been developed and evaluated in pre-clinical trials. Available data suggest that vaccines should be based on the the 180kDa viral spike protein, S, the only significant neutralization antigen capable of inducing protective immune responses in animals. In the absence of clinical cases of SARS, candidate vaccines should be evaluated for efficacy in animal models, and although it is uncertain whether the United States Food and Drug Administration's “animal rule” would apply to licensure of a SARS vaccine, it is important to develop standardized animal models and immunological assays in preparation for this eventuality. This report summarizes the recommendations from a WHO Technical Meeting on Animal Models and Antibody Assays for Evaluating Candidate SARS Vaccines held on 25–26 August 2005 in South Mimms, UK, provides guidance on the use of animal models, and outlines the steps to develop standard reagents and assays for immunological evaluation of candidate SARS vaccines. url: https://www.sciencedirect.com/science/article/pii/S0264410X06008231 doi: 10.1016/j.vaccine.2006.07.009 id: cord-347706-r0rs3ls1 author: Roberts, Anjeanette title: Animal Models for Sars date: 2006 words: 3013.0 sentences: 139.0 pages: flesch: 43.0 cache: ./cache/cord-347706-r0rs3ls1.txt txt: ./txt/cord-347706-r0rs3ls1.txt summary: Mice that recover from infection develop a neutralizing antibody response and are protected from subsequent challenge; antibody alone is sufficient to protect mice from replication of SARS-CoV in the lower respiratory tract and NK, NK-T, T, and B cells are not required for viral clearance. 13, 13b CoV disease, with weight loss and pneumonitis that begins with acute bronchiolitis and In summary, SARS-CoV replicates efficiently in the respiratory tract of young viremia occurs 1 to 2 days following infection and virus is detected in the liver and spleen in hamsters. As seen with the other animal models, the course of infection in experimentally infected nonhuman primates is short, with a rapid peak in viral replication and clearance of virus from the lungs by days 4 to 7 in different species. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037579/ doi: 10.1007/978-0-387-33012-9_83 id: cord-290690-53t7df81 author: Roberts, David J. title: Life in Times of COVID‐19 date: 2020-05-13 words: 1448.0 sentences: 69.0 pages: flesch: 60.0 cache: ./cache/cord-290690-53t7df81.txt txt: ./txt/cord-290690-53t7df81.txt summary: The articles by CK Lee from Hong Kong 2 and Dana Devine 3 from Canada describe how blood services in two very different epidemiological settings responded to the epidemic. However, the measures implemented for SARS in Hong Kong in 2003, namely social distancing, use of personal protective equipment and screening of donors, laid the foundation for many blood services'' response to this current epidemic. Similarly, the methods developed by Dr Lee in the SARS epidemic in 2002 described in this issue, have enable Hong Kong to maintain the blood supply in this COVID-19 pandemic and have been shared by webinar and have helped many blood services cope with the current crisis (https://education.isbtweb.org/isbt/#!*menu=8*browseby=8*sortby=2*label=19776) (Accessed 1st May 2020). Perhaps the wider lesson from the experience of Hong Kong and Canada was that very real threat posed by SARS in 2003 prompted improved pandemic planning. abstract: nan url: https://doi.org/10.1111/tme.12688 doi: 10.1111/tme.12688 id: cord-272566-rtnhndw3 author: Robertson, M. title: A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort date: 2020-05-04 words: 5158.0 sentences: 323.0 pages: flesch: 55.0 cache: ./cache/cord-272566-rtnhndw3.txt txt: ./txt/cord-272566-rtnhndw3.txt summary: Following baseline questionnaire completion, study participants will be contacted monthly (for 6 months) to complete assessments of engagement in non-pharmaceutical interventions (e.g., use of cloth masks, avoiding large gatherings); COVID-19 symptoms; SARS/COV2 testing and diagnosis; hospitalizations; healthcare access; and uptake of health messaging. 2, 3 In response to the COVID-19 pandemic the CUNY Institute for Implementation Science in Population Health (ISPH) launched the Communities, Households and SARS/COV-2 Epidemiology (CHASING) COVID Cohort "C 3 " study on March 28, 2020 . For analyses to assess subsequent disease after Month 1, incident COVID-19 disease will be defined as development of new COVID-like symptoms > 7 days after the first (positive or negative) SARS/COV2 serologic test result. The C 3 cohort is geographically and socio-demographically diverse, and includes participants from many active hotspots during the recruitment period (March 28-April 20, 2020), as well as frontline health care workers and other essential employees, and individuals who are vulnerable to severe outcomes associated with SARS/COV2 infection. abstract: Introduction: The Chasing COVID Cohort (C3) study is a US-based, geographically and socio-demographically diverse sample of adults (18 and older) enrolled into a prospective cohort study during the upswing of the U.S. COVID-19 pandemic. Methods: We used internet-based strategies to enroll C3 participants beginning March 28th, 2020. Following baseline questionnaire completion, study participants will be contacted monthly (for 6 months) to complete assessments of engagement in non-pharmaceutical interventions (e.g., use of cloth masks, avoiding large gatherings); COVID-19 symptoms; SARS/COV2 testing and diagnosis; hospitalizations; healthcare access; and uptake of health messaging. Dried blood spot (DBS) specimens will be collected at the first follow-up assessment (last week of April 2020) and at month 3 (last week of June 2020) and stored until a validated serologic test is available. Results: As of April 20, 2020, the number of people that completed the baseline survey and provided contact information for follow-up was 7,070. Participants resided in all 50 US states, the District of Columbia, Puerto Rico, and Guam. At least 24% of participants were frontline workers (healthcare and other essential workers). Twenty-three percent (23%) were 60+ years, 24% were Black or Hispanic, 52% were men, and 52% were currently employed. Nearly 20% reported recent COVID-like symptoms (cough, fever or shortness of breath) and a high proportion reported engaging in non-pharmaceutical interventions that reduce SARS/COV2 spread (93% avoided groups >20, 58% wore masks; 73% quarantined). More than half (54%) had higher risk for severe COVID-19 illness should they become infected with SARS/COV2 based on age, underlying health conditions (e.g., chronic lung disease), or daily smoking. Discussion: A geographically and socio-demographically diverse group of participants was rapidly enrolled in the C3 during the upswing of the SARS/COV2 pandemic. Strengths of the C3 include the potential for direct observation of, and risk factors for, seroconversion and incident COVID disease (among those with or without antibodies to SARS/COV2) in areas of active transmission. url: https://doi.org/10.1101/2020.04.28.20080630 doi: 10.1101/2020.04.28.20080630 id: cord-316845-k9zvsfvj author: Robertson, Mary M. title: Gilles de la Tourette Syndrome: advice in the times of COVID-19 date: 2020-04-28 words: 3763.0 sentences: 212.0 pages: flesch: 53.0 cache: ./cache/cord-316845-k9zvsfvj.txt txt: ./txt/cord-316845-k9zvsfvj.txt summary: These include the coronaviruses, which have caused multiple major public health events that resulted in global pandemics such as severe acute respiratory syndrome (SARS; or "bat SARS"), Middle East respiratory syndrome (MERS) and the current coronavirus disease (COVID-19) (Kandeel et al., 2020). GTS, as a complex neuropsychiatric disorder, offers many angles of attack for the current COVID-19 pandemic and its consequences (social distancing, home schooling, confinement/quarantine, and living in a general climate of fear). The authors discuss similarities of COVID-19 and tics in GTS and outline specific problems that may result from the pandemic for this group of patients. I like this small paper and find it interesting to read, since it alerts us that the current pandemic may be much more challenging for patients with GTS compared to healthy people. Also in Table 1 : "Viral infection -Coronavirus 19" please change in "SARS-CoV-2".The authors describe the different symptoms associated with COVID-19 including neurological complications. abstract: The novel coronavirus disease (COVID-19) was identified as the cause of an outbreak of respiratory disease in China at the end of 2019. It then spread with enormous rapidity and by mid-March 2020 was declared a world pandemic. Gilles de la Tourette Syndrome (GTS) is a childhood-onset neurodevelopmental disorder with a worldwide prevalence of about 1% of the population. The clinical symptoms include multiple motor and one or more phonic (vocal) tics. Germane to this communication is that 85% of patients with GTS have associated psychiatric co-morbidities, many of which are being exacerbated in the current global health crisis. In addition, several symptoms of GTS may mimic COVID-19, such as a dry cough and sniffing (phonic tics), while other symptoms such as spitting, inappropriate touching of others and “non-obscene socially inappropriate symptoms” can potentially get patients with GTS into trouble with the law. We suggest that a clear explanation of the COVID-19 illness and GTS is important to enable colleagues of various specialities who tend to patients with GTS. It is important to acknowledge at the outset that the information available on the COVID-19 pandemic changes daily, including cases infected, deaths reported, and how various national health systems are planning and or coping or not. It is fair to say that having read the current medical and lay press we conclude that it is not easy to reassure our patients with absolute certainty. However, notwithstanding that, we hope our documentation is of some assistance. url: https://doi.org/10.12688/f1000research.23275.2 doi: 10.12688/f1000research.23275.2 id: cord-288070-qwax5tg9 author: Robilotti, E. V. title: Determinants of Severity in Cancer Patients with COVID-19 Illness date: 2020-05-08 words: 2652.0 sentences: 166.0 pages: flesch: 48.0 cache: ./cache/cord-288070-qwax5tg9.txt txt: ./txt/cord-288070-qwax5tg9.txt summary: Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. On multivariate analysis, age ≥ 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. In this study, we report on the epidemiology of COVID-19 illness experienced at our cancer center over the last month, during the height of incident cases in New York City, and offer an analysis of risk factors for severe infection that is pertinent to cancer patient populations. abstract: New York State had 180,458 cases of SARS-CoV-2 and 9385 reported deaths as of April 10th, 2020. Patients with cancer comprised 8.4% of deceased individuals1. Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. This information is critical to balance the competing safety considerations of reducing SARS-CoV-2 exposure and cancer treatment continuation. Since March 10th, 2020 Memorial Sloan Kettering Cancer Center performed diagnostic testing for SARS-CoV-2 in symptomatic patients. Overall, 40% out of 423 patients with cancer were hospitalized for COVID-19 illness, 20% developed severe respiratory illness, including 9% that required mechanical ventilation, and 9% that died. On multivariate analysis, age [≥] 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Association between ICI and COVID-19 outcomes will need interrogation in tumor-specific cohorts. url: https://www.ncbi.nlm.nih.gov/pubmed/32511541/ doi: 10.1101/2020.05.04.20086322 id: cord-329844-w969lczb author: Robson, B. title: Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date: 2020-06-08 words: 15903.0 sentences: 664.0 pages: flesch: 49.0 cache: ./cache/cord-329844-w969lczb.txt txt: ./txt/cord-329844-w969lczb.txt summary: The location of any sialic acid glycan binding region of SARS-CoV-2 is, a priori unclear, although intuitively (a) it would likely be associated with the cap or knob at the outer end of the spike protein, or (b) at least not involve exactly the same domain as is required for other important functions. An algorithm for predicting the domains and proteins involved in sialic acid glycan binding is developed in the course of the project described in Results Section 4, but this is primarily of a highly empirical nature. This, plus a sequence rather than three dimensional structure perspective, and a specific focus on binding sialic acid glycans rather than sugars in general, resulted in a substantial difference in scores from another major method of predicting sugar binding regions of proteins also discussed later below. abstract: SARS-CoV and SARS-CoV-2 do not appear to have functions of a hemagglutinin and neuraminidase. This is a mystery, because sugar binding activities appear essential to many other viruses including influenza and even most other coronaviruses in order to bind to and escape from the glycans (sugars, oligosaccharides or polysaccharides) characteristic of cell surfaces and saliva and mucin. The S1 N terminal Domains (S1-NTD) of the spike protein, largely responsible for the bulk of the characteristic knobs at the end of the spikes of SARS-CoV and SARS-CoV-2, are here predicted to be “hiding” sites for recognizing and binding glycans containing sialic acid. This may be important for infection and the ability of the virus to locate ACE2 as its known main host cell surface receptor, and if so it becomes a pharmaceutical target. It might even open up the possibility of an alternative receptor to ACE2. The prediction method developed, which uses amino acid residue sequence alone to predict domains or proteins that bind to sialic acids, is naïve, and will be advanced in future work. Nonetheless, it was surprising that such a very simple approach was so useful, and it can easily be reproduced in a very few lines of computer program to help make quick comparisons between SARS-CoV-2 sequences and to consider the effects of viral mutations. url: https://www.ncbi.nlm.nih.gov/pubmed/32658736/ doi: 10.1016/j.compbiomed.2020.103849 id: cord-333262-xvfl7ycj author: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 words: 21671.0 sentences: 953.0 pages: flesch: 50.0 cache: ./cache/cord-333262-xvfl7ycj.txt txt: ./txt/cord-333262-xvfl7ycj.txt summary: The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). abstract: Abstract This paper continues a recent study of the spike protein sequence of the COVID-19 virus (SARS-CoV-2). It is also in part an introductory review to relevant computational techniques for tackling viral threats, using COVID-19 as an example. Q-UEL tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. Subsequence KRSFIEDLLFNKV of the S2′ spike glycoprotein proteolytic cleavage site continues to appear important. Here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. Its function or functions thus seem important to the coronaviruses. It might represent SARS-CoV-2 Achilles’ Heel, less likely to acquire resistance by mutation, as has happened in some early SARS vaccine studies discussed in the previous paper. Preliminary conformational analysis of the receptor (ACE2) binding site of the spike protein is carried suggesting that while it is somewhat conserved, it appears to be more variable than KRSFIEDLLFNKV. However compounds like emodin that inhibit SARS entry, apparently by binding ACE2, might also have functions at several different human protein binding studies. The enzyme 11β-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. Perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets. url: https://doi.org/10.1016/j.compbiomed.2020.103749 doi: 10.1016/j.compbiomed.2020.103749 id: cord-343586-28ezisog author: Rocca, María Florencia title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date: 2020-05-07 words: 1498.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-343586-28ezisog.txt txt: ./txt/cord-343586-28ezisog.txt summary: title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied. These preliminary results suggest that MALDI-TOF MS coupled with ClinProTools software represents an interesting alternative as a screening tool for diagnosis of SARS-CoV-2, especially because of the good performance and accuracy obtained with samples in which viral presence was not detected. abstract: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid, sensitive and specific diagnosis of SARS-CoV-2 by fast and unambiguous testing is widely recognized to be critical in responding to the ongoing outbreak. Since the current testing capacity of RT-PCR-based methods is being challenged due to the extraordinary demand of supplies, such as RNA extraction kits and PCR reagents worldwide, alternative and/or complementary testing assays should be developed. Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied. url: https://doi.org/10.1101/2020.05.07.082925 doi: 10.1101/2020.05.07.082925 id: cord-258221-pn8gh73b author: Rocha, José Lucas Martins title: Mesenchymal Stromal Cells in Viral Infections: Implications for COVID-19 date: 2020-09-07 words: 8950.0 sentences: 487.0 pages: flesch: 42.0 cache: ./cache/cord-258221-pn8gh73b.txt txt: ./txt/cord-258221-pn8gh73b.txt summary: Abbreviations: ANG, Angiogenin; ANGPT1, Angiopoietin 1; bFGF, Basic fibroblast growth factor; BV/BR, Biliverdin and Bilirubin; COX2, Cyclooxygenase-2; DAMPs, Damage-associated molecular pattern; EGF, Epidermal growth factor; ESM1, Endothelial Cell Specific Molecule 1; FAS/FASL, apoptosis antigen 1 receptor and ligand; HGF, Hepatocyte growth factor; HLA-G, Human leukocyte antigen G; HO-1, Heme oxygenase 1; IDO, Indoleamine 2,3-dioxygenase; ISGs, Interferon-stimulated genes; Kyn, Kynurenin; LIF, Leukemia inhibitory factor; LPS, Lipopolysaccharide; miRNAs, micro RNA; MMPs, Matrix metalloproteinases; MSC-EV, Extracellular vesicles from MSC; PAMPs, Pathogen-associated molecular pattern; PGE2, Prostaglandin E2; PD-1/PD-L1, Programmed death receptor and ligand; ROS, Reactive oxygen species; SOD, Superoxide dismutase; sHLA-G, Soluble human leukocyte antigen G; sPD-L1/2, Soluble Programmed death ligands 1 and 2; TGF-β, Transforming growth factor β; TLR, Toll-like receptor; TNF-α, Tumor necrosis factor α; Trp , Tryptophan; TSG-6, TNFstimulated gene 6 Similarly, long-lasting FASL interactions enable MSCs to induce T cell apoptosis [39] . abstract: Mesenchymal stromal cells (MSCs) constitute a heterogeneous population of stromal cells with immunomodulatory and regenerative properties that support their therapeutic use. MSCs isolated from many tissue sources replicate vigorously in vitro and maintain their main biological properties allowing their widespread clinical application. To date, most MSC-based preclinical and clinical trials targeted immune-mediated and inflammatory diseases. Nevertheless, MSCs have antiviral properties and have been used in the treatment of various viral infections in the last years. Here, we revised in detail the biological properties of MSCs and their preclinical and clinical applications in viral diseases, including the disease caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection (COVID-19). Notably, rapidly increasing numbers of MSC-based therapies for COVID-19 have recently been reported. MSCs are theoretically capable of reducing inflammation and promote lung regeneration in severe COVID-19 patients. We critically discuss the rationale, advantages and disadvantages of MSC-based therapies for viral infections and also specifically for COVID-19 and point out some directions in this field. Finally, we argue that MSC-based therapy may be a promising therapeutic strategy for severe COVID-19 and other emergent respiratory tract viral infections, beyond the viral infection diseases in which MSCs have already been clinically applied. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12015-020-10032-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12015-020-10032-7 doi: 10.1007/s12015-020-10032-7 id: cord-288644-ywaefpe8 author: Rodon, Jordi title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 words: 7571.0 sentences: 449.0 pages: flesch: 50.0 cache: ./cache/cord-288644-ywaefpe8.txt txt: ./txt/cord-288644-ywaefpe8.txt summary: We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. abstract: There is an urgent need to identify novel drugs against the new coronavirus. Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still under evaluation. Here, we have screened existing drugs approved for human use in a variety of diseases, to compare how they counteract SARS-CoV-2-induced cytopathic effect and viral replication in vitro. Among the potential 72 antivirals tested herein that were previously proposed to inhibit SARS-CoV-2 infection, only 18% had in vitro antiviral activity. Moreover, only eight families had an IC50 below 25 µM or 102 IU/mL. These include chloroquine derivatives and remdesivir, along with plitidepsin, cathepsin inhibitors, nelfinavir mesylate hydrate, interferon 2-alpha, interferon-gamma, fenofibrate and camostat. Plitidepsin was the only clinically approved drug displaying nanomolar efficacy. Four of these families, including novel cathepsin inhibitors, blocked viral entry in a cell-type specific manner. Since the most effective antivirals usually combine therapies that tackle the virus at different steps of infection, we also assessed several drug combinations. Although no particular synergy was found, inhibitory combinations did not reduce their antiviral activity. Thus, these combinations could decrease the potential emergence of resistant viruses. Antivirals prioritized herein identify novel compounds and their mode of action, while independently replicating the activity of a reduced proportion of drugs which are mostly approved for clinical use. Combinations of these drugs should be tested in animal models to inform the design of fast track clinical trials. url: https://doi.org/10.1101/2020.04.23.055756 doi: 10.1101/2020.04.23.055756 id: cord-353161-mtq6yh25 author: Rodrigues, João PGLM title: Insights on cross-species transmission of SARS-CoV-2 from structural modeling date: 2020-06-05 words: 6169.0 sentences: 369.0 pages: flesch: 56.0 cache: ./cache/cord-353161-mtq6yh25.txt txt: ./txt/cord-353161-mtq6yh25.txt summary: We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Collectively, our results provide a structural framework that explains why certain animal species are not susceptible to SARS-CoV-2 infection, and also suggests potential mutations that can enhance binding to the viral RBD. Although it is well-known that docking scores do not quantitatively correlate with experimental binding affinities [19] , these scores suggest that SARS-CoV-2 neg species lack one or more key ACE2 residues that contribute significantly to the interaction with RBD. Models of SARS-CoV-2 neg species -chicken, duck, guinea pig, mouse, and rat -generally have higher (worse) HADDOCK scores than average (Figure 2 ), suggesting that these species'' non-susceptibility to infection could stem from deficient RBD binding to ACE2. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global pandemic that has infected more than 6 million people in more than 180 countries worldwide. Like other coronaviruses, SARS-CoV-2 is thought to have been transmitted to humans from wild animals. Given the scale and widespread geographical distribution of the current pandemic, the question emerges whether human-to-animal transmission is possible and if so, which animal species are most at risk. Here, we investigated the structural properties of several ACE2 orthologs bound to the SARS-CoV-2 spike protein. We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Our models also predict affinity-enhancing mutations that could be used to design ACE2 variants for therapeutic purposes. Finally, our study provides a blueprint for modeling viral-host protein interactions and highlights several important considerations when designing these computational studies and analyzing their results. url: https://www.ncbi.nlm.nih.gov/pubmed/32577636/ doi: 10.1101/2020.06.05.136861 id: cord-347090-sqw7n1v2 author: Rodriguez-Gonzalez, Moises title: New onset severe right ventricular failure associated with COVID-19 in a young infant without previous heart disease date: 2020-06-16 words: 1816.0 sentences: 110.0 pages: flesch: 44.0 cache: ./cache/cord-347090-sqw7n1v2.txt txt: ./txt/cord-347090-sqw7n1v2.txt summary: We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. abstract: We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. He did not present signs of toxin-mediated disease or Kawasaki disease. He was finally diagnosed with SARS-CoV-2 infection. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. url: https://doi.org/10.1017/s1047951120001857 doi: 10.1017/s1047951120001857 id: cord-290254-m9l8ntur author: Rodriguez-Manzano, J. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 words: 5622.0 sentences: 340.0 pages: flesch: 54.0 cache: ./cache/cord-290254-m9l8ntur.txt txt: ./txt/cord-290254-m9l8ntur.txt summary: In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Currently, reverse transcriptase polymerase chain reaction using real-time benchtop platform (RT-qPCR) is considered the gold standard for COVID-19 diagnosis due to its capability to detect the presence of SARS-CoV-2 RNA close to the onset of symptomatic illness which is critical for isolation. In this paper, we combined LAMP with an in-house LoC device to develop a rapid PoC diagnostic test (< 20 min) for the detection of SARS-CoV-2 RNA from extracted samples. abstract: The COVID-19 pandemic is a global health emergency characterized by the high rate of transmission and ongoing increase of cases globally. Rapid point-of-care (PoC) diagnostics to detect the causative virus, SARS-CoV-2, are urgently needed to identify and isolate patients, contain its spread and guide clinical management. In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. The developed LAMP assay was tested on a real-time benchtop instrument (RT-qLAMP) showing a lower limit of detection of 10 RNA copies per reaction. It was validated against 183 clinical samples including 127 positive samples (screened by the CDC RT-qPCR assay). Results showed 90.55% sensitivity and 100% specificity when compared to RT-qPCR and average positive detection times of 15.45 {+/-} 4.43 min. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Paired with a smartphone for results visualization and geo-localization, this portable diagnostic platform with secure cloud connectivity will enable real-time case identification and epidemiological surveillance. url: http://medrxiv.org/cgi/content/short/2020.06.29.20142349v1?rss=1 doi: 10.1101/2020.06.29.20142349 id: cord-319833-u9uuuu38 author: Rodriguez-Martinez, Carlos E. title: Decontamination and reuse of N95 filtering facemask respirators: a systematic review of the literature date: 2020-07-08 words: 7259.0 sentences: 380.0 pages: flesch: 47.0 cache: ./cache/cord-319833-u9uuuu38.txt txt: ./txt/cord-319833-u9uuuu38.txt summary: METHODS: We performed a systematic review of the literature in order to identify studies reporting outcomes of at least one decontamination method for inactivating or removing any potentially infectious material from the surface of N95 FFRs, specifically addressing issues related to reduction of the microbial threat (including SARS-CoV-2 when available), maintaining the function of N95 FFRs and a lack of residual toxicity. 10 Although various decontamination methods have been used, there are concerns over certain characteristics of the N95 FFRs with respect to their utilization, such as alterations in their physical appearance/odor, structural integrity, filtration efficiency, fit and seal and filter airflow resistance, degradation of their material, and chemical residues that are potentially toxic or irritate the skin (due to the chemical disinfectants required for rinsing and drying). abstract: INTRODUCTION: As has happened in other emerging respiratory pandemics, demand for N95 filtering facemask respirators (FFRs) has far exceeded their manufacturing production and availability in the context of the SARS-CoV-2 pandemic. One of the proposed strategies for mitigating the massive demand for N95 FFRs is their reuse after a process of decontamination that allows the inactivation of any potentially infectious material on their surfaces. This article aims to summarize all of the available evidence on the different decontamination methods that might allow disposable N95 FFRs to be reused, with emphasis on decontamination from SARS-CoV-2. METHODS: We performed a systematic review of the literature in order to identify studies reporting outcomes of at least one decontamination method for inactivating or removing any potentially infectious material from the surface of N95 FFRs, specifically addressing issues related to reduction of the microbial threat (including SARS-CoV-2 when available), maintaining the function of N95 FFRs and a lack of residual toxicity. RESULTS: We identified a total of 14 studies reporting on the different decontamination methods that might allow disposable N95 FFRs to be reused, including small-scale energetic methods and disinfecting solutions/spray/wipes. Among these decontamination methods, ultraviolet germicidal irradiation (UVGI) and vaporized hydrogen peroxide (VHP) seem to be the most promising decontamination methods for N95 FFRs, based on their biocidal efficacy, filtration performance, fitting characteristics, and residual chemical toxicity, as well as other practical aspects such as the equipment required for their implementation and the maximum number of decontamination cycles. CONCLUSIONS: Although all the methods for the decontamination and reuse of N95 FFRs have advantages and disadvantages, UVGI and VHP seem to be the most promising methods. url: https://doi.org/10.1016/j.ajic.2020.07.004 doi: 10.1016/j.ajic.2020.07.004 id: cord-031497-pp0p3en6 author: Rodríguez-Fuster, Alberto title: Tracheal trauma in the context of the current infection by COVID-19. About 2 cases() date: 2020-09-06 words: 1153.0 sentences: 79.0 pages: flesch: 53.0 cache: ./cache/cord-031497-pp0p3en6.txt txt: ./txt/cord-031497-pp0p3en6.txt summary: Various authors and scientific societies have recommended limiting the number of airway procedures and manipulations and introducing stringent protection measures for health personnel in order to minimize the risk of infection. [2] [3] [4] We report 2 cases of patients diagnosed with SARS-CoV-2 infection and tracheal iatrogenic rupture following airway manipulation. She required OTI + MV for respiratory failure, and during the procedure she incurred a tracheal lesion confirmed by computed tomography and fiberoptic bronchoscopy to be a rupture of the pars membranacea measuring approximately 2 cm. To minimize the risk of aerosols, the patient was maintained in complete muscle relaxation throughout the procedure; preoxygenation and ventilatory pauses-apneas-were performed (as far as possible) in accordance with the recommendations described for tracheotomy. Emergency tracheal intubation in 202 patients with COVID-19 in Wuhan, China: lessons learnt and international expert recommendations Tracheal trauma after difficult airway management in morbidly obese patients with COVID-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474846/ doi: 10.1016/j.arbr.2020.08.007 id: cord-280697-tovty20e author: Rodríguez‐Martínez, Carlos E. title: Efficacy, safety and cost‐effectiveness of hydroxychloroquine in children with COVID‐19: A call for evidence date: 2020-06-03 words: 929.0 sentences: 55.0 pages: flesch: 48.0 cache: ./cache/cord-280697-tovty20e.txt txt: ./txt/cord-280697-tovty20e.txt summary: Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including pediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for pediatric patients) at present time (2). 1 Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including paediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for paediatric patients) at present time. We would therefore encourage nations where the undertaking of high-quality clinical trials in children during the current SARS-CoV-2 pandemic is possible, to ensure that putative treatments that would be available and affordable in low-to middle-income countries (LMICs), such as hydroxychloroquine, are included wherever possible. At a time of great uncertainty, evidence is urgently needed to inform treatment options, and therefore, randomised controlled trials are necessary to clarify further the clinical benefit of HCQ in paediatric patients with SARS-CoV-2 infections. abstract: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic poses a serious threat to public health and local economies around the globe. This has created an urgent need to identify effective medications for its prevention and treatment (1). Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including pediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for pediatric patients) at present time (2). url: https://www.ncbi.nlm.nih.gov/pubmed/32438459/ doi: 10.1111/apa.15373 id: cord-309633-1cd74xdl author: Rogers, Julia H. title: Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study date: 2020-09-15 words: 4018.0 sentences: 241.0 pages: flesch: 53.0 cache: ./cache/cord-309633-1cd74xdl.txt txt: ./txt/cord-309633-1cd74xdl.txt summary: MEASUREMENTS: The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. CONCLUSION: Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. Surge testing was initiated on 30 March 2020 (and continued through 24 April) in collaboration with Public Health-Seattle & King County''s Communicable Disease Epidemiology Team to conduct contact tracing at 6 shelters where cases of SARS-CoV-2 were previously detected ( Figure 2 ). We calculated the test positivity rate of SARS-CoV-2 infection at shelters by dividing the number of positive cases by the total number of participant encounters in the study period. Overall, 2% of participant encounters involved positive SARS-CoV-2 results, with most cases detected through surge testing events. abstract: BACKGROUND: Homeless shelters are a high-risk setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission because of crowding and shared hygiene facilities. OBJECTIVE: To investigate SARS-CoV-2 case counts across several adult and family homeless shelters in a major metropolitan area. DESIGN: Cross-sectional, community-based surveillance study. (ClinicalTrials.gov: NCT04141917) SETTING: 14 homeless shelters in King County, Washington. PARTICIPANTS: A total of 1434 study encounters were done in shelter residents and staff, regardless of symptoms. INTERVENTION: Two strategies were used for SARS-CoV-2 testing: routine surveillance and contact tracing (“surge testing”) events. MEASUREMENTS: The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. Sociodemographic, clinical, and virologic variables were assessed as correlates of viral positivity. RESULTS: Among 1434 encounters, 29 (2% [95% CI, 1.4% to 2.9%]) cases of SARS-CoV-2 infection were detected across 5 shelters. Most (n = 21 [72.4%]) were detected during surge testing events rather than routine surveillance, and most (n = 21 [72.4% {CI, 52.8% to 87.3%}]) were asymptomatic at the time of sample collection. Persons who were positive for SARS-CoV-2 were more frequently aged 60 years or older than those without SARS-CoV-2 (44.8% vs. 15.9%). Eighty-six percent of persons with positive test results slept in a communal space rather than in a private or shared room. LIMITATION: Selection bias due to voluntary participation and a relatively small case count. CONCLUSION: Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. The findings suggest an unmet need for routine viral testing outside of clinical settings for homeless populations. PRIMARY FUNDING SOURCE: Gates Ventures. url: https://doi.org/10.7326/m20-3799 doi: 10.7326/m20-3799 id: cord-252473-i4pmux28 author: Rogers, Sharon title: Why can''t I visit? The ethics of visitation restrictions – lessons learned from SARS date: 2004-08-31 words: 1908.0 sentences: 83.0 pages: flesch: 42.0 cache: ./cache/cord-252473-i4pmux28.txt txt: ./txt/cord-252473-i4pmux28.txt summary: It could be argued that visitation restrictions, in light of a potential outbreak of a contagious disease, are ethically sound because of the compelling need to protect public health. In a health care institution, visitation restrictions not only affect inpatients but also have an impact on ambulatory patients who must come for diagnostic tests or interventions and who, if deprived access, might develop urgent or emergent conditions. Furthermore, to be consistent with expectations of transparency, the criteria by which exceptionality to the rules of visitation restriction exists should also be published openly throughout the organization for staff, patients and visitors. For example, although current policy allows for specific times of visitation and numbers of visitors per day, a sudden outbreak might dictate a quick lockdown of the facility without patients or family members receiving prior notice. It is ethical to accept that public health protection trumps individual rights to liberal visitation. abstract: Patients want, need and expect that their relatives will be able to visit them during inpatient admissions or accompany them during ambulatory visits. The sudden outbreak of severe acute respiratory syndrome (SARS), or a similar contagious pathogen, will restrict the number of people entering the hospital. The ethical values that underlie visitor restrictions are discussed here. url: https://www.ncbi.nlm.nih.gov/pubmed/15469583/ doi: 10.1186/cc2930 id: cord-263167-es806qhz author: Rogers, Thomas F. title: Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model date: 2020-06-15 words: 4512.0 sentences: 249.0 pages: flesch: 53.0 cache: ./cache/cord-263167-es806qhz.txt txt: ./txt/cord-263167-es806qhz.txt summary: We showed that passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters, as revealed by maintained weight and low lung viral titers in treated animals. Donor plasma were tested for binding to recombinant SARS-CoV-2 and SARS-CoV-1 S and receptor binding domain (RBD) proteins, for binding to cell surface expressed spikes and for neutralization in both live replicating virus and pseudovirus assays (Fig. 2, B to D, and fig. The bulk-transformed ligation products for both the heavy chain and light chain were transfected and tested for binding to RBD and S protein, and for neutralization in the SARS-CoV-2 pseudovirus assay using HeLa-ACE2 target cells ( fig. To investigate the relationship between in vitro neutralization and protection in vivo against SARS-CoV-2, we selected two mAbs for passive transfer/challenge experiments in a Syrian hamster animal model based on a summary of the nAb data (table S3 and fig. abstract: Countermeasures to prevent and treat COVID-19 are a global health priority. We enrolled a cohort of SARS-CoV-2-recovered participants, developed neutralization assays to interrogate antibody responses, adapted our high-throughput antibody generation pipeline to rapidly screen over 1800 antibodies, and established an animal model to test protection. We isolated potent neutralizing antibodies (nAbs) to two epitopes on the receptor binding domain (RBD) and to distinct non-RBD epitopes on the spike (S) protein. We showed that passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters, as revealed by maintained weight and low lung viral titers in treated animals. The study suggests a role for nAbs in prophylaxis, and potentially therapy, of COVID-19. The nAbs define protective epitopes to guide vaccine design. url: https://doi.org/10.1126/science.abc7520 doi: 10.1126/science.abc7520 id: cord-335040-1qa6pe4v author: Rogstam, Annika title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-10-06 words: 7408.0 sentences: 385.0 pages: flesch: 59.0 cache: ./cache/cord-335040-1qa6pe4v.txt txt: ./txt/cord-335040-1qa6pe4v.txt summary: The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. observed SARS nsp10 in the same space group as reported here, I213, reporting a monomer in the asymmetric unit but a dimer in solution, as was determined by size exclusion Residues shaded in red are fully conserved, while residues with text in red indicate a change to a similar residue. We determined the crystal structure and behaviour in solution of SARS-CoV-2 nsp10 in its unbound form. abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing Coronavirus Disease 19 (COVID-19), emerged at the end of 2019 and quickly spread to cause a global pandemic with severe socio-economic consequences. The early sequencing of its RNA genome revealed its high similarity to SARS, likely to have originated from bats. The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. Here, we report the biophysical characterization and 1.6 Å resolution structure of the unbound form of nsp10 from SARS-CoV-2 and compare it to the structures of its SARS homologue and the complex-bound form with nsp16 from SARS-CoV-2. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/33036230/ doi: 10.3390/ijms21197375 id: cord-287501-7it4kh0e author: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 words: 2964.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-287501-7it4kh0e.txt txt: ./txt/cord-287501-7it4kh0e.txt summary: We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. 33 In this study, we report a novel approach for the inhibitor screening of SARS-CoV N protein using a quantum dots (QDs)-conjugated oligonucleotide system with wide applicability for facile and sensitive imaging analysis on a biochip. To the best of our knowledge, this is the first report on the inhibition effects of (-)-catechin gallate and (-)-gallocatechin gallate on SARS-CoV N protein using an optical nanoparticle-based RNA oligonucleotide platform. Among the polyphenolic compounds screened, (-)-catechin gallate and (-)-gallocatechin gallate showed high anti-SARS-CoV N protein activity. At a concentration of 0.05 µg mL -1 , (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a QDs-RNA oligonucleotide biochip platform. abstract: Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS), and the rate of global death from SARS has remarkably increased. Hence, the development of efficient drug treatments for the biological effects of SARS is highly needed. We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. In this study, we found that a designed biochip could analyze inhibitors of the SARS-CoV N protein using nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. (−)-catechin gallate and (−)-gallocatechin gallate attenuated the binding affinity in a concentrated manner as evidenced by QDs-conjugated RNA oligonucleotide on a designed biochip. At a concentration of 0.05 μg mL(−1), (−)-catechin gallate and (−)-gallocatechin gallate showed more than 40% inhibition activity on a nanoparticle-based RNA oligonucleotide biochip system. url: https://doi.org/10.2147/ijn.s31379 doi: 10.2147/ijn.s31379 id: cord-285979-ha5nszxi author: Rojas, Manuel title: Convalescent plasma in Covid-19: Possible mechanisms of action date: 2020-05-05 words: 5818.0 sentences: 334.0 pages: flesch: 44.0 cache: ./cache/cord-285979-ha5nszxi.txt txt: ./txt/cord-285979-ha5nszxi.txt summary: CP early administered after symptoms onset showed a reduction in mortality compared with placebo or no therapy in severe acute respiratory infections of viral etiology like influenza and SARS-CoV, however, a similar response in Ebola disease was not observed [20, 25] . This was demonstrated in B cells, where the upregulation of FCRIIB was associated with treatment efficacy for acute rejection after kidney transplantation [81] , and was J o u r n a l P r e -p r o o f a key determinant for IVIg response in patients with Kawasaki disease [82] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible of the coronavirus disease 2019 (COVID-19) pandemic. Therapeutic options including antimalarials, antivirals, and vaccines are under study. Meanwhile the current pandemic has called attention over old therapeutic tools to treat infectious diseases. Convalescent plasma (CP) constitutes the first option in the current situation, since it has been successfully used in other coronaviruses outbreaks. Herein, we discuss the possible mechanisms of action of CP and their repercussion in COVID-19 pathogenesis, including direct neutralization of the virus, control of an overactive immune system (i.e., cytokine storm, Th1/Th17 ratio, complement activation) and immunomodulation of a hypercoagulable state. All these benefits of CP are expected to be better achieved if used in non-critically hospitalized patients, in the hope of reducing morbidity and mortality. url: https://www.sciencedirect.com/science/article/pii/S1568997220301166?v=s5 doi: 10.1016/j.autrev.2020.102554 id: cord-322456-5at1euqm author: Rokohl, Alexander C. title: Die Rolle der Augenheilkunde in der COVID-19-Pandemie date: 2020-06-09 words: 1837.0 sentences: 210.0 pages: flesch: 47.0 cache: ./cache/cord-322456-5at1euqm.txt txt: ./txt/cord-322456-5at1euqm.txt summary: Im Dezember 2019 wurde Dr. Li Wenliang, ein Augenarzt aus der Volksrepublik China, in seinem Krankenhaus auf 7 Patienten, die alle unter einem schweren akuten Atemnotsyndrom litten und vorher einen Großmarkt in Wuhan besuchten, aufmerksam. Das COVID-19 auslösende Severe-Acute-Respiratory-Syndrome-related Coronavirus-2 (SARS-CoV-2) wurde durch die Coronavirus-Studiengruppe des Internationalen Komitees zur Taxonomie von Viren (International Committee on Taxonomy of Viruses) aufgrund der sehr engen Verwandtschaft zum Sars-Virus (Sars-CoV), an dem 2002/2003 Hunderte Menschen gestorben waren, benannt. Auch Dr. Li Wenliang, der Augenarzt, der die COVID-19 als einer der Ersten entdeckte und später auch an der Krankheit verstarb, könnte von einem asymptomatischen Patienten infiziert worden sein [23] . Zudem konnte in mehreren Studien mit hospitalisierten COVID-19-Patienten SARS-CoV-2-RNA in der Tränenflüssigkeit nachgewiesen werden [2, 28, 30, 32] . Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV-2. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 19 (COVID-19) has led to a worldwide pandemic. This pandemic presents a huge challenge for the healthcare system and also for ophthalmologists. Previous studies and case reports indicated that SARS-CoV‑2 also infects the conjunctiva resulting in conjunctivitis. In addition, infectious virus particles in the tear fluid can be potential sources of infection; however, the detection of SARS-CoV‑2 RNA in the tear fluid has rarely been successful. Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV‑2. Therefore, protective and hygiene measures should currently be consistently followed to minimize the risk of spreading the virus. Currently, there are no treatment recommendations for conjunctivitis associated with COVID-19. Tear substitutes might be helpful for symptom relief but there is no evidence for a topical antiviral therapy. In the future ophthalmologists could play a decisive role in the screening of maculopathies that might occur during COVID-19 treatment using chloroquine or hydroxychloroquine. url: https://www.ncbi.nlm.nih.gov/pubmed/32519117/ doi: 10.1007/s00347-020-01148-9 id: cord-350992-l6l24pco author: Roldan, Eugenia Quiros title: The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against Sars-Cov-2 infection (COVID-19): A role for iron homeostasis? date: 2020-05-13 words: 8037.0 sentences: 393.0 pages: flesch: 40.0 cache: ./cache/cord-350992-l6l24pco.txt txt: ./txt/cord-350992-l6l24pco.txt summary: Here we review what is currently known on the mechanisms of action of CQ and HCQ as anti-viral, anti-inflammatory and anti-thrombotic drugs and discuss the up-to-date experimental evidence on the potential mechanisms of action of CQ/HCQ in Sars-Cov2 infection and the current clinical knowledge on their efficacy in the treatment of COVID-19 patients. We also propose a different insight into some of CQ and HCQ effects, suggesting a potential role of iron homeostasis in Sars-Cov-2 disease (COVID-19), similarly to several other human viral infections [2] [3] [4] . The search strategy was to use different search terms alone and in any combination, such as "Sars-Cov-2 disease", "COVID-19", "Sars-Cov-2", "coronavirus", "clinical trial", "treatment", "drug", "chloroquine", "hydroxychloroquine", "iron", "virus", "viral entry", "viral spread", "anti-viral activity", "infection", "inflammation", "immunity", "innate immunity", "cytokine", "IL-6", "TNF-", "IL-1", "adaptive immunity", "thrombosis", "in vitro". abstract: The anti-malarial drugs chloroquine (CQ) and primarily the less toxic hydroxychloroquine (HCQ) are currently used to treat autoimmune diseases for their immunomodulatory and anti-thrombotic properties. They have also been proposed for the treatment of several viral infections, due to their anti-viral effects in cell cultures and animal models, and, currently, for the treatment of coronavirus disease 2019 (COVID-19), the pandemic severe acute respiratory syndrome caused by coronavirus 2 (Sars-Cov-2) infection that is spreading all over the world. Although in some recent studies a clinical improvement in COVID-19 patients has been observed, the clinical efficacy of CQ and HCQ in COVID-19 has yet to be proven with randomized controlled studies, many of which are currently ongoing, also considering pharmacokinetics, optimal dosing regimen, therapeutic level and duration of treatment and taking into account patients with different severity degrees of disease. Here we review what is currently known on the mechanisms of action of CQ and HCQ as anti-viral, anti-inflammatory and anti-thrombotic drugs and discuss the up-to-date experimental evidence on the potential mechanisms of action of CQ/HCQ in Sars-Cov2 infection and the current clinical knowledge on their efficacy in the treatment of COVID-19 patients. Given the role of iron in several human viral infections, we also propose a different insight into a number of CQ and HCQ pharmacological effects, suggesting a potential involvement of iron homeostasis in Sars-Cov-2 infection and COVID-19 clinical course. url: https://www.sciencedirect.com/science/article/pii/S1043661820312123?v=s5 doi: 10.1016/j.phrs.2020.104904 id: cord-349556-k312qkvh author: Roldán-Santiago, Ernesto title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 words: 1831.0 sentences: 148.0 pages: flesch: 64.0 cache: ./cache/cord-349556-k312qkvh.txt txt: ./txt/cord-349556-k312qkvh.txt summary: title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient''s cervical LN. abstract: A woman with mild Covid-19 developed cervical adenopathy, being diagnosed of Epstein−Barr virus infectious mononucleosis. After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. url: https://doi.org/10.1093/cid/ciaa1422 doi: 10.1093/cid/ciaa1422 id: cord-318920-njurbf3d author: Romana Ponziani, Francesca title: Liver involvement is not associated with mortality: results from a large cohort of SARS‐CoV‐2 positive patients date: 2020-07-06 words: 2267.0 sentences: 131.0 pages: flesch: 50.0 cache: ./cache/cord-318920-njurbf3d.txt txt: ./txt/cord-318920-njurbf3d.txt summary: CONCLUSIONS: In SARS‐CoV‐2 positive patients without pre‐existing severe chronic liver disease, baseline liver tests abnormalities are associated with the risk of ICU admission and tend to normalize over time. To investigate the prevalence of liver damage in our cohort of patients, serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT), gamma glutamyl transferase (GGT), alkaline phosphatase (ALP), total bilirubin and albumin were collected at baseline, then on the date closest to 15 days from the admission. This study demonstrates that in patients without severe chronic liver disease liver involvement during SARS-CoV-2 infection is usually mild, is not associated with increased risk of ICU admission or mortality, and tends to resolve over time. Baseline liver tests abnormalities can be found in more than 30% of cases, especially in patients with ARDS; these alterations are associated with the risk of ICU admission but not with mortality, and tend to normalize over time. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is frequently associated with liver tests abnormalities. AIMS: To describe the evolution of liver involvement during SARS‐CoV‐2 infection and its effect on clinical course and mortality. METHODS: Data of 515 SARS‐CoV‐2 positive patients were collected at baseline and during follow‐up, last evaluation or death. Stratification based on need for hospitalization, severe disease and admission to intensive care unit (ICU) was performed. The association between liver tests abnormalities (baseline and peak values) and ICU admission or death was also explored. RESULTS: Liver tests abnormalities were found in 161 (31.3%) patients. Aspartate aminotransferase (AST), alanine aminotransferase (ALT) and gamma glutamyl transferase (GGT) were increased in 20.4%, 19% and 13.6% of patients, respectively. Baseline liver tests abnormalities were associated with increased risk of ICU admission (OR 2.19 [95%CI 1.24‐3.89], p=0.007) but not with mortality (OR 0.84 [95%CI 0.49‐1.41], p=0.51). Conversely, ALP peak values were correlated with the risk of death (OR 1.007 [95%CI 1.002‐1.01], p=0.005) along with age, multiple comorbidities, acute respiratory distress syndrome (ARDS), ICU admission, and C‐reactive protein. Alterations of liver tests worsened within 15 days after hospitalization; however, in patients with the longest median follow‐up, the prevalence of liver tests alterations decreased over time, returning similar to that of baseline. CONCLUSIONS: In SARS‐CoV‐2 positive patients without pre‐existing severe chronic liver disease, baseline liver tests abnormalities are associated with the risk of ICU admission and tend to normalize over time. ALP peak value seems to be predictive of a worse prognosis. url: https://doi.org/10.1111/apt.15996 doi: 10.1111/apt.15996 id: cord-278618-7tu5c7m1 author: Romano-Bertrand, Sara title: Sustainability of SARS-CoV-2 in aerosols: Should we worry about airborne transmission? date: 2020-06-12 words: 1340.0 sentences: 70.0 pages: flesch: 45.0 cache: ./cache/cord-278618-7tu5c7m1.txt txt: ./txt/cord-278618-7tu5c7m1.txt summary: This is based on previous knowledge [1] and the doctrine that: a patient positive for SARS-CoV-2 is contagious by respiratory secretions (>10μm in size) that disseminate only on short distance (<1m); SARS-CoV-2 carried on large droplets settles onto local surfaces and is not stable in the air; SARS-CoV-2 aerosol dispersion is possible during AGPs which extensively expose HCWs and therefore HCWs need to wear a respirator for a higher respiratory protection during AGPs. However, an experimental study of van Doremalen et al, [2] assessed the sustainability of SARS-CoV-2 in aerosols (<5μm at 65% of hygrometry (expressed in %RH for relative humidity)) performed using a high-powered machine that does not reflect normal cough conditions (https://www.who.int/publications-detail/modes-of-transmission-of-virus-causing-covid-19-implicationsfor-ipc-precaution-recommendations). They showed that SARS-CoV-2 remained viable and infective at least 3 hours in aerosols, which opened the debate on SARS-CoV-2 transmission through longdistance aerosols (>1m), and questioned the appropriateness of respiratory protection for HCWs. An individual who is well, emits 10 to 10 4 particles per liter of expired air, including 95% of <1μm-size particles [3] . abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0195670120303030?v=s5 doi: 10.1016/j.jhin.2020.06.018 id: cord-273408-jtpaue0z author: Romeyke, Tobias title: COVID-19 Case Report: An 84-Year-Old Man with Exacerbation of Multiple Comorbidities Due to COVID-19 Managed by a Multidisciplinary Team Using Patient-Reported Outcomes date: 2020-08-21 words: 3045.0 sentences: 201.0 pages: flesch: 48.0 cache: ./cache/cord-273408-jtpaue0z.txt txt: ./txt/cord-273408-jtpaue0z.txt summary: Patient: Male, 84-year-old Final Diagnosis: Acute bronchitis • chronic multiple pain with spondylosis with radiculopathy: lumbar region • chronic renal failure CKD 4 • derailed type 2 diabetes mellitus • diabetes mellitus type 2 • eart failure • hyperuricaemia • progressive aortic stenosis • pulmonary hypertension • SARS-CoV2 Symptoms: Appetite loss • fever • pain • sore throat Medication: — Clinical Procedure: — Specialty: General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: When treating patients with comorbidities who are infected with severe acute respiratory syndrome as a result of SARS-CoV-2, it is crucial to offer multidisciplinary treatment that takes into consideration all of the health conditions with which they have been diagnosed. We collected clinical and patient-reported data on quality of life, physical functions, the sensation of pain, psychological well-being, and symptoms while taking into account the degree of chronicity of the conditions, the level of the patient''s pain, and his hospitalization in an isolation ward. abstract: Patient: Male, 84-year-old Final Diagnosis: Acute bronchitis • chronic multiple pain with spondylosis with radiculopathy: lumbar region • chronic renal failure CKD 4 • derailed type 2 diabetes mellitus • diabetes mellitus type 2 • eart failure • hyperuricaemia • progressive aortic stenosis • pulmonary hypertension • SARS-CoV2 Symptoms: Appetite loss • fever • pain • sore throat Medication: — Clinical Procedure: — Specialty: General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: When treating patients with comorbidities who are infected with severe acute respiratory syndrome as a result of SARS-CoV-2, it is crucial to offer multidisciplinary treatment that takes into consideration all of the health conditions with which they have been diagnosed. In particular, clinicians should not lose sight of the patient experience, which we can be assessed with the help of patient-reported outcomes (PROs). CASE REPORT: An 84-year-old man infected with SARS-CoV-2 was already suffering from multiple health conditions, including Type 2 diabetes mellitus. He most likely was receiving cortisone therapy and had chronic pain with spondylosis with radiculopathy, bilateral gonarthrosis following total knee replacement, malaise, and fatigue. The patient received acute inpatient care in a hospital that provides complementary medical therapies. We collected clinical and patient-reported data on quality of life, physical functions, the sensation of pain, psychological well-being, and symptoms while taking into account the degree of chronicity of the conditions, the level of the patient’s pain, and his hospitalization in an isolation ward. We stabilized clinical parameters related to the patient’s main underlying health conditions (blood glucose and pain levels and oxygen saturation). The PROs we collected demonstrated a significant improvement on discharge. CONCLUSIONS: Applying PROs can be helpful in obtaining a more comprehensive picture of a patient with COVID-19, in which “the patient is given a voice,” in addition to being assessed by others. The knowledge gained can then be made available to the interdisciplinary treatment team to be incorporated into the treatment plan. url: https://doi.org/10.12659/ajcr.926694 doi: 10.12659/ajcr.926694 id: cord-333805-xmqs2ax7 author: Romoli, Michele title: A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date: 2020-06-05 words: 4025.0 sentences: 257.0 pages: flesch: 44.0 cache: ./cache/cord-333805-xmqs2ax7.txt txt: ./txt/cord-333805-xmqs2ax7.txt summary: BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. This study therefore aimed to identify clinical cases of confirmed nervous system invasion or postinfectious neurological disease in the available COVID-19 literature on the basis of a systematic review. A systematic review was carried out to study all cases reporting nervous system involvement in patients with proven SARS-CoV2 infection. There were just 2 cases with positive SARS-CoV-2 PCR in CSF among 27 patients with potential neurologic symptoms and proven COVID-19. In this regard, we see a clear need for the use of precise case definitions and focused diagnostic work-up to distinguish nonspecific complications of severe disease and focused reporting of neurological involvement in association with SARS-CoV-2 infection. abstract: BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. METHODS: We followed PRISMA guidelines and used the MEDLINE, EMBASE, Google Scholar, MedRxiv and ChinaXiv databases to search for papers on COVID‐19 and nervous system involvement which were published from January 1(st) to April 24(th) 2020. Data on design, sample size, neurologic assessment and related work‐up were extracted. Biases were assessed with the Newcastle‐Ottawa scale. RESULTS: We analysed 27 publications on potential neuroinvasive or parainfectious neurological complications of COVID‐19. The reports focused on smell and taste (n=5) and evaluation of neurological symptoms and signs in cohorts (n=5). There were cases of Guillain‐Barré syndrome/Miller‐Fisher syndrome/cranial neuropathy (7 cases), meningitis/encephalitis (9 cases) and various other conditions (5 cases). Patients with cerebrospinal fluid (CSF) examination and in particular SARS‐CoV‐2 PCR was negligible. Amongst, two had a positive SARS‐CoV‐2 PCR exam of CSF specimen. The study of potential parenchymal involvement with magnetic resonance imaging was rare. Only 4 reports received a rating for the highest quality standards. CONCLUSION: This systematic review failed to establish comprehensive insights to nervous system manifestations of COVID‐19 beyond immune‐mediated complications as aftermath of respiratory symptoms. The authors therefore provide guidance for more careful clinical, diagnostic and epidemiological studies to characterize the manifestations and burden of neurological disease caused by SARS‐CoV‐2 on behalf of the Infectious Disease Panel of the European Academy of Neurology. url: https://doi.org/10.1111/ene.14382 doi: 10.1111/ene.14382 id: cord-014897-rnrlslfh author: Rong-bing, Wang title: Therapeutic effects of integrated traditional Chinese medicine and western medicine in treating severe acute respiratory syndrome date: 2003 words: 2324.0 sentences: 103.0 pages: flesch: 52.0 cache: ./cache/cord-014897-rnrlslfh.txt txt: ./txt/cord-014897-rnrlslfh.txt summary: The comprehensive effect on relieving fever, cell-mediated immunity, pulmonary inflammation and secondary infection was compared between the two groups.Results: The therapeutic effect in the ICWM group was better than that in the control group in such aspects as steadily lowering body temperature, alleviating general symptoms, accelerating the absorption of pulmonary infiltration and easing cellular immunity suppression.Conclusion: The therapeutic effect of ICWM is better in treating SARS than that of western medicine alone. In order to elevate the therapeutic effects, lighten patients" symptoms, improve the pulmonary inflammation and cellular immune inhibition that occurred in the course of the illness, a clinical study of the treatment of 68 SARS patients with integrated traditional Chinese and western medicine (ICWM), which was controlled with 67 patients treated with western medicine alone, was carried out. abstract: Objective: To improve the effects of treatment of severe acute respiratory syndrome (SARS) and to explore the clinical significance of integrated traditional Chinese medicine and western medicine (ICWM) in the treatment of SARS and its influence on the chief indexes in the process of the disease.Methods: The clinical study involving observation of 135 patients of SARS was conducted in the randomized, synchronously controlled and open way. The patients were divided into two groups, 68 in the ICWM group and 67 in the control group, all of whom were treated with the same basic treatment of western medicine, but to the ICWM group, Chinese drugs for clearing Heat, detoxifying and removing Dampness were given additionally. The comprehensive effect on relieving fever, cell-mediated immunity, pulmonary inflammation and secondary infection was compared between the two groups.Results: The therapeutic effect in the ICWM group was better than that in the control group in such aspects as steadily lowering body temperature, alleviating general symptoms, accelerating the absorption of pulmonary infiltration and easing cellular immunity suppression.Conclusion: The therapeutic effect of ICWM is better in treating SARS than that of western medicine alone. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089471/ doi: 10.1007/bf02838610 id: cord-306733-df36w6l7 author: Rosales-Mendoza, Sergio title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 words: 8591.0 sentences: 420.0 pages: flesch: 39.0 cache: ./cache/cord-306733-df36w6l7.txt txt: ./txt/cord-306733-df36w6l7.txt summary: Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. abstract: The emergence of new pathogenic viral strains is a constant threat to global health, with the new coronavirus strain COVID-19 as the latest example. COVID-19, caused by the SARS-CoV-2 virus has quickly spread around the globe. This pandemic demands rapid development of drugs and vaccines. Plant-based vaccines are a technology with proven viability, which have led to promising results for candidates evaluated at the clinical level, meaning this technology could contribute towards the fight against COVID-19. Herein, a perspective in how plant-based vaccines can be developed against COVID-19 is presented. Injectable vaccines could be generated by using transient expression systems, which offer the highest protein yields and are already adopted at the industrial level to produce VLPs-vaccines and other biopharmaceuticals under GMPC-processes. Stably-transformed plants are another option, but this approach requires more time for the development of antigen-producing lines. Nonetheless, this approach offers the possibility of developing oral vaccines in which the plant cell could act as the antigen delivery agent. Therefore, this is the most attractive approach in terms of cost, easy delivery, and mucosal immunity induction. The development of multiepitope, rationally-designed vaccines is also discussed regarding the experience gained in expression of chimeric immunogenic proteins in plant systems. url: https://www.ncbi.nlm.nih.gov/pubmed/32295153/ doi: 10.3390/vaccines8020183 id: cord-323094-zugrtvyo author: Rose, R. title: Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies date: 2020-04-29 words: 1774.0 sentences: 119.0 pages: flesch: 58.0 cache: ./cache/cord-323094-zugrtvyo.txt txt: ./txt/cord-323094-zugrtvyo.txt summary: Here, we quantify and characterize intra-host variation in SARS-CoV-2 raw sequence data uploaded to SRA as of 14 April 2020, and compare results between two sequencing methods (amplicon and RNA-Seq). While mutations resulting from amplification and/or sequencing errors cannot be excluded, the observation of shared polymorphic sites with high MAF across multiple samples and sequencing methods is consistent with true underlying variation. Our goal in this study was to quantify and characterize intra-host variation in all SARS-CoV-2 raw sequence data available in SRA as of 14 April 2020, and compare results between two All rights reserved. . https://doi.org/10.1101/2020.04.24.20078691 doi: medRxiv preprint 5 percent of the genome covered at 10x and 25x remained high with the amplicon data (10x IQR: 0.987 -0.997; 25x IQR: 0.980 -0.997), the range was much broader for the RNA-Seq data (10x IQR: 0.240 -0.997; 25x IQR: 0.024 -0.993). abstract: Despite the potential relevance to clinical outcome, intra-host dynamics of SARS-CoV-2 are unclear. Here, we quantify and characterize intra-host variation in SARS-CoV-2 raw sequence data uploaded to SRA as of 14 April 2020, and compare results between two sequencing methods (amplicon and RNA-Seq). Raw fastq files were quality filtered and trimmed using Trimmomatic, mapped to the WuhanHu1 reference genome using Bowtie2, and variants called with bcftools mpileup. To ensure sufficient coverage, we only included samples with 10X coverage for >90% of the genome (n=406 samples), and only variants with a depth >=10. Derived (i.e. non-reference) alleles were found at 408 sites. The number of polymorphic sites (i.e. sites with multiple alleles) within samples ranged from 0-13, with 72% of samples (295/406) having at least one polymorphic site. Correlation between number of polymorphic sites and coverage was very low for both sequencing methods (R2 < 0.1, p < 0.05). Polymorphisms were observed >1 sample at 66 sites (range: 2-38 samples). The minor allele frequency (MAF) at each shared polymorphic site was 0.03% - 48.5%. 33/66 sites occurred in ORF1a1b, and 37/66 changes were non-synonymous. At 10/66 sites, derived alleles were found in samples sequenced using both methods. Polymorphic amplicon samples were found at 10/10 positions, while polymorphic RNA-Seq samples were found at 7/10 positions. In conclusion, our results suggest that intra-host variation is prevalent among clinical samples. While mutations resulting from amplification and/or sequencing errors cannot be excluded, the observation of shared polymorphic sites with high MAF across multiple samples and sequencing methods is consistent with true underlying variation. Further investigation into intra-host evolutionary dynamics, particularly with longitudinal sampling, is critical for broader understanding of disease progression. url: https://doi.org/10.1101/2020.04.24.20078691 doi: 10.1101/2020.04.24.20078691 id: cord-347472-n6811ens author: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 words: 6252.0 sentences: 344.0 pages: flesch: 51.0 cache: ./cache/cord-347472-n6811ens.txt txt: ./txt/cord-347472-n6811ens.txt summary: The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. abstract: Testing for RNA viruses such as SARS-CoV-2 requires careful handling of inherently labile RNA during sample collection, clinical processing, and molecular analysis. Tests must include fail-safe controls that affirmatively report the presence of intact RNA and demonstrate success of all steps of the assay. A result of “no virus signal” is insufficient for clinical interpretation: controls must also say “The reaction worked as intended and would have found virus if present.” Unfortunately, a widely used test specified by the US Centers for Disease Control and Prevention (CDC) incorporates a control that does not perform as intended and claimed. Detecting SARS-CoV-2 with this assay requires both intact RNA and successful reverse transcription. The CDC-specified control does not require either of these, due to its inability to differentiate human genomic DNA from reverse-transcribed RNA. Patient DNA is copurified from nasopharyngeal swabs during clinically-approved RNA extraction and is sufficient to return an “extraction control success” signal using the CDC design. As such, this assay fails-unsafe: truly positive patient samples return a false-negative result of “no virus detected, control succeeded” following any of several readily-encountered mishaps. This problem affects tens-of-millions of patients worth of shipped assays, but many of these flawed reagents have not yet been used. There is an opportunity to improve this important diagnostic tool. As demonstrated here, a re-designed transcript-specific control correctly monitors sample collection, extraction, reverse transcription, and qPCR detection. This approach can be rapidly implemented and will help reduce truly positive patients from being incorrectly given the all-clear. One Sentence Summary A widely-used COVID-19 diagnostic is mis-designed and generates false-negative results, dangerously confusing “No” with “Don’t know” – but it’s fixable url: https://doi.org/10.1101/2020.05.13.094839 doi: 10.1101/2020.05.13.094839 id: cord-351189-56am76lb author: Rosen, Melissa H title: Management of Acute Severe Ulcerative Colitis in a Pregnant Woman With COVID-19 Infection: A Case Report and Review of the Literature date: 2020-05-12 words: 2373.0 sentences: 136.0 pages: flesch: 47.0 cache: ./cache/cord-351189-56am76lb.txt txt: ./txt/cord-351189-56am76lb.txt summary: As the patient was improving on steroids and given the rapidly increasing rate of COVID-19 infected patients at our institution, the decision was made to discharge the patient home on an oral prednisone taper on hospital day 5 with plans to start infliximab as an outpatient. Although intravenous steroids are the mainstay of treatment for acute severe UC in the hospitalized patient, the use of steroids in the first trimester of pregnancy may be associated with a risk of cleft lip or cleft palate. The necessity for guidance was addressed by the International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) in their publication, "Management of Patients with Crohn''s Disease and Ulcerative Colitis During the COVID-19 Pandemic: Results of an International Meeting." 9 The recommendation is to continue biologic therapy in the absence of SARS-CoV-2 infection. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes abstract: First detected in Wuhan, China, the novel 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped RNA beta-coronavirus responsible for an unprecedented, worldwide pandemic caused by COVID-19. Optimal management of immunosuppression in inflammatory bowel disease (IBD) patients with COVID-19 infection currently is based on expert opinion, given the novelty of the infection and the corresponding lack of high-level evidence in patients with immune-mediated conditions. There are limited data regarding IBD patients with COVID-19 and no data regarding early pregnancy in the era of COVID-19. This article describes a patient with acute severe ulcerative colitis (UC) during her first trimester of pregnancy who also has COVID-19. The case presentation is followed by a review of the literature to date on COVID-19 in regard to inflammatory bowel disease and pregnancy, respectively. url: https://www.ncbi.nlm.nih.gov/pubmed/32393973/ doi: 10.1093/ibd/izaa109 id: cord-274761-c2hgkbg6 author: Rosenberg, Eli S. title: Cumulative incidence and diagnosis of SARS-CoV-2 infection in New York date: 2020-06-17 words: 3431.0 sentences: 178.0 pages: flesch: 44.0 cache: ./cache/cord-274761-c2hgkbg6.txt txt: ./txt/cord-274761-c2hgkbg6.txt summary: SARS-CoV-2 cumulative incidence was estimated from antibody reactivity by first post-stratification weighting then adjusting by antibody test characteristics. CONCLUSIONS: From the largest US serosurvey to date, we estimated > 2 million adult New York residents were infected through late March, with substantial disparities, although cumulative incidence remained below herd immunity thresholds. Cumulative incidence among non-institutionalized adults, by geographic and demographic features, was estimated from weighted reactivity rates that were adjusted for validated test characteristics. We estimated SARS-Cov-2 cumulative incidence from observed antibody reactivity using two sequential steps: 1) post-stratification weighting to standardize to the New York State population and 2) adjustment by estimated antibody test characteristics. Test-characteristic adjusted cumulative incidence values were multiplied by the one-and two-way non-institutionalized adult populations (e.g. excluding settings such as prisons and nursing homes) from the American Community Survey 2014-2018 Public Use Microdata Sample file [23] . abstract: PURPOSE: New York State (NYS) is an epicenter of the SARS-CoV-2 pandemic in the United States. Reliable estimates of cumulative incidence in the population are critical to tracking the extent of transmission and informing policies. METHODS: We conducted a statewide seroprevalence study among a 15,101 patron convenience sample at 99 grocery stores in 26 counties throughout NYS. SARS-CoV-2 cumulative incidence was estimated from antibody reactivity by first post-stratification weighting then adjusting by antibody test characteristics. The percent diagnosed was estimated by dividing diagnoses by estimated infection-experienced adults. RESULTS: Based on 1,887 of 15,101 reactive results (12.5%), estimated cumulative incidence through March 29 was 14.0% (95% CI: 13.3-14.7%), corresponding to 2,139,300 (95% CI: 2,035,800-2,242,800) infection-experienced adults. Cumulative incidence was highest in New York City (NYC) 22.7% (95% CI: 21.5-24.0%) and higher among Hispanic/Latino (29.2%), non-Hispanic black/African American (20.2%), and non-Hispanic Asian (12.4%) than non-Hispanic white adults (8.1%, p<.0001). An estimated 8.9% (95% CI: 8.4-9.3%) of infections in NYS were diagnosed, with diagnosis highest among adults ≥55 years (11.3%, 95% CI: 10.4-12.2%). CONCLUSIONS: From the largest US serosurvey to date, we estimated > 2 million adult New York residents were infected through late March, with substantial disparities, although cumulative incidence remained below herd immunity thresholds. Monitoring, testing, and contact tracing remain essential public health strategies. url: https://api.elsevier.com/content/article/pii/S1047279720302015 doi: 10.1016/j.annepidem.2020.06.004 id: cord-336522-y9nzsv95 author: Rosenke, Kyle title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date: 2020-09-30 words: 1723.0 sentences: 121.0 pages: flesch: 54.0 cache: ./cache/cord-336522-y9nzsv95.txt txt: ./txt/cord-336522-y9nzsv95.txt summary: title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers Cell viability was 33 evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR 34 and TCID50 infectivity assays. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. In this study, five PPMO were designed to target the 5'' UTR 107 and first translation start site-region of SARS-CoV-2 positive sense genomic RNA ( Table 1) . abstract: Background SARS-CoV-2 is the causative agent of COVID-19 and a pathogen of immense global public health importance. Development of innovative direct-acting antiviral agents is sorely needed to address this virus. Peptide-conjugated morpholino oligomers (PPMO) are antisense agents composed of a phosphordiamidate morpholino oligomer covalently conjugated to a cell-penetrating peptide. PPMO require no delivery assistance to enter cells and are able to reduce expression of targeted RNA through sequence-specific steric blocking. Objectives and Methods Five PPMO designed against sequences of genomic RNA in the SARS-CoV-2 5’-untranslated region and a negative control PPMO of random sequence were synthesized. Each PPMO was evaluated for its effect on the viability of uninfected cells and its inhibitory effect on the replication of SARS-CoV-2 in Vero-E6 cell cultures. Cell viability was evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR and TCID50 infectivity assays. Results PPMO designed to base-pair with sequence in the 5’-terminal region or the leader transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, in a non-toxic and dose-responsive manner. Conclusion The data indicate that PPMO have the ability to potently and specifically suppress SARS-CoV-2 growth and are promising candidates for further pre-clinical development. url: https://doi.org/10.1101/2020.09.29.319731 doi: 10.1101/2020.09.29.319731 id: cord-296148-za3j19k5 author: Rosenzweig, Ivana title: Does damage to hypothalamic paraventricular nucleus underlie symptoms of ultradian rhythm disorder and an increased anxiety in coronavirus disease 2019? date: 2020-08-17 words: 1706.0 sentences: 80.0 pages: flesch: 34.0 cache: ./cache/cord-296148-za3j19k5.txt txt: ./txt/cord-296148-za3j19k5.txt summary: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may directly target parts of the brain, more specifically the hypothalamus and its paraventricular nucleus, and possibly lead to increased prevalence of anxiety disorders. Any changes in the PVN circuitries, due to their major control over most of neuro-endocrine axes and neuronal autonomic centers, may cause robust alteration in homeostatic regulation, and through influence on regulatory brain centers impact on sleep and wakefulness, increased propensity to affective disorders and anxiety, and alteration of ultradian rhythms. We correspondingly argue a direct SARS-CoV-2 effect on the specific part of the brain''s hypothalamic paraventricular nucleus (PVN) circuitry ( Figure 1 ) as a neurologic mechanism that may, at least in part, underlie previously reported ultradian disruption, and that may lead to an increased anxiety symptomatology (7) . We propose that SARS-CoV-2 may target the distinct ACE2-tagged part of the PVN-subcircuitry (8), via a direct monosynaptic subfornical route (Figure 1 ), leading to the pleomorphic dysautonomic ultradian presentation, which is further compounded with nocturnal sleep fragmentation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32881437/ doi: 10.3325/cmj.2020.61.377 id: cord-356009-emn2w8if author: Roshandel, M. R. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 words: 4687.0 sentences: 292.0 pages: flesch: 49.0 cache: ./cache/cord-356009-emn2w8if.txt txt: ./txt/cord-356009-emn2w8if.txt summary: Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. The searches included medical subject headings (MeSH) and keywords for SARS-CoV-2, COVID, Corona, together with shedding, persistence, urine, urinary, specimen, viral load, or RNA body fluids. We completed the data abstraction process using created forms to record study characteristics, clinical data, and laboratory data including study year and design, country of study origin, total initial population size, test type for disease diagnosis, test type for samples (urine/stool/rectal swab/blood), patients age (including mean and range), number of positive and total patients and/or (wherever applicable) number of positive and total specimens collected for each test category, disease severity, ICU admission, and fatality rate. abstract: Objective:Investigating the infectivity of body fluid can be useful for preventative measures in the community and ensuring safety in the operating rooms and on the laboratory practices. Methods:We performed a literature search of clinical trials, cohorts, and case series using PubMed/MEDLINE, Google Scholar, and Cochrane library, and downloadable database of CDC. We excluded case reports and searched all language articles for review and repeated until the final drafting. The search protocol was registered in the PROSPERO database. Results: Thirty studies with urinary sampling for viral shedding were included. A total number of 1,271 patients were enrolled initially, among which 569 patients had undergone urinary testing. Nine studies observed urinary viral shedding in urine from 41 patients. The total incidence of urinary SARS-CoV-2 shedding was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively. The summarized risk ratio (RR) estimates for urine positive rates compared to the pharyngeal rate was 0.08. The pertaining RR urine compared to blood and stool positive rates were 0.20 and 0.33 respectively. Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. Moreover, the findings in our review ?suggest that a larger population size may reveal more positive urinary cases possibly by ?minimizing biases. However, it is important to notice that it is the naso-pharyngeal specimens, ?stool, and serum that show more possibilities to became positive, respectively. url: https://doi.org/10.1101/2020.10.08.20209544 doi: 10.1101/2020.10.08.20209544 id: cord-290148-6cxndab8 author: Rossi, Gian Paolo title: Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients date: 2020-04-06 words: 3145.0 sentences: 156.0 pages: flesch: 46.0 cache: ./cache/cord-290148-6cxndab8.txt txt: ./txt/cord-290148-6cxndab8.txt summary: The discovery of angiotensin converting enzyme-2 (ACE-2) as the receptor for SARSCoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) has implicated the renin-angiotensin-aldosterone system in acute respiratory distress syndrome (ARDS) and respiratory failure in patients with coronavirus disease-19 (COVID-19). However, they differ markedly: ACE-1 cleaves the dipeptide His-Leu from angiotensin I, thus generating angiotensin (Ang) II, which causes vaso-and broncho-constriction, increases vascular permeability, inflammation, and fibrosis and thereby promotes the development of ARDS and lung failure in patients infected with the SARS-CoV and SARS-CoV-2 (Yang et al., 2015) (Figure 1, panel B) . In one commentary ACE-2 was suggested to be secreted at higher amounts in patients with cardiovascular disease than in healthy individuals, and in another, it was also stated that ''ACE-2 levels can be increased by the use of ACEIs'' , albeit no evidence of this occurring in the lungs Mechanisms of COVID-19 by which the SARS-COV-2 virus infects the lower airway cells and modalities to increase circulating soluble ACE-2 for therapeutic use. abstract: The discovery of angiotensin converting enzyme-2 (ACE-2) as the receptor for SARS- CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) has implicated the renin-angiotensin-aldosterone system in acute respiratory distress syndrome (ARDS) and respiratory failure in patients with coronavirus disease-19 (COVID-19). The angiotensin converting enzyme-1–angiotensin II–angiotensin AT(1) receptor pathway contributes to the pathophysiology of ARDS, whereas activation of the ACE-2–angiotensin(1-7)-angiotensin AT(2) receptor and the ACE-2–angiotensin(1-7)–Mas receptor pathways have been shown to be protective. Here we propose and discuss therapeutic considerations how to increase soluble ACE-2 in plasma in order for ACE-2 to capture and thereby inactivate SARS-CoV-2. This could be achieved by administering recombinant soluble ACE-2. We also discuss why and how ACEIs and ARBs provide cardiovascular, renal and also pulmonary protection in SARS-CoV-2- associated ARDS. Discontinuing these medications in COVID-19 patients may therefore potentially be harmful. url: https://www.ncbi.nlm.nih.gov/pubmed/32250244/ doi: 10.7554/elife.57278 id: cord-331571-v01kstbr author: Rossoff, Jenna title: Benign course of SARS‐CoV‐2 infection in a series of pediatric oncology patients date: 2020-06-23 words: 722.0 sentences: 49.0 pages: flesch: 51.0 cache: ./cache/cord-331571-v01kstbr.txt txt: ./txt/cord-331571-v01kstbr.txt summary: Repeat SARS-CoV-2 testing the next day was again negative, and blood cultures grew both Acinetobacter junii and Pseudomonas aeruginosa. He had an uncomplicated hospital course, but still tested positive for SARS-CoV-2 on the day of discharge and again 5 days later. Repeat testing after another 10 days, 6 weeks after symptom onset, was negative. Our series of pediatric oncology patients with relatively benign courses of SARS-CoV-2 infection is consistent with reports from both Italy and New York city, where five and 20 pediatric cancer patients, respectively, were identified as having mild or asymptomatic SARS-CoV-2 infection, 8, 9 and mirror the experience in some patients on biologics for immune-mediated inflammatory disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China Patients with cancer appear more vulnerable to SARS-COV-2: a multi-center study during the COVID-19 outbreak abstract: nan url: https://doi.org/10.1002/pbc.28504 doi: 10.1002/pbc.28504 id: cord-294571-qd0qjo3y author: Rothan, Hussin A. title: Molecular Aspects of COVID-19 Differential Pathogenesis date: 2020-07-06 words: 3246.0 sentences: 173.0 pages: flesch: 43.0 cache: ./cache/cord-294571-qd0qjo3y.txt txt: ./txt/cord-294571-qd0qjo3y.txt summary: Angiotensin-converting enzyme-2 (ACE2) represents the primary SARS-CoV-2 entry receptor, and its physiological role is crucial in the progress of COVID-19 illness. Previous studies on SARS-CoV-1 reported that the binding of viral spike (S) protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . The levels of ACE2 expression, which could be sex-and age-dependent, have a protective role against lung and kidney injuries that could impact the severity of COVID-19 illness in male vs. The susceptibility of cardio-metabolic patients to develop severe COVID-19 illness and the high mortality rate could be linked to the ACE2 function during SARS-CoV-2 infection and the cardio-metabolic treatments that may interfere with ACE2-virus interaction. Previous studies on SARS-COV-1 reported that the binding of viral S protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . abstract: In the absence of therapeutic interventions, and a possible vaccine candidate, the spread of COVID-19 disease and associated fatalities are on the rise. The high mutation frequency in the genomic material of these viruses supports their ability to adapt to new environments, resulting in an efficient alteration in tissue tropism and host range. Therefore, the coronavirus’ health threats could be relevant for the long-term. The epidemiological data indicate that age, sex, and cardio-metabolic disease have a significant impact on the spread and severity of COVID-19. In this review, we highlight recent updates on the pathogenesis of SARS-CoV-2 among men and women, including children. We also discuss the role of the cellular receptors and coreceptors used by the virus to enter host cells on differential infection among men, women, and cardio-metabolic patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32640525/ doi: 10.3390/pathogens9070538 id: cord-309289-vm0k7hfx author: Rothan, Hussin A. title: The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date: 2020-04-14 words: 1463.0 sentences: 91.0 pages: flesch: 46.0 cache: ./cache/cord-309289-vm0k7hfx.txt txt: ./txt/cord-309289-vm0k7hfx.txt summary: title: The FDAapproved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, antiinflammatory and anti-ROS properties. We investigated the anti-viral activity of auranofin against SARS-CoV-2 and its effect on virus-induced inflammation in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury. abstract: SARS-COV-2 has recently emerged as a new public health threat. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Treatment of cells with auranofin resulted in a 95% reduction in the viral RNA at 48 hours after infection. Auranofin treatment dramatically reduced the expression of SARS-COV-2-induced cytokines in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Auranofin has a well-known toxicity profile and is considered safe for human use. url: https://doi.org/10.1101/2020.04.14.041228 doi: 10.1101/2020.04.14.041228 id: cord-315637-7td617dm author: Rothe, M. title: A systematic review of mask disinfection and reuse for SARS-CoV-2 date: 2020-11-12 words: 3849.0 sentences: 234.0 pages: flesch: 53.0 cache: ./cache/cord-315637-7td617dm.txt txt: ./txt/cord-315637-7td617dm.txt summary: However, results show it is possible to achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) disinfection on N95 masks. However, results did show that it is possible to 160 achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical 161 (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) 162 disinfection. Given the wide differences in test conditions, results are 185 summarized by disinfection agent for N95s only, for agents with >5 samples or those agents identified in 186 the disinfection efficacy section as achieving >3 log reduction of SARS-CoV-2, including ethanol, 187 hydrogen peroxide, peracetic acid, PX-UV, UVGI, autoclaving, and heat. abstract: We conducted a systematic review of hygiene intervention effectiveness against SARS-CoV-2, including developing inclusion criteria, conducting the search, selecting articles for inclusion, and summarizing included articles. We reviewed 104,735 articles, and 109 articles meeting inclusion criteria were identified, with 33 additional articles identified from reference chaining. Herein, we describe results from 58 mask disinfection and reuse studies, where the majority of data were collected using N95 masks. Please note, no disinfection method consistently removed >3 log of virus irrespective of concentration, contact time, temperature, and humidity. However, results show it is possible to achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) disinfection on N95 masks. N95 mask reuse and failure data indicate that hydrogen peroxide, heat, and UV-GI are promising for mask reuse, peracetic acid and PX-UV need more data, and autoclaving and ethanol lead to mask durability failures. Data on other mask types is limited. We thus recommend focusing guidelines and further research on the use of heat, hydrogen peroxide, and UVGI for N95 mask disinfection/reuse. All of these disinfection options could be investigated for use in LMIC and humanitarian contexts. url: http://medrxiv.org/cgi/content/short/2020.11.11.20229880v1?rss=1 doi: 10.1101/2020.11.11.20229880 id: cord-333868-qrnsmhws author: Rothman, Richard E. title: Respiratory Hygiene in the Emergency Department date: 2006-08-23 words: 7437.0 sentences: 362.0 pages: flesch: 35.0 cache: ./cache/cord-333868-qrnsmhws.txt txt: ./txt/cord-333868-qrnsmhws.txt summary: These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection. abstract: The emergency department (ED) is an essential component of the public health response plan for control of acute respiratory infectious threats. Effective respiratory hygiene in the ED is imperative to limit the spread of dangerous respiratory pathogens, including influenza, severe acute respiratory syndrome, avian influenza, and bioterrorism agents, particularly given that these agents may not be immediately identifiable. Sustaining effective respiratory control measures is especially challenging in the ED because of patient crowding, inadequate staffing and resources, and ever-increasing numbers of immunocompromised patients. Threat of contagion exists not only for ED patients but also for visitors, health care workers, and inpatient populations. Potential physical sites for respiratory disease transmission extend from out-of-hospital care, to triage, waiting room, ED treatment area, and the hospital at large. This article presents a summary of the most current information available in the literature about respiratory hygiene in the ED, including administrative, patient, and legal issues. Wherever possible, specific recommendations and references to practical information from the Centers for Disease Control and Prevention are provided. The “Administrative Issues” section describes coordination with public health departments, procedures for effective facility planning, and measures for health care worker protection (education, staffing optimization, and vaccination). The patient care section addresses the potentially infected ED patient, including emergency medical services concerns, triage planning, and patient transport. “Legal Issues” discusses the interplay between public safety and patient privacy. Emergency physicians play a critical role in early identification, treatment, and containment of potentially lethal respiratory pathogens. This brief synopsis should help clinicians and administrators understand, develop, and implement appropriate policies and procedures to address respiratory hygiene in the ED. url: https://www.sciencedirect.com/science/article/pii/S0196064406007037 doi: 10.1016/j.annemergmed.2006.05.018 id: cord-336677-h62angfw author: Rousseau, Antoine title: Sars-Cov-2, Covid-19 Et Œil: Le Point Sur Les Données Publiées date: 2020-05-30 words: 3187.0 sentences: 298.0 pages: flesch: 60.0 cache: ./cache/cord-336677-h62angfw.txt txt: ./txt/cord-336677-h62angfw.txt summary: Par ailleurs, la protéine Spike de SARS-CoV-2 comprend aussi un site de clivage compatible avec l''action de la furine, une autre protéase membranaire déjà connue pour être impliquée dans la pénétration d''autres coronavirus [14, 20] , et là encore, des inhibiteurs spécifiques de la furine sont à l''étude pour connaître leur propriété antivirale sur SARS-CoVUn second récepteur cellulaire semble jouer un rôle important dans la sensibilité au virus, il s''agit du récepteur CD147, aussi nommé basigine ou encore EMMPRIN (extracellular matrix metalloproteinase inducer). Les propriétés antivirales de l''hydroxychloroquine ont d''ailleurs été suspectées pour un grand nombre d''autres virus que SARS-CoV-2, mais jusqu''à présent, aucun des essais thérapeutiques chez l''homme n''a montré son efficacité dans ces autres infections [25] . Les essais thérapeutiques visant à réguler cette réaction immunitaire exacerbée représentent une part importante de l''effort de recherche clinique sur les formes sévères de COVID-19, et c''est d''ailleurs dans ce domaine que l''un des premiers essais randomisés contrôlé a montré des résultats préliminaires encourageants, (mais qui restent encore à confirmer) à propos d''un inhibiteur de l''interleukine 6 (le tocilizumab) [38] . abstract: Abstract The COVID-19 pandemic has dramatically changed our daily lives as ophthalmologists. This general review firstly provides a better understanding of the virus responsible for the pandemic: the SARS-CoV-2, and the clinical manifestations of the COVID-19 disease. The second part is detailing the pathophysiology, clinical signs and challenges of ocular involvement, which seems rare and not functionally severe, but which may be a potential source of contamination. Finally, we discuss the preventive measures that need to be implemented in our daily practice to avoid any viral dissemination. url: https://api.elsevier.com/content/article/pii/S0181551220302291 doi: 10.1016/j.jfo.2020.05.003 id: cord-262276-5nue46dm author: Roussel, Yanis title: SARS-CoV-2: fear versus data date: 2020-03-19 words: 1860.0 sentences: 119.0 pages: flesch: 55.0 cache: ./cache/cord-262276-5nue46dm.txt txt: ./txt/cord-262276-5nue46dm.txt summary: The first, severe acute respiratory syndrome (SARS) coronavirus, had very little impact on global morbidity and mortality, with more than 80 0 0 recognized cases and 774 deaths [15 , 16] . Among the Organisation for Economic Co-operation and Development (OECD) countries, 7476 patients have tested positive for SARS-CoV-2, with 96 deaths (mortality rate 1.3%) ( Table 3 ). In France, 191 people have tested positive for SARS-CoV-2, with three deaths (mortality rate 1.6%). If the extrapolation of deaths in AP-HM hospitals is correct, in metropolitan France, this would represent 543/0.8 * 100 = 67 875 cases of patients hospitalized with a respiratory infection with common coronaviruses in 2 months, which is almost as many cases as for SARS-CoV-2 worldwide. Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China abstract: SARS-CoV-2, the novel coronavirus from China, is spreading around the world, causing a huge reaction despite its current low incidence outside China and the Far East. Four common coronaviruses are in current circulation and cause millions of cases worldwide. This article compares the incidence and mortality rates of these four common coronaviruses with those of SARS-CoV-2 in Organisation for Economic Co-operation and Development countries. It is concluded that the problem of SARS-CoV-2 is probably being overestimated, as 2.6 million people die of respiratory infections each year compared with less than 4000 deaths for SARS-CoV-2 at the time of writing. url: https://www.ncbi.nlm.nih.gov/pubmed/32201354/ doi: 10.1016/j.ijantimicag.2020.105947 id: cord-305262-23qylbmg author: Rowan, Neil J. title: Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic – Implications for efficacy, re-use and sustainable waste management date: 2020-09-10 words: 9978.0 sentences: 575.0 pages: flesch: 46.0 cache: ./cache/cord-305262-23qylbmg.txt txt: ./txt/cord-305262-23qylbmg.txt summary: Important countermeasures for preventing COVID-19 transmission include mitigating potential high risk aerosol transmission in healthcare setting using medical PPE (such as filtering facepiece respirators (FFRs)) and the appropriate use of face coverings by the general public that carries a lower transmission risk. Given that disposable, plastic-based, PPE (gowns, eye protection, gloves, face masks, filtering facepiece respirators (FFRs)) are heat sensitive, existing healthcare technologies were considered to be either not available, unsuitable or not configured for reprocessing of PPE in healthcare for emergency use (Rowan and Laffey, 2020) . However, potential solutions for effective reprocessing of PPE that considered virus inactivation, material compatibility and device functionality (filtration efficacy, penetration, fit test and so forth) post processing included use of low temperature hydrogen peroxide vapour (VH2O2), ultraviolet germicidal light (UVGI), moist heat, and use of weak bleach for liquid decontamination (Rowan and Laffey, 2020; CDC, 2020) . abstract: Currently, there is no effective vaccine for tackling the ongoing COVID-19 pandemic caused by SARS-CoV-2 with the occurrence of repeat waves of infection frequently stretching hospital resources beyond capacity. Disease countermeasures rely upon preventing person-to-person transmission of SARS-CoV2 so as to protect front-line healthcare workers (HCWs). COVID-19 brings enormous challenges in terms of sustaining the supply chain for single-use-plastic personal and protective equipment (PPE). Post-COVID-19, the changes in medical practice will drive high demand for PPE. Important countermeasures for preventing COVID-19 transmission include mitigating potential high risk aerosol transmission in healthcare setting using medical PPE (such as filtering facepiece respirators (FFRs)) and the appropriate use of face coverings by the general public that carries a lower transmission risk. PPE reuse is a potential short term solution during COVID-19 pandemic where there is increased evidence for effective deployment of reprocessing methods such as vaporized hydrogen peroxide (30 to 35% VH2OH) used alone or combined with ozone, ultraviolet light at 254 nm (2000 mJ/cm2) and moist heat (60 °C at high humidity for 60 min). Barriers to PPE reuse include potentially trust and acceptance by HCWs. Efficacy of face coverings are influenced by the appropriate wearing to cover the nose and mouth, type of material used, number of layers, duration of wearing, and potentially superior use of ties over ear loops. Insertion of a nose clip into cloth coverings may help with maintaining fit. Use of 60 °C for 60 min (such as, use of domestic washing machine and spin dryer) has been advocated for face covering decontamination. Risk of virus infiltration in improvised face coverings is potentially increased by duration of wearing due to humidity, liquid diffusion and virus retention. Future sustained use of PPE will be influenced by the availability of recyclable PPE and by innovative biomedical waste management. url: https://api.elsevier.com/content/article/pii/S0048969720357880 doi: 10.1016/j.scitotenv.2020.142259 id: cord-263090-29n9tsk9 author: Roy, Susmita title: Dynamical asymmetry exposes 2019-nCoV prefusion spike date: 2020-04-21 words: 4573.0 sentences: 331.0 pages: flesch: 57.0 cache: ./cache/cord-263090-29n9tsk9.txt txt: ./txt/cord-263090-29n9tsk9.txt summary: In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. A number of Cryo-EM structures captured the ''up'' and ''down'' conformations of the RBD domain of spike proteins of other coronaviruses including SARS-CoV-2 where the S1 subunit undergoes a hinge-like conformational movement prerequisite for receptor binding (Fig. 2C) (7, 8, 10, 17) . Analysis of all the simulations yields the 2-D free energy landscape of the trimeric spike protein of SARS-CoV-2 ( Fig 3B) with its all possible conformations. This generates a homo-trimeric SARS-CoV-2 spike where this initial structure has important components in terms of intra and inter-chain contacts (interaction) leading to an ''S1-head-up'' and an ''S1-head-down'' conformation for each protomer. abstract: The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets. One Sentence Summary Inter-chain-interaction driven rapid symmetry breaking strategy adopted by the prefusion trimeric spike protein likely to make 2019-nCoV highly infective. url: https://doi.org/10.1101/2020.04.20.052290 doi: 10.1101/2020.04.20.052290 id: cord-306901-uuwgpuhw author: Roy, Sylvie title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date: 2020-09-16 words: 4215.0 sentences: 251.0 pages: flesch: 58.0 cache: ./cache/cord-306901-uuwgpuhw.txt txt: ./txt/cord-306901-uuwgpuhw.txt summary: title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. High amounts of SARS-CoV-2 DS protein are incorporated into MLV VLPs released 142 from stable producer cells. A VLP-derived SARS CoV-2 vaccine will be a viable option if 143 sufficient amounts of S protein are incorporated at the surface of the released particles. In conclusion, we have developed and characterized a new MLV VLP platform that can 243 efficiently incorporate the S protein from SARS-CoV-2, and that has the potential to produce a pan-244 coronavirus vaccine. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that started in China at the end of 2019 has rapidly spread to become pandemic. Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. First, we showed that a codon optimized version of the S protein could migrate efficiently to the cell membrane. However, efficient production of infectious viral particles was only achieved with stable expression of a shorter version of S in its C-terminal domain (ΔS) in 293 cells that express MLV Gag-Pol (293GP). The incorporation of ΔS was 15-times more efficient into VLPs as compared to the full-length version, and that was not due to steric interference between the S cytoplasmic tail and the MLV capsid. Indeed, a similar result was also observed with extracellular vesicles released from parental 293 and 293GP cells. The amount of ΔS incorporated into VLPs released from producer cells was robust, with an estimated 1.25 μg/ml S2 equivalent (S is comprised of S1 and S2). Thus, a scalable platform that has the potential for production of pan-coronavirus VLP vaccines has been established. The resulting nanoparticles could potentially be used alone or as a boost for other immunization strategies for COVID-19. IMPORTANCE Several candidate COVID-19 vaccines have already been tested in humans, but their protective effect and long-term efficacy are uncertain. Therefore, it is necessary to continue developing new vaccine strategies that could be more potent and/or that would be easier to manufacture in large-scale. Virus-like particle (VLP) vaccines are considered highly immunogenic and have been successfully developed for human papilloma virus as well as hepatitis and influenza viruses. In this study, we report the generation of a robust Moloney murine leukemia virus platform that produces VLPs containing the spike of SARS-CoV-2. This vaccine platform that is compatible with lyophilization could simplify storage and distribution logistics immensely. url: https://doi.org/10.1101/2020.09.16.298992 doi: 10.1101/2020.09.16.298992 id: cord-018057-p1l6xtsq author: Ruan, Li title: SARS Epidemic: SARS Outbreaks in Inner-land of China date: 2008 words: 7509.0 sentences: 359.0 pages: flesch: 49.0 cache: ./cache/cord-018057-p1l6xtsq.txt txt: ./txt/cord-018057-p1l6xtsq.txt summary: Since 2002, SARS has broken out three times: the first epidemic spread worldwide from November 2002 to July 2003 (WHO, 2004) ; the second spread locally in Guangdong province between December 2003 and February 2004 (Liang et al., 2004) ; and the third developed on a small scale from laboratory infection in the inner-land of China from March to April 2004 (Ministry of Health, People''s Republic of China, 2004) . A study in Guangdong found SARS cases among people, such as restaurant cooks and meat animal''s vendors or purchasers, who had no history of contact with SARS patients but had been in contact with wild animals Peng et al., 2003; Yang et al., 2003 ; Leadership Group of SARS Prevention and Control in Beijing, Epidemiological features of severe acute respiratory syndrome in Beijing, 2003; Chinese Center for Disease Control and Prevention, 2003) . abstract: Severe Acute Respiratory Syndrome (SARS), also known in China as Infectious Atypical Pneumonia (IAP), is the 21st century’s first infectious disease to severely threaten the public health of the human population (WHO, 2003a). A respiratory transmitted disease caused by a virus, SARS is highly infectious and is rapidly transmitted, inflicting severe complications and a high case fatality rate. The first round of the SARS pandemic led to global panic and billions of dollars economic losses, for due to lack of effective SARS drugs, governments throughout the world had to take rigid steps toward prevention and treatment of the disease. The SARS epidemic began with the first reported case in Guangzhou, China (Wang et al., 2004), on 16 November 2002. Eight months later, the disease had spread to 26 countries in Asia, America, and Europe, resulting in a reported 8,096 cases and 774 deaths (WHO, 2004). In this global epidemic, China, with 7,429 cases and 685 deaths, accounted for 91.8% of the world’s reported cases and 88.5% of the deaths (5,327 SARS cases and 349 deaths were reported in 24 provinces in the inner-land of China – mostly in Beijing and Guangzhou, which, with a combined 4,033 cases, accounted for 75.7% of the total number in the inner-land of China; Hong Kong had 1,755 cases, 299 deaths; Taiwan: 346 cases, 37 deaths; Macao: 1 case, 0 deaths) (He et al., 2003; Peng et al., 2003; Yang et al., 2003; Leadership Group of SARS Prevention and Control in Beijing, 2003; Chinese Center for Disease Control and Prevention, 2003). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122843/ doi: 10.1007/978-0-387-75722-3_5 id: cord-347458-za7cot2n author: Ruan, Qiurong title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China date: 2020-03-03 words: 915.0 sentences: 53.0 pages: flesch: 59.0 cache: ./cache/cord-347458-za7cot2n.txt txt: ./txt/cord-347458-za7cot2n.txt summary: title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China Using the database of Jin Yin-tan Hospital and Tongji Hospital, we conducted a retrospective multicenter study of 68 death cases (68/150, 45%) and 82 discharged cases (82/150, 55%) with laboratory-confirmed infection of SARS-CoV-2. Patients met the discharge criteria if they had no fever for at least 3 days, significantly improved respiratory function, and had negative SARS-CoV-2 laboratory test results twice in succession. It should be noted that patients with cardiovascular diseases have a significantly increased risk of death when they are infected with SARS-CoV-2 (p < 0.001). Based on the analysis of the clinical data, we confirmed that some patients died of fulminant myocarditis. KY, WXW, LYJ and JXS contributed to the analysis and interpretation of the data. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32125452/ doi: 10.1007/s00134-020-05991-x id: cord-267013-nbwrl4g3 author: Ruan, R title: Subacute Thyroiditis might be a complication triggered by SARS-CoV-2 date: 2020-10-13 words: 884.0 sentences: 81.0 pages: flesch: 66.0 cache: ./cache/cord-267013-nbwrl4g3.txt txt: ./txt/cord-267013-nbwrl4g3.txt summary: The actual coronavirus disease 2019 (COVID-19) pandemia, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached more than 16 million confirmed cases worldwide, being the United Kingdom, Spain and Italy the most affected countries in Europe. We describe a clinical case of SAT following SARS-CoV-2 infection. Thyroid scintigraphy with 5.73 mCi of 99m Tc-pertechnetate was performed on May 26th, which showed absence of uptake in the gland (figure 1). To date, four cases of subacute thyroiditis during or shortly after SARS-CoV2 infection have been reported 2-5 . SAT is a clinical entity that must be suspected in patients that experience a sudden onset of neck pain and tenderness, during or after COVID-19 disease. Subacute thyroiditis in a patient infected with SARS-COV-2: an endocrine complication linked to the COVID-19 pandemic Hormones (Athens) A case of subacute thyroiditis associated with Covid-19 infection SARS-CoV-2: a potential trigger for subacute thyroiditis? Subacute Thyroiditis After Sars-COV-2 Infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33139217/ doi: 10.1016/j.endinu.2020.09.002 id: cord-300149-djclli8n author: Ruan, Yijun title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection date: 2003-05-24 words: 4355.0 sentences: 226.0 pages: flesch: 54.0 cache: ./cache/cord-300149-djclli8n.txt txt: ./txt/cord-300149-djclli8n.txt summary: title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection METHODS: We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations. All genetic variations of Singapore isolates identified when compared with available SARS-CoV genome sequences were further confirmed by primer extension genotyping technology (Sequenom, San Diego, CA, USA). These sequences showed that the genomes of SARS-CoV isolated in Singapore are comprised of 29 711 bases, with the exception of a five-nucleotide deletion in strain SIN2748 and a six-nucleotide deletion in SIN2677. abstract: BACKGROUND: The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus. Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines. METHODS: We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). These sequences were compared with the isolates from Canada (TOR2), Hong Kong (CUHK-W1 and HKU39849), Hanoi (URBANI), Guangzhou (GZ01), and Beijing (BJ01, BJ02, BJ03, BJ04). FINDINGS: We identified 129 sequence variations among the 14 isolates, with 16 recurrent variant sequences. Common variant sequences at four loci define two distinct genotypes of the SARS virus. One genotype was linked with infections originating in Hotel M in Hong Kong, the second contained isolates from Hong Kong, Guangzhou, and Beijing with no association with Hotel M (p<0.0001). Moreover, other common sequence variants further distinguished the geographical origins of the isolates, especially between Singapore and Beijing. INTERPRETATION: Despite the recent onset of the SARS epidemic, genetic signatures are emerging that partition the worldwide SARS viral isolates into groups on the basis of contact source history and geography. These signatures can be used to trace sources of infection. In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations. Published online May 9, 2003 http://image.thelancet.com/extras/03art4454web.pdf url: https://www.ncbi.nlm.nih.gov/pubmed/12781537/ doi: 10.1016/s0140-6736(03)13414-9 id: cord-282920-s4yixzuy author: Rubin, Elizabeth S. title: Detection of COVID-19 in a Vulvar Lesion date: 2020-07-02 words: 969.0 sentences: 54.0 pages: flesch: 49.0 cache: ./cache/cord-282920-s4yixzuy.txt txt: ./txt/cord-282920-s4yixzuy.txt summary: While current research suggests COVID-19 viral antigen is not found in vaginal secretions, its detectability in the female lower genital tract may have clinical implications for obstetric and gynecologic care for women. While vertical transmission has largely not been reported, the presence of detectable virus in the female lower genital tract makes this a continued possibility and area of study. Given her other reported symptoms, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nasopharyngeal test was also ordered, and the patient was instructed to have the test performed at an offsite outpatient testing site specifically designated for this purpose. This patient represents the first reported case of SARS-CoV-2 viral shedding detected in a vulvar lesion. [4] [5] [6] Finally, while vertical transmission of COVID-19 to fetuses and newborns has not been definitively shown, 7-9 the presence of detectable virus in the lower genital tract should prompt continued studies into this possibility. SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection abstract: As new information about coronavirus disease 2019 (COVID-19) is rapidly discovered, clinicians are better equipped to make informed decisions for their patients. While current research suggests COVID-19 viral antigen is not found in vaginal secretions, its detectability in the female lower genital tract may have clinical implications for obstetric and gynecologic care for women. We present a case of a woman at 31 weeks' gestation with simultaneous upper respiratory symptoms and vulvovaginitis. She was found to have a vulvar lesion positive for severe acute respiratory syndrome-COVID by viral swab. This case shows that COVID-19 is detectable in the vulva. This may have implications for health care workers' exposure and personal protective equipment needs. While vertical transmission has largely not been reported, the presence of detectable virus in the female lower genital tract makes this a continued possibility and area of study. Key Points: COVID-19 is detectable in the female lower genital tract. The detection of COVID-19 in the vulva may have implications for personal protective equipment use. The detection of COVID-19 in vulvovaginal lesions makes vertical transmission a continued possibility. url: https://www.ncbi.nlm.nih.gov/pubmed/32615620/ doi: 10.1055/s-0040-1713665 id: cord-311044-kjx0z1hc author: Rubio-Pérez, Inés title: COVID-19: key concepts for the surgeon date: 2020-05-28 words: 4652.0 sentences: 301.0 pages: flesch: 51.0 cache: ./cache/cord-311044-kjx0z1hc.txt txt: ./txt/cord-311044-kjx0z1hc.txt summary: Abstract In view of the current pandemic by SARS-CoV-2 it deems essential to understand the key concepts about the infection: its epidemiological origin, presentation, clinical course, diagnosis and treatment (still experimental in many cases). The authors have provided a narrative review of the literature available for certain key aspects of COVID-19 epidemiology, clinical presentation, diagnosis and treatment, which are of special interest to the readers of the journal. Decisions on whether or not to proceed with elective surgery in cancer patients currently depend on the local epidemiological situation, availability of operating rooms J o u r n a l P r e -p r o o f and ICU at the corresponding hospital, disease status and the risk of progression or complications (individualized), assessment of surgical risk and potential complications of the procedure. abstract: Abstract In view of the current pandemic by SARS-CoV-2 it deems essential to understand the key concepts about the infection: its epidemiological origin, presentation, clinical course, diagnosis and treatment (still experimental in many cases). The knowledge about the virus is still limited, but as the pandemic progresses and the physiopathology of the disease is understood, new evidence is being massively published. Surgical specialists are facing an unprecedented situation: they must collaborate in the ER or medical wards attending these patients, while still needing to make decisions about surgical patients with probable COVID-19. The present narrative review aims to summarize the most relevant aspects and synthetize concepts on COVID-19 for surgeons. url: https://api.elsevier.com/content/article/pii/S2173507720301101 doi: 10.1016/j.cireng.2020.05.009 id: cord-345864-87b5qdjx author: Rudolph, James L. title: Temperature in Nursing Home Residents Systematically Tested for SARS-CoV-2 date: 2020-06-09 words: 1482.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-345864-87b5qdjx.txt txt: ./txt/cord-345864-87b5qdjx.txt summary: Abstract Objectives Many nursing home residents infected with SARS-CoV-2 fail to be identified with standard screening for the associated COVID-19 syndrome. The objective of this study is to describe the temperature changes before and after universal testing for SARS-CoV-2 in nursing home residents. We report the temperature in window of the 14 days before and after universal SARS-CoV-2 testing among CLC residents. Administration Community Life Centers (CLCs) infected with SARS-CoV-2 do have 57 temperature elevations well ahead of a confirmatory test, but also that peak temperatures will not 58 typically meet the current screening criterion threshold of 38°C that follows the Centers for 59 Disease Control''s (CDC) guidance. The purpose of this analysis is to compare temperature 73 trends and identify maximum temperatures in nursing home residents fourteen days prior to and 74 following systematic testing for SARS-CoV-2 throughout VHA CLCs. 75 abstract: Abstract Objectives Many nursing home residents infected with SARS-CoV-2 fail to be identified with standard screening for the associated COVID-19 syndrome. Current nursing home COVID-19 screening guidance includes assessment for fever defined as a temperature of at least 38.0°C. The objective of this study is to describe the temperature changes before and after universal testing for SARS-CoV-2 in nursing home residents. Design Cohort study Setting and Participants: The Veterans Administration (VA) operates 134 Community Living Centers (CLC), similar to nursing homes, that house residents who cannot live independently. VA guidance to CLCs directed daily clinical screening for COVID-19 that included temperature assessment. Measures All CLC residents (n=7325) underwent SARS-CoV-2 testing. We report the temperature in window of the 14 days before and after universal SARS-CoV-2 testing among CLC residents. Baseline temperature was calculated for 5 days prior to the study window. Results SARS-CoV-2 was identified in 443 (6.0%) residents. The average maximum temperature in SARS-CoV-2 positive residents was 37.66 (0.69) compared to 37.11 (0.36) (p=0.001) in SARS-CoV-2 negative residents. Temperatures in those with SARS-CoV-2 began rising 7 days prior to testing and remained elevated during the 14-day follow up. Among SARS-CoV-2 positive residents, only 26.6% (n=118) met the fever threshold of 38.0°C during the survey period. Most residents (62.5%, n=277) with confirmed SARS-CoV-2 did experience two or more 0.5°C elevations above their baseline values. One cohort of SARS-CoV-2 residents’ (20.3%, n=90) temperatures never deviated >0.5°C from baseline. Conclusions and Implications A single screening for temperature is unlikely to detect nursing home residents with SARS-CoV-2. Repeated temperature measurement with a patient-derived baseline can increase sensitivity. The current fever threshold as a screening criteria for SARS-CoV-2 infection should be reconsidered. url: https://doi.org/10.1016/j.jamda.2020.06.009 doi: 10.1016/j.jamda.2020.06.009 id: cord-302160-4yfvspaq author: Ruetalo, Natalia title: Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date: 2020-10-07 words: 1853.0 sentences: 108.0 pages: flesch: 56.0 cache: ./cache/cord-302160-4yfvspaq.txt txt: ./txt/cord-302160-4yfvspaq.txt summary: Strikingly, short exposure of high titer surface dried virus (3*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total reduction of SARS-CoV-2 infectivity. We hence conducted a "real-life" application approach simulating the 66 inactivation of dried surface residing infectious SARS-CoV-2 by a mobile handheld UV-C 67 emitting device and an UV-C box designed to decontaminate medium-size objects. Simulating the situation that exhaled droplets or aerosols from infected 115 individuals contaminate surfaces, we produced a high-titer SARS-CoV-2 infectious stock and 116 dried 35µL of this stock corresponding to ~4*10^6 IU/ml in each well of a 6-well plate. Of note, even short UV-C treatment of the dried virus in the context of the moving "fast" 135 regimen completely inactivated SARS-CoV-2, as no infected cells were detected based on 136 fluorescence protein expression (Fig. 1b) . Altogether, our data 143 demonstrate that UV-C regimens that expose high-titer SARS-CoV-2 to doses down to 16 144 mJ/cm² are sufficient to achieve complete inactivation of the virus. abstract: The SARS-CoV-2 pandemic urges for cheap, reliable and rapid technologies for disinfection and decontamination. We here evaluated the efficiency of UV-C irradiation to inactivate surface dried SARS-CoV-2. Drying for two hours did not have a major impact on the infectivity of SARS-CoV-2, indicating that exhaled virus in droplets or aerosols stays infectious on surfaces at least for a certain amount of time. Strikingly, short exposure of high titer surface dried virus (3*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total reduction of SARS-CoV-2 infectivity. Together, our results demonstrate that SARS-CoV-2 is rapidly inactivated by relatively low doses of UV-C irradiation. Hence, UV-C treatment is an effective non-chemical possibility to decontaminate surfaces from high-titer infectious SARS-CoV-2. url: https://doi.org/10.1101/2020.09.22.308098 doi: 10.1101/2020.09.22.308098 id: cord-319933-yp9ofhi8 author: Ruiz, Sara I. title: Chapter 38 Animal Models of Human Viral Diseases date: 2013-12-31 words: 28834.0 sentences: 1797.0 pages: flesch: 46.0 cache: ./cache/cord-319933-yp9ofhi8.txt txt: ./txt/cord-319933-yp9ofhi8.txt summary: An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. abstract: Abstract As the threat of exposure to emerging and reemerging viruses within a naive population increases, it is vital that the basic mechanisms of pathogenesis and immune response be thoroughly investigated. By using animal models in this endeavor, the response to viruses can be studied in a more natural context to identify novel drug targets, and assess the efficacy and safety of new products. This is especially true in the advent of the Food and Drug Administration's animal rule. Although no one animal model is able to recapitulate all the aspects of human disease, understanding the current limitations allows for a more targeted experimental design. Important facets to be considered before an animal study are the route of challenge, species of animals, biomarkers of disease, and a humane endpoint. This chapter covers the current animal models for medically important human viruses, and demonstrates where the gaps in knowledge exist. url: https://api.elsevier.com/content/article/pii/B9780124158948000385 doi: 10.1016/b978-0-12-415894-8.00038-5 id: cord-353548-kf4om6iu author: Ruiz-Manriquez, J. title: Knowledge of Latin American gastroenterologists and endoscopists regarding SARS-CoV-2 infection date: 2020-05-31 words: 2749.0 sentences: 180.0 pages: flesch: 53.0 cache: ./cache/cord-353548-kf4om6iu.txt txt: ./txt/cord-353548-kf4om6iu.txt summary: An electronic questionnaire was applied that was designed to evaluate the knowledge of symptoms, risk groups for severe disease, prevention measures, and the reprocessing of endoscopes utilized in patients with COVID-19. [10] [11] The aim of the present study was to evaluate the knowledge of Latin American gastroenterology and endoscopy professionals in relation to the characteristics of SARS-CoV-2 infection and the prevention measures recommended during patient care and the performance of endoscopic procedures, including the reprocessing of equipment utilized on patients with the disease. We conducted a cross-sectional study on gastroenterologists and endoscopists (residents and specialists) working in public hospitals from nine Latin American countries (Mexico, Costa Rica, Ecuador, Paraguay, Peru, Guatemala, Uruguay, Honduras, and the Dominican Republic). The present study described the current knowledge of 133 Latin American residents and specialists in gastroenterology and endoscopy about symptoms, risk groups, transmission, and endoscopic equipment reprocessing in relation to COVID-19. abstract: Abstract Introduction After the World Health Organization declared the COVID-19 outbreak a pandemic, the number of patients with confirmed SARS-CoV-2 infection (COVID-19) has increased exponentially, and gastroenterologists and other specialists most likely will be involved in the care of those patients. Aim To evaluate the knowledge Latin American gastroenterologists and endoscopists (staff physicians and residents) have about the characteristics of COVID-19, as well as the prevention measures to be taken during endoscopic procedures. Materials and methods We conducted a cross-sectional study that included gastroenterologists and endoscopists from 9 Latin American countries. An electronic questionnaire was applied that was designed to evaluate the knowledge of symptoms, risk groups for severe disease, prevention measures, and the reprocessing of endoscopes utilized in patients with COVID-19. Results Information was obtained from 133 physicians. Ninety-five percent of them correctly identified the most frequent symptoms of the virus, and 60% identified the 3 risk groups for severe disease. Sixty-six percent of those surveyed did not consider it necessary to use standard precautions during endoscopic procedures, and 30% did not consider contact precautions necessary. Forty-eight percent of the participants surveyed were not familiar with the protocol for reprocessing the endoscopes utilized in patients with COVID-19. Conclusion The majority of the gastroenterologists and endoscopists surveyed were familiar with the signs and symptoms of COVID-19 and the populations at risk for complications. There was a lack of knowledge about prevention measures (during clinical care and endoscopic procedures) and the reprocessing of endoscopic equipment by 70% and 48%, respectively, of those surveyed. Dissemination and teaching strategies that increase the knowledge of specific biosafety measures must be carried out. url: https://doi.org/10.1016/j.rgmxen.2020.04.002 doi: 10.1016/j.rgmxen.2020.04.002 id: cord-310411-l0slp1wa author: Rusanen, J. title: Rapid homogeneous assay for detecting antibodies against SARS-CoV-2 date: 2020-11-04 words: 2117.0 sentences: 162.0 pages: flesch: 57.0 cache: ./cache/cord-310411-l0slp1wa.txt txt: ./txt/cord-310411-l0slp1wa.txt summary: 73 We have previously set up rapid homogeneous (wash-free) immunoassays utilizing time(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In this study we introduce rapid wash-free LFRET assays for detection of antibodies 114 against SARS-CoV-2 N and S antigens and compare them with ELISAs and 115 microneutralization. ; https://doi.org/10.1101/2020.11.01.20224113 doi: medRxiv preprint 119 LFRET assays for SARS-CoV-2 S and N were set up using Eu-labeled in-house antigens 120 and AF-labeled protein L. 140 In order to compare the performance of LFRET with classical serology, we tested the set (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. After overnight incubation at Protein expression and purification 299 We initially attempted producing SARS-CoV-2 S protein in Expi293F cells utilizing the (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: Accurate and rapid diagnostic tools are needed for management of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Antibody tests enable detection of individuals past the initial phase of infection and will help to examine possible vaccine responses. The major targets of human antibody response in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the spike glycoprotein (S) and nucleocapsid protein (N). We have developed a rapid homogenous approach for antibody detection termed LFRET (protein L-based time-resolved Forster resonance energy transfer immunoassay). In LFRET, fluorophore-labeled protein L and antigen are brought to close proximity by antigen-specific patient immunoglobulins of any isotype, resulting in TR-FRET signal generation. We set up LFRET assays for antibodies against S and N and evaluated their diagnostic performance using a panel of 77 serum/plasma samples from 44 individuals with COVID-19 and 52 negative controls. Moreover, using a previously described S construct and a novel N construct, we set up enzyme linked immunosorbent assays (ELISAs) for antibodies against SARS-CoV-2 S and N. We then compared the LFRET assays with these enzyme immunoassays and with a SARS-CoV-2 microneutralization test (MNT). We found the LFRET assays to parallel ELISAs in sensitivity (90-95% vs. 90-100%) and specificity (100% vs. 94-100%). In identifying individuals with or without a detectable neutralizing antibody response, LFRET outperformed ELISA in specificity (91-96% vs. 82-87%), while demonstrating an equal sensitivity (98%). In conclusion, this study demonstrates the applicability of LFRET, a 10-minute 'mix and read' assay, to detection of SARS-CoV-2 antibodies. url: http://medrxiv.org/cgi/content/short/2020.11.01.20224113v1?rss=1 doi: 10.1101/2020.11.01.20224113 id: cord-320587-936cavob author: Ruscio, M. title: Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay date: 2020-11-07 words: 4092.0 sentences: 221.0 pages: flesch: 46.0 cache: ./cache/cord-320587-936cavob.txt txt: ./txt/cord-320587-936cavob.txt summary: This analytical assessment encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, and comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using DiaSorin Liaison SARS-CoV-2 S1/S2 IgG and Roche Elecsys Anti-SARS-CoV-2 total antibodies. The assessment of this novel Beckman Coulter Access SARS-CoV-2 IgG immunoassay on UniCel DxI800 has originally encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, as well as comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using two other commercial anti-SARS-CoV-2 immunoassays, as comprehensively described below. As for the diagnostic performance calculated using manufacturers'' cut-off, the AUCs of Beckman Coulter Access SARS-CoV-2 IgG (p<0.001) and Roche Elecsys Anti-SARS-CoV-2 (p=0.01) antibodies titers were found to be both significantly higher than that of DiaSorin Liaison SARS-CoV-2 S1/S2 IgG, whilst they were not significantly different between them (p=0.785). abstract: Background. The approach to diagnosing, treating and monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies strongly on laboratory resources, with serological testing representing the mainstay for studying the onset, nature and persistence of humoral immune response. This study was aimed at evaluating the analytical performance of the novel Beckman Coulter anti-SARS-CoV-2 IgG chemiluminescent immunoassay. Methods. This analytical assessment encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, and comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using DiaSorin Liaison SARS-CoV-2 S1/S2 IgG and Roche Elecsys Anti-SARS-CoV-2 total antibodies. Diagnostic performance was also tested against results of molecular testing on nasopharyngeal swabs, collected over the previous 4 months. Results. Intra-assay, inter-assay and total imprecision of Beckman Coulter anti-SARS-CoV-2 IgG were between 4.3-4.8%, 2.3-3.9% and 4.9-6.2%, respectively. The linearity of the assay was excellent between 0.11-18.8 antibody titers. The LOB, LOD and functional sensitivity were 0.02, 0.02 and 0.05, respectively. The diagnostic accuracy (area under the curve; AUC) of Beckman Coulter anti-SARS-CoV-2 IgG compared to molecular testing was 0.87 (95% CI, 0.84-0.91; p<0.001) using manufacturer's cut-off, and increased to 0.90 (95% CI, 0.86-0.94; p<0.001) with antibody titers. The AUC was non-significantly different from that of Roche Elecsys Anti-SARS-CoV-2, but was always higher than that of DiaSorin Liaison SARS-CoV-2 S1/S2 IgG. The correlation of Beckman Coulter Access SARS-CoV-2 IgG was 0.80 (95% CI, 0.75-0.84; p<0.001) with Roche Elecsys Anti-SARS-CoV-2 and 0.72 (95% CI, 0.66-0.77; p<0.001) with DiaSorin Liaison SARS-CoV-2 S1/S2 IgG, respectively. Conclusions. The results of this analytical evaluation of Beckman Coulter Access anti-SARS-CoV-2 IgG suggests that this fully-automated chemiluminescent immunoassay represents a valuable resource for large and accurate seroprevalence surveys. url: https://doi.org/10.1101/2020.11.05.20226555 doi: 10.1101/2020.11.05.20226555 id: cord-291505-vt5vpp60 author: Rusconi, Chiara title: SARS-CoV-2 Interstitial Pneumonia Treated With Tocilizumab in a Patient Affected by Classical Hodgkin Lymphoma date: 2020-09-01 words: 1769.0 sentences: 111.0 pages: flesch: 40.0 cache: ./cache/cord-291505-vt5vpp60.txt txt: ./txt/cord-291505-vt5vpp60.txt summary: [5] [6] [7] We therefore report a case of SARS-CoV-2 interstitial pneumonia in a patient with classical Hodgkin Lymphoma (cHL) successfully treated with tocilizumab. 6, 7 More recently, a series of hematological cancer patients SARS-CoV-2 infected has been described: 3 out of 25 patients received tocilizumab, in 2 cases together with steroids, and a successful outcome has been reported for two of them. The first cHL patient affected by COVID-19 has been described by O''Kelly and colleagues: at symptoms onset, a PD-1 inhibitors induced pneumonitis was suspected, and treatment against SARS-CoV-2 was started after NPS test resulted positive. 14 To the best of our knowledge, this is the first extended report on successful tocilizumab treatment for a lymphoma patient affected by COVID-19; immunocompromised subjects may mount an antibody response and overcome SARS-CoV-2 infection, even in case of severe interstitial pneumonia. abstract: nan url: https://doi.org/10.1097/hs9.0000000000000472 doi: 10.1097/hs9.0000000000000472 id: cord-029813-o2uzcuai author: Rusconi, Stefano title: COVID-19: studying the global pandemic – foreword date: 2020-07-27 words: 2723.0 sentences: 131.0 pages: flesch: 43.0 cache: ./cache/cord-029813-o2uzcuai.txt txt: ./txt/cord-029813-o2uzcuai.txt summary: This special issue of Future Virology contains nine articles on diverse aspects of the COVID-19 pandemic and its causative agent, SARS-CoV-2. The topics range from basic virology on coronavirus evolution and replication to identification of repurposed therapeutics for clinical testing to public health issues including the conundrums of asymptomatic viral transmission and risks to homeless populations. The Commentary by Parvez [1] briefly reviews the detection of SARS-CoV-2 RNA in fecal samples, including its persistence, and the finding of gastrointestinal complaints in a minority of hospitalized patients. While it is clear that this phytochemical has multiple pharmacological activities, as reviewed previously [10] , this in silico report does not provide biologic data on rutin''s possible effects in SARS-CoV-2 infection. Detection of relatively high SARS-CoV-2 RNA loads in upper respiratory tract samples has been reported in both presymptomatic (late incubation period) and truly asymptomatic infected persons. Transmission and clinical characteristics of asymptomatic patients with SARS-CoV-2 infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386404/ doi: 10.2217/fvl-2020-0211 id: cord-289890-sf2uxubd author: Rushworth, S. A. title: Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay date: 2020-06-12 words: 3954.0 sentences: 195.0 pages: flesch: 52.0 cache: ./cache/cord-289890-sf2uxubd.txt txt: ./txt/cord-289890-sf2uxubd.txt summary: We evaluated the FDA approved SARS-CoV-2 immunoassay (developed at Mount Sinai, by Krammer and colleagues) for the identification of COVID-19 seroconversion and potential cross-reactivity of the assay in a United Kingdom (UK) National Health Service (NHS) hospital setting. In summary, we report that the Mount Sinai IgG ELISA assay is highly sensitive test for SARS-Cov-2 infection, however modification of thresholding was required to minimise false positive results. Figure 2A shows that 42/47 samples from this group were established as negative for SARS-CoV-2 IgG antibody in the first RBD screening test step, and 5/47 required confirmatory assessment with the second dilution assay. On testing of the control group, 70/72 patient samples were identified as being negative for SARS-CoV-2 IgG antibody following the RBD step of the assay using the 5 SD threshold. To conclude, here we report that the Mount Sinai IgG ELISA assay is highly sensitive and apparent cost-effective test for SARS-Cov-2 infection in a UK NHS acute hospital laboratory setting. abstract: We evaluated the FDA approved SARS-CoV-2 immunoassay (developed at Mount Sinai, by Krammer and colleagues) for the identification of COVID-19 seroconversion and potential cross-reactivity of the assay in a United Kingdom (UK) National Health Service (NHS) hospital setting. In our "set up" cohort we found that the SARS-CoV-2 IgG was detectable in 100% of patients tested 14 days post positive COVID-19 nucleic acid test. Serum samples taken from pregnant women in 2018 were used as a negative control group with zero false positives. We also analysed samples from patients with non-COVID-19 viral infections, paraproteinaemia or autoantibodies and found false positive results in 6/179. Modification of the sensitivity threshold to five standard deviations from the mean of the control group eliminated all false positive result in the set up cohort. We confirmed the validity of the test with a revised threshold on an independent prospective "validation cohort" of patient samples. Taking data from both cohorts we report a sensitivity of the Mount Sinai assay of 96.6% (28/29) and specificity of 100% (299/299) using a revised threshold cut-off, at a time point at least 14 days since the diagnostic antigen test. Finally, we conducted a health economic probabilistic sensitivity analysis (PSA) on the costs of producing the tests, and the mean cost we estimate to be 13.63 pounds sterling (95%CI 9.63 - 18.40), allowing its cost effectiveness to be tested against other antibody tests. In summary, we report that the Mount Sinai IgG ELISA assay is highly sensitive test for SARS-Cov-2 infection, however modification of thresholding was required to minimise false positive results. url: https://doi.org/10.1101/2020.06.11.20128306 doi: 10.1101/2020.06.11.20128306 id: cord-158628-71n1tgrw author: Russo, Giulia title: In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform date: 2020-05-05 words: 5596.0 sentences: 296.0 pages: flesch: 50.0 cache: ./cache/cord-158628-71n1tgrw.txt txt: ./txt/cord-158628-71n1tgrw.txt summary: Recently, specific findings about the genome sequencing of SARS-CoV-2 in different countries where cases of infection were registered, revealed its relative intrinsic genomic variability, its virus dynamics and the related host response mechanisms, unveiling interesting knowledge useful for the formulation of innovative strategies for preventive vaccination. Specifically, SARS-CoV-2 sequencing along with its relative intrinsic genomic variability [10] , the presence of minority variants generated during SARS-CoV-2 replication [11] , the involved cellular factors that favors SARS-CoV-2 cell entry [12] , the timing in which viral load peaks (during the first week of illness), its gradual decline (over the second week) and the increasing of both IgG and IgM antibodies (around day 10 after symptom onset) represent some of the relevant insights so far delineated and considered by research community about SARS-CoV-2 virus [13] . UISS is an immune system simulation platform that was designed to be applied to several and different scenarios, especially to carry on in silico trials to predict the efficacy of a specific prophylactic or therapeutic vaccine against a particular disease. abstract: SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this, outbreak specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. Here, we present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS- CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. UISS is then potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2. url: https://arxiv.org/pdf/2005.02289v1.pdf doi: nan id: cord-344714-0cam9ipf author: Russo, Maria title: Roles of flavonoids against coronavirus infection date: 2020-07-28 words: 8395.0 sentences: 394.0 pages: flesch: 46.0 cache: ./cache/cord-344714-0cam9ipf.txt txt: ./txt/cord-344714-0cam9ipf.txt summary: Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Inhibition of TMPRSS2 and Furin protease activities can be considered an interesting therapeutic option against coronavirus infection, especially COVID-19, allowing the block and/or prevention of SARS-CoV-2 infection, as recently reported [28] . Based on these observations, it is not surprising that molecular docking approach, summarized in Fig. 3 , supports the role of flavonoids in the inhibition of SARS-CoV 3CL pro by binding His41 and Cys145 of the catalytic site and other active site residues (e.g., Met49, Gly143, His163, His164, Glu166, Pro168, and Gln89), stimulating their validation by in vitro and in vivo studies. abstract: In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of “savage” protocols, based on “old” anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenols family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections. url: https://doi.org/10.1016/j.cbi.2020.109211 doi: 10.1016/j.cbi.2020.109211 id: cord-298350-pq1dcz3a author: Ryan, Jeffrey R. title: Category C Diseases and Agents date: 2016-03-25 words: 7266.0 sentences: 451.0 pages: flesch: 57.0 cache: ./cache/cord-298350-pq1dcz3a.txt txt: ./txt/cord-298350-pq1dcz3a.txt summary: Specific examples explored in this chapter include Nipah virus, hantavirus, West Nile fever virus, and the coronaviruses that cause severe acute respiratory syndrome and Middle East respiratory syndrome. Remarkably, researchers noted that human case patients had an association with infected animals from a concurrent and severe outbreak of respiratory disease in pigs and that there was a notable absence of illness in children. Research shows that many HPS case patients acquired the virus after having been in frequent contact with rodents or their droppings for long periods (Centers for Disease Control and Prevention, Special Pathogens Branch, 2007) . Initially, Saint Louis encephalitis virus was believed to be the cause of the human infections until WNV was isolated from the human and animal specimens. Patients infected with the SARS-coronavirus disease are likely to present to health-care facilities. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia abstract: This chapter covers Category C diseases and agents. These emerging diseases present a very unique challenge to public health officials and infectious disease specialists. Perhaps they have been with us for millions of years, lurking in a dark corner of the environment, waiting for an opportunity to jump from their natural cycle of transmission to a human host. Or they may represent something totally new. Regardless of their origin, an emerging disease pathogen must be characterized quickly by molecular biologists and microbiologists. The dynamics of disease transmission must be investigated by teams of epidemiologists. Treatment regimens must be formulated by clinicians working on the frontlines of the outbreak. Disease prevention strategies and risk communications must be quickly formulated by public health officials. Finally, media attention for emerging disease outbreaks forces government officials at all levels to address the problem with planning and preparedness activities aimed at preserving the health of the public. Specific examples explored in this chapter include Nipah virus, hantavirus, West Nile fever virus, and the coronaviruses that cause severe acute respiratory syndrome and Middle East respiratory syndrome. url: https://www.sciencedirect.com/science/article/pii/B9780128020296000050 doi: 10.1016/b978-0-12-802029-6.00005-0 id: cord-337511-20yaol5r author: Ryan, Paul MacDaragh title: COVID-19 and relative angiotensin-converting enzyme 2 deficiency: role in disease severity and therapeutic response date: 2020-06-11 words: 3244.0 sentences: 182.0 pages: flesch: 37.0 cache: ./cache/cord-337511-20yaol5r.txt txt: ./txt/cord-337511-20yaol5r.txt summary: Interestingly, comparative analysis of two successive SARS epidemics in early 2000s showed that increased affinity of the SARS virus for human ACE2 receptor strongly predicted severity of clinical disease suggesting that spike protein conformation is potentially a key determinant of virulence. 15 Interestingly, in several Wuhan cohorts cardiac injury and arrythmia were prominent in high-risk Figure 3 Homeostasis of RAS-ACE2 under normal healthy conditions 10 19 ; perturbation of RAS-ACE2 homeostasis in cardiovascular disease, hypertension and diabetes mellitus 22 27 ; COVID-19 may potentially further upregulate RAS in CVD patients and deplete ACE2 33 ; proposition that rhACE2 replacement therapy improves RAS-ACE2 balance by augmenting ACE2 and decreasing RAS activation. 35 If the same holds true for SARS-CoV-2, then soluble rhACE2 may reduce ongoing SARS-CoV-2 access to membrane-bound ACE2 receptor, alter favourably local AngII/Ang1-7 levels and inhibit deleterious RAS effects on remaining at risk tissues in COVID-19 patients. abstract: nan url: https://doi.org/10.1136/openhrt-2020-001302 doi: 10.1136/openhrt-2020-001302 id: cord-325055-todb1d4x author: Rychter, Anna Maria title: Should patients with obesity be more afraid of COVID‐19? date: 2020-06-24 words: 3270.0 sentences: 217.0 pages: flesch: 49.0 cache: ./cache/cord-325055-todb1d4x.txt txt: ./txt/cord-325055-todb1d4x.txt summary: Furthermore, obesity is increasingly considered as a yet another risk factor, particularly, because it has been observed that people suffering from excessive body weight may experience a more severe course of COVID‐19 infection. Although the data regarding the impact of SARS-CoV-2 in individuals with obesity are limited and their association has not been fully defined yet, it has been observed that people suffering from excessive body weight may experience a more serious COVID-19 infection. 68 Whether the obesity paradox will be present among COVID-19 patients remains to be seen, nevertheless, the phenomenon was reported among other respiratory diseases, such as COPD or ARDS. 53, 69 Its pathophysiological basis remains unknown; however, an increased BMI seems to be associated with a better survival and a slower decline in the lung function in patients with a mild course of chronic obstructive pulmonary disease. Obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Association of obesity with disease severity among patients with COVID-19. abstract: COVID‐19 crisis has lasted since the late 2019 to the present day. The severity of the disease is positively correlated with several factors, such as age and coexisting diseases. Furthermore, obesity is increasingly considered as a yet another risk factor, particularly, because it has been observed that people suffering from excessive body weight may experience a more severe course of COVID‐19 infection. On the basis of current research, in our nonsystematic review, we have investigated the extent to which obesity can affect the SARS‐CoV‐2 course and identify the potential mechanisms of the disease. We have also described the role of proper nutrition, physical activity and other aspects relevant to the management of obesity. url: https://doi.org/10.1111/obr.13083 doi: 10.1111/obr.13083 id: cord-315181-emf4i6ir author: Ryoo, Nayoung title: Coping with Dementia in the Middle of the COVID-19 Pandemic date: 2020-10-27 words: 7135.0 sentences: 400.0 pages: flesch: 42.0 cache: ./cache/cord-315181-emf4i6ir.txt txt: ./txt/cord-315181-emf4i6ir.txt summary: • Home based exercise and planned outdoor activities, avoiding densely populated areas, with caregivers are encouraged • Have more organized daily plans that include enjoyable therapeutic activities • Create a new routine which fits within the context of the current circumstances • Prevent overuse or addiction to TV/video by scheduling and restricting daily use • Counselling for behavioural management of FTD via telephone hotlines is helpful • Providing self-help guidance for reducing stress through electronic media can result in beneficial effects for FTD patients ADL = activities of daily living, PPE = personal protective equipment, COVID-19 = coronavirus disease 2019, BPSD = behavioral and psychological symptoms of dementia, VD = vascular dementia, AD = Alzheimer''s disease, FTD = frontotemporal dementia, ICU = intensive care unit, DLB = diffuse Lewy body. abstract: Multiple neurological complications have been associated with the coronavirus disease-19 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2. This is a narrative review to gather information on all aspects of COVID-19 in elderly patients with cognitive impairment. First, the following three mechanisms have been proposed to underlie the neurological complications associated with COVID-19: 1) direct invasion, 2) immune and inflammatory reaction, and 3) hypoxic brain damage by COVID-19. Next, because the elderly dementia patient population is particularly vulnerable to COVID-19, we discussed risk factors and difficulties associated with cognitive disorders in this vulnerable population. We also reviewed the effects of the patient living environment in COVID-19 cases that required intensive care unit (ICU) care. Furthermore, we analyzed the impact of stringent social restrictions and COVID-19 pandemic-mediated policies on dementia patients and care providers. Finally, we provided the following strategies for working with elderly dementia patients: general preventive methods; dementia care at home and nursing facilities according to the activities of daily living and dementia characteristics; ICU care after COVID-19 infection; and public health care system and government response. We propose that longitudinal follow-up studies are needed to fully examine COVID-19 associated neurological complications, such as dementia, and the efficacy of telemedicine/telehealth care programs. url: https://www.ncbi.nlm.nih.gov/pubmed/33140593/ doi: 10.3346/jkms.2020.35.e383 id: cord-267482-afqfymbq author: Ryu, Seungjin title: Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date: 2020-09-12 words: 8189.0 sentences: 476.0 pages: flesch: 49.0 cache: ./cache/cord-267482-afqfymbq.txt txt: ./txt/cord-267482-afqfymbq.txt summary: Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs. Also, initial studies that employ lung ciliated epithelial cell-specific HFH4/FOXJ1 promoter driven hACE2 transgenic mice show SARS-CoV-2 infection induces weight loss, lung inflammation and approximately 50% mortality rate, suggesting the usefulness of this model to understand the mechanism of immune dysregulation (Jiang et al., 2020) . Moreover, given our recent findings that ketogenesis inhibits inflammation and expands tissue resident ϒδ T cells (Goldberg et al., 2019) while SARS-CoV-2 infection in patients is associated with depletion of ϒδ T cells (Lei et al., 2020; Rijkers et al., 2020) , we next tested whether elevating BHB by feeding a ketogenic diet (KD) protects against mCoV-A59-driven inflammatory damage in aged mice. abstract: Increasing age is the strongest predictor of risk of COVID-19 severity. Unregulated cytokine storm together with impaired immunometabolic response leads to highest mortality in elderly infected with SARS-CoV-2. To investigate how aging compromises defense against COVID-19, we developed a model of natural murine beta coronavirus (mCoV) infection with mouse hepatitis virus strain MHV-A59 (mCoV-A59) that recapitulated majority of clinical hallmarks of COVID-19. Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs. Ketogenic diet increases beta-hydroxybutyrate, expands tissue protective γδ T cells, deactivates the inflammasome and decreases pathogenic monocytes in lungs of infected aged mice. These data underscore the value of mCoV-A59 model to test mechanism and establishes harnessing of the ketogenic immunometabolic checkpoint as a potential treatment against COVID-19 in the elderly. Highlights - Natural MHV-A59 mouse coronavirus infection mimics COVID-19 in elderly. - Aged infected mice have systemic inflammation and inflammasome activation - Murine beta coronavirus (mCoV) infection results in loss of pulmonary γδ T cells. - Ketones protect aged mice from infection by reducing inflammation. eTOC Blurb Elderly have the greatest risk of death from COVID-19. Here, Ryu et al report an aging mouse model of coronavirus infection that recapitulates clinical hallmarks of COVID-19 seen in elderly. The increased severity of infection in aged animals involved increased inflammasome activation and loss of γδ T cells that was corrected by ketogenic diet. url: https://doi.org/10.1101/2020.09.11.294363 doi: 10.1101/2020.09.11.294363 id: cord-316788-4x5l2h4d author: Ryu, Young Bae title: Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition date: 2010-11-15 words: 3222.0 sentences: 173.0 pages: flesch: 59.0 cache: ./cache/cord-316788-4x5l2h4d.txt txt: ./txt/cord-316788-4x5l2h4d.txt summary: Following bioactivity-guided fractionation, eight diterpenoids (1–8) and four biflavonoids (9–12) were isolated and evaluated for SARS-CoV 3CL(pro) inhibition using fluorescence resonance energy transfer analysis. As part of an ongoing investigation of potential SARS-CoV 3CL pro inhibitors from medicinal plants, we performed an initial screen of ethanol extracts of the leaves of Torreya nucifera using a fluorescence resonance energy transfer (FRET) assay. We isolated 12 phytochemicals-eight diterpenoids and four biflavonoids-with SARS-CoV 3CL pro inhibitory activity from the ethanol extracts of the leaves of T. Of the isolated compounds, biflavonoid amentoflavone (9) was identified as a potent inhibitor of SARS-CoV 3CL pro , exhibiting an IC 50 value of 8.3 lM. nucifera, is an effective inhibitor of SARS-CoV 3CL pro and is more effective than the corresponding flavones (apigenin and luteolin) and biflavonoid derivatives containing various numbers of methoxy groups. abstract: As part of our search for botanical sources of SARS-CoV 3CL(pro) inhibitors, we selected Torreya nucifera, which is traditionally used as a medicinal plant in Asia. The ethanol extract of T. nucifera leaves exhibited good SARS-CoV 3CL(pro) inhibitory activity (62% at 100 μg/mL). Following bioactivity-guided fractionation, eight diterpenoids (1–8) and four biflavonoids (9–12) were isolated and evaluated for SARS-CoV 3CL(pro) inhibition using fluorescence resonance energy transfer analysis. Of these compounds, the biflavone amentoflavone (9) (IC(50) = 8.3 μM) showed most potent 3CL(pro) inhibitory effect. Three additional authentic flavones (apigenin, luteolin and quercetin) were tested to establish the basic structure–activity relationship of biflavones. Apigenin, luteolin, and quercetin inhibited 3CL(pro) activity with IC(50) values of 280.8, 20.2, and 23.8 μM, respectively. Values of binding energy obtained in a molecular docking study supported the results of enzymatic assays. More potent activity appeared to be associated with the presence of an apigenin moiety at position C-3′ of flavones, as biflavone had an effect on 3CL(pro) inhibitory activity. url: https://www.sciencedirect.com/science/article/pii/S0968089610008722 doi: 10.1016/j.bmc.2010.09.035 id: cord-321714-yhruzu7f author: Ryu, Young Bae title: SARS-CoV 3CL(pro) inhibitory effects of quinone-methide triterpenes from Tripterygium regelii date: 2010-03-15 words: 1933.0 sentences: 114.0 pages: flesch: 59.0 cache: ./cache/cord-321714-yhruzu7f.txt txt: ./txt/cord-321714-yhruzu7f.txt summary: Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). We then further characterized the inhibitory mechanism of the isolated quinone-methide triterpenes against SARS-CoV 3CL pro activity. Although all isolated quinone-methide triterpenes has previously been known compounds, this is the first time it has been shown to possess SARS-CoV 3CL pro inhibitory activity. abstract: Quinone-methide triterpenes, celastrol (1), pristimerin (2), tingenone (3), and iguesterin (4) were isolated from Triterygium regelii and dihydrocelastrol (5) was synthesized by hydrogenation under palladium catalyst. Isolated quinone-methide triterpenes (1–4) and 5 were evaluated for SARS-CoV 3CL(pro) inhibitory activities and showed potent inhibitory activities with IC(50) values of 10.3, 5.5, 9.9, and 2.6 μM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC(50) = 21.7 μM). As a result, quinone-methide moiety in A-ring and more hydrophobic E-ring assist to exhibit potent activity. Also, all quinone-methide triterpenes 1–4 have proven to be competitive by the kinetic analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/20167482/ doi: 10.1016/j.bmcl.2010.01.152 id: cord-307463-bheq9p5w author: Rödel, Franz title: Low-dose radiation therapy for COVID-19 pneumopathy: what is the evidence? date: 2020-05-09 words: 2006.0 sentences: 97.0 pages: flesch: 43.0 cache: ./cache/cord-307463-bheq9p5w.txt txt: ./txt/cord-307463-bheq9p5w.txt summary: Due to the current lack of effective pharmacological concepts, this situation has caused interest in (re)considering historical reports on the treatment of patients with low-dose radiation therapy for pneumonia. Although these historical reports are of low-level evidence per se, hampering recommendations for decision-making in the clinical setting, they indicate effectiveness in the dose range between 0.3 and 1 Gy, similar to more recent dose concepts in the treatment of acute and chronic inflammatory/degenerative benign diseases with, e.g., a single dose per fraction of 0.5 Gy. This concise review aims to critically review the evidence for low-dose radiation treatment of COVID-19 pneumopathy and discuss whether it is worth investigating in the present clinical situation. This situation has caused interest in (re)considering the historical treatment of patients with low-dose radiation therapy for pneumonia. This review on 15 reports covers 863 patients with severe pneumonia of K different pathogeneses, including two studies of viral origin treated with low doses of kilovoltage X-rays. abstract: In the current dismal situation of the COVID-19 pandemic, effective management of patients with pneumonia and acute respiratory distress syndrome is of vital importance. Due to the current lack of effective pharmacological concepts, this situation has caused interest in (re)considering historical reports on the treatment of patients with low-dose radiation therapy for pneumonia. Although these historical reports are of low-level evidence per se, hampering recommendations for decision-making in the clinical setting, they indicate effectiveness in the dose range between 0.3 and 1 Gy, similar to more recent dose concepts in the treatment of acute and chronic inflammatory/degenerative benign diseases with, e.g., a single dose per fraction of 0.5 Gy. This concise review aims to critically review the evidence for low-dose radiation treatment of COVID-19 pneumopathy and discuss whether it is worth investigating in the present clinical situation. url: https://doi.org/10.1007/s00066-020-01635-7 doi: 10.1007/s00066-020-01635-7 id: cord-281294-dnaith3a author: Röhr, Susanne title: Psychosoziale Folgen von Quarantänemaßnahmen bei schwerwiegenden Coronavirus-Ausbrüchen: ein Rapid Review date: 2020-04-27 words: 3068.0 sentences: 424.0 pages: flesch: 47.0 cache: ./cache/cord-281294-dnaith3a.txt txt: ./txt/cord-281294-dnaith3a.txt summary: Im April 2020 unterstand weltweit mehr als ein Drittel der Menschheit Quarantänemaßnahmen, um die Ausbreitung des neuartigen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) einzudämmen. Die durch die Infektion mit SARS-CoV-2 ausgelöste Atemwegserkrankung Corona Virus Disease 2019 (COVID19) wurde erstmals im Dezember 2019 in der chinesischen Millionenstadt Wuhan beschrieben und entwickelte sich bereits im Januar 2020 zur Epidemie in China [1] . Evidenz über psychosoziale Folgen von Quarantänemaßnahmen im Zusammenhang mit den genannten Ausbrüchen können Grundlage für entsprechende Untersuchungsansätze und Handlungsempfehlungen im Rahmen der COVID-19-Pandemie sein. Insgesamt konnten 13 Studien identifiziert werden, die konsistent psychosoziale Folgen von Quarantäne-und Isolationsmaßnahmen bei der SARS-Pandemie 2002/2003 und lokalen MERS-CoV-Ausbrüchen in den Zehnerjahren beschrieben, darunter Depressivität, Ängstlichkeit, Wut, Stress, Schlafstörungen, Sorgen, soziale Isolation, Einsamkeit und Stigmatisierung. Erste Fallstudien aus Deutschland bestätigen erhöhte psychische Belastungen infolge von COVID-19 und unterstreichen den Bedarf für eine Public-Health-Agenda, die Maßnahmen zum Schutz der psychosozialen Gesundheit während der Massenquarantäne hierzulande forciert [46] . abstract: Objective Review of the evidence on the psychosocial impact of quarantine measures during serious coronavirus outbreaks before COVID-19. Such information is highly relevant in regard to the COVID-19 pandemic. Methods Search of the MEDLINE database for relevant studies related to SARS-CoV and MERS-CoV outbreaks. Results Across 13 identified studies, quarantine measures were consistently associated with negative psychosocial outcomes, including depressive symptoms, anxiety, anger, stress, posttraumatic stress, social isolation, loneliness and stigmatization. Determinants comprised duration of quarantine measures and income losses. Health care workers constituted a particularly vulnerable group. Conclusion Quarantine measures during serious coronavirus outbreaks have extensive negative consequences for mental health. Prevention and intervention approaches to attenuate the psychosocial impact should be an integral component of crisis response during pandemic conditions. url: https://doi.org/10.1055/a-1159-5562 doi: 10.1055/a-1159-5562 id: cord-292985-w62xaa4f author: Römer, Rudolf A. title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 words: 5201.0 sentences: 341.0 pages: flesch: 61.0 cache: ./cache/cord-292985-w62xaa4f.txt txt: ./txt/cord-292985-w62xaa4f.txt summary: We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. abstract: The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank (PDB). We study their flexibility, rigidity and mobility, an important first step in trying to ascertain their dynamics for further drug-related docking studies. We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. For example, for the SARS-CoV-2 spike protein in the open configuration, our method identifies a possible further opening and closing of the S1 subunit through movement of SB domain. With full structural information of this process available, docking studies with possible drug structures are then possible in silico. In our study, we present full results for the more than 200 thus far published SARS-CoV-2-related protein structures in the PDB. url: https://doi.org/10.1101/2020.07.12.199364 doi: 10.1101/2020.07.12.199364 id: cord-260503-yq4dtf8n author: SAMARANAYAKE, LAKSHMAN P. title: Severe acute respiratory syndrome and dentistry A retrospective view date: 2004-09-30 words: 6836.0 sentences: 383.0 pages: flesch: 54.0 cache: ./cache/cord-260503-yq4dtf8n.txt txt: ./txt/cord-260503-yq4dtf8n.txt summary: Objectives The authors trace the emergence of the SARS outbreak from southern China and its spread worldwide, discuss the viral etiology of the infection and its clinical features, and review the infection control guidelines issued during the outbreak by the health authorities in Hong Kong, the Centers for Disease Control and Prevention, the World Health Organization and the American Dental Association. Conclusions and Clinical Implications Researchers believe that a combination of factors, including the universal infection control measures that the dental community has implemented and/or the low degree of viral shedding in the prodromal phase of SARS, may have obviated the spread of the disease in dental settings. Interim domestic infection control precautions for aerosol-generating procedures on C L I N I C A L P R A C T I C E patients with severe acute respiratory syndrome (SARS) abstract: ABSTRACT Background Severe acute respiratory syndrome, or SARS, which has created panic in Asia and in some parts of North America, is the first epidemic of the new century. Although it has been well-contained, sporadic cases continue to emerge. Objectives The authors trace the emergence of the SARS outbreak from southern China and its spread worldwide, discuss the viral etiology of the infection and its clinical features, and review the infection control guidelines issued during the outbreak by the health authorities in Hong Kong, the Centers for Disease Control and Prevention, the World Health Organization and the American Dental Association. They also review the prospects for a new outbreak and preventive measures. Overview The disease, which is caused by a novel coronavirus termed the “SARS coronavirus,” or SARS-CoV, essentially spreads through droplet infection and affects people of any age. It has a mortality rate ranging from 10 to 15 percent. A major hallmark of this disease has been the rate at which it has affected health care workers through nosocomial transmission; in some countries, up to one-fourth to one-third of those infected were in this category. However, no dental health care worker has been affected by SARS in a nosocomial or dental setting. Conclusions and Clinical Implications Researchers believe that a combination of factors, including the universal infection control measures that the dental community has implemented and/or the low degree of viral shedding in the prodromal phase of SARS, may have obviated the spread of the disease in dental settings. The dental community should reflect on this outbreak to reinforce the currently applied infection control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/15493394/ doi: 10.14219/jada.archive.2004.0405 id: cord-355477-7xd93aqv author: SATIJA, NAMITA title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 words: 4946.0 sentences: 279.0 pages: flesch: 52.0 cache: ./cache/cord-355477-7xd93aqv.txt txt: ./txt/cord-355477-7xd93aqv.txt summary: abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells abstract: abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). The SARS epidemic in 2003 resulted in more than 8400 SARS cases and approximately 800 deaths. Existing in non‐identified animal reservoirs, SARS‐CoV continues to represent a threat to humans although more than four years have passed since a large outbreak of SARS, and no new cases have been reported. However, we cannot exclude the possibility of reemergence of SARS. It is hence necessary to understand the biology of the SARS‐CoV to deal adequately with the next outbreak, whenever it happens. The SARS‐CoV is a novel coronavirus with a large (∼30 thousand nucleotides) positive‐sense, single‐stranded RNA containing 14 functional open reading frames (ORFs) of which 2 large ORFs constitute the replicase gene which encodes proteins required for viral RNA syntheses. The remaining 12 ORFs encode the 4 structural proteins: spike, membrane, nucleocapsid and envelope; and eight accessory proteins. The viral genome and its expression within the host cell undergoes extensive translational and enzymatic processing to form the 4 structural, 8 accessory and 16 nonstructural proteins. In an effort to understand the molecular mechanisms or capsid assembly and viral pathogenesis, laboratories around the world have adopted a variety of approaches to answering these trivial questions. It has been our effort to consolidate all information known to date about the molecular mechanisms of the SARS‐CoV into this chapter to update our readership on the current status of research. url: https://www.ncbi.nlm.nih.gov/pubmed/17470909/ doi: 10.1196/annals.1408.002 id: cord-257022-6vw88jib author: SHANG, Lei title: Polymorphism of SARS-CoV Genomes date: 2006-04-30 words: 2739.0 sentences: 144.0 pages: flesch: 61.0 cache: ./cache/cord-257022-6vw88jib.txt txt: ./txt/cord-257022-6vw88jib.txt summary: Abstract In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. In this work, the genome of one SARS-CoV isolated directly from the stool sample of a SARS patient was completely sequenced. We aligned 116 complete genome sequences of SARS-CoV (including BJ202 ) to analyze their single nucleotide polymorphism (SNPs). The 21.9-23.9 kb region, which falls into OrfS, had the third highest mutation frequency, in which 39 polymorphic sites were found in the nearly 2 kb stretch of genomic sequence (1 9.5 SNPs in 1 kb). Although it was reported that the in vitro mutation rate of the SARS-CoV in Vero cell passage was negligible[''81, there might be difference between the genomic sequences obtained directly from clinical samples and from isolates of the cell culture. In this work, we completed the sequencing of SARS-CoV genome directly from the stool sample and analyzed the polymorphism of the SARS-CoV genome. abstract: Abstract In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI Gen-Bank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3′ end (19.0 kb-29.7 kb). Regions encoding Orf10–11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27 700–28 000) which encodes parts of the putative ORF9 and ORF10–11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. BJ202 was phylogeneticly closer to BJ01 and LLJ-2004. url: https://www.ncbi.nlm.nih.gov/pubmed/16625834/ doi: 10.1016/s0379-4172(06)60061-9 id: cord-288651-bgo8istm author: SHI, Yi title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date: 2005-03-17 words: 3062.0 sentences: 242.0 pages: flesch: 62.0 cache: ./cache/cord-288651-bgo8istm.txt txt: ./txt/cord-288651-bgo8istm.txt summary: RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. The results show that all siRNA duplexes specifically reduced SARS-CoV genes expression to different extents compared with the control (Fig. 1) . Kinetic study results (Fig. 2B ) revealed a continuous increase in the specific inhibition of SARS-CoV genes expression by No. 5, No. 6, and No. 16 siRNA from 24 to 72 h after transfection. abstract: RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. dsRNA-mediated RNAi can be used in a wide variety of eucaryotes to induce the sequence-specific inhibition of gene expression. Synthetic 21-23 nucleotide (nt) small interfering RNA (siRNA) with 2 nt 3′ overhangs was recently found to mediate efficient sequence-specific mRNA degradation in mammalian cells. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Among total 26 siRNA duplexes, we obtained 3 siRNA duplexes which could sequence-specifically reduce target genes expression over 80% at the concentration of 60 nM in Vero E6 cells. The downregulation effect was in correlation with the concentrations of the siRNA duplexes in a range of 0∼60 nM. Our results also showed that many inactive siRNA duplexes may be brought to life simply by unpairing the 5' end of the antisense strands. Results suggest that siRNA is capable of inhibiting SARS coronavirus genes expression and thus may be a new therapeutic strategy for treatment of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15780182/ doi: 10.1038/sj.cr.7290286 id: cord-286072-kgpvdb42 author: Sa Ribero, Margarida title: Interplay between SARS-CoV-2 and the type I interferon response date: 2020-07-29 words: 7026.0 sentences: 360.0 pages: flesch: 43.0 cache: ./cache/cord-286072-kgpvdb42.txt txt: ./txt/cord-286072-kgpvdb42.txt summary: While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection. IFN, interferon; IFNAR, interferon alpha and beta receptor; IκB, inhibitor of nuclear factor κB; IKKε, IκB kinase-ε; IRF, IFN regulatory factor; ISG, IFN-stimulated gene; JAK, Janus kinase; M, membrane; MAVS, mitochondrial antiviral signaling protein; MDA5, melanoma differentiation-associated gene 5; N, nucleocapsid; Nsp, nonstructural protein; ORF, open reading frame; P, phosphate; PLP, papain-like protease; RIG-I, retinoic acid-inducible gene 1; SARS-CoV, severe acute respiratory syndrome coronavirus; STAT, signal transducer and activator of transcription; TANK, TRAF family member associated NF-κB activator; TBK1, TANK-binding kinase 1; TRAF3, tumor necrosis factor receptor-associated factor 3; TYK2, tyrosine kinase 2. abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. An unbalanced immune response, characterized by a weak production of type I interferons (IFN-Is) and an exacerbated release of proinflammatory cytokines, contributes to the severe forms of the disease. SARS-CoV-2 is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2003 and 2013, respectively. Although IFN treatment gave some encouraging results against SARS-CoV and MERS-CoV in animal models, its potential as a therapeutic against COVID-19 awaits validation. Here, we describe our current knowledge of the complex interplay between SARS-CoV-2 infection and the IFN system, highlighting some of the gaps that need to be filled for a better understanding of the underlying molecular mechanisms. In addition to the conserved IFN evasion strategies that are likely shared with SARS-CoV and MERS-CoV, novel counteraction mechanisms are being discovered in SARS-CoV-2–infected cells. Since the last coronavirus epidemic, we have made considerable progress in understanding the IFN-I response, including its spatiotemporal regulation and the prominent role of plasmacytoid dendritic cells (pDCs), which are the main IFN-I–producing cells. While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection. url: https://doi.org/10.1371/journal.ppat.1008737 doi: 10.1371/journal.ppat.1008737 id: cord-296494-6kn4mr04 author: Saban-Ruiz, J. title: COVID-19: A Personalized Cardiometabolic Approach for Reducing Complications and Costs. The Role of Aging Beyond Topics date: 2020-05-12 words: 6444.0 sentences: 326.0 pages: flesch: 50.0 cache: ./cache/cord-296494-6kn4mr04.txt txt: ./txt/cord-296494-6kn4mr04.txt summary: Bearing this in mind, it is quite likely, that if we have fewer complications, particularly severe ones (cardiac arrest, ventricular tachyarrhythmia, acute heart failure, acute coronary syndrome, haemorrhagic or massive ischaemic stroke), this integrated approach could cut down the elevated mortality in the highest risk group (cancer, COPD and oldest subjects with comorbidities), usually preceded by a multi-organ failure. In aged COVID-19 patients or with history of coronary artery disease (CAD) an acute coronary syndrome (ACS) can also be seen for plaque vulnerability in the presence of a pro-inflammatory state with cytokine release (71) but from the experience in animals, could it be plausible that any of them could be due to arteritis? The third aspect would be the combination of T2DM and Heart failure (HF) (the most frequent cardiac complication in any of the phases of the disease), which is present in a high percentage of patients, especially those at higher risk. abstract: COVID 19 is much more than an infectious disease by SARS-CoV-2 followed by a disproportionate immune response. An older age, diabetes and history of cardiovascular disease, especially hypertension, but also chronic heart failure and coronary artery disease among others, are between the most important risk factors. In addition, during the hospitalization both hyperglycaemia and heart failure are frequent. Less frequent are acute coronary syndrome, arrhythmias and stroke. Accordingly, not all prolonged stays or even deaths are due directly to SARS-CoV-2. To our knowledge, this is the first review, focusing both on cardiovascular and metabolic aspects of this dreadful disease, in an integrated and personalized way, following the guidelines of the Cardiometabolic Health/Medicine. Therefore, current personalized aspects such as ACEIs and ARBs, the place of statins and the most appropriate management of heart failure in diabetics are analysed. Aging, better than old age, as a dynamic process, is also considered in this review for the first time in the literature, and not only as a risk factor attributed to cardiovascular and non-cardiovascular comorbidities. Immunosenescence is also approached to build healthier elders, so they can resist present and future infectious diseases, and not only in epidemics or pandemics. In addition, to do this we must start knowing the molecular mechanisms that underlying Aging process in general, and immunosenescence in particular. Surprisingly, the endoplasmic reticulum stress and autophagy are implicated in both process. Finally, with a training in all the aspects covered in this review, not only the hospital stay, complications and costs of this frightening disease in high-risk population should be reduced. Likely, this paper will open a gate to the future for open-minded physicians. url: https://doi.org/10.1007/s12603-020-1385-5 doi: 10.1007/s12603-020-1385-5 id: cord-296214-xeezt6f7 author: Sabatino, Jolanda title: Women''s perspective on the COVID-19 pandemic: Walking into a post-peak phase date: 2020-08-13 words: 2699.0 sentences: 160.0 pages: flesch: 49.0 cache: ./cache/cord-296214-xeezt6f7.txt txt: ./txt/cord-296214-xeezt6f7.txt summary: Therefore, we discussed the impact of COVID-19 pandemic on women, children and young patients, particularly those with underlying cardiovascular comorbidities or congenital heart disease. Although the so far evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is likely to have a lower fatality rate in women, the course of the disease during pregnancy is not fully understood. Indeed, in rat lungs a higher expression of ACE2 has been observed in younger females animals than in adult males [26] Despite adult patients with cardiovascular co-morbidities have a worse course of the disease, and higher mortality rate, when we look at children infected by SARS-CoV-2 with concomitant congenital heart disease (CHD), they seem to have the same clinical trend and mortality of peers without CHD. An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes abstract: The pandemic of Novel Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has provoked hundreds of thousands of deaths, resulting in catastrophe for humans. Although some insights have been garnered in studies on women, children and young adults infected with COVID-19, these often remain fragmented in literature. Therefore, we discussed the impact of COVID-19 pandemic on women, children and young patients, particularly those with underlying cardiovascular comorbidities or congenital heart disease. Furthermore, we gathered and distilled the existing body of literature that describes their cardiovascular complications and the recommended actions in favour of those patients toward the post-peak pandemic period. Although many questions still require answers, this article is sought to help the practicing clinician in the understanding and management of the threatening disease in special populations. url: https://doi.org/10.1016/j.ijcard.2020.08.025 doi: 10.1016/j.ijcard.2020.08.025 id: cord-294440-zd0arwmr author: Sacco, Guillaume title: COVID-19 in seniors: Findings and lessons from mass screening in a nursing home date: 2020-06-26 words: 3981.0 sentences: 216.0 pages: flesch: 52.0 cache: ./cache/cord-294440-zd0arwmr.txt txt: ./txt/cord-294440-zd0arwmr.txt summary: CONCLUSIONS: The pauci-symptomatic expression of COVID-19 in older residents, together with the high prevalence of asymptomatic forms in caregivers, justifies mass screening in nursing homes, possibly prioritizing residents with suggestive combinations of clinical signs including dyspnea, falls, anorexia and/or altered consciousness. The objective of the present study was to clarify symptoms and chronological aspects of the propagation of the SARS-CoV-2 in a nursing home, both in residents and staff members. The study consisted in a five-week retrospective observational cohort study in a middle-sized nursing home in Maine-et-Loire, West of France, having performed COVID-19 mass screening of residents (n=87) and staff members (n=92). The present report of COVID-19 mass screening in a nursing home showed a high prevalence of asymptomatic infected staff members, and confirmed that older residents exhibit few and mainly nonspecific symptoms. abstract: BACKGROUND/OBJECTIVE: The COVID-19 epidemic is particularly serious in older adults. The symptomatology and epidemic profile remain little known in this population, especially in disabled oldest-old people with chronic diseases living in nursing homes. The objective of the present study was to comprehensively describe symptoms and chronological aspects of the diffusion of the SARS-CoV-2 virus in a nursing home, among both residents and caregivers. DESIGN: Five-week retrospective cohort study. SETTING: A middle-sized nursing home in Maine-et-Loire, west of France. PARTICIPANTS: Eighty-seven frail older residents (87.9 ± 7.2years; 71% female) and 92 staff members (38.3 ± 11.7years; 89% female) were included. MEASUREMENTS: Mass screening for SARS-CoV-2 was performed in both residents and staff. Attack rate, mortality rate, and symptoms among residents and staff infected with SARS-CoV-2 were recorded. RESULTS: The attack rate of COVID-19 was 47% in residents (case fatality rate, 27%), and 24% in staff. Epidemic curves revealed that the epidemic started in residents before spreading to caregivers. Residents exhibited both general and respiratory signs (59% hyperthermia, 49% cough, 42% polypnea) together with geriatric syndromes (15% falls, 10% altered consciousness). The classification tree revealed 100% COVID-19 probability in the following groups: i) residents younger than 90 with dyspnea and falls; ii) residents older than 90 with anorexia; iii) residents older than 90 without anorexia but with altered consciousness. Finally, 41% of staff members diagnosed with COVID-19 were asymptomatic. CONCLUSIONS: The pauci-symptomatic expression of COVID-19 in older residents, together with the high prevalence of asymptomatic forms in caregivers, justifies mass screening in nursing homes, possibly prioritizing residents with suggestive combinations of clinical signs including dyspnea, falls, anorexia and/or altered consciousness. url: https://www.sciencedirect.com/science/article/pii/S0378512220303194?v=s5 doi: 10.1016/j.maturitas.2020.06.023 id: cord-179749-qdbmpi7j author: Sacks, Daniel W. title: What can we learn about SARS-CoV-2 prevalence from testing and hospital data? date: 2020-08-01 words: 10732.0 sentences: 621.0 pages: flesch: 56.0 cache: ./cache/cord-179749-qdbmpi7j.txt txt: ./txt/cord-179749-qdbmpi7j.txt summary: We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on who gets tested, using Indiana data on hospital inpatient records linked to SARS-CoV-2 virological tests. In this paper, we propose a new approach to measuring the point-in-time prevalence of active SARS-CoV-2 infections in the overall population using data on patients who are hospitalized for non-COVID reasons. The combination of these assumptions with linked testinghospital data leads to relatively tight upper and lower bounds on the prevalence of active SARS-CoV-2 infections in the overall population in Indiana in each week from mid-March to mid-June. We maintain the test monotonicity assumption throughout, and we derive upper and lower bounds on prevalence in the population under two alternative assumptions about the representativeness of non-COVID hospitalizations for the broader population. Equivalently, the independence assumption implies that SARS-CoV-2 prevalence is the same among people who are hospitalized for non-COVID conditions and the general population. abstract: Measuring the prevalence of active SARS-CoV-2 infections is difficult because tests are conducted on a small and non-random segment of the population. But people admitted to the hospital for non-COVID reasons are tested at very high rates, even though they do not appear to be at elevated risk of infection. This sub-population may provide valuable evidence on prevalence in the general population. We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on who gets tested, using Indiana data on hospital inpatient records linked to SARS-CoV-2 virological tests. The non-COVID hospital population is tested fifty times as often as the general population. By mid-June, we estimate that prevalence was between 0.01 and 4.1 percent in the general population and between 0.6 to 2.6 percent in the non-COVID hospital population. We provide and test conditions under which this non-COVID hospitalization bound is valid for the general population. The combination of clinical testing data and hospital records may contain much more information about the state of the epidemic than has been previously appreciated. The bounds we calculate for Indiana could be constructed at relatively low cost in many other states. url: https://arxiv.org/pdf/2008.00298v1.pdf doi: nan id: cord-286301-7sjw5ci7 author: Sadasivan, Jibin title: Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date: 2017-04-18 words: 6243.0 sentences: 289.0 pages: flesch: 48.0 cache: ./cache/cord-286301-7sjw5ci7.txt txt: ./txt/cord-286301-7sjw5ci7.txt summary: SARS-S-Y was absent from surface in most of the cells and localized at the intracellular compartments (figure 5a), and OC43-S protein was mainly localized in distinct puncta that could represent endocytic structures following internalization from the plasma membrane (figure 5b). Our studies clearly demonstrated that the KXHXX motif is the major intracellular localization signal of the full-length SARS-S protein and the C-terminal proximity is not essential. Our alanine mutation studies on the KXHXX motif confirm the importance of the lysine and histidine in the full-length wild-type HCoV-SARS S protein; the mutant protein showed localization in plasma membrane instead of the usual ER and ERGIC. In contrast, Lysosomal acid phosphatase, also a type I membrane protein with a cytosolic tail GYXXØ motif located 7 residues from both transmembrane domain and the carboxy termini (Tm-RMQAQPPGYRHVADGEDHA) delivered mainly via the cell surface (Braun et al. abstract: Intracellular trafficking and localization studies of spike protein from SARS and OC43 showed that SARS spike protein is localized in the ER or ERGIC compartment and OC43 spike protein is predominantly localized in the lysosome. Differential localization can be explained by signal sequence. The sequence alignment using Clustal W shows that the signal sequence present at the cytoplasmic tail plays an important role in spike protein localization. A unique GYQEL motif is identified at the cytoplasmic terminal of OC43 spike protein which helps in localization in the lysosome, and a novel KLHYT motif is identified in the cytoplasmic tail of SARS spike protein which helps in ER or ERGIC localization. This study sheds some light on the role of cytoplasmic tail of spike protein in cell-to-cell fusion, coronavirus host cell fusion and subsequent pathogenicity. url: https://www.ncbi.nlm.nih.gov/pubmed/28569247/ doi: 10.1007/s12038-017-9676-7 id: cord-300783-pvn2qq0f author: Sadykov, Mukhtar title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date: 2020-08-07 words: 933.0 sentences: 91.0 pages: flesch: 61.0 cache: ./cache/cord-300783-pvn2qq0f.txt txt: ./txt/cord-300783-pvn2qq0f.txt summary: title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5''-UCG-3'' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins. One such 34 mechanism is the CpG dinucleotide reduction observed in many single-stranded RNA 35 fraction of the observed C>U changes represent multiple, independent events ( Figure S3 ). CpG Dinucleotides in SARS-CoV-2 Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host 396 antiviral defense Multi-site co-398 mutations and 5''UTR CpG immunity escape drive the evolution of SARS-CoV-2 abstract: RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5’-UCG-3’ motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins. url: https://doi.org/10.1101/2020.06.19.161687 doi: 10.1101/2020.06.19.161687 id: cord-345304-n74m5ucs author: Safadi, Marco Aurelio Palazzi title: THE CHALLENGING AND UNPREDICTABLE SPECTRUM OF COVID-19 IN CHILDREN AND ADOLESCENTS date: 2020-09-07 words: 1855.0 sentences: 95.0 pages: flesch: 39.0 cache: ./cache/cord-345304-n74m5ucs.txt txt: ./txt/cord-345304-n74m5ucs.txt summary: 6 Based on current evidence, older adults and people of all ages with underlying medical conditions, including severe obesity, chronic lung disease, cardiovascular disease, diabetes mellitus, chronic kidney disease, liver disease, active cancer, transplantation and immunocompromised have been associated with poor clinical outcomes and higher fatality rates from COVID-19. One of the largest pediatric cancer programs in the USA, in New York city, reported that 20/178 (11%) children and adolescents with cancer had positive test for SARS-CoV-2. 11 The overwhelmed public health systems by the COVID-19 pandemic represents a serious risk for pediatric general health, limiting access of children and adolescents to basic health care, compromising immunization coverages and postponing consultations for patients with underlying conditions. Clinical characteristics of 58 children with a pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 Clinical characteristics and outcomes of hospitalized and critically Ill children and adolescents with coronavirus disease 2019 (COVID-19) at a tertiary care medical center in New York City abstract: nan url: https://doi.org/10.1590/1984-0462/2020/38/2020192 doi: 10.1590/1984-0462/2020/38/2020192 id: cord-104507-xx7t26rl author: Safari, Saeid title: Extracorporeal Hemoperfusion as a Potential Therapeutic Option for Severe COVID-19 patients; a Narrative Review date: 2020-08-22 words: 3425.0 sentences: 173.0 pages: flesch: 31.0 cache: ./cache/cord-104507-xx7t26rl.txt txt: ./txt/cord-104507-xx7t26rl.txt summary: Based on previous experience of blood purification to treat cytokine storm syndrome (CSS) in severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), here we aimed to review the current literature on extracorporeal hemoperfusion as a potential therapeutic option for CSS-associated conditions, with a focus on severe COVID-19. To date, various centers in different countries including Italy, China, USA, Germany, and Iran have reported or are investigating the beneficial effects of different hemoperfusion systems, including HA380/HA330 cartridges, CytoSorb, and polymyxin B immobilized fiber column in treatment of critically-ill COVID-19 patients. To date, a large number of experimental and clinical data, mostly from case reports and case series, have introduced CytoSorb as an effective rescue therapy for removal of inflammatory cytokines and achievement of hemodynamic stabilization in critically ill patients with septic shock and kidney failure (47) (48) (49) . abstract: The 2019 novel coronavirus (officially known as severe acute respiratory syndrome coronavirus 2, SARS-CoV2) was first found in Wuhan, China. On February 11, 2020, the World Health Organization (WHO) has declared the outbreak of the disease caused by SARS-CoV2, named coronavirus disease 2019 (COVID-19), as an emergency of international concern. Based on the current epidemiological surveys, some COVID-19 patients with severe infection gradually develop impairment of the respiratory system, acute kidney injury (AKI), multiple organ failure, and ultimately, death. Currently, there is no established pharmacotherapy available for COVID-19. As seen in influenza, immune damage mediated by excessive production of inflammatory mediators contributes to high incidence of complications and poor prognosis. Thus, removal or blocking the overproduction of these mediators potentially aids in reducing the deleterious cytokine storm and improving critically ill patients’ outcomes. Based on previous experience of blood purification to treat cytokine storm syndrome (CSS) in severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), here we aimed to review the current literature on extracorporeal hemoperfusion as a potential therapeutic option for CSS-associated conditions, with a focus on severe COVID-19. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587998/ doi: nan id: cord-286269-vrjyj2y1 author: Sagheb, Setareh title: Two seriously ill neonates born to mothers with COVID-19 pneumonia- a case report date: 2020-09-21 words: 2778.0 sentences: 168.0 pages: flesch: 61.0 cache: ./cache/cord-286269-vrjyj2y1.txt txt: ./txt/cord-286269-vrjyj2y1.txt summary: They evaluated cord blood, amniotic fluid and even breast milk samples of mothers diagnosed with COVID-19 pneumonia, but SARS-COV-2 tests were negative in all cases. Consequently, because of performing all the aforementioned droplet and contact precautions during hospitalization, having high LDH, lymphopenia and SIADH soon after birth may be due to early-onset infection of SARS-COV-2. Furthermore, another study conducted on a limited number of patients showed a high level of SARS-COV-2 IgM in neonates born from COVID-19 infected mothers within 2 first hours of their birth [7] , which may indicate infection transmission from mother to fetus. It is worth noting that, although our neonates'' RT-PCR tests'' results for SARS-COV-2 were negative 1 hour after their birth, they tested positive on day 7 and 12. Neonatal Early-Onset Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in Wuhan, China abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19), a highly contagious viral disease has spread from Wuhan, Hubei Province, China to all over the world from its first recognition on December 2019. To date, only a few neonatal early-onset sepsis by SARS-COV-2 has been reported worldwide. CASE PRESENTATION: In this report, we present two seriously ill neonates who were born from mothers with stablished COVID-19 pneumonia. Laboratory tests showed lymphopenia with high LDH and hypocalcemia right after the birth. They had fever for days without responding to antibiotics and despite ruling out other potential causes. Both patients had positive RTPCR for SARS-COV-2 in the second round of testing but the first assay tested was negative. Hydroxychloroquine was used to treat both patients; the first patient was treated with it over a period of 14 days before showing signs of improvement. The second patient responded to the treatment over a period of 5 days. CONCLUSION: Although based on the available evidences, vertical transmission of COVID-19 is less likely, many aspects of pathogenesis and transmission of this novel virus are still unclear. Therefore we cannot rule out the vertical transmission totally. Further investigations are warranted to determine the exact mechanisms and routes of transmission. url: https://doi.org/10.1186/s13052-020-00897-2 doi: 10.1186/s13052-020-00897-2 id: cord-335467-0b0m8v5r author: Saha, Asit title: Novel coronavirus SARS‐CoV‐2 (Covid‐19) dynamics inside the human body date: 2020-07-19 words: 2617.0 sentences: 162.0 pages: flesch: 51.0 cache: ./cache/cord-335467-0b0m8v5r.txt txt: ./txt/cord-335467-0b0m8v5r.txt summary: A time‐dependent nonlinear system of ordinary differential equations model was constructed involving type‐I cells, type‐II cells, SARS‐CoV‐2 virus, inflammatory mediators, interleukins along with host pulmonary gas exchange rate, thermostat control, and mean pressure difference. The cybernetic model can simulate a dynamic response to the reduced pulmonary alveolar gas exchange rate, thermostat control, and mean pressure difference under a very critical condition based on equilibrium (steady state) values of the inflammatory mediators and system parameters. 13, 14 In the present study, we aim to understand the chain of events after the SARS-CoV-2 virus invaded the human body, creating chaos in the respiratory system, thermostat control, and multiple organ failure systematic networks using the knowledge-based cybernetic model. abstract: A knowledge‐based cybernetic framework model representing the dynamics of SARS‐CoV‐2 inside the human body has been studied analytically and in silico to explore the pathophysiologic regulations. The following modeling methodology was developed as a platform to introduce a predictive tool supporting a therapeutic approach to Covid‐19 disease. A time‐dependent nonlinear system of ordinary differential equations model was constructed involving type‐I cells, type‐II cells, SARS‐CoV‐2 virus, inflammatory mediators, interleukins along with host pulmonary gas exchange rate, thermostat control, and mean pressure difference. This formalism introduced about 17 unknown parameters. Estimating these unknown parameters requires a mathematical association with the in vivo sparse data and the dynamic sensitivities of the model. The cybernetic model can simulate a dynamic response to the reduced pulmonary alveolar gas exchange rate, thermostat control, and mean pressure difference under a very critical condition based on equilibrium (steady state) values of the inflammatory mediators and system parameters. In silico analysis of the current cybernetical approach with system dynamical modeling can provide an intellectual framework to help experimentalists identify more active therapeutic approaches. url: https://doi.org/10.1002/rmv.2140 doi: 10.1002/rmv.2140 id: cord-269187-lt0uo7q3 author: Saha, Indrajit title: Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date: 2020-07-11 words: 2305.0 sentences: 142.0 pages: flesch: 58.0 cache: ./cache/cord-269187-lt0uo7q3.txt txt: ./txt/cord-269187-lt0uo7q3.txt summary: Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. Based on this information, they developed an SNP-based PCR assay to show differentiation between To address the above facts, we have analyzed publicly available 566 Indian complete or near complete SARS-CoV-2 genomes in order to find the mutation points as substitution, deletion J o u r n a l P r e -p r o o f and insertion. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs. The genomic sequences of Indian SARS-CoV-2 virus was collected from Global Initiative on Sharing All Influenza Data (GISAID) 1 in fasta format on 11th June 2020. abstract: The wave of COVID-19 is a big threat to the human population. Presently, the world is going through different phases of lock down in order to stop this wave of pandemic; India being no exception. We have also started the lock down on 23rd March 2020. In this current situation, apart from social distancing only a vaccine can be the proper solution to serve the population of human being. Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. This fast motivated us to analyze publicly available 566 Indian complete or near complete SARS-CoV-2 genomes to find the mutation points as substitution, deletion and insertion. In this regard, we have performed the multiple sequence alignment in presence of reference sequence from NCBI. After the alignment, a consensus sequence is build to analyze each genome in order to identify the mutation points. As a consequence, we have found 933 substitutions, 2449 deletions and 2 insertions, in total 3384 unique mutation points, in 566 genomes across 29.9 K bp. Further, it has been classified into three groups as 100 clusters of mutations (mostly deletions), 1609 point mutations as substitution, deletion and insertion and 64 SNPs. These outcomes are visualized using BioCircos and bar plots as well as plotting entropy value of each genomic location. Moreover, phylogenetic analysis has also been performed to see the evolution of SARS-CoV-2 virus in India. It also shows the wide variation in tree which indeed vivid in genomic analysis. Finally, these SNPs can be the useful target for virus classification, designing and defining the effective dose of vaccine for the heterogeneous population. url: https://www.sciencedirect.com/science/article/pii/S1567134820302884?v=s5 doi: 10.1016/j.meegid.2020.104457 id: cord-196608-k4f79dr4 author: Saha, Sovan title: Computational modeling of Human-nCoV protein-protein interaction network date: 2020-05-05 words: 4387.0 sentences: 262.0 pages: flesch: 51.0 cache: ./cache/cord-196608-k4f79dr4.txt txt: ./txt/cord-196608-k4f79dr4.txt summary: Our developed computational model of nCoV-Human PPIN contains high quality interactions (HQI) and proteins identified by Fuzzy affinity thresholding and spreadability index validated by SIS model respectively. With the gradual progress of the work, it has been observed that the selected human spreader nodes, identified by our proposed model, emerge as the potential protein targets of the FDA approved drugs for COVID-19. Target proteins of the potential FDA drugs for COVID-19 are found to overlap with the spreader nodes of the proposed computational nCoV-Human protein interaction model. Target proteins of seven potential FDA drugs: Lopinavir 30 , Ritonavir 31 , Hydroxychloroquine 32, 33 , Azithromycin 33 , Remdesivir 34-36 , Favipiravir 37, 38 and Darunavir 39 for COVID-19 as mentioned in the DrugBank white paper 26 overlap with the spreader nodes of the proposed in silico nCoV-Human protein interaction model (see Figure 5 ). abstract: COVID-19 has created a global pandemic with high morbidity and mortality in 2020. Novel coronavirus (nCoV), also known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), is responsible for this deadly disease. International Committee on Taxonomy of Viruses (ICTV) has declared that nCoV is highly genetically similar to SARS-CoV epidemic in 2003 (89% similarity). Limited number of clinically validated Human-nCoV protein interaction data is available in the literature. With this hypothesis, the present work focuses on developing a computational model for nCoV-Human protein interaction network, using the experimentally validated SARS-CoV-Human protein interactions. Initially, level-1 and level-2 human spreader proteins are identified in SARS-CoV-Human interaction network, using Susceptible-Infected-Susceptible (SIS) model. These proteins are considered as potential human targets for nCoV bait proteins. A gene-ontology based fuzzy affinity function has been used to construct the nCoV-Human protein interaction network at 99.98% specificity threshold. This also identifies the level-1 human spreaders for COVID-19 in human protein-interaction network. Level-2 human spreaders are subsequently identified using the SIS model. The derived host-pathogen interaction network is finally validated using 7 potential FDA listed drugs for COVID-19 with significant overlap between the known drug target proteins and the identified spreader proteins. url: https://arxiv.org/pdf/2005.04108v1.pdf doi: nan id: cord-255755-5jccb3nh author: Saha, Sovan title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date: 2020-04-23 words: 3668.0 sentences: 212.0 pages: flesch: 59.0 cache: ./cache/cord-255755-5jccb3nh.txt txt: ./txt/cord-255755-5jccb3nh.txt summary: title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network The new network attribute spreadability index along with generated SIS values of selected top spreader nodes when compared with the other network centrality based methodologies like Degree centrality (DC), Closeness centrality (CC), Local average centrality (LAC) and Betweeness centrality (BC) is found to perform relatively better than the existing-state-of-art. In the proposed methodology, Protein-protein interaction network (PPIN) has been used as the central component in identification of spreader nodes in SARS-CoV. Once it is formed, spreader nodes are identified in each of SARS-CoV proteins, its level 1 and level 2 of human network by the application of a new network attribute i.e. spreadability index which is a combination of three terminologies: 1) edge ratio [28] 2) neighborhood density [28] and 3) node weight [29] . abstract: The entire world has recently witnessed the commencement of coronavirus disease 19 (COVID-19) pandemic. It is caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It has exploited human vulnerabilities to coronavirus outbreak. SARS-CoV-2 promotes fatal chronic respiratory disease followed by multiple organ failure which ultimately puts an end to human life. No proven vaccine for n-CoV is available till date in spite of significant research efforts worldwide. International Committee on Taxonomy of Viruses (ICTV) has reached to a consensus that the virus SARS-CoV-2 is highly genetically similar to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) outbreak of 2003. It has been reported that SARS-CoV has ∼89% genetic similarities with n-CoV. With this hypothesis, the current work focuses on the identification of spreader nodes in SARS-CoV protein interaction network. Various network characteristics like edge ratio, neighborhood density and node weight have been explored for defining a new feature spreadability index by virtue of which spreader nodes and edges are identified. The selected top spreader nodes having high spreadability index have been also validated by Susceptible-Infected-Susceptible (SIS) disease model. Initially, the proposed method is applied on a synthetic protein interaction network followed by SARS-CoV-human protein interaction network. Hence, key spreader nodes and edges (ranked edges) are unmasked in SARS-CoV proteins and its connected level 1 and level 2 human proteins. The new network attribute spreadability index along with generated SIS values of selected top spreader nodes when compared with the other network centrality based methodologies like Degree centrality (DC), Closeness centrality (CC), Local average centrality (LAC) and Betweeness centrality (BC) is found to perform relatively better than the existing-state-of-art. url: https://doi.org/10.1101/2020.04.12.038216 doi: 10.1101/2020.04.12.038216 id: cord-275360-uphdzj5l author: Sahajpal, Nikhil Shri title: Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date: 2020-07-30 words: 1675.0 sentences: 92.0 pages: flesch: 49.0 cache: ./cache/cord-275360-uphdzj5l.txt txt: ./txt/cord-275360-uphdzj5l.txt summary: Herein, we propose a mass population screening approach, based on sample pooling strategy for rapid and wide-scale population screening that may be adopted by laboratories currently using RT-PCR based methods to test for SARS-CoV-2. The strategy we propose leverages on existing high throughput systems that employ high analytically sensitive [limit of detection (LOD) 5-20 copies/ml] real-time PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. 6 The advantages of this approach include the potential to catch up with huge testing deficits, reducing turnaround times and most importantly ensuring enormous savings through the most efficient use of RNA extraction and/or testing kits, which even today are in significant short supply. The strategy we propose leverages existing high throughput systems which employ analytically high sensitive RT-PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. abstract: Testing for SARS-CoV-2 has lagged behind in many countries due to lack of adequate test kits and bottlenecks in the analytical process. The aim of this study was to investigate the feasibility and accuracy of a sample pooling approach for wide-scale population screening for COVID-19. A total of 940 nasopharyngeal-swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were de-identified and assigned random numbers for analysis. From this, 94 pools of 10 samples each were created. Automated RNA extraction followed by RT-PCR was carried out in a 96 well plate. Positive pools were identified and the individual samples were re-analyzed. url: https://www.sciencedirect.com/science/article/pii/S1525157820304074?v=s5 doi: 10.1016/j.jmoldx.2020.07.001 id: cord-356370-jjl1hbeb author: Sahajpal, Nikhil Shri title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 words: 1602.0 sentences: 77.0 pages: flesch: 41.0 cache: ./cache/cord-356370-jjl1hbeb.txt txt: ./txt/cord-356370-jjl1hbeb.txt summary: In response to the outbreak, several state authorities and commercial companies have developed diagnostic assays to test individuals for the SARS-CoV-2 infection. In the US, clinical laboratories are required to perform ''bridging studies'' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. Although, the reverse transcription-polymerase chain reaction (RT-PCR) based assays for the detection of SARS-CoV-2 nucleic acid regions might be the most practical approach at present, qualitative assays are far from providing insights into the evolution of the virus and the varied immune response in different populations. In addition, the RT-PCR based assays provide a unique opportunity to implement pooling sample strategy for wide-scale population screening for SARS-CoV-2. Several studies, including from our laboratory (under review) have demonstrated that pooling sample strategy is a practical and feasible method for screening populations for SARS-CoV-2 [2] . Laboratories should therefore prime for serologic testing by validating assays using RT-PCR confirmed COVID-19 samples. abstract: nan url: https://doi.org/10.4155/fmc-2020-0129 doi: 10.4155/fmc-2020-0129 id: cord-153725-jjefjlx2 author: Sahoo, Suban K title: Computational evidence on repurposing the anti-influenza drugs baloxavir acid and baloxavir marboxil against COVID-19 date: 2020-09-02 words: 2219.0 sentences: 116.0 pages: flesch: 55.0 cache: ./cache/cord-153725-jjefjlx2.txt txt: ./txt/cord-153725-jjefjlx2.txt summary: In this communication, molecular docking analyses of two influenza antiviral drugs baloxavir acid (BXA) and baloxavir marboxil (BXM) were performed with the three therapeutic target proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp). Considering the need of new potential drugs to repurpose against COVID-19 pandemic, this research was carried out to investigate the effective binding of the drugs BMX and BXA with the three functional proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The molecular docking of the drugs were performed with the therapeutic target proteins and their affinity of binding at the active site was compared. Therefore, to provide computational evidence on the comparative potency of the two influenza antiviral drugs BXA and BXM (Fig. 1) , the molecular docking experiments were performed in Autodock Vina with the therapeutic target proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The blind molecular docking was performed where the grid box was selected to cover the whole protein structure. abstract: The main reasons for the ongoing COVID-19 (coronavirus disease 2019) pandemic are the unavailability of recommended efficacious drugs or vaccines along with the human to human transmission nature of SARS-CoV-2 virus. So, there is urgent need to search appropriate therapeutic approach by repurposing approved drugs. In this communication, molecular docking analyses of two influenza antiviral drugs baloxavir acid (BXA) and baloxavir marboxil (BXM) were performed with the three therapeutic target proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp). The molecular docking results of both the drugs BXA and BXM were analysed and compared. The investigational drug BXA binds at the active site of Mpro and RdRp, whereas the approved drug BXM binds only at the active site of RdRp. Also, comparison of dock score revealed that BXA is binding more effectively at the active site of RdRp than BXM. The computational molecular docking revealed that the drug BXA may be more effective against COVID-19 as compared to BXM. url: https://arxiv.org/pdf/2009.01094v1.pdf doi: nan id: cord-339727-q8pjwl3s author: Sahu, Kamal Kant title: Mesenchymal Stem Cells in COVID-19: A Journey from Bench to Bedside date: 2020-07-30 words: 3325.0 sentences: 214.0 pages: flesch: 48.0 cache: ./cache/cord-339727-q8pjwl3s.txt txt: ./txt/cord-339727-q8pjwl3s.txt summary: Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. [6] [7] [8] [9] [10] Recently, a few studies have examined the role of mesenchymal stem cells (MSCs) in critically ill patients with COVID-19. Because H7N9 and SARS-CoV-2 share similar complications-ARDS, hypoxic respiratory failure, severe inflammation, overt immune response, and multiorgan dysfunction syndrome-MSCs therapy may be beneficial for patients with COVID-19 pneumonia as well. Rationale for the clinical use of adipose-derived mesenchymal stem cells for COVID-19 patients Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use abstract: The COVID-19 pandemic has led to a major setback in both the health and economic sectors across the globe. The scale of the problem is enormous because we still do not have any specific anti-SARS-CoV-2 antiviral agent or vaccine. The human immune system has never been exposed to this novel virus, so the viral interactions with the human immune system are completely naive. New approaches are being studied at various levels, including animal in vitro models and human-based studies, to contain the COVID-19 pandemic as soon as possible. Many drugs are being tested for repurposing, but so far only remdesivir has shown some positive benefits based on preliminary reports, but these results also need further confirmation via ongoing trials. Otherwise, no other agents have shown an impactful response against COVID-19. Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. The patients belonging to this subset are most likely beyond the point where they could benefit from an antiviral therapy because most of their illness at this stage of disease is driven by inflammatory (over)response of the immune system. In this review, we discuss the potential of MSCs as a therapeutic option for patients with COVID-19, based on the encouraging results from the preliminary data showing improved outcomes in the progression of COVID-19 disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32729620/ doi: 10.1093/labmed/lmaa049 id: cord-307671-f9l2l8fi author: Said, Mohammed title: The Forgotten Element in the Resumption of Elective Bariatric Surgery During the COVID-19 Pandemic: the Patient Consent! date: 2020-09-19 words: 2199.0 sentences: 123.0 pages: flesch: 39.0 cache: ./cache/cord-307671-f9l2l8fi.txt txt: ./txt/cord-307671-f9l2l8fi.txt summary: The aim was to assess their knowledge and expectations regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A total of 233 (87.6%) candidates believed that they were prone to a higher risk of severe SARS-CoV-2 infection, and 24.4% of them believed that bariatric surgery, during the pandemic, would improve their immunity. The present study aims to help in answering these questions through an assessment of patients'' concepts regarding bariatric surgery resumption after the peak of the COVID-19 pandemic. The following four questions assessed the patient opinion regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Bariatric teams need to ensure that candidates for surgery share the required knowledge regarding the methods of transmission of SARS-CoV-2 infection and are willing to follow the protective measures. abstract: Safety comes first, and the sympathy with the postponed bariatric patients should not come at the expense of the proper standard of care. This study presents a survey of 266 bariatric candidates who were rescheduled for bariatric surgery after postponement during the COVID-19 pandemic. The aim was to assess their knowledge and expectations regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A total of 233 (87.6%) candidates believed that they were prone to a higher risk of severe SARS-CoV-2 infection, and 24.4% of them believed that bariatric surgery, during the pandemic, would improve their immunity. A total of 27.8% of candidates attributed the responsibility regarding potential perioperative SARS-CoV-2 infection to the medical personnel, and 10.7% of them believed it to be the surgeon’s responsibility. url: https://www.ncbi.nlm.nih.gov/pubmed/32949001/ doi: 10.1007/s11695-020-04976-5 id: cord-277830-6fsz9iy7 author: Saikatendu, Kumar Singh title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 words: 6555.0 sentences: 344.0 pages: flesch: 56.0 cache: ./cache/cord-277830-6fsz9iy7.txt txt: ./txt/cord-277830-6fsz9iy7.txt summary: The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. A view of the proposed active site of SARS ADRP along with the superimposed structures of AF1521 and yeast Ymx7 are shown in Figure 4B , highlighting the interactions that are likely between residues of the protein with the ligand. abstract: The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. The structure of this “X” domain, seen in many single-stranded RNA viruses, reveals a three-layered α/β/α core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1″-phosphate (Appr-1″-p). The SARS nsP3 domain readily removes the 1″ phosphate group from Appr-1″-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. url: https://api.elsevier.com/content/article/pii/S0969212605003138 doi: 10.1016/j.str.2005.07.022 id: cord-262441-slh52nxm author: Sakai, Yusuke title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 words: 6120.0 sentences: 261.0 pages: flesch: 52.0 cache: ./cache/cord-262441-slh52nxm.txt txt: ./txt/cord-262441-slh52nxm.txt summary: To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3. abstract: Infection with coronavirus rearranges the host cell membrane to assemble a replication/transcription complex in which replication of the viral genome and transcription of viral mRNA occur. Although coexistence of nsp3 and nsp4 is known to cause membrane rearrangement, the mechanisms underlying the interaction of these two proteins remain unclear. We demonstrated that binding of nsp4 with nsp3 is essential for membrane rearrangement and identified amino acid residues in nsp4 responsible for the interaction with nsp3. In addition, we revealed that the nsp3-nsp4 interaction is not sufficient to induce membrane rearrangement, suggesting the participation of other factors such as host proteins. Finally, we showed that loss of the nsp3-nsp4 interaction eliminated viral replication by using an infectious cDNA clone and replicon system of SARS-CoV. These findings provide clues to the mechanism of the replication/transcription complex assembly of SARS-CoV and could reveal an antiviral target for the treatment of betacoronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/28738245/ doi: 10.1016/j.virol.2017.07.019 id: cord-301080-xr7kl573 author: Sakanashi, Daisuke title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 date: 2020-09-30 words: 1623.0 sentences: 102.0 pages: flesch: 54.0 cache: ./cache/cord-301080-xr7kl573.txt txt: ./txt/cord-301080-xr7kl573.txt summary: title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Therefore, the present study aimed to compare nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19. Among them, five patients had been diagnosed with COVID-19 by reverse transcription real-time polymerase chain reaction (rRT-PCR) of nasopharyngeal swabs and were hospitalized before the first collection of paired specimens, whereas seven were outpatients suspected to have COVID-19 based on their clinical symptoms. abstract: Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Here, we investigated suitability of saliva as a non-invasively obtained specimen for molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19. In total, 28 paired clinical specimens of saliva and nasopharyngeal swabs were collected from 12 patients at various time points after symptom onset. Each specimen was assayed using reverse transcription real-time polymerase chain reaction (rRT-PCR) on the BD MAX open system using primers and probes targeting the N-gene. The saliva and nasopharyngeal swab specimens showed 19 and 15 positive results, respectively. No invalid (PCR inhibition) result was observed for any specimen. The qualitative results of each specimen obtained in the period immediately after symptom onset were similar. Three convalescent patients presented saliva-positive results, whereas their nasopharyngeal swabs were negative at four different time points, suggesting that saliva may be superior to nasopharyngeal swabs in terms of obtaining stable assay result of SARS-CoV-2. In conclusion, our results suggest that saliva can potentially serve as an alternative to nasopharyngeal swabs as a specimen for SARS-CoV-2 rRT-PCR. As saliva can be collected by patients themselves, it may be an effective way to overcome the shortage of personal protective equipment and specimen sampling tools. url: https://www.sciencedirect.com/science/article/pii/S1341321X20303470?v=s5 doi: 10.1016/j.jiac.2020.09.027 id: cord-291954-wormplcu author: Sakulkonkij, Parichart title: A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date: 2020-08-08 words: 4424.0 sentences: 304.0 pages: flesch: 48.0 cache: ./cache/cord-291954-wormplcu.txt txt: ./txt/cord-291954-wormplcu.txt summary: A novel betacoronavirus, the seventh member of coronaviruses, which is shown to infect humans and lately named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an ongoing outbreak of respiratory illness that began in December 2019 in China called coronavirus disease 2019 . On admission, a nasopharyngeal and throat swabs for SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) revealed a positive result, other laboratory findings included white blood cell count (WBC) 2480 cells/mm 3 , lymphocyte (L) 18%, neutrophil (N) 78%, and C-reactive protein (CRP) 62.7 mg/L. Although acute hypoxemic respiratory failure from COVID-19 in elderly and KT recipients in our cohort seemed to be prominent, early investigation in high-risk populations, prompt initiation of potential therapy, and intensive supportive care are important to prevent adverse consequences and mortality. Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? abstract: INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes an ongoing outbreak of respiratory illness called coronavirus disease 2019 (COVID‐19). The clinical course could be ranging from mild to severe illness especially the individuals with an immunocompromised condition such as solid organ transplant recipients. METHOD: We described a family cluster of COVID‐19 patients who were admitted during 3rd April 2020 to 30th April 2020. COVID‐19 was confirmed by a presence of SARS‐CoV‐2 ribonucleic acid in the respiratory specimens detected by a qualitative, real‐time reverse transcription‐polymerase chain reaction. The study focused on the clinical course and management of our cases. RESULTS: A family cluster of four laboratory‐confirmed COVID‐19 patients, one of those carried an underlying kidney transplant (KT) receiving immunosuppressants. Clinical presentation and severity of our case series are variable depending on each individual immune status. By far, a KT recipient seems to develop more severity despite antiviral therapy, cessation of immunosuppressant, and aggressive intensive care support. CONCLUSION: Our case series plausibly affirmed a person‐to‐person transmission and potentially severe disease in the transplant population. Clinicians who are encountering with transplant recipients should be aware of possible transmission among family members. url: https://www.ncbi.nlm.nih.gov/pubmed/32770646/ doi: 10.1002/iid3.337 id: cord-312401-y1tat1bf author: Sakurai, Aki title: Natural History of Asymptomatic SARS-CoV-2 Infection date: 2020-06-12 words: 918.0 sentences: 56.0 pages: flesch: 52.0 cache: ./cache/cord-312401-y1tat1bf.txt txt: ./txt/cord-312401-y1tat1bf.txt summary: On February 1, a passenger from Hong Kong, who traveled for 5 days from Yokohama and left the ship at Hong Kong on January 25, tested positive for SARS-CoV-2. Ten of 31 symptomatic passengers, crew and their cabinmates tested positive for SARS-CoV-2 on February 5, when the quarantine was implemented off the coast. Given the circumstances, a decision was made to accommodate some of the asymptomatic SARS-CoV-2 confirmed cases, both passengers and crew as well as their cabinmates who tested negative on the ship, at this hospital to continue their isolation and observation off the ship. Asymptomatic confirmed cases were cohorted on two floors, while their cabinmates who tested positive on the ship were isolated in private rooms on a separate floor to prevent further transmission. If the test was positive, they were cohorted with asymptomatic SARS-CoV-2 confirmed cases. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32530584/ doi: 10.1056/nejmc2013020 id: cord-337089-ksh62ni0 author: Salajegheh Tazerji, Sina title: Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review date: 2020-09-21 words: 4901.0 sentences: 293.0 pages: flesch: 53.0 cache: ./cache/cord-337089-ksh62ni0.txt txt: ./txt/cord-337089-ksh62ni0.txt summary: In addition to the considerable COVID-19 cases, hospitalizations, and deaths in humans, several cases of SARS-CoV-2 infections in animal hosts (dog, cat, tiger, lion, and mink) have been reported. Therefore, this study aimed to gather information about the reported cases of COVID-19 transmission in animals through a literary review of works published in scientific journals and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. However, based on recently published findings, other authors hypothesized that an immunological cross-protection between SARS-CoV-2 and canine respiratory coronavirus (CRCoV) exists due to the high homology between the spike protein epitopes of the two taxonomicallyrelated coronaviruses [21] . The objective of the present study was to gather, present, and discuss information on the reported cases of COVID-19 in animals focusing on the virus transmission cases in pets and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. abstract: COVID-19 caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan (Hubei province, China) during late 2019. It has spread across the globe affecting nearly 21 million people with a toll of 0.75 million deaths and restricting the movement of most of the world population during the past 6 months. COVID-19 became the leading health, economic, and humanitarian challenge of the twenty-first century. In addition to the considerable COVID-19 cases, hospitalizations, and deaths in humans, several cases of SARS-CoV-2 infections in animal hosts (dog, cat, tiger, lion, and mink) have been reported. Thus, the concern of pet owners is increasing. Moreover, the dynamics of the disease requires further explanation, mainly concerning the transmission of the virus from humans to animals and vice versa. Therefore, this study aimed to gather information about the reported cases of COVID-19 transmission in animals through a literary review of works published in scientific journals and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. Although many instances of transmission of the SARS-CoV-2 have been reported, caution and further studies are necessary to avoid the occurrence of maltreatment in animals, and to achieve a better understanding of the dynamics of the disease in the environment, humans, and animals. Future research in the animal–human interface can help formulate and implement preventive measures to combat the further transmission of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32957995/ doi: 10.1186/s12967-020-02534-2 id: cord-335652-v98gv5uf author: Salazar, Cecilia title: Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date: 2020-05-10 words: 2063.0 sentences: 131.0 pages: flesch: 48.0 cache: ./cache/cord-335652-v98gv5uf.txt txt: ./txt/cord-335652-v98gv5uf.txt summary: Methods We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region. This global health emergency has deployed international efforts to apply genomic epidemiology to track the spread of SARS-CoV-2 in real time. The recent development of targeted sequencing protocols by the ARTIC Network [3] , open sharing of genomic data through the GISAID (www.gisaid.org) database and straightforward bioinformatic tools for viral phylogenomics [4] , provides the opportunity to reconstruct global spatio-temporal dynamics of the COVID-19 pandemic with unprecedented comprehensiveness and resolution. We therefore aimed to characterize the spatio-temporal dynamics of SARS-CoV-2 by sequencing around 10% of cases occurred during the first week of outbreak in Montevideo, allowing us to identify transmission patterns, geographic origins and genetic variation among local strains. abstract: Background After its emergence in China in December 2019, the new coronavirus disease (COVID-19) caused by SARS-CoV-2, has rapidly spread infecting more than 3 million people worldwide. South America is among the last regions hit by COVID-19 pandemic. In Uruguay, first cases were detected on March 13 th 2020 presumably imported by travelers returning from Europe. Methods We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Then, we applied genomic epidemiology using a global dataset to reconstruct the local spatio-temporal dynamics of SARS-CoV-2. Results Our phylogeographic analysis showed three independent introductions of SARS-CoV-2 from different continents. Also, we evidenced regional circulation of viral strains originally detected in Spain. Introduction of SARS-CoV-2 in Uruguay could date back as early as Feb 20th. Identification of specific mutations showed rapid local genetic differentiation. Conclusions We evidenced early independent introductions of SARS-CoV-2 that likely occurred before first cases were detected. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region. url: https://doi.org/10.1101/2020.05.09.086223 doi: 10.1101/2020.05.09.086223 id: cord-321784-nubu5fuz author: Salazar, E. title: Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas date: 2020-05-13 words: 3560.0 sentences: 224.0 pages: flesch: 58.0 cache: ./cache/cord-321784-nubu5fuz.txt txt: ./txt/cord-321784-nubu5fuz.txt summary: Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. 22 We performed the present study to provide additional data on these initial clinical observations of patients'' clinical course and subsequent improvement after receiving convalescent plasma therapy for COVID-19. Although our study has limitations, the data indicate that transfusion of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Our study was performed to evaluate the safety and potential benefit of transfusing convalescent plasma to patients with severe COVID-19 disease. Outcomes from this case series of 25 patients indicates that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. abstract: Background: COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years. Methods: Patients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 to April 14, 2020. Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 post-transfusion. Clinical improvement was assessed based on a modified World Health Organization 6-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. Results: At baseline, all patients were receiving supportive care, including anti-inflammatory and anti-viral treatments, and all patients were on oxygen support. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. By day 14 post-transfusion, 19 (76%) patients had at least a 1-point improvement in clinical status and 11 were discharged. No adverse events as a result of plasma transfusion were observed. The whole genome sequencing data did not identify a strain genotype-disease severity correlation. Conclusions: The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Randomized, controlled trials are needed to determine its efficacy. url: https://doi.org/10.1101/2020.05.08.20095471 doi: 10.1101/2020.05.08.20095471 id: cord-343333-4krrmjio author: Salazar, Martín title: COVID-19, Hipertensión y Enfermedad cardiovascular date: 2020-06-18 words: 2412.0 sentences: 249.0 pages: flesch: 52.0 cache: ./cache/cord-343333-4krrmjio.txt txt: ./txt/cord-343333-4krrmjio.txt summary: Las comunicaciones provenientes de China en el inicio de la pandemia de COVID-19 mostraron una marcada asociación de los casos severos y la mortalidad con la edad avanzada, la hipertensión arterial, las enfermedades cardiovasculares y la diabetes. Las estimaciones de China coinciden con estos datos: que mientras la mortalidad sin comorbilidades fue de 0,9%, se incrementó a 10,5% con enfermedad Page 4 of 13 J o u r n a l P r e -p r o o f 4 cardiovascular, 6,3% con enfermedad pulmonar obstructiva crónica, 6% con hipertensión arterial y 5,6% con cáncer. En el reporte Morbidity and Mortality Weekly Report (MMWR), con datos al 28 de marzo, 78% de los pacientes internados en terapia intensiva por COVID-19 tenían comorbilidades, las más frecuentes eran la enfermedad cardiovascular (29%) y la enfermedad pulmonar crónica (21%). peor evolución del COVID-19, encontrando que la prevalencia de esta patología entre quienes fallecen o requieren cuidados críticos debido a la infección por SARS-CoV-2 es elevada, rondando entre un 7,5 y 39,5%, según los distintos reportes. abstract: Resumen La asociación entre patología cardiovascular y mala evolución de la infección por SARS-CoV-2 resulta llamativa. Estudios publicados en diferentes países muestran que la hipertensión, diabetes, enfermedad cerebrovascular y cardiopatía isquémica son marcadamente más frecuentes en aquellos pacientes que requieren cuidados críticos o fallecen por COVID-19. Un posible nexo causal sería el daño y disfunción miocárdica producidos por el SARS-CoV-2, evidenciado en los frecuentes hallazgos de elevación de la troponina y anormalidades electrocardiográficas. Por otra parte, existen hipótesis a favor y en contra de un posible efecto deletéreo de los inhibidores de la enzima convertidora y los bloqueantes del receptor de angiotensina 2 en esta patología, no habiendo actualmente evidencia sólida que respalde contundentemente una u otra, resultando impostergable la necesidad de estudios que diluciden este interrogante. Los pacientes con enfermedad cardiovascular deberían evitar especialmente la exposición al SARS-CoV-2, no automedicarse y consultar rápidamente ante la aparición de síntomas. Abstract The association between hypertension, diabetes, cardio and cerebrovascular disease and severe and fatal COVID-19, described in different countries, is remarkable. Myocardial damage and myocardial dysfunction are postulated as a possible causal nexus. Frequent findings of elevated troponin levels and electrocardiographic anomalies support this concept. On the other hand, hypotheses in favour and against a deleterious effect of angiotensin converting enzyme inhibitors and angiotensin receptor blockers, a usual treatment for cardiovascular disease, have been raised. There is currently no solid evidence and thus properly designed studies on this subject are urgently needed. In this context, patients with cardiovascular disease should especially avoid being exposed to the virus, should not self-medicate and rapidly seek medical advice should they show symptoms of infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32591283/ doi: 10.1016/j.hipert.2020.06.003 id: cord-297832-picpuzvo author: Salazar, Rafael title: Decreased Mortality in Patients With Severe Bronchospasm Associated With SARS-CoV-2: An Alternative to Invasive Mechanical Ventilation date: 2020-10-06 words: 1768.0 sentences: 110.0 pages: flesch: 47.0 cache: ./cache/cord-297832-picpuzvo.txt txt: ./txt/cord-297832-picpuzvo.txt summary: The number of patients with acute episodes of severe bronchospasm needing intubation and ventilatory support has increased rapidly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus disease 2019 (COVID-19) pandemic. Anteroposterior chest X-ray at the time of acute bronchospasm with Radiographic Assessment of Lung Edema (RALE) score 2 The initial management comprised placing the patient in the prone position and administering oxygen at high flow through a non-rebreather mask with flow between 10 and 15 liters per minute until reaching 100% FiO 2 . To improve ventilatory mechanics and ultimately postpone the need for IMV due to acute bronchospasm in patients diagnosed with COVID-19, we put in place a therapeutic approach consisting of early respiratory therapy and pharmacological bronchospasm rescue approach. The therapeutic bundle of early respiratory therapy, consisting of deep inspiration with inspiratory hold, and pharmacological bronchospasm rescue decreased the need for invasive mechanical ventilation in patients with bronchospasm associated with SARS-CoV-2 and reduced the mortality rate. abstract: The number of patients with acute episodes of severe bronchospasm needing intubation and ventilatory support has increased rapidly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus disease 2019 (COVID-19) pandemic. Although medical consensus upholds the use of ventilatory support in this pathology, its survival benefits remain unclear. To improve the outcomes and survival rates, a bundle of early respiratory therapy with a pharmacological rescue regimen was provided to four patients with bronchospasm secondary to COVID-19. This therapeutic approach successfully delayed the need for invasive mechanical ventilation for 48 hours and decreased the mortality rate in all cases. url: https://www.ncbi.nlm.nih.gov/pubmed/33173630/ doi: 10.7759/cureus.10822 id: cord-259925-g28sx9qu author: Saleemi, Mansab Ali title: Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date: 2020-10-06 words: 6875.0 sentences: 375.0 pages: flesch: 51.0 cache: ./cache/cord-259925-g28sx9qu.txt txt: ./txt/cord-259925-g28sx9qu.txt summary: The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. Up to date, it is unclear how SARS-CoV-2 interacts with the host antiviral immunity, hence lessons can be learned from previous studies of other members of the coronavirus family and also human pathogenic viruses, such as human immunodeficiency viruses and severe acute respiratory syndrome (SARS) CoV known as human CoVs (HCoVs) due to their ability to cause human infections (Andersen et al., 2020) . abstract: The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S1567134820304147?v=s5 doi: 10.1016/j.meegid.2020.104583 id: cord-332595-874tpi09 author: Salehi, Najmeh title: Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients date: 2020-09-08 words: 1800.0 sentences: 111.0 pages: flesch: 61.0 cache: ./cache/cord-332595-874tpi09.txt txt: ./txt/cord-332595-874tpi09.txt summary: To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). On the other hand, nineteen sequences of the full genome sequence of SARS-CoV-2 on the GISAID database from patients in different countries that had a travel history to Iran or contacts with Iranian cases were retrieved from the database. In this study, the full genome sequences of SARS-CoV-2 from the 20 Iranian related COVID-19 patients were profiled in detail. B. The nucleotide and protein mutations, the number of mutation events in data from the 20 Iranian related patients, the entropy values of these mutations in all 3927 SARS-CoV-2 sequences, and the corresponded proteins are depicted. abstract: The etiologic agent SARS-CoV-2 has caused the outbreak of COVID-19 which is spread widely around the world. It is vital to uncover and investigate the full genome sequence of SARS-CoV-2 throughout the world to track changes in this virus. To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). R207C, V378I, M2796I, L3606F, and A6407V in ORF1ab were common mutations in these sequences. Also, some of the detected mutations only were found in Iranian data in comparison with all the available sequences of SARS-CoV-2. The position of S protein mutations showed they were far from the binding site of this protein with angiotensin-converting enzyme-2 (ACE2) as the host cell receptor. These results can be helpful to design specific diagnostic tests, trace the SARS-CoV-2 sequence changes in Iran, and explore therapeutic drugs and vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/32779445/ doi: 10.22074/cellj.2020.7524 id: cord-338543-q6cl5kjp author: Salguero, Francisco J. title: Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date: 2020-09-17 words: 1093.0 sentences: 59.0 pages: flesch: 56.0 cache: ./cache/cord-338543-q6cl5kjp.txt txt: ./txt/cord-338543-q6cl5kjp.txt summary: Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Throat swabs from cynomolgus macaques contained 147 higher levels of viral RNA early in infection (one to three dpc) and remained ≥4.5 x 148 10 4 copies/ml for all animals between four and nine dpc. However viral RNA 159 levels above the LLOQ were detected at both three dpc and five dpc in cynomolgus 160 macaques in comparison to two dpc and three dpc in rhesus macaques ( Figure 2D ). abstract: A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. Immune responses against SARS-CoV-2 were also similar in both species and equivalent to those reported in milder infections and convalescent human patients. Importantly, we have devised a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks. url: https://doi.org/10.1101/2020.09.17.301093 doi: 10.1101/2020.09.17.301093 id: cord-346299-2s9j01q7 author: Salim Khan, S Muhammad title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date: 2020-09-04 words: 1407.0 sentences: 102.0 pages: flesch: 55.0 cache: ./cache/cord-346299-2s9j01q7.txt txt: ./txt/cord-346299-2s9j01q7.txt summary: title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. 65 Besides, assuming that antibodies provide partial or total immunity, seroprevalence surveys give Here, we present the results of a cross-sectional seroprevalence study in District Srinagar, 70 conducted between 1 st and 15 th July 2020, to estimate the prevalence of IgG antibodies against 71 SARS-CoV-2 among adults using a sensitive and specific chemiluminescent microparticle 72 immunoassay (CMIA)-based test. 156 We estimated the number of infections till two weeks before the study period, i.e., 15 th June 2020 157 to 30 th June 2020, by applying the age-and gender-specific seroprevalence rates found in the Table) . abstract: Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. Methods 2906 persons >18 years of age selected from hospital visitors across District Srinagar participated in the study. We tested samples for the presence of SARS-CoV-2 specific IgG antibodies using a chemiluminescent microparticle immunoassay-based serologic test. Results Age- and gender-standardized seroprevalence was 3.6% (95% CI 2.9% to 4.3%). Age 30-69 years, a recent history of symptoms of an influenza-like-illness, and a history of being placed under quarantine were significantly related to higher odds of the presence of SARS-CoV-2 specific IgG antibodies. The estimated number of SARS-CoV-2 infections during the two weeks preceding the study, adjusted for test performance, was 32602 with an estimated (median) infection-to-known-case ratio of 46 (95% CI 36 to 57). Conclusions The seroprevalence of SARS-CoV-2 specific IgG antibodies is low in the District. A large proportion of the population is still susceptible to the infection. A sizeable number of infections remain undetected, and a substantial proportion of people with symptoms compatible with COVID-19 are not tested. url: https://doi.org/10.1101/2020.09.04.282640 doi: 10.1101/2020.09.04.282640 id: cord-294427-6eiligyy author: Salimi, Ali title: The North American Layman''s Understanding of COVID-19: Are We Doing Enough? date: 2020-07-03 words: 5699.0 sentences: 217.0 pages: flesch: 46.0 cache: ./cache/cord-294427-6eiligyy.txt txt: ./txt/cord-294427-6eiligyy.txt summary: Methods: In this cross-sectional observational study, an online survey targeted to North Americans focused on the public''s knowledge of COVID-19, risk perception, and precautionary behaviors taken in response to this pandemic. The results of this study highlight that this relatively young and educated sample of North Americans had a high level of knowledge about COVID-19 and a large proportion of them were taking the precautionary measures against this pandemic. To that end, this study aimed to compare and contrast the level of knowledge, risk perception, and precautionary measures taken in response to COVID-19, between populations of the United States of America (US) and Canada. To date, the US has reported the highest rate of COVID-19 positive cases in the world and therefore, by understanding the public''s attitude and risk perception toward the current pandemic, we hope to provide valuable information to help develop adequate populationtailored communication protocols that are effective in disease prevention and containment. abstract: Background: In the absence of an effective vaccine, public health policies are aimed at awareness, and education of the general public in order to contain the quickly spreading COVID-19 pandemic. Most of the recommended precautionary measures are dependent on human behaviors and therefore their effectiveness largely depends on peoples' perception and attitudes toward the disease. This study aimed to assess the level of knowledge, risk perception, and precautionary measures taken in response to COVID-19 in North America. Methods: In this cross-sectional observational study, an online survey targeted to North Americans focused on the public's knowledge of COVID-19, risk perception, and precautionary behaviors taken in response to this pandemic. Descriptive analyses were performed for the whole population and the subgroup analyses contrasted the differences between Americans and Canadians. Results: The cohort comprised 1,264 relatively young participants with an average age of 28.6 ± 9.8 years. The vast majority (>90%) were knowledgeable about COVID-19. Regarding risk perception, about a quarter assumed to be at less risk to contract the disease, and 42.8% considered themselves to be less contagious than others. While the vast majority avoided performing risky behaviors, only a small proportion (13.2%) wore a face mask—which is in line with the public health recommendations of the two countries at the time of data collection. Overall, a larger proportion of Canadian participants (55.8%) were satisfied with the performance of their national public health in response to the current pandemic, compared to their American counterparts (12.2%). Discussion: Data regarding the public's knowledge of COVID-19, risk perception, and behaviors in response to this pandemic is limited. The results of this study highlight that this relatively young and educated sample of North Americans had a high level of knowledge about COVID-19 and a large proportion of them were taking the precautionary measures against this pandemic. However, a significant number of individuals believe to be at less risk of contracting the disease compared to the general population. Educating the public that no one is safe from this disease, could play a role in further limiting risky behaviors and ultimately facilitating disease containment. url: https://www.ncbi.nlm.nih.gov/pubmed/32719768/ doi: 10.3389/fpubh.2020.00358 id: cord-273451-xnce010o author: Salisbury-Afshar, Elizabeth M. title: Vulnerable Populations: Weathering the Pandemic Storm date: 2020-04-22 words: 1658.0 sentences: 97.0 pages: flesch: 47.0 cache: ./cache/cord-273451-xnce010o.txt txt: ./txt/cord-273451-xnce010o.txt summary: Yet, even with awareness that all individuals deserve access to services, and that supporting marginalized populations will slow the spread of SARS-CoV-2, resource limitations will demand difficult allocation determinations. 3 Many individuals experiencing homelessness with SARS-CoV-2 will not meet hospitalization criteria and will be discharged into the general population. 11 In response to SARS-CoV-2, the Substance Abuse and Mental Health Services Administration has developed emergency regulations to support medication for opioid use disorder via telehealth, 12 and temporarily waived the requirement for in-person physical exam to be able to initiate buprenorphine. These often forgotten populations-people incarcerated, homeless, or using drugs-are likely to experience higher risk of exposure to SARS-CoV-2 because of their social circumstances. Planning should incorporate dedicated efforts, funding, and policies/guidelines specific to individuals who experience homelessness, are incarcerated, or are coping with substance use disorders both because these populations deserve care and services, and because not doing so poses great risk to the broader community. abstract: nan url: https://doi.org/10.1016/j.amepre.2020.04.002 doi: 10.1016/j.amepre.2020.04.002 id: cord-255872-e2b7ox6b author: Sallam, M. title: Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study date: 2020-08-25 words: 5129.0 sentences: 380.0 pages: flesch: 61.0 cache: ./cache/cord-255872-e2b7ox6b.txt txt: ./txt/cord-255872-e2b7ox6b.txt summary: This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Similar to other RNA viruses, SARS-CoV-2 can be the subject of phylogenetic analysis due to its high evolutionary rate, and the application of molecular clock analysis might be of value to determine the timing of introductions of large clusters that imply networks of transmission (Duffy et al., 2008; Forster et al., 2020; Pybus and Rambaut, 2009 ). The total number of MENA SARS-CoV-2 S gene sequences that were included in final analysis was 553, distributed as follows: Oman (n=159), KSA (n=140), Egypt (Table 1) . Phylogenetic analysis of the MENA S gene SARS-CoV-2 sequences showed a relatively low level of phylogenetic clustering (15%), which hints to a large number of virus introductions into the region. abstract: Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G=435, Q677H=8, and V6F=5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p<0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 x 10-3 substitutions/site/year based on large clusters' Bayesian analyses. The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported. url: http://medrxiv.org/cgi/content/short/2020.08.24.20176792v1?rss=1 doi: 10.1101/2020.08.24.20176792 id: cord-267134-5gz2dotn author: Sallenave, Jean-Michel title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 words: 5347.0 sentences: 239.0 pages: flesch: 39.0 cache: ./cache/cord-267134-5gz2dotn.txt txt: ./txt/cord-267134-5gz2dotn.txt summary: The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus abstract: COVID-19 is caused by the Severe Acute Respiratory Syndrome (SARS) coronavirus (Cov)-2, an enveloped virus with a positive-polarity, single-stranded RNA genome. The initial outbreak of the pandemic began in December 2019, and it is affecting the human health of the global community. In common with previous pandemics (Influenza H1N1 and SARS-CoV) and the epidemics of Middle east respiratory syndrome (MERS)-CoV, CoVs target bronchial and alveolar epithelial cells. Virus protein ligands (e.g., haemagglutinin or trimeric spike glycoprotein for Influenza and CoV, respectively) interact with cellular receptors, such as (depending on the virus) either sialic acids, Dipeptidyl peptidase 4 (DPP4), or angiotensin-converting enzyme 2 (ACE2). Host proteases, e.g., cathepsins, furin, or members of the type II transmembrane serine proteases (TTSP) family, such as Transmembrane protease serine 2 (TMPRSS2), are involved in virus entry by proteolytically activating virus ligands. Also involved are Toll Like Receptor (TLR) family members, which upregulate anti-viral and pro-inflammatory mediators [interleukin (IL)-6 and IL-8 and type I and type III Interferons among others], through the activation of Nuclear Factor (NF)-kB. When these events (virus cellular entry and innate immune responses) are uncontrolled, a deleterious systemic response is sometimes encountered in infected patients, leading to the well-described “cytokine storm” and an ensuing multiple organ failure promoted by a downregulation of dendritic cell, macrophage, and T-cell function. We aim to describe how the lung and systemic host innate immune responses affect survival either positively, through downregulating initial viral load, or negatively, by triggering uncontrolled inflammation. An emphasis will be put on host cellular signaling pathways and proteases involved with a view on tackling these therapeutically. url: https://www.ncbi.nlm.nih.gov/pubmed/32574272/ doi: 10.3389/fimmu.2020.01229 id: cord-025119-201ac32t author: Salman, Saad title: Virtual screening of immunomodulatory medicinal compounds as promising anti-SARS-COV-2 inhibitors date: 2020-05-21 words: 3144.0 sentences: 162.0 pages: flesch: 37.0 cache: ./cache/cord-025119-201ac32t.txt txt: ./txt/cord-025119-201ac32t.txt summary: Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Here, we analyzed different medicinal compounds using a virtual screening method to obtain promising inhibitors for these viral proteins that could be further utilized for SARS-COV-2 treatment. More than 300 medicinal compounds with immunomodulatory and antiviral activity were added to the Raccoon2 plugin of Autodock vina to perform virtual screening to obtain promising inhibitors for SARS-COV-2 proteins. This study aimed to obtain novel drug candidates that have the capability to interact with the active site of all of these viral proteins and should possess efficient pharmacokinetic profile with low toxicity to ensure safety during administration. • Docking interaction of immunomodulatory medicinal compounds library filtered six promising medicinal compounds against severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) viral proteins. abstract: Aim: Severe acute respiratory syndrome coronavirus-2 (SARS-COV-2), a pernicious viral disease, causes acute respiratory distress responsible for mortality and morbidity worldwide. To screen different immunomodulatory medicinal compounds to unravel their interaction with SARS-COV-2 viral proteins. Materials & methods: A library of immunomodulatory medicinal compounds with antiviral capability were analyzed against SARS proteases, spike protein and nonstructural proteins (NSP-9, 15) using Autodock vina. Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Further ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis showed good pharmacokinetic properties and low acute toxicity of these compounds. Conclusion: The current study provides convincing evidence that these medicinal compounds exert antiviral activity against the SARS-COV-2 virus and could be further exploited for the treatment of this disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7243912/ doi: 10.2217/fvl-2020-0079 id: cord-033333-880jx1bt author: Salman, Saad title: In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date: 2020-10-08 words: 3431.0 sentences: 226.0 pages: flesch: 53.0 cache: ./cache/cord-033333-880jx1bt.txt txt: ./txt/cord-033333-880jx1bt.txt summary: The molecular docking was performed for these inhalers including human neutralizing S230 light chain-antibody (monoclonal antibodies [mAbs]), alpha-1-antitrypsin (AAT), short-palate-lung and nasal-epithelial clone-1-derived peptides (SPLUNC1) and dornase-alfa (DA) against spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to assess their inhibitory activity. Protein-protein interaction (PPI) of COVID-19 spike glycoprotein with alpha-1-antitrypsin (1atu), dornase-alfa (4AWN), angiotensin-converting enzyme-2 (ACE-2) (PDB ID:1R4L), human palate, lung and nasal epithelium clone protein (SPLUNC1) (4n4x) and human neutralizing the S230 light chain antibody was evaluated through HawkDock. We attempted to address this issue by analyzing a variety of protein/peptide-based inhalers/antimucolytic agents and previously utilized mAb (used in asthma) to observe their possible interaction with the SARS-CoV-2 spike protein. • Molecular docking analysis of protein/peptide-based inhalers revealed that the S230 light chain antibody and dornase-alfa demonstrated a strong affinity for SARS-CoV-2 spike protein. abstract: Aim: Peptide/protein-based inhalers are excessively used to treat respiratory disorders. The molecular docking was performed for these inhalers including human neutralizing S230 light chain-antibody (monoclonal antibodies [mAbs]), alpha-1-antitrypsin (AAT), short-palate-lung and nasal-epithelial clone-1-derived peptides (SPLUNC1) and dornase-alfa (DA) against spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to assess their inhibitory activity. Materials & methods: HawkDock was used to dock these biologics against SARS-CoV-2 spike-glycoprotein. Results: Results showed that DA, AAT and mAb were quite active against spike glycoprotein with a binding free energy of -26.35 and -22.94 kcal/mol. Conclusion: mAB and AAT combined with DA can be used in the treatment of coronavirus disease of 2019 as a potential anti-SARS-CoV-2 agent. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543042/ doi: 10.2217/fvl-2020-0119 id: cord-319408-841c0g1c author: Salvatore, Christine M title: Neonatal management and outcomes during the COVID-19 pandemic: an observation cohort study date: 2020-07-23 words: 4636.0 sentences: 232.0 pages: flesch: 55.0 cache: ./cache/cord-319408-841c0g1c.txt txt: ./txt/cord-319408-841c0g1c.txt summary: [8] [9] [10] [11] [12] [13] [14] We aimed to follow up neonates born to mothers positive for SARS-CoV-2 at time of delivery, to elucidate best practices regarding infection control and identify potential risk factors associated with transmission. For this observational cohort study, we identified all neonates born between March 22 and May 17, 2020, at New York Presbyterian-Komansky Children''s Hospital, Weill Cornell Medicine, New York Presbyterian-Lower Manhattan Hospital, and New York Presbyterian-Queens in New York City to mothers who tested positive for SARS-CoV-2 from a nasopharyngeal swab sample at the time of delivery. Data collected included demographics, neonatal and maternal clinical presentation at time of delivery, during hospit alisation, and once discharged, microbiology results (SARS-CoV-2 rtPCR testing), and infection control practices in the hospital and at home. abstract: BACKGROUND: The risk of vertical and perinatal transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, which causes COVID-19), the most appropriate management, and the neonate's risk of developing COVID-19 during the perinatal period are unknown. Therefore, we aimed to elucidate best practices regarding infection control in mother–newborn dyads, and identify potential risk factors associated with transmission. METHODS: In this observational cohort study, we identified all neonates born between March 22 and May 17, 2020, at three New York Presbyterian Hospitals in New York City (NY, USA) to mothers positive for SARS-CoV-2 at delivery. Mothers could practice skin-to-skin care and breastfeed in the delivery room, but had to wear a surgical mask when near their neonate and practice proper hand hygiene before skin-to-skin contact, breastfeeding, and routine care. Unless medically required, neonates were kept in a closed Giraffe isolette in the same room as their mothers, and were held by mothers for feeding after appropriate hand hygiene, breast cleansing, and placement of a surgical mask. Neonates were tested for SARS-CoV-2 by use of real-time PCR on nasopharyngeal swabs taken at 24 h, 5–7 days, and 14 days of life, and were clinically evaluated by telemedicine at 1 month of age. We recorded demographics, neonatal, and maternal clinical presentation, as well as infection control practices in the hospital and at home. FINDINGS: Of 1481 deliveries, 116 (8%) mothers tested positive for SARS-CoV-2; 120 neonates were identified. All neonates were tested at 24 h of life and none were positive for SARS-CoV-2. 82 (68%) neonates completed follow-up at day 5–7 of life. Of the 82 neonates, 68 (83%) roomed in with the mothers. All mothers were allowed to breastfeed; at 5–7 days of life, 64 (78%) were still breastfeeding. 79 (96%) of 82 neonates had a repeat PCR at 5–7 days of life, which was negative in all; 72 (88%) neonates were also tested at 14 days of life and none were positive. None of the neonates had symptoms of COVID-19. INTERPRETATION: Our data suggest that perinatal transmission of COVID-19 is unlikely to occur if correct hygiene precautions are undertaken, and that allowing neonates to room in with their mothers and direct breastfeeding are safe procedures when paired with effective parental education of infant protective strategies. FUNDING: None. url: https://doi.org/10.1016/s2352-4642(20)30235-2 doi: 10.1016/s2352-4642(20)30235-2 id: cord-277410-lt19mijb author: Salvatore, Phillip P title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date: 2020-09-28 words: 3282.0 sentences: 206.0 pages: flesch: 52.0 cache: ./cache/cord-277410-lt19mijb.txt txt: ./txt/cord-277410-lt19mijb.txt summary: METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). Given the paucity of data examining associations of these factors with Ct value at the time of diagnosis, we sought to identify relationships between Ct values and time since onset, demographic factors, and symptoms among laboratory-confirmed COVID-19 cases identified in a multistate investigation of SARS-CoV-2 household transmission. Cycle threshold (Ct) values for SARS-CoV-2 rRT-PCR target probes N1 and N2 are plotted against the time elapsed between symptom onset and NP specimen collection in panel 1A. abstract: BACKGROUND: Detection of SARS-CoV-2 infection has principally been performed through the use of real-time reverse-transcription PCR (rRT-PCR) testing. Results of such tests can be reported as cycle threshold (Ct) values, which may provide semi-quantitative or indirect measurements of viral load. Previous reports have examined temporal trends in Ct values over the course of a SARS-CoV-2 infection. METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. RESULTS: We found Ct values are lowest (corresponding to higher viral RNA concentration) soon after symptom onset and are significantly correlated with time elapsed since onset (p<0.001); within 7 days after symptom onset, the median Ct value was 26.5 compared with a median Ct value of 35.0 occurring 21 days after onset. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). CONCLUSIONS: These results emphasize the importance of early testing for SARS-CoV-2 among individuals with symptoms of respiratory illness and allows cases to be identified and isolated when their viral shedding may be highest. url: https://www.ncbi.nlm.nih.gov/pubmed/32986120/ doi: 10.1093/cid/ciaa1469 id: cord-340049-6rqmc89u author: Salvatori, Giovanni title: SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines date: 2020-06-03 words: 1411.0 sentences: 86.0 pages: flesch: 44.0 cache: ./cache/cord-340049-6rqmc89u.txt txt: ./txt/cord-340049-6rqmc89u.txt summary: Evidence of the key role played by the S protein in counteracting coronavirus infection came from studies on human-neutralizing antibodies from rare memory B cells of individuals infected with SARS-CoV [2] or MERS-CoV [3] . Journal of Translational Medicine antibody responses, and vigorously neutralized SARS-CoV-2 S-mediated entry into cells, thus further encouraging the use of this molecular target for vaccination and immunotherapies [4] . Given the above and that the coronavirus S glycoprotein is surface-exposed and mediates entry into host cells by interacting with angiotensin-converting enzyme 2 (ACE2), it rapidly became the main target of neutralizing antibodies and the focus of therapeutic and vaccine design. Several companies and research institutes have started developing a vaccine that has the SARS-CoV-2 protein S as its target (see Table 1 ), although the various vaccination strategies show a differing ability to induce in the host both an antibody-mediated humoral response and a cell response mediated by CD4 or CD8 T lymphocytes in preclinical models. abstract: COVID-19 has rapidly spread all over the world, progressing into a pandemic. This situation has urgently impelled many companies and public research institutes to concentrate their efforts on research for effective therapeutics. Here, we outline the strategies and targets currently adopted in developing a vaccine against SARS-CoV-2. Based on previous evidence and experience with SARS and MERS, the primary focus has been the Spike protein, considered as the ideal target for COVID-19 immunotherapies. url: https://www.ncbi.nlm.nih.gov/pubmed/32493510/ doi: 10.1186/s12967-020-02392-y id: cord-343919-n8884bli author: Salvio, Gianmaria title: Bone Metabolism in SARS-CoV-2 Disease: Possible Osteoimmunology and Gender Implications date: 2020-09-01 words: 3908.0 sentences: 183.0 pages: flesch: 39.0 cache: ./cache/cord-343919-n8884bli.txt txt: ./txt/cord-343919-n8884bli.txt summary: We present a brief review of the molecular mechanisms linking inflammatory diseases to increased fracture risk/osteoporosis and of the therapeutic strategies that can prevent bone resorption in patients with inflammatory disease, focusing on the RANK-RANKL system. A subsequent in vitro study showed that a specific SARS-CoV protein, 3a/X1, directly promotes osteoclastogenesis, accelerating osteoclast differentiation from monocyte/macrophage precursors, enhancing the expression of receptor activator of NF-kB ligand (RANKL) and inflammatory cytokines such as TNF-α, which indirectly promote osteoclastogenesis [20] . As will be explained later in the text, IL-6 represents an important cofactor for bone resorption in inflammatory diseases; therefore, during SARS-CoV-2 infection, men, though less affected by osteoporosis, may experience more bone metabolism alterations than women for higher levels of IL-6 resulting from the lack of suppression by estrogen. abstract: Even though inflammatory conditions are known to exert adverse effects on bone metabolism, there are no published data regarding SARS-CoV-2 infection and subsequent fracture risk. We present a brief review of the molecular mechanisms linking inflammatory diseases to increased fracture risk/osteoporosis and of the therapeutic strategies that can prevent bone resorption in patients with inflammatory disease, focusing on the RANK-RANKL system. We also make some considerations on gender differences in infection response and on their implications for survival and for the consequences of COVID-19. Several inflammatory cytokines, especially IL-1, IL-6, and TNF-α, stimulate osteoclast activity, favoring bone resorption through the RANK-RANKL system. Data from the previous SARS-CoV outbreak suggest that the present disease also has the potential to act directly on bone resorption units, although confirmation is clearly needed. Even though the available data are limited, the RANK-RANKL system may provide the best therapeutic target to prevent bone resorption after COVID-19 disease. Vitamin D supplementation in case of deficiency could definitely be beneficial for bone metabolism, as well as for the immune system. Supplementation of vitamin D in case of deficiency could be further advantageous. In COVID-19 patients, it would be useful to measure the bone metabolism markers and vitamin D. Targeting the RANK-RANKL system should be a priority, and denosumab could represent a safe and effective choice. In the near future, every effort should be made to investigate the fracture risk after SARS-CoV-2 infection. url: https://doi.org/10.1007/s12018-020-09274-3 doi: 10.1007/s12018-020-09274-3 id: cord-311429-adcmgd1i author: Salzberger, B. title: Epidemiologie von SARS-CoV-2/COVID 19: Aktueller Stand date: 2020-10-29 words: 1795.0 sentences: 212.0 pages: flesch: 51.0 cache: ./cache/cord-311429-adcmgd1i.txt txt: ./txt/cord-311429-adcmgd1i.txt summary: Die Basisreproduktionszahl R0 (Mittelwert der Zahl von Personen, die von Tab. 1 Kennzahlen der Epidemiologie von SARS("severe acute respiratory syndrome")-CoV("coronavirus")-2 Die Altersverteilung kann sich über die Zeit ändern, in Deutschland ist ein deutlicher Trend zu sehen: Infektionen nach Mai treten überwiegend bei jüngeren auf, die Infektionsraten bei diesen Gruppen sind in der Periode nach der ersten Welle höher als in der ersten Periode (. Der Anteil der Infektionen bei Personen des medizinischen Personals lag in China bei 2,7 %, in Italien bei 11,1 % und in Deutschland bei 5,8 % [9, 18, 27] . Die Ausbreitung lag bei den genannten Influenzapandemien zwischen 9 und 40 % der Gesamtbevölkerung -eine starke Motivation zur effektiven Kontrolle der SARS-CoV-2-Infektion. SARS-CoV-2 hat sich nach dem ersten Ausbruch in Wuhan rasch international verbreitet, und eine Verbreitung und eine Übertragung sind auf allen Kontinenten zu verzeichnen. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus, which first appeared in 2019 and rapidly spread causing a worldwide pandemic. Here we present a nonsystematic review of the current knowledge on its epidemiological features. The SARS-CoV‑2 replicates mainly in the upper and lower respiratory tract and is mainly transmitted by droplets and aerosols from asymptomatic and symptomatic infected subjects. The estimate for the basic reproduction number (R0) is between 2 and 3 and the median incubation period is 6 days (range 2–14 days). Similar to the related coronaviruses SARS and Middle East respiratory syndrome (MERS), superspreading events play an important role in spreading the disease. The majority of infections run an uncomplicated course but 5–10% of those infected develop pneumonia or a systemic inflammation leading to hospitalization, respiratory and potentially multiorgan failure. The most important risk factors for a complicated disease course are age, hypertension, diabetes, chronic cardiovascular and pulmonary diseases and immunodeficiency. The current infection fatality rate over all age groups is between 0.5% and 1% and the rate rises after the sixth decade of life. Nosocomial transmission and infections in medical personnel have been reported. A drastic reduction of social contacts has been implemented in many countries with outbreaks of SARS-CoV‑2, leading to rapid reductions in R0. Most interventions have used bundles and which of the measures have been more effective is still unknown. Using mathematical models an incidence of 0.4%–1.8% can be estimated for the first wave in Germany. url: https://www.ncbi.nlm.nih.gov/pubmed/33144889/ doi: 10.1007/s11377-020-00479-y id: cord-324963-zg3ghl2m author: Salzberger, B. title: COVID-19 – eine neue und vielseitige Herausforderung date: 2020-08-03 words: 877.0 sentences: 127.0 pages: flesch: 46.0 cache: ./cache/cord-324963-zg3ghl2m.txt txt: ./txt/cord-324963-zg3ghl2m.txt summary: Affinität zum ACE2-Rezeptor kann die Infektion in den oberen Atemwegen stattfinden Das Virus ist ein neues β-Coronavirus, das vermutlich von Fledermäusen auf eine noch unbekannte Säugerspezies übergesprungen ist. Es bindet wie SARS-CoV an den Angiotensinconverting-enzyme-2(ACE2)-Rezeptor, aber mit einer sehr viel höheren Affinität, sodass die Infektion in den oberen Atemwegen stattfinden kann. In einer ersten großen genomweiten Studie konnten einige genetische Faktoren als Risiken identifiziert werden, für eine individuelle Risikoabschätzung sind alle diese Daten jedoch noch nicht geeignet [5] . Die schweren Krankheitsverläufe einer Infektionskrankheit mit der realen Gefahr nosokomialer Infektionen konnten spezialisierte Infektions-oder Intensivmediziner nicht allein behandeln, es waren breit interdisziplinäre Teams im Einsatz, die von der Diagnostik über die Therapie bis zu Isolations-und Quarantänestrategien ein breites Portfolio von klinischen und organisatorischen Aufgaben lösten. Immunmodulatorische Therapien sind bisher kaum systematisch evaluiert worden, in einer randomisierten Studie aus Großbritannien konnte gerade erstmals gezeigt werden, dass Dexamethason bei schwer verlaufender COVID-19-Erkrankung die Prognose verbessert [9] . Epidemiologie von SARS-CoV-2-Infektion und COVID-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32748001/ doi: 10.1007/s00108-020-00851-8 id: cord-353092-4hz2yyl5 author: Sama, Iziah E title: Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin–angiotensin–aldosterone inhibitors date: 2020-05-14 words: 3472.0 sentences: 182.0 pages: flesch: 49.0 cache: ./cache/cord-353092-4hz2yyl5.txt txt: ./txt/cord-353092-4hz2yyl5.txt summary: CONCLUSION: In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. We therefore investigated plasma concentrations of ACE2 in two large and independent cohorts of men and women with heart failure according to the use of RAAS inhibitors. In two large independent cohorts of patients with heart failure, we found that plasma ACE2 concentrations were higher in men than in women. In two large cohorts of patients with heart failure, plasma ACE2 concentrations were higher in men than in women, possibly reflecting higher tissue expression of this receptor for SARS coronavirus infections. abstract: AIMS: The current pandemic coronavirus SARS-CoV-2 infects a wide age group but predominantly elderly individuals, especially men and those with cardiovascular disease. Recent reports suggest an association with use of renin–angiotensin–aldosterone system (RAAS) inhibitors. Angiotensin-converting enzyme 2 (ACE2) is a functional receptor for coronaviruses. Higher ACE2 concentrations might lead to increased vulnerability to SARS-CoV-2 in patients on RAAS inhibitors. METHODS AND RESULTS: We measured ACE2 concentrations in 1485 men and 537 women with heart failure (index cohort). Results were validated in 1123 men and 575 women (validation cohort). The median age was 69 years for men and 75 years for women. The strongest predictor of elevated concentrations of ACE2 in both cohorts was male sex (estimate = 0.26, P < 0.001; and 0.19, P < 0.001, respectively). In the index cohort, use of ACE inhibitors, angiotensin receptor blockers (ARBs), or mineralocorticoid receptor antagonists (MRAs) was not an independent predictor of plasma ACE2. In the validation cohort, ACE inhibitor (estimate = –0.17, P = 0.002) and ARB use (estimate = –0.15, P = 0.03) were independent predictors of lower plasma ACE2, while use of an MRA (estimate = 0.11, P = 0.04) was an independent predictor of higher plasma ACE2 concentrations. CONCLUSION: In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. These data might explain the higher incidence and fatality rate of COVID-19 in men, but do not support previous reports suggesting that ACE inhibitors or ARBs increase the vulnerability for COVID-19 through increased plasma ACE2 concentrations. url: https://www.ncbi.nlm.nih.gov/pubmed/32388565/ doi: 10.1093/eurheartj/ehaa373 id: cord-328557-f6o1aynz author: Samad, Abdus title: Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach date: 2020-07-17 words: 7593.0 sentences: 423.0 pages: flesch: 50.0 cache: ./cache/cord-328557-f6o1aynz.txt txt: ./txt/cord-328557-f6o1aynz.txt summary: So, targeting S-protein can provide an immunogenic response in the human host, and has been chosen for designing a multi-epitopes vaccine candidate against the SARS-CoV-2. For the prediction of CTLs epitope, the sequence of the selected protein was submitted into the NetCTL v1.2 server available at http://www.cbs.dtu. For this purpose, we submitted the refined vaccine model as ligand and TLR4 protein as immunological receptor into the ClusPro v2.0 server, available at https://cluspro.bu.edu/, for molecular docking (Kozakov et al., 2017) . Due to the high number of potential epitopes, we selected the top four CTL epitopes for the final vaccine construction based on the antigenicity score (Table 1) . Likewise, we considered the top four HTL epitopes for incorporating into the final vaccine construct based on the antigenic score (Table 2) . In this study, we designed an epitope-based vaccine that could provide a strong immune response against SARS-CoV-2, thereby, preventing the COVID-19 pandemic. abstract: Ongoing COVID-19 outbreak has raised a drastic challenge to global public health security. Most of the patients with COVID-19 suffer from mild flu-like illnesses such as cold and fever; however, few percentages of the patients progress from severe illness to death, mostly in an immunocompromised individual. The causative agent of COVID-19 is an RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite these debilitating conditions, no medication to stop the disease progression or vaccination is available till now. Therefore, we aimed to formulate a multi-epitope vaccine against SARS-CoV-2 by utilizing an immunoinformatics approach. For this purpose, we used the SARS-CoV-2 spike glycoprotein to determine the immunodominant T- and B-cell epitopes. After rigorous assessment, we designed a vaccine construct using four potential epitopes from each of the three epitope classes such as cytotoxic T-lymphocytes, helper T-lymphocyte, and linear B-lymphocyte epitopes. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. More importantly, the predicted vaccine structure was similar to the native protein. Further investigations indicated a strong and stable binding interaction between the vaccine and the toll-like receptor (TLR4). Strong binding stability and structural compactness were also evident in molecular dynamics simulation. Furthermore, the computer-generated immune simulation showed that the vaccine could trigger real-life-like immune responses upon administration into humans. Finally, codon optimization based on Escherichia coli K12 resulted in optimal GC content and higher CAI value followed by incorporating it into the cloning vector pET28+(a). Overall, these results suggest that the designed peptide vaccine can serve as an excellent prophylactic candidate against SARS-CoV-2. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1792347 doi: 10.1080/07391102.2020.1792347 id: cord-313684-61hkogdh author: Samaddar, Arghadip title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 words: 11700.0 sentences: 585.0 pages: flesch: 42.0 cache: ./cache/cord-313684-61hkogdh.txt txt: ./txt/cord-313684-61hkogdh.txt summary: Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. abstract: Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. To date, there are no proven drugs or vaccines against this virus. Hence, the situation demands an urgent need to explore all potential therapeutic strategies that can be made available to prevent the disease progression and improve patient outcomes. In absence of clinically proven treatment guidelines, several repurposed drugs and investigational agents are currently being evaluated in clinical trials for their probable benefits in the treatment of COVID-19. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. Moreover, there is a need to clearly define the patient populations who warrant therapy and also the timing of initiation of treatment. Understanding the disease pathology responsible for the clinical manifestations of COVID-19 is imperative to identify the potential targets for drug development. This review explains the pathophysiology of COVID-19 and summarizes the potential treatment candidates, which can provide guidance in developing effective therapeutic strategies. url: https://doi.org/10.3389/fphar.2020.585888 doi: 10.3389/fphar.2020.585888 id: cord-334550-xb0alubj author: Samaddar, Arghadip title: The Enigma of Low COVID-19 Fatality Rate in India date: 2020-07-28 words: 6405.0 sentences: 367.0 pages: flesch: 48.0 cache: ./cache/cord-334550-xb0alubj.txt txt: ./txt/cord-334550-xb0alubj.txt summary: These include some ongoing mutations that can alter the virulence of the circulating SARS-CoV-2 strains, host factors like innate immunity, genetic diversity in immune responses, epigenetic factors, genetic polymorphisms of ACE2 receptors, micro RNAs and universal BCG vaccination, and environmental factors like high temperature and humidity which may alter the viability and transmissibility of the strain. Researchers from Translational Bioinformatics Group at International Center for Genetic Engineering and Biotechnology (ICGEB) in collaboration with the Department of Biochemistry, Jamia Hamdard, New Delhi, India, performed an integrated mutational analysis of SARS-CoV-2 genomes from different geographical locations, including India, Italy, United States, Nepal and Wuhan, and observed a novel mutation in S protein (A930V, 24351C>T) of the Indian strain, which was absent in other strains (Sardar et al., 2020) . While this apparent protection among Indians is largely attributed to non-heritable influences as discussed earlier, a safe and effective vaccine against SARS-CoV-2 can reduce disease severity, control transmission, and prevent future infections across all populations. abstract: Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly evolved into a pandemic. Though its origin has been linked to the Wuhan City of China’s Hubei Province in December 2019, recent reports claim that the original animal-to-human transmission of the virus probably happened sometime between September and October 2019 in Guangdong Province, rather than Hubei. As of July 3, 2020, India has reported a case positivity rate of 6.5% and a fatality rate of 2.8%, which are among the lowest in the world. Also, the severity of the disease is much less among Indians as evidenced by the low rate of ICU admission (15.3%) and the need for mechanical ventilation (4.16%). As per the World Health Organization (WHO) situation report 165 on July 3, 2020, India has one of the lowest deaths per 100,000 population (1.32 deaths against a global average of 6.04). Several factors related to the pathogen, host and environment might have some role in reducing the susceptibility of Indians to COVID-19. These include some ongoing mutations that can alter the virulence of the circulating SARS-CoV-2 strains, host factors like innate immunity, genetic diversity in immune responses, epigenetic factors, genetic polymorphisms of ACE2 receptors, micro RNAs and universal BCG vaccination, and environmental factors like high temperature and humidity which may alter the viability and transmissibility of the strain. This perspective -highlights the potential factors that might be responsible for the observed low COVID-19 fatality rate in Indian population. It puts forward several hypotheses which can be a ground for future studies determining individual and population susceptibility to COVID-19 and thus, may offer a new dimension to our current understanding of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32849833/ doi: 10.3389/fgene.2020.00854 id: cord-026792-jsqa4pmu author: Samanta, Jayanta title: 2019 Novel Coronavirus Infection: Gastrointestinal Manifestations date: 2020-05-16 words: 3792.0 sentences: 218.0 pages: flesch: 51.0 cache: ./cache/cord-026792-jsqa4pmu.txt txt: ./txt/cord-026792-jsqa4pmu.txt summary: The modern world is facing a major public health crisis due to novel corona virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) which has caused a pandemic involving at least 210 countries. The extrapulmonary effects and modes of transmission gained attention when the first confirmed case of SARS-CoV-2 reported from the United States had gastrointestinal (GI) complaints of nausea and vomiting followed later by diarrhea and patient''s fecal specimen tested positive on day 7 of illness. This review aims to comprehensively outline the GI manifestations of this virus, its potential to spread via the feco-oral route and its implications and an overview of management strategies for other GI diseases, such as inflammatory bowel disease (IBD) coexisting with coronavirus-19 disease (COVID-19) infection. abstract: The world is witnessing a major public health crisis in the wake of the third coronavirus strain pandemic, a novel coronavirus (severe acute respiratory syndrome coronavirus 2). Although initially thought to be a pure respiratory pathogen, recent reports have highlighted not only the extrapulmonary effects of the virus but also, importantly, the gastrointestinal tract (GIT) effects. Various studies have looked into the effects of this novel coronavirus infection (coronavirus-19 disease [COVID-19]) on GIT involvement with reports of more frequent involvement than previously expected. With feco-oral transmission, debate being conclusively proven with fecal samples testing positive for COVID-19 and longer shedding time, it only underlines the importance of GIT involvement. Moreover, the presence of other GI diseases, such as inflammatory bowel disease, with COVID-19 infection might wreak havoc leading to poor patient outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295271/ doi: 10.1055/s-0040-1712077 id: cord-297693-lqyc49t6 author: Samec, Matthew J title: 80-year-old man with dyspnoea and bilateral groundglass infiltrates: an elusive case of COVID-19 date: 2020-05-27 words: 2821.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-297693-lqyc49t6.txt txt: ./txt/cord-297693-lqyc49t6.txt summary: COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a ''crazy paving'' pattern on chest CT imaging and a negative initial infectious workup. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a ''crazy paving'' pattern on chest CT imaging and a negative initial infectious workup. The case was reviewed with the institutional infection prevention and control team who recommended repeating SARS-CoV-2 PCR 48 hours from the initial test. 14 There have been three published case reports of initially negative COVID-19 PCR tests in patients subsequently new disease determined to have COVID-19 infection. abstract: COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. COVID-19 has spread rapidly and is now considered a global pandemic. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a ‘crazy paving’ pattern on chest CT imaging and a negative initial infectious workup. However, given persistent dyspnoea and labs suggestive of COVID-19 infection, the patient remained hospitalised for further monitoring. Forty-eight hours after initial testing, the PCR test was repeated and returned positive for COVID-19. This case illustrates the importance of clinical vigilance to retest patients for COVID-19, particularly in the absence of another compelling aetiology. As COVID-19 testing improves to rapidly generate results, selective retesting of patients may uncover additional COVID-19 cases and strengthen measures to minimise the spread of COVID-19. url: https://doi.org/10.1136/bcr-2020-236069 doi: 10.1136/bcr-2020-236069 id: cord-259229-e8m8m4ut author: Samidurai, Arun title: Cardiovascular Complications Associated with COVID-19 and Potential Therapeutic Strategies date: 2020-09-16 words: 10768.0 sentences: 530.0 pages: flesch: 38.0 cache: ./cache/cord-259229-e8m8m4ut.txt txt: ./txt/cord-259229-e8m8m4ut.txt summary: Emerging evidence reveals a direct interplay between COVID-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. Respiratory illness and acute cardiac injury are major clinical manifestations observed in patients infected with SARS-CoV-2 during the late stage complications of the disease [38] . Based on the available clinical data, potential myocardial injury is a relevant challenge among hospitalized patients with COVID-19 with increased risk of mortality; therefore, it is essential for multidisciplinary assessment, including blood pressure control in hypertensive patients as well as cardiovascular evaluation and therapy to reduce the morality for COVID-19 infection. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China abstract: The outbreak of coronavirus disease 2019 (COVID-19), an infectious disease with severe acute respiratory syndrome, has now become a worldwide pandemic. Despite the respiratory complication, COVID-19 is also associated with significant multiple organ dysfunction, including severe cardiac impairment. Emerging evidence reveals a direct interplay between COVID-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. The proposed pathophysiological mechanisms of myocardial impairment include invasion of SARS-CoV-2 virus via angiotensin-converting enzyme 2 to cardiovascular cells/tissue, which leads to endothelial inflammation and dysfunction, de-stabilization of vulnerable atherosclerotic plaques, stent thrombosis, cardiac stress due to diminish oxygen supply and cardiac muscle damage, and myocardial infarction. Several promising therapeutics are under investigation to the overall prognosis of COVID-19 patients with high risk of cardiovascular impairment, nevertheless to date, none have shown proven clinical efficacy. In this comprehensive review, we aimed to highlight the current integrated therapeutic approaches for COVID-19 and we summarized the potential therapeutic options, currently under clinical trials, with their mechanisms of action and associated adverse cardiac events in highly infectious COVID-19 patients. url: https://doi.org/10.3390/ijms21186790 doi: 10.3390/ijms21186790 id: cord-326929-ytix4l1o author: Samillan, V. J. title: Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru date: 2020-09-18 words: 4344.0 sentences: 214.0 pages: flesch: 48.0 cache: ./cache/cord-326929-ytix4l1o.txt txt: ./txt/cord-326929-ytix4l1o.txt summary: In this study, we explored the relationship between the cumulative number of infections and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection and mortality of SARS-CoV-2 in Peru. Although more studies are necessary, the rate of infection and the severity of the diseases seems different for people living in cities at high altitudes, where not only hipoxia is a major factor, but other factors such as air quality, solar radiation, and population density, could play a role in SARS-CoV-2 person-to-person transmission. The main objectives of this study was to explore the relationship between SARS-CoV-2 infection and mortality cases, case-fatality rates with a set of climate (temperature, precipitation, solar radiation, water vapor pressure, and wind), environmental data (elevation, NDVI, PM 2.5 and NO 2 concentration), and population density in Peru. abstract: The role of the environment and climate in the transmission and case-fatality rates of SARS-CoV-2 is still being investigated. Elevation and air quality are believed to be significant factors in the current development of the pandemic, but the influence of additional environmental factors remain unclear. In this study, we explored the relationship between the cumulative number of infections and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Using the data from confirmed cases of infection from 1287 districts and confirmed cases of mortality in 479 districts, we used Spearman's correlations to assess the correlation between environmental and climatic factors with cumulative infection cases, cumulative mortality and case-fatality rate. We also explored district cases by the ecozones of coast, sierra, high montane forest and lowland rainforest. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection and mortality of SARS-CoV-2 in Peru. The case-fatality rate was weakly associated with elevation. Our results also strongly suggest that exposure to poor air quality is a significant factor in the mortality of individuals with SARS-CoV-2 below the age of 30. We conclude that environmental and climatic factors do play a significant role in the transmission and case-fatality rates in Peru, however further study is required to see if these relationships are maintained over time. url: http://medrxiv.org/cgi/content/short/2020.09.16.20196170v1?rss=1 doi: 10.1101/2020.09.16.20196170 id: cord-333320-ndmmbckb author: Samore, M. title: SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample date: 2020-10-27 words: 7433.0 sentences: 403.0 pages: flesch: 53.0 cache: ./cache/cord-333320-ndmmbckb.txt txt: ./txt/cord-333320-ndmmbckb.txt summary: Probability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah. Although seroprevalence has been touted as a more standardized way to estimate the incidence of SaRS-COV-2 infection across different populations, it also presents challenges because of inconsistencies in test performance and sampling methods. Using a statistical sampling frame and adjusting for test performance and non-response, we estimated the prevalence of IgG antibody to SARS-CoV-2 in four urban counties in Utah between May and June to be only 0.8%. We used a serological test that is reported by the manufacturer to have a specificity at 99.6%; however, even at this level of accuracy, statistically accounting for false positives is necessary given the low population prevalence of IgG antibody to SARS-CoV-2. abstract: This project's aim was to generate an unbiased estimate of the incidence of SARS-CoV-2 infection in four urban counties in Utah. A multi-stage sampling design was employed to randomly select community-representative participants 12 years and over. Between May 4 and June 30, 2020, surveys were completed and sera drawn from 8,108 individuals belonging to 5,125 households. A qualitative chemiluminescent microparticle immunoassay was used to detect the presence of IgG antibody to SARS-CoV-2. The overall prevalence of IgG antibody to SARS-CoV-2 was estimated at 0.8%. The estimated seroprevalence-to-case count ratio was 2.4, corresponding to a detection fraction of 42%. Only 0.2% of individuals who had a nasopharyngeal swab collected were reverse transcription polymerase chain reaction (RT-PCR) positive. The prevalence of antibodies to SARS-CoV-2 in Utah urban areas between May and June was low and the prevalence of positive RT-PCR even lower. The detection fraction for COVID-19 in Utah was comparatively high. Probability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah. url: https://doi.org/10.1101/2020.10.26.20219907 doi: 10.1101/2020.10.26.20219907 id: cord-261025-y49su5uc author: Sampathkumar, Priya title: SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date: 2003-07-31 words: 3952.0 sentences: 200.0 pages: flesch: 49.0 cache: ./cache/cord-261025-y49su5uc.txt txt: ./txt/cord-261025-y49su5uc.txt summary: Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus. It appears to be spread primarily by large droplet transmission. There is no specific therapy, and management consists of supportive care. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. url: https://www.sciencedirect.com/science/article/pii/S002561961162689X doi: 10.4065/78.7.882 id: cord-320964-1gg33gdn author: Sampieri, Clara Luz title: Revisión de nuevas evidencias acerca de la posible transmisión vertical de la COVID-19 date: 2020-06-20 words: 4036.0 sentences: 363.0 pages: flesch: 60.0 cache: ./cache/cord-320964-1gg33gdn.txt txt: ./txt/cord-320964-1gg33gdn.txt summary: En el contexto de la pandemia por COVID-19 se ha generado nueva evidencia tras la publicación de la guía de la Organización Mundial de la Salud, el 13 de marzo de 2020 14 , por lo que efectuamos una revisión sistemática de la literatura en PubMed de estudios revisados por pares publicados entre el 27 de marzo y el 21 de mayo de 2020, enfocándonos en aquellos trabajos que incluyeran análisis de muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical y Se identificaron 107 registros, de los cuales dos condujeron a la misma referencia y uno indicó una ruta de acceso no válida. En los estudios incluidos se identificó la etapa en que la madre tuvo la confirmación de la infección por SARS-CoV-2 o el diagnóstico clínico de COVID-19, el pronóstico del binomio madre-hijo/a, los resultados del análisis de SARS-CoV-2 del bebé, y las muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical o leche humana. abstract: ABSTRACT Objective: To conduct a systematic review of original peer-reviewed studies, containing data on the identification of SARS-CoV-2 in clinical samples of amniotic fluid, placenta or membranes, umbilical cord blood, and human milk, from women with a clinically or confirmed diagnosis of COVID-19. These studies should have been published after the guide for the management of patients with COVID-19 from World Health Organization guide (available in March 13, 2020). Results: Seventeen studies were included, in which 143 clinical samples were identified (38 of amniotic fluid; 34 of placentas or membranes; 39 from umbilical cord blood and 32 from human milk). Among the 143 samples, nine were positive for SARS-CoV-2 RNA (one amniotic fluid sample obtained before rupturing the membranes; six samples of placenta or membranes, although authors indicate the possibility of contamination by maternal blood in three of these, and two samples of human milk). Conclusions: Following our search criteria, we found no studies that demonstrate the detection of SARS-CoV-2, in conjunction with viral isolation and the evaluation of the infective capacity of viral particles, in clinical samples of amniotic fluid, placenta or membranes, umbilical cord blood and human milk, from women with a confirmed or clinical diagnosis of COVID-19. However, vertical transmission cannot be ruled out, larger studies are required that ideally locate in situ RNA and protein of SARS-CoV-2, as well as isolation that demonstrate the infective capacity of the viral particles. url: https://www.ncbi.nlm.nih.gov/pubmed/32711871/ doi: 10.1016/j.gaceta.2020.06.005 id: cord-319920-vn5si7xm author: Sampogna, Gianluca title: Spinal cord dysfunction after COVID-19 infection date: 2020-09-30 words: 2524.0 sentences: 164.0 pages: flesch: 47.0 cache: ./cache/cord-319920-vn5si7xm.txt txt: ./txt/cord-319920-vn5si7xm.txt summary: INTRODUCTION: We observed individuals affected by spinal cord dysfunction (SCD) after coronavirus disease 2019 (COVID-19). Case 1, aged 69 years, experienced T10 AIS B paraplegia upon awakening due to spinal cord ischemia from T8 to conus medullaris, besides diffuse thromboses, 27 days after the onset of COVID-19 symptoms. Prior to SCD, all three individuals suffered from respiratory failure due to COVID-19, required mechanical ventilation, had cardiovascular risk factors, experienced lymphopenia, and received tocilizumab (TCZ). The aim of our report is to provide our initial experience with people experiencing SCD after COVID-19 in a referral USU in the Northern Italian region most affected by the SARS-CoV-2 infection. As a consequence of the neurotropic and neuro-invasive potential of this virus, it has been reported that 36.4% of patients with COVID-19 suffer from neurological complications, and up to 45.5% patients in case of severe SARS-CoV-2 infection [14] . abstract: INTRODUCTION: We observed individuals affected by spinal cord dysfunction (SCD) after coronavirus disease 2019 (COVID-19). The aim of our report is to provide our initial experience with individuals experiencing SCD after COVID-19 in a referral center in Northern Italy, from February 21 to July 15, 2020. CASE PRESENTATION: We report on three men with SCD after COVID-19. Case 1, aged 69 years, experienced T10 AIS B paraplegia upon awakening due to spinal cord ischemia from T8 to conus medullaris, besides diffuse thromboses, 27 days after the onset of COVID-19 symptoms. Case 2, aged 56 years, reported progressive cervicalgia 29 days after COVID-19 onset associated with C3 AIS C tetraplegia. Magnetic resonance imaging (MRI) revealed a C4–C6 spinal epidural abscess (SEA) requiring a C3–C4 left hemilaminectomy. Case 3, aged 48 years, reported backache together with lower limb muscle weakness on day 16 after being diagnosed with COVID-19. Exam revealed T2 AIS A paraplegia and an MRI showed a T1–T7 SEA. He underwent a T3–T4 laminectomy. Prior to SCD, all three individuals suffered from respiratory failure due to COVID-19, required mechanical ventilation, had cardiovascular risk factors, experienced lymphopenia, and received tocilizumab (TCZ). DISCUSSION: To our knowledge, this is the first report of SCD after COVID-19. Based on our experience, we did not observe a direct viral infection, but there were two different etiologies. In Case 1, the individual developed spinal cord ischemia, whereas in Cases 2 and 3 SEAs were likely related to the use of TCZ used to treat COVID-19. url: https://doi.org/10.1038/s41394-020-00341-x doi: 10.1038/s41394-020-00341-x id: cord-313084-l7odplqg author: Sampson, Victoria title: Could there be a link between oral hygiene and the severity of SARS-CoV-2 infections? date: 2020-06-26 words: 3352.0 sentences: 203.0 pages: flesch: 42.0 cache: ./cache/cord-313084-l7odplqg.txt txt: ./txt/cord-313084-l7odplqg.txt summary: The risk factors already identified for developing complications from a COVID-19 infection are age, gender and comorbidities such as diabetes, hypertension, obesity and cardiovascular disease. This paper investigates the potential link between SARS-CoV-2 and bacterial load, questioning whether bacteria may play a role in bacterial superinfections and complications such as pneumonia, acute respiratory distress syndrome and sepsis. 1 While COVID-19 has a viral origin, it is suspected that in severe cases, bacterial superinfections may contribute to causing complications such as pneumonia and acute respiratory distress syndrome (ARDS). 18 It is common for respiratory viral infections to predispose patients to bacterial superinfections, leading to increased disease severity and mortality; for example, during the influenza pandemic in 1918, where the primary cause of death was not from the virus itself but from bacterial superinfections. Bacteria present in patients with severe COVID-19 are associated with the oral cavity and improved oral hygiene may play a part in reducing the risk of complications. abstract: On 30 January 2020, the World Health Organisation identified COVID-19, caused by the virus SARS-CoV-2, to be a global emergency. The risk factors already identified for developing complications from a COVID-19 infection are age, gender and comorbidities such as diabetes, hypertension, obesity and cardiovascular disease. These risk factors, however, do not account for the other 52% of deaths arising from COVID-19 in often seemingly healthy individuals. This paper investigates the potential link between SARS-CoV-2 and bacterial load, questioning whether bacteria may play a role in bacterial superinfections and complications such as pneumonia, acute respiratory distress syndrome and sepsis. The connection between COVID-19 complications and oral health and periodontal disease is also examined, as the comorbidities at highest risk of COVID-19 complications also cause imbalances in the oral microbiome and increase the risk of periodontal disease. We explore the connection between high bacterial load in the mouth and post-viral complications, and how improving oral health may reduce the risk of complications from COVID-19. url: https://doi.org/10.1038/s41415-020-1747-8 doi: 10.1038/s41415-020-1747-8 id: cord-289588-n61gz7pi author: Samudrala, Pavan Kumar title: Virology, pathogenesis, diagnosis and in-line treatment of COVID-19 date: 2020-07-17 words: 3898.0 sentences: 253.0 pages: flesch: 56.0 cache: ./cache/cord-289588-n61gz7pi.txt txt: ./txt/cord-289588-n61gz7pi.txt summary: Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. As far as safety is a major concern, 424 Gilead Sciences announced phase III clinical trial of remdesivir to prove its safety and 425 efficacy in COVID-19 infection (Keown, 16 .03.2020). Epidemiology, causes, clinical manifestation and 687 diagnosis, prevention and control of coronavirus disease (COVID-19) during the early 688 outbreak period: a scoping review First known person-to-784 person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 785 the USA Clinical 803 features of patients infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 (COVID-19) Vaccine Development and Production: An 817 Severe acute respiratory 845 syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The 846 epidemic and the challenges Unique epidemiological and clinical features 949 of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control 950 measures abstract: SARS-CoV-2, a newly emerged pathogen in December 2019, marked as one of the highly pathogenic Coronavirus, and altogether this is the third coronavirus attack that crossed the species barrier. As of 1(st) July 2020, it is spreading around 216 countries, areas or territories, and a total of 10,185,374 and 503,862 confirmed cases and death reports, respectively. The SARS-CoV-2 virus entered into the target cells by binding with the hACE2 receptors. Spike glycoprotein promotes the entry of the virus into host target cells. Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. These modifications may be the probable reason for the extreme transmission and pathogenicity of the virus. A hasty spread of COVID-19 throughout the world is highly threatening, but still, scientists do not have a proper therapeutic measure to fight with it. Scientists are endeavoring across the world to find effective therapy to combat COVID 19. Several drugs such as Remdesivir, Hydroxychloroquine, Chloroquine, Ribavirin, Ritonavir, Lopinavir, Favipiravir, Interferons, Bevacizumab, Azithromycin, etc. are currently under clinical trials. Vaccine development from various pharmaceutical companies and research institutes is under progress, and more than ten vaccine candidates are in the various phases of clinical trials. This review work highlighted the origin, emergence, structural features, pathogenesis, and clinical features of COVID-19. We have also discussed the in-line treatment strategies, preventive measures, and vaccines to combat the emergence of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0014299920304672?v=s5 doi: 10.1016/j.ejphar.2020.173375 id: cord-334425-6zrmavps author: SanJuan-Reyes, Sindy title: COVID-19 in the environment date: 2020-08-14 words: 2084.0 sentences: 139.0 pages: flesch: 50.0 cache: ./cache/cord-334425-6zrmavps.txt txt: ./txt/cord-334425-6zrmavps.txt summary: The WHO has named it COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV2). New studies provide information of the role of the environment in COVID-19 transmission process, mortality related to this infectious disease and the impact on human health. The following review aims to analyze information on the implications of COVID-19 infection on human health and the impact of its presence on the environment, from its transmission capacity and the role of air pollutants and climatological factors to reducing the air pollution during confinement. Until now, there are no specific pharmacological treatment or vaccines against COVID-19 infection 104 for potential therapy in humans, so extensive isolation measures and the use of disinfection products 105 have been implemented to reduce their transmission from person to person. First known person-to-person transmission of severe acute 593 respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA abstract: Abstract In recent months, the presence of an emerging disease of infectious etiology has paralyzed everyone, already being a public health problem due to its high rate of infection, a life-threatening disease. The WHO has named it COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV2). New studies provide information of the role of the environment in COVID-19 transmission process, mortality related to this infectious disease and the impact on human health. The following review aims to analyze information on the implications of COVID-19 infection on human health and the impact of its presence on the environment, from its transmission capacity and the role of air pollutants and climatological factors to reducing the air pollution during confinement. Likewise, it provides a vision of the impact on the environment and human health of exposure to disinfectants and the presence of COVID-19 in wastewater, among other actions. url: https://api.elsevier.com/content/article/pii/S0045653520321688 doi: 10.1016/j.chemosphere.2020.127973 id: cord-280172-6o1gqe8v author: Sanami, Samira title: Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date: 2020-07-15 words: 5835.0 sentences: 307.0 pages: flesch: 55.0 cache: ./cache/cord-280172-6o1gqe8v.txt txt: ./txt/cord-280172-6o1gqe8v.txt summary: In this research, first, the CTL, HTL, and B-cell epitopes of the S protein were predicted using ProPred-1, ProPred, and ABCPred servers, respectively, and then were selected base on antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Next, the physicochemical properties of the construct were investigated, the 3D structure of the protein was predicted, and finally, its affinity to the MHC I and II molecules was investigated through docking, following that, was performed the molecular dynamics (MD) simulation of docking complexes. The antigenicity of the epitopes were calculated by VaxiJen v2.0 server (http://www.ddgpharmfac.net/vaxijen/VaxiJen/VaxiJen.html), which is based on the transformation of the protein sequences auto cross-covariance (ACC) into uniform vectors of main amino acid properties. selected N, M, and S proteins as the target antigen for the prediction of T and B-cell epitopes and designed a multi-epitope vaccine against SARS-CoV-2 [48] . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused COVID-19 disease in China. So far, no vaccine has licensed to protect against infection with COVID-19, therefore an effective COVID-19 vaccine needed. The aim of this study was to predict antigenic peptides of SARS-CoV-2 for designing the COVID-19 vaccine using immunoinformatic analysis. In this study, T and B-cell epitopes of S protein were predicted and screened based on the antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. The epitopes were joined by the appropriate linker. LT-IIc as an adjuvant was attached to the end of the structure. The secondary and 3D structure of the vaccine was predicted. The refinement process was performed to improve the quality of the 3D model structure; the validation process is performed using the Ramachandran plot and ProSA z-score. The proposed vaccine's binding affinity to the HLA-A11: 01 and HLA-DRB1_01: 01 molecule was evaluated by molecular docking. Using molecular dynamics, the stability of vaccine-HLA complexes was also evaluated. Finally, in silico gene cloning was performed in the pET30a (+) vector. The findings suggest that the current vaccine may be a promising vaccine to prevent SARS-CoV-2 infection. url: https://doi.org/10.1016/j.ijbiomac.2020.07.117 doi: 10.1016/j.ijbiomac.2020.07.117 id: cord-146091-kpvxdhcu author: Sanchez-Lorenzo, Arturo title: Anomalous atmospheric circulation favored the spread of COVID-19 in Europe date: 2020-04-26 words: 3235.0 sentences: 166.0 pages: flesch: 52.0 cache: ./cache/cord-146091-kpvxdhcu.txt txt: ./txt/cord-146091-kpvxdhcu.txt summary: In this study we show that an unusual persistent anticyclonic situation prevailing in southwestern Europe during February 2020 (i.e. anomalously strong positive phase of the North Atlantic and Arctic Oscillations) could have resulted in favorable conditions, in terms of air temperature and humidity, in Italy and Spain for a quicker spread of the virus compared with the rest of the European countries. These results evidence that it seems plausible that the positive phase of the NAO, and the atmospheric conditions associated with it, provided optimal conditions for the spread of the COVID-19 in southern countries like Spain and Italy, where both the start and the most severe impacts of the outbreak in Europe were located. Taking into account these results, we claim that the major initial outbreaks of COVID-19 in Europe (i.e., Italy and Spain) may be favored by an anomalous atmospheric circulation pattern in February, characterized by a positive phase of the NAO and AO. abstract: The current pandemic caused by the coronavirus SARS-CoV-2 is having negative health, social and economic consequences worldwide. In Europe, the pandemic started to develop strongly at the end of February and beginning of March 2020. It has subsequently spread over the continent, with special virulence in northern Italy and inland Spain. In this study we show that an unusual persistent anticyclonic situation prevailing in southwestern Europe during February 2020 (i.e. anomalously strong positive phase of the North Atlantic and Arctic Oscillations) could have resulted in favorable conditions, in terms of air temperature and humidity, in Italy and Spain for a quicker spread of the virus compared with the rest of the European countries. It seems plausible that the strong atmospheric stability and associated dry conditions that dominated in these regions may have favored the virus's propagation, by short-range droplet transmission as well as likely by long-range aerosol (airborne) transmission. url: https://arxiv.org/pdf/2004.12503v1.pdf doi: nan id: cord-283372-c20i99qa author: Sanchis-Gomar, Fabian title: Amiodarone in the COVID-19 Era: Treatment for Symptomatic Patients Only, or Drug to Prevent Infection? date: 2020-08-01 words: 2612.0 sentences: 126.0 pages: flesch: 37.0 cache: ./cache/cord-283372-c20i99qa.txt txt: ./txt/cord-283372-c20i99qa.txt summary: Amiodarone, one of the most widely prescribed antiarrhythmic drugs to treat both ventricular and supraventricular arrhythmias, has been identified as a candidate drug for use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We present the rationale of using amiodarone in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe coronavirus disease 2019 (COVID-19), based on current evidence. However, amiodarone is not free of secondary adverse effects, contraindications and interactions with other drugs, including the potential to cause pulmonary toxicity and fibrosis, thyroid disease, hepatic toxicity, increased creatine levels, QT interval prolongation, and bradyarrhythmia [9] . We present here the rationale for amiodarone use in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe COVID-19, based on current evidence. abstract: Amiodarone, one of the most widely prescribed antiarrhythmic drugs to treat both ventricular and supraventricular arrhythmias, has been identified as a candidate drug for use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We present the rationale of using amiodarone in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe coronavirus disease 2019 (COVID-19), based on current evidence. url: https://doi.org/10.1007/s40256-020-00429-7 doi: 10.1007/s40256-020-00429-7 id: cord-102920-z5q3wo7v author: Sang, Eric R. title: Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date: 2020-06-28 words: 6437.0 sentences: 316.0 pages: flesch: 44.0 cache: ./cache/cord-102920-z5q3wo7v.txt txt: ./txt/cord-102920-z5q3wo7v.txt summary: Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Along with showing a broad susceptibility potential across mammalian species based on structural analysis [26] [27] [28] , our results further reveal that domestic animals including dogs, pigs, cattle and goats may evolve previously unexamined immunogenetic diversity to restrict SARS-CoV2 infections. In addition to structural analysis of simulated S-RBD-ACE2 interaction, we propose that several immunogenetic factors, including the evolution of S-binding-void ACE2 isoforms in some domestic animals, the species-specific IFN system, and epigenetic regulation of IFN-stimulated property of host ACE2 genes, contribute to the viral susceptibility and the development of COVID-19-like symptoms in certain animal species [15, 38, 39, 49] . abstract: The current new coronavirus disease (COVID-19) has caused globally near 0.4/6 million confirmed deaths/infected cases across more than 200 countries. As the etiological coronavirus (a.k.a. SARS-CoV2) may putatively have a bat origin, our understanding about its intermediate reservoir between bats and humans, especially its tropism in wild and domestic animals, are mostly unknown. This constitutes major concerns in public health for the current pandemics and potential zoonosis. Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. Through integration of key immunogenetic factors, including the existence of S-binding-void ACE2 isoforms and the disparity of ACE2 expression upon early innate immune response, we further refine the SARS-CoV2 susceptibility prediction to fit recent experimental validation. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Thus, we propose that domestic animals may be unlikely to play a role as amplifying hosts unless the virus has further species-specific adaptation. These findings may relieve relevant public concerns regarding COVID-19-like risk in domestic animals, highlight virus-host coevolution, and evoke disease intervention through targeting ACE2 molecular diversity and interferon optimization. url: https://doi.org/10.1101/2020.06.27.174961 doi: 10.1101/2020.06.27.174961 id: cord-265697-bbvlowyo author: Sang, Eric R. title: Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date: 2020-08-31 words: 7298.0 sentences: 333.0 pages: flesch: 46.0 cache: ./cache/cord-265697-bbvlowyo.txt txt: ./txt/cord-265697-bbvlowyo.txt summary: Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. (C) We also detected several short ACE2 isoforms (underlined) in the domestic animals including dog, pig, goat and cattle, which have an N-terminal truncation spanning 10-13 key residues in the contacting network to S-RBD but keeping the enzyme active sites (indicated by Yellow triangles), thus resulting in little engagement by the viral S protein and predicting an unexpected evolutionary advantage for relieving potential COVID-19 risk caused by the viral engagement and functional distortion on the classical long ACE2 isoforms in these animal species. abstract: The current new coronavirus disease (COVID-19) has caused globally near 0.4/6 million confirmed deaths/infected cases across more than 200 countries. As the etiological coronavirus (a.k.a. SARS-CoV2) may putatively have a bat origin, our understanding about its intermediate reservoir between bats and humans, especially its tropism in wild and domestic animals are mostly unknown. This constitutes major concerns in public health for the current pandemics and potential zoonosis. Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. Through integration of key immunogenetic factors, including the existence of S-binding-void ACE2 isoforms and the disparity of ACE2 expression upon early innate immune response, we further refine the SARS-CoV2 susceptibility prediction to fit recent experimental validation. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Thus, we propose that domestic animals may be unlikely to play a role as amplifying hosts unless the virus has further species-specific adaptation. Findings may relieve relevant public concerns regarding COVID-19-like risk in domestic animals, highlight virus-host coevolution, and evoke disease intervention through targeting ACE2 molecular diversity and interferon optimization. url: https://www.ncbi.nlm.nih.gov/pubmed/32904785/ doi: 10.1016/j.heliyon.2020.e04818 id: cord-314679-lmfalzni author: Sangith, Nikhil title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions date: 2020-06-24 words: 585.0 sentences: 43.0 pages: flesch: 43.0 cache: ./cache/cord-314679-lmfalzni.txt txt: ./txt/cord-314679-lmfalzni.txt summary: title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. aureus)coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. The role of the fibrinogen-binding motif of N-protein in formation of blood clots and 142 mimicking functions of Efb for pathogen survival in host will be investigated. Staphylococcus aureus secretes coagulase 187 and von Willebrand factor binding protein to modify the coagulation cascade and establish 188 host infections abstract: Novel Coronavirus (SARS CoV-2), the etiological agent for the highly contagious Corona virus disease-2019 (COVID-19) pandemic has threatened global health and economy infecting around 5.8 million people and causing over 359,200 deaths (as of 28(th) May, 2020, https://www.worldometers.info/coronavirus/). The clinical manifestations of infected patients generally range from asymptomatic or mild to severe illness, or even death. The ability of the virus to evade the host immune response have been major reasons for high morbidity and mortality. One of the important clinical observations under conditions of critical illness show increased risk of developing disseminated intravascular coagulation. Molecular mechanisms of how SARS CoV-2 induces such conditions still remain unclear. This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. This is based on an established function of secretory proteins in Staphylococcus aureus (S. aureus)- coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. It is hypothesized that having protein interaction motifs that are homologous to these S. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. However, this hypothesis needs to be tested in vitro. Considering the overwhelming increase in the incidence of SARS CoV-2 infection globally, this information may be useful for further investigation and could help in deducing new therapeutic strategies to combat advanced stages of this disease. url: https://api.elsevier.com/content/article/pii/S0306987720313621 doi: 10.1016/j.mehy.2020.110030 id: cord-263292-qjfe2t9v author: Sansone, A. title: Addressing male sexual and reproductive health in the wake of COVID-19 outbreak date: 2020-07-13 words: 3912.0 sentences: 210.0 pages: flesch: 39.0 cache: ./cache/cord-263292-qjfe2t9v.txt txt: ./txt/cord-263292-qjfe2t9v.txt summary: Despite being a trivial matter for patients in intensive care units (ICUs), erectile dysfunction (ED) is a likely consequence of COVID-19 for survivors, and considering the high transmissibility of the infection and the higher contagion rates among elderly men, a worrying phenomenon for a large part of affected patients. Testicular function in COVID-19 patients requires careful investigation for the unclear association with testosterone deficiency and the possible consequences for reproductive health. However, independently of whether testosterone is a friend or foe for COVID-19, it should be acknowledged that the testis is a target for SARS-CoV-2 and the possibility for long-lasting consequences on the endocrine function exists, even for recovered patients. Drugs such as β-blockers and antihypertensive agents, routinely used in COVID-19 patients, have the potential to impair sexual function [41] ; therefore, both the cardiovascular consequences and their treatment might ease progression from subclinical to a clinically overt ED [42, 43] . abstract: PURPOSE: The COVID-19 pandemic, caused by the SARS-CoV-2, represents an unprecedented challenge for healthcare. COVID-19 features a state of hyperinflammation resulting in a “cytokine storm”, which leads to severe complications, such as the development of micro-thrombosis and disseminated intravascular coagulation (DIC). Despite isolation measures, the number of affected patients is growing daily: as of June 12th, over 7.5 million cases have been confirmed worldwide, with more than 420,000 global deaths. Over 3.5 million patients have recovered from COVID-19; although this number is increasing by the day, great attention should be directed towards the possible long-term outcomes of the disease. Despite being a trivial matter for patients in intensive care units (ICUs), erectile dysfunction (ED) is a likely consequence of COVID-19 for survivors, and considering the high transmissibility of the infection and the higher contagion rates among elderly men, a worrying phenomenon for a large part of affected patients. METHODS: A literature research on the possible mechanisms involved in the development of ED in COVID-19 survivors was performed. RESULTS: Endothelial dysfunction, subclinical hypogonadism, psychological distress and impaired pulmonary hemodynamics all contribute to the potential onset of ED. Additionally, COVID-19 might exacerbate cardiovascular conditions; therefore, further increasing the risk of ED. Testicular function in COVID-19 patients requires careful investigation for the unclear association with testosterone deficiency and the possible consequences for reproductive health. Treatment with phosphodiesterase-5 (PDE5) inhibitors might be beneficial for both COVID-19 and ED. CONCLUSION: COVID-19 survivors might develop sexual and reproductive health issues. Andrological assessment and tailored treatments should be considered in the follow-up. url: https://doi.org/10.1007/s40618-020-01350-1 doi: 10.1007/s40618-020-01350-1 id: cord-350235-yoy3hj3j author: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 words: 2988.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-350235-yoy3hj3j.txt txt: ./txt/cord-350235-yoy3hj3j.txt summary: Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. abstract: What is COVID‐19? What are the causes, parameters, and effects of this disease? What are the short‐ and long‐term prospects? Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32259394/ doi: 10.15252/emmm.202012463 id: cord-323424-86wh4u6l author: Santos, M. M. title: Survival and predictors of deaths of patients hospitalised due to COVID-19 from a retrospective and multicentre cohort study in Brazil date: 2020-09-07 words: 3746.0 sentences: 163.0 pages: flesch: 47.0 cache: ./cache/cord-323424-86wh4u6l.txt txt: ./txt/cord-323424-86wh4u6l.txt summary: The co-variables used to compare survival curves were socioeconomic factors (age, sex, race, education and area of residence), clinical signs and symptoms (fever, cough, sore throat, diarrhoea and vomiting), hospital variables (influenza-like outbreak, hospital-acquired infection, dyspnoea, respiratory distress, O 2 saturation <95%, intensive care unit (ICU) admission, ICU length of stay and X-ray result), chronic disease (heart disease, haematology, Down''s syndrome, liver disease, asthma, diabetes mellitus, neurological disease, pneumopathy, immunodepression, kidney disease and body mass index (BMI)), if the patient has had a flu vaccine, use of antiviral against influenza and what is the type of such antiviral. This multicentre retrospective cohort study of patients hospitalised with COVID-19 found important differences in survival times, as well as risk factors or protection for the death of patients in Brazilian hospitals. abstract: This study aimed to analyse the survival of patients admitted to Brazilian hospitals due to the COVID-19 and estimate prognostic factors. This is a retrospective, multicentre cohort study, based on data from 46 285 hospitalisations for COVID-19 in Brazil. Survival functions were calculated using the Kaplan–Meier's method. The log-rank test compared the survival functions for each variable and from that, hazard ratios (HRs) were calculated, and the proportional hazard model was used in Cox multiple regression. The smallest survival curves were the ones for patients at the age of 68 years or more, black/mixed race, illiterate, living in the countryside, dyspnoea, respiratory distress, influenza-like outbreak, O(2) saturation <95%, X-ray change, length of stay in the intensive care unit (ICU), invasive ventilatory support, previous heart disease, pneumopathy, diabetes, Down's syndrome, neurological disease and kidney disease. Better survival was observed in the influenza-like outbreak and in an asthmatic patient. The multiple model for increased risk of death when they were admitted to the ICU HR 1.28, diabetes HR 1.17, neurological disease HR 1.34, kidney disease HR 1.11, heart disease HR 1.14, black or mixed race of HR 1.50, asthma HR 0.71 and pneumopathy HR 1.12. This reinforces the importance of socio-demographic and clinical factors as a prognosis for death. url: https://www.ncbi.nlm.nih.gov/pubmed/32892789/ doi: 10.1017/s0950268820002034 id: cord-291363-re45w37d author: Sanville, Bradley title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date: 2020-03-30 words: 1308.0 sentences: 86.0 pages: flesch: 53.0 cache: ./cache/cord-291363-re45w37d.txt txt: ./txt/cord-291363-re45w37d.txt summary: title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32227197/ doi: 10.1093/cid/ciaa347 id: cord-269202-re2djjrc author: Sapino, Anna title: The autopsy debate during the COVID-19 emergency: the Italian experience date: 2020-04-29 words: 1140.0 sentences: 63.0 pages: flesch: 48.0 cache: ./cache/cord-269202-re2djjrc.txt txt: ./txt/cord-269202-re2djjrc.txt summary: "in patients dying with SARS-CoV-2 infection, the autopsies can confirm laboratory and radiological findings and can contribute to an accurate diagnosis and to a better understanding of mechanisms of the disease." In the meantime, the SIAPC Board accepted to collaborate with the Scientific Society of Hospital Forensic Medicine of the National Health System (COMLAS) to produce a joint document, which was available on the SIAPEC web site on March 22 [2] . In addition, in cases of autopsies without apparent SARS-CoV-2 infection, we recommend (i) to discuss with the clinicians the reason why the post-mortem examination is requested; (ii) and if available, to perform nasal-oropharyngeal swabs on corpses This article is part of the Topical Collection on Quality in Pathology * Mattia Barbareschi mattia.barbareschi@apss.tn.it within 2 h of death to assess the presence of SARS-CoV-2 infection to implement the safety measures [3] . abstract: nan url: https://doi.org/10.1007/s00428-020-02828-2 doi: 10.1007/s00428-020-02828-2 id: cord-317707-r0q7ipa6 author: Saracco, Margherita title: Carrying on with Liver Transplantation during the COVID-19 emergency: Report from Piedmont Region date: 2020-08-07 words: 2843.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-317707-r0q7ipa6.txt txt: ./txt/cord-317707-r0q7ipa6.txt summary: We aimed to analyze the number of LT performed between February 24 th , 2020 and April 17 th , 2020 with the same period of time in 2019, in our high-volume transplant Center (median 150 LT/year). Furthermore, among the 5 intensive care units of our hospital, the one dedicated to transplants was maintained COVID-free, by testing each transplant recipient in advance with SARS-CoV-2 RNA in NPS or BAL, starting from the 22 nd of March. Between February 24 th , 2020 and April 17 th , 2020, among 22 admissions in our 7-bed sub-intensive liver unit, a 40-year-old woman, who was listed during hospitalization, developed fever during hospitalization and tested positive for SARS-CoV-2 RNA in NPSs. Immediately transferred to a COVID unit, she came back to our unit after 7 days and 2 negative SARS-CoV-2 RNA in NPS and underwent LT the day after readmission to our unit. Despite all our efforts to maintain a transplant COVID-free pathway, two transplant patients, one before and one after LT were tested SARS-CoV-2 virus positive during hospitalization and both were safely discharged home. abstract: BACKGROUND: The COVID-19 pandemic is an emergency worldwide. In Italy, Liver transplant activity was carried on, but despite all efforts, a 25% reduction of procured organs has already been observed during the first 4 weeks of the outbreak. AIMS: To analyze if our strategy and organization of LT pathway during the first two months of the COVID-19 emergency succeeded in keeping a high level of LT activity, comparing the number of LT in the first two months with the same period of time in 2019. METHODS: We compared the Liver transplants performed in our Center between February 24(th) and April 17(th), 2020 with Liver transplants performed in the same period in 2019. RESULTS: In 2020, 21 patients underwent Liver transplantation from deceased donors, exactly as the year before, without statistically significant difference. All patients survived in both groups, and the rate of early graft dysfunction was 24% in 2020 and 33% in 2019. In 2020 Median MELD was higher (17vs 13). We were able to perform 3 multiorgan transplants and one acute liver failure. Nobody died on waiting list. The performance of our Center, despite the maxi-emergency situation, was steady and this was the result of a tremendous team working within the hospital and in our Region. CONCLUSIONS: Team working allowed our Center to maintain its activity level, taking care of patients before and after Liver transplantation. Sharing our experience, we hope to be helpful to other Centers that are facing the pandemic and, if another pandemic comes, to be more prepared to deal with it. url: https://api.elsevier.com/content/article/pii/S2210740120302072 doi: 10.1016/j.clinre.2020.07.017 id: cord-029167-bq6ogxyq author: Sarada, B. V. title: Fight Against COVID-19: ARCI’s Technologies for Disinfection date: 2020-07-14 words: 2831.0 sentences: 137.0 pages: flesch: 47.0 cache: ./cache/cord-029167-bq6ogxyq.txt txt: ./txt/cord-029167-bq6ogxyq.txt summary: In this context, ARCI has quickly made efforts to develop disinfection systems including a UVC-based disinfection trolley, honeycomb air heater and a fogging chamber using UVC germicidal lamps, dry heat sterilization and HOCl-based chemical disinfectant to provide rapid and effective inactivation of microorganisms causing the pandemic. Though the virus survives as aerosols and on environmental surfaces for various durations of time, it can easily be inactivated by several types of physical and chemical disinfection methods (Mackenzie 2020) including UVC disinfection (Malayeri et al. Physical, dry heat and chemical disinfection methods have been developed by using UVC lamps, honeycomb air heater and HOCl fogging system, respectively. (MIL), has co-developed a UVC disinfection trolley to fight against COVID-19 by a simple physical process where rapid cleaning is possible within few minutes especially in hospital settings avoiding the use of harsh chemicals. abstract: COVID-19 (SARS-CoV-2) is causing a huge concern to the global population due to its highly contagious properties. The SARS-CoV-2 is a new variant in the coronavirus family. The world is focussing on several methods to battle against this novel corona virus, including control of its spread. In this context, ARCI has quickly made efforts to develop disinfection systems including a UVC-based disinfection trolley, honeycomb air heater and a fogging chamber using UVC germicidal lamps, dry heat sterilization and HOCl-based chemical disinfectant to provide rapid and effective inactivation of microorganisms causing the pandemic. These systems have been successfully deployed at different hospitals for their validation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358699/ doi: 10.1007/s41403-020-00153-3 id: cord-268795-tjmx6msm author: Sardar, Rahila title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date: 2020-03-21 words: 2257.0 sentences: 128.0 pages: flesch: 47.0 cache: ./cache/cord-268795-tjmx6msm.txt txt: ./txt/cord-268795-tjmx6msm.txt summary: title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Our analysis shows unique host-miRNAs targeting SARS-CoV2 virus genes. CELLO2GO (7)server was used to infer biological function for each protein of SARS-CoV2 genome with their localization prediction. Assembled SARS-CoV2 genomes sequences in FASTA format from India, USA, China, Italy and Nepal used for coronavirus typing tool analysis. For the phylogenetic analysis, we compared the sequences of 6 SARS-CoV2 isolates from different countries namely, Wuhan, India, Italy, USA and Nepal along with other corona virus species ( Figure 1 ). abstract: The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes url: https://doi.org/10.1101/2020.03.21.001586 doi: 10.1101/2020.03.21.001586 id: cord-354349-hbk2p6ej author: Sardar, Sundus title: COVID-19 and Plasmodium vivax malaria co-infection date: 2020-06-20 words: 1722.0 sentences: 118.0 pages: flesch: 49.0 cache: ./cache/cord-354349-hbk2p6ej.txt txt: ./txt/cord-354349-hbk2p6ej.txt summary: With its variety of clinical manifestations including, but not limited to, fever, cough, diarrhea, vomiting, headache, myalgia and fatigue, it may be challenging to distinguish COVID-19 from a spectrum of diseases with similar presentations, such as malaria, especially in endemic areas. The coronavirus infection 2019 (COVID-19), which is caused by SARS-CoV-2, emerged in Wuhan, China in December 2019 and has since reached pandemic proportions affecting more than 8 million cases worldwide with total deaths exceeding 400,000 [1] . SARS-CoV-2, COVID-19, malaria, Plasmodium vivax, co-infection, artesunate In this case, artesunate and artemether were initiated as the treatment regimen; whether these agents offered protective effects from respiratory deterioration or multi-organ involvement despite SARS-CoV-2 infection is unclear and should be further explored. Our case highlights the importance of identifying possible underlying secondary infections in concurrence with SARS-CoV-2, which may be otherwise overlooked amidst the challenges of the current unprecedented COVID-19 pandemic. abstract: The ongoing outbreak of COVID-19 poses an unprecedented global health challenge. With its variety of clinical manifestations including, but not limited to, fever, cough, diarrhea, vomiting, headache, myalgia and fatigue, it may be challenging to distinguish COVID-19 from a spectrum of diseases with similar presentations, such as malaria, especially in endemic areas. Risk of concomitant infections also remains a concern owing to overburdening of healthcare services and possible scarcity of resources. We present the first reported case of confirmed COVID and malaria co-infection. In this case, we emphasize the need for vigilance from frontline clinicians for timely diagnosis and appropriate clinical management of potential co-infections in the COVID era. url: https://www.sciencedirect.com/science/article/pii/S2214250920301876?v=s5 doi: 10.1016/j.idcr.2020.e00879 id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 words: 4869.0 sentences: 230.0 pages: flesch: 41.0 cache: ./cache/cord-292416-3hhi4wps.txt txt: ./txt/cord-292416-3hhi4wps.txt summary: Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. abstract: At the time of writing, in July 2020, the recently emerging SARS-CoV-2 pandemic has attracted major attention to viral diseases, in particular coronaviruses. In spite of alarming molecular evidence, documentation of interspecies transmission in livestock, and the emergence of two new and relatively virulent human coronaviruses within a 10-year period, many gaps remain in the study and understanding of this family of viruses. This paper provides an overview of our knowledge regarding the coronavirus family, while highlighting their key biological properties in the context of our overall understanding of viral diseases. url: https://doi.org/10.5041/rmmj.10414 doi: 10.5041/rmmj.10414 id: cord-267666-i7uuf3ck author: Sarkar, Bishajit title: Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach date: 2020-11-11 words: 1873.0 sentences: 129.0 pages: flesch: 50.0 cache: ./cache/cord-267666-i7uuf3ck.txt txt: ./txt/cord-267666-i7uuf3ck.txt summary: Therefore, in this study, immunoinformatics methods were exploited to design a novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. Thereafter, several in silico validations i.e., the molecular docking, molecular dynamics simulation (including the RMSF and RMSD studies), and immune simulation studies were also performed which predicted that the designed vaccine should be quite safe, effective, and stable within the biological environment. The MHC class-I and class-II epitopes were predicted from the target protein sequences for 503 constructing the vaccine. Exploring Leishmania secretory proteins 1232 to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach Immunoinformatics approaches 1236 to explore Helicobacter Pylori proteome (Virulence Factors) to design B and T cell multi-epitope 1237 subunit vaccine. Immunoinformatics-guided designing of 1405 epitope-based subunit vaccine against the SARS Coronavirus-2 (SARS-CoV-2) abstract: As the number of infections and deaths caused by the recent COVID-19 pandemic is increasing dramatically day-by-day, scientists are rushing towards developing possible countermeasures to fight the deadly virus, SARS-CoV-2. Although many efforts have already been put forward for developing potential vaccines, however, most of them are proved to possess negative consequences. Therefore, in this study, immunoinformatics methods were exploited to design a novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. The highly antigenic, non-allergenic, non-toxic, non-human homolog, and 100% conserved (across other isolates from different regions of the world) epitopes were used for constructing the vaccine. In total, fourteen CTL epitopes and eighteen HTL epitopes were used to construct the vaccine. Thereafter, several in silico validations i.e., the molecular docking, molecular dynamics simulation (including the RMSF and RMSD studies), and immune simulation studies were also performed which predicted that the designed vaccine should be quite safe, effective, and stable within the biological environment. Finally, in silico cloning and codon adaptation studies were also conducted to design an effective mass production strategy of the vaccine. However, more in vitro and in vivo studies are required on the predicted vaccine to finally validate its safety and efficacy. url: https://api.elsevier.com/content/article/pii/S2352914820306298 doi: 10.1016/j.imu.2020.100478 id: cord-102833-hh4641o0 author: Sarkis-Onofre, Rafael title: Decontamination of N95 respirators against SARS-CoV-2: a scoping review date: 2020-11-13 words: 5948.0 sentences: 343.0 pages: flesch: 38.0 cache: ./cache/cord-102833-hh4641o0.txt txt: ./txt/cord-102833-hh4641o0.txt summary: These masks are intended for single use and, based on the manufacturer''s instructions, they are heat sensitive and not designed to be sterilized; however, due to their high costs and limited availability [6, 13] , different methods to decontaminate N95 [5, 13, [15] [16] [17] [18] [19] respirators have been discussed to allow multiple usages. (2020) performed an in vitro study and compared the use of a high-level decontamination cabinet that generates aerosolized peracetic acid and hydrogen peroxide with ultraviolet C light and dry heat at 70 °C for 30 minutes. Decontamination and Reuse of N95 Respirators with Hydrogen Peroxide Vapor to Address Worldwide Personal Protective Equipment Shortages During the SARS-CoV-2 (COVID-19) Pandemic Decontamination and reuse of surgical masks and N95 filtering facepiece respirators during COVID-19 pandemic: a systematic review Decontamination of face masks and filtering facepiece respirators via ultraviolet germicidal irradiation, hydrogen peroxide vaporisation, and use of dry heat inactivates an infectious SARS-CoV-2 surrogate virus abstract: Objectives This scoping review aimed to map and compile the available evidence regarding the effectiveness of decontaminating N95 respirators against the novel coronavirus (SARS-CoV-2). Data We selected studies written in English assessing or discussing the decontamination strategies of N95 respirators against SARS-CoV-2. Two independent researchers performed the search and study screening. A descriptive analysis was carried out considering the study design of the included studies. Sources PubMed, SCOPUS, and Preprint platforms (bioRxiv and medRxiv). Study selection We included 55 reports from PubMed and SCOPUS. Nine articles were letters to the editors, 21 were in vitro studies, 16 were literature reviews, and 9 were classified as other study designs. We included 37 preprints. Two articles were letters to the editors, 24 were in vitro studies, 3 were literature reviews, and 8 were classified as other study designs. In general, vaporized hydrogen peroxide and ultraviolet irradiation were the strategies most cited and most promising. However, there is a lack of evidence and consensus related to the best method of N95 respirator decontamination. Conclusion The evidence regarding decontamination strategies of N95 respirators against SARS-CoV-2 remains scarce. Vaporized hydrogen peroxide and ultraviolet irradiation seem to be the current standard for N95 respirator decontamination. Clinical significance Vaporized hydrogen peroxide and ultraviolet irradiation appear to be the most promising methods for N95 respirator decontamination. url: https://api.elsevier.com/content/article/pii/S0300571220302827 doi: 10.1016/j.jdent.2020.103534 id: cord-262149-qrjprsv5 author: Sarode, Gargi S. title: Clinical status determines the efficacy of salivary and nasopharyngeal samples for detection of SARS-CoV-2 date: 2020-10-12 words: 824.0 sentences: 67.0 pages: flesch: 58.0 cache: ./cache/cord-262149-qrjprsv5.txt txt: ./txt/cord-262149-qrjprsv5.txt summary: To draw a meaningful conclusion in this regard, the most important study design would be a comparative cross-sectional analysis of salivary and nasopharyngeal samples (NPSs) in the detection of SARS-CoV-2 RNA with a cycle threshold value. (Table 1 ) All the studies projected saliva as potential sampling material for the detection and diagnosis of SARS-CoV-2 RNA using RT-PCR. In asymptomatic cases, the sensitivity and detection rate was more in salivary samples as compared to NPS [2, 7] . On the contrary, in asymptomatic cases, NPS could not be a representative sample (probably due to absent or limited viral localization) for the detection of SARS-CoV-2. Looking at this discriminative trend, prescription of saliva samples for asymptomatic cases and NPS for symptomatic cases would be a valuable recommendation subject to validation in future randomized prospective studies. A direct comparison of enhanced saliva to nasopharyngeal swab for the detection of SARS-CoV-2 in symptomatic patients abstract: nan url: https://doi.org/10.1007/s00784-020-03630-9 doi: 10.1007/s00784-020-03630-9 id: cord-296392-2u9mz6d3 author: Sarıgül, Figen title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 words: 3891.0 sentences: 209.0 pages: flesch: 51.0 cache: ./cache/cord-296392-2u9mz6d3.txt txt: ./txt/cord-296392-2u9mz6d3.txt summary: title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic This value being higher than 0.73 coefficient obtained through comparison of RdRps of the two kits only, showed that inclusion of a secondary biomarker by Diagnovital improved the correlation of different kits. In this study, we investigated the compatibility between the two different SARS-CoV-2 PCR kits produced in Turkey during the COVID-19 pandemic. Nevertheless, the strong correlation of the two kit results suggested that two different RNA targeting gene assays were appropriate as suggested by WHO in the diagnosis of COVID-19 disease [20] . showed that similar results were found; the PCR kit with two different genes of the SARS-CoV-2 had a higher yield than the other two kits performing one gene analysis [21] . abstract: AIM: In the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse transcriptase-PCR (RT-PCR) technique is often used. We evaluated the compatibility of SARS-CoV-2 RT-PCR kits containing different gene targets during the pandemic. MATERIALS & METHODS: Samples were tested by Bio-Speddy(®) (RdRp gene) and Diagnovital(®) (RdRp + E genes). The correlation between two assays were determined by Deming regression analysis and chi-square analyses. RESULTS: Diagnovital PCR kit showed amplification in a narrow Ct range and conveniently sharper exponential amplification curves than Bio-Speedy PCR kit. While the correlation between the findings of the two kits was apparent even with single gene target, this correlation increased when a secondary biomarker was added to the correlation calculations. CONCLUSION: We have observed high correlation between different PCR kits, however, using different PCR kits during the pandemic may provide a more accurate diagnosis of SARS-CoV-2, since despite correlation there are a number of patients showing contradicting diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/33005213/ doi: 10.2217/fvl-2020-0169 id: cord-323839-a4oejky0 author: Sasaki, Michihito title: SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date: 2020-08-28 words: 2100.0 sentences: 128.0 pages: flesch: 63.0 cache: ./cache/cord-323839-a4oejky0.txt txt: ./txt/cord-323839-a4oejky0.txt summary: These results indicated that S gene mutants are resistant to the 1 5 9 treatment with TMPRRSS2 inhibitors, but are sensitive to antivirals that target post entry In an effort to understand the selection mechanisms underlying the generation of these 1 6 4 mutant variants, we estimated the frequency of S gene mutants in virus population of 1 6 5 SARS-CoV-2 that had undergone serial passage in cultured cells. In contrast, nucleotide sequence 1 7 2 deletions around the S1/S2 cleavage site corresponding to del1 and del2 mutants were 1 7 3 observed in all three biological replicates of SARS-CoV-2 populations passaged in Vero 1 7 4 cells (Fig. 5a) . Moreover, we must be very objective when interpreting the results 2 3 0 from studies using Vero-passaged virus, especially those focused on S protein cleavage, Cells were infected with either WT or S mutants of SARS-CoV-2 at an MOI of 1. abstract: The spike (S) protein of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) binds to a host cell receptor which facilitates viral entry. A polybasic motif detected at the cleavage site of the S protein has been shown to broaden the cell tropism and transmissibility of the virus. Here we examine the properties of SARS-CoV-2 variants with mutations at the S protein cleavage site that undergo inefficient proteolytic cleavage. Virus variants with S gene mutations generated smaller plaques and exhibited a more limited range of cell tropism compared to the wild-type strain. These alterations were shown to result from their inability to utilize the entry pathway involving direct fusion mediated by the host type II transmembrane serine protease, TMPRSS2. Notably, viruses with S gene mutations emerged rapidly and became the dominant SARS-CoV-2 variants in TMPRSS2-deficient cells including Vero cells. Our study demonstrated that the S protein polybasic cleavage motif is a critical factor underlying SARS-CoV-2 entry and cell tropism. As such, researchers should be alert to the possibility of de novo S gene mutations emerging in tissue-culture propagated virus strains. url: https://doi.org/10.1101/2020.08.28.271163 doi: 10.1101/2020.08.28.271163 id: cord-332207-dmxbk7ad author: Sastry, Sangeeta R. title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence date: 2020-07-23 words: 1202.0 sentences: 78.0 pages: flesch: 41.0 cache: ./cache/cord-332207-dmxbk7ad.txt txt: ./txt/cord-332207-dmxbk7ad.txt summary: title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence In 2 New York City (NYC) hospitals, 13.7% of asymptomatic pregnant women admitted for delivery tested positive for SARS-CoV-2 virus. 3 Universal screening of healthcare populations may prevent in-hospital transmission of SARS-CoV-2 virus. Upon developing real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) tests in-house with >98% sensitivity, as well as increasing the availability of PPE at our institution, we initiated universal screening of patients on hospital admission using nasopharyngeal swabs to identify and isolate asymptomatic positive patients to prevent in-hospital transmission of SARS-CoV-2. On April 27, 2020, our 1,000-bed academic center instituted universal SARS-CoV-2 testing of patients on hospital admission. Universal screening for the detection of SARS-CoV-2 at our institution revealed that during the study period, the number of asymptomatic persons admitted to the hospital was relatively small. abstract: nan url: https://doi.org/10.1017/ice.2020.358 doi: 10.1017/ice.2020.358 id: cord-342786-dl8vjwfn author: Sattar, Yasar title: COVID-19 Cardiovascular Epidemiology, Cellular Pathogenesis, Clinical Manifestations and Management date: 2020-07-14 words: 5268.0 sentences: 349.0 pages: flesch: 37.0 cache: ./cache/cord-342786-dl8vjwfn.txt txt: ./txt/cord-342786-dl8vjwfn.txt summary: Abstract Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. The infected patients may also present with cardiovascular disease (CVD) like acute coronary syndrome(ACS) and congestive cardiac failure(CHF) [6] . The systemic inflammation in COVID-19 may also dysregulate the post-translational modification of cardiac ion channels resulting in arrhythmia [25, 26] It is also noteworthy that viral proteins of SARS-CoV-2, ORF3 and ORF8, activate NLRP3 inflammasomes which inturn promotes atrial fibrillation [27, 28] . abstract: Abstract Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. These cardiovascular effects are worse in patients who have pre-existing cardiac conditions such as coronary artery disease, hypertension, diabetes mellitus, and coagulation abnormalities. Other predisposing risk factors include advanced age, immunocompromised state, and underlying systemic inflammatory conditions. Here we review the cellular pathophysiology, clinical manifestations and treatment modalities of the cardiac manifestations seen in patients with COVID-19. url: https://api.elsevier.com/content/article/pii/S2352906720302876 doi: 10.1016/j.ijcha.2020.100589 id: cord-335958-dtvlo0kz author: Satyam, Rohit title: Deciphering the SSR incidences across viral members of Coronaviridae family date: 2020-09-21 words: 4611.0 sentences: 274.0 pages: flesch: 55.0 cache: ./cache/cord-335958-dtvlo0kz.txt txt: ./txt/cord-335958-dtvlo0kz.txt summary: Thus, the aims of the current study were 1) to analyze various facets of the distribution and dynamics of SSRs in the genomes of Coronaviridae members, 2) to identify patterns of SSR incidences across genomes, if any i.e the underrepresentation/overrepresentation of specific repeat motif classes, 3) the preferential genomic localization of SSRs & 4) to investigate if SSRs serves as mutation hotspots in SARS-CoV-2, a novel SARS strain causing COVID-19 outbreak. Additionally, the attributes of SSRs across genomes under study were quite similar in terms of length (preferentially found to be 12-13 nucleotides long with polyA repeats of varying lengths), GC composition, abundance (SSR frequency didn''t exceed 2 irrespective of genome size) and localization. The BED files (eg.sequence_perf_default.tsv) so produced by PERF comprise of SSRs genomic coordinates (Column 1-3) followed by repeat class, repeat Length, repeat Strand, motif Number & actual repeat (more details: https://github.com/RKMlab/perf) and were used for the downstream analysis. abstract: Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae members. We successfully identified 919 SSRs with length≥12 bp across 55 reference genomes majority of which (838 S SRs) were found abundant in genic regions. The in-silico analysis further identified the preferential abundance of hexameric SSRs than any other size-based motif class. Our analysis shows that the genome size and GC content of the genome had a weak influence on SSR frequency and density. However, we find a positive correlation of SSRs GC content with genomic GC content. We also report relatively low abundances of all theoretically possible 501 repeat motif classes in all the genomes of Coronaviridae. The majority of SSRs were AT-rich. Overall, we see an underrepresentation of SSRs across the genomes of Coronaviridae. Besides, our integrative study highlights the presence of SSRs in ORF1ab (nsp3, nsp4, nsp5A_3CLpro and nsp5B_3CLpro, nsp6, nsp10, nsp12, nsp13, & nsp15 domains), S, ORF3a, ORF7a, N & 3′ UTR regions of SARS-CoV-2 and harbours multiple mutations (3′UTR and ORF1ab SSRs serving as major mutational hotspots). This indicates the genic SSRs are under selection pressure against mutations that might alter the reading frame and at the same time responsible for rapid protein evolution. Our preliminary results indicate the significance of the limited repertoire of SSRs in the genomes of Coronaviridae. url: https://doi.org/10.1016/j.cbi.2020.109226 doi: 10.1016/j.cbi.2020.109226 id: cord-275438-drywzvx8 author: Satış, Hasan title: Prognostic value of interleukin-18 and its association with other inflammatory markers and disease severity in COVID-19 date: 2020-09-29 words: 3539.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-275438-drywzvx8.txt txt: ./txt/cord-275438-drywzvx8.txt summary: Serum IL-18 levels were remarkably higher in COVID-19 patients compared to healthy subjects with being highest in severe pneumonia group (p < 0.001). According to the disease course, COVID-19 patients may be roughly divided into two groups; asymptomatic or mild cases that usually recover and severe cases that develop multi organ failure, primarily respiratory failure, requiring intensive care unit (ICU) admission [5, 6] . In this study, we found that both IL-6 and serum IL-18 concentrations are remarkably increased in patients with COVID-19 and correlated with other inflammatory markers and disease severity. There are differences in cytokine production among COVID-19 patients, such as men are more susceptible to SARS-CoV-2 infection than women and children, in whom it could present as Kawasaki disease [29, 30] , as well as serum cytokine levels tend to be higher in men explaining their worse prognosis [29] . abstract: BACKGROUND: The effectual immune response is crucial to defeat viral infections. However, exuberant immune response with features of macrophage activation syndrome (MAS) lead detrimental consequences in COVID-19 patients. Interleukin (IL)-18 is one of the leading cytokines in MAS which has not been studied in COVID-19. OBJECTIVE: To investigate the association of IL-18 with the other inflammatory markers and disease severity in COVID-19 for predicting disease prognosis. METHODS: Patients with COVID-19 who had confirmed diagnosis with SARS-CoV-2 nucleic acid RT-PCR were enrolled into the study. Data on demographic and clinical characteristics, and laboratory values of CRP, ferritin, d-dimer and procalcitonin were measured on admission. Patients were followed up prospectively with a standardized approach until hospital discharge or death. Individuals were classified as asymptomatic, mild and severe pneumonia according to their clinical, laboratory and radiological characteristics. Worse outcome was defined as requirement of intensive care unit (ICU) admission or death. Blood samples were collected at enrollment and serum levels of IL-6 and IL-18 were determined by ELISA. Association between IL-18 and other inflammatory markers and prognosis were analyzed. RESULTS: There were 58 COVID-19 patients (50% male) with a median age of 43 (min 22-max 81) years. Twenty age and sex matched healthy subjects were served as control group. The study population was divided into three groups according to disease severity: asymptomatic (n = 20), mild pneumonia group (n = 27) and a severe group (n = 11). During follow up nine (15.5%) patients required ICU admission and three of them were died eventually. Serum IL-18 were correlated with other inflammatory markers and biochemical markers of organ injury; creatinine, liver enzymes and troponin. Serum IL-18 levels were remarkably higher in COVID-19 patients compared to healthy subjects with being highest in severe pneumonia group (p < 0.001). IL-18 serum concentrations were almost four-fold higher in patients with worse outcome compared to good outcome (p < 0.001). Serum IL-18 above the cut off value of 576 pg/mL on admission was associated with 11.7 fold increased risk of ICU admission. CONCLUSIONS: The serum concentrations of IL-18 correlate with other inflammatory markers and reflect disease severity. Results of the present study shed light on role of IL-18 on COVID-19 pathogenesis and might provide an evidence for the clinical trials on IL-18 antagonists for the treatment of severe COVID-19 patients. url: https://doi.org/10.1016/j.cyto.2020.155302 doi: 10.1016/j.cyto.2020.155302 id: cord-253472-3s142p6u author: Saurabh, Suman title: Author’s reply to correspondence regarding the article ‘Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals’ date: 2020-09-18 words: 735.0 sentences: 60.0 pages: flesch: 57.0 cache: ./cache/cord-253472-3s142p6u.txt txt: ./txt/cord-253472-3s142p6u.txt summary: title: Author''s reply to correspondence regarding the article ''Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals'' 1 This is since 95% SARS-CoV-2 infected individuals (including both symptomatics and asymptomatics) were found to have virus persistence of up to 20.92 days. 1 Further, they go on to state that ''as per test-based strategy for asymptomatic patients, two respiratory specimens (≥ 24 hours apart) are required to be negative, irrespective of initial date of COVID-19 detection''. Test-based discharge is not practicable with an overwhelming number of SARS-CoV-2 infected individuals and a large proportion of them undergoing home isolation. Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32946582/ doi: 10.1093/qjmed/hcaa269 id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 words: 6361.0 sentences: 313.0 pages: flesch: 48.0 cache: ./cache/cord-015376-z739ifu5.txt txt: ./txt/cord-015376-z739ifu5.txt summary: These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. abstract: Coronavirus replication offers several attractive targets for chemotherapy. These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. Lessons should be learnt from AIDS research for choosing the best strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103690/ doi: 10.1517/13543776.16.9.1269 id: cord-282384-qbcqbhk4 author: Savastano, Alfonso title: Peripapillary Retinal Vascular Involvement in Early Post-COVID-19 Patients date: 2020-09-08 words: 3740.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-282384-qbcqbhk4.txt txt: ./txt/cord-282384-qbcqbhk4.txt summary: Furthermore, we performed an additional analysis within the post-COVID-19 group correlating the primary outcome measures with the other examined variables to detect potential risk factors for RPCP impairment in post SARS-CoV-2 patients. Spearman''s Test revealed a statistically significant linear correlation between RNFL average thickness and both RPCP perfusion density (p < 0.001) ( Figure 3 ) and RPCP flow index (p < 0.001) (Figure 4) within the post-COVID-19 group. Our study examined this aspect outlining the correlation of the RPCP perfusion density and RPCP flow index with the RNFL average thickness also in early post-COVID-19 patients. In this regard, it is interesting to notice that patients in the post-COVID-19 group showed a lower mean age, a lower prevalence of diabetes and systemic arterial hypertension, and a higher prevalence of females (typically affected by milder manifestations of the disease) compared to the reported SARS-CoV-2 epidemiologic data [38] . abstract: The ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2′s) to cause multi-organ ischemia and coronavirus-induced posterior segment eye diseases in mammals gave concern about potential sight-threatening ischemia in post coronavirus disease 2019 patients. The radial peripapillary capillary plexus (RPCP) is a sensitive target due to the important role in the vascular supply of the peripapillary retinal nerve fiber layer (RNFL). Eighty patients one month after SARS-CoV-2 infection and 30 healthy patients were selected to undergo structural OCT (optical coherence tomography) and OCTA (optical coherence tomography angiography) exams. Primary outcome was a difference in RPCP perfusion density (RPCP-PD) and RPCP flow index (RPCP-FI). No significant difference was observed in age, sex, intraocular pressure (IOP) and prevalence of myopia. RPCP-PD was lower in post SARS-CoV-2 patients compared to controls. Within the post-COVID-19 group, patients with systemic arterial hypertension had lower RPCP-FI and age was inversely correlated to both RPCP-FI and RPCP-PD. Patients treated with lopinavir + ritonavir or antiplatelet therapy during admission had lower RPCP-FI and RPCP-PD. RNFL average thickness was linearly correlated to RPCP-FI and RPCP-PD within post-COVID-19 group. Future studies will be needed to address the hypothesis of a microvascular retinal impairment in individuals who recovered from SARS-CoV-2 infection. url: https://doi.org/10.3390/jcm9092895 doi: 10.3390/jcm9092895 id: cord-279750-if9vphb2 author: Savić, Dragan title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report date: 2020-07-27 words: 2041.0 sentences: 138.0 pages: flesch: 50.0 cache: ./cache/cord-279750-if9vphb2.txt txt: ./txt/cord-279750-if9vphb2.txt summary: title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report We are presenting a case of a 13-year-old girl with a ruptured cerebral pseudoaneurysm of the left middle cerebral artery (M2 segment) with severe intracerebral hemorrhage as the earliest manifestation of COVID-19 infection. There are rare case reports of adult patients (the youngest was a 31-year-old male, other patients over 60 years old) with COVID-19 infection and ruptured cerebral aneurysm with subarachnoid hemorrhage [1, 16, 19] . In this paper, we present an adolescent girl with COVID-19 infection, who developed an intracerebral hematoma due to cerebral pseudoaneurysm rupture. As far as we know, this is the first reported case of an adolescent with ruptured cerebral pseudoaneurysm as the initial presentation of COVID-19 infection. As a consequence of the infection, a multisystem inflammatory syndrome or the direct damage by the virus has resulted in severe brain hemorrhage attributable to the ruptured pseudoaneurysm. abstract: The clinical manifestations of coronavirus disease 2019 (COVID-19) are non-specific and multi-inflammatory. They vary from mild to severe manifestations that can be life-threatening. The association of SARS-CoV-2 infection and pseudoaneurysm formation or rupture of an already existing aneurysm is still unexplored. Several mechanisms may be involved, including the direct destruction to the artery by the viral infection or through the release of the inflammatory cytokines. We are presenting a case of a 13-year-old girl with a ruptured cerebral pseudoaneurysm of the left middle cerebral artery (M2 segment) with severe intracerebral hemorrhage as the earliest manifestation of COVID-19 infection. url: https://doi.org/10.1007/s00701-020-04510-7 doi: 10.1007/s00701-020-04510-7 id: cord-260077-xf4sofyc author: Sawalha, Amr H. title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients date: 2020-04-08 words: 2598.0 sentences: 143.0 pages: flesch: 45.0 cache: ./cache/cord-260077-xf4sofyc.txt txt: ./txt/cord-260077-xf4sofyc.txt summary: title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Examining whole-genome DNA methylation data generated using an array-based approach, we observe significant hypomethylation in the ACE2 gene in this T cell subset compared to KIR − CD11a low T cells isolated from the same lupus patients (Fig. 1A) . Therefore, it is reasonable to suggest the possibility that the DNA methylation defect in lupus patients, exacerbated by oxidative stress generated from SARS-CoV-2 infection, will further enhance viral entry in lupus patients through epigenetic de-repression of ACE2 and increased ACE2 expression. abstract: Infection caused by SARS-CoV-2 can result in severe respiratory complications and death. Patients with a compromised immune system are expected to be more susceptible to a severe disease course. In this report we suggest that patients with systemic lupus erythematous might be especially prone to severe COVID-19 independent of their immunosuppressed state from lupus treatment. Specifically, we provide evidence in lupus to suggest hypomethylation and overexpression of ACE2, which is located on the X chromosome and encodes a functional receptor for the SARS-CoV-2 spike glycoprotein. Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. In addition, demethylation of interferon-regulated genes, NFκB, and key cytokine genes in lupus patients might exacerbate the immune response to SARS-CoV-2 and increase the likelihood of cytokine storm. These arguments suggest that inherent epigenetic dysregulation in lupus might facilitate viral entry, viremia, and an excessive immune response to SARS-CoV-2. Further, maintaining disease remission in lupus patients is critical to prevent a vicious cycle of demethylation and increased oxidative stress, which will exacerbate susceptibility to SARS-CoV-2 infection during the current pandemic. Epigenetic control of the ACE2 gene might be a target for prevention and therapy in COVID-19. url: https://api.elsevier.com/content/article/pii/S1521661620302394 doi: 10.1016/j.clim.2020.108410 id: cord-024133-zv0ysi8m author: Saxena, Shailendra K. title: Current Insight into the Novel Coronavirus Disease 2019 (COVID-19) date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SARS-CoV-2 is a novel strain of coronavirus that has not been previously identified in humans. It has been declared a pandemic and has infected at least 1,844,683 individuals and caused 117,021 deaths as of 14th April 2020. Transmission among humans occurs via close contact with an infected individual that produces respiratory droplets. Patients have been shown to undergo acute respiratory distress syndrome, which is defined as cytokine storm. The diagnosis relies on detection of nucleic acid, IgG/IgM antibodies, and a chest radiograph of the suspected individuals. The genome of SARS-CoV-2 is similar to other coronaviruses that comprise of ten open reading frames (ORFs). SARS-CoV-2 spike protein exhibits higher affinity to ACE2 receptor as compared with SARS-CoV. Repurposing drugs like favipiravir, remdesivir, chloroquine, and TMPRSS2 protease inhibitors have been shown to be effective for the treatment of COVID-19. Personal protective measures should be followed to prevent SARS-CoV-2 infection. In addition, a clinical trial of SARS-CoV-2 vaccine, mRNA-1273, has been started. This chapter provides a glimpse of advancements made in the area of SARS-CoV-2 infection by proving recent clinical and research trials in the field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189397/ doi: 10.1007/978-981-15-4814-7_1 id: cord-316003-xt59voyt author: Say, Daphne S. title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol date: 2020-03-31 words: 1465.0 sentences: 77.0 pages: flesch: 40.0 cache: ./cache/cord-316003-xt59voyt.txt txt: ./txt/cord-316003-xt59voyt.txt summary: title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol Endoscopists face risk for infection with viruses like SARS-CoV-2, as the aerosol generating nature of endoscopy diffuses respiratory disease that can be spread via an airborne and droplet route. It is unclear how much of the risk was related to community transmission or to breaches in use of personal protective equipment (PPE) during the care of patients with COVID-19. Given initial limitations in the availability of testing for SARS-CoV-2 infection, however, our institution''s current screening algorithm specifies testing only individuals with influenza-like illness and exposure to a patient with known COVID-19. If viral testing for SARS-CoV-2 infection is not available, patient risk stratification before endoscopy may be accomplished based on symptoms and sick contacts. At minimum, those in the pediatric endoscopy suite will require use of gloves, water-resistant gowns, surgical face masks, eye protection, and hair coverings for all endoscopic procedures. abstract: SARS-CoV-2, the novel coronavirus causing coronavirus disease 2019 (COVID-19), is now a global pandemic. Human-to-human transmission has been documented to occur through respiratory secretions, feces, aerosols, and contaminated environmental surfaces. Pediatric patients present a unique challenge as they may have minimal symptoms and yet transmit disease. Endoscopists face risk for infection with viruses like SARS-CoV-2, as the aerosol generating nature of endoscopy diffuses respiratory disease that can be spread via an airborne and droplet route. We describe our center's methodology for pediatric patient risk stratification to facilitate responsible use of endoscopic resources during this crisis. We also describe our recommendations for use of personal protective equipment by endoscopists, with the goal of ensuring the safety of ourselves, our anesthesiology and endoscopy staff, and our patients. url: https://doi.org/10.1097/mpg.0000000000002731 doi: 10.1097/mpg.0000000000002731 id: cord-332179-du1zjupf author: Sayed, Shomoita title: COVID-19 and Diabetes; possible role of polymorphism and rise of telemedicine date: 2020-08-31 words: 4009.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-332179-du1zjupf.txt txt: ./txt/cord-332179-du1zjupf.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is facilitated by interaction with Angiotensin Converting Enzyme-2 (ACE2) and possible polymorphisms in ACE2 can be a determining factor in host-viral protein interaction. Another population study in England showed a 31.4% mortality rate for type 2 diabetes (T2D) patients suffering from COVID-19 infection [17] . So, increased viral entry via increased ACE2 expression and circulating proteases, lymphocytopenia and concurrent increase of inflammatory cytokines can exacerbate SARS-CoV-2 infection in patients with diabetes [23] . Diabetic patients on medication with abovementioned drugs with their elevated ACE2 expression can be susceptible to facilitated SARS-CoV-2 entry, leading to increased chances of disease severity. Whether the polymorphisms have more pronounced effects among diabetic patients with COVID-19 infection should be taken into consideration while exploring the possible role of viral entry in hosts. abstract: BACKGROUND: Diabetes has been found to be one of the leading comorbidities associated with fatality in COVID-19 patients. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is facilitated by interaction with Angiotensin Converting Enzyme-2 (ACE2) and possible polymorphisms in ACE2 can be a determining factor in host-viral protein interaction. A significant shift of healthcare towards ‘Telemedicine’ is also on the rise. In this review, the possible effects of ACE2 polymorphisms on SARS-CoV-2 entry along with the escalation of ‘telemedicine’ is discussed. METHOD: An expansive literature search using keywords: “COVID-19”, “SARS-CoV-2”, “diabetes”, “type 2 diabetes’’, “type 1 diabetes”, “ACE2”, “polymorphism”, “DPP4” and “telemedicine” was conducted on Pubmed and EMBASE till 7(th) August, 2020. RESULT: Possible polymorphisms in ACE2 gene can play a role in influencing the virus entry in host body. Telemedicine can be bring a new revolution for medical sector. CONCLUSION: COVID-19 severity is more heinous among diabetic population. So far, the in-silico studies involving human ACE2-viral Spike (S) interaction showed inconsistent predictions regarding some SNPs. But without actual in-vivo studies, a holistic understanding can’t be established. url: https://www.ncbi.nlm.nih.gov/pubmed/32912711/ doi: 10.1016/j.pcd.2020.08.018 id: cord-339431-kyr5lv15 author: Saçar Demirci, Müşerref Duygu title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 words: 2323.0 sentences: 163.0 pages: flesch: 52.0 cache: ./cache/cord-339431-kyr5lv15.txt txt: ./txt/cord-339431-kyr5lv15.txt summary: In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. abstract: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that have been found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs that would target their own genes or alter the host gene expression, there are examples of miRNAs functioning as an antiviral defense mechanism. In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Our PANTHER gene function analysis results indicate that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription. For instance, a transcriptional regulator, STAT1 and transcription machinery might be targeted by virus-derived miRNAs. In addition, many known human miRNAs appear to be able to target viral genes. Considering the fact that miRNA-based therapies have been successful before, comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics. url: https://doi.org/10.1101/2020.03.15.992438 doi: 10.1101/2020.03.15.992438 id: cord-266512-xh6zed03 author: Scala, Enrico title: Atopic statusprotects from severe complications of COVID‐19 date: 2020-08-16 words: 1297.0 sentences: 70.0 pages: flesch: 44.0 cache: ./cache/cord-266512-xh6zed03.txt txt: ./txt/cord-266512-xh6zed03.txt summary: In infection, the Th2 response counteractsthe microbicidal Th1 response, which could limit the tissue damage induced by Th1-mediated inflammation (4) on one hand, but also cause a less efficient anti-virus response, as shown in a study on experimental Coronavirus 229E infection in healthy volunteers, where atopy appeared to be associated with a more severe rhinitis score (5) .Further, atopic subjects show a reduced expression of ACE2, the SARS-CoV-2 receptor, which could be associated with reduced susceptibility to the virus (6) . The multiple logistic regression analysis(details in supplementary material) confirmed a significant association between atopic status andmilder COVID-19;non-atopic patients had a significantly higher risk of having severe Covid-19 (OR adj 3.0, 95% CI 1.6-5.7, p =0.001) ( Table 1) In severe SARS-CoV-2 infection hyper-expressed cytokines include IFN-gamma, TNF-alpha, and IL-6, which cause fever, fatigue, flu-like symptoms, vascular leakage due to endothelial dysfunction, cardiomyopathy, hypotension, lung injury, activation of the coagulation cascade, and diffuse intravascular coagulation (7) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32799364/ doi: 10.1111/all.14551 id: cord-313227-6zwkfzab author: Scala, Stefania title: Fighting the Host Reaction to SARS-COv-2 in Critically Ill Patients: The Possible Contribution of Off-Label Drugs date: 2020-05-27 words: 3872.0 sentences: 202.0 pages: flesch: 36.0 cache: ./cache/cord-313227-6zwkfzab.txt txt: ./txt/cord-313227-6zwkfzab.txt summary: Interestingly, in patients infected by SARS-COv-2, there is an increase in IL1β, IFNγ, IP10, and MCP1, probably leading to activated T-helper-1 (TH1) cell responses, and increased production of T-helper-2 (TH2) immunosuppressive cytokines, such as IL4 and IL10 (18) . Peripheral blood examinations on admission in the majority of patients with COVID-19 displayed lymphopenia, elevated infection-related biomarkers (i.e., procalcitonin, erythrocyte sedimentation rate, serum ferritin, and C-reactive protein) (20) and several elevated inflammatory cytokines (i.e., tumor necrosis factor (TNF)-α, interleukin (IL)-2R and IL-6). Despite markedly reducing virus titers, anti-S-IgG caused lung injury during the early stages of infection, impairing the wound-healing macrophage response and TGF-β production, while promoting pro inflammatory cytokine IL-8, MCP1 production, and inflammatory macrophage accumulation (22) . Another proteasome inhibitor, VR23, possess powerful antiinflammatory activity reducing IL-6 in synovial cells from RA patients, and improving LPS-induced acute lung injury by decreasing neutrophil migration, TNF-α secretion, and tissue inflammation in a mice model (52) . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-COv-2) is the etiologic agent of the 2019 coronavirus disease (COVID19). The majority of infected people presents flu like symptoms and among them 15–20% develops a severe interstitial pneumonitis (IP) that may eventually evolve in acute respiratory distress syndrome (ARDS). IP is caused by the viral glycoprotein spike (S) binding to the angiotensin converting enzyme 2 (ACE2) expressed on the surface of alveolar pneumocytes. The virus is recognized by the “pattern recognition receptors” (PRR) of the immune cells that release cytokines activating more immune cells that produce a large number of pro-inflammatory cytokines, tissue factors and vasoactive peptides. Affected patients might develop the “cytokine storm syndrome,” a fulminant and fatal hypercytokinaemia with multiorgan failure. In patients infected by SARS-COv-2 increase in T-helper 2 (TH2) cytokines (IL-4 and IL10) are reported in addition to the T-helper 1 (TH1) cytokines (IL1B, IFNγ, IP10, and MCP1) previously detected in other coronavirus infections. Cytokines and other molecules involved in immune response and inflammation are conceivable therapeutic targets for IP and ARDS, improving symptoms and decreasing intensive care unit admissions. To this aim off label drugs may be used taking into consideration the window timing for immunosuppressive drugs in virus infected patients. Some off label therapeutic options and preclinical evidence drugs are herein considered. url: https://www.ncbi.nlm.nih.gov/pubmed/32574268/ doi: 10.3389/fimmu.2020.01201 id: cord-252506-8u9oiqoc author: Scarfò, Lydia title: COVID-19 severity and mortality in patients with chronic lymphocytic leukemia: a joint study by ERIC, the European Research Initiative on CLL, and CLL Campus date: 2020-07-09 words: 4023.0 sentences: 248.0 pages: flesch: 49.0 cache: ./cache/cord-252506-8u9oiqoc.txt txt: ./txt/cord-252506-8u9oiqoc.txt summary: authors: Scarfò, Lydia; Chatzikonstantinou, Thomas; Rigolin, Gian Matteo; Quaresmini, Giulia; Motta, Marina; Vitale, Candida; Garcia-Marco, Jose Antonio; Hernández-Rivas, José Ángel; Mirás, Fatima; Baile, Mónica; Marquet, Juan; Niemann, Carsten U.; Reda, Gianluigi; Munir, Talha; Gimeno, Eva; Marchetti, Monia; Quaglia, Francesca Maria; Varettoni, Marzia; Delgado, Julio; Iyengar, Sunil; Janssens, Ann; Marasca, Roberto; Ferrari, Angela; Cuéllar-García, Carolina; Itchaki, Gilad; Špaček, Martin; De Paoli, Lorenzo; Laurenti, Luca; Levin, Mark-David; Lista, Enrico; Mauro, Francesca R.; Šimkovič, Martin; Van Der Spek, Ellen; Vandenberghe, Elisabeth; Trentin, Livio; Wasik-Szczepanek, Ewa; Ruchlemer, Rosa; Bron, Dominique; De Paolis, Maria Rosaria; Del Poeta, Giovanni; Farina, Lucia; Foglietta, Myriam; Gentile, Massimo; Herishanu, Yair; Herold, Tobias; Jaksic, Ozren; Kater, Arnon P.; Kersting, Sabina; Malerba, Lara; Orsucci, Lorella; Popov, Viola Maria; Sportoletti, Paolo; Yassin, Mohamed; Pocali, Barbara; Barna, Gabor; Chiarenza, Annalisa; dos Santos, Gimena; Nikitin, Eugene; Andres, Martin; Dimou, Maria; Doubek, Michael; Enrico, Alicia; Hakobyan, Yervand; Kalashnikova, Olga; Ortiz Pareja, Macarena; Papaioannou, Maria; Rossi, Davide; Shah, Nimish; Shrestha, Amit; Stanca, Oana; Stavroyianni, Niki; Strugov, Vladimir; Tam, Constantine; Zdrenghea, Mihnea; Coscia, Marta; Stamatopoulos, Kostas; Rossi, Giuseppe; Rambaldi, Alessandro; Montserrat, Emili''; Foà, Robin; Cuneo, Antonio; Ghia, Paolo Of the 190 patients studied, four Spanish cases were previously published in extenso [12] , 47 patients were included in a report describing the impact of SARS-CoV-2 pandemic infection on the practical management of CLL in Italy with only limited clinical data [18] . abstract: Chronic lymphocytic leukemia (CLL) is a disease of the elderly, characterized by immunodeficiency. Hence, patients with CLL might be considered more susceptible to severe complications from COVID-19. We undertook this retrospective international multicenter study to characterize the course of COVID-19 in patients with CLL and identify potential predictors of outcome. Of 190 patients with CLL and confirmed COVID-19 diagnosed between 28/03/2020 and 22/05/2020, 151 (79%) presented with severe COVID-19 (need of oxygen and/or intensive care admission). Severe COVID-19 was associated with more advanced age (≥65 years) (odds ratio 3.72 [95% CI 1.79–7.71]). Only 60 patients (39.7%) with severe COVID-19 were receiving or had recent (≤12 months) treatment for CLL at the time of COVID-19 versus 30/39 (76.9%) patients with mild disease. Hospitalization rate for severe COVID-19 was lower (p < 0.05) for patients on ibrutinib versus those on other regimens or off treatment. Of 151 patients with severe disease, 55 (36.4%) succumbed versus only 1/38 (2.6%) with mild disease; age and comorbidities did not impact on mortality. In CLL, (1) COVID-19 severity increases with age; (2) antileukemic treatment (particularly BTK inhibitors) appears to exert a protective effect; (3) age and comorbidities did not impact on mortality, alluding to a relevant role of CLL and immunodeficiency. url: https://doi.org/10.1038/s41375-020-0959-x doi: 10.1038/s41375-020-0959-x id: cord-351367-ral9sbfy author: Scarlattei, Maura title: Unknown SARS-CoV-2 pneumonia detected by PET/CT in patients with cancer date: 2020-06-22 words: 3010.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-351367-ral9sbfy.txt txt: ./txt/cord-351367-ral9sbfy.txt summary: METHODS: We report 5 patients with unknown SARS-CoV-2 infection undergoing positron emission tomography (PET)/computed tomography (CT) with radiopharmaceuticals targeting different tumor processes: (18)F-FDG, (18)F-choline (FCH), and (68)Ga-PSMA. Correct management of a PET session presents many difficulties because of the coexistence of asymptomatic SARS-CoV-2 infection and patients with mild symptoms before the PET scan (https://www.sirm.org/2020/03/30/ covid-19-caso-69/), mostly not tested on RT-PCR, but variably presenting with chest CT findings compatible with pulmonary interstitial infiltrates, potentially associated with infection or drug-related reactions. In this study, we report 5 patients (Table 1) with unknown SARS-CoV-2 infection undergoing PET/CT scan for restaging breast and prostate cancer (patients 1, 3, 4), characterization of lung nodule (patient 2), and focal splenic lesions (patient 5). Recent case series about PET in patients with SARS-CoV-2 pneumonia showed high 18 F-FDG uptake in lung lesions accompanied by nodal involvement detectable on PET/CT images. abstract: INTRODUCTION: In January 2020, the coronavirus disease 2019 (COVID-19) outbreak in Italy necessitated rigorous application of more restrictive safety procedures in the management and treatment of patients with cancer to ensure patient and staff protection. Identification of respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was a challenge during the pandemic owing to a large number of asymptomatic or mildly symptomatic patients. METHODS: We report 5 patients with unknown SARS-CoV-2 infection undergoing positron emission tomography (PET)/computed tomography (CT) with radiopharmaceuticals targeting different tumor processes: (18)F-FDG, (18)F-choline (FCH), and (68)Ga-PSMA. RESULTS: In all patients, PET/CT showed increased tracer uptake in the lungs corresponding to CT findings of SARS-CoV-2 pneumonia. Quantitative assessment of tracer uptake showed more elevated values for the glucose analogue (18)F-FDG (mean SUVmax 5.4) than for the other tracers (mean SUVmax 3.5). CONCLUSIONS: Our findings suggest that PET/CT is a sensitive modality to hypothesize SARS-CoV-2 pneumonia in patients with cancer, even when asymptomatic. More data are needed to verify the correlation among immune response to SARS-CoV-2 infection, clinical evolution, and PET results. Under the strict safety measures implemented at the PET center, the number of potentially SARS-CoV-2–positive patients undergoing PET/CT was very low (1.6%), and no staff member has been diagnosed with infection as of April 30, 2020. url: https://www.ncbi.nlm.nih.gov/pubmed/32567505/ doi: 10.1177/0300891620935983 id: cord-327661-osx42wdh author: Schaefer, E. J. title: Coronavirus Disease-2019 Case, Death, and Testing Rates in the United States and Worldwide: Primary Data and Review date: 2020-10-14 words: 3995.0 sentences: 232.0 pages: flesch: 60.0 cache: ./cache/cord-327661-osx42wdh.txt txt: ./txt/cord-327661-osx42wdh.txt summary: ABSTRACT Coronavirus disease-2019 (COVID-19), due to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been associated with a world-wide pandemic, with the United States (US) having the largest total number of cases and deaths (>7 million and >200,000, respectively) at this time. We assessed data as of September 1, 2020 from our combined laboratories and as reported for selected states and countries for case, death, and testing rates per 1 million in the population. Our positive rates per state agreed reasonably well with reported Centers for Disease Control and Prevention (CDC) data (r=0.609, P<0.0001) based on 19,898 cases, 593 deaths, and 271,637 tests, all per 1 million in the US population. 7 Our goals were to assess our own data as well as available US and worldwide data in terms of cases, deaths, and testing per 1 million in the population, in order to examine potential causes for the large rate differences observed between states and countries. abstract: ABSTRACT Coronavirus disease-2019 (COVID-19), due to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been associated with a world-wide pandemic, with the United States (US) having the largest total number of cases and deaths (>7 million and >200,000, respectively) at this time. We assessed data as of September 1, 2020 from our combined laboratories and as reported for selected states and countries for case, death, and testing rates per 1 million in the population. Our goal was to elucidate potential causes for the large rate differences observed. SARS-CoV-2 naso-pharyngeal (NP) RNA swab testing in 985,219 US subjects referred to our laboratories by healthcare providers revealed an overall 10.1% positive rate, comparable to the 7.3% rate reported nationwide. In a small subset of 91 subjects, all of whom had been positive for SARS-CoV-2 RNA in NP swabs 2-4 weeks earlier, NP swab testing was twice as likely to be positive (58.6%) as saliva samples (21.5%), based on paired sampling. Our positive rates per state agreed reasonably well with reported Centers for Disease Control and Prevention (CDC) data (r=0.609, P<0.0001) based on 19,898 cases, 593 deaths, and 271,637 tests, all per 1 million in the US population. Louisiana had the highest case rate; New Jersey had the highest death rate; and Rhode Island had the highest testing rate. Of 47 countries, including all countries with populations >50 million, Qatar had the highest case rate; Peru had the highest death rate; and Israel had the highest testing rate for SARS-CoV-2 infection. Correlations between case rates and death rates as well as testing rates were 0.473 and 0.398 for US states and 0.473 and 0.476 for the various countries, respectively (all P<0.0001). In conclusion, outpatient saliva testing is not as sensitive as NP testing for SARS-CoV-2 RNA detection. While testing is important, without adequate public health measures, it is unlikely that we will get this pandemic under adequate control until vaccines become available. url: http://medrxiv.org/cgi/content/short/2020.10.13.20172957v1?rss=1 doi: 10.1101/2020.10.13.20172957 id: cord-340010-t1m7dxzc author: Schaefer, Esperance A. K. title: Interrelationship Between Coronavirus Infection and Liver Disease date: 2020-05-21 words: 1416.0 sentences: 97.0 pages: flesch: 43.0 cache: ./cache/cord-340010-t1m7dxzc.txt txt: ./txt/cord-340010-t1m7dxzc.txt summary: Several published studies have characterized the frequency and severity of liver biochemistry abnormalities on presentation, and a few have determined whether these abnormalities are associated with increased disease-related morbidity or death, as summarized in Table 1 . 9, 10, [12] [13] [14] [16] [17] [18] [19] [20] [21] [22] [23] [24] The largest published study to date encompassed 5700 hospitalized patients in New York and examined admission serologies: aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were both frequently elevated (58.4% and 39.0% of subjects, respectively), and a separate large cohort found elevations to be more common in severe disease. 28 Thus, the liver injury observed in COVID-19 may reflect a direct viral effect, but other potential contributors must be considered, both at the time of initial presentation and during disease progression and management. Hepatic injury from SARS-CoV2 infection is observed from the time of initial contact with the medical system, suggesting that the primary insult is unrelated to medical management but rather due to either direct effect of the virus or a consequence of the systemic disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32489653/ doi: 10.1002/cld.967 id: cord-313282-z5cues67 author: Schaefer, Inga-Marie title: In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19 date: 2020-06-19 words: 3975.0 sentences: 189.0 pages: flesch: 41.0 cache: ./cache/cord-313282-z5cues67.txt txt: ./txt/cord-313282-z5cues67.txt summary: Among five patients with acute-phase DAD (≤7 days from onset of respiratory failure), SARS-CoV-2 was detected in pulmonary pneumocytes and ciliated airway cells (N = 5), and in upper airway epithelium (N = 2). The findings suggest that SARS-CoV-2 infection of epithelial cells in lungs and airways of patients with COVID-19 who developed respiratory failure can be detected during the acute phase of lung injury and is absent in the organizing phase. The aim of this study was to examine the gross and histologic patterns of tissue injury in correlation with viral protein expression in the conducting airways and lungs at autopsy in a series of patients with confirmed SARS-CoV-2 infection. Overall, the different stages of DAD observed histologically correspond to the estimated time interval from onset of respiratory failure to death; however, the exact timing of severe lung injury may be difficult to determine in certain cases given reports of silent hypoxemia in COVID-19 infected patients [27, 28] . abstract: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has led to a global public health crisis. In elderly individuals and those with comorbidities, COVID-19 is associated with high mortality, frequently caused by acute respiratory distress syndrome. We examine in situ expression of SARS-CoV-2 in airways and lung obtained at autopsy of individuals with confirmed COVID-19 infection. Seven autopsy cases (male, N = 5; female, N = 2) with reverse transcriptase-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection and a median age of 66 years (range, 50–77 years) were evaluated using a rabbit polyclonal antibody against SARS Nucleocapsid protein in correlation with clinical parameters. The median time from symptom onset to death was 9 days (range, 6–31 days), from hospitalization 7 days (range, 1–21 days), from positive RT-PCR 7 days (range, 0–18 days), and from intensive care unit admission defining onset of respiratory failure 3 days (range, 1–18 days). Chest imaging identified diffuse airspace disease in all patients corresponding to acute and (N = 5) or organizing (N = 2) diffuse alveolar damage (DAD) on histologic examination. Among five patients with acute-phase DAD (≤7 days from onset of respiratory failure), SARS-CoV-2 was detected in pulmonary pneumocytes and ciliated airway cells (N = 5), and in upper airway epithelium (N = 2). In two patients with organizing DAD (>14 days from onset of respiratory failure), no virus was detected in lungs or airways. No endothelial cell infection was observed. The findings suggest that SARS-CoV-2 infection of epithelial cells in lungs and airways of patients with COVID-19 who developed respiratory failure can be detected during the acute phase of lung injury and is absent in the organizing phase. url: https://www.ncbi.nlm.nih.gov/pubmed/32561849/ doi: 10.1038/s41379-020-0595-z id: cord-034371-j3xxmkjd author: Schellack, Natalie title: COVID-19: Guidelines for pharmacists in South Africa date: 2020-06-10 words: 5039.0 sentences: 344.0 pages: flesch: 54.0 cache: ./cache/cord-034371-j3xxmkjd.txt txt: ./txt/cord-034371-j3xxmkjd.txt summary: This evidence-based review is aimed at providing guidance for pharmacists in community, hospital and other settings in South Africa, on the management of patients with suspected or confirmed coronavirus disease 2019, or COVID-19. • Epidemiology • The virus, its modes of transmission and incubation period • Symptom identification, including the differentiation between influenza, allergic rhinitis, sinusitis and COVID-19 • Social media myths and misinformation • Treatment guidelines and medicines that may need to be kept in stock • Treatment and prevention options, including an update on vaccine development • The case for and against the use of NSAIDs, ACE-inhibitors and angiotensin receptor blockers (ARBs) in patients with COVID-19 • Interventions and patient counselling by the pharmacist. The current NDoH/NICD guidelines do not recommend the use of chloroquine (CQ)/ hydroxychloroquine (HCQ), due to insufficient evidence, in the treatment of patients with suspected or confirmed COVID-19. abstract: Epidemiology. The virus, its modes of transmission and incubation period. Symptom identification, including the differentiation between influenza, allergic rhinitis, sinusitis and COVID-19. Social media myths and misinformation. Treatment guidelines and medicines that may need to be kept in stock. Treatment and prevention options, including an update on vaccine development. The case for and against the use of NSAIDs, ACE-inhibitors and angiotensin receptor blockers (ARBs) in patients with COVID-19. Interventions and patient counselling by the pharmacist. World Health Organization (WHO): https://www.who.int/emergencies/diseases/novel-coronavirus-2019. National Institute for Communicable Diseases (NICD): https://www.nicd.ac.za/diseases-a-z-index/covid-19/. National Department of Health (NDoH): http://www.health.gov.za/index.php/outbreaks/145-corona-virus-outbreak/465-corona-virus-outbreak; https://sacoronavirus.co.za/; url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577345/ doi: 10.4102/sajid.v35i1.206 id: cord-296649-h6oyjz56 author: Scherf-Clavel, Oliver title: Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date: 2020-11-06 words: 5076.0 sentences: 263.0 pages: flesch: 53.0 cache: ./cache/cord-296649-h6oyjz56.txt txt: ./txt/cord-296649-h6oyjz56.txt summary: In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. The value obtained from our experiments falls in that range and is comparable to the V z obtained in mice from blood concentrations and to plasma V z measured in humans (see Table 4 ). abstract: Background and Objectives Remdesivir and hydroxychloroquine are or were among the most promising therapeutic options to tackle the current SARS-CoV-2 pandemic. Besides the use of the prodrug remdesivir itself, the direct administration of GS-441 524, the resulting main metabolite of remdesivir, could be advantageous and even more effective. All substances were not originally developed for the treatment of COVID-19 and especially for GS-441 524 little is known about its pharmacokinetic and physical-chemical properties. To justify the application of new or repurposed drugs in humans, pre-clinical in vivo animal models are mandatory to investigate relevant PK and PD properties and their relationship to each other. In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. Methods GS-441 524 and HCQ were administered intravenously as a single injection to male mice. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. In vitro experiments were conducted to investigate the degradation of remdesivir in human plasma and blood. All pharmacokinetic analyses were performed with R Studio using non-compartmental analysis. Results High tissue to plasma ratios for GS-441 524 and HCQ were found, indicating a significant distribution into the examined tissue, except for the central nervous system and fat. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. For HCQ, relatively high in vitro EC50 values are reported, which were not reached in all tissues. Facing its slow tissue distribution, HCQ might not lead to sufficient tissue saturation for a reliable antiviral effect. Conclusion The mouse model was able to characterise the PK and tissue distribution of both model substances and is a suitable tool to investigate early drug candidates against SARS-CoV-2. Furthermore, we could demonstrate a high tissue distribution of GS-441 524 even if not administered as the prodrug remdesivir. url: https://doi.org/10.1101/2020.09.16.299537 doi: 10.1101/2020.09.16.299537 id: cord-348243-e5tdb08v author: Schermer, Bernhard title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 words: 3958.0 sentences: 236.0 pages: flesch: 56.0 cache: ./cache/cord-348243-e5tdb08v.txt txt: ./txt/cord-348243-e5tdb08v.txt summary: METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. abstract: BACKGROUND: Rapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose. METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). RESULTS: Whilst specificity of standard RT-LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed RT-LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel RT-LAMP assays with SHERLOCK. CONCLUSION: In summary, this approach reveals one-step multiplexed RT-LAMP assays as a prime-option for the development of easy and cheap POC test kits. url: https://doi.org/10.1371/journal.pone.0238612 doi: 10.1371/journal.pone.0238612 id: cord-191741-2vuiafv0 author: Schifanella, L. title: Massive viral replication and cytopathic effects in early COVID-19 pneumonia date: 2020-04-30 words: 1953.0 sentences: 94.0 pages: flesch: 46.0 cache: ./cache/cord-191741-2vuiafv0.txt txt: ./txt/cord-191741-2vuiafv0.txt summary: Here we show that SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes causes focal lung injury in an individual with no history of pulmonary symptoms. Ground glass opacities or patchy infiltrates in the lungs in CT images of asymptomatic SARS-CoV-2 infected individuals [5] [6] [7] suggest that lung infection and associated tissue injury may be detectable in individuals who did not have severe pneumonia or respiratory failure 7 . We have already shown images that suggested that vRNA+ macrophages could acquire vRNA by phagocytosis of infected type II pneumocytes or vRNA released from lysed cells (Fig. 1, 2) , and now show further evidence in support of that conclusion. We show in a SARS-CoV-2 infected individual with ostensibly early infection, who had no known history of pulmonary symptoms, that there was a region of the lung with focal pneumonia in which massive SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes directly contributes to lung pathology. abstract: SARS-CoV-2 is the cause of COVID-19 acute respiratory illness that like its predecessors, MERS and SARS, can be severe and fatal 1-4. By April of 2020, COVID-19 infections had become a worldwide pandemic with nearly 3 million infections and over 200,000 deaths. The relative contributions of virus replication and cytopathic effects or immunopathological host responses to the severe and fatal outcomes of COVID-19 lung infections have as yet to be determined. Here we show that SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes causes focal lung injury in an individual with no history of pulmonary symptoms. These findings point to the potential benefit of early effective antiviral treatment to prevent progression to severe and fatal COVID-19 pneumonia. url: https://arxiv.org/pdf/2005.00004v1.pdf doi: nan id: cord-016921-64mfqks9 author: Schillmeier, Michael title: Risiko-Akteur-Netzwerke date: 2009-08-07 words: 3555.0 sentences: 398.0 pages: flesch: 55.0 cache: ./cache/cord-016921-64mfqks9.txt txt: ./txt/cord-016921-64mfqks9.txt summary: Should SARS continue to spread, the global economic consequences -already estimated at around US $ 30 billion -could be great in a closely interconnected and interdependent world." (WHO 2003: 5) Die Welt bekam es mit einem Akteur zu tun, der in der Lage war, gesellschaftliches und individuelles Leben zu tangieren, zu bedrohen oder gar zu vernichten. Gerade die Möglichkeit, dass wir Menschen mit Hilfe von Flugzeugen weltweit schnell von einem Ort zum anderen reisen können, machte die Gefährlichkeit des SARS-Virus aus, da dieser das Risiko darstellte, als eine Art blinder Passagier mitzureisen und sich so ebenso global entlang dieser Flugrouten und darüber hinaus auszubreiten. SARS markiert ein "kosmo-politisches Ereignis" (Schillmeier & Pohler 2006) : Es stellt einen grenzüberschreitenden, öffentlichen Akteur dar, der nicht nur gesellschaftliche Ordnungsmuster, sondern auch die etablierten Routinen seiner Beschreibung kontingent erscheinen lässt und reformuliert. Bereits an dieser Stelle lässt sich erkennen, dass mit dem Risiko-Akteur SARS eine prozessuale, man könnte auch sagen, eine propagationale Perspektive von Handlung erforderlich ist, die sich der klassischen Konzeptionen und Begrifflichkeiten sozialwissenschaftlicher Methode entziehen. abstract: Einen Monat nach dem globalen Ausbruch einer bisher unbekannten, jedoch hochgradig ansteckenden und lebensbedrohlichen atypischen „Lungenkrankheit“ – die Rede ist von SARS, einer Krankheit, die zum ersten Mal im Februar 2003 in einer südchinesischen Provinz beobachtet wurde – beschreibt David L. Heymann, Leiter der Abteilung Emerging and other Communicable Diseasesder World Health Organization(WHO), das spezifische Risiko- und Gefahrenpotential des Severe Acute Respiratory Syndrom: „SARS is emerging in ways that suggest great potential for rapid international spread under the favorable conditions created by a highly mobile, closely interconnected world. Anecdotal data indicate an incubation period of 2 to 10 days (average 2 to 7 days), allowing the infectious agent to be transported, unsuspected und undetected, in a symptomless air traveler from one city in the world to any other city having an international airport. Person-to-person transmission through close contact with respiratory secretions has been demonstrated. The initial symptoms are nonspecific and common. The concentration of cases in previously healthy staff and the proportion of patients requiring intensive care are particularly alarming. The „21 century“ disease could have other consequences as well. Should SARS continue to spread, the global economic consequences – already estimated at around US $ 30 billion – could be great in a closely interconnected and interdependent world.“ (WHO 2003: 5) url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121357/ doi: 10.1007/978-3-531-91674-3_16 id: cord-281551-0aj2zwx8 author: Schlagenhauf, Patricia title: Repurposing antimalarials and other drugs for COVID-19 date: 2020-04-02 words: 1433.0 sentences: 80.0 pages: flesch: 50.0 cache: ./cache/cord-281551-0aj2zwx8.txt txt: ./txt/cord-281551-0aj2zwx8.txt summary: A French paper reporting on the use of drug combinations in infected patients highlighted the possibility that hydroxychloroquine is effective in the treatment of COVID-19 patients [4] particularly in combination with azithromycin. For instance, teicoplanin was proposed as a potential treatment in COVID-19 patients and has already shown inhibitory effects on cell entry of Ebola virus, SARS-CoV and MERS-CoV in the past. However, it has to be acknowledged that in this and other cases, it is a long, expensive and time-consuming way, even if there is an accelerated avenue to expedite promising developments, from in vitro assays indicative of antiviral effects to the initiation steps of safety and efficacy assessments in humans, Finding compounds that can block the entry of the virus into the cell could be an important approach to find potential therapies for COVID-19. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) abstract: nan url: https://api.elsevier.com/content/article/pii/S1477893920301265 doi: 10.1016/j.tmaid.2020.101658 id: cord-103112-m6cg67lz author: Schloer, Sebastian title: Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date: 2020-08-16 words: 1554.0 sentences: 91.0 pages: flesch: 51.0 cache: ./cache/cord-103112-m6cg67lz.txt txt: ./txt/cord-103112-m6cg67lz.txt summary: As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. abstract: The Corona Virus Disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Related Coronavirus 2 (SARS-CoV-2) is a global health emergency. As only very limited therapeutic options are clinically available, there is an urgent need for the rapid development of safe, effective, and globally available pharmaceuticals that inhibit SARS-CoV-2 entry and ameliorate COVID-19. In this study, we explored the use of small compounds acting on the homeostasis of the endolysosomal host-pathogen interface, to fight SARS-CoV-2 infection. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity against two currently circulating influenza A virus subtypes, an effect which was also observed upon treatment with the FIASMAs amiodarone and imipramine. Mechanistically, fluoxetine induced both impaired endolysosomal acidification and the accumulation of cholesterol within the endosomes. As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19. url: https://doi.org/10.1101/2020.07.27.222836 doi: 10.1101/2020.07.27.222836 id: cord-270329-t60t639i author: Schloer, Sebastian title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date: 2020-10-16 words: 1053.0 sentences: 77.0 pages: flesch: 52.0 cache: ./cache/cord-270329-t60t639i.txt txt: ./txt/cord-270329-t60t639i.txt summary: title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. While drugs 87 directly acting on virus structures are much more likely to completely eliminate the 88 pathogens in shorter treatment time, emerging viral resistance to these antivirals is a major 89 concern, as observed with the influenza neuraminidase inhibitor oseltamivir (Kim et al., itraconazole antiviral activity in SARS-CoV-2 infected Vero cells (Fig. 1b) . abstract: The SARS-COV-2 pandemic and the global spread of coronavirus disease 2019 (COVID-19) urgently calls for efficient and safe antiviral treatment strategies. A straightforward approach to speed up drug development at lower costs is drug repurposing. Here we investigated the therapeutic potential of targeting the host- SARS-CoV-2 interface via repurposing of clinically licensed drugs and evaluated their use in combinatory treatments with virus- and host-directed drugs. We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Drug treatments were well-tolerated and potent impaired viral replication was observed with all drug treatments. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. Itraconazole-Remdesivir and Fluoxetine-Remdesivir combinations are promising therapeutic options to control SARS-CoV-2 infection and severe progression of COVID-19. url: https://doi.org/10.1101/2020.10.16.342410 doi: 10.1101/2020.10.16.342410 id: cord-287289-zgehbwve author: Schmidt, M. title: FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity date: 2020-05-01 words: 2381.0 sentences: 154.0 pages: flesch: 60.0 cache: ./cache/cord-287289-zgehbwve.txt txt: ./txt/cord-287289-zgehbwve.txt summary: title: FACTFrankfurt adjusted COVID-19 testinga novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity We applied a novel protocol to NAT testing of respiratory swabs for SARS-CoV-2: First, to evaluate for suitability of different mini-pool sizes, swabs were contaminated with a defined SARS-CoV-2 virus concentration of 1x10 4 copies/ml, and then placed in a series of 10 tubes with lysis buffer for 5 minutes each. P-value for individuals sample and mini pool NAT was 0.299 and 0.354 for the ORF region and E-gene, respectively, which we consider not statistically significant. Ct-values did not differ significantly between mini-pool and the single sample testing (p-value for the ORF region and E gene were 0.44 and 0.46, respectively) (table 4). Here, we present an alternate protocol (FACT) that is based on incubation of a respiratory swab first in a single sample tube, and then again in a mini-pool tube. abstract: Background: In the pandemic, testing for SARS-CoV-2 by RT-PCR in one of the pillars on which countermeasures are based. Factors limiting the output of laboratories interfere with the effectiveness of public health measures. Conserving reagents by pooling samples in low-probability settings is proposed, but may cause dilution and loss of sensitivity. Methods: We tested an alternate approach (FACT) by simultaneously incubating multiple respiratory swabs in a single tube. This protocol was evaluated by serial incubation of a respiratory swab in up to 10 tubes. The analytics validity of this concept was demonstrated in a five-sample mini pool set-up. It was consequently applied in the testing of 50 symptomatic patients (five-sample pools) as well as 100 asymptomatic residents of a nursing home (ten-sample pools). Results: Serial incubation of a respiratory swab in up to 10 tubes did not lead to a significant decline in viral concentration. The novel FACT-protocol did not cause a false negative result in a five-sample mini-pool setup, with non-significantly differing Ct values between single sample and mini-pool NAT. In two routine applications, all mini pools containing positive patient samples were correctly identified. Conclusions: Our proposed FACT- protocol did not cause a significant loss in analytic or diagnostic sensitivity compared to single sample testing in multiple setups. It reduced the amount of reagents needed by up to 40%, and also reduced hands-on time. This method could enhance testing efficiency, especially in groups with a low pretest-probability, such as systemically relevant professional groups. url: https://doi.org/10.1101/2020.04.28.20074187 doi: 10.1101/2020.04.28.20074187 id: cord-318738-7dgbc4um author: Schmidt, Marco Florian title: Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening date: 2008-03-17 words: 1957.0 sentences: 93.0 pages: flesch: 47.0 cache: ./cache/cord-318738-7dgbc4um.txt txt: ./txt/cord-318738-7dgbc4um.txt summary: A potential anti‐SARS drug has been developed by dynamic ligation screening (DLS), by which nucleophilic fragments are directed to the protein''s active site by reversible reaction with an aldehyde inhibitor. To establish DLS for site-directed identification of inhibitory fragments, at first a fluorescence-based assay [4] for SARS-CoV M pro activity was developed by employing the substrate Ac-TSAVLQ-AMCA (1). To obtain an entirely non-peptidic inhibitor of SARS-CoV M pro targeting both the S1'' and S1 pockets, the dynamic ligation screening was conducted iteratively in a "reverted" mode ( Table 2 ). Dynamic ligation screening for the S1'' site was performed for a library of 234 nucleophilic fragments using 1 mm of SARS-CoV M pro , 200 mm 1, 400 mm of one nucleophilic fragment per well, and 50 mm of the peptide aldehyde inhibitor Ac-DSFDQ-H (2) on a 384-well microtiter plate. abstract: A potential anti‐SARS drug has been developed by dynamic ligation screening (DLS), by which nucleophilic fragments are directed to the protein's active site by reversible reaction with an aldehyde inhibitor. Their inhibitory effect is detected by competition with a fluorogenic enzyme substrate. With this concept, low‐affinity fragments binding specifically to the active site are quickly identified in a functional enzyme assay.[Image: see text] url: https://doi.org/10.1002/anie.200704594 doi: 10.1002/anie.200704594 id: cord-291264-akuvt5ig author: Schnichels, Sven title: Kann SARS-CoV-2 das Auge infizieren? – Ein Überblick über den Rezeptorstatus in okularem Gewebe date: 2020-06-24 words: 2764.0 sentences: 326.0 pages: flesch: 61.0 cache: ./cache/cord-291264-akuvt5ig.txt txt: ./txt/cord-291264-akuvt5ig.txt summary: At the time of the research, angiotensin-converting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV‑2. Auch in dieser Studie war die exprimierte Menge von ACE2 in der epithelialen Kornea zwischen 5-und 20-mal geringer als in den anderen untersuchten Geweben (Hoden, Dünndarm, Herz) [22] . Des Weiteren wurde TMPRSS2 auch in Proben der Konjunktiva und Hornhaut nachgewiesen, mit einem im Vergleich zu ACE2 ubiquitäreren Färbungsmuster. At the time of the research, angiotensinconverting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV-2. Aufgrund der geringeren ACE2-und TMPRSS2-Expression ist das Auge nicht als Hochrisikogewebe anzusehen. Expression of SARS coronavirus S protein functional receptor-Angiotensin-converting enzyme 2 in human cornea and conjunctiva abstract: Is the new coronavirus SARS-CoV‑2 able to infect ocular tissue and thus poses a risk of infection through the tissue in addition to the risk of contact? This is the question that has occupied ophthalmologists since the beginning of the outbreak. In order to infect a certain type of tissue specific receptors for each virus and sometimes also coreceptors or other proteins must be present. The aim of this review was to summarize and reflect the current state of research with the help of the currently available literature as of 28 May 2020. At the time of the research, angiotensin-converting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV‑2. In the eye both ACE2 and TMPRSS2 are expressed, although sometimes very weakly and with varying degrees in different tissues. It is noteworthy that very different results were obtained with different methods. Several reasons can account for this effect: Firstly, the method of detection or preservation of the tissue, secondly, the possibly different expression of the tested tissue samples and thirdly, a possibly rapid loss of receptor expression post-mortem. Therefore, an infection of the eye seems possible, which has already been reported in various publications. The amount of virus or receptor expression necessary to cause an infection is not known. According to current state of knowledge the eye is not considered to be a high-risk tissue due to the low ACE2 and TMPRSS2 expression. Nevertheless, appropriate protective measures are necessary for both medical personnel and patients. In cases of corneal transplantation an infection of the donor tissue with SARS-CoV‑2 must be excluded. url: https://doi.org/10.1007/s00347-020-01160-z doi: 10.1007/s00347-020-01160-z id: cord-294789-07hto8qn author: Schoch-Spana, Monica title: The public’s role in COVID-19 vaccination: human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States date: 2020-10-29 words: 5808.0 sentences: 272.0 pages: flesch: 37.0 cache: ./cache/cord-294789-07hto8qn.txt txt: ./txt/cord-294789-07hto8qn.txt summary: Members of the working group-listed as authors on this paper-included national figures in public health and social science with research, policy, and practice expertise in vaccinology, vaccine hesitancy/confidence, health disparities, infectious disease, bioethics, epidemiology, bioinformatics, public health law, pandemic mitigation, public health preparedness, mass vaccination campaigns, community engagement, and crisis and emergency risk communication. A combination of literature reviews on vaccination, pandemic planning, and health crisis communication; an assessment of current news and social media trends regarding COVID-19 vaccines; and key informant interviews with each working group member focusing on their respective expertise formed the basis of the research presented in this article. To ensure a successful COVID-19 vaccination campaign, it is necessary for sponsors to invest in time-critical investigations on human factors related to vaccine acceptance, and for public health authorities and other stakeholders to act on the social and behavioral findings of this research. abstract: Given the social and economic upheavals caused by the COVID-19 pandemic, political leaders, health officials, and members of the public are eager for solutions. One of the most promising, if they can be successfully developed, is vaccines. While the technological development of such countermeasures is currently underway, a key social gap remains. Past experience in routine and crisis contexts demonstrates that uptake of vaccines is more complicated than simply making the technology available. Vaccine uptake, and especially the widespread acceptance of vaccines, is a social endeavor that requires consideration of human factors. To provide a starting place for this critical component of a future COVID-19 vaccination campaign in the United States, the 23-person Working Group on Readying Populations for COVID-19 Vaccines was formed. One outcome of this group is a synthesis of the major challenges and opportunities associated with a future COVID-19 vaccination campaign and empirically-informed recommendations to advance public understanding of, access to, and acceptance of vaccines that protect against SARS-CoV-2. While not inclusive of all possible steps than could or should be done to facilitate COVID-19 vaccination, the working group believes that the recommendations provided are essential for a successful vaccination program. url: https://api.elsevier.com/content/article/pii/S0264410X20313682 doi: 10.1016/j.vaccine.2020.10.059 id: cord-018460-wbtaoo0o author: Schomburg, Dietmar title: SARS coronavirus main proteinase 3.4.22.69 date: 2013 words: 6007.0 sentences: 743.0 pages: flesch: 70.0 cache: ./cache/cord-018460-wbtaoo0o.txt txt: ./txt/cord-018460-wbtaoo0o.txt summary: abstract: EC number 3.4.22.69 Recommended name SARS coronavirus main proteinase Synonyms 3C-like protease <2,3> [9,16,38,49,51] 3CL protease <2> [14,48] 3cLpro <1,2,3> [7,11,13,16,19,28,38,49,51] C30.004 (Merops-ID) Mpro SARS 3C-like protease <2> [17] SARS 3C-like proteinase <2> [15,18,27] SARS 3CL protease <2> [31] SARS 3CLpro <2> [49] SARS CoV main proteinase <2> [1,2,4,5] SARS CoVMpro <2> [33] SARS Mpro <2> [25] SARS coronavirus 3C-like protease <2> [48] SARS coronavirus 3C-like proteinase <2> [50] SARS coronavirus 3CL protease <2> [20] SARS coronavirus main peptidase <2> [23] SARS coronavirus main protease <2> [25] SARS coronavirus main proteinase <2> [5,33] SARS main protease <2> [12,25] SARS-3CL protease <2> [48] SARS-3CLpro <2> [29,50] SARS-CoV 3C-like peptidaseSARS-CoV 3C-like peptidase<2> [24] SARS-CoV 3C-like protease<1> [19] SARS-CoV 3CL protease <2> [22,30,44,46] SARS-CoV 3CLpro <2> [32,36,38,44,45] SARS-CoV 3CLpro enzyme <2> [11] SARS-CoV Mpro <2> [21,40] SARS-CoV main protease <2> [21,26,43] SARS-coronavirus 3CL protease <2> [8] SARS-coronavirus main protease <2> [47] TGEV Mpro coronavirus 3C-like protease <1> [19] porcine transmissible gastroenteritis virus Mpro severe acute respiratory syndrome coronavirus 3C-like protease <2> [41,42] severe acute respiratory syndrome coronavirus main protease <2> [21] severe acute respiratory syndrome coronavirus main proteinase <2> [33] CAS registry number 218925-73-6 37353-41-6 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123336/ doi: 10.1007/978-3-642-36260-6_3 id: cord-355728-wivk0bm0 author: Schoof, Michael title: An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date: 2020-08-17 words: 3613.0 sentences: 377.0 pages: flesch: 68.0 cache: ./cache/cord-355728-wivk0bm0.txt txt: ./txt/cord-355728-wivk0bm0.txt summary: Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Class I nanobodies emerged with highly 144 variable activity in this assay with Nb6 and Nb11 as two of the most potent clones with IC50 145 values of 370 and 540 nM, respectively (Table 1) To define the binding sites of Nb6 and Nb11, we determined their cryogenic electron 156 microscopy (cryo-EM) structures bound to Spike* ( Fig. 2A state RBDs only contacts a single RBD (Fig. 2D) . 277 278 mNb6-tri displays further gains in potency in both pseudovirus and live SARS-CoV-2 infection 279 assays with IC50 values of 120 pM (5.0 ng/mL) and 54 pM (2.3 ng/mL), respectively (Fig. 4H-I, 280 Table 1). abstract: Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains stability and function after aerosolization, lyophilization, and heat treatment. These properties may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century. url: https://doi.org/10.1101/2020.08.08.238469 doi: 10.1101/2020.08.08.238469 id: cord-294590-1niaplc2 author: Schrag, Stephanie J. title: SARS Surveillance during Emergency Public Health Response, United States, March–July 2003 date: 2004-02-17 words: 4720.0 sentences: 214.0 pages: flesch: 44.0 cache: ./cache/cord-294590-1niaplc2.txt txt: ./txt/cord-294590-1niaplc2.txt summary: In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003 , a total of 398 (27%) met clinical and epidemiologic SARS case criteria. On March 14, 2003 , the U.S. Centers for Disease Control and Prevention (CDC) launched an emergency public health response and established national surveillance for SARS to identify case-patients in the United States and determine if domestic transmission was occurring. abstract: In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003, a total of 398 (27%) met clinical and epidemiologic SARS case criteria. Of these, 72 (18%) were probable cases with radiographic evidence of pneumonia. Eight (2%) were laboratory-confirmed SARS-coronavirus (SARS-CoV) infections, 206 (52%) were SARS-CoV negative, and 184 (46%) had undetermined SARS-CoV status because of missing convalescent-phase serum specimens. Thirty-one percent (124/398) of case-patients were hospitalized; none died. Travel was the most common epidemiologic link (329/398, 83%), and mainland China was the affected area most commonly visited. One case of possible household transmission was reported, and no laboratory-confirmed infections occurred among healthcare workers. Successes and limitations of this emergency surveillance can guide preparations for future outbreaks of SARS or respiratory diseases of unknown etiology. url: https://www.ncbi.nlm.nih.gov/pubmed/15030681/ doi: 10.3201/eid1002.030752 id: cord-351305-6vtv2xuh author: Schramm, Markus A. title: COVID-19 in a Severely Immunosuppressed Patient With Life-Threatening Eosinophilic Granulomatosis With Polyangiitis date: 2020-08-28 words: 1260.0 sentences: 64.0 pages: flesch: 38.0 cache: ./cache/cord-351305-6vtv2xuh.txt txt: ./txt/cord-351305-6vtv2xuh.txt summary: The current pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compels clinicians to develop recommendations for successful clinical management and surveillance of immunocompromised patients at high risk for severe disease progression. With only few case studies published on SARS-CoV-2 infection in patients with rheumatic diseases, we report a 25-year-old male who developed moderate coronavirus disease 2019 (COVID-19) with fever, mild dyspnea, and no major complications despite having received high-dose prednisolone, cyclophosphamide, and rituximab for the treatment of highly active, life-threatening eosinophilic granulomatosis with polyangiitis (EGPA). Thus, due to severity and refractory disease the previously healthy patient was continuously hospitalized from January to March 2020, receiving intravenous cyclophosphamide (CYCLOPS-protocol, cumulative dose 4.76 g), rituximab (4 × 375 mg/m 2 ), and a long-term, slowly tapered high-dose prednisolone treatment (up to 1 g/day). Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients abstract: Immunosuppressive therapies increase the susceptibility of patients to infections. The current pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compels clinicians to develop recommendations for successful clinical management and surveillance of immunocompromised patients at high risk for severe disease progression. With only few case studies published on SARS-CoV-2 infection in patients with rheumatic diseases, we report a 25-year-old male who developed moderate coronavirus disease 2019 (COVID-19) with fever, mild dyspnea, and no major complications despite having received high-dose prednisolone, cyclophosphamide, and rituximab for the treatment of highly active, life-threatening eosinophilic granulomatosis with polyangiitis (EGPA). url: https://www.ncbi.nlm.nih.gov/pubmed/32983161/ doi: 10.3389/fimmu.2020.02086 id: cord-312955-gs65c3fy author: Schreiber, Gideon title: The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date: 2020-09-30 words: 8418.0 sentences: 467.0 pages: flesch: 48.0 cache: ./cache/cord-312955-gs65c3fy.txt txt: ./txt/cord-312955-gs65c3fy.txt summary: Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I–receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Thereby, it inhibits the nuclear transport of phosphorylated STAT1, rendering cells refractory to IFN-Is. Another example of viral mechanisms that evolved to eliminate IFN-I functions in inducing innate immunity is given by the SARS corona virus, where both the production of IFNb and the IFN-I induced signaling are attenuated. This gene was found to preferentially cleave the ubiquitin-like modifier interferon-stimulated gene 15 (ISG15), FIGURE 4 | SARS-CoV-2 has multiple effects on the immune system, including inhibition of IFNb production, which results in ISGs not to be produced, CD4+ and CD8+ exhaustion and increased levels of pro-inflammatory proteins (TNFa, IL6, NF-kB). abstract: Type I interferons (IFN-I) were first discovered over 60 years ago in a classical experiment by Isaacs and Lindenman, who showed that IFN-Is possess antiviral activity. Later, it became one of the first approved protein drugs using heterologous protein expression systems, which allowed its large-scale production. It has been approved, and widely used in a pleiotropy of diseases, including multiple-sclerosis, hepatitis B and C, and some forms of cancer. Preliminary clinical data has supported its effectiveness against potential pandemic pathogens such as Ebola and SARS. Still, more efficient and specific drugs have taken its place in treating such diseases. The COVID-19 global pandemic has again lifted the status of IFN-Is to become one of the more promising drug candidates, with initial clinical trials showing promising results in reducing the severity and duration of the disease. Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I–receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Furthermore, I discuss how these may guide the optimized use IFN-Is in combatting COVID-19. url: https://doi.org/10.3389/fimmu.2020.595739 doi: 10.3389/fimmu.2020.595739 id: cord-284478-c1uj3jra author: Schub, David title: High levels of SARS-CoV-2–specific T cells with restricted functionality in severe courses of COVID-19 date: 2020-10-15 words: 7277.0 sentences: 364.0 pages: flesch: 48.0 cache: ./cache/cord-284478-c1uj3jra.txt txt: ./txt/cord-284478-c1uj3jra.txt summary: RESULTS: Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2–specific T cells as compared with convalescent individuals. So far, mainly nonspecific general changes in the number and functionality of blood cells have been described, whereas specific T cell immunity directed against SARS-CoV-2 has as yet not been studied as extensively (7) (8) (9) (10) (11) , especially in patients with different disease severity. As shown in Figure 3A , the percentage of multifunctional, SARS-CoV-2-specific CD4 + T cells with the ability to simultaneously produce all 3 cytokines was significantly lower in patients with severe courses as compared with convalescent individuals. Nevertheless, the SEB-reactive and SARS-CoV-2-specific cytokine profiles exhibited similar differences between patients with severe disease and convalescent individuals ( Figure 3A ). We also analyzed expression of cytotoxic T lymphocyte antigen 4 (CTLA-4) on SARS-CoV-2-specific and SEB-reactive T cells as phenotypical correlates of altered functionality commonly observed during active infections. abstract: BACKGROUND: Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) differ in the severity of disease. We hypothesized that characteristics of SARS-CoV-2–specific immunity correlate with disease severity. METHODS: In this study, SARS-CoV-2–specific T cells and antibodies were characterized in uninfected controls and patients with different coronavirus disease 2019 (COVID-19) disease severity. SARS-CoV-2–specific T cells were flow cytometrically quantified after stimulation with SARS-CoV-2 peptide pools and analyzed for expression of cytokines (IFN-γ, IL-2, and TNF-α) and markers for activation, proliferation, and functional anergy. SARS-CoV-2–specific IgG and IgA antibodies were quantified using ELISA. Moreover, global characteristics of lymphocyte subpopulations were compared between patient groups and uninfected controls. RESULTS: Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2–specific T cells as compared with convalescent individuals. SARS-CoV-2–specific CD4(+) T cells dominated over CD8(+) T cells and closely correlated with the number of plasmablasts and SARS-CoV-2–specific IgA and IgG levels. Unlike in convalescent patients, SARS-CoV-2–specific T cells in patients with severe disease showed marked alterations in phenotypical and functional properties, which also extended to CD4(+) and CD8(+) T cells in general. CONCLUSION: Given the strong induction of specific immunity to control viral replication in patients with severe disease, the functionally altered characteristics may result from the need for contraction of specific and general immunity to counteract excessive immunopathology in the lung. FUNDING: The study was supported by institutional funds to MS and in part by grants of Saarland University, the State of Saarland, and the Rolf M. Schwiete Stiftung. url: https://www.ncbi.nlm.nih.gov/pubmed/32937615/ doi: 10.1172/jci.insight.142167 id: cord-305589-ofpna4k1 author: Schubert, Katharina title: SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date: 2020-07-07 words: 4090.0 sentences: 229.0 pages: flesch: 55.0 cache: ./cache/cord-305589-ofpna4k1.txt txt: ./txt/cord-305589-ofpna4k1.txt summary: By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. Based on these results we assembled in vitro a 40S-Nsp1 complex and determined its structure at 2.8 Å resolution using cryo-EM (Extended Data Fig. 2 ). As observed in the high-resolution structure of the 40S-Nsp1 complex, the C-terminal part of Nsp1 in the mRNA entrance channel (Fig. 1e ) folds into two helices that interact with h18 of the 18S rRNA as well as proteins uS3 in the head and uS5 and eS30 in the body, respectively ( Fig. 1f; Fig. 2a ). Our structural data suggest that SARS-CoV-2 Nsp1 inhibits translation by sterically occluding the entrance region of the mRNA channel and interfering with binding of cellular mRNAs (Fig. 4a,b) . abstract: The non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, is the first viral protein that is synthesized in SARS-CoV-2 infected human cells to suppress host innate immune functions1,2. By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. The protein inserts its C-terminal domain at the entrance to the mRNA channel where it interferes with mRNA binding. We observe potent translation inhibition in the presence of Nsp1 in lysates from human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5’ untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines inhibition of translation by Nsp1 with efficient translation of the viral mRNA to achieve expression of viral genes3. url: https://doi.org/10.1101/2020.07.07.191676 doi: 10.1101/2020.07.07.191676 id: cord-332303-0bbw64p5 author: Schuit, Michael title: Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date: 2020-06-11 words: 3598.0 sentences: 241.0 pages: flesch: 54.0 cache: ./cache/cord-332303-0bbw64p5.txt txt: ./txt/cord-332303-0bbw64p5.txt summary: This study examined the effect of simulated sunlight, relative humidity, and suspension matrix on the stability of SARS-CoV-2 in aerosols. Therefore, the present study examined the influence of both simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in different liquid matrices. Two different environmentally controlled rotating drum aerosol chambers, with volumes of 16-L and 208-L, were used in the present study to expose aerosols containing SARS-CoV-2 to controlled levels of temperature, relative humidity, and simulated sunlight. The present study examined the influence of simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in either simulated saliva or culture medium at 20°C. The half-lives estimated from the mean decay constants across all relative humidity levels without simulated sunlight present were 55 and 86 minutes for aerosols generated from virus suspended in culture medium and simulated saliva, respectively. abstract: Aerosols represent a potential route of transmission of COVID-19. This study examined the effect of simulated sunlight, relative humidity, and suspension matrix on the stability of SARS-CoV-2 in aerosols. Both simulated sunlight and matrix significantly affected the decay rate of the virus. Relative humidity alone did not affect the decay rate; however, minor interactions between relative humidity and the other factors were observed. Decay rates in simulated saliva, under simulated sunlight levels representative of late winter/early fall and summer were 0.121±0.017 min(-1) (90% loss: 19 minutes) and 0.379±0.072 min(-1) (90% loss: 6 minutes), respectively. The mean decay rate without simulated sunlight across all relative humidity levels was 0.008±0.011 min(-1) (90% loss: 125 minutes). These results suggest that the potential for aerosol transmission of SARS-CoV-2 may be dependent on environmental conditions, particularly sunlight. These data may be useful to inform mitigation strategies to minimize the potential for aerosol transmission. url: https://doi.org/10.1093/infdis/jiaa334 doi: 10.1093/infdis/jiaa334 id: cord-347428-2isuaiyx author: Schulz-Stübner, Sebastian title: Hygiene in der Anästhesie in Zeiten der SARS-CoV-2-Pandemie date: 2020-07-31 words: 1435.0 sentences: 177.0 pages: flesch: 50.0 cache: ./cache/cord-347428-2isuaiyx.txt txt: ./txt/cord-347428-2isuaiyx.txt summary: Im Verlauf kann es bei etwa 20 % der Patienten zu einer klinischen Verschlechterung kommen, mit Entwicklung von Dyspnoe und/oder Hypoxämien, typischerweise ca. In einer systematischen Übersicht aus dem Jahr 2016 wurde gezeigt, dass N95-Atemschutzmasken (entspricht FFP2) zwar im Laborversuch einen größeren Schutz gegen die Erreger akuter Atemwegsinfektionen einschließlich pandemischer Influenza zu bieten scheinen als chirurgische Masken, dass sich mittels Metaanalyse aber kein höherer Schutzeffekt für medizinisches Personal bei klinischer Anwendung nachweisen lässt [8] . Sie berichtet retrospektiv, in einer Gondelbahn neben einer Person mit Symptomen einer viralen Atemwegsinfektion gesessen zu haben, sie entwickelt 4 Tage nach Arbeitsbeginn selbst Symptome und wird positiv auf SARS-CoV-2 getestet. Effectiveness of N95 respirators versus surgical masks in protecting health care workers from acute respiratory infection: a systematic review and meta-analysis Medical masks vs N95 respirators for preventing COVID-19 in healthcare workers: A systematic review and meta-analysis of randomized trials. abstract: It is necessary to discuss the sometimes competing goals of sufficient critical care capacity, maintenance of regular patient care, protection of medical staff, interruption of infectious chains within the general public and individual aspects of patient care in anesthesia and the operating room in times of the SARS CoV-2 pandemic, given the uncertainty of many data on which decisions need to be based. Basic hygiene remains the cornerstone of infection prevention especially when resources are sparse and SARS-CoV-2 specific additional measures need to be taken according to a risk analysis taking the dynamic of the pandemic as well as local factors into account. url: https://www.ncbi.nlm.nih.gov/pubmed/32736389/ doi: 10.1055/a-1174-7359 id: cord-281677-pspmmrq7 author: Schulze-Koops, Hendrik title: Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie e. V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 date: 2020-08-05 words: 1199.0 sentences: 117.0 pages: flesch: 43.0 cache: ./cache/cord-281677-pspmmrq7.txt txt: ./txt/cord-281677-pspmmrq7.txt summary: V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Daten aus COVID-19-Registern, Fallserien und Fallberichten legen aber nach derzeitigem Wissensstand nahe, dass Patienten mit ERE im Vergleich zur nicht rheumatisch erkrankten Bevölkerung kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 aufweisen [7] [8] [9] [10] [11] . unten) -die medikamentöse antirheumatische Therapie ein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt [11] . Abstract A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Aktuelle Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie für die Betreuung von Patienten mit rheumatischen Erkrankungen während der SARS-CoV-2/Covid 19-Pandemie abstract: A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). These first recommendations were based on an expert consensus and were largely non-evidence-based. Now that the first scientific data from registers, cross-sectional studies, case reports and case series are available, the present update is intended to update the previous recommendations and to add new findings. The current recommendations are based on a literature search of publications available up to 15 June 2020 and address preventive measures (such as hygiene measures or vaccinations) and the use of immunomodulatory/immunosuppressive drugs. An important goal of the current recommendations is also to prevent harm to patients with IRD through unjustified restriction of care. The DGRh will continue to update its recommendations in the case of new aspects and will publish them as well as further information on the COVID-19 pandemic on its homepage (www.dgrh.de) in an ongoing process. url: https://doi.org/10.1007/s00393-020-00851-x doi: 10.1007/s00393-020-00851-x id: cord-347262-q88g1561 author: Schutzer‐Weissmann, J. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 words: 4753.0 sentences: 279.0 pages: flesch: 39.0 cache: ./cache/cord-347262-q88g1561.txt txt: ./txt/cord-347262-q88g1561.txt summary: Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review abstract: The protection of healthcare workers from the risk of nosocomial severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is a paramount concern. SARS‐CoV‐2 is likely to remain endemic and measures to protect healthcare workers against nosocomial infection will need to be maintained. This review aims to inform the assessment and management of the risk of SARS‐CoV‐2 transmission to healthcare workers involved in elective peri‐operative care. In the absence of data specifically related to the risk of SARS‐CoV‐2 transmission in the peri‐operative setting, we explore the evidence‐base that exists regarding modes of viral transmission, historical evidence for the risk associated with aerosol‐generating procedures and contemporaneous data from the COVID‐19 pandemic. We identify a significant lack of data regarding the risk of transmission in the management of elective surgical patients, highlighting the urgent need for further research. url: https://doi.org/10.1111/anae.15221 doi: 10.1111/anae.15221 id: cord-124012-5zxkd2jy author: Schwab, Patrick title: predCOVID-19: A Systematic Study of Clinical Predictive Models for Coronavirus Disease 2019 date: 2020-05-17 words: 5098.0 sentences: 247.0 pages: flesch: 38.0 cache: ./cache/cord-124012-5zxkd2jy.txt txt: ./txt/cord-124012-5zxkd2jy.txt summary: Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. In addition, [48] performed a cohort study for clinical and laboratory predictors of COVID-19 related inhospital mortality that identified baseline neutrophil count, age Fig. 2 : The presented multistage machine-learning pipeline consists of preprocessing (light purple) the input data x, developing multiple candidate models using the given dataset (orange), selecting the best candidate model for evaluation (blue), and evaluating the selected best model''s outputsŷ. Owing to the recent emergence of SARS-CoV-2, there currently exists, to the best of our knowledge, no prior systematic study on clinical predictive models that predict likelihood of a positive SARS-CoV-2 test, hospital and intensive care unit admission from clinical, demographic and blood analysis data that accounts for the missingness that is characteristic for the clinical setting. abstract: Coronavirus Disease 2019 (COVID-19) is a rapidly emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the rapid human-to-human transmission of SARS-CoV-2, many healthcare systems are at risk of exceeding their healthcare capacities, in particular in terms of SARS-CoV-2 tests, hospital and intensive care unit (ICU) beds and mechanical ventilators. Predictive algorithms could potentially ease the strain on healthcare systems by identifying those who are most likely to receive a positive SARS-CoV-2 test, be hospitalised or admitted to the ICU. Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. To evaluate the predictive performance of our models, we perform a retrospective evaluation on clinical and blood analysis data from a cohort of 5644 patients. Our experimental results indicate that our predictive models identify (i) patients that test positive for SARS-CoV-2 a priori at a sensitivity of 75% (95% CI: 67%, 81%) and a specificity of 49% (95% CI: 46%, 51%), (ii) SARS-CoV-2 positive patients that require hospitalisation with 0.92 AUC (95% CI: 0.81, 0.98), and (iii) SARS-CoV-2 positive patients that require critical care with 0.98 AUC (95% CI: 0.95, 1.00). In addition, we determine which clinical features are predictive to what degree for each of the aforementioned clinical tasks. Our results indicate that predictive models trained on routinely collected clinical data could be used to predict clinical pathways for COVID-19, and therefore help inform care and prioritise resources. url: https://arxiv.org/pdf/2005.08302v1.pdf doi: nan id: cord-327501-8s6dvanf author: Schwaiger, Julia title: No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date: 2020-09-17 words: 2367.0 sentences: 124.0 pages: flesch: 52.0 cache: ./cache/cord-327501-8s6dvanf.txt txt: ./txt/cord-327501-8s6dvanf.txt summary: Testing 54 intravenous immunoglobulin preparations, produced from plasma collected in Europe and the United States, confirmed highly potent neutralization of a seasonal coronavirus; however, no cross-neutralization of the new SARS-CoV-2 was seen. The question is of significant clinical relevance, as SARS-CoV-2 cross-neutralizing antibodies in IVIGs, if they were present, might afford some protection to people with immune deficiencies and may even represent a treatment option for coronavirus disease 2019 (COVID-19) patients. The current study tested a representative number of IVIG lots for nAbs against SARS-CoV-2 and the longer-circulating HCoV-229E, to establish clarity about cross-neutralization of the pandemic virus by antibodies induced by earlier circulating seasonal coronaviruses. SARS-CoV-2 nAb titers were below the limit of detection for all 54 IVIG lots tested, irrespective of geographic origin of the plasma (Europe vs United States) and plasma collection modality (recovered vs source) ( Figure 1A) . abstract: The 2020 SARS-CoV-2 pandemic is caused by a zoonotic coronavirus transmitted to humans, similar to earlier events. Whether the other, seasonally circulating coronaviruses induce cross-reactive, potentially even cross-neutralizing, antibodies to the new species in humans is unclear. The question is particularly relevant for people with immune deficiencies, as their health depends on treatment with immunoglobulin preparations that need to contain neutralizing antibodies against the pathogens in their environment. Testing 54 intravenous immunoglobulin preparations, produced from plasma collected in Europe and the United States, confirmed highly potent neutralization of a seasonal coronavirus; however, no cross-neutralization of the new SARS-CoV-2 was seen. url: https://www.ncbi.nlm.nih.gov/pubmed/32941626/ doi: 10.1093/infdis/jiaa593 id: cord-342739-iy9vjpuh author: Schwartz, David A. title: Potential Maternal and Infant Outcomes from Coronavirus 2019-nCoV (SARS-CoV-2) Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections date: 2020-02-10 words: 8414.0 sentences: 406.0 pages: flesch: 49.0 cache: ./cache/cord-342739-iy9vjpuh.txt txt: ./txt/cord-342739-iy9vjpuh.txt summary: In order to assess the potential of the Wuhan 2019-nCoV to cause maternal, fetal and neonatal morbidity and other poor obstetrical outcomes, this communication reviews the published data addressing the epidemiological and clinical effects of SARS, MERS, and other coronavirus infections on pregnant women and their infants. The most common adverse obstetrical outcomes associated with maternal pneumonias from all causes include This newly recognized coronavirus, producing a disease that has been termed COVID-19, is rapidly spreading throughout China, has crossed international borders to infect persons in neighboring countries, and humans infected by the virus are travelling via commercial airlines to other continents. Pregnant women may develop severe disease and fatal maternal and/or fetal outcomes as a result of MERS-CoV infection; however, little is known of the pathophysiology of this infection during pregnancy. abstract: In early December 2019 a cluster of cases of pneumonia of unknown cause was identified in Wuhan, a city of 11 million persons in the People’s Republic of China. Further investigation revealed these cases to result from infection with a newly identified coronavirus, initially termed 2019-nCoV and subsequently SARS-CoV-2. The infection moved rapidly through China, spread to Thailand and Japan, extended into adjacent countries through infected persons travelling by air, eventually reaching multiple countries and continents. Similar to such other coronaviruses as those causing the Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS), the new coronavirus was reported to spread via natural aerosols from human-to-human. In the early stages of this epidemic the case fatality rate is estimated to be approximately 2%, with the majority of deaths occurring in special populations. Unfortunately, there is limited experience with coronavirus infections during pregnancy, and it now appears certain that pregnant women have become infected during the present 2019-nCoV epidemic. In order to assess the potential of the Wuhan 2019-nCoV to cause maternal, fetal and neonatal morbidity and other poor obstetrical outcomes, this communication reviews the published data addressing the epidemiological and clinical effects of SARS, MERS, and other coronavirus infections on pregnant women and their infants. Recommendations are also made for the consideration of pregnant women in the design, clinical trials, and implementation of future 2019-nCoV vaccines. url: https://doi.org/10.3390/v12020194 doi: 10.3390/v12020194 id: cord-308356-ojx3tasi author: Schwarz, Silke title: Corona bei Kindern: Die Co-Ki Studie: Relevanz von SARS-CoV-2 in der ambulanten pädiatrischen Versorgung in Deutschland date: 2020-11-03 words: 1258.0 sentences: 172.0 pages: flesch: 64.0 cache: ./cache/cord-308356-ojx3tasi.txt txt: ./txt/cord-308356-ojx3tasi.txt summary: Hintergrund Die aktuelle Studienlage deutet darauf hin, dass Kinder und Jugendliche eine geringere Rate symptomatischer SARS-CoV-2-Infektionen (COVID-19) aufweisen als Erwachsene und mehrheitlich keine oder nur milde Symptome entwickeln [1] [2] [3] . Darüber hinaus ist leider nicht bekannt, wie viele der vom RKI erfassten Kinder symptomatisch waren, und ob ihre etwaigen Symptome auf SARS-CoV-2 zurückzuführen sind. Diese KJÄ meldeten insgesamt 9803 Kinder und Jugendliche, die aufgrund eines Verdachts der Eltern oder eines Kontaktes mit einem SARS-CoV-2-Infizierten in der Sprechstunde vorgestellt wurden. Die KJÄ ihrerseits hatten den klinischen Verdacht auf eine SARS-CoV-2-Infektion bei 3654 Kindern, wobei einzelne KJÄ mehr eigene Verdachtsfälle als Vorstellungen mit Verdacht meldeten, und das Wort "ebenfalls" in Frage 4 wohl ignorierten, weshalb die 3654 nicht eine reine Teilmenge von den 9803 sind. Die höhere Rate an Antikörperpositivität hängt mit der Tatsache zusammen, dass mehr Kinder getestet wurden, die zuvor Symptome und/oder einen positiven PCR-Test hatten. abstract: BACKGROUND: In Germany over 80% of children and adolescents are in the ambulatory care of registered pediatricians. These have a specific perspective on the COVID-19 pandemic. METHODS: For this reason, this professional group initiated a central recording of case numbers, individual case descriptions and observations on infections and illnesses with SARS-CoV‑2 (www.co-ki.de). RESULTS: So far 557 pediatricians have participated. Together they care for ca. 670,000 children. They reported 9803 children who presented as suspected cases. The pediatricians themselves had a clinical suspicion of SARS-CoV‑2 infections in 3654 children. In 7707 children PCR tests were carried out using nose/throat swabs of which 198 (2.6%) were positive. In addition, 731 children were tested for SARS-CoV‑2 antibodies with detection in 82 cases (11.2%). Despite initially positive PCR tests, 47 children had a negative antibody test at least 2 weeks later. Our query as to infections of adults by children yielded only one case, which a telephone enquiry revealed as unlikely. DISCUSSION: From an outpatient pediatric perspective COVID-19 is rare. There was no convincing evidence that children are a relevant source of infection for SARS-CoV‑2 nor that they are relevantly at risk. url: https://www.ncbi.nlm.nih.gov/pubmed/33162611/ doi: 10.1007/s00112-020-01050-3 id: cord-331666-iwkuwnun author: Schweitzer, Wolf title: Implications for forensic death investigations from first Swiss post-mortem CT in a case of non-hospital treatment with COVID-19 date: 2020-06-30 words: 3810.0 sentences: 191.0 pages: flesch: 49.0 cache: ./cache/cord-331666-iwkuwnun.txt txt: ./txt/cord-331666-iwkuwnun.txt summary: Comment: With the pandemic impact of SARS-COV-2, a range of issues unfolds, also for medicolegal investigations into deaths, as we report the first Swiss case with post-mortem CT where death had occurred due to a SARS-COV-2 infection, with features of a severe acute respiratory distress syndrome, as an outpatient. Control: Case of a 24 year old woman who had no acute respiratory distress syndrome related findings at all; there was post-mortem hypostasis dorsally at the right lung. While this man''s subjective report apparently did not include dyspnea, even less than a day prior to his death, the pulmonary pathology of this outpatient, as evidenced by PMCT, appears to extend beyond the severity shown in descriptions of currently published SARS-CoV-2-related fatalities, all of which apparently had obtained prior hospital and intensive-care treatment [39] [40] [41] . As post-mortem RT-PCR testing for SARS-CoV-2 in a forensic setting may not be available or too slow, PMCT may identify lung changes possibly related to COVID-19. abstract: Abstract Case details: A case of a 50-year old HIV-positive man is presented, with focus on visualization of post-mortem computed tomography (PMCT) of the lungs, in comparison to a forensic control case. He had been found dead at home, a day after his nasopharyngeal swab had returned positive for SARS-COV-2, three days after the sample had been taken as an outpatient, over five weeks after first exhibiting possible symptoms. 3D-visualization was performed by visually discriminating correlates for aerated, poorly aerated and non-aerated lung regions. The visual side-by-side comparison with a control case shows the deterioration beyond any ”normal” post-mortem finding, however. The PMCT findings in the lungs resemble those of patients with acute respiratory distress syndrome (ARDS), while histologically identified inflammation also shows, in part binuclear, lymphocytes. In addition, acute liver dystrophy and acute tubular necrosis in the kidneys were found. Except coronary artery atherosclerosis, there appeared to be no remarkable pathology of the heart. Comment: With the pandemic impact of SARS-COV-2, a range of issues unfolds, also for medicolegal investigations into deaths, as we report the first Swiss case with post-mortem CT where death had occurred due to a SARS-COV-2 infection, with features of a severe acute respiratory distress syndrome, as an outpatient. As this pandemic from the view of risk assessment does constitute a black swan, underestimated fat tails as technical reason should be addressed by also analyzing apparent extreme single observations. This case of an outpatient (without hospital or intensive-care treatment) shows a pulmonary progression beyond the typical findings of COVID-19, to a non-specific picture of ARDS, where histologically, in part binuclear lymphocytes were remarked. What appeared to be an initially slow progression with final rapid escalation raises the question whether nasopharyngeal swabs alone or added pulmonary CT might be better for screening high-risk patients. The reported symptoms and relatively late medical consultation in this case appeared to contrast with the extensive pathology, raising the question whether any search for super-spreaders should not just focus on asymptomatic but under-reported symptomatic patients, and whether their prolonged circulation in everyday life would justify measures such as for example more extensive face mask policies. As post-mortem testing for SARS-COV-2 may not be available for every case, PMCT may provide sensitive testing for lung changes related to COVID-19. In order to allow for more precise medicolegal investigations in the context of COVID-19, however, any more specific extra tests may have to be financed by stakeholders in epidemiology, infectious disease or policy. url: https://api.elsevier.com/content/article/pii/S2666225620300270 doi: 10.1016/j.fri.2020.200378 id: cord-319799-h9kot3og author: Schäfer, Alexandra title: Epigenetic Landscape during Coronavirus Infection date: 2017-02-15 words: 10080.0 sentences: 465.0 pages: flesch: 33.0 cache: ./cache/cord-319799-h9kot3og.txt txt: ./txt/cord-319799-h9kot3og.txt summary: By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host''s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. By utilizing Calu3 cells, we have developed a robust human model platform to study innate immune regulatory control and epigenetics following emerging coronavirus and influenza virus infections as well as other highly pathogenic viruses ( Figure 6 ). Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. abstract: Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus–host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype. Epigenetic modifications, such as histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, function as important regulators that remodel host chromatin, altering host expression patterns and networks in a highly flexible manner. For most of the past two and a half decades, research has focused on the molecular mechanisms by which RNA viruses antagonize the signaling and sensing components that regulate induction of the host innate immune and antiviral defense programs upon infection. More recently, a growing body of evidence supports the hypothesis that viruses, even lytic RNA viruses that replicate in the cytoplasm, have developed intricate, highly evolved, and well-coordinated processes that are designed to regulate the host epigenome, and control host innate immune antiviral defense processes, thereby promoting robust virus replication and pathogenesis. In this article, we discuss the strategies that are used to evaluate the mechanisms by which viruses regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus infections as a model. By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host’s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/28212305/ doi: 10.3390/pathogens6010008 id: cord-284867-p4jgyusp author: Schöler, Lara title: A Novel In-Cell ELISA Assay Allows Rapid and Automated Quantification of SARS-CoV-2 to Analyze Neutralizing Antibodies and Antiviral Compounds date: 2020-10-09 words: 4328.0 sentences: 235.0 pages: flesch: 42.0 cache: ./cache/cord-284867-p4jgyusp.txt txt: ./txt/cord-284867-p4jgyusp.txt summary: Altogether, the SARS-CoV-2 icELISA test allows rapid (<48 h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs and antiviral drugs using reagents and equipment present in most routine diagnostics departments. The fact that the infection and the resulting icELISA signal were neutralized by NAbs present in immune sera indicated that the fast and automated icELISA format is applicable for icNTs. Although most SARS-CoV-2 NTs have not been formally validated and certified, classic plaque reduction neutralization tests (PRNT) are currently considered to represent the gold standard for the detection of SARS-CoV-2-specific NAbs. Various commercially available IgM, IgA, and IgG ELISAs have been compared to PRNTs [e.g., (30) ]. Given the excellent signal-to-noise ratio between infected and uninfected cells, the test was applicable to quantify the efficacy of antiviral compounds, here shown for IFNb, and SARS-CoV-2-specific NAbs present in immune sera. abstract: The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most pressing medical and socioeconomic challenge. Constituting important correlates of protection, the determination of virus-neutralizing antibodies (NAbs) is indispensable for convalescent plasma selection, vaccine candidate evaluation, and immunity certificates. In contrast to standard serological ELISAs, plaque reduction neutralization tests (PRNTs) are laborious, time-consuming, expensive, and restricted to specialized laboratories. To replace microscopic counting-based SARS-CoV-2 PRNTs by a novel assay exempt from genetically modified viruses, which are inapplicable in most diagnostics departments, we established a simple, rapid, and automated SARS-CoV-2 neutralization assay employing an in-cell ELISA (icELISA) approach. After optimization of various parameters such as virus-specific antibodies, cell lines, virus doses, and duration of infection, SARS-CoV-2-infected cells became amenable as direct antigen source for quantitative icELISA. Antiviral agents such as human sera containing NAbs or antiviral interferons dose dependently reduced the SARS-CoV-2-specific signal. Applying increased infectious doses, the icELISA-based neutralization test (icNT) was superior to PRNT in discriminating convalescent sera with high from those with intermediate neutralizing capacities. In addition, the icNT was found to be specific, discriminating between SARS-CoV-2-specific NAbs and those raised against other coronaviruses. Altogether, the SARS-CoV-2 icELISA test allows rapid (<48 h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs and antiviral drugs using reagents and equipment present in most routine diagnostics departments. url: https://doi.org/10.3389/fimmu.2020.573526 doi: 10.3389/fimmu.2020.573526 id: cord-324919-ciamusjs author: Scialo, Filippo title: ACE2: The Major Cell Entry Receptor for SARS-CoV-2 date: 2020-11-10 words: 5356.0 sentences: 257.0 pages: flesch: 42.0 cache: ./cache/cord-324919-ciamusjs.txt txt: ./txt/cord-324919-ciamusjs.txt summary: Since the beginning of the COVID-19 pandemic, hypertension and diabetes have been correlated with higher risk of mortality, and initial reports speculated that angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs), which are commonly used therapeutic agents for these conditions, would up-regulate ACE2 expression, thus increasing the risk of severe illness [37] . Binding of S1 subunit of the Spike protein of SARS-CoV-2 to the ACE2 receptor triggers the cleavage of ACE2 by ADAM17/tumor necrosis factorconverting enzyme (TACE) at the ectodomain sites [41] and a soluble form that retains its catalytic activity (sACE2) is produced [42] . ACE2 shedding can be stimulated by proinflammatory cytokines such as IL-1β and tumor necrosis factor (TNF)-α, and endotoxin [47] that could result in a positive effect reducing SARS-CoV-2 entry, but at the same time, may cause an increase in AngII and further activation of the AngII/AT1R axis worsening inflammation (discussed below) (Fig. 1) . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: Despite the unprecedented effort of the scientific community, the novel SARS-CoV-2 virus has infected more than 46 million people worldwide, killing over one million two hundred thousand. Understanding the mechanisms by which some individuals are more susceptible to SARS-CoV-2 infection and why a subgroup of them are prone to experience severe pneumonia, and death should lead to a better approach and more effective treatments for COVID-19. Here, we focus our attention on ACE2, a primary receptor of SARS-CoV-2. We will discuss its biology, tissue expression, and post-translational regulation that determine its potential to be employed by SARS-CoV-2 for cell entry. Particular attention will be given to how the ACE2 soluble form can have a great impact on disease progression and thus be used in a potential therapeutic strategy. Furthermore, we will discuss repercussions that SARS-CoV-2/ACE2 binding has on the renin–angiotensin system and beyond. Indeed, although mostly neglected, ACE2 can also act on [des-Arg 937]-bradykinin of the kinin–kallikrein system regulating coagulation and inflammation. Thorough comprehension of the role that ACE2 plays in different pathways will be the key to assess the impact that SARS-CoV-2/ACE2 binding has on organismal physiology and will help us to find better therapies and diagnostic tools. url: https://doi.org/10.1007/s00408-020-00408-4 doi: 10.1007/s00408-020-00408-4 id: cord-275979-cx2h5bsw author: Scutelnic, Adrian title: Vascular Events, Vascular Disease and Vascular Risk Factors—Strongly Intertwined with COVID-19 date: 2020-10-08 words: 6747.0 sentences: 342.0 pages: flesch: 46.0 cache: ./cache/cord-275979-cx2h5bsw.txt txt: ./txt/cord-275979-cx2h5bsw.txt summary: According to the INTERSTROKE study, the 10 most frequent modifiable vascular risk factors are arterial hypertension, physical inactivity, overweight, dyslipidaemia, smoking, unhealthy diet, cardiac pathologies, diabetes mellitus, stress/depression and overconsumption of alcohol. Also, a higher rate of infection with COVID-19, severe COVID-19 and bad outcome has been demonstrated in patients with pre-existing vascular disease and vascular risk factors. A higher rate of infection with COVID-19, severe COVID-19, and worse outcome has been demonstrated in patients with pre-existing vascular disease and risk factors, compared with young and healthy persons [1, 6, 8-11, 28, 29] . Several potential mechanisms increasing this risk of COVID-19 in patients with diabetes mellitus have been proposed: (1) higher affinity of cellular binding of SARS-CoV-2 and higher levels of circulating furin facilitating virus entry, (2) increased ACE2 expression in the lungs, (3) decreased viral clearance, (4) diminished T cell function, (5) increased susceptibility to inflammation and cytokine storm syndrome and (6) co-existence of vascular disease and risk factors [5] . abstract: PURPOSE OF REVIEW: To elucidate the intertwining of vascular events, vascular disease and vascular risk factors and COVID-19. RECENT FINDINGS: Strokes are a leading cause of disability and death worldwide. Vascular risk factors are important drivers of strokes. There are unmodifiable vascular risk factors such as age and ethnicity and modifiable vascular risk factors. According to the INTERSTROKE study, the 10 most frequent modifiable vascular risk factors are arterial hypertension, physical inactivity, overweight, dyslipidaemia, smoking, unhealthy diet, cardiac pathologies, diabetes mellitus, stress/depression and overconsumption of alcohol. Also, infection and inflammation have been shown to increase the risk of stroke. There is high-quality evidence for the clinical benefits of optimal primary and secondary stroke prevention. The COVID-19 pandemic brought a new perspective to this field. Vascular events, vascular disease and vascular risk factors—and COVID-19—are strongly intertwined. An increased risk of vascular events—by multifactorial mechanisms—has been observed in COVID-19 patients. Also, a higher rate of infection with COVID-19, severe COVID-19 and bad outcome has been demonstrated in patients with pre-existing vascular disease and vascular risk factors. SUMMARY: At present, we suggest that regular interactions between healthcare professionals and patients should include education on COVID-19 and on primary and secondary vascular prevention in order to reduce the burden of disease in our ageing populations. url: https://doi.org/10.1007/s11940-020-00648-y doi: 10.1007/s11940-020-00648-y id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 words: 8320.0 sentences: 382.0 pages: flesch: 36.0 cache: ./cache/cord-306424-gf0bglm0.txt txt: ./txt/cord-306424-gf0bglm0.txt summary: Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus abstract: The potential health risks associated with (re-)emerging positive-strand RNA (+RNA) viruses emphasizes the need for understanding host-pathogen interactions for these viruses. The innate immune system forms the first line of defense against pathogenic organisms like these and is responsible for detecting pathogen-associated molecular patterns (PAMPs). Viral RNA is a potent inducer of antiviral innate immune signaling, provoking an antiviral state by directing expression of interferons (IFNs) and pro-inflammatory cytokines. However, +RNA viruses developed various methods to avoid detection and downstream signaling, including isolation of viral RNA replication in membranous viral replication organelles (ROs). These structures therefore play a central role in infection, and consequently, loss of RO integrity might simultaneously result in impaired viral replication and enhanced antiviral signaling. This review summarizes the first indications that the innate immune system indeed has tools to disrupt viral ROs and other non- or aberrant-self membrane structures, and may do this by marking these membranes with proteins such as microtubule-associated protein 1A/1B-light chain 3 (LC3) and ubiquitin, resulting in the recruitment of IFN-inducible GTPases. Further studies should evaluate whether this process forms a general effector mechanism in +RNA virus infection, thereby creating the opportunity for development of novel antiviral therapies. url: https://api.elsevier.com/content/article/pii/S1359610117300667 doi: 10.1016/j.cytogfr.2017.05.007 id: cord-284234-9cd2v6bt author: Sebastian, S title: Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date: 2020-06-10 words: 4483.0 sentences: 256.0 pages: flesch: 44.0 cache: ./cache/cord-284234-9cd2v6bt.txt txt: ./txt/cord-284234-9cd2v6bt.txt summary: Understandable concerns have been raised on the safety of steroids, immunosuppressive drugs, and biologics used in patients for a variety of indications including immune mediated inflammatory disease such as inflammatory bowel diseases (IBD), which do increase the risk of opportunistic bacterial, viral and fungal infections (5) . Therefore, continuing concerns remain both from IBD patients and the A c c e p t e d M a n u s c r i p t clinicians managing them, regarding the potential of IBD related drugs causing more frequent infections by SARS-CoV2, and increased risk of severe complications from COVID-19 (13) . Corticosteroids are thought to have a divergent effect on viral infections including SARS COV viruses; on one hand they inhibit host immune response acting on migration and chemokines production leading to impaired viral clearance and the resultant prolonged Moreover, a prospective, randomized double-blinded, placebo-controlled trial compared early hydrocortisone treatment (before day seven of the illness) with a placebo and found that early hydrocortisone therapy was associated with a higher subsequent plasma viral load (61) . abstract: The Coronavirus 2019 (COVID-19) pandemic has posed challenges in the routine care of patients with inflammatory bowel disease. One of the key challenges needing addressing is the quantification of the risks of immunosuppressive and biologic therapies in IBD patients during the pandemic. The similarities and differences between the previous coronavirus outbreaks and the pathobiology of the infections can give useful information in understanding the risks, and perhaps potential beneficial aspects of drugs used in IBD. Although clinical, immunological and pharmacological data from the experience with the previous coronavirus outbreaks cannot be automatically translated to predict the safety of IBD therapies during COVID-19 pandemic, the signals so far from these outbreaks on IBD patients who are on immunomodulators and biologics are reassuring to patients and clinicians alike. url: https://doi.org/10.1093/ecco-jcc/jjaa120 doi: 10.1093/ecco-jcc/jjaa120 id: cord-284589-j1609xlu author: Sedova, Mayya title: Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence date: 2020-05-29 words: 1302.0 sentences: 85.0 pages: flesch: 55.0 cache: ./cache/cord-284589-j1609xlu.txt txt: ./txt/cord-284589-j1609xlu.txt summary: RESULTS: Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context. At the same time, with the exception of the spike protein mutations, there are no publicly available resources that provide analysis for all the other structurally characterized regions of the SARS-CoV-2 proteins. For commercial re-use, please contact journals.permissions@oup.com MN908947.3), with information on boundaries of the predicted proteins, currently available SARS-CoV-2 structures and a histogram of the aminoacid mutation frequency. The first of the lower level panels (Figure 1b) provides interactive visualization of the selected structure or model, with an option for coloring the chain according to the mutation frequency. The Coronavirus3D server was designed to provide users with information and tools to carry out their own analysis of how mutations in the SARS-CoV-2 proteins may affect their 3D-structures and their functions. abstract: MOTIVATION: As the COVID-19 pandemics is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome. RESULTS: Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context. AVAILABILITY: Coronavirus3D server is freely available at https://coronavirus3d.org. url: https://doi.org/10.1093/bioinformatics/btaa550 doi: 10.1093/bioinformatics/btaa550 id: cord-284163-3jmqzemf author: Seffer, Malin-Theres title: Heparin 2.0: A New Approach to the Infection Crisis date: 2020-07-02 words: 2982.0 sentences: 156.0 pages: flesch: 43.0 cache: ./cache/cord-284163-3jmqzemf.txt txt: ./txt/cord-284163-3jmqzemf.txt summary: This narrative review will give a brief overview regarding some of the extracorporeal devices that could be used to treat COVID-19 patients, including the Seraph® 100 Microbind® Affinity Blood Filter, produced by ExThera Medical (Martinez, CA, USA), first licensed in the European Economic Area in 2019. Bacteria, viruses, fungi, and toxins have been shown to bind to the immobilized heparin in a similar way to the interaction with heparan sulfate on the cell surface. Of note, it has recently been demonstrated that SARS-CoV-2 attaches to heparin through its surface protein Spike 1 receptor-binding domain [21] . The Seraph ® 100 Microbind ® Affinity Blood Filter is an extracorporeal hemoperfusion device whose functional core, that is, polyethylene beads (diameter of 0.3 mm) with immobilized heparin bound to it, mimics a naturally mammalian cell surface (Fig. 1) . Cytokines in blood from septic patients interact with surface-immobilized heparin abstract: In April 2020, the US Food and Drug Administration granted emergency use authorization for certain medical devices to be used in patients with coronavirus disease 2019 (CO­VID-19). This included extracorporeal blood purification devices. This narrative review will give a brief overview regarding some of the extracorporeal devices that could be used to treat COVID-19 patients, including the Seraph® 100 Microbind® Affinity Blood Filter, produced by ExThera Medical (Martinez, CA, USA), first licensed in the European Economic Area in 2019. The Seraph® 100 contains ultrahigh molecular weight polyethylene beads with end point-attached heparin and is approved for the reduction of pathogens from the bloodstream either as a single agent or as an adjunct to conventional anti-infective agents. Bacteria, viruses, fungi, and toxins have been shown to bind to the immobilized heparin in a similar way to the interaction with heparan sulfate on the cell surface. This binding is nonreversible and as such, the pathogens are removed from the bloodstream. In this review, we describe the pathophysiological basis and rationale for using heparin for pathogen removal from the blood as well as exploring the technology behind the adaptation of heparin to deprive it of its systemic anticoagulant activity. In addition, we summarize the in vitro data as well as the available preclinical testing and published clinical reports. Finally, we discuss the enormous potential of this technology in an era of increasing antibiotic resistance and high mortality associated with sepsis and consider the application of this as a possible treatment option for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32615569/ doi: 10.1159/000508647 id: cord-309418-dx6e0lri author: Segalés, Joaquim title: Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain date: 2020-10-06 words: 3135.0 sentences: 178.0 pages: flesch: 48.0 cache: ./cache/cord-309418-dx6e0lri.txt txt: ./txt/cord-309418-dx6e0lri.txt summary: Several models for SARS-CoV-2 infection have been so far developed in animals, including Egyptian fruit bat, ferret, golden Syrian hamster, cat, humanized angiotensin-converting enzyme 2 (ACE2) transgenic mice (hACE2 mice), and some nonhuman primate species (3) (4) (5) (6) (7) (8) . The clinical condition was finally attributed to a feline hypertrophic cardiomyopathy, but the animal was also infected by SARS-CoV-2. The detection of SARS-CoV-2 RNA in several samples of C1, all of them with Ct values over 30 (low viral load), and presence of antibodies (neutralizing and nonneutralizing) in both C1 and C2, indicated both animals suffered from a productive viral infection, probably linked to the exposure of the cats to COVID-19−affected owners. These experimental results, together with the few reports on SARS-CoV-2 detection in domestic cats and wild felids, indicate that felines are susceptible to infection by the novel coronavirus. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is considered a zoonotic pathogen mainly transmitted human to human. Few reports indicate that pets may be exposed to the virus. The present report describes a cat suffering from severe respiratory distress and thrombocytopenia living with a family with several members affected by COVID-19. Clinical signs of the cat prompted humanitarian euthanasia and a detailed postmortem investigation to assess whether a COVID-19−like disease was causing the condition. Necropsy results showed the animal suffered from feline hypertrophic cardiomyopathy and severe pulmonary edema and thrombosis. SARS-CoV-2 RNA was only detected in nasal swab, nasal turbinates, and mesenteric lymph node, but no evidence of histopathological lesions compatible with a viral infection were detected. The cat seroconverted against SARS-CoV-2, further evidencing a productive infection in this animal. We conclude that the animal had a subclinical SARS-CoV-2 infection concomitant to an unrelated cardiomyopathy that led to euthanasia. url: https://doi.org/10.1073/pnas.2010817117 doi: 10.1073/pnas.2010817117 id: cord-312178-tojgojjf author: Segars, James title: Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known? date: 2020-04-16 words: 5355.0 sentences: 309.0 pages: flesch: 48.0 cache: ./cache/cord-312178-tojgojjf.txt txt: ./txt/cord-312178-tojgojjf.txt summary: Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a pandemic of Coronavirus Disease 2019 (COVID-19) across the globe. The novel SARS-CoV-2 virus spreads rapidly, with 2-3 people infected from every index case, a reproduction number (R 0 ) or transmission rate of 2.24 -3.58 (2) . The aim of this review is to summarize what is currently known about the impact of prior coronaviruses and the novel SARS-CoV-2 infection on reproduction and pregnancy. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: Report of two cases & review of the literature An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes abstract: Structured Abstract Objective To summarize current understanding of the effects of novel and prior coronaviruses on human reproduction, specifically male and female gametes, and in pregnancy. Design Review of English publications in PubMed and Embase to April 6, 2020. Methods Manuscripts were screened for reports including coronavirus, reproduction, including pathophysiology and pregnancy. Intervention(s) None. Main Outcome Measure(s) Reproductive outcomes; effects on gametes; pregnancy outcomes; neonatal complications. Results Seventy-nine reports formed the basis of the review. Coronavirus binding to cells involves the S1 domain of the spike protein to receptors present in reproductive tissues, including angiotensin converting enzyme-2 (ACE2), CD26, Ezrin, and cyclophilins. SARS-CoV-1 may cause severe orchitis leading to germ cell destruction in males. Reports indicate decreased sperm concentration and motility for 72-90 days following COVID-19 infection. Gonadotropin-dependent expression of ACE2 was found in human ovaries, but it is unclear whether SARS-CoV-2 adversely affects female gametogenesis. Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. COVID-19 infections in pregnancy are associated with preterm delivery. Postpartum neonatal transmission from mother to child has been reported. Conclusion COVID-19 infection may adversely affect some pregnant women and their offspring. Additional studies are needed to assess effects of SARS-CoV-2 infection on male and female fertility. url: https://www.ncbi.nlm.nih.gov/pubmed/32482250/ doi: 10.1016/j.fertnstert.2020.04.025 id: cord-295794-glcg36si author: Seghers, Victor J. title: After the initial COVID-19 surge: a phased radiology departmental re-opening plan date: 2020-08-22 words: 4747.0 sentences: 201.0 pages: flesch: 37.0 cache: ./cache/cord-295794-glcg36si.txt txt: ./txt/cord-295794-glcg36si.txt summary: Social distancing, stay home/work safe orders, protective measures for vulnerable individuals (e.g., immunocompromised patients), masking protocols, visitation policies, testing and many more measures resulted in an accelerated but necessary ramping down of elective hospital services [4] [5] [6] [7] [8] [9] . While the radiologist-in-chief also participates in daily meetings with other clinical service chiefs and executive leadership for the hospital, the radiologist-in-chief is an integral member of the systemwide "Phased Recovery and Redesign Team" as well, which includes team captains for infection control, surgery, anesthesia, emergency and urgent care centers, radiology, pathology, ambulatory medicine, specialty care centers, e-health, revenue cycle and billing, and marketing and public relations. This can include patient-directed online scheduling and expanded access to imaging, offering same-day service with hours and locations adapted to the patient and family lifestyle; improved use of virtual dashboards to more easily track various metrics including MR efficiency, sedation utilization, and length of patient stay in the imaging department; and investment in Table 2 Radiology: the opportunity to re-design operations post COVID-19 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32827259/ doi: 10.1007/s00247-020-04792-0 id: cord-274948-ze6scnae author: Segondy, Michel title: Les Coronavirus humains date: 2020-10-31 words: 2469.0 sentences: 262.0 pages: flesch: 64.0 cache: ./cache/cord-274948-ze6scnae.txt txt: ./txt/cord-274948-ze6scnae.txt summary: Toutefois, à côté de ces infections à coronavirus endémiques, ont récemment émergé chez l''homme, à partir de réservoirs animaux, des coronavirus responsables de syndromes respiratoires sévères avec un taux de mortalité élevé [2] . Ce sont des virus enveloppés dont le génome est un ARN de polarité positive d''une taille de l''ordre de 30 kilobases, ce qui en fait le génome le plus grand chez les virus à ARN [3] . Des coronavirus génétiquement très proches du Mers-CoV ont été identifiés chez des chauves-souris qui représentent le réservoir de virus [29] . Bien que le plus souvent inapparente ou bénigne chez le jeune enfant, l''infection par le Sars-CoV-2 peut être à l''origine d''un syndrome hyper inflammatoire similaire à la maladie de Kawasaki [38] . ◗t Les coronavirus émergents sont responsables d''infections respiratoires sévères avec une mortalité élevée. En moins de vingt ans, ce sont trois coronavirus responsables d''infections respiratoires sévères avec une mortalité élevée qui ont émergé dans la population humaine. abstract: Four coronaviruses cause frequent and most often mild respiratory infections in humans: HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU 1. In addition to these endemic human coronaviruses, three new coronaviruses of zoonotic origin have emerged in the human population over the past 20 years. SARS-CoV (-1) appeared in 2003, MERS-CoV appeared in 2012, and SARS-CoV-2 appeared in 20l9. These three coronaviruses are the causative agents of a severe respiratory syndrome. The epidemic of the severe acute respiratory syndrome (SARS) due to SARS-CoV-l affected approximately 8,000 individuals and caused approximately 800 deaths but was brought under control within a few months. MERS-CoV has caused more than 2,500 cases since 20l2 with a mortality of around 35 %. SARS-CoV-2 is currently responsible for a major pandemic with significant mortality in the elderly or in patients with underlying diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/33163102/ doi: 10.1016/s1773-035x(20)30311-7 id: cord-322417-9e95m4kz author: Segovia-Juarez, Jose title: High altitude reduces infection rate of COVID-19 but not case-fatality rate date: 2020-07-15 words: 1256.0 sentences: 88.0 pages: flesch: 59.0 cache: ./cache/cord-322417-9e95m4kz.txt txt: ./txt/cord-322417-9e95m4kz.txt summary: authors: Segovia-Juarez, Jose; Castagnetto, Jesús M.; Gonzales, Gustavo F. title: High altitude reduces infection rate of COVID-19 but not case-fatality rate It is suggested that life at high altitude may reduce COVID infections and case-fatality rates (cases/deaths). A recent paper with data as of April 7th from the Tibet, Bolivia and Ecuador suggests that high-altitude (HA) may provide protection from pathogenesis of SAR-CoV-2 infection (Arias-Reyes et al, 2020). The current study has been designed to determine COVID-19 cases, deaths by COVID-19 and case-fatality rates in Peru in an altitude range from 3 to 4,342 meters above sea level. The sex ratio (male/female) for positive cases of COVID-19 is maintained at any altitude of residence ( Figure 1D ). Another important finding from our study is that the cumulative case-fatality rate (cumulative deaths/cumulative positive cases) by COVID-19 does not appear to change with altitude of residence ( Figure 3 ). abstract: Coronavirus disease 19 (COVID-19) is a pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It is suggested that life at high altitude may reduce COVID infections and case-fatality rates (cases/deaths). We study data from Peru COVID-19 pandemics, which first case was recorded on March 6th, 2020. By June 13, 2020 there were 6498 deaths, and 224,132 SARS-CoV-2 positives. Using data from 185 capitals of provinces with altitudes ranging from 3 to 4342 m, we confirm previous reports that infection with COVID-19 at high altitude is reduced. However, case-fatality rate is not dependent of altitude. We have also presented first evidence that female protection towards death by COVID-19 is reduced as altitude of residence increases. url: https://api.elsevier.com/content/article/pii/S156990482030152X doi: 10.1016/j.resp.2020.103494 id: cord-308075-1ftswsm8 author: Segura, Patricia Sanz title: Involvement of the digestive system in COVID-19. A review date: 2020-10-09 words: 4829.0 sentences: 247.0 pages: flesch: 47.0 cache: ./cache/cord-308075-1ftswsm8.txt txt: ./txt/cord-308075-1ftswsm8.txt summary: 4 Recent studies have indicated detection of SARS-CoV-2 by PCR in the faeces of infected patients, with a higher prevalence in those with gastrointestinal symptoms, in particular diarrhoea. Moreover, the cohort studies that have analysed the course of COVID-19 in patients with viral hepatitis (hepatitis B) 41 and those that have assessed the impact of non-alcoholic fatty liver disease on the disease due to the novel coronavirus, especially in the absence of obesity, have concluded that there is a higher risk of developing a serious form of pneumonia and having more prolonged hospital stays, 42 although the available data in this regard remain insufficient. abstract: The SARS-CoV-2 pandemic is leading to high mortality and a global health crisis. The primary involvement is respiratory; however, the virus can also affect other organs, such as the gastrointestinal tract and liver. The most common symptoms are anorexia and diarrhea. In about half of the cases, viral RNA could be detected in the stool, which is another line of transmission and diagnosis. COVID19 has a worse prognosis in patients with comorbidities, although there is not enough evidence in case of previous digestive diseases. Digestive endoscopies may give rise to aerosols, which make them techniques with a high risk of infection. Experts and scientific organizations worldwide have developed guidelines for preventive measures. The available evidence on gastrointestinal and hepatic involvement, the impact on patients with previous digestive diseases and operating guidelines for Endoscopy Units during the pandemic are reviewed. url: https://www.sciencedirect.com/science/article/pii/S2444382420301565 doi: 10.1016/j.gastre.2020.06.004 id: cord-319571-fspmgg4s author: Sehailia, Moussa title: Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 date: 2020-07-22 words: 4894.0 sentences: 232.0 pages: flesch: 49.0 cache: ./cache/cord-319571-fspmgg4s.txt txt: ./txt/cord-319571-fspmgg4s.txt summary: Although, functional importance of different targets has been linked to the viral replication and maturation of coronaviruses'' family such as Chymotrypsin-like protease(3CLpro) or known as Mpro (Khan et al., 2020; Muralidharan et al., 2020) or Envelope protein (E) (Gupta et al., 2020; Boopathi et al., 2020) but it has been confirmed that the binding of the viral trimeric surface spike glycoprotein (SProtein) of SARS-CoV-2 to the human receptor angiotensin-converting enzyme 2 (hACE2) is the first step in host infection . Therefore, it is very likely that selective interaction of HCQ with the surface of SARS-CoV-2 SProtein through the formation of an inclined tape over the hydrophobic pocket responsible for hosting the Lys353 hotspot (the OH group in this case is acting like a hook by forming a hydrogen bond with Asn501), can be responsible for the prevention of tighter binding with hACE2 protein via restricting penetration of Lys353 into its finally assigned destination on the SProtein RBD (Figure 2 ). abstract: Medicinal herbs have proved along history to be a source of multiple cures. In this paper, we demonstrate how hydroxychloroquine can act as a good inhibitor of SARS-CoV-2 Spike protein receptor-binding-domain using molecular docking studies. We also unveil how hydroxychloroquine can interfere in the prevention of Lys353 in hACE2 from interacting with the corresponding binding hotspot present on the Spike protein. Further screening of artemisinin & derived compounds produced better Vina docking score than hydroxychloroquine (-7.1 kcal mol(−1) for artelinic acid vs. −5.5 kcal mol(−1) for hydroxychloroquine). Artesunate, artemisinin and artenimol, showed two mode of interactions with Lys353 and Lys31 binding hotspots of the Spike protein. Molecular dynamics analysis confirmed that the formed complexes are able to interact and remain stable in the active site of their respective targets. Given that these molecules are effective antivirals with excellent safety track records in humans against various ailment, we recommend their potential repurposing for the treatment of SARS-CoV-2 patients after successful clinical studies. In addition, an extraction protocol for artemisinin from Artemisia annua L. is proposed in order to cope with the potential urgent global demand. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32696720/ doi: 10.1080/07391102.2020.1796809 id: cord-336722-41eqt97y author: Sehmi, P. title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review date: 2020-06-29 words: 1688.0 sentences: 131.0 pages: flesch: 59.0 cache: ./cache/cord-336722-41eqt97y.txt txt: ./txt/cord-336722-41eqt97y.txt summary: title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review Recent studies have confirmed the presence of SARS-CoV-2 nucleic acids in feces of Coronavirus disease 2019 (COVID-19) patients using RT-PCR tests. Larger studies are needed to corroborate these findings, as well as to determine its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. . https://doi.org/10.1101/2020.06.27.20105429 doi: medRxiv preprint A total of 4 studies describing isolation of live SARS-CoV-2 virus in fecal samples of COVID-19 patients were included. The findings from these four studies, though limited by the small sample sizes, confirm that live SARS-CoV-2 virus is present in fecal samples of COVID-19 patients, and therefore supports the hypothesis that COVID-19 could potentially be transmitted via the feco-oral route. Larger high-quality studies are urgently needed to better characterize the magnitude of live SARS-CoV-2 viral shedding in feces, as well as its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. abstract: Coronavirus disease 2019 (COVID-19) is a rapidly escalating pandemic that has spread to many parts of the world. The disease has already affected over 6 million individuals, with over 400,000 fatalities. Recent studies have confirmed the presence of SARS-CoV-2 nucleic acids in feces of Coronavirus disease 2019 (COVID-19) patients using RT-PCR tests. It is however, still unclear as to whether or not live SARS-CoV-2 virus is actually present in feces of these patients. In this rapid review, we systematically analyzed literature to establish any evidence of live SARS-CoV-2 virus in fecal samples of COVID-19 patients. We identified 4 studies (one case report, 2 case series and 1 cohort study) where the SARS-CoV-2 was successfully isolated from fecal samples of COVID-19 patients using culture techniques. Therefore, there is some evidence COVID-19 could shed live SARS-CoV-2 virus via the gastro-intestinal tract. Larger studies are needed to corroborate these findings, as well as to determine its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. url: https://doi.org/10.1101/2020.06.27.20105429 doi: 10.1101/2020.06.27.20105429 id: cord-353373-zhkqnu0w author: Seidu, Samuel title: The impact of obesity on severe disease and mortality in people with SARS‐CoV‐2: A systematic review and meta‐analysis date: 2020-08-14 words: 2872.0 sentences: 159.0 pages: flesch: 50.0 cache: ./cache/cord-353373-zhkqnu0w.txt txt: ./txt/cord-353373-zhkqnu0w.txt summary: BACKGROUND: Obesity accompanied by excess ectopic fat storage has been postulated as a risk factor for severe disease in people with SARS‐CoV‐2 through the stimulation of inflammation, functional immunologic deficit and a pro‐thrombotic disseminated intravascular coagulation with associated high rates of venous thromboembolism. METHODS: Observational studies in COVID‐19 patients reporting data on raised body mass index at admission and associated clinical outcomes were identified from MEDLINE, Embase, Web of Science and the Cochrane Library up to 16 May 2020. 2 Recent studies have increasingly described obesity as an associating factor for people at an increased risk of severe disease. 15 In order to attempt to quantify the relationship between raised body weight and severe outcomes from COVID-19, we conducted a systematic review and meta-analysis to determine whether people with overweight or obesity and with SARS-CoV-2 have different outcomes compared to those within normal weight thresholds. abstract: BACKGROUND: Obesity accompanied by excess ectopic fat storage has been postulated as a risk factor for severe disease in people with SARS‐CoV‐2 through the stimulation of inflammation, functional immunologic deficit and a pro‐thrombotic disseminated intravascular coagulation with associated high rates of venous thromboembolism. METHODS: Observational studies in COVID‐19 patients reporting data on raised body mass index at admission and associated clinical outcomes were identified from MEDLINE, Embase, Web of Science and the Cochrane Library up to 16 May 2020. Mean differences and relative risks (RR) with 95% confidence intervals (CIs) were aggregated using random effects models. RESULTS: Eight retrospective cohort studies and one cohort prospective cohort study with data on of 4,920 patients with COVID‐19 were eligible. Comparing BMI ≥ 25 vs <25 kg/m(2), the RRs (95% CIs) of severe illness and mortality were 2.35 (1.43‐3.86) and 3.52 (1.32‐9.42), respectively. In a pooled analysis of three studies, the RR (95% CI) of severe illness comparing BMI > 35 vs <25 kg/m(2) was 7.04 (2.72‐18.20). High levels of statistical heterogeneity were partly explained by age; BMI ≥ 25 kg/m(2) was associated with an increased risk of severe illness in older age groups (≥60 years), whereas the association was weaker in younger age groups (<60 years). CONCLUSIONS: Excess adiposity is a risk factor for severe disease and mortality in people with SARS‐CoV‐2 infection. This was particularly pronounced in people 60 and older. The increased risk of worse outcomes from SARS‐CoV‐2 infection in people with excess adiposity should be taken into account when considering individual and population risks and when deciding on which groups to target for public health messaging on prevention and detection measures. Systematic review registration: PROSPERO 2020: CRD42020179783. url: https://www.ncbi.nlm.nih.gov/pubmed/32904932/ doi: 10.1002/edm2.176 id: cord-326375-8m4110k3 author: Seitzman, Gerami D. title: No Time for Tears date: 2020-03-26 words: 968.0 sentences: 77.0 pages: flesch: 52.0 cache: ./cache/cord-326375-8m4110k3.txt txt: ./txt/cord-326375-8m4110k3.txt summary: In this issue, Jun et al, 1 (https:// www.aaojournal.org/article/S0161-6420(20)30311-0/fulltext) from the National Health Care Group Eye Institute in Singapore, report that they were unable to detect SARS-CoV-2 in the tears of 17 patients diagnosed with COVID-19. 2, 3 In a separate study that evaluated conjunctival swabs of 30 patients with COVID-19 pneumonia in China, only 1 patient demonstrated conjunctivitis, and those swabs showed positive results for SARS-CoV-2 by reverse-transcriptase polymerase chain reaction analysis. Patients who seek treatment from an ophthalmologist and screen positive for signs, symptoms, or both of COVID-19 should forgo an eye examination for prompt SARS-CoV-2 screening. Patients with conjunctivitis seeking treatment from ophthalmology departments should be considered contagious, and SARS-CoV-2 precautions should be taken. Assessing viral shedding and infectivity of tears in coronavirus disease 2019 (COVID-19) patients SARS-CoV-2 viral load in upper respiratory specimens of infected patients Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32303374/ doi: 10.1016/j.ophtha.2020.03.030 id: cord-312115-foy3dsq4 author: Sekine, Takuya title: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 date: 2020-08-14 words: 4891.0 sentences: 272.0 pages: flesch: 52.0 cache: ./cache/cord-312115-foy3dsq4.txt txt: ./txt/cord-312115-foy3dsq4.txt summary: In line with these data, we found that CD8 + T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) more commonly expressed CD38, but not HLA-DR, Ki-67, or PD-1, in patients with acute moderate or severe COVID-19 compared with convalescent individuals and healthy blood donors, indicating limited bystander activation and proliferation during the early phase of infection with SARS-CoV-2 ( Figure 2A , B and Figure S3C ). On the basis of these observations, we quantified functional SARS-CoV-2-specific memory T cell responses across five distinct cohorts, including healthy individuals who donated blood either before or during the pandemic, family members who shared a household with convalescent individuals and were exposed at the time of symptomatic disease, and individuals in the convalescent phase after mild or severe COVID-19. These donors exhibited robust memory T cell responses months after infection, even in the absence of detectable circulating antibodies specific for SARS-CoV-2, indicating a previously unanticipated degree of population-level immunity against COVID-19. abstract: Summary SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19. We here systematically mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in unexposed individuals, exposed family members, and individuals with acute or convalescent COVID-19. Acute phase SARS-CoV-2-specific T cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent phase SARS-CoV-2-specific T cells were polyfunctional and displayed a stem-like memory phenotype. Importantly, SARS-CoV-2-specific T cells were detectable in antibody-seronegative exposed family members and convalescent individuals with a history of asymptomatic and mild COVID-19. Our collective dataset shows that SARS-CoV-2 elicits robust, broad and highly functional memory T cell responses, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0092867420310084?v=s5 doi: 10.1016/j.cell.2020.08.017 id: cord-309541-2vqk7fx1 author: Sekizuka, Tsuyoshi title: Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak date: 2020-08-18 words: 3302.0 sentences: 161.0 pages: flesch: 50.0 cache: ./cache/cord-309541-2vqk7fx1.txt txt: ./txt/cord-309541-2vqk7fx1.txt summary: Here, we have generated a haplotype network of the SARS-CoV-2 outbreak using genome-wide single nucleotide variations (SNVs), identifying the genotypes of isolates that disseminated in the DP cruise ship after quarantine on February 5, 2020. The frequencies of SNVs suggested that all 73 isolates shared a SNV: The G nucleotide at the 11,083 position on the Wuhan-Hu-1 genome sequence was mutated to T (G 11083 T transversion), leading to a nonsynonymous amino Significance On February 5, 2020, the Diamond Princess cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed to have coronavirus disease 2019. Maximum-likelihood (ML) phylogenetic analysis including other SARS-CoV-2 genome sequences that are publicly available on GISAID and haplotype networks from genomic SNVs (HN-GSNVs) were used to map the genotypes of the SARS-CoV-2 isolates that disseminated in the DP cruise ship after isolation of the passengers on February 5, 2020 (Fig. 2) . abstract: The Diamond Princess cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed as a coronavirus disease 2019 case. We performed whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from PCR(+) clinical specimens and conducted a phylogenetic analysis of the outbreak. All tested isolates exhibited a transversion at G(11083)T, suggesting that SARS-CoV-2 dissemination on the Diamond Princess originated from a single introduction event before the quarantine started. Although further spreading might have been prevented by quarantine, some progeny clusters could be linked to transmission through mass-gathering events in the recreational areas and direct transmission among passengers who shared cabins during the quarantine. This study demonstrates the usefulness of haplotype network/phylogeny analysis in identifying potential infection routes. url: https://www.ncbi.nlm.nih.gov/pubmed/32723824/ doi: 10.1073/pnas.2006824117 id: cord-310392-fmobf1f1 author: Sekizuka, Tsuyoshi title: SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date: 2020-06-05 words: 2410.0 sentences: 132.0 pages: flesch: 59.0 cache: ./cache/cord-310392-fmobf1f1.txt txt: ./txt/cord-310392-fmobf1f1.txt summary: A field FIGURE 1 | Summary of travel history, clinical course, and PCR testing for 10 SARS-CoV-2-positive travelers who returned to Japan from Egypt, as well as the associated patients who were their close contacts. In this study, we have evaluated viral genome sequences from SARS-CoV-2-positive travelers who returned from Egypt, and characterized the haplotype networks to demonstrate possible routes of the spread. SARS-CoV-2 genome sequences with nearly fulllength information (≥ 29 kb) were retrieved from the GISAID EpiCoV database on March 30, 2020, and we generated haplotype networks by median-joining network analysis using PopART software 3 to highlight and trace a potential infectious route among COVID-19 patient populations. P2-1 and P2-2 had visited Egypt together and traveled aboard the same Nile River cruise ship, and SARS-CoV-2 genome sequences isolated from them are identical with that of P1 (Figure 3) . abstract: Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries. url: https://doi.org/10.3389/fmicb.2020.01316 doi: 10.3389/fmicb.2020.01316 id: cord-315085-rucfowvv author: Sekulic, Miroslav title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date: 2020-05-26 words: 5025.0 sentences: 302.0 pages: flesch: 47.0 cache: ./cache/cord-315085-rucfowvv.txt txt: ./txt/cord-315085-rucfowvv.txt summary: In this study we report postmortem findings and detection and sequencing of SARS-CoV-2 viral RNA from formalin-fixed paraffinembedded (FFPE) samples of multiple organs collected in 2 patients with antemortem detection of SARS-CoV-2. The patient''s medical history was otherwise notable for dementia, radiologic evidence of a left lung mass (managed with hospice care), coronary artery disease (status post coronary artery bypass grafting), atrial fibrillation (biventricular pacemaker implanted), congestive heart failure, peripheral artery disease (status post iliac stenting), diabetes mellitus, hypertension, dyslipidemia, chronic kidney disease, gout, smoking, cerebrovascular accidents, and urinary tract infections. On day 1 after admission, ❚Image 2❚ (Case 1) Postmortem microscopic examination of the lungs showed diffuse alveolar damage characterized by hyaline membrane formation (A, ×100) and scattered squamous metaplasia of distal airways (B, ×100) on a background of emphysematous changes. abstract: OBJECTIVES: To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals. METHODS: Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks. RESULTS: Postmortem examinations revealed diffuse alveolar damage, while no viral-associated hepatic, cardiac, or renal damage was observed. Viral RNA was detected in lungs, bronchi, lymph nodes, and spleen in both cases using qRT-PCR method. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation. CONCLUSIONS: SARS-CoV-2 testing and viral sequencing can be performed from FFPE tissue. Detection and sequencing of SARS-CoV-2 in combination with morphological findings from postmortem tissue examination can aid in gaining a better understanding of the virus’s pathophysiologic effects on human health. url: https://doi.org/10.1093/ajcp/aqaa091 doi: 10.1093/ajcp/aqaa091 id: cord-289255-qwzg7prx author: Seligman, Stephen J. title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date: 2007-02-15 words: 642.0 sentences: 43.0 pages: flesch: 55.0 cache: ./cache/cord-289255-qwzg7prx.txt txt: ./txt/cord-289255-qwzg7prx.txt summary: title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants have reported data on a 386-nt deletion in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) [1] . Because 1 patient had both the L386del variant and the wild-type variant in the same specimen, they raised the possibility that SARS-CoV exists as a quasi species, at least in some patients. Previous authors studying single-nucleotide variants from Beijing-area isolates in 2003 [2] and from the Singapore 2004 outbreak [3] have also found multiple viral sequences in the same sample that they attributed to quasi species. Although these 3 studies clearly establish the presence of a diversity of SARS-CoV genomes in individual patients, the issue of whether SARS-CoV quasi species exists remains open, particularly with respect to the 386-nt deletion. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? SARS-associated coronavirus quasispecies in individual patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17230423/ doi: 10.1086/510917 id: cord-310063-8nbmrjrw author: Selva, K. J. title: Distinct systems serology features in children, elderly and COVID patients date: 2020-05-18 words: 3779.0 sentences: 218.0 pages: flesch: 55.0 cache: ./cache/cord-310063-8nbmrjrw.txt txt: ./txt/cord-310063-8nbmrjrw.txt summary: . https://doi.org/10.1101 /2020 6 147 To interrogate Ab functionality and cross-reactivity between antigens of selected CoV signatures, we 148 conducted a correlation network analysis, focusing upon significant correlations of Ab features 149 selected by Elastic-Net. The children''s network (Figure 1f ) demonstrates how SARS-CoV-2 Abs that 150 engaged FcγRIIa-H131 are associated with SARS-CoV-2 IgG, specifically of IgG1 subclass. In particular, we found that in the majority of COVID-19 190 patients, the SARS-CoV-2 antigen-specific Abs bound to FcγRIIIaV158 and FcγRIIaH131 soluble 191 dimers at high levels, even at 1:800 plasma titrations, suggesting potent ADCC and ADCP CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.05.11.20098459 doi: medRxiv preprint 8 notably being the healthy exposed SARS-CoV-2 PCR-negative individual (Figure 3d) The majority of COVID-19 moderate/severe samples were collected upon hospital presentation, 235 whereas mild samples were collected upon convalescence (Extended Data Table 3 ). abstract: SARS-CoV-2, the pandemic coronavirus that causes COVID-19, has infected millions worldwide, causing unparalleled social and economic disruptions. COVID-19 results in higher pathogenicity and mortality in the elderly compared to children. Examining baseline SARS-CoV-2 cross-reactive coronavirus immunological responses, induced by circulating human coronaviruses, is critical to understand such divergent clinical outcomes. The cross-reactivity of coronavirus antibody responses of healthy children (n=89), adults (n=98), elderly (n=57), and COVID-19 patients (n=19) were analysed by systems serology. While moderate levels of cross-reactive SARS-CoV-2 IgG, IgM, and IgA were detected in healthy individuals, we identified serological signatures associated with SARS-CoV-2 antigen-specific Fc{gamma} receptor binding, which accurately distinguished COVID-19 patients from healthy individuals and suggested that SARS-CoV-2 induces qualitative changes to antibody Fc upon infection, enhancing Fc{gamma} receptor engagement. Vastly different serological signatures were observed between healthy children and elderly, with markedly higher cross-reactive SARS-CoV-2 IgA and IgG observed in elderly, whereas children displayed elevated SARS-CoV-2 IgM, including receptor binding domain-specific IgM with higher avidity. These results suggest that less-experienced humoral immunity associated with higher IgM, as observed in children, may have the potential to induce more potent antibodies upon SARS-CoV-2 infection. These key insights will inform COVID-19 vaccination strategies, improved serological diagnostics and therapeutics. url: http://medrxiv.org/cgi/content/short/2020.05.11.20098459v1?rss=1 doi: 10.1101/2020.05.11.20098459 id: cord-336177-p7b7yw28 author: Selvi, Valeria title: Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives date: 2020-09-22 words: 5461.0 sentences: 265.0 pages: flesch: 45.0 cache: ./cache/cord-336177-p7b7yw28.txt txt: ./txt/cord-336177-p7b7yw28.txt summary: Regarding the pandemic 2009 influenza A H1N1, the results from the prospective cohort study by Hung and colleagues showed that plasma treatment reduced mortality (the patients involved in the study were seriously ill and required intensive care); no adverse events were observed [4, 8, 20] . A meta-analysis by Mair-Jenkins and colleagues, including 32 studies of SARS coronavirus and severe influenza, reported that convalescent plasma reduced mortality and it was safe (no relevant adverse events or complications after treatment were reported). Based on the evidence from past experience in passive immunization, the BRN explained that there was a considerable possibility that the application of whole blood (as well as plasma, serum, or immunoglobulin concentrates) from convalescent persons could be effective in the treatment/prevention of infectious disease. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection abstract: On March 11(th), 2020, the World Health Organization declared COVID-19 infection as a pandemic. Since it is a novel virus, there are basically no proven drugs or therapies; although many laboratories in different countries are working to develop a vaccine, it will take time to make it available. Passive immunization is the therapy born from the intuition of Behring and Kisato in the late 19(th) century. It was widely used for the treatment of bacterial infections until the discovery of antibiotics, as well as during the viral pandemics of the 20(th) century and of the beginning of the 21(st); it still has clinical applications (e.g., tetanus prevention). This paper summarizes the basic principles of passive immunization, with particular reference to convalescent plasma. The literature concerning its use during past epidemics and the results of the first clinical studies concerning its use during the current pandemic are discussed too. A large section is dedicated to the analysis of the possible, although rare, side effects. Recently, in 2017, the WHO Blood Regulators Network (BRN) published a position paper, recommending convalescent plasma as the first-choice treatment to be tested in the absence of authorized drugs; however, this strategy has not been followed. In the current epidemic, the principle of passive immunization through convalescent plasma has been applied in several circumstances and particularly in patients with serious complications. The first reported results are encouraging and confirm the effectiveness of plasma therapy and its safety. Also, the FDA has proposed plasma treatment in order to face the increasingly complex situation and manage patients with serious or immediately life-threatening COVID-19 disease. Several studies and clinical programs are still ongoing. url: https://doi.org/10.1155/2020/2606058 doi: 10.1155/2020/2606058 id: cord-269496-tnw7sxlh author: Sen Gupta, Parth Sarthi title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 words: 4910.0 sentences: 246.0 pages: flesch: 53.0 cache: ./cache/cord-269496-tnw7sxlh.txt txt: ./txt/cord-269496-tnw7sxlh.txt summary: Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). Together, being conserved and a necessary component for the replication of coronavirus, a multi-functional protein, Nsp13-helicase, is another vital SARS-COV-2 target (Jia et al., 2019) , which can be considered further for antiviral drug discovery provided a very small number of Nsp13 inhibitors reported to date . Molecular docking of Ivermectin with twelve SARS-COV-2''s targets along with Importin-a was carried out, followed by binding mechanism exploration and structural stability analysis using molecular dynamics (MD) simulation through the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g ), and binding free energy of the complexes of Ivermectin with the best targets. abstract: While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ∼5000 folds within 48 h, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets along with Importin-α studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting −10.4 kcal/mol and −9.6 kcal/mol, respectively, followed by Importin-α with −9.0 kcal/mol. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. url: https://doi.org/10.1080/07391102.2020.1839564 doi: 10.1080/07391102.2020.1839564 id: cord-280922-w6a5ec06 author: Sen, Sanjana title: Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date: 2020-10-29 words: 4134.0 sentences: 289.0 pages: flesch: 55.0 cache: ./cache/cord-280922-w6a5ec06.txt txt: ./txt/cord-280922-w6a5ec06.txt summary: Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Furthermore, a recent review on antibody-dependent enhancement of SARS-CoV-2 stated, "At present, there are no known clinical findings, immunological assays or biomarkers that can differentiate any severe infection from immune-enhanced disease, whether by measuring antibodies, T cells or intrinsic host responses (7) ." This conclusion inspired our study. The results demonstrate that Abs to a specific epitope from N protein plus disease risk factors strongly correlate with COVID-19 disease severity. The DRFS of patients with αEp9 Abs strongly correlates with COVID-19 disease severity (Pearson''s r = 0.72, p-value <0.0001, and R 2 = 0.52) (Fig. 4A) . abstract: Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the ICU, requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within six days post-symptom onset and sometimes within one day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patient’s comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 Likelihood Ratio (96.72% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention. url: https://doi.org/10.1101/2020.10.15.341743 doi: 10.1101/2020.10.15.341743 id: cord-340138-u8hxyfml author: Seneviratne, Chaminda Jayampath title: The Role of Dentists in COVID-19 Is Beyond Dentistry: Voluntary Medical Engagements and Future Preparedness date: 2020-10-06 words: 3861.0 sentences: 217.0 pages: flesch: 46.0 cache: ./cache/cord-340138-u8hxyfml.txt txt: ./txt/cord-340138-u8hxyfml.txt summary: Keywords: COVID-19, dentistry, voluntary work, preparedness, infection control BACKGROUND The emergence of the highly infectious novel coronavirus has led to a global pandemic in a span of just 3 months. Thus, the robust training of clinical medicine in dentistry strengthens the candidature of dentists to volunteer services for COVID-19 control and spread. Many dentists have therefore discontinued the provision of elective dental treatment, in accordance with guidelines released by national-level government healthcare authorities such as the Centers for Disease Control and Prevention (CDC) in the US and National Health Service (NHS) in the UK. In this context, dental clinics that are well equipped with facilities to control aerosol spread of infections, such as negative pressure rooms and high-volume excavators, can offer help to augment the capacity for COVID-19 screening. Precautions when providing dental care during Coronavirus Disease 2019 (COVID-19) pandemic abstract: The emergence of the highly infectious novel coronavirus SARS-CoV-2 has led to a global COVID-19 pandemic. Since the outbreak of COVID-19, worldwide healthcare systems have been severely challenged. The rapid and explosive surge of positive cases has significantly increased the demand for medical care. Herein we provide a perspective on the role dentists can play in voluntary medical assistance and future preparedness for a similar pandemic. Though dentists and physicians have different scopes of practice, their trainings share many similarities. Hence, dental professionals, with their knowledge of basic human science and sterile surgical techniques, are an invaluable resource in the COVID-19 pandemic response. Overall, it is commendable that many dentists have risen to the challenge in the fight against COVID-19. For example, in Singapore, National Dental Centre Singapore (NDCS) deployed dental clinicians as well as volunteers from research laboratories to screen for suspected cases, provide consultations as well as conduct swabbing operations. Dental practice will be considerably changed in the post-COVID-19 era. There is a greater need to have refresher courses for practicing dentists on new infection control strategies. Moreover, the curriculum in dental schools should be expanded to include competencies in pandemic and disaster relief. In addition, voluntary medical work should be made a part of the community dentistry curriculum. This volunteerism will leave a positive impact on developing the careers of young dentists. Hence, the contribution of dentists beyond dental practice in this pandemic situation will be appreciated by future generations. url: https://www.ncbi.nlm.nih.gov/pubmed/33117825/ doi: 10.3389/fmed.2020.00566 id: cord-301547-d4wt9dqp author: Seng, J. J. B. title: Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics date: 2020-05-11 words: 5400.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-301547-d4wt9dqp.txt txt: ./txt/cord-301547-d4wt9dqp.txt summary: Study selection Studies which evaluated health literacy related to novel coronavirus disease 2019 (COVID-19), Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS) Data extraction Data on the characteristics of study designs, instruments, participants and level of health literacy were collected. Keywords employed in the search strategy included terms related to health literacy as well as the viruses and syndromes implicated in the three coronavirus pandemics which were namely COVID-19, MERS and SARS. Studies which evaluated health literacy related to COVID-19, SARS or MERS among adult participants aged ≥ 18 years old from the general population, healthcare sectors and infected patients were included. Questions from instruments used across included studies were classified into three main themes, which were 1) knowledge, 2) attitudes and 3) practices, to help guide future development of standardised COVID-19 and pandemic health literacy tools. abstract: Background: Health literacy plays an essential role in ones ability to acquire and understand critical medical information in the COVID-19 infodemic and other pandemics. Purpose: To summarize the assessment, levels and determinants of pandemic related health literacy and its associated clinical outcomes. Data sources: Medline, Embase, PsychINFO, CINAHL, arXiv, bioRxiv, medRxiv, and Social Science Research Network. The start date was unrestricted and current as of 22 April 2020. Study selection Studies which evaluated health literacy related to novel coronavirus disease 2019 (COVID-19), Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS) Data extraction Data on the characteristics of study designs, instruments, participants and level of health literacy were collected. Items used in instruments were grouped under the themes of knowledge, attitudes and practices. Determinants of health literacy were grouped into five domains (socio-demographic, medical, psychological/psychiatric, health systems related and others). Data synthesis: Of 2,065 articles screened, 70 articles were included. 21, 17 and 32 studies evaluated health literacy related to COVID-19, SARS and MERS, respectively. The rates of low pandemic health literacy ranged from 4.3 to 57.9% among medical-related populations and 4.0% to 82.5% among non-medical populations. Knowledge about symptoms and transmission of infection; worry about infection and, practices related to mask usage and hand hygiene was most frequently evaluated. Socio-demographic determinants of health literacy were most studied, where higher education level, older age and female gender were associated with better health literacy. No studies evaluated outcomes associated with health literacy. Limitations Non-English articles were excluded. Conclusion: The level of pandemic related health literacy is sub-optimal. Healthcare administrators need to be aware of health literacy determinants when formulating policies in pandemics. url: https://doi.org/10.1101/2020.05.07.20094227 doi: 10.1101/2020.05.07.20094227 id: cord-342756-rgm9ffpk author: Senger, Mario Roberto title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 words: 16108.0 sentences: 1024.0 pages: flesch: 51.0 cache: ./cache/cord-342756-rgm9ffpk.txt txt: ./txt/cord-342756-rgm9ffpk.txt summary: Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. abstract: Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/33027420/ doi: 10.1590/0074-02760200254 id: cord-333632-i2bjap7m author: Senthil Kumar, K. J. title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells date: 2020-06-19 words: 3864.0 sentences: 227.0 pages: flesch: 49.0 cache: ./cache/cord-333632-i2bjap7m.txt txt: ./txt/cord-333632-i2bjap7m.txt summary: title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells The results suggest that geranium and lemon essential oils and their derivative compounds are valuable natural anti-viral agents that may contribute to the prevention of the invasion of SARS-CoV-2/COVID-19 into the human body. To the best of our knowledge, this is the first report indicating that geranium and lemon essential oils and their major components citronellol, geraniol, limonene, linalool, and neryl acetate downregulate ACE2 receptor activity in virus-host epithelial cells. In this study, we presented the first piece of evidence that geranium and lemon essential oils and their major compounds, citronellol, geraniol, limonene, linalool, and neryl acetate, could downregulate ACE2 expression in epithelial cells, thereby blocking virus entry into host cells, and eventually preventing viral infection. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease-2019 (COVID-19), is a pandemic disease that has been declared as modern history’s gravest health emergency worldwide. Until now, no precise treatment modality has been developed. The angiotensin-converting enzyme 2 (ACE2) receptor, a host cell receptor, has been found to play a crucial role in virus cell entry; therefore, ACE2 blockers can be a potential target for anti-viral intervention. In this study, we evaluated the ACE2 inhibitory effects of 10 essential oils. Among them, geranium and lemon oils displayed significant ACE2 inhibitory effects in epithelial cells. In addition, immunoblotting and qPCR analysis also confirmed that geranium and lemon oils possess potent ACE2 inhibitory effects. Furthermore, the gas chromatography-mass spectrometry (GC–MS) analysis displayed 22 compounds in geranium oil and 9 compounds in lemon oil. Citronellol, geraniol, and neryl acetate were the major compounds of geranium oil and limonene that represented major compound of lemon oil. Next, we found that treatment with citronellol and limonene significantly downregulated ACE2 expression in epithelial cells. The results suggest that geranium and lemon essential oils and their derivative compounds are valuable natural anti-viral agents that may contribute to the prevention of the invasion of SARS-CoV-2/COVID-19 into the human body. url: https://doi.org/10.3390/plants9060770 doi: 10.3390/plants9060770 id: cord-320848-bz9pf2p6 author: Sepehrinezhad, Ali title: COVID-19 virus may have neuroinvasive potential and cause neurological complications: a perspective review date: 2020-05-16 words: 2758.0 sentences: 186.0 pages: flesch: 52.0 cache: ./cache/cord-320848-bz9pf2p6.txt txt: ./txt/cord-320848-bz9pf2p6.txt summary: Here, we reviewed the evidence of the neuroinvasive potential of coronaviruses and discussed the possible pathogenic processes in CNS infection by COVID-19 to provide a precise insight for future studies. Therefore, the aim of the present study was to review neuroinvasive potential and neurotropism effects of human coronaviruses (HCoVs) and discuss the probable neurological complication followed by COVID-19 to give an insight for future studies. We used the terms "coronavirus," "SARS," "SARS-CoV-2," "MERS," "229E-CoV," and "COVID-19," w i t h c o m bi n a t i o n th e t e r m s " n er vo us sy s t e m , " "neuroinvasion," and "neurological manifestation." In vitro studies on neurotropism potentials of CoVs on neural or glial cells cultures were considered. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 abstract: Coronavirus disease 2019 (COVID-19) was reported at the end of 2019 in China for the first time and has rapidly spread throughout the world as a pandemic. Since COVID-19 causes mild to severe acute respiratory syndrome, most studies in this field have only focused on different aspects of pathogenesis in the respiratory system. However, evidence suggests that COVID-19 may affect the central nervous system (CNS). Given the outbreak of COVID-19, it seems necessary to perform investigations on the possible neurological complications in patients who suffered from COVID-19. Here, we reviewed the evidence of the neuroinvasive potential of coronaviruses and discussed the possible pathogenic processes in CNS infection by COVID-19 to provide a precise insight for future studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32418055/ doi: 10.1007/s13365-020-00851-2 id: cord-330626-0aidit63 author: Sepulveda, Jorge title: Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City date: 2020-07-23 words: 2695.0 sentences: 125.0 pages: flesch: 47.0 cache: ./cache/cord-330626-0aidit63.txt txt: ./txt/cord-330626-0aidit63.txt summary: A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase in blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity. Frequent ordering of blood cultures for patients with COVID-19 may overwhelm a laboratory''s capacity to perform and process these tests, which may negatively impact the overall benefit of testing for the entire medical center. abstract: A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase in blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We sought to evaluate the utilization and diagnostic yield of blood cultures during the COVID-19 pandemic to determine prevalence and common etiologies of bacteremia and to inform a diagnostic approach to relieve blood culture overutilization. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Ordering volume increased by 34.8% in the second half of March 2020 compared to the level in the first half of the month. The rate of bacteremia was significantly lower among COVID-19 patients (3.8%) than among COVID-19-negative patients (8.0%) and those not tested (7.1%) (P < 0.001). COVID-19 patients had a high proportion of organisms reflective of commensal skin microbiota, which, when excluded, reduced the bacteremia rate to 1.6%. More than 98% of all positive cultures were detected within 4 days of incubation. Bloodstream infections are very rare for COVID-19 patients, which supports the judicious use of blood cultures in the absence of compelling evidence for bacterial coinfection. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity. url: https://www.ncbi.nlm.nih.gov/pubmed/32404482/ doi: 10.1128/jcm.00875-20 id: cord-346370-jdfsacds author: Sergi, Consolato M. title: The Facemask in Public and Healthcare Workers– A Need not a Belief date: 2020-05-13 words: 1186.0 sentences: 63.0 pages: flesch: 51.0 cache: ./cache/cord-346370-jdfsacds.txt txt: ./txt/cord-346370-jdfsacds.txt summary: Strict isolation and social distancing measures can flatten the coronavirus infectious curve, and the use of facemask needs to be encouraged and facilitated in crowded places, particularly in hospitals where the 6-feet social distancing cannot be adopted because of physical barriers. I If most people wear a mask in public at any time the transmission rate can easily decrease beneath 1.0, thus stopping the spread of the disease and limit the long-standing Lockdown measures 13 . It is important to emphasize that while a protective mask may reduce the likelihood of infection, it will not eliminate the risk, particularly when a disease has more than one route of transmission, as identified in SARS-Cov-2. While strict isolation and social distancing measures can flatten the infectious curve, the use of facemask needs to be encouraged and facilitated where the 6-feet social distancing cannot be implemented because of physical barriers. abstract: Abstract Since the declaration of the COVID-19 pandemic, a lot of data has invaded our lives, and the conflicting findings have caused us to be frantic about the correct course action. Strict isolation and social distancing measures can flatten the coronavirus infectious curve, and the use of facemask needs to be encouraged and facilitated in crowded places, particularly in hospitals where the 6-feet social distancing cannot be adopted because of physical barriers. url: https://www.ncbi.nlm.nih.gov/pubmed/32405099/ doi: 10.1016/j.puhe.2020.05.009 id: cord-301921-i1o18nmw author: Sernicola, Alvise title: How to Deal With Post-viral Cutaneous Eruptions in the Era of Coronavirus Infection date: 2020-05-12 words: 1144.0 sentences: 53.0 pages: flesch: 41.0 cache: ./cache/cord-301921-i1o18nmw.txt txt: ./txt/cord-301921-i1o18nmw.txt summary: In our routine clinical practice during the COVID-19 outbreak, we are observing a growing number of post viral cutaneous eruptions in apparently healthy individuals in the second or third decade of life that we feel is remarkable compared to the usual local epidemiology of this season. A dermatopathologist from our country has shared the report of skin biopsies performed on two patients with COVID-19 disease, matching the histology of Giannotti-Crosti syndrome, that is a non-specific manifestation of a viral infection (11) . These observations hint at the possible role of specific genetic factors that, while a predisposition to the development of skin eruptions, may protect from severely symptomatic presentations of coronavirus infection. In our current cases of atypical skin eruptions, in which a relationship with conventional viral agents has been ruled out by laboratory testing and clinical history, molecular testing with PCR could be performed on pharynx swabs to support the hypothesis of a possible association with the novel coronavirus. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32574325/ doi: 10.3389/fmed.2020.00224 id: cord-262282-9xh51cd1 author: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 words: 4323.0 sentences: 260.0 pages: flesch: 57.0 cache: ./cache/cord-262282-9xh51cd1.txt txt: ./txt/cord-262282-9xh51cd1.txt summary: Without going into details concerning live vaccine production via eukaryotic viruses, I think it reasonable to assume that eukaryotic virus production is more difficult, more expensive and less rapid than the production of phages. However, current efforts to human-engineer improved antigens for anti-RNA virus vaccines have shown that neutralizing antibodies typically react with viral proteins that are in states that are context dependent and unstable [12, 13, 15, 20] . I take the liberty of responding here to the obvious objection that no membrane-covered, single-stranded RNA phage has ever been isolated [21] and that the pandemic viruses include influenza, Zika-type and coronaviruses, all in this category. A non-specialist observer reasonably concludes that DNA and RNA vaccines, when viewed in the context of our overall objective, are examples of type 2 strategy options. Given that eukaryotic viruses have doubling times much greater than those of phages (2-5 min for typical coliphages), meeting this objective implies that a live virus vaccine has to be already present in the environment. abstract: Recently, the research community has had a real-world look at reasons for improving vaccine responses to emerging RNA viruses. Here, a vaccine non-specialist suggests how this might be done. I propose two alternative options and compare the primary alternative option with current practice. The basis of comparison is feasibility in achieving what we need: a safe, mass-produced, emerging virus-targeted vaccine on 2–4 week notice. The primary option is the following. (1) Start with a platform based on live viruses that infect bacteria, but not humans (bacteriophages, or phages). (2) Isolate phages (to be called pathogen homologs) that resemble and provide antigenic context for membrane-covered, pathogenic RNA viruses; coronavirus-phage homologs will probably be found if the search is correctly done. (3) Upon isolating a viral pathogen, evolve its phage homolog to bind antibodies neutralizing for the viral pathogen. Vaccinate with the evolved phage homolog by generating a local, non-hazardous infection with the phage host and then curing the infection by propagating the phage in the artificially infecting bacterial host. I discuss how this alternative option has the potential to provide what is needed after appropriate platforms are built. url: https://www.ncbi.nlm.nih.gov/pubmed/32429032/ doi: 10.3390/antibiotics9050255 id: cord-338741-gy3ovkrt author: Sethi, Atin title: Evaluation of Current Therapies for COVID-19 Treatment date: 2020-07-22 words: 5580.0 sentences: 333.0 pages: flesch: 47.0 cache: ./cache/cord-338741-gy3ovkrt.txt txt: ./txt/cord-338741-gy3ovkrt.txt summary: No survival benefit for those not requiring respiratory support [22] Convalescent plasma n = 10 severely ill patients Treatment: 200 mL IV In all 10 patients, fever, cough, shortness of breath, and chest pain disappeared or largely improved within 1-3 days of therapy initiation [23] In vitro study determining the activity of convalescent plasma from a recovered SARS-1 patient against SARS-CoV-2 Although the focus of this study was not to explore the efficacy of hydroxychloroquine/azithromycin, it outlines the importance of appropriate risk-benefit analysis while treating patients with COVID-19. This randomized control trial [10] of 199 patients explored the efficacy of lopinavir-ritonavir in hospitalized COVID-19 patients with relatively mild respiratory illness. Efficacy of hydroxychloroquine in patients with COVID-19: Results of a randomized clinical trial Clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-19 patients with at least a six-day follow up: A pilot observational study abstract: The virus SARS-CoV-2, the etiological agent of COVID-19, is responsible for more than 400,000 deaths worldwide as of 10 June 2020. As a result of its recent appearance (December 2019), an efficacious treatment is not yet available. Although considered a lung infection since its emergence, COVID-19 is now causing multiple organ failure, requiring a continuous adjustment in the procedures. In this review, we summarize the current literature surrounding unproven therapies for COVID-19. Analyses of the clinical trials were grouped as chemotherapy, serotherapy, anticoagulant, and the use of human recombinant soluble ACE2 therapies. We conclude that, while no agent has hit the threshold for quality of evidence to demonstrate efficacy and safety, preliminary data show potential benefits. Moreover, there is a possibility for harm with these unproven therapies, and the decision to treat should be based on a comprehensive risk–benefit analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/32707942/ doi: 10.3390/microorganisms8081097 id: cord-257613-o0q7hvn3 author: Shafiee, Abbas title: Coronavirus disease 2019: A tissue engineering and regenerative medicine perspective date: 2020-08-21 words: 3427.0 sentences: 199.0 pages: flesch: 43.0 cache: ./cache/cord-257613-o0q7hvn3.txt txt: ./txt/cord-257613-o0q7hvn3.txt summary: To date, numerous studies have been conducted to evaluate the safety and efficacy of tissue engineering and regenerative medicine (TERM) products, including mesenchymal stem cells (MSCs), and their derivatives (eg, exosomes) for coronavirus infections, which could be applied for the COVID‐19. Over the COVID-19 outbreak, the funding for many TERM projects is being cut, which has a significant impact on the present and future of Current clinical trials highlight the potential benefits of stem cell therapies for COVID-19 patients. Effective multi-institutional collaboration and adequate funding from government and nongovernment sources are also needed to collect and analyze the data from ongoing and new human trials, to better understand the potential benefits of stem cell therapies for COVID-19 patients. Clinical study of mesenchymal stem cell treating acute respiratory distress syndrome induced by epidemic Influenza A (H7N9) infection, a hint for COVID-19 treatment. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial abstract: Current therapies for novel coronavirus disease (COVID‐19) are generally used to manage rather than cure this highly infective disease. Therefore, there is a significant unmet medical need for a safe and effective treatment for COVID‐19. Inflammation is the driving force behind coronavirus infections, and the majority of deaths caused by COVID‐19 are the result of acute respiratory distress syndrome (ARDS). It is crucial to control the inflammation as early as possible. To date, numerous studies have been conducted to evaluate the safety and efficacy of tissue engineering and regenerative medicine (TERM) products, including mesenchymal stem cells (MSCs), and their derivatives (eg, exosomes) for coronavirus infections, which could be applied for the COVID‐19. In this review, first, the impacts of COVID‐19 pandemic in the present and future of TERM research and products are briefly presented. Then, the recent clinical trials and the therapeutic benefits of MSCs in coronavirus‐induced ARDS are critically reviewed. Last, the recent advances in the field of tissue engineering relevant to the coronavirus infections, including three‐dimensional platforms to study the disease progression and test the effects of antiviral agents are described. Moreover, the application of biomaterials for vaccine technology, and drug delivery are highlighted. Despite promising results in the preclinical and clinical applications of MSC therapy for coronavirus infections, the controversy still exists, and thus further investigation is required to understand the efficacy of these therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/32820868/ doi: 10.1002/sctm.20-0197 id: cord-341045-75of9ys6 author: Shah, Abdullah title: Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries date: 2020-09-14 words: 1041.0 sentences: 64.0 pages: flesch: 56.0 cache: ./cache/cord-341045-75of9ys6.txt txt: ./txt/cord-341045-75of9ys6.txt summary: By multiple sequence alignment of amino acids, we observed substitutions and deletion in S protein at 13 different sites in the isolates of five countries (China, USA, Finland, India and Australia) as compared to the reference sequence. Interestingly, in ORF8 substitution of Leucine, a nonpolar to Serine a polar amino acid at same position (aa84 L to S) in 23 isolates of five countries i.e. China, USA, Spain, Taiwan and India were observed, which may affect the conformation of peptides. Thus, we observed several mutations in the isolates thereafter the first sequencing of SARS-CoV-2 isolate, NC_045512.2, which suggested that this virus might be a threat to the whole world and therefore further studies are needed to characterize how these mutations in different proteins affect the functionality and pathogenesis of SARS-CoV-2. Thus, further studies are required to characterize how these amino acids substitutions in different proteins affect the functionality and pathogenesis of SARS-CoV-2. abstract: Since December 2019, a severe pandemic of pneumonia, COVID-19 associated with a novel coronavirus (SARS-CoV-2), have emerged in Wuhan, China and spreading throughout the world. As RNA viruses have a high mutation rate therefore we wanted to identify whether this virus is also prone to mutations. For this reason we selected four major structural (Spike protein (S), Envelope protein (E), Membrane glycoprotein (M), Nucleocapsid phosphoprotein (N)) and ORF8 protein of 100 different SARS-CoV-2 isolates of fifteen countries from NCBI database and compared these to the reference sequence, Wuhan NC_045512.2, which was the first isolate of SARS-CoV-2 that was sequenced. By multiple sequence alignment of amino acids, we observed substitutions and deletion in S protein at 13 different sites in the isolates of five countries (China, USA, Finland, India and Australia) as compared to the reference sequence. Similarly, alignment of N protein revealed substitutions at three different sites in isolates of China, Spain and Japan. M protein exhibits substitution only in one isolates from USA, however, no mutation was observed in E protein of any isolate. Interestingly, in ORF8 substitution of Leucine, a nonpolar to Serine a polar amino acid at same position (aa84 L to S) in 23 isolates of five countries i.e. China, USA, Spain, Taiwan and India were observed, which may affect the conformation of peptides. Thus, we observed several mutations in the isolates thereafter the first sequencing of SARS-CoV-2 isolate, NC_045512.2, which suggested that this virus might be a threat to the whole world and therefore further studies are needed to characterize how these mutations in different proteins affect the functionality and pathogenesis of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S2452014420303009?v=s5 doi: 10.1016/j.genrep.2020.100886 id: cord-285569-ei9w19i7 author: Shah, Aditya title: Guide to Understanding the 2019 Novel Coronavirus date: 2020-02-28 words: 2060.0 sentences: 141.0 pages: flesch: 53.0 cache: ./cache/cord-285569-ei9w19i7.txt txt: ./txt/cord-285569-ei9w19i7.txt summary: A cluster of cases of pneumonia caused by a novel coronavirus, COVID-19, was first reported in Wuhan in the Hubei province in China in late December 2019. 1 Beta coronaviruses include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the coronavirus variant COVID-19 virus first described in Wuhan. SARS-CoV disproportionately impacted health care workers (HCWs) in countries with the most reported cases. Similar to SARS-CoV, presentation is typically fever with symptoms of lower respiratory tract infection and radiographic evidence of pneumonia or ARDS. 16 The Centers for Disease Control and Prevention (CDC) has issued interim guidance for HCWs. 17 Novel coronavirus should be suspected if patients meet the criteria described in Table 1 . Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: nan url: https://doi.org/10.1016/j.mayocp.2020.02.003 doi: 10.1016/j.mayocp.2020.02.003 id: cord-317240-d7ioosi6 author: Shah, Niyati title: Review: An insight into coronaviruses: Challenges, security and scope date: 2020-08-04 words: 2285.0 sentences: 151.0 pages: flesch: 59.0 cache: ./cache/cord-317240-d7ioosi6.txt txt: ./txt/cord-317240-d7ioosi6.txt summary: In principle, a molecule can act as an anti-viral drug if it inhibits some stage of the virus replication cycle, without being too toxic to the body cells. Out of these, the data of 8 patients could not be analyzed F I G U R E 2 A general mechanism of viral replication in host cells and functions of inhibitors at various stages during the process. A drug which is designed to be a fusion inhibitor will function at this stage by preventing the virus from binding with the receptor. This trial reported reduced mortality rates and also clinical improvements in 68% of the patients by the use of remdesivir. In cell culture, chloroquine shows activity against the SARS-CoV-2 virus, but the dosage requirements are usually high which may lead to serious toxicities if administered to humans. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (H1N1) 2009 virus infection abstract: SARS‐CoV2 is a novel coronavirus; the seventh of its species to infect humans. The spread of this virus emerged in Wuhan, China in late December, 2019. Since then, this virus has spread to more than 200 countries and has caused a worldwide pandemic. Being a new species of coronaviruses, any cure or vaccines for this virus has not yet been obtained. A large amount of scientific studies and clinical trials are being carried out across the world to find a potential vaccine for this virus. Current work reports a review of potential drugs and vaccines that may be effective against this virus. Different scientific therapies that may potentially be effective against the SARS‐CoV2 virus are also reviewed. The mechanisms of various drugs, their efficiency in various clinical trials and their side effects are also studied. url: https://www.ncbi.nlm.nih.gov/pubmed/32754974/ doi: 10.1002/rmv.2138 id: cord-302238-l8j1vy0y author: Shah, Prakesh S. title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates date: 2020-04-21 words: 943.0 sentences: 55.0 pages: flesch: 42.0 cache: ./cache/cord-302238-l8j1vy0y.txt txt: ./txt/cord-302238-l8j1vy0y.txt summary: title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. Vertical transmission of coronavirus Disease 19 (COVID-19) from infected pregnant mothers to neonates: a review Neonatal early-onset infection with SARS-CoV-2 in 33 neonates born to mothers with COVID-19 in Wuhan, China. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn abstract: The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. It has implications for the mother, fetus, and neonate, as well as for healthcare providers present at the time of birth and caring for the child during the neonatal period, including obstetricians, midwives, family doctors, anesthetists, pediatricians, neonatologists, nurses, and respiratory therapists. At present the evidence for intrauterine transmission from mother to fetus or intrapartum transmission from mother to the neonate is sparse. There are limitations associated with sensitivity and specificity of diagnostic tests used and classification of patients based on test results has also been questioned. url: https://www.ncbi.nlm.nih.gov/pubmed/32277845/ doi: 10.1111/aogs.13870 id: cord-282867-kbyxdegu author: Shah, Sayed Zulfiqar Ali title: Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date: 2020-08-26 words: 4542.0 sentences: 247.0 pages: flesch: 39.0 cache: ./cache/cord-282867-kbyxdegu.txt txt: ./txt/cord-282867-kbyxdegu.txt summary: The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living. abstract: Coronavirus is an RNA virus, which attacks the respiratory system causing complications including severe respiratory distress and pneumonia and many other symptoms. Recently, a novel coronavirus (COVID-19) outbreak emerged in Wuhan, which caused a significant number of infections in China and resulted in a global pandemic. The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. Based on the evidence presented, we conclude that certain physical rehabilitation techniques and modalities could be of great support in the management of COVID-19-associated pneumonia. The safety of staff and patients when applying rehabilitation intervention requires attention. The combination of physical rehabilitation and medical treatment would result in improved treatment outcomes, faster recovery, and shorter hospital stay. Many rehabilitation techniques are safe and feasible and can be easily incorporated into the management protocol of COVID-19 victims. Decisions of early rehabilitation induction should be based on the patient's medical condition and tolerability. url: https://doi.org/10.1155/2020/3642143 doi: 10.1155/2020/3642143 id: cord-268483-joiajgs4 author: Shah, Vibhuti Kumar title: Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past date: 2020-08-07 words: 10644.0 sentences: 477.0 pages: flesch: 43.0 cache: ./cache/cord-268483-joiajgs4.txt txt: ./txt/cord-268483-joiajgs4.txt summary: As there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like SARS, MERS, HIV, ebola, malaria, and tuberculosis are being given to COVID-19 patients, and clinical trials for many such drugs have already begun. An ELISA-based time kinetics study to detect the COVID-19 specific humoral immune response showed that the patients produced IgM and IgG antibodies that did not cross-react with other human coronaviruses except SARS-CoV. A case study on pediatric patients reports that 5 out of 6 children showed a protective humoral response, with neutralizing IgG and IgM antibodies targeting the N and S-RBD proteins of SARS-CoV-2 (65) . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice abstract: After the 1918 flu pandemic, the world is again facing a similar situation. However, the advancement in medical science has made it possible to identify that the novel infectious agent is from the coronavirus family. Rapid genome sequencing by various groups helped in identifying the structure and function of the virus, its immunogenicity in diverse populations, and potential preventive measures. Coronavirus attacks the respiratory system, causing pneumonia and lymphopenia in infected individuals. Viral components like spike and nucleocapsid proteins trigger an immune response in the host to eliminate the virus. These viral antigens can be either recognized by the B cells or presented by MHC complexes to the T cells, resulting in antibody production, increased cytokine secretion, and cytolytic activity in the acute phase of infection. Genetic polymorphism in MHC enables it to present some of the T cell epitopes very well over the other MHC alleles. The association of MHC alleles and its downregulated expression has been correlated with disease severity against influenza and coronaviruses. Studies have reported that infected individuals can, after recovery, induce strong protective responses by generating a memory T-cell pool against SARS-CoV and MERS-CoV. These memory T cells were not persistent in the long term and, upon reactivation, caused local damage due to cross-reactivity. So far, the reports suggest that SARS-CoV-2, which is highly contagious, shows related symptoms in three different stages and develops an exhaustive T-cell pool at higher loads of viral infection. As there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like SARS, MERS, HIV, ebola, malaria, and tuberculosis are being given to COVID-19 patients, and clinical trials for many such drugs have already begun. A classical immunotherapy of convalescent plasma transfusion from recovered patients has also been initiated for the neutralization of viremia in terminally ill COVID-19 patients. Due to the limitations of plasma transfusion, researchers are now focusing on developing neutralizing antibodies against virus particles along with immuno-modulation of cytokines like IL-6, Type I interferons (IFNs), and TNF-α that could help in combating the infection. This review highlights the similarities of the coronaviruses that caused SARS and MERS to the novel SARS-CoV-2 in relation to their pathogenicity and immunogenicity and also focuses on various treatment strategies that could be employed for curing COVID-19. url: https://doi.org/10.3389/fimmu.2020.01949 doi: 10.3389/fimmu.2020.01949 id: cord-331472-kd4uxcve author: Shahid, Zainab title: COVID‐19 and Older Adults: What We Know date: 2020-04-20 words: 2314.0 sentences: 153.0 pages: flesch: 53.0 cache: ./cache/cord-331472-kd4uxcve.txt txt: ./txt/cord-331472-kd4uxcve.txt summary: Studies have shown that this virus causes worse outcomes and a higher mortality rate in older adults and those with comorbidities such as hypertension, cardiovascular disease, diabetes, chronic respiratory disease, and chronic kidney disease (CKD). 5 The Centers for Disease Control and Prevention (CDC) reported that although individuals older than age 65 comprise 17% of the total population in the United States, they make up 31% of COVID-19 infections, 45% of hospitalizations, 53% of intensive care unit admissions, and 80% of deaths caused by this infection. 15, 16 These symptoms are also common in older adults; one study on 21 critically ill patients with SARS-CoV-2 infection, with a mean age of 70 years, found that the most common presenting symptoms were shortness of breath (76%), fever (52%), and cough (48%). 19 One study on 46 fatal cases of SARS-CoV-2, in which 84% of patients were older than age 60, found that diabetes is likely associated with increased mortality. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a novel virus that causes COVID‐19 infection, has recently emerged and caused a deadly pandemic. Studies have shown that this virus causes worse outcomes and a higher mortality rate in older adults and those with comorbidities such as hypertension, cardiovascular disease, diabetes, chronic respiratory disease, and chronic kidney disease (CKD). A significant percentage of older American adults have these diseases, putting them at a higher risk of infection. Additionally, many adults with hypertension, diabetes, and CKD are placed on angiotensin‐converting enzyme (ACE) inhibitors and angiotensin II receptor blockers. Studies have shown that these medications upregulate the ACE‐2 receptor, the very receptor that the SARS‐CoV‐2 virus uses to enter host cells. Although it has been hypothesized that this may cause a further increased risk of infection, more studies on the role of these medications in COVID‐19 infections are necessary. In this review, we discuss the transmission, symptomatology, and mortality of COVID‐19 as they relate to older adults, and possible treatments that are currently under investigation. J Am Geriatr Soc 68:926–929, 2020 url: https://doi.org/10.1111/jgs.16472 doi: 10.1111/jgs.16472 id: cord-271469-lozvq3y6 author: Shaikh, Faiq title: Current landscape of Imaging and the potential role for Artificial intelligence in the management of COVID-19 date: 2020-06-27 words: 3042.0 sentences: 171.0 pages: flesch: 42.0 cache: ./cache/cord-271469-lozvq3y6.txt txt: ./txt/cord-271469-lozvq3y6.txt summary: The clinical presentation of COVID-19 COVID-19 is primarily a respiratory tract infection caused by the SARS-CoV2 virus. Currently, the imaging features related to the neurologic complications of the virus are consistent with stroke related to large vessel occlusion and encephalopathy (Fig. 5) with reported leptomeningeal enhancement and cranial nerve palsies [25, 26] , which in the vast majority are seen in subjects with severe alternate manifestations of Covid-19 infection [27, 28] . Given that it has been shown to be useful for imaging lung infections, such as tuberculosis and atypical pneumonia [33] , its potential role in COVID19 management, albeit small may be extrapolated (Fig. 6) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response Severity assessment of coronavirus disease 2019 (COVID-19) using quantitative features from chest CT images abstract: The clinical management of COVID-19 is challenging. Medical imaging plays a critical role in the early detection, clinical monitoring and outcomes assessment of this disease. Chest x-ray radiography (CXR) and computed tomography (CT) are the standard imaging modalities used for the structural assessment of the disease status, while functional imaging (namely, positron emission tomography) has had limited application. Artificial intelligence (AI) can enhance the predictive power and utilization of these imaging approaches and new approaches focusing on detection, stratification and prognostication are showing encouraging results. We review the current landscape of these imaging modalities and AI approaches as applied in COVID-19 management. url: https://www.ncbi.nlm.nih.gov/pubmed/32703538/ doi: 10.1067/j.cpradiol.2020.06.009 id: cord-324246-liyk6mna author: Shakoor, Hira title: Be well: A potential role for vitamin B in COVID-19 date: 2020-08-15 words: 2240.0 sentences: 132.0 pages: flesch: 40.0 cache: ./cache/cord-324246-liyk6mna.txt txt: ./txt/cord-324246-liyk6mna.txt summary: Vitamin B assists in proper activation of both the innate and adaptive immune responses, reduces pro-inflammatory cytokine levels, improves respiratory function, maintains endothelial integrity, prevents hypercoagulability and can reduce the length of stay in hospital [7, 8] . In a recent preprint it is suggested that PLP supplementation mitigates COVID-19 symptoms by regulating immune responses, decreasing pro-inflammatory cytokines, maintaining endothelial integrity and preventing hypercoagulability [22] . J o u r n a l P r e -p r o o f Vitamin B not only helps to build and maintain a healthy immune system but it could potentially prevent or reduce COVID-19 symptoms or treat SARS-CoV-2 infection. In particular, vitamin B modulates immune response by downregulating pro-inflammatory cytokines and inflammation, reducing breathing difficulty and gastrointestinal problems, preventing hypercoagulability, potentially improving outcomes and reducing the length of stay in the hospital for COVID-19 patients. abstract: nan url: http://www.maturitas.org/article/S0378512220303480/pdf doi: 10.1016/j.maturitas.2020.08.007 id: cord-293543-87ulnpdm author: Shalhoub, Sarah title: Interferon beta-1b for COVID-19 date: 2020-05-10 words: 957.0 sentences: 57.0 pages: flesch: 53.0 cache: ./cache/cord-293543-87ulnpdm.txt txt: ./txt/cord-293543-87ulnpdm.txt summary: 8 In The Lancet, Ivan Fan-Ngai Hung and colleagues 9 present the results of an open-label, randomised, phase 2 trial that examined the effect of a triple combination regimen of interferon beta-1b 8 million international units (0·25 mg) on alternate days, lopinavir 400 mg plus ritonavir 100 mg every 12 h, and ribavirin 400 mg every 12 h, compared with lopinavir 400 mg plus ritonavir 100 mg every 12 h alone. However, as the authors acknowledge, future studies to examine the efficacy of interferon beta-1b alone or in combination with other drugs to treat severe or critically ill patients with confirmed COVID-19 compared with placebo are warranted. Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study Triple combination of interferon beta-1b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial abstract: nan url: https://doi.org/10.1016/s0140-6736(20)31101-6 doi: 10.1016/s0140-6736(20)31101-6 id: cord-314669-lvibjx97 author: Shang, Guifang title: Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 date: 2007-11-26 words: 4044.0 sentences: 186.0 pages: flesch: 53.0 cache: ./cache/cord-314669-lvibjx97.txt txt: ./txt/cord-314669-lvibjx97.txt summary: title: Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 STUDY DESIGN AND METHODS: Case onset dates from the 2003 Shenzhen SARS epidemic and investigational results from Taiwan on viremia in humans are used to estimate the number of cases that were viremic throughout the epidemic. RESULTS: Based on data from Shenzhen, Hongkong and Taiwan, the maximum and mean risk (per million) of SARS-CoV transmission from donors in Shenzhen were estimated as 23.57 (95% CI: 6.83–47.69) and 14.11 (95% CI: 11.00–17.22), respectively. Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 Then, using this information and information on the asymptomatic or subclinical SARS-CoV infection-to-clinically confirmed SARS ratio (R), the proportion of infected individuals who remain asymptomatic (A), and the population size, we estimated the risk of SARS-CoV transmission by transfusion from a unit of blood donated at time t during the epidemic. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a newly recognized infectious disease that caused an outbreak in south China in 2003. The cause of SARS was identified as a novel coronavirus (CoV). The existence of asymptomatic seroconvertors and the detection of the SARS-CoV RNA in plasma during the course of infection all suggest that SARS could, as least theoretically, be transmitted by transfusion. An estimate of the risk of SARS transmission through blood transfusion will contribute to decisions concerning blood safety monitoring and may be useful in the design of strategies to decrease the risk of transfusion-transmitted infections. STUDY DESIGN AND METHODS: Case onset dates from the 2003 Shenzhen SARS epidemic and investigational results from Taiwan on viremia in humans are used to estimate the number of cases that were viremic throughout the epidemic. Estimates of the asymptomatic-to-clinically confirmed SARS-CoV infection ratio, the proportion of asymptomatic infections reported in a seroprevalence survey in Hongkong, and the population size of Shenzhen are used to infer the SARS-CoV transfusion–transmission risk. Statistical resampling methods are used. RESULTS: Based on data from Shenzhen, Hongkong and Taiwan, the maximum and mean risk (per million) of SARS-CoV transmission from donors in Shenzhen were estimated as 23.57 (95% CI: 6.83–47.69) and 14.11 (95% CI: 11.00–17.22), respectively. The estimated risk peaked on April 02, 2003. CONCLUSIONS: Although there are currently no confirmed reports of the transmission of SARS-CoV from asymptomatic individuals, recent research data indicate that transfusion-transmitted SARS-CoV is at least theoretically possible. Although the risk is low, with its rapid spread of the disease, appearance of alarmingly high infectivity and high fatality rate, public health authorities need to consider strategies for blood donor recruitment and virus inactivation during an epidemic to further ensure blood safety. url: https://www.ncbi.nlm.nih.gov/pubmed/18036985/ doi: 10.1016/j.transci.2007.09.004 id: cord-316647-jj8anf5g author: Shang, You title: Management of critically ill patients with COVID-19 in ICU: statement from front-line intensive care experts in Wuhan, China date: 2020-06-06 words: 13583.0 sentences: 668.0 pages: flesch: 39.0 cache: ./cache/cord-316647-jj8anf5g.txt txt: ./txt/cord-316647-jj8anf5g.txt summary: RESULTS: A comprehensive document with 46 statements are presented, including protection of medical personnel, etiological treatment, diagnosis and treatment of tissue and organ functional impairment, psychological interventions, immunity therapy, nutritional support, and transportation of critically ill COVID-19 patients. Statement 8 Convalescent plasma therapy should probably be used for severe and critically ill patients with COVID-19 (Grade 2+, weak recommendation). However, critically ill patients with COVID-19 have a longer mechanical ventilation time, and daily sedatives interruption is not suggested for patients receiving deep sedation in order to reduce lung damage during early stage of severe ARDS. Light sedation is suggested for severe COVID-19 patients receiving HFNC oxygen therapy and non-invasive mechanical ventilation, and also for critically ill patients in the recovering stage (expert opinion). Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial abstract: BACKGROUND: The ongoing coronavirus disease 2019 (COVID-2019) pandemic has swept all over the world, posing a great pressure on critical care resources due to large number of patients needing critical care. Statements from front-line experts in the field of intensive care are urgently needed. METHODS: Sixteen front-line experts in China fighting against the COVID-19 epidemic in Wuhan were organized to develop an expert statement after 5 rounds of expert seminars and discussions to provide trustworthy recommendation on the management of critically ill COVID-19 patients. Each expert was assigned tasks within their field of expertise to provide draft statements and rationale. Parts of the expert statement are based on epidemiological and clinical evidence, without available scientific evidences. RESULTS: A comprehensive document with 46 statements are presented, including protection of medical personnel, etiological treatment, diagnosis and treatment of tissue and organ functional impairment, psychological interventions, immunity therapy, nutritional support, and transportation of critically ill COVID-19 patients. Among them, 5 recommendations were strong (Grade 1), 21 were weak (Grade 2), and 20 were experts’ opinions. A strong agreement from voting participants was obtained for all recommendations. CONCLUSION: There are still no targeted therapies for COVID-19 patients. Dynamic monitoring and supportive treatment for the restoration of tissue vascularization and organ function are particularly important. url: https://doi.org/10.1186/s13613-020-00689-1 doi: 10.1186/s13613-020-00689-1 id: cord-305856-xt3zxajf author: Shanmugam, Chandrakumar title: COVID-2019 – A comprehensive pathology insight date: 2020-09-18 words: 4597.0 sentences: 325.0 pages: flesch: 46.0 cache: ./cache/cord-305856-xt3zxajf.txt txt: ./txt/cord-305856-xt3zxajf.txt summary: Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. The current pandemic of corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2) led to complete lockdown in many countries contributing to major socio-economic crisis and irreparable recession, globally. [22, 31, 32, 33] Similar to SARS CoV, a recent study reported non-O blood group specifically group A had higher infection and death rates due to COVID-19 owing to absence of protective anti-A IgM antibodies. Pulmonary pathology of early phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer The clinical pathology of severe acute respiratory syndrome (SARS): a report from China abstract: Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. The lungs are the main organs affected leading to pneumonia and respiratory failure in severe cases that may need mechanical ventilation. Occasionally patient may present with gastro-intestinal, cardiac and neurologic symptoms with or without lung involvement. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. Other organs like liver and kidneys may be involved secondarily. Currently the treatment is principally symptomatic and prevention by proper use of personal protective equipment and other measures is crucial to limit the spread. In the midst of pandemic there is paucity of literature on pathological features including pathogenesis, hence in this review we provide the current pathology centered understanding of COVID-19. Furthermore, the pathogenetic pathway is pivotal in the development of therapeutic targets. url: https://www.ncbi.nlm.nih.gov/pubmed/32979742/ doi: 10.1016/j.prp.2020.153222 id: cord-330827-gu2mt6zp author: Shanmugaraj, Balamurugan title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 words: 3730.0 sentences: 175.0 pages: flesch: 40.0 cache: ./cache/cord-330827-gu2mt6zp.txt txt: ./txt/cord-330827-gu2mt6zp.txt summary: The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. abstract: Novel Coronavirus (2019-nCoV) is an emerging pathogen that was first identified in Wuhan, China in late December 2019. This virus is responsible for the ongoing outbreak that causes severe respiratory illness and pneumonia-like infection in humans. Due to the increasing number of cases in China and outside China, the WHO declared coronavirus as a global health emergency. Nearly 35,000 cases were reported and at least 24 other countries or territories have reported coronavirus cases as early on as February. Inter-human transmission was reported in a few countries, including the United States. Neither an effective anti-viral nor a vaccine is currently available to treat this infection. As the virus is a newly emerging pathogen, many questions remain unanswered regarding the virus’s reservoirs, pathogenesis, transmissibility, and much more is unknown. The collaborative efforts of researchers are needed to fill the knowledge gaps about this new virus, to develop the proper diagnostic tools, and effective treatment to combat this infection. Recent advancements in plant biotechnology proved that plants have the ability to produce vaccines or biopharmaceuticals rapidly in a short time. In this review, the outbreak of 2019-nCoV in China, the need for rapid vaccine development, and the potential of a plant system for biopharmaceutical development are discussed. url: https://doi.org/10.3390/pathogens9020148 doi: 10.3390/pathogens9020148 id: cord-351837-vasuu70k author: Shannon, Ashleigh title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 words: 6507.0 sentences: 349.0 pages: flesch: 50.0 cache: ./cache/cord-351837-vasuu70k.txt txt: ./txt/cord-351837-vasuu70k.txt summary: title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 . abstract: The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32943628/ doi: 10.1038/s41467-020-18463-z id: cord-296390-jv86w4j9 author: Shao, Chen title: Evolution of SARS-Co-2 RNA test results in a fatal Covid-19 patient: a case report date: 2020-05-11 words: 1436.0 sentences: 99.0 pages: flesch: 53.0 cache: ./cache/cord-296390-jv86w4j9.txt txt: ./txt/cord-296390-jv86w4j9.txt summary: On day 9 after admission, chest CT scan showed diffuse ground-glass shadows in patient''s bilateral lungs. How SARS-CoV-2-infected patients progress to critical disease is a key issue in clinical practice. He was confirmed as Covid-19 positive in February 2 nd by qPCR analysis for SARS-CoV-2RNA of samples collected by nasopharyngeal swabs. He progressed to septic shock, severe metabolic acidosis and respiratory acidosis occurred successively and then, the patient died on February 14 th . It is worthy to note that the patient received SARS-CoV-2 RNA tests by nasopharyngeal swabs six times ( Table 1 ). Since February 6 th , four times SARS-CoV-2 RNA testing by nasopharyngeal swabs were negative (Table 1) . Given the missed diagnosis of the potential bacterial infection, antibiotics treatment was started too later in this patient, which might have resulted in multi-organ failure due to a septic shock. Clinical manifestation and lung histological alteration showed that this patient suffered from SARS-CoV-2 viral pneumonia. abstract: A 65 year-old man was hospitalized due to fever (38.6°C) and dry cough since 4 days. He visited Wuhan 8 days ago. At admission, nasopharyngeal swabs sample were taken and PCR analysis confirmed SARS-CoV-2RNA positivity. On day 9 after admission, chest CT scan showed diffuse ground-glass shadows in patient’s bilateral lungs. On day 11, his respiratory symptoms worsened. Subsequently, type 1 respiratory failure was diagnosed, coinciding with kidney injury, and subsequently, type 2 respiratory failure occurred, coupled with multi-organ failure including heart and liver. However, patient constitution worsened although SARS-CoV-2 tests were negative since day 13. He died on day 21. Lung biopsy showed areas of diffuse alveolar damage, characterized by extensive acute alveolitis with numerous intra-alveolar neutrophils, lymphocytes and macrophages infiltrations. Microthrombi were seen in the dilated pulmonary capillaries. Immunohistochemistry stainings for SARS-CoV-2-N protein was negative. Taken together, the patient died of multiorgan failure although the SARS-CoV-2 infection was cleared already, implicating that for disease worsening, no active SARS-CoV-2 infection is required. url: https://doi.org/10.1016/j.humpath.2020.04.015 doi: 10.1016/j.humpath.2020.04.015 id: cord-286429-voem879q author: Shao, Yi‐Ming title: Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors date: 2007-08-23 words: 2043.0 sentences: 100.0 pages: flesch: 49.0 cache: ./cache/cord-286429-voem879q.txt txt: ./txt/cord-286429-voem879q.txt summary: Optimization of TL-3 as an inhibitor against the 3CL protease by replacement of the peripheral Val-Ala residues or the two central phenyl groups was based on the rationale that the binding mode of TL-3 in the protein-ligand complex mainly involves at least a dipeptide scaffold. We thus synthesized two compounds to test the binding mode hypothesis: one with two Trp groups adjacent to the central diol (4, Scheme 1) and the other with two additional Val-Ala residues as in 9. The consensus complex structure was compared with the differential density map, which shows the superimposition of the differential electron density map and the modeled binding mode of compound 4. The ligand-protein complex shown in Figure 1 B was different from the top-ranked Trp-Trp binding mode predicted from the preliminary modeling task (for differences see Figure S2 ). The subsequent refinement of the complex structure significantly improved the accuracy of the binding model, and provided a working model for further optimization of the lead compounds. abstract: In a successful example of lead optimization by computer modeling prediction, computational technology was used to optimize a lead inhibitor (TL‐3) of the SARS‐CoV 3CL protease. A novel C (2)‐symmetric diol (1) was then designed and synthesized, and displayed higher affinity than the original lead compound by one order of magnitude in its inhibition constant (0.6→0.073 μm). We believe that this approach has provided a platform for further lead optimization.[Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/17722121/ doi: 10.1002/cbic.200700254 id: cord-305025-pqye1ebh author: Sharifi, Majid title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 words: 3583.0 sentences: 226.0 pages: flesch: 44.0 cache: ./cache/cord-305025-pqye1ebh.txt txt: ./txt/cord-305025-pqye1ebh.txt summary: The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 637 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 638 RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Rapid COVID-19 detection causative virus (SARS-CoV-2) in human 933 nasopharyngeal swab specimens using field-effect transistor-based biosensor abstract: The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In fact, statistical reports of diagnostic tools show that their accuracy, specificity and sensitivity in the detection of COVID-face challenges that can be eliminated by using nanoparticles (NPs). In this study, we aimed to present an overview on the most important way to diagnose different kinds of viruses followed by the introduction of nanobiosensors. Afterward, some methods of coronavirus detection such as imaging, laboratory and kit-based diagnostic tests are surveyed. Furthermore, nucleic acids/protein- and-immunoglobulin (Ig)-based nanobiosensors for the COVID-19 detection infection are reviewed. Finally, current challenges and future perspective for the development of diagnostic or monitoring technologies in the control of COVID-19 are discussed to persuade the scientists in advancing their technologies beyond imagination. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. url: https://api.elsevier.com/content/article/pii/S0039914020309954 doi: 10.1016/j.talanta.2020.121704 id: cord-309794-scqkyr5g author: Sharif‐Askari, Fatemeh Saheb title: Are patients with chronic rhinosinusitis with nasal polyps at a decreased risk of COVID‐19 infection? date: 2020-08-05 words: 1885.0 sentences: 105.0 pages: flesch: 52.0 cache: ./cache/cord-309794-scqkyr5g.txt txt: ./txt/cord-309794-scqkyr5g.txt summary: In fact, higher SARS-CoV-2 viral load was detected in nasal compared to throat swabs obtained from COVID-19 infected patients [4] , and that was attributed to the difference in ACE2 expression between both tissues. Interestingly, a significant reduction in the expression of ACE2 and TMPRSS2 was observed in the nasal polyps of CRSwNPs patients compared to healthy controls ( Figure 1A ). This data suggest that eosinophilic inflammation and the associated type 2 cytokines downregulate the expression of ACE2 in nasal tissue of CRS patients and thus may have a protective role against COVID-19 infection. In conclusion, as presented in Figure 2 , our data suggest that the type of inflammation underlying CRS, as well as corticosteroid treatment, may modulate ACE2 and TEMPRSS2 gene expression levels in the nasal polyps of CRSwNPs patients. abstract: nan url: https://doi.org/10.1002/alr.22672 doi: 10.1002/alr.22672 id: cord-324480-7u5lh4jx author: Sharma, A. title: Structural stability of SARS-CoV-2 degrades with temperature date: 2020-10-14 words: 1541.0 sentences: 88.0 pages: flesch: 51.0 cache: ./cache/cord-324480-7u5lh4jx.txt txt: ./txt/cord-324480-7u5lh4jx.txt summary: Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter. However an understanding of how SARS-CoV-2 survives different environmental conditions is still incomplete and mechanisms of virus particle degradation are poorly mapped out. A key challenge in studying SARS-CoV-2 is the extreme level of threat associated with the live virus and the resultant need for high safety standards for such work. Here we used this technology to study the stability of the viral envelope and associated proteins (M, E, and S) under different environmental conditions. Environmental stability of SARS-CoV-2 on different types of surfaces under indoor and seasonal climate conditions abstract: SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter. Statement of Scientific Significance The economic and public health impact of the COVID-19 pandemic are very significant. However scientific information needed to underpin policy decisions are limited partly due to novelty of the SARS-CoV-2 pathogen. There is therefore an urgent need for mechanistic studies of both COVID-19 disease and the SARS-CoV-2 virus. We show that individual virus particles suffer structural destabilization at relatively mild but elevated temperatures. Our nanoscale results are consistent with recent observations at larger scales. Our work strengthens the case for COVID-19 resurgence in winter. url: https://doi.org/10.1101/2020.10.12.336818 doi: 10.1101/2020.10.12.336818 id: cord-026130-ki7bn67o author: Sharma, Anand Kumar title: Novel Coronavirus Disease (COVID-19) date: 2020-06-05 words: 5073.0 sentences: 330.0 pages: flesch: 57.0 cache: ./cache/cord-026130-ki7bn67o.txt txt: ./txt/cord-026130-ki7bn67o.txt summary: In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. abstract: The present outbreak of the novel coronavirus initially called as “2019 novel coronavirus” or “2019-nCoV” by the World Health Organization (WHO), is also known as “Wuhan coronavirus” or “Wuhan pneumonia”, as it started in the Wuhan city of China in early December of 2019. This new coronavirus-associated acute respiratory deadly disease is now officially named as Corona Virus Disease-19 (COVID-19) by the WHO. From China, this epidemic has now spread to all over the world. On 11 March 2020, the WHO recognised COVID-19 as a pandemic. A pandemic refers to a disease that has spread to several countries, continents, if not worldwide. While the information available on this newly identified virus is limited and evolving, here is a quick run-down of what has been figured out so far. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274062/ doi: 10.1007/s12045-020-0981-3 id: cord-283120-hyzk59qv author: Sharma, Ashish title: Liver disease and outcomes among COVID-19 hospitalized patients- a systematic review and meta-analysis date: 2020-10-16 words: 2630.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-283120-hyzk59qv.txt txt: ./txt/cord-283120-hyzk59qv.txt summary: In this meta-analysis, we aim to study the occurrence and association of liver injury, comorbid liver disease and elevated liver enzymes in COVID-19 confirmed hospitalizations with outcomes. MATERIALS AND METHODS: Data from observational studies describing comorbid chronic liver disease, acute liver injury, elevated aspartate aminotransferase (AST), alanine aminotransferase (ALT) levels and outcomes of COVID-19 hospitalized patients from December 1, 2019, to June 30, 2020 was extracted following PRISMA guidelines. The aim of the study is to evaluate the role of the comorbid chronic liver disease (CM-CLD), elevated liver enzymes and COVID-19 associated acute liver injury (COVID-19 ALI) in predicting the outcomes in confirmed COVID-19 hospitalized patients. The Maentel-Haenszel formula was used to calculate dichotomous variables to obtain odds ratios (ORs) along with its 95% confidence intervals to describe the association of comorbid liver disease, elevated liver enzymes, acute liver injury and outcomes of COVID-19 patients in each study. abstract: INTRODUCTION AND OBJECTIVES: The coronavirus disease 2019 (COVID-19) pandemic has been a challenge globally. In severe acute respiratory syndrome (SARS) epidemic 60% of patients had hepatic injury, due to phylogenetic similarities of the viruses it is assumed that COVID-19 is associated with acute liver injury. In this meta-analysis, we aim to study the occurrence and association of liver injury, comorbid liver disease and elevated liver enzymes in COVID-19 confirmed hospitalizations with outcomes. MATERIALS AND METHODS: Data from observational studies describing comorbid chronic liver disease, acute liver injury, elevated aspartate aminotransferase (AST), alanine aminotransferase (ALT) levels and outcomes of COVID-19 hospitalized patients from December 1, 2019, to June 30, 2020 was extracted following PRISMA guidelines. Adverse outcomes were defined as admission to intensive care unit (ICU), oxygen saturation <90%, invasive mechanical ventilation (IMV), severe disease and in-hospital mortality. Odds ratio (OR) and 95% confidence interval (95%CI) were obtained. RESULTS: 24 studies with 12882 confirmed COVID-19 patients were included. Overall prevalence of CM-CLD was 2.6%, COVID-19-ALI was 26.5%, elevated AST was 41.1% and elevated ALT was 29.1%. CM-CLD had no significant association with poor outcomes (pooledOR:0.96;95%CI:0.71–1.29; p = 0.78). COVID-19-ALI (1.68;1.04–2.70; p = 0.03), elevated AST (2.98;2.35–3.77; p < 0.00001) and elevated ALT (1.85;1.49–2.29; p < 0.00001) were significantly associated with higher odds of poor outcomes. CONCLUSION: Our meta-analysis suggests that acute liver injury and elevated liver enzymes were significantly associated with COVID-19 severity. Future studies should evaluate changing levels of biomarkers amongst liver disease patients to predict poor outcomes of COVID-19 and causes of liver injury during COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33075578/ doi: 10.1016/j.aohep.2020.10.001 id: cord-312708-9ywu6r2t author: Sharma, Dhruv title: Cadaveric Simulation of Otologic Procedures: An Analysis of Droplet Splatter Patterns During the COVID-19 Pandemic date: 2020-05-19 words: 2222.0 sentences: 124.0 pages: flesch: 47.0 cache: ./cache/cord-312708-9ywu6r2t.txt txt: ./txt/cord-312708-9ywu6r2t.txt summary: OBJECTIVE: The otolaryngology community has significant concerns regarding the spread of SARS-CoV-2 through droplet contamination and viral aerosolization during head and neck examinations and procedures. RESULTS: There were no fluorescein droplets or splatter contamination observed in the measured surgical field in any direction after myringotomy and insertion of ventilation tube. 7 As a result, the American Academy of Otolaryngology-Head and Neck Surgery has issued a position statement to limit elective procedures requiring interaction with upper airway mucosal surfaces or those with increased risk of aerosolization, which may include otologic procedures such as myringotomy and mastoidectomy. Since the upper respiratory tract harbors a high viral load, 3 otolaryngologists are vulnerable to SARS-CoV-2 transmission while performing head and neck procedures that utilize suction and powered instrumentation, such as the surgical drill, especially if they are doing so without appropriate protective personal equipment. abstract: OBJECTIVE: The otolaryngology community has significant concerns regarding the spread of SARS-CoV-2 through droplet contamination and viral aerosolization during head and neck examinations and procedures. The objective of this study was to investigate the droplet and splatter contamination from common otologic procedures. STUDY DESIGN: Cadaver simulation series. SETTING: Dedicated surgical laboratory. METHODS: Two cadaver heads were prepped via bilateral middle cranial fossa approaches to the tegmen (n = 4). Fluorescein was instilled through a 4-mm burr hole drilled into the middle cranial fossa floor, and presence in the middle ear was confirmed via microscopic ear examination. Myringotomy with ventilation tube placement and mastoidectomy were performed, and the distribution and distance of resulting droplet splatter patterns were systematically evaluated. RESULTS: There were no fluorescein droplets or splatter contamination observed in the measured surgical field in any direction after myringotomy and insertion of ventilation tube. Gross contamination from the surgical site to 6 ft was noted after complete mastoidectomy, though, when performed in standard fashion. CONCLUSION: Our results show that there is no droplet generation during myringotomy with ventilation tube placement in an operating room setting. Mastoidectomy, however, showed gross contamination 3 to 6 ft away in all directions measured. Additionally, there was significantly more droplet and splatter generation to the left of the surgeon when measured at 1 and 3 ft as compared with all other measured directions. url: https://doi.org/10.1177/0194599820930245 doi: 10.1177/0194599820930245 id: cord-322446-ddv86eoy author: Sharma, Kulbhushan title: SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date: 2011-05-27 words: 8437.0 sentences: 512.0 pages: flesch: 56.0 cache: ./cache/cord-322446-ddv86eoy.txt txt: ./txt/cord-322446-ddv86eoy.txt summary: We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. Analysis of 9b-YFP localization showed that in addition to the extranuclear region, some amount of 9b was also present within the nucleus similar to the SARS-CoV infected cells (Fig. S1 , panel (i), (ii) and (iii)). Panel (ii) shows that even in in-vitro transport assay, SARS-CoV 9b protein localizes in both cytoplasm as well as nucleus. As shown in panel (v), the SARS-CoV 9b protein was able to enter the nucleus even in the presence of WGA showing that its entry is independent of active transport pathway. The SARS-CoV 9b protein triggers caspase 3 mediated apoptosis when retained in the nucleus of mammalian cells While performing pulse-chase assays, we found that a significant number of Vero E6 cells, in which nuclear export of 9b has been inhibited (either by treating with LMB or using NES deficient 9b), were showing caspase 3 dependent apoptosis. abstract: BACKGROUND: 9b is an accessory protein of the SARS-CoV. It is a small protein of 98 amino acids and its structure has been solved recently. 9b is known to localize in the extra-nuclear region and has been postulated to possess a nuclear export signal (NES), however the role of NES in 9b functioning is not well understood. PRINCIPAL FINDINGS/METHODOLOGY: In this report, we demonstrate that 9b in the absence of any nuclear localization signal (NLS) enters the nucleus by passive transport. Using various cell cycle inhibitors, we have shown that the nuclear entry of 9b is independent of the cell cycle. Further, we found that 9b interacts with the cellular protein Crm1 and gets exported out of the nucleus using an active NES. We have also revealed that this NES activity influences the half-life of 9b and affects host cell death. We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. CONCLUSION/SIGNIFICANCE: Here, we showed that nuclear shuttling of 9b and its interaction with Crm1 are essential for the proper degradation of 9b and blocking the nuclear export of this protein induces apoptosis. This phenomenon may be critical in providing a novel role to the 9b accessory protein of SARS-CoV. url: https://doi.org/10.1371/journal.pone.0019436 doi: 10.1371/journal.pone.0019436 id: cord-336103-ufvq0ngl author: Sharma, R. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 words: 1563.0 sentences: 125.0 pages: flesch: 64.0 cache: ./cache/cord-336103-ufvq0ngl.txt txt: ./txt/cord-336103-ufvq0ngl.txt summary: 2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2 abstract: The SARS-CoV-2 pandemic situation has presented multiple imminent challenges to the nations around the globe. While health agencies around the world are exploring various options to contain the spread of this fatal viral infection, multiple strategies and guidelines are being issued to boost the fight against the disease. Identifying and isolating infected individuals at an early phase of the disease has been a very successful approach to stop the chain of transmission. But this approach faces a practical challenge of limited resources. Sample pooling solves this enigma by significantly improving the testing capacity and result turn around time while using no extra resources. However, the general sample pooling method also has the scope of significant improvements. This article describes a process to further optimize the resources with optimal sample pooling. This is a user-friendly technique, scalable on a national or international scale. A mathematical model has been built and validated for its performance using clinical data. url: http://medrxiv.org/cgi/content/short/2020.07.03.20145953v1?rss=1 doi: 10.1101/2020.07.03.20145953 id: cord-320704-rrq6x25k author: Sharma, Shruti title: COVID-19: A Concern for Cardiovascular Disease Patients date: 2020-07-29 words: 3068.0 sentences: 189.0 pages: flesch: 46.0 cache: ./cache/cord-320704-rrq6x25k.txt txt: ./txt/cord-320704-rrq6x25k.txt summary: The organism responsible for the cause of disease is Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Coronavirus Disease (COVID-19) is a recently emerged disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2), a novel coronavirus that leads to adverse pulmonary pathological features [1] . Therefore, in the present review, the role of ACE2 receptors in the viral entry into the host cell, the effect of COVID-19 on the symptoms and prognosis of CVDs, impact of ACE inhibitors (ACEI), and angiotensin receptor blockers (ARBs) on patients of CVDs suffering from COVID-19 have been discussed. Various cardiac complications like cardiovascular disease, arrhythmia (ventricular tachyarrhythmia, atrial fibrillation and ventricular fibrillation), hypertension, cardiac injury, heart failure, and fulminant myocarditis have been found to influence the mortality of the COVID -19 patients [27] . There is a possibility that polymorphism in ACE2 gene, linked to hypertension, particularly, in Asian populations, affects the susceptibility of SARS-CoV-2 infection and COVID-19 disease outcome. ACE2 receptor polymorphism: Susceptibility to SARS-CoV-2, hypertension, multi-organ failure, and COVID-19 disease outcome abstract: Coronavirus disease 2019 (COVID-19) is declared as a pandemic that has spread worldwide, affecting 205 countries. The disease affected 1, 40, 43, 176 individuals and caused 5, 97, 583 deaths around the globe. The organism responsible for the cause of disease is Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). SARS-CoV-2 enters into the cell via receptors present on the cell surface named angiotensin-converting enzyme 2 (ACE2) receptor. Notwithstanding ACE2 receptors acts as a gateway for infection, and most of the cardiovascular patients are treated with the ACE inhibitors. Thus, the role of ACE inhibitors or angiotensin receptor blockers may play a critical role in the severity or outcome of disease. Also, the effect of ACE inhibitors varies with the polymorphism in ACE2 receptors present in the individuals. Hence, it is the need of the hour to investigate the mechanisms which could better aid in the treatment of COVID-19-infected cardiovascular disease (CVD) patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32729064/ doi: 10.1007/s12012-020-09596-0 id: cord-257008-7q5s1vu1 author: Sharma, Virender K. title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 words: 1326.0 sentences: 85.0 pages: flesch: 42.0 cache: ./cache/cord-257008-7q5s1vu1.txt txt: ./txt/cord-257008-7q5s1vu1.txt summary: In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) abstract: nan url: https://doi.org/10.1007/s10311-020-01017-6 doi: 10.1007/s10311-020-01017-6 id: cord-290472-w77cmljm author: Sharon, Donald title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 words: 8665.0 sentences: 393.0 pages: flesch: 39.0 cache: ./cache/cord-290472-w77cmljm.txt txt: ./txt/cord-290472-w77cmljm.txt summary: These markers, such as protein (including autoantibodies, which are antibodies specific to self-antigens [43] ), hormonal markers (such as lack of insulin in Type I diabetic patients [89] ), and genetic/genomic markers (such as BRCA1 mutation in breast cancer patients [52] ), enable clinicians to diagnose the disease while it is still at early stages, to ensure appropriate surgical intervention, efficient drug treat-ment and monitoring, and to predict an individual''s risk of developing specific diseases before they experience symptoms. Scientists, such as the group led by Gil Mor at Yale University, recruited proteomics-based approaches using antibody-based protein microarrays to identify new serum biomarkers, which, in combination with CA-125, may enhance the early detection of ovarian cancer [48, 66, 110] . To date, no studies that attempt to identify novel breast cancer markers have been performed using high-density protein microarrays. abstract: Our understanding of human disease and potential therapeutics is improving rapidly. In order to take advantage of these developments it is important to be able to identify disease markers. Many new high-throughput genomics and proteomics technologies are being implemented to identify candidate disease markers. These technologies include protein microarrays, next-generation DNA sequencing and mass spectrometry platforms. Such methods are particularly important for elucidating the repertoire of molecular markers in the genome, transcriptome, proteome and metabolome of patients with diseases such as cancer, autoimmune diseases, and viral infections, resulting from the disruption of many biological pathways. These new technologies have identified many potential disease markers. These markers are expected to be valuable to achieve the promise of truly personalized medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/20534906/ doi: 10.3233/dma-2010-0707 id: cord-281937-yztlb0fn author: Sheahan, Timothy P title: The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health date: 2020-06-04 words: 2456.0 sentences: 120.0 pages: flesch: 54.0 cache: ./cache/cord-281937-yztlb0fn.txt txt: ./txt/cord-281937-yztlb0fn.txt summary: A new paradigm for human coronavirology was born with the emergence of severe acute respiratory syndrome CoV (SARS-CoV) in November 2002 in Guangdong Province, China. The epidemic strain of SARS-CoV, is believed to have emerged from a bat reservoir through a civet intermediate host in live animal markets and then spilled over into humans 2 . This notion of CoV emergence was further solidified with discovery of the novel highly pathogenic Middle East respiratory syndrome CoV (MERS-CoV) in 2012, which also likely emerged from an ancestral bat-CoV but through a camel intermediate host which continues to seed human MERS-CoV infections to this day 2,3 . Given the diversity and prevalence of CoV circulating among wild birds and mammals, it is not surprising that the potential for emerging CoV to cause severe disease outbreaks and epidemics is not limited to humans. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence abstract: A new coronavirus (CoV) called SARS-CoV-2 emerged in Wuhan, China in December 2019 as the etiological agent of a viral pneumonia called COVID-19. The global spread of SARS-CoV-2 has been so extensive that the WHO declared COVID-19 a pandemic on March 11, 2020. Below, we discuss the emergence of SARS-CoV-2 and provide the historical context, which strongly suggests emerging CoVs provide an immediate threat to global public health and will continue to do so in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32569751/ doi: 10.1016/j.coviro.2020.05.010 id: cord-300608-eju7wnb9 author: Sheervalilou, Roghayeh title: COVID‐19 under spotlight: A close look at the origin, transmission, diagnosis, and treatment of the 2019‐nCoV disease date: 2020-05-26 words: 7391.0 sentences: 384.0 pages: flesch: 47.0 cache: ./cache/cord-300608-eju7wnb9.txt txt: ./txt/cord-300608-eju7wnb9.txt summary: 2.1 | Respiratory system SARS-CoV-2 tends to infect the respiratory tract, thus, pneumonia is a primary clinical finding in patients with COVID-19 Li, Guan, et al., 2020; Zhu et al., 2020) . A number of investigations recently conducted on COVID-19 have reported that IL-6 levels was actually higher in the patients with severe disease (Cai, 2020; Chen, Liu, et al., 2020; Xiang et al., 2020) . Impaired liver function tests have been reported for a number of patients with SARS-CoV-2 infection, suggesting hepatic damage as an extrapulmonary complication of COVID-19 in almost one half of the patients (Chen, Zhou, et al., 2020; Wang, Hu, et al., 2020) . Since H7N9 and SARS-CoV-2 can result in similar complications, for example, ARDS and respiratory failure, MSC-based therapy might lead to a new path in treatment of COVID-19-associated pneumonia . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Months after the outbreak of a new flu‐like disease in China, the entire world is now in a state of caution. The subsequent less‐anticipated propagation of the novel coronavirus disease, formally known as COVID‐19, not only made it to headlines by an overwhelmingly high transmission rate and fatality reports, but also raised an alarm for the medical community all around the globe. Since the causative agent, SARS‐CoV‐2, is a recently discovered species, there is no specific medicine for downright treatment of the infection. This has led to an unprecedented societal fear of the newly born disease, adding a psychological aspect to the physical manifestation of the virus. Herein, the COVID‐19 structure, epidemiology, pathogenesis, etiology, diagnosis, and therapy have been reviewed. url: https://doi.org/10.1002/jcp.29735 doi: 10.1002/jcp.29735 id: cord-263450-v6vdg8os author: Shegogue, Daniel title: Object-oriented biological system integration: a SARS coronavirus example date: 2005-05-15 words: 4930.0 sentences: 260.0 pages: flesch: 38.0 cache: ./cache/cord-263450-v6vdg8os.txt txt: ./txt/cord-263450-v6vdg8os.txt summary: Results: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. In addition, applying a well-defined software engineering process and object-oriented methodology provide an effective means to capture specifications from experimental data and integrate the biological system information. Finally, this process provides a guideline for the development of an integrated biological system, represented as an object-oriented software architecture, in a widely accepted objectoriented modeling language (such as UML), which can facilitate communication about complex systems among software engineers, biologists and other users. To demonstrate the efficacy of a well-defined software engineering process in the translation of a biological system to a model grounded in object-oriented principles, we used UML in the development of a severe acquired respiratory syndrome-coronavirus (SARS-CoV) model. abstract: Motivation: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary. Results: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems. Availability: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm Contact: zhengw@musc.edu Supplementary information: Supplemental data: Table 1 and Figures 1–16. url: https://www.ncbi.nlm.nih.gov/pubmed/15731211/ doi: 10.1093/bioinformatics/bti344 id: cord-033551-eojpkxz9 author: Shekh, Shamasoddin title: In silico allicin induced S-thioallylation of SARS-CoV-2 main protease date: 2020-09-16 words: 3910.0 sentences: 248.0 pages: flesch: 54.0 cache: ./cache/cord-033551-eojpkxz9.txt txt: ./txt/cord-033551-eojpkxz9.txt summary: In the current report, using virtual screening methods, reactive sulfur species allicin is subjecting for covalent docking at the active site of SARS-CoV-2 M(pro) using PX-12 as a benchmark reference compound. Figure 1a shows the structure of SARS-CoV-2 M pro with free cysteine thiols and active site dyad residues. Figure 2b shows the formation of cysteine allyl disulfide at the Cys-145 residue of SARS-CoV-2 M pro after covalent docking with allicin. Figure 4b and c show the formation of cysteine allyl disulfide at Cys-85 and Cys-156 residue of SARS-CoV-2 M pro after covalent docking with allyl sulfenic acid. Table-S2 provides a summary of covalent docking of allicin/PX-12/allyl sulfenic acid at cysteine thiols of four different co-crystal structures of SARS-CoV-2 M pro . Figure 5b shows the sulfur mediated hydrogen bonding by the sulfur of allyl disulfide formed after covalent docking of allicin at the active site of SARS-CoV-2 M pro . abstract: Coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused due to new coronavirus infection with (3)716075 deaths across the world as reported by the World Health Organization (WHO). SARS-CoV-2 main protease (M(pro)) plays a vital role in the replication of coronavirus and thus an attractive target for the screening of inhibitors for the therapy of COVID-19. The preclinical drugs ebselen and PX-12 are potent inhibitors of SARS-CoV-2 M(pro) and covalently modifies the active site Cys-145 residue of M(pro) through selenosulfide/disulfide. In the current report, using virtual screening methods, reactive sulfur species allicin is subjecting for covalent docking at the active site of SARS-CoV-2 M(pro) using PX-12 as a benchmark reference compound. The results indicate that allicin induces dual S-thioallylation of Cys-145 and Cys-85/ Cys-156 residues of SARS-CoV-2 M(pro). Using density functional theory (DFT), Gibbs free energy change (DG) is calculated for the putative reactions between N-acetylcysteine amide thiol and allicin/allyl sulfenic acid. The overall reaction is exergonic and allyl disulfide of Cys-145 residue of M(pro) is involved in a sulfur mediated hydrogen bond. The results indicate that allicin causes dual S-thioallylation of SARS-CoV-2 M(pro) which may be of interest for treatment and attenuation of ongoing coronavirus infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544924/ doi: 10.1080/17415993.2020.1817457 id: cord-299156-1dwsm3ie author: Shemer, Asaf title: Ocular involvement in coronavirus disease 2019 (COVID-19): a clinical and molecular analysis date: 2020-09-14 words: 3509.0 sentences: 214.0 pages: flesch: 56.0 cache: ./cache/cord-299156-1dwsm3ie.txt txt: ./txt/cord-299156-1dwsm3ie.txt summary: The aim of this study was to assess the clinical and molecular ocular involvement among patients with confirmed COVID-19 admitted to a tertiary care facility. CONCLUSIONS: Among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was noted in one out of five cases, and was associated with loss of smell and taste. Among patients with COVID-19, active conjunctival injection was associated with loss of smell and loss of taste as part of the clinical presentation (66.7% vs 7.7%, p = 0.018). In this study, we evaluated the ocular signs and symptoms, as well as the presence of SARS-CoV-2 in conjunctival swab samples among patients with COVID-19 in one tertiary referral center during March and April of 2020. To conclude, among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was present in 19% of cases and was associated with loss of smell and taste as part of the clinical presentation. abstract: PURPOSE: Coronavirus disease 2019 (COVID-19) caused a global pandemic with millions infected worldwide. Little is known on the ocular involvement associated with the disease. The aim of this study was to assess the clinical and molecular ocular involvement among patients with confirmed COVID-19 admitted to a tertiary care facility. METHODS: Consecutive patients admitted to the COVID-19 Ward of the Shamir Medical Center in Israel during March and April, 2020 were included. The control group included patients negative for COVID-19 admitted during a similar period to a different ward. Patients were examined by trained Ophthalmologists. SARS-CoV-2 conjunctival swab samples were obtained. RESULTS: Included were 48 patients, 16 with confirmed COVID-19 and 32 controls. Median patient age was 68.5 (interquartile range: 31.5, mean: 63 ± 21) years and 48% were male. Active conjunctival injection was present in three patients (19%) with COVID-19, compared to none in the controls (p = 0.034). Patients with COVID-19 were more likely to complain of foreign body sensation (31.3% vs 3.1%, p = 0.005) and redness of the eye (25% vs 0%, p = 0.003). Conjunctival injection was associated with loss of smell and taste (75% vs 7.7%, p = 0.018). Viral conjunctival swab tests all showed negative results for all three viral genes tested (E, N, and RdRp). CONCLUSIONS: Among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was noted in one out of five cases, and was associated with loss of smell and taste. Conjunctival swabs for viral RNA were negative in patients with and without ocular involvement. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10792-020-01592-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10792-020-01592-1 doi: 10.1007/s10792-020-01592-1 id: cord-312533-4u3bmb0e author: Shen, Li Wen title: TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections date: 2017-08-01 words: 4771.0 sentences: 251.0 pages: flesch: 42.0 cache: ./cache/cord-312533-4u3bmb0e.txt txt: ./txt/cord-312533-4u3bmb0e.txt summary: Recently, a great deal of evidence has suggested that a transmembrane protease, serine 2 (TMPRSS2), a type II transmembrane serine protease (TTSP), plays a critical role in SARS and Abbreviations: ARE, androgen receptor element; AEBSF, 4-(2-Aminomethyl) benzenesulfonyl fluoride hydrochloride; BHH, Bromhexine hydrochloride; CoV, coronavirus; DESC1, serine protease DESC1; EST, (2S,3S)-trans-Epoxysuccinyl-Lleucylamido-3-methylbutane ethyl ester; FDA, Food and Drug Administration; HAT, human airway trypsin-like protease; HAI-2, hepatocyte growth factor activator inhibitor 2; HGF, hepatocyte growth factor; IFITM, Interferon-induced transmembrane protein; MMP-2, matrix metalloproteinase-2; MSPL, transmembrane protease, serine 13; PAI-1, plasminogen activator inhibitor 1; PAR-2, protease activated receptor 2; PPMO, peptide-conjugated phosphorodiamidate morpholino oligomer; RBS, receptor binding subdomain; THE, human tracheal epithelial; TMPRSS2, transmembrane protease, serine 2; TMPRSS4, transmembrane protease serine 4; TTSP, type II transmembrane serine protease; vRNPs, viral ribonucleoproteins. Although FDA-approved inhibitors that specifically inhibit TMPRSS2 are not yet available, some drugs such as camostat and nafamostat that have inhibitory activity against a variety of serine proteases have been approved for the treatment of other diseases and also suppress influenza virus and coronavirus infections. abstract: Influenza virus and coronavirus epidemics or pandemics have occurred in succession worldwide throughout the early 21st century. These epidemics or pandemics pose a major threat to human health. Here, we outline a critical role of the host cell protease TMPRSS2 in influenza virus and coronavirus infections and highlight an antiviral therapeutic strategy targeting TMPRSS2. url: https://doi.org/10.1016/j.biochi.2017.07.016 doi: 10.1016/j.biochi.2017.07.016 id: cord-327318-qhrsli0b author: Shen, Qian title: Consensus recommendations for the care of children receiving chronic dialysis in association with the COVID-19 epidemic date: 2020-04-24 words: 3149.0 sentences: 160.0 pages: flesch: 46.0 cache: ./cache/cord-327318-qhrsli0b.txt txt: ./txt/cord-327318-qhrsli0b.txt summary: In turn, a set of recommendations for the prevention and control of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 in pediatric hemodialysis (HD) centers and in home peritoneal dialysis (PD) settings have been proposed. The recommendations are based on the epidemiological features of the SARS-CoV-2 virus and COVID-19 disease, susceptibility factors, and preventive and control strategies. In turn, the factors associated with an increased risk for contracting SARS-CoV-2 infection among pediatric chronic dialysis patients, especially those who receive in-center HD, include the following: (a) compromised immune system (the result of long-term malnutrition, uremia, and/or immunosuppressants); (b) close proximity to other Preventive and control strategies for in-center HD Staff management (Table 2 ) In order to effectively prevent and control the transmission of SARS-CoV-2 among children who receive maintenance dialysis, we formulated this set of recommendations based on infectious disease guidelines and our experience with the COVID-19 epidemic, which healthcare staff in pediatric dialysis centers can refer to. abstract: Coronavirus disease 2019 (COVID-19) has rapidly spread not only in China but throughout the world. Children with kidney failure (chronic kidney disease (CKD) stage 5) are at significant risk for COVID-19. In turn, a set of recommendations for the prevention and control of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 in pediatric hemodialysis (HD) centers and in home peritoneal dialysis (PD) settings have been proposed. The recommendations are based on the epidemiological features of the SARS-CoV-2 virus and COVID-19 disease, susceptibility factors, and preventive and control strategies. These recommendations will be updated as new information regarding SARS-CoV-2 and COVID-19 becomes available. url: https://www.ncbi.nlm.nih.gov/pubmed/32333285/ doi: 10.1007/s00467-020-04555-x id: cord-350957-10wcqgaq author: Shen, Zu T. title: SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice date: 2016-06-28 words: 5609.0 sentences: 265.0 pages: flesch: 48.0 cache: ./cache/cord-350957-10wcqgaq.txt txt: ./txt/cord-350957-10wcqgaq.txt summary: Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). Previously, we reported that incorporation of another immunomodulatory peptide, GF9, that employs the SCHOOL mechanisms of action and targets triggering receptor expressed on myeloid cells 1 (TREM-1), into synthetic HDL-like nanoparticles of spherical shape (sHDL) significantly reduces the effective therapeutic dosage of GF9 in animal models of sepsis, lung cancer, and RA 33, 34 . As expected from the anti-arthritic activities demonstrated in animal models of autoimmune arthritis for TCR CP 20,21,23 and HIV gp41 FP 18 , the SARS-CoV FP-derived peptide sequence MG11 significantly suppresses CIA in mice: the peptide at 25 mg/kg/day inhibits inflammation in CIA as assessed by clinical evaluation and scoring of the disease (Fig. 2) . abstract: During the co-evolution of viruses and their hosts, the viruses have evolved numerous strategies to counter and evade host antiviral immune responses in order to establish a successful infection, replicate and persist in the host. Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). This family includes T cell receptor (TCR) that is critically involved in immune diseases such as autoimmune arthritis. In the present study, we provide compelling experimental in vivo evidence in support of our hypothesis. Using the SCHOOL approach and the SARS-CoV fusion peptide sequence, we rationally designed a novel immunomodulatory peptide that targets TCR. We showed that this peptide ameliorates collagen-induced arthritis in DBA/1J mice and protects against bone and cartilage damage. Incorporation of the peptide into self-assembling lipopeptide nanoparticles that mimic native human high density lipoproteins significantly increases peptide dosage efficacy. Together, our data further confirm that viral immune evasion strategies that target MIRRs can be transferred to therapeutic strategies that require similar functionalities. url: https://doi.org/10.1038/srep28672 doi: 10.1038/srep28672 id: cord-276327-wyevh4xv author: Sheng, Calvin C title: Canakinumab to reduce deterioration of cardiac and respiratory function in SARS‐CoV‐2 associated myocardial injury with heightened inflammation (canakinumab in Covid‐19 cardiac injury: The three C study) date: 2020-08-24 words: 3239.0 sentences: 192.0 pages: flesch: 37.0 cache: ./cache/cord-276327-wyevh4xv.txt txt: ./txt/cord-276327-wyevh4xv.txt summary: We designed a proof‐of‐concept randomized controlled trial to evaluate whether treatment with canakinumab prevents progressive respiratory failure and worsening cardiac dysfunction in patients with SARS‐CoV2 infection, myocardial injury, and high levels of inflammation. The three C Study is a prospective, IRB approved, blinded randomized-controlled Phase II study designed to evaluate whether treatment with canakinumab prevents progressive heart and respiratory failure in patients with Covid-19 associated myocardial injury and increased inflammation. This blinded randomized controlled trial is designed as a proof of concept study to demonstrate whether IL-1β antagonism can dampen the deleterious autoinflammatory response to SARS-CoV2 infection in patients with myocardial injury and heightened inflammation. In evaluating this hypothesis, the Three C study will help inform whether targeting inappropriate activation of the innate immune system should be investigated in larger clinical trials to improve survival in patients with Covid-19 and myocardial injury. abstract: BACKGROUND: In patients with Covid‐19, myocardial injury and increased inflammation are associated with morbidity and mortality. We designed a proof‐of‐concept randomized controlled trial to evaluate whether treatment with canakinumab prevents progressive respiratory failure and worsening cardiac dysfunction in patients with SARS‐CoV2 infection, myocardial injury, and high levels of inflammation. HYPOTHESIS: The primary hypothesis is that canakiumab will shorten time to recovery. METHODS: The three C study (canakinumab in Covid‐19 Cardiac Injury, NCT04365153) is a double‐blind, randomized controlled trial comparing canakinumab 300 mg IV, 600 mg IV, or placebo in a 1:1:1 ratio in hospitalized Covid‐19 patients with elevations in troponin and C‐reactive protein (CRP). The primary endpoint is defined as the time in days from randomization to either an improvement of two points on a seven category ordinal scale or discharge from the hospital, whichever occurs first up to 14 days postrandomization. The secondary endpoint is mortality at day 28. A total of 45 patients will be enrolled with an anticipated 5 month follow up period. RESULTS: Baseline characteristics for the first 20 randomized patients reveal a predominantly male (75%), elderly population (median 67 years) with a high prevalence of hypertension (80%) and hyperlipidemia (75%). CRPs have been markedly elevated (median 16.2 mg/dL) with modest elevations in high‐sensitivity troponin T (median 21 ng/L), in keeping with the concept of enrolling patients with early myocardial injury. CONCLUSIONS: The three C study will provide insights regarding whether IL‐1β inhibition may improve outcomes in patients with SARS‐CoV2 associated myocardial injury and increased inflammation. url: https://www.ncbi.nlm.nih.gov/pubmed/32830894/ doi: 10.1002/clc.23451 id: cord-333897-isodrtly author: Shenoy, Niraj title: Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting? date: 2020-08-19 words: 2833.0 sentences: 150.0 pages: flesch: 39.0 cache: ./cache/cord-333897-isodrtly.txt txt: ./txt/cord-333897-isodrtly.txt summary: Finally, it discusses potential implications of specific clinical observations and considerations in COVID-19 patients on target oxygen saturation, such as diffuse systemic endothelitis and microthrombi playing an important pathogenic role in the wide range of systemic manifestations, exacerbation of hypoxic pulmonary vasoconstriction in the setting of pulmonary vascular endothelitis/microthrombi, the phenomenon of "silent hypoxemia" with some patients presenting to the hospital with severe hypoxemia disproportional to symptoms, and overburdened health systems and public health resources in many parts of the world with adverse implications on outpatient monitoring and early institution of oxygen supplementation. -The LOCO-2 trial [2] where ARDS (acute respiratory distress syndrome) patients were randomized to conservative (target partial pressure of arterial oxyHere, we examine the above two studies guiding current target oxygen saturation recommendations for COVID-19; discuss, with supporting transcriptomic analyses, the influence of hypoxia on ACE2 (angiotensin converting enzyme-2, target receptor for SARS-CoV-2 entry) expression; reflect on relevant clinical observations and considerations in COVID-19 patients; and propose a reevaluation of target oxygen saturation in these patients-both in the inpatient and outpatient settings. abstract: BACKGROUND: The current target oxygen saturation range for patients with COVID-19 recommended by the National Institutes of Health is 92–96%. MAIN BODY: This article critically examines the evidence guiding current target oxygen saturation recommendation for COVID-19 patients, and raises important concerns in the extrapolation of data from the two studies stated to be guiding the recommendation. Next, it examines the influence of hypoxia on upregulation of ACE2 (target receptor for SARS-CoV-2 entry) expression, with supporting transcriptomic analysis of a publicly available gene expression profile dataset of human renal proximal tubular epithelial cells cultured in normoxic or hypoxic conditions. Finally, it discusses potential implications of specific clinical observations and considerations in COVID-19 patients on target oxygen saturation, such as diffuse systemic endothelitis and microthrombi playing an important pathogenic role in the wide range of systemic manifestations, exacerbation of hypoxic pulmonary vasoconstriction in the setting of pulmonary vascular endothelitis/microthrombi, the phenomenon of “silent hypoxemia” with some patients presenting to the hospital with severe hypoxemia disproportional to symptoms, and overburdened health systems and public health resources in many parts of the world with adverse implications on outpatient monitoring and early institution of oxygen supplementation. CONCLUSIONS: The above factors and analyses, put together, call for an urgent exploration and re-evaluation of target oxygen saturation in COVID-19 patients, both in the inpatient and outpatient settings. Until data from such trials become available, where possible, it may be prudent to target an oxygen saturation at least at the upper end of the recommended 92–96% range in COVID-19 patients both in the inpatient and outpatient settings (in patients that are normoxemic at pre-COVID baseline). Home pulse oximetry, tele-monitoring, and earlier institution of oxygen supplementation for hypoxemic COVID-19 outpatients could be beneficial, where public health resources allow for their implementation. url: https://doi.org/10.1186/s12916-020-01735-2 doi: 10.1186/s12916-020-01735-2 id: cord-338648-5evr2v3r author: Shental, Noam title: Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers date: 2020-09-11 words: 5352.0 sentences: 274.0 pages: flesch: 56.0 cache: ./cache/cord-338648-5evr2v3r.txt txt: ./txt/cord-338648-5evr2v3r.txt summary: We developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, which identifies all positive subjects within a set of samples using a single round of testing. Here, we developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, using a single-stage nonadaptive group-testing approach, which significantly reduces the number of tests required to identify all positive subjects within a large set of samples. PCR results for each of the pools are provided to the detection algorithm (see Methods), which identifies all positive carriers without the need for an additional testing stage (Fig. 1 , A to C). RNA was extracted from each single sample and pools and was then tested for SARS-CoV-2 using the Seegene COVID-19 diagnostic kit. Using a pooling scheme designed for a carrier rate of ~1%, we showed that our method correctly identified all positive carriers in sets of 384 samples pooled into 48 pools, thereby providing an eightfold reduction in the number of required tests. abstract: Recent reports suggest that 10 to 30% of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) infected patients are asymptomatic and that viral shedding may occur before symptom onset. Therefore, there is an urgent need to increase diagnostic testing capabilities to prevent disease spread. We developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, which identifies all positive subjects within a set of samples using a single round of testing. Each sample is assigned into multiple pools using a combinatorial pooling strategy based on compressed sensing. We pooled sets of 384 samples into 48 pools, providing both an eightfold increase in testing efficiency and an eightfold reduction in test costs, while identifying up to five positive carriers. We then used P-BEST to screen 1115 health care workers using 144 tests. P- BEST provides an efficient and easy-to-implement solution for increasing testing capacity that can be easily integrated into diagnostic laboratories. url: https://www.ncbi.nlm.nih.gov/pubmed/32917716/ doi: 10.1126/sciadv.abc5961 id: cord-346711-2k736hvr author: Shetty, Rohit title: Stem cell therapy in COVID-19 – current evidence and future potential date: 2020-11-09 words: 3231.0 sentences: 225.0 pages: flesch: 45.0 cache: ./cache/cord-346711-2k736hvr.txt txt: ./txt/cord-346711-2k736hvr.txt summary: Acute respiratory distress syndrome (ARDS) caused by an unregulated host inflammatory response towards the viral infection, followed by multi-organ dysfunction or failure, is one of the primary causes of deaths in severe cases of COVID-19 infection. Expanded Umbilical Cord Mesenchymal Stem Cells (UC-MSCs) as a Therapeutic Strategy in Managing Critically Ill COVID-19 Patients: The Case for Compassionate Use Clinical remission of a critically ill COVID-19 patient treated by human umbilical cord mesenchymal stem cells FDA approved mesenchymal stem cell (MSC) treatments as compassionate use in the very sickest COVID-19 patients Adipose-derived mesenchymal stromal cells for the treatment of patients with severe SARS-CoV-2 pneumonia requiring mechanical ventilation. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial, The Lancet Therapeutic Effects of Human Umbilical Cord-Derived Mesenchymal Stem Cells in Acute Lung Injury Mice abstract: The end of 2019 saw the beginning of the COVID-19 pandemic that soared in 2020, affecting 215 countries worldwide with no signs of abating. In an effort to contain the spread of the disease and treat the infected, researchers are racing against several odds to find an effective solution. The unavailability of timely and affordable or definitive treatment has caused significant morbidity and mortality. Acute respiratory distress syndrome (ARDS) caused by an unregulated host inflammatory response towards the viral infection, followed by multi-organ dysfunction or failure, is one of the primary causes of deaths in severe cases of COVID-19 infection. Currently, empirical management of respiratory and hematological manifestations along with anti-viral agents are being used to treat the infection. The quest is on for both a vaccine and more a definitive management protocol to curtail the spread. Researchers and clinicians are also exploring the possibility of using cell therapy for severe cases of COVID-19 with ARDS. Mesenchymal stem cells are known to have immunomodulatory properties and have previously been used to treat viral infections. This review explores the potential of mesenchymal stem cells as cell therapy for ARDS. url: https://www.sciencedirect.com/science/article/pii/S1465324920309324?v=s5 doi: 10.1016/j.jcyt.2020.11.001 id: cord-290978-e7imc11r author: Shevachman, M. title: A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic date: 2020-08-07 words: 4777.0 sentences: 283.0 pages: flesch: 51.0 cache: ./cache/cord-290978-e7imc11r.txt txt: ./txt/cord-290978-e7imc11r.txt summary: A long-lasting sanitizing skin protectant that can effectively inactivate SARS-CoV-2 and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. Hence, development of an effective hand sanitizer that can generate long-lasting protective effects can offer significant benefits in minimizing rampant viral transmissions and maximize virus inactivation in a pandemic situation like SARS-CoV-2 outbreak [15, [17] [18] [19] . In order to determine the prolonged protective effects of IonLAST TM in contrast to the currently marketed products containing 70% ethyl alcohol, an in-vitro efficacy study was conducted using E. We evaluated the virucidal effects of IonLAST TM gel and the active CG-101 (5% w/w in purified water) against human Coronavirus strain 229E (hCoV229E) using a virucidal suspension test (in-vitro time-kill method) based on industry/regulatory-relevant global standardized methodologies (ASTM E1052-20). abstract: The recent outbreak and rapid spread of coronavirus disease 2019 (COVID-19) is a global pandemic and a massive public health crisis. COVID-19 has also had a severe impact on the quality of life and mental health. While different health authorities such as WHO and CDC are encouraging adoption of strategies including hand washing and use of facemasks to reduce the spread of the pathogens and infections, adoption of these approaches requires substantial commitment. Current hand sanitizers based on ethanol provide immediate protection, however, the protection rendered by such sanitizers is very short-lived due to their rapid evaporation. A long-lasting sanitizing skin protectant that can effectively inactivate SARS-CoV-2 and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. Herein, we describe a skin protectant, IonLASTTM, based on an ionic liquid/deep eutectic solvent, formed by GRAS materials, choline and geranic acid (CAGE, CG-101), that provides protection for at least 4h after a single application. IonLASTTM was formulated as a gel that facilitates easy application on the skin. Tolerance of CG-101 was substantiated through a study in human volunteers. In vitro studies confirmed that IonLASTTM effectively inactivates a human coronavirus hCoV229E. A second human clinical study established that a single application of IonLASTTM imparts protection against microbes that lasts up to several hours. url: http://medrxiv.org/cgi/content/short/2020.08.04.20161067v1?rss=1 doi: 10.1101/2020.08.04.20161067 id: cord-270591-0szbkhiz author: Shi, Chen title: Comprehensive Landscape of Heparin Therapy for COVID-19 date: 2020-10-22 words: 6198.0 sentences: 354.0 pages: flesch: 41.0 cache: ./cache/cord-270591-0szbkhiz.txt txt: ./txt/cord-270591-0szbkhiz.txt summary: Clinical observations found that systemic symptoms caused by SARS-CoV-2 infection are attenuated when using the anticoagulant agent heparin, indicating that heparin may play other roles in managing COVID-19, in addition to prevention of pulmonary thrombosis. This review discusses the pharmacological mechanisms of heparin regarding its anticoagulant, anti-inflammatory and direct antiviral activities, providing current evidence concerning the effectiveness and safety of heparin therapy for this major public health emergency. In addition to its anticoagulant and anti-inflammatory activity, heparin may possess a direct antiviral effect to SARS-CoV-2, based on the preclinical studies for other viral infections. There are both preclinical evidence and clinical data to demonstrate the benefits of heparin therapy for SARS-CoV-2 infection.With anticoagulant and anti-inflammatory effects, heparin can offer supportive treatment and alleviate the systematic symptoms of COVID-19. abstract: The pandemic coronavirus disease 2019 (COVID-19), caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rapidly spreading globally. Clinical observations found that systemic symptoms caused by SARS-CoV-2 infection are attenuated when using the anticoagulant agent heparin, indicating that heparin may play other roles in managing COVID-19, in addition to prevention of pulmonary thrombosis. Several biochemical studies show strong binding of heparin and heparin-like molecules to the Spike protein, which resulted in inhibition of viral infection to cells. The clinical observations and in vitro studies argue for a potential multiple-targeting effects of heparin. However, adverse effects of heparin administration and some of the challenges using heparin therapy for SARS-CoV-2 infection need to be considered. This review discusses the pharmacological mechanisms of heparin regarding its anticoagulant, anti-inflammatory and direct antiviral activities, providing current evidence concerning the effectiveness and safety of heparin therapy for this major public health emergency. url: https://api.elsevier.com/content/article/pii/S0144861720314053 doi: 10.1016/j.carbpol.2020.117232 id: cord-333429-bq7kfpby author: Shi, Ding title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 words: 3513.0 sentences: 251.0 pages: flesch: 57.0 cache: ./cache/cord-333429-bq7kfpby.txt txt: ./txt/cord-333429-bq7kfpby.txt summary: title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. abstract: BACKGROUND: Despite the ongoing spread of COVID-19, knowledge about factors affecting prolonged viral excretion is limited. METHODS: In this study, we retrospectively collected data from 99 hospitalized patients with COVID-19 between January 19 and February 17 in Zhejiang Province, China. We classified them into two groups based on whether the virus test results eventually became negative. Cox proportional hazards regression was used to evaluate factors associated with SARS-CoV-2 shedding. RESULTS: Among 99 patients, 61 patients had SARS-CoV-2 clearance (virus-negative group), but 38 patients had sustained positive results (virus-positive group). The median duration of SARS-CoV-2 excretion was 15 days (IQR 12-19) among the virus-negative patients. The shedding time was significantly increased if fecal SARS-CoV-2 RNA test results was positive. Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. Antiviral therapy and corticosteroid treatment were not independent factors. CONCLUSIONS: SARS-CoV-2 RNA clearance time was associated with sex, disease severity and lymphocyte function. The current antiviral protocol and low-to-moderate dosage of corticosteroid had little effect on the duration of viral excretion. url: https://doi.org/10.1093/infdis/jiaa388 doi: 10.1093/infdis/jiaa388 id: cord-320175-w00rcvd8 author: Shi, Jiahai title: The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain date: 2006-02-08 words: 5485.0 sentences: 261.0 pages: flesch: 51.0 cache: ./cache/cord-320175-w00rcvd8.txt txt: ./txt/cord-320175-w00rcvd8.txt summary: Based on this, a super‐active triple‐mutant STI/A with a 3.7‐fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild‐type (WT) and STI/A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Based on this, a super-active triple-mutant STI ⁄ A with a 3.7-fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild-type (WT) and STI ⁄ A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Dynamic light scattering (DLS) was used to measure the apparent molecular mass resulting from monomer-dimer equilibrium of the wild-type and mutated proteases at three different NaCl concentrations. abstract: The 3C‐like protease of the severe acute respiratory syndrome (SARS) coronavirus has a C‐terminal extra domain in addition to the chymotrypsin‐fold adopted by piconavirus 3C proteases hosting the complete catalytic machinery. Previously we identified the extra domain to be involved in enzyme dimerization which has been considered essential for the catalytic activity. In an initial attempt to map out the extra‐domain residues critical for dimerization, we have systematically generated 15 point mutations, five deletions and one triple mutation and subsequently characterized them by enzymatic assay, dynamic light scattering, CD and NMR spectroscopy. The results led to identification of four regions critical for enzyme dimerization. Interestingly, Asn214Ala mutant with a significant tendency to form a monomer still retained ≈ 30% activity, indicating that the relationship between the activity and dimerization might be very complex. Very surprisingly, two regions (one over Ser284–Thr285–Ile286 and another around Phe291) were discovered on which Ala‐mutations significantly increased the enzymatic activities. Based on this, a super‐active triple‐mutant STI/A with a 3.7‐fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild‐type (WT) and STI/A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. We rationalized these results based on the enzyme structure and consequently observed an interesting picture: the majority of the dimerization‐critical residues plus Ser284–Thr285–Ile286 and Phe291 are clustered together to form a nano‐scale channel passing through the central region of the enzyme. We therefore speculate that this channel might play a role in relaying regulatory effects from the extra domain to the catalytic machinery. url: https://www.ncbi.nlm.nih.gov/pubmed/16478476/ doi: 10.1111/j.1742-4658.2006.05130.x id: cord-263847-kyak5cy4 author: Shi, Tzu-Hau title: Andrographolide and its fluorescent derivative inhibit the main proteases of 2019-nCoV and SARS-CoV through covalent linkage date: 2020-08-25 words: 3093.0 sentences: 162.0 pages: flesch: 45.0 cache: ./cache/cord-263847-kyak5cy4.txt txt: ./txt/cord-263847-kyak5cy4.txt summary: We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (AndroNBD), suppressed the main protease (M(pro)) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys(145) of either 2019-nCoV M(pro) or SARS-CoV M(pro). Moreover, lopinavir/ritonavir, previously identified as HIV protease inhibitors and found to exhibit anti-SARS-CoV activity in vitro and in clinical, have been proposed to bind 2019-nCoV M pro and are being investigated for COVID-19 treatments [6, 7] . Lopinavir/ritonavir, the HIV protease inhibitors previously identified with anti-SARS-CoV activity in vitro and in clinical, was proposed to bind 2019-nCoV M pro and thus has been investigated for COVID-19 treatments [6, 7] . In this study, we revealed that andrographolide and its derivative inhibits the activity of main protease and thus likely to impair the replication of SARS-CoV and 2019-nCoV. abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by 2019 novel coronavirus (2019-nCoV) has been a crisis of global health, whereas the effective vaccines against 2019-nCoV are still under development. Alternatively, utilization of old drugs or available medicine that can suppress the viral activity or replication may provide an urgent solution to suppress the rapid spread of 2019-nCoV. Andrographolide is a highly abundant natural product of the medicinal plant, Andrographis paniculata, which has been clinically used for inflammatory diseases and anti-viral therapy. We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (Andro- NBD), suppressed the main protease (M(pro)) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Moreover, Andro-NBD was shown to covalently link its fluorescence to these proteases. Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys(145) of either 2019-nCoV M(pro) or SARS-CoV M(pro). Consistently, molecular modeling analysis supported the docking of andrographolide within the catalytic pockets of both viral M(pro)s. Considering that andrographolide is used in clinical practice with acceptable safety and its diverse pharmacological activities that could be beneficial for attenuating COVID-19 symptoms, extensive investigation of andrographolide on the suppression of 2019-nCoV as well as its application in COVID-19 therapy is suggested. url: https://www.sciencedirect.com/science/article/pii/S0006291X20316831?v=s5 doi: 10.1016/j.bbrc.2020.08.086 id: cord-349365-2ot1kf2k author: Shi, Yi title: Antisense downregulation of SARS‐CoV gene expression in Vero E6 cells date: 2004-11-15 words: 3217.0 sentences: 175.0 pages: flesch: 52.0 cache: ./cache/cord-349365-2ot1kf2k.txt txt: ./txt/cord-349365-2ot1kf2k.txt summary: Cells were then treated with the antisense oligonucleotides used by adding them to the culture medium, which then reached the nuclei and resulted in sequence-specific antisense downregulation of SARS-CoV gene expression. We conclude that the antisense PS-ODNs could effectively and sequence-specifically downregulate SARS-CoV gene expression in a dose-dependent manner. In this work, we have evaluated the down-regulation effects of 26 antisense PS-ODNs targeting different sites along the open reading frames (ORFs) of E, M, and N proteins and obtained 12 antisense oligos which could reduce target gene expression by over 50% in Vero E6 cells at the concentration of 50 µM in the culture medium. Our present results indicate a sequencespecific down-regulation effect of antisense PS-ODN (20mer) in Vero E6 cells, and we found an effective range of concentrations, where the antisense oligo inhibited expression of the E, M, and N genes of SARS-CoV in a concentration-dependent manner. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is caused by a novel coronavirus (SARS‐CoV). It is an enveloped, single‐stranded, plus‐sense RNA virus with a genome of ∼30 kb. The structural proteins E, M and N of SARS‐CoV play important roles during host cell entry and viral morphogenesis and release. Therefore, we have studied whether expression of these structural proteins can be down‐regulated using an antisense technique. METHODS: Vero E6 cells were transfected with plasmid constructs containing exons of the SARS‐CoV structural protein E, M or N genes or their exons in frame with the reporter protein EGFP. The transfected cell cultures were treated with antisense phosphorothioated oligonucleotides (antisense PS‐ODN, 20mer) or a control oligonucleotide by addition to the culture medium. RESULTS: Among a total of 26 antisense PS‐ODNs targeting E, M and N genes, we obtained six antisense PS‐ODNs which could sequence‐specifically reduce target genes expression by over 90% at the concentration of 50 µM in the cell culture medium tested by RT‐PCR. The antisense effect was further proved by down‐regulating the expression of the fusion proteins containing the structural proteins E, M or N in frame with the reporter protein EGFP. In Vero E6 cells, the antisense effect was dependent on the concentrations of the antisense PS‐ODNs in a range of 0–10 µM or 0–30 µM. CONCLUSIONS: The antisense PS‐ODNs are effective in downregulation of SARS. The findings indicate that antisense knockdown of SARS could be a useful strategy for treatment of SARS, and could also be suitable for studies of the pathological function of SARS genes in a cellular model system. Copyright © 2004 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/15543523/ doi: 10.1002/jgm.640 id: cord-103940-a2cqw8kg author: Shi, Yuejun title: Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date: 2020-06-09 words: 3207.0 sentences: 216.0 pages: flesch: 63.0 cache: ./cache/cord-103940-a2cqw8kg.txt txt: ./txt/cord-103940-a2cqw8kg.txt summary: Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. In this study, 130 we selected SARS-CoV, SARS-CoV-2, and HCoV-229E as models, which adopt the 131 two RBD states, and evaluated and compared immune responses to the S trimers and 132 7 RBDs of these coronaviruses through immunological and bioinformatics approaches. 133 We also investigated the mechanism through which the HCoV-229E S trimer 134 produced effective nAbs. Finally, we provide possible vaccine strategies for alphaTo address this issue, we performed B-cell epitope predictions for the S trimers 152 and RBDs of alpha-CoV (HCoV-229E) and beta-CoVs (SARS-CoV and 153 SARS-CoV-2). Taken together, these results showed that the intact and stable S1 subunit of 240 HCoV-229E is a prerequisite for the production of effective nAbs. Furthermore, our experimental results show that RBD has a higher ability to bind 242 12 to the receptor hAPN (Fig. 4B) , which indicates that the characteristics of RBD itself 243 may lead to the generation of less neutralizing antibodies. abstract: Coronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. However, no commercial vaccines against the coronaviruses that can infect humans are available. The spike (S) homotrimers bind to their receptors through the receptor-binding domain (RBD), which is believed to be a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs were observed to adopt two different conformational states (lying or standing). Then, structural and immunological analyses were used to explore differences in the immune response with RBDs among these coronaviruses. Our results showed that more RBD-specific antibodies were induced by the S trimer with the RBD in the “standing” state (SARS-CoV and SARS-CoV-2) than the S trimer with the RBD in the “lying” state (HCoV-229E), and the affinity between the RBD-specific antibodies and S trimer was also higher in the SARS-CoV and SARS-CoV-2. In addition, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was much lower and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus. Our findings will provide important implications for future development of coronavirus vaccines. Importance Outbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. Here, we tested the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that Beta-CoVs RBDs are in a standing state, and their S proteins can induce more neutralizing antibodies targeting RBD. However, HCoV-229E RBD is in a lying state, and its S protein induces a low level of neutralizing antibody targeting RBD. Our results indicate that Alpha-coronavirus is more conducive to escape host immune recognition, and also provide novel ideas for the development of vaccines targeting S protein. url: https://doi.org/10.1101/2020.06.09.141580 doi: 10.1101/2020.06.09.141580 id: cord-335955-2bw2sly8 author: Shi, Yuejun title: A Dimerization-Dependent Mechanism Drives the Endoribonuclease Function of Porcine Reproductive and Respiratory Syndrome Virus nsp11 date: 2016-04-14 words: 7045.0 sentences: 383.0 pages: flesch: 53.0 cache: ./cache/cord-335955-2bw2sly8.txt txt: ./txt/cord-335955-2bw2sly8.txt summary: The crystal structures of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp15 and murine hepatitis virus (MHV) nsp15 show that the biological unit of nsp15 is a hexamer (19, 21) and that the N-terminal domain (NTD) is important for oligomerization (23) . We report the crystal structure of PRRSV endoribonuclease nsp11 and demonstrate that the folding of NendoU active site residues is widely conserved among members of the order Nidovirales (families Arteriviridae and Coronaviridae). Additionally, the structural comparison demonstrated that residues His129, His144, Lys173, Thr177, Asp180, Asp204, and Tyr219 from nsp11 superimpose well onto the corresponding residues of coronavirus nsp15 (Fig. 5 and 6 ), indicating the relative conservation of key active site residues and similar endoribonuclease cleavage mechanisms shared among nidoviruses (families Arteriviridae and Coronaviridae). In this study, endoribonuclease activity of the wild-type and mutant nsp11 protein was measured, and the results are shown in Fig. 7C . abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) RNA endoribonuclease nsp11 belongs to the XendoU superfamily and plays a crucial role in arterivirus replication. Here, we report the first crystal structure of the arterivirus nsp11 protein from PRRSV, which exhibits a unique structure and assembles into an asymmetric dimer whose structure is completely different from the hexameric structure of coronavirus nsp15. However, the structures of the PRRSV nsp11 and coronavirus nsp15 catalytic domains were perfectly superimposed, especially in the “active site loop” (His129 to His144) and “supporting loop” (Val162 to Thr179) regions. Importantly, our biochemical data demonstrated that PRRSV nsp11 exists mainly as a dimer in solution. Mutations of the major dimerization site determinants (Ser74 and Phe76) in the dimerization interface destabilized the dimer in solution and severely diminished endoribonuclease activity, indicating that the dimer is the biologically functional unit. In the dimeric structure, the active site loop and supporting loop are packed against one another and stabilized by monomer-monomer interactions. These findings may help elucidate the mechanism underlying arterivirus replication and may represent great potential for the development of antiviral drugs. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is a member of the family Arteriviridae, order Nidovirales. PRRSV is a major agent of respiratory diseases in pigs, causing tremendous economic losses to the swine industry worldwide. The PRRSV nsp11 endoribonuclease plays a vital role in arterivirus replication, but its precise roles and mechanisms of action are poorly understood. Here, we report the first dimeric structure of the arterivirus nsp11 from PRRSV at 2.75-Å resolution. Structural and biochemical experiments demonstrated that nsp11 exists mainly as a dimer in solution and that nsp11 may be fully active as a dimer. Mutagenesis and structural analysis revealed NendoU active site residues, which are conserved throughout the order Nidovirales (families Arteriviridae and Coronaviridae) and the major determinants of dimerization (Ser74 and Phe76) in Arteriviridae. Importantly, these findings may provide a new structural basis for antiviral drug development. url: https://doi.org/10.1128/jvi.03065-15 doi: 10.1128/jvi.03065-15 id: cord-354893-tku1dr32 author: Shi, Zhengli title: Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology date: 2010-12-24 words: 5894.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-354893-tku1dr32.txt txt: ./txt/cord-354893-tku1dr32.txt summary: Comparative genome sequence analysis indicated that SARS-CoVs civets experience rapid ongoing mutation, suggesting that the viruses were still adapting to the host rather than persisting in equilibrium expected for viruses in their natural reservoir species Song et al., 2005) . Analysis of all the viral sequences available from human patients and animals revealed two major hallmarks of rapid virus evolution during the initial stages of the 2002À2003 outbreaks: (1) All isolates from early patients and market animals contained a 29-nt sequence in ORF8 that is absent in most of the publicly available human SARS-CoV sequences derived from later phases of the outbreaks; (2) a characteristic motif of single-nucleotide variations (SNVs) were identified in SARS-CoV of different phases, and all these SNVs were located in the S gene that codes for the spike protein responsible for attachment to host cellular receptor . Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections abstract: This chapter discusses the evolution of severe acute respiratory syndrome (SARS) coronavirus and the relevance of modern molecular epidemiology. The first case was reported in China in November 2002 and led to a disastrous worldwide pandemic. An international SARS network was established by WHO to rapidly identify the causative agent. In March 2003, the SARS coronavirus was identified. The majority of the early cases were limited to the Guangdong province of China, which have a unique dietary tradition favoring freshly slaughtered game meat; therefore, studies were conducted in those markets for evidence of SARS-CoV. Antibodies against SARS-CoV were detected in masked palm civets. By using serological and PCR surveillance, it was discovered that SARS-like CoV or SL-CoVs were present in different horseshoe bats in the genus Rhinolophus and that they are the likely natural reservoir hosts of bat SL-CoVs. There are more than 60 different horseshoe species around the world, and one or more of them may serve as the natural reservoir of SARS-CoV and/or its progenitor virus(es). It is therefore likely that another outbreak could occur on a similar scale as that of the SARS-CoV outbreaks but our response to a future outbreak caused by any bat-borne coronavirus will be much more effective. SARS is an example demonstrating the evolution of an animal virus into a human pathogen responsible for one of the most severe global pandemic. It is paramount that from now we include active surveillance of wild animals as part of an integrated infectious disease prevention and control strategy. url: https://api.elsevier.com/content/article/pii/B9780123848901000273 doi: 10.1016/b978-0-12-384890-1.00027-3 id: cord-355514-2qjbc3bd author: Shibata, Shun title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection date: 2020-07-25 words: 2044.0 sentences: 117.0 pages: flesch: 48.0 cache: ./cache/cord-355514-2qjbc3bd.txt txt: ./txt/cord-355514-2qjbc3bd.txt summary: title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 1 High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 2 Because of high incidence of false positive RIAT results, cross antigenicity between human common cold coronaviruses and SARS-CoV-2 can be considered. We experienced a patient suffering human coronavirus HKU1 pneumonia who showed false-positive results for IgG against SARS-CoV-2 using an RIAT. We performed RIAT using a commercially available kit for IgM and IgG against SARS-CoV-2 in serum samples of 24 patients with laboratory-confirmed COVID-19 (admitted from February to April 2020), 7 patients with human common cold coronavirus pneumonia (Table 1) and IgM with median 12 days from illness onset was compatible with previous reports [3, 4] . abstract: We experienced a 72-year-old man who developed laboratory-confirmed human coronavirus HKU1 pneumonia. PCR testing for SARS-CoV-2 from a nasopharyngeal specimen was negative twice, and rapid immunochromatographic antibody test (RIAT) using a commercially available kit for IgM and IgG against SARS-CoV-2 showed him turning positive for IgG against SARS-CoV-2. We then performed RIAT in stored serum samples from other patients who suffered laboratory-confirmed human common cold coronaviruses (n = 6) and viruses other than coronavirus (influenza virus, n = 3; rhinovirus, n = 3; metapneumovirus, n = 1; adenovirus, n = 1) admitted until January 2019. Including the present case, four of 7 (57%) showed false-positive RIAT results due to human common cold coronaviruses infection. Two of the 4 patients showed initial negative to subsequent positive RIAT results, indicating seroconversion. RIAT was positive for IgG and IgM in viruses other than coronavirus in 2 (25.0%) and 1 (12.5%) patient. Because of high incidence of false positive RIAT results, cross antigenicity between human common cold coronaviruses and SARS-CoV-2 can be considered. Results of RIAT should be interpreted in light of epidemics of human common cold coronaviruses infection. Prevalence of past SARS-CoV-2 infection may be overestimated due to high incidence of false-positive RIAT results. url: https://doi.org/10.1016/j.rmcr.2020.101180 doi: 10.1016/j.rmcr.2020.101180 id: cord-346816-xys0g8b8 author: Shichijo, S. title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity date: 2004-10-20 words: 1141.0 sentences: 61.0 pages: flesch: 54.0 cache: ./cache/cord-346816-xys0g8b8.txt txt: ./txt/cord-346816-xys0g8b8.txt summary: title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity Abstract: In order to determine highly immunogenic severe acute respiratory syndrome coronavirus (SARS‐CoV) epitope peptides capable of inducing long‐lasting immunity, we first screened immunoglobulin‐G (IgG) antibodies reactive to 197 different overlapping 15‐mers from the SARS‐CoV proteins in the sera of three infected patients. The significantly higher levels of IgG antibodies specific to three (S791, M207 and N161) of 42 peptides were detectable in the post‐infection sera from 23 (51%), 27 (60%) and 19 (42%) of 45 patients, respectively. In contrast to these four peptides, significant levels of IgG reactive to the remaining 36 peptides were either scarcely or not detected in the patients (Table 1) Fig. 5 . Dynamic observation IgG and IgM antibodies in patients with severe acute respiratory syndrome abstract: Abstract: In order to determine highly immunogenic severe acute respiratory syndrome coronavirus (SARS‐CoV) epitope peptides capable of inducing long‐lasting immunity, we first screened immunoglobulin‐G (IgG) antibodies reactive to 197 different overlapping 15‐mers from the SARS‐CoV proteins in the sera of three infected patients. Forty‐two peptides among them were reactive to the sera from all three patients. Consequently, we tested for the reactivity of these 42 peptides to patients' sera (n = 45) at 6‐month post‐infection. The significantly higher levels of IgG antibodies specific to three (S791, M207 and N161) of 42 peptides were detectable in the post‐infection sera from 23 (51%), 27 (60%) and 19 (42%) of 45 patients, respectively. These three peptides, recognized by their long‐lasting immunity, may provide a better understanding of the immunogenicity of SARS‐CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/15496204/ doi: 10.1111/j.1399-0039.2004.00314.x id: cord-352080-3rcqbgl7 author: Shidham, Vinod B. title: Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date: 2020-04-10 words: 3486.0 sentences: 227.0 pages: flesch: 50.0 cache: ./cache/cord-352080-3rcqbgl7.txt txt: ./txt/cord-352080-3rcqbgl7.txt summary: It is therefore mandatory to practice all the universal/standard precautions with basic protective measures while handling any biological specimen irrespective of SARS-CoV-2 status [Tables 1 -3] . [16] Although, appropriate disinfectants and precautions related to cytopathological/histological fixation and processing of samples during the current COVID 19 pandemic are not known, information can likely be extrapolated from other recent coronaviruses (e.g., SARS and MERS). 5. If the diagnostic testing specimens are processed outside of a BSL-2 laboratory, [33] such as preparation of cytology direct smears, rinsing of FNAB aspirates for cell block, the Standard Precautions (similar to those mentioned under Table 1 ) should be practiced as a barrier between the specimen and personnel. [14, 15] In cases suspected or positive for SARS-CoV-2 virus-perform the processing in certified Class II [35] Biological Safety Cabinet FNAB procedure [22] Based on the aforementioned, SARS-CoV-2 in any specimen processed with routine fixatives in cytopathology should be inactivated [ Table 5 ]. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32395151/ doi: 10.25259/cytojournal_24_2020 id: cord-355760-2a12nsnl author: Shields, A. M. title: SARS-CoV-2 seroconversion in health care workers date: 2020-05-19 words: 3159.0 sentences: 178.0 pages: flesch: 44.0 cache: ./cache/cord-355760-2a12nsnl.txt txt: ./txt/cord-355760-2a12nsnl.txt summary: Conclusions In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. Evidence before the study To date, no study has examined the cross-sectional seroprevalence of anti-SARS-CoV-2 antibodies in health care workers during the COVID-19 pandemic. We conducted a cross-sectional study of 554 staff at UHBFT to determine the incidence of infection and seroconversion in health care workers and their relationship to prior symptoms of COVID-19. In light of further evidence of asymptomatic infection and seroconversion, the impact of mandatory screening of health care workers should be thoroughly investigated [12] The seroprevalence of SARS-CoV-2 antibodies amongst the UK general population remains unknown and few studies have considered seroprevalence in other populations. In conclusion, we provide evidence of SARS-CoV-2 seroconversion in health care workers with and without prior symptomatic illness. abstract: Background The correlates of protection against SARS-CoV-2 and their longevity remain unclear. Studies in severely ill individuals have identified robust cellular and humoral immune responses against the virus. Asymptomatic infection with SARS-CoV-2 has also been described, but it is unknown whether this is sufficient to produce antibody responses. Methods We performed a cross-sectional study recruiting 554 health care workers from University Hospitals Birmingham NHS Foundation Trust who were at work and asymptomatic. Participants were tested for current infection with SARS-CoV-2 by nasopharyngeal swab for real-time polymerase chain reaction and for seroconversion by the measurement of anti-SARS-CoV-2 spike glycoprotein antibodies by enzyme linked immunosorbent assay. Results were interpreted in the context of previous, self-reported symptoms of illness consistent with COVID-19. Results The point prevalence of infection with SARS-CoV-2, determined by the detection of SARS-CoV-2 RNA on nasopharnygeal swab was 2.39% (n=13/544). Serum was available on 516 participants. The overall rate of seroconversion in the cohort was 24.4% (n=126/516). Individuals who had previously experienced a symptomatic illness consistent with COVID-19 had significantly greater seroconversion rates than those who had remained asymptomatic (37.5% vs 17.1%, {chi}2 =21.1034, p<0.0001). In the week preceding peak COVID-19-related mortality at UHBFT, seroconversion rates amongst those who were suffering from symptomatic illnesses peaked at 77.8%. Prior symptomatic illness generated quantitatively higher antibody responses than asymptomatic seroconversion. Seroconversion rates were highest amongst those working in housekeeping (34.5%), acute medicine (33.3%) and general internal medicine (30.3%) with lower rates observed in participants working in intensive care (14.8%) and emergency medicine (13.3%). Conclusions In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. The identification that the potential for seroconversion in health-care workers can associate differentially with certain hospital departments may inform future infection control and occupational health practices. url: http://medrxiv.org/cgi/content/short/2020.05.18.20105197v1?rss=1 doi: 10.1101/2020.05.18.20105197 id: cord-325966-0g7a9s5z author: Shih, Hsin-I. title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 words: 7324.0 sentences: 365.0 pages: flesch: 39.0 cache: ./cache/cord-325966-0g7a9s5z.txt txt: ./txt/cord-325966-0g7a9s5z.txt summary: Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. However, these clinical, laboratory, and imaging findings are nonspecific and cannot differentiate COVID-19 from other viral respiratory infections; viral diagnostic methods specific for SARS-CoV-2 should be applied for disease confirmation. An open-label study published in 2004 suggested, by comparison with a control group that received only ribavirin, that the addition of lopinavir-ritonavir (400 mg and 100 mg, respectively) to ribavirin reduced the risk of adverse clinical outcomes (acute respiratory distress syndrome or death) and viral load among patients with SARS [29] . Some available candidate drugs targeting different levels of human responses to COVID-19, such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, IL-6 blocker and convalescent plasma, may improve the clinical outcomes of critical COVID-19 patients. abstract: The COVID-19 pandemic caused by a novel coronavirus, SARS-CoV-2, has infected more than 4.9 million individuals and resulted in over 300,000 deaths globally. The rapid spread of the virus and the precipitously increasing numbers of cases necessitate the urgent development of accurate diagnostic methods, effective treatments, and vaccines. Here, we review the progress of developing diagnostic methods, therapies, and vaccines for SARS-CoV-2 with a focus on current clinical trials and their challenges. For diagnosis, nucleic acid amplification tests remain the mainstay diagnostics for laboratory confirmation of SARS-CoV-2 infection, while serological antibody tests are used to aid contact tracing, epidemiological, and vaccine evaluation studies. Viral isolation is not recommended for routine diagnostic procedures due to safety concerns. Currently, no single effective drug or specific vaccine is available against SARS-CoV-2. Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. Other supportive care measures for critical patients are still necessary. Advances in genetic sequencing and other technological developments have sped up the establishment of a variety of vaccine platforms. Accordingly, numerous vaccines are under development. Vaccine candidates against SARS-CoV-2 are mainly based upon the viral spike protein due to its vital role in viral infectivity, and most of these candidates have recently moved into clinical trials. Before the efficacy of such vaccines in humans is demonstrated, strong international coordination and collaboration among studies, pharmaceutical companies, regulators, and governments are needed to limit further damage due the emerging SARS-CoV-2 virus. url: https://doi.org/10.1016/j.bj.2020.05.021 doi: 10.1016/j.bj.2020.05.021 id: cord-337867-hqmf6r7t author: Shim, Byoung-Shik title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses date: 2010-12-31 words: 3762.0 sentences: 221.0 pages: flesch: 54.0 cache: ./cache/cord-337867-hqmf6r7t.txt txt: ./txt/cord-337867-hqmf6r7t.txt summary: title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses RESULTS: In the present study, the immune responses of BALB/c mice immunized via intranasal (i.n.) route with SARS DNA vaccine (pci-S) in a PEI/pci-S complex form have been examined. The result showed that SARS S-specific IgA antibody response was significantly (P < 0.01) increased in lung wash from mice immunized with PEI/pci-S complexes ( Figure 2B ). B220 + cells from mice immunized with PEI/pci-S complexes were highly proliferated after in vitro re-stimulation with SARS-CoV S protein ( Figure 2C ). The surface expression of CD80 and CD86 co-stimulatory molecules were significantly (P < 0.05) higher on DCs from mice treated with PEI/pci-S complexes than those from SARS-CoV DNA S vaccine alone ( Figure 3 ). DNA vaccine encoding full-length S protein has shown to induce humoral, cellular and protective immune responses against SARS-CoV [6] . abstract: BACKGROUND: Immunization with the spike protein (S) of severe acute respiratory syndrome (SARS)-coronavirus (CoV) in mice is known to produce neutralizing antibodies and to prevent the infection caused by SARS-CoV. Polyethylenimine 25K (PEI) is a cationic polymer which effectively delivers the plasmid DNA. RESULTS: In the present study, the immune responses of BALB/c mice immunized via intranasal (i.n.) route with SARS DNA vaccine (pci-S) in a PEI/pci-S complex form have been examined. The size of the PEI/pci-S nanoparticles appeared to be around 194.7 ± 99.3 nm, and the expression of the S mRNA and protein was confirmed in vitro. The mice immunized with i.n. PEI/pci-S nanoparticles produced significantly (P < 0.05) higher S-specific IgG1 in the sera and mucosal secretory IgA in the lung wash than those in mice treated with pci-S alone. Compared to those in mice challenged with pci-S alone, the number of B220(+ )cells found in PEI/pci-S vaccinated mice was elevated. Co-stimulatory molecules (CD80 and CD86) and class II major histocompatibility complex molecules (I-A(d)) were increased on CD11c(+ )dendritic cells in cervical lymph node from the mice after PEI/pci-S vaccination. The percentage of IFN-γ-, TNF-α- and IL-2-producing cells were higher in PEI/pci-S vaccinated mice than in control mice. CONCLUSION: These results showed that intranasal immunization with PEI/pci-S nanoparticles induce antigen specific humoral and cellular immune responses. url: https://www.ncbi.nlm.nih.gov/pubmed/21194475/ doi: 10.1186/1471-2172-11-65 id: cord-275746-3sgbpn13 author: Shimamoto, Yasuhiro title: Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors date: 2015-02-15 words: 6600.0 sentences: 347.0 pages: flesch: 66.0 cache: ./cache/cord-275746-3sgbpn13.txt txt: ./txt/cord-275746-3sgbpn13.txt summary: After the reaction mixture was cooled to room temperature, water was added and the whole was extracted with AcOEt. The organic layer was washed with 1 M HCl and brine, dried over MgSO 4 , filtered, and concentrated. After the mixture was stirred for 12 h, the reaction was quenched with saturated aqueous NH 4 Cl and the whole was extracted with AcOEt. The organic layer was washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by silica gel column chromatography (hexane/AcOEt = 3:1) to give a title alcohol ( 21 .0 mmol) in CH 2 Cl 2 (50 mL), and the mixture was stirred for 8 h at room temperature. The residue was purified by silica gel column chromatography (hexane/AcOEt = 6:1) to give 32 ( Tris-HCl buffer pH 7.5 containing 7 mM DTT) was incubated with the R188I SARS 3CL pro28 (56 nM) at 37°C for 60 min in the presence of various inhibitor concentrations at 37°C for 60 min. abstract: The design and evaluation of a novel decahydroisoquinolin scaffold as an inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)) are described. Focusing on hydrophobic interactions at the S(2) site, the decahydroisoquinolin scaffold was designed by connecting the P(2) site cyclohexyl group of the substrate-based inhibitor to the main-chain at the α-nitrogen atom of the P(2) position via a methylene linker. Starting from a cyclohexene enantiomer obtained by salt resolution, trans-decahydroisoquinolin derivatives were synthesized. All decahydroisoquinolin inhibitors synthesized showed moderate but clear inhibitory activities for SARS 3CL(pro), which confirmed the fused ring structure of the decahydroisoquinolin functions as a novel scaffold for SARS 3CL(pro) inhibitor. X-ray crystallographic analyses of the SARS 3CL(pro) in a complex with the decahydroisoquinolin inhibitor revealed the expected interactions at the S(1) and S(2) sites, as well as additional interactions at the N-substituent of the inhibitor. url: https://api.elsevier.com/content/article/pii/S0968089614008761 doi: 10.1016/j.bmc.2014.12.028 id: cord-281101-gv1sgbk1 author: Shin, Gu-Choul title: Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date: 2006-08-30 words: 5929.0 sentences: 279.0 pages: flesch: 52.0 cache: ./cache/cord-281101-gv1sgbk1.txt txt: ./txt/cord-281101-gv1sgbk1.txt summary: Severe acute respiratory syndrome-coronavirus nucleocapsid (SARS-CoV N) protein has been found to be important to the processes related to viral pathogenesis, such as virus replication, interference of the cell process and modulation of host immune response; detection of the antigen has been used for the early diagnosis of infection. Reactivity of SARS-N mAbs with SARS-CoV infected cells was determined by immunofluorescence assay, performed according to the instructions of the manufacturer (Euroimmun, Germany). To further assess the specificity of the mAbs, antigen-capture ELISA was performed with human coronavirus-infected cell lysates and BrSARS-N protein as positive control (Fig. 6B) . (B) Cross-reactivity of SARS-N mAbs was examined by antigen-capture ELISA using human coronavirus OC43 lysates (256 HA unit), BrSARS-N protein (500 ng/well) and PBST buffer with 1% BSA as control. These mAbs were available for use in detecting SARS-CoV N protein by various diagnostic methods, such as immunoblot assay, immunofluorescence assay and antigen-capture ELISA (Table 3) . abstract: Severe acute respiratory syndrome-coronavirus nucleocapsid (SARS-CoV N) protein has been found to be important to the processes related to viral pathogenesis, such as virus replication, interference of the cell process and modulation of host immune response; detection of the antigen has been used for the early diagnosis of infection. We have used recombinant N protein expressed in insect cells to generate 17 mAbs directed against this protein. We selected five mAbs that could be used in various diagnostic assays, and all of these mAbs recognized linear epitopes. Three IgG(2b) mAbs were recognized within the N-terminus of N protein, whereas the epitope of two IgG(1) mAbs localized within the C-terminus. These mAbs were found to have significant reactivity with both non-phosphorylated and phosphorylated N proteins, which resulted in high reactivity with native N protein in virus-infected cells; however, they did not show cross-reactivity with human coronavirus. Therefore, these results suggested that these mAbs would be useful in the development of various diagnostic kits and in future studies of SARS-CoV pathology. url: https://www.ncbi.nlm.nih.gov/pubmed/16942813/ doi: 10.1016/j.virusres.2006.07.004 id: cord-303661-etb19d6y author: Shin, Hyoung-Shik title: Empirical Treatment and Prevention of COVID-19 date: 2020-06-22 words: 4019.0 sentences: 212.0 pages: flesch: 42.0 cache: ./cache/cord-303661-etb19d6y.txt txt: ./txt/cord-303661-etb19d6y.txt summary: Though the COVID-19 showed pandemic spread and unexpected clinical manifestations characterized by various symptoms throughout the whole body, SARS-CoV-2 seems to be less virulent especially in children and adolescents, in whom the disease mimics common cold caused by seasonal coronaviruses [7] . At the early stage of the epidemic, it had been recommended to apply the treatment regimen of middle east respiratory syndrome coronavirus (MERS-CoV) in the case of the patients with severe symptoms [23] . Considering that the infection can be asymptomatic and as it can rapidly spread across national borders, studies-to elucidate the life cycle of SARS-CoV-2, innate and adaptive immune responses to the virus, and side effects of medicationsshould be conducted on a global scale; this would help in developing appropriate treatment strategies. abstract: The rapid spread of severe acute respiratory coronavirus syndrome 2 (SARS-CoV-2) in the population and throughout the cells within our body has been developing. Another major cycle of coronavirus disease 2019 (COVID-19), which is expected in the coming fall, could be even more severe than the current one. Therefore, effective countermeasures should be developed based on the already obtained clinical and research information about SARS-CoV-2. The aim of this review was to summarize the data on the empirical treatment of COVID-19 acquired during this SARS-CoV-2 infection cycle; this would aid the establishment of an appropriate healthcare policy to meet the challenges in the future. The infectious disease caused by SARS-CoV-2 is characterized by common cold along with hypersensitivity reaction. Thus, in addition to treating common cold, it is essential to minimize the exposure of cells to the virus and to mitigate the uncontrolled immune response. A proper combination of antiviral agents, immune modulators such as prednisolone, and anticoagulants such as heparin and anti-C5a antagonists could be employed to minimize lung damage and prevent systemic involvements. Finally, strategies to achieve population immunity against SARS-CoV-2 should be developed through understanding of the interaction between the immune system and the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32476308/ doi: 10.3947/ic.2020.52.2.142 id: cord-350679-69lv4wbz author: Shinde, Rajesh S. title: To Do or Not to Do?—A Review of Cancer Surgery Triage Guidelines in COVID-19 Pandemic date: 2020-05-11 words: 3474.0 sentences: 176.0 pages: flesch: 44.0 cache: ./cache/cord-350679-69lv4wbz.txt txt: ./txt/cord-350679-69lv4wbz.txt summary: In the absence of actual data on cancer surgery care during this pandemic, clinical decisions should be based on careful consideration of disease-related and patient-related factors. As cancer surgeries involve significant healthcare resources in terms of infrastructure, intensive care unit beds, blood products and manpower, surgical oncologists face a dilemma regarding the triage of surgical patients during this period of uncertainty. A particular concern for a cancer surgeon is to weigh the risk of deferring cancer surgery versus the risk of COVID-19 exposure and infection to patients as well as health care providers. Smoking, one of the commonest risk factors in lung cancer, has not been independently shown to affect the mortality in SARS-CoV-2 patient; however, pre-existing chronic obstructive lung disease is associated with increased mortality [4] . Clinical management of lung cancer patients during the outbreak of 2019 novel coronavirus disease (COVID-19) abstract: COVID-19 pandemic has emerged as a global health emergency involving more than 200 countries so far. The number of affected population is on rising, so is the mortality. This crisis has overwhelmed the healthcare infrastructures in many affected countries. Due to overall rising cancer incidence and specific concerns, a cohort of cancer patients forms a distinct subset of the population in whom a correct and timely treatment has a huge impact on the outcome. During this period, oncology care is definitely affected owing to many factors like lockdowns, reduced beds and deferral of elective cases to halt the spread of the pandemic. Surgery remains the best line of defence in many solid organ tumours especially in early stage and is potentially curative. China, the source of this pandemic, has taken more than 3 months to enter the post transitional phase of this pandemic. Deferring cancer surgeries for this long period may have a direct impact on the long-term outcomes of cancer patients. Many surgical oncology associations across the globe have come up with triage guidelines for surgical care of cancer patients; however, these are based on expert opinion rather than actual data. Herein, we intend to review these guidelines with respect to the risk of disease progression in cancer patients. In the absence of actual data on cancer surgery care during this pandemic, clinical decisions should be based on careful consideration of disease-related and patient-related factors. While some of the cancer surgeries can be safely delayed for some time, how long we can delay surgeries safely cannot be answered/ explained by any means. Thorough evaluation and discussion by an expert and experienced multidisciplinary team appears to be the most effective way forward. url: https://www.ncbi.nlm.nih.gov/pubmed/32395064/ doi: 10.1007/s13193-020-01086-7 id: cord-254464-6l7fwylu author: Shingare, Ashay title: COVID‐19 in recent kidney transplant recipients date: 2020-06-08 words: 1712.0 sentences: 114.0 pages: flesch: 54.0 cache: ./cache/cord-254464-6l7fwylu.txt txt: ./txt/cord-254464-6l7fwylu.txt summary: Younger age, absence of other comorbidities and lower dose of anti‐thymocyte globulin (ATG) used as induction possibly contributed to good outcome in our recent LDKT recipients compared with earlier published cases of recent deceased donor kidney transplant recipients with COVID‐19. Sooner or later we would need to restart transplant programs, both LDKT & deceased donor kidney transplant (DDKT), as dust settles on the acute era to a post-COVID-19 new normal, where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will be a possibility. During the further follow-up over next 2 months, 2 of these 7 patients tested positive for SARS-CoV-2 by nasopharyngeal swab real-time reverse transcription polymerase chain reaction (rRT-PCR), 3 tested negative and 2 were not tested as they were asymptomatic. Due to intensive immunosuppression, recent transplant recipients (< 3 months post-transplant) are at increased risk of developing severe disease due to COVID-19. abstract: As coronavirus disease 2019 (COVID‐19) pandemic spread across the globe, transplant programs suffered a setback. We report the first experience of COVID‐19 infection within 1 month of living donor kidney transplant (LDKT). We describe 2 LDKT recipients who were detected positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection at day 19 and day 7 post‐transplant. They had minimal symptoms at diagnosis and did not develop any respiratory complications or allograft dysfunction. Immunosuppression was de‐escalated; however, nasopharyngeal swab real‐time reverse transcription polymerase chain reaction (rRT‐PCR) remained positive for SARS‐CoV‐2 for a prolonged time. Younger age, absence of other comorbidities and lower dose of anti‐thymocyte globulin (ATG) used as induction possibly contributed to good outcome in our recent LDKT recipients compared with earlier published cases of recent deceased donor kidney transplant recipients with COVID‐19. url: https://doi.org/10.1111/ajt.16120 doi: 10.1111/ajt.16120 id: cord-355788-6hteott0 author: Shirvani, Edris title: Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2 date: 2020-07-29 words: 4090.0 sentences: 220.0 pages: flesch: 50.0 cache: ./cache/cord-355788-6hteott0.txt txt: ./txt/cord-355788-6hteott0.txt summary: In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Currently, a number of DNA and RNA virus vector platforms are under evaluation for a SARS-CoV-2 vaccine, including attenuated vaccinia virus, replication-defective adenovirus, vesicular stomatitis virus, human parainfluenza viruses, and alphavirus replicons. Keeping these limitations in mind, we think Newcastle disease virus (NDV), as avian virus, has a number of characteristics that make it suitable for use as a vaccine vector for SARS-CoV-2. The effectiveness of NDV-vectored vaccines has already been evaluated against SARS-CoV in monkeys [8] , against MERS-CoV in camels [9] , and against avian infectious bronchitis virus (IBV) in chickens, a natural host challenge model [10] . Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 16 million infections and more than 600,000 deaths worldwide. There is an urgent need to develop a safe and effective vaccine against SARS-CoV-2. Currently, several strategies are being pursued to develop a safe and effective SARS-CoV-2 vaccine. However, each vaccine strategy has distinct advantages and disadvantages. Therefore, it is important to evaluate multiple vaccine platforms to select the most efficient vaccine platform for SARS-CoV-2. In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Here, we elaborate on the idea of considering NDV as a vaccine vector for SARS-CoV-2. url: https://doi.org/10.3390/pathogens9080619 doi: 10.3390/pathogens9080619 id: cord-254636-3lr008th author: Shishir, Tushar Ahmed title: In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date: 2020-08-16 words: 2974.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-254636-3lr008th.txt txt: ./txt/cord-254636-3lr008th.txt summary: We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. We conducted comparative analysis of publicly available genome sequences of SARS-CoV-2 from 27 countries to predict the origin of viruses in Bangladesh by studying a time-4 resolved phylogenetic relationship. Later, we analyzed the variants present in different isolates of Bangladesh to understand the pattern of mutations in relation to the ancestral Wuhan strain, find unique mutations, and possible effect of these mutations on the stability of encoded proteins, and selection pressure on genes. abstract: The COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh. url: https://doi.org/10.1101/2020.07.20.212563 doi: 10.1101/2020.07.20.212563 id: cord-350095-hsl1hfds author: Shiu, Stephen Y. W. title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? date: 2003-06-16 words: 1326.0 sentences: 66.0 pages: flesch: 40.0 cache: ./cache/cord-350095-hsl1hfds.txt txt: ./txt/cord-350095-hsl1hfds.txt summary: title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? Since the end of February of this year, global health is being threatened by the emergence of a new infectious disease, severe acute respiratory syndrome (SARS), caused by a novel coronavirus [1] [2] [3] . However, the most immediate concerns to the health authorities of Hong Kong and mainland China are to contain the spread of the disease and to reduce the mortality of those SARS patients who succumb to acute respiratory failure. While health officials are working hard to contain the spread of the disease in the hard-hit places such as China, Hong Kong [4] , Singapore and Canada [5] , clinicians are racing against time to find effective drugs to rescue SARS patients from serious illness and death. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/12823616/ doi: 10.1034/j.1600-079x.2003.00068.x id: cord-295302-vwrxentv author: Shivarov, Velizar title: Potential SARS-CoV-2 Preimmune IgM Epitopes date: 2020-04-30 words: 2397.0 sentences: 118.0 pages: flesch: 50.0 cache: ./cache/cord-295302-vwrxentv.txt txt: ./txt/cord-295302-vwrxentv.txt summary: While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. For the present study, the degrees of the vertices representing the natural SARS-CoV-2 epitopes, all of which belonged to the giant component, were used as the number of adjacent mimotopes parameter. A simple comparison for exact matches to peptides from the SARS-CoV-2 proteome yielded 3 heptapeptides-two in the open reading frame 1ab ( 3518 AQTGIAV 3524 and 5198 TKGPHEF 5204 ) and one in the spike protein ( 108 TTLDSKT 114 ). This loop is adjacent to the loop representing the epitope of the neutralizing antibody LCA60 on the SARS-CoV spike (8, 9) . Thus, it is quite possible that the SARS-CoV-2 spike epitope TTLDSKT is bound by B cells that will contribute to the induced immune response. abstract: While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. Joining the efforts to fast track SARS-CoV-2 vaccine development, here we describe briefly these potential epitopes in comparison to mimotopes representing peptides of SARS-CoV, HCoV 229E and OC43. url: https://www.ncbi.nlm.nih.gov/pubmed/32425955/ doi: 10.3389/fimmu.2020.00932 id: cord-276058-1mpp7sbt author: Shlomai, A. title: Global versus focused isolation during the SARS-CoV-2 pandemic-A cost-effectiveness analysis date: 2020-04-01 words: 3798.0 sentences: 232.0 pages: flesch: 56.0 cache: ./cache/cord-276058-1mpp7sbt.txt txt: ./txt/cord-276058-1mpp7sbt.txt summary: Objective: To compare the cost-effectiveness of global isolation of the whole population to focused isolation of individuals at high risk of being exposed, augmented by thorough PCR testing. We used R0=2.4 (range 1.4-3.9) (13), we assumed that the recovery time is 26 days, thus the transmission rate from infected (carrier) patients to susceptible population (β) was 0.09 (range 0.031 to 0.186)(13). In strategy 1, r1_HR_c represents the proportion of the population under relaxed isolation due to a high risk of contact with SARS-CoV-2 patients (0.7%). We next tested our model with a strategy of strict isolation of all infected individuals, relaxed isolation for two weeks of the high-risk group and a global quarantine of the susceptible population (strategy 1). https://doi.org/10.1101/2020.03.30.20047860 doi: medRxiv preprint each high-risk individual during the 14 days of isolation, and therefore ~10,000-15,000 tests will be needed daily for a country the size of Israel. abstract: Background: The novel coronavirus (SARS-CoV-2) pandemic is driving many countries to adopt global isolation measures in an attempt to slow-down its spread. These extreme measures are associated with extraordinary economic costs. Objective: To compare the cost-effectiveness of global isolation of the whole population to focused isolation of individuals at high risk of being exposed, augmented by thorough PCR testing. Design: We applied a modified Susceptible, Exposed, Infectious, Removed (SEIR) model to compare two different strategies in controlling the SARS-CoV-2 spread. Data sources and target population: We modeled the dynamics in Israel, a small country with ~ 9 million people. Time horizon: 200 days. Interventions: 1. Global isolation of the whole population (strategy 1) 2. Focused isolation of people at high risk of exposure with extensive PCR testing (strategy 2). Outcome measures: Number of deaths and the cost per one avoided death in strategy 1 vs 2. Results of Base-Case analysis: The number of expected deaths is 389 in strategy 1 versus 432 in strategy 2. The incremental cost-effectiveness ratio (ICER) in case of adhering to global isolation will be $ 102,383,282 to prevent one case of death. Results of sensitivity analysis: The ICER value is between $ 22.5 million to over $280 million per one avoided death. Conclusions: According to our model, global isolation will save ~43 more lives compared to a strategy of focused isolation and extensive screening. This benefit is implicated in tremendous costs that might result in overwhelming economic effects. Limitations: Compartment models do not necessarily fit to countries with heterogeneous populations. In addition, we rely on current published parameters that might not reliably reflect infection dynamics. url: https://doi.org/10.1101/2020.03.30.20047860 doi: 10.1101/2020.03.30.20047860 id: cord-355912-ioihqf0r author: Shomuradova, A. S. title: SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors date: 2020-05-25 words: 8632.0 sentences: 494.0 pages: flesch: 57.0 cache: ./cache/cord-355912-ioihqf0r.txt txt: ./txt/cord-355912-ioihqf0r.txt summary: Here we assayed both antibody and T-cell reactivity to SARS-CoV-2 antigens in COVID-19 convalescent patients and healthy donors sampled before and during the pandemic. 20.20107813 doi: medRxiv preprint Analysis of the humoral immune response to SARS-CoV-2 demonstrated that the IgG antibodies of the majority of COVID-19 -CPs were specific to one or more viral antigens. To describe the structure and clonality of SARS-CoV-2 directed T-cell immune response we performed analysis of T-cell receptor (TCR) repertoires of FACS-sorted IFNγ-secreting CD8+/CD4+ cells and MHC-tetramer-positive populations as well as the total fraction of PBMC by high throughput sequencing using the Illumina platform. Two patients (p1472 and p1473) had no detectable antibody levels in the serum to any of the tested SARS-CoV-2 antigens and no T-cellular response to any of the peptide pools, albeit they had T-cells reactive to the recombinant S-protein. abstract: Understanding the determinants of adaptive immune response to SARS-CoV-2 is critical for fighting the ongoing COVID-19 pandemic. Here we assayed both antibody and T-cell reactivity to SARS-CoV-2 antigens in COVID-19 convalescent patients and healthy donors sampled before and during the pandemic. Our results show that while anti-SARS-CoV-2 antibodies can distinguish convalescent patients from healthy donors, the magnitude of T-cell response was more pronounced in healthy donors sampled during COVID-19 pandemic than in donors sampled before the outbreak. This hints at the possibility that some individuals have encountered the virus but were protected by T-cell cross-reactivity observed. A public and diverse T-cell response was observed for two A*02-restricted SARS-CoV-2 epitopes, revealing a set of T-cell receptor motifs displaying germline-encoded features. Bulk CD4+ and CD8+ T-cell response to SARS-CoV-2 glycoprotein S is characterized by multiple groups of homologous T-cell receptor sequences some of which are shared across multiple donors, indicating the existence of immunodominant epitopes. Overall, our findings indicate that T cells form an efficient response to SARS-CoV-2 and alongside the antibodies can serve as a useful biomarker for surveying SARS-CoV-2 exposure and immunity. We hope that data, including the set of specific T-cell receptors identified in this study can serve as a basis for future developments of SARS-CoV-2 vaccinations and monitoring. url: https://doi.org/10.1101/2020.05.20.20107813 doi: 10.1101/2020.05.20.20107813 id: cord-255909-m94j1rh4 author: Shree, Priya title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study date: 2020-08-27 words: 5495.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-255909-m94j1rh4.txt txt: ./txt/cord-255909-m94j1rh4.txt summary: title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study Molecular docking study showed six probable inhibitors against SARS-CoV-2 M(pro) (Main protease), two from Withania somnifera (Ashwagandha) (Withanoside V [10.32 kcal/mol] and Somniferine [9.62 kcal/mol]), one from Tinospora cordifolia (Giloy) (Tinocordiside [8.10 kcal/mol]) and three from Ocimum sanctum (Tulsi) (Vicenin [8.97 kcal/mol], Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte [8.55 kcal/mol] and Ursolic acid [8.52 kcal/mol]). Active phytoconstituents of Ayurvedic medicinal plants Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) predicted to significantly hinder main protease (M(pro) or 3Cl(pro)) of SARS-CoV-2. Through molecular docking and molecular dynamic simulation study, Withanoside V, Somniferine, Tinocordiside, Vicenin, Ursolic acid and Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte were anticipated to impede the activity of SARS-CoV-2 M(pro). abstract: COVID-19 (Coronavirus disease 2019) is a transmissible disease initiated and propagated through a new virus strain SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) since 31(st) December 2019 in Wuhan city of China and the infection has outspread globally influencing millions of people. Here, an attempt was made to recognize natural phytochemicals from medicinal plants, in order to reutilize them against COVID-19 by the virtue of molecular docking and molecular dynamics (MD) simulation study. Molecular docking study showed six probable inhibitors against SARS-CoV-2 M(pro) (Main protease), two from Withania somnifera (Ashwagandha) (Withanoside V [10.32 kcal/mol] and Somniferine [9.62 kcal/mol]), one from Tinospora cordifolia (Giloy) (Tinocordiside [8.10 kcal/mol]) and three from Ocimum sanctum (Tulsi) (Vicenin [8.97 kcal/mol], Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte [8.55 kcal/mol] and Ursolic acid [8.52 kcal/mol]). ADMET profile prediction showed that the best docked phytochemicals from present work were safe and possesses drug-like properties. Further MD simulation study was performed to assess the constancy of docked complexes and found stable. Hence from present study it could be suggested that active phytochemicals from medicinal plants could potentially inhibit M(pro) HIGHLIGHTS: Holistic approach of Ayurvedic medicinal plants to avenge against COVID-19 pandemic. Active phytoconstituents of Ayurvedic medicinal plants Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) predicted to significantly hinder main protease (M(pro) or 3Cl(pro)) of SARS-CoV-2. Through molecular docking and molecular dynamic simulation study, Withanoside V, Somniferine, Tinocordiside, Vicenin, Ursolic acid and Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte were anticipated to impede the activity of SARS-CoV-2 M(pro). Drug-likeness and ADMET profile prediction of best docked compounds from present study were predicted to be safe, drug-like compounds with no toxicity. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1810778 doi: 10.1080/07391102.2020.1810778 id: cord-331611-pwj226j0 author: Shrimp, Jonathan H. title: An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date: 2020-06-23 words: 3894.0 sentences: 216.0 pages: flesch: 45.0 cache: ./cache/cord-331611-pwj226j0.txt txt: ./txt/cord-331611-pwj226j0.txt summary: We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan for pancreatitis due to their inhibition of trypsin-like proteases. The structurally related trypsin-like serine protease inhibitor nafamostat was shown to similarly inhibit spike protein-mediated cell fusion of MERS-CoV 7 . Herein we report the development of a TMPRSS2 fluorogenic biochemical assay and testing of clinical repurposing candidates for COVID19. To identify inhibitors of TMPRSS2 that may be used to validate its role in SARS-CoV-2 entry and potentially expedite to clinical trials, we developed a biochemical assay using active TMPRSS2 protease and a fluorogenic peptide substrate ( Figure 1B) . We developed a fluorogenic biochemical assay for measuring recombinant human TMPRSS2 activity for high-throughput screening that can be readily replicated and used to demonstrate that nafamostat is a more potent inhibitor than camostat and gabexate. abstract: SARS-CoV-2 is the viral pathogen causing the COVID19 global pandemic. Consequently, much research has gone into the development of pre-clinical assays for the discovery of new or repurposing of FDA-approved therapies. Preventing viral entry into a host cell would be an effective antiviral strategy. One mechanism for SARS-CoV-2 entry occurs when the spike protein on the surface of SARS-CoV-2 binds to an ACE2 receptor followed by cleavage at two cut sites (“priming”) that causes a conformational change allowing for viral and host membrane fusion. This fusion event is proceeded by release of viral RNA within the host cell. TMPRSS2 has an extracellular protease domain capable of cleaving the spike protein to initiate membrane fusion. Additionally, knock-out studies in mice have demonstrated reduced infection in the absence of TMPRSS2 with no detectable physiological impact; thus, TMPRSS2 is an attractive target for therapeutic development. A validated inhibitor of TMPRSS2 protease activity would be a valuable tool for studying the impact TMPRSS2 has in viral entry and potentially be an effective antiviral therapeutic. To enable inhibitor discovery and profiling of FDA-approved therapeutics, we describe an assay for the biochemical screening of recombinant TMPRSS2 suitable for high throughput application. We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan for pancreatitis due to their inhibition of trypsin-like proteases. Nafamostat and camostat are currently in clinical trials against COVID19. The rank order potency for the three inhibitors is: nafamostat (IC(50) = 0.27 nM), camostat (IC(50) = 6.2 nM) and gabexate (IC(50) = 130 nM). Further profiling of these three inhibitors against a panel of proteases provides insight into selectivity and potency. url: https://www.ncbi.nlm.nih.gov/pubmed/32596694/ doi: 10.1101/2020.06.23.167544 id: cord-317761-tkqmu1va author: Shukla, Ashutosh M title: Chloroquine and hydroxychloroquine in the context of COVID-19 date: 2020-04-28 words: 4111.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-317761-tkqmu1va.txt txt: ./txt/cord-317761-tkqmu1va.txt summary: This review aims to present the available in vitro and clinical data for the role of chloroquine/hydroxychloroquine in COVID-19 and attempts to put them into perspective, especially in relation to the different risks/benefits particular to each patient who may require treatment. 1 These agents have also shown a promising role in viral infections, and with the recent declaration on March 12th, 2020, by the World Health Organization that coronavirus disease (COVID) of 2019 (COVID-19) is a pandemic, these compounds have rapidly gained worldwide attention for their ability to control the causative virus, severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2). 1 These include inhibition of ligand-based toll-like receptor stimulation, inhibition of nuclear factor kappalight-chain-enhancer of activated B cells (NFkB) pathways in macrophages with resultant reduction in the generation of pro-inflammatory cytokines, reduced processing of the endogenous and exogenous ligands through lysosomes and endosomes with resultant reduction in the availability of processed antigens for presentation to the major ISSN: 1740-4398 REVIEW -Chloroquine, hydroxychloroquine, and COVID-19 drugsincontext.com histocompatibility complex-T cell receptor interactions, and downstream activation of cellular immunity. abstract: Chloroquine and closely related structural analogs, employed initially for the treatment of malaria, are now gaining worldwide attention due to the rapidly spreading pandemic caused by severe acute respiratory syndrome-coronavirus-2, named coronavirus disease (COVID) of 2019 (COVID-19). Although much of this attention has a mechanistic basis, the hard efficacy data for chloroquine/hydroxychloroquine in the management of the clinical syndrome of COVID-19 have been limited thus far. This review aims to present the available in vitro and clinical data for the role of chloroquine/hydroxychloroquine in COVID-19 and attempts to put them into perspective, especially in relation to the different risks/benefits particular to each patient who may require treatment. url: https://doi.org/10.7573/dic.2020-4-5 doi: 10.7573/dic.2020-4-5 id: cord-308342-ycdok8fc author: Shutler, J. title: Risk of SARS-CoV-2 infection from contaminated water systems date: 2020-06-20 words: 3147.0 sentences: 196.0 pages: flesch: 57.0 cache: ./cache/cord-308342-ycdok8fc.txt txt: ./txt/cord-308342-ycdok8fc.txt summary: Collectively this evidence suggests that SARS-CoV-2 virus can survive 45 within water and the viral loads within untreated sewage effluent are likely high in countries 46 of high infection rates, a portion of which is viable virus, and therefore water contaminated 47 We note that adenoviruses are 122 known to be particularly resilient, and therefore likely to represent an upper estimate, but 123 also that our selected range is consistent with the 10 -3 value used elsewhere for assessing 124 viral risk in water systems (eg 14 ), including one assessment for SARS CoV-2 transmission 125 risk to wastewater workers 18 . Collectively this means that if a drinking water source 156 was to become infected with SARS-CoV-2 the standard virus removal and disinfection 157 approaches of ultraviolet exposure and chlorination may not reduce the virus below 158 detectable limits. abstract: Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in China, airborne water droplets (aerosols) have been identified as the main transmission route, although other transmission routes are likely to exist. We quantify SARS-CoV-2 virus survivability within water and the risk of infection posed by faecal contaminated water within 39 countries. We identify that the virus can remain stable within water for up to 25 days, and country specific relative risk of infection posed by faecal contaminated water is related to the environment. Faecal contaminated rivers, waterways and water systems within countries with high infection rates can provide infectious doses >100 copies within 100 ml of water. The implications for freshwater systems, the coastal marine environment and virus resurgence are discussed. url: http://medrxiv.org/cgi/content/short/2020.06.17.20133504v1?rss=1 doi: 10.1101/2020.06.17.20133504 id: cord-017516-qbksb83c author: Si, Yain-Whar title: Hidden Cluster Detection for Infectious Disease Control and Quarantine Management date: 2009-09-30 words: 3358.0 sentences: 158.0 pages: flesch: 46.0 cache: ./cache/cord-017516-qbksb83c.txt txt: ./txt/cord-017516-qbksb83c.txt summary: Our prototype Infectious Disease Detection and Quarantine Management System (IDDQMS), which can identify and trace clusters of infection by mining patients'' history, is introduced in this paper. The SARS (Severe Acute Respiratory Syndrome) outbreak in 2003 and recent world-wide avian flu infections have contributed to the urgent need to search for efficient methods for prevention and control of highly infectious diseases. Given this background, this research aims to develop a decision support system which can be used to locate the source of an outbreak by mining clusters and communities from the patients'' past activities (testimonies) using techniques from infectious disease control, information visualization, and database management systems. IDDQMS (see Figure 1 ) consists of four modules; information extraction, data analysis, hidden cluster detection, and quarantine management. In this paper, we have described our novel prototype system on Infectious Disease Detection and Quarantine Management, which can be used to identify and trace clusters of infection by mining patients'' history. abstract: Infectious diseases that are caused by pathogenic microorganisms can spread fast and far, from one person to another, directly or indirectly. Prompt quarantining of the infected from the rest, coupled with contact tracing, has been an effective measure to encounter outbreaks. However, urban life and international travel make containment difficult. Furthermore, the length of incubation periods of some contagious diseases like SARS enable infected passengers to elude health screenings before first symptoms appear and thus to carry the disease further. Detecting and visualizing contact–tracing networks, and immediately identifying the routes of infection, are thus important. We apply information visualization and hidden cluster detection for finding cliques of potentially infected people during incubation. Preemptive control and early quarantine are hence possible by our method. Our prototype Infectious Disease Detection and Quarantine Management System (IDDQMS), which can identify and trace clusters of infection by mining patients’ history, is introduced in this paper. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122094/ doi: 10.1007/978-1-4419-0312-9_10 id: cord-278055-v2ed3tei author: Sia, Sin Fun title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 words: 5396.0 sentences: 292.0 pages: flesch: 56.0 cache: ./cache/cord-278055-v2ed3tei.txt txt: ./txt/cord-278055-v2ed3tei.txt summary: Previous study of SARS-CoV (Urbani strain) in 5-weeks-old golden Syrian hamsters showed robust viral replication with peak viral titers detected in the lungs on 2 dpi, followed by rapid viral clearance by 7 dpi, but without weight loss or evidence of disease in the inoculated animals 20 . Our results indicate that the golden Syrian hamster is a suitable experimental animal model for SARS-CoV-2, as there is apparent weight loss in the inoculated and naturally-infected hamsters and evidence of efficient viral replication in the nasal mucosa and lower respiratory epithelial cells. c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. e, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one donor on 6 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. abstract: SARS-CoV-2, a novel coronavirus with high nucleotide identity to SARS-CoV and SARS-related coronaviruses detected in horseshoe bats, has spread across the world and impacted global healthcare systems and economy1,2. A suitable small animal model is needed to support vaccine and therapy development. We report the pathogenesis and transmissibility of the SARS-CoV-2 in golden Syrian hamsters. Immunohistochemistry demonstrated viral antigens in nasal mucosa, bronchial epithelial cells, and in areas of lung consolidation on days 2 and 5 post-inoculation (dpi), followed by rapid viral clearance and pneumocyte hyperplasia on 7 dpi. Viral antigen was also found in the duodenum epithelial cells with viral RNA detected in feces. Notably, SARS-CoV-2 transmitted efficiently from inoculated hamsters to naïve hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was less efficient. Although viral RNA was continuously detected in the nasal washes of inoculated hamsters for 14 days, the communicable period was short and correlated with the detection of infectious virus but not viral RNA. Inoculated and naturally-infected hamsters showed apparent weight loss, and all animals recovered with the detection of neutralizing antibodies. Our results suggest that SARS-CoV-2 infection in golden Syrian hamsters resemble features found in humans with mild infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32408338/ doi: 10.1038/s41586-020-2342-5 id: cord-287477-aios0h8s author: Sicari, Daria title: Role of the early secretory pathway in SARS-CoV-2 infection date: 2020-07-28 words: 6483.0 sentences: 359.0 pages: flesch: 44.0 cache: ./cache/cord-287477-aios0h8s.txt txt: ./txt/cord-287477-aios0h8s.txt summary: CoV-2 infection starts when its spike (S) protein binds to angiotensin I-converting enzyme 2 (ACE2) receptors on the host cell membrane (Lake, 2020; Letko et al., 2020) . Thus, virion spread critically depends on recruiting the most efficient secretory machineries of host cells (Su et al., 2016; Proteins of the early secretory pathway bound by SARS-CoV-2 As the entire world asks for ways to stop CoV-2, many laboratories are investigating the virus''s Achilles heel(s). The role of glycosylation and protein quality control in SARS-CoV-2 infections Most CoVs bud at the ERGIC level ( Fig. 1) and are then transported along the exocytic pathway (Klumperman et al., 1994; Stertz et al., 2007) . We observed enrichment for five host-derived virus-interacting proteins (GOLGB1, PDE4DIP, TOR1A, HMOX1, and HYOU1) involved in different processes and related to quality control and ER-Golgi homeostasis maintenance. abstract: Similar to other RNA viruses, SARS-CoV-2 must (1) enter a target/host cell, (2) reprogram it to ensure its replication, (3) exit the host cell, and (4) repeat this cycle for exponential growth. During the exit step, the virus hijacks the sophisticated machineries that host cells employ to correctly fold, assemble, and transport proteins along the exocytic pathway. Therefore, secretory pathway–mediated assemblage and excretion of infective particles represent appealing targets to reduce the efficacy of virus biogenesis, if not to block it completely. Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications. url: https://doi.org/10.1083/jcb.202006005 doi: 10.1083/jcb.202006005 id: cord-355674-mhi85px5 author: Siddiqi, Hasan K. title: Increased prevalence of myocardial injury in patients with SARS-CoV-2 viremia. date: 2020-11-10 words: 1731.0 sentences: 134.0 pages: flesch: 48.0 cache: ./cache/cord-355674-mhi85px5.txt txt: ./txt/cord-355674-mhi85px5.txt summary: The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. Conclusions: Hospitalized COVID-19 patients with SARS-CoV-2 viremia have a significantly higher prevalence of detectable troponin and myocardial injury during their hospitalization, compared to non-viremic patients. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. abstract: BACKGROUND: Patients with COVID-19 have a high prevalence of detectable troponin and myocardial injury. In addition, a subset of COVID-19 patients have detectable SARS-CoV-2 viral loads. The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. METHODS: SARS-CoV-2 plasma viral load was measured in plasma samples drawn from patients hospitalized for COVID-19 at two academic medical centers. Baseline characteristics and clinically obtained high-sensitivity cardiac troponin T (hs-cTnT) values were abstracted from the medical record. The main outcome was detectable hs-cTnT (≥6ng/mL) and myocardial injury (hs-cTnT ≥14ng/mL; >99th percentile for assay). RESULTS: 70 hospitalized COVID-19 patients were included in this study, with 39% females and median age 58 +/- 17 years. 21 patients (30%) were found to have detectable SARS-CoV-2 viral load and were classified in the viremia group. Patients with viremia were significantly older than those without viremia. 100% of viremic patients had detectable troponin during hospitalization, compared to 59% of non-viremic patients (p=0.0003). Myocardial injury was seen in 76% of viremic patients and 38% of non-viremic patients (p=0.004). CONCLUSIONS: Hospitalized COVID-19 patients with SARS-CoV-2 viremia have a significantly higher prevalence of detectable troponin and myocardial injury during their hospitalization, compared to non-viremic patients. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. url: https://doi.org/10.1016/j.amjmed.2020.09.046 doi: 10.1016/j.amjmed.2020.09.046 id: cord-333144-gyuh2fvl author: Siddiqui, Arif Jamal title: Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 date: 2020-08-05 words: 7806.0 sentences: 436.0 pages: flesch: 50.0 cache: ./cache/cord-333144-gyuh2fvl.txt txt: ./txt/cord-333144-gyuh2fvl.txt summary: Therefore, this review focuses on the current use of various drugs as single agents (hydroxychloroquine, ivermectin, azithromycin, favipiravir, remdesivir, umifenovir, teicoplanin, nitazoxanide, doxycycline, and dexamethasone) or in combinations with immunomodulators additionally. While some drugs have shown therapeutic effect against COVID-19 infection such as hydroxychloroquine (Al-Kofahi et al., 2020; Choudhary & Sharma 2020; Liu et al., 2020; Sinha & Balayla 2020) , azithromycin, (Andreani et al., 2020a; Choudhary & Sharma 2020) ivermectin (Caly et al., 2020; Chaccour et al., 2020; Choudhary & Sharma 2020) and some other antivirals (Asai et al., 2020; Boopathi et al., 2020; Lian et al., 2020) . Consequently, this review will provide an insight and comprehensive view on different therapeutic approaches including combining of different known anti-parasitic drugs, as well as proposing novel suggestions of chemoprophylaxis drug therapy, which can be used in the current treatment and vaccine development strategies against COVID-19 disease. abstract: The spread of new coronavirus infection starting December 2019 as novel SARS-CoV-2, identified as the causing agent of COVID-19, has affected all over the world and been declared as pandemic. Approximately, more than 8,807,398 confirmed cases of COVID-19 infection and 464,483 deaths have been reported globally till the end of 21 June 2020. Until now, there is no specific drug therapy or vaccine available for the treatment of COVID-19. However, some potential antimalarial drugs like hydroxychloroquine and azithromycin, antifilarial drug ivermectin and antiviral drugs have been tested by many research groups worldwide for their possible effect against the COVID-19. Hydroxychloroquine and ivermectin have been identified to act by creating the acidic condition in cells and inhibiting the importin (IMPα/β1) mediated viral import. There is a possibility that some other antimalarial drugs/antibiotics in combination with immunomodulators may help in combatting this pandemic disease. Therefore, this review focuses on the current use of various drugs as single agents (hydroxychloroquine, ivermectin, azithromycin, favipiravir, remdesivir, umifenovir, teicoplanin, nitazoxanide, doxycycline, and dexamethasone) or in combinations with immunomodulators additionally. Furthermore, possible mode of action, efficacy and current stage of clinical trials of various drug combinations against COVID-19 disease has also been discussed in detail. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1802345 doi: 10.1080/07391102.2020.1802345 id: cord-315198-v4ay9kwg author: Siddiqui, Ruqaiyyah title: SARS-CoV-2: The Increasing Importance of Water Filtration against Highly Pathogenic Microbes date: 2020-08-13 words: 1412.0 sentences: 78.0 pages: flesch: 46.0 cache: ./cache/cord-315198-v4ay9kwg.txt txt: ./txt/cord-315198-v4ay9kwg.txt summary: Additionally, the frequent use of contaminated water for bathing, nasal irrigation, swimming, and ablution can be a risk factor in contracting infectious agents such as the brain-eating amoebae and possibly SARS-CoV-2. For example, the observation of primary amoebic meningoencephalitis due to brain-eating amoebae (i.e., Naegleria fowleri) is mostly unnoticed, especially in rural areas and disadvantaged communities, and is known to be associated with nasal irrigation for cleansing, ritual ablution, bathing, and swimming. Thus, the contamination of human waste as well as human wastewater into drinking water supplies highlights a major risk factor in contracting infectious agents such as brain-eating amoeba and possibly COVID-19, especially for developing countries. The use of simple tap water filters in households prior to ablution or nasal irrigation ( Figure 1E ,F) can be effective in eradicating microbial contaminants. abstract: [Image: see text] The presence of SARS-CoV-2 in human wastewater together with poor quality of public drinking water supplies in developing countries is of concern. Additionally, the frequent use of contaminated water for bathing, nasal irrigation, swimming, and ablution can be a risk factor in contracting infectious agents such as the brain-eating amoebae and possibly SARS-CoV-2. The use of appropriate tap water filters should be encouraged to remove pathogenic microbes, together with restrained nasal irrigation (not forcing water inside nostrils vigorously) during ritual ablution or bathing to avoid dangerous consequences for populations residing in developing countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32790273/ doi: 10.1021/acschemneuro.0c00468 id: cord-331087-kpze9xux author: Siddiqui, S. title: SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting date: 2020-09-03 words: 3245.0 sentences: 179.0 pages: flesch: 49.0 cache: ./cache/cord-331087-kpze9xux.txt txt: ./txt/cord-331087-kpze9xux.txt summary: To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW. We conducted a prospective longitudinal observational study to estimate the prevalence of anti SARS-CoV-2 antibodies among workers of a private hospital in Delhi with different levels of exposure to COVID-19 cases. The present study was conducted to estimate the seroprevalence of SARS-CoV-2 infection in Delhi and to observe how long the antibodies persist in the body. In a recently published brief report from Mumbai, India, conducted among the HCWs of three hospitals, highlighted that SARS-CoV-2 antibodies are not detected after 50 days, in RT-PCR positive individuals contrasting our observations 24 . abstract: Background: SARS-CoV-2 infection has caused 64,469 deaths in India, with 7, 81, 975 active cases till 30th August 2020, lifting it to 3rd rank globally. To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. Various studies have been conducted worldwide to assess the antibody stability. However, there is very limited data available from India. Healthcare workers (HCW) are the frontline workforce and more exposed to the COVID-19 infection (SARS-CoV-2) compared to the community. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW. Methods: Staff of a tertiary care hospital in Delhi and individuals visiting that hospital were recruited between April to August 2020. Venous blood sample, demographic, clinical, COVID-19 symptoms, and RT-PCR data was collected from all participants. Serological testing was performed using the electro-chemiluminescence based assay developed by Roche Diagnostics, in Cobas Elecsys 411. Seropositive participants were followed- upto 83 days to check for the presence of antibodies. Results: A total of 780 participants were included in this study, which comprised 448 HCW and 332 individuals from the general population. Among the HCW, seroprevalence rates increased from 2.3% in April to 50.6% in July. The cumulative prevalence was 16.5% in HCW and 23.5% (78/332) in the general population with a large number of asymptomatic individuals. Out of 74 seropositive HCWs, 51 were followed-up for the duration of this study. We observed that in all seropositive cases the antibodies were sustained even up to 83 days. Conclusion: The cumulative prevalence of seropositivity was lower in HCWs than the general population. There were a large number of asymptomatic cases and the antibodies developed persisted through the duration of the study. More such longitudinal serology studies are needed to better understand the antibody response kinetics. url: http://medrxiv.org/cgi/content/short/2020.09.02.20186486v1?rss=1 doi: 10.1101/2020.09.02.20186486 id: cord-312473-7i7efdp2 author: Sidhom, John-William title: Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date: 2020-06-20 words: 1181.0 sentences: 62.0 pages: flesch: 46.0 cache: ./cache/cord-312473-7i7efdp2.txt txt: ./txt/cord-312473-7i7efdp2.txt summary: We first examined the distribution of TCRs within the McPas database over the types of pathogens present in the database and cross-referenced the SARS-CoV-2 specific TCRs into the McPas database ( Figure 1A) , and we noted that there was a statistically significant enrichment (from 17.3% to 32.9%) of SARS-CoV-2 specific TCRs that had known specificity to the immunodominant M1 GILGFVFTL epitope We then examined the distribution of TCRs within the ImmuneCode database across the various open readings frames (orfs) and mapped the M1 specific TCRs within this database ( Figure 1B) . In conclusion, while these results are preliminary in a small cohort of individuals, we have identified a set of TCRs that is known to both recognize an immunodominant epitope derived from Influenza and SARS-CoV-2, suggesting that immune control of one infection may play a role in the control of the other. abstract: Adaptive Biotechnologies and Microsoft have recently partnered to release ImmuneCode, a database containing SARS-CoV-2 specific T-cell receptors derived through MIRA, a T-cell receptor (TCR) sequencing based sequencing approach to identify antigen-specific TCRs. Herein, we query the extent of cross reactivity between these derived SARS-CoV-2 specific TCRs and other known antigens present in McPas-TCR, a manually curated catalogue of pathology-associated TCRs. We reveal cross reactivity between SARS-CoV-2 specific TCRs and the immunodominant Influenza GILGFVFTL M1 epitope, suggesting the importance of further work in characterizing the implications of prior Influenza exposure or co-exposure to the pathology of SARS-CoV-2 illness. url: https://doi.org/10.1101/2020.06.20.160499 doi: 10.1101/2020.06.20.160499 id: cord-276234-2nkeq4ud author: Siedlecki, Jakob title: COVID-19: Ophthalmological Aspects of the SARS-CoV 2 Global Pandemic date: 2020-05-06 words: 3702.0 sentences: 227.0 pages: flesch: 46.0 cache: ./cache/cord-276234-2nkeq4ud.txt txt: ./txt/cord-276234-2nkeq4ud.txt summary: Indeed, ophthalmologists seem to rank among the medical specialties with the highest risk for COVID-19 infection, probably due to close patient contact during examination, e.g., at the slit lamp [4] , and possible conjunctival involvement during the course of the disease [5, 6] . In this paper, a systematic review of current COVID-19 literature relevant for ophthalmological practice is performed, with a special focus on modes of transmission, the prevention thereof, structural adjustments of clinical care required during the pandemic, and possible ocular manifestations of this novel disease. The novel coronavirus SARS-CoV 2, currently causing the COVID-19 pandemic, has severe implications for ophthalmologybe it because the eyes represent an important route of infection, most probably through lacrimal drainage into the nasal mucosa, or because of ocular manifestations, which, even if rather rare, can represent the first symptoms of this novel disease [29] . abstract: Purpose To perform a systematic analysis of articles on the ophthalmological implications of the global COVID-19 pandemic. Methods PubMed.gov was searched for relevant articles using the keywords “COVID-19”, “coronavirus”, and “SARS-CoV-2” in conjunction with “ophthalmology” and “eye”. Moreover, official recommendations of ophthalmological societies were systematically reviewed, with a focus on the American Academy of Ophthalmology (AAO) and the Royal College of Ophthalmologists (RCOphth). Results As of April 16, 2020, in total, 21 peer-reviewed articles on the ophthalmological aspects of COVID-19 were identified. Of these, 12 (57.1%) were from Asia, 6 (28.6%) from the United States of America, and 3 (14.3%) from Europe. There were 5 (23.8%) original studies, 10 (47.6%) letters, 3 (14.2%) case reports, and 3 (14.2%) reviews. These articles could be classified into the topics “Modes and prevention of (ocular) transmission”, “Ophthalmological manifestations of COVID-19”, “Clinical guidance concerning ophthalmological practice during the COVID-19 pandemic”, and “Practical recommendations for clinical infrastructure”. Practical recommendations could be extracted from official statements of the AAO and the RCOphth. Conclusion Within a short period, a growing body of articles has started to elucidate the ophthalmological implications of COVID-19. As the eye can represent a route of infection (actively via tears and passively via the nasoacrimal duct), ophthalmological care has to undergo substantial modifications during this pandemic. In the eye, COVID-19 can manifest as keratoconjunctivitis. url: https://doi.org/10.1055/a-1164-9381 doi: 10.1055/a-1164-9381 id: cord-276758-k2imddzr author: Siegel, Jane D. title: 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date: 2007-12-07 words: 46228.0 sentences: 2479.0 pages: flesch: 35.0 cache: ./cache/cord-276758-k2imddzr.txt txt: ./txt/cord-276758-k2imddzr.txt summary: Activities currently assigned to ICPs in response to emerging challenges include (1) surveillance and infection prevention at facilities other than acute care hospitals (eg, ambulatory clinics, day surgery centers, LTCFs, rehabilitation centers, home care); (2) oversight of employee health services related to infection prevention (eg, assessment of risk and administration of recommended treatment after exposure to infectious agents, tuberculosis screening, influenza vaccination, respiratory protection fit testing, and administration of other vaccines as indicated, such as smallpox vaccine in 2003); (3) preparedness planning for annual influenza outbreaks, pandemic influenza, SARS, and bioweapons attacks; (4) adherence monitoring for selected infection control practices; (5) oversight of risk assessment and implementation of prevention measures associated with construction and renovation; (6) prevention of transmission of MDROs; (7) evaluation of new medical products that could be associated with increased infection risk (eg, intravenous infusion materials); (8) communication with the public, facility staff, and state and local health departments concerning infection control-related issues; and (9) participation in local and multicenter research projects. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18068815/ doi: 10.1016/j.ajic.2007.10.007 id: cord-260257-phmd0u6d author: Siegler, Aaron J title: Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date: 2020-06-30 words: 3710.0 sentences: 237.0 pages: flesch: 54.0 cache: ./cache/cord-260257-phmd0u6d.txt txt: ./txt/cord-260257-phmd0u6d.txt summary: METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. 8, 9 Calls for home-based specimen collection or drive-through specimen collection models to address SARS-CoV-2 virus test scale-up have cogently argued that these approaches have the benefit of (1) avoiding burdening hospitals at a critical time, (2) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), (3) likely lowering costs, and (4) potentially achieving rapid scale-up due to laboratory centralization. We conducted an online survey to assess patient willingness to use the following SARS-CoV-2 testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. Across a diverse sample of 1,435 participants, one-third more persons reported that they would be willing to collect specimens at home for SARS-CoV-2 testing if they experienced illness, compared to clinic-based testing. abstract: BACKGROUND: SARS-CoV-2 virus testing for persons with COVID-19 symptoms, and contact tracing for those testing positive, will be critical to successful epidemic control. Willingness of persons experiencing symptoms to seek testing may determine the success of this strategy. METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. Instructions clarified that home-collected specimens would be mailed to a laboratory for testing. We presented similar willingness questions regarding testing during follow-up care. RESULTS: Of 1435 participants, comprising a broad range of sociodemographic groups, 92% were willing to test with a home saliva specimen, 88% with home swab, 71% with drive-through swab, and 60% with clinic collected swab. Moreover, 68% indicated they would be more likely to get tested if there was a home testing option. There were no significant differences in willingness items across sociodemographic variables or for those currently experiencing COVID-19 symptoms. Results were nearly identical for willingness to receive testing for follow-up COVID-19 care. CONCLUSIONS: We observed a hierarchy of willingness to test for SARS-CoV-2, ordered by the degree of contact required. Home specimen collection options could result in up to one-third more symptomatic persons seeking testing, facilitating contact tracing and optimal clinical care. Remote specimen collection options may ease supply chain challenges and decrease the likelihood of nosocomial transmission. As home specimen collection options receive regulatory approval, they should be scaled rapidly by health systems. url: https://doi.org/10.1093/ofid/ofaa269 doi: 10.1093/ofid/ofaa269 id: cord-277812-4cz2hziz author: Sieni, Elena title: Favourable outcome of coronavirus disease 2019 in a 1‐year‐old girl with acute myeloid leukaemia and severe treatment‐induced immunosuppression date: 2020-05-19 words: 1345.0 sentences: 75.0 pages: flesch: 48.0 cache: ./cache/cord-277812-4cz2hziz.txt txt: ./txt/cord-277812-4cz2hziz.txt summary: Since the beginning of coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults.1 Few cases of infection in children with cancer are described; also in these patients, except for one reported case,2 the disease was largely asymptomatic.3 Nevertheless, the management of COVID-19 in young patients with comorbidities, particularly cancer, remains a challenge for the clinician; further data are required to optimize the clinical approach to these cases. Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults. On day 18, routine laboratory testing further improved (WBC 2080 cells/µl with 48% neutrophils, Hb 112 g/l, PLTs correspondence 297 000/µl, negative CRP), and she was finally discharged, despite persistent positivity for SARS-CoV-2 at nasal swab, with oral prophylactic anti-microbial therapy. abstract: Since the beginning of coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults.1 Few cases of infection in children with cancer are described; also in these patients, except for one reported case,2 the disease was largely asymptomatic.3 Nevertheless, the management of COVID-19 in young patients with comorbidities, particularly cancer, remains a challenge for the clinician; further data are required to optimize the clinical approach to these cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32369615/ doi: 10.1111/bjh.16781 id: cord-308077-hbxpn5a1 author: Siepmann, Timo title: Variability of symptoms in neuralgic amyotrophy following infection with SARS‐CoV‐2 date: 2020-10-01 words: 493.0 sentences: 38.0 pages: flesch: 46.0 cache: ./cache/cord-308077-hbxpn5a1.txt txt: ./txt/cord-308077-hbxpn5a1.txt summary: The report of Cacciavillani and colleagues contributes to the discussion of the possibility of peripheral nerve involvement in coronavirus disease 2019 (COVID-1 9) and adds to our observation of neuralgic amyotrophy following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Interestingly, research prior to the COVID-19 pandemic showed that earlier coronaviruses such as hemagglutinating encephalomyelitis virus may first enter peripheral nerve terminals before traveling to the central nervous system (CNS) via synapse-connected routes. In fact, peripheral nerve damage might occur in almost 10% of patients hospitalized for SARS-CoV-2 infection. Whether peripheral nervous system complications following COVID-19 such as neuralgic amyotrophy result from direct neuroinvasion or from an auto-immune post-infectious mechanism needs to be elucidated. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients abstract: nan url: https://doi.org/10.1002/mus.27084 doi: 10.1002/mus.27084 id: cord-289144-d6fgs8qg author: Sieńko, Jerzy title: COVID-19: The Influence of ACE Genotype and ACE-I and ARBs on the Course of SARS-CoV-2 Infection in Elderly Patients date: 2020-07-21 words: 5129.0 sentences: 320.0 pages: flesch: 49.0 cache: ./cache/cord-289144-d6fgs8qg.txt txt: ./txt/cord-289144-d6fgs8qg.txt summary: Moreover, there is evidence that ACE genotype affects the outcomes of acute respiratory distress syndrome (ARDS) treatment, the most severe consequence of SARS-CoV-2 infection. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 63 This upregulation of the ACE2 receptor causes an increase in SARS-CoV-2 binding sites, which can lead to COVID-19 infection. Association of inpatient use of angiotensin converting enzyme inhibitors and angiotensin II receptor blockers with mortality among patients with hypertension hospitalized with COVID-19 abstract: Since the beginning of 2020, the whole world has been struggling with the pandemic of Coronavirus Disease 2019 (COVID-19) caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 infection depends on ACE2, TMPRSS2, and CD147, which are expressed on host cells. Several studies suggest that some single nucleotide polymorphisms (SNPs) of ACE2 might be a risk factor of COVID-19 infection. Genotypes affect ACE2 structure, its serum concentration, and levels of circulating angiotensin (1-7). Moreover, there is evidence that ACE genotype affects the outcomes of acute respiratory distress syndrome (ARDS) treatment, the most severe consequence of SARS-CoV-2 infection. COVID-19 morbidity, infection course, and mortality might depend on ACE D allele frequency. The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. There is no direct evidence yet for ACE-I or ARBs in the treatment of COVID-19. However, for those already taking these medications, both the European Society of Cardiology and the American College of Cardiology recommend continuing the treatment, because at present, there is no clear clinical or scientific evidence to justify the discontinuation of ACE-I or ARBs. Individualized treatment decisions should be based on the clinical condition and co-morbidities of each patient. url: https://www.ncbi.nlm.nih.gov/pubmed/32764907/ doi: 10.2147/cia.s261516 id: cord-296997-ba7f2mf3 author: Sikora, Mateusz title: Map of SARS-CoV-2 spike epitopes not shielded by glycans date: 2020-07-03 words: 5818.0 sentences: 371.0 pages: flesch: 55.0 cache: ./cache/cord-296997-ba7f2mf3.txt txt: ./txt/cord-296997-ba7f2mf3.txt summary: To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. Our simulation system contained four membrane-embedded SARS-CoV-2 S proteins assembled from resolved structures where available and models for the missing parts (SI Appendix, Fig. S5 ). In the ray analysis, we illuminated the protein model by diffuse light; in the Fab docking analysis, we performed rigid body Monte Carlo simulations of S and the SARS-CoV-2 antibody CR3022 Fab to determine the steric accessibility to an antibody Fab. To account for protein and glycan mobility, we performed both analyses individually for 4 × 193 snapshots taken at 10 ns time intervals from the 1.93 µs MD simulation with four glycosylated S proteins. abstract: The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping. url: https://doi.org/10.1101/2020.07.03.186825 doi: 10.1101/2020.07.03.186825 id: cord-354101-8a7tohcx author: Silva de Oliveira, Daniela title: Immune response in COVID-19: What do we currently know? date: 2020-09-09 words: 553.0 sentences: 53.0 pages: flesch: 53.0 cache: ./cache/cord-354101-8a7tohcx.txt txt: ./txt/cord-354101-8a7tohcx.txt summary: In 2002/2003 there was a pandemic denominate SARS (severe acute respiratory syndrome), caused by the SARS-CoV virus that belongs to the genera Betacoranavirus and the family Coronaviridae, generally responsible for influenza infections. In mid of 2019, a new disease by the coronavirus named by COVID-19 (SARS-CoV-2) emerged, both infections have flu symptoms, however they are infections that variable intensity, being medium to severe. The acute respiratory syndrome is a disease caused by the SARS-CoV-2 virus (COVID-37 19), where symptoms include difficulty breathing, high fever, and cough (WHO, 2020). Clinicopathologic, immunohistochemical, and ultrastructural findings of 673 a fatal case of Middle East respiratory syndrome coronavirus infection in the United 674 Immune responses in COVID-19 700 and potential vaccines: Lessons learned from SARS and MERS epidemic Middle East respiratory syndrome coronavirus Middle East respiratory syndrome coronavirus 766 (MERS-CoV) sheets/detail/middle-east-respiratory-syndrome-coronavirus-(mers-cov)> Access Pathological findings of COVID-19 associated with acute respiratory 786 distress syndrome. abstract: In 2002/2003 there was a pandemic denominate SARS (severe acute respiratory syndrome), caused by the SARS-CoV virus that belongs to the genera Betacoranavirus and the family Coronaviridae, generally responsible for influenza infections. In mid of 2019, a new disease by the coronavirus named by COVID-19 (SARS-CoV-2) emerged, both infections have flu symptoms, however they are infections that variable intensity, being medium to severe. In medium infections individuals have the virus and exhibit symptoms, however hospitalization is not necessary, in severe infections, individuals are hospitalized, have high pathology and in some cases progress to death. The virus is formed by simple positive RNA, enveloped, non-segmented, and presenting the largest genome of viruses constituting 32 Kb, consisting of envelope proteins, membrane, nucleocapsid and spike protein, which is essential in the interaction with the host cells. As for the origin of this virus, research has been intensified to determine this paradox and although the similarity with SARS-CoV, this virus did not has necessarily the same place of origin. As for the immune system, it is currently unknown how this new virus interacts. In this brief review, we demonstrate important considerations about the responses to this infection. url: https://api.elsevier.com/content/article/pii/S0882401020308500 doi: 10.1016/j.micpath.2020.104484 id: cord-260871-dtn5t8ka author: Silva, Marcus Tulius T. title: SARS-CoV-2: Should We Be Concerned about the Nervous System? date: 2020-07-17 words: 4110.0 sentences: 263.0 pages: flesch: 43.0 cache: ./cache/cord-260871-dtn5t8ka.txt txt: ./txt/cord-260871-dtn5t8ka.txt summary: Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system abstract: The COVID-19 pandemic has proved to be an enormous challenge to the health of the world population with tremendous consequences for the world economy. New knowledge about COVID-19 is being acquired continuously. Although the main manifestation of COVID-19 is SARS, dysfunction in other organs has been described in the last months. Neurological aspects of COVID-19 are still an underreported subject. However, a plethora of previous studies has shown that human CoVs might be neurotropic, neuroinvasive, and neurovirulent, highlighting the importance of this knowledge by physicians. Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Therefore, we should be watchful, searching for early evidence of neurological insults and promoting clinical protocols to investigate them. Our objectives are to review the potential neuropathogenesis of this new CoV and the neurological profile of COVID-19 patients described so far. url: https://doi.org/10.4269/ajtmh.20-0447 doi: 10.4269/ajtmh.20-0447 id: cord-252991-gvlyn6j7 author: Silva, V. O. title: PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL date: 2020-10-21 words: 4148.0 sentences: 277.0 pages: flesch: 57.0 cache: ./cache/cord-252991-gvlyn6j7.txt txt: ./txt/cord-252991-gvlyn6j7.txt summary: To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. . https://doi.org/10.1101 Professionals from laboratory areas were 25% while workers who had no direct contact with patients (administrative areas, security and cleaning staff) had a higher infection rate, especially in the areas of logistics (Faíco-Filho, et al., 2020) In our study, we chose to use a rapid test for preliminary results, despite the its reported performance (Sensitivity: 86, 43% [95% CI: 82, 51%~89, 58%] and Specificity: 99, 57% [95% CI: 97, 63%~99,92%]).. abstract: Background: Covid-19 Serology may document exposure and perhaps protection to the virus, and serological test may help understand epidemic dynamics. To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. Methods: This study was performed among professionals of Adolfo Lutz Institute in Sao Paulo, Brazil and some administrative areas of the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. Results: A total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA.. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity. Conclusions: We documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, with higher rates among outsourced workers and those with referring cohabitation with COVID-19 patients. COVID samples handling was not related to increased seropositivity. Some symptoms how strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings. url: http://medrxiv.org/cgi/content/short/2020.10.19.20213421v1?rss=1 doi: 10.1101/2020.10.19.20213421 id: cord-295765-c7o2ukm6 author: Silvas, Jesus A. title: Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date: 2020-07-20 words: 2234.0 sentences: 145.0 pages: flesch: 53.0 cache: ./cache/cord-295765-c7o2ukm6.txt txt: ./txt/cord-295765-c7o2ukm6.txt summary: VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. As SARS-CoV-2 replication 174 damages the cell monolayer, impedance measurements decrease over time, providing a detailed 175 assessment of infection kinetics. Based on the toxicity window of 1-20 221 h.p.t. determined with the VPS34 inhibitors, neither Triacsin C nor Orlistat induced early 222 cytotoxic effects, even at the highest concentrations of 50uM and 500uM, respectively ( Figure 223 3A and 3C). Here, we demonstrate that two VPS34 inhibitors, Orlistat, and Triacsin C each have clear effects 308 on SARS-CoV-2 replication and the morphology of viral replication centers. In contrast, the compounds did not exhibit any activity against 384 SARS-CoV-2 in Vero E6 cells whereas Triacsin C did. abstract: Therapeutics targeting replication of SARS coronavirus 2 (SARS-CoV-2) are urgently needed. Coronaviruses rely on host membranes for entry, establishment of replication centers and egress. Compounds targeting cellular membrane biology and lipid biosynthetic pathways have previously shown promise as antivirals and are actively being pursued as treatments for other conditions. Here, we tested small molecule inhibitors that target membrane dynamics or lipid metabolism. Included were inhibitors of the PI3 kinase VPS34, which functions in autophagy, endocytosis and other processes; Orlistat, an inhibitor of lipases and fatty acid synthetase, is approved by the FDA as a treatment for obesity; and Triacsin C which inhibits long chain fatty acyl-CoA synthetases. VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. Of these the VPS34 inhibitors exhibit the most potent activity. url: https://doi.org/10.1101/2020.07.18.210211 doi: 10.1101/2020.07.18.210211 id: cord-344070-17oac3bg author: Silverman, Justin D title: Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date: 2020-04-03 words: 5095.0 sentences: 284.0 pages: flesch: 59.0 cache: ./cache/cord-344070-17oac3bg.txt txt: ./txt/cord-344070-17oac3bg.txt summary: ILI correlates with known patterns of SARS-CoV-2 spread across states within the US, suggesting the surge is unlikely to be due to other endemic respiratory pathogens, yet is orders of magnitude larger than the number of confirmed COVID cases reported. We find that as the seasonal surge of endemic non-influenza respiratory pathogens declines, this excess ILI correlates more strongly with state-level patterns of newly confirmed COVID cases suggesting that 75 this surge is a reflection of ILI due to SARS-CoV-2 (Pearson ρ = 0.8 and p < 10 −10 for the last two weeks; Figure S1 ). However, if we assume the excess non-influenza ILI is almost entirely due to SARS-CoV-2, an assumption that becomes more valid as the virus becomes more prevalent, we can use the excess non-influenza ILI to understand the constraints and mutual dependence of exponential growth rates, the rate of subclinical infections, and the time 95 between the onset of infectiousness and a patient reporting as ILI Figure 3 . abstract: Detection of SARS-CoV-2 infections to date has relied on RT-PCR testing. However, a failure to identify early cases imported to a country, bottlenecks in RT-PCR testing, and the existence of infections which are asymptomatic, sub-clinical, or with an alternative presentation than the standard cough and fever have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how publicly available CDC influenza-like illness (ILI) outpatient surveillance data can be repurposed to estimate the detection rate of symptomatic SARS-CoV-2 infections. We find a surge of non-influenza ILI above the seasonal average and show that this surge is correlated with COVID case counts across states. By quantifying the number of excess ILI patients in March relative to previous years and comparing excess ILI to confirmed COVID case counts, we estimate the syndromic case detection rate of SARS-CoV-2 in the US to be less than 13%. If only 1/3 of patients infected with SARS-CoV-2 sought care, the ILI surge would correspond to more than 8.7 million new SARS-CoV-2 infections across the US during the three week period from March 8 to March 28. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to be doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID epidemic in the US in which rapid spread across the US are combined with a large population of infected patients with presumably mild-to-moderate clinical symptoms. We emphasize the importance of testing these findings with seroprevalence data, and discuss the broader potential to use syndromic time series for early detection and understanding of emerging infectious diseases. url: https://doi.org/10.1101/2020.04.01.20050542 doi: 10.1101/2020.04.01.20050542 id: cord-347079-1zbsbcdd author: Silverman, Justin D. title: Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date: 2020-06-22 words: 6234.0 sentences: 266.0 pages: flesch: 49.0 cache: ./cache/cord-347079-1zbsbcdd.txt txt: ./txt/cord-347079-1zbsbcdd.txt summary: To estimate the proportion and magnitude of the March 2020 US ILI surge attributable to SARS-CoV-2 infections, we made the following three assumptions: (1) that the patient population reported by sentinel providers is representative of their state each week; (2) that changes in care-seeking behavior of ILI patients is occurring at a similar rate as that of other non-ILI patients; and (3) that the total number of patients in the US who require medical care over the course of a year has not substantially changed since 2018. The goal of our study was to use publicly available data to estimate the number of patients seeking care for non-influenza ILI in excess of seasonal trends during the three weeks spanning March 8 to March 28, 2020 and then use this ILI surge to estimate COVID-19 incidence in March and parameterize epidemiological model growth rates and clinical rates. abstract: Detection of SARS-CoV-2 infections to date has relied heavily on RT-PCR testing. However, limited test availability, high false-negative rates, and the existence of asymptomatic or sub-clinical infections have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how influenza-like illness (ILI) outpatient surveillance data can be used to estimate the prevalence of SARS-CoV-2. We found a surge of non-influenza ILI above the seasonal average in March 2020 and showed that this surge correlated with COVID-19 case counts across states. If 1/3 of patients infected with SARS-CoV-2 in the US sought care, this ILI surge would have corresponded to more than 8.7 million new SARS-CoV-2 infections across the US during the three-week period from March 8 to March 28, 2020. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to have been doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID-19 epidemic in the US characterized by rapid spread across the US with over 80% infected patients remaining undetected. We emphasize the importance of testing these findings with seroprevalence data and discuss the broader potential to use syndromic surveillance for early detection and understanding of emerging infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32571980/ doi: 10.1126/scitranslmed.abc1126 id: cord-260365-neili1bd author: Silverstein, Jenna S. title: Acute Respiratory Decompensation Requiring Intubation in Pregnant Women with SARS-CoV-2 (COVID-19) date: 2020-06-04 words: 2205.0 sentences: 134.0 pages: flesch: 50.0 cache: ./cache/cord-260365-neili1bd.txt txt: ./txt/cord-260365-neili1bd.txt summary: Data from China suggest that pregnant women with COVID-19 have favorable maternal and neonatal outcomes, with rare cases of critical illness or respiratory compromise. However, we report two cases of pregnant women diagnosed with COVID-19 in the late preterm period admitted to tertiary care hospitals in New York City for respiratory indications. 8 We report here two pregnant women with no medical comorbidities, one under 18 years of age, diagnosed with COVID-19 at 34 and 36 weeks of gestation, respectively, who rapidly decompensated and underwent caesarean delivery under general anesthesia followed by prolonged mechanical ventilation. The risks and benefits of delivery in pregnant patients with critical respiratory illness from COVID-19 infections are not yet known, but prior experience with maternal acute respiratory distress syndrome (ARDS) and viral 2009/H1N1 influenza requiring mechanical ventilation in pregnancy reveals increased risk of fetal HR abnormalities, as well as fetal and neonatal mortality. abstract: There is a current paucity of information about the obstetric and perinatal outcomes of pregnant novel coronavirus disease 2019 (COVID-19) patients in North America. Data from China suggest that pregnant women with COVID-19 have favorable maternal and neonatal outcomes, with rare cases of critical illness or respiratory compromise. However, we report two cases of pregnant women diagnosed with COVID-19 in the late preterm period admitted to tertiary care hospitals in New York City for respiratory indications. After presenting with mild symptoms, both quickly developed worsening respiratory distress requiring intubation, and both delivered preterm via caesarean delivery. These cases highlight the potential for rapid respiratory decompensation in pregnant COVID-19 patients and the maternal-fetal considerations in managing these cases. url: https://doi.org/10.1055/s-0040-1712925 doi: 10.1055/s-0040-1712925 id: cord-326257-rcv8sh22 author: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 words: 3499.0 sentences: 172.0 pages: flesch: 47.0 cache: ./cache/cord-326257-rcv8sh22.txt txt: ./txt/cord-326257-rcv8sh22.txt summary: C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5''U/A and 3''U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). abstract: The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations. url: https://doi.org/10.1101/2020.05.01.072330 doi: 10.1101/2020.05.01.072330 id: cord-325481-uzch2hwd author: Simmons, Graham title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date: 2011-05-01 words: 7139.0 sentences: 315.0 pages: flesch: 49.0 cache: ./cache/cord-325481-uzch2hwd.txt txt: ./txt/cord-325481-uzch2hwd.txt summary: For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) . abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) poses a considerable threat to human health. Activation of the viral spike (S)-protein by host cell proteases is essential for viral infectivity. However, the cleavage sites in SARS-S and the protease(s) activating SARS-S are incompletely defined. We found that R667 was dispensable for SARS-S-driven virus-cell fusion and for SARS-S-activation by trypsin and cathepsin L in a virus-virus fusion assay. Mutation T760R, which optimizes the minimal furin consensus motif 758-RXXR-762, and furin overexpression augmented SARS-S-activity, but did not result in detectable SARS-S cleavage. Finally, SARS-S-driven cell-cell fusion was independent of cathepsin L, a protease essential for virus-cell fusion. Instead, a so far unknown leupeptin-sensitive host cell protease activated cellular SARS-S for fusion with target cells expressing high levels of ACE2. Thus, different host cell proteases activate SARS-S for virus-cell and cell-cell fusion and SARS-S cleavage at R667 and 758-RXXR-762 can be dispensable for SARS-S activation. url: https://www.sciencedirect.com/science/article/pii/S0042682211000924 doi: 10.1016/j.virol.2011.02.020 id: cord-339344-qd73h1ie author: Simon, David title: Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion date: 2020-07-24 words: 4094.0 sentences: 202.0 pages: flesch: 43.0 cache: ./cache/cord-339344-qd73h1ie.txt txt: ./txt/cord-339344-qd73h1ie.txt summary: To test whether differences in social exposure between the groups account for the low prevalence of SARS-CoV-2 IgG responses in IMID patients treated with cytokine inhibitors, we assessed exposure risk variables (contact with persons with a respiratory infection, presence at workplace outside home, travel to risk areas) of IMID patient groups and control groups. The low seroprevalence of SARS-CoV-2 in anti-cytokine treated IMIDs could have two principle explanations: While (i) the four groups were recruited in the same region, (ii) the HC control group having the highest prevalence for SARS-CoV-2 IgG was in direct contact with the IMID patients and (iii) all participants were exposed to similar detailed information regarding social behavior during the outbreak of the COVID-19 pandemic in Germany, IMID patients may have followed an even more stringent exposure prophylaxis than healthy individuals. abstract: Immune-mediated inflammatory diseases (IMIDs) of the joints, gut and skin are treated with inhibitors of inflammatory cytokines. These cytokines are involved in the pathogenesis of coronavirus disease 2019 (COVID-19). Investigating anti-SARS-CoV-2 antibody responses in IMIDs we observe a reduced incidence of SARS-CoV-2 seroconversion in IMID patients treated with cytokine inhibitors compared to patients receiving no such inhibitors and two healthy control populations, despite similar social exposure. Hence, cytokine inhibitors seem to at least partially protect from SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32709909/ doi: 10.1038/s41467-020-17703-6 id: cord-281285-5g1rw202 author: Simonis, Alexander title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 words: 9501.0 sentences: 504.0 pages: flesch: 46.0 cache: ./cache/cord-281285-5g1rw202.txt txt: ./txt/cord-281285-5g1rw202.txt summary: Based on its MOA, repurposed drugs with anti-SARS-CoV-2 activity can be divided into substances that prevent viral entry into host cells (1-2) and inhibit viral proteases (3) and inhibitors of viral replicase (4). The disappointing clinical results might be related to sub-therapeutic levels for inhibition of SARS-COV-2 because application of 400/100 mg of lopinavir/ritonavir twice daily was shown to yield median serum concentrations of 7.2 mg/l (11.5 µM) in patients with HIV (van der Lugt et al, 2009), which is significantly lower than the observed EC 50 in the in vitro studies. In this comparative review, we focus on repurposed drugs with antiviral effects against SARS-CoV-2 in cell-based assays as those substances offer great opportunities for a treatment early in the course of COVID-19 by inhibition of viral replication and might be even suitable for preventive strategies as shown for neuraminidase inhibitors in case of influenza (Jefferson et al, 2014) . abstract: The ongoing SARS‐CoV‐2 pandemic stresses the need for effective antiviral drugs that can quickly be applied in order to reduce morbidity, mortality, and ideally viral transmission. By repurposing of broadly active antiviral drugs and compounds that are known to inhibit viral replication of related viruses, several advances could be made in the development of treatment strategies against COVID‐19. The nucleoside analog remdesivir, which is known for its potent in vitro activity against Ebolavirus and other RNA viruses, was recently shown to reduce the time to recovery in patients with severe COVID‐19. It is to date the only approved antiviral for treating COVID‐19. Here, we provide a mechanism and evidence‐based comparative review of remdesivir and other repurposed drugs with proven in vitro activity against SARS‐CoV‐2. url: https://doi.org/10.15252/emmm.202013105 doi: 10.15252/emmm.202013105 id: cord-355589-3zdv9zim author: Simons, David title: The association of smoking status with SARS‐CoV‐2 infection, hospitalisation and mortality from COVID‐19: A living rapid evidence review with Bayesian meta‐analyses (version 7) date: 2020-10-02 words: 5236.0 sentences: 322.0 pages: flesch: 46.0 cache: ./cache/cord-355589-3zdv9zim.txt txt: ./txt/cord-355589-3zdv9zim.txt summary: However, early data from the COVID-19 pandemic have not provided clear evidence for a negative impact of current or former smoking on SARS-CoV-2 infection or COVID-19 disease outcomes, such as hospitalisation or mortality 11 . We aimed to produce a rapid synthesis of available evidence pertaining to the rates of infection, hospitalisation, disease severity and mortality from SARS-CoV-2/COVID-19 stratified by smoking status. Sixty studies reported disease severity in hospitalised patients stratified by smoking status (see Table 4 ). Current smokers were at reduced risk of testing positive for SARS-CoV-2 and former smokers were at increased risk of hospitalisation, disease severity and mortality compared with never smokers. Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: a Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: AIMS: To estimate the association of smoking status with rates of i) infection, ii) hospitalisation, iii) disease severity, and iv) mortality from SARS‐CoV‐2/COVID‐19 disease. DESIGN: Living rapid review of observational and experimental studies with random‐effects hierarchical Bayesian meta‐analyses. Published articles and pre‐prints were identified via MEDLINE and medRxiv. SETTING: Community or hospital. No restrictions on location. PARTICIPANTS: Adults who received a SARS‐CoV‐2 test or a COVID‐19 diagnosis. MEASUREMENTS: Outcomes were SARS‐CoV‐2 infection, hospitalisation, disease severity and mortality stratified by smoking status. Study quality was assessed (i.e. ‘good’, ‘fair’ and ‘poor’). FINDINGS: Version 7 (searches up to 25 August 2020) included 233 studies with 32 ‘good’ and ‘fair’ quality studies included in meta‐analyses. Fifty‐seven studies (24.5%) reported current, former and never smoking status. Recorded smoking prevalence among people with COVID‐19 was generally lower than national prevalence. Current compared with never smokers were at reduced risk of SARS‐CoV‐2 infection (RR=0.74, 95% Credible Interval (CrI) = 0.58‐0.93, τ = 0.41). Data for former smokers were inconclusive (RR=1.05, 95% CrI = 0.95‐1.17, τ = 0.17) but favoured there being no important association (21% probability of RR ≥1.1). Former compared with never smokers were at somewhat increased risk of hospitalisation (RR=1.20, CrI = 1.03‐1.44, τ = 0.17), greater disease severity (RR=1.52, CrI = 1.13‐2.07, τ = 0.29), and mortality (RR=1.39, 95% CrI = 1.09‐1.87, τ = 0.27). Data for current smokers were inconclusive (RR=1.06, CrI = 0.82‐1.35, τ = 0.27; RR=1.25, CrI = 0.85‐1.93, τ = 0.34; RR=1.22, 95% CrI = 0.78‐1.94, τ = 0.49 respectively) but favoured there being no important associations with hospitalisation and mortality (35% and 70% probability of RR ≥1.1, respectively) and a small but important association with disease severity (79% probability of RR ≥1.1). CONCLUSIONS: Compared with never smokers, current smokers appear to be at reduced risk of SARS‐CoV‐2 infection while former smokers appear to be at increased risk of hospitalisation, increased disease severity and mortality from COVID‐19. However, it is uncertain whether these associations are causal. url: https://doi.org/10.1111/add.15276 doi: 10.1111/add.15276 id: cord-297217-pe6mehjv author: Simpson, A. Hamish R. W. title: COVID-19: potential transmission through aerosols in surgical procedures and blood products date: 2020-07-23 words: 1324.0 sentences: 73.0 pages: flesch: 48.0 cache: ./cache/cord-297217-pe6mehjv.txt txt: ./txt/cord-297217-pe6mehjv.txt summary: A six-fold increased risk of transmission of viral diseases, such as severe acute respiratory syndrome (SARS) has been reported during anaesthetic procedures such as endotracheal intubation. 2 no definite transmission has been reported due to surgical procedures, however unlike other viral diseases such as SARS and middle east respiratory syndrome (meRS), CoVid-19 appears to be both severe and highly transmissible and therefore could pose a far higher risk to surgeons and operating room staff. 9, 11 in comparison to SARS, in which only very low plasma levels of virus have been reported, 12 the blood of CoVid-19 patients is likely to have a higher potential for aerosols produced during surgical procedures to carry the virus. there is increasing evidence that a significant number of potentially up to 50% or more of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) are asymptomatic. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32728423/ doi: 10.1302/2046-3758.94.bjr-2020-0130 id: cord-308080-1heu9vuv author: Simulundu, Edgar title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date: 2020-10-06 words: 1714.0 sentences: 99.0 pages: flesch: 52.0 cache: ./cache/cord-308080-1heu9vuv.txt txt: ./txt/cord-308080-1heu9vuv.txt summary: title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient''s household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient''s SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. abstract: Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. Whilst African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa.. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that lineage B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. url: https://doi.org/10.1016/j.ijid.2020.09.1480 doi: 10.1016/j.ijid.2020.09.1480 id: cord-293259-o51fnvuw author: Sinaei, Reza title: Why COVID-19 is less frequent and severe in children: a narrative review date: 2020-09-25 words: 7043.0 sentences: 359.0 pages: flesch: 44.0 cache: ./cache/cord-293259-o51fnvuw.txt txt: ./txt/cord-293259-o51fnvuw.txt summary: Thus far, only a small number of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection have involved children, so that they have accounted for only 1-5% of total patients [2, [6] [7] [8] [9] [10] . Severe SARS-CoV-2 infection is characterized by a hyperproinflammatory response or cytokine storm state that results to acute respiratory distress syndrome (ARDS) and multisystem inflammatory syndrome (MIS). The search strategy was constructed based on searching terms 2019 novel coronavirus, COVID-19, SARS-CoV-2 with using and/or, also the terms of child, pediatric, newborn, infant, adolescence, adult, age, age groups, severity, epidemiology, prevalence, difference, immune system, etiology, reasons in title, abstract, and key words. The first results stem from some considerations that children have a less vigorous immune response to the virus than adults because the cytokine storm is thought to be important in the pathogenesis of severe SARS-CoV-2 infections [28] . abstract: BACKGROUND: Despite the streaks of severity, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection is, in general, less frequent and severe in children than in adults. We searched for causal evidence of this mystery. DATA SOURCES: An extensive search strategy was designed to identify papers on coronavirus disease 2019 (COVID-19). We searched Ovid MEDLINE, PubMed, EMBASE databases, and Cochrane library and carried out a review on the causes of this dilemma. RESULTS: Our searches produced 81 relevant articles. The review showed that children accounted for a lower percentage of reported cases, and they also experienced less severe illness courses. Some potential explanations, including the tendency to engage the upper airway, the different expression in both receptors of angiotensin-converting enzyme and renin–angiotensin system, a less vigorous immune response, the lower levels of interleukin (IL)-6, IL-10, myeloperoxidase, and P-selectin and a higher intracellular adhesion molecule-1, a potential protective role of lymphocytes, and also lung infiltrations might have protective roles in the immune system–respiratory tract interactions. Finally, what have shed light on this under representation comes from two studies that revealed high-titer immunoglobulin-G antibodies against respiratory syncytial virus and mycoplasma pneumonia, may carry out cross-protection against SARS-CoV-2 infection, just like what suggested about the vaccines. CONCLUSIONS: These results require an in-depth look. Properties of the immune system including a less vigorous adaptive system beside a preliminary potent innate response and a trained immunity alongside a healthier respiratory system, and their interactions, might protect children against SARS-CoV-2 infection. However, further studies are needed to explore other possible causes of this enigma. url: https://doi.org/10.1007/s12519-020-00392-y doi: 10.1007/s12519-020-00392-y id: cord-331022-tek4u751 author: Sinderewicz, Emilia title: Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience? date: 2020-09-09 words: 8464.0 sentences: 427.0 pages: flesch: 46.0 cache: ./cache/cord-331022-tek4u751.txt txt: ./txt/cord-331022-tek4u751.txt summary: The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. The current study reviewed the role of interleukins (ILs) with tumor necrosis factors (TNFs), chemokines and interferons (IFNs) in the immune response to HCoVs. A comparison of the content of proinflammatory Th1 and Th2 cytokines in the serum of SARS patients with healthy controls documented a significantly greater concentration of TNF-α, IL-6, IL-8, IL-10, and IL-12 in the early stage of the SARS-CoV infection [32, 40] . abstract: The global range and high fatality rate of the newest human coronavirus (HCoV) pandemic has made SARS-CoV-2 the focus of the scientific world. Next-generation sequencing of the viral genome and a phylogenetic analysis have shown the high homology of SARS-CoV-2 to other HCoVs that have led to local epidemics in the past. The experience acquired in SARS and MERS epidemics may prove useful in understanding the SARS-CoV-2 pathomechanism and lead to effective treatment and potential vaccine development. This study summarizes the immune response to SARS-CoV, MERS-CoV, and SARS-CoV-2 and focuses on T cell response, humoral immunity, and complement system activation in different stages of HCoVs infections. The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. The role of interferons in the therapy of these infections is also discussed. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. url: https://doi.org/10.3390/pathogens9090739 doi: 10.3390/pathogens9090739 id: cord-290290-wyx9ib7s author: Sinegubova, Maria V. title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date: 2020-11-05 words: 5978.0 sentences: 304.0 pages: flesch: 49.0 cache: ./cache/cord-290290-wyx9ib7s.txt txt: ./txt/cord-290290-wyx9ib7s.txt summary: title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. Previously we have developed the plasmid vector p1.1, containing large fragments of non-coding DNA from the EEF1A1 gene of the Chinese hamster and fragment of the Epstein-Barr virus long terminal repeat concatemer [21] and employed it for unusually high-level expression of various proteins in CHO cells, including blood clotting factors VIII [22] , IX [23] , and heterodimeric follicle-stimulating hormone [24] . We have proposed that SARS-CoV-2 RBD, suitable for in vitro diagnostics use, may be expressed in large quantities by stably transfected CHO cells, bearing the EEF1A1-based plasmid. abstract: The spike (S) protein is one of the three proteins forming the coronaviruses’ viral envelope. The S protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has a spatial structure similar to the S proteins of other mammalian coronaviruses, except for a unique receptor-binding domain (RBD), which is a significant inducer of host immune response. Recombinant SARS-CoV-2 RBD is widely used as a highly specific minimal antigen for serological tests. Correct exposure of antigenic determinants has a significant impact on the accuracy of such tests – the antigen has to be correctly folded, contain no potentially antigenic non-vertebrate glycans, and, preferably, should have a glycosylation pattern similar to the native S protein. Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. RBDv1 contained a native viral signal peptide, RBDv2 – human tPA signal peptide. We transfected a CHO DG44 cell line, selected stably transfected cells, and performed a few rounds of methotrexate-driven amplification of the genetic cassette in the genome. For the RBDv2 variant, a high-yield clonal producer cell line was obtained. We developed a simple purification scheme that consistently yielded up to 30 mg of RBD protein per liter of the simple shake flask cell culture. Purified proteins were analyzed by polyacrylamide gel electrophoresis in reducing and non-reducing conditions and gel filtration; for RBDv2 protein, the monomeric form content exceeded 90% for several series. Deglycosylation with PNGase F and mass spectrometry confirmed the presence of N-glycosylation. The antigen produced by the described technique is suitable for serological tests and similar applications. url: https://doi.org/10.1101/2020.11.04.368092 doi: 10.1101/2020.11.04.368092 id: cord-350972-0n4dumgg author: Sing, Chor-Wing title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 words: 1789.0 sentences: 143.0 pages: flesch: 59.0 cache: ./cache/cord-350972-0n4dumgg.txt txt: ./txt/cord-350972-0n4dumgg.txt summary: title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. abstract: Use of high-dose glucocorticoids for coronavirus disease 2019 (COVID-19; caused by SARS-CoV-2) is controversial because of safety concerns. We examined long-term consequences in severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) survivors. Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. url: https://doi.org/10.1093/cid/ciaa992 doi: 10.1093/cid/ciaa992 id: cord-254207-uru7bkr4 author: Singanayagam, Anika title: Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020 date: 2020-08-13 words: 2290.0 sentences: 112.0 pages: flesch: 51.0 cache: ./cache/cord-254207-uru7bkr4.txt txt: ./txt/cord-254207-uru7bkr4.txt summary: Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Understanding the duration of infectiousness in persons who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to developing evidence-based public health policies on isolation, contact tracing and return to work. In the first 3 months of the COVID-19 pandemic in the United Kingdom (UK) (late January to early April 2020), we received 754 URT samples from 425 symptomatic cases that tested positive for SARS-CoV-2 by RT-PCR targeting the RNA-dependent RNA polymerase (RdRp) gene [1] and that had a clear record of the dates of symptom onset and sample collection. abstract: Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32794447/ doi: 10.2807/1560-7917.es.2020.25.32.2001483 id: cord-271871-8grkln6o author: Singer, J. S. title: Low Prevalence (0.13%) of COVID-19 Infection in Asymptomatic Pre-operative/Pre-procedure Patients at a Large Academic Medical Center Informs Approaches to Perioperative Care date: 2020-08-14 words: 2842.0 sentences: 158.0 pages: flesch: 43.0 cache: ./cache/cord-271871-8grkln6o.txt txt: ./txt/cord-271871-8grkln6o.txt summary: Abstract Background The COVID-19 pandemic has resulted in reduced performance of elective surgeries and procedures at medical centers across the U.S. Awareness of the prevalence of asymptomatic disease is critical for guiding safe approaches to operative/procedural services. Conclusions These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to inform perioperative protocols during the COVID-19 pandemic. These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic 117 population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to 118 inform perioperative protocols during the COVID-19 pandemic. As a large urban referral center, we adopted the CDC and ACS recommendations early in the pandemic, 327 suspending elective surgical and interventional procedures, and later relaxing those suspensions while 328 balancing local/regional COVID-19 epidemiology, data regarding our pre-operative/pre-procedure 329 testing results, and health system resources and priorities. abstract: Abstract Background The COVID-19 pandemic has resulted in reduced performance of elective surgeries and procedures at medical centers across the U.S. Awareness of the prevalence of asymptomatic disease is critical for guiding safe approaches to operative/procedural services. As COVID-19 PCR testing has been limited largely to symptomatic patients, healthcare workers (HCWs), or to those in communal care centers, data regarding asymptomatic viral disease carriage are limited. Study Design In this retrospective observational case series evaluating UCLA Health patients enrolled in pre-operative/pre-procedure protocol COVID-19 RT-PCR testing between 4/7/20 – 5/21/20, we determine the prevalence of COVID-19 infection in asymptomatic patients scheduled for surgeries and procedures. Results Primary outcomes include the prevalence of COVID-19 infection in this asymptomatic population. Secondary data analysis includes overall population testing results and population demographics. 18 of 4751 (0.38%) patients scheduled for upcoming surgeries and high risk procedures had abnormal (positive/inconclusive) COVID-19 RT-PCR testing results. 6/18 patients were confirmed asymptomatic. 4/18 had inconclusive results. 8/18 had positive results in the setting of recent symptoms or known COVID-19 infection. The prevalence of asymptomatic COVID-19 infection was 0.13%. More than 90% of patients had residential addresses within a 67 mile geographic radius of our medical center, the median age was 58, and there was equal male/female distribution. Conclusions These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to inform perioperative protocols during the COVID-19 pandemic. Testing protocols like ours may prove valuable for other health systems in their approaches to safe procedural practices during COVID-19. url: http://www.surgjournal.com/article/S0039606020305213/pdf doi: 10.1016/j.surg.2020.07.048 id: cord-289114-ifnk41oq author: Singh, Angaraj title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 words: 6894.0 sentences: 470.0 pages: flesch: 54.0 cache: ./cache/cord-289114-ifnk41oq.txt txt: ./txt/cord-289114-ifnk41oq.txt summary: The SARS-CoV-2 infected patients with the cardiovascular problem have a higher fatality rate as compared to general COVID-19 patients. The ACE-2 has been suggested as a medicine for the treatment of diabetes because it reduces inflammation .Therefore, the diabetes and COVID-19 patients treated with ACE-2 have higher risk of infection (Zachary, 2020) . Although, the specific drug for SARS-CoV-2 is not discovered till date, the medical observers are attempting with different antiviral drugs for the treatment of COVID-19 infection . All rights reserved patients demonstrated that the combination of a new antiviral drug remdesivir and chloroquine slowed down the growth of SARS-CoV-2 (Abdul et al., 2017) . Convalescent plasma therapy has been observed as a better alternative for the treatment of severely infected COVID-19 patients. A research report suggested that plasma treatment is more effective at the initial stage (within 14 days of symptoms) of COVID-19 infection. abstract: The entire world is suffering from a new type of viral disease, occurred by severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2). The present article briefly discussed the genome sequencing and interaction of host cells with SARS‐CoV‐2. The influence of pre‐existing diseases such as diabetes, heart disease and age of the patients on COVID‐19 infection is reviewed. The possible treatments of SARS‐CoV‐2 including antiviral drugs, Chinese traditional treatment and plasma therapy are elaborately discussed. The proper vaccine for COVID‐19 is not available till date. However, the trials of pre‐existing antiviral vaccines such as, chloroquine/hydroxychloroquine, remdesivir, ritonavir and lopinavir and their consequences are briefly presented. Further, the importance of new materials and devices for the detection and treatment of COVID‐19 has also been reviewed. The polymerase chain reaction (PCR)‐based, and non‐PCR based devices are used for the detection of COVID‐19 infection. The non‐PCR based devices provide rapid results as compared to PCR based devices. url: https://www.ncbi.nlm.nih.gov/pubmed/33173852/ doi: 10.1002/mds3.10140 id: cord-254452-gqqdx2r5 author: Singh, Awadhesh Kumar title: Remdesivir in COVID-19: A critical review of pharmacology, pre-clinical and clinical studies date: 2020-05-12 words: 3162.0 sentences: 163.0 pages: flesch: 47.0 cache: ./cache/cord-254452-gqqdx2r5.txt txt: ./txt/cord-254452-gqqdx2r5.txt summary: METHODS: We systematically searched the PubMed, ClinicalTrial.Org and MedRxiv database up till May 5, 2020 using specific key words such as "Remdesivir" or ''GS-5734″ AND "COVID-19" or "SARS-CoV-2" and retrieved all the article published in English language, that have reported the pharmacology and the clinical outcomes of remdesivir in patients with COVID-19. A preliminary report (April 29, 2020) from an interim analysis of an ongoing double-blind randomized controlled trial (RCT) recently suggested that remdesivir had a 31% faster time to recovery, compared to the placebo (p<0.001), in patients with COVID-19 [15] . In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) No evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for COVID-19 infection with oxygen requirement: results of a study using routinely collected data to emulate a target trial abstract: BACKGROUND & AIMS: Remdesivir is a broad spectrum anti-viral drug that has shown to inhibit SARS-CoV-2, in vitro and in vivo. In absence of any effective treatment for SARS-CoV-2 infection (COVID-19), remdesivir has been tried for a compassionate use in severe COVID-19. Newer randomized controlled studies that have recently become available, showed a mixed result. We aimed to systematically search the literature to understand the pharmacology and clinical effects of remdesivir in patients with COVID-19. METHODS: We systematically searched the PubMed, ClinicalTrial.Org and MedRxiv database up till May 5, 2020 using specific key words such as “Remdesivir” or ‘GS-5734″ AND “COVID-19” or “SARS-CoV-2” and retrieved all the article published in English language, that have reported the pharmacology and the clinical outcomes of remdesivir in patients with COVID-19. RESULTS: Initial compassionate use of remdesivir has shown a fairly good result, but difficult to quantify, in the absence of control arm. While the very first double-blind, placebo-controlled, randomized trial conducted in Wuhan, did not find any significant benefit compared to the control, the preliminary result of another similar multi-country trial has shown a significant faster time to recovery but without any difference in mortality. CONCLUSIONS: Remdesivir has shown a mixed result in patients with COVID-19 with an acceptable side effect. However, jury is still out while awaiting the results from the forthcoming trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32428865/ doi: 10.1016/j.dsx.2020.05.018 id: cord-286638-bqxyb61p author: Singh, Awadhesh Kumar title: Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations date: 2020-04-09 words: 4824.0 sentences: 281.0 pages: flesch: 46.0 cache: ./cache/cord-286638-bqxyb61p.txt txt: ./txt/cord-286638-bqxyb61p.txt summary: The disease burden of coronavirus infectious disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) has been increasing continuously with more than a million confirmed patients and more than 45 thousand deaths globally [1] . Emerging data suggests that COVID-19 is common in patients with diabetes, hypertension, and cardiovascular disease (CVD), although the prevalence rate varied in different studies as well in country-wise data. Evolving data also suggest that patients of COVID-19 with diabetes are more often associated with severe or critical disease varying from 14 to 32% in different studies [15e18, 20, 22, 24] . Though there is limited data about the association of blood glucose levels with disease course in COVID-19 at present, data from other infections like SARS and influenza H1N1 has shown that patients with poor glycemic control have increased risk of complications and death [60, 61] . abstract: BACKGROUND AND AIMS: High prevalence of diabetes makes it an important comorbidity in patients with COVID-19. We sought to review and analyze the data regarding the association between diabetes and COVID-19, pathophysiology of the disease in diabetes and management of patients with diabetes who develop COVID-19 infection. METHODS: PubMed database and Google Scholar were searched using the key terms ‘COVID-19’, ‘SARS-CoV-2’, ‘diabetes’, ‘antidiabetic therapy’ up to April 2, 2020. Full texts of the retrieved articles were accessed. RESULTS: There is evidence of increased incidence and severity of COVID-19 in patients with diabetes. COVID-19 could have effect on the pathophysiology of diabetes. Blood glucose control is important not only for patients who are infected with COVID-19, but also for those without the disease. Innovations like telemedicine are useful to treat patients with diabetes in today’s times. url: https://doi.org/10.1016/j.dsx.2020.04.004 doi: 10.1016/j.dsx.2020.04.004 id: cord-295973-41jqgsv0 author: Singh, Awadhesh Kumar title: Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries date: 2020-03-26 words: 3461.0 sentences: 163.0 pages: flesch: 50.0 cache: ./cache/cord-295973-41jqgsv0.txt txt: ./txt/cord-295973-41jqgsv0.txt summary: In this review article, we have systematically searched the medical data base until and collated all the available evidences that have emerged so far on the efficacy of chloroquine and hydroxychloroquine, in the treatment of patients with COVID19 , with or without diabetes and present a perspective on both these compounds. A Chinese study involving more than 100 patients of COVID-19 found chloroquine superior to the control group in reducing symptom duration, exacerbation of pneumonia including radiological improvement and promoting virus-negative seroconversion without any severe side effects [18] . The expert consensus from the Department of Science and Technology and Health Commission of Guangdong province published on 20th February (based on in vitro evidence and still unpublished clinical experience) chloroquine phosphate tablet at a dose of 500 mg twice per day for 10 days for patients diagnosed as mild, moderate and severe cases of SARS-CoV-2 pneumonia in the absence of contraindication to the drug [21] . abstract: BACKGROUND AND AIMS: No drugs are currently approved for Coronavirus Disease-2019 (COVID-19), although some have been tried. In view of recent studies and discussion on chloroquine and hydroxychloroquine (HCQ), we aimed to review existing literature and relevant websites regarding these drugs and COVID-19, adverse effects related to drugs, and related guidelines. AIMS AND METHODS: We systematically searched the PubMed database up till March 21, 2020 and retrieved all the articles published on chloroquine and HCQ and COVID-19. RESULTS: Two small human studies have been conducted with both these drugs in COVID-19, and have shown significant improvement in some parameters in patients with COVID-19. CONCLUSION: Considering minimal risk upon use, a long experience of use in other diseases, cost-effectiveness and easy availability across India, we propose that both these drugs are worthy of fast track clinical trial for treatment, and may be carefully considered for clinical use as experimental drugs. Since HCQ has been approved for treatment of diabetes in India, it should be further researched in diabetes and COVID-19, a subgroup where significant mortality has been shown. url: https://www.ncbi.nlm.nih.gov/pubmed/32247211/ doi: 10.1016/j.dsx.2020.03.011 id: cord-338417-7kw9lws0 author: Singh, Awadhesh Kumar title: Comorbidities in COVID-19: Outcomes in hypertensive cohort and controversies with renin angiotensin system blockers date: 2020-04-09 words: 3212.0 sentences: 172.0 pages: flesch: 48.0 cache: ./cache/cord-338417-7kw9lws0.txt txt: ./txt/cord-338417-7kw9lws0.txt summary: RESULTS: From the pooled data of all ten available Chinese studies (n = 2209) that have reported the characteristics of comorbidities in patients with COVID-19, hypertension was present in nearly 21%, followed by diabetes in nearly 11%, and established cardiovascular disease (CVD) in approximately 7% of patients. Emerging data suggests that older COVID-19 patients with other comorbid conditions such as diabetes, hypertension, cardiac and pulmonary disease are in particular more susceptible, compared to general populations and have higher mortality. We have systematically searched the PubMed medical database up till March 27, 2020 using MeSH key words that include Covid-19, coronavirus, hypertension, diabetes, cardiovascular disease, angiotensin receptor blockers, angiotensin converting enzyme inhibitors. Interestingly, in the pooled data from the ten Chinese studies (n ¼ 2209) that have reported the characteristics of comorbidities in patients with COVID-19; associations of hypertension, diabetes and presence of established cardiovascular disease (CVD) are larger, varying from 15 to 30% (average 21%), 5e20% (average 11%) and 2e40% (average 7%) respectively (Table 1) . abstract: BACKGROUND AND AIMS: COVID-19 is already a pandemic. Emerging data suggest an increased association and a heightened mortality in patients of COVID-19 with comorbidities. We aimed to evaluate the outcome in hypertensive patients with COVID-19 and its relation to the use of renin-angiotensin system blockers (RASB). METHODS: We have systematically searched the medical database up to March 27, 2020 and retrieved all the published articles in English language related to our topic using MeSH key words. RESULTS: From the pooled data of all ten available Chinese studies (n = 2209) that have reported the characteristics of comorbidities in patients with COVID-19, hypertension was present in nearly 21%, followed by diabetes in nearly 11%, and established cardiovascular disease (CVD) in approximately 7% of patients. Although the emerging data hints to an increase in mortality in COVID-19 patients with known hypertension, diabetes and CVD, it should be noted that it was not adjusted for multiple confounding factors. Harm or benefit in COVID-19 patients receiving RASB has not been typically assessed in these studies yet, although mechanistically and plausibly both, benefit and harm is possible with these agents, given that COVID-19 expresses to tissues through the receptor of angiotensin converting enzyme-2. CONCLUSION: Special attention is definitely required in patients with COVID-19 with associated comorbidities including hypertension, diabetes and established CVD. Although the role of RASB has a mechanistic equipoise, patients with COVID-19 should not stop these drugs at this point of time, as recommended by various world organizations and without the advice of health care provider. url: https://doi.org/10.1016/j.dsx.2020.03.016 doi: 10.1016/j.dsx.2020.03.016 id: cord-319241-div9rzax author: Singh, Bhuchitra title: Severe Acute Respiratory Syndrome‐Corona Virus‐2 (SARS‐CoV‐2) and its Effect on Gametogenesis and Early Pregnancy date: 2020-09-23 words: 4386.0 sentences: 305.0 pages: flesch: 50.0 cache: ./cache/cord-319241-div9rzax.txt txt: ./txt/cord-319241-div9rzax.txt summary: There is also evidence of significant placental pathology in SARS‐CoV‐2 infection, but it is unclear what effects there may be for early pregnancy, though available data suggest less severe effects compared to other respiratory virus outbreaks. We searched for articles that contained information related to SARS-CoV-2 and reproductive tissues (ovaries, testes), gametes, placentation, and early pregnancy in humans. Our search phrases included: "severe acute respiratory syndrome coronavirus 2", "2019 ncov", "sarscov 2", "SARS-Cov-2", "pregnancy", "gravidity", "abortion", "germ cells", "oocytes", "gametes", "embryonic structures", "embryo", "fertility", "testes", "miscarriage"(See Appendix 1 for completed list of databases search strategy and Figure 1 for PRISMA table). Specifically, 10 women with severe COVID-19 were tested or SARS-CoV-2 in vaginal fluid, with all samples negative for virus [48] . Another study performed during the 2002-2003 SARS pandemic showed that 4 of 7 (57%) pregnant women infected with SARS-CoV had a spontaneous miscarriage in the first trimester of pregnancy [55] , though notably no viral inclusion bodies or particles were detected in the products of conception. abstract: SARS‐CoV‐2 infection and pregnancy has been the topic of hundreds of publications over the last several months, however, few studies have focused on the implications of infection in early pregnancy and reproductive tissues. Here we analyzed available evidence pertaining to SARS‐CoV‐2 infection, early pregnancy, and reproductive tissues. We searched PubMed and Embase databases in accordance with guidelines of Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) for publications from inception to June 4, 2020. Four reviewers screened titles and abstracts, and obtained full text articles for analysis. 62 studies were included in the review. Biological plausibility for infection with SARS‐CoV‐2 exists in testis, ovaries, and placenta as they express ACE2 receptor activity. In males, SARS‐CoV‐2 infection could lead to functional abnormalities leading to spermatogenic failure and male infertility. In females, an alteration of the ACE2 cascade via SARS‐CoV‐2 infection could lead to impairment in important follicular and luteal processes. There is also evidence of significant placental pathology in SARS‐CoV‐2 infection, but it is unclear what effects there may be for early pregnancy, though available data suggest less severe effects compared to other respiratory virus outbreaks. Further investigation is needed regarding SARS‐CoV‐2 in reproductive function and early pregnancy. url: https://www.ncbi.nlm.nih.gov/pubmed/32969123/ doi: 10.1111/aji.13351 id: cord-263245-2qub96mz author: Singh, D. title: Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date: 2020-09-29 words: 4779.0 sentences: 234.0 pages: flesch: 41.0 cache: ./cache/cord-263245-2qub96mz.txt txt: ./txt/cord-263245-2qub96mz.txt summary: This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . abstract: The pandemic due to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has emerged as a serious global public health issue. Since the start of the outbreak, the importance of hand-hygiene and respiratory protection to prevent the spread of the virus has been the prime focus for infection control. Health regulatory organisations have produced guidelines for the formulation of hand sanitisers to the manufacturing industries. This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. url: https://doi.org/10.1017/s0950268820002319 doi: 10.1017/s0950268820002319 id: cord-256872-jekx1czw author: Singh, Manvendra title: A single-cell RNA expression map of human coronavirus entry factors date: 2020-09-03 words: 4554.0 sentences: 6938.0 pages: flesch: 74.0 cache: ./cache/cord-256872-jekx1czw.txt txt: ./txt/cord-256872-jekx1czw.txt summary: To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell transcriptomics across various healthy human tissues. Evidence of impaired gonadal function in male COVID-19 patients was also recently presented The high level of TMPRSS2, ACE2 and other coronavirus receptors such as ANPEP in the trophectoderm, which gives rise to the placenta, combined with low levels of IFITMs in this lineage (Figure 2A and Figure S1A ) raises the possibility that the developing placenta may be vulnerable to SARS-CoV-2 infection. Our study, along with several others (Table S1 ) have tapped into vast amount of publicly available scRNA-seq data to profile the expression of host factors thought to be important for entry of SARS-CoV-2 in healthy tissues. abstract: To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell transcriptomics across various healthy human tissues. SCARFs include cellular factors both facilitating and restricting viral entry. Intestinal goblet cells, enterocytes and kidney proximal tubule cells appear highly permissive to SARS-CoV-2, consistent with clinical data. Our analysis also predicts non-canonical entry paths for lung and brain infections. Spermatogonial cells and prostate endocrine cells also appear to be permissive to SARS-CoV-2 infection, suggesting male-specific vulnerabilities. Both pro- and anti-viral factors are highly expressed within the nasal epithelium, with potential age-dependent variation, predicting an important battleground for coronavirus infection. Our analysis also suggests that early embryonic and placental development are at moderate risk of infection. Lastly, SCARF expression appears broadly conserved across a subset of primate organs examined. Our study establishes a resource for investigations of coronavirus biology and pathology. url: https://www.sciencedirect.com/science/article/pii/S2211124720311645?v=s5 doi: 10.1016/j.celrep.2020.108175 id: cord-285636-cs26uuwx author: Singh, N. K. title: Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer date: 2020-09-25 words: 7858.0 sentences: 486.0 pages: flesch: 53.0 cache: ./cache/cord-285636-cs26uuwx.txt txt: ./txt/cord-285636-cs26uuwx.txt summary: In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads as benchmarked by RT-qPCR within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). The major hurdle in repurposing a glucometer for direct detection of SARS-CoV-2 is that the target biomarkers (e.g., protein N and S) are present at low concentrations in biological samples The average CoVID-19 viral load in nasal/throat, sputum, and saliva samples is 3×10 6 , 7.50×10 5 , and 3.5×10 7 copies/ml 24, 25 , respectively, necessitating signal amplification to generate product (i.e. glucose) in quantities similar to physiological levels in human blood (i.e. 10-600 mg/dL or 0.6-33 mM) 21, 26 . To transduce antigen binding SARS-CoV-2 N or S protein specific biotinylated aptamer is conjugated to streptavidin coated magnetic bead (MB) and pre-hybridized with a complementary antisense oligonucleotide strand that is covalently attached to an invertase enzyme. abstract: Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based screening efforts required to contain the COVID-19 pandemic in the absence of effective antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer. The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect to smartphones providing an opportunity to integrate with contract tracing apps, medical providers, and electronic medical records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as benchmarked by RT-qPCR - within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach can provide an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale. url: http://medrxiv.org/cgi/content/short/2020.09.24.20200394v1?rss=1 doi: 10.1101/2020.09.24.20200394 id: cord-334540-ggnkdnky author: Singh, Pankaj title: Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie date: 2020-07-01 words: 1593.0 sentences: 203.0 pages: flesch: 45.0 cache: ./cache/cord-334540-ggnkdnky.txt txt: ./txt/cord-334540-ggnkdnky.txt summary: title: Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie Bei infizierten Patienten lässt sich regelhaft (auch schon in der Anfangsphase der Erkrankung) eine hohe Viruslast in den oberen und unteren Atemwegen nachweisen. Im Eingangsbereich zum Haupthaus des Klinikums werden alle Patienten nach dem MTS "triagiert" [4, 5] und bezüglich einer möglichen COVID-Erkrankung befragt. Ergibt sich der Verdacht auf eine CO-VID-19-Erkrankung, wird der Patient abgestrichen und bei möglicher ambulanter Behandlung mit Medikation nach Hause geschickt. B. einer pp-Vitrektomie bei Amotio retinae, die in Intubationsnarkose stattfinden sollen, erfolgt unmittelbar vor stationärer Aufnahme des Patienten ein Rachen-/Nasenabstrich zum Nachweis/Ausschluss von SARS-CoV-2. Auch im Op.-Bereich sind die Patienten so terminiert worden, dass zwischen den Op.s ein ausreichender Zeitabstand eingehalten werden kann, entsteht und der genügend Zeit für die Einhaltung und Umsetzung aller Hygienestandards lässt. Implementierung eines Betriebskonzeptes in einer HNO-Klinik im Rahmen der SARS-CoV-2-Pandemie. abstract: The SARS-CoV‑2 pandemic poses major challenges for the entire medical care system. Especially in maximum care clinical facilities, a higher exposure to potentially infectious patients or positively tested COVID-19 patients is to be expected. A hospital facility concept was developed in the Department of Ophthalmology, Goethe University, Frankfurt am Main, Germany with the aim of achieving maximum patient safety with maximum employee protection. The current infection control hygiene recommendations of the Robert Koch Institute (RKI), the leading specialist association, were taken into consideration along with the existing hospital hygiene plan of the University Hospital Frankfurt am Main. Incorporated into the developmental process were the Institute for Medical Microbiology and Hospital Hygiene, the occupational medical service department and the board of the University Hospital Frankfurt am Main. The operational concept with individualized measures ensures that (i) the care of outpatients; (ii) the performance of outpatient operations; (iii) and the care of admitted patients and patients undergoing surgery are also guaranteed during the COVID-19 pandemic. All measures have been documented in writing in the clinic’s internal quality manual and are thus accessible to all employees. The concept is regularly checked for functionality, so-called stress tests and hygiene inspections are carried out and improvements are made as necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/32613255/ doi: 10.1007/s00347-020-01156-9 id: cord-281005-6gi18vka author: Singh, Praveen Kumar title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date: 2020-09-01 words: 3161.0 sentences: 203.0 pages: flesch: 57.0 cache: ./cache/cord-281005-6gi18vka.txt txt: ./txt/cord-281005-6gi18vka.txt summary: title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. In this study, we aimed to predict the mutations in the spike protein (S) of SARS-CoV-2 genomes available in the database (whole genome sequences as well as partial coding sequences of spike protein) and analyze the effect of each mutation on the antigenicity of the predicted epitopes. abstract: Objectives The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has been unprecedentedly fast, spreading to more than 180 countries within 3 months with variable severity. One of the major reasons attributed to this variation is genetic mutation. Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. Materials and Methods Several research groups have generated whole genome sequencing data which are available in the public repositories. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. Further, the antigenicity of the predicted mutations inferred, and the epitopes were superimposed on the structure of the spike protein. Results The sequence analysis resulted in high SNPs frequency. The significant variations in the predicted epitopes showing high antigenicity were A348V, V367F and A419S in receptor binding domain (RBD). Other mutations observed within RBD exhibiting low antigenicity were T323I, A344S, R408I, G476S, V483A, H519Q, A520S, A522S and K529E. The RBD T323I, A344S, V367F, A419S, A522S and K529E are novel mutations reported first time in this study. Moreover, A930V and D936Y mutations were observed in the heptad repeat domain and one mutation D1168H was noted in heptad repeat domain 2. Conclusion S protein is the major target for vaccine development, but several mutations were predicted in the antigenic epitopes of S protein across all genomes available globally. The emergence of various mutations within a short period might result in the conformational changes of the protein structure, which suggests that developing a universal vaccine may be a challenging task. url: https://doi.org/10.1055/s-0040-1715790 doi: 10.1055/s-0040-1715790 id: cord-353494-72fvkx7f author: Singh, Rajveer title: Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study date: 2020-10-10 words: 4677.0 sentences: 267.0 pages: flesch: 54.0 cache: ./cache/cord-353494-72fvkx7f.txt txt: ./txt/cord-353494-72fvkx7f.txt summary: The RMSD plots of all the three ligand-protein complexes showed very stable conformation throughout the simulation study, which demonstrates that it has a huge impact on the Mpro target ( Figure S2A ) as the reference compound N3. RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). The molecular dynamic simulation showed that the selected natural compounds bind and stabilized the active site of both the proteins such as Mpro and TMPRSS2. abstract: The current pandemic, caused by SARS-CoV-2 virus, is a severe challenge for human health and the world economy. There is an urgent need for development of drugs that can manage this pandemic, as it has already infected 19 million people and led to the death of around 711,277 people worldwide. At this time, in-silico studies are providing lots of preliminary data about potential drugs, which can be a great help in further in-vitro and in-vivo studies. Here, we have selected three polyphenolic compounds, mangiferin, glucogallin, and phlorizin. These compounds are isolated from different natural sources but share structural similarities and have been reported for their antiviral activity. The objective of this study is to analyze and predict the anti-protease activity of these compounds on SARS-CoV-2main protease (Mpro) and TMPRSS2 protein. Both the viral protein and the host protein play an important role in the viral life cycle, such as post-translational modification and viral spike protein priming. This study has been performed by molecular docking of the compounds using PyRx with AutoDock Vina on the two aforementioned targets chosen for this study, i.e., SARS-CoV-2 Mpro and TMPRSS2. The compounds showed good binding affinity and are further analyzed by (Molecular dynamic) MD and Molecular Mechanics Poisson-Boltzmann Surface Area MM-PBSA study. The MD-simulation study has predicted that these natural compounds will have a great impact on the stabilization of the binding cavity of the Mpro of SARS-CoV-2. The predicted pharmacokinetic parameters also show that these compounds are expected to have good solubility and absorption properties. Further predictions for these compounds also showed no involvement in drug-drug interaction and no toxicity. url: https://doi.org/10.3390/molecules25204604 doi: 10.3390/molecules25204604 id: cord-026340-2nf97zvc author: Singh, Ranjana title: Chloroquine: A Potential Drug in the COVID-19 Scenario date: 2020-06-07 words: 7542.0 sentences: 412.0 pages: flesch: 55.0 cache: ./cache/cord-026340-2nf97zvc.txt txt: ./txt/cord-026340-2nf97zvc.txt summary: In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19'' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell''s receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. abstract: Today, the whole world is fighting a public health emergency called ‘COVID-19’ caused by a new infectious virus called SARS-CoV2. Any person can catch COVID-19 from an infected person via aerosol droplets when the person coughs, sneezes, or speaks. To limit such a transmission, World Health Organization (WHO) has recommended people to wear masks and physically distance themselves by staying at least 1 m (3 feet) away from others. As aerosol droplets (by cough or sneeze) land on objects and surfaces around the person such as tables, doorknobs and handrails, and remain active on these surfaces for hours to days, people are advised to use soaps for at least 20 s. and alcohol-based sanitizers as well. As the public made efforts, clinicians and researchers investigated and found that drugs which were initially used to treat other diseases may work as a treatment option for COVID-19. One of those drugs was Chloroquine and its related derivative called hydroxychloroquine. In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19’ and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. These data have been acquired mostly from PubMed and websites of WHO and Indian Council for Medical Research (ICMR). We did a systematic search and found that the properties of chloroquine are very much essential for the COVID-19 scenario. We also bring to you some evidence that the anti-lysosomal activity of chloroquine may be increased by botanicals like betulinic acid. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275976/ doi: 10.1007/s41403-020-00114-w id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 words: 13032.0 sentences: 690.0 pages: flesch: 44.0 cache: ./cache/cord-336554-n8n5ii5k.txt txt: ./txt/cord-336554-n8n5ii5k.txt summary: Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . abstract: Currently, there are no treatment options available for the deadly contagious disease, coronavirus disease 2019 (COVID-19). Drug repurposing is a process of identifying new uses for approved or investigational drugs and it is considered as a very effective strategy for drug discovery as it involves less time and cost to find a therapeutic agent in comparison to the de novo drug discovery process. The present review will focus on the repurposing efficacy of the currently used drugs against COVID-19 and their mechanisms of action, pharmacokinetics, dosing, safety, and their future perspective. Relevant articles with experimental studies conducted in-silico, in-vitro, in-vivo, clinical trials in humans, case reports, and news archives were selected for the review. Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. These drugs either act through virus-related targets such as RNA genome, polypeptide packing and uptake pathways or target host-related pathways involving angiotensin-converting enzyme-2 (ACE2) receptors and inflammatory pathways. Using the basic knowledge of viral pathogenesis and pharmacodynamics of drugs as well as using computational tools, many drugs are currently in pipeline to be repurposed. In the current scenario, repositioning of the drugs could be considered the new avenue for the treatment of COVID-19. url: https://doi.org/10.1007/s43440-020-00155-6 doi: 10.1007/s43440-020-00155-6 id: cord-317092-5qba9jiq author: Singh, Tulika title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date: 2020-05-08 words: 4971.0 sentences: 355.0 pages: flesch: 49.0 cache: ./cache/cord-317092-5qba9jiq.txt txt: ./txt/cord-317092-5qba9jiq.txt summary: The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children''s immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. abstract: The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Consistent epidemiologic evidence of reduced severity of infection in children across different populations and countries suggests there are underlying biologic differences between children and adults that mediate differential disease pathogenesis. This presents a unique opportunity to learn about disease modifying host factors from pediatric populations. Our review summarizes the current knowledge of pediatric clinical disease, role in transmission, risks for severe disease, protective immunity, as well as novel therapies and vaccine trials for children. We then define key hypotheses and areas for future research that can use the pediatric model of disease, transmission, and immunity to develop preventive and therapeutic strategies for people of all age groups. url: https://www.ncbi.nlm.nih.gov/pubmed/32382748/ doi: 10.1093/cid/ciaa547 id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 words: 7194.0 sentences: 381.0 pages: flesch: 58.0 cache: ./cache/cord-280427-smqc23vr.txt txt: ./txt/cord-280427-smqc23vr.txt summary: The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. abstract: Coronaviruses are a large family of viruses that are known to infect both humans and animals. However, the evidence of inter-transmission of coronavirus between humans and companion animals is still a debatable issue. There is substantial evidence that the virus outbreak is fueled by zoonotic transmission because this new virus belongs to the same family of viruses as SARS-CoV associated with civet cats, and MERS-CoV associated with dromedary camels. While the whole world is investigating the possibility about the transmission of this virus, the transmission among humans is established, but the interface between humans and animals is not much evident. Not only are the lives of human beings at risk, but there is an equal potential threat to the animal world. With multiple reports claiming about much possibility of transmission of COVID-19 from humans to animals, there has been a significant increase in the number of pets being abandoned by their owners. Additionally, the risk of reverse transmission of COVID-19 virus from companion pets like cats and dogs at home is yet another area of concern. The present article highlights different evidence of human-animal interface and necessitates the precautionary measures required to combat with the consequences of this interface. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have suggested various ways to promote awareness and corroborate practices for helping people as well as animals to stay secure and healthy. url: https://www.ncbi.nlm.nih.gov/pubmed/32926266/ doi: 10.1007/s11259-020-09781-0 id: cord-026788-4d3r9rj8 author: Singla, Vikas title: Hepatobiliary and Pancreatic Manifestations of Coronavirus Disease 2019 date: 2020-05-16 words: 1952.0 sentences: 133.0 pages: flesch: 50.0 cache: ./cache/cord-026788-4d3r9rj8.txt txt: ./txt/cord-026788-4d3r9rj8.txt summary: The disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the Coronaviridae family. Drugs used to treat severe COVID-19 may cause liver injury and may have an effect on the underlying disease activity. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has spread throughout the globe in a very short span of time, which is beyond the imagination of most of us. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in November 2002 and resulted in more than 800 deaths. Patients with decompensated liver disease may be more prone to infection by SARS-CoV-2 because of underlying immunocompromised state, and the disease may be severe in these patients. In conclusion, SARS-CoV2 can cause hepatic and pancreatic injury, which is more common in patients with severe disease. abstract: Coronavirus disease 2019 (COVID-19) is a new infectious disease that has spread rapidly throughout the world. The disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the Coronaviridae family. Though the pulmonary involvement is a major cause of morbidity and mortality, involvement of the gastrointestinal tract, liver, and pancreas has been explained in these patients. The literature is rapidly changing because of influx of new information with every passage of time. The most common hepatic presentation is mild elevation of aspartate transaminase and alanine transaminase, which does not require specific treatment. Occasionally, patients can have severe liver injury. Because of underlying predisposing factors such as diabetes mellitus, hypertension, and obesity, patients with nonalcoholic liver disease may be at risk of severe disease. Patients with decompensated liver disease may also be vulnerable to severe disease. Behavior of SARS-CoV-2 in patients with chronic hepatitis B and C, autoimmune hepatitis, primary sclerosing cholangitis, and primary biliary cirrhosis is yet to be seen. The prevalence and severity of COVID-19 patients with the aforementioned diseases may be different. The effect of SARS-CoV-2 on an underlying liver disease is not known. COVID-19 may complicate the peritransplant period and throw new challenges in these patients. Drugs used to treat severe COVID-19 may cause liver injury and may have an effect on the underlying disease activity. Both hepatic and pancreatic involvement is related to the severity of COVID-19 disease. Serum amylase and lipase levels may be elevated in patients with severe COVID-19 disease. The involvement of pancreatic islet cells may lead to deranged blood sugar levels and potentially predispose to future diabetes mellitus. There are many unknown facts that will unfold with the passage of time. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295265/ doi: 10.1055/s-0040-1712079 id: cord-266350-yybunc6z author: Sinha, Saurabh K. title: An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets date: 2020-05-13 words: 3180.0 sentences: 165.0 pages: flesch: 48.0 cache: ./cache/cord-266350-yybunc6z.txt txt: ./txt/cord-266350-yybunc6z.txt summary: From the binding energy and interaction studies, the Saikosaponins U and V showed the best affinity towards both the proteins suggesting them to be future research molecule as they mark the desire interaction with NSP15, which is responsible for replication of RNA and also with 2019-nCoV spike glycoprotein which manage the connection with ACE2. The docking simulation study of total 23 Saikosaponins (Supplementary file) was performed on the 1.9 A crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the complex with a citrate (PDB ID: 6W01) and prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up (PDB ID: 6VSB) which was retrieved from protein data bank (https://www.rcsb.org). Our observations revealed that, the Saikosaponin V having two oxane rings substituted with 3 hydroxyl group and the side chain contains 4 hydroxyl and an ester linkage showed very high binding with active site having a furrow between the two b-sheets, carries amino acids Lys290, Thr341, Tyr343 and Ser29. abstract: The Public Health Emergency of International Concern declared the widespread outbreak of SARS-CoV-2 as a global pandemic emergency, which has resulted in 1,773,086 confirmed cases including 111,652 human deaths, as on 13 April 2020, as reported to World Health Organization. As of now, there are no vaccines or antiviral drugs declared to be officially useful against the infection. Saikosaponin is a group of oleanane derivatives reported in Chinese medicinal plants and are described for their anti-viral, anti-tumor, anti-inflammatory, anticonvulsant, antinephritis and hepatoprotective activities. They have also been known to have anti-coronaviral property by interfering the early stage of viral replication including absorption and penetration of the virus. Thus, the present study was undertaken to screen and evaluate the potency of different Saikosaponins against different sets of SARS-CoV-2 binding protein via computational molecular docking simulations. Docking was carried out on a Glide module of Schrodinger Maestro 2018-1 MM Share Version on NSP15 (PDB ID: 6W01) and Prefusion 2019-nCoV spike glycoprotein (PDB ID: 6VSB) from SARS-CoV-2. From the binding energy and interaction studies, the Saikosaponins U and V showed the best affinity towards both the proteins suggesting them to be future research molecule as they mark the desire interaction with NSP15, which is responsible for replication of RNA and also with 2019-nCoV spike glycoprotein which manage the connection with ACE2. [Image: see text] Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32345124/ doi: 10.1080/07391102.2020.1762741 id: cord-351446-j4ambec5 author: Sinonquel, P. title: COVID‐19 and gastrointestinal endoscopy: what should be taken into account? date: 2020-04-26 words: 2673.0 sentences: 178.0 pages: flesch: 51.0 cache: ./cache/cord-351446-j4ambec5.txt txt: ./txt/cord-351446-j4ambec5.txt summary: With this report we aim to provide recommendations and practical relevant information for gastroenterologists based on the limited amount of available data and local experience, to guarantee a high‐quality patient care and adequate infection prevention in the gastroenterology clinic. [6] SARS-CoV-2 virus spreads via droplets and aerosols, and indirectly by contact with contaminated surfaces which implies the absolute need of personal protective equipment (PPE) for both patients and health care workers/professionals, especially those operating in the aero-digestive tract. The aim of this report is to provide a practical guide for the protective management when performing endoscopic/endoluminal procedures of the GI tract in emergency, ambulatory or hospitalized patients, based upon the current available information worldwide and local experience in our tertiary university hospital. Before any procedure can be performed, the patient should wear a surgical mask and should be questioned about contact with COVID-19 positive individuals and recent or present symptoms like fever, cough and dyspnea, rhinitis, sudden loss of smell and/or taste. abstract: On March 11(th) 2020 the World Health Organisation (WHO) declared COVID‐19 pandemic, leading to a subsequent impact on the entire world and health care system. Since the causing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) houses in the aerodigestive tract, activities in the gastrointestinal outpatient clinic and endoscopy unit should be limited to emergencies only. Health care professionals are faced with the need to perform endoscopic or endoluminal emergency procedures in patients with a confirmed positive or unknown COVID‐19 status. With this report we aim to provide recommendations and practical relevant information for gastroenterologists based on the limited amount of available data and local experience, to guarantee a high‐quality patient care and adequate infection prevention in the gastroenterology clinic. url: https://doi.org/10.1111/den.13706 doi: 10.1111/den.13706 id: cord-300320-07tdrd4w author: Siordia, Juan A. title: Systematic and Statistical Review of Coronavirus Disease 19 Treatment Trials date: 2020-07-15 words: 4829.0 sentences: 372.0 pages: flesch: 44.0 cache: ./cache/cord-300320-07tdrd4w.txt txt: ./txt/cord-300320-07tdrd4w.txt summary: Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, tocilizumab, favipiravir, heparin, and dexamethasone. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Medical therapies investigated included lopinavir/ritonavir, arbidol, hydroxychloroquine, remdesivir, favipiravir, heparin, glucocorticoids, interferon, ivermectin, and convalescent plasma. Key words included COVID-19, SARS-CoV2, randomized, This article is part of the Topical Collection on Covid-19 controlled, human, retrospective, prospective, trial, chloroquine, hydroxychloroquine, lopinavir, ritonavir, arbidol, umifenovir, tocilizumab, favipiravir, steroids, dexamethasone, glucocorticoids, interferon, ivermectin, remdesivir, azithromycin, heparin, and low-molecular weight heparin. Lopinavir/ritonavir, arbidol, hydroxychloroquine, favipiravir, remdesivir, and heparin are medications that have been tested in human controlled trials for COVID-19 treatment. In human trials, arbidol shows no significant positive-negative conversion rate or recovery time compared to standard therapy or lopinavir/ritonavir [4, 9] . Combining T, treatment group (remdesivir); C, control group all the hydroxychloroquine human trials showed no benefit with reducing COVID-19 viral shedding time. abstract: The following systematic review and meta-analysis compile the current data regarding human controlled COVID-19 treatment trials. An electronic search of the literature compiled studies pertaining to human controlled treatment trials with COVID-19. Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, tocilizumab, favipiravir, heparin, and dexamethasone. Statistical analyses were performed for common viral clearance endpoints whenever possible. Lopinavir/ritonavir showed no significant effect on viral clearance for COVID-19 cases (OR 0.95 [95% CI 0.50–1.83]). Hydroxychloroquine also showed no significant effect on COVID-19 viral clearance rates (OR 2.16 [95% CI 0.80–5.84]). Arbidol showed no 7-day (OR 1.63 [95% CI 0.76–3.50]) or 14-day viral (OR 5.37 [95% CI 0.35–83.30]) clearance difference compared to lopinavir/ritonavir. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Tocilizumab showed mixed results regarding survival. Favipiravir showed quicker symptom improvement compared to lopinavir/ritonavir and arbidol. Heparin and dexamethasone showed improvement with severe COVID-19 cases requiring supplemental oxygenation. Current medications do not show significant effect on COVID-19 viral clearance rates. Tocilizumab showed mixed results regarding survival. Favipiravir shows favorable results compared to other tested medications. Heparin and dexamethasone show benefit especially for severe COVID-19 cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32838169/ doi: 10.1007/s42399-020-00399-6 id: cord-334715-902pfxyz author: Sirico, Domenico title: Cardiac imaging in congenital heart disease during the coronavirus disease-2019 pandemic: recommendations from the Working Group on Congenital Heart Disease of the Italian Society of Cardiology date: 2020-06-01 words: 2547.0 sentences: 130.0 pages: flesch: 41.0 cache: ./cache/cord-334715-902pfxyz.txt txt: ./txt/cord-334715-902pfxyz.txt summary: The aim of this position paper is to provide clinical recommendation regarding the execution of imaging investigations for the cardiac diagnostic work-up of paediatric patients with suspected or confirmed infection. In particular, the Echo-Lab leading team along with referring physicians should identify all those investigations that have an urgent/emergent indication and reschedule all the elective ones, especially for patients at higher risk of infection and low priority for echocardiogram. Echocardiogram execution Echocardiographic studies performed on paediatric patients with suspected or confirmed COVID-19 should be as focused as necessary to be of any diagnostic value. In the case of an echocardiogram in a suspected or confirmed COVID-19 hospital inpatient, a bedside investigation with a portable machine in the isolated room should be preferred, avoiding moving patients within the clinic or hospital. In this setting (suspected/confirmed COVID-19 and signs of myocarditis), CMR can be performed, considering the risk/benefit ratio according to the patient''s hemodynamic status and exam''s therapeutic impact. abstract: The recent outbreak of 2019 severe acute respiratory syndrome coronavirus-2 is having major repercussions on healthcare services provision in Italy and worldwide. Data suggest the virus has a strong impact on the cardiovascular system, and cardiac imaging will play an important role in patients affected by coronavirus disease-2019. Although paediatric patients are mildly affected, they represent a clear accelerator in spreading the virus, and healthcare workers are at higher risk of infection. The aim of this position paper is to provide clinical recommendation regarding the execution of imaging investigations for the cardiac diagnostic work-up of paediatric patients with suspected or confirmed infection. url: https://doi.org/10.2459/jcm.0000000000000990 doi: 10.2459/jcm.0000000000000990 id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 words: 8918.0 sentences: 582.0 pages: flesch: 44.0 cache: ./cache/cord-260225-bc1hr0fr.txt txt: ./txt/cord-260225-bc1hr0fr.txt summary: Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). abstract: [Image: see text] SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. url: https://doi.org/10.1021/acs.jproteome.0c00421 doi: 10.1021/acs.jproteome.0c00421 id: cord-311835-dmqfij6j author: Siu, Kam-Leung title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 date: 2014-01-13 words: 4917.0 sentences: 306.0 pages: flesch: 55.0 cache: ./cache/cord-311835-dmqfij6j.txt txt: ./txt/cord-311835-dmqfij6j.txt summary: title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 We and others have previously shown that severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis virus (MHV) spike (S) proteins induce ER stress and activate cellular unfolded protein response (UPR) in the ER [3] [4] [5] . We compared the UPR-activating activity of SARS-CoV and HCoV-HKU1 S proteins in terms of their influence on the expression of UPR effectors Grp78, Grp94, CHOP and PERK. To analyze further whether PERK activity is required for transcriptional activation of Grp78 and Grp94 promoters by SARS-CoV and HCoV-HKU1 S proteins, we made use of a dominant negative (DN) mutant of PERK which constitutively inhibits PERK kinase activity [48] . To determine whether the UPR-activating property of SARS-CoV S protein is mediated by S1 (amino acids 1-770) or S2 (amino acids 771-1255) subunit, we expressed them in 293FT cells ( Figure 6A, lanes 2 and 3) . abstract: BACKGROUND: Whereas severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) is associated with severe disease, human coronavirus HKU1 (HCoV-HKU1) commonly circulates in the human populations causing generally milder illness. Spike (S) protein of SARS-CoV activates the unfolded protein response (UPR). It is not understood whether HCoV-HKU1 S protein has similar activity. In addition, the UPR-activating domain in SARS-CoV S protein remains to be identified. RESULTS: In this study we compared S proteins of SARS-CoV and HCoV-HKU1 for their ability to activate the UPR. Both S proteins were found in the endoplasmic reticulum. Transmembrane serine protease TMPRSS2 catalyzed the cleavage of SARS-CoV S protein, but not the counterpart in HCoV-HKU1. Both S proteins showed a similar pattern of UPR-activating activity. Through PERK kinase they activated the transcription of UPR effector genes such as Grp78, Grp94 and CHOP. N-linked glycosylation was not required for the activation of the UPR by S proteins. S1 subunit of SARS-CoV but not its counterpart in HCoV-HKU1 was capable of activating the UPR. A central region (amino acids 201–400) of SARS-CoV S1 was required for this activity. CONCLUSIONS: SARS-CoV and HCoV-HKU1 S proteins use distinct UPR-activating domains to exert the same modulatory effects on UPR signaling. url: https://www.ncbi.nlm.nih.gov/pubmed/24410900/ doi: 10.1186/2045-3701-4-3 id: cord-338320-jc00ulx5 author: Siu, Kam-Leung title: Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain date: 2014-02-10 words: 3684.0 sentences: 238.0 pages: flesch: 53.0 cache: ./cache/cord-338320-jc00ulx5.txt txt: ./txt/cord-338320-jc00ulx5.txt summary: title: Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain We have previously shown that severe acute respiratory syndrome (SARS) coronavirus M protein suppresses type I interferon (IFN) production by impeding the formation of functional TRAF3-containing complex. 12 , 13 We have previously reported that SARS coronavirus M protein suppresses type I IFN production potently by preventing the formation of functional TRAF3-TANK-TBK1/IKKe complex. IFN antagonism of SARS coronavirus M protein was mediated by N-terminal TM1 (amino acids 1-38), which targets M protein to the Golgi complex and associates with TRAF3 to prevent it from interacting with TANK, TBK1 and IKKe. Our findings provide additional molecular details for suppression of type I IFN production by SARS coronavirus M protein. Notably, human coronavirus HKU1 M protein also targets the Golgi complex, interacts with TRAF3, but does not suppress IFN production. abstract: Coronaviruses have developed various measures to evade innate immunity. We have previously shown that severe acute respiratory syndrome (SARS) coronavirus M protein suppresses type I interferon (IFN) production by impeding the formation of functional TRAF3-containing complex. In this study, we demonstrate that the IFN-antagonizing activity is specific to SARS coronavirus M protein and is mediated through its first transmembrane domain (TM1) located at the N terminus. M protein from human coronavirus HKU1 does not inhibit IFN production. Whereas N-linked glycosylation of SARS coronavirus M protein has no influence on IFN antagonism, TM1 is indispensable for the suppression of IFN production. TM1 targets SARS coronavirus M protein and heterologous proteins to the Golgi apparatus, yet Golgi localization is required but not sufficient for IFN antagonism. Mechanistically, TM1 is capable of binding with RIG-I, TRAF3, TBK1 and IKKε, and preventing the interaction of TRAF3 with its downstream effectors. Our work defines the molecular architecture of SARS coronavirus M protein required for suppression of innate antiviral response. url: https://doi.org/10.1038/cmi.2013.61 doi: 10.1038/cmi.2013.61 id: cord-337681-579cz2tc author: Sk, Md Fulbabu title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations date: 2020-06-01 words: 5882.0 sentences: 340.0 pages: flesch: 53.0 cache: ./cache/cord-337681-579cz2tc.txt txt: ./txt/cord-337681-579cz2tc.txt summary: title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations In the present work, we have elucidated the mechanism of binding of two inhibitors, namely α-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. The initial coordinates for our molecular dynamics simulations were obtained from the X-ray crystallographic structure of the SARS-CoV-2 3CL pro complexed with the inhibitors a-ketoamide (PDB: 6Y2G) and Z31792168 (PDB: 5R84) (Berman et al., 2002; Zhang et al., 2020) . Next, in our study, the binding affinity of a-ketoamide was further evaluated and compared with the FDA approved anti-HIV protease inhibitors, such as lopinavir and darunavir, which has been reported as potent drugs against 3CL pro of SARS-CoV-2. abstract: The recent outbreak of novel “coronavirus disease 2019” (COVID-19) has spread rapidly worldwide, causing a global pandemic. In the present work, we have elucidated the mechanism of binding of two inhibitors, namely α-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. We calculated the total binding free energy (ΔG(bind)) of both inhibitors and further decomposed ΔG(bind) into various forces governing the complex formation using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal that α-ketoamide is more potent (ΔG(bind)= − 9.05 kcal/mol) compared to Z31792168 (ΔG(bind)= − 3.25 kcal/mol) against COVID-19 3CL(pro). The increase in ΔG(bind) for α-ketoamide relative to Z31792168 arises due to an increase in the favorable electrostatic and van der Waals interactions between the inhibitor and 3CL(pro). Further, we have identified important residues controlling the 3CL(pro)-ligand binding from per-residue based decomposition of the binding free energy. Finally, we have compared ΔG(bind) of these two inhibitors with the anti-HIV retroviral drugs, such as lopinavir and darunavir. It is observed that α-ketoamide is more potent compared to lopinavir and darunavir. In the case of lopinavir, a decrease in van der Waals interactions is responsible for the lower binding affinity compared to α-ketoamide. On the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic and van der Waals interactions contributes to lower affinity compared to α-ketoamide. Our study might help in designing rational anti-coronaviral drugs targeting the SARS-CoV-2 main protease. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32396767/ doi: 10.1080/07391102.2020.1768149 id: cord-329643-hhk900c1 author: Skalina, K. A. title: Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date: 2020-05-20 words: 1869.0 sentences: 114.0 pages: flesch: 49.0 cache: ./cache/cord-329643-hhk900c1.txt txt: ./txt/cord-329643-hhk900c1.txt summary: Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. determined that short delays (up to 4 days) in processing influenza nasal and throat swabs did not significantly affect the ability to detect viral particles by real-time RT-PCR.(5) More recently the stability of SARS-CoV-2 detection in different types of storage media over a 14-day period was evaluated. This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. abstract: With the global outbreak of the novel coronavirus disease 2019, the demand for testing rapidly increased and quickly exceeded the testing capacities for many laboratories. Clinical tests which receive CE and FDA authorizations cannot always be tested thoroughly in a real-world environment. Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. url: https://doi.org/10.1101/2020.05.16.20104158 doi: 10.1101/2020.05.16.20104158 id: cord-268476-3lxsh1zz author: Skoog, Hunter title: Tracheotomy in the SARS‐CoV‐2 pandemic date: 2020-04-29 words: 1504.0 sentences: 91.0 pages: flesch: 44.0 cache: ./cache/cord-268476-3lxsh1zz.txt txt: ./txt/cord-268476-3lxsh1zz.txt summary: The severe acute respiratory syndrome (SARS)‐CoV‐2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. The severe acute respiratory syndrome (SARS)-CoV-2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. Our priorities in establishing these guidelines included: optimal patient care, protection of medical personnel, minimizing further spread of the virus and preservation of important resources (ICU beds, ventilators, and PPE). Due to the paucity of data regarding the current SARS-CoV-2 epidemic, the literature from the SARS epidemic of In Canada, 43% of cases occurred in health care workers as a result of AGPs. 1,2 One instance involved a difficult intubation of a patient who was under investigation for SARS. There are multiple reports 3,4 of safely performing tracheotomy on patients with SARS without infecting health care workers. abstract: The severe acute respiratory syndrome (SARS)‐CoV‐2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. As such, surgeons will be called upon to perform tracheotomy for a subset of these chronically intubated patients. As seen during the SARS and the SARS‐CoV‐2 outbreaks, aerosol‐generating procedures (AGP) have been associated with higher rates of infection of medical personnel and potential acceleration of viral dissemination throughout the medical center. Therefore, a thoughtful approach to tracheotomy (and other AGPs) is imperative and maintaining traditional management norms may be unsuitable or even potentially harmful. We sought to review the existing evidence informing best practices and then develop straightforward guidelines for tracheotomy during the SARS‐CoV‐2 pandemic. This communication is the product of those efforts and is based on national and international experience with the current SARS‐CoV‐2 pandemic and the SARS epidemic of 2002/2003. url: https://www.ncbi.nlm.nih.gov/pubmed/32342565/ doi: 10.1002/hed.26214 id: cord-273253-rgqvdzna author: Skowronski, D. M. title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 date: 2020-07-15 words: 4173.0 sentences: 265.0 pages: flesch: 50.0 cache: ./cache/cord-273253-rgqvdzna.txt txt: ./txt/cord-273253-rgqvdzna.txt summary: title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 The goal of these serial snapshots was to establish baseline and early pandemic sero-prevalence for future attack rate comparison; to estimate cumulative incidence, residual susceptibility and the extent to which community transmission was suppressed; and to assess surveillance underascertainment across the winter-spring 2020 period in BC. Two of 869 sera were dual-assay positive at the March snapshot giving a crude seroprevalence of 0.23% (95%CI=0.03-0.83) and age-standardized sero-prevalence of 0.28% (95%CI=0.03-0.95). We estimated sero-prevalence based on dual-assay positivity and report cumulative incidence of 0.28% by the start of first wave population-level measures in March. Results of SARS-CoV-2 sero-survey screening by chemiluminescent assay for antibodies to spike (S1) and nucleocapsid proteins, by age group, March and May 2020 snapshots, Lower Mainland, BC, Canada Table 2 . abstract: Background: The province of British Columbia (BC) has been recognized for successful SARS-CoV-2 control, with surveillance data showing amongst the lowest case and death rates in Canada. We estimate sero-prevalence for two periods flanking the start (March) and end (May) of first-wave mitigation measures in BC. Methods: Serial cross-sectional sampling was conducted using anonymized residual sera obtained from an outpatient laboratory network, including children and adults in the Greater Vancouver Area (population ~3 million) where community attack rates were expected to be highest. Screening used two chemiluminescent immuno-assays for spike (S1) and nucleocapsid antibodies. Samples sero-positive on either screening assay were assessed by a third assay targeting the S1 receptor binding domain plus a neutralization assay. Age-standardized sero-prevalence estimates were based on dual-assay positivity. The May sero-prevalence estimate was extrapolated to the source population to assess surveillance under-ascertainment, quantified as the ratio of estimated infections versus reported cases. Results: Serum collection dates spanned March 5-13 and May 15-27, 2020. In March, two of 869 specimens were dual-assay positive, with age-standardized sero-prevalence of 0.28% (95%CI=0.03-0.95). Neither specimen had detectable neutralizing antibodies. In May, four of 885 specimens were dual-assay positive, with age-standardized sero-prevalence of 0.55% (95%CI=0.15-1.37%). All four specimens had detectable neutralizing antibodies. We estimate ~8 times more infections than reported cases. Conclusions: Less than 1% of British Columbians had been infected with SARS-CoV-2 when first-wave mitigation measures were relaxed in May 2020. Our findings indicate successful suppression of community transmission in BC, but also substantial residual susceptibility. Further sero-survey snapshots are planned as the pandemic unfolds. url: https://doi.org/10.1101/2020.07.13.20153148 doi: 10.1101/2020.07.13.20153148 id: cord-269213-tsm6zoe3 author: Slaughter, Laura title: A framework for capturing the interactions between laypersons’ understanding of disease, information gathering behaviors, and actions taken during an epidemic date: 2005-01-30 words: 8435.0 sentences: 449.0 pages: flesch: 52.0 cache: ./cache/cord-269213-tsm6zoe3.txt txt: ./txt/cord-269213-tsm6zoe3.txt summary: This paper provides a description of a methodological framework designed to capture the inter-relationships between the lay publics'' understanding of health-related processes, information gathering behaviors, and actions taken during an outbreak. This methodological framework, based on narrative analysis, is a tool for learning about how laypersons use information to build representations of an epidemic situation and how the results of this process influence their decisions to act. For example, the interview texts also result in a list of information needs expressed by the lay public concerning an outbreak as well as a general list of actions taken for SARS prevention. The arrangement of the interview into time periods (before, during, and upcoming events related to the epidemic) facilitates the data analysis when looking at the interactions and influences between informa-tion received, lay understanding, and actions taken. abstract: This paper provides a description of a methodological framework designed to capture the inter-relationships between the lay publics’ understanding of health-related processes, information gathering behaviors, and actions taken during an outbreak. We developed and refined our methods during a study involving eight participants living in severe acute respiratory syndrome (SARS)-affected areas (Hong Kong, Taiwan, and Toronto). The framework is an adaptation of narrative analysis, a qualitative method that is used to investigate a phenomenon through interpretation of the stories people tell about their experiences. From our work, several hypotheses emerged that will contribute to future research. For example, our findings showed that many decisions in an epidemic are carefully considered and involve use of significant information gathering. Having a good model of lay actions based on information received and beliefs held will contribute to the development of more effective information support systems in the event of a future epidemic. url: https://www.sciencedirect.com/science/article/pii/S153204640500002X doi: 10.1016/j.jbi.2004.12.006 id: cord-272759-dqkjofw2 author: Small, Michael title: Super-spreaders and the rate of transmission of the SARS virus date: 2006-03-15 words: 7581.0 sentences: 508.0 pages: flesch: 62.0 cache: ./cache/cord-272759-dqkjofw2.txt txt: ./txt/cord-272759-dqkjofw2.txt summary: The main conclusions of this study are: (i) "super-spreaders" may occur even if the infectiousness of all infected individuals is constant; (ii) consistent with previous reports, extended exposure time beyond 3–5 days (i.e. significant nosocomial transmission) was the key factor in the severity of the SARS outbreak in Hong Kong; and, (iii) the spread of SARS can be effectively controlled by either limiting long range links (imposing a partial quarantine) or enforcing rapid hospitalisation and isolation of symptomatic individuals. 1 Two characteristic features were observed during the SARS outbreak in Hong Kong in 2003 (see Fig. 1 ) [3, 4] : so-called super-spread events (SSE), in which a single individual initiates a large number of cases; and persistent transmission within the community. In this paper, we apply these methods to the modelling of the spread of SARS in Hong Kong; transmission is only allowed to occur along a limited number of direct links between individuals. abstract: We describe a stochastic small-world network model of transmission of the SARS virus. Unlike the standard Susceptible-Infected-Removed models of disease transmission, our model exhibits both geographically localised outbreaks and “super-spreaders”. Moreover, the combination of localised and long range links allows for more accurate modelling of partial isolation and various public health policies. From this model, we derive an expression for the probability of a widespread outbreak and a condition to ensure that the epidemic is controlled. Moreover, multiple simulations are used to make predictions of the likelihood of various eventual scenarios for fixed initial conditions. The main conclusions of this study are: (i) “super-spreaders” may occur even if the infectiousness of all infected individuals is constant; (ii) consistent with previous reports, extended exposure time beyond 3–5 days (i.e. significant nosocomial transmission) was the key factor in the severity of the SARS outbreak in Hong Kong; and, (iii) the spread of SARS can be effectively controlled by either limiting long range links (imposing a partial quarantine) or enforcing rapid hospitalisation and isolation of symptomatic individuals. url: https://api.elsevier.com/content/article/pii/S0167278906000479 doi: 10.1016/j.physd.2006.01.021 id: cord-355318-qm79gz8w author: Smit, Albertus J. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 words: 15419.0 sentences: 706.0 pages: flesch: 41.0 cache: ./cache/cord-355318-qm79gz8w.txt txt: ./txt/cord-355318-qm79gz8w.txt summary: Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Thus, if climate factors do play a role in COVID-19 infection rates, the concurrence of transition of southern hemisphere countries to their winter season with the mid-stages of the disease transmission trajectory is of concern, especially with respect to containment policy and health system resource allocation. Environmental variables considered in preprint and peer-reviewed publications as modulators of SARS-CoV-2 transmission rates include mean, minimum and/or maximum daily temperature, and diurnal temperature range; an undefined ''humidity'' variable, relative humidity, specific humidity and absolute humidity; dew point temperature; rainfall; wind speed or wind power; air pressure; some metric of solar or UV radiation; and ''air quality'' (Supplementary Tables S1 and S2 ). The general prevalence of climatologically-coupled seasonal signals and environmental variable modulation seen in the majority of other viral respiratory diseases creates the expectation for a similar effect on SARS-CoV-2 and in COVID-19 epidemiology. abstract: SARS-CoV-2 virus infections in humans were first reported in December 2019, the boreal winter. The resulting COVID-19 pandemic was declared by the WHO in March 2020. By July 2020, COVID-19 was present in 213 countries and territories, with over 12 million confirmed cases and over half a million attributed deaths. Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Many studies on the environmental sensitivity of COVID-19 are appearing online, and some have been published in peer-reviewed journals. Initially, these studies raised the hypothesis that climatic conditions would subdue the viral transmission rate in places entering the boreal summer, and that southern hemisphere countries would experience enhanced disease spread. For the latter, the COVID-19 peak would coincide with the peak of the influenza season, increasing misdiagnosis and placing an additional burden on health systems. In this review, we assess the evidence that environmental drivers are a significant factor in the trajectory of the COVID-19 pandemic, globally and regionally. We critically assessed 42 peer-reviewed and 80 preprint publications that met qualifying criteria. Since the disease has been prevalent for only half a year in the northern, and one-quarter of a year in the southern hemisphere, datasets capturing a full seasonal cycle in one locality are not yet available. Analyses based on space-for-time substitutions, i.e., using data from climatically distinct locations as a surrogate for seasonal progression, have been inconclusive. The reported studies present a strong northern bias. Socio-economic conditions peculiar to the ‘Global South’ have been omitted as confounding variables, thereby weakening evidence of environmental signals. We explore why research to date has failed to show convincing evidence for environmental modulation of COVID-19, and discuss directions for future research. We conclude that the evidence thus far suggests a weak modulation effect, currently overwhelmed by the scale and rate of the spread of COVID-19. Seasonally modulated transmission, if it exists, will be more evident in 2021 and subsequent years. url: https://doi.org/10.3390/ijerph17165634 doi: 10.3390/ijerph17165634 id: cord-346345-jc9bq0zu author: Smith, Colin M title: COVID-19-associated brief psychotic disorder date: 2020-08-11 words: 2601.0 sentences: 144.0 pages: flesch: 43.0 cache: ./cache/cord-346345-jc9bq0zu.txt txt: ./txt/cord-346345-jc9bq0zu.txt summary: This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. Here, we report a case of symptomatic COVID-19-related psychosis in a patient with no personal or family history of mental illness and briefly discuss the relevant literature on coronavirus-associated psychosis. 8 However, all patients were incidentally found to have positive SARS-CoV-2 test and did not present with other symptoms to suggest infection, calling into question whether the diagnosis of COVID-19 was related to the psychosis. abstract: A 36-year-old previously healthy woman with no personal or family history of mental illness presented with new-onset psychosis after a diagnosis of symptomatic COVID-19. Her psychotic symptoms initially improved with antipsychotics and benzodiazepines and further improved with resolution of COVID-19 symptoms. This is the first case of COVID-19-associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. url: https://www.ncbi.nlm.nih.gov/pubmed/32784244/ doi: 10.1136/bcr-2020-236940 id: cord-351974-1najtyui author: Smith, E. title: Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation date: 2020-08-05 words: 2661.0 sentences: 181.0 pages: flesch: 60.0 cache: ./cache/cord-351974-1najtyui.txt txt: ./txt/cord-351974-1najtyui.txt summary: 1 2 Transmission of SARS-CoV-2 may be possible up to two-days prior to the appearance of typical symptoms yet older patients frequently have atypical presentation, 3-5 making recognition and control of infection in care homes difficult. SARS-CoV-2 has highlighted serious gaps in data intelligence surrounding care homes, 13 with regional test results typically not available to local authorities until 2 July 2020. In addition, for SARS-CoV-2-positive residents who were asymptomatic at the point of test, data on any symptoms recorded in the 14-day post-test period were extracted. Data for residents and staff tests comprised unique ID, care home ID, date of SARS-CoV-2 test(s) and test outcome(s). Early screening of residents and staff after ingress into care homes identified prevalence of truly asymptomatic infections and symptom presentation in residents relatively early in the UK COVID-19 outbreak. Early testing and screening of staff and residents in care homes can accurately identify outbreaks, prevalence of infection and death, and cause of death. abstract: Background COVID-19 has especially affected care home residents. Aim To evaluate a nurse-led Enhanced Care Home Team (ECHT) enhanced SARS-CoV-2 testing strategy. Design and setting Service evaluation in care homes in Norfolk UK. Method Residents and staff received nose and throat swab tests (7 April to 29 June 2020). Resident test results were linked with symptoms on days 0-14 after test and mortality to 13 July 2020. Results Residents (n=518) in 44 homes and staff (n=340) in 10 care homes were tested. SARS-CoV-2 positivity was identified in 103 residents in 14 homes and 49 staff in seven homes. Of 103 SARS-CoV-2+ residents, just 38 had typical symptom(s) at time of test (new cough and/or fever). Amongst 54 residents who were completely asymptomatic when tested, 12 (22%) developed symptoms within 14 days. Compared to SARS-CoV-2 negative residents, SARS-CoV-2+ residents were more likely to exhibit typical symptoms (new cough (n=26, p=0.001); fever (n=24, p=<0.001)) or as generally-unwell (n=18, p=0.001). Of 38 resident deaths, 21 (55%) were initially attributed to SARS-CoV-2, all of whom tested SARS-CoV-2+. One death not initially attributed to SARS-CoV-2 also tested positive. Conclusion Testing identified asymptomatic and pre-symptomatic SARS-CoV-2+ residents and staff. Being generally-unwell was common amongst symptomatic residents and may indicate SARS-CoV-2 infection in older people in the absence of more typical symptoms. Where a resident appears generally unwell SARS-CoV-2-infection should be suspected. Protocols for testing involved integrated health and social care teams. url: http://medrxiv.org/cgi/content/short/2020.08.04.20165928v1?rss=1 doi: 10.1101/2020.08.04.20165928 id: cord-267397-b7ogeokm author: Smith, E. R. title: Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods date: 2020-11-12 words: 5612.0 sentences: 401.0 pages: flesch: 53.0 cache: ./cache/cord-267397-b7ogeokm.txt txt: ./txt/cord-267397-b7ogeokm.txt summary: Given the scarcity of COVID data in pregnancy, differences in data collection protocols globally, and potential risks for severe illnesses in this population, there is an urgent need to rapidly generate high quality information to make evidence-based decisions and create guidelines on the prevention and treatment of COVID-19 illness in pregnant women and infants. We updated the data modules in September 2020 to reflect evolving understanding of SARS-CoV-2 infection in newborns and to reflect and an updated generic protocol developed by WHO for COVID-related pregnancy cohort studies (Supplementary File 3) . Studies will be eligible to contribute data to the PMA when they have accrued at least 25 confirmed cases with completed follow up including obtaining maternal and neonatal outcomes. Given the current state of limited, high-quality evidence to inform public health guidance and healthcare strategies for pregnant women and newborn, the proposed study will contribute timely and necessary evidence-based data for decision-making in the context of COVID-19 and maternal and neonatal health. abstract: Background. We urgently need answers to basic epidemiological questions regarding COVID-19 infection in pregnant women and newborns. While many national registries, health facilities, and research groups are collecting relevant data, we need a collaborative and methodologically appropriate approach to utilize these data to generate answers. Methods. We propose that a sequential, prospective meta-analysis (PMA) is the best approach to rapidly generate policy and practice-oriented guidelines. As the pandemic is rapidly evolving, studies identified retrospectively through a living systematic review will also be invited to participate. The primary analysis will pool data using a two-stage meta-analysis with generic inverse-variance methods. The meta-analyses will be updated as additional data accrues in each contributing study and as additional studies meet study-specific time or data accrual thresholds for sharing. Participating Studies. At the time of publication, there are 19 studies being conducted in 21 countries that prospectively agreed to pool data for this analysis. Among the 19 included studies, ten are COVID-19 registry studies, seven are cohort or surveillance studies, and two are case-control studies. More than 74,000 pregnant women are expected to contribute to the completed analysis. Dissemination: Protocols and updates will be maintained publicly. Results will be shared with key stakeholders including the World Health Organization (WHO) Maternal, Newborn, Child, and Adolescent Health (MNCAH) Research Working Group. Scientific publications will be published in open access journals on an ongoing basis. url: https://doi.org/10.1101/2020.11.08.20228056 doi: 10.1101/2020.11.08.20228056 id: cord-296378-ki93iltt author: Smith, Joan C. title: Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract date: 2020-05-16 words: 10042.0 sentences: 595.0 pages: flesch: 54.0 cache: ./cache/cord-296378-ki93iltt.txt txt: ./txt/cord-296378-ki93iltt.txt summary: Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination. In total, our results demonstrate that exposure to cigarette smoke increases the expression of the coronavirus receptor ACE2 in rodent and human respiratory tissue, and this upregulation is potentially reversible. To investigate a potential link between inflammation and the expression of the host factors required for coronavirus infections, we first examined the levels of ACE2 in published datasets of respiratory epithelial cells challenged with different viruses. To further verify these results, we re-analyzed a published gene expression dataset of airway epithelial cells exposed to IFN-β, and we found a similar increase in ACE2 levels following interferon treatment ( Figure 5H ) (Rusinova et al., 2013; Shapira et al., 2009) . abstract: Abstract The factors mediating fatal SARS-CoV-2 infections are poorly understood. Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Using single-cell sequencing data, we demonstrate that ACE2 is expressed in a subset of secretory cells in the respiratory tract. Chronic smoke exposure triggers the expansion of this cell population and a concomitant increase in ACE2 expression. In contrast, quitting smoking decreases the abundance of these secretory cells and reduces ACE2 levels. Finally, we demonstrate that ACE2 expression is responsive to inflammatory signaling and can be upregulated by viral infections or interferon treatment. Taken together, these results may partially explain why smokers are particularly susceptible to severe SARS-CoV-2 infections. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination. url: https://doi.org/10.1016/j.devcel.2020.05.012 doi: 10.1016/j.devcel.2020.05.012 id: cord-277731-thazunob author: Smith, Matthew L. title: Biosurfactants: A Covid-19 Perspective date: 2020-06-09 words: 4700.0 sentences: 207.0 pages: flesch: 38.0 cache: ./cache/cord-277731-thazunob.txt txt: ./txt/cord-277731-thazunob.txt summary: In this case, the use of biosurfactants in dealing with this pandemic justifies extensive study with their potential applications being in the prevention of viral spread; dealing with the symptoms that develop after the incubation period; directly targeting viral infected cells and preventing the spread of the virus throughout the host, all in addition to also acting as potential drug delivery systems and cleaning agents. The use of biosurfactants will therefore be considered in handwashes and cleaning agents to prevent the spread of the virus; targeting and relieving the symptoms after infection; acting as drug delivery systems and additionally their use in other important areas with a key example being the production reliable antiviral facemasks. This structure will be significant in directly targeting the virus, impacting its overall emulsification activity, while also being crucial in our application of biosurfactants in drug delivery. abstract: The recent outbreak in severe acute respiratory syndrome – coronavirus-2 (SARS-CoV-2) has demonstrated the complete inability of nations across the world to cope with the pressures of a global pandemic, especially one in which the only current feasible treatments are those which deal with the symptoms alone and not the viral cause. As the death toll rises, scientists begin to fall toward new avenues of research, with novelty showing itself to be an incredible and so far, underrated resource. In this case, the use of biosurfactants in dealing with this pandemic justifies extensive study with their potential applications being in the prevention of viral spread; dealing with the symptoms that develop after the incubation period; directly targeting viral infected cells and preventing the spread of the virus throughout the host, all in addition to also acting as potential drug delivery systems and cleaning agents. This extensive avenue of biosurfactants owes to the simplicity in their amphiphilic structure which permits them to interact directly with the lipid membrane of the coronavirus, in a way which wouldn't be of significant threat to the host. Although it could possibly interact and affect the virus, it could also affect human internal organs/cells by interacting with lipid membrane, if (biosurfactant is) ingested, and it still needs further studies in human models. The structure of the coronavirus, in this case SARS-CoV-2, is detrimentally dependent on the integrity of its lipid membrane which encloses its vital proteins and RNA. Biosurfactants possess the innate ability to threaten this membrane, a result of their own hydrophobic domains across their amphiphilic structure. With biosurfactants additionally being both natural and sustainable, while also possessing a remarkably low cytotoxicity, it is of no doubt that they are going to be of increasing significance in dealing with the current pandemic. url: https://doi.org/10.3389/fmicb.2020.01341 doi: 10.3389/fmicb.2020.01341 id: cord-033780-184e64tr author: Smith, Rasheid title: Implications of current and future approaches to coronavirus disease 2019 testing date: 2020-10-13 words: 3266.0 sentences: 154.0 pages: flesch: 44.0 cache: ./cache/cord-033780-184e64tr.txt txt: ./txt/cord-033780-184e64tr.txt summary: The current reality is that SARS-CoV-2 is a highly transmissible airborne disease with a broad presentation of symptoms and leaves lasting damage in severe cases, and for which there is a scarcity of effective medications to treat it. Using the cycle threshold value in this manner only informs as to the presence of the virus and may not reveal disease progression, severity and viral load in the sample; and as such the results are largely qualitative despite the inherent quantitative nature of real-time RT-PCR [27] . Nevertheless, initial studies have demonstrated that chest CT imaging is more accurate than RT-PCR at detecting SARS-CoV-2 patients [32] with 97.2% versus 83% in the early stages of infection [33] . Immunoassays (antibody serum tests), such as enzyme-linked immunosorbent assays (ELISAs), are used to detect the presence of serum antibodies (either IgA, IgG or IgM) to viral proteins and can indicate when a person has developed an immune response to SARS-CoV-2. Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560716/ doi: 10.2217/fvl-2020-0318 id: cord-341287-i1hyk962 author: Smith, Trevor R. F. title: Immunogenicity of a DNA vaccine candidate for COVID-19 date: 2020-05-20 words: 7803.0 sentences: 446.0 pages: flesch: 54.0 cache: ./cache/cord-341287-i1hyk962.txt txt: ./txt/cord-341287-i1hyk962.txt summary: Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. In subjects immunized with INO-4700 (MERS-CoV S protein DNA vaccine) durable neutralizing antibodies (nAbs) and T cell immune responses were measured, and a seroconversion rate of 96% was observed and immunity was followed for 60 weeks in most study volunteers 9 . We followed the induction of immunity by the selected immunogen in mice and guinea pigs, measuring SARS-CoV-2 S protein-specific antibody levels in serum and in the lung fluid, and antibody functionality through competitive inhibition of ACE2 binding, pseudovirus and live virus neutralization. In summary, humoral immunogenicity testing in both mice and guinea pigs revealed the COVID-19 vaccine candidate, INO-4800, was capable of eliciting functional blocking antibody responses to SARS-CoV-2 spike protein. abstract: The coronavirus family member, SARS-CoV-2 has been identified as the causal agent for the pandemic viral pneumonia disease, COVID-19. At this time, no vaccine is available to control further dissemination of the disease. We have previously engineered a synthetic DNA vaccine targeting the MERS coronavirus Spike (S) protein, the major surface antigen of coronaviruses, which is currently in clinical study. Here we build on this prior experience to generate a synthetic DNA-based vaccine candidate targeting SARS-CoV-2 S protein. The engineered construct, INO-4800, results in robust expression of the S protein in vitro. Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. This preliminary dataset identifies INO-4800 as a potential COVID-19 vaccine candidate, supporting further translational study. url: https://www.ncbi.nlm.nih.gov/pubmed/32433465/ doi: 10.1038/s41467-020-16505-0 id: cord-299133-09mbiqrr author: Smither, Sophie J. title: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity date: 2020-06-22 words: 1391.0 sentences: 81.0 pages: flesch: 57.0 cache: ./cache/cord-299133-09mbiqrr.txt txt: ./txt/cord-299133-09mbiqrr.txt summary: title: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity In this study, the ability of SARS-CoV-2 to survive in the dark, at two different relative humidity values and within artificial saliva, a clinically relevant matrix, was investigated. SARS-CoV-2 was found to be stable, in the dark, in a dynamic small particle aerosol under the four experimental conditions we tested and viable virus could still be detected after 90 minutes. A recent study has shown the Washington variant of SARS-CoV-2 remains viable in a small particle aerosol for long periods [2] . Here we extend that research to look at a UK variant of SARS-CoV-2 in aerosols, at different relative humidity values, and in artificial saliva. SARS-CoV-2 England-2 variant was aerosolised in tissue culture media or in artificial saliva and maintained in a dynamic aerosol at medium RH (40-60%) or high RH (68-88%) (Supplementary Material: Table 1 ). abstract: SARS-CoV-2, the causative agent of the COVID-19 pandemic, may be transmitted via airborne droplets or contact with surfaces onto which droplets have deposited. In this study, the ability of SARS-CoV-2 to survive in the dark, at two different relative humidity values and within artificial saliva, a clinically relevant matrix, was investigated. SARS-CoV-2 was found to be stable, in the dark, in a dynamic small particle aerosol under the four experimental conditions we tested and viable virus could still be detected after 90 minutes. The decay rate and half-life was determined and decay rates ranged from 0.4 to 2.27 % per minute and the half lives ranged from 30 to 177 minutes for the different conditions. This information can be used for advice and modelling and potential mitigation strategies. url: https://doi.org/10.1080/22221751.2020.1777906 doi: 10.1080/22221751.2020.1777906 id: cord-283430-k1ex9fes author: Smithgall, Marie C. title: Third Trimester Placentas of SARS‐CoV‐2‐Positive Women: Histomorphology, including Viral Immunohistochemistry and in Situ Hybridization date: 2020-07-21 words: 1277.0 sentences: 100.0 pages: flesch: 39.0 cache: ./cache/cord-283430-k1ex9fes.txt txt: ./txt/cord-283430-k1ex9fes.txt summary: CONCLUSIONS: In this study, third trimester placentas from SARS‐CoV‐2‐positive women were more likely to show evidence of maternal/fetal vascular malperfusion; however, no evidence of direct viral involvement or vertical transmission was noted by ISH and IHC. Studies to date regarding SARS-CoV-2 and placental pathology have been limited by the number of SARS-CoV-2 positive cases, 4, 5 and only one with a sample size of 5 cases has utilized in-situ hybridization (ISH) and immunohistochemistry (IHC) analyses. 6 In our study, we compared placental histopathology from 51 SARS-CoV-2-positive and 25 SARS-CoV-2negative women in their third-trimesters presenting to L&D, and tested placentas from SARS-CoV-2-positive mothers using ISH and/or IHC. Placentas from SARS-CoV-2-positive women showed non-specific evidence of maternal/fetal vascular malperfusion, including subchorionic thrombi (Fig.1A) , intervillous thrombi (Fig.1B) , infarction (Fig.1C) , chorangiosis, segmental avascular-villi (Fig.1D) , fetal thrombotic vasculopathy (Fig.1E) , and villous agglutination (Fig.1F ). abstract: AIMS: The wide‐variety of affected organ‐systems associated with SARS‐CoV‐2 infection highlights the need for tissue‐specific evaluation. We compared placentas from SARS‐CoV‐2‐positive and negative women in our hospital in New York City, which became the epicenter of the COVID‐19 pandemic in March 2020. While some limited studies have been published on placentas from SARS‐CoV‐2‐positive women to date, this study, in addition to describing histomorphology, utilizes in‐situ hybridization (ISH) for the S‐gene encoding the spike‐protein and immunohistochemistry (IHC) with the monoclonal‐SARS‐CoV‐2 spike‐antibody 1A9 for placental evaluation. METHODS AND RESULTS: In this study, 51 singleton, third‐trimester placentas from SARS‐CoV‐2‐positive women and 25 singleton, third‐trimester placentas from SARS‐CoV‐2‐negative women were examined histomorphologically using the Amsterdam Criteria as well as with ISH and/or IHC. Corresponding clinical findings and neonatal outcomes also were recorded. While no specific histomorphologic changes related to SARS‐CoV‐2 were noted in the placentas, evidence of maternal/fetal vascular malperfusion was identified, with placentas from SARS‐CoV‐2‐positive women significantly more likely to show villous agglutination (p=0.003) and subchorionic thrombi (p=0.026) than placentas from SARS‐CoV‐2‐negative women. No evidence of direct viral involvement was identified using ISH and IHC. CONCLUSIONS: In this study, third trimester placentas from SARS‐CoV‐2‐positive women were more likely to show evidence of maternal/fetal vascular malperfusion; however, no evidence of direct viral involvement or vertical transmission was noted by ISH and IHC. url: https://doi.org/10.1111/his.14215 doi: 10.1111/his.14215 id: cord-289740-nsiycudn author: Smithgall, Marie C. title: Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2 date: 2020-05-13 words: 2230.0 sentences: 141.0 pages: flesch: 57.0 cache: ./cache/cord-289740-nsiycudn.txt txt: ./txt/cord-289740-nsiycudn.txt summary: OBJECTIVE: This study aimed to compare two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2, to the Roche cobas SARS-CoV-2 assay for samples with low, medium, and high viral concentrations. STUDY DESIGN: A total of 113 nasopharyngeal swabs from remnant patient samples were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. CONCLUSIONS: While Xpert showed high agreement with cobas across a wide range of viral concentrations, this study highlights an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Utilizing the high volume of patient testing performed at our medical center in New York City, we sought to evaluate and compare the performance of these two rapid assays across a wide range of clinical samples. Deidentified remnant patient samples that underwent routine clinical testing with the cobas SARS-CoV-2 assay on the 6800 platform (Roche Diagnostics, Indianapolis, IN) were used to evaluate the Xpert and ID Now assays. abstract: BACKGROUND: The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. However, robust data are lacking on the relative performance of available rapid molecular tests across a full range of viral concentrations. OBJECTIVE: This study aimed to compare two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2, to the Roche cobas SARS-CoV-2 assay for samples with low, medium, and high viral concentrations. STUDY DESIGN: A total of 113 nasopharyngeal swabs from remnant patient samples were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. RESULTS: Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. CONCLUSIONS: While Xpert showed high agreement with cobas across a wide range of viral concentrations, this study highlights an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs url: https://www.ncbi.nlm.nih.gov/pubmed/32434706/ doi: 10.1016/j.jcv.2020.104428 id: cord-341416-6bh08901 author: Smithgall, Marie C. title: Laboratory Testing of SARS CoV-2: A New York Institutional Experience date: 2020-07-19 words: 2923.0 sentences: 161.0 pages: flesch: 47.0 cache: ./cache/cord-341416-6bh08901.txt txt: ./txt/cord-341416-6bh08901.txt summary: The World Health Organization developed the first quantitative RT-PCR test for detecting SARS-CoV-2 and subsequently the U.S. Centers for Disease Control and Prevention (CDC) began shipping its own RT-PCR test kits after receiving Emergency Use Authorization (EUA) by the U.S. Food and Drug Administration (FDA) on February 4, 2020. To date there are more than 80 commercial laboratories and/or test kit manufacturers that have received approval for emergency use by the Federal Drug Administration (FDA) for SARS-CoV-2 testing with molecular assays accounting for the vast majority [6] . In addition, the FDA recently granted EUA for an RT-PCR lab developed test for qualitative detection of SARS-CoV-2 in saliva specimens and a test that uses a home collection kit with nasal swabs [6] for details see https://www.fda.gov/emergency-preparednessand-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization]. During this time, termed the "window period," a patient who is infected with SARS-CoV-2, but has not yet produced antibodies, would test negative on such an assay. abstract: nan url: https://api.elsevier.com/content/article/pii/S258940802030003X doi: 10.1016/j.yamp.2020.07.002 id: cord-333176-6v7ficfk author: Snell, Jonathan title: SARS-CoV-2 infection and its association with thrombosis and ischemic stroke: A review COVID-19, thrombosis, and ischemic stroke date: 2020-09-30 words: 2059.0 sentences: 122.0 pages: flesch: 45.0 cache: ./cache/cord-333176-6v7ficfk.txt txt: ./txt/cord-333176-6v7ficfk.txt summary: SARS-CoV-2 infection is well-documented to cause severe pneumonia, however, thrombosis and thrombotic complications, such as ischemic stroke, have also been documented in a variety of patient demographics. 5,6 This is likely due to the presence of asymptomatic or mildly symptomatic transmission of SARS-CoV-2, and its current prevalence in the human population supports the infective potential of this novel coronavirus. 37 Imbalance of the interactions between ACE2 and the RAS axis may also contribute to the thromboembolic events seen in SARS-CoV-2 infection. 44, 45 Ischemic stroke due to occlusion of large arteries has been a documented complication of SARS-CoV infection in patients with minimal to no risk factors. 46 SARS-CoV-2 infection seems to also increase risk of developing ischemic stroke, among other neurological consequences. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: A report of five cases Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Ischemic Stroke abstract: This review of current literature provides background to the COVID-19 pandemic, as well as an examination of potential pathophysiologic mechanisms behind development of thrombosis and ischemic stroke related to COVID-19. SARS-CoV-2 infection is well-documented to cause severe pneumonia, however, thrombosis and thrombotic complications, such as ischemic stroke, have also been documented in a variety of patient demographics. SARS-CoV-2 infection is known to cause a significant inflammatory response, as well as invasion of vascular endothelial cells, resulting in endothelial dysfunction. These factors, coupled with imbalance of ACE2 and RAS axis interactions, have been shown to create a prothrombotic environment, favoring thromboembolic events. Ischemic stroke is a severe complication of COVID-19 and may be a presenting symptom in some patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33036853/ doi: 10.1016/j.ajem.2020.09.072 id: cord-259603-bh198xgl author: Snijder, E.J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 words: 24187.0 sentences: 1090.0 pages: flesch: 50.0 cache: ./cache/cord-259603-bh198xgl.txt txt: ./txt/cord-259603-bh198xgl.txt summary: Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein''s importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V''Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme''s activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. abstract: Coronaviruses are animal and human pathogens that can cause lethal zoonotic infections like SARS and MERS. They have polycistronic plus-stranded RNA genomes and belong to the order Nidovirales, a diverse group of viruses for which common ancestry was inferred from the common principles underlying their genome organization and expression, and from the conservation of an array of core replicase domains, including key RNA-synthesizing enzymes. Coronavirus genomes (~ 26–32 kilobases) are the largest RNA genomes known to date and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. The primary functions that direct coronavirus RNA synthesis and processing reside in nonstructural protein (nsp) 7 to nsp16, which are cleavage products of two large replicase polyproteins translated from the coronavirus genome. Significant progress has now been made regarding their structural and functional characterization, stimulated by technical advances like improved methods for bioinformatics and structural biology, in vitro enzyme characterization, and site-directed mutagenesis of coronavirus genomes. Coronavirus replicase functions include more or less universal activities of plus-stranded RNA viruses, like an RNA polymerase (nsp12) and helicase (nsp13), but also a number of rare or even unique domains involved in mRNA capping (nsp14, nsp16) and fidelity control (nsp14). Several smaller subunits (nsp7–nsp10) act as crucial cofactors of these enzymes and contribute to the emerging “nsp interactome.” Understanding the structure, function, and interactions of the RNA-synthesizing machinery of coronaviruses will be key to rationalizing their evolutionary success and the development of improved control strategies. url: https://api.elsevier.com/content/article/pii/S0065352716300471 doi: 10.1016/bs.aivir.2016.08.008 id: cord-263438-9ra94uda author: Snowden, Frank M. title: Emerging and reemerging diseases: a historical perspective date: 2008-09-19 words: 14393.0 sentences: 608.0 pages: flesch: 47.0 cache: ./cache/cord-263438-9ra94uda.txt txt: ./txt/cord-263438-9ra94uda.txt summary: Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. In 1996, in addition, President Bill Clinton (28) issued a fact sheet entitled ''Addressing the Threat of Emerging Infectious Diseases'' in which he declared them ''one of the most significant health and security challenges facing the global community.'' There were also highly visible hearings on emerging infections in the US Congress (29) . The Rand Corporation intelligence report The Global Threat of New and Reemerging Infectious Diseases: Reconciling U.S. National Security and Public Health Policy (53) had two leading themes. abstract: Summary: Between mid‐century and 1992, there was a consensus that the battle against infectious diseases had been won, and the Surgeon General announced that it was time to close the book. Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The increasing virulence of dengue fever with dengue hemorrhagic fever and dengue shock syndrome disproved the theory of the evolution toward commensalism, and the discovery of the microbial origins of peptic ulcer demonstrated the reach of infectious diseases. The Institute of Medicine coined the term ‘emerging and reemerging diseases’ to explain that the world had entered an era in which the vulnerability to epidemics in the United States and globally was greater than ever. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. These mechanisms were tested by severe acute respiratory syndrome in 2003, and a series of practical and conceptual blind spots in preparedness were revealed. url: https://www.ncbi.nlm.nih.gov/pubmed/18837773/ doi: 10.1111/j.1600-065x.2008.00677.x id: cord-295800-w0dup04b author: So, Loletta K-Y title: Development of a standard treatment protocol for severe acute respiratory syndrome date: 2003-05-10 words: 2401.0 sentences: 140.0 pages: flesch: 50.0 cache: ./cache/cord-295800-w0dup04b.txt txt: ./txt/cord-295800-w0dup04b.txt summary: Add combination treatment with ribavirin and methylprednisolone when: q Extensive or bilateral chest radiographic involvement q Or persistent chest radiographic involvement and persistent high fever for 2 days q Or clinical, chest radiographic, or laboratory findings suggestive of worsening q Or oxygen saturation <95% in room air Standard corticosteroid regimen for 21 days q Methylprednisolone 1 mg/kg every 8 h (3 mg/kg daily) intravenously for 5 days q Then methylprednisolone 1 mg/kg every 12 h (2 mg/kg daily) intravenously for 5 days q Then prednisolone 0·5 mg/kg twice daily (1 mg/kg daily) orally for 5 days q Then prednisolone 0·5 mg/kg daily orally for 3 days q Then prednisolone 0·25 mg/kg daily orally for 3 days q Then off Ribavirin regimen for 10-14 days q Ribavirin 400 mg every 8 h (1200 mg daily) intravenously for at least 3 days (or until condition becomes stable) q Then ribavirin 1200 mg twice daily (2400 mg daily) orally Pulsed methylprednisolone q Give pulsed methylprednisolone if clinical condition, chest radiograph, or oxygen saturation worsens (at least two of these), and lymphopenia persists q Give as methylprednisolone 500 mg twice daily intravenously for 2 days, then back to standard corticosteroid regimen Ventilation q Consider non-invasive ventilation or mechanical ventilation if oxygen saturation <96% while on >6 L per min oxygen or if patient complains of increasing shortness of breath conditioning) was increased to 10-12 changes per h. abstract: A series of 31 patients with probable SARS, diagnosed from WHO criteria, were treated according to a treatment protocol consisting of antibacterials and a combination of ribavirin and methylprednisolone. Through experience with the first 11 patients, we were able to finalise standard dose regimens, including pulsed methylprednisolone. One patient recovered on antibacterial treatment alone, 17 showed rapid and sustained responses, and 13 achieved improvement with step-up or pulsed methylprednisolone. Four patients required short periods of non-invasive ventilation. No patient required intubation or mechanical ventilation. There was no mortality or treatment morbidity in this series. url: https://www.ncbi.nlm.nih.gov/pubmed/12747883/ doi: 10.1016/s0140-6736(03)13265-5 id: cord-276820-l7bd5y8y author: So, Winnie K.W. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong date: 2004-11-30 words: 4507.0 sentences: 225.0 pages: flesch: 55.0 cache: ./cache/cord-276820-l7bd5y8y.txt txt: ./txt/cord-276820-l7bd5y8y.txt summary: authors: So, Winnie K.W.; Chan, Sophia S.C.; Lee, Angel C.K.; Tiwari, Agnes F.Y. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong Abstract The study aims to examine the knowledge and the practice of the precautionary measures taken by older adults in Hong Kong against the outbreak of severe acute respiratory syndrome (SARS). The aim of the study is to describe the knowledge about SARS and precautionary measures taken by older adults in Hong Kong. Understanding older adults'' knowledge level and adherence to the government''s recommended precautionary measures to prevent transmission of SARS is an essential step in being able to design similar promotion programmes for this population in the future. (1) What demographic variables influenced older adults'' knowledge level, beliefs, and precautionary measures taken to prevent transmission of SARS? abstract: Abstract The study aims to examine the knowledge and the practice of the precautionary measures taken by older adults in Hong Kong against the outbreak of severe acute respiratory syndrome (SARS). Overall, more than half the participants responded correctly that droplet transmission is one of the main transmission routes of SARS. Those who received formal education demonstrated that they acquired greater knowledge of the sources and precautionary measures for SARS. The types of precautionary measures used and the factors affecting their behaviours were discussed. The results of the study could help the health-care professionals develop appropriate health promotion and disease prevention programmes for older adults. url: https://api.elsevier.com/content/article/pii/S0020748904000677 doi: 10.1016/j.ijnurstu.2004.04.004 id: cord-345225-2s5xd1oc author: Soares, F. title: A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence date: 2020-04-14 words: 4558.0 sentences: 236.0 pages: flesch: 51.0 cache: ./cache/cord-345225-2s5xd1oc.txt txt: ./txt/cord-345225-2s5xd1oc.txt summary: We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). Based on this data, we built an artificial intelligence classification framework, ER-CoV, aiming at determining which patients were more likely to be negative for SARS-CoV-2 when visiting an ER and that were categorized as a suspect case by medical professionals. Considering the aforementioned successes in integrating AI and medicine, we propose ER-CoV, an artificial intelligence-based screening method that uses blood exams to triage patients suspect of COVID-19 arriving at emergency rooms. abstract: Background: The SARS-CoV-2 virus responsible for COVID-19 poses a significant challenge to healthcare systems worldwide. Despite governmental initiatives aimed at containing the spread of the disease, several countries are experiencing unmanageable increases in the demand for ICU beds, medical equipment, and larger testing capacity. Efficient COVID-19 diagnosis enables healthcare systems to provide better care for patients while protecting caregivers from the disease. However, many countries are constrained by the limited amount of test kits available, the lack of equipment and trained professionals. In the case of patients visiting emergency rooms (ERs) with a suspect of COVID-19, a prompt diagnosis can improve the outcome and even provide information for efficient hospital management. In this context, a quick, inexpensive and readily available test to perform an initial triage at ER could help to smooth patient flow, provide better patient care, and reduce the backlog of exams. Methods: In this Case-control quantitative study, we developed a strategy backed by artificial intelligence to perform an initial screening of suspect COVID-19 cases. We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). Based on this initial classification, positive cases can be referred for further highly sensitive testing (e.g. CT scan, or specific antibodies). We used publicly available data from the Albert Einstein Hospital in Brazil from 5,644 patients. Focussing on using simple blood exams, a sample of 599 subjects that had the fewest missing values for 16 common exams were selected. From these 599 patients, only 81 were positive for SARS-CoV-2 (determined by RT-PCR). Based on this data, we built an artificial intelligence classification framework, ER-CoV, aiming at determining which patients were more likely to be negative for SARS-CoV-2 when visiting an ER and that were categorized as a suspect case by medical professionals. The primary goal of this investigation is to develop a classifier with high specificity and high negative predictive values, with reasonable sensitivity. Findings: We identified that our framework achieved an average specificity of 92.16% [95% CI 91.73 - 92.59] and negative predictive value (NPV) of 95.29% [95% CI 94.65% - 95.90%]. Those values are completely aligned with our goal of providing an effective low-cost system to triage suspected patients at ERs. As for sensitivity, our model achieved an average of 63.98% [95% CI 59.82% - 67.50%] and positive predictive value (PPV) of 48.00% [95% CI 44.88% - 51.56%]. An error analysis identified that, on average, 45% of the false negative results would have been hospitalized anyway, thus the model is making mistakes for severe cases that would not be overlooked, partially mitigating the fact that the test is not high-sensitive. All code for our AI model, called ER-CoV is publicly available at https://github.com/soares-f/ER-CoV. Interpretation: Based on the capacity of our model to accurately predict which cases are negative from suspected patients arriving at emergency rooms, we envision that this framework can play an important role in patient triage. Probably the most important outcome is related to testing availability, which at this point is extremely low in many countries. Considering the achieved specificity, we would reduce by at least 90% the number of SARS-CoV-2 tests performed at emergency rooms, with the chance of getting a false negative at around 5%. The second important outcome is related to patient management in hospitals. Patients predicted as positive by our framework could be immediately separated from the other patients while waiting for the results of confirmatory tests. This could reduce the spread rate inside hospitals since in many hospitals all suspected cases are kept in the same ward. In Brazil, where the data was collected, rate infection is starting to quickly spread, the lead time of a SARS-CoV-2 can be up to 2 weeks. Funding: University of Sheffield provided financial support for the Ph.D scholarship for Felipe Soares. url: https://doi.org/10.1101/2020.04.10.20061036 doi: 10.1101/2020.04.10.20061036 id: cord-296977-yzhsdz9c author: Soares, R. R. G. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 words: 6533.0 sentences: 391.0 pages: flesch: 55.0 cache: ./cache/cord-296977-yzhsdz9c.txt txt: ./txt/cord-296977-yzhsdz9c.txt summary: ; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 . abstract: With its origin estimated around December 2019 in Wuhan, China, the ongoing 2020 SARS-CoV-2 pandemic is a major global health challenge, resulting in more than 45 million infections and 1.2 million deaths. The demand for scalable, rapid and sensitive viral diagnostics is thus particularly pressing at present to help contain the rapid spread of infection and prevent overwhelming the capacity of health systems. While high-income countries have managed to rapidly expand diagnostic capacities, such is not the case in resource-limited settings of low- to medium-income countries. Aiming at developing cost-effective viral load detection systems for point-of-care COVID-19 diagnostics in resource-limited and resource-rich settings alike, we report the development of an integrated modular centrifugal microfluidic platform to perform loop-mediated isothermal amplification (LAMP) of viral RNA directly from heat-inactivated nasopharyngeal swab samples. The discs were pre-packed with dried n-benzyl-n-methylethanolamine modified agarose beads used as a versatile post-nucleic acid amplification signal enhancement strategy, allowing fluorescence detection via a smartphone camera and simple optics. The platform provided sample-to-answer analysis within 1 hour from sample collection and a detection limit between 100 and 1000 RNA copies in 10 L reaction volume. Furthermore, direct detection of non-extracted SARS-CoV-2 RNA in nasopharyngeal swab samples from patients with Ct values below 26 (n=25 plus 6 PCR negative samples) was achieved with ~94% sensitivity and 100% specificity, thus being fit-for-purpose to diagnose patients with a high risk of viral transmission. These results show significant promise towards bringing routine point-of-care COVID-19 diagnostics closer to resource-limited settings. url: http://medrxiv.org/cgi/content/short/2020.11.04.20225888v1?rss=1 doi: 10.1101/2020.11.04.20225888 id: cord-032928-m0awip9y author: Sobh, Eman title: Novel coronavirus disease 2019 (COVID-19) non-respiratory involvement date: 2020-10-01 words: 4021.0 sentences: 242.0 pages: flesch: 43.0 cache: ./cache/cord-032928-m0awip9y.txt txt: ./txt/cord-032928-m0awip9y.txt summary: Coronavirus disease 2019 (COVID-19) is caused by a novel single-strand ribonucleic acid (RNA) coronavirus known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 primary attacks the lower respiratory system causing viral pneumonia, but it may also affect the heart, gastrointestinal system, liver, kidney, and central nervous system leading to multiple organ failure [3] . Other researchers found elevated serum troponin levels in many patients infected with COVID-19, and it was associated with more severe disease and poor prognosis [21] . The mechanism behind acute myocardial injury caused by SARS-CoV-2 infection might be related to human angiotensin-converting enzyme 2 receptor (ACE2) [20] which are highly expressed in the heart [11] . The results of previous reports indicate that cardiac injury, arrhythmia, and venous thromboembolism should be considered in any suspected or confirmed COVID-19 case and the patient should undergo a prompt clinical evaluation. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a newly emerging pandemic that affected millions of people worldwide caused by novel coronavirus SARS-CoV-2. The first cases reported suffered from respiratory symptoms. MAIN BODY: Various extrapulmonary manifestations were linked to COVID-19 in several reports including cardiovascular, genitourinary, gastrointestinal, and skin. It is important that every clinician should be aware of these non-respiratory manifestations for early diagnosis and prompt management. This review aims to summarize the different extrapulmonary manifestations of COVID-19 disease and highlight the importance of multidisciplinary care. CONCLUSION: COVID-19 is a disease of multi-organ involvement. Manifestations may vary depending on which organ is involved. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527290/ doi: 10.1186/s43168-020-00030-1 id: cord-263801-01goni72 author: Sobral, Marcos Felipe Falcão title: Association between climate variables and global transmission oF SARS-CoV-2 date: 2020-08-10 words: 2957.0 sentences: 173.0 pages: flesch: 46.0 cache: ./cache/cord-263801-01goni72.txt txt: ./txt/cord-263801-01goni72.txt summary: In this study, we aimed at analyzing the associations between transmission of and deaths caused by SARS-CoV-2 and meteorological variables, such as average temperature, minimum temperature, maximum temperature, and precipitation. On the basis of the assumption that different climatic conditions play a significant role in the course of COVID-19, it is essential to identify associations between environmental factors, such as average, maximum, and minimum temperatures; precipitation; and demographic density, and SARS-CoV-2 transmission and COVID-19 mortality in humans. Even with the complete specification that includes two binary variables capturing specific effects for the months of the year and controlling for population density, the results suggest that an increase in temperature is associated with a decrease in the number of infections. This study aimed to identify the associations between environmental variables and SARS-CoV-2 transmission/COVID-19 mortality. We examined the associations between climatic variables and SARS-CoV-2 transmission and COVID-19 mortality. abstract: In this study, we aimed at analyzing the associations between transmission of and deaths caused by SARS-CoV-2 and meteorological variables, such as average temperature, minimum temperature, maximum temperature, and precipitation. Two outcome measures were considered, with the first aiming to study SARS-CoV-2 infections and the second aiming to study COVID-19 mortality. Daily data as well as data on SARS-CoV-2 infections and COVID-19 mortality obtained between December 1, 2019 and March 28, 2020 were collected from weather stations around the world. The country's population density and time of exposure to the disease were used as control variables. Finally, a month dummy variable was added. Daily data by country were analyzed using the panel data model. An increase in the average daily temperature by one degree Fahrenheit reduced the number of cases by approximately 6.4 cases/day. There was a negative correlation between the average temperature per country and the number of cases of SARS-CoV-2 infections. This association remained strong even with the incorporation of additional variables and controls (maximum temperature, average temperature, minimum temperature, and precipitation) and fixed country effects. There was a positive correlation between precipitation and SARS-CoV-2 transmission. Countries with higher rainfall measurements showed an increase in disease transmission. For each average inch/day, there was an increase of 56.01 cases/day. COVID-19 mortality showed no significant association with temperature. url: https://doi.org/10.1016/j.scitotenv.2020.138997 doi: 10.1016/j.scitotenv.2020.138997 id: cord-308100-tvk47fd7 author: Soetikno, Roy title: Considerations in performing endoscopy during the COVID-19 pandemic date: 2020-03-27 words: 2705.0 sentences: 224.0 pages: flesch: 54.0 cache: ./cache/cord-308100-tvk47fd7.txt txt: ./txt/cord-308100-tvk47fd7.txt summary: Based on experiences and the literature, our objective is to provide practical suggestions for performing endoscopy in the setting of COVID-19 pandemic. 6 It is unknown how much of the risk was related to the direct care of infected patients or to the inadequate use of personal protective equipment (PPE). 9 With numbers of COVID-19 cases continuing to rise in North America and Europe, we aim to provide practical suggestions to potentially avoid the transmissions of COVID-19 in the endoscopy unit. Possible routes of SARS-CoV-2 transmission include (1) person-to-person, (2) respiratory droplets, (3) aerosols generated during endoscopy, and (4) contact with contaminated surroundings and body fluids. 13 Recently, the World Health Organization (WHO) has published an extensive guideline on the rational use of personal protective equipment (PPE) for COVID-19 and provided specific instructions for healthcare workers performing AGP on patients with COVID-19. 17 Note that as an AGP, endoscopy of PUI/COVID patients requires the use of respiratory protection. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0016510720340335?v=s5 doi: 10.1016/j.gie.2020.03.3758 id: cord-350903-nwagvvc5 author: Softic, Laurent title: Inhibition of SARS-CoV-2 Infection by the Cyclophilin Inhibitor Alisporivir (Debio 025) date: 2020-06-23 words: 1398.0 sentences: 80.0 pages: flesch: 47.0 cache: ./cache/cord-350903-nwagvvc5.txt txt: ./txt/cord-350903-nwagvvc5.txt summary: Alisporivir reduced SARS-CoV-2 RNA production in a dose-dependent manner in Vero E6 cells, with a 50% effective concentration (EC(50)) of 0.46 ± 0.04 μM. For instance, chloroquine has been shown to bear potent antiviral properties against SARS-CoV-2 in vitro, and several clinical trials are under way to assess its efficacy in patients with COVID-19. Cyclosporine A (CsA), a potent cyclophilin inhibitor, blocks the replication of various coronaviruses in vitro, including HCoV-229E, HCoV-NL63, FPIV, mouse hepatitis virus (MHV), avian infectious bronchitis virus, and SARS-CoV (5, (8) (9) (10) . The antiviral effectiveness of increasing concentrations of alisporivir was measured in Vero E6 cells infected with a clinical isolate of SARS-CoV-2 at a multiplicity of infection (MOI) of 0.02 (Fig. 1A) . These results justify rapidly conducting a proof-of-concept phase 2 trial to assess the antiviral properties and the effect of alisporivir on COVID-19 clinical outcomes in infected patients. abstract: Cyclophilins play a key role in the life cycle of coronaviruses. Alisporivir (Debio 025) is a nonimmunosuppressive analogue of cyclosporine with potent cyclophilin inhibition properties. Alisporivir reduced SARS-CoV-2 RNA production in a dose-dependent manner in Vero E6 cells, with a 50% effective concentration (EC(50)) of 0.46 ± 0.04 μM. Alisporivir inhibited a postentry step of the SARS-CoV-2 life cycle. These results justify rapidly conducting a proof-of-concept phase 2 trial with alisporivir in patients with SARS-CoV-2 infection. url: https://doi.org/10.1128/aac.00876-20 doi: 10.1128/aac.00876-20 id: cord-323930-pl3qlcpo author: Sohail, Ayesha title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 words: 1497.0 sentences: 95.0 pages: flesch: 53.0 cache: ./cache/cord-323930-pl3qlcpo.txt txt: ./txt/cord-323930-pl3qlcpo.txt summary: The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. abstract: In December 2019, an atypical pneumonia invaded the city of Wuhan, China, and the causative agent of this disease turned out to be a new coronavirus. In January 2020, the World Health Organization named the new coronavirus 2019-nCoV and subsequently it is referred to as SARS-CoV2 and the related disease as CoViD-19 [9]. Very quickly, the epidemic led to a pandemic and it is now a worldwide emergency requiring the creation of new antiviral therapies and a related vaccine. The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the “entry receptor” for the infection process involving membrane fusion [10]. A reverse engineering process uses the formalism of the Hill function to represent the functions related to the dynamics of the biochemical interactions of the viral infection process. Then, using a logical evaluation of viral density that measures the rate at which the cells are hijacked by the virus (and they provide a place for the virus to replicate) and considering the “time delay” given by the interaction between cell and virus, the expected duration of the incubation period is predicted. The conclusion is that the density of the virus varies from the “exposure time” to the “interaction time” (virus-cells). This model can be used both to evaluate the infectious condition and to analyze the incubation period. BACKGROUND: The ongoing threat of the new coronavirus SARS-CoV2 pandemic is alarming and strategies for combating infection are highly desired. This RNA virus belongs to the β-coronavirus genus and is similar in some features to SARS-CoV. Currently, no vaccine or approved medical treatment is available. The complex dynamics of the rapid spread of this virus can be demonstrated with the aid of a computational framework. METHODS: A mathematical model based on the principles of cell-virus interaction is developed in this manuscript. The amino acid sequence of S proein and its interaction with the ACE-2 protein is mimicked with the aid of Hill function. The mathematical model with delay is solved with the aid of numerical solvers and the parametric values are obtained with the help of MCMC algorithm. RESULTS: A delay differential equation model is developed to demonstrate the dynamics of target cells, infected cells and the SARS-CoV2. The important parameters and coefficients are demonstrated with the aid of numerical computations. The resulting thresholds and forecasting may prove to be useful tools for future experimental studies and control strategies. CONCLUSIONS: From the analysis, I is concluded that control strategy via delay is a promising technique and the role of Hill function formalism in control strategies can be better interpreted in an inexpensive manner with the aid of a theoretical framework. url: https://api.elsevier.com/content/article/pii/S0079610720300262 doi: 10.1016/j.pbiomolbio.2020.04.002 id: cord-322184-kgv9f58a author: Sohn, Yujin title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 words: 3476.0 sentences: 182.0 pages: flesch: 55.0 cache: ./cache/cord-322184-kgv9f58a.txt txt: ./txt/cord-322184-kgv9f58a.txt summary: Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In this study, we attempted to confirm the presence of viable virus by performing RT-PCR assay and culture using salivary and nasopharyngeal swabs of asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease and admitted to a CTC at least two weeks previously. Therefore, based on the evidence that the virus is rarely detected in respiratory specimens after 10 days following the onset of symptoms, especially in mild or asymptomatic cases of SARS-CoV-2 infection, even if viral shedding is sustained in the later phase of COVID-19, it can be expected that the transmission risk of the virus is low. abstract: Background: The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a major global public health issue. SARS-CoV-2 infection is confirmed by the detection of viral RNA using reverse transcription polymerase chain reaction (RT-PCR). Prolonged viral shedding has been reported in patients with SARS-CoV-2 infection, but the presence of viral RNA does not always correlate with infectivity. Therefore, the present study aimed to confirm the presence of viable virus in asymptomatic or mildly symptomatic patients in the later phase of the disease, more than two weeks after diagnosis. Method: Asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease at least two weeks previously and admitted to a community treatment center (CTC) from 15 March to 10 April 2020 were enrolled in this study. Nasopharyngeal and salivary swab specimens were collected from each patient. Using these specimens, RT-PCR assay and viral culture were performed. Result: In total, 48 patients were enrolled in this study. There were no significant differences in baseline characteristics between the asymptomatic and mildly symptomatic patient groups. RT-PCR assay and viral culture of SARS-CoV-2 were performed using nasopharyngeal and salivary swabs. The results of RT-PCR performed using salivary swab specimens, in terms of cycle threshold (Ct) values, were similar to those of RT-PCR using nasopharyngeal swab specimens. In addition, no viable virus could be cultured from swab specimens collected from the late-phase COVID-19 patients with prolonged viral RNA shedding. Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In addition, saliva can be used as a reliable specimen for the diagnosis of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32927798/ doi: 10.3390/jcm9092924 id: cord-266866-z98x80zj author: Sohpal, Vipan Kumar title: Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA date: 2020-09-24 words: 2027.0 sentences: 139.0 pages: flesch: 53.0 cache: ./cache/cord-266866-z98x80zj.txt txt: ./txt/cord-266866-z98x80zj.txt summary: Hence the purpose of the present work is to assess the genomic relationship on the basis of statistical techniques between MERS-CoV, SARS-CoV, and SARS-CoV-2 with an objective to (1) maximized value of likelihood function of nucleotide substitution models, (2) transition/transversion bias and frequencies computation using maximum likelihood (ML) technique, (3) analyze the probability rate of substitution using ML. ML of different nucleotide substitution models BIC and AICc are the most important parameters for statistical analysis of ML to analyze the biological data. It indicates ML method accurately fits of 24 different nucleotide substitution models for biological data of SARS-CoV-2, MERS-CoV, and SARS-CoV under neutral evolution. In broad, the transitional/transversional varies from 0.57 (GTR model) to 0.89 (T92 + G + I), higher values indicate proportion of invariable sites (+I) and/or rate of variation across sites (+G) are more dominating in T92 model for SARS-CoV-2, SARS-CoV, and MERSCoV biological sequence. Six different nucleotide substitution models were simulated for biological sequence data of SARS-CoV, MERS-CoV and SARS-CoV-2. abstract: The novel coronavirus pandemic that has originated from China and spread throughout the world in three months. Genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) predecessor, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) play an important role in understanding the concept of genetic variation. In this paper, the genomic data accessed from National Center for Biotechnology Information (NCBI) through Molecular Evolutionary Genetic Analysis (MEGA) for statistical analysis. Firstly, the Bayesian information criterion (BIC) and Akaike information criterion (AICc) are used to evaluate the best substitution pattern. Secondly, the maximum likelihood method used to estimate of transition/transversions (R) through Kimura-2, Tamura-3, Hasegawa-Kishino-Yano, and Tamura-Nei nucleotide substitutions model. Thirdly and finally nucleotide frequencies computed based on genomic data of NCBI. The results indicate that general times reversible model has the lowest BIC and AICc score 347,394 and 347,287, respectively. The transition/transversions bias for nucleotide substitutions models varies from 0.56 to 0.59 in MEGA output. The average nitrogenous bases frequency of U, C, A, and G are 31.74, 19.48, 28.04, and 20.74, respectively in percentages. Overall the genomic data analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV highlights the close genetic relationship. url: https://doi.org/10.5808/gi.2020.18.3.e30 doi: 10.5808/gi.2020.18.3.e30 id: cord-279989-swsxez0a author: Sokolov, Elisaveta title: Non-convulsive status epilepticus: COVID-19 or clozapine induced? date: 2020-10-04 words: 2664.0 sentences: 165.0 pages: flesch: 54.0 cache: ./cache/cord-279989-swsxez0a.txt txt: ./txt/cord-279989-swsxez0a.txt summary: We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We highlight seizure disorders as a possible manifestation of SARS-CoV2 infection and describe the complexity of these presentations in the intensive care setting, especially in the context of atypical antipsychotics such as Clozapine. These two scans were done when the Findings that shed new light on the possible pathogenesis of a disease or an adverse effect patient was noted not to be waking following extubation, first as she was quadriplegic at this time and second to consider if there were any MRI features known to be associated with COVID-19. abstract: We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We discuss the presentation, investigations, differential diagnosis and management. In particular, we focus on the electroencephalogram (EEG) findings seen in this case and the electroclinical response to antiepileptic medication. We review the literature and discuss the relevance of this case to the SARS-CoV-2 global pandemic. We emphasise the importance of considering possible neurological manifestations of SARS-CoV-2 infection and highlight seizure disorder as one of the possible presentations. In addition, we discuss the possible effects of clozapine on the electroclinical presentation by way of possible seizure induction as well as discuss the possible EEG changes and we highlight that this needs to be kept in mind especially during rapid titration. url: https://doi.org/10.1136/bcr-2020-239015 doi: 10.1136/bcr-2020-239015 id: cord-323095-q8tj826i author: Sokolowska, Milena title: Outsmarting SARS-CoV-2 by empowering a decoy ACE2 date: 2020-11-03 words: 1473.0 sentences: 85.0 pages: flesch: 50.0 cache: ./cache/cord-323095-q8tj826i.txt txt: ./txt/cord-323095-q8tj826i.txt summary: Along with the current efforts to develop high-affinity neutralizing antibodies, Chan and colleagues engineered the soluble variant of human ACE2 with enhanced binding to the spike protein, outranking the soluble wild-type protein in blocking SARS-CoV-2 infection in vitro. There are currently a few therapeutic approaches focused on blocking SARS-CoV-2 binding to its key receptor, an angiotensin-converting enzyme 2 (ACE2), or on inhibition of virus spike cleavage (Fig. 1a) . 2 Therefore, other approaches are also intensively studied including soluble recombinant human ACE2 (rhACE2) or peptide-based binders, developed to block SARS-CoV-2-RBD-ACE2 binding interface or small molecule inhibitors blocking the host cell proteases, such as TMPRSS2 or furin, block virus fusion with the host cell. Therefore, in designing the soluble ACE2 (sACE2) variant the authors introduced the combinations of 3-7 mutations, which gave the large increases in S binding. Engineered soluble construct of ACE2 with enhanced affinity to SARS-CoV-2 spike RBD opens up several possibilities of its usage in the current pandemics. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33144557/ doi: 10.1038/s41392-020-00370-w id: cord-301603-gdxvbspx author: Sokouti, Massoud title: Comparative Global Epidemiological Investigation of SARS-CoV-2 and SARS-CoV Diseases Using Meta-MUMS Tool Through Incidence, Mortality, and Recovery Rates date: 2020-04-15 words: 1884.0 sentences: 113.0 pages: flesch: 57.0 cache: ./cache/cord-301603-gdxvbspx.txt txt: ./txt/cord-301603-gdxvbspx.txt summary: In this meta-analysis, a random effect model of relations of incidence, mortality, and recovery rates of COVID-19 and SARS world infections were determined. The meta-analysis and forest plots of two viral world infections showed that the incidence rate of COVID-19 infection is more than SARS infections, while recovery and mortality event rates of SARS-CoV are more than COVID-19 infection. In the current study, the comparisons between incidence and mortality, as well as recovery and death rates among the countries for COVID-19 and SARS-CoV with the higher incidence rates, were performed using the meta-analysis approach developed in the Meta-MUMS tool. The incidence event rates of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 1A , showing the relationships between two infectious diseases. Recovery event rate of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 2A , showing the relations between both diseases. abstract: COVID-19 is a novel coronavirus that was reported by the world health organization in late December 2019. As an unexplained respiratory disease epidemic, which is similar to respiratory syndrome coronavirus SARS-CoV, it rapidly spread all over the world. The study aims to compare several parameters of COVID-19 and SARS-CoV infectious diseases in terms of incidence, mortality, and recovery rates. The publicly available dataset Worldometer (extracted on April 5, 2020) confirmed by WHO report was available for meta-analysis purposes using the Meta-MUMS tool. And, the reported outcomes of the analysis used a random-effects model to evaluate the event rate, and risk ratios thorough subgroup analysis forest plots. Seventeen countries for COVID-19 and eight countries of SARS infections, including COVID-19 group n = 1124243, and SARS-CoV group n = 8346, were analyzed. In this meta-analysis, a random effect model of relations of incidence, mortality, and recovery rates of COVID-19 and SARS world infections were determined. The meta-analysis and forest plots of two viral world infections showed that the incidence rate of COVID-19 infection is more than SARS infections, while recovery and mortality event rates of SARS-CoV are more than COVID-19 infection. And subgroup analysis showed that the mortality and recovery rates were higher in both SARS-CoV wand COVID-19 in comparison to incidence and mortality rates, respectively. In conclusion, the meta-analysis approach on the abovementioned dataset revealed the epidemiological and statistical analyses for comparing COVID-19 and SARS-CoV outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32331787/ doi: 10.1016/j.arcmed.2020.04.005 id: cord-334188-bggt1i2e author: Solari, Domenico title: The nose lid for the endoscopic endonasal procedures during COVID-19 era: technical note date: 2020-08-11 words: 2604.0 sentences: 122.0 pages: flesch: 44.0 cache: ./cache/cord-334188-bggt1i2e.txt txt: ./txt/cord-334188-bggt1i2e.txt summary: We describe peculiar surgical technique modifications and the use of an endonasal face mask, i.e., the nose lid, to be applied to the patient during transnasal procedures for skull base pathologies as a further possible COVID-19 mitigation strategy. CONCLUSIONS: Transnasal surgery, transgressing respiratory mucosa, can definitely increase the risk of virus transmission: we find that adopting further precautions, above all limiting high-speed drill can help preventing or at least reducing aerosol/droplets. After usual nasal pyramid sterile draping, an endonasal surgery facial mask, namely a nose lid, is assembled: a sterile non-latex glove layer is used to cover nostril and fixed with adhesive protection film over the nasal bridge; initially, two and then three narrow slit cut are placed over the nares to let instruments enter the nostrils (Figs. abstract: BACKGROUND: COVID-19 pandemic has disrupted the global health systems worldwide. According to the tremendous rate of interhuman transmission via aerosols and respiratory droplets, severe measures have been required to contain contagion spread. Accordingly, medical and surgical maneuvers involving the respiratory mucosa and, among them, transnasal transsphenoidal surgery have been charged of maximum risk of spread and contagion, above all for healthcare professionals. METHOD: Our department, according to the actual COVID-19 protocol national guidelines, has suspended elective procedures and, in the last month, only three patients underwent to endoscopic endonasal procedures, due to urgent conditions (a pituitary apoplexy, a chondrosarcoma causing cavernous sinus syndrome, and a pituitary macroadenoma determining chiasm compression). We describe peculiar surgical technique modifications and the use of an endonasal face mask, i.e., the nose lid, to be applied to the patient during transnasal procedures for skull base pathologies as a further possible COVID-19 mitigation strategy. RESULTS: The nose lid is cheap, promptly available, and can be easily assembled with the use of few tools available in the OR; this mask allows to both operating surgeon and his assistant to perform wider surgical maneuvers throughout the slits, without ripping it, while limiting the nostril airflow. CONCLUSIONS: Transnasal surgery, transgressing respiratory mucosa, can definitely increase the risk of virus transmission: we find that adopting further precautions, above all limiting high-speed drill can help preventing or at least reducing aerosol/droplets. The creation of a non-rigid face mask, i.e., the nose lid, allows the comfortable introduction of instruments through one or both nostrils and, at the same time, minimizes the release of droplets from the patient’s nasal cavity. url: https://www.ncbi.nlm.nih.gov/pubmed/32779028/ doi: 10.1007/s00701-020-04518-z id: cord-338889-7hd3iibk author: Solbakk, Jan Helge title: Back to WHAT? The role of research ethics in pandemic times date: 2020-11-03 words: 11689.0 sentences: 709.0 pages: flesch: 53.0 cache: ./cache/cord-338889-7hd3iibk.txt txt: ./txt/cord-338889-7hd3iibk.txt summary: 10 Of the 10 standards laid down in this Code, and with which physician-researchers must comply when carrying out experiments on human subjects, standard 5, in particular, has become highly relevant these days due to pressure from influential medical stakeholders, agencies and bioethicists to permit the conduct of controlled human infection studies (CHIs), also labeled human challenge trials (HCTs), or challenge studies (CSs) to possibly shorten the development time of vaccines to protect against Covid-19 caused by the SARS-CoV-2 virus. abstract: The Covid-19 pandemic creates an unprecedented threatening situation worldwide with an urgent need for critical reflection and new knowledge production, but also a need for imminent action despite prevailing knowledge gaps and multilevel uncertainty. With regard to the role of research ethics in these pandemic times some argue in favor of exceptionalism, others, including the authors of this paper, emphasize the urgent need to remain committed to core ethical principles and fundamental human rights obligations all reflected in research regulations and guidelines carefully crafted over time. In this paper we disentangle some of the arguments put forward in the ongoing debate about Covid-19 human challenge studies (CHIs) and the concomitant role of health-related research ethics in pandemic times. We suggest it might be helpful to think through a lens differentiating between risk, strict uncertainty and ignorance. We provide some examples of lessons learned by harm done in the name of research in the past and discuss the relevance of this legacy in the current situation. url: https://www.ncbi.nlm.nih.gov/pubmed/33141289/ doi: 10.1007/s11019-020-09984-x id: cord-301677-b6mnn27h author: Soleimanian, Saeede title: Harnessing Memory NK Cell to Protect Against COVID-19 date: 2020-08-20 words: 9746.0 sentences: 462.0 pages: flesch: 42.0 cache: ./cache/cord-301677-b6mnn27h.txt txt: ./txt/cord-301677-b6mnn27h.txt summary: In this regard, Natural Killer (NK) cells as essential front-line responders to many viral infections in humans have been proposed for a suitable therapeutic approach in severe COVID-19 patients, and several clinical trials have begun (Market et al., 2020) . In this line, Type I IFNs have a critical role in concert with pattern PRR signaling to prime innate and adaptive antiviral responses such as stimulating natural killer (NK) cells, macrophages, and production of proinflammatory cytokines (Samuel, 2001; Murira and Lamarre, 2016) . The detection of both SARS-CoV-2 nucleic acid and specific antibodies to viral proteins have thus far become significant for primary diagnosis infection and immunity in COVID-19 patients, respectively. in a pneumonia model of SARS in mice, mimicking features of the human disease, illustrated that mice depleted of both CD4 and CD8T cells, had the ability to control SARS-CoV replication in the lungs, suggesting an immune mechanism independent of T cells, and a role for innate antiviral response and NK cells, in viral clearance. abstract: The worldwide struggle against the coronavirus disease 2019 (COVID-19) as a public health crisis continues to sweep across the globe. Up to now, effective antiviral treatment against COVID-19 is not available. Therefore, throughout virus infections, a thorough clarification of the virus-host immune system interactions will be most probably helpful to encounter these challenges. Emerging evidence suggests that just like SARS and MERS, COVID-19 primarily suppresses the innate immune system, enabling its stable propagation during the early stage of infection. Consequently, proinflammatory cytokines and chemokines have been increasing during infection progression associated with severe lung pathology. It is imperative to consider hyper inflammation in vaccine designing, as vaccine-induced immune responses must have a protective role against infection without leading to immunopathology. Among the front-line responders to viral infections, Natural Killer (NK) cells have immense therapeutic potential, forming a bridge between innate and adaptive responses. A subset of NK cells exhibits putatively increased effector functions against viruses following pathogen-specific and immunization. Memory NK cells have higher cytotoxicity and effector activity, compared with the conventional NK cells. As a pioneering strategy, prompt accumulation and long‐term maintenance of these memory NK cells could be an efficacious viral treatment. According to the high prevalence of human cytomegalovirus (HCMV) infection in the world, it remains to be determined whether HCMV adaptive NK cells could play a protective role against this new emerging virus. In addition, the new adaptive-like KIR+NKG2C+ NK cell subset (the adaptive-like lung tissue residue [tr]NK cell) in the context of the respiratory infection at this site could specifically exhibit the expansion upon COVID-19. Another aspect of NK cells we should note, utilizing modified NK cells such as allogeneic off-the-shelf CAR-NK cells as a state-of-the-art strategy for the treatment of COVID-19. In this line, we speculate introducing NKG2C into chimeric antigen receptors in NK cells might be a potential approach in future viral immunotherapy for emerging viruses. In this contribution, we will briefly discuss the current status and future perspective of NK cells, which provide to successfully exploit NK cell-mediated antiviral activity that may offer important new tools in COVID-19 treatment. url: https://doi.org/10.3389/fphar.2020.01309 doi: 10.3389/fphar.2020.01309 id: cord-306826-vbfdxoc2 author: Solerte, Sebastiano Bruno title: Dipeptidyl peptidase-4 (DPP4) inhibition in COVID-19 date: 2020-06-06 words: 2251.0 sentences: 112.0 pages: flesch: 41.0 cache: ./cache/cord-306826-vbfdxoc2.txt txt: ./txt/cord-306826-vbfdxoc2.txt summary: CONCLUSIONS: The use of DPP4 inhibitors, such as gliptins, in patients with COVID-19 with, or even without, type 2 diabetes, may offer a simple way to reduce the virus entry and replication into the airways and to hamper the sustained cytokine storm and inflammation within the lung in patients diagnosed with COVID-19 infection. The novel beta-coronavirus 2019 (SARS-CoV-2) has recently emerged as a threat for human kind, causing severe respiratory syndrome , associated with other systemic complications (i.e., intestinal infections, renal and heart failure) and with a relative high mortality [1] . The co-expression of ACE2 and DPP4/CD26 as receptors of spike glycoproteins could hypothesize that different human coronaviruses (CoVs) target similar cell types across different human tissues and explain the presence of similar clinical features in patients infected with different CoVs. In another case, it was shown that DPP4 acted for CoV co-receptor, thus suggesting a potential similar mechanism of entry for SARS-CoV-2 [5] . abstract: AIMS: SARS–CoV-2 causes severe respiratory syndrome (COVID-19) with high mortality due to a direct cytotoxic viral effect and a severe systemic inflammation. We are herein discussing a possible novel therapeutic tool for COVID-19. METHODS: Virus binds to the cell surface receptor ACE2; indeed, recent evidences suggested that SARS–CoV-2 may be using as co-receptor, when entering the cells, the same one used by MERS–Co-V, namely the DPP4/CD26 receptor. The aforementioned observation underlined that mechanism of cell entry is supposedly similar among different coronavirus, that the co-expression of ACE2 and DPP4/CD26 could identify those cells targeted by different human coronaviruses and that clinical complications may be similar. RESULTS: The DPP4 family/system was implicated in various physiological processes and diseases of the immune system, and DPP4/CD26 is variously expressed on epithelia and endothelia of the systemic vasculature, lung, kidney, small intestine and heart. In particular, DPP4 distribution in the human respiratory tract may facilitate the entrance of the virus into the airway tract itself and could contribute to the development of cytokine storm and immunopathology in causing fatal COVID-19 pneumonia. CONCLUSIONS: The use of DPP4 inhibitors, such as gliptins, in patients with COVID-19 with, or even without, type 2 diabetes, may offer a simple way to reduce the virus entry and replication into the airways and to hamper the sustained cytokine storm and inflammation within the lung in patients diagnosed with COVID-19 infection. url: https://doi.org/10.1007/s00592-020-01539-z doi: 10.1007/s00592-020-01539-z id: cord-305745-9lngdjow author: Solnier, Julia title: Flavonoids: A complementary approach to conventional therapy of COVID-19? date: 2020-09-18 words: 9494.0 sentences: 469.0 pages: flesch: 48.0 cache: ./cache/cord-305745-9lngdjow.txt txt: ./txt/cord-305745-9lngdjow.txt summary: Chalcones isolated from Angelica keiskei were shown to inhibit both SARS-CoV proteases PLpro and 3CLpro in enzymatic, FRET-based (Table 2) and molecular docking studies (Park et al. As Table 2 demonstrates, the compounds showed generally higher inhibitory potential against SARS-CoV PLpro than when tested against the other viral proteases using fluorogenic methods, which is likely related to genomic variations in the single amino acid sequences. In particular, herbacetin, quercetin and isobavachalcone (Fig. 3) were identified as promising antiviral leads against SARS-and MERS-CoV based on their broad-spectrum activity against the viral proteases 3CL and PL of both CoVs, the number of relevant literature data, and the availability of the compounds from different plant sources. However, despite some promising inhibitory activities of flavonoids against SARS-and MERS-CoV in vitro, none of these compounds have been tested in vivo using animal and/or human cell models. abstract: COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential. url: https://doi.org/10.1007/s11101-020-09720-6 doi: 10.1007/s11101-020-09720-6 id: cord-279290-wtnnlp4i author: Solorio-Pineda, Saúl title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? date: 2020-09-25 words: 1370.0 sentences: 95.0 pages: flesch: 50.0 cache: ./cache/cord-279290-wtnnlp4i.txt txt: ./txt/cord-279290-wtnnlp4i.txt summary: title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? BACKGROUND: In December 2019, in Wuhan, a new virus emerged, causing severe acute respiratory syndrome (SARS) secondary to infection by a type of coronavirus, causing coronavirus disease (COVID-19). A new virus emerged, causing severe acute respiratory syndrome (SARS) originated in the city of Wuhan, China, in December 2019. [6, 9] We decided to present the following remarkable case from a patient with pituitary tumor apoplexy infected with SARS-CoV-2. Unfortunately, given the patient''s condition and his timely isolation in the coronavirus disease (COVID-19) floor, it was not possible to perform a brain MRI scan. e CNS involvement in COVID-19 infection includes cerebrovascular events due to endothelial dysfunction, with pituitary apoplexy being an unusual presentation, a situation that should be confirmed in the future. Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? abstract: BACKGROUND: In December 2019, in Wuhan, a new virus emerged, causing severe acute respiratory syndrome (SARS) secondary to infection by a type of coronavirus, causing coronavirus disease (COVID-19). The pandemic caused by the new coronavirus has had implications in the central nervous system. COVID-19 is known to be characterized by coagulation activation and endothelial dysfunction, causing ischemic and hemorrhagic vascular syndromes. CASE DESCRIPTION: A 27-year-old male patient case with progressive decrease in visual acuity, associated with respiratory symptoms and intense headache. Multilobar infiltrate with a reticulonodular pattern is evident on chest CT scan. Brain CT scan with pituitary macroadenoma apoplexy was shown. SARS-Cov2 was confirmed, and respiratory support initiated. However, the patient died shortly afterward, secondary to pulmonary complications. CONCLUSION: The angiotensin-converting enzyme (ACE) II receptor is expressed in circumventricular organs and in cerebrovascular endothelial cells, which play a role in vascular autoregulation and cerebral blood flow. For this reason, is rational the hypothesize that brain ACE II could be involved in COVID-19 infection. Underlying mechanisms require further elucidation in the future. url: https://doi.org/10.25259/sni_305_2020 doi: 10.25259/sni_305_2020 id: cord-285490-tpsf05ca author: Solís, José Gabriel title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm date: 2020-07-29 words: 1793.0 sentences: 130.0 pages: flesch: 39.0 cache: ./cache/cord-285490-tpsf05ca.txt txt: ./txt/cord-285490-tpsf05ca.txt summary: title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm He developed acute kidney injury requiring renal replacement therapy without reversibility, despite optimal treatment. 2 We report the case of a patient with confirmed SARS-CoV-2 infection who presented with rhabdomyolysis as a cardinal manifestation, discuss the possible mechanisms, and propose a diagnostic-therapeutic algorithm. Laboratory tests revealed grade 3 acute kidney injury (AKI) with a creatinine level of 11 mg/dL (basal value 0.7 mg/dL); increased blood levels of creatine kinase (CK) (> 400,000 U/L), lactate dehydrogenase (LDH), aspartate aminotransferase, alanine aminotransferase; and electrolyte disturbances with hyperkalemia, hyperphosphatemia, hypocalcemia, and severe metabolic acidosis. The underlying cause of muscle injury must be identified and treated, which is difficult in patients with COVID-19 because there is no specific therapy. Kidney disease is associated with in-hospital death of patients with COVID-19 Acute kidney injury due to rhabdomyolysis and renal replacement therapy: a critical review abstract: COVID-19 represents the greatest health challenge of modern years. The spectrum of illness comprises respiratory and non-respiratory manifestations. We report the case of an adult man with COVID-19 who presented with rhabdomyolysis as a principal extrapulmonary manifestation. Our patient presented with dyspnea, fever, and muscle pain. After a comprehensive approach, the diagnosis of COVID-19 and rhabdomyolysis was made. He developed acute kidney injury requiring renal replacement therapy without reversibility, despite optimal treatment. We performed a literature search for similar cases, discuss the potential mechanisms implied, and propose a diagnostic-therapeutic algorithm. url: https://doi.org/10.4269/ajtmh.20-0692 doi: 10.4269/ajtmh.20-0692 id: cord-321664-3qlfsei6 author: Somsen, G Aernout title: Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission date: 2020-05-27 words: 1244.0 sentences: 59.0 pages: flesch: 55.0 cache: ./cache/cord-321664-3qlfsei6.txt txt: ./txt/cord-321664-3qlfsei6.txt summary: title: Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission Globally, health-care authorities are searching for effective measures to prevent community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, aerosols containing a small concentration of virus in poorly ventilated spaces, combined with low humidity and high temperature, 6 might result in an infectious dose over time. To better understand the spreading of respiratory droplets and possible preventive measures, we analysed droplet production due to coughs and speech by measuring the droplet size distribution, travel distance and velocity, and the airborne time in relation to the level of air ventilation. Although we only studied healthy volunteers and did not study patients with COVID-19 or virus-laden aerosol droplets directly, our data on droplet size distribution and persistence does have implications on requirements to use face masks to prevent virus transmission. The persistence of small respiratory droplets in such poorly ventilated spaces could contribute to the spread of SARS-CoV-2. abstract: nan url: https://api.elsevier.com/content/article/pii/S2213260020302459 doi: 10.1016/s2213-2600(20)30245-9 id: cord-319935-ni6a8vje author: Somsen, G. A. title: Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters date: 2020-10-14 words: 1846.0 sentences: 114.0 pages: flesch: 56.0 cache: ./cache/cord-319935-ni6a8vje.txt txt: ./txt/cord-319935-ni6a8vje.txt summary: To demonstrate the usefulness of our novel method, we perform measurements in typical public spaces that can play a role in aerosol transmission of SARS-CoV-2, each differing in volume, number of people and ventilation rate. Using this easily applicable method, aerosol concentrations can be measured in any public space which is important to determine the risk is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Using the half-times as measured by us, we calculate that the decrease in the number of aerosol particles after these 6 minutes will vary between 50 and 100%, depending on the ventilation method and the size of the public space. Small droplet aerosols in poorly ventilated spaces; the need for specific measures to prevent SARS-CoV-2 transmission abstract: We investigate the role of aerosols in the transmission of SARS-CoV-2 in public spaces. Direct measurement of aerosol concentrations however has proven technically difficult; we propose the use of handheld particle counters as a novel and easily applicable method to measure aerosol concentrations. This allow us to perform measurements in typical public spaces, each differing in volume, number of people and ventilation rate. These data are used to estimate the relation between aerosol persistence time and the risk of infection with SARS-CoV-2. url: http://medrxiv.org/cgi/content/short/2020.10.13.20211839v1?rss=1 doi: 10.1101/2020.10.13.20211839 id: cord-277197-njy99jh4 author: Song, Fang title: COVID‐19: Recommended sampling sites at different stage of the disease date: 2020-04-16 words: 545.0 sentences: 45.0 pages: flesch: 49.0 cache: ./cache/cord-277197-njy99jh4.txt txt: ./txt/cord-277197-njy99jh4.txt summary: At present, it mainly relies on Real‐time RT‐PCR to detect SARS‐CoV‐2 virus nucleic acid collected from the clinical specimens of patients as the standard for diagnosis, discontinuation of quarantine and discharge.(1,2) This article is protected by copyright. 13 Different from the suspected cases with typical clinical characteristics, the diagnosis rate can be improved by detecting the nucleic acid in fecal samples, the latest discharge standards in China still requires only the collection of respiratory specimens 1 . But it has been emphasized in the discharge standard to collect "nasal swab, sputum" and other upper and lower respiratory tract specimens at the same Based on the improvement of clinical symptoms and CT imaging, the guidelines require only two consecutive negative nucleic acid tests (≥24 hours) before discharge can be considered. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan abstract: Coronavirus Disease 2019 (COVID‐19) is mainly an acute respiratory infectious disease caused by a novel coronavirus (officially named Severe acute respiratory syndrome coronavirus 2, SARS‐CoV‐2) in December 2019, which is currently a worldwide pandemic, mainly causes the novel coronavirus pneumonia (NCP). At present, it mainly relies on Real‐time RT‐PCR to detect SARS‐CoV‐2 virus nucleic acid collected from the clinical specimens of patients as the standard for diagnosis, discontinuation of quarantine and discharge.(1,2) This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32297981/ doi: 10.1002/jmv.25892 id: cord-268075-kbislbx0 author: Song, Limin title: Cardiovascular Changes in Patients With COVID-19 From Wuhan, China date: 2020-09-02 words: 4052.0 sentences: 224.0 pages: flesch: 44.0 cache: ./cache/cord-268075-kbislbx0.txt txt: ./txt/cord-268075-kbislbx0.txt summary: Alternatively, ascending aortic dilation and LA enlargement might be present before infection but characterized the patient at risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Epidemiological studies have demonstrated that acute pneumonia is associated with an increased risk for cardiac complications at all levels of infection severity (4) . In this study, we retrospectively collected and analyzed detailed clinical data from patients with laboratory-confirmed COVID-19 who were admitted to the Union Hospital (Wuhan, China). Myocardial injury associated with the SARS-CoV-2 occurred in five of the first 41 patients diagnosed with COVID-19 in Wuhan, which mainly manifested as an increase in high-sensitivity cardiac troponin I levels (2) . In summary, we have shown that hypertension is a common comorbidity among hospitalized patients with COVID-19 in Wuhan, China, and cardiac injury was the most common complication. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China abstract: Background: Coronavirus disease 2019 (COVID-19) is rapidly spreading and resulting in a significant loss of life around the world. However, specific information characterizing cardiovascular changes in COVID-19 is limited. Methods: In this single-centered, observational study, we enrolled 38 adult patients with COVID-19 from February 10 to March 13, 2020. Clinical records, laboratory findings, echocardiography, and electrocardiogram reports were collected and analyzed. Results: Of the 38 patients enrolled, the median age was 68 years [interquartile range (IQR), 55–74] with a slight female majority (21, 55.3%). Nineteen (50.0%) patients had hypertension. Seven (33.3%) had ST-T segment and T wave changes, and four (19%) had sinus tachycardia. Twenty (52.6%) had an increase in ascending aorta (AAO) diameter, 22 (57.9%) had an increase in left atrium (LA) size, and 28 (73.7%) presented with ventricular diastolic dysfunction. Correlation analysis showed that the AAO diameter was significantly associated with C-reactive protein (r = 0.4313) and creatine kinase-MB (r = 0.0414). LA enlargement was significantly associated with C-reactive protein (r = 0.4377), brain natriuretic peptide (r = 0.7612), creatine kinase-MB (r = 0.4940), and aspartate aminotransferase (r = 0.2947). Lymphocyte count was negatively associated with the AAO diameter (r = −0.5329) and LA enlargement (r = −0.3894). Conclusions: Hypertension was a common comorbidity among hospitalized patients with COVID-19, and cardiac injury was the most common complication. Changes in cardiac structure and function manifested mainly in the left heart and AAO in these patients. Abnormal AAO and LA size were found to be associated with severe inflammation and cardiac injury. Alternatively, ascending aortic dilation and LA enlargement might be present before infection but characterized the patient at risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. url: https://www.ncbi.nlm.nih.gov/pubmed/33102532/ doi: 10.3389/fcvm.2020.00150 id: cord-256702-lwxt4587 author: Song, Lingjie title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date: 2020-04-06 words: 2037.0 sentences: 144.0 pages: flesch: 57.0 cache: ./cache/cord-256702-lwxt4587.txt txt: ./txt/cord-256702-lwxt4587.txt summary: title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. Although the nucleic acid test was negative or single-target positive, the low number of white blood cells and lymphocytes in laboratory tests, and GGO in the lungs by CT examination indicated SARS-CoV-2 infection. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. We report the epidemiological history and clinical information of a patient with negative (or single-target positive) SARS-CoV-2 infection with multiple RT-PCR tests. abstract: In 2019, a novel coronavirus (SARS-CoV-2) was first discovered in Wuhan, Hubei, China, causing severe respiratory disease in humans, and has been identified as a public health emergency of international concern. With the spread of the virus, there are more and more false negative cases of RT-PCR nucleic acid detection in the early stage of potential infection. In this paper, we collected the epidemiological history, clinical manifestations, outcomes, laboratory results and images of a SARS-CoV-2 carrier with no significant past medical history. The patient was quarantined because of her colleague had been diagnosed. After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. In addition to coughing up phlegm during her stay in the hospital, she did not develop chills, fever, abdominal pain, diarrhea and other clinical symptoms. Since initial antiviral treatment, the lung lesions were absorbed. But the sputum nucleic acid test was still positive. In combination with antiviral and immune therapy, the patient tested negative for the virus. Notably, SARS-CoV-2 was detected only in the lower respiratory tract samples (sputum) throughout the diagnosis and treatment period. This is a confirmed case of SARS-CoV-2 infection with common symptoms, and her diagnosis has undergone multiple false negatives ,suggesting that it is difficult to identify certain carriers of the virus and that such patients may also increase the spread of the SARS-CoV-2. url: https://doi.org/10.1101/2020.03.31.20045401 doi: 10.1101/2020.03.31.20045401 id: cord-284879-sjkni2uc author: Song, Suk-Kyoon title: IgG Seroprevalence of COVID-19 among Individuals without a History of the Coronavirus Disease Infection in Daegu, Korea date: 2020-07-16 words: 2559.0 sentences: 146.0 pages: flesch: 51.0 cache: ./cache/cord-284879-sjkni2uc.txt txt: ./txt/cord-284879-sjkni2uc.txt summary: METHODS: Serologic testing for immunoglobulin G antibody based on immunochromatographic assay was conducted in 103 patients and 95 guardians aged 18 to 82 years without any history of COVID-19 diagnosis, who visited outpatient clinics of a single university-affiliated hospital from May 25 to June 5, 2020. 4-15 However, a significant fraction of the population has developed antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suggesting that the infection is much more pervasive than implied by the number of confirmed cases. Next, we compared seroprevalence among subgroups stratified by characteristics of study subjects, including age (< 40, 40-59, ≥ 60 years), gender, body mass index (BMI) (< 25, ≥ 25 kg/m 2 ), smoking history (current, previous, never), history of doctor-diagnosed diabetes or hypertension (yes, no), reason for the current hospital visit (patient, guardian), and the presence of COVID-19 confirmed cases among close contacts (yes, no). abstract: BACKGROUND: Seroprevalence studies of coronavirus disease 2019 (COVID-19) from many countries have shown that the number of undiagnosed missing cases is much larger than that of confirmed cases, irrespective of seroprevalence levels. Considering the strategy of Korea entailing massive testing and contact tracing from the beginning of epidemic, the number of undiagnosed missing cases in Korea may be negligible. This study was conducted to estimate the seroprevalence of COVID-19 among individuals who were never diagnosed with COVID-19 in Daegu, the epicenter of COVID-19 epidemic in Korea. METHODS: Serologic testing for immunoglobulin G antibody based on immunochromatographic assay was conducted in 103 patients and 95 guardians aged 18 to 82 years without any history of COVID-19 diagnosis, who visited outpatient clinics of a single university-affiliated hospital from May 25 to June 5, 2020. RESULTS: The estimated seroprevalence was 7.6% (95% confidence interval, 4.3%–12.2%) with 15 positive cases. Among them, only one had a polymerase chain reaction (PCR)-confirmed case among their close contacts and 13 did not experience COVID-19-related symptoms. Seroprevalence was similar between patients and guardians. Based on this figure, the number of undiagnosed missing cases in Daegu was estimated to be a dozen times more than the number of confirmed cases based on PCR testing. CONCLUSION: Despite the limitation of a small and unrepresentative sample, this is the first study on seroprevalence of COVID-19 in Korea. Our study suggested that the number of undiagnosed missing cases was substantial even with the stringent strategy adopted in Korea, similar to that of other countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32715672/ doi: 10.3346/jkms.2020.35.e269 id: cord-305858-gp1u4kh7 author: Song, Xiang title: High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date: 2020-07-19 words: 4896.0 sentences: 268.0 pages: flesch: 49.0 cache: ./cache/cord-305858-gp1u4kh7.txt txt: ./txt/cord-305858-gp1u4kh7.txt summary: To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. To determine whether platelets were directly targeted by SARS-CoV-2 or trigged by viral inflammatory reactions, we examined the ACE2 expression on the highly-purified CD41b + CD42a + platelets from human peripheral blood ( Figure 3A Our previous work established that platelets could release mitochondria contributing to the immune modulation and islet b-cell regeneration [13] . Thus, the virus-infected alveolar macrophages play a critical role in the pathogenesis of COVID-19 and SARS [28] [29] [30] and may recruit the lung infiltration of additional immune cells through predominantly releasing cytokines and chemokines [31, 32] , resulting in pulmonary edema and hypoxemia: the hallmark of acute respiratory distress syndrome (ARDS) ( Figure 6 ). abstract: Angiotensin-converting enzyme-2 (ACE2) has been recognized as the binding receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that infects host cells, causing the development of the new coronavirus infectious disease (COVID-19). To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. Flow cytometry demonstrated that there was little to no expression of ACE2 on most of the human peripheral blood-derived immune cells including CD4+ T, CD8+ T, activated CD4+ T, activated CD8+ T, CD4+CD25+CD127low/− regulatory T cells (Tregs), Th17 cells, NKT cells, B cells, NK cells, monocytes, dendritic cells (DCs), and granulocytes. Additionally, there was no ACE2 expression (< 1%) found on platelets. Compared with interleukin-4-treated type 2 macrophages (M2), the ACE2 expression was markedly increased on the activated type 1 macrophages (M1) after the stimulation with lipopolysaccharide (LPS). Immunohistochemistry demonstrated that high expressions of ACE2 were colocalized with tissue macrophages, such as alveolar macrophages found within the lungs and Kupffer cells within livers of mice. Flow cytometry confirmed the very low level of ACE2 expression on human primary pulmonary alveolar epithelial cells. These data indicate that alveolar macrophages, as the frontline immune cells, may be directly targeted by the SARS-CoV-2 infection and therefore need to be considered for the prevention and treatment of COVID-19. url: https://doi.org/10.1101/2020.07.18.210120 doi: 10.1101/2020.07.18.210120 id: cord-320632-369kax2m author: Song, Yang title: COVID-19 Treatment: Close to a Cure? – A Rapid Review of Pharmacotherapies for the Novel Coronavirus date: 2020-07-04 words: 5659.0 sentences: 335.0 pages: flesch: 45.0 cache: ./cache/cord-320632-369kax2m.txt txt: ./txt/cord-320632-369kax2m.txt summary: The selection of medications in this review is based the 7 th edition of COVID-19 diagnosis and treatment guideline issued by the National Health Commission (NHC) of the People''s Republic of China ( Table 2) and relevant clinical studies. In a phase 2 open-label COVID-19 trial, which enrolled 127 patients from 6 Hong Kong hospitals, Hung and his colleagues compared triple therapy (lopinavir/ritonavir 400/100 mg PO every 12 hours, ribavirin 400 mg PO every 12 hours, and interferon β-1b 8 million IU SQ on alternative days) with a control group of LPV/r [33] . During the 2013 SARS epidemic, observational studies and case reports described IVIG for the treatment of critically ill patients in combination with antiviral therapies. In a COVID-19 case series study, the combination of umifenovir, lopinavir/ritonavir and traditional Chinese medicine alleviated pneumonia symptoms in all four patients and decreased viral load to undetectable in two [68] . abstract: Currently, there is no approved therapy for COVID-19. The World Health Organization therefore endorse supportive care only. However, frontline clinicians and researchers have been experimenting with several virus-based and host-based therapeutics since the outbreak in China. China's National Health Commission has issued the first COVID-19 Treatment Guideline with therapy suggestions (7(th) edition attached) which inspired following clinical studies worldwide. Major therapeutics are evaluated in this review. Key evidence from in vitro researches, animal models and clinical researches in emerging coronaviruses are examined. Antiviral therapies remdesivir, lopinavir/ritonavir and umifenovir, if considered, could be initiated before the peak of viral replication for optimal outcomes. Ribavirin may be beneficial as an add-on therapy and is ineffective as a monotherapy. Corticosteroids use should be limited to indicating comorbidities. IVIG is not recommended due to lack of data in COVID-19. Xuebijing may benefit patients with complications of bacterial pneumonia or sepsis. The efficacy of interferon is unclear due to conflicting outcomes in coronavirus studies. Chloroquine and hydroxychloroquine have shown in vitro inhibition of SARS-CoV-2, and the studies on clinical efficacy and whether the benefits outweigh the risk of dysrhythmias remain inconclusive. For patients who developed cytokine release syndrome, interleukin-6 inhibitors may be beneficial. url: https://www.ncbi.nlm.nih.gov/pubmed/32634603/ doi: 10.1016/j.ijantimicag.2020.106080 id: cord-325045-ak7rouhb author: Sotgiu, Giovanni title: Advanced forecasting of SARS‐CoV‐2‐related deaths in Italy, Germany, Spain, and New York State date: 2020-05-11 words: 718.0 sentences: 37.0 pages: flesch: 52.0 cache: ./cache/cord-325045-ak7rouhb.txt txt: ./txt/cord-325045-ak7rouhb.txt summary: Based on this model, we aimed at predicting SARS-Cov-2-related mortality in Italy, 7 Germany, 8 Spain, 9 and New York State. 10 To validate the model, we calculated R 2 correlations for Italy (0.995), Germany (0.996), Spain (0.988), and New York State (0.998) after 30, 18, 11, and 10 days of prediction, respectively, thus confirming the reliability of our modeling approach during the first month of this outbreak in each of these countries ( Figure 1A) . Instead, the expected SARS-Cov-2related mortality is more closely related to early events within the first days of the outbreak and to timing to regional/national interventions (eg, social distancing, confinement), which suggests that superspreading events (eg Lombardia region, Italy) deeply impact on the magnitude of the curve and, in turn, on the number of deaths. Figure 1B illustrates the curves of the expected deaths based on daily peak after 28 and 21 days in Italy, Germany, Spain, and New York State. abstract: nan url: https://doi.org/10.1111/all.14327 doi: 10.1111/all.14327 id: cord-261921-c97ygxq2 author: Souders, Colby P. title: Considerations for Bedside Urologic Procedures in Patients with Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-04-24 words: 1826.0 sentences: 94.0 pages: flesch: 42.0 cache: ./cache/cord-261921-c97ygxq2.txt txt: ./txt/cord-261921-c97ygxq2.txt summary: METHODS: Urologic trainees and attending physicians at our institution, who are familiar with existing safety recommendations and guidelines regarding the care of infected patients, were queried regarding their experiences to determine an expert consensus on best practices for bedside procedures for SARS-CoV-2 positive patients. RESULTS: Our team developed the following general recommendations for urologic interventions on SARS-CoV-2 positive patients: maximize use of telehealth (even for inpatient consults), minimize in-room time, use personal protective equipment appropriately, enlist a colleague to assist, and acquire all supplies that may be needed and maintain them outside the room. Our aim is to share our experiences performing bedside urologic procedures on SARS-CoV-2positive patients and offer considerations to maximize the safety of the patients and providers involved and conserve supplies while maintaining a high standard of care. Outlined above are our experiences with inpatient consultations and bedside procedures in SARS-CoV-2 patients and how we have attempted to address urologic challenges that have emerged with this pandemic. abstract: OBJECTIVE: To provide guidance when performing bedside urologic procedures on SARS-CoV-2 positive patients and offer considerations to maximize the safety of the patients and providers, conserve supplies, and provide optimal management of urologic issues. METHODS: Urologic trainees and attending physicians at our institution, who are familiar with existing safety recommendations and guidelines regarding the care of infected patients, were queried regarding their experiences to determine an expert consensus on best practices for bedside procedures for SARS-CoV-2 positive patients. RESULTS: Our team developed the following general recommendations for urologic interventions on SARS-CoV-2 positive patients: maximize use of telehealth (even for inpatient consults), minimize in-room time, use personal protective equipment appropriately, enlist a colleague to assist, and acquire all supplies that may be needed and maintain them outside the room. Detailed recommendations were also developed for difficult urethral catheterization, bedside cystoscopy, incision and drainage of abscesses, and gross hematuria/clot irrigations. CONCLUSIONS: As patients hospitalized with SARS-CoV-2 infection are predominantly men over 50 years old, there are significant urologic challenges common in this population that have emerged with this pandemic. While there is tremendous variation in how different regions have been affected, the demographics of SARS-CoV-2 mean that urologists will continue to have a unique role in helping to manage these patients. Here, we summarize recommendations for bedside urologic interventions specific to SARS-CoV-2 positive patients based on experiences from a large metropolitan hospital system. Regulations and requirements may differ on an institutional basis, so these guidelines are intended to augment specific local protocols. url: https://www.ncbi.nlm.nih.gov/pubmed/32339561/ doi: 10.1016/j.urology.2020.04.066 id: cord-339817-qqitdrz6 author: Sousa Gonçalves, Catarina title: Erythematous Papular Rash: A Dermatological Feature of COVID-19 date: 2020-06-10 words: 871.0 sentences: 56.0 pages: flesch: 44.0 cache: ./cache/cord-339817-qqitdrz6.txt txt: ./txt/cord-339817-qqitdrz6.txt summary: COVID-19 is the clinical expression of the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection. The cutaneous clinical spectrum is wide and includes maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, and pityriasis rosea-like, violaceous and pustular lesions. Clinicians should be aware of patients presenting only with cutaneous symptoms, which in some cases are the initial clinical feature of COVID-19. The clinical presentation of SARS-CoV-2 infection is called COVID-19 and has a wide spectrum of clinical manifestations. As with other viral infections, SARS-CoV-2 may also have cutaneous manifestations. In the absence of other possible syndromes and diseases, the skin rash was very likely due to SARS-CoV-2 infection. The cutaneous manifestations include maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, pityriasis rosea-like and violaceous lesions, and vesicular and maculopapular pustular lesions (as in other viral infections). abstract: COVID-19 is the clinical expression of the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection. Most patients have mild symptoms, but a significant proportion have severe or critical disease, which can include cardiac injury, sepsis, acute kidney failure and respiratory failure. It is also worth highlighting the increasing number of reported COVID-19 cases with dermatological disease/manifestations. The cutaneous clinical spectrum is wide and includes maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, and pityriasis rosea-like, violaceous and pustular lesions. Until the physiological mechanism is fully understood, it is important to describe these manifestations, which could help identify a typical pattern. This report describes a cutaneous manifestation in a COVID-19 patient. LEARNING POINTS: SARS-CoV-2 presents with multiple symptoms with the dermatological manifestations currently under-recognized. Clinicians should be aware of patients presenting only with cutaneous symptoms, which in some cases are the initial clinical feature of COVID-19. url: https://doi.org/10.12890/2020_001768 doi: 10.12890/2020_001768 id: cord-267402-kca05rvz author: South, Kieron title: Preceding infection and risk of stroke: An old concept revived by the COVID-19 pandemic date: 2020-07-24 words: 6248.0 sentences: 335.0 pages: flesch: 41.0 cache: ./cache/cord-267402-kca05rvz.txt txt: ./txt/cord-267402-kca05rvz.txt summary: What follows herein is a detailed summary of the current literature surrounding COVID-19, encompassing the immune and inflammatory responses to infection, thrombotic manifestations and vascular consequences of infection with a focus on possible mechanisms by which these elements may contribute to acute stroke events. 89 This is not the case in COVID-19 (and the previous SARS outbreak) and a recent retrospective cohort study has suggested an incidence of stroke 7-8 times higher in patients hospitalized with COVID-19 infection compared with those hospitalized by influenza, 90 supporting the possibility of a SARS-CoV-2-driven hyper-coagulant state. [91] [92] [93] Obesity, in particular, is emerging as a prominent risk factor in the development of severe COVID-19 disease and is generally associated with increased incidence and increased severity of respiratory viral infection. Notably, the cytokine IL-33 is persistently elevated in obese individuals and is capable of stimulating endothelial cells to release pro-coagulant tissue factor 97 which may expose them to more severe COVID-19 disease and/or stroke. abstract: Anecdotal reports and clinical observations have recently emerged suggesting a relationship between COVID-19 disease and stroke, highlighting the possibility that infected individuals may be more susceptible to cerebrovascular events. In this review we draw on emerging studies of the current pandemic and data from earlier, viral epidemics, to describe possible mechanisms by which SARS-CoV-2 may influence the prevalence of stroke, with a focus on the thromboinflammatory pathways, which may be perturbed. Some of these potential mechanisms are not novel but are, in fact, long-standing hypotheses linking stroke with preceding infection that are yet to be confirmed. The current pandemic may present a renewed opportunity to better understand the relationship between infection and stroke and possible underlying mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/32618498/ doi: 10.1177/1747493020943815 id: cord-314229-9k2dd95b author: Spaccaferri, G. title: Cas groupés d’infections au nouveau coronavirus (SARS-CoV-2) aux Contamines-Montjoie, Haute-Savoie, janvier–février 2020 date: 2020-09-30 words: 1971.0 sentences: 212.0 pages: flesch: 69.0 cache: ./cache/cord-314229-9k2dd95b.txt txt: ./txt/cord-314229-9k2dd95b.txt summary: Matériels et méthodes Un cas possible était défini comme tout patient présentant des signes cliniques d''infection respiratoire aiguë et ayant un lien avec le cas index ou avec un cas confirmé lié à ce cas index ; un cas confirmé était un cas possible avec un prélèvement positif par RT-PCR à SARS-CoV-2. Cinq autres touristes anglais ayant séjourné dans le chalet après le départ du cas index ont été en contact avec les cas confirmés symptomatiques : l''un d''eux a été confirmé positif à SARS-CoV-2 le 15/02, traduisant une seconde chaîne de transmission au sein du chalet ; aucun des 6 cas confirmés en France ne présentaient alors de signe de gravité. Introduction Peu de cas de COVID-19 chez des patients infectés par le VIH ont été rapportés dans la littérature. abstract: Introduction Le 7/02/2020, Santé publique France a été informée via European Early Warning and Response System (EWRS) d’un cas confirmé d’infection au nouveau coronavirus (SARS-CoV-2) chez un anglais infecté à Singapour. Ce cas index était symptomatique durant son séjour en Haute-Savoie du 24 au 28/01 où il a résidé dans 2 logements successifs. Il ne s’est signalé qu’après son retour en Angleterre, où le diagnostic de COVID-19 a été confirmé. Matériels et méthodes Un cas possible était défini comme tout patient présentant des signes cliniques d’infection respiratoire aiguë et ayant un lien avec le cas index ou avec un cas confirmé lié à ce cas index ; un cas confirmé était un cas possible avec un prélèvement positif par RT-PCR à SARS-CoV-2. Les cas confirmés ont été interrogés par Santé publique France et l’Agence régionale de santé pour documenter les caractéristiques cliniques et identifier leurs contacts durant leur période symptomatique. Les sujets contacts identifiés ont été interrogés pour évaluer leur niveau d’exposition permettant de les classer en 3 catégories de risque (modéré/élevé, faible et négligeable) puis de leur transmettre les consignes (adaptées à leur catégorie de risque) d’isolement et de surveillance de leur état de santé. Résultats Le cas index a séjourné dans un chalet avec 10 autres touristes anglais et une famille de 5 anglais (2 adultes et 3 enfants) résidant en France dans un autre appartement de ce chalet. Parmi ces 16 personnes, 12 ont été testées positives pour le SARS-CoV-2 : 6 en Angleterre (dont le cas index), 5 en France (dont un enfant) et 1 en Espagne, soit un taux d’attaque global de 75 %. Cinq autres touristes anglais ayant séjourné dans le chalet après le départ du cas index ont été en contact avec les cas confirmés symptomatiques : l’un d’eux a été confirmé positif à SARS-CoV-2 le 15/02, traduisant une seconde chaîne de transmission au sein du chalet ; aucun des 6 cas confirmés en France ne présentaient alors de signe de gravité. Au 16/02, 169 sujets contacts ont été recensés dont 70 ont rapporté des symptômes et classés comme cas possibles : 67 ont été testés négatifs. Parmi ces contacts, 46 % étaient en lien avec trois écoles et un club sportif fréquentés par le cas pédiatrique confirmé. Conclusion Il s’agit du premier cluster large documenté en France qui aura été remarquable par le nombre élevé de cas dans l’environnement confiné du chalet (au 16/02, n =13 : 1 cas index, 11 cas secondaires et 1 cas tertiaire), le nombre important de sujets contacts suivis, et son caractère international (3 pays concernés). url: https://www.sciencedirect.com/science/article/pii/S0399077X20303061 doi: 10.1016/j.medmal.2020.06.142 id: cord-274510-fo7p98np author: Spadera, Lucrezia title: Potential Role of GcMAF in suppressing the severity of COVID-19-induced immune responses: lesson learned from HIV date: 2020-09-24 words: 4050.0 sentences: 217.0 pages: flesch: 40.0 cache: ./cache/cord-274510-fo7p98np.txt txt: ./txt/cord-274510-fo7p98np.txt summary: Based on the aforementioned findings and on documented analogies between SARS-CoV-2 and HIV [13] , we hypothesized that the reduced conversion activity of the Gc protein (human groupspecific component (Gc)) into the macrophage activating factor (MAF) could have a key role in the dysregulate immune response induced by SARS-CoV-2, just like for HIV infected patients [14] [15] . In particular, based on their antiviral activity [68] , chloroquine and hydroxychloroquine, initially conceived as antimalarial therapeutics, were proposed to treat patients hospitalized with COVID-19, better if associated to azithromycin, showing promising efficacy in "inhibiting the exacerbation of pneumonia, improving lung imaging findings, promoting a virus negative conversion and shortening the disease course" [69] [70] . So, in sight of this, given its multifunctional properties, we believe that GcMAF could have a very important role in the pathophysiology of organ damage induced by SARS-CoV-2, providing explanations which are consistent with the clinical, radiological and histopathological findings observed in patients with COVID-19. Effects of vitamin D(3)-binding protein-derived macrophage activating factor (GcMAF) on angiogenesis abstract: nan url: https://www.sciencedirect.com/science/article/pii/S030698772031392X?v=s5 doi: 10.1016/j.mehy.2020.110293 id: cord-281500-5mm1nnwv author: Spadera, Lucrezia title: Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey date: 2020-08-04 words: 3619.0 sentences: 184.0 pages: flesch: 51.0 cache: ./cache/cord-281500-5mm1nnwv.txt txt: ./txt/cord-281500-5mm1nnwv.txt summary: The questionnaire was composed of five sections: (a) respondents'' workplace, age, and sex of the patient; (b) general information about the risk of exposure to COVID-19, asking to specify if the patient is a healthcare professional; (c) clinical information: onset of symptoms, grade of olfactory loss (OL) with three subjective levels (mild, moderate, and severe/complete), presence or absence of: ageusia, hypogeusia and/or dysgeusia gathered together under the name of "taste symptoms"; nasal discharge and/or congestion, other accompanying symptoms (e.g., fever, fatigue, dry cough, dyspnoea, and myalgia), comorbidities and complications; d) execution and results of nasopharyngeal (NP)/oropharyngeal (OP) swab; e) short description about the clinical case. The mean time of SOL onset before or after the first typical COVID-19 symptom (fever, dry cough, and dyspnoea) was 2.4 days (SD ± 2.7); anosmia/hyposmia occurred as the first symptom in 46.7% of cases, as sole symptom in 16.7% of cases or in association with other clinical manifestations in 31.2% of patients. abstract: PURPOSE: The presence of many asymptomatic COVID-19 cases may increase the risks of disease dissemination, mainly for physicians. There are numerous reports on the frequent findings of sudden anosmia or hyposmia, before or at the same time of the typical COVID-19 symptoms onset. The aim of this study was to verify the association of olfactory impairment and COVID-19, providing a basis for subsequent research in the field of COVID-19 clinical heterogeneity. METHODS: We developed a 15-item online questionnaire on “Sudden Olfactory Loss (SOL) and COVID-19” that was administered during March 2020 to Italian general practitioners registered to a social media group. RESULTS: One hundred and eighty responses were received. SOL was identified as a significant sign of infection in COVID-19 patients, mainly aged between 30 and 40 years, even in the absence of other symptoms. SOL was present as an initial symptom in 46.7% of subjects, and in 16.7%, it was the only symptom. Among the COVID-19 confirmed cases, SOL occurred as the only symptom in 19.2% of patients. CONCLUSION: SOL could represent a possible early symptom in otherwise asymptomatic COVID-19 subjects. Subjects affected by SOL should be considered as potential COVID-19 cases. LEVEL OF EVIDENCE: 4. url: https://www.ncbi.nlm.nih.gov/pubmed/32749606/ doi: 10.1007/s00405-020-06252-9 id: cord-294498-fv545rfa author: Spiegel, Martin title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein date: 2004-07-31 words: 1276.0 sentences: 83.0 pages: flesch: 59.0 cache: ./cache/cord-294498-fv545rfa.txt txt: ./txt/cord-294498-fv545rfa.txt summary: title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein In this study, we demonstrated that multiplication of SARS-CoV in cell culture can be strongly inhibited by pretreatment with interferon-beta. In this study, we investigated the potential of different IFNs to inhibit replication of SARS-CoV in cell culture and determined whether the human MxA protein contributes to the antiviral effect of type I IFNs. African green monkey kidney (Vero) cells were grown in Dulbecco''s modified Eagle''s medium containing 10% fetal calf serum. We investigated the inhibitory effect of type I and II IFNs on SARS-CoV multiplication in cell culture. Therefore, we tested growth of SARS-CoV in Vero cell lines which stably express MxA (Frese et al., 1995) . Thus, the search for antiviral effects against SARS-CoV should focus on other IFN-induced proteins such as PKR or RNase L. abstract: Abstract Severe acute respiratory syndrome (SARS) is caused by a novel coronavirus termed SARS-CoV. No antiviral treatment has been established so far. Interferons are cytokines which induce the synthesis of several antivirally active proteins in the cell. In this study, we demonstrated that multiplication of SARS-CoV in cell culture can be strongly inhibited by pretreatment with interferon-beta. Interferon-alpha and interferon-gamma, by contrast, were less effective. The human MxA protein is one of the most prominent proteins induced by interferon-beta. Nevertheless, no interference with SARS-CoV replication was observed in Vero cells stably expressing MxA. Therefore, other interferon-induced proteins must be responsible for the strong inhibitory effect of interferon-beta against SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/15135736/ doi: 10.1016/j.jcv.2003.11.013 id: cord-320729-imyfo83x author: Spiga, Ottavia title: Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein date: 2003-10-10 words: 2919.0 sentences: 122.0 pages: flesch: 50.0 cache: ./cache/cord-320729-imyfo83x.txt txt: ./txt/cord-320729-imyfo83x.txt summary: The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. After sequence alignment of SARS S protein (SwissProt Accession Number P59594) with the corresponding ones from human and canine coronaviruses, model building of S1 and S2 subunits was obtained by using the latter two pdb files and shuffled PsiPred runs [13] , with subsequent manual optimisation to enhance the overlapping between the predicted and observed secondary structure elements. As a final remark, it should be underlined that the consistent series of structural features, exhibited by the proposed models for the S1 and S2 subunits of the SARS_CoV spike protein, supports their reliability as a possible rational starting point for anti-viral drug design. abstract: The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. An indirect search for a protein structure to be used as a template for 3D modelling has been performed on the basis of the genomic organisation similarity generally exhibited by coronaviruses. The crystal structure of Clostridium botulinum neurotoxin B appeared to be structurally adaptable to human and canine coronavirus spike protein sequences and it was successfully used to model the two subunits of SARS coronavirus spike glycoprotein. The overall shape and the surface hydrophobicity of the two subunits in the obtained models suggest the localisation of the most relevant regions for their activity. url: https://www.sciencedirect.com/science/article/pii/S0006291X03017340 doi: 10.1016/j.bbrc.2003.08.122 id: cord-278453-ogbmaw3o author: Spiller, Tobias R. title: Development of health care workers'' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies date: 2020-08-13 words: 1502.0 sentences: 101.0 pages: flesch: 58.0 cache: ./cache/cord-278453-ogbmaw3o.txt txt: ./txt/cord-278453-ogbmaw3o.txt summary: title: Development of health care workers'' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies BACKGROUND: Virus outbreaks such as the current SARS-CoV-2 pandemic are challenging for health care workers (HCWs), affecting their workload and their mental health. Since both, workload and HCW''s well-being are related to the quality of care, continuous monitoring of working hours and indicators of mental health in HCWs is of relevance during the current pandemic. METHODS: We conducted two cross-sectional online studies among Swiss HCWs assessing working hours, depression, anxiety, and burnout. With this study, we aimed to assess changes in working hours and mental health (assessed as symptoms of anxiety, depression, and burnout) in Swiss HCWs at the height of the SARS-CoV-2 pandemic (T1) and again after its flattening (T2). In the conducted network analyses burnout and anxiety were both independently related to lower perceived support by the employer in both studies, a well-described association also in non-pandemic contexts (Shanafelt & Noseworthy, 2017) . abstract: BACKGROUND: Virus outbreaks such as the current SARS-CoV-2 pandemic are challenging for health care workers (HCWs), affecting their workload and their mental health. Since both, workload and HCW's well-being are related to the quality of care, continuous monitoring of working hours and indicators of mental health in HCWs is of relevance during the current pandemic. The existing investigations, however, have been limited to a single study period. We examined changes in working hours and mental health in Swiss HCWs at the height of the pandemic (T1) and again after its flattening (T2). METHODS: We conducted two cross-sectional online studies among Swiss HCWs assessing working hours, depression, anxiety, and burnout. From each study, 812 demographics-matched participants were included into the analysis. Working hours and mental health were compared between the two samples. RESULTS: Compared to prior to the pandemic, the share of participants working less hours was the same in both samples, whereas the share of those working more hours was lower in the T2 sample. The level of depression did not differ between the samples. In the T2 sample, participants reported more anxiety, however, this difference was below the minimal clinically important difference. Levels of burnout were slightly higher in the T2 sample. CONCLUSIONS: Two weeks after the health care system started to transition back to normal operations, HCWs' working hours still differed from their regular hours in non-pandemic times. Overall anxiety and depression among HCWs did not change substantially over the course of the current SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32787976/ doi: 10.1017/s0033291720003128 id: cord-275784-n6jv72l7 author: Spina, Alfio title: The Management Of Neurosurgical Patients During The Covid-19 Pandemic date: 2020-04-30 words: 2228.0 sentences: 131.0 pages: flesch: 45.0 cache: ./cache/cord-275784-n6jv72l7.txt txt: ./txt/cord-275784-n6jv72l7.txt summary: An adequate management protocol can reduce hospital viral spread, improving safety both for patients and healthcare professionals. 1 The management of an ever-increasing number of patients, particularly those suffering from coronavirus disease 2019 (COVID-19) pneumonia has deeply affected the organization of healthcare facilities. 11 In a single-center Chinese case series of 138 hospitalized patients, presumed hospitalrelated infection of COVID-19 was suspected in 41% of patients, with a reported mortality of 4.3% and an intensive care unit admission rate of 26%. 12 Furthermore, COVID-19 transmission rate to healthcare worker was reported up to 20% 13 These data suggest that, inadequate hospital setting may represent a relevant route of SARS-CoV-2 spread both for patients and healthcare professionals. Whenever possible, elective surgery for confirmed cases (i.e. Group 1) should be rescheduled, because of this class of patients show higher risks of intensive care need and death. abstract: ABSTRACT The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is, to date, the major challenge for healthcare systems worldwide. Hospital represents one of main vector amplifying the spread of the disease among both patients and healthcare professionals. Adequate department organization is pivotal to reduce hazards while still ensuring the highest quality of care. In this document we aim to share the recent experience of a Neurosurgery department located in one of the first and largest coronavirus disease 2019 (COVID-19) pandemic epicenters. A review of the available literature was also performed. Case selection, operating room and postoperative management of neurosurgical patients were discussed. COVID-19 pandemic has upset healthcare organizations, requiring a deep reorganization in many respects. An adequate management protocol can reduce hospital viral spread, improving safety both for patients and healthcare professionals. url: https://api.elsevier.com/content/article/pii/S1878875020308706 doi: 10.1016/j.wneu.2020.04.161 id: cord-269902-sbp18486 author: Springer, Steffen title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin date: 2020-05-06 words: 790.0 sentences: 54.0 pages: flesch: 63.0 cache: ./cache/cord-269902-sbp18486.txt txt: ./txt/cord-269902-sbp18486.txt summary: title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin tigris) in the Bronx Zoo were reported [Gollakner & Capua, 2020] , corresponding peaks were revealed in search queries by Google Trends, in particular for the unusual transmission to lions and tigers (figure 1). For the Pearson correlation coefficient, a high correlation between the search terms "CoViD-19" and "tiger" (r = 0.669, p < 0.05) was found for the period from 1 st January 2020 to 24 th April 2020. For the search term "palm civet" a low Pearson correlation coefficient was found (r=0.148; p < 0.05). Our data support that the main interest of the population is currently rather in the medical therapeutic direction and, apart from anecdotal individual reports (e.g. Bronx Zoo cats), there is less interest in possible virus carriers or the animal origin and reservoir. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0889159120307820?v=s5 doi: 10.1016/j.bbi.2020.05.005 id: cord-338544-eph89g47 author: Spuntarelli, Valerio title: COVID-19: is it just a lung disease? A case-based review date: 2020-07-28 words: 2279.0 sentences: 142.0 pages: flesch: 44.0 cache: ./cache/cord-338544-eph89g47.txt txt: ./txt/cord-338544-eph89g47.txt summary: COVID-19 pandemic reached 3.78 million confirmed reported cases worldwide, and it is generally associated to the acronym that precedes its name: severe acute respiratory syndrome (SARS). A prospective study investigating left ventricular performance in 46 patients with severe acute respiratory syndrome showed subclinical diastolic impairment without systolic involvement [3] . Pathological findings of COVID-19 associated with acute respiratory distress syndrome showed few interstitial mononuclear inflammatory infiltrates, but no other substantial damage in the heart tissue [7] . A case report highlights myocarditis as a complication associated with COVID-19, even without symptoms and signs of interstitial pneumonia in an otherwise healthy 53-year-old white woman [8] . The authors concluded that the presence of the characteristic features of symmetric, multifocal lesions with thalamic involvement suggests that this is a case of acute necrotizing hemorrhagic encephalopathy associated with COVID-19. Guillain Barre syndrome associated with COVID-19 infection: a case report abstract: Due to its extreme virulence, COVID-19 virus has rapidly spread, developing a severe pandemic. SARS-COV-2 mostly affected the respiratory tract, causing a severe acute lung failure. Although the infection of airways, COVID-19 can be associated with chronic and systemic damages still not so much known. The purpose of this research is to collect recent evidence in literature about systemic diseases caused by COVID-19. The format of the present article has features of a systematic case-based review (level of evidence), and it is structured as a case series report (patients of our COVID-19 Medicine Ward have been selected as cases). Data for this review have been selected systematically, taking evidence only from indexed journals and databases: PubMed, Scopus, MEDLINE, and Cochrane systems. Papers chosen included systematic reviews, case series, clinical cases, meta-analysis studies, and RCTs. We start collecting studies since 2003. The main keywords used were “COVID-19” “OR” “SARS” “OR” “SARS – COV 2” “AND” “systemic disease” / “nephropathy” / “cardiac pathology” / “central nervous system.” Clinical cases belong to our COVID-19 Medicine Ward. One of the most severe COVID-19 clinical presentations includes cardiovascular problems, like myocarditis, pericarditis, and acute hearth failure. Cytokine release syndrome caused by COVID-19 develops severe acute kidney failure. It is still unknown the way coronavirus damages the liver, brain, and reproductive system. Considering the majority of the new studies about this pathology, it issues that COVID-19 is considered to be a multi-organ disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32838177/ doi: 10.1007/s42399-020-00418-6 id: cord-299635-bxdf27sv author: Squire, M. M. title: Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions date: 2020-08-24 words: 5088.0 sentences: 317.0 pages: flesch: 47.0 cache: ./cache/cord-299635-bxdf27sv.txt txt: ./txt/cord-299635-bxdf27sv.txt summary: The objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. Hence, hospital operations require the assessment of energy efficiency when evaluating Coronavirus Disease 2019 (COVID19) intervention measures, due to COVID-19 being caused by the Severe Acute Respiratory Disease Coronavirus-2 (SARS-CoV-2). As potential infection control interventions for COVID-19 are considered, information that pertains to energy consumption at hospitals provides additional context on costs related to implementation of mitigation strategies for person-to-person transmission, as well as environmental contamination. This paper evaluates the energy implications and impact of NP and XP-UV infection control measures on decreasing secondary transmission of SARS-CoV-2 in acute care hospitals. 21.20178855 doi: medRxiv preprint This study seamlessly combines projections of COVID-19 hospitalizations, evaluation of energy use, and the impact of infection control measures among three different hospital sizes. abstract: The objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. The intervention control measures evaluated include use of negative pressure (NP) treatment rooms and xenon pulsed ultraviolet (XP-UV) infection control equipment. After projecting COVID-19 hospitalizations, a Hospital Energy Model and Infection De-escalation Models are applied to quantify increases in energy demand and reductions in secondary infections. The scope of the interventions consisted of implementing NP in 11, 22, and 44 rooms (at small, medium, and large hospitals) while the XP-UV equipment was used eight, nine, and ten hours a day, respectively. The annum kilowatt-hours (kWh) for NP (and costs were at $0.1015 per kWh) were 116,700 ($11,845), 332,530 ($33,752), 795,675 ($80,761) for small, medium, and large hospitals ($1,077, $1,534, $1,836 added annum energy cost per NP room). For XP-UV, the annum kilowatt-hours and costs were 438 ($45), 493 ($50), 548 ($56) for small, medium, and large hospitals. There are other initial costs associated with the purchase and installation of the equipment, with XP-UV having a higher initial cost. XP-UV had a greater reduction in secondary COVID-19 infections in large and medium hospitals. NP rooms had a greater reduction in secondary SARS-CoV-2 transmission in small hospitals. Early implementation of interventions can result in realized cost savings through reduced hospital-acquired infections. url: http://medrxiv.org/cgi/content/short/2020.08.21.20178855v1?rss=1 doi: 10.1101/2020.08.21.20178855 id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 words: 6118.0 sentences: 309.0 pages: flesch: 51.0 cache: ./cache/cord-301823-fbeb1nw1.txt txt: ./txt/cord-301823-fbeb1nw1.txt summary: Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. abstract: The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame. url: https://www.ncbi.nlm.nih.gov/pubmed/33134554/ doi: 10.12688/wellcomeopenres.15937.2 id: cord-331429-mh2hd5fe author: Srikantiah, Padmini title: SARS Clinical Features, United States, 2003 date: 2005-01-17 words: 1948.0 sentences: 100.0 pages: flesch: 48.0 cache: ./cache/cord-331429-mh2hd5fe.txt txt: ./txt/cord-331429-mh2hd5fe.txt summary: We compared the clinical features of 8 U.S. case-patients with laboratory-confirmed severe acute respiratory syndrome (SARS) to 65 controls who tested negative for SARS coronavirus (SARS-CoV) infection. Shortness of breath, vomiting, diarrhea, progressive bilateral infiltrates on chest radiograph, and need for supplemental oxygen were significantly associated with confirmed SARS-CoV infection. Case-patients with laboratory-confirmed SARS were compared to a convenience sample of persons who met the clinical and epidemiologic criteria for suspected or probable SARS but subsequently tested negative for SARS-CoV infection. Controls had negative findings on all testing performed for SARS-CoV, including the absence of antibody against the virus in convalescent-phase serum samples obtained >21 days after onset of symptoms. Over the course of their illness, findings suggestive of a lower respiratory tract infection developed in all 8 patients with laboratory-confirmed SARS; these findings included dyspnea (n = 8), rales (n = 5), and hypoxia (n = 5) (Table 1) . abstract: We compared the clinical features of 8 U.S. case-patients with laboratory-confirmed severe acute respiratory syndrome (SARS) to 65 controls who tested negative for SARS coronavirus (SARS-CoV) infection. Shortness of breath, vomiting, diarrhea, progressive bilateral infiltrates on chest radiograph, and need for supplemental oxygen were significantly associated with confirmed SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15705339/ doi: 10.3201/eid1101.040585 id: cord-300625-fvirvpyl author: Srinivasan, Suhas title: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date: 2020-03-25 words: 5902.0 sentences: 285.0 pages: flesch: 41.0 cache: ./cache/cord-300625-fvirvpyl.txt txt: ./txt/cord-300625-fvirvpyl.txt summary: In addition to the global structural genomics, an initiative that focuses on determining the 3D structures of individual proteins on a genome scale [34] , as well as to the specific efforts aimed at rapid structural characterization of proteins in emerging viruses [35] [36] [37] [38] , multiple works have used comparative modeling to predict the structures of protein-protein interaction complexes [39] [40] [41] , facilitate structure-based drug discovery [33, 42, 43] , infer protein functions [44] , determine the macromolecular interaction network [45] [46] [47] [48] , and provide molecular insights into the viral evolution [49] [50] [51] . To do so, we structurally characterized individual proteins as well as intra-viral and human-virus protein complexes, extracted the information on their interaction interfaces and ligand binding, and superposed the evolutionary difference and conservation information with the binding information. abstract: During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge, we leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community. url: https://www.ncbi.nlm.nih.gov/pubmed/32218151/ doi: 10.3390/v12040360 id: cord-327392-9psblokc author: Srivastava, A.K. title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 words: 4055.0 sentences: 218.0 pages: flesch: 52.0 cache: ./cache/cord-327392-9psblokc.txt txt: ./txt/cord-327392-9psblokc.txt summary: Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new virus in coronavirus family that causes coronavirus disease (COVID-19), emerges as a big threat to the human race. To date, there is no medicine and vaccine available for COVID-19 treatment. While the development of medicines and vaccines are essentially and urgently required, what is also extremely important is the repurposing of smart materials to design effective systems for combating COVID-19. Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. In this article, we discuss the potential of graphene and GRMs for healthcare applications and how they may contribute to fighting against COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2468519420301452?v=s5 doi: 10.1016/j.mtchem.2020.100385 id: cord-274053-406dfdih author: Srivastava, Kamna title: Association between COVID-19 and cardiovascular disease date: 2020-07-14 words: 2574.0 sentences: 166.0 pages: flesch: 46.0 cache: ./cache/cord-274053-406dfdih.txt txt: ./txt/cord-274053-406dfdih.txt summary: SARS-CoV-2 infects host cells through ACE2 receptors, leading to COVID-19-related pneumonia. Search methods and strategies for identification of studies Literature search was performed in WHO reports, PubMed, Scopus, Science Direct and also in American Heart Association journals, Nature, JAMA, BMJ and THE LANCET journals using following terms:ACE2, coronavirus, COVID-19 and 2019-nCoV, COVID-19 and CVD, Cardiovascular Risk and Diseases to find articles published from January 05 to May 20, 2020. SARS-CoV-2 shares both high sequence similarity and the use of the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV). In another study [43] , we have reported the role of Angiotensin type I receptor in patients with essential hypertension and normal healthy controls as pathological and physiological differential expression at mRNA and protein levels. In a report by Huang et al [3] myocardial injury associated with the SARS-CoV-2 was found in 5 of the first 41 patients diagnosed with COVID-19 in Wuhan. abstract: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19) has reached a pandemic level. SARS-CoV-2 infects host cells through ACE2 receptors, leading to COVID-19-related pneumonia. The rapid increase in confirmed cases makes the prevention and control of COVID-19 extremely serious. Real-time reverse transcription-PCR (RT-PCR) assays remain the molecular test of choice for the etiologic diagnosis of SARS-CoV-2 infection while radiographic findings (chest computed tomography [CT]) and antibody-based techniques are being introduced as supplemental tools. Novel virus also cause chronic damage to the cardiovascular system, and attention should be given to cardiovascular protection during treatment for COVID-19. Acute cardiac injury determined by elevated high-sensitivity troponin levels is commonly observed in severe cases and is strongly associated with mortality. This review suggests that cardiovascular comorbidities are common in patients with COVID-19 and such patients are at higher risk of morbidity and mortality. The continuation of clinically indicated ACE inhibitor and ARB medications is recommended in COVID-19. We review the basics of coronaviruses, novel molecular targets for the coronaviruses with a focus on COVID-19, along with their effects on the cardiovascular system. url: https://www.sciencedirect.com/science/article/pii/S2352906720302815?v=s5 doi: 10.1016/j.ijcha.2020.100583 id: cord-340432-vm6m0kb4 author: Srivastava, Sukrit title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date: 2020-09-06 words: 2661.0 sentences: 199.0 pages: flesch: 54.0 cache: ./cache/cord-340432-vm6m0kb4.txt txt: ./txt/cord-340432-vm6m0kb4.txt summary: title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide Methodology A novel reverse epitomics approach, "overlapping-epitope-clusters-to-patches" method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. Multi-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, "Overlapping-epitope-clusters-to-patches" method. In the present study, we have reported a novel method to design a 1170 vaccine against SARS-CoV-2 by utilizing multiple antigenic patches from the viral 1171 proteins. The designed MPVs from the antigenic patches of SARS-CoV-2 proteins 1182 have several advantages over to the subunit and multi-epitope based vaccines. Design of multi epitope-based peptide vaccine against E 1409 protein of human 2019-nCoV: An immunoinformatics approach Multi-epitope based peptide 1549 vaccine design against SARS-CoV-2 using its spike protein In silico approach for designing of a multi-epitope based 1587 vaccine against novel Coronavirus (SARS-COV-2) abstract: Background The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a positive-sense single-stranded RNA coronavirus responsible for the ongoing 2019-2020 COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. In present study we have designed and theoretically validated novel Multi-Patch Vaccines against SARS-CoV-2. Methodology A novel reverse epitomics approach, “overlapping-epitope-clusters-to-patches” method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are here termed as “Ag-Patch or Ag-Patches”, for Antigenic Patch or Patches. The identification of Ag-Patches is based on clusters of overlapping epitopes rising from a particular region of SARS-CoV-2 protein. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel methodology for vaccine design and development. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. Results We identified 73 CTL (Cytotoxic T-Lymphocyte), 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 (518 CTL and 250 HTL) overlapping epitopes targeting different HLA alleles. Such large number of epitope coverage is not possible for multi-epitope vaccines. The large number of epitopes covered implies large number of HLA alleles targeted, and hence large ethnically distributed human population coverage. The MPVs:Toll-Like Receptor ectodomain complex shows stable nature with numerous hydrogen bond formation and acceptable root mean square deviation and fluctuation. Further, the cDNA analysis favors high expression of the MPVs constructs in human cell line. Conclusion Highly immunogenic novel Ag-Patches are identified from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach. We conclude that the novel Multi-Patch Vaccines could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide. ABSTRACT FIGURE: A Multi-Patch Vaccine design to combat SARS-CoV-2 and a method to prepare thereof. Multi-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, “Overlapping-epitope-clusters-to-patches” method. url: https://doi.org/10.1101/2020.09.06.284992 doi: 10.1101/2020.09.06.284992 id: cord-282317-k9mtf6yl author: Srivastava, Vivek title: Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2 date: 2020-10-14 words: 3964.0 sentences: 190.0 pages: flesch: 51.0 cache: ./cache/cord-282317-k9mtf6yl.txt txt: ./txt/cord-282317-k9mtf6yl.txt summary: The main objective of the present study is to carry out molecular docking analysis of Glycyrrhiza glabra active compounds, Glycyrrhizic acid, Liquiritigenin and Glabridin against the main protease (M pro ) one by one followed by molecular interaction study (hydrogen bond prediction between target and drugs), drug-likeness behaviour and ADMET prediction to confirm the efficiency and efficacy of these active compound against SARS-CoV2. The molecular docked pose of the minimum binding affinity conformer of the Gg active compounds that is glycyrrhizic acid, Glabridin and Liquiritigenin demonstrated that they also firmly goes and bind to the active site of the M pro protein of the SARS-CoV-2 ( figure 4 and table 2 ). Molecular docking indicated that the three active compounds of Glycyrrhiza glabra namely glycyrrhizic acid, Liquiritigenin, and Glabridin successfully docked with the amino acid molecule at the catalytic site of the M pro with a high negative binding affinity and formed several molecular interaction with the main protease of SARS-CoV2. abstract: Recent pandemic situation of COVID-19 is caused due to SARS-CoV2 and almost all the countries of the world has been affected by this highly contagious virus. Main protease (M(pro)) of this virus is a highly attractive drug target among various other enzymes due to its ability to process poly-protein that is the translated product of the SARS-CoV2 RNA. The aim of the present study demonstrates molecular docking study of Glycyrrhiza glabra (Gg) active compounds such as Glycyrrhizic acid (GA), Liquiritigenin (L) and Glabridin (G) against the M(pro). Docking studies shows that these active compounds bind strongly with some of the amino acid residues in the active site of M(pro) and inhibits the enzyme strongly. GA, L, and G are proposed to be strong inhibitors of the enzyme and the amino acids: His(41), Gly(143), Gln(189), Glu (166), Cys (145), Thr(25), Asn(142), Met(49), Cys(44), Thr(45) and pro(168) present in the active site of M(pro) were shown to make non-covalent interaction with these compounds. In silico ADMET properties prediction also shows that Gg active compounds had good solubility, absorption, permeation, non-toxic, and non- carcinogenic characteristics. Our finding concludes that all of the three active compounds of Gg could have the potential to be strong inhibitors for M(pro) of SARS-CoV2 but glycyrrhizic acid have a high binding affinity of -8.0 Kcal/mol and glycyrrhizic acid have good ADMET properties than the other two. url: https://api.elsevier.com/content/article/pii/S2214785320376227 doi: 10.1016/j.matpr.2020.10.055 id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 words: 2735.0 sentences: 147.0 pages: flesch: 41.0 cache: ./cache/cord-261961-u4d0vvmq.txt txt: ./txt/cord-261961-u4d0vvmq.txt summary: To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. abstract: Key steps of viral replication take place at host cell membranes, but the detection of membrane-associated protein-protein interactions using standard affinity-based approaches (e.g. immunoprecipitation coupled with mass spectrometry, IP-MS) is challenging. To learn more about SARS-CoV-2 - host protein interactions that take place at membranes, we utilized a complementary technique, proximity-dependent biotin labeling (BioID). This approach uncovered a virus-host topology network comprising 3566 proximity interactions amongst 1010 host proteins, highlighting extensive virus protein crosstalk with: (i) host protein folding and modification machinery; (ii) membrane-bound vesicles and organelles, and; (iii) lipid trafficking pathways and ER-organelle membrane contact sites. The design and implementation of sensitive mass spectrometric approaches for the analysis of complex biological samples is also important for both clinical and basic research proteomics focused on the study of COVID-19. To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. Together, these datasets comprise a valuable resource for MS-based SARS-CoV-2 research, and identify novel virus-host protein interactions that could be targeted in COVID-19 therapeutics. url: https://doi.org/10.1101/2020.08.28.269175 doi: 10.1101/2020.08.28.269175 id: cord-272690-r8lv1zzx author: St. John, Ronald K. title: Border Screening for SARS date: 2005-01-17 words: 2643.0 sentences: 139.0 pages: flesch: 51.0 cache: ./cache/cord-272690-r8lv1zzx.txt txt: ./txt/cord-272690-r8lv1zzx.txt summary: With the rapid international spread of severe acute respiratory syndrome (SARS) from March through May 2003, Canada introduced various measures to screen airplane passengers at selected airports for symptoms and signs of SARS. Because of the continuing outbreak in Toronto, domestic spread in other affected countries in Southeast Asia, and international spread to other countries, Health Canada intensified its initial response by instituting both inbound and outbound passenger screening to identify persons with symptoms or signs compatible with SARS. In parallel to these measures, Health Canada initiated a pilot study on May 8, 2003 , on the use of infrared thermal scanning machines to detect temperatures >38°C in selected international arriving and departing passengers at Vancouver''s International and Toronto''s Pearson International airports. Careful analysis of the travel histories of suspected and probable SARS patients who traveled to Canada showed that persons became ill after arrival and would not have been detected by airport screening measures. abstract: With the rapid international spread of severe acute respiratory syndrome (SARS) from March through May 2003, Canada introduced various measures to screen airplane passengers at selected airports for symptoms and signs of SARS. The World Health Organization requested that all affected areas screen departing passengers for SARS symptoms. In spite of intensive screening, no SARS cases were detected. SARS has an extremely low prevalence, and the positive predictive value of screening is essentially zero. Canadian screening results raise questions about the effectiveness of available screening measures for SARS at international borders. url: https://www.ncbi.nlm.nih.gov/pubmed/15705315/ doi: 10.3201/eid1101.040835 id: cord-261941-xf1k5uj1 author: Stackhouse, Robin A. title: Severe acute respiratory syndrome and tuberculosis date: 2005-03-01 words: 5420.0 sentences: 306.0 pages: flesch: 55.0 cache: ./cache/cord-261941-xf1k5uj1.txt txt: ./txt/cord-261941-xf1k5uj1.txt summary: Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients abstract: Respiratory infectious diseases such as severe acute respiratory syndrome and tuberculosis create unique risks for anyone who may be exposed. A brief history of each disease is discussed in this article. The pathogenesis, manifestations, and therapy (where applicable) are also addressed. Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. url: https://www.ncbi.nlm.nih.gov/pubmed/15325712/ doi: 10.1016/j.atc.2004.06.002 id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 words: 5146.0 sentences: 248.0 pages: flesch: 51.0 cache: ./cache/cord-329493-ueqlhgn0.txt txt: ./txt/cord-329493-ueqlhgn0.txt summary: A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralysed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again. url: https://www.ncbi.nlm.nih.gov/pubmed/15035025/ doi: 10.1038/nrmicro775 id: cord-279642-0j5828ah author: Stafford, Emma G. title: Pharmacovigilance in Patients with Diabetes: A Data-Driven Analysis Identifying Specific RAS Antagonists with Adverse Pulmonary Safety Profiles That Have Implications for COVID-19 Morbidity and Mortality date: 2020-06-01 words: 1918.0 sentences: 97.0 pages: flesch: 48.0 cache: ./cache/cord-279642-0j5828ah.txt txt: ./txt/cord-279642-0j5828ah.txt summary: Angiotensin converting enzyme inhibitors (ACEIs) and angiotensin-II receptor blockers (ARBs) are considered first-line agents in diabetics due to their nephroprotective effects but administration of these drugs leads to upregulation of angiotensin-converting-enzyme-2 (ACE2), responsible for viral entry of severe-acute-respiratory-distress-syndrome, coronavirus-2 (SARS-CoV-2). In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. abstract: ABSTRACT OBJECTIVES Current demographic information from China reports that 10-19% of patients hospitalized with COVID-19 were diabetic. Angiotensin converting enzyme inhibitors (ACEIs) and angiotensin-II receptor blockers (ARBs) are considered first-line agents in diabetics due to their nephroprotective effects but administration of these drugs leads to upregulation of angiotensin-converting-enzyme-2 (ACE2), responsible for viral entry of severe-acute-respiratory-distress-syndrome, coronavirus-2 (SARS-CoV-2). Data is lacking to determine what pulmonary effects ACEIs/ARBs may have in patients with diabetes, which could be relevant in the management of patients infected with SARS-CoV-2. In this study, the aim was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory illness, such as SARS-CoV-2 infection. METHODS 1DATA, a unique data platform resulting from collaboration across veterinary and human healthcare, utilized an intelligent medicine recommender system (1DrugAssist) developed using several national and international databases, to evaluate all ADEs reported to the FDA for patients with diabetes taking ACEIs or ARBs. RESULTS Mining of this data elucidated the proportion of a cluster of pulmonary ADEs associated with specific medications in these classes, which may aid healthcare professionals in understanding how these medications could worsen or predispose patients with diabetes to infections affecting the respiratory system specifically, COVID-19. Based on this data mining, Captopril was found to have a statistically significantly higher incidence of pulmonary ADEs compared to other ACEIs (P = 0.005) as well as ARBs (P = 0.012), though other specific drugs also had important pulmonary ADEs associated with their use. CONCLUSION These analyses suggest that pharmacists and clinicians will need to consider specific medication’s adverse event profile, particularly captopril, and how this profile may affect infections and other acute disease states that alter pulmonary function, such as COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32561317/ doi: 10.1016/j.japh.2020.05.018 id: cord-303741-1ou0cy5k author: Stafstrom, Carl E. title: COVID-19: Neurological Considerations in Neonates and Children date: 2020-09-10 words: 7035.0 sentences: 369.0 pages: flesch: 40.0 cache: ./cache/cord-303741-1ou0cy5k.txt txt: ./txt/cord-303741-1ou0cy5k.txt summary: An especially apropos case demonstrated maternal viremia, placental infection shown by immunohistochemistry, and high placental viral load with subsequent neonatal viremia, implying transplacental transfer of SARS-CoV-2 from pregnant mother to fetus [24] ; this newborn presented with neurological symptoms as discussed in Section 3. The lack of unequivocal reports of SARS-CoV-2 being recovered from the CSF of individuals affected with presumed neurological involvement nor in brain tissue from the limited number of autopsied cases strengthens the possibility that the virus does not often directly cause the symptoms but rather, that the neurological sequelae are secondary to hypoxia, cytokine involvement, or some other non-direct mechanism (see Section 6). Finally, 4 of 27 children with COVID-19 associated MIS-C developed new neurologic symptoms including encephalopathy, headache, weakness, ataxia, and dysarthria [81] ; two patients had lumbar punctures and CSF was negative for SARS-CoV-2 in both. abstract: The ongoing worldwide pandemic of the novel human coronavirus SARS-CoV-2 and the ensuing disease, COVID-19, has presented enormous and unprecedented challenges for all medical specialists. However, to date, children, especially neonates, have been relatively spared from the devastating consequences of this infection. Neurologic involvement is being increasingly recognized among adults with COVID-19, who can develop sensory deficits in smell and taste, delirium, encephalopathy, headaches, strokes, and peripheral nervous system disorders. Among neonates and children, COVID-19-associated neurological manifestations have been relatively rare, yet reports involving neurologic dysfunction in this age range are increasing. As discussed in this review, pediatric neurologists and other pediatric specialists should be alert to potential neurological involvement by this virus, which might have neuroinvasive capability and carry long-term neuropsychiatric and medical consequences. url: https://www.ncbi.nlm.nih.gov/pubmed/32927628/ doi: 10.3390/children7090133 id: cord-314798-n6oofe3i author: Stall, N. M. title: Sex-specific differences in COVID-19 testing, cases and outcomes: a population-wide study in Ontario, Canada date: 2020-05-06 words: 1020.0 sentences: 68.0 pages: flesch: 57.0 cache: ./cache/cord-314798-n6oofe3i.txt txt: ./txt/cord-314798-n6oofe3i.txt summary: In this population-wide study in Ontario, Canada we report on all 194,372 unique residents who received testing for SARS-CoV-2 between January 23, 2020 and April 28, 2020. This population-wide cohort study included all residents of Ontario, Canada who received a nasopharyngeal swab for SARS-CoV-2 between January 23, 2020 (date swab was performed for first reported case of COVID-19 in Canada) and April 28, 2020. We obtained data for this study from the Ontario Ministry of Health as part of the province''s emergency "modeling table", including deidentified line level data on all SARS-CoV-2 testing via the Ontario Laboratories Information System (OLIS) and from the integrated Public Health Information System (iPHIS) for all reported COVID-19 cases and related clinical outcomes. We reported sex-and age-disaggregated data on SARS-CoV-2 testing, COVID-19 cases and related rates of hospitalization, intensive care unit (ICU) admission and death. abstract: In this population-wide study in Ontario, Canada we report on all 194,372 unique residents who received testing for SARS-CoV-2 between January 23, 2020 and April 28, 2020. We found that while more women than men were tested for SARS-CoV-2, men had a higher rate of laboratory-confirmed COVID-19 infection, hospitalization, ICU admission and death. These findings were consistent even with age adjustment, suggesting that the observed differences in outcomes between women and men were not explained by age or systematic differences in testing by sex. Instead, they may be due to sex-based immunological or other gendered differences, such as higher rates of smoking leading to cardiovascular disease. url: https://doi.org/10.1101/2020.04.30.20086975 doi: 10.1101/2020.04.30.20086975 id: cord-342942-1s32o9m8 author: Stamatakis, George title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 words: 4074.0 sentences: 209.0 pages: flesch: 47.0 cache: ./cache/cord-342942-1s32o9m8.txt txt: ./txt/cord-342942-1s32o9m8.txt summary: Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. abstract: Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes. url: https://doi.org/10.1101/2020.06.22.164681 doi: 10.1101/2020.06.22.164681 id: cord-253331-z443e8lk author: Stanhope, Michael J. title: Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV date: 2004-03-31 words: 2564.0 sentences: 105.0 pages: flesch: 44.0 cache: ./cache/cord-253331-z443e8lk.txt txt: ./txt/cord-253331-z443e8lk.txt summary: Based on evolutionary analyses of coronavirus DNA sequences, encompassing an approximately 13kb stretch of the SARS-TOR2 genome, we provide evidence that SARS-CoV has a recombinant history with lineages of types I and III coronavirus. Our results act to both corroborate and extend their findings, adding further support to the idea that SARS has had a recombinant history involving different coronavirus lineages and suggest the possibility that the genome could have arisen through a combination of host jumping and recombination events in a manner analogous to previous outbreaks of influenzae (Gregory et al., 2003; Zhou et al., 1999) . Our results indicate that SARS-CoV recombined with a member of the group III lineage, suggesting that an avian coronavirus was involved, a further point of general agreement between our results and that of Rest and Mindell (2003) . abstract: Abstract The origins and evolutionary history of the Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS-CoV) remain an issue of uncertainty and debate. Based on evolutionary analyses of coronavirus DNA sequences, encompassing an approximately 13kb stretch of the SARS-TOR2 genome, we provide evidence that SARS-CoV has a recombinant history with lineages of types I and III coronavirus. We identified a minimum of five recombinant regions ranging from 83 to 863bp in length and including the polymerase, nsp9, nsp10, and nsp14. Our results are consistent with a hypothesis of viral host jumping events, concomitant with the reassortment of bird and mammalian coronaviruses, a scenario analogous to earlier outbreaks of influenzae. url: https://www.ncbi.nlm.nih.gov/pubmed/15019585/ doi: 10.1016/j.meegid.2003.10.001 id: cord-275690-83nrzfon author: Stanifer, Megan L. title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date: 2020-04-24 words: 4696.0 sentences: 256.0 pages: flesch: 52.0 cache: ./cache/cord-275690-83nrzfon.txt txt: ./txt/cord-275690-83nrzfon.txt summary: title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, and in agreement with the results observed in cells depleted of the type III IFN receptor, this increase in infectivity was also associated with an increase in infectious denovo virus particle production ( Fig. 3G ). All together, these results strongly support a model where the type III IFN mediated signaling controls SARS-CoV-2 infection in human intestinal epithelial cells. All together these results show that human colon organoids can support SARS-CoV-2 infection, replication and spread and that the type III IFN response plays a critical role in controlling virus replication. abstract: SARS-CoV-2 is an unprecedented worldwide health problem that requires concerted and global approaches to better understand the virus in order to develop novel therapeutic approaches to stop the COVID-19 pandemic and to better prepare against potential future emergence of novel pandemic viruses. Although SARS-CoV-2 primarily targets cells of the lung epithelium causing respiratory infection and pathologies, there is growing evidence that the intestinal epithelium is also infected. However, the importance of the enteric phase of SARS-CoV-2 for virus-induced pathologies, spreading and prognosis remains unknown. Here, using both colon-derived cell lines and primary non-transformed colon organoids, we engage in the first comprehensive analysis of SARS-CoV-2 lifecycle in human intestinal epithelial cells. Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, we identified intestinal epithelial cells as the best culture model to propagate SARS-CoV-2. We found that viral infection elicited an extremely robust intrinsic immune response where, interestingly, type III interferon mediated response was significantly more efficient at controlling SARS-CoV-2 replication and spread compared to type I interferon. Taken together, our data demonstrate that human intestinal epithelial cells are a productive site of SARS-CoV-2 replication and suggest that the enteric phase of SARS-CoV-2 may participate in the pathologies observed in COVID-19 patients by contributing in increasing patient viremia and by fueling an exacerbated cytokine response. url: https://doi.org/10.1101/2020.04.24.059667 doi: 10.1101/2020.04.24.059667 id: cord-277549-sg7tzhdm author: Stanley, Kate E. title: Coronavirus disease (COVID-19) and fertility: viral host entry protein expression in male and female reproductive tissues date: 2020-05-08 words: 5364.0 sentences: 249.0 pages: flesch: 47.0 cache: ./cache/cord-277549-sg7tzhdm.txt txt: ./txt/cord-277549-sg7tzhdm.txt summary: Single cell RNA sequencing (scRNAseq) in human and non-human primate respiratory tissues have shown co-expression of ACE2 and TMPRSS2 in pneumocytes in the lungs and goblet secretory cells in the nose (6) , indicating that these cell types may serve as foci for infection and potentially explaining the range of respiratory symptoms associated with COVID-19. Cell-type specific expression patterns of genes that produce viral host entry proteins, and identification of potential loci of infection within the reproductive system, are therefore necessary in order to predict whether SARS-CoV-2 is likely to have any impact on fertility. Categorizations for protein expression correspond to the categorizations given by the Human Protein Atlas and the Human Proteome Map. Published scRNAseq datasets in human testicular (18) and non-human primate ovarian (19) tissue were used to assess the cell-type specific expression pattern of SARS-CoV-2 entry receptor ACE2 and entry-associated protease TMPRSS2 and their coexpression. abstract: Abstract Objective To identify cell types in the male and female reproductive systems at risk of SARS-CoV-2 infection due to expression of host genes and proteins used by the virus for cell entry. Design Descriptive analysis of transcriptomic and proteomic data. Setting Academic research department and clinical diagnostic laboratory. Patients/Animals None. Focused on previously generated gene and protein expression data. Intervention(s) None. Main Outcome Measure(s) Identification of cell types co-expressing the key ACE2 and TMPRSS2 genes and proteins, as well as other candidates potentially involved in SARS-CoV-2 cell entry. Results Based on single cell RNA sequencing data, co-expression of ACE2 and TMPRSS2 was not detected in testicular cells, including sperm. A subpopulation of oocytes in non-human primate ovarian tissue were found to express ACE2 and TMPRSS2, but co-expression was not observed in ovarian somatic cells. RNA expression of TMPRSS2 in 18 samples of human cumulus cells was shown to be low or absent. There was general agreement between publicly available bulk RNA and protein datasets in terms of ACE2 and TMPRSS2 expression patterns in testis, ovary, endometrial and placental cells. Conclusion These analyses suggest that SARS-CoV-2 infection is unlikely to have long-term effects on male and female reproductive function. While the results cannot be considered definitive they imply that procedures in which oocytes are collected and fertilized in vitro are associated with very little risk of viral transmission from gametes to embryos and may indeed have the potential to minimize exposure of susceptible reproductive cell types to infection when compared to natural conception. url: https://doi.org/10.1016/j.fertnstert.2020.05.001 doi: 10.1016/j.fertnstert.2020.05.001 id: cord-283850-kt8n6pg2 author: Steardo, Luca title: Psychiatric face of COVID-19 date: 2020-07-30 words: 7886.0 sentences: 374.0 pages: flesch: 32.0 cache: ./cache/cord-283850-kt8n6pg2.txt txt: ./txt/cord-283850-kt8n6pg2.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similarly to other coronaviruses demonstrate neurotropism; the viral infection of the brain stem may complicate the course of the disease through damaging central cardio-respiratory control. Post-mortem analysis of nervous tissue from tissue of a 54 years-old man who died from severe respiratory failure associated with COVID-19 identified SARS-COV-2 viral particles in the olfactory nerve, in the gyrus rectus and in the brainstem with signs of profound damage to all elements of the tissue including glial cells, neurones, their axons and myelin 37 . Infection with SARS-CoV-2 (even in moderate clinical cases) thus promotes cognitive disorders with emergence of delirium, acute psychosis, exacerbation of mild cognitive impairment or with accelerating of dementia associated with various neurodegenerative conditions, including Alzheimer''s disease (AD) 85, 86 . Patients with COVID-19 could present with a wide range of neuropsychiatric symptoms, which result from systemic inflammation, CNS effects of cytokines, infection of neural cells by SARS-COV-2, neuroinflammation, glial dysfunction or aberrant epigenetic modifications of stress-related genes. abstract: The Coronavirus Disease 2019 (COVID-19) represents a severe multiorgan pathology which, besides cardio-respiratory manifestations, affects the function of the central nervous system (CNS). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similarly to other coronaviruses demonstrate neurotropism; the viral infection of the brain stem may complicate the course of the disease through damaging central cardio-respiratory control. The systemic inflammation as well as neuroinflammatory changes are associated with massive increase of the brain pro-inflammatory molecules, neuroglial reactivity, altered neurochemical landscape and pathological remodelling of neuronal networks. These organic changes, emerging in concert with environmental stress caused by experiences of intensive therapy wards, pandemic fears and social restrictions, promote neuropsychiatric pathologies including major depressive disorder, bipolar disorder (BD), various psychoses, obsessive-compulsive disorder and post-traumatic stress disorder. The neuropsychiatric sequelae of COVID-19 represent serious clinical challenge that has to be considered for future complex therapies. url: https://doi.org/10.1038/s41398-020-00949-5 doi: 10.1038/s41398-020-00949-5 id: cord-290195-8uaai9nv author: Stebbing, Justin title: Mechanism of baricitinib supports artificial intelligence‐predicted testing in COVID‐19 patients date: 2020-05-30 words: 6584.0 sentences: 326.0 pages: flesch: 46.0 cache: ./cache/cord-290195-8uaai9nv.txt txt: ./txt/cord-290195-8uaai9nv.txt summary: Furthermore, baricitinib treatment resulted in a significant reduction (p<0.05) from baseline in plasma IL-6 at week 12 in patients with active RA who had an inadequate response to methotrexate from a phase 2b (Tanaka, Emoto et al., 2016) , randomized, placebo-controlled, dose-ranging study (Fig. 1B) . As shown in Figure 3A , all four patients showed improvement with baricitinib treatment in signs and symptoms such as cough, fever, and reduction in plasma IL-6 levels, along with a reduction in the SARS-CoV-2 RNA viral load, as detected by the real-time reverse-transcriptase-polymerase chain reaction (RT-PCR) signal from the nasopharyngeal carriage. Therefore, the impact of baricitinib on the subsequent development of protective humoral and cell-mediated anti-viral immunity in COVID-19 patients must be evaluated in randomized clinical trials (Ottoviani & Stebbing, 2020) . The finding that baricitinib is a potent AAK1/BIKE/GAK inhibitor that may reduce host cell infectivity, along with reaffirmation of its anti-cytokine profile, provide reasons to study this intervention in randomized clinical trials. abstract: Baricitinib, is an oral Janus kinase (JAK)1/JAK2 inhibitor approved for the treatment of rheumatoid arthritis (RA) that was independently predicted, using artificial intelligence (AI)‐algorithms, to be useful for COVID‐19 infection via a proposed anti‐cytokine effects and as an inhibitor of host cell viral propagation. We evaluated the in vitro pharmacology of baricitinib across relevant leukocyte subpopulations coupled to its in vivo pharmacokinetics and showed it inhibited signaling of cytokines implicated in COVID‐19 infection. We validated the AI‐predicted biochemical inhibitory effects of baricitinib on human numb‐associated kinase (hNAK) members measuring nanomolar affinities for AAK1, BIKE, and GAK. Inhibition of NAKs led to reduced viral infectivity with baricitinib using human primary liver spheroids. These effects occurred at exposure levels seen clinically. In a case series of patients with bilateral COVID‐19 pneumonia, baricitinib treatment was associated with clinical and radiologic recovery, a rapid decline in SARS‐CoV‐2 viral load, inflammatory markers, and IL‐6 levels. Collectively, these data support further evaluation of the anti‐cytokine and anti‐viral activity of baricitinib and supports its assessment in randomized trials in hospitalized COVID‐19 patients. url: https://doi.org/10.15252/emmm.202012697 doi: 10.15252/emmm.202012697 id: cord-302616-1uwrcvjx author: Steenblock, Charlotte title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis date: 2020-05-07 words: 3872.0 sentences: 201.0 pages: flesch: 41.0 cache: ./cache/cord-302616-1uwrcvjx.txt txt: ./txt/cord-302616-1uwrcvjx.txt summary: title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis Furthermore, it has to be considered that certain therapies impacting expression of ACE2 might also influence the RAAS and the neuroendocrine stress axis, which may lead to long-term consequences, as prolonged exposure to stressors increases the risk to develop major depressive, anxiety and post-traumatic stress disorders [42] . In addition to contributing to the progression of the immune response against viral infection, cytokines activate the HPA axis, resulting in the release of adrenal glucocorticoids [43] . In relation to coronavirus infections, it was shown that pulmonary stem/progenitor cells that express ACE2 are targeted by SARS-CoV in primary cultures [73] . Increasing brain angiotensin converting enzyme 2 activity Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis decreases anxiety-like behavior in male mice by activating central Mas receptors abstract: nan url: https://doi.org/10.1038/s41380-020-0758-9 doi: 10.1038/s41380-020-0758-9 id: cord-290796-x9xqqcj6 author: Stefanelli, P. title: Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento date: 2020-11-13 words: 3142.0 sentences: 212.0 pages: flesch: 55.0 cache: ./cache/cord-290796-x9xqqcj6.txt txt: ./txt/cord-290796-x9xqqcj6.txt summary: All individuals above ten years of age resident in 5 municipalities of the Autonomous Province of Trento, northern Italy, who resulted IgG positive for anti-SARS-CoV-2 nucleocapsid (NC) antibodies in a serosurvey conducted on May 2020 were retested after 4 months. The duration of protection against infection with common human coronaviruses appears to be rather short 2, 3 , and there are studies showing declines in IgG antibodies against SARS-CoV-2 among both symptomatic and asymptomatic individuals 4, 5 . In order to evaluate the persistence of SARS-CoV-2 antibodies, we repeated a serosurvey in five municipalities of the Autonomous Province (AP) of Trento, Italy, recruiting those individuals who had resulted positive in a large population-based seroprevalence study conducted 4 months before 14 . The analyser automatically calculates SARS-CoV-2 NC IgG antibody concentration expressed as an is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint abstract: Background. There are conflicting results about the duration of antibodies induced by SARS-CoV-2, but several studies show a rapid decay in a few months after infection. To evaluate antibody decline, we re-evaluated the presence of anti-SARS-CoV-2 antibodies among individuals found seropositive in a first population survey conducted 4 months before. Methods. All individuals above ten years of age resident in 5 municipalities of the Autonomous Province of Trento, northern Italy, who resulted IgG positive for anti-SARS-CoV-2 nucleocapsid (NC) antibodies in a serosurvey conducted on May 2020 were retested after 4 months. Anti-SARS-CoV-2 antibodies were detected using the Abbott SARS-CoV-2 IgG assay (Abbott Diagnostics, USA) detecting anti-NC antibodies. Samples that gave a negative result were re-tested using the same test plus Liaison SARS-CoV-2 IgG assay (DiaSorin, Italy) to assess anti-spike (S) S1/S2 IgG antibodies. Seroprevalence was calculated as the proportion of positive people on the total number of tested. A neutralizing assay was performed on a subgroup of formerly positives sera using fifty-percent tissue culture infective dose (TCID50) as endpoint dilution to produce a cytopathic effect in 50% of inoculated Vero E6 cells culture. In all the analyses a p value < 0.05 were considered statistically significant. Statistical analysis was performed by STATA version 16.1 (STATA Corp., College Station, Texas, USA). Findings. Overall, 1159 out of 1402 initially anti-NC seropositive participants were enrolled in the study. Of them, 480 (41.1%) became seronegative for anti-NC IgG antibodies. When 479 negative sera were tested for anti-S IgG, 373 samples (77.9%) resulted positives. A functional neutralization assay was performed on 106 sera showing high concordance with anti-S antibodies positivity. Interpretation. A decline of anti-NC IgG values was recorded 4 months after the first evaluation. Worth of note, a high proportion of anti-NC seronegative individuals were positive for anti-spike IgG antibodies, which appear to persist longer and to better correlate with neutralization activity. url: https://doi.org/10.1101/2020.11.11.20229062 doi: 10.1101/2020.11.11.20229062 id: cord-303868-aes92l6s author: Steffen, Tara L. title: The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date: 2020-08-22 words: 6098.0 sentences: 300.0 pages: flesch: 46.0 cache: ./cache/cord-303868-aes92l6s.txt txt: ./txt/cord-303868-aes92l6s.txt summary: In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. This suggests that polyclonal antibody binding to the RBD domain of the spike protein represents the key target of neutralizing antibody to SARS-CoV-2 after natural infection. Most importantly, our antigen-specific antibody depletion approach demonstrated that the RBD domain of the spike protein is responsible for 70% +/-18.9% of the human polyclonal neutralizing antibody activity to spike after natural SARS-CoV-2 infection. Although our study shows that the dominant target of IgG neutralizing antibody response after natural SARS-CoV-2 infection is the RBD domain of the spike protein, we have evaluated a limited number (n=10) of patients by antigen-specific antibody depletion. abstract: Natural infection of SARS-CoV-2 in humans leads to the development of a strong neutralizing antibody response, however the immunodominant targets of the polyclonal neutralizing antibody response are still unknown. Here, we functionally define the role SARS-CoV-2 spike plays as a target of the human neutralizing antibody response. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. Using an ELISA format, we assessed binding of human sera to spike subunit 1 (S1), spike subunit 2 (S2) and the receptor binding domain (RBD) of spike. To functionally identify the key target of neutralizing antibody, we depleted sera of subunit-specific antibodies to determine the contribution of these individual subunits to the antigen-specific neutralizing antibody response. We show that epitopes within RBD are the target of a majority of the neutralizing antibodies in the human polyclonal antibody response. These data provide critical information for vaccine development and development of sensitive and specific serological testing. url: https://doi.org/10.1101/2020.08.21.261727 doi: 10.1101/2020.08.21.261727 id: cord-345014-qp13h0un author: Stein, Richard Albert title: The 2019 coronavirus: Learning curves, lessons, and the weakest link date: 2020-03-13 words: 2268.0 sentences: 155.0 pages: flesch: 57.0 cache: ./cache/cord-345014-qp13h0un.txt txt: ./txt/cord-345014-qp13h0un.txt summary: 14 In the most recent of the three coronavirus outbreaks, several clusters of patients with pneumonia started to be reported on December 8, 2019 from Wuhan, China, and most of them were epidemiologically linked to the Huanan Seafood Wholesale Market. 24, 25 The virus shares >70% genetic similarity with the 2002-2003 SARS-CoV strain, 5 is most closely related to coronaviruses of bat origin, 17 its spike glycoprotein gene appears to have emerged by recombination between a bat coronavirus and a coronavirus of unknown origins, and relative synonymous codon usage bias analyses indicate that snakes may be a potential reservoir. 26 The SARS-CoV spike protein receptor binds the angiotensin-converting enzyme 2 (ACE2) on host cells, an interaction that shapes cross-species and human-to-human transmission. 10,58-60 Every outbreak brings something new, provides opportunities to reap the benefits gained from past epidemics and pandemics, and provides novel lessons that will shape the framework to manage emerging infectious diseases. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in Wuhan, China abstract: In the space of just six weeks, a new coronavirus, from a family that historically was not viewed as a global health concern, has become daily headline news around the globe. The 21st century marked its arrival with the emergence of three previously unknown coronaviruses. SARS-CoV (severe acute respiratory syndrome coronavirus) was recognized in November 2002 [1, 2], MERS-CoV (Middle East respiratory syndrome coronavirus) in June 2012 [3, 4], and 2019-nCoV in December 2019 [5]. Previously, human coronaviruses, known since the 1960s, were viewed as being only marginally relevant to the clinic, except for infants, the elderly, and immunocompromised individuals [1, 6, 7]. url: https://doi.org/10.1111/ijcp.13488 doi: 10.1111/ijcp.13488 id: cord-328778-mjzsz7rz author: Steinchen, N. title: Biologikatherapie nach COVID-19-Infektion: Keine Reaktivierung einer COVID-19-Infektion bei positivem Antikörperstatus SARS-CoV-2 unter Biologikatherapie date: 2020-06-08 words: 1126.0 sentences: 180.0 pages: flesch: 40.0 cache: ./cache/cord-328778-mjzsz7rz.txt txt: ./txt/cord-328778-mjzsz7rz.txt summary: In der kurzen Beobachtungszeit zeigten sich bis heute erfreulicherweise keine klinischen Hinweise auf eine Reaktivierung der COVID-19-Infektion, die bDMARD-Therapie wurde nebenwirkungsfrei vertragen. Die Fragen, ob bei Vorliegen einer entzündlich rheumatischen Erkrankung eine besondere Gefahr besteht, sich mit SARS-CoV-2 zu infizieren, und im Fall einer Infektion diese auch schwerer verläuft, sind bis heute aufgrund begrenzter Daten nicht sicher zu beantworten. Die Patienten*innen standen alle unter einer Zytokinhemmertherapie und wiesen im Vergleich zu den 2 Kontrollen (ohne Anti-Zytokin-Therapie) keine Antikörper gegen SARS-CoV-2 auf, während bei 2 % des nichtmedizinisch tätigen und 4 % des medizinisch tätigen Kontrollpersonals Antikörper gegen Corona-Virus detektierbar waren. Ursache des geringen Antikörpernachweises gegen SARS-CoV-2 in der Gruppe der Patienten*innen mit entzündlich rheumatischen Erkrankungen unter Anti-Zytokin-Therapie könnte sein, dass im Vergleich zu den anderen beiden Gruppen die RKI-Abstands-und Hygieneempfehlungen konsequenter aus Furcht vor einer Ansteckung unter immunsuppressiver Therapie umgesetzt wurden. Andererseits kann die Schlussfolgerung, dass eine Biologikatherapie vor einer SARS-CoV-2-Infektion mit einem schweren Verlauf möglicherweise schützt, aus den Daten nicht abgeleitet werden. abstract: A case with rheumatoid arthritis and insufficient compensation under disease-modifying combined long-term therapy with methotrexate and leflunomide is reported. After recovery from a COVID-19 infection, a tumor necrosis factor (TNF) inhibitor therapy was initiated. Until now no reactivation of the COVID-19 infection with positive SARS-CoV‑2 antibody status has occurred. url: https://doi.org/10.1007/s00393-020-00824-0 doi: 10.1007/s00393-020-00824-0 id: cord-353209-qkhfp66l author: Steiner, Daniel J. title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date: 2020-06-16 words: 2517.0 sentences: 129.0 pages: flesch: 45.0 cache: ./cache/cord-353209-qkhfp66l.txt txt: ./txt/cord-353209-qkhfp66l.txt summary: We report a multiplex label-free antigen microarray on the Arrayed Imaging Reflectometry (AIR) platform for detection of antibodies to SARS-CoV-2, SARS-CoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43) and three strains of influenza. Aminereactive substrates for fabrication of AIR arrays were provided by Adarza BioSystems, Inc. For ELISA assays, SARS-CoV-2 full-length spike and RBD were produced in-house using a mammalian expression system, 20,21 as was influenza A/H1N1/California 2009 hemagglutinin. To that end, we have presented preliminary data on a 15-plex array on the AIR platform, developed in response to the need to study SARS-CoV-2 but incorporating antigens for other coronaviruses and influenza. Responses to SARS-CoV-2 antigens on the array effectively discriminated between serum samples from uninfected and COVID-19 convalescent subjects, with generally good correlation to ELISA data. abstract: Detection of antibodies to upper respiratory pathogens is critical to surveillance, assessment of the immune status of individuals, vaccine development, and basic biology. The urgent need for antibody detection tools has proven particularly acute in the COVID-19 era. We report a multiplex label-free antigen microarray on the Arrayed Imaging Reflectometry (AIR) platform for detection of antibodies to SARS-CoV-2, SARS-CoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43) and three strains of influenza. We find that the array is readily able to distinguish uninfected from convalescent COVID-19 subjects, and provides quantitative information about total Ig, as well as IgG- and IgM-specific responses. url: https://doi.org/10.1101/2020.06.15.153064 doi: 10.1101/2020.06.15.153064 id: cord-335386-eflyypev author: Steinman, Jonathan Baruch title: Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics date: 2020-10-06 words: 5373.0 sentences: 287.0 pages: flesch: 48.0 cache: ./cache/cord-335386-eflyypev.txt txt: ./txt/cord-335386-eflyypev.txt summary: Exploring why the pediatric population is generally far less likely to develop COVID-19, even though their rate of infection is similar to adults (10), may offer productive clues, enabling strategies for (1) Coronavirus associated with common colds in children may offer some protection due to cross-reactive T cell immunity and crossreactive antibody immunity between common coronaviruses and SARS-CoV-2, and due to reduced ACE2 in nasal mucosa of children. A reasonable conjecture might be that, if ACE2 and/or TMPRSS2 expression is diminished in children, then viral infection of respiratory cells by SARS-CoV-2 might be less likely at any given viral load, and, additionally, there might be reduced expression of associated inflammatory modules. T[h]2 inflammation may predispose individuals to experience better COVID-19 outcomes through a decrease in airway levels of ACE2 that override any countervailing effect from increased expression of TMPRSS2." It is indeed surprising that the Th2 immune type associated with allergic diseases including asthma, and with eosinophilia, provides some protection to COVID-19 in children. abstract: The reduced development of COVID-19 for children compared to adults provides some tantalizing clues on the pathogenesis and transmissibility of this pandemic virus. First, ACE2, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, is reduced in the respiratory tract in children. Second, coronavirus associated with common colds in children may offer some protection, due to cross-reactive humoral immunity and T cell immunity between common coronaviruses and SARS-CoV-2. Third, T helper 2 immune responses are protective in children. Fourth, surprisingly, eosinophilia, associated with T helper 2, may be protective. Fifth, children generally produce lower levels of inflammatory cytokines. Finally, the influence of the downturn in the global economy, the impact of living in quarters among families who are the most at risk, and factors including the openings of some schools, are considered. Those most disadvantaged socioeconomically may suffer disproportionately with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32883878/ doi: 10.1073/pnas.2012358117 id: cord-277529-z2r14w2k author: Stella, Alessandro title: Familial Mediterranean Fever and COVID-19: Friends or Foes? date: 2020-09-18 words: 3634.0 sentences: 194.0 pages: flesch: 42.0 cache: ./cache/cord-277529-z2r14w2k.txt txt: ./txt/cord-277529-z2r14w2k.txt summary: We were intrigued by the remarkable overlap between these clinical manifestations and some of the typical manifestations of Familial Mediterranean Fever (FMF), a largely recessively inherited monogenic inflammasomopathy (autoinflammatory disorder involving the inflammasome) caused by mutations in the MEFV gene that is particularly prevalent in the Mediterranean basin (14) . It is tempting to speculate that FMF patients carrying V726A and R761H variants-which represents the wild type residues in all bats and pangolin sequences-might modulate better their cytokine response to SARS-CoV-2 infection. Thus, the severity of COVID-19 disease in FMF patients, once infected, might be influenced, at least partially, depending on specific MEFV genotypes which shows country-specific differences. FMF, in which Pyrin activity and consequent ASC oligomerization are increased because of MEFV pathogenic variants, may therefore represent a unique opportunity as a disease model to investigate the regulation of the inflammatory response to novel emerging viruses. abstract: Familial Mediterranean Fever (FMF) and COVID-19 show a remarkable overlap of clinical symptoms and similar laboratory findings. Both are characterized by fever, abdominal/chest pain, elevation of C-reactive protein, and leukocytosis. In addition, colchicine and IL-1 inhibitors treatments that are effective in controlling inflammation in FMF patients have recently been proposed for off-label use in COVID-19 patients. Thus, FMF may resemble a milder recapitulation of the cytokine storm that is a hallmark of COVID-19 patients progressing to severe disease. We analyzed the sequence of the MEFV-encoded Pyrin protein – whose mutations cause FMF- in mammals, bats and pangolin. Intriguingly, although Pyrin is extremely conserved in species that are considered either a reservoir or intermediate hosts for SARS-CoV-2, some of the most common FMF-causing variants in humans are present as wildtype residues in these species. We propose that in humans, Pyrin may have evolved to fight highly pathogenic infections. url: https://doi.org/10.3389/fimmu.2020.574593 doi: 10.3389/fimmu.2020.574593 id: cord-316894-zhmuzv7z author: Stetzenbach, L.D. title: Airborne Infectious Microorganisms date: 2009-02-17 words: 4393.0 sentences: 259.0 pages: flesch: 40.0 cache: ./cache/cord-316894-zhmuzv7z.txt txt: ./txt/cord-316894-zhmuzv7z.txt summary: Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. abstract: Inhalation exposes the upper and lower respiratory tracts of humans to a variety of airborne particles and vapors. Airborne transmission of pathogenic microorganisms to humans from the environment, animals, or other humans can result in disease. Inhalation is an important route of exposure as the lung is more susceptible to infection than the gastrointestinal tract. Ingested microorganisms must past through the acidic environment of the stomach before they can colonize tissue while inhaled microorganisms are deposited directly on the moist surfaces of the respiratory tract. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Following inhalation, infectious viruses, bacteria, and fungi can establish in host cells of the respiratory tract. Some are translocated and infect the gastrointestinal tract and other tissues. This chapter discusses human viral, bacterial, and fungal diseases transmitted via aerosols. Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Bacterial diseases are Legionnaires’ disease, tuberculosis, and nontubercule mycobacterial disease. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Fungal diseases included are histoplasmosis, coccidiomycosis, blastomycosis, cryptococcosis, and aspergillosis. The threat of bioterrorism with airborne infectious agents is also briefly presented. url: https://www.sciencedirect.com/science/article/pii/B9780123739445001772 doi: 10.1016/b978-012373944-5.00177-2 id: cord-326710-vc9wkcro author: Stevens, Bryan title: Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA date: 2020-08-06 words: 1796.0 sentences: 107.0 pages: flesch: 50.0 cache: ./cache/cord-326710-vc9wkcro.txt txt: ./txt/cord-326710-vc9wkcro.txt summary: BACKGROUND: Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). METHODS: A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. CONCLUSIONS: The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. In this study, we demonstrated comparable test performance between the Cepheid Xpert Xpress SARS-CoV-2 assay and the Panther Fusion SARS-CoV-2 assay, with an overall agreement of 99%. abstract: BACKGROUND: Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). Limited data are available comparing the test performance characteristics of these assays. METHODS: A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. Agreement between the two assays was assessed by overall, positive, and negative percent agreement and Cohen’s kappa coefficient. RESULTS: A total of 104 (54 positive and 50 negative) clinical nasopharyngeal samples were tested by both assays. Using the Panther Fusion as a reference standard, the Xpert demonstrated an overall agreement of 99.0% (95% confidence interval (CI): 94.8 – 100), positive percent agreement of 98.1% (95% CI: 90.1 – 100), and a negative percent agreement of 100% (95% CI: 94.2 – 100). The kappa coefficient was 0.98 (95% CI: 0.94 – 1.0). One sample positive by the Panther Fusion with a cycle threshold (Ct) of 38.6 was found to be reproducibly negative by the Xpert assay. CONCLUSIONS: The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. url: https://doi.org/10.1093/jalm/jfaa135 doi: 10.1093/jalm/jfaa135 id: cord-318339-j35w1vsw author: Stockman, Lauren J title: SARS: Systematic Review of Treatment Effects date: 2006-09-12 words: 4388.0 sentences: 233.0 pages: flesch: 50.0 cache: ./cache/cord-318339-j35w1vsw.txt txt: ./txt/cord-318339-j35w1vsw.txt summary: METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients. abstract: BACKGROUND: The SARS outbreak of 2002–2003 presented clinicians with a new, life-threatening disease for which they had no experience in treating and no research on the effectiveness of treatment options. The World Health Organization (WHO) expert panel on SARS treatment requested a systematic review and comprehensive summary of treatments used for SARS-infected patients in order to guide future treatment and identify priorities for research. METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. We also searched for clinical trial evidence of treatment for acute respiratory distress syndrome. Sources of data were the literature databases MEDLINE, EMBASE, BIOSIS, and the Cochrane Central Register of Controlled Trials (CENTRAL) up to February 2005. Data from publications were extracted and evidence within studies was classified using predefined criteria. In total, 54 SARS treatment studies, 15 in vitro studies, and three acute respiratory distress syndrome studies met our inclusion criteria. Within in vitro studies, ribavirin, lopinavir, and type I IFN showed inhibition of SARS-CoV in tissue culture. In SARS-infected patient reports on ribavirin, 26 studies were classified as inconclusive, and four showed possible harm. Seven studies of convalescent plasma or IVIG, three of IFN type I, and two of LPV/r were inconclusive. In 29 studies of steroid use, 25 were inconclusive and four were classified as causing possible harm. CONCLUSIONS: Despite an extensive literature reporting on SARS treatments, it was not possible to determine whether treatments benefited patients during the SARS outbreak. Some may have been harmful. Clinical trials should be designed to validate a standard protocol for dosage and timing, and to accrue data in real time during future outbreaks to monitor specific adverse effects and help inform treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/16968120/ doi: 10.1371/journal.pmed.0030343 id: cord-299443-nggl87u6 author: Stockman, Lauren J. title: Coronavirus Antibodies in Bat Biologists date: 2008-06-17 words: 1009.0 sentences: 55.0 pages: flesch: 59.0 cache: ./cache/cord-299443-nggl87u6.txt txt: ./txt/cord-299443-nggl87u6.txt summary: To address the possibility that the antibodies from this serum sample were not specifi c to SARS-CoV, we tested it against recombinant N proteins of human CoVs, HCoV-229E, HCoV-OC43, NL63, and HKU-1. If the antibodies were induced by a SARS-like CoV infection, we would expect to have also detected antibodies against recombinant S protein (9) or recombinant fragments representing antigenically distinct regions of the N protein of SARS-CoV. We did not detect either; instead, we detected antibodies against the antigenically distinct N fragments from group 1 and 2 human CoVs. Thus, this survey of a sample of bat biologists, who were exposed primarily to North American bats but also to bats from Asia and Africa, showed no evidence of SARSlike CoV infection. Recombinant protein-based assays for detection of antibodies to severe acute respiratory syndrome coronavirus spike and nucleocapsid proteins. Antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (SARS) coronavirus and polyclonal antisera of antigenic group I animal coronaviruses: implication for SARS diagnosis abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18507931/ doi: 10.3201/eid1406.070964 id: cord-338589-1ent68fx author: Stoddard, Shana V. title: Optimization Rules for SARS-CoV-2 M(pro) Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site date: 2020-08-26 words: 11437.0 sentences: 606.0 pages: flesch: 55.0 cache: ./cache/cord-338589-1ent68fx.txt txt: ./txt/cord-338589-1ent68fx.txt summary: The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 M(pro) active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 −log(10)(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M(pro) [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The use of multiple conformations when using docking will assist in the prediction of new antivirals agents targeting SARS-CoV-2 M pro as the diversity of accessible variations can produce distinct binding poses for an inhibitor compound. abstract: Coronaviruses are viral infections that have a significant ability to impact human health. Coronaviruses have produced two pandemics and one epidemic in the last two decades. The current pandemic has created a worldwide catastrophe threatening the lives of over 15 million as of July 2020. Current research efforts have been focused on producing a vaccine or repurposing current drug compounds to develop a therapeutic. There is, however, a need to study the active site preferences of relevant targets, such as the SARS-CoV-2 main protease (SARS-CoV-2 M(pro)), to determine ways to optimize these drug compounds. The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 M(pro) active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. A total of 220 compounds were docked into both the 5R7Z and 6LU7 SARS-CoV-2 M(pro) crystal structures. Several key preferences for strong binding to the four subsites (S1, S1′, S2, and S4) were identified, such as accessing hydrogen binding hotspots, hydrophobic patches, and utilization of primarily aliphatic instead of aromatic substituents. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 −log(10)(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. Using the optimization guidelines, the SARS-CoV-2 M(pro) inhibitor cinanserin was optimized resulting in an increase in binding affinity of 4.59 −log(10)(Kd) and increased protease inhibitor bioactivity. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M(pro) [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The enhanced binding affinity produced demonstrates the utility of the design guidelines described. The work described herein will assist scientists in developing potent COVID-19 antivirals. url: https://doi.org/10.3390/v12090942 doi: 10.3390/v12090942 id: cord-304372-6eqnr52t author: Stolle, Claudia title: Bedarfe der Langzeitpflege in der COVID-19-Pandemie date: 2020-10-28 words: 2696.0 sentences: 359.0 pages: flesch: 46.0 cache: ./cache/cord-304372-6eqnr52t.txt txt: ./txt/cord-304372-6eqnr52t.txt summary: Hier wiesen die Befragten auf eine Lücke bei notwendigen Informationen und Verfah-renshinweisen im Umgang mit kognitiv beeinträchtigten und verhaltensveränderten Pflegebedürftigen während der COVID-19-Pandemie hin. 70 % der Befragten, zusammengefasst in der Unterkategorie SARS-CoV-2-Testungen, forderten die Durchführung von "systematischen" und "regelmäßigen" Reihentestungen (n = 72) zum einen beim Personal der Einrichtungen und zum anderen bei den Pflegebedürftigen. 22 % der Befragten gaben an, dass entsprechende Kontaktpersonen nicht immer ausreichend qualifiziert erschienen, um mit praxisnahen Problemlösungen in den Einrichtungen weiterhelfen zu können, sodass ein Bedarf an einer fachlich "kompetenten Beratung" bestehe (n = 16). Dazu äußerten die Befragten einen konkreten Bedarf an "Beratung zur Umsetzung" (n = 12) der Vorgaben und Empfehlungen in den Einrichtungen. Mit der Dynamik und den steigenden Erkenntnissen in der Pandemie wurden auch die Empfehlungen zum Umgang SARS-CoV-2 in den Pflegeeinrichtungen seitens des RKI angepasst. Um die vulnerable Gruppe der Pflegebedürftigen und die Mitarbeitenden von Pflegeeinrichtungen in der aktuellen Situation vor SARS-CoV-2-Infektionen zu schützen, ergeben sich aus den Ergebnissen v. abstract: The SARS-CoV‑2 virus and the associated disease COVID-19 pose major challenges to healthcare systems worldwide. Especially the vulnerable group of people in need of long-term care is at risk of suffering a severe course of the disease or of dying from the infection. In a nationwide cross-sectional study the situation and needs of inpatient and outpatient long-term care facilities during the SARS-CoV‑2 pandemic were assessed and analyzed using an online survey. Participants from 531 institutions postulated the need for uniform recommendations for action on SARS-CoV‑2, adequate and affordable protective and hygiene materials, serial tests in the institutions, well-founded advice on the implementation of interventions, a specific pandemic plan and supporting public relations work by the media. This calls for higher nursing remuneration, better staffing levels and greater appreciation of the nursing profession. In order to protect the vulnerable group of people in need of nursing care from a SARS-CoV‑2 infection, long-term care must be given a stronger focus in health policy measures during the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/33113017/ doi: 10.1007/s00391-020-01801-7 id: cord-305496-t8ykkekl author: Stone, E. Taylor title: Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date: 2020-08-21 words: 7227.0 sentences: 391.0 pages: flesch: 60.0 cache: ./cache/cord-305496-t8ykkekl.txt txt: ./txt/cord-305496-t8ykkekl.txt summary: One such tool for evaluating neutralizing antibody response is a 88 plaque/focus neutralization reduction test (PRNT/FRNT), which evaluates the ability of polyclonal 89 sera samples to prevent or reduce infection of a cell monolayer in vitro. We examined the impact of cell density on foci formation for both Vero WHO and Vero E6 cells 144 by plating identical dilutions of SARS-CoV-2 virus stocks on 96-well plates seeded with differing 145 numbers of WHO or E6 cells (3 × 104, 1.5 × 104 or 3 × 104 cells/well) one day prior to infection 146 of the cell monolayer. To determine the optimal time frame for infection of SARS-CoV-2 on a Vero WHO cell 172 monolayer to form individual foci, we tested a variety of incubation times. The FFA relies on an immunostaining protocol of an infected cell monolayer in order to 197 quantify infectious virus titer and is therefore dependent upon SARS-CoV-2-specific antibody 198 abstract: The SARS-CoV-2 outbreak and subsequent COVID-19 pandemic have highlighted the urgent need to determine what cells are susceptible to infection and for assays to detect and quantify SARS-CoV-2. Furthermore, the ongoing efforts for vaccine development have necessitated the development of rapid, high-throughput methods of quantifying infectious SARS-CoV-2, as well as the ability to screen human polyclonal sera samples for neutralizing antibodies against SARS-CoV-2. To this end, our lab has adapted focus forming assays for SARS-CoV-2 using Vero CCL-81 cells, referred to in this text as Vero WHO. Using the focus forming assay as the basis for screening cell susceptibility and to develop a focus reduction neutralization test. We have shown that this assay is a sensitive tool for determining SARS-CoV-2 neutralizing antibody titer in human, non-human primate, and mouse polyclonal sera following SARS-CoV-2 exposure. Additionally, we describe the viral growth kinetics of SARS-CoV-2 in a variety of different immortalized cell lines and demonstrate via human ACE2 and viral spike protein expression that these cell lines can support viral entry and replication. url: https://doi.org/10.1101/2020.08.20.259838 doi: 10.1101/2020.08.20.259838 id: cord-342796-f7n8sxbu author: Stowe, J. title: Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design date: 2020-09-18 words: 3923.0 sentences: 218.0 pages: flesch: 48.0 cache: ./cache/cord-342796-f7n8sxbu.txt txt: ./txt/cord-342796-f7n8sxbu.txt summary: Findings: The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible pathogenic competition between the two viruses. The odds of ventilator use or death and ICU admission or death was greatest among coinfection patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Severity and risk of death among individuals with a coinfection: The mortality rate among individuals with a SARS-CoV-2 and influenza coinfection and those with SARS-CoV-2 infection who tested negative for influenza was calculated by dividing the number of deaths by the total number of individuals tested by age group. We also found strong evidence that coinfection with influenza and SARS-CoV-2 was associated with an increased risk of death or severe disease and that this appears to be beyond the additive effect of the two viruses acting independently. abstract: Background: The potential impact of COVID-19 alongside influenza on morbidity, mortality and health service capacity is a major concern as the Northern Hemisphere winter approaches. This study investigates the interaction between influenza and COVID-19 during the latter part of the 2019-20 influenza season in England. Methods: Individuals tested for influenza and SARS-CoV-2 were extracted from national surveillance systems between 20/01/2020 and 25/04/2020. To estimate influenza infection on the risk of SARS-CoV-2 infection, univariable and multivariable analyses on the odds of SARS-CoV-2 in those who tested positive for influenza compared to those who tested negative for influenza. To assess whether a coinfection was associated with severe SARS-CoV-2 outcome, univariable and multivariable analyses on the odds of death adjusted for age, sex, ethnicity, comorbidity and coinfection status. Findings: The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible pathogenic competition between the two viruses. Patients with a coinfection had a risk of death of 5.92 (95% CI, 3.21-10.91) times greater than among those with neither influenza nor SARS-CoV-2 suggesting possible synergistic effects in coinfected individuals. The odds of ventilator use or death and ICU admission or death was greatest among coinfection patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Interpretation: Cocirculation of these viruses could have a significant impact on morbidity, mortality and health service demand. Testing for influenza alongside SARS-CoV-2 and maximising influenza vaccine uptake should be prioritised to mitigate these risks. url: http://medrxiv.org/cgi/content/short/2020.09.18.20189647v1?rss=1 doi: 10.1101/2020.09.18.20189647 id: cord-317359-7yuygcew author: Straccia, Patrizia title: Description of a new biosafe procedure for cytological specimens from patients with COVID‐19 processed by liquid‐based preparations date: 2020-08-07 words: 1782.0 sentences: 99.0 pages: flesch: 43.0 cache: ./cache/cord-317359-7yuygcew.txt txt: ./txt/cord-317359-7yuygcew.txt summary: CONCLUSIONS: Despite some minor changes in the morphology of the cells, the results of this study highlight that the adoption of the new protocol for the biosafety of LBC‐processed samples in pathology laboratories is important for minimizing the risk for personnel, trainees, and cytopathologists without impairing the diagnostic efficacy of the technique. 8 The new coronavirus, Cancer Cytopathology Month 2020 originally called 2019 novel coronavirus (2019-nCoV) and officially renamed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and the disease it causes, namely coronavirus disease 2019 (COVID-19), have quickly become of tremendous concern worldwide. Because the laboratory personnel might be exposed to contamination during the preparation and handling of fresh specimens from such patients, a new procedure for the sterilization of material to be processed by liquid-based cytology (LBC) has been applied. abstract: BACKGROUND: Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and represents the causative agent of a potentially fatal disease. The spread of the infection and the severe clinical disease have led to the widespread adoption of social distancing measures. Special attention and efforts to protect or reduce transmission have been applied at all social levels, including health care operators. Hence, this reports focuses on the description of a new protocol for the safe management of cytological samples processed by liquid‐based cytology (LBC) with an evaluation of the changes in terms of morphology and immunoreactivity. METHODS: From March 11 to April 25, 2020, 414 cytological cases suspicious for SARS‐CoV‐2 were processed with a new virus‐inactivating method suggested by Hologic, Inc, for all LBC specimens. RESULTS: The samples showed an increased amount of fibrin in the background. A slight decrease in cellular size was also observed in comparison with the standard method of preparation. Nonetheless, the nuclear details of the neoplastic cells were well identified, and the immunoreactivity of the majority of those cells was maintained. The cell blocks did not show significant differences in morphology, immunoreactivity, or nucleic acid stability. CONCLUSIONS: Despite some minor changes in the morphology of the cells, the results of this study highlight that the adoption of the new protocol for the biosafety of LBC‐processed samples in pathology laboratories is important for minimizing the risk for personnel, trainees, and cytopathologists without impairing the diagnostic efficacy of the technique. url: https://doi.org/10.1002/cncy.22341 doi: 10.1002/cncy.22341 id: cord-295144-tyyc81uc author: Stradner, Martin H. title: Rheumatic Musculoskeletal Diseases and COVID-19 A Review of the First 6 Months of the Pandemic date: 2020-10-09 words: 9901.0 sentences: 442.0 pages: flesch: 39.0 cache: ./cache/cord-295144-tyyc81uc.txt txt: ./txt/cord-295144-tyyc81uc.txt summary: In this review, we summarize the published cases of COVID-19 infections in RMD patients, including patients with inflammatory arthritis and connective tissue diseases as well as anti-phospholipid syndrome and Kawasaki syndrome. It also reviews the general risk of viral infections in patients with RMD, the impact of disease modifying anti-rheumatic drugs (DMARDs) on the outcome of infections, and gives a comparison between present and previous coronavirus pandemics. This argues against a protective role of HCQ (in the usually administered dose for RMD patients) in SARS-CoV-2 infection, which is also supported by pharmacological in vitro data describing a much higher level needed for effective viral inhibition (61) . In conclusion, data published in the first 6 months do not consistently describe a higher risk for infection with SARS-CoV-2 or a more severe course of COVID-19 in patients with either inflammatory arthritis or connective tissue diseases. abstract: In December 2019, a cluster of severe pneumonia was observed in China, with the subsequent discovery of a new beta-coronavirus (SARS-CoV-2) as the causative agent. The elicited disease COVID-19 is characterized by fever, dry cough, myalgia, or fatigue and has a favorable outcome in the majority of cases. However, in some patients COVID-19 leads to severe pneumonia and sepsis with subsequent respiratory failure and gastrointestinal, hematological, neurological, and cardiovascular complications. A higher risk of infection is intrinsic to active rheumatic and musculoskeletal diseases (RMD) and the use of biological disease modifying anti-rheumatic drugs (DMARDs). With an increasing number of reports on COVID-19 in RMD patients, we are beginning to appraise their risks. In this review, we summarize the published cases of COVID-19 infections in RMD patients, including patients with inflammatory arthritis and connective tissue diseases as well as anti-phospholipid syndrome and Kawasaki syndrome. Overall, patients with inflammatory arthritis do not seem to be at a higher risk for infection or a severe course of COVID-19. Risk for critical COVID-19 in patients with systemic inflammatory diseases such as SLE or vasculitis might be increased, but this needs further confirmation. Furthermore, we summarize the data on DMARDs used to fight SARS-CoV-2 infection and hyperinflammation. url: https://www.ncbi.nlm.nih.gov/pubmed/33154972/ doi: 10.3389/fmed.2020.562142 id: cord-258431-8zgwj2fa author: Strafella, Claudia title: Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications date: 2020-07-03 words: 4055.0 sentences: 203.0 pages: flesch: 42.0 cache: ./cache/cord-258431-8zgwj2fa.txt txt: ./txt/cord-258431-8zgwj2fa.txt summary: The eQTLs analysis located in and targeting ACE2 revealed a high distribution of eQTL variants in different brain tissues, suggesting a possible link between ACE2 genetic variability and the neurological complications in patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. Moreover, they found a higher allelic frequency of eQTL variants, which is associated with higher ACE2 expression in tissues, suggesting a different susceptibility or response to SARS-Cov-2 infection with respect to other populations under similar conditions [28] . abstract: Angiotensin-converting enzyme 2 (ACE2) has been recognized as the entry receptor of the novel severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Structural and sequence variants in ACE2 gene may affect its expression in different tissues and determine a differential response to SARS-Cov-2 infection and the COVID-19-related phenotype. The present study investigated the genetic variability of ACE2 in terms of single nucleotide variants (SNVs), copy number variations (CNVs), and expression quantitative loci (eQTLs) in a cohort of 268 individuals representative of the general Italian population. The analysis identified five SNVs (rs35803318, rs41303171, rs774469453, rs773676270, and rs2285666) in the Italian cohort. Of them, rs35803318 and rs2285666 displayed a significant different frequency distribution in the Italian population with respect to worldwide population. The eQTLs analysis located in and targeting ACE2 revealed a high distribution of eQTL variants in different brain tissues, suggesting a possible link between ACE2 genetic variability and the neurological complications in patients with COVID-19. Further research is needed to clarify the possible relationship between ACE2 expression and the susceptibility to neurological complications in patients with COVID-19. In fact, patients at higher risk of neurological involvement may need different monitoring and treatment strategies in order to prevent severe, permanent brain injury. url: https://www.ncbi.nlm.nih.gov/pubmed/32635188/ doi: 10.3390/genes11070741 id: cord-343864-0258nh92 author: Straughn, Alex R. title: Withaferin A: a potential therapeutic agent against COVID-19 infection date: 2020-07-19 words: 2916.0 sentences: 141.0 pages: flesch: 45.0 cache: ./cache/cord-343864-0258nh92.txt txt: ./txt/cord-343864-0258nh92.txt summary: Therefore, WFA demonstrates real potential as a therapeutic agent to treat or prevent the spread of COVID-19 due to the reported interference in viral S-protein to host receptor binding and its lack of effect on ACE2 expression in the lungs. Data from four SARS-CoV-2 hot spots (the United States, Italy, Spain and China) has shown that cancer patients infected with the novel coronavirus have a significantly increased risk of admission to an intensive care unit (ICU) and/or requiring mechanical ventilation, as well as an increase in patient mortality [15, [17] [18] [19] . Withaferin A alone or in combination with drugs, such as: hydroxychloroquine, dexamethasone or other treatments (under clinical trials), could be developed into an attractive therapeutic agent for both the general population and cancer patients due to its anti-tumorigenic properties and the preliminary studies showing that it is capable of binding to the Sprotein of SARS-CoV-2, thereby potentially inhibiting infection and/or spread of the disease. abstract: The outbreak and continued spread of the novel coronavirus disease 2019 (COVID-19) is a preeminent global health threat that has resulted in the infection of over 11.5 million people worldwide. In addition, the pandemic has claimed the lives of over 530,000 people worldwide. Age and the presence of underlying comorbid conditions have been found to be key determinants of patient mortality. One such comorbidity is the presence of an oncological malignancy, with cancer patients exhibiting an approximate two-fold increase in mortality rate. Due to a lack of data, no consensus has been reached about the best practices for the diagnosis and treatment of cancer patients. Interestingly, two independent research groups have discovered that Withaferin A (WFA), a steroidal lactone with anti-inflammatory and anti-tumorigenic properties, may bind to the viral spike (S-) protein of SARS-CoV-2. Further, preliminary data from our research group has demonstrated that WFA does not alter expression of ACE2 in the lungs of tumor-bearing female mice. Downregulation of ACE2 has recently been demonstrated to increase the severity of COVID-19. Therefore, WFA demonstrates real potential as a therapeutic agent to treat or prevent the spread of COVID-19 due to the reported interference in viral S-protein to host receptor binding and its lack of effect on ACE2 expression in the lungs. url: https://www.ncbi.nlm.nih.gov/pubmed/32684166/ doi: 10.1186/s13048-020-00684-x id: cord-327273-7ntp7x8d author: Street, Renée title: COVID-19 wastewater surveillance: An African perspective date: 2020-07-03 words: 842.0 sentences: 61.0 pages: flesch: 54.0 cache: ./cache/cord-327273-7ntp7x8d.txt txt: ./txt/cord-327273-7ntp7x8d.txt summary: Abstract The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water, and sanitation in public health. In the current COVID-19 pandemic, tracking of wastewater has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease [11, 12] . Thus SARS-CoV-2 surveillance through water-based epidemiology (WBE) is a potential complimentary and cost-effective approach to enable wide scale screening which would reduce labor intensive and costly personal COVID-19 testing and tracings [11, 17, 18] . Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges abstract: Abstract The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. This short communication on wastewater surveillance in sub-Saharan Africa highlights challenges, opportunities and alternatives taken into account the local context. url: https://api.elsevier.com/content/article/pii/S0048969720342418 doi: 10.1016/j.scitotenv.2020.140719 id: cord-353749-2vlc11rx author: Stricker, Raphael B title: Flattening the Risk: Pre-Exposure Prophylaxis for COVID-19 date: 2020-10-19 words: 3090.0 sentences: 200.0 pages: flesch: 50.0 cache: ./cache/cord-353749-2vlc11rx.txt txt: ./txt/cord-353749-2vlc11rx.txt summary: 24 In one uncontrolled study, HCQ prophylaxis in a hospital setting with a known SARS-CoV-2 exposure prevented dissemination of viral infection. 40 The second case-control study of HCWs found that four or more weekly doses of HCQ resulted in significantly less infection with SARS-CoV-2 (adjusted odds ratio 0.44, p<0.001). 45 In a retrospective cohort study of 32,109 rheumatic disease patients from the US Veterans Health Administration, the incidence of SARS-CoV-2 infection was equivalent regardless of chronic HCQ use (0.3% in users versus 0.4% in non-users), but mortality was significantly decreased in patients taking HCQ (odds ratio 0.70, p=0.0031). SARS-CoV-2 infection in a patient on chronic hydroxychloroquine therapy: implications for prophylaxis Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study Hydroxychloroquine in the COVID-19 pandemic era: in pursuit of a rational use for prophylaxis of SARS-CoV-2 infection abstract: To date, more than 35 million people worldwide have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), and more than one million have died in the COVID-19 pandemic. International economies are stalled and social isolation based on palpable fear of death remains the order of the day. The United States and other countries are moving toward resuming work activities and social interaction to boost economic recovery. While this makes financial sense, from a medical perspective our population has already suffered and will continue to suffer severe losses in the absence of a viable aggressive prophylaxis strategy for SARS-CoV-2. Herein, we present a plan to address this problem. url: https://doi.org/10.2147/idr.s264831 doi: 10.2147/idr.s264831 id: cord-266348-tbr2ynx0 author: Stroemer, A. title: Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera date: 2020-06-17 words: 2893.0 sentences: 215.0 pages: flesch: 61.0 cache: ./cache/cord-266348-tbr2ynx0.txt txt: ./txt/cord-266348-tbr2ynx0.txt summary: Here, we compare the diagnostic accuracy of six commercially available SARS-CoV-2 IgG (Abbott SARS-CoV-2 IgG; Diasorin Liaison SARS-CoV-2 S1/2 IgG; Epitope EDI Novel Coronavirus COVID-19 IgG ELISA Kit; Euroimmun Anti-SARS-CoV-2 ELISA (IgG); Mikrogen recomWell SARS-CoV-2 IgG) or total SARS-CoV-2 antibody assays (Roche Elecsys Anti-SARS-CoV-2). The majority of assay results were confirmed in a laboratory-developed plaque reduction neutralization test and by a SARS-CoV-2 IgG-specific line assay including measurement of generally low IgG avidities (Mikrogen recomLine Coronavirus IgG [Aviditaet], prototype). Out 132 of the remaining 34 samples, only one serum (#20; Figure 1 ) which was obtained ten days after a positive 133 RT-PCR was tested negative for SARS-CoV-2 IgG/total antibodies in the six assays. Six of them -including three family members of a 153 confirmed COVID-19 case (#22; Figure 1 ) -were classified SARS-CoV-2 IgG/total antibody positive by the 154 majority of the tests. abstract: The reliable detection of immunoglobulin G (IgG) or total antibodies directed against the novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is important for clinical diagnostics and epidemiological studies. Here, we compare the diagnostic accuracy of six commercially available SARS-CoV-2 IgG (Abbott SARS-CoV-2 IgG; Diasorin Liaison SARS-CoV-2 S1/2 IgG; Epitope EDI Novel Coronavirus COVID-19 IgG ELISA Kit; Euroimmun Anti-SARS-CoV-2 ELISA (IgG); Mikrogen recomWell SARS-CoV-2 IgG) or total SARS-CoV-2 antibody assays (Roche Elecsys Anti-SARS-CoV-2). The test sensitivities were analyzed with a set of 34 sera obtained from 26 patients after PCR-confirmed SARS-CoV-2 infection and varied from 76.9% (Euroimmun) to 96.2% (Abbott). The majority of assay results were confirmed in a laboratory-developed plaque reduction neutralization test and by a SARS-CoV-2 IgG-specific line assay including measurement of generally low IgG avidities (Mikrogen recomLine Coronavirus IgG [Aviditaet], prototype). Moreover, 100 stored sera collected during summer 2018 (N = 50) and winter season 2018/2019 (N = 50) were included to demonstrate test specificities. These varied from 96.0% (DiaSorin) to 100% (Epitope EDI). A subset of sera were retested with a lateral flow test (STANDARD Q COVID-19 IgM/IgG Duo) and a considerably lower sensitivity was noted. Overall, the diagnostic accuracy of the six SARS-CoV-2 IgG/total antibody assays was good and varied from 92.9% (Euroimmun) to 98.4% (Abbott). Due to the different specificities, results of commercially available SARS-CoV-2 antibody tests should be interpreted with caution. A high proportion of antibody-positive patient sera demonstrated neutralizing capacity against SARS-CoV-2. url: https://doi.org/10.1101/2020.06.15.20131672 doi: 10.1101/2020.06.15.20131672 id: cord-297072-f5lmstyn author: Struck, Anna-Winona title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 date: 2012-01-16 words: 5088.0 sentences: 302.0 pages: flesch: 61.0 cache: ./cache/cord-297072-f5lmstyn.txt txt: ./txt/cord-297072-f5lmstyn.txt summary: title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 Peptide (438)YKYRYL(443) is part of the receptor-binding domain (RBD) of the spike protein of SARS-CoV. The interaction of SARS-CoV with its receptor ACE2 is an attractive drug target as epitopes of the RBD on the spike protein may serve as leads for the design of effective entry inhibitors (Du et al., 2009) . This method allows the determination of the binding specificity, as Table 2 Synthetic peptide library of fourteen 6mer peptides comprising RBD-residues N435-E452 and A471-S500 of SARS-CoV spike protein. We found a hexapeptide in the receptor-binding domain (RBD) of the S protein of SARS-CoV that carries a significant portion of the binding affinity of the virus to the human cell. Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein abstract: In vitro infection of Vero E6 cells by SARS coronavirus (SARS-CoV) is blocked by hexapeptide Tyr-Lys-Tyr-Arg-Tyr-Leu. The peptide also inhibits proliferation of coronavirus NL63. On human cells both viruses utilize angiotensin-converting enzyme 2 (ACE2) as entry receptor. Blocking the viral entry is specific as alpha virus Sindbis shows no reduction in infectivity. Peptide (438)YKYRYL(443) is part of the receptor-binding domain (RBD) of the spike protein of SARS-CoV. Peptide libraries were screened by surface plasmon resonance (SPR) to identify RBD binding epitopes. (438)YKYRYL(443) carries the dominant binding epitope and binds to ACE2 with K(D) = 46 μM. The binding mode was further characterized by saturation transfer difference (STD) NMR spectroscopy and molecular dynamic simulations. Based on this information the peptide can be used as lead structure to design potential entry inhibitors against SARS-CoV and related viruses. url: https://api.elsevier.com/content/article/pii/S0166354211005481 doi: 10.1016/j.antiviral.2011.12.012 id: cord-279725-d82sj80v author: Ströher, Ute title: Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date: 2004-04-01 words: 2235.0 sentences: 126.0 pages: flesch: 52.0 cache: ./cache/cord-279725-d82sj80v.txt txt: ./txt/cord-279725-d82sj80v.txt summary: We evaluated the susceptibility of the SARS-related coronavirus (SARS CoV) to ribavirin and interferon (IFN)-α in vitro by use of cytopathic effect, plaque assay, and immunoblot analysis. To support the search for effective antiviral treatments, we evaluated the susceptibility of SARS CoV isolates (detailed studies were performed with the Tor2 isolate [Toronto, Canada]) to ribavirin and interferon (IFN)-a-2b in vitro. Our data indicate that ribavirin does not inhibit the virus at concentrations attainable in human serum but that IFN-a-2b may be useful and deserves further evaluation as a therapeutic agent. To quantify the effect of IFN-a-2b on the replication of the SARS CoV, Vero E6 cells were infected at an MOI of 0.001 and were incubated in the presence IFN-a-2b (0-5000 IU/mL), as described above. Whether combined therapy with IFN-a-2b and ribavirin would inhibit the replication of the SARS CoV in vitro has not yet been evaluated; the combination is more effective than either agent used alone for the treatment of HCV infection in humans. abstract: Current treatment schemes for severe acute respiratory syndrome (SARS) include broad-spectrum antibiotics, glucocorticoids, and ribavirin. We evaluated the susceptibility of the SARS-related coronavirus (SARS CoV) to ribavirin and interferon (IFN)-α in vitro by use of cytopathic effect, plaque assay, and immunoblot analysis. Ribavirin did not inhibit viral growth at concentrations attainable in human serum. In contrast, IFN-α showed an in vitro inhibitory effect starting at concentrations of 1000 IU/mL. In conclusion, ribavirin alone is unlikely to be beneficial in the prophylaxis or treatment of SARS CoV infections. Clinical trials with IFN-α might be justified to determine a beneficial effect on the outcome of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15031783/ doi: 10.1086/382597 id: cord-346532-4xpnd93d author: Strömich, Léonie title: Allosteric Hotspots in the Main Protease of SARS-CoV-2 date: 2020-11-06 words: 2370.0 sentences: 145.0 pages: flesch: 60.0 cache: ./cache/cord-346532-4xpnd93d.txt txt: ./txt/cord-346532-4xpnd93d.txt summary: Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Bond-to-bond propensities have been shown to successfully detect allosteric sites on proteins [43] and we here present 141 the results in the SARS-CoV-2 M pro to that effect. After a full Bond-to-bond propensity analysis and quantile regression to rank all residues, we are able to score the active 156 site to obtain a measure for the connectivity towards the catalytic center (Tab. S8). A complementary, node-based method, Markov Transient analysis (MTA) 276 identifies areas of the protein that are significantly connected to a site of interest, the source, such as the active site, and 277 obtains the signal propagation that connects the two sites at the atomistic level. abstract: Inhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting. url: https://doi.org/10.1101/2020.11.06.369439 doi: 10.1101/2020.11.06.369439 id: cord-252965-30pl5tx3 author: Stutt, Richard O. J. H. title: A modelling framework to assess the likely effectiveness of facemasks in combination with ‘lock-down’ in managing the COVID-19 pandemic date: 2020-06-10 words: 8015.0 sentences: 341.0 pages: flesch: 48.0 cache: ./cache/cord-252965-30pl5tx3.txt txt: ./txt/cord-252965-30pl5tx3.txt summary: The current COVID-19 pandemic, caused by the virus species severe acute respiratory syndromerelated coronavirus, named SARS-CoV-2 [1] , has stimulated considerable controversy over the potential benefits of facemask use by the public and the timing of the initiation and termination of ''lock-down'' periods. The currently available control measures to combat SARS-Cov-2, therefore, include: physical distancing, population lock-down periods, good sanitation/hand washing/surface disinfecting, good ventilation, facemask and visor protection, as well as diagnostics followed by contact tracing and quarantine of infected and exposed individuals. We use two complementary modelling approaches to test the effectiveness of facemask wearing by sections of the population in reducing the transmission rate of SARS-Cov-2 and hence in reducing the effective reproduction number, R e (the expected number of new cases caused by a single infectious individual at a given point in the epidemic). abstract: COVID-19 is characterized by an infectious pre-symptomatic period, when newly infected individuals can unwittingly infect others. We are interested in what benefits facemasks could offer as a non-pharmaceutical intervention, especially in the settings where high-technology interventions, such as contact tracing using mobile apps or rapid case detection via molecular tests, are not sustainable. Here, we report the results of two mathematical models and show that facemask use by the public could make a major contribution to reducing the impact of the COVID-19 pandemic. Our intention is to provide a simple modelling framework to examine the dynamics of COVID-19 epidemics when facemasks are worn by the public, with or without imposed ‘lock-down’ periods. Our results are illustrated for a number of plausible values for parameter ranges describing epidemiological processes and mechanistic properties of facemasks, in the absence of current measurements for these values. We show that, when facemasks are used by the public all the time (not just from when symptoms first appear), the effective reproduction number, R(e), can be decreased below 1, leading to the mitigation of epidemic spread. Under certain conditions, when lock-down periods are implemented in combination with 100% facemask use, there is vastly less disease spread, secondary and tertiary waves are flattened and the epidemic is brought under control. The effect occurs even when it is assumed that facemasks are only 50% effective at capturing exhaled virus inoculum with an equal or lower efficiency on inhalation. Facemask use by the public has been suggested to be ineffective because wearers may touch their faces more often, thus increasing the probability of contracting COVID-19. For completeness, our models show that facemask adoption provides population-level benefits, even in circumstances where wearers are placed at increased risk. At the time of writing, facemask use by the public has not been recommended in many countries, but a recommendation for wearing face-coverings has just been announced for Scotland. Even if facemask use began after the start of the first lock-down period, our results show that benefits could still accrue by reducing the risk of the occurrence of further COVID-19 waves. We examine the effects of different rates of facemask adoption without lock-down periods and show that, even at lower levels of adoption, benefits accrue to the facemask wearers. These analyses may explain why some countries, where adoption of facemask use by the public is around 100%, have experienced significantly lower rates of COVID-19 spread and associated deaths. We conclude that facemask use by the public, when used in combination with physical distancing or periods of lock-down, may provide an acceptable way of managing the COVID-19 pandemic and re-opening economic activity. These results are relevant to the developed as well as the developing world, where large numbers of people are resource poor, but fabrication of home-made, effective facemasks is possible. A key message from our analyses to aid the widespread adoption of facemasks would be: ‘my mask protects you, your mask protects me’. url: https://doi.org/10.1098/rspa.2020.0376 doi: 10.1098/rspa.2020.0376 id: cord-326883-j7pbe50g author: Stöbe, Stephan title: Echocardiographic characteristics of patients with SARS-CoV-2 infection date: 2020-08-14 words: 4812.0 sentences: 265.0 pages: flesch: 39.0 cache: ./cache/cord-326883-j7pbe50g.txt txt: ./txt/cord-326883-j7pbe50g.txt summary: RESULTS AND METHODS: An extended echocardiographic image acquisition protocol was performed in 18 patients with SARS-CoV-2 infection assessing LV longitudinal, radial, and circumferential deformation including rotation, twist, and untwisting. The present paper describes the experience at the Leipzig University Hospital in detecting myocardial involvement in SARS-CoV-2-infected patients by echocardiography using a specialized extended imaging and analysis protocol to analyze different components of myocardial deformation [19] . In contrast to conventional echocardiography, deformation imaging (n = 14) revealed several interesting findings potentially documenting myocardial involvement in SARS-CoV-2-infected patients with mild/moderate and severe symptoms ( Table 2 ; Figs. The finding of a "reverse basal tako-tsubo-like syndrome" of basal LV segments might also be explained by the edema, which leads to abnormal basal rRS curves without any alterations Fig. 2 Rotational deformation pattern of the same SARS-CoV-2-infected patient with COVID-19 pulmonary disease as in Fig. 1 : normal radial strain patterns are documented in apical (a) and basal (b) left-ventricular (LV) segments. abstract: BACKGROUND: Myocardial involvement induced by SARS-CoV-2 infection might be important for long-term prognosis. The aim of this observational study was to characterize the myocardial effects during SARS-CoV-2 infections by echocardiography. RESULTS AND METHODS: An extended echocardiographic image acquisition protocol was performed in 18 patients with SARS-CoV-2 infection assessing LV longitudinal, radial, and circumferential deformation including rotation, twist, and untwisting. Furthermore, LV deformation was analyzed in an age-matched control group of healthy individuals (n = 20). The most prevalent finding was a reduced longitudinal strain observed predominantly in more than one basal LV segment (n = 10/14 patients, 71%). This pattern reminded of a “reverse tako-tsubo” morphology that is not typical for other viral myocarditis. Additional findings included a biphasic pattern with maximum post-systolic or negative regional radial strain predominantly basal (n = 5/14 patients, 36%); the absence or dispersion of basal LV rotation (n = 6/14 patients, 43%); a reduced or positive regional circumferential strain in more than one segment (n = 7/14 patients, 50%); a net rotation showing late post-systolic twist or biphasic pattern (n = 8/14 patients, 57%); a net rotation showing polyphasic pattern and/or higher maximum net values during diastole (n = 8/14 patients, 57%). CONCLUSION: Myocardial involvement due to SARS-CoV-2-infection was highly prevalent in the present cohort—even in patients with mild symptoms. It appears to be characterized by specific speckle tracking deformation abnormalities in the basal LV segments. These data set the stage to prospectively test whether these parameters are helpful for risk stratification and for the long-term follow-up of these patients. url: https://doi.org/10.1007/s00392-020-01727-5 doi: 10.1007/s00392-020-01727-5 id: cord-291710-ixun0c8g author: Su, Haixia title: Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date: 2020-04-14 words: 2572.0 sentences: 154.0 pages: flesch: 53.0 cache: ./cache/cord-291710-ixun0c8g.txt txt: ./txt/cord-291710-ixun0c8g.txt summary: A crystal structure of SARS-CoV-2 3CLpro in complex with baicalein, the first non-covalent, non-peptidomimetic small-molecule inhibitor, was also determined, revealing a unique binding mode of this natural product with the protease. To validate the binding of baicalin and baicalein with SARS-CoV-2 3CLpro and exclude the suspicion of being the pan-assay interference compounds (PAINS) (15) , their binding affinities with the protease were measured by isothermal titration calorimetry (ITC), widely known as an invaluable tool used to determine thermodynamic parameters of protein-ligand interactions such as Kd (Fig. 1, A and B ; Table 1 ). Moreover, the ITC profiles in combination with their chemical structures suggest that baicalin and baicalein act as noncovalent inhibitors of SARS-CoV-2 3CLpro with a high ligand binding efficiency. The mode of action of baicalein and the structural determinants associated with its binding with SARS-CoV-2 3CLpro were further explored using X-ray protein crystallography. abstract: Human infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause coronavirus disease 19 (COVID-19) and there is currently no cure. The 3C-like protease (3CLpro), a highly conserved protease indispensable for replication of coronaviruses, is a promising target for development of broad-spectrum antiviral drugs. To advance the speed of drug discovery and development, we investigated the inhibition of SARS-CoV-2 3CLpro by natural products derived from Chinese traditional medicines. Baicalin and baicalein were identified as the first non-covalent, non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography is distinctly different from those of known inhibitors. Baicalein is perfectly ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to prevent the peptide substrate approaching the active site. The simple chemical structure, unique mode of action, and potent antiviral activities in vitro, coupled with the favorable safety data from clinical trials, emphasize that baicalein provides a great opportunity for the development of critically needed anti-coronaviral drugs. url: https://doi.org/10.1101/2020.04.13.038687 doi: 10.1101/2020.04.13.038687 id: cord-267261-8z4aqfff author: Su, John R. title: Emerging viral infections date: 2005-03-01 words: 6882.0 sentences: 400.0 pages: flesch: 45.0 cache: ./cache/cord-267261-8z4aqfff.txt txt: ./txt/cord-267261-8z4aqfff.txt summary: In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients abstract: "Emerging infections" have been defined as infections that have newly appeared, that have appeared previously but are expanding in incidence and geographic range, or that threaten to increase in the near future. This article focuses on nine emerging viral infectious agents. These viruses illustrate how such agents emerge: by encroaching on previously unvisited habitats (eg, hantaviruses), by air travel (eg, SARS), and by accidental importation (eg, monkeypox). Additionally, the example of SARS demonstrates not only how quickly emerging viral infections can spread but also how quickly they can be identified and contained with motivated cooperation. url: https://www.sciencedirect.com/science/article/pii/S0272271204000587 doi: 10.1016/j.cll.2004.05.002 id: cord-285965-mar8zt2t author: Su, Liang title: The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19 date: 2020-03-25 words: 2751.0 sentences: 160.0 pages: flesch: 57.0 cache: ./cache/cord-285965-mar8zt2t.txt txt: ./txt/cord-285965-mar8zt2t.txt summary: This study aims to analyze the different clinical characteristics between children and their families infected with severe acute respiratory syndrome coronavirus 2. Here, we report the clinical manifestations, laboratory test results, imaging characteristics, and treatment regimen of nine SARS-CoV-2 infected children and their families in Jinan, Shandong province to increase awareness of this disease, especially in children. A retrospective review was conducted of the clinical, lab tests, and radiologic findings for nine children and their families admitted to the Jinan Infectious Diseases Hospital identified to be nucleic acid-positive for SARS-CoV-2 from 24 January 2020 to 24 February 2020. All the patients were recorded with basic information and epidemiological histories [4] including (1) History of travel or residence in Wuhan and surrounding areas or other reported cases within 14 days of onset; (2) History of contact with new coronavirus infection (nucleic acid-positive) 14 days before onset; (3) history of contact with patients with fever or respiratory symptoms from Wuhan and surrounding areas, or from communities with case reports within 14 days before onset; (4) Cluster onset, along with disease condition changes. abstract: This study aims to analyze the different clinical characteristics between children and their families infected with severe acute respiratory syndrome coronavirus 2. Clinical data from nine children and their 14 families were collected, including general status, clinical, laboratory test, and imaging characteristics. All the children were detected positive result after their families onset. Three children had fever (22.2%) or cough (11.2%) symptoms and six (66.7%) children had no symptom. Among the 14 adult patients, the major symptoms included fever (57.1%), cough (35.7%), chest tightness/pain (21.4%), fatigue (21.4%) and sore throat (7.1%). Nearly 70% of the patients had normal (71.4%) or decreased (28.6%) white blood cell counts, and 50% (7/14) had lymphocytopenia. There were 10 adults (71.4%) showed abnormal imaging. The main manifestations were pulmonary consolidation (70%), nodular shadow (50%), and ground glass opacity (50%). Five discharged children were admitted again because their stool showed positive result in SARS-CoV-2 PCR. COVID-19 in children is mainly caused by family transmission, and their symptoms are mild and prognosis is better than adult. However, their PCR result in stool showed longer time than their families. Because of the mild or asymptomatic clinical process, it is difficult to recognize early for pediatrician and public health staff. url: https://doi.org/10.1080/22221751.2020.1744483 doi: 10.1080/22221751.2020.1744483 id: cord-293701-u4ntxo0y author: Su, Shan title: Learning from the past: development of safe and effective COVID-19 vaccines date: 2020-10-16 words: 8201.0 sentences: 390.0 pages: flesch: 40.0 cache: ./cache/cord-293701-u4ntxo0y.txt txt: ./txt/cord-293701-u4ntxo0y.txt summary: In this Perspective, we summarize examples of vaccine-associated disease enhancement in the history of developing vaccines against respiratory syncytial virus, dengue virus, SARS-CoV and Middle East respiratory syndrome coronavirus, which highlight the importance of a robust safety and efficacy profile, and present recommendations for preclinical and clinical evaluation of COVID-19 vaccine candidates as well as for vaccine design and optimization. One month later, five more candidates had also entered phase I clinical trials, and more than 100 COVID-19 vaccine candidates were in results, all of these vaccines induced antibodies against the spike protein (S protein) and the receptor-binding domain (RBD), including antibodies that neutralized pseudotyped and live SARS-CoV-2. We summarize examples of VADE in the history of the development of vaccines against respiratory syncytial virus (RSV), dengue virus (DENV), SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), each of which provides clues for safe COVID-19 vaccine development and highlights the need for rigorous preclinical and clinical safety testing. abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has elicited an equally rapid response aiming to develop a COVID-19 vaccine. These efforts are encouraging; however, comprehensive efficacy and safety evaluations are essential in the development of a vaccine, and we can learn from previous vaccine development campaigns. In this Perspective, we summarize examples of vaccine-associated disease enhancement in the history of developing vaccines against respiratory syncytial virus, dengue virus, SARS-CoV and Middle East respiratory syndrome coronavirus, which highlight the importance of a robust safety and efficacy profile, and present recommendations for preclinical and clinical evaluation of COVID-19 vaccine candidates as well as for vaccine design and optimization. url: https://doi.org/10.1038/s41579-020-00462-y doi: 10.1038/s41579-020-00462-y id: cord-344330-zsx7wfyj author: Su, Shuo title: Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses date: 2016-03-21 words: 4537.0 sentences: 227.0 pages: flesch: 49.0 cache: ./cache/cord-344330-zsx7wfyj.txt txt: ./txt/cord-344330-zsx7wfyj.txt summary: Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans. In humans, CoV infections primarily involve the upper respiratory tract and the gastrointestinal tract, and vary from mild, self-limiting disease, such as the common cold, to more severe manifestations, such as bronchitis and pneumonia with renal involvement [15] . A recent investigation discovered that multiple HCoV species, including MERS-CoV, beta-CoV group A, and a 229E-like virus, circulate amongst dromedary camels in Saudi Arabia [62] . Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection abstract: Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans. url: https://www.sciencedirect.com/science/article/pii/S0966842X16000718 doi: 10.1016/j.tim.2016.03.003 id: cord-316616-j82q99in author: Su, Yen-Bo title: Cardiovascular manifestation and treatment in COVID-19 date: 2020-05-19 words: 4445.0 sentences: 243.0 pages: flesch: 36.0 cache: ./cache/cord-316616-j82q99in.txt txt: ./txt/cord-316616-j82q99in.txt summary: The novel coronavirus disease 2019 (COVID-19), with first presentation of atypical pneumonia, has spread rapidly from Wuhan, China, on December 12, 2019 to over 200 countries, caused 2 310 572 infected individuals and 158 691 mortalities, updated on April 19, 2020. 33, 41 In a small singlearm study of patients with confirmed COVID-19, treatment with hydroxychloroquine was associated with a significant difference in clearing of viral nasopharyngeal carriage of SARS-CoV2 within 3 to 6 days when compared with untreated controls. ACE2 levels are increased following treatment with ACE inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), which yield the concerns that using these medications might increase the severity of COVID-19, especially in patients with existing cardiovascular diseases. Patients with comorbidities including hypertension, cardiovascular diseases, and diabetes tend to have higher risk for having severe COVID-19 which leads to acute respiratory distress syndrome (ARDS) and mortality. Risk factors associated with acute respiratory distress syndrome and death in patients With coronavirus disease 2019 pneumonia in Wuhan, China abstract: The novel coronavirus disease 2019 (COVID-19), with first presentation of atypical pneumonia, has spread rapidly from Wuhan, China, on December 12, 2019 to over 200 countries, caused 2 310 572 infected individuals and 158 691 mortalities, updated on April 19, 2020. Many studies have published timely to help global healthcare workers to understand and control the disease. Vulnerable patients with risk factors such as elderly, cardiovascular diseases (eg, hypertension, coronary disease, or cardiomyopathy), diabetes, and chronic kidney disease have worse outcomes after COVID-19 infection. COVID-19 could directly cause cardiovascular injuries such as pericarditis, myocarditis, myocardial infarction, heart failure, arrhythmias, or thromboembolic events, which urge cardiologists to be involved in the frontline to practice. Here, we provide a review of COVID-19 on cardiovascular system to assist clinical cardiologists to better understand the disease and being capable of providing comprehensive medical support. url: https://doi.org/10.1097/jcma.0000000000000352 doi: 10.1097/jcma.0000000000000352 id: cord-339686-oybnk1j8 author: Suassuna, José Hermógenes Rocco title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine date: 2020-08-26 words: 5770.0 sentences: 281.0 pages: flesch: 41.0 cache: ./cache/cord-339686-oybnk1j8.txt txt: ./txt/cord-339686-oybnk1j8.txt summary: title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine We produced this document to bring pertinent information to the practice of nephrology, as regards to the renal involvement with COVID-19, the management of acute kidney injury cases, and practical guidance on the provision of dialysis support.As information on COVID-19 evolves at a pace never before seen in medical science, these recommendations, although based on recent scientific evidence, refer to the present moment. Every professional involved in nephrological care must provide the best possible assistance to the patients under their responsibility, adopt practices that minimize their personal risk of contamination, that of their patients and the whole range of other professionals who participate in hospital kidney support, including nurses and technicians, dialysis staff, healthcare professionals from all areas (for example, doctors and nurses in intensive care medicine), laboratory and radiology technicians, cleaning and transport staff, etc. abstract: We produced this document to bring pertinent information to the practice of nephrology, as regards to the renal involvement with COVID-19, the management of acute kidney injury cases, and practical guidance on the provision of dialysis support.As information on COVID-19 evolves at a pace never before seen in medical science, these recommendations, although based on recent scientific evidence, refer to the present moment. The guidelines may be updated when published data and other relevant information become available. url: https://doi.org/10.1590/2175-8239-jbn-2020-s107 doi: 10.1590/2175-8239-jbn-2020-s107 id: cord-311446-afhw0450 author: Suhandynata, Raymond T title: Multi-platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19 date: 2020-08-07 words: 3328.0 sentences: 194.0 pages: flesch: 56.0 cache: ./cache/cord-311446-afhw0450.txt txt: ./txt/cord-311446-afhw0450.txt summary: Diazyme, Roche, and Abbott SARS-CoV-2 serology assays were compared by correlating the raw quantitative values from each platform for all samples from PCR positive patients ( Supplementary Figure 2A-C) . The impact of disease prevalence on the PPV and negative predictive value (NPV) for the Diazyme, Roche, and Abbott SARS-CoV-2 serology platforms were calculated using the PPA and NPA of the ≥ 15 day patient group ( Table 4 and Supplementary Table 4 ). The prevalence for COVID-19 in the ≥ 15 day patient group was 12.3%, and the observed PPV for the Diazyme IgM/IgG panel, the Roche total Ig, and the Abbott IgG assays were 89.3%, 96.0%, and 92.6%, respectively. We evaluated longitudinal samples from 16 SARS-CoV-2 PCR positive patients with the Diazyme, Roche, and Abbott serology platforms (Figure 2A -2D) . We evaluated the PPA and NPA of the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays using the same samples across all three platforms. abstract: BACKGROUND: COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel beta-coronavirus that is responsible for the 2019 coronavirus pandemic. Acute infections should be diagnosed by polymerase chain reaction (PCR) based tests, but serology tests can demonstrate previous exposure to the virus. METHODS: We compared the performance of the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays using 179 negative subjects to determine negative percent agreement (NPA) and in 60 SARS-CoV-2 PCR confirmed positive patients to determine positive percent agreement (PPA) at three different timeframes following a positive SARS-CoV-2 PCR result. RESULTS: At ≥ 15 days, the PPA (95% CI) was 100 (86.3–100)% for the Diazyme IgM/IgG panel, 96.0 (79.7–99.9)% for the Roche total Ig assay, and 100 (86.3–100)% for the Abbott IgG assay. The NPA (95% CI) was 98.3 (95.2–99.7)% for the Diazyme IgM/IgG panel, 99.4 (96.9–100)% for the Roche total Ig assay, and 98.9 (96.0–99.9)% for the Abbott IgG assay. When the Roche total Ig assay was combined with either the Diazyme IgM/IgG panel or the Abbott IgG assay, the positive predictive value was 100% while the negative predictive value remained greater than 99%. CONCLUSIONS: Our data demonstrates that the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays have similar clinical performance. We demonstrated a low false positive rate across all three platforms and observed that false positives observed on the Roche platform are unique compared to those observed on the Diazyme or Abbott assays. Using multiple platforms in tandem increases the PPVs which is important when screening populations with low disease prevalence. url: https://doi.org/10.1093/jalm/jfaa139 doi: 10.1093/jalm/jfaa139 id: cord-261029-befymalm author: Sultan, Keith title: Review of inflammatory bowel disease and COVID-19 date: 2020-10-07 words: 3257.0 sentences: 153.0 pages: flesch: 48.0 cache: ./cache/cord-261029-befymalm.txt txt: ./txt/cord-261029-befymalm.txt summary: Early reports of the virus, now known as severe acute respiratory syndrome coronavirus 2, and its clinical disease coronavirus disease 2019 (COVID-19), has shown higher rates of morbidity and mortality in the elderly and those with pre-existing medical conditions. The authors also reported that there had been no cases of IBD/SARS-CoV-2 infected patients in the three largest tertiary IBD centers in Wuhan (Tongji Hospital, Union Hospital, and Zhongnan Hospital) at the time their manuscript was prepared, March 8, 2020. Rodriguez-Lago et al [29] reported on 40 cases of IBD (21 hospitalized) with confirmed positive tests for SARS-CoV-2 from 5 sites in the Basque Country (Spain), median age 59 years, 60% male, 32% Crohn''s disease (CD), with 28% on immune therapy, 18% biologic, and 10% systemic corticosteroids. To date, the largest national case reporting has come from a combined 24 IBD referral centers in Italy, affiliated with the Italian Group for the Study of Inflammatory Bowel Disease (IG-IBD) [32] . abstract: The first cases of a novel corona virus infection were reported in Wuhan China in December of 2019, followed by the declaration of an international pandemic by the World Health Organization in March 2020. Early reports of the virus, now known as severe acute respiratory syndrome coronavirus 2, and its clinical disease coronavirus disease 2019 (COVID-19), has shown higher rates of morbidity and mortality in the elderly and those with pre-existing medical conditions. Of particular concern is the safety of those with compromised immune systems. Inflammatory Bowel disease (IBD) is itself caused by a disordered immune response, with the most effective medical therapies being immune suppressing or modifying. As such, the risk of COVID-19, virus related outcomes, and appropriate management of IBD patients during the global pandemic is of immediate concern to gastroenterologists worldwide. There has been a rapid accumulation of clinical data and expert opinion on the topic. This review will highlight the latest source information on clinical observation/outcomes of the IBD population and provide a concise summary of the most up to date perspectives on IBD management in the age of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33088153/ doi: 10.3748/wjg.v26.i37.5534 id: cord-331558-6rqd3fmj author: Sun, Chuan-bin title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 words: 5459.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-331558-6rqd3fmj.txt txt: ./txt/cord-331558-6rqd3fmj.txt summary: Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. abstract: The outbreak of the current 2019 novel coronavirus (2019-nCoV, now named SARS-CoV-2) infection has become a worldwide health threat. Currently, more information is needed so as to further understand the transmission and clinical characteristics of 2019-nCoV infection and the infection control procedures required. Recently, the role of the eye in transmitting 2019-nCoV has been intensively discussed. Previous investigations of other highly infectious human CoVs, that is, severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV), may provide useful information. In this review, we describe the genomics and morphology of human CoVs, the epidemiology, systemic and ophthalmic manifestations, and mechanisms of human CoV infection, and recommendations for infection control procedures. The role of the eye in the transmission of 2019-nCoV is discussed in detail. Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. This suggests that the eye is neither a preferred organ of human CoV infection nor a preferred gateway of entry for human CoVs for infecting the respiratory tract. However, pathogens that the ocular surface is exposed to might be transported to nasal and nasopharyngeal mucosa by constant tear rinsing through the lacrimal duct system and then cause respiratory tract infection. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs by droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. url: https://doi.org/10.3389/fpubh.2020.00155 doi: 10.3389/fpubh.2020.00155 id: cord-352304-tt2q5mgs author: Sun, Dan title: Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center’s observational study date: 2020-03-19 words: 3229.0 sentences: 194.0 pages: flesch: 52.0 cache: ./cache/cord-352304-tt2q5mgs.txt txt: ./txt/cord-352304-tt2q5mgs.txt summary: METHODS: We included eight severe or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children''s Hospital from January 24 to February 24. The outbreak of coronavirus disease 2019 (COVID-19, previously known as 2019-nCoV) caused by SARS-CoV-2 infection in Wuhan City, China, has spread around the world [1] . We included eight severely or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children''s Hospital from January 24 to February 24. Critically ill COVID-19 was defined when the pediatric patients met any of the following criteria: (1) respiratory failure which requires mechanical ventilation; (2) septic shock, and (3) accompanied by other organ failure that needs ICU monitoring and treatment. Demographic information and clinical characteristics including exposure history, anamnesis, signs and symptoms, chest computed tomographic (CT) scan or X-ray results, complications, treatments, clinical outcomes, and laboratory findings of each patient were obtained from the Electronic Medical Record System of Wuhan Children''s Hospital. abstract: BACKGROUND: An outbreak of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 was first detected in Wuhan, Hubei, China. People of all ages are susceptible to SARS-CoV-2 infection. No information on severe pediatric patients with COVID-19 has been reported. We aimed to describe the clinical features of severe pediatric patients with COVID-19. METHODS: We included eight severe or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children’s Hospital from January 24 to February 24. We collected information including demographic data, symptoms, imaging data, laboratory findings, treatments and clinical outcomes of the patients with severe COVID-19. RESULTS: The onset age of the eight patients ranged from 2 months to 15 years; six were boys. The most common symptoms were polypnea (8/8), followed by fever (6/8) and cough (6/8). Chest imaging showed multiple patch-like shadows in seven patients and ground-glass opacity in six. Laboratory findings revealed normal or increased whole blood counts (7/8), increased C-reactive protein, procalcitonin and lactate dehydrogenase (6/8), and abnormal liver function (4/8). Other findings included decreased CD16 + CD56 (4/8) and Th/Ts*(1/8), increased CD3 (2/8), CD4 (4/8) and CD8 (1/8), IL-6 (2/8), IL-10 (5/8) and IFN-γ (2/8). Treatment modalities were focused on symptomatic and respiratory support. Two critically ill patients underwent invasive mechanical ventilation. Up to February 24, 2020, three patients remained under treatment in ICU, the other five recovered and were discharged home. CONCLUSIONS: In this series of severe pediatric patients in Wuhan, polypnea was the most common symptom, followed by fever and cough. Common imaging changes included multiple patch-like shadows and ground-glass opacity; and a cytokine storm was found in these patients, which appeared more serious in critically ill patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32193831/ doi: 10.1007/s12519-020-00354-4 id: cord-298406-7wfdwou8 author: Sun, Haifang title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus date: 2003-12-31 words: 2678.0 sentences: 161.0 pages: flesch: 60.0 cache: ./cache/cord-298406-7wfdwou8.txt txt: ./txt/cord-298406-7wfdwou8.txt summary: title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus To facilitate the studies regarding the functions and structures of SARS_3CLpro, in this report the synthetic genes encoding 3CLpro of SARS_CoV were assembled, and the plasmid was constructed using pQE30 as vector and expressed in Escherichia coli M15 cells. In our previous work [24, 25] , we reported a 3D model of SARS_3CL pro and its inhibitor design by virtual screening, as well as the cloning, expression, and purification of the E protein of SARS_CoV. In this article, we would like to present the results describing the molecular cloning, expression and purification of 3CL pro of SARS_CoV, and the preliminary study on its mass spectrometric characterization is also reported. Expression and purification of SARS_3CL pro Escherichia coli M15 cells transformed with the plasmid pQE30-SARS_3CL pro were grown in 100 ml LB medium containing ampicillin (100 mg/L) and kanamycin (25 mg/L) at 37°C overnight and then inoculated into 1 L LB supplemented with both the antibiotics. abstract: Abstract Severe acute respiratory syndrome (SARS) is an acute respiratory illness, which has broken out in China. It has been known that SARS coronavirus (SARS_CoV) is a novel human coronavirus and is responsible for SARS infection. Belonging to one of the major proteins associated with SARS_CoV, SARS 3C-like protease (SARS_3CLpro) functions as a cysteine protease engaging in the proteolytic cleavage of the viral precursor polyprotein to a series of functional proteins required for coronavirus replication and is considered as an appealing target for designing anti-SARS agents. To facilitate the studies regarding the functions and structures of SARS_3CLpro, in this report the synthetic genes encoding 3CLpro of SARS_CoV were assembled, and the plasmid was constructed using pQE30 as vector and expressed in Escherichia coli M15 cells. The highly yielded (∼15mg/L) expressed protease was purified by use of NTA-Ni2+ affinity chromatography and FPLC system, and its sequence was determined by LC/MS with the residue coverage of 46.4%. url: https://api.elsevier.com/content/article/pii/S1046592803002614 doi: 10.1016/j.pep.2003.08.016 id: cord-281727-elartlro author: Sun, Jing title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient date: 2020-05-18 words: 974.0 sentences: 60.0 pages: flesch: 58.0 cache: ./cache/cord-281727-elartlro.txt txt: ./txt/cord-281727-elartlro.txt summary: title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. A novel coronavirus SARS-CoV-2 emerged to cause a major outbreak of severe pneumonia in humans in China and has spread to over 100 other countries [1] . Although viral RNA can be detected in multiple organs in COVID-19 patients, infectious SARS-CoV-2 has only been isolated from respiratory specimens [3, 4] . The urine sample tested positive for SARS-CoV-2 RNA on day 12 post infection (p.i.) (February 5th) for the first time and had periodically showed positive results in RT-PCR test until March 6th. Although it is hard to determine whether the kidney, the testis or the bladder were infected and produced infectious virus from current study, isolation of infectious SARS-CoV-2 in urine raises the possibility of fecal/urine-respiratory transmission. abstract: SARS-CoV-2 caused a major outbreak of severe pneumonia (COVID-19) in humans. Viral RNA was detected in multiple organs in COVID-19 patients. However, infectious SARS-CoV-2 was only isolated from respiratory specimens. Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. The virus isolated could infect new susceptible cells and was recognized by its’ own patient sera. Appropriate precautions should be taken to avoid transmission from urine. url: https://doi.org/10.1080/22221751.2020.1760144 doi: 10.1080/22221751.2020.1760144 id: cord-275340-q8d7rvnj author: Sun, JingKang title: Advances in the use of chloroquine and hydroxychloroquine for the treatment of COVID-19 date: 2020-06-21 words: 6629.0 sentences: 285.0 pages: flesch: 47.0 cache: ./cache/cord-275340-q8d7rvnj.txt txt: ./txt/cord-275340-q8d7rvnj.txt summary: CQ/HCQ may synergistically exert antiviral and immunomodulatory effects on COVID-19 through multiple mechanisms including hindering the receptor recognition process by influencing the affinity of ACE2 and S protein, and the affinity for sialic acid and ganglioside; inhibiting the membrane fusion process by suppressing endolysosome acidification; suppressing the p38 activation and affecting host defense machinery, and preventing MHC class II expression (block expression of CD154 on the surface of CD4 + T cell) and TLR signaling and reducing the production of cytokines through inhibiting the activation of T cells and B cells. ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; CQ, chloroquine; HCQ, hydroxychloroquine; CoVs, coronaviruses; MAPK, mitogen-activated protein kinase; MHC-II, major histocompatibility complex class II; TLR, toll-like receptor; cGAS, cyclic GMP-AMP synthase; IFN, interferon; IL, interleukin; TNF-α, tumor necrosis factor-α. The authors deemed that the anti-inflammatory effect of low-dose HCQ and the activity of inhibiting viral replication may have important significance in critically ill patients with COVID-19. abstract: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading worldwide. Antiviral therapy is the most important treatment for COVID-19. Among the drugs under investigation, anti-malarials, chloroquine (CQ) and hydroxychloroquine (HCQ), are being repurposed as treatment for COVID-19. CQ/HCQ were shown to prevent receptor recognition by coronaviruses, inhibit endosome acidification, which interferes with membrane fusion, and exhibit immunomodulatory activity. These multiple mechanisms may work together to exert a therapeutic effect on COVID-19. A number of in vitro studies revealed inhibitory effects of CQ/HCQ on various coronaviruses, including SARS-CoV-2 although conflicting results exist. Several clinical studies showed that CQ/HCQ alone or in combination with a macrolide may alleviate the clinical symptoms of COVID-19, promote viral conversion, and delay disease progression, with less serious adverse effects. However, recent studies indicated that the use of CQ/HCQ, alone or in combination with a macrolide, did not show any favorable effect on patients with COVID-19. Adverse effects, including prolonged QT interval after taking CQ/HCQ, may develop in COVID-19 patients. Therefore, current data are not sufficient enough to support the use of CQ/HCQ as therapies for COVID-19 and increasing caution should be taken about the application of CQ/HCQ in COVID-19 before conclusive findings are obtained by well-designed, multi-center, randomized, controlled studies. url: https://doi.org/10.1080/00325481.2020.1778982 doi: 10.1080/00325481.2020.1778982 id: cord-330045-4gj9d181 author: Sun, Jiufeng title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date: 2020-08-17 words: 1541.0 sentences: 93.0 pages: flesch: 57.0 cache: ./cache/cord-330045-4gj9d181.txt txt: ./txt/cord-330045-4gj9d181.txt summary: We recruited hospitalized patients with COVID-19 from 2 designated provincial emergency hospitals for e merging infectious diseases in Guangdong, China, and tested specimens by real-time reverse transcription PCR (rRT-PCR) to estimate the duration of the detection of SARS-CoV-2 RNA in various body fluids, using an accelerated failure time (AFT)-based modeling study. We used parametric Weibull regression models (AFT) to estimate the time until the loss of SARS-CoV-2 RNA detection in each body fluid and reported findings in medians and 95th percentiles using R software version 3.6.1 with flexsurv, survival, and survminer packages (9) . We used Weibull models to estimate the median and the 95th percentile for the time until the loss of SARS-CoV-2 RNA detection in swab, sputum, and fecal samples (Table; Figures 1, 2) . In this study, we estimated the time for COVID-19 case-patients to clear SARS-CoV-2 RNA in the acute phase of infection through an AFT-based modeling study. abstract: We prospectively assessed 49 coronavirus disease cases in Guangdong, China, to estimate the frequency and duration of detectable severe acute respiratory syndrome coronavirus 2 RNA in human body fluids. The prolonged persistence of virus RNA in various body fluids may guide the clinical diagnosis and prevention of onward virus transmission. url: https://doi.org/10.3201/eid2608.201097 doi: 10.3201/eid2608.201097 id: cord-319447-xanewi59 author: Sun, Jiya title: Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date: 2020-05-01 words: 3250.0 sentences: 163.0 pages: flesch: 52.0 cache: ./cache/cord-319447-xanewi59.txt txt: ./txt/cord-319447-xanewi59.txt summary: To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. In this study, we used the SARS-CoV-2 strain isolated from patients [11] to infect in vitro Calu-3 cells, and performed RNA sequencing to determine the time-series transcriptome profiling data of the host. Next, to gain possible explanations for the distinct patterns in host antiviral capacity and cytokine production during SARS-CoV-2 infection, dynamic expression of four types of key genes were evaluated, including virus receptors for cell entry, pathogen recognition receptors (PRRs) for an innate immune startup, regulator genes for induction of antiviral-related genes and interferon production (Figure 4) . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a widespread outbreak of highly pathogenic COVID-19. It is therefore important and timely to characterize interactions between the virus and host cell at the molecular level to understand its disease pathogenesis. To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. Our analysis results showed that the rapid growth of the virus was accompanied by an early intensive response of host genes. We also systematically compared the molecular footprints of the host cells in response to SARS-CoV-2, SARS-CoV and MERS-CoV. Upon infection, SARS-CoV-2 induced hundreds of up-regulated host genes hallmarked by a significant cytokine production followed by virus-specific host antiviral responses. While the cytokine and antiviral responses triggered by SARS-CoV and MERS-CoV were only observed during the late stage of infection, the host antiviral responses during the SARS-CoV-2 infection were gradually enhanced lagging behind the production of cytokine. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. Taken together, our findings provide novel molecular insights into the mechanisms underlying the infectivity and pathogenicity of SARS-CoV-2. url: https://doi.org/10.1101/2020.04.30.071274 doi: 10.1101/2020.04.30.071274 id: cord-268740-ldz5366v author: Sun, Mei title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients date: 2020-08-14 words: 2389.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-268740-ldz5366v.txt txt: ./txt/cord-268740-ldz5366v.txt summary: title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients We propose anal swabs as the potentially optimal specimen for SARS-CoV-2 detection for evaluation of hospital discharge of COVID-19 patients. In this study, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of a few cured patients, which challenges the current standards for discharge and termination of compulsory isolation for COVID-19 patients. In summary, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of several cured patients. • SARS-CoV-2 detection is positive in anal swabs but negative in throat swabs and sputum swabs of a few discharged patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. abstract: Since December 2019, an outbreak of SARS coronavirus 2 (SARS-CoV-2) began in Wuhan, and has rapidly spread worldwide. Previously, discharged patients with coronavirus disease 2019 (COVID-19) patients met the criteria of China’s pneumonia diagnosis and treatment program of novel coronavirus infection (trial version 7) for cure of viral infection. Nevertheless, positive detection of SARS-CoV-2 has been found again in several cured COVID-19 patients, leading to conflicts with current criteria. Here, we report clinically cured cases with positive results only in anal swabs, and investigate the clinical value of anal swabs for SARS-CoV-2 detection. url: https://doi.org/10.2217/fmb-2020-0090 doi: 10.2217/fmb-2020-0090 id: cord-345275-h0hvaxgx author: Sun, Mengyao title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 words: 5308.0 sentences: 286.0 pages: flesch: 56.0 cache: ./cache/cord-345275-h0hvaxgx.txt txt: ./txt/cord-345275-h0hvaxgx.txt summary: title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection abstract: Abstract Background Convalescent plasma (CP) has been used successfully to treat many types of infectious diseases, and it has shown initial effects in the treatment of the emerging 2019 coronavirus disease (COVID-19). However, its curative effect and feasibility have yet to be confirmed by formal evaluation and well-designed clinical trials. To explore the effectiveness of treatment and predict the potential effect of CP for COVID-19, studies of different types of infectious diseases treated with CP were included in this systematic review and meta-analysis. Methods Related studies were obtained from databases and screened based on the inclusion criteria. The data quality was assessed, and the data were extracted and pooled for analysis. Results We included 40 studies on CP treatment for infectious diseases We found that CP treatment could reduce the risk of mortality with a low incidence of adverse events, promote the production of antibodies, show the decline in viral load, and shorten the disease course. A meta-analysis of 15 controlled studies showed that there was a significantly lower mortality rate in the group treated with CP (pooled OR = 0.32, 95% CI: 0.19-0.52, P < 0.001, I2 = 54%) than in the control groups. Studies were mostly of low or very low quality with a moderate or high risk of bias. The sources of clinical and methodological heterogeneity were identified. The exclusion of heterogeneity indicated that the results were stable. Conclusions CP therapy has some curative effect and is well tolerated to treat infectious diseases. It is a potentially effective treatment for COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305427?v=s5 doi: 10.1016/j.ijid.2020.06.107 id: cord-307263-znuqdzdp author: Sun, Niuniu title: A Qualitative Study on the Psychological Experience of Caregivers of COVID-19 Patients date: 2020-04-08 words: 4478.0 sentences: 250.0 pages: flesch: 50.0 cache: ./cache/cord-307263-znuqdzdp.txt txt: ./txt/cord-307263-znuqdzdp.txt summary: Previous studies have shown that during sudden natural disasters and infectious diseases, nurses will sacrifice their own needs to actively participate in the anti-epidemic work and make selfless contributions out of moral and professional responsibility [7] . Previous studies have shown that when nurses are in close contact with patients with emerging infectious diseases such as SARS [9] , MERS-Cov [10, 11] , Ebola [12] , H1N1 [13] , they will suffer from loneliness, anxiety, fear, fatigue, sleep disorders, and other physical and mental health problems. This study explored the psychological experience of caregivers of patients with COVID-19 using phenomenological methods and we summarised our findings into four themes: significant amounts of negative emotions at an early stage, self-coping styles, growth under stress, and positive emotions that occur simultaneously or progressively with negative emotions. abstract: BACKGROUND: The coronavirus disease 2019 (COVID-19) is spreading rapidly, bringing pressure and challenges to nursing staff. OBJECTIVE: To explore the psychology of nurses caring for COVID-19 patients. METHOD: Using a phenomenological approach, we enrolled 20 nurses who provided care for COVID-19 patients in the First Affiliated Hospital of Henan University of Science and Technology from 20 January to 10 February 2020. The interviews were conducted face-to-face or by telephone and were analysed by Colaizzi's 7-step method. RESULTS: The psychological experience of nurses caring for COVID-19 patients can be summarized into four themes. Firstly, negative emotions present in early stage consisting of fatigue, discomfort, and helplessness was caused by high-intensity work, fear and anxiety, and concern for patients and family members. Secondly, self-coping styles included psychological and life adjustment, altruistic acts, team support, and rational cognition. Thirdly, we found growth under pressure, which included increased affection and gratefulness, development of professional responsibility, and self-reflection. Finally, we showed that positive emotions occurred simultaneously with negative emotions. CONCLUSIONS: During an epidemic outbreak, positive and negative emotions of the front-line nurses interweaved and coexisted. In the early stage, negative emotions were dominant and positive emotions appeared gradually. Self-coping styles and psychological growth played an important role in maintaining mental health of nurses. url: https://www.sciencedirect.com/science/article/pii/S0196655320302017?v=s5 doi: 10.1016/j.ajic.2020.03.018 id: cord-325452-2sywbgje author: Sun, Pengfei title: Understanding of COVID‐19 based on current evidence date: 2020-03-05 words: 963.0 sentences: 68.0 pages: flesch: 57.0 cache: ./cache/cord-325452-2sywbgje.txt txt: ./txt/cord-325452-2sywbgje.txt summary: A study by Wang et al 12 In the absence of effective treatments, the best way to deal with the SARS-CoV-2 epidemic is to control the sources of infection. 9 According to the official Chinese data, the case fatality rate among the SARS-CoV-2-infected patients was much lower than that of SARS and MERS. These studies will help further reduce the case fatality and transmission rates among SARS-CoV-2-infected patients. Moreover, super-spreaders were reported during the SARS and MERS epidemics. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in Wuhan, China Updated understanding of the outbreak of 2019 novel coronavirus (2019-nCoV) in Wuhan Clinical features of patients infected with 2019 novel coronavirus in Wuhan Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 Clinical characteristics of 2019 novel coronavirus infection in China abstract: Since December 2019, a series of unexplained pneumonia cases have been reported in Wuhan, China. On 12 January 2020, the World Health Organization (WHO) temporarily named this new virus as the 2019 novel coronavirus (2019‐nCoV). On 11 February 2020, the WHO officially named the disease caused by the 2019‐nCoV as coronavirus disease (COVID‐19). The COVID‐19 epidemic is spreading all over the world, especially in China. Based on the published evidence, we systematically discuss the characteristics of COVID‐19 in the hope of providing a reference for future studies and help for the prevention and control of the COVID‐19 epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32096567/ doi: 10.1002/jmv.25722 id: cord-346677-20ky3t6y author: Sun, Pengfei title: Clinical characteristics of hospitalized patients with SARS‐CoV‐2 infection: A single arm meta‐analysis date: 2020-03-11 words: 1647.0 sentences: 112.0 pages: flesch: 52.0 cache: ./cache/cord-346677-20ky3t6y.txt txt: ./txt/cord-346677-20ky3t6y.txt summary: OBJECTIVE: We aim to summarize reliable evidence of evidence‐based medicine for the treatment and prevention of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) by analyzing all the published studies on the clinical characteristics of patients with SARS‐CoV‐2. Since December 2019, the epidemic of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infectious pneumonia in Wuhan, China. To acquire more accurate conclusions on the clinical characteristics and mortality of patients with SARS-CoV-2 infection, we searched the relevant literatures and carried out single-arm metaanalysis. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 17 hospitalized patients with 2019 novel coronavirus infections outside Wuhan, China. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: A single arm meta-analysis abstract: OBJECTIVE: We aim to summarize reliable evidence of evidence‐based medicine for the treatment and prevention of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) by analyzing all the published studies on the clinical characteristics of patients with SARS‐CoV‐2. METHODS: PubMed, Cochrane Library, Embase, and other databases were searched. Several studies on the clinical characteristics of SARS‐CoV‐2 infection were collected for meta‐analysis. RESULTS: Ten studies were included in Meta‐analysis, including a total number of 50466 patients with SARS‐CoV‐2 infection. Meta‐analysis shows that, among these patients, the incidence of fever was 0.891 (95% CI: 0.818, 0.945), the incidence of cough was 0.722 (95% CI: 0.657, 0.782), and the incidence of muscle soreness or fatigue was 0.425 (95% CI: 0.213, 0.652). The incidence of acute respiratory distress syndrome (ARDS) was 0.148 (95% CI: 0.046, 0.296), the incidence of abnormal chest computer tomography (CT) was 0.966 (95% CI: 0.921, 0.993), the percentage of severe cases in all infected cases was 0.181 (95% CI: 0.127, 0.243), and the case fatality rate of patients with SARS‐CoV‐2 infection was 0.043 (95% CI: 0.027, 0.061). CONCLUSION: Fever and cough are the most common symptoms in patients with SARS‐CoV‐2 infection, and most of these patients have abnormal chest CT examination. Several people have muscle soreness or fatigue as well as ARDS. Diarrhea, hemoptysis, headache, sore throat, shock, and other symptoms are rare. The case fatality rate of patients with SARS‐CoV‐2 infection is lower than that of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). This meta‐analysis also has limitations, so the conclusions of this Meta‐analysis still need to be verified by more relevant studies with more careful design, more rigorous execution, and larger sample size. url: https://doi.org/10.1002/jmv.25735 doi: 10.1002/jmv.25735 id: cord-312305-ll29frwc author: Sun, Shihui title: Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date: 2020-11-11 words: 4720.0 sentences: 270.0 pages: flesch: 52.0 cache: ./cache/cord-312305-ll29frwc.txt txt: ./txt/cord-312305-ll29frwc.txt summary: Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. We further characterized the in vivo replication dynamics of MASCp6 in both young and aged mice, and the results from qRT-PCR showed that high levels of SARS-CoV-2 subgenomic RNAs were persistent in the lung and tracheas till 4 day post infection (dpi) in aged mice (Fig. 1E) . The skewed age distribution of COVID-19 disease was reproduced in the MASCp36 infected mouse model where more severe symptoms were observed in aged mice when compared to young mice. In addition to the age-related skewed distribution of COVID-19, gender-related differences in distribution of COVID-19 disease is also recapitulated in this MASCp36 infected mouse model with increased susceptibility and enhanced pathogenicity observed in male mice when compared to their female counterparts. abstract: The ongoing SARS-CoV-2 pandemic has brought an urgent need for animal models to study the pathogenicity of the virus. Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. Particularly, this model exhibits age and gender related skewed distribution of mortality akin to severe COVID-19, and the 50% lethal dose (LD50) of MASCp36 was ∼100 PFU in aged, male BALB/c mice. Deep sequencing identified three amino acid mutations, N501Y, Q493H, and K417N, subsequently emerged at the receptor binding domain (RBD) of MASCp36, which significantly enhanced the binding affinity to its endogenous receptor, mouse ACE2 (mACE2). Cryo-electron microscopy (cryo-EM) analysis of mACE2 in complex with the RBD of MASCp36 at 3.7-angstrom resolution elucidates molecular basis for the receptor-binding switch driven by amino acid substitutions. Our study not only provides a robust platform for studying the pathogenesis of severe COVID-19 and rapid evaluation of coutermeasures against SARS-CoV-2, but also unveils the molecular mechanism for the rapid adaption and evolution of SARS-CoV-2 in mice. One sentence summary A mouse adapted SARS-CoV-2 strain that harbored three amino acid substitutions in the RBD of S protein showed 100% mortality in aged, male BALB/c mice. url: https://doi.org/10.1101/2020.11.10.377333 doi: 10.1101/2020.11.10.377333 id: cord-272019-4uua0zgp author: Sun, Wei title: Changes in coagulation and fibrinolysis of post-SARS osteonecrosis in a Chinese population date: 2006-03-18 words: 2231.0 sentences: 125.0 pages: flesch: 46.0 cache: ./cache/cord-272019-4uua0zgp.txt txt: ./txt/cord-272019-4uua0zgp.txt summary: The purpose of this study was to detect changes in coagulation and fibrinolysis of post-severe acute respiratory syndrome (SARS) Chinese patients with osteonecrosis, investigate the aetiology of post-SARS osteonecrosis (ON), and select the sensitive molecular markers for identifying the susceptible population. Of 88 patients with post-SARS, 78 (88.64%) were found to have at least one coagulopathy versus 36.54% of controls (p<0.01); PC, APC-R, AT-III, PAI, and PLG were significantly different between the two groups (Tables 1 and 2 ). [28] studied risk factors for pulmonary emboli after total hip or knee arthroplasty, 21 serological measures and five genes associated with thrombophilia and/or hypofibrinolysis were assessed: 13 of 27 (48%) in the control group also had at least one abnormality. In this study, we did not detect any coagulation abnormalities in a small proportion of the patients; this may reflect limitations in our understanding of the causes of thrombosis and hypofibrinolysis. Risk factors potentially activating intravascular coagulation and causing nontraumatic osteonecrosis abstract: The purpose of this study was to detect changes in coagulation and fibrinolysis of post-severe acute respiratory syndrome (SARS) Chinese patients with osteonecrosis, investigate the aetiology of post-SARS osteonecrosis (ON), and select the sensitive molecular markers for identifying the susceptible population. For this study, blood samples were collected from 88 patients with post-SARS ON and 52 healthy people. Activated partial thromboplastin time (APTT), protein C (PC), antithrombin III (AT–III), plasminogen activator inhibitor (PAI), activated protein C resistance (APC–R), plasminogen (PLG), von Willebrand’s factor(vWF), D–dimer (D–D), fibrinogen (Fib), and homocysteine (HCY) were examined by enzyme-linked immunosorbent assay (ELISA). We noted that blood agents of patients with ON changed obviously. APTT, PC, AT–III, PAI, APC–R, and PLG were significantly different between the two groups. Hypercoagulation and hypofibrinolysis were found in patients with post-SARS ON. Therefore, these examinations can be used to screen a population susceptible to ON. Measurements of APTT, PC, AT–III, PAI, APC–R, and PLG are sensitive blood tests for screening purposes. url: http://europepmc.org/articles/pmc2532088?pdf=render doi: 10.1007/s00264-005-0067-6 id: cord-326666-melz5fq4 author: Sun, Weitao title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date: 2020-09-03 words: 1723.0 sentences: 138.0 pages: flesch: 62.0 cache: ./cache/cord-326666-melz5fq4.txt txt: ./txt/cord-326666-melz5fq4.txt summary: title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. 578 shown with special markers at the top of colored blocks representing ORFs. Mutation 623 10818G>T in ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which 624 results in amino acid M37F mutation in transmembrane protein nsp6. ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which results in amino 631 acid M37F mutation in transmembrane protein nsp6. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense single-stranded virus approximately 30 kb in length, causes the ongoing novel coronavirus disease-2019 (COVID-19). Studies confirmed significant genome differences between SARS-CoV-2 and SARS-CoV, suggesting that the distinctions in pathogenicity might be related to genomic diversity. However, the relationship between genomic differences and SARS-CoV-2 fitness has not been fully explained, especially for open reading frame (ORF)-encoded accessory proteins. RNA viruses have a high mutation rate, but how SARS-CoV-2 mutations accelerate adaptation is not clear. This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. A power law relationship was discovered between the HGS of ORF3b, ORF6, and N and the expression of interferon (IFN)-sensitive response element (ISRE)-containing promoters. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. The 10818G>T caused the amino acid mutation M37F in the transmembrane protein nsp6. The results suggest that the ORF6 and ORF8 genes and the mutation M37F may play important roles in causing COVID-19. The findings demonstrate that HGS analysis is a promising way to identify important genes and mutations in adaptive strains, which may help in searching potential targets for pharmaceutical agents. url: https://doi.org/10.1101/2020.09.03.280727 doi: 10.1101/2020.09.03.280727 id: cord-267735-y3832u9e author: Sun, Wuping title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date: 2020-09-24 words: 3073.0 sentences: 178.0 pages: flesch: 40.0 cache: ./cache/cord-267735-y3832u9e.txt txt: ./txt/cord-267735-y3832u9e.txt summary: title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic It has been reported that hyper-immunity individuals have received treatment with immunosuppressive or modulatory agents; these approaches may increase the possibility of SARS-CoV-2 infection (Cai et al., 2020) . These results demonstrated that SARS-CoV-2 infection-induced immune alteration in COVID-19 patients. These studies suggested that SARS-CoV-2 infection-induced immune alteration could further result in the concurrence of chronic pain since it affects the nervous system. Acquired immune deficiency syndrome (AIDS) is associated with various infection symptoms, and peripheral neuropathic pain is the most common and severe neurological manifestation that has been reported in HIV-positive, immunocompromised individuals (Amaniti et al., 2019) . Chronic pain patients have received limited treatment and discounted services during the COVID-19 outbreak due to limit the spread of SARS-CoV-2 infection. Chronic pain patients may also have increased infection risks to SARS-CoV-2 due to complicated reasons. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33072033/ doi: 10.3389/fmicb.2020.572318 id: cord-333018-2h8y118z author: Sun, Xingxing title: Safety Considerations for Neuraxial Anaesthesia in Parturients with COVID-19 date: 2020-05-14 words: 649.0 sentences: 43.0 pages: flesch: 42.0 cache: ./cache/cord-333018-2h8y118z.txt txt: ./txt/cord-333018-2h8y118z.txt summary: To decide the mode of anaesthesia for parturients with COVID-19, one should evaluate neurological symptoms in addition to respiratory symptoms. Angiotensin-converting enzyme 2 (ACE2) is the functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); 7 it is expressed in the cell membrane of various tissues and organs including lung, small intestine, and brain. When deciding on anaesthetic strategy for patients with COVID-19, we think that one should consider the possible deleterious effects on the nervous system by neuraxial anaesthesia. For patients with apparent central or peripheral nervous system symptoms, although direct evidence is still lacking, general anaesthesia might be an acceptable alternative. However, general anaesthesia can impair the blood-brain barrier 10 , which might facilitate the invasion of SARS-CoV-2 into the central nervous system. Emergency Caesarean delivery in a patient with confirmed coronavirus disease 2019 under spinal anaesthesia abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32410737/ doi: 10.1016/j.bja.2020.05.005 id: cord-318364-5bmdzgla author: Sun, Xinjuan title: Cytokine storm intervention in the early stages of COVID-19 pneumonia date: 2020-04-25 words: 3102.0 sentences: 158.0 pages: flesch: 40.0 cache: ./cache/cord-318364-5bmdzgla.txt txt: ./txt/cord-318364-5bmdzgla.txt summary: In a retrospective study of 41 patients with COVID-19, most patients with SARS-CoV-2 infection developed mild symptoms, whereas some patients later developed aggravated disease symptoms, and eventually passed away because of multiple organ dysfunction syndrome (MODS), as a consequence of a severe cytokine storm. In view of the severe morbidity and mortality of COVID-19 pneumonia, we review the current understanding of treatment of human coronavirus infections from the perspective of a dysregulated cytokine and immune response. In support of the above observations, a retrospective study of 41 patients with COVID-19 2 showed that most SARS-CoV-2 infected patients present clinically with mild symptoms, while a minority of patients progressively declined from the infection and eventually died of acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MOD). Severe pneumonia caused by pathogenic human coronaviruses (HCoV) are often associated with induced hypercytokinemia, also termed cytokine storm, in immunocompetent individuals; uncontrolled overproduction of inflammatory cytokines contributes to acute lung injury and acute respiratory distress syndrome (ARDS). abstract: Clinical intervention in patients with corona virus disease 2019 (COVID-19) has demonstrated a strong upregulation of cytokine production in patients who are critically ill with SARS-CoV2-induced pneumonia. In a retrospective study of 41 patients with COVID-19, most patients with SARS-CoV-2 infection developed mild symptoms, whereas some patients later developed aggravated disease symptoms, and eventually passed away because of multiple organ dysfunction syndrome (MODS), as a consequence of a severe cytokine storm. Guidelines for the diagnosis and treatment of SARS-CoV-2 infected pneumonia were first published January 30(th), 2020; these guidelines recommended for the first time that cytokine monitoring should be applied in severely ill patients to reduce pneumonia related mortality. The cytokine storm observed in COVID-19 illness is also an important component of mortality in other viral diseases, including SARS, MERS and influenza. In view of the severe morbidity and mortality of COVID-19 pneumonia, we review the current understanding of treatment of human coronavirus infections from the perspective of a dysregulated cytokine and immune response. url: https://api.elsevier.com/content/article/pii/S1359610120300484 doi: 10.1016/j.cytogfr.2020.04.002 id: cord-301227-ica5x0r1 author: Sun, Yi-Sheng title: A SARS-CoV-2 variant with the 12-bp deletion at E gene date: 2020-10-29 words: 4410.0 sentences: 236.0 pages: flesch: 65.0 cache: ./cache/cord-301227-ica5x0r1.txt txt: ./txt/cord-301227-ica5x0r1.txt summary: In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. In this paper, we isolated two SARS-CoV-2 strains with both wild-type and mutant E genes from the same sample using plaque purification. To explore whether other clinical samples contained a similar SARS-CoV-2 strain lacking a 12-bp sequence in the E gene, we used RT-PCR to detect the mutant E gene specifically. Our results indicated that both the F8 and 8X strains can infect Vero cells, however, the S protein content of the F8 viral culture was higher than that of 8X. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. abstract: The coronavirus disease 2019 (COVID-19) pandemic is still ongoing and has become an important public health threat. This disease is caused by a new coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, and so far, little is known about this virus. In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. There was no significant difference in the viral titer and infectivity of these two strains. The S protein content of the F8 viral culture was 0.39 μg/ml, much higher than that of 8X. An inactivated vaccine made from the F8 strain could trigger high levels of the IgG titer and neutralizing antibody titer, which could last for at least 6 weeks and were significantly higher than those from the 8X strain at 1 and 3 weeks post vaccination, respectively. In conclusion, we reported that both the E gene mutant and wild-type SARS-CoV-2 strains were isolated from the same clinical sample by plaque purification. A 12-bp deletion in the E gene was important for SARS-CoV-2 replication and immunogenicity. url: https://doi.org/10.1080/22221751.2020.1837017 doi: 10.1080/22221751.2020.1837017 id: cord-336093-ic6q6ke8 author: Sun, Ying title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 words: 6321.0 sentences: 361.0 pages: flesch: 57.0 cache: ./cache/cord-336093-ic6q6ke8.txt txt: ./txt/cord-336093-ic6q6ke8.txt summary: Abbreviations: SARS, severe acute respiratory syndrome; SARS-CoV, SARS coronavirus; nsp, nonstructural protein; N7-MTase, guanine-N7-methyltransferase; 2 0 -O-MTase, 2 0 -O-methyltransferase; AdoMet, S-adenosyl-L-methionine; AdoHcy, S-adenosyl-L-homocysteine; ATA, aurintricarboxylic acid; IC 50 , inhibitory concentration at 50% activity. A single transformed colony of the YBS40 strain containing plasmids expressing human N7-MTase (MT-Human), SARS-CoV N7-MTase (MT-SARS), N7-MTases of other coronaviruses (MT-MHV, MT-TGEV, and MT-IBV), and the pMceK294A vector as control (representing the yeast N7-MTase [MT-Yeast]), were inoculated separately into 5 ml of a basic medium (Min SD Base) lacking tryptophan and incubated at 30°C for 21-24 h until reaching a similar final cell density in the stationary phase (0.5-1.0 Â 10 8 cells/ml) (Chrebet et al., 2005) . Although AdoHcy, ATA and sinefungin, were previously reported to be inhibitors of coronavirus RNA MTases in vitro , only sinefungin significantly suppressed the growth of the MT-yeast, MT-human, and MT-SARS yeast cells (Fig. 3 ). abstract: The 5′-cap structure is a distinct feature of eukaryotic mRNAs and is important for RNA stability and protein translation by providing a molecular signature for the distinction of self or non-self mRNA. Eukaryotic viruses generally modify the 5′-end of their RNAs to mimic the cellular mRNA structure, thereby facilitating viral replication in host cells. However, the molecular organization and biochemical mechanisms of the viral capping apparatus typically differ from its cellular counterpart, which makes viral capping enzymes attractive targets for drug discovery. Our previous work showed that SARS coronavirus (SARS-CoV) non-structural protein 14 represents a structurally novel and unique guanine-N7-methyltransferase (N7-MTase) that is able to functionally complement yeast cellular N7-MTase. In the present study, we developed a yeast-based system for identifying and screening inhibitors against coronavirus N7-MTase using both 96-well and 384-well microtiter plates. The MTase inhibitors previously identified by in vitro biochemical assays were tested, and some, such as sinefungin, effectively suppressed N7-MTase in the yeast system. However, other compounds, such as ATA and AdoHcy, did not exert an inhibitory effect within a cellular context. These results validated the yeast assay system for inhibitor screening yet also demonstrated the difference between cell-based and in vitro biochemical assays. The yeast system was applied to the screening of 3000 natural product extracts, and three were observed to more potently inhibit the activity of coronavirus than human N7-MTase. url: https://api.elsevier.com/content/article/pii/S0166354214000369 doi: 10.1016/j.antiviral.2014.02.002 id: cord-330715-olypwdoq author: Sun, Zeyu title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date: 2020-08-30 words: 5567.0 sentences: 275.0 pages: flesch: 50.0 cache: ./cache/cord-330715-olypwdoq.txt txt: ./txt/cord-330715-olypwdoq.txt summary: title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications In this study, we report a comprehensive N-glycosylation profile-as well as other PTMs-of the HCoV-19 S protein and hACE2, elucidated by high-resolution mass spectrometry (MS) analyses. To resolve glycan camouflage on the surface of the HCoV-19 S protein and hACE2, intact glycopeptides derived from protease digestion and fractionated by HILIC were directly subjected to LC-MSMS analysis specifically designed to detect peptides with extra molecular weight due to N-glycan attachment. Fig. 2 (c) provides a summary of the most dominant N-glycan composition and predicted structure for each site of the HCoV-19 spike protein and hACE2. When the spike proteins from HCoV-19 and SARS-CoV were compared, it was noticeable that the majority of differences in the glycosylation sites occurred in the distal S1 subunit, resulting in a significant difference in the glycan profile in the outermost canopy of the virus formed by spike trimer clusters. abstract: The COVID-19 pandemic has led to worldwide efforts to understand the biological traits of the newly identified HCoV-19 virus. In this mass spectrometry (MS)-based study, we reveal that out of 21 possible glycosites in the HCoV-19 S protein, 20 are completely occupied by N-glycans, predominantly of the oligomannose type. All seven glycosylation sites in human angiotensin I converting enzyme 2 (hACE2) were found to be completely occupied, mainly by complex N-glycans. However, glycosylation did not directly contribute to the binding affinity between HCoV-19 S and hACE2. Additional post-translational modification (PTM) was identified, including multiple methylated sites in both proteins and multiple sites with hydroxylproline in hACE2. Refined structural models of HCoV-19 S and hACE2 were built by adding N-glycan and PTMs to recently published cryogenic electron microscopy (cryo-EM) structures. The PTM and glycan maps of HCoV-19 S and hACE2 provide additional structural details for studying the mechanisms underlying host attachment and the immune response of HCoV-19, as well as knowledge for developing desperately needed remedies and vaccines. url: https://www.sciencedirect.com/science/article/pii/S2095809920302344?v=s5 doi: 10.1016/j.eng.2020.07.014 id: cord-352909-s11tpfoq author: Sun, Zhiping title: Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions date: 2020-08-14 words: 1747.0 sentences: 106.0 pages: flesch: 66.0 cache: ./cache/cord-352909-s11tpfoq.txt txt: ./txt/cord-352909-s11tpfoq.txt summary: Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions Zhiping Sun 1 , Xia Cai 1 , Chenjian Gu 2 , Rong Zhang 2 , Wendong Han 1 , Yun Qian 1 , Yuyan Wang 2 , Wei Xu 2 , Yang Wu 2 , Xunjia Cheng 2 , Zhenghong Yuan 2 , Youhua Xie 2 and Di Qu 1, 2 Dear Editor, The pneumonia caused by a novel coronavirus was first reported in December 2019 in Wuhan of China, and since then has become a pandemic 1, 2 . Here, we first investigated the infectivity of SARS-COV-2 using a plaque-purified strain nCoV-SH01 isolated from a patient in Shanghai (GenBank MT121215) 6 , studied subsequently its stability in liquid medium, on dry filter paper, and under acidic condition (pH2.2) at RT. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32821426/ doi: 10.1038/s41421-020-00191-9 id: cord-351651-6dbt99h0 author: Sun, Zhong title: Potential Factors Influencing Repeated SARS Outbreaks in China date: 2020-03-03 words: 4985.0 sentences: 260.0 pages: flesch: 55.0 cache: ./cache/cord-351651-6dbt99h0.txt txt: ./txt/cord-351651-6dbt99h0.txt summary: Thus, if bats were the natural hosts of SARS-CoVs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. A study on the genome sequence of diseased pangolins smuggled from Malaysia to China found that pangolins carry coronavirus, suggesting that pangolins may be intermediate hosts for SARS-COV-2 [35] . However, the only source of bats that have been publicly identified as carrying virus phylogenetically close to SARS-CoV-2 is far away from Wuhan in Zhoushan, Zhejiang. However, to confirm this scenario, it is necessary to find wild bats in Wuhan and its neighboring areas that carry CoVs identical to those isolated from various SARS-2 patients. This mini-review evaluated the common epidemiological patterns of both SARS epidemics in China and identified cold, dry winter as a common environmental condition conducive for SARS virus infection to human beings. abstract: Within last 17 years two widespread epidemics of severe acute respiratory syndrome (SARS) occurred in China, which were caused by related coronaviruses (CoVs): SARS-CoV and SARS-CoV-2. Although the origin(s) of these viruses are still unknown and their occurrences in nature are mysterious, some general patterns of their pathogenesis and epidemics are noticeable. Both viruses utilize the same receptor—angiotensin-converting enzyme 2 (ACE2)—for invading human bodies. Both epidemics occurred in cold dry winter seasons celebrated with major holidays, and started in regions where dietary consumption of wildlife is a fashion. Thus, if bats were the natural hosts of SARS-CoVs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. The widespread existence of these bat-carried or -released viruses might have an easier time in breaking through human defenses when harsh winter makes human bodies more vulnerable. Once succeeding in making some initial human infections, spreading of the disease was made convenient with increased social gathering and holiday travel. These natural and social factors influenced the general progression and trajectory of the SARS epidemiology. However, some unique factors might also contribute to the origination of SARS in Wuhan. These factors are discussed in different scenarios in order to promote more research for achieving final validation. url: https://www.ncbi.nlm.nih.gov/pubmed/32138266/ doi: 10.3390/ijerph17051633 id: cord-278457-yrm5hi3v author: Sung, Heungsup title: Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea date: 2020-10-17 words: 3722.0 sentences: 187.0 pages: flesch: 45.0 cache: ./cache/cord-278457-yrm5hi3v.txt txt: ./txt/cord-278457-yrm5hi3v.txt summary: EQAs using pooled respiratory samples spiked with inactivated cultured SARS-CoV-2 had indicated the possible effects of these variations on assay performance, thereby allowing External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. abstract: External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. A total of 110 (93.2%) laboratories reported correct results for all qualitative tests; 29 (24.6%) laboratories had >1 outliers according to cycle threshold values. Our EQA panel identified the potential weaknesses of currently available commercial reagent kits. The methodology we used can provide practical experience for those planning to conduct evaluations for testing of SARS-CoV-2 and other emerging pathogens in the future. url: https://doi.org/10.3201/eid2610.202551 doi: 10.3201/eid2610.202551 id: cord-303934-8gh3q7p3 author: Sungnak, Waradon title: SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways date: 2020-03-13 words: 3044.0 sentences: 170.0 pages: flesch: 47.0 cache: ./cache/cord-303934-8gh3q7p3.txt txt: ./txt/cord-303934-8gh3q7p3.txt summary: To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA-sequencing (scRNA-seq) datasets from healthy individuals generated by the Human Cell Atlas consortium. To clarify the expression patterns of ACE2 and TMPRSS2 and analyze the expression of the other potential genes associated with SARS-CoV-2 pathogens at cellular resolution, we interrogated single-cell transcriptome expression data from published scRNA-seq datasets from healthy donors generated by the Human Cell Atlas consortium 24 . While we cannot rule out the possibility that the virus uses alternative proteases for entry in such contexts, or that lung fetal tissue expresses the relevant genes, these results are at least consistent with early reports that fail to detect evidence of intrauterine infection through vertical transmission in women who develop COVID-19 pneumonia in late pregnancy 38 . abstract: The SARS-CoV-2 coronavirus, the etiologic agent responsible for COVID-19 coronavirus disease, is a global threat. To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA-sequencing (scRNA-seq) datasets from healthy individuals generated by the Human Cell Atlas consortium. We found that ACE2, as well as the protease TMPRSS2, are differentially expressed in respiratory and gut epithelial cells. In-depth analysis of epithelial cells in the respiratory tree reveals that nasal epithelial cells, specifically goblet/secretory cells and ciliated cells, display the highest ACE2 expression of all the epithelial cells analyzed. The skewed expression of viral receptors/entry-associated proteins towards the upper airway may be correlated with enhanced transmissivity. Finally, we showed that many of the top genes associated with ACE2 airway epithelial expression are innate immune-associated, antiviral genes, highly enriched in the nasal epithelial cells. This association with immune pathways might have clinical implications for the course of infection and viral pathology, and highlights the specific significance of nasal epithelia in viral infection. Our findings underscore the importance of the availability of the Human Cell Atlas as a reference dataset. In this instance, analysis of the compendium of data points to a particularly relevant role for nasal goblet and ciliated cells as early viral targets and potential reservoirs of SARS-CoV-2 infection. This, in turn, serves as a biological framework for dissecting viral transmission and developing clinical strategies for prevention and therapy. url: https://arxiv.org/pdf/2003.06122v1.pdf doi: 10.1038/s41591-020-0868-6 id: cord-330779-mso2zfom author: Sunkari, Emmanuel Daanoba title: Sources and routes of SARS-CoV-2 transmission in water systems in Africa: Are there any sustainable remedies? date: 2020-09-09 words: 4162.0 sentences: 200.0 pages: flesch: 50.0 cache: ./cache/cord-330779-mso2zfom.txt txt: ./txt/cord-330779-mso2zfom.txt summary: Hence, it is proposed that governments in Africa must put measures like improved WASH facilities and public awareness campaigns, suburbanization of wastewater treatment facilities, utilizing low-cost point-of-use water treatment systems, legally backed policy interventions, and Community-Led Total Sanitation (CLTS). Overall, since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water is very high and thus, the sources and routes of community spread of the virus, which is currently being reported must be critically re-examined. Since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water from wastewater systems is very high. abstract: Governments across the globe are currently besieged with the novel coronavirus (COVID-19) pandemic caused by SARS-CoV-2. Although some countries have been largely affected by this pandemic, others are only slightly affected. In this regard, every government is taking precautionary measures to mitigate the adverse effects of COVID-19. SARS-CoV-2 has been detected in wastewater raising an alarm for Africa due to the poor water, sanitation, and hygiene (WASH) facilities. Also, most countries in Africa do not have resilient policies governing sanitation and water management systems, which expose them to higher risk levels for the transmission of SARS-CoV-2. Therefore, this study unearthed the likely sources and routes of SARS-CoV-2 transmission in water systems (mainly wastewater) in Africa through a holistic review of published works. This provided the opportunity to propose sustainable remedial measures, which can be extrapolated to most developing countries in the world. The principal sources and routes of potential transmission of SARS-CoV-2 in water systems are hospital sewage, waste from isolation and quarantine centres, faecal-oral transmission, contaminated surface and groundwater sources, and contaminated sewage. The envisioned overwhelming impact of these sources on the transmission of SARS-CoV-2 through water systems in Africa suggests that governments need to put stringent and sustainable measures to curtail the scourge. Hence, it is proposed that governments in Africa must put measures like improved WASH facilities and public awareness campaigns, suburbanization of wastewater treatment facilities, utilizing low-cost point-of-use water treatment systems, legally backed policy interventions, and Community-Led Total Sanitation (CLTS). SARS-CoV-2 in water systems can be inactivated and destroyed by integrating ozonation, chlorination, UV irradiation, and sodium hypochlorite in low-cost point-of-use treatment systems. These proposed sustainable remedial measures can help policymakers in Africa to effectively monitor and manage the untoward impact of SARS-CoV-2 on water systems and consequently, on the health of the general public. url: https://api.elsevier.com/content/article/pii/S0048969720358277 doi: 10.1016/j.scitotenv.2020.142298 id: cord-354773-u86bdmvf author: Suo, Tao title: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date: 2020-06-07 words: 4490.0 sentences: 242.0 pages: flesch: 57.0 cache: ./cache/cord-354773-u86bdmvf.txt txt: ./txt/cord-354773-u86bdmvf.txt summary: To improve the diagnostic accuracy of nucleic acid detection of SARS-Cov-2 in low viral load samples using droplet digital PCR, we compared the dynamic range and the limit of detection (LoD) with a 95% repeatable probability between ddPCR and RT-PCR in laboratory, and tested the clinical samples from 77 patients by both ddPCR and RT-PCR for head to head comparison. Throat swab samples of each patient were firstly collected for official approved RT-PCR diagnosis in hospitals and blinding laboratory RT-PCR and ddPCR tests simultaneously with the same primers/probe sets approved by Chinese CDC. As shown in Figure 3 , throat swab samples of each suspected outpatient were firstly collected for laboratory RT-PCR, ddPCR tests and official approved RT-PCR diagnosis in hospitals simultaneously with the same primers/probe sets approved by Chinese CDC (Table 1) . In this study, two throat swab samples of each supposed convalescent were collected for laboratory RT-PCR, ddPCR and official approved RT-PCR tests simultaneously with the same primers/probe sets (Table 2) . abstract: Quantitative real time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant numbers of false negative reports are inevitable, which results in failure to timely diagnose, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 RNA from 77 patients, and compared with RT-PCR in terms of the diagnostic accuracy based on the results of follow-up survey. 26 patients of COVID-19 with negative RT-PCR reports were reported as positive by ddPCR. The sensitivity, specificity, PPV, NPV, negative likelihood ratio (NLR) and accuracy were improved from 40% (95% CI: 27–55%), 100% (95% CI: 54–100%), 100%, 16% (95% CI: 13–19%), 0.6 (95% CI: 0.48–0.75) and 47% (95% CI: 33–60%) for RT-PCR to 94% (95% CI: 83–99%), 100% (95% CI: 48–100%), 100%, 63% (95% CI: 36–83%), 0.06 (95% CI: 0.02–0.18), and 95% (95% CI: 84–99%) for ddPCR, respectively. Moreover, 6/14 (42.9%) convalescents were detected as positive by ddPCR at 5–12 days post discharge. Overall, ddPCR shows superiority for clinical diagnosis of SARS-CoV-2 to reduce the false negative reports, which could be a powerful complement to the RT-PCR. url: https://www.ncbi.nlm.nih.gov/pubmed/32438868/ doi: 10.1080/22221751.2020.1772678 id: cord-023865-6rafp3x3 author: Surjit, Milan title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 words: 9210.0 sentences: 448.0 pages: flesch: 45.0 cache: ./cache/cord-023865-6rafp3x3.txt txt: ./txt/cord-023865-6rafp3x3.txt summary: Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese''s laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells abstract: As in other coronaviruses, the nucleocapsid protein is one of the core components of the SARS coronavirus (CoV). It oligomerizes to form a closed capsule, inside which the genomic RNA is securely stored thus providing the SARS-CoV genome with its first line of defense from the harsh conditions of the host environment and aiding in replication and propagation of the virus. In addition to this function, several reports have suggested that the SARS-CoV nucleocapsid protein modulates various host cellular processes, so as to make the internal milieu of the host more conducive for survival of the virus. This article will analyze and discuss the available literature regarding these different properties of the nucleocapsid protein. Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176212/ doi: 10.1007/978-3-642-03683-5_9 id: cord-316880-hbw6jbz5 author: Sutton, Melissa title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 date: 2020-08-14 words: 517.0 sentences: 43.0 pages: flesch: 48.0 cache: ./cache/cord-316880-hbw6jbz5.txt txt: ./txt/cord-316880-hbw6jbz5.txt summary: title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 to the Oregon State Public Health Laboratory for testing with the Abbott Architect Laboratories SARS-CoV-2 IgG immunoassay. Antibodies to SARS-CoV-2 were detected in nine of 897 specimens, yielding an unadjusted seroprevalence of 1.0% (95% confidence interval = 0.2%-1.8%). The estimated seroprevalence of SARS-CoV-2 antibodies in a convenience sample of adult Oregonians was approximately 10 times the measured cumulative COVID-19 incidence obtained by nucleic acid testing, consistent with results from seven other U.S. states and geographic areas (4). Population point prevalence of SARS-CoV-2 infection based on a statewide random sample-Indiana Estimated community seroprevalence of SARS-CoV-2 antibodies-two Georgia counties Seroprevalence of antibodies to SARS-CoV-2 in 10 sites in the United States All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32790658/ doi: 10.15585/mmwr.mm6932a4 id: cord-285944-8lapwnuw author: Suwanwongse, Kulachanya title: Hyperpyrexia in COVID‐19 patients date: 2020-06-10 words: 2171.0 sentences: 124.0 pages: flesch: 39.0 cache: ./cache/cord-285944-8lapwnuw.txt txt: ./txt/cord-285944-8lapwnuw.txt summary: We propose three possible underlying mechanisms based on our current knowledge: 1) direct brain injury from SARS-CoV-2, 2) persistent immune dysfunction and dysregulation of cytokines, and 3) vascular thrombosis. According to our case series, the lack of normal daily temperature variation in patient 4 and 5, and the presence of hypothermia in patient 1 and 5 support the hypothesis that direct brain injury from SARS-CoV-2 leads to hyperpyrexia. SARS-CoV-2 may cause injury to the brain-stem respiratory center explaining why COVID-19 patients often report lesser perception of dyspnea than the actual degree of hypoxia and the extent of lung pathology [15] . Our case series also highlights the need to determine underlying mechanisms of hyperpyrexia in COVID-19 patients as each cause requires different management. The underlying mechanisms of hyperpyrexia in COVID-19 are unknown but may be a result of SARS-CoV-2 related brain injury, exuberant immune response, and thrombus formation. abstract: Coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a global health emergency, in which its effective treatment and prevention remain obscured. Hyperpyrexia is an elevation of body temperature (BT) above 106.7 °F (41.5 °C) due to an abnormally increased hypothalamic thermo‐regulatory set. The pathophysiology, impact, and outcomes of hyperpyrexia in COVID‐19 patients have not yet been studied. Herein, we present clinical features and outcomes of six COVID‐19 patients who had developed hyperpyrexia during hospitalization. All patients expired shortly after the onset of hyperpyrexia. Hyperpyrexia seems to adversely impact the outcomes and mortality in patients with COVID‐19. The underlying mechanisms of developing hyperpyrexia in COVID‐19 are mysterious. We propose it may be caused by SARS‐CoV‐2 related brain injury, exuberant immune response, and thrombus formation. More research is needed to verify our results. Understanding the association between hyperpyrexia and SARS‐CoV‐2 will help to elucidate the COVID‐19 pathogenesis, which is mandatory for developing effective treatment strategies. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26154 doi: 10.1002/jmv.26154 id: cord-302786-ibt7mupq author: Suwanwongse, Kulachanya title: Fatal Outcome in a Kidney-Pancreas Transplant Recipient With COVID-19 date: 2020-06-18 words: 2229.0 sentences: 138.0 pages: flesch: 47.0 cache: ./cache/cord-302786-ibt7mupq.txt txt: ./txt/cord-302786-ibt7mupq.txt summary: Despite a growing report on clinical characteristics and prognosis of patients with COVID-19, the data in the special population, including transplant recipients, is still limited. We proposed that the pre-existing T-cell dysfunction from the long-term use of immunosuppressive agents in organ transplant recipients adversely affects COVID-19 prognosis and worsens COVID-19 mortality. However, impaired immune functions may paradoxically protect transplant patients from the hyper-inflammatory response to SARS-CoV-2 and thus dampen the disease severity. Long-term immunosuppressive therapy in organ transplant recipients may alter clinical features and outcomes of COVID-19. The long-term use of immunosuppressive medications in organ transplant recipients is associated with the decrease in T-cell number and function; TAC and MMF preferentially inhibit T-cell response. However, in this report, immunosuppressive agents were discontinued in patients with severe disease, presumably with high mortality risks. Preexisting T-cell immune response deficits from long-term use of immunosuppressive agents may worsen the prognosis of COVID-19 in transplant recipients. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious pathogen causing the novel coronavirus disease 2019 (COVID-19), the ongoing unprecedented pandemic in 2020. SARS-CoV-2 primarily targets the respiratory systems, so acute respiratory distress syndrome is the major cause of death. Clinical courses of COVID-19 are variable and unpredictable, while some epidemiologic and clinical factors have been found to have a negative impact on the disease prognosis. Despite a growing report on clinical characteristics and prognosis of patients with COVID-19, the data in the special population, including transplant recipients, is still limited. Herein we report on the clinical features and fatal outcome of COVID-19 in a dual pancreas-kidney transplant recipient (with failure of the pancreas graft). Our case illustrates the similarities and differences of the COVID-19 disease course between transplant recipients and the general population. We proposed that the pre-existing T-cell dysfunction from the long-term use of immunosuppressive agents in organ transplant recipients adversely affects COVID-19 prognosis and worsens COVID-19 mortality. url: https://doi.org/10.7759/cureus.8691 doi: 10.7759/cureus.8691 id: cord-308279-gsk4qel5 author: Suzuki, Yuichiro J. title: The viral protein fragment theory of COVID-19 pathogenesis date: 2020-09-11 words: 1397.0 sentences: 70.0 pages: flesch: 44.0 cache: ./cache/cord-308279-gsk4qel5.txt txt: ./txt/cord-308279-gsk4qel5.txt summary: I herein propose the viral protein fragment theory of COVID-19 pathogenesis based on my observations in cultured human vascular cells that SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I hypothesize that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling without the rest of the viral components. This hypothesis is based on my experimental observations in cultured human vascular cells that the recombinant full length S1 subunit of SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I propose a scenario that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the current pandemic of coronavirus disease 2019 (COVID-19) that have killed nearly one million people so far. While this appears to be a respiratory virus, surprisingly, it has been recognized that patients with cardiovascular disease are likely to be affected severely and die of COVID-19. This phenomenon cannot be explained by the generally accepted logic that the SARS-CoV-2 infection/replication is the sole determinant of the actions of the virus to define the fate of host cells. I herein propose the viral protein fragment theory of COVID-19 pathogenesis based on my observations in cultured human vascular cells that SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. It is generally thought that SARS-CoV-2 and other single-stranded RNA viruses attach to the host cells through the interactions between surface proteins of the viral capsid and the host cell receptors; the fusion and the entry of the viral components, resulting in the replication of the viruses; and the host cell responses are the consequence of these events. I hypothesize that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling without the rest of the viral components. Thus, COVID-19 patients are subjected to the intact virus infecting the host cells for the replication and the amplification as well as the spike protein fragment that are capable of affecting the host cells. I propose that cell signaling elicited by the spike protein fragment that occurs on cardiovascular cells would predispose infected individuals to develop complications that are seen in severe and fatal COVID-19 conditions. If this hypothesis is correct, then the strategies to treat COVID-19 should include, in addition to giving agents that inhibit the viral replication, therapeutics that inhibit the virus fragment-mediated cell signaling on cardiovascular cells. url: https://api.elsevier.com/content/article/pii/S0306987720326943 doi: 10.1016/j.mehy.2020.110267 id: cord-313805-6mnclfeg author: Suzuki, Yuichiro J. title: SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date: 2020-10-12 words: 2299.0 sentences: 128.0 pages: flesch: 56.0 cache: ./cache/cord-313805-6mnclfeg.txt txt: ./txt/cord-313805-6mnclfeg.txt summary: Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. Our results showing that SARS-CoV-2 spike protein is capable of activating the MEK/ERK pathway in pulmonary artery smooth muscle and endothelial cells suggest that cell growth signaling may be triggered in the pulmonary vascular walls in response to SARS-CoV-2. The major finding of this study is that the SARS-CoV-2 spike protein without the rest of the virus can elicit cell signaling, specifically the activation of the MEK/ERK pathway, in human host lung vascular smooth muscle and endothelial cells. abstract: Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. So far, 30 million people have been infected with SARS-CoV-2, and nearly 1 million people have died because of COVID-19 worldwide, causing serious health, economical, and sociological problems. However, the mechanism of the effect of SARS-CoV-2 on human host cells has not been defined. The present study reports that the SARS-CoV-2 spike protein alone without the rest of the viral components is sufficient to elicit cell signaling in lung vascular cells. The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. The activation kinetics was transient with a peak at 10 min. The recombinant protein that contains only the ACE2 receptor-binding domain of SARS-CoV-2 spike protein S1 subunit (Arg319 – Phe541), on the other hand, did not cause this activation. Consistent with the activation of cell growth signaling in lung vascular cells by SARS-CoV-2 spike protein, pulmonary vascular walls were found to be thickened in COVID-19 patients. Thus, SARS-CoV-2 spike protein-mediated cell growth signaling may participate in adverse cardiovascular/pulmonary outcomes, and this mechanism may provide new therapeutic targets to combat COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33052333/ doi: 10.1101/2020.10.12.335083 id: cord-275199-y7b12vml author: Suárez-Fariñas, Mayte title: Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date: 2020-09-25 words: 5683.0 sentences: 331.0 pages: flesch: 47.0 cache: ./cache/cord-275199-y7b12vml.txt txt: ./txt/cord-275199-y7b12vml.txt summary: The RISK cohort 18 : ACE2 and TMPRSS2 in treatment-free pediatric CD (<17 years of age) patients was studied using RNA-seq expression profiles from GSE57945, which includes ileal biopsies from endoscopically defined inflamed samples (n=160), non-inflamed (n=53) and non-IBD controls (n=42). Genes differentially expressed in blood 22 , lung NHBE/A549 23 or human small intestinal organoids 24 (hSIO) following SARS-CoV-2 infection; IBD inflammation; or response to medications were separately projected onto various BGRNs allowing for 1 or 2 nearest neighbors depending on the signature sizes. The expression of ACE2 and TMPRSS2 was similar when comparing active smokers to non-smokers, either between healthy controls or IBD patients (data not shown) and no significant interactions with inflammation status, region or other covariates were found. We observed that genes: up-regulated with inflammation, or positively associated with macroscopic or microscopic measures of disease, or associated with the risk of IBD, were significantly enriched with genes up-regulated by SARS-CoV2 infection of lung epithelial cells ( Figure S10e ). abstract: Background and Aims The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication within enterocytes. Methods Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation and IBD treatment. Results A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and non-biologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. Additionally, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. Conclusions These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0016508520352100?v=s5 doi: 10.1053/j.gastro.2020.09.029 id: cord-327912-wfjdxgxh author: Swann, Heather title: Minimal system for assembly of SARS-CoV-2 virus like particles date: 2020-08-24 words: 1695.0 sentences: 98.0 pages: flesch: 59.0 cache: ./cache/cord-327912-wfjdxgxh.txt txt: ./txt/cord-327912-wfjdxgxh.txt summary: Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. Non-infectious virus like particles (VLPs) displaying essential viral proteins can be used to study the structural properties of the SARS-CoV-2 virions and due to their maximum immunogenicity are also vaccine candidates 2, 3 . Similarly, expression of M, E and S proteins are shown to result in release of morphologically identical particles to wild type SARS-CoV virus 9, 10 . We then tested the structural integrity of the SARS-CoV-2 VLPs attached to dry glass using Atomic Force Microscopy (AFM), since SARS-CoV-2 virions have been reported to survive on solid surfaces in dry conditions for many hours 13 . SARS-CoV-2 M, S and E protein genes were identified from the full genome sequence of the virus 1 , these genes were then humanized and inserted in CMV driven mammalian expression vectors (see supplement for complete plasmid sequences). abstract: SARS-CoV-2 virus is the causative agent of COVID-19. Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. The assembled SARS-CoV-2 VLPs possess S protein spikes on particle exterior, making them ideal for vaccine development. The particles range in shape from spherical to elongated with a characteristic size of 129 ± 32 nm. We further show that SARS-CoV-2 VLPs dried in ambient conditions can retain their structural integrity upon repeated scans with Atomic Force Microscopy up to a peak force of 1 nN. url: https://doi.org/10.1101/2020.06.01.128058 doi: 10.1101/2020.06.01.128058 id: cord-299565-shlhreve author: Sweileh, Waleed M. title: Global research trends of World Health Organization’s top eight emerging pathogens date: 2017-02-08 words: 6058.0 sentences: 393.0 pages: flesch: 52.0 cache: ./cache/cord-299565-shlhreve.txt txt: ./txt/cord-299565-shlhreve.txt summary: According to WHO, the list of pathogens, which required urgent attention for research and development pertaining to preparedness, included "Crimean Congo haemorrhagic fever, Ebola virus, Marburg, Lassa fever, Middle East respiratory syndrome (MERS) and Severe acute respiratory syndrome (SARS) coronavirus diseases, Nipah, and Rift Valley fever" [1] . ( TITLE ( "Crimean-Congo" OR ebola OR "Middle East Respiratory Syndrome" OR "Severe acute respiratory syndrome" OR lassa OR nipah OR "Rift valley" OR marburg OR mers OR merscov OR sars OR ebolavirus OR crimean ) AND TITLE-ABS ( virus OR viral OR fever OR hemorrhagic OR haemorrhagic OR corona* OR coronavirus OR infection OR infectious ) AND TITLE ( vaccin* ) ) AND PUBYEAR > 1995 AND PUBYEAR < 2016 AND ( LIMIT-TO ( SRCTYPE , "j" ) ) AND ( EXCLUDE ( DOCTYPE , "er" ) ) N = 472 abstract: BACKGROUND: On December 8(th), 2015, World Health Organization published a priority list of eight pathogens expected to cause severe outbreaks in the near future. To better understand global research trends and characteristics of publications on these emerging pathogens, we carried out this bibliometric study hoping to contribute to global awareness and preparedness toward this topic. METHOD: Scopus database was searched for the following pathogens/infectious diseases: Ebola, Marburg, Lassa, Rift valley, Crimean-Congo, Nipah, Middle Eastern Respiratory Syndrome (MERS), and Severe Respiratory Acute Syndrome (SARS). Retrieved articles were analyzed to obtain standard bibliometric indicators. RESULTS: A total of 8619 journal articles were retrieved. Authors from 154 different countries contributed to publishing these articles. Two peaks of publications, an early one for SARS and a late one for Ebola, were observed. Retrieved articles received a total of 221,606 citations with a mean ± standard deviation of 25.7 ± 65.4 citations per article and an h-index of 173. International collaboration was as high as 86.9%. The Centers for Disease Control and Prevention had the highest share (344; 5.0%) followed by the University of Hong Kong with 305 (4.5%). The top leading journal was Journal of Virology with 572 (6.6%) articles while Feldmann, Heinz R. was the most productive researcher with 197 (2.3%) articles. China ranked first on SARS, Turkey ranked first on Crimean-Congo fever, while the United States of America ranked first on the remaining six diseases. Of retrieved articles, 472 (5.5%) were on vaccine – related research with Ebola vaccine being most studied. CONCLUSION: Number of publications on studied pathogens showed sudden dramatic rise in the past two decades representing severe global outbreaks. Contribution of a large number of different countries and the relatively high h-index are indicative of how international collaboration can create common health agenda among distant different countries. url: https://doi.org/10.1186/s12992-017-0233-9 doi: 10.1186/s12992-017-0233-9 id: cord-033901-itj6v1jl author: Syambani Ulhaq, Z. title: Recurrent positive SARS-CoV-2 RNA tests in recovered and discharged patients() date: 2020-10-17 words: 819.0 sentences: 66.0 pages: flesch: 55.0 cache: ./cache/cord-033901-itj6v1jl.txt txt: ./txt/cord-033901-itj6v1jl.txt summary: The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic remains a global concern that requires a comprehensive approach to reduce rapid transmission, starting from case detection, inpatient care, as well as post-hospital management. However, concerns have risen over recent reports of increasing re-detectable positive (RP) SARS-CoV-2 RNA tests observed among recovered and discharged patients 1-2 . Aiming to summarize the current evidence, a meta-analysis was performed to estimate the prevalence of RP SARS-CoV-2 RNA tests among recovered patients, in addition to the days of RNA-positive conversion since last negative/discharge. A comprehensive literature search was conducted through an electronic database dated up to May 2020, with search terms such as "recovered/discharged patients", "coronavirus 2019/COVID-19", "SARS-CoV-2", "positive PCR" used in combination without language restriction. 1. Observational studies or case reports that described some RP SARS-CoV-2 RNA tests among recovered/discharged patients. Positive SARS-Cov-2 test in a woman with COVID-19 at 22 days after hospital discharge: A case report abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568126/ doi: 10.1016/j.rceng.2020.06.005 id: cord-279106-3ffa9djf author: Syatila Ab Ghani, Nur title: Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date: 2020-10-21 words: 6970.0 sentences: 404.0 pages: flesch: 52.0 cache: ./cache/cord-279106-3ffa9djf.txt txt: ./txt/cord-279106-3ffa9djf.txt summary: In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed. 33 In this work, amino acid side chain similarity searching was utilized to propose alternative target sites in 34 SARS-CoV-2 protein structures for drug repositioning. abstract: Structures of protein-drug-complexes provide an atomic level profile of drug-target interactions. In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. We were able to identify 22 target sites for the repositioning of 16 approved drug compounds as potential therapeutics for COVID-19. Using the same approach, we were also able to investigate the potentially promiscuous binding of the 16 compounds to off-target sites that could be implicated in toxicity and side effects that had not been provided by any previous studies. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. The intention of this work is not to explicitly identify candidate compounds but to present how an integrated drug repositioning and potential toxicity pipeline using side chain similarity searching algorithms are of great utility in epidemic scenarios involving novel pathogens. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed. url: https://www.ncbi.nlm.nih.gov/pubmed/33101604/ doi: 10.1016/j.csbj.2020.10.013 id: cord-354538-vqi67h6a author: Sydney, Elana R. title: Antibody evidence of SARS-CoV-2 infection in healthcare workers in the Bronx date: 2020-08-26 words: 793.0 sentences: 68.0 pages: flesch: 50.0 cache: ./cache/cord-354538-vqi67h6a.txt txt: ./txt/cord-354538-vqi67h6a.txt summary: 5. What is the prevalence of antibodies in those healthcare workers with self-reported positive and negative SARS-CoV-2 PCR tests? In total, 1,700 healthcare workers were tested for SARS-CoV-2 IgG antibody between April 28 and May 4, 2020. We analyzed the data by looking at those healthcare workers that had positive antibodies and stratified it based on department, presence or absence of symptoms, and previously reported positive PCR. Notably, 12% of those who tested positive for the presence of IgG reported a negative SARS-CoV-2 PCR result. As expected, 92% of individuals that reported a positive PCR test developed IgG antibodies. A small number of individuals, representing 1% of those reporting a positive SARS-CoV-2 PCR test prior to being tested, had a negative antibody test. 6 Our results reflect a higher overall rate of SARS-CoV-2 antibody development among healthcare workers in the Bronx compared to reported rates in NYC healthcare workers. abstract: nan url: https://doi.org/10.1017/ice.2020.437 doi: 10.1017/ice.2020.437 id: cord-255631-516epnjw author: Syeda, H. B. title: The Role of Machine Learning Techniques to Tackle COVID-19 Crisis: A Systematic Review. date: 2020-08-25 words: 6751.0 sentences: 469.0 pages: flesch: 46.0 cache: ./cache/cord-255631-516epnjw.txt txt: ./txt/cord-255631-516epnjw.txt summary: Results: The 128 publications selected were classified into three themes based on ML applications employed to combat the COVID-19 crisis: Computational Epidemiology (CE), Early Detection and Diagnosis (EDD), and Disease Progression (DP). This study focused on peer-reviewed publications, as well as, preprints that applied ML techniques to analyze and address COVID-19 crisis on different scales including diagnostics, prognostics, disease spread forecast, omics, and drug development. We identified forty studies that primarily focused on diagnosing COVID-19 in patients with suspected infection mostly using chest radiological images such as Computed Tomography (CT), X-Radiation (X-Ray), and Lung Ultrasound (LUS). In our review, we identified one study by Roy et al [126] who used a deep learning model on annotated LUS COVID-19 dataset to predict disease severity. The goal of the study was to develop a decision support tool that integrates readily available lab results from EHRs. The novel coronavirus (COVID-19) pandemic has strained global healthcare systems, especially ICUs, due to hospitalized patients having higher ICU transfer rates [133] . abstract: Background: The novel coronavirus responsible for COVID-19 has caused havoc with patients presenting a spectrum of complications forcing the healthcare experts around the globe to explore new technological solutions, and treatment plans. Machine learning (ML) based technologies have played a substantial role in solving complex problems, and several organizations have been swift to adopt and customize them in response to the challenges posed by the COVID-19 pandemic. Objective: The objective of this study is to conduct a systematic literature review on the role of ML as a comprehensive and decisive technology to fight the COVID-19 crisis in the arena of epidemiology, diagnosis, and disease progression. Methods: A systematic search in PubMed, Web of Science, and CINAHL databases was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines to identify all potentially relevant studies published and made available between December 1, 2019, and June 27, 2020. The search syntax was built using keywords specific to COVID-19 and ML. A total of 128 qualified articles were reviewed and analyzed based on the study objectives. Results: The 128 publications selected were classified into three themes based on ML applications employed to combat the COVID-19 crisis: Computational Epidemiology (CE), Early Detection and Diagnosis (EDD), and Disease Progression (DP). Of the 128 studies, 70 focused on predicting the outbreak, the impact of containment policies, and potential drug discoveries, which were grouped into the CE theme. For the EDD, we grouped forty studies that applied ML techniques to detect the presence of COVID-19 using the patient's radiological images or lab results. Eighteen publications that focused on predicting the disease progression, outcomes (recovery and mortality), Length of Stay (LOS), and number of Intensive Care Unit (ICU) days for COVID-19 positive patients were classified under the DP theme. Conclusions: In this systematic review, we assembled the current COVID-19 literature that utilized ML methods to provide insights into the COVID-19 themes, highlighting the important variables, data types, and available COVID-19 resources that can assist in facilitating clinical and translational research. url: http://medrxiv.org/cgi/content/short/2020.08.23.20180158v1?rss=1 doi: 10.1101/2020.08.23.20180158 id: cord-344213-j3yextjl author: Sze, Shirley title: The need for improved discharge criteria for hospitalised patients with COVID-19—implications for patients in long term care facilities date: 2020-09-19 words: 1195.0 sentences: 76.0 pages: flesch: 52.0 cache: ./cache/cord-344213-j3yextjl.txt txt: ./txt/cord-344213-j3yextjl.txt summary: In the COVID-19 pandemic, patients who are older and residents of long term care facilities (LTCF) are at greatest risk of worse clinical outcomes. We reviewed discharge criteria for hospitalised COVID-19 patients from ten countries with the highest incidence of COVID-19 cases as of 26th July 2020. We recommend a unified, simpler discharge criteria, based on current studies which suggest that most SARS-CoV-2 loses its infectivity by 10 days post-symptom onset. This represents a practical compromise between unnecessarily prolonged admissions and returning highly infectious patients back to their care facilities, and is of particular importance in older patients discharged to LTCFs, residents of which may be at greatest risk of transmission and worse clinical outcomes.  Current evidence suggests that most patients are non-infective 10 days post symptom onset or after first positive PCR result COVID-19 is a global pandemic. abstract: In the COVID-19 pandemic, patients who are older and residents of long term care facilities (LTCF) are at greatest risk of worse clinical outcomes. We reviewed discharge criteria for hospitalised COVID-19 patients from ten countries with the highest incidence of COVID-19 cases as of 26th July 2020. Five countries (Brazil, Mexico, Peru, Chile and Iran) had no discharge criteria; the remaining five (United States of America, India, Russia, South Africa and the United Kingdom) had discharge guidelines with large inter-country variability. India and Russia recommend discharge for a clinically recovered patient with two negative reverse transcription polymerase chain reaction (RT-PCR) tests 24 hours apart; the USA offers either a symptom based strategy—clinical recovery and ten days after symptom onset, or the same test-based strategy. The UK suggests that patients can be discharged when patients have clinically recovered; South Africa recommends discharge 14 days after symptom onset if clinically stable. We recommend a unified, simpler discharge criteria, based on current studies which suggest that most SARS-CoV-2 loses its infectivity by 10 days post-symptom onset. In asymptomatic cases, this can be taken as 10 days after the first positive PCR result. Additional days of isolation beyond this should be left to the discretion of individual clinician. This represents a practical compromise between unnecessarily prolonged admissions and returning highly infectious patients back to their care facilities, and is of particular importance in older patients discharged to LTCFs, residents of which may be at greatest risk of transmission and worse clinical outcomes. url: https://doi.org/10.1093/ageing/afaa206 doi: 10.1093/ageing/afaa206 id: cord-252687-7084pfqm author: Szelenberger, Rafal title: Ischemic Stroke among the Symptoms Caused by the COVID-19 Infection date: 2020-08-19 words: 7334.0 sentences: 378.0 pages: flesch: 37.0 cache: ./cache/cord-252687-7084pfqm.txt txt: ./txt/cord-252687-7084pfqm.txt summary: Many clinical studies have shown an association between SARS-CoV-2 infection and hypercoagulability diagnosed on the basis of abnormal coagulation parameters, including activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer and C-reactive protein level. In this review, the potential mechanism and the effect of the SARS-CoV-2 viral infection on the development of ischemic stroke in COVID-19 patients were carefully studied. study, in which most non-survivor COVID-19 patients'' (71.4%) blood tests showed prolonged prothrombin time and an increased D-dimer levels, which indicated the state after activation of the plasma coagulation system [14] . The accumulation of immune cells in the vascular wall in response to the viral infection, especially among patients with ischemic risk factors, induces endothelial dysfunction, migration and proliferation of cells, activation of coagulation cascade and production of fibrous plaques. abstract: The 2019 global pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a public health emergency of international concern by the World Health Organization (WHO). The WHO recognized the spread of COVID-19 as a pandemic on 11 March 2020. Based on statistics from 10 August 2020, more than 20.2 million cases of COVID-19 have been reported resulting in more than 738,000 deaths. This completely new coronavirus has spread worldwide in a short period, causing economic crises and healthcare system failures worldwide. Initially, it was thought that the main health threat was associated with respiratory system failures, but since then, SARS-CoV-2 has been linked to a broad spectrum of symptoms indicating neurological manifestations, including ischemic stroke. Current knowledge about SARS-CoV-2 and its complications is very limited because of its rapidly evolving character. However, further research is undoubtedly necessary to understand the causes of neurological abnormalities, including acute cerebrovascular disease. The viral infection is inextricably associated with the activation of the immune system and the release of pro-inflammatory factors, that can stimulate the host organism to defend itself. However, the body’s immune response is a double-edged sword that on one hand, destroys the virus but also disrupts the homeostasis leading to serious complications, including thrombosis. Numerous studies have linked coagulopathies with COVID-19, however, there is great uncertainty regarding it functions on the molecular level. In this review, a detailed insight into the biological processes associated with ischemic stroke in COVID-19 patients and suggest a possible explanation for this phenomenon is provided. url: https://www.ncbi.nlm.nih.gov/pubmed/32825182/ doi: 10.3390/jcm9092688 id: cord-262454-bccrvapy author: Szente Fonseca, Silvia Nunes title: Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis date: 2020-10-31 words: 4700.0 sentences: 249.0 pages: flesch: 53.0 cache: ./cache/cord-262454-bccrvapy.txt txt: ./txt/cord-262454-bccrvapy.txt summary: With all that, we developed a protocol for early recognition and treatment of high-risk patients (in our population, age greater than 40 years because of generally poorer health standards, or with comorbidities) who would come to our outpatient network of emergency rooms with influenza-like symptoms: fever, cough, myalgia and headache, among others, and receive early treatment, provided to patients at the first doctor visit, using physician discretion from among HCQ, azithromycin, ivermectin, oseltamivir, zinc sulfate, nitazoxanide and prednisone (the last starting on day-6 of symptoms). On March 28, 2020, the FDA issued an emergency use authorization for remdesivir and HCQ for patients in both clinical trials and with severe hospitalized disease (31) . We found early outpatient use of HCQ and prednisone, both as individual prescriptions and used together, to lower the risk of hospitalization in symptomatic high-risk COVID-19 patients presenting for primary care at the emergency rooms of our large HMO in Brazil. abstract: BACKGROUND: For the past few months, HMOs have faced crowded emergency rooms and insufficient hospital and intensive-care-unit beds, all from the worst pandemic of this century, COVID-19. METHODS: In a large HMO in Brazil, our approach was to allow treating physicians to prescribe antiviral medications immediately at presentation, and prednisone starting on day-6 of symptoms to treat pulmonary inflammation. We implemented this COVID-19 protocol for outpatients and studied 717 consecutive SARS-CoV-2-positive patients age 40 years or older presenting at our emergency rooms. RESULTS: Use of hydroxychloroquine (HCQ), prednisone or both significantly reduced hospitalization risk by 50-60%. Ivermectin, azithromycin and oseltamivir did not substantially reduce risk further. Hospitalization risk was doubled for people with type-2 diabetes or obesity, increased by two-thirds for people with heart disease, and by 75% for each decade of age over age 40. Similar magnitudes of reduced risk with HCQ and prednisone use were seen for mortality risk, though were not significant because of only 11 deaths among the 717 patients. No cardiac arrhythmias requiring medication termination were observed for any of the medications. CONCLUSIONS: This work adds to the growing literature of studies that have found substantial benefit for use of HCQ combined with other agents in the early outpatient treatment of COVID-19, and adds the possibility of steroid use to enhance treatment efficacy. url: https://www.sciencedirect.com/science/article/pii/S1477893920304026?v=s5 doi: 10.1016/j.tmaid.2020.101906 id: cord-349721-wdjlr4z4 author: Szpiro, L. title: Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection date: 2020-08-25 words: 3991.0 sentences: 190.0 pages: flesch: 42.0 cache: ./cache/cord-349721-wdjlr4z4.txt txt: ./txt/cord-349721-wdjlr4z4.txt summary: To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. In an attempt to better understand and thus better control the transmission of SARS-CoV-2 behind the recent and ongoing pandemic, the impact of body fluid secretions, from coughing or sneezing corresponding to an artificial mixture containing nasal mucus and saliva, on the surface stability of SARS-CoV-2 and the virucidal efficiency of disinfectant were tested. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers (according to the EN14476 standard suspension test) and 1 surface chemical disinfectant (according to the virucidal surface quantitative EN16777 test) against SARS-CoV-2, HCoV-229E and FCoV was then measured. The virucidal activity of three commercial hand rub products against SARS-CoV-2, HCoV-229E and FCoV was determined using the quantitative suspension test according to EN 14476, comparing standardized interfering substance (clean condition, 0.3 g/l BSA) and our artificial mucus/saliva mixture. abstract: Contaminated environmental surfaces are considered to represent a significant vector for hospital-acquired viral infections. In this study, we have evaluated the impact of interfering substances on SARS-CoV-2 surface stability and virucidal efficiency of hand sanitizers and surface disinfectant. To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers and 1 surface chemical disinfectant against SARS-CoV-2, HCoV-229E and FCoV was then measured. Our results indicate that mucus/saliva mixture did not demonstrate a beneficial effect on the surface survival of tested viruses, with temperature being an important parameter. In addition, we demonstrated that interfering substances may play an important role in the virucidal efficacy of hand sanitizers and disinfectants, highlighting the need for adapted testing protocols that better reflect current - real life -conditions of use. url: https://doi.org/10.1101/2020.08.22.20180042 doi: 10.1101/2020.08.22.20180042 id: cord-251581-8ubyveyt author: Szymkowiak, Andrzej title: In-store epidemic behavior: scale development and validation date: 2020-05-04 words: 6038.0 sentences: 297.0 pages: flesch: 51.0 cache: ./cache/cord-251581-8ubyveyt.txt txt: ./txt/cord-251581-8ubyveyt.txt summary: All identified factors significantly correlated with the in-store infection threat which reiterates the importance of providing information revealing the true scale of the pandemic and not leaving space for individuals to create subjective probability judgments. Nonetheless, one must also bear in mind that grocery stores are a place for possible transmission of many bacterial and viral pathogens (Bell et al., 2009; Dalton, New, & Health, 2006; Sinclair, Fahnestock, Feliz, Patel, & Perry, 2018) , causing consumers to undertake various behavioral changes in their approach to shopping. Based on the analysis of this limited quantity of research related to consumer behavioral changes in response to epidemics, it is clear that there is a gap in research on how the fear of contagion and not budgetary limitations can impact consumer willingness to shop at stationery stores. Moreover, the questionnaire was performed during the outbreak of the COVID-19 pandemic which limits the possibility of comparing the results for in-shop behaviors with a time from before the epidemic. abstract: Epidemics of infectious diseases have accompanied humans for a long time and, depending on the scale, cause various undesirable social and economic consequences. During the ongoing COVID-19 pandemic, governments of many countries impose restrictions to inhibit spreading of infection. Isolation and limiting interpersonal contacts are particularly recommended actions. Adhering to the rule of isolation may involve restrictions in freedom during daily activities, such as shopping. The aim of the study was to develop a scale of in-store pandemic behavior. The whole process involved 3 stages: qualitative inquiry, scale purification and scale validation, which were based on 3 studies: 1 qualitative (20 in-depth interviews) 2 two quantitative (373 and 584 respondents, respectively), and allowed to identify 8 factors. Following, a theoretical model was created to investigate the impact of in-store infection threat on identified variables. All identified factors significantly correlated with the in-store infection threat which reiterates the importance of providing information revealing the true scale of the pandemic and not leaving space for individuals to create subjective probability judgments. The developed scale can help counteract disinformation and assess consumer behavior compliance and understanding of the official recommendations imposed by governments, enabling more efficient educational efforts. url: https://arxiv.org/pdf/2005.02764v1.pdf doi: nan id: cord-292874-6zjqflhz author: SØRENSEN, MORTEN DRÆBY title: Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date: 2006-05-10 words: 1560.0 sentences: 110.0 pages: flesch: 54.0 cache: ./cache/cord-292874-6zjqflhz.txt txt: ./txt/cord-292874-6zjqflhz.txt summary: abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV. In February 2003, the new and previously unknown deadly coronavirus causing severe acute respiratory syndrome (SARS-CoV) was brought to the attention of the World Health Organization (WHO) by Dr. Carlo Urbani and his colleagues. Creation of immune phage-display libraries for immunized donors has shown a particular efficiency in selecting neutralizing antibodies (NABs) against different viruses, for example, rabies, 39 varicella-zoster, 40 hepatitis A 41 and E, 42 measles, 43 and respiratory syncytial virus. abstract: abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. For reasons unknown, the SARS virus is less severe and the clinical progression a great deal milder in children younger than 12 years of age. In contrast, the mortality rate can exceed 50% for persons at or above the age of 60. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/16804033/ doi: 10.1196/annals.1354.072 id: cord-288051-wp8v2mc5 author: Sánchez-González, Álvaro title: What Should Be Known by a Urologist About the Medical Management of COVID-19’s Patients? date: 2020-09-01 words: 3616.0 sentences: 267.0 pages: flesch: 47.0 cache: ./cache/cord-288051-wp8v2mc5.txt txt: ./txt/cord-288051-wp8v2mc5.txt summary: Seven days after the clinical onset, the risk of transmission decreases in mildsymptomatic patients, but it may be extended over 24 days in severe cases [11•, 15] . The clinical spectrum of SARS-CoV-2 infection varies widely, including asymptomatic infection, mild upper respiratory tract illness, severe viral pneumonia with respiratory failure, and even death [9, 11•] (Fig. 1) . Corticosteroids are recommended in the treatment of septic shock, exacerbation of chronic obstructive respiratory disease and these COVID-19''s patients with respiratory deterioration and quick radiological progression associated with sings of cytokine storm (cytopenia, maintained fever, an increase of inflammatory reactants: D-dimer > 1000 ng/mL, ferritin > 1000 ng/mL, fibrinogen > 100 ng/mL, IL-6 > 40 pg/mL) [6, 23••] . Results from 237 patients, 158 assigned to remdesivir, showed no differences in time to clinical improvement, 28day mortality, oxygen support, hospitalization, or viral load. Clinical management of severe acute respiratory infection (SARI) when COVID-19 disease is suspected. Effective treatment of severe COVID-19 patients with tocilizumab abstract: PURPOSE OF REVIEW: The alarming number of confirmed COVID-19 cases put a strain on the healthcare systems, which had to reallocate human and technical resources to respond to the emergency. Many urologists became integrated into multidisciplinary teams, dealing with this respiratory illness and its unknown management. It aims to summarize the epidemiological, clinical, diagnostical, and therapeutical characteristics of COVID-19, from a practical perspective, to ease COVID-19 management to non-physician staff. RECENT FINDINGS: We performed a narrative review of the literature regarding COVID-19, updated to May 8th, 2020, at PubMed and COVID resource platforms of the main scientific editorials. COVID-19, characterized by fever, myalgias, dyspnea, and dry cough, varies widely from asymptomatic infection to death. Arrhythmias and thrombotic events are prevalent. Lymphopenia and inflammatory reactant elevation on laboratory, as well as bilateral and peripheral ground-glass opacities or consolidations on X-Ray, are usually found in its assessment. Little is known about SARS-CoV-2 immunology. To date, no therapy has demonstrated efficacy in COVID-19. Of-level or compassionate-use therapies are prescribed in the context of clinical trials. We should become familiar with specific adverse events and pharmacological interactions. SUMMARY: The COVID-19 pandemic has paralyzed the urological activity, and its long-term consequences are unpredictable. Despite not being used to deal with respiratory diseases, the urologists become easily qualified to manage COVID-19 by following protocols and being integrated into multidisciplinary teams, helping to overcome the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32870407/ doi: 10.1007/s11934-020-00995-y id: cord-332013-bl5d4xkc author: Sánchez-Álvarez, J. Emilio title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) date: 2020-04-27 words: 3619.0 sentences: 214.0 pages: flesch: 54.0 cache: ./cache/cord-332013-bl5d4xkc.txt txt: ./txt/cord-332013-bl5d4xkc.txt summary: title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) Conclusions SARS-CoV-2 infection already affects a significant number of Spanish patients on RRT, mainly those on ICH, hospitalization rates are very high and mortality is high; age and the development of pneumonia are factors associated with mortality. As of April 11, data from 868 patients on RRT with documented SARS-CoV-2 coronavirus infection had been entered into the Registry. The analysis of data collected during the first three weeks of the Covid-19 Registry of SEN shows that the SARS-CoV-2 infection affects a significant number of Spanish patients on RRT, mainly those that are in HDC . Nevertheless our registry show that , hydroxychloroquine and other commonly used drugs in the SARS-CoV infection-2 are used more frequently in transplant than in dialysis patients. abstract: Summary The recent appearance of the SARS-CoV-2 coronavirus pandemic has had a significant impact on the general population. Patients on renal replacement therapy (RRT) have not been unaware of this situation and due to their characteristics they are especially vulnerable. We present the results of the analysis of the COVID-19 Registry of the Spanish Society of Nephrology. Material and methods The Registry began operating on March 18th, 2020. It collects epidemiological variables, contagion and diagnosis data, signs and symptoms, treatments and outcomes. It is an “online” registry. Patients were diagnosed with SARS-Cov-2 infection based on the results of the PCR of the virus, carried out both in patients who had manifested compatible symptoms or had suspicious signs, as well as in those who had undergone screening after some contact. acquainted with another patient. Results As of April 11, the Registry had data on 868 patients, from all the Autonomous Communities. The most represented form of TRS is in-center hemodialysis (ICH) followed by transplant patients. Symptoms are similar to the general population. A very high percentage (85%) required hospital admission, 8% in intensive care units. The most used treatments were hydroxychloroquine, lopinavir-ritonavir, and steroids. Mortality is high and reaches 23%; deceased patients were more frequently on ICH, developed pneumonia more frequently, and received less frequently lopinavir-ritonavir and steroids. Age and pneumonia were independently associated with the risk of death. Conclusions SARS-CoV-2 infection already affects a significant number of Spanish patients on RRT, mainly those on ICH, hospitalization rates are very high and mortality is high; age and the development of pneumonia are factors associated with mortality. url: https://api.elsevier.com/content/article/pii/S201325142030050X doi: 10.1016/j.nefroe.2020.04.002 id: cord-297381-1upz6dsy author: Sánchez‐Duque, Jorge A. title: Are we now observing an increasing number of coinfections between SARS‐CoV‐2 and other respiratory pathogens? date: 2020-05-29 words: 1015.0 sentences: 83.0 pages: flesch: 60.0 cache: ./cache/cord-297381-1upz6dsy.txt txt: ./txt/cord-297381-1upz6dsy.txt summary: Then, we would like to take the opportunity to discuss some of them, 1-10 as there are not yet reviews on this emerging issue of Currently, the evidence suggests that the coinfection rates between SARS-CoV-2 and other respiratory pathogens would be higher than initially expected, which represents a challenge for the diagnosis and treatment. Of patients with confirmed SARS-CoV-2 infection, 20.7% (n=24) were positive for one or more additional pathogens, of which the most common were rhinovirus/enterovirus (6.9%; n=8), respiratory syncytial virus (5.2%; n=6) and other Coronaviruses (4.3%; n=5). 2 Another study by Ding et al., 3 included 115 patients with SARS-CoV-2 infection, 4.35% (n=5) had influenza coinfection (3 for influenza A; 2 for influenza B) 9 . 6 Arashiro et al., 4 published a case report of a patient who debuted with severe acute respiratory distress associated with This article is protected by copyright. abstract: We have recently read the article by Chaung et al.,(1) describing a case of SARS‐CoV‐2 and HCoV‐HKU1 coinfection. The HCoV‐HKU1 is also a member of the Betacoronavirus. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32470211/ doi: 10.1002/jmv.26089 id: cord-280528-7ivw72l0 author: TUFAN, Abdurrahman title: COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs date: 2020-04-21 words: 7053.0 sentences: 364.0 pages: flesch: 42.0 cache: ./cache/cord-280528-7ivw72l0.txt txt: ./txt/cord-280528-7ivw72l0.txt summary: In this review, to gain better information about appropriate anti-inflammatory treatments, mostly used in rheumatology for COVID-19, we have focused the attention on the structural features of SARS-CoV-2, the host immune response against SARS-CoV-2 and its association with the cytokine storm. The effective antiviral responses of the host innate and adaptive immunity, including the production of various proinflammatory cytokines, the activation of T cells, CD4 and CD8+ T cells, are essential for controlling the viral replication, limiting the spread of virus, inflammation and cleaning the infected cells [31, 32] . Few retrospective studies have revealed that the lung injury reported with Murray score is strongly associated with the level of IL-1α, IL-1ra, IL-2, IL-7, IL-10, IL-17, IFN-ɣ, inducible interferon protein (IP)-10, G-CSF, and MCP-3 and these cytokines and chemokines excluding MCP-3 are positively related to SARS-CoV-2 viral load 2 [7] . abstract: In the Wuhan Province of China, in December 2019, the novel coronavirus 2019 (COVID-19) has caused a severe involvement of the lower respiratory tract leading to an acute respiratory syndrome. Subsequently, coronavirus 2 (SARS-CoV-2) provoked a pandemic which is considered a life-threatening disease. The SARS-CoV-2, a family member of betacoronaviruses, possesses single-stranded positive-sense RNA with typical structural proteins, involving the envelope, membrane, nucleocapsid and spike proteins that are responsible for the viral infectivity, and nonstructural proteins. The effectual host immune response including innate and adaptive immunity against SARS-Cov-2 seems crucial to control and resolve the viral infection. However, the severity and outcome of the COVID-19 might be associated with the excessive production of proinflammatory cytokines “cytokine storm” leading to an acute respiratory distress syndrome. Regretfully, the exact pathophysiology and treatment, especially for the severe COVID-19, is still uncertain. The results of preliminary studies have shown that immune-modulatory or immune-suppressive treatments such as hydroxychloroquine, interleukin (IL)-6 and IL-1 antagonists, commonly used in rheumatology, might be considered as treatment choices for COVID-19, particularly in severe disease. In this review, to gain better information about appropriate anti-inflammatory treatments, mostly used in rheumatology for COVID-19, we have focused the attention on the structural features of SARS-CoV-2, the host immune response against SARS-CoV-2 and its association with the cytokine storm. url: https://www.ncbi.nlm.nih.gov/pubmed/32299202/ doi: 10.3906/sag-2004-168 id: cord-253987-83h861lp author: Tada, Takuya title: A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date: 2020-09-17 words: 6830.0 sentences: 349.0 pages: flesch: 50.0 cache: ./cache/cord-253987-83h861lp.txt txt: ./txt/cord-253987-83h861lp.txt summary: The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. In SARS-CoV-2 entry, the virus attaches to the target cell through the interaction of the spike glycoprotein (S) with its receptor, the angiotensin-converting enzyme 2 (ACE2) (Li, 2015; Li et al., 2005; Li et al., 2003) , a plasma membrane protein carboxypeptidase that degrades angiotensin II to angiotensin-(1-7) [Ang-(1-7)] a vasodilator that promotes sodium transport in the regulation of cardiac function and blood pressure (Kuba et al., 2010; Riordan, 2003; Tikellis and Thomas, 2012) . To determine the relative antiviral activity of soluble ACE2 and the ACE2 microbody proteins, we tested their ability to block the infection SARS-CoV-2 Δ19 S protein pseudotyped GFP/luciferase reporter virus. abstract: Soluble forms of ACE2 have recently been shown to inhibit SARS-CoV-2 infection. We report on an improved soluble ACE2, termed a “microbody” in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. The ACE2 microbody inhibited the entry of ACE2-specific β coronaviruses and viruses with the high infectivity variant D614G spike. The ACE2 microbody may be a valuable therapeutic for COVID-19 that is active against SARS-CoV-2 variants and future coronaviruses that may arise. url: https://doi.org/10.1101/2020.09.16.300319 doi: 10.1101/2020.09.16.300319 id: cord-343712-gn7fw891 author: Taglauer, Elizabeth title: Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads date: 2020-08-25 words: 1497.0 sentences: 86.0 pages: flesch: 41.0 cache: ./cache/cord-343712-gn7fw891.txt txt: ./txt/cord-343712-gn7fw891.txt summary: title: Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads Parenchymal changes of placentas from COVID-19 infected mothers have been reported by several groups, but the localization and relative abundance of SARS-CoV-2 viral proteins and cellular entry machinery has not been fully characterized within larger placental tissue cohorts. Overall this study provides an important basis for the ongoing evaluation of SARS-CoV-2 physiology in pregnancy and highlights the importance of the placenta as a key source of primary human tissue for ongoing diagnostic and therapeutic research efforts to reduce the global burden of COVID-19. While ACE2 was consistently found in the sTB layer of all tissues 148 surveyed (COVID-19 Maternal and controls), TMPRSS2 expression was absent in both groups of 149 placentas (Fig. 3 A,B) . Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of 301 the placenta in pregnancies with COVID-19 positive mothers and neonates at birth abstract: INTRODUCTION: While the COVID-19 pandemic continues to have a significant global health impact, rates of maternal to infant vertical transmission remain low (<5%). Parenchymal changes of placentas from COVID-19 infected mothers have been reported by several groups, but the localization and relative abundance of SARS-CoV-2 viral proteins and cellular entry machinery has not been fully characterized within larger placental tissue cohorts. METHODS: An extended placental tissue cohort including samples from 15 COVID-19 positive maternal-fetal dyads (with n = 5 cases with evidence of fetal transmission) in comparison with 10 contemporary COVID-19 negative controls. Using comparative immunofluorescence, we examined the localization and relative tissue abundance of SARS-CoV2 spike glycoprotein (CoV2 SP) along with the co-localization of two SARS-CoV2 viral entry proteins angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). RESULTS/CONCLUSIONS: CoV2 SP was present within the villous placenta in COVID-19 positive pregnancies with and without evidence of fetal transmission. We further identified the predominance of ACE2 expression in comparison with TMPRSS2. Importantly, both CoV2 SP and ACE2 expression consistently localized primarily within the outer syncytiotrophoblast layer placental villi, a key physiologic interface between mother and fetus. Overall this study provides an important basis for the ongoing evaluation of SARS-CoV-2 physiology in pregnancy and highlights the importance of the placenta as a key source of primary human tissue for ongoing diagnostic and therapeutic research efforts to reduce the global burden of COVID-19. url: https://doi.org/10.1016/j.placenta.2020.08.015 doi: 10.1016/j.placenta.2020.08.015 id: cord-287497-93oiiqqi author: Tagliamento, Marco title: Italian survey on managing immune checkpoint inhibitors in oncology during COVID‐19 outbreak date: 2020-06-14 words: 3228.0 sentences: 199.0 pages: flesch: 49.0 cache: ./cache/cord-287497-93oiiqqi.txt txt: ./txt/cord-287497-93oiiqqi.txt summary: The objectives of this survey were to examine the impact of COVID-19 outbreak on the perception of Italian physicians involved in the administration of ICIs about SARS-CoV-2 related risks in cancer patients receiving these therapies, and their attitudes towards the management of ICIs in oncology. The perception of respondents regarding the potential increased risk of severe events related to SARS-CoV-2 infection in cancer patients treated with ICIs is displayed in Figure 1B . 17 Moreover, besides the overlapping between cancer-related signs/symptoms or side effects of oncological treatments (including irAEs) and COVID-19 manifestations, additional issues could emerge from the differential diagnosis between radiological findings of lung involvement from SARS-CoV-2 and pneumonitis induced by ICIs. 9, 24 To the best of our knowledge, this is the first study exploring the perception of physicians towards these unsolved issues, and whether the outbreak has modified the clinical practice in managing the treatment with ICIs in oncology. abstract: BACKGROUND: During COVID‐19 outbreak, oncological care has been reorganized. Cancer patients have been reported to experience a more severe COVID‐19 syndrome; moreover, there are concerns of an interference between immune checkpoint inhibitors (ICIs) and SARS‐CoV‐2 pathogenesis. MATERIALS AND METHODS: Between May 6 and 16, 2020, a 22‐item survey was sent to Italian physicians involved in administering ICIs. It aimed to explore the perception about SARS‐CoV‐2 related risks in cancer patients receiving ICIs, and the attitudes towards their management. RESULTS: The 104 respondents had a median age of 35.5 years, 58.7% were females and 71.2% worked in Northern Italy. 47.1% of respondents argued a synergism between ICIs and SARS‐CoV‐2 pathogenesis leading to worse outcomes, but 97.1% would not deny an ICI only for the risk of infection. During COVID‐19 outbreak, to reduce hospital visits, 55.8% and 30.8% opted for the highest labeled dose of each ICI (55.8%) and/or, among different ICIs for the same indication, for the one with the longer interval between cycles, respectively. 53.8% of respondents suggested testing for SARS‐CoV‐2 every cancer patient candidate to ICIs. 71.2% declared to manage patients with onset of dyspnea and cough as SARS‐CoV‐2 infected until otherwise proven; however, 96.2% did not reduce the use of steroids to manage immune‐related toxicities. The administration of ICIs in specific situations for different cancer types has not been drastically conditioned. CONCLUSIONS: These results highlight the confusion around the perception of a potential interference between ICIs and COVID‐19, supporting the need of focused studies on this topic. url: https://doi.org/10.1111/eci.13315 doi: 10.1111/eci.13315 id: cord-337595-0p5f5o5v author: Tagliamento, Marco title: Call for ensuring cancer care continuity during COVID-19 pandemic date: 2020-05-07 words: 874.0 sentences: 48.0 pages: flesch: 50.0 cache: ./cache/cord-337595-0p5f5o5v.txt txt: ./txt/cord-337595-0p5f5o5v.txt summary: On 11 March 2020, WHO declared the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to be a pandemic, and the related syndrome was then named coronavirus disease 2019 (COVID-19). At a median follow-up of 15 days since the confirmed diagnosis of SARS-CoV-2 infection, the case fatality rate was 24%: four patients out of 17 died due to severe COVID-19, two of whom were on oncological follow-up (ie, off therapy). Widespread testing for SARS-CoV-2 among patients with cancer and their healthcare providers could also help to control the potential negative consequences of this outbreak on cancer care. With the current uncertainty, the important aim behind this decision is to ensure continuity of care to those selected patients who can reasonably receive oncological treatments in spite of SARS-CoV-2 positivity, balancing the risks associated with the infection and the disruption of proper antineoplastic strategies. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan abstract: nan url: https://doi.org/10.1136/esmoopen-2020-000783 doi: 10.1136/esmoopen-2020-000783 id: cord-302414-g5onwhg1 author: Tahir ul Qamar, Muhammad title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 words: 6780.0 sentences: 434.0 pages: flesch: 47.0 cache: ./cache/cord-302414-g5onwhg1.txt txt: ./txt/cord-302414-g5onwhg1.txt summary: Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) linked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause severe illness and life-threatening pneumonia in humans. The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection. Therefore, the present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19. METHODS: Structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) of SARS-CoV-2 are responsible for its prime functions. Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B- and T- cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. RESULTS: Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%. Taken together, 276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes (CTL), 6 helper T lymphocyte (HTL) and 4 B-cell epitopes with suitable adjuvant and linkers. The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV. Finally, MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system, to ensure its increased expression. CONCLUSION: The MESV developed in this study is capable of generating immune response against COVID-19. Therefore, if designed MESV further investigated experimentally, it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19. url: https://doi.org/10.1186/s40249-020-00752-w doi: 10.1186/s40249-020-00752-w id: cord-273614-qmp2tqtb author: Tahir, Faryal title: Cardiac Manifestations of Coronavirus Disease 2019 (COVID-19): A Comprehensive Review date: 2020-05-08 words: 7164.0 sentences: 413.0 pages: flesch: 53.0 cache: ./cache/cord-273614-qmp2tqtb.txt txt: ./txt/cord-273614-qmp2tqtb.txt summary: However, multiple studies that highlight the clinical features, laboratory findings, and prognosis of acute myocardial injury (AMI) in COVID-19-affected individuals have been published. The study concluded that severe respiratory illness with 2019n-CoV infection with deteriorating complications was associated with ICU admission and a higher mortality rate [24] . This study concluded that patients with very severe COVID-19 have a higher percentage of increased cTnI levels and their mortality rate can be improved by protecting them from myocardial injury [40] . The study concluded that cardiac injury is a prevalent condition among hospitalized patients with COVID-19 in Wuhan, China, and it is associated with a higher risk of in-hospital mortality [41] . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study (Epub ahead of print) Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China (Epub ahead of print) abstract: Since its origin in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become a pandemic and spread to 209 countries. As coronavirus disease 2019 (COVID-19) is a very rapidly emerging disease, organ-specific studies related to it have been reported. Apart from respiratory findings, some studies have highlighted inflammatory consequences in the heart, kidney, and/or liver as well. Cardiac involvement in COVID-19 seems to be a result of an inflammatory storm in response to the infection. Moreover, direct viral invasion of cardiomyocytes, as well as a myocardial injury due to oxidative stress, may account for acute cardiac injury in COVID-19. Nevertheless, the mechanism of heart injury in COVID-19 is not clear yet. However, multiple studies that highlight the clinical features, laboratory findings, and prognosis of acute myocardial injury (AMI) in COVID-19-affected individuals have been published. In this review, we have summarized the findings of all those studies as well as the clinical features and management of cardiac injury discussed by some case reports. url: https://www.ncbi.nlm.nih.gov/pubmed/32528760/ doi: 10.7759/cureus.8021 id: cord-280050-fktc778q author: Tahir, Shumaila title: Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan date: 2020-06-17 words: 3423.0 sentences: 182.0 pages: flesch: 53.0 cache: ./cache/cord-280050-fktc778q.txt txt: ./txt/cord-280050-fktc778q.txt summary: Methods We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. The primary aim of this retrospective observational study was to report the epidemiological features and statistics of individuals infected with COVID-19 from February 26 to April 24 from East Karachi, Pakistan, and contribute towards an accurate collection of figures from the country. The suspected or confirmed cases were clinically classified as asymptomatic, mild, moderate, severe, and critical, according to the National Institute of Health, Pakistan guidelines and are defined below in Table 1 [9]. Candidates with fever, symptoms of lower respiratory illness, and a travel history to Wuhan, China or other countries with uncontrolled COVID-19 cases or who have been in contact with an individual suspected of COVID-19 or with laboratory-confirmed COVID-19 in the preceding 14 days should be isolated and tested for the infection promptly [19] . abstract: Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to almost every country on the globe, and each country is reporting the symptomatic presentation of their patients to give better insight into the various clinical presentations of SARS-CoV-2. However, the epidemiological literature from Pakistan is scanty. Methods We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. Patients' demographics, symptoms, travel and contact history, and outcomes were recorded. All statistical analysis was performed using the Statistical Package for the Social Sciences (SPSS) version 22 (IBM SPSS Statistics for Windows, IBM Corp, Armonk, NY). Results Most of the patients were male (64.6%), the majority (43.3%) belonging to the 21- to 40-year age group. Most of the patients (65.5%) were residents of Gulshan Iqbal. A total of 15.8% of the patients were admitted to the hospital, and 3.9% of patients expired. The three most common presenting symptoms were fever (74.8%), cough (60.4%), and flu (35.5%). The majority of patients (89.3%) gave a history of contact with SARS-CoV-2 patients. Conclusion The number of SARS-CoV-2 cases is rapidly increasing in Karachi, Pakistan. There is a need to educate the population about the most common sign and symptoms of the virus so that individuals can identify these symptoms and get themselves tested. The concerned authorities should devise an adequate and effective plan to flatten the infectivity curve. url: https://www.ncbi.nlm.nih.gov/pubmed/32699679/ doi: 10.7759/cureus.8679 id: cord-335118-oa9jfots author: Taka, E. title: Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date: 2020-09-21 words: 5264.0 sentences: 344.0 pages: flesch: 61.0 cache: ./cache/cord-335118-oa9jfots.txt txt: ./txt/cord-335118-oa9jfots.txt summary: By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Initial studies have constructed a homology model of SARS-CoV-2 RBD in complex with ACE2, based on the SARS-CoV crystal structure (8, 14) and performed conventional MD (cMD) simulations totaling 10 ns (15, 16) and 100 ns (17, 18) in length to estimate binding free energies (15, 16) and interaction scores (18) . In this study, we performed a comprehensive set of all-atom MD simulations totaling 16.5 µs in length using the recently-solved structure of the RBD of the SARS-CoV-2 S protein in complex with the PD of ACE2 (7) . In 20 SMD simulations (each 15 ns, totaling 300 ns in length, table S1), the average work applied to unbind RBD from PD was 71.1 ± 12.7 kcal/mol (mean ± s.d.), demonstrating that the S protein binds stably to ACE2 (Fig. 3B) . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors and causes the Coronavirus disease 2019 (COVID-19). Therapeutic approaches to prevent SARS-CoV-2 infection are mostly focused on blocking S-ACE2 binding, but critical residues that stabilize this interaction are not well understood. By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Mutagenesis of these residues on the RBD was not sufficient to destabilize binding but reduced the average work to unbind the S protein from ACE2. In particular, the hydrophobic end of RBD serves as the main anchor site and unbinds last from ACE2 under force. We propose that blocking this site via neutralizing antibody or nanobody could prove an effective strategy to inhibit S-ACE2 interactions. url: https://doi.org/10.1101/2020.09.21.305490 doi: 10.1101/2020.09.21.305490 id: cord-312414-g5px0b65 author: Takagi, Akira title: An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date: 2020-09-19 words: 4076.0 sentences: 230.0 pages: flesch: 61.0 cache: ./cache/cord-312414-g5px0b65.txt txt: ./txt/cord-312414-g5px0b65.txt summary: As shown in Fig. 2 , the intracellular cytokine staining (ICS) assay showed that 173 significant numbers of IFN--producing CD8+ T cells were elicited in mice immunized 174 with 18 liposomal peptides including pp1a-38, -52, -84, -103, -445, -597, -641, -1675, 175 -2785, -2884, -3083, -3403, -3467, -3583, -3662, -3710, -3732, and -3886, revealing that 176 these 18 peptides are HLA-A*02:01-restricted CTL epitopes derived from SARS-CoV-2 177 pp1a. However, any of 18 185 epitopes are not found in the amino acid sequence of either MERS-CoV or the four 186 common cold human coronaviruses involving HCoV-OC43, In the 18 positive peptides, 10 peptides including pp1a-38, -84, -641, -1675, -2884, 189 -3467, -3583, -3662, -3710, and -3732 were selected for the following analyses because 190 of the high ratios of IFN- + cells in CD8 + T cells (Fig. 2) . At first glance, the graphs of CD107a ( Taken together, 10 peptides differed significantly in their ability to induce 226 SARS-CoV-2 pp1a-specific CTLs when mice were immunized with the mixture of 10 227 peptides in liposomes. abstract: COVID-19 vaccines are being rapidly developed and human trials are underway. Almost all of these vaccines have been designed to induce antibodies targeting spike protein of SARS-CoV-2 in expectation of neutralizing activities. However, non-neutralizing antibodies are at risk of causing antibody-dependent enhancement. Further, the longevity of SARS-CoV-2-specific antibodies is very short. Therefore, in addition to antibody-induced vaccines, novel vaccines on the basis of SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs) should be considered in the vaccine development. Here, we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Eighty-two peptides were firstly predicted as epitope candidates on bioinformatics. Fifty-four in 82 peptides showed high or medium binding affinities to HLA-A*02:01. HLA-A*02:01 transgenic mice were then immunized with each of the 54 peptides encapsulated into liposomes. The intracellular cytokine staining assay revealed that 18 out of 54 peptides were CTL epitopes because of the induction of IFN-γ-producing CD8+ T cells. In the 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant CTL epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant over the other peptides. Surprisingly, all mice immunized with the liposomal 10 peptide mixture did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines. Importance For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines. url: https://doi.org/10.1101/2020.09.18.304493 doi: 10.1101/2020.09.18.304493 id: cord-339670-lq46nj8j author: Takahashi, Nozomi title: Clinical course of a critically ill patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-06-16 words: 1746.0 sentences: 98.0 pages: flesch: 43.0 cache: ./cache/cord-339670-lq46nj8j.txt txt: ./txt/cord-339670-lq46nj8j.txt summary: Although several studies have reported on the clinical and epidemiological characteristics of the patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinical course of the most severe cases requiring treatment in ICU have been insufficiently reported. A 73-year-old man traveling on a cruise ship with history of hypertension and dyslipidemia developed high fever, dyspnea and cough after 7 days of steroid treatment for sudden sensorineural hearing loss, and tested positive for SARS-CoV-2 in sputa polymerase chain reaction (PCR) examination. The sustained excessive inflammatory cytokines in the present case might have led to the exacerbation of the disease, requiring vigorous organ support therapies to allow for survival and recovery from the rapid progression of multiple organ dysfunctions and severe respiratory failure. (SARS-CoV-2), who developed multiple organ dysfunctions, treated with artificial organ supports including mechanical ventilation, extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT). abstract: Although several studies have reported on the clinical and epidemiological characteristics of the patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinical course of the most severe cases requiring treatment in ICU have been insufficiently reported. A 73-year-old man traveling on a cruise ship with history of hypertension and dyslipidemia developed high fever, dyspnea and cough after 7 days of steroid treatment for sudden sensorineural hearing loss, and tested positive for SARS-CoV-2 in sputa polymerase chain reaction (PCR) examination. His respiratory function deteriorated despite treatments with lopinavir/ritonavir, oseltamivir, azithromycin and meropenem at a regional hospital. He was intubated and transferred to the ICU in the tertiary university hospital on day 10 (ICU day 1). Interferon beta-1b subcutaneous injection was initiated immediately to enhance anti-viral therapy, and favipiravir on ICU day 10 upon availability. Progression of organ dysfunctions necessitated inhalation of nitrogen oxide for respiratory dysfunction, noradrenaline for cardiovascular dysfunction and continuous renal replacement therapy for renal dysfunction. His blood samples PCR also tested positive for SARS-CoV-2, indicating viremia, concomitantly with elevated IL-6 levels. VV-ECMO was initiated after sudden exacerbation of respiratory dysfunction on ICU day 7 to maintain oxygenation. The sustained excessive inflammatory cytokines in the present case might have led to the exacerbation of the disease, requiring vigorous organ support therapies to allow for survival and recovery from the rapid progression of multiple organ dysfunctions and severe respiratory failure. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10047-020-01183-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32556649/ doi: 10.1007/s10047-020-01183-y id: cord-315849-e16lln3f author: Takayama, Kazuo title: In vitro and Animal Models for SARS-CoV-2 research date: 2020-05-30 words: 1167.0 sentences: 94.0 pages: flesch: 54.0 cache: ./cache/cord-315849-e16lln3f.txt txt: ./txt/cord-315849-e16lln3f.txt summary: An in vitro cell model for SARS-CoV-2 research is essential for understanding the viral life cycle, for amplifying and isolating the virus for further research and for preclinical evaluation of therapeutic molecules. This section lays out the cell lines used to replicate and isolate SARS-CoV-2, as well as organoids that can be used to examine the effects of SARS-CoV-2 infection on specific human tissues (Table 1A, Figure 1 ). They showed that their organoids were permissive to the SARS-CoV-2 infection and could evaluate anti-viral effects of COVID-19 candidate therapeutic compounds including camostat [17] . who conducted SARS-CoV-2 infection experiments using HeLa cells that expressed ACE2 proteins taken from multiple animal species from mice to humans [11] . The team found that such mice after SARS-CoV-2 infection, showed weight loss, virus replication in the lungs, and interstitial pneumonia [25] . Human ACE2 transgenic mice After SARS-CoV-2 infection, the mice show weight loss, virus replication in the lungs, and interstitial pneumonia. abstract: Abstract Basic research on SARS-CoV-2 is essential to understand its detailed pathophysiology and identify best drug targets. Models that can faithfully reproduce the viral life cycle and reproduce the pathology of COVID-19 are required. Here, we briefly review the cell lines, organoids, and animal models that are currently being used in COVID-19 research. url: https://www.ncbi.nlm.nih.gov/pubmed/32553545/ doi: 10.1016/j.tips.2020.05.005 id: cord-352557-l7sahv5t author: Takla, Michael title: Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety date: 2020-11-13 words: 7587.0 sentences: 347.0 pages: flesch: 43.0 cache: ./cache/cord-352557-l7sahv5t.txt txt: ./txt/cord-352557-l7sahv5t.txt summary: In contrast, only 58% of observational studies employing an endpoint specific to efficacy recorded no significant difference in the attainment of outcomes, such as duration of hospital stay, need for mechanical ventilation, and probability of transfer to an intensive care unit (ICU), between COVID-19 patients given a range of CQ and/or HCQ doses, and the control groups. Indeed, of the remaining papers, 60% found evidence of a higher probability of discharge rate (Sbidian et al., 2020) , viral clearance and shorter symptom duration (Huang et al., 2020a) in a therapeutic context, and a lower incidence of SARS-CoV-2 infection in a prophylactic context (Bhattacharya et al., 2020 Although 60% of clinical trials found evidence of higher mild adverse drug-related events in the treatment group, none of those specifically focusing on cardiac-side effects discovered any significant difference relative to the control. abstract: The COVID-19 pandemic has required clinicians to urgently identify new treatment options or the re-purposing of existing drugs. Of particular interest are chloroquine (CQ) and hydroxychloroquine (HCQ). The aims of this systematic review are to systematically identify and collate 24 studies describing the use of CQ and HCQ in human clinical trials and to provide a detailed synthesis of evidence of its efficacy and safety. Of clinical trials, 100% showed no significant difference in the probability of viral transmission or clearance in prophylaxis or therapy, respectively, compared to the control group. Among observational studies employing an endpoint specific to efficacy, 58% concurred with the finding of no significant difference in the attainment of outcomes. Three-fifths of clinical trials and half of observational studies examining an indicator unique to drug safety discovered a higher probability of adverse events in those treated patients suspected of, and diagnosed with, COVID-19. Of the total papers focusing on cardiac side-effects, 44% found a greater incidence of QTc prolongation and/or arrhythmias, 44% found no evidence of a significant difference, and 11% mixed results. The strongest available evidence points towards the inefficacy of CQ and HCQ in prophylaxis or in the treatment of hospitalised COVID-19 patients. url: https://api.elsevier.com/content/article/pii/S1319016420302644 doi: 10.1016/j.jsps.2020.11.003 id: cord-333092-78vo7i6v author: Taksande, Amar title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age date: 2020-08-11 words: 475.0 sentences: 35.0 pages: flesch: 56.0 cache: ./cache/cord-333092-78vo7i6v.txt txt: ./txt/cord-333092-78vo7i6v.txt summary: title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age The authors studied the SARS-CoV-2 infection in infants under 1 year of age in Wuhan City, China. [2] reported that the prevalence of malnutrition in elderly patients with coronavirus disease 2019 (COVID-19) was high, and nutritional support should be strengthened during treatment. Have the authors used any cardiac biomarkers, such as troponin-T or echocardiography (tissue Doppler imaging), to assess myocardial function in the infants? The authors found that 61.11% of infants have bilateral pneumonia and that 41.67% have received antibiotics treatment. This means that procalcitonin is a better indicator of inflammation than CRP in infants with SARS-CoV-2 infection. To my knowledge, this is the best study of the SARS-CoV-2 infection in infants under 1 year of age carried out by the author. SARS-CoV-2 infection in infants under 1 year of age in Wuhan City abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32780313/ doi: 10.1007/s12519-020-00384-y id: cord-316432-xemz7zn9 author: Talaie, Haleh title: Is there any potential management against COVID-19? A systematic review and meta-analysis date: 2020-08-18 words: 5089.0 sentences: 261.0 pages: flesch: 38.0 cache: ./cache/cord-316432-xemz7zn9.txt txt: ./txt/cord-316432-xemz7zn9.txt summary: METHODS: Pubmed, Embase, Scopus, Cochrane, and Scholar databases were searched from inception to July 1, 2020, to identify studies reporting the current treatment process and medications (e.g. hydroxychloroquine, antiviral therapy, convalescent plasma, and immunomodulatory agents) for COVID-19. Zhong et al., provided a systematic review and meta-analysis including the therapies for severe acute respiratory syndrome (SARS), Middle Eastern respiratory syndrome (MERS) mainly besides COVID-19 and assessed their safety and efficacy profiles [31] . All types of studies i.e. randomized controlled trials (RCTs), prospective or retrospective cohort studies, and the case series that investigated clinical outcomes and/or viral clearance among adult patients were included to conduct this study. In agreement with previous researches, our meta-analysis results showed that the administration of immunomodulatory agents (especially tocilizumab and anakinra) significantly decreased the mortality rate and ameliorate clinical symptoms in patients with COVID-19 [113, 114] . Virological and clinical cure in COVID-19 patients treated with hydroxychloroquine: a systematic review and meta-analysis abstract: PURPOSE: A recent survey has shown that the COVID-19 pandemic has culminated in dramatical and critical treatment particularly in acute infected patients. In fact, this systematic review-meta-analysis was directly pertained to estimation at the efficient value of some clinical managements to confront the COVID-19 infection. METHODS: Pubmed, Embase, Scopus, Cochrane, and Scholar databases were searched from inception to July 1, 2020, to identify studies reporting the current treatment process and medications (e.g. hydroxychloroquine, antiviral therapy, convalescent plasma, and immunomodulatory agents) for COVID-19. A random-effects model meta-analysis was performed to calculate the relative risk (RR) with 95% confidence intervals (CI). The outcomes of this study were the frequency of negative conversion cases, clinical improvements, mechanical ventilation demand, intensive care unit (ICU) entry, and mortality. The standard treatment refers to the published guidelines and specialist experience which varies in different articles, and the proposed treatment refers to the kind of interest suggested in the included studies. RESULTS: A number of 45 articles met the eligibility criteria (out of 6793 articles). Among them, 26 articles involving 3263 patients were included in quantitative analysis. Anti-COVID-19 interventions could significantly increase clinical improvement (RR 1.17, 95% CI 1.08–1.27; I(2) = 49.8%) and reduce the mortality rate (RR 0.58, 95% CI 0.35–0.95; I(2) = 74.8%). Although in terms of negative conversion, ICU entry, and mechanical ventilation demand, clinical intervention had no beneficial effect. The clinical effect of immunomodulatory agents (especially tocilizumab and anakinra) was noticeable compared to other medications with RR of 0.22 (95% CI 0.09–0.53; I(2) = 40.9%) for mortality and 1.25 (95% CI 1.07–1.46; I(2) = 45.4%) for clinical improvement. Moreover, Antivirals (RR 1.13, 95% CI 1.01–1.26; I(2) = 47.0%) and convalescent plasma therapy (RR 1.41, 95% CI 1.01–1.98; I(2) = 66.6%) had significant beneficial effects on clinical improvement. CONCLUSION: Based on our findings, all the included interventions significantly declined the mortality and enhanced clinical improvements with no effect on negative conversion and mechanical ventilation demand. Especially, immunomodulators and plasma therapy showed favorable outcomes. GRAPHICAL ABSTRACT: [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40199-020-00367-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s40199-020-00367-4 doi: 10.1007/s40199-020-00367-4 id: cord-267511-tb69dwg8 author: Talebian, Sepehr title: Why Go NANO on COVID-19 Pandemic? date: 2020-09-02 words: 1964.0 sentences: 100.0 pages: flesch: 46.0 cache: ./cache/cord-267511-tb69dwg8.txt txt: ./txt/cord-267511-tb69dwg8.txt summary: This will be essential to find viral particles in an efficient way and target them for destruction by developing NANOvaccines involved in host cell protection and immune and immunity response and/or anti-viral NANOagents, involved in inhibiting viral attachment, cell entry, and systemic infection (Figure 1 ). 6 Hence, one could imagine the realization of an oral multi-modal NANOvaccine for targeted delivery of a synthetic mRNA of the virus to the respiratory tract, with the purpose of enhancing the immunostimulatory activity of the vaccine, by simply including antibodies or small molecules that could target the interaction sites between ACE2 and SARS-CoV. Considering that viruses could be phylogenetically unrelated and structurally different, and given that most vaccines are virus specific, a promising approach would be that of developing broad-spectrum anti-viral NANOparticles to fight COVID-19 and future pandemics. Potential Therapeutic Approaches by which NANOtechnology Can Contribute against COVID-19 abstract: Although treating COVID-19 is shown to be challenging, NANOtechnology is around the corner to overcome potential drawbacks. The use of NANOtechnologies will definitely shape the worldwide approaches and tools to treat COVID-19. Here we highlight the importance of going NANO on the COVID-19 pandemic. url: https://api.elsevier.com/content/article/pii/S259023852030432X doi: 10.1016/j.matt.2020.08.005 id: cord-296232-6zj99nuw author: Talukdar, Jayanta title: Potential of natural astaxanthin in alleviating the risk of cytokine storm in COVID-19 date: 2020-10-16 words: 7622.0 sentences: 435.0 pages: flesch: 41.0 cache: ./cache/cord-296232-6zj99nuw.txt txt: ./txt/cord-296232-6zj99nuw.txt summary: We present reports where ASX is shown to prevent against oxidative damage and attenuate exacerbation of the inflammatory responses by regulating signaling pathways like NF-ĸB, NLRP3 and JAK/STAT. Studies including human trials have shown that ASX effectively regulates immunity and disease etiology, suggesting its wide array of potential therapeutic and nutritional support in prevention and treatment of various pathogenic diseases and metabolic disorders, all of which have elements of oxidative stress and/or inflammation in the pathogenesis [8, 10, 17] . [9] found that the administration of ASX provides both preventive and curative anti-inflammatory effects against LPS-induced inflammation in the human gingival keratinocyte line NDUSD-1 by suppressing the production of IL-6 via inhibiting activation of the NF-ĸB signaling pathway. Evidence from these studies suggest that ASX is a potent antioxidant and a natural anti-inflammatory compound having efficient immunomodulatory action that exerts potential therapeutic benefits against oxidative and inflammation induced tissue damage. abstract: Host excessive inflammatory immune response to SARS-CoV-2 infection is thought to underpin the pathogenesis of COVID-19 associated severe pneumonitis and acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). Once an immunological complication like cytokine storm occurs, anti-viral based monotherapy alone is not enough. Additional anti-inflammatory treatment is recommended. It must be noted that anti-inflammatory drugs such as JAK inhibitors, IL-6 inhibitors, TNF-α inhibitors, colchicine, etc., have been either suggested or are under trials for managing cytokine storm in COVID-19 infections. Natural astaxanthin (ASX) has a clinically proven safety profile and has antioxidant, anti-inflammatory, and immunomodulatory properties. There is evidence from preclinical studies that supports its preventive actions against ALI/ARDS. Moreover, ASX has a potent PPARs activity. Therefore, it is plausible to speculate that ASX could be considered as a potential adjunctive supplement. Here, we summarize the mounting evidence where ASX is shown to exert protective effect by regulating the expression of pro-inflammatory factors IL-1β, IL-6, IL-8 and TNF-α. We present reports where ASX is shown to prevent against oxidative damage and attenuate exacerbation of the inflammatory responses by regulating signaling pathways like NF-ĸB, NLRP3 and JAK/STAT. These evidences provide a rationale for considering natural astaxanthin as a therapeutic agent against inflammatory cytokine storm and associated risks in COVID-19 infection and this suggestion requires further validation with clinical studies. url: https://www.sciencedirect.com/science/article/pii/S0753332220310787?v=s5 doi: 10.1016/j.biopha.2020.110886 id: cord-322980-rembksdr author: Talwar, Shivangi title: Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020 date: 2020-10-22 words: 4536.0 sentences: 233.0 pages: flesch: 48.0 cache: ./cache/cord-322980-rembksdr.txt txt: ./txt/cord-322980-rembksdr.txt summary: The severe acute respiratory syndrome coronavirus (SARS-CoV-2019) emerged in 2019 in the month of December in Wuhan city of China, which again made the life of humans miserable with numerous fatal health issues and slowly and gradually this virus entrapped the whole world [2, 3] . Before the doctors, scientists, and researchers could study and come up with a cure for treatment, this virus had already infected more than lakhs of people across the world with the human coronavirus pathogens, i.e., HCoV-22E and HCoV-OC43, which affects the upper respiratory tract. Because of broad reach, presently, remdesivir and its in vitro studies against coronavirus help in treating SARS-CoV-2 with EC50 and EC90 estimations of 0.77 μM and 1.76 μM, respectively, and are proved to be a fruitful expected treatment for COVID-19 [ abstract: PURPOSE OF REVIEW: In the last month of 2019, i.e., December, COVID-19 hit Wuhan city in China. Since then, it has infected more than 210 countries and nearly about 33.4 million people with one million deaths globally. It is a viral disease with flu-like symptoms; hence, prevention and management is the best option to be adopted for its cure. RECENT FINDINGS: Many healthcare systems, scientists, and researchers are fighting for the cure of this pandemic. Ayurvedic and allopathic treatments have been studied extensively and approached for the cure of COVID-19. In addition to ayurvedic treatments, the Ministry of Ayush, India, has also recommended many remedies to boost up immunity. Allopathic studies involved several antiviral drugs which were used in different combinations for the treatment of COVID-19. SUMMARY: Comparative analysis of Ayurveda and allopathic treatment strategies were carried out in the present study. Depending upon the patient’s conditions and symptoms, Ayurveda is useful for the treatment of COVID-19. Allopathic treatments inhibit viral infection by targeting majorly endocytosis, and angiotensin-converting enzyme (Ace) receptor signaling. In this article, we summarize different ayurvedic and allopathic medicines and treatment strategies which have been used for the treatment of COVID-19, a global pandemic. url: https://doi.org/10.1007/s40495-020-00245-2 doi: 10.1007/s40495-020-00245-2 id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 words: 1606.0 sentences: 135.0 pages: flesch: 61.0 cache: ./cache/cord-294718-n3gx862b.txt txt: ./txt/cord-294718-n3gx862b.txt summary: title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. abstract: SARS-CoV-2 is a novel coronavirus and causative pathogen to the pandemic illness COVID-19. Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. url: https://doi.org/10.1093/cid/ciaa673 doi: 10.1093/cid/ciaa673 id: cord-281571-vob1bu9c author: Tam, Theresa W.S title: The Canadian Pandemic Influenza Plan: an evolution to the approach for national communicable disease emergencies date: 2004-06-30 words: 1843.0 sentences: 77.0 pages: flesch: 34.0 cache: ./cache/cord-281571-vob1bu9c.txt txt: ./txt/cord-281571-vob1bu9c.txt summary: The general concepts incorporated into the CPIP may be utilised in the contingency planning for a bioterrorism event or other communicable disease emergencies, including: a national, coordinated approach in planning; an emergency management structure to conduct the response; the use of common terminology to facilitate communication and response coordination, and the establishment of specific technical, communications and operational response groups and networks in advance. After the Hong Kong influenza A/H5N1 incident in 1997, the pandemic plan evolved to include a more comprehensive approach, incorporating the following key components: surveillance, vaccine programs, and use of antivirals, health services, emergency services, public health measures and communications. The general concepts incorporated into the CPIP that may be utilised in the contingency planning for other infectious disease emergencies include: a national, coordinated approach to planning; an emergency management structure to coordinate and conduct the response; the need for common terminology (e.g. using the same response phases), and the need to have specific technical, communications and operational response groups and networks formed in advance. abstract: Abstract Advance planning for a large-scale and widespread health emergency is required to optimize health care delivery during an influenza pandemic. The Canadian Pandemic Influenza Plan (CPIP) is an example of a successful communicable disease emergency plan that ensures a national, coordinated approach to preparedness, response and recovery activities in the event of an influenza pandemic. The general concepts incorporated into the CPIP may be utilised in the contingency planning for a bioterrorism event or other communicable disease emergencies, including: a national, coordinated approach in planning; an emergency management structure to conduct the response; the use of common terminology to facilitate communication and response coordination, and the establishment of specific technical, communications and operational response groups and networks in advance. The multinational outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003 offered the opportunity for the testing of these concepts. The experiences and lessons learnt during the SARS response may be utilised to strengthen communicable disease preparedness and response capacity. url: https://www.sciencedirect.com/science/article/pii/S0531513104000391 doi: 10.1016/j.ics.2004.01.036 id: cord-350328-wu1ygt6w author: Tambyah, P. A. title: SARS: responding to an unknown virus date: 2004-07-14 words: 4855.0 sentences: 221.0 pages: flesch: 53.0 cache: ./cache/cord-350328-wu1ygt6w.txt txt: ./txt/cord-350328-wu1ygt6w.txt summary: The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. The severe acute respiratory syndrome (SARS) is a newly recognized coronavirus infection that emerged in southern China [1] with subsequent global spread to 29 countries [2] [3] [4] [5] . The newly infected individuals traveled onward to their homes or next destinations in the USA, Canada, Singapore, Hong Kong and Ireland sparking off epidemics of varying degrees of severity in each of those countries, mainly in hospitals but also in their respective communities. A directive had gone out from the Hong Kong Department of Health on 21 February 2003 to maintain strict infection control with droplet precautions for all cases of "atypical" community-acquired pneumonia because of concerns that highly pathogenic avian influenza might be easily transmissible from person to person. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. In early 2003, through a single incident, it spread to Hong Kong, Singapore, Canada and Vietnam. For busy clinicians in large public hospitals, the response to the virus was initially based on ensuring a high level of protection for staff. However, as the epidemic progressed and more information became available about the virus, procedures were rationalized and the virus is currently under control worldwide. There are, however, numerous unanswered questions concerning super-spreading events, the modes of transmission of the virus and, perhaps most importantly, the rapid detection of the virus early in the course of disease. These issues need to be addressed in case the virus becomes more widespread in the near future. url: https://www.ncbi.nlm.nih.gov/pubmed/15252720/ doi: 10.1007/s10096-004-1175-8 id: cord-264924-ds6jv5ek author: Tambyah, Paul A title: Severe acute respiratory syndrome from the trenches, at a Singapore university hospital date: 2004-11-30 words: 5458.0 sentences: 274.0 pages: flesch: 53.0 cache: ./cache/cord-264924-ds6jv5ek.txt txt: ./txt/cord-264924-ds6jv5ek.txt summary: Summary The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The severe acute respiratory syndrome (SARS) coronavirus is a novel pathogen that emerged in southern China at the end of 2002 and because of a single event in a hotel in Hong Kong one night in February 2003, spread to three continents. Mild illness associated with severe acute respiratory syndrome coronavirus infection: lessons from a prospective seroepidemiologic study of health-care workers in a teaching hospital in Singapore abstract: Summary The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. However, there have been few reports of the problems that infectious disease clinicians encounter when dealing with the protean manifestations of this pathogen. This is a qualitative account of some of the issues faced by an infectious disease physician when identifying and treating patients with SARS as well as protecting other healthcare workers and patients, including: identification of the chain of contagion, early recognition of the disease in the absence of a reliable and rapid diagnostic test, appropriate use of personal protective equipment, and the use of isolation to prevent super-spreading events. Many issues need to be addressed if clinicians are to be able to manage the virus should it reappear. url: https://www.ncbi.nlm.nih.gov/pubmed/15522681/ doi: 10.1016/s1473-3099(04)01175-2 id: cord-351283-1y9dfobn author: Tan, Bai‐Hong title: The possible impairment of respiratory‐related neural loops may be associated with the silent pneumonia induced by SARS‐CoV‐2 date: 2020-06-11 words: 1364.0 sentences: 66.0 pages: flesch: 38.0 cache: ./cache/cord-351283-1y9dfobn.txt txt: ./txt/cord-351283-1y9dfobn.txt summary: As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID‐19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit stay for those requiring invasive mechanical ventilation. In view of the findings for H5N1 influenza virus, the silence of pneumonia induced by SARS-CoV-2 may be due to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID-19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit (ICU) stay for those requiring invasive mechanical ventilation. Therefore, we propose that the peculiar manifestations in COVID-19 patients may be attributed to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. abstract: As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID‐19 patients, including the “silence” of pneumonia in both mild and severe cases and a long intensive care unit stay for those requiring invasive mechanical ventilation. Similar silent pneumonia has been documented in the infection induced by H5N1 influenza virus HK483, and was found to result from the direct attack of the virus on the bronchopulmonary C‐fibers at the early stage and the final infection in the brainstem at the late stage. The long stay of critical patients in the intensive care unit is possibly due to the depression of central respiratory drive, which resulted in the failure to wean from the mechanic ventilation. Carotid and aortic bodies and bronchopulmonary C‐fibers are two key peripheral components responsible for the chemosensitive responses in the respiratory system, while triggering respiratory reflexes depends predominantly on the putative chemosensitive neurons located in the pontomedullary nuclei. In view of the findings for H5N1 influenza virus, the silence of pneumonia induced by SARS‐CoV‐2 may be due to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory‐related central neurons. (195 words) This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26158 doi: 10.1002/jmv.26158 id: cord-269939-8nvrt5y7 author: Tan, Boon Fei title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore date: 2020-04-23 words: 1927.0 sentences: 109.0 pages: flesch: 53.0 cache: ./cache/cord-269939-8nvrt5y7.txt txt: ./txt/cord-269939-8nvrt5y7.txt summary: title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore Abstract COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. On 23 January 2020, Singapore reported its first imported case of the novel coronavirus infection, officially named COVID-19, [AQ1]which was later declared a global pandemic by the World Health Organization (WHO) [1] . The division serves about 61% of the country''s population who require radiotherapy, treating about 280-300 patients per day, including inpatients from SGH and other hospitals within the healthcare cluster. Should any patient who is quarantined for 14 days due to close contact with confirmed COVID-19 cases or those with a Stay Home Notice (SHN) due to recent entry from abroad as of 20 March 2020 require radiotherapy, it will be conducted in a highly controlled manner with close collaboration with the Ministry of Health. abstract: Abstract COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. It has impacted the world medically, financially, politically and socially, with countries such as China and Italy adopting a full lockdown of their cities to mitigate the transmission. The current mortality rate is 5.4%, with 1 056 159 people infected worldwide. The disease is reminiscent of SARS in 2002, from which the healthcare system of Singapore has garnered many lessons and applied them in the current climate. As a result of the high transmissibility of the virus, hospitals in Singapore have reduced clinic loads and elective treatments to halt propagation of the virus and also to allow redistribution of healthcare workforce to the frontline. Cancer patients, who are often immunocompromised, are at risk of contracting the disease and becoming seriously ill. At the same time, delaying treatment such as radiotherapy in cancer patients can be detrimental. Here, we describe our experience as a large radiation oncology department in Singapore, including the challenges we encountered and how we managed our patient flow. url: https://api.elsevier.com/content/article/pii/S093665552030162X doi: 10.1016/j.clon.2020.04.006 id: cord-309934-kcyao9i9 author: Tan, Emily L.C. title: Inhibition of SARS Coronavirus Infection In Vitro with Clinically Approved Antiviral Drugs date: 2004-04-17 words: 3489.0 sentences: 180.0 pages: flesch: 47.0 cache: ./cache/cord-309934-kcyao9i9.txt txt: ./txt/cord-309934-kcyao9i9.txt summary: Here we report that certain interferon subtypes exhibit in vitro inhibitory activity against SARS-CoV and are candidates for follow-up studies in animal models and patients to determine their efficacy in vivo. A collection of 19 antiviral drugs was tested in the SARS-CoV CPE inhibition assay ( Table 2) . Because the criteria for ascertaining anti-SARS-CoV activity in this screen were set at 100% inhibition of CPE, and as high doses of interferons may result in severe clinical side effects, we chose to conduct further evaluations only in the interferons that showed complete inhibition from initial screen, namely, Wellferon, Multiferon, Betaferon, and Alferon. Betaferon, Alferon, Multiferon, Wellferon, and ribavirin inhibited CPE in SARS-CoV-infected Vero E6 cells, in decreasing order of potency. Ribavirin, a drug widely used in initial efforts to manage SARS infections, inhibited CPE completely at 500-5,000 µg/mL at virus loads of 100-10,000 PFU per well. abstract: Severe acute respiratory syndrome (SARS) is an infectious disease caused by a newly identified human coronavirus (SARS-CoV). Currently, no effective drug exists to treat SARS-CoV infection. In this study, we investigated whether a panel of commercially available antiviral drugs exhibit in vitro anti–SARS-CoV activity. A drug-screening assay that scores for virus-induced cytopathic effects on cultured cells was used. Tested were 19 clinically approved compounds from several major antiviral pharmacologic classes: nucleoside analogs, interferons, protease inhibitors, reverse transcriptase inhibitors, and neuraminidase inhibitors. Complete inhibition of cytopathic effects of SARS-CoV in culture was observed for interferon subtypes, β-1b, α-n1, α-n3, and human leukocyte interferon α. These findings support clinical testing of approved interferons for the treatment of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15200845/ doi: 10.3201/eid1004.030458 id: cord-346335-el45v0a5 author: Tan, H.S. title: Fourier spectral density of the coronavirus genome date: 2020-08-11 words: 4646.0 sentences: 224.0 pages: flesch: 56.0 cache: ./cache/cord-346335-el45v0a5.txt txt: ./txt/cord-346335-el45v0a5.txt summary: We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density. An example of a seminal paper in this subject is that of Voss in [2] where the author found that the spectral density of the genome of many different species follows a power law of the form 1/k β in the low-frequency domain, with the exponent β potentially related to the organism''s evolutionary category. We develop a few models to characterize the typical spectrum, and in the process stumble upon a linear scaling law between a measure of the complexity of each genome and the power-law exponent that describes the enveloping curve of the low-frequency domain. abstract: We present an analysis of the coronavirus RNA genome via a study of its Fourier spectral density based on a binary representation of the nucleotide sequence. We find that at low frequencies, the power spectrum presents a small and distinct departure from the behavior expected from an uncorrelated sequence. We provide a couple of simple models to characterize such deviations. Away from a small low-frequency domain, the spectrum presents largely stochastic fluctuations about fixed values which vary inversely with the genome size generally. It exhibits no other peaks apart from those associated with triplet codon usage. We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density. url: https://doi.org/10.1101/2020.06.30.180034 doi: 10.1101/2020.06.30.180034 id: cord-268718-tt07cwrf author: Tan, Heng Wee title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 words: 6346.0 sentences: 400.0 pages: flesch: 52.0 cache: ./cache/cord-268718-tt07cwrf.txt txt: ./txt/cord-268718-tt07cwrf.txt summary: 54 Virus infectivity study has indicated that the SARS-CoV-2 is able to utilize ACE2 of human, Chinese horseshoe bats, civet, and pig but was not able to use mouse ACE2. The roles of ACE2 expression in SARS-CoV-2 pathogenesis and human COVID-19 susceptibility are largely unknown. B, ACE2 expression in lung cancer patients with different smoking histories analyzed using similar methods as described previously 106 other symptoms in addition to respiratory symptoms, suggesting that SARS-CoV-2 could perhaps infect other organs (Figure 3 ). 118 In addition to sputum, SARS-CoV-2 RNA has been detected in the stools of a COVID-19 patient, 119 F I G U R E 3 Tissue distribution of angiotensin-converting enzyme 2 (ACE2) expression and potential COVID-19 susceptibility. Expression of elevated levels of proinflammatory cytokines in SARS-CoV-infected ACE2 + cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS abstract: Coronavirus (CoV) disease 2019 (COVID‐19) is an ongoing pandemic caused by severe acute respiratory syndrome CoV 2 (SARS‐CoV‐2). The highly contagious SARS‐CoV‐2 belongs to the genus Betacoronavirus, and it is phylogenetically closely related to SARS‐CoV, a human CoV that caused an outbreak back in 2002 to 2003. Both SARS‐CoV‐2 and SARS‐CoV enter human cells via the interactions between viral crown‐like spike protein and human angiotensin‐converting enzyme 2 (ACE2) receptor. Here, we aim to review the involvement of ACE2 in human CoV infections by discussing the roles of ACE2 in CoV evolution, cross‐species transmissibility, and COVID‐19 susceptibility. We also provide our perspectives on COVID‐19 treatment and prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/32602627/ doi: 10.1002/rmv.2122 id: cord-311383-1aqt65cc author: Tan, Jinzhi title: The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes date: 2009-05-15 words: 7613.0 sentences: 391.0 pages: flesch: 58.0 cache: ./cache/cord-311383-1aqt65cc.txt txt: ./txt/cord-311383-1aqt65cc.txt summary: However, within the large Nsp3 (1922 amino-acid residues), the structure and function of the so-called SARS-unique domain (SUD) have remained elusive. The SARS-CoV genome is devoid of G-stretches longer than 5–6 nucleotides, but more extended G-stretches are found in the 3′-nontranslated regions of mRNAs coding for certain host-cell proteins involved in apoptosis or signal transduction, and have been shown to bind to SUD in vitro. In this communication, we describe the crystal structures at 2.2 Å and 2.8 Å resolution (monoclinic and triclinic form, respectively) of the core of the SARS-unique domain (SUD core , Nsp3 residues 389-652). One potential binding site for G-quadruplexes might be in a cleft between two consecutive SUD core dimers as they occur in both the monoclinic and triclinic crystal forms ( Figure S2B ), but for confirmation, any of these models will have to await crystallographic determination of the complex. abstract: Since the outbreak of severe acute respiratory syndrome (SARS) in 2003, the three-dimensional structures of several of the replicase/transcriptase components of SARS coronavirus (SARS-CoV), the non-structural proteins (Nsps), have been determined. However, within the large Nsp3 (1922 amino-acid residues), the structure and function of the so-called SARS-unique domain (SUD) have remained elusive. SUD occurs only in SARS-CoV and the highly related viruses found in certain bats, but is absent from all other coronaviruses. Therefore, it has been speculated that it may be involved in the extreme pathogenicity of SARS-CoV, compared to other coronaviruses, most of which cause only mild infections in humans. In order to help elucidate the function of the SUD, we have determined crystal structures of fragment 389–652 (“SUD(core)”) of Nsp3, which comprises 264 of the 338 residues of the domain. Both the monoclinic and triclinic crystal forms (2.2 and 2.8 Å resolution, respectively) revealed that SUD(core) forms a homodimer. Each monomer consists of two subdomains, SUD-N and SUD-M, with a macrodomain fold similar to the SARS-CoV X-domain. However, in contrast to the latter, SUD fails to bind ADP-ribose, as determined by zone-interference gel electrophoresis. Instead, the entire SUD(core) as well as its individual subdomains interact with oligonucleotides known to form G-quadruplexes. This includes oligodeoxy- as well as oligoribonucleotides. Mutations of selected lysine residues on the surface of the SUD-N subdomain lead to reduction of G-quadruplex binding, whereas mutations in the SUD-M subdomain abolish it. As there is no evidence for Nsp3 entering the nucleus of the host cell, the SARS-CoV genomic RNA or host-cell mRNA containing long G-stretches may be targets of SUD. The SARS-CoV genome is devoid of G-stretches longer than 5–6 nucleotides, but more extended G-stretches are found in the 3′-nontranslated regions of mRNAs coding for certain host-cell proteins involved in apoptosis or signal transduction, and have been shown to bind to SUD in vitro. Therefore, SUD may be involved in controlling the host cell's response to the viral infection. Possible interference with poly(ADP-ribose) polymerase-like domains is also discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/19436709/ doi: 10.1371/journal.ppat.1000428 id: cord-275888-6u1o6414 author: Tan, Kian Teo title: N95 acne date: 2004-06-29 words: 2073.0 sentences: 146.0 pages: flesch: 52.0 cache: ./cache/cord-275888-6u1o6414.txt txt: ./txt/cord-275888-6u1o6414.txt summary: 1 The giant porokeratosis lesion on the left hand of our patient was totally excised and grafted. A diagnosis of sarcoidosis involving the central nervous system, lacrimal gland, nasal septum, vocal cord, lung and scalp was made, and the patient was treated with 20 mg of methylprednisone on alternate days with intralesional triamcinolone injection for skin lesions. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. abstract: Two women, aged 27 and 45 years, presented to the Dermatology Outpatient Clinic with acne vulgaris. Both had nodular acne in a similar distribution over the cheeks, chin, and perioral areas (Fig. 1). Each had a history of acne vulgaris as a teenager. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. They were treated with topical retinoid and systemic antimicrobials, and both responded well. url: https://www.ncbi.nlm.nih.gov/pubmed/15230894/ doi: 10.1111/j.1365-4632.2004.02338.x id: cord-301079-n1nytr6k author: Tan, Li title: Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date: 2020-07-27 words: 3556.0 sentences: 205.0 pages: flesch: 60.0 cache: ./cache/cord-301079-n1nytr6k.txt txt: ./txt/cord-301079-n1nytr6k.txt summary: Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. abstract: Abstract Background Few studies have explored the air and surface contamination by SARS-CoV-2 virus in healthcare settings. Methods We collected air and surface samples from the isolation wards and intensive care units designated for COVID-19 patients. The clinical data and tests result of nasopharyngeal specimens and serum antibodies were also collected from the sampling patients. Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Only one air sample taken during the intubation procedure tested positive. High-touch surfaces were slightly more likely contaminated by the RNA of the SARS-CoV-2 virus than low-touch surfaces. Contamination rates was slightly higher near severe/critical patients compared to those near mild patients, although not statistically significant (p <0.05). Surface contamination was still found near the patients with both positive IgG and IgM. Conclusions Air and surface contamination of the viral RNA was relatively low in healthcare settings after enhancement of infection prevention and control. Environmental contamination could still be found near seroconverted patients, suggesting the needs of maintaining constant vigilance in healthcare settings to reduce healthcare associated infection during the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32730827/ doi: 10.1016/j.ijid.2020.07.027 id: cord-267971-xgwmda8e author: Tan, Shing Cheng title: Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients date: 2020-04-07 words: 2851.0 sentences: 204.0 pages: flesch: 57.0 cache: ./cache/cord-267971-xgwmda8e.txt txt: ./txt/cord-267971-xgwmda8e.txt summary: Background: Numerous groups have reported the clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) cases; however, the data remained inconsistent. Understanding the clinical and 46 epidemiological characteristics of the disease is important for informing public health decision 47 making, which would enable improvement of surveillance and effective planning of treatment. (4) found that the male-to-female ratio among the 81 patients included 56 was close to 1:1, indicating that both genders were equally susceptible to 57 the World Health Organization (WHO) has declared COVID-19 a global pandemic and the 58 contagion shows no sign of slowing down (13). In this 60 study, a systematic review and pooled analysis was performed to characterize the clinical and 61 epidemiological features of COVID-19 patients. In this work, a systematic review and pooled analysis was 137 performed to combine data from 69 previous reports, in order to yield a more accurate summary 138 of the clinical and epidemiological characteristics of COVID-19 patients. abstract: Background: Numerous groups have reported the clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) cases; however, the data remained inconsistent. This paper aimed to pool the available data to provide a more complete picture of the characteristics of COVID-19 patients. Methods: A systematic review and pooled analysis was performed. Eligible studies were identified from database and hand searches up to March 2, 2020. Data on clinical (including laboratory and radiological) and epidemiological (including demographic) characteristics of confirmed COVID-19 cases were extracted and combined by simple pooling. Results: Of 644 studies identified, 69 studies (involving 48,926 patients) were included in the analysis. The average age of the patients was 49.16 years. A total of 51.46% of the patients were men and 52.32% were non-smokers. Hypertension (50.82%) and diabetes (20.89%) were the most frequent comorbidities observed. The most common symptoms were fever (83.21%), cough (61.74%), and myalgia or fatigue (30.22%). Altered levels of blood and biochemical parameters were observed in a proportion of the patients. Most of the patients (78.50%) had bilateral lung involvements, and 5.86% showed no CT findings indicative of viral pneumonia. Acute respiratory distress syndrome (28.36%), acute cardiac injury (7.89%) and acute kidney injury (7.60%) were the most common complications recorded. Conclusions: Clinical and epidemiological characteristics of COVID-19 patients were mostly heterogeneous and non-specific. This is the most comprehensive report of the characteristics of COVID-19 patients to date. The information presented is important for improving our understanding of the spectrum and impact of this novel disease. url: https://doi.org/10.1101/2020.04.02.20050989 doi: 10.1101/2020.04.02.20050989 id: cord-023473-ofwdzu5t author: Tan, Wei‐Jiat title: Managing threats in the global era: The impact and response to SARS date: 2006-06-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In early 2003, the SARS virus brought disruption of public and business activities in many areas of the world, particularly Asia. As a result of its impact, SARS quickly established itself as a new kind of global uncertainty and posed challenges for traditional methods of risk management. This article examines the impact that SARS has had through means of a case study and builds on this to provide recommendations for how uncertainty may be managed in an increasingly globalized world. Reconsideration of strategic and risk‐management approaches have become necessary. Supply‐chain management and corporate strategy require a fundamental rethink to balance the pursuit of efficiency with increased responsiveness and flexibility. Unpredictability and turbulence in the international business environment suggest that traditional planning approaches that assume linear growth may give way to more scenario‐based planning. This will encourage firms to contemplate a variety of possible futures and better prepare them for unanticipated events. Similarly, contingent‐based continuity plans help businesses continue running even during a crisis. © 2006 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169807/ doi: 10.1002/tie.20107 id: cord-339303-feiy6xed author: Tan, Xiaodong title: Severe Acute Respiratory Syndrome epidemic and change of people''s health behavior in China date: 2004-10-17 words: 1733.0 sentences: 100.0 pages: flesch: 58.0 cache: ./cache/cord-339303-feiy6xed.txt txt: ./txt/cord-339303-feiy6xed.txt summary: title: Severe Acute Respiratory Syndrome epidemic and change of people''s health behavior in China Severe Acute Respiratory Syndrome (SARS) has become a new worldwide epidemic whose origin was until recently unknown. This study presents an inquiry into people''s knowledge and self-reported changes in behavior in response to the epidemic. Most respondents took action to avoid being infected by SARS, including, most commonly, efforts to improve indoor ventilation, to disinfect the indoor environment and to increase hand-washing frequency. Severe Acute Respiratory Syndrome (SARS) is a new flu-like disease that made its appearance in late 2002 and spread to over 30 countries by mid-2003. The adoption of these measures, due to the initially unclear nature of SARS transmission, actually increased panic among the Chinese people who began wearing masks, reducing the chances of outdoor activities, disinfecting the environment and washing their hands. Seven questions about health behavior change in the previous 2 weeks addressed recent preventive measures generally and hand-washing specifically. abstract: Severe Acute Respiratory Syndrome (SARS) has become a new worldwide epidemic whose origin was until recently unknown. It is the unpredictable nature of this epidemic that makes people want answers to some important questions about what they can do to protect themselves. This study presents an inquiry into people's knowledge and self-reported changes in behavior in response to the epidemic. Respondents were drawn from seven major occupational groups in the large central city of Wuhan. Although most respondents knew of SARS, there was still 8.4% who did not know about it. Knowledge was lowest among farmers who had come to the city for temporary work. Most respondents took action to avoid being infected by SARS, including, most commonly, efforts to improve indoor ventilation, to disinfect the indoor environment and to increase hand-washing frequency. Self-reported increases in hand-washing frequency were significant; however, among the seven occupational groups, reports of increased hand-washing were consistently greater among commercial service workers, students and farmers. While it seems that possible fears induced by the epidemic led to these changes, there are still about one-third of respondents who do not wash their hands as frequently as desired. There is also the challenge of devising strategies for maintaining the desired frequency of hand-washing among those who did change. url: https://www.ncbi.nlm.nih.gov/pubmed/15150138/ doi: 10.1093/her/cyg074 id: cord-317123-0tdfvlqd author: Tan, Xiaotian title: Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date: 2020-04-21 words: 4154.0 sentences: 220.0 pages: flesch: 52.0 cache: ./cache/cord-317123-0tdfvlqd.txt txt: ./txt/cord-317123-0tdfvlqd.txt summary: Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. In this work, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, and sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen -S protein, both of which are spiked in serum, as a model system. For the anti-S1 IgG detection experiments (see Figure S2 (B) for the detailed protocol), various concentrations of monoclonal antibodies were prepared by diluting the stock solutions with 50 times diluted human serum (the serum was diluted with 1× reagent diluent, which correlates to 1% BSA). abstract: COVID-19 pandemic has caused tens of thousands of deaths and is now a severe threat to global health. Clinical practice has demonstrated that the SARS-CoV-2 S1 specific antibodies and viral antigens can be used as diagnostic and prognostic markers of COVID-19. However, the popular point-of-care biomarker detection technologies, such as the lateral-flow test strips, provide only yes/no information and have very limited sensitivities. Thus, it has a high false negative rate and cannot be used for the quantitative evaluation of patient’s immune response. Conventional ELISA (enzyme-linked immunosorbent assay), on the other hand, can provide quantitative, accurate, and sensitive results, but it involves complicated and expensive instruments and long assay time. In addition, samples need to be sent to centralized labs, which significantly increases the turn-around time. Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. Furthermore, we demonstrated that our microfluidic ELISA platform can be used for rapid affinity evaluation of monoclonal anti-S1 antibodies. The microfluidic ELISA device is highly portable and requires less than 10 μL of samples for each channel. Therefore, our technology will greatly facilitate rapid and quantitative analysis of COVID-19 patients and vaccine recipients at point-of-care. url: https://doi.org/10.1101/2020.04.20.052233 doi: 10.1101/2020.04.20.052233 id: cord-332276-gs80celr author: Tan, Yee‐Joo title: Regulation of cell death during infection by the severe acute respiratory syndrome coronavirus and other coronaviruses date: 2007-08-20 words: 5790.0 sentences: 272.0 pages: flesch: 48.0 cache: ./cache/cord-332276-gs80celr.txt txt: ./txt/cord-332276-gs80celr.txt summary: In two independent studies, it was demonstrated that the inhibition of apoptosis, either by caspase inhibitors or by overexpression of the Bcl-2 protein, did not affect SARS-CoV replication in Vero cells (Ren et al., 2005; Bordi et al., 2006) , suggesting that apoptosis does not play a role in facilitating viral release. The mechanisms for induction of apoptosis by these SARS-CoV proteins are unclear, although in some cases, it could be related to their abilities to interfere with cellular functions, such as blocking cell cycle progression, altering membrane permeability, activating signal transduction pathways, upregulating transcription factors and other regulatory genes (Table 1 ). (2007) The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) gene 7 products contribute to virus-induced apoptosis. Over-expression of 7a, a protein specifically encoded by the severe acute respiratory syndrome (SARS) -coronavirus, induces apoptosis via a caspase-dependent pathway abstract: Both apoptosis and necrosis have been observed in cells infected by various coronaviruses, suggesting that the regulation of cell death is important for viral replication and/or pathogenesis. Expeditious research on the severe acute respiratory syndrome (SARS) coronavirus, one of the latest discovered coronaviruses that infect humans, has provided valuable insights into the molecular aspects of cell‐death regulation during infection. Apoptosis was observed in vitro, while both apoptosis and necrosis were observed in tissues obtained from SARS patients. Viral proteins that can regulate apoptosis have been identified, and many of these also have the abilities to interfere with cellular functions. Occurrence of cell death in host cells during infection by other coronaviruses, such as the mouse hepatitis virus and transmissible porcine gastroenteritis virus, has also being extensively studied. The diverse cellular responses to infection revealed the complex manner by which coronaviruses affect cellular homeostasis and modulate cell death. As a result of the complex interplay between virus and host, infection of different cell types by the same virus does not necessarily activate the same cell‐death pathway. Continuing research will lead to a better understanding of the regulation of cell death during viral infection and the identification of novel antiviral targets. url: https://www.ncbi.nlm.nih.gov/pubmed/17714515/ doi: 10.1111/j.1462-5822.2007.01034.x id: cord-321315-bzmokdzk author: Tanacan, Atakan title: The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey date: 2020-07-30 words: 2136.0 sentences: 136.0 pages: flesch: 54.0 cache: ./cache/cord-321315-bzmokdzk.txt txt: ./txt/cord-321315-bzmokdzk.txt summary: title: The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey OBJECTIVE: To investigate the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. CONCLUSION: Healthcare professionals should be cautious in the labor and delivery of high-risk pregnant women during the pandemic period and universal testing for COVID-19 may be considered in selected populations. The aim of this study is to investigate the rate of SARS-CoV-2 positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. Maternal age, gravidity, parity, number of previous miscarriages, body mass index (BMI) (kg/m2), gestational age at birth, birth weight, 1st-5th minute Apgar scores, route of delivery (spontaneous vaginal deliver yor cesarean section) and SARS-CoV-2 positivity rates were compared between the healthy and high-risk pregnant women. abstract: OBJECTIVE: To investigate the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. STUDY DESIGN: This prospective cohort study was conducted in Ankara City Hospital between April, 15, 2020 and June, 5, 2020. A total of 206 asymptomatic pregnant women (103 low-risk pregnant women without any defined risk factor and 103 high-risk pregnant women) were screened for SARS-CoV-2 positivity upon admission to hospital for delivery. Detection of SARS-CoV2 in nasopharyngeal samples was performed by Real Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) method targeting RdRp (RNA dependent RNA polymerase) gene. Two groups were compared in terms of demographic features, clinical characteristics and SARS-CoV-2 positivity. RESULTS: Three of the 206 pregnant women participating in the study had positive RT-PCR tests (1.4%) and all positive cases were in the high-risk pregnancy group. Although, one case in the high-risk pregnancy group had developed symptoms highly suspicious for COVID-19, two repeated RT-PCR tests were negative. SARS-CoV-2 RT-PCR positivity rate was significantly higher in the high-risk pregnancy group (2.9% vs 0%, p = 0.04). CONCLUSION: Healthcare professionals should be cautious in the labor and delivery of high-risk pregnant women during the pandemic period and universal testing for COVID-19 may be considered in selected populations. url: https://api.elsevier.com/content/article/pii/S0301211520304930 doi: 10.1016/j.ejogrb.2020.07.051 id: cord-301811-ykpiorgo author: Tanaka, Takuma title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date: 2020-10-28 words: 5530.0 sentences: 296.0 pages: flesch: 55.0 cache: ./cache/cord-301811-ykpiorgo.txt txt: ./txt/cord-301811-ykpiorgo.txt summary: title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing We estimated the numbers of undiagnosed symptomatic patients and the lower bound of the number of total infected individuals per diagnosed patient before and after the declaration of the state of emergency in Hokkaido, Japan. The present analysis uses the distributions of the cluster size and patients'' time from onset to diagnosis, which are released by the health officials, to estimate the model parameters. At the same time, the nodes in the connected component containing the diagnosed node are also removed from the network, which corresponds to the contact tracing of the infected individuals (Fig 2, gray open circles) . In this paper, we have formulated a model to describe the spreading of infection and the quarantine of infected individuals, and estimated the number of undiagnosed symptomatic and asymptomatic COVID-19 patients in Hokkaido. abstract: Estimating the percentages of undiagnosed and asymptomatic patients is essential for controlling the outbreak of SARS-CoV-2, and for assessing any strategy for controlling the disease. In this paper, we propose a novel analysis based on the birth-death process with recursive full tracing. We estimated the numbers of undiagnosed symptomatic patients and the lower bound of the number of total infected individuals per diagnosed patient before and after the declaration of the state of emergency in Hokkaido, Japan. The median of the estimated number of undiagnosed symptomatic patients per diagnosed patient decreased from 1.7 to 0.77 after the declaration, and the median of the estimated lower bound of the number of total infected individuals per diagnosed patient decreased from 4.2 to 2.4. We will discuss the limitations and possible expansions of the model. url: https://www.ncbi.nlm.nih.gov/pubmed/33112895/ doi: 10.1371/journal.pone.0241170 id: cord-322051-89wgv100 author: Tanasa, Ingrid Andrada title: Anosmia and ageusia associated with coronavirus infection (COVID-19) - what is known? date: 2020-05-28 words: 2260.0 sentences: 132.0 pages: flesch: 44.0 cache: ./cache/cord-322051-89wgv100.txt txt: ./txt/cord-322051-89wgv100.txt summary: This study summarizes the existing data regarding the association of anosmia and ageusia with the SARS-CoV-2 infection. In a retrospective observational study, Klopfenstein et al (20) reported that 54 patients (47%) with confirmed SARS-CoV-2 infection developed anosmia, 4.4 (±1.9) days after infection onset, and that was the third symptom to manifest in 38% (22/52) of the cases. Some authors reported three mechanisms for anosmia in COVID-19 patients: i) local infection of support cells and vascular pericytes in the nose and olfactory bulb that may affect the function of bipolar neurons or mitral cells; ii) damage to support cells in the sensory epithelium that may indirectly influence the signaling pathway from sensory neurons to the brain; and iii) damage to sustentacular cells and Bowman''s gland cells that could lead to diffuse morphological damage to the olfactory sensory epithelium and altering of smell perception (28, 29) . Further research is needed to demonstrate the association between anosmia and ageusia with SARS-CoV-2 infection, the clinical manifestations determined by variants of ACE2 receptor, and recovery rates of olfactory and gustative dysfunction, and specific treatment protocols of these manifestations. abstract: In 2020 a new pandemic caused by the SARS-CoV-2 coronavirus is affecting the lives of millions of patients and healthcare workers worldwide. The clinical picture of this infection is in a dynamic process of discovery, and more symptoms emerge as the clinicians observe and diagnose manifestations that affect multiple organs. Anosmia (loss of smell), and ageusia (loss of taste) become more frequently cited as independent symptoms or in association with the most common manifestations of the disease, such as fever, cough and dyspnea. A thorough screening program will prevent most nosocomial and community-acquired infections by promoting efficient triage and specific measures such as isolation of the patients. Therefore, it is important to include frequent symptoms in the anamnesis and questionnaires to select those patients who might benefit from testing, isolation, and treatment. This study summarizes the existing data regarding the association of anosmia and ageusia with the SARS-CoV-2 infection. It also aims to describe manifestations of these, particularly in the clinical picture of all symptomatic patients. url: https://doi.org/10.3892/etm.2020.8808 doi: 10.3892/etm.2020.8808 id: cord-260407-jf1dnllj author: Tang, Catherine So-kum title: Factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult Chinese in Hong Kong date: 2004-06-11 words: 4503.0 sentences: 219.0 pages: flesch: 47.0 cache: ./cache/cord-260407-jf1dnllj.txt txt: ./txt/cord-260407-jf1dnllj.txt summary: This study aimed to determine factors associating with individuals'' practice of the target SARS preventive behavior (facemask wearing). Three of the five components of the Health Belief Model, namely, perceived susceptibility, cues to action, and perceived benefits, were significant predictors of facemask-wearing even after considering effects of demographic characteristics. Overall, perceived benefits, perceived barriers, and perceived susceptibility are the three most powerful components of the Health Belief Model in influencing whether individuals practice different preventive behaviors [21, 29, 30] . A logistic regression with odds ratios was conducted to test the efficacy of the Health Belief Model in predicting the wearing of facemasks to prevent SARS. Similar to previous research [15 -26] , this study found the Health Belief Model useful in identifying major determinants of the wearing of facemasks to prevent contracting and spreading SARS. The remaining two components of the Health Belief Model, perceived severity and perceived barriers, were found to be nonsignificant determinants of the target SARS preventive behavior in this study. abstract: Background. The global outbreak of the severe acute respiratory syndrome (SARS) in 2003 has been an international public health threat. Quick diagnostic tests and specific treatments for SARS are not yet available; thus, prevention is of paramount importance to contain its global spread. This study aimed to determine factors associating with individuals' practice of the target SARS preventive behavior (facemask wearing). Methods. A total of 1329 adult Chinese residing in Hong Kong were surveyed. The survey instrument included demographic data, measures on the five components of the Health Belief Model, and the practice of the target SARS preventive behavior. Logistic regression analyses were conducted to determine rates and predictors of facemask wearing. Results. Overall, 61.2% of the respondents reported consistent use of facemasks to prevent SARS. Women, the 50–59 age group, and married respondents were more likely to wear facemasks. Three of the five components of the Health Belief Model, namely, perceived susceptibility, cues to action, and perceived benefits, were significant predictors of facemask-wearing even after considering effects of demographic characteristics. Conclusions. The Health Belief Model is useful in identifying determinants of facemask wearing. Findings have significant implications in enhancing the effectiveness of SARS prevention programs. url: https://www.ncbi.nlm.nih.gov/pubmed/15539054/ doi: 10.1016/j.ypmed.2004.04.032 id: cord-024614-6bu3zo01 author: Tang, Daxing title: Prevention and control strategies for emergency, limited-term, and elective operations in pediatric surgery during the epidemic period of COVID-19 date: 2020-03-26 words: 5846.0 sentences: 300.0 pages: flesch: 43.0 cache: ./cache/cord-024614-6bu3zo01.txt txt: ./txt/cord-024614-6bu3zo01.txt summary: Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the "Technical Guidelines for the Prevention and Control of New Coronavirus Infection in Medical Institutions (First Edition)," 17 "Diagnosis and Treatment Plan on the New Coronavirus inflicted pneumonia (Sixth trial edition, revised)" 2 (both released by the National Health Commission of China), "Recommendations for the Prevention and Control of General Surgery in the Background of New Coronavirus Outbreak," 6 and other relevant latest reports, we propose the following control measures and practical strategies for pediatric surgery practice during the COVID-19 epidemic. abstract: The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to more than 100 countries. Children approved to be susceptible to SARS-CoV-2 infection. Preventing and controlling the epidemic while ensuring orderly flows of pediatric surgery clinical work has proven to be a big challenge for both patients and clinicians during the epidemic. Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211106/ doi: 10.1136/wjps-2020-000122 id: cord-344967-t88pedeb author: Tang, Hon Lok title: Severe acute respiratory syndrome in haemodialysis patients: a report of two cases date: 2003-10-17 words: 1666.0 sentences: 107.0 pages: flesch: 64.0 cache: ./cache/cord-344967-t88pedeb.txt txt: ./txt/cord-344967-t88pedeb.txt summary: A 49-year-old male, who had end-stage renal failure and was receiving chronic haemodialysis twice weekly, was admitted to the Princess Margaret Hospital on April 6, 2003, because of fever, chills, rigors and cough for 1 day. In view of his contact history with SARS patients, he was put on anti-viral therapy with i.v. ribavirin on day 5. Despite ribavirin treatment, the patient ran a persistently low-grade fever and a chest radiograph on day 21 revealed new shadows over the right lower zone. We report two cases of SARS occurring in end-stage renal failure patients. The diagnosis of SARS was based on his strong contact history, chest radiograph shadows and the second RT-PCR assay for coronavirus of his throat and nasal swabs on day 24. The optimal ribavirin dose for treating SARS in patients with end-stage renal failure and in those receiving haemodialysis is unknown. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/13679500/ doi: 10.1093/ndt/gfg454 id: cord-255252-md0avnqg author: Tang, Julian W. title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date: 2007-07-02 words: 5317.0 sentences: 326.0 pages: flesch: 70.0 cache: ./cache/cord-255252-md0avnqg.txt txt: ./txt/cord-255252-md0avnqg.txt summary: SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. Post-mortem tissues were collected with great care from the major organs including heart, kidney, liver, spleen, lung, small bowel, psoas (skeletal) muscle, and bone marrow. Figures 1-6 show the results, using semi-log plots, for each organ: heart, kidney, liver, spleen, lung, and small bowel, respectively, for SARS-CoV, GAPDH and the SARS-CoV/GAPDH RNA ratio. In the organspecific viral load results, the overall picture made up from the data points from the seven different patients with different durations of SARS illness, generally, the SARS-CoV/GAPDH RNA ratio never reached above one in heart, kidney, liver, and spleen tissue for all x-axis parameters analyzed. abstract: Few post‐mortem studies have been performed on patients who have died from severe acute respiratory syndrome (SARS). No studies have examined how the SARS‐associated coronavirus (SARS‐CoV) loads in different organs with respect to time, post‐mortem. The aim of this study was to determine the quantitative temporal‐spatial distribution of SARS‐CoV in the post‐mortem tissue samples of seven patients. Quantitation of a house‐keeping gene, glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) was undertaken to standardize the amount of tissue tested. SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. The SARS‐CoV/GAPDH RNA ratio remained relatively stable in most organ tissue types for all these time durations. The ratio reached the highest value of equal to or greater than one for lung and small bowel, whereas those for heart, liver, spleen, and kidney were always less than one. It is concluded that SARS‐CoV viral loads in these organs remain relatively stable, post‐mortem. This quantitative assessment further supports SARS‐CoV has a specific tropism for the human respiratory and gastrointestinal tracts, which may be related to the density of SARS‐CoV receptors. J. Med. Virol. 79:1245–1253, 2007. © Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17607787/ doi: 10.1002/jmv.20873 id: cord-353099-38bz0acw author: Tang, Mei San title: Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date: 2020-07-02 words: 1034.0 sentences: 70.0 pages: flesch: 51.0 cache: ./cache/cord-353099-38bz0acw.txt txt: ./txt/cord-353099-38bz0acw.txt summary: Methods 67 specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Results The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46 respectively. Conclusion COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. The correlation of the SARS-CoV-2 neutralizing titer with the ratio reported by the 162 Roche, Abbott, and EI assays was 0.29, 0.47, and 0.46 respectively (Figure 2A-C) . Increased neutralizing antibody titers were also higher in patients that were intubated, 201 had cardiac injury, or AKI relative to those with milder COVID-19 symptoms ( Figure 202 4B-D). abstract: Introduction Commercially available SARS-CoV-2 serological assays based on different viral antigens have been approved for the qualitative determination of anti-SARS-CoV-2 antibodies. However, there is limited published data associating the results from commercial assays with neutralizing antibodies. Methods 67 specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Correlation, concordance, positive percent agreement (PPA), and negative percent agreement (NPA) were calculated at several cutoffs. Results were compared in patients categorized by clinical outcomes. Results The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46 respectively. At an EC50 of 1:32, the concordance kappa with Roche was 0.49 (95% CI; 0.23-0.75), with Abbott was 0.52 (0.28-0.77), and with EUROIMMUN was 0.61 (0.4-0.82). At the same neutralizing titer, the PPA and NPA for the Roche was 100% (94-100) & 56% (30-80); Abbott was 96% (88-99) & 69% (44-86); and EUROIMMUN was 91% (80-96) & 81% (57-93) for distinguishing neutralizing antibodies. Patients who died, were intubated, or had a cardiac injury from COVID-19 infection had significantly higher neutralizing titers relative to those with mild symptoms. Conclusion COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. Nevertheless, commercial serological assays have poor NPA for SARS-CoV-2 neutralization, making them imperfect proxies for neutralization. url: https://doi.org/10.1101/2020.07.01.182220 doi: 10.1101/2020.07.01.182220 id: cord-277278-lg38l5gh author: Tang, Olive title: Outcomes of nursing home COVID-19 patients by initial symptoms and comorbidity: Results of universal testing of 1,970 residents date: 2020-10-14 words: 2160.0 sentences: 125.0 pages: flesch: 53.0 cache: ./cache/cord-277278-lg38l5gh.txt txt: ./txt/cord-277278-lg38l5gh.txt summary: Residents who were positive for COVID-19 and had multiple symptoms at the time of testing had the highest risk of mortality (HR 4.44; 95% CI: 2.97, 6.65) and hospitalization (SHR 2.38; 95% CI: 1.70, 3.33), even after accounting for comorbidity burden. Of 52 SARS-CoV-2 positive residents who were asymptomatic at the time of testing and were closely monitored for 14 days at one facility, only 6 (11.6%) developed symptoms. Conclusions and Implications Asymptomatic infection with SARS-CoV-2 in the nursing home setting was associated with increased risk of death suggesting a need for closer monitoring of these residents, particularly those with underlying cardiovascular and respiratory comorbidities. A 78 cohort of all residents at one facility who were asymptomatic at the time of testing were closely 79 monitored by nursing home staff for development of symptoms over a 14 day period; this was 80 documented in a dedicated line list and included as a sub-analysis. abstract: Objective Clinical implications of asymptomatic cases of the novel coronavirus disease 2019 (COVID-19) in nursing homes remain poorly understood. We assessed the association of symptom status and medical comorbidities on mortality and hospitalization risk associated with COVID-19 in residents of a large nursing home system. Design Retrospective cohort study. Setting and Participants 1,970 residents from 15 nursing home facilities with universal COVID-19 testing in Maryland. Methods We used descriptive statistics to compare baseline characteristics, logistic regression to assess the association of comorbidities with COVID-19, and Cox regression to assess the association of asymptomatic and symptomatic COVID-19 with mortality and hospitalization. We assessed the association of comorbidities with mortality and hospitalization risk. Symptom status was assessed at the time of the first test. Maximum follow-up was 94 days. Results Among the 1,970 residents (mean age 73.8, 57% female, 68% Black), 752 (38.2%) were positive on their first test. Residents who were positive for COVID-19 and had multiple symptoms at the time of testing had the highest risk of mortality (HR 4.44; 95% CI: 2.97, 6.65) and hospitalization (SHR 2.38; 95% CI: 1.70, 3.33), even after accounting for comorbidity burden. Cases who were asymptomatic at testing had a higher risk of mortality (HR 2.92; 95% CI: 1.95, 4.35), but not hospitalization (HR 1.06; 95% CI: 0.82, 1.38) compared to those who were negative for COVID-19. Of 52 SARS-CoV-2 positive residents who were asymptomatic at the time of testing and were closely monitored for 14 days at one facility, only 6 (11.6%) developed symptoms. Conclusions and Implications Asymptomatic infection with SARS-CoV-2 in the nursing home setting was associated with increased risk of death suggesting a need for closer monitoring of these residents, particularly those with underlying cardiovascular and respiratory comorbidities. url: https://www.ncbi.nlm.nih.gov/pubmed/33153910/ doi: 10.1016/j.jamda.2020.10.011 id: cord-338041-gl65i3s0 author: Tang, Qin title: Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date: 2015-11-26 words: 4455.0 sentences: 230.0 pages: flesch: 53.0 cache: ./cache/cord-338041-gl65i3s0.txt txt: ./txt/cord-338041-gl65i3s0.txt summary: Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Based on the data matrix of nucleotide composition, the MD and SVM were applied to predict hosts of coronaviruses. The data matrix with 19 factors as columns and 730 samples as rows was fitted to SVM and MD models, all predictions in leave-one-out cross-validations were listed in Supplementary Table S2 and summarized in Table 1 according to host species. Cross-host evolution research of SARS-CoV in palm civet and humans indicated that the variations in spike genes seemed to be essential for the transition of coronavirus from animal-to-human transmission to human-to-human transmission 25 . The MD correctly predicts bats as the natural hosts of the three viruses, and the SVM indicates that Rs3367 and SL-CoV-WIV1 are harmful to humans. abstract: Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at http://bioinfo.ihb.ac.cn/seq2hosts. url: https://doi.org/10.1038/srep17155 doi: 10.1038/srep17155 id: cord-352768-16vgnq14 author: Tang, Qingquan title: Application of siRNA Against SARS in the Rhesus Macaque Model date: 2008 words: 4389.0 sentences: 274.0 pages: flesch: 48.0 cache: ./cache/cord-352768-16vgnq14.txt txt: ./txt/cord-352768-16vgnq14.txt summary: Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen''s genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. A pair of siRNAs showing prominent prophylactic and therapeutic activities in the cell culture study (29), referred to as siSC2 and siSC5, were further evaluated in vivo, first in mice using a reporter gene assay and subsequently using a clinically acceptable intranasal administration in the recently established rhesus macaque SARS model (23-26). abstract: Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen's genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. The prophylactic and therapeutic efficacies resulted in relief of animals from SCV infection-induced fever, diminished SCV in upper airway and lung alveoli, and milder acute diffuse alveoli damage (DAD). The dosages of siRNA used, 10 to 40 mg/kg, did not show any sign of siRNA-induced toxicity. These results support that a clinical investigation of this anti-SARS siRNA therapeutic agent is warranted. The study also illustrates the capability of siRNA to enable a massive reduction in development time for novel targeted therapeutic agents. We detail a representative example of large-mammal siRNA use. url: https://doi.org/10.1007/978-1-59745-191-8_11 doi: 10.1007/978-1-59745-191-8_11 id: cord-104081-a3fx8tyd author: Tang, Tiffany title: Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date: 2020-10-05 words: 4004.0 sentences: 206.0 pages: flesch: 57.0 cache: ./cache/cord-104081-a3fx8tyd.txt txt: ./txt/cord-104081-a3fx8tyd.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Our results demonstrate that S1/S2 pre-cleavage is essential for plasma membrane entry into Calu-3 cells, a model lung epithelial cell line, but not for endosomal entry Vero E6 cells, a model cell culture line, and that other proteases in addition to furin are responsible for processing SARS-CoV-2 S1/S2. dec-RVKR-CMK treatment had no significant impact on SARS-CoV S mediated infection of Vero E6 and Calu-3 cells (Figure 6A and 6B) , suggesting that dec-RVKR-CMK impacts on SARS-CoV-2 S is due to inhibiting the S1/S2 pre-cleavage and not due to some general effect on protein expression. Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2 Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Cleavage of the S protein at the S1/S2 and/or S2’ site is known to activate the S protein for viral entry, which can occur at either the cell plasma membrane or the endosomal membrane. Previous studies show that SARS-CoV-2 has a unique insert at the S1/S2 site that can be cleaved by furin, which expands viral tropism to lung cells. Here, we analyze the presence of a furin S1/S2 site in related CoVs and offer thoughts on the implications of SARS-CoV-2’s unique insert on its origin. We also utilized viral pseudoparticles to study the impact of the S1/S2 cleavage on infectivity. Our results demonstrate that S1/S2 pre-cleavage is essential for plasma membrane entry into Calu-3 cells, a model lung epithelial cell line, but not for endosomal entry Vero E6 cells, a model cell culture line, and that other proteases in addition to furin are responsible for processing SARS-CoV-2 S1/S2. url: https://doi.org/10.1101/2020.10.04.325522 doi: 10.1101/2020.10.04.325522 id: cord-269275-b7xxk48t author: Tang, Xiaojia title: Neurological manifestations in COVID-19 and its possible mechanism date: 2020-09-27 words: 4631.0 sentences: 260.0 pages: flesch: 44.0 cache: ./cache/cord-269275-b7xxk48t.txt txt: ./txt/cord-269275-b7xxk48t.txt summary: SARS-CoV-2 has been reported to be associated with Guillain-Barré syndrome, rhabdomyolysis, acute cerebrovascular disease, central nervous system infections and other neurological diseases. Four formal reports have described neurological problems in SARS patients, including polyneuropathy [35] , myopathy and rhabdomyolysis [36] , large artery ischemic stroke [37] and central nervous system infections [38] . In a study by Mao et al., 214 patients diagnosed with COVID-19 were enrolled, and six (2.80%) of them developed acute cerebrovascular disease (five cases of ischemic stroke and one case of cerebral hemorrhage). Strokes are not uncommon in critically ill patients with multiple comorbidities, so SARS-CoV-2 infections in humans may increase the risk of stroke. Since some COVID-19 patients have complained of headaches, nausea etc, care providers should be alert for central nervous system infections caused by SARS-CoV-2 if such patients also exhibit symptoms such as a fever, epilepsy and disturbances of consciousness. abstract: In December 2019, the first cases of the acute respiratory illness now known as Corona Virus Disease 2019 (COVID-19) occurred in Wuhan, Hubei Province, China. The main clinical manifestations of COVID-19 are a fever, dry cough and general weakness, although in some patients, a headache, tight chest, diarrhea, etc. are the first clinical manifestations. Neurological practice is involved in all aspects of medicine, from primary care for patients with migraines to consultations with patients in the intensive care unit. Few disorders spare the nervous system, and newly emerging infections are no exception. As neurologists, we are concerned about the effects of SARS-CoV-2 infections on the nervous system. Multiple neuropathy, rhabdomyolysis, cerebrovascular disease, central nervous system infections and other common neurological diseases require attention during this outbreak. url: https://doi.org/10.18632/aging.103732 doi: 10.18632/aging.103732 id: cord-015503-j99cgsjt author: Tang, Xiaolu title: On the origin and continuing evolution of SARS-CoV-2 date: 2020-03-03 words: 5243.0 sentences: 292.0 pages: flesch: 59.0 cache: ./cache/cord-015503-j99cgsjt.txt txt: ./txt/cord-015503-j99cgsjt.txt summary: Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Further, the genomic sequences of SARS-CoV-2 viruses isolated from a number of patients share sequence identity higher than 99.9%, suggesting a very recent host shift into humans [1] [2] [3] . abstract: The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure. These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (COVID-19). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107875/ doi: 10.1093/nsr/nwaa036 id: cord-353887-f4yd7guj author: Tang, Yujun title: Cytokine Storm in COVID-19: The Current Evidence and Treatment Strategies date: 2020-07-10 words: 8532.0 sentences: 461.0 pages: flesch: 44.0 cache: ./cache/cord-353887-f4yd7guj.txt txt: ./txt/cord-353887-f4yd7guj.txt summary: Besides, corticosteroids, programmed cell death protein (PD)-1/PD-L1 checkpoint inhibition, cytokine-adsorption devices, intravenous immunoglobulin, and antimalarial agents could be potentially useful and reliable approaches to counteract cytokine storm in COVID-19 patients. In this review, we referred COVID-19 associated cytokine storm as the patients who are severely ill along with a high concentration of pro-inflammatory cytokines. The innate and adaptive immune responses activated by SARS-CoV-2 infection lead to uncontrolled inflammatory responses and ultimately cause the cytokine storm (14) . MERS-CoV infects the cells mentioned above to induce delayed (but increased) levels of pro-inflammatory cytokines (e.g., IL-2) and chemokines (e.g., CCL2, CCL3) (27, 30) . Although SARS-CoV is abortive in macrophages and DCs, the virus induces an increase in levels of pro-inflammatory cytokines and chemokines (31, 32) . A comment and a meta-analysis, which mainly bases on the evidence of SARS and MERS (64, 65) , stated that corticosteroid would increase mortality and delayed clearance of viral in coronavirus infection diseases. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) is the pathogen that causes coronavirus disease 2019 (COVID-19). As of 25 May 2020, the outbreak of COVID-19 has caused 347,192 deaths around the world. The current evidence showed that severely ill patients tend to have a high concentration of pro-inflammatory cytokines, such as interleukin (IL)-6, compared to those who are moderately ill. The high level of cytokines also indicates a poor prognosis in COVID-19. Besides, excessive infiltration of pro-inflammatory cells, mainly involving macrophages and T-helper 17 cells, has been found in lung tissues of patients with COVID-19 by postmortem examination. Recently, increasing studies indicate that the “cytokine storm” may contribute to the mortality of COVID-19. Here, we summarize the clinical and pathologic features of the cytokine storm in COVID-19. Our review shows that SARS-Cov-2 selectively induces a high level of IL-6 and results in the exhaustion of lymphocytes. The current evidence indicates that tocilizumab, an IL-6 inhibitor, is relatively effective and safe. Besides, corticosteroids, programmed cell death protein (PD)-1/PD-L1 checkpoint inhibition, cytokine-adsorption devices, intravenous immunoglobulin, and antimalarial agents could be potentially useful and reliable approaches to counteract cytokine storm in COVID-19 patients. url: https://doi.org/10.3389/fimmu.2020.01708 doi: 10.3389/fimmu.2020.01708 id: cord-308994-4nljzm8a author: Tang, Zhongmin title: Insights from nanotechnology in COVID-19 treatment date: 2020-11-04 words: 3239.0 sentences: 177.0 pages: flesch: 36.0 cache: ./cache/cord-308994-4nljzm8a.txt txt: ./txt/cord-308994-4nljzm8a.txt summary: We focus specifically on SARS-CoV-2 and the detailed role that nanotechnology can play in addressing this pandemic, including i) using FDA-approved nanomaterials for drug/vaccine delivery, including further exploration of the inhalation pathway; ii) introducing promising nanomaterials currently in clinical trials for drug/vaccine delivery; iii) designing novel biocompatible nanomaterials to combat the virus via interfering in its life cycle; and iv) promoting the utilization of nanomaterials in pneumonia treatment. To summarize, the advantages of nanotechnology in antiviral research include the following: 1) promotes the delivery of water-insoluble drugs; [39] 2) enhances the circulation time of drugs in vivo; [40] 3) achieves co-delivery of drugs; [40] 4) improves drug utilization efficiency and reduce side effects through targeting antibody modification; [41] 5) protects DNA and mRNA vaccines, overcoming bottlenecks for in vivo applications; [42] and 6) the physicochemical properties of nanomaterials can also be employed directly against viruses. abstract: In just a few months, SARS-CoV-2 and the disease it causes, COVID-19, created a worldwide pandemic. Virologists, biologists, pharmacists, materials scientists, and clinicians are collaborating to develop efficient treatment strategies. Overall, in addition to the use of clinical equipment to assist patient rehabilitation, antiviral drugs and vaccines are the areas of greatest focus. Given the physical size of SARS-CoV-2 and the vaccine delivery platforms currently in clinical trials, the relevance of nanotechnology is clear, and previous antiviral research using nanomaterials also supports this connection. Herein we briefly summarize current representative strategies regarding nanomaterials in antiviral research. We focus specifically on SARS-CoV-2 and the detailed role that nanotechnology can play in addressing this pandemic, including i) using FDA-approved nanomaterials for drug/vaccine delivery, including further exploration of the inhalation pathway; ii) introducing promising nanomaterials currently in clinical trials for drug/vaccine delivery; iii) designing novel biocompatible nanomaterials to combat the virus via interfering in its life cycle; and iv) promoting the utilization of nanomaterials in pneumonia treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/33178330/ doi: 10.1016/j.nantod.2020.101019 id: cord-286466-scokdxp2 author: Tani, Hideki title: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date: 2020-08-23 words: 2558.0 sentences: 155.0 pages: flesch: 54.0 cache: ./cache/cord-286466-scokdxp2.txt txt: ./txt/cord-286466-scokdxp2.txt summary: The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The neutralization values of the serum 31 samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative 32 donors against the pseudotyped virus infection evaluated by the CRNT were compared with 33 was designated as pCAG-SARS-CoV-2. Vero cells were treated with serially diluted sera or whole blood of convalescent patients with 145 COVID-19 or PCR-negative donors and then inoculated with Sfullpv, St19pv, or VSVpv. To 146 remove hematopoietic cells from whole blood samples, centrifugation was performed at 2,000 × g 147 for 5 min. To determine the specificity of infection of Sfullpv and St19pv, a neutralization assay of the 183 pseudotyped viruses was performed using sera of two hospitalized COVID-19 patients. abstract: SARS-CoV-2 is a novel coronavirus that emerged in 2019 and is now classified in the genus Coronavirus with closely related SARS-CoV. SARS-CoV-2 is highly pathogenic in humans and is classified as a biosafety level (BSL)-3 pathogen, which makes manipulating it relatively difficult due to its infectious nature. To circumvent the need for BSL-3 laboratories, an alternative assay was developed that avoids live virus and instead uses a recombinant VSV expressing luciferase and possesses the full length or truncated spike proteins of SARS-CoV-2. Furthermore, to measure SARS-CoV-2 neutralizing antibodies under BSL2 conditions, a chemiluminescence reduction neutralization test (CRNT) for SARS-CoV-2 was developed. The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The CRNT, which used whole blood collected from hospitalized patients with COVID-19, was also examined. As a result, the inhibition of pseudotyped virus infection was specifically observed in both serum and whole blood and was also correlated with the results of the IFA. In conclusion, the CRNT for COVID-19 is a convenient assay system that can be performed in a BSL-2 laboratory with high specificity and sensitivity for evaluating the occurrence of neutralizing antibodies against SARS-CoV-2. url: https://doi.org/10.1101/2020.08.21.262295 doi: 10.1101/2020.08.21.262295 id: cord-352073-rdhjj72g author: Taniwaki, S.A title: Resource optimization in COVID-19 diagnosis date: 2020-06-26 words: 1910.0 sentences: 98.0 pages: flesch: 57.0 cache: ./cache/cord-352073-rdhjj72g.txt txt: ./txt/cord-352073-rdhjj72g.txt summary: The emergence and rapid dissemination worldwide of a novel Coronavirus (SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This manuscript reports on the optimization of the Charité and the CDC RT-qPCR protocols for SARS-CoV-2 detection regarding concentration and volumes of reagents for both probe and intercalant agent-based platforms, as well as on the substitution of rayon swabs for cotton swabs for sample collection. Performance of E and RdRp genes of SARS-CoV-2 RT-qPCRs, based on final reaction volume of 10 µL with 2 µL of RNA (Table 1) , were verified with a relative standard curve built with 10 -2 to 10 -8 dilutions of positive RNA control. Tabela 4 -Probe-based RT-qPCR to the E gene of serial dilutions of SARS-CoV-2 sampled with cotton and rayon swabs. abstract: The emergence and rapid dissemination worldwide of a novel Coronavirus (SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This scenario, showed the requirement of improve de diagnostic capacity, so the aim of this study were to verify the possibility of reducing the reaction volume of RT-qPCR and to test cotton swabs as alternative for sample collection. RT-qPCR volumes and RNA sample concentration were optimized without affecting the sensitivity of assays, using both probe-based and intercalation dyes methods. Although rayon swabs showed better performance, cotton swabs could be used as alternative type for clinical sample collection. COVID-19 laboratory diagnosis is important to isolate and restrict the dissemination of virus, so seek for alternatives to decrease the coast of assays improve the control of disease. url: https://doi.org/10.1101/2020.06.25.172528 doi: 10.1101/2020.06.25.172528 id: cord-254777-h8hw4m9f author: Tanner, Tamara title: Hyperinflammation and the utility of immunomodulatory medications in children with COVID-19 date: 2020-07-29 words: 4731.0 sentences: 248.0 pages: flesch: 42.0 cache: ./cache/cord-254777-h8hw4m9f.txt txt: ./txt/cord-254777-h8hw4m9f.txt summary: Cytokine storm syndromes include various entities, depending on the inciting factor: primary Hemophagocytic Lymphohistiocytosis [HLH] in children with specific genetic mutations; secondary HLH due to infection or malignancy, macrophage activation syndrome due to rheumatologic disease and cytokine release syndrome (CRS) when hyperinflammation is due to CAR T-cell therapy. Although still under investigation, ADE has been proposed as a potential mechanism underlying the newly described MIS-C, based on the observation that a majority of the patients have evidence of existing antibodies to SARS-CoV-2 and the inflammatory condition seems to lag behind the COVID-19 infection peak by approximately 4-6 weeks. The rationale for use of IL-6 blockade in serious COVID-19 infections is based on the observation that for the subset of patients with severe manifestations, IL-6 is most likely one of the drivers of the cytokine storm, and elevated levels of IL-6 have been consistently shown [14] . abstract: The rapid spread of SARS-CoV-2 infection globally coupled with the relatively high case-fatality rate has led to immediate need for therapeutic intervention to prevent and treat COVID-19 disease. There is accumulating evidence that morbidity and mortality in COVID-19 may be exacerbated by a dysregulated host immune response resulting in significant hyperinflammation and cytokine release. The aim of this review is to describe the basis for the immune dysregulation caused by SARS-CoV-2 infection and to examine current investigations into immunomodulatory therapies aimed at targeting the excessive host immune response. url: https://doi.org/10.1016/j.prrv.2020.07.003 doi: 10.1016/j.prrv.2020.07.003 id: cord-288818-6uvb4qsk author: Tanveer, Faouzia title: Ethics, pandemic and environment; looking at the future of low middle income countries date: 2020-10-15 words: 6998.0 sentences: 322.0 pages: flesch: 45.0 cache: ./cache/cord-288818-6uvb4qsk.txt txt: ./txt/cord-288818-6uvb4qsk.txt summary: From the restrictions on public freedom and burgeoning socio-economic impacts to the rationing of scarce medical resources, the spread of COVID-19 is an extraordinary ethical dilemma for resource constrained nations with less developed health and research systems. International regimes are on high alert to stop its spread, however, as far as the global scenario is concerned, countries and governments are clueless in stopping the expanding pandemic as not much is known about SARS-CoV-2, while left only with implementing nationwide lock downs and curfews which opened new economic fronts and social challenges. COVID-19 has presented itself as a test case for the humanity in terms of global fraternity, decision making, technology and expertise sharing, rapid pandemic response mechanisms, stability, crises management and policy making. abstract: COVID-19 which started in Wuhan, China and swiftly expanded geographically worldwide, including to Low to Middle Income Countries (LMICs). This in turn raised numerous ethical concerns in preparedness, knowledge sharing, intellectual property rights, environmental health together with the serious constraints regarding readiness of health care systems in LMICs to respond to this enormous public health crisis. From the restrictions on public freedom and burgeoning socio-economic impacts to the rationing of scarce medical resources, the spread of COVID-19 is an extraordinary ethical dilemma for resource constrained nations with less developed health and research systems. In the current crisis, scientific knowledge and technology has an important role to play in effective response. Emergency preparedness is a shared responsibility of all countries with a moral obligation to support each other. This review discusses the ethical concerns regarding the national capacities and response strategies in LMICs to deal with the COVID-19 pandemic as well as the deep link between the environment and the increasing risk of pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/33059674/ doi: 10.1186/s12939-020-01296-z id: cord-293059-2iwzieqm author: Tao, Huaqiang title: Dysimmunity and inflammatory storm: Watch out for bone lesions in COVID-19 infection date: 2020-10-06 words: 1818.0 sentences: 104.0 pages: flesch: 38.0 cache: ./cache/cord-293059-2iwzieqm.txt txt: ./txt/cord-293059-2iwzieqm.txt summary: It has been approved that inflammation-induced pathogenesis in COVID-19 infection has a strong correlation with incidence of cardiovascular metabolic diseases and gastrointestinal injury (1) . However, studies on the correlation between pro-inflammatory cytokine responses and bone metabolism in COVID-19 patients are still lacking. In this special background, will inflammatory disorder and immune imbalance affect bone metabolism after COVID-19 infection? Simultaneously, hypoxia inducible factor (HIF-1) was proven to facilitate osteoclast differentiation by overexpressing RANKL and nuclear factor of activated T cells cytoplasmic 1 (NFATc1) (14) . As osteoblasts and osteoclasts exist in approach with immune cells in medullary cavity, it''s no wonder that immune system shares massive regulatory cytokines, signaling molecules and transcription factors with bone biology. Apart from that, NF-κB and AP-1 stimulate the expression of many elements which required for inflammatory cytokines, driving up osteoclast activity and usually implicated inhibition on proliferation and differentiation of osteoblasts (22) . abstract: At the end of 2019, a new kind of pneumonia which was proven to be supported by novel coronaviruses named SARS-CoV-2 emerges and it seems to be more complicate in its clinical course and management. Related researches have demonstrated that SARS-CoV-2 serves roles in respiratory, intestinal and neuronal diseases. Given the growing cases of COVID-19, analyzing the relevance between COVID-19 and fragile patients who suffer from bone destruction is entirely indispensable. Accordingly, the recapitulatory commentary is necessary to advance our knowledge on COVID-19 and orthopedics. In this article, we particularly clarify the possible relationship between the newly COVID-19 infection and bone lesions from the standpoints of dysimmunity and inflammatory storm. url: https://api.elsevier.com/content/article/pii/S030698772032973X doi: 10.1016/j.mehy.2020.110332 id: cord-103662-a4ok5wqc author: Tarek, M. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 words: 8116.0 sentences: 454.0 pages: flesch: 45.0 cache: ./cache/cord-103662-a4ok5wqc.txt txt: ./txt/cord-103662-a4ok5wqc.txt summary: When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. abstract: Computational prediction of immunogenic epitopes is a promising platform for therapeutic and preventive vaccine design. A potential target for this strategy is human immunodeficiency virus (HIV-1), for which, despite decades of efforts, no vaccine is available. In particular, a therapeutic vaccine devised to eliminate infected cells would represent a key component of cure strategies. HIV peptides designed based on individual viro-immunological data from people living with HIV/AIDS have recently shown able to induce post-therapy viral set point abatement. However, the reproducibility and scalability of this method is curtailed by the errors and arbitrariness associated with manual peptide design as well as by the time-consuming process. We herein introduce Custommune, a user-friendly web tool to design personalized and population-targeted vaccines. When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. Of note, Custommune predictions compared favorably with manually designed peptides administered in a recent phase II clinical trial (NCT02961829). Furthermore, we utilized Custommune to design preventive vaccines targeted for populations highly affected by COVID-19. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Overall, our data describe a new tool for rapid development of personalized or population-based immunotherapy against chronic and acute viral infections. url: http://medrxiv.org/cgi/content/short/2020.04.25.20079426v1?rss=1 doi: 10.1101/2020.04.25.20079426 id: cord-306832-w8s282nq author: Tarragón, Blanca title: FRACASO RENAL AGUDO EN PACIENTES HOSPITALIZADOS POR COVID-19 date: 2020-10-09 words: 3471.0 sentences: 362.0 pages: flesch: 59.0 cache: ./cache/cord-306832-w8s282nq.txt txt: ./txt/cord-306832-w8s282nq.txt summary: La mediana de estancia fue de 12 días (RIC 9-23), y el 22% fallecieron-Los pacientes que desarrollaron FRA durante el ingreso presentaron valores más altos de proteína C-reactiva, LDH o dímero D, una afectación pulmonar más grave, más necesidad de ingreso en UCI, más tratamiento con lopinavir/ritonavir y fármacos biológicos y mayor necesidad de TSR. Además, esta afectación en pacientes COVID-19 no es uniforme según lo comunicado por los hospitales chinos y puede estar condicionada por la estrategia de detección de casos de cada sistema de salud, la política de ingresos de cada hospital, la definición de daño renal e incluso los factores genéticos y ambientales de las diversas poblaciones afectadas. El FRA se ha definido como factor de peor pronóstico y mayor mortalidad en pacientes ingresados con infección por SARS-Cov-2 9,10 . abstract: Antecedentes y objetivo: En diciembre de 2019 surgió en Wuhan, China, la COVID-19 causada por SARS-CoV-2, declarada pandemia global por la OMS en marzo de 2020. Es una infección respiratoria con complicaciones a nivel cardiaco, hematológico, digestivo, neurológico y renal. El fracaso renal agudo (FRA) en pacientes hospitalizados por COVID-19 se presenta en el 0,5-25% y es un factor de mal pronóstico. Los mecanismos de afectación renal no están completamente aclarados. Presentamos la evolución clínica de pacientes ingresados por COVID-19 con FRA que requirieron atención por nefrología en un hospital terciario de la comunidad de Madrid, España. Métodos: Éste es un estudio observacional prospectivo de todos los casos que ingresaron por COVID-19 entre el 6 de marzo y el 12 de mayo de 2020 y requirieron atención por Nefrología. Se recogieron datos clínicos y analíticos de características basales, evolución de la COVID-19 y del FRA. Resultados: Se analizaron 41 pacientes con edad media de 66,8 años (DE 2,1), el 90,2% varones, y con enfermedad renal crónica previa en el 36,6%. El 56,1% presentaron neumonía grave o síndrome de distrés respiratorio agudo y el 31,7% requirió ingreso en UCI. El FRA fue de etiología prerrenal en el 61%, necrosis tubular aguda en contexto de sepsis en el 24,4%, glomerular en el 7,3% y por toxicidad tubular en el 7,3%. Se registró proteinuria en el 88,9% y hematuria en el 79,4%. El 48,8% de los pacientes requirió terapia de sustitución renal (TSR). La mediana de estancia fue de 12 días (RIC 9-23), y el 22% fallecieron-Los pacientes que desarrollaron FRA durante el ingreso presentaron valores más altos de proteína C-reactiva, LDH o dímero D, una afectación pulmonar más grave, más necesidad de ingreso en UCI, más tratamiento con lopinavir/ritonavir y fármacos biológicos y mayor necesidad de TSR. Conclusiones: La hipovolemia y deshidratación son una causa frecuente de FRA en pacientes COVID-19. Aquellos que desarrollan FRA intrahospitalario presentan un perfil de peor pronóstico respiratorio, analítico y renal. Creemos que la monitorización de marcadores renales, así como el manejo individualizado de la volemia pueden ser determinantes para prevenir el FRA. Background and aim: In December 2019, a coronavirus 2019 (COVID-19) outbreak, caused by SARS-CoV-2, took place in Wuhan and was declared a global pandemic in March 2020 by the World Health Organization (WHO). It is a prominently respiratory infection, with potential cardiological, hematological, gastrointestinal and renal complications. Acute kidney injury (AKI) is found in 0.5-25% of hospitalized COVID-19 patients and constitutes a negative prognostic factor. Renal damage mechanisms are not completely clear. We report the clinical evolution of hospitalized COVID-19 patients who presented with AKI requiring attention from the Nephrology team in a tertiary hospital in Madrid, Spain. Methods: This is an observational prospective study including all COVID-19 cases that required hospitalization and Nephrology management from March 6th to May 12th. We collected clinical and analytical data of baseline characteristics, COVID-19 and AKI evolutions. Results: We analyzed 41 patients with a mean age of 66.8 years (SD 2.1), 90.2% males, and with a history of chronic kidney disease (CKD) in 36.6%. 56.1% of patients presented with sever pneumonia or acute respiratory distress syndrome (ARDS), and 31.7% required intensive care. AKI etiology was prerenal in 61%, acute tubular necrosis in the context of sepsis in 24.4%, glomerular in 7.3% and tubular toxicity in 7.3% of the cases. We reported proteinuria in 88.9% and hematuria in 79.4% of patients. 48.8% of patients required renal replacement therapy (RRT). Median length of stay was 12 days (interquartilic range 9-23) and 22% of the population died. Patients who developed AKI during hospital stay presented with higher C-reactive protein, Lactate dehydrogenase-LDH and D-dimer values, more severe pulmonary damage, more frequent intensive care unit-ICU admission, treatment with lopinavir/ritonavir and biological drugs and RRT requirement. Conclusions: Hypovolemia and dehydration are a frequent cause of AKI among COVID-19 patients. Those who develop AKI during hospitalization display worse prognostic factors in terms of pulmonary damage, renal damage, and analytical findings. We believe that monitorization of renal markers as well as individualized fluid management can play a key role in AKI prevention. url: https://doi.org/10.1016/j.nefro.2020.08.005 doi: 10.1016/j.nefro.2020.08.005 id: cord-296031-r6iqiy1n author: Tattan-Birch, H. title: COVID-19, smoking, vaping and quitting: A representative population survey in England date: 2020-06-30 words: 5196.0 sentences: 343.0 pages: flesch: 59.0 cache: ./cache/cord-296031-r6iqiy1n.txt txt: ./txt/cord-296031-r6iqiy1n.txt summary: Aims: To explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home. Conclusions: In a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In this study, we will use a representative population sample of adults in England to estimate: 1) associations between suspected SARS-CoV-2 infection and smoking status, e-cigarette use and NRT use; . https://doi.org/10.1101/2020.06.29.20142661 doi: medRxiv preprint A1: Logistic regression was used to estimate the association between suspected SARS-CoV-2 infection and (i) smoking status, (ii) e-cigarette use and (iii) NRT use, with and without adjustment for potential confounders. abstract: Aims: To explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home. Design: Cross-sectional household surveys of a representative sample of the population in England from April-May 2020. Participants: The sample included 3,285 adults aged [≥]18 years. Measurements: Participants who reported they definitely or think they had coronavirus were classified as having a suspected SARS-CoV-2 infection. Participants were asked how often they wash their hands after returning home, before eating, before preparing foods or before touching their face. They were also asked whether, due to COVID-19, they had i) attempted to quit smoking, ii) attempted to quit vaping, and iii) changed the amount they smoke inside the home. Findings: Odds of suspected SARS-CoV-2 infection were significantly greater among current smokers (20.9%, adjusted odds ratio [ORadj]=1.34, 95% confidence interval [CI]=1.04-1.73) and long-term (>1-year) ex-smokers (16.1%, ORadj=1.33, 95%CI=1.05-1.68) than never smokers (14.5%). Recent (<1-year) ex-smokers had non-significantly greater odds of suspected infection (22.2%, ORadj=1.50, 95%CI=0.85-2.53, Bayes factor=0.55-1.17). Bayes factors indicated there was sufficient evidence to rule out large differences in suspected SARS-CoV-2 infection by NRT use and medium differences by e-cigarette use. With the exception of hand washing before face touching, engagement in hand washing behaviours was high (>85%) regardless of nicotine use. A minority (12.2%) of past-year smokers who made a quit attempt in the past three months were triggered by COVID-19, and approximately one-in-ten current e-cigarette users reported attempting to quit vaping because of COVID-19. Most people reported smoking the same amount inside the home. Conclusions: In a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In general, engagement in hand washing was high regardless of nicotine or tobacco use. A minority of past-year smokers and current e-cigarette users, respectively, attempted to quit smoking/vaping due to COVID-19. url: https://doi.org/10.1101/2020.06.29.20142661 doi: 10.1101/2020.06.29.20142661 id: cord-299999-jra1yu6a author: Tattar, R. title: COVID PDPs date: 2020-05-22 words: 1630.0 sentences: 94.0 pages: flesch: 48.0 cache: ./cache/cord-299999-jra1yu6a.txt txt: ./txt/cord-299999-jra1yu6a.txt summary: However, a structure needs to be developed to account for the disruption in training COVID-19 has caused and facilitate the progression of the trainees without compromising the quality and integrity of the respected specialities. The New England Journal of Medicine case report of the first COVID-19 patient in the USA detected high SARS-CoV-2 viral load in their stool sample. At present, PDPs are not a routine part of the undergraduate curricula 3 and as such, newly qualified dentists will be faced with the new challenge of having to proactively plan their CPD to fulfil outstanding competencies from their current training course. Whilst CPD cycles are five years, the need to complete certain key foundation skills to ensure adequate competence and baseline knowledge to facilitate progression through postgraduate training pathways will result in trainees having to meet such objectives sooner. Urgent dental care for patients during the COVID-19 pandemic Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic abstract: nan url: https://doi.org/10.1038/s41415-020-1696-2 doi: 10.1038/s41415-020-1696-2 id: cord-262598-zk192s0x author: Tatu, Laurent title: Guillain–Barré syndrome in the COVID-19 era: another occasional cluster? date: 2020-06-23 words: 702.0 sentences: 51.0 pages: flesch: 55.0 cache: ./cache/cord-262598-zk192s0x.txt txt: ./txt/cord-262598-zk192s0x.txt summary: entitled ''Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster?'' [1] . The authors reported an unusual cluster of seven patients affected by Guillain-Barré syndrome (GBS) in an Italian region (Friuli Venezia-Giulia), which coincided with the descending curve of the COVID-19 pandemic. In the public health crisis of March-April 2020, we encountered an unusually high number of GBS cases, admitting seven patients. Some authors report a possible correlation between acute symptomatic COVID-19 infection and GBS [4, 5] . Nevertheless, the issue raised by Gigli''s cases and those in this series is different: an abnormally high frequency of GBS amid the SARS-CoV-2 pandemic in patients without a COVID infection. Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster? Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré syndrome related to COVID-19 infection abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32577868/ doi: 10.1007/s00415-020-10005-3 id: cord-274841-rcdoewwv author: Tay, Matthew Zirui title: The trinity of COVID-19: immunity, inflammation and intervention date: 2020-04-28 words: 7186.0 sentences: 383.0 pages: flesch: 43.0 cache: ./cache/cord-274841-rcdoewwv.txt txt: ./txt/cord-274841-rcdoewwv.txt summary: Monoclonal antibodies targeting the When severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells expressing the surface receptors angiotensin-converting enzyme 2 (ACE2) and TMPRSS2, the active replication and release of the virus cause the host cell to undergo pyroptosis and release damageassociated molecular patterns, including ATP, nucleic acids and ASC oligomers. While there are no clinical trials specifically testing these drugs against COVID-19 at the time of writing, when camostat mesylate was tested on SARS-CoV-2 isolated from a patient, it prevented entry of the virus into lung cells 44, 50 . Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Neutralizing antibodies in patients with severe acute respiratory syndrome-associated Nature reviews | Immunology coronavirus infection abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the fundamental physiological and immunological processes underlying the clinical manifestations of COVID-19 is vital for the identification and rational design of effective therapies. Here, we provide an overview of the pathophysiology of SARS-CoV-2 infection. We describe the interaction of SARS-CoV-2 with the immune system and the subsequent contribution of dysfunctional immune responses to disease progression. From nascent reports describing SARS-CoV-2, we make inferences on the basis of the parallel pathophysiological and immunological features of the other human coronaviruses targeting the lower respiratory tract — severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Finally, we highlight the implications of these approaches for potential therapeutic interventions that target viral infection and/or immunoregulation. url: https://www.ncbi.nlm.nih.gov/pubmed/32346093/ doi: 10.1038/s41577-020-0311-8 id: cord-255734-038xu4hq author: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 words: 5334.0 sentences: 263.0 pages: flesch: 44.0 cache: ./cache/cord-255734-038xu4hq.txt txt: ./txt/cord-255734-038xu4hq.txt summary: The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets abstract: The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Researchers around the world pooled their scientific resources and shared early data in an unprecedented manner in light of the impending public health crisis. There are still large gaps in knowledge about the pathogenesis of this virus. While significant advances have been made in the development of animal models, the practicality of their use may be hampered by a lack of pathological similarity with human disease. Described here are issues related to progress in vaccine development and the obstacles that lie ahead for both researchers and regulatory agencies. url: https://www.ncbi.nlm.nih.gov/pubmed/16191455/ doi: 10.1016/j.vaccine.2005.08.102 id: cord-018441-r6wwpfcy author: Taylor, Milton W. title: Emerging Viruses date: 2014-07-22 words: 3674.0 sentences: 210.0 pages: flesch: 63.0 cache: ./cache/cord-018441-r6wwpfcy.txt txt: ./txt/cord-018441-r6wwpfcy.txt summary: Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). abstract: Emerging viruses are viruses that appear suddenly in the human population. These are viruses to which man has no history of exposure and thus no or limited immunity; they are not new evolutionary creations, but are viruses than man meets due to environmental changes, such as deforestation, entering into new habitats, or viruses that are transmitted from one species of animal to humans. Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of “new” respiratory viruses infecting man. It is possible that unknown emerging viruses are the cause of death, often listed as “death due to an unknown cause,” as in the retrospective cases of HIV. Emerging viruses might also include poliovirus and influenza, since their introduction into the human population is (was) often sudden and due to changes in the environment or due to contact with other animal species. For examples, polio was a result of changes in sanitation in the countries of North America and Western Europe, and influenza is constantly jumping from aquatic birds to man and other animal species where genomic reassortment occurs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123315/ doi: 10.1007/978-3-319-07758-1_20 id: cord-102456-6jt4ksha author: Taylor-Cousar, Jennifer L. title: How I Do It: Restarting Respiratory Clinical Research in the Era of the COVID19 Pandemic date: 2020-11-13 words: 4068.0 sentences: 168.0 pages: flesch: 35.0 cache: ./cache/cord-102456-6jt4ksha.txt txt: ./txt/cord-102456-6jt4ksha.txt summary: However, now that we have navigated the initial surge of SARS-CoV-2 cases, many are considering how to reintroduce non-COVID-19 clinical research conduct while protecting participants, staff and ensuring data integrity. Here we review key considerations and suggest a step-wise approach for resuming clinical research including observational research, registry trials, and interventional trials, as well as potential data confounding related to COVID-19 infections that are important to consider as research studies restart and data are analyzed. In the spirit of "Do No Harm", it is critical that institutional policies and processes are in place to ensure that there is no significant additional risk of contracting viral respiratory or other infections in the normal course of participation in research studies; now during the COVID-19 pandemic, these principles are even more critical. Throughout the subject''s participation in clinical research during the pandemic, she expressed her appreciation for the opportunity to continue in the study from which she believed she was benefiting, with minimal risk of exposure to infection from SARS-CoV-2. abstract: The clinical research we do to improve our understanding of disease and development of new therapies has temporarily been paused or delayed as the global healthcare enterprise has focused its attention on those impacted by COVID-19. While rates of SARS-CoV-2 infection are decreasing in many areas, many locations continue to have a high prevalence of infection. Nonetheless, research must continue and institutions are considering approaches to re-starting non-COVID related clinical investigation. Those restarting respiratory research must navigate the added planning challenges that take into account outcome measures that require aerosol generating procedures. Such procedures potentially increase risk of transmission of SARS-CoV-2 to research staff, utilize limited personal protective equipment, and require conduct in negative pressure rooms. One must also be prepared to address the potential for COVID-19 resurgence. With research subject and staff safety and maintenance of clinical trial data integrity as the guiding principles, here we review key considerations and suggest a step-wise approach for resuming respiratory clinical research. url: https://api.elsevier.com/content/article/pii/S0012369220351400 doi: 10.1016/j.chest.2020.11.001 id: cord-344383-7s4gnxs4 author: Tee, Augustine K.H. title: Atypical SARS in Geriatric Patient date: 2004-02-17 words: 2056.0 sentences: 125.0 pages: flesch: 52.0 cache: ./cache/cord-344383-7s4gnxs4.txt txt: ./txt/cord-344383-7s4gnxs4.txt summary: We describe an atypical presentation of severe acute respiratory syndrome (SARS) in a geriatric patient with multiple coexisting conditions. On the basis of epidemiologic data (contact tracing linking her to one of the three original index cases in Singapore) (12) , the index patient''s cause of death was determined to be SARS (Figure 3 ). Since the issue of a global alert on atypical pneumonia by the World Health Organization on March 12, reported cases of SARS increased daily and appeared in other countries, including Canada, the United States, Europe, and Africa. Our case serves to highlight atypical signs and symptoms of SARS, especially the resolving fever, delay in establishing a positive contact history, and the nonspecific chest radiographic appearance that could be affected by concurrent coexisting conditions, such as cardiac failure. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: We describe an atypical presentation of severe acute respiratory syndrome (SARS) in a geriatric patient with multiple coexisting conditions. Interpretation of radiographic changes was confounded by cardiac failure, with resolution of fever causing delayed diagnosis and a cluster of cases. SARS should be considered even if a contact history is unavailable, during an ongoing outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/15030694/ doi: 10.3201/eid1002.030322 id: cord-302813-963ypqow author: Tegally, H. title: Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. date: 2020-10-30 words: 3543.0 sentences: 200.0 pages: flesch: 59.0 cache: ./cache/cord-302813-963ypqow.txt txt: ./txt/cord-302813-963ypqow.txt summary: Through the unprecedented sharing of SARS-CoV-2 sequences during this pandemic, including from one of the first cases in Wuhan, China (MN908947.3) 2 , genomic epidemiology investigations globally are playing a major role in characterizing and understanding this emerging virus [4] [5] [6] [7] [8] [9] . The profile of SARS-CoV-2 epidemiological progression in South Africa was largely influenced by the implementation of lockdown measures in the early phases of the epidemic and the subsequent easing of these measures. We focused on the three largest monophyletic lineage clusters (C.1, B.1.1.54, B.1.1.56,) that spread in South Africa during lockdown and then grew into large transmission clusters during the peak infections phase of the epidemic (Fig 1C) . Our analysis therefore shows that a number of SARS-CoV-2 lineages, each with unique mutations, emerged within localized epidemics during lockdown even as the introduction of new lineages from outside South Africa was being curbed. abstract: In March 2020, the first cases of COVID-19 were reported in South Africa. The epidemic spread very fast despite an early and extreme lockdown and infected over 600,000 people, by far the highest number of infections in an African country. To rapidly understand the spread of SARS-CoV-2 in South Africa, we formed the Network for Genomics Surveillance in South Africa (NGS-SA). Here, we analyze 1,365 high quality whole genomes and identify 16 new lineages of SARS-CoV-2. Most of these unique lineages have mutations that are found hardly anywhere else in the world. We also show that three lineages spread widely in South Africa and contributed to ~42% of all of the infections in the country. This included the first identified C lineage of SARS-CoV-2, C.1, which has 16 mutations as compared with the original Wuhan sequence. C.1 was the most geographically widespread lineage in South Africa, causing infections in multiple provinces and in all of the eleven districts in KwaZulu-Natal (KZN), the most sampled province. Interestingly, the first South-African specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were controlled. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify and control the spread of SARS-CoV-2. url: http://medrxiv.org/cgi/content/short/2020.10.28.20221143v1?rss=1 doi: 10.1101/2020.10.28.20221143 id: cord-331825-dwi350c0 author: Teherani, Mehgan F title: Burden of illness in households with SARS-CoV-2 infected children date: 2020-08-11 words: 1629.0 sentences: 117.0 pages: flesch: 63.0 cache: ./cache/cord-331825-dwi350c0.txt txt: ./txt/cord-331825-dwi350c0.txt summary: We investigated the dynamics of illness among household members of SARS-CoV-2 infected children that received medical care (n=32). To address this knowledge gap, we utilized a prospective registry of laboratory-confirmed pediatric COVID-19 cases and conducted contact tracing of household members to characterize the presumed transmission before and after the child''s diagnosis. We defined the suspected index case as the first person (child or adult) to report symptoms or test positive for SARS-CoV-2 in the household, documented 14 days prior to, during, or after symptoms of other family members. Because pediatric patients are more likely to be asymptomatic or show mild symptoms, it has been challenging to define their role in SARS-CoV-2 household transmission, which this study aimed to address. In our study of child-to-adult transmission cases, children were symptomatic for at least 4 days prior to seeking care, the time period when they were most likely to be infectious to other household members 5,9 . abstract: We investigated the dynamics of illness among household members of SARS-CoV-2 infected children that received medical care (n=32). We identified 144 household contacts (HCs): 58 children and 86 adults. Forty-six percent of HCs developed symptoms consistent with COVID-19 disease. Child-to-adult transmission was suspected in 7 cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32780809/ doi: 10.1093/jpids/piaa097 id: cord-016844-lq2bgu7a author: Teksam, Ozlem title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective date: 2013-05-29 words: 3932.0 sentences: 206.0 pages: flesch: 45.0 cache: ./cache/cord-016844-lq2bgu7a.txt txt: ./txt/cord-016844-lq2bgu7a.txt summary: title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective Invasive mechanical ventilation (IMV) is a critical intervention in many cases of acute respiratory failure (ARF), but there are absolute risks associated with endotracheal intubation (ETI). Additionally, the World Health Organization''s interim guidelines on the prevention and control of acute respiratory diseases associated with health care have included NIV among the aerosol-generating procedures in which there is possibly an increased risk of respiratory pathogen transmission [ 11 ] . Nonetheless, after the most important two viral pandemics during the last decade, especially the last one with infl uenza A(H1N1), most of the societies including above-mentioned and the European Respiratory Society, European Society of Intensive Care Medicine, and The American Association for Respiratory Care have recommended that NIV not be used to treat ARF due to H1N1, particularly in severely ill patients. abstract: Respiratory problems are common symptoms in children and common reason for visits to the pediatric emergency department (PED) and admission to the pediatric intensive care unit (PICU). Although the great majority of cases are benign and self-limited, requiring no intervention, some patients need respiratory support. Invasive mechanical ventilation (IMV) is a critical intervention in many cases of acute respiratory failure (ARF), but there are absolute risks associated with endotracheal intubation (ETI). On the other hand, noninvasive ventilation (NIV) is an extremely valuable alternative to IMV. A major reason for the increasing use of NIV has been the desire to avoid the complications of IMV. It is generally much safer than IMV and has been shown to decrease resource utilization. Its use also avoids the complications and side effects associated with ETI, including upper airway trauma, laryngeal swelling, postextubation vocal cord dysfunction, nosocomial infections, and ventilator-associated pneumonia. There are a number of advantages of NIV including leaving the upper airway intact, preserving the natural defense mechanisms of the upper airways, decreasing the need for sedation, maintaining the ability to talk while undergoing NIV, and reducing the length of hospitalization and its associated costs [1–3]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121261/ doi: 10.1007/978-3-7091-1496-4_29 id: cord-350352-wgppovfx author: Temmam, Sarah title: Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus date: 2020-08-29 words: 2470.0 sentences: 125.0 pages: flesch: 54.0 cache: ./cache/cord-350352-wgppovfx.txt txt: ./txt/cord-350352-wgppovfx.txt summary: In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others (n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc.) compatible with COVID-19 infection. We investigated the presence of SARS-CoV-2 infection of domestic cats (n = 9) and dogs (n = 12) living in close contact with a cluster of French veterinary students, their owners (n = 18), whose median age was 23 years (21-28 years). Although based on a small cluster of 21 domestic pets, our cross-sectional study based on the antibody response one month after exposure to the index case points to J o u r n a l P r e -p r o o f Journal Pre-proof undetectable interspecific transmission of the SARS-CoV-2 virus between COVID-19 patients and domestic dogs or cats under natural exposure conditions. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, in 2019, is responsible for the COVID-19 pandemic. It is now accepted that the wild fauna, probably bats, constitute the initial reservoir of the virus, but little is known about the role pets can play in the spread of the disease in human communities, knowing the ability of SARS-CoV-2 to infect some domestic animals. In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others (n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc.) compatible with COVID-19 infection. Although a few pets presented many clinical signs indicative for a coronavirus infection, no antibodies against SARS-CoV-2 were detectable in their blood one month after the index case was reported, using an immunoprecipitation assay. These original data can serve a better evaluation of the host range of SARS-CoV-2 in natural environment exposure conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/32904469/ doi: 10.1016/j.onehlt.2020.100164 id: cord-269568-vwkawh6x author: Ten Hulzen, Richard D. title: Impact of Hearing Loss and Universal Face Masking in the COVID-19 Era. date: 2020-08-03 words: 1084.0 sentences: 65.0 pages: flesch: 48.0 cache: ./cache/cord-269568-vwkawh6x.txt txt: ./txt/cord-269568-vwkawh6x.txt summary: Abbreviations: COVID-19 = coronavirus disease 2019; dB = decibel; ED = Emergency Department; FFP = filtering face piece; FM = frequency modulation; Hz = Hertz; ICU = Intensive Care Unit; N95 mask = a particulate-filtering face mask that filters at least 95% of airborne particles; PPE = personal protective equipment; PSAPs -personal sound amplification products; SARS-CoV-2 = severe acute respiratory syndrome-coronavirus-2. We''d like to call attention to the negative impacts of universal masking and social distancing in both health-care and community settings for individuals with hearing loss. Social Healthcare professionals should recognize that, with the loss of visual cues (i.e., lip reading) and support systems (e.g., family members), current COVID-19 policies such as universal masking, social distancing, and unaccompanied patients may "unmask" significant hearing loss-related issues that previously had been diminished or ignored. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0025619620308430?v=s5 doi: 10.1016/j.mayocp.2020.07.027 id: cord-313082-n3bo9jw1 author: Tenenbein, Paul title: The case for routine screening for SARS-CoV-2 before surgery date: 2020-06-03 words: 3816.0 sentences: 269.0 pages: flesch: 58.0 cache: ./cache/cord-313082-n3bo9jw1.txt txt: ./txt/cord-313082-n3bo9jw1.txt summary: Herein, we focus on one specific aspect of this question, namely whether all surgical patients should, in addition to detailed clinical screening (i.e., exposure risk and symptoms) for COVID-19, undergo routine preoperative testing for SARS-CoV-2 with nasopharyngeal swabbing and nucleicacid-based testing. Dans cet éditorial, nous nous intéressons à un aspect en particulier de cette question : faudrait-il faire passer un test préopératoire systématique pour dépister le SARS-CoV-2 à l''aide d''un écouvillon nasopharyngé et d''un test d''amplification des acides nucléiques à tous les patients chirurgicaux, en plus du dépistage clinique détaillé (c.-à-d. É tant donné le risque que la COVID-19 pose aux patients chirurgicaux, il est conseillé de remettre toute intervention qui peut être retardée en toute sécurité ou d''envisager des options thérapeutiques non chirurgicales, le cas échéant, pour tout patient positif au SARS-CoV-2. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32495121/ doi: 10.1007/s12630-020-01730-4 id: cord-289719-64ugdvfe author: Tenforde, Mark W. title: Characteristics of Adult Outpatients and Inpatients with COVID-19 — 11 Academic Medical Centers, United States, March–May 2020 date: 2020-07-03 words: 3166.0 sentences: 148.0 pages: flesch: 46.0 cache: ./cache/cord-289719-64ugdvfe.txt txt: ./txt/cord-289719-64ugdvfe.txt summary: During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. To explore the spectrum of illness across health care settings and potential community SARS-CoV-2 exposures after issuance of national social distancing guidelines on March 16, 2020 (4), 11 academic medical centers in nine states conducted telephone-based surveys of a sample of patients with positive SARS-COV-2 test results during April 15-May 24, 2020 (testing dates = March 31-May 10, 2020). abstract: Descriptions of coronavirus disease 2019 (COVID-19) in the United States have focused primarily on hospitalized patients. Reports documenting exposures to SARS-CoV-2, the virus that causes COVID-19, have generally been described within congregate settings, such as meat and poultry processing plants (1) and long-term care facilities (2). Understanding individual behaviors and demographic characteristics of patients with COVID-19 and risks for severe illness requiring hospitalization can inform efforts to reduce transmission. During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. Respondents were contacted 14-21 days after SARS-CoV-2 testing and asked about their demographic characteristics, underlying chronic conditions, symptoms experienced on the date of testing, and potential exposures to SARS-CoV-2 during the 2 weeks before illness onset (or the date of testing among those who did not report symptoms at the time of testing). Among 350 interviewed patients (271 [77%] outpatients and 79 [23%] inpatients), inpatients were older, more likely to be Hispanic and to report dyspnea than outpatients. Fewer inpatients (39%, 20 of 51) reported a return to baseline level of health at 14-21 days than did outpatients (64%, 150 of 233) (p = 0.001). Overall, approximately one half (46%) of patients reported known close contact with someone with COVID-19 during the preceding 2 weeks. This was most commonly a family member (45%) or a work colleague (34%). Approximately two thirds (64%, 212 of 333) of participants were employed; only 35 of 209 (17%) were able to telework. These findings highlight the need for screening, case investigation, contact tracing, and isolation of infected persons to control transmission of SARS-CoV-2 infection during periods of community transmission. The need for enhanced measures to ensure workplace safety, including ensuring social distancing and more widespread use of cloth face coverings, are warranted (3). url: https://doi.org/10.15585/mmwr.mm6926e3 doi: 10.15585/mmwr.mm6926e3 id: cord-290863-f0wpsaip author: Tenforde, Mark W. title: Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 date: 2020-07-31 words: 2969.0 sentences: 146.0 pages: flesch: 51.0 cache: ./cache/cord-290863-f0wpsaip.txt txt: ./txt/cord-290863-f0wpsaip.txt summary: During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. At 14-21 days from the test date, CDC personnel interviewed the randomly sampled patients or their proxies by telephone to obtain self-reported baseline demographic, socioeconomic, and underlying health information, including the presence of chronic medical conditions. abstract: Prolonged symptom duration and disability are common in adults hospitalized with severe coronavirus disease 2019 (COVID-19). Characterizing return to baseline health among outpatients with milder COVID-19 illness is important for understanding the full spectrum of COVID-19-associated illness and tailoring public health messaging, interventions, and policy. During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. Interviews were conducted 14-21 days after the test date. Respondents were asked about demographic characteristics, baseline chronic medical conditions, symptoms present at the time of testing, whether those symptoms had resolved by the interview date, and whether they had returned to their usual state of health at the time of interview. Among 292 respondents, 94% (274) reported experiencing one or more symptoms at the time of testing; 35% of these symptomatic respondents reported not having returned to their usual state of health by the date of the interview (median = 16 days from testing date), including 26% among those aged 18-34 years, 32% among those aged 35-49 years, and 47% among those aged ≥50 years. Among respondents reporting cough, fatigue, or shortness of breath at the time of testing, 43%, 35%, and 29%, respectively, continued to experience these symptoms at the time of the interview. These findings indicate that COVID-19 can result in prolonged illness even among persons with milder outpatient illness, including young adults. Effective public health messaging targeting these groups is warranted. Preventative measures, including social distancing, frequent handwashing, and the consistent and correct use of face coverings in public, should be strongly encouraged to slow the spread of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32730238/ doi: 10.15585/mmwr.mm6930e1 id: cord-325324-kh2aal5n author: Teng, Shaolei title: ACE2 Enhance Viral Infection or Viral Infection Aggravate the Underlying Diseases date: 2020-08-06 words: 4403.0 sentences: 274.0 pages: flesch: 53.0 cache: ./cache/cord-325324-kh2aal5n.txt txt: ./txt/cord-325324-kh2aal5n.txt summary: SARS-CoV-2 spike protein (S) is cleaved by the human furin enzyme to generate S1, which binds to the host receptor, ACE-2. It is possible that the released free spike or the cleaved S1 protein in the blood might bind to cellular membrane ACE2 of heart, artery and alveolar lung cells to block the conversion of Angiotensin II to Ang-(1-7) and/or Angiotensin I to Ang-(1-9), which is consistent with a previous experimental result on SARS-CoV-1 (59) . Therefore, our hypothesis, as shown in the right side of Fig. 1 as "Viral aggravating existing diseases", is that comorbidities in COVID-19 patients are aggravated by the infection of SARS-CoV-2 to causes higher fatalities because the viral S protein interacts with ACE2 to inhibit ACE2 function. The claims that COVID-19 disproportionately affects the individuals of minority groups and aged people are not only supported by reported data but also by our hypothesis that SARS-CoV-2 infection generates spike protein that interacts with ACE2 to either exhaust ACE2 or inhibit ACE2 function or both so that the comorbidities are aggravated (Figure 1 ). abstract: ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32832038/ doi: 10.1016/j.csbj.2020.08.002 id: cord-315760-9g8901v6 author: Teng, Xufei title: Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date: 2020-08-30 words: 3532.0 sentences: 182.0 pages: flesch: 59.0 cache: ./cache/cord-315760-9g8901v6.txt txt: ./txt/cord-315760-9g8901v6.txt summary: Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. We have further examined the compositional subtleties among the clades and clusters with 304 a focus on G+C and purine content variability as both contents appear drifting toward optima 305 in SARS-CoV-2 and its relatives ( Figure 5C and 5D). abstract: COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months and a global fight against both is still going on. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. (2) The second abundance group includes: three negative-strand mutations U-to-C, A-to-G, G-to-A and a positive-strand mutation G-to-U generated through an identical mechanism as C-to-U. (3) A clade-associated and biased mutation trend is found attributable to elevated level of the negative-sense strand synthesis. (4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a bioinformatics platform where emerging mutations are mapped on to mostly subtle but fast-adjusting viral proteomes and transcriptomes to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such thoughts and actions are in desperate need, especially in the middle of the War against COVID-19. url: https://doi.org/10.1101/2020.08.26.267781 doi: 10.1101/2020.08.26.267781 id: cord-328695-nptfd6c2 author: Tengs, Torstein title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date: 2020-06-29 words: 1969.0 sentences: 102.0 pages: flesch: 51.0 cache: ./cache/cord-328695-nptfd6c2.txt txt: ./txt/cord-328695-nptfd6c2.txt summary: title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. The presence of s2m in the SARS-CoV-2 genome (GenBank accession MN908947, position 29727-29768) and other members of this group is probably the result of a single horizontal transfer event, predating the divergence of the SARS-related viruses (Tengs, et al. The insect species that contain s2m (and the associated protein) are distantly related, indicating either a deep evolutionary origin with multiple losses or that this genetic construct is also a mobile element, perhaps using viruses as a vector . abstract: Unprecedented quantities of sequence data have been generated from the newly emergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of COVID-19. We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. url: https://doi.org/10.1101/2020.06.29.177030 doi: 10.1101/2020.06.29.177030 id: cord-264970-232stxxo author: Testa, Sophie title: Switch from oral anticoagulants to parenteral heparin in SARS-CoV-2 hospitalized patients date: 2020-04-15 words: 1421.0 sentences: 67.0 pages: flesch: 28.0 cache: ./cache/cord-264970-232stxxo.txt txt: ./txt/cord-264970-232stxxo.txt summary: The development of COVID-19 syndrome in anticoagulated patients, and especially their admission to intensive-care units with acute severe respiratory syndrome (SARS-CoV-2), expose them to specific problems related to their therapy, in addition to those associated with the acute viral infection. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral heparin to avoid the risk of over/under treatment. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease, and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral low-molecular-weight heparin (LMWH) or unfractionated heparin (UH) to avoid the risk of over/under treatment. abstract: The development of COVID-19 syndrome in anticoagulated patients, and especially their admission to intensive-care units with acute severe respiratory syndrome (SARS-CoV-2), expose them to specific problems related to their therapy, in addition to those associated with the acute viral infection. Patients on VKA hospitalized with SARS-CoV-2 show high instability of PT INR due to the variability of vitamin K metabolism, diet, fasting, co-medications, liver impairment, and heart failure. Patients on DOAC are exposed to under/over treatment caused by significant pharmacological interferences. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral heparin to avoid the risk of over/under treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32297089/ doi: 10.1007/s11739-020-02331-1 id: cord-302075-ctd9sutv author: Tetro, Jason A. title: Is COVID-19 receiving ADE from other coronaviruses? date: 2020-02-22 words: 1267.0 sentences: 70.0 pages: flesch: 44.0 cache: ./cache/cord-302075-ctd9sutv.txt txt: ./txt/cord-302075-ctd9sutv.txt summary: One of the most perplexing questions regarding the current COVID-19 coronavirus epidemic is the discrepancy between the severity of cases observed in the Hubei province of China and those occurring elsewhere in the world. ADE also requires prior exposure to similar antigenic epitopes, presumably circulating in local viruses, making it a possible explanation for the observed geographic limitation of severe cases and deaths. Notably, these observations in COVID-19 patients are similar to those who suffered from severe acute respiratory syndrome (SARS) during the 2003 epidemic [4] . Based on this information and the similarity of symptoms to SARS, COVID-19 appears to constitute a major threat to human health justifying the World Health Organization''s declaration of a Public Health Emergency of International Concern. Cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis Anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a pH-and cysteine protease-independent FcgR pathway abstract: One of the most perplexing questions regarding the current COVID-19 coronavirus epidemic is the discrepancy between the severity of cases observed in the Hubei province of China and those occurring elsewhere in the world. One possible answer is antibody dependent enhancement (ADE) of SARS-CoV-2 due to prior exposure to other coronaviruses. ADE modulates the immune response and can elicit sustained inflammation, lymphopenia, and/or cytokine storm, one or all of which have been documented in severe cases and deaths. ADE also requires prior exposure to similar antigenic epitopes, presumably circulating in local viruses, making it a possible explanation for the observed geographic limitation of severe cases and deaths. url: https://www.sciencedirect.com/science/article/pii/S1286457920300344 doi: 10.1016/j.micinf.2020.02.006 id: cord-336938-03366q9t author: Thacker, Vivek V title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date: 2020-08-10 words: 2818.0 sentences: 169.0 pages: flesch: 49.0 cache: ./cache/cord-336938-03366q9t.txt txt: ./txt/cord-336938-03366q9t.txt summary: title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model A combination of qRT-PCR, RNAscope, immunofluorescence, and ELISA measurements are used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 delivered to the apical surface of the epithelial face maintained at an air-liquid interface. We therefore establish a human lung-on-chip model for SARS-CoV-2 infections, and probe the viral growth kinetics, cellular localization and responses to a low dose infection using qRT-PCR, ELISA, RNAscope, immunofluorescence and confocal imaging (Fig. 1J) . Nevertheless, total RNA extracted from the apical and vascular channels of an infected LoC without macrophages at 1 dpi revealed >10 4 genomes in both epithelial and endothelial cells (Fig. 2C ) and genome copy numbers exceeded those for cellular housekeeping gene RNAseP (Fig. 2D ). Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors abstract: Background Severe manifestations of COVID-19 include hypercoagulopathies and systemic endothelialitis. The underlying dynamics of damage to the vasculature, and whether it is a direct consequence of endothelial infection or an indirect consequence of immune cell mediated cytokine storms is unknown. This is in part because in vitro infection models are typically monocultures of epithelial cells or fail to recapitulate vascular physiology. Methods We establish a vascularised lung-on-chip infection model consisting of a co-culture of primary human alveolar epithelial cells (‘epithelial’) and human lung microvascular endothelial cells (‘endothelial’), with the optional addition of CD14+ macrophages to the epithelial side. A combination of qRT-PCR, RNAscope, immunofluorescence, and ELISA measurements are used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 delivered to the apical surface of the epithelial face maintained at an air-liquid interface. Findings SARS-CoV-2 inoculation does not lead to a productive amplification of infectious virions. However, both genomic and antisense viral RNA can be found in endothelial cells within 1-day post infection (dpi) and persist upto 3 dpi. This generates an NF-KB inflammatory response typified by IL-6 secretion and a weak antiviral interferon response even in the absence of immune cells. Endothelial inflammation leads to a progressive loss of barrier integrity, a subset of cells also shows a transient hyperplasic phenotype. Administration of Tocilizumab slows the loss of barrier integrity but does not reduce the occurrence of the latter. Interpretation Endothelial infection can occur through basolateral transmission from infected epithelial cells at the air-liquid interface. SARS-CoV-2 mediated inflammation occurs despite the lack of rapid viral replication and the consequences are cell-type dependent. Infected endothelial cells might be a key source of circulating IL-6 in COVID-19 patients. Vascular damage occurs independently of immune-cell mediated cytokine storms, whose effect would only exacerbate the damage. Finding Core support from EPEL. url: https://doi.org/10.1101/2020.08.10.243220 doi: 10.1101/2020.08.10.243220 id: cord-322503-fynprt6f author: Thakur, Aarzoo title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 words: 3527.0 sentences: 210.0 pages: flesch: 48.0 cache: ./cache/cord-322503-fynprt6f.txt txt: ./txt/cord-322503-fynprt6f.txt summary: Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. To address this possibility, we utilized physiologically-based pharmacokinetic (PBPK) modeling to simulate the unbound lung concentration of lopinavir achieved by 400/100 mg twice daily dose of lopinavir/ritonavir in both Caucasians and Chinese populations. 14, 15 Therefore, we derived unbound EC 50 (EC 50,unbound ) values against SARS-CoV-2 from various literature reports and compared it against the predicted C u,lung values to determine if clinically used doses of 400/100 mg twice a day would reach efficacious lung concentrations in Caucasian and Chinese populations. The impact of protein binding on PK/PD assessments were then assessed by comparing the predicted total and unbound lung concentrations of 400/100 mg twice daily lopinavir/ritonavir with EC 50 and EC 50,unbound values of lopinavir against SARS-CoV-2 respectively. abstract: Lopinavir/ritonavir, originally developed for treating the human immunodeficiency virus (HIV), is currently undergoing clinical studies for treating the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Although recent reports suggest that lopinavir exhibits in vitro efficacy against SARS‐CoV‐2, it is a highly protein bound drug and it remains unknown if it reaches adequate in vivo unbound (free) concentrations in lung tissue. We built a physiologically‐based pharmacokinetic (PBPK) model of lopinavir/ritonavir in Caucasian and Chinese populations. Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. The model was validated against multiple observed clinical datasets for single and repeated dosing of lopinavir/ritonavir. Predicted pharmacokinetic parameters such as the maximum plasma concentration, area under the plasma concentration‐time profile, oral clearance, half‐life and minimum plasma concentration at steady state were within two‐fold of clinical values for both populations. Using the current lopinavir/ritonavir regimen of 400/100 mg twice daily, lopinavir does not achieve sufficient free lung concentrations for efficacy against SARS‐CoV‐2. Although the Chinese population reaches greater plasma and lung concentrations as compared to Caucasians, our simulations suggest that a significant dose increase from the current clinically used dosing regimen is necessary to reach the EC(50,unbound) value for both populations. Based on safety data, higher doses would likely lead to QT prolongation and gastrointestinal disorders (nausea, vomiting and diarrhea), thus, any dose adjustment must be carefully weighed alongside these safety concerns. url: https://www.ncbi.nlm.nih.gov/pubmed/32767755/ doi: 10.1002/cpt.2014 id: cord-345929-z7yfegr5 author: Thakur, Suman S. title: Proteomics and Its Application in Pandemic Diseases date: 2020-11-06 words: 1355.0 sentences: 94.0 pages: flesch: 39.0 cache: ./cache/cord-345929-z7yfegr5.txt txt: ./txt/cord-345929-z7yfegr5.txt summary: found that the antimalarial drug metaquine and anti-HIV antiretroviral saquinavir interact with four SARS-CoV-2 receptors, including Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S protein), interacting with human ACE2; therefore, they may be repurposed for COVID-19 treatment. Furthermore, Maffucci and Contini used an in silico approach to find drug candidates against the main proteinase and spike protein of SARS-CoV-2. suggested that the antigenic peptides generated from the S1 spike glycoprotein of SARS-CoV-2 using aminopeptidases ERAP1, ERAP2, and IRAP might be helpful in selecting better epitopes for immunogenic studies and the design of a vaccine for COVID-19. Interestingly, a computational method was used to find an allosteric site on the SARS-CoV-2 spike protein by Di Paola et al., as its detection would weaken the spike−ACE2 interaction and thereby reduce the viral infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33153265/ doi: 10.1021/acs.jproteome.0c00824 id: cord-277907-x6387i7b author: Tham, Sai Meng title: Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020 date: 2020-11-17 words: 922.0 sentences: 59.0 pages: flesch: 50.0 cache: ./cache/cord-277907-x6387i7b.txt txt: ./txt/cord-277907-x6387i7b.txt summary: Coronavirus disease (COVID-19) and tuberculosis (TB) developed in 4 foreign workers living in dormitories in Singapore during April–May 2020. Clinical manifestations and atypical radiographic features of COVID-19 led to the diagnosis of TB through positive interferon-gamma release assay and culture results. Pleural fluid analysis revealed a lymphocytic exudative effusion with an adenosine deaminase (ADA) level of 130 U/L (reference range <40 U/L), but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 112 U/L and interleukin-6 (IL-6) level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 62 U/L and an IL-6 level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. tuberculosis and SARS-CoV-2 in patients with atypical radiographic features of COVID-19. abstract: Coronavirus disease (COVID-19) and tuberculosis (TB) developed in 4 foreign workers living in dormitories in Singapore during April–May 2020. Clinical manifestations and atypical radiographic features of COVID-19 led to the diagnosis of TB through positive interferon-gamma release assay and culture results. During the COVID-19 pandemic, TB should not be overlooked. url: https://www.ncbi.nlm.nih.gov/pubmed/32667283/ doi: 10.3201/eid2611.202752 id: cord-277496-9ss09g6h author: Thaweerat, Wajana title: Current evidence on pancreatic involvement in SARS-CoV-2 infection date: 2020-05-27 words: 945.0 sentences: 66.0 pages: flesch: 42.0 cache: ./cache/cord-277496-9ss09g6h.txt txt: ./txt/cord-277496-9ss09g6h.txt summary: SARS-CoV-2, the infectious agent of COVID-19, attached to angiotensin-converting enzyme 2 (ACE2) at cell surface which act as a receptor for viral entry into host cells. 5 Chinese case series reported 9 patients with mild elevation of pancreatic enzymes less than triple of upper limit of normal which does not reach the cut-point for diagnosis and did not provide other supported evidence to fulfill the criteria of diagnosing acute pancreatitis such as characteristics of abdominal pain or imaging findings. 8 Acute pancreatitis in severe COVID-19 patients may result from direct attack of SARS-CoV-2 to pancreatic acinar cells or uncontrollable systemic inflammatory response from cytokine storm syndrome leading to multi-organ dysfunction including pancreatic injury. 14 Therefore, further autopsy of COVID-19 cases still required to provide histological evidence of SARS-CoV-2 infection in pancreatic cells. In conclusion, current evidence of pancreatic manifestation in COVID-19 patients are limited which further investigation is essential to unravel consequences of SARS-CoV-2 infection to both endocrine and exocrine function of pancreas. abstract: nan url: https://doi.org/10.1016/j.pan.2020.05.015 doi: 10.1016/j.pan.2020.05.015 id: cord-026111-pb3r74uq author: Thede, Christian title: Mögliche Therapiestrategien bei Covid-19-Erkrankungen mit chinesischen Arzneimitteln date: 2020-06-05 words: 7593.0 sentences: 1140.0 pages: flesch: 61.0 cache: ./cache/cord-026111-pb3r74uq.txt txt: ./txt/cord-026111-pb3r74uq.txt summary: Abschließend werden vorläufige Behandlungsvorschläge mit chinesischen Arzneimitteln für das offenbar zentrale Dysharmoniemuster -eine Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) und der Transformation von Flüssigkeiten im Rahmen einer Akkumulation von humor ("Feuchtigkeit", shi) mit Toxischem − für die sich bei schweren Verläufen entwickelnde Pneumonie vorgestellt. Wie in den meisten anderen Rezepturen aus diesem Therapieprotokoll findet sich auch hier Ephedrae herba (Mahuang) in Kombination mit aromatischen Arzneien sowohl zur Elimination der Akkumulation von humor ("Feuchtigkeit", shi) als auch der Entfaltung des qi pulmonale (Qi des Fk "Lunge", feiqi). Obwohl das Krankheitsmuster "yidu" (Epidemisch-Toxisches) genannt wird, wird auch hier primär die Kombination von "Dekokt mit Ephedra, Prunus armeniaca, Gypsum und Glycyrrhiza" (Maxing shigan tang) mit aromatischen und diuretischen Arzneien zur Lösung der humor-Akkumulation ("Feuchtigkeit", shi) und somit der Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) eingesetzt. abstract: In view of the severe corona virus pandemic and the not yet foreseeable availability of causal therapy approaches (vaccination, antiviral drugs), it is of great importance to know what Chinese medicine can contribute to the treatment of Covid 19. According to a WHO report published in 2004, concerning the 2003 SARS epidemic caused by SARS-CoV-1, Chinese medicine was used in China both preventively and therapeutically in addition to Western medicine. In both these preventive and curative roles, treatment proved to be significantly effective. During the current outbreak of SARS-CoV-2, about 60,000 Covid 19 patients were treated with Chinese medicine in the Wuhan region alone by the end of February 2020. The first part of this paper provides a summarizing overview of a number of sources with treatment recommendations and experiences of different clinics, working groups and official bodies. In the second part - based on currently known information — the author voices his own considerations on pathophysiology and important therapeutic principles. Finally, he presents preliminary treatment proposals using Chinese medicinal remedies for what appear to be the central pattern of the disorder - a blockage of pulmonary qi and the transformation of fluids in the context of an accumulation of dampness /humor with toxicity and, in severe cases, development into pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273822/ doi: 10.1007/s00052-020-0260-0 id: cord-034021-6h5h3zow author: Thede, Christian title: COVID-19 – Therapiemöglichkeiten mit chinesischen Arzneimitteln in der Akutphase und Rekonvaleszenz date: 2020-10-20 words: 1599.0 sentences: 204.0 pages: flesch: 46.0 cache: ./cache/cord-034021-6h5h3zow.txt txt: ./txt/cord-034021-6h5h3zow.txt summary: Wenngleich diese Berichte noch mit einer gewissen Vorsicht zu betrachten sind und die Ergebnisse erster kontrollierter randomisierter Studien zum Einsatz von CAM bei COVID-19 noch ausstehen, kann der Einsatz chinesischer Medizin eine Bereicherung des zur Zeit noch sehr kargen Spektrums an Therapiemöglichkeiten bei SARS-CoV-2-Infektionen darstellen. In der vorliegenden Arbeit sollen, basierend auf dem in China entwickelten Konsens zum dominierenden Krankheitsmechanismus und der daraufhin unter der Ägide der staatlichen Gesundheitsbehörden entwickelten Therapieprotokolle [5] , Therapieoptionen für ausgewählte Krankheitsphasen einer COVID-19-Erkrankung vorgestellt werden: zum einen für die Phase der beginnenden Pneumonie, also für spätambulante bis frühstationäre Stadien, und zum anderen für mögliche Entwicklungen nach überstandener Akuterkrankung, also poststationäre Stadien mit klinischen Problemen. Dazu gehören persistierende restriktive Ventilationsstörungen oder eine Fatigue-Symptomatik, die angesichts der zunehmenden Zahl von Personen, die eine COVID-19-Erkrankung durchgemacht haben, wachsende Bedeutung erlangen und für welche die etablierte Medizin bisher keine Lösungen gefunden hat. Während coronavirusassoziierte Fatigue-Symptomatik bisAngesichts der persistierenden SARS-CoV-2-Pandemie und noch immer mangelnder Therapieoptionen werden in der vorliegenden Arbeit Therapiemöglichkeiten mit chinesischen Arzneimitteln erörtert, die sich in ersten Beobachtungsstudien als Erfolg versprechend erwiesen haben. abstract: In light of the persistent SARS-CoV‑2 pandemic and the current lack of treatment options, this work discusses therapeutic options using Chinese herbal medicines that have shown promise in initial observational studies. In addition, a therapeutic option for the increasing number of postinfectious states of weakness (fatigue symptoms) is presented, which in selected cases can be viewed as a “lesser yang syndrome” and treated with promise. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574989/ doi: 10.1007/s42212-020-00316-x id: cord-352796-6einbent author: Theodore Coroneo, Minas title: The eye as the discrete but defensible portal of coronavirus infection date: 2020-05-21 words: 5340.0 sentences: 259.0 pages: flesch: 44.0 cache: ./cache/cord-352796-6einbent.txt txt: ./txt/cord-352796-6einbent.txt summary: The virus may bind to corneal and conjunctival angiotensin converting enzyme 2 (ACE2) receptors and potentially to the lipophilic periocular skin and superficial tear film with downstream carriage into the nasopharynx and subsequent access to the lungs and gut. A combination such as hydroxychloroquine, azithromycin and zinc, all of which have previously been used topically in the eye and which work at least in part by blocking ACE2 receptors, may offer a safe, cost-effective and resource-sparing intervention. At the height of the 1918 world influenza epidemic, a landmark paper appeared, proposing transmission of acute respiratory infections via the eye and lacrimal-nasal pathway (5) (Figure 1) . Table 2 summarises the drugs that have been identified as potential treatments for coronavirus infection, their efficacy (in vitro and in vivo) and for which there is data (for that agent or a related compound) for previous topical ocular surface usage. abstract: Oculo-centric factors may provide a key to understanding invasion success by SARS-CoV-2, a highly contagious, potentially lethal, virus with ocular tropism. Respiratory infection transmission via the eye and lacrimal-nasal pathway elucidated during the 1918 influenza pandemic, remains to be explored in this crisis. The eye and its adnexae represent a large surface area directly exposed to airborne viral particles and hand contact. The virus may bind to corneal and conjunctival angiotensin converting enzyme 2 (ACE2) receptors and potentially to the lipophilic periocular skin and superficial tear film with downstream carriage into the nasopharynx and subsequent access to the lungs and gut. Adenoviruses and influenza viruses share this ocular tropism and despite differing ocular and systemic manifestations and disease patterns, common lessons, particularly in management, emerge. Slit lamp usage places ophthalmologists at particular risk of exposure to high viral loads (and poor prognosis) and as for adenoviral epidemics, this may be a setting for disease transmission. Local, rather than systemic treatments blocking virus binding in this pathway (advocated for adenovirus) are worth considering. This pathway is accessible with eye drops or aerosols containing drugs which appear efficacious via systemic administration. A combination such as hydroxychloroquine, azithromycin and zinc, all of which have previously been used topically in the eye and which work at least in part by blocking ACE2 receptors, may offer a safe, cost-effective and resource-sparing intervention. url: https://api.elsevier.com/content/article/pii/S1542012420300896 doi: 10.1016/j.jtos.2020.05.011 id: cord-342951-nirue1x4 author: Theophanous, Christos title: Bell’s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-09-04 words: 1454.0 sentences: 92.0 pages: flesch: 52.0 cache: ./cache/cord-342951-nirue1x4.txt txt: ./txt/cord-342951-nirue1x4.txt summary: title: Bell''s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) This is the first reported pediatric case of Bell''s palsy in the setting of SARS-CoV-2 infection. [5, 6] There are limited reports of an association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and Bell''s palsy in adults but this seems to be rare with only two cases reports at the time of this report. Herein, we report the first case of a pediatric patient presenting with acute onset Bell''s Palsy in the setting of SARS-CoV-2 infection. To our knowledge, this is the first report of an association between Bell''s palsy and SARS-CoV-2 in a pediatric patient. Few cases of Bell''s palsy in the setting of SARS-CoV2 infection have been reported in adults and appear to be very infrequent [9, 10] . Our patient''s history of hyper-IgM syndrome may complicate his response to a SARS-CoV-2 infection. abstract: Bell’s palsy is an acute facial paralysis with known association to viral infections. We describe a medically complex 6-year-old male with hyper IgM syndrome who presented with unilateral facial droop and positive SARS-CoV-2 RT-PCR. This is the first reported pediatric case of Bell’s palsy in the setting of SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S0387760420302606 doi: 10.1016/j.braindev.2020.08.017 id: cord-340415-6fte7krp author: Thevarajan, Irani title: Clinical presentation and management of COVID‐19 date: 2020-07-17 words: 4287.0 sentences: 244.0 pages: flesch: 43.0 cache: ./cache/cord-340415-6fte7krp.txt txt: ./txt/cord-340415-6fte7krp.txt summary: In the face of high health care demand during the peak of a pandemic, safe management of low risk patients in the community will likely be essential to preserve hospital capacity for the more severely ill. This position is endorsed by the Australasian Society for Infectious Diseases interim guidelines for the clinical management of COVID-19 in adults, 20 guidelines for the clinical care of people with COVID-19, 19 which state that even where conditional recommendations for use of disease modifying agents are made, whenever possible these should be administered in the context of randomised trials with appropriate ethical approval. 37, 38 However, given the current lack of evidence of clinical benefit and reports of significant limitations of supply of hydroxychloroquine for patients with rheumatological conditions, in March 2020, the Pharmaceutical Society of Australia and the Australasian Society for Infectious Diseases called for immediate cessation of prescribing and dispensing of hydroxychloroquine for indications relating to COVID-19, outside use in approved clinical trials. Specific antiviral therapy in the clinical management of acute respiratory infection with SARS-CoV-2 (COVID-19). abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 led to the declaration of a global pandemic within 3 months of its emergence. The majority of patients presenting with coronavirus disease 2019 (COVID‐19) experience a mild illness that can usually be managed in the community. Patients require careful monitoring and early referral to hospital if any signs of clinical deterioration occur. Increased age and the presence of comorbidities are associated with more severe disease and poorer outcomes. Treatment for COVID‐19 is currently predominantly supportive care, focused on appropriate management of respiratory dysfunction. Clinical evidence is emerging for some specific therapies (including antiviral and immune‐modulating agents). Investigational therapies for COVID‐19 should be used in the context of approved randomised controlled trials. Australian clinicians need to be able to recognise, diagnose, manage and appropriately refer patients affected by COVID‐19, with thousands of cases likely to present over the coming years. url: https://www.ncbi.nlm.nih.gov/pubmed/32677734/ doi: 10.5694/mja2.50698 id: cord-275960-1m6poddy author: Thieme, C. J. title: The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity date: 2020-05-16 words: 3244.0 sentences: 217.0 pages: flesch: 52.0 cache: ./cache/cord-275960-1m6poddy.txt txt: ./txt/cord-275960-1m6poddy.txt summary: Analyzing a cohort of COVID-19 patients with moderate, severe, and critical disease severity, we show that overlapping peptide pools (OPP) of all three proteins can activate SARS-CoV-2-reactive T-cells with a stronger response of CD4+ compared to CD8+ T-cells. Accordingly, very recent studies identified SARS-CoV-2 S-protein reactive T cell responses in patients suffering from moderate, severe, and critical COVID-19 4, 10 . Surprisingly, and in contrast to the endemic SARS-CoV infection, we detected the highest magnitude of CD4 + and CD8 + T cells reactive to S-, M-, and N-proteins in critical COVID-19 (Fig. 3) . Polyfunctional T cells showed higher frequencies in critical COVID-19 patients compared to moderate and severe cases (Fig. 3e ,f,n,o). In line with data showing an association between polyfunctionality and the stage of phenotypic differentiation 17 , we observed higher frequencies of CD8 + T cells with effector memory (TEM)/TEMRA phenotype in critical COVID-19 patients compared to moderate and severe cases (Fig S4) . abstract: Identification of immunogenic targets of SARS-CoV-2 is crucial for monitoring of antiviral immunity and vaccine design. Currently, mainly anti-spike (S)-protein adaptive immunity is investigated. However, also the nucleocapsid (N)- and membrane (M)-proteins should be considered as diagnostic and prophylactic targets. The aim of our study was to explore and compare the immunogenicity of SARS-CoV-2 S-, M- and N-proteins in context of different COVID-19 manifestations. Analyzing a cohort of COVID-19 patients with moderate, severe, and critical disease severity, we show that overlapping peptide pools (OPP) of all three proteins can activate SARS-CoV-2-reactive T-cells with a stronger response of CD4+ compared to CD8+ T-cells. Although interindividual variations for the three proteins were observed, M protein induced the highest frequencies of CD4+ T-cells, suggesting its relevance as diagnostic and vaccination target. Importantly, patients with critical COVID-19 demonstrated the strongest T-cell response, including the highest frequencies of cytokine-producing bi- and trifunctional T-cells, for all three proteins. Although the higher magnitude and superior functionality of SARS-CoV-2-reactive T-cells in critical patients can also be a result of a stronger immunogenicity provided by severe infection, it disproves the hypothesis of insufficient SARS-CoV-2-reactive immunity in critical COVID-19. To this end, activation of effector T-cells with differentiated memory phenotype found in our study could cause hyper-reactive response in critical cases leading to immunopathogenesis. Conclusively, since the S-, M-, and N-proteins induce T-cell responses with individual differences, all three proteins should be evaluated for diagnostics and therapeutic strategies to avoid underestimation of cellular immunity and to deepen our understanding of COVID-19 immunity. url: https://doi.org/10.1101/2020.05.13.20100636 doi: 10.1101/2020.05.13.20100636 id: cord-282821-qvtvpnrr author: Thijsen, Steven title: Elevated nucleoprotein-induced interferon-γ release in COVID-19 patients detected in a SARS-CoV-2 enzyme-linked immunosorbent spot assay date: 2020-06-12 words: 784.0 sentences: 45.0 pages: flesch: 58.0 cache: ./cache/cord-282821-qvtvpnrr.txt txt: ./txt/cord-282821-qvtvpnrr.txt summary: (2) (3) (4) The objective of the present study was to determine the functional T-cell responses to SARS-CoV-2 antigens (mosaic surface protein and nucleoprotein), by using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay, in patients with RT-PCR confirmed COVID-19 (n=27) and healthy controls (n=16). Our results show that the SARS-CoV-2-specific T-cell response measured in the ELISpot versus the dps induced by the mosaic surface protein and the nucleoprotein showed different patterns. In all but one of the 27 COVID-19 cases the T-cell response against the mosaic surface protein was absent or weak, as shown by the ELISpot results which were lower than 20 spot forming cells (SFC). In contrast, the Tcell response against the nucleoprotein measured by the ELISpot assay was elevated (10-150 SFC) in 12 of 19 patients (63%) that were sampled at ≥14 dps ( Fig. 1b) . abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320303959?v=s5 doi: 10.1016/j.jinf.2020.06.015 id: cord-309323-yflng8m3 author: Thomas, T. title: COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status date: 2020-05-16 words: 6928.0 sentences: 387.0 pages: flesch: 40.0 cache: ./cache/cord-309323-yflng8m3.txt txt: ./txt/cord-309323-yflng8m3.txt summary: Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). The current study provides the first comprehensive targeted and untargeted metabolomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to inflammatory markers and renal function. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint described impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients (44), though they also described that progressive increases in disease severity, from mild to severe to critical, correlated with the levels of transcripts for JAK1, STAT1 and 2, interferon alpha 2, interferon alpha receptors 1 and 2, and interferon regulatory factors 1, 4, 5 and 7. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint Serum levels of free fatty acids and acylcarnitines were significantly different when comparing COVID-19positive patients and controls. abstract: Previous studies suggest a role for systemic reprogramming of host metabolism during viral pathogenesis to fuel rapidly expanding viral proliferation, for example by providing free amino acids and fatty acids as building blocks. In addition, general alterations in metabolism can provide key understanding of pathogenesis. However, little is known about the specific metabolic effects of SARS-COV-2 infection. The present study evaluated the serum metabolism of COVID-19 patients (n=33), identified by a positive nucleic acid test of a nasopharyngeal swab, as compared to COVID-19-negative control patients (n=16). Targeted and untargeted metabolomics analyses specifically identified alterations in the metabolism of tryptophan into the kynurenine pathway, which is well-known to be involved in regulating inflammation and immunity. Indeed, the observed changes in tryptophan metabolism correlated with serum interleukin-6 (IL-6) levels. Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). Increased circulating levels of glucose and free fatty acids were also observed, consistent with altered carbon homeostasis in COVID-19 patients. Metabolite levels in these pathways correlated with clinical laboratory markers of inflammation and disease severity (i.e., IL-6 and C-reactive protein) and renal function (i.e., blood urea nitrogen). In conclusion, this initial observational study of the metabolic consequences of COVID-19 infection in a clinical cohort identified amino acid metabolism (especially kynurenine and cysteine/taurine) and fatty acid metabolism as correlates of COVID-19, providing mechanistic insights, potential markers of clinical severity, and potential therapeutic targets. url: https://doi.org/10.1101/2020.05.14.20102491 doi: 10.1101/2020.05.14.20102491 id: cord-309629-7jtnhn65 author: Thomas, Viju title: International society for gynecologic endoscopy (ISGE) guidelines and recommendations on gynecological endoscopy during the evolutionary phases of the SARS-CoV-2 pandemic date: 2020-08-26 words: 4633.0 sentences: 306.0 pages: flesch: 50.0 cache: ./cache/cord-309629-7jtnhn65.txt txt: ./txt/cord-309629-7jtnhn65.txt summary: We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports'' closure (such as using gas filters and smoke evacuation systems). We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports'' closure (such as using gas filters and smoke evacuation systems). did assess the risk of open and laparoscopic surgery to be the same provided the gas/smoke was evacuated safely and water lock filters were used or if gasless laparoscopy was performed [24] . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has raised some important interrogations on minimally invasive gynaecological surgery. The International Society of gynaecological Endoscopists (ISGE) has taken upon itself the task of providing guidance and best practice policies for all practicing gynaecological endoscopists. Factors affecting decision making processes in minimal invasive surgery (MIS) vary depending on factors such as the phase of the pandemic, policies on control and prevention, expertise and existing infrastructure. Our responsibility remains ensuring the safety of all health care providers, ancillary staff and patients during this unusual period. We reviewed the current literature related to gynecological and endoscopic surgery during the Coronavirus Disease 19 (COVID-19) crisis. Regarding elective surgery, universal testing for SARS-CoV-2 infection should be carried out wherever possible 40 h prior to surgery. In case of confirmed positive case of SARS-CoV-2, surgery should be delayed. Priority should be given to relatively urgent cases such as malignancies. ISGE supports medical optimization and delaying surgery for benign non-life-threatening surgeries. When possible, we recommend to perform cases by laparoscopy and to allow early discharges. Any procedure with risk of bowel involvement should be performed by open surgery as studies have found a high amount of viral RNA (ribonucleic acid) in stool. Regarding urgent surgery, each unit should create a risk assessment flow chart based on capacity. Patients should be screened for symptoms and symptomatic patients must be tested. In the event that a confirmed case of SARS-CoV-2 is found, every attempt should be made to optimize medical management and defer surgery until the patient has recovered and only emergency or life-threatening surgery should be performed in these cases. We recommend to avoid intubation and ventilation in SARS-CoV-2 positive patients and if at all possible local or regional anesthesia should be utilized. Patients who screen or test negative may have general anesthesia and laparoscopic surgery while strict protocols of infection control are upheld. Surgery in screen-positive as well as SARS-CoV-2 positive patients that cannot be safely postponed should be undertaken with full PPE with ensuring that only essential personnel are exposed. If available, negative pressure theatres should be used for patients who are positive or screen high risk. During open and vaginal procedures, suction can be used to minimize droplet and bioaerosol spread. In a patient who screens low risk or tests negative, although carrier and false negatives cannot be excluded, laparoscopy should be strongly considered. We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports’ closure (such as using gas filters and smoke evacuation systems). During the post-peak period of pandemic, debriefing and mental health screening for staff is recommended. Psychological support should be provided as needed. In conclusion, based on the existent evidence, ISGE largely supports the current international trends favoring laparoscopy over laparotomy on a case by case risk evaluation basis, recognizing the different levels of skill and access to minimally invasive procedures across various countries. url: https://www.sciencedirect.com/science/article/pii/S0301211520305509?v=s5 doi: 10.1016/j.ejogrb.2020.08.039 id: cord-333487-zem2d4y6 author: Thomaz Ugliara Barone, Mark title: The Impact of COVID-19 on People with Diabetes in Brazil date: 2020-07-03 words: 4658.0 sentences: 216.0 pages: flesch: 47.0 cache: ./cache/cord-333487-zem2d4y6.txt txt: ./txt/cord-333487-zem2d4y6.txt summary: Methods In a convenience sampling study, data were collected from 1701 individuals, aged 18 or above; 75.54% female participants; 60.73% T1D and 30.75% T2D, between April 22nd and May 4th, using an anonymous and untraceable survey containing 20 multiple choice questions (socio-demographic; health status and habits of life during COVID-19 pandemic). Conclusions This study provides a firsthand revelation of the severity of COVID-19 on individuals with diabetes in Brazil, altering their habits, which impacted their glycemia, potentially increasing their risk of poor outcomes if infected by SARS-CoV-2. This also harmed adjustments to continue the proper follow-up and management of other diseases, including both communicable and NCDs. For these reasons, the present study aims to investigate challenges encountered by people living with diabetes in Brazil during the COVID-19 pandemic. abstract: Abstract The present study aims atidentifying main barriers faced by people living with diabetes in Brazil during the COVID-19 pandemic. Methods In a convenience sampling study, data were collected from 1701 individuals, aged 18 or above; 75.54% female participants; 60.73% T1D and 30.75% T2D, between April 22nd and May 4th, using an anonymous and untraceable survey containing 20 multiple choice questions (socio-demographic; health status and habits of life during COVID-19 pandemic). Relationship between variables was established using the multiple correspondence analysis technique. Results 95.1% of respondents reduced their frequency of going outside of their homes; among those who monitored blood glucose at home during the pandemic (91.5%), the majority (59.4%) experienced an increase, a decrease or a higher variability in glucose levels; 38.4% postponed their medical appointments and/or routine examinations; and 59.5% reduced their physical activity. T1D, the youngest group, was more susceptible to presenting COVID-19 symptoms despite not being testing; whilst the TD2 group had higher frequency of comorbidities that are additional risk factors for COVID-19 severity. Conclusions This study provides a firsthand revelation of the severity of COVID-19 on individuals with diabetes in Brazil, altering their habits, which impacted their glycemia, potentially increasing their risk of poor outcomes if infected by SARS-CoV-2. url: https://doi.org/10.1016/j.diabres.2020.108304 doi: 10.1016/j.diabres.2020.108304 id: cord-048335-5fl0rk90 author: Thompson, Alison K title: Pandemic influenza preparedness: an ethical framework to guide decision-making date: 2006-12-04 words: 7950.0 sentences: 380.0 pages: flesch: 45.0 cache: ./cache/cord-048335-5fl0rk90.txt txt: ./txt/cord-048335-5fl0rk90.txt summary: The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The significance of this ethical framework is a) in the unique collaborative approach taken to its development that involved ethicists with different areas of expertise and a variety of health care stakeholders, and b) that it fills an important need in pandemic planning for an ethical framework to guide decision-making that has been unmet in most pandemic planning processes world wide. The second part of the framework identifies ten key ethical values that should inform the pandemic influenza planning process and decision-making during an outbreak. abstract: BACKGROUND: Planning for the next pandemic influenza outbreak is underway in hospitals across the world. The global SARS experience has taught us that ethical frameworks to guide decision-making may help to reduce collateral damage and increase trust and solidarity within and between health care organisations. Good pandemic planning requires reflection on values because science alone cannot tell us how to prepare for a public health crisis. DISCUSSION: In this paper, we present an ethical framework for pandemic influenza planning. The ethical framework was developed with expertise from clinical, organisational and public health ethics and validated through a stakeholder engagement process. The ethical framework includes both substantive and procedural elements for ethical pandemic influenza planning. The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. We discuss the merits and limits of an applied ethical framework for hospital decision-making, as well as the robustness of the framework. SUMMARY: The need for reflection on the ethical issues raised by the spectre of a pandemic influenza outbreak is great. Our efforts to address the normative aspects of pandemic planning in hospitals have generated interest from other hospitals and from the governmental sector. The framework will require re-evaluation and refinement and we hope that this paper will generate feedback on how to make it even more robust. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698926/ doi: 10.1186/1472-6939-7-12 id: cord-351278-nm2bq717 author: Thompson, Craig title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure date: 2020-04-17 words: 2995.0 sentences: 204.0 pages: flesch: 55.0 cache: ./cache/cord-351278-nm2bq717.txt txt: ./txt/cord-351278-nm2bq717.txt summary: title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors a pilot study of the value of serology to determine population exposure We performed a serological study of recent blood donors in Scotland to detect antibodies to SARS-CoV-2 as a marker of past infection. Serial follow up studies are needed to track infection and seroconversion in this and other similar populations However, these data indicate that sero-surveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic like the current SARS-CoV-2 outbreak. Since the first reports in December, 2019, infections with SARS-CoV-2 have been reported from an increasing number of countries worldwide, with particularly high incidence of diagnosed infections and associated deaths from respiratory disease initially in China but more recently in Italy, Iran, Spain, France and the USA (https://www.who.int/emergencies/diseases/novel-coronavirus-2019). abstract: Background. The extent of spread of SARS coronavirus 2 (SARS-CoV-2) in the UK and elsewhere is unknown because typically only symptomatic individuals are diagnosed. We performed a serological study of recent blood donors in Scotland to detect antibodies to SARS-CoV-2 as a marker of past infection. Methods. A pseudotyped SARS-CoV-2 virus microneutralisation assay was used to detect neutralising antibodies to SARS-CoV-2. The study group comprised samples from 1000 blood donors collected in Scotland during March, 2020. Controls were collected from 100 donors in Scotland during 2019. Findings. All samples collected on the 17th March, 2020 (n=500) were negative in the pseudotyped SARS-CoV-2 virus microneutralisation assay. Neutralising antibodies were detected in 5 of the 500 samples collected 21st to 23rd March; one further sample was reactive in an anti-spike ELISA. Interpretation. Although we cannot use the rise in numbers seropositive to infer the contemporary seroprevalence or the growth rate of the epidemic, we note that they are consistent with frequency of reported diagnosed infections and SARS-CoV-2-associated deaths reported in that time period in Scotland, given that seroconversion takes up to 2-3 weeks. It should also be noted that blood donors are not representative of the general population; in particular, those with a history of recent respiratory infections are deferred. Finally, it is unknown what proportion of infected individuals seroconvert and become reactive in the assays used. Serial follow up studies are needed to track infection and seroconversion in this and other similar populations However, these data indicate that sero-surveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic like the current SARS-CoV-2 outbreak. url: https://doi.org/10.1101/2020.04.13.20060467 doi: 10.1101/2020.04.13.20060467 id: cord-287499-zcizdc7s author: Thompson, Hayley A title: SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China date: 2020-08-24 words: 1399.0 sentences: 72.0 pages: flesch: 46.0 cache: ./cache/cord-287499-zcizdc7s.txt txt: ./txt/cord-287499-zcizdc7s.txt summary: title: SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China Highlight: We estimated SARS-CoV-2 infection prevalence in cohorts of repatriated citizens from Wuhan to be 0.44% (95% CI: 0.19%-1.03%). Although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in Wuhan City, China, in the absence of large-scale population testing early in the epidemic. By focusing on flights where all passengers were tested for SARS-CoV-2 infection with real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR), regardless of symptoms, a more accurate estimate of infection prevalence can be obtained compared to relying on symptomatic surveillance testing alone. 8 The repatriation flights we considered represent a globally diverse population of foreign nationals who were residing in Wuhan City leading up to the outbreak for variable periods of time and for a variety of reasons: students, work-related travel, visiting friends and families and tourism. High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries abstract: We estimated SARS-CoV-2 infection prevalence in cohorts of repatriated citizens from Wuhan to be 0.44% (95% CI: 0.19%–1.03%). Although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in Wuhan City, China, in the absence of large-scale population testing early in the epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32830853/ doi: 10.1093/jtm/taaa135 id: cord-303651-fkdep6cp author: Thompson, Robin N. title: Key questions for modelling COVID-19 exit strategies date: 2020-08-12 words: 11567.0 sentences: 587.0 pages: flesch: 40.0 cache: ./cache/cord-303651-fkdep6cp.txt txt: ./txt/cord-303651-fkdep6cp.txt summary: This leads to a roadmap for future research (figure 1) made up of three key steps: (i) improve estimation of epidemiological parameters using outbreak data from different countries; (ii) understand heterogeneities within and between populations that affect virus transmission and interventions; and (iii) focus on data needs, particularly data collection and methods for planning exit strategies in low-to-middle-income countries (LMICs) where data are often lacking. Three key steps are required: (i) improve estimates of epidemiological parameters (such as the reproduction number and herd immunity fraction) using data from different countries ( §2a-d); (ii) understand heterogeneities within and between populations that affect virus transmission and interventions ( §3a-d); and (iii) focus on data requirements for predicting the effects of individual interventions, particularly-but not exclusively-in data-limited settings such as LMICs ( §4a-c). abstract: Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute ‘Models for an exit strategy’ workshop (11–15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health. url: https://arxiv.org/pdf/2006.13012v4.pdf doi: 10.1098/rspb.2020.1405 id: cord-333099-hy4nmy7l author: Thoms, Matthias title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 date: 2020-07-17 words: 3441.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-333099-hy4nmy7l.txt txt: ./txt/cord-333099-hy4nmy7l.txt summary: Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. To elucidate the molecular interaction of SARS-CoV-2 Nsp1 with human ribosomes, we reconstituted a complex from purified, recombinant Nsp1 and purified human 40S ribosomal subunits and determined its structure by cryo-EM at an average resolution of 2.6 Å (Fig. 2, A and B , and figs. To characterize the ribosomal targets and the mode of interaction of Nsp1 in human cells, we expressed N-terminally 3xFLAG tagged Nsp1 in HEK293T cells and affinity purified associated native complexes for analysis by cryo-EM and mass spectrometry (Fig. 2E , figs. The second major population of Nsp1-bound 80S ribosomes (Fig. 2 , M and N) lacked CCDC124, but contained the cell growth regulating nucleolar protein LYAR, which has been implicated in processing of pre-rRNA and in negative regulation of antiviral innate immune responses (34, 35) . abstract: SARS-CoV-2 is the causative agent of the current COVID-19 pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1) which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. Structural analysis by cryo-electron microscopy (cryo-EM) of in vitro reconstituted Nsp1-40S and various native Nsp1-40S and -80S complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks RIG-I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2. url: https://doi.org/10.1126/science.abc8665 doi: 10.1126/science.abc8665 id: cord-321166-nvphu1fm author: Thomson, Emma C. title: The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date: 2020-11-05 words: 9813.0 sentences: 514.0 pages: flesch: 55.0 cache: ./cache/cord-321166-nvphu1fm.txt txt: ./txt/cord-321166-nvphu1fm.txt summary: We find that the N439K mutation is associated with a similar clinical spectrum of disease and slightly higher viral loads in vivo compared with isolates with the wild-type N439 residue, and that it results in immune escape from polyclonal sera from a proportion of recovered individuals and a panel of neutralizing mAbs. N439K provides a sentinel example of immune escape, indicating that RBM variants must be evaluated when considering vaccines and the therapeutic or prophylactic use of mAbs. Long term control of the pandemic will require systematic monitoring of immune escape variants and selection of strategies that address the variants circulating in targeted populations. Fitness of this variant, N439K, was demonstrated by repeated emergence by convergent evolution, spread to multiple countries and significant representation in the SARS-CoV-2 sequence databases, the fact that the N439K RBD retains a high affinity interaction with the hACE2 receptor, efficient viral replication in cultured cells, and no disease attenuation in a large cohort of infected individuals. abstract: SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics. Herein we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is the most divergent region of S, and provide epidemiological, clinical, and molecular characterization of a prevalent RBM variant, N439K. We demonstrate that N439K S protein has enhanced binding affinity to the hACE2 receptor, and that N439K virus has similar clinical outcomes and in vitro replication fitness as compared to wild- type. We observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, including one in clinical trials, as well as from polyclonal sera from a sizeable fraction of persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics. url: https://doi.org/10.1101/2020.11.04.355842 doi: 10.1101/2020.11.04.355842 id: cord-328505-5fkpnbdb author: Thornton, Jeanine Rempe title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab date: 2020-06-26 words: 997.0 sentences: 75.0 pages: flesch: 48.0 cache: ./cache/cord-328505-5fkpnbdb.txt txt: ./txt/cord-328505-5fkpnbdb.txt summary: title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab We report a series of two MS patients who developed COVID-19 while on Ocrelizumab therapy and subsequently exhibited negative SARS-CoV-2 serology. The sensitivity may be diminished by inadequate timing of testing following an infection, but the most recent literature suggests that the vast majority of patients with symptomatic COVID-19 produce antibodies within the first two to three weeks after symptom onset (Long et al., 2020) . In MS, a possible concern is the impact of certain DMTs, such as CD-20 monoclonal antibodies In this article, we report serology results from the first two patients at our center to have undergone SARS-CoV-2 antibody testing after developing COVID-19 while on Ocrelizumab therapy. In this case series, we present negative results from the first two MS patients at our site who underwent SARS-CoV-2 antibody testing after developing PCR-confirmed COVID-19 while on Ocrelizumab. abstract: BACKGROUND: It is unknown whether MS disease modifying therapies impact ability to mount an antibody response to SARS-CoV-2. METHODS: Case series and literature review. We report a series of two MS patients who developed COVID-19 while on Ocrelizumab therapy and subsequently exhibited negative SARS-CoV-2 serology. RESULTS: A 42-year-old man and 39-year-old woman with MS developed COVID-19 while on Ocrelizumab therapy. Neither patient required hospitalization. The man exhibited negative serology at 7- and 9-weeks post-infection. The woman exhibited negative serology at 6- and 12-weeks post-infection. CONCLUSIONS: Large studies are essential to determine whether certain DMTs may blunt SARS-CoV-2 antibody production. url: https://www.ncbi.nlm.nih.gov/pubmed/32622338/ doi: 10.1016/j.msard.2020.102341 id: cord-331910-s474ecvk author: Thota, Sai Manohar title: Natural products as home‐based prophylactic and symptom management agents in the setting of COVID‐19 date: 2020-08-17 words: 8669.0 sentences: 457.0 pages: flesch: 37.0 cache: ./cache/cord-331910-s474ecvk.txt txt: ./txt/cord-331910-s474ecvk.txt summary: Natural products like ginger, turmeric, garlic, onion, cinnamon, lemon, neem, basil, and black pepper have been scientifically proven to have therapeutic benefits against acute respiratory tract infections including pulmonary fibrosis, diffuse alveolar damage, pneumonia, and acute respiratory distress syndrome, as well as associated septic shock, lung and kidney injury, all of which are symptoms associated with COVID‐19 infection. In this context, this review highlights the potential beneficial effects of natural products that are actively used in alternative/ traditional medicines to treat many of the acute pulmonary infections, routinely seen in COVID-19 patients. Importantly, these pre-clinical studies highlight the efficacy of garlic in mitigating pulmonary fibrosis, lung injury, and sepsis-associated organ failure, all of which are symptoms observed in patients with advanced COVID-19 infection. Taken together, preclinical and clinical studies suggest that vitamin-C could have promising therapeutic benefits in individuals with pulmonary fibrosis, pneumonia, ARDS, sepsis, acute lung injury, and multiple organ dysfunction all of which are observed in advanced COVID-19 patients. abstract: Coronavirus disease (COVID‐19) caused by the novel coronavirus (SARS‐CoV‐2) has rapidly spread across the globe affecting 213 countries or territories with greater than six million confirmed cases and about 0.37 million deaths, with World Health Organization categorizing it as a pandemic. Infected patients present with fever, cough, shortness of breath, and critical cases show acute respiratory infection and multiple organ failure. Likelihood of these severe indications is further enhanced by age as well as underlying comorbidities such as diabetes, cardiovascular, or thoracic problems, as well as due to an immunocompromised state. Currently, curative drugs or vaccines are lacking, and the standard of care is limited to symptom management. Natural products like ginger, turmeric, garlic, onion, cinnamon, lemon, neem, basil, and black pepper have been scientifically proven to have therapeutic benefits against acute respiratory tract infections including pulmonary fibrosis, diffuse alveolar damage, pneumonia, and acute respiratory distress syndrome, as well as associated septic shock, lung and kidney injury, all of which are symptoms associated with COVID‐19 infection. This review highlights the potential of these natural products to serve as home‐based, inexpensive, easily accessible, prophylactic agents against COVID‐19. url: https://doi.org/10.1002/ptr.6794 doi: 10.1002/ptr.6794 id: cord-317928-doj39520 author: Thum, Thomas title: SARS-CoV-2 receptor ACE2 expression in the human heart: cause of a post-pandemic wave of heart failure? date: 2020-05-14 words: 1462.0 sentences: 85.0 pages: flesch: 48.0 cache: ./cache/cord-317928-doj39520.txt txt: ./txt/cord-317928-doj39520.txt summary: A number of pre-clinical studies have shown various organ systems to express the primary SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2). Potentially, the COVID-19 outbreak will also lead to an increase of long-term complications of patients with CVD such as heart failure in both patients infected with SARS-CoV-2 and those that are not infected but that were treated suboptimally during the ongoing pandemic ( Figure 1 ). In conclusion, Nicin and co-workers report here an important observation with future implications in both research and, potentially, treatment of SARS-CoV-2-infected cardiovascular patients. These novel data at least suggest that it will be important to monitor SARS-CoV-2-infected patients for cardiovascular complications and assess the impact of ARB/ACE inhibitor therapy in more detail. Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 abstract: nan url: https://doi.org/10.1093/eurheartj/ehaa410 doi: 10.1093/eurheartj/ehaa410 id: cord-300272-95o8yd7h author: Thépaut, Michel title: DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date: 2020-08-10 words: 6862.0 sentences: 356.0 pages: flesch: 53.0 cache: ./cache/cord-300272-95o8yd7h.txt txt: ./txt/cord-300272-95o8yd7h.txt summary: In the context of the current COVID-19 pandemic, attention is now focused on the SARS-CoV-2 virus Zhou et al., 2020) .Coronaviruses use a homotrimeric glycosylated spike (S) protein protruding from their viral envelope to interact with cell membranes and promote fusion upon proteolytic activation. Additionally, in the case of SARS-CoV-2, a new paradigm is needed to untangle the complex clinical picture, resulting in a vast range of possible symptoms and in a spectrum of disease severity associated on one hand with active viral replication and cell infection through interaction with ACE2 along the respiratory tract, and, on the other hand, to the development of excessive immune activation, i.e. the so called "cytokine storm", that is related to additional tissue damage and potential fatal outcomes. These observations prompted us to investigate the potential interaction of C-type lectins receptors, notably DC/L-SIGN with SARS-CoV-2, through glycan recognition of the spike envelope glycoprotein, as well at their potential role in SARS-CoV-2 transmission. abstract: The efficient spread of SARS-CoV-2 resulted in a pandemic that is unique in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in air mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. Thus, we described a mechanism potentiating viral capture and spreading of infection. Early involvement of APCs opens new avenues for understanding and treating the imbalanced innate immune response observed in COVID-19 pathogenesis url: https://doi.org/10.1101/2020.08.09.242917 doi: 10.1101/2020.08.09.242917 id: cord-355395-rckzi8vz author: Tian, Dandan title: Hepatic complications of COVID‐19 and its treatment date: 2020-05-21 words: 2896.0 sentences: 137.0 pages: flesch: 40.0 cache: ./cache/cord-355395-rckzi8vz.txt txt: ./txt/cord-355395-rckzi8vz.txt summary: SARS‐CoV‐2 can cause liver injury through systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia‐reperfusion injury, side effects of treatment drugs, and underlying liver disease and can attack liver cells directly via ACE2. Considering limited number of autopsy cases in patients with COVID-19 studied and the relatively low expression of ACE2 in liver, liver damage directly caused by SARS-CoV-2 infection of hepatocytes deserves further investigation. It was speculated that in addition to the virus itself causing liver injury, immune injury, systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia and hypoxia reperfusion injury, and drug-induced injury may be the main mechanisms that cause secondary liver injury in patients with COVID-19 [11] [12] 14, 27 . Patients with COVID-19 have varying degrees of hypoxemia, with more than 40% requiring oxygen therapy 5 Drug hepatotoxicity( Figure 2) In China, the incidence of drug-induced liver injury is second only to viral hepatitis and fatty liver disease (including alcoholic and non-alcoholic). abstract: COVID‐19 is highly contagious and has a variety of clinical manifestations, it can affect a number of other organs in addition to the lungs, and liver injury may occur. SARS‐CoV‐2 can cause liver injury through systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia‐reperfusion injury, side effects of treatment drugs, and underlying liver disease and can attack liver cells directly via ACE2. Clinical studies have found that liver injury in COVID‐19 patients mainly manifests as abnormal liver biochemical indicators, but there have been no reports of liver failure caused by this disease. The number of COVID‐19 patients with liver injury is increasing, and the incidence of liver injury in COVID‐19 patients with severe disease are higher than in patients with mild disease. Liver injury may be a risk factor for progresses and worsens in patients with COVID‐19, and it is necessary to pay attention to the occurrence of liver injury in the diagnosis and treatment of COVID‐19. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32437004/ doi: 10.1002/jmv.26036 id: cord-297826-2nruf2g7 author: Tian, Jing-Hui title: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date: 2020-06-30 words: 2660.0 sentences: 171.0 pages: flesch: 60.0 cache: ./cache/cord-297826-2nruf2g7.txt txt: ./txt/cord-297826-2nruf2g7.txt summary: In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). Mice 171 immunized with 10 μg dose of NVX-CoV2373/Matrix-M induced antibodies that blocked 172 hACE2 receptor binding to S-protein and virus neutralizing antibodies 21-28-days after 173 a single priming dose ( Fig. 4B and 4C ). Importantly, we found the frequency 254 of IFN-γ + , TNF-α + , and IL-2 + cytokine-secreting CD4 + and CD8 + T cells was 255 significantly higher (p <0.0001) in spleens from the NVX-CoV2373/Matrix-M immunized 256 mice compared to mice immunized without adjuvant ( Fig. 6B and 6C) . Anti-S protein IgG titers were detected within 21-days of a single priming immunization 288 in animals immunized with NVX-CoV2373/Matrix-M across all the dose levels (GMT = 289 1,249-19,000). abstract: The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd immunity to control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length spike (S) protein, stabilized in the prefusion conformation. Purified NVX-CoV2373 S form 27.2nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). NVX-CoV2373 vaccine also elicits multifunctional CD4+ and CD8+ T cells, CD4+ T follicular helper T cells (Tfh), and the generation of antigen-specific germinal center (GC) B cells in the spleen. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2327 with Matrix-M (NCT04368988). url: https://doi.org/10.1101/2020.06.29.178509 doi: 10.1101/2020.06.29.178509 id: cord-270665-z4l3lq39 author: Tian, Qing title: Endoscopic mask innovation and protective measures changes during the COVID‐19 pandemic: experience from a Chinese hepato‐biliary‐pancreatic unit date: 2020-07-23 words: 1833.0 sentences: 115.0 pages: flesch: 44.0 cache: ./cache/cord-270665-z4l3lq39.txt txt: ./txt/cord-270665-z4l3lq39.txt summary: However, due to the distinctive epidemiological characteristics of SARS‐CoV‐2 (the virus causing COVID‐19), healthcare providers are exposed to the patient''s respiratory and gastrointestinal fluids, rendering endoscopy a high risk for transmitting a nosocomial infection. This article introduces preventive measures for endoscopic treatment enacted in our medical center during COVID‐19, including the adjustment of indications, the application of endoscope protective equipment, the design and application of endoscopic masks and splash‐proof films, and novel recommendations for bedside endoscope pre‐sterilization. During the COVID-19 pandemic, due to the distinctive epidemiological characteristics of SARS-CoV-2, endoscopy poses a high risk of nosocomial infection, since healthcare providers are exposed to the patient''s respiratory and gastrointestinal fluids 6 . 6) All medical personnel who a) have fever or respiratory symptoms, b) had contact with suspected or confirmed COVID-19 patients, c) live in or had contact with individuals residing in areas where the disease is prevalent, or d) recently returned from a high-pandemic area or country should undergo self-isolation for 14 days. abstract: Endoscopy is widely used as a clinical diagnosis and treatment method for certain hepatobiliary and pancreatic diseases. However, due to the distinctive epidemiological characteristics of SARS‐CoV‐2 (the virus causing COVID‐19), healthcare providers are exposed to the patient’s respiratory and gastrointestinal fluids, rendering endoscopy a high risk for transmitting a nosocomial infection. This article introduces preventive measures for endoscopic treatment enacted in our medical center during COVID‐19, including the adjustment of indications, the application of endoscope protective equipment, the design and application of endoscopic masks and splash‐proof films, and novel recommendations for bedside endoscope pre‐sterilization. url: https://www.ncbi.nlm.nih.gov/pubmed/32702176/ doi: 10.1111/den.13799 id: cord-314574-3e6u4aza author: Tian, Xiaolong title: Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody date: 2020-02-17 words: 1816.0 sentences: 88.0 pages: flesch: 49.0 cache: ./cache/cord-314574-3e6u4aza.txt txt: ./txt/cord-314574-3e6u4aza.txt summary: Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3] , CR3014 [4] , CR3022 [5] , as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15] , and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)) . abstract: The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 11,900 laboratory-confirmed human infections, including 259 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD. These results suggest that CR3022 may have the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. url: https://doi.org/10.1080/22221751.2020.1729069 doi: 10.1080/22221751.2020.1729069 id: cord-267509-w7nfbnbb author: Tian, Yuan title: Review article: gastrointestinal features in COVID‐19 and the possibility of faecal transmission date: 2020-03-31 words: 1577.0 sentences: 107.0 pages: flesch: 52.0 cache: ./cache/cord-267509-w7nfbnbb.txt txt: ./txt/cord-267509-w7nfbnbb.txt summary: METHODS: We have reviewed gastrointestinal features of, and faecal test results in, COVID‐19 from case reports and retrospective clinical studies relating to the digestive system published since the outbreak. 7, 11, 17 Gastrointestinal symptoms were also present in critically ill children, 28 Early studies indicated that individuals infected with SARS-CoV-2 might shed and spread the virus while they were pre-symptomatic or asymptomatic. Manifestations of digestive system in hospitalized patients with novel coronavirus pneumonia in Wuhan, China: a single-center, descriptive study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: BACKGROUND: There is little published evidence on the gastrointestinal features of COVID‐19. AIMS: To report on the gastrointestinal manifestations and pathological findings of patients with COVID‐19, and to discuss the possibility of faecal transmission. METHODS: We have reviewed gastrointestinal features of, and faecal test results in, COVID‐19 from case reports and retrospective clinical studies relating to the digestive system published since the outbreak. RESULTS: With an incidence of 3% (1/41)‐79% (159/201), gastrointestinal symptoms of COVID‐19 included anorexia 39.9% (55/138)‐50.2% (101/201), diarrhoea 2% (2/99)‐49.5% (146/295), vomiting 3.6% (5/138)‐66.7% (4/6), nausea 1% (1/99)‐29.4% (59/201), abdominal pain 2.2% (3/138)‐6.0% (12/201) and gastrointestinal bleeding 4% (2/52)‐13.7% (10/73). Diarrhoea was the most common gastrointestinal symptom in children and adults, with a mean duration of 4.1 ± 2.5 days, and was observed before and after diagnosis. Vomiting was more prominent in children. About 3.6% (5/138)‐15.9% (32/201) of adult and 6.5% (2/31)‐66.7% (4/6) of children patients presented vomiting. Adult and children patients can present with digestive symptoms in the absence of respiratory symptoms. The incidence of digestive manifestations was higher in the later than in the early stage of the epidemic, but no differences in digestive symptoms among different regions were found. Among the group of patients with a higher proportion of severe cases, the proportion of gastrointestinal symptoms in severe patients was higher than that in nonsevere patients (anorexia 66.7% vs 30.4%; abdominal pain 8.3% vs 0%); while in the group of patients with a lower severe rate, the proportion with gastrointestinal symptoms was similar in severe and nonsevere cases (nausea and vomiting 6.9% vs 4.6%; diarrhoea 5.8% vs 3.5%). Angiotensin converting enzyme 2 and virus nucleocapsid protein were detected in gastrointestinal epithelial cells, and infectious virus particles were isolated from faeces. Faecal PCR testing was as accurate as respiratory specimen PCR detection. In 36% (5/14)‐53% (39/73) faecal PCR became positive, 2‐5 days later than sputum PCR positive. Faecal excretion persisted after sputum excretion in 23% (17/73)‐82% (54/66) patients for 1‐11 days. CONCLUSIONS: Gastrointestinal symptoms are common in patients with COVID‐19, and had an increased prevalence in the later stage of the recent epidemic in China. SARS‐CoV‐2 enters gastrointestinal epithelial cells, and the faeces of COVID‐19 patients are potentially infectious. url: https://doi.org/10.1111/apt.15731 doi: 10.1111/apt.15731 id: cord-282635-ffq8kpij author: Tierraseca, Melody Sánchez title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) date: 2020-05-11 words: 535.0 sentences: 64.0 pages: flesch: 50.0 cache: ./cache/cord-282635-ffq8kpij.txt txt: ./txt/cord-282635-ffq8kpij.txt summary: title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) Como se describe en el manuscrito al que hace referencia el título, así como series publicadas desde enero de 2020, la mayoría de los niños infectados por SARS-CoV-2 presentan clínica respiratoria leve 2,3 . Aún no disponemos de suficiente información de la clínica gastrointestinal exclusiva por SARS-CoV-2 y los protocolos actuales están dirigidos al manejo de las manifestaciones respiratorias quedando muchas incógnitas sobre otras manifestaciones. Sin embargo, se ha descrito la posibilidad de su transmisión por la excreción fecal 2,3 por la detección del ARN viral en las heces de pacientes infectados, incluso varias semanas tras su negativización en muestras respiratorias. Actualización de la situación epidemiológica de la infección por SARS-CoV-2 en España. Infección por coronavirus(COVID-19) en Anales de Pediatría Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and abstract: nan url: https://api.elsevier.com/content/article/pii/S1695403320301788 doi: 10.1016/j.anpedi.2020.04.021 id: cord-297842-hkr1wm3k author: Tilley, Kimberly title: A Cross-Sectional Study Examining the Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in a University Student Population date: 2020-10-15 words: 3894.0 sentences: 197.0 pages: flesch: 43.0 cache: ./cache/cord-297842-hkr1wm3k.txt txt: ./txt/cord-297842-hkr1wm3k.txt summary: PURPOSE: The aim of the study was to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in a university student population. METHODS: This was a cross-sectional survey study based on the World Health Organization population-based seroepidemiological investigational protocol for SARS-CoV-2 conducted between April 29, 2020, and May 8, 2020, examining SARS-CoV-2 antibody prevalence among 790 university students in Los Angeles, CA. With the goal of having the sample distributions match distributions in the population, these strata were selected based on internal university data, indicating that females are more likely to participate in health-related research projects compared with males, and fewer undergraduates (36.4%) spent the end of the Spring 2020 semester in Los Angeles relative to graduate students (76.5%). Seroprevalence of SARS-CoV-2 antibodies in a Los Angeles university student population as of May 8, 2020, was estimated to be 4.0%. abstract: PURPOSE: The aim of the study was to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in a university student population. METHODS: This was a cross-sectional survey study based on the World Health Organization population-based seroepidemiological investigational protocol for SARS-CoV-2 conducted between April 29, 2020, and May 8, 2020, examining SARS-CoV-2 antibody prevalence among 790 university students in Los Angeles, CA. Participants completed a questionnaire on potential risk factors before blood sampling. Samples were analyzed using the EUROIMMUN Anti-SARS-CoV-2 ELISA (IgG) for the qualitative detection of IgG class antibodies to SARS-CoV-2 in human serum or plasma. RESULTS: The estimated prevalence of SARS-CoV-2 antibody was 4.0% (3.0%, 5.1%). Factors associated with having a positive test included history of anosmia and/or loss of taste (95% CI: 1.4–9.6). A history of respiratory symptoms, with or without fever, was not associated with a positive antibody test. CONCLUSIONS: Prevalence of SARS-CoV-2 antibodies in the undergraduate and graduate student university population was similar to community prevalence. url: https://www.sciencedirect.com/science/article/pii/S1054139X2030522X doi: 10.1016/j.jadohealth.2020.09.001 id: cord-264974-hspek930 author: Timmis, Kenneth title: The COVID‐19 pandemic: some lessons learned about crisis preparedness and management, and the need for international benchmarking to reduce deficits date: 2020-05-03 words: 7222.0 sentences: 275.0 pages: flesch: 35.0 cache: ./cache/cord-264974-hspek930.txt txt: ./txt/cord-264974-hspek930.txt summary: If, despite the explicit warning of the World Health Organization in 2011 that ''The world is ill-prepared to respond to a severe influenza pandemic or to any similarly global, sustained and threatening public-health emergency'' (https://apps.who.int/gb/ebwha/pdf_files/WHA64/A64_10en.pdf), it was not apparent to those in charge, and to the general public-i.e., those suffering from COVID-19 infections and the funders of health services (tax/insurance payers)-that existing health systems had inherent vulnerabilities which could prove to be devastating when seriously stressed, the SARS-CoV-2 pandemic (e.g., see Brüssow, 2020 ) has brutally exposed it now. International benchmarking is mandatory, because it has become clear that there is a wide range of effectiveness in the ability of different countries with developed economies to respond to this crisis (and probably others), and the tax-paying public has no compelling reason to tolerate perpetuation of factors underlying poor responses to crises. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32319151/ doi: 10.1111/1462-2920.15029 id: cord-337430-c2vdnml7 author: Timpka, Toomas title: Sports Health During the SARS-Cov-2 Pandemic date: 2020-05-02 words: 2261.0 sentences: 122.0 pages: flesch: 47.0 cache: ./cache/cord-337430-c2vdnml7.txt txt: ./txt/cord-337430-c2vdnml7.txt summary: In December 2019, the Chinese city of Wuhan reported an outbreak of SARS-Cov-2 (severe acute respiratory syndrome coronavirus-2) infection that causes the Covid-19 disease, an atypical pneumonia [1] . The national public health agencies choose social distancing regulations based on an overall assessment of how critical certain activities are for society as a whole and whether motivation to comply with the rules can be assumed. During the SARS-Cov-2 pandemic, effectively all population-level interventions include the recommendation that social contacts with the elderly, and especially the senior elderly, are to be reduced to an absolute minimum. Sports organisations should develop a pandemic response strategy that addresses the needs of its athletes and coaches, while complying with the regulations and recommendations issued by the government and national public health agency. The temporary frameworks for organised sports practice and competitions must be developed based on the social distancing and quarantine protocols activated during the pandemic. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32361898/ doi: 10.1007/s40279-020-01288-7 id: cord-255440-ls1l2mlg author: Tindle, Courtney title: Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date: 2020-10-18 words: 9951.0 sentences: 525.0 pages: flesch: 53.0 cache: ./cache/cord-255440-ls1l2mlg.txt txt: ./txt/cord-255440-ls1l2mlg.txt summary: Besides the approaches described so far, there are a few more approaches used for modeling COVID-19-(i) 3D organoids from bronchospheres and tracheospheres have been established before (Hild and Jaffe, 2016; Rock et al., 2009; Tadokoro et al., 2016) and are now used in apical-out cultures for infection with SARS-COV-2 (Suzuki et al., 2020); (ii) the most common model used for drug screening is the air-liquid interphase (ALI model) in which pseudo-stratified primary bronchial or small airway epithelial cells are used to recreate the multilayered mucociliary epithelium (Mou et al., 2016; Randell et al., 2011) ; (iii) several groups have also generated 3D airway models from iPSCs or tissue-resident stem cells (Dye et al., 2015; Ghaedi et al., 2013; Konishi et al., 2016; McCauley et al., 2017; Miller et al., 2019; Wong et al., 2012) ; (iv) others have generated AT2 cells from iPSCs using closely overlapping protocols of sequential differentiation starting with definitive endoderm, anterior foregut endoderm, and distal alveolar expression (Chen et al., 2017; Gotoh et al., 2014; Huang et al., 2014; Jacob et al., 2017; Jacob et al., 2019; Yamamoto et al., 2017) . abstract: SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. GRAPHIC ABSTRACT HIGHLIGHTS Human lung organoids with mixed proximodistal epithelia are created Proximal airway cells are critical for viral infectivity Distal alveolar cells are important for emulating host response Both are required for the overzealous response in severe COVID-19 IN BRIEF An integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33106807/ doi: 10.1101/2020.10.17.344002 id: cord-281561-r10y2sgb author: Tiwari, Nidhi title: Novel β-Coronavirus (SARS-CoV-2): Current and Future Aspects of Pharmacological Treatments date: 2020-08-27 words: 6877.0 sentences: 384.0 pages: flesch: 45.0 cache: ./cache/cord-281561-r10y2sgb.txt txt: ./txt/cord-281561-r10y2sgb.txt summary: Another invitro study reported that Ribavirin, analogue of guanosine nucleotide having wide spectrum of antiviral activity, used along with LPV/RTV to treat SARS-COV-2 viral infection in china (ChiCTR2000029387) . reported remdesivir shows possible efficacy better as compared to placebo group in hospitalized patients for the treatment of SARS-CoV-2 virus. The effectiveness and safety concern of darunavir/cobicistat combination is being evaluated under development of clinical trials phase 3 by enrolling 30 COVID-19 patients and estimated completion of study on December 31, 2020. Recently, retrospective cohort study showed high dose of anakinra (5 mg/kg, BD,iv) produces beneficial and efficacious effects in 72% Covid-19 infected patients associated with ARDS (Cavalli et al., 2020) . Based on case study of patients with SARS-CoV2 infection and also confirmed severe pneumonia and ARDS treated with i.v. infusion of eculizumab along with anticoagulant therapy (Enoxaparin 4000 IU/day s.c), antiviral therapy (LPV 800 mg/day + RTV 200 mg/day), hydroxychloroquine 400 mg/day, ceftriaxone 2 g/day IV, vitamin C 6 g/day for 4 days. abstract: The novel coronavirus outbreak has reported to be rapidly spreading across the countries and becomes a foremost community health alarm. At present, no vaccine or specific drug is on hand for the treatment of this infectious disease. This review investigates the drugs, which are being evaluated and found to be effective against nCOVID-19 infection. A thorough literature search was performedon the recently published research papers in between January 2020 to May 2020, through various databases like “Science Direct”, “Google Scholar”, “PubMed”,“Medline”, “Web of Science”, and “World Health Organization (WHO)”. We reviewed and documented the information related with the current and future aspects for the management and cure of COVID-19. As of 21st July, 2020 a total of 14,562,550 confirmed cases of coronavirus and 607,781 deaths have been reported world-wide. The main clinical feature of COVID-19 ranges from asymptomatic disease to mild lower respiratory tract illness to severe pneumonia, acute lung injury, acute respiratory distress syndrome (ARDS), multiple organ dysfunction, and death. The drugs at present used in COVID-19 patients and ongoing clinical trials focusing on drug repurposing of various therapeutic classes of drug e.g. antiviral, anti-inflammatory and/or immunomodulatory drugs along with adjuvant/supportive care. Many drugs on clinical trials shows effective results on preliminary scale and now used currently in patients. Adjuvant/ supportive care therapy are used in patients to get the best results in order to minimize the short and long-term complications. However, further studies and clinical trials are needed on large scale of population to reach any firm conclusion in terms of its efficacy and safety. url: https://doi.org/10.1016/j.jsps.2020.08.015 doi: 10.1016/j.jsps.2020.08.015 id: cord-291987-zpkzzldu author: To, Kelvin KW title: False-positive SARS-CoV-2 serology in three children with Kawasaki disease date: 2020-07-17 words: 1397.0 sentences: 98.0 pages: flesch: 53.0 cache: ./cache/cord-291987-zpkzzldu.txt txt: ./txt/cord-291987-zpkzzldu.txt summary: Recent reports showed that children with KD-like disease from KD low prevalence regions had positive SARS-CoV-2 serology despite a negative SARS-CoV-2 polymerase chain reaction (PCR) in respiratory samples. To describe three paediatric Kawasaki Disease patients with false positive SARS-CoV-2 serology. We aim to describe three paediatric Kawasaki Disease patients diagnosed during the COVID-19 outbreak with false positive SARS-CoV-2 serology. Blood (5 mL) was collected from each patient and serum was obtained for the detection of IgG against SARS-CoV-2 nucleoprotein (NP) and spike protein receptor binding domain (RBD) using a microsphere-based antibody assay as described previously. Three Chinese children, who had no epidemiological links with COVID-19 patients were diagnosed with typical KD during the peak of COVID-19 outbreak in Hong Kong (Table 1) 10 11 We believe the false positive SARS-CoV-2 serology results were unrelated to the administration of IVIG for treating KD. abstract: BACKGROUND: Kawasaki disease (KD) is an acute febrile and eruptive disease with systemic vasculitis predominantly affecting young East Asian children. Recent reports showed that children with KD-like disease from KD low prevalence regions had positive SARS-CoV-2 serology despite a negative SARS-CoV-2 polymerase chain reaction (PCR) in respiratory samples. OBJECTIVES: To describe three pediatric Kawasaki Disease patients with false positive SARS-CoV-2 serology. STUDY DESIGN: We retrospectively recruited children with KD diagnosed during the COVID-19 outbreak in Hong Kong. Clinical characteristics and laboratory test results including SARS-CoV-2 PCR results were retrieved. We performed a microparticle-based immunoassay for the detection of IgG against nucleoprotein (NP) and spike protein receptor binding domain (RBD), and a microneutralization assay for the detection of neutralizing antibodies. RESULTS: Three Chinese children with typical KD were identified. They had no epidemiological links with COVID-19 patients and tested negative for SARS-CoV-2 NPA PCR. They were treated with IVIG and aspirin, and were discharged without complications. Subsequently two of them were tested positive against anti-RBD and anti-NP antibodies and one was tested positive against anti- RBD antibodies. However, microneutralization assay showed that neutralizing antibodies were absent, suggesting a false-positive IgG result. CONCLUSION: Detection of neutralizing antibodies is recommended to confirm previous SARS-CoV-2 infection in IgG-positive but PCR-negative patients. url: https://api.elsevier.com/content/article/pii/S0732889320305186 doi: 10.1016/j.diagmicrobio.2020.115141 id: cord-254478-scc9wee0 author: To, Kelvin Kai-Wang title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date: 2020-03-23 words: 5189.0 sentences: 294.0 pages: flesch: 53.0 cache: ./cache/cord-254478-scc9wee0.txt txt: ./txt/cord-254478-scc9wee0.txt summary: title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. We present findings of an observational cohort study of the temporal profile of viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from posterior oropharyngeal saliva samples and serum antibody responses, dated by symptom onset and correlated with clinical findings. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. METHODS: We did a cohort study at two hospitals in Hong Kong. We included patients with laboratory-confirmed COVID-19. We obtained samples of blood, urine, posterior oropharyngeal saliva, and rectal swabs. Serial viral load was ascertained by reverse transcriptase quantitative PCR (RT-qPCR). Antibody levels against the SARS-CoV-2 internal nucleoprotein (NP) and surface spike protein receptor binding domain (RBD) were measured using EIA. Whole-genome sequencing was done to identify possible mutations arising during infection. FINDINGS: Between Jan 22, 2020, and Feb 12, 2020, 30 patients were screened for inclusion, of whom 23 were included (median age 62 years [range 37–75]). The median viral load in posterior oropharyngeal saliva or other respiratory specimens at presentation was 5·2 log(10) copies per mL (IQR 4·1–7·0). Salivary viral load was highest during the first week after symptom onset and subsequently declined with time (slope −0·15, 95% CI −0·19 to −0·11; R(2)=0·71). In one patient, viral RNA was detected 25 days after symptom onset. Older age was correlated with higher viral load (Spearman's ρ=0·48, 95% CI 0·074–0·75; p=0·020). For 16 patients with serum samples available 14 days or longer after symptom onset, rates of seropositivity were 94% for anti-NP IgG (n=15), 88% for anti-NP IgM (n=14), 100% for anti-RBD IgG (n=16), and 94% for anti-RBD IgM (n=15). Anti-SARS-CoV-2-NP or anti-SARS-CoV-2-RBD IgG levels correlated with virus neutralisation titre (R(2)>0·9). No genome mutations were detected on serial samples. INTERPRETATION: Posterior oropharyngeal saliva samples are a non-invasive specimen more acceptable to patients and health-care workers. Unlike severe acute respiratory syndrome, patients with COVID-19 had the highest viral load near presentation, which could account for the fast-spreading nature of this epidemic. This finding emphasises the importance of stringent infection control and early use of potent antiviral agents, alone or in combination, for high-risk individuals. Serological assay can complement RT-qPCR for diagnosis. FUNDING: Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, and Sanming Project of Medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/32213337/ doi: 10.1016/s1473-3099(20)30196-1 id: cord-269973-sntnmqqd author: To, Kelvin Kai-Wang title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date: 2020-08-05 words: 1860.0 sentences: 139.0 pages: flesch: 63.0 cache: ./cache/cord-269973-sntnmqqd.txt txt: ./txt/cord-269973-sntnmqqd.txt summary: However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. abstract: After two months of relative quiescence, a large COVID-19 outbreak occurred in Hong Kong in July 2020 after gradual relaxation of social distancing policy. Two unique SARS-CoV-2 phylogenetic clusters have been identified among locally-acquired cases, with most genomes belonging to cluster HK1 which is phylogenetically related to SARS-CoV-2 reported overseas. url: https://www.ncbi.nlm.nih.gov/pubmed/32756996/ doi: 10.1093/cid/ciaa1119 id: cord-295525-emrwcx0m author: To, Kelvin Kai-Wang title: Consistent Detection of 2019 Novel Coronavirus in Saliva date: 2020-02-12 words: 1912.0 sentences: 110.0 pages: flesch: 55.0 cache: ./cache/cord-295525-emrwcx0m.txt txt: ./txt/cord-295525-emrwcx0m.txt summary: The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. abstract: The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. Serial saliva viral load monitoring generally showed a declining trend. Live virus was detected in saliva by viral culture. Saliva is a promising noninvasive specimen for diagnosis, monitoring, and infection control in patients with 2019-nCoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32047895/ doi: 10.1093/cid/ciaa149 id: cord-325614-e9hnhzfg author: Todorov, German title: A Possible Path towards Rapid Development of Live-Attenuated SARS-CoV-2 Vaccines: Plunging into the Natural Pool date: 2020-10-14 words: 3122.0 sentences: 145.0 pages: flesch: 41.0 cache: ./cache/cord-325614-e9hnhzfg.txt txt: ./txt/cord-325614-e9hnhzfg.txt summary: Our proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, which may lead to a shorter cycle of vaccine development, as well as higher vaccine effectiveness. The proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, potentially leading to a more rapid cycle of vaccine development, as well as higher vaccine effectiveness. If the candidate attenuated SARS-CoV-2 strain is easily transmissible, we would need to evaluate whether a live-attenuated virus that causes a very mild form of infection but is easy to transmit can be considered sufficiently safe for use as a vaccine, or whether it needs to be further attenuated in the lab, which could slow down the development of the vaccine. All in all, at present there are too many unknowns to predict how much screening of suitable individuals in high-risk subpopulations will be required to find naturally-evolved candidate strains for the development of live-attenuated vaccines. abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic spreading around the world, causing massive distress to the world’s economy and affecting healthcare systems worldwide. Although some exposed individuals have no symptoms and most symptomatic infections are not severe, COVID-19 cases span a wide spectrum, ranging from mild to critical and sometimes resulting in life-threatening complications, such as pneumonia, severe respiratory distress and cardiac problems. Currently, there is no curative drug for COVID-19 and vaccines are still under development. We are presenting here a strategy for the fast development of natural live-attenuated SARS-CoV-2 vaccines. Our proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, which may lead to a shorter cycle of vaccine development, as well as higher vaccine effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/33066343/ doi: 10.3390/biom10101438 id: cord-312509-m3p9fuq0 author: Tohidinia, Maryam title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 date: 2020-08-21 words: 2722.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-312509-m3p9fuq0.txt txt: ./txt/cord-312509-m3p9fuq0.txt summary: title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 The main aim of the 91 current is to use of bioinformatics tool to identify potential B-and T-cell epitope(s) of S protein with high 92 antigenicity that could be used to develop promising vaccines [20] . In 161 addition, Bcepred server at http://www.imtech.res.in/raghava/bcepred/ [32] was employed to predict linear B-162 cell epitopes in a protein sequence. Therefore, the usage of several tools to predict linear B-168 cell epitopes in protein sequences are more reliable. Ellipro at http://tools.immuneepitope.org [33] was used to 169 predict linear and discontinuous antibody epitopes based on a protein antigen''s 3D structure. The spike protein on the surface of the viral particle plays key roles in the binding of the cell receptor and 459 membrane fusion, by which the host range is firmly determined. abstract: Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus that it disease spreads in over the world. Coronaviruses are single-stranded, positive-sense RNA viruses with a genome of approximately 30 KD, the largest genome among RNA viruses. Most people infected with the COVID-19 virus will experience mild to moderate respiratory illness and recover without requiring special treatment. Older people and those with underlying medical problems like cardiovascular disease, diabetes, chronic respiratory disease, and cancer are more likely to develop serious illness. At this time, there are no specific vaccines or treatments for COVID-19. So, there is an emergency need for vaccines and antiviral strategies. The spike protein is the major surface protein that it uses to bind to a receptor of another protein that acts as a doorway into a human cell. The putative antigenic epitopes may prove effective as novel vaccines for eradication and combating of COV19 infection. A combination of available bioinformatics tools are used to synthesis of such peptides that are important for the development of a vaccine. In conclusion, amino acids 250–800 were selected as effective B cell epitopes, T cell epitopes, and functional exposed amino acids in order to a recombinant vaccine against coronavirus. url: https://doi.org/10.1016/j.micpath.2020.104459 doi: 10.1016/j.micpath.2020.104459 id: cord-252049-rgdynmla author: Tomar, Sakshi title: Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CL(pro)): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS date: 2015-06-08 words: 11805.0 sentences: 601.0 pages: flesch: 56.0 cache: ./cache/cord-252049-rgdynmla.txt txt: ./txt/cord-252049-rgdynmla.txt summary: All coronaviruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the proteolytic activity of the nsp5 protease (also known as 3C-like protease, 3CL(pro)) during virus replication, making it a high value target for the development of anti-coronavirus therapeutics. Therefore, we determined the dependence of the enzymatic activity of MERS-CoV 3CL pro on the total enzyme concentration and compared it with other 3CL pro enzymes from HKU4, HKU5, and SARS coronaviruses (Fig. 2) . The kinetic data for all four 3CL pro enzymes, MERS-CoV, HKU4-CoV, HKU5-CoV, and SARS-CoV, fit well to this model, and the resulting values for the monomer-dimer equilibrium dissociation constant, K d , and apparent turnover number, k cat , for each enzyme are provided in Table 2 . Compound 11 also forms two direct and one water-mediated hydrogen bond interactions with amino acids in the MERS-CoV 3CL pro active site (Fig. 6E) . abstract: All coronaviruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the proteolytic activity of the nsp5 protease (also known as 3C-like protease, 3CL(pro)) during virus replication, making it a high value target for the development of anti-coronavirus therapeutics. Kinetic studies indicate that in contrast to 3CL(pro) from other β-CoV 2c members, including HKU4 and HKU5, MERS-CoV 3CL(pro) is less efficient at processing a peptide substrate due to MERS-CoV 3CL(pro) being a weakly associated dimer. Conversely, HKU4, HKU5, and SARS-CoV 3CL(pro) enzymes are tightly associated dimers. Analytical ultracentrifugation studies support that MERS-CoV 3CL(pro) is a weakly associated dimer (K(d) ∼52 μm) with a slow off-rate. Peptidomimetic inhibitors of MERS-CoV 3CL(pro) were synthesized and utilized in analytical ultracentrifugation experiments and demonstrate that MERS-CoV 3CL(pro) undergoes significant ligand-induced dimerization. Kinetic studies also revealed that designed reversible inhibitors act as activators at a low compound concentration as a result of induced dimerization. Primary sequence comparisons and x-ray structural analyses of two MERS-CoV 3CLpro and inhibitor complexes, determined to 1.6 Å, reveal remarkable structural similarity of the dimer interface with 3CL(pro) from HKU4-CoV and HKU5-CoV. Despite this structural similarity, substantial differences in the dimerization ability suggest that long range interactions by the nonconserved amino acids distant from the dimer interface may control MERS-CoV 3CL(pro) dimerization. Activation of MERS-CoV 3CL(pro) through ligand-induced dimerization appears to be unique within the genogroup 2c and may potentially increase the complexity in the development of MERS-CoV 3CL(pro) inhibitors as antiviral agents. url: https://www.ncbi.nlm.nih.gov/pubmed/26055715/ doi: 10.1074/jbc.m115.651463 id: cord-271551-bj2db91j author: Tomczyk, Samuel title: Social Distancing and Stigma: Association Between Compliance With Behavioral Recommendations, Risk Perception, and Stigmatizing Attitudes During the COVID-19 Outbreak date: 2020-08-11 words: 5338.0 sentences: 242.0 pages: flesch: 37.0 cache: ./cache/cord-271551-bj2db91j.txt txt: ./txt/cord-271551-bj2db91j.txt summary: Latent class analysis examined patterns of compliance, and subsequent multinomial logistic regression models tested sociodemographic (age, gender, country of origin, level of education, region, and number of persons per household) and psychosocial (knowledge about preventive behaviors, risk perception, stigmatizing attitudes) predictors. However, to our knowledge, only one study applied latent class analysis to population behaviors following a novel virus outbreak [i.e., influenza A (H7N9)] in Hong Kong (Liao et al., 2015) , despite the method''s statistical advantages in modeling behavioral patterns (e.g., flexibility, integration of measurement error). Via an online survey, a community sample of 157 German adults [80% female; M (SD) age = 27.82 (11.01)] provided information about their knowledge of preventive measures, risk perception, intentions to comply with official behavioral recommendations and guidelines as well as their stigmatizing attitudes toward people suffering from COVID-19. abstract: Introduction: Following behavioral recommendations is key to successful containment of the COVID-19 pandemic. Therefore, it is important to identify causes and patterns of non-compliance in the population to further optimize risk and health communication. Methods: A total of 157 participants [80% female; mean age = 27.82 years (SD = 11.01)] were surveyed regarding their intention to comply with behavioral recommendations issued by the German government. Latent class analysis examined patterns of compliance, and subsequent multinomial logistic regression models tested sociodemographic (age, gender, country of origin, level of education, region, and number of persons per household) and psychosocial (knowledge about preventive behaviors, risk perception, stigmatizing attitudes) predictors. Results: Three latent classes were identified: high compliance (25%) with all recommendations; public compliance (51%), with high compliance regarding public but not personal behaviors; and low compliance (24%) with most recommendations. Compared to high compliance, low compliance was associated with male gender [relative risk ratio (RRR) = 0.08 (0.01; 0.85)], younger age [RRR = 0.72 (0.57; 0.93)], and lower public stigma [RRR = 0.21 (0.05; 0.88)]. Low compliers were also younger than public compliers [RRR = 0.76 (0.59; 0.98)]. Discussion: With 25% of the sample reporting full compliance, and 51% differing in terms of public and personal compliance, these findings challenge the sustainability of strict regulatory measures. Moreover, young males were most likely to express low compliance, stressing the need for selective health promotion efforts. Finally, the positive association between public stigma and compliance points to potential othering effects of stigma during a pandemic, but further longitudinal research is required to examine its impact on health and social processes throughout the pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32849073/ doi: 10.3389/fpsyg.2020.01821 id: cord-008841-r17qhfsj author: Tomlinson, Brian title: SARS: experience at Prince of Wales Hospital, Hong Kong date: 2003-05-03 words: 1754.0 sentences: 108.0 pages: flesch: 58.0 cache: ./cache/cord-008841-r17qhfsj.txt txt: ./txt/cord-008841-r17qhfsj.txt summary: THE LANCET • Vol 361 • May 3, 2003 • www.thelancet.com COMMENTARY The Prince of Wales Hospital (PWH) has been at the forefront of the outbreak of severe acute respiratory syndrome (SARS) in Hong Kong. Three major reasons for spread of infection to health-care workers have been: failure to apply isolation precautions to cases not yet identified as SARS, breaches of procedure, and inadequate precautions. "Super-spreaders" may be prone to carry a high viral load because of defects in their COMMENTARY SARS: experience at Prince of Wales Hospital, Hong Kong immune system, as could be the case in the patient with end-stage renal failure implicated in the Amoy Gardens outbreak and another with renal failure at the centre of an outbreak in Singapore. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134636/ doi: 10.1016/s0140-6736(03)13218-7 id: cord-315972-5g2hnk1x author: Tong, Suxiang title: Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya date: 2009-03-17 words: 1691.0 sentences: 87.0 pages: flesch: 58.0 cache: ./cache/cord-315972-5g2hnk1x.txt txt: ./txt/cord-315972-5g2hnk1x.txt summary: The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans. Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identifi ed from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species (6) (7) (8) (9) (10) (11) . To characterize the overall diversity of CoV sequences, in this study a phylogenetic tree (Figure 2 ) of the 121-bp fragment of RdRp was generated from 39 coronaviruses from bats in Kenya and 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database based on the Bayesian Monte Carlo Markov Chain method (14) . bats (location 17) were closely related to a SARS-like CoV cluster, including 1 sequence shown in Figure 2 (BtKY15) and another (BtKY16) that was 1 of the 3 low-quality sequences excluded from the tree. abstract: Diverse coronaviruses have been identified in bats from several continents but not from Africa. We identified group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans. url: https://www.ncbi.nlm.nih.gov/pubmed/19239771/ doi: 10.3201/eid1503.081013 id: cord-332537-rtdu4jae author: Tong, Tommy R. title: Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date: 2005-05-01 words: 1162.0 sentences: 68.0 pages: flesch: 48.0 cache: ./cache/cord-332537-rtdu4jae.txt txt: ./txt/cord-332537-rtdu4jae.txt summary: Airborne transmission of the severe acute respiratory syndrome (SARS) coronavirus (CoV) has been the favored explanation for its transmission on an aircraft [1] and appeared to explain a large community outbreak of SARS in the Amoy Gardens in Hong Kong [2] . in this issue of the Journal of Infectious Diseases [3] suggests that airborne dissemination of SARS-CoV may also occur in the health-care setting. However, if SARS-CoV is naturally airborne (produced by breathing and coughing), as was shown by Booth et al., then there is sufficient concern that it can be transmitted successfully by air. Acknowledgment of the fact that SARS-CoV can be aerosolized justifies the actions of those who have already committed resources for providing a safer environment in terms of preventing airborne transmission of infectious diseases and might provide the needed pressure for others to follow suit. Evidence of airborne transmission of the severe acute respiratory syndrome virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15809896/ doi: 10.1086/429637 id: cord-294385-6dlgv3tb author: Tong, Xin title: Surveillance of SARS‐CoV‐2 infection among frontline health care workers in Wuhan during COVID‐19 outbreak date: 2020-08-20 words: 1380.0 sentences: 92.0 pages: flesch: 58.0 cache: ./cache/cord-294385-6dlgv3tb.txt txt: ./txt/cord-294385-6dlgv3tb.txt summary: The radiological analysis revealed that there was no typical chest CT scan of COVID‐19 among 222 HCWs. Consistently, anti‐SARS‐CoV‐2 IgM or IgG was also found to be negative among 191 HCWs. CONCLUSIONS: There was no nosocomial infection of SARS‐CoV‐2 among our cohort of the frontline HCWs, suggesting that zero occupational infection is an achievable goal with appropriate training, strict compliance, and psychological support for the frontline HCWs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging infectious disease, first described in Wuhan, China, has rapidly spread throughout worldwide. 2 The ever-increasing number of COVID-19 cases, overwhelming workload, the depletion of personal protection equipment (PPE), physical fatigue, and psychological stress during the early outbreak has resulted in at least 22 073 cases of COVID-19 among HCWs. 3 A study from China Center for Disease Control and Prevention (CDC) showed that as of 17 February 2020, 3.8% confirmed COVID-19 cases were among HCWs. 4 A report from Italy revealed 11% of COVID-19 cases were HCWs. 5 All the evidence suggested a high risk of occupational infection of SARS-CoV-2. abstract: INTRODUCTION: As an emerging infectious disease, coronavirus disease 2019 (COVID‐19) has rapidly spread throughout worldwide. Health care workers (HCWs) on frontline directly participated in the diagnosis, treatment, and care of COVID‐19 patients are at high risk of getting infected with the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the novel coronavirus that causes COVID‐19. In Nanjing Drum Tower Hospital, a total of 222 medical staff went to Wuhan city for support. In this study, we aimed to determine any nosocomial infection among our cohort of HCWs who worked in Wuhan. METHODS: Throat swab samples were obtained for RNA testing on day 1 and 14 of their quarantine upon their return to Nanjing. Radiological assessments were performed by chest computed tomography (CT) on day 14 of their quarantine. The blood was collected from 191 HCWs between May 12 and May 15. Anti‐SARS‐CoV‐2 immunoglobulin M (IgM) and IgG antibody responses were determined by a chemiluminescence immunoassay. RESULTS: All the throat swab specimens were found negative for SARS‐CoV‐2. The radiological analysis revealed that there was no typical chest CT scan of COVID‐19 among 222 HCWs. Consistently, anti‐SARS‐CoV‐2 IgM or IgG was also found to be negative among 191 HCWs. CONCLUSIONS: There was no nosocomial infection of SARS‐CoV‐2 among our cohort of the frontline HCWs, suggesting that zero occupational infection is an achievable goal with appropriate training, strict compliance, and psychological support for the frontline HCWs. url: https://www.ncbi.nlm.nih.gov/pubmed/32816387/ doi: 10.1002/iid3.340 id: cord-274536-fv7mltj7 author: Tong, Yongqing title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 words: 3120.0 sentences: 188.0 pages: flesch: 59.0 cache: ./cache/cord-274536-fv7mltj7.txt txt: ./txt/cord-274536-fv7mltj7.txt summary: RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn''t be detected in other types of specimen in this study. Firstly, we analyzed the possible sites of infection in hospitalized patients with COVID-19 by detecting viral RNA with 12 different types of specimens, including nasopharyngeal swab, oropharyngeal swab, sputum, bronchoalveolar lavage fluid (BALF), stool, anal swab, urine, peritoneal dialysis fluid (PDF), blood, sweat, cerebrospinal fluid (CSF) and corneal secretion. The 20 discharged cases of COVID-19, the criteria [12] for which was the SARS-CoV-2 virus RNA detection negative in two consecutive respiratory specimens (at least 1 day of time interval of sampling) for patients who have reached the standards of isolation period (14 days) after clinical cured, during the isolation period were selected to detect SARS-CoV-2 RNA with multiple specimens including nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and blood. abstract: BACKGROUND: The SARS-CoV-2 RNA was detected positive again after discharged from hospital in some COVID-19 patients, with or without clinical symptoms such as fever or dry cough. METHODS: 1008 severe COVID-19 patients, with SARS-CoV-2 RNA positive detected with the mixed specimen of nasopharyngeal swab and oropharyngeal swab by real-time fluorescence quantitative PCR (RT-qPCR), were selected to monitor SARS-CoV-2 RNA with the 12 types of specimens by RT-qPCR during hospitalization. All of 20 discharged cases with COVID-19 were selected to detect SARS-CoV-2 RNA in isolation period with 7 types of specimens by RT-qPCR before releasing the isolation period. RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn’t be detected in other types of specimen in this study. Of the 20 discharged cases during the isolation period, the positive rate of SARS-CoV-2 RNA was 30% (6/20): 2 cases were positive in sputum at the eighth and ninth day after discharge, respectively, 1 case was positive in nasopharynx swab at the sixth day after discharge, 1 case was positive in anal swab at the eighth day after discharge, and 1 case was positive in 3 specimens (nasopharynx swab, oropharynx swab and sputum) simultaneously at the fourth day after discharge, and no positive SARS-CoV-2 RNA was detected in other specimens including stool, urine and blood at the discharged patients. CONCLUSIONS: SARS-CoV-2 RNA should be detected in multiple specimens, such as nasopharynx swab, oropharynx swab, sputum, and if necessary, stool and anal swab specimens should be performed simultaneously at discharge when the patients were considered for clinical cure and before releasing the isolation period. url: https://doi.org/10.1186/s12967-020-02580-w doi: 10.1186/s12967-020-02580-w id: cord-283786-d65njv7b author: Toptan, Tuna title: Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date: 2020-06-20 words: 5258.0 sentences: 235.0 pages: flesch: 53.0 cache: ./cache/cord-283786-d65njv7b.txt txt: ./txt/cord-283786-d65njv7b.txt summary: The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). Therefore, we additionally compared the performance of two research kits (New England Biolabs, Ipswich, MA, USA) and one In conclusion, our M-gene-based qRT-PCR detection of SARS-CoV-2 RNA was at least as specific as the RdRP PCR recommended for confirmation by the WHO but showed a significantly higher sensitivity. abstract: The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19, which has become a global concern due to its rapid spread. Meanwhile, increased demand for testing has led to a shortage of reagents and supplies and compromised the performance of diagnostic laboratories in many countries. Both the World Health Organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate the interpretation of the test results, especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in diagnostics as well as in research labs using a low-cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infections and performed RT-PCR assays along with successive dilutions of RNA standards to determine the limit of detection. We identified an M-gene binding primer and probe pair highly suitable for the quantitative detection of SARS-CoV-2 RNA for diagnostic and research purposes. url: https://www.ncbi.nlm.nih.gov/pubmed/32575728/ doi: 10.3390/ijms21124396 id: cord-325479-2r4oomdp author: Torii, Shotaro title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 words: 5881.0 sentences: 363.0 pages: flesch: 58.0 cache: ./cache/cord-325479-2r4oomdp.txt txt: ./txt/cord-325479-2r4oomdp.txt summary: This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. This study aims (1) to compare the combination of primary concentration (UF, EMV, and PEG) and RNA extraction (QIAamp Viral RNA Mini Kit and TRIzol) for the whole process recovery of nonenveloped and enveloped virus surrogates and (2) to test the applicability of the method providing the highest φ6 recovery to detect SARS-CoV-2 abstract: The primary concentration and molecular process are critical to implement wastewater-based epidemiology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the previously developed methods were optimized for nonenveloped viruses. Few studies evaluated if the methods are applicable to the efficient recovery of enveloped viruses from various types of raw sewage. This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. Among the tested combinations, PEG+TRIzol provided the highest φ6 recovery ratio of 29.8% to 49.8% (geometric mean). UF+QIAamp Viral RNA Mini Kit provided the second highest φ6 recovery of 6.4% to 35.8%. The comparable φ6 recovery was observed for UF+TRIzol (13.8 – 30.0 %). PEG+QIAamp Viral RNA Mini Kit provided only 1.4% to 3.0% of φ6 recovery, while coliphage MS2, a surrogate for nonenveloped viruses, was recovered comparably with PEG+TRIzol. This indicated that the nonenveloped surrogate (MS2) did not necessarily validate the efficient recovery for enveloped viruses. EMV+QIAamp Viral RNA Mini Kit provided significantly different φ6 recovery (1.6 – 21 %) among the types of raw sewage. Then, the applicability of modified PEG+TRIzol was examined for the raw sewage collected in Tokyo, Japan. Of the 12 grab samples, 4 were positive for SARS-CoV-2 CDC N1 and N3 assay. Consequently, PEG+TRIzol provided the highest φ6 recovery and allowed for the detection of SARS-CoV-2 RNA from raw sewage. url: https://www.ncbi.nlm.nih.gov/pubmed/33131851/ doi: 10.1016/j.scitotenv.2020.143067 id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 words: 4202.0 sentences: 222.0 pages: flesch: 53.0 cache: ./cache/cord-266150-wox7pnkr.txt txt: ./txt/cord-266150-wox7pnkr.txt summary: Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. abstract: BACKGROUND: A SARS-CoV-2 outbreak affecting 52 people from a large school community in Santiago, Chile was identified (March 12), nine days after the first country case. We assessed the magnitude of the outbreak and the role students and staff played using a self-administered antibody detection test and survey. METHODS: The school was closed on March 13, and the entire community was placed under quarantine. We implemented a home-delivery, self-administered, IgG/IgM antibody test and survey to a classroom stratified sample of students and all staff from May 4-19. We aimed to determine overall seroprevalence rates by age group, reported symptoms, contact exposure and to explore dynamics of transmission. RESULTS: Antibody positivity rates were 9.9% (95%CI: 8.2-11.8) for 1,009 students and 16.6% (95%CI: 12.1-21.9) for 235 staff. Among students, positivity was associated with younger age (P=0.01), lower grade level (P=0.05), prior RT-PCR positivity (P=0.03), and history of contact with a confirmed case (P<0.001). Among staff, positivity was higher in teachers (P=0.01) and in those previously RT-PCR positive (P<0.001). Excluding RT-PCR positive individuals, antibody positivity was associated with fever in adults and children (P=0.02; P=0.002), abdominal pain in children (P=0.001), and chest pain in adults (P=0.02). Within antibody positive individuals, 40% of students and 18% of staff reported no symptoms (P=0.01). CONCLUSIONS: Teachers were more affected during the outbreak and younger children were at higher infection risk, likely because index case(s) were teachers and/or parents from preschool. Self-administered antibody testing, supervised remotely, proved to be a suitable and rapid tool. Our study provides useful information for school re-openings. url: https://doi.org/10.1093/cid/ciaa955 doi: 10.1093/cid/ciaa955 id: cord-356150-ivso91ln author: Torretta, Sara title: Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature date: 2020-08-31 words: 3497.0 sentences: 195.0 pages: flesch: 48.0 cache: ./cache/cord-356150-ivso91ln.txt txt: ./txt/cord-356150-ivso91ln.txt summary: 2 Despite suboptimal detection rates, 3 collection of secretions from the upper airway by means of NPS/OPS still represents the first-line diagnostic modality to test patients and otherwise asymptomatic population for COVID-19, provided that it is early and adequately performed after onset of symptoms. 2 As a fact, reduced detection rates reflect analytical sensitivity of RT-PCR test and the epidemiologic characteristics of COVID-19, given that a false negative RT-PCR result could be possibly obtained both in the initial phase of the disease (ie, a few days before symptom onset) and at the ''''tail end'''' of SARS-CoV-2 infection (ie, from 20 days after symptom onset) due to a low viral load and a viral shedding below analytical RT-PCR sensitivity threshold. 3 On the basis of the reported detection rates, 4 the US Center for Disease Control and Prevention (US-CDC) has recommended the collection of sole upper respiratory NPS, 2 but the US Food and Drug Administration pointed out that a negative RT-PCR test result does not completely rule out SARS-CoV-2 infection and it shall not be used as a single element for patient management decisions. abstract: OBJECTIVE: The most widely used diagnostic technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is real-time reverse transcriptase-polymerase chain reaction (RT-PCR). It can be done on different samples: nasopharyngeal swabs (NPS) or oropharyngeal swabs (OPS), and self-collected saliva. However, negative findings do not rule out infection. METHODS: A review was conceived to discuss advantages and limitations of the available diagnostic modalities for nonserologic diagnosis of SARS-CoV-2 based on RT-PCR; the article also proposes some practical suggestions to improve diagnostic reliability. RESULTS: A total of 16 papers (corresponding to 452 patients) of the 56 initially identified were included. Most of the papers describe findings from different samples obtained in limited case series; comparative studies are missing. CONCLUSIONS: Diagnostic accuracy of NPS and OPS is suboptimal and the risk of contaminated aerosol dispersal is not negligible. The SARS-CoV-2 RNA can be found in self-collected saliva specimens of many infected patients within 7 to 10 days after symptom onset. There is an urgent need for comparative trials to define the diagnostic modality of choice. Adequate education and training of health care personnel is mandatory. url: https://doi.org/10.1177/0145561320953231 doi: 10.1177/0145561320953231 id: cord-270064-hidirfkv author: Tort, Fernando L. title: A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date: 2020-04-12 words: 4314.0 sentences: 257.0 pages: flesch: 61.0 cache: ./cache/cord-270064-hidirfkv.txt txt: ./txt/cord-270064-hidirfkv.txt summary: In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. In order to gain insight into the emergence, evolution, adaptation and spread of the SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. To gain insight into the biology and evolution of emerging SARS-CoV-2, a comprehensive analysis of genome composition, codon and amino acid usage of βCoV strains isolated in China from humans, bats, civets and ferret hosts was performed, including SARS-CoV-2 strains recently isolated from current outbreak. The results of these studies revealed that SARS-CoV-2 strains enrolled in these analyses have a distinct genome composition in relation to other βCoV strains isolated from human (SARS-CoV), bats, civets and ferrets (see Fig. 1 ). abstract: An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences. url: https://www.ncbi.nlm.nih.gov/pubmed/32294518/ doi: 10.1016/j.virusres.2020.197976 id: cord-260981-647wfa8z author: Torti, Lorenza title: Impact of SARS CoV-2 in Hemoglobinopathies with Immune Disfunction and Epidemiology. A Protective Mechanism from Beta Chain Hemoglobin Defects? date: 2020-07-01 words: 1291.0 sentences: 83.0 pages: flesch: 54.0 cache: ./cache/cord-260981-647wfa8z.txt txt: ./txt/cord-260981-647wfa8z.txt summary: A novel coronavirus (SARS-CoV-2) has rapidly overspread infecting in few months all continents and representing a medical emergency, with 20% of patients with severe clinical manifestations. 2 The transcribed, non-structural SARS-CoV-2 proteins ORF 8, 3a, and 10 play critical roles during infection (viral replication) and disease pathogenesis (stimulate NF-kB mediated inflammation and immune responses). Of the 105 patients who were in contact with the infected staff, only 7 reported symptoms, all mild, in the two months surveillance, and only 1 of the 7 tested positive on the swab. The SARS-CoV-2 positive patient, a female aged 59 with Beta-Thalassemia Major(TM)(IVS-6/745) received a transfusion on March 5, and after being notified, called the hospital on March 21 reporting mild temperature (37 o C). So, our case of SARS-CoV-2 infection in TM patient was revealed during an endemic outbreak, which involved 24 symptomatic HCPs out of a staff of 52. Recently a multicentric Iranian experience of 18350 Beta-thalassemic patients (only fifteen confirmed cases) reported mild to moderate disease of COVID-19. abstract: nan url: https://doi.org/10.4084/mjhid.2020.052 doi: 10.4084/mjhid.2020.052 id: cord-256300-emsvxxs5 author: Tortorici, M. Alejandra title: Structural insights into coronavirus entry date: 2019-08-22 words: 6535.0 sentences: 325.0 pages: flesch: 49.0 cache: ./cache/cord-256300-emsvxxs5.txt txt: ./txt/cord-256300-emsvxxs5.txt summary: We review here our current understanding of the mechanism used by CoVs to infect host cells based on recent structural and biochemical studies of S glycoprotein ectodomains in prefusion and postfusion states as well as complexes with known receptors or neutralizing antibodies. Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al., 2017; Kirchdoerfer et al., 2018; Song et al., 2018; Walls et al., 2019; Yuan et al., 2017) . Major antigenic determinants of MHV and SARS-CoV S overlap with the fusion peptide region (Daniel et al., 1993; Zhang et al., 2004) and binding of neutralizing antibodies to this site could putatively prevent fusogenic conformational changes, as proposed for influenza virus hemagglutinin or HIV envelope (Corti et al., 2011; Kong et al., 2016; Lang et al., 2017) . abstract: Coronaviruses (CoVs) have caused outbreaks of deadly pneumonia in humans since the beginning of the 21st century. The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and was responsible for an epidemic that spread to five continents with a fatality rate of 10% before being contained in 2003 (with additional cases reported in 2004). The Middle-East respiratory syndrome coronavirus (MERS-CoV) emerged in the Arabian Peninsula in 2012 and has caused recurrent outbreaks in humans with a fatality rate of 35%. SARS-CoV and MERS-CoV are zoonotic viruses that crossed the species barrier using bats/palm civets and dromedary camels, respectively. No specific treatments or vaccines have been approved against any of the six human coronaviruses, highlighting the need to investigate the principles governing viral entry and cross-species transmission as well as to prepare for zoonotic outbreaks which are likely to occur due to the large reservoir of CoVs found in mammals and birds. Here, we review our understanding of the infection mechanism used by coronaviruses derived from recent structural and biochemical studies. url: https://www.sciencedirect.com/science/article/pii/S0065352719300284 doi: 10.1016/bs.aivir.2019.08.002 id: cord-321742-cstub5zz author: Tovar, Isabel title: Rationale for the Use of Radiation-Activated Mesenchymal Stromal/Stem Cells in Acute Respiratory Distress Syndrome date: 2020-09-02 words: 6896.0 sentences: 292.0 pages: flesch: 36.0 cache: ./cache/cord-321742-cstub5zz.txt txt: ./txt/cord-321742-cstub5zz.txt summary: We have previously shown that the combination of radiotherapy with human umbilical-cord-derived mesenchymal stromal/stem cells (MSCs) cell therapy significantly reduces the size of the xenotumors in mice, both in the directly irradiated tumor and in the distant nonirradiated tumor or its metastasis. Knowing the role of annexin A1 in the control of hypoxia and inflammation that is characteristic of acute respiratory-distress syndrome (ARDS), we designed a hypothetical therapeutic strategy, based on the transplantation of mesenchymal stromal/stem cells stimulated with radiation, to alleviate the symptoms of patients who, due to pneumonia caused by SARS-CoV-2, require to be admitted to an intensive care unit for patients with life-threatening conditions. Supposedly a vectorized signaling system, we now believe that the exosomes released from radiation-activated-MSCs cells can reach other organs different from the lungs, where they will be up-taken after intravenous injection and thus extend the anti-inflammatory and antimicrobiological effects of the treatment, to cover systemic problems such as the treatment of patients with septic shock in general and for COVID-19 at this particular time. abstract: We have previously shown that the combination of radiotherapy with human umbilical-cord-derived mesenchymal stromal/stem cells (MSCs) cell therapy significantly reduces the size of the xenotumors in mice, both in the directly irradiated tumor and in the distant nonirradiated tumor or its metastasis. We have also shown that exosomes secreted from MSCs preirradiated with 2 Gy are quantitatively, functionally and qualitatively different from the exosomes secreted from nonirradiated mesenchymal cells, and also that proteins, exosomes and microvesicles secreted by MSCs suffer a significant change when the cells are activated or nonactivated, with the amount of protein present in the exosomes of the preirradiated cells being 1.5 times greater compared to those from nonirradiated cells. This finding correlates with a dramatic increase in the antitumor activity of the radiotherapy when is combined with MSCs or with preirradiated mesenchymal stromal/stem cells (MSCs*). After the proteomic analysis of the load of the exosomes released from both irradiated and nonirradiated cells, we conclude that annexin A1 is the most important and significant difference between the exosomes released by the cells in either status. Knowing the role of annexin A1 in the control of hypoxia and inflammation that is characteristic of acute respiratory-distress syndrome (ARDS), we designed a hypothetical therapeutic strategy, based on the transplantation of mesenchymal stromal/stem cells stimulated with radiation, to alleviate the symptoms of patients who, due to pneumonia caused by SARS-CoV-2, require to be admitted to an intensive care unit for patients with life-threatening conditions. With this hypothesis, we seek to improve the patients’ respiratory capacity and increase the expectations of their cure. url: https://www.ncbi.nlm.nih.gov/pubmed/32887260/ doi: 10.3390/cells9092015 id: cord-346445-hgqohdct author: Toyoshima, Yujiro title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 words: 3553.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-346445-hgqohdct.txt txt: ./txt/cord-346445-hgqohdct.txt summary: Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. abstract: The coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly expanded to a global pandemic. However, numbers of infected cases, deaths, and mortality rates related to COVID-19 vary from country to country. Although many studies were conducted, the reasons of these differences have not been clarified. In this study, we comprehensively investigated 12,343 SARS-CoV-2 genome sequences isolated from patients/individuals in six geographic areas and identified a total of 1234 mutations by comparing with the reference SARS-CoV-2 sequence. Through a hierarchical clustering based on the mutant frequencies, we classified the 28 countries into three clusters showing different fatality rates of COVID-19. In correlation analyses, we identified that ORF1ab 4715L and S protein 614G variants, which are in a strong linkage disequilibrium, showed significant positive correlations with fatality rates (r = 0.41, P = 0.029 and r = 0.43, P = 0.022, respectively). We found that BCG-vaccination status significantly associated with the fatality rates as well as number of infected cases. In BCG-vaccinated countries, the frequency of the S 614G variant had a trend of association with the higher fatality rate. We also found that the frequency of several HLA alleles, including HLA-A*11:01, were significantly associated with the fatality rates, although these factors were associated with number of infected cases and not an independent factor to affect fatality rate in each country. Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. url: https://doi.org/10.1038/s10038-020-0808-9 doi: 10.1038/s10038-020-0808-9 id: cord-258435-lhn34tc4 author: Tracy, C Shawn title: Public perceptions of quarantine: community-based telephone survey following an infectious disease outbreak date: 2009-12-16 words: 3724.0 sentences: 180.0 pages: flesch: 47.0 cache: ./cache/cord-258435-lhn34tc4.txt txt: ./txt/cord-258435-lhn34tc4.txt summary: CONCLUSION: To engender strong public support for quarantine and other restrictive measures, government officials and public health policy-makers would do well to implement a comprehensive system of supports and safeguards, to educate and inform frontline public health workers, and to engage the public at large in an open dialogue on the ethical use of restrictive measures during infectious disease outbreaks. In view of the evidence of potential adverse effects on individual well-being and psychosocial health, and owing to the critical necessity of high compliance in the event of a major infectious disease outbreak, it is increasingly important to understand how quarantine is perceived by the general public. The data reported in this paper are derived from a subset of 15 survey items specifically designed to measure public attitudes towards the use of quarantine during infectious disease outbreaks. abstract: BACKGROUND: The use of restrictive measures such as quarantine draws into sharp relief the dynamic interplay between the individual rights of the citizen on the one hand and the collective rights of the community on the other. Concerns regarding infectious disease outbreaks (SARS, pandemic influenza) have intensified the need to understand public perceptions of quarantine and other social distancing measures. METHODS: We conducted a telephone survey of the general population in the Greater Toronto Area in Ontario, Canada. Computer-assisted telephone interviewing (CATI) technology was used. A final sample of 500 individuals was achieved through standard random-digit dialing. RESULTS: Our data indicate strong public support for the use of quarantine when required and for serious legal sanctions against those who fail to comply. This support is contingent both on the implementation of legal safeguards to protect against inappropriate use and on the provision of psychosocial supports for those affected. CONCLUSION: To engender strong public support for quarantine and other restrictive measures, government officials and public health policy-makers would do well to implement a comprehensive system of supports and safeguards, to educate and inform frontline public health workers, and to engage the public at large in an open dialogue on the ethical use of restrictive measures during infectious disease outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/20015400/ doi: 10.1186/1471-2458-9-470 id: cord-266450-g9vihgbk author: Tran, Michael title: SARS-CoV-2 and pulmonary embolism: who stole the platelets? date: 2020-09-03 words: 1498.0 sentences: 93.0 pages: flesch: 38.0 cache: ./cache/cord-266450-g9vihgbk.txt txt: ./txt/cord-266450-g9vihgbk.txt summary: Careful attention to his daily platelet count suggested the possibility of immune mediated heparin-induced thrombocytopenia (HIT) which was confirmed by laboratory testing and resolved when anticoagulation was switched to a direct thrombin inhibitor. CONCLUSIONS: Since excessive platelet activation and in situ thrombosis occur in HIT, this case underscores the need to consider that thrombocytopenia in patients with SARS-CoV-2—most of whom receive heparinoids—may be unrecognized HIT. Emerging reports suggest the possibility of HIT developing in SARS-CoV-2 patients receiving heparin anticoagulation [4, 5] . The patient''s platelet count decreased from 487 k/uL to a nadir of 91 k/uL over the following 4 days, raising the concern for heparin induced thrombocytopenia (HIT) with an intermediate pretest probability by the 4Ts score of 4 ( Table 1 ). Platelet count and time points for anticoagulation administration and laboratory testing COVID-19 patients receiving heparin-involved treatment. abstract: BACKGROUND: Patients infected with SARS-CoV-2 often develop venous and arterial thrombosis. The high patient mortality is partly attributed to thrombotic events. An emerging trend is the presence of immunological phenomena including antiphospholipid antibodies which may promote thrombosis. The mechanism for these observations is not clear though many patients with SARS-CoV-2 develop thrombocytopenia. CASE PRESENTATION: We describe a patient with SARS-CoV-2 pneumonitis who presented with intermediate risk pulmonary embolism (PE). Careful attention to his daily platelet count suggested the possibility of immune mediated heparin-induced thrombocytopenia (HIT) which was confirmed by laboratory testing and resolved when anticoagulation was switched to a direct thrombin inhibitor. CONCLUSIONS: Since excessive platelet activation and in situ thrombosis occur in HIT, this case underscores the need to consider that thrombocytopenia in patients with SARS-CoV-2—most of whom receive heparinoids—may be unrecognized HIT. A central role for the platelet in the etiology of thrombosis during the COVID-19 pandemic should be explored. url: https://www.ncbi.nlm.nih.gov/pubmed/32905282/ doi: 10.1186/s12959-020-00229-8 id: cord-329971-09ubsq2k author: Tranoulis, Anastasios title: Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic date: 2020-06-30 words: 665.0 sentences: 38.0 pages: flesch: 43.0 cache: ./cache/cord-329971-09ubsq2k.txt txt: ./txt/cord-329971-09ubsq2k.txt summary: title: Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic To date, there is no clear evidence concerning the impact of SARS-CoV-2 on tubo-ovarian cancer care. Generally, cancer patients are seemingly at increased risk of SARS-CoV-2 infection owing to the underlying immunosuppression. According to the cases treated using the ''do no harm'' principle, we believe that the following situations should be considered for surgery: (1) To conclude, the effects of SARS-CoV-2 pandemic can be mitigated to a certain degree for patients with ovarian cancer, by adopting a careful and individualised triage and treatment management. A rigorous counseling concerning the risk of undergoing surgery during SARS-CoV-2 pandemic should be done, whilst the national and international health bodies recommendations will supportively guide clinicians prioritise ovarian cancer care. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan abstract: nan url: https://doi.org/10.1016/j.ejso.2020.06.043 doi: 10.1016/j.ejso.2020.06.043 id: cord-334988-brumg6jh author: Traugott, Marianna title: Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in Different Stages of Infection: Comparison of Commercial Enzyme-Linked Immunosorbent Assays and Rapid Tests date: 2020-05-30 words: 2236.0 sentences: 103.0 pages: flesch: 51.0 cache: ./cache/cord-334988-brumg6jh.txt txt: ./txt/cord-334988-brumg6jh.txt summary: We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction–confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. In the current study, we compared the diagnostic ability of 4 enzyme-linked immunosorbent assays (ELISAs), which assess SARS-CoV-2-specific antibodies of different immunoglobulin (Ig) classes (Euroimmun SARS-CoV-2 IgA and IgG and Wantai SARS-CoV-2 IgM and total antibody), and 2 rapid tests (Wantai SARS-CoV-2 Ab Rapid Test and Hangzhou AllTest Biotech 2019-nCoV IgG/IgM Rapid Test) in 77 patients with symptomatic SARS-CoV-2 infection. Of the 77 patients with PCR-confirmed SARS-CoV-2 infection, 30 individuals (12 female, 18 male; median age, 58 years; age range, 15-83 years) provided serum/plasma samples that were obtained at symptom onset or 1-5 days after the onset of disease (group 1). abstract: We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction–confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. Although test sensitivities were low (<40%) within the first 5 days after disease onset, immunoglobulin (Ig) M, IgA, and total antibody ELISAs increased in sensitivity to >80% between days 6 and 10 after symptom onset. The evaluated tests (including IgG and rapid tests) provided positive results in all patients at or after the 11th day after onset of disease. The specificities of the ELISAs were 83% (IgA), 98% (IgG), and 97% (IgM and total antibody). url: https://doi.org/10.1093/infdis/jiaa305 doi: 10.1093/infdis/jiaa305 id: cord-289535-srrfr1es author: Tregoning, J. S. title: Vaccines for COVID‐19 date: 2020-10-18 words: 14329.0 sentences: 793.0 pages: flesch: 44.0 cache: ./cache/cord-289535-srrfr1es.txt txt: ./txt/cord-289535-srrfr1es.txt summary: One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial abstract: Since the emergence of COVID‐19, caused by the SARS‐CoV‐2 virus at the end of 2019, there has been an explosion of vaccine development. By 24 September 2020, a staggering number of vaccines (more than 200) had started preclinical development, of which 43 had entered clinical trials, including some approaches that have not previously been licensed for human vaccines. Vaccines have been widely considered as part of the exit strategy to enable the return to previous patterns of working, schooling and socializing. Importantly, to effectively control the COVID‐19 pandemic, production needs to be scaled‐up from a small number of preclinical doses to enough filled vials to immunize the world’s population, which requires close engagement with manufacturers and regulators. It will require a global effort to control the virus, necessitating equitable access for all countries to effective vaccines. This review explores the immune responses required to protect against SARS‐CoV‐2 and the potential for vaccine‐induced immunopathology. We describe the profile of the different platforms and the advantages and disadvantages of each approach. The review also addresses the critical steps between promising preclinical leads and manufacturing at scale. The issues faced during this pandemic and the platforms being developed to address it will be invaluable for future outbreak control. Nine months after the outbreak began we are at a point where preclinical and early clinical data are being generated for the vaccines; an overview of this important area will help our understanding of the next phases. url: https://www.ncbi.nlm.nih.gov/pubmed/32935331/ doi: 10.1111/cei.13517 id: cord-345405-ngpsgn63 author: Tremiliosi, Guilherme C. title: Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date: 2020-06-26 words: 6259.0 sentences: 339.0 pages: flesch: 46.0 cache: ./cache/cord-345405-ngpsgn63.txt txt: ./txt/cord-345405-ngpsgn63.txt summary: An adaptation of ISO 18184 Determination of antiviral activity of textile products Standard Method [23] was used as a reference for a quantitative method to evaluate the treated polycotton''s ability to inactivate the SARS-CoV-2 virus particles (SARS-CoV-2/human/BRA/SP02cc/2020 -MT350282), under the tested conditions, at two different time intervals (2 and 5 minutes of contact time). The antiviral activity test was designed to determine the inactivation of viral particles upon short exposure to the products, which in this case were the Ag-based treated polycotton samples incubated in liquid media. Table 6 shows the number of copies of the control media without any fabric sample, non-treated polycotton, and the two Ag-based treated polycotton samples at the two different tested time periods. Application of silver nanoparticles to cotton fabric as an antibacterial textile finish Fibers Polym Antibacterial properties of cotton fabric treated with silver nanoparticles abstract: Pathogens (bacteria, fungus and virus) are becoming a potential threat to the health of human beings and environment worldwide. They widely exist in the environment, with characteristics of variety, spreading quickly and easily causing adverse reactions. In this work, an Ag-based material is used to be incorporated and functionalized in polycotton fabrics using pad-dry-cure method. This composite proved to be effective for inhibiting the SARS-CoV-2 virus, decreasing the number of replicates in 99.99% after an incubation period of 2 minutes. In addition, it caused 99.99% inhibition of the pathogens S. aureus, E. coli and C. albicans, preventing cross-infections and does not cause allergies or photoirritation processes, demonstrating the safety of its use. url: https://doi.org/10.1101/2020.06.26.152520 doi: 10.1101/2020.06.26.152520 id: cord-328122-nfvbog77 author: Tresoldi, Ilaria title: SARS‐COV‐2 and infectivity: Possible increase in infectivity associated to integrin motif expression date: 2020-04-10 words: 698.0 sentences: 48.0 pages: flesch: 48.0 cache: ./cache/cord-328122-nfvbog77.txt txt: ./txt/cord-328122-nfvbog77.txt summary: It has been proposed that SARS-COV-2 has acquired the spike glycoprotein RGD (KGD in SARS-CoV) 1 integrin-binding site which is considered significant for the virus transmission efficiency. The most common of these motifs is the minimal peptide sequence for binding integrins, RGD, which is known for its role in virus infection via its ability to interact with over half of the more than 20 known integrins. 4 Besides the fibronectin binding motif RGD, other integrinbinding sites are specifically expressed in SARS-COV-2, and, particularly, a change from a LDV to a LDI motif is likely significant. 5 We investigated the protein sequence of the human coronavirus and compared it to SARS and bat coronavirus to identify any eventual overexpression of other integrin-binding sites. Orf1ab polyprotein has many integrin-binding motifs implicated in cell adhesion with binding sites on Fibronectin, Tenascin_C, and VCAM. abstract: SARS-COV2 represents the causal agent of a potentially fatal disease (COVID-19) that is actually of great global public health concern. SARS-COV2 has diffused throughout the world surprisingly fast demonstrating a far greater infectivity than previously known human coronaviruses and it is also responsible for an unusual high variety of symptoms in affected patients. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32246503/ doi: 10.1002/jmv.25831 id: cord-274416-bmvazgj7 author: Trevisanuto, Daniele title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan date: 2020-04-24 words: 3761.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-274416-bmvazgj7.txt txt: ./txt/cord-274416-bmvazgj7.txt summary: title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection. Although it is unlikely that neonates born from SARS-CoV-2-infected mothers require an intensive care management related to the maternal infection [18, 19] , coronaviruses may result in adverse outcomes for the fetus and infant (intrauterine growth restriction, preterm delivery, admission to the neonatal intensive care unit (NICU), spontaneous abortion and perinatal death) [16, 17, 25] . Our designated approach for the management of women with suspected or confirmed CO-VID-19 and their infants before, during, and after delivery provides cues to reduce the chance of neonatal infection and therefore potential negative outcomes in the newborn. abstract: Coronavirus disease 2019 (COVID-19), caused by the novel SARS-CoV-2 virus, is rapidly spreading across the world. As the number of infections increases, those of infected pregnant women and children will rise as well. Controversy exists whether COVID-19 can be transmitted in utero and lead to disease in the newborn. As this chance cannot be ruled out, strict instructions for the management of mothers and newborn infants are mandatory. This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection. url: https://doi.org/10.1159/000507935 doi: 10.1159/000507935 id: cord-284429-d7qxfo6d author: Trezza, Alfonso title: An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors date: 2020-08-17 words: 4720.0 sentences: 244.0 pages: flesch: 47.0 cache: ./cache/cord-284429-d7qxfo6d.txt txt: ./txt/cord-284429-d7qxfo6d.txt summary: We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein – ACE2 interaction inhibitor. By combining molecular dynamics simulations (MD), Supervised MD (SuMD), Steered MD (SMD) and interaction energy calculations, we showed that Simeprevir and Lumacaftor bind RDB with high affinity and prevent ACE2 interaction. In order to identify possible PPI inhibitors the transient pocket that contained key residues involved in hACE2 recognition and binding (Fig. 1A ) was selected and used for the virtual screening of 1582 FDA-approved drugs. In order to understand if Simeprevir and Lumacaftor are able to interfere and prevent the binding between the S glycoprotein and ACE2, we ran a Supervised Molecular Dynamics (SuMD) simulations. Using SuMD it is possible to simulate the full binding process of ACE2 to RBD in presence of Simeprevir or Lumacaftor in an unbiased way (i.e. independently from starting relative positions), taking into account hydration patterns and drug binding-unbinding events. abstract: The Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The virus has rapidly spread in humans, causing the ongoing Coronavirus pandemic. Recent studies have shown that, similarly to SARS-CoV, SARS-CoV-2 utilises the Spike glycoprotein on the envelope to recognise and bind the human receptor ACE2. This event initiates the fusion of viral and host cell membranes and then the viral entry into the host cell. Despite several ongoing clinical studies, there are currently no approved vaccines or drugs that specifically target SARS-CoV-2. Until an effective vaccine is available, repurposing FDA approved drugs could significantly shorten the time and reduce the cost compared to de novo drug discovery. In this study we attempted to overcome the limitation of in silico virtual screening by applying a robust in silico drug repurposing strategy. We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein – ACE2 interaction inhibitor. Our data showed that Simeprevir and Lumacaftor bind the receptor-binding domain of the Spike protein with high affinity and prevent ACE2 interaction. url: https://doi.org/10.1038/s41598-020-70863-9 doi: 10.1038/s41598-020-70863-9 id: cord-327511-e3idvknz author: Trifan, G. title: Characteristics of a Diverse Cohort of Stroke Patients with SARS-CoV-2 and Outcome by Sex date: 2020-09-11 words: 3482.0 sentences: 233.0 pages: flesch: 52.0 cache: ./cache/cord-327511-e3idvknz.txt txt: ./txt/cord-327511-e3idvknz.txt summary: CONCLUSION: In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this multicenter study of patients with stroke and SARS-CoV-2 infection admitted to comprehensive stroke centers in the Chicagoland area, males were more likely than females to have severe COVID-19 manifestations and worse ischemic stroke outcome at hospital discharge. abstract: BACKGROUND AND PURPOSE: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is associated with stroke. The role of sex on stroke outcome has not been investigated. To objective of this paper is to describe the characteristics of a diverse cohort of acute stroke patients with COVID-19 disease and determine the role of sex on outcome. METHODS: This is a retrospective study of patients with acute stroke and SARS-CoV-2 infection admitted between March 15 to May 15, 2020 to one of the six participating comprehensive stroke centers. Baseline characteristics, stroke subtype, workup, treatment and outcome are presented as total number and percentage or median and interquartile range. Outcome at discharge was determined by the modified Rankin Scale Score (mRS). Variables and outcomes were compared for males and females using univariate and multivariate analysis. RESULTS: The study included 83 patients, 47% of which were Black, 28% Hispanics/Latinos, and 16% whites. Median age was 64 years. Approximately 89% had at least one preexisting vascular risk factor (VRF). The most common complications were respiratory failure (59%) and septic shock (34%). Compared with females, a higher proportion of males experienced severe SARS-CoV-2 symptoms requiring ICU hospitalization (73% vs. 49%; p=0.04). When divided by stroke subtype, there were 77% ischemic, 19% intracerebral hemorrhage and 3% subarachnoid hemorrhage. The most common ischemic stroke etiologies were cryptogenic (39%) and cardioembolic (27%). Compared with females, males had higher mortality (38% vs. 13%; p=0.02) and were less likely to be discharged home (12% vs. 33%; p=0.04). After adjustment for age, race/ethnicity, and number of VRFs, mRS was higher in males than in females (OR=1.47, 95% CI=1.03-2.09). CONCLUSION: In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. url: https://api.elsevier.com/content/article/pii/S1052305720307321 doi: 10.1016/j.jstrokecerebrovasdis.2020.105314 id: cord-253422-m18ngwbt author: Trimarchi, Hernán title: COVID-19 and acute kidney injury in pediatric subjects: is there a place for eculizumab treatment? date: 2020-09-29 words: 976.0 sentences: 47.0 pages: flesch: 39.0 cache: ./cache/cord-253422-m18ngwbt.txt txt: ./txt/cord-253422-m18ngwbt.txt summary: One of the reasons we found this case of particular interest is that it reminds us of a similar experience by one of the authors who observed a dramatic effect of eculizumab in a 4-year-old child with diffuse proliferative lupus nephritis who developed complement-mediated TMA and AKI [6] . She fully recovered but needed chronic eculizumab treatment for atypical hemolytic uremic syndrome (aHUS). In both cases the initial disease was a severe multisystem inflammatory syndrome due to SARS-CoV-2 or systemic lupus erythematosus. He was admitted with severe diffuse bilateral SARS-CoV-2 pneumonia [9] and elevated D-dimer and fibrinogen concentrations, suggesting a pro-coagulant state due to pulmonary microthrombosis, as described in autopsies of subjects with COVID-19 infections [1] , despite ongoing chronic eculizumab treatment. However, while waiting for further follow-up, the present report deserves our utmost interest because it highlights the role of the complement system activation in SARS-COV-2 infection and the pharmacological interventions to attenuate the micro-thrombotic complications associated with COVID-19. Eculizumab, SARS-COV-2 and atypical hemolytic uremic syndrome abstract: nan url: https://doi.org/10.1007/s40620-020-00859-1 doi: 10.1007/s40620-020-00859-1 id: cord-329853-kf3kh26y author: Trimarchi, Hernán title: Eculizumab, SARS-CoV-2 and atypical hemolytic uremic syndrome date: 2020-09-27 words: 1097.0 sentences: 64.0 pages: flesch: 39.0 cache: ./cache/cord-329853-kf3kh26y.txt txt: ./txt/cord-329853-kf3kh26y.txt summary: Complement activation is thought to contribute to endothelial injury and there are at least seven ongoing clinical trials testing six different anti-complement strategies for coronavirus disease 2019 (COVID-19), including eculizumab. We herein report on a kidney transplant patient with aHUS on chronic eculizumab therapy that developed severe COVID-19 despite eculizumab administration early in the course of the disease. Although eculizumab was unable to prevent the development of severe endothelial cell injury, as assessed by increasing D-dimer levels from 292 to 10 586 ng/mL, the patient eventually recovered following dexamethasone and convalescent plasma administration. To our knowledge, this is the first report of a kidney transplant recipient with aHUS on eculizumab therapy who developed SARS-CoV-2 infection. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: a report of five cases abstract: Atypical hemolytic uremic syndrome (aHUS) treatment consists of eculizumab. Severe acute respiratory syndrome coronavirus 2 causes severe pneumonia and endothelial injury that leads to a prothrombotic state that may be complicated by macrovascular and microvascular thrombosis. Complement activation is thought to contribute to endothelial injury and there are at least seven ongoing clinical trials testing six different anti-complement strategies for coronavirus disease 2019 (COVID-19), including eculizumab. We herein report on a kidney transplant patient with aHUS on chronic eculizumab therapy that developed severe COVID-19 despite eculizumab administration early in the course of the disease. Although eculizumab was unable to prevent the development of severe endothelial cell injury, as assessed by increasing D-dimer levels from 292 to 10 586 ng/mL, the patient eventually recovered following dexamethasone and convalescent plasma administration. url: https://www.ncbi.nlm.nih.gov/pubmed/33117528/ doi: 10.1093/ckj/sfaa166 id: cord-305091-tfn2pyc6 author: Tripathi, Praveen Kumar title: Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2 date: 2020-12-01 words: 4026.0 sentences: 240.0 pages: flesch: 52.0 cache: ./cache/cord-305091-tfn2pyc6.txt txt: ./txt/cord-305091-tfn2pyc6.txt summary: We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL(Pro) of SARS-CoV-2. COVID-19 is an infectious disease caused by a newly discovered positive-sense single-stranded RNA virus called the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The involvement of H-bond donors and acceptors around hydrophobic sites compel the Teicoplanin molecule to interact within the inhibitor binding pocket of the 3CL Pro protease. In a recent MD simulation study, it was reported that Teicoplanin in complex with SARS-CoV-2 main protease has stable ligand-protein complex and intermolecular interactions during the simulated trajectory [21] . We report Teicoplanin as an effective drug against 3CL Pro which works at a micromolar concentration of 1.5 µM (Fig. 2) and acts by blocking the active site of the protease (Fig. 4F) . abstract: The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a global catastrophe. The virus requires main protease for processing the viral polyproteins PP1A and PP1AB translated from the viral RNA. In search of a quick, safe and successful therapeutic agent; we screened various clinically approved drugs for the in-vitro inhibitory effect on 3CL(Pro) which may be able to halt virus replication. The methods used includes protease activity assay, fluorescence quenching, surface plasmon resonance (SPR), Thermofluor® Assay, Size exclusion chromatography and in-silico docking studies. We found that Teicoplanin as most effective drug with IC(50) ~ 1.5 μM. Additionally, through fluorescence quenching Stern–Volmer quenching constant (K(SV)) for Teicoplanin was estimated as 2.5 × 10(5) L·mol(−1), which suggests a relatively high affinity between Teicoplanin and 3CL(Pro) protease. The SPR shows good interaction between Teicoplanin and 3CL(Pro) with K(D) ~ 1.6 μM. Our results provide critical insights into the mechanism of action of Teicoplanin as a potential therapeutic against COVID-19. We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL(Pro) of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32853604/ doi: 10.1016/j.ijbiomac.2020.08.166 id: cord-319983-e4f2sfl4 author: Tripathi, Shweta title: The COVID-19: Current understanding date: 2020-09-26 words: 4293.0 sentences: 261.0 pages: flesch: 53.0 cache: ./cache/cord-319983-e4f2sfl4.txt txt: ./txt/cord-319983-e4f2sfl4.txt summary: Till the date of writing this article (August 15, 2020), a total number of 2526192+65002 laboratory-confirmed cases of COVID-19 from 35 states and Union Territories, out of which 1,915,580 (71.91%) recovered, while 50,924 (1.93%) deaths are reported in India [8, 10] . According to the Ministry of Family and Health Welfare of India; a suspected case is defined as a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, and shortness of breath) and a history of travel to or residence in a location reporting community transmission of COVID-19, 14 days prior of the beginning of symptoms. However, more clinical trials are needed to prove the safety and effectiveness of convalescent plasma transfusion in SARS-CoV-2 infected patients [48] . Epidemiological and clinical characteristics of 99 cases of 2019 novel Coronavirus pneumonia in Wuhan, China: A descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel Coronavirus-infected pneumonia in Wuhan, China abstract: In December 2019, China reported several cases of a new coronavirus disease (COVID-19). The COVID-19 outbreak, which was initially limited to Wuhan, China, has rapidly spread worldwide. Infection of the disease occurs through exposure to the virus through inhalation of respiratory droplets or if a person touches a mucosal surface after touching an object with the virus on it. The common symptoms of COVID-19 are fever, dry cough, dyspnea (difficult or labored breathing), fatigue, chest pain, and myalgia (muscle pain), etc. Real-time polymerase chain reaction is used to detect the virus in sputum, throat, nasal swabs, and secretion of lower respiratory samples. Early diagnosis, isolation, and supportive care are necessary for the treatment of the patients. The present review aims to provide recent information on COVID-19 related to its epidemiology, clinical symptoms, and management. This article also summarizes the current understanding of severe acute respiratory syndrome coronavirus-2 and its history of origin. url: https://www.ncbi.nlm.nih.gov/pubmed/33132617/ doi: 10.14202/vetworld.2020.1998-2005 id: cord-333234-yvixy77x author: Triposkiadis, Filippos title: Renin-angiotensin-system inhibition in the context of corona virus disease-19: experimental evidence, observational studies, and clinical implications date: 2020-09-01 words: 3226.0 sentences: 153.0 pages: flesch: 46.0 cache: ./cache/cord-333234-yvixy77x.txt txt: ./txt/cord-333234-yvixy77x.txt summary: While the potential for benefit with the use of renin-angiotensin-aldosterone system inhibitors (RAASi) and the risks from stopping them is more evident, potential harm by RAΑSi may also be caused by the increase in the activity of the ACE2 receptor, the inefficient counter regulatory axis in the lungs in which the proinflammatory prolyloligopeptidase (POP) is the main enzyme responsible for the conversion of deleterious angiotensin (ANG) II to protective ANG [1–7] and the proinflammatory properties of ACE2(+) cells infected with SARS-CoV-2. In a recent statement of the European Medicinal Agencies (EMA), it is emphasized (10 June 2020 EMA/284513/2020): "Recent observational studies of angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs, also called sartans) have not shown an effect of these medicines on the risk of becoming infected with severe acute respiratory syndrome coronavirus 2 (the virus causing COVID-19) and do not indicate a negative impact on the outcome for patients with COVID-19 disease. abstract: Coronavirus disease 2019 (COVID-19) is due to severe acute respiratory syndrome coronavirus (SARS-CoV)-2 which binds and enters the host cells through the angiotensin-converting enzyme (ACE)2. While the potential for benefit with the use of renin-angiotensin-aldosterone system inhibitors (RAASi) and the risks from stopping them is more evident, potential harm by RAΑSi may also be caused by the increase in the activity of the ACE2 receptor, the inefficient counter regulatory axis in the lungs in which the proinflammatory prolyloligopeptidase (POP) is the main enzyme responsible for the conversion of deleterious angiotensin (ANG) II to protective ANG [1–7] and the proinflammatory properties of ACE2(+) cells infected with SARS-CoV-2. Acknowledging the proven RAΑSi benefit in patients with several diseases such as hypertension, heart failure, coronary disease, and diabetic kidney disease in the non-COVID-19 era, it is a reasonable strategy in this period of uncertainty to use these agents judiciously with careful consideration and to avoid the use of RAASi in select patients whenever possible, until definitive evidence becomes available. url: https://www.ncbi.nlm.nih.gov/pubmed/32875490/ doi: 10.1007/s10741-020-10022-4 id: cord-317067-u90zkjk9 author: Trottein, François title: Potential causes and consequences of gastrointestinal disorders during a SARS-CoV-2 infection date: 2020-07-03 words: 639.0 sentences: 48.0 pages: flesch: 44.0 cache: ./cache/cord-317067-u90zkjk9.txt txt: ./txt/cord-317067-u90zkjk9.txt summary: Intensive research on the pathogenic mechanisms used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed – notably in order to identify potential drug targets. Here, we review gastrointestinal disorders in patients with COVID-19, suggest hypothetical mechanisms leading to gut symptoms, and discuss the potential consequences of gastrointestinal disorders on the outcome of the disease. Lastly, we discuss the role of the gut microbiota during respiratory viral infections and suggest that targeting gut dysbiosis may help to control the pathogenesis of COVID-19. In this review, Trottein & Sokol present hypothetical mechanisms leading to gut symptoms in patients with COVID-19 and discuss their potential consequences on disease severity. They also discuss the role of the gut microbiota in disease and the potential interest of targeting it to improve COVID-19 pathogenesis. Clinical characteristics of 138 hospitalized patients with 2019 novel 589 coronavirus-infected pneumonia in Wuhan, China abstract: Summary Coronaviruses cause several human diseases, including severe acute respiratory syndrome. The global coronaviruses disease 2019 (COVID-19) pandemic has become a huge threat to humans. Intensive research on the pathogenic mechanisms used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed – notably in order to identify potential drug targets. Clinical studies of patients with COVID-19 have shown that gastrointestinal disorders appear to precede or follow the respiratory symptoms. Here, we review gastrointestinal disorders in patients with COVID-19, suggest hypothetical mechanisms leading to gut symptoms, and discuss the potential consequences of gastrointestinal disorders on the outcome of the disease. Lastly, we discuss the role of the gut microbiota during respiratory viral infections and suggest that targeting gut dysbiosis may help to control the pathogenesis of COVID-19. url: https://doi.org/10.1016/j.celrep.2020.107915 doi: 10.1016/j.celrep.2020.107915 id: cord-283895-1p5uog38 author: Trottier, J. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 words: 1925.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-283895-1p5uog38.txt txt: ./txt/cord-283895-1p5uog38.txt summary: Indeed, several reports indicate that SARS-CoV-2 RNA was readily detected in wastewater, and it is proposed that such approach could anticipate the occurrence of novel COVID-19 outbreaks in low prevalence regions , La Rosa et al., 2020 , Medema et al., 2020 , Orive et al., 2020 , Randazzo et al., 2020 . First, we showed that the Ebola standard (Ebo Std) primer/probe set was not detecting RNA from SARS-CoV-2-infected Vero E6 cells (Table 1) . . https://doi.org/10.1101/2020.07.08.20148882 doi: medRxiv preprint Next, we measured the SARS-CoV-2 RNA levels using N1 and N3 primer/probe sets in wastewater collected upstream of the main WWTP of the Montpellier metropolitan area on May 7 th , 18 th , 26 th , June 4 th , 15 th and 25 th (Figure 2A ). This intriguing result is reminiscent of a recent Spanish study, in which the authors could detect SARS-CoV-2 RNA in wastewater weeks before the first COVID-19 cases were reported (Randazzo et al., 2020) . abstract: The evolution of the COVID-19 pandemic can be monitored through the detection of SARS-CoV-2 RNA in sewage. Here, we measured the amount of SARS-CoV-2 RNA at the inflow point of the main waste water treatment plant (WWTP) of Montpellier, France. We collected samples 4 days before the end of lockdown and up to 45 days post-lockdown. We detected increased amounts of SARS-CoV-2 RNA at the WWTP, which was not correlated with the number of newly diagnosed patients. Future epidemiologic investigations may explain such asynchronous finding. url: https://doi.org/10.1101/2020.07.08.20148882 doi: 10.1101/2020.07.08.20148882 id: cord-339152-wfakzb6w author: Trovato, Maria title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 words: 12000.0 sentences: 540.0 pages: flesch: 38.0 cache: ./cache/cord-339152-wfakzb6w.txt txt: ./txt/cord-339152-wfakzb6w.txt summary: Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. abstract: In the last decades, a number of infectious viruses have emerged from wildlife or re-emerged, generating serious threats to the global health and to the economy worldwide. Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. Vaccination is probably the most effective tool in helping the immune system to activate protective responses against pathogens, reducing morbidity and mortality, as proven by historical records. Under health emergency conditions, new and alternative approaches in vaccine design and development are imperative for a rapid and massive vaccination coverage, to manage a disease outbreak and curtail the epidemic spread. This review gives an update on the current vaccination strategies for some of the emerging/re-emerging viruses, and discusses challenges and hurdles to overcome for developing efficacious vaccines against future pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/33013898/ doi: 10.3389/fimmu.2020.02130 id: cord-323685-gjocoa60 author: Tsai, Shang-Jui title: Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date: 2020-11-06 words: 5332.0 sentences: 289.0 pages: flesch: 49.0 cache: ./cache/cord-323685-gjocoa60.txt txt: ./txt/cord-323685-gjocoa60.txt summary: The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Conclusion Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins. These antigen-responsive CD4+ and CD8+ populations were present nearly two months after the final boost injection, indicating that LSNME/S W1 vaccination had elicited a sustained cellular immune response to both of these SARS-CoV-2 structural proteins. As for the future development of the LSNME/S W1 vaccine, we anticipate that follow-on studies in larger animal models at doses comparable to other mRNA vaccines will demonstrate a desirable combination of safety, balanced immune responses, and when challenged, protection against SARS-CoV-2 infection and/or disease. abstract: Background In less than a year from its zoonotic entry into the human population, SARS-CoV-2 has infected more than 45 million people, caused 1.2 million deaths, and induced widespread societal disruption. Leading SARS-CoV-2 vaccine candidates immunize with the viral spike protein delivered on viral vectors, encoded by injected mRNAs, or as purified protein. Here we describe a different approach to SARS-CoV-2 vaccine development that uses exosomes to deliver mRNAs that encode antigens from multiple SARS-CoV-2 structural proteins. Approach Exosomes were purified and loaded with mRNAs designed to express (i) an artificial fusion protein, LSNME, that contains portions of the viral spike, nucleocapsid, membrane, and envelope proteins, and (ii) a functional form of spike. The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Results Immunized mice developed CD4+, and CD8+ T-cell reactivities that respond to both the SARS-CoV-2 nucelocapsid protein and the SARS-CoV-2 spike protein. These responses were apparent nearly two months after the conclusion of vaccination, as expected for a durable response to vaccination. In addition, the spike-reactive CD4+ T-cells response was associated with elevated expression of interferon gamma, indicative of a Th1 response, and a lesser induction of interleukin 4, a Th2-associated cytokine. Vaccinated mice showed no sign of altered growth, injection-site hypersensitivity, change in white blood cell profiles, or alterations in organ morphology. Consistent with these results, we also detected moderate but sustained anti-nucleocapsid and anti-spike antibodies in the plasma of vaccinated animals. Conclusion Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins. url: https://doi.org/10.1101/2020.11.06.371419 doi: 10.1101/2020.11.06.371419 id: cord-292337-74c69z28 author: Tsai, Shin-Han title: Transporting Patient with Suspected SARS date: 2004-07-17 words: 1471.0 sentences: 90.0 pages: flesch: 57.0 cache: ./cache/cord-292337-74c69z28.txt txt: ./txt/cord-292337-74c69z28.txt summary: Because medical facilities are limited on these islands, the Department of Health authorized the National Aeromedical Consultation Center (NACC), a physician-based 24-hour control center that coordinates all aeromedical transport of critically ill or injured patients within Taiwan, to coordinate transporting these patients to designated SARS hospitals in Taipei. When leaving the pre-isolation room, the physician and the PIU were sprayed with a sodium hypochloride solution before the first layer of personal protective equipment was removed. Although one report by Christopher and Eitzen (2) suggested the value of an aeromedical team to evacuate patients with suspected lethal, infectious diseases, limited evidence supported a safer means of transportation that would possibly reduce transmission of SARS to persons taking part in the mission. Interim guidance: air medical transport for severe acute respiratory syndromes (SARS) patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15338533/ doi: 10.3201/1007.030608 id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 words: 4920.0 sentences: 297.0 pages: flesch: 35.0 cache: ./cache/cord-333730-qsx0m68e.txt txt: ./txt/cord-333730-qsx0m68e.txt summary: However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial abstract: There have been several episodes of viral infection evolving into epidemics in recent decades, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the latest example. Its high infectivity and moderate mortality have resulted in an urgent need to find an effective treatment modality. Although the category of immunosuppressive drugs usually poses a risk of infection due to interference of the immune system, some of them have been found to exert antiviral properties and are already used in daily practice. Recently, hydroxychloroquine and baricitinib have been proposed as potential drugs for SARS-CoV-2. In fact, there are other immunosuppressants known with antiviral activities, including cyclosporine A, hydroxyurea, minocycline, mycophenolic acid, mycophenolate mofetil, leflunomide, tofacitinib, and thalidomide. The inherent antiviral activity could be a treatment choice for patients with coexisting rheumatological disorders and infections. Clinical evidence, their possible mode of actions and spectrum of antiviral activities are included in this review article. LAY SUMMARY: Immunosuppressants often raise the concern of infection risks, especially for patients with underlying immune disorders. However, some disease-modifying antirheumatic drugs (DMARDs) with inherent antiviral activity would be a reasonable choice in the situation of concomitant viral infections and flare up of autoimmune diseases. This review covers DMARDs of treatment potential for SARS-CoV-2 in part I, and antiviral mechanisms plus trial evidence for viruses other than SARS-CoV-2 in part II. url: https://www.ncbi.nlm.nih.gov/pubmed/32952617/ doi: 10.1177/1759720x20947296 id: cord-354948-q5eouyi2 author: Tsao, Kuo‐Chien title: False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome date: 2005-09-19 words: 2812.0 sentences: 161.0 pages: flesch: 63.0 cache: ./cache/cord-354948-q5eouyi2.txt txt: ./txt/cord-354948-q5eouyi2.txt summary: title: False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome An earlier serum collected from the same patient on the 3rd day after disease onset was retested, and it was found that the results were negative for both SARS-CoV and HTLV antibodies. It was speculated that some SARS-CoV peptides common to HTLV might be responsible for the false positive results observed in HTLV antibody detection. These four common peptides were synthesized and tested the cross-reactivity of antibodies in the sera of SARS versus HTLV-infected patients. These four common peptides were synthesized further and tested for crossreactivity of antibodies in the sera of SARS versus HTLV infected-patients. This finding suggests that among the antibodies in the sera of SARS patients, those with cross-reactivity with HTLV peptides might disappear Six SARS coronavirus genomes are TW1/ay291451, CUHK-W1/ay278554, TOR2/nc_004718, CUHK-Su10/ay282752, BJ01/ay278488, and Urbani /ay278741. abstract: Taiwan suffered from the outbreak of severe acute respiratory syndrome (SARS) in 2003. Our laboratory performed a series of virology and serology tests for SARS patients admitted to our hospital. Cross‐reactivity was found when testing for antibody against human T‐cell lymphotropic virus (HTLV) in one patient with SARS. Therefore, antibodies against HTLV were examined in paired‐sera from 26 SARS patients. ELISA and a neutralization test were used to measure anti‐SARS antibodies. Seroconversion for antibody against SARS‐CoV was observed in all patients. Surprisingly, with the use of ELISA for HTLV, sera for 13 patients were positive for HTLV (50%), and seroconversion for HTLV was also observed in 10 patients (38.5%). Western blot for HTLV on those 26 paired‐sera from 13 HTLV‐positive patients displayed 5 positive results for HTLV‐I, 7 positive results for HTLV‐II, 1 positive result for both HTLV‐I and II, 9 negative results for either HTLV‐I or HTLV‐II, and 4 “indeterminate” results. The findings that antibody to HTLV can be detected in blood samples collected from SARS patients provide important information for safe handling of blood products. Without such knowledge, blood products can be discarded mistakenly even though they contain anti‐SARS‐CoV antibodies that may be potentially valuable for SARS therapy. J. Med. Virol. 77:331–336, 2005. © 2005 Wiley‐Liss, inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16173022/ doi: 10.1002/jmv.20460 id: cord-349827-0trvostt author: Tse, Alan C.B. title: Crisis management and recovery: how restaurants in Hong Kong responded to SARS date: 2005-01-29 words: 2934.0 sentences: 154.0 pages: flesch: 55.0 cache: ./cache/cord-349827-0trvostt.txt txt: ./txt/cord-349827-0trvostt.txt summary: This article reviews a typology of crises, examines the crisis response of restaurants in Hong Kong, illustrates how local restaurants deal with this unprecedented situation and develop strategies for management and recovery. Restaurants in Hong Kong have already been put under great pressure to survive in the harsh market environment resulting from the Asian financial crisis of 1997, but the Severe Acute Respiratory Syndrome (SARS) outbreak in March 2003 was a death sentence to the industry. The SARS instance in Hong Kong had indirectly generated crises of the social environment because many restaurants experienced liquidity problems after the outbreak, and had to lay off thousands of staff or force them to take no-pay leave. In the SARS outbreak, for example, restaurant managers'' attempt to lay off staff without proper compensation to improve their cash flow position may lead to confrontation with the labour, which may subsequently cause a crisis of the social environment type. abstract: The 2003 Severe Acute Respiratory Syndrome (SARS) outbreak constitutes an example of the many crises that a restaurant may encounter. This article reviews a typology of crises, examines the crisis response of restaurants in Hong Kong, illustrates how local restaurants deal with this unprecedented situation and develop strategies for management and recovery. The lessons and experience gained from dealing with the SARS crisis serve as references for restaurants in other destinations when they face similar crises in future. url: https://api.elsevier.com/content/article/pii/S0278431904001203 doi: 10.1016/j.ijhm.2004.12.001 id: cord-348071-0zlzblwi author: Tseng, Jen-Yu title: Potential implications of SARS-CoV-2 on pregnancy date: 2020-05-13 words: 509.0 sentences: 33.0 pages: flesch: 62.0 cache: ./cache/cord-348071-0zlzblwi.txt txt: ./txt/cord-348071-0zlzblwi.txt summary: The Wuhan Coronavirus (recently named SARS-CoV-2) has been making headline news around the world as there are over 60,000 confirmed cases and a total of over 1300 deaths in China alone since the start of the outbreak [1]. In a review of previous coronavirus infections in pregnancy, there were 13 cases of SARS-CoV and 11 cases of MERS-CoV reported in the literature [3, 4] . Maternal outcome of the 13 cases: 4 cases had miscarriage, 2 opted for termination of pregnancy, 2 succumbed to SARS, 2 required mechanical ventilation, and 3 were treated conservatively. Maternal outcome of the 11 MERS-CoV cases: 2 were asymptomatic, 3 succumbed to MERS, 2 required mechanical ventilation, 3 were treated conservatively, and 1 refused treatment. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature abstract: nan url: https://doi.org/10.1016/j.tjog.2020.03.025 doi: 10.1016/j.tjog.2020.03.025 id: cord-303880-zv4nbz9p author: Tsikala Vafea, Maria title: Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19 date: 2020-06-24 words: 5485.0 sentences: 328.0 pages: flesch: 42.0 cache: ./cache/cord-303880-zv4nbz9p.txt txt: ./txt/cord-303880-zv4nbz9p.txt summary: RESULTS: Key focus areas include the applications of artificial intelligence, the use of Big Data and Internet of Things, the importance of mathematical modeling for predictions, utilization of technology for community screening, the use of nanotechnology for treatment and vaccine development, the utility of telemedicine, the implementation of 3D-printing to manage new demands and the potential of robotics. The technologies in this review include: artificial intelligence (AI), machine learning and deep learning, nanomedicine, novel technologies for vaccines development and therapeutics, novel mathematical modeling, big data, internet of things (IoT), telemedicine, robots, and 3D printing technology. Mei et al proposed an AI system based on machine learning and deep learning models that combines demographic (age, sex) and clinical information (laboratory test results, reported symptoms, history of exposure etc.) with chest imaging findings for rapid identification of patients with COVID-19. abstract: INTRODUCTION: The COVID-19 pandemic has caused an unprecedented health and economic worldwide crisis. Innovative solutions are imperative given limited resources and immediate need for medical supplies, healthcare support and treatments. AIM: The purpose of this review is to summarize emerging technologies being implemented in the study, diagnosis, and treatment of COVID-19. RESULTS: Key focus areas include the applications of artificial intelligence, the use of Big Data and Internet of Things, the importance of mathematical modeling for predictions, utilization of technology for community screening, the use of nanotechnology for treatment and vaccine development, the utility of telemedicine, the implementation of 3D-printing to manage new demands and the potential of robotics. CONCLUSION: The review concludes by highlighting the need for collaboration in the scientific community with open sharing of knowledge, tools, and expertise. url: https://www.ncbi.nlm.nih.gov/pubmed/32837582/ doi: 10.1007/s12195-020-00629-w id: cord-264013-8jnae6ig author: Tsilingiris, Dimitrios title: Telomere length, epidemiology, and pathogenesis of severe COVID‐19 date: 2020-08-09 words: 1905.0 sentences: 115.0 pages: flesch: 46.0 cache: ./cache/cord-264013-8jnae6ig.txt txt: ./txt/cord-264013-8jnae6ig.txt summary: Cohen et al reported that in a relatively selected population of healthy adults aged between 18 and 55 years, following experimental exposure to Rhinovirus 39 (a single-stranded RNA virus), a shorter telomer length in PBMCs, total lymphocytes, as well as CD4+ and CD8+ Tlymphocyte subsets was associated with an increased probability of upper respiratory infection 23 . A diminishing telomere length in human lymphocytes is related to the process of their replicative senescence (or biological "aging") 26 . 29 Conversely, CD8+ lymphocyte senescence associated with critical telomere shortening induces a state of "hyper-function" with evasion of apoptosis, increased secretion of pro-inflammatory cytokines such as Tumor Necrosis Factor-alpha and interleukin-6 and loss of surface CD28, a co-stimulatory receptor necessary for the mobilization of targeted T-cell immune responses. We further speculate that this observation is driven by a complex immune dysregulation tracing back to immune cell senescence associated with telomere shortening, leading to increased susceptibility to infection and clinical disease (particularly pneumonia) by SARS-CoV-2, as well as unfavorable disease progression potentially marked by cytokine storm syndrome. abstract: In December of 2019, an outbreak of pneumonia of unknown cause was reported in Wuhan, Hubei Province, China. By January 2020 a novel coronavirus ‐ that was named severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) ‐ was isolated from patients in Wuhan and was identified as the causative pathogen of the disease, which was named Coronavirus disease of 2019 (COVID‐19). In the middle of March the World Health Organization (WHO) announced COVID‐19 outbreak a pandemic. According to the daily report of the WHO, as of 18 July 2020, COVID‐19 has spread rapidly to infect more than 14000000 people and has caused roughly 597000 deaths globally. url: https://www.ncbi.nlm.nih.gov/pubmed/32880939/ doi: 10.1111/eci.13376 id: cord-289716-nleql08z author: Tsitsilonis, Ourania E. title: Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report date: 2020-09-21 words: 3225.0 sentences: 143.0 pages: flesch: 44.0 cache: ./cache/cord-289716-nleql08z.txt txt: ./txt/cord-289716-nleql08z.txt summary: Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. According to the manufacturer''s package insert, Elecsys ® Anti-SARS-CoV-2 exhibits high overall clinical specificity of 99.81% with no cross-reactivity to the common cold coronaviruses; clinical sensitivity, determined by testing a total of 204 samples from 69 symptomatic patients with a PCR-confirmed SARS-CoV-2 infection, is 100% for samples collected ≥14 days after PCR confirmation in this collective; these values were verified in our study by measuring 25 RT-qPCR SARS-CoV-2 positive and 25 negative samples. abstract: Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. The National and Kapodistrian University of Athens (ΝΚUA), especially its health-care/medical personnel, has been actively involved in the first line of state responses to COVID-19. To estimate the prevalence of antibodies (Igs) against SARS-CoV-2 among NKUA members, we designed a five consecutive monthly serosurvey among randomly selected NKUA consenting volunteers. Here, we present the results from the first 2500 plasma samples collected during June–July 2020. Twenty-five donors were tested positive for anti-SARS-CoV-2 Igs; thus, the overall seroprevalence was 1.00%. The weighted overall seroprevalence was 0.93% (95% CI: 0.27, 2.09) and varied between males [1.05% (95% CI: 0.18, 2.92)] and females [0.84% (95% CI: 0.13, 2.49)], age-groups and different categories (higher in participants from the School of Health Sciences and in scientific affiliates/faculty members/laboratory assistants), but no statistical differences were detected. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. Given that approximately one in three infections was asymptomatic, continuous monitoring of the progression of the pandemic by assessing Ig seroprevalence is needed. url: https://doi.org/10.3390/life10090214 doi: 10.3390/life10090214 id: cord-331930-w2055c42 author: Tso, Eugene Y. K. title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date: 2004-05-01 words: 529.0 sentences: 34.0 pages: flesch: 61.0 cache: ./cache/cord-331930-w2055c42.txt txt: ./txt/cord-331930-w2055c42.txt summary: title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15127357/ doi: 10.1086/383580 id: cord-314124-yk4y0kea author: Tsou, Ian Y. title: Severe acute respiratory syndrome (SARS) in a paediatric cluster in Singapore date: 2003-08-20 words: 1955.0 sentences: 117.0 pages: flesch: 55.0 cache: ./cache/cord-314124-yk4y0kea.txt txt: ./txt/cord-314124-yk4y0kea.txt summary: BACKGROUND: Severe acute respiratory syndrome (SARS) is a major infectious disease pandemic that occurred in early 2003, and one of the diagnostic criteria is the presence of chest radiographic findings. Severe acute respiratory syndrome (SARS) is a new form of atypical pneumonia, and is an infectious disease which has caused a pandemic with significant public health concerns. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Chest radiographic findings of a case of severe acute respiratory syndrome (SARS) in Singapore abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a major infectious disease pandemic that occurred in early 2003, and one of the diagnostic criteria is the presence of chest radiographic findings. OBJECTIVE: To describe the radiographic features of SARS in a cluster of affected children. MATERIALS AND METHODS: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. RESULTS: Ill-defined air-space shadowing was the common finding in all the children. The distribution was unifocal or multifocal. No other findings were seen on the radiographs. None of the children developed radiographic findings consistent with acute respiratory distress syndrome. All four children showed significant resolution of the radiographic findings 4–6 days after the initial radiograph. CONCLUSIONS: Early recognition of these features is important in implementing isolation and containment measures to prevent the spread of infection. SARS in children appears to manifest as a milder form of the disease as compared to adults. url: https://www.ncbi.nlm.nih.gov/pubmed/12928757/ doi: 10.1007/s00247-003-1042-2 id: cord-330908-402eb8wg author: Tsuji, Motonori title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease date: 2020-05-29 words: 2619.0 sentences: 148.0 pages: flesch: 48.0 cache: ./cache/cord-330908-402eb8wg.txt txt: ./txt/cord-330908-402eb8wg.txt summary: title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease Additional docking simulations for predicted compounds with high binding affinity with M(pro) suggested that 28 bioactive compounds may have potential as effective anti‐SARS‐CoV‐2 drug candidates. Additional docking simulations for predicted compounds with high binding affinity with M pro suggested that 28 bioactive compounds may have potential as effective anti-SARS-CoV-2 drug candidates. In this study, I performed stepwise structure-based virtual screenings using two different docking simulations in order to discover potential drugs that target M pro using the ChEMBL database [4] , which mainly lists drugs and known bioactive compounds. Structure-based virtual screenings were performed using RDOCK (2013) [11] and AUTODOCK VINA version 1.1.2 [12] ; both interfaces are available in Docking Study with HYPER-CHEM (DSHC) software [5, 13] , and the resulting docking modes filtered by the RDOCK score threshold were more precisely simulated using AUTODOCK VINA. abstract: A novel coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), or 2019 novel coronavirus] has been identified as the pathogen of coronavirus disease 2019. The main protease (M(pro), also called 3‐chymotrypsin‐like protease) of SARS‐CoV‐2 is a potential target for treatment of COVID‐19. A M(pro) homodimer structure suitable for docking simulations was prepared using a crystal structure (PDB ID: https://doi.org/10.2210/pdb6Y2G/pdb; resolution 2.20 Å). Structural refinement was performed in the presence of peptidomimetic α‐ketoamide inhibitors, which were previously disconnected from each Cys145 of the M(pro) homodimer, and energy calculations were performed. Structure‐based virtual screenings were performed using the ChEMBL database. Through a total of 1 485 144 screenings, 64 potential drugs (11 approved, 14 clinical, and 39 preclinical drugs) were predicted to show high binding affinity with M(pro). Additional docking simulations for predicted compounds with high binding affinity with M(pro) suggested that 28 bioactive compounds may have potential as effective anti‐SARS‐CoV‐2 drug candidates. The procedure used in this study is a possible strategy for discovering anti‐SARS‐CoV‐2 drugs from drug libraries that may significantly shorten the clinical development period with regard to drug repositioning. url: https://www.ncbi.nlm.nih.gov/pubmed/32374074/ doi: 10.1002/2211-5463.12875 id: cord-274205-e2r38v29 author: Tsunetsugu-Yokota, Yasuko title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen date: 2007-11-28 words: 2170.0 sentences: 165.0 pages: flesch: 66.0 cache: ./cache/cord-274205-e2r38v29.txt txt: ./txt/cord-274205-e2r38v29.txt summary: title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen In general, a whole virion serves as a simple vaccine antigen and often essential material for the analysis of immune responses against virus infection. In order to develop an effective vaccine and diagnostic tools, we prepared UV-inactivated SARS coronavirus on a large scale under the strict Biosafety Level 3 (BSL3) regulation. We have demonstrated that subcutaneously administered UV-inactivated SARS-CoV elicits a high level of IgG-type neutralizing antibodies and weak T-cell responses in mice (4). Here we describe our protocol for the largescale preparation of UV-inactivated SARS-CoV virion under the strict Biosafety Level 3 (BSL3) regulation. In order to increase the safety of this UV-inactivated SARS-CoV, we inactivated the virion vaccine using both UV and formalin. Severe acute respiratory syndrome (SARS) coronavirus: application of monoclonal antibodies and development of an effective vaccine abstract: In general, a whole virion serves as a simple vaccine antigen and often essential material for the analysis of immune responses against virus infection. However, to work with highly contagious pathogens, it is necessary to take precautions against laboratory-acquired infection. We have learned many lessons from the recent outbreak of severe acute respiratory syndrome (SARS). In order to develop an effective vaccine and diagnostic tools, we prepared UV-inactivated SARS coronavirus on a large scale under the strict Biosafety Level 3 (BSL3) regulation. Our protocol for large-scale preparation of UV-inactivated SARS-CoV including virus expansion, titration, inactivation, and ultracentrifugation is applicable to any newly emerging virus we might encounter in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/19057880/ doi: 10.1007/978-1-59745-181-9_11 id: cord-338333-yvm3d6xy author: Tu, Danna title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 date: 2020-07-25 words: 1067.0 sentences: 67.0 pages: flesch: 47.0 cache: ./cache/cord-338333-yvm3d6xy.txt txt: ./txt/cord-338333-yvm3d6xy.txt summary: title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. Here we would like to share our finding about the serum antibodies analyzed in a special group of pediatric medical workers exposed to varying levels of SARS-CoV-2 after Wuhan severe epidemic of COVID-19. The overall positive rate for SARS-CoV-2 IgG and IgM antibodies in the pediatric medical workers was 43.08 and 5.85%, respectively. This research revealed that pediatric medical workers are a high-risk group for infection by SARS-CoV-2, and the higher the exposure levels to COVID-19 patients and aerosol production, the greater chance of being infected. Table 1 Test results of serum antibodies in pediatric medical workers exposed to different levels of SARS-CoV-2 High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients abstract: • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. • ELISA and dual-target fluorescence accurately detect SARS-CoV-2 antibodies indicated that antibody detection should be considered as an auxiliary diagnosis of COVID-19. • Antibody positive subjects tested negative for SARS-CoV-2 neutralizing antibodies and SARS-CoV-2 antibodies diminish to near undetectable levels within two months. url: https://api.elsevier.com/content/article/pii/S0163445320305041 doi: 10.1016/j.jinf.2020.07.023 id: cord-282433-p6jl9gxf author: Tu, Xinyi title: Functional polymorphisms of the CCL2 and MBL genes cumulatively increase susceptibility to severe acute respiratory syndrome coronavirus infection date: 2015-03-27 words: 4611.0 sentences: 213.0 pages: flesch: 45.0 cache: ./cache/cord-282433-p6jl9gxf.txt txt: ./txt/cord-282433-p6jl9gxf.txt summary: RESULTS: Both the high-CCL2-producing GG genotype and the low-MBL-producing B allele were consistently associated with increased risks of SARS-CoV infection in all 4 case–control populations (joint P = 1.6 × 10(−4) and 4.9 × 10(−8), for CCL2 and MBL respectively), with no interaction between polymorphisms could be detected. 3À10 In particular, our previous two independent association studies have implicated that a functional polymorphism at codon 54 in exon 1 (rs1800450, G230A, denoted as A/B variant) of mannose binding lectin (MBL), which encodes a protein belonging to the family of collectin and plays a critical role in the innate immune response, conferred a significantly increased susceptibility to SARS-CoV infection. Taken together, the large size of the investigation, the consistency of the observations in 4 independent caseecontrol series and the low P values distinguish our study from previous studies investigating the influence of different other polymorphisms on the development of SARS, and strengthen the association between the CCL2 G-2518A and MBL codon 54 variant (A/B) and susceptibility to SARS-CoV infection. abstract: OBJECTIVES: To assess associations between the functional polymorphisms G-2518A at the chemokine (C–C motif) ligand 2 gene (CCL2) and mannose binding lectin (MBL) codon 54 variant (A/B) and susceptibility to SARS. METHODS: We genotyped the CCL2 G-2518A and MBL codon 54 variant (A/B) in 4 case–control populations of Chinese descent, totally consisting of 932 patients with SARS and 982 control subjects. RESULTS: Both the high-CCL2-producing GG genotype and the low-MBL-producing B allele were consistently associated with increased risks of SARS-CoV infection in all 4 case–control populations (joint P = 1.6 × 10(−4) and 4.9 × 10(−8), for CCL2 and MBL respectively), with no interaction between polymorphisms could be detected. Furthermore, all the 4 case–control studies demonstrated a cumulative effect on risk of SARS-CoV infection for the combination of polymorphisms (joint P = 1.3 × 10(−10)). However, tests using the area under the curve (AUC) indicated that at this stage, the polymorphisms were unlikely to be appropriate for risk prediction testing because of low AUC values (all <66%). Additionally, no association was observed between the polymorphisms and severity of SARS. CONCLUSIONS: The CCL2 G-2518A and MBL codon 54 variant have a significantly cumulative effect on increased risk of SARS-CoV infection. url: https://doi.org/10.1016/j.jinf.2015.03.006 doi: 10.1016/j.jinf.2015.03.006 id: cord-278467-c0jw9dkw author: Tulchinsky, Mark title: The American College of Nuclear Medicine Guidance on Operating Procedures for a Nuclear Medicine Facility During COVID-19 Pandemic date: 2020-05-01 words: 2101.0 sentences: 147.0 pages: flesch: 45.0 cache: ./cache/cord-278467-c0jw9dkw.txt txt: ./txt/cord-278467-c0jw9dkw.txt summary: During the COVID-19 pandemic, 5 scheduling of examinations should be judicious, equipment disinfection should be practiced before each patient, medical service sustainability should be optimized, all aerosol-generating tests must be avoided, and time of staff-patient contact should be minimized for each test in order to contain the contagion. 3. Provide to the patient and/or guardian as much information as possible by phone in advance of arrival to an NMF, including screening questions for COVID-19 risk and explanation of the test or therapy to be performed, in order to minimize the time spent in close in-person contact. Although the outlined principles are universal, their practical applications and implementation are dependent on prevalence dynamics of COVID-19 at specific locations and resources available to individual NMFs. A novel coronavirus from patients with pneumonia in China Incidental findings suggestive of COVID-19 in asymptomatic patients undergoing nuclear medicine procedures in a high-prevalence region abstract: The novel coronavirus 2 pandemic is causing widespread disruption in everyday life necessitating urgent and radical adaptations in operating procedures at Nuclear Medicine facilities. The potential for causing severe illness, COVID-19, calls for strict observance of preventive measures aimed to mitigate the spread of the virus. The threat of COVID-19 is particularly serious as there is no vaccine and no specific antiviral therapy. Further complications are introduced by shortages of personal protective equipment for healthcare workers who have direct contact with patients and effective testing to identify infected patients, raising the need for delaying some testing and therapies. Certain vulnerable segments of the general population have been identified (advanced age and certain comorbidities), which should heighten further their preventive efforts. Therefore, this guidance is intended to be operationalized depending on a facility’s specific needs and local disease prevalence. url: https://www.ncbi.nlm.nih.gov/pubmed/32358234/ doi: 10.1097/rlu.0000000000003146 id: cord-304176-yloqrblw author: Tunesi, S. title: Prescribing COVID-19 treatments: what we should never forget date: 2020-05-13 words: 701.0 sentences: 42.0 pages: flesch: 51.0 cache: ./cache/cord-304176-yloqrblw.txt txt: ./txt/cord-304176-yloqrblw.txt summary: authors: Tunesi, S.; Bourgarit, A. COVID-19-induced proinflammatory status looks to trigger most severe SARS-CoV-2 forms (2). Many drugs have been hypothesized to be directly active against COVID-19 only because of a supposed antiviral activity: remdesivir, a molecule originally tested against Ebola virus, shows in vivo activity against MERS-CoV (5) but there is actually no real evidence of in vivo activity against COVID-19; lopinavir/ritonavir, a well-known protease inhibitor used in HIV treatment, has been widely used before randomized clinical trials showed his inefficacy in mortality reduction (6); chloroquine and hydroxychloroquine, which are largely used in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) treatment, show modest antiviral effects, but mortality due to QT elongation-related cardiac events is a matter of concern (7). Conversely, preliminary data about a potential role of ACE inhibitors in favouring the onset of severe forms of SARS-CoV-2 infection induced a massive change in antihypertensive drugs prescription that caused the onset of severe cardiovascular events (9). abstract: nan url: https://doi.org/10.1016/j.jinf.2020.05.018 doi: 10.1016/j.jinf.2020.05.018 id: cord-028363-7pmro8bu author: Tung-Chen, Yale title: Acute pericarditis due to COVID-19 infection: An underdiagnosed disease? date: 2020-07-10 words: 1427.0 sentences: 83.0 pages: flesch: 51.0 cache: ./cache/cord-028363-7pmro8bu.txt txt: ./txt/cord-028363-7pmro8bu.txt summary: 4 Gradually a therapeutic scheme is being established that would include hydroxychloroquine and azithromycin 5 (or in other cases lopinavir/ritonavir) in the early stages of moderate disease that does not require treatment in ICU (Intensive Care Unit) but given the analytical indication (elevation of ddimer) and imaging (thrombosis in CTPA) in many cases, should be evaluated the early inclusion of low molecular weight heparin (LMWH) at doses of at least high-risk prophylaxis in all these patients without thrombopenia <20,000 platelets or acute bleeding and manifesting high d-dimer. 5 In another study, 83 patients with severe and critical COVID-19 infection underwent a CT scan, 6 chest pain was reported in 6% of the patients and pericardial effusion was found in 4.8%, which suggests that acute pericarditis could be an under diagnosed pathology, and therefore, not correctly managed and treated. This is the first case report to describe an acute pericarditis episode due to SARS-CoV-2, which might be an under diagnosed condition in this pandemic, and therefore not correctly managed. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333598/ doi: 10.1016/j.medcle.2020.06.001 id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 words: 2438.0 sentences: 173.0 pages: flesch: 48.0 cache: ./cache/cord-351559-az4pgi9k.txt txt: ./txt/cord-351559-az4pgi9k.txt summary: Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. abstract: Background Since December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. Results Our analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. url: https://doi.org/10.1101/2020.06.29.177204 doi: 10.1101/2020.06.29.177204 id: cord-317423-3nkzp1z2 author: Turk, Can title: In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus date: 2020-06-03 words: 4303.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-317423-3nkzp1z2.txt txt: ./txt/cord-317423-3nkzp1z2.txt summary: RESULTS: The whole-genome expression data of the lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were analyzed, and a total of 15 RAS family and 29 immune genes were found to be highly correlated with the exposure time to the virus in the studied groups. 13, 21 The main purpose of this present in silico genomic study was to assess how the expressions of the RAS gene family changes after cellular infection with SARS-CoV in the lung epithelial cell culture. The whole normalized gene expression data of lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were compared between different groups in order to determine significantly and differentially expressed RAS family genes. Based on our results, in this phase, as the exposure time to SARS-CoV increases, EGFR and IGF2R, two receptors with key roles in the RAS signaling pathway, were significantly down-regulated in the infected human bronchial epithelial cells. abstract: INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified coronavirus family member that triggers a respiratory disease similar to severe acute respiratory syndrome coronavirus (SARS-CoV). SARS-CoV and SARS-CoV-2 are very similar to each other in many respects, such as structure, genetics, and pathobiology. We hypothesized that coronaviruses could affect pulmonary tissues via integration with the critical immune genes after their interaction with renin–angiotensin system (RAS) elements. The aim of the present bioinformatics study was to assess expression changes of the RAS and non-RAS genes, particularly immune response genes, in the lung epithelial cells after infection with SARS-CoV. METHODS: Linear regression, hierarchical clustering, pathway analysis, and network analysis were performed using the E-GEOD-17400 data set. RESULTS: The whole-genome expression data of the lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were analyzed, and a total of 15 RAS family and 29 immune genes were found to be highly correlated with the exposure time to the virus in the studied groups. CONCLUSION: RAS genes are important at the initiation of the infections caused by coronavirus family members and may have a strong relationship with the exchange of immune genes in due course following the infection. url: https://doi.org/10.1177/1470320320928872 doi: 10.1177/1470320320928872 id: cord-306760-05my504t author: Turner, Dan title: Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date: 2020-03-31 words: 3832.0 sentences: 209.0 pages: flesch: 46.0 cache: ./cache/cord-306760-05my504t.txt txt: ./txt/cord-306760-05my504t.txt summary: METHODS: An electronic reporting system of children with IBD infected with SARS-CoV-2 has been circulated among 102 PIBD centres affiliated with the Porto and Interest-group of ESPGHAN. Standard IBD treatments including biologics should continue at present through the pandemic, especially in children who generally have more severe IBD course on one hand, and milder SARS-CoV-2 infection on the other. In light of the hyperinflammatory immune response seen in patients with COVID-19 it is highly relevant that blockade of IL-6R with tocilizumab resulted in clinical improvement associated with normalisation of fever, lymphocyte counts, and CRP in a retrospective group of 21 adults with severe SARS-CoV-2 infection (20) . Therefore, uninfected children should generally continue their medical treatment, including immunomodulators and biologic therapies, as the risk of a disease flare outweighs any estimated risk of SARS-CoV2 infection. abstract: INTRODUCTION: With the current coronavirus disease 2019 (COVID-19) pandemic, concerns have been raised about the risk to children with inflammatory bowel diseases (IBD). We aimed to collate global experience and provide provisional guidance for managing paediatric IBD (PIBD) in the era of COVID-19. METHODS: An electronic reporting system of children with IBD infected with SARS-CoV-2 has been circulated among 102 PIBD centres affiliated with the Porto and Interest-group of ESPGHAN. A survey has been completed by major PIBD centres in China and South-Korea to explore management during the pandemic. A third survey collected current practice of PIBD treatment. Finally, guidance points for practice have been formulated and voted upon by 37 PIBD authors and Porto group members. RESULTS: Eight PIBD children had COVID-19 globally, all with mild infection without needing hospitalization despite treatment with immunomodulators and/or biologics. No cases have been reported in China and South Korea but biologic treatment has been delayed in 79 children, of whom 17 (22%) had exacerbation of their IBD. Among the Porto group members, face-to-face appointments were often replaced by remote consultations but almost all did not change current IBD treatment. Ten guidance points for clinicians caring for PIBD patients in epidemic areas have been endorsed with consensus rate of 92% to 100%. CONCLUSIONS: Preliminary data for PIBD patients during COVID-19 outbreak are reassuring. Standard IBD treatments including biologics should continue at present through the pandemic, especially in children who generally have more severe IBD course on one hand, and milder SARS-CoV-2 infection on the other. SUPPLEMENTAL DIGITAL CONTENT: An infographic accompanying this article can be found at. url: https://doi.org/10.1097/mpg.0000000000002729 doi: 10.1097/mpg.0000000000002729 id: cord-339241-e2nl766y author: Turriziani, Ombretta title: SARS‐CoV‐2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period date: 2020-08-02 words: 1290.0 sentences: 93.0 pages: flesch: 53.0 cache: ./cache/cord-339241-e2nl766y.txt txt: ./txt/cord-339241-e2nl766y.txt summary: The study retrospectively included 6565 subjects tested for SARS‐CoV‐2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. This analysis allowed to gather comprehensive information on SARS‐CoV‐2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown. In this scenario this paper aims to take a snapshot of the epidemiological characteristics of the population resulted positive for SARS-CoV-2 at Sapienza University Hospital "Policlinico Umberto I" in Rome starting from 6 March until 4 May. This study includes all individuals (n = 6565) who have been tested 2.1 | Statistical analysis χ 2 Test was used to analyze the differences in positivity between groups. abstract: Italy was one of the most affected nations by coronavirus disease 2019 outside China. The infections, initially limited to Northern Italy, spread to all other Italian regions. This study aims to provide a snapshot of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) epidemiology based on a single‐center laboratory experience in Rome. The study retrospectively included 6565 subjects tested for SARS‐CoV‐2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. Positivity to SARS‐CoV‐2 was detected in 8% (527/6565) of individuals, increased with age, and was higher in male patients (P < .001). The number of new confirmed cases reached a peak on 18 March and then decreased. The virus was detected in respiratory samples, in stool and in pleural fluids, while none of gargle lavage or cerebrospinal fluid samples gave a positive result. This analysis allowed to gather comprehensive information on SARS‐CoV‐2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown. url: https://doi.org/10.1002/jmv.26332 doi: 10.1002/jmv.26332 id: cord-274824-kaefedl1 author: Turski, Waldemar A. title: AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date: 2020-09-24 words: 5928.0 sentences: 284.0 pages: flesch: 36.0 cache: ./cache/cord-274824-kaefedl1.txt txt: ./txt/cord-274824-kaefedl1.txt summary: as pro viral factor TiPARP, and to the modulation of cytokine gene expression, specifically, interleukin 1␤ (IL-1␤), IL-10, and TNF-␣ ( Fig. 1) , which is consistent with the role for AhR activation in the host response to CoV infection Grunewald, Shaban, Mackin, Fehr, & Perlman, 2020; Neavin, Liu, Ray, & Weinshilboum, 2018) . Since CoV persistently activate AhRs, this may lead to up-regulation of multiple sets of downstream effectors resulting in different pathologies (Fig. 2) depending on time after infection, individuals overall state of health, comorbidities, and environmental factors affecting AhRs. We believe it is therefore appropriate to describe this disease as a systemic AhR activation syndrome (SAAS), which can manifest in an acute (current pandemic), and perhaps later, in a chronic form, in survivors. abstract: Covid-19 is the acute illness caused by SARS-CoV-2 with initial clinical symptoms such as cough, fever, malaise, headache, and anosmia. After entry into cells, corona viruses (CoV) activate aryl hydrocarbon receptors (AhRs) by an indoleamine 2,3-dioxygenase (IDO1)-independent mechanism, bypassing the IDO1-kynurenine-AhR pathway. The IDO1-kynurenine-AhR signaling pathway is used by multiple viral, microbial and parasitic pathogens to activate AhRs and to establish infections. AhRs enhance their own activity through an IDO1-AhR-IDO1 positive feedback loop prolonging activation induced by pathogens. Direct activation of AhRs by CoV induces immediate and simultaneous up-regulation of diverse AhR-dependent downstream effectors, and this, in turn, results in a “Systemic AhR Activation Syndrome” (SAAS) consisting of inflammation, thromboembolism, and fibrosis, culminating in multiple organ injuries, and death. Activation of AhRs by CoV may lead to diverse sets of phenotypic disease pictures depending on time after infection, overall state of health, hormonal balance, age, gender, comorbidities, but also diet and environmental factors modulating AhRs. We hypothesize that elimination of factors known to up-regulate AhRs, or implementation of measures known to down-regulate AhRs, should decrease severity of infection. Although therapies selectively down-regulating both AhR and IDO1 are currently lacking, medications in clinical use such as dexamethasone may down-regulate both AhR and IDO1 genes, as calcitriol/vitamin D(3) may down-regulate the AhR gene, and tocopherol/vitamin E may down-regulate the IDO1 gene. Supplementation of calcitriol should therefore be subjected to epidemiological studies and tested in prospective trials for prevention of CoV infections, as should tocopherol, whereas dexamethasone could be tried in interventional trials. Because lack of physical exercise activates AhRs via the IDO1-kynurenine-AhR signaling pathway increasing risk of infection, physical exercise should be encouraged during quarantines and stay-at-home orders during pandemic outbreaks. Understanding which factors affect gene expression of both AhR and IDO1 may help in designing therapies to prevent and treat humans suffering from Covid-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32597823/ doi: 10.3233/rnn-201042 id: cord-280068-rszu1c48 author: Twomey, Julianne D. title: COVID-19 update: The race to therapeutic development date: 2020-10-24 words: 6195.0 sentences: 331.0 pages: flesch: 42.0 cache: ./cache/cord-280068-rszu1c48.txt txt: ./txt/cord-280068-rszu1c48.txt summary: We highlight two major lines of therapeutic strategies for COVID-19 treatment: 1) repurposing the existing drugs for use in COVID-19 patients, such as antiviral medications (e.g., remdesivir) and immunomodulators (e.g., dexamethasone) which were previously approved for other disease conditions, and 2) novel biological products that are designed to target specific molecules that are involved in SARS-COV-2 viral entry, including neutralizing antibodies against the spike protein of SARS-COV-2, such as REGN-COV2 (an antibody cocktail) and LY-COV555, as well as recombinant human soluble ACE2 protein to counteract SARS-COV-2 binding to the transmembrane ACE2 receptor in target cells. The current review highlights the potential therapeutic strategies for the treatment of COVID-19, including small molecule drugs and therapeutic proteins to target the SARS-CoV-2 viral entry, viral amplification or the host immune responses. abstract: The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents an unprecedented challenge to global public health. At the time of this review, COVID-19 has been diagnosed in over 40 million cases and associated with 1.1 million deaths worldwide. Current management strategies for COVID-19 are largely supportive, and while there are more than 2000 interventional clinical trials registered with the U.S. National Library of Medicine (clinicaltrials.gov), results that can clarify benefits and risks of candidate therapies are only gradually becoming available. We herein describe recent advances in understanding SARS-COV-2 pathobiology and potential therapeutic targets that are involved in viral entry into host cells, viral spread in the body, and the subsequent COVID-19 progression. We highlight two major lines of therapeutic strategies for COVID-19 treatment: 1) repurposing the existing drugs for use in COVID-19 patients, such as antiviral medications (e.g., remdesivir) and immunomodulators (e.g., dexamethasone) which were previously approved for other disease conditions, and 2) novel biological products that are designed to target specific molecules that are involved in SARS-COV-2 viral entry, including neutralizing antibodies against the spike protein of SARS-COV-2, such as REGN-COV2 (an antibody cocktail) and LY-COV555, as well as recombinant human soluble ACE2 protein to counteract SARS-COV-2 binding to the transmembrane ACE2 receptor in target cells. Finally, we discuss potential drug resistance mechanisms and provide thoughts regarding clinical trial design to address the diversity in COVID-19 clinical manifestation. Of note, preventive vaccines, cell and gene therapies are not within the scope of the current review. url: https://doi.org/10.1016/j.drup.2020.100733 doi: 10.1016/j.drup.2020.100733 id: cord-252305-rstxyofq author: Tyan, Kevin title: Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting date: 2020-08-31 words: 2062.0 sentences: 156.0 pages: flesch: 49.0 cache: ./cache/cord-252305-rstxyofq.txt txt: ./txt/cord-252305-rstxyofq.txt summary: We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. While this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. Some products on List N do not have an emerging viral pathogen claim but have been included because they 1) demonstrate efficacy against another human coronavirus similar to SARS-CoV-2 or 2) are EPA-approved against select viruses that are harder-to-kill [5] . The publication of the EPA List N was an important step in providing a resource for selecting disinfectants against SARS-CoV-2 and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability. abstract: Proper disinfection using adequate disinfecting agents will be necessary for infection control strategies against COVID-19. However, limited guidance exists on effective surface disinfectants or best practices for their use against SARS-CoV-2. We outlined a process of fully characterizing over 350 products on the EPA List N, including pH, method of delivery, indication for equipment sterilization, and purchase availability. We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. This resource guides the evaluation of ideal disinfectants amidst practical considerations posed by the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32989420/ doi: 10.1093/ofid/ofaa396 id: cord-269723-gm65p1op author: Tzeng, Nian-Sheng title: What could we learn from SARS when facing the mental health issues related to the COVID-19 outbreak? A nationwide cohort study in Taiwan date: 2020-10-06 words: 4370.0 sentences: 198.0 pages: flesch: 46.0 cache: ./cache/cord-269723-gm65p1op.txt txt: ./txt/cord-269723-gm65p1op.txt summary: There were several studies about the psychiatric and mental health issues related to the severe adult respiratory syndrome (SARS) outbreak in 2003, however, the association between SARS and the overall risk of psychiatric disorders and suicides has, as yet, to be studied in Taiwan. A total of 285 patients with SARS and 2850 controls without SARS (1:10) matched for sex, age, insurance premium, comorbidities, residential regions, level of medical care, and index date were selected between February 25 and June 15, 2003 from the Inpatient Database Taiwan''s National Health Insurance Research Database. To the best of our knowledge, this is the first study on the association between SARS and increased risk in developing psychiatric disorders and suicide, in a 12-year follow-up, from a nationwide, population-based database. abstract: There were several studies about the psychiatric and mental health issues related to the severe adult respiratory syndrome (SARS) outbreak in 2003, however, the association between SARS and the overall risk of psychiatric disorders and suicides has, as yet, to be studied in Taiwan. The aim of this study is to examine as to whether SARS is associated with the risk of psychiatric disorders and suicide. A total of 285 patients with SARS and 2850 controls without SARS (1:10) matched for sex, age, insurance premium, comorbidities, residential regions, level of medical care, and index date were selected between February 25 and June 15, 2003 from the Inpatient Database Taiwan’s National Health Insurance Research Database. During the 12-year follow-up, in which 79 in the SARS cohort and 340 in the control group developed psychiatric disorders or suicide (4047.41 vs. 1535.32 per 100,000 person-years). Fine and Gray’s survival analysis revealed that the SARS cohort was associated with an increased risk of psychiatric disorders and suicide, and the adjusted subdistribution HR (sHR) was 2.805 (95% CI: 2.182–3.605, p < 0.001) for psychiatric disorders and suicide. The SARS cohort was associated with anxiety, depression, sleep disorders, posttraumatic stress disorder/acute stress disorder (PTSD/ASD), and suicide. The sensitivity analysis revealed that the SARS group was associated with anxiety, depression, sleep disorders, PTSD/ASD, and suicide after the individuals with a diagnosis of psychiatric disorders and suicide were excluded within the first year, and with anxiety, depression, and sleep disorders, while those in the first five years were excluded. In conclusion, SARS was associated with the increased risk of psychiatric disorders and suicide. url: https://doi.org/10.1038/s41398-020-01021-y doi: 10.1038/s41398-020-01021-y id: cord-338436-0z828org author: Tzou, Philip L. title: Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds date: 2020-09-09 words: 8193.0 sentences: 522.0 pages: flesch: 46.0 cache: ./cache/cord-338436-0z828org.txt txt: ./txt/cord-338436-0z828org.txt summary: Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. Figure 4 displays EC 50 values for many of the directly acting antiviral compounds currently in clinical trials for the treatment of COVID-19 including six polymerase inhibitors (remdesivir, EIDD-2801, favipiravir, ribavirin, galidesivir, and sofosbuvir), three HIV-1 protease inhibitors (lopinavir, atazanavir, and darunavir), and three entry inhibitors (receptor binding monoclonal antibodies, soluble recombinant human ACE2, and umifenovir). Viruses 2020, 12, x FOR PEER REVIEW 11 of 22 Table 4 describes a set of the most promising compounds for the treatment of SARS-CoV-2 based on the following criteria: (i) act by a validated direct or indirect antiviral mechanism, (ii) display submicromolar activity in vitro and/or inhibitory activity in an animal model, and (iii) have a record of safety and favorable pharmacokinetics in human subjects. abstract: Background: To prioritize the development of antiviral compounds, it is necessary to compare their relative preclinical activity and clinical efficacy. Methods: We reviewed in vitro, animal model, and clinical studies of candidate anti-coronavirus compounds and placed extracted data in an online relational database. Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. SARS-CoV-2, SARS-CoV, and MERS-CoV account for 85% of the data. Approximately 75% of experiments involved compounds with known or likely mechanisms of action, including monoclonal antibodies and receptor binding inhibitors (21%), viral protease inhibitors (17%), miscellaneous host-acting inhibitors (10%), polymerase inhibitors (9%), interferons (7%), fusion inhibitors (5%), and host protease inhibitors (5%). Of 975 compounds with known or likely mechanism, 135 (14%) are licensed in the U.S. for other indications, 197 (20%) are licensed outside the U.S. or are in human trials, and 595 (61%) are pre-clinical investigational compounds. Conclusion: CoV-RDB facilitates comparisons between different candidate antiviral compounds, thereby helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development. url: https://www.ncbi.nlm.nih.gov/pubmed/32916958/ doi: 10.3390/v12091006 id: cord-335492-od3c25qg author: UGUREL, Osman Mutluhan title: An updated analysis of variations in SARS-CoV-2 genome date: 2020-06-21 words: 4971.0 sentences: 273.0 pages: flesch: 57.0 cache: ./cache/cord-335492-od3c25qg.txt txt: ./txt/cord-335492-od3c25qg.txt summary: In this study; we have used these data to analyse the mutations on SARS-CoV-2 genome using a software based on multiple sequence alignment (Strategy Based Local Alignment Tool: ODOTool) that have been originally developed for bacterial SNP determination in our studies. Now, we targeted to analyse the mutations that have emerged in at least 10% of SARS-CoV-2 genomes in all 30366 sequences submitted in GISAID by May 20th, 2020 using the ODOTool in terms of date and location they occurred, the relationship with each other and their effect on the primary protein structure. Despite the Strategy Based Local Alignment Tool (ODOTool) used in this study was originally developed by our group for bacterial single nucleotide polymorphism (SNP) determination, it was reasonable to test the abilities of the tool using a different dataset with the emergence of SARS-CoV-2 causing COVID-19 pandemic and this is applied in the present study to analyse variations in viral genome. abstract: A novel pathogen, named SARS-CoV-2, has caused an unprecedented worldwide pandemic in the first half of 2020. As the SARS-CoV-2 genome sequences have become available, one of the important focus of scientists has become tracking variations in the viral genome. In this study, 30366 SARS-CoV-2 isolate genomes were aligned using the software developed by our group (ODOTool) and 11 variations in SARS-CoV-2 genome over 10% of whole isolates were discussed. Results indicated that, frequency rates of these 11 variations change between 3.56%–88.44 % and these rates differ greatly depending on the continents they have been reported. Despite some variations being in low frequency rate in some continents, C14408T and A23403G variations on Nsp12 and S protein, respectively, observed to be the most prominent variations all over the world, in general, and both cause missense mutations. It is also notable that most of isolates carry C14408T and A23403 variations simultaneously and also nearly all isolates carrying the G25563T variation on ORF3a, also carry C14408T and A23403 variations, although their location distributions are not similar. All these data should be considered towards development of vaccine and antiviral treatment strategies as well as tracing diversity of virus in all over the world. url: https://doi.org/10.3906/biy-2005-111 doi: 10.3906/biy-2005-111 id: cord-305632-xbji6g5x author: Uccelli, Matteo title: COVID-19 and Obesity: Is Bariatric Surgery Protective? Retrospective Analysis on 2145 Patients Undergone Bariatric-Metabolic Surgery from High Volume Center in Italy (Lombardy) date: 2020-10-31 words: 2889.0 sentences: 167.0 pages: flesch: 49.0 cache: ./cache/cord-305632-xbji6g5x.txt txt: ./txt/cord-305632-xbji6g5x.txt summary: There are also emerging data indicating that obesity is an independent predictor of intensive care unit (ICU) admission, mechanical ventilation, and death [6, 11, 12] , and in a recent report from a large cohort of COVID-19 patients in New York, obesity was found to be one of the most common associated comorbidities in hospitalized patients [13, 14] . We therefore analyzed a significant number of patients to evaluate the spread and the effects of the SARS-CoV-2 infection in a population of patients who had undergone bariatric surgery. Therefore, our data are encouraging, considering that these patients were obese: bariatric surgery and the consequent weight loss seem to significantly lower the risk of serious consequences due to COVID infection. Bariatric surgery, therefore, can be considered a protective factor with respect to the onset of severe respiratory disease resulting from infection with SARS-CoV-2. abstract: INTRODUCTION: On February 20, 2020, a severe case of pneumonia due to SARS-CoV-2 was diagnosed in northern Italy (Lombardy). Some studies have identified obesity as a risk factor for severe disease in patients with COVID-19. The purpose of this study was to investigate the incidence of SARS-CoV-2 infection and its severity in patients who have undergone bariatric surgery. MATERIAL AND METHODS: During the lockdown period (until May 2020), we contacted operated patients by phone and social networks (e.g., Facebook) to maintain constant contact with them; in addition, we gave the patients a dedicated phone number at which to call us for emergencies. We produced telemedicine and educational videos for obese and bariatric patients, and we submitted a questionnaire to patients who had undergone bariatric surgery in the past. RESULTS: A total of 2145 patients (313 male; 1832 female) replied to the questionnaire. Mean presurgical BMI: 44.5 ± 6.8 kg/m(2). Mean age: 44.0 ± 10.0 year. Mean BMI after surgery: 29.3 ± 5.5 kg/m(2) (p < 0.05). From February to May 2020, 8.4% of patients reported that they suffered from at least one symptom among those identified as related to SARS-CoV-2 infection. Thirteen patients (0.6%) tested positive for COVID-19. Six patients (0.3%) were admitted to the COVID Department, and 2 patients (0.1%) were admitted to the ICU. CONCLUSIONS: Although the reported rates of symptoms and fever were high, only 0.6% of patients tested positive for COVID-19. Among more than 2000 patients who underwent bariatric surgery analyzed in this study, only 0.1% needed ICU admission. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11695-020-05085-z. url: https://doi.org/10.1007/s11695-020-05085-z doi: 10.1007/s11695-020-05085-z id: cord-328856-1l7x72j7 author: Ucciferri, Claudio title: Pidotimod in Paucisymptomatic SARS-CoV2 Infected Patients date: 2020-07-01 words: 1207.0 sentences: 83.0 pages: flesch: 45.0 cache: ./cache/cord-328856-1l7x72j7.txt txt: ./txt/cord-328856-1l7x72j7.txt summary: Several studies on COVID-19 are focusing on severe forms; however, the most frequent SARS-CoV-2 clinical presentation is a mild disease with or without pneumonia in about 80% of patients. Notwithstanding immune response appeared fundamental for SARS infection resolution, SARS-Cov-2 disease present increased levels of plasma pro-inflammatory mediators, as a consequence of an induced dysregulated cytokine storm. We enrolled SARS-CoV2 positive patients (Brescia-COVID Respiratory Severity Scale 0), with fever and cough without acute respiratory failure or sign of pneumonia from March to April 2020 at the Infectious Diseases Clinic, University ''G. 9 In our study, in the outpatient population affected by SARS-CoV2 infection, pidotimod appears as a valid option to reduce the duration of symptoms in patients, as an earlier defervescence of fever and it could prevent the cytokine cascade activation. In conclusion, in ambulatorial adult patients with SARS-Cov2 infection without pneumonia, pidotimod could be considered an option, well tolerated and associated with a rapid reduction of systemic symptoms of disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32670526/ doi: 10.4084/mjhid.2020.048 id: cord-331243-0u65qguq author: Ucciferri, Claudio title: Role of monoclonal antibody drugs in the treatment of COVID-19 date: 2020-10-06 words: 1695.0 sentences: 94.0 pages: flesch: 39.0 cache: ./cache/cord-331243-0u65qguq.txt txt: ./txt/cord-331243-0u65qguq.txt summary: Evidence suggests that elevated cytokine levels, reflecting a hyperinflammatory response secondary to SARS-CoV-2 infection, are responsible for multi-organ damage in patients with COVID-19. These studies suggest that tocilizumab may be a candidate to improve the outcome of patients with severe COVID-19 infections. Recent data on anakinra showed that, in a cohort of patients with COVID-19 and Acute respiratory distress syndrome managed with non-invasive mechanical ventilation, treatment with highdose anakinra was safe and associated with clinical improvement [16, 17] . Currently available data on SARS-CoV-2 infection show that the extent of the inflammatory response correlates with disease progression and subsequent organ damage. Tocilizumab for the treatment of severe COVID-19 pneumonia with hyperinflammatory syndrome and acute respiratory failure: A single center study of 100 patients in Interleukin-1 blockade with high-dose anakinra in patients with COVID-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study abstract: Currently clinicians all around the world are experiencing a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The clinical presentation of this pathology includes fever, dry cough, fatigue and acute respiratory distress syndrome that can lead to death infected patients. Current studies on coronavirus disease 2019 (COVID-19) continue to highlight the urgent need for an effective therapy. Numerous therapeutic strategies have been used until now but, to date, there is no specific effective treatment for SARS-CoV-2 infection. Elevated inflammatory cytokines have been reported in patients with COVID-19. Evidence suggests that elevated cytokine levels, reflecting a hyperinflammatory response secondary to SARS-CoV-2 infection, are responsible for multi-organ damage in patients with COVID-19. For these reason, numerous randomized clinical trials are currently underway to explore the effectiveness of biopharmaceutical drugs, such as, interleukin-1 blockers, interleukin-6 inhibitors, Janus kinase inhibitors, in COVID-19. The aim of the present paper is to briefly summarize the pathogenetic rationale and the state of the art of therapeutic strategy blocking hyperinflammation. url: https://doi.org/10.12998/wjcc.v8.i19.4280 doi: 10.12998/wjcc.v8.i19.4280 id: cord-269283-jm18lj5t author: Uddin, Md Bashir title: Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date: 2020-07-01 words: 2736.0 sentences: 169.0 pages: flesch: 50.0 cache: ./cache/cord-269283-jm18lj5t.txt txt: ./txt/cord-269283-jm18lj5t.txt summary: Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. As the outbreak of the 2019 novel coronavirus (COVID-19 [SARS-CoV-2]) is expanding rapidly, analysis of epidemiological data of COVID-19 is necessary to explore the measures of burden associated with the disease and to simultaneously gather information on determinants and interventions. Moreover, the conservancy study of immunogenic peptides predicted from the SARS-CoV-2 proteins was also compared against other human coronavirus strains (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1 and MERS-CoV). Cross-checked conservancy analysis of COVID-19 antigenic epitopes with SARS-CoV proteins showed that conservancy when crosschecked with other coronaviruses, including BufCoV-HKU26 of Bangladesh origin, was not significant ( Table 3) . abstract: SARS-CoV-2, a new coronavirus strain responsible for COVID-19 has emerged in Wuhan City, China and still continuing its worldwide pandemic nature. Considering the severity of the disease, a number of studies are underway, and full genomic sequences have already been released in the last few weeks to enable the understanding of the evolutionary origin and molecular characteristics of this virus. Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. Based on currently available genomic information, a phylogeny study was employed focusing four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings clearly demonstrated that SARS-CoV-2 exhibited evolutionary convergent relation with previously reported SARS-CoV. It was also found that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed lower level of similarity and identical patterns. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. url: https://www.sciencedirect.com/science/article/pii/S1567134820302719?v=s5 doi: 10.1016/j.meegid.2020.104440 id: cord-299711-m5gb03is author: Udrea, Ana-Maria title: Laser irradiated phenothiazines: New potential treatment for COVID-19 explored by molecular docking date: 2020-08-15 words: 2191.0 sentences: 153.0 pages: flesch: 54.0 cache: ./cache/cord-299711-m5gb03is.txt txt: ./txt/cord-299711-m5gb03is.txt summary: In this study we predict, using molecular docking, the binding affinity of 15 phenothiazines (antihistaminic and antipsychotic drugs) when interacting with the main protease (M(pro)) of SARS-CoV-2. For identifying a treatment of COVID-19 disease, we used molecular docking procedure to predict the inhibitory activity (against SARS-CoV-2) M pro of some compounds from phenothiazines drug class. To simulate the interaction between SARS-CoV-2 and drugs from the class of phenothiazines including TZ and CPZ photoproducts we have used the virus M pro from RCSB Protein Data Bank: PDB code 6LU7 [15] . The 2D/3D chemical structure of compounds from Phenothiazines class and TZ and CPZ photoproducts that resulted during laser irradiation; 2D chemical structure, lowest EFEB (kcal/mol) for each compound resulted after 100 runs using molecular docking simulation, predicted KI (nM) and pKI values are also presented. Our results suggest that TZ and TZ photoproducts obtained by laser irradiation, have significant biological activity on SARS-CoV-2 M pro and could be used in a potent treatment in COVID-19 disease. abstract: The worldwide infection with the new Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) demands urgently new potent treatment(s). In this study we predict, using molecular docking, the binding affinity of 15 phenothiazines (antihistaminic and antipsychotic drugs) when interacting with the main protease (M(pro)) of SARS-CoV-2. Additionally, we tested the binding affinity of photoproducts identified after irradiation of phenothiazines with Nd:YAG laser beam at 266 nm respectively 355 nm. Our results reveal that thioridazine and its identified photoproducts (mesoridazine and sulforidazine) have high biological activity on the virus M(pro). This shows that thioridazine and its two photoproducts might represent new potent medicines to be used for treatment in this outbreak. Such results recommend these medicines for further tests on cell cultures infected with SARS-CoV-2 or animal model. The transition to human subjects of the suggested treatment will be smooth due to the fact that the drugs are already available on the market. url: https://www.ncbi.nlm.nih.gov/pubmed/32829256/ doi: 10.1016/j.jphotobiol.2020.111997 id: cord-035026-2qcsfd87 author: Ugwueze, Chidiebere V. title: COVID-19 and Diabetes Mellitus: The Link and Clinical Implications date: 2020-10-23 words: 5413.0 sentences: 329.0 pages: flesch: 44.0 cache: ./cache/cord-035026-2qcsfd87.txt txt: ./txt/cord-035026-2qcsfd87.txt summary: The effect of glucocorticoids and catecholamines, invasion of the pancreatic islet cells, drugs used in the treatment of COVID-19, and the lockdown policy may impact negatively on glycemic control of diabetic patients. [40] showed that the clinical outcomes in COVID-19-positive patients with coexisting diabetes and hypertension who use ACE inhibitor or angiotensin II receptor blocker were comparable to those not using the drugs. A clinical trial (NCT04318418) was designed to determine the effect of ACE inhibitors and angiotensin II type 1 receptor blockers on the severity of COVID-19 infection [41] . Some authors have considered the rapidity of worsening glycemic control in stable diabetic patients with CO-VID-19 requiring the use of high insulin dose and suggested the possibility of pancreatic invasion by the SARS-CoV-2 [57, 58] . Once the entry of the virus is established, there is a downregulation of ACE2 receptor and a corresponding Ugwueze/Ezeokpo/Nnolim/Agim/ Anikpo/Onyekachi Dubai Diabetes Endocrinol J 6 DOI: 10.1159/000511354 activation of renin-angiotensin-aldosterone system, which is responsible for the cardiac and pulmonary complications of COVID-19 infection [75] . abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a pandemic viral infection that has ravaged the world in recent times, and the associated morbidity and mortality have been much more pronounced in those with noncommunicable disease. Diabetes mellitus is one of commonest noncommunicable diseases associated with worsening clinical status in COVID-19 patients. SUMMARY: The aim of this review was to evaluate the receptors and pathogenetic link between diabetes and COVID-19. Both disease conditions involve inflammation with the release of inflammatory markers. The roles of angiotensin-converting enzyme molecule and dipeptidyl peptidase were explored to show their involvement in COVID-19 and diabetes. Pathogenetic mechanisms such as impaired immunity, microangiopathy, and glycemic variability may explain the effect of diabetes on recovery of COVID-19 patients. The effect of glucocorticoids and catecholamines, invasion of the pancreatic islet cells, drugs used in the treatment of COVID-19, and the lockdown policy may impact negatively on glycemic control of diabetic patients. The outcome studies between diabetic and nondiabetic patients with COVID-19 were also reviewed. Some drug trials are still ongoing to determine the suitability or otherwise of some drugs used in diabetic patients with COVID-19, such as dapagliflozin trial and linagliptin trial. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649685/ doi: 10.1159/000511354 id: cord-319540-kivk3h1k author: Uhe, Tobias title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy date: 2020-07-13 words: 849.0 sentences: 61.0 pages: flesch: 48.0 cache: ./cache/cord-319540-kivk3h1k.txt txt: ./txt/cord-319540-kivk3h1k.txt summary: title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy An 84-year-old male patient with known ischemic cardiomyopathy was admitted to the emergency department of Leipzig University Hospital with typical signs and symptoms of an acute coronary syndrome in the midst of the SARS-Cov2 pandemic on April 22, 2020. Echocardiography (Fig. 2) showed wall motion abnormalities with apical septal dyskinesis, mid ubiquitous akinesia and basal septal and anterior hypokinesis. Due to media reports, she was highly afraid of SARS-CoV2 infections for her husband and herself, because age and hypertension were communicated as high risk for a severe course of COVID-19. Her condition acutely and severely exacerbated when her husband was admitted to the hospital, which she felt would place him at a high risk of death, and because she was not allowed to visit him due to the SARS-CoV2-specific regulations. The patient was provided with psychological support and the SARS-CoV2-negative couple was allowed to meet. abstract: nan url: https://doi.org/10.1007/s00392-020-01706-w doi: 10.1007/s00392-020-01706-w id: cord-263279-afdmegq0 author: Uhteg, Katharine title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 words: 3175.0 sentences: 186.0 pages: flesch: 51.0 cache: ./cache/cord-263279-afdmegq0.txt txt: ./txt/cord-263279-afdmegq0.txt summary: Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. abstract: In December 2019, a novel coronavirus (SARS-CoV-2) was first isolated from Wuhan city, China and within three months, the global community was challenged with a devastating pandemic. The rapid spread of the virus challenged diagnostic laboratories to rapidly develop molecular diagnostic methods. As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. This study compares the validation of three different molecular assays at the Johns Hopkins Molecular Virology laboratory: the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. Overall, our studies indicate a comparable analytical performance of the three assays for the detection of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32361285/ doi: 10.1016/j.jcv.2020.104384 id: cord-019076-4qu9j953 author: Ulferts, Rachel title: Expression and Functions of SARS Coronavirus Replicative Proteins date: 2009-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The discovery of a previously unknown coronavirus as the causative agent of the SARS epidemic in 2002/2003 stimulated a large number of studies into the molecular biology of SARS coronavirus (SARS-CoV) and related viruses. This research has provided significant new insight into the functions and activities of the coronavirus replicase–transcriptase complex, a multiprotein complex that directs coordinated processes of both continuous and discontinuous RNA synthesis to replicate and transcribe the large coronavirus genome, a single-stranded, positive-sense RNA of ~30 kb. In this chapter, we review our current understanding of the expression and functions of key replicative enzymes, such as RNA polymerases, helicase, ribonucleases, ribose-2′-O-methyltransferase and other replicase gene-encoded proteins involved in genome expression, virus–host interactions and other processes. Collectively, these recent studies reveal fascinating details of an enzymatic machinery that, in the RNA virus world, is unparalleled in terms of the number and nature of virally encoded activities involved in virus replication and host interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124140/ doi: 10.1007/978-3-642-03683-5_6 id: cord-313541-fpqwzf9k author: Ulloa, S. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 words: 1776.0 sentences: 104.0 pages: flesch: 55.0 cache: ./cache/cord-313541-fpqwzf9k.txt txt: ./txt/cord-313541-fpqwzf9k.txt summary: The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Thus, the four different media used in this study (UTM, PBS 1x solution, Hanks medium and DNA/RNA Shield TM ) did not affect analytical results, because all precipitated samples were able to be detected by rRT-PCR using the whole viral panel (Orf1ab, N and S genes) and the internal control gene. Here, a simple protocol to detect SARS-CoV-2 from NPSs using rRT-PCR after a heat inactivation and a precipitation/concentration step is proposed. abstract: The World Health Organization (WHO) has declared a pandemic caused by a new coronavirus named SARS-CoV-2. The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. Although the recommendation is to use automated methods for nucleic acid extraction, alternatives are necessary to replace commercial kits. However, these alternatives should be as reliable as automated methods. This work describes a simple method to detect SARS-CoV-2 from specimens collected in different preservation media. Samples were previously inactivated by heating and precipitating with a PEG/NaCl solution before rRT-PCR assays for Orf1ab, N and S genes. The new method was compared with an automated protocol of nucleic acid extraction. Both procedures showed similar analytical results. Consequently, this simple and inexpensive method is a suitable procedure for laboratory diagnosis of SARS-CoV-2 infection. url: https://doi.org/10.1016/j.jviromet.2020.113960 doi: 10.1016/j.jviromet.2020.113960 id: cord-032552-rjuug7er author: Umviligihozo, Gisele title: Sub-Saharan Africa preparedness and response to the COVID-19 pandemic: A perspective of early career African scientists date: 2020-07-08 words: 5927.0 sentences: 290.0 pages: flesch: 46.0 cache: ./cache/cord-032552-rjuug7er.txt txt: ./txt/cord-032552-rjuug7er.txt summary: As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. abstract: Emerging highly transmissible viral infections such as SARS-CoV-2 pose a significant global threat to human health and the economy. Since its first appearance in December 2019 in the city of Wuhan, Hubei province, China, SARS-CoV-2 infection has quickly spread across the globe, with the first case reported on the African continent, in Egypt on February 14 (th), 2020. Although the global number of COVID-19 infections has increased exponentially since the beginning of the pandemic, the number of new infections and deaths recorded in African countries have been relatively modest, suggesting slower transmission dynamics of the virus on the continent, a lower case fatality rate, or simply a lack of testing or reliable data. Notably, there is no significant increase in unexplained pneumonias or deaths on the continent which could possibly indicate the effectiveness of interventions introduced by several African governments. However, there has not yet been a comprehensive assessment of sub-Saharan Africa’s (SSA) preparedness and response to the COVID-19 pandemic that may have contributed to prevent an uncontrolled outbreak so far. As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. Our perspective is based on extensive review of the available scientific publications, official technical reports and announcements released by governmental and non-governmental health organizations as well as from our personal experiences as workers on the COVID-19 battlefield in SSA. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499400/ doi: 10.12688/wellcomeopenres.16070.1 id: cord-017463-repm1vw9 author: Ungchusak, Kumnuan title: Public Health Surveillance: A Vital Alert and Response Function date: 2018-07-27 words: 5671.0 sentences: 273.0 pages: flesch: 40.0 cache: ./cache/cord-017463-repm1vw9.txt txt: ./txt/cord-017463-repm1vw9.txt summary: We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. abstract: Ungchusak, Heymann and Pollack address the critical global issue of public health surveillance. They describe how epidemiologists collect and use surveillance data to detect unusual events or outbreaks and to guide control programmes. Drawing on their combined international experience, the authors explain the vital role that data play in alerting authorities to respond to outbreaks such as Severe Acute Respiratory Syndrome, Ebola, Zika virus and Avian influenza. They point to the importance of sharing information globally while ensuring equal benefits to providers of data, coordinating surveillance activities across sectors, building capacity for surveillance and coordinating national surveillance activities. The authors emphasise the need for enhanced global cooperation to prepare for future public health emergencies of international concern. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122032/ doi: 10.1057/978-1-137-54984-6_10 id: cord-345628-a4c46m2w author: Unudurthi, Sathya D. title: Cardiac inflammation in COVID-19: Lessons from heart failure date: 2020-09-21 words: 7725.0 sentences: 413.0 pages: flesch: 41.0 cache: ./cache/cord-345628-a4c46m2w.txt txt: ./txt/cord-345628-a4c46m2w.txt summary: Autopsies of COVID-19 patients reveal an infiltration of inflammatory mononuclear cells in the myocardium, confirming the role of the immune system in mediating cardiovascular damage in response to COVID-19 infection and also suggesting potential causal mechanisms for the development of new cardiac pathologies and/or exacerbation of underlying CVDs in infected patients. Myocyte damage and lymphocytic myocarditis have also been independently confirmed by recent autopsies carried out on multiple COVID-19 patients from Seattle and Germany (Bradley et al., 2020; Wichmann et al., 2020) Recently, SARS-CoV-2 viral particles have been identified in cardiac macrophages, suggesting that these cells can be directly infected by the virus, potentially transmitting the disease systemically to multiple tissues (Tavazzi et al., 2020) . abstract: Cardiovascular disease (CVD) is the most common co-morbidity associated with COVID-19 and the fatality rate in COVID-19 patients with CVD is highest compared to other comorbidities, such as hypertension and diabetes. Preliminary data suggest that COVID-19 may also cause or worsen cardiac injury in infected patients through multiple mechanisms such as ‘cytokine storm’, endotheliosis, thrombosis, lymphocytopenia etc. Autopsies of COVID-19 patients reveal an infiltration of inflammatory mononuclear cells in the myocardium, confirming the role of the immune system in mediating cardiovascular damage in response to COVID-19 infection and also suggesting potential causal mechanisms for the development of new cardiac pathologies and/or exacerbation of underlying CVDs in infected patients. In this review, we discuss the potential underlying molecular mechanisms that drive COVID-19-mediated cardiac damage, as well as the short term and expected long-term cardiovascular ramifications of COVID-19 infection in patients. url: https://api.elsevier.com/content/article/pii/S0024320520312352 doi: 10.1016/j.lfs.2020.118482 id: cord-340323-xz6v95yy author: Urbach, Horst title: Notfällige Neurointerventionen, Covid-19 und Thorax-CT: SOP und Literaturübersicht date: 2020-05-07 words: 1427.0 sentences: 154.0 pages: flesch: 51.0 cache: ./cache/cord-340323-xz6v95yy.txt txt: ./txt/cord-340323-xz6v95yy.txt summary: Bei Schlaganfall-und anderen Notfallpatienten kann das Ergebnis einer RT-PCR zum Nachweis von SARS-CoV-2, dem Erreger der COVID-19, aus einem Abstrich in der Mehrzahl der Fälle nicht abgewartet werden. Ein solcher Patient wird also wie ein COVID-19-Verdacht betrachtet, auch wenn die Wahrscheinlichkeit, dass er mit SARS-CoV-2 infiziert ist, eher gering erscheint. Das wünschenswerte Szenario ist nun, dass der Patient die Bereiche Computertomographie (CT), Angiographie und Intensivstation wie ein COVID-19-Patient durchläuft sowie Isolierung und Verdacht nach negativem RT-PCR-Ergebnis aufgehoben werden [1] [2] [3] . V. eine Umfrage darüber gestartet, welche diagnostischen und Schutzmaßnahmen in den einzelnen Kliniken bei Patienten mit möglicher SARS-CoV-2-Infektion getroffen werden. Das unterschiedliche Vorgehen neuroradiologischer Abteilungen in Deutschland spiegelt die Unsicherheit im Umgang mit Schlaganfallpatienten und möglicher "coronavirus disease 2019" (COVID-19) wider. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 abstract: BACKGROUND AND PURPOSE: To analyze standard operating procedures (SOP) of acute stroke imaging and interventions during COVID-19 pandemic with special emphasis on chest CT within a multimodal stroke protocol. METHODS: A questionnaire was distributed via email to members of the Professional Organization of German Neuroradiologists (Berufsverband Deutscher Neuroradiologen e.V.). RESULTS: Answers were received from 25 units: eleven of them acquire chest CT, three in any patient and eight, when COVID-19 is suspected due to body temperature increase, patient’s history or when the latter cannot be sufficiently obtained. Preliminary data indicate a high sensitivity and moderate negative predictive value. CONCLUSION: Different SOP reflect an uncertainty whether chest CT should be acquired as part of a multimodal stroke protocol. Accuracy of low dose chest CT cannot be determined yet. The strengths and limitations of chest CT are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32382877/ doi: 10.1007/s00062-020-00911-4 id: cord-351492-8jv7ip67 author: Urwin, S. G. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 words: 7241.0 sentences: 397.0 pages: flesch: 53.0 cache: ./cache/cord-351492-8jv7ip67.txt txt: ./txt/cord-351492-8jv7ip67.txt summary: Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. In this systematic review and pooled analysis of IPD, we found that the FebriDx LFD had a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) for COVID-19 across two studies performed within acute hospitals in the UK when compared to RT-PCR on nose and throat swabs during the first wave of the SARS-CoV-2 pandemic. abstract: Background: Point-of-care (POC) tests for COVID-19 could relieve pressure on isolation resource, support infection prevention and control, and help commence more timely and appropriate treatment. We aimed to undertake a systematic review and pooled diagnostic test accuracy study of available individual patient data (IPD) to evaluate the diagnostic accuracy of a commercial POC test (FebriDx) in patients with suspected COVID-19. Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Studies were screened for risk of bias. IPD were sought from studies meeting the inclusion and exclusion criteria. Logistic regression was performed to investigate the study effect on the outcome of the RT-PCR test result in order to determine whether it was appropriate to pool results. Diagnostic accuracy statistics were calculated with 95% confidence intervals (CIs). Results: 15 studies were screened, and we included two published studies with 527 hospitalised patients. 523 patients had valid FebriDx results for Myxovirus resistance protein A (MxA), an antiviral host response protein. The FebriDx test produced a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) compared with RT-PCR, where there was an estimated true COVID-19 prevalence of 0.405 (0.364-0.448) and overall FebriDx test yield was 99.2%. Patients were tested at a median of 4 days [interquartile range: 2:9] after symptom onset. No differences were found in a sub-group analysis of time tested since the onset of symptoms. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. More research is required to determine how FebriDx would perform in other healthcare settings with higher or lower COVID-19 prevalence, different patient populations, or when other respiratory infections are in circulation. url: http://medrxiv.org/cgi/content/short/2020.10.15.20213108v1?rss=1 doi: 10.1101/2020.10.15.20213108 id: cord-257802-vgizgq2y author: Uttamchandani, Mahesh title: Applications of microarrays in pathogen detection and biodefence date: 2008-11-12 words: 6568.0 sentences: 305.0 pages: flesch: 35.0 cache: ./cache/cord-257802-vgizgq2y.txt txt: ./txt/cord-257802-vgizgq2y.txt summary: Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] . abstract: The microarray is a platform with wide-ranging potential in biodefence. Owing to the high level of throughput attainable through miniaturization, microarrays have accelerated the ability to respond in an epidemic or crisis. Extending beyond diagnostics, recent studies have applied microarrays as a research tool towards understanding the etiology and pathogenicity of dangerous pathogens, as well as in vaccine development. The original emphasis was on DNA microarrays, but the range now includes protein, antibody and carbohydrate microarrays, and research groups have exploited this diversity to further extend microarray applications in the area of biodefence. Here, we discuss the impact and contributions of the growing range of microarrays and emphasize the concepts that might shape the future of biodefence research. url: https://doi.org/10.1016/j.tibtech.2008.09.004 doi: 10.1016/j.tibtech.2008.09.004 id: cord-348342-iqq8kmn0 author: Uyoga, S. title: Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors date: 2020-07-29 words: 3103.0 sentences: 198.0 pages: flesch: 58.0 cache: ./cache/cord-348342-iqq8kmn0.txt txt: ./txt/cord-348342-iqq8kmn0.txt summary: Methods We measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance. Based on these data, we defined anti-SARS-CoV-2 IgG seropositivity as an OD ratio >2 and selected the spike ELISA for this study; the sensitivity and specificity of this threshold was 83% (95% CI: 59-96%) and 99.0% (95% CI 98.1-99.5%), respectively (Table 1, Figure S3 panels A & B). The Bayesian population-weighted and test-adjusted seroprevalence for Kenya was 5.2% (95% CI 3.7-7.1%, Table 3 ) and the posterior sensitivity and specificity estimates were 82.5% (95% CI 69.6-91.2%) and 99.2 (95% CI 98.7-99.6%), respectively. In this anti-SARS-CoV-2 IgG seroprevalence study of blood donors in Kenya, the crude prevalence was 5.6% and the population-weighted test-adjusted seroprevalence was 5.2%. abstract: Background There are no data on SARS-CoV-2 seroprevalence in Africa though the COVID-19 epidemic curve and reported mortality differ from patterns seen elsewhere. We estimated the anti-SARS-CoV-2 antibody prevalence among blood donors in Kenya. Methods We measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. Assay sensitivity and specificity were 83% (95% CI 59, 96%) and 99.0% (95% CI 98.1, 99.5%), respectively. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance. Results Complete data were available for 3098 of 3174 donors, aged 15-64 years. By comparison with the Kenyan population, the sample over-represented males (82% versus 49%), adults aged 25-34 years (40% versus 27%) and residents of coastal Counties (49% versus 9%). Crude overall seroprevalence was 5.6% (174/3098). Population-weighted, test-adjusted national seroprevalence was 5.2% (95% CI 3.7, 7.1%). Seroprevalence was highest in the 3 largest urban Counties; Mombasa (9.3% [95% CI 6.4, 13.2%)], Nairobi (8.5% [95% CI 4.9, 13.5%]) and Kisumu (6.5% [95% CI 3.3, 11.2%]). Conclusions We estimate that 1 in 20 adults in Kenya had SARS-CoV-2 antibodies during the study period. By the median date of our survey, only 2093 COVID-19 cases and 71 deaths had been reported through the national screening system. This contrasts, by several orders of magnitude, with the numbers of cases and deaths reported in parts of Europe and America when seroprevalence was similar. url: https://doi.org/10.1101/2020.07.27.20162693 doi: 10.1101/2020.07.27.20162693 id: cord-311673-z4hkw17g author: Uzzan, Mathieu title: Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis date: 2020-06-23 words: 2969.0 sentences: 154.0 pages: flesch: 40.0 cache: ./cache/cord-311673-z4hkw17g.txt txt: ./txt/cord-311673-z4hkw17g.txt summary: As the visceral fat possesses an intense immune activity, is involved in metabolic syndrome and is at the crossroad between the intestines, the systemic circulation and the lung, we hypothesized that it plays a major role in severe forms of SARS-CoV-2 infection. Several factors may increase intestinal permeability including, direct enterocyte damage by SARS-CoV2, systemic inflammatory response syndrome (SIRS) and epithelial ischemia secondary to SARS-CoV2associated endothelial dysfunction. This increase permeability further leads to translocation of microbial components such as MAMPS (microbial-associated molecular pattern), triggering an inflammatory immune response by TLR-expressing cells of the mesentery fat (mostly macrophages and adipocytes). As the increased volume of mesentery fat in overweight men play a key role in the occurrence of metabolic syndrome [8] , we hypothesized that the visceral adipose tissue plays a central role in severe forms of COVID-19. abstract: Consistent observations report increased severity of SARS-CoV-2 infection in overweight men with cardiovascular factors. As the visceral fat possesses an intense immune activity, is involved in metabolic syndrome and is at the crossroad between the intestines, the systemic circulation and the lung, we hypothesized that it plays a major role in severe forms of SARS-CoV-2 infection. SARS-CoV2 presents the ability to infect epithelial cells of the respiratory tract as well as the intestinal tract. Several factors may increase intestinal permeability including, direct enterocyte damage by SARS-CoV2, systemic inflammatory response syndrome (SIRS) and epithelial ischemia secondary to SARS-CoV2- associated endothelial dysfunction. This increase permeability further leads to translocation of microbial components such as MAMPS (microbial-associated molecular pattern), triggering an inflammatory immune response by TLR-expressing cells of the mesentery fat (mostly macrophages and adipocytes). The pro-inflammatory cytokines produced by the mesentery fat mediates systemic inflammation and aggravate acute respiratory distress syndrome (ARDS) through the mesenteric lymph drainage. url: https://www.sciencedirect.com/science/article/pii/S0306987720316662?v=s5 doi: 10.1016/j.mehy.2020.110023 id: cord-323618-d09b65gd author: Vabret, A. title: Coronavirus humains (HCoV) date: 2008-05-05 words: 6301.0 sentences: 541.0 pages: flesch: 63.0 cache: ./cache/cord-323618-d09b65gd.txt txt: ./txt/cord-323618-d09b65gd.txt summary: La survenue récente, en 2002 à 2003, de l''épidémie de SRAS (ou syndrome respiratoire aigu sévère), et l''identification de l''agent pathogène responsable, un coronavirus émergent dans la population humaine, ont conduit à un vif regain d''intérêt et une intensification importante des recherches sur ces virus. Certaines données expérimentales sont inattendues : malgré des séquences en aminoacides conservées au niveau de la protéine S1 des HCoV 229E et NL63, ces deux coronavirus humains utilisent des récepteurs différents (APN et ACE2, respectivement) ; par ailleurs, le SARS-CoV utilise le même récepteur cellulaire que NL63 alors que les séquences S1 sont éloignées, cependant le RBD des deux virus semble proche et il est absent chez les SL-CoV. Une des conséquences biologiques de cette grande délétion est le changement de tropisme du virus qui, d''entérique pour le TGEV, est devenu respiratoire pour le PRCV [36] De nombreuses études ont été menées à la recherche du réservoir animal du SARS-CoV. abstract: Coronaviruses are a large group of viruses and infect a lot of species of mammals and birds. Five coronaviruses currently infect humans: HCoVs 229E and OC43, identified in the 1960s, SARS-CoV identified in March 2003 during the SARS epidemic, and the HCoVs NL63 and HKU1, identified in 2004 and 2005 respectively. The genome of the coronaviruses is a linear, non-segmented, positive-sense single-stranded RNA molecule of approximately 30 kb. The evolution of these viruses occurs through some features: the generation of multiple mutants during the replication resulting on a quasispecies structure of the viral population, the demonstrated ability of coronaviruses to establish persistent infections, the flexibility of the genome due to a high frequency of homologue or heterologue recombinations, the ability to jump barrier species and to adapt to the new environment. Two epidemiologic pictures of HCoV infections have to be distinguished: as suggested by recent studies, HCoVs except SARS-CoV, are distributed worldwide and cocirculate during seasonal outbreaks. The distribution of the different HCoV species varies according to the geographic area and season. In contrast, the SARS-CoV is responsible of the first emerging infectious disease of this millennium, infecting more than 8000 people between November 2002 and July 2003. Its circulation has been stopped by drastic public health policy. Human coronaviruses may be also involved in enteric and neurologic diseases. The detection of these viruses is difficult and mainly based on molecular assays (RT-PCR). There is no established specific therapy to date. url: https://www.ncbi.nlm.nih.gov/pubmed/18456429/ doi: 10.1016/j.patbio.2008.02.018 id: cord-253077-61fmul8c author: Vabret, Nicolas title: Immunology of COVID-19: current state of the science date: 2020-05-06 words: 20227.0 sentences: 1120.0 pages: flesch: 45.0 cache: ./cache/cord-253077-61fmul8c.txt txt: ./txt/cord-253077-61fmul8c.txt summary: Lastly, Nonhuman primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific IgG responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into pro-inflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012; Liu et al., 2019) . Collectively, these data suggest that cross-talk with monocytes might impair NK cell recognition and killing of SARS-CoV-2infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients ( Figure 2 ). However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human coronaviruses, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020) . abstract: Abstract The coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of COVID19 pathophysiology. In this review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32505227/ doi: 10.1016/j.immuni.2020.05.002 id: cord-259185-qg4jwbes author: Vadlamani, B. S. title: Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-09-09 words: 3988.0 sentences: 249.0 pages: flesch: 51.0 cache: ./cache/cord-259185-qg4jwbes.txt txt: ./txt/cord-259185-qg4jwbes.txt summary: In this work, we report the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor and its efficacy for rapid detection of spike glycoprotein of SARS-CoV-2 by examining S-RBD protein as the reference material. Our manuscript reports the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor for rapid detection of spike glycoprotein of SARS-CoV-2. . https://doi.org/10.1101/2020.09.07.20190173 doi: medRxiv preprint asymptomatic individuals are needed, which is feasible only after the development of a simple, portable and rapid point-of-use sensor for the detection of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data showed that cobalt functionalized TNTs could selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~ 30 secs. abstract: The coronavirus disease (COVID-19) is a newly emerging viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rapid increase in the number of COVID-19 cases worldwide led the WHO declare pandemic within a few month after the first case of infection. Due to the lack of a prophylactic measure to control the virus infection and spread, early diagnosis and quarantining of infected as well as the asymptomatic individuals are necessary for the containment of this pandemic. However, the current methods for SARS-CoV-2 diagnosis are expensive and time consuming although some promising and inexpensive technologies are coming out for emergency use. In this work, we report the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor and its efficacy for rapid detection of spike glycoprotein of SARS-CoV-2 by examining S-RBD protein as the reference material. A simple, low-cost, and one-step electrochemical anodization route was used to synthesize TNTs, followed by an incipient wetting method for cobalt functionalization of the TNTs platform, which is connected to a potentiostat for data collection. The sensor specifically detected the S-RBD protein of SARS-CoV-2 even at very low concentration (range of 14 nM to 1400 nM). Additionally, our sensor showed linear response in the detection of viral protein with concentration. In summary, our Co-TNT sensor is highly effective in detecting SARS-CoV-2 S-RBD protein in approximately 30 seconds, which can be explored for developing a point of care diagnostics for rapid detection of SARS-CoV-2 in nasal secretions or saliva samples. url: https://doi.org/10.1101/2020.09.07.20190173 doi: 10.1101/2020.09.07.20190173 id: cord-344180-v8xs5ej8 author: Vadlamani, Bhaskar S. title: Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date: 2020-10-17 words: 5150.0 sentences: 280.0 pages: flesch: 52.0 cache: ./cache/cord-344180-v8xs5ej8.txt txt: ./txt/cord-344180-v8xs5ej8.txt summary: In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO(2) nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. In this study, we developed a Co-metal functionalized TNT as a sensing material for electrochemical detection of SARS-CoV-2 infection through the detection of the receptor binding domain (RBD) of spike glycoprotein. abstract: The COronaVIrus Disease (COVID-19) is a newly emerging viral disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rapid increase in the number of COVID-19 cases worldwide led the WHO to declare a pandemic within a few months after the first case of infection. Due to the lack of a prophylactic measure to control the virus infection and spread, early diagnosis and quarantining of infected as well as the asymptomatic individuals are necessary for the containment of this pandemic. However, the current methods for SARS-CoV-2 diagnosis are expensive and time consuming, although some promising and inexpensive technologies are becoming available for emergency use. In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO(2) nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. A simple, low-cost, and one-step electrochemical anodization route was used for synthesizing TNTs, followed by an incipient wetting method for cobalt functionalization of the TNTs platform, which was connected to a potentiostat for data collection. This sensor specifically detected the S-RBD protein of SARS-CoV-2 even at very low concentration (range of 14 to 1400 nM (nano molar)). Additionally, our sensor showed a linear response in the detection of viral protein over the concentration range. Thus, our Co-TNT sensor is highly effective in detecting SARS-CoV-2 S-RBD protein in approximately 30 s, which can be explored for developing a point of care diagnostics for rapid detection of SARS-CoV-2 in nasal secretions and saliva samples. url: https://doi.org/10.3390/s20205871 doi: 10.3390/s20205871 id: cord-355422-c4odhdql author: Vaira, Luigi Angelo title: Potential pathogenesis of ageusia and anosmia in COVID‐19 patients date: 2020-04-27 words: 1008.0 sentences: 67.0 pages: flesch: 49.0 cache: ./cache/cord-355422-c4odhdql.txt txt: ./txt/cord-355422-c4odhdql.txt summary: From the first reports, ageusia and anosmia appear to be frequent clinical features in coronavirus disease 19 (COVID‐19) patients. 3 We report our survey of the literature up to April 14, 2020 , analyzing the possible causes of these chemosensory alterations, which may be useful as a starting point for specific future studies. Moreover, the Middle East Respiratory Syndrome (MERS) coronavirus may bind to the sialic acid receptors 9 , an ability which has also recently been described for SARS-CoV-2 10 . In such a way, SARS-CoV-2 could therefore occupy the binding sites of sialic acid on the taste buds, accelerating the degradation of the gustatory particles. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia abstract: From the first reports, ageusia and anosmia appear to be frequent clinical features in coronavirus disease 19 (COVID‐19) patients. We have performed a survey of the literature, analyzing the possible causes of these chemosensory alterations, which may be useful as a starting point for specific further studies. This article is protected by copyright. All rights reserved url: https://doi.org/10.1002/alr.22593 doi: 10.1002/alr.22593 id: cord-293544-nemw29r7 author: Valdivia, Arantxa title: Qualitative assessment of SARS‐CoV‐2‐specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay date: 2020-08-02 words: 765.0 sentences: 57.0 pages: flesch: 45.0 cache: ./cache/cord-293544-nemw29r7.txt txt: ./txt/cord-293544-nemw29r7.txt summary: Here, we carried out qualitative assessment of SARS‐CoV‐2‐specific antibody avidity using an urea (6M) dissociation test performed on a lateral flow immunochromatographic IgG/IgM device. 2 Although serology testing is mainly aimed at identifying individuals who have previously been exposed to SARS-CoV-2, it may also aid in diagnosis of ongoing COVID-19, particularly in RT-PCR negative patients who present at relatively late times after infection. 3 Knowledge of the precise timing of infection may be of clinical and epidemiological relevance as viral shedding in the upper respiratory tract seems to continue up to 7 to 9 days after onset of symptoms in patients presenting with mild or moderate COVID-19. T A B L E 2 Qualitative assessment of SARS-CoV-2-specific antibody avidity in serial serum samples from patients with COVID Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay abstract: Knowledge of the precise timing of SARS‐CoV‐2 infection may be of clinical and epidemiological relevance. The presence of low‐avidity IgGs has conventionally been considered an indicator of recent infection. Here, we carried out qualitative assessment of SARS‐CoV‐2‐specific antibody avidity using an urea (6M) dissociation test performed on a lateral flow immunochromatographic IgG/IgM device. We included a total of 76 serum specimens collected from 57 COVID‐19 patients, of which 39 tested positive for both IgG and IgM and 37 only for IgG. Sera losing IgG reactivity after urea treatment (n = 28) were drawn significantly earlier (P = .04) after onset of symptoms than those which preserved it (n = 48). This assay may be helpful to estimate the time of acquisition of infection in patients with mild to severe COVID‐19. url: https://www.ncbi.nlm.nih.gov/pubmed/32706420/ doi: 10.1002/jmv.26344 id: cord-331002-7uojryqz author: Valent, Francesca title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date: 2020-09-06 words: 784.0 sentences: 64.0 pages: flesch: 59.0 cache: ./cache/cord-331002-7uojryqz.txt txt: ./txt/cord-331002-7uojryqz.txt summary: METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. The main finding of our study is the long duration of SARS-CoV-2 positivity in a population 133 including patients ranging from asymptomatic to acute respiratory distress syndrome requiring ICU 134 care. SARS-CoV-2 Viral Load in Upper 236 Respiratory Specimens of Infected Patients abstract: OBJECTIVES: Duration of SARS-CoV-2 in upper respiratory tract is extremely variable, but its relation to disease severity is unknown. We investigated such relation in the 530,000-inhabitant North-Eastern Italian province of Udine. METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Duration of viral positivity was assessed from the first positive test to the day of the first of two consecutive negative tests. Univariate and multivariate analyses were conducted to investigate differences in the four groups. RESULTS: From March 1 to April 30, 39,483 RT-PCR tests for SARS-CoV-2 were conducted on 23,778 persons. 974 subjects had a positive test result. Among those with multiple tests (N=878), mean time to negativity was 23.7 days (standard error 0.3639) (median 23, interquartile range: 16-30 days). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. CONCLUSIONS: Disease control measures should not be adjusted to account for differences in viral shedding according to symptomatic status. url: https://api.elsevier.com/content/article/pii/S1198743X20305255 doi: 10.1016/j.cmi.2020.08.041 id: cord-310061-nro623aa author: Valitutto, Marc T. title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 words: 3678.0 sentences: 192.0 pages: flesch: 48.0 cache: ./cache/cord-310061-nro623aa.txt txt: ./txt/cord-310061-nro623aa.txt summary: Historically, bats have been linked to highly pathogenic viruses that pose a serious threat to human health, including the coronaviruses responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), the hemorrhagic ebola and Marburg filoviruses, and paramyxoviruses such as Nipah virus [10, 11, [13] [14] [15] [16] [17] [18] . The 2002-2003 SARS epidemic, the emergence of MERS in people in 2012, and the ongoing COVID-19 pandemic have prompted substantial interest in detecting coronaviruses of bat origin due to public health concern and their pandemic potential [10, [13] [14] [15] [16] [17] [18] . In addition to human-associated CoVs, bats are also hosts of coronaviruses that infect production animals, and have been implicated in the emergence and origin of swine acute diarrhea syndrome (SADS), transmissible gastroenteritis virus (TGEV) in pigs, and porcine epidemic diarrhea (PED), which can cause considerable losses [23] [24] [25] [26] . abstract: The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales. url: https://www.ncbi.nlm.nih.gov/pubmed/32271768/ doi: 10.1371/journal.pone.0230802 id: cord-327653-2gn9h4i2 author: Vallinoto, Antonio Carlos Rosário title: The challenges of COVID-19 in the Brazilian Amazonian communities and the importance of seroepidemiological surveillance studies date: 2020-08-15 words: 1721.0 sentences: 74.0 pages: flesch: 36.0 cache: ./cache/cord-327653-2gn9h4i2.txt txt: ./txt/cord-327653-2gn9h4i2.txt summary: Since the elimination of beta-coronavirus circulation requires a minimum herd immunity (indications 50-66%) [7] , the information for which is still unknown at the local, national or global levels, conducting seroepidemiological and surveillance studies on SARS-CoV-2 in geographic areas such as the Amazon is extremely important, as it will allow for the assessment of the prevalence and titre of antibodies anti-SARS-CoV-2, mortality and case fatality rates and the epidemiological aspects of risk of exposure in communities from different population strata, such as riberinhos (riverain communities), quilombola (Afro-descendant communities) and indigenous peoples, providing an improvement in the decisionmaking of future epidemics. abstract: The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has alarmed the world with its high rate of transmission and the ability to cause severe and fatal disease. The impact of this pandemic may be even greater in populations where the absence of health services is a chronic aspect, as reported with populations living in the Brazilian Amazon. In this article, we address the perspective of possible impacts of the pandemic on these populations and the importance of conducting seroepidemiological surveillance studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32799872/ doi: 10.1186/s12939-020-01256-7 id: cord-283485-xit6najq author: Van Damme, Wim title: The COVID-19 pandemic: diverse contexts; different epidemics—how and why? date: 2020-07-27 words: 9627.0 sentences: 633.0 pages: flesch: 53.0 cache: ./cache/cord-283485-xit6najq.txt txt: ./txt/cord-283485-xit6najq.txt summary: Since its emergence in Wuhan, China, in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 4 It was soon discovered that the virus is easily transmitted, can cause Summary box ► Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 88 Box 2 On the use of mathematical models during epidemics A dominant way of studying the transmission dynamics of an infectious disease such as COVID-19, and predicting the amplitude and peak of the epidemic in a population (city, province, country) and analysing the effect of control measures is using mathematical models. abstract: It is very exceptional that a new disease becomes a true pandemic. Since its emergence in Wuhan, China, in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. However, in different countries, the COVID-19 epidemic takes variable shapes and forms in how it affects communities. Until now, the insights gained on COVID-19 have been largely dominated by the COVID-19 epidemics and the lockdowns in China, Europe and the USA. But this variety of global trajectories is little described, analysed or understood. In only a few months, an enormous amount of scientific evidence on SARS-CoV-2 and COVID-19 has been uncovered (knowns). But important knowledge gaps remain (unknowns). Learning from the variety of ways the COVID-19 epidemic is unfolding across the globe can potentially contribute to solving the COVID-19 puzzle. This paper tries to make sense of this variability—by exploring the important role that context plays in these different COVID-19 epidemics; by comparing COVID-19 epidemics with other respiratory diseases, including other coronaviruses that circulate continuously; and by highlighting the critical unknowns and uncertainties that remain. These unknowns and uncertainties require a deeper understanding of the variable trajectories of COVID-19. Unravelling them will be important for discerning potential future scenarios, such as the first wave in virgin territories still untouched by COVID-19 and for future waves elsewhere. url: https://doi.org/10.1136/bmjgh-2020-003098 doi: 10.1136/bmjgh-2020-003098 id: cord-344751-i4qnrtjq author: Van Praet, Jens T. title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 words: 2399.0 sentences: 119.0 pages: flesch: 49.0 cache: ./cache/cord-344751-i4qnrtjq.txt txt: ./txt/cord-344751-i4qnrtjq.txt summary: Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. To evaluate the specificity of the immuno-assays, we used a set of serum samples from control patients with recent respiratory viral or atypical bacterial infections. To this end, we tested for cross-reactivity with sera of patients with other respiratory viral or atypical bacterial infections, including common coronavirus infections, since these may present with clinical and radiological findings similar to Covid-19. Our study focused on the clinical sensitivity and specificity of four commercial immuno-assays for anti-SARS-COV-2 IgG in the subset of patients presenting with negative RT-PCR and suspect CT findings. In summary, we found good clinical sensitivity of anti-SARS-Cov-2 IgG immunoassays for Covid-19 in the subset of patients with negative RT-PCR 14 days after onset of symptoms. abstract: A subset of patients with Covid-19 presents with negative RT-PCR screening but suspect CT findings. Using four commercially available anti-SARS-CoV-2 IgG immuno-assays, we found this subset constituted 9.2% of all consecutively admitted outpatients with Covid-19 in our hospital. Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s15010-020-01523-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s15010-020-01523-3 doi: 10.1007/s15010-020-01523-3 id: cord-326148-9wpxm5of author: Van Walle, I. title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date: 2020-09-18 words: 3790.0 sentences: 218.0 pages: flesch: 49.0 cache: ./cache/cord-326148-9wpxm5of.txt txt: ./txt/cord-326148-9wpxm5of.txt summary: title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Studies containing potentially usable data on clinical performance of SARS-CoV-2 nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. abstract: We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Analogously, 9 nucleic acid tests and 25 antibody tests, among which 12 point of care tests, had a clinical specificity of [≤]98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Manufacturer reported clinical performance was significantly higher than independently assessed in 11/32 (34.4%) and 4/34 (11.8%) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. Continuous monitoring of clinical performance within more clearly defined target populations is needed. url: http://medrxiv.org/cgi/content/short/2020.09.16.20195917v1?rss=1 doi: 10.1101/2020.09.16.20195917 id: cord-243806-26n22jbx author: Vandelli, Andrea title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 words: 5252.0 sentences: 317.0 pages: flesch: 52.0 cache: ./cache/cord-243806-26n22jbx.txt txt: ./txt/cord-243806-26n22jbx.txt summary: Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5'' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . abstract: Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of>2500 coronaviruses and computed>100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are the most structured elements in the viral genome and the 5 prime end has the strongest propensity to associate with human proteins. The domain encompassing nucleotides 23000-24000 is highly conserved both at the sequence and structural level, while the region upstream varies significantly. These two sequences code for a domain of the viral protein Spike S that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2) and has the potential to bind sialic acids. Our predictions indicate that the first 1000 nucleotides in the 5 prime end can interact with proteins involved in viral RNA processing such as double-stranded RNA specific editases and ATP-dependent RNA-helicases, in addition to other high-confidence candidate partners. These interactions, previously reported to be also implicated in HIV, reveal important information on host-virus interactions. The list of transcriptional and post-transcriptional elements recruited by SARS-CoV-2 genome provides clues on the biological pathways associated with gene expression changes in human cells. url: https://arxiv.org/pdf/2003.13655v4.pdf doi: nan id: cord-297652-ut6e1ysz author: Vanden Eynde, Jean Jacques title: COVID-19: A Brief Overview of the Discovery Clinical Trial date: 2020-04-10 words: 3140.0 sentences: 191.0 pages: flesch: 58.0 cache: ./cache/cord-297652-ut6e1ysz.txt txt: ./txt/cord-297652-ut6e1ysz.txt summary: The study is entitled "Trial of Treatments for COVID-19 in Hospitalized Adults (DisCoVeRy)" (NCT04315948) [4] . In a MERS-CoV mouse model, the combination lopinavir/ritonavir/interferon β-1a, used as prophylactic and curative treatments, revealed no significant decrease in the viral load [9] . The results of an ongoing clinical trial (NCT Pharmaceuticals 2020, 13, 65 5 of 8 02845843 [4]), entitled "MERS-CoV infection treated with a combination of lopinavir/ritonavir and interferon Beta-1b", are eagerly awaited, but will not be disclosed before 2021. On March 28, the FDA issued an Emergency Use Authorization for use of hydroxychloroquine and chloroquine for patients who do not have access to the drugs via clinical trials [36] . The first cases of COVID-19 emerged in Wuhan, China, in late 2019, and to date there is no approved specific drug to cure patients infected by SARS-CoV-2. In Vitro Antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) abstract: The outbreak of COVID-19 is leading to a tremendous search for curative treatments. The urgency of the situation favors a repurposing of active drugs but not only antivirals. This short communication focuses on four treatments recommended by WHO and included in the first clinical trial of the European Discovery project. url: https://doi.org/10.3390/ph13040065 doi: 10.3390/ph13040065 id: cord-335932-0phqok4g author: Vanhems, Philippe title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit date: 2020-03-30 words: 579.0 sentences: 46.0 pages: flesch: 60.0 cache: ./cache/cord-335932-0phqok4g.txt txt: ./txt/cord-335932-0phqok4g.txt summary: title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit Lyon Study Group on Covid19 infection (Geriatric sectionAlphabetic order): Adrait, A, Benoist F, Castel-Kremer E, Chuzeville M, Dupin AC, Doh S, Kim B, Favrelle L, Hilliquin D, Kanafer N, Marion E, Martin-Gaujard G, Moyenin Y, Paulet-Lafuma H, Ricanet A, Saadatian-Elahi M, Vanhems P. To the Editor-SARS-CoV2 nosocomial transmission has been reported among healthcare professionals and patients. The nasal swab previously collected was retested on March 6 and confirmed positive for SARS-CoV2 by RT-PCR. Strict infection control measures and close monitoring of suspected cases of patients and healthcare professionals were subsequently performed to contain the intraunit transmission of the SARS-Cov-2 virus. The rapid spread of nosocomial COVID-19 in this ward confirms the contagiousness of SARS-CoV-2 in healthcare settings and the high mortality rates in this population. Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit abstract: Lyon Study Group on Covid19 infection (Geriatric section- Alphabetic order): Adrait, A, Benoist F, Castel-Kremer E, Chuzeville M, Dupin AC, Doh S, Kim B, Favrelle L, Hilliquin D, Kanafer N, Marion E, Martin-Gaujard G, Moyenin Y, Paulet-Lafuma H, Ricanet A, Saadatian-Elahi M, Vanhems P. url: https://www.ncbi.nlm.nih.gov/pubmed/32223768/ doi: 10.1017/ice.2020.99 id: cord-300763-3ateeei3 author: Vannabouathong, Christopher title: Novel Coronavirus COVID-19: Current Evidence and Evolving Strategies date: 2020-05-06 words: 6137.0 sentences: 308.0 pages: flesch: 52.0 cache: ./cache/cord-300763-3ateeei3.txt txt: ./txt/cord-300763-3ateeei3.txt summary: The term PHEIC is defined as 27 : "an extraordinary event which is determined to constitute a public health risk to other States through the international spread of disease; and to potentially require a coordinated international response." Also, according to the WHO 28 , "This definition implies a situation that is serious, unusual, or unexpected; carries implications for public health beyond the affected state''s national border; and may require immediate international action." Eleven days later, on February 10, 2020, there were, cumulatively, 40,554 confirmed cases and 910 deaths globally across 25 countries, and the majority were identified in the People''s Republic of China 29 . In a cross-sectional analysis that included 1,023 COVID-19-related deaths in the People''s Republic of China, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team 43 found that >80% were patients ‡60 years of age; when extending this range to those who were ‡50 years of age, this number increased to >90% 44 . abstract: COVID-19 is a global pandemic that has currently infected >300,000 globally. Fever and cough are the most common symptoms of the disease, and it is important to remember that the virus can even be transmitted by individuals who test positive for the disease but do not have any symptoms. Currently reported mortality rates vary because of the rapid spread of the disease and different approaches to calculating this estimate, but it is clear that the risk of death is associated with age and the presence of underlying conditions. Risk mitigation techniques (i.e., hand washing, social distancing, and self-isolation) have already been emphasized across major news outlets. It is essential that we continue these practices, as the outbreak is currently expected to last for many more months and we must be mindful of the lessons learned from past pandemics to prevent a second wave from occurring. url: https://www.ncbi.nlm.nih.gov/pubmed/32379112/ doi: 10.2106/jbjs.20.00396 id: cord-296109-kco85lqn author: Vanuytsel, Kim title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 words: 2499.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-296109-kco85lqn.txt txt: ./txt/cord-296109-kco85lqn.txt summary: Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. In the United States, significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate COVID-19 patient care and public health management of the pandemic (Sharfstein et al., 2020) , impacting the timely mapping of the dynamics of viral spread in the general population, and more topically, the conservation of personal protective equipment. Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). abstract: Summary The COVID-19 pandemic is a global public health crisis. Significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate public health management of the disease, impacting the timely mapping of viral spread and the conservation of personal protective equipment. Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. Here, we report the implementation of a SARS-CoV-2 diagnostic RT-PCR assay with rapid turnaround time enabling more informed decisions with personal and public health ramifications. This work provides a blueprint for academic centers and community hospitals lacking capital-intensive automated laboratory machinery to implement in-house testing. url: https://www.sciencedirect.com/science/article/pii/S2666634020300039?v=s5 doi: 10.1016/j.medj.2020.05.001 id: cord-265724-fdt00qw1 author: Varadarajan, Saranya title: EMMPRIN/BASIGIN as a biological modulator of oral cancer and COVID-19 interaction: novel propositions date: 2020-07-09 words: 1761.0 sentences: 105.0 pages: flesch: 39.0 cache: ./cache/cord-265724-fdt00qw1.txt txt: ./txt/cord-265724-fdt00qw1.txt summary: Apart from ACE-2, recently EMMPRIN, has been regarded as a target for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attachment and entry into the host cell. Since one of the routes of entry for the virus is the oral cavity, it becomes imperative to percept oral comorbidities such oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMDs) in terms of EMMPRIN as a target for SARS-CoV-2. 1 Angiotensin-Converting Enzyme 2 (ACE-2) on the host cells is the attachment protein for the spike receptor present on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [4] [5] [6] Apart from ACE-2, recently extracellular matrix metalloproteinase inducer (EMMPRIN), which is also called BASIGIN/CD147, has been regarded as a target for SARS-CoV-2 attachment and its entry into the host cell. OSCC, by the virtue of upregulation of EMMPRIN expression (potential and alternative site for ''S'' receptor), increases the susceptibility to SARS-CoV-2 infection. abstract: Extracellular matrix metalloproteinase inducer (EMMPRIN), which is also called BASIGIN/CD147, is a cell surface glycoprotein that belongs to the immunoglobulin superfamily and plays a significant role in intercellular recognition in immunology, cellular differentiation and development. Apart from ACE-2, recently EMMPRIN, has been regarded as a target for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attachment and entry into the host cell. Since one of the routes of entry for the virus is the oral cavity, it becomes imperative to percept oral comorbidities such oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMDs) in terms of EMMPRIN as a target for SARS-CoV-2. In the present paper, it is proposed that OSCC, by the virtue of upregulation of EMMPRIN expression, increases the susceptibility to coronavirus disease (COVID-19). In turn, COVID-19 in OSCC patients causes exhaustion of EMMPRIN receptor due to binding with ‘S’ receptor leading to a downregulation of related carcinogenesis events. We proposed that in the ACE-2 depleted situation in OSCC, EMMPRIN receptor might get high jacked by the COVID-19 virus for the entry into the host cells. Apart from the anti-monoclonal antibody, it is recommended to explore the use of grape seed and skin containing mouthwash as an adjunct, which could also have anti EMMPRIN effects in patients with OSCC and OPMDs. url: https://www.sciencedirect.com/science/article/pii/S0306987720319721?v=s5 doi: 10.1016/j.mehy.2020.110089 id: cord-257766-z7vcdtcq author: Varadhachary, Atul title: Salivary anti-SARS-CoV-2 IgA as an accessible biomarker of mucosal immunity against COVID-19 date: 2020-08-11 words: 8470.0 sentences: 455.0 pages: flesch: 50.0 cache: ./cache/cord-257766-z7vcdtcq.txt txt: ./txt/cord-257766-z7vcdtcq.txt summary: To minimize risk to lab personnel of exposure to SARS-CoV-2, our clinical study was limited to salivary samples collected from individuals who were at least a month post-symptom onset, so we cannot report on when IgA levels first appear in saliva, though that work is currently underway. Individual Immunity and Clinical Implications: Our observations that (i) we see a large variation in salivary IgA titer, even in pre-COVID-19 samples; (ii) elevated IgA levels appear to persist for at least 2-3 months; and (iii) individuals may develop mucosal IgA without an overt SARS-CoV-2 infection, each raise intriguing questions. . https://doi.org/10.1101/2020.08.07.20170258 doi: medRxiv preprint Community Surveillance and Herd Immunity: Reports that systemic IgA may be detectable earlier than IgG or IgM, 22,23 as early as two days after symptom onset are consistent with the early-response role played by IgA, as well as with our anecdotal observations that individuals can muco-convert to positive salivary IgA contemporaneously with viral detection by PCR. abstract: BACKGROUND: Mucosal immunity, including secretory IgA (sIgA), plays an important role in early defenses against respiratory pathogens. Salivary testing, the most convenient way to measure sIgA, has been used to characterize mucosal immune responses to many viral infections including SARS, MERS, influenza, HIV, and RSV. However, its role has not yet been characterized in the COVID-19 pandemic. Here, we report development and validation of a rapid immunoassay for measuring salivary IgA against the SARS-CoV-2 virus, and report quantitative results in both pre-COVID-19 and muco-converted subjects. METHODS: We developed and refined a specific test for salivary IgA against SARS-CoV-2 on the Brevitest platform, a rapid immunoassay system designed for point-of-care use. A qualitative test was validated as per FDA guidelines with saliva obtained from subjects prior to the emergence of COVID-19, and from PCR-confirmed COVID-19 patients. We also generated a quantitative measure of anti-SARS-CoV-2 salivary IgA. Time taken for saliva self-collection was measured and its ease-of-use assessed. RESULTS: We successfully validated a qualitative salivary assay for SARS-CoV-2 IgA antibodies, with positive and negative predictive values of 92% and 97%, respectively, and no observable cross-reactivity with any of seven potential confounders. Pre-COVID-19 saliva samples showed an 8-fold range of IgA concentrations, suggesting a broad continuum of natural antibody resistance against the novel virus, though at levels lower than that observed in COVID-19 PCR-confirmed subjects. Samples from muco-positive subjects also shown a ~9-fold variation in salivary IgA levels, with elevated salivary IgA observed beyond three months after onset of symptoms. We observed a correlation (r=0.4405) between salivary IgA levels and COVID-19 disease severity. In anecdotal observations, we observed individuals who exhibited antibodies early in the course of their disease, contemporaneously with a positive PCR test, as well as individuals who muco-converted despite no known direct exposure to a COVID-19 patient, no symptoms, and negative molecular and/or serum antibody tests. Salivary collection took 5–10 minutes, and was reported as being easy (mean of 1.1 on a scale of 1 to 10). IMPLICATIONS: Mucosal immunity, including secretory IgA, plays an important role in host defense against respiratory pathogens, and our early data suggest it may do so in COVID-19. Salivary IgA, an accessible marker of mucosal immunity, may be a useful indicator of several key parameters including individual and community immune response, disease severity, clinical risk, and herd immunity. The non-invasive nature and ease of saliva collection facilitates its potential use as a biomarker for ongoing patient assessment and management, as well as a community surveillance tool. By measuring mucosal immune responses directly and systemic immune responses indirectly, salivary IgA could be useful in developing and deploying a vaccine(s) against COVID-19. Quantitative IgA assessment could also potentially serve as a tool to segment the population into different risk categories and inform individual and collective decisions relating to appropriate activities and vaccine prioritization/delivery. These data reinforce the importance of further investigation into the role of mucosal immunity and IgA in host responses against COVID-19. url: http://medrxiv.org/cgi/content/short/2020.08.07.20170258v1?rss=1 doi: 10.1101/2020.08.07.20170258 id: cord-329363-kaw3h5xm author: Vardeny, Orly title: Applying the Lessons of Influenza to COVID-19 During a Time of Uncertainty date: 2020-05-26 words: 1030.0 sentences: 42.0 pages: flesch: 30.0 cache: ./cache/cord-329363-kaw3h5xm.txt txt: ./txt/cord-329363-kaw3h5xm.txt summary: For patients with underlying cardiovascular disease, other opportunities for minimizing complications from infection include remaining up to date on other immunizations, including influenza vaccine, which is available and effective, and pneumococcal vaccine, as secondary bacterial infections often lead to hospitalizations among those with primary viral infections. Because viral illness has been shown to exacerbate underlying cardiac illness and can lead to acute events such as acute myocardial infarction or decompensated heart failure, efforts should be made to optimize guideline-directed treatment strategies that have been shown to improve clinical status in high-risk patients, and thus reduce the risk of worsening symptoms or acute events in case of infection. In patients without known or suspected COVID-19, this includes all evidence-based therapies in cardiovascular disease, such as aspirin, statins, and β-blockers for secondary prevention in patients with coronary disease, and guideline-directed medical therapy in those with heart failure. abstract: nan url: https://doi.org/10.1161/circulationaha.120.046837 doi: 10.1161/circulationaha.120.046837 id: cord-296095-onereai5 author: Vardhan, Seshu title: In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 date: 2020-07-28 words: 5483.0 sentences: 274.0 pages: flesch: 48.0 cache: ./cache/cord-296095-onereai5.txt txt: ./txt/cord-296095-onereai5.txt summary: Considering the published literature on medicinal importance, 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). In this manuscript, 154 phytochemicals from limonoids and triterpenoids were selected by considering their known medicinal importance to search potential hits for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). Our recent molecular docking study on searching inhibitors for COVID-19 revealed that the phytochemical limonin known for inhibiting the replication of retroviruses like HTLV-I and HIV-1 showed the higher dock score towards the protein targets RdRp and ACE2 of SARS-CoV-2, and comparatively higher than the drug hydroxychloroquine [17] . abstract: Virtual screening of phytochemicals was performed through molecular docking, simulations, in silico ADMET and drug-likeness prediction to identify the potential hits that can inhibit the effects of SARS-CoV-2. Considering the published literature on medicinal importance, 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). The in silico computational results revealed that the phytochemicals such as glycyrrhizic acid, limonin, 7-deacetyl-7-benzoylgedunin, maslinic acid, corosolic acid, obacunone and ursolic acid were found to be effective against the target proteins of SARS-CoV-2. The protein-ligand interaction study revealed that these phytochemicals bind with the amino acid residues at the active site of the target proteins. Therefore, the core structure of these potential hits can be used for further lead optimization to design drugs for SARS-CoV-2. Also, the medicinal plants containing these phytochemicals like licorice, neem, tulsi, citrus and olives can be used to formulate suitable therapeutic approaches in traditional medicines. url: https://www.sciencedirect.com/science/article/pii/S0010482520302729 doi: 10.1016/j.compbiomed.2020.103936 id: cord-272681-u3p0hsla author: Vargas-Gandica, Jair title: Ageusia and anosmia, a common sign of COVID-19? A case series from four countries date: 2020-07-14 words: 1508.0 sentences: 84.0 pages: flesch: 53.0 cache: ./cache/cord-272681-u3p0hsla.txt txt: ./txt/cord-272681-u3p0hsla.txt summary: As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to evolve, novel signs and symptoms continue to emerge and expand the clinical manifestations of coronavirus disease 2019 (COVID-19) (Rodriguez-Morales et al. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. As we observed in our patients, deficits in olfactory and taste function were usually of acute onset and at early stages of the disease, presenting for most cases as the initial clinical manifestation throughout the first days (Beltran-Corbellini et al. Anosmia as a presenting symptom of SARS-CoV-2 infection in healthcare workers -a systematic review of the literature, case series, and recommendations for clinical assessment and management abstract: Over the course of the pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), multiple new clinical manifestations, as the consequence of the tropism of the virus, have been recognized. That includes now the neurological manifestations and conditions, such as headache, encephalitis, as well as olfactory and taste disorders. We present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. url: https://doi.org/10.1007/s13365-020-00875-8 doi: 10.1007/s13365-020-00875-8 id: cord-274802-7ioiwsd8 author: Varghese, Praveen Mathews title: Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies date: 2020-08-19 words: 19657.0 sentences: 1033.0 pages: flesch: 42.0 cache: ./cache/cord-274802-7ioiwsd8.txt txt: ./txt/cord-274802-7ioiwsd8.txt summary: Proteomic and transcriptomic studies on bronchoalveolar lavage (BAL) samples from COVID-19 patients have also revealed considerable insights into the expression of SARS-CoV-2 receptors, co-receptors, immune responses, as well as risk factors for severe disease e.g. age and co-morbidities. Furthermore, treatment with a recombinant C5a antibody on 2 male COVID-19 patients aged 54 and 67 years showed significant benefit in suppressing complement hyperactivation, which contributes to the excessive immune response causing aggravated inflammatory lung injury, a hallmark of SARS-CoV-2 pathogenesis and lethality (242) . Consistent with endothelial injury, the significantly elevated levels of von Willebrand factor found in the patient with severe COVID-19 has led to the idea that the infection of the ACE2 expressing endothelium by SARS-CoV-2 induces injury and activates the complement , which sets up a feedback loop that maintains a state of inflammation (243, (268) (269) (270) . Initial clinical studies in China involving 100 SARS-CoV-2 infected patients, who were treated with Chloroquine, showed amelioration of pneumonia, shortened disease progression, increased resolution of lung lesions on CT, and a better virus-negative conversion (313, 314) . abstract: Abstract The current coronavirus pandemic, COVID-19, is the third outbreak of disease caused by the coronavirus family, after Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. It is an acute infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 Virus (SARS-CoV-2). The severe disease is characterised by acute respiratory distress syndrome, septic shock, metabolic acidosis, coagulation dysfunction, and multiple organ dysfunction syndromes. Currently, no drugs or vaccine exist against the disease and the only course of treatment is symptom management involving mechanical ventilation, immune suppressants, and repurposed drugs. As such the severe form of the disease has a relatively high mortality rate. Last 6 months have seen an explosion of information related to the host receptors, virus transmission, virus structure-function relationships, pathophysiology, co-morbidities, immune response, treatment and most promising vaccines. This review takes a critically comprehensive look at various aspects of host-pathogen interaction in COVID-19. We examine genomic aspects of SARS-CoV-2, modulation of innate and adaptive immunity, complement-triggered microangiopathy, and host transmission modalities. We also examine its pathophysiological impact during pregnancy, in addition to various gaps in our knowledge. The lessons learnt from various clinical trials involving repurposed drugs have been summarised. We also highlight the rationale and likely success of the most promising vaccine candidates. url: https://www.ncbi.nlm.nih.gov/pubmed/33130519/ doi: 10.1016/j.imbio.2020.152008 id: cord-323185-n0rubc72 author: Varshney, Bhavna title: SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date: 2012-01-12 words: 5667.0 sentences: 345.0 pages: flesch: 51.0 cache: ./cache/cord-323185-n0rubc72.txt txt: ./txt/cord-323185-n0rubc72.txt summary: Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. In this study, we confirmed the putative interaction of 3b and RUNX1b and observed in vivo recruitment of 3b on the RUNX1 binding element on the IL2 promoter in transiently transfected human T, jurkat cells. We next determined the positive effect of 3b-RUNX1b interaction on the expression of RUNX1b regulated chemokine MIP-1a, reported to be upregulated in SARS-CoV infected monocyte derived dendritic cells. To investigate whether 3b-RUNX1b interaction leads to the recruitment of 3b on RUNX1 binding elements on the endogenous IL2 promoter, ChIP assays were performed in RUNX1b/CBFb endogenously expressing jurkat cells that are abortively infected by SARS-CoV. To investigate the effect of SARS-CoV 3b protein on the RUNX1b transcriptional activity, reporter gene assays were performed using the mouse IL2 promoter. abstract: BACKGROUND: The causative agent of severe acute respiratory syndrome, SARS coronavirus (SARS-CoV) genome encodes several unique group specific accessory proteins with unknown functions. Among them, accessory protein 3b (also known as ORF4) was lately identified as one of the viral interferon antagonist. Recently our lab uncovered a new role for 3b in upregulation of AP-1 transcriptional activity and its downstream genes. Thus, we believe that 3b might play an important role in SARS-CoV pathogenesis and therefore is of considerable interest. The current study aims at identifying novel host cellular interactors of the 3b protein. METHODOLOGY/PRINCIPAL FINDINGS: In this study, using yeast two-hybrid and co-immunoprecipitation techniques, we have identified a host transcription factor RUNX1b (Runt related transcription factor, isoform b) as a novel interacting partner for SARS-CoV 3b protein. Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. Kinase assay and pharmacological inhibitor treatment implied that 3b also affect RUNX1b transcriptional activity by regulating its ERK dependent phosphorylation levels. Additionally, mRNA levels of MIP-1α, a RUNX1b target gene upregulated in SARS-CoV infected monocyte-derived dendritic cells, were found to be elevated in 3b expressing U937 monocyte cells. CONCLUSIONS/SIGNIFICANCE: These results unveil a novel interaction of SARS-CoV 3b with the host factor, RUNX1b, and speculate its physiological relevance in upregulating cytokines and chemokine levels in state of SARS virus infection. url: https://doi.org/10.1371/journal.pone.0029542 doi: 10.1371/journal.pone.0029542 id: cord-318625-hf7fgtnp author: Vashi, Yoya title: Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens date: 2020-05-27 words: 2923.0 sentences: 180.0 pages: flesch: 57.0 cache: ./cache/cord-318625-hf7fgtnp.txt txt: ./txt/cord-318625-hf7fgtnp.txt summary: The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. The potential epitope regions were predicted using the sequence of the S protein of SARS-CoV-2 that showed the least variability (GenBank accession number NC_045512). We identified 18 linear epitopes, predicted by ElliPro (IEDB), which contained regions from 19 of our selected peptides (highlighted in red in Table 2 ). The study could help us to use the predicted peptide as an immunogen for the development of diagnostics and vaccines against SARS-CoV-2. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2. abstract: The 2019 novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak has caused a large number of deaths, with thousands of confirmed cases worldwide. The present study followed computational approaches to identify B- and T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. We identified 24 peptide stretches on the SARS-CoV-2 S protein that are well conserved among the reported strains. The S protein structure further validated the presence of predicted peptides on the surface, of which 20 are surface exposed and predicted to have reasonable epitope binding efficiency. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. Also, identified T-cell epitopes might be considered for incorporation in vaccine designs. url: https://api.elsevier.com/content/article/pii/S1567134820302136 doi: 10.1016/j.meegid.2020.104382 id: cord-265322-3854ddb9 author: Vavougios, George D. title: A data-driven hypothesis on the epigenetic dysregulation of host metabolism by SARS coronaviral infection: potential implications for the SARS-CoV-2 modus operandi date: 2020-04-23 words: 1252.0 sentences: 72.0 pages: flesch: 41.0 cache: ./cache/cord-265322-3854ddb9.txt txt: ./txt/cord-265322-3854ddb9.txt summary: Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host''s metabolism as part of its lifecycle. In the literature, SARS-CoV has been known to cause de novo diabetes by ACE2-dependent uptake on pancreatic isle cells, and furthermore dysregulate lipid autophagy in favor of the viral lifecycle. Their study provided the foundation for a hypothesis put forth by Fang and colleagues indicating that diabetic and hypertensive patients exposed to ACE2 inhibitors may be at an increased risk of more severe COVID-19 (7) . In another study, SARS-CoV was shown to cause diabetes by ACE2-dependent infection of pancreatic isle cells (10) . Future studies should determine SARS-CoV-2 interaction and effect on the human transcriptome, further identifying drug targets using pharmacogenomic enrichment analyses. Natural small molecules as inhibitors of coronavirus lipid-dependent attachment to host cells: a possible strategy for reducing SARS-COV-2 infectivity? abstract: COVID-19, the disease caused by the novel SARS-CoV-2, a betacoronavirus structurally similar to SARS-CoV. Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host’s metabolism as part of its lifecycle. This hypothesis is evaluated by (a) exploratory analysis of SARS-CoV / human transcriptomic interaction data and gene set enrichment analysis (b) a confirmatory, focused review of the literature based on the findings by (a). A STRING Viruses (available search for human – SARS-CoV (NCBI taxonomy Id: 9606 vs. NCBI taxonomy Id: 694009) genomic interactions reveals ten human proteins, interacting with SARS-CoV: SGTA, FGL2, SPECC1, STAT3, PHB, BCL2L1, PPP1CA, CAV1, JUN, XPO1. Gene set enrichment analyses (GSEA) with STRING on this network revealed their role as a putative protein – protein interaction network (PPI; Enrichment p-value=0.0296) mediating, viral parasitism, interleukin as well as insulin signaling, diabetes and triglyceride catabolism. In the literature, SARS-CoV has been known to cause de novo diabetes by ACE2-dependent uptake on pancreatic isle cells, and furthermore dysregulate lipid autophagy in favor of the viral lifecycle. Conversely, currently there are only non-causative, observational evidence of worse outcomes for COVID-19 patients with comorbid diabetes or hyperglycemia. No study has reported on the lipid profiles of COVID-19 patients; however, lipid-targeting molecules have been proposed as agents against SARS-CoV-2. Future studies, reporting on lipid and glucose metabolism of COVID-19 patients could help elucidate the disease’s seculae and aid drug design. url: https://www.sciencedirect.com/science/article/pii/S0306987720305600?v=s5 doi: 10.1016/j.mehy.2020.109759 id: cord-035203-dnoc0xcv author: Vaňková, Eva title: Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic date: 2020-10-29 words: 5754.0 sentences: 290.0 pages: flesch: 43.0 cache: ./cache/cord-035203-dnoc0xcv.txt txt: ./txt/cord-035203-dnoc0xcv.txt summary: Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. In the present study, we have investigated FDM 3D-printed PLA structure and porosity after exposure to common chemical disinfectants including ethanol, isopropanol and a commercial disinfectant containing sodium hypochlorite, which are easily accessible. In addition, we examined the efficiency of PLA disinfection after artificial contamination with bacteria (Staphylococcus epidermidis, Escherichia coli), a yeast fungus (Candida albicans), viruses (SARS-CoV-2 and human adenovirus -HAdV) or natural contamination by wearing the masks. The effect of immersing in three chemical disinfectants (96% ethanol, 70% isopropanol and the commercial disinfectant and bleach SAVO Original, Unilever ČR s.r.o., Czech Republic containing 0.85% sodium hypochlorite diluted with water (2:9)) was tested by repeated (5 × 15 min) cycles and long-term (24 h) exposure. Effect of ethanol, isopropanol and sodium hypochlorite on disinfection of PLA material contaminated with bacteria, yeast fungus or viruses abstract: A critical lack of personal protective equipment has occurred during the COVID-19 pandemic. Polylactic acid (PLA), a polyester made from renewable natural resources, can be exploited for 3D printing of protective face masks using the Fused Deposition Modelling technique. Since the possible high porosity of this material raised questions regarding its suitability for protection against viruses, we have investigated its microstructure using scanning electron microscopy and aerosol generator and photometer certified as the test system according to the standards EN 143 and EN 149. Moreover, the efficiency of decontaminating PLA surfaces by conventional chemical disinfectants including 96% ethanol, 70% isopropanol, and a commercial disinfectant containing 0.85% sodium hypochlorite has been determined. We confirmed that the structure of PLA protective masks is compact and can be considered a sufficient barrier protection against particles of a size corresponding to microorganisms including viruses. Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. Natural contamination of PLA masks worn by test persons was decontaminated easily and efficiently by ethanol. No disinfectant caused major changes to the PLA surface properties, and the pore size did not change despite severe mechanical damage of the surface. Therefore, PLA may be regarded as a suitable material for 3D printing of protective masks during the current or future pandemic crises. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603793/ doi: 10.7717/peerj.10259 id: cord-326514-7plamtl8 author: Veerus, Piret title: Seroprevalence of SARS‐CoV‐2 antibodies among pregnant women in Estonia: a call for epidemiological studies date: 2020-09-24 words: 662.0 sentences: 37.0 pages: flesch: 51.0 cache: ./cache/cord-326514-7plamtl8.txt txt: ./txt/cord-326514-7plamtl8.txt summary: On April 7, 2020 Mehreen Zaigham and Ola Andersson published a systematic review of maternal and perinatal outcomes in 108 pregnancies with Covid‐19 concluding that careful monitoring of such pregnancies and is warranted.(1) We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS‐CoV‐2) causing Covid‐19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. 1 We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS-CoV-2) causing Covid-19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. In comparison with available data from Spain, 9 seroprevalence of SARS-CoV-2 antibodies among pregnant women in Estonia was 10 times lower than among the general population in Spain indicating the possibility of regional differences in the incidence of COVID-19 across Europe. abstract: On April 7, 2020 Mehreen Zaigham and Ola Andersson published a systematic review of maternal and perinatal outcomes in 108 pregnancies with Covid‐19 concluding that careful monitoring of such pregnancies and is warranted.(1) We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS‐CoV‐2) causing Covid‐19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. url: https://www.ncbi.nlm.nih.gov/pubmed/32970836/ doi: 10.1111/aogs.13995 id: cord-343757-e4hmo4yc author: Velavan, Thirumalaisamy P. title: The COVID‐19 epidemic date: 2020-02-16 words: 1307.0 sentences: 74.0 pages: flesch: 45.0 cache: ./cache/cord-343757-e4hmo4yc.txt txt: ./txt/cord-343757-e4hmo4yc.txt summary: The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People''s Republic of China, has spread to many other countries. The initial clinical sign of the SARS-CoV-2-related disease COVID-19 which allowed case detection was pneumonia. A combination of the antiretroviral drugs lopinavir and ritonavir significantly improved the clinical condition of SARS-CoV patients [17] and might be an option in COVID-19 infections. Repurposing these available drugs for immediate use in treatment in SARS-CoV-2 infections could improve the currently available clinical management. Given the fragile health systems in most sub-Saharan African countries, new and re-emerging disease outbreaks such as the current COVID-19 epidemic can potentially paralyse health systems at the expense of primary healthcare requirements. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Clinical characteristics of 2019 novel coronavirus infection in China. abstract: The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People's Republic of China, has spread to many other countries. On January 30, 2020, the WHO Emergency Committee declared a global health emergency based on growing case notification rates at Chinese and international locations. The case detection rate is changing hourly and daily and can be tracked in almost real time on website provided by Johns Hopkins University [1] and other websites. As of early February 2020, China bears the large burden of morbidity and mortality, whereas the incidence in other Asian countries, in Europe and North America remains low so far. url: https://doi.org/10.1111/tmi.13383 doi: 10.1111/tmi.13383 id: cord-303054-s1clwunc author: Velly, Lionel title: Guidelines: Anaesthesia in the context of COVID-19 pandemic date: 2020-06-05 words: 9239.0 sentences: 471.0 pages: flesch: 42.0 cache: ./cache/cord-303054-s1clwunc.txt txt: ./txt/cord-303054-s1clwunc.txt summary: Operating theatre 12 R1.3.1 -Experts suggest that healthcare professionals involved in airway management (intubation, extubation, supraglottic airway insertion and/or removal…), or those who could be brought to do so in some given situations, wear a fit tested respirator mask (Respirator N95 or FFP2 standard, or equivalent) in addition to a disposable face shield or at least, in the absence of the latter, safety goggles, regardless of the patient''s COVID-19 status (Table 1) The presence of major (i.e., very frequent or relatively characteristic) and/or minor (i.e. more inconsistent and/or less specific) symptoms allows to orient the preoperative COVID-19 status assessment, and then to estimate the benefit/risk balance of maintaining or postponing the surgery, taking into account the risk of contamination of health personnel and others patients within the care structure. abstract: ABSTRACT Objectives: The world is currently facing an unprecedented healthcare crisis caused by COVID-19 pandemic. The objective of these guidelines is to produce a framework to facilitate the partial and gradual resumption of intervention activity in the context of the COVID-19 pandemic. Methods: The group has endeavoured to produce a minimum number of recommendations to highlight the strengths to be retained in the 7 predefined areas: (1) Protection of staff and patients; (2) Benefit/Risk and Patient Information; (3) Pre-operative assessment and decision on intervention; (4) Modalities of the pre-anaesthesia consultation; (5) Specificity of anaesthesia and analgesia; (6) Dedicated circuits and (7) Containment Exit Type of Interventions. Results: The SFAR Guideline panel provides 51 statements on anaesthesia management in the context of COVID-19 pandemic. After one round of discussion and various amendments, a strong agreement was reached for 100% of the recommendations and algorithms. Conclusion: We present suggestions for how the risk of transmission by and to anaesthetists can be minimised and how personal protective equipment policies relate to COVID-19 pandemic context url: https://doi.org/10.1016/j.accpm.2020.05.012 doi: 10.1016/j.accpm.2020.05.012 id: cord-255178-mb784dam author: Velu, P. title: Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution date: 2020-06-08 words: 2351.0 sentences: 159.0 pages: flesch: 60.0 cache: ./cache/cord-255178-mb784dam.txt txt: ./txt/cord-255178-mb784dam.txt summary: NP and sputum samples were tested on the altona RealStar® rRT-PCR 145 assay to ensure the absence of SARS-CoV-2 and pooled for use as a matrix for spiking 146 in RNA for LOD studies and accuracy studies. Probit analysis was applied to the NP data after an additional five replicates 187 of testing were performed at 0.8, 0.6, 0.5, 0.4, and 0.2 gene copies/reaction, and 188 narrowed the LOD to 2.7 gene copies/reaction at 95% detection rate (Figure 2) The in silico analysis for inclusivity that was performed by the manufacturer of the kit 197 found 100% homology of the E gene and S gene forward and reverse primers and probes 198 with 563 whole-genome sequences of SARS-CoV-2 published in GISAID and NCBI as of 199 3/16/2020 [9] . abstract: An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital system following the emergency use authority (EUA) guidance issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=124) using newly designed dual-target rRT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting of SARS-CoV-2 in upper respiratory and lower respiratory tract specimens, including bronchoalveolar lavage and tracheal aspirates. Accuracy testing demonstrated excellent assay agreement between expected and observed values. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 tests from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Our findings demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarizes clinical data from early in the epidemic in New York City. url: http://medrxiv.org/cgi/content/short/2020.06.05.20109637v1?rss=1 doi: 10.1101/2020.06.05.20109637 id: cord-309876-l0xginsa author: Vena, Antonio title: Prevalence of Antibodies to SARS-CoV-2 in Italian Adults and Associated Risk Factors date: 2020-08-27 words: 3065.0 sentences: 168.0 pages: flesch: 45.0 cache: ./cache/cord-309876-l0xginsa.txt txt: ./txt/cord-309876-l0xginsa.txt summary: A generalized estimating equations model showed that the main risk factors associated with SARS-CoV-2 seroprevalence were the following: an occupational exposure to the virus [Odd ratio (OR) = 2.36; 95% CI 1.59–3.50, p = 0.001], being a long-term care facility resident (OR = 4.53; 95% CI 3.19–6.45, p = 0.001), and reporting previous symptoms of influenza-like illness (OR = 4.86; 95% CI 3.75–6.30, p = 0.001) or loss of sense of smell or taste (OR = 41.00; 95% CI 18.94–88.71, p = 0.001). In the present observational study performed on a large sample of subject in northern Italy, we found the following: (1) the overall seroprevalence of anti-SARS-CoV-2 antibodies (IgG and/or IgM) was 11.0%; (2) occupational exposure to the virus, long-term care facility residency, as well as previous symptoms of influenza-like illness or loss of sense of smell or taste were independently associated with anti-SARS-CoV-2 positivity. abstract: We aimed to assess the prevalence of and factors associated with anti- severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) positivity in a large population of adult volunteers from five administrative departments of the Liguria and Lombardia regions. A total of 3609 individuals were included in this analysis. Participants were tested for anti-SARS-CoV-2 antibodies [Immunoglobulin G (IgG) and M (IgM) class antibodies] at three private laboratories (Istituto Diganostico Varelli, Medical Center, and Casa della Salute di Genova). Demographic data, occupational or private exposure to SARS-CoV-2-infected patients, and prior medical history consistent with SARS-CoV-2 infection were collected according to a preplanned analysis. The overall seroprevalence of anti-SARS-CoV-2 antibodies (IgG and/or IgM) was 11.0% [398/3609; confidence interval (CI) 10.0%–12.1%]. Seroprevalence was higher in female inmates than in male inmates (12.5% vs. 9.2%, respectively, p = 0.002), with the highest rate observed among adults aged >55 years (13.2%). A generalized estimating equations model showed that the main risk factors associated with SARS-CoV-2 seroprevalence were the following: an occupational exposure to the virus [Odd ratio (OR) = 2.36; 95% CI 1.59–3.50, p = 0.001], being a long-term care facility resident (OR = 4.53; 95% CI 3.19–6.45, p = 0.001), and reporting previous symptoms of influenza-like illness (OR = 4.86; 95% CI 3.75–6.30, p = 0.001) or loss of sense of smell or taste (OR = 41.00; 95% CI 18.94–88.71, p = 0.001). In conclusion, we found a high prevalence (11.0%) of SARS-CoV-2 infection that is significantly associated with residing in long-term care facilities or occupational exposure to the virus. These findings warrant further investigation into SARS-CoV-2 antibody prevalence among the Italian population. url: https://www.ncbi.nlm.nih.gov/pubmed/32867328/ doi: 10.3390/jcm9092780 id: cord-284950-qqje5s04 author: Venkataraman, Thiagarajan title: The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis date: 2017-07-31 words: 6622.0 sentences: 335.0 pages: flesch: 45.0 cache: ./cache/cord-284950-qqje5s04.txt txt: ./txt/cord-284950-qqje5s04.txt summary: In this article, we summarize pulmonary fibrotic changes observed after a SARS-CoV infection, discuss the extent to which other respiratory viruses induce fibrosis, describe available animal models to study the development of SARS-CoV induced fibrosis and review evidence that pulmonary fibrosis is caused by a hyperactive host response to lung injury mediated by epidermal growth factor receptor (EGFR) signaling. In this article, we summarize observations of pulmonary fibrosis during and after the SARS epidemic, note the extent to which fibrosis occurs after other pulmonary viral infections, describe efforts to recapitulate fibrotic changes in mouse models of SARS, and review evidence that the condition represents a hyperactive response to lung injury, driven by proinflammatory mediators acting through epidermal growth factor receptor (EGFR) signaling. After an illness lasting 1e2 weeks, most patients resolve the infection, however about one-third develop severe pulmonary complications leading to acute lung injury and acute respiratory distress syndrome (ARDS), resulting in intubation and prolonged hospitalization (Tsui et al., 2003) . abstract: Abstract Many survivors of the 2003 outbreak of severe acute respiratory syndrome (SARS) developed residual pulmonary fibrosis with increased severity seen in older patients. Autopsies of patients that died from SARS also showed fibrosis to varying extents. Pulmonary fibrosis can be occasionally seen as a consequence to several respiratory viral infections but is much more common after a SARS coronavirus (SARS-CoV) infection. Given the threat of future outbreaks of severe coronavirus disease, including Middle East respiratory syndrome (MERS), it is important to understand the mechanisms responsible for pulmonary fibrosis, so as to support the development of therapeutic countermeasures and mitigate sequelae of infection. In this article, we summarize pulmonary fibrotic changes observed after a SARS-CoV infection, discuss the extent to which other respiratory viruses induce fibrosis, describe available animal models to study the development of SARS-CoV induced fibrosis and review evidence that pulmonary fibrosis is caused by a hyperactive host response to lung injury mediated by epidermal growth factor receptor (EGFR) signaling. We summarize work from our group and others indicating that inhibiting EGFR signaling may prevent an excessive fibrotic response to SARS-CoV and other respiratory viral infections and propose directions for future research. url: https://doi.org/10.1016/j.antiviral.2017.03.022 doi: 10.1016/j.antiviral.2017.03.022 id: cord-297671-3d3gcn6k author: Venn, April M.R. title: A case series of pediatric croup with COVID-19 date: 2020-09-15 words: 2360.0 sentences: 153.0 pages: flesch: 59.0 cache: ./cache/cord-297671-3d3gcn6k.txt txt: ./txt/cord-297671-3d3gcn6k.txt summary: We describe three previously healthy children, admitted from our emergency department (ED) to our free-standing children''s hospital, as the first documented cases of croup as a manifestation of SARS-CoV-2 infection. All three cases (ages 11 months, 2 years, and 9 years old) presented with non-specific upper-respiratory-tract symptoms that developed into a barky cough with associated stridor at rest and respiratory distress. The novel 2019 coronavirus SARS-CoV-2, responsible for COVID-19 disease, commonly presents in children with fever, cough or shortness of breath. [7] After an electronic health record database review, we describe this ca 1 se series of our ED''s only three cases, between March 1, 2020 and July 31, 2020, of children who received nebulized racemic epinephrine (NRE) and had a positive SARS-CoV-2 infection. [15] Pediatric croup patients who received ≥3 NRE in one children''s hospital were more likely to need intensive care management. abstract: We describe three previously healthy children, admitted from our emergency department (ED) to our free-standing children's hospital, as the first documented cases of croup as a manifestation of SARS-CoV-2 infection. All three cases (ages 11 months, 2 years, and 9 years old) presented with non-specific upper-respiratory-tract symptoms that developed into a barky cough with associated stridor at rest and respiratory distress. All were diagnosed with SARS-CoV-2 by polymerase chain reaction testing from nasopharyngeal samples that were negative for all other pathogens including the most common etiologies for croup. Each received multiple (≥3) doses of nebulized racemic epinephrine with minimal to no improvement shortly after medication. All had a prolonged period of time from ED presentation until the resolution of their stridor at rest (13, 19, and 21 h). All received dexamethasone early in their ED treatment and all were admitted. All three received at least one additional dose of dexamethasone, an atypical treatment occurrence in our hospital, due to each patient's prolonged duration of symptoms. One child required heliox therapy and admission to intensive care. All patients were eventually discharged. Pathogen testing is usually not indicated in croup, but with “COVID-19 croup,” SARS-CoV-2 testing should be considered given the prognostic significance and prolonged quarantine implications. Our limited experience with this newly described COVID-19 croup condition suggests that cases can present with significant pathology and might not improve as rapidly as those with typical croup. url: https://api.elsevier.com/content/article/pii/S0735675720308299 doi: 10.1016/j.ajem.2020.09.034 id: cord-334300-hnrmaytm author: Ventura Fernandes, Bianca H title: Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date: 2020-10-20 words: 1799.0 sentences: 126.0 pages: flesch: 50.0 cache: ./cache/cord-334300-hnrmaytm.txt txt: ./txt/cord-334300-hnrmaytm.txt summary: Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus. 169 In the global task to develop the vaccine and possible therapeutic approaches for 170 COVID-19, several animal models have been proposed, such as mice 10 , hACE2 171 transgenic mice 11 , alpaca 12 , golden Syrian hamsters, ferrets, dogs, pigs, chickens, and 172 cats 9 , and species of non-human primates 10 . abstract: Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. We produced a recombinant N-terminal fraction of the Spike SARS-CoV-2 protein and injected it into adult female zebrafish. The specimens generated humoral immunity and passed the antibodies to the eggs. However, they presented adverse reactions and inflammatory responses similar to severe cases of human COVID-19. The analysis of the structure and function of zebrafish and human Angiotensin-converting enzyme 2, the main human receptor for virus infection, presented remarkable sequence similarities. Moreover, bioinformatic analysis predicted protein-protein interaction of the Spike SARS-CoV-2 fragment and the Toll-like receptor pathway. It might help in the choice of future therapeutic pharmaceutical drugs to be studied. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus. url: https://doi.org/10.1101/2020.10.20.346262 doi: 10.1101/2020.10.20.346262 id: cord-280821-kc0ut4oy author: Venturini, Elisabetta title: Treatment of children with COVID-19: position paper of the Italian Society of Pediatric Infectious Disease date: 2020-09-24 words: 5481.0 sentences: 315.0 pages: flesch: 45.0 cache: ./cache/cord-280821-kc0ut4oy.txt txt: ./txt/cord-280821-kc0ut4oy.txt summary: The Italian Society of Pediatric Infectious Diseases steering and scientific committee developed a position paper on treatment of children with COVID-19, reviewing the current literature on this topic and providing indications based on the available literature data. Currently, American guidelines on COVID-19 treatment published in May 2020, recommend both in children and adults to use lopinavir/ritonavir only in the context of clinical trials, given the lack of effectiveness reported now in literature [9, 12] . The latest Chinese guidelines on SARS-Cov-2 pneumoniae do not recommend the use of a specific antiviral for the treatment of COVID-19, and nevertheless include lopinavir/ritonavir among the available therapeutic options for hospitalized patients [29] . In May 2020, following an assessment of the emergency use authorization criteria and available scientific evidence, the FDA issued an emergency use authorization allowing for the administration of remdesivir intravenously by health care providers for the treatment of COVID-19 suspected or laboratoryconfirmed in adults and pediatric patients hospitalized with severe disease [34] . abstract: A statement of consensus was formulated after reviewing available literature on pediatric treatment strategies for COVID-19 by the Steering and Scientific Committee of the Italian Society of Infectious Pediatric Diseases in connection with the Italian Society of Paediatrics. url: https://doi.org/10.1186/s13052-020-00900-w doi: 10.1186/s13052-020-00900-w id: cord-275004-qzg03dvg author: Veras, Flavio Protasio title: SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology date: 2020-09-14 words: 6380.0 sentences: 383.0 pages: flesch: 51.0 cache: ./cache/cord-275004-qzg03dvg.txt txt: ./txt/cord-275004-qzg03dvg.txt summary: The concentration of NETs was augmented in plasma, tracheal aspirate, and lung autopsies tissues from COVID-19 patients, and their neutrophils released higher levels of NETs. Notably, we found that viable SARS-CoV-2 can directly induce the release of NETs by healthy neutrophils. The well-known similarities between sepsis and key events involved in the COVID-19 pathophysiology, such as cytokine overproduction (Mehta et al., 2020) , microthrombosis (Magro et al., 2020; Dolhnikoff et al., 2020) , and acute respiratory distress syndrome (Lai et al., 2020) , led us to hypothesize that NETs are triggered during SARS-CoV-2 infection and might contribute to tissue injury in COVID-19 patients. In summary, in the present study, we demonstrated that in COVID-19 patients, circulating and lung-infiltrating neutrophils are releasing higher levels of NETs. We also showed that SARS-CoV-2 directly stimulates neutrophils to release NETs in mechanisms dependent on ACE2 and serine protease activity axis and effective viral replication. abstract: Severe COVID-19 patients develop acute respiratory distress syndrome that may progress to cytokine storm syndrome, organ dysfunction, and death. Considering that neutrophil extracellular traps (NETs) have been described as important mediators of tissue damage in inflammatory diseases, we investigated whether NETs would be involved in COVID-19 pathophysiology. A cohort of 32 hospitalized patients with a confirmed diagnosis of COVID-19 and healthy controls were enrolled. The concentration of NETs was augmented in plasma, tracheal aspirate, and lung autopsies tissues from COVID-19 patients, and their neutrophils released higher levels of NETs. Notably, we found that viable SARS-CoV-2 can directly induce the release of NETs by healthy neutrophils. Mechanistically, NETs triggered by SARS-CoV-2 depend on angiotensin-converting enzyme 2, serine protease, virus replication, and PAD-4. Finally, NETs released by SARS-CoV-2–activated neutrophils promote lung epithelial cell death in vitro. These results unravel a possible detrimental role of NETs in the pathophysiology of COVID-19. Therefore, the inhibition of NETs represents a potential therapeutic target for COVID-19. url: https://doi.org/10.1084/jem.20201129 doi: 10.1084/jem.20201129 id: cord-322148-sfr9twfa author: Verbeek, P. Richard title: Loss of Paramedic Availability in an Urban Emergency Medical Services System during a Severe Acute Respiratory Syndrome Outbreak date: 2008-06-28 words: 2481.0 sentences: 142.0 pages: flesch: 55.0 cache: ./cache/cord-322148-sfr9twfa.txt txt: ./txt/cord-322148-sfr9twfa.txt summary: Objectives: To describe the loss of paramedic availability to Toronto Emergency Medical Services during a biphasic (SARS‐1 and SARS‐2) outbreak of severe acute respiratory syndrome (SARS). [3] [4] [5] Ontario 8, 9 In response to the SARS outbreak, a program of contact tracing, quarantine, and medical surveillance of paramedics was implemented by Toronto Emergency Medical Services (EMS) and base hospital of Sunnybrook and Women''s College Health Sciences Centre. Paramedics were advised to wear gloves, mask, and gown for patients with ''''an acute Home quarantine (HQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital or to a patient with suspect/probable SARS under home observation for ten days from the last known exposure date. Work quarantine (WQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital during the SARS-2 outbreak on duty while wearing PPE at all times. abstract: Objectives: To describe the loss of paramedic availability to Toronto Emergency Medical Services during a biphasic (SARS‐1 and SARS‐2) outbreak of severe acute respiratory syndrome (SARS). Methods:During the SARS outbreak, a dedicated paramedic surveillance and quarantine program was developed. The authors determined the number of paramedics on quarantine each day, the type of quarantine (either home quarantine [HQ] or work quarantine [WQ]), and the development of SARS‐like symptoms. Results: During the SARS outbreak, there were five cases of probable SARS and three cases of suspect SARS. SARS‐1 lasted 30 days, during which 234 paramedics were placed on HQ. The total number of HQ days was 1,615. During the five peak days of SARS‐1, the total number of HQ days was 664. SARS‐2 lasted 18 days, during which 292 paramedics were placed on either HQ or WQ, for a combined number of quarantine days of 1,637. During the five peak days of SARS‐2, the combined number of quarantine days was 910. Of these, paramedics were available for duty on 708 days (78%) due to the WQ program. The primary reason for quarantine was unprotected exposure to a health care institution experiencing a SARS outbreak. Under quarantine, SARS‐like symptoms developed in 68 paramedics, including cough (53 [78%]), myalgia (33 [48%]), fatigue (30 [44%]), headache (29 [43%]), fever (11 [16%]), and shortness of breath (7 [10%]). Conclusions: Paramedics were among the health care workers who developed SARS. During SARS‐2, WQ optimized the number of days on which paramedics were available for duty. Many paramedics developed SARS‐like symptoms without being diagnosed as having SARS. A dedicated paramedic surveillance and quarantine program provided a useful means to manage the paramedic resource during the SARS outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/15347550/ doi: 10.1197/j.aem.2004.03.021 id: cord-286015-oonfpa0c author: Verbeure, Birgit title: Patent pools and diagnostic testing date: 2006-01-27 words: 4328.0 sentences: 187.0 pages: flesch: 42.0 cache: ./cache/cord-286015-oonfpa0c.txt txt: ./txt/cord-286015-oonfpa0c.txt summary: Recent studies have reported on the licensing practices of the owners of patents for genetic inventions [3] [4] [5] [6] , and concerns have been raised that patent thickets, resulting in royalty stacking (see Glossary), block access to patented technology through the accumulated license fees that a downstream inventor has to pay to upstream patent holders. In the late 1990s, several patent pools were formed in the electronics and telecommunications industries, starting with the moving picture experts group (MPEG)-2 pool in 1997 for inventions relating to the MPEG-2 standard (see Klein [15] and the Guidelines on the Application of Article 81 of the EC Treaty to Technology Transfer Agreements [16] . The Organization for Economic Co-operation and Development (OECD; www.oecd.org) considers the concept of a patent pool to be an interesting one for biotechnology but has some doubts as to whether the technologies and markets for genetic inventions are amenable to patent pools [20] . abstract: There is increasing concern that overlapping patents in the field of genetics will create a costly and legally complex situation known as a patent thicket, which, along with the associated issues of accumulating royalty payments, can act as a disincentive for innovation. One potential means of preventing this is for the patent holders to enter into a so-called patent pool, such as those established in the electronics and telecommunications industries. Precedents for these also exist in the field of genetics, notably with the patents pertaining to the SARS genome. In this review, we initially address the patent pool concept in general and its application in genetics. Following this, we will explore patent pools in the diagnostic field in more detail, and examine some existing and novel examples of patent pools in genetics. url: https://www.ncbi.nlm.nih.gov/pubmed/16443296/ doi: 10.1016/j.tibtech.2006.01.002 id: cord-266558-vd41u2t1 author: Verdecchia, Paolo title: The pivotal link between ACE2 deficiency and SARS-CoV-2 infection date: 2020-04-20 words: 4690.0 sentences: 316.0 pages: flesch: 48.0 cache: ./cache/cord-266558-vd41u2t1.txt txt: ./txt/cord-266558-vd41u2t1.txt summary: Clinical reports of patients infected with SARS-CoV-2 show that several features associated with infection and severity of the disease (i.e., older age, hypertension, diabetes, cardiovascular disease) share a variable degree of ACE2 deficiency. The entry of SARS-CoV-2 into cells is mediated by the efficient binding of the spike (S) viral protein, a 1273 amino acid long protein which belongs to the viral envelope and protrudes outwards with a ''corona'' like appearance, to the angiotensin converting enzyme 2 (ACE2) receptors. In the current pandemic of SARS-CoV-2 infection with associated pulmonary inflammation and Acute Respiratory Distress Syndrome (ARDS), it is interesting to note that angiotensin II also interferes with adaptive immunity by activating machrophages [24] and other cells of the immune system, with consequent increased production of IL-6, [25] TNFα and other inflammatory citokynes. The authors found that even the isolated spike viral protein induced down-regulation of ACE2 receptors with concomitant increase of angiotensin II in the lung tissue and precipitation of severe pulmonary inflammatory lesions. abstract: Angiotensin converting enzyme-2 (ACE2) receptors mediate the entry into the cell of three strains of coronavirus: SARS-CoV, NL63 and SARS-CoV-2. ACE2 receptors are ubiquitous and widely expressed in the heart, vessels, gut, lung (particularly in type 2 pneumocytes and macrophages), kidney, testis and brain. ACE2 is mostly bound to cell membranes and only scarcely present in the circulation in a soluble form. An important salutary function of membrane-bound and soluble ACE2 is the degradation of angiotensin II to angiotensin(1-7). Consequently, ACE2 receptors limit several detrimental effects resulting from binding of angiotensin II to AT1 receptors, which include vasoconstriction, enhanced inflammation and thrombosis. The increased generation of angiotensin(1-7) also triggers counter-regulatory protective effects through binding to G-protein coupled Mas receptors. Unfortunately, the entry of SARS-CoV2 into the cells through membrane fusion markedly down-regulates ACE2 receptors, with loss of the catalytic effect of these receptors at the external site of the membrane. Increased pulmonary inflammation and coagulation have been reported as unwanted effects of enhanced and unopposed angiotensin II effects via the ACE→Angiotensin II→AT1 receptor axis. Clinical reports of patients infected with SARS-CoV-2 show that several features associated with infection and severity of the disease (i.e., older age, hypertension, diabetes, cardiovascular disease) share a variable degree of ACE2 deficiency. We suggest that ACE2 down-regulation induced by viral invasion may be especially detrimental in people with baseline ACE2 deficiency associated with the above conditions. The additional ACE2 deficiency after viral invasion might amplify the dysregulation between the ‘adverse’ ACE→Angiotensin II→AT1 receptor axis and the ‘protective’ ACE2→Angiotensin(1-7)→Mas receptor axis. In the lungs, such dysregulation would favor the progression of inflammatory and thrombotic processes triggered by local angiotensin II hyperactivity unopposed by angiotensin(1-7). In this setting, recombinant ACE2, angiotensin(1-7) and angiotensin II type 1 receptor blockers could be promising therapeutic approaches in patients with SARS-CoV-2 infection. url: https://www.sciencedirect.com/science/article/pii/S0953620520301515 doi: 10.1016/j.ejim.2020.04.037 id: cord-291356-df5n5v09 author: Verma, Saguna title: ACE2 receptor expression in testes: implications in coronavirus disease 2019 pathogenesis date: 2020-05-19 words: 1279.0 sentences: 71.0 pages: flesch: 49.0 cache: ./cache/cord-291356-df5n5v09.txt txt: ./txt/cord-291356-df5n5v09.txt summary: Expression of angiotensin-converting enzyme 2, receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is high in the testes, therefore SARS-CoV-2 infection and its association with male reproductive health should be investigated in male coronavirus disease 2019 patients. SARS-CoV-2 infection is robust in cells expressing angiotensinconverting enzyme 2 (ACE2) receptor, a type I integral membrane protein that controls cardiac and kidney functions by negatively regulating renin-angiotensin systems [2] . High ACE2 expression may augment virus infection in the lung, heart, and small intestine that might explain the pathophysiology of acute lung and myocardial injury, and gastrointestinal symptoms reported in COVID-19 patients [1] . Cytokines and chemokines induced by SARS-CoV-2 entry into the LC and SC may recruit peripheral immune cells including macrophages and virus-specific T cells that may further potentiate inflammation and orchitis in accordance with reported symptoms from 19% of patients in study by Pan et al. abstract: Expression of angiotensin-converting enzyme 2, receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is high in the testes, therefore SARS-CoV-2 infection and its association with male reproductive health should be investigated in male coronavirus disease 2019 patients. url: https://doi.org/10.1093/biolre/ioaa080 doi: 10.1093/biolre/ioaa080 id: cord-303585-8py6joh6 author: Verma, Surjeet title: Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19) date: 2020-09-25 words: 10884.0 sentences: 562.0 pages: flesch: 50.0 cache: ./cache/cord-303585-8py6joh6.txt txt: ./txt/cord-303585-8py6joh6.txt summary: The objective of this review was to collate information regarding the potential of plants and natural products to inhibit coronavirus and targets associated with infection in humans and to highlight known drugs, which may have potential activity against SARS-CoV-2. Finally, this review discusses the potential use of Southern African medicinal plants, which have traditionally been used for the treatment of symptoms related to respiratory viral infections, and influenza, to inhibit SARS-CoV-2. The selective index (SI) values of compounds 1-6 were found to be 58, >510, 111, 193, 180 , and >667, respectively, indicating that these plants were able to inhibit viral replication without having a cytotoxic effect on the host cells. A chalcone, xanthoangelol E (8), isolated from the ethanolic leaf extract of Angelica keiskei (Miq.) Koidz., showed inhibitory activity against SARS-CoV 3CL pro and a papain-like protease (PL pro ) with IC 50 values of 11.4 and 1.2 µM, respectively, using cell-free assays. abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), known to cause the disease COVID-19, was declared a pandemic in early 2020. The objective of this review was to collate information regarding the potential of plants and natural products to inhibit coronavirus and targets associated with infection in humans and to highlight known drugs, which may have potential activity against SARS-CoV-2. Due to the similarity in the RNA genome, main proteases, and primary host receptor between SARS-CoV and SARS-CoV-2, a review was conducted on plants and secondary metabolites, which have shown activity against SARS-CoV. Numerous scientific reports on the potential of plants and secondary metabolites against SARS-CoV infection were found, providing important information on their possible activity against SARS-CoV-2. Based on current literature, 83 compounds have been identified with the potential to inhibit COVID-19. The most prominent selectivity was found for the alkaloid, lycorine, the lignan, savinin, and the abietane terpenoid, 8-beta-hydroxyabieta-9(11),13-dien-12-one with selectivity index values greater than 945, 667, and 510, respectively. Plants and their secondary metabolites, with activity against targets associated with the SARS-CoV infection, could provide valuable leads for the development into drugs for the novel SARS-CoV-2. The prospects of using computational methods to screen secondary metabolites against SARS-CoV targets are briefly discussed, and the drawbacks have been highlighted. Finally, we discuss plants traditionally used in Southern Africa for symptoms associated with respiratory viral infections and influenza, such as coughs, fever, and colds. However, only a few of these plants have been screened against SARS-CoV. Natural products hold a prominent role in discovering novel therapeutics to mitigate the current COVID-19 pandemic; however, further investigations regarding in vitro, in vivo, pre-clinical, and clinical phases are still required. url: https://www.ncbi.nlm.nih.gov/pubmed/33101023/ doi: 10.3389/fphar.2020.561334 id: cord-305703-ypeibwje author: Veronese, Nicola title: Use of Corticosteroids in Coronavirus Disease 2019 Pneumonia: A Systematic Review of the Literature date: 2020-04-24 words: 2878.0 sentences: 144.0 pages: flesch: 37.0 cache: ./cache/cord-305703-ypeibwje.txt txt: ./txt/cord-305703-ypeibwje.txt summary: For each article, we extracted data regarding authors, year of publication, country, city or region in which the study was conducted, the period of observation, how the diagnosis of COVID-19 was obtained, the stage of COVID-19 infection (asymptomatic forms, pneumonia, acute respiratory distress syndrome (ARDS), requiring intensive care unit, ICU; convalescent), sample size included, number of males and females, mean age and its standard deviation (or similar information such as median and range), the percentage of people treated with corticosteroids in the sample as a whole, and, if possible, the route of administration and type of corticosteroid considered. Overall, two studies reported negative findings regarding these medications, one reported no significant association between corticosteroids and clinical outcomes, and one concluded that methylprednisolone was associated with a significant reduction of mortality in patients with COVID-19 pneumonia developing ARDS. abstract: The aim was to investigate the effectiveness of glucocorticoid therapy in patients with COVID-19. A systematic search of the literature across nine databases was conducted from inception until 15th March 2020, following the PRISMA guidelines. Patients with a validated diagnosis of COVID-19 and using corticosteroids were included, considering all health outcomes. Four studies with 542 Chinese participants were included. Two studies reported negative findings regarding the use of corticosteroids in patients with COVID-19, i.e., corticosteroids had a detrimental impact on clinical outcomes. One study reported no significant association between the use of corticosteroids and clinical outcomes. However, one study, on 201 participants with different stages of pneumonia due to COVID-19, found that in more severe forms, the administration of methylprednisolone significantly reduced the risk of death by 62%. The literature to date does not fully support the routine use of corticosteroids in COVID-19, but some findings suggest that methylprednisolone could lower mortality rate in more severe forms of the condition. url: https://doi.org/10.3389/fmed.2020.00170 doi: 10.3389/fmed.2020.00170 id: cord-286901-whvq8y1p author: Vidali, Sofia title: D-dimer as an indicator of prognosis in SARS-CoV-2 infection: a systematic review date: 2020-07-13 words: 4272.0 sentences: 228.0 pages: flesch: 37.0 cache: ./cache/cord-286901-whvq8y1p.txt txt: ./txt/cord-286901-whvq8y1p.txt summary: This study aims to highlight the correlation between elevated D-dimer (an indirect thrombosis marker) and the increased rate of poor prognosis-associated conditions, and to introduce D-dimer-labelled anticoagulant administration as a potentially useful tool to prevent complications and positively influence coronavirus disease 2019 (COVID-19) course. The keywords and their variants (differently combined) used for the search were "COVID-19", "2019-nCoV", "2019 novel coronavirus", "SARS-CoV-2", "D-dimer", "coagulation", "hypercoagulative state", "laboratory analysis", "ARDS", "haemostasis", "thrombosis", "pulmonary embolism", "disseminated intravascular coagulation (DIC)", "heparin" and "anti-coagulation". The alterations of coagulation factors during SARS-CoV-2 infection and specifically that of D-dimer are, as documented in the clinical experiences described here, severe, constant and correlated with prognosis, complications and CEP rates. Among the factors that were demonstrated to be connected to the clinical outcome of COVID-19 patients, the presence of comorbidities may represent a confounding factor for the interpretation of D-dimer and other coagulation parameter alterations, especially considering the heterogeneous aetiology of thrombotic and thrombophilic states. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulates pro-thrombotic changes. This, combined with its tropism for endothelium and lung structures, may explain its association with thrombotic events, reduction of pulmonary gas exchange, acute respiratory distress syndrome (ARDS) and a composite end-point (intensive care unit, invasive ventilation, death). This study aims to highlight the correlation between elevated D-dimer (an indirect thrombosis marker) and the increased rate of poor prognosis-associated conditions, and to introduce D-dimer-labelled anticoagulant administration as a potentially useful tool to prevent complications and positively influence coronavirus disease 2019 (COVID-19) course. METHODS: An online database search (PubMed, Google Scholar, Scopus, Web of Science and Cochrane) was performed between 13 March and 10 April 2020. The most relevant keywords were “D-dimer”, “SARS-CoV-2”, “COVID-19”, “thrombosis” and “ARDS”. Selection was independently conducted by three reviewers. References and previews of accepted articles were evaluated. Data inclusion/extraction inaccuracy was limited by the work of three reviewers. Selection bias reduction was addressed by thoughtfully designing the search protocol. Quality assessment was performed with the Newcastle–Ottawa Scale. The systematic review protocol was not registered because we anticipated the very limited available evidence on the topic and due to the urgency of the study. RESULTS: 16 studies were evaluated. Good-quality criteria were reached in 13 out of 16 studies. D-dimer was increased and significantly higher in COVID-19 patients compared with healthy controls, in COVID-19 patients with severe disease or a composite end-point compared with non-severe disease, in ARDS compared with non-ARDS patients and in deceased ARDS patients compared with ARDS patients who survived (all p<0.001). COVID-19 patients treated with anticoagulants demonstrated lower mortality compared with those not treated (p=0.017). CONCLUSIONS: Correlations exist between COVID-19 infection, severe elevation of D-dimer levels, and increase in the rate of complications and composite end-point. The appropriateness of early and continuous D-dimer monitoring and labelled anticoagulation as management tools for COVID-19 disease deserves accurate investigation, to prevent complications and reduce interventions. url: https://www.ncbi.nlm.nih.gov/pubmed/32685436/ doi: 10.1183/23120541.00260-2020 id: cord-330690-cupy89gl author: Vierucci, Francesco title: How COVID-19 Pandemic Changed Children and Adolescents Use of the Emergency Department: the Experience of a Secondary Care Pediatric Unit in Central Italy date: 2020-09-23 words: 4321.0 sentences: 211.0 pages: flesch: 43.0 cache: ./cache/cord-330690-cupy89gl.txt txt: ./txt/cord-330690-cupy89gl.txt summary: During phase 1 (national lockdown period, March 9th-May 3rd, 2020) the Italian Ministry of Health recommended to avoid direct access to the emergency department (ED) in case of fever and/or cough or other respiratory symptoms, favoring home care or phone consultation for ill patients without compromised general conditions [10] . The aims of this study were to (1) evaluate the impact of COVID-19 pandemic on the activity of a secondary care Italian Pediatric Unit assessing, in particular, the characteristics of pediatric ED consultations performed in 2020 before and after the beginning of lockdown; (2) evaluate the prevalence of SARS-CoV-2 infection in children and adolescents referred to ED; and (3) compare pediatric ED activity during the same period of 2019 and 2020. abstract: Italy was the first European country hit by SARS-CoV-2 infection, particularly northern regions. After the beginning of national lockdown (March 9th, 2020), we observed a significant decrease in pediatric emergency department consultations (daily pediatric visits; pre-lockdown, 16 (11–22); lockdown, 3 (1–3); phase 2, 3 (3–5), p < 0.0001). On the other hand, the percentage of children discharged right after pediatric visit significantly decreased from 80% in January to 50% in April. After March 9th, we registered a change in the diagnoses of emergency department visits, with an increase in the percentage of non-infectious acute conditions and a decrease in infectious diseases, with two cases of a noteworthy delayed access to hospital care. We performed a retrospective analysis of consultations requested to our pediatric unit for children and adolescents referred to the general Emergency Department of San Luca Hospital of Lucca (Tuscany, Central Italy) from January 1st to May 31st, 2020. We split data in two different time periods according to consultations performed before (January 1st–March 8th) and after the beginning of lockdown (March 9th–May 31st). Analyzing the number of children hospitalized from January to May 2020 in comparison with the same period in 2019, a decreased hospitalization became evident after March (March − 74.6%, April − 71.6%, May − 58.6%). Nasopharyngeal swabs done in 115 children showed only one case of COVID-19. Even if COVID-19 outbreak more seriously affected Northern Italy, utilization of pediatric emergency services significantly changed also in Central Italy with consequent reduced demand and increased appropriateness. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42399-020-00532-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32984767/ doi: 10.1007/s42399-020-00532-5 id: cord-325320-v9e2axf4 author: Vigil‐De Gracia, P. title: Pregnancies recovered from SARS‐CoV‐2 infection in the second and third trimesters: obstetric evolution date: 2020-09-30 words: 811.0 sentences: 46.0 pages: flesch: 54.0 cache: ./cache/cord-325320-v9e2axf4.txt txt: ./txt/cord-325320-v9e2axf4.txt summary: However we do not know the maternal and perinatal results of pregnant women recovered from SARS-CoV-2 infection continuing the pregnancy. This first report of pregnant women infected with COVID-19 and recovered allows us to know that the patient continues to be at high obstetric risk, especially due to the PROM and labor before 39 weeks. A study of 16 placentas from SARS-CoV-2 patients reports an increase in the rates of maternal and fetal vascular malperfusion features; two cases were more than 30 days after the appearance of symptoms and these placentas showed fetal vascular malperfusion (clustered avascular villi, hipercoiled umbilical cord, chorangiosis) 3 . In our opinion, in pregnant patients infected and recovered with SARS-CoV-2, there is a "placental inflammatory syndrome" characterized by spontaneous onset of labor, premature births, premature rupture of membranes, alteration in the cardiotocograph trace, fetal distress, death and placental alterations. Fetal deaths in pregnancies with SARS-CoV-2 infection in Brazil: A case series. abstract: nan url: https://doi.org/10.1002/uog.23134 doi: 10.1002/uog.23134 id: cord-316702-dj2fo8sn author: Vignesh, Ramachandran title: Is Herd Immunity Against SARS-CoV-2 a Silver Lining? date: 2020-09-30 words: 3250.0 sentences: 169.0 pages: flesch: 45.0 cache: ./cache/cord-316702-dj2fo8sn.txt txt: ./txt/cord-316702-dj2fo8sn.txt summary: Since many studies from different geographical locations are documenting preexisting immunity to SARS-CoV-2, it will be important to define specificities of these T and B cell immune response carefully to assess their association with COVID-19 disease severity. This preexisting cross-reactive T and B cell immunity to SARS-CoV-2 may have wide implications as this could explain differential clinical outcomes in COVID-19 patients, disease severity, vaccine development, and important in accessing herd immunity for SARS-CoV-2 viral infection/COVID-19 disease. Several studies have provided strong evidence for the importance of SARS-CoV-2 specific CTLs, and T helper cells in mild and moderate patients compared to severe COVID-19 disease (27, 28, (31) (32) (33) . Several studies have provided strong evidence for the importance of SARS-CoV-2specific neutralizing antibodies in association with less disease severity in COVID-19 patients (38, 39) . A recent modelling study has estimated that about one in five individuals worldwide would be at increased risk of severe COVID-19, upon infection with SARS-CoV-2, owing to the underlying conditions. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33101320/ doi: 10.3389/fimmu.2020.586781 id: cord-320266-7gzx6ljt author: Vigneshwar, Navin G. title: Positive tracheal SARS-CoV-2 RNA test after three negative SARS-CoV-2 RNA tests in a patient with COVID-19 date: 2020-06-12 words: 939.0 sentences: 70.0 pages: flesch: 52.0 cache: ./cache/cord-320266-7gzx6ljt.txt txt: ./txt/cord-320266-7gzx6ljt.txt summary: Perioperative guidelines for patients with suspected coronavirus disease (COVID-19) often rely on nasopharyngeal swab testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Herein, we report the case of a patient with three consecutive negative nasopharyngeal swab tests followed by a positive tracheal aspirate test for SARS-CoV-2 RNA (Figure 1 ). On admission, a viral respiratory panel and two nasopharyngeal swab SARS-CoV-2 RT-PCR tests separated by four hours were negative. On hospital day 1, the patient''s hypoxia improved, and results from a repeat SARS-CoV-2 RT-PCR test from a nasopharyngeal swab were negative. During the novel influenza A (H1N1) pandemic, approximately 10% of patients showed positive RT-PCR test results in respiratory secretions after intubation when prior tests on nasopharyngeal swab gave negative results. Following further deterioration of the patient''s respiratory status and endotracheal intubation, a tracheal sample was positive for SARS-CoV-2 RNA. abstract: nan url: https://doi.org/10.1007/s12630-020-01742-0 doi: 10.1007/s12630-020-01742-0 id: cord-343604-v986m9jd author: Vijayakumar, Balaji Gowrivel title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 words: 1258.0 sentences: 90.0 pages: flesch: 47.0 cache: ./cache/cord-343604-v986m9jd.txt txt: ./txt/cord-343604-v986m9jd.txt summary: title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. Coronavirus main 403 proteinase (3CLpro) structure: basis for design of anti-SARS drugs Structural basis for inhibition 675 of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is distinctly infective and there is an ongoing effort to find a cure for this pandemic. Flavonoids exist in many diets as well as in traditional medicine, and their modern subset, indole-chalcones, are effective in fighting various diseases. Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Interactions were studied with respect to biology and function of SARS-CoV-2 proteins for activity. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The results reveal that 30 compounds are capable of M(pro) deactivation as well as potentially lowering the efficiency of M(pro) function. Cyanidin may inhibit RNA polymerase function and, Quercetin is found to block interaction sites on the viral spike. These results suggest flavonoids and their modern pharmaceutical cousins, indole chalcones are capable of fighting SARS-CoV-2. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. url: https://api.elsevier.com/content/article/pii/S0014299920305409 doi: 10.1016/j.ejphar.2020.173448 id: cord-221611-eeybl35x author: Vijayan, Ramachandran title: Structure-based inhibitor screening of natural products against NSP15 of SARS- CoV-2 revealed Thymopentin and Oleuropein as potent inhibitors date: 2020-07-28 words: 3083.0 sentences: 190.0 pages: flesch: 48.0 cache: ./cache/cord-221611-eeybl35x.txt txt: ./txt/cord-221611-eeybl35x.txt summary: Here, we screened Selleckchem Natural product database of compounds against the NSP15, Thymopentin and Oleuropein showed highest binding energies. The structure of SARS-CoV-2 NSP15 protein is very similar to other Coronavirus NSP15 monomers, consisting of mainly three regions: the N-terminal domain, a subsequent middle domain, and a catalytic C-terminal nidoviral RNA uridylate-specific endoribonuclease domain. In order to design specific inhibitors against the Non-structural protein 15 (NSP15), Libraries of Selleckchem Natural products (https://www.selleckchem.com/screening/natural-productlibrary.html) were chosen for Virtual screening [24] [25] [26] . After the docking studies, the Molecular dynamic simulation [25] [26] [27] was performed for the top five screened compounds (Thymopentin, Ginsenoside, Oleuropein, Akebia Saponin D and Keampferitrin), to understand the binding stability of the docked complexes. In this study, structure based virtual screening followed by the validation through Molecular dynamic simulation approaches were carried out to find antiviral leads against NSP15 of SARS-CoV-2. abstract: Coronaviruses are enveloped, non-segmented positive-sense RNA viruses that have the largest genome among RNA viruses. The genome contains a large replicase ORF encodes nonstructural proteins (NSPs), structural and accessory genes. NSP15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) has C-terminal catalytic domain. The endoribonuclease activity of NSP15 interferes with the innate immune response of the host. Here, we screened Selleckchem Natural product database of compounds against the NSP15, Thymopentin and Oleuropein showed highest binding energies. The binding of these molecules was further validated by Molecular dynamic simulation and found very stable complexes. These drugs might serve as effective counter molecules in the reduction of virulence of this virus. Future validation of both these inhibitors are worth consideration for patients being treated for COVID -19. url: https://arxiv.org/pdf/2007.14375v1.pdf doi: nan id: cord-259267-trpo5w11 author: Vilibic-Cavlek, Tatjana title: Severe acute respiratory syndrome coronavirus 2 seroprevalence among personnel in the healthcare facilities of Croatia, 2020 date: 2020-08-26 words: 1490.0 sentences: 94.0 pages: flesch: 48.0 cache: ./cache/cord-259267-trpo5w11.txt txt: ./txt/cord-259267-trpo5w11.txt summary: From April 25 to May 24, 2020, when the COVID-19 epidemic curve was approaching the end of the first wave in Croatia, a total of 592 serum samples from HCWs and allied/auxiliary HCWs were tested for the presence of SARS-CoV-2 antibodies. Two studies from the United Kingdom showed that 18% of symptomatic HCWs 6 and 3% of asymptomatic HCWs tested RT-PCR-positive for SARS-CoV-2 7 . Data are limited on the seroprevalence of COVID-19 among HCWs. In this study, using ELISA, SARS-CoV-2 IgG antibodies were detected in 2.7% of participants, while neutralizing antibodies were detected in 1.5% of participants, indicating a low seroprevalence among HCWs in Croatia. In the present study, three seropositive HCWs reported experiencing COVID-19-consistent clinical symptoms, while six were asymptomatic. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients abstract: nan url: https://doi.org/10.1590/0037-8682-0458-2020 doi: 10.1590/0037-8682-0458-2020 id: cord-344798-q34j4zxu author: Villalba, María Caridad Montalvo title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients date: 2020-08-29 words: 4141.0 sentences: 232.0 pages: flesch: 44.0 cache: ./cache/cord-344798-q34j4zxu.txt txt: ./txt/cord-344798-q34j4zxu.txt summary: title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients The aim of this study was evaluate inflammatory response using the expression of immune mediators with antiviral, immunosuppression and chemotactic functions in the primary site of SARS-CoV-2 replication, at early stage of infection. J o u r n a l P r e -p r o o f Taking into account that Ct value has a correlation with the amount of RNA present in the samples, it was found that medians and IQR of SARS-CoV-2 viral titer was similar in asymptomatic (33.00, 29.00-37.00) and symptomatic (30, 27 .00-37.00) cases; and comparison between groups did not show difference (p=0.4373). As show our results, SARS-CoV-2 infection induced high IFN-γ expression in swabbed cells from upper airway; its expression was higher in symptomatic patients in comparison with asymptomatic individuals. Also, positive correlation between IFN-γ and TGF-β1 provided evidence of immune response control could determinate the asymptomatic presentation of SARS-CoV-2 infection. abstract: Upper respiratory tract is the primary site of SARS-CoV-2 replication. Releasing of pro and anti-inflammatory mediators plays an important role in the immunopathogenesis of Coronavirus Disease 2019 (COVID-19). The aim of this study was to evaluate the early inflammatory response in upper airway by measuring of IFN-γ, TGF-β1 and RANTES at mRNA level. Forty five SARS-CoV-2 infected patients were enrolled, whose were divided in two groups: asymptomatic and symptomatic. Twenty healthy persons, SARS-CoV-2 negative were included as controls. Higher IFN-γ expression was detected in SARS-CoV-2 infected patients in comparison with controls (p = 0,0393). IFN-γ expression was increased in symptomatic patients (p = 0,0165). TGF-β1 and RANTES expressions were lower in SARS-CoV-2 infected patients than controls (p < 0,0001; p = 0,0011, respectively). A significant correlation between IFN-γ and TGF-β1 was observed in SARS-CoV-2 asymptomatic patients (r = +0,61, p = 0,0014). The findings suggest that imbalance between IFN-γ and TGF-β1 expression could be an impact in clinical expression of SARS-CoV-2 infection. url: https://api.elsevier.com/content/article/pii/S1521661620307361 doi: 10.1016/j.clim.2020.108576 id: cord-331375-tbuijeje author: Villalobos, Carlos title: SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives date: 2020-09-25 words: 7205.0 sentences: 354.0 pages: flesch: 48.0 cache: ./cache/cord-331375-tbuijeje.txt txt: ./txt/cord-331375-tbuijeje.txt summary: This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). By weighting the age-stratified IFRs by the country population agegroups shares in each country, it is possible to obtain countryspecific IFRs. The relevance of this study is 3-fold: Firstly, the estimation of the true number of infections includes not only confirmed cases but COVID-19 undetected cases, as well as SARS-CoV-2infected individuals without the disease, or in a pre-symptomatic stage. In order to provide reliable estimates of the number of SARS-CoV-2 infections and of the cumulative detection rates, it is necessary that governments provide real-time information about the number of COVID-19 deaths. abstract: This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Worldwide, on July 20, it has been estimated above 160 million individuals infected by SARS-CoV-2. Moreover, it is found that only about 1 out of 11 infected individuals are detected. In an information context in which population-based seroepidemiological studies are not frequently available, this study shows a parsimonious alternative to provide estimates of the number of SARS-CoV-2 infected individuals. By comparing our estimates with those provided by the population-based seroepidemiological ENE-COVID study in Spain, we confirm the utility of our approach. Then, using a cross-country regression, we investigated if differences in detection rates are associated with differences in the cumulative number of deaths. The hypothesis investigated in this study is that higher levels of detection of SARS-CoV-2 infections can reduce the risk exposure of the susceptible population with a relatively higher risk of death. Our results show that, on average, detecting 5 instead of 35 percent of the infections is associated with multiplying the number of deaths by a factor of about 6. Using this result, we estimated that 120 days after the pandemic outbreak, if the US would have tested with the same intensity as South Korea, about 85,000 out of their 126,000 reported deaths could have been avoided. url: https://www.ncbi.nlm.nih.gov/pubmed/33102412/ doi: 10.3389/fpubh.2020.00489 id: cord-292173-95t89yee author: Villani, Federico Alcide title: COVID-19 and Dentistry: Prevention in Dental Practice, a Literature Review date: 2020-06-26 words: 4583.0 sentences: 260.0 pages: flesch: 49.0 cache: ./cache/cord-292173-95t89yee.txt txt: ./txt/cord-292173-95t89yee.txt summary: Several authors have highlighted the importance of telephone triage and/or clinic questionnaires, body temperature measurement, usage of personal protective equipment, surface disinfection with ethanol between 62% and 71%, high-speed instruments equipped with an anti-retraction system, four-handed work, and large-volume cannulas for aspiration. The aim of this narrative review is to investigate preventive measures in dental practice by assessing the operator and patient health protection during the new COVID-19 emergency by considering past experiences in terms of prevention, as the virus was only recently discovered. In addition, a second search was made: "masks" OR "disinfectants" OR "PPE" OR "dental equipment" AND "Covid-19" OR "coronavirus" OR "SARS-CoV-2". instead obtained diametrically opposing results; they showed, through a randomized controlled clinical study on 3591 subjects, that health workers who used N95 masks continuously during the shift or in situations considered to be at high risk, presented an 85% chance of not contracting a viral infection transmitted via droplets [36] . abstract: SARS-CoV-2 is a member of the family of coronaviruses. The first cases were recorded in Wuhan, China, between December 2019 and January 2020. Italy is one of the most affected countries in Europe. COVID-19 is a new challenge in modern dentistry. New guidelines are required in dental clinics to avoid contagion caused by cross-infections. A narrative review was performed using both primary sources, such as scientific articles and secondary ones, such as bibliographic indexes, web pages, and databases. The main search engines were PubMed, SciELO, and Google Scholar. Twelve articles were selected to develop the bibliographic review by applying pre-established inclusion and exclusion criteria. Precautionary measures should be applied to control COVID-19 in clinical practice. Several authors have highlighted the importance of telephone triage and/or clinic questionnaires, body temperature measurement, usage of personal protective equipment, surface disinfection with ethanol between 62% and 71%, high-speed instruments equipped with an anti-retraction system, four-handed work, and large-volume cannulas for aspiration. Clinically, the use of a rubber dam is essential. FFP2 (or N95) and FFP3 respirators, if compared to surgical masks, provide greater protection for health workers against viral respiratory infections. Further accurate studies are needed to confirm this. url: https://www.ncbi.nlm.nih.gov/pubmed/32604906/ doi: 10.3390/ijerph17124609 id: cord-354612-7f91l0n9 author: Villar, Livia Melo title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS date: 2020-07-23 words: 572.0 sentences: 51.0 pages: flesch: 65.0 cache: ./cache/cord-354612-7f91l0n9.txt txt: ./txt/cord-354612-7f91l0n9.txt summary: title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS A total of four individuals (two hepatitis cases and two without liver disease) were negative to SARS CoV-2 in NPS and saliva (100% of specificity). Positive concordant results in NPS and saliva were observed in seven individuals (two hepatitis cases and 5 without liver disease) until 7 days after onset of symptoms (100% of sensitivity). This is the first report of SARS CoV-2 detection in saliva samples among liver disease patients showing best results until 7 days of beginning of symptoms. In addition, there is no information regarding the usefulness of saliva for detecting SARS CoV-2 RNA in individuals presenting comorbidities, such as liver disease. Since saliva can be collected easily, SARS CoV-2 RNA detection in saliva can be useful strategy to increase the access of sample collection for the diagnosis of COVID-19 in patients with liver disease. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320304916?v=s5 doi: 10.1016/j.jinf.2020.07.017 id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 words: 15780.0 sentences: 708.0 pages: flesch: 42.0 cache: ./cache/cord-281281-knelqmzx.txt txt: ./txt/cord-281281-knelqmzx.txt summary: The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. abstract: On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32906733/ doi: 10.3390/molecules25184086 id: cord-263803-0n41gylj author: Villoutreix, Bruno O. title: Prevention of COVID-19 by drug repurposing: rationale from drugs prescribed for mental disorders date: 2020-06-25 words: 1287.0 sentences: 72.0 pages: flesch: 49.0 cache: ./cache/cord-263803-0n41gylj.txt txt: ./txt/cord-263803-0n41gylj.txt summary: We also compared these 18 drugs with published molecules known to have in vitro antiviral activities [1, 2] using various chemoinformatics strategies (e.g., computation of molecular descriptors and compounds clustering carried out on J o u r n a l P r e -p r o o f about 300 molecules with in vitro antiviral activities on various viruses including SARS-CoV-2). Overall, our analysis suggests that the most commonly prescribed psychotropic drugs, including some antihistamine agents used as anxiolytics, possess in vitro antiviral activity ( Table 1 ). In summary, we propose that some of the drugs commonly prescribed to psychiatric patients could protect them from SARS-CoV-2 infection via the modulation of the endo-lysosomal pathway, membrane fusion and yet to be characterized interactions with specific receptors (e.g., nAChR, ACE2 and Sigma receptors, Fig. 1 ). Based upon the above analysis, we suggest that one of these CAD molecules or a combination could be used as preventive treatment against SARS-CoV-2 infection, especially drugs with reduced adverse effects (e.g., low dosage nicotine patch associated with an antihistamine agent). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32593662/ doi: 10.1016/j.drudis.2020.06.022 id: cord-286168-019rcbpg author: Vindegaard, Nina title: COVID-19 pandemic and mental health consequences: systematic review of the current evidence date: 2020-05-30 words: 4106.0 sentences: 217.0 pages: flesch: 45.0 cache: ./cache/cord-286168-019rcbpg.txt txt: ./txt/cord-286168-019rcbpg.txt summary: Out of these, only two studies evaluated patients with confirmed COVID-19 infection, whereas 41 evaluated the indirect effect of the pandemic (2 on patients with preexisting psychiatric disorders, 20 on medical health care workers, and 19 on the general public). 23, 24 We aimed to systematically review the literature in order to provide an overview of the psychiatric complications to COVID-19 infection (direct effect) and how COVID-19 are currently affecting mental health among psychiatric patients and general public (indirect effect) alongside with factors altering the risk of psychiatric symptoms in both groups. A variety of factors were associated with higher risk of psychiatric symptoms and/or low psychological well-being of the general public including female gender, front-line health care workers, and poor self-rated health. From previous studies of the SARS CoV-1 epidemic it is known that health care workers are at risk of anxiety and depressive symptoms, which the current studies indicate also is the case of COVID19 . abstract: BACKGROUND: During the COVID-19 pandemic general medical complications have received the most attention, whereas only few studies address the potential direct effect on mental health of SARS-CoV-2 and the neurotropic potential. Furthermore, the indirect effects of the pandemic on general mental health are of increasing concern, particularly since the SARS-CoV-1 epidemic (2002-2003) was associated with psychiatric complications. METHODS: We systematically searched the database Pubmed including studies measuring psychiatric symptoms or morbidities associated with COVID-19 among infected patients and among none infected groups the latter divided in psychiatric patients, health care workers and non-health care workers. RESULTS: A total of 43 studies were included. Out of these, only two studies evaluated patients with confirmed COVID-19 infection, whereas 41 evaluated the indirect effect of the pandemic (2 on patients with preexisting psychiatric disorders, 20 on medical health care workers, and 19 on the general public). 18 of the studies were case-control studies/compared to norm, while 25 of the studies had no control groups. The two studies investigating COVID-19 patients found a high level of post-traumatic stress symptoms (PTSS) (96.2%) and significantly higher level of depressive symptoms (p=0.016). Patients with preexisting psychiatric disorders reported worsening of psychiatric symptoms. Studies investigating health care workers found increased depression/depressive symptoms, anxiety, psychological distress and poor sleep quality. Studies of the general public revealed lower psychological well-being and higher scores of anxiety and depression compared to before COVID-19, while no difference when comparing these symptoms in the initial phase of the outbreak to four weeks later. A variety of factors were associated with higher risk of psychiatric symptoms and/or low psychological well-being including female gender, poor-self-related health and relatives with COVID-19. CONCLUSION: Research evaluating the direct neuropsychiatric consequences and the indirect effects on mental health is highly needed to improve treatment, mental health care planning and for preventive measures during potential subsequent pandemics. url: https://www.sciencedirect.com/science/article/pii/S0889159120309545?v=s5 doi: 10.1016/j.bbi.2020.05.048 id: cord-343766-hlg7t5i5 author: Vinken, Mathieu title: A putative AOP for pneumonia related to COVID-19 date: 2020-07-20 words: 994.0 sentences: 59.0 pages: flesch: 47.0 cache: ./cache/cord-343766-hlg7t5i5.txt txt: ./txt/cord-343766-hlg7t5i5.txt summary: In order to further encourage research in this direction, an updated version of the putative AOP for pneumonia linked to COVID-19 is proposed, which encompasses new knowledge that is rapidly accumulating (Fig. 1) . One of the major MIEs in this AOP is the binding of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor at the plasma membrane surface of type II pneumocytes lining the alveoli in lung. Such AOP network should comprise the mechanisms driving the multi-organ failure frequently observed in severe COVID-19 patients, for which the causes (i.e. MIEs) are as yet not entirely clear or delineated. Thus, liver failure may be caused by the direct binding and actions of SARS-CoV-2 in hepatocytes or cholangiocytes, but could also be an indirect consequence of the systemic inflammatory response syndrome associated with COVID-19. A putative AOP for pneumonia linked to COVID-19 abstract: nan url: https://doi.org/10.1007/s00204-020-02860-w doi: 10.1007/s00204-020-02860-w id: cord-279439-h4ji0ttm author: Viotti, Manuel title: HUMAN PRE-IMPLANTATION EMBRYOS ARE PERMISSIVE TO SARS-COV-2 ENTRY date: 2020-09-30 words: 517.0 sentences: 41.0 pages: flesch: 49.0 cache: ./cache/cord-279439-h4ji0ttm.txt txt: ./txt/cord-279439-h4ji0ttm.txt summary: DESIGN: Assessment of expression levels of SARS-CoV-2 entry mediators in human embryo biopsies by RNAseq analysis, and infection of cultured embryos with SARS-CoV-2 Spike glycoprotein pseudotyped reporter virions expressing green fluorescent protein (GFP). MATERIALS AND METHODS: Trophectoderm biopsies from blastocyst-stage embryos (n¼24) were processed for RNAseq using a commercial kit and sequenced; results were analyzed for expression of factors implicated in SARS-CoV-2 cellular entry. For viral infection experiments, blastocyst-stage embryos (n¼94) were hatched from zonas mechanically, and infected by spinoculation with GFP-reporter virions pseudotyped with the SARS-CoV-2 Spike glycoprotein (required for SARS-CoV-2 entry). RESULTS: Cells collected from blastocyst-stage embryos robustly expressed the canonical SARS-CoV-2 entry receptor ACE2 and the putative activator protease TMPRSS2, in addition to other reported entry factors. Embryos exposed to reporter virions pseudotyped with SARS-CoV-2 Spike glycoprotein displayed robust GFP signal, often in numerous cells with cytoplasmic localization. CONCLUSIONS: Our results indicate that cells present in preimplantation embryos are permissive to the canonical Spike-ACE2 viral entry mechanism utilized by SARS-CoV-2. abstract: nan url: https://api.elsevier.com/content/article/pii/S0015028220323281 doi: 10.1016/j.fertnstert.2020.09.127 id: cord-006890-81wv1s33 author: Viret, Jean-Francois title: Development of a SARS vaccine: an industrial perspective on the global race against a global disease date: 2014-01-09 words: 2069.0 sentences: 78.0 pages: flesch: 38.0 cache: ./cache/cord-006890-81wv1s33.txt txt: ./txt/cord-006890-81wv1s33.txt summary: The high profile of SARS in the international news media contributed to early public disease awareness but also caused fear in both affected and unaffected populations, placing additional political and economic pressure on authorities to act on the threat despite of an insufficient basis for informed decisions. Once the global scale of the outbreak became fully apparent, the scientific community, supported by the WHO, committed to ''...the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models and correlates of protection in humans.'' an unparalleled collaborative effort. More specifically, in spite of the fortunate capability to propagate the SARS-CoV on a well-accepted cell substrate (VERO), the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models of persistent infection and correlates of protection in humans. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103677/ doi: 10.1586/14760584.2.4.465 id: cord-296426-upwsdgso author: Virmani, Sarthak title: Identifying a Kidney Transplant Recipient COVID Phenotype to Aid Test Utilization in the Setting of Limited Testing Availability - Does One Exist? date: 2020-06-20 words: 4402.0 sentences: 222.0 pages: flesch: 49.0 cache: ./cache/cord-296426-upwsdgso.txt txt: ./txt/cord-296426-upwsdgso.txt summary: While it is true that other non-novel viruses tend to cause more severe disease in immunocompromised patients [1] , no conclusive data is available to suggest an increased susceptibility or severity of SARS-Cov-2 infection in immunosuppressed kidney transplant recipients (KTRs). This was a single center, retrospective chart review performed as a QAPI project to assess similarities in kidney transplant recipients who tested positive for SARS-CoV-2 as compared to those who tested negative, and guide testing recommendations in the setting of limited testing availability during the COVID-19 pandemic. We did not observe any significant association between patient gender, level of education, or history of diabetes on the SARS-CoV-2 test result. Our cohort of KTRs showed no significant difference in ALC between patients who tested positive and negative for SARS-CoV-2 (Table 3 ). Though statistically significant in our small patient cohort, larger studies of KTRs with COVID-19 disease and a history of BKV will be required to confirm and better understand this association. abstract: Abstract: The high morbidity and mortality of COVID-19 in immunocompetent patients raises significant concern for immunosuppressed kidney transplant recipients (KTRs). This level of concern, both on the part of the KTRs and transplant professionals, is heightened by a lack of prior knowledge on how SARS-CoV-2 may manifest differently in immunosuppressed patients. Characterizing how KTRs may present differently than the general population would allow for more targeted and timely evaluation and treatment of KTRs with COVID-19 infection. Methods Without prior knowledge of how this virus would affect our transplant center’s delivery of care to KTRs who are SARS-CoV-2 positive or Patients Under Investigation (PUIs), and in the setting of limited testing availability, we initiated a Quality Assurance and Improvement Project (QAPI) to track KTRs followed at our transplant center through the SARS-CoV-2 testing process. Results Of the 53 symptomatic patients, 20 (38%) tested positive for SARS-CoV-2 either on presentation to the emergency department, or referral to a designated outpatient testing center. In addition, 16 (80%) of the 20 patients who tested positive required inpatient treatment. Intriguingly, patients with a history of polyoma BK viremia (BKV) had a higher incidence of testing positive for SARS-CoV-2 compared to patients without history of BKV (80% and 28%, respectively; p= 0.002). The Positive Predictive Value and Likelihood ratio was 80% and 6.6 for this association, respectively. Among our KTRs tested, those receiving belatacept had a lower likelihood of testing positive for SARS-CoV-2. This finding approached, but did not achieve, statistical significance (p=0.06). url: https://doi.org/10.1016/j.transproceed.2020.05.033 doi: 10.1016/j.transproceed.2020.05.033 id: cord-346055-7fa57pmf author: Visani, Giuseppe title: SARS-CoV-2 impact in a community-based hematological ward in an Italian Red Zone date: 2020-06-13 words: 741.0 sentences: 48.0 pages: flesch: 49.0 cache: ./cache/cord-346055-7fa57pmf.txt txt: ./txt/cord-346055-7fa57pmf.txt summary: Initial reports from China suggested that patients with cancer had an estimated two-fold increased risk of contracting SARS-CoV-2 than the general population and, if infected, also had a higher risk of either ICU admission, invasive ventilation, or death, compared to patients without cancer [2] . Up to now, 5924 cases resulted SARS-CoV-2 positive in Marche Region (out of 30,543 test done), with a rhythm of infection and death toll five times superior those of China [4] ; 845 patients died (452 in Pesaro Area) due to Covid-19, with high case-fatality rate (14%). Finally, we implemented testing with nasopharyngeal swabs and a quantitative polymerase-chain-reaction test to detect SARS-CoV-2 infection in patients admitted for chemotherapy/stem cell transplantation. Thirty-five HCPs, working exclusively at our Center, were tested: none of them resulted SARS-CoV-2 positive by nasopharyngeal swab. Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China abstract: nan url: https://doi.org/10.1007/s00277-020-04116-0 doi: 10.1007/s00277-020-04116-0 id: cord-317000-bfc51e0m author: Visci, G. title: Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date: 2020-10-27 words: 2663.0 sentences: 142.0 pages: flesch: 51.0 cache: ./cache/cord-317000-bfc51e0m.txt txt: ./txt/cord-317000-bfc51e0m.txt summary: In the present study we aimed to analyze the prevalence of positive serology testing following positive RT-PCR or the appearance of symptoms suggestive of Covid-19 among high-risk HCWs employed in public hospitals of Bologna, Northern Italy, an area at high incidence of infection with SARS-CoV-2 and mortality from Covid-19, and to compare the sensitivity of different types of serological tests, including chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA). An additional group of healthcare workers who developed symptoms related to Covid-19, but did not have a positive RT-PCR result, was included in the surveillance program (based on clinical diagnostic criteria). Based on the results reported in Table 2 , and sensitivity of LFIA test equal to 75.2%, we estimated that 73.4% of HCWs with Covid-19 related symptoms, who were not tested with RT-PCR, were not infected with SARS-CoV-2. abstract: Background. Limited information is available on prevalence and determinants of serologic response to SARS-CoV-2 infection among healthcare workers (HCWs). Methods. We analyzed the results of serologic testing with chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA) test among 544 HCWs with at least one positive RT-PCR test and 157 HCWs with Covid-19 related symptoms without a positive RT-PCR test from public hospitals in Bologna, Northern Italy. Tests were performed between March and August 2020. We fitted multivariate logistic regression models to identify determinants of positive serology. Results. The sensitivity of SARS-CoV-2 was 75.2% (LFIA) and 90.6% (CLIA). No differences in seropositivity were observed by sex, while older HCWs had higher positivity than other groups, and nurses had higher positivity compared to physicians, but not other HCWs. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2. Conclusions. Our study provides the best available data on sensitivity of serologic tests and on determinants of serologic response among HCWs positive for SARS-CoV-2, and provide evidence on the low specificity of Covid-19 related symptoms to identify infected HCWs. url: http://medrxiv.org/cgi/content/short/2020.10.25.20219113v1?rss=1 doi: 10.1101/2020.10.25.20219113 id: cord-253665-1dn3ek34 author: Vishnubalaji, Radhakrishnan title: Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response date: 2020-07-07 words: 5427.0 sentences: 301.0 pages: flesch: 42.0 cache: ./cache/cord-253665-1dn3ek34.txt txt: ./txt/cord-253665-1dn3ek34.txt summary: Coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared a global pandemic by the World Health Organization (WHO) on Phenomenal changes in ncRNA expression are also seen within host cells, which can play a major role in respiratory virus pathogenesis, with long non-coding RNAs (lncRNAs) exhibiting higher tissue specificity than coding genes [30] . Disease and function analysis on the differentially expressed genes revealed the most significant enrichment in pathways related to reactive oxygen species, induction of apoptosis and necrosis, as well as activation of neutrophils in SARS-CoV-2 infected NHBE cells (Figure 3a,b) . The top ten activated upstream regulator networks (CST5, IFNG, IFNL1, IFNA2, SPI1, RNY3, PRL, TGM2 , miR-122 and miR-122-5p) in lung tissue derived from COVID-19 patient based on transcriptome and IPA analyses, revealed the enrichment of functions related to immune system associated JAK-STAT cascade, type 1 interferon receptor binding, cytokine receptor binding, and MHC 1 biosynthesis (Figure 6a and Supplementary Table S10 ). abstract: The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated. url: https://doi.org/10.3390/genes11070760 doi: 10.3390/genes11070760 id: cord-341783-e7xz4utr author: Vistisen, Simon T. title: Risk and prognosis of COVID-19 in patients treated with renin–angiotensin–aldosterone inhibitors date: 2020-07-06 words: 1907.0 sentences: 99.0 pages: flesch: 47.0 cache: ./cache/cord-341783-e7xz4utr.txt txt: ./txt/cord-341783-e7xz4utr.txt summary: 2 Because ACE2 plays an important role in the renin-angiotensin system and also acts as a receptor for SARS-CoV-2 cell entry, hypotheses about an association between ACEi/ARBs and COVID-19 outcomes were rapidly generated. Nevertheless, based on these initial observational findings, there seems to be no increased risk of SARS-CoV-2 infection for ACEi/ARB users. Four studies examined the prognosis of COVID-19 patients and uniformly found that risk of severe outcomes was not higher for the collapsed group of ACEi and ARB 740 Vistisen et al. The transmembrane angiotensin-converting enzyme 2 receptor allows SARS-CoV-2 entry and leads to virus replication, activation of innate immune system/complement, cytokine formation followed by neutrophils/lymphocytes in the lung and development of acute respiratory distress syndrome (ARDS). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32769503/ doi: 10.1097/eja.0000000000001277 id: cord-303959-e1654g5j author: Vitiello, Antonio title: COVID-19 Patients with Pulmonary Fibrotic Tissue: Clinical Pharmacological Rational of Antifibrotic Therapy date: 2020-08-27 words: 1917.0 sentences: 89.0 pages: flesch: 38.0 cache: ./cache/cord-303959-e1654g5j.txt txt: ./txt/cord-303959-e1654g5j.txt summary: In this direction, the use of a pharmacological approach to reduce or prevent fibrotic status, with antifibrotic agents such as pirfenidone, used with demonstrated clinical efficacy in idiopathic pulmonary fibrosis [4] can be a valuable aid in the prevention of serious or fatal complications from COVID-19 in patients with ongoing infection, or in those already healed with residual fibrotic lung lesions [5] . Although many patients who develop SARS-CoV-2 respiratory distress syndrome survive the acute phase of the Fig. 1 Antifibrotic therapy, pleiotropic effects of Pirfenidone disease, data have shown that some of them die from progressive pulmonary fibrosis [19] . Several reports suggest, however, that there are differences between IPF and COVID-19-induced pulmonary fibrosis, diversity in the rapid evolution of the fibrotic and inflammatory state, and a highly developed procoagulant effect in SARS-CoV-2 viral infection [22, 23] . abstract: In December 2019, the first data emerged from Wuhan, China, of a serious acute respiratory disease caused by a new coronavirus, SARS-CoV-2 (COVID-19). In a short time, the health emergency became a global pandemic. To date, there are about 18.8 million infected people and about 700,000 deaths. There are currently no effective vaccines, and treatments are mostly experimental. The symptoms associated with COVID-19 are different, ranging from mild upper respiratory tract symptoms to severe acute respiratory distress syndrome (SARS). Data from previous coronavirus outbreaks such as SARS-CoV (2003 outbreak) and emerging epidemiological data from the current global COVID-19 pandemic suggest that there could be substantial tissue fibrotic consequences following SARS-CoV-2 infection, responsible for severe and in some cases fatal lung lesions. Some data show that even patients cured of viral infection have lung fibrotic tissue residues responsible for incorrect respiratory function even after healing. The role of antifibrotic drug therapy in patients with ongoing SARS-CoV-2 infection or in patients cured of residual pulmonary fibrosis is still to be defined and unclear; the scientific rationale for initiating, continuing, or discontinuing therapy is poorly defined. In this article, we describe the advantages of antifibrotic therapy in patients with ongoing SARS-CoV-2 viral infection to prevent the worsening and aggravation of the clinical situation, and the advantages it could have in the role of preventing pulmonary fibrosis after SARS-CoV-2 infection, and in accelerating the complete healing process. url: https://doi.org/10.1007/s42399-020-00487-7 doi: 10.1007/s42399-020-00487-7 id: cord-332778-rf47ptj6 author: Vivarelli, Silvia title: Cancer Management during COVID-19 Pandemic: Is Immune Checkpoint Inhibitors-Based Immunotherapy Harmful or Beneficial? date: 2020-08-10 words: 7447.0 sentences: 374.0 pages: flesch: 44.0 cache: ./cache/cord-332778-rf47ptj6.txt txt: ./txt/cord-332778-rf47ptj6.txt summary: It was demonstrated that cancer patients have an increased risk of developing a worse symptomatology upon severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV-2) infection, often leading to hospitalization and intensive care. Given their immune-compromised status, cancer patients infected by SARS-CoV-2 might be at a higher risk of developing severe and critical consequences upon COVID-19, including ARDS, septic shock and acute myocardial infarction [29] [30] [31] . Nevertheless, cancer patients, when infected by SARS-CoV-2 might develop more severe outcomes, if anti-cancer treatments induce a weakening of the host immune health [38] . Since the beginning of this pandemic, nine independent clinical studies have been published about the risks possibly related to SARS-CoV-2 infection in patients with cancer. In line with this concept, three additional independent clinical studies are currently enrolling non-cancer COVID-19 patients to test the efficacy of administering ICIs to reshape the impaired immune system of SARS-CoV-2 infected individuals (i.e., NCT04268537; NCT04356508 and NCT04413838). abstract: The coronavirus disease 2019 (COVID-19) is currently representing a global health threat especially for fragile individuals, such as cancer patients. It was demonstrated that cancer patients have an increased risk of developing a worse symptomatology upon severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV-2) infection, often leading to hospitalization and intensive care. The consequences of this pandemic for oncology are really heavy, as the entire healthcare system got reorganized. Both oncologists and cancer patients are experiencing rescheduling of treatments and disruptions of appointments with a concurrent surge of fear and stress. In this review all the up-to-date findings, concerning the association between COVID-19 and cancer, are reported. A remaining very debated question regards the use of an innovative class of anti-cancer molecules, the immune checkpoint inhibitors (ICIs), given their modulating effects on the immune system. For that reason, administration of ICIs to cancer patients represents a question mark during this pandemic, as its correlation with COVID-19-associated risks is still under investigation. Based on the mechanisms of action of ICIs and the current evidence, we suggest that ICIs not only can be safely administered to cancer patients, but they might even be beneficial in COVID-19-positive cancer patients, by exerting an immune-stimulating action. url: https://doi.org/10.3390/cancers12082237 doi: 10.3390/cancers12082237 id: cord-332278-2p64ab2z author: Vivas, David title: Recomendaciones sobre el tratamiento antitrombótico durante la pandemia COVID-19. Posicionamiento del Grupo de Trabajo de Trombosis Cardiovascular de la Sociedad Española de Cardiología date: 2020-06-19 words: 3074.0 sentences: 166.0 pages: flesch: 46.0 cache: ./cache/cord-332278-2p64ab2z.txt txt: ./txt/cord-332278-2p64ab2z.txt summary: Thus, even patients who are not infected with SARS-CoV-2 are being affected by the pandemic, which is having a strong influence on the optimization of antithrombotic therapy due to the current health care situation. Its aim is to summarize the available information and provide simple guidelines for the use of antithrombotic drugs in order to guarantee optimal care for patients infected by the SARS-CoV-2 virus. Patients with SARS-CoV-2 infection are at increased risk of thromboembolic events, especially VTE, which is associated with the critical situation and immobilization entailed by this disease. Figure 2 shows an algorithm for the treatment approach to patients with prior oral anticoagulation therapy admitted for COVID-19 infection, in which a change to parenteral anticoagulation is proposed (mainly due to the severe situation or to interactions with COVID-19 drugs). abstract: Abstract The new coronavirus SARS-CoV-2, which gives rise to the highly contagious COVID-19 disease, has caused a pandemic that is overwhelming health care systems worldwide. Affected patients have been reported to have a heightened inflammatory state that increases their thrombotic risk. However, there is very scarce information on the management of thrombotic risk, coagulation disorders, and anticoagulant therapy. In addition, the situation has also greatly influenced usual care in patients not infected with COVID-19. This article by the Working Group on Cardiovascular Thrombosis of the Spanish Society of Cardiology aims to summarize the available information and to provide a practical approach to the management of antithrombotic therapy. Full English text available from: www.revespcardiol.org/en url: https://www.ncbi.nlm.nih.gov/pubmed/32694078/ doi: 10.1016/j.rec.2020.04.025 id: cord-336373-xb3jrg75 author: Vivas, Esther X. title: COVID19 and Otology/Neurotology date: 2020-08-22 words: 1981.0 sentences: 105.0 pages: flesch: 49.0 cache: ./cache/cord-336373-xb3jrg75.txt txt: ./txt/cord-336373-xb3jrg75.txt summary: The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. In the following text I will review some of the changes to the practice of otology and neurotology in the US, in the context of the COVID-19 pandemic. In general, it is safe to say that while N95s have been used extensively, the role of CAPR and PAPR is limited for routine otologic and neurotologic procedures, but may be necessary on COVID-19 positive patients. Another change to standard operating procedures has been the implementation of pre-operative COVID-19 testing for all patients undergoing surgery. The COVID-19 pandemic has required otologists and neurotologists to implement several changes into our practice. abstract: The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. The effects have been particularly palpable in the practice of medicine. The medical community now has to re-evaluate everything we do on a daily basis, practices once deemed routine are now scrutinized. The field of otolaryngology has not been spared. We’ve had to significantly alter the way we provide care to patients, changes that are likely to become a new norm for the foreseeable future. This chapter will highlight some of the changes as they apply to otology/neurotology. Although this is written from the perspective of an academic physician, it is also applicable to private practice colleagues. url: https://doi.org/10.1016/j.otc.2020.08.003 doi: 10.1016/j.otc.2020.08.003 id: cord-286655-5vorrnq3 author: Vivek-Ananth, R.P. title: In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection date: 2020-08-22 words: 12942.0 sentences: 693.0 pages: flesch: 55.0 cache: ./cache/cord-286655-5vorrnq3.txt txt: ./txt/cord-286655-5vorrnq3.txt summary: Lastly, we filtered the subset of phytochemicals whose binding energy in the best docked pose with TMPRSS2 (respectively, cathepsin L) is ≤−8.5 kcal/mol (respectively, ≤−8.0 In the third stage, we performed protein-ligand docking using AutoDock Vina [34] . Finally, in the fifth stage, for the top three inhibitors of TMPRSS2 namely, T1 (qingdainone), T2 (edgeworoside C) and T3 (adlumidine), and of cathepsin L namely, C1 (ararobinol), C2 ((+)-oxoturkiyenine) and C3 (3α,17α-cinchophylline), their respective protein-ligand complexes were analyzed using 180 ns MD simulation (Section 3; Figures 8 and 9; Supplementary Figures S1 and S2) and their interaction binding energy was computed using MM-PBSA method (Section 3; Table 3 ). As mentioned above, we have identified 96 potential natural product inhibitors of TMPRSS2 by computational screening of 14,011 phytochemicals produced by Indian medicinal plants, and these 96 compounds labelled T1-T96 are listed in Supplementary Table S1 along with their PubChem identifier, common name, IUPAC name and structure in SMILES format. abstract: Presently, there are no approved drugs or vaccines to treat COVID-19, which has spread to over 200 countries and at the time of writing was responsible for over 650,000 deaths worldwide. Recent studies have shown that two human proteases, TMPRSS2 and cathepsin L, play a key role in host cell entry of SARS-CoV-2. Importantly, inhibitors of these proteases were shown to block SARS-CoV-2 infection. Here, we perform virtual screening of 14,011 phytochemicals produced by Indian medicinal plants to identify natural product inhibitors of TMPRSS2 and cathepsin L. AutoDock Vina was used to perform molecular docking of phytochemicals against TMPRSS2 and cathepsin L. Potential phytochemical inhibitors were filtered by comparing their docked binding energies with those of known inhibitors of TMPRSS2 and cathepsin L. Further, the ligand binding site residues and non-covalent interactions between protein and ligand were used as an additional filter to identify phytochemical inhibitors that either bind to or form interactions with residues important for the specificity of the target proteases. This led to the identification of 96 inhibitors of TMPRSS2 and 9 inhibitors of cathepsin L among phytochemicals of Indian medicinal plants. Further, we have performed molecular dynamics (MD) simulations to analyze the stability of the protein-ligand complexes for the three top inhibitors of TMPRSS2 namely, qingdainone, edgeworoside C and adlumidine, and of cathepsin L namely, ararobinol, (+)-oxoturkiyenine and 3α,17α-cinchophylline. Interestingly, several herbal sources of identified phytochemical inhibitors have antiviral or anti-inflammatory use in traditional medicine. Further in vitro and in vivo testing is needed before clinical trials of the promising phytochemical inhibitors identified here. url: https://www.ncbi.nlm.nih.gov/pubmed/32842606/ doi: 10.3390/molecules25173822 id: cord-304306-rxjahqwh author: Vlachakis, Dimitrios title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 words: 8517.0 sentences: 459.0 pages: flesch: 48.0 cache: ./cache/cord-304306-rxjahqwh.txt txt: ./txt/cord-304306-rxjahqwh.txt summary: The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response abstract: The novel coronavirus SARS-CoV-2 has emerged as a severe threat against public health and global economies. COVID-19, the disease caused by this virus, is highly contagious and has led to an ongoing pandemic. SARS-CoV-2 affects, mainly, the respiratory system, with most severe cases primarily showcasing acute respiratory distress syndrome. Currently, no targeted therapy exists, and since the number of infections and death toll keeps rising, it has become a necessity to study possible therapeutic targets. Antiviral drugs can target various stages of the viral infection, and in the case of SARS-CoV-2, both structural and non-structural proteins have been proposed as potential drug targets. This review focuses on the most researched SARS-CoV-2 proteins, their structure, function, and possible therapeutic approaches. url: https://doi.org/10.1016/j.fct.2020.111805 doi: 10.1016/j.fct.2020.111805 id: cord-264515-nle4axad author: Vlachos, J. title: School closures and SARS-CoV-2. Evidence from Sweden''s partial school closure date: 2020-10-14 words: 7580.0 sentences: 407.0 pages: flesch: 56.0 cache: ./cache/cord-264515-nle4axad.txt txt: ./txt/cord-264515-nle4axad.txt summary: To study the broad impact of school closures on the transmission of the virus, we estimate differences in infection rates between parents exposed to lower and upper secondary students. We estimate differences in infections among parents, teachers, and teachers'' partners who were differently exposed to lower (open) and upper (online) secondary schools using linear probability models (OLS) and logistic regressions. We find that parental exposure to open rather than closed schools is associated with a somewhat higher rate of PCR-confirmed SARS-CoV-2 infections The positive association for PCR-confirmed cases could partly reflect other behavioral differences between households with slightly younger and older children, but if treated as a causal the estimates indicate that a hypothetical closure of lower secondary schools in Sweden would have resulted in 341 fewer detected cases among the 312 575 parents in our sample. abstract: To reduce the transmission of SARS-CoV-2 most countries closed schools, despite uncertainty if school closures are an effective containment measure. At the onset of the pandemic, Swedish upper secondary schools moved to online instruction while lower secondary school remained open. This allows for a comparison of parents and teachers differently exposed to open and closed schools, but otherwise facing similar conditions. Leveraging rich Swedish register data, we connect all students and teachers in Sweden to their families and study the impact of moving to online instruction on the incidence of SARS-CoV-2 and COVID-19. We find that among parents, exposure to open rather than closed schools resulted in a small increase in PCR-confirmed infections [OR 1.15; CI95 1.03-1.27]. Among lower secondary teachers the infection rate doubled relative to upper secondary teachers [OR 2.01; CI95 1.52-2.67]. This spilled over to the partners of lower secondary teachers who had a higher infection rate than their upper secondary counterparts [OR 1.30; CI95 1.00-1.68]. When analyzing COVID-19 diagnoses from healthcare visits and the incidence of severe health outcomes, results are similar for teachers but somewhat weaker for parents and teachers' partners. The results for parents indicate that keeping lower secondary schools open had minor consequences for the transmission of SARS-CoV-2 in society. The results for teachers suggest that measures to protect teachers could be considered. url: https://doi.org/10.1101/2020.10.13.20211359 doi: 10.1101/2020.10.13.20211359 id: cord-303787-dx1n8jap author: Vonck, Kristl title: Neurological manifestations and neuro‐invasive mechanisms of the severe acute respiratory syndrome coronavirus type 2 date: 2020-05-16 words: 3806.0 sentences: 208.0 pages: flesch: 42.0 cache: ./cache/cord-303787-dx1n8jap.txt txt: ./txt/cord-303787-dx1n8jap.txt summary: RESULTS: Neurological manifestations potentially related to COVID‐19 have been reported in large studies, case series and case reports and include acute cerebrovascular diseases, impaired consciousness, cranial nerve manifestations and auto‐immune disorders such as Guillain‐Barré Syndrome often present in patients with more severe COVID‐19. Neurological symptoms were more common in patients with severe infection according to their respiratory status (45.5% vs 30.2% in non-severe cases) and fell into 3 categories: central nervous system (CNS) manifestations (dizziness, headache, impaired consciousness, acute cerebrovascular disease, ataxia, and seizure), cranial and peripheral nervous system manifestations (taste impairment, smell impairment, vision impairment, and neuropathy), and skeletal muscular injury manifestations. This is illustrated by a recent report of a COVID-19 patient with an acute necrotizing encephalopathy, a rare complication observed in infections with viruses including influenza, and related to a cytokine storm in the brain without direct viral invasion 26 . abstract: INTRODUCTION: Infections with coronaviruses are not always confined to the respiratory tract and various neurological manifestations have been reported. The aim of this study was to perform a review to describe neurological manifestations in patients with COVID‐19 and possible neuro‐invasive mechanisms of Sars‐CoV‐2. METHODS: Pubmed, WebOfScience and Covid‐dedicated databases were searched for the combination of COVID‐19 terminology and neurology terminology up to May 10(th) 2020. Social media channels were followed‐up between March 15(th) and May 10(th) 2020 for postings with the same scope. Neurological manifestations were extracted from the identified manuscripts and combined to provide a useful summary for the neurologist in clinical practice. RESULTS: Neurological manifestations potentially related to COVID‐19 have been reported in large studies, case series and case reports and include acute cerebrovascular diseases, impaired consciousness, cranial nerve manifestations and auto‐immune disorders such as Guillain‐Barré Syndrome often present in patients with more severe COVID‐19. Cranial nerve symptoms such as olfactory and gustatory dysfunctions are highly prevalent in patients with mild‐to‐moderate COVID‐19 even without associated nasal symptoms and often present in an early stage of the disease. CONCLUSION: Physicians should be aware of the neurological manifestations in patients with COVID‐19, especially when rapid clinical deterioration occurs. The neurological symptoms in COVID‐19 patients may be due to direct viral neurological injury or indirect neuroinflammatory and autoimmune mechanisms. No antiviral treatments against the virus or vaccines for its prevention are available and the long‐term consequences of the infection on human health remain uncertain especially with regards to the neurological system. url: https://www.ncbi.nlm.nih.gov/pubmed/32416028/ doi: 10.1111/ene.14329 id: cord-337674-mb6ue2hl author: Voulgaris, Athanasios title: Sleep medicine and COVID-19. Has a new era begun? date: 2020-07-17 words: 4544.0 sentences: 207.0 pages: flesch: 47.0 cache: ./cache/cord-337674-mb6ue2hl.txt txt: ./txt/cord-337674-mb6ue2hl.txt summary: This is especially important for the treatment of patients with sleep disordered breathing (SDB) since the application of positive airway pressure (PAP) can induce spread of aerosol and increase substantially the risk of infection [6] . A group of experts in SDB from the Chinese Thoracic Society provided feedback on the management of patients with OSA and suggested that sleep studies and initiation of PAP application should be continued only in regions with low incidence of COVID-19, preferably with the use of home sleep apnea tests (HSAT) [19] . In case where in-laboratory sleep studies are necessary, especially for PAP titration or insurance demands, these could be performed only after patients'' negative screening for COVID-19, according to local recommendations and hospital guidelines, with the personnel using all necessary personal protective equipment (PPE) and keeping safe distances, as previously mentioned and according to WHO infection prevention and control guidance [34] . abstract: Since late December 2019, COVID-19, the disease caused by the novel coronavirus, SARS-CoV-2, has spread rapidly around the world, causing unprecedented changes in provided health care services. Patients diagnosed with sleep-disordered breathing (SDB) are subject to a higher risk for worse outcomes from COVID-19, due to the high prevalence of coexistent comorbidities. Additionally, treatment with positive airway treatment devices (PAP) can also be challenging because of the greater transfer of PAP-induced droplets and aerosol. In this context, sleep medicine practices are entering a new era and need to adapt rapidly in these circumstances, so as to provide the best care for patients with SDB. Novel approaches like the application of telemedicine may play an important role in the management of patients with SDB during the COVID-19 pandemic. url: https://www.sciencedirect.com/science/article/pii/S1389945720303117?v=s5 doi: 10.1016/j.sleep.2020.07.010 id: cord-263031-cco2vh0f author: Vultaggio, Alessandra title: Considerations on Biologicals for Patients with allergic disease in times of the COVID‐19 pandemic: an EAACI Statement date: 2020-06-05 words: 2870.0 sentences: 177.0 pages: flesch: 41.0 cache: ./cache/cord-263031-cco2vh0f.txt txt: ./txt/cord-263031-cco2vh0f.txt summary: We discuss immunological and clinical considerations for patients on biologic agents (biologicals)targeting the type 2 inflammatory response due to difficult-to-treat allergic diseases in the context of COVID-19. In other coronavirus infections such as severe acute respiratory syndrome (SARS), type I IFN are critical for the initiation of immune response and virus clearance. In line with a paucity of mechanistic data on COVID-19 in the context of type 2 inflammation, knowledge on the disease course in patients treated with biologicals targeting type 2 inflammation due to severe asthma or other atopic diseases, such as CSU, AD and CRSwNP, is scarce to absent. In the past years, new biological therapies for severe asthma, atopic dermatitis (AD), chronicrhinosinusitis with nasal polyps (CRSwNP) and chronic spontaneous urticaria (CSU) have been developed targeting different aspects of the type 2 immune response. abstract: The outbreak of the SARS‐CoV‐2‐induced Coronavirus Disease 2019 (COVID‐19) pandemic re‐shaped doctor‐patient interaction and challenged capacities of healthcare systems. It created many issues around the optimal and safest way to treat complex patients with severe allergic disease. A significant numberof the patients are on treatment with biologicals and clinicians face the challenge to provide optimal care during the pandemic. Uncertainty of the potential risks for these patients is related to the fact that the exact sequence of immunological events during SARS‐CoV‐2 is not known. Severe COVID‐19 patients may experience a “cytokine storm” and associated organ damage characterized by an exaggerated release of proinflammatory type 1 and type 3 cytokines. These inflammatory responses are potentially counteracted by anti‐inflammatory cytokines and type 2 responses. This expert based EAACI statement aims to provide guidance on the application of biologicals targeting type 2 inflammation in patients with allergic disease. Currently, there is very little evidence for an enhanced risk of patients with allergic diseases to develop severe COVID‐19 with studies focusing on severe allergic phenotypes lacking. At present, non‐infected patients on biologicals for the treatment of asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps or chronic spontaneous urticaria should continue their biologicals targeting type 2 inflammation via self‐application. In case of an active SARS‐CoV‐2 infection, biological treatment needs to be stopped until clinical recovery and SARS‐CoV‐2 negativity is established and treatment with biologicals should be re‐initiated. Maintenance of add‐on therapy and a constant assessment of disease control, apart from acute management is demanded. url: https://www.ncbi.nlm.nih.gov/pubmed/32500526/ doi: 10.1111/all.14407 id: cord-314947-fy1lqk00 author: WU, Xiao Dong title: The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells date: 2004-10-17 words: 3908.0 sentences: 211.0 pages: flesch: 60.0 cache: ./cache/cord-314947-fy1lqk00.txt txt: ./txt/cord-314947-fy1lqk00.txt summary: title: The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells In order to investigate the maturation and proteolytic processing of the S protein of SARS CoV, we generated S1 and S2 subunit specific antibodies (Abs) as well as N, E and 3CL protein-specific Abs. Our results showed that the antibodies could efficiently and specifically bind to their corresponding proteins from E.coli expressed or lysate of SARS-CoV infected Vero-E6 cells by Western blot analysis. When S2 Ab was used to perform immune precipitation with lysate of SARS-CoV infected cells, a cleaved S2 fragment was detected with S2-specific mAb by Western blot analysis. Furthermore, antibodies against S1, S2, N protein could detect their corresponding proteins from the lysates of SARS-CoV infected Vero E6 cells. To First, S2-specific mAb was directly used to detect native S2 fragment or full length of S protein in the lysate of SARS-CoV infected Vero E6 cells. abstract: Spike protein is one of the major structural proteins of severe acute respiratory syndrome-coronavirus. It is essential for the interaction of the virons with host cell receptors and subsequent fusion of the viral envelop with host cell membrane to allow infection. Some spike proteins of coronavirus, such as MHV, HCoV-OC43, AIBV and BcoV, are proteolytically cleaved into two subunits, S1 and S2. In contrast, TGV, FIPV and HCoV-229E are not. Many studies have shown that the cleavage of spike protein seriously affects its function. In order to investigate the maturation and proteolytic processing of the S protein of SARS CoV, we generated S1 and S2 subunit specific antibodies (Abs) as well as N, E and 3CL protein-specific Abs. Our results showed that the antibodies could efficiently and specifically bind to their corresponding proteins from E.coli expressed or lysate of SARS-CoV infected Vero-E6 cells by Western blot analysis. Furthermore, the anti-S1 and S2 Abs were proved to be capable of binding to SARS CoV under electron microscope observation. When S2 Ab was used to perform immune precipitation with lysate of SARS-CoV infected cells, a cleaved S2 fragment was detected with S2-specific mAb by Western blot analysis. The data demonstrated that the cleavage of S protein was observed in the lysate, indicating that proteolytic processing of S protein is present in host cells. url: https://www.ncbi.nlm.nih.gov/pubmed/15450134/ doi: 10.1038/sj.cr.7290240 id: cord-342765-rw8valjp author: Wacharapluesadee, Supaporn title: Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19 date: 2020-05-13 words: 2125.0 sentences: 123.0 pages: flesch: 52.0 cache: ./cache/cord-342765-rw8valjp.txt txt: ./txt/cord-342765-rw8valjp.txt summary: Additionally, NT specimens with PCR cycle threshold (Ct) greater than 35 were pooled to determine the limit of detection and sensitivity of pooling samples to test for SARS-CoV-2. Previously positive specimens with high and low-concentrations of RNA, as determined by PCR Ct values at the time of detection, were selected to determine the effect of viral load on pooling to ensure that the sensitivity and accuracy of the assay was maintained (Table 1) The fifteen 1X (L>35) pools were tested by performing duplicate (replicates I and II) qPCR assays to determine the limit of detection of specimen pooling when compared to individual testing. This study demonstrates that specimen pooling (either 1X or 2X pooling ratios) does not compromise the sensitivity of detecting SARS-CoV-2 provided the Ct value of the individually tested sample is lower than 35. abstract: In the age of a pandemic, such as the ongoing one caused by SARS‐CoV‐2, the world faces a limited supply of tests, personal protective equipment, and factories and supply chains are struggling to meet the growing demands. This study aimed to evaluate the efficacy of specimen pooling for testing of SARS‐CoV‐2 virus, to determine whether costs and resource savings could be achieved without impacting the sensitivity of the testing. Ten previously tested nasopharyngeal and throat swab specimens by real‐time PCR, were pooled for testing, containing either one or two known positive specimens of varying viral concentrations. Specimen pooling did not affect the sensitivity of detecting SARS‐CoV‐2 when the PCR cycle threshold (Ct) of original specimen was lower than 35. In specimens with low viral load (Ct>35), 2 out of 15 pools (13.3%) were false negative. Pooling specimens to test for COVID‐19 infection in low prevalence (≤1%) areas or in low risk populations can dramatically decrease the resource burden on laboratory operations by up to 80%. This paves the way for large‐scale population screening, allowing for assured policy decisions by governmental bodies to ease lockdown restrictions in areas with a low incidence of infection, or with lower risk populations. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26005 doi: 10.1002/jmv.26005 id: cord-263002-f3itn0sb author: Wagener, Frank A. D. T. G. title: Targeting the Heme-Heme Oxygenase System to Prevent Severe Complications Following COVID-19 Infections date: 2020-06-19 words: 3943.0 sentences: 248.0 pages: flesch: 39.0 cache: ./cache/cord-263002-f3itn0sb.txt txt: ./txt/cord-263002-f3itn0sb.txt summary: Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. These predisposing conditions, and inflammation in general, downregulate HO-1 expression and activity [67, 74, [100] [101] [102] [103] [104] [105] [106] , further supporting that this compromised protection and diminished tolerance against inflammatory and oxidative stress promotes adverse clinical outcome in COVID-19 patients. Since dexamethasone reduces hemolysis and induces HO-1 in macrophages [113] , it is tempting to speculate that this increased protection against free heme attenuates the severity of disease in COVID-19 patients. abstract: SARS-CoV-2 is causing a pandemic resulting in high morbidity and mortality. COVID-19 patients suffering from acute respiratory distress syndrome (ARDS) are often critically ill and show lung injury and hemolysis. Heme is a prosthetic moiety crucial for the function of a wide variety of heme-proteins, including hemoglobin and cytochromes. However, injury-derived free heme promotes adhesion molecule expression, leukocyte recruitment, vascular permeabilization, platelet activation, complement activation, thrombosis, and fibrosis. Heme can be degraded by the anti-inflammatory enzyme heme oxygenase (HO) generating biliverdin/bilirubin, iron/ferritin, and carbon monoxide. We therefore postulate that free heme contributes to many of the inflammatory phenomena witnessed in critically ill COVID-19 patients, whilst induction of HO-1 or harnessing heme may provide protection. HO-activity not only degrades injurious heme, but its effector molecules possess also potent salutary anti-oxidative and anti-inflammatory properties. Until a vaccine against SARS-CoV-2 becomes available, we need to explore novel strategies to attenuate the pro-inflammatory, pro-thrombotic, and pro-fibrotic consequences of SARS-CoV-2 leading to morbidity and mortality. The heme-HO system represents an interesting target for novel “proof of concept” studies in the context of COVID-19. url: https://doi.org/10.3390/antiox9060540 doi: 10.3390/antiox9060540 id: cord-289079-m417oxpc author: Waggershauser, Constanze H. title: Letter: immunotherapy in IBD patients in a SARS‐CoV‐2 endemic area date: 2020-08-14 words: 405.0 sentences: 35.0 pages: flesch: 58.0 cache: ./cache/cord-289079-m417oxpc.txt txt: ./txt/cord-289079-m417oxpc.txt summary: Editors, With interest, we read the article of Taxonera et al on symptoms and the risk of COVID-19 in inflammatory bowel disease (IBD). 1 We would like to provide data from our IBD centre during the outbreak of SARS-CoV-2 concerning patients receiving immunotherapies. 2 Therefore, soon two questions raised great concern: are IBD patients who receive immunotherapies more susceptible to SARS-CoV-2 infections than the general population and are infected patients exposed to a more severe course? Since the estimated number of silent SARS-CoV-2 infections is high 7 and most individuals show only moderate symptoms of respiratory tract infection, we called or invited our patients to fill-in a questionnaire, 8 Our data confirm the recommended practice that immunotherapies should not be stopped or delayed during the COVID-19 crisis. Daniel Szokodi has served as a speaker for Pfizer. 2019 novel coronavirus disease (COVID-19) in patients with inflammatory bowel diseases abstract: LINKED CONTENT This article is linked to Taxonera et al papers. To view these articles, visit https://doi.org/10.1111/apt.15804 and https://doi.org/10.1111/apt.15955 url: https://www.ncbi.nlm.nih.gov/pubmed/32852838/ doi: 10.1111/apt.15897 id: cord-284102-rovyvv45 author: Wagner, Teresa R. title: NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date: 2020-09-28 words: 2910.0 sentences: 190.0 pages: flesch: 53.0 cache: ./cache/cord-284102-rovyvv45.txt txt: ./txt/cord-284102-rovyvv45.txt summary: Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Considering that Nbs targeting diverse epitopes within the RBD:ACE2 interface are beneficial 201 in both reducing viral infectivity and preventing mutational escape, we next combined the most 202 potent inhibitory and neutralizing candidates derived from Nb-Set1 (NM1226, NM1228) and 203 We incubated our previously generated color-coded beads 232 comprising RBD, S1 domain or homotrimeric spike with serum samples from patients or non-233 infected individuals, in addition to dilution series of the combinations NM1226/ NM1230 or 234 NM1228/ NM1230 and used this to detect patient-derived IgGs bound to the respective 235 antigens. As a result, we modified our previously described multiplex immunoassay 303 (MULTICOV-AB, 20 ) and developed a novel diagnostic test called NeutrobodyPlex to monitor 304 the presence and the emergence of neutralizing antibodies in serum samples of SARS-CoV-2 305 infected individuals. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block 681 interaction with ACE2 abstract: As the COVID-19 pandemic escalates, the need for effective vaccination programs, diagnosis tools and therapeutic intervention ever increases. Neutralizing binding molecules have become important tools for acute treatment of COVID-19 and also provide a unique possibility to monitor the emergence and presence of a neutralizing immune response in infected or vaccinated individuals. Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Of these, 8 effectively block the RBD:ACE2 interface. Via competitive binding analysis and detailed epitope mapping, we grouped all Nbs into 3 sets and demonstrated their neutralizing effect. Combinations from different sets showed a profound synergistic effect by simultaneously targeting different epitopes within the RBD. Finally, we established a competitive multiplex binding assay (“NeutrobodyPlex”) enabling the detection of neutralizing antibodies in serum of infected patients. Overall, our Nbs have high potential for prophylactic and therapeutic options and provide a novel approach to screen for a neutralizing immune response in infected or vaccinated individuals, helping to monitor immune status or guide vaccine design. url: https://doi.org/10.1101/2020.09.22.308338 doi: 10.1101/2020.09.22.308338 id: cord-348301-bk80pps9 author: Wahl, Angela title: Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801 date: 2020-09-24 words: 4279.0 sentences: 238.0 pages: flesch: 47.0 cache: ./cache/cord-348301-bk80pps9.txt txt: ./txt/cord-348301-bk80pps9.txt summary: Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Human lung tissues of LoM were inoculated with SARS-CoV-2 and titers of replication competent virus determined 2, 6, and 14 days post-exposure (Fig. 1c , Extended Data Table 2 ). Collectively, our results indicate that LoM re ect the pathogenic effects in icted by SARS-CoV-2 on the human lung and demonstrate their utility as a single in vivo platform to evaluate and compare the replication and pathogenesis of past, present, and future pre-emergent, epidemic, and pandemic coronaviruses accelerating the development and testing of pre-exposure prophylaxis agents such as EIDD-2801. abstract: All known recently emerged human coronaviruses likely originated in bats. Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Virus replication in this model occurs in bona fide human lung tissue and does not require any type of adaptation of the virus or the host. Our results indicate that bats harbor endogenous coronaviruses capable of direct transmission into humans. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Acute SARS-CoV-2 infection was highly cytopathic and induced a robust and sustained Type I interferon and inflammatory cytokine/chemokine response. Finally, we evaluated a pre-exposure prophylaxis strategy for coronavirus infection. Our results show that prophylactic administration of EIDD-2801, an oral broad spectrum antiviral currently in phase II clinical trials for the treatment of COVID-19, dramatically prevented SARS-CoV-2 infection in vivo and thus has significant potential for the prevention and treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32995766/ doi: 10.21203/rs.3.rs-80404/v1 id: cord-275894-puwaty70 author: Wajnberg, A. title: SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months date: 2020-07-17 words: 2493.0 sentences: 190.0 pages: flesch: 61.0 cache: ./cache/cord-275894-puwaty70.txt txt: ./txt/cord-275894-puwaty70.txt summary: Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. In order to determine if antibodies induced against the spike protein exert neutralizing activity, we 111 performed a well-established, quantitative microneutralization assay (18) based on authentic 112 SARS-CoV-2 with 120 samples of known ELISA titers ranging from ''negative'' to 1:2880. . https://doi.org/10.1101/2020.07.14.20151126 doi: medRxiv preprint with authentic SARS-CoV-2 virus, and the vast majority of individuals with antibody titers of 1:320 167 or higher show neutralizing activity in their serum. abstract: SARS-CoV-2 has caused a global pandemic with millions infected and numerous fatalities. Questions regarding the robustness, functionality and longevity of the antibody response to the virus remain unanswered. Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggests that more than 90% of seroconverters make detectible neutralizing antibody responses and that these titers are stable for at least the near-term future. url: http://medrxiv.org/cgi/content/short/2020.07.14.20151126v1?rss=1 doi: 10.1101/2020.07.14.20151126 id: cord-262328-q7mt0xve author: Wajnberg, Ania title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 words: 4419.0 sentences: 216.0 pages: flesch: 54.0 cache: ./cache/cord-262328-q7mt0xve.txt txt: ./txt/cord-262328-q7mt0xve.txt summary: In this observational study, we ran an outreach programme in the New York City (NY, USA) area, including parts of Connecticut and New Jersey, to identify people who had recovered from SARS-CoV-2 infection for nasopharyngeal PCR (cobas 6800; Roche Diagnostics, Indianapolis, IN, USA) and serum IgG titre measurement (ELISA; Icahn School of Medicine at Mount Sinai, New York, NY, USA). We did not find reports of ELISA antibody assays as large as this one from areas with major COVID-19 hotspots, and found mixed and growing reports of IgG response to and PCR positivity for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over time. In the 584 participants for whom both nasopharyngeal PCR testing and serum antibody testing was available, SARS-CoV-2 RNA was detected in 249 (43%) at a median of 20 days (IQR 18-23) from symptom onset and 12 days (9-14) from symptom resolution. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. The proportion of infected individuals who seroconvert is still an open question. In addition, it has been shown in some individuals that viral genome can be detected up to 3 months after symptom resolution. We investigated both seroconversion and PCR positivity in a large cohort of convalescent serum donors in the New York City (NY, USA) region. METHODS: In this observational study, we ran an outreach programme in the New York City area. We recruited participants via the REDCap (Vanderbilt University, Nashville, TN, USA) online survey response. Individuals with confirmed or suspected SARS-CoV-2 infection were screened via PCR for presence of viral genome and via ELISA for presence of anti-SARS-CoV-2 spike antibodies. One-way ANOVA and Fisher's exact test were used to measure the association of age, gender, symptom duration, and days from symptom onset and resolution with positive antibody results. FINDINGS: Between March 26 and April 10, 2020, we measured SARS-CoV-2 antibody titres in 1343 people. Of the 624 participants with confirmed SARS-CoV-2 infection who had serologies done after 4 weeks, all but three seroconverted to the SARS-CoV-2 spike protein, whereas 269 (37%) of 719 participants with suspected SARS-CoV-2 infection seroconverted. PCR positivity was detected up to 28 days from symptom resolution. INTERPRETATION: Most patients with confirmed COVID-19 seroconvert, potentially providing immunity to reinfection. We also report that in a large proportion of individuals, viral genome can be detected via PCR in the upper respiratory tract for weeks after symptom resolution, but it is unclear whether this signal represents infectious virus. Analysis of our large cohort suggests that most patients with mild COVID-19 seroconvert 4 weeks after illness, and raises questions about the use of PCR to clear positive individuals. FUNDING: None. url: https://www.ncbi.nlm.nih.gov/pubmed/33015652/ doi: 10.1016/s2666-5247(20)30120-8 id: cord-015181-875gf11z author: Walgate, Robert title: SARS escaped Beijing lab twice date: 2004-04-27 words: 614.0 sentences: 42.0 pages: flesch: 71.0 cache: ./cache/cord-015181-875gf11z.txt txt: ./txt/cord-015181-875gf11z.txt summary: Email: Walgate@scienceanalysed.com The latest outbreak of severe acute respiratory syndrome (SARS) in China, with eight confirmed or suspected cases so far and hundreds quarantined, involves two researchers who were working with the virus in a Beijing research lab, the World Health Organization (WHO) said on Monday (April 26). "We suspect two people, a 26-year-old female postgraduate student and a 31-year-old male postdoc, were both infected, apparently in two separate incidents," Bob Dietz, WHO spokesman in Beijing, told us. China has level three research guidelines and rules in place for handling the SARS virus, which are "of acceptable quality" to WHO, Dietz told us. They are going to go into the labs with Ministry of Health people and find out what happened here," Dietz said. " We''ve been told we''ll have full access, be able to test all the surfaces, interview people who worked there, and look at documentation to find out what was being done," Dietz said. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7096887/ doi: 10.1186/gb-spotlight-20040427-03 id: cord-015183-1eytelxn author: Walgate, Robert title: Latest SARS evidence date: 2003-04-07 words: 1055.0 sentences: 68.0 pages: flesch: 71.0 cache: ./cache/cord-015183-1eytelxn.txt txt: ./txt/cord-015183-1eytelxn.txt summary: The outbreak of SARS (Severe Acute Respiratory Syndrome) that originated in China is, with "95-97% certainty," caused by a completely new type of coronavirus, according to Julie Hall, who is responsible for the World Health Organization''s Global Alert, Response and Operations Network. In patients, we''d also like to see the curves of IgM [specific to this virus], to show people have an acute response, and then IgG, which takes two to three weeks to level up, and stays with you, to show that it wasn''t just a passing extraneous infection." Moreover "We have lots of blood samples to test this in now," Hall said, so the results should not be long coming. Günther said he and Drosten had isolated three short DNA sequences from the coronavirus in a tissue sample from the "index case" (first case) of SARS in Germany, by a random amplification, lowstringency PCR approach. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7096924/ doi: 10.1186/gb-spotlight-20030407-01 id: cord-326198-6okk3u49 author: Walker, A. title: Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events date: 2020-04-30 words: 1943.0 sentences: 94.0 pages: flesch: 46.0 cache: ./cache/cord-326198-6okk3u49.txt txt: ./txt/cord-326198-6okk3u49.txt summary: An analysis (Supplementary Text) of other publicly available SARS-CoV-2 sequences did not reveal an obvious origin of the Heinsberg outbreak (Supplementary Table S4 ); the Heinsberg isolates are not related to early sequences from other German outbreak areas (Bavaria, Baden Wuerttemberg), and, despite intense Dutch viral sampling efforts (585 available viral genomes from the Netherlands at the time of analysis), our analysis identified only 2 closely related isolates from the Netherlands (one collected on 21 st March, the other with undefined collection date). A minimum spanning tree analysis of unambiguously resolved viral sequences ( Figure 1 ) showed that there were at least 5 clusters of viral haplotypes circulating in the Düsseldorf area; the number of variant positions relative to the SARS-CoV-2 reference genome in the Düsseldorf samples varied between 2 and 13 (Supplementary Table 2 ). abstract: We whole-genome sequenced 55 SARS-CoV-2 isolates from Western Germany and investigated the genetic structure of SARS-CoV-2 outbreaks in the Heinsberg district and Dusseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflective of superspreading dynamics during the carnival season, distinct viral strains are circulating in Dusseldorf, reflecting the city's international links. Limited detection of Heinsberg strains in the Dusseldorf area despite geographical proximity may reflect efficient containment and contact tracing efforts. url: http://medrxiv.org/cgi/content/short/2020.04.25.20079517v1?rss=1 doi: 10.1101/2020.04.25.20079517 id: cord-314107-x6e1jhcd author: Walker, M. title: SARS-CoV-2 Infection and Stroke: Coincident or Causal? date: 2020-07-29 words: 656.0 sentences: 44.0 pages: flesch: 55.0 cache: ./cache/cord-314107-x6e1jhcd.txt txt: ./txt/cord-314107-x6e1jhcd.txt summary: Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Consistent with global reports, we observed a regional reduction in overall stroke volume during the COVID-19 pandemic peak. Surprisingly, less than 0.1% of patients suffered coincident SARS-CoV-2 infection and ischemic stroke. We also found no association between SARS-CoV-2 infection and stroke in younger patients. Similarly, a retrospective review in the UK during this same period [4] failed to identify a causal relationship in six patients with large vessel strokes and coincident SARS-CoV-2 infection because competing vascular risk factors were present. Regional data from five U.S. states suggests that among patients who sought care or were hospitalized during the peak of COVID-19, acute ischemic stroke in the setting of SARS-CoV-2 infection is rare and may be coincident. Large-Vessel Stroke as a Presenting Feature of Covid-19 in the Young abstract: Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Data collected during peak of the Covid-19 pandemic from stroke centers in five states reveal few similarities to what has recently been published. Given the diversity in phenotype, we caution policymakers and health care providers when considering cerebrovascular complications from SARS-CoV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.07.17.20156463v1?rss=1 doi: 10.1101/2020.07.17.20156463 id: cord-293382-uyat0w58 author: Walker, Susanne N. title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients date: 2020-10-21 words: 4793.0 sentences: 274.0 pages: flesch: 55.0 cache: ./cache/cord-293382-uyat0w58.txt txt: ./txt/cord-293382-uyat0w58.txt summary: title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients The first assay is surface plasmon resonance (SPR) based and can quantitate both antibody binding to the SARS-CoV-2 spike protein and blocking to the Angiotensin-converting enzyme 2 (ACE2) receptor in a single experiment. The second assay is enzyme-linked immunosorbent assay (ELISA) based and can measure competition and blocking of the ACE2 receptor to the SARS-CoV-2 spike protein with antispike antibodies. Four of the six guinea pigs immunized against SARS-CoV-2 spike showed statistically significant ACE2 blocking, and importantly, the pooled sera was comparable to the average AUC from all six serum samples (Fig. 3F, Fig. S2D ). First, we showed that an ELISA-based assay could be employed to measure receptor blocking antibodies in animals vaccinated with the SARS-CoV-2 spike protein. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of COVID-19, resulting in cases of mild to severe respiratory distress and significant mortality. The global outbreak of this novel coronavirus has now infected >20 million people worldwide, with >5 million cases in the United States (11 August 2020). The development of diagnostic and research tools to determine infection and vaccine efficacy is critically needed. We have developed multiple serologic assays using newly designed SARS-CoV-2 reagents for detecting the presence of receptor-binding antibodies in sera. The first assay is surface plasmon resonance (SPR) based and can quantitate both antibody binding to the SARS-CoV-2 spike protein and blocking to the Angiotensin-converting enzyme 2 (ACE2) receptor in a single experiment. The second assay is enzyme-linked immunosorbent assay (ELISA) based and can measure competition and blocking of the ACE2 receptor to the SARS-CoV-2 spike protein with antispike antibodies. The assay is highly versatile, and we demonstrate the broad utility of the assay by measuring antibody functionality of sera from small animals and nonhuman primates immunized with an experimental SARS-CoV-2 vaccine. In addition, we employ the assay to measure receptor blocking of sera from SARS-CoV-2-infected patients. The assay is shown to correlate with pseudovirus neutralization titers. This type of rapid, surrogate neutralization diagnostic can be employed widely to help study SARS-CoV-2 infection and assess the efficacy of vaccines. url: https://doi.org/10.1128/jcm.01533-20 doi: 10.1128/jcm.01533-20 id: cord-318938-7d731q65 author: Wallentin, Lars title: Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation date: 2020-09-27 words: 4630.0 sentences: 229.0 pages: flesch: 43.0 cache: ./cache/cord-318938-7d731q65.txt txt: ./txt/cord-318938-7d731q65.txt summary: In unadjusted analyses and after adjustment for clinical variables and medical treatment, male sex, diabetes, congestive heart failure, prior myocardial infarction, and age were consistently associated with higher sACE2 levels in both cohorts ( Figure 3A ; Supplementary material online, Table S2 ). The results showed that higher levels of sACE2 were associated with male sex, cardiovascular disease, diabetes, and older age, which are also the main risk factors for complications and mortality of COVID-19 infections. The indication that male sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes might be associated with a specific mechanism leading to higher risk of more severe SARS-CoV-2 infection might be useful for risk stratification concerning COVID-19. The close association between biomarkers and the sACE2 level suggests that biological ageing and cardiovascular disease and dysfunction might lead to increased ACE2 expression and a potentially higher risk for SARS-CoV-2 binding and more severe COVID-19 infection. abstract: AIMS: The global COVID-19 pandemic is caused by the SARS-CoV-2 virus entering human cells using angiotensin-converting enzyme 2 (ACE2) as a cell surface receptor. ACE2 is shed to the circulation, and a higher plasma level of soluble ACE2 (sACE2) might reflect a higher cellular expression of ACE2. The present study explored the associations between sACE2 and clinical factors, cardiovascular biomarkers, and genetic variability. METHODS AND RESULTS: Plasma and DNA samples were obtained from two international cohorts of elderly patients with atrial fibrillation (n = 3999 and n = 1088). The sACE2 protein level was measured by the Olink Proteomics(®) Multiplex CVD II(96 × 96) panel. Levels of the biomarkers high-sensitive cardiac troponin T (hs-cTnT), N-terminal probrain natriuretic peptide (NT-proBNP), growth differentiation factor 15 (GDF-15), C-reactive protein, interleukin-6, D-dimer, and cystatin-C were determined by immunoassays. Genome-wide association studies were performed by Illumina chips. Higher levels of sACE2 were statistically significantly associated with male sex, cardiovascular disease, diabetes, and older age. The sACE2 level was most strongly associated with the levels of GDF-15, NT-proBNP, and hs-cTnT. When adjusting for these biomarkers, only male sex remained associated with sACE2. We found no statistically significant genetic regulation of the sACE2 level. CONCLUSIONS: Male sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes are associated with higher sACE2 levels. The levels of GDF-15 and NT-proBNP, which are associated both with the sACE2 level and a higher risk for mortality and cardiovascular disease, might contribute to better identification of risk for severe COVID-19 infection. url: https://doi.org/10.1093/eurheartj/ehaa697 doi: 10.1093/eurheartj/ehaa697 id: cord-310195-am3u7z76 author: Waller, J. title: Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date: 2020-05-10 words: 4813.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-310195-am3u7z76.txt txt: ./txt/cord-310195-am3u7z76.txt summary: Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. This study was designed to test two hypotheses: describing a test indicating the presence of antibodies using the term Immunity (vs Antibody), and describing test results as Passports or Certificates (vs Test), increases the likelihood that those with this test result erroneously perceive they have no risk of becoming infected in the future with coronavirus. . https://doi.org/10.1101/2020.05.06.20093401 doi: medRxiv preprint Primary outcome Proportion of participants perceiving an antibody-positive test result to mean no risk of catching coronavirus in the future, assessed in response to a question with four response options. abstract: Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Design: 2 by 3 experimental design. Setting: Online with data collected between 28th April and 1st May 2020. Participants: 1,204 adults registered with a UK research panel. Intervention: Participants were randomised to receive one of six descriptions of an antibody test and results showing SARS-CoV-2 antibodies, differing in the terms used to describe the type of test (Immunity vs Antibody) and the test result (Passport vs Certificate vs Test). Main outcome measures: The primary outcome was the proportion of participants perceiving no risk of becoming infected with SARS-CoV-2 given an antibody positive test result. Other outcomes include intended changes to frequency of hand washing and physical distancing. Results: When using the term Immunity (vs Antibody), 19.1% of participants [95% CI: 16.1 to 22.5] (vs 9.8% [95% CI: 7.5 to 12.4]) perceived no risk of catching coronavirus at some point in the future given an antibody-positive test result (AOR: 2.91 [95% CI: 1.52 to 5.55]). Using the terms Passport or Certificate, as opposed to Test, had no significant effect (AOR: 1.24 [95% CI: 0.62 to 2.48] and AOR: 0.96 [95% CI: 0.47 to 1.99] respectively). There was no significant interaction between the effects of the test and result terminology. Across groups, perceiving no risk of infection was associated with an intention to wash hands less frequently (AOR: 2.32 [95% CI: 1.25 to 4.28]) but there was no significant association with intended avoidance of physical contact with others outside of the home (AOR: 1.37 [95% CI: 0.93 to 2.03]). Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. The way antibody testing is described may have implications for the likely impact of testing on transmission rates. url: https://doi.org/10.1101/2020.05.06.20093401 doi: 10.1101/2020.05.06.20093401 id: cord-322834-rl6yum7n author: Wallinga, Jacco title: Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures date: 2004-09-15 words: 4139.0 sentences: 185.0 pages: flesch: 46.0 cache: ./cache/cord-322834-rl6yum7n.txt txt: ./txt/cord-322834-rl6yum7n.txt summary: The available epidemic curves for SARS show marked differences between the affected regions with respect to the total number of cases and epidemic duration, even for those regions in which outbreaks started almost simultaneously and similar control measures were implemented at the same time. In this paper, we interpret the observed epidemic curves with regard to disease transmission potential and effectiveness of control measures, and we compare the epidemiologic profiles of SARS outbreaks in Hong Kong, Vietnam, Singapore, and Canada. The model uses values of k t = 0.18 for cases with a symptom onset date before March 12, 2003 , and k t = 0.08 for cases with a symptom onset date on or after March 12, 2003 ; these values correspond to the distribution of the number of secondary infections per case as observed during the severe acute respiratory syndrome (SARS) outbreak in Singapore (4). abstract: Severe acute respiratory syndrome (SARS) has been the first severe contagious disease to emerge in the 21st century. The available epidemic curves for SARS show marked differences between the affected regions with respect to the total number of cases and epidemic duration, even for those regions in which outbreaks started almost simultaneously and similar control measures were implemented at the same time. The authors developed a likelihood-based estimation procedure that infers the temporal pattern of effective reproduction numbers from an observed epidemic curve. Precise estimates for the effective reproduction numbers were obtained by applying this estimation procedure to available data for SARS outbreaks that occurred in Hong Kong, Vietnam, Singapore, and Canada in 2003. The effective reproduction numbers revealed that epidemics in the various affected regions were characterized by markedly similar disease transmission potentials and similar levels of effectiveness of control measures. In controlling SARS outbreaks, timely alerts have been essential: Delaying the institution of control measures by 1 week would have nearly tripled the epidemic size and would have increased the expected epidemic duration by 4 weeks. url: https://www.ncbi.nlm.nih.gov/pubmed/15353409/ doi: 10.1093/aje/kwh255 id: cord-308428-zw26usmh author: Walter, Justin D. title: Highly potent bispecific sybodies neutralize SARS-CoV-2 date: 2020-11-10 words: 10526.0 sentences: 580.0 pages: flesch: 54.0 cache: ./cache/cord-308428-zw26usmh.txt txt: ./txt/cord-308428-zw26usmh.txt summary: Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. However, binders of the isolated RBD may not effectively engage the aforementioned pre-fusion conformation of the spike protein, which could account for the poor neutralization ability of recently described single-domain antibodies that were raised against the RBD of SARS-CoV-2 spike protein [29] . Since Sb#15 and Sb#68 can bind simultaneously to the RBD and the full-length spike protein, we mixed Sb#15 and Sb#68 together to investigate potential additive or synergistic neutralizing activity of these two independent sybodies. To gain structural insights into how Sb#15 and Sb#68 recognize the RBD, we performed single particle cryo-EM analysis of the spike protein in complex with the sybodies. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 abstract: The COVID-19 pandemic has resulted in a global crisis. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. Cryo-EM analyses of the spike protein in complex with both sybodies revealed symmetrical and asymmetrical conformational states. In the symmetric complex each of the three RBDs were bound by both sybodies, and adopted the up conformation. The asymmetric conformation, with three Sb#15 and two Sb#68 bound, contained one down RBD, one up-out RBD and one up RBD. Bispecific fusions of the sybodies increased the neutralization potency 100-fold, as compared to the single binders. Our work demonstrates that linking two binders that recognize spatially-discrete binding sites result in highly potent SARS-CoV-2 inhibitors for potential therapeutic applications. url: https://doi.org/10.1101/2020.11.10.376822 doi: 10.1101/2020.11.10.376822 id: cord-318444-sgm24q1i author: Walter, Justin D. title: Sybodies targeting the SARS-CoV-2 receptor-binding domain date: 2020-05-16 words: 5902.0 sentences: 416.0 pages: flesch: 49.0 cache: ./cache/cord-318444-sgm24q1i.txt txt: ./txt/cord-318444-sgm24q1i.txt summary: Two independently prepared RBD constructs were used for in vitro sybody selections, and resulting single clones that could bind the full spike ectodomain were sequenced, expressed, and purified. Six unique sybodies show favorable binding affinity to the SARS-CoV-2 spike, and five of these were also found to substantially attenuate the interaction between the viral RBD and human ACE2. While this purified pre-fusion spike (PFS) had not yet been available for binder selections and characterization by grating-coupled interferometry, it was used to conduct ELISAs in order to identify selected sybodies which recognize the RBD in the pre-fusion context (see below). Since virulence of SARS-CoV-2 is dependent on the ability of the viral RBD to bind to human ACE2 (hACE2), we sought to determine which of the 57 selected sybodies that were well-behaved upon purification could inhibit interaction between the isolated RBD and purified hACE2. abstract: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has resulted in a global health and economic crisis of unprecedented scale. The high transmissibility of SARS-CoV-2, combined with a lack of population immunity and prevalence of severe clinical outcomes, urges the rapid development of effective therapeutic countermeasures. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2. In an expeditious process taking only twelve working days, sybodies were selected entirely in vitro from three large combinatorial libraries, using ribosome and phage display. We obtained six strongly enriched sybody pools against the isolated RBD and identified 63 unique anti-RBD sybodies which also interact in the context of the full-length SARS-CoV-2 spike ectodomain. Among the selected sybodies, six were found to bind to the viral spike with double-digit nanomolar affinity, and five of these also showed substantial inhibition of RBD interaction with human angiotensin-converting enzyme 2 (ACE2). Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. It is anticipated that compact binders such as these sybodies could feasibly be developed into an inhalable drug that can be used as a convenient prophylaxis against COVID-19. Moreover, generation of polyvalent antivirals, via fusion of anti-RBD sybodies to additional small binders recognizing secondary epitopes, could enhance the therapeutic potential and guard against escape mutants. We present full sequence information and detailed protocols for the identified sybodies, as a freely accessible resource. url: https://doi.org/10.1101/2020.04.16.045419 doi: 10.1101/2020.04.16.045419 id: cord-255940-chb4iuis author: Walton, David A. title: Facility-Level Approaches for COVID-19 When Caseload Surpasses Surge Capacity date: 2020-06-26 words: 1801.0 sentences: 99.0 pages: flesch: 49.0 cache: ./cache/cord-255940-chb4iuis.txt txt: ./txt/cord-255940-chb4iuis.txt summary: We present two COVID-19 treatment center designs that leverage lessons learned from previous outbreaks of communicable infectious diseases and provide potential solutions when caseload exceeds existing capacity, with and without access to SARS-CoV-2 testing. These designs are intended for settings in which health facilities and testing resources for COVID-19 are surpassed during the pandemic, are adaptable to local conditions and constraints, and mitigate the likelihood of nosocomial transmission while offering an option to care for hospitalized patients. To respond to the immediate crisis facing health workers and patients, we propose a COVID-19 treatment center design ( Figure 1 ) that harnesses lessons learned from other outbreaks and adheres to infection prevention and control principles recommended by the WHO for the novel coronavirus. The design assumes that two thresholds have been reached: first, the health center no longer has space to individually isolate COVID-19 patients, and second, laboratory capacity is limited or surpassed, such that rapid, accurate testing for COVID-19 may not be available, as is the reality facing our colleagues in Haiti. abstract: As COVID-19 cases continue to increase globally, fragile health systems already facing challenges with health system infrastructure, SARS-CoV-2 diagnostic capacity, and patient isolation capabilities may be left with few options to effectively care for acutely ill patients. Haiti—with only two laboratories that can perform reverse transcriptase PCR for SARS-CoV-2, a paucity of hospital beds, and an exponential increase in cases—provides an example that underpins the need for immediate infrastructure solutions for the crisis. We present two COVID-19 treatment center designs that leverage lessons learned from previous outbreaks of communicable infectious diseases and provide potential solutions when caseload exceeds existing capacity, with and without access to SARS-CoV-2 testing. These designs are intended for settings in which health facilities and testing resources for COVID-19 are surpassed during the pandemic, are adaptable to local conditions and constraints, and mitigate the likelihood of nosocomial transmission while offering an option to care for hospitalized patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32597389/ doi: 10.4269/ajtmh.20-0681 id: cord-257142-q79yy6o5 author: Wambier, Carlos Gustavo title: Androgen sensitivity gateway to COVID‐19 disease severity date: 2020-05-15 words: 3188.0 sentences: 172.0 pages: flesch: 43.0 cache: ./cache/cord-257142-q79yy6o5.txt txt: ./txt/cord-257142-q79yy6o5.txt summary: Similarly, we believe that shorter CAG repeats in the androgen receptor gene may be associated with increased COVID-19 disease severity and mortality. A spectrum of androgenic activity would imply in polar pauciviral COVID-19 (e.g., children < 7), with null airway/fecal transmission potential, women with normal androgen activity would have low transmission potential (borderline pauciviral COVID-19), male teenagers and adults would have high transmission potential (borderline multiviral , and infected individuals with abnormally high androgen receptor activity (genetic or acquired) would represent the multiviral COVID-19 pole of the spectrum, with extremely high transmission To further test this hypothesis, it would be interesting to observe for severe COVID cases in female patients who present with increase androgens, for example, females with metabolic syndrome, or whom are using birth control methods with progestogen hormones that bind to androgen receptor. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated abstract: In this communication, we present arguments for androgen sensitivity as a likely determinant of COVID‐19 disease severity. The androgen sensitivity model explains why males are more likely to develop severe symptoms while children are ostensibly resistant to infection. Further, the model explains the difference in COVID‐19 mortality rates among different ethnicities. Androgen sensitivity is determined by genetic variants of the androgen receptor. The androgen receptor regulates transcription of the transmembrane protease, serine 2 (TMPRSS2), which is required for SARS‐CoV‐2 infectivity. TMPRSS2 primes the Spike protein of the virus, which has two consequences: diminishing viral recognition by neutralizing antibodies and activating SARS‐CoV‐2 for virus‐cell fusion. Genetic variants that have been associated with androgenetic alopecia, prostate cancer, benign prostatic hyperplasia and polycystic ovary syndrome could be associated with host susceptibility. In addition to theoretical epidemiological and molecular mechanisms, there are reports of high rates of androgenetic alopecia of from hospitalized COVID‐19 patients due to severe symptoms. Androgen sensitivity is a likely determinant of COVID‐19 disease severity. We believe that the evidence presented in this communication warrants the initiation of trials using anti‐androgen agents. url: https://doi.org/10.1002/ddr.21688 doi: 10.1002/ddr.21688 id: cord-352934-ypls4zau author: Wan, Jinkai title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date: 2020-07-03 words: 2406.0 sentences: 151.0 pages: flesch: 59.0 cache: ./cache/cord-352934-ypls4zau.txt txt: ./txt/cord-352934-ypls4zau.txt summary: title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection We screened sera samples from 11 patients recently recovered from COVID-19, and 119 found all individuals showed certain levels of serological responses, with #507 and 120 #501 being the weakest, to SARS-CoV-2 Spike RBD and S1 proteins ( Figure 1A ). We 121 also found that 10 sera, except for 507, showed neutralization abilities against 122 SARS-CoV-2 pseudoviral infection of HEK293T cells stably expressing human ACE2 123 ( Figure 1B ). In order to screen for SARS-CoV-2 spike antigen specific monoclonal antibodies, we 143 used two primary assays based on ELISA (enzyme linked immunosorbent assay) and 144 FCA (flow cytometry assay), respectively. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin 561 converting enzyme 2 receptor A potent neutralizing human antibody reveals the N-terminal domain of the 564 Spike protein of SARS-CoV-2 as a site of vulnerability Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific 612 human monoclonal antibody abstract: Summary COVID-19 has become a worldwide threat to humans, and neutralizing antibodies have therapeutic potential. We have purified more than one thousand memory B cells specific to SARS-CoV-2 S1 or RBD (receptor binding domain), and obtain 729 paired heavy and light chain fragments. Among these, 178 antibodies test positive for antigen binding, and the majority of the top 17 binders with EC50 below 1 nM are RBD binders. Furthermore, we identify 11 neutralizing antibodies, 8 of which show an IC50 within 10 nM, and the best one, 414-1, with IC50 of 1.75 nM. Through epitope mapping, we find 3 main epitopes in RBD recognized by these antibodies, and epitope B antibody 553-15 could substantially enhance the neutralizing abilities of most of the other antibodies. We also find that 515-5 could cross-neutralize the SARS-CoV pseudovirus. Altogether, our study provides 11 potent human neutralizing antibodies for COVID-19 as therapeutic candidates. url: https://api.elsevier.com/content/article/pii/S2211124720308998 doi: 10.1016/j.celrep.2020.107918 id: cord-305263-fgwf6wy3 author: Wang, Ben X. title: The yin and yang of viruses and interferons date: 2012-02-07 words: 6285.0 sentences: 294.0 pages: flesch: 38.0 cache: ./cache/cord-305263-fgwf6wy3.txt txt: ./txt/cord-305263-fgwf6wy3.txt summary: IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. abstract: Interferons (IFNs)-α/β are critical effectors of the innate immune response to virus infections. Through activation of the IFN-α/β receptor (IFNAR), they induce expression of IFN-stimulated genes (ISGs) that encode antiviral proteins capable of suppressing viral replication and promoting viral clearance. Many highly pathogenic viruses have evolved mechanisms to evade an IFN response and the balance between the robustness of the host immune response and viral antagonistic mechanisms determines whether or not the virus is cleared. Here, we discuss IFNs as broad-spectrum antivirals for treatment of acute virus infections. In particular, they are useful for treatment of re-emerging virus infections, where direct-acting antivirals (DAAs) have limited utility due to DAA-resistant mutations, and for newly emerging virus strains in which the time to vaccine availability precludes vaccination at the onset of an outbreak. url: https://doi.org/10.1016/j.it.2012.01.004 doi: 10.1016/j.it.2012.01.004 id: cord-306486-y6a4u0vh author: Wang, Bin title: Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients date: 2020-05-05 words: 847.0 sentences: 52.0 pages: flesch: 50.0 cache: ./cache/cord-306486-y6a4u0vh.txt txt: ./txt/cord-306486-y6a4u0vh.txt summary: 5 To fulfill the pressing need, we examined antibody generation and virus clearance in 26 patients with SARS-CoV-2-induced COVID-19. Thus, this is the first report to state that innate immunity plays an essential role in SARS-CoV-2 clearance, which The disease severity and fatality were increased with age in COVID-19 patients, which may be explained by the augmentation of proinflammatory responses and the reduction of antiviral cytokines in elder individuals. Taken together, we showed that SARS-CoV-2 could coexist with virus-specific IgG antibodies in COVID-19 patients for an unexpectedly long time and, without adaptive immunity, innate immunity may still be powerful enough to eliminate SARS-CoV-2. The long-term coexistence of IgG with SARS-CoV-2 in the human body raises the question of whether patients with antibodies are still at risk for reinfection, which may make COVID-19 "immunity passports" Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients abstract: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection causing coronavirus disease 2019 (COVID‐19) has spread worldwide. Whether antibodies are important for the adaptive immune responses against SARS‐CoV‐2 infection needs to be determined. Here, 26 cases of COVID‐19 in Jinan, China, were examined and shown to be mild or with common clinical symptoms, and no case of severe symptoms was found among these patients. Strikingly, a subset of these patients had SARS‐CoV‐2 and virus‐specific IgG coexist for an unexpectedly long time, with two cases for up to 50 days. One COVID‐19 patient who did not produce any SARS‐CoV‐2–bound IgG successfully cleared SARS‐CoV‐2 after 46 days of illness, revealing that without antibody‐mediated adaptive immunity, innate immunity alone may still be powerful enough to eliminate SARS‐CoV‐2. This report may provide a basis for further analysis of both innate and adaptive immunity in SARS‐CoV‐2 clearance, especially in nonsevere cases. url: https://doi.org/10.1002/jmv.25946 doi: 10.1002/jmv.25946 id: cord-274668-lh7c9izt author: Wang, Chaofu title: Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients date: 2020-06-20 words: 4584.0 sentences: 253.0 pages: flesch: 45.0 cache: ./cache/cord-274668-lh7c9izt.txt txt: ./txt/cord-274668-lh7c9izt.txt summary: BACKGROUND: The novel coronavirus pneumonia COVID-19 caused by SARS-CoV-2 infection could lead to a serious of clinical symptoms and severe illness, including acute respiratory distress syndrome (ARDS) and fatal organ failure. INTERPRETATION: Infection of Alveolar macrophage by SARS-CoV-2 might be drivers of the "cytokine storm", which might result in damages in pulmonary tissues, heart and lung, and leading to the failure of multiple organs . One case report showed the pathological characteristics of a patient who died from severe infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by postmortem biopsies. Moreover, type II alveolar epithelial cells and macrophages in alveoli and pulmonary hilum lymphoid tissue were infected by SARS-CoV-2, as revealed by immunohistochemistry using Rp3-NP specific antibodies (Figs. [10] In the case of COVID-19, the viral infection of aggregated alveolar macrophages was obvious from early phase to the late stage, according to our study and the results in recent reports of pulmonary pathology [17, 20] . abstract: BACKGROUND: The novel coronavirus pneumonia COVID-19 caused by SARS-CoV-2 infection could lead to a serious of clinical symptoms and severe illness, including acute respiratory distress syndrome (ARDS) and fatal organ failure. We report the fundamental pathological investigation in the lungs and other organs of fatal cases for the mechanistic understanding of severe COVID-19 and the development of specific therapy in these cases. METHODS: The autopsy and pathological investigations of specimens were performed on bodies of two deceased cases with COVID-19. Gross anatomy and histological investigation by Hematoxylin and eosin (HE) stained were reviewed on each patient. Alcian blue/periodic acid-Schiff (AB-PAS) staining and Masson staining were performed for the examinations of mucus, fibrin and collagen fiber in lung tissues. Immunohistochemical staining were performed on the slides of lung tissues from two patients. Real-time PCR was performed to detect the infection of SARS-CoV-2. Flow cytometry analyses were performed to detect the direct binding of S protein and the expression of ACE2 on the cell surface of macrophages. FINDINGS: The main pathological features in lungs included extensive impairment of type I alveolar epithelial cells and atypical hyperplasia of type II alveolar cells, with formation of hyaline membrane, focal hemorrhage, exudation and pulmonary edema, and pulmonary consolidation. The mucous plug with fibrinous exudate in the alveoli and the dysfunction of alveolar macrophages were characteristic abnormalities. The type II alveolar epithelial cells and macrophages in alveoli and pulmonary hilum lymphoid tissue were infected by SARS-CoV-2. S protein of SARS-CoV-2 directly bound to the macrophage via the S-protein-ACE2 interaction. INTERPRETATION: Infection of Alveolar macrophage by SARS-CoV-2 might be drivers of the “cytokine storm”, which might result in damages in pulmonary tissues, heart and lung, and leading to the failure of multiple organs . FUNDING: Shanghai Guangci Translational Medical Research Development Foundation, Shanghai, China url: https://www.sciencedirect.com/science/article/pii/S2352396420302085 doi: 10.1016/j.ebiom.2020.102833 id: cord-253035-tijcxtwx author: Wang, Chen title: A novel coronavirus outbreak of global health concern date: 2020-01-24 words: 1834.0 sentences: 92.0 pages: flesch: 45.0 cache: ./cache/cord-253035-tijcxtwx.txt txt: ./txt/cord-253035-tijcxtwx.txt summary: Early in the SARS coronavirus outbreak, frontline health workers became infected, which amplified transmission to patients in hospitals where outbreaks were occurring. 4 Early evidence from the initial MERS outbreaks suggested that health workers were likewise being infected, but that their infections were less severe than those of patients in hospitals who became infected and had comorbidities such as diabetes or chronic respiratory disease. 3 In The Lancet, Chaolin Huang and colleagues 7 report clinical features of the first 41 patients admitted to the designated hospital in Wuhan who were confirmed to be infected with 2019-nCoV by Jan 2, 2020. Considering that substantial numbers of patients with SARS and MERS were infected in health-care settings, precautions need to be taken to prevent nosocomial spread of the virus. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/31986257/ doi: 10.1016/s0140-6736(20)30185-9 id: cord-349656-baoqgu8v author: Wang, Chen title: Intrauterine vertical transmission of SARS‐CoV‐2: what we know so far date: 2020-04-07 words: 735.0 sentences: 62.0 pages: flesch: 68.0 cache: ./cache/cord-349656-baoqgu8v.txt txt: ./txt/cord-349656-baoqgu8v.txt summary: [2] In a study by Chen et al., [3] paired neonatal pharyngeal swab samples and placental tissues of three pregnant women with COVID-19 were used as samples to evaluate the potential risk of intrauterine vertical transmission, and all samples tested negative for SARS-CoV-2 RNA. Notably, a neonate born to a pregnant woman with COVID-19 tested positive for SARS-CoV-2 RNA in the pharyngeal swab sample at 36 hours after birth was subsequently confirmed that the qRT-PCR testing of the placenta and cord blood was negative for SARS-CoV-2, suggesting that intrauterine vertical transmission might not have occurred. Furthermore, in a cohort study by Zeng et al., [13] 3 of 33 (9%) infants were diagnosed with neonatal early-onset infection with SARS-CoV-2 based on positive qRT-PCR results of the nasopharyngeal and anal swabs in two consecutive tests at day 2 and 4 of age. Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32266753/ doi: 10.1002/uog.22045 id: cord-351115-dy81dtnk author: Wang, Chen title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 words: 6133.0 sentences: 310.0 pages: flesch: 50.0 cache: ./cache/cord-351115-dy81dtnk.txt txt: ./txt/cord-351115-dy81dtnk.txt summary: This study addresses both by utilizing evolutionary information from SARS-CoV-2 sequence and structural data to search for actionable functional sites for each protein in the SARS-CoV-2 genome. Here we systematically suggest potential drug target sites for most SARS-CoV-2 proteins based on evolutionary information. This relative ranking re ects the variation entropy of each sequence position within and across the branches of an associated phylogenetic tree, revealing evolutionary pressure points that correspond to functional and structural determinants, and the protein sites at which they often cluster (30) . As in our approach to discover ET drug sites, we combined ET residue ranking information with sequencing data from SARS-CoV-2 isolates to arrive at linear peptides along the proteome that are evolutionarily important and also show little variation in the current outbreak ( Figure S6 , Dataset S5). The data include, for example, multiple sequence alignments, precalculated ET ranks, and predicted epitopes (both linear and structural) for all SARS-CoV-2 proteins. abstract: Since the first recognized case of COVID-19, more than 30 million people have been infected worldwide. Despite global efforts in drug and vaccine development to fight the disease, there is currently no vaccine or drug cure for COVID-19, though some drugs reduce severity and hasten recovery. Here we interrogate the evolutionary history of the entire SARS-CoV-2 proteome to identify functional sites that can inform the search for treatments. Combining this information with the mutations observed in the current COVID-19 outbreak, we systematically and comprehensively define evolutionarily stable sites that are useful drug targets. Several experimentally-validated effective drugs interact with these proposed target sites. In addition, the same evolutionary information can prioritize cross reactive antigens that are useful in directing multi-epitope vaccine strategies to illicit broadly neutralizing immune responses to the betacoronavirus family. Although the results are focused on SARS-CoV-2, these approaches are based upon evolutionary principles and are agnostic to organism or infective agent. url: https://doi.org/10.21203/rs.3.rs-95030/v1 doi: 10.21203/rs.3.rs-95030/v1 id: cord-259935-xyo2pe4g author: Wang, Ching-Ying title: SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date: 2017-05-02 words: 4628.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-259935-xyo2pe4g.txt txt: ./txt/cord-259935-xyo2pe4g.txt summary: To examine the association of SARS-CoV PLpro-induced TGF-β1 production with the collagen up-regulation, A549 lung epithelial cells transiently transfected with pcDNA3.1 and pSARS-PLpro were analyzed the production of TGF-β1 and type I collagen using Western blot, realtime RT-PCR and Sirius red staining assays (Fig. 1) . To examine whether SMAD-dependent pathways involve in TGF-β1mediated up-regulation of Type I collagen in response SARS-CoV PLpro, subcellular localization of receptor-regulated SMAD3 and inhibitory SMAD7 in transfected cells were detected using the immunofluorescent and DAPI staining (Fig. 4) . To examine the possible pathways involved in TGF-β1-dependent up-regulation of Type I collagen by SARS-CoV PLpro, the profiles of ubiquitin-conjugated proteins in transfected cells with vector control and pSARS-PLpro were determined using immune-precipitation and nanoLC-MS/MS. Subcellular localization analysis demonstrated that SMAD3 was predominant in cytoplasmic, but not in the nucleus in transfected cells with pSARS-PLpro compared to vector control (Fig. 4) , revealing that canonical Smad-dependent signaling pathway was not involved in PLpro-induced TGF-β1-dependent upregulation of Type I collagen. abstract: SARS coronavirus (CoV) papain-like protease (PLpro) reportedly induced the production of TGF-β1 through p38 MAPK/STAT3-meidated Egr-1-dependent activation (Sci. Rep. 6, 25754). This study investigated the correlation of PLpro-induced TGF-β1 with the expression of Type I collagen in human lung epithelial cells and mouse pulmonary tissues. Specific inhibitors for TGF-βRI, p38 MAPK, MEK, and STAT3 proved that SARS-CoV PLpro induced TGF-β1-dependent up-regulation of Type I collagen in vitro and in vivo. Subcellular localization analysis of SMAD3 and SMAD7 indicated that non-SMAD pathways in TGF-β1 signaling involved in the production of Type I collagen in transfected cells with pSARS-PLpro. Comprehensive analysis of ubiquitin-conjugated proteins using immunoprecipitation and nanoLC–MS/MS indicated that SARS-CoV PLpro caused the change in the ubiquitination profile of Rho GTPase family proteins, in which linked with the increase of Rho-like GTPase family proteins. Moreover, selective inhibitors TGF-βRI and STAT6 (AS1517499) ascertained that STAT6 activation was required for PLpro-induced TGF-β1-dependent up-regulation of Type I collagen in human lung epithelial cells. The results showed that SARS-CoV PLpro stimulated TGF-β1-dependent expression of Type I collagen via activating STAT6 pathway. url: https://www.ncbi.nlm.nih.gov/pubmed/28414040/ doi: 10.1016/j.virusres.2017.04.008 id: cord-320788-ln8ddyuj author: Wang, Chun-Hua title: Persistence of lung inflammation and lung cytokines with high-resolution CT abnormalities during recovery from SARS date: 2005-05-11 words: 4399.0 sentences: 229.0 pages: flesch: 49.0 cache: ./cache/cord-320788-ln8ddyuj.txt txt: ./txt/cord-320788-ln8ddyuj.txt summary: BACKGROUND: During the acute phase of severe acute respiratory syndrome (SARS), mononuclear cells infiltration, alveolar cell desquamation and hyaline membrane formation have been described, together with dysregulation of plasma cytokine levels. In the current study, we conducted a study to examine HRCT changes in patients who recovered from the acute phase of SARS at days 60 and 90, and measured the associated inflammatory profiles directly by examining bronchoalveolar lavage fluid (BALF). At 60 days, compared to normal subjects, there was a significant increase in total cell counts in BAL fluid from SARS patients (Table 3 ) with a significant increase in alveolar macrophages (AM) and lymphocytes., The proportion of CD8+ T cells was increased to a greater extent than CD4+ T cells, leading to a significant decrease in CD4/CD8 ratio (Table 4 ). Coronavirus infected cells were not detected in any of SARS patients with low HRCT score or in normal subjects (Table 1) . abstract: BACKGROUND: During the acute phase of severe acute respiratory syndrome (SARS), mononuclear cells infiltration, alveolar cell desquamation and hyaline membrane formation have been described, together with dysregulation of plasma cytokine levels. Persistent high-resolution computed tomography (HRCT) abnormalities occur in SARS patients up to 40 days after recovery. METHODS: To determine further the time course of recovery of lung inflammation, we investigated the HRCT and inflammatory profiles, and coronavirus persistence in bronchoalveolar lavage fluid (BALF) of 12 patients at recovery at 60 and 90 days. RESULTS: At 60 days, compared to normal controls, SARS patients had increased cellularity of BALF with increased alveolar macrophages (AM) and CD8 cells. HRCT scores were increased and correlated with T-cell numbers and their subpopulations, and inversely with CD4/CD8 ratio. TNF-α, IL-6, IL-8, RANTES and MCP-1 levels were increased. Viral particles in AM were detected by electron microscopy in 7 of 12 SARS patients with high HRCT score. On day 90, HRCT scores improved significantly in 10 of 12 patients, with normalization of BALF cell counts in 6 of 12 patients with repeat bronchoscopy. Pulse steroid therapy and prolonged fever were two independent factors associated with delayed resolution of pneumonitis, in this non-randomized, retrospective analysis. CONCLUSION: Resolution of pneumonitis is delayed in some patients during SARS recovery and may be associated with delayed clearance of coronavirus, Complete resolution may occur by 90 days or later. url: https://www.ncbi.nlm.nih.gov/pubmed/15888207/ doi: 10.1186/1465-9921-6-42 id: cord-283127-jetmocvk author: Wang, Denong title: Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date: 2015-03-12 words: 3983.0 sentences: 212.0 pages: flesch: 45.0 cache: ./cache/cord-283127-jetmocvk.txt txt: ./txt/cord-283127-jetmocvk.txt summary: In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). One intriguing question is whether human viruses of distinct phylogenetic origins, such as HIV-1 and SARS-CoV, may display conserved glycan targets that are suitable for broad virus neutralization. Subsequently, we performed a comparative carbohydrate microarray analysis to characterize the glycan-binding profiles of 2G12 and GNA and to pinpoint specific glyco-epitopes they recognize. To support exploration of the potential GNA glyco-epitopes in this study, we produced a set of comprehensive antigen microarrays, which include a large-panel of carbohydrates, lipids/liposomes, and protein antigens (Supplementary Table S1 ). Using carbohydrate microarrays and ELISA-based viral glycan-profiling analysis, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and lectin GNA. abstract: Identifying molecular targets for eliciting broadly virus-neutralizing antibodies is one of the key steps toward development of vaccines against emerging viral pathogens. Owing to genomic and somatic diversities among viral species, identifying protein targets for broad-spectrum virus neutralization is highly challenging even for the same virus, such as HIV-1. However, viruses rely on host glycosylation machineries to synthesize and express glycans and, thereby, may display common carbohydrate moieties. Thus, exploring glycan-binding profiles of broad-spectrum virus-neutralizing agents may provide key information to uncover the carbohydrate-based virus-neutralizing epitopes. In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. Although these agents were known to be specific for oligomannosyl antigens, they differ strikingly in virus-binding activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). In carbohydrate microarray analyses, we explored the molecular basis underlying the striking differences in the spectrum of anti-virus activities of the two probes. Unlike 2G12, which is strictly specific for the high-density Man(9)GlcNAc(2)Asn (Man9)-clusters, GNA recognizes a number of N-glycan cryptic sugar moieties. These include not only the known oligomannosyl antigens but also previously unrecognized tri-antennary or multi-valent GlcNAc-terminating N-glycan epitopes (Tri/m-Gn). These findings highlight the potential of N-glycan cryptic sugar moieties as conserved targets for broad-spectrum virus neutralization and suggest the GNA-model of glycan-binding warrants focused investigation. url: https://www.ncbi.nlm.nih.gov/pubmed/25774492/ doi: 10.3390/molecules20034610 id: cord-294212-nlekz39f author: Wang, Dongliang title: Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date: 2020-07-03 words: 6072.0 sentences: 305.0 pages: flesch: 54.0 cache: ./cache/cord-294212-nlekz39f.txt txt: ./txt/cord-294212-nlekz39f.txt summary: Linear B-cell epitopes of the SARS-CoV-2 S protein were predicted by BepiPred 2.0 in IEDB (BepiPred 2.0., Immune Epitope Database and Analysis Resource, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA) with a threshold of 0.55 (corresponding specificity > 0.817 and sensitivity < 0.292), and only the epitopes with more than 8 residues were considered for subsequent antigenicity analysis. Discontinuous B-cell epitopes were predicted via the DiscoTope 2.0 server tool in IEDB with a default threshold of −3.7 (corresponding specificity > 0.75 and sensitivity < 0.47), based on the 3-dimensional (3D) structures of the SARS-CoV-2 S protein (PDB ID: 6VYB, B chain) and the SARS-CoV-2 S protein RBD (PDB ID: 6M0J, B chain). It is worth noting that one epitope ( 786 QILPDPLKPTKRSFIEDLLFNKVTLA 811 ) located in the S2 subunit of the SARS-CoV S protein is an important linear B-cell epitope capable of eliciting the production of a neutralizing antibody (NAb) identified in patients who recovered from SARS-CoV infection (Table S2 ) [13] . abstract: Currently, there is limited knowledge about the immunological profiles of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We used computer-based immunoinformatic analysis and the newly resolved 3-dimensional (3D) structures of the SARS-CoV-2 S trimeric protein, together with analyses of the immunogenic profiles of SARS-CoV, to anticipate potential B-cell and T-cell epitopes of the SARS-CoV-2 S protein for vaccine design, particularly for peptide-driven vaccine design and serological diagnosis. Nine conserved linear B-cell epitopes and multiple discontinuous B-cell epitopes composed of 69 residues on the surface of the SARS-CoV-2 trimeric S protein were predicted to be highly antigenic. We found that the SARS-CoV-2 S protein has a different antigenic profile than that of the SARS-CoV S protein due to the variations in their primary and 3D structures. Importantly, SARS-CoV-2 may exploit an immune evasion mechanism through two point mutations in the critical and conserved linear neutralization epitope (overlap with fusion peptide) around a sparsely glycosylated area. These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein. In addition, 62 T-cell epitopes in the SARS-CoV-2 S protein were predicted in our study. The structure-based immunoinformatic analysis for the SARS-CoV-2 S protein in this study may improve vaccine design, diagnosis, and immunotherapy against the pandemic of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32635180/ doi: 10.3390/vaccines8030355 id: cord-254469-7q6xi2xx author: Wang, Fuzhou title: An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development date: 2020-05-05 words: 4737.0 sentences: 245.0 pages: flesch: 48.0 cache: ./cache/cord-254469-7q6xi2xx.txt txt: ./txt/cord-254469-7q6xi2xx.txt summary: In March 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US). However, on March 16 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US), conducted by Moderna and the Vaccine Research Center (VRC) of the National Institute of Allergy and Infectious Diseases (NIAID) [12, 13] . Although mRNA vaccines are commencing human clinical trials, due to the rapid global spread of this new viral pandemic, it may not be possible to develop a safe and effective vaccine for SARS-CoV-2 in time to prevent the increasing number of deaths due to this novel RNA virus. abstract: The first outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred in Wuhan, Hubei Province, China, in late 2019. The subsequent COVID-19 pandemic rapidly affected the health and economy of the world. The global approach to the pandemic was to isolate populations to reduce the spread of this deadly virus while vaccines began to be developed. In March 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US). The production of mRNA-based vaccines is a promising recent development in the production of vaccines. However, there remain significant challenges in the development and testing of vaccines as rapidly as possible to control COVID-19, which requires international collaboration. This review aims to describe the background to the rationale for the development of mRNA-based SARS-CoV-2 vaccines and the current status of the mRNA-1273 vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/32366816/ doi: 10.12659/msm.924700 id: cord-320417-01l27d99 author: Wang, Hai-Long title: The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date: 2020-10-14 words: 5013.0 sentences: 257.0 pages: flesch: 52.0 cache: ./cache/cord-320417-01l27d99.txt txt: ./txt/cord-320417-01l27d99.txt summary: I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intraand inter-viral clades. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination. SARS-CoV-2 is an RNA virus with limited genome length, but its high mutation rate and homologous genetic recombination nonetheless gave rise to exponentially increased variants. This is why all previously reported recombination events of SARS-Cov-2 have relied on clade-defining SNPs. The 2D co-occurring variant mapping is a simple way to display inter-clade hybrid lineages, and it can be used to directly compare distributions of populations for intra-and inter-clade from different geographic locations or the same location but at a different time point. I downloaded ~18,000 SARS-CoV-2 genome sequences from NCBI (on September 2 nd ) and used the same criterion as before to search for inter-clade co-occurring SNP pairs (see method for details). abstract: I performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide. I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intra- and inter-viral clades. This method is highly advantageous for the new era of “big-data” when high-throughput sequencing is becoming readily available. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination. url: https://doi.org/10.1101/2020.10.13.338038 doi: 10.1101/2020.10.13.338038 id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 words: 2579.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-339976-tg2jkss7.txt txt: ./txt/cord-339976-tg2jkss7.txt summary: title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient''s clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15229153/ doi: 10.1373/clinchem.2004.031237 id: cord-322212-8xrehbd1 author: Wang, Hanyin title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock date: 2020-04-23 words: 1467.0 sentences: 112.0 pages: flesch: 51.0 cache: ./cache/cord-322212-8xrehbd1.txt txt: ./txt/cord-322212-8xrehbd1.txt summary: title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock We report the case of an 88-year-old man with coronavirus disease 2019 (COVID-19) who presented with ARDS and septic shock. 1 An estimated 5.0% of patients with coronavirus disease 2019 (COVID-19) required ICU admission, 2.3% underwent mechanical ventilation, and 1.1% had septic shock. 2 Angiotensin II (Ang-2) is a synthetic vasopressor that received US Food and Drug Administration approval in 2017 for treatment of refractory vasodilatory shock. We report our experience with Ang-2 for septic shock in a critically ill patient with COVID-19. He became hypotensive and required ABBREVIATIONS: ACE = angiotensin-converting enzyme; ACE2 = angiotensin-converting enzyme 2; Ang-2 = angiotensin II; COVID-19 = coronavirus disease 2019; SARS-CoV = severe acute respiratory syndrome-related coronavirus; SARS-CoV-2 = 2019 novel coronavirus On ICU day 2, the SARS-CoV-2 polymerase chain reaction result was positive. abstract: We report the case of an 88-year-old man with coronavirus disease 2019 (COVID-19) who presented with ARDS and septic shock. The patient had exquisite BP sensitivity to low-dose angiotensin II (Ang-2), allowing for rapid liberation from high-dose vasopressors. We hypothesize that sensitivity to Ang-2 might be related to biological effect of severe acute respiratory syndrome coronavirus 2 infection. The case is suggestive of a potential role for synthetic Ang-2 for patients with COVID-19 and septic shock. Further studies are needed to confirm our observed clinical efficacy. url: https://doi.org/10.1016/j.chest.2020.04.015 doi: 10.1016/j.chest.2020.04.015 id: cord-273373-5elel6qo author: Wang, Haofeng title: Recent progress in the discovery of inhibitors targeting coronavirus proteases date: 2016-02-19 words: 3083.0 sentences: 165.0 pages: flesch: 50.0 cache: ./cache/cord-273373-5elel6qo.txt txt: ./txt/cord-273373-5elel6qo.txt summary: The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. Structural analyses revealed that the substrate-binding pockets of various CoV M pro s are highly conserved, which led to the concept of "widespectrum inhibitors" for targeting all CoVs. Through a structure-based drug design, we have identified a lead compound named N3 with potent inhibitory activity against all M pro s tested ( Figure 2D) . Structurebased design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome-coronavirus papain-like protease Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Papain-like protease 2 (PLP2) from severe acute respiratory syndrome coronavirus (SARS-CoV): expression, purification, characterization, and inhibition abstract: Coronaviruses (CoVs) can cause highly prevalent diseases in humans and animals. The fatal outbreak of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) highlights the threat posed by this unique virus subfamily. However, no specific drugs have been approved to treat CoV-associated diseases to date. The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. This review summarizes the recent advances in biological and structural studies, together with the development of inhibitors targeting CoV proteases, particularly main proteases (M(pro)s), which could help develop effective treatments to prevent CoV infection. [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/26920707/ doi: 10.1007/s12250-015-3711-3 id: cord-271505-eot38721 author: Wang, Hongliang title: Molecular pathogenesis of severe acute respiratory syndrome date: 2006-09-28 words: 4959.0 sentences: 229.0 pages: flesch: 48.0 cache: ./cache/cord-271505-eot38721.txt txt: ./txt/cord-271505-eot38721.txt summary: demonstrated that the angiotensin-converting enzyme 2 (ACE2) is a functional cellular receptor of SARS-CoV, by using coimmunoprecipitation of the virus glycoprotein (S1) with lysates from cells that are susceptible to virus infection (Vero E6 cells) followed by mass spectrometry analysis [7] . In the case of SARS, apoptosis was observed in patients'' lung epithelial cells; thus, SARS-CoV induced apoptosis would certainly have a deleterious pathogenic role, leading to severe tissue damage [26] . This model system allowed us to avoid possible secondary effects resulting from viral replication or infections in vivo and to directly test whether SARS-CoV spike protein might adversely affect acute lung injury through modulation of ACE2. SARS-CoV infection or spike protein treatment can down-regulate the expression of ACE2, and thus aggravate lung injury. Nabel, pH-dependent entry of severe acute respiratory syndrome coronavirus is mediated by the spike glycoprotein and enhanced by dendritic cell transfer through DC-SIGN abstract: The global outbreak in 2002–2003 of severe acute respiratory syndrome (SARS) posed a serious threat to public health and had a significant impact on socioeconomic stability. Although the global outbreak of SARS has been contained, there are serious concerns over its re-emergence and bioterrorism potential, and up to date, no specific treatment exists for this disease. Here we review the progress of studies on the pathogenesis of the disease, in particular, studies on the molecular level. url: https://www.ncbi.nlm.nih.gov/pubmed/17142081/ doi: 10.1016/j.micinf.2006.06.012 id: cord-260508-z11exbyu author: Wang, Hongru title: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date: 2020-10-12 words: 4698.0 sentences: 272.0 pages: flesch: 58.0 cache: ./cache/cord-260508-z11exbyu.txt txt: ./txt/cord-260508-z11exbyu.txt summary: Phylogenetic analyses (Fig. 2 ) in genomic regions with all recombination tracts 6 (Supplementary Table 5 ) masked using Maximum-likelihood (Fig. 2a) and Neighbor-joining 7 based on synonymous (Fig. 2b ) or non-synoymous (Fig. 2c ) mutation distance metrics, 8 consistently support RmYN02 as the nearest outgroup to human SARS-CoV-2, in contrast to 9 previous analyses before the discovery of RmYN02, which instead found RaTG13 to be the 10 nearest outgroup ). Notice that the divergences 14 between human SARS-CoV-2 and the bat viral sequences, RaTG13 and RmYN02, in most 15 regions of the genome, are quite low compared to the other comparisons. While the overall divergence in the S gene encoding the spike protein could suggest the 10 presence of recombination in the region, previous study ) reported that the tree 11 based on synonymous substitutions supported RaTG13 as the sister taxon to the human SARS-12 abstract: Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin isolated strain, GD410721, in the receptor binding domain (RBD) of the spike protein, a pattern that can be caused by either recombination or by convergent amino acid evolution driven by natural selection. We perform a detailed analysis of the synonymous divergence, which is less likely to be affected by selection than amino acid divergence, between human SARS-CoV-2 and related strains. We show that the synonymous divergence between the bat derived viruses and SARS-CoV-2 is larger than between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for the recombination hypothesis. However, the synonymous divergence between pangolin strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent recombination between them, instead it suggests a recombination into RaTG13. We also find a 14-fold increase in the dN/dS ratio from the lineage leading to SARS-CoV-2 to the strains of the current pandemic, suggesting that the vast majority of non-synonymous mutations currently segregating within the human strains have a negative impact on viral fitness. Finally, we estimate that the time to the most recent common ancestor of SARS-CoV-2 and RaTG13 or RmYN02 based on synonymous divergence, is 51.71 years (95% C.I., 28.11-75.31) and 37.02 years (95% C.I., 18.19-55.85), respectively. url: https://doi.org/10.1101/2020.04.20.052019 doi: 10.1101/2020.04.20.052019 id: cord-034354-4xu97je3 author: Wang, Hongye title: SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution date: 2020-10-21 words: 3678.0 sentences: 245.0 pages: flesch: 53.0 cache: ./cache/cord-034354-4xu97je3.txt txt: ./txt/cord-034354-4xu97je3.txt summary: The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. Using the SARS-CoV-2 proteome microarray, we screened IgM and IgG antibodies in the serum of 10 COVID-19 patients who were in the early stage of infection (days of symptoms onset, 3.0 ± 5.92) (Supporting Information, Table S2 ) to construct a landscape of humoral responses to the SARS-CoV-2 proteome (Figure 2 ). Sixty-one (61) IgG and IgM antibody epitopes were identified in seven SARS-CoV-2 proteins (M, N, S, Orf1ab, Orf3a, Orf7a, and Orf8) with a Z-score higher than 3 in at least one COVID-19 patient (Table 1) . Furthermore, we constructed the first landscape of B-cell epitopes of serum IgM and IgG antibodies, representing the comprehensive antibody response of COVID-19 patients to SARS-CoV-2 infection (Figures 2−4) . abstract: [Image: see text] Comprehensive profiling of humoral antibody response to severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) proteins is essential in understanding the host immunity and in developing diagnostic tests and vaccines. To address this concern, we developed a SARS-CoV-2 proteome peptide microarray to analyze antibody interactions at the amino acid resolution. With the array, we demonstrate the feasibility of employing SARS-CoV-1 antibodies to detect the SARS-CoV-2 nucleocapsid phosphoprotein. The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. With array data and structural analysis, a peptide epitope for neutralizing antibodies within the SARS-CoV-2 spike receptor-binding domain’s interaction interface with the angiotensin-converting enzyme 2 receptor was predicted. All the results demonstrate the utility of our microarray as a platform to determine the changes of antibody responses in COVID-19 patients and animal models as well as to identify potential targets for diagnosis and treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7586461/ doi: 10.1021/acscentsci.0c00742 id: cord-291388-tt9eq7e0 author: Wang, Jann-Tay title: Clinical Manifestations, Laboratory Findings, and Treatment Outcomes of SARS Patients date: 2004-05-17 words: 4355.0 sentences: 226.0 pages: flesch: 50.0 cache: ./cache/cord-291388-tt9eq7e0.txt txt: ./txt/cord-291388-tt9eq7e0.txt summary: Previous reports have described some major clinical findings of SARS, including the temporal progression of clinical symptoms and chest radiography, the outcomes, suggested treatment protocol, and risk factors for death (4, 5) . We report on the clinical features of our SARS patients with pneumonia, with emphasis on temporal progression of laboratory findings, treatment outcome, and risk factors for poor prognosis. Methylprednisolone was usually administered in the second week of the disease if any of the following occurred: a flare of fever, progression of clinical symptoms (such as dyspnea or diarrhea), a surge or resurge of CRP level, or rapid deterioration of chest radiographic findings (development of new infiltration). A previous study reported the temporal progression of clinical and radiologic findings in SARS patients and indicated that several parameters would become more severe in the second and third week of disease (5). abstract: Clinical and laboratory data on severe acute respiratory syndrome (SARS), particularly on the temporal progression of abnormal laboratory findings, are limited. We conducted a prospective study on the clinical, radiologic, and hematologic findings of SARS patients with pneumonia, who were admitted to National Taiwan University Hospital from March 8 to June 15, 2003. Fever was the most frequent initial symptom, followed by cough, myalgia, dyspnea, and diarrhea. Twenty-four patients had various underlying diseases. Most patients had elevated C-reactive protein (CRP) levels and lymphopenia. Other common abnormal laboratory findings included leukopenia, thrombocytopenia, and elevated levels of aminotransferase, lactate dehydrogenase, and creatine kinase. These clinical and laboratory findings were exacerbated in most patients during the second week of disease. The overall case-fatality rate was 19.7%. By multivariate analysis, underlying disease and initial CRP level were predictive of death. url: https://www.ncbi.nlm.nih.gov/pubmed/15200814/ doi: 10.3201/eid1005.030640 id: cord-277816-ncdy9qgb author: Wang, Ji-gan title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis date: 2020-10-20 words: 3600.0 sentences: 202.0 pages: flesch: 48.0 cache: ./cache/cord-277816-ncdy9qgb.txt txt: ./txt/cord-277816-ncdy9qgb.txt summary: title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis In order to understand the clinical manifestations and incidence of gastrointestinal symptoms of coronavirus disease (COVID-19) in children and discuss the importance of fecal nucleic acid testing.We retrospectively analyzed studies on gastrointestinal symptoms and fecal nucleic acid detection in pediatric COVID-19 patients from January 1, 2020 to August 10, 2020, including prospective clinical studies and case reports. Stata12.0 software was used for meta-analysis.The results showed that the most common gastrointestinal symptoms in children with COVID-19 were vomiting and diarrhea, with a total incidence of 17.7% (95% Cl 13.9–21.5%). At present, there is no relevant study on whether there is a difference in the positive rate of fecal nucleic acid testing in COVID-19 children with and without diarrhea. Clinical features of 33 cases in children infected with SARS-CoV-2 in Anhui Province, China: a multi-center retrospective cohort study. abstract: In order to understand the clinical manifestations and incidence of gastrointestinal symptoms of coronavirus disease (COVID-19) in children and discuss the importance of fecal nucleic acid testing.We retrospectively analyzed studies on gastrointestinal symptoms and fecal nucleic acid detection in pediatric COVID-19 patients from January 1, 2020 to August 10, 2020, including prospective clinical studies and case reports. The results of fecal nucleic acid detection were analyzed systematically. Stata12.0 software was used for meta-analysis.The results showed that the most common gastrointestinal symptoms in children with COVID-19 were vomiting and diarrhea, with a total incidence of 17.7% (95% Cl 13.9–21.5%). However, the prevalence of gastrointestinal symptoms in other countries (21.1%, 95% CI 16.5–25.7%) was higher compared to China (12.9%, 95% CI 8–17.7%). In Wuhan, the pooled prevalence was much higher (41.3%, 95% CI 3.2–79.4%) compared to areas outside Wuhan in China (7.1%, 95% CI 4.0–10.3%). The positive rate of fecal nucleic acid testing in COVID-19 children was relatively high at 85.8% (91/106). Additionally, 71.2% (52/73) were still positive for fecal nucleic acid after respiratory tract specimens turned negative. One and two weeks after the respiratory tract specimens turned nucleic acid-negative, 45.2% (33/73) and 34.2% (25/73) patients, respectively, remained fecal nucleic acid-positive. The longest interval between the respiratory tract specimens turning negative and fecal specimens turning negative exceeded 70 days. Conclusions and relevance: gastrointestinal symptoms in pediatric COVID-19 are relatively common. Attention should be paid to the detection of fecal nucleic acids in children. Fecal nucleic acid-negative status should be considered as one of the desegregation standards. url: https://www.ncbi.nlm.nih.gov/pubmed/33082472/ doi: 10.1038/s41598-020-74913-0 id: cord-296362-9vi8xwu7 author: Wang, Jian-Min title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function date: 2008-09-12 words: 3490.0 sentences: 199.0 pages: flesch: 57.0 cache: ./cache/cord-296362-9vi8xwu7.txt txt: ./txt/cord-296362-9vi8xwu7.txt summary: title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. For in-depth study of functions of different viral proteins and regulatory sequence elements by reverse genetics, full-length infectious cDNA clones have been established using various techniques including bacterial artificial chromosome (BAC) vector [23] [24] [25] and SARS-CoV replicon cell lines [26] , which can also be used for antiviral drug screening. Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis abstract: Abstract Severe acute respiratory syndrome virus (SARS-CoV) was the causative agent of the SARS outbreaks in 2002–2003. A safer in vitro system is desirable for conducting research on SARS-CoV and to screen for antiviral drugs against the virus. Based on the infectious cDNA clone of rSARS-CoV-ΔE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. Successful replication was achieved as evident from continuous expression of eGFP detected by both fluorescence and Western blot. Treatment with antiviral drugs demonstrated that the replication could be significantly inhibited by 0.4mg/ml of cysteine proteinase inhibitor E-64D, but not by ribavirin. The same replicons containing further deletion of the coding regions for non-structural proteins (nsp) 1, 2 or 16 confirmed previous observation that nsp16, but not nsp1 or nsp2, was essential for efficient viral replication or transcription. url: https://www.sciencedirect.com/science/article/pii/S0006291X08012916 doi: 10.1016/j.bbrc.2008.06.129 id: cord-258859-iaiosjlu author: Wang, Jiao title: Mask use during COVID-19: A risk adjusted strategy() date: 2020-06-25 words: 2683.0 sentences: 159.0 pages: flesch: 53.0 cache: ./cache/cord-258859-iaiosjlu.txt txt: ./txt/cord-258859-iaiosjlu.txt summary: In the context of Coronavirus Disease (2019) (COVID-19) cases globally, there is a lack of consensus across cultures on whether wearing face masks is an effective physical intervention against disease transmission. This study 1) illustrates transmission routes of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); 2) addresses controversies surrounding the mask from perspectives of attitude, effectiveness, and necessity of wearing the mask with evidence that the use of mask would effectively interrupt the transmission of infectious diseases in both hospital settings and community settings; and 3) provides suggestion that the public should wear the mask during COVID-19 pandemic according to local context. The mask is generally used 278 by general public, while the respirator or a filtering face piece, which is designed to 279 protect the wearer from exposure to airborne contaminants, is mainly used by health care 280 workers especially during AGP (European Centre for Disease Prevention and Control, 281 2020). abstract: In the context of Coronavirus Disease (2019) (COVID-19) cases globally, there is a lack of consensus across cultures on whether wearing face masks is an effective physical intervention against disease transmission. This study 1) illustrates transmission routes of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); 2) addresses controversies surrounding the mask from perspectives of attitude, effectiveness, and necessity of wearing the mask with evidence that the use of mask would effectively interrupt the transmission of infectious diseases in both hospital settings and community settings; and 3) provides suggestion that the public should wear the mask during COVID-19 pandemic according to local context. To achieve this goal, government should establish a risk adjusted strategy of mask use to scientifically publicize the use of masks, guarantee sufficient supply of masks, and cooperate for reducing health resources inequities. url: https://www.sciencedirect.com/science/article/pii/S0269749120334862?v=s5 doi: 10.1016/j.envpol.2020.115099 id: cord-300532-4d6fnjt8 author: Wang, Jiao title: Disinfection technology of hospital wastes and wastewater: Suggestions for disinfection strategy during coronavirus Disease 2019 (COVID-19) pandemic in China date: 2020-04-24 words: 6421.0 sentences: 331.0 pages: flesch: 38.0 cache: ./cache/cord-300532-4d6fnjt8.txt txt: ./txt/cord-300532-4d6fnjt8.txt summary: For each ward and restroom of an infectious disease hospital or the infectious disease area of a general Table 1 Comparison of Disinfection technologies for hospital wastewater (Fan et al., 2017; Kühn et al., 2003; Kleinb€ ohl et al., 2018; Messerle et al., 2018; Yu et al., 2013 The ability of decoloring and deodorizing and quick decomposition of microorganisms High operation costs and hazardous by-products hospital, 1 kg of bleaching powder containing 25% of available chlorine per 10 beds should be added 3 to 4 times before further disinfection. From the perspective of investment and operation costs as well as economic and social benefits, high temperature incineration is still one of the most valuable hospital waste disinfection technology in China. Recently, RNA of SARS-CoV-2 has been found in feces of patients, which triggered concern to the disinfection of wastes and wastewater of designated hospitals during COVID-19 pandemic in China. abstract: Hospitals are important sources of pollutants resulted from diagnostic, laboratory and research activities as well as medicine excretion by patients, which include active component of drugs and metabolite, chemicals, residues of pharmaceuticals, radioactive markers, iodinated contrast media, etc. The discharge of hospital wastes and wastewater, especially those without appropriate treatment would expose the public in danger of infection. In particular, under the Coronavirus Disease 2019 (COVID-19) pandemic context in China, it is of great significance to reduce the health risks to the public and environment. In this study, technologies of different types of hospital wastes and wastewater disinfection have been summarized. Liquid chlorine, sodium hypochlorite, chlorine dioxide, ozone, and ultraviolet irradiation disinfection are commonly used for hospital wastewater disinfection. While incineration, chemical disinfection, and physical disinfection are commonly used for hospital wastes disinfection. In addition, considering the characteristics of various hospital wastes, the classification and selection of corresponding disinfection technologies are discussed. On this basis, this study provides scientific suggestions for management, technology selection, and operation of hospital wastes and wastewater disinfection in China, which is of great significance for development of national disinfection strategy for hospital wastes and wastewater during COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32443202/ doi: 10.1016/j.envpol.2020.114665 id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 words: 2771.0 sentences: 166.0 pages: flesch: 51.0 cache: ./cache/cord-302409-40ktyt5q.txt txt: ./txt/cord-302409-40ktyt5q.txt summary: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs'' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. abstract: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. METHODS: Surfaces of objects were routinely wiped with 1000 mg/L chlorine containing disinfectant. Air and sewage disinfection was proceeded routinely and strictly. Hospital environmental surfaces and PPE of staffs in isolation wards were sampled using swabs. The sewage from various inlet and outlets were sampled. The respiratory and stool specimens of patients were collected. The respiratory specimens of staffs in the isolation wards were also sampled once a week. Quantitative real-time reverse transcription PCR (qRT-PCR) methods were used to confirm the existence of SARS-Cov-2 RNA. Viral culture was done for the samples positive for SARS-Cov-2 RNA. RESULTS: During the study period, 33 laboratory-confirmed patients were hospitalized in isolation wards in the hospital. None of SARS-Cov-2 RNA was detected among the 36 objects surface samples and 9 staffs PPE samples in isolation wards. Though the 3 sewage samples from the inlet of preprocessing disinfection pool were positive for SARS-CoV-2 RNA and the sample from the outlet of preprocessing disinfection pool was weakly positive, the sewage sample from the outlet of the last disinfection pool was negative. All of the 5 sewage samples from various points were negative by viral culture of SARS-Cov-2. None of the respiratory specimens of staffs in the isolation wards were positive. CONCLUSIONS: Though SARS-Cov-2 RNA of the sewage samples were positive from inlets of the sewage disinfection pool and negative from the outlet of the last sewage disinfection pool, no viable virus was detected by culture. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. url: https://www.ncbi.nlm.nih.gov/pubmed/32311449/ doi: 10.1016/j.ijid.2020.04.024 id: cord-304379-4mfyxp6h author: Wang, Jin title: Mathematical models for COVID-19: applications, limitations, and potentials date: 2020-06-25 words: 1561.0 sentences: 77.0 pages: flesch: 35.0 cache: ./cache/cord-304379-4mfyxp6h.txt txt: ./txt/cord-304379-4mfyxp6h.txt summary: (5) conducted computational modeling of potential epidemic trajectories to estimate the outbreak size in Wuhan, China, and their results indicated that control measures need to block well over 60% of transmission to be effective in containing the outbreak. Incorporating such an environment-tohuman route into mathematical modeling may better characterize the transmission dynamics of COVID-19 and potentially gain deeper understanding of its epidemic patterns. For example, many countries (China in particular) implemented strong disease control measures, including large-scale quarantine, intensive tracking of movement and contact, strict isolation of infected individuals, expanded medical facilities, and social distancing, which can effectively (and, in some places, rapidly) reduce the transmissibility of the virus. Mathematical epidemic models are well positioned to incorporate the economic impact of COVID-19, to quantify the interaction of epidemiological and economic factors, and to suggest an optimal balance between the pandemic control and economic development. abstract: nan url: https://doi.org/10.21037/jphe-2020-05 doi: 10.21037/jphe-2020-05 id: cord-281161-u896icp9 author: Wang, Jing title: The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date: 2012-05-17 words: 6854.0 sentences: 317.0 pages: flesch: 49.0 cache: ./cache/cord-281161-u896icp9.txt txt: ./txt/cord-281161-u896icp9.txt summary: We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. As shown in Table 2 , similar IgG1 and IgG2a humoral immune responses against the influenza viruses were induced in the mice vaccinated previously with rRBD plus rOv-ASP-1 adjuvant and those administered with PBS only. As shown in Table 3 , all of the NHPs vaccinated with rRBD protein plus 50 mg (n = 2), 100 mg rOv-ASP-1 (n = 2) or 500 mg CpG (n = 1) as the adjuvant developed RBDspecific IgG antibody response with increasing antibody level after each boost. Secondly, using two concentration of the rOv-ASP-1 adjuvant, 50 or 100 mg, and rRBD as the vaccine antigen, we were able to induce after three immunizations high titers of neutralizing antibodies (1:3,500-1:6,392) that much exceed what is needed for protection against SARS-CoV infection in vivo (.1:500) [56] . abstract: Adjuvants potentiate antigen-specific protective immune responses and can be key elements promoting vaccine effectiveness. We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. With a few vaccine antigens, it also promoted a Th1-biased response based on pronounced induction of Th1-associated IgG2a and IgG2b antibody responses and the upregulated production of Th1 cytokines, including IL-2, IFN-γ, TNF-α and IL-6. However, because it is a protein, the rOv-ASP-1 adjuvant may also induce anti-self-antibodies. Therefore, it was important to verify that the host responses to self will not affect the adjuvanticity of rOv-ASP-1 when it is used in subsequent vaccinations with the same or different vaccine antigens. In this study, we have established rOv-ASP-1's adjuvanticity in mice during the course of two sequential vaccinations using two vaccine model systems: the receptor-binding domain (RBD) of SARS-CoV spike protein and a commercial influenza virus hemagglutinin (HA) vaccine comprised of three virus strains. Moreover, the adjuvanticity of rOv-ASP-1 was retained with an efficacy similar to that obtained when it was used for a first vaccination, even though a high level of anti-rOv-ASP-1 antibodies was present in the sera of mice before the administration of the second vaccine. To further demonstrate its utility as an adjuvant for human use, we also immunized non-human primates (NHPs) with RBD plus rOv-ASP-1 and showed that rOv-ASP-1 could induce high titres of functional and protective anti-RBD antibody responses in NHPs. Notably, the rOv-ASP-1 adjuvant did not induce high titer antibodies against self in NHPs. Thus, the present study provided a sound scientific foundation for future strategies in the development of this novel protein adjuvant. url: https://doi.org/10.1371/journal.pone.0037019 doi: 10.1371/journal.pone.0037019 id: cord-325449-fl6ob5ja author: Wang, Jing title: COVID-19 and diabetes: the contributions of hyperglycemia date: 2020-10-01 words: 3424.0 sentences: 164.0 pages: flesch: 42.0 cache: ./cache/cord-325449-fl6ob5ja.txt txt: ./txt/cord-325449-fl6ob5ja.txt summary: Thus, following SARS-CoV-2 infection, poor-controlled blood glucose in diabetes patients may promote macrophage inflammation and antigen presentation impairment in DCs, resulting in a great increase in the secretion of inflammatory cytokines and chemokines from immune cells and ultimately cytokine storm and increased mortality (Figure 1) . The exact mechanisms linking diabetes and COVID-19 remain to be further elucidated, but available clinical/laboratory observations suggest that hyperglycemia-induced immune dysfunction, cytokines storm, and elevated lactate levels may play critical roles in the severity of COVID-19 in patients with pre-existing diabetes. A large body of evidence shows that hyperglycemia or diabetes may impair immune response mediated by macrophages, monocytes, and DCs, weaken T-cell function, and promote cytokine storm, ultimately resulting in increased susceptibility of SARS-CoV-2 infection and COVID-19-associated mortality. Hyperglycemia may also increase lactate production via HIF-1α, which suppresses the innate immune RLR signaling by targeting MAVS, leading to delayed clearance of SARS-CoV-2 and thus severe outcomes in diabetes patients with COVID-19, including ARDS, septic shock, and MODS. abstract: Coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has now evolved into a worldwide crisis that triggers substantial morbidity and mortality. COVID-19 occurs more frequently and has more serious complications in patients with diabetes mellitus, but the underlying mechanisms remain largely elusive. Here, we summarize current and evolving concepts on the detrimental effect of hyperglycemia on SARS-CoV-2 infection and consequences, focusing on several key mechanisms underlying the link between diabetes and COVID-19. A better understanding of the mechanisms by which hyperglycemia worsens the prognosis of COVID-19 is critical for reducing the risk of SARS-CoV-2 infection and its associated mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/33002109/ doi: 10.1093/jmcb/mjaa054 id: cord-337208-6rs1sgx1 author: Wang, Jingbo title: Enlightenments of Asymptomatic Cases of SARS-CoV-2 Infection date: 2020-06-30 words: 1529.0 sentences: 83.0 pages: flesch: 61.0 cache: ./cache/cord-337208-6rs1sgx1.txt txt: ./txt/cord-337208-6rs1sgx1.txt summary: They both had normal lymphocyte counts and CT scans, without clinical symptoms; however, their qRT-PCR results of throat swabs and sputum samples both showed positive for SARS-CoV-2. The wife, daughter, and son-in-law of Case 1 were successively diagnosed with novel coronavirus-infected pneumonia, all of which were common types, and all had clinical symptoms such as fever, cough, sore throat, decreased lymphocyte count, and the CT examination of both lungs showed typical ground-glass and patchy shadows, and qRT-PCR results of pharyngeal brush and sputum specimens were positive for SARS-CoV-2. Among them, infected patients 1, 2 and 3 had clinical symptoms (fever, cough, sore throat, etc.), lymphocyte count decreased, lung CT scan showed typical ground-glass and patch shadows, and qRT-PCR tests of pharyngeal swabs and sputum specimens revealed positive for SARS-CoV-2. On February 2, Case 2 had tested positive for SARS-CoV-2 by qRT-PCR of pharyngeal swabs, and was hospitalized in isolation. abstract: This article reports two asymptomatic cases of SARS-CoV-2 infection. Both cases came from Hubei Province. One was a 63-year-old male and the other was a 29-year-old female. Both were diagnosed with SARS-CoV-2 infection during the screening of high-risk personnel from the affected areas. During the 14-day isolation medical observation, they had no symptoms, their blood lymphocyte count and lung CT examinations were normal. An asymptomatic infection had been diagnosed, however, it was not “asymptomatic infection” state in incubation period. Due to the timely and effective isolation measures taken for the two cases, no other persons have been infected by them. Therefore, effective control of the source of infection, cutting off the route of transmission, and protecting vulnerable populations are currently effective measures to prevent the spread of coronavirus infected disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32983934/ doi: 10.2478/jtim-2020-0017 id: cord-262268-gm99cadh author: Wang, Jingqiang title: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date: 2003-12-01 words: 4027.0 sentences: 189.0 pages: flesch: 49.0 cache: ./cache/cord-262268-gm99cadh.txt txt: ./txt/cord-262268-gm99cadh.txt summary: Consequently, we thoroughly investigated the immunoreactivities with patient sera of a series of synthesized peptides from SARS-coronavirus structural proteins. Results: Four epitopic sites, S599, M137, N66, and N371-404, located in the SARS-coronavirus S, M, and N proteins, respectively, were detected by screening synthesized peptides. The peptides representing the COOH terminus of the N protein, in particular N371 and N385, had high absorbance/cutoff value ratios with the highest positive detection rate and the lowest hydrophobicity score among all of the synthesized peptides (Fig. 1C, and Fig. 3 in the online Data Supplement). The other 17 peptides reacted only slightly with the sera from SARS patients and gave low detection rates, suggesting that the regions of the S protein covered by these peptides have no epitopic site. The patient sera preincubated with 4 mg/L S599 or N385 gave a 25-30% lower response in the ELISA (data not shown), suggesting that the two peptides could compete with SARS coronavirus for binding to the antibodies in SARS serum. abstract: Background: The widespread threat of severe acute respiratory syndrome (SARS) to human life has spawned challenges to develop fast and accurate analytical methods for its early diagnosis and to create a safe antiviral vaccine for preventive use. Consequently, we thoroughly investigated the immunoreactivities with patient sera of a series of synthesized peptides from SARS-coronavirus structural proteins. Methods: We synthesized 41 peptides ranging in size from 16 to 25 amino acid residues of relatively high hydrophilicity. The immunoreactivities of the peptides with SARS patient sera were determined by ELISA. Results: Four epitopic sites, S599, M137, N66, and N371-404, located in the SARS-coronavirus S, M, and N proteins, respectively, were detected by screening synthesized peptides. Notably, N371 and N385, located at the COOH terminus of the N protein, inhibited binding of antibodies to SARS-coronavirus lysate and bound to antibodies in >94% of samples from SARS study patients. N385 had the highest affinity for forming peptide-antibody complexes with SARS serum. Conclusions: Five peptides from SARS structural proteins, especially two from the COOH terminus of the N protein, appear to be highly immunogenic and may be useful for serologic assays. The identification of these antigenic peptides contributes to the understanding of the immunogenicity and persistence of SARS coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/14633869/ doi: 10.1373/clinchem.2003.023184 id: cord-269718-e1mxmo3a author: Wang, Jingquan title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China date: 2020-11-13 words: 862.0 sentences: 59.0 pages: flesch: 49.0 cache: ./cache/cord-269718-e1mxmo3a.txt txt: ./txt/cord-269718-e1mxmo3a.txt summary: title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China Considering the live SARS-CoV-2 was detected and isolated from the excrement and urine of infected patients, the potential public health risk of its waterborne transmission should be paid broad and close attention. The purpose of the current study is to investigate the associations between COVID-19 incidences and hydrological factors such as lake area, river length, precipitation and volume of water resources in 30 regions of China. Based on the results of descriptive analysis and nonlinear regression analysis, positive associations with COVID-19 confirmed numbers were observed for migration scale index (MSI), river length, precipitation and volume of water resources, but negative associations for population density. length, precipitation and volume of water resources, but negative associations for 21 population density. Impact of meteorological factors on the COVID-19 transmission: 435 A multi-city study in China Water transmission oF SARS-CoV-2 abstract: Considering the live SARS-CoV-2 was detected and isolated from the excrement and urine of infected patients, the potential public health risk of its waterborne transmission should be paid broad and close attention. The purpose of the current study is to investigate the associations between COVID-19 incidences and hydrological factors such as lake area, river length, precipitation and volume of water resources in 30 regions of China. All confirmed cases for each areas were divided into two clusters including first cases cluster driven by imported cases during the period of January 20th to January 29th, 2020 and second cases cluster driven by local cases during the period of January 30th to March 1st, 2020. Based on the results of descriptive analysis and nonlinear regression analysis, positive associations with COVID-19 confirmed numbers were observed for migration scale index (MSI), river length, precipitation and volume of water resources, but negative associations for population density. The correlation coefficient in the second stage cases cluster is apparently higher than that in the first stage cases cluster. Then, the negative binomial-generalized linear model (NB-GLM) was fitted to estimate area-specific effects of hydrological variables on relative risk (RR) with the incorporation of additional variables (e.g., MSI) and the effects of exposure-lag-response. The statistically significant associations between RR and river length, the volume of water resources, precipitation were obtained by meta-analysis as 1.24 (95% CI: 1.22, 1.27), 2.56 (95% CI: 2.50, 2.61) and 1.59 (95% CI: 1.56, 1.62), respectively. The possible water transmission routes of SARS-CoV-2 and the potential capacity of long-distance transmission of SARS-CoV-2 in water environment was also discussed. Our results could provide a better guidance for local and global authorities to broaden the mind for understanding the natural-social system or intervening measures for COVID-19 control at the current or futural stage. url: https://www.sciencedirect.com/science/article/pii/S0013935120313712?v=s5 doi: 10.1016/j.envres.2020.110474 id: cord-007581-nu1shltl author: Wang, Jiun-Ling title: Rhabdomyolysis associated with probable SARS date: 2003-10-01 words: 1197.0 sentences: 87.0 pages: flesch: 59.0 cache: ./cache/cord-007581-nu1shltl.txt txt: ./txt/cord-007581-nu1shltl.txt summary: Four type II patients were treated with angiotensin-converting enzyme (ACE) inhibitors when they had the first angioedema attack, as compared with none with type I disease. Previous studies have pointed out that patients with probable SARS may have abnormal laboratory examination results, including elevated creatine kinase levels (2-4). We report 3 patients with probable SARS who developed rhabdomyolysis. The first patient was a 38-year-old woman who suffered from probable SARS during a nosocomial outbreak in Taiwan (5) . Serum creatine kinase level increased from 378 to 7659 U/L from April 24 to 30, and renal failure developed. Elevated serum creatine kinase levels of up to 3000 U/L have been noted in previous patients with SARS. We conclude that rhabdomyolysis-associated renal failure may be another unusual but severe presentation of SARS. Patients with SARS should have their creatine kinase levels monitored carefully, even if initial levels are only slightly elevated. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119401/ doi: 10.1016/s0002-9343(03)00448-0 id: cord-288862-upcsvjuo author: Wang, Junmei title: Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study date: 2020-04-21 words: 4369.0 sentences: 269.0 pages: flesch: 54.0 cache: ./cache/cord-288862-upcsvjuo.txt txt: ./txt/cord-288862-upcsvjuo.txt summary: Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson–Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Flexible docking and MM-PBSA-weighted solvent-accessible surface area (WSAS) were applied as the first and second filters, respectively, to improve the efficiency and accuracy of HVS in inhibitor identification for SARS-CoV-2 main protease. MD simulations were first performed for a docking hit for two purposes: (1) studying the relative stability of the ligand residing in the binding pocket; (2) sampling a set of conformations for MM-PBSA-WSAS binding free energy calculations and MM-GBSA residue−ligand binding free energy decomposition analysis. abstract: [Image: see text] The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D structures of key viral proteins are resolved. The virus causing COVID-19 is SARS-CoV-2. Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson–Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Rev.2019, 119, 947831244000; Wang, Curr. Comput.-Aided Drug Des.2006, 2, 287; Wang; HouJ. Chem. Inf. Model., 2012, 52, 119922497310). Several promising known drugs stand out as potential inhibitors of SARS-CoV-2 main protease, including carfilzomib, eravacycline, valrubicin, lopinavir, and elbasvir. Carfilzomib, an approved anticancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, −13.8 kcal/mol. The second-best repurposing drug candidate, eravacycline, is synthetic halogenated tetracycline class antibiotic. Streptomycin, another antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (−3.8 kcal/mol) is not nearly as low as that of the neutral form (−7.9 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of −12.9 kcal/mol. Detailed receptor–ligand interactions were analyzed and hot spots for the receptor–ligand binding were identified. I found that one hot spot residue, His41, is a conserved residue across many viruses including SARS-CoV, SARS-CoV-2, MERS-CoV, and hepatitis C virus (HCV). The findings of this study can facilitate rational drug design targeting the SARS-CoV-2 main protease. url: https://doi.org/10.1021/acs.jcim.0c00179 doi: 10.1021/acs.jcim.0c00179 id: cord-333688-bykbyojs author: Wang, Junxue title: Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report date: 2020-08-21 words: 2618.0 sentences: 146.0 pages: flesch: 49.0 cache: ./cache/cord-333688-bykbyojs.txt txt: ./txt/cord-333688-bykbyojs.txt summary: RATIONALE: Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. We report the case of a patient with mild symptoms of coronavirus disease (COVID-19), who achieved clinical recovery but showed persistently positive SARS-CoV-2 nucleic acid test results until Day 92 after disease onset. The third scenario is that the COVID-19-related symptoms have disappeared and the patient has entered the convalescent phase, but SARS-CoV-2 nucleic acid test results are positive for a long period of time. [4] In this study, we report the case of a patient with COVID-19 who achieved clinical recovery but showed persistently positive results on the SARS-CoV-2 nucleic acid test for up to 92 days after disease onset. Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. abstract: RATIONALE: Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. We report the case of a patient with mild symptoms of coronavirus disease (COVID-19), who achieved clinical recovery but showed persistently positive SARS-CoV-2 nucleic acid test results until Day 92 after disease onset. PATIENT CONCERNS: The patient is a 50-year-old man with mild symptoms of coronavirus disease (COVID-19). DIAGNOSES: COVID-19 pneumonia. INTERVENTIONS: The patient was quarantined for 105 days. Of these, inpatient quarantine lasted for 75 days. When the nucleic acid test results were negative for 3 consecutive days, the patient was discharged at Day 75 after disease onset. During this period, multiple samples were collected from the patient's body surface, the surrounding environment, and physical surfaces, but none of these tested positive for SARS-CoV-2. These samples included those from anal swabs, hands, inner surface of mask, cell phone, bed rails, floor around the bed, and toilet bowl surface. However, nucleic acid retest results on Day 80 and Day 92 after disease onset were positive for SARS-CoV-2 nucleic acids. OUTCOMES: The patient continued with quarantine and observation at home. After the test results on Days 101 and 105 after disease onset were negative, quarantine was terminated at last. LESSONS: Per our knowledge, this is the longest known time that a patient has tested positive for SARS-CoV-2 nucleic acids. No symptoms were observed during follow-up. During hospitalization, the SARS-CoV-2 nucleic acid positivity was not observed in samples from the body surface and surrounding environment, and no verified transmission event occurred during the quarantine at home. After undergoing clinical recovery a minority of patients with COVID-19 have shown long-term positive results for the presence of the SARS-CoV-2 nucleic acid. This has provided new understanding and research directions for coronavirus infection. Long-term follow-up and quarantine measures have been employed for such patients. Further studies are required to analyze potential infectivity in such patients and determine whether more effective antiviral drugs or regimens to enable these patients to completely clear viral infection should be researched. url: https://doi.org/10.1097/md.0000000000021865 doi: 10.1097/md.0000000000021865 id: cord-278491-cnqxsno8 author: Wang, K. title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-07-17 words: 3139.0 sentences: 216.0 pages: flesch: 57.0 cache: ./cache/cord-278491-cnqxsno8.txt txt: ./txt/cord-278491-cnqxsno8.txt summary: Methods Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. 9, 10 However, the dynamics and roles of SARS-CoV-2specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Our study may provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases and aid in the development of vaccines against SARS-CoV-2. 15, 16 The short-term humoral immune response in COVID-19 patients is also highly consistent with that observed in patients infected with SARS-CoV and MERS-CoV, 17, 18 who show a rapid decrease in virus-specific antibody titers within 3-4 months. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. abstract: Background Coronavirus disease 2019 (COVID-19) is a global pandemic with no licensed vaccine or specific antiviral agents for therapy. Little is known about the longitudinal dynamics of SARS-CoV-2-specific neutralizing antibodies (NAbs) in COVID-19 patients. Methods Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. Results SARS-CoV-2-specific NAb titers were low for the first 7-10 d after symtom onset and increased after 2-3 weeks. The median peak time for NAbs was 33 d (IQR 24-59 d) after symptom onset. NAb titers in 93.3% (28/30) of the patients declined gradually over the 3-month study period, with a median decrease of 34.8% (IQR 19.6-42.4%). NAb titers increased over time in parallel with the rise in IgG antibody levels, correlating well at week 3 (r = 0.41, p < 0.05). The NAb titers also demonstrated a significant positive correlation with levels of plasma proinflammatory cytokines, including SCF, TRAIL, and M-CSF. Conclusions These data provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases. url: http://medrxiv.org/cgi/content/short/2020.07.14.20151159v1?rss=1 doi: 10.1101/2020.07.14.20151159 id: cord-279550-7u2hksxm author: Wang, Kai title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-08-03 words: 2656.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-279550-7u2hksxm.txt txt: ./txt/cord-279550-7u2hksxm.txt summary: METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. Thus, serological testing, especially to detect NAbs, is essential in determining the onset of the serological immune response, evaluating the potential capacity of the host body for viral clearance, and identifying donors for passive antibody therapy trials. 12, 13 However, the dynamics and roles of SARS-CoV-2-specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Furthermore, to determine if there was a statistical correlation between NAb levels and virus-specific IgG levels in COVID-19 patients, serum samples were grouped by time (weeks) after symptom onset. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a global pandemic with no licensed vaccine or specific antiviral agents for therapy. Little is known about the longitudinal dynamics of SARS-CoV-2-specific neutralizing antibodies (NAbs) in COVID-19 patients. METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. RESULTS: SARS-CoV-2-specific NAb titers were low for the first 7–10 d after symptom onset and increased after 2–3 weeks. The median peak time for NAbs was 33 d (IQR 24–59 d) after symptom onset. NAb titers in 93·3% (28/30) of the patients declined gradually over the 3-month study period, with a median decrease of 34·8% (IQR 19·6–42·4%). NAb titers increased over time in parallel with the rise in IgG antibody levels, correlating well at week 3 (r = 0·41, p & 0·05). The NAb titers also demonstrated a significant positive correlation with levels of plasma proinflammatory cytokines, including SCF, TRAIL, and M-CSF. CONCLUSIONS: These data provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases. url: https://doi.org/10.1093/cid/ciaa1143 doi: 10.1093/cid/ciaa1143 id: cord-349392-r71g2e9y author: Wang, L. -F. title: Bats, Civets and the Emergence of SARS date: 2007 words: 7011.0 sentences: 301.0 pages: flesch: 52.0 cache: ./cache/cord-349392-r71g2e9y.txt txt: ./txt/cord-349392-r71g2e9y.txt summary: Virological and serological studies indicated that masked palm civets ( Paguma larvata ), together with two other wildlife animals, sampled from a live animal market were infected with SARS-CoV or a closely related virus. Here, we review studies by different groups demonstrating that SARS-CoV succeeded in spillover from a wildlife reservoir (probably bats) to human population via an intermediate host(s) and that rapid virus evolution played a key role in the adaptation of SARS-CoVs in at least two nonreservoir species within a short period. Recently, two groups independently demonstrated that bats in the genus Rhinolophus are natural reservoirs of SARS-like viruses , providing strong evidence that SARS-CoV is indeed a new zoonotic virus with a wildlife origin. (2003) , SARS-CoV-like viruses were isolated from palm civets and a raccoon dog in a live animal market in southern China and serologic evidence indicted that a third species, the Chinese ferret-badger, was also infected by a similar virus. abstract: Severe acute respiratory syndrome (SARS) was the first pandemic transmissible disease of previously unknown aetiology in the twenty-first century. Early epidemiologic investigations suggested an animal origin for SARS-CoV. Virological and serological studies indicated that masked palm civets ( Paguma larvata ), together with two other wildlife animals, sampled from a live animal market were infected with SARS-CoV or a closely related virus. Recently, horseshoe bats in the genus Rhinolophus have been identified as natural reservoir of SARS-like coronaviruses. Here, we review studies by different groups demonstrating that SARS-CoV succeeded in spillover from a wildlife reservoir (probably bats) to human population via an intermediate host(s) and that rapid virus evolution played a key role in the adaptation of SARS-CoVs in at least two nonreservoir species within a short period. url: https://www.ncbi.nlm.nih.gov/pubmed/17848070/ doi: 10.1007/978-3-540-70962-6_13 id: cord-309302-n6cd2fc3 author: Wang, Li title: Clinical management of lung cancer patients during the outbreak of COVID-19 epidemic date: 2020-09-23 words: 5674.0 sentences: 318.0 pages: flesch: 46.0 cache: ./cache/cord-309302-n6cd2fc3.txt txt: ./txt/cord-309302-n6cd2fc3.txt summary: In this review, we focus on the epidemiological characteristics, early diagnosis, patient management and mental health of lung cancer patients during the COVID-19 epidemic. According to China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), drugs with potential antiviral effects should be used early in the course of the disease, and it is recommended to focus on patients with high risk factors for severe illness patients. However, hydroxychloroquine or combined azithromycin is not recommended for COVID-19 patients base on China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). In addition, convalescent plasma is suitable for patients with rapid disease progression, severe and critically ill patients base on China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). According to China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), Tocilizumab can be tried for patients with extensive lung disease and elevated IL-6 levels in the laboratory. abstract: The rapid growth of 2019 novel coronavirus (COVID-19) outbreak in Wuhan, China, at the early December 2019. COVID-19 spread all over the word just a few months. The outbreak of COVID-19 infection poses major threat to international health and economy. World Health Organization (WHO) announced that the new coronavirus was an international public health emergency on January 30, 2020. However, with the spread of COVID-19, the routine medical care of lung cancer patients was affected. Because lung cancer patients have low immunity after anti-tumor treatment, they should become the main targets for epidemic prevention. Lung cancer patients are increasingly concerned about the prevention of COVID-19. It is necessary to provide individualized medical treatment and management for lung cancer patients based on patients’ conditions and regional epidemic patterns. url: https://doi.org/10.1186/s13027-020-00322-7 doi: 10.1186/s13027-020-00322-7 id: cord-258160-v08cs51n author: Wang, Lin-Fa title: Review of Bats and SARS date: 2006-12-17 words: 3793.0 sentences: 171.0 pages: flesch: 50.0 cache: ./cache/cord-258160-v08cs51n.txt txt: ./txt/cord-258160-v08cs51n.txt summary: Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Although in 1 live animal market, 3 species were found to be infected by viruses related to SARS-CoV (9), all subsequent studies have focused mainly on palm civets, possibly because the rate of detection was higher in civets or because the number of civets traded in southern People''s Republic of China exceeds that of other wildlife groups. abstract: Bats have been identified as a natural reservoir for an increasing number of emerging zoonotic viruses, including henipaviruses and variants of rabies viruses. Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Our current research focused on the identification of the reservoir species for the progenitor virus of the SARS coronaviruses responsible for outbreaks during 2002–2003 and 2003–2004. In addition to SARS-like coronaviruses, many other novel bat coronaviruses, which belong to groups 1 and 2 of the 3 existing coronavirus groups, have been detected by PCR. The discovery of bat SARS-like coronaviruses and the great genetic diversity of coronaviruses in bats have shed new light on the origin and transmission of SARS coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17326933/ doi: 10.3201/eid1212.060401 id: cord-277309-kelebqr6 author: Wang, Lin-Fa title: Viruses in bats and potential spillover to animals and humans date: 2019-01-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission. url: https://www.sciencedirect.com/science/article/pii/S187962571830107X doi: 10.1016/j.coviro.2018.12.007 id: cord-277759-zbmzjsvs author: Wang, Luwen title: Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China date: 2020-03-31 words: 3233.0 sentences: 190.0 pages: flesch: 53.0 cache: ./cache/cord-277759-zbmzjsvs.txt txt: ./txt/cord-277759-zbmzjsvs.txt summary: BACKGROUND: Whether the patients with coronavirus disease 19 (COVID-19) infected by severe acute respiratory syndrome (SARS)-CoV-2 would commonly develop acute kidney injury (AKI) is an important issue worthy of clinical attention. This study aimed to explore the effects of SARS-CoV-2 infection on renal function through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. As shown in Table 2 , 111 COVID-19-confirmed patients without CKD did not develop obvious abnormal renal function after infection with SARS-CoV-2 and during the treatment of pneumonia. SARS-CoV-2 RNA in urine sediments of COVID-19-confirmed 53 patients, including 5 CKD cases, enrolled in this study was examined by real-time RT-PCR. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. abstract: BACKGROUND: Whether the patients with coronavirus disease 19 (COVID-19) infected by severe acute respiratory syndrome (SARS)-CoV-2 would commonly develop acute kidney injury (AKI) is an important issue worthy of clinical attention. This study aimed to explore the effects of SARS-CoV-2 infection on renal function through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. METHODS: One hundred sixteen COVID-19-confirmed patients enrolled in this study were hospitalized in the Department of Infectious Diseases, Renmin Hospital of Wuhan University from January 14 to February 13, 2020. The recorded information includes demographic data, medical history, contact history, potential comorbidities, symptoms, signs, laboratory test results, chest computer tomography scans, and treatment measures. SARS-CoV-2 RNA in 53 urine sediments of enrolled patients was detected by real-time reverse transcription-polymerase chain reaction. RESULTS: Twelve (10.8%) patients showed mild increase of blood urea nitrogen or creatinine (<26 μmol/L within 48 h), and 8 (7.2%) patients showed trace or 1+ albuminuria in 111 COVID-19-confirmed patients without chronic kidney disease (CKD). All these patients did not meet the diagnostic criteria of AKI. In addition, 5 patients with CKD who were undergone regular continuous renal replacement therapy (CRRT) before admission were confirmed infection of SARS-CoV-2 and diagnosed as COVID-19. In addition to therapy for COVID-19, CRRT was also applied 3 times weekly during hospitalization for these 5 patients with CKD. In the course of treatment, the renal function indicators showed stable state in all 5 patients with CKD, without exacerbation of CKD, and pulmonary inflammation was gradually absorbed. All 5 patients with CKD were survived. Moreover, SARS-CoV-2 RNA in urine sediments was positive only in 3 patients from 48 cases without CKD, and 1 patient had a positive for SARS-CoV-2 open reading frame 1ab from 5 cases with CKD. CONCLUSION: AKI was uncommon in COVID-19. SARS-CoV-2 infection does not result in AKI, or aggravate CKD in the COVID-19 patients. url: https://doi.org/10.1159/000507471 doi: 10.1159/000507471 id: cord-332672-fbwz8oxp author: Wang, Manli title: Bats as animal reservoirs for the SARS coronavirus: Hypothesis proved after 10 years of virus hunting date: 2013-10-30 words: 1114.0 sentences: 51.0 pages: flesch: 61.0 cache: ./cache/cord-332672-fbwz8oxp.txt txt: ./txt/cord-332672-fbwz8oxp.txt summary: It was suggested that the previously known bat SL-CoV stains cannot jump from bats to civets or humans owing to the significant differences between their RBDs (Li F, 2013); 2) although SL-CoVs have been identified from different bat species, isolation of a live SL-CoVs from bats never succeed; 3) no native SL-CoV from bats could use ACE2 as receptors and infect human cells, only when its RBD is replaced with the counterpart from a human SARS-CoV strain (Li W, et al, 2003; Becker M M, et al, 2008; Ren W, et al, 2008) . The residue 479 is known to be an asparagine only in human SAR-CoVs, but not in the previously identified bat SL-CoVs or civet SAR-CoVs. It is proposed that an asparagine at position 479 has a higher binding affinity with human ACE2 and is likely to determine whether the virus can infect humans (Li F, 2013) . abstract: Recently, the team led by Dr. Zhengli Shi from Wuhan Institute of Virology, Chinese Academy of Sciences, and Dr. Peter Daszak from Ecohealth Alliance identified SL-CoVs in Chinese horseshoe bats that were 95% identical to human SARS-CoV and were able to use human angiotensin-converting enzyme 2 (ACE2) receptor for docking and entry. Remarkably, they isolated the first known live bat SL-CoV that replicates in human and related cells. Their findings provide clear evidence that some SL-CoVs circulating in bats are capable of infecting and replicating in human (Ge X Y, et al., 2013). url: https://www.ncbi.nlm.nih.gov/pubmed/24174406/ doi: 10.1007/s12250-013-3402-x id: cord-349545-w7c2tu5a author: Wang, Mengmeng title: Analytical performance evaluation of five RT‐PCR kits for severe acute respiratory syndrome coronavirus 2 date: 2020-10-27 words: 1838.0 sentences: 126.0 pages: flesch: 55.0 cache: ./cache/cord-349545-w7c2tu5a.txt txt: ./txt/cord-349545-w7c2tu5a.txt summary: BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT‐PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS‐CoV‐2 infection. 8 Pan et al found that thermal inactivation adversely affected the efficiency of RT-PCR for SARS-CoV-2 detection samples with low viral loads. In the work, we presented the analytical performance evaluations of five RT-PCR kits using nasopharyngeal swabs samples from patients with confirmed SARS-CoV-2 infection, and negative nasopharyngeal swabs samples ( Figure 1 ). To further confirm the detection ability of the five kits, a positive clinical specimen (Ct: ORF1ab 26.99, N: 28.19) was diluted with 5-fold using RNase-free water, and the resulting dilution is considered as Level 1. No positive result was obtained in testing of 30 negative clinical samples by using five kits for ORF1ab and N gene. abstract: BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT‐PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. METHODS: A total of 20 COVID‐19 confirmed patients and 30 negative nasopharyngeal swab specimens were analyzed by five kits. The detection ability of five RT‐PCR kits was evaluated with 5 concentration gradients diluted by a single positive sample. The limit of detection was evaluated by N gene fragment solid standard. Two positive clinical specimens were used to evaluate the repeatability and imprecision. Finally, we used six human coronaviruses plasmid and four respiratory pathogens plasmid to check for cross‐reactivity. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS‐CoV‐2 infection. The coincidence rate of five kits in 10 negative samples was 100%. The detection rate of target genes for Daan, BioGerm, Liferiver, and Yaneng was 100% from Level 1 to Level 3. In Level 4, only Daan detection rate was 100%. In Level 5, five kits presented poor positive rate. The limit of detection declared by each manufacturer was verified. The repeatability for target genes was less than 5% and so did the total imprecision. There is no cross‐reactivity of five kits with six human coronaviruses and four respiratory pathogens for ORF1ab and N gene. CONCLUSIONS: Five RT‐PCR kits assessed in this study showed acceptable analytical performance characteristics and are useful tools for the routine diagnosis of SARS‐CoV‐2. url: https://www.ncbi.nlm.nih.gov/pubmed/33107116/ doi: 10.1002/jcla.23643 id: cord-318387-s4d442kx author: Wang, Ming title: Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses date: 2020-03-06 words: 4680.0 sentences: 304.0 pages: flesch: 56.0 cache: ./cache/cord-318387-s4d442kx.txt txt: ./txt/cord-318387-s4d442kx.txt summary: COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. https://doi.org/10.1101/2020.03.04.20029538 doi: medRxiv preprint read numbers of the test sample to those of the negative control (with "0" in the negative control 129 calculated as "1"), we defined that a ratio of ≥10 indicates a positive result for that fragment, 130 scoring 1; ≥3 to 10 fold is inconclusive, scoring 0.4; and <3 is negative, scoring 0. The 4 h sequencing output data (Fig. 4a ) revealed that all 153 19 samples defined as positive by qPCR were recognized SARS-CoV-2-infected by NTS, 154 abstract: The ongoing novel coronavirus pneumonia COVID-19 outbreak in Wuhan, China, has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Combining the advantages of target amplification and long-read, real-time nanopore sequencing, we developed nanopore target sequencing (NTS) to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. NTS is thus suitable for contemporary COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses or pathogens. url: https://doi.org/10.1101/2020.03.04.20029538 doi: 10.1101/2020.03.04.20029538 id: cord-327124-kzavc4ez author: Wang, Ming title: SARS-CoV Infection in a Restaurant from Palm Civet date: 2005-12-17 words: 3408.0 sentences: 172.0 pages: flesch: 60.0 cache: ./cache/cord-327124-kzavc4ez.txt txt: ./txt/cord-327124-kzavc4ez.txt summary: Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003–2004 were a waitress at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant a short distance from animal cages. Only 5 signature nt variations (SNVs) were observed in the 5 complete S gene sequences from palm civets determined in this study, indicating that SARS-CoV sequences from civets at the restaurant were not different from those of the original animal SARS source. These most recent SARS patients were therefore infected by SARS-CoV that is most closely related to virus isolates from palm civets at the restaurant (Figure) (6) . When the complete genomes of SARS-CoV from palm civets at the restaurant were compared with sequences of human isolates, 62 SNVs were identified. However, when the complete genome was compared with sequences of virus isolated from palm civets from animal markets in the 2003 epidemic, only 37 SNVs were identified. abstract: Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003–2004 were a waitress at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant a short distance from animal cages. All 6 palm civets at the restaurant were positive for SARS-associated coronavirus (SARS-CoV). Partial spike (S) gene sequences of SARS-CoV from the 2 patients were identical to 4 of 5 S gene viral sequences from palm civets. Phylogenetic analysis showed that SARS-CoV from palm civets in the restaurant was most closely related to animal isolates. SARS cases at the restaurant were the result of recent interspecies transfer from the putative palm civet reservoir, and not the result of continued circulation of SARS-CoV in the human population. url: https://www.ncbi.nlm.nih.gov/pubmed/16485471/ doi: 10.3201/eid1112.041293 id: cord-299148-uge5uodk author: Wang, Qiang title: A Method To Prevent SARS-CoV-2 IgM False Positives in Gold Immunochromatography and Enzyme-Linked Immunosorbent Assays date: 2020-05-26 words: 2874.0 sentences: 124.0 pages: flesch: 47.0 cache: ./cache/cord-299148-uge5uodk.txt txt: ./txt/cord-299148-uge5uodk.txt summary: We set out to investigate the interference factors that led to false-positive novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgM detection results using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions. GICA and ELISA were used to detect SARS-CoV-2 IgM in 86 serum samples, including 5 influenza A virus (Flu A) IgM-positive sera, 5 influenza B virus (Flu B) IgM-positive sera, 5 Mycoplasma pneumoniae IgM-positive sera, 5 Legionella pneumophila IgM-positive sera, 6 sera of HIV infection patients, 36 rheumatoid factor IgM (RF-IgM)-positive sera, 5 sera from hypertensive patients, 5 sera from diabetes mellitus patients, and 14 sera from novel coronavirus infection disease 19 (COVID-19) patients. At a urea dissociation concentration of 4 mol/liter and with affinity index (AI) levels lower than 0.371 set to negative, SARS-CoV-2 IgM results were positive in 3 mid-to-high-level-RF-IgM-positive sera and in 14 COVID-19 patient sera detected using ELISA. abstract: We set out to investigate the interference factors that led to false-positive novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgM detection results using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions. GICA and ELISA were used to detect SARS-CoV-2 IgM in 86 serum samples, including 5 influenza A virus (Flu A) IgM-positive sera, 5 influenza B virus (Flu B) IgM-positive sera, 5 Mycoplasma pneumoniae IgM-positive sera, 5 Legionella pneumophila IgM-positive sera, 6 sera of HIV infection patients, 36 rheumatoid factor IgM (RF-IgM)-positive sera, 5 sera from hypertensive patients, 5 sera from diabetes mellitus patients, and 14 sera from novel coronavirus infection disease 19 (COVID-19) patients. The interference factors causing false-positive reactivity with the two methods were analyzed, and the urea dissociation test was employed to dissociate the SARS-CoV-2 IgM-positive serum using the best dissociation concentration. The two methods detected positive SARS-CoV-2 IgM in 22 mid-to-high-level-RF-IgM-positive sera and 14 sera from COVID-19 patients; the other 50 sera were negative. At a urea dissociation concentration of 6 mol/liter, SARS-CoV-2 IgM results were positive in 1 mid-to-high-level-RF-IgM-positive serum and in 14 COVID-19 patient sera detected using GICA. At a urea dissociation concentration of 4 mol/liter and with affinity index (AI) levels lower than 0.371 set to negative, SARS-CoV-2 IgM results were positive in 3 mid-to-high-level-RF-IgM-positive sera and in 14 COVID-19 patient sera detected using ELISA. The presence of RF-IgM at mid-to-high levels could lead to false-positive reactivity of SARS-CoV-2 IgM detected using GICA and ELISA, and urea dissociation tests would be helpful in reducing SARS-CoV-2 IgM false-positive results. url: https://doi.org/10.1128/jcm.00375-20 doi: 10.1128/jcm.00375-20 id: cord-297332-rzf0cw1x author: Wang, Qidi title: Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates date: 2016-04-11 words: 8688.0 sentences: 431.0 pages: flesch: 56.0 cache: ./cache/cord-297332-rzf0cw1x.txt txt: ./txt/cord-297332-rzf0cw1x.txt summary: 15 Other observations include evidence of ADE reported here for the first time induced by an inactivated SARS-CoV vaccine in rhesus macaques ( Figure 1 ) and by antisera from SARS patients (Table S1) , as well as ADE in other coronavirus infections. Herein, we discovered that a peptide of the viral sequence simultaneously elicits the antibodies of disparate functions in protection and enhancement against SARS-CoV infection by the studies with host Vero E6 cells in vitro and in non-human primates. In contrast, the immunized monkeys in the Vac3 group had a strongly increased ability to control SARS-CoV infection in association with induction of high levels of anti-S 604−625 antibodies ( Figure 7E ). 44 This study demonstrates for the first time that an antibody (mAb43-3-14) targeting a specific linear epitope (S 597−603 ) of the SARS-CoV spike protein can mediate enhancement of virus infection both in vitro and in non-human primates via an epitope sequence-dependent mechanism. abstract: [Image: see text] Severe acute respiratory syndrome (SARS) is caused by a coronavirus (SARS-CoV) and has the potential to threaten global public health and socioeconomic stability. Evidence of antibody-dependent enhancement (ADE) of SARS-CoV infection in vitro and in non-human primates clouds the prospects for a safe vaccine. Using antibodies from SARS patients, we identified and characterized SARS-CoV B-cell peptide epitopes with disparate functions. In rhesus macaques, the spike glycoprotein peptides S(471–503), S(604–625), and S(1164–1191) elicited antibodies that efficiently prevented infection in non-human primates. In contrast, peptide S(597–603) induced antibodies that enhanced infection both in vitro and in non-human primates by using an epitope sequence-dependent (ESD) mechanism. This peptide exhibited a high level of serological reactivity (64%), which resulted from the additive responses of two tandem epitopes (S(597–603) and S(604–625)) and a long-term human B-cell memory response with antisera from convalescent SARS patients. Thus, peptide-based vaccines against SARS-CoV could be engineered to avoid ADE via elimination of the S(597–603) epitope. We provide herein an alternative strategy to prepare a safe and effective vaccine for ADE of viral infection by identifying and eliminating epitope sequence-dependent enhancement of viral infection. url: https://www.ncbi.nlm.nih.gov/pubmed/27627203/ doi: 10.1021/acsinfecdis.6b00006 id: cord-291076-p350i54m author: Wang, Renxi title: The role of C5a in acute lung injury induced by highly pathogenic viral infections date: 2015-05-06 words: 5790.0 sentences: 373.0 pages: flesch: 42.0 cache: ./cache/cord-291076-p350i54m.txt txt: ./txt/cord-291076-p350i54m.txt summary: Unregulated complement activation is likely to play a crucial role in the pathogenesis of acute lung injury (ALI) induced by highly pathogenic virus including influenza A viruses H5N1, H7N9, and severe acute respiratory syndrome (SARS) coronavirus. [1] [2] [3] In addition, the complement system has been implicated in the development of acute lung diseases induced by highly pathogenic viruses including influenza A virus H1N1, 4 H5N1, 5 H7N9, 6 severe acute respiratory syndrome coronavirus (SARS-Cov), 7 Middle East respiratory syndrome coronavirus (MERS-Cov). C5a-mediated release of reactive oxygen species C5a is a strong chemoattractant for neutrophils and monocytes; it then activates these cells to generate oxidative burst with release of 10 A study demonstrated that ROS are primary pathogenic molecules in pneumonia from mice infected with influenza virus. Inhibition of Complement Activation Alleviates Acute Lung Injury Induced by Highly Pathogenic Avian Influenza H5N1 Virus Infection abstract: The complement system, an important part of innate immunity, plays a critical role in pathogen clearance. Unregulated complement activation is likely to play a crucial role in the pathogenesis of acute lung injury (ALI) induced by highly pathogenic virus including influenza A viruses H5N1, H7N9, and severe acute respiratory syndrome (SARS) coronavirus. In highly pathogenic virus-induced acute lung diseases, high levels of chemotactic and anaphylatoxic C5a were produced as a result of excessive complement activaiton. Overproduced C5a displays powerful biological activities in activation of phagocytic cells, generation of oxidants, and inflammatory sequelae named “cytokine storm”, and so on. Blockade of C5a signaling have been implicated in the treatment of ALI induced by highly pathogenic virus. Herein, we review the literature that links C5a and ALI, and review our understanding of the mechanisms by which C5a affects ALI during highly pathogenic viral infection. In particular, we discuss the potential of the blockade of C5a signaling to treat ALI induced by highly pathogenic viruses. url: https://doi.org/10.1038/emi.2015.28 doi: 10.1038/emi.2015.28 id: cord-193489-u6ewlh16 author: Wang, Rui title: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date: 2020-04-29 words: 6066.0 sentences: 419.0 pages: flesch: 62.0 cache: ./cache/cord-193489-u6ewlh16.txt txt: ./txt/cord-193489-u6ewlh16.txt summary: Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. Genetic identification and characterization of the geographic distribution, intercontinental evolution, and global trends of SARS-CoV-2 is the most efficient approach for studying COVID-19 genomic epidemiology and offer the molecular foundation for region-specific SARS-CoV-2 vaccine design, drug discovery, and diagnostic development [10] . We use K-means methods to cluster SARS-CoV-2 mutations, which provides the updated molecular information for the region-specific design of vaccines, drugs, and diagnoses. Table 5 presents the statistics of single mutations on various SARS-CoV-2 proteins that occurred in the recorded genomes between January 5, 2020, and April 24, 2020. Specifically, nucleocapsid protein has both the highest number of mutations per residues of 0.56 and the highest h-index of 27, suggesting that it is the most non-conservative protein in SARS-CoV-2 genomes. abstract: Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. We introduce mutation ratio and mutation $h$-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively non-conservative. In particular, the nucleocapsid protein has more than half its genes changed in the past few months, signaling devastating impacts on the ongoing development of COVID-19 diagnosis, vaccines, and drugs. url: https://arxiv.org/pdf/2004.14114v1.pdf doi: nan id: cord-206006-8l7hrany author: Wang, Rui title: Mutations on COVID-19 diagnostic targets date: 2020-05-05 words: 1605.0 sentences: 94.0 pages: flesch: 56.0 cache: ./cache/cord-206006-8l7hrany.txt txt: ./txt/cord-206006-8l7hrany.txt summary: Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on the genotyping of 7818 SARS-CoV-2 genome samples collected up to May 1, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have had mutations. We further show that SARS-CoV-2 has the most devastating mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been unfortunately used by countries around the world to diagnose COVID-19. It is interesting to note that N-China-F [10] is the most inefficient reagent among all primers/probes and its SARS-CoV-2 target has eight mutations involving samples in all five clusters, which may explain many media reports about the inefficiency of certain COVID-19 diagnostic kits made in China. abstract: Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It would be an absolute tragedy if currently used diagnostic reagents are undermined in any manner. Based on the genotyping of 7818 SARS-CoV-2 genome samples collected up to May 1, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have had mutations. We further show that SARS-CoV-2 has the most devastating mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been unfortunately used by countries around the world to diagnose COVID-19. Our findings explain what has seriously gone wrong with a specific diagnostic reagent made in China. To understand whether SARS-CoV-2 genes have mutated unevenly, we have computed the mutation ratio and mutation $h$-index of all SARS-CoV genes, indicating that the N gene is the most non-conservative gene in the SARS-CoV-2 genome. Our findings enable researchers to target the most conservative SARS-CoV-2 genes and proteins for the design and development of COVID-19 diagnostic reagents, preventive vaccines, and therapeutic medicines. url: https://arxiv.org/pdf/2005.02188v1.pdf doi: nan id: cord-277774-kec1o4ys author: Wang, Shangqian title: The need for urogenital tract monitoring in COVID-19 date: 2020-04-20 words: 1528.0 sentences: 84.0 pages: flesch: 48.0 cache: ./cache/cord-277774-kec1o4ys.txt txt: ./txt/cord-277774-kec1o4ys.txt summary: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, which invades a cell through binding to the ACE2 receptor and TMPRSS2 priming. Most patients with severe COVID-19 present with pneumonia-related symptoms, but some patients with severe disease could develop serious urinary complications including acute kidney injury (AKI), which requires continuous renal replacement therapy (CRRT) 1 . Furthermore, male reproductive systems are vulnerable to infection; dramatic changes in sex hormones in patients with COVID-19 have been observed, suggesting gonadal function impairment 2 . Similar findings were also observed in autopsy kidney samples from patients with MERS-CoV infection 4 , which showed degeneration of the renal tubules, including ectasia changes and necrosis, sloughing, and loss of brush surface in the proximal tubular epithelial cells. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection abstract: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, which invades a cell through binding to the ACE2 receptor and TMPRSS2 priming. Patients with severe disease predominantly present with pneumonia-related symptoms. However, evidence suggests that COVID-19 infection also has implications for the urogenital tract. Thus, urogenital organs should be considered when treating COVID-19. url: https://doi.org/10.1038/s41585-020-0319-7 doi: 10.1038/s41585-020-0319-7 id: cord-296250-7ln7p715 author: Wang, Sheng-Fan title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date: 2020-05-20 words: 4962.0 sentences: 302.0 pages: flesch: 43.0 cache: ./cache/cord-296250-7ln7p715.txt txt: ./txt/cord-296250-7ln7p715.txt summary: Increasing evidence showed potential therapeutic agents directly acting against SARS-CoV-2 virus, such as interferon, RNA-dependent RNA polymerase inhibitors, protease inhibitors, viral entry blockers, neuraminidase inhibitor, vaccine, antibody agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitor. Increasing evidence reveals potential therapeutic agents acting directly against SARS-CoV-2, such as interferon (IFN), RdRp inhibitors, protease inhibitors, coronaviral protease inhibitor, viral entry blocker, neuraminidase inhibitor, vaccine, antibody, agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitors. The novel specific anti-SARS-CoV-2 agents might comprise inhibitors interfering with the viral replication cycle, antibody targeting the host receptor and virus S protein, and inhibitors of host cellular proteases involved in the virus endocytosis pathway. 33, 34 Moreover, evidence showed that diarylheptanoids, the natural products derived from Japanese alder (Alnus japonica), can inhibit the papain-like protease and restore the host innate immunity response against SARS-CoV through maintaining the function of IFNs. 31 Therefore, specific coronaviral proteases might be good candidate targets for developing new drugs to fight COVID-19. abstract: Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was quickly identified as the causal pathogen leading to the outbreak of SARS-like illness all over the world. As the SARS-CoV-2 infection pandemic proceeds, many efforts are being dedicated to the development of diverse treatment strategies. Increasing evidence showed potential therapeutic agents directly acting against SARS-CoV-2 virus, such as interferon, RNA-dependent RNA polymerase inhibitors, protease inhibitors, viral entry blockers, neuraminidase inhibitor, vaccine, antibody agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitor. To date, several direct anti-SARS-CoV-2 agents have demonstrated promising in vitro and clinical efficacy. This article reviews the current and future development of direct acting agents against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32433345/ doi: 10.1097/jcma.0000000000000353 id: cord-311610-uniz8tuc author: Wang, Shi-Yi title: The impact on neonatal mortality of shifting childbirth services among levels of hospitals: Taiwan''s experience date: 2009-06-08 words: 3476.0 sentences: 161.0 pages: flesch: 44.0 cache: ./cache/cord-311610-uniz8tuc.txt txt: ./txt/cord-311610-uniz8tuc.txt summary: This evidence indicates that the neonatal mortality rate in areas with large hospitals was significantly lower than predicted, despite the shift of childbirth services to local community hospitals during the SARS epidemic. Furthermore, this study''s large sample size of 1,848 observations allows us to demonstrate clearly that the shifting of childbirth services among hospitals associated with the SARS epidemic did not increase the risk of neonatal deaths. Although it has not been documented conclusively whether or not advanced hospitals provide better care for normal birthweight deliveries than small maternity units [7] [8] [9] [10] [11] [12] [13] [14] [15] , this study has demonstrated that childbirth outcomes were not influenced by the shift in maternity services to local community hospitals during the SARS epidemic in Taiwan. abstract: BACKGROUND: There is considerable discussion surrounding whether advanced hospitals provide better childbirth care than local community hospitals. This study examines the effect of shifting childbirth services from advanced hospitals (i.e., medical centers and regional hospitals) to local community hospitals (i.e., clinics and district hospitals). The sample population was tracked over a seven-year period, which includes the four months of the 2003 severe acute respiratory syndrome (SARS) epidemic in Taiwan. During the SARS epidemic, pregnant women avoided using maternity services in advanced hospitals. Concerns have been raised about maintaining the quality of maternity care with increased demands on childbirth services in local community hospitals. In this study, we analyzed the impact of shifting maternity services among hospitals of different levels on neonatal mortality and maternal deaths. METHODS: A population-based study was conducted using data from Taiwan's National Health Insurance annual statistics of monthly county neonatal morality rates. Based on a pre-SARS sample from January 1998 to December 2002, we estimated a linear regression model which included "trend," a continuous variable representing the effect of yearly changes, and two binary variables, "month" and "county," controlling for seasonal and county-specific effects. With the estimated coefficients, we obtained predicted neonatal mortality rates for each county-month. We compared the differences between observed mortality rates of the SARS period and predicted rates to examine whether the shifting in maternity services during the SARS epidemic significantly affected neonatal mortality rates. RESULTS: With an analysis of a total of 1,848 observations between 1998 and 2004, an insignificantly negative mean of standardized predicted errors during the SARS period was found. The result of a sub-sample containing areas with advanced hospitals showed a significant negative mean of standardized predicted errors during the SARS period. These findings indicate that despite increased use of local community hospitals, neonatal mortality during the SARS epidemic did not increase, and even decreased in areas with advanced hospitals. CONCLUSION: An increased use of maternity services in local community hospitals occurred during the SARS epidemic in Taiwan. However, we observed no increase in neonatal and maternity mortality associated with these increased demands on local community hospitals. url: https://doi.org/10.1186/1472-6963-9-94 doi: 10.1186/1472-6963-9-94 id: cord-321564-6950p8i9 author: Wang, Shiu‐Mei title: Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date: 2019-07-10 words: 2794.0 sentences: 148.0 pages: flesch: 42.0 cache: ./cache/cord-321564-6950p8i9.txt txt: ./txt/cord-321564-6950p8i9.txt summary: BST2 is a component of innate immune response in the form of restricted enveloped virion release, and many viruses have evolved specific antagonists to counteract BST2 antiviral activity: HIV-1 Vpu, HIV-2 Env, simian immunodeficiency virus (SIV) Nef and Env, Ebola and Sendai virus GP, Kaposi''s sarcoma-associated herpesvirus K5, and influenza virus neuraminidase are all capable of antagonizing BST2. 23 We also found that the SARS-CoV spike (S) protein is capable of downmodulating BST2, thus mitigating the BST2-mediated restriction of virus-like particle (VLP) release, and suggesting that SARS-CoV and other enveloped viruses are capable of evolving additional anti-BST2 factors. BST2, bone marrow stromal antigen 2; SARS-CoV, severe acute respiratory syndrome coronavirus SARS-CoV virion release is mitigated by SARS-CoV S, it is possible that a number of enveloped viruses have developed supplementary anti-BST2 factors over time-note that in addition to Vpu, HIV-1 Nef is capable of overcoming BST2 restrictions on virus release under certain conditions. abstract: BST2/tetherin, an interferon‐inducible antiviral factor, can block the cellular release of various enveloped viruses. We previously reported that human coronavirus 229E (HCoV‐229E) infection can alleviate the BST2 tethering of HIV‐1 virions by downregulating cell surface BST2, suggesting that coronaviruses are capable of encoding anti‐BST2 factors. Here we report our new finding that severe acute respiratory syndrome coronavirus (SARS‐CoV) spike (S) glycoprotein, similar to Vpu, is capable of antagonizing the BST2 tethering of SARS‐CoV, HCoV‐229E, and HIV‐1 virus‐like particles via BST2 downregulation. However, unlike Vpu (which downmodulates BST2 by means of proteasomal and lysosomal degradation pathways), BST2 downregulation is apparently mediated by SARS‐CoV S through the lysosomal degradation pathway only. We found that SARS‐CoV S colocalized with both BST2 and reduced cell surface BST2, suggesting an association between SARS‐CoV S and BST2 that targets the lysosomal degradation pathway. According to one recent report, SARS‐CoV ORF7a antagonizes BST2 by interfering with BST2 glycosylation(1). Our data provide support for the proposal that SARS‐CoV and other enveloped viruses are capable of evolving supplementary anti‐BST2 factors in a manner that requires virus replication. Further experiments are required to determine whether the BST2‐mediated restriction of authentic SARS‐CoV virions is alleviated by the SARS‐CoV spike protein. url: https://doi.org/10.1002/jmv.25518 doi: 10.1002/jmv.25518 id: cord-346669-7n75m669 author: Wang, Shixin title: Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date: 2008-02-29 words: 3814.0 sentences: 200.0 pages: flesch: 53.0 cache: ./cache/cord-346669-7n75m669.txt txt: ./txt/cord-346669-7n75m669.txt summary: This study was to investigate the relationship between tumor necrosis factor (TNF)-α gene polymorphisms with the occurrence of SARS-CoV infection and its role in prognosis of patients with lung interstitial fibrosis and femoral head osteonecrosis. METHODS: The association between genetic polymorphisms of TNF-α gene and susceptibility to severe acute respiratory syndromes (SARS) was conducted in a hospital-based case-control study including 75 SARS patients, 41 health care workers and 92 healthy controls. Relationships of TNF-α gene polymorphisms with interstitial lung fibrosis and femoral head osteonecrosis were carried out in two case-case studies in discharged SARS patients. In this paper, we aimed to study whether polymorphisms in TNF-α promoter region were associated with SARS-CoV infection, development, and progression of interstitial lung fibrosis and femoral head necrosis in cure SARS patients. Considered that the progression of interstitial lung fibrosis or femoral head necrosis may be affected by hormone therapy, hormone using dosage, method and lasting period were considered in this study when analyzing the associations between gene polymorphisms with disease. abstract: BACKGROUND: Host genetic factors may play a role in the occurrence and progress of SARS-Cov infection. This study was to investigate the relationship between tumor necrosis factor (TNF)-α gene polymorphisms with the occurrence of SARS-CoV infection and its role in prognosis of patients with lung interstitial fibrosis and femoral head osteonecrosis. METHODS: The association between genetic polymorphisms of TNF-α gene and susceptibility to severe acute respiratory syndromes (SARS) was conducted in a hospital-based case-control study including 75 SARS patients, 41 health care workers and 92 healthy controls. Relationships of TNF-α gene polymorphisms with interstitial lung fibrosis and femoral head osteonecrosis were carried out in two case-case studies in discharged SARS patients. PCR sequencing based typing (PCR-SBT) method was used to determine the polymorphisms of TNF-α gene in locus of the promoter region and univariate logistic analysis was conducted in analyzing the collected data. RESULTS: Compared to TT genotype, the CT genotype at the -204 locus was found associated with a protective effect on SARS with OR(95%CI) of 0.95(0.90–0.99). Also, TT genotype, CT and CC were found associated with a risk effect on femoral head necrosis with ORs(95%CI) of 5.33(1.39–20.45) and 5.67(2.74–11.71), respectively and the glucocorticoid adjusted OR of CT was 5.25(95%CI 1.18–23.46) and the combined (CT and CC) genotype OR was 6.0 (95%CI 1.60–22.55) at -1031 site of TNF-α gene. At the same time, the -863 AC genotype was manifested as another risk effect associated with femoral head necrosis with OR(95%CI) of 6.42(1.53–26.88) and the adjusted OR was 8.40(95%CI 1.76–40.02) in cured SARS patients compared to CC genotype. CONCLUSION: SNPs of TNF-α gene of promoter region may not associate with SARS-CoV infection. And these SNPs may not affect interstitial lung fibrosis in cured SARS patients. However, the -1031CT/CC and -863 AC genotypes may be risk factors of femoral head necrosis in discharged SARS patients. url: https://doi.org/10.1186/1471-2334-8-27 doi: 10.1186/1471-2334-8-27 id: cord-269862-krcu3hfa author: Wang, Shui-Mei title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date: 2009-05-25 words: 6895.0 sentences: 379.0 pages: flesch: 58.0 cache: ./cache/cord-269862-krcu3hfa.txt txt: ./txt/cord-269862-krcu3hfa.txt summary: We previously demonstrated that HIV-1 Gag mutants containing severe acute respiratory syndrome coronavirus nucleocapsid (SARS-CoV N) coding sequences as NC substitutes can effectively assemble VLPs . Given that SARS-CoV N possesses a RNA-binding property, it is likely that assembly-competent chimeras containing a replacement of HIV-1 NC by an SARS-CoV N sequence may support the incorporation of hA3G into VLPs. Here we demonstrate that the carboxyl-terminal half of the SARS-CoV or human coronavirus 229E (HCoV-229E) N protein not only enables efficient VLP production, but also confers the ability to efficiently package human APOBEC3G (hA3G) when substituted for HIV-1 NC. As the results in Fig. 6B indicate, the carboxyl-terminal half of HCoV-229E N (which also contains a putative self-association domain) (Tswen-Kei Tang, 2005) was capable of replacing the HIV-1 NC function with respect to VLP assembly and hA3G packaging-that is, substantial amounts of VLPs and hA3G were detected in NC(229EN2) transfectant supernatant (lane 4). abstract: We previously reported that replacing HIV-1 nucleocapsid (NC) domain with SARS-CoV nucleocapsid (N) residues 2–213, 215–421, or 234–421 results in efficient virus-like particle (VLP) production at a level comparable to that of wild-type HIV-1. In this study we demonstrate that these chimeras are capable of packaging large amounts of human APOBEC3G (hA3G), and that an HIV-1 Gag chimera containing the carboxyl-terminal half of human coronavirus 229E (HCoV-229E) N as a substitute for NC is capable of directing VLP assembly and efficiently packaging hA3G. When co-expressed with SARS-CoV N and M (membrane) proteins, hA3G was efficiently incorporated into SARS-CoV VLPs. Data from GST pull-down assays suggest that the N sequence involved in N–hA3G interactions is located between residues 86 and 302. Like HIV-1 NC, the SARS-CoV or HCoV-229E N-associated with hA3G depends on the presence of RNA, with the first linker region essential for hA3G packaging into both HIV-1 and SARS-CoV VLPs. The results raise the possibility that hA3G is capable of associating with different species of viral structural proteins through a potentially common, RNA-mediated mechanism. url: https://api.elsevier.com/content/article/pii/S0042682209001834 doi: 10.1016/j.virol.2009.03.010 id: cord-296672-i267t23m author: Wang, Shui-Mei title: Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain date: 2008-07-01 words: 5504.0 sentences: 300.0 pages: flesch: 52.0 cache: ./cache/cord-296672-i267t23m.txt txt: ./txt/cord-296672-i267t23m.txt summary: We replaced the HIV-1 nucleocapsid (NC) domain with different N-coding sequences to test SARS-CoV nucleocapsid (N) self-interaction capacity, and determined the capabilities of each chimera to direct virus-like particle (VLP) assembly. Each mutant was transiently transfected into 293T cells and subjected to Western immunoblotting to determine its ability to assemble and release VLPs. As shown in Fig. 2b , chimeric proteins with predicted molecular weights corresponding to Pr55 gag containing a SARS-CoV N coding sequence insertion in the NC region were readily detected. The above results suggest that HIV-1 Gag containing a large sequence of approximately 200-400 residues inserted into the NC region is still capable of assembling and releasing VLPs. Since the cultured 293T transfectant supernatant was centrifuged through 20% sucrose cushions for 40 min, we believe the recovered viral proteins in the pelleted medium are virus-associated. abstract: We replaced the HIV-1 nucleocapsid (NC) domain with different N-coding sequences to test SARS-CoV nucleocapsid (N) self-interaction capacity, and determined the capabilities of each chimera to direct virus-like particle (VLP) assembly. Analysis results indicate that the replacement of NC with the carboxyl-terminal half of the SARS-CoV N resulted in the production of wild type (wt)-level virus-like particles (VLPs) with the density of a wt HIV-1 particle. When co-expressed with SARS-CoV N, chimeras containing the N carboxyl-terminal half sequence efficiently packaged N. However, the same was not true for the chimera bearing the N amino-terminal half sequence, despite its production of substantial amounts of VLPs. According to further analysis, HIV-1 NC replacement with N residues 2–213, 215–421, or 234–421 resulted in efficient VLP production at levels comparable to that of wt HIV-1, but replacement with residues 215–359, 302–421, 2–168, or 2–86 failed to restore VLP production to wild-type levels. The results suggest that the domain conferring the ability to direct VLP assembly and release in SARS-CoV N is largely contained between residues 168 and 421. url: https://doi.org/10.1007/s11373-008-9265-8 doi: 10.1007/s11373-008-9265-8 id: cord-335619-t3yv5y7h author: Wang, Song-mi title: Screening of SARS-CoV-2 in 299 Hospitalized Children with Hemato-oncological Diseases: A Multicenter Survey in Hubei, China date: 2020-08-07 words: 2426.0 sentences: 131.0 pages: flesch: 48.0 cache: ./cache/cord-335619-t3yv5y7h.txt txt: ./txt/cord-335619-t3yv5y7h.txt summary: A cross-sectional study was performed to investigate the clinical characteristics, lung CT scan, SARS-CoV-2 nucleic acid test and serum antibodies of hospitalized children with hemato-oncological diseases from January 23 to April 24, 2020. A cross-sectional study was performed to inves-tigate the SARS-CoV-2 infection status of children with hemato-oncological diseases hospitalized in three medical institutions from January 23 to April 24, 2020. The findings of this study showed that the SARS-CoV-2 infection rate in enrolled children with hematological malignancies was 0.33%. Zhang [3] reported that 53.6% of COVID-19infected cancer patients had serious clinical events, with a mortality rate of 28.6%. Therefore, for patients with hematological malignancies, the possibility of COVID-19 cannot be ruled out by negative antibody detection, which needs to be combined with multiple nucleic acid test, epidemiological history, and lung imaging to assist in the diagnosis. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: The SARS-CoV-2 infection status of hospitalized children was surveyed in the department of pediatric hematology and oncology in three different hospitals of epidemic areas in Hubei, China. A cross-sectional study was performed to investigate the clinical characteristics, lung CT scan, SARS-CoV-2 nucleic acid test and serum antibodies of hospitalized children with hemato-oncological diseases from January 23 to April 24, 2020. 299 children were enrolled in this study, including 176 males (58.9%) and 123 females (41.1%), aged from 2 months to 16 years. 255 cases (85.3%) received chemotherapy or other immunosuppressive therapies, and there were 44 cases (14.7%) of other benign diseases. Nucleic acid test was performed on 258 children (86.3%) and one case was positive. 163 cases (54.5%) were tested for serum antibodies, and all of them were negative. Lung CT scan was performed on 247 children (82.6%), and 107 of them showed infectious changes. Only one case (0.33%) of COVID-19 was diagnosed in the group. The prevalence rate of COVID-19 in enrolled children with hemato-oncological diseases in Hubei was 0.33%. Immunosuppressed patients are not prone to produce related antibodies. Comprehensive protective measures and ward management can reduce the risk of SARS-CoV-2 infection in the group patients. url: https://doi.org/10.1007/s11596-020-2228-7 doi: 10.1007/s11596-020-2228-7 id: cord-268193-xwptzgvl author: Wang, Tzong-Luen title: Establishing a clinical decision rule of severe acute respiratory syndrome at the emergency department() date: 2003-12-29 words: 3218.0 sentences: 157.0 pages: flesch: 50.0 cache: ./cache/cord-268193-xwptzgvl.txt txt: ./txt/cord-268193-xwptzgvl.txt summary: Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Methods: According to the clinical characteristics and initial laboratory findings of 175 suspected cases defined by the WHO criteria (20 confirmed as cases of SARS) in 3 university teaching hospitals in Taipei between March 1 and April 20, 2003, the scoring system for SARS was designed by multivariate analysis and stepwise logistic regression as the simple arithmetic sum of point values assigned to 7 parameters. abstract: STUDY OBJECTIVE: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. METHODS: According to the clinical characteristics and initial laboratory findings of 175 suspected cases defined by the WHO criteria (20 confirmed as cases of SARS) in 3 university teaching hospitals in Taipei between March 1 and April 20, 2003, the scoring system for SARS was designed by multivariate analysis and stepwise logistic regression as the simple arithmetic sum of point values assigned to 7 parameters. We thereafter applied the scoring system for SARS to the consecutive 232 patients (the validation group) who met the WHO criteria of suspected cases from April 21 to May 22, 2003. Final diagnosis of SARS was determined by the results of real-time polymerase chain reaction and paired serum. RESULTS: The scoring system for SARS was defined as radiographic findings of multilobar or bilateral infiltrates (3 points), sputum monocyte predominance (3 points), lymphocytopenia (2 points), history of exposure (1 point), lactate dehydrogenase more than 450 U/L (1 point), C-reactive protein more than 5.0 mg/dL (1 point), and activated partial prothrombin time more than 40 seconds (1 point). Of the validation group, 60 patients (group A) were confirmed as having cases of SARS, and the other 172 (group B) patients tested negative for SARS. The total points of the scoring system for SARS at initial presentation were significantly higher in the SARS group (median 9; range 6 to 11) than in the non-SARS group (median 4; range 3 to 7; P<.001). At the cutoff value of 6 points, the sensitivity and specificity of the scoring system for SARS in diagnosing SARS were 100% and 93%, respectively. The positive and negative predictive values of the scoring system for SARS were 83% and 100%, respectively. CONCLUSION: The scoring system for SARS can provide a rapid and reliable clinical decision to help emergency physicians detect cases of SARS more accurately in the endemic area. url: https://api.elsevier.com/content/article/pii/S0196064403008254 doi: 10.1016/j.annemergmed.2003.08.002 id: cord-344364-vu389d88 author: Wang, Wei title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 words: 1754.0 sentences: 115.0 pages: flesch: 61.0 cache: ./cache/cord-344364-vu389d88.txt txt: ./txt/cord-344364-vu389d88.txt summary: Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. abstract: COVID‐19 is a respiratory disease caused by a novel coronavirus and is currently a global pandemic. HLA variation is associated with COVID‐19 because HLA plays a pivotal role in the immune response to pathogens. Here, 82 individuals with COVID‐19 were genotyped for HLA‐A, ‐B, ‐C, ‐DRB1, ‐DRB3/4/5, ‐DQA1, ‐DQB1, ‐DPA1, and ‐DPB1 loci using next‐generation sequencing (NGS). Frequencies of the HLA‐C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID‐19 patients than in the control population, with uncorrected statistical significance. Only HLA‐C*07:29 and B*15:27 were significant when the corrected P‐value was considered. These data suggested that some HLA alleles may be associated with the occurrence of COVID‐19. url: https://doi.org/10.1111/tan.13941 doi: 10.1111/tan.13941 id: cord-354394-zojhdnlu author: Wang, Wei-Kung title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 words: 3972.0 sentences: 175.0 pages: flesch: 56.0 cache: ./cache/cord-354394-zojhdnlu.txt txt: ./txt/cord-354394-zojhdnlu.txt summary: We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. Using a quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay and fractionation experiment, we investigated the load of SARS-CoV in these samples and different components of the throat wash. As shown in Table 1 , SARS-CoV RNA was detected in the cell-associated component of the throat wash from all 16 specimens examined. abstract: The severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to be transmitted primarily through dispersal of droplets, but little is known about the load of SARS-CoV in oral droplets. We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. Immunofluorescence study showed replication of SARS-CoV in the cells derived from throat wash, demonstrating the possibility of developing a convenient antigen detection assay. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/15324540/ doi: 10.3201/eid1007.031113 id: cord-348526-g3asp1ps author: Wang, Wenjun title: WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019 date: 2020-02-26 words: 2341.0 sentences: 149.0 pages: flesch: 63.0 cache: ./cache/cord-348526-g3asp1ps.txt txt: ./txt/cord-348526-g3asp1ps.txt summary: We plotted daily data on the frequencies of keywords related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from WeChat, a Chinese social media. Using WeChat Index, we obtained daily data from Nov 17, 2019 to Feb 14, 2020 for the keywords related to the SARS-Cov-2 disease such as "SARS", "Feidian (Chinese abbreviation for severe acute respiratory syndrome)", "pneumonia", "fever", "cough", "shortness of breath", "dyspnea", "fatigue", "stuffy nose", "runny nose", "diarrhea", "coronavirus", "novel coronavirus", and "infection" (see the raw data in Appendix A). By exploring daily data from WeChat, a Chinese social media, we found that the frequencies of several keywords related to the SARS-Cov-2 disease behaved abnormally during a period ahead of the outbreak in China, 2019. Gathering and analyzing data from social media, Internet search queries, news wires and web sites represents a novel approach to early warning and detection of disease outbreaks and is a supplementary to traditional surveillance systems [6] . abstract: We plotted daily data on the frequencies of keywords related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from WeChat, a Chinese social media. Using 'Feidian', Chinese abbreviation for SARS, may detect the SARS-CoV-2 outbreak in 2019 two weeks earlier. WeChat offered a new approach to early detect disease outbreaks. url: https://doi.org/10.1101/2020.02.24.20026682 doi: 10.1101/2020.02.24.20026682 id: cord-338790-rvdoq616 author: Wang, Xiaowen title: Be aware of acute kidney injury in critically ill children with COVID-19 date: 2020-08-26 words: 2904.0 sentences: 155.0 pages: flesch: 47.0 cache: ./cache/cord-338790-rvdoq616.txt txt: ./txt/cord-338790-rvdoq616.txt summary: BACKGROUND: Acute kidney injury (AKI) is a common complication of critically ill adult patients with COVID-19. METHODS: By extracting data from electronic medical records, we conducted a retrospective observational study of kidney involvement in confirmed pediatric COVID-19 cases in Wuhan Children''s Hospital during the coronavirus outbreak, from January 24 to March 20, 2020. The AWARE (Assessment of Worldwide Acute Kidney Injury, Renal Angina, and Epidemiology) study, which enrolled ICUs in 32 hospitals in Asia, Australia, Europe, and North America, showed that the overall incidence of AKI in 4683 critically ill children was 26.9%, and the incidence of severe AKI (KDIGO stage 2 or 3) was 11.6% [8, 14] . The correlation between IL-6 titer and serum creatinine level in our patients suggests that cytokine storm might play a more important role in critically ill COVID-19 children with AKI, in addition to the prerenal and intrarenal injuries. abstract: BACKGROUND: Acute kidney injury (AKI) is a common complication of critically ill adult patients with COVID-19. However, currently, no studies investigate kidney impairment in children with COVID-19. We investigated incidence and treatment of AKI in pediatric patients with COVID-19 in Wuhan Children’s Hospital during the early stages of the COVID-19 pandemic and discuss possible mechanisms of AKI related to SARS-CoV-2 infection. METHODS: By extracting data from electronic medical records, we conducted a retrospective observational study of kidney involvement in confirmed pediatric COVID-19 cases in Wuhan Children’s Hospital during the coronavirus outbreak, from January 24 to March 20, 2020. Clinical presentations, clinical courses, laboratory findings, and medical interventions are described below. RESULTS: Among 238 confirmed COVID-19 cases, only three were critically ill and needed intensive care unit (ICU) admission. All three developed AKI, but AKI was not detected in any non-critically ill patients outside the ICU. Two of the three patients with AKI had prodromal gastrointestinal symptoms. Significantly elevated interleukin-6 (IL-6) levels and complement activation were observed in these patients with AKI. The three patients with AKI were treated with plasma exchange (PE) and continuous kidney replacement therapy (CKRT), resulting in one complete recovery, one partial recovery, and one mortality due to critical illness. CONCLUSIONS: Critically ill children with COVID-19 may develop AKI, especially following prodromal gastrointestinal symptoms. An inflammatory storm and complement-mediated injury may underlie AKI development in children with COVID-19. Our study supports implantation of PE and CKRT in management of critically ill patients with AKI. url: https://www.ncbi.nlm.nih.gov/pubmed/32844290/ doi: 10.1007/s00467-020-04715-z id: cord-336711-bnb62wa6 author: Wang, Xiaoyang title: CT findings of patients infected with SARS-CoV-2 date: 2020-06-23 words: 2043.0 sentences: 143.0 pages: flesch: 61.0 cache: ./cache/cord-336711-bnb62wa6.txt txt: ./txt/cord-336711-bnb62wa6.txt summary: BACKGROUND: We aimed to describe the chest CT findings in sixty-seven patients infected by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The typical CT findings in hospitalized patients with SARS-CoV-2 infection were ground glass opacities (42/54), lesions located in the peripheral area (50/54), multiple lesions (46/54), and lesions located in the lower lobes (42/54). There were less typical CT findings, including air bronchogram (18/54), pleural thickening or pleural effusion (14/54), consolidation (12/54), lesions in the upper lobes (12/54), interlobular septal thickening (11/54), reversed halo sign (9/54), single lesion (8/54), air cavities (4/54), bronchial wall thickening (3/54), and intrathoracic lymph node enlargement (2/54). The chest CT image shows ground glass opacities occupying the left lower lobe (blue arrow) Fig. 4 A female patient infected with SARS-CoV-2. Chest CT images showed the enlargement of ground glass opacity (red arrows) and intrathoracic lymph node (blue arrows) after 10-day treatment found in the patients infected with SARS-CoV-2 ( Table 2 ). abstract: BACKGROUND: We aimed to describe the chest CT findings in sixty-seven patients infected by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We retrospectively reviewed 67 patients hospitalized in Ruian People’s Hospital. All the patients received the positive diagnosis of SARS-CoV-2 infection. The CT and clinical data were collected between January 23rd, 2020 and February 10th, 2020. The CT images were analyzed by the senior radiologists. RESULTS: There are 54 patients with positive CT findings and 13 patients with negative CT findings. The typical CT findings in hospitalized patients with SARS-CoV-2 infection were ground glass opacities (42/54), lesions located in the peripheral area (50/54), multiple lesions (46/54), and lesions located in the lower lobes (42/54). There were less typical CT findings, including air bronchogram (18/54), pleural thickening or pleural effusion (14/54), consolidation (12/54), lesions in the upper lobes (12/54), interlobular septal thickening (11/54), reversed halo sign (9/54), single lesion (8/54), air cavities (4/54), bronchial wall thickening (3/54), and intrathoracic lymph node enlargement (2/54). CONCLUSIONS: CT features can play an important role in the early diagnosis and follow-up of COVID-19 patients. url: https://doi.org/10.1186/s12880-020-00471-6 doi: 10.1186/s12880-020-00471-6 id: cord-277113-pykf7iw1 author: Wang, Xingyu title: The Clinical Features and Outcomes of Discharged Coronavirus Disease 2019 Patients：A Prospective Cohort Study date: 2020-05-22 words: 3565.0 sentences: 232.0 pages: flesch: 57.0 cache: ./cache/cord-277113-pykf7iw1.txt txt: ./txt/cord-277113-pykf7iw1.txt summary: By gathering detailed information of symptoms and treatments, reexamined outcomes, distribution of quarantine locations and close contact history post hospitalization, we aimed to track the course of clinical outcomes of COVID-19 patients after discharge, and to evaluate their transmissibility during the period of observation, therefore to make improvement on post-discharge management if necessary. All of the discharged COVID-19 patients met the discharge criteria as follows: afebrile for at least three days, respiratory symptoms significantly improved, improvement in the radiological abnormalities on chest radiograph or CT, and two consecutive negative SARS-CoV-2 tests more than 24 hours apart [6] . However, the clinical characteristics of Patient 2 was not in line with other 7 patients, who retested with positive SARS-CoV-2 but were only associated with mild symptoms as dry cough or intermittent fever and ultimately pronounced negative tests and improved chest CT during 4 weeks of follow-up period. abstract: BACKGROUND: COVID-19 is a global pandemic but the follow-up data of discharged patients was barely described. AIMS: To investigate clinical outcomes, distribution of quarantine locations, and the infection status of the contacts of COVID-19 patients after discharge. DESIGN: A prospective cohort study METHODS: Demographics, baseline characteristics of 131 COVID-19 patients discharged from February 3 to 21, 2020 in Wuhan, China were collected and analyzed by reviewing the medical records retrospectively. Post-hospitalization data related to clinical outcomes, quarantine locations and close contact history were obtained by following up the patients every week up to 4 weeks. RESULTS: 53 (40.05%) patients on discharge had cough (29.01%), fatigue (7.63%), expectoration (6.11%), chest tightness (6.11%), dyspnea (3.82%), chest pain (3.05%), and palpitation (1.53%). These symptoms constantly declined in 4 weeks post discharge. Transient fever recurred in 11 (8.4%) patients. 78 (59.5%) discharged patients underwent chest CT and 2 (1.53%) showed deterioration. 94 (71.8%) patients received SARS-CoV-2 retest and 8 (6.10%) reported positive. 7 (2.29%) patients were re-admitted because of fever or positive SARS-CoV-2 retest. 121 (92.37%) and 4 (3.05%) patients were self-quarantined at home or community spots following discharge, with totally 167 closely contacted persons free of COVID-19 at the endpoint of study. CONCLUSIONS: The majority of COVID-19 patients after discharge were in the course of recovery. Readmission was required in rare cases due to suspected recurrence of COVID-19. Although no contacted infection observed, appropriate self-quarantine and regular reexamination are necessary, particularly for those who have recurred symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/32442308/ doi: 10.1093/qjmed/hcaa178 id: cord-280627-dfnc9g2c author: Wang, Xiong title: Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 words: 1846.0 sentences: 111.0 pages: flesch: 53.0 cache: ./cache/cord-280627-dfnc9g2c.txt txt: ./txt/cord-280627-dfnc9g2c.txt summary: The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). abstract: Abstract Background Since the outbreak of coronavirus disease (COVID-19) in Wuhan in December 2019, by March 10, 2020, a total of 80,932 confirmed cases have been reported in China. Two consecutively negative RT-PCR test results in respiratory tract specimens is required for the evaluation of discharge from hospital, and oropharyngeal swabs were the most common sample. However, false negative results occurred in the late stage of hospitalization, and avoiding false negative result is critical essential. Methods We reviewed the medical record of 353 patients who received tests with both specimens simultaneously, and compared the performance between nasopharyngeal and oropharyngeal swabs. Results Of the 353 patients (outpatients, 192; inpatients, 161) studied, the median age was 54 years, and 177 (50.1%) were women. Higher positive rate (positive tests/total tests) was observed in nasopharyngeal swabs than oropharyngeal swabs, especially in inpatients. Nasopharyngeal swabs from inpatients showed higher positive rate than outpatients. Nasopharyngeal swabs from male showed higher positive rate than female, especially in outpatients. Detection with both specimens slightly increased the positive rate than nasopharyngeal swab only. Moreover, the consistency between from nasopharyngeal and oropharyngeal swabs were poor (Kappa=0.308). Conclusion In conclusion, our study suggests that nasopharyngeal swabs may be more suitable than oropharyngeal swab at this stage of COVID-19 outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32315809/ doi: 10.1016/j.ijid.2020.04.023 id: cord-279476-h7zi82a8 author: Wang, Xueliang title: Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) date: 2020-04-13 words: 596.0 sentences: 35.0 pages: flesch: 57.0 cache: ./cache/cord-279476-h7zi82a8.txt txt: ./txt/cord-279476-h7zi82a8.txt summary: title: Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) To cope with the COVID-19 epidemic, the China National Medical Products Administration (NMPA) approved six RT-PCR kits for SARS-CoV-2, and some of which subsequently received CE marking. To verify its applicability, the viral RNA was tested with the six kits provided by Shanghai Liferiver Bio-tech Co., Ltd, Wuhan Huada Bio-tech Co., Ltd, Shanghai GeneoDx Biotech Co., Ltd, DAAN Gene Co., Ltd of Sun Yat-sen University, Sansure Biotech Inc., and Shanghai BioGerm Medical Co., Ltd. The different target genes ( Table 1 ) produced typical S-shaped amplification curves, indicating that the RNA could be used in the six kits to evaluate their LoDs. The viral RNA concentration was determined with RT-droplet digital PCR (RT-ddPCR), which allows the absolute quantification of viral RNA by counting single molecules, without reference to an external standard curve. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR We acknowledge the six manufacturers for providing the SARS-CoV-2 RT-PCR detection kits. abstract: nan url: https://doi.org/10.1093/clinchem/hvaa099 doi: 10.1093/clinchem/hvaa099 id: cord-305223-go75cs6r author: Wang, Yafei title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China date: 2020-08-25 words: 3218.0 sentences: 180.0 pages: flesch: 52.0 cache: ./cache/cord-305223-go75cs6r.txt txt: ./txt/cord-305223-go75cs6r.txt summary: title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China OBJECTIVES: The aim of this study was to explore the clinical characteristics and risk factors of severe pneumonia caused by the SARS-CoV-2 in Wuhan, China. SPSS was used for data analysis to explore the clinical characteristics and risk factors of patients with severe pneumonia caused by SARS-CoV-2. Statistical analysis showed that advanced age, increased D-Dimer, and decreased lymphocytes were characteristics of the patients with severe pneumonia. Severe pneumonia usually progresses rapidly, and many clinical indicators can change in a short time, especially lymphocyte count, D-Dimer and serum albumin values, and chest CT manifestations. The result suggests that advanced age, lymphocyte decline, and D-dimer elevation are independent risk factors for patients with severe COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China abstract: BACKGROUND: A new virus broke out in Wuhan, Hubei, China, that was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The clinical characteristics of severe pneumonia caused by SARS-CoV-2 are still not clear. OBJECTIVES: The aim of this study was to explore the clinical characteristics and risk factors of severe pneumonia caused by the SARS-CoV-2 in Wuhan, China. METHODS: The study included patients hospitalized at the Central Hospital of Wuhan who were diagnosed with COVID-19. Clinical features, chronic comorbidities, demographic data, laboratory examinations, and chest computed tomography (CT) scans were reviewed through electronic medical records. SPSS was used for data analysis to explore the clinical characteristics and risk factors of patients with severe pneumonia caused by SARS-CoV-2. RESULTS: A total of 110 patients diagnosed with COVID-19 were included in the study, including 38 with severe pneumonia and 72 with nonsevere pneumonia. Statistical analysis showed that advanced age, increased D-Dimer, and decreased lymphocytes were characteristics of the patients with severe pneumonia. Moreover, in the early stage of the disease, chest CT scans of patients with severe pneumonia showed that the illness can progress rapidly. CONCLUSIONS: Advanced age, decreased lymphocytes, and D-Dimer elevation are important characteristics of patients with severe COVID-19. Clinicians should focus on these characteristics to identify high-risk patients at an early stage. url: https://doi.org/10.1159/000507940 doi: 10.1159/000507940 id: cord-304718-w469n0o8 author: Wang, Yan title: Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection date: 2009-05-01 words: 2595.0 sentences: 161.0 pages: flesch: 51.0 cache: ./cache/cord-304718-w469n0o8.txt txt: ./txt/cord-304718-w469n0o8.txt summary: One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. A few case-control studies have reported an association between SARS susceptibility and human leucocyte antigen (HLA) and MBL [8] [9] [10] [11] . With regard to SARS-CoV infection, the codon 54 variant of the MBL gene has been shown to be associated with infection susceptibility but not with disease severity [11] . As the downstream protein of MBL, variants of the MASP2 gene may be associated with SARS-CoV infection. Genomic DNA from 30 individuals with SARS was chosen for analysis of MASP2 gene polymorphisms. abstract: BACKGROUND: The pathogenesis of severe acute respiratory disease syndrome (SARS) is not fully understood. One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. METHODS: Thirty individuals with SARS were chosen for analysis of MASP2 polymorphisms by means of PCR direct sequencing. Tag single nucleotide polymorphisms (tagSNPs) were chosen using pairwise tagging algorithms. The frequencies of four tag SNPs (rs12711521, rs2261695, rs2273346 and rs7548659) were ascertained in 376 SARS patients and 523 control subjects, using the Beckman SNPstream Ultra High Throughput genotyping platform. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. Diplotype (rs2273346 and rs12711521)were analyzed for association with susceptibility to SARS, no statistically significant evidence of association was observed. The Beijing and Guangzhou sample groups were homogeneous regarding demographic and genetic parameters, a joined analysis also showed no statistically significant evidence of association. CONCLUSION: Our data do not suggest a role for MASP2 polymorphisms in SARS susceptibility in northern and southern China. url: https://doi.org/10.1186/1471-2334-9-51 doi: 10.1186/1471-2334-9-51 id: cord-258113-mnou31j3 author: Wang, Yaping title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date: 2020-05-19 words: 3898.0 sentences: 215.0 pages: flesch: 54.0 cache: ./cache/cord-258113-mnou31j3.txt txt: ./txt/cord-258113-mnou31j3.txt summary: title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. [5] studied the clinical features of 99 patients with COVID-19 and found that SARS-Cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ARDS). Among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, PCT, LDH, CK, ALB, AST, and D-dimer were associated with disease severity. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: BACKGROUND: The clinical manifestations and factors associated with the severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections outside of Wuhan are not clearly understood. METHODS: All laboratory-confirmed cases with SARS-Cov-2 infection who were hospitalized and monitored in Guangzhou Eighth People’s Hospital were recruited from January 20 to February 10. RESULTS: A total of 275 patients were included in this study. The median patient age was 49 years, and 63.6% had exposure to Wuhan. The median virus incubation period was 6 days. Fever (70.5%) and dry cough (56.0%) were the most common symptoms. A decreased albumin level was found in 51.3% of patients, lymphopenia in 33.5%, and pneumonia based on chest computed tomography in 86%. Approximately 16% of patients (n = 45) had severe disease, and there were no deaths. Compared with patients with nonsevere disease, those with severe disease were older, had a higher frequency of coexisting conditions and pneumonia, and had a shorter incubation period (all P < .05). There were no differences between patients who likely contacted the virus in Wuhan and those who had no exposure to Wuhan. Multivariate logistic regression analysis indicated that older age, male sex, and decreased albumin level were independently associated with disease severity. CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. url: https://doi.org/10.1093/ofid/ofaa187 doi: 10.1093/ofid/ofaa187 id: cord-346015-bzeqs5oh author: Wang, Yeming title: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial date: 2020-04-29 words: 5233.0 sentences: 246.0 pages: flesch: 46.0 cache: ./cache/cord-346015-bzeqs5oh.txt txt: ./txt/cord-346015-bzeqs5oh.txt summary: Although several approved drugs and investigational agents have shown antiviral activity against SARS-CoV-2 in vitro, 6, 7 at present there are no antiviral therapies of proven effectiveness in treating severely ill patients with A multicentre, open-label, randomised controlled trial (RCT) of hydroxychloroquine involving 150 adults admitted to hospital for COVID-19 reported no significant effect of the drug on accelerating viral clearance. This was an investigator-initiated, individually randomised, placebo-controlled, double-blind trial to assess the effectiveness and safety of intravenous remdesivir in adults (aged ≥18 years) admitted to hospital with severe COVID-19. Our study is the first randomised, double-blind, placebocontrolled clinical trial assessing the effect of intravenous remdesivir in adults admitted to hospital with severe COVID-19. Future studies of remdesivir, including earlier treatment in patients with COVID-19 and higher-dose regimens or in combination with other antivirals or SARS-CoV-2 neutralising antibodies in those with severe COVID-19 are needed to better understand its potential effectiveness. abstract: BACKGROUND: No specific antiviral drug has been proven effective for treatment of patients with severe coronavirus disease 2019 (COVID-19). Remdesivir (GS-5734), a nucleoside analogue prodrug, has inhibitory effects on pathogenic animal and human coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, and inhibits Middle East respiratory syndrome coronavirus, SARS-CoV-1, and SARS-CoV-2 replication in animal models. METHODS: We did a randomised, double-blind, placebo-controlled, multicentre trial at ten hospitals in Hubei, China. Eligible patients were adults (aged ≥18 years) admitted to hospital with laboratory-confirmed SARS-CoV-2 infection, with an interval from symptom onset to enrolment of 12 days or less, oxygen saturation of 94% or less on room air or a ratio of arterial oxygen partial pressure to fractional inspired oxygen of 300 mm Hg or less, and radiologically confirmed pneumonia. Patients were randomly assigned in a 2:1 ratio to intravenous remdesivir (200 mg on day 1 followed by 100 mg on days 2–10 in single daily infusions) or the same volume of placebo infusions for 10 days. Patients were permitted concomitant use of lopinavir–ritonavir, interferons, and corticosteroids. The primary endpoint was time to clinical improvement up to day 28, defined as the time (in days) from randomisation to the point of a decline of two levels on a six-point ordinal scale of clinical status (from 1=discharged to 6=death) or discharged alive from hospital, whichever came first. Primary analysis was done in the intention-to-treat (ITT) population and safety analysis was done in all patients who started their assigned treatment. This trial is registered with ClinicalTrials.gov, NCT04257656. FINDINGS: Between Feb 6, 2020, and March 12, 2020, 237 patients were enrolled and randomly assigned to a treatment group (158 to remdesivir and 79 to placebo); one patient in the placebo group who withdrew after randomisation was not included in the ITT population. Remdesivir use was not associated with a difference in time to clinical improvement (hazard ratio 1·23 [95% CI 0·87–1·75]). Although not statistically significant, patients receiving remdesivir had a numerically faster time to clinical improvement than those receiving placebo among patients with symptom duration of 10 days or less (hazard ratio 1·52 [0·95–2·43]). Adverse events were reported in 102 (66%) of 155 remdesivir recipients versus 50 (64%) of 78 placebo recipients. Remdesivir was stopped early because of adverse events in 18 (12%) patients versus four (5%) patients who stopped placebo early. INTERPRETATION: In this study of adult patients admitted to hospital for severe COVID-19, remdesivir was not associated with statistically significant clinical benefits. However, the numerical reduction in time to clinical improvement in those treated earlier requires confirmation in larger studies. FUNDING: Chinese Academy of Medical Sciences Emergency Project of COVID-19, National Key Research and Development Program of China, the Beijing Science and Technology Project. url: https://api.elsevier.com/content/article/pii/S0140673620310229 doi: 10.1016/s0140-6736(20)31022-9 id: cord-252671-uf96jgig author: Wang, Yi title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism date: 2016-02-09 words: 7390.0 sentences: 389.0 pages: flesch: 52.0 cache: ./cache/cord-252671-uf96jgig.txt txt: ./txt/cord-252671-uf96jgig.txt summary: title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. The result of a dual-luciferase assay using the Renilla luciferase gene as a transfection control demonstrated that the SARS-CoV M gene rather than the S and E genes markedly increased IFN-␤ promoter activity (Fig. 1D) , whereas the valineto-alanine alteration at residue 68 of M protein completely abolished this induction, indicating that the specificity of M gene products played a role in this process. Taken together, our data indicate for the first time that SARS-CoV M protein may function as a novel cytosolic PAMP to activate IFN-␤ induction through an intracellular TLR-related signaling pathway in a TRAF3-independent manner. abstract: Most of the intracellular pattern recognition receptors (PRRs) reside in either the endolysosome or the cytoplasm to sense pathogen-derived RNAs, DNAs, or synthetic analogs of double-stranded RNA (dsRNA), such as poly(I:C). However, it remains elusive whether or not a pathogen-derived protein can function as a cytosolic pathogen-associated molecular pattern (PAMP). In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. Both NF-κB and TBK1-IRF3 signaling cascades are activated by M gene products. M protein rather than M mRNA is responsible for M-mediated IFN-β induction that is preferentially associated with the activation of the Toll-like receptor (TLR) adaptor proteins MyD88, TIRAP, and TICAM2 but not the RIG-I signaling cascade. Blocking the secretion of M protein by brefeldin A (BFA) failed to reverse the M-mediated IFN-β induction. The antagonist of both TLR2 and TLR4 did not impede M-mediated IFN-β induction, indicating that the driving force for the activation of IFN-β production was generated from inside the cells. Inhibition of TRAF3 expression by specific small interfering RNA (siRNA) did not prevent M-mediated IFN-β induction. SARS-CoV pseudovirus could induce IFN-β production in an M rather than M(V68A) dependent manner, since the valine-to-alanine alteration at residue 68 in M protein markedly inhibited IFN-β production. Overall, our study indicates for the first time that a pathogen-derived protein is able to function as a cytosolic PAMP to stimulate type I interferon production by activating a noncanonical TLR signaling cascade in a TRAF3-independent manner. url: https://www.ncbi.nlm.nih.gov/pubmed/26861016/ doi: 10.1128/mbio.01872-15 id: cord-027650-pl6qsojf author: Wang, Yijin title: SARS-CoV-2 infection in liver-Author’s reply date: 2020-06-23 words: 1065.0 sentences: 64.0 pages: flesch: 40.0 cache: ./cache/cord-027650-pl6qsojf.txt txt: ./txt/cord-027650-pl6qsojf.txt summary: In light of the low percentage of hepatocytes expressing ACE2, but not absolute absence, it is not surprisingly that SARS-CoV-2 is capable of causing liver injury directly. It is therefore assumed that viral direct effect in liver might not operate absolutely through ACE2 expression, and other receptors could not be excluded. Alternatively, the finding of up-regulated ACE2 expression in hepatocytes in cirrhotic liver inspired us to speculate that SARS-CoV-2 infection might induce compensatory hyperplasia of hepatocytes, which are possibly derived from highly expressed ACE2 cholangiocytes [16] . All in all, our data fully support a direct role of SARS-CoV-2 in COVID-19 related hepatic impairment. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309894/ doi: 10.1016/j.jhep.2020.06.028 id: cord-317647-vcktnsv8 author: Wang, Yinhua title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis date: 2020-09-18 words: 1766.0 sentences: 152.0 pages: flesch: 53.0 cache: ./cache/cord-317647-vcktnsv8.txt txt: ./txt/cord-317647-vcktnsv8.txt summary: title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis We plan to systematically review the use of ribavirin in patients with coronavirus-related pneumonia and meta-analyze the data with updated studies. Therefore, we aim to systematically review the use of ribavirin on coronavirus-related pneumonia (SARS, MERSS, and COVID-19) and meta-analyze the data with the results of the updated RCTs to provide advanced evidence. We aim to assess the safety and efficacy of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19). Our systematic review and meta-analysis will include these updated results and re-assess the efficacy and safety of ribavirin in patients with coronavirus-related pneumonia. Efficacy and safety of antiviral treatment for COVID-19 from evidence in studies of SARSCoV-2 and other acute viral infections: a systematic review and meta-analysis abstract: BACKGROUND: The new coronavirus-related pneumonia is causing a global pandemic without specific antiviral drug. Ribavirin has activity against extensive RNA and DNA viruses. We plan to systematically review the use of ribavirin in patients with coronavirus-related pneumonia and meta-analyze the data with updated studies. METHODS: EMBASE, PubMed, Cochrane Library, and China National Knowledge Infrastructure will be searched from 2002 to June 2021 without language restriction to identify randomized controlled trials. Subjects consist of patients with coronavirus-related pneumonia. Ribavirin of any dose or route will be compared with the control group of other medication, placebo, or no medication. The primary outcome is the hospital mortality. The secondary outcome includes the hospital length of stay, ventilator-free days in 28 days, median time from start of study treatment to negative nasopharyngeal swab, and adverse events. The Mantel-Haenszel method will be used for analysis of dichotomous data and the risk ratios will be reported with 95% confidence interval; the inverse-variance method will be used for continuous data and the mean differences will be reported. Sensitivity and subgroup analyses will be further performed. The funnel plots or Egger test will be used for detection of publication bias. The GRADE methodology will be used for summarizing the quality of evidence. The trial sequential analysis will be conducted to test whether the current meta-analysis is conclusive. RESULTS: The efficacy and safety of ribavirin for treatment of coronavirus-related pneumonia will be systematically reviewed and summarized. The forthcoming results of the ongoing studies focusing on ribavirin in patients with the 2019 noel coronavirus disease will also be included. CONCLUSION: The relevant studies will be summarized and advanced evidence will be provided. PROSPERO REGISTRATION NUMBER: CRD42020178900 url: https://www.ncbi.nlm.nih.gov/pubmed/32957417/ doi: 10.1097/md.0000000000022379 id: cord-292236-eudcs9t2 author: Wang, Yishan title: Asymptomatic cases with SARS‐CoV‐2 infection date: 2020-05-22 words: 901.0 sentences: 60.0 pages: flesch: 43.0 cache: ./cache/cord-292236-eudcs9t2.txt txt: ./txt/cord-292236-eudcs9t2.txt summary: On 31 March 2020, Chinese Health Authorization announced that numbers of asymptomatic cases with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection will be made to the public daily. Currently, asymptomatic cases are not included in the confirmed patients in everyday-report according to the "Novel Coronavirus Pneumonia Diagnosis and Treatment Protocol (7th edition, trial)." Another study reported that the asymptomatic ratio was estimated at 30.8% among evacuees tested positive for SARS-CoV-2 using the information on Japanese nationals that were evacuated from Wuhan, China. Studies from single-center reported 4% to 6% cases with SARS-CoV-2 did not develop any symptom during the course of the disease. Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data. Alert for non-respiratory symptoms of Coronavirus Disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection abstract: On 31 March 2020, Chinese Health Authorization announced that numbers of asymptomatic cases with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection will be made to the public daily. This was a very important step since different counties have different capacities for the detection of SARS‐CoV‐2 infection and control strategy for the Coronavirus Disease 2019 outbreak. We summarized the characteristics of asymptomatic SARS‐CoV‐2 infections and the transmission potential of asymptomatic cases. Then we provided guidelines for the management of asymptomatic cases through quarantine and nucleic acid/serology tests. url: https://www.ncbi.nlm.nih.gov/pubmed/32383171/ doi: 10.1002/jmv.25990 id: cord-323481-uz6usokd author: Wang, Yixuan title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures date: 2020-03-29 words: 2943.0 sentences: 210.0 pages: flesch: 50.0 cache: ./cache/cord-323481-uz6usokd.txt txt: ./txt/cord-323481-uz6usokd.txt summary: title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures By 27 February 2020, the outbreak of coronavirus disease 2019 (COVID‐19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (SARS) (8273 cases, 775 deaths) and Middle East respiratory syndrome (MERS) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China The guidelines for diagnosis and treatment of novel coronavirus (2019-nCoV) infected pneumonia (the sixth edition draft) issued by the National Health Commission of China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection abstract: By 27 February 2020, the outbreak of coronavirus disease 2019 (COVID‐19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (SARS) (8273 cases, 775 deaths) and Middle East respiratory syndrome (MERS) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. COVID‐19 has spread to 46 countries internationally. Total fatality rate of COVID‐19 is estimated at 3.46% by far based on published data from the Chinese Center for Disease Control and Prevention (China CDC). Average incubation period of COVID‐19 is around 6.4 days, ranges from 0 to 24 days. The basic reproductive number (R(0)) of COVID‐19 ranges from 2 to 3.5 at the early phase regardless of different prediction models, which is higher than SARS and MERS. A study from China CDC showed majority of patients (80.9%) were considered asymptomatic or mild pneumonia but released large amounts of viruses at the early phase of infection, which posed enormous challenges for containing the spread of COVID‐19. Nosocomial transmission was another severe problem. A total of 3019 health workers were infected by 12 February 2020, which accounted for 3.83% of total number of infections, and extremely burdened the health system, especially in Wuhan. Limited epidemiological and clinical data suggest that the disease spectrum of COVID‐19 may differ from SARS or MERS. We summarize latest literatures on genetic, epidemiological, and clinical features of COVID‐19 in comparison to SARS and MERS and emphasize special measures on diagnosis and potential interventions. This review will improve our understanding of the unique features of COVID‐19 and enhance our control measures in the future. url: https://doi.org/10.1002/jmv.25748 doi: 10.1002/jmv.25748 id: cord-266914-3eatplc2 author: Wang, Yongjin title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date: 2010-06-02 words: 4005.0 sentences: 220.0 pages: flesch: 53.0 cache: ./cache/cord-266914-3eatplc2.txt txt: ./txt/cord-266914-3eatplc2.txt summary: The group II coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis coronavirus (MHV) encode a number of proteins that antagonize host innate immunity. Innate immune signal transduction was stimulated by NDV infection in cells transfected with plasmids-expressing nsp1 from HCoV-229E, HCoV-NL63 or SARS-CoV, or with a control plasmid. Luciferase reporter assays showed that synthesis of the innate immune promoter IFN-band ISG15-driven genes was suppressed by 5-20-folds in HCoV-229E and HCoV-NL63 nsp1-expressing 293 cells (Fig. 4A) . Synthesis of non-immune promoter-driven genes, including for SV40, HSV-TK and CMV promoters, was inhibited to a similar extent by the two group I coronavirus nsp1 proteins (Fig. 4B) . These results indicate that group I coronaviruses have evolved a mechanism strikingly similar to SARS-CoV for antagonizing host cell proliferation and innate immunity using nsp1. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells abstract: The nsp1 protein of the highly pathogenic SARS coronavirus suppresses host protein synthesis, including genes involved in the innate immune system. A bioinformatic analysis revealed that the nsp1 proteins of group I and SARS coronaviruses have similar structures. Nsp1 proteins of group I coronaviruses interacted with host ribosomal 40S subunit and did not inhibit IRF-3 activation. However, synthesis of host immune and non-immune proteins was inhibited by nsp1 proteins at both transcriptional and translational levels, similar to SARS coronavirus nsp1. These results indicate that different coronaviruses might employ the same nsp1 mechanism to antagonize host innate immunity and cell proliferation. However, nsp1 may not be the key determinant of viral pathogenicity, or the factor used by the SARS coronavirus to evade host innate immunity. url: https://www.sciencedirect.com/science/article/pii/S1567134810001371 doi: 10.1016/j.meegid.2010.05.014 id: cord-294558-cqa58db8 author: Wang, Yubo title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 words: 2858.0 sentences: 214.0 pages: flesch: 57.0 cache: ./cache/cord-294558-cqa58db8.txt txt: ./txt/cord-294558-cqa58db8.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. Asymptomatic infections are also an important source of infection. Here, we aimed to further clarify the epidemiologic and clinical characteristics of asymptomatic SARS-CoV-2 infections. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. We stratified this cohort by normal versus abnormal findings on chest CT, and compared the strata regarding comorbidities, demographics, laboratory findings, viral transmission and other factors. RESULTS: Between January and March, 2020, we identified and hospitalized 279 RT-PCR+ contacts of COVID-19 patients. Of these, 63 (23%) remained asymptomatic until discharge; 29 had abnormal and 34 had normal chest CT findings. The mean cohort age was 39.3 years, and 87.3% had no comorbidities. Mean time to diagnosis after close contact with a COVID-19 index patient was 16.0 days (range 1 to 29), and 13.4 days and 18.7 days for those with abnormal and normal CT findings, respectively (p < 0.05). Nine subjects (14.3%) transmitted the virus to others; 4 and 5 were in the abnormal and normal CT strata, respectively. The median length of nucleic acid turning negative in asymptomatic COVID-19 patients was 13 days, compared to 10.4 days in those with normal chest CT (p < 0.05). CONCLUSIONS: A portion of these asymptomatic individuals, with and without abnormal chest CT scans, were capable of transmitting the virus to others. Given the frequency and potential infectiousness of asymptomatic infections, testing of traced contacts is essential. Studies of the impact of treatment on asymptomatic RT-PCR+ individuals on disease progression and transmission should be undertaken. url: https://doi.org/10.1093/cid/ciaa629 doi: 10.1093/cid/ciaa629 id: cord-299082-s8bm40vy author: Wang, Yueying title: Cardiac arrhythmias in patients with COVID‐19 date: 2020-07-26 words: 3714.0 sentences: 247.0 pages: flesch: 40.0 cache: ./cache/cord-299082-s8bm40vy.txt txt: ./txt/cord-299082-s8bm40vy.txt summary: 5, 6, 9, 10, [12] [13] [14] [15] Several investigators have reported cardiac function and structural abnormalities in patients with SARS-CoV-2 infection, including acute heart failure (HF), 3,10,16 takotsubo syndrome, 17 ,18 viral myocarditis, 19 and acute myocardial infarction. In addition to exacerbating the previous cardiomyopathy and conduction disorders, inducing arrhythmia events, SARS-CoV-2 may also induce electrophysiological abnormalities in patients with no previous history of heart disease under a variety of mechanisms. Clinical features and mechanism of heart injury in patients suffered from severe acute respiratory syndrome. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial Risk of QT interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease 2019 (COVID-19) abstract: The emergence of coronavirus disease 2019 (COVID‐19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become a major global public health concern. Although SARS‐CoV‐2 causes primarily respiratory problems, concurrent cardiac injury cannot be ignored since it may be an independent predictor for adverse outcomes. Cardiac arrhythmias are often observed in patients with COVID‐19, especially in severe cases, and more likely contribute to the high risk of adverse outcomes. Arrhythmias should be regarded as one of the main complications of COVID‐19. Mechanistically, a number of ion channels can be adversely affected in COVID‐19, leading to alterations in cardiac conduction and/or repolarization properties, as well as calcium handling, which can predispose to cardiac arrhythmogenesis. In addition, several antimicrobials that are currently used as potential therapeutic agents for COVID‐19, such as chloroquine, hydroxychloroquine and azithromycin, have uncertain benefit, and yet may induce electrocardiographic QT prolongation with potential ventricular pro‐arrhythmic effects. Continuous electrocardiogram monitoring, accurate and prompt recognition of arrhythmias are important. The present review focuses on cardiac arrhythmias in patients with COVID‐19, its underlying mechanisms, and proposed preventive and therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/33024460/ doi: 10.1002/joa3.12405 id: cord-282142-76jr4p7n author: Wang, Yun title: Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date: 2020-08-07 words: 5495.0 sentences: 292.0 pages: flesch: 47.0 cache: ./cache/cord-282142-76jr4p7n.txt txt: ./txt/cord-282142-76jr4p7n.txt summary: Pregnant women are susceptible to respiratory pathogens and the development of severe pneumonia, suggesting the urgent need to assess the potential maternal and infant outcome of pregnancy with COVID-19. Therefore, the effect of SARS-CoV-2 infection on maternal and infant outcomes needs to be explored, especially the intrauterine vertical transmission potential of COVID-19. SARS-CoV infection during pregnancy was associated with a risk of adverse maternal and neonatal complications, including intrauterine growth restriction, preterm delivery, spontaneous miscarriage, severe maternal illnesses, such as, admission to the intensive care unit (ICU), renal failure, and disseminated intravascular coagulopathy, and death (4, 6, 13, (42) (43) (44) (45) (46) . The samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples from six patients tested negative for SARS-CoV-2 (5), suggesting no intrauterine vertical transmission of SARS-CoV-2 in the nine pregnant COVID-19 patients. abstract: The coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is highly infectious and its ongoing outbreak has been declared a global pandemic by the WHO. Pregnant women are susceptible to respiratory pathogens and the development of severe pneumonia, suggesting the urgent need to assess the potential maternal and infant outcome of pregnancy with COVID-19. The intrauterine vertical transmission potential of SARS-CoV-2 also remains controversial. Herein, we discuss the potential effect of COVID-19 on maternal and infant outcomes based on current studies, including those published in Chinese, in a total of 80 mothers with COVID-19 and 80 infants. We also comprehensively explored the mother-to-child transmission routes of SARS-CoV-2, in particular the route of intrauterine vertical transmission. Given SARS-CoV-2 is a sister to SARS-CoV, of the SARS-related coronavirus species, we made a comprehensive comparison between them to learn from experiences with SARS. Although there is no evidence supporting the intrauterine vertical transmission of SARS-CoV-2, our comprehensive analysis suggests that the adverse maternal and infant outcomes caused by COVID-19 cannot be underestimated. Further, we speculated that the inconsistency between nucleic acids and serological characteristics IgM to SARS-CoV-2 of infants' specimens may be caused by the disruption of the amniotic barrier by the inflammatory factors induced by SARS-CoV-2 infection. Our review is beneficial to understand the effect of SARS-CoV-2 on maternal and infant outcomes. url: https://doi.org/10.3389/fped.2020.00511 doi: 10.3389/fped.2020.00511 id: cord-312278-rin733w4 author: Wang, Yung‐Chih title: Current diagnostic tools for coronaviruses–From laboratory diagnosis to POC diagnosis for COVID‐19 date: 2020-08-13 words: 2250.0 sentences: 171.0 pages: flesch: 53.0 cache: ./cache/cord-312278-rin733w4.txt txt: ./txt/cord-312278-rin733w4.txt summary: 22 For detecting the presence of novel infectious diseases, the gold standard method has been the use of qRT-PCR for the detection of 29 Saliva has also been approved as a noninvasive specimen for detecting SARS-CoV-2. Another well-known test is the Vivalytic COVID-19 test (Bosch, Germany), which delivers results in less than 2.5 hr using multiplex PCR and μArray-detection to identify SARS-CoV-2. All of these tests employ PCR to detect the presence of SARS-CoV-2 RNA, and can provide results within 72 hr. Second, all of these at-home kits are designed to detect SARS-CoV-2 RNA during early-stage infection, but they are not used to determine the presence of antibodies. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using fieldeffect transistor-based biosensor Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis abstract: The Coronavirus‐2019 (COVID‐19) pandemic has put tremendous strain on healthcare systems worldwide. It is challenging for clinicians to differentiate COVID‐19 from other acute respiratory tract infections via clinical symptoms because those who are infected display a wide range of symptoms. An effective, point‐of‐care (POC) diagnostic tool could mitigate healthcare system strain, protect healthcare professionals, and support quarantine efforts. We believe that a POC tool can be developed that would be rapid, easy to use, and inexpensive. It could be used in the home, in resource‐limited areas, and even in clinical settings. In this article, we summarize the current state of POC tools and propose an all‐in‐one, highly sensitive POC assay that integrates antibody detection, protein detection, and serum cytokine detection to diagnose COVID‐19 infection. We believe this article will provide insight into the current state of POC diagnostics for COVID‐19, and promote additional research and tool development that could be exceptionally impactful. url: https://doi.org/10.1002/btm2.10177 doi: 10.1002/btm2.10177 id: cord-343566-epvswt7f author: Wang, Zhao-Hua title: Critically Ill Patients with Coronavirus Disease 2019 in a Designated ICU: Clinical Features and Predictors for Mortality date: 2020-07-20 words: 3291.0 sentences: 198.0 pages: flesch: 50.0 cache: ./cache/cord-343566-epvswt7f.txt txt: ./txt/cord-343566-epvswt7f.txt summary: CONCLUSION: Critically ill COVID-19 patients aged higher than 70, arrhythmia, or a SOFA score above 4 have a high risk of mortality, and need prior medical intervention. In the present study, we present details of 59 critically ill patients with SARS-CoV-2 infection, admitted to the intensive care unit (ICU) of Caidian Branch of Tongji Hospital, and then identified prognostic factors for mortality of these critically ill patients. 3, 4 According to the WHO interim guidance and Diagnostic and Treatment Program of COVID-19 (Version 7.0) published by the National Health Commission of the People''s Republic of China, all patients were diagnosed with severe pneumonia induced by SARS-CoV-2 infection who required mechanical ventilation, had inspiratory oxygen fraction (FiO₂) ≥60%, or had the shock or organ failure. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a worldwide pandemic outbreak with a high mortality. Prognostic factors of critically ill patients with COVID-19 have not been fully elucidated yet. METHODS: In the present study, 59 patients with COVID-19 from the intensive care unit of the Caidian Branch of Tongji Hospital were enrolled. Epidemiological, demographic, clinical, laboratory, radiological, treatment data, and clinical outcomes were collected. Prognostic factors were statistically defined. RESULTS: Of the 59 patients studied (67.4±11.3 years), 38 patients were male, 51 had underlying diseases, and 41 patients died during admission. Compared with the survivors, the deceased patients were of older age, had more smoking history, severer fatigue, and diarrhea, a higher incidence of multiple organ injuries, more deteriorative lymphopenia and thrombocytopenia, remarkably impaired cellular immune response, and strengthened cytokine release. Age higher than 70 (OR=2.76, 95% CI=1.45–5.23), arrhythmia (OR=4.76, 95% CI=1.59–14.25), and a Sequential Organ Failure Assessment (SOFA) score above 4 (OR=5.16, 95% CI=1.29–20.55) were identified as risk factors for mortality of patients. CONCLUSION: Critically ill COVID-19 patients aged higher than 70, arrhythmia, or a SOFA score above 4 have a high risk of mortality, and need prior medical intervention. url: https://www.ncbi.nlm.nih.gov/pubmed/32765138/ doi: 10.2147/rmhp.s263095 id: cord-312991-ypgrw78s author: Wang, Zhi-Gang title: Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV date: 2005-09-12 words: 3744.0 sentences: 224.0 pages: flesch: 64.0 cache: ./cache/cord-312991-ypgrw78s.txt txt: ./txt/cord-312991-ypgrw78s.txt summary: In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. According to 5 polymorphism sites, 63 SARS-CoV genomes were divided into early, middle and late phase genotype groups [19] . Key mutation loci are shown in Table 3 (identified by using nucleotide-nucleotide BLAST program at NEBI and Clustalw 1.83), and the phylogenetic tree of 174 loci ( Fig. 1) showed that, according to the polymorphism sites of C9404T, C9479T, G17564T, G19838A, A21721G, C22222T, G22517A, G23823T, T27243C and C27827T, the SARS-CoV genomes of the first epidemic can be divided into two genotypes, genotype C and T. among the genotypes and the groups The genetic characteristics of the genotypes were further analyzed based on the sequence polymorphism of the spike protein genes ( Table 4 ). SARS-CoV GD03T0013 was from the patient with ''''mild clinical symptoms'''', and its genome sequence was similar to that of the sub-genotype C1. abstract: In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1–C4 and T1–T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor. url: https://www.sciencedirect.com/science/article/pii/S0014579305009439 doi: 10.1016/j.febslet.2005.07.075 id: cord-253990-m75xwrz9 author: Wang, Zhiguo title: Covid‐19: From structure to therapeutic targeting in studying approved drugs and local DNA vaccination date: 2020-10-29 words: 1125.0 sentences: 62.0 pages: flesch: 48.0 cache: ./cache/cord-253990-m75xwrz9.txt txt: ./txt/cord-253990-m75xwrz9.txt summary: The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represent one of the major challenges in controlling the disease severity, keeping to pose a huge threat to the global health. The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represents one of the major challenges in controlling the disease severity and consequences, posing a huge threat to the global health. In this article, we highlight several previously approved drugs for potential effect on combating SARS-CoV-2 coronavirus infection, and modulating pulmonary inflammation and immune response. Despite unprecedented efforts to contain the virus spread and prevent infection, SARS-CoV-2 pneumonitis can still rapidly strike to incapacitate the lung causing severe acute respiratory distress syndrome (ARDS), resulting in severe disease aftermath and sometimes death. abstract: The coronavirus disease 2019 (COVID-19) pandemic presents an unprecedented threat to global public health. The spread of the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infections in a global scale has affected more than 30.6 million people suffering the COVID-19, resulting in more than 955,000 deaths globally as of the 20 September 2020. The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represent one of the major challenges in controlling the disease severity, keeping to pose a huge threat to the global health. url: https://doi.org/10.1111/1440-1681.13409 doi: 10.1111/1440-1681.13409 id: cord-332832-kjppd6uz author: Ward, B. J. title: Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants date: 2020-11-06 words: 7024.0 sentences: 466.0 pages: flesch: 58.0 cache: ./cache/cord-332832-kjppd6uz.txt txt: ./txt/cord-332832-kjppd6uz.txt summary: (ClinicalTrials.gov number NCT04450004) Methods: The study was a randomized, partially-blinded, prime-boost 21 days apart, dose-escalation Phase 1 study intended to assess the safety, tolerability, and immunogenicity of CoVLP at three dose levels (3.75 microgram, 7.5 microgram, and 15 microgram) unadjuvanted or adjuvanted with either CpG 1018 or AS03 in 180 SARS-CoV-2 seronegative healthy adults 18 to 55 years of age. We report here the results of a Phase 1 study initiated in July 2020 evaluating the safety, 203 tolerability and immunogenicity of two doses, 21-days apart of 3.75, 7.5 or 15 µg of a virus-204 like-particle vaccine candidate for Covid-19 produced in plants (hereafter called CoVLP). ; https://doi.org/10.1101/2020.11.04.20226282 doi: medRxiv preprint Like any early-phase clinical trial, this study has several limitations beyond the obvious 459 concern regarding small group size when testing multiple dose levels and formulations 460 (n=20/group). abstract: Background: The stabilized prefusion form of the SARS-CoV-2 spike protein is produced by transient expression in Nicotiana benthamiana. The trimeric spike glycoproteins are displayed at the surface of self-assembling Virus-Like-Particles that mimic the shape and the size of the virus. The candidate vaccine (CoVLP) administered alone or with AS03 or CpG1018 adjuvants was evaluated in a Phase 1 trial in healthy adults. (ClinicalTrials.gov number NCT04450004) Methods: The study was a randomized, partially-blinded, prime-boost 21 days apart, dose-escalation Phase 1 study intended to assess the safety, tolerability, and immunogenicity of CoVLP at three dose levels (3.75 microgram, 7.5 microgram, and 15 microgram) unadjuvanted or adjuvanted with either CpG 1018 or AS03 in 180 SARS-CoV-2 seronegative healthy adults 18 to 55 years of age. Enrollment was staggered for dose-escalation. At each dose level, the vaccine was initially administered to a small number of subjects. Vaccination of the remaining subjects at the same dose level and the next higher vaccine dose level was administered with approval of an Independent Data Monitoring Committee (IDMC). The same procedure was followed for the second vaccine administration. Monitoring of safety signals was performed throughout the study with pre-determined pausing/stopping rules if there was clear evidence of harmful effects such as severe adverse events (AEs) related to the treatment. The primary endpoints were the safety and tolerability of the vaccine after each dose and the immunogenicity as assessed by neutralizing antibody responses assessed using a vesicular stomatitis virus (VSV) pseudovirion assay and interferon-gamma and interleukin-4 (IL-4) ELISpot assays at Days 0, 21 and 42. Secondary endpoints were anti-spike antibody responses by ELISA and neutralizing antibodies measured by live virus plaque reduction neutralization test (PRNT) assay at Days 0, 21 and 42 and immunogenicity with additional safety and immunogenicity endpoints planned for 6-months following the last vaccination. The anti-spike and neutralizing antibody responses were compared with 23 convalescent serum samples from symptomatic Covid-19 patients. We performed a primary analysis at day 42. Results: A total of 180 subjects (102 females: 78 males: average 34.3 years) were recruited to the study and interim safety and immunogenicity data up to day 42 after the first dose are reported here. There was no obvious CoVLP dose effect in safety outcomes for any of the formulations tested and all formulations were generally well-tolerated. Most solicited local and systemic AEs were mild-moderate and transient. Reactogenicity was increased in all adjuvanted formulations and was generally highest in the CoVLP+AS03 groups. Local and systemic adverse events were reported with similar frequency after the first and second doses in subjects who received either CoVLP alone or CoVLP+CpG1018 but increased in both frequency and severity after the second dose in the CoVLP+AS03 groups. CoVLP alone only elicited a weak total anti-spike IgG response at the highest dose level and little-to-no neutralization antibody response, even after the second dose. Cellular responses in the CoVLP alone groups (IFN-gamma and IL-4) were detectable after the second dose but were still only marginally above background levels. The addition of either adjuvant substantially increased both antibody and cellular responses at most CoVLP dose levels and changes were most pronounced after the second dose. However, a substantial neutralizing antibody response after the first dose was only seen in all CoVLP+AS03 groups. After the second dose, both total anti-spike IgG and neutralizing antibody titers in the CoVLP+AS03 groups were higher than those in the CoVLP+CpG1018 groups. The antibody titers achieved were either similar to (CoVLP+CpG1018) or at least 10-times higher (CoVLP+AS03) than those seen in convalescent plasma. Administration of CoVLP with either adjuvant also significantly increased the cellular responses. After 2 doses, both IFN-gamma and IL-4 responses were significantly increased in the CoVLP+CpG1018 groups. In the CoVLP+AS03 groups, significant increases in the cellular responses were observed after the first dose while IFN-gamma and IL-4 increased further in both magnitude and number of subjects responding after the second dose. Again, the cellular responses in the CoVLP+AS03 groups were higher than those seen in the CoVLP+CpG1018 groups. Conclusion: These data demonstrate that CoVLP administered with either CpG1018 or AS03 has a safety profile similar to other candidate vaccines for SARS-CoV-2. When administered with either AS03 or CpG1018, several of the CoVLP dose levels elicited strong humoral and T cell responses after the second dose. When administered with AS03, even the 3.75 microgram CoVLP dose elicited neutralizing antibody titers that were ~10-times higher than those observed in individuals recovering from Covid-19 as well as consistent and balanced IFN-gamma and IL-4 responses. Although many CoVLP formulations were immunogenic, in the absence of established correlates of protection and given the advantages of dose-sparing in the context of the on-going pandemic, these findings suggest that CoVLP (3.75 microgram)+AS03 has a good benefit/risk ratio and support the transition of this formulation to studies in expanded populations and to efficacy evaluations url: https://doi.org/10.1101/2020.11.04.20226282 doi: 10.1101/2020.11.04.20226282 id: cord-316617-8cqxz3wi author: Ward, Michael P. title: SARS‐CoV‐2, where to now? date: 2020-06-19 words: 1239.0 sentences: 69.0 pages: flesch: 45.0 cache: ./cache/cord-316617-8cqxz3wi.txt txt: ./txt/cord-316617-8cqxz3wi.txt summary: (2020) present the results of a SARS-CoV-2 serological survey in 35 animal species in China, including the dog of a COVID-19 patient and an additional two in-contact dogs. Tests available for the detection of SARS-CoV-2 are comprehensively described in this issue of Transboundary and Emerging Diseases (Li & Ren, 2020) . In addition to the publication of new knowledge about SARS-CoV-2 in this issue of Transboundary and Emerging Diseases, new ideas are also presented. A key enabler of such a shift in our thinking and approach to disease emergence and spread is a One Health workforce capable of undertaking integrated monitoring, surveillance, risk assessment and response activities. The COVID-19 pandemic could be a catalyst for such a seismic shift in how we approach emerging infectious diseases and One Health. We can be sure, even when the current COVID-19 pandemic is resolved, that the need for surveillance, response and prevention of transboundary and emerging diseases will remain. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32562349/ doi: 10.1111/tbed.13654 id: cord-333326-n9ifhw5s author: Wardell, Hanna title: Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Febrile Neonates date: 2020-07-09 words: 2919.0 sentences: 173.0 pages: flesch: 44.0 cache: ./cache/cord-333326-n9ifhw5s.txt txt: ./txt/cord-333326-n9ifhw5s.txt summary: Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in pediatric patients are mild or asymptomatic. We report a case series of 4 full-term neonates hospitalized with fever and found to have SARS-CoV-2 infection with a spectrum of illness severities. Herein we present a case series of 4 full-term neonates who were hospitalized with fever and found to be infected with SARS-CoV-2. Due to the concern for end-organ involvement with possibly evolving acute myocardial injury as well as a supplemental oxygen requirement, the patient was initiated on therapy with remdesivir on inpatient day 4 via an expanded-access program from the manufacturer after approval from the US Food and Drug Administration and local institutional review board, with informed consent. In this report, we present 4 febrile neonates hospitalized with SARS-CoV-2 infection with favorable outcomes. SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress abstract: Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in pediatric patients are mild or asymptomatic. However, infants have emerged at higher risk of hospitalization and severe outcomes in pediatric coronavirus disease 2019 (COVID-19). We report a case series of 4 full-term neonates hospitalized with fever and found to have SARS-CoV-2 infection with a spectrum of illness severities. Two neonates required admission to the intensive care unit for respiratory insufficiency and end organ involvement. Half of the patients were found to have a coinfection. One neonate received antiviral therapy with remdesivir and is, to our knowledge, the youngest patient to receive this drug for COVID-19. All neonates had favorable outcomes. url: https://doi.org/10.1093/jpids/piaa084 doi: 10.1093/jpids/piaa084 id: cord-258681-66ct8nod author: Warnock, David G. title: Clinical Trials during the SARS-CoV-2 Pandemic date: 2020-04-14 words: 731.0 sentences: 43.0 pages: flesch: 52.0 cache: ./cache/cord-258681-66ct8nod.txt txt: ./txt/cord-258681-66ct8nod.txt summary: The primary outcome measures of this trial include the incidence of active COVID-19-related disease at 14 days post-enrollment, and a COVID-19 Disease Severity Scale self-reported by participants at 14 days post-enrollment: no COVID-19-related disease (score of 1); COVID-19-related disease with no hospitalization (score of 2); or COVID-19-related disease with hospitalization or death (score of 3).The goal is to enroll and randomize 1,500 subjects into each of the active-drug and placebo arms, followed by a 6-day treatment course with hydroxychloroquine. Secondary outcome measures include 14-day incidence of hospitalization, 14-day incidence of confirmed SARS-CoV-2 infection, the number of participants in each arm who discontinue or withdraw from the protocol, and 90-day incidence of death related to COVID-19-related disease. The trial includes a chartered Data Safety Monitoring Board with defined stopping rules for clinical futility or statistically significant improvement in the primary outcome measures comparing the active-drug group to the placebo group (personal communication, March 22, 2020: covid19faq COVID-1-Post-Exposure Prophylaxis FAQ Account). abstract: nan url: https://doi.org/10.1159/000507582 doi: 10.1159/000507582 id: cord-315440-he7sm7nj author: Wassie, Gizachew Tadesse title: Incubation period of SARS-CoV-2: A systematic review and meta-analysis date: 2020-10-11 words: 3756.0 sentences: 232.0 pages: flesch: 51.0 cache: ./cache/cord-315440-he7sm7nj.txt txt: ./txt/cord-315440-he7sm7nj.txt summary: Since there is no effective COVID-19 vaccine available yet, it is increasingly important to understand the average incubation period of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to design appropriate preventive and control strategies. Therefore, this systematic review and meta-analysis was designed to estimate the pooled average incubation period of SARS-CoV-2. We included peer-reviewed research studies written in the English language on the incubation period of SARS-CoV-2 using pre-defined quality and inclusion criteria. With regard to studies published in peer-reviewed journals or found in grey literature, all observational study designs (i.e. cross-sectional, case-control, and cohort), studies involving humans, and studies reporting the incubation period of SARS-CoV-2 were eligible for inclusion in this systematic review and meta-analysis. Studies with no accessible full text after using all the PRISMA-P search strategies and studies not reporting a specific incubation period for SARS-CoV-2 were excluded from this systematic review and meta-analysis. abstract: Background: Coronavirus disease (COVID-19) has currently become a major global public health problem. The prevalence of COVID-19 has increased rapidly worldwide. Since there is no effective COVID-19 vaccine available yet, it is increasingly important to understand the average incubation period of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to design appropriate preventive and control strategies. Therefore, this systematic review and meta-analysis was designed to estimate the pooled average incubation period of SARS-CoV-2. Methods: We conducted a systematic electronic web-based search of online databases including PubMed, Google Scholar, EMBASE, and the World Health Organization's HINARI portal. We included peer-reviewed research studies written in the English language on the incubation period of SARS-CoV-2 using pre-defined quality and inclusion criteria. STATA version 15 statistical software was used to analyze the data. Joanna Briggs Institute (JBI) critical appraisal quality assessment tool for observational studies was utilized to evaluate the included studies. We extracted relevant data and presented in a tabular form. The I(2) test was used to assess heterogeneity across studies. Funnel plot asymmetry and Egger's tests were used to check for publication bias. The final effect size was determined by applying a random-effects model. Results: Our search identified 206 studies, amongst which 18 studies, representing 22,595 participants were included in the final analysis. The pooled average incubation period of SARS-CoV-2 was 5.7 days (95% CI: 5.1, 6.4). Subgroup analyses by geographic location showed that the pooled average incubation period of SARS-CoV-2 was 6.1 days (95% CI: 5.34, 6.94) in China and 4.54 (95% CI: 3.9, 5.2) in other countries (Singapore, South Korea, and globally). Conclusion: The pooled average incubation period of SARS-CoV-2 was about six days. The longest incubation period was observed in China. The global health initiatives as well as local health planners should consider, this average incubation period while designing optimal prevention and control strategies for SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0011393X20300333 doi: 10.1016/j.curtheres.2020.100607 id: cord-263452-y2ral8nx author: Watanabe, Yasunori title: Site-specific glycan analysis of the SARS-CoV-2 spike date: 2020-05-04 words: 2073.0 sentences: 121.0 pages: flesch: 50.0 cache: ./cache/cord-263452-y2ral8nx.txt txt: ./txt/cord-263452-y2ral8nx.txt summary: To resolve the site-specific glycosylation of SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo-electron microscopy (cryo-EM) structure, albeit without glycan processing blockade using kifunensine (4). The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27) , influenza HA (28, 29) , and LASV GPC (24). For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34) . This suggests that SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies. SARS-CoV-2 spike site-specific N-linked glycan analysis abstract: The emergence of the betacoronavirus, SARS-CoV-2, the causative agent of COVID-19, represents a significant threat to global human health. Vaccine development is focused on the principal target of the humoral immune response, the spike (S) glycoprotein, which mediates cell entry and membrane fusion. SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in protein folding and immune evasion. Here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant SARS-CoV-2 S immunogen. This analysis enables mapping of the glycan-processing states across the trimeric viral spike. We show how SARS-CoV-2 S glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design. url: https://www.ncbi.nlm.nih.gov/pubmed/32366695/ doi: 10.1126/science.abb9983 id: cord-317786-iv1br2oj author: Waterfield, T. title: Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study. date: 2020-09-02 words: 3769.0 sentences: 271.0 pages: flesch: 54.0 cache: ./cache/cord-317786-iv1br2oj.txt txt: ./txt/cord-317786-iv1br2oj.txt summary: Discussion In this study children demonstrated similar antibody titres in response to SARS-CoV-2 irrespective of age. The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. Participants and their parents provided information at enrollment relating to age, sex, previous health and potential predictors of SARS-CoV-2 infection including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/antibody testing. Seroprevalence of SARS-CoV-2 antibodies in children of healthcare workers-A prospective multicentre cohort study protocol -Accepted for publication abstract: Background Studies based on molecular testing of oral/nasal swabs underestimate SARS-CoV-2 infection due to issues with test sensitivity and timing of testing. The objective of this study was to report the presence of SARS-CoV-2 antibodies, consistent with previous infection, and to report the symptomatology of infection in children. Design This multicentre observational cohort study, conducted between 16th April - 3rd July 2020 at 5 UK sites, aimed to recruit 900 children aged 2 to 15 years of age. Participants provided blood samples for SARS-CoV-2 antibody testing and data were gathered regarding unwell contacts and symptoms. Results 1007 participants were enrolled, and 992 were included in the final analysis. The median age of participants was 10.1 years. There were 68 (6.9%) participants with positive SARS-CoV-2 antibody tests indicative of previous SARS-CoV-2 infection. Of these, 34/68 (50%) reported no symptoms. The presence of antibodies and the mean antibody titre was not influenced by age. Following multivariate analysis 4 independent variables were identified as significantly associated with SARS-CoV-2 infection. These were: known infected household contact; fatigue; gastrointestinal symptoms; and changes in sense of smell or taste. Discussion In this study children demonstrated similar antibody titres in response to SARS-CoV-2 irrespective of age. The symptoms of SARS-CoV-2 infection in children were subtle but of those reported, fatigue, gastrointestinal symptoms and changes in sense of smell or taste were most strongly associated with antibody positivity. Registration This study was registered at https://www.clinicaltrials.gov (trial registration: NCT04347408) on the 15/04/2020. url: https://doi.org/10.1101/2020.08.31.20183095 doi: 10.1101/2020.08.31.20183095 id: cord-326706-75mjs6vm author: Waterfield, Thomas title: Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study date: 2020-11-10 words: 3573.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-326706-75mjs6vm.txt txt: ./txt/cord-326706-75mjs6vm.txt summary: Following multivariable analysis four independent variables were identified as significantly associated with SARS-CoV-2 seropositivity: known infected household contact OR=10.9 (95% CI 6.1 to 19.6); fatigue OR=16.8 (95% CI 5.5 to 51.9); gastrointestinal symptoms OR=6.6 (95% CI 3.0 to 13.8); and changes in sense of smell or taste OR=10.0 (95% CI 2.4 to 11.4). The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. 26 Participants and their parents provided information at enrolment relating to age, sex, previous health and potential predictors of SARS-CoV-2 seropositivity including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/ antibody testing. abstract: BACKGROUND: Studies based on molecular testing of oral/nasal swabs underestimate SARS-CoV-2 infection due to issues with test sensitivity, test timing and selection bias. The objective of this study was to report the presence of SARS-CoV-2 antibodies, consistent with previous infection. DESIGN: This multicentre observational cohort study, conducted between 16 April to 3 July 2020 at 5 UK sites, recruited children of healthcare workers, aged 2–15 years. Participants provided blood samples for SARS-CoV-2 antibody testing and data were gathered regarding unwell contacts and symptoms. RESULTS: 1007 participants were enrolled, and 992 were included in the final analysis. The median age of participants was 10·1 years. There were 68 (6.9%) participants with positive SARS-CoV-2 antibody tests indicative of previous SARS-CoV-2 infection. Of these, 34/68 (50%) reported no symptoms prior to testing. The presence of antibodies and the mean antibody titre was not influenced by age. Following multivariable analysis four independent variables were identified as significantly associated with SARS-CoV-2 seropositivity: known infected household contact OR=10.9 (95% CI 6.1 to 19.6); fatigue OR=16.8 (95% CI 5.5 to 51.9); gastrointestinal symptoms OR=6.6 (95% CI 3.0 to 13.8); and changes in sense of smell or taste OR=10.0 (95% CI 2.4 to 11.4). DISCUSSION: Children demonstrated similar antibody titres in response to SARS-CoV-2 irrespective of age. Fatigue, gastrointestinal symptoms and changes in sense of smell or taste were the symptoms most strongly associated with SARS-CoV-1 antibody positivity. TRIAL REGISTRATION NUMBER: https://www.clinicaltrials.gov (trial registration: NCT0434740) on the 15 April 2020. url: https://doi.org/10.1136/archdischild-2020-320558 doi: 10.1136/archdischild-2020-320558 id: cord-282964-dmc8mlxu author: Wathore, Roshan title: Understanding air and water borne transmission and survival of coronavirus: Insights and way forward for SARS-CoV-2 date: 2020-08-04 words: 3366.0 sentences: 176.0 pages: flesch: 44.0 cache: ./cache/cord-282964-dmc8mlxu.txt txt: ./txt/cord-282964-dmc8mlxu.txt summary: This has spurred efforts to characterize the coronavirus and understand the factors impacting its transmission and survival such as aerosols, air quality, meteorology, chemical compositions and characteristics of particles and surfaces, which are directly or indirectly associated with coronaviruses infection spread. Nonetheless, many peer-reviewed articles have studied these aspects but mostly in isolation; a complete array of coronavirus survival and transmission from an infected individual through airand water-borne channels and its subsequent intractions with environmental factors, surfaces, particulates and chemicals is not comprehensively explored. Finally, this study outlines probable air and water borne routes and suggest a way forward highlighting the need for investigating the effect of particulate matter characteristics on survival and transmission of SARS-CoV-2 due to the prominent presence of PM in ambient, spaces, and on the surfaces. abstract: Abstract The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in unprecedented disease burden, healthcare costs, and economic impacts worldwide. Despite several measures, SARS-CoV-2 has been extremely impactful due to its extraordinary infection potential mainly through coronavirus-borne saliva respiratory and droplet nuclei of an infected person and its considerable stability on surfaces. Although the disease has affected over 180 countries, its extent and control are significantly different across the globe, making it a strong case for exploration of its behavior and dependence across various environmental pathways and its interactions with the virus. This has spurred efforts to characterize the coronavirus and understand the factors impacting its transmission and survival such as aerosols, air quality, meteorology, chemical compositions and characteristics of particles and surfaces, which are directly or indirectly associated with coronaviruses infection spread. Nonetheless, many peer-reviewed articles have studied these aspects but mostly in isolation; a complete array of coronavirus survival and transmission from an infected individual through air- and water-borne channels and its subsequent intractions with environmental factors, surfaces, particulates and chemicals is not comprehensively explored. Particulate matter (PM) is omnipresent with variable concentrations, structures and composition, while most of the surfaces are also covered by PM of different characteristics. Learning from the earlier coronavirus studies, including SARS and MERS, an attempt has been made to understand the survival of SARS-CoV-2 outside of the host body and discuss the probable air and water-borne transmission routes and its interactions with the outside environment. The present work 1) Helps appreciate the role of PM, its chemical constituents and surface characteristics and 2) Further identifies gaps in this field and suggests possible domains to work upon for better understanding of transmission and survival of this novel coronavirus. url: https://api.elsevier.com/content/article/pii/S0048969720350154 doi: 10.1016/j.scitotenv.2020.141486 id: cord-282133-5dzzm9s8 author: Watzky, Manon title: Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry date: 2020-10-15 words: 5706.0 sentences: 337.0 pages: flesch: 50.0 cache: ./cache/cord-282133-5dzzm9s8.txt txt: ./txt/cord-282133-5dzzm9s8.txt summary: In here, exploiting a large panel of publicly available genome-wide data, we investigated whether the human receptor ACE2 and human proteases TMPRSS2, FURIN and CATHEPSINs (B, L and V), which are involved in SARS-CoV-2 cell entry, are transcriptionally regulated by environmental cues. We queried the comparative toxicogenomics database (CTD) to identify studies reporting changes in expression levels of human genes encoding receptor and proteases J o u r n a l P r e -p r o o f important for SARS-CoV-2 cell entry upon chemical exposure (Davis et al., 2019) . Using these criteria, we identified several chemical exposures regulating the expression of receptor ACE2 and human proteases TMPRSS2, FURIN and Cathepsins genes in human cells and tissues (Figure 2; Supplementary Table S2 ). Our analysis suggests that expression of human receptor and proteases of SARS-CoV-2 spike S glycoprotein are not directly regulated by cigarette smoke at the transcriptional level in lung cells, nor that PIR and ACE2 are coregulated upon cigarette smoke exposure. abstract: The role of environmental condition on the infection by the novel pathogenic SARS-CoV-2 virus remains uncertain. In here, exploiting a large panel of publicly available genome-wide data, we investigated whether the human receptor ACE2 and human proteases TMPRSS2, FURIN and CATHEPSINs (B, L and V), which are involved in SARS-CoV-2 cell entry, are transcriptionally regulated by environmental cues. We report that more than 50 chemicals modulate the expression of ACE2 or human proteases important for SARS-CoV-2 cell entry. We further demonstrate that transcription factor AhR, which is commonly activated by pollutants, binds to the promoter of TMPRSS2 and enhancers and/or promoters of Cathepsin B, L and V encoding genes. Our exploratory study documents an influence of environmental exposures on the expression of genes involved in SARS-CoV-2 cell entry. These results could be conceptually and medically relevant to our understanding of the COVID-19 disease, and should be further explored in laboratory and epidemiologic studies. url: https://www.ncbi.nlm.nih.gov/pubmed/33069705/ doi: 10.1016/j.envres.2020.110317 id: cord-327616-uu9uygic author: Wazny, Vanessa title: Vascular underpinning of COVID-19 date: 2020-08-27 words: 6970.0 sentences: 359.0 pages: flesch: 33.0 cache: ./cache/cord-327616-uu9uygic.txt txt: ./txt/cord-327616-uu9uygic.txt summary: Coronavirus disease 2019 (COVID-19) case study reports have called attention to the overrepresentation of cardiovascular diseases, in addition to respiratory diseases, among patients at risk of critical illness and mortality following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection [1] [2] [3] [4] [5] [6] [7] [8] . Initial concerns were also raised regarding the medical treatment of hypertension with adverse COVID-19 outcomes, as studies in animals have shown that the use of renin-angiotensin system blockers-angiotensin-converting enzyme inhibitors and angiotensin receptor blockers result in the upregulation of angiotensin-converting enzyme 2 (ACE2) expression, which is an entry factor for SARS-CoV-2 [13] . Collectively, these case reports of confirmed COVID-19 hospitalized patients strongly indicate a strong association between underlying cardiovascular diseases and diabetes with severe health outcomes and fatality following SARS-CoV-2 infection. In COVID-19 research, nasal and alveolar epithelial cells are generally believed to be the primary sites of viral infection due to the high expressions of SARS-CoV-2 entry factors [51] . abstract: COVID-19 management guidelines have largely attributed critically ill patients who develop acute respiratory distress syndrome, to a systemic overproduction of pro-inflammatory cytokines. Cardiovascular dysfunction may also represent a primary phenomenon, with increasing data suggesting that severe COVID-19 reflects a confluence of vascular dysfunction, thrombosis and dysregulated inflammation. Here, we first consolidate the information on localized microvascular inflammation and disordered cytokine release, triggering vessel permeability and prothrombotic conditions that play a central role in perpetuating the pathogenic COVID-19 cascade. Secondly, we seek to clarify the gateways which SARS-CoV-2, the causative COVID-19 virus, uses to enter host vascular cells. Post-mortem examinations of patients' tissues have confirmed direct viral endothelial infection within several organs. While there have been advances in single-cell RNA sequencing, endothelial cells across various vascular beds express low or undetectable levels of those touted SARS-CoV-2 entry factors. Emerging studies postulate alternative pathways and the apicobasal distribution of host cell surface factors could influence endothelial SARS-CoV-2 entry and replication. Finally, we provide experimental considerations such as endothelial polarity, cellular heterogeneity in organoids and shear stress dynamics in designing cellular models to facilitate research on viral-induced endothelial dysfunctions. Understanding the vascular underpinning of COVID-19 pathogenesis is crucial to managing outcomes and mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/32847471/ doi: 10.1098/rsob.200208 id: cord-262760-mf1pn587 author: Weber, Stefanie title: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date: 2020-09-24 words: 4664.0 sentences: 264.0 pages: flesch: 59.0 cache: ./cache/cord-262760-mf1pn587.txt txt: ./txt/cord-262760-mf1pn587.txt summary: By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first identified in Wuhan, China late in 2019. Nine months later (Sept. 18, 2020), the virus has infected > 30 million people world-wide and caused > 944.000 (3.15 %) fatalities in 220 countries and territories. Research on the genetics of the SARS-CoV-2 genome, its mutants and their penetrance can aid future defense strategies. By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. During world-wide spreading among human populations, at least 10 distinct hotspot mutations had been selected and found in up to > 80 % of viral genomes. Many of these mutations led to amino acid exchanges in replication-relevant viral proteins. Mutations in the SARS-CoV-2 genome would also impinge upon the secondary structure of the viral RNA molecule and its repertoire of interactions with essential cellular and viral proteins. The increasing frequency of SARS-CoV-2 mutation hotspots might select for dangerous viral pathogens. Alternatively, in a 29.900 nucleotide-genome, there might be a limit to the number of mutable and selectable sites which, when exhausted, could prove disadvantageous to viral survival. The speed, at which novel SARS-CoV-2 mutants are selected and dispersed around the world, could pose problems for the development of vaccines and therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/32979477/ doi: 10.1016/j.virusres.2020.198170 id: cord-315585-bjij8ds7 author: Wee, Liang En title: Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore date: 2020-05-08 words: 3960.0 sentences: 215.0 pages: flesch: 50.0 cache: ./cache/cord-315585-bjij8ds7.txt txt: ./txt/cord-315585-bjij8ds7.txt summary: METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. 15 Here, we report our experience with a novel concept, a respiratory surveillance ward (RSW), which was introduced as a strategy for admission, triage and disposition of patients presenting with respiratory syndromes during a SARS-CoV-2 outbreak. Respiratory surveillance wards (RSWs): Admissions criteria, layout, infection control, and transfer criteria At our institution, high-risk patients that fulfilled suspect case criteria for COVID-19 were admitted to an isolation ward with 37 negative-pressure rooms. During an outbreak of SARS-CoV-2 with local transmission, an RSW to cohort all inpatients admitted from the community with respiratory symptoms may enhance case detection and reduce the potential of nosocomial transmission. abstract: OBJECTIVES: Patients with COVID-19 may present with respiratory syndromes indistinguishable from those caused by common viruses. Early isolation and containment is challenging. Although screening all patients with respiratory symptoms for COVID-19 has been recommended, the practicality of such an effort has yet to be assessed. METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a “respiratory surveillance ward” (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. Patients could be transferred when SARS-CoV-2 tests were negative on 2 consecutive occasions, 24 hours apart. RESULTS: Over the study period, 1,178 patients were admitted to the RSWs. The mean length-of-stay (LOS) was 1.89 days (SD, 1.23). Among confirmed cases of pneumonia admitted to the RSW, 5 of 310 patients (1.61%) tested positive for SARS-CoV-2. This finding was comparable to the pickup rate from our isolation ward. In total, 126 HCWs were potentially exposed to these cases; however, only 3 (2.38%) required quarantine because most used appropriate PPE. In addition, 13 inpatients overlapped with the index cases during their stay in the RSW; of these 13 exposed inpatients, 1 patient subsequently developed COVID-19 after exposure. No patient–HCW transmission was detected despite intensive surveillance. CONCLUSIONS: Our institution successfully utilized the strategy of an RSW over a 6-week period to contain a cluster of COVID-19 cases and to prevent patient–HCW transmission. However, this method was resource-intensive in terms of testing and bed capacity. url: https://doi.org/10.1017/ice.2020.207 doi: 10.1017/ice.2020.207 id: cord-310594-i0586vfw author: Weemaes, Matthias title: Laboratory information system requirements to manage the COVID-19 pandemic: a report from the Belgian national reference testing center date: 2020-04-29 words: 2537.0 sentences: 136.0 pages: flesch: 34.0 cache: ./cache/cord-310594-i0586vfw.txt txt: ./txt/cord-310594-i0586vfw.txt summary: OBJECTIVE: To describe the development, implementation and requirements of laboratory information system (LIS) functionality to manage test ordering, registration, sample flow, and result reporting during the COVID-19 pandemic. RESULTS: We outline the design, implementation and requirements of LIS functionality related to managing increased test demand during the COVID-19 crisis, including tools for test ordering, standardized order sets integrated into a computerized provider order entry module, notifications on shipping requirements, automated triaging based on digital metadata forms, and the establishment of databases with contact details of other laboratories and primary care physicians to enable automated reporting. DISCUSSION: Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turn-around-time of SARS-CoV-2 testing. During the early stages of the COVID-19 outbreak, our laboratory was the only SARSNotably, the large majority of our expanded work force (30 of the 38 additional FTE) was assigned to help with administrative tasks (sample reception, triaging, patient registration, result validation and reporting, and epidemiological studies), and not directly involved in expanding analytical capacity (i.e. PCR analysis) ( Figure 2 ). abstract: OBJECTIVE: To describe the development, implementation and requirements of laboratory information system (LIS) functionality to manage test ordering, registration, sample flow, and result reporting during the COVID-19 pandemic. CONTEXT AND SETTING: Our large (>12,000,000 tests/year) academic hospital laboratory is the Belgian National Reference Center (NRC) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We performed a moving total of > 25,000 SARS-CoV-2 PCR tests in parallel to standard routine testing since the start of the outbreak. A LIS implementation team dedicated to develop tools to remove the bottlenecks, primarily situated in the pre- and post-analytical phase, was established early in the crisis. RESULTS: We outline the design, implementation and requirements of LIS functionality related to managing increased test demand during the COVID-19 crisis, including tools for test ordering, standardized order sets integrated into a computerized provider order entry module, notifications on shipping requirements, automated triaging based on digital metadata forms, and the establishment of databases with contact details of other laboratories and primary care physicians to enable automated reporting. We also describe our approach to data mining and reporting of actionable daily summary statistics to governing bodies and other policymakers. DISCUSSION: Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turn-around-time of SARS-CoV-2 testing. It will be important to maintain an environment that is conducive for the rapid adoption of meaningful LIS tools post-COVID crisis. url: https://doi.org/10.1093/jamia/ocaa081 doi: 10.1093/jamia/ocaa081 id: cord-315652-hct9yh3n author: Wehbe, Zena title: Molecular Insights Into SARS COV-2 Interaction With Cardiovascular Disease: Role of RAAS and MAPK Signaling date: 2020-06-03 words: 6560.0 sentences: 372.0 pages: flesch: 41.0 cache: ./cache/cord-315652-hct9yh3n.txt txt: ./txt/cord-315652-hct9yh3n.txt summary: As such, a thorough understanding of the signaling pathways common to the pathogenesis of CVD and SARS-CoV-2 infection is necessary to identify crucial sites of crosstalk and direct future investigation of potential therapeutic interventions mitigating both COVID-19 complications in CVD patients as well as short-and long-term viral-induced cardiovascular impairment. The chronic nature and gradual development timeframe of these diseases might argue that the crosstalk among increased MAPK signaling cascades and SARS-CoV-2 pathogenesis leads to increased infection severity and complications in patients with established CVD rather than being involved in viraltriggered cardiovascular involvement. This raises the possibility for a beneficial effect of eplerenone or other aldosterone receptor antagonists in reducing risk of severe COVID-19 infection in CVD patients or to mitigate the cardiovascular burden of SARS-CoV-2 infection. abstract: In December 2019, reports of viral pneumonia came out of Wuhan city in Hubei province in China. In early 2020, the causative agent was identified as a novel coronavirus (CoV) sharing some sequence similarity with SARS-CoV that caused the severe acute respiratory syndrome outbreak in 2002. The new virus, named SARS-CoV-2, is highly contagious and spread rapidly across the globe causing a pandemic of what became known as coronavirus infectious disease 2019 (COVID-19). Early observations indicated that cardiovascular disease (CVD) patients are at higher risk of progression to severe respiratory manifestations of COVID-19 including acute respiratory distress syndrome. Moreover, further observations demonstrated that SARS-CoV-2 infection can induce de novo cardiac and vascular damage in previously healthy individuals. Here, we offer an overview of the proposed molecular pathways shared by the pathogenesis of CVD and SARS-CoV infections in order to provide a mechanistic framework for the observed interrelation. We examine the crosstalk between the renin-angiotensin-aldosterone system and mitogen activated kinase pathways that potentially links cardiovascular predisposition and/or outcome to SARS-CoV-2 infection. Finally, we summarize the possible effect of currently available drugs with known cardiovascular benefit on these pathways and speculate on their potential utility in mitigating cardiovascular risk and morbidity in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32581799/ doi: 10.3389/fphar.2020.00836 id: cord-345603-mirsz6m8 author: Wehrhahn, Michael C. title: Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic date: 2020-05-04 words: 2345.0 sentences: 125.0 pages: flesch: 57.0 cache: ./cache/cord-345603-mirsz6m8.txt txt: ./txt/cord-345603-mirsz6m8.txt summary: Self-collected swabs in the community for SARS-CoV-2, the agent of COVID-19, and for other respiratory viruses offers potential significant benefit in the current pandemic by J o u r n a l P r e -p r o o f reducing requirement for PPE, limiting exposure of patients and staff to infection, increased convenience and access for patients and timeliness of a sample receipt. 9 Recent reports on SARS-CoV-2 in respiratory specimens indicate early high viral loads in symptomatic and asymptomatic patients in a variety of clinical specimens including nasal and throat swabs, sputum and saliva samples. The aim of this study was to compare prospectively the performance of HC with separate SC nasal (SCN) and throat swabs (SCT) and the combination of the two (SCNT) for respiratory viruses including SARS-CoV-2. abstract: OBJECTIVES: To evaluate the reliability of self-collection for SARS-CoV-2 and other respiratory viruses because swab collections for SARS-CoV-2 put health workers at risk of infection and require use of personal protective equipment (PPE). METHODS: In a prospective study, patients from two states in Australia attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) throat and nasal swabs (SCNT) prior to health worker collect (HC) using throat and nasal swabs (Site 1) or throat and nasopharyngeal swabs (Site 2). Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohen's kappa (κ) and Cycle threshold (Ct) values were recorded for all positive results as a surrogate measure for viral load. RESULTS: Of 236 patients sampled by HC and SC, 25 had SARS-CoV-2 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 y SC). SC was highly concordant with HC (κ = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method (κ = 0.959 vs 0.933). Mean SARS-CoV-2 E-gene and N-gene, rhinovirus and parainfluenza Ct values did not differ between HC and SCNT. CONCLUSIONS: Self-collection of throat and nasal swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other respiratory viruses and provides patients with easier access to testing, reduces exposure of the community and health workers to those being tested and reduces requirement for PPE. url: https://www.ncbi.nlm.nih.gov/pubmed/32403007/ doi: 10.1016/j.jcv.2020.104417 id: cord-256940-yuja99jg author: Wei, Bo title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 words: 1994.0 sentences: 136.0 pages: flesch: 56.0 cache: ./cache/cord-256940-yuja99jg.txt txt: ./txt/cord-256940-yuja99jg.txt summary: title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. However, some COVID-19 patients have been reported to have long-term positivity for SARS-CoV-2 ribonucleic acid (RNA). On April 5, after three consecutive negative nucleic acid test results, he was discharged and transferred to another hospital for further treatment of comorbidities. Thus, DNVr may be a potential antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. abstract: Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a pandemic. We herein report four COVID-19 cases with long-term positive viral ribonucleic acid (RNA) for about 61 days. Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. url: https://doi.org/10.1590/0037-8682-0372-2020 doi: 10.1590/0037-8682-0372-2020 id: cord-310201-70fj4fhr author: Wei, D.-Q. title: Anti-SARS drug screening by molecular docking date: 2006-05-22 words: 3577.0 sentences: 202.0 pages: flesch: 60.0 cache: ./cache/cord-310201-70fj4fhr.txt txt: ./txt/cord-310201-70fj4fhr.txt summary: (2003) and Chou (2004) found the fitting problem of AG7088 to the binding pocket of SARS CoV Mpro, and they suggested its derivative KZ7088 as a better starting point. Furthermore, the intermolecular hydrogen bonds and electrostatic interaction, whose effects have already been counted in the binding energy, were also investigated in order to find useful information for drug design. In contrast, if ranking the docking results according to the binding free energy which includes the torsional term as shown in Rank 2 of Table 1 , it was found that most of the top-20 ligands interacted quite well with the receptor in the pocket. A comparison of the results between Ranks 1 and 2 suggests that the binding free energy is more reliable as a criterion for the virtual screening via molecular docking. Hydrogen bonds between ligand 4 and the involved residues of SARS CoV Mpro. abstract: Starting from a collection of 1386 druggable compounds obtained from the 3D pharmacophore search, we performed a similarity search to narrow down the scope of docking studies. The template molecule is KZ7088 (Chou et al., 2003, Biochem Biophys Res Commun 308: 148–151). The MDL MACCS keys were used to fingerprint the molecules. The Tanimoto coefficient is taken as the metric to compare fingerprints. If the similarity threshold was 0.8, a set of 50 unique hits and 103 conformers were retrieved as a result of similarity search. The AutoDock 3.011 was used to carry out molecular docking of 50 ligands to their macromolecular protein receptors. Three compounds, i.e., C(28)H(34)O(4)N(7)Cl, C(21)H(36)O(5)N(6), and C(21)H(36)O(5)N(6), were found that may be promising candidates for further investigation. The main feature shared by these three potential inhibitors as well as the information of the involved side chains of SARS Cov Mpro may provide useful insights for the development of potent inhibitors against SARS enzyme. url: https://www.ncbi.nlm.nih.gov/pubmed/16715412/ doi: 10.1007/s00726-006-0361-7 id: cord-276402-ymxvtyll author: Wei, Jia title: SARS-CoV-2 infection in immunocompromised patients: humoral versus cell-mediated immunity date: 2020-07-29 words: 3517.0 sentences: 212.0 pages: flesch: 49.0 cache: ./cache/cord-276402-ymxvtyll.txt txt: ./txt/cord-276402-ymxvtyll.txt summary: BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic placed unprecedented pressure on various healthcare systems, including departments that use immunotherapies such as chimeric antigen receptor (CAR) T-cell therapy and immunosuppression therapy in organ transplantation units. The true impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on immunocompromised CAR T-cell therapy recipients and kidney transplant recipients (KTRs) has not yet been established. His virus clearance failure and life-threating cytokine storm during SARS-CoV-2 infection suggested that any decision to proceed CAR T-cell therapy during COVID-19 pandemics will require extensive discussion of potential risks and benefits. 3 Coronavirus disease 2019 (COVID-19) is a heterogeneous disease population, of which most patients exhibit mild to moderate symptoms, however approximately 15% progress to severe pneumonia, while 5% were eventually admitted to intensive care units (ICU) due to the resultant acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure. abstract: BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic placed unprecedented pressure on various healthcare systems, including departments that use immunotherapies such as chimeric antigen receptor (CAR) T-cell therapy and immunosuppression therapy in organ transplantation units. The true impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on immunocompromised CAR T-cell therapy recipients and kidney transplant recipients (KTRs) has not yet been established. CASE PRESENTATION: In this report, we compare two patients with severe COVID-19 pneumonia in either the humoral or cell-mediated immunodeficient states. The first patient was a man in his early 30s who was diagnosed with refractory multiple myeloma. He received fully humanized, anti-B-cell maturation antigen, CAR T-cell therapy before 4 months and achieved strict complete remission. He was infected with SARS-CoV-2 starting on January 26, 2019 and gradually progressed to severe pneumonia. Throughout the clinical progression of the disease, SARS-CoV-2 could not be cleared due to his humoral immunodeficient state. During this period of his severe COVID-19 pneumonia, elevated cytotoxic T-cells were observed in this patient’s peripheral blood while elevated plasma levels of interleukin (IL)-2R, IL-6, tumor necrosis factor α, and ferritin were observed in his cytokine profiles. This patient eventually progressed into acute respiratory distress syndrome and recieved non-invasive ventilatory support. He failed to generate specific SARS-CoV-2 antibodies and died of respiratory failure on day 33 (d33). The second patient was a 52-year-old kidney transplant recipient (KTR) who took ciclosporin after renal transplantation for more than 7 years. He confirmed SARS-CoV-2 infection on January 20, 2019 and gradually progressed into severe pneumonia on d16 with a slightly elevated B-cell percentage and normal T-lymphocyte subsets. Viral clearance occurred together with the generation of specific anti-immunoglobulin G-SARS-CoV-2 antibodies after 2 weeks of treatment. He was symptom-free and discharged from the hospital on d42. CONCLUSION: We report a CAR T-cell therapy recipient diagnosed with COVID-19 for the first time. His virus clearance failure and life-threating cytokine storm during SARS-CoV-2 infection suggested that any decision to proceed CAR T-cell therapy during COVID-19 pandemics will require extensive discussion of potential risks and benefits. Immunosuppressant treatment based on ciclosporin could be relatively safe for KTRs diagnosed with COVID-19. TRIAL REGISTRATION NUMBER: ChiCTR-OPN-1800018137. url: https://doi.org/10.1136/jitc-2020-000862 doi: 10.1136/jitc-2020-000862 id: cord-335338-wzxjn5ip author: Wei, Lan title: Pathology of the thyroid in severe acute respiratory syndrome() date: 2006-09-25 words: 3536.0 sentences: 169.0 pages: flesch: 44.0 cache: ./cache/cord-335338-wzxjn5ip.txt txt: ./txt/cord-335338-wzxjn5ip.txt summary: To further investigate the effects of SARS associated coronavirus (CoV) on the thyroid, we have undertaken a detailed study of the thyroid gland with special attention to the pattern of cellular and architectural alterations on parafollicular and follicular cells. In contrast to normal thyroid, the thyroid glands from patients with SARS consistently showed destruction of the follicular epithelium and exfoliation of epithelial cells into the follicle. Our study has demonstrated that thyroid glands in patients with SARS were significantly affected by the disease with extensive injury to the follicular epithelial cells and the parafollicular cells. The extent of morphological injury and the large quantity of cells undergoing apoptosis that we observed in the thyroid follicular epithelium provide an explanation for the diminished serum T3 and T4 levels in patients with SARS. Evaluation and observation of serum thyroid hormone and parathyroid hormone in patients with severe acute respiratory syndrome The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells abstract: The severe acute respiratory syndrome (SARS) epidemic started in November 2002 and spread worldwide. The pathological changes in several human organs of patients with SARS have been extensively described. However, to date, little has been reported about the effects of this infection on the thyroid gland. Femoral head necrosis and low serum triiodothyronine and thyroxine levels, commonly found in patients with SARS, raise the possibility of thyroid dysfunction. We have undertaken this study to evaluate for any potential injury to the thyroid gland caused by SARS on tissue samples obtained from 5 SARS autopsies. The terminal deoxynucleotidyl transferase-mediated dUPT nick end–labeling assay was performed to identify apoptotic cells. The follicular epithelium was found to be damaged with large numbers of cells exfoliated into the follicle. The terminal deoxynucleotidyl transferase-mediated dUPT nick end–labeling assay demonstrated many cells undergoing apoptosis. Follicular architecture was altered and showed distortion, dilatation, and collapse. No distinct calcitonin-positive cells were detectable in the SARS thyroids. In conclusion, both parafollicular and follicular cells were injured. This may provide an explanation both for low serum triiodothyronine and thyroxine levels and the osteonecrosis of the femoral head associated with patients with SARS. Apoptosis may play a role in the pathogenesis of SARS associated coronavirus infection in the thyroid gland. url: https://www.sciencedirect.com/science/article/pii/S0046817706003807 doi: 10.1016/j.humpath.2006.06.011 id: cord-268065-mxvbbkc4 author: Wei, Maoti title: Epidemiology of Coronavirus Disease 2019 (COVID-19) Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-05-18 words: 4409.0 sentences: 246.0 pages: flesch: 57.0 cache: ./cache/cord-268065-mxvbbkc4.txt txt: ./txt/cord-268065-mxvbbkc4.txt summary: Shortly after the virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the epidemic of coronavirus disease 2019 (COVID-19) broke out, and an information storm occurred. Based on information of SARS, Middle East respiratory syndrome (MERS), and COVID-19, the components of the epidemic (the sources, the routes of infection, and the susceptible population) will be discussed, as well as the role of natural and social factors involved. S ince the end of 2019, a novel coronavirus, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID19) , appeared in Wuhan, Hubei Province, China. Recent results showed that SARS-CoV-2 persists longer with a higher viral load and peaks later in the respiratory tissue of patients with severe disease; this phenomenon highlights the need for the prevention and control of the epidemic. Some experts commented that people with mild or asymptomatic SARS-CoV-2 infection were not identified by epidemic prevention measures, thus accelerating the spread of the disease. abstract: In December, 2019, an infectious outbreak of unknown cause occurred in Wuhan, which attracted intense attention. Shortly after the virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the epidemic of coronavirus disease 2019 (COVID-19) broke out, and an information storm occurred. At that time, 2 important aspects, that is, the stages of spread and the components of the epidemic, were unclear. Answers to the questions (1) what are the sources, (2) how do infections occur, and (3) who will be affected should be clarified as the outbreak continues to evolve. Furthermore, components of the epidemic and the stages of spread should be explored and discussed. Based on information of SARS, Middle East respiratory syndrome (MERS), and COVID-19, the components of the epidemic (the sources, the routes of infection, and the susceptible population) will be discussed, as well as the role of natural and social factors involved. Epidemiologic characteristics of patients will be traced based on current information. url: https://www.ncbi.nlm.nih.gov/pubmed/32418549/ doi: 10.1017/dmp.2020.155 id: cord-304254-67brxejx author: Wei, Ping title: The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase date: 2006-01-20 words: 4577.0 sentences: 240.0 pages: flesch: 47.0 cache: ./cache/cord-304254-67brxejx.txt txt: ./txt/cord-304254-67brxejx.txt summary: As we have reported previously, the peptide cleavage assay shows that the specific activity for proteolysis decreases linearly with the decrease of enzyme concentration, suggesting that the dimer is the major form for biological activity and that the dimeric interface could be targeted for structural-based drug design against SARS 3CL proteinase [18] . The crystal structure of SARS 3CL proteinase indicates that the N-finger fragment plays an important role in the dimerization and maintenance of the active form of the enzyme [16] . The dimer dissociation constants of the SARS 3CL proteinase and N-terminal mutants were determined by sedimentation velocity and equilibrium methods. In summary, we have carried out a mutational study on the N-finger of SARS 3CL proteinase and determined the dimer dissociation constants for the wild-type protein and the mutants using sedimentation velocity and equilibrium techniques. abstract: Abstract The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. Accurate determination of the dimer dissociation constant and the role of the N-finger (residues 1–7) will provide more insights into the enzyme catalytic mechanism of SARS 3CL proteinase. The dimer dissociation constant of the wild-type protein was determined to be 14.0μM by analytical ultracentrifugation method. The N-finger fragment of the enzyme plays an important role in enzyme dimerization as shown in the crystal structure. Key residues in the N-finger have been studied by site-directed mutagenesis, enzyme assay, and analytical ultracentrifugation. A single mutation of M6A was found to be critical to maintain the dimer structure of the enzyme. The N-terminal octapeptide N8 and its mutants were also synthesized and tested for their potency as dimerization inhibitors. Peptide cleavage assay confirms that peptide N8 is a dimerization inhibitor with a K i of 2.20mM. The comparison of the inhibitory activities of N8 and its mutants indicates that the hydrophobic interaction of Met-6 and the electrostatic interaction of Arg-4 contribute most for inhibitor binding. This study describes the first example of inhibitors targeting the dimeric interface of SARS 3CL proteinase, providing a novel strategy for drug design against SARS and other coronaviruses. url: https://api.elsevier.com/content/article/pii/S0006291X05026331 doi: 10.1016/j.bbrc.2005.11.102 id: cord-323389-8vp57c1o author: Wei, S. title: Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2. date: 2020-06-16 words: 1563.0 sentences: 105.0 pages: flesch: 62.0 cache: ./cache/cord-323389-8vp57c1o.txt txt: ./txt/cord-323389-8vp57c1o.txt summary: We developed an assay that detects single copies of SARS-CoV-2 virus directly from saliva and swab samples in 30 min using a simple, one-step protocol that utilizes only a heat block and microcentrifuge tube prefilled with a mixture containing the necessary reagents and has a sensitivity and specificity of 97% and 100%, respectively. To determine which primer set was most sensitive and specific to SARS-CoV-2, we tested the eight primer sets that we designed, along with previously published primer sets 9, 10 , using serial dilutions of 500 to 0.5 copies of SARS-CoV-2 RNA standard spiked into a 25 μ L RT-LAMP reaction ( Figure 1C ). . https://doi.org/10.1101/2020.06.13.20129841 doi: medRxiv preprint necessary for testing clinical samples ( Figure 1D ). In summary, we developed HP-LAMP, which enables rapid detection of SARS-CoV-2 directly from saliva in 30 min using a simple one-step protocol with a LoD of 2 viral copies per μ L of saliva and a sensitivity and specificity of 97% and 100%, respectively. abstract: Abstract Rapid, scalable, point-of-need, COVID-19 diagnostic testing is necessary to safely re-open economies and prevent future outbreaks. We developed an assay that detects single copies of SARS-CoV-2 virus directly from saliva and swab samples in 30 min using a simple, one-step protocol that utilizes only a heat block and microcentrifuge tube prefilled with a mixture containing the necessary reagents and has a sensitivity and specificity of 97% and 100%, respectively. url: http://medrxiv.org/cgi/content/short/2020.06.13.20129841v1?rss=1 doi: 10.1101/2020.06.13.20129841 id: cord-262796-syu4wbpi author: Wei, Xiao-Shan title: Diarrhea is associated with prolonged symptoms and viral carriage in COVID-19 date: 2020-04-18 words: 2863.0 sentences: 174.0 pages: flesch: 57.0 cache: ./cache/cord-262796-syu4wbpi.txt txt: ./txt/cord-262796-syu4wbpi.txt summary: Abstract Background & Aims We compared clinical, laboratory, radiological, and outcome features of patients with SARS-CoV-2 infection (COVID-19) with pneumonia, with vs without diarrhea. Methods We performed a retrospective, single-center analysis of 84 patients with SARS-CoV-2 pneumonia in Wuhan Union Hospital, China, from January 19 through February 7, 2020. Of 76 patients with a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039). On admission to hospital, all confirmed COVID patients were tested for SARS-CoV-2 RNA from stool samples. Of 76 COVID-19 patients who had a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039) ( Table 5) . abstract: Abstract Background & Aims We compared clinical, laboratory, radiological, and outcome features of patients with SARS-CoV-2 infection (COVID-19) with pneumonia, with vs without diarrhea. Methods We performed a retrospective, single-center analysis of 84 patients with SARS-CoV-2 pneumonia in Wuhan Union Hospital, China, from January 19 through February 7, 2020. Cases were confirmed by real-time reverse-transcriptase PCR of nasal and pharyngeal swab specimens for SARS-CoV-2 RNA. Blood samples were analyzed for white blood cell count, lymphocyte count, alanine aminotransferase, creatine kinase, lactate dehydrogenase, D-dimer, C-reactive protein, and in some cases, immunoglobulins, complement, lymphocyte subsets, and cytokines. Virus RNA was detected in stool samples by real-time PCR. Results Of the 84 patients with SARS-CoV-2 pneumonia, 26 (31%) had diarrhea. The duration of fever and dyspnea in patients with diarrhea was significantly longer than those without diarrhea (all P<.05). Stool samples from a higher proportion of patients with diarrhea tested positive for virus RNA (69%) than from patients without diarrhea (17%) (P<.001). As of February 19, a lower proportion of patients with diarrhea had a negative result from the latest throat swab for SARS-CoV-2 (77%) than patients without diarrhea (97%) (P=.010), during these patients’ hospitalization. Of 76 patients with a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039). Conclusions At a single center in Wuhan, China, 31% of patients with SARS-CoV-2 pneumonia had diarrhea. A significantly higher proportion of patients with diarrhea have virus RNA in stool than patients without diarrhea. Elimination of SARS-CoV-2 from stool takes longer than elimination from the nose and throat. url: https://api.elsevier.com/content/article/pii/S1542356520305267 doi: 10.1016/j.cgh.2020.04.030 id: cord-138439-wvynetna author: Wei, Xiyi title: Sex Differences in Severity and Mortality Among Patients With COVID-19: Evidence from Pooled Literature Analysis and Insights from Integrated Bioinformatic Analysis date: 2020-03-30 words: 4720.0 sentences: 290.0 pages: flesch: 50.0 cache: ./cache/cord-138439-wvynetna.txt txt: ./txt/cord-138439-wvynetna.txt summary: Objective: To conduct a meta-analysis of current studies that examined sex differences in severity and mortality in patients with COVID-19, and identify potential mechanisms underpinning these differences. Methods: We performed a systematic review to collate data from observational studies examining associations of sex differences with clinical outcomes of COVID-19. Conclusions: This meta-analysis detected an increased severity and mortality rate in the male populations with COVID-19, which might be attributable to the sex-based differences in cellular compositions and immunological microenvironments of the lung. However, whether the sex difference is related to the risk factors for infection, severity, and mortality of COVID-19 is still lacking a comprehensive analysis based on the integration of new studies. ACE2 as a receptor of SARS-CoV and spike protein can be primed by TMPRSS2 are exploited to entry into target cells, which play an vital role in coronavirus pneumonia infection. abstract: Objective: To conduct a meta-analysis of current studies that examined sex differences in severity and mortality in patients with COVID-19, and identify potential mechanisms underpinning these differences. Methods: We performed a systematic review to collate data from observational studies examining associations of sex differences with clinical outcomes of COVID-19. PubMed, Web of Science and four preprint servers were searched for relevant studies. Data were extracted and analyzed using meta-analysis where possible, with summary data presented otherwise. Publicly available bulk RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data were analyzed to explore the potential mechanisms underlying the observed association. Results: 39 studies met inclusion criteria, representing 77932 patients, of which 41510 (53.3%) were males. Men were at a markedly increased risk of developing severe cases compared with women. Furthermore, the pooled odds ratio (OR) of mortality for male group compared with the female group indicated significant higher mortality rate for male. Data from scRNA-seq suggest that men have a higher amount of ACE2-expressing pulmonary alveolar type II cells than women. Sex-based immunological differences exist. The expression of androgen receptor (AR) is positively correlated with ACE2, and there is evidence that AR may directly regulate the expression of ACE2. Conclusions: This meta-analysis detected an increased severity and mortality rate in the male populations with COVID-19, which might be attributable to the sex-based differences in cellular compositions and immunological microenvironments of the lung. The host cell receptor ACE2 is likely regulated by AR signaling pathway, which is identified as a potential target for prevention and treatment of SARS-Cov-2 infections in men. url: https://arxiv.org/pdf/2003.13547v1.pdf doi: nan id: cord-332109-ont0tqpn author: Wei, Yufeng title: Substance Use Disorder in the COVID-19 Pandemic: A Systematic Review of Vulnerabilities and Complications date: 2020-07-18 words: 11728.0 sentences: 668.0 pages: flesch: 39.0 cache: ./cache/cord-332109-ont0tqpn.txt txt: ./txt/cord-332109-ont0tqpn.txt summary: The immunosuppression reduces antibody production, cytotoxicity, and T cell-mediated immune responses, and is linked to higher incidences of pathogen infections, slowed recovery, and severe disease progression in COVID-19. Due to compromised immune responses, cocaine abusers have considerably high incidences of viral infections, including human immunodeficiency virus (HIV), influenza, and potentially SARS-CoV-2. Cardiac arrhythmias and acute MI; oxygen imbalance; microvascular diseases and thrombosis [122] [123] [124] [125] [126] [127] [129] [130] [131] [132] Increased severity and mortality [12, 37, 38] Immune system Stimulating HPA axis; immunosuppression; defects in antibody formation, lymphocyte proliferation, macrophage and NK activation [141, 142] High incidence of viral infection [142] CNS Increased BBB permeability due to loss of tight junction proteins; rearrangement of cytoskeleton structure [143] [144] [145] [146] Endotheliitis and CNS infection [53, [55] [56] [57] Amphetamine, METH, MDMA abstract: As the world endures the coronavirus disease 2019 (COVID-19) pandemic, the conditions of 35 million vulnerable individuals struggling with substance use disorders (SUDs) worldwide have not received sufficient attention for their special health and medical needs. Many of these individuals are complicated by underlying health conditions, such as cardiovascular and lung diseases and undermined immune systems. During the pandemic, access to the healthcare systems and support groups is greatly diminished. Current research on COVID-19 has not addressed the unique challenges facing individuals with SUDs, including the heightened vulnerability and susceptibility to the disease. In this systematic review, we will discuss the pathogenesis and pathology of COVID-19, and highlight potential risk factors and complications to these individuals. We will also provide insights and considerations for COVID-19 treatment and prevention in patients with SUDs. url: https://doi.org/10.3390/ph13070155 doi: 10.3390/ph13070155 id: cord-327520-qj7coqfr author: Wei, Yulong title: Coronavirus genomes carry the signatures of their habitats date: 2020-06-13 words: 1395.0 sentences: 93.0 pages: flesch: 54.0 cache: ./cache/cord-327520-qj7coqfr.txt txt: ./txt/cord-327520-qj7coqfr.txt summary: Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Here we compared the CpG and U content 327 of these coronaviruses and found that viruses that regularly infect AVP-rich tissues tend to Based on global sequence comparison, figure 4a shows that most SNPs are C->U substitutions. abstract: Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of COVID-19. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter deaminates C into U residues leading to dysfunctional transcripts. We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas viruses that do not infect tissues with abundant AVPs do not share these sequence hallmarks. In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Furthermore, over four months of SARS-CoV-2 evolutionary history, we observed a marked increase in C to U substitutions in the 5’ UTR and ORF1ab regions. This suggests that the two regions could be under constant C to U deamination by APOBEC3. The evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development. url: https://doi.org/10.1101/2020.06.13.149591 doi: 10.1101/2020.06.13.149591 id: cord-014938-7evmiuv5 author: Wei-ming, Yan title: Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model date: 2008-01-13 words: 1092.0 sentences: 64.0 pages: flesch: 43.0 cache: ./cache/cord-014938-7evmiuv5.txt txt: ./txt/cord-014938-7evmiuv5.txt summary: title: Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model To evaluate the role of murine fibrinogen like protein 2 (mfgl2) /fibroleukin in lung impairment in Severe acute respiratory syndrome (SARS), a murine SARS model induced by Murine hepatitis virus strain 3 (MHV-3) through trachea was established. In a separate experiment, tissues including lungs, spleen, liver, kidneys, intestine, heart, brain were collected at a series of time points from Balb/cJ mice infected with MHV-3 through trachea. Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung The clinical pathology of severe acute respiratory syndrome (SARS): a report from China Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR A novel coronavirus associated with severe acute respiratory syndrome abstract: To evaluate the role of murine fibrinogen like protein 2 (mfgl2) /fibroleukin in lung impairment in Severe acute respiratory syndrome (SARS), a murine SARS model induced by Murine hepatitis virus strain 3 (MHV-3) through trachea was established. Impressively, all the animals developed interstitial pneumonia with extensive hyaline membranes formation within alveoli, and presence of micro-vascular thrombosis in the pulmonary vessels. MHV-3 nucleocapsid gene transcripts were identified in multiple organs including lungs, spleen etc. As a representative proinflammatory gene, mfgl2 prothrombinase expression was evident in terminal and respiratory bronchioles, alveolar epithelia and infiltrated cells in the lungs associated with fibrin deposition and micro-vascular thrombosis. In summary, the established murine SARS model could mimic the pathologic characteristics of lungs in patients with SARS. Besides the physical damages due to virus replication in organs, the up-regulation of novel gene mfgl2 in lungs may play a vital role in the development of SARS associated lung damage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091223/ doi: 10.1007/s12250-007-0020-5 id: cord-261470-sqxdwu6j author: Weichmann, Franziska title: Projected supportive effects of Pycnogenol® in patients suffering from multi-dimensional health impairments after a SARS-CoV2 infection date: 2020-10-09 words: 5918.0 sentences: 308.0 pages: flesch: 38.0 cache: ./cache/cord-261470-sqxdwu6j.txt txt: ./txt/cord-261470-sqxdwu6j.txt summary: Two London based hospitals also found increasing numbers of patients with Kawasaki-like symptoms in communities with high rates of COVID 19, which was provisionally called pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) [68] [70] . Another double-blind, placebo-controlled study reported similar effects when supplementing type II diabetes and hypertensive patients, taking ACE inhibitor medication together with 125 mg Pycnogenol ® daily for 3 months. Regarding endotheliitis, Pycnogenol ® studies offer good evidence for potential beneficial effects for patients suffering from COVID-19 by improving endothelial function. As Pycnogenol ® offers antioxidant and anti-inflammatory activities and positively influences endothelial cell function as well as microcirculation and platelet reactivity, a supplementation might support the management of COVID-19 patients. We hypothesize possible additional beneficial effects of Pycnogenol ® in patients infected with the new coronavirus SARS-CoV2 and those who suffer from abiding health problems, when complemented to the standard treatment also upon the first day of symptoms or infection. abstract: Corona Virus Disease 2019 (COVID-19) is triggered by the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV2) and has rapidly developed into a worldwide pandemic. Unlike other SARS viruses, SARS-CoV2 does not solely impact the respiratory system, but additionally leads to inflammation of endothelial cells, microvascular injuries and coagulopathies, thereby affecting multiple organs. Recent reports of patients that were infected with SARS-CoV2 suggest persistent health problems even months after the initial infection. In over 90 human clinical studies, the French maritime pine bark extract Pycnogenol® demonstrated anti-inflammatory, vascular and endothelium-protective effects. We propose that Pycnogenol® may be beneficial in supporting recovery and mitigating symptoms and long-term consequences resulting from a SARS-CoV2 infection in COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S0924857920303976?v=s5 doi: 10.1016/j.ijantimicag.2020.106191 id: cord-339508-nf6ov39g author: Weil, Ana A. title: Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle date: 2020-09-01 words: 3734.0 sentences: 207.0 pages: flesch: 48.0 cache: ./cache/cord-339508-nf6ov39g.txt txt: ./txt/cord-339508-nf6ov39g.txt summary: In this study, we describe the results of cross-sectional resident and employee SARS-CoV-2 testing, and infection control and personnel policies associated with 16 Seattle area SNFs. Through two testing strategies, a total of 16 SNFs offered testing to either residents, employees, or both. For employees tested through the Seattle Flu Study, data included participant date of birth, date of testing, race and ethnicity, location and nature of work, new symptoms experienced during the last 7 days, and history of SARS-CoV-2 testing (Appendix 1 in the Supplementary Material). For employees, positive or inconclusive SARS-CoV-2 test results were reported directly to participants by phone within 48 h and to the Washington State Department of Health. We report the results of a large cross-sectional study evaluating SARS-CoV-2 prevalence in skilled nursing facilities (SNFs) in the Seattle area during the spring 2020 peak of the COVID-19 pandemic. abstract: BACKGROUND: Skilled nursing facilities (SNFs) are high-risk settings for SARS-CoV-2 transmission. Infection rates among employees are infrequently described. OBJECTIVE: To describe SARS-CoV-2 rates among SNF employees and residents during a non-outbreak time period, we measured cross-sectional SARS-CoV-2 prevalence across multiple sites in the Seattle area. DESIGN: SARS-CoV-2 testing was performed for SNF employees and residents using quantitative real-time reverse transcription polymerase chain reaction. A subset of employees completed a sociodemographic and symptom questionnaire. PARTICIPANTS: Between March 29 and May 13, 2020, we tested 1583 employees and 1208 residents at 16 SNFs for SARS-CoV-2. MAIN MEASURE: SARS-CoV-2 testing results and symptom report among employees and residents. KEY RESULTS: Eleven of the 16 SNFs had one or more resident or employee test positive. Overall, 46 (2.9%) employees had positive or inconclusive testing for SARS-CoV-2, and among those who completed surveys, most were asymptomatic and involved in direct patient care. The majority of employees tested were female (934, 73%), and most employees were Asian (392, 30%), Black (360, 28%), or white (360, 28%). Among the 1208 residents tested, 110 (9.1%) had positive or inconclusive results. There was no association between the presence of positive residents and positive employees within a SNF (p = 0.62, McNemar’s test). CONCLUSIONS: In the largest study of SNFs to date, SARS-CoV-2 infections were detected among both employees and residents. Employees testing positive were often asymptomatic and involved in direct patient care. Surveillance testing is needed for SNF employees and residents during the pandemic response. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11606-020-06165-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32875494/ doi: 10.1007/s11606-020-06165-7 id: cord-277210-xaj2623u author: Weinkove, Robert title: Managing haematology and oncology patients during the COVID‐19 pandemic: interim consensus guidance date: 2020-05-13 words: 6044.0 sentences: 315.0 pages: flesch: 38.0 cache: ./cache/cord-277210-xaj2623u.txt txt: ./txt/cord-277210-xaj2623u.txt summary: • Adopt measures within cancer centres to reduce risk of nosocomial SARS-CoV-2 acquisition; support population-wide social distancing; reduce demand on acute services; ensure adequate staffing; and provide culturally safe care. Patients with cancer could be at elevated risk of severe COVID-19, while delivery of cancer therapies could be disrupted by quarantines, social distancing measures, and interruption of routine health care delivery by the pandemic. 38 Community spread of COVID-19 has the potential to diminish the donor pool, to threaten the capacity of cancer services to provide routine transfusion support, and to increase the risks that transfusion-dependent patients will come into contact with other individuals with SARS-CoV-2. We present interim guidance for clinicians caring for patients with cancer who may be particularly vulnerable both to severe COVID-19 and the potential impact of the pandemic on the provision of cancer investigations and treatment. abstract: INTRODUCTION: A pandemic coronavirus, SARS‐CoV‐2, causes COVID‐19, a potentially life‐threatening respiratory disease. Patients with cancer may have compromised immunity due to their malignancy and/or treatment, and may be at elevated risk of severe COVID‐19. Community transmission of COVID‐19 could overwhelm health care services, compromising delivery of cancer care. This interim consensus guidance provides advice for clinicians managing patients with cancer during the pandemic. MAIN RECOMMENDATIONS: During the COVID‐19 pandemic: In patients with cancer with fever and/or respiratory symptoms, consider causes in addition to COVID‐19, including other infections and therapy‐related pneumonitis. For suspected or confirmed COVID‐19, discuss temporary cessation of cancer therapy with a relevant specialist. Provide information on COVID‐19 for patients and carers. Adopt measures within cancer centres to reduce risk of nosocomial SARS‐CoV‐2 acquisition; support population‐wide social distancing; reduce demand on acute services; ensure adequate staffing; and provide culturally safe care. Measures should be equitable, transparent and proportionate to the COVID‐19 threat. Consider the risks and benefits of modifying cancer therapies due to COVID‐19. Communicate treatment modifications, and review once health service capacity allows. Consider potential impacts of COVID‐19 on the blood supply and availability of stem cell donors. Discuss and document goals of care, and involve palliative care services in contingency planning. CHANGES IN MANAGEMENT AS A RESULT OF THIS STATEMENT: This interim consensus guidance provides a framework for clinicians managing patients with cancer during the COVID‐19 pandemic. In view of the rapidly changing situation, clinicians must also monitor national, state, local and institutional policies, which will take precedence. ENDORSED BY: Australasian Leukaemia and Lymphoma Group; Australasian Lung Cancer Trials Group; Australian and New Zealand Children's Haematology/Oncology Group; Australia and New Zealand Society of Palliative Medicine; Australasian Society for Infectious Diseases; Bone Marrow Transplantation Society of Australia and New Zealand; Cancer Council Australia; Cancer Nurses Society of Australia; Cancer Society of New Zealand; Clinical Oncology Society of Australia; Haematology Society of Australia and New Zealand; National Centre for Infections in Cancer; New Zealand Cancer Control Agency; New Zealand Society for Oncology; and Palliative Care Australia. url: https://doi.org/10.5694/mja2.50607 doi: 10.5694/mja2.50607 id: cord-300793-tuq8z6gm author: Weiss, Robin A title: Social and environmental risk factors in the emergence of infectious diseases date: 2004 words: 5853.0 sentences: 273.0 pages: flesch: 47.0 cache: ./cache/cord-300793-tuq8z6gm.txt txt: ./txt/cord-300793-tuq8z6gm.txt summary: About 30 new diseases have been identified, including Legionnaires'' disease, human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS), hepatitis C, bovine spongiform encephalopathy (BSE)/variant Creutzfeldt-Jakob disease (vCJD), Nipah virus, several viral hemorrhagic fevers and, most recently, severe acute respiratory syndrome (SARS) and avian influenza. Emerging infectious diseases in humans comprise the following: first, established diseases undergoing increased incidence or geographic spread, for example, Tuberculosis and Dengue fever; second, newly discovered infections causing known diseases, for example, hepatitis C and Helicobacter pylori; and third, newly emerged diseases, for example, HIV/AIDS and SARS. Although some of the apparent increase in infectious disease may be attributable to better diagnostic methods and surveillance, there seems little doubt that more incidents are occurring, and have the potential to spread more widely than 50 years ago, as outbreaks and spread of infections like Nipah virus and SARS would not have passed unnoticed. abstract: Fifty years ago, the age-old scourge of infectious disease was receding in the developed world in response to improved public health measures, while the advent of antibiotics, better vaccines, insecticides and improved surveillance held the promise of eradicating residual problems. By the late twentieth century, however, an increase in the emergence and re-emergence of infectious diseases was evident in many parts of the world. This upturn looms as the fourth major transition in human–microbe relationships since the advent of agriculture around 10,000 years ago. About 30 new diseases have been identified, including Legionnaires' disease, human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS), hepatitis C, bovine spongiform encephalopathy (BSE)/variant Creutzfeldt-Jakob disease (vCJD), Nipah virus, several viral hemorrhagic fevers and, most recently, severe acute respiratory syndrome (SARS) and avian influenza. The emergence of these diseases, and resurgence of old ones like tuberculosis and cholera, reflects various changes in human ecology: rural-to-urban migration resulting in high-density peri-urban slums; increasing long-distance mobility and trade; the social disruption of war and conflict; changes in personal behavior; and, increasingly, human-induced global changes, including widespread forest clearance and climate change. Political ignorance, denial and obduracy (as with HIV/AIDS) further compound the risks. The use and misuse of medical technology also pose risks, such as drug-resistant microbes and contaminated equipment or biological medicines. A better understanding of the evolving social dynamics of emerging infectious diseases ought to help us to anticipate and hopefully ameliorate current and future risks. url: https://www.ncbi.nlm.nih.gov/pubmed/15577934/ doi: 10.1038/nm1150 id: cord-321938-pda4a5n7 author: Weisshoff, Hardy title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 words: 5076.0 sentences: 266.0 pages: flesch: 57.0 cache: ./cache/cord-321938-pda4a5n7.txt txt: ./txt/cord-321938-pda4a5n7.txt summary: We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). In the Spike protein of SARS-CoV-2, several sequences which are highly susceptible to interaction with DNA (multiple amino acids with positive charged side chains) were identified, in particular at the angiotensin I-converting enzyme 2 (ACE2)-receptor binding domain (RBD): YRLFRK (SARS-CoV-2 specific from protein data bank (PDB) data base entry PBD ID: 6VXX, source: [23] ), as well as NRKRISN (PBD ID: 6VXX) and KIKRMK (PDB ID: 5X5B source: [24] ). This enabled us to exploit NMR-spectroscopy to investigate whether the selected peptide-sequences from SARS-CoV-2 proteins bind to this clinically advanced aptamer (BC 007), forcing it into its well described quadruple structure just by molecular interaction. abstract: Corona virus disease 2019 (COVID-19) is a respiratory disease caused by a new coronavirus (SARS-CoV-2) which causes significant morbidity and mortality. The emergence of this novel and highly pathogenic SARS-CoV-2 and its rapid international spread poses a serious global public health emergency. To date 32,174,627 cases, of which 962,613 (2.99%) have died, have been reported (https://www.who.int/westernpacific/health-topics/coronavirus, accessed 23 Sep 2020). The outbreak was declared a Public Health Emergency of International Concern on 30 January 2020. There are still not many SARS-CoV-2-specific and effective treatments or vaccines available. A second round of infection is obviously unavoidable. Aptamers had already been at the centre of interest in the fight against viruses before now. The selection and development of a new aptamer is, however, a time-consuming process. We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). Indeed, several such sequence-sections have been identified. In particular for two of these sequences, BC 007 showed specific binding in a therapy-relevant concentration range, as shown in Nuclear magnetic resonance (NMR)- and Circular dicroism (CD)-spectroscopy and isothermal titration calorimetry (ITC). The excellent clinical toxicity and tolerability profile of this substance opens up an opportunity for rapid clinical testing of its COVID-19 effectiveness. url: https://www.sciencedirect.com/science/article/pii/S2405844020322647 doi: 10.1016/j.heliyon.2020.e05421 id: cord-297197-klr208kp author: Weizman, Yehuda title: Use of Wearable Technology to Enhance Response to the COVID-19 Pandemic date: 2020-07-01 words: 1361.0 sentences: 73.0 pages: flesch: 50.0 cache: ./cache/cord-297197-klr208kp.txt txt: ./txt/cord-297197-klr208kp.txt summary: ABSTRACT Introduction As part of the COVID-19 outbreak response, numerous technology-based solutions have been created to enable contact tracing, track movements of the population and ensure social control. The bracelet would facilitate 3 functions; screening on a population level, digital contact tracing and real-time immunity status tracking. The bracelet would employ the IoT to transfer data over a network to an interactive web-based dashboard that tracks COVID-19 in real-time. If an individual then tested positive for SARS-CoV-2, the database could automatically trace back anyone they had come in contact with in the past 14 days using a GPS feature (described below). In this instance, the biometric bracelet''s GPS feature would continuously track movements of individuals within a geographical area and communicate back to the Covid-19 database platform saving input on the population whereabouts at each timepoint. As the coronavirus pandemic continues to spread, some Privacy Commissioners are lifting data restrictions for health officials to keep track of the outbreak. abstract: ABSTRACT Introduction As part of the COVID-19 outbreak response, numerous technology-based solutions have been created to enable contact tracing, track movements of the population and ensure social control. Wearable biometric bracelets are widespread and commonly used in the form of wrist-worn activity trackers that are both familiar and liked by the general population. Objectives/Study Design/Methods The authors propose an innovative approach - a wearable bracelet that can be used to curb the spread of Covid-19. The bracelet would facilitate 3 functions; screening on a population level, digital contact tracing and real-time immunity status tracking. Results/Conclusions Utilising the Internet of Things, data would then be transfer over a network to interactive web-based dashboard and big data analytics employed to augment response within a defined geographic region. url: https://www.sciencedirect.com/science/article/pii/S0033350620302869?v=s5 doi: 10.1016/j.puhe.2020.06.048 id: cord-256982-t6urqus7 author: Wellinghausen, Nele title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 words: 2514.0 sentences: 131.0 pages: flesch: 51.0 cache: ./cache/cord-256982-t6urqus7.txt txt: ./txt/cord-256982-t6urqus7.txt summary: The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. A comparison of five commercial immunoassays in serum samples taken at least ten days after onset of symptoms from 51 PCR-confirmed COVID-19 outpatients revealed an overall sensitivity of the assays from 74.5% to 88.2%. abstract: Commercially available immunoassays have been developed for sensitive and specific detection of antibodies against SARS-CoV-2. While high sensitivity has been reported in hospitalized COVID-19 patients, little is known about the performance of the assays in ambulatory patients. Therefore, we evaluated the SARS-CoV-2-IgG response in 51 SASR-CoV-2-PCR-confirmed outpatients with five commercial immunoassays. The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. The sensitivity in serum samples, collected >20 days after onset of symptoms, varied between 75.0% and 90.0%, and in samples, collected at least 28 days after onset of symptoms, did not increase, except in the Anti-SARS-CoV-2-ELISA IgG by Euroimmun (90.0%). There was not an obvious association between the type of the antigen (N versus S protein) and the overall sensitivity of the assays. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. In asymptomatic persons the SARS-CoV-2-IgG response may even be absent in a relevant percentage of persons. url: https://www.ncbi.nlm.nih.gov/pubmed/32983837/ doi: 10.3205/id000066 id: cord-308256-jy20xtwx author: Wells, P. M. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-07-30 words: 4262.0 sentences: 235.0 pages: flesch: 52.0 cache: ./cache/cord-308256-jy20xtwx.txt txt: ./txt/cord-308256-jy20xtwx.txt summary: Methods: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. abstract: Background: Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. Methods: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. Findings: We demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. Interpretation: Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. Funding: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC url: http://medrxiv.org/cgi/content/short/2020.07.29.20162701v1?rss=1 doi: 10.1101/2020.07.29.20162701 id: cord-322812-9u3ptqjs author: Wells, Philippa M. title: Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date: 2020-10-15 words: 3730.0 sentences: 197.0 pages: flesch: 51.0 cache: ./cache/cord-322812-9u3ptqjs.txt txt: ./txt/cord-322812-9u3ptqjs.txt summary: METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. abstract: BACKGROUND: Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. FINDINGS: We demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. INTERPRETATION: Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FUNDING: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC url: https://api.elsevier.com/content/article/pii/S0163445320306538 doi: 10.1016/j.jinf.2020.10.011 id: cord-260925-puuqv6zk author: Wen, Feng title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 date: 2020-03-05 words: 1171.0 sentences: 70.0 pages: flesch: 56.0 cache: ./cache/cord-260925-puuqv6zk.txt txt: ./txt/cord-260925-puuqv6zk.txt summary: title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 The sequences NC_004718.3 of SARS coronavirus 6 genes were utilized to define the protein products of SARS-CoV-2. First, the protein sequences of SARS-CoV-2 were compared with RaTG13, human SARS (NC_004718.3), bat SARS (DQ022305.2), and human MERS (NC_019843.3) by calculating the similarity in a given sliding window ( Fig. 1 A) . These results suggested that there had probably been no hyper-variable genomic hotspot in the SARS-CoV-2 population until now. The hyper-variable genomic hotspot has been established in the SARS-CoV-2 population at the nucleotide but not the amino acid level, suggesting that there have been no beneficial mutations. mutations in nsp1, nsp3, nsp15, and gene S that identified in this study would be associated with the SARS-CoV-2 epidemic and was worthy of further study. The genome sequence of the SARS-associated coronavirus abstract: nan url: https://doi.org/10.1016/j.jinf.2020.02.027 doi: 10.1016/j.jinf.2020.02.027 id: cord-033406-xoyt7esk author: Wen, Wen title: Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient date: 2020-09-11 words: 358.0 sentences: 30.0 pages: flesch: 58.0 cache: ./cache/cord-033406-xoyt7esk.txt txt: ./txt/cord-033406-xoyt7esk.txt summary: title: Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient The patient presented to Anqing Municipal Hospital (Anhui province) with a positive result on nasopharyngeal swabs for SARS-CoV-2 and discharged in good clinical condition after consecutive negative results On February 9, 2020. 3 In our report, the patient recovered from COVID-19 and developed a lung infection with GGO 82 days later after being discharged from hospital. This study is part of the project of "Construction of a bio-information platform for novel coronavirus pneumonia Chest computed tomography show completely absorbed lesion when he was discharged on May 28, 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543505/ doi: 10.1093/pcmedi/pbaa033 id: cord-259033-op94wuy4 author: Wendling, Daniel title: Can SARS-CoV-2 trigger reactive arthritis? date: 2020-10-27 words: 1193.0 sentences: 73.0 pages: flesch: 42.0 cache: ./cache/cord-259033-op94wuy4.txt txt: ./txt/cord-259033-op94wuy4.txt summary: The potential mechanisms at the origin of arthritis in a context of viral infection by SARS-CoV-2 remain at the hypothesis stage. The mechanism of reactive arthritis is plausible, due to the clinical presentation, the delay between the onset (or diagnosis) of COVID and the onset of rheumatological manifestations, the usual negativation of nasopharyngeal RT-PCR at the time of onset of rheumatological involvement. However, cases of symptomatic SARS-CoV-2 infection have been reported in patients treated with an anti IL-17 monoclonal antibody for spondyloarthritis [19] . Arthritis may be reactive to a masked pulmonary or digestive infection as a consequence of COVID [13] , or it may be a non-specific consequence of the "cytokine storm" that accompanies the symptomatic forms of the disease [20] . This new infectious disease may induce rheumatological manifestations, with the possibility of reactive arthritis. Patient-reported Disease Activity in an Axial Spondyloarthritis Cohort during the COVID-19 Pandemic. A Case of Reactive Arthritis Secondary to Coronavirus Disease 2019 Infection Case of acute arthritis following SARS-CoV-2 infection abstract: nan url: https://api.elsevier.com/content/article/pii/S1297319X20301937 doi: 10.1016/j.jbspin.2020.105086 id: cord-318766-vx0dnnxh author: Wendt, Ralph title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany date: 2020-06-03 words: 1553.0 sentences: 91.0 pages: flesch: 50.0 cache: ./cache/cord-318766-vx0dnnxh.txt txt: ./txt/cord-318766-vx0dnnxh.txt summary: title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany We investigated potential transmissions of a symptomatic SARS-CoV-2–positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. We tested all 254 potential contacts of the symptomatic SARS-CoV-2-positive index physician, including 67 patients, and 187 nurses and doctors, technical and medical assistants, and other healthcare staff, on day 5 after the exposure by specific RT-PCR from nose and throat swabs or pharyngeal lavage, irrespective of reported symptoms. We tested a large number of possible contact persons of a symptomatic SARS-CoV-2-infected physician among HCWs and patients on day 5 after exposure; all were negative. 6 For further analysis and confirmation of our results, we investigated the serum of all high-risk contacts (n = 23) on days 15 or 16 and 22 or 23 for SARS-CoV-2-specific antibodies. abstract: We investigated potential transmissions of a symptomatic SARS-CoV-2–positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. No in-hospital transmissions occurred, despite 254 contacts among patients and healthcare workers. In conclusion, exposed hospital staff continued work, accompanied by close clinical and virologic monitoring. url: https://doi.org/10.1017/ice.2020.268 doi: 10.1017/ice.2020.268 id: cord-258281-gxwk8jq9 author: Wenling, Yao title: Pregnancy and COVID-19: management and challenges date: 2020-08-31 words: 5015.0 sentences: 263.0 pages: flesch: 46.0 cache: ./cache/cord-258281-gxwk8jq9.txt txt: ./txt/cord-258281-gxwk8jq9.txt summary: Based on recently published literature and official documents, this review provides an introduction to the pathogenesis, pathology, and clinical features of COVID-19 and has focused on the current researches on clinical features, pregnancy outcomes and placental histopathological analysis from pregnant women infected with SARS-CoV-2 in comparison with SARS-CoV and MERS-CoV. Although there is no unequivocal evidence to support the fetal infection by intrauterine vertical transmission of SARS, MERS and SARS-CoV-2 so far, more and more articles began to report maternal deaths due to COVID-19. There were no cases of vertical transmission identified among pregnant women infected with SARS 44-49 so far, but SARS during pregnancy is associated with high incidences of spontaneous miscarriage, preterm delivery, intrauterine growth restriction, endotracheal intubation and admission to the neonatal intensive care unit [44] [45] [46] . This is a review on pregnant women infected by SARS-CoV-2, SARS, and MERS, including their pathogenesis, clinical manifestations and pregnancy outcomes. Middle East respiratory syndrome coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature abstract: The consequences of COVID-19 infecting pregnant women and the potential risks of vertical transmission have become a major issue. Since little is currently known about COVID-19 in pregnancy, the understanding of COVID-19 in this particular group will be updated in time, and a comprehensive review will be useful to evaluate the impact of COVID-19 in pregnancy. Based on recently published literature and official documents, this review provides an introduction to the pathogenesis, pathology, and clinical features of COVID-19 and has focused on the current researches on clinical features, pregnancy outcomes and placental histopathological analysis from pregnant women infected with SARS-CoV-2 in comparison with SARS-CoV and MERS-CoV. These viruses trigger a cytokine storm in the body, produce a series of immune responses, and cause changes in peripheral leukocytes and immune system cells leading to pregnancy complications that may be associated with viral infections. The expression of ACE2 receptors in the vascular endothelium may explain the histological changes of placentas from pregnant women infected by SARS-CoV-2. Pregnant women with COVID-19 pneumonia show similar clinical characteristics compared with non-pregnant counterparts. Although there is no unequivocal evidence to support the fetal infection by intrauterine vertical transmission of SARS, MERS and SARS-CoV-2 so far, more and more articles began to report maternal deaths due to COVID-19. In particular, from February 26, 2020 (date of the first COVID-19 case reported in Brazil) until June 18, 2020, Brazil reported 124 maternal deaths. Therefore, pregnant women and neonates require special attention regarding the prevention, diagnosis and management of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32876296/ doi: 10.1590/s1678-9946202062062 id: cord-320455-doup2bqq author: Werion, Alexis title: SARS-CoV-2 Causes a Specific Dysfunction of the Kidney Proximal Tubule date: 2020-08-10 words: 2871.0 sentences: 182.0 pages: flesch: 44.0 cache: ./cache/cord-320455-doup2bqq.txt txt: ./txt/cord-320455-doup2bqq.txt summary: Coronavirus disease 2019 (COVID-19) is commonly associated with kidney damage, and the angiotensin converting enzyme 2 (ACE2) receptor for SARS-CoV-2 is highly expressed in the proximal tubule cells. At the structural level, kidneys from patients with COVID-19 showed prominent tubular injury, including in the initial part of the proximal tubule, with brush border loss, acute tubular necrosis, intraluminal debris, and a marked decrease in the expression of megalin in the brush border. Thus, our data establish that SARS-CoV-2 causes specific manifestations of proximal tubule dysfunction and provide novel insights into COVID-19 severity and outcome. The angiotensin converting enzyme 2 (ACE2), the receptor mediating the entry of SARS-CoV-2 in human cells, is expressed in the lung, heart, intestine and kidney, providing a rationale for the systemic manifestations of the disease [4] [5] [6] [7] . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection abstract: Coronavirus disease 2019 (COVID-19) is commonly associated with kidney damage, and the angiotensin converting enzyme 2 (ACE2) receptor for SARS-CoV-2 is highly expressed in the proximal tubule cells. Whether patients with COVID-19 present specific manifestations of proximal tubule dysfunction remains unknown. To test this, we examined a cohort of 49 patients requiring hospitalization in a large academic hospital in Brussels, Belgium. There was evidence of proximal tubule dysfunction in a subset of patients with COVID-19, as attested by low-molecular-weight proteinuria (70-80%), neutral aminoaciduria (46%), and defective handling of uric acid (46%) or phosphate (19%). None of the patients had normoglycemic glucosuria. Proximal tubule dysfunction was independent of pre-existing comorbidities, glomerular proteinuria, nephrotoxic medications or viral load. At the structural level, kidneys from patients with COVID-19 showed prominent tubular injury, including in the initial part of the proximal tubule, with brush border loss, acute tubular necrosis, intraluminal debris, and a marked decrease in the expression of megalin in the brush border. Transmission electron microscopy identified particles resembling coronaviruses in vacuoles or cisternae of the endoplasmic reticulum in proximal tubule cells. Among features of proximal tubule dysfunction, hypouricemia with inappropriate uricosuria was independently associated with disease severity and with a significant increase in the risk of respiratory failure requiring invasive mechanical ventilation using Cox (adjusted hazard ratio 6.2, 95% CI 1.9-20.1) or competing risks (adjusted sub-distribution hazard ratio 12.1, 95% CI 2.7-55.4) survival models. Thus, our data establish that SARS-CoV-2 causes specific manifestations of proximal tubule dysfunction and provide novel insights into COVID-19 severity and outcome. url: https://api.elsevier.com/content/article/pii/S0085253820309121 doi: 10.1016/j.kint.2020.07.019 id: cord-304487-ycvu5l5f author: Wertheim, Joel O title: A glimpse into the origins of genetic diversity in SARS-CoV-2 date: 2020-03-04 words: 1202.0 sentences: 74.0 pages: flesch: 43.0 cache: ./cache/cord-304487-ycvu5l5f.txt txt: ./txt/cord-304487-ycvu5l5f.txt summary: Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32129842/ doi: 10.1093/cid/ciaa213 id: cord-252922-cdhnlvxv author: West, Erin A. title: Corona Immunitas: study protocol of a nationwide program of SARS-CoV-2 seroprevalence and seroepidemiologic studies in Switzerland date: 2020-10-24 words: 5479.0 sentences: 321.0 pages: flesch: 47.0 cache: ./cache/cord-252922-cdhnlvxv.txt txt: ./txt/cord-252922-cdhnlvxv.txt summary: We describe here the protocol of Corona Immunitas, a centrally coordinated research program consisting of repeated cross-sectional and longitudinal seroprevalence and seroepidemiological studies conducted across several regions and populations in Switzerland, whose aim is to generate reliable data to inform policy-making. Specific aims are to: (1) estimate the number of individuals infected with SARS-CoV-2 in the population with or without symptoms at several points in time; (2) compare the seroprevalence between the general population and specific subpopulations; (3) investigate the characteristics, duration, and extent of immunity after infection; (4) assess the association between participant characteristics and behaviors with their risk of infection; and (5) quantify the association between the pandemic and participants'' mental and physical health. Corona Immunitas is a research program coordinated by SSPH?, conducting longitudinal, population-based seroprevalence studies covering a number of Swiss Cantons as well as several seroepidemiological studies in specific subpopulations. abstract: OBJECTIVES: Seroprevalence studies to assess the spread of SARS-CoV-2 infection in the general population and subgroups are key for evaluating mitigation and vaccination policies and for understanding the spread of the disease both on the national level and for comparison with the international community. METHODS: Corona Immunitas is a research program of coordinated, population-based, seroprevalence studies implemented by Swiss School of Public Health (SSPH+). Over 28,340 participants, randomly selected and age-stratified, with some regional specificities will be included. Additional studies in vulnerable and highly exposed subpopulations are also planned. The studies will assess population immunological status during the pandemic. RESULTS: Phase one (first wave of pandemic) estimates from Geneva showed a steady increase in seroprevalence up to 10.8% (95% CI 8.2–13.9, n = 775) by May 9, 2020. Since June, Zurich, Lausanne, Basel City/Land, Ticino, and Fribourg recruited a total of 5973 participants for phase two thus far. CONCLUSIONS: Corona Immunitas will generate reliable, comparable, and high-quality serological and epidemiological data with extensive coverage of Switzerland and of several subpopulations, informing health policies and decision making in both economic and societal sectors. ISRCTN Registry: https://www.isrctn.com/ISRCTN18181860. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00038-020-01494-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00038-020-01494-0 doi: 10.1007/s00038-020-01494-0 id: cord-309856-flkjl1dm author: Westblade, Lars F. title: SARS-CoV-2 Viral Load Predicts Mortality in Patients with and Without Cancer Who Are Hospitalized with COVID-19 date: 2020-09-15 words: 1971.0 sentences: 96.0 pages: flesch: 52.0 cache: ./cache/cord-309856-flkjl1dm.txt txt: ./txt/cord-309856-flkjl1dm.txt summary: For data generated using the cobas assay, we used viral load cutoffs based on C T values for the 123 ORF1ab gene target that were previously shown to correlate with in-hospital mortality among 124 hospitalized patients with COVID-19: high, C T value <25; medium, C T value 25-30, low, C T value 125 >30 (Magleby et al., 2020) . In the overall cohort, using assay-specific C T value cutoffs, 38.8% of patients with a high viral 156 load died during their hospitalization, compared to 24.1% of patients with a medium viral load, active cancer that adjusted for age and need for supplemental oxygen within 3 hours of 169 presentation to the ED (Table 4) , we found that having a high viral load was independently 170 associated with increased in-hospital mortality (aOR 5.00; 95% CI: 1. In conclusion, using two different diagnostic platforms, we found that admission SARS-CoV-2 277 viral load, as assessed by C T values that are generated by routine RT-PCR diagnostic assays, 278 was highly associated with in-hospital mortality in COVID-19 patients with and without cancer. abstract: Patients with cancer may be at increased risk of severe coronavirus disease 2019 (COVID-19), but the role of viral load on this risk is unknown. We measured SARS-CoV-2 viral load using cycle threshold (C T ) values from reverse transcription-polymerase chain reaction assays applied to nasopharyngeal swab specimens in 100 patients with cancer and 2914 without cancer who were admitted to three New York City hospitals. Overall, the in-hospital mortality rate was 38.8% among patients with a high viral load, 24.1% among patients with a medium viral load, and 15.3% among patients with a low viral load (P<0.001). Similar findings were observed in patients with cancer (high, 45.2% mortality; medium, 28.0%; low, 12.1%; P=0.008). Patients with hematologic malignancies had higher median viral loads (C T =25.0) than patients without cancer (C T =29.2; P=0.0039). SARS-CoV-2 viral load results may offer vital prognostic information for patients with and without cancer who are hospitalized with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32997958/ doi: 10.1016/j.ccell.2020.09.007 id: cord-310606-msmh7d8m author: Westerhuis, B. M. title: Severe COVID-19 patients display a back boost of seasonal coronavirus-specific antibodies date: 2020-10-12 words: 4297.0 sentences: 306.0 pages: flesch: 65.0 cache: ./cache/cord-310606-msmh7d8m.txt txt: ./txt/cord-310606-msmh7d8m.txt summary: . https://doi.org/10.1101/2020.10.10.20210070 doi: medRxiv preprint All patients mounted a strong SARS-CoV-2 immune response shown by rising IgG titers against 174 SARS2-SECTO, SARS2-S1 and SARS2-SRBD which peaked around 4 weeks post onset of clinical 175 symptoms ( Figure 1A and Supplementary figure 1A for individual patients). Besides the SARS-CoV-2 IgG response, serum IgG reactivity towards various, but not 183 all seasonal CoV antigens, increased in longitudinally analyzed COVID-19 patients ( Figure 1A is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint However, cross-reactivity 282 between OC43-SECTO and SARS-CoV-2 S antigens showed significant weak negative 283 correlations (range R=-0.038 --0.088, range p=4,7x10 -6 -0.014) suggesting that OC43-S ECTO 284 specific clones are unlikely to cross-react with SARS-CoV-2 S in severe COVID-19 patients 285 ( Figure 3B ). abstract: Severe acquired respiratory syndrome coronavirus-2 (SARS-CoV-2) is the cause of coronavirus disease (COVID-19). In severe COVID-19 cases, higher antibody titers against seasonal coronaviruses have been observed than in mild cases. To investigate antibody cross-reactivity as potential explanation for severe disease, we determined the kinetics, breadth, magnitude and level of cross-reactivity of IgG against SARS-CoV-2 and seasonal CoV nucleocapsid and spike from 17 severe COVID-19 cases at the clonal level. Although patients mounted a mostly type-specific SARS-CoV-2 response, B-cell clones directed against seasonal CoV dominated and strongly increased over time. Seasonal CoV IgG responses that did not neutralize SARS-CoV-2 were boosted well beyond detectable cross-reactivity, particularly for HCoV-OC43 spike. These findings support a back-boost of poorly protective coronavirus-specific antibodies in severe COVID-19 patients that may negatively impact de novo SARS-CoV-2 immunity, reminiscent of original antigenic sin. url: https://doi.org/10.1101/2020.10.10.20210070 doi: 10.1101/2020.10.10.20210070 id: cord-258595-bk35vxlr author: Westhaus, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 words: 4965.0 sentences: 305.0 pages: flesch: 57.0 cache: ./cache/cord-258595-bk35vxlr.txt txt: ./txt/cord-258595-bk35vxlr.txt summary: Inoculation of differentiated Caco-2 cells for ten days with purified and concentrated wastewater (P2, P5, P11, and P12) did not result in the production of infectious SARS-CoV-2 particles (data not shown), which suggests that treated sewage appears to be non-infectious even though viral RNA fragments can be detected. Inter-comparing these nine catchment areas, we plotted the estimated cumulative and the acute prevalence against the measured SARS-CoV-2 load (Figure 8 ), the latter calculated from RT-qPCR measured M-gene copy concentration ( Figure 4 ) and the actual wastewater flow Q actual on the day of sampling (Table 2) . In contrast, plotting the incidence against SARS-CoV-2 concentration did not yield a conclusive correlation (not shown), likely because the precision of the qPCR employed was not sufficient to discriminate relatively minor differences in the incidence prevailing in the studied catchment areas at the time of sampling, ranging from 30 to 174 cases per 100,000 residents (less than an order of magnitude, Figure 8C and D). abstract: Abstract Wastewater-based monitoring of the spread of the new SARS-CoV-2 virus, also referred to as wastewater-based epidemiology (WBE), has been suggested as a tool to support epidemiology. An extensive sampling campaign, including nine municipal wastewater treatment plants, has been conducted in different cities of the Federal State of North Rhine-Westphalia (Germany) on the same day in April 2020, close to the first peak of the corona crisis. Samples were processed and analysed for a set of SARS-CoV-2-specific genes, as well as pan-genotypic gene sequences also covering other coronavirus types, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Additionally, a comprehensive set of chemical reference parameters and bioindicators was analysed to characterize the wastewater quality and composition. Results of the RT-qPCR based gene analysis indicate the presence of SARS-CoV-2 genetic traces in different raw wastewaters. Furthermore, selected samples have been sequenced using Sanger technology to confirm the specificity of the RT-qPCR and the origin of the coronavirus. A comparison of the particle-bound and the dissolved portion of SARS-CoV-2 virus genes shows that quantifications must not neglect the solid-phase reservoir. The infectivity of the raw wastewater has also been assessed by viral outgrowth assay with a potential SARS-CoV2- host cell line in vitro, which were not infected when exposed to the samples. This first evidence suggests that wastewater might be no major route for transmission to humans. Our findings draw attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater. url: https://api.elsevier.com/content/article/pii/S0048969720352797 doi: 10.1016/j.scitotenv.2020.141750 id: cord-293991-x5zdo8t2 author: Wheatley, A. K. title: Evolution of immunity to SARS-CoV-2 date: 2020-09-10 words: 4622.0 sentences: 333.0 pages: flesch: 56.0 cache: ./cache/cord-293991-x5zdo8t2.txt txt: ./txt/cord-293991-x5zdo8t2.txt summary: While SARS-CoV-2 specific B and T cell responses are readily induced by infection, the longitudinal dynamics of these key memory populations remains poorly resolved. We find that binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection, as expected, with a similar decline in S-specific CD4+ and circulating T follicular helper (cTFH) frequencies. Serum inhibition of RBD-ACE2 binding and S1-specific IgG 106 responses in early infection were also well correlated with neutralisation titre in late 107 convalescence (Spearman rho=0.79, 0.81, respectively; Extended Data Fig 3) . S-specific cTFH and conventional CD4+ 152 and CD8+ memory T cells (Tmem), were quantified using activation induced marker 153 (AIM) assays 19,22 (Methods) following stimulation with overlapping S (split into S1 154 or S2) peptide pools (Fig. 3A, 3B ). SARS-CoV-2 infection induces sustained humoral immune 623 responses in convalescent patients following symptomatic COVID-19. abstract: The durability of infection-induced SARS-CoV-2 immunity has major implications for public health mitigation and vaccine development. Animal studies and the scarcity of confirmed re-infection suggests immune protection is likely, although the durability of this protection is debated. Lasting immunity following acute viral infection requires maintenance of both serum antibody and antigen-specific memory B and T lymphocytes and is notoriously pathogen specific, ranging from life-long for smallpox or measles4, to highly transient for common cold coronaviruses (CCC). Neutralising antibody responses are a likely correlate of protective immunity and exclusively recognise the viral spike (S) protein, predominantly targeting the receptor binding domain (RBD) within the S1 sub-domain. Multiple reports describe waning of S-specific antibodies in the first 2-3 months following infection. However, extrapolation of early linear trends in decay might be overly pessimistic, with several groups reporting that serum neutralisation is stable over time in a proportion of convalescent subjects. While SARS-CoV-2 specific B and T cell responses are readily induced by infection, the longitudinal dynamics of these key memory populations remains poorly resolved. Here we comprehensively profiled antibody, B and T cell dynamics over time in a cohort recovered from mild-moderate COVID-19. We find that binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection, as expected, with a similar decline in S-specific CD4+ and circulating T follicular helper (cTFH) frequencies. In contrast, S-specific IgG+ memory B cells (MBC) consistently accumulate over time, eventually comprising a significant fraction of circulating MBC. Modelling of the concomitant immune kinetics predicts maintenance of serological neutralising activity above a titre of 1:40 in 50% of convalescent subjects to 74 days, with probable additive protection from B and T cells. Overall, our study suggests SARS-CoV-2 immunity after infection is likely t 66 o be transiently protective at a population level. SARS-CoV-2 vaccines may require greater immunogenicity and durability than natural infection to drive long-term protection. url: http://medrxiv.org/cgi/content/short/2020.09.09.20191205v1?rss=1 doi: 10.1101/2020.09.09.20191205 id: cord-275128-620wf0pb author: White, J. R. title: PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection date: 2020-09-03 words: 2388.0 sentences: 173.0 pages: flesch: 47.0 cache: ./cache/cord-275128-620wf0pb.txt txt: ./txt/cord-275128-620wf0pb.txt summary: We performed a statistical evaluation of in vitro gene expression profiles reflecting exposure to 1,835 drugs, and found topoisomerase inhibitors and PI3K/mTOR pathway inhibitors among the strongest candidates for reduced expression of ACE2, a host gene associated with SARS-CoV-2 infection. We next performed a retrospective review of clinical records to evaluate the frequency of SARS-CoV-2 infection in patients on these ACE2-associated antineoplastics. Retrospective data was obtained from an IRB-approved study of adult cancer patients tested for SARS-CoV-2 receiving active antineoplastic therapy at Memorial Sloan Kettering Cancer Center (MSKCC) during the COVID-19 epidemic period (n=4,040 patients; Table S2 ). Patients receiving ACE2-associated therapies demonstrated a lower univariate odds ratio (0.65, 95% CI 0.00-0.98, P=0.04) for a positive SARS-CoV-2 test during active antineoplastic therapy compared to patients on other agents (Table S3) . Cancer patients taking these potential ACE2-associated agents showed lower rates of a positive SARS-CoV-2 test compared to patients taking other forms of active antineoplastic therapy. abstract: There is an urgent need to identify therapies to prevent and treat SARS-CoV-2 infection. We performed a statistical evaluation of in vitro gene expression profiles reflecting exposure to 1,835 drugs, and found topoisomerase inhibitors and PI3K/mTOR pathway inhibitors among the strongest candidates for reduced expression of ACE2, a host gene associated with SARS-CoV-2 infection. Retrospective clinical data suggest that patients on these agents may be less likely to test positive for SARS-CoV-2. url: http://medrxiv.org/cgi/content/short/2020.09.02.20186783v1?rss=1 doi: 10.1101/2020.09.02.20186783 id: cord-354720-fu19u2b0 author: White-Dzuro, Gabrielle title: Multisystem effects of COVID-19: a concise review for practitioners date: 2020-11-04 words: 5088.0 sentences: 285.0 pages: flesch: 35.0 cache: ./cache/cord-354720-fu19u2b0.txt txt: ./txt/cord-354720-fu19u2b0.txt summary: It is important that clinicians managing critically ill COVID-19 patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. It is important that clinicians managing these critically ill patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. The indirect effects of the virus result from the host''s response to the viral infection, and are associated with a cytokine storm characterized by very high circulating levels of pro-inflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukins, granulocyte-colony stimulating factor, and chemokines [9] . include direct viral damage of nervous tissue, injury resulting from the excessive inflammatory response, unintended host immune response effects after the acute infection (e.g., Guillain-Barré syndrome as reported in a case series of four patients [24] ), and injury resulting from the effects of systemic illness. abstract: While COVID-19 has primarily been characterized by the respiratory impact of viral pneumonia, it affects every organ system and carries a high consequent risk of death in critically ill patients. Higher sequential organ failure assessment (SOFA) scores have been associated with increased mortality in patients critically ill patients with COVID-19. It is important that clinicians managing critically ill COVID-19 patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. We review the multisystem complications of COVID-19 and associated treatment strategies to improve the care of critically ill COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32921198/ doi: 10.1080/00325481.2020.1823094 id: cord-284791-bgodmbru author: Whitworth, Carrie title: Persistence of Bacteriophage Phi 6 on Porous and Nonporous Surfaces and the Potential for Its Use as an Ebola Virus or Coronavirus Surrogate date: 2020-08-18 words: 5152.0 sentences: 250.0 pages: flesch: 55.0 cache: ./cache/cord-284791-bgodmbru.txt txt: ./txt/cord-284791-bgodmbru.txt summary: The persistence of phi 6 was evaluated as a surrogate for Ebola virus (EBOV) and coronaviruses on porous and nonporous hospital surfaces. Under these laboratory-simulated Western indoor hospital conditions, we assessed the suitability of phi 6 as a surrogate for environmental persistence research related to enveloped viruses, including EBOV and coronaviruses. This study evaluated the persistence of phi 6 in the presence of artificial test soil (ATS) as a potential surrogate for EBOV or coronaviruses at two absolute humidity (AH) conditions on four potential fomites: nonporous stainless steel (SS) and plastic (PL) and two types of porous hospital curtain fabrics. found that the Phi 6 was shown here in the current study to be a conservative surrogate for EBOV in a laboratory-simulated Western hospital room condition of 3.0 g/m 3 AH, persisting longer than the Makona-C05 variant (AH ϭ 3.3 g/m 3 ), with decay rates of 0.06 log 10 /d and 0.79 log 10 /h, respectively (Table 1 ). abstract: The infection of health care workers during the 2013 to 2016 Ebola outbreak raised concerns about fomite transmission. In the wake of the coronavirus disease 2019 (COVID-19) pandemic, investigations are ongoing to determine the role of fomites in coronavirus transmission as well. The bacteriophage phi 6 has a phospholipid envelope and is commonly used in environmental studies as a surrogate for human enveloped viruses. The persistence of phi 6 was evaluated as a surrogate for Ebola virus (EBOV) and coronaviruses on porous and nonporous hospital surfaces. Phi 6 was suspended in a body fluid simulant and inoculated onto 1-cm(2) coupons of steel, plastic, and two fabric curtain types. The coupons were placed at two controlled absolute humidity (AH) levels: a low AH of 3.0 g/m(3) and a high AH of 14.4 g/m(3). Phi 6 declined at a lower rate on all materials under low-AH conditions, with a decay rate of 0.06-log(10) PFU/day to 0.11-log(10) PFU/day, than under the higher AH conditions, with a decay rate of 0.65-log(10) PFU/h to 1.42-log(10) PFU/day. There was a significant difference in decay rates between porous and nonporous surfaces at both low AH (P < 0.0001) and high AH (P < 0.0001). Under these laboratory-simulated conditions, phi 6 was found to be a conservative surrogate for EBOV under low-AH conditions in that it persisted longer than Ebola virus in similar AH conditions. Additionally, some coronaviruses persist longer than phi 6 under similar conditions; therefore, phi 6 may not be a suitable surrogate for coronaviruses. IMPORTANCE Understanding the persistence of enveloped viruses helps inform infection control practices and procedures in health care facilities and community settings. These data convey to public health investigators that enveloped viruses can persist and remain infective on surfaces, thus demonstrating a potential risk for transmission. Under these laboratory-simulated Western indoor hospital conditions, we assessed the suitability of phi 6 as a surrogate for environmental persistence research related to enveloped viruses, including EBOV and coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32591388/ doi: 10.1128/aem.01482-20 id: cord-267124-8efdzlc0 author: Wichmann, Dominic title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 words: 4062.0 sentences: 240.0 pages: flesch: 50.0 cache: ./cache/cord-267124-8efdzlc0.txt txt: ./txt/cord-267124-8efdzlc0.txt summary: In response to the pandemic spread of SARS-CoV-2, the authorities of the German federal state of Hamburg ordered mandatory autopsies in all patients dying with a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR). During autopsy, tissue samples for histology were taken from the following organs: heart, lungs, liver, kidneys, spleen, pancreas, brain, prostate and testes (in males), ovaries (in females), small bowel, saphenous vein, common carotid artery, pharynx, and muscle. In this autopsy study of 12 consecutive patients who died of COVID-19, we found a high incidence of deep venous thrombosis (58%). In studies that examined deceased patients with COVID-19 without relying on autopsy, no increased rates of pulmonary embolism were observed clinically. To our knowledge, only 3 case reports have been published on patients with COVID-19 who have undergone complete autopsy and a few more in which only lung tissue was examined (7, 8) . abstract: BACKGROUND: The new coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS–CoV-2), has caused more than 210 000 deaths worldwide. However, little is known about the causes of death and the virus's pathologic features. OBJECTIVE: To validate and compare clinical findings with data from medical autopsy, virtual autopsy, and virologic tests. DESIGN: Prospective cohort study. SETTING: Autopsies performed at a single academic medical center, as mandated by the German federal state of Hamburg for patients dying with a polymerase chain reaction–confirmed diagnosis of COVID-19. PATIENTS: The first 12 consecutive COVID-19–positive deaths. MEASUREMENTS: Complete autopsy, including postmortem computed tomography and histopathologic and virologic analysis, was performed. Clinical data and medical course were evaluated. Results: Median patient age was 73 years (range, 52 to 87 years), 75% of patients were male, and death occurred in the hospital (n = 10) or outpatient sector (n = 2). Coronary heart disease and asthma or chronic obstructive pulmonary disease were the most common comorbid conditions (50% and 25%, respectively). Autopsy revealed deep venous thrombosis in 7 of 12 patients (58%) in whom venous thromboembolism was not suspected before death; pulmonary embolism was the direct cause of death in 4 patients. Postmortem computed tomography revealed reticular infiltration of the lungs with severe bilateral, dense consolidation, whereas histomorphologically diffuse alveolar damage was seen in 8 patients. In all patients, SARS–CoV-2 RNA was detected in the lung at high concentrations; viremia in 6 of 10 and 5 of 12 patients demonstrated high viral RNA titers in the liver, kidney, or heart. LIMITATION: Limited sample size. CONCLUSION: The high incidence of thromboembolic events suggests an important role of COVID-19–induced coagulopathy. Further studies are needed to investigate the molecular mechanism and overall clinical incidence of COVID-19–related death, as well as possible therapeutic interventions to reduce it. PRIMARY FUNDING SOURCE: University Medical Center Hamburg-Eppendorf. url: https://www.ncbi.nlm.nih.gov/pubmed/32374815/ doi: 10.7326/m20-2003 id: cord-264031-0y7xbgun author: Wierbowski, Shayne D. title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date: 2020-10-13 words: 5066.0 sentences: 291.0 pages: flesch: 42.0 cache: ./cache/cord-264031-0y7xbgun.txt txt: ./txt/cord-264031-0y7xbgun.txt summary: title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. Further, we explore the utility of our interactome modeling approach in identifying key 99 interactions undergoing evolution along viral protein interfaces, highlighting population variants on 100 human interfaces that could modulate the strength of viral-host interactions to confer protection from or 101 susceptibility to COVID-19, and prioritizing drug candidates predicted to bind competitively at viral-102 human interaction interfaces. abstract: The recent COVID-19 pandemic has sparked a global public health crisis. Vital to the development of informed treatments for this disease is a comprehensive understanding of the molecular interactions involved in disease pathology. One lens through which we can better understand this pathology is through the network of protein-protein interactions between its viral agent, SARS-CoV-2, and its human host. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV can be explained by rapid evolution along the interface between the Spike protein and its human receptor (ACE2) leading to increased binding affinity. Sequence divergences that modulate other protein-protein interactions may further explain differences in transmission and virulence in this novel coronavirus. To facilitate these comparisons, we combined homology-based structural modeling with the ECLAIR pipeline for interface prediction at residue resolution, and molecular docking with PyRosetta. This enabled us to compile a novel 3D structural interactome meta-analysis for the published interactome network between SARS-CoV-2 and human. This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. All predictions are available online† for easy access and are continually updated when new interactions are published. † Some sections of this pre-print have been redacted to comply with current bioRxiv policy restricting the dissemination of purely in silico results predicting potential therapies for SARS-CoV-2 that have not undergone thorough peer-review. The results section titled “Prioritization of Candidate Inhibitors of SARS-CoV-2-Human Interactions Through Binding Site Comparison,” Figure 4, Supplemental Table 9, and all links to our web resource have been removed. Blank headers left in place to preserve structure and item numbering. Our full manuscript will be published in an appropriate journal following peer-review. url: https://doi.org/10.1101/2020.10.13.308676 doi: 10.1101/2020.10.13.308676 id: cord-276995-b003vcdc author: Wiese, Andrew D title: Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date: 2020-06-20 words: 818.0 sentences: 54.0 pages: flesch: 39.0 cache: ./cache/cord-276995-b003vcdc.txt txt: ./txt/cord-276995-b003vcdc.txt summary: And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. abstract: nan url: https://doi.org/10.1093/cid/ciaa834 doi: 10.1093/cid/ciaa834 id: cord-291677-zcbyhsf1 author: Wilamowski, M. title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 words: 5348.0 sentences: 308.0 pages: flesch: 56.0 cache: ./cache/cord-291677-zcbyhsf1.txt txt: ./txt/cord-291677-zcbyhsf1.txt summary: To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex abstract: The genome of the SARS-CoV-2 coronavirus contains 29 proteins, of which 15 are nonstructural. Nsp10 and Nsp16 form a complex responsible for the capping of mRNA at the 5′ terminus. In the methylation reaction the S-adenosyl-L-methionine serves as the donor of the methyl group that is transferred to Cap-0 at the first transcribed nucleotide to create Cap-1. The presence of Cap-1 makes viral RNAs mimic the host transcripts and prevents their degradation. To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We determined crystal structures of Nsp10/16 that revealed the states before and after the methylation reaction, for the first time illustrating coronavirus Nsp10/16 complexes with the m7GpppAm2′-O Cap-1, where 2′OH of ribose is methylated. We compare these structures with structures of Nsp10/16 at 297 K and 100 K collected from a single crystal. This data provide important mechanistic insight and can be used to design small molecules that inhibit viral RNA maturation making SARS-CoV-2 sensitive to host innate response. url: https://doi.org/10.1101/2020.08.14.251421 doi: 10.1101/2020.08.14.251421 id: cord-022473-l4jniccw author: Wilder-Smith, Annelies title: As Travel Medicine Practitioner during the SARS Outbreak in Singapore date: 2009-11-16 words: 2887.0 sentences: 184.0 pages: flesch: 71.0 cache: ./cache/cord-022473-l4jniccw.txt txt: ./txt/cord-022473-l4jniccw.txt summary: In the first week after our first cases, the WHO named the disease "SARS", and they sent out global alerts. In Singapore, the outbreak was initially only hospital based, but in April the news was out that SARS had affected a large vegetable market. The news of the death of Carlo Urbani, the Italian WHO doctor who was instrumental in the control of SARS in Vietnam, sent our hospital staff into depression. In total, we lost a total of five healthcare workers to SARS in Singapore: 2 doctors, 1 nursing officer, 1 nursing aide and 1 hospital attendant. Two to three weeks into the epidemic it became clear, that infection control measures were effective; no more new cases occurred amongst the staff of our hospital. The SARS outbreak in Singapore can be traced to the first imported case. New imported SARS cases therefore need not lead to major outbreaks if systems are in place to identify and isolate them early. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155737/ doi: 10.1016/b978-0-08-045359-0.50041-5 id: cord-252292-qz9msrl7 author: Wilder-Smith, Annelies title: Experience of Severe Acute Respiratory Syndrome in Singapore: Importation of Cases, and Defense Strategies at the Airport date: 2006-03-08 words: 2165.0 sentences: 107.0 pages: flesch: 58.0 cache: ./cache/cord-252292-qz9msrl7.txt txt: ./txt/cord-252292-qz9msrl7.txt summary: METHODS: Information on imported cases of SARS and measures taken at entry points to Singapore was retrieved from the Ministry of Health and the Civil Aviation Authority of Singapore. The large outbreaks in Hong Kong, Toronto, Singapore and Vietnam were initiated by cases that were imported before this new disease had been identified and before appropriate measures had been put in place to prevent transmission. Information on measures taken at the national airport (Changi Airport), seaports and road entry points to reduce the importation of further cases was obtained from the Civil Aviation Authority of Singapore (CAAS) and from the websites of the Ministry of Health, Singapore (http://www.moh.gov.sq/sars/news/chronology.html; accessed 15 June). She became very unwell and breathless on her return flight from Beijing to Singapore on 26 March, but no precautions were taken on the airplane,as her diagnosis was not known.Immediately after arrival, her mother took her in a taxi to Tan Tock Seng Hospital,where she was isolated in the Intensive Care Unit. abstract: BACKGROUND: The importation of SARS was responsible for the outbreaks in Singapore, Hong Kong, Vietnam and Canada at a time when this new disease had not been identified. We report the incidence and impact of cases of SARS imported to Singapore between 25 February and 31 May 2003, and describe national measures to prevent further importation. METHODS: Information on imported cases of SARS and measures taken at entry points to Singapore was retrieved from the Ministry of Health and the Civil Aviation Authority of Singapore. RESULTS: Of the 6 imported cases, which all occurred before screening measures were implemented at the airport, only the first resulted in extensive secondary transmission. Of 442,973 air passengers screened after measures were implemented, 136 were sent to a designated hospital for further SARS screening; none was diagnosed as having SARS. CONCLUSIONS: The SARS outbreak in Singapore can be traced to the first imported case. The absence of transmission from the other imported cases was probably a result of relatively prompt identification and isolation of cases, together with a low potential for transmission. New imported SARS cases therefore need not lead to major outbreaks if systems are in place to identify and isolate them early. Screening at entry points is costly, has a low yield and is not sufficient in itself, but may be justified in light of the major economic, social and international impact which even a single imported SARS case may have. url: https://www.ncbi.nlm.nih.gov/pubmed/14531977/ doi: 10.2310/7060.2003.2676 id: cord-279001-l5ogbl5p author: Wilder-Smith, Annelies title: Can we contain the COVID-19 outbreak with the same measures as for SARS? date: 2020-03-05 words: 4387.0 sentences: 241.0 pages: flesch: 53.0 cache: ./cache/cord-279001-l5ogbl5p.txt txt: ./txt/cord-279001-l5ogbl5p.txt summary: COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. In November, 2002, the severe acute respiratory syn drome coronavirus (SARSCoV) emerged in China causing global anxiety as the outbreak rapidly spread, and by July, 2003, had resulted in over 8000 cases in 26 countries. In the absence of vaccines and specific treatment, the only available public health tools to control persontoperson transmittable diseases are isolation and quarantine, social distancing, and community containment measures. Isolation, quarantine, social distancing and community containment: pivotal role for oldstyle public health measures in the novel coronavirus (2019nCoV) outbreak Public health measures to control the spread of the severe acute respiratory syndrome during the outbreak in Toronto abstract: The severe acute respiratory syndrome (SARS) outbreak in 2003 resulted in more than 8000 cases and 800 deaths. SARS was eventually contained by means of syndromic surveillance, prompt isolation of patients, strict enforcement of quarantine of all contacts, and in some areas top-down enforcement of community quarantine. By interrupting all human-to-human transmission, SARS was effectively eradicated. By contrast, by Feb 28, 2020, within a matter of 2 months since the beginning of the outbreak of coronavirus disease 2019 (COVID-19), more than 82 000 confirmed cases of COVID-19 have been reported with more than 2800 deaths. Although there are striking similarities between SARS and COVID-19, the differences in the virus characteristics will ultimately determine whether the same measures for SARS will also be successful for COVID-19. COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. Exportations to other countries need not result in rapid large-scale outbreaks, if countries have the political will to rapidly implement countermeasures. url: https://www.ncbi.nlm.nih.gov/pubmed/32145768/ doi: 10.1016/s1473-3099(20)30129-8 id: cord-295061-58tj4csz author: Wilder‐Smith, Annelies title: Short communication: Low risk of transmission of severe acute respiratory syndrome on airplanes: the Singapore experience date: 2003-10-22 words: 1321.0 sentences: 60.0 pages: flesch: 57.0 cache: ./cache/cord-295061-58tj4csz.txt txt: ./txt/cord-295061-58tj4csz.txt summary: The risk of transmission of severe acute respiratory syndrome (SARS) on airplanes is of major concern to the public and airline industry. Seven airplanes with nine passengers on board later diagnosed as suffering from probable SARS (based on WHO criteria) arrived in Singapore between 25 February and 31 May 2003: three were from Hong Kong (with five cases of SARS), one from Beijing, one from New York, one from East Malaysia and one from Indonesia. However, only three airplanes (with four passengers) had symptomatic cases of SARS on board, whereas the passengers of the other flights developed symptoms within the first 2 days after arrival in Singapore. The third flight with one passenger with severe symptoms of SARS (fever, cough, shortness of breath) arrived after the Infectious Disease Act had been invoked: all crew members and 46 of 47 passengers were contactable and quarantined with active surveillance for 10 days; none developed SARS. abstract: The risk of transmission of severe acute respiratory syndrome (SARS) on airplanes is of major concern to the public and airline industry. We examined data from flights to Singapore with SARS patients on board in order to assess this risk. In‐flight transmission occurred only in one of the three flights with symptomatic SARS patients on board. The incidence was estimated to be 1 out of 156 passengers. The risk of in‐flight transmission of SARS appears to be far lower than that reported for influenza, but may be increased with superspreaders on board. url: https://www.ncbi.nlm.nih.gov/pubmed/14629772/ doi: 10.1046/j.1360-2276.2003.01133.x id: cord-323980-rcyjthze author: Willems, Laurent M. title: SARS-CoV-2-related rapid reorganization of an epilepsy outpatient clinic from personal appointments to telemedicine services: A German single-center experience date: 2020-10-06 words: 4373.0 sentences: 186.0 pages: flesch: 40.0 cache: ./cache/cord-323980-rcyjthze.txt txt: ./txt/cord-323980-rcyjthze.txt summary: METHODS: Documentations of telephone contacts and telemedicine consultations at the Epilepsy Center Frankfurt Rhine-Main were recorded in detail between March and May 2020 and analyzed for acceptance, feasibility, and satisfaction of the conversion from personal to telemedicine appointments from both patients'' and medical professionals'' perspectives. The aim of this study was to analyze the acceptance, feasibility, and satisfaction of the SARS-CoV-2-related conversion from face-to-face to telemedicine appointments from the perspectives of both patients and medical professionals. General understanding and acceptance of cancelations of elective face-to-face ambulatory visits and of the option to have telemedicine consultations during the SARS-CoV-2 pandemic in Germany was high, especially in patients with very urgent or urgent appointment priority. abstract: INTRODUCTION: When the SARS-CoV-2 pandemic reached Europe in 2020, a German governmental order forced clinics to immediately suspend elective care, causing a problem for patients with chronic illnesses such as epilepsy. Here, we report the experience of one clinic that converted its outpatient care from personal appointments to telemedicine services. METHODS: Documentations of telephone contacts and telemedicine consultations at the Epilepsy Center Frankfurt Rhine-Main were recorded in detail between March and May 2020 and analyzed for acceptance, feasibility, and satisfaction of the conversion from personal to telemedicine appointments from both patients' and medical professionals' perspectives. RESULTS: Telephone contacts for 272 patients (mean age: 38.7 years, range: 17–79 years, 55.5% female) were analyzed. Patient-rated medical needs were either very urgent (6.6%, n = 18), urgent (23.5%, n = 64), less urgent (29.8%, n = 81), or nonurgent (39.3%, n = 107). Outpatient service cancelations resulted in a lack of understanding (9.6%, n = 26) or anger and aggression (2.9%, n = 8) in a minority of patients, while 88.6% (n = 241) reacted with understanding, or relief (3.3%, n = 9). Telemedicine consultations rather than a postponed face-to-face visit were requested by 109 patients (40.1%), and these requests were significantly associated with subjective threat by SARS-CoV-2 (p = 0.004), urgent or very urgent medical needs (p = 0.004), and female gender (p = 0.024). Telemedicine satisfaction by patients and physicians was high. Overall, 9.2% (n = 10) of patients reported general supply problems due to SARS-CoV-2, and 28.4% (n = 31) reported epilepsy-specific problems, most frequently related to prescriptions, or supply problems for antiseizure drugs (ASDs; 22.9%, n = 25). CONCLUSION: Understanding and acceptance of elective ambulatory visit cancelations and the conversion to telemedicine consultations was high during the coronavirus disease 2019 (COVID-19) lockdown. Patients who engaged in telemedicine consultations were highly satisfied, supporting the feasibility and potential of telemedicine during the COVID-19 pandemic and beyond. url: https://www.ncbi.nlm.nih.gov/pubmed/33181898/ doi: 10.1016/j.yebeh.2020.107483 id: cord-315424-i3nnennw author: Willer, Brittany L. title: The otolaryngologist’s and anesthesiologist’s collaborative role in a pandemic: a large quaternary pediatric center’s experience with COVID-19 preparation and simulation date: 2020-06-10 words: 2607.0 sentences: 145.0 pages: flesch: 36.0 cache: ./cache/cord-315424-i3nnennw.txt txt: ./txt/cord-315424-i3nnennw.txt summary: Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be intimately familiar with strategies to mitigate the high-risk periods of viral contamination that are posed to the environment and healthcare personnel during tracheal intubation and extubation procedures. Since both the pediatric otolaryngologist and anesthesiologist are directly involved in emergency airway interventions, both specialties impact the safety of caring for COVID-19 patients and are a part of overall hospital pandemic preparedness. The pediatric otolaryngologist and anesthesiologist will encounter the COVID-19 patient in a variety of clinical settings (perioperative/operative, intensive care unit, emergency department, and radiology suite) and situations (emergent airway management, urgent or emergent surgical intervention, diagnostic or interventional radiology, and critical care resuscitation). Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be welleducated in and familiar with strategies to mitigate these high risk periods of viral contamination that are posed to the environment and healthcare personnel during endotracheal intubation and extubation procedures [9] . abstract: There has been a rapid global spread of a novel coronavirus, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which originated in Wuhan China in late 2019. A serious threat of nosocomial spread exists and as such, there is a critical necessity for well-planned and rehearsed processes during the care of the COVID-19 positive and suspected patient to minimize transmission and risk to healthcare providers and other patients. Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be intimately familiar with strategies to mitigate the high-risk periods of viral contamination that are posed to the environment and healthcare personnel during tracheal intubation and extubation procedures. Since both the pediatric otolaryngologist and anesthesiologist are directly involved in emergency airway interventions, both specialties impact the safety of caring for COVID-19 patients and are a part of overall hospital pandemic preparedness. We describe our institutional approach to COVID-19 perioperative pandemic planning at a large quaternary pediatric hospital including operating room management and remote airway management. We outline our processes for the safe and effective care of these patients with emphasis on simulation and pathways necessary to protect healthcare workers and other personnel from exposure while still providing safe, effective, and rapid care. url: https://doi.org/10.1016/j.ijporl.2020.110174 doi: 10.1016/j.ijporl.2020.110174 id: cord-264052-uph136sn author: Wilson, Mitchell P title: Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature date: 2020-04-23 words: 2110.0 sentences: 141.0 pages: flesch: 44.0 cache: ./cache/cord-264052-uph136sn.txt txt: ./txt/cord-264052-uph136sn.txt summary: title: Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature A search of MEDLINE, J o u r n a l P r e -p r o o f EMBASE, Scopus, and the Cochrane Library (including the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and the Cochrane Special Collections) from inception to April 7, 2020 was performed in order to identify articles evaluating both COVID-19 and neurology or neurosurgery. A total of 10 articles including 4 articles discussing clinical symptomatology and/or the neuroinvasive potential of SARS-CoV-2 (5-8) and 6 articles discussing recommendations for modified neurosurgical (9-11), stroke (12) , and spine (13) (14) practices during the COVID-19 crisis. Thus far, early experience and recommendations in neurosurgical (9) (10) (11) 33) , stroke (12) , and spine (13, 14) practices have been reported (Table 2) As an early scoping review of available literature to date, this study has certain limitations. abstract: Coronavirus disease 2019 (COVID-19) is a devastating respiratory illness that has dramatically changed the medical landscape around the world. In parallel with a rise in the number of cases globally, the COVID-19 literature has rapidly expanded with experts around the world disseminating knowledge and collaborating on best practices. To date, the literature has predominantly consisted of case reports, case series, and systemic protocols for dealing with this deadly disease from a plethora of specialties with larger observational and randomized studies only now starting to emerge. This scoping review of MEDLINE, EMBASE, SCOPUS, and the Cochrane Library aims to evaluate and summarize the current status of the COVID-19 literature at it applies to neurology and neurosurgery. Neurological symptomatology, neurological risk factors for poor prognosis, pathophysiology for neuroinvasion, and actions taken by neurological or neurosurgical services to manage the current COVID-19 crisis are reviewed. url: https://api.elsevier.com/content/article/pii/S0303846720302092 doi: 10.1016/j.clineuro.2020.105866 id: cord-331927-b7pfm3i0 author: Winn, Soe P title: Diabetic Ketoacidosis in Coronavirus Disease Patients With Type 2 Diabetes Mellitus date: 2020-08-14 words: 1772.0 sentences: 97.0 pages: flesch: 53.0 cache: ./cache/cord-331927-b7pfm3i0.txt txt: ./txt/cord-331927-b7pfm3i0.txt summary: Since the emergence of the coronavirus disease (COVID-19) pandemic, we have seen many cases and studies on the underlying pathophysiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia with or without respiratory failure. We have also learned that the angiotensin-converting enzyme receptor is one of the major entry sites of SARS-CoV-2 infection, and it might be one of the causes that predispose patients to DKA. also stated that the human pancreas also expresses ACE2, and therefore, patients with diabetes are more vulnerable to SARS-CoV-2 infection than the general population [9] . In our cases, the transient damage of pancreatic beta-cell function leading to reduced levels of serum C peptide may be the reason for our patients experiencing acute insulin-dependent DKA for a brief period during the course of COVID-19. COVID-19 may cause DKA by increasing insulin requirement induced by ACE2-mediated destruction of pancreatic beta cells, as evidenced by reversible decreased serum C peptide levels or other unexplored mechanisms. abstract: The occurrence of diabetes is increasing globally and carries a variety of complications, such as thromboembolism, acute cerebrovascular accidents, and diabetic ketoacidosis (DKA). Although DKA is not commonly associated with type 2 diabetes (T2D), it can manifest in patients who have underlying comorbidities predisposed to DKA. Since the emergence of the coronavirus disease (COVID-19) pandemic, we have seen many cases and studies on the underlying pathophysiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia with or without respiratory failure. We have also learned that the angiotensin-converting enzyme receptor is one of the major entry sites of SARS-CoV-2 infection, and it might be one of the causes that predispose patients to DKA. However, few studies exist that explore the development of DKA in T2D with SARS-CoV-2 infection. We present two cases of patients with DKA and COVID-19 treated with an insulin regimen with no further complications. url: https://www.ncbi.nlm.nih.gov/pubmed/32953287/ doi: 10.7759/cureus.9731 id: cord-310946-rjwyirld author: Wiseman, Jessica title: False negative SARS-CoV-2 PCR - A case report and literature review date: 2020-07-06 words: 1690.0 sentences: 98.0 pages: flesch: 53.0 cache: ./cache/cord-310946-rjwyirld.txt txt: ./txt/cord-310946-rjwyirld.txt summary: The first case of the novel Coronavirus Diseases (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected in Wuhan, China in December 2019. A nasopharyngeal SARS-CoV-2 PCR was obtained on day 1 of his admission and was negative. This case highlights multiple negative nasopharyngeal SARS-CoV-2 PCR swabs in a patient with high clinical suspicion for SARS-CoV-2, who ultimately tested positive when deep sputum was sent for PCR nine days into his admission (10 days after respiratory symptoms started). Therefore, to improve the odds of making a definitive diagnosis, additional testing methods such as sputum for PCR and serology testing should be considered in patients with a high clinical suspicion of COVID-19 who have a negative nasopharyngeal PCR. Subsequently [7] , conducted a study on 127 patients in Beijing Ditan Hospital comparing RT-PCR versus droplet digital PCR (ddPCR) testing, which is reported as being more sensitive in virus detection, in addition to assessing viral load with disease progression. abstract: The first case of the novel Coronavirus Diseases (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected in Wuhan, China in December 2019. On January 30, 2020, the World Health Organization declared a global health emergency. Countries around the world advised social distancing, businesses and schools closed, while health care workers faced a viral war. With the declaration of a global emergency, a test to rapidly detect the SARS-CoV-2 was developed to ensure swift isolation of infected persons to prevent spread of disease. Currently, the gold standard for test is Reverse Transcriptase Polymerase Chain Reaction (RT-PCR); however, patients with a high clinical suspicion for COVID-19 can sometimes have multiple negative tests. We discuss a patient under investigation (PUI) who had classic findings of COVID-19 but repeatedly tested negative from nasopharyngeal swabs until a fifth sample obtained from a deep suctioning was tested. url: https://doi.org/10.1016/j.rmcr.2020.101140 doi: 10.1016/j.rmcr.2020.101140 id: cord-309869-gk0svt2f author: Wiwanitkit, Viroj title: SARS-CoV-2 in Semen date: 2020-10-23 words: 233.0 sentences: 23.0 pages: flesch: 64.0 cache: ./cache/cord-309869-gk0svt2f.txt txt: ./txt/cord-309869-gk0svt2f.txt summary: key: cord-309869-gk0svt2f cord_uid: gk0svt2f Dear Editor, I would like to discuss the publication "Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection" [1] . [1] concluded that "although all semen samples were obtained in the acute stage of the infection when the nasopharyngeal swab test was positive, we did not detect SARS-CoV-2 in semen." In fact, there are some previous reports showing no existence of pathogen in semen samples [2, 3] . Nevertheless, a recent meta-analysis still noted that there is still a requirement for caution on the possibility of COVID-19 transmission via sexual contact [4] . Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection Italian males recovering from mild COVID-19 show no evidence of SARS-CoV-2 in semen despite prolonged nasopharyngeal swab positivity Atypical modes of COVID-19 transmission: how likely are they? abstract: nan url: https://doi.org/10.1159/000511616 doi: 10.1159/000511616 id: cord-348010-m3a3utvz author: Wolff, Michael title: On build‐up of epidemiologic models—Development of a SEI(3)RSD model for the spread of SARS‐CoV‐2 date: 2020-10-13 words: 13018.0 sentences: 991.0 pages: flesch: 61.0 cache: ./cache/cord-348010-m3a3utvz.txt txt: ./txt/cord-348010-m3a3utvz.txt summary: (Adequate contacts, reproduction and contact numbers) (i) A contact is called adequate (also effective), if it leads to a transmission of the pathogen from an infectious person to another one, and, if the affected individual is susceptible, then an infection is provoked. In the case of concrete models one uses generally contact and replacement numbers, and , which reflect the current infection behaviour. (i) (Closed-population model) An assumed constant number of community members (see Remark 2.2) seems to be justified, if the infection spreads quickly, approximately within a year, and/or, if there is a balance between births, migration and non-disease-related deaths. (Using , there arise difficulties with the dot indicating the time derivation.) If the model is to be to take a latent period into account, the class of infected is divided into subclasses in the following way. abstract: The present study investigates essential steps in build‐up of models for description of the spread of infectious diseases. Combining these modules, a SEI(3)RSD model will be developed, which can take into account a possible passive immunisation by vaccination as well as different durations of latent and incubation periods. Besides, infectious persons with and without symptoms can be distinguished. Due to the current world‐wide SARS‐CoV‐2 pandemic (COVID‐19 pandemic) models for description of the spread of infectious diseases and their application for forecasts have become into the focus of the scientific community as well as of broad public more than usual. Currently, many papers and studies have appeared and appear dealing with the virus SARS‐CoV‐2 and the COVID‐19 disease caused by it. This occurs under medical, virological, economic, sociological and further aspects as well as under mathematical points of view. Concerning the last‐mentioned point, the main focus lies on the application of existing models and their adaptation to data about the course of infection available at the current time. Clearly, the aim is to predict the possible further development, for instance in Germany. It is of particular interest to investigate how will be the influence of political and administrative measures like contact restrictions, closing or rather re‐opening of schools, restaurants, hotels etc. on the course of infection. The steps considered here for building up suitable models are well‐known for long time. However, understandably they will not be dealt with in an extended way in current application‐oriented works. Therefore, it is the aim of this study to present some existing steps of modelling without any pretension of completeness. Thus, on the one hand we give assistance and, on the other hand, we develop a model capable to take already known properties of COVID‐19 as well as a later possible passive immunisation by vaccination and a possible loss of immunity of recovered persons into account. url: https://doi.org/10.1002/zamm.202000230 doi: 10.1002/zamm.202000230 id: cord-313754-f4sq45gy author: Wong, Chi-Yan title: Practice of habitual and volitional health behaviors to prevent severe acute respiratory syndrome among Chinese adolescents in Hong Kong date: 2005-03-31 words: 4713.0 sentences: 228.0 pages: flesch: 43.0 cache: ./cache/cord-313754-f4sq45gy.txt txt: ./txt/cord-313754-f4sq45gy.txt summary: Abstract Purpose To explore factors relating to the practice of habitual and volitional health behaviors against the severe acute respiratory syndrome (SARS) among Chinese adolescents in Hong Kong. Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy). Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy) ( Table 1) . For volitional health behaviors of facemask-wearing to prevent SARS, environmental cues, practice of habitual health behaviors, and perceived threat were positive correlates (r ϭ .40, .38, and .27, respectively; p Ͻ .05). This study showed that among six components of the HBM, perceived threat and cues to action were more salient correlates of SARS preventive health behaviors among Chinese adolescents. abstract: Abstract Purpose To explore factors relating to the practice of habitual and volitional health behaviors against the severe acute respiratory syndrome (SARS) among Chinese adolescents in Hong Kong. Methods A community telephone survey was conducted with 230 Chinese adolescents. Random-digit dialing of the local residential telephone directory was used to select respondents, who were asked to provide information on their practice of SARS preventive health behaviors and associated factors as specified by the Health Belief Model. These factors included perceived threat of SARS, perceived benefits and barriers in practicing SARS preventive health behaviors, cues to action, knowledge of SARS, and self-efficacy. Hierarchical regression analyses were conducted to determine salient correlates of habitual and volitional health behaviors against SARS. Results About 54.8% of respondents reported practicing all three recommended habitual health behaviors. Another 47.8% indicated consistent practice of volitional health behavior of facemask-wearing to prevent SARS. Results of hierarchical regression analyses showed that habitual health behaviors against SARS were related to perceived health threat and environmental cues. For facemask-wearing, salient correlates were environmental cues, rates of SARS habitual health behaviors, younger age, and perceived health threat. Conclusions The Health Belief Model is useful in understanding Chinese adolescents’ practice of health behaviors, especially volitional health behaviors. url: https://www.ncbi.nlm.nih.gov/pubmed/15737774/ doi: 10.1016/j.jadohealth.2004.02.024 id: cord-296517-414grqif author: Wong, Gary title: MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease date: 2015-10-14 words: 2880.0 sentences: 129.0 pages: flesch: 50.0 cache: ./cache/cord-296517-414grqif.txt txt: ./txt/cord-296517-414grqif.txt summary: In September 2012, Middle East Respiratory Syndrome coronavirus (MERS-CoV) emerged as a novel virus that can result in severe respiratory disease with renal failure, with a case fatality rate of up to 38%. Notably, between May and July 2015, an outbreak of MERS-CoV centered in South Korea killed 36 people out of 186 confirmed cases (Promedmail.org, 2015) , with thousands quarantined as health authorities attempted to control virus spread. The 2015 MERS-CoV outbreak in South Korea began from an imported case, a 68-year-old male with a recent travel history to several Middle Eastern countries, including Bahrain, the United Arab Emirates, Saudi Arabia, and Qatar. Thus, the MERS-CoV outbreak in South Korea was driven primarily by three infected individuals, and approximately 75% of cases can be traced back to three super-spreaders who have each infected a disproportionately high number of contacts ( Figure 1A ). abstract: Super-spreading occurs when a single patient infects a disproportionate number of contacts. The 2015 MERS-CoV, 2003 SARS-CoV, and to a lesser extent 2014–15 Ebola virus outbreaks were driven by super-spreaders. We summarize documented super-spreading in these outbreaks, explore contributing factors, and suggest studies to better understand super-spreading. url: https://doi.org/10.1016/j.chom.2015.09.013 doi: 10.1016/j.chom.2015.09.013 id: cord-272633-2vmdf9j6 author: Wong, Gary W.K. title: Out of the East – Emerging infections date: 2006-06-05 words: 1364.0 sentences: 106.0 pages: flesch: 51.0 cache: ./cache/cord-272633-2vmdf9j6.txt txt: ./txt/cord-272633-2vmdf9j6.txt summary: Severe Acute respiratory syndrome (SARS) originated from southern China and rapidly spread to many countries in early 2003 with over 8000 cases worldwide. 1 Human infection due to a highly pathogenic avian influenza A (H5N1) virus was first described in a mini-outbreak from Hong Kong in 1997. The first outbreak of human disease of avian influenza occurred in 1997 with 18 cases and 6 deaths. 2 Unlike SARS, human disease of avian influenza has a high mortality in both adults and children. Epidemiology of severe acute respiratory syndrome (SARS): adults and children Avian influenza virus infections in humans Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus Outbreak of avian influenza A (H5N1) virus infection in Hong Kong in 1997 Pathology of fatal human infection associated with avian influenza A H5N1 virus abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1526054206002491 doi: 10.1016/j.prrv.2006.04.194 id: cord-282947-3hgku2e4 author: Wong, Hui Hui title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date: 2017-12-30 words: 8714.0 sentences: 423.0 pages: flesch: 46.0 cache: ./cache/cord-282947-3hgku2e4.txt txt: ./txt/cord-282947-3hgku2e4.txt summary: title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins. abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) is an inefficient inducer of interferon (IFN) response. It expresses various proteins that effectively circumvent IFN production at different levels via distinct mechanisms. Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. We also found that proteins 8b and 8ab could physically interact with IRF3. Overexpression of 8b and 8ab resulted in the reduction of poly (I:C)-induced IRF3 dimerization and inhibition of the IFN-β signaling pathway. This counteracting effect was partially mediated by protein 8b/8ab-induced degradation of IRF3 in a ubiquitin-proteasome-dependent manner. Taken together, we propose that SARS-CoV may exploit the unique functions of proteins 8b and 8ab as novel mechanisms to overcome the effect of IFN response during virus infection. url: https://api.elsevier.com/content/article/pii/S0042682217304427 doi: 10.1016/j.virol.2017.12.028 id: cord-319501-a2x1hvkk author: Wong, Lok-Yin Roy title: A molecular arms race between host innate antiviral response and emerging human coronaviruses date: 2016-01-15 words: 7759.0 sentences: 460.0 pages: flesch: 51.0 cache: ./cache/cord-319501-a2x1hvkk.txt txt: ./txt/cord-319501-a2x1hvkk.txt summary: Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. This suggests SARS-CoV N may interfere with RNA recognition by host immune sensors such as RIG-I and MDA5 thus achieving suppressive role in IFN production. Our group demonstrated that MERS-CoV ORF4a interacts with PACT, a cellular dsRNA-binding protein that optimally activates RIG-Iand MDA5-induced type I IFN production, in an RNAdependent manner (Siu et al., 2014c) . Infection with SARS-CoV and MERS-CoV has been accompanied with suppression of innate immune response, most notably with the suppression of type I IFN production and signaling pathways. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses pact-induced activation of RIG-I and MDA5 in the innate antiviral response abstract: Coronaviruses have been closely related with mankind for thousands of years. Communityacquired human coronaviruses have long been recognized to cause common cold. However, zoonotic coronaviruses are now becoming more a global concern with the discovery of highly pathogenic severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses causing severe respiratory diseases. Infections by these emerging human coronaviruses are characterized by less robust interferon production. Treatment of patients with recombinant interferon regimen promises beneficial outcomes, suggesting that compromised interferon expression might contribute at least partially to the severity of disease. The mechanisms by which coronaviruses evade host innate antiviral response are under intense investigations. This review focuses on the fierce arms race between host innate antiviral immunity and emerging human coronaviruses. Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. On the other hand, the counter-measures evolved by SARS and MERS coronaviruses to circumvent host defense are also dissected. With a better understanding of the dynamic interaction between host and coronaviruses, it is hoped that insights on the pathogenesis of newly-identified highly pathogenic human coronaviruses and new strategies in antiviral development can be derived. [Image: see text] url: https://doi.org/10.1007/s12250-015-3683-3 doi: 10.1007/s12250-015-3683-3 id: cord-257698-ed2tqn35 author: Wong, Raymond S.M. title: Index Patient and SARS Outbreak in Hong Kong date: 2004-02-17 words: 1495.0 sentences: 86.0 pages: flesch: 53.0 cache: ./cache/cord-257698-ed2tqn35.txt txt: ./txt/cord-257698-ed2tqn35.txt summary: During the global outbreak of severe acute respiratory syndrome (SARS) in 2003, treatment was empiric. We report the case history of the index patient in a hospital outbreak of SARS in Hong Kong. Other laboratory tests were performed, including blood, sputum, and urine cultures, nasopharyngeal aspirate for influenza and parainfluenza, indirect immunofluorescence for respiratory syncytial viral antigen detection, and atypical pneumonia titer (for adenovirus, Chlamydia psittaci, Q fever, influenza A and B, and Mycoplasma). Our patient was identified as the index case-patient 5 days after the onset of this large outbreak at the Prince of Wales Hospital, as he was the first patient who had the characteristic clinical, radiologic, and laboratory features of SARS and had epidemiologic links with other infected persons. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: During the global outbreak of severe acute respiratory syndrome (SARS) in 2003, treatment was empiric. We report the case history of the index patient in a hospital outbreak of SARS in Hong Kong. The patient recovered after conventional antimicrobial therapy. Further studies are needed to address treatment of SARS, which has high attack and death rates. url: https://www.ncbi.nlm.nih.gov/pubmed/15030708/ doi: 10.3201/eid1002.030645 id: cord-312730-4ejjmab4 author: Wong, Rebecca S. Y. title: The SARS-CoV-2 Outbreak: an Epidemiological and Clinical Perspective date: 2020-09-29 words: 6475.0 sentences: 301.0 pages: flesch: 51.0 cache: ./cache/cord-312730-4ejjmab4.txt txt: ./txt/cord-312730-4ejjmab4.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started with the detection of an increasing number of pneumonia cases of unknown origin in Wuhan, China, since December 2019. In response to the rapidly growing number of confirmed cases and deaths, some measures taken by the Chinese authorities include the quarantine of millions of its citizens with the unprecedented lockdown of many cities, in an attempt to contain the virus and slow down the spread of the disease [3] . One study in China reported a young 22-year-old male who spread SARS-CoV-2 infection to his contacts (1 relative and 6 classmates, all of which were youngsters from 16 to 23 years) just after a few-hour contact during the incubation period, when he was totally asymptomatic [18] , suggesting that the disease is highly infectious during the incubation period. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started with the detection of an increasing number of pneumonia cases of unknown origin in Wuhan, China, since December 2019. The disease caused by SAS-CoV-2 was subsequently named coronavirus disease 2019 (COVID-19). Currently, the ongoing COVID-19 pandemic poses a global health concern with more than 28.9 million confirmed cases, taking away the lives of more than 900,000 people worldwide. To prevent further spread of the disease, an understanding of the clinical characteristics and how the disease spread is essential, especially for an emerging disease like COVID-19. Individuals who are infected with SARS-CoV-2 show diverse clinical features, and the disease severity can range from asymptomatic to death. The disease has been shown to affect not just the respiratory system but also other systems of the body. This review will discuss the pulmonary and extra-pulmonary clinical manifestations of COVID-19 in general, as well as the clinical characteristics in different groups of patients such as children, the elderly, pregnant women, patients with comorbidities and those with a compromised immunity. It will also critically examine existing evidence from relevant studies and discuss the SARS-CoV-2 outbreak from an epidemiological perspective. With the easing of control measures in many countries after months of lockdown, it is important to revisit the lessons learnt from research, as the world enters a new normal with the coexistence of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/33015553/ doi: 10.1007/s42399-020-00546-z id: cord-289947-z2dw2eaz author: Wong, River Chun-Wai title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay date: 2020-08-16 words: 800.0 sentences: 75.0 pages: flesch: 64.0 cache: ./cache/cord-289947-z2dw2eaz.txt txt: ./txt/cord-289947-z2dw2eaz.txt summary: title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens. The overall performance of Xpert Xpress SARS-CoV-2 assay was satisfactory when tested with DTS and LRT specimens. To our knowledge, this is the first report to evaluate the use of PBS for sample homogenization of DTS prior to testing with Xpert Xpress SARS-CoV-2 assay. These procedures can minimize the mucus and viscous substances among non-validated specimen types and broaden the testing scope of Xpert Xpress SARS-CoV-2 assay. abstract: BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86% & 100% respectively while the negative percent agreement (NPA) was 100% for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens. url: https://www.ncbi.nlm.nih.gov/pubmed/32823131/ doi: 10.1016/j.jcv.2020.104593 id: cord-311604-qsc3nks6 author: Wong, River Chun‐Wai title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date: 2020-09-30 words: 932.0 sentences: 61.0 pages: flesch: 56.0 cache: ./cache/cord-311604-qsc3nks6.txt txt: ./txt/cord-311604-qsc3nks6.txt summary: title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens This study aims to evaluate the diagnostic performance of PF assay for detection of SARS-CoV-2 in comparison to the TIB-Molbiol LightMix® SarbecoV E-gene assay (TIB-Molbiol assay) (TIB-Molbiol, Berlin, Germany) using DTS, NP and LRT specimens. Despite the manufacturer of TIB Miobiol regarded results with Ct <36 as positive, when use as an initial screening test in our laboratory, sample with any Ct value will be tested supplementary with Xpert Xpress assay. Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens abstract: Tremendous increase in workload due to COVID‐19 pandemic has caused intense strain on laboratory service. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32997347/ doi: 10.1002/jmv.26574 id: cord-268750-kox3uah2 author: Wong, S. F. title: Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures date: 2004-01-08 words: 1584.0 sentences: 87.0 pages: flesch: 55.0 cache: ./cache/cord-268750-kox3uah2.txt txt: ./txt/cord-268750-kox3uah2.txt summary: When the operations were performed, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga., USA) had not yet prepared guidelines for the prevention of SARS transmission during Caesarean sections. For the three Caesarean sections performed on mothers with SARS, the number of healthcare workers was limited to a minimum, with only those personnel essential to carry out the operation, neonatal resuscitation, and cleanup being involved (i.e., 2 senior obstetricians, 2 senior neonatologists, 1 senior anaesthetist, 1 theatre assistant, a team of 4 senior midwives, and 2 cleansing staff). The participating HCWs wore appropriate PPE according to the hospital''s guidelines prior to the arrival of the patient from the intensive care unit. In conclusion, the procedures described above were sufficient to prevent our healthcare workers from contracting SARS while performing these very high-risk operations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/14712366/ doi: 10.1007/s10096-003-1068-2 id: cord-022776-fz7m177w author: Wong, S.F. title: Severe Acute Respiratory Syndrome and pregnancy date: 2003-12-22 words: 1463.0 sentences: 92.0 pages: flesch: 56.0 cache: ./cache/cord-022776-fz7m177w.txt txt: ./txt/cord-022776-fz7m177w.txt summary: Severe Acute Respiratory Syndrome (SARS) has already had an enormous impact on society and medical practice but presents special problems in pregnancy. The following comments are based on the experience of those in Hong Kong caring for patients with SARS in pregnancy of which there have been 10 at the time of writing in May 2003. The risk of cross infection is particularly high at the time of vaginal or operative deliveries, especially when there is maternal viraemia. There have not been any fetal problems reported in the very few women given ribavarin in the second half of pregnancy 2,3 . Our own experience with SARS in Hong Kong is in keeping with the extra risk of pregnancy in viral illness. Therefore, it is tempting to recommend early delivery or termination of pregnancy in pregnant women who are seriously ill with SARS. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161769/ doi: 10.1046/j.1471-0528.2003.03008.x id: cord-322603-8ajckhzc author: Wongsawat, Jurai title: Risk of novel coronavirus 2019 transmission from children to caregivers: A case series date: 2020-06-22 words: 923.0 sentences: 86.0 pages: flesch: 62.0 cache: ./cache/cord-322603-8ajckhzc.txt txt: ./txt/cord-322603-8ajckhzc.txt summary: World Health Organization (WHO) characterised coronavirus disease 2019 (COVID-19) as a pandemic on 11 March 2020. [4] [5] [6] The potential risk of transmission from infected children to adults is of concern due to prolonged detection of the SARS-CoV-2 RNA in respiratory specimens and faeces. Children were allowed to be discharged when their swabs turned negative for SARS-CoV-2 RNA on 2 consecutive days; this happened on days 15, 23 and 27 of illness for cases 1, 2 and 3, respectively. 8, 9 While our study revealed no evidence of transmission from mildly ill, afebrile children to their caregivers despite prolonged positivity of the SARS-CoV-2 RNA in their respiratory specimens, our findings are consistent with WHO''s recommendations for alternatively managing patients with mild COVID-19 disease at home. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: An observational cohort study SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics abstract: nan url: https://doi.org/10.1111/jpc.14965 doi: 10.1111/jpc.14965 id: cord-268572-uhak283t author: Woo, Marcel S. title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients date: 2020-07-11 words: 1304.0 sentences: 92.0 pages: flesch: 51.0 cache: ./cache/cord-268572-uhak283t.txt txt: ./txt/cord-268572-uhak283t.txt summary: title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients However, few details about the effect of individual immunotherapies have been reported, which could instruct us about the immunological control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we report on two individuals with underlying neuroimmunological diseases who were under stable rituximab therapy-a B cell-depleting monoclonal antibody [6, 7] -when confirmed COVID-19 developed. Patient 2 was a 68-year-old female with neuromyelitis optica spectrum disorder (NMOSD, diagnosed 2014, EDSS 6.0), who was directly admitted to our intensive care unit (ICU) on March 29th, 2020 with progressive respiratory failure and infection of the urinary tract. She had a B cell count of 25/µL (Ref. 80-500/µL, Supplementary Table 2) at the day of admission and tested negative for SARS-CoV-2-specific antibodies (3.5 AU/mL; Ref. In summary, we report on two patients who developed COVID-19 while under treatment with rituximab due to neuroimmunological diseases. Antibody responses to SARS-CoV-2 in patients with COVID-19 abstract: nan url: https://doi.org/10.1007/s00415-020-10046-8 doi: 10.1007/s00415-020-10046-8 id: cord-287210-sars5dmi author: Woo, Patrick C. Y. title: Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia date: 2005-12-01 words: 3345.0 sentences: 206.0 pages: flesch: 56.0 cache: ./cache/cord-287210-sars5dmi.txt txt: ./txt/cord-287210-sars5dmi.txt summary: However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. All prospectively collected NPAs from patients with community-acquired pneumonia that were sent to the clinical microbiology laboratories of 4 hospitals in Hong Kong during a 12-month period (22 March 2003 [the beginning of the SARS epidemic in Hong Kong] to 21 March 2004) for detection of SARS-CoV and were found to be negative for SARS-CoV RNA, by reverse-transcription polymerase chain reaction (RT-PCR) [20] , were included in the study. Sequence analysis revealed 0%-2% nucleotide differences between the sequences of the fragments and the sequence of the pol gene from The epidemiological, clinical, and radiological characteristics of the 10 patients with CoV-HKU1-associated community-acquired pneumonia are summarized in table 2. abstract: BackgroundRecently, we described the discovery of a novel group 2 coronavirus, coronavirus HKU1 (CoV-HKU1), from a patient with pneumonia. However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. The epidemiological, clinical, and laboratory characteristics of patients with CoV-HKU1–associated pneumonia were analyzed. The pol spike (S), and nucleocapsid (N) genes were also sequenced ResultsNPAs from 10 (2.4%) of 418 patients with community-acquired pneumonia were found to be positive for CoV-HKU1. All 10 cases occurred in spring and winter. Nine of these patients were adults, and 4 had underlying diseases of the respiratory tract. In the 6 patients from whom serum samples were available, all had a 4-fold change in immunoglobulin (Ig) G titer and/or presence of IgM against CoV-HKU1. The 2 patients who died had significantly lower hemoglobin levels, monocyte counts, albumin levels, and oxygen saturation levels on admission and had more-extensive involvement visible on chest radiographs. Sequence analysis of the pol S, and N genes revealed 2 genotypes of CoV-HKU1 ConclusionsCoV-HKU1 accounts for 2.4% of community-acquired pneumonia, with 2 genotypes in the study population. Without performance of diagnostic tests, the illness was clinically indistinguishable from other community-acquired pneumonia illnesses url: https://www.ncbi.nlm.nih.gov/pubmed/16267760/ doi: 10.1086/497151 id: cord-264968-ctx39vhi author: Woo, Patrick CY title: Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia date: 2004-03-13 words: 3570.0 sentences: 171.0 pages: flesch: 47.0 cache: ./cache/cord-264968-ctx39vhi.txt txt: ./txt/cord-264968-ctx39vhi.txt summary: An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. Assessment of recombinant nucleocapsid protein ELISA Serum samples from 149 healthy blood donors who donated blood 3 years previously (aged 18 years or older) and 106 patients with pneumonia positive for antibodies against SARS-CoV detected by our indirect immunofluorescence assay 1 were used for the assessment of the ELISA-based IgG antibody test. abstract: BACKGROUND: Although the genome of severe acute respiratory syndrome coronavirus (SARS-CoV) has been sequenced and a possible animal reservoir identified, seroprevalence studies and mass screening for detection of subclinical and non-pneumonic infections are still lacking. METHODS: We cloned and purified the nucleocapsid protein and spike polypeptide of SARS-CoV and examined their immunogenicity with serum from patients with SARS-CoV pneumonia. An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. The seroprevalence of SARS-CoV was studied with the ELISA in healthy blood donors who donated during the SARS outbreak in Hong Kong, non-pneumonic hospital inpatients, and symptom-free health-care workers. All positive samples were confirmed by two separate western-blot assays (with recombinant nucleocapsid protein and recombinant spike polypeptide). FINDINGS: Western-blot analysis showed that the nucleocapsid protein and spike polypeptide of SARS-CoV are highly immunogenic. The specificity of the IgG antibody test (ELISA with positive samples confirmed by the two western-blot assays) was 100%, and the sensitivity was 94·3%. Three of 400 healthy blood donors who donated during the SARS outbreak and one of 131 non-pneumonic paediatric inpatients were positive for IgG antibodies, confirmed by the two western-blot assays (total, 0·48% of our study population). INTERPRETATION: Our findings support the existence of subclinical or non-pneumonic SARS-CoV infections. Such infections are more common than SARS-CoV pneumonia in our locality. url: https://www.sciencedirect.com/science/article/pii/S0140673604157292 doi: 10.1016/s0140-6736(04)15729-2 id: cord-276403-yomjm2gg author: Woo, Patrick CY title: Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections date: 2006-10-30 words: 3636.0 sentences: 178.0 pages: flesch: 50.0 cache: ./cache/cord-276403-yomjm2gg.txt txt: ./txt/cord-276403-yomjm2gg.txt summary: title: Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections In this review, these two severe zoonotic viral infections transmitted by the respiratory route, with pandemic potential, are used as models to illustrate the role of Chinese wet-markets in their emergence, amplification and dissemination. The outbreak of avian influenza A H5N1 virus human infections in Hong Kong in 1997, with 18 cases and six deaths [6] , serves as another excellent example to illustrate the role of Chinese wet-markets in the emergence of zoonotic severe respiratory viral infections (Fig. 4) . China, with one-quarter of the world''s population, 16 of the 20 most polluted cities of the world and a huge diversity of animals closely associated with the human population, is one of the countries with the greatest potential for the emergence and spread of infectious diseases, such as SARS and avian influenza. abstract: In China, close contacts between humans and food animals have resulted in the transmission of many microbes from animals to humans. The two most notable infectious diseases in recent years are severe acute respiratory syndrome and avian influenza. In this review, these two severe zoonotic viral infections transmitted by the respiratory route, with pandemic potential, are used as models to illustrate the role of Chinese wet-markets in their emergence, amplification and dissemination. RECENT FINDINGS: Two research groups independently discovered the presence of severe acute respiratory syndrome coronavirus-like viruses in horseshoe bats. An astonishing diversity of coronaviruses was also discovered in different species of bats. For the recent and still ongoing avian influenza H5N1 outbreak that originated in Southeast Asia, from 2003 to 21 April 2006, 204 humans have been infected, with 113 deaths. Most patients had recent direct contacts with poultry. SUMMARY: In Chinese wet-markets, unique epicenters for transmission of potential viral pathogens, new genes may be acquired or existing genes modified through various mechanisms such as genetic reassortment, recombination and mutation. The wet-markets, at closer proximity to humans, with high viral burden or strains of higher transmission efficiency, facilitate transmission of the viruses to humans. url: https://www.ncbi.nlm.nih.gov/pubmed/16940861/ doi: 10.1097/01.qco.0000244043.08264.fc id: cord-258725-z79gel8h author: Wood, R. title: Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland date: 2020-09-22 words: 5315.0 sentences: 272.0 pages: flesch: 53.0 cache: ./cache/cord-258725-z79gel8h.txt txt: ./txt/cord-258725-z79gel8h.txt summary: Methods Using a Scotland-wide record-linkage based occupational cohort comprising healthcare workers and members of their households, we examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalisation with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). Similar, but slightly stronger associations were found when the analysis was restricted to households where at least one member of staff had a patient-facing role (fully adjusted model, HR per child 0.83; 95% CI 0.68-1.02, Supplementary Table S3), a group with greater occupational exposure to SARS-CoV-2 than non-patient facing healthcare workers, although on formally testing for an interaction between patient facing and non-patient facing groups, the coefficient included the null, (P-value for interaction = 0.80). abstract: Background Children are relatively protected from novel coronavirus infection (COVID-19). The reasons for this protection are not well understood but differences in the immune response to Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) have been implicated. If such differences are due to differential exposure to non-SARS-CoV-2 infectious agents, adults who are close contacts of children may partly share in this protection. Such a protective effect would have important implications for the lives of children, not least in terms of schooling. Methods Using a Scotland-wide record-linkage based occupational cohort comprising healthcare workers and members of their households, we examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalisation with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). All healthcare workers directly employed by the National health Service (NHS) in Scotland, or contracted to provide general practice services, were included. Outcome and covariate data were obtained via linkage to Scotland-wide microbiology, drug prescribing, hospitalisation and death data. Results 241,266 adults did not share a household with young children; 41,198, 23,783 and 3,850 shared a household with 1, 2 and 3 or more young children respectively. The risk of hospitalisation with COVID-19 was lower in those with one child and lower still in those with two or more children, adjusting for age the hazard ratio (HR) was 0.83 per child (95% CI 0.70-0.99). On additionally adjusting for sex, socioeconomic deprivation, occupation, professional role, staff/non-staff status, the number of adults and adolescents in each household, and comorbidity, the HR was 0.89 per child (95% CI 0.74-1.06). An association of the same magnitude, but more precisely estimated, was obtained for any case of COVID-19 (fully adjusted model, HR per child 0.89; 95% CI 0.84-0.95). Conclusion Increased household exposure to young children was associated with an attenuated risk of testing positive for SARS-CoV-2 and appeared to also be associated with an attenuated risk of COVID-19 disease severe enough to require hospitalisation. url: http://medrxiv.org/cgi/content/short/2020.09.21.20196428v1?rss=1 doi: 10.1101/2020.09.21.20196428 id: cord-265599-903w782b author: Woods, R. title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection date: 2020-10-21 words: 2254.0 sentences: 188.0 pages: flesch: 58.0 cache: ./cache/cord-265599-903w782b.txt txt: ./txt/cord-265599-903w782b.txt summary: title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection Conclusion: Inaccurate specimen collection from poor swab technique could contribute to false negative rate of testing for SARS-CoV-2. 8, 9 A study was performed to assess nasopharyngeal swab technique of staff in a major academic institution. Accurate specimen collection is critical to ensure optimal sensitivity of testing for SARS-CoV-2 but depends on the skill of the person performing the swab.  There is little evidence on the accuracy of swabbing technique in peer-reviewed published medical literature  This study uses a novel tool to evaluate a crucial aspect of public health measures to control the spread of SARS-CoV-2  The low success rate of accurately swabbing the nasopharynx implies that better training is necessary  Better training may improve specimen collection and sensitivity of testing for SARS-CoV-2  Standardised training videos with description of the relevant anatomy would likely be useful to improve testing . abstract: Background: The COVID-19 pandemic has caused huge pressure on healthcare systems worldwide. Public health measures to control the virus are reliant on testing, including appropriate collection of specimens for analysis. Methods: A prospective study of nasopharyngeal swab technique by staff in an academic tertiary referral centre was carried out. Nasopharyngeal swab technique was evaluated by a novel design of a navigated swab on a three-dimensional model head. Results: Swab technique of 228 participants was assessed. Technique was poor, with a success rate of nasopharyngeal swabbing at 38.6%. Angle and length of insertion were significantly different between those with successful and unsuccessful technique. Doctors were significantly more accurate than nurses and non-healthcare professionals (p<0.01). Conclusion: Inaccurate specimen collection from poor swab technique could contribute to false negative rate of testing for SARS-CoV-2. Specific training in nasopharyngeal anatomy and swab technique may improve the accuracy of nasopharyngeal swabbing. url: http://medrxiv.org/cgi/content/short/2020.10.19.20213140v1?rss=1 doi: 10.1101/2020.10.19.20213140 id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 words: 4329.0 sentences: 253.0 pages: flesch: 52.0 cache: ./cache/cord-337673-1nau263l.txt txt: ./txt/cord-337673-1nau263l.txt summary: Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . abstract: Until the appearance of severe acute respiratory syndrome (SARS), caused by the SARS coronavirus (SARS-CoV) in early 2003, coronavirus infection was not considered to be serious enough to be controlled by either vaccination or specific antiviral therapy. It is now believed that the availability of antiviral drugs effective against SARS-CoV will be crucial for the control of future SARS outbreaks. Recently, RNA interference has been successfully used as a more specific and efficient method for gene silencing. RNA interference induced by small interfering RNA can inhibit the expression of viral antigens and so provides a new approach to the therapy of pathogenic viruses. This review provides an overview of current information on coronavirus and the application of small interfering RNA in viral therapeutics, with particular reference to SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/16433589/ doi: 10.1517/13543784.15.2.89 id: cord-024613-yump76qu author: Wu, Chunxing title: Recommendations for control and prevention of infections for pediatric orthopedics during the epidemic period of COVID-19 date: 2020-04-23 words: 3818.0 sentences: 273.0 pages: flesch: 43.0 cache: ./cache/cord-024613-yump76qu.txt txt: ./txt/cord-024613-yump76qu.txt summary: Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares, for clinical practices of pediatric orthopedics according to the physicochemical properties of SARS-CoV-2. Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares for pediatric orthopedics, pediatric surgery and others. reCommendAtion formAtion proCeSS Given the high demand of patients for medical treatment and the need to protect medical staff from infectious diseases, a recommendation working group "Recommendation Formulating Team for Pediatric Orthopedic Infection controls during the Epidemic''s Period of COVID-19" (including all authors) was formed to focus on relevant issues for protection of medical staff in pediatric surgery, pediatric orthopedics, infectious diseases department, anesthesiology department, and nursing department to hospital administrators. abstract: The outbreak of Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged and spread rapidly throughout the world. As of February 29, 2020, 79 389 cases of COVID-19 have been reported, and the outbreak is linked to 2838 deaths. The population is generally susceptible to the disease, and differences in incubation periods after infection exist among individuals. These two aspects of COVID-19 pose significant challenges to pediatric orthopedic diagnosis and treatment. As a dedicated center for managing pediatric cases of SARS-CoV-2 in Shanghai, our hospital has mobilized all branches and departments to undertake joint actions for scientific prevention and control, precise countermeasure and comprehensive anti-epidemic efforts. Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares, for clinical practices of pediatric orthopedics according to the physicochemical properties of SARS-CoV-2. It may serve as practical references and recommendations for managing SARS-CoV-2 infection in other pediatric specialties and in other hospitals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211102/ doi: 10.1136/wjps-2020-000124 id: cord-335859-k37jivp6 author: Wu, Daphne C. title: Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date: 2020-10-21 words: 3112.0 sentences: 160.0 pages: flesch: 52.0 cache: ./cache/cord-335859-k37jivp6.txt txt: ./txt/cord-335859-k37jivp6.txt summary: To understand the socio-demographic predictors of COVID symptoms, we conducted a logistic regression analysis where the outcome was self-reported symptoms suggestive of COVID infection which we defined in this study as the respondent reporting himself/herself and/or at least one member of the household having had a combination of fever (with or without hallucinations) and any of i) difficulty breathing/shortness of breath or ii) dry cough so severe that it disrupts sleep or iii) a loss of a sense of smell in the past month; and the explanatory variables were gender (male, female, or other), education level (high school and under, or some college/ university and higher), province, age, ethnicity (Indigenous, English and other European, or others), visible minority (defined as persons, other than Aboriginal peoples, who are nonwhite in race or colour) [6] , and number of household members. abstract: Random population-based surveys to estimate prevalence of SARS-CoV2 infection causing coronavirus disease (COVID-19) are useful to understand distributions and predictors of the infection. In April 2020, the first-ever nationally representative survey in Canada polled 4,240 adults age 18 years and older about self-reported COVID experience in March, early in the epidemic. We examined the levels and predictors of COVID symptoms, defined as fever plus difficulty breathing/shortness of breath, dry cough so severe that it disrupts sleep, and/or loss of sense of smell; and testing for SARS-CoV-2 by respondents and/or household members. About 8% of Canadians reported that they and/or one or more household members experienced COVID symptoms. Symptoms were more common in younger than in older adults, and among visible minorities. Overall, only 3% of respondents and/or household members reported testing for SARS-CoV-2. Being tested was associated with having COVID symptoms, Indigenous identity, and living in Quebec. Periodic nationally representative surveys of symptoms, as well as SARS-CoV-2 antibodies, are required in many countries to understand the pandemic and prepare for the future. url: https://doi.org/10.1371/journal.pone.0240778 doi: 10.1371/journal.pone.0240778 id: cord-273675-0oiq44gl author: Wu, Di title: To alert coinfection of COVID-19 and dengue virus in developing countries in the dengue-endemic area date: 2020-05-04 words: 568.0 sentences: 38.0 pages: flesch: 66.0 cache: ./cache/cord-273675-0oiq44gl.txt txt: ./txt/cord-273675-0oiq44gl.txt summary: At the meantime, dengue was endemic in the Southeast Asia and South America, and a part of the patients shared the same symptoms, so, we write this paper to alert the clinicians to distinguish these two diseases. 1 Gabriel Yan et al 2 reported 2 cases of COVID-19 patients coinfected with dengue fever in Singapore. Joob et al 3 also reported a patient coinfected with SARS-CoV-2 and dengue virus in Thailand. These 3 cases raise concern that patients with fever can be infected with both SARS-CoV-2 and dengue at the same time in dengue-endemic areas such as Singapore, Thailand, and Malaysia in Southeast Asia and Brazil in South America. Some patients present only with fever when infected with SARS-CoV-2. Therefore, measures should be taken to distinguish patients with fever and headache from dengue fever and COVID-19, and these atypical symptoms should trigger alerts, especially in developing countries with a high incidence of dengue fever, as in Southeast Asia and South American. abstract: Coronavirus disease 2019 (CoVID-19) is a new outbreak infectious disease caused by SARS-CoV-2, which was originated from Wuhan in China and has now spread to the whole world. At the meantime, dengue was endemic in the Southeast Asia and South America, and a part of the patients shared the same symptoms, so, we write this paper to alert the clinicians to distinguish these two diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32362302/ doi: 10.1017/ice.2020.187 id: cord-277911-x916hsg6 author: Wu, Di title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) date: 2020-04-13 words: 615.0 sentences: 50.0 pages: flesch: 56.0 cache: ./cache/cord-277911-x916hsg6.txt txt: ./txt/cord-277911-x916hsg6.txt summary: title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated from Wuhan in China and has now spread globally. However, despite the concern focused on SARS-CoV-2, influenza virus continues to circulate and cause disease. The SARS-COV-2 outbreak in late December of 2019 in Wuhan, China, has caused many infections and deaths globally. 1 In China, several respiratory viruses are also now active including influenza, parainfluenza virus, respiratory syncytial virus, adenovirus, and now SARS-COV-2. The current World Health Organization (WHO)/ECDC definition of suspected case is not focused on pediatric population. Considering the large number of patients referring to pediatric hospital because of acute respiratory infections in winter season, the strict adoption of WHO/ECDC criteria can lead to a congestion of our hospitals. Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32287051/ doi: 10.1097/inf.0000000000002688 id: cord-334973-jemeyudi author: Wu, Dingye title: Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center date: 2020-07-22 words: 2429.0 sentences: 151.0 pages: flesch: 54.0 cache: ./cache/cord-334973-jemeyudi.txt txt: ./txt/cord-334973-jemeyudi.txt summary: title: Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center Hospitalization days, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid positive days, minimal lymphocyte count, and occurrence time were collected and comparatively analyzed. In addition, a multiple linear regression model was used to analyze the effect of diabetes on minimal lymphocyte count and its emergence time, patient''s hospitalization days, and SARS-CoV-2 nucleic acid positive days by adjusting for potential confounding factors including age; gender; BMI; SBP; DBP; and ALT, AST, and Cr levels. This single center, observational, retrospective study of patients with COVID-19 showed that, patients with T2DM have higher CRP, lower level and more rapid decline in lymphocyte count, and longer hospitalization time than those without T2DM. Our study found a decrease in lymphocyte count in patients with COVID-19, and the lower the lymphocyte count, the longer SARS-CoV-2 nucleic acid positive days and hospitalization days. abstract: Abstract Objective To investigate the characteristics of lymphocytes in type 2 diabetic patients with coronavirus disease (COVID-19). Methods Patients with COVID-19 admitted to hospital in Wuxi, China from January 29 to March 15 were included in the study. Lymphocytes were measured and recorded at admission and during treatment. Hospitalization days, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid positive days, minimal lymphocyte count, and occurrence time were collected and comparatively analyzed. Correlations between minimal lymphocyte count and hospitalization days as well as SARS-CoV-2 nucleic acid positive days were analyzed. Results A total of 63 patients were included in the study, with 16 in the diabetic group and 47 in the non-diabetic group. After adjusting for potential confounding factors, we observed lower minimal lymphocyte count (0.67 ± 0.36*109/L vs. 1.30 ± 0.54*109/L, adjusted P = 0.001), earlier occurrence of the minimal lymphocyte count (2.68 ± 2.33 days vs. 5.29 ± 4.95 days, adjusted P = 0.042), and longer hospitalization time (20.44 ± 5.24 days vs. 17.11 ± 4.78 days, adjusted P = 0.047) in the diabetic group than in the non-diabetic group. There was a negative correlation between minimal lymphocyte count and hospitalization days (R = -0.600, P < 0.05) as well as SARS-CoV-2 nucleic acid positive days (R = -0.420, P < 0.05). Conclusions The diabetic group with COVID-19 had lower lymphocyte count, reached the minimal count faster, and had longer hospital stays than the non-diabetic group. Hospitalization days and SARS-CoV-2 nucleic acid positive days were negatively correlated with the minimal lymphocyte count. url: https://doi.org/10.1016/j.diabres.2020.108340 doi: 10.1016/j.diabres.2020.108340 id: cord-308302-5yns1hg9 author: Wu, Gang title: A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings date: 2020-08-20 words: 2966.0 sentences: 202.0 pages: flesch: 48.0 cache: ./cache/cord-308302-5yns1hg9.txt txt: ./txt/cord-308302-5yns1hg9.txt summary: We used machine learning for processing laboratory findings of 110 patients with SARS-CoV-2 pneumonia (including 51 non-survivors and 59 discharged patients). Thus it is feasible to establish an accurate prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings. Laboratory tests for SARS-CoV-2 pneumonia included: blood routine test, serum biochemical (including glucose, renal and liver function, creatine kinase, lactate dehydrogenase, and electrolytes), coagulation profile, cytokine test, markers of myocardial injury, infection-related makers, and other enzymes. 68 discharged patients with SARS-CoV-2 pneumonia whose age and gender matched the non-survivors were selected (46 male, median age 66 years). A number of laboratory features were compared between non-survivors and discharged patients with SARS-CoV-2 pneumonia. With machine learning methods previously used in radiomics, a prediction model combining seven out of thirty-eight laboratory features was built for predicting the outcome of SARS-CoV-2 pneumonia. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in thousands of deaths in the world. Information about prediction model of prognosis of SARS-CoV-2 infection is scarce. We used machine learning for processing laboratory findings of 110 patients with SARS-CoV-2 pneumonia (including 51 non-survivors and 59 discharged patients). The maximum relevance minimum redundancy (mRMR) algorithm and the least absolute shrinkage and selection operator logistic regression model were used for selection of laboratory features. Seven laboratory features selected in the model were: prothrombin activity, urea, white blood cell, interleukin-2 receptor, indirect bilirubin, myoglobin, and fibrinogen degradation products. The signature constructed using the seven features had 98% [93%, 100%] sensitivity and 91% [84%, 99%] specificity in predicting outcome of SARS-CoV-2 pneumonia. Thus it is feasible to establish an accurate prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings. url: https://www.ncbi.nlm.nih.gov/pubmed/32820210/ doi: 10.1038/s41598-020-71114-7 id: cord-285865-1gsy43a0 author: Wu, Guang title: Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species date: 2004-12-09 words: 4309.0 sentences: 214.0 pages: flesch: 53.0 cache: ./cache/cord-285865-1gsy43a0.txt txt: ./txt/cord-285865-1gsy43a0.txt summary: Randomly predictable present type of amino-acid pair with unpredictable frequency There are 84 alanines (A) in the spike glycoprotein from human SARS-CoV. In view of the unpredictable portion whose actual value is smaller than its predicted value (left panel), the spike glycoproteins have the largest percentages in both unpredictable type and frequency among different coronavirus proteins. With respect to the second line of evidence, we find that the spike glycoprotein has a larger percentage of unpredictable types and frequencies whose actual values are smaller than the predicted values in Fig. 2 . Comparison with the first nine proteins in Table 2 (columns V, VI, VII and VIII in Table 2 , similar to Fig. 3) shows that the difference between actual and predicted values is statistically larger in spike glycoproteins regarding unpredictable types and is statistically smaller regarding unpredictable frequency. abstract: In this study, we used the probabilistic models developed by us over the last several years to analyze 158 proteins from coronaviruses in order to determine which protein is more vulnerable to mutations. The results provide three lines of evidence suggesting that the spike glycoprotein is different from the other coronavirus proteins: (1) the spike glycoprotein is more sensitive to mutations, this is the current state of the spike glycoprotein, (2) the spike glycoprotein has undergone more mutations in the past, this is the history of spike glycoprotein, and (3) the spike glycoprotein has a bigger potential towards future mutations, this is the future of spike glycoprotein. Furthermore, this study gives a clue on the species susceptibility regarding different proteins. Figure Predictable and unpredictable portions in coronavirus proteins. The data are presented as median with interquartile range. * the predictable and unpredictable portions in spike glycoprotein group are statistically different from any other protein groups at p<0.05 level, except for hemagglutinin-esterase precursor group. # the predictable and unpredictable portions in spike glycoprotein group are statistically different from hemagglutinin-esterase precursor, membrane protein and nucleocapsid protein groups at p<0.05 level. † the predictable and unpredictable portions in spike glycoprotein group are statistically different from hemagglutinin-esterase precursor, and membrane protein groups at p<0.05 level. Electronic Supplementary Material is available for this article if you access the article at http://dx.doi.org/10.1007/s00894-004-0210-0. url: https://www.ncbi.nlm.nih.gov/pubmed/15592899/ doi: 10.1007/s00894-004-0210-0 id: cord-314102-8jf3fnqe author: Wu, Jie title: Advances in research on ACE2 as a receptor for 2019-nCoV date: 2020-08-11 words: 8322.0 sentences: 389.0 pages: flesch: 47.0 cache: ./cache/cord-314102-8jf3fnqe.txt txt: ./txt/cord-314102-8jf3fnqe.txt summary: Although 2019-nCoV and SARS-CoV are very similar viruses genomically and structurally, the huge number of severe cases and deaths now being caused by 2019-nCoV infections has understandably prompted intense research on the receptor used by it to enter human cells. Angiotensin converting enzyme 2 (ACE2), a functional receptor for SARS-CoV, now appears likely to mediate 2019-nCoV entry into human cells. Some recent studies have suggested Cellular and Molecular Life Sciences * Xiuhong Yang yangxiuhong@ncst.edu.cn 1 that 2019-nCoV may infect host cells through the ACE2 receptor, as has already been established for SARS-CoV [7] [8] [9] [10] . In this review, the latest advances in our understanding of the roles played by ACE2 in enzyme catalysis, CoV invasion, cellular expression changes after viral-host cell binding, and its relationships with viral transmission and population susceptibility are described in the context of the pathogenesis of COVID-19. Therefore, it is speculated that like SARS-CoV, 2019-nCoV infects host cells via the mediating effects of its S protein and ACE2 receptors on the surfaces of human cells. abstract: Currently, a novel coronavirus (SARS-CoV-2, also called 2019-nCoV) has triggered pandemic Coronavirus Disease 2019 (COVID-19), an acute infectious respiratory disease that first became epidemic in Wuhan (China) and is now spreading worldwide. Although 2019-nCoV and SARS-CoV are very similar viruses genomically and structurally, the huge number of severe cases and deaths now being caused by 2019-nCoV infections has understandably prompted intense research on the receptor used by it to enter human cells. Angiotensin converting enzyme 2 (ACE2), a functional receptor for SARS-CoV, now appears likely to mediate 2019-nCoV entry into human cells. In this review, we describe the roles performed by ACE2 as an enzymatic catalyst and as a receptor for this novel coronavirus. We also summarize the latest research pertaining to the changes noted in ACE2 expression after viral binding, and the relationships relating to virus transmission and population susceptibility to it. Lastly, we speculate on the pathogenesis of COVID-19 and provide a useful reference for drug development against this aggressive virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32780149/ doi: 10.1007/s00018-020-03611-x id: cord-315656-asvf4roo author: Wu, Junjiao title: Revisiting the Immune Balance Theory: A Neurological Insight Into the Epidemic of COVID-19 and Its Alike date: 2020-10-15 words: 5937.0 sentences: 286.0 pages: flesch: 37.0 cache: ./cache/cord-315656-asvf4roo.txt txt: ./txt/cord-315656-asvf4roo.txt summary: However, in the central nervous system (CNS), the activation of resident immune cells including microglia and astrocytes may lead to chronic immune imbalance, which underlies the potential long-term effects in synaptic changes and neuropsychiatric impairments. (II) Multiple organ failure in severe COVID-19 is caused by the systemic acute immune responses, the cytokine storm, and unsurprisingly caused the brain inflammation and led to encephalitis. Apart from the direct infection of the brain, SARS-CoV-2 may cause neurological disorders indirectly by triggering an over-activated immune responses, characterized as cytokine storm. Although with exciting benefits, the inhibition of IL-6 pathway works mostly for severe cases, the long-term treatment strategy against the SARS-CoV-2 infection requires the rapid development of effective anti-viral drugs and, more importantly, vaccines. However, in addition to protective effects, microglia may also mediate hippocampal presynaptic membrane damage through complement system, resulting in long-term memory impairment and cognitive decline in patients with encephalitis, caused by coronavirus or human immunodeficiency virus (HIV) infection (69) . abstract: As the pandemic of COVID-19 is raging around the world, the mysteriousness of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) coronavirus is being revealed by the concerted endeavors of scientists. Although fever and pneumonia are typical symptoms, COVID-19 patients exhibit multiple neurological complications. In this interim review, we will summarize the neurological manifestations and their potential causes in COVID-19. Similar to the other two fatal respiratory coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 also shows to be neuroinvasive that may spread from the periphery to brain, probably by the retrograde axonal transport. The invaded viruses may directly disrupt the complex neural circuits, and raise a chronic activation of immune responses. In another hand, multiple organ failure in severe COVID-19 is caused by the systemic acute immune responses, and unsurprisingly caused the brain inflammation and led to encephalitis. However, in the central nervous system (CNS), the activation of resident immune cells including microglia and astrocytes may lead to chronic immune imbalance, which underlies the potential long-term effects in synaptic changes and neuropsychiatric impairments. The neuroinvasive biology also provides a possible link with the Braak staging of neurodegenerative diseases such as Parkinson's disease (PD). Although with considerable advances, the neurotropic potential and chronic neurological effects caused by SARS-CoV-2 infections merit further investigations. url: https://doi.org/10.3389/fneur.2020.566680 doi: 10.3389/fneur.2020.566680 id: cord-197818-asd39zbj author: Wu, Kai title: Magnetic Immunoassays: A Review of Virus and Pathogen Detection Before and Amidst the Coronavirus Disease-19 (COVID-19) date: 2020-07-09 words: 5625.0 sentences: 344.0 pages: flesch: 41.0 cache: ./cache/cord-197818-asd39zbj.txt txt: ./txt/cord-197818-asd39zbj.txt summary: In this review, magnetic biosensors'' application in virus and pathogen detection will be summarized and discussed based on the different working principle of the technologies. [69] The key take-away point here is that several experimental demonstrations of the magnetic assays for virus detection based on GMRs and the reported LOD indicate that GMR-based bioassay is one of the promising candidates for onsite, rapid, and sensitive detection of COVID-19. reported the volume-based MPS immunoassay platform utilizing the polyclonal antibodies induced cross-linking of MNPs for one-step, wash-free detection of H1N1 nucleoprotein molecules. In this section, we reviewed some representative works that use magnetic materials are auxiliary tools for high sensitivity virus and pathogen detections, as summarized in Table 3 . We reviewed the magnetic immunoassay literatures prior to COVID-19 and highlighted some promising tools for detecting pathogens as well as viruses with high specificity and sensitivity. Magnetic quantum dot based lateral flow assay biosensor for multiplex and sensitive detection of protein toxins in food samples abstract: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is a threat to the global healthcare system and economic security. As of July 2020, no specific drugs or vaccines are yet available for COVID-19, fast and accurate diagnosis for SARS-CoV-2 is essential in slowing down the spread of COVID-19 and for efficient implementation of control and containment strategies. Magnetic immunoassay is a novel and emerging topic representing the frontiers of current biosensing and magnetics areas. The past decade has seen rapid growth in applying magnetic tools for biological and biomedical applications. Recent advances in magnetic materials and nanotechnologies have transformed current diagnostic methods to nanoscale and pushed the detection limit to early stage disease diagnosis. Herein, this review covers the literatures of magnetic immunoassay platforms for virus and pathogen detections, before COVID-19. We reviewed the popular magnetic immunoassay platforms including magnetoresistance (MR) sensors, magnetic particle spectroscopy (MPS), and nuclear magnetic resonance (NMR). Magnetic Point-of-Care (POC) diagnostic kits are also reviewed aiming at developing plug-and-play diagnostics to manage the SARS-CoV-2 outbreak as well as preventing future epidemics. In addition, other platforms that use magnetic materials as auxiliary tools for enhanced pathogen and virus detections are also covered. The goal of this review is to inform the researchers of diagnostic and surveillance platforms for SARS-CoV-2 and their performances. url: https://arxiv.org/pdf/2007.04809v1.pdf doi: nan id: cord-327997-noqbcxua author: Wu, Kevin E. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 words: 7201.0 sentences: 377.0 pages: flesch: 42.0 cache: ./cache/cord-327997-noqbcxua.txt txt: ./txt/cord-327997-noqbcxua.txt summary: We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5'' and 3'' viral untranslated regions contain the strongest, most distinct localization signals. As previously discussed, since much of the APEX-seq mitochondrial data used to train RNA-GPS actually consists of nuclear-encoded transcripts likely picked up as the APEX-COX4 fusion protein is transported to the mitochondria, we hypothesize that our predicted mitochondrial residency is alluding to similarity in localization pathways, rather than localization destination. To further validate the robustness of these results, we also trained a different predictive algorithm (a recurrent neural network, see STAR Methods for additional details) on the APEX-seq data and performed a similar set of experiments, comparing SARS-CoV-2 dominant subcellular residency predictions to human and coronavirus baselines ( Figure S3A /B). abstract: Abstract/Summary SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral RNA could thus play important roles in viral replication and host antiviral immune response. We perform computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes to the human transcriptome and other coronaviruses. We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5’ and 3’ viral untranslated regions contain the strongest, most distinct localization signals. We interpret the mitochondrial residency signal as an indicator of intracellular RNA trafficking with respect to double-membrane vesicles, a critical stage in the coronavirus life cycle. Our computational analysis serves as a hypothesis generation tool to suggest models for SARS-CoV-2 biology and inform experimental efforts to combat the virus. A record of this paper’s Transparent Peer Review process is included in the Supplemental Information. url: https://www.sciencedirect.com/science/article/pii/S2405471220302374?v=s5 doi: 10.1016/j.cels.2020.06.008 id: cord-279616-8gtumtxb author: Wu, Kitty K. title: Posttraumatic Stress after SARS date: 2005-08-17 words: 1746.0 sentences: 86.0 pages: flesch: 55.0 cache: ./cache/cord-279616-8gtumtxb.txt txt: ./txt/cord-279616-8gtumtxb.txt summary: We used 2 Chinese self-report measures to examine features of PTSD, anxiety, and depression in 131 survivors of severe acute respiratory syndrome at 1 month and 3 months after discharge from the hospital. The first category included pre-SARS variables: sex, age, education level, family income, availability of emotional support as indicated by the number of persons with whom one could talk and share worries, and whether one was a healthcare worker. The measures used in the study include the Chinese versions of the Impact of Event Scale -Revised (IES-R) (7, 8) and the Hospital Anxiety and Depression Scale (HADS) (8) (9) (10) . Results of Pearson correlations (Table 2) showed that the level of SaO 2 , the number of persons with whom one could talk and share worries, and the rating on perceived threat were significantly related to various IES-R and HADS subscale scores. abstract: Posttraumatic stress disorder (PTSD) can arise in patients with medical illness. We used 2 Chinese self-report measures to examine features of PTSD, anxiety, and depression in 131 survivors of severe acute respiratory syndrome at 1 month and 3 months after discharge from the hospital. Risk factors associated with psychological distress were identified. url: https://www.ncbi.nlm.nih.gov/pubmed/16102324/ doi: 10.3201/eid1108.041083 id: cord-324938-2lu9z5b2 author: Wu, Li-Ping title: Duration of Antibody Responses after Severe Acute Respiratory Syndrome date: 2007-10-17 words: 1478.0 sentences: 84.0 pages: flesch: 60.0 cache: ./cache/cord-324938-2lu9z5b2.txt txt: ./txt/cord-324938-2lu9z5b2.txt summary: Among 176 patients who had had severe acute respiratory syndrome (SARS), SARS-specific antibodies were maintained for an average of 2 years, and significant reduction of immunoglobulin G–positive percentage and titers occurred in the third year. Both the OD readings (0.93) and positive percentages peaked at 90-120 days; however, the rate of reduction of the average OD readings was much faster, dropping by 22% (0.73) and 40% (0.54) at 1 and 2 years, respectively, after symptom onset (Figure 1) . Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Longitudinal profi le of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus Longitudinal analysis of severe acute respiratory syndrome (SARS) coronavirus-specifi c antibody in SARS patients abstract: Among 176 patients who had had severe acute respiratory syndrome (SARS), SARS-specific antibodies were maintained for an average of 2 years, and significant reduction of immunoglobulin G–positive percentage and titers occurred in the third year. Thus, SARS patients might be susceptible to reinfection >3 years after initial exposure. url: https://www.ncbi.nlm.nih.gov/pubmed/18258008/ doi: 10.3201/eid1310.070576 id: cord-308224-cqi1x92w author: Wu, Lianhua title: Clinical study on the related markers of blood coagulation in the patients with ANFH after SARS date: 2007-10-01 words: 1634.0 sentences: 96.0 pages: flesch: 54.0 cache: ./cache/cord-308224-cqi1x92w.txt txt: ./txt/cord-308224-cqi1x92w.txt summary: The expression of CD31, CD61, CD62p, CD63 and PAC-1 on platelet membrane was measured respectively by flowcytometry, and the plasma prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and fibrinogen (Fbg) were measured by blood clotting instrument in 26 patients with ANFH after SARS and in 17 healthy adults. When patients experienced discomfort or pain at the site of hip-joint four to six months after administration of hormone, their blood samples were taken intravenously under the condition of fasting to measure CD31, CD61, CD62P, CD63, PAC-1 on platelet membrane and coagulation four indices including PT, APTT, Fbg and TT. It was found that, in these patients with ANFH after SARS, the expression of glycoprotein CD31, CD61, CD62P, CD63 and PAC-1 on platelet membrane decreased; coagulation four indices including PT, APTT and TT time were all normal. abstract: The aim of this research was to investigate the blood coagulation function in the patients with avascular necrosis of the femoral head (ANFH) after severe acute respiratory syndrome (SARS). The expression of CD31, CD61, CD62p, CD63 and PAC-1 on platelet membrane was measured respectively by flowcytometry, and the plasma prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and fibrinogen (Fbg) were measured by blood clotting instrument in 26 patients with ANFH after SARS and in 17 healthy adults. The expression of CD31, CD61, CD 62p, CD63 and PAC-1 on platelet membrane in 26 patients was all lower than that in 17 healthy subjects (P < 0.01). The levels of PT, APTT, TT and Fbg in 26 patients were all normal. There is no significant difference (P > 0.05) in those markers between patients and 17 healthy adults. The blood may not be in hypercoagulable state in patients with ANFH after SARS. url: https://doi.org/10.1007/s11684-007-0080-9 doi: 10.1007/s11684-007-0080-9 id: cord-332522-adul9nzf author: Wu, Qingfa title: Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date: 2004-04-02 words: 2810.0 sentences: 143.0 pages: flesch: 62.0 cache: ./cache/cord-332522-adul9nzf.txt txt: ./txt/cord-332522-adul9nzf.txt summary: In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. To compare the sensitivities of these 12 sets of nested primers, serial 10-fold di-lution genome cDNA of BJ01 that reverse transcribed with random primer was used as the template to carry out the nested PCR. abstract: Severe acute respiratory syndrome (SARS) is an acute newly emerged infectious respiratory illness. The etiologic agent of SARS was named ‘SARS-associated coronavirus’ (SARS-CoV) that can be detected with reverse transcription-polymerase chain reaction (RT-PCR) assays. In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Based on the sensitivity and simplicity of results, the no. 73 primer set was chosen as the candidate primer set for clinical diagnoses. To specify the amplicon to minimize false positive results, a Taqman RT-nested PCR system of no. 73 nested primer set was developed. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. url: https://www.ncbi.nlm.nih.gov/pubmed/15109816/ doi: 10.1016/j.jviromet.2004.02.011 id: cord-354824-7fdcu2f0 author: Wu, Renyi title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 words: 9652.0 sentences: 504.0 pages: flesch: 42.0 cache: ./cache/cord-354824-7fdcu2f0.txt txt: ./txt/cord-354824-7fdcu2f0.txt summary: Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. This estimated 20% of patients developing more severe disease with SARS-CoV-2 infection are most likely due to genetics, epigenetics, and or other factors, with dampened innate immune response to fight the virus coupled with enhanced viral load leading to cytokine storm, severe inflammatory/oxidative stress response, and severe lung injury secondary to ARDS. Chloroquine can inhibit the entry of SARS-CoV-2 and prevent virus-cell fusion by interfering with glycosylation of ACE2 receptor and its binding with spike protein, suggesting that chloroquine treatment might be more effective in the early stage of infection, before COVID-19 reduces ACE2 expression and activity [30, 38, 39] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, doubleblinded, phase IIb clinical trial (CloroCovid-19 Study) abstract: The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has presented unprecedented challenges to the healthcare systems in almost every country around the world. Currently, there are no proven effective vaccines or therapeutic agents against the virus. Current clinical management includes infection prevention and control measures and supportive care including supplemental oxygen and mechanical ventilatory support. Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. In this review, we will update and summarize the most common and plausible drugs for the treatment of COVID-19 patients. These drugs and therapeutic agents include antiviral agents (remdesivir, hydroxychloroquine, chloroquine, lopinavir, umifenovir, favipiravir, and oseltamivir), and supporting agents (Ascorbic acid, Azithromycin, Corticosteroids, Nitric oxide, IL-6 antagonists), among others. We hope that this review will provide useful and most updated therapeutic drugs to prevent, control, and treat COVID-19 patients until the approval of vaccines and specific drugs targeting SARS-CoV-2. url: https://doi.org/10.1007/s40495-020-00216-7 doi: 10.1007/s40495-020-00216-7 id: cord-331807-ooym5eh3 author: Wu, Tao title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date: 2020-07-29 words: 556.0 sentences: 48.0 pages: flesch: 51.0 cache: ./cache/cord-331807-ooym5eh3.txt txt: ./txt/cord-331807-ooym5eh3.txt summary: title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA abstract: The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. A rapid, highly sensitive, specific, and simple operational method was needed for the detection of SARS-CoV-2. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. The primers and probe were designed based on the nucleocapsid protein gene (N gene) sequence of SARS-CoV-2. The detection limit was 10 copies per reaction in this assay, which could be conducted within 15 min at a constant temperature (39 °C), without any cross-reactions with other respiratory tract pathogens, such as other coronaviruses. Furthermore, compared with commercial real-time RT-PCR assay, it showed a kappa value of 0.959 (p < 0.001) from 150 clinical specimens. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0042682220301331 doi: 10.1016/j.virol.2020.07.006 id: cord-301303-44sk478e author: Wu, Vin-Cent title: Renal hypouricemia is an ominous sign in patients with severe acute respiratory syndrome date: 2008-02-21 words: 3128.0 sentences: 193.0 pages: flesch: 54.0 cache: ./cache/cord-301303-44sk478e.txt txt: ./txt/cord-301303-44sk478e.txt summary: Conclusion: One fourth of patients with SARS developed hypouricemia, which might result from a defect in renal UA handling and was associated with a high serum IL-8 level. Serum levels of the proinflammatory cytokines IL-6, IL-8, and TNF-␣ were measured in 16 patients (6 hypouricemic, 10 normouricemic) during their UA excretion studies. The inverse correlation between serum UA level and FE UA indicates that the hypouricemia in patients with SARS resulted from an abnormal increase in UA excretion during SARS-CoV infection. 27 Our study showed that the lowest serum UA level occurred days 7 to 9 after fever onset, when the cytokine storm of patients with SARS usually occurred. 19 The present study shows that hypouricemic patients with SARS had a poor outcome, especially in terms of respiratory failure, compared with normouricemic patients. In summary, hypouricemia resulting from abnormal renal urate handling is not rare in patients with SARS-CoV infection and may reflect the severity of disease and predict poor patient outcomes. abstract: Background: The purpose of this study is to determine the incidence and significance of hypouricemia in patients with severe acute respiratory syndrome (SARS). Pulmonary lesions in patients with SARS are thought to result from proinflammatory cytokine dysregulation. Acute renal failure has been reported in patients with SARS, but whether cytokines can injure renal tubules is unknown. Methods: Sixty patients diagnosed with SARS in Taiwan in April 2003 were studied. Patients were identified as hypouricemic when their serum uric acid (UA) level was less than 2.5 mg/dL (<149 μmol/L) within 15 days after fever onset. Urine UA and creatinine levels were available for 43 patients; the serum cytokines interleukin-6 (IL-6), IL-8, and tumor necrosis factor-α (TNF-α) were measured in 16 patients. Results: Sixteen patients (26.7%) had hypouricemia (UA, 1.68 ± 0.52 mg/dL [100 ± 31 μmol/L]). No differences in age, sex, symptoms, vital signs, hemogram, or other biochemistry data existed between the hypouricemic and normouricemic groups. Fractional excretion (FE) of UA (FE(UA)) in 12 hypouricemic patients was 39.6% ± 23.4%, significantly greater than that of 31 normouricemic patients (16.4% ± 11.4%; P < 0.0001). After adjustments for age and sex, high FE(UA) was significantly associated with the lowest blood oxygenation (P = 0.001; r = −0.624). The number of catastrophic outcomes (endotracheal intubation and/or death) adjusted for older age and sex showed that hypouremic patients had an odds ratio of 10.57 (confidence interval, 2.33 to 47.98; P = 0.002). Kaplan-Meier curves for catastrophic outcome–free results showed significant differences between patients with normouricemia or hypouricemia (P = 0.01). Serum IL-8 levels correlated significantly with FE(UA) (P < 0.001; r = 0.785) and inversely with serum UA level (P = 0.044; r = −0.509); neither IL-6 nor TNF-α level showed such correlations. Conclusion: One fourth of patients with SARS developed hypouricemia, which might result from a defect in renal UA handling and was associated with a high serum IL-8 level. Renal hypouricemia is an ominous sign in patients with SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15696447/ doi: 10.1053/j.ajkd.2004.09.031 id: cord-351269-xjy6chia author: Wu, Y title: Coronavirus disease 2019 among pregnant Chinese women: case series data on the safety of vaginal birth and breastfeeding date: 2020-05-26 words: 3516.0 sentences: 208.0 pages: flesch: 50.0 cache: ./cache/cord-351269-xjy6chia.txt txt: ./txt/cord-351269-xjy6chia.txt summary: METHODS: We collected clinical data, vaginal secretions, stool specimens and breast milk from SARS‐CoV‐2‐infected women during different stages of pregnancy and collected neonatal throat and anal swabs. 2 Previous studies have suggested that SARS-CoV infection during pregnancy may carry severe complications including maternal death, spontaneous miscarriage, preterm delivery and intrauterine growth restriction; 3 and MERS has been associated with intrauterine fetal demise and stillbirth. All pregnant women with SARS-CoV-2 admitted to Renmin Hospital of Wuhan University in China between 31 We extracted demographic information, clinical course, laboratory indices and imaging results of infected pregnant women from the medical records, maternal throat swabs were collected upon admission. None of the newborns delivered in our study was infected, a result consistent with previous reports (e.g. negative tests for the novel coronavirus nucleic acid in pharyngeal swab samples from 19 neonates born to mothers with COVID-19 pneumonia, and for three placental samples 13, 14 ) . abstract: OBJECTIVE: To assess whether vaginal secretions and breast milk of women with coronavirus disease 2019 (COVID‐19) contain severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). DESIGN: Single centre cohort study. SETTING: Renmin Hospital of Wuhan University, Wuhan, Hubei province, China. POPULATION: We studied 13 SARS‐CoV‐2‐infected pregnant women diagnosed between 31 January and 9 March 2020. METHODS: We collected clinical data, vaginal secretions, stool specimens and breast milk from SARS‐CoV‐2‐infected women during different stages of pregnancy and collected neonatal throat and anal swabs. MAIN OUTCOMES AND MEASURES: We assessed viral presence in different biosamples. RESULTS: Of the 13 women with COVID‐19, five were in their first trimester, three in their second trimester and five in their third trimester. Of the five women in their third trimester who gave birth, all delivered live newborns. Among these five deliveries, the primary adverse perinatal outcomes included premature delivery (n = 2) and neonatal pneumonia (n = 2). One of nine stool samples was positive; all 13 vaginal secretion samples, and five throat swabs and four anal swabs collected from neonates, were negative for the novel coronavirus. However, one of three samples of breast milk was positive by viral nucleic acid testing. CONCLUSIONS: In this case series of 13 pregnant women with COVID‐19, we observed negative viral test results in vaginal secretion specimens, suggesting that a vaginal delivery may be a safe delivery option. However, additional research is urgently needed to examine breast milk and the potential risk for viral contamination. TWEETABLE ABSTRACT: New evidence for the safety of vaginal delivery and breastfeeding in pregnant women infected with SARS‐CoV‐2, positive viral result in a breast‐milk sample. url: https://www.ncbi.nlm.nih.gov/pubmed/32369656/ doi: 10.1111/1471-0528.16276 id: cord-303143-4sksz6xz author: Wu, Y. P. title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients date: 2009-03-19 words: 4222.0 sentences: 243.0 pages: flesch: 50.0 cache: ./cache/cord-303143-4sksz6xz.txt txt: ./txt/cord-303143-4sksz6xz.txt summary: title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients The diagnosis was further confirmed using the ELISA assay for plasma SARS-CoV protein N IgG measurement (described below). Anti-SARS-CoV N protein IgG levels were [median (95% CI)] 0.97 (0.81-1.58) versus 0.05 (0.04-0.06) and 0.05 (0.04-0.07) units (OD450) in patients with SARStype pneumonia, patients with CAP (S. A significant correlation between plasma SP-D and anti-SARS-CoV N protein IgG measured in SARS patients was observed using linear regression (r 2 = 0.5995, P = 0.02) (Fig. 5) . This was further confirmed by the measures of lung injury reported in the present study showing no significant differences in pulmonary infiltrate, chest radiographic score, thrombocytopenia and leucocytopenia between SARS patients and the bacterial-type pneumonia patients. Plasma surfactant protein levels and clinical outcomes in patients with acute lung injury abstract: Pulmonary SP‐D is a defence lectin promoting clearance of viral infections. SP‐D is recognized to bind the S protein of SARS‐CoV and enhance phagocytosis. Moreover, systemic SP‐D is widely used as a biomarker of alveolar integrity. We investigated the relation between plasma SP‐D, SARS‐type pneumonia and the SARS‐specific IgG response. Sixteen patients with SARS, 19 patients with community‐acquired pneumonia (CAP) (Streptococcus pneumonia) and 16 healthy control subjects were enrolled in the study. Plasma SP‐D and anti‐SARS‐CoV N protein IgG were measured using ELISA. SP‐D was significantly elevated in SARS‐type pneumonia [median (95% CI), 453 (379–963) ng/ml versus controls 218 (160–362) ng/ml, P < 0.05] like in patients with CAP. SP‐D significantly correlated with anti‐SARS‐CoV N protein IgG (r (2) = 0.5995, P = 0.02). The possible re‐emergence of SARS or SARS‐like infections suggests a need for minimal traumatic techniques for following the alveolar compartment, e.g. during testing of antivirals. We suggest that monitoring systemic SP‐D may be useful in monitoring the alveolar integrity in SARS‐type pneumonia. The significant correlation between plasma SP‐D and anti‐SARS‐CoV‐specific antibodies support the role for SP‐D in interlinking innate and adaptive immune pathways. url: https://doi.org/10.1111/j.1365-3083.2009.02245.x doi: 10.1111/j.1365-3083.2009.02245.x id: cord-350130-c4u0gxp5 author: Wu, Yi-Chi title: The outbreak of COVID-19: An overview date: 2020-02-12 words: 3325.0 sentences: 228.0 pages: flesch: 57.0 cache: ./cache/cord-350130-c4u0gxp5.txt txt: ./txt/cord-350130-c4u0gxp5.txt summary: In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus#, emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The 2019-nCoV, SARS-CoV, and bat SARS-like CoV belong to Abstract: In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus # , emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The virus has a preferential tropism to human airway epithelial cells and the cellular receptor, The first confirmed nCoV case in Wuhan (no Huanan seafood market exposure) December 10 abstract: In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus#, emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The disease is officially named as Coronavirus Disease-2019 (COVID-19, by WHO on February 11, 2020). It is also named as Severe Pneumonia with Novel Pathogens on January 15, 2019 by the Taiwan CDC, the Ministry of Health and is a notifiable communicable disease of the fifth category. COVID-19 is a potential zoonotic disease with low to moderate (estimated 2%–5%) mortality rate. Person-to-person transmission may occur through droplet or contact transmission and if there is a lack of stringent infection control or if no proper personal protective equipment available, it may jeopardize the first-line healthcare workers. Currently, there is no definite treatment for COVID-19 although some drugs are under investigation. To promptly identify patients and prevent further spreading, physicians should be aware of the travel or contact history of the patient with compatible symptoms. url: https://doi.org/10.1097/jcma.0000000000000270 doi: 10.1097/jcma.0000000000000270 id: cord-354529-k8p2u7iq author: Wu, Yongran title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 words: 3753.0 sentences: 223.0 pages: flesch: 57.0 cache: ./cache/cord-354529-k8p2u7iq.txt txt: ./txt/cord-354529-k8p2u7iq.txt summary: Clinical information of patients was collected from the electronic medical information system of Jinyintan Hospital, including the following factors: demographic data; date of symptom onset, admission, first CP infusion and discharge; laboratory data before and after infusion of CP, including white blood cell count, neutrophil count, lymphocyte count, liver and kidney function test, and inflammatory factors such as high sensitive C-reaction protein (HsCRP); results of SARS-CoV-2 test and cycle threshold value (Ct value) of quantitative reverse transcription-polymerase chain reaction; patients'' status and treatments before or after the CP therapy, including the vital signs, anti-virus therapy, oxygen therapy, and other treatments; total volume dose of CP; pulmonary imaging examination data; information on complications such as transfusion-related adverse reactions. Clinical Benefit and Outcome of Patients with Prolonged Positivity of SARS-CoV-2 RNA after CP Therapy As shown in Table 3 , the median and interquartile ranged total volume of CP transfusion was 400 (200-400) mL in EN group and 400 (400-800) mL in LN group. abstract: Convalescent plasma therapy has been implemented in a few cases of severe coronavirus disease 2019. No report about convalescent plasma therapy in treating patients with prolonged positivity of SARS-CoV-2 RNA has been published. In this study, we conducted a retrospective observational study in 27 patients with prolonged positivity of SARS-CoV-2 RNA, the clinical benefit of convalescent plasma therapy were analyzed. qRT-PCR test of SARS-CoV-2 RNA turned negative (≤ 7 days) in a part of patients (early negative group, n = 15) after therapy, others (late negative group, n = 12) turned negative in more than 7 days. Pulmonary imaging improvement was confirmed in 7 patients in early negative group and 8 in late negative group after CP therapy. Viral load decreased in early negative group compared with late negative group at day 3, 5, 7 after implementing convalescent plasma therapy. Patients in early negative group had a shorter median length of hospital stay. In conclusion, convalescent plasma therapy might help eliminate virus and shorten length of hospital stay in patients with prolonged positivity of SARS-CoV-2 RNA. url: https://www.ncbi.nlm.nih.gov/pubmed/32865701/ doi: 10.1007/s12250-020-00281-8 id: cord-302485-hhsa76k8 author: Wu, Yuntao title: SARS-CoV-2 is an appropriate name for the new coronavirus date: 2020-03-06 words: 853.0 sentences: 51.0 pages: flesch: 59.0 cache: ./cache/cord-302485-hhsa76k8.txt txt: ./txt/cord-302485-hhsa76k8.txt summary: be significantly attenuated to the point of becoming a new low-pathogenic or non-patho genic virus, such attenuated viral isolates could be named as lowpathogenic human coronaviruses, such as LPH-CoV. We believe that the naming of SARS-CoV-2 by the Coronavirus Study Group is aligned with the goals of the International Committee on Taxonomy of Viruses to facilitate good practice and scientific exchange. We have read with great interest the Correspondence by Shibo Jiang and colleagues, 1 in which they propose a name change for the newly emerged coronavirus, 2 which was recently designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. 4 Through DivErsity pArtitioning by hieRarchical Clustering-based analyses, 5 the newly emerged coronavirus was deemed not sufficiently novel but is a sister virus to SARS-CoV, the primary viral isolate defining the species. abstract: nan url: https://doi.org/10.1016/s0140-6736(20)30557-2 doi: 10.1016/s0140-6736(20)30557-2 id: cord-268645-5op2m7pu author: Wu, Zhiqiang title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 words: 5949.0 sentences: 277.0 pages: flesch: 49.0 cache: ./cache/cord-268645-5op2m7pu.txt txt: ./txt/cord-268645-5op2m7pu.txt summary: However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . abstract: Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs. url: https://www.ncbi.nlm.nih.gov/pubmed/26262818/ doi: 10.1038/ismej.2015.138 id: cord-288756-r96izsyq author: Wu, Zhiqiang title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date: 2016-02-15 words: 2253.0 sentences: 108.0 pages: flesch: 55.0 cache: ./cache/cord-288756-r96izsyq.txt txt: ./txt/cord-288756-r96izsyq.txt summary: title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus Several lineage B betacoronaviruses termed severe acute respiratory syndrome (SARS)–like CoVs (SL-CoVs) were identified from Rhinolophus bats in China. The nucleotide sequences in the ORF1ab, E, M, and N genes in these bat-borne lineage B beta-CoVs are 89%-93% similar to those in the SARS-CoVs from humans. Furthermore, genetic evidence for the identical ORF8 is needed to trace the origin of SARS-CoVs to bat SL-CoVs. All genome sequences were submitted to GenBank. In this study, a systematic survey of bat-borne CoVs was performed using bat virome data from throughout China, described in our previous report [6] , to obtain genetic evidence indicating the source of SARS-CoVs. Fifteen SL-CoVs were identified from 9 bat species in 11 provinces ( Figure 1A ) [6] . sinicus have nearly identical ORF8s and similar backbone genes to those in SARS-CoVs in Yunnan and Guangxi provinces. abstract: Several lineage B betacoronaviruses termed severe acute respiratory syndrome (SARS)–like CoVs (SL-CoVs) were identified from Rhinolophus bats in China. These viruses are characterized by a set of unique accessory open reading frames (ORFs) that are located between the M and N genes. Among unique accessory ORFs, ORF8 is most hypervariable. In this study, the ORF8s of all SL-CoVs were classified into 3 types, and, for the first time, it was found that very few SL-CoVs from Rhinolophus sinicus have ORF8s that are identical to that of human SARS-CoV. This finding provides new genetic evidence for Chinese horseshoe bats as the source of human SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/26433221/ doi: 10.1093/infdis/jiv476 id: cord-308576-iw8oobbe author: Wuxing, Dai title: Expression and purification of SARS coronavirus membrane protein date: 2004 words: 1785.0 sentences: 130.0 pages: flesch: 67.0 cache: ./cache/cord-308576-iw8oobbe.txt txt: ./txt/cord-308576-iw8oobbe.txt summary: To construct a recombinant plasmid Pet23a-M, the gene encoding severe acute respiratory syndrome (SARS) coronavirus membrane protein was amplified by RT-PCR and cloned into the expression plasmid Pet23a. To screen and prepare effective SARS virus vaccine and diagnostic antigens, we designed a pair of primers to amplify the gene encoding SARS coronavirus membrane protein and cloned it into an expression plasmid Pet23a. Coli BI.21 ( D E 3 ) and induced by I P T G , Western-blot showed that the expressed 27 kD protein which was characterized by SDS-PAGE and purified by metal chelated chromatography could react with antibodies in sera of SARS patients during convalescence, demonstrating the recombinant protein possessed the biological activity of membrane protein. abstract: To construct a recombinant plasmid Pet23a-M, the gene encoding severe acute respiratory syndrome (SARS) coronavirus membrane protein was amplified by RT-PCR and cloned into the expression plasmid Pet23a. Results of restriction endonuclease analysis, PCR detection and DNA sequencing analysis revealed that the cloned DNA sequence was the same as that reported. The recombinants were transformed intoEscherichia coli (E. Coli) BL21 (DE3) and induced by Isopropyl-β-D-thiogalactopyranoside (IPTG). The expression of 27 kD (1 kD=0.992 1 ku) protein was detected by SDS-PAGE and pured by metal chelated chromatography. Results of Western-blot showed that this expressed protein could react with antibodies in sera of SARS patients during convalescence. This provided the basis for the further study on SARS virus vaccine and diagnostic agents. url: https://www.ncbi.nlm.nih.gov/pubmed/15641679/ doi: 10.1007/bf02831095 id: cord-348391-xytmq2f2 author: Wyganowska-Swiatkowska, Marzena title: Influence of Herbal Medicines on HMGB1 Release, SARS-CoV-2 Viral Attachment, Acute Respiratory Failure, and Sepsis. A Literature Review date: 2020-06-30 words: 8077.0 sentences: 461.0 pages: flesch: 41.0 cache: ./cache/cord-348391-xytmq2f2.txt txt: ./txt/cord-348391-xytmq2f2.txt summary: While long term proteinase and ACE-2 inhibition could be detrimental to cellular function and bodily homeostasis, targeted treatment partially reducing the effectiveness of coronavirus S protein attachment to the ACE2 or to the priming proteinase could have the potential to drop the SARS-CoV-2 viral load before a state of septic shock is reached at the peak of infection. Aspalathin and nothofagin extracted from Rooibos have been shown to effectively inhibit LPS-induced release of HMGB1, and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules [124] . The effect and mechanism of salidroside on sepsis-induced acute lung injury is mediated by the inhibition of inflammatory responses and HMGB1 production in bacterial LPS-treated macrophages and mice. Study has shown that pelargonidin (PEL) had effectively inhibited LPS-induced release of HMGB1 and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules. abstract: By attaching to the angiotensin converting enzyme 2 (ACE2) protein on lung and intestinal cells, Sudden Acute Respiratory Syndrome (SARS-CoV-2) can cause respiratory and homeostatic difficulties leading to sepsis. The progression from acute respiratory failure to sepsis has been correlated with the release of high-mobility group box 1 protein (HMGB1). Lack of effective conventional treatment of this septic state has spiked an interest in alternative medicine. This review of herbal extracts has identified multiple candidates which can target the release of HMGB1 and potentially reduce mortality by preventing progression from respiratory distress to sepsis. Some of the identified mixtures have also been shown to interfere with viral attachment. Due to the wide variability in chemical superstructure of the components of assorted herbal extracts, common motifs have been identified. Looking at the most active compounds in each extract it becomes evident that as a group, phenolic compounds have a broad enzyme inhibiting function. They have been shown to act against the priming of SARS-CoV-2 attachment proteins by host and viral enzymes, and the release of HMGB1 by host immune cells. An argument for the value in a nonspecific inhibitory action has been drawn. Hopefully these findings can drive future drug development and clinical procedures. url: https://doi.org/10.3390/ijms21134639 doi: 10.3390/ijms21134639 id: cord-102842-51n5mnjb author: Węglarz-Tomczak, Ewelina title: Ebselen as a highly active inhibitor of PLProCoV2 date: 2020-05-17 words: 3320.0 sentences: 196.0 pages: flesch: 56.0 cache: ./cache/cord-102842-51n5mnjb.txt txt: ./txt/cord-102842-51n5mnjb.txt summary: In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range. Here, we demonstrate that ebselen inhibits activity of the essential viral enzyme, namely, papain-like protease (PL pro ) from SARS-CoV-2 (PL pro CoV2) in low micromolar range. We applied ebselen as a possible inhibitor and, indeed, it suppresses PL Pro activity from CoV2 with inhibition constants approximately equal 2 μM (Table 1 and Figure 3 ). Our results were further illustrated by the use of molecular modeling to study the binding mode of ebselen with PL Pro SARS ( Figure 4 ) and PL Pro CoV2 (Figure 4 and 5) . This study confirmed our primary assumption that ebselen binds to the PL Pro CoV2 active site covalently and, thus, convinced us of our hypothesis about an irreversible mechanism of inhibition. abstract: Since December 2019 a novel a coronavirus identified as SARS-CoV-2 or COV2 has been spreading around the world. On the 16th of May around 4.5 million people got infected and over 300,000 died due to the infection of COV2. The effective treatment remains a challenge. Targeted therapeutics are still under investigation. The papain-like protease (PLPro) from the human SARS-CoV-2 coronavirus is a cysteine protease that plays a critical role in virus replication. Its activity is required to process the viral polyprotein into functional, mature subunits. Moreover, COV2 uses this enzyme to modulate the host’s immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. In this work, we discovered that ebselen, a synthetic organoselenium drug molecule with anti-inflammatory, anti-oxidant and cytoprotective activity in mammalian cells and cytotoxicity in lower organisms, is a highly active inhibitor of PLProCoV2. We proved that ebselen is a covalent, fast-binding inhibitor of PLProCoV2 exhibiting a low micromolar potency. Furthermore, we identified a difference between PLPro from SARS-CoV-1 (the corona virus which caused the 2002–2004 outbreak, SARS) and SARS-CoV-2 that allows to explain the difference in dynamics of the replication, and, thus, the disease progression. Namely, we present that they show differences in the binding affinity of substrates that we observed through kinetics and molecular docking studies. Using a novel Approximate Bayesian Computation method we were able to find kinetic constants for both enzymes. Molecular modeling study on the structure of the active site and binding mode of the ebselen with SARS and COV2 showed also significant differences that could explain our observation that ebselen is less active and slower bounding with SARS than COV2. In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range. url: https://doi.org/10.1101/2020.05.17.100768 doi: 10.1101/2020.05.17.100768 id: cord-355811-aq7p1uxo author: Węglarz-Tomczak, Ewelina title: Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date: 2020-05-21 words: 2008.0 sentences: 151.0 pages: flesch: 57.0 cache: ./cache/cord-355811-aq7p1uxo.txt txt: ./txt/cord-355811-aq7p1uxo.txt summary: A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). In recent studies, peptide analogues [11] and ebselen [12] have been identified as highly active inhibitors for PL pro . We show that some of them indeed possess higher activity than ebselen, that has been recently reported as PL pro CoV2 inhibitor [12] , and, thus, could be considered as novel potential drugs against COVID-19. In this work, we used the ebselen derivatives/analogues library and performed a comprehensive inhibition study of PL pro CoV2. In the case of PL pro SARS, none of the presented ebselen derivatives was able to block the enzyme. Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design Ebselen as a highly active inhibitor of PL pro CoV2 abstract: A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). This cysteine protease, being responsible for the hydrolysis of peptide bonds between specific amino acids, plays a critical role in CoV2 replication and in assembly of new viral particles within human cells. The activity of the PLpro CoV2 is essential for the progression of coronavirus disease 2019 (COVID-19) and it constitutes a key target for the development of anti-COVID-19 drugs. Here, we identified four strong inhibitors that bind favorably to the PLpro CoV2 with the IC50 in the nanomolar range. url: https://doi.org/10.1101/2020.05.20.107052 doi: 10.1101/2020.05.20.107052 id: cord-286130-4f7otdx1 author: Xavier, Joilson title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing date: 2020-08-11 words: 4670.0 sentences: 233.0 pages: flesch: 50.0 cache: ./cache/cord-286130-4f7otdx1.txt txt: ./txt/cord-286130-4f7otdx1.txt summary: title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing To better understand the recent epidemic in the second most populous state in southeast Brazil Minas Gerais (MG) we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Initial phylogenetic analysis using the first two SARS-CoV-2 complete genomes isolated in São Paulo from travellers returning from Italy revealed two independent introductions into the country relative to the data set available at that time [13] . Herein, we present a summary of epidemiological data and the generation and analysis of 40 new SARS-CoV-2 genome sequences isolated from clinical samples of confirmed cases from MG. abstract: The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country. To better understand the recent epidemic in the second most populous state in southeast Brazil - Minas Gerais (MG) - we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into MG. Epidemiological estimates of the reproductive number (R) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in R from the first reported case to the end of April 2020. The estimated date of SARS-CoV-2 introduction into Brazil was consistent with epidemiological data from the first case of a returned traveller from Lombardy, Italy. These findings highlight the nature of the COVID-19 epidemic in MG and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens.. url: https://doi.org/10.1080/22221751.2020.1803146 doi: 10.1080/22221751.2020.1803146 id: cord-317593-tajy3p9e author: Xi, AIqi title: Epidemiological and clinical characteristics of discharged patients infected with SARS-CoV-2 on the Qinghai plateau date: 2020-04-29 words: 3146.0 sentences: 212.0 pages: flesch: 56.0 cache: ./cache/cord-317593-tajy3p9e.txt txt: ./txt/cord-317593-tajy3p9e.txt summary: Since the outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, a series of confirmed cases of COVID-19 were found on the Qinghai-Tibet plateau. Coronavirus disease 2019 , caused by infection with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, Hubei, China in December 2019 [1] [2] [3] [4] and rapidly spread worldwide. For this retrospective study, we enrolled all 18 patients infected with SARS-CoV-2 from the hospitals designated for treatment by the Health Commission of Qinghai Province from Jan 21 to April 6, 2020. Convalescent plasma has been used to improve the survival rate of patients with severe acute respiratory syndrome (SARS) coronavirus infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China abstract: Since the outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, a series of confirmed cases of COVID-19 were found on the Qinghai-Tibet plateau. We aimed to describe the epidemiological, clinical characteristics, and outcomes of all confirmed cases in Qinghai, a province at high altitude. With efficient measures to stop the spread of coronavirus, no new cases were found in Qinghai Province for 60 consecutive days between Feb 6 and April 6, 2020. Of all 18 patients with confirmed SARS-CoV-2 infection, 15 patients comprising 4 transmission clusters were identified. Three patients were infected by direct contact without travel history to Wuhan. Seven patients were asymptomatic on admission. Of 18 patients, 10 patients showed bilateral pneumonia and 2 patients showed no abnormalities. Three patients with comorbidities such as hypertension, liver diseases or diabetes developed severe illness. High C-reactive protein levels and elevations of both ALT and AST were observed in 3 severely ill patients on admission. All 18 patients were eventually discharged, including the 3 severe patients who recovered after treatment with non-invasive mechanical ventilation, convalescent plasma and other therapies. Our findings confirmed human-to-human transmission of SARS-CoV-2 in clusters. The strategies of early diagnosis, early isolation, and early treatment are important to prevent the spread of COVID-19 and improve the cure rate. Patients with comorbidities are more likely to develop severe illness and could benefit from convalescent plasma transfusion. url: https://doi.org/10.1101/2020.04.23.20077644 doi: 10.1101/2020.04.23.20077644 id: cord-355306-fj8utkfe author: Xia Chao, Yin title: The role of IgA in COVID-19 date: 2020-05-23 words: 832.0 sentences: 52.0 pages: flesch: 51.0 cache: ./cache/cord-355306-fj8utkfe.txt txt: ./txt/cord-355306-fj8utkfe.txt summary: Secretory IgA plays a crucial role in the immune defense of mucosal surfaces, the first point of entry of SARS-CoV-2. Reported serology tests focus on IgM, IgG and total immunoglobulins although IgA is playing an important role in mucosal immunity. As an immune barrier, secretory IgA can neutralize SARS-CoV-2 before they reach and bind the epithelial cells (Figure1) . Mucosal vaccine targeting SARS-CoV-2 RBD given via oral or nasal targets to induce secretion of IgA within the mucosa may be a therapeutic strategy for preventing COVID-19 development. Plasma cells, which can be the target of mucosal vaccine, produce IgA and secreted into the mucus where they meet and neutralize the invaded virus through binding to the Spike protein on the surface of SARS-Cov-2. Other neutralization antibodies can also bind to SARS-Cov-2 to prevent it from infecting other cells. abstract: nan url: https://doi.org/10.1016/j.bbi.2020.05.057 doi: 10.1016/j.bbi.2020.05.057 id: cord-280518-2tl0mtb8 author: Xia, Jianhua title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection date: 2020-03-12 words: 1359.0 sentences: 108.0 pages: flesch: 60.0 cache: ./cache/cord-280518-2tl0mtb8.txt txt: ./txt/cord-280518-2tl0mtb8.txt summary: title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. On 7 January 2020, the Chinese Center for Disease Control and Prevention isolated and confirmed this pathogen as a novel type of coronavirus through a throat swab. Study Group of the International Committee on Taxonomy of Viruses named 2019-nCoV severe acute respiratory syndrome-related coronavirus 2, or SARS-CoV-2. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection abstract: OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. At an interval of 2 to 3 days, tear and conjunctival secretions were collected twice with disposable sampling swabs for reverse‐transcription polymerase chain reaction (RT‐PCR) assay. RESULTS: Twenty‐one common‐type and nine severe‐type NCP patients were enrolled. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. Fifty‐eight samples from other patents were all negative. CONCLUSION: We speculate that SARS‐CoV‐2 may be detected in the tears and conjunctival secretions in NCP patients with conjunctivitis. url: https://doi.org/10.1002/jmv.25725 doi: 10.1002/jmv.25725 id: cord-324926-3c5ab73l author: Xia, Shuai title: A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike date: 2019-04-10 words: 10849.0 sentences: 515.0 pages: flesch: 55.0 cache: ./cache/cord-324926-3c5ab73l.txt txt: ./txt/cord-324926-3c5ab73l.txt summary: Therefore, it is reasonable to speculate that HR1 could also be a good target for the development of fusion inhibitors against highly pathogenic HCoVs. We and others have reported that peptides derived from the HR2 regions of SARS-CoV and MERS-CoV S proteins can competitively inhibit viral 6-HB formation, thereby preventing viral fusion and entry into host cells (18, 27) . Moreover, structural studies of EK1 in complex with HR1s from different HCoVs explain the conserved basis for the HR1-EK1 interaction, further indicating that HR1 region could serve as a promising target site for the development of broad-spectrum pan-CoV fusion inhibitors. On the other hand, HR2P peptides derived from the two -HCoVs, i.e., 229E and NL63, showed potent and broad inhibitory activity against -HCoV S-mediated cell-cell fusion with IC 50 values ranging from 0.13 to 0.51 M or from 0.21 to 0.56 M, respectively, but no effective inhibitory activity against -HCoVs (including MERS-CoV, SARS-CoV, and OC43) S-mediated fusion ( Fig. 1D and table S1 ). abstract: Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site. url: https://www.ncbi.nlm.nih.gov/pubmed/30989115/ doi: 10.1126/sciadv.aav4580 id: cord-329186-0eoz4npg author: Xia, Shuai title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin date: 2020-06-12 words: 1742.0 sentences: 112.0 pages: flesch: 64.0 cache: ./cache/cord-329186-0eoz4npg.txt txt: ./txt/cord-329186-0eoz4npg.txt summary: title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin It has been speculated that RRAR, a unique furin-like cleavage site (FCS) in the spike protein (S), which is absent in other lineage B βCoVs, such as SARS-CoV, is responsible for its high infectivity and transmissibility. Then, by calculating the ratio of the fused cells, we can assess the fusogenic capacity of the S protein in the presence or absence of exogenous trypsin or human airway trypsin-like protease (HAT). Next, we compared the fusogenic capacity of SARS-CoV-2-S, SARS-CoV-S and their mutants via an S-mediated cell-cell fusion assay in the absence of exogenous trypsin or human airway trypsin-like protease (HAT). © The Author(s) 2020 Fig. 1 The function of furin cleavage site in SARS-CoV-2-S mediated fusion. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion abstract: nan url: https://doi.org/10.1038/s41392-020-0184-0 doi: 10.1038/s41392-020-0184-0 id: cord-298734-h286m32c author: Xia, Siyu title: Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury date: 2020-06-29 words: 4766.0 sentences: 302.0 pages: flesch: 53.0 cache: ./cache/cord-298734-h286m32c.txt txt: ./txt/cord-298734-h286m32c.txt summary: title: Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury In this study, we successfully established long term cultures of normal human kidney proximal tubule epithelial cells (KPTECs) in 2D and 3D culture systems using conditional reprogramming (CR) and organoids techniques. Due to the lack of specific detection of ACE2 mRNA and protein expression in human kidney tubule cells, it is hard to confirm the direct infection of SARS-CoV-2. In this study, we firstly established long term cell cultures of KPTECs using 2D CR and 3D organoids technologies, which maintained the lineage function, and the ability to differentiate and repair DNA damage. In terms of the questions above, we need model systems to study infection of SARS-CoVs in ACE2 expressing cell types, especially in kidney epithelial cells (Hamming et al. abstract: The mechanism of how SARS-CoV-2 causes severe multi-organ failure is largely unknown. Acute kidney injury (AKI) is one of the frequent organ damage in severe COVID-19 patients. Previous studies have shown that human renal tubule cells could be the potential host cells targeted by SARS-CoV-2. Traditional cancer cell lines or immortalized cell lines are genetically and phenotypically different from host cells. Animal models are widely used, but often fail to reflect a physiological and pathogenic status because of species tropisms. There is an unmet need for normal human epithelial cells for disease modeling. In this study, we successfully established long term cultures of normal human kidney proximal tubule epithelial cells (KPTECs) in 2D and 3D culture systems using conditional reprogramming (CR) and organoids techniques. These cells had the ability to differentiate and repair DNA damage, and showed no transforming property. Importantly, the CR KPTECs maintained lineage function with expression of specific transporters (SLC34A3 and cubilin). They also expressed angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoV and SARS-CoV-2. In contrast, cancer cell line did not express endogenous SLC34A3, cubilin and ACE2. Very interestingly, ACE2 expression was around twofold higher in 3D organoids culture compared to that in 2D CR culture condition. Pseudovirion assays demonstrated that SARS-CoV spike (S) protein was able to enter CR cells with luciferase reporter. This integrated 2D CR and 3D organoid cultures provide a physiological ex vivo model to study kidney functions, innate immune response of kidney cells to viruses, and a novel platform for drug discovery and safety evaluation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-020-00253-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12250-020-00253-y doi: 10.1007/s12250-020-00253-y id: cord-262844-qeheeqe3 author: Xia, Xuhua title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date: 2020-04-14 words: 3305.0 sentences: 204.0 pages: flesch: 53.0 cache: ./cache/cord-262844-qeheeqe3.txt txt: ./txt/cord-262844-qeheeqe3.txt summary: The zinc finger antiviral protein (ZAP, known as ZC3HAV1 in mammals or hZAP in human), a key component in mammalian interferon-mediated immune response, binds specifically to CpG dinucleotides in viral RNA genomes via its RNA-binding domain (Meagher et al., 2019) . If a coronavirus infects a different host tissue with different ZAP abundance, then its RNA genome will experience different selection pressure against its CpG. The most striking pattern in Fig. 1 is an isolated but dramatic shift in the lineage leading to BatCoV RaTG13 which was reported (Zhou et al., 2020) (Theys et al., 2018) , but also in experimentally CpG dinucleotide-enriched viral genomes (Antzin-Anduetza et al., 2017; Burns et al., 2009; Fros et al., 2017; Trus et al., 2019; Tulloch et al., 2014; Wasson et al., 2017) . To search for a mammalian host with the potential to select viral lineages with low Poder, 2011; Pratelli, 2006) , have genomic ICpG and GC% values similar to those observed in SARS-CoV-2 and BatCoV RaTG13 (Fig. 3A) . abstract: Wild mammalian species, including bats, constitute the natural reservoir of Betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. I show that SARS-CoV-2 has the most extreme CpG deficiency in all known Betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (Alphacoronavirus) as possessing the most extreme CpG deficiency, comparable to that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts. url: https://www.ncbi.nlm.nih.gov/pubmed/32289821/ doi: 10.1093/molbev/msaa094 id: cord-275250-ilmgy7ce author: Xia, Yong title: Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date: 2020-05-17 words: 728.0 sentences: 52.0 pages: flesch: 63.0 cache: ./cache/cord-275250-ilmgy7ce.txt txt: ./txt/cord-275250-ilmgy7ce.txt summary: As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. abstract: nan url: https://api.elsevier.com/content/article/pii/S1201971220303490 doi: 10.1016/j.ijid.2020.05.042 id: cord-293503-e7be12qb author: Xiang, Chao title: CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation date: 2020-08-15 words: 3312.0 sentences: 193.0 pages: flesch: 50.0 cache: ./cache/cord-293503-e7be12qb.txt txt: ./txt/cord-293503-e7be12qb.txt summary: COVID-19 leads to respiratory infections similar to those of SARS and MERS, causing pneumonia, severe acute respiratory syndrome, kidney failure, and even death. The CT image characteristics were recorded as follows: (a) lesion''s location (segment), (b) morphology (patchy, nodular, and linear), (c) distribution (single or multiple, peripheral or/and central), (d) type (ground-glass opacity, consolidation, and linear opacity), (e) pattern (reticulation, parenchymal bands, crazy-paving, and interlobular thickening), (f) atelectasis, (g) cavitation, (h) pleural effusion, (i) hilar or mediastinal lymphadenopathy, (j) bronchiectasis, and (k) air bronchogram. Although a patient with exposure history may be asymptomatic and obtained negative results of CT findings and viral nucleic acid test at initial presentation, the potential infection cannot be totally excluded, and performing repeating CT scan and coronavirus RNA test is needed. Ground-glass opacity and consolidation with multiple, bilateral, and lower lobe distribution are the main features of COVID-19 pneumonia at initial CT scan. abstract: BACKGROUND: COVID-19 first broke out in China and spread rapidly over the world. OBJECTIVES: To describe the CT features of COVID-19 pneumonia and to share our experience at initial diagnoses. Patients and Methods. Data from 53 patients (31 men, 22 women; mean age, 53 years; age range, 16-83 years) with confirmed COVID-19 pneumonia were collected. Their complete clinical data was reviewed, and their CT features were recorded and analyzed. RESULTS: The average time between onset of illness and the initial CT scan was six days (range, 1-42 days). A total of 399 segments were involved and distributed bilaterally (left lung: 186 segments [46.6%], right lung: 213 segments [53.4%]) and peripherally (38 [71.7%] patients). Multiple lobes (45 [84.9%]) and bilateral lower lobes (left lower lobe: 104 [26.1%], right lower lobe: 107 [26.8%], and total: 211 [52.9%]) were the most commonly involved. Ground-glass opacity with consolidation (24 [45.3%]) and pure ground-glass opacity (28 [52.8%]) were the main findings. The other findings were crazy-paving (14 [26.4%]), bronchiectasis (12 [22.6%]), atelectasis (7 [13.2%]), parenchymal bands (6 [11.3%]), air bronchogram (6 [11.3%]), interlobular thickening (5 [9.4%]), reticular pattern (1 [1.9%]), and pleural effusion (1 [1.9%]). CONCLUSIONS: Most COVID-19 pneumonia patients had abnormalities on chest CT images at initial presentation. Imaging features combined with patient's exposure history and onset symptoms could facilitate the identification of the suspected patient for further examinations. url: https://www.ncbi.nlm.nih.gov/pubmed/32851078/ doi: 10.1155/2020/5436025 id: cord-270474-jaurhjvr author: Xiang, Zhen title: Glucocorticoids improve severe or critical COVID-19 by activating ACE2 and reducing IL-6 levels date: 2020-06-27 words: 4417.0 sentences: 258.0 pages: flesch: 46.0 cache: ./cache/cord-270474-jaurhjvr.txt txt: ./txt/cord-270474-jaurhjvr.txt summary: We verified the efficacy of nine chemicals on regulating ACE2 expression in human GES-1, an upper digestive tract epithelial cell line, and THP-1, a human monocyte cell line, and found that several glucocorticoids imparted activating effects on ACE2 in both cell lines. We retrospectively analyzed the therapeutic efficacy of nine severe or critical patients from a cohort of 90 COVID-19 cases, who received medium to small doses of glucocorticoids from our integrated medical team in Wuhan. This study provides experimental and clinical evidence that medium-to-low-dose glucocorticoids may play a protective role in the respiratory and digestive systems by activating ACE2 and suppressing cytokine storm. Because the epithelial cells of the respiratory and digestive tracts are susceptible targets of SARS-CoV-2, we verified the regulatory effects of several candidate agonists of ACE2 expression on available normal human epithelial cells. Compared to the blank control, hydrocortisone revealed the strongest activating effect on ACE2 expression, followed by prednisolone, dexamethasone, and methylprednisolone. abstract: COVID-19 is a public health emergency that has rapidly spread to over 200 countries and regions, and no effective treatment has been established to date. Severe and critical cases have been associated with higher mortality due to acute respiratory distress syndrome (ARDS) and cytokine storm. Based on the novelty and recent emergence of COVID-19, no effective treatment regimen has been identified, thus prompting clinicians to engage in drug repurposing to address the immediate therapeutic need. This study focused on the molecular target angiotensin-converting enzyme 2 (ACE2) of SARS-CoV-2 and screened a group of ACE2 agonists by bioinformatics. Glucocorticoids are a type of ACE2 activator. We verified the efficacy of nine chemicals on regulating ACE2 expression in human GES-1, an upper digestive tract epithelial cell line, and THP-1, a human monocyte cell line, and found that several glucocorticoids imparted activating effects on ACE2 in both cell lines. The drugs triciribine and kinetin riboside activate ACE2 expression or inhibit IL-6 production in macrophages to some extent. In addition, we compared the efficacies of several glucocorticoids. Hydrocortisone showed the strongest effect on ACE2 activation, followed by prednisolone, dexamethasone, and methylprednisolone. We retrospectively analyzed the therapeutic efficacy of nine severe or critical patients from a cohort of 90 COVID-19 cases, who received medium to small doses of glucocorticoids from our integrated medical team in Wuhan. Seven out of nine patients revealed significant improvement in clinical parameters and chest CT images. This study provides experimental and clinical evidence that medium-to-low-dose glucocorticoids may play a protective role in the respiratory and digestive systems by activating ACE2 and suppressing cytokine storm. url: https://www.ncbi.nlm.nih.gov/pubmed/32760206/ doi: 10.7150/ijbs.47652 id: cord-251995-nbqukjzv author: Xiao, Fei title: Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 date: 2020-08-17 words: 1447.0 sentences: 94.0 pages: flesch: 53.0 cache: ./cache/cord-251995-nbqukjzv.txt txt: ./txt/cord-251995-nbqukjzv.txt summary: title: Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged in China, causing a major outbreak of severe pneumonia and spreading to >200 other countries (1) . A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. The viral load was higher in feces than in respiratory specimens collected at multiple time points (17-28 days after symptom onset) (Appendix Figure, panel D) . We attempted to isolate SARS-CoV-2 virus from 3 of the viral RNA-positive patients. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient abstract: Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. Confirmation of infectious virus in feces affirms the potential for fecal–oral or fecal–respiratory transmission and warrants further study. url: https://doi.org/10.3201/eid2608.200681 doi: 10.3201/eid2608.200681 id: cord-339752-o6atz33c author: Xiao, Li title: ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel? date: 2020-04-28 words: 3937.0 sentences: 257.0 pages: flesch: 49.0 cache: ./cache/cord-339752-o6atz33c.txt txt: ./txt/cord-339752-o6atz33c.txt summary: According to a report based on 72,314 cases (test confirmed cases: 44,672 (62%) from the Chinese Center for Disease Control and Prevention, 81% of COVID-19 patients have cold-like symptoms and mild pneumonia, 14% have severe respiratory inflammation, and 5% have critical conditions including respiratory failure, septic shock, and/or multiple organ dysfunction or failure. Similar to SARS (severe acute respiratory syndrome, [2002] [2003] coronavirus (SARS-CoV) [3] , SARS-CoV-2 primarily uses the S protein to invade host cells through ACE2, an enzyme which is known to be important in the renin-angiotensin-aldosterone system (RAAS) [4, 5] . Since TMPRSS2 plays a very important role in SARS-CoV-2 cell entry and ACE2 dysfunction, blocking the activity of TMPRSS2 should be the primary strategy for preventing severe and critical conditions of COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: Recently, the SARS-CoV-2 induced disease COVID-19 has spread all over the world. Nearly 20% of the patients have severe or critical conditions. SARS-CoV-2 exploits ACE2 for host cell entry. ACE2 plays an essential role in the renin–angiotensin–aldosterone system (RAAS), which regulates blood pressure and fluid balance. ACE2 also protects organs from inflammatory injuries and regulates intestinal functions. ACE2 can be shed by two proteases, ADAM17 and TMPRSS2. TMPRSS2-cleaved ACE2 allows SARS-CoV-2 cell entry, whereas ADAM17-cleaved ACE2 offers protection to organs. SARS-CoV-2 infection-caused ACE2 dysfunction worsens COVID-19 and could initiate multi-organ failure. Here, we will explain the role of ACE2 in the pathogenesis of severe and critical conditions of COVID-19 and discuss auspicious strategies for controlling the disease. url: https://doi.org/10.3390/v12050491 doi: 10.3390/v12050491 id: cord-299491-8rfm0jxh author: Xiao, Shenglan title: Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date: 2017-07-20 words: 4765.0 sentences: 218.0 pages: flesch: 53.0 cache: ./cache/cord-299491-8rfm0jxh.txt txt: ./txt/cord-299491-8rfm0jxh.txt summary: Like many other respiratory viruses, the SARS-CoV is suspected to spread from an infected person to the susceptible via three basic transmission routes, i.e., the long-range airborne, close contact and fomite routes [14] [15] [16] , as shown in Fig 1. Several studies have proposed probable evidence for the airborne spread of the SARS-CoV based on the consistencies between bio-aerosol concentration distributions and reported attack rates [19] [20] [21] , but no mechanism-based investigations exist for the fomite route. To investigate the role the fomite route plays in SARS-CoV transmission, we conducted a detailed modelling study of the largest hospital outbreak in Hong Kong [20] , in which the distribution of reported attack rates of inpatients showed a statistically significant spatial pattern. A multi-agent model ( Fig 2) was developed to simulate the possible spread of the viruses from the index patient to the susceptible by air flow and surface touching, and to calculate the possible exposure doses and infection risks for each hypothesis. abstract: The epidemic of severe acute respiratory syndrome (SARS) had a significant effect on global society in the early 2000s and the potential of its resurgence exists. Studies on the modes of transmission of SARS are limited though a number of outbreak studies have revealed the possible airborne route. To develop more specific and effective control strategies, we conducted a detailed mechanism-based investigation that explored the role of fomite transmission in the well-known Ward 8A outbreak. We considered three hypothetical transmission routes, i.e., the long-range airborne, fomite and combined routes, in 1,744 scenarios with combinations of some important parameters. A multi-agent model was used to predict the infection risk distributions of the three hypothetical routes. Model selection was carried out for different scenarios to compare the distributions of infection risk with that of the reported attack rates and select the hypotheses with the best fitness. Our results reveal that under the assumed conditions, the SARS coronavirus was most possible to have spread via the combined long-range airborne and fomite routes, and that the fomite route played a non-negligible role in the transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/28727803/ doi: 10.1371/journal.pone.0181558 id: cord-326721-2v5wkjrq author: Xiao, Wenlei title: A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks date: 2020-03-17 words: 4478.0 sentences: 282.0 pages: flesch: 57.0 cache: ./cache/cord-326721-2v5wkjrq.txt txt: ./txt/cord-326721-2v5wkjrq.txt summary: Distinguished with other epidemiological models, such as SIR, SEIR, etc., that compute the theoretical number of infected people in a closed population, CDIM considers the immigration and emigration population as system inputs, and administrative and medical resources as dynamic control variables. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint : Effective infectious increment (can be negative); : Total non-isolated cases (asymptomatic carriers); : Patient increment (symptom onset); : Total isolated cases (confirmed patients after symptom onset); Figure 4 : Basic principle of the cybernetics-based dynamic infection model be made. In the view of this, we used the data from Shanghai, a relatively well controlled city, to identify and calibrate the key parameters of the incubation period and the basic reproductive number. In Shanghai Model, there is no worry about the shortage of medical supplies, so a negative summation channel performs a direct control effect on the positive feedback infection loop, which is thus of paramount importance in reducing the number of total infectious cases. abstract: Since December 2019, COVID-19 has raged in Wuhan and subsequently all over China and the world. We propose a Cybernetics-based Dynamic Infection Model (CDIM) to the dynamic infection process with a probability distributed incubation delay and feedback principle. Reproductive trends and the stability of the SARS-COV-2 infection in a city can then be analyzed, and the uncontrollable risks can be forecasted before they really happen. The infection mechanism of a city is depicted using the philosophy of cybernetics and approaches of the control engineering. Distinguished with other epidemiological models, such as SIR, SEIR, etc., that compute the theoretical number of infected people in a closed population, CDIM considers the immigration and emigration population as system inputs, and administrative and medical resources as dynamic control variables. The epidemic regulation can be simulated in the model to support the decision-making for containing the outbreak. City case studies are demonstrated for verification and validation. url: https://doi.org/10.1101/2020.03.13.20034082 doi: 10.1101/2020.03.13.20034082 id: cord-325420-e9fjo7tl author: Xiao, Xia title: Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date: 2020-07-06 words: 1282.0 sentences: 78.0 pages: flesch: 58.0 cache: ./cache/cord-325420-e9fjo7tl.txt txt: ./txt/cord-325420-e9fjo7tl.txt summary: Here we performed a high throughput screen of approximately 1700 US FDA approved compounds to identify novel therapeutic agents that can effectively inhibit replication of coronaviruses including SARS-CoV-2. These screens have identified 24 anti-SARS-CoV-2 drugs including previously reported compounds such as hydroxychloroquine, amlodipine, arbidol hydrochloride, tilorone 2HCl, dronedarone hydrochloride, and merfloquine hydrochloride. Positive compounds from the initial screen were tested for their antiviral 120 efficacy against SARS-CoV-2 in Vero cells. Our data show that 24 of these compounds show significant 124 efficacy in inhibiting SARS-CoV-2 replication with sub micromolar IC50 for many of these 125 drugs such as nilotinib, clofazimine and raloxifene. This screen identified five new compounds that 187 are highly efficacious in inhibiting the viral replication of SARS-CoV-2 with SI >600. The positively identified drugs from this screen were used to perform dose response curves 220 against OC43 on LLC-MK2 and against SARS-CoV-2 using Vero cells as described below. abstract: COVID-19 pandemic has infected millions of people with mortality exceeding 300,000. There is an urgent need to find therapeutic agents that can help clear the virus to prevent the severe disease and death. Identifying effective and safer drugs can provide with more options to treat the COVID-19 infections either alone or in combination. Here we performed a high throughput screen of approximately 1700 US FDA approved compounds to identify novel therapeutic agents that can effectively inhibit replication of coronaviruses including SARS-CoV-2. Our two-step screen first used a human coronavirus strain OC43 to identify compounds with anti-coronaviral activities. The effective compounds were then screened for their effectiveness in inhibiting SARS-CoV-2. These screens have identified 24 anti-SARS-CoV-2 drugs including previously reported compounds such as hydroxychloroquine, amlodipine, arbidol hydrochloride, tilorone 2HCl, dronedarone hydrochloride, and merfloquine hydrochloride. Five of the newly identified drugs had a safety index (cytotoxic/effective concentration) of >600, indicating wide therapeutic window compared to hydroxychloroquine which had safety index of 22 in similar experiments. Mechanistically, five of the effective compounds were found to block SARS-CoV-2 S protein-mediated cell fusion. These FDA approved compounds can provide much needed therapeutic options that we urgently need in the midst of the pandemic. url: https://doi.org/10.1101/2020.07.06.188953 doi: 10.1101/2020.07.06.188953 id: cord-282895-85if4mnu author: Xiao, Xiaodong title: The SARS-CoV S glycoprotein: expression and functional characterization date: 2003-12-26 words: 3819.0 sentences: 182.0 pages: flesch: 54.0 cache: ./cache/cord-282895-85if4mnu.txt txt: ./txt/cord-282895-85if4mnu.txt summary: Fragments containing the N-terminal amino acid residues 17–537 and 272–537 but not 17–276 bound specifically to Vero E6 cells and purified soluble receptor, ACE2, recently identified by M. Here we report cloning, expression, and characterization of the SARS-CoV fulllength S glycoprotein and various soluble fragments, demonstration of its fusogenic function at neutral pH, development of a quantitative cell fusion reporter gene-based assay, and localization of the RBD in the N-terminal 303-537 residues. We have not observed measurable cytopathic effects in cells transfected with any of the constructs we developed (data not shown) indicating the possibility that the full-length and soluble fragments of the S glycoprotein may not have direct cytopathic effects. In an attempt to localize the receptor-binding domain (RBD) of the S glycoprotein prior to the identification of the SARS-CoV receptor, we developed an assay based on the binding of various soluble fragments to receptor expressing Vero E6 cells. abstract: We have cloned, expressed, and characterized the full-length and various soluble fragments of the SARS-CoV (Tor2 isolate) S glycoprotein. Cells expressing S fused with receptor-expressing cells at neutral pH suggesting that the recombinant glycoprotein is functional, its membrane fusogenic activity does not require other viral proteins, and that low pH is not required for triggering membrane fusion; fusion was not observed at low receptor concentrations. S and its soluble ectodomain, S(e), were not cleaved to any significant degree. They ran at about 180–200 kDa in SDS gels suggesting post-translational modifications as predicted by previous computer analysis and observed for other coronaviruses. Fragments containing the N-terminal amino acid residues 17–537 and 272–537 but not 17–276 bound specifically to Vero E6 cells and purified soluble receptor, ACE2, recently identified by M. Farzan and co-workers [Nature 426 (2003) 450–454]. Together with data for inhibition of binding by antibodies developed against peptides from S, these findings suggest that the receptor-binding domain is located between amino acid residues 303 and 537. These results also confirm that ACE2 is a functional receptor for the SARS virus and may help in the elucidation of the mechanisms of SARS-CoV entry and in the development of vaccine immunogens and entry inhibitors. url: https://api.elsevier.com/content/article/pii/S0006291X03024136 doi: 10.1016/j.bbrc.2003.11.054 id: cord-271243-8cfyen86 author: Xiao, Y. title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus date: 2008-05-31 words: 3375.0 sentences: 179.0 pages: flesch: 52.0 cache: ./cache/cord-271243-8cfyen86.txt txt: ./txt/cord-271243-8cfyen86.txt summary: title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus Summary Masked palm civets are highly susceptible to infection with the severe acute respiratory syndrome coronavirus (SARS-CoV). The present study describes the spectrum of histopathological changes in the lung, spleen, lymph node, liver, small intestine, kidney and cerebrum of civets infected experimentally with SARS-CoV. One animal from each group was sacrificed at 3, 13, 23, 34 and 35 days post-infection (dpi), and lung, spleen, lymph node, small intestine, kidney, trachea, cerebrum, pancreas, sex glands, stomach and heart were collected from each animal. In summary, the data presented in this study further corroborate previous findings (Wu et al., 2005) in demonstrating that civets are more susceptible to SARS-CoV infection than other animals, as implied by their clinical symptoms, pathological changes and virus distribution within tissues. abstract: Summary Masked palm civets are highly susceptible to infection with the severe acute respiratory syndrome coronavirus (SARS-CoV). Infected animals become less aggressive and develop pyrexia, lethargy and diarrhoea. The present study describes the spectrum of histopathological changes in the lung, spleen, lymph node, liver, small intestine, kidney and cerebrum of civets infected experimentally with SARS-CoV. In-situ hybridization (ISH) with probes specific for the RNA polymerase gene demonstrated viral RNA in the lung, small intestine and cerebrum only. In-situ labelling was employed in order to demonstrate cellular apoptosis in the cerebrum, but there was no evidence of apoptosis within the myocardium. These results indicate that SARS-CoV causes multi-organ pathology in civets, similar to that observed in human SARS patients. These parallels suggest that civets may be used as an animal model of this infection to gain insight into the pathogenesis of SARS and for evaluation of candidate vaccines and antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/18343398/ doi: 10.1016/j.jcpa.2007.12.005 id: cord-279976-juz9jnfk author: Xie, Mingxuan title: Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date: 2020-04-01 words: 3863.0 sentences: 228.0 pages: flesch: 50.0 cache: ./cache/cord-279976-juz9jnfk.txt txt: ./txt/cord-279976-juz9jnfk.txt summary: METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". abstract: BACKGROUND: The rapid spread of the coronavirus disease 2019 (COVID-19), caused by a zoonotic beta-coronavirus entitled 2019 novel coronavirus (2019-nCoV), has become a global threat. Awareness of the biological features of 2019-nCoV should be updated in time and needs to be comprehensively summarized to help optimize control measures and make therapeutic decisions. METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. RESULTS: The genome of 2019-nCoV partially resembled SARS-CoV and MERS-CoV, and indicating a bat origin. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Clinical presentation and pathology of COVID-19 greatly resembled SARS and MERS, with less upper respiratory and gastrointestinal symptoms, and more exudative lesions in post-mortems. Potential treatments included remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). CONCLUSION: The initial experience from the current pandemic and lessons from the previous two pandemics can help improve future preparedness plans and combat disease progression. url: https://www.sciencedirect.com/science/article/pii/S1201971220302046?v=s5 doi: 10.1016/j.ijid.2020.03.071 id: cord-343876-2inr4mcy author: Xie, Qin title: COVID-19 patients managed in psychiatric inpatient settings due to first-episode mental disorders in Wuhan, China: clinical characteristics, treatments, outcomes, and our experiences date: 2020-10-02 words: 4834.0 sentences: 215.0 pages: flesch: 40.0 cache: ./cache/cord-343876-2inr4mcy.txt txt: ./txt/cord-343876-2inr4mcy.txt summary: During the outbreak of COVID-19, the selection of an appropriate treatment setting for COVID-19 patients with mental disorders is a dilemma: in respiratory treatment settings these patients are more likely to not adhere with The main findings of this comparative study are 1) adjustment disorder and acute and transient psychotic disorders, with associated acute stress were the main clinical diagnoses in the COVID-19 group and some other disorders had their organic basis such as delirium due to infection and chloroquine-induced psychosis, while serious mental illnesses (SMIs) and alcohol use disorders were overrepresented in the control group, a common feature of inpatients of most Chinese psychiatric hospitals; 2) a wide range of psychiatric symptoms were found in COVID-19 patients with mental disorders on admission, including psychotic symptoms, aggressive behaviors, and anxiety symptoms; 3) the most common respiratory symptom of COVID-19 patients was cough, followed by fever, chills, and fatigue; and 4) mental disorders and COVID-19 of most patients were successfully treated after symptomatic and supportive treatments, including conventional psychotropic treatment and antiviral treatment, and, COVID-19 patients left the hospital earlier than psychiatric patients without COVID-19, on average by 16 days after admission. abstract: Data are scarce regarding the comorbid mental disorders and their management among COVID-19 patients. This study described the clinical characteristics and management of COVID-19 patients treated in psychiatric inpatient settings due to comorbid first-onset mental disorders in Wuhan, China. This electronic medical records-based study included 25 COVID-19 patients with first-onset mental disorders and 55 patients with first-onset mental disorders without COVID-19 (control group). Data collected included ICD-10 diagnoses of mental disorders, psychiatric and respiratory symptoms, treatments, and outcomes. Adjustment disorder (n = 11, 44.0%) and acute and transient psychotic disorders, with associated acute stress (n = 6, 24.0%) were main clinical diagnoses in the COVID-19 group while serious mental illnesses (i.e., schizophrenia, 24.5%) and alcohol use disorders (10.9%) were overrepresented in the control group. On admission, the most common psychiatric symptom in COVID-19 patients was insomnia symptoms (n = 18, 72.0%), followed by aggressive behaviors (n = 16, 64.0%), delusion (n = 10, 40.0%), and severe anxiety (n = 9, 36.0%). In addition to respiratory treatments, 76.0% COVID-19 patients received antipsychotics, 40.0% sedative-hypnotics, and 24.0% mood stabilizers. At the end of inpatient treatment, 4 (16.0%) COVID-19 patients were transferred to other hospitals to continue respiratory treatment after their psychiatric symptoms were controlled while the remaining 21 (84.0%) all recovered. Compared to the control group, COVID-19 group had significantly shorter length of hospital stay (21.2 vs. 37.4 days, P < 0.001). Adjustment disorder and acute and transient psychotic disorders are the main clinical diagnoses of COVID-19 patients managed in psychiatric inpatient settings. The short-term prognosis of these patients is good after conventional psychotropic treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/33009366/ doi: 10.1038/s41398-020-01022-x id: cord-298899-lkrmg5qr author: Xie, Yewei title: Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date: 2020-08-31 words: 6242.0 sentences: 368.0 pages: flesch: 53.0 cache: ./cache/cord-298899-lkrmg5qr.txt txt: ./txt/cord-298899-lkrmg5qr.txt summary: To fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, CT results, and risk factors of the COVID-19. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study abstract: BACKGROUND: The COVID-19 pandemic has affected the world deeply, with more than 14,000,000 people infected and nearly 600,000 deaths. This review aimed to summarize the epidemiologic traits, clinical spectrum, CT results and laboratory findings of the COVID-19 pandemic. METHODS: We scoped for relevant literatures published during 1st December 2019 to 16th July 2020 based on three databases using English and Chinese languages. We reviewed and analyzed the relevant outcomes. RESULTS: The COVID-19 pandemic was found to have a higher transmission rate compared to SARS and MERS and involved 4 stages of evolution. The basic reproduction number (R(0)) is 3.32 (95% CI:3.24–3.39), the incubation period was 5.24 days (95% CI:3.97–6.50, 5 studies) on average, and the average time for symptoms onset varied by countries. Common clinical spectrums identified included fever (38.1–39.0 °C), cough and fatigue, with Acute Respiratory Distress Syndrome (ARDS) being the most common complication reported. Body temperatures above 39.0 °C, dyspnea, and anorexia were more common symptoms in severe patients. Aged over 65 years old, having co-morbidities, and developing complications were the commonest high-risk factors associated with severe conditions. Leucopenia and lymphopenia were the most common signs of infection while liver and kidney damage were rare but may cause bad outcomes for patients. The bilateral, multifocal Ground-Glass Opacification (GGO) on peripheral, and the consolidative pulmonary opacity were the most frequent CT results and the tendency of mortality rates differed by region. CONCLUSIONS: We provided a bird’s-eye view of the COVID-19 during the current pandemic, which will help better understanding the key traits of the disease. The findings could be used for disease’s future research, control and prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/32867706/ doi: 10.1186/s12879-020-05371-2 id: cord-289134-ne3tjt5g author: Xing, Yue title: Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein date: 2020-07-17 words: 1628.0 sentences: 93.0 pages: flesch: 58.0 cache: ./cache/cord-289134-ne3tjt5g.txt txt: ./txt/cord-289134-ne3tjt5g.txt summary: By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. From 45828 SARS-CoV-2 genome sequences available in the GISAID database as of June 13, 2020, 103 strains of SARS-CoV-2 1 https://www.ncbi.nlm.nih.gov/Class/Structure/aa/aa_explorer.cgi carried various DNA mutations including 25 unique ones that may affect the furin cleavage site located at the amino acid residual positions 680-689 (S1/S2 region) (Coutard et al., 2020; Wang et al., 2020; Zhang et al., 2020) of the SARS-CoV-2 spike protein (Figure 1 , Table 1, and Supplementary Table 1) . We uncovered 103 SARS-CoV-2 strains from multiple geographic regions, 81 of which carried 25 unique mutations that may affect the furin cleavage site in the spike glycoprotein. abstract: The furin cleavage site in the spike glycoprotein of the SARS-CoV-2 coronavirus is considered important for the virus to enter the host cells. By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. Our results revealed that the furin cleavage site might not be required for SARS-CoV-2 to enter human cells in vivo. The identified mutants may represent a new subgroup of SARS-CoV-2 coronavirus with reduced tropism and transmissibility as potential live-attenuated vaccine candidates. url: https://doi.org/10.3389/fgene.2020.00783 doi: 10.3389/fgene.2020.00783 id: cord-309577-438fotfd author: Xing, Yuhan title: Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase date: 2020-04-10 words: 965.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-309577-438fotfd.txt txt: ./txt/cord-309577-438fotfd.txt summary: 1 We would like to share findings from our paediatric patients who were positive for nucleic acid testing for SARS-CoV-2 in stools up to 8-20 days after clearance of viral RNA in respiratory specimens. Surprisingly, we found SARS-CoV-2 remained detectable in faeces of paediatric patients for approximately 4 weeks, whereas negative conversion of viral RNA in respiratory specimens occurred within 2 weeks after disease onset. Two children showed negative results for faecal detection of SARS-CoV-2 20 days after clear-ance of viral RNA in the respiratory tract, while another child persistently tested positive on faecal samples even 8 days after respiratory samples turning negative. Faecal shedding of viral RNA has been constantly reported in patients infected with SARS-CoV-2. 7 -10 One study reported over half of the 17 patients had faecal samples positive for SARS-CoV-2 detection, although virus copies in stools were less than those in respiratory specimens. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32283149/ doi: 10.1016/j.jinf.2020.03.049 id: cord-345299-4k7qymqd author: Xiong, Hua-Long title: Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date: 2020-06-05 words: 1471.0 sentences: 88.0 pages: flesch: 47.0 cache: ./cache/cord-345299-4k7qymqd.txt txt: ./txt/cord-345299-4k7qymqd.txt summary: To identify drugs that are potentially used for the treatment of COVID-19, the potency of 1403 FDA-approved drugs were evaluated using a robust pseudovirus assay and the candidates were further confirmed by authentic SARS-CoV-2 assay. Four compounds, Clomiphene (citrate), Vortioxetine, Vortioxetine (hydrobromide) and Asenapine (hydrochloride), showed potent inhibitory effects in both pseudovirus and authentic virus assay. In this study, the anti-SARS-Cov-2 potentiality of 1403 FDA approved drugs were quantitatively evaluated by the pseudovirus-based assay. In the second round of screening, inhibition of VSV-SARS-CoV-2-Sdel18 virus infection and cell cytotoxicity were both detected (Supplementary Figure 1) . The robust assay based on VSV-SARS-CoV-2-Sdel18 pseudovirus screened out the potential drugs with high efficiency, then the inhibitory effect was confirmed by authentic SARS-CoV-2 assay. The relative value or inhibition rate of candidate drugs were calculated according to the decrease of GFP positive cell number (for pseudovirus-based assay) or cytopathic effect (for authentic SARS-CoV-2-based assay). abstract: To identify drugs that are potentially used for the treatment of COVID-19, the potency of 1403 FDA-approved drugs were evaluated using a robust pseudovirus assay and the candidates were further confirmed by authentic SARS-CoV-2 assay. Four compounds, Clomiphene (citrate), Vortioxetine, Vortioxetine (hydrobromide) and Asenapine (hydrochloride), showed potent inhibitory effects in both pseudovirus and authentic virus assay. The combination of Clomiphene (citrate), Vortioxetine and Asenapine (hydrochloride) is much more potent than used alone, with IC50 of 0.34 μM. url: https://doi.org/10.1101/2020.06.05.135996 doi: 10.1101/2020.06.05.135996 id: cord-345499-hq5um68k author: Xiong, Rui title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date: 2020-03-12 words: 5275.0 sentences: 317.0 pages: flesch: 53.0 cache: ./cache/cord-345499-hq5um68k.txt txt: ./txt/cord-345499-hq5um68k.txt summary: title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. We identified that targeting DHODH offers broad-spectrum antiviral efficacies against various RNA viruses, including the DAA-resistant influenza virus and the newly emerged coronavirus SARS-CoV-2. abstract: Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of coronavirus SARS-CoV-2. Existing direct-acting antiviral (DAA) drugs cannot be applied immediately to new viruses because of virus-specificity, and the development of new DAA drugs from the beginning is not timely for outbreaks. Thus, host-targeting antiviral (HTA) drugs have many advantages to fight against a broad spectrum of viruses, by blocking the viral replication and overcoming the potential viral mutagenesis simultaneously. Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knocking-out cells. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. Notably, S416 is reported to be the most potent inhibitor with an EC50 of 17nM and SI value >5882 in SARS-CoV-2-infected cells so far. This work demonstrates that both our self-designed candidates and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-repression may have clinical potentials not only to influenza but also to COVID-19 circulating worldwide, no matter such viruses mutate or not. url: https://doi.org/10.1101/2020.03.11.983056 doi: 10.1101/2020.03.11.983056 id: cord-337809-bxvgr6qg author: Xiong, Yong title: Family cluster of three recovered cases of pneumonia due to severe acute respiratory syndrome coronavirus 2 infection date: 2020-05-04 words: 1738.0 sentences: 122.0 pages: flesch: 53.0 cache: ./cache/cord-337809-bxvgr6qg.txt txt: ./txt/cord-337809-bxvgr6qg.txt summary: Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. [2] [3] [4] [5] [6] [7] [8] This report describes the epidemiological and clinical features of coronavirus disease (COVID-19) among three members of a family following SARS-CoV-2 infection. On 10 and 11 January 2020, a family of three, comprising the father (65 years), the mother (61 years) and the son (38 years), were admitted to the Department of Infectious Disease at the Zhongnan Hospital of Wuhan University with symptoms of cough and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: The coronavirus disease (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, in late 2019 and has affected more than 1 270 000 people worldwide. The numbers of reported cases continue to rise and threaten global health. Transmissions among family members are frequently observed, although the route of transmission is partially known. Here we report three cases of SARS-CoV-2 infection within one family. Sequencing of the S gene of the viral genome showed 100% identity among samples, suggesting that the same strain caused the infection. Following treatment with oseltamivir and short-term methylprednisolone combined with symptomatic management, all three patients recovered within 3 weeks, as evidenced by the disappearance of their symptoms, clearance of pulmonary infiltrates and consecutive negative molecular diagnostic test findings. Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/moderate pneumonia in COVID-19 cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32371416/ doi: 10.1136/bcr-2020-235302 id: cord-321918-9jwma2y6 author: Xiu, Siyu title: Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities date: 2020-06-15 words: 10526.0 sentences: 621.0 pages: flesch: 52.0 cache: ./cache/cord-321918-9jwma2y6.txt txt: ./txt/cord-321918-9jwma2y6.txt summary: The spike protein can be divided into two domains; S1 is responsible for angiotensin-converting enzyme II(ACE2) recognition, the recently identified host cell receptor, and S2 mediates membrane fusion (Figure 2 ). 98 99 On the basis of this approach, they identified two small molecules, TGG (12, Table 4 ) and luteolin (13) , that can bind avidly to the SARS-CoV S2 protein and inhibit viral entry of SARS-CoV into Vero E6 cells with IC 50 values of 4.5 and 10.6 μM, respectively. 113 A high-throughput screen (HTS) of a 1000-compound library that resulted in the identification of MDL28170 (17 , Table 4 ) by Bates et al., and in an antiviral activity assay, 17 specifically inhibited cathepsin L-mediated substrate cleavage and blocked SARS-CoV viral entry, with an IC 50 value of 2.5 nM and EC 50 value in the range of 100 nM. abstract: [Image: see text] Recently, a novel coronavirus initially designated 2019-nCoV but now termed SARS-CoV-2 has emerged and raised global concerns due to its virulence. SARS-CoV-2 is the etiological agent of “coronavirus disease 2019”, abbreviated to COVID-19, which despite only being identified at the very end of 2019, has now been classified as a pandemic by the World Health Organization (WHO). At this time, no specific prophylactic or postexposure therapy for COVID-19 are currently available. Viral entry is the first step in the SARS-CoV-2 lifecycle and is mediated by the trimeric spike protein. Being the first stage in infection, entry of SARS-CoV-2 into host cells is an extremely attractive therapeutic intervention point. Within this review, we highlight therapeutic intervention strategies for anti-SARS-CoV, MERS-CoV, and other coronaviruses and speculate upon future directions for SARS-CoV-2 entry inhibitor designs. url: https://doi.org/10.1021/acs.jmedchem.0c00502 doi: 10.1021/acs.jmedchem.0c00502 id: cord-261877-4y37676n author: Xu, Cong title: Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date: 2020-06-30 words: 8754.0 sentences: 505.0 pages: flesch: 60.0 cache: ./cache/cord-261877-4y37676n.txt txt: ./txt/cord-261877-4y37676n.txt summary: Recent cryoelectron microscopy (cryo-EM) studies on the stabilized ectodomain of SARS-CoV-2 S protein revealed a closed state of S trimer with three RBD domains in "down" conformation (Walls et al., 2020) , as well as an open state with one RBD in the "up" conformation, corresponding to the receptor-accessible state (Walls et al., 2020; Wrapp et al., 2020) . To gain a thorough picture on how the receptor ACE2 binding induces conformational dynamics of the SARS-CoV-2 S trimer and triggers transition towards the postfusion state, we determine the cryo-EM structure of SARS-CoV-2 S trimer in complex with human ACE2 PD domain to 3.8 Å resolution (termed SARS-CoV-2 S-ACE2, Figs. Based on the data, we put forward a mechanism of ACE2 binding-induced conformational transitions of SARS-CoV-2 S trimer from the tightly closed ground prefusion state transforming towards the postfusion state (Fig. 6) . Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding abstract: The recent outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid international spread pose a global health emergency. The trimeric spike (S) glycoprotein interacts with its receptor human ACE2 to mediate viral entry into host-cells. Here we present cryo-EM structures of an uncharacterized tightly closed SARS-CoV-2 S-trimer and the ACE2-bound-S-trimer at 2.7-Å and 3.8-Å-resolution, respectively. The tightly closed S-trimer with inactivated fusion peptide may represent the ground prefusion state. ACE2 binding to the up receptor-binding domain (RBD) within S-trimer triggers continuous swing-motions of ACE2-RBD, resulting in conformational dynamics of S1 subunits. Noteworthy, SARS-CoV-2 S-trimer appears much more sensitive to ACE2-receptor than SARS-CoV S-trimer in terms of receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and residue Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2, and provided structural basis of the spike D614G-mutation induced enhanced infectivity. Our findings offer a thorough picture on the mechanism of ACE2-induced conformational transitions of S-trimer from ground prefusion state towards postfusion state, thereby providing important information for development of vaccines and therapeutics aimed to block receptor binding. url: https://doi.org/10.1101/2020.06.30.177097 doi: 10.1101/2020.06.30.177097 id: cord-317523-idji1l0a author: Xu, Huanzhou title: SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date: 2020-10-27 words: 1192.0 sentences: 59.0 pages: flesch: 42.0 cache: ./cache/cord-317523-idji1l0a.txt txt: ./txt/cord-317523-idji1l0a.txt summary: With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. To assess if ORF3a also 135 mediates activation of other prominent inflammasomes including NLRP1 and NLRC4, we 136 depleted each of these molecules but were unable to block cleavage of pro-caspase 1 (Fig.2G) , 137 indicating that ORF3a predominantly activates the NLRP3 inflammasome. In summary, an essential viroporin required for release of SARS-CoV-2 from infected cells is also 178 able to prime and activate the NLRP3 inflammasome, the machinery responsible for much of the abstract: Cytokine storm resulting from a heightened inflammatory response is a prominent feature of severe COVID-19 disease. This inflammatory response results from assembly/activation of a cell-intrinsic defense platform known as the inflammasome. We report that the SARS-CoV-2 viroporin encoded by ORF3a activates the NLRP3 inflammasome, the most promiscuous of known inflammasomes. ORF3a triggers IL-1β expression via NFκB, thus priming the inflammasome while also activating it via ASC-dependent and -independent modes. ORF3a-mediated inflammasome activation requires efflux of potassium ions and oligomerization between NEK7 and NLRP3. With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. Summary Development of anti-SARS-CoV-2 therapies is aimed predominantly at blocking infection or halting virus replication. Yet, the inflammatory response is a significant contributor towards disease, especially in those severely affected. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. We also define key amino acid residues on ORF3a needed to activate the inflammatory response, and likely to facilitate virus release, and find that they are conserved in virus isolates across continents. These findings reveal ORF3a and NLRP3 to be attractive targets for therapy. url: https://doi.org/10.1101/2020.10.27.357731 doi: 10.1101/2020.10.27.357731 id: cord-338973-73a7uvyz author: Xu, Jiabao title: Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV date: 2020-02-22 words: 7110.0 sentences: 426.0 pages: flesch: 57.0 cache: ./cache/cord-338973-73a7uvyz.txt txt: ./txt/cord-338973-73a7uvyz.txt summary: After the outbreak of the severe acute respiratory syndrome (SARS) in the world in 2003, human coronaviruses (HCoVs) have been reported as pathogens that cause severe symptoms in respiratory tract infections. Recently, a new emerged HCoV isolated from the respiratory epithelium of unexplained pneumonia patients in the Wuhan seafood market caused a major disease outbreak and has been named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The source of unexplained pneumonia was first discovered in Wuhan in Dec, 2019, and SARS-CoV-2, a new coronavirus, was isolated from the respiratory epithelium of patients. Hong Kong scholars found that, compared with ribavirin alone, patients treated with lopinavir/ritonavir and ribavirin had lower risk of acute respiratory distress syndrome (ARDS) or death caused by SARS-CoV [76, 77] . A high-resolution crystal structure of SARS-CoV-2 coronavirus 3CL hydrolase (Mpro) was announced after the outbreak of COVID-19 in the world [80] , and human coronaviruses (HCoVs) have been treated as severe pathogens in respiratory tract infections. abstract: After the outbreak of the severe acute respiratory syndrome (SARS) in the world in 2003, human coronaviruses (HCoVs) have been reported as pathogens that cause severe symptoms in respiratory tract infections. Recently, a new emerged HCoV isolated from the respiratory epithelium of unexplained pneumonia patients in the Wuhan seafood market caused a major disease outbreak and has been named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus causes acute lung symptoms, leading to a condition that has been named as “coronavirus disease 2019” (COVID-19). The emergence of SARS-CoV-2 and of SARS-CoV caused widespread fear and concern and has threatened global health security. There are some similarities and differences in the epidemiology and clinical features between these two viruses and diseases that are caused by these viruses. The goal of this work is to systematically review and compare between SARS-CoV and SARS-CoV-2 in the context of their virus incubation, originations, diagnosis and treatment methods, genomic and proteomic sequences, and pathogenic mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/32098422/ doi: 10.3390/v12020244 id: cord-021055-ebcu3ywq author: Xu, Jianguo title: Inaugural editorial: Towards evidence-based biosafety and biosecurity date: 2019-02-20 words: 826.0 sentences: 61.0 pages: flesch: 42.0 cache: ./cache/cord-021055-ebcu3ywq.txt txt: ./txt/cord-021055-ebcu3ywq.txt summary: China has experienced significant biosecurity and biosafety challenges and is the only nation that has been subjected to a bioweapon assault. 2 The SARS epidemic served as a timeous practical reminder to both China and the world that emerging infectious diseases could significantly threaten national and global safety and security. [3] [4] [5] [6] [7] The 2004 SARS outbreak in North China resulted from a series of flaws in the biosafety protocol at a national institute in Beijing, 5 resulting in infection of four laboratory workers. We propose that the scope of biosecurity and biosafety should include all relevant areas with the potential to cause death, social disruption and panic, economic breakdown, and/or national crisis (e.g. emerging infectious diseases, bioweapons, bioterror, laboratory biosafety, antibiotic-resistant bacterial super-strains, harmful invasive plant or animal species, misuse of synthetic biological technology, misuse of human genetic information, etc.). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148918/ doi: 10.1016/j.jobb.2019.01.008 id: cord-252933-bu4oihem author: Xu, Jieqing Jessica title: Renal Infarct in a COVID‐19 Positive Kidney‐Pancreas Transplant Recipient date: 2020-06-01 words: 1391.0 sentences: 93.0 pages: flesch: 38.0 cache: ./cache/cord-252933-bu4oihem.txt txt: ./txt/cord-252933-bu4oihem.txt summary: The novel coronavirus disease 2019 (COVID‐19) is associated with increased risk of thromboembolic events, but the extent and duration of this hypercoagulable state remains unknown. We describe the first case report of renal allograft infarction in a 46‐year‐old kidney‐pancreas transplant recipient with no prior history of thromboembolism, who presented 26 days after diagnosis of COVID‐19. Since we are the first to report this complication, further investigation is required before making recommendations for thromboembolic prophylaxis in all solid organ transplant recipients with COVID-19. In summary, we present the case of a kidney-pancreas transplant recipient with moderate to severe COVID-19 complicated by late kidney allograft segmental infarction. This is the first case of a thromboembolic event in a SARS-CoV-2 positive solid organ recipient. High incidence of venous thromboembolic events in anticoagulated severe CoVID-19 patients Case report of CoVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? abstract: The novel coronavirus disease 2019 (COVID‐19) is associated with increased risk of thromboembolic events, but the extent and duration of this hypercoagulable state remains unknown. We describe the first case report of renal allograft infarction in a 46‐year‐old kidney‐pancreas transplant recipient with no prior history of thromboembolism, who presented 26 days after diagnosis of COVID‐19. At the time of renal infarct, he was COVID‐19 symptom free and repeat test for SARS‐CoV‐2 was negative. This case report suggests that a hypercoagulable state may persist even after resolution of COVID‐19. Further studies are required to determine thromboprophylaxis indications and duration in solid organ transplant recipients with COVID‐19. url: https://doi.org/10.1111/ajt.16089 doi: 10.1111/ajt.16089 id: cord-310331-29srzbuk author: Xu, Jiuyang title: 2019 novel Coronavirus outbreak: a quiz or final exam? date: 2020-03-20 words: 2004.0 sentences: 107.0 pages: flesch: 51.0 cache: ./cache/cord-310331-29srzbuk.txt txt: ./txt/cord-310331-29srzbuk.txt summary: Armed with experience from previous epidemics in the last two decades, clinicians, scientists, officials, and citizens in China are all contributing to the prevention of further 2019-nCoV transmission. The 2019 novel coronavirus (2019-nCoV) outbreak is currently bringing challenges to China and the whole world. Since direct human transmission and asymptomatic infection have been revealed for 2019-nCoV [3] , health authorities in China are facing an enormous challenge on disease management and control. Realizing the severity of SARS-CoV as a respiratory virus, the detection of pneumonia of unknown origin in 2019-nCoV outbreak enabled relatively early alarm from health authorities and raised awareness for medical staff to equip personal protection methods when dealing with suspected cases. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: The 2019 novel Coronavirus (2019-nCoV) is an emerging pathogen and is threatening the global health. Strikingly, more than 28 000 cases and 550 deaths have been reported within two months from disease emergence. Armed with experience from previous epidemics in the last two decades, clinicians, scientists, officials, and citizens in China are all contributing to the prevention of further 2019-nCoV transmission. Efficient preliminary work has enabled us to understand the basic characteristics of 2019-nCoV, but there are still many unanswered questions. It is too early now to judge our performance in this outbreak. Continuous and strengthened efforts should be made not only during the epidemic, but also afterwards in order to prepare for any incoming challenges. url: https://doi.org/10.1007/s11684-020-0753-1 doi: 10.1007/s11684-020-0753-1 id: cord-315056-ohyb6oa0 author: Xu, Juanjuan title: Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset date: 2020-10-29 words: 4426.0 sentences: 247.0 pages: flesch: 50.0 cache: ./cache/cord-315056-ohyb6oa0.txt txt: ./txt/cord-315056-ohyb6oa0.txt summary: title: Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset This retrospective study presents the clinical, laboratory, and radiological profiles, treatments, and outcomes of atypical COVID-19 patients without respiratory symptoms or fever at onset. The study examined ten atypical patients out of 909 severe or critical patients diagnosed with COVID-19 in Wuhan Union Hospital West Campus between 25 January 2020 and 10 February 2020. Chest computed tomography (CT) scan and nucleic acid detection should be performed immediately on close contacts of COVID-19 patients to screen out those with atypical infections, even if the contacts present without respiratory symptoms or fever at onset. In this study, we aimed to describe the clinical, laboratory, and radiological characteristics, treatments, and outcomes of severe or critical COVID-19 patients who presented no respiratory symptoms or fever at onset. An atypical patient was defined as a patient with laboratory-confirmed COVID-19 but without characteristic fever or respiratory symptoms before hospital admission. abstract: It is difficult to identify suspected cases of atypical patients with coronavirus disease 2019 (COVID-19), and data on severe or critical patients are scanty. This retrospective study presents the clinical, laboratory, and radiological profiles, treatments, and outcomes of atypical COVID-19 patients without respiratory symptoms or fever at onset. The study examined ten atypical patients out of 909 severe or critical patients diagnosed with COVID-19 in Wuhan Union Hospital West Campus between 25 January 2020 and 10 February 2020. Data were obtained from the electronic medical records of severe or critical patients without respiratory symptoms or fever at onset. Outcomes were followed up to discharge or death. Among 943 COVID-19 patients, 909 (96.4%) were severe or critical type. Of the severe or critical patients, ten (1.1%) presented without respiratory symptoms or fever at admission. The median age of the ten participants was 63 years (interquartile range (IQR): 57–72), and seven participants were men. The median time from symptom onset to admission was 14 d (IQR: 7–20). Eight of the ten patients had chronic diseases. The patients had fatigue (n = 5), headache or dizziness (n = 4), diarrhea (n = 5), anorexia (n = 3), nausea or vomiting (n = 3), and eye discomfort (n = 1). Four patients were found to have lymphopenia. Imaging examination revealed that nine patients had bilateral pneumonia and one had unilateral pneumonia. Eventually, two patients died and eight were discharged. In the discharged patients, the median time from admission to discharge lasted 24 d (IQR: 13–43). In summary, some severe or critical COVID-19 patients were found to have no respiratory symptoms or fever at onset. All such atypical cases should be identified and quarantined as early as possible, since they tend to have a prolonged hospital stay or fatal outcomes. Chest computed tomography (CT) scan and nucleic acid detection should be performed immediately on close contacts of COVID-19 patients to screen out those with atypical infections, even if the contacts present without respiratory symptoms or fever at onset. url: https://www.ncbi.nlm.nih.gov/pubmed/33163252/ doi: 10.1016/j.eng.2020.09.009 id: cord-266775-4npowkkz author: Xu, Jun title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 words: 3449.0 sentences: 167.0 pages: flesch: 46.0 cache: ./cache/cord-266775-4npowkkz.txt txt: ./txt/cord-266775-4npowkkz.txt summary: In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . abstract: Background. Previous studies have shown that common human coronavirus might be neurotropic, although it was first isolated as a pathogen of the respiratory tract. We noticed that a few patients with severe acute respiratory syndrome (SARS) experienced central nervous symptoms during the course of illness. In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. Methods. Using transmission electronic microscopy and nested reverse transcription–polymerase chain reaction, the causative pathogen was identified in cultures of a brain tissue specimen obtained from the patient with SARS. Histopathologic examination of the brain tissue was performed using the methods of immunohistochemistry analysis and double immunofluorescence staining. Fifteen cytokines and chemokines were detected in the blood of the patient with SARS by means of a bead-based multiassay system. Results. A fragment specific for SARS human coronavirus was amplified from cultures of the brain suspension, and transmission electronic microscopy revealed the presence of an enveloped virus morphologically compatible with a coronavirus isolated in the cultures. Pathologic examination of the brain tissue revealed necrosis of neuron cells and broad hyperplasia of gliocytes. Immunostaining demonstrated that monokine induced by interferon-Γ (Mig) was expressed in gliocytes with the infiltration of CD68(+) monocytes/macrophages and CD3(+) T lymphocytes in the brain mesenchyme. Cytokine/chemokine assay revealed that levels of interferon-Γ–inducible protein 10 and Mig in the blood were highly elevated, although the levels of other cytokines and chemokines were close to normal. Conclusions. This study provides direct evidence that SARS human coronavirus is capable of infecting the central nervous system, and that Mig might be involved in the brain immunopathology of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/16163626/ doi: 10.1086/444461 id: cord-286121-ltaxmp3u author: Xu, Ke title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date: 2009-06-05 words: 5289.0 sentences: 287.0 pages: flesch: 56.0 cache: ./cache/cord-286121-ltaxmp3u.txt txt: ./txt/cord-286121-ltaxmp3u.txt summary: In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein. abstract: Eight accessory proteins have been identified in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). They are believed to play roles in the viral life cycle and may contribute to the pathogenesis and virulence. ORF9b as one of these accessory proteins is located in subgenomic mRNA9 and encodes a 98 amino acid protein. However, whether 9b protein is a structural component of SARS-CoV particles remains unknown. In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. Further analysis shows that sufficient incorporation of 9b protein into VLPs is dependent upon the co-expression of E and M proteins, but not upon the presence of either S or N protein. Our data indicate that 9b protein of SARS-CoV is another virion-associated accessory protein. This finding will lead to a better understanding of the properties of the SARS-CoV 9b protein. url: https://doi.org/10.1016/j.virol.2009.03.032 doi: 10.1016/j.virol.2009.03.032 id: cord-350317-a9qd3xdr author: Xu, Qiannan title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 date: 2020-11-05 words: 700.0 sentences: 49.0 pages: flesch: 58.0 cache: ./cache/cord-350317-a9qd3xdr.txt txt: ./txt/cord-350317-a9qd3xdr.txt summary: title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 The expression of ACE2 is associated with the potential risk of making the target tissue susceptible to infection by SARS-CoV-2. Elevated ACE2 expression and detection of SARS-CoV-2 in the skin 4 of COVID-19 patients implied skin was a potential host of SARS-CoV-2. After IL-17 antibody treatment, the skin ACE2 expression was downregulated which meant IL-17 antibody could lower the risk of COVID-19 through lessening the cells which could interact with SARS-CoV-2. Additionally, IL-17 antibody could reverse the deteriorated barrier and inflammatory status in the skin of psoriasis patient which meant less microbe infection.Herein, the specific microbe could be SARS-CoV-2. Thus, whether IL-17 antibody could reduce the COVID-19 risk through reversing the inflammatory skin status with deteriorated barrier and preventing SARS-CoV-2 transmitting should be further discussed. Skin is a potential host of SARS-CoV-2: a clinical, single-cell transcriptome-profiling and histological study abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0190962220329054?v=s5 doi: 10.1016/j.jaad.2020.10.084 id: cord-298098-4dfqlebp author: Xu, Ruodan title: Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System date: 2020-07-30 words: 3326.0 sentences: 173.0 pages: flesch: 53.0 cache: ./cache/cord-298098-4dfqlebp.txt txt: ./txt/cord-298098-4dfqlebp.txt summary: In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Construction of SARS-CoV-2 VLPs was performed by co-transfecting cells with S, M, E, and N with molar ratio at 8:6:8:3 as shown in Figure 1 . To get better understanding of the secretory features of four SARS-CoV-2 structural proteins, we first transfected HEK-293T and Vero E6 cells with vectors expressing S, M, E, or N, respectively. In the current study, we described the efficient construction of SARS-CoV-2 VLPs by plasmid-driven transfection of viral structural proteins in mammalian cells. abstract: Virus-like particle (VLP) is a self-assembled nanostructure incorporating key viral structural proteins. VLP resembles molecular and morphological features of authentic viruses but is non-infectious and non-replicating due to lack of genetic materials. Successful applications of VLP has been shown in vaccinological and virological research. As an accessibly safe and relevant substitute of naturally pathogenic viruses, the construction of SARS-CoV-2 VLPs is much in demand in the ongoing fight against 2019 Coronavirus disease (COVID-19) pandemics. In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Our data demonstrate that SARS-CoV-2 VLPs possess molecular and morphological properties of native virion particles, which endow such VLPs with a promising vaccine candidate and a powerful tool for the research of SARS-CoV-2. url: https://doi.org/10.3389/fbioe.2020.00862 doi: 10.3389/fbioe.2020.00862 id: cord-034351-5br4faov author: Xu, Shuang-Fei title: Cross-Sectional Seroepidemiologic Study of Coronavirus Disease 2019 (COVID-19) among Close Contacts, Children, and Migrant Workers in Shanghai date: 2020-10-02 words: 3445.0 sentences: 187.0 pages: flesch: 51.0 cache: ./cache/cord-034351-5br4faov.txt txt: ./txt/cord-034351-5br4faov.txt summary: (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. Since the first known case of pneumonia infected with the novel coronavirus was reported in the city of Wuhan in late December of 2019, Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and announced by the World Health Organization on 11 February 2020, unexpectedly and quickly spread in China and many other countries with rapid geographical expansion and a sudden increase in the number of cases [1, 2] . abstract: (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. (2) Method: This is a cross-sectional seroepidemiologic study. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. A multi-stage sampling method will be employed to acquire an adequate sample size. Assessments that include questionnaires and blood, nasopharyngeal specimens, and feces collection will be performed via home-visit survey. (3) Ethics and Dissemination: The study was approved by the Institute Review Board of School of Public Health, Fudan University (IRB#2020-04-0818). Before data collection, written informed consent will be obtained from all participants. The manuscripts from this work will be submitted for publication in quality peer-reviewed journals and presented at national or international conferences. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7579139/ doi: 10.3390/ijerph17197223 id: cord-332962-8y3t0r2d author: Xu, Xi title: Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 date: 2020-02-28 words: 2439.0 sentences: 145.0 pages: flesch: 50.0 cache: ./cache/cord-332962-8y3t0r2d.txt txt: ./txt/cord-332962-8y3t0r2d.txt summary: We aimed to report the imaging and clinical characteristics of these patients infected with SARS-CoV-2 in Guangzhou, China. CONCLUSION: SARS-CoV-2 infection can be confirmed based on the patient''s history, clinical manifestations, imaging characteristics, and laboratory tests. Image analysis, focused on the lesion features of each patient, included (a) distribution characteristics, (b) number of lobes involved, (c) lobe of lesion distribution, (d) Fig. 1 A 49-year-old man with history of recent travel to Wuhan presented with fever and cough for 6 days. Our study showed some common CT imaging features in patients affected by SARS-CoV-2 pneumonia: bilateral, multifocal ground glass opacities, with peripheral distribution. In our study, few patients initially negative for SARS-CoV-2 nucleic acid test had bilateral ground glass opacities in chest CT scans. In a patient with a history of close contact with a SARS-CoV-2-infected patient, early manifestation of bilateral, multifocal, and peripheral ground glass opacities on a chest CT scan might be a sign of a 2019 novel coronavirus infection. abstract: BACKGROUND: The pneumonia caused by the 2019 novel coronavirus (SARS-CoV-2, also called 2019-nCoV) recently break out in Wuhan, China, and was named as COVID-19. With the spread of the disease, similar cases have also been confirmed in other regions of China. We aimed to report the imaging and clinical characteristics of these patients infected with SARS-CoV-2 in Guangzhou, China. METHODS: All patients with laboratory-identified SARS-CoV-2 infection by real-time polymerase chain reaction (PCR) were collected between January 23, 2020, and February 4, 2020, in a designated hospital (Guangzhou Eighth People’s Hospital). This analysis included 90 patients (39 men and 51 women; median age, 50 years (age range, 18–86 years). All the included SARS-CoV-2-infected patients underwent non-contrast enhanced chest computed tomography (CT). We analyzed the clinical characteristics of the patients, as well as the distribution characteristics, pattern, morphology, and accompanying manifestations of lung lesions. In addition, after 1–6 days (mean 3.5 days), follow-up chest CT images were evaluated to assess radiological evolution. FINDINGS: The majority of infected patients had a history of exposure in Wuhan or to infected patients and mostly presented with fever and cough. More than half of the patients presented bilateral, multifocal lung lesions, with peripheral distribution, and 53 (59%) patients had more than two lobes involved. Of all included patients, COVID-19 pneumonia presented with ground glass opacities in 65 (72%), consolidation in 12 (13%), crazy paving pattern in 11 (12%), interlobular thickening in 33 (37%), adjacent pleura thickening in 50 (56%), and linear opacities combined in 55 (61%). Pleural effusion, pericardial effusion, and lymphadenopathy were uncommon findings. In addition, baseline chest CT did not show any abnormalities in 21 patients (23%), but 3 patients presented bilateral ground glass opacities on the second CT after 3–4 days. CONCLUSION: SARS-CoV-2 infection can be confirmed based on the patient’s history, clinical manifestations, imaging characteristics, and laboratory tests. Chest CT examination plays an important role in the initial diagnosis of the novel coronavirus pneumonia. Multiple patchy ground glass opacities in bilateral multiple lobular with periphery distribution are typical chest CT imaging features of the COVID-19 pneumonia. url: https://doi.org/10.1007/s00259-020-04735-9 doi: 10.1007/s00259-020-04735-9 id: cord-306373-61snvddh author: Xu, Xiao-Wei title: Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series date: 2020-02-19 words: 3594.0 sentences: 204.0 pages: flesch: 56.0 cache: ./cache/cord-306373-61snvddh.txt txt: ./txt/cord-306373-61snvddh.txt summary: OBJECTIVE: To study the clinical characteristics of patients in Zhejiang province, China, infected with the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) responsible for coronavirus disease 2019 (covid-2019). Since the outbreak of covid-19, strict precautionary measures have been implemented in Zhejiang province, including the creation of fever clinics that exclusively receive patients with suspected SARS-Cov-2 infection, defined as presenting with a fever or any respiratory symptoms, including dry cough, and especially in those with a history of travel to Wuhan or exposure to infected people within two weeks before the onset of illness since January 2020. The incubation period was defined as the time from exposure to the onset of illness, which was estimated among patients who could provide the exact date of close contact with individuals from Wuhan with confirmed or suspected SARS-Cov-2 infection. abstract: OBJECTIVE: To study the clinical characteristics of patients in Zhejiang province, China, infected with the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) responsible for coronavirus disease 2019 (covid-2019). DESIGN: Retrospective case series. SETTING: Seven hospitals in Zhejiang province, China. PARTICIPANTS: 62 patients admitted to hospital with laboratory confirmed SARS-Cov-2 infection. Data were collected from 10 January 2020 to 26 January 2020. MAIN OUTCOME MEASURES: Clinical data, collected using a standardised case report form, such as temperature, history of exposure, incubation period. If information was not clear, the working group in Hangzhou contacted the doctor responsible for treating the patient for clarification. RESULTS: Of the 62 patients studied (median age 41 years), only one was admitted to an intensive care unit, and no patients died during the study. According to research, none of the infected patients in Zhejiang province were ever exposed to the Huanan seafood market, the original source of the virus; all studied cases were infected by human to human transmission. The most common symptoms at onset of illness were fever in 48 (77%) patients, cough in 50 (81%), expectoration in 35 (56%), headache in 21 (34%), myalgia or fatigue in 32 (52%), diarrhoea in 3 (8%), and haemoptysis in 2 (3%). Only two patients (3%) developed shortness of breath on admission. The median time from exposure to onset of illness was 4 days (interquartile range 3-5 days), and from onset of symptoms to first hospital admission was 2 (1-4) days. CONCLUSION: As of early February 2020, compared with patients initially infected with SARS-Cov-2 in Wuhan, the symptoms of patients in Zhejiang province are relatively mild. url: https://doi.org/10.1136/bmj.m606 doi: 10.1136/bmj.m606 id: cord-255907-t7gpi2vo author: Xu, Yifei title: Unveiling the Origin and Transmission of 2019-nCoV date: 2020-02-24 words: 1330.0 sentences: 71.0 pages: flesch: 54.0 cache: ./cache/cord-255907-t7gpi2vo.txt txt: ./txt/cord-255907-t7gpi2vo.txt summary: A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Unveiling the Origin and Transmission of 2019-nCoV Yifei Xu 1, * A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Regardless of its initial source, it is likely that 2019-nCoV was introduced into a small cluster of humans from a cluster of infected animals and, from there, the virus acquired the capacity for human-tohuman transmission, spreading in the city before the cluster of patients from the Huanan market was identified. abstract: A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. url: https://www.sciencedirect.com/science/article/pii/S0966842X20300251 doi: 10.1016/j.tim.2020.02.001 id: cord-266033-gbx48scp author: Xu, Yu-Huan title: Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 date: 2020-02-25 words: 3082.0 sentences: 153.0 pages: flesch: 55.0 cache: ./cache/cord-266033-gbx48scp.txt txt: ./txt/cord-266033-gbx48scp.txt summary: Based on the fifth edition of the China Guidelines for the Diagnosis and Treatment Plan of Novel Coronavirus (2019-nCoV) Infection by the National Health Commission (Trial Version 5), 6 the NCP was classified into four types: mild with slight clinical symptoms but no imaging presentations of pneumonia; common with fever, respiratory symptoms and imaging presentations of pneumonia; severe type with any of the following: respiratory distress with RR > 30 times/minutes, oxygen saturation at rest < 93%, or PaO2/FiO2 < 300 mmHg (1 mmHg = 0.133 kPa); critically severe type with any of the following: respiratory failure needing mechanical ventilation, shock, or combination with other organ failure needing ICU intensive care. Fifty patients with NCP caused by infection of the SARS-CoV-2 virus were enrolled and had high-resolution pulmonary CT scanning, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three ( Table 1 ). abstract: PURPOSE: To investigate the clinical and imaging characteristics of computed tomography (CT) in novel coronavirus pneumonia (NCP) caused by SARS-CoV-2. MATERIALS AND METHODS: A retrospective analysis was performed on the imaging findings of patients confirmed with COVID-19 pneumonia who had chest CT scanning and treatment after disease onset. The clinical and imaging data were analyzed. RESULTS: Fifty patients were enrolled, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three. Mild patients (29 years) were significantly (P<0.03) younger than either common (44.5 years) or severe (54.7) and critically severe (65.7 years) patients, and common patients were also significantly (P<0.03) younger than severe and critically severe patients. Mild patients had low to moderate fever (<39.1 °C), 49 (98%) patients had normal or slightly reduced leukocyte count, 14 (28%) had decreased counts of lymphocytes, and 26 (52%) patients had increased C-reactive protein. Nine mild patients were negative in CT imaging. For all the other types of NCP, the lesion was in the right upper lobe in 30 cases, right middle lobe in 22, right lower lobe in 39, left upper lobe in 33 and left lower lobe in 36. The lesion was primarily located in the peripheral area under the pleura with possible extension towards the pulmonary hilum. Symmetrical lesions were seen in 26 cases and asymmetrical in 15. The density of lesion was mostly uneven with ground glass opacity as the primary presentation accompanied by partial consolidation and fibrosis. CONCLUSION: CT imaging presentations of NCP are mostly patchy ground glass opacities in the peripheral areas under the pleura with partial consolidation which will be absorbed with formation of fibrotic stripes if improved. CT scanning provides important bases for early diagnosis and treatment of NCP. url: https://www.sciencedirect.com/science/article/pii/S0163445320301006 doi: 10.1016/j.jinf.2020.02.017 id: cord-032222-i6gfp4me author: Xue, Ling title: A quick look at the latest developments in the COVID-19 pandemic date: 2020-09-10 words: 2867.0 sentences: 206.0 pages: flesch: 49.0 cache: ./cache/cord-032222-i6gfp4me.txt txt: ./txt/cord-032222-i6gfp4me.txt summary: Later, the Coronavirus Study Group of the International Committee on Taxonomy of Viruses formally named this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is a novel coronavirus, and an effective vaccine has yet to be developed. 51 A recombinant adenovirus type 5 vector vaccine, developed by Chen Wei''s team, showed good safety and immunogenicity in a phase I clinical trial, rapidly inducing both humoral and T-cell responses against SARS-CoV-2 in most participants. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia abstract: In December 2019, a new respiratory disease manifesting as viral pneumonia emerged in Wuhan, China. Isolation and identification of the virus showed that the pathogen causing this disease was a novel coronavirus. On January 12, 2020, the World Health Organization named the novel coronavirus causing the outbreak 2019 novel coronavirus (2019-nCoV). The disease caused by the virus was named coronavirus disease 2019 (COVID-19). Later, the Coronavirus Study Group of the International Committee on Taxonomy of Viruses formally named this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus shows strong infectivity and high lethality, arousing widespread concern. As an emerging virus, a comprehensive understanding of SARS-CoV-2 is missing. To provide a reference and a theoretical basis for further study of SARS-CoV-2, recent advances in our understanding of the virus are summarized in this review. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488894/ doi: 10.1177/0300060520943802 id: cord-279518-z3k7zaw4 author: Xue, Xiaotong title: High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2 date: 2020-05-23 words: 1506.0 sentences: 89.0 pages: flesch: 52.0 cache: ./cache/cord-279518-z3k7zaw4.txt txt: ./txt/cord-279518-z3k7zaw4.txt summary: High ACE2 expression was identified in the type II alveolar cells (AT2), bronchial transient secretory cells, small intestinal epithelium cells and the oral epithelial cells in accordance with respiratory clinical manifestations and rare clinical manifestations such as gastrointestinal symptoms, suggesting the respiratory droplet, digestive ２ and fecal-oral transmission routes of SARS-CoV-2 (Lukassen et al., 2020; Liang et al., 2020; Xu et al., 2020a) . Therefore, we hypothesized that the expression and distribution of ACE2 in human organs and tissues could reflect the potential infection routes of SARS-CoV-2. However, scRNA-seq has not yet been applied to examine the ACE2 expression in the cells of skin tissues, and the transmission of this virus by percutaneous routes remains unclear. In conclusion, the high expression of ACE2 on keratinocytes in human skin indicated that percutaneous transmission might be a potential risk route for SARS-CoV-2 infection, especially in condition of skin barrier dysfunction. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0022202X2031602X?v=s5 doi: 10.1016/j.jid.2020.05.087 id: cord-342091-xus5kxs0 author: YAVARIAN, Jila title: First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report date: 2020-08-17 words: 1241.0 sentences: 80.0 pages: flesch: 59.0 cache: ./cache/cord-342091-xus5kxs0.txt txt: ./txt/cord-342091-xus5kxs0.txt summary: In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. Here we report the first cases of SARS-CoV-2 infections in Qom, central Iran in Feb 2020. Collectively seven patients'' residents of Qom City were positive for SARS-CoV-2 on Feb 19 in Iran. We identified the first cases of SARS-CoV-2 in Qom city, Iran with unclear transmission route. Futureresearch should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. abstract: In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Iran was included in the affected countries. Throat swab specimens were collected and tested by using real-time reverse transcription PCR (RT-PCR) kit targeting the E region for screening and RNA dependent RNA polymerase for confirmation. Conventional RT-PCR was conducted for the N region and the PCR products were sequenced by Sanger sequencing. The first seven cases of SARS-CoV-2 infections were identified in Qom, Iran. This report describes the clinical and epidemiological features of the first cases of SARS-CoV-2 confirmed in Iran. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. url: https://www.ncbi.nlm.nih.gov/pubmed/33083334/ doi: 10.18502/ijph.v49i8.3903 id: cord-291627-5dqwyd9r author: Yadav, Rakhee title: SARS-CoV-2-host dynamics: Increased risk of adverse outcomes of COVID-19 in obesity date: 2020-07-21 words: 4361.0 sentences: 269.0 pages: flesch: 48.0 cache: ./cache/cord-291627-5dqwyd9r.txt txt: ./txt/cord-291627-5dqwyd9r.txt summary: 11 Many recent studies are now reporting obesity as one of the risk factors for severity of COVID-19 in USA, Brazil, UK, Italy, Spain and France [12] [13] [14] [15] [16] [17] [18] 67 (summarised in the In the current scenario, since USA has become the epi-centre of the COVID-19 pandemic; the dynamics of patient characteristics in terms of associated complications is showing a difference from the initial data put out by China. During the present pandemic, till now, it has been well established that cardiovascular diseases and diabetes are the major risk factors for poor outcomes but considering a higher BMI to be a forerunner for both these co-morbidities, the inclusion of obesity and overweight individuals as candidates for poor COVID-19 outcomes becomes very important. 58 Thus, the interaction between ACE2-RAS system, adipose tissue and the SARS-CoV-2 could, at least partially, explain the higher morbidity and mortality risk of COVID-19 in obese patients. abstract: BACKGROUND AND AIM: The pandemic of COVID-19 has put forward the public health system across countries to prepare themselves for the unprecedented outbreak of the present time. Recognition of the associated risks of morbidity and mortality becomes not only imperative but also fundamental to determine the prevention strategies as well as targeting the high-risk populations for appropriate therapies. METHODS: We reviewed, collated and analysed the online database i.e. Pubmed, Google scholar, Researchgate to highlight the demographic and mechanistic link between obesity and associated risks of severity in COVID-19. RESULTS: We observed a changing dynamic in the reporting from the time of initial pandemic in China to currently reported research. While, initially body mass index (BMI) did not find a mention in the data, it is now clearly emerging that obesity is one of the profound risk factors for complications of COVID-19. CONCLUSION: Our review will help clinicians and health policy makers in considering the importance of obesity in making the prevention and therapeutic strategies of COVID-19. An extra attention and precaution for patients with obesity in COVID-19 pandemic is recommended. url: https://api.elsevier.com/content/article/pii/S1871402120302782 doi: 10.1016/j.dsx.2020.07.030 id: cord-262783-uhfnv532 author: Yamamoto, Fumiichiro title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression date: 2020-09-23 words: 1683.0 sentences: 107.0 pages: flesch: 52.0 cache: ./cache/cord-262783-uhfnv532.txt txt: ./txt/cord-262783-uhfnv532.txt summary: title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression The ABO blood group polymorphism was previously shown to influence the susceptibility to SARS with individuals in groups A and O having a higher and lower risk, respectively [6] . Since 11 March 2020, several papers reported the association between ABO blood groups and SARS-CoV-2/COVID-19. The authors compared ABO blood group distribution among 265 SARS-CoV-2-infected patients and 3,694 healthy controls. The SARS-CoV-2 viruses produced in individuals of groups A, B, AB and O express A, B, A and B antigens, and none, respectively. For example, SARS-CoV-2 viruses produced in group A individuals may express A antigens and infect group A or AB individuals without such antigen-antibody reactions. Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies Association between ABO blood groups and risk of SARS-CoV-2 pneumonia ABO blood groups and SARS-CoV-2 infection. abstract: nan url: https://doi.org/10.1111/vox.13004 doi: 10.1111/vox.13004 id: cord-352562-qfb478sf author: Yamamoto, Lidia title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 words: 7315.0 sentences: 341.0 pages: flesch: 45.0 cache: ./cache/cord-352562-qfb478sf.txt txt: ./txt/cord-352562-qfb478sf.txt summary: In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. They identified 191 cases in hospitalized patients younger than 21 years of age, reported by hospitals in the New York State with the diagnosis of Kawasaki disease, toxic shock syndrome, myocarditis, and suspected multisystem inflammatory syndrome associated with COVID-19 in children (MIS-C). The laboratory diagnosis of COVID-19 are based on the detection of viral RNA by real time amplifications (RT-PCR) 40 or the detection of antibodies (immunoglobulins) anti-SARS-CoV-2 from the classes IgM, IgA and IgG, produced by the host''s immune system. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review abstract: This narrative review summarizes the main aspects underlying the new coronavirus SARS-CoV-2, its epidemiology, pathophysiology, pointing to differences of SARS-CoV-2 main receptors ACE2, in terms of expression and the amount of soluble ACE2 in the circulation of children, men and women, and also in those with risk factors such as the smokers and pregnant women or presenting with comorbidities (diabetes, obesity, hypertension and other cardiovascular diseases, renal and CNS pre-existing diseases). Clinical manifestations in adults and children were also described, emphasizing the particularities already seen in children, regarding signs, symptoms, viral excretion time and the involvement of all organs and systems. The COVID-19 in the pediatric population was divided into two sections: one dedicated to previously healthy children and adolescents with COVID-19, and the other to those who live with comorbidities and acquired COVID-19. A few paragraphs were reserved to the recently described severe multisystemic inflammatory syndrome associated with COVID-19 (MIS-C) that shares certain characteristics with Kawasaki disease. Some studies on the infection in pregnant and postpartum women, as well as neonates were shown. This review has also covered the laboratory diagnosis of COVID-19, passing through the imaging diagnosis made by the chest tomography revealing ground glass patching opacities, and results of non-specific exams such as the total blood with lymphopenia, the coagulation tests with increased prothrombin times, as well as marked increments of the D-dimer, troponin and proinflammatory cytokines. In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. In the end, the management of pediatric patients with COVID-19 based mainly on supportive measures has been briefly commented. url: https://doi.org/10.1590/s1678-9946202062065 doi: 10.1590/s1678-9946202062065 id: cord-315576-bgcqkz0p author: Yamamoto, Naoki title: Apparent difference in fatalities between Central Europe and East Asia due to SARS-COV-2 and COVID-19: Four hypotheses for possible explanation date: 2020-08-05 words: 6114.0 sentences: 280.0 pages: flesch: 51.0 cache: ./cache/cord-315576-bgcqkz0p.txt txt: ./txt/cord-315576-bgcqkz0p.txt summary: The comparison of the numbers of cases and deaths due to SARS-CoV-2 / COVID-19 shows that people in Central Europe are much more affected than people in East Asia where the disease originally occurred. Trying to explain this difference, this communication presents four hypotheses that propose the following reasons for the observed findings: 1) Differences in social behaviors and cultures of people in the two regions; 2) Possible outbreak of virulent viruses in Central Europe due to multiple viral infection, and the involvement of immuno-virological factors associated with it, 3) Possibility of corona resistance gene mutation occurring among East Asians as a result of long-term co-evolution of virus and host, and 4) possible involvement of hygienic factors. For the analysis of the difference regarding the number of infected people and the death tolls due to COVID-19 between Central European and East Asian 5 countries, we have chosen Italy, Spain, France, Germany and UK from Central Europe and China, South Korea, Japan, and Taiwan from South East Asia. abstract: The comparison of the numbers of cases and deaths due to SARS-CoV-2 / COVID-19 shows that people in Central Europe are much more affected than people in East Asia where the disease originally occurred. Trying to explain this difference, this communication presents four hypotheses that propose the following reasons for the observed findings: 1) Differences in social behaviors and cultures of people in the two regions; 2) Possible outbreak of virulent viruses in Central Europe due to multiple viral infection, and the involvement of immuno-virological factors associated with it, 3) Possibility of corona resistance gene mutation occurring among East Asians as a result of long-term co-evolution of virus and host, and 4) possible involvement of hygienic factors. Direct or indirect supportive evidences for each one of our hypotheses are presented and experimental approaches for their evaluation are discussed. Finally, we suggest that the dynamics of the pandemic also shows that the problems of the new coronavirus can be overcome due to people's awareness of the epidemics, rational viral diagnostics and a high level of medical care. url: https://www.sciencedirect.com/science/article/pii/S0306987720314912?v=s5 doi: 10.1016/j.mehy.2020.110160 id: cord-276361-77cylm1o author: Yamamoto, Norio title: HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus date: 2004-06-04 words: 2267.0 sentences: 129.0 pages: flesch: 55.0 cache: ./cache/cord-276361-77cylm1o.txt txt: ./txt/cord-276361-77cylm1o.txt summary: title: HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus Here we report that the HIV-1 protease inhibitor, nelfinavir, strongly inhibited replication of the SARS coronavirus (SARS-CoV). Experiments with various timings of drug addition revealed that nelfinavir exerted its effect not at the entry step, but at the post-entry step of SARS-CoV infection. We found that nelfinavir, a widely used HIV-1 protease inhibitor, could inhibit SARS-CoV replication efficiently. We screened our chemical library and found that nelfinavir could inhibit SARS-CoV replication in Vero E6 cells. Nelfinavir clearly inhibited the cytopathic effect (CPE) induced by infection with SARS-CoV (Fig. 1A) . Nelfinavir significantly inhibited SARS-CoV replication when used before infection (Figs. The other protease inhibitors including ritonavir had no effect on replication of SARS-CoV CC 50 , cytotoxic concentration of the compound that reduced cell viability to 50%. Our studies have clearly shown that nelfinavir can strongly inhibit the replication of SARS-CoV in Vero E6 cells. abstract: A novel coronavirus has been identified as an etiological agent of severe acute respiratory syndrome (SARS). To rapidly identify anti-SARS drugs available for clinical use, we screened a set of compounds that included antiviral drugs already in wide use. Here we report that the HIV-1 protease inhibitor, nelfinavir, strongly inhibited replication of the SARS coronavirus (SARS-CoV). Nelfinavir inhibited the cytopathic effect induced by SARS-CoV infection. Expression of viral antigens was much lower in infected cells treated with nelfinavir than in untreated infected cells. Quantitative RT-PCR analysis showed that nelfinavir could decrease the production of virions from Vero cells. Experiments with various timings of drug addition revealed that nelfinavir exerted its effect not at the entry step, but at the post-entry step of SARS-CoV infection. Our results suggest that nelfinavir should be examined clinically for the treatment of SARS and has potential as a good lead compound for designing anti-SARS drugs. url: https://www.sciencedirect.com/science/article/pii/S0006291X04008150 doi: 10.1016/j.bbrc.2004.04.083 id: cord-283818-4m9p717r author: Yan, Chao title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 words: 1589.0 sentences: 119.0 pages: flesch: 60.0 cache: ./cache/cord-283818-4m9p717r.txt txt: ./txt/cord-283818-4m9p717r.txt summary: title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase 23 chain reaction (RT-PCR). The main findings of this study is that we established a rapid, sensitive, and 199 specific assay for SARS-CoV-2 detection by RT-LAMP. Rapid and sensitive detection of 311 novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated 312 isothermal amplification combined with a lateral-flow device A real-time 326 reverse transcription loop-mediated isothermal amplification assay for the rapid 327 detection of yellow fever virus abstract: OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). METHODS: We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay. And, this assay was evaluated for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation. RESULTS: The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) time was 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivity was 2×10(1) copies and 2×10(2) copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with other 60 respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensiticity was 100% (95% CI 92.3% - 100%), specificity 100% (95% CI 93.7% - 100%). This assay detected SARS-CoV-2 in the mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation. CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts, and high-risk groups. url: https://www.ncbi.nlm.nih.gov/pubmed/32276116/ doi: 10.1016/j.cmi.2020.04.001 id: cord-314932-edf9xjwr author: Yan, Junqiang title: Research Progress of Drug Treatment in Novel Coronavirus Pneumonia date: 2020-05-13 words: 2940.0 sentences: 161.0 pages: flesch: 41.0 cache: ./cache/cord-314932-edf9xjwr.txt txt: ./txt/cord-314932-edf9xjwr.txt summary: Studies have found that 2019-nCoV is a single-stranded RNA beta coronavirus similar to SARS and MERS (12) , so current treatment is mainly based on the treatment experience of these two diseases (13) and further development of new targeted drugs. Currently, the drugs studied for the treatment of 2019-nCoV mainly include antivirals, antimalarials, glucocorticoids, plasma therapy, biological agents, and traditional Chinese medicine, among which lopinavir/ritonavir, ribavirin, remdesivir, chloroquine phosphate, and interferon are the main drugs. Recent studies have shown that chloroquine can inhibit 2019-nCoV by increasing the endosome pH required for viral cell fusion (26) , and its antiviral and antiinflammatory activity considerations are also involved (36) . New research shows that interferon-α nebulization, injection of interferon-α2b (57) , and α-interferon combined with lopinavir/ritonavir drugs (58) may be applicable to the current treatment of 2019-nCoV infection. Current studies have shown that the drug treatment of 2019-nCoV-related pneumonia mainly includes antivirals, antimalarials, and interferon. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro abstract: As of March 10, 2020, more than 100,000 novel coronavirus pneumonia cases have been confirmed globally. With the continuous spread of the new coronavirus pneumonia epidemic in even the world, prevention and treatment of the disease have become urgent tasks. The drugs currently being developed are not adequate to deal with this critical situation. In addition to being controlled through effective isolation, we need a rapid response from the healthcare and biotechnology industries to accelerate drug treatment research. By reviewing the currently available literature published at home and abroad, we summarize the current research progress of drug treatment during the epidemic period. At present, the drugs that can be used for treatment mainly include antiviral drugs, antimalarials, glucocorticoids, plasma therapy, biological agents, and traditional Chinese medicine. The effectiveness and safety of drug therapy need to be confirmed by more clinical studies. url: https://doi.org/10.1208/s12249-020-01679-z doi: 10.1208/s12249-020-01679-z id: cord-339568-th2xmhb6 author: Yan, Meitian title: Analysis of the diagnostic value of serum specific antibody testing for coronavirus disease 2019 date: 2020-06-27 words: 1869.0 sentences: 114.0 pages: flesch: 53.0 cache: ./cache/cord-339568-th2xmhb6.txt txt: ./txt/cord-339568-th2xmhb6.txt summary: The detection of antibodies produced during the immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has become an important laboratory method for the diagnosis of COVID‐19. In this study, retrospective analysis was used to explore the dynamic changes of serum IgM and IgG antibody and factors affecting diagnostic efficacy, so as to provide a theoretical basis for clinical diagnosis and treatment. Serum IgM antibodies against SARS-CoV can be detected 3-6 days after infection, but levels rapidly decrease thereafter. The positive rates of IgM and IgG antibodies in the non-severe group (71.62% and 71.14%, respectively) were higher than that in the severe group (28.38% and 28.86%, respectively), but these differences were not statistically significant (p > 0.05). Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis abstract: The coronavirus disease 2019 (COVID‐19) pandemic has spread to various regions worldwide. As of 27 April 2020, according to real‐time statistics released by the World Health Organization, there have been 84,341 confirmed cases and 4,643 deaths in China, with more than 2,979,484 confirmed cases and 206,450 deaths outside China. The detection of antibodies produced during the immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has become an important laboratory method for the diagnosis of COVID‐19. However, at present, little research on these specific antibodies has been conducted. In this study, retrospective analysis was used to explore the dynamic changes of serum IgM and IgG antibody and factors affecting diagnostic efficacy, so as to provide a theoretical basis for clinical diagnosis and treatment. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26230 doi: 10.1002/jmv.26230 id: cord-342294-x18xmrji author: Yan, Nao title: Medium Term Follow-Up of 337 Patients With Coronavirus Disease 2019 (COVID-19) in a Fangcang Shelter Hospital in Wuhan, China date: 2020-07-03 words: 2707.0 sentences: 147.0 pages: flesch: 48.0 cache: ./cache/cord-342294-x18xmrji.txt txt: ./txt/cord-342294-x18xmrji.txt summary: Risk factors of nucleic acid re-positivity including the number of lobes infiltration (odds ratio[OR], 1.14; 95% CI, 1.09–1.19), distribution (OR, 0.16; 95% CI, 0.13–0.19), CT imaging feature of patchy shadowing accompanying with consolidation (OR, 9.36; 95% CI, 7.84–11.17), respiratory symptoms of cough accompanying with expectoration (OR, 1.39; 95% CI, 1.28–1.52), and chest congestion accompanying by dyspnea (OR, 1.42; 95% CI, 1.28–1.57). Considering the high infectious characteristics of the SARS-CoV-2 virus, all recovered patients continue to undergo 14 days postdischarge quarantine at designated locations, which is required by the diagnosis and treatment program for novel coronavirus pneumonia (Trial Version 6). All patients were detected to be SARS-CoV-2 nucleic acid positive by a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and classified as mild to moderate cases on admission based on the criteria issued by the National Health Commission (NHC) of the People''s Republic of China. abstract: Background: With the adoption of powerful preventive and therapeutic measures, a large number of patients with COVID-19 have recovered and been discharged from hospitals in Wuhan, China. Prevention of epidemic rebound is a top priority of current works. However, information regarding post-discharge quarantine and surveillance of recovered patients with COVID-19 is scarce. Methods: This study followed up 337 patients with COVID-19 in a Wuhan East-West Lake Fangcang shelter hospital during the post-discharge quarantine. Demographic, clinical characteristics, comorbidities, and chest computed tomography (CT) image, mental state, medication status, and nucleic acid test data were summarized and analyzed. Results: 21/337 (6.2%) patients were SARS-CoV-2 nucleic acid re-positive, and 4 /337(1.2%) patients were suspected positive. The median day interval between the discharge to nucleic acid re-positivity was 7.5 days (IQR, 6–13), ranging from 6 to 13 days. Cough/expectoration are the most common symptoms, followed by chest congestion/dyspnea during the 2 weeks post-discharge quarantine. Risk factors of nucleic acid re-positivity including the number of lobes infiltration (odds ratio[OR], 1.14; 95% CI, 1.09–1.19), distribution (OR, 0.16; 95% CI, 0.13–0.19), CT imaging feature of patchy shadowing accompanying with consolidation (OR, 9.36; 95% CI, 7.84–11.17), respiratory symptoms of cough accompanying with expectoration (OR, 1.39; 95% CI, 1.28–1.52), and chest congestion accompanying by dyspnea (OR, 1.42; 95% CI, 1.28–1.57). Conclusion: The 2 weeks post-discharge quarantine may be an effective measure to prevent the outbreak from rebounding from the recovered patients. The second week is a critical period during post-discharge quarantine. Special attention should be paid to cough, expectoration, chest congestion, and dyspnea in recovered COVID-19 patients. A few recovered patients may prolong the quarantine based on clinical symptoms and signs and nucleic acid results in the 2 weeks of medical observation. url: https://www.ncbi.nlm.nih.gov/pubmed/32719806/ doi: 10.3389/fmed.2020.00373 id: cord-309206-kq77whdx author: Yan, Victoria C. title: Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment date: 2020-06-23 words: 2300.0 sentences: 155.0 pages: flesch: 49.0 cache: ./cache/cord-309206-kq77whdx.txt txt: ./txt/cord-309206-kq77whdx.txt summary: 13 Seeing that the enzymes involved in McGuigan prodrug hydrolysis are hardly expressed in the lungs undermines its utility in the context of a primarily respiratory disease such as Covid-19. 4−6 For the fleeting duration of time that remdesivir is in the blood (prior to hydrolysis to GS-441524), the expression of bioactivating enzymes for McGuigan prodrugs suggests that the highest concentrations of NTP formation by remdesivirrather than GS-441524 would occur in cell types with high expression of CES1/ CTSA/HINT1. 26 At the time of publication, a study by Agostini and colleagues is the only report that has compared the antiviral activities of GS-441524 and remdesivir in primary human airway epithelial (HAE) cells, the most clinically relevant in vitro model of the lung, infected with either SARS-CoV or MERS-CoV. 1 Above all else, premature hydrolysis of the McGuigan prodrug, followed by dephosphorylation in serum such that GS-441524 is the predominant metabolite 4,5,29 compels studies investigating its utility in patients with Covid-19. abstract: [Image: see text] While remdesivir has garnered much hope for its moderate anti-Covid-19 effects, its parent nucleoside, GS-441524, has been overlooked. Pharmacokinetic analysis of remdesivir evidences premature serum hydrolysis to GS-441524; GS-441524 is the predominant metabolite reaching the lungs. With its synthetic simplicity and in vivo efficacy in the veterinary setting, we contend that GS-441524 is superior to remdesivir for Covid-19 treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32665809/ doi: 10.1021/acsmedchemlett.0c00316 id: cord-253006-r2a2ozrc author: Yan, Xiquan title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers date: 2020-05-24 words: 493.0 sentences: 39.0 pages: flesch: 57.0 cache: ./cache/cord-253006-r2a2ozrc.txt txt: ./txt/cord-253006-r2a2ozrc.txt summary: title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers Notably, patient 2 carried SARS-CoV-2 viral for 32 days continuously after exposure to COVID-19 and tested positive for viral RNA in the respiratory sample for 13 days after first positive test onset. The results indicate that asymptomatic human can carry SARS-CoV-2 viral RNA after exposure to COVID-19, and the carriage seems long-lived. Further study is needed to determine the potential for and mode of contagion of asymptomatic carriers to develop more scientific control strategies. The long duration of asymptomatic infection with SARS-CoV-2 may warrant a reassessment of quarantine as the current outbreak. The US Centers for Disease Control and Prevention recommends that contacts of asymptomatic carriers self-isolate for 14 days [4] . Quarantine of asymptomatic carriers and identification of contacts are a crucial part of these control efforts. There is a great need for further studies on the mechanism by which asymptomatic carriers could acquire and carry SARS-CoV-2 that causes COVID-19. abstract: nan url: https://doi.org/10.1186/s13054-020-02952-0 doi: 10.1186/s13054-020-02952-0 id: cord-318235-2e5er0x0 author: Yanai, Hidekatsu title: Adiposity is the Crucial Enhancer of COVID-19 date: 2020-08-01 words: 884.0 sentences: 49.0 pages: flesch: 42.0 cache: ./cache/cord-318235-2e5er0x0.txt txt: ./txt/cord-318235-2e5er0x0.txt summary: A very recent study showed that patients with overweight and obesity admitted in a medical ward for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related pneumonia, despite their younger age, required more frequently assisted ventilation and access to intensive care units (ICUs) or semi-ICU than normal-weight patients [1] . Increased DPP4 expression was observed in vascular endothelial cells, adipose tissue and liver in obese people [8] , which can also make it easy for SARS-CoV-2 to enter human tissues. It has been proposed that the increase of secretion of interleukin-6 and tumor necrosis factor-alpha by adipose tissue in obesity-induced insulin resistance, could underlie the associations of insulin resistance with endothelial dysfunction and coagulopathy [9] . Elevation of inflammatory cytokines, endothelial dysfunction and procoagulant state already exist in obese people even before SARS-CoV-2 infection. In conclusion, obese people have various factors including high likelihood of entry of SARS-CoV-2 into human vital tissues, elevated cytokines, endothelial dysfunction and procoagulant state, which may enhance the severity of COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32849972/ doi: 10.14740/cr1118 id: cord-259620-qigfstxt author: Yang, Chen title: Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date: 2020-10-10 words: 3373.0 sentences: 205.0 pages: flesch: 54.0 cache: ./cache/cord-259620-qigfstxt.txt txt: ./txt/cord-259620-qigfstxt.txt summary: Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Studies have indicated direct infection of SARS-CoV-2 in kidney in addition to lung 5, 31 , however, ACE2 remains the only confirmed receptor which may mediate this invasion. Notably, our results suggest that SARS-CoV-2-RBD binds KIM1 and ACE2 via two distinct pockets, implicating that KIM1 and ACE2 may synergistically mediate the invasion of SARS-CoV-2 in kidney cells; which may explain the strong renal tropism, as well as the high incidence of acute kidney injury in COVID-19 patients 5 . ACE2 is the most well-studied receptor for SARS-CoV-2 so far, yet it is not an ideal therapeutic target for COVID-19 since it is widely expresses in multiple organs, and plays crucial roles in regulating blood pressure and preventing heart/kidney injury 36, 37 . abstract: COVID-19 patients present high incidence of kidney abnormalities, which are associated with poor prognosis and high mortality. Identification of SARS-CoV-2 in kidney of COVID-19 patients suggests renal tropism and direct infection. Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Kidney injury molecule-1 (KIM1) is a transmembrane protein that drastically up-regulated after renal injury. Here, binding between SARS-CoV2-RBD and the extracellular Ig V domain of KIM1 was identified by molecular simulations and co-immunoprecipitation, which was comparable in affinity to that of ACE2 to SARS-CoV-2. Moreover, KIM1 facilitated cell entry of SARS-CoV2-RBD, which was potently blockaded by a rationally designed KIM1-derived polypeptide. Together, the findings suggest KIM1 may mediate and exacerbate SARS-CoV-2 infection in a ‘vicious cycle’, and KIM1 could be further explored as a therapeutic target. url: https://doi.org/10.1101/2020.10.09.334052 doi: 10.1101/2020.10.09.334052 id: cord-333999-k92fmnq7 author: Yang, Chih-Jen title: Remdesivir Use in the Coronavirus Disease 2019 Pandemic: A Mini-Review date: 2020-10-05 words: 2581.0 sentences: 158.0 pages: flesch: 47.0 cache: ./cache/cord-333999-k92fmnq7.txt txt: ./txt/cord-333999-k92fmnq7.txt summary: In this mini-review, we summarize the current evidence on the efficacy and challenges of remdesivir for the treatment of coronavirus disease 2019 (COVID-19). J o u r n a l P r e -p r o o f Based on several clinical trials and reports on its compassionate use, remdesivir is considered by many to be the most promising drug for the treatment of COVID-19 [44] [45] [46] . First, to evaluate the efficacy and safety of remdesivir in patients with COVID-19, a randomized, placebo-controlled, double-blind, multicenter, phase 3 clinical trial was launched on February 5, 2020, in China 30, 60 . Clinically, common adverse drug reactions (ADRs) noted during the compassionate use of remdesivir in patients with COVID-19 reported by Grein et al. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative viral pathogen of coronavirus disease 2019 (COVID-19), appears to have various clinical presentations and may result in severe respiratory failure. The global SARS-CoV-2-associated viral pneumonia pandemic was first reported in December 2019 in China. Based on known pharmacological mechanisms, many therapeutic drugs have been repurposed to target SARS-CoV-2. Among these drugs, remdesivir appears to be the currently most promising according to several clinical trials and reports of compassionate use. In this mini-review, we summarize the current evidence on the efficacy and challenges of remdesivir for the treatment of coronavirus disease 2019 (COVID-19). url: https://api.elsevier.com/content/article/pii/S168411822030236X doi: 10.1016/j.jmii.2020.09.002 id: cord-310774-rpc8hrrx author: Yang, Chongtu title: Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia date: 2020-08-28 words: 1671.0 sentences: 117.0 pages: flesch: 52.0 cache: ./cache/cord-310774-rpc8hrrx.txt txt: ./txt/cord-310774-rpc8hrrx.txt summary: We designed this study to investigate the association between carcinoembryonic antigen (CEA) elevation and SARS-CoV-2 infection. METHODS: We retrospectively analyzed 177 patients with confirmed SARS-CoV-2 infection who received plasma CEA assays during hospitalization. CONCLUSION: SARS-CoV-2 infection might be another cause of CEA elevation, with nearly 20% of patients experienced transient and marked CEA increment during COVID-19 pneumonia. We found a portion of patients with COVID-19 pneumonia had raised serum of CEA, and we designed this study to investigate the association between CEA elevation and SARS-CoV-2 infection. However, as none of our participants had any clinical indication of malignancy, further studies are needed to investigate the role of CEA level in COVID-19 patients accompanied with colorectal cancer. In conclusion, SARS-CoV-2 infection might cause transient and marked CEA elevation especially in non-survivors, and this abnormal increment was not correlated with the severity of inflammation. abstract: PURPOSE: Coronavirus disease 2019 (COVID-19) tends to affect multiple organs and induce abnormal laboratory parameters. We designed this study to investigate the association between carcinoembryonic antigen (CEA) elevation and SARS-CoV-2 infection. METHODS: We retrospectively analyzed 177 patients with confirmed SARS-CoV-2 infection who received plasma CEA assays during hospitalization. Patients with other causes of CEA elevation were excluded. Data regarding epidemiological and demographical characteristics, clinical symptoms, laboratory tests, and outcomes were analyzed. Linear regression analysis was used to evaluate the correlation between CEA levels and inflammation severity. RESULTS: 171 patients were included in the final study and 32 patients (18.7%) had raised serum of CEA (> 5 ng/ml), with a median (range) age of 66 (53–86). The median [interquartile range (IQR)] CEA level was 11.4 ng/ml (8.1–21.6), which was significantly higher than the upper limit of reference range. CEA level between 5–10 ng/ml was in 11 patients, 10–15 ng/ml in 10 patients, and > 15 ng/ml in 11 patients. No correlation was found between CEA levels and lymphocyte (R(2) = 0.055; P = 0.10) nor CRP (R(2) = 0.026; P = 0.38). The median levels of CEA were 20.0 ng/ml (IQR, 14.7–23.0) in non-survivors and 10.9 ng/ml (IQR 7.5–16.1) in survivors, and the difference between two groups was statistically significant (P = 0.048). CONCLUSION: SARS-CoV-2 infection might be another cause of CEA elevation, with nearly 20% of patients experienced transient and marked CEA increment during COVID-19 pneumonia. The false-positive results of CEA elevation might have clinical significance for patients with colorectal cancer. url: https://www.ncbi.nlm.nih.gov/pubmed/32857179/ doi: 10.1007/s00432-020-03350-3 id: cord-303171-u5jrbsii author: Yang, Gee-Gwo title: SARS-associated Coronavirus Infection in Teenagers date: 2004-02-17 words: 1226.0 sentences: 83.0 pages: flesch: 66.0 cache: ./cache/cord-303171-u5jrbsii.txt txt: ./txt/cord-303171-u5jrbsii.txt summary: On April 28, when a student (case-patient 1) visited the school nurse on the first day that he had a fever, an infection specialist from affiliated Tzu-Chi Medical Center immediately responded. All nine schoolmates underwent chest x-ray examinations and were tested for SARS-associated coronavirus (SARS -CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (4) and DNA sequencing. Six schoolmates were positive for SARS-CoV by RT-PCR, confirmed later by DNA sequencing for replicase. No new cases of fever have occurred in Tzu-Chi High School in the 2 months since these patients'' isolation. Six schoolmates with fever were confirmed by real-time RT-PCR and DNA sequences to have SARS-CoV infection. Worldwide, SARS-CoV infection has been clinically severe, characterized by respiratory distress and a 15% average mortality rate (6) (7) (8) . Our teenagers with presumed SARS-CoV infection had very mild courses. The benign course of SARS-CoV infection in our teenage students supports the WHO finding of less-severe disease in younger persons. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15043016/ doi: 10.3201/eid1002.030485 id: cord-329069-ejdunj41 author: Yang, He S title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-08-21 words: 2361.0 sentences: 134.0 pages: flesch: 50.0 cache: ./cache/cord-329069-ejdunj41.txt txt: ./txt/cord-329069-ejdunj41.txt summary: METHOD: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual''s SARS-CoV-2 infection status. CONCLUSION: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. In this study, we hypothesized that the results of routine laboratory tests performed within a short time frame as the RT-PCR testing, in conjunction with a limited number of previously identified predictive demographic factors (age, gender, race) (17), can predict SARS-CoV-2 infection status. Laboratory tests were selected to construct the input feature vectors of the prediction model based on the following criteria: 1) a result available for at least 30% of the patients two days before a specific SARS-CoV-2 RT-PCR test, and 2) showing a significant difference (P-value, P-value after Bonferroni correction, P-value after demographics adjustment all less than 0.05) between patients with positive and negative RT-PCR results. abstract: BACKGROUND: Accurate diagnostic strategies to rapidly identify SARS-CoV-2 positive individuals for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours. METHOD: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual’s SARS-CoV-2 infection status. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital. RESULTS: The model achieved an area under the receiver operating characteristic curve (AUC) of 0.854 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within two days. CONCLUSION: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. It may play an important role in assisting the identification of SARS-COV-2 infected patients in areas where RT-PCR testing is not accessible due to financial or supply constraints. url: https://www.ncbi.nlm.nih.gov/pubmed/32821907/ doi: 10.1093/clinchem/hvaa200 id: cord-351028-p5cq2is5 author: Yang, Jia-Wei title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond date: 2020-06-27 words: 1058.0 sentences: 85.0 pages: flesch: 40.0 cache: ./cache/cord-351028-p5cq2is5.txt txt: ./txt/cord-351028-p5cq2is5.txt summary: IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Corticosteroid therapy for 386 critically ill patients with the Middle East respiratory syndrome: a multicenter 387 retrospective cohort study Epidemiological and clinical characteristics of 432 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive 433 study Clinical course and outcomes of critically ill patients 449 with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, 450 observational study abstract: BACKGROUND: Corticosteroids are commonly used as adjuvant therapy for acute respiratory distress syndrome (ARDS) by many clinicians due to their perceived anti-inflammatory effects. However, for patients with severe viral pneumonia, the corticosteroid treatment is highly controversial. OBJECTIVES: The purpose of this review is to systematically evaluate the effect and potential mechanism of corticosteroid administration in pandemic viral pneumonia. SOURCES: We comprehensively searched all manuscripts on corticosteroids therapy for influenza, SARS, MERS and SARS-CoV-2 viral pneumonia from the PubMed, EMBASE, Web of Science and Cochrane Library databases. CONTENT: We systematic summarized the effects of corticosteroids therapy for pandemic viral pneumonia and the potential mechanism of corticosteroid worked in COVID-19. IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Limited data on corticosteroid therapy for COVID-19 were reported. Corticosteroids were used in about a fifth of patients (670/2995, 22.4%). Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Compared with non-severe patients, severe patients were more likely to receive corticosteroid therapy (201/382, 52.6% vs 201/1310, 15.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Excessive inflammatory response and lymphopenia might be critical factors associated with disease severity and mortality of COVID-19. Sufficiently powered randomized controlled trials with rigorous inclusion/exclusion criteria and standardized dose and duration of corticosteroids are needed to verify the effectiveness and safety of corticosteroid therapy. url: https://api.elsevier.com/content/article/pii/S1198743X20303645 doi: 10.1016/j.cmi.2020.06.020 id: cord-274280-x5s4l0pp author: Yang, Jinsung title: Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor date: 2020-09-11 words: 7278.0 sentences: 403.0 pages: flesch: 56.0 cache: ./cache/cord-274280-x5s4l0pp.txt txt: ./txt/cord-274280-x5s4l0pp.txt summary: Here, we analyze the biophysical properties of the SARS-CoV-2 S-glycoprotein binding, on model surfaces and on living cells, to ACE2 receptors using force-distance (FD) curve-based atomic force microscopy (FD-curve-based AFM) (Fig. 1c) . used FD-curve-based AFM to evaluate at the single-molecule level the binding strength of the interaction established between the glycosylated S1 subunit and ACE2 receptors on model surfaces (Fig. 2a) . To investigate the properties of the binding complex, force-distance (FD) curves were recorded by repeatedly approaching and withdrawing the S1 subunit or RBD-functionalized tip from the ACE2 model surface (Fig. 2a, b) . To this end, we synthetized four different peptides (sequences provided in Supplementary Fig. 9 ), which have been selected to mimic the regions of ACE2 that interact with the S1 subunit as determined by the crystal structure 29 , and we tested their binding inhibition properties using our single-molecule force spectroscopy approach (Fig. 4a, b) . abstract: Study of the interactions established between the viral glycoproteins and their host receptors is of critical importance for a better understanding of virus entry into cells. The novel coronavirus SARS-CoV-2 entry into host cells is mediated by its spike glycoprotein (S-glycoprotein), and the angiotensin-converting enzyme 2 (ACE2) has been identified as a cellular receptor. Here, we use atomic force microscopy to investigate the mechanisms by which the S-glycoprotein binds to the ACE2 receptor. We demonstrate, both on model surfaces and on living cells, that the receptor binding domain (RBD) serves as the binding interface within the S-glycoprotein with the ACE2 receptor and extract the kinetic and thermodynamic properties of this binding pocket. Altogether, these results provide a picture of the established interaction on living cells. Finally, we test several binding inhibitor peptides targeting the virus early attachment stages, offering new perspectives in the treatment of the SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32917884/ doi: 10.1038/s41467-020-18319-6 id: cord-270019-er70ehk4 author: Yang, Kunyu title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study date: 2020-05-29 words: 4268.0 sentences: 242.0 pages: flesch: 48.0 cache: ./cache/cord-270019-er70ehk4.txt txt: ./txt/cord-270019-er70ehk4.txt summary: title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study METHODS: We did a retrospective, multicentre, cohort study of 205 patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and with a pathological diagnosis of a malignant tumour in nine hospitals within Hubei, China, from Jan 13 to March 18, 2020. Multivariable regression analysis showed that receiving chemotherapy within 4 weeks before symptom onset (odds ratio [OR] 3·51 [95% CI 1·16–10·59]; p=0·026) and male sex (OR 3·86 [95% CI 1·57–9·50]; p=0·0033) were risk factors for death during admission to hospital. 5 In particular, male sex and receiving chemotherapy within 4 weeks before symptom onset were identified as risk factors for death in patients with cancer who were diagnosed with COVID-19. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China abstract: BACKGROUND: Patients with cancer are a high-risk population in the COVID-19 pandemic. We aimed to describe clinical characteristics and outcomes of patients with cancer and COVID-19, and examined risk factors for mortality in this population. METHODS: We did a retrospective, multicentre, cohort study of 205 patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and with a pathological diagnosis of a malignant tumour in nine hospitals within Hubei, China, from Jan 13 to March 18, 2020. All patients were either discharged from hospitals or had died by April 20, 2020. Clinical characteristics, laboratory data, and cancer histories were compared between survivors and non-survivors by use of χ(2) test. Risk factors for mortality were identified by univariable and multivariable logistic regression models. FINDINGS: Between Jan 13 and Mar 18, 2020, 205 patients with cancer and laboratory-confirmed SARS-CoV-2 infection were enrolled (median age 63 years [IQR 56–70; range 14–96]; 109 [53%] women). 183 (89%) had solid tumours and 22 (11%) had haematological malignancies. The median duration of follow-up was 68 days (IQR 59–78). The most common solid tumour types were breast (40 [20%] patients), colorectal (28 [14%]), and lung cancer (24 [12%]). 54 (30%) of 182 patients received antitumour therapies within 4 weeks before symptom onset. 30 (15%) of 205 patients were transferred to an intensive care unit and 40 (20%) died during hospital admission. Patients with haematological malignancies had poorer prognoses than did those with solid tumours: nine (41%) of 22 patients with haematological malignancies died versus 31 (17%) of 183 patients with solid tumours (hazard ratio for death 3·28 [95% CI 1·56–6·91]; log rank p=0·0009). Multivariable regression analysis showed that receiving chemotherapy within 4 weeks before symptom onset (odds ratio [OR] 3·51 [95% CI 1·16–10·59]; p=0·026) and male sex (OR 3·86 [95% CI 1·57–9·50]; p=0·0033) were risk factors for death during admission to hospital. INTERPRETATION: Patients with cancer and COVID-19 who were admitted to hospital had a high case-fatality rate. Unfavourable prognostic factors, including receiving chemotherapy within 4 weeks before symptom onset and male sex, might help clinicians to identify patients at high risk of fatal outcomes. FUNDING: National Natural Science Foundation of China. url: https://www.ncbi.nlm.nih.gov/pubmed/32479787/ doi: 10.1016/s1470-2045(20)30310-7 id: cord-256893-3sh87h2x author: Yang, Li title: COVID-19: immunopathogenesis and Immunotherapeutics date: 2020-07-25 words: 5347.0 sentences: 300.0 pages: flesch: 42.0 cache: ./cache/cord-256893-3sh87h2x.txt txt: ./txt/cord-256893-3sh87h2x.txt summary: The recent novel coronavirus disease (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is seeing a rapid increase in infected patients worldwide. SARS-CoV-2 not only activates antiviral immune responses, but can also cause uncontrolled inflammatory responses characterized by marked pro-inflammatory cytokine release in patients with severe COVID-19, leading to lymphopenia, lymphocyte dysfunction, and granulocyte and monocyte abnormalities. The number of people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is rapidly increasing worldwide. The effect of elevated cytokine production on clinical manifestations Increasing evidence shows that viral infection can induce severe syndromes of shock and organ failure; 8,57 this phenomenon was also investigated for COVID-19. Treg cell-based therapy The dysregulated inflammatory processes caused by SARS-CoV-2 in patients with severe COVID-19 are partially due to the dysfunction of Tregs, which are responsible for inhibiting inflammation. abstract: The recent novel coronavirus disease (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is seeing a rapid increase in infected patients worldwide. The host immune response to SARS-CoV-2 appears to play a critical role in disease pathogenesis and clinical manifestations. SARS-CoV-2 not only activates antiviral immune responses, but can also cause uncontrolled inflammatory responses characterized by marked pro-inflammatory cytokine release in patients with severe COVID-19, leading to lymphopenia, lymphocyte dysfunction, and granulocyte and monocyte abnormalities. These SARS-CoV-2-induced immune abnormalities may lead to infections by microorganisms, septic shock, and severe multiple organ dysfunction. Therefore, mechanisms underlying immune abnormalities in patients with COVID-19 must be elucidated to guide clinical management of the disease. Moreover, rational management of the immune responses to SARS-CoV-2, which includes enhancing anti-viral immunity while inhibiting systemic inflammation, may be key to successful treatment. In this review, we discuss the immunopathology of COVID-19, its potential mechanisms, and clinical implications to aid the development of new therapeutic strategies against COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32712629/ doi: 10.1038/s41392-020-00243-2 id: cord-295508-yhdj5m0e author: Yang, Li-Tao title: Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients date: 2006-06-16 words: 4422.0 sentences: 241.0 pages: flesch: 64.0 cache: ./cache/cord-295508-yhdj5m0e.txt txt: ./txt/cord-295508-yhdj5m0e.txt summary: title: Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients In this study, we found that memory T-cell responses against the spike (S) protein were persistent for more than 1 year after SARS-CoV infection by detecting the production of IFN-γ using ELISA and ELISpot assays. In this study, we analyzed CD4 + and CD8 + T-cell responses in peripheral blood of recovered SARS patients to a pool of 169 overlapping SARS-CoV S peptides and characterized the phenotype of memory T-cell subpopulations. In this study, we performed phenotypic characterization of antiviral T-cell responses specific for SARS-CoV S peptides on the basis of their ability to secrete IFN-g and the expression of CD45RO, CCR7 and CD62L. Consistent with observations in HIV infection, we showed that SARS-CoV S-specific CD8 + T cells produced IFN-g but not IL-2 and predominantly displayed CD45RO À CCR7 À phenotype which might represent terminally differentiated effector memory T cells [25] . abstract: The role of cell-mediated immunity in human SARS-CoV infection is still not well understood. In this study, we found that memory T-cell responses against the spike (S) protein were persistent for more than 1 year after SARS-CoV infection by detecting the production of IFN-γ using ELISA and ELISpot assays. Flow cytometric analysis showed that both CD4(+) and CD8(+) T cells were involved in cellular responses against SARS-CoV infection. Interestingly, most of SARS-CoV S-specific memory CD4(+) T cells were central memory cells expressing CD45RO(+) CCR7(+) CD62L(−). However, the majority of memory CD8(+) T cells revealed effector memory phenotype expressing CD45RO(−) CCR7(−) CD62L(−). Thus, our study provides the evidence that SARS-CoV infection in humans can induce cellular immune response that is persistent for a long period of time. These data may have an important implication in the possibility of designing effective vaccine against SARS-CoV infection, specifically in defining T-cell populations that are implicated in protective immunity. url: https://www.sciencedirect.com/science/article/pii/S1521661606007352 doi: 10.1016/j.clim.2006.05.002 id: cord-293858-dk4snw9r author: Yang, Lin title: Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date: 2019-02-14 words: 4083.0 sentences: 195.0 pages: flesch: 46.0 cache: ./cache/cord-293858-dk4snw9r.txt txt: ./txt/cord-293858-dk4snw9r.txt summary: Annual excess rates of mortality or hospitalization associated with influenza in the older population were estimated for the pre-SARS (reference period), post-SARS and post-pandemic period, respectively. We constructed time series segmented regression models to estimate cause-specific mortality or hospitalization risks associated with influenza in the older population during the pre-SARS, post-SARS, and post-pandemic periods for Hong Kong and Brisbane. Compared to Hong Kong, during the study period Brisbane had higher mortality rates for all-cause (81.7 vs 66.5 per 100,000 population), cardiorespiratory diseases (CRD, 42.1 vs 33.8), stroke (9.5 vs 6.5) and ischemic heart diseases (IHD, 17.0 vs 7.5), but a lower rate for pneumonia and influenza (P&I, 2.8 vs 9.9), and a comparable rate for chronic obstructive pulmonary disease (COPD, 3.9 vs 4.2) (Additional file 1: Appendix 3). In this study, we estimated excess rates of mortality or hospitalizations attributable to influenza in different periods (pre-SARS, post-SARS, and post-pandemic) for two subtropical cities Hong Kong and Brisbane. abstract: BACKGROUND: Influenza and pneumococcal vaccine uptake in the older population aged 65 years or over of Hong Kong dramatically increased since the 2003 SARS outbreak. This study is aimed to evaluate the impact of increased coverage of influenza and pneumococcal vaccines by comparing the change of disease burden in the older population of Hong Kong, with the burden in the older population of Brisbane with relatively high vaccine coverage in the past fifteen years. METHODS: Time series segmented regression models were applied to weekly numbers of cause-specific mortality or hospitalization of Hong Kong and Brisbane. Annual excess rates of mortality or hospitalization associated with influenza in the older population were estimated for the pre-SARS (reference period), post-SARS and post-pandemic period, respectively. The rate ratios (RRs) between these periods were also calculated to assess the relative change of disease burden. RESULTS: Compared to the pre-SARS period, excess rates of mortality associated with influenza during the post-SARS period in Hong Kong decreased for cardiorespiratory diseases (RR = 0.90, 95% CI 0.80, 1.01), stroke (RR = 0.74, 95% CI 0.50, 1.09), and ischemic heart diseases (RR = 0.45, 95% CI 0.34, 0.58). The corresponding RRs in Brisbane were 0.79 (95% CI 0.54, 1.15), 0.33 (0.13, 0.80), and 1.09 (0.62, 1.90), respectively. Only the mortality of ischemic heart diseases showed a greater reduction in Hong Kong than in Brisbane. During the post-pandemic period, excess rates of all-cause mortality increased in Hong Kong, but to a lesser extent than in Brisbane (RR = 1.41 vs 2.39). CONCLUSION: A relative decrease (or less of an increase) of influenza disease burden was observed in the older population of Hong Kong after increased coverage of influenza and pneumococcal vaccines in this population, as compared to those of Brisbane where vaccination rates remained stable. The lack of significant findings in some disease categories highlights the challenges of evaluating the benefits of vaccination at the population level. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-3735-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30764779/ doi: 10.1186/s12879-019-3735-7 id: cord-321468-nkl2mls8 author: Yang, Mo title: Thrombopoietin levels increased in patients with severe acute respiratory syndrome date: 2008-03-07 words: 2433.0 sentences: 118.0 pages: flesch: 53.0 cache: ./cache/cord-321468-nkl2mls8.txt txt: ./txt/cord-321468-nkl2mls8.txt summary: Using a ELISA method, we found an increase in thrombopoietin (TPO) levels in the plasma of convalesced SARS patients (290 ± 53 pg/ml) and active SARS patients (251 ± 23 pg/ml) comparing to that from normal control patients (228 ± 17 pg/ml). Severe Acute Respiratory Syndrome (SARS) is a recently emerged human disease caused by the infection of a novel coronavirus (SARS-CoV) [1] . In this study, TPO levels in plasmas from SARS patients, the effect of these plasmas on in vitro megakaryocytopoiesis, and whether SARS-CoV can directly infect hematopoietic stem cells and megakaryocytic cells are investigated. To study the correlation of platelet counts and the plasma TPO levels, linear regression analyses were carried out for the normal, convalesced SARS and active SARS patient groups respectively. The present study showed that there was an increase of TPO levels in the plasma of convalescence SARS patients comparing to those from normal control and active SARS patients. abstract: Hematological changes in patients with Severe Acute Respiratory Syndrome (SARS) are common and frequently include thrombocytopenia. Using a ELISA method, we found an increase in thrombopoietin (TPO) levels in the plasma of convalesced SARS patients (290 ± 53 pg/ml) and active SARS patients (251 ± 23 pg/ml) comparing to that from normal control patients (228 ± 17 pg/ml). In addition, the plasma from active SARS patients had an inhibitory effect on CFU-MK formation, which could be neutralized by anti-TGF-β antibodies. In the experiment to determine whether SARS-CoV can directly infect hematopoietic stem cells and megakaryocytic cells, incubation of the cells with SARS-CoV did not show active infection. Our findings of increased TPO levels in the plasma of SARS patients provide a possible explanation for the genesis of thrombocytosis, which frequently develops from thrombocytopenia in SARS patients. url: https://www.sciencedirect.com/science/article/pii/S0049384807004896 doi: 10.1016/j.thromres.2007.12.021 id: cord-299472-pmqqemku author: Yang, Naibin title: In-flight Transmission Cluster of COVID-19: A Retrospective Case Series date: 2020-03-30 words: 3591.0 sentences: 279.0 pages: flesch: 66.0 cache: ./cache/cord-299472-pmqqemku.txt txt: ./txt/cord-299472-pmqqemku.txt summary: No data were available about the risk of SARS-CoV-2 transmission on aircraft and clinical characteristics and outcomes of these COVID-19 patients. We conducted a retrospective study focused on the clinical characteristics of ten patients with COVID-19 successively admitted to Xiaoshan First People''s Hospital after having been on a flight. Epidemiology data were collected by interviewing each patient including exposure history, dates of illness onset, hospital admissions and All rights reserved. Patients were discharged from hospital when the results of two RT-PCR tests taken 24 hours apart were negative for SARS-CoV-2 and symptoms improved obviously according to China guidelines 10 . . https://doi.org/10.1101/2020.03.28.20040097 doi: medRxiv preprint SARS-CoV-2 transmission on aircraft were similar to those without in-flight history, as previously reported [4, 7, 14] . Notably, the symptoms of COVID-19 patients infected in this flight were relatively mild, outcomes were inclined to be better, and the risk to passengers was higher compared with transmission of SARS on aircraft [15-17]. abstract: Objectives: No data were available about in-flight transmission of SARS-CoV-2. Here, we report an in-flight transmission cluster of COVID-19 and describe the clinical characteristics of these patients. Methods: After a flight, laboratory-confirmed COVID-19 was reported in 12 patients. Ten patients were admitted to the designated hospital. Data were collected from 25th January to 28th February 2020. Clinical information was retrospectively collected. Results: All patients are passengers without flight attendants. The median age was 33 years, and 70% were females. None was admitted to intensive care unit, and no patients succumbed through 28th February. The median incubation period was 3.0 days and from illness onset to hospital admission was 2 days. The most common symptom was fever. Two patients were asymptomatic and negative for chest CT scan throughout the disease course. On admission, initial RT-PCR were positive in 9 patients, however initial chest CT were positive in only half patients. The median lung total severity score of chest CT was 6. Notably, Crazy-Paving pattern, pleural effusion, and ground-glass nodules were also seen. Conclusion: It is potential for COVID-19 transmission by airplane, but the symptoms are mild. Passengers and attendants must be protected during the flight. url: https://doi.org/10.1101/2020.03.28.20040097 doi: 10.1101/2020.03.28.20040097 id: cord-288670-1vlowf2n author: Yang, Naidi title: Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19 date: 2020-03-15 words: 4511.0 sentences: 207.0 pages: flesch: 45.0 cache: ./cache/cord-288670-1vlowf2n.txt txt: ./txt/cord-288670-1vlowf2n.txt summary: As a result, the endocytic pathway including endosome and lysosome has become important targets for development of therapeutic strategies in combating diseases caused by CoVs. In this mini-review, we will focus on the importance of the endocytic pathway as well as the autophagy process in viral infection of several pathogenic CoVs inclusive of SARS-CoV, MERS-CoV and the new CoV named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and discuss the development of therapeutic agents by targeting these processes. Further studies also demonstrated that either ATG5 or ATG7, two of the key autophagy proteins in control of autophagosome biogenesis, is not required for viral replication in cells infected by MHV [28, 29] or by SARS-CoVs [30] . Taken together, establishing the role of endocytic pathway in viral entry is a major breakthrough in the mechanistic understanding of the CoVs infection, which offers great opportunity in development of novel therapeutic strategies for treatment of diseases such as SARS and COVID-19. abstract: Coronaviruses (CoVs) are a group of enveloped, single-stranded positive genomic RNA viruses and some of them are known to cause severe respiratory diseases in human, including Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS) and the ongoing coronavirus disease-19 (COVID-19). One key element in viral infection is the process of viral entry into the host cells. In the last two decades, there is increasing understanding on the importance of the endocytic pathway and the autophagy process in viral entry and replication. As a result, the endocytic pathway including endosome and lysosome has become important targets for development of therapeutic strategies in combating diseases caused by CoVs. In this mini-review, we will focus on the importance of the endocytic pathway as well as the autophagy process in viral infection of several pathogenic CoVs inclusive of SARS-CoV, MERS-CoV and the new CoV named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and discuss the development of therapeutic agents by targeting these processes. Such knowledge will provide important clues for control of the ongoing epidemic of SARS-CoV-2 infection and treatment of COVID-19. url: https://doi.org/10.7150/ijbs.45498 doi: 10.7150/ijbs.45498 id: cord-265877-dund6unq author: Yang, Q. title: Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis date: 2020-06-03 words: 3757.0 sentences: 237.0 pages: flesch: 52.0 cache: ./cache/cord-265877-dund6unq.txt txt: ./txt/cord-265877-dund6unq.txt summary: We extracted data from eligible studies to summarize the clinical manifestations and laboratory indexes of kidney injury on COVID-19 infection patients and further compared the prevalence of acute kidney injury (AKI) and the mean differences of three biomarkers between in ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint "SARS-CoV-2", "clinical", "laboratory", "kidney", "Acute Kidney Injury", "proteinuria" and "hematuria". To identify the risk factors for critical illnesses of COVID-19 patients, we then analyzed the relevance of the AKI and the three laboratory indexes with the clinical severity through comparing the incidences of AKI and mean differences of those biomarkers between ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint Due to the restriction of clinic information and most of the studies did not include in the death cases and the mortality of COVID-19, the association between kidney impairment and COVID-19-induced death was not be analyzed in our meta-analysis. abstract: Background: The novel coronavirus is pandemic around the world. Several researchers have given the evidence of impacts of COVID-19 on the respiratory, cardiovascular and gastrointestinal system. Studies still have debated on kidney injury of COVID-19 patients. The purpose of the meta-analysis was to evaluate the association of kidney impairment with the development of COVID-19. Methods: The PubMed, Embase and MedRxiv databases were searched until April 1, 2020. We extracted data from eligible studies to summarize the clinical manifestations and laboratory indexes of kidney injury on COVID-19 infection patients and further compared the prevalence of acute kidney injury (AKI) and the mean differences of three biomarkers between in ICU/severe and non-ICU/non-severe cases. Heterogeneity was evaluated using the I2 method. Results: In the sum of 19 studies with 4375 patients were included in this analysis. The pooled prevalence of AKI, increased serum creatinine (Scr), increased blood urea nitrogen (BUN), increased D-dimer, proteinuria and hematuria in patients with COVID-19 were 7.7%, 6.6%, 6.2%, 49.8%, 42% and 30.3% respectively. Moreover, the means of Scr, BUN and D-dimer were shown 6-folds, 1.8-folds and 0.68-folds, respectively, higher in ICU/severe cases than in corresponding non-ICU/non-severe patients. The prevalence of AKI was about 17 folds higher in ICU/severe patients compared with the non-ICU/non-severe cases. Conclusions: Overall, we assessed the incidences of the clinic and laboratory features of kidney injury in COVID-19 patients. And kidney dysfunction may be a risk factor for COVID-19 patients developing into the severe condition. In reverse, COVID-19 can also cause damage to the kidney. url: https://doi.org/10.1101/2020.05.28.20116400 doi: 10.1101/2020.05.28.20116400 id: cord-267887-ntwvquqz author: Yang, Ren title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro date: 2020-08-21 words: 1308.0 sentences: 81.0 pages: flesch: 51.0 cache: ./cache/cord-267887-ntwvquqz.txt txt: ./txt/cord-267887-ntwvquqz.txt summary: title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro Previously, researchers had developed a pseudotyped virus system for SARS-CoV and MERS-CoV, based on HIV-1 core, bearing virus spike protein. Furthermore, the neutralization results for ppSARS-2 were consistent with those of live SARS-CoV-2 and determined using the serum samples from convalescent patients. In conclusion, we have developed an easily accessible and reliable tool for studying the neutralizing efficiency of antibodies against SARS-CoV-2 and the entry process of the virus in a BSL-2 laboratory. Development and optimization of a sensitive pseudovirus-based assay for HIV-1 neutralizing antibodies detection using A3R5 cells A safe and convenient pseudovirus-based inhibition assay to detect neutralizing antibodies and screen for viral entry inhibitors against the novel human coronavirus MERS-CoV Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig abstract: With the development of the COVID-19 epidemic, there is an urgent need to establish a system for determining the effectiveness and neutralizing activity of vaccine candidates in biosafety level 2 (BSL-2) facilities. Previously, researchers had developed a pseudotyped virus system for SARS-CoV and MERS-CoV, based on HIV-1 core, bearing virus spike protein. During the development of a pseudotyped SARS-CoV-2 system, a eukaryotic expression plasmid expressing SARS-CoV-2 spike (S) protein was constructed and then co-transfected with HIV-1 based plasmid which containing the firefly luciferase reporter gene, into HEK293T cells to prepare the pseudotyped SARS-CoV-2 virus (ppSARS-2). We have successfully established the pseudotyped SARS-CoV-2 system for neutralization and entry inhibition assays. Huh7.5 cell line was found to be the most susceptible to our pseudotyped virus model. Different levels of neutralizing antibodies were detected in convalescent serum samples of COVID-19 patients using ppSARS-2. The recombinant, soluble, angiotensin-converting enzyme 2 protein was found to inhibit the entry of ppSARS-2 in Huh7.5 cells effectively. Furthermore, the neutralization results for ppSARS-2 were consistent with those of live SARS-CoV-2 and determined using the serum samples from convalescent patients. In conclusion, we have developed an easily accessible and reliable tool for studying the neutralizing efficiency of antibodies against SARS-CoV-2 and the entry process of the virus in a BSL-2 laboratory. url: https://www.sciencedirect.com/science/article/pii/S2590053620300884?v=s5 doi: 10.1016/j.bsheal.2020.08.004 id: cord-330873-hwbdreul author: Yang, Wan title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal date: 2020-07-07 words: 810.0 sentences: 47.0 pages: flesch: 47.0 cache: ./cache/cord-330873-hwbdreul.txt txt: ./txt/cord-330873-hwbdreul.txt summary: title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal After infectious SARS-CoV-2 was isolated from COVID-19 patients'' feces and urines, the corresponding RNA in the wastewater and sewage sludge was also observed (Randazzo et al., 2020) , implying the possibility of transmission of SARS-CoV-2 through the wastewater treatment plants (WWTP). Therefore, it is imperative to understand the potential exposure and transmission risk of this virus in sludge for the sake of public health. While limited evidence was found that sludge would play an essential role in SARS-CoV-2 transmission, there is still a need to understand the fate of coronaviruses outside the human host, including their persistence and inactivation mechanisms in 5 sludge, which would help to reveal their potential risks during sludge treatment and disposal. Aerosol Transmission Figure 1 The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal abstract: nan url: https://doi.org/10.1016/j.resconrec.2020.105043 doi: 10.1016/j.resconrec.2020.105043 id: cord-292002-g0v0xc21 author: Yang, Wenjing title: The role of imaging in 2019 novel coronavirus pneumonia (COVID-19) date: 2020-04-15 words: 4642.0 sentences: 228.0 pages: flesch: 45.0 cache: ./cache/cord-292002-g0v0xc21.txt txt: ./txt/cord-292002-g0v0xc21.txt summary: Imaging features of multiple patchy areas of ground glass opacity and consolidation predominately in the periphery of the lungs are characteristic manifestations on chest CT and extremely helpful in the early detection and diagnosis of this disease, which aids prompt diagnosis and the eventual control of this emerging global health emergency. • Among the infected patients, characteristic findings on CT imaging include multiple, patchy, ground-glass opacity, crazy-paving pattern, and consolidation shadows, mainly distributed in the peripheral and subpleural areas of both lungs, which are very helpful for the frontline clinicians. The typical chest CT imaging characteristics of COVID-19 include multiple, peripheral, bilateral, patchy, sub-segmental, or segmental ground glass opacities and areas of consolidation, which are mostly distributed along the bronchovascular bundles and subpleural space. Furthermore, in the currently available reports, the most common chest CT findings in COVID-19 patients are the peripheral areas of ground glass opacity/consolidation (without subpleural sparing) which are bilateral in distribution [21] [22] [23] . abstract: Almost the entire world, not only China, is currently experiencing the outbreak of a novel coronavirus that causes respiratory disease, severe pneumonia, and even death. The outbreak began in Wuhan, China, in December of 2019 and is currently still ongoing. This novel coronavirus is highly contagious and has resulted in a continuously increasing number of infections and deaths that have already surpassed the SARS-CoV outbreak that occurred in China between 2002 and 2003. It is now officially a pandemic, announced by WHO on the 11th of March. Currently, the 2019 novel coronavirus (SARS-CoV-2) can be identified by virus isolation or viral nucleic acid detection; however, false negatives associated with the nucleic acid detection provide a clinical challenge and thus make the imaging examination crucial. Imaging exams have been a main clinical diagnostic criteria for the 2019 novel coronavirus disease (COVID-19) in China. Imaging features of multiple patchy areas of ground glass opacity and consolidation predominately in the periphery of the lungs are characteristic manifestations on chest CT and extremely helpful in the early detection and diagnosis of this disease, which aids prompt diagnosis and the eventual control of this emerging global health emergency. Key Points • In December 2019, China, an outbreak of pneumonia caused by a novel, highly contagious coronavirus raised grave concerns and posed a huge threat to global public health. • Among the infected patients, characteristic findings on CT imaging include multiple, patchy, ground-glass opacity, crazy-paving pattern, and consolidation shadows, mainly distributed in the peripheral and subpleural areas of both lungs, which are very helpful for the frontline clinicians. • Imaging examination has become the indispensable means not only in the early detection and diagnosis but also in monitoring the clinical course, evaluating the disease severity, and may be presented as an important warning signal preceding the negative RT-PCR test results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00330-020-06827-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32296940/ doi: 10.1007/s00330-020-06827-4 id: cord-257876-nzjp1hrz author: Yang, Wenzhong title: Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality date: 2020-09-14 words: 3319.0 sentences: 192.0 pages: flesch: 55.0 cache: ./cache/cord-257876-nzjp1hrz.txt txt: ./txt/cord-257876-nzjp1hrz.txt summary: Genomic annotation of the BLAST hits also showed that viruses from geographic regions with severe infections tended to have more dynamic genomic regions in the SARS-CoV-2 receptor-binding domain (RBD) and receptor-binding motif (RBM) of the spike protein (S protein). We collected all available raw sequencing data for SARS-CoV-2 from the four sequencing platforms (Illumina, BGI, Ion-Torrent and Nanopore) deposited in the National Center for Biotechnology Information (NCBI) Short Reads Archive (SRA) database as of 15 April 2020 (Supplementary Table S1 ). The BLAST hit score (BHS) is a metric based on the similarity between a high-quality read of a SARS-CoV-2 sample and each assembled genome in the coronavirus databases (Methods). To investigate the dynamic binding between RBM and ACE2, we implemented protein structure dockings between the modeled S proteins (with and without the ''hidden mutations'' in the alignments of 4I.C1) and human ACE2 protein using HDOCK [26] The threshold for the high-quality reads from BGI and Illumina platforms is 0.9 (marked by a dash line) and that for Ion-Torrent and Nanopore is 0.2 (marked by a dash line). abstract: There is an urgent public health need to better understand Severe Acute Respiratory Syndrome (SARS)-CoV-2/COVID-19, particularly how sequences of the viruses could lead to diverse incidence and mortality of COVID-19 in different countries. However, because of its unknown ancestors and hosts, elucidating the genetic variations of the novel coronavirus, SARS-CoV-2, has been difficult. Without needing to know ancestors, we identified an uneven distribution of local genome similarities among the viruses categorized by geographic regions, and it was strongly correlated with incidence and mortality. To ensure unbiased and origin-independent analyses, we used a pairwise comparison of local genome sequences of virus genomes by Basic Local Alignment Search Tool (BLAST). We found a strong statistical correlation between dominance of the SARS-CoV-2 in distributions of uneven similarities and the incidence and mortality of illness. Genomic annotation of the BLAST hits also showed that viruses from geographic regions with severe infections tended to have more dynamic genomic regions in the SARS-CoV-2 receptor-binding domain (RBD) and receptor-binding motif (RBM) of the spike protein (S protein). Dynamic domains in the S protein were also confirmed by a canyon region of mismatches coincident with RBM and RBD, without hits of alignments of 100% matching. Thus, our origin-independent analysis suggests that the dynamic and unstable SARS-CoV-2-RBD could be the main reason for diverse incidence and mortality of COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32924062/ doi: 10.1093/bib/bbaa208 id: cord-327690-di7hfghi author: Yang, Xiaobo title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study date: 2020-02-24 words: 3848.0 sentences: 241.0 pages: flesch: 53.0 cache: ./cache/cord-327690-di7hfghi.txt txt: ./txt/cord-327690-di7hfghi.txt summary: title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study METHODS: In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. In this study, we investigated critically ill patients with confirmed SARS-CoV-2 pneumonia who were admitted to Wuhan Jin Yin-tan hospital. The baseline SARS-CoV-2-associated morbidity and mortality data from this study will be of considerable value for the early identification of individuals who are at risk of becoming critically ill and who are most likely to benefit from intensive care treatment. During the outbreak of SARS-CoV-2 infection, the number of critically ill patients exceeded the capacity of ICUs. Therefore, two provisional ICUs were urgently established in Jin Yin-tan hospital and hence most mechanical ventilator settings and recordings were not recorded, except records of positive end-expiratory pressure in some cases. abstract: BACKGROUND: An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (SARS-CoV-2) started in December, 2019, in Wuhan, China. Information about critically ill patients with SARS-CoV-2 infection is scarce. We aimed to describe the clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia. METHODS: In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected. Data were compared between survivors and non-survivors. The primary outcome was 28-day mortality, as of Feb 9, 2020. Secondary outcomes included incidence of SARS-CoV-2-related acute respiratory distress syndrome (ARDS) and the proportion of patients requiring mechanical ventilation. FINDINGS: Of 710 patients with SARS-CoV-2 pneumonia, 52 critically ill adult patients were included. The mean age of the 52 patients was 59·7 (SD 13·3) years, 35 (67%) were men, 21 (40%) had chronic illness, 51 (98%) had fever. 32 (61·5%) patients had died at 28 days, and the median duration from admission to the intensive care unit (ICU) to death was 7 (IQR 3–11) days for non-survivors. Compared with survivors, non-survivors were older (64·6 years [11·2] vs 51·9 years [12·9]), more likely to develop ARDS (26 [81%] patients vs 9 [45%] patients), and more likely to receive mechanical ventilation (30 [94%] patients vs 7 [35%] patients), either invasively or non-invasively. Most patients had organ function damage, including 35 (67%) with ARDS, 15 (29%) with acute kidney injury, 12 (23%) with cardiac injury, 15 (29%) with liver dysfunction, and one (2%) with pneumothorax. 37 (71%) patients required mechanical ventilation. Hospital-acquired infection occurred in seven (13·5%) patients. INTERPRETATION: The mortality of critically ill patients with SARS-CoV-2 pneumonia is considerable. The survival time of the non-survivors is likely to be within 1–2 weeks after ICU admission. Older patients (>65 years) with comorbidities and ARDS are at increased risk of death. The severity of SARS-CoV-2 pneumonia poses great strain on critical care resources in hospitals, especially if they are not adequately staffed or resourced. FUNDING: None. url: https://www.sciencedirect.com/science/article/pii/S2213260020300795 doi: 10.1016/s2213-2600(20)30079-5 id: cord-275862-1aqtqaod author: Yang, Xiaodong title: A case of COVID-19 patient with the diarrhea as initial symptom and literature review date: 2020-04-15 words: 1316.0 sentences: 93.0 pages: flesch: 57.0 cache: ./cache/cord-275862-1aqtqaod.txt txt: ./txt/cord-275862-1aqtqaod.txt summary: authors: Yang, Xiaodong; Zhao, Jie; Yan, Qiang; Zhang, Shangxin; Wang, Yigao; Li, Yongxiang Here we reported a case of 2019 novel coronavirus-infected patient (NCIP) with diarrhea as the initial symptom. Laboratory examination shows that the absolute number of leukocytes, neutrophils and lymphocytes decrease in most patients, while CRP increases significantly and procalcitonin is usually normal [7] . In our case, the patient suffered from diarrhea as the initial symptom, which was relatively rare in NCIP. In conclusion, we reported the clinic feature and laboratory examination of a NCIP patient with diarrhea as the initial symptom. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China abstract: Since Dec 2019, a cluster of pneumonia outbreak in Wuhan, Hubei province, China, and soon spread to all province of China. The pathogen was proved to be a novel betacoronavirus called 2019 novel coronavirus (officially named by the World Health Organization as COVID-19). The typical clinical manifestations were fever, cough, dyspnea, and myalgia or fatigue. Less common symptoms included headache, diarrhea, nausea and vomiting. However diarrhea as the first symptom is rarely reported. Here we reported a case of 2019 novel coronavirus-infected patient (NCIP) with diarrhea as the initial symptom. Image of CT scan and laboratory examination and careful collected as well as detection of viral RNA in pharynx. The case demonstrate that gastrointestinal symptoms ware not rare in NCIP, and diarrhea could be the initial symptom. url: https://doi.org/10.1016/j.clinre.2020.03.013 doi: 10.1016/j.clinre.2020.03.013 id: cord-267579-gkvd0fol author: Yang, Xiaoyu title: Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period date: 2020-07-27 words: 470.0 sentences: 37.0 pages: flesch: 52.0 cache: ./cache/cord-267579-gkvd0fol.txt txt: ./txt/cord-267579-gkvd0fol.txt summary: title: Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period The 2019 novel coronavirus disease (COVID-19) causing acute infectious pneumonia has widely spread in China and other countries in the world. Studies have documented that novel coronavirus spread through human-to-human transmission in hospital and family setting 2,3 . Nevertheless, the transmission of the novel coronavirus from an asymptomatic carrier should be considered as a source of the infection of COVID-19 as well 4 . Therefore, it is of significance to identify and isolate asymptomatic carriers as well as patients with mild symptoms to prevent the spread of the virus. Clinical Characteristics of Coronavirus Disease 2019 in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients abstract: nan url: https://doi.org/10.1016/j.wneu.2020.07.144 doi: 10.1016/j.wneu.2020.07.144 id: cord-273751-61eeykj1 author: Yang, Zhenwei title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis date: 2020-04-10 words: 3003.0 sentences: 204.0 pages: flesch: 52.0 cache: ./cache/cord-273751-61eeykj1.txt txt: ./txt/cord-273751-61eeykj1.txt summary: title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis The inclusion criteria in this meta-analysis were as follows: (1) subjects in each study were patients with coronavirus infection; (2) the patients were divided into the experimental group using corticosteroids and the control group not using corticosteroids; (3) the outcomes included the use of corticosteroids in critical and noncritical patients, mortality, length of stay (LOS) and adverse reactions to corticosteroids. We extracted the following variables: the authors, the publication year, the study design, viral type, population, treatment details (including corticosteroid use, types and doses of corticosteroids, and other treatments), and outcome measures such as the use of corticosteroids in critical and non-critical patients, mortality, LOS and adverse reactions to corticosteroids (including bacterial infection, hyperglycemia, hypocalcemia and hypokalemia). In this systematic review and meta-analysis, the result indicated that patients with severe conditions were more likely to require corticosteroids therapy. abstract: OBJECTIVES: An outbreak of novel coronavirus in 2019 threatens the health of people, and there is no proven pharmacological treatment. Although corticosteroids were widely used during outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, their efficacy remainedhighly controversial. We aimed to further evaluate the influence of corticosteroids on patients with coronavirus infection. METHODS: We conducted a comprehensive search of literature published in PubMed, Embase, Cochrane library, and China National Knowledge Infrastructure (CNKI) from January 1, 2002 to March 15, 2020. All statistical analyses in this study were performed on stata14.0. RESULTS: A total of 5270 patients from 15 studies were included in this meta-analysis. The result indicated that critical patients were more likely to require corticosteroids therapy (risk ratio [RR] = 1.56, 95% confidence interval [CI] = 1.28-1.90, P<0.001). However, corticosteroid treatment was associated with higher mortality (RR = 2.11, 95%CI = 1.13-3.94, P = 0.019), longer length of stay (weighted mean difference [WMD] = 6.31, 95%CI = 5.26–7.37, P<0.001), a higher rate of bacterial infection (RR = 2.08, 95%CI = 1.54–2.81, P<0.001), and hypokalemia (RR = 2.21, 95%CI = 1.07–4.55, P = 0.032) but not hyperglycemia (RR = 1.37, 95%CI=0.68–2.76, P = 0.376) or hypocalcemia (RR = 1.35, 95%CI = 0.77–2.37, P = 0.302). CONCLUSIONS: Patients with severe conditions are more likely to require corticosteroids. Corticosteroid use is associated with increased mortality in patients with coronavirus pneumonia. url: https://doi.org/10.1016/j.jinf.2020.03.062 doi: 10.1016/j.jinf.2020.03.062 id: cord-282106-7k088cqv author: Yang, Zhi-yong title: A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice date: 2004 words: 3739.0 sentences: 193.0 pages: flesch: 48.0 cache: ./cache/cord-282106-7k088cqv.txt txt: ./txt/cord-282106-7k088cqv.txt summary: Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Immunization and challenge were performed in mice as described previously 18 , and viral replication (mean log 10 TCID 50 per g tissue with standard error) in the lower (a) and upper (b) respiratory tract after challenge with SARS-CoV was measured for five immunized animals inoculated with SDCD, SDTM or empty plasmid vector control. abstract: Public health measures have successfully identified and contained outbreaks of the severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV)(1,2,3,4,5), but concerns remain over the possibility of future recurrences. Finding a vaccine for this virus therefore remains a high priority. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Alternative forms of S were analysed by DNA immunization. These expression vectors induced robust immune responses mediated by CD4 and CD8 cells, as well as significant antibody titres, measured by enzyme-linked immunosorbent assay. Moreover, antibody responses in mice vaccinated with an expression vector encoding a form of S that includes its transmembrane domain elicited neutralizing antibodies. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Gene-based vaccination for the SARS-CoV elicits effective immune responses that generate protective immunity in an animal model. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature02463) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/15024391/ doi: 10.1038/nature02463 id: cord-261688-njlxrxv6 author: Yang, Ziwei title: Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date: 2020-08-12 words: 2508.0 sentences: 166.0 pages: flesch: 52.0 cache: ./cache/cord-261688-njlxrxv6.txt txt: ./txt/cord-261688-njlxrxv6.txt summary: Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA. Based on our existing experimental data, we propose a simple working model to illustrate how NSP8 218 negatively regulates innate immune responses by inhibiting MDA5 K63-linked polyubiquitination (Fig.5c) . abstract: Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Upon recognition of viral dsRNA, MDA5 is activated with K63-linked polyubiquitination and then triggers the recruitment of MAVS and activation of TBK1 and IKK, subsequently leading to IRF3 and NF-κB phosphorylation. Great numbers of symptomatic and severe infections of SARS-CoV-2 are spreading worldwide, and the poor efficacy of treatment with type I interferon and antiviral agents indicates that SARS-CoV-2 escapes from antiviral immune responses via an unknown mechanism. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. It downregulates the expression of type I IFNs, IFN-stimulated genes and proinflammatory cytokines by binding to MDA5 and impairing its K63-linked polyubiquitination. Our findings reveal that NSP8 mediates innate immune evasion during SARS-CoV-2 infection and may serve as a potential target for future therapeutics for SARS-CoV-2 infectious diseases. Importance The large-scale spread of COVID-19 is causing mass casualties worldwide, and the failure of antiviral immune treatment suggests immune evasion. It has been reported that several nonstructural proteins of severe coronaviruses suppress antiviral immune responses; however, the immune suppression mechanism of SARS-CoV-2 remains unknown. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA. url: https://doi.org/10.1101/2020.08.12.247767 doi: 10.1101/2020.08.12.247767 id: cord-350242-4u1iyf0p author: Yaniv, K. title: City-level SARS-CoV-2 sewage surveillance date: 2020-10-21 words: 2017.0 sentences: 140.0 pages: flesch: 61.0 cache: ./cache/cord-350242-4u1iyf0p.txt txt: ./txt/cord-350242-4u1iyf0p.txt summary: In this study we sampled an urban wastewater infrastructure in the city of Ashkelon, Israel, during the end of the first COVID-19 wave in May 2020 when the number of infections seemed to be waning. Using the linear equation, we calculated copy number of N1 gene in sewage samples reported in this study. If the sampling is extended to 24 hours, then the NVL can be expressed as number of SARS-CoV-2 RNA copies per 1,000 people per day. Ashkelon was chosen for surveillance of SARS-CoV-2 in sewage due to a relatively low COVID-19 prevalence during the time of study following a national lockdown period during Table S1 ). In conclusion, we present a proof-of-concept study demonstrating the feasibility of SARS-CoV-2 RNA detection in raw sewage originating from the city sewer system that reflects virus circulation in the assessed area. abstract: The COVID-19 pandemic created a global crisis impacting not only healthcare systems, but also world economies and society. Recent data have indicated that fecal shedding of SARS-CoV-2 is common, and that viral RNA can be detected in wastewater. This suggests that wastewater monitoring is a potentially efficient tool for both epidemiological surveillance, and early warning for SARS-CoV-2 circulation at the population level. In this study we sampled an urban wastewater infrastructure in the city of Ashkelon, Israel, during the end of the first COVID-19 wave in May 2020 when the number of infections seemed to be waning. We were able to show varying presence of SARS-CoV-2 RNA in wastewater from several locations in the city during two sampling periods. This was expressed as a new index, Normalized Viral Load (NVL), which can be used in different area scales to define levels of virus activity such as red (high) or green (no), and to follow morbidity in the population at tested area. Our index showed the rise in viral load between the two sampling periods (one week apart) and indicated an increase in morbidity that was evident a month later in the population. Thus, this methodology may provide an early indication for SARS-CoV-2 infection outbreak in a population before an outbreak is clinically apparent. url: https://doi.org/10.1101/2020.10.19.20215244 doi: 10.1101/2020.10.19.20215244 id: cord-102364-t5bt2eb4 author: Yao, Dehui title: Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date: 2020-06-08 words: 1852.0 sentences: 104.0 pages: flesch: 54.0 cache: ./cache/cord-102364-t5bt2eb4.txt txt: ./txt/cord-102364-t5bt2eb4.txt summary: In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor. Antibodies targeting the spike glycoprotein of SARS-CoV and MERS-CoV, especially its receptor-binding domain (RBD), was found to efficiently neutralize virus infection [1, 2] . In this work, we engineered a human ferritin heavy chain (HFtn) by fusing and presenting the RBM of its spike glycoprotein as potential vaccine of SARS-CoV-2. abstract: The outbreak of COVID-19 has so far inflicted millions of people all around the world and will have a long lasting effect on every aspect of everyone’s life. Yet there is no effective approved treatment for the disease. In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor. url: https://doi.org/10.1101/2020.05.25.115618 doi: 10.1101/2020.05.25.115618 id: cord-267426-3eu9umx5 author: Yao, Hangping title: Patient-derived mutations impact pathogenicity of SARS-CoV-2 date: 2020-04-19 words: 4615.0 sentences: 314.0 pages: flesch: 62.0 cache: ./cache/cord-267426-3eu9umx5.txt txt: ./txt/cord-267426-3eu9umx5.txt summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously referred to as 32 2019-nCoV), associated with the ongoing outbreak of atypical pneumonia, has already 33 caused a global pandemic, despite China''s extensive systematic effort to contain the 34 All rights reserved. 75 To address this, we characterized 11 SARS-CoV-2 viral isolates from patients (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.04.14.20060160 doi: medRxiv preprint 16 sequences and Taijima''s D is -2.8874 with a nucleotide diversity (π) of 0.000641 (p < 229 0.05 according to simulations performed in (Tajima, 1989) , indicating that the 230 SARS-CoV-2 genome has an excess of low-frequency alleles due to recent population 231 expansions, consistent with the repeated bottlenecking events during viral infections. abstract: The sudden outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity. Here we report functional characterizations of 11 patient-derived viral isolates, all of which have at least one mutation. Importantly, these viral isolates show significant variation in cytopathic effects and viral load, up to 270-fold differences, when infecting Vero-E6 cells. We observed intrapersonal variation and 6 different mutations in the spike glycoprotein (S protein), including 2 different SNVs that led to the same missense mutation. Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity. url: https://doi.org/10.1101/2020.04.14.20060160 doi: 10.1101/2020.04.14.20060160 id: cord-345103-b2wkm03g author: Yao, Hangping title: Molecular architecture of the SARS-CoV-2 virus date: 2020-09-06 words: 5755.0 sentences: 313.0 pages: flesch: 54.0 cache: ./cache/cord-345103-b2wkm03g.txt txt: ./txt/cord-345103-b2wkm03g.txt summary: Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). The postfusion S observed on the SARS-CoV-2 virus may come from 1) products of occasional, spontaneous dissociation of S1 (Cai et al., 2020) , which was cleaved by host proteinases; 2) syncytium naturally formed on infected cells , when budding progeny virions carried a few residual postfusion S from the cell surface; 3) sample preparation procedure, as cryo-EM images of ßpropiolactone fixed viruses showed most spikes present on the virus are postfusion-like Gao et al., 2020) . Three representative SARS-CoV-2 virus (Figures 1B and 4D ) and a bundle of postfusion S ( Figure 3B ) were reconstructed by projecting all spikes and RNPs onto their refined coordinates and merging the structures using Jsubtomo (Huiskonen et al., 2014) . Structures and distributions of SARS-CoV-2 spike proteins on intact virions abstract: SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in both pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass-spectrometry, which revealed highly similar overall processing states of the native glycans to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNP) and its higher-order assemblies were revealed. Overall, these characterizations have revealed the architecture of the SARS-CoV-2 virus in exceptional detail, and shed lights on how the virus packs its ∼30 kb long single-segmented RNA in the ∼80 nm diameter lumen. url: https://www.ncbi.nlm.nih.gov/pubmed/32979942/ doi: 10.1016/j.cell.2020.09.018 id: cord-354868-pqn59ojj author: Yao, Hebang title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date: 2020-09-25 words: 3231.0 sentences: 236.0 pages: flesch: 58.0 cache: ./cache/cord-354868-pqn59ojj.txt txt: ./txt/cord-354868-pqn59ojj.txt summary: title: A high-affinity RBD-targeting nanobody improves fusion partner''s potency against SARS-CoV-2 Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. A high-affinity RBD binder without neutralizing activity 85 Previously, we generated 99 sybodies from three highly diverse synthetic libraries by ribosome and phage display with in vitro selections against the SARS-CoV-2 RBD. Consistent with its inability to neutralize SARS-CoV-2 pseudovirus, SR31 did not affect RBD-ACE2 binding (Fig. 1C) . Most RBD-targeting neutralizing antibodies, including neutralizing nanobodies characterized so far (8, 13-15, 19, 20, 22-24, 26-28, 34, 35, 37) , engage the RBD at the receptor-binding motif (RBM) (Fig. 3A) , thus competing off ACE2 and preventing viral entry. Taken together, the structural data rationalize the high-affinity binding between SR31 and RBD, and its inability to neutralize SARS-CoV-2. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 abstract: A key step to the SARS-CoV-2 infection is the attachment of its Spike receptor-binding domain (S RBD) to the host receptor ACE2. Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. Simple and effective strategies to increase potency are desirable for such studies when antibodies are only modestly effective. Here, we identify and characterize a high-affinity synthetic nanobody (sybody, SR31) as a fusion partner to improve the potency of RBM-antibodies. Crystallographic studies reveal that SR31 binds to RBD at a conserved and ‘greasy’ site distal to RBM. Although SR31 distorts RBD at the interface, it does not perturb the RBM conformation, hence displaying no neutralizing activities itself. However, fusing SR31 to two modestly neutralizing sybodies dramatically increases their affinity for RBD and neutralization activity against SARS-CoV-2 pseudovirus. Our work presents a tool protein and an efficient strategy to improve nanobody potency. url: https://doi.org/10.1101/2020.09.24.312595 doi: 10.1101/2020.09.24.312595 id: cord-322005-70snojec author: Yao, Pingping title: Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell date: 2020-06-19 words: 890.0 sentences: 71.0 pages: flesch: 65.0 cache: ./cache/cord-322005-70snojec.txt txt: ./txt/cord-322005-70snojec.txt summary: title: Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell In a recent report, 149 mutations were found among 103 sequenced isolates of SARS-CoV-2 . To investigate whether our viruses show mutations different from other reported SARS-CoV-2, all the seven isolates were sequenced at the 3rd passage and the sequences were aligned with coding sequence (CDS) of SARS-CoV-2 Wuhan-Hu-1 (NC_045512). It is interesting to note that these seven patients infected with SARS-CoV-2 have high viral load in the early stage of clinical sign, which is consistent with previous reports (Kim et al. A The cytopathic effect was observed in Vero cells infected with the isolated viruses at 5 dpi. In conclusion, seven SARS-CoV-2 strains were isolated, sequenced and characterized in Vero cells, and a deletion mutation was identified after short passage in Vero cells. Viral load kinetics of SARS-CoV-2 infection in first two patients in Korea SARS-CoV-2 viral load in upper respiratory specimens of infected patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32562199/ doi: 10.1007/s12250-020-00241-2 id: cord-353103-sdij1d90 author: Yao, Xueting title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 words: 3449.0 sentences: 191.0 pages: flesch: 52.0 cache: ./cache/cord-353103-sdij1d90.txt txt: ./txt/cord-353103-sdij1d90.txt summary: title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug''s safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. abstract: BACKGROUND: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) first broke out in Wuhan (China) and subsequently spread worldwide. Chloroquine has been sporadically used in treating SARS-CoV-2 infection. Hydroxychloroquine shares the same mechanism of action as chloroquine, but its more tolerable safety profile makes it the preferred drug to treat malaria and autoimmune conditions. We propose that the immunomodulatory effect of hydroxychloroquine also may be useful in controlling the cytokine storm that occurs late-phase in critically ill SARS-CoV-2 infected patients. Currently, there is no evidence to support the use of hydroxychloroquine in SARS-CoV-2 infection. METHODS: The pharmacological activity of chloroquine and hydroxychloroquine was tested using SARS-CoV-2 infected Vero cells. Physiologically-based pharmacokinetic models (PBPK) were implemented for both drugs separately by integrating their in vitro data. Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug’s safety profile. RESULTS: Hydroxychloroquine (EC(50)=0.72 μM) was found to be more potent than chloroquine (EC(50)=5.47 μM) in vitro. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. CONCLUSIONS: Hydroxychloroquine was found to be more potent than chloroquine to inhibit SARS-CoV-2 in vitro. url: https://www.ncbi.nlm.nih.gov/pubmed/32150618/ doi: 10.1093/cid/ciaa237 id: cord-261472-qcu73sdu author: Yao, Yong Xiu title: Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date: 2004-07-01 words: 3851.0 sentences: 159.0 pages: flesch: 47.0 cache: ./cache/cord-261472-qcu73sdu.txt txt: ./txt/cord-261472-qcu73sdu.txt summary: Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. The possible use of insect cell-displayed S protein for diagnostic application was assessed by examining fragment reactivity with serum samples from patients infected with human CoV 229E and also with serum from a patient with suspected but clinically unconfirmed SARS (serum sample 3118). Of the 2 assay formats we used, nondenatured S protein present on the cell surface provided the most sensitive detection of antibodies, with clear shifts in fluorescence for serum samples from patients with suspected but clinically unconfirmed SARS. abstract: Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. S protein could be cleaved by exogenous trypsin but not by coexpressed furin, suggesting that the protein is not normally processed during infection. Reactivity was evident by both flow cytometry and Western blot assays, but the pattern of reactivity varied according to assay and sequence of the antigen. The antibody response to SCoV S protein involves antibodies to both linear and conformational epitopes, with linear epitopes associated with the carboxyl domain and conformational epitopes associated with the amino terminal domain. Recombinant SCoV S protein appears to be a suitable antigen for the development of an efficient and sensitive diagnostic test for SARS, but our data suggest that assay format and choice of S antigen are important considerations. url: https://www.ncbi.nlm.nih.gov/pubmed/15195247/ doi: 10.1086/421280 id: cord-289711-4ab3d00h author: Yarmarkovich, Mark title: Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date: 2020-06-08 words: 5290.0 sentences: 252.0 pages: flesch: 46.0 cache: ./cache/cord-289711-4ab3d00h.txt txt: ./txt/cord-289711-4ab3d00h.txt summary: Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 abstract: Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. We further prioritize genomic regions that generate highly dissimilar peptides from the human proteome, and are also predicted to produce B cell epitopes. We propose sixty-five 33mer peptide sequences, a subset of which can be tested using DNA or mRNA delivery strategies. These include peptides that are contained within evolutionarily divergent regions of the spike protein reported to increase infectivity through increased binding to the ACE2 receptor and within a newly evolved furin cleavage site thought to increase membrane fusion. Validation and implementation of this vaccine concept could specifically target specific vulnerabilities of SARS-CoV-2 and should engage a robust adaptive immune response in the vast majority of the population. url: https://doi.org/10.1016/j.xcrm.2020.100036 doi: 10.1016/j.xcrm.2020.100036 id: cord-253457-gawn4s9g author: Yau, Kevin title: COVID-19 Outbreak in an Urban Hemodialysis Unit date: 2020-07-15 words: 2215.0 sentences: 145.0 pages: flesch: 47.0 cache: ./cache/cord-253457-gawn4s9g.txt txt: ./txt/cord-253457-gawn4s9g.txt summary: Patients with SARS-CoV-2 infection including asymptomatic individuals were treated with droplet and contact precautions until confirmation of negative SARS-CoV-2 RT-PCR testing. Nasopharyngeal swabs were performed by physicians, nurse practitioners, and staff from the hospital''s COVID-19 Assessment Centre under droplet and contact precautions in the hemodialysis unit with curtains drawn around the dialysis station at which the patient was being swabbed. At the time of testing, six (55%) patients and six (55%) staff positive for SARS-CoV-2 were asymptomatic. Patients with confirmed SARS-CoV-2 infection including asymptomatic individuals were dialyzed in a dedicated room separate from the main hemodialysis unit for the duration of their infection and maintained on droplet and contact precautions. Five hemodialysis staff were allowed to return to work following symptom resolution and documentation of two negative SARS-CoV-2 nasopharyngeal swabs performed 14 days from symptom onset. Infection control authorities concluded that SARS-CoV-2 transmission during an outbreak at the St. Michael''s Hospital hemodialysis unit was likely to have originated from two index cases. abstract: RATIONALE & OBJECTIVE: Hemodialysis patients are at increased risk for COVID-19 transmission due, in part, to difficulty maintaining physical distancing. Our hemodialysis unit experienced a COVID-19 outbreak despite following symptom-based screening guidelines. We describe the course of the COVID-19 outbreak and the infection control measures taken for mitigation. STUDY DESIGN: Retrospective cohort study SETTING & PARTICIPANTS: 237 maintenance hemodialysis patients and 93 hemodialysis staff at a single hemodialysis centre in Toronto, Canada. EXPOSURE: Universal screening of patients and staff with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). OUTCOMES: The primary outcome was detection of SARS-CoV-2 in nasopharyngeal samples from patients and staff using reverse transcriptase-polymerase chain reaction (RT-PCR) . ANALYTICAL APPROACH: Descriptive statistics were used for clinical characteristics and the primary outcome. RESULTS: Eleven (4.6%) of 237 hemodialysis patients and 11 of 93 (12%) staff members had a positive RT-PCR test for SARS-CoV-2. Among individuals testing positive, 12 of 22 (55%) were asymptomatic at time of testing, and 7 of 22 (32%) were asymptomatic for the duration of follow-up. One patient was hospitalized at the time of SARS-CoV-2 infection and four additional patients with positive tests were subsequently hospitalized. Two patients (18%) required admission to the intensive care unit. After 30 days follow-up no patients had died or required mechanical ventilation. No hemodialysis staff required hospitalization. Universal droplet and contact precautions were implemented during the outbreak. Hemodialysis staff with SARS-CoV-2 infection were placed on home quarantine regardless of symptom status. Patients with SARS-CoV-2 infection including asymptomatic individuals were treated with droplet and contact precautions until confirmation of negative SARS-CoV-2 RT-PCR testing. Analysis of the outbreak identified two index cases with subsequent nosocomial transmission within the dialysis unit and in shared shuttle buses to the hemodialysis unit. LIMITATIONS: Single centre study. CONCLUSIONS: Universal SARS-CoV-2 testing and universal droplet and contact precautions in the setting of an outbreak appeared to be effective in preventing further transmission. url: https://api.elsevier.com/content/article/pii/S0272638620308118 doi: 10.1053/j.ajkd.2020.07.001 id: cord-270528-3rsv3jlh author: Yazdanpanah, Fereshteh title: The immune system and COVID-19: Friend or foe? date: 2020-06-02 words: 3134.0 sentences: 192.0 pages: flesch: 48.0 cache: ./cache/cord-270528-3rsv3jlh.txt txt: ./txt/cord-270528-3rsv3jlh.txt summary: The pathogenesis of this virus is not yet clearly understood, but there is evidence of a hyper-inflammatory immune response in critically ill patients, which leads to acute respiratory distress syndrome (ARDS) and multi-organ failure. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID19) , and has affected people''s lives globally, since first observed in Wuhan, China in the last days of 2019 (1, 2) . On the other hand, the hyper-inflammatory and cytokine release syndrome (CRS) typical of COVID-19 causes tissue damage to the lung epithelium and ARDS (32); therefore, immunosuppressive drugs may be useful as there is some evidence that an anti-IL-6 approach is effective in critically ill patients in the ICU (33) . Also, due to the overexpression of ACE2 in islet cells of the pancreas, SARS-CoV-2 may be a diabetogenic virus that causes severe instability in the blood glucose levels of diabetes patients, which worsens the inflammatory imbalance (37) . abstract: AIM: Coronavirus disease 2019 (COVID-19) is a novel highly contagious infection caused by SARS-CoV-2, which has been became a global public health challenge. The pathogenesis of this virus is not yet clearly understood, but there is evidence of a hyper-inflammatory immune response in critically ill patients, which leads to acute respiratory distress syndrome (ARDS) and multi-organ failure. MATERIAL AND METHODS: A literature review was performed to identify relevant articles on COVID-19 published up to April 30, 2020. The search resulted in 361 total articles. After reviewing the titles and abstracts for inclusion, some irrelevant papers were excluded. Additional relevant articles were identified from a review of citations referenced. KEY FINDINGS: SARS-CoV-2, directly and indirectly, affects the immune system and avoids being eliminated in early stages. On the other hand, the secretion of inflammatory cytokines creates critical conditions that lead to multi-organ failure. SIGNIFICANCE: The immune system which is affected by the virus tries to respond via a cytokine storm and hyperinflammation, which itself leads to further multi-organ damage and even death. url: https://www.ncbi.nlm.nih.gov/pubmed/32502542/ doi: 10.1016/j.lfs.2020.117900 id: cord-314111-bqmfmcfm author: Yazdanpanah, Yazdan title: Les antirétroviraux ont-ils une place dans le traitement du syndrome respiratoire aigu sévère ? date: 2006-01-31 words: 1902.0 sentences: 180.0 pages: flesch: 67.0 cache: ./cache/cord-314111-bqmfmcfm.txt txt: ./txt/cord-314111-bqmfmcfm.txt summary: Dans le traitement du syndrome respiratoire aigu sévère (SRAS) liés à severe acute respiratory syndrome-Coronavirus (SARS-CoV), l''évaluation de l''efficacité des anti-VIH était essentiellement motivée par l''absence d''alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Dans le traitement du SARS-CoV, l''évaluation de l''efficacité des anti-VIH, le virus pour lequel il existe le plus grand nombre de molécules, était essentiellement motivée par l''absence d''alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Compte tenu de ces observations, 2 hypothèses ont été proposées: l''interférence de l''infection par le VIH avec la réplication du SARS-CoV pouvant empêcher le développement du SRAS, et/ou un éventuel effet prophylactique des traitements antirétroviraux. Les auteurs ont observé un nombre significativement moins important de syndromes respiratoires aigus et de décès (2,4 %) chez 41 patients atteints de SRAS recevant dès l''admission un traitement par lopinavir/ritonavir (400/100 mg x 2/j) et ribavirine que dans une cohorte historique de 111 patients ayant reçu la ribavirine seule à leur admission (28,8 %). abstract: Points essentiels L’inhibition d’une protéase ou d’une protéine de fusion est une approche générale en chimiothérapie antivirale et n’est pas spécifique du VIH. Les molécules qui provoquent ces phénomènes sont, en général, très spécifiques d’un virus ou d’une famille virale. Dans le traitement du syndrome respiratoire aigu sévère (SRAS) liés à severe acute respiratory syndrome-Coronavirus (SARS-CoV), l’évaluation de l’efficacité des anti-VIH était essentiellement motivée par l’absence d’alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Aucun des traitements commercialisés dans la prise en charge des patients vivant avec le VIH ne semble efficace dans le traitement du du SARS-CoV. Les données in vitro sont non concluantes et les données cliniques fragiles. Des résultats préliminaires sur les inhibiteurs de protéase et les inhibiteurs d’entrée à un stade précoce de développement, très en amont des phases cliniques, ouvrent des perspectives intéressantes. Key points Inhibition of viral assembly (protease inhibitors) and of fusion of viral and target membranes (fusion inhibitors) are general approaches to antiviral treatment, not specific for HIV. Nonetheless, the agents that induce these phenomena are most often specific for a given virus or virus family. Drugs developed for HIV treatment were reevaluated for use against severe acute respiratory syndrome-coronavirus (SARS-CoV) during and after the epidemic in 2003, in view of the absence of any other available treatment. Of the protease and entry inhibitors approved for treating HIV-infected patients, none was effective against SARS-CoV, although in vitro activity against this virus was reported for the protease inhibitor lopinavir/ritonavir, in results that have not been confirmed in the most recent studies. The epidemiologic methods used to assess this drug's efficacy are not robust. Preliminary results for SARS treatment with protease and entry inhibitors, although at early stages of development, are promising. url: https://www.sciencedirect.com/science/article/pii/S0755498206745316 doi: 10.1016/s0755-4982(06)74531-6 id: cord-356005-zhwtlik6 author: Yazhini, Arangasamy title: D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date: 2020-11-02 words: 2626.0 sentences: 142.0 pages: flesch: 47.0 cache: ./cache/cord-356005-zhwtlik6.txt txt: ./txt/cord-356005-zhwtlik6.txt summary: Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ''closed'' and ''partially open'' conformations. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant. To study the effect of D614G variation on the thermodynamic stability of the spike protein trimer, we calculated free energy changes upon aspartate to glycine substitution using buildmodel function in FoldX (Schymkowitz et al., 2005) . The table contains details of frustration index of inter-residue contacts present at 614th position of spike protein trimer in closed and partially open conformations. abstract: SARS-CoV-2 spike protein with D614G substitution has become the dominant variant in the ongoing COVID-19 pandemic. Several studies to characterize the new virus expressing G614 variant show that it exhibits increased infectivity compared to the ancestral virus having D614 spike protein. Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ‘closed’ and ‘partially open’ conformations. We find that the local interactions mediated by aspartate at the 614th position are energetically frustrated and create unfavourable environment. Whereas, glycine at the same position confers energetically favourable environment and strengthens intra-as well as inter-protomer association. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant. url: https://doi.org/10.1101/2020.11.02.364273 doi: 10.1101/2020.11.02.364273 id: cord-291012-y0ufzx93 author: Ye, Qing title: SARS-CoV-2 infection causes transient olfactory dysfunction in mice date: 2020-11-10 words: 1846.0 sentences: 125.0 pages: flesch: 51.0 cache: ./cache/cord-291012-y0ufzx93.txt txt: ./txt/cord-291012-y0ufzx93.txt summary: Robust viral nucleocapsid (N) protein was detected in the 89 lung from SARS-CoV-2 infected hACE2 mice, but not from the control animals 90 ( Figure S1B ). Remarkably, a significantly increased latency (152.8 s v.s. 81.8 s; p=0.022) to locate 103 food pellets was observed in SARS-CoV-2 infected mice as compared with the control 104 animals on 2 dpi ( Figure 1D ). Further RT-qPCR assay showed a dozen of 211 OR genes were significantly down regulated in response to SARS-CoV-2 infection 212 ( Figure 5E ), which may also attribute to the observed olfactory dysfunction. Interestingly, SARS-CoV-2 positive signals were also observed in mOSNs and HBCs 245 of infected animals, although we didn''t detect any hACE2 expression in these cells. A) Representative multiplex immunofluorescent staining shows SARS-CoV-2 674 (SARS-CoV-2 N protein-positive) infects sustentacular cells (CK8-positive, yellow 675 arrows), Bowman''s gland cells (Sox9/CK8-positive, white arrows), microvillar cells 676 (CD73/CK8-positive, cyan arrows), HBCs (CK5-postitive, gold arrows) and iOSNs 677 (GAP43-positive abstract: Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowman’s gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19. url: https://doi.org/10.1101/2020.11.10.376673 doi: 10.1101/2020.11.10.376673 id: cord-279766-s3ms5f56 author: Ye, Zhongde title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis date: 2008-07-28 words: 3408.0 sentences: 181.0 pages: flesch: 46.0 cache: ./cache/cord-279766-s3ms5f56.txt txt: ./txt/cord-279766-s3ms5f56.txt summary: title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis All these data suggest that ORF-6 induces apoptosis via Caspase-3 mediated, ER stress and JNK-dependent pathways. We observed that ORF-6 was able to induce apoptosis when overexpressed in Vero E6 and COS-7 cells (Fig. 1A and B) . The death rates were comparable to the rates caused by the overexpression of Bax, a well-known pro-apoptotic member of the Bcl-family, and ORF-7a, a SARS protein that has been shown to induce apoptosis [19] . Our observation suggests that overexpression of ORF-6 induced apoptosis via a Caspase-3-dependent pathway. One of the possible mechanisms for SARS protein-induced cell death is via the JNK pathway. Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells G0/G1 arrest and apoptosis induced by SARS-CoV 3b protein in transfected cells abstract: Severe acute respiratory syndrome (SARS) coronavirus (CoV) spread from China to more than 30 countries, causing severe outbreaks of atypical pneumonia and over 800 deaths worldwide. CoV primarily infects the upper respiratory and gastrointestinal tract; however, SARS-CoV has a unique pathogenesis because it infects both the upper and lower respiratory tracts and leads to human respiratory diseases. SARS-CoV genome has shown containing 14 open reading frames (ORFs) and 8 of them encode novel proteins. Previous reports show that overexpression of ORF-3a, ORF-3b and ORF-7a induce apoptosis. In this report, we demonstrate that overexpression of ORF-6 also induces apoptosis and that Caspase-3 inhibitor and JNK inhibitor block ORF-6 induced apoptosis. Importantly, the protein level of ER chaperon protein, GRP94, was up-regulated when ORF-6 was overexpressed. All these data suggest that ORF-6 induces apoptosis via Caspase-3 mediated, ER stress and JNK-dependent pathways. url: https://api.elsevier.com/content/article/pii/S0304416508001608 doi: 10.1016/j.bbagen.2008.07.009 id: cord-353704-lfndq85x author: Ye, Zi-Wei title: Zoonotic origins of human coronaviruses date: 2020-03-15 words: 8096.0 sentences: 434.0 pages: flesch: 54.0 cache: ./cache/cord-353704-lfndq85x.txt txt: ./txt/cord-353704-lfndq85x.txt summary: In contrast, SARS-CoV, MERS-CoV and the newly-identified SARS-CoV-2 are highly pathogenic, causing severe lower respiratory tract infection in relatively more patients with a higher chance to develop acute respiratory distress syndrome (ARDS) and extrapulmonary manifestations. The 2019 novel HCoV (2019-nCoV), which has subsequently been renamed SARS-CoV-2, is the causative agent of the ongoing epidemic of coronavirus disease 2019 (COVID19) , which has claimed more than 3,120 lives and infected more than 91,000 people as of March 3, 2020 [19] . All these four communityacquired HCoVs have been well adapted to humans and are generally less likely to mutate to cause highly pathogenic diseases, though accidents did occur for unknown reasons as in the rare case of a more virulent subtype of HCoV-NL63, which has recently been reported to cause severe lower respiratory tract infection in China [38] . Alternatively, whereas bat alpha-CoVs serve as the gene pool of HCoV-229E, alpacas and dromedary camels might serve as intermediate hosts that transmit viruses to humans, exactly as in the case of MERS-CoV [69] . abstract: Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted. url: https://www.ncbi.nlm.nih.gov/pubmed/32226286/ doi: 10.7150/ijbs.45472 id: cord-266755-y2lf7ssp author: Yehualashet, Awgichew Shewasinad title: ACEIs and ARBs and Their Correlation with COVID-19: A Review date: 2020-09-16 words: 4160.0 sentences: 221.0 pages: flesch: 46.0 cache: ./cache/cord-266755-y2lf7ssp.txt txt: ./txt/cord-266755-y2lf7ssp.txt summary: 21, 22 Both ACE-1 and ACE-2 cleave angiotensin peptides in that ACE-1 cleaves angiotensin I and generating angiotensin (Ang) II, which causes vasoconstriction, bronchoconstriction, increases vascular permeability, inflammation, and fibrosis and enhance the development of acute respiratory disease syndrome (ARDS) and lung failure in patients infected with SARS-CoV-2. 36 The probable rational proposed for the possible relation between the use of ACEIs/ARBs, and progression to ARDS in COVID-19 is the increased availability of ACE-2 attached to surface in the lung endothelium, an inherent effect of these two classes, leading to enhanced coupling of SARS-CoV2 to ACE-2 and its consequent cell entry. Based on prior animal studies, it was suggested that proposed ACEIs and ARBs can enhance ACE2 activity and thereby increase infectivity of COVID-19 virus. 48 In severe lung injury animal models, preclinical studies have showed that ACE2 is significantly downregulated and it has been shown that the inhibition of the angiotensin type 1 receptor by ARB like losartan reduces severe acute lung injury in mice administered with the spike glycoprotein of SARS-CoV. abstract: Although some animal studies suggested that the use of ACEIs/ARBs could contribute for the prevention and treatment of the effects of the COVID-19 infection, there are also contradictory scenarios indicating that their use may exacerbate the deleterious conditions of the infection. As a result of the paradoxical issue of using ACEIs/ARBs during COVID-19, it is still an area requiring extended investigation to prove. Additionally, a trial evidence of their efficacy and the possible benefit risk analysis of these conventional drugs during COVID-19 in connection with other comorbidities like hypertension, heart failure, and renal disease associated with diabetes should also be addressed. url: https://doi.org/10.2147/idr.s264882 doi: 10.2147/idr.s264882 id: cord-301388-p3juk2vv author: Yen, Muh-Yong title: Recommendations for protecting against and mitigating the COVID-19 pandemic in long-term care facilities date: 2020-04-10 words: 3933.0 sentences: 225.0 pages: flesch: 47.0 cache: ./cache/cord-301388-p3juk2vv.txt txt: ./txt/cord-301388-p3juk2vv.txt summary: 5, 6 It is therefore essential that the health care community develop infection control guidelines on prevention measures to address pandemic preparedness and response in LTCFs. 7, 8 Here we offer recommendations based on what we consider the "gold standard" for pandemic preparedness and response in LTCFs. However, we recognize that the ideal response we describe is likely not an option for LTCFs in the midst of the current COVID-19 pandemic. 18 Given the significant vulnerability of LTCF residents and staff to the COVID-19 pandemic, here we recommend adopting eTCB, and adapting it to LTCFs. Enhanced TCB protects LTCF staff and residents from droplet, contact and fomite transmission through a process including triage prior to entering the facility, separate zones of risk within the facility and checkpoint hand hygiene throughout. abstract: The COVID-19 outbreak has drawn heightened attention from public health scholars researching ways to limit its spread. Much of the research has been focused on minimizing transmission in hospitals and in the general community. However, a particularly vulnerable community that has received relatively little attention is elders residing in long-term care facilities (LTCFs). In this article we address this relative lack of attention, arguing that enhanced traffic control bundling (eTCB) can and should be adopted and implemented as a means of protecting LTCF residents and staff. Enhanced TCB has been widely applied in hospital settings and has proven effective at limiting droplet and fomite transmissions both within hospitals and between hospitals and the general community. By effectively adapting eTCB to LTCF conditions, particularly by incorporating compartmentalization within zones plus active surveillance, COVID-19 transmission into and throughout LTCFs can be minimized, thereby saving numerous lives among an especially vulnerable population. url: https://www.ncbi.nlm.nih.gov/pubmed/32303480/ doi: 10.1016/j.jmii.2020.04.003 id: cord-033204-v17d98c9 author: Yen, Wei‐Ting title: Taiwan’s COVID‐19 Management: Developmental State, Digital Governance, and State‐Society Synergy date: 2020-09-23 words: 6583.0 sentences: 387.0 pages: flesch: 53.0 cache: ./cache/cord-033204-v17d98c9.txt txt: ./txt/cord-033204-v17d98c9.txt summary: The country''s success mainly lies in three factors: (1) reliance on the mask policy as the main disease prevention measure and the ability to quickly expand mask production capacity; (2) use of big data and technology to enhance effective implementation of disease prevention and detection measures; and (3) strong state‐society relations favoring transparency, communication, and collaboration. I then turn to the crisis management framework, discussing how the developmental state foundations and the democratic regime lead to Taiwan''s success on mask policy, digital governance, and strong state-society collaboration and communication. Moreover, the capacity of a government to define and communicate the uncertainty the crisis brings is also an essential element in an effective response because collective sense-making can help increase citizens'' voluntary compliance. Specifically, during COVID-19, digital governance helped improve disease detection through integrated databases of people''s health records and travel history, through more accurate contact tracing, and through active surveillance tracking for people under quarantine. abstract: This article examines the reasons behind Taiwan’s effective COVID‐19 response. While some have argued that Taiwan’s success with COVID‐19 is based on its experience with SARS, I argue that we should not attribute Taiwan’s effective response solely to its SARS experience. The country’s success mainly lies in three factors: (1) reliance on the mask policy as the main disease prevention measure and the ability to quickly expand mask production capacity; (2) use of big data and technology to enhance effective implementation of disease prevention and detection measures; and (3) strong state‐society relations favoring transparency, communication, and collaboration. The first two factors can trace their roots to the country’s developmental state model. Democracy provides the institutional underpinning for a vibrant civil society and the synergy between state and civil society, strengthening Taiwan’s crisis governance legitimacy and increasing citizens’ voluntary compliance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7537052/ doi: 10.1111/aspp.12541 id: cord-332292-n7k4va9k author: Yen, Yung-Feng title: Olfactory disorder in patients infected with SARS-CoV-2 date: 2020-08-20 words: 1239.0 sentences: 86.0 pages: flesch: 57.0 cache: ./cache/cord-332292-n7k4va9k.txt txt: ./txt/cord-332292-n7k4va9k.txt summary: Therefore, we conducted this cohort study to characterize the clinical course of olfactory disorder in COVID-19 patients in Taiwan. Two patients exhibited anosmia as the main symptom at the onset of SARS-CoV-2 infection, while one patient had hyposmia 4 days after the onset of COVID-19. 7 All patients with olfactory disorder in our study fully recovered their olfactory function before the RT-PCR results for SARS-CoV-2 turned negative. This cohort study was the first to characterize the clinical course of olfactory disorder in COVID-19 patients. 2 Limited COVID-19 cases in this study may preclude this J o u r n a l P r e -p r o o f analysis from estimating the precise prevalence of olfactory disorder in patients infected with SARS-CoV-2. However, consistent with a current report, 7 the findings of our study suggest that olfactory disorder is not an uncommon symptom in COVID-19 patients. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study abstract: Abstract Three (60%) of five patients with coronavirus disease 2019 (COVID-19) had olfactory disorder. Two exhibited anosmia at the onset of COVID-19, while one had hyposmia 4 days after the onset of COVID-19. All patients with olfactory disorder were completely recovered with a mean recovery length of 11.3 days. url: https://api.elsevier.com/content/article/pii/S1684118220302085 doi: 10.1016/j.jmii.2020.08.010 id: cord-275552-ijxxeo27 author: Yen, Zui-Shen title: How much would you be willing to pay for preventing a new dangerous infectious disease: A willingness-to-pay study in medical personnel working in the emergency department date: 2007-10-10 words: 2704.0 sentences: 166.0 pages: flesch: 56.0 cache: ./cache/cord-275552-ijxxeo27.txt txt: ./txt/cord-275552-ijxxeo27.txt summary: The objective of this study was to estimate the median amount of money ED personnel would be willing to pay for preventing nosocomial severe acute respiratory syndrome (SARS). 9 In this study, CVM was used to estimate the median amount emergency medical personnel would be willing to pay for a hypothetical vaccine to prevent developing nosocomial SARS. We used this study as an example to demonstrate that medical personnel would be willing to pay substantial monetary amounts to avert the risk of nosocomial SARS infection. However, we found that the median amount medical personnel in the ED would be willing to pay for a SARS vaccine was US $1,762, which was exceedingly high compared to the usual cost of a vaccine and equal to 14% of the 2002 Taiwan gross domestic product per capita (US $12,588). abstract: BACKGROUND: The risk of developing nosocomial infectious diseases among medical personnel in the emergency department (ED) can result in tremendous psychologic stress. The objective of this study was to estimate the median amount of money ED personnel would be willing to pay for preventing nosocomial severe acute respiratory syndrome (SARS). METHODS: A contingent valuation approach with close-ended format was used. During the study period from June 15, 2003 through June 30, 2003, a convenience sample of all medical personnel working in the ED of National Taiwan University Hospital was carried out. Participants were interviewed by a standard questionnaire and were asked to choose whether or not they would pay at a specified price to purchase a hypothetical SARS vaccine. A logistic regression model was created to evaluate the relationship between willingness-to-pay and the log of the price offered in the bid questions. The median and mean amounts of willingness-to-pay were calculated. RESULTS: A total of 115 subjects were interviewed and most were nurses (68.7%). The median and mean amount subjects reported being willing to pay for a SARS vaccine was US $1762 and US $720, respectively. Subject responses were significantly related to the price of vaccination and their type of job. CONCLUSIONS: Medical personnel in the ED reported that they would be willing to pay substantial monetary amounts for preventing nosocomial SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/17936142/ doi: 10.1016/j.ajic.2006.09.008 id: cord-355807-q3bngari author: Yepes-Pérez, Andres F. title: Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling date: 2020-10-29 words: 8807.0 sentences: 453.0 pages: flesch: 48.0 cache: ./cache/cord-355807-q3bngari.txt txt: ./txt/cord-355807-q3bngari.txt summary: Molecular modeling was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (cat''s claw) focusing on the binding interface of the RBD–ACE-2 and the viral spike protein. tomentosa against focusing both on the binding interface of the RBD-ACE-2 and inside SARS-CoV-2 RBD spike protein, (2) simulations of ligand pathway of the best predicted compounds from step 1 to evaluate convenient entrance mechanism of the compounds to the binding site, (3) MD simulation to assess the stability of the best protein-ligand complexes from 1, (4) calculation of pharmacokinetics parameters for the most qualified compounds resulting from the previous parts of the docking protocol. Next, we used the cryo-EM structure of SARS-CoV-2 spike protein (PDB code: 6VYB) in their open state (Lipinski et al., 2012) to explore the potential inhibition of components of the cat''s claw, selecting ACE-2-binding pocket to this study. abstract: COVID-19 is a novel severe acute respiratory syndrome coronavirus. Currently, there is no effective treatment and vaccines seem to be the solution in the future. Virtual screening of potential drugs against the S protein of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has provided small molecular compounds with a high binding affinity. Unfortunately, most of these drugs do not attach with the binding interface of the receptor-binding domain (RBD)–angiotensin-converting enzyme-2 (ACE-2) complex in host cells. Molecular modeling was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (cat’s claw) focusing on the binding interface of the RBD–ACE-2 and the viral spike protein. The in silico approach starts with protein–ligand docking of 26 Cat’s claw key components followed by molecular dynamics simulations and re-docked calculations. Finally, we carried out drug-likeness calculations for the most qualified cat’s claw components. The structural bioinformatics approaches led to the identification of several bioactive compounds of U. tomentosa with potential therapeutic effect by dual strong interaction with interface of the RBD–ACE-2 and the ACE-2 binding site on SARS-CoV-2 RBD viral spike. In addition, in silico drug-likeness indices for these components were calculated and showed good predicted therapeutic profiles of these phytochemicals found in U. tomentosa (cat’s claw). Our findings suggest the potential effectiveness of cat’s claw as complementary and/or alternative medicine for COVID-19 treatment. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1837676 doi: 10.1080/07391102.2020.1837676 id: cord-351687-6otr8zl3 author: Yesilkaya, Umit Haluk title: Neuroimmune correlates of the nervous system involvement of COVID-19: A commentary date: 2020-05-27 words: 934.0 sentences: 62.0 pages: flesch: 40.0 cache: ./cache/cord-351687-6otr8zl3.txt txt: ./txt/cord-351687-6otr8zl3.txt summary: • Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Strikingly, they postulated that enhanced inflammatory signalling and immune-mediated processes which are activated by SARS-CoV-2 might imitate the molecular architecture of self-directed immunity in the peripheral nervous system and might lead to Guillain Barre syndrome (GBS), an autoimmune disorder. It should be considered that neuropsychiatric manifestations related to human coronaviruses including SARS-CoV-2 might be associated with the involvement of both neuroimmune response and direct viral transmission.  Pathophysiological underpinnings of nervous system involvement of SARS-CoV-2 are yet to be elucidated  Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Severe Acute Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the Absence of Encephalitis in Mice Transgenic for Human ACE2 The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients abstract: • Uncommon clinical presentations of COVID-19 pandemic including neuropsychiatric manifestations have been started reporting. • Pathophysiological underpinnings of nervous system involvement of SARS-CoV-2 are yet to be elucidated. • Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. url: https://doi.org/10.1016/j.jocn.2020.05.056 doi: 10.1016/j.jocn.2020.05.056 id: cord-253844-y6xdcf20 author: Yesudhas, Dhanusha title: COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date: 2020-09-04 words: 7165.0 sentences: 422.0 pages: flesch: 51.0 cache: ./cache/cord-253844-y6xdcf20.txt txt: ./txt/cord-253844-y6xdcf20.txt summary: In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. SUMMARY: The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs. The sequence similarity between SARS-CoV-2 and SARS-CoV spike proteins explains the possibility of binding to the same receptor angiotensin converting enzyme 2 (ACE2) in the host cell [14] . In this review, we discuss the history of coronaviruses in both humans and animals, their transmissions, mechanism of host cell entry and the structural studies, explaining active and inactive receptor binding of spike protein and the key residues playing an important role in the receptor binding. During viral infection, spike protein (~ 1300 amino acid residues) is cleaved by host proteases into receptor binding subunit S1 and membrane fusion subunit S2. abstract: PURPOSE: The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions. METHODS: We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included. RESULTS: Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. SUMMARY: The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs. url: https://doi.org/10.1007/s15010-020-01516-2 doi: 10.1007/s15010-020-01516-2 id: cord-305422-t8azymo7 author: Yi, Ye title: COVID-19: what has been learned and to be learned about the novel coronavirus disease date: 2020-03-15 words: 8300.0 sentences: 446.0 pages: flesch: 53.0 cache: ./cache/cord-305422-t8azymo7.txt txt: ./txt/cord-305422-t8azymo7.txt summary: The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. The virus is highly homologous to the coronavirus (CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003; thus, it was named SARS-CoV-2 by the World Health Organization (WHO) on February 11, 2020, and the associated disease was named CoV Disease-19 (COVID-19) [1] . Whenever possible, we will try to compare COVID-19 with SARS and another CoV-caused disease, Middle East respiratory syndrome (MERS, an outbreak in 2012). Due to the lack of experience with the novel CoV, physicians can mainly provide supportive care to COVID-19 patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other CoVs such as SARS-CoV and MERS-CoV and other viral diseases ( Table 2) . abstract: The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. Similar to its homologous virus, SARS-CoV, which caused SARS in thousands of people in 2003, SARS-CoV-2 might also be transmitted from the bats and causes similar symptoms through a similar mechanism. However, COVID-19 has lower severity and mortality than SARS but is much more transmissive and affects more elderly individuals than youth and more men than women. In response to the rapidly increasing number of publications on the emerging disease, this article attempts to provide a timely and comprehensive review of the swiftly developing research subject. We will cover the basics about the epidemiology, etiology, virology, diagnosis, treatment, prognosis, and prevention of the disease. Although many questions still require answers, we hope that this review helps in the understanding and eradication of the threatening disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32226295/ doi: 10.7150/ijbs.45134 id: cord-297918-840thddt author: Yilmaz, Umut title: COVID-19: neurologische Manifestationen: Was wir bisher wissen date: 2020-09-02 words: 1333.0 sentences: 172.0 pages: flesch: 48.0 cache: ./cache/cord-297918-840thddt.txt txt: ./txt/cord-297918-840thddt.txt summary: So wurde in einer ersten Studie mit 214 COVID-19-Patienten aus Wuhan eine neurologische Beteiligung in 36,4 % der Fälle beschrieben [1] . Eine Studie mit 58 aufgrund eines akuten Lungenversagens ("acute respiratory distress syndrome", ARDS) intensivmedizinisch behandelten COVID-19-Patienten aus Straßburg berichtet von neurologischen Komplikationen in 84 % der Fälle. Im weiteren Verlauf der Pandemie sind in den letzten Monaten zahlreiche Fallberichte und Fallserien publiziert worden, die von unterschiedlichen neurologischen Manifestationen bei CO-VID-19-Patienten berichten. Daher wurden in einer aktuellen Metaanalyse von Fallberichten und Studien zu neurologischen Komplikationen standardisierte Falldefinitionen für die Wahrscheinlichkeit eines Zusammenhangs zur COVID-19-Infektion gefordert [7] . Eine PCR-Analyse des Liquors auf SARS-CoV-2 wurde in 4 Fällen durchgeführt und fiel bei einem Patienten positiv aus. In einer europäischen Studie mit 417 Patienten wird von Störungen des Geruchs-oder Geschmackssinnes in über 85 % der Fälle mit bestätigter Infektion berichtet [2] . Saggese und Kollegen berichten von einem 62-jährigen COVID-19-positiven Patienten mit multiplen vaskulären Risikofaktoren, der aufgrund eines Schlaganfalls behandelt wurde. abstract: Shortly after the beginning of the global COVID-19 pandemic there was also an increasing number of reports of neurological complications in infected patients. Many case reports and case series described associated diseases of the central and peripheral nervous systems and cerebrovascular complications. This review article provides a short overview of the currently confusing picture of recent findings. url: https://www.ncbi.nlm.nih.gov/pubmed/32880004/ doi: 10.1007/s00117-020-00748-5 id: cord-257403-jujrazsr author: Yin, Changchuan title: Genotyping coronavirus SARS-CoV-2: Methods and implications date: 2020-04-27 words: 2614.0 sentences: 179.0 pages: flesch: 53.0 cache: ./cache/cord-257403-jujrazsr.txt txt: ./txt/cord-257403-jujrazsr.txt summary: Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. In this study, we use the Jaccard distance of the SNP mutations of SARS-CoV-2 genomes to measure the dissimilarity of virus isolates. From the SNP profiles of SARS-CoV-2 strain, high-frequency mutations predominate in the virus isolations, therefore, these high-frequency mutations probably contribute to increased transmissibility. This study employs the substitutions variants in genotyping for understanding the evolution and transmission of SARS-CoV-2, however, structural variants including insertions, deletions, and copy number variation are critical for virus pathogenicity [40] and human pathology [41, 42] . In this study, the complete genomes of SARS-CoV-2 are used for SNP genotype calling. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. To understand the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. This study presents an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The single-nucleotide polymorphism (SNP) genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. The proposed method serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control. url: https://api.elsevier.com/content/article/pii/S0888754320303189 doi: 10.1016/j.ygeno.2020.04.016 id: cord-283376-6wolrfvk author: Yin, M. title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study date: 2020-04-11 words: 4109.0 sentences: 301.0 pages: flesch: 56.0 cache: ./cache/cord-283376-6wolrfvk.txt txt: ./txt/cord-283376-6wolrfvk.txt summary: For this retrospective cohort study, we reviewed clinical records, laboratory findings, and chest CT scans from 31 pregnant women and 35 non-pregnant women from Jan 28 to Feb 28, 2020 to evaluate the effects of SARS-CoV-2 infection during pregnancy. 4, [7] [8] [9] Although numerous studies have illuminated the clinical characteristics and outcomes of general population with COVID-19, 2, 8 little has been reported about the effects of SARS-CoV-2 infection on pregnant women. Considering that inflammatory cytokine storm was the main lethal factor of infectious pneumonia such as SARS and Middle East Respiratory Syndrome (MERS), 18-21 we compared the levels of interleukin (IL)-6 and some inflammatory indices including NLR, LMR, PLR, SII, ANRI and APRI, in pregnant and non-pregnant patients ( author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 12 However, we found a shorter interval from onset to hospitalization and severer COVID-19 in pregnant patients than non-pregnant patients with SARS-CoV-2 infection. abstract: Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the cause of the ongoing worldwide epidemic of Coronavirus Disease 2019 (COVID-19) in China and worldwide. However, there were few studies about the effects of SARS-CoV-2 infection on pregnant women. Methods In this retrospective cohort study, we enrolled 31 pregnant women and 35 non-pregnant women from Jan 28 to Feb 28, 2020 to evaluate the effects of SARS-CoV-2 infection during pregnancy. Inflammatory indices were used to assess the severity of COVID-19. Evidence of vertical transmission was determined by laboratory confirmation of SARS-CoV-2 in amniotic fluid, placenta, neonatal throat and anal swab and breastmilk samples. Findings Compared with non-pregnant women, pregnant women had a significantly lower proportion of fever (54.8% vs. 87.5%, p= 0.006), a shorter average interval from onset to hospitalization, and a higher proportion of severe or critical COVID-19 (32.3% vs. 11.4%, p=0.039). Neutrophil-to-lymphocyte ratio (NLR) and systematic immune-inflammation-based prognostic index (SII) were significantly higher on admission in severe/critical pneumonia group than moderate pneumonia group. We could not detect the presence of SARS-CoV-2 by RT-PCR in amniotic fluid, placenta, neonatal throat and anal swab and breastmilk samples. Conclusions The clinical symptoms of COVID-19 in pregnant women were insidious and atypical, compared with those in non-pregnant patients. SII and NLR could be a useful marker to evaluate the severity of COVID-19. There was no evidence of vertical transmission during pregnancy with SARS-CoV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.04.07.20053744v1?rss=1 doi: 10.1101/2020.04.07.20053744 id: cord-301978-9uu318tp author: Yin, Xiaoping title: A mild type of childhood Covid-19 - A case report date: 2020-03-27 words: 1216.0 sentences: 85.0 pages: flesch: 56.0 cache: ./cache/cord-301978-9uu318tp.txt txt: ./txt/cord-301978-9uu318tp.txt summary: This case is about a 9-year-old child diagnosed with COVID-19, with a history of epidemiology; SARS-CoV-2 nucleic acids testing was positive, while chest CT examination was negative. Because the child had lived in Wuhan two weeks before the onset of the disease and had a fever, SARS-CoV-2 infection was not excluded. Children and teenagers infected with SARS-CoV-2 have mild clinical symptoms and radiological manifestations [4] , and are rarely severe or critical. If children and adolescents have a history of living or traveling in epidemic areas within one to two weeks, or they have had contact with confirmed or suspected cases, or stay in an aggregated disease environment, the possibility of their infection with SARS-CoV-2 cannot be ruled out, even when their clinical symptoms are mild and there is no typical chest imaging manifestation. SARS-CoV-2 nucleic acid or gene testing is required for these patients. Preliminary study on clinical imaging features of 2019 novel coronavirus (2019-nCoV) pneumonia in Wuhan. abstract: This case is about a 9-year-old child diagnosed with COVID-19, with a history of epidemiology; SARS-CoV-2 nucleic acids testing was positive, while chest CT examination was negative. The clinical classification was light. Nonetheless, isolation measures should still be taken to avoid infecting others. url: https://www.ncbi.nlm.nih.gov/pubmed/32363226/ doi: 10.1016/j.jrid.2020.03.004 id: cord-325172-a8ntxnmm author: Yip, Ming Shum title: Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus date: 2014-05-06 words: 5791.0 sentences: 253.0 pages: flesch: 44.0 cache: ./cache/cord-325172-a8ntxnmm.txt txt: ./txt/cord-325172-a8ntxnmm.txt summary: More recently, we demonstrated that anti-Spike antibody potentiates infection of both monocytic and lymphoid immune cell lines, not only by SARS-CoVpp but also by replication-competent SARS-coronavirus [16] , thus providing evidence for a novel and versatile mechanism by which SARS-CoV can enter into target cells that do not express the conventional ACE2 virus receptor and are otherwise refractory to the virus. Finally, we have provided evidence that the intracellular signaling motifbut not the IgG binding motifof the FcγR is the key molecular determinant for triggering ADE of SARS-CoVpp. Our findings conclusively demonstrate that anti-spike serum promotes internalization of SARS-CoV by human macrophages. All the endodomain-truncated constructs (FcγRIIA-H.ΔIC, FcγRIIA-R.ΔIC and FcγRIIB.ΔIC, corresponding to constructs 2, 6, 11 respectively) were not susceptible to ADE of infection, indicating that binding of anti-Spike IgG-SARS-CoVpp immune complexes was not sufficient to mediate entry and that the signaling-competent endodomain was required. abstract: BACKGROUND: Public health risks associated to infection by human coronaviruses remain considerable and vaccination is a key option for preventing the resurgence of severe acute respiratory syndrome coronavirus (SARS-CoV). We have previously reported that antibodies elicited by a SARS-CoV vaccine candidate based on recombinant, full-length SARS-CoV Spike-protein trimers, trigger infection of immune cell lines. These observations prompted us to investigate the molecular mechanisms and responses to antibody-mediated infection in human macrophages. METHODS: We have used primary human immune cells to evaluate their susceptibility to infection by SARS-CoV in the presence of anti-Spike antibodies. Fluorescence microscopy and real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR) were utilized to assess occurrence and consequences of infection. To gain insight into the underlying molecular mechanism, we performed mutational analysis with a series of truncated and chimeric constructs of fragment crystallizable γ receptors (FcγR), which bind antibody-coated pathogens. RESULTS: We show here that anti-Spike immune serum increased infection of human monocyte-derived macrophages by replication-competent SARS-CoV as well as Spike-pseudotyped lentiviral particles (SARS-CoVpp). Macrophages infected with SARS-CoV, however, did not support productive replication of the virus. Purified anti-viral IgGs, but not other soluble factor(s) from heat-inactivated mouse immune serum, were sufficient to enhance infection. Antibody-mediated infection was dependent on signaling-competent members of the human FcγRII family, which were shown to confer susceptibility to otherwise naïve ST486 cells, as binding of immune complexes to cell surface FcγRII was necessary but not sufficient to trigger antibody-dependent enhancement (ADE) of infection. Furthermore, only FcγRII with intact cytoplasmic signaling domains were competent to sustain ADE of SARS-CoVpp infection, thus providing additional information on the role of downstream signaling by FcγRII. CONCLUSIONS: These results demonstrate that human macrophages can be infected by SARS-CoV as a result of IgG-mediated ADE and indicate that this infection route requires signaling pathways activated downstream of binding to FcγRII receptors. url: https://doi.org/10.1186/1743-422x-11-82 doi: 10.1186/1743-422x-11-82 id: cord-288692-v471648u author: Yip, Shea Ping title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 words: 2387.0 sentences: 117.0 pages: flesch: 51.0 cache: ./cache/cord-288692-v471648u.txt txt: ./txt/cord-288692-v471648u.txt summary: title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus We designed a 1-step real-time quantitative RT-PCR assay for SARS-CoV with the use of 2 TaqMan probes, instead of 1 probe, hybridizing to the same PCR product to further improve the sensitivity. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Quantitation of severe acute respiratory syndrome coronavirus genome by real-time polymerase chain reaction assay using minor groove binder DNA probe technology Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested-polymerase chain reaction abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/16189379/ doi: 10.1373/clinchem.2005.054106 id: cord-261253-btwx2vxo author: Yip, Timothy T. C. title: Application of ProteinChip Array Profiling in Serum Biomarker Discovery for Patients Suffering From Severe Acute Respiratory Syndrome date: 2007 words: 3836.0 sentences: 310.0 pages: flesch: 66.0 cache: ./cache/cord-261253-btwx2vxo.txt txt: ./txt/cord-261253-btwx2vxo.txt summary: By protein chip array profiling technology, a number of serum biomarkers that might be useful in monitoring the clinical course of SARS patients were identified. The serum profiling spectra in SARS patients were acquired, baseline subtracted and analyzed in parallel with those from the control subjects by Ciphergen ProteinChip Software 3.0.2 with their peak intensities compared by a nonparametric two sample Mann-Whitney-U test. More than twelve peaks were differentially expressed in SARS patients with one at m/z of 11,695 (later identified to be serum amyloid A protein), which had increase in peak intensity correlating with the extent of SARS-coronavirus induced pneumonia as defined by a serial chest X-ray opacity score. In a recent article, the discovery of 12 upor downregulated serum biomarkers were reported in SARS patients by a novel protein chip array profiling approach (1014) with one biomarker appears to be useful in monitoring the extent of pneumonia (15) . abstract: A new strain of coronavirus has caused an outbreak of severe acute respiratory syndrome (SARS) from 2002 to 2003 resulting in 774 deaths worldwide. By protein chip array profiling technology, a number of serum biomarkers that might be useful in monitoring the clinical course of SARS patients were identified. This book chapter describes how the protein chip array profiling was carried out for this study. Briefly, SARS patients’ serum samples were first fractionated in Q Ceramic HyperD ion exchange sorbent beads by buffers at different pH. Serum protein fractions thus obtained were then bound onto a copper (II) immobilized metal affinity capture (IMAC30 Cu [II]) ProteinChip® Array or a weak cation-exchange (CM10) ProteinChip Array. After washing and addition of sinapinic acid, the chips were read in a Protein Biological System (PBS) IIc mass spectrometer. Ions were generated by laser shots and flied in a time of flight mode to the ion detector according to their mass over charge (m/z) ratio. The serum profiling spectra in SARS patients were acquired, baseline subtracted and analyzed in parallel with those from the control subjects by Ciphergen ProteinChip Software 3.0.2 with their peak intensities compared by a nonparametric two sample Mann-Whitney-U test. More than twelve peaks were differentially expressed in SARS patients with one at m/z of 11,695 (later identified to be serum amyloid A protein), which had increase in peak intensity correlating with the extent of SARS-coronavirus induced pneumonia as defined by a serial chest X-ray opacity score. The remaining biomarkers could also be useful in the study of other clinical parameters in SARS patients. url: https://www.ncbi.nlm.nih.gov/pubmed/18220240/ doi: 10.1007/978-1-59745-304-2_20 id: cord-288398-vnra553x author: Yogeswaran, Athiththan title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study date: 2020-07-23 words: 1166.0 sentences: 78.0 pages: flesch: 54.0 cache: ./cache/cord-288398-vnra553x.txt txt: ./txt/cord-288398-vnra553x.txt summary: authors: Yogeswaran, Athiththan; Gall, Henning; Tello, Khodr; Grünig, Ekkehard; Xanthouli, Panagiota; Ewert, Ralf; Kamp, Jan C.; Olsson, Karen M.; Wißmüller, Max; Rosenkranz, Stephan; Klose, Hans; Harbaum, Lars; Lange, Tobias J.; Opitz, Christian F.; Waelde, Andrea; Milger, Katrin; Sommer, Natascha; Seeger, Werner; Ghofrani, Hossein Ardeschir; Richter, Manuel J. title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study This multi-centre study provides evidence for a negative influence of these restrictions on patient care in pulmonary hypertension expert referral centres. The impact of SARS-CoV-2 associated restrictions on PH out-patient departments in Germany, however, has not been systematically evaluated. This study provides evidence for the significant impact of SARS-CoV-2 and the related restrictions on the medical care of patients with (suspected and subsequently confirmed) PH in Germany. Of note, the relative fraction of patients with subsequently initiated PH-specific therapy remained constant during the SARS-CoV-2 pandemic. abstract: Pulmonary hypertension is frequently underdiagnosed, and referral is delayed with subsequent impact on outcomes. During the SARS-CoV-2 pandemic, restrictions on daily life and changes in hospitals' daily routine care were introduced in Germany. This multi-centre study provides evidence for a negative influence of these restrictions on patient care in pulmonary hypertension expert referral centres. url: https://www.ncbi.nlm.nih.gov/pubmed/32754309/ doi: 10.1177/2045894020941682 id: cord-310096-a242g5kg author: Yokota, I. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 words: 1956.0 sentences: 131.0 pages: flesch: 49.0 cache: ./cache/cord-310096-a242g5kg.txt txt: ./txt/cord-310096-a242g5kg.txt summary: Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (self-collected saliva and NPS) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. abstract: Background COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Results In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence, 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. Conclusion Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons. url: https://doi.org/10.1101/2020.08.13.20174078 doi: 10.1101/2020.08.13.20174078 id: cord-278045-hr3r17mz author: Yokota, Isao title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-09-25 words: 2271.0 sentences: 156.0 pages: flesch: 52.0 cache: ./cache/cord-278045-hr3r17mz.txt txt: ./txt/cord-278045-hr3r17mz.txt summary: METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (NPS and self-collected saliva) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. abstract: BACKGROUND: COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. CONCLUSION: Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons. url: https://doi.org/10.1093/cid/ciaa1388 doi: 10.1093/cid/ciaa1388 id: cord-267476-j59tm40d author: Yong, Sarah Ee Fang title: Connecting clusters of COVID-19: an epidemiological and serological investigation date: 2020-04-21 words: 3562.0 sentences: 187.0 pages: flesch: 49.0 cache: ./cache/cord-267476-j59tm40d.txt txt: ./txt/cord-267476-j59tm40d.txt summary: We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection. Serological testing had a crucial role in establishing a link between clusters, showing its use in identifying convalescent COVID-19 cases and supporting epidemiological investigations. In our epidemiological investigation, we used RT-PCR and serological testing to diagnose cases of COVID-19 and establish links between clusters. This investigation shows how SARS-CoV-2 serological analysis (ELISA detecting IgG and VNT detecting neutralising antibodies), in addition to use of traditional epidemiological methods, was important in establishing links among locally transmitted COVID-19 cases and tracing the transmission chain to an imported source. abstract: BACKGROUND: Elucidation of the chain of disease transmission and identification of the source of coronavirus disease 2019 (COVID-19) infections are crucial for effective disease containment. We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19. METHODS: In Singapore, active case-finding and contact tracing were undertaken for all COVID-19 cases. Diagnosis for acute disease was confirmed with RT-PCR testing. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection. FINDINGS: Three clusters of COVID-19, comprising 28 locally transmitted cases, were identified in Singapore; these clusters were from two churches (Church A and Church B) and a family gathering. The clusters in Church A and Church B were linked by an individual from Church A (A2), who transmitted SARS-CoV-2 infection to the primary case from Church B (F1) at a family gathering they both attended on Jan 25, 2020. All cases were confirmed by RT-PCR testing because they had active disease, except for A2, who at the time of testing had recovered from their illness and tested negative. This individual was eventually diagnosed with past infection by serological testing. ELISA assays showed an optical density of more than 1·4 for SARS-CoV-2 nucleoprotein and receptor binding domain antigens in titres up to 1/400, and viral neutralisation was noted in titres up to 1/320. INTERPRETATION: Development and application of a serological assay has helped to establish connections between COVID-19 clusters in Singapore. Serological testing can have a crucial role in identifying convalescent cases or people with milder disease who might have been missed by other surveillance methods. FUNDING: National Research Foundation (Singapore), National Natural Science Foundation (China), and National Medical Research Council (Singapore). url: https://doi.org/10.1016/s1473-3099(20)30273-5 doi: 10.1016/s1473-3099(20)30273-5 id: cord-304101-b9na3yf6 author: Yong, Suh Kuan title: Molecular Targets for the Testing of COVID‐19 date: 2020-05-18 words: 1777.0 sentences: 97.0 pages: flesch: 46.0 cache: ./cache/cord-304101-b9na3yf6.txt txt: ./txt/cord-304101-b9na3yf6.txt summary: This diagnostic panel is working with Applied Biosystems 7500 Fast DX Real-Time PCR Instrument with SDS 1.4 software; 2) "New coronavirus nucleic acid assay" which targeted on ORF1ab and N genes was developed by Chinese National Institute for Viral Disease Control and Prevention; 3) Molecular test kits from four companies such as Seegene Inc., Kogene Biotech Co. Ltd., Sd Biosensor Inc., and Solgent Co. were approved by Ministry Food and Drug Safety and Korea Centers for Disease Control and Prevention which are now widely being used in South Korea. A probe, usually a specific antibody, is needed before a successful viral protein detection method can be developed. As aforementioned, the serology testing of COVID-19 is not targeting the virus itself but the antibodies such as immunoglobulin M (IgM) and immunoglobulin G (IgG) induced following viral infection. Serology testings targeting on viral-induced antibodies are given different information as those for viral RNA and proteins from SARS-CoV-2. abstract: The pandemic outbreaks of coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), spread all over the world in a short period of time. Efficient identification of the infection by SARS‐CoV‐2 has been one of the most important tasks to facilitate all the following counter measurements in dealing with the infectious disease. In Taiwan, a COVID‐19 Open Science Platform adheres to the spirit of open science: sharing sources, data, and methods to promote progress in academic research while corroborating findings from various disciplines has established in mid‐February 2020, for collaborative research in support of the development of detection methods, therapeutics, and a vaccine for COVID‐19. Research priorities include infection control, epidemiology, clinical characterization and management, detection methods (including viral RNA detection, viral antigen detection, and serum antibody detection), therapeutics (neutralizing antibody and small molecule drugs), vaccines, and SARS‐CoV‐2 pathogenesis. In addition, research on social ethics and the law are included to take full account of the impact of the COVID‐19 virus. url: https://doi.org/10.1002/biot.202000152 doi: 10.1002/biot.202000152 id: cord-304550-6j1pb1pu author: Yongchen, Zhang title: Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients date: 2020-05-02 words: 2032.0 sentences: 108.0 pages: flesch: 43.0 cache: ./cache/cord-304550-6j1pb1pu.txt txt: ./txt/cord-304550-6j1pb1pu.txt summary: Here, we conducted a serial investigation on 21 individuals infected with SARS-CoV-2 in two medical centres from Jiangsu Province, including 11 non-severe COVID-19 patients, and 5 severe COVID-19 patients and 5 asymptomatic carriers based on nucleic acid test and clinical symptoms. In this respective study, we serially analysed the virus RNA test results in swab samples, along with anti-SARS-CoV-2 IgM and IgG responses among 21 COVID-19 patients at the Second Hospital of Nanjing and the Affiliated Hospital of Xuzhou Medical University in Jiangsu Province, China. Our serial SARS-CoV-2 RNA testing identified a prolonged viral shedding for asymptomatic cases compared to COVID-19 patients, suggesting the importance of early identification and timely quarantine for these asymptomatic carriers. It is possible that significantly high level of SARS-CoV-2 viral load observed in severe cases [8, 9] drives an early antibody response produced by immediate activation of extrafollicular B cells during acute infection [10, 11] . abstract: Effective strategy to mitigate the ongoing pandemic of 2019 novel coronavirus (COVID-19) require a comprehensive understanding of humoral responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emerging virus causing COVID-19. The dynamic profile of viral replication and shedding along with viral antigen specific antibody responses among COVID-19 patients started to be reported but there is no consensus on their patterns. Here, we conducted a serial investigation on 21 individuals infected with SARS-CoV-2 in two medical centres from Jiangsu Province, including 11 non-severe COVID-19 patients, and 5 severe COVID-19 patients and 5 asymptomatic carriers based on nucleic acid test and clinical symptoms. The longitudinal swab samples and sera were collected from these people for viral RNA testing and antibody responses, respectively. Our data revealed different pattern of seroconversion among these groups. All 11 non-severe COVID-19 patients and 5 severe COVID-19 patients were seroconverted during hospitalization or follow-up period, suggesting that serological testing is a complementary assay to nucleic acid test for those symptomatic COVID-19 patients. Of note, immediate antibody responses were identified among severe cases, compared to non-severe cases. On the other hand, only one were seroconverted for asymptomatic carriers. The SARS-CoV-2 specific antibody responses were well-maintained during the observation period. Such information is of immediate relevance and would assist COVID-19 clinical diagnosis, prognosis and vaccine design. url: https://doi.org/10.1080/22221751.2020.1756699 doi: 10.1080/22221751.2020.1756699 id: cord-289598-t8upoq9a author: Yoon, Jane C title: COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date: 2020-09-08 words: 2980.0 sentences: 197.0 pages: flesch: 56.0 cache: ./cache/cord-289598-t8upoq9a.txt txt: ./txt/cord-289598-t8upoq9a.txt summary: BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. Risk of SARS-CoV-2 infection, the virus that causes COVID-19, may be higher among people experiencing homelessness (PEH) because of challenges in preventing respiratory disease transmission in congregate shelter settings. Our finding of decreased prevalence in four shelters during repeat testing is consistent with reports from skilled nursing facilities and correctional facilities, supporting the use of universal (facility-wide) testing for early identification and isolation of those with positive SARS-CoV-2 as a strategy to interrupt transmission in congregate settings [23] [24] [25] . abstract: BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. A subset of PEH and staff was screened for symptoms. Shelter assessments were conducted concurrently at a convenience sample of shelters using a standardized questionnaire RESULTS: Overall, 2,875 individuals at 24 shelters and nine unsheltered outreach events underwent SARS-CoV-2 testing and 2,860 (99.5%) had conclusive test results. SARS-CoV-2 prevalence was 2.1% (36/1,684) among PEH living sheltered, 0.5% (3/628) among PEH living unsheltered, and 1.3% (7/548) among staff. Reporting fever, cough, or shortness of breath in the last week during symptom screening was 14% sensitive and 89% specific for identifying COVID-19 cases compared with RT-PCR. Prevalence by shelter ranged 0%–27.6%. Repeat testing 3–4 weeks later at four shelters documented decreased SARS-CoV-2 prevalence (0%–3.9%). Nine of 24 shelters completed shelter assessments and implemented IPC measures as part of the COVID-19 response CONCLUSIONS: PEH living in shelters experienced higher SARS-CoV-2 prevalence compared with PEH living unsheltered. Facility-wide testing in congregate settings allowed for identification and isolation of COVID-19 cases and is an important strategy to interrupt SARS-CoV-2 transmission url: https://doi.org/10.1093/cid/ciaa1340 doi: 10.1093/cid/ciaa1340 id: cord-258792-4lakgpxp author: Yoon, Sung‐Won title: Sovereign Dignity, Nationalism and the Health of a Nation: A Study of China''s Response in Combat of Epidemics date: 2008-04-08 words: 7935.0 sentences: 341.0 pages: flesch: 50.0 cache: ./cache/cord-258792-4lakgpxp.txt txt: ./txt/cord-258792-4lakgpxp.txt summary: Unless and until the Chinese leadership examines the nationalistic element embedded in their approach towards growing disease Sung-Won Yoon: Sovereign Dignity, Nationalism and the Health of a Nation epidemics and globalising health challenges, China''s ascendance to great power status will actually be harmed rather than helped. A major factor behind the government''s recent change in its attitude towards the AIDS epidemic seemed to be the outbreak of SARS in China in Studies in Ethnicity and Nationalism: Vol. 8, No. 1, 2008 2003, which exposed the dangers of not reacting to emerging infectious diseases. It is argued that global health governance may influence the nation''s response to the threats posed by emerging infectious diseases such as SARS or AIDS as a mode of building political compromises but does not considerably alter the nation''s behaviour, at least for China. abstract: This paper seeks to understand the role of nationalism in China's policy towards the combat of emerging infectious diseases. By locating nationalism as a factor which facilitates or impedes global governance and international collaboration, this paper explores how nationalism influences China's political decision‐making. Given her historical experience, China has in its national psyche an impulse never to become ‘the sick man of the East’ again. Today, China's willingness to co‐operate with international bodies emanates out of reputational concerns rather than technical‐medical considerations. This was clearly manifested in her handling of two epidemics in recent years: the Severe Acute Respiratory Syndrome (SARS) and HIV/AIDS episodes. This paper concludes that China's nationalism plays an inhibiting role in China's attempts to further incorporate herself into the architecture of global health governance in the long run. url: https://doi.org/10.1111/j.1754-9469.2008.00009.x doi: 10.1111/j.1754-9469.2008.00009.x id: cord-283249-pk5sc2ca author: Yoshida, Wataru title: Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers date: 2006-09-15 words: 5356.0 sentences: 235.0 pages: flesch: 56.0 cache: ./cache/cord-283249-pk5sc2ca.txt txt: ./txt/cord-283249-pk5sc2ca.txt summary: The structural change of the enzyme-inhibiting aptamer site induces a change in the inhibitory activity of the AES, which enables us to detect a target molecule by measuring the enzymatic activity of the whole aptameric complex in a homogeneous solution without bound/free separation. The stem-and-loop structure bearing the probe DNA sequence was inserted into the 3 0 -end T-T loop of the G-quartet structure of the 31-mer thrombin-inhibiting aptamer. We also inserted two additional T bases between the thrombin-inhibiting aptamer and the stem-and-loop structure in all AESs except AES 1, since the diameter of the DNA double helix is different from the distance between two Gs of the G-quartet structure (approximately 17 and 20 Å , respectively). For the measurement of the CD spectra of AES SARS 1, a stem-and-loop structure to be inserted into the 31-mer thrombin-inhibiting aptamer on AES SARS 1 was synthesized. abstract: Abstract A novel aptameric enzyme subunit (AES) which can detect target DNAs has been developed. AES is an enzyme-inhibiting aptamer bearing a target-molecule binding site which can allosterically control enzymatic activity. The thrombin-inhibiting aptamer bearing a G-quartet structure was chosen as the enzyme-inhibiting aptamer. The stem-and-loop structure, which contains a strand complementary to the target DNA, was inserted into the G-quartet structure of the thrombin-inhibiting aptamer to disrupt the G-quartet structure through the hybridization of the target DNA with the complementary strand in the AES. The disruption of the G-quartet structure led to a decrease of the inhibitory activity of the whole aptameric complex. Using this designed aptamer, we were able to detect target DNAs by measuring the thrombin activity in a homogeneous solution without bound/free separation, and the lower detection limit was 20nM. url: https://www.sciencedirect.com/science/article/pii/S0006291X06015956 doi: 10.1016/j.bbrc.2006.07.069 id: cord-321858-c5m4dj9m author: Yoshizawa, Shin-ichiro title: Evaluation of an octahydroisochromene scaffold used as a novel SARS 3CL protease inhibitor date: 2020-02-15 words: 6519.0 sentences: 337.0 pages: flesch: 56.0 cache: ./cache/cord-321858-c5m4dj9m.txt txt: ./txt/cord-321858-c5m4dj9m.txt summary: The inhibitory activities of the diastereoisomerically-pure inhibitors (3a–d) strongly suggest that a specific stereo-isomer of the octahydroisochromene scaffold, (1S, 3S) 3b, directs the P1 site imidazole, the warhead aldehyde, and substituent at the 1-position of the fused ring to their appropriate pockets in the protease. To access whether the octahydroisochromene derivatives containing substituents at the 1-position of the ring system function as a novel inhibitor scaffold, the inhibitory activity of compounds 16a-d toward SARS 3CL pro was preliminary evaluated by the IC 50 values obtained using the procedure described below. To determine the configuration of each diastereomer (13a and 13b), the major product obtained after the asymmetric dihydroxylation reaction using (DHQ) 2 Pyr as the chiral ligand (Table 2, entry 3) was isolated and purified using preparative thin layer chromatography (PTLC). abstract: An octahydroisochromene scaffold has been introduced into a known SARS 3CL protease inhibitor as a novel hydrophobic core to interact with the S2 pocket of the protease. An alkyl or aryl substituent was also introduced at the 1-position of the octahydroisochromene scaffold and expected to introduce additional interactions with the protease. Sharpless–Katsuki asymmetric epoxidation and Sharpless asymmetric dihydroxylation were employed to construct the octahydroisochromene scaffold. The introductions of the P1 site His-al and the substituent at 1-position was achieved using successive reductive amination reactions. Our initial evaluations of the diastereo-isomeric mixtures (16a–d) revealed that the octahydroisochromene moiety functions as a core hydrophobic scaffold for the S2 pocket of the protease and the substituent at the 1-position may form additional interactions with the protease. The inhibitory activities of the diastereoisomerically-pure inhibitors (3a–d) strongly suggest that a specific stereo-isomer of the octahydroisochromene scaffold, (1S, 3S) 3b, directs the P1 site imidazole, the warhead aldehyde, and substituent at the 1-position of the fused ring to their appropriate pockets in the protease. url: https://api.elsevier.com/content/article/pii/S0968089619319637 doi: 10.1016/j.bmc.2019.115273 id: cord-282372-nmii30mc author: Youk, Jeonghwan title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 words: 5124.0 sentences: 294.0 pages: flesch: 53.0 cache: ./cache/cord-282372-nmii30mc.txt txt: ./txt/cord-282372-nmii30mc.txt summary: Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . abstract: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global pandemic, infects human lung alveolar cells (hACs). Characterising the pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hACs limits the study. Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Further tracing of viral mutations acquired during transmission identifies full infection of individual cells effectively from a single viral entry. Our study provides deep insights into the pathogenesis of SARS-CoV-2, and the application of long-term 3D hAT2 cultures as models for respiratory diseases. url: https://doi.org/10.1101/2020.07.10.194498 doi: 10.1101/2020.07.10.194498 id: cord-345679-ydwcp75s author: Younas, Amber title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN date: 2020-08-24 words: 2370.0 sentences: 148.0 pages: flesch: 59.0 cache: ./cache/cord-345679-ydwcp75s.txt txt: ./txt/cord-345679-ydwcp75s.txt summary: title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN Despite the prevailing pandemic, there are no recommendations available as yet for testing SARS-CoV-2 antibodies as part of blood screening. In our study, we conducted specific serological testing (total antibodies) to identify prevalence of SARS-2-CoV antibodies among the healthy blood donors who visited Blood Bank at our Institute.Their results were compared with specific serologic results of blood donors that came before the onset of pandemic(October, 2019). In July 2020, we tested 300 healthy blood donors, 113 donors (37.7%) were found to be reactive for anti-SARS-CoV-2antibodies. Another study in Northern France reported 25.8% of population positive for COVID-19 antibody(19)but they also did not exclude previously symptomatic cases. To conclude, seroprevalence of SARS-COV-2 antibodies has increased in Pakistan over a period of time and could help in recognizing the actual number of COVID-19 cases. The prevalence of antibodies to SARS-CoV-2 among blood donors in China.medRxiv abstract: BACKGROUND: Covid-19 spread through blood transfusion has not yet been reported. Despite the prevailing pandemic, there are no recommendations available as yet for testing SARS-CoV-2 antibodies as part of blood screening. OBJECTIVE: To determine the seroprevalence of SAR-CoV-2 antibodies, its clinical significance and to identify if total antibodies(IgA, IgM, IgG) should be tested or just the specific IgG antibodies only. METHOD: Consecutive blood donors donated were screened for standard serological panel of HbsAg, Anti-HCV, Anti-HIV and Syphilis using Cobas-411 analyser and Malaria. All seronegative donors were then screened for COVID serology using the same instrument. These results were compared with the blood donors’ seroprevalence checked in a cohort in the first week of June 2020. Pre-COVID-19 period (October 2019) blood donors’ archived samples were also compared. Donors who were positive on ECLIA were then tested for specific antibodies (IgM or IgG) by ELISA. RESULTS: A total of 380 healthy blood donors were included. All were males with the mean age being 30.6 ± 6.3 years. Ten pre-pandemic samples did not show COVID-19 antibodies, whereas out of 70 samples in the3(rd) week of June, only 15 (21.4%)were positive. However, in July out of the 300 blood donors, 113 (37.7%) were found to be reactive. To reconfirm our findings, these 113 donors were then tested on ELISA for presence of IgG specifically. Out of these 128 samples, 81 were IgG positive, 23 were borderline positive and 24 were negative. CONCLUSION: Almost 40% of blood donors are now seroconverted for COVID-19. This is a reflection of widespread seroprevalence in the adult male population. url: https://www.sciencedirect.com/science/article/pii/S1473050220302378?v=s5 doi: 10.1016/j.transci.2020.102923 id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 words: 3612.0 sentences: 253.0 pages: flesch: 52.0 cache: ./cache/cord-258724-1qhen1bj.txt txt: ./txt/cord-258724-1qhen1bj.txt summary: METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). In this multi-pronged study, we describe the serologic evolution, inflammatory response and pattern of viral shedding and viability in patients with virologically confirmed COVID-19 in Singapore, and analyse the contributions these make to severe infections. Serum collected during the acute and convalescent phases of infection were tested for SARS-CoV-2 receptor binding domain specific IgM and IgG using capture ELISA (details in Supplementary Appendix). The central role of the immune response to SARS-CoV-2 in COVID-19 was evident from the strong correlation between disease severity and levels of IgG/IgM and inflammatory immune mediators in our cohort. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study abstract: BACKGROUND: Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. RESULTS: 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. CONCLUSION: We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32856707/ doi: 10.1093/cid/ciaa1280 id: cord-300923-5cyxr98s author: Younger, David S title: Postmortem Neuropathology in Covid‐19 date: 2020-10-23 words: 631.0 sentences: 46.0 pages: flesch: 42.0 cache: ./cache/cord-300923-5cyxr98s.txt txt: ./txt/cord-300923-5cyxr98s.txt summary: This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid‐19) due to severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) from among 250 reported patients succumbing to Covid‐19 illness (1‐7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid‐19 illness, and are important in the development of effective treatment strategies. This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid-19) due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from among 250 reported patients succumbing to Covid-19 illness (1-7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid-19 illness, and are important in the development of effective treatment strategies. As shown in Table 1 , older age, male gender, increased serum cytokine and pro-coagulation markers, and critical care hospitalization for ≤10 days prior to death characterized the cohort. Neuropathologic features of four autopsied COVID-19 patients The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 abstract: This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid‐19) due to severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) from among 250 reported patients succumbing to Covid‐19 illness (1‐7) who underwent detailed postmortem neuropathological studies. This disease, which starts in the lungs, is a multisystem disorder affecting all major organs including the brain. These cases provide a more complete picture of Covid‐19 illness, and are important in the development of effective treatment strategies. url: https://doi.org/10.1111/bpa.12915 doi: 10.1111/bpa.12915 id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 words: 3221.0 sentences: 179.0 pages: flesch: 50.0 cache: ./cache/cord-294335-qnu19ru5.txt txt: ./txt/cord-294335-qnu19ru5.txt summary: We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . abstract: BACKGROUND: Improved understanding of SARS-CoV-2 spectrum of disease is essential for clinical and public health interventions. There are limited data on mild or asymptomatic infections, but recognition of these individuals is key as they contribute to viral transmission. We describe the symptom profiles from individuals with mild or asymptomatic SARS-CoV-2 infection. METHODS: From March 22 to April 22, 2020 in Wisconsin and Utah, we enrolled and prospectively observed 198 household contacts exposed to SARS-CoV-2. We collected and tested nasopharyngeal (NP) specimens by RT-PCR two or more times during a 14-day period. Contacts completed daily symptom diaries. We characterized symptom profiles on the date of first positive RT-PCR test and described progression of symptoms over time. RESULTS: We identified 47 contacts, median age 24 (3-75) years, with detectable SARS-CoV-2 by RT-PCR. The most commonly reported symptoms on the day of first positive RT-PCR test were upper respiratory (n=32, 68%) and neurologic (n=30, 64%); fever was not commonly reported (n=9, 19%). Eight (17%) individuals were asymptomatic at the date of first positive RT-PCR collection; two (4%) had preceding symptoms that resolved and six (13%) subsequently developed symptoms. Children less frequently reported lower respiratory symptoms (age <18: 21%, age 18-49: 60%, age 50+ years: 69%; p=0.03). CONCLUSIONS: Household contacts with lab-confirmed SARS-CoV-2 infection reported mild symptoms. When assessed at a single time-point, several contacts appeared to have asymptomatic infection; however, over time all developed symptoms. These findings are important to inform infection control, contact tracing, and community mitigation strategies. url: https://doi.org/10.1093/cid/ciaa1072 doi: 10.1093/cid/ciaa1072 id: cord-352256-qxdakdk0 author: Yousefi, Bahman title: A global treatments for coronaviruses including COVID‐19 date: 2020-05-11 words: 4017.0 sentences: 213.0 pages: flesch: 48.0 cache: ./cache/cord-352256-qxdakdk0.txt txt: ./txt/cord-352256-qxdakdk0.txt summary: Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Chloroquine inhibits SARS-CoV entry, which exerts its inhibitory effect by altering glycosylation of the ACE2 receptor and spike protein. | 5 in a MERS-CoV rhesus macaque model were promising, with the results of the trial and the effect of ribavirin and IFN (either α2a or β1) on MERS-CoV infected patients it was different, however, ribavirin lowers hemoglobin concentrations in respiratory patients and therefore reduces its potential as an antiviral against SARS-CoV-2 (Arabi et al., 2017; Falzarano et al., 2013) . abstract: In late December 2019 in Wuhan, China, several patients with viral pneumonia were identified as 2019 novel coronavirus (2019‐nCoV). So far, there are no specific treatments for patients with coronavirus disease‐19 (COVID‐19), and the treatments available today are based on previous experience with similar viruses such as severe acute respiratory syndrome‐related coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), and Influenza virus. In this article, we have tried to reach a therapeutic window of drugs available to patients with COVID‐19. Cathepsin L is required for entry of the 2019‐nCoV virus into the cell as target teicoplanin inhibits virus replication. Angiotensin‐converting‐enzyme 2 (ACE2) in soluble form as a recombinant protein can prevent the spread of coronavirus by restricting binding and entry. In patients with COVID‐19, hydroxychloroquine decreases the inflammatory response and cytokine storm, but overdose causes toxicity and mortality. Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Ribavirin reduces hemoglobin concentrations in respiratory patients, and remdesivir improves respiratory symptoms. Use of ribavirin in combination with LPV/r in patients with SARS‐CoV reduces acute respiratory distress syndrome and mortality, which has a significant protective effect with the addition of corticosteroids. Favipiravir increases clinical recovery and reduces respiratory problems and has a stronger antiviral effect than LPV/r. currently, appropriate treatment for patients with COVID‐19 is an ACE2 inhibitor and a clinical problem reducing agent such as favipiravir in addition to hydroxychloroquine and corticosteroids. url: https://doi.org/10.1002/jcp.29785 doi: 10.1002/jcp.29785 id: cord-298242-iuskpoug author: Yu, Alvin title: A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date: 2020-10-02 words: 3604.0 sentences: 204.0 pages: flesch: 47.0 cache: ./cache/cord-298242-iuskpoug.txt txt: ./txt/cord-298242-iuskpoug.txt summary: Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. In this paper, we construct a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion from the currently available structural and atomistic simulation data on SARS-CoV-2 proteins. In this work, we detail several of our CG methods used to iteratively develop a CG model for the full SARS-CoV-2 virion, in which molecular interactions between CG particles are derived using a combination of phenomenological, experimental, and atomistic simulation approaches. In recent cryo-EM images of SARS-CoV-2 particles, the S1 domain of the S protein was found to transiently open and close in order to bind the ACE-2 receptor (3, 5) , which are subtle conformational changes that are difficult to sample in atomistic simulations. abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely “bottom-up” coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion. Significance Statement This study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions. url: https://www.ncbi.nlm.nih.gov/pubmed/33024966/ doi: 10.1101/2020.10.02.323915 id: cord-340635-8wki7noy author: Yu, Bin title: Innate and adaptive immunity of murine neural stem cell-derived piRNA exosomes/microvesicles against pseudotyped SARS-CoV-2 and HIV-based lentivirus date: 2020-11-13 words: 6017.0 sentences: 300.0 pages: flesch: 56.0 cache: ./cache/cord-340635-8wki7noy.txt txt: ./txt/cord-340635-8wki7noy.txt summary: Through testing pseudotyped SARS-CoV-2 and HIV-based lentivirus, this study reports that exosomes/microvesicles (Ex/Mv) isolated from murine hypothalamic neural stem/progenitor cells (htNSC) or subtype htNSCPGHM as well as hippocampal NSC have innate immunity-like actions against these RNA viruses. We then measured some of these piRNAs in NSC Ex/Mv (using htNSC PGHM and J o u r n a l P r e -p r o o f hpNSC as the representative) compared to the levels in MSC Ex/Mv. As shown in Fig. S2B and S3, most of these piRNAs were present in these NSC Ex/Mv but were much less detectable in MSC Ex/Mv. Our additional assays showed that htNSC PGHM were comparable or slightly stronger than htNSC in producing these piRNAs. Thus, based on the information from wildtype and pseudotyped SARS-CoV-2, NSC Ex/Mv contain piRNAs against the genomic sequences of both viruses, although these NSC were not previously exposed to either virus, suggesting that mouse species has evolved to establish large antiviral piRNA libraries in NSC Ex/Mv. We asked if an initial pre-exposure of a specific virus to NSC could lead to an enhancement or enrichment of specific antiviral piRNAs in NSC Ex/Mv. Thus, we treated these NSCs with pseudotyped SARS-CoV-2 virus for 2 generations, and then maintained them under normal culture for about 5 generations. abstract: Through testing pseudotyped SARS-CoV-2 and HIV-based lentivirus, this study reports that exosomes/microvesicles (Ex/Mv) isolated from murine hypothalamic neural stem/progenitor cells (htNSC) or subtype htNSCPGHM as well as hippocampal NSC have innate immunity-like actions against these RNA viruses. These extracellular vesicles also have a cell-free innate antiviral action through attacking and degrading viruses. We further generated the induced versions of Ex/Mv through prior viral exposure to NSCs and found that these induced Ex/Mv were stronger than basal Ex/Mv in reducing the infection of these viruses, suggesting the involvement of an adaptive immunity-like antiviral function. These NSC Ex/Mv were found to be characterized by producing large libraries of piRNAs against genomes of various viruses, and some of these piRNAs were enriched during the adaptive immunity-like reaction, possibly contributing to the antiviral effects of these Ex/Mv. In conclusion, NSC Ex/Mv have antiviral immunity and could potentially be developed to combat against various viruses. url: https://api.elsevier.com/content/article/pii/S2589004220310038 doi: 10.1016/j.isci.2020.101806 id: cord-309517-yh4d414y author: Yu, Chao title: Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study date: 2020-08-12 words: 3498.0 sentences: 188.0 pages: flesch: 38.0 cache: ./cache/cord-309517-yh4d414y.txt txt: ./txt/cord-309517-yh4d414y.txt summary: In addition, some asymptomatic patients can develop symptoms during hospitalization [6] , and the characteristics of these presymptomatic patients and their independent risk factors have not been addressed yet. Therefore, in the present study, we investigated 79 asymptomatic patients to analyze their clinical characteristics, disease progression, and recurrence of positive SARS-CoV2 RNA after discharge. No intergroup differences were observed in other radiographic characteristics, and patchy shadowing was the most common abnormality Meanwhile, the asymptomatic carriers had normal levels of other markers related to liver damage, renal dysfunction, inflammation, and coagulation, which were comparable with those of the symptomatic patients. Although the presymptomatic patients developed symptoms during hospitalization, these patients had similar viral RNA shedding duration compared with the asymptomatic carriers (14 days [IQR 7-25 days] vs. In our study, the recurrence rate of positive SARS-CoV-2 nucleic acid in the asymptomatic carriers after discharge was lower than that in the symptomatic patients (10.12% vs. abstract: Novel coronavirus disease 2019 (COVID-19), caused by novel coronavirus SARS-CoV-2, has spread globally since the end of 2019. Asymptomatic carriers are of great concern as they can undermine the interventions to stop the pandemic. However, there is limited information about the characteristics and outcomes of the asymptomatic patients. Therefore, we conducted this retrospective study and retrieved data of 79 asymptomatic COVID-19 patients at admission from three designated hospitals in Wuhan, China. The asymptomatic patients could happen at any age, ranged from 9 to 96 years. These patients also had lower levels of alanine aminotransferase and C-reactive protein. Patchy shadowing was the most common manifestation in computed tomography scan. Some asymptomatic carriers developed mild or moderate symptoms during hospitalization. Age and comorbidities, especially hypertension, may be predictive factors for symptom development in the initially asymptomatic carriers at admission. Early detection and treatment for these presymptomatic patients before symptom onset can shorten the communicable period for the coronavirus and reduce the occurrence of severe cases. url: https://doi.org/10.1080/21505594.2020.1802194 doi: 10.1080/21505594.2020.1802194 id: cord-265723-6k8196p2 author: Yu, Chengjun title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis date: 2020-06-25 words: 2622.0 sentences: 136.0 pages: flesch: 41.0 cache: ./cache/cord-265723-6k8196p2.txt txt: ./txt/cord-265723-6k8196p2.txt summary: title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis Therefore, we conducted this updated systematic review and meta-analysis to recapitulate relevant studies to evaluate the safety, efficacy, tolerability and treatment-related outcomes of type I IFNs for coronavirus infection in clinical practice, with expectation to provide more robust evidence whether IFNs should be served as first-line agents for coronavirus infection, including the SARS-CoV-2. Each included article was thoroughly reviewed, and the following baseline information were extracted (Table 1) : first author, publication year, region, study type, participants, diagnostic method of coronavirus, data collection method, time from admission to treatment start, time from diagnosis to treatment start, primary endpoints, and treatment-related adverse effects. Critically ill defined as coronavirus-infected patients with other severe comorbidities, respiratory distress or failure, directly or indirectly transferred to ICU, needing intubation, mechanical ventilation, or extracorporeal membrane oxygenation (ECMO), when admitted to primary treatment. abstract: BACKGROUND: There is no vaccine or specific antiviral treatment for HCoVs infection. The use of type I interferons for coronavirus is still under great debate in clinical practice. MATERIALS AND METHODS: A literature search of all relevant studies published on PubMed, Cochrane library, Web of Science database, Science Direct, Wanfang Data, and China National Knowledge Infrastructure (CNKI) until February 2020 was performed. RESULTS: Of the 1081 identified articles, only 15 studies were included in the final analysis. Comorbidities and delay in diagnosis were significantly associated with case mortality. Type I interferons seem to improve respiratory distress, relieve lung abnormalities, present better saturation, reduce needs for supplemental oxygen support. Type I interferons seem to be well tolerated, and don’t increase life threating adverse effects. Data on IFNs in HCoVs are limited, heterogenous and mainly observational. CONCLUSIONS: Current data do not allow making regarding robust commendations for the use of IFNs in HCoVs in general or in specific subtype. But we still recommend type I interferons serving as first-line antivirals in HCoVs infections within local protocols, and interferons may be adopted to the treatments of the SARS-CoV-2 as well. Well-designed large-scale prospective randomized control trials are greatly needed to provide more robust evidence on this topic. url: https://www.sciencedirect.com/science/article/pii/S1567576920315526?v=s5 doi: 10.1016/j.intimp.2020.106740 id: cord-339934-g6ufz29l author: Yu, Hai-qiong title: Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients date: 2020-05-13 words: 993.0 sentences: 55.0 pages: flesch: 45.0 cache: ./cache/cord-339934-g6ufz29l.txt txt: ./txt/cord-339934-g6ufz29l.txt summary: In the case of respiratory infection, while IgM and IgG isotypes have been the primary emphasis in characterizing immunity, mucosal and systemic IgA responses that may play a critical role in the disease pathogenesis, have received much less attention. This pattern of humoral immune response is different in case of SARS-CoV infection, in which IgM and IgA showed similar chronological profiles in terms of both seroconversion time and antibody titres [5] , in line with the knowledge that viremia is common in SARS. Upregulated IgA production may be the result of increased levels of TGF-β and IL-10 that promote antibody switching in SARS-CoV-2 infection. Considering the roles of mucosal and systemic IgA in COVID-19, inducing IgA production, e.g. using Lactoferrin to activate canonical TGF-β signaling [13] , or retinoic acid to enhance lactoferrin-induced IgA responses [14] , has been proposed as novel therapies for severe COVID-19. abstract: Humoral immune response to SARS-CoV-2 showed an early response of IgA, instead of IgM, in COVID-19 patients. As highlighted by our study, enhanced IgA responses observed in severe COVID-19 might confer damaging effects in severe COVID-19. url: https://doi.org/10.1183/13993003.01526-2020 doi: 10.1183/13993003.01526-2020 id: cord-299122-djfj4262 author: Yu, Hua title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date: 2007-03-15 words: 5459.0 sentences: 273.0 pages: flesch: 52.0 cache: ./cache/cord-299122-djfj4262.txt txt: ./txt/cord-299122-djfj4262.txt summary: title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown). abstract: Antibodies to SARS-Coronavirus (SARS-CoV)-specific B cell epitopes might recognize the pathogen and interrupt its adherence to and penetration of host cells. Hence, these epitopes could be useful for diagnosis and as vaccine constituents. Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. After a bioinformatics tool was used to analyze these epitopes, four epitope-based S protein dodecapeptides corresponding to the predominant epitopes were chosen for synthesis. Their antigenic specificities and immunogenicities were studied in vitro and in vivo. Flow cytometry and ELISPOT analysis of lymphocytes as well as a serologic analysis of antibody showed that these peptides could trigger a rapid, highly effective, and relatively safe immune response in BALB/c mice. These findings might aid development of SARS diagnostics and vaccines. Moreover, the role of S and M proteins as important surface antigens is confirmed. url: https://www.ncbi.nlm.nih.gov/pubmed/17055022/ doi: 10.1016/j.virol.2006.09.016 id: cord-281726-s1o5l7ns author: Yu, Ignatius T. S. title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date: 2005-05-01 words: 3528.0 sentences: 181.0 pages: flesch: 56.0 cache: ./cache/cord-281726-s1o5l7ns.txt txt: ./txt/cord-281726-s1o5l7ns.txt summary: We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Layout of the ward where the index case patient with severe acute respiratory syndrome (SARS) was hospitalized, showing the location of beds, air supply diffusers, and exhaust grilles. The relationships between SARS and bed location, date of exposure, duration of exposure, smoking To explore the possible roles of HCWs in the outbreak of infection, all nurses working on the ward during the study period were interviewed in person between 28 March and 8 April with a questionnaire to collect information on symptoms, contacts, and working practices. The analysis of the temporal-spatial spread of SARS from the index case patient to other inpatients in the ward suggested that airborne spread through virus-laden aerosols possibly played an important role. abstract: Background. We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Methods. All inpatients who had stayed in the same ward as the initial index case patient for any duration before isolation were recruited into a cohort and followed up to document the occurrence of SARS. The normalized concentration of virus-laden aerosols at different locations of the ward was estimated by use of computational fluid dynamics modeling. The attack rates in the various subgroups stratified by bed location were calculated. Multivariate Cox proportional hazards regression was used to document important risk factors. Results. The overall attack rate of SARS was 41% (30 of 74 subjects). It was 65%, 52%, and 18% in the same bay, adjacent bay, and distant bays, respectively (P = .001). Computation fluid dynamics modeling indicated that the normalized concentration of virus-laden aerosols was highest in the same bay and lowest in the distant bays. Cox regression indicated that staying in the ward on 6 or 10 March entailed higher risk, as well as staying in the same or adjacent bays. The epidemic curve showed 2 peaks, and stratified analyses by bed location suggested >1 generation of spread. Conclusions. The temporal-spatial spread of SARS in the ward was consistent with airborne transmission, as modeled by use of computational fluid dynamics. Infected health care workers likely acted as secondary sources in the latter phase of the outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/15825024/ doi: 10.1086/428735 id: cord-338359-pd4bfjet author: Yu, J. title: Risk assessment of admission procedures for cancer patients during the convalescence of COVID-19 date: 2020-09-30 words: 1094.0 sentences: 74.0 pages: flesch: 49.0 cache: ./cache/cord-338359-pd4bfjet.txt txt: ./txt/cord-338359-pd4bfjet.txt summary: Conclusions: Unbiased proteomic profiling of COVID-19 patient serum identified a panel of candidate protein biomarkers that associate with tocilizumab treatment response as well as the ensuing course of the disease. Background: There are limited data on cancer patients (pts) and the novel coronavirus (SARS-CoV2) respiratory disease (COVID-19). We aim to evaluate the frequency of ILI in cancer pts during the pandemic, and to identify high-risk subjects to test for COVID-19. Results: Overall, 562 pts were enrolled: 13 (2%) pts had a positive SARS-CoV2 swab, none of which performed on the basis of triage procedures or questionnaires, rather detected through telephone communications and triage; 52 (9%) pts reported suspect symptoms and/or laboratory tests. The incidence of both COVID-19 diagnosis (2%), and SARS-CoV2 Ab positivity in pts tested on the basis of suspect symptoms (<1%), were similar to those observed in the general population. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0923753420417557 doi: 10.1016/j.annonc.2020.08.1759 id: cord-253179-pi5uq90z author: Yu, Jing title: SARS-CoV-2 transmission in cancer patients of a tertiary hospital in Wuhan date: 2020-02-25 words: 1332.0 sentences: 82.0 pages: flesch: 53.0 cache: ./cache/cord-253179-pi5uq90z.txt txt: ./txt/cord-253179-pi5uq90z.txt summary: Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. 3 Among the different disease types, cancer patients are often recalled to the hospital for treatment and disease surveillance, and therefore, they may be at an elevated risk of contracting SARS-CoV-2. https://doi.org/10.1101/2020.02.22.20025320 doi: medRxiv preprint real-time reverse transcription polymerase chain reaction assay for SARS-CoV-2 and eight by the clinical criteria of fever and radiological computed tomography changes; Table 1 ). For cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China abstract: In December 2019, an outbreak of atypical pneumonia known as 2019 novel coronavirus disease (COVID-19) occurred in Wuhan, China. This new type of pneumonia is characterized by rapid human-to-human transmission. Among the different disease types, cancer patients are often recalled to the hospital for treatment and disease surveillance, and the majority of cancer treatments such as chemotherapy and radiotherapy are immunosuppressive. This prompts us to consider if cancer patients were at an elevated risk of SARS-CoV-2 infection. A total of 1,524 cancer patients who were managed at our tertiary cancer institution-Zhongnan hospital of Wuhan University were reviewed during the period of Dec 30, 2019 to Feb 17, 2020. It was found that cancer patients had an estimated 2-fold increased risk of COVID-19 than the general population. We identified twelve patients who were infected with SARS-CoV-2, with two recorded deaths (16.7%), albeit one patient passed away from a COVID-19 unrelated cause. Interestingly, only five of these patients were ongoing treatment at the time of contracting the virus, suggesting that hospital visitation was the likely factor contributing to the elevated incidence in cancer patients. Moreover, we also observed that the incidence of severe COVID-19 was not higher than in the general population. Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. url: https://doi.org/10.1101/2020.02.22.20025320 doi: 10.1101/2020.02.22.20025320 id: cord-319337-w9zyshzb author: Yu, Jingyou title: DNA vaccine protection against SARS-CoV-2 in rhesus macaques date: 2020-05-20 words: 2719.0 sentences: 156.0 pages: flesch: 50.0 cache: ./cache/cord-319337-w9zyshzb.txt txt: ./txt/cord-319337-w9zyshzb.txt summary: Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. Following vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log(10) reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with sham controls. S3 and S4), including 1.92 and 2.16 log 10 reductions of median peak viral RNA in BAL and NS, respectively, in S vaccinated animals compared with sham controls (P = 0.02 and P = 0.04, two-sided Mann-Whitney tests) ( fig. Viral RNA assays were confirmed by PFU assays, which similarly showed lower infectious virus titers in S vaccinated animals compared with sham controls (P = 0.04, two-sided Mann-Whitney test) ( fig. In this study, we generated a series of prototype DNA vaccines expressing various S immunogens and assessed protective efficacy against intranasal and intratracheal SARS-CoV-2 challenge in rhesus macaques. abstract: The global COVID-19 pandemic caused by the SARS-CoV-2 virus has made the development of a vaccine a top biomedical priority. In this study, we developed a series of DNA vaccine candidates expressing different forms of the SARS-CoV-2 Spike (S) protein and evaluated them in 35 rhesus macaques. Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. Following vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log(10) reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with sham controls. Vaccine-elicited neutralizing antibody titers correlated with protective efficacy, suggesting an immune correlate of protection. These data demonstrate vaccine protection against SARS-CoV-2 in nonhuman primates. url: https://doi.org/10.1126/science.abc6284 doi: 10.1126/science.abc6284 id: cord-332300-5osg046o author: Yu, Luo title: Catching and killing of airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system date: 2020-07-07 words: 2756.0 sentences: 125.0 pages: flesch: 55.0 cache: ./cache/cord-332300-5osg046o.txt txt: ./txt/cord-332300-5osg046o.txt summary: Traditional air-conditioner filters based on fiberglass or aluminum (Al) mesh are difficult to heat or have large pores (about 1 centimeter in size), so they cannot effectively catch and kill the virus contained in aerosols (generally smaller than 5 µm in size) [23] or other airborne highly infectious agents, such as anthrax spores. In order to realize a filter for preventing the spread of SARS-CoV-2 and anthrax spores, here we designed and fabricated a filter device consisting of folded pieces of Ni foam in multiple compartments connected electrically in series to efficiently increase the resistance to a manageable level so that a temperature up to 250 was able to be achieved, and found that the filter device exhibits almost 100% ability to catch and kill aerosolized SARS-CoV-2 and anthrax spores in air passed once through the Ni foam heated up to 200 (temperature optimization will be addressed in a future study). abstract: Abstract Airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via air-conditioning systems poses a significant threat for the continued escalation of the current coronavirus disease (COVID-19) pandemic. Considering that SARS-CoV-2 cannot tolerate temperatures above 70 °C, here we designed and fabricated efficient filters based on heated nickel (Ni) foam to catch and kill SARS-CoV-2. Virus test results revealed that 99.8% of the aerosolized SARS-CoV-2 was caught and killed by a single pass through a novel Ni-foam-based filter when heated up to 200 °C. Additionally, the same filter was also used to catch and kill 99.9% of Bacillus anthracis, an airborne spore. This study paves the way for preventing transmission of SARS-CoV-2 and other highly infectious airborne agents in closed environments. url: https://api.elsevier.com/content/article/pii/S2542529320300730 doi: 10.1016/j.mtphys.2020.100249 id: cord-330324-4hqhty5o author: Yu, Meng title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date: 2008-02-29 words: 5799.0 sentences: 284.0 pages: flesch: 50.0 cache: ./cache/cord-330324-4hqhty5o.txt txt: ./txt/cord-330324-4hqhty5o.txt summary: title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. In this study we identified and characterized the major immunodominant domains of the SARS-CoV N and S proteins recognized by different animal species, and then developed competition ELISAs based on these findings. The specificity of the antibody was further confirmed using Western blot against viral antigen (data not shown) and IFAT using SARS-CoV infected Vero cells. One of the main aims of this study was to assess the feasibility of developing a competition ELISA for detection of SARS-CoV antibodies from different animal species. Inhibition of binding of mono-specific chicken antibodies to SARS-CoV by sera from different species. abstract: Abstract Knowledge of immunodominant regions in major viral antigens is important for rational design of effective vaccines and diagnostic tests. Although there have been many reports of such work done for SARS–CoV, these were mainly focused on the immune responses of humans and mice. In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. Twelve overlapping recombinant protein fragments were produced in Escherichia coli, six each for the S and N proteins, which covered the entire coding region of the two proteins. Using a membrane-strip based Western blot approach, the reactivity of each antigen fragment against a panel of animal sera was determined. Immunodominant regions containing linear epitopes, which reacted with sera from all the species tested, were identified for both proteins. The S3 fragment (aa 402–622) and the N4 fragment (aa 220–336) were the most immunodominant among the six S and N fragments, respectively. Antibodies raised against the S3 fragment were able to block the binding of a panel of S-specific monoclonal antibodies (mAb) to SARS–CoV in ELISA, further demonstrating the immunodominance of this region. Based on these findings, one-step competition ELISAs were established which were able to detect SARS–CoV antibodies from human and at least seven different animal species. Considering that a large number of animal species are known to be susceptible to SARS–CoV, these assays will be a useful tool to trace the origin and transmission of SARS–CoV and to minimise the risk of animal-to-human transmission. url: https://doi.org/10.1016/j.jim.2007.11.009 doi: 10.1016/j.jim.2007.11.009 id: cord-333712-sdtxi8xw author: Yu, Ping title: Geographical structure of bat SARS-related coronaviruses date: 2019-02-06 words: 3662.0 sentences: 163.0 pages: flesch: 53.0 cache: ./cache/cord-333712-sdtxi8xw.txt txt: ./txt/cord-333712-sdtxi8xw.txt summary: In 2005, the discovery of novel CoVs related to human SARS-CoVs in Chinese horseshoe bats (genus Rhinolophus), named SARS-related coronaviruses (SARSr-CoVs), provided new clue that bats may be the natural host for SARS-CoV (Lau et al., 2005; Li et al., 2005) . SARS-CoV and SARSr-CoVs belong to lineage B of genus Betacoronavirus in the family Coronaviridae and share the same genomic organization with other coronaviruses, including genes coding for 16 nonstructural proteins (nsp, in ORF1ab domain), the structural proteins like spike protein (S), envelope (E), membrane (M), nucleocapsid (N) and other several genes (Perlman and Netland, 2009; Woo et al., 2009) . Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China abstract: Bats are the natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) which caused the outbreak of human SARS in 2002–2003. We introduce the genetic diversity of SARS-related coronaviruses (SARSr-CoVs) discovered in bats and provide insights on the bat origin of human SARS. We also analyze the viral geographical structure that may improve our understanding of the evolution of bat SARSr-CoVs. url: https://www.sciencedirect.com/science/article/pii/S156713481830902X doi: 10.1016/j.meegid.2019.02.001 id: cord-323882-127c5bve author: Yu, Wen-Bin title: Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data date: 2020-05-17 words: 5560.0 sentences: 282.0 pages: flesch: 57.0 cache: ./cache/cord-323882-127c5bve.txt txt: ./txt/cord-323882-127c5bve.txt summary: Of the 93 genomes of SARS-CoV-2, 39 (41.93%) were from infected patients in 11 countries outside China and encoded 31 haplotypes (H d =0.987±0.009 (SD), P i =0.16×10 -3 ± 0.01×10 -3 ), with 27 nationally/regionally private haplotypes. Three different datasets were used to infer evolutionary networks, which consistently supported H13 and H38 as the potentially ancestral haplotypes, i.e., the outgroup bat-RaTG13-CoV could connect to both H13 and H38, or H38 alone, or through a medium vector mv1 (an intermediate host or the first infected humans) connected to both H13 and H38 by single mutations at positions 18067 (S, synonymous substitution) and/or 29102 (S), referring to the numbering of the alignment length 29 910 bp ( Figure 5 ). To clarify the exact origins of these haplotypes outside China, we need more epidemiological investigative efforts and more SARS-CoV-2 genomic data from patients at the early stage of transmissions. abstract: The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu(TM) database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32351056/ doi: 10.24272/j.issn.2095-8137.2020.022 id: cord-330743-o11d0aa1 author: Yu, Xi title: Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date: 2020-05-25 words: 4470.0 sentences: 245.0 pages: flesch: 54.0 cache: ./cache/cord-330743-o11d0aa1.txt txt: ./txt/cord-330743-o11d0aa1.txt summary: Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). Incubation of the culture supernatant but not the bacterial lysates resulted in significant suppression of DENV ( Figure 1B ) and ZIKV ( Figure 1C ) infectivity in Vero cells, indicating that an extracellular effector(s) secreted by Csp_BJ was responsible for viral inhibition. DENV, ZIKV, HSV-1 and SARS-CoV-2 virus stocks were diluted to 50 plaque-forming units (pfu) per ml and incubated untreated or with a serial dilution of the CbAEs in five-fold steps at 37°C for 1 hr before being added onto Vero cell monolayers for 2 hr of infection. abstract: Viruses are the major aetiological agents of acute and chronic severe human diseases that place a tremendous burden on global public health and economy; however, for most viruses, effective prophylactics and therapeutics are lacking, in particular, broad-spectrum antiviral agents. Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). The CbAEs potently blocked viral infection in the extracellular milieu through their lipase activity. Mechanistic studies showed that this lipase activity directly disrupted the viral envelope structure, thus inactivating infectivity. A mutation of CbAE-1 in its lipase motif fully abrogated the virucidal ability. Furthermore, CbAE-2 presented low toxicity in vivo and in vitro, highlighting its potential as a broad-spectrum antiviral drug. url: https://doi.org/10.1101/2020.05.22.109900 doi: 10.1101/2020.05.22.109900 id: cord-295603-mk9oartb author: Yu, Xiaoqi title: Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness date: 2020-07-05 words: 1991.0 sentences: 97.0 pages: flesch: 49.0 cache: ./cache/cord-295603-mk9oartb.txt txt: ./txt/cord-295603-mk9oartb.txt summary: However, it is unclear whether there has been cryptic transmission before these early officially confirmed cases, we therefore retrospectively screened for the SARS-CoV-2 RNA in 1271 nasopharyngeal swab samples, as well as the prevalence of IgM, IgG, and total antibodies against SARS-CoV-2 in 357 matched serum samples collected from hospitalized patients with influenza-like illness between 1 December 2018 and 31 March 2020 in Shanghai Ruijin Hospital. Additionally, among 6662 patients with influenza-like illness from 1 December 2017 to 31 March 2020, the overall number of patients positive for influenza and other respiratory viruses during the COVID-19 period decreased significantly when compared with that in the same period of the last two years, reflecting that public health interventions can effectively control the spread of common respiratory viruses. The nasopharyngeal swab samples for this study were collected from 1271 hospitalized patients with influenza-like illness from 1 December 2018 to 31 March 2020 in Ruijin Hospital (Shanghai, China). abstract: Since the first report of the coronavirus disease (COVID-19) in late December 2019, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now widely spread to more than 187 countries and regions. However, it is unclear whether there has been cryptic transmission before these early officially confirmed cases, we therefore retrospectively screened for the SARS-CoV-2 RNA in 1271 nasopharyngeal swab samples, as well as the prevalence of IgM, IgG, and total antibodies against SARS-CoV-2 in 357 matched serum samples collected from hospitalized patients with influenza-like illness between 1 December 2018 and 31 March 2020 in Shanghai Ruijin Hospital. The onset date of the earliest COVID-19 case in this study was 25 January 2020. Before this time point, the presence of SARS-CoV-2 was not observed, which limited the possibility that SARS-CoV-2 has already spread among the population before the large-scale outbreak. Additionally, among 6662 patients with influenza-like illness from 1 December 2017 to 31 March 2020, the overall number of patients positive for influenza and other respiratory viruses during the COVID-19 period decreased significantly when compared with that in the same period of the last two years, reflecting that public health interventions can effectively control the spread of common respiratory viruses. url: https://doi.org/10.1080/22221751.2020.1785952 doi: 10.1080/22221751.2020.1785952 id: cord-295375-nakxfhxk author: Yu, Yang title: Assessment of the quality of systematic reviews on COVID‐19: A comparative study of previous coronavirus outbreaks date: 2020-04-28 words: 2455.0 sentences: 143.0 pages: flesch: 48.0 cache: ./cache/cord-295375-nakxfhxk.txt txt: ./txt/cord-295375-nakxfhxk.txt summary: In this comparative study, we investigated the present status of conducting SRs on COVID-19, MERS, and SARS, appraised the methodological quality of these SRs using the a measurement tool to assess systematic reviews (AMSTAR 2), and performed a preliminary examination of the potential risk factors associated with the quality of SRs, with the aim of providing suggestions from the aspects of methodological quality for conducting and using SRs during the COVID-19 pandemic. AMSTAR, a measurement tool to assess systematic reviews; MA, meta-analysis quality of most SRs is unsatisfactory, and those on COVID-19 have higher risks of poor quality, despite the rapid actions taken to conduct SRs. Teams that may want to conduct a SR should focus on the study design and focus on improving the quality of the SR. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis abstract: Several systematic reviews (SRs) have been conducted on the COVID‐19 outbreak, which together with the SRs on previous coronavirus outbreaks, form important sources of evidence for clinical decision and policy making. Here, we investigated the methodological quality of SRs on COVID‐19, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Online searches were performed to obtain SRs on COVID‐19, SARS, and MERS. The methodological quality of the included SRs was assessed using the AMSTAR‐2 tool. Descriptive statistics were used to present the data. In total, of 49 SRs that were finally included in our study, 17, 16, and 16 SRs were specifically on COVID‐19, MERS, and SARS, respectively. The growth rate of SRs on COVID‐19 was the highest (4.54/month) presently. Of the included SRs, 6, 12, and 31 SRs were of moderate, low, and critically low quality, respectively. SRs on SARS showed the optimum quality among the SRs on the three diseases. Subgroup analyses showed that the SR topic (P < .001), the involvement of a methodologist (P < .001), and funding support (P = .046) were significantly associated with the methodological quality of the SR. According to the adherence scores, adherence to AMSTAR‐2 items sequentially decreased in SRs on SARS, MERS, and COVID‐19. The methodological quality of most SRs on coronavirus outbreaks is unsatisfactory, and those on COVID‐19 have higher risks of poor quality, despite the rapid actions taken to conduct SRs. The quality of SRs should be improved in the future. Readers must exercise caution in accepting and using the results of these SRs. url: https://www.ncbi.nlm.nih.gov/pubmed/32301508/ doi: 10.1002/jmv.25901 id: cord-282058-it0ojdk3 author: Yu, Yuanqiang title: Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review date: 2020-05-15 words: 7461.0 sentences: 389.0 pages: flesch: 50.0 cache: ./cache/cord-282058-it0ojdk3.txt txt: ./txt/cord-282058-it0ojdk3.txt summary: References for this review were identified through searches of PubMed for articles published from January 1, 2003, to May 1, 2020, by use of the terms "coronavirus, " "neonate, " "children, " "COVID19, " and "SARS-CoV-2." Relevant articles published between 2003 and 2020 were identified through searches in the authors'' personal files. The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The symptoms of COVID-19 appear to be less severe in infants and children than in adult patients, similar to the SARS-CoV infection (15) (16) (17) . Of the 34 pregnant women who were confirmed with the SARS-CoV-2 infection in multiple hospitals in Wuhan, including one pregnant woman with a negative nucleic acid test result, 30 had a fever and 16 had a cough (54) (55) (56) (57) . abstract: At the end of 2019, a novel coronavirus began to spread in Wuhan, Hubei Province, China. The confirmed cases increased nationwide rapidly, in part due to the increased population mobility during the Chinese Lunar New Year festival. The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Soon, transmission from person to person was confirmed and the virus spread to many other countries. To date, many cases have been reported in the pediatric age group, most of which were from China. The management and treatment strategies have also been improved, which we believe would be helpful to pediatric series in other countries as well. However, the characteristics of neonatal and childhood infection still have not been evaluated in detail. This review summarizes the current understanding of SARS-CoV-2 infection in neonates and children from January 24 to May 1, as an experience from China. url: https://www.ncbi.nlm.nih.gov/pubmed/32574286/ doi: 10.3389/fped.2020.00287 id: cord-317563-mu47vvma author: Yuan, Chunhui title: Viral loads in throat and anal swabs in children infected with SARS-CoV-2 date: 2020-06-09 words: 2297.0 sentences: 108.0 pages: flesch: 50.0 cache: ./cache/cord-317563-mu47vvma.txt txt: ./txt/cord-317563-mu47vvma.txt summary: Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay on anal swabs was recently reported to be persistently positive even after throat testing was negative during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Furthermore, viral loads detected on both throat and anal swabs also showed no significant difference (P = 0.9511) and correlation (Pearson r = 0.0434, P = 0.8406), and exhibited an inconsistent kinetic change through the course of SARS-CoV-2 infection. These findings revealed that RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune state in paediatric patients. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay has been widely used for clinical diagnosis and SARS-CoV-2 has been detected in specimens from multiple sites, including bronchoalveolar lavage fluid, sputum, nasal, anal, and throat swabs of patients with COVID-19 [2] . In conclusion, RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune states in paediatric patients. abstract: Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay on anal swabs was recently reported to be persistently positive even after throat testing was negative during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, data about the consistent performance of RT-PCR assay on throat and anal swabs remain limited in paediatric patients. Here, we retrospectively reviewed RT-PCR-testing results of 212 paediatric patients with suspected SARS-CoV-2 infection at Wuhan Children’s Hospital. The diagnostic potential of these two types of specimens showed significant difference (positive rate: 78.2% on throat swabs vs. 52.6% on anal swabs, McNemar Test P = 0.0091) and exhibited a weak positive consistency (Kappa value was 0.311, P < 0.0001) in paediatric patients. Furthermore, viral loads detected on both throat and anal swabs also showed no significant difference (P = 0.9511) and correlation (Pearson r = 0.0434, P = 0.8406), and exhibited an inconsistent kinetic change through the course of SARS-CoV-2 infection. Besides, viral loads in the throat and anal swabs were correlated with different types of immune states, immune-reactive phase, and the resolution phase/immunologic tolerance, respectively. These findings revealed that RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune state in paediatric patients. url: https://doi.org/10.1080/22221751.2020.1771219 doi: 10.1080/22221751.2020.1771219 id: cord-273126-gceffbfp author: Yuan, Kehu title: Suppression of SARS-CoV entry by peptides corresponding to heptad regions on spike glycoprotein date: 2004-07-02 words: 3263.0 sentences: 174.0 pages: flesch: 58.0 cache: ./cache/cord-273126-gceffbfp.txt txt: ./txt/cord-273126-gceffbfp.txt summary: Subsequently, the highly conserved heptad repeat (HR) regions (HR1 and HR2) in the glycoprotein interact with each other to form a six-helix bundle structure, which facilitates the juxtaposition of the virus and cell membranes, leading to membrane fusion [9] . Based on the fusion mechanism described above, we used an approach that was successfully used for studying other enveloped viruses, such as HIV-1 and MHV, to identify the potent inhibitor for virus entry [16, 18, 19, 25] . Screened through the pseudotyped virus infection assay [7, [26] [27] [28] and validated with wild-typed virus infection, two peptides were identified, HR1-1 and HR2-18, which were able to inhibit the SARS-CoV entry process. Although we designed a series of peptides overlapping the HR2 region, only one peptide HR2-18 was identified to inhibit the entry of SARS-CoV with low inhibitor activity. abstract: Heptad repeat regions (HR1 and HR2) are highly conserved sequences located in the glycoproteins of enveloped viruses. They form a six-helix bundle structure and are important in the process of virus fusion. Peptides derived from the HR regions of some viruses have been shown to inhibit the entry of these viruses. SARS-CoV was also predicted to have HR1 and HR2 regions in the S2 protein. Based on this prediction, we designed 25 peptides and screened them using a HIV-luc/SARS pseudotyped virus assay. Two peptides, HR1-1 and HR2-18, were identified as potential inhibitors, with EC(50) values of 0.14 and 1.19 μM, respectively. The inhibitory effects of these peptides were validated by the wild-type SARS-CoV assay. HR1-1 and HR2-18 can serve as functional probes for dissecting the fusion mechanism of SARS-CoV and also provide the potential of further identifying potent inhibitors for SARS-CoV entry. url: https://www.ncbi.nlm.nih.gov/pubmed/15184046/ doi: 10.1016/j.bbrc.2004.05.046 id: cord-330473-f03ka7bd author: Yuan, Meng title: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date: 2020-03-14 words: 1563.0 sentences: 107.0 pages: flesch: 65.0 cache: ./cache/cord-330473-f03ka7bd.txt txt: ./txt/cord-330473-f03ka7bd.txt summary: In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. ONE SENTENCE SUMMARY Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain. A recent study has shown that CR3022, which is a human 49 neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4), Nonetheless, despite having a 70 high conservation in the epitope residues, CR3022 Fab binds to SARS-CoV RBD (K d = 1 71 nM) with a much higher affinity than to SARS-CoV-2 RBD (K d = 115 nM) (Table 1 Previous cryo-EM studies have also shown that the recombinant SARS-CoV S 121 protein is mostly found in the none-"up", single-"up", or double-"up" conformations (19, 122 21), but rarely in the triple-"up" conformation, even with ACE2 receptor bound (21, 22) . abstract: The outbreak of COVID-19, which is caused by SARS-CoV-2 virus, continues to spread globally, but there is currently very little understanding of the epitopes on the virus. In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. CR3022 targets a highly conserved epitope that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding site can only be accessed when at least two RBDs on the trimeric S protein are in the “up” conformation. Overall, this study provides structural and molecular insight into the antigenicity of SARS-CoV-2. ONE SENTENCE SUMMARY Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain. url: https://doi.org/10.1101/2020.03.13.991570 doi: 10.1101/2020.03.13.991570 id: cord-342902-y1v8wzxq author: Yuan, Shuofeng title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 words: 5692.0 sentences: 291.0 pages: flesch: 45.0 cache: ./cache/cord-342902-y1v8wzxq.txt txt: ./txt/cord-342902-y1v8wzxq.txt summary: Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. We found that co-application of clofazimine and remdesivir impacts SARS-CoV-2 replication in a manner that extends beyond the additive combinatorial activity predicted by the Bliss independence model (maximal Bliss Synergy Score of 44.28; Figure 5a , Extended Data Figure 2) , and indicates these two drugs harbor a synergistic antiviral relationship. abstract: COVID-19 pandemic is the third zoonotic coronavirus (CoV) outbreak of the century after severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) since 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. The FDA-approved molecule was found to inhibit multiple steps of viral replication, suggesting multiple underlying antiviral mechanisms. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Additionally, clofazimine exhibited synergy when administered with remdesivir. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. Taken together, our data provide evidence that clofazimine may have a role in the control of the current pandemic SARS-CoV-2, endemic MERS-CoV in the Middle East, and, possibly most importantly, emerging CoVs of the future. url: https://doi.org/10.21203/rs.3.rs-86169/v1 doi: 10.21203/rs.3.rs-86169/v1 id: cord-351489-tzmev77c author: Yuan, Shuofeng title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 words: 5002.0 sentences: 238.0 pages: flesch: 40.0 cache: ./cache/cord-351489-tzmev77c.txt txt: ./txt/cord-351489-tzmev77c.txt summary: They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. In this primary screening, chloroquine, lopinavir, and remdesivir which were recently reported to have anti-SARS-CoV-2 activity, exhibited about 1.3-2.0 log10 copies/mL reduction in viral RNA load ( Figure 1 ). In comparison, recombinant IFN-β demonstrated the most potent anti-SARS-CoV-2 activity, with Avonex (IFN-β1a), Rebif (IFN-β1a), and Betaferon (IFN-β1b) each achieving about 3 log10 copies/mL reduction in viral load. In our primary screening using a fixed antiviral agent concentration and virus inoculum, we identified recombinant IFNs and lipogenesis modulators to be the most potent anti-SARS-CoV-2 agents among 22 broad-spectrum antivirals. abstract: The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) signals an urgent need for an expansion in treatment options. In this study, we investigated the anti-SARS-CoV-2 activities of 22 antiviral agents with known broad-spectrum antiviral activities against coronaviruses and/or other viruses. They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. Betaferon (interferon-β1b) exhibited the most potent anti-SARS-CoV-2 activity in viral antigen expression, viral load reduction, and plaque reduction assays among the recombinant interferons. The lipogenesis modulators 25-hydroxycholesterol and AM580 exhibited EC(50) at low micromolar levels and selectivity indices of >10.0. Combinational use of these host-based antiviral agents with virus-based antivirals to target different processes of the SARS-CoV-2 replication cycle should be evaluated in animal models and/or clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32532085/ doi: 10.3390/v12060628 id: cord-320054-wqpr8v3p author: Yuan, Xianlin title: The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date: 2020-08-24 words: 2588.0 sentences: 156.0 pages: flesch: 58.0 cache: ./cache/cord-320054-wqpr8v3p.txt txt: ./txt/cord-320054-wqpr8v3p.txt summary: In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. To explore these questions, here we report 94 to used these immuno-bioinformatic tools from the IEDB and related resources to 95 predict the B cell epitopes of S protein from the prototype and mutated strains of 96 SARS-CoV-2 and compare the changes of the likely epitope sites from dominant and 97 rare mutations of S protein. The major variation sequences were available 409 from The Global Initiative for Sharing All Influenza Data (GISAID) [26] and GenBank 446 We used the sequence from early onset SARS-CoV-2 as the wildtype or prototype and 447 the recent variant virus as mutation strains to predict the B-cell epitopes of S protein. abstract: SARS-CoV-2 has rapidly transmitted worldwide and results in the COVID-19 pandemic. Spike glycoprotein on surface is a key factor of viral transmission, and has appeared a lot of variants due to gene mutations, which may influence the viral antigenicity and vaccine efficacy. Here, we used bioinformatic tools to analyze B-cell epitopes of prototype S protein and its 9 common variants. 12 potential linear and 53 discontinuous epitopes of B-cells were predicted from the S protein prototype. Importantly, by comparing the epitope alterations between prototype and variants, we demonstrate that B-cell epitopes and antigenicity of 9 variants appear significantly different alterations. The dominant D614G variant impacts the potential epitope least, only with moderately elevated antigenicity, while the epitopes and antigenicity of some mutants(V483A, V367F, etc.) with small incidence in the population change greatly. These results suggest that the currently developed vaccines should be valid for a majority of SARS-CoV-2 infectors. This study provides a scientific basis for large-scale application of SARS-CoV-2 vaccines and for taking precautions against the probable appearance of antigen escape induced by genetic variation after vaccination. Author Summary The global pandemic of SARS-CoV-2 has lasted for more than half a year and has not yet been contained. Until now there is no effective treatment for SARS-CoV-2 caused disease (COVID-19). Successful vaccine development seems to be the only hope. However, this novel coronavirus belongs to the RNA virus, there is a high mutation rate in the genome, and these mutations often locate on the Spike proteins of virus, the gripper of the virus entering the cells. Vaccination induce the generation of antibodies, which block Spike protein. However, the Spike protein variants may change the recognition and binding of antibodies and make the vaccine ineffective. In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. We discovered the variability in antigenicity among the mutants, for instance, in the more widespread D614G variant the change of epitope was least affected, only with slight increase of antigenicity. However, the antigenic epitopes of some mutants change greatly. These results could be of potential importance for future vaccine design and application against SARS-CoV2 variants. url: https://doi.org/10.1101/2020.08.24.264895 doi: 10.1101/2020.08.24.264895 id: cord-289377-2vqqabum author: Yubero, P. title: Evidence for immunity to SARS-CoV-2 from epidemiological data series date: 2020-07-24 words: 4972.0 sentences: 268.0 pages: flesch: 53.0 cache: ./cache/cord-289377-2vqqabum.txt txt: ./txt/cord-289377-2vqqabum.txt summary: We then estimate the capacity of EAKF techniques to infer the duration of this memory and then apply this approach to mortality time series from New York City, discerning immunity times against SARS-CoV-2 with reasonable accuracy. (B) The value of the synthetic infection rate β synth (dotted line) is captured by the protocol β model (blue) after some data assimilation steps, and prior to the pandemic peak. . https://doi.org/10.1101/2020.07.22.20160028 doi: medRxiv preprint uity of a strong reduction of the infection rate during the initial days of the epidemic in all data sets that we studied (results of Belgium, Spain and France are available in Fig. S4 ). In our case, the time-dependent state variables are the infection rate β , the immunity memory τ and the population in each compartment of the model. abstract: The duration of immunity to SARS-CoV-2 is uncertain. Delineating immune memory typically requires longitudinal serological studies that track antibody prevalence in the same cohort for an extended time. However, this information is needed in faster timescales. Notably, the dynamics of an epidemic where recovered patients become immune for any period should differ significantly from those of one where the recovered promptly become susceptible. Here, we exploit this difference to provide a reliable protocol that can estimate immunity early in an epidemic. We verify this protocol with synthetic data, discuss its limitations, and then apply it to evaluate human immunity to SARS-CoV-2 in mortality data series from New York City. Our results indicate that New York's mortality figures are incompatible with immunity lasting anything below 105 or above 211 days (90% CI.), and set an example on how to assess immune memory in emerging pandemics before serological studies can be deployed. url: https://doi.org/10.1101/2020.07.22.20160028 doi: 10.1101/2020.07.22.20160028 id: cord-252771-6kwfulqe author: Yue, Jing-Li title: Mental health services for infectious disease outbreaks including COVID-19: a rapid systematic review date: 2020-11-05 words: 7935.0 sentences: 412.0 pages: flesch: 41.0 cache: ./cache/cord-252771-6kwfulqe.txt txt: ./txt/cord-252771-6kwfulqe.txt summary: Group-based cognitive behavioral therapy, psychological first aid, community-based psychosocial arts program, and other culturally adapted interventions were reported as being effective against the mental health impacts of COVID-19, Ebola, and SARS. Specifically, mental health professionals including psychiatrists, psychiatric nurses, and psychologists were deployed to provide psychological counseling and support for vulnerable populations (e.g. frontline healthcare workers, confirmed COVID-19 patients, suspected COVID-19 cases and their families) in China and for people in quarantine in South Korea. For example, group-based CBT (Waterman et al., 2018; Waterman et al., 2019) , PFA, PTL (Decosimo et al., 2019) , culturally adapted interventions such as SMART (Ng et al., 2006) , ultra-brief psychological interventions (Ping et al., 2020) and peer supports (Rastegar Kazerooni et al., 2020) have been reported to effectively mitigate the emotional impacts of COVID-19, EVD, and SARS outbreaks. Culturally-adapted and cost-effective mental health emergency systems based on evidence-based intervention methods integrated into public health emergency responses at the national and global levels are recommended to reduce the psychological impacts of infectious disease outbreaks, especially for COVID-19. abstract: The upsurge in the number of people affected by the COVID-19 is likely to lead to increased rates of emotional trauma and mental illnesses. This article systematically reviewed the available data on the benefits of interventions to reduce adverse mental health sequelae of infectious disease outbreaks, and to offer guidance for mental health service responses to infectious disease pandemic. PubMed, Web of Science, Embase, PsycINFO, WHO Global Research Database on infectious disease, and the preprint server medRxiv were searched. Of 4278 reports identified, 32 were included in this review. Most articles of psychological interventions were implemented to address the impact of COVID-19 pandemic, followed by Ebola, SARS, and MERS for multiple vulnerable populations. Increasing mental health literacy of the public is vital to prevent the mental health crisis under the COVID-19 pandemic. Group-based cognitive behavioral therapy, psychological first aid, community-based psychosocial arts program, and other culturally adapted interventions were reported as being effective against the mental health impacts of COVID-19, Ebola, and SARS. Culturally-adapted, cost-effective, and accessible strategies integrated into the public health emergency response and established medical systems at the local and national levels are likely to be an effective option to enhance mental health response capacity for the current and for future infectious disease outbreaks. Tele-mental healthcare services were key central components of stepped care for both infectious disease outbreak management and routine support; however, the usefulness and limitations of remote health delivery should also be recognized. url: https://www.ncbi.nlm.nih.gov/pubmed/33148347/ doi: 10.1017/s0033291720003888 id: cord-009697-dq4y89ab author: Yuen, Eddie title: Role of absolute lymphocyte count in the screening of patients with suspected SARS date: 2003-07-25 words: 1510.0 sentences: 92.0 pages: flesch: 59.0 cache: ./cache/cord-009697-dq4y89ab.txt txt: ./txt/cord-009697-dq4y89ab.txt summary: 3 This multicentre, placebo-controlled, randomized, double-blind trial in 6213 patients with acute ST-elevation myocardial infarct (STEMI) found that magnesium sulphate, (2 g intravenous bolus over 15 min followed by a 17 g infusion over 24 h), administered within 6 hours of onset of symptoms did not have any effect on the primary end-point of 30 day all-cause mortality when compared with placebo (15.3% 30 day mortality in the magnesium group vs 15.2% in the placebo group; odds ratio 1.0; 95% CI 0.9-1.2; P = 0.96). As the investigators point out in the discussion of their paper, this means that 68 684 patients have been studied over the past 22 years in 14 randomized trials of magnesium in myocardial infarction. Second, a multicentre, placebo-controlled, randomized, double-blind trial of intravenous magnesium sulphate in 248 patients with acute severe asthma was recently reported. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163475/ doi: 10.1046/j.1442-2026.2003.00486_3.x id: cord-322877-jy1uvwre author: Yuen, Kenneth S.C. title: Ocular screening in severe acute respiratory syndrome date: 2004-03-30 words: 1260.0 sentences: 86.0 pages: flesch: 56.0 cache: ./cache/cord-322877-jy1uvwre.txt txt: ./txt/cord-322877-jy1uvwre.txt summary: To investigate the ocular manifestations of patients with severe acute respiratory syndrome (SARS) and to monitor the possible ocular complications arising from the treatment regimen with high-dose systemic corticosteroid drugs. In March 2003, Hong Kong was seriously affected by a massive outbreak of SARS, and we took that opportunity to conduct a prospective observational study to investigate the probable ocular manifestations arising from SARS and the possible short-term complications resulting from the pulse or high-dose corticosteroid therapy. Patients were assessed with a comprehensive ocular examination including best-corrected visual acuity, intraocular pressure (IOP) by noncontact tonometer ([NCT] Xpert Noncontact Tonometer Plus; Reichert Ophthalmic Instruments, New York, New York, USA), slit-lamp, and binocular indirect ophthalmoscopy at baseline and at 2 months and 3 months. 2 With the unremarkable ophthalmologic findings of this study, routine ocular screening in patients with SARS for diagnosis or for complications may not be worthwhile. abstract: To investigate the ocular manifestations of patients with severe acute respiratory syndrome (SARS) and to monitor the possible ocular complications arising from the treatment regimen with high-dose systemic corticosteroid drugs. DESIGN: Prospective, observational cohort case series. METHODS: Ninety eyes from 45 patients with the diagnosis of SARS during an epidemic outbreak in Hong Kong were analyzed. Relevant medical and ophthalmic histories were taken. Ophthalmic examinations, including best-corrected visual acuity, intraocular pressure, slit-lamp, and indirect ophthalmoscopy examination, were performed at baseline and at 2-month and 3-month follow-up. SETTING: Faculty practice in university hospital. RESULTS: Only two patients had mild elevated intraocular pressure at baseline and at subsequent follow-up. There was no loss of visual acuity, cataract progression, or increased cup–disk ratio. Fundus examinations were unremarkable in all patients. CONCLUSIONS: Our study did not demonstrate any ocular manifestations in patients with SARS. The treatment regimen of high-dose corticosteroid also did not show any significant ocular complications. Routine ocular screening of patients with SARS for diagnosis or for complications might not be indicated. url: https://www.ncbi.nlm.nih.gov/pubmed/15059730/ doi: 10.1016/j.ajo.2003.09.060 id: cord-028525-0ckagrt1 author: Yung, Chee Fu title: Household Transmission of SARS-CoV-2 from Adults to Children date: 2020-07-04 words: 1706.0 sentences: 89.0 pages: flesch: 56.0 cache: ./cache/cord-028525-0ckagrt1.txt txt: ./txt/cord-028525-0ckagrt1.txt summary: Beginning on March 5, because of concern that infected children might not display symptoms, the Ministry of Health Singapore implemented screening for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction from nasopharyngeal swabs for all pediatric household contacts (regardless of symptoms) of persons with laboratory-confirmed COVID-19. During March and April, among 137 households with a total of 223 adults (index patients) with laboratory-confirmed COVID-19, 213 children aged ≤16 years were tested for SARS-6 CoV-2; 13 cases were detected in seven households, for an attack rate of 6.1% among children and 5.2% of households with confirmed exposure to COVID-19 (Table) . Based on systematic surveillance and screening of children who were household contacts of persons with confirmed COVID-19, the attack rate of SARS-CoV-2 infection in children was 6.1%. The low attack rate suggests that strict compliance with infection control may be able to eliminate or reduce the risk of transmission from adults to children in household settings. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334921/ doi: 10.1016/j.jpeds.2020.07.009 id: cord-269555-29t956ik author: Zaconeta, Alberto title: Letter to the editor“SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?” date: 2020-09-22 words: 187.0 sentences: 24.0 pages: flesch: 55.0 cache: ./cache/cord-269555-29t956ik.txt txt: ./txt/cord-269555-29t956ik.txt summary: key: cord-269555-29t956ik title: Letter to the editor"SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?" journal: Placenta DOI: 10.1016/j.placenta.2020.09.063 cord_uid: 29t956ik transmission of SARS-CoV-2. After discussing anatomical and molecular differences between 36 the alveolar-capillary and syncytium-capillary barriers, the authors presented the well-37 considered hypothesis that the absence of caveolin expression in the syncytium is one of the 38 most important mechanisms preventing the transplacental passage of this virus (1) . their masterful analysis, we would like to extend the discussion to another important risk factor 40 for vertical transmission, namely viral load in blood. Factors preventing 55 materno-fetal transmission of SARS-CoV-2 Detection of SARS-CoV-2 in 58 different types of clinical specimens Clinical features of patients 61 infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not 65 associated with infectious virus The trinity of COVID-19: immunity, 68 inflammation and intervention abstract: nan url: https://doi.org/10.1016/j.placenta.2020.09.063 doi: 10.1016/j.placenta.2020.09.063 id: cord-339506-pkusvf82 author: Zaki, N. title: The estimations of the COVID-19 incubation period: a systematic review of the literature date: 2020-05-23 words: 5969.0 sentences: 280.0 pages: flesch: 50.0 cache: ./cache/cord-339506-pkusvf82.txt txt: ./txt/cord-339506-pkusvf82.txt summary: One reason for this is that generally we can only discover the times when the patient was in contact with persons carrying the virus, and then assume that the incubation period runs from the earliest date of exposure to the appearance of clinical symptoms or medical diagnosis. et al [15] researched the early data regarding transmission dynamics for the virus in Wuhan, estimating the mean incubation period at 5.2 days (95% CI: 4.1-7.0), with the distribution''s 95 th percentile being 12.5 days. They took individual patient histories from COVID-19 subjects in China (not from Hubei Province) for estimating the distribution of the time for generation, incubation, and the time span between onset of symptoms and isolation/diagnosis. The researchers undertook analysis of clinical data for 34 subjects submitting to elective surgery during the COVID-19 incubation period at four Chinese hospitals (Renmin, Tongji, Zhongnan, and Central) in Wuhan between January 1 and February 5, 2020. abstract: Objective: to undertake a review and critical appraisal of all published/preprint reports that offer an estimation of incubation periods for novel coronavirus (COVID-19). Design: a rapid and systematic review/critical appraisal Data sources: COVID-19 Open Research Dataset supplied by Georgetown's Centre for Security and Emerging Technology as well as PubMed and Embase via Arxiv, medRxiv, and bioRxiv. Results: screening was undertaken 44,000 articles with a final selection of 25 studies referring to 18 different experimental projects related to the estimation of the incubation period of COVID-19. Findings: The majority of extant published estimates offer empirical evidence showing that the incubation period for the virus is a mean of 7.8 days, with a median of 5.01 days, which falls into the ranges proposed by the WHO (0 to 14 days) and the ECDC (2 to 12 days). Nevertheless, a number of authors proposed that quarantine time should be a minimum of 14 days and that for estimates of mortality risks a median time delay of 13 days between illness and mortality should be under consideration. It is unclear as to whether any correlation exists between the age of patients and the length of time they incubate the virus. Finally, it is generally agreed that robust precautions must be put in place for the prevention and/or mitigation of asymptomatic transmission to high-risk patients caused by those incubating the virus. url: http://medrxiv.org/cgi/content/short/2020.05.20.20108340v1?rss=1 doi: 10.1101/2020.05.20.20108340 id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 words: 19585.0 sentences: 1132.0 pages: flesch: 36.0 cache: ./cache/cord-016990-ot1wi3xi.txt txt: ./txt/cord-016990-ot1wi3xi.txt summary: 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. abstract: The lungs are among the most vulnerable to microbial assault of all organs in the body. From a contemporary vantage, lower respiratory tract infections are the greatest cause of infection-related mortality in the United States, and rank seventh among all causes of deaths in the United States.2,3 From a global and historic perspective, the scope and scale of lower respiratory tract infection is greater than any other infectious syndrome, and viral pneumonias have proven to be some of the most lethal and dramatic of human diseases. The 1918–1919 influenza pandemic, perhaps the most devastating infectious disease pandemic in recorded history, resulted in an estimated 40 million deaths worldwide, including 700,000 deaths in the U.S.4 The global outbreak of severe acute respiratory syndrome (SARS) during 2003, although considerably smaller in scale, resulted in 8098 cases and 774 deaths5 and is a dramatic contemporary example of the ability of viral pneumonias to rapidly disseminate and cause severe disease in human populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121437/ doi: 10.1007/978-0-387-68792-6_11 id: cord-304115-xs54f295 author: Zamaniyan, Marzieh title: Preterm delivery in pregnant woman with critical COVID‐19 pneumonia and vertical transmission date: 2020-04-17 words: 1793.0 sentences: 98.0 pages: flesch: 51.0 cache: ./cache/cord-304115-xs54f295.txt txt: ./txt/cord-304115-xs54f295.txt summary: Given the patient''s history and fever and cough, two nasal and throat swab samples were taken and tested to be positive for SARS-CoV-2 with SuperScript III Platinum, Quantitive Real-time PCR system Kits (Invitrogen company, USA) 4 . The RT-PCR tests was positive for amniotic fluid and neonate, suggesting the infant might have been affected intrauterine by COVID-19; therefore, once more, it raised the concerns regarding possible vertical transmission of the virus in mothers with serious illness. In some previous studies, the authors reported 21 healthy babies delivered by infected mothers to COVID-19, but they could not detect the virus in any of the feto-maternal parts namely placenta, amniotic fluid and cord blood [9] [10] [11] . The current case study, once again, raises concerns regarding possible vertical transmission of COVID-19 in pregnant women infected by SARS CoV-2 in contrast to the findings reported in some small studies published previously. abstract: nan url: https://doi.org/10.1002/pd.5713 doi: 10.1002/pd.5713 id: cord-276061-7b8h2sjw author: Zammit, M title: A rise in facial nerve palsies during the coronavirus disease 2019 pandemic date: 2020-10-01 words: 2478.0 sentences: 146.0 pages: flesch: 56.0 cache: ./cache/cord-276061-7b8h2sjw.txt txt: ./txt/cord-276061-7b8h2sjw.txt summary: OBJECTIVE: An increase in spontaneous lower motor neuron facial nerve (VIIth cranial nerve) palsies was seen during the severe acute respiratory syndrome coronavirus 2 outbreak in our emergency clinic. • There was an increased incidence of spontaneous lower motor neuron facial nerve palsy in our emergency ENT clinic • Only two prior case reports have referenced an association between VIIth cranial nerve palsy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) • Facial nerve palsy incidence of 3.5 per cent was seen in clinic during 2020, 2.7 times higher than the previous year at 1.3 per cent • A SARS-CoV-2 incidence of 11.8 per cent was seen in our cohort, contrasting with that of the Liverpool population of 0.5 per cent • It is important for clinicians to be aware that facial nerve palsy may be an initial presentation of the disease abstract: OBJECTIVE: An increase in spontaneous lower motor neuron facial nerve (VIIth cranial nerve) palsies was seen during the severe acute respiratory syndrome coronavirus 2 outbreak in our emergency clinic. This led us to perform a single-centre cohort review. METHODS: A retrospective review was conducted of VIIth cranial nerve palsies from January to June 2020 and the findings were compared to those cases reviewed in the previous year. The severe acute respiratory syndrome coronavirus 2 incidence of the cohort was compared with that of the Liverpool population. RESULTS: Our VIIth cranial nerve palsy incidence in the 2020 period was 3.5 per cent (30 out of 852), 2.7 higher than last year's rate of 1.3 per cent (14 out of 1081), which was a statistically significant difference (p < 0.01). Two of the 17 patients in our cohort tested positive for severe acute respiratory syndrome coronavirus 2 (11.8 per cent), contrasting with Liverpool's severe acute respiratory syndrome coronavirus 2 incidence (0.5 per cent). CONCLUSION: Severe acute respiratory syndrome coronavirus 2 may be responsible for an increased number of facial nerve palsies; it is important for clinicians to be aware that this may being an initial presentation of the disease. url: https://doi.org/10.1017/s0022215120002121 doi: 10.1017/s0022215120002121 id: cord-347484-7vn93t58 author: Zamoto, Aya title: Identification of Ferret ACE2 and its Receptor Function for Sars-Coronavirus date: 2006 words: 773.0 sentences: 50.0 pages: flesch: 61.0 cache: ./cache/cord-347484-7vn93t58.txt txt: ./txt/cord-347484-7vn93t58.txt summary: Severe acute respiratory syndrome associated coronavirus (SARS-CoV) was the causative agent of SARS, which occurred as an emerging pneumonic disease in 2002. Amplification of partial ACE2 gene by RT-PCR: RNAs were extracted from heart, lung, kidney, and small intestine of a ferret. Determination of nucleotide sequence of ferret ACE2 (feACE2): Two overlapping regions of feACE2 genes were amplified by RT-PCR from kidney RNA. The partial feACE2 gene was amplified from RNAs isolated from the lung, heart, kidney, and small intestine by RT-PCR. HeLa cells expressing feACE2 supported SARS-CoV replication to the same extent as those expressing human ACE2 (Fig. 3) . From these observations, it is postulated that animal species whose ACE2 functions as an efficient SARS-CoV receptor would be a susceptible in feACE2 expressing HeLa cells was over 10 times more efficient than that in mouse efficiently. Furthermore, transgenic mouse expressing ferret or human ACE2 may serve a useful animal model for SARS-CoV infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037589/ doi: 10.1007/978-0-387-33012-9_93 id: cord-286001-pu1fetq7 author: Zang, Ruochen title: TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date: 2020-04-23 words: 2049.0 sentences: 145.0 pages: flesch: 50.0 cache: ./cache/cord-286001-pu1fetq7.txt txt: ./txt/cord-286001-pu1fetq7.txt summary: In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. Importantly, we found that 160 expression of TMPRSS4 but not ST14 also resulted in a significant increase in the levels of viral RNA and infectious virus titers in the presence of ACE2 ( Fig. 3B and S3C) . Collectively, we have shown that TMPRSS2 and TMPRSS4 activate SARS-CoV-2 S and 187 enhance membrane fusion and viral endocytosis into host cells. Importantly, abrogating TMPRSS4 expression led 209 to a 4-fold reduction in SARS-CoV-2 chimera virus replication in human enteroid, even 210 more significant than TMPRSS2 knockout (Fig. 4B) , highlighting its importance in 211 mediating virus replication in primary cells. It is possible that in the 293 small intestine, whereas SARS-CoV-2 is relatively stable, additional proteases such as 294 trypsin likely enhance viral pathogenesis by triggering more robust IEC fusion (Fig. S2A) . abstract: Both gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA have been frequently observed in COVID-19 patients. However, whether SARS-CoV-2 replicate in the human intestine and its clinical relevance to potential fecal-oral transmission remain unclear. Here, we demonstrate productive infection of SARS-CoV-2 in ACE2+ mature enterocytes in human small intestinal enteroids. In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. However, newly synthesized viruses released into the intestinal lumen were rapidly inactivated by human colonic fluids and no infectious virus was recovered from the stool specimens of COVID-19 patients. Our results highlight the intestine as a potential site of SARS-CoV-2 replication, which may contribute to local and systemic illness and overall disease progression. url: https://doi.org/10.1101/2020.04.21.054015 doi: 10.1101/2020.04.21.054015 id: cord-258268-7ypq0t3d author: Zanin, Luca title: SARS-CoV-2 can induce brain and spine demyelinating lesions date: 2020-05-04 words: 1481.0 sentences: 113.0 pages: flesch: 47.0 cache: ./cache/cord-258268-7ypq0t3d.txt txt: ./txt/cord-258268-7ypq0t3d.txt summary: On January 24, 2020, a new virus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been identified, quickly gaining worldwide attention [21] . Similarly to other Coronavirus, SARS-CoV-2 can attack the olfactory bulb and then affect the central nervous system (CNS) through the olfactory tract in the early stages of infection [5] . Neurological impairment and demyelinating reaction appear as complications in case of severe Coronavirus Disease 2019 (COVID-19) [10] . Our patient showed symptoms consistent with a neurological involvement consequent to SARS-CoV-2 infection. In SARS-CoV-2 infection, neurological impairment was observed only in case of severe COVID-19 [10] . SARS-CoV-2 was not detected in the CSF probably because the neurological damage was sustained by a delayed immune response that occurred after the viremia. Sudden neurological impairment with seizures in COVID-19 patients may be sustained by CNS involvement and demyelinating lesions. Neurologic features in severe SARS-CoV-2 infection abstract: SARS-CoV-2 can attack the central nervous system in the early stages of infection. Headache, anosmia, and dysgeusia are common symptoms. Disturbance of consciousness and seizures can occur as complications in case of severe COVID-19. We described the case of a COVID-19 patient admitted for interstitial pneumonia and seizures. MRI showed newly diagnosed demyelinating lesions. High-dose steroid treatment allowed neurological and respiratory recovery. We speculated a delayed immune response induced by SARS-CoV-2. The virus may lead to a SIRS-like immune disorder or play a role of infective trigger. Prompt invasive treatment should be adopted to avoid hypoxic neurotoxicity and prevent CNS injuries. url: https://doi.org/10.1007/s00701-020-04374-x doi: 10.1007/s00701-020-04374-x id: cord-026806-pn4lwhr7 author: Zargar, Showkat Ali title: Gastrointestinal Endoscopy during COVID: Do Some, Leave Most date: 2020-05-16 words: 1498.0 sentences: 91.0 pages: flesch: 54.0 cache: ./cache/cord-026806-pn4lwhr7.txt txt: ./txt/cord-026806-pn4lwhr7.txt summary: Therefore, these guidelines cannot be applied uniformly all over India and more or less usual business can start with caveat of complete adherence to standard operating procedure of infectious control protocols in combination with adherence to social distancing, frequent hand washing, use of protective gears, and organization of endoscopy teams and space in green zones. Chinese data are testimony to the fact that in Wuhan, China-epicenter of COVID-19-that in the initial weeks HCWs accounted for large number of total cases which was significantly reduced following adherence to infectious control practices. The informed consent requires "detailed and transparent" discussion on issues as follows: (1) acquisition of infection by HCWs from asymptomatic COVID-19 patient and also patient may develop full-fledged infection in postprocedure period blaming the endoscopist; (2) chances of acquisition of infection despite of adherence to infectious control protocols; and (3) risks involved in postponing otherwise medically indicated, time-sensitive procedure and reasons for delaying it. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295292/ doi: 10.1055/s-0040-1712337 id: cord-347548-h5fk64p8 author: Zarza, José title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection date: 2020-08-21 words: 1843.0 sentences: 122.0 pages: flesch: 51.0 cache: ./cache/cord-347548-h5fk64p8.txt txt: ./txt/cord-347548-h5fk64p8.txt summary: title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection Coronavirus disease 2019 (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which has sparked growing interest and concern in the international community. 1 We present a case of COVID-19 associated with Evans syndrome (hemolytic anemia plus thrombocytopenia, both with autoimmune causes) and antiphospholipid antibodies. With these findings, her diagnoses upon admission were SARS-COV-2 infection, SLE with associated antiphospholipid antibodies, and Evans syndrome. We present the case of a young patient who was apparently in good health but had a history of venous thrombosis of unknown cause in her childhood, which started with Evans syndrome and a high titer of antiphospholipid antibodies, in coincidence with a SARS-COV-2 infection. 4 Although the decreased platelet count is usually mild in COVID-19, some cases of severe thrombocytopenia have been reported in the context of disseminated intravascular coagulation in these patients. abstract: nan url: https://api.elsevier.com/content/article/pii/S2531137920301164 doi: 10.1016/j.htct.2020.08.003 id: cord-309931-cpzp33b3 author: Zawawi, Ayat title: The impact of COVID-19 pandemic on malaria elimination date: 2020-10-20 words: 4183.0 sentences: 219.0 pages: flesch: 48.0 cache: ./cache/cord-309931-cpzp33b3.txt txt: ./txt/cord-309931-cpzp33b3.txt summary: As lowand middle-income countries shift increasingly to focus on identifying and treating COVID-19, questions are emerging about the impact this shift in focus will have on ongoing efforts to control other infectious diseases, such as malaria. This review discusses how the spread of SARS-CoV-2 in lowand middle-income countries might impact these efforts, focusing in particular on the effects of co-infection and the use of antimalarial drugs used to treat malaria as therapeutic interventions for COVID-19. This review addresses this gap in the literature by discussing how the spread of SARS-CoV-2 in low-and middle-income countries might impact efforts to control malaria. Despite the CQ and HCQ treatment potential for COVID-19, the use of these two drugs could pose many challenges in low-and middle-income countries and not just in malaria-endemic areas. abstract: SARS-CoV-2 has spread throughout the world and become the cause of the infectious coronavirus disease 2019 (COVID-19). As low- and middle-income countries shift increasingly to focus on identifying and treating COVID-19, questions are emerging about the impact this shift in focus will have on ongoing efforts to control other infectious diseases, such as malaria. This review discusses how the spread of SARS-CoV-2 in low- and middle-income countries might impact these efforts, focusing in particular on the effects of co-infection and the use of antimalarial drugs used to treat malaria as therapeutic interventions for COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2405673120300568?v=s5 doi: 10.1016/j.parepi.2020.e00187 id: cord-328011-6lf3no6u author: Zayed, Hatem title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics date: 2020-08-14 words: 1449.0 sentences: 84.0 pages: flesch: 49.0 cache: ./cache/cord-328011-6lf3no6u.txt txt: ./txt/cord-328011-6lf3no6u.txt summary: title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics Since coronaviruses are increasing alarmingly, there is an urgent need for a safe and effective vaccine to prevent the spread of the virus during pandemic outbreaks, and stop deaths associated with the virulent COVID-19. We now know that SARS-CoV-2 shares 88% identity with two SARS-like coronaviruses (bat-SL-CoVZXC21 and bat-SL-CoVZC45) that both originated in China, and use the same human angiotensin-converting enzyme 2 receptor for cell entry during the process of infection (3). In response to such forewarnings from scientists, a predictive vaccine could have been designed and developed for the potential virus pandemic. Thereafter, during the time of pandemic, suitable stored transgenic cell lines could be used, based on the Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; VLP, virus-like particle; WHO, World Health Organization. abstract: nan url: https://doi.org/10.3389/fimmu.2020.02051 doi: 10.3389/fimmu.2020.02051 id: cord-353628-f6ew980g author: Zayet, Souheil title: Encephalopathy in patients with COVID‐19: ‘Causality or coincidence?’ date: 2020-05-19 words: 1521.0 sentences: 102.0 pages: flesch: 51.0 cache: ./cache/cord-353628-f6ew980g.txt txt: ./txt/cord-353628-f6ew980g.txt summary: Since its discovery in December 2019, the novel coronavirus disease 2019 (COVID-19) has caused several clinical presentations: mainly respiratory, rarely gastrointestinal, and exceptionally neurological. In addition to the usual symptoms (general, respiratory and otorhinolaryngological) of the infection with SARS-CoV-2, several authors have described neurological manifestations as headache, nausea, and vomiting. These viruses can invade brainstem via a synapse-connected route from the lungs and airways 9 .Considering the high similarity between SARS-CoV-2 and others CoVs 10 , it is still not clearly known whether the potential neuro-invasion of SARS-CoV2 is partially responsible for respiratory failure in patients with COVID-19 9,11,12 . Therefore, in the context of COVID pandemic, it would be reasonable to perform a thoracic CT and a RT-PCR for SARS-CoV-2 in case of encephalopathy with normal lumbar puncture and brain imaging. The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients abstract: The main tropism of the novel coronavirus disease 2019 (COVID‐19) is respiratory. Increasing evidences show that SARS‐CoV‐2 is not always confined to the respiratory tract but can also invade the central nervous system (CNS) and induce neurological diseases. We report two cases illustrating this phenomenon. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32427357/ doi: 10.1002/jmv.26027 id: cord-305341-nokybn2a author: Zeng, Fanya title: Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments date: 2004-03-19 words: 3954.0 sentences: 192.0 pages: flesch: 51.0 cache: ./cache/cord-305341-nokybn2a.txt txt: ./txt/cord-305341-nokybn2a.txt summary: title: Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments Another interesting finding was that mouse antibodies elicited separately by plasmids encoding S1 and S2 subunits cooperatively neutralized SARS-CoV but neither the S1 nor S2 specific antibodies did, suggesting the possible role of both S1 and S2 subunits in host cell docking and entry. Animals vaccinated with DNA encoding secreting form of E2 glycoprotein of classical swine fever virus (CSFV) showed both CSFV specific antibody response and protection upon viral challenge though the native E2 was anchor membrane protein ( [28, 29] and Zeng et al., unpublished data). In the mice experiment, it was demonstrated that SARS-CoV specific antibodies could be induced by immunization with plasmids encoding S1, S2 and fragment of S1 subunit. The first paper on immunizing masques with structural genes of SARS-CoV, however, reported that co-delivery of three viral genes encoding S1, nucleocapsid (N), and membrane (M) protein could elicit a high titer of neutralizing antibody and T-cell response [24] . abstract: The immunological characteristics of SARS-CoV spike protein were investigated by administering mice with plasmids encoding various S gene fragments. We showed that the secreting forms of S1, S2 subunits and the N-terminus of S1 subunit (residues 18–495) were capable of eliciting SARS-CoV specific antibodies and the region immediate to N-terminus of matured S1 protein contained an important immunogenic determinant for elicitation of SARS-CoV specific antibodies. In addition, mice immunized with plasmids encoding S1 fragment developed a Th1-mediated antibody isotype switching. Another interesting finding was that mouse antibodies elicited separately by plasmids encoding S1 and S2 subunits cooperatively neutralized SARS-CoV but neither the S1 nor S2 specific antibodies did, suggesting the possible role of both S1 and S2 subunits in host cell docking and entry. These results provide insights into understanding the immunological characteristics of spike protein and the development of subunit vaccines against SARS-CoV. url: https://www.sciencedirect.com/science/article/pii/S0006291X04002104 doi: 10.1016/j.bbrc.2004.01.166 id: cord-275185-9br8lwma author: Zeng, Hao title: The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date: 2020-10-06 words: 6613.0 sentences: 360.0 pages: flesch: 53.0 cache: ./cache/cord-275185-9br8lwma.txt txt: ./txt/cord-275185-9br8lwma.txt summary: Following CP transfusion, six out of eight patients showed improved oxygen support status; chest CT indicated varying degrees of absorption of pulmonary lesions in six patients within 8 days; the viral load was decreased to a negative level in five patients who had the previous viremia; other laboratory parameters also tended to improve, including increased lymphocyte counts, decreased C-reactive protein, procalcitonin, and indicators for liver function. Herein, we performed a retrospective observational study involving eight critical or severe patients with COVID-19 from four designated hospitals in the southwest region of China, aiming to explore the potential efficacy and safety of CP therapy, and to provide more evidence for the quality control of donated plasma and reasonable clinical application of CP transfusion. 23 Assessing the effects of neutralizing activity of CP on the patients'' clinical efficacy, we found that patients treated by CP with high NAT50 (>1:640) had more obvious improvement than patients receiving low NAT50 value (≤1:640) of CP, including shorter negative conservation time of viral RNA, and higher increment of IgG level after CP transfusion. abstract: Convalescent plasma (CP) transfusion has been indicated as a promising therapy in the treatment for other emerging viral infections. However, the quality control of CP and individual variation in patients in different studies make it rather difficult to evaluate the efficacy and risk of CP therapy for coronavirus disease 2019 (COVID-19). We aimed to explore the potential efficacy of CP therapy, and to assess the possible factors associated with its efficacy. We enrolled eight critical or severe COVID-19 patients from four centers. Each patient was transfused with 200–400 mL of CP from seven recovered donors. The primary indicators for clinical efficacy assessment were the changes of clinical symptoms, laboratory parameters, and radiological image after CP transfusion. CP donors had a wide range of antibody levels measured by serology tests which were to some degree correlated with the neutralizing antibody (NAb) level. No adverse events were observed during and after CP transfusion. Following CP transfusion, six out of eight patients showed improved oxygen support status; chest CT indicated varying degrees of absorption of pulmonary lesions in six patients within 8 days; the viral load was decreased to a negative level in five patients who had the previous viremia; other laboratory parameters also tended to improve, including increased lymphocyte counts, decreased C-reactive protein, procalcitonin, and indicators for liver function. The clinical efficacy might be associated with CP transfusion time, transfused dose, and the NAb levels of CP. This study indicated that CP might be a potential therapy for severe patients with COVID-19. url: https://doi.org/10.1038/s41392-020-00329-x doi: 10.1038/s41392-020-00329-x id: cord-336752-cpxnof1b author: Zeng, Qi‐Qiang title: Radiomics‐based model for accurately distinguishing between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) and influenza A infected pneumonia date: 2020-08-13 words: 3366.0 sentences: 186.0 pages: flesch: 39.0 cache: ./cache/cord-336752-cpxnof1b.txt txt: ./txt/cord-336752-cpxnof1b.txt summary: Patients were excluded if they met any of the following criteria: (a) history of American Society of Anesthesiologists (ASA) score of more than 2; (b) history of existing respiratory disease prior to outbreak of SARS-CoV-2; (c) pneumonia of etiology other than SARS-CoV-2 or influenza A virus by measuring nucleic acid by fluorogenic quantitative PCR of serum samples and/or oropharyngeal swab samples in conjunction to radiographic evidence and clinically established diagnosis; or (d) absent of obvious pulmonary lesions on radiographic imaging. Abbreviation: ASA score, American society of anesthesiologists score F I G U R E 2 Radiomics-based machine learning workflow, including computed tomography (CT) images acquisition and region-of-interest (ROI) segmentation of inflammatory lesions; radiomic feature extraction by LIFEx; features selection by least absolute shrinkage and selection operator (LASSO) with 10-fold cross-validation; radiomics prediction score and calibration; and nomogram development for a more clinicianfriendly application, and support vector machine (SVM) were used to distinguish these two kinds of diseases effectively drawn to compare the predicted outcome versus observed outcome of each patient in order to illustrate the probability of NCP. abstract: Clinicians have been faced with the challenge of differentiating between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) infected pneumonia (NCP) and influenza A infected pneumonia (IAP), a seasonal disease that coincided with the outbreak. We aim to develop a machine‐learning algorithm based on radiomics to distinguish NCP from IAP by texture analysis based on computed tomography (CT) imaging. Forty‐one NCP and 37 IAP patients admitted from January to February 6, 2019 admitted to two hospitals in Wenzhou, China. All patients had undergone chest CT examination and blood routine tests prior to receiving medical treatment. NCP was diagnosed by real‐time RT‐PCR assays. Eight of 56 radiomic features extracted by LIFEx were selected by least absolute shrinkage and selection operator regression to develop a radiomics score and subsequently constructed into a nomogram to predict NCP with area under the operating characteristics curve of 0.87 (95% confidence interval: 0.77‐0.93). The nomogram also showed excellent calibration with Hosmer‐Lemeshow test yielding a nonsignificant statistic (P = .904). The novel nomogram may efficiently distinguish between NCP and IAP patients. The nomogram may be incorporated to existing diagnostic algorithm to effectively stratify suspected patients for SARS‐CoV‐2 pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/32838396/ doi: 10.1002/mco2.14 id: cord-297324-me5ff1pb author: Zeng, Rong title: Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date: 2004-07-30 words: 4579.0 sentences: 223.0 pages: flesch: 57.0 cache: ./cache/cord-297324-me5ff1pb.txt txt: ./txt/cord-297324-me5ff1pb.txt summary: Analysis of the genomic organization of SARS-CoV showed that a gene locus containing ORF3a and 3b located between the S and E genes, 6 -8 is frequently found in different members of the coronavirus family (see Figure 4A ). According to the genomic sequence information for SARS-CoV, ORF 3a encoded a putative 31 kDa protein containing 274 amino acid residues. 6, 7 In order to confirm the result by shot-gun assay, the collected cytosol of SARS-CoV-infected Vero E6 cells was separated with SDS-PAGE, and then the gel slice around the 31 kDa region was excised and analyzed by capillary liquid chromatography electrospray tandem mass spectrometry (mLC-ESI-MS/MS). Interestingly, comparison with S protein sequences of the coronavirus family also shows a cysteinerich region overlapping the junction of the membrane-spanning domain and the cytoplasmic tail, which is a conserved motif of spike proteins in all analyzed coronaviruses (see Figure 3 of Marra et al. abstract: Proteomics was used to identify a protein encoded by ORF 3a in a SARS-associated coronavirus (SARS-CoV). Immuno-blotting revealed that interchain disulfide bonds might be formed between this protein and the spike protein. ELISA indicated that sera from SARS patients have significant positive reactions with synthesized peptides derived from the 3a protein. These results are concordant with that of a spike protein-derived peptide. A tendency exists for co-mutation between the 3a protein and the spike protein of SARS-CoV isolates, suggesting that the function of the 3a protein correlates with the spike protein. Taken together, the 3a protein might be tightly correlated to the spike protein in the SARS-CoV functions. The 3a protein may serve as a new clinical marker or drug target for SARS treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/15312778/ doi: 10.1016/j.jmb.2004.06.016 id: cord-256152-8wla6ne4 author: Zeng, Xiang title: Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? date: 2020-05-18 words: 775.0 sentences: 60.0 pages: flesch: 54.0 cache: ./cache/cord-256152-8wla6ne4.txt txt: ./txt/cord-256152-8wla6ne4.txt summary: title: Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? Furthermore, scientists and researchers should always adhere to the conflict-of-interest guidelines during the crisis era. Finally, scientist and researchers need an unbiased interpretation of the findings. For example, while taking care of respiratory emergency is the priority, researchers were also concerned about the damage to the nervous system caused by SARS-CoV-2 infection. 5 Nonetheless, alterations of sex-related hormone levels in reproductive-aged men with SARS-CoV-2 infection may indicate a decline in gonadal function. Such proactive, forward-looking studies render a new perspective on comprehensive understanding of disease and get us prepared for drug discovery, and offer important references for the decision of public health policies. All in all, the scientific community is now taking on new challenges in the era of COVID-19 pandemic. Neurologic features in severe SARS-CoV-2 infection Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study abstract: nan url: https://doi.org/10.14245/ns.2040212.106 doi: 10.14245/ns.2040212.106 id: cord-313268-j51zyodw author: Zeng, Xiangxiang title: Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning date: 2020-07-12 words: 4081.0 sentences: 217.0 pages: flesch: 42.0 cache: ./cache/cord-313268-j51zyodw.txt txt: ./txt/cord-313268-j51zyodw.txt summary: Using Amazon''s AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. 10−12 Deep learning has also recently demonstrated its better performance than classic machine learning methods to assist drug repurposing, 13 −16 yet without foreknowledge of the complex networks connecting drugs, targets, SARS-CoV-2, and diseases, the development of affordable approaches for the effective treatment of COVID-19 is challenging. Via systematic validation using transcriptomics and proteomics data generated from SARS-CoV-2-infected human cells and the ongoing clinical trial data, we successfully identified 41 drug candidates that can be further tested in large-scale randomized control trials for the potential treatment of COVID-19. Using Amazon''s AWS computing resources, we identified 41 high-confidence repurposed drug candidates (including dexamethasone, indomethacin, niclosamide, and toremifene) for COVID-19, which were validated by an enrichment analysis of gene expression and proteomics data in SARS-CoV-2 infected human cells. abstract: [Image: see text] There have been more than 2.2 million confirmed cases and over 120 000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there is currently a lack of proven effective medications against COVID-19. Drug repurposing offers a promising route for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep-learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, proteins/genes, pathways, and expression from a large scientific corpus of 24 million PubMed publications. Using Amazon’s AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. Whereas this study by no means recommends specific drugs, it demonstrates a powerful deep-learning methodology to prioritize existing drugs for further investigation, which holds the potential to accelerate therapeutic development for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32654489/ doi: 10.1021/acs.jproteome.0c00316 id: cord-024319-isbqs7hg author: Zeng, Xin title: Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The infection of the novel coronavirus SARS-CoV-2 has caused more than 200,000 deaths, but no vaccine or therapeutic monoclonal antibody is currently available. SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. High-affinity antibodies were enriched after the first round using a standard panning process in which RBD-His was immobilized as a bait. At the next two rounds, immobilized ACE2-Fc and free RBD-His were mixed with the enriched phage antibodies. Antibodies binding to RBD at epitopes different from ACE2-binding site were captured by the immobilized ACE2-Fc, forming a “sandwich” complex. Only antibodies competed with ACE2 can bind to the free RBD-His in the supernatant and be subsequently separated by the Ni-NTA magnetic beads. Top 1 lead from the competitive biopanning of our synthetic antibody library, Lib AB1, was produced as the full-length IgG1 format. It was proved to competitively block the binding of RBD to ACE2 and potently inhibit SARS-CoV-2 pseudovirus infection with IC(50) values of 12 nM. Nevertheless, top 1 lead from the standard biopanning can only bind to RBD in vitro, but not have the blocking or neutralization activity. Our strategy can efficiently isolate the blocking antibodies of RBD, and it would speed up the discovery of neutralizing antibodies against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197610/ doi: 10.1093/abt/tbaa008 id: cord-253447-4w6caxwu author: Zeng, Xin title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date: 2020-04-20 words: 2866.0 sentences: 161.0 pages: flesch: 54.0 cache: ./cache/cord-253447-4w6caxwu.txt txt: ./txt/cord-253447-4w6caxwu.txt summary: title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. A high-affinity antibody against the target protein can be screened from a phage display antibody library using the standard biopanning process, but its binding epitopes are identified by some extra steps, such as epitope mapping and competitive ELISA. abstract: The infection of the novel coronavirus SARS-CoV-2 have caused more than 150,000 deaths, but no vaccine or specific therapeutic antibody is currently available. SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. High-affinity antibodies were enriched after the first round using a standard panning process in which RBD-His recombinant protein was immobilized as a bait. At the next two rounds, immobilized ACE2-Fc and free RBD-His proteins were mixed with the enriched phage antibodies. Antibodies binding to RBD at epitopes different from ACE2-binding site were captured by the immobilized ACE2-Fc, forming a “sandwich” complex. Only antibodies competed with ACE2 for recognizing RBD at the same or similar epitopes can bind to the free RBD-His in the supernatant and be subsequently separated by the Ni-NTA magnetic beads. Top 1 lead from the competitive biopanning of a synthetic antibody library, Lib AB1, was produced as the full-length IgG1 format. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Nevertheless, top 1 lead from the standard biopanning of Lib AB1, can only bind to RBD in vitro but not have the blocking or neutralization activity. Our strategy can efficiently isolate the blocking antibodies of RBD, and it would speed up the discovery of neutralizing antibodies against SARS-CoV-2. url: https://doi.org/10.1101/2020.04.19.049643 doi: 10.1101/2020.04.19.049643 id: cord-320207-cwt7dswz author: Zeng, Yingchun title: The nucleocapsid protein of SARS-associated coronavirus inhibits B23 phosphorylation date: 2008-05-02 words: 3129.0 sentences: 173.0 pages: flesch: 53.0 cache: ./cache/cord-320207-cwt7dswz.txt txt: ./txt/cord-320207-cwt7dswz.txt summary: B23 protein is also identified as one of the substrates of CDK2/cyclin E and plays a critical role in centrosome duplication during cell cycle progression, which is regulated by the phosphorylation of B23 at Thr199 [26, 27] . The overlayed result indicated that the SARS-CoV N protein co-localized with B23 protein in the perinuclear region of HeLa cells (Fig. 1f) . In our previous research, we found that SARS-CoV N protein contained three NLS motifs and a nuclear export signal, acting as a shuttle protein between nucleus and cytoplasm, and it could arrest the cell cycle progression [10] . B23 protein can bind NLS, facilitate protein nuclear import and play a role in centrosome duplication during cell cycle progression [20, 21, 26] . In our previous research, we have shown that the N protein of SARS-CoV can arrest cell cycle progression [10] , which is in accordance with the result of Surjit et al. abstract: Abstract Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is responsible for SARS infection. Nucleocapsid (N) protein of SARS-CoV encapsidates the viral RNA and plays an important role in virus particle assembly and release. In this study, the N protein of SARS-CoV was found to associate with B23, a phosphoprotein in nucleolus, in vitro and in vivo. Mapping studies localized the critical N sequences for this interaction to amino acid residues 175–210, which included a serine/arginine (SR)-rich domain. In vitro phosphorylation assay showed that the N protein inhibited the B23 phosphorylation at Thr199. url: https://www.ncbi.nlm.nih.gov/pubmed/18243139/ doi: 10.1016/j.bbrc.2008.01.096 id: cord-293265-qqxlwpju author: Zeng, Yong title: Clinical characteristics of 9 cancer patients with SARS-CoV-2 infection date: 2020-05-14 words: 1370.0 sentences: 89.0 pages: flesch: 51.0 cache: ./cache/cord-293265-qqxlwpju.txt txt: ./txt/cord-293265-qqxlwpju.txt summary: D-dimmer rise, infection index rise, and chest CT(computed tomography) progression may be clinical warning indicators for severe patients, in our study, more 50% of patients had elevated levels of these indicators, but only 44% (including the dead) of patients had received treatment in the intensive care unit. Cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may be effective in the prevention and treatment of novel coronavirus-infected pneumonia (NICP). Studies [10] found that the combination of traditional Chinese medicine and western medicine was effective in the prevention and treatment of NICP in all stages, and the response rate of symptoms such as fever, cough and fatigue were significantly increased in ordinary patients after taking lianhua qingwen granules. By analyzing 9 cancer patients with SARS-CoV-2 infection, cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may abstract: In December 2019, a cluster of pneumonia cases was caused by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China. Cancer patients are a special group, the immunity of them will be suppressed because of various anti-tumor treatments, and the risk of infection will be greatly increased, so we will report clinical features of 9 cancer patients with SARS-CoV-2 infection. 5 (56%) patients were ordinary type, 3 (33%) were severe type, and 1 (11%) was critical type. A total of 8 patients received combined therapy of traditional Chinese medicines and western medicines. From the clinical outcomes of these 8 patients, western combined therapy of traditional Chinese medicine was indeed an effective treatment method. D-dimmer rise, infection index rise, and chest CT(computed tomography) progression may be clinical warning indicators for severe patients, in our study, more 50% of patients had elevated levels of these indicators, but only 44% (including the dead) of patients had received treatment in the intensive care unit. 5 (56%) ordinary type patients had been discharged, while the 1 (11%) critical type patient died 3 days after admission. Cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may be effective in the prevention and treatment of novel coronavirus-infected pneumonia (NICP). url: https://doi.org/10.1186/s13020-020-00328-8 doi: 10.1186/s13020-020-00328-8 id: cord-270462-d9l3agr0 author: Zeng, Zhi title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion date: 2020-05-06 words: 2734.0 sentences: 186.0 pages: flesch: 54.0 cache: ./cache/cord-270462-d9l3agr0.txt txt: ./txt/cord-270462-d9l3agr0.txt summary: title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion The aim of this study was to explore pulmonary pathology of early phase COVID‐19 pneumonia in a patient with a benign lung lesion. METHODS AND RESULTS: We analyzed the pathological changes of lung tissue from a 55‐year‐old female patient with early phase SARS‐CoV‐2 infection. CONCLUSION: The results highlighted the pulmonary pathological changes of early phase SARS‐CoV‐2 infection and suggested a role of immune dysfunction in the pathogenesis of COVID‐19 pneumonia. [8] [9] [10] However, the pathological changes in the lungs caused by SARS-CoV-2, especially in the early stage of infection, have seldom been described. Combining epidemiological characteristics, clinical presentation, nucleic acid testing and intracytoplasmic viral-like inclusions, it is reasonable to speculate that this case represents an early stage of lung injury secondary to SARS-CoV-2 infection. Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer abstract: AIMS: An ongoing outbreak of 2019 novel coronavirus (SARS‐CoV‐2) diseases (COVID‐19) has been spreading in multiple countries. One of the reasons for the rapid spread is that the virus can be transmitted from infected individuals without symptoms. Revealing the pathological features of early phase COVID‐19 pneumonia is important to the understanding of its pathogenesis. The aim of this study was to explore pulmonary pathology of early phase COVID‐19 pneumonia in a patient with a benign lung lesion. METHODS AND RESULTS: We analyzed the pathological changes of lung tissue from a 55‐year‐old female patient with early phase SARS‐CoV‐2 infection. In this case, right lower lobectomy was performed for a benign pulmonary nodule. Detailed clinical, laboratory and radiological data were also described. This case was confirmed to have preoperative SARS‐CoV‐2 infection by real‐time RT‐PCR and RNA in situ hybridization on surgically removed lung tissues. Histologically, COVID‐19 pneumonia was characterized by exudative inflammation. The closer to the visceral pleura, the more severe the exudation of monocytes and lymphocytes. Perivascular inflammatory infiltration, intraalveolar multinucleated giant cells, pneumocyte hyperplasia and intracytoplasmic viral‐like inclusion bodies were seen. However, fibrinous exudate and hyaline membrane formation, which were typical pulmonary features of SARS pneumonia, were not evident in this case. Immunohistochemical staining results showed that an abnormal accumulation of CD4+ helper T lymphocytes and CD163+ M2 macrophages in the lung tissue. CONCLUSION: The results highlighted the pulmonary pathological changes of early phase SARS‐CoV‐2 infection and suggested a role of immune dysfunction in the pathogenesis of COVID‐19 pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/32374419/ doi: 10.1111/his.14138 id: cord-281106-vzb5xzza author: Zerwes, S. title: COVID-19-Infektion – Risiko für thrombembolische Komplikationen date: 2020-09-01 words: 1929.0 sentences: 204.0 pages: flesch: 38.0 cache: ./cache/cord-281106-vzb5xzza.txt txt: ./txt/cord-281106-vzb5xzza.txt summary: According to current data, the risk of thromboembolic events in hospitalized COVID-19 patients is significantly increased, making thrombosis prophylaxis with low molecular weight or unfractionated heparin necessary. Neben den bekannten Ursachen der Thromboseentstehung, wurden bei der COVID-Erkrankung spezielle Pathomechanismen beobachtet, die zur Bildung von Thrombosen sowohl im venösen als auch im arteriellen System beitragen können. Auch wenn die Mechanismen noch nicht in Ihrer Gesamtheit erfasst sind, so ist bereits jetzt ersichtlich, dass die thrombembolischen Komplikationen im Zusammenhang mit dem SARS-CoV-2-Virus auf eine exzessive Inflammationsreaktion, Veränderung von Blutflusseigenschaften, direkte virusbedingte Thrombozytenaktivierung und Endothelschädigung zurückzuführen sind [3] . Diese Hypothese wird von nahezu allen bisher publizierten Arbeiten zu thrombembolischen Ereignissen bei COVID-19-Patienten postuliert und könnte eine Erklärung für die deutlich erhöhte Anzahl von TVT bieten [1, 7, 17, 28, 39] . Eine einheitliche Nomenklatur besteht noch nicht, die Pu-blikationmitdergrößtenSerie benennt es als "Pediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2" (PIMS-TS) [36] . abstract: While the COVID-19 syndrome triggered by the SARS CoV‑2 was initially seen predominantly as a pulmonary disease, the number of reports of vascular complications has recently increased. The aim of the present review article is to summarize the most relevant vascular complications in COVID-19 patients. These include venous and arterial thromboembolic events as well as local thromboses, which can form directly on the endothelium at the site of cytokine release. A generalized coagulopathy also appears to promote this thrombogenic condition. With a rate of approximately 20%, deep vein thrombosis (DVT) of the leg is one of the most common thromboembolic events in COVID-19 patients requiring intensive care treatment. In addition, arterial events, such as stroke or acute coronary syndrome were also observed in COVID-19 patients with pre-existing vascular disease. Children rarely have vascular complications, but a systemic immune response similar to the Kawasaki syndrome and toxic shock syndrome has been reported. According to current data, the risk of thromboembolic events in hospitalized COVID-19 patients is significantly increased, making thrombosis prophylaxis with low molecular weight or unfractionated heparin necessary. If pharmaceutical thrombosis prophylaxis is contraindicated, intermittent pneumatic compression should be used. In addition, in patients admitted to the hospital with suspected or proven SARS-CoV‑2 infection, the determination of D‑dimers and, in the case of positive results, broad indication for compression sonography of the deep leg veins are recommended. This allows to detect and treat DVT at an early stage. The treatment of thromboses should be carried out according to current guidelines with therapeutic anticoagulation. Further studies and registries are needed to improve the understanding of the relationship between COVID-19 infection and the occurrence of thromboembolic events. url: https://www.ncbi.nlm.nih.gov/pubmed/32905019/ doi: 10.1007/s00772-020-00687-4 id: cord-339077-pxf2u68u author: Zerwes, Sebastian title: Erhöhtes Risiko für tiefe Beinvenenthrombosen bei Intensivpatienten mit CoViD-19-Infektion? – Erste Daten date: 2020-06-05 words: 1558.0 sentences: 195.0 pages: flesch: 44.0 cache: ./cache/cord-339077-pxf2u68u.txt txt: ./txt/cord-339077-pxf2u68u.txt summary: BACKGROUND: The incidence of deep vein thrombosis (DVT) in CoViD-19 patients in intensive care units (ICU) has so far been investigated in only a few studies. MATERIAL AND METHODS: In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. Es ist bekannt, dass intensivpflichtige Patienten per se ein erhöhtes Risiko für thrombembolische Ereignisse aufweisen: So treten bei Intensivpatienten Thrombosen je nach Grunderkrankung mit einer Wahrscheinlichkeit von 10-80 % auf; 10-15 % der Patienten entwickeln trotz Thromboseprophylaxe eine tiefe Beinvenenthrombosen (TVT; [8, 9] ). In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. abstract: BACKGROUND: The incidence of deep vein thrombosis (DVT) in CoViD-19 patients in intensive care units (ICU) has so far been investigated in only a few studies. Prospective comparative studies with non-CoViD-19 ICU patients are completely lacking. OBJECTIVE: Evaluation of the incidence of DVT in ICU patients with CoViD-19 compared to non-CoViD-19 ICU patients who were treated in the University Hospital Augsburg during the same period. In addition, the aim was to investigate what type of anticoagulation was present in CoViD-19 patients at the time the DVT occurred and to what extent DVT is associated with increased mortality in this patient population. MATERIAL AND METHODS: In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. For this purpose, demographic data, laboratory parameters, and clinical outcomes were recorded and evaluated. RESULTS: The rate of DVT in the investigated patient collective was markedly higher in patients with SARS-CoV2 (CoViD-19 patients 20% vs. non-CoViD-19 patients 5%). Both DVT and elevated D‑dimer levels were associated with increased mortality in the present study. CONCLUSION: We recommend the determination of D‑dimer levels and, in the case of elevated levels, the broad indication for compression sonography of the deep leg veins on admission of patients with suspected or confirmed SARS-CoV2. In this way DVT in the setting of CoViD-19 can be recognized early and therapeutic anticoagulation can be started. All inpatient CoViD-19 patients should receive thrombosis prophylaxis with low molecular weight heparin. Further studies on point of care methods (TEG®, ROTEM®) for the detection of hypercoagulability in SARS-CoV2 are necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/32504106/ doi: 10.1007/s00104-020-01222-7 id: cord-308310-wtmjt3hf author: Zha, Lisha title: Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date: 2020-05-14 words: 2012.0 sentences: 110.0 pages: flesch: 54.0 cache: ./cache/cord-308310-wtmjt3hf.txt txt: ./txt/cord-308310-wtmjt3hf.txt summary: Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. The receptor binding domain (RBD) of the SARS spike protein binds to ACE2 and is an important target for neutralizing antibodies [5] [6] [7] . Hence, the RBD-CuMVTT vaccine candidate is able to induce high levels of SARS-CoV-2 neutralizing antibodies. Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine abstract: The recently ermerging disease COVID-19 is caused by the new SARS-CoV-2 virus first detected in the city of Wuhan, China. From there it has been rapidly spreading inside and outside China. With initial death rates around 4%, COVID-19 patients at longer distances from Wuhan showed reduced mortality as was previously observed for the SARS coronavirus. However, the new coronavirus spreads more strongly, as it sheds long before onset of symptoms or may be transmitted by people without symptoms. Rapid development of a protective vaccine against COVID-19 is therefore of paramount importance. Here we demonstrate that recombinantly expressed receptor binding domain (RBD) of the spike protein homologous to SARS binds to ACE2, the viral receptor. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. url: https://doi.org/10.1101/2020.05.06.079830 doi: 10.1101/2020.05.06.079830 id: cord-301324-2tyl1r2l author: Zhan, Jing title: Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() date: 2020-09-09 words: 543.0 sentences: 43.0 pages: flesch: 45.0 cache: ./cache/cord-301324-2tyl1r2l.txt txt: ./txt/cord-301324-2tyl1r2l.txt summary: title: Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() The emergence of a novel coronavirus named by SARS-CoV-2 during December, 2019, has caused the global outbreak of coronavirus disease 2019 (COVID-19), which is officially announced to be a pandemic by the World Health Organization (WHO). Understanding the transmission, survival, and evolution of the virus in the environment will assist in the prevention, control, treatment and eradication of its infection. Herein, we aimed to elucidate the environmental impacts on the transmission and evolution of SARS-CoV-2, based on briefly introducing this respiratory virus. This review should be of great help to prevent and control the epidemics caused by emerging respiratory coronaviruses (CoVs). Summary: More knowledge on the transmission and evolution of SARS-CoV-2 in the environment is urgently needed. High infectivity and pathogenicity of influenza A 620 virus via aerosol and droplet transmission abstract: The emergence of a novel coronavirus named by SARS-CoV-2 during December, 2019, has caused the global outbreak of coronavirus disease 2019 (COVID-19), which is officially announced to be a pandemic by the World Health Organization (WHO). The increasing burden from this pandemic is seriously affecting everyone’s life, and threating the global public health. Understanding the transmission, survival, and evolution of the virus in the environment will assist in the prevention, control, treatment and eradication of its infection. Herein, we aimed to elucidate the environmental impacts on the transmission and evolution of SARS-CoV-2, based on briefly introducing this respiratory virus. Future research objectives for the prevention and control of these contagious viruses and their related diseases are highlighted from the perspective of environmental science. This review should be of great help to prevent and control the epidemics caused by emerging respiratory coronaviruses (CoVs). Summary: More knowledge on the transmission and evolution of SARS-CoV-2 in the environment is urgently needed. url: https://api.elsevier.com/content/article/pii/S0269749120363090 doi: 10.1016/j.envpol.2020.115621 id: cord-320860-qt84oicg author: Zhang, Aining title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date: 2020-09-15 words: 2359.0 sentences: 131.0 pages: flesch: 47.0 cache: ./cache/cord-320860-qt84oicg.txt txt: ./txt/cord-320860-qt84oicg.txt summary: title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis abstract: Background To figure out whether abnormal coagulation parameters are associated with disease severity and poor prognosis in patients with 2019 Corona Virus Disease (COVID-19). Methods A systematic literature search was conducted using the databases PubMed, Embase, and Web of sciences until April 25, 2020. We included a total of 15 studies with 2277 patients. Platelet count (PLT), prothrombin time (PT), activated partial thromboplastin time (APTT), D-dimer (D-D) and fibrinogen (FIB) were collected and analyzed. The statistical results were expressed the effect measure by mean difference (MD) with the related 95% confidence interval (CI). Results The PLT level of severe patients was lower than that of mild patients, while the levels of PT, D-D and FIB were higher than those of mild patients (P < 0.05). The level of APTT had no statistical difference between two groups (P > 0.05). Compared to Non-ICU patients, PT of ICU patients was significantly longer (P < 0.05). In Non-survivors, PT and D-D were higher, yet PLT was lower than survivors (P < 0.05). There was no significant difference in APTT between survivors and Non-survivors (P > 0.05). The funnel plot and Egger's Regression test demonstrated that there was no publication bias. Conclusions Our data support the notion that coagulopathy could be considered as a risk factor for disease severity and mortality of COVID-19, which may help clinicians to identify the incidence of poor outcomes in COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S1201971220307372?v=s5 doi: 10.1016/j.ijid.2020.09.021 id: cord-259238-n2uuaof6 author: Zhang, Bao-Zhong title: SARS-CoV-2 infects human neural progenitor cells and brain organoids date: 2020-08-04 words: 1887.0 sentences: 136.0 pages: flesch: 51.0 cache: ./cache/cord-259238-n2uuaof6.txt txt: ./txt/cord-259238-n2uuaof6.txt summary: To explore the direct involvement of SARS-CoV-2 in the CNS in physiologically relevant models, we assessed SARS-CoV-2 infection in induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and brain organoids. Importantly, extensive SARS-CoV-2 antigen was detected in the infected samples at 72 hpi (Fig. 1f) , indicating that SARS-CoV-2 directly infected the brain organoids. The results demonstrated SARS-CoV-2 RdRp gene copy number increased in a timedependent manner, suggesting active release of progeny virus particles from infected brain organoids (Fig. 1g, left) . Plaque assays performed on supernatant samples from brain organoids infected with SARS-CoV-2 showed that the infectious virus titer peaked at 24 hpi and were continuously detected at 48 and 72 hpi. h Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and TUJ1. i Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and NESTIN. abstract: nan url: https://doi.org/10.1038/s41422-020-0390-x doi: 10.1038/s41422-020-0390-x id: cord-352020-9wxwktck author: Zhang, Baoshan title: A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone date: 2020-10-23 words: 4914.0 sentences: 266.0 pages: flesch: 46.0 cache: ./cache/cord-352020-9wxwktck.txt txt: ./txt/cord-352020-9wxwktck.txt summary: To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses. To improve protein solubility and expression, we added glycans to the surface of the nanoparticles, designing a panel of LuS and ferritin constructs with SpyTag and SpyCatcher (Table 1 and Supplementary Table S1 ). To demonstrate the versatility of our SpyTag-displaying nanoparticles in immunogen development, we conjugated them to three viral antigens of vaccine interest, the DS2-preF stabilized RSV F 33 , a DS2-stabilized version of PIV3 F 34 , and the 2P-stabilized version of SARS-CoV-2 spike 24 . abstract: Antigens displayed on self-assembling nanoparticles can stimulate strong immune responses and have been playing an increasingly prominent role in structure-based vaccines. However, the development of such immunogens is often complicated by inefficiencies in their production. To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. LuS and ferritin coupled to SpyTag expressed well in a mammalian expression system when an N-linked glycan was added to the nanoparticle surface. The respiratory syncytial virus fusion (F) glycoprotein trimer—stabilized in the prefusion conformation and fused with SpyCatcher—could be efficiently conjugated to LuS-SpyTag or ferritin-SpyTag, enabling multivalent display of F trimers with prefusion antigenicity. Similarly, F-glycoprotein trimers from human parainfluenza virus-type 3 and spike-glycoprotein trimers from SARS-CoV-2 could be displayed on LuS nanoparticles with decent yield and antigenicity. Notably, murine vaccination with 0.08 µg of SARS-CoV-2 spike-LuS nanoparticle elicited similar neutralizing responses as 2.0 µg of spike, which was ~ 25-fold higher on a weight-per-weight basis. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses. url: https://www.ncbi.nlm.nih.gov/pubmed/33097791/ doi: 10.1038/s41598-020-74949-2 id: cord-252288-klkoerfn author: Zhang, Bicheng title: Immune Phenotyping Based on the Neutrophil-to-Lymphocyte Ratio and IgG Level Predicts Disease Severity and Outcome for Patients With COVID-19 date: 2020-07-03 words: 3245.0 sentences: 194.0 pages: flesch: 57.0 cache: ./cache/cord-252288-klkoerfn.txt txt: ./txt/cord-252288-klkoerfn.txt summary: This disease is initiated by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and uncontrolled cytokine storm, but it remains unknown as to whether a robust antibody response is related to clinical deterioration and poor outcome in COVID-19 patients. Immune response phenotyping based on the late IgG levels and neutrophil-to-lymphocyte ratio (NLR) was characterized to stratified patients into different disease severities and outcomes. Here, we evaluated antibody response within 35 days after symptom onset in laboratory-confirmed cases with COVID-19 as one component of an overall exaggerated immune activation in severe SARS-CoV-2 infection, and developed an immune phenotyping based on the late IgG response and NLR that could help determine disease severity and clinical outcome for COVID-19 patients. Using two immune responserelated indicators NLR and IgG levels detected in sera at late stage, we developed a combined immune response phenotype, which could predict disease severity and the outcome of COVID-19 patients. abstract: Introduction: A recently emerging respiratory disease named coronavirus disease 2019 (COVID-19) has quickly spread across the world. This disease is initiated by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and uncontrolled cytokine storm, but it remains unknown as to whether a robust antibody response is related to clinical deterioration and poor outcome in COVID-19 patients. Methods: Anti-SARS-CoV-2 IgG and IgM antibodies were determined by chemiluminescence analysis (CLIA) in COVID-19 patients at a single center in Wuhan. Median IgG and IgM levels in acute and convalescent-phase sera (within 35 days) for all included patients were calculated and compared between severe and non-severe patients. Immune response phenotyping based on the late IgG levels and neutrophil-to-lymphocyte ratio (NLR) was characterized to stratified patients into different disease severities and outcomes. Results: A total of 222 patients were included in this study. IgG was first detected on day 4 of illness, and its peak levels occurred in the fourth week. Severe cases were more frequently found in patients with high IgG levels, compared to those with low IgG levels (51.8 vs. 32.3%; p = 0.008). Severity rates for patients with NLR(hi)IgG(hi), NLR(hi)IgG(lo), NLR(lo)IgG(hi), and NLR(lo)IgG(lo) phenotype were 72.3, 48.5, 33.3, and 15.6%, respectively (p < 0.0001). Furthermore, severe patients with NLR(hi)IgG(hi), NLR(hi)IgG(lo) had higher inflammatory cytokines levels including IL-2, IL-6 and IL-10, and decreased CD4+ T cell count compared to those with NLR(lo)IgG(lo) phenotype (p < 0.05). Recovery rates for severe patients with NLR(hi)IgG(hi), NLR(hi)IgG(lo), NLR(lo)IgG(hi), and NLR(lo)IgG(lo) phenotype were 58.8% (20/34), 68.8% (11/16), 80.0% (4/5), and 100% (12/12), respectively (p = 0.0592). Dead cases only occurred in NLR(hi)IgG(hi) and NLR(hi)IgG(lo) phenotypes. Conclusions: COVID-19 severity is associated with increased IgG response, and an immune response phenotyping based on the late IgG response and NLR could act as a simple complementary tool to discriminate between severe and non-severe COVID-19 patients, and further predict their clinical outcome. url: https://doi.org/10.3389/fmolb.2020.00157 doi: 10.3389/fmolb.2020.00157 id: cord-327028-dbvucvy3 author: Zhang, Cantong title: Controversial treatments: An updated understanding of the coronavirus disease 2019 date: 2020-04-10 words: 1898.0 sentences: 123.0 pages: flesch: 40.0 cache: ./cache/cord-327028-dbvucvy3.txt txt: ./txt/cord-327028-dbvucvy3.txt summary: To reduce the case‐fatality rate among coronavirus disease 2019 patients, we should not ignore the complications, such as RNAaemia, acute respiratory distress syndrome, and multiple organ dysfunction. To help understand the advantages and limitations of differential treatments, we provide a timely review and discuss the complications and corresponding major treatments, especially controversial ones such as antiviral therapy (remdesivir, ribavirin, and chloroquine), glucocorticoid therapy, extracorporeal support including an artificial liver system, and extracorporeal membrane oxygenation based on available evidence. Furthermore, we list a table to conclude the mechanism, advantages, and limitations for different treatments mentioned in this review (Table 2) The mechanism of remdesivir against the virus showed that the drug effectively inhibited the Ebola virus RNA-dependent RNA polymerase (RdRp) complex. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China abstract: An outbreak of severe acute respiratory syndrome‐related coronavirus 2 infection has posed significant threats to international health and the economy. In the absence of specific treatment for this virus, there is an urgent need to learn from the experience and lessons in China. To reduce the case‐fatality rate among coronavirus disease 2019 patients, we should not ignore the complications, such as RNAaemia, acute respiratory distress syndrome, and multiple organ dysfunction. To help understand the advantages and limitations of differential treatments, we provide a timely review and discuss the complications and corresponding major treatments, especially controversial ones such as antiviral therapy (remdesivir, ribavirin, and chloroquine), glucocorticoid therapy, extracorporeal support including an artificial liver system, and extracorporeal membrane oxygenation based on available evidence. As a result, we suggest that antiviral therapy and organ function support are vital to reduce mortality for mild patients and critical patients, respectively. url: https://www.ncbi.nlm.nih.gov/pubmed/32219882/ doi: 10.1002/jmv.25788 id: cord-030654-8yxa1r1c author: Zhang, Changhui title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date: 2020-08-20 words: 4281.0 sentences: 289.0 pages: flesch: 62.0 cache: ./cache/cord-030654-8yxa1r1c.txt txt: ./txt/cord-030654-8yxa1r1c.txt summary: This structure was revealed to be a horseshoe-like tetramer, which may play an essential role in nsp9 oligomerization and in the regulation of viral nucleic acid binding during the replication of the virus. The initial structure solved by molecular replacement showed that six SARS-CoV-2 nsp9 protomers form an OB-fold cluster in an asymmetric unit ( Supplementary Fig. 1a ). To obtain more information about the protein interfaces and the likely biological assemblies of the OB-fold cluster, we calculated the structure of SARS-CoV-2 nsp9 using PDBe-PISA [27] . These three contact surfaces in interface I b/c contribute a hydrophobic base with eight hydrogen bonds and one salt bridge, making the SARS-CoV-2 nsp9 tetramer extremely stable in the crystal structure. In this present study, we observed the nucleic acid-binding ability of SARS-CoV-2 nsp9, using the electrophoretic mobility The molecules in these two interfaces are shown as cartoons and colored and labeled as in Fig. 2a . abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of a potentially fatal disease named coronavirus disease 2019 (COVID-19), has raised significant public health concerns globally. To date, the COVID-19 pandemic has caused millions of people to be infected with SARS-CoV-2 worldwide. It has been known since the 2003 SARS epidemic that coronaviruses (CoVs) have large RNA genomes, the replication of which requires an RNA-dependent RNA replication/transcription complex. CoV nonstructural proteins (Nsps) play pivotal roles in the assembly of this complex and associated enzymatic functions in virus genomic replication. Several smaller nonenzymatic Nsps assist with RNA-dependent RNA polymerase function. In this study, we determined the structure of SARS-CoV-2 nonstructural protein 9 (nsp9), an RNA-binding protein that is essential for CoV replication. Its homotetrameric structure with two stable dimeric interfaces provids a structural basis for understanding the mechanisms of RNA-binding protein self-assembly, which may be essential for the regulation of viral RNA replication and transcription. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438161/ doi: 10.1186/s43556-020-00005-0 id: cord-273349-penb65x7 author: Zhang, Chao title: Liver injury in COVID-19: management and challenges date: 2020-05-31 words: 1541.0 sentences: 82.0 pages: flesch: 44.0 cache: ./cache/cord-273349-penb65x7.txt txt: ./txt/cord-273349-penb65x7.txt summary: The severity, mortality, and incidence of complications in these patients, including secondary infection, hepatic encephalopathy, upper gastrointestinal bleeding, and liver failure, need to be examined in large-cohort clinical studies. As the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread from China to other countries, governments and the medical community are taking steps to prevent transmission, from common sense recommendations to radical quarantine measures. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalised patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study abstract: nan url: https://doi.org/10.1016/s2468-1253(20)30057-1 doi: 10.1016/s2468-1253(20)30057-1 id: cord-253456-u9num2o9 author: Zhang, Che title: Clinical and epidemiological characteristics of pediatric SARS-CoV-2 infections in China: A multicenter case series date: 2020-06-16 words: 4540.0 sentences: 260.0 pages: flesch: 49.0 cache: ./cache/cord-253456-u9num2o9.txt txt: ./txt/cord-253456-u9num2o9.txt summary: Suspected patients with clinical and/or radiological features of pneumonia were quarantined prior to SARS-CoV-2 nucleic acid detection according to WHO guidelines for cases with suspected infection [8] as well as the instructions from the Pediatric Branch of the Hubei Medical Association for pediatric cases [9] . Specifically, suspected cases of SARS-CoV-2 infection should meet 1 of the following criteria [10] : (1) at least 1 clinical symptom, including fever, expectation, tachypnea, lethargy, poor feeding, cough, vomiting, and diarrhea; (2) chest radiologic abnormalities consistent with viral pneumonia. Patients were discharged when all the following criteria were met [10] : (1) fever had recovered for at least 3 days; (2) upper respiratory symptoms were alleviated; (3) the exudative lesion was alleviated significantly according to radiological evidence; (4) negative results were obtained for SARS-CoV-2 nucleic acid detection in 2 consecutive tests performed with an interval of 24 hours. abstract: BACKGROUND: As of April 18, 2020, over 2,000,000 patients had been diagnosed with coronavirus disease-2019 (COVID-19) globally, and more than 140,000 deaths had been reported. The clinical and epidemiological characteristics of adult patients have been documented recently. However, information on pediatric patients is limited. We describe the clinical and epidemiological characteristics of pediatric patients to provide valuable insight into the early diagnosis and assessment of COVID-19 in children. METHODS AND FINDINGS: This retrospective, observational study involves a case series performed at 4 hospitals in West China. Thirty-four pediatric patients with COVID-19 were included from January 27 to February 23, 2020. The final follow-up visit was completed by March 16, 2020. Clinical and epidemiological characteristics were analyzed on the basis of demographic data, medical history, laboratory tests, radiological findings, and treatment information. Data analysis was performed for 34 pediatrics patients with COVID-19 aged from 1 to 144 months (median 33.00, interquartile range 10.00–94.25), among whom 14 males (41%) were included. All the patients in the current study presented mild (18%) or moderate (82%) forms of COVID-19. A total of 48% of patients were noted to be without a history of exposure to an identified source. Mixed infections of other respiratory pathogens were reported in 16 patients (47%). Comorbidities were reported in 6 patients (18%). The most common initial symptoms were fever (76%) and cough (62%). Expectoration (21%), vomiting (12%), and diarrhea (12%) were also reported in a considerable portion of cases. A substantial increase was detected in serum amyloid A for 17 patients (among 20 patients with available data; 85%) and in high-sensitivity C-reactive protein for 17 patients (among 29 patients with available data; 59%), whereas a decrease in prealbumin was noticed in 25 patients (among 32 patients with available data; 78%). In addition, significant increases in the levels of lactate dehydrogenase and α-hydroxybutyrate dehydrogenase were detected in 28 patients (among 34 patients with available data; 82%) and 25 patients (among 34 patients with available data; 74%), respectively. Patchy lesions in lobules were detected by chest computed tomographic scans in 28 patients (82%). Ground-glass opacities, which were a typical feature in adults, were rare in pediatric patients (3%). Rapid radiologic progression and a late-onset pattern of lesions in the lobules were also noticed. Lesions in lobules still existed in 24 (among 32 patients with lesions; 75%) patients that were discharged, although the main symptoms disappeared a few days after treatment. All patients were discharged, and the median duration of hospitalization was 10.00 (8.00–14.25) days. The current study was limited by the small sample size and a lack of dynamic detection of inflammatory markers. CONCLUSIONS: Our data systemically presented the clinical and epidemiological features, as well as the outcomes, of pediatric patients with COVID-19. Stratified analysis was performed between mild and moderate cases. The findings offer new insight into early identification and intervention in pediatric patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32544155/ doi: 10.1371/journal.pmed.1003130 id: cord-327084-r12copka author: Zhang, Chenxi title: Survey of Insomnia and Related Social Psychological Factors Among Medical Staff Involved in the 2019 Novel Coronavirus Disease Outbreak date: 2020-04-14 words: 4087.0 sentences: 198.0 pages: flesch: 49.0 cache: ./cache/cord-327084-r12copka.txt txt: ./txt/cord-327084-r12copka.txt summary: A multiple binary logistic regression model revealed that insomnia symptoms were associated with an education level of high school or below (OR = 2.69, p = 0.042, 95% CI = 1.0–7.0), being a doctor (OR = 0.44, p = 0.007, 95% CI = 0.2–0.8), currently working in an isolation unit (OR = 1.71, p = 0.038, 95% CI = 1.0–2.8), is worried about being infected (OR = 2.30, p < 0.001, 95% CI = 1.6–3.4), perceived lack of helpfulness in terms of psychological support from news or social media with regard to COVID-19 (OR = 2.10, p = 0.001, 95% CI = 1.3–3.3), and having very strong uncertainty regarding effective disease control (OR = 3.30, p = 0.013, 95% CI = 1.3–8.5). abstract: OBJECTIVE: The outbreak of the 2019 novel coronavirus disease (COVID-19) not only caused particularly large public health problems, but also caused great psychological distress, especially for medical staff. We aimed to investigate the prevalence rate of insomnia and to confirm the related social psychological factors among medical staff in hospitals during the COVID-19 outbreak. METHOD: Medical staff members in China were recruited, including frontline medical workers. The questionnaire, administered through the WeChat program, obtained demographic data and asked self-design questions related to the COVID-19 outbreak, insomnia/depressive/anxiety symptoms, and stress-related symptoms. We used a logistic regression analysis to examine the associations between sociodemographic factors and insomnia symptoms. RESULT: There were a total of 1,563 participants in our study. Five-hundred-and-sixty-four (36.1%) participants had insomnia symptoms according to the Insomnia Severity Index (ISI) (total score ≥ 8). A multiple binary logistic regression model revealed that insomnia symptoms were associated with an education level of high school or below (OR = 2.69, p = 0.042, 95% CI = 1.0–7.0), being a doctor (OR = 0.44, p = 0.007, 95% CI = 0.2–0.8), currently working in an isolation unit (OR = 1.71, p = 0.038, 95% CI = 1.0–2.8), is worried about being infected (OR = 2.30, p < 0.001, 95% CI = 1.6–3.4), perceived lack of helpfulness in terms of psychological support from news or social media with regard to COVID-19 (OR = 2.10, p = 0.001, 95% CI = 1.3–3.3), and having very strong uncertainty regarding effective disease control (OR = 3.30, p = 0.013, 95% CI = 1.3–8.5). CONCLUSION: Our study found that more than one-third of the medical staff suffered insomnia symptoms during the COVID-19 outbreak. The related factors included education level, an isolation environment, psychological worries about the COVID-19 outbreak, and being a doctor. Interventions for insomnia among medical staff are needed considering the various sociopsychological factors at play in this situation. url: https://doi.org/10.3389/fpsyt.2020.00306 doi: 10.3389/fpsyt.2020.00306 id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 words: 3745.0 sentences: 208.0 pages: flesch: 49.0 cache: ./cache/cord-104162-fe51v2pt.txt txt: ./txt/cord-104162-fe51v2pt.txt summary: Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). abstract: Base order, not composition, best reflects local evolutionary pressure for folding of single-stranded nucleic acids. The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 “Achilles heel,” the signal can be targeted by a recently described antiviral compound (NSC 260594) or by synthetic oligonucleotides. Thus, a conserved base-order-rich region of HIV-1 may facilitate therapeutic attack. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential “Achilles heels” for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The region of the FSE scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein. url: https://doi.org/10.1101/2020.10.22.343673 doi: 10.1101/2020.10.22.343673 id: cord-295850-nb6miso7 author: Zhang, Chuan-hai title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain date: 2005-05-02 words: 2930.0 sentences: 161.0 pages: flesch: 55.0 cache: ./cache/cord-295850-nb6miso7.txt txt: ./txt/cord-295850-nb6miso7.txt summary: title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain The immunogenicity of a candidate-inactivated vaccine prepared from SARS-CoV F69 strain was evaluated in Balb/c mice. The present study was performed with the objective of determining the immunogenicity of a candidate-inactivated SARS-CoV vaccine made from F69 strain in Balb/c mice. In test groups, anti-SARS-CoV specific IgM antibodies were induced by the inactivated vaccine. The results showed that SARS-CoV F69 strain inactivated vaccine could induce potent humoral immune responses in Balb/c mice. In present study, the specificity of serum antibodies induced by F69 strain inactivated vaccine was identified by Western blot assay. A convalescent serum of SARS patient was used, and the same positive result was obtained (lane 3, Fig. 4) , which further demonstrated the specificity of the antibodies induced with the inactivated vaccine produced from F69 strain. abstract: The immunogenicity of a candidate-inactivated vaccine prepared from SARS-CoV F69 strain was evaluated in Balb/c mice. Potent humoral immune responses were induced under the elicitation of three times of immunizations at 2-week intervals with this vaccine, combined with three types of adjuvants (Freund's adjuvant, Al(OH)(3) adjuvant and CpG adjuvant). Titers of specific IgG antibodies in three test groups all peaked in the sixth week after first vaccination, but significant differences existed in the kinetics of specific IgG antibody levels. The strong neutralizing capacity exhibited in micro-cytopathic effect neutralization tests indicated the specific antibodies are protective. Western blot assay further demonstrated the specificity of the induced serum antibodies. url: https://www.sciencedirect.com/science/article/pii/S0264410X05000939 doi: 10.1016/j.vaccine.2004.11.073 id: cord-293080-b4pxjrcj author: Zhang, Chunyan title: Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method date: 2020-09-18 words: 4173.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-293080-b4pxjrcj.txt txt: ./txt/cord-293080-b4pxjrcj.txt summary: Immunological diagnosis of COVID-19 is mainly achieved through testing specific antibody IgM and IgG responses after human infection with SARS-CoV-2 and is based on antigen-antibody capturemethods. Such methods include lateral flow assays and provide the advantages of easy operation, quick test results, no need of a special laboratory site with (complex) instruments, and high sensitivity and specificity, and is suitable for carrying out large-scale SARS-CoV-2 infection/screening as point-of-care sites [7] . Based on the process of SARS-CoV-2 infection and the production of specific antibody responses, a diagnostic IgG and IgM detection assay would be the most useful method to diagnosis the occurrence of COVID-19 and development of pulmonary disease. In the present study, the recombinant protein and test strip for detecting the SARS-CoV-2 antibody by the antigen capturing method, and its preparation method were provided, supporting a new method for SARS-CoV-2 infection screening, diagnosis, disease monitoring and prognosis evaluation. abstract: COVID-19 is caused by SARS-CoV-2 infection and was initially discovered in Wuhan. This outbreak quickly spread all over China and then to more than 20 other countries. SARS-CoV-2 fluorescent microsphere immunochromatographic test strips were prepared by the combination of time-resolved fluorescence immunoassay with a lateral flow assay. The analytical performance and clinical evaluation of this testing method was done and the clinical significance of the testing method was verified. The LLOD of SARS-CoV-2 antibody IgG and IgM was 0.121U/L and 0.366U/L. The specificity of IgM and IgG strips in healthy people and in patients with non-COVID-19 disease was 94%, 96.72% and 95.50%, 99.49%, respectively; and sensitivity of IgM and IgG strips for patients during treatment and follow-up was 63.02%, 37.61% and 87.28%, 90.17%, respectively. The SARS-CoV-2 antibody test strip can provide rapid, flexible and accurate testing, and is able to meet the clinical requirement for rapid on-site testing of virus. The ability to detect IgM and IgG provided a significant benefit for the detection and prediction of clinical course with COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32799618/ doi: 10.1080/22221751.2020.1811161 id: cord-256500-nlavfnpt author: Zhang, Dan title: COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome date: 2020-03-26 words: 3501.0 sentences: 198.0 pages: flesch: 50.0 cache: ./cache/cord-256500-nlavfnpt.txt txt: ./txt/cord-256500-nlavfnpt.txt summary: Background: Excessive monocyte/macrophage activation with the development of a cytokine storm and subsequent acute lung injury, leading to acute respiratory distress syndrome (ARDS) is a feared consequence of infection with COVID-19. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), also known as Corona Virus Disease-19 (COVID-19) is a new coronavirus, first identified in Wuhan, China in December 2019, which frequently induces fatal inflammatory responses and acute lung injury. Herein we describe novel observations in relation to changes in monocyte morphology and activation status, which correlate with the prognosis and severity of COVID-19 infection and which can be readily quantified by flow cytometry with the concurrent measurement of forward scatter (FSC) and (SSC), which measure cell size and complexity, respectively. We have shown that simple assessment of FSC by flow cytometry in the context of COVID-19 infection can rapidly identify those patients with an increasing proportion of large, activated, IL-6 and TNF secreting monocytes, who have severe disease and are at greatest risk of ICU admission. abstract: Background: Excessive monocyte/macrophage activation with the development of a cytokine storm and subsequent acute lung injury, leading to acute respiratory distress syndrome (ARDS) is a feared consequence of infection with COVID-19. The ability to recognize and potentially intervene early in those patients at greatest risk of developing this complication could be of great clinical utility. Methods: We performed detailed flow cytometric analysis of peripheral blood samples from 28 COVID-19 patients treated at Xian No.8 Hospital and the First Affiliated Hospital of Xian Jiaotong University in early 2020 in an attempt to identify factors that could help predict severity of disease and patient outcome. Findings: While we did not detect significant differences in the number of monocytes between patients with COVID-19 and normal healthy individuals,we did identify significant morphological and functional differences, which are more pronounced in patients requiring prolonged hospitalization and ICU admission. Patients with COVID-19 have larger than normal monocytes, easily identified on forward scatter, side scatter analysis by routine flow cytometry,with the presence of a distinct population of monocytes with high forward scatter (FSC-high). On more detailed analysis, these FSC-high monocytes are CD11b+, CD14+, CD16+, CD68+, CD80+, CD163+, CD206+ and secrete IL-6, IL-10 and TNF-alpha, consistent with an inflammatory phenotype. Conclusions: The detection and serial monitoring of this subset of inflammatory monocytes using flow cytometry could be of great help in guiding the prognostication and treatment of patients with COVID-19 and merits further evaluation. url: https://doi.org/10.1101/2020.03.24.20042655 doi: 10.1101/2020.03.24.20042655 id: cord-338243-njkhwkwk author: Zhang, Dayi title: Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital date: 2020-06-23 words: 2831.0 sentences: 158.0 pages: flesch: 51.0 cache: ./cache/cord-338243-njkhwkwk.txt txt: ./txt/cord-338243-njkhwkwk.txt summary: title: Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital In this study, we evaluated the presence of SARS-CoV-2 viral RNA in septic tanks of Wuchang Cabin Hospital and found a striking high level of (0.5–18.7) × 103 copies/L after disinfection with sodium hypochlorite. In septic tanks, disinfection achieved free chlorine > 6.5 mg/L for 1.5 hours when the dosage of sodium hypochlorite was 800 g/m 3 , meeting well with the guideline for emergency treatment of medical sewage containing SARS-CoV-2 suggested by China CDC. Septic tanks can behave as a long-term source J o u r n a l P r e -p r o o f to release SARS-CoV-2 viral RNA into waters when disinfection is not sufficient and challenges public health via potentially spreading viruses in drainage pipelines. abstract: Abstract The outbreak of coronavirus infectious disease-2019 (COVID-19) pneumonia raises the concerns of effective deactivation of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in medical wastewater by disinfectants. In this study, we evaluated the presence of SARS-CoV-2 viral RNA in septic tanks of Wuchang Cabin Hospital and found a striking high level of (0.5–18.7) × 103 copies/L after disinfection with sodium hypochlorite. Embedded viruses in stool particles might be released in septic tanks, behaving as a secondary source of SARS-CoV-2 and potentially contributing to its spread through drainage pipelines. Current recommended disinfection strategy (free chlorine ≥0.5 mg/L after at least 30 min suggested by World Health Organization; free chlorine above 6.5 mg/L after 1.5-h contact by China Centers for Disease Control and Prevention) needs to be reevaluated to completely remove SARS-CoV-2 viral RNA in non-centralized disinfection system and effectively deactivate SARS-CoV-2. The effluents showed negative results for SARS-CoV-2 viral RNA when overdosed with sodium hypochlorite but had high a level of disinfection by-product residuals, possessing significant ecological risks. url: https://doi.org/10.1016/j.scitotenv.2020.140445 doi: 10.1016/j.scitotenv.2020.140445 id: cord-103709-86hv27vh author: Zhang, Dong Yan title: Prefusion spike protein stabilization through computational mutagenesis date: 2020-06-19 words: 3243.0 sentences: 184.0 pages: flesch: 53.0 cache: ./cache/cord-103709-86hv27vh.txt txt: ./txt/cord-103709-86hv27vh.txt summary: The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We subject the selected residues to computational redesign using Eris to find the stabilizing mutations by calculating the change in free energy ∆∆ = ∆ − ∆ , where ∆ and ∆ are the free energies of the mutant protein and wild type proteins correspondingly. After the designation of the mutation sites, the pipeline utilizes Eris to determine the changes in free energies of the mutants. We analyze the conservation score, RMSF, and SASA of residues in the spike protein through the pipeline. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes abstract: A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) has emerged as a human pathogen, causing global pandemic and resulting in over 400,000 deaths worldwide. The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Due to the critical role in viral-host interaction and the exposure of spike protein, it has been a focus of most vaccines’ developments. However, the structural and biochemical studies of the spike protein are challenging because it is thermodynamically metastable1. Here, we develop a new pipeline that automatically identifies mutants that thermodynamically stabilize the spike protein. Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We then utilize our previously developed protein design tool, Eris, to predict thermodynamically stabilizing mutations in proteins. We validate the ability of our pipeline to identify protein stabilization mutants through known prefusion spike protein mutants. We finally utilize the pipeline to identify new prefusion spike protein stabilization mutants. url: https://doi.org/10.1101/2020.06.17.157081 doi: 10.1101/2020.06.17.157081 id: cord-285755-zblitbo0 author: Zhang, F. title: Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study date: 2020-03-24 words: 3069.0 sentences: 164.0 pages: flesch: 42.0 cache: ./cache/cord-285755-zblitbo0.txt txt: ./txt/cord-285755-zblitbo0.txt summary: [Results] A total of 110 patients with confirmed (n=80) or suspected (n=30) COVID-19 were screened and 48 patients (female 31.3%, mean age 70.58{+/-}13.38 year old) among them with high-sensitivity cardiac troponin I (hs-cTnI) test within 48 hours after admission were included, of whom 17 (17/48, 35.4%) died in hospital while 31 (31/48, 64.6%) were discharged or transferred to other hospital. [Conclusions] Cardiac injury defined by hs-cTnI elevation and elevated d-dimer on admission were risk factors for in-hospital death, while higher SpO2 could be seen as a protective factor, which could help clinicians to identify patients with adverse outcome at the early stage of COVID-19. Short-term prognosis of COVID-19 patients are discrepancy and in-hospital mortality risk are high in severe cases[1] [2] Although previous study had indicated that several risk factors were independently associated with short-term mortality, such as elevated d-dimer, older age and higher Sequential Organ Failure Assessment (SOFA) score [2] , few studies focused on cardiac injury with COVID-19 patients. abstract: [Background] Since December 2019, a cluster of coronavirus disease 2019 (COVID-19) occurred in Wuhan, Hubei Province, China and spread rapidly from China to other countries. In-hospital mortality are high in severe cases and cardiac injury characterized by elevated cardiac troponin are common among them. The mechanism of cardiac injury and the relationship between cardiac injury and in-hospital mortality remained unclear. Studies focused on cardiac injury in COVID-19 patients are scarce. [Objectives] To investigate the association between cardiac injury and in-hospital mortality of patients with confirmed or suspected COVID-19. [Methods] Demographic, clinical, treatment, and laboratory data of consecutive confirmed or suspected COVID-19 patients admitted in Wuhan No.1 Hospital from 25th December, 2019 to 15th February, 2020 were extracted from electronic medical records and were retrospectively reviewed and analyzed. Univariate and multivariate Cox regression analysis were used to explore the risk factors associated with in-hospital death. [Results] A total of 110 patients with confirmed (n=80) or suspected (n=30) COVID-19 were screened and 48 patients (female 31.3%, mean age 70.58{+/-}13.38 year old) among them with high-sensitivity cardiac troponin I (hs-cTnI) test within 48 hours after admission were included, of whom 17 (17/48, 35.4%) died in hospital while 31 (31/48, 64.6%) were discharged or transferred to other hospital. High-sensitivity cardiac troponin I was levated in 13 (13/48, 27.1%) patents. Multivariate Cox regression analysis showed pulse oximetry of oxygen saturation (SpO2) on admission (HR 0.704, 95% CI 0.546-0.909, per 1% decrease, p=0.007), elevated hs-cTnI (HR 10.902, 95% 1.279-92.927, p=0.029) and elevated d-dimer (HR 1.103, 95%CI 1.034-1.176, per 1mg/L increase, p=0.003) on admission were independently associated with in-hospital mortality. [Conclusions] Cardiac injury defined by hs-cTnI elevation and elevated d-dimer on admission were risk factors for in-hospital death, while higher SpO2 could be seen as a protective factor, which could help clinicians to identify patients with adverse outcome at the early stage of COVID-19. url: http://medrxiv.org/cgi/content/short/2020.03.21.20040121v1?rss=1 doi: 10.1101/2020.03.21.20040121 id: cord-325348-yi6yu5l1 author: Zhang, G. title: Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date: 2020-06-17 words: 2664.0 sentences: 160.0 pages: flesch: 54.0 cache: ./cache/cord-325348-yi6yu5l1.txt txt: ./txt/cord-325348-yi6yu5l1.txt summary: Recent cryo-electron microscopy (cryo-EM) structural studies of the SARS-CoV-2 spike protein 68 receptor binding domain (RBD) in complex with full-length human ACE2 receptor revealed key 69 amino acid residues at the contact interface between the two proteins and estimated the binding 70 affinity at ~15 nM [7, 8] . The results of this MD simulation suggest 108 that SBP1 and SBP2 peptides derived from the ACE-PD α1 helix may alone potentially bind the 109 SARS-CoV-2 spike RBD protein with sufficient affinity to disrupt the associated PPI. However, competition was not observed when using non-biotinylated SBP1 pre-140 mixed in solution with Sino Biological insect-derived SARS-CoV-2-RBD, even with a 1000-fold 141 excess of the peptide (Fig. 3C, 3E ). In conclusion, a biotinylated peptide sequence derived from human ACE2 was found to 205 bind Sino Biological insect-derived SARS-CoV-2 spike protein RBD with micromolar affinity, but 206 did not associate with SARS-CoV-2-RBD variants obtained from other commercial sources. abstract: Coronavirus disease 19 (COVID-19) is an emerging global health crisis. With over 7 million confirmed cases to date, this pandemic continues to expand, spurring research to discover vaccines and therapies. SARS-CoV-2 is the novel coronavirus responsible for this disease. It initiates entry into human cells by binding to angiotensin-converting enzyme 2 (ACE2) via the receptor binding domain (RBD) of its spike protein (S). Disrupting the SARS-CoV-2-RBD binding to ACE2 with designer drugs has the potential to inhibit the virus from entering human cells, presenting a new modality for therapeutic intervention. Peptide-based binders are an attractive solution to inhibit the RBD-ACE2 interaction by adequately covering the extended protein contact interface. Using molecular dynamics simulations based on the recently solved cryo-EM structure of ACE2 in complex with SARS-CoV-2-RBD, we observed that the ACE2 peptidase domain (PD) α1 helix is important for binding SARS-CoV-2-RBD. Using automated fast-flow peptide synthesis, we chemically synthesized a 23-mer peptide fragment of the ACE2 PD α1 helix (SBP1) composed entirely of proteinogenic amino acids. Chemical synthesis of SBP1 was complete in 1.5 hours, and after work up and isolation >20 milligrams of pure material was obtained. Bio-layer interferometry (BLI) revealed that SBP1 associates with micromolar affinity to insect-derived SARS-CoV-2-RBD protein obtained from Sino Biological. Association of SBP1 was not observed to an appreciable extent to HEK cell-expressed SARS-CoV-2-RBD proteins and insect-derived variants acquired from other vendors. Moreover, competitive BLI assays showed SBP1 does not outcompete ACE2 binding to Sino Biological insect-derived SARS-CoV-2-RBD. Further investigations are ongoing to gain insight into the molecular and structural determinants of the variable binding behavior to different SARS-CoV-2-RBD protein variants. url: https://doi.org/10.1101/2020.03.19.999318 doi: 10.1101/2020.03.19.999318 id: cord-293082-fw7deem8 author: Zhang, Guangzhi title: Animal coronaviruses and SARS‐CoV‐2 date: 2020-08-16 words: 2068.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-293082-fw7deem8.txt txt: ./txt/cord-293082-fw7deem8.txt summary: As of April 7, just four months since its first outbreak, more 48 than 3.4 million confirmed cases and 238,000 deaths have been recorded in 215 countries, areas, 49 and territories, and moreover it seems that severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2) that causes COVID-19 will probably continue to circulate around the globe 51 (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/). The health 52 authorities and governments of affected countries have paid attention to current pandemic and 53 have taken immediate measures to block COVID-19 transmission, including utilization of personal 54 protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis 55 and sharing, public health education, maintaining social distance, the creation of diagnostics, 56 therapeutics, and vaccines, etc (Xiao and Torok 2020) . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain abstract: COVID‐19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). It has rapidly spread to 216 countries and territories since first outbreak in December of 2019, posing a substantial economic losses and extraordinary threats to the public health worldwide. Although bats have been suggested as the natural host of SARS‐CoV‐2, transmission chains of this virus, role of animals during cross‐species transmission, and future concerns remain unclear. Diverse animal coronaviruses have extensively been studied since the discovery of avian coronavirus in 1930s. The current article comprehensively reviews and discusses the current understanding about animal coronaviruses and SARS‐CoV‐2 for their emergence, transmission, zoonotic potential, alteration of tissue/host tropism, evolution, status of vaccines, and surveillance. This study aims at providing guidance for control of COVID‐19 and preventative strategies for possible future outbreaks of zoonotic coronavirus via cross‐species transmission. url: https://doi.org/10.1111/tbed.13791 doi: 10.1111/tbed.13791 id: cord-349774-898tmq14 author: Zhang, Haiyang title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date: 2020-06-16 words: 3172.0 sentences: 188.0 pages: flesch: 52.0 cache: ./cache/cord-349774-898tmq14.txt txt: ./txt/cord-349774-898tmq14.txt summary: title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein Here, we report for the first time that the 11S proteasomal activator PA28γ regulates the intracellular abundance of the SARS-CoV-2 N protein (nCoV N). These results suggest that PA28γ binding is important in regulating 20S proteasome activity, which in turn regulates levels of the critical nCoV N nucleocapsid protein of SARS-CoV-2, furthering our understanding of the pathogenesis of COVID-19. The SARS-CoV-2 nucleocapsid protein (hereafter, referred to as nCoV N) accounts for the largest proportion of viral structure proteins and is the most abundant protein in virus-infected cells. PA28γ could be critical for degrading the SARS-CoV-19 nCoV N protein in the nucleus as part of the 20S proteasome, which acts to degrade proteins in a ubiquitin-independent manner, such as seen in the hepatitis C virus (HCV) core protein [11] . Interactions of SARS Coronavirus Nucleocapsid Protein with the host cell proteasome subunit p42 abstract: The nucleocapsid protein is significant in the formation of viral RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), accounting for the largest proportion of viral structural proteins. Here, we report for the first time that the 11S proteasomal activator PA28γ regulates the intracellular abundance of the SARS-CoV-2 N protein (nCoV N). Furthermore, we have identified proteasome activator PA28γ as a nCoV N binding protein by co-immunoprecipitation assay. As a result of their interaction, nCoV N could be degraded by PA28γ-20S in vitro degradation assay. This was also demonstrated by blocking de novo protein synthesis with cycloheximide. The stability of nCoV N in PA28γ-knockout cells was greater than in PA28γ-wildtype cells. Notably, immunofluorescence staining revealed that knockout of the PA28γ gene in cells led to the transport of nCoV N from the nucleus to the cytoplasm. Overexpression of PA28γ enhanced proteolysis of nCoV N compared to that in PA28γ-N151Y cells containing a dominant-negative PA28γ mutation, which reduced this process. These results suggest that PA28γ binding is important in regulating 20S proteasome activity, which in turn regulates levels of the critical nCoV N nucleocapsid protein of SARS-CoV-2, furthering our understanding of the pathogenesis of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32703419/ doi: 10.1016/j.bbrc.2020.06.058 id: cord-266324-uvsmbrbf author: Zhang, Hu title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases date: 2020-05-08 words: 2336.0 sentences: 131.0 pages: flesch: 48.0 cache: ./cache/cord-266324-uvsmbrbf.txt txt: ./txt/cord-266324-uvsmbrbf.txt summary: title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases A cohort study of 140 COVID-19 patients showed that gastrointestinal symptoms were observed in 39.6% of the patients, including nausea (17.3%), diarrhoea (12.9%) and vomiting (5.0%) [4] . Therefore, we determined that a retrospective analysis of cases might be useful for clinicians to identify the clinical characteristics of COVID-19 patients with gastrointestinal symptoms. In this study, red and white blood cells were not identified in the faeces of patients who experienced gastrointestinal symptoms, a finding characteristic of viral infections. Second, this study was the lack of the result of SARS-CoV-2 RNA in the stool of COVID-19 patients, so we did not determine the hypothesis that the severity of gastrointestinal symptoms may be related to the presence of viral replication in stool. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan abstract: OBJECTIVE: To explore the clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms. METHODS: The clinical data of 164 COVID-19 patients with gastrointestinal symptoms were extracted and analysed retrospectively. RESULTS: In total, 505 COVID-19 patients were divided into two groups: those with gastrointestinal symptoms (G group) and those without gastrointestinal symptoms (NG group). Common gastrointestinal symptoms included inappetence, diarrhoea, nausea, abdominal pain, and vomiting. Significantly higher proportions of patients with fever, dizziness, myalgia, and fatigue were noted in group G than in group NG. Compared with patients without fever, there was a significant difference between G group and NG group in moderate fever or above, while there was no significant difference between the two groups in low fever. The laboratory results showed that patients in the G group had significantly higher C-reactive protein, lactate dehydrogenase, and α-hydroxybutyrate dehydrogenase levels than those in the NG group. Moreover, the proportion of patients with severe pneumonia was significantly higher in the G group than in the NG group. CONCLUSION: In Wuhan, the proportion of COVID-19 patients who experience gastrointestinal symptoms is relatively high. Patients who experience gastrointestinal symptoms are more likely to suffer from severe pneumonia, which may help clinicians identify patients at high risk of COVID-19 and thus reduce the incidence of this condition. url: https://www.ncbi.nlm.nih.gov/pubmed/32507692/ doi: 10.1016/j.dld.2020.04.034 id: cord-309513-dleo9rpl author: Zhang, Huilan title: Histopathologic Changes and SARS–CoV-2 Immunostaining in the Lung of a Patient With COVID-19 date: 2020-03-12 words: 609.0 sentences: 44.0 pages: flesch: 51.0 cache: ./cache/cord-309513-dleo9rpl.txt txt: ./txt/cord-309513-dleo9rpl.txt summary: Biopsy lung sections were analyzed with hematoxylineosin staining, and immunostaining for SARS-CoV-2 was conducted as reported elsewhere (1) . In contrast, viral protein expression was minimally detectable on blood vessels ( Figure 2 , B, dashed black line) or in the interstitial areas between alveoli (Figure 2, B, bottom panel, blue arrows) . Immu-nostaining of Huh7 cells infected with SARS-CoV and of lung sections from an HIV-positive patient who died of fungal infection served as positive and negative staining controls, respectively (Figure 2, C) . A. Histopathologic examination revealing diffuse alveolar damage, organizing phase (A-1); denudation of alveolar lining cells (arrow 1), with presence of reactive type II pneumocyte hyperplasia (arrow 2) (A-2); intra-alveolar fibrinous exudates (arrow 3) and interstitial loose fibrosis with chronic inflammatory infiltrates (arrow 4) (A-3); and intra-alveolar loose fibrous plugs (arrow 5) (A-4). B. Immunostaining of SARS-CoV-2 in lung sections. abstract: nan url: https://doi.org/10.7326/m20-0533 doi: 10.7326/m20-0533 id: cord-317129-wa1j2f6b author: Zhang, Jia title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 words: 2319.0 sentences: 117.0 pages: flesch: 58.0 cache: ./cache/cord-317129-wa1j2f6b.txt txt: ./txt/cord-317129-wa1j2f6b.txt summary: This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. This single-step sequential primer extension was expected to yield mainly final templates with no intermediate products. As shown in Figure 1 , DNA fragments in lengths of 182 and 204 bp were obtained from primers of set A and set B, respectively, by the single-step sequential primer extension where each reaction contained four partially overlapping a The expected products were extended from reverse primers (AR or BR) to the first forward primers. De novo synthesis of the PCR template complimentary to a viral genome provides a tool for the rapid development of early diagnostic assays for any new pathogen as soon as its sequence is known. abstract: A novel coronavirus was identified as the cause for severe acute respiratory syndrome (SARS). The complete sequence of SARS genome has provided an opportunity for the development of molecular diagnostic assays. To restrain further outbreak of SARS, the World Health Organization has posted several pairs of polymerase chain reaction (PCR) primers for early diagnosis and urged more research to be done on PCR protocols. Here we report a strategy for the de novo synthesis of PCR templates complimentary to the SARS virus genome, which has the advantage of working on PCR templates without concern about viral infection and also has the advantage that it can be used by those who do not have access to the SARS virus. This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. url: https://www.ncbi.nlm.nih.gov/pubmed/14526121/ doi: 10.1385/mb:25:2:107 id: cord-252980-1e28zj1d author: Zhang, Jiahao title: Insights into the cross-species evolution of 2019 novel coronavirus date: 2020-03-04 words: 1045.0 sentences: 75.0 pages: flesch: 62.0 cache: ./cache/cord-252980-1e28zj1d.txt txt: ./txt/cord-252980-1e28zj1d.txt summary: 5 Although humans and bats live in different environments, some wildlife species were susceptible to the novel coronaviruses in nature, highlighting that the need of tracing its origin of SARS-CoV-2 in wild animals. The similarity analysis of SARS-CoV-2 and the animal-origin coronaviruses demonstrated that recombination events were likely to occur in bat-and pangolin-origin coronaviruses (Supplementary Figure S1) . Although the S amino acid identities of pangolin-origin coronavirus exhibited lower amino acid identities with bat/RaTG13, it was noteworthy that six amino acids associated with the receptor binding preference of human receptor angiotensin converting enzyme II-464 L, 495F, 502Q, 503S, 510 N, and 514Y (SARS-CoV-2 numbering)-in the pangolin/1 coronavirus were the same as that of SARS-CoV-2 ( Fig. 2 ), but were distinct from that of the bat-origin coronaviruses. Besides, the PRRA-motif insertion was occurred in the S1/S2 junction of SARS-CoV-2; however, the PRRA-motif insertion in the pangolin-and bat-origin coronaviruses was missing (Supplementary Figure S4 ), suggesting that the convergent cross-species evolution of SARS-CoV-2-related coronaviruses. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320301067 doi: 10.1016/j.jinf.2020.02.025 id: cord-285440-srtkqr13 author: Zhang, Jianguo title: Web-based electronic patient records for collaborative medical applications date: 2004-12-20 words: 3525.0 sentences: 169.0 pages: flesch: 46.0 cache: ./cache/cord-285440-srtkqr13.txt txt: ./txt/cord-285440-srtkqr13.txt summary: We developed a web-based system to interactively display electronic patient records (EPR), such as DICOM images, graphics, and structure reports and therapy records, for intranet and internet collaborative medical applications. Second, we present a new design of web-based interactive system architecture and its major components, which support EPR display and manipulation and operate in a central mode for collaborative applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. abstract: We developed a web-based system to interactively display electronic patient records (EPR), such as DICOM images, graphics, and structure reports and therapy records, for intranet and internet collaborative medical applications. This system has three major components, a C/S (client/server) architecture for EPR data acquisition and authoring, and a Web B/S architecture for data delivering. The Web viewer of this system integrates multi-media display modules and remote control module together to provide interactive EPR display and manipulation functions for collaborative applications. We have successfully used this system two times to provide teleconsultation for severe acute respiratory syndrome (SARS) patients in Shanghai Infection Hospital and Xinhua Hospital. During the consultation, both the physicians in infection control area and the experts outside the control area could use this system interactively to manipulate and navigate the EPR objects of the SARS patients to facilitate a more precise diagnosis. This paper gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use Web technology and DICOM standard to build an open architecture for collaborative medical applications. The system can be used for both intranet and internet medical applications such as tele-diagnosis, teleconsultation, and distant learning. url: https://api.elsevier.com/content/article/pii/S0895611104001132 doi: 10.1016/j.compmedimag.2004.09.005 id: cord-316623-tv5yyfak author: Zhang, Jianmin title: Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase date: 2008-03-04 words: 4944.0 sentences: 258.0 pages: flesch: 65.0 cache: ./cache/cord-316623-tv5yyfak.txt txt: ./txt/cord-316623-tv5yyfak.txt summary: The product was purified by column chromatography (50:50 EtOAc/hexanes) to yield 12a as a solid (16 mg To a solution of 11a (10 mg, 0.045 mmol) in dry THF (5 mL) was added LiHMDS (0.1 mL, 1.0 M solution in THF, 0.1 mmol) over a period of 5 min. The mixture was stirred for 1 h at À78°C, and a solution of NFSi (32 mg, 0.1 mmol) in dry THF (3 mL) was added dropwise over 10 min. After 3 h of stirring at 20°C, the solvent was removed in vacuo and the product was purified by column chromatography on silica gel (25:75 EtOAc/hexanes) to yield 21 as a solid (1.35 g, 68%) Based on our previous modeling studies [10b,23], the three-ringed esters utilize a non-covalent and reversible mechanism of inhibition in a S4-S1 binding mode, by blocking entry of substrates into the active site of SARS-CoV 3CL pro . abstract: The severe acute respiratory syndrome (SARS) virus depends on a chymotrypsin-like cysteine proteinase (3CL(pro)) to process the translated polyproteins to functional viral proteins. This enzyme is a target for the design of potential anti-SARS drugs. A series of ketones and corresponding mono- and di-fluoro ketones having two or three aromatic rings were synthesized as possible reversible inhibitors of SARS 3CL(pro). The design was based on previously established potent inhibition of the enzyme by oxa analogues (esters), which also act as substrates. Structure–activity relationships and modeling studies indicate that three aromatic rings, including a 5-bromopyridin-3-yl moiety, are key features for good inhibition of SARS 3CL(pro). Compound 11d, 2-(5-bromopyridin-3-yl)-1-(5-(4-chlorophenyl)furan-2-yl)ethanone and its α-monofluorinated analogue 12d, gave the best reversible inhibition with IC(50) values of 13 μM and 28 μM, respectively. In contrast to inhibitors having two aromatic rings, α-fluorination of compounds with three rings unexpectedly decreased the inhibitory activity. url: https://api.elsevier.com/content/article/pii/S0045206808000035 doi: 10.1016/j.bioorg.2008.01.001 id: cord-251943-jzaeaxam author: Zhang, Jian‐San title: A serological survey on neutralizing antibody titer of SARS convalescent sera date: 2005-08-24 words: 2542.0 sentences: 139.0 pages: flesch: 50.0 cache: ./cache/cord-251943-jzaeaxam.txt txt: ./txt/cord-251943-jzaeaxam.txt summary: A seroepidemiologic study was conducted in North China in 2003 to determine the neutralizing antibody titer of severe acute respiratory syndrome (SARS) convalescent sera. A total of 99 SARS convalescent serum samples were collected from patients from the Inner Mongolia Autonomous Region, Hebei Province, and Beijing 35–180 days after the onset of symptoms. To gain a comprehensive understanding of the antibody to SARS-CoV, we report the anti-SARS antibody titer of 87 SARS convalescent sera determined by neutralization assay. These 87 serum samples were confirmed to be positive for anti-SARS antibodies with the combination of ELISA, neutralization, and Western blot, so they were pooled to form a convalescent sera database for the further analysis of neutralizing antibody titer. The anti-SARS neutralizing antibody titer of 87 positive convalescent sera was analyzed quantitatively by the neutralization assay. In our laboratory, a combination of ELISA, neutralization assay, and Western blot were performed on 99 SARS convalescent sera. abstract: A seroepidemiologic study was conducted in North China in 2003 to determine the neutralizing antibody titer of severe acute respiratory syndrome (SARS) convalescent sera. A total of 99 SARS convalescent serum samples were collected from patients from the Inner Mongolia Autonomous Region, Hebei Province, and Beijing 35–180 days after the onset of symptoms. The anti‐SARS antibodies were detected by enzyme‐linked immunosorbent assay (ELISA), neutralization assay, and Western blot. Eighty‐seven serum samples were confirmed to be positive for SARS antibodies. The neutralizing antibody titer of the 87 positive sera was analyzed quantitatively by neutralization assay. The geometric mean titer (GMT) of the 87 convalescent sera was 1:61. The Kolmogorov–Smirnov test showed that the neutralizing antibody titers conform to normal distribution, which suggests that the average anti‐SARS antibody level in this study was representative of the convalescent antibody level of the SARS population. This result could be useful for the development and quality control of SARS vaccines. J. Med. Virol. 77:147–150, 2005. © 2005 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16121363/ doi: 10.1002/jmv.20431 id: cord-016120-pz2q62i7 author: Zhang, Jie title: Chai Jing: The Power of Vulnerability date: 2019-02-16 words: 7940.0 sentences: 335.0 pages: flesch: 52.0 cache: ./cache/cord-016120-pz2q62i7.txt txt: ./txt/cord-016120-pz2q62i7.txt summary: This uneasiness with emotion, which is perceived to be opposite to journalistic objectivity, as well as the questioning of Chai''s sincerity, which is an innate paradox of the new documentary movement itself (some questioned whether the filmmakers are using the stories of the marginalized people for their own identity politics), provides a lens into the media consumption habits of the Chinese public in the first two decades of the twenty-first century. Chai left the CCTV in 2014 and returned to the public sphere in 2015 with her documentary Under the Dome, which uses a TED talk format to combine personal testimonials, graphs and data, animation, and interviews to investigate the causes of China''s air pollution. Chai''s embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. abstract: In the past seventeen years Chai Jing has risen from China’s official media to become a recognized investigative journalist, public intellectual, author, and more recently, an independent filmmaker and environmental activist. Her experience and work reflect how China’s news apparatus has reformed to adapt to the drastic societal changes with emotion being used to open up new ways of news communication. Her documentary Under the Dome further shows how the internet has transformed the ecology of media and provided innovative platforms for social engagement. Chai’s embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. Her leaving the CCTV can be viewed as a self-marginalization that helps her sustain that vulnerability, through which she gains resilience and critical power. The use of maternal voice in Under the Dome exemplifies her use of the power of vulnerability in its most mature form. The controversiality about that voice signals that post-socialist China remains a space where environmental and gender discourses are contested and negotiated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120306/ doi: 10.1007/978-981-13-5980-4_3 id: cord-316180-g3lfecp0 author: Zhang, Jingshu title: Membrane heist: Coronavirus host membrane remodeling during replication date: 2020-10-25 words: 1790.0 sentences: 122.0 pages: flesch: 43.0 cache: ./cache/cord-316180-g3lfecp0.txt txt: ./txt/cord-316180-g3lfecp0.txt summary: Here we review the current knowledge of the structure, lipid composition, function, and biogenesis of coronavirus-induced DMVs, highlighting the druggable viral and cellular factors that are involved in the formation and function of DMVs. Prior to the emergence of Coronavirus Disease-2019 (COVID-19) caused by severe 2 acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the outbreak of highly approximately 50 to 250 nm of these DMVs as described in detail elsewhere 9, 10 . Severe 503 acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 504 induce double-membrane vesicles Mutation in 521 murine coronavirus replication protein nsp4 alters assembly of double 522 membrane vesicles Expression and cleavage of middle east respiratory 537 syndrome coronavirus nsp3-4 polyprotein induce the formation of double-538 membrane vesicles that mimic those associated with coronaviral RNA 539 replication The N-terminal region of severe acute respiratory syndrome 546 coronavirus protein 6 induces membrane rearrangement and enhances virus 547 replication abstract: The ongoing pandemic of COVID-19 (Coronavirus Disease-2019), a respiratory disease caused by the novel coronavirus strain, SARS-CoV-2, has affected more than 30 million people already, with more than 900 thousand deaths worldwide (as of September 28, 2020). We are in urgent need of therapeutic interventions that target the host-virus interface, which requires a molecular understanding of the SARS-CoV-2 life-cycle. Like other positive-sense RNA viruses, coronaviruses remodel intracellular membranes to form specialized viral replication compartments, including double-membrane vesicles (DMVs), where viral RNA genome replication takes place. Here we review the current knowledge of the structure, lipid composition, function, and biogenesis of coronavirus-induced DMVs, highlighting the druggable viral and cellular factors that are involved in the formation and function of DMVs. url: https://api.elsevier.com/content/article/pii/S0300908420302686 doi: 10.1016/j.biochi.2020.10.010 id: cord-324623-x6eom6kh author: Zhang, Jingyi title: Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review date: 2020-04-22 words: 4246.0 sentences: 286.0 pages: flesch: 56.0 cache: ./cache/cord-324623-x6eom6kh.txt txt: ./txt/cord-324623-x6eom6kh.txt summary: This rapid review aims to explore the clinical effectiveness and safety of IVIG in the treatment of children with severe COVID-19. Methods: We systematically searched the literature on the use of IVIG in patients with COVID-19, Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS), including both adults and children. Results: A total of 1519 articles were identified by initial literature search, and finally six studies, included one randomized controlled trial (RCT), four case series and one case report involving 198 patients. The risk of death was not associated with the use of IVIG in the patients with ARDS (31) .A case report of three adults with COVID-19 reported that a high dose IVIG (25 g/d for 5 days) administered at the appropriate point could successfully block the progression of disease cascade (result of the clinical symptoms, laboratory inspection indicators and chest CT scan), and finally improve the outcome of COVID 19 (32) . abstract: Background: Intravenous immunoglobulin (IVIG) is usually used as supportive therapy, but the treatment of COVID-19 by IVIG is controversial. This rapid review aims to explore the clinical effectiveness and safety of IVIG in the treatment of children with severe COVID-19. Methods: We systematically searched the literature on the use of IVIG in patients with COVID-19, Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS), including both adults and children. We assessed the risk of bias and quality of evidence and reported the main findings descriptively. Results: A total of 1519 articles were identified by initial literature search, and finally six studies, included one randomized controlled trial (RCT), four case series and one case report involving 198 patients. One case series showed the survival of COVID-19 patients with acute respiratory distress syndrome (ARDS) was not improved by IVIG. One case report showed high-dose IVIG could improve the outcome of COVID-19 adults. Three observational studies showed inconsistent results of the effect of IVIG on SARS patients. One RCT showed that IVIG did not reduce mortality or the incidence of nosocomial infection in adults with severe SARS. The quality of evidence was between low and very low. Conclusions: The existing evidence is insufficient to support the efficacy or safety of IVIG in the treatment of COVID-19. Keywords: COVID-19; children; intravenous immunoglobulin; rapid review. url: https://doi.org/10.1101/2020.04.17.20064444 doi: 10.1101/2020.04.17.20064444 id: cord-319718-blqzi69t author: Zhang, L. title: Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route date: 2020-05-03 words: 1689.0 sentences: 110.0 pages: flesch: 62.0 cache: ./cache/cord-319718-blqzi69t.txt txt: ./txt/cord-319718-blqzi69t.txt summary: Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. . https://doi.org/10.1101 /2020 Based on the position and nucleotide variation of the phylogenetic tree, 104 we compared the evolutionary variation between SARS-CoV-2 representative 105 strains. abstract: In the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations. url: https://doi.org/10.1101/2020.04.27.20081349 doi: 10.1101/2020.04.27.20081349 id: cord-327005-7zgolyqf author: Zhang, Lan title: Clinical Features of 33 Cases in Children Infected With SARS-CoV-2 in Anhui Province, China–A Multi-Center Retrospective Cohort Study date: 2020-06-16 words: 3747.0 sentences: 213.0 pages: flesch: 57.0 cache: ./cache/cord-327005-7zgolyqf.txt txt: ./txt/cord-327005-7zgolyqf.txt summary: Here, we report 33 patients under the age of 19 years with confirmed COVID-19 infection from Anhui province, China, and describe the clinical features, laboratory, and radiological characteristics of a chest CT, treatment, and clinical outcome. Information recorded included demographic data, medical history, familial clustering, details of the confirmed patients, if any, in the family, whether they were residents of Wuhan, or traveled to Wuhan, whether they came in contact with confirmed patients, signs, and symptoms, including pharyngodynia, fever, cough, vomiting and diarrhea, fatigue, tightness in the chest, total WBC and lymphocyte percentages, levels of C-reactive protein (CRP), IL-6, liver function, CKMB, a marker of myocardial injury, chest CT, administration of INF a, lopinavir and ritonavir, ribavirin, or arbidol, and titers of Mp-IgM, anti-parainfluenza virus IgM, anti-influenza virus IgM, and anti-adenovirus IgM. A retrospective cohort study was used to analyze the epidemiological data, clinical symptoms, and signs, changes in WBC and total lymphocyte counts, chest CT, and the different treatments in children infected with SARS-COV-2. abstract: Background: As of 23rd February 2020, China had 77,048 patients with confirmed SARS-CoV-2 infections, and only 2. 1% of patients were under the age of 19 years. Morbidity among children was much lower, with milder or absent signs and symptoms; chest CT scans showed milder symptoms, if at all, compared to adults. Objective: Report the epidemiological, clinical features, laboratory, radiological characteristics, and treatment of SARS-CoV-2 infections. Compare additional signs and symptoms, investigate familial clustering, compare laboratory results, and find out relevance between age and typical chest CT scans in patients. Methods: We studied 33 young patients with laboratory-confirmed SARS-CoV-2 infection in Anhui Province of China by 16th February 2020. Their signs, symptoms, and familial clustering were analyzed. We compared the laboratory test results, age, and gender among three parts based on their chest CT scans. Results: Familial clustering was seen in 30 (30/33; 90.91%) patients; three families had seven confirmed members infected with the disease. Eight (8/33; 24.24%) patients had no symptoms, 12 (12/33; 36.36%) patients had only fever, nine (9/33; 27.27%) patients had fever and additional symptoms, and 12 (12/33; 36.36%) patients had no fever. Dry cough was the most common additional symptom. In 25 (25/33; 75.76%) patients, the percent of lymphocytes decreased; 26 (26/33; 78.79%) patients were older than 7 years. More male than female patients and patients older than 8 years showed typical abnormalities in the chest CT scans (P = 0.038). Only two 18 years old patients had hepatic injury. Conclusion: Children's infection is mild and familial clustering was the most common channel. The older patients had more typical ground glass opacity (GGO) or consolidation in chest CT scans. Cases without fever strongly suggested that non-symptomatic children should not be assumed to be free of infection when their family members have confirmed infection. Most children showed clinical features distinguishable from adults and with increased susceptibility within family members. url: https://www.ncbi.nlm.nih.gov/pubmed/32612971/ doi: 10.3389/fpubh.2020.00255 id: cord-299989-p59u6qa0 author: Zhang, Lei title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date: 2020-06-18 words: 1282.0 sentences: 69.0 pages: flesch: 49.0 cache: ./cache/cord-299989-p59u6qa0.txt txt: ./txt/cord-299989-p59u6qa0.txt summary: title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. Interestingly, our finding that ACE2 was highly expressed in breast appears to be in contrast to a retrospective study on nine pregnant women with COVID-19 in the third trimester, in which the colostrum from six patients tested negative for SARS-CoV-2 (H. abstract: The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global public health emergency. SARS-CoV-2 employs the host cell receptor ACE2 for cellular entry. Nonetheless, the differences in ACE2 expression pattern in lung versus other normal and solid tumor tissues remain incompletely characterized. Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. url: https://doi.org/10.1016/j.meegid.2020.104428 doi: 10.1016/j.meegid.2020.104428 id: cord-303917-2tu707ng author: Zhang, Lei title: Potential interventions for novel coronavirus in China: A systematic review date: 2020-03-03 words: 5433.0 sentences: 369.0 pages: flesch: 46.0 cache: ./cache/cord-303917-2tu707ng.txt txt: ./txt/cord-303917-2tu707ng.txt summary: We suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children''s RNA‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. In addition, Semba et al 12 had reported that vitamin A supplementation reduced morbidity and mortality in different infectious diseases, such as measles, diarrheal disease, measles-related pneumonia, human immunodeficiency virus (HIV) infection, and malaria. 15 The mechanism by which vitamin A and retinoids inhibit measles replication is upregulating elements of the innate immune response in uninfected bystander cells, making them refractory to productive infection during subsequent rounds of viral replication. Remdesivir (RDV), a nucleoside analog GS-5734, had been reported to inhibit human and zoonotic coronavirus in vitro and to restrain severe acute respiratory syndrome coronavirus (SARS-CoV) in vivo. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association abstract: An outbreak of a novel coronavirus (COVID‐19 or 2019‐CoV) infection has posed significant threats to international health and the economy. In the absence of treatment for this virus, there is an urgent need to find alternative methods to control the spread of disease. Here, we have conducted an online search for all treatment options related to coronavirus infections as well as some RNA‐virus infection and we have found that general treatments, coronavirus‐specific treatments, and antiviral treatments should be useful in fighting COVID‐19. We suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children's RNA‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. In addition, convalescent plasma should be given to COVID‐19 patients if it is available. In conclusion, we suggest that all the potential interventions be implemented to control the emerging COVID‐19 if the infection is uncontrollable. url: https://www.ncbi.nlm.nih.gov/pubmed/32052466/ doi: 10.1002/jmv.25707 id: cord-351512-h4vigeuy author: Zhang, Lin title: How scientific research reacts to international public health emergencies: a global analysis of response patterns date: 2020-06-09 words: 7123.0 sentences: 347.0 pages: flesch: 49.0 cache: ./cache/cord-351512-h4vigeuy.txt txt: ./txt/cord-351512-h4vigeuy.txt summary: In the present paper, we attempt to characterise, quantify and measure the response of academia to international public health emergencies in a comparative bibliometric study of multiple outbreaks. From our analysis of six infectious disease outbreaks since 2000, including COVID-19, we find that academia always responded quickly to public health emergencies with a sharp increase in the number of publications immediately following the declaration of an outbreak by the WHO. Researches in the fields of virology, infectious diseases and immunology are the most active, and we identified two characteristic patterns in global science distinguishing research in Europe and America that is more focused on public health from that conducted in China and Japan with more emphasis on biomedical research and clinical pharmacy, respectively. From the perspective of countries and world regions, funding agencies in the USA, China, and the UK contributed most to supporting research in response to public health emergencies, as shown in Fig. 11 . abstract: As of the middle of April 2020, the unprecedented COVID-19 pandemic has claimed more than 137,000 lives (https://coronavirus.jhu.edu/map.html). Because of its extremely fast spreading, the attention of the global scientific community is now focusing on slowing down, containing and finally stopping the spread of this disease. This requires the concerted action of researchers and practitioners of many related fields, raising, as always in such situations the question, of what kind of research has to be conducted, what are the priorities, how has research to be coordinated and who needs to be involved. In other words, what are the characteristics of the response of the global research community on the challenge? In the present paper, we attempt to characterise, quantify and measure the response of academia to international public health emergencies in a comparative bibliometric study of multiple outbreaks. In addition, we provide a preliminary review of the global research effort regarding the defeat of the COVID-19 pandemic. From our analysis of six infectious disease outbreaks since 2000, including COVID-19, we find that academia always responded quickly to public health emergencies with a sharp increase in the number of publications immediately following the declaration of an outbreak by the WHO. In general, countries/regions place emphasis on epidemics in their own region, but Europe and North America are also concerned with outbreaks in other, developed and less developed areas through conducting intensive collaborative research with the core countries/regions of the outbreak, such as in the case of Ebola in Africa. Researches in the fields of virology, infectious diseases and immunology are the most active, and we identified two characteristic patterns in global science distinguishing research in Europe and America that is more focused on public health from that conducted in China and Japan with more emphasis on biomedical research and clinical pharmacy, respectively. Universities contribute slightly less than half to the global research output, and the vast majority of research funding originates from the public sector. Our findings on how academia responds to emergencies could be beneficial to decision-makers in research and health policy in creating and adjusting anti-epidemic/-pandemic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32836522/ doi: 10.1007/s11192-020-03531-4 id: cord-294831-pem059zk author: Zhang, Ling-Pu title: Focus on a 2019-novel coronavirus (SARS-CoV-2) date: 2020-06-11 words: 6173.0 sentences: 378.0 pages: flesch: 54.0 cache: ./cache/cord-294831-pem059zk.txt txt: ./txt/cord-294831-pem059zk.txt summary: A report of five patients in a family cluster who traveled to Wuhan and were infected with SARS-CoV-2 was the first report directly illustrating that the virus is capable of person-to-person transmission in hospital and family settings [23] . Xiao and colleagues showed that 53.42% of 73 hospitalized COVID-19 patients had SARS-CoV-2 RNA in stool specimens, and the duration time of positive stool results ranged from 1 to 12 days [27] . In a study published in The Lancet, 41 of 41 patients who were identified as positive for SARS-CoV-2 infection presented with pneumonia and abnormal chest computed tomography (CT) [6] . An article reported in Science shows that SARS-CoV-2 can replicate in the upper respiratory tract of ferrets, indicating that ferrets represent an ideal animal model for evaluating antiviral drugs or vaccine candidates against COVID-19 [64] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: A new coronavirus, severe acute respiratory syndrome coronavirus 2, was first discovered in Wuhan, China, in December 2019. As of April 7, 2020, the new coronavirus has spread quickly to 184 countries and aroused the attention of the entire world. No targeted drugs have yet been available for intervention and treatment of this virus. The sharing of academic information is crucial to risk assessment and control activities in outbreak countries. In this review, we summarize the epidemiological, genetic and clinical characteristics of the virus as well as laboratory testing and treatments to understand the nature of the virus. We hope this review will be helpful to prevent viral infections in outbreak countries and regions. url: https://doi.org/10.2217/fmb-2020-0063 doi: 10.2217/fmb-2020-0063 id: cord-298777-hit7rs6q author: Zhang, Linjie title: What we know so far about Coronavirus Disease 2019 in children: A meta‐analysis of 551 laboratory‐confirmed cases date: 2020-06-10 words: 3869.0 sentences: 250.0 pages: flesch: 58.0 cache: ./cache/cord-298777-hit7rs6q.txt txt: ./txt/cord-298777-hit7rs6q.txt summary: We conducted this systematic review and meta-analysis of currently available studies to summarize what we know so far about the epidemiological, clinical, radiological, and laboratory features, as well as therapeutic and prognostic aspects, of COVID-19 in children. To be included in this review, studies needed to meet the following criteria: (a) Study design: randomized trials, observational studies (cross-sectional, cohort and case-control), case series or case reports, and research letters; (b) Participants: children up to 18 years of age with laboratory-confirmed COVID-19; (c) Variables: epidemiological and demographic characteristics, clinical, radiological and laboratory findings, treatments, and prognosis. Thus, 46 articles [7] [8] [9] 14, 15, reporting 551 laboratory-confirmed cases of COVID-19 in children were included in the review (Figure 1 ). A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study abstract: AIM: To summarize what we know so far about coronavirus disease (COVID‐19) in children. METHOD: We searched PubMed, Scientific Electronic Library Online, and Latin American and Caribbean Center on Health Sciences Information from 1 January 2020 to 4 May 2020. We selected randomized trials, observational studies, case series or case reports, and research letters of children ages birth to 18 years with laboratory‐confirmed COVID‐19. We conducted random‐effects meta‐analyses to calculate the weighted mean prevalence and 95% confidence interval (CI) or the weighted average means and 95% CI. RESULT: Forty‐six articles reporting 551 cases of COVID‐19 in children (aged 1 day‐17.5 years) were included. Eighty‐seven percent (95% CI: 77%‐95%) of patients had household exposure to COVID‐19. The most common symptoms and signs were fever (53%, 95% CI: 45%‐61%), cough (39%, 95% CI: 30%‐47%), and sore throat/pharyngeal erythema (14%, 95% CI: 4%‐28%); however, 18% (95% CI: 11%‐27%) of cases were asymptomatic. The most common radiographic and computed tomography (CT) findings were patchy consolidations (33%, 95% CI: 23%‐43%) and ground glass opacities (28%, 95% CI: 18%‐39%), but 36% (95% CI: 28%‐45%) of patients had normal CT images. Antiviral agents were given to 74% of patients (95% CI: 52%‐92%). Six patients, all with major underlying medical conditions, needed invasive mechanical ventilation, and one of them died. CONCLUSION: Previously healthy children with COVID‐19 have mild symptoms. The diagnosis is generally suspected from history of household exposure to COVID‐19 case. Children with COVID‐19 and major underlying condition are more likely to have severe/critical disease and poor prognosis, even death. url: https://doi.org/10.1002/ppul.24869 doi: 10.1002/ppul.24869 id: cord-294931-a77g9rjo author: Zhang, Linqi title: Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals date: 2005-11-18 words: 4013.0 sentences: 193.0 pages: flesch: 52.0 cache: ./cache/cord-294931-a77g9rjo.txt txt: ./txt/cord-294931-a77g9rjo.txt summary: While there is no systematic evaluation of cytotoxic T-cell (CTL) activity in infected patients, there are some reports showing detection of binding antibodies to nucleocapsid (N) and spike (S) glycoprotein after about 2 weeks, remaining detectable for as long as 210 days after the onset of symptoms [Shi et al., 2003 Huang et al., 2004; Leung et al., 2004; Liu et al., 2004; Nie et al., 2004a; Temperton et al., 2005] . In this report, using both the ELISA-based and pseudotyped retrovirus-based neutralization systems, we characterized temporal changes in N protein-specific antibody and S glycoprotein-specific Nab responses in infected patients who have either recovered from or succumb to SARS-CoV infection. Since the 293/ACE2 cell line is the most susceptible to entry of the pseudotyped retrovirus bearing S glycoprotein, we chose this cell line for studies of neutralization antibody (Nab) activities of serum samples collected from SARS-CoV-infected patients. abstract: Most of the SARS‐CoV‐infected patients spontaneously recovered without clinical intervention while a small percentage succumbed to the disease. Here, we characterized temporal changes in N protein‐specific and S glycoprotein‐specific neutralizing antibody (Nab) responses in infected patients who have either recovered from or succumbed to SARS‐CoV infection. Recovered patients were found to have higher and sustainable levels of both N protein‐specific and S glycoprotein‐specific Nab responses, suggesting that antibody responses likely play an important role in determining the ultimate disease outcome of SARS‐CoV‐infected patients. J. Med. Virol. 78:1–8, 2006. © 2005 Wiley‐Liss, inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16299724/ doi: 10.1002/jmv.20499 id: cord-261075-wqtxhiy8 author: Zhang, Meng title: The nervous system——a new territory being explored of SARS-CoV-2 date: 2020-10-28 words: 3716.0 sentences: 216.0 pages: flesch: 41.0 cache: ./cache/cord-261075-wqtxhiy8.txt txt: ./txt/cord-261075-wqtxhiy8.txt summary: However, there is growing evidence that SARS-CoV-2 can result in a broad spectrum of neurologic diseases (6) (7) (8) (9) , which is not surprising, as neurological manifestations have been reported in other respiratory viral infections, including coronavirus, but the nervous system manifestations of COVID-19 are more common and disabling, raising the worldwide concerns about its potential long-term complications to humans (10, 11) . In particular, we focused on its neurological manifestations and specific pathogenesis, as well as its comparison with other viral respiratory infections.Finally, we further summarized the significance of the neuroinvasion and the follow-up issues that need to be paid attention to by scientists, so as to help neurologists understand the influence of SARS-CoV-2 on nervous system better and promote the accurate diagnosis and efficient treatment of COVID-19. abstract: In December 2019, COVID-19 outbroke in Wuhan, then sweeping the mainland of China and the whole world rapidly. On March 4, Beijing Ditan Hospital confirmed the existence of SARS-CoV-2 in the cerebrospinal fluid by gene sequencing, indicating the neurotropic involvement of SARS-CoV-2. Meanwhile, neurological manifestations in the central nervous system, peripheral nervous system and skeletal muscular were also observed, indicating the potential neuroinvasion of SARS-CoV-2. In particular, we focused on its neurological manifestations and specific pathogenesis, as well as its comparison with other viral respiratory infections.Finally, we further summarized the significance of the neuroinvasion and the follow-up issues that need to be paid attention to by scientists, so as to help neurologists understand the influence of SARS-CoV-2 on nervous system better and promote the accurate diagnosis and efficient treatment of COVID-19. url: https://api.elsevier.com/content/article/pii/S0967586820316155 doi: 10.1016/j.jocn.2020.10.056 id: cord-317085-qc8bfb9g author: Zhang, Nan title: Risk Factors for Poor Outcomes of Diabetes Patients With COVID-19: A Single-Center, Retrospective Study in Early Outbreak in China date: 2020-09-24 words: 4754.0 sentences: 241.0 pages: flesch: 53.0 cache: ./cache/cord-317085-qc8bfb9g.txt txt: ./txt/cord-317085-qc8bfb9g.txt summary: In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In the present study, the clinical characteristics of 52 diabetic patients with COVID-19 from a designated hospital in Wuhan, China are described, and the risk factors associated with severe clinical events which were defined as the patients'' admission to ICU, the use of mechanical ventilation, or death are investigated. abstract: Background: Diabetes has been found to increase severity and mortality under the current pandemic of coronavirus disease of 2019 (COVID-19). Up to date, the clinical characteristics of diabetes patients with COVID-19 and the risk factors for poor clinical outcomes are not clearly understood. Methods: The study was retrospectively carried out on enrolled diabetes patients with laboratory confirmed COVID-19 infection from a designated medical center for COVID-19 from January 25th, 2020 to February 14th, 2020 in Wuhan, China. The medical record was collected and reviewed. Univariate and multivariate analyses were performed to assess the risk factors associated with the severe events which were defined as a composite endpoint of admission to intensive care unit, the use of mechanical ventilation, or death. Results: A total of 52 diabetes patients with COVID-19 were finally included in the study. 21 (40.4%) patients had developed severe events in 27.50 (IQR 12.25–35.75) days follow-up, 15 (28.8%) patients experienced life-threatening complications and 8 patients died with a recorded mortality rate of 15.4%. Only 13 patients (41.9%) were in optimal glycemic control with HbA1c value of <7.0%. In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. Mild higher level of cardiac troponin I (cTNI) (32.0 pg/ml; IQR 16.80–55.00) and D-dimer (1.70 μg/L, IQR 0.70–2.40) were found in diabetes patients with severe events as compared to the non-severe patients (cTNI:20.00 pg/ml, IQR5.38–30.00, p = 0.019; D-dimer: 0.70 μg/L, IQR 0.30–2.40, p = 0.037). After adjusting age and sex, increased level of cTNI was found to significantly associate with the incidence of severe events (HR: 1.007; 95% CI: 1.000–1.013; p = 0.048), Furthermore, using of α-glucosidase inhibitors was found to be the potential protectant for severe events (HR: 0.227; 95% CI: 0.057–0.904; p = 0.035). Conclusion: Diabetes patients with COVID-19 showed poor clinical outcomes. Vigorous monitoring of cTNI should be recommended for the diabetes patients with COVID-19. Usage of α-glucosidase inhibitors could be a potential protectant for the diabetes patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33071977/ doi: 10.3389/fendo.2020.571037 id: cord-338152-e8e3lv79 author: Zhang, Peilin title: Detection of SARS-CoV-2 in placentas with pathology and vertical transmission date: 2020-08-03 words: 610.0 sentences: 50.0 pages: flesch: 55.0 cache: ./cache/cord-338152-e8e3lv79.txt txt: ./txt/cord-338152-e8e3lv79.txt summary: We examined 364 consecutive placentas from the mothers tested in our facilities since the universal testing policy was adopted in March 2020 including 74 positive and 290 negative for SARS-CoV2 by nasopharyngeal swab PCR method as previously described [1] . One positive placenta for SARS-CoV2 by ISH was delivered by C-section at 35 weeks 6 days due to placental previa 4 associated with placental infarcts, and the newborn baby was tested positive by swab PCR at 24 hours, 48 hours and 7 days. The other positive placenta was from a mother with 40 week gestation associated with no significant clinical and pathological features, and the baby was tested negative for SARS-CoV2 by swab PCR method within the first 24 hours. The current study showed that SARS-COV2 viral particles are uncommon in placentas from PCR-positive mothers at late gestation. Neonatal testing for SARS-CoV2 by swab PCR also showed rare positive cases from positive mothers. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32838273/ doi: 10.1016/j.ajogmf.2020.100197 id: cord-268760-31i0mpvn author: Zhang, Qian title: Anosmia and Ageusia as the Only Indicators of Coronavirus Disease 2019 (COVID-19) date: 2020-05-01 words: 2109.0 sentences: 125.0 pages: flesch: 54.0 cache: ./cache/cord-268760-31i0mpvn.txt txt: ./txt/cord-268760-31i0mpvn.txt summary: There is currently a lack of published case reports describing COVID-19 patients with the sole symptoms of anosmia and ageusia in the United States of America. This case report details a 60year-old woman with the chief complaint of right-sided headache along with anosmia and ageusia but was eventually found to be SARS-COV-2 positive. The most common COVID-19 symptoms include fever (43.8% on initial presentation and 88.7% during hospitalization), cough (67.8%), nasal congestion (4.8%), nausea or vomiting (5.0%), and diarrhea (3.8%) based on a research study of 1099 patients from China. Our patient had a very low clinical suspicion of COVID-19 infection, as she was afebrile along with no respiratory symptoms despite having anosmia and ageusia in the setting of headache caused by trigeminal neuralgia. Awareness of a possible COVID-19 infection should be raised in patients with the sole presentation of anosmia and ageusia despite the lack of published case reports or research findings on its exact mechanisms of action. abstract: The patient is a 60-year-old woman with a history of vertigo and seasonal allergies who presented to the hospital with the chief complaint of headache. Radiological findings were negative for intracranial abnormalities. The headache was due to trigeminal neuralgia. She had concurrent complaints of anosmia and ageusia without fever, respiratory symptoms, or obvious risk factors. However, it was determined to test the patient for coronavirus disease 2019 (COVID-19) infection despite extremely low clinical suspicion. Unfortunately, she was found to be COVID-19 positive after she was discharged from the hospital while she remained asymptomatic. There is currently a lack of published case reports describing COVID-19 patients with the sole symptoms of anosmia and ageusia in the United States of America. url: https://www.ncbi.nlm.nih.gov/pubmed/32494532/ doi: 10.7759/cureus.7918 id: cord-254968-czrgzyr3 author: Zhang, Qiang title: A serological survey of SARS-CoV-2 in cat in Wuhan date: 2020-09-17 words: 3148.0 sentences: 180.0 pages: flesch: 56.0 cache: ./cache/cord-254968-czrgzyr3.txt txt: ./txt/cord-254968-czrgzyr3.txt summary: Here, we investigated the infection of SARS-CoV-2 in cats during COVID-19 outbreak in Wuhan by serological detection methods. Our data demonstrated that SARS-CoV-2 has infected cats in Wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of COVID-19. Here, we investigated the serological prevalence of SARS-CoV-2 in cats by an indirect ELISA and virus neutralization tests (VNT), and monitored the serum antibody dynamics of cats infected SARS-CoV-2, providing a basis for further understanding the infection of SARS-CoV-2 in cats. In this study, we detected the presence of SARS-CoV-2 antibodies in cats in Wuhan during the COVID-19 outbreak with ELISA, VNT and western blot. Virus neutralization test and Western blot assay of cat serum samples for SARS-CoV-2 (A) Cat#14, Cat#15 and Cat#4 sera were 3-fold serially diluted and mixed with SARS-CoV-2; after incubated at 37°C for 1 h, the mixture was used to infect Vero E6 cells, and replaced with semi-solid media 1 h later. abstract: COVID-19 is a new respiratory illness caused by SARS-CoV-2, and has constituted a global public health emergency. Cat is susceptible to SARS-CoV-2. However, the prevalence of SARS-CoV-2 in cats remains largely unknown. Here, we investigated the infection of SARS-CoV-2 in cats during COVID-19 outbreak in Wuhan by serological detection methods. A cohort of serum samples were collected from cats in Wuhan, including 102 sampled after COVID-19 outbreak, and 39 prior to the outbreak. Fifteen sera collected after the outbreak were positive for the receptor binding domain (RBD) of SARS-CoV-2 by indirect enzyme linked immunosorbent assay (ELISA). Among them, 11 had SARS-CoV-2 neutralizing antibodies with a titer ranging from 1/20 to 1/1080. No serological cross-reactivity was detected between SARS-CoV-2 and type I or II feline infectious peritonitis virus (FIPV). In addition, we continuously monitored serum antibody dynamics of two positive cats every 10 days over 130 days. Their serum antibodies reached the peak at 10 days after first sampling, and declined to the limit of detection within 110 days. Our data demonstrated that SARS-CoV-2 has infected cats in Wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of COVID-19. url: https://doi.org/10.1080/22221751.2020.1817796 doi: 10.1080/22221751.2020.1817796 id: cord-294199-o8w35pdy author: Zhang, Qiangzhe title: Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity date: 2020-06-17 words: 2222.0 sentences: 132.0 pages: flesch: 48.0 cache: ./cache/cord-294199-o8w35pdy.txt txt: ./txt/cord-294199-o8w35pdy.txt summary: Inspired by the fact that the infectivity of SARS-CoV-2 relies on its binding with the protein receptors, either known or unknown, on the target cells, we create cellular nanosponges as a medical countermeasure to the coronavirus. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) and CD147 expressed on the host cells, such as human alveolar epithelial type II cells, as receptors for cellular entry. To further verify that the inhibition was indeed due to epithelial cell or macrophage membrane coating, control nanosponges made from membranes of red blood cells (denoted "RBC-NS") were also tested in parallel for viral inhibition but were not effective in neutralizing SARS-CoV-2 infection of Vero E6 cells ( Figure 3C ). In principle, as long as the target of the virus remains the identified host cell, the nanosponges will be able to neutralize the infection, providing a broad-acting countermeasure resistant to mutations and protection against this and other emerging coronaviruses. abstract: [Image: see text] We report cellular nanosponges as an effective medical countermeasure to the SARS-CoV-2 virus. Two types of cellular nanosponges are made of the plasma membranes derived from human lung epithelial type II cells or human macrophages. These nanosponges display the same protein receptors, both identified and unidentified, required by SARS-CoV-2 for cellular entry. It is shown that, following incubation with the nanosponges, SARS-CoV-2 is neutralized and unable to infect cells. Crucially, the nanosponge platform is agnostic to viral mutations and potentially viral species, as well. As long as the target of the virus remains the identified host cell, the nanosponges will be able to neutralize the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32551679/ doi: 10.1021/acs.nanolett.0c02278 id: cord-356154-ifb3qiz7 author: Zhang, Rong title: A Study of Two Cases Co-Infected with SARS-CoV-2 and Human Immunodeficiency Virus date: 2020-09-07 words: 1066.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-356154-ifb3qiz7.txt txt: ./txt/cord-356154-ifb3qiz7.txt summary: CT scan results in early February indicated lesions in bilateral lungs (Supplementary Table S1 ), but the result of the SARS-CoV-2 nucleic acid test was negative. However, the patient''s condition deteriorated again on February 20, and the nucleic acid test results were single positive for COVID-19 SARS-CoV-2. Notes: ND, no data; ?, positive; -, negative We assumed that HIV infection had damaged their immune systems; this could also explain why the patient tested negative for SARS-CoV-2 antibodies in the late stages of treatment when the disease became worse. In general, the blocking of the IL-6 receptor with tocilizumab has a particular effect on the treatment of COVID-19 patients with severe disease, but it may have little effect on patients with Fig. 1 The clinical courses of two cases co-infected with SARS-CoV-2 and HIV. COVID-19 patients with immunodeficiency disease may cause more severe illness and poor treatment response due to the destruction of the immune system. abstract: nan url: https://doi.org/10.1007/s12250-020-00280-9 doi: 10.1007/s12250-020-00280-9 id: cord-321155-dty18esg author: Zhang, Rongxin title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 words: 4927.0 sentences: 331.0 pages: flesch: 57.0 cache: ./cache/cord-321155-dty18esg.txt txt: ./txt/cord-321155-dty18esg.txt summary: We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. abstract: The Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery. url: https://doi.org/10.1101/2020.06.05.135749 doi: 10.1101/2020.06.05.135749 id: cord-280961-fka8c69p author: Zhang, Rui title: CT features of SARS-CoV-2 pneumonia according to clinical presentation: a retrospective analysis of 120 consecutive patients from Wuhan city date: 2020-04-11 words: 3651.0 sentences: 211.0 pages: flesch: 50.0 cache: ./cache/cord-280961-fka8c69p.txt txt: ./txt/cord-280961-fka8c69p.txt summary: METHODS: This was a retrospective analysis of the clinical and thoracic CT features of 120 consecutive patients with confirmed SARS-CoV-2 pneumonia admitted to a tertiary university hospital between January 10 and February 10, 2020, in Wuhan city, China. (c) Unenhanced axial CT images of a 27-year-old male doctor with a history of exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), nonproductive cough, dyspnea, and myalgia (c1) who progressed to a severe case requiring oxygen supplementation (c2). (d) Unenhanced axial CT images of a 52-year-old male doctor with asthma and exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), non-productive cough, dyspnea, and myalgia who rapidly progressed to a severe form requiring mechanical ventilation. In this study, we reported the clinical characteristics and chest CT findings at presentation for all types of SARS-CoV-2 pneumonia severity. abstract: OBJECTIVES: To characterize the chest computed tomography (CT) findings of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) according to clinical severity. We compared the CT features of common cases and severe cases, symptomatic patients and asymptomatic patients, and febrile and afebrile patients. METHODS: This was a retrospective analysis of the clinical and thoracic CT features of 120 consecutive patients with confirmed SARS-CoV-2 pneumonia admitted to a tertiary university hospital between January 10 and February 10, 2020, in Wuhan city, China. RESULTS: On admission, the patients generally complained of fever, cough, shortness of breath, and myalgia or fatigue, with diarrhea often present in severe cases. Severe patients were 20 years older on average and had comorbidities and an elevated lactate dehydrogenase (LDH) level. There were no differences in the CT findings between asymptomatic and symptomatic common type patients or between afebrile and febrile patients, defined according to Chinese National Health Commission guidelines. CONCLUSIONS: The clinical and CT features at admission may enable clinicians to promptly evaluate the prognosis of patients with SARS-CoV-2 pneumonia. Clinicians should be aware that clinically silent cases may present with CT features similar to those of symptomatic common patients. KEY POINTS: • The clinical features and predominant patterns of abnormalities on CT for asymptomatic, typic common, and severe cases were summarized. These findings may help clinicians to identify severe patients quickly at admission. • Clinicians should be cautious that CT findings of afebrile/asymptomatic patients are not better than the findings of other types of patients. These patients should also be quarantined. • The use of chest CT as the main screening method in epidemic areas is recommended. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00330-020-06854-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00330-020-06854-1 doi: 10.1007/s00330-020-06854-1 id: cord-320681-b3ui95vx author: Zhang, Rui title: COVID-19: Melatonin as a potential adjuvant treatment date: 2020-06-01 words: 4138.0 sentences: 219.0 pages: flesch: 39.0 cache: ./cache/cord-320681-b3ui95vx.txt txt: ./txt/cord-320681-b3ui95vx.txt summary: Based on clinical features, pathology, the pathogenesis of acute respiratory disorder induced by either highly homogenous coronaviruses or other pathogens, the evidence suggests that excessive inflammation, oxidation, and an exaggerated immune response very likely contribute to COVID-19 pathology. Herein, we review the evidence indicating that melatonin will have supportive adjuvant utility in treating COVID-19 induced pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In SARS-CoV and MERS-CoV infected animal model, marked inflammatory and immune responses may activate a "cytokine storm", and apoptosis of epithelial cells and endothelial cells; subsequently, vascular leakage, abnormal T cell and macrophages responses ensue and induce ALI/ARDS or even death [13] . The amplification of the inflammatory response would promote cellular apoptosis or We postulated that lungs infected by SARS-CoV-2, and a suppressed immune response, elevated inflammation and excessive oxidation stress proceed unabated, this results in the activation of the cytokine storm. abstract: Abstract This article summarizes the likely benefits of melatonin in the attenuation of COVID-19 based on its putative pathogenesis. The recent outbreak of COVID-19 has become a pandemic with tens of thousands of infected patients. Based on clinical features, pathology, the pathogenesis of acute respiratory disorder induced by either highly homogenous coronaviruses or other pathogens, the evidence suggests that excessive inflammation, oxidation, and an exaggerated immune response very likely contribute to COVID-19 pathology. This leads to a cytokine storm and subsequent progression to acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) and often death. Melatonin, a well-known anti-inflammatory and anti-oxidative molecule, is protective against ALI/ARDS caused by viral and other pathogens. Melatonin is effective in critical care patients by reducing vessel permeability, anxiety, sedation use, and improving sleeping quality, which might also be beneficial for better clinical outcomes for COVID-19 patients. Notably, melatonin has a high safety profile. There is significant data showing that melatonin limits virus-related diseases and would also likely be beneficial in COVID-19 patients. Additional experiments and clinical studies are required to confirm this speculation. url: https://www.ncbi.nlm.nih.gov/pubmed/32217117/ doi: 10.1016/j.lfs.2020.117583 id: cord-298426-hhly45md author: Zhang, Shan-Yan title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China date: 2020-07-08 words: 3726.0 sentences: 207.0 pages: flesch: 52.0 cache: ./cache/cord-298426-hhly45md.txt txt: ./txt/cord-298426-hhly45md.txt summary: title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China CONCLUSIONS: Clinicians should pay close attention to these features in patients with COVID-19 including older age, male, fever, cough, hemoptysis, gastrointestinal symptoms and hypertension to identify the severity of illness as early as possible. Hence, the aim of our study is to summarize the epidemiologic and clinical characteristics, laboratory and radiograph findings, treatments, and outcomes of different subtypes of patients with COVID-19 in Zhejiang Province. We conducted a retrospective study investigating on the epidemiological, clinical, laboratory, radiograph, treatments and outcomes characteristics of confirmed cases of COVID-19 in Zhejiang Province from 17 January to 12 February 2020. Several risk factors for the severity of illness in patients with COVID-19 were identified in our study including male, fever, cough, hemoptysis, gastrointestinal symptoms, hypertension, and higher age-grading. abstract: BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) is now becoming an enormous threat to public health. The clinical spectrum of COVID-19 is extensive, of which critical cases are with rapid disease progression and high mortality. The aim of our study is to summarize the characteristics of different subtypes and explore risk factors of illness severity for early identification and prompt treatment. METHODS: In this retrospective study, we collected data of patients confirmed COVID-19 in Zhejiang Province from 17 January to 12 February 2020. According to the definition of clinical classification, we divided confirmed cases into four types, and summarize epidemiological and clinical characteristics, laboratory and radiograph findings, treatments, and outcomes, respectively. Moreover, we used univariate and multivariate ordinal logistic regression models to explore risk factors for the severity of illness in patients with COVID-19. RESULTS: A total of 788 patients were enrolled in our study, of whom 52 cases (6.6%) were mild type, 658 cases (83.5%) were common type, 61 cases (7.2%) were severe type, and 17 cases (2.2%) were critical type. Multivariate ordinal logistic regression demonstrated increasing odds of the severity of illness in patients with COVID-19 associated with male (odds ratio [OR] = 1.7, 95% confidence interval [CI]: 1.2–2.6 P = 0.008), fever (OR = 3.6, 95% CI: 2.1–6.3, P < 0.001), cough (OR = 1.7, 95% CI: 1.0–2.9, P = 0.041), hemoptysis (OR = 3.4, 95% CI: 1.1–10.3, P = 0.032), gastrointestinal symptoms (OR = 1.9, 95% CI: 1.0–3.5, P = 0.047), hypertension (OR = 2.6, 95% CI: 1.2–5.6, P = 0.013). With the increase of age-grading, risk for the severity of illness was gradually higher (≤ 18 years [OR = 1.0], 19–40 years [OR = 12.7, 95% CI: 4.5–36.0, P < 0.001], 41–65 years [OR = 14.8, 95% CI: 5.2–42.1, P < 0.001], ≥ 66 years [OR = 56.5, 95% CI: 17.1–186.5, P < 0.001]). CONCLUSIONS: Clinicians should pay close attention to these features in patients with COVID-19 including older age, male, fever, cough, hemoptysis, gastrointestinal symptoms and hypertension to identify the severity of illness as early as possible. url: https://www.ncbi.nlm.nih.gov/pubmed/32641121/ doi: 10.1186/s40249-020-00710-6 id: cord-302166-tah3jdw0 author: Zhang, Shen-Ying title: Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity? date: 2020-06-18 words: 1601.0 sentences: 88.0 pages: flesch: 41.0 cache: ./cache/cord-302166-tah3jdw0.txt txt: ./txt/cord-302166-tah3jdw0.txt summary: We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. Studies since 1996 have identified a number of monogenic inborn errors of immunity (IEIs) underlying life-threatening infectious diseases, including specific viral diseases, in previously healthy patients 1,3-6 . The search for monogenic IEIs conferring predisposition to severe COVID-19 in previously healthy children and young or even middle-aged adults should therefore involve the genome-wide, agnostic testing of genetic hypotheses (see also COVID Human Genetic Effort) 10 . The discovery of monogenic IEIs to SARS-CoV-2 should help unravel the mechanistic basis of the immunopathogenesis of severe COVID-19 in young, previously healthy individuals. A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection abstract: Severe COVID-19 is rare in previously healthy individuals who are less than 50 years of age, affecting probably no more than 1 in 1,000 such infected individuals. We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. url: https://doi.org/10.1038/s41577-020-0373-7 doi: 10.1038/s41577-020-0373-7 id: cord-030535-8o7rzb98 author: Zhang, Sheng title: Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists date: 2020-08-12 words: 2718.0 sentences: 178.0 pages: flesch: 59.0 cache: ./cache/cord-030535-8o7rzb98.txt txt: ./txt/cord-030535-8o7rzb98.txt summary: The tutorial begins with the X-ray crystallographic structure of the main protease (Mpro) of the SARS coronavirus (SARS-CoV) bound to a peptide substrate and then uses the UCSF Chimera software to modify the substrate to create a cyclic peptide inhibitor within the Mpro active site. In this tutorial, we will use the X-ray crystallographic structure of the homologous SARS-CoV M pro bound to a protein substrate to recapitulate the design of a cyclic peptide inhibitor of the SARS-CoV-2 M pro . 8 We will first use the molecular modeling software UCSF Chimera to visualize the X-ray crystallographic structure of the SARS-CoV M pro bound to the protein substrate. In structure-based drug design, we would typically now synthesize the cyclic peptide inhibitor and evaluate its activity experimentally through studying its ability to block the cleavage of a fluorogenic peptide substrate by SARS-CoV-2 M pro . abstract: This paper describes the structure-based design of a preliminary drug candidate against COVID-19 using free software and publicly available X-ray crystallographic structures. The goal of this tutorial is to disseminate skills in structure-based drug design and to allow others to unleash their own creativity to design new drugs to fight the current pandemic. The tutorial begins with the X-ray crystallographic structure of the main protease (Mpro) of the SARS coronavirus (SARS-CoV) bound to a peptide substrate and then uses the UCSF Chimera software to modify the substrate to create a cyclic peptide inhibitor within the Mpro active site. Finally, the tutorial uses the molecular docking software AutoDock Vina to show the interaction of the cyclic peptide inhibitor with both SARS-CoV Mpro and the highly homologous SARS-CoV-2 Mpro. The supporting information (supplementary material) provides an illustrated step-by-step guide for the inhibitor design, to help readers design their own drug candidates for COVID-19 and the coronaviruses that will cause future pandemics. An accompanying preprint in bioRxiv [https://doi.org/10.1101/2020.08.03.234872] describes the synthesis of the cyclic peptide and the experimental validation as an inhibitor of SARS-CoV-2 Mpro. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430054/ doi: 10.26434/chemrxiv.12791954 id: cord-294410-iy57tjx5 author: Zhang, Shengnan title: (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain date: 2010-12-23 words: 1013.0 sentences: 60.0 pages: flesch: 65.0 cache: ./cache/cord-294410-iy57tjx5.txt txt: ./txt/cord-294410-iy57tjx5.txt summary: title: (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain The main protease (M(pro)) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. Here, we reported the NMR assignments of the SARS-CoV M(pro) N-terminal domain alone, which are essential for its solution structure determination. The backbone resonance chemical shift assignments were based on 2D 1 H-15 N HSQC, 3D HNCA, HN(CO)CA, HNCACB, CBCA(CO)HN, HNCO, HN(CA)CO and HBHA(CO)NH NMR spectra. The side chain resonance chemical shift assignments were based on 3D HCCH-COSY, HCCH-TOCSY, (H)CCH-COSY, and (H)CCH-TOCSY NMR experiments data. Without its n-finger, SARS-CoV main protease can form a novel dimer through its C-terminal domain C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer abstract: The main protease (M(pro)) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. SARS-CoV M(pro) is composed of a catalytic N-terminal domain and an α-helical C-terminal domain linked by a long loop. Even though the N-terminal domain of SARS-CoV M(pro) adopts a similar chymotrypsin-like fold as that of piconavirus 3C protease, the extra C-terminal domain is required for SARS-CoV M(pro) to be enzymatically active. Here, we reported the NMR assignments of the SARS-CoV M(pro) N-terminal domain alone, which are essential for its solution structure determination. url: https://www.ncbi.nlm.nih.gov/pubmed/21181312/ doi: 10.1007/s12104-010-9287-9 id: cord-294392-a8s66g96 author: Zhang, Shuai title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date: 2020-09-07 words: 985.0 sentences: 65.0 pages: flesch: 46.0 cache: ./cache/cord-294392-a8s66g96.txt txt: ./txt/cord-294392-a8s66g96.txt summary: title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. 12 Two studies showed that tracheal intubation procedure was related to increased risk of 120 transmission SARS-CoV-1 and SARS-CoV-2 to HCWs. 13,14 Face mask and eye protection especially 121 N95 respirators were most consistently with reduced COVID-19 infection among HCWs. 14,15 Face 122 mask was also reported to be associated with asymptomatic SARS-CoV-2 infection based on several 123 uncontrolled reports. The univariable logistic regression analysis showed worked in high-risk departments, 169 hand washing consistently and consistent use of isolation gown, N95 respirators, gloves, hair cover, 170 and eye protection were associated with an increased likelihood of asymptomatic infection (Table S1) . abstract: OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. METHODS: All HCWs in Wuhan Union Hospital and Wuhan Red Cross Hospital with either positive SARS-CoV-2 nucleic acid or antibody test before April 18, 2020 were included. Exposure, epidemiologic, demographic information were retrospectively collected by a structured questionnaire. Medical records were also reviewed for clinical characteristics and CT images in HCWs. RESULTS: As of April 18, 2020, a total of 424 HCWs were identified. Among them, 276 (65.1%) were symptomatic and 148 (34.9%) were asymptomatic. 55 (19.9%) families of the symptomatic HCWs and 16 (10.8%) families of the asymptomatic HCWs were infected with SARS-CoV-2. HCWs with infected family members tend to be symptomatic cases (Odds ratio [OR], 2.053 [95% confidence interval (CI), 1.130-3.730]; P=0.018). Multivariable logistic regression analysis exhibited that performing tracheal intubation or extubation (OR, 4.057 [95% CI, 1.183-13.909]; P=0.026) was associated with an increased likelihood of symptomatic SARS-CoV-2 infection, while consistent use of N95 respirators (OR, 0.369 [95% CI, 0.201-0.680]; P=0.001) and eye protection (OR, 0.217 [95% CI, 0.116-0.404]; P<0.001) were associated with an increased likelihood of asymptomatic SARS-CoV-2 infection. CONCLUSIONS: Asymptomatic SARS-CoV-2 infection in HCWs occupies a considerable proportion during the pandemic of COVID-19. Those who have performed tracheal intubation or extubation were most likely to develop related symptoms, while those taking aggressive measures including consistent use of N95 masks, and eye protection tended to be asymptomatic cases. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305218?v=s5 doi: 10.1016/j.cmi.2020.08.038 id: cord-332185-a96r1k7a author: Zhang, Shuyuan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 words: 1228.0 sentences: 103.0 pages: flesch: 63.0 cache: ./cache/cord-332185-a96r1k7a.txt txt: ./txt/cord-332185-a96r1k7a.txt summary: title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. Cryo-electron microscopy structures of the SARS-CoV spike 464 glycoprotein reveal a prerequisite conformational state for receptor binding Cryo-EM structure of the SARS 467 coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Cryo-EM structures of MERS-CoV and SARS-CoV spike 495 glycoproteins reveal the dynamic receptor binding domains abstract: In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the “down” conformation, indicating they are more prone to adopt this receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. These results collectively indicate that strong RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection. url: https://doi.org/10.1101/2020.09.21.307439 doi: 10.1101/2020.09.21.307439 id: cord-297236-wnuvofwr author: Zhang, Si title: SARS-CoV-2 binds platelet ACE2 to enhance thrombosis in COVID-19 date: 2020-09-04 words: 10404.0 sentences: 646.0 pages: flesch: 50.0 cache: ./cache/cord-297236-wnuvofwr.txt txt: ./txt/cord-297236-wnuvofwr.txt summary: SARS-CoV-2 and its Spike protein directly enhanced platelet activation such as platelet aggregation, PAC-1 binding, CD62P expression, α granule secretion, dense granule release, platelet spreading, and clot retraction in vitro, and thereby Spike protein enhanced thrombosis formation in wild-type mice transfused with hACE2 transgenic platelets, but this was not observed in animals transfused with wild-type platelets in vivo. However, similar to the results from the SARS-CoV-2 virus experiments, we were able to demonstrate that the Spike protein dose-dependently enhanced platelet aggregation and ATP release (Additional file 1: Online Figure 6 ). In addition, the Spike protein potentiated platelet aggregation and ATP release in response to agonists in vitro and enhanced thrombosis formation in vivo on hACE2 transgenic mice, while it had no effect on wild-type mice ( Fig. 6c and Additional file 1: Online Figure 8 ). abstract: BACKGROUND: Critically ill patients diagnosed with COVID-19 may develop a pro-thrombotic state that places them at a dramatically increased lethal risk. Although platelet activation is critical for thrombosis and is responsible for the thrombotic events and cardiovascular complications, the role of platelets in the pathogenesis of COVID-19 remains unclear. METHODS: Using platelets from healthy volunteers, non-COVID-19 and COVID-19 patients, as well as wild-type and hACE2 transgenic mice, we evaluated the changes in platelet and coagulation parameters in COVID-19 patients. We investigated ACE2 expression and direct effect of SARS-CoV-2 virus on platelets by RT-PCR, flow cytometry, Western blot, immunofluorescence, and platelet functional studies in vitro, FeCl(3)-induced thrombus formation in vivo, and thrombus formation under flow conditions ex vivo. RESULTS: We demonstrated that COVID-19 patients present with increased mean platelet volume (MPV) and platelet hyperactivity, which correlated with a decrease in overall platelet count. Detectable SARS-CoV-2 RNA in the blood stream was associated with platelet hyperactivity in critically ill patients. Platelets expressed ACE2, a host cell receptor for SARS-CoV-2, and TMPRSS2, a serine protease for Spike protein priming. SARS-CoV-2 and its Spike protein directly enhanced platelet activation such as platelet aggregation, PAC-1 binding, CD62P expression, α granule secretion, dense granule release, platelet spreading, and clot retraction in vitro, and thereby Spike protein enhanced thrombosis formation in wild-type mice transfused with hACE2 transgenic platelets, but this was not observed in animals transfused with wild-type platelets in vivo. Further, we provided evidence suggesting that the MAPK pathway, downstream of ACE2, mediates the potentiating role of SARS-CoV-2 on platelet activation, and that platelet ACE2 expression decreases following SARS-COV-2 stimulation. SARS-CoV-2 and its Spike protein directly stimulated platelets to facilitate the release of coagulation factors, the secretion of inflammatory factors, and the formation of leukocyte–platelet aggregates. Recombinant human ACE2 protein and anti-Spike monoclonal antibody could inhibit SARS-CoV-2 Spike protein-induced platelet activation. CONCLUSIONS: Our findings uncovered a novel function of SARS-CoV-2 on platelet activation via binding of Spike to ACE2. SARS-CoV-2-induced platelet activation may participate in thrombus formation and inflammatory responses in COVID-19 patients. url: https://doi.org/10.1186/s13045-020-00954-7 doi: 10.1186/s13045-020-00954-7 id: cord-327499-4aps0kvp author: Zhang, Wei title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes date: 2020-02-17 words: 1962.0 sentences: 131.0 pages: flesch: 62.0 cache: ./cache/cord-327499-4aps0kvp.txt txt: ./txt/cord-327499-4aps0kvp.txt summary: It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Human samples, including oral swabs, anal swabs and blood samples were collected by Wuhan pulmonary hospital with the consent from all patients and approved by the ethics committee of the designated hospital for emerging infectious diseases. We conducted a molecular investigation to patients in Wuhan pulmonary hospital, who were detected as oral swabs positive for 2019-nCoV upon admission. We collected blood, oral swabs and anal swabs for 2019-nCoV qPCR test using previously established method [5] . We detected the virus in oral swabs, anal swabs and blood, thus infected patients can potentially shed this pathogen through respiratory, fecal-oral or body fluid routes. Above all, we strongly suggest using viral IgM and IgG serological test to confirm an infection, considering the unreliable results from oral swabs detection. abstract: In December 2019, a novel coronavirus (2019-nCoV) caused an outbreak in Wuhan, China, and soon spread to other parts of the world. It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Likewise, patient will be released upon two times of negative detection from oral swabs. However, many coronaviruses can also be transmitted through oral–fecal route by infecting intestines. Whether 2019-nCoV infected patients also carry virus in other organs like intestine need to be tested. We conducted investigation on patients in a local hospital who were infected with this virus. We found the presence of 2019-nCoV in anal swabs and blood as well, and more anal swab positives than oral swab positives in a later stage of infection, suggesting shedding and thereby transmitted through oral–fecal route. We also showed serology test can improve detection positive rate thus should be used in future epidemiology. Our report provides a cautionary warning that 2019-nCoV may be shed through multiple routes. url: https://doi.org/10.1080/22221751.2020.1729071 doi: 10.1080/22221751.2020.1729071 id: cord-316126-j51dik7f author: Zhang, X. Sophie title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles date: 2020-10-28 words: 12434.0 sentences: 576.0 pages: flesch: 42.0 cache: ./cache/cord-316126-j51dik7f.txt txt: ./txt/cord-316126-j51dik7f.txt summary: title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles Since the beginning of the COVID-19 pandemic, there has been intense debate over SARS-CoV-2''s mode of transmission and appropriate personal protective equipment for health care workers in low-risk settings. This review attempts to summarize current cumulative data on SARS-CoV-2''s modes of transmission and identify gaps in research while offering preliminary answers to the question on everyone''s mind: is the airborne route significant and should we modify our COVID-19 PPE recommendations for frontline workers in low-risk settings? Given that substantial disagreement persists on the importance of natural aerosol generation by COVID-19 patients, and consequently, the necessary level of respiratory protection in non-AGP contexts, our review will focus on transmission and PPE in low-risk health care settings. abstract: Since the beginning of the COVID-19 pandemic, there has been intense debate over SARS-CoV-2’s mode of transmission and appropriate personal protective equipment for health care workers in low-risk settings. The objective of this review is to identify and appraise the available evidence (clinical trials and laboratory studies on masks and respirators, epidemiological studies, and air sampling studies), clarify key concepts and necessary conditions for airborne transmission, and shed light on knowledge gaps in the field. We find that, except for aerosol-generating procedures, the overall data in support of airborne transmission—taken in its traditional definition (long-distance and respirable aerosols)—are weak, based predominantly on indirect and experimental rather than clinical or epidemiological evidence. Consequently, we propose a revised and broader definition of “airborne,” going beyond the current droplet and aerosol dichotomy and involving short-range inhalable particles, supported by data targeting the nose as the main viral receptor site. This new model better explains clinical observations, especially in the context of close and prolonged contacts between health care workers and patients, and reconciles seemingly contradictory data in the SARS-CoV-2 literature. The model also carries important implications for personal protective equipment and environmental controls, such as ventilation, in health care settings. However, further studies, especially clinical trials, are needed to complete the picture. url: https://doi.org/10.1128/cmr.00184-20 doi: 10.1128/cmr.00184-20 id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 words: 3023.0 sentences: 152.0 pages: flesch: 52.0 cache: ./cache/cord-316525-uadfehr6.txt txt: ./txt/cord-316525-uadfehr6.txt summary: Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). abstract: The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure. url: https://www.ncbi.nlm.nih.gov/pubmed/15480857/ doi: 10.1007/s00705-004-0413-9 id: cord-263739-xoum5e0k author: Zhang, X.-Y. title: Analysis of the effect of proton pump inhibitors on the course of common COVID-19 date: 2020-06-09 words: 2581.0 sentences: 179.0 pages: flesch: 66.0 cache: ./cache/cord-263739-xoum5e0k.txt txt: ./txt/cord-263739-xoum5e0k.txt summary: In the proton pump inhibitors group and the control group, the duration of SARS-CoV-2 clearance were 7(6-9) and 7(6-11) days, and the duration of hospital stay was 21(16-25) and 20(15-26) days, respectively. Case exclusion criteria: (1) the patients used drugs to inhibit the secretion of 179 gastric acid within 30 days before admission; (2) Specimens used for SARS-CoV-180 2 nucleic acid testing were collected at an interval of more than 48 hours; (3) 181 The demographic and clinical data included age and sex of the patients, The nucleic acid test specimens of SARS-CoV-2 in this study were 209 The cumulative probability of SARS-CoV-2 clearance or discharge from 224 COVID-19 cases were conducted through Kaplan-Meier statistics, and the 225 difference was examined by Log-rank test. Cumulative probability of SARS-CoV-2 clearance and discharge in COVID-19 676 patients between PPIs group and control group by 1:1 PS-matching analysis abstract: Background/aims: To evaluate the effect of proton pump inhibitors on the course of common COVID-19. Methods: Clinical data of common COVID-19 patients admitted to the Shanghai public health clinical center for treatment from January 20, 2020 to March 16, 2020 were collected. A retrospective study was conducted and the patients were divided into two groups according to whether they used proton pump inhibitors or not. The differences in SARS-CoV-2 clearance and hospital stay between the two groups were compared by univariate and multivariate analyses. Results: A total of 154 COVID-19 common cases were included in this study, including 80 males (51.9%), 35 patients (22.7%) in the proton pump inhibitors group, and 119 patients (77.3%) in the control group. In the proton pump inhibitors group and the control group, the duration of SARS-CoV-2 clearance were 7(6-9) and 7(6-11) days, and the duration of hospital stay was 21(16-25) and 20(15-26) days, respectively. There was no significant difference between the two groups in the cumulative incidence of SARS-CoV-2 clearance and the cumulative incidence of discharge, and the same after Propensity Score Match, all P > 0.05. Multivariate analysis suggested that chronic gastropathy prolonged the duration of SARS-CoV-2 clearance, the HR was 20.924(3.547-123.447). Hypertension, chronic obstructive pulmonary disease, chronic liver disease and malignant tumor all increased the duration of hospital stay for COVID-19, and the HR were 1.820 (1.073-3.085), 4.370 (1.205-15.844), 9.011 (2.681-30.290) and 5.270 (1.237-22.456), respectively; the duration of hospital stay in COVID-19 patients was shortened by SARS-CoV-2 clearance, and the HR was 0.907 (0.869-0.947); all P < 0.05. Conclusion: Proton pump inhibitors use have no effect on the prolonging or shortening of the course of adults hospitalized with COVID-19. url: https://doi.org/10.1101/2020.06.07.20124776 doi: 10.1101/2020.06.07.20124776 id: cord-296375-gf0mgz5x author: Zhang, Xi title: Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date: 2020-10-30 words: 3275.0 sentences: 164.0 pages: flesch: 53.0 cache: ./cache/cord-296375-gf0mgz5x.txt txt: ./txt/cord-296375-gf0mgz5x.txt summary: CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. Therefore, in this study, by collecting the daily numbers of newly confirmed COVID-19 and SARS cases during the two epidemics, we aimed to determine the spatial behavior and temporal features of the COVID-19 spread in mainland China and compared them with respective features from the SARS epidemic using spatiotemporal analysis. Incident cases infected by COVID-19 were extracted from the daily briefings on novel coronavirus cases from January 20 to March 4, 2020, provided on the official website of the National Health Commission of the People''s Republic of China [5] . Incident cases of SARS were extracted from daily situation reports for mainland China from April 21 to August 3, 2003 , which were posted by China.org.cn (in Chinese) and were also provided by the National Health Commission. abstract: BACKGROUND: Both coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) are caused by coronaviruses and have infected people in China and worldwide. We aimed to investigate whether COVID-19 and SARS exhibited similar spatial and temporal features at provincial level in mainland China. METHODS: The number of people infected by COVID-19 and SARS were extracted from daily briefings on newly confirmed cases during the epidemics, as of Mar. 4, 2020 and Aug. 3, 2003, respectively. We depicted spatiotemporal patterns of the COVID-19 and SARS epidemics using spatial statistics such as Moran’s I and the local indicators of spatial association (LISA). RESULTS: Compared to SARS, COVID-19 had a higher overall incidence. We identified 3 clusters (predominantly located in south-central China; the highest RR = 135.08, 95% CI: 128.36–142.08) for COVID-19 and 4 clusters (mainly in Northern China; the highest RR = 423.51, 95% CI: 240.96–722.32) for SARS. Fewer secondary clusters were identified after the “Wuhan lockdown”. The LISA cluster map detected a significantly high-low (Hubei) and low-high spatial clustering (Anhui, Hunan, and Jiangxi, in Central China) for COVID-19. Two significant high-high (Beijing and Tianjin) and low-high (Hebei) clusters were detected for SARS. CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-020-05537-y. url: https://doi.org/10.1186/s12879-020-05537-y doi: 10.1186/s12879-020-05537-y id: cord-353537-skeajydw author: Zhang, Xian title: Asymptomatic Subclinical Cases of Coronavirus Disease 2019 without Viral Transmission in Three Independent Families date: 2020-09-24 words: 2098.0 sentences: 119.0 pages: flesch: 49.0 cache: ./cache/cord-353537-skeajydw.txt txt: ./txt/cord-353537-skeajydw.txt summary: Their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected by SARS-CoV-2. Three medical staff diagnosed with asymptomatic SARS-CoV-2 infection by serological tests after returning to work and their family members were recruited for this study. The patients and their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected with SARS-CoV-2. All their family members-including four old people, three young persons, and three children-showed no symptoms of COVID-19, and their nucleic acid and antibody tests were negative, indicating that they were not infected. During the following 2 months more, almost covering the whole disease process, from the incubation period to the recovery period, the indexes lived together with their family members, including a nasopharyngeal carcinoma patient who is theoretically vulnerable to SARS-CoV-2 infection due to impaired immune function as a result of radiotherapy or chemotherapy, without taking any protective measures. abstract: PURPOSE: There is increasing evidence indicating that considerable fractions of cases of SARS-CoV-2 infection are asymptomatic. We traced three asymptomatic clusters to investigate the infectivity of subclinical cases of coronavirus disease 2019 (COVID-19). PATIENTS AND METHODS: Three medical staff who were asymptomatic were diagnosed with coronavirus disease 2019 by serological tests. Their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected by SARS-CoV-2. RESULTS: None of the staff’s close contacts, including 10 family members, were infected by the indexes, even though no protective measures were taken. CONCLUSION: The infectivity of asymptomatic subclinical infection patients of coronavirus disease 2019 seems to be low. url: https://www.ncbi.nlm.nih.gov/pubmed/33061473/ doi: 10.2147/idr.s261304 id: cord-300445-qzu4gz2d author: Zhang, Xiao-lei title: Pharmacological and cardiovascular perspectives on the treatment of COVID-19 with chloroquine derivatives date: 2020-09-23 words: 7247.0 sentences: 376.0 pages: flesch: 37.0 cache: ./cache/cord-300445-qzu4gz2d.txt txt: ./txt/cord-300445-qzu4gz2d.txt summary: Chloroquine phosphate and its derivative hydroxychloroquine, which have been used in the treatment and prevention of malaria and autoimmune diseases for decades, were found to inhibit SARS-CoV-2 infection with high potency in vitro and have shown clinical and virologic benefits in COVID-19 patients. However, chloroquine phosphate and its derivative hydroxychloroquine, which have been used for decades in the treatment and prevention of malaria and chronic inflammatory diseases such as rheumatoid arthritis and systemic lupus erythematosus, were discovered to have a high inhibitory potency against SARS-CoV-2 infection in vitro [2] [3] [4] [5] and favorable clinical and virologic benefits in COVID-19 patients [6] [7] [8] [9] [10] , and they have emerged as important therapies for COVID-19 in several countries, including China, France, USA, and India, although the mechanisms of their anti-COVID-19 effects remain unclear. abstract: The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) and an ongoing severe pandemic. Curative drugs specific for COVID-19 are currently lacking. Chloroquine phosphate and its derivative hydroxychloroquine, which have been used in the treatment and prevention of malaria and autoimmune diseases for decades, were found to inhibit SARS-CoV-2 infection with high potency in vitro and have shown clinical and virologic benefits in COVID-19 patients. Therefore, chloroquine phosphate was first used in the treatment of COVID-19 in China. Later, under a limited emergency-use authorization from the FDA, hydroxychloroquine in combination with azithromycin was used to treat COVID-19 patients in the USA, although the mechanisms of the anti-COVID-19 effects remain unclear. Preliminary outcomes from clinical trials in several countries have generated controversial results. The desperation to control the pandemic overrode the concerns regarding the serious adverse effects of chloroquine derivatives and combination drugs, including lethal arrhythmias and cardiomyopathy. The risks of these treatments have become more complex as a result of findings that COVID-19 is actually a multisystem disease. While respiratory symptoms are the major clinical manifestations, cardiovascular abnormalities, including arrhythmias, myocarditis, heart failure, and ischemic stroke, have been reported in a significant number of COVID-19 patients. Patients with preexisting cardiovascular conditions (hypertension, arrhythmias, etc.) are at increased risk of severe COVID-19 and death. From pharmacological and cardiovascular perspectives, therefore, the treatment of COVID-19 with chloroquine and its derivatives should be systematically evaluated, and patients should be routinely monitored for cardiovascular conditions to prevent lethal adverse events. url: https://doi.org/10.1038/s41401-020-00519-x doi: 10.1038/s41401-020-00519-x id: cord-324727-bj8oei0v author: Zhang, Xiaomei title: Management of Digestive Disorders and Procedures Associated With COVID-19 date: 2020-06-03 words: 1864.0 sentences: 129.0 pages: flesch: 42.0 cache: ./cache/cord-324727-bj8oei0v.txt txt: ./txt/cord-324727-bj8oei0v.txt summary: The Chinese Gastroenterology Expert Group, comprising experts from the gastroenterology units and national medical aid teams of the epidemic region of Wuhan, along with the Chinese Society of Gastroenterology introduce and recommend this management consensus for digestive disorders in patients with COVID-19. Liver injury in patients with COVID-19 may be caused by either systemic inflammation or direct effects of SARS-CoV-2 on the angiotensin-converting enzyme 22 of cholangiocytes (13) . To prevent or control the transmission of SARS-CoV-2 in epidemic communities, gastroenterological procedures such as esophageal pH test, gastrointestinal motility, hydrogen breath test, fecal microbiota transplantation, Helicobacter pylori breath test, and stool antigen detection are recommended for suspension or postponement until the epidemic is under control. Don''t overlook digestive symptoms in patients with 2019 novel coronavirus disease (COVID-19) Digestive symptoms in COVID-19 patients with mild disease severity: Clinical presentation, stool viral RNA testing, and outcomes abstract: nan url: https://doi.org/10.14309/ajg.0000000000000728 doi: 10.14309/ajg.0000000000000728 id: cord-276991-gv1k7u7j author: Zhang, Xu title: Strategies to trace back the origin of COVID-19 date: 2020-04-08 words: 745.0 sentences: 49.0 pages: flesch: 58.0 cache: ./cache/cord-276991-gv1k7u7j.txt txt: ./txt/cord-276991-gv1k7u7j.txt summary: The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2, had raised great concern. Chinese authorities originally announced that the first infection case was reported on December 31, 2019, and many of the initial cases were linked directly to Huanan seafood market in Wuhan, in the Hubei province. The hypothesis that the outbreak originated at the market, with its initial transmission from live animals to human beings followed by rapid human-to-human transmission, is suggested to be most likely and convincing. Emergence of SARS-like coronavirus poses new challenge in China Novel coronavirus disease (Covid-19): the first two patients in the UK with person to person transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Emergence of SARS-like coronavirus in china: an update abstract: nan url: https://doi.org/10.1016/j.jinf.2020.03.032 doi: 10.1016/j.jinf.2020.03.032 id: cord-329707-89zyu8bl author: Zhang, Xue title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date: 2006-11-30 words: 3212.0 sentences: 210.0 pages: flesch: 54.0 cache: ./cache/cord-329707-89zyu8bl.txt txt: ./txt/cord-329707-89zyu8bl.txt summary: We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. abstract: OBJECTIVE: Severe acute respiratory syndrome (SARS) is a highly contagious and lethal disease caused by a new type of coronavirus, SARS-associated coronavirus (SARS-CoV). Currently, there is no efficient treatment and prevention for this disease. We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. Effective shRNA molecules to the viral genes were screened and identified, and then constructed into adenovirus vectors. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. With availability of high titers of adenoviruses and uniform and rapid infection, this approach would have foreseeable wide applications both in experimental biology and molecular medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/17139181/ doi: 10.1159/000097391 id: cord-336605-d4loia11 author: Zhang, Xue Wu title: Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs date: 2004-05-15 words: 1566.0 sentences: 87.0 pages: flesch: 58.0 cache: ./cache/cord-336605-d4loia11.txt txt: ./txt/cord-336605-d4loia11.txt summary: To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Except four drugs (lopinavir, ritonavir, niclosamide and promazine), we also conducted the docking studies of two other molecules, PNU and UC2, for their molecular formulas are close to those of niclosamide and promazine, respectively (Fig. 2) , and they both are the inhibitors of HIV-1 reverse transcriptase. Figure 3 displays the overall structures of docking for four drugs (lopinavir, ritonavir, niclosamide and promazine) and two inhibitors (PNU and UC2) to SARS-CoV main proteinase. Thus, the four drugs and two inhibitors studied here can basically bind to the active site of SARS-CoV main proteinase, a cleft between domains I and II. abstract: The SARS-associated coronavirus (SARS-CoV) main proteinase is a key enzyme in viral polyprotein processing. To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Our results suggest that these drugs and another two HIV inhibitors (PNU and UC2) could be used as templates for designing SARS-CoV proteinase inhibitors. url: https://api.elsevier.com/content/article/pii/S0968089604002214 doi: 10.1016/j.bmc.2004.03.035 id: cord-275216-dnt88ycw author: Zhang, Xue-Yan title: Biological, clinical and epidemiological features of COVID-19, SARS and MERS and AutoDock simulation of ACE2 date: 2020-07-20 words: 4893.0 sentences: 259.0 pages: flesch: 51.0 cache: ./cache/cord-275216-dnt88ycw.txt txt: ./txt/cord-275216-dnt88ycw.txt summary: This review is intended to summarize the research on this new coronavirus, to analyze the similarities and differences between COVID-19 and previous outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and to provide guidance regarding new methods of prevention, diagnosis and clinical treatment based on autodock simulations. Given that the epidemic is still spreading and the evidence that there are similarities among the three coronaviruses in terms of their biological, clinical and epidemiological features, a comparison among the three is very helpful to guide the improvement of treatment and prevention measures, and the similarities and differences among the three are likely to provide the key to addressing the COVID-19 epidemic. In 2002-2003, SARS-CoV caused an epidemic of severe acute respiratory diseases in China; MERS-CoV was found in the Middle East in 2012 [9, 10] . abstract: BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) has caused a public catastrophe and global concern. The main symptoms of COVID-19 are fever, cough, myalgia, fatigue and lower respiratory tract infection signs. Almost all populations are susceptible to the virus, and the basic reproduction number (R(0)) is 2.8–3.9. The fight against COVID-19 should have two aspects: one is the treatment of infected patients, and the other is the mobilization of the society to avoid the spread of the virus. The treatment of patients includes supportive treatment, antiviral treatment, and oxygen therapy. For patients with severe acute respiratory distress syndrome (ARDS), extracorporeal membrane oxygenation (ECMO) and circulatory support are recommended. Plasma therapy and traditional Chinese medicine have also achieved good outcomes. This review is intended to summarize the research on this new coronavirus, to analyze the similarities and differences between COVID-19 and previous outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and to provide guidance regarding new methods of prevention, diagnosis and clinical treatment based on autodock simulations. METHODS: This review compares the multifaceted characteristics of the three coronaviruses including COVID-19, SARS and MERS. Our researchers take the COVID-19, SARS, and MERS as key words and search literatures in the Pubmed database. We compare them horizontally and vertically which respectively means concluding the individual characteristics of each coronavirus and comparing the similarities and differences between the three coronaviruses. RESULTS: We searched for studies on each outbreak and their solutions and found that the main biological differences among SARS-CoV-2, SARS-CoV and MERS-CoV are in ORF1a and the sequence of gene spike coding protein-S. We also found that the types and severity of clinical symptoms vary, which means that the diagnosis and nursing measures also require differentiation. In addition to the common route of transmission including airborne transmission, these three viruses have their own unique routes of transmission such as fecal-oral route of transmission COVID-19. CONCLUSIONS: In evolutionary history, these three coronaviruses have some similar biological features as well as some different mutational characteristics. Their receptors and routes of transmission are not all the same, which makes them different in clinical features and treatments. We discovered through the autodock simulations that Met124 plays a key role in the efficiency of drugs targeting ACE2, such as remdesivir, chloroquine, ciclesonide and niclosamide, and may be a potential target in COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32690096/ doi: 10.1186/s40249-020-00691-6 id: cord-328187-9zd79gai author: Zhang, Yali title: Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date: 2020-07-22 words: 3018.0 sentences: 165.0 pages: flesch: 55.0 cache: ./cache/cord-328187-9zd79gai.txt txt: ./txt/cord-328187-9zd79gai.txt summary: The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. 22 On 293T-ACE2iRb3 cells, both the SARS-CoV2-RBG and SARS-CoV2-STG 23 probes showed effective-binding to the cells, as membrane-bound and hACE2-24 mRuby3-colocalized mGam signals were observed after a 6-min incubation with the 25 cells ( Figure 2C ). Compared with 3 samples from healthy donors (n=40), all COVID-19-convalescent plasmas showed 4 significant cMFI inhibition on CSBT assay, whereas only 12 samples (37.5%) had 5 detectable CRBT activity ( Figure 3A ). Among the antibody titers derived from various assays, the 10 CSBT titer showed the best correlation with LVppNAT ( Figure 3D and Table S2, 11 r=0.832, p<0.001), and it also well correlated (r=0.959, p<0.001, Figure 3D ) with the 12 neutralization activity against authentic SARS-CoV-2 virus in 12 representative 13 samples (Table S3) . abstract: The ongoing COVID-19 pandemic, caused by SARS-CoV-2 infection, has resulted in hundreds of thousands of deaths. Cellular entry of SARS-CoV-2, which is mediated by the viral spike protein and host ACE2 receptor, is an essential target for the development of vaccines, therapeutic antibodies, and drugs. Using a mammalian cell expression system, we generated a recombinant fluorescent protein (Gamillus)-fused SARS-CoV-2 spike trimer (STG) to probe the viral entry process. In ACE2-expressing cells, we found that the STG probe has excellent performance in the live-cell visualization of receptor binding, cellular uptake, and intracellular trafficking of SARS-CoV-2 under virus-free conditions. The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. This approach may also be adapted to develop a viral entry visualization system for other viruses. url: https://doi.org/10.1101/2020.07.22.215236 doi: 10.1101/2020.07.22.215236 id: cord-327721-y39751g4 author: Zhang, Yan title: Emotional “inflection point” in public health emergencies with the 2019 New Coronavirus Pneumonia (NCP) in China date: 2020-07-19 words: 5385.0 sentences: 276.0 pages: flesch: 55.0 cache: ./cache/cord-327721-y39751g4.txt txt: ./txt/cord-327721-y39751g4.txt summary: BACKGROUND: The outbreak of the new coronavirus pneumonia (NCP) in Wuhan, Hubei, has caused very serious consequences and severely affected people''s lives and mental health. METHODS: This study used self-designed questionnaires and artificial intelligence (AI) to assess and analyze the emotional state of over 30,000 college students during the outbreak period in January (T1) and home quarantine in February (T2). From these data, it indicated that during the period of home isolation, college students in Hubei Province showed more negative emotions due to their long-term exposure to the epidemic. There is also the stress symptom of "seeming as being infected" caused by too much browsing of the relevant news every day, which directly affects the emotions of students, they became more sensible and anxious to disease, this is a mental tension (Peng et al., 2019) . This survey found that there is an emotional "infection point" in February among college students, especially in the Hubei area. abstract: BACKGROUND: The outbreak of the new coronavirus pneumonia (NCP) in Wuhan, Hubei, has caused very serious consequences and severely affected people's lives and mental health. The outbreak will cause bad emotions such as tension, anxiety, fear, and so on. College students who have returned home from school face infection, isolation, and delay in starting school, and thus, their emotional stress should be observed. METHODS: This study used self-designed questionnaires and artificial intelligence (AI) to assess and analyze the emotional state of over 30,000 college students during the outbreak period in January (T1) and home quarantine in February (T2). This survey used online questionnaire (www.wjx.cn) to investigate the emotion information of college students. RESULTS: In the T1 survey, the "Typhoon Eye Effect" appeared. College students in Hubei are calmer than those outside Hubei in T1. However, in T2, an emotional "infection point" appeared, there was an "Exposure Effect", the negative emotions of students in Hubei largely increased and became higher than students outside Hubei. CONCLUSION: This survey found that there is an emotional "infection point" in February among college students, especially in the Hubei area. College students in Hubei are calmer than those outside Hubei in T1. In contrast, college students in Hubei were more nervous and scared than those outside Hubei in T2. This epidemic has caused the students to experience significant pressure and negative emotions. Therefore, universities and society should pay attention to their emotional adjustment, there are some suggestions such as establish the mental health organizations, test students' emotion status regularly. url: https://api.elsevier.com/content/article/pii/S0165032720325428 doi: 10.1016/j.jad.2020.07.097 id: cord-334378-dqtnj3y3 author: Zhang, Yi title: Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2 date: 2020-06-10 words: 1452.0 sentences: 86.0 pages: flesch: 55.0 cache: ./cache/cord-334378-dqtnj3y3.txt txt: ./txt/cord-334378-dqtnj3y3.txt summary: How does RBD of the SARS-CoV-2 spike protein binds to the human receptor ACE2? The precise binding interface of the SARS-CoV-2 spike RBD and ACE2 can be dissected from the crystal structures of the complex determined by Shang et al. Analysis of the crystal structures of RBD from the SARS-CoV spike protein in complex with established SARS-CoV neutralizing human m396 and 80R antibodies reveals that the antibodies are bound in the same binding site as ACE2 9,10 , implying that their neutralizing mechanism is a direct blockage of receptor binding. Proteolytic cleavage of the SARS-CoV-2 spike protein by the human serine protease TMPRSS2 is a critical step in the virus entry through the plasma membrane fusion mechanism (Fig. 2) , as shown by Hoffmann et al. In addition to targeting components of the viral attachment and the membrane fusion machinery, other strategies to eliminate SARS-CoV-2 include impeding virus entry into the host cell through the endosomal pathway and disrupting activities of viral proteins. abstract: Amid the COVID-19 pandemic, scientists around the globe have been working resolutely to find therapies to treat patients and avert the spreading of the SARS-CoV-2 virus. In this commentary, we highlight some of the latest studies that provide atomic-resolution structural details imperative for the development of vaccines and antiviral therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/32523109/ doi: 10.1038/s41467-020-16779-4 id: cord-268144-maa8c4a4 author: Zhang, Yuan title: Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization date: 2007-02-17 words: 2548.0 sentences: 129.0 pages: flesch: 44.0 cache: ./cache/cord-268144-maa8c4a4.txt txt: ./txt/cord-268144-maa8c4a4.txt summary: The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. As an envelope glycoprotein, the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) plays a key role in the viral entry and neutralization (Bartlam et al., 2005; Denison, 2004; Lau and Peiris, 2005; Xu and Gao, 2004; Zhu, 2004) . Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association abstract: The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational characterization and design of RBD-mediated receptor recognition and antibody neutralization. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics protocols. And the calculations predict a number of single substitutions on RBD, receptor or antibody that could remarkably elevate the binding affinities of those complexes. It is reasonable to anticipate our structure-based computation-derived hypotheses could be informative to the future biochemical and immunological tests. url: https://api.elsevier.com/content/article/pii/S1476927107000266 doi: 10.1016/j.compbiolchem.2007.02.005 id: cord-316066-pge0vx04 author: Zhang, Zheng title: Longitudinal alteration of circulating dendritic cell subsets and its correlation with steroid treatment in patients with severe acute respiratory syndrome date: 2005-06-16 words: 5115.0 sentences: 251.0 pages: flesch: 52.0 cache: ./cache/cord-316066-pge0vx04.txt txt: ./txt/cord-316066-pge0vx04.txt summary: In this study, we found that 74 patients with severe acute respiratory syndrome (SARS) exhibited a rapid, dramatic decrease in numbers of circulating myeloid and plasmacytoid dendritic cells (mDCs and pDCs) during the first 2 weeks of illness (5.3and 28.4-fold reductions for mDCs and pDCs compared with 25 healthy individuals, respectively), with slow return to normal cell numbers during convalescence (weeks 5–7 of illness on average). A marked lymphocytopenia occurred in most patients during the acute phase of SARS, with CD4 and CD8 T-cell subsets particularly affected, and the degree of reduction of circulating T lymphocyte counts was found to be associated with disease severity, indicating that host immune functional changes are involved in the initiation and progression of SARS [3 -6] . In addition, our findings suggest that acute SARS-CoV infection may contribute to the rapid initial reduction of both circulating mDCs and pDCs. Subsequently, steroid administration, particularly at high doses over weeks, probably exacerbated and prolonged the decrease in numbers of DC subset as well as T-cell subsets. abstract: In this study, we found that 74 patients with severe acute respiratory syndrome (SARS) exhibited a rapid, dramatic decrease in numbers of circulating myeloid and plasmacytoid dendritic cells (mDCs and pDCs) during the first 2 weeks of illness (5.3- and 28.4-fold reductions for mDCs and pDCs compared with 25 healthy individuals, respectively), with slow return to normal cell numbers during convalescence (weeks 5–7 of illness on average). In addition, numbers of circulating CD4 and CD8 T cells exhibited milder reductions (2.1- and 1.8-fold at week 1) and earlier return to normal at a mean of weeks 3 and 4, respectively. A significant inverse correlation was found between numbers of DC and T-cell subsets and high-dose steroid treatment. Our novel findings thus suggest that the acute SARS-coronavirus infection probably contributes to the initial reduction of DC and T-cell subsets in blood, and that high-dose steroid administration may subsequently exacerbate and prolong low expression of the cell subsets. These findings will aid the framing of further studies of the immunopathogenesis of SARS. url: https://api.elsevier.com/content/article/pii/S1521661605001518 doi: 10.1016/j.clim.2005.04.015 id: cord-324518-a346cjx4 author: Zhang, Zhibin title: The outbreak pattern of the SARS cases in Asia date: 2004 words: 1935.0 sentences: 118.0 pages: flesch: 54.0 cache: ./cache/cord-324518-a346cjx4.txt txt: ./txt/cord-324518-a346cjx4.txt summary: The increase rate of SARS cases is expected to decrease with the cumulative SARS cases, as described by the traditional logistical model, which is widely used in population dynamic studies. The maximum instantaneous rate of increase, basic reproductive number, and maximum cumulative SARS cases were also calculated by using the logistic model. The outbreak pattern of cumulative SARS cases is likely of a logistic type because at the initial stage, it grows exponentially, later due to the increasing control effort by people and/or due to depletion of susceptible individuals, the infection will be slowed down. significant and negative linear "density dependency" of the instantaneous rate of increase on the cumulative cases of SARS indicates that the outbreak pattern of SARS can be well described by the logistic model( Fig. 1(a) and (b) ). abstract: The severe acute respiratory syndrome (SARS) caused tremendous damage to many Asia countries, especially China. The transmission process and outbreak pattern of SARS is still not well understood. This study aims to find a simple model to describe the outbreak pattern of SARS cases by using SARS case data commonly released by governments. The outbreak pattern of cumulative SARS cases is expected to be a logistic type because the infection will be slowed down due to the increasing control effort by people and/or due to depletion of susceptible individuals. The increase rate of SARS cases is expected to decrease with the cumulative SARS cases, as described by the traditional logistical model, which is widely used in population dynamic studies. The instantaneous rate of increases were significantly and negatively correlated with the cumulative SARS cases in mainland of China (including Beijing, Hebei, Tianjin, Shanxi, the Autonomous Region of Inner Mongolia) and Singapore. The basic reproduction numberR (0) in Asia ranged from 2.0 to 5.6 (except for Taiwan, China). TheR (0) of Hebei and Tianjin were much higher than that of Singapore, Hongkong, Beijing, Shanxi, Inner Mongolia, indicating SARS virus might have originated differently or new mutations occurred during transmission. We demonstrated that the outbreaks of SARS in many regions of Asia were well described by the logistic model, and the control measures implemented by governments are effective. The maximum instantaneous rate of increase, basic reproductive number, and maximum cumulative SARS cases were also calculated by using the logistic model. url: https://doi.org/10.1007/bf03183407 doi: 10.1007/bf03183407 id: cord-310091-x31g02xw author: Zhang, Zhilan title: Pan-cancer analysis reveals that ACE2 is positively associated with immunotherapy response and is a potential protective factor for cancer progression date: 2020-09-02 words: 2941.0 sentences: 169.0 pages: flesch: 42.0 cache: ./cache/cord-310091-x31g02xw.txt txt: ./txt/cord-310091-x31g02xw.txt summary: Using cancer genomics datasets from the Cancer Genome Atlas (TCGA) program, we performed computational analyses of associations between ACE2 expression and antitumor immunity, immunotherapy response, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in 13 cancer cohorts. A recent study [9] showed that ACE2 expression was associated with increased tumor immune infiltration and was a positive prognostic factor in uterine corpus endometrial and renal papillary cell cancers. Despite these previous studies, a systemic investigation into the association between ACE2 expression and antitumor immunity, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in pan-cancer remains lacking. We also explored associations between ACE2 expression and multiple tumor phenotypes, including cell proliferation, stemness, epithelial-mesenchymal transition (EMT), oncogenic signaling, and clinical outcomes in these cancer cohorts. We found that ACE2 expression levels inversely correlated with the activity of cell cycle, mismatch repair, TGF-β, Wnt, VEGF, and Notch signaling pathways in 10, 7, 9, 7, 5, and 7 individual cancer types, respectively (Spearman''s correlation test, FDR < 0.05) ( Fig. 2A) . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 13 million people and has caused more than 570,000 deaths worldwide as of July 14, 2020. The SARS-CoV-2 human cell receptor ACE2 has recently received extensive attention for its role in SARS-CoV-2 infection. Many studies have also explored the association between ACE2 and cancer. However, a systemic investigation into associations between ACE2 and oncogenic pathways, tumor progression, and clinical outcomes in pan-cancer remains lacking. Using cancer genomics datasets from the Cancer Genome Atlas (TCGA) program, we performed computational analyses of associations between ACE2 expression and antitumor immunity, immunotherapy response, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in 13 cancer cohorts. We found that ACE2 upregulation was associated with increased antitumor immune signatures and PD-L1 expression, and favorable anti-PD-1/PD-L1/CTLA-4 immunotherapy response. ACE2 expression levels inversely correlated with the activity of cell cycle, mismatch repair, TGF-β, Wnt, VEGF, and Notch signaling pathways. Moreover, ACE2 expression levels had significant inverse correlations with tumor proliferation, stemness, and epithelial-mesenchymal transition. ACE2 upregulation was associated with favorable survival in pan-cancer and in multiple individual cancer types. These results suggest that ACE2 is a potential protective factor for cancer progression. Our data may provide potential clinical implications for treating cancer patients infected with SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S2001037020303779?v=s5 doi: 10.1016/j.csbj.2020.08.024 id: cord-265164-ybh5yljw author: Zhao, Bin title: Numerical study of the transport of droplets or particles generated by respiratory system indoors date: 2004-11-24 words: 2613.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-265164-ybh5yljw.txt txt: ./txt/cord-265164-ybh5yljw.txt summary: The drift flux model, which considers the settling of particles or droplets under the effect of gravitational sedimentation, is adopted to simulate the droplets transport and distribution indoors during respiration and sneezing or coughing process, while the simplified model for solving the continuous fluid flow is combined. The results show that droplets or particles generated by normal breathing process transport a relatively short distance, while droplets or particles generated during coughing or sneezing may travel much longer distances, which may pose adverse effect on human bodies for defending the SARS or other infectious diseases. To calculate the three-dimensional and non-isothermal airflow inside ventilated rooms, a well validated simplified methodology combined with N-point air supply opening model [4] , a zero equation turbulence model [5] is applied. Numerical studies on the transport and distribution of particles or droplets generated by normal respiration and sneezing or coughing indoors result in the following conclusions: abstract: The outbreak of atypical pneumonia, referred to as severe acute respiratory syndrome (SARS), has spread to many countries in the world. SARS may infect human bodies by the tiny droplets or particles carrying various virus and bacteria, which are generated by the respiratory system of infected patients. This paper presents the numerical analysis of the influence of generating ways of the droplets or particles on the transport and distribution of the droplets or particles indoors. The drift flux model, which considers the settling of particles or droplets under the effect of gravitational sedimentation, is adopted to simulate the droplets transport and distribution indoors during respiration and sneezing or coughing process, while the simplified model for solving the continuous fluid flow is combined. Two different cases considering the normal respiration and coughing or sneezing are studied, respectively, and two different outlet velocities from the mouth for the sneezing or coughing process are considered. The results show that droplets or particles generated by normal breathing process transport a relatively short distance, while droplets or particles generated during coughing or sneezing may travel much longer distances, which may pose adverse effect on human bodies for defending the SARS or other infectious diseases. url: https://www.sciencedirect.com/science/article/pii/S0360132304003038 doi: 10.1016/j.buildenv.2004.09.018 id: cord-333140-cdikbi1l author: Zhao, Helong title: Imatinib is not a potent anti-SARS-CoV-2 drug date: 2020-09-30 words: 913.0 sentences: 52.0 pages: flesch: 43.0 cache: ./cache/cord-333140-cdikbi1l.txt txt: ./txt/cord-333140-cdikbi1l.txt summary: We tested the effects of imatinib and asciminib, a highly specific and potent ABL inhibitor binding to the myristate pocket of the kinase domain [7] , on SARS-CoV-2 infection and replication in the naturally susceptible ACE2 + human Caco-2 cells [5] . We then performed the standard viral replication assay using the USA-WA1/2020 strain of SARS-CoV-2 to test imatinib and asciminib in a blinded fashion, including remdesivir as a positive control. Therefore, our data indicate that, within clinically achievable dose ranges, imatinib and asciminib have no significant effect on SARS-CoV-2 infection and replication. These data support additional prospective investigations into the potential beneficial effect of imatinib and possibly other ABL inhibitors on COVID-19, but provide insufficient evidence for the off-label use of imatinib in patients with COVID-19. Prevalence of COVID-19 diagnosis in Dutch CML patients during the 2020 SARS-CoV2 pandemic. Imatinib is not a potent anti-SARS-CoV-2 drug abstract: nan url: https://doi.org/10.1038/s41375-020-01045-9 doi: 10.1038/s41375-020-01045-9 id: cord-347767-aq9niccc author: Zhao, Jie title: Yidu-toxicity blocking lung decoction ameliorates inflammation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome by eliminating IL-6 and TNF-a date: 2020-06-19 words: 3538.0 sentences: 198.0 pages: flesch: 49.0 cache: ./cache/cord-347767-aq9niccc.txt txt: ./txt/cord-347767-aq9niccc.txt summary: The present study investigates the differences in inflammatory agents alterations, immune function, and leukocyte differential count evaluation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome after the recommended Chinese medicine prescription of Yidu-toxicity blocking lung decoction. A total of 40 patients with yidu-toxicity blocking lung syndrome, diagnosed as severe pneumonia of SARS-COV-2 following the latest Chinese national recommendations for the diagnosis and treatment of pneumonia caused by SARS-COV-2 (the 5th edition), were recruited. To characterize the effect of herbal medicine, immune function, and inflammatory agents, levels of white blood cells were detected for all patients according to the manufacturer''s instructions at the beginning and at the end of the two weeks. In conclusion, our study suggests that the 5th edition recommendation''s CM prescription, can be safely used in the treatment of severe pneumonia of SARS-COV-2 with yidu-toxicity blocking lung syndrome. abstract: The present study investigates the differences in inflammatory agents alterations, immune function, and leukocyte differential count evaluation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome after the recommended Chinese medicine prescription of Yidu-toxicity blocking lung decoction. A total of 40 patients with yidu-toxicity blocking lung syndrome, diagnosed as severe pneumonia of SARS-COV-2 following the latest Chinese national recommendations for the diagnosis and treatment of pneumonia caused by SARS-COV-2 (the 5th edition), were recruited. They were randomly divided into the pure western medicine therapy group (PWM) and integrated into Chinese and Western medicine therapy group (ICW). The general strategies were given to both groups according to the national recommendations, and the ICW group was given Yidu-toxicity blocking lung decoction extraorally. A radioimmunoassay method was adopted to detect the content of IL-6, IL-8,IL-2R,TNF-α, procalcitonin (PCT) and high-sensitivity C-reactive protein (hs-CRP) in sera. Flow cytometry was used to determine the peripheral blood lymphocyte subsets (the levels of CD3+, CD4+, CD8+, and the ratios of CD4+/CD8+). The white blood cell counts (WBC#), neutrophils count(N#), and lymphocyte counts (L#) were measured using a fully automatic blood rheological instrument. The t test or Rank Sum Test and Spearman analysis were conducted to evaluate the differences. The results showed that IL-6 (P = 0.013) and TNF-α (P = 0.035) levels in the PWM group were significantly higher than those in the ICW group after treatment. Infection related indicators such as WBC#, N#, L#, hs-CRP showed no differences. The analysis showed that there was no statistical difference in the values of CD4 and CD8 between the two groups. By the end of Day 29, all patients were discharged and the final cure rate for both group were 100%. Taken together, we conclude that Yidu-toxicity blocking lung decoction could relieve inflammation of SARS-COV-2 patients with yidu-toxicity blocking lung syndrome by eliminating inflammatory agents. CM can serve as a complementary medication to western medicine, which should be highlighted in clinical settings. url: https://www.sciencedirect.com/science/article/pii/S0753332220306296?v=s5 doi: 10.1016/j.biopha.2020.110436 id: cord-316723-srenbxa7 author: Zhao, Jincun title: Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus date: 2004-11-23 words: 3093.0 sentences: 180.0 pages: flesch: 64.0 cache: ./cache/cord-316723-srenbxa7.txt txt: ./txt/cord-316723-srenbxa7.txt summary: Amino acid residues 450–650 of the spike (S) glycoprotein of SARS-CoV (S450-650) contains dominant epitopes for anti-viral antibodies (Abs) in patient sera. However, so far there is no enzyme-linked immunosorbent assay (ELISA) available for easier and more sensitive detection of anti-S Abs. Our computer-assisted analysis suggested that amino acid residues 450-650 of the S glycoprotein (S450-650) of SARS-CoV is largely solvent accessible and likely to contain dominant B cell epitopes. (2004) showing that residues 441-700 of the S protein of SARS-CoV contained dominant epitope(s) for anti-S Abs in patient sera, as determined in WB assays. All patient sera were tested for anti-SARS-CoV IgG Abs using an ELISA kit produced by Huada Institute (see below). Sera from three convalescent SARS patients and two healthy individuals were serial diluted and tested in the S450-650-based ELISAs, which detected anti-S IgG Abs in a specific and sensitive manner, with the reactivity end point from 1:400 to 1:800 diluted patient sera (Fig. 2) . abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is caused by infection with SARS-associated coronavirus (CoV). Amino acid residues 450–650 of the spike (S) glycoprotein of SARS-CoV (S450-650) contains dominant epitopes for anti-viral antibodies (Abs) in patient sera. OBJECTIVES: To develop and evaluate an ELISA system for detection of anti-S Abs in patient sera. STUDY DESIGN: Express recombinant S450-650 in E. Coli and evaluate the sensitivity and specificity of an ELISA system based on the S450-650 polypeptide. RESULTS: The S450-650-based ELISA detected IgG Abs in 41 out of 51 serum samples from 22 hospitalized patients with probable SARS, a result closely correlated with that obtained with a virus-based ELISA (r = 0.75, k = 0.8). Differential anti-S IgG responses were observed amongst SARS patients. Some of them produced anti-S Abs early during their infection, while others failed to make IgG Abs against the S450-650 polypeptide. None of the serum samples from 100 healthy blood donors was positive in the S450-650-based assay. CONCLUSION: The S450-650-based ELISA can detect anti-S IgG Abs with high sensitivity and specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/15797360/ doi: 10.1016/j.jcv.2004.09.024 id: cord-333515-llqpfhwg author: Zhao, Juanjuan title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 words: 3575.0 sentences: 230.0 pages: flesch: 56.0 cache: ./cache/cord-333515-llqpfhwg.txt txt: ./txt/cord-333515-llqpfhwg.txt summary: Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. To mitigate this knowledge gap, and to provide scientific analysis on the benefit of antibody testing when used in combination with the current RNA testing, this study investigates the dynamics of total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 in serial blood samples collected from 173 confirmed COVID-19 patients and provides discussion on the clinical value of antibody testing. A total of 535 plasma samples collected during the hospitalization period of the 173 patients were tested for antibodies against SARS-CoV-2. In addition to the diagnosis value of Ab test, our study revealed a strong positive correlation between clinical severity and antibody titer since 2-week after illness onset, for the first time in COVID-19 patients. abstract: Summary Background The novel coronavirus SARS-CoV-2 is a newly emerging virus. The antibody response in infected patient remains largely unknown, and the clinical values of antibody testing have not been fully demonstrated. Methods A total of 173 patients with confirmed SARS-CoV-2 infection were enrolled. Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. The dynamics of antibodies with the progress and severity of disease was analyzed. Findings Among 173 patients, the seroconversion rate for Ab, IgM and IgG was 93.1% (161/173), 82.7% (143/173) and 64.7% (112/173), respectively. Twelve patients who had not seroconverted were those only blood samples at the early stage of illness were collected. The seroconversion sequentially appeared for Ab, IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. The presence of antibodies was < 40% among patients in the first 7 days of illness, and then rapidly increased to 100.0%, 94.3% and 79.8% for Ab, IgM and IgG respectively since day 15 after onset. In contrast, the positive rate of RNA decreased from 66.7% (58/87) in samples collected before day 7 to 45.5% (25/55) during days 15 to 39. Combining RNA and antibody detections significantly improved the sensitivity of pathogenic diagnosis for COVID-19 patients (p < 0.001), even in early phase of 1-week since onset (p = 0.007). Moreover, a higher titer of Ab was independently associated with a worse clinical classification (p = 0.006). Interpretation The antibody detection offers vital clinical information during the course of SARS-CoV-2 infection. The findings provide strong empirical support for the routine application of serological testing in the diagnosis and management of COVID-19 patients. url: https://doi.org/10.1101/2020.03.02.20030189 doi: 10.1101/2020.03.02.20030189 id: cord-298461-tyhtdawb author: Zhao, L. title: COVID-19: Effects of weather conditions on the propagation of respiratory droplets date: 2020-05-25 words: 7832.0 sentences: 475.0 pages: flesch: 55.0 cache: ./cache/cord-298461-tyhtdawb.txt txt: ./txt/cord-298461-tyhtdawb.txt summary: This study investigates the influence of weather conditions including temperature, humidity and wind velocity, on the transmission of SARS-CoV-2-containing respiratory droplets. We suggest that the current pandemic may not ebb over the summer without continuous and proper public health intervention, because (1) in hot and dry weather, respiratory droplets more easily evaporate into aerosol particles capable of long-range transmission; (2) infectious PM2.5 that can infiltrate deeply into our lung has a longer suspension time in hot and dry weather; (3) many public spaces implement air-conditioning systems that can still operate at temperature and humidity setpoints that favor droplet transport. . https://doi.org/10.1101/2020.05.24.20111963 doi: medRxiv preprint Key parameters considered in the model include the distribution of initial droplet size d0, initial velocity v0, environmental temperature T ∞ , relative humidity RH, air velocity Vair, whose values are given here. abstract: As the number of confirmed cases of Coronavirus disease 2019 (COVID-19) continues to increase, there has been a rising concern regarding the effect of weather conditions, especially over the upcoming summer, on the transmission of this disease. In this study, we assess the transmission of COVID-19 under different weather conditions by investigating the propagation of infectious respiratory droplets. A comprehensive mathematical model is established to explore their evaporation, heat transfer and kinematics under different temperature, humidity and ventilation conditions. The transmitting pathway of COVID-19 through respiratory droplets is divided into short-range droplet contacts and long-range aerosol exposure. We show that the effect of weather conditions is not monotonic: low temperature and high humidity facilitate droplet contact transmission, while high temperature and low humidity promote the formation of aerosol particles and accumulation of particles with a diameter of 2.5 m or less (PM2.5). Our model suggests that the 6 ft of social distance recommended by the Center for Disease Control and Prevention (CDC) may be insufficient in certain environmental conditions, as the droplet spreading distance can be as long as 6 m (19.7 ft) in cold and humid weather. The results of this study suggest that the current pandemic may not ebb in the summer of the northern hemisphere without proper intervention, as there is an increasing chance of aerosol transmission. We also emphasize that the meticulous design of building ventilation systems is critical in containing both the droplet contact infections and aerosol exposures. url: https://doi.org/10.1101/2020.05.24.20111963 doi: 10.1101/2020.05.24.20111963 id: cord-328686-5ik5em5a author: Zhao, L. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 words: 1606.0 sentences: 110.0 pages: flesch: 61.0 cache: ./cache/cord-328686-5ik5em5a.txt txt: ./txt/cord-328686-5ik5em5a.txt summary: In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint From the findings of this study, during the middle risk period, positive samples were detected both in 83 municipal and hospital wastewater systems. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Although SARS-CoV-2 RNA surveillance in wastewaters is a useful WBE drive, the public health risk associated 109 with water cycle is unclear since viral particles infectivity in sewage and faeces is yet to be determined in 110 addition to its probable fecal-oral transmission. abstract: Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community. Congruently, SARS-CoV-2 virus, the etiologic agent of COVID-19, has been demonstrated to infect the gastrointestinal tissues, and be shed in feces. In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. One sludge sample collected from Hospital 4; which was obtained during low risk period, was positive for SARS-CoV-2 RNA. These study findings demonstrate the significance of WBE in continuous surveilling and monitoring of SARS-CoV-2 at the community level, even when the COVID19 prevalence is low. Therefore, the application of WBE is principally useful in tracking the level of infections in communities and the risk assessment of the secondary environment. url: https://doi.org/10.1101/2020.08.19.20172924 doi: 10.1101/2020.08.19.20172924 id: cord-328040-5qd05e4r author: Zhao, Xin-Ying title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date: 2020-04-29 words: 3416.0 sentences: 191.0 pages: flesch: 54.0 cache: ./cache/cord-328040-5qd05e4r.txt txt: ./txt/cord-328040-5qd05e4r.txt summary: title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study Since December 2019, several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were first reported the virus has caused an outbreak in a short time by human-to-human transmission throughout China, especially in Hubei Province. A considerable proportion of COVID-19 patients develop severe pneumonia, pulmonary edema, acute respiratory distress syndrome, and even multiple organ failure within a short time. Patients suspected of having COVID-19 were admitted and quarantined, and throat swab samples were collected and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative polymerase chain reaction assay (qPCR). Clinical data [age, previous chronic disease, epidemiological history, symptoms, vital signs, computed tomography (CT) images, virus load, laboratory tests, complications, and treatment process] of the 91 patients involved in this study were collected. abstract: BACKGROUND: Since December 2019, the 2019 coronavirus disease (COVID-19) has expanded to cause a worldwide outbreak that more than 600,000 people infected and tens of thousands died. To date, the clinical characteristics of COVID-19 patients in the non-Wuhan areas of Hubei Province in China have not been described. METHODS: We retrospectively analyzed the clinical characteristics and treatment progress of 91 patients diagnosed with COVID-19 in Jingzhou Central Hospital. RESULTS: Of the 91 patients diagnosed with COVID-19, 30 cases (33.0%) were severe and two patients (2.2%) died. The severe disease group tended to be older (50.5 vs. 42.0 years; p = 0.049) and have more chronic disease (40% vs. 14.8%; p = 0.009) relative to mild disease group. Only 73.6% of the patients were quantitative polymerase chain reaction (qPCR)-positive on their first tests, while typical chest computed tomography images were obtained for each patient. The most common complaints were cough (n = 75; 82.4%), fever (n = 59; 64.8%), fatigue (n = 35; 38.5%), and diarrhea (n = 14; 15.4%). Non-respiratory injury was identified by elevated levels of aspartate aminotransferase (n = 18; 19.8%), creatinine (n = 5; 5.5%), and creatine kinase (n = 14; 15.4%) in laboratory tests. Twenty-eight cases (30.8%) suffered non-respiratory injury, including 50% of the critically ill patients and 21.3% of the mild patients. CONCLUSIONS: Overall, the mortality rate of patients in Jingzhou was lower than that of Wuhan. Importantly, we found liver, kidney, digestive tract, and heart injuries in COVID-19 cases besides respiratory problems. Combining chest computed tomography images with the qPCR analysis of throat swab samples can improve the accuracy of COVID-19 diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/32345226/ doi: 10.1186/s12879-020-05010-w id: cord-324344-dxuabscn author: Zhao, Xuesen title: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date: 2020-04-05 words: 3152.0 sentences: 186.0 pages: flesch: 48.0 cache: ./cache/cord-324344-dxuabscn.txt txt: ./txt/cord-324344-dxuabscn.txt summary: In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. Finally, the findings that LY6E inhibits human CoV entry cannot be evaded by ectopic 284 expression of membrane-associated serine protease TMPRSS2 and compromised by AmphoB 285 treatment strongly indicate that LY6E modulates virus entry via a distinct mechanism from that 286 IFITM proteins do (Figs. abstract: C3A is a sub-clone of human hepatoblastoma HepG2 cell line with the strong contact inhibition of growth. We fortuitously found that C3A was more susceptible to human coronavirus HCoV-OC43 infection than HepG2, which was attributed to the increased efficiency of virus entry into C3A cells. In an effort to search for the host cellular protein(s) mediating the differential susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and LY6E, three cellular proteins with known activity of interfering virus entry, expressed at significantly higher levels in HepG2 cells. Functional analyses revealed that ectopic expression of LY6E, but not GILT or ADAP2, in HEK 293 cells inhibited the entry of HCoV-OC43. While overexpression of LY6E in C3A and A549 cells efficiently inhibited the infection of HCoV-OC43, knockdown of LY6E expression in HepG2 significantly increased its susceptibility to HCoV-OC43 infection. Moreover, we found that LY6E also efficiently restricted the entry mediated by the envelope spike proteins of other human coronaviruses, including the currently pandemic SARS-CoV-2. Interestingly, overexpression of serine protease TMPRSS2 or amphotericin treatment significantly neutralized the IFITM3 restriction of human coronavirus entry, but did not compromise the effect of LY6E on the entry of human coronaviruses. The work reported herein thus demonstrates that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis via a distinct mechanism. Importance Virus entry into host cells is one of the key determinants of host range and cell tropism and is subjected to the control by host innate and adaptive immune responses. In the last decade, several interferon inducible cellular proteins, including IFITMs, GILT, ADAP2, 25CH and LY6E, had been identified to modulate the infectious entry of a variety of viruses. Particularly, LY6E was recently identified as host factors to facilitate the entry of several human pathogenic viruses, including human immunodeficiency virus, influenza A virus and yellow fever virus. Identification of LY6E as a potent restriction factor of coronaviruses expands the biological function of LY6E and sheds new light on the immunopathogenesis of human coronavirus infection. url: https://doi.org/10.1101/2020.04.02.021469 doi: 10.1101/2020.04.02.021469 id: cord-350627-4pgish5x author: Zhao, Yu title: Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date: 2020-01-26 words: 1865.0 sentences: 129.0 pages: flesch: 56.0 cache: ./cache/cord-350627-4pgish5x.txt txt: ./txt/cord-350627-4pgish5x.txt summary: Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. These studies showed that in normal human lung, ACE2 is mainly expressed by type II and type I alveolar epithelial cells. In total, we analyzed 43,134 cells derived from normal lung tissue of To further understand the special population of ACE2-expressing AT2, we performed gene ontology enrichment analysis to study which biological processes are involved with this cell population by comparing them with the AT2 cells not expressing ACE2. Of note, the 2 male donors have a higher ACE2-expressing cell ratio than all other 6 female author/funder. We also noticed that the only Asian donor (male) has a much higher ACE2Altogether, in the current study, we report the RNA expression profile of ACE2 in the human lung at single-cell resolution. https://doi.org/10.1101/2020.01.26.919985 doi: bioRxiv preprint author/funder. abstract: A novel coronavirus SARS-CoV-2 was identified in Wuhan, Hubei Province, China in December of 2019. According to WHO report, this new coronavirus has resulted in 76,392 confirmed infections and 2,348 deaths in China by 22 February, 2020, with additional patients being identified in a rapidly growing number internationally. SARS-CoV-2 was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-CoV. Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. The result indicates that the ACE2 virus receptor expression is concentrated in a small population of type II alveolar cells (AT2). Surprisingly, we found that this population of ACE2-expressing AT2 also highly expressed many other genes that positively regulating viral entry, reproduction and transmission. This study provides a biological background for the epidemic investigation of the COVID-19, and could be informative for future anti-ACE2 therapeutic strategy development. url: https://doi.org/10.1101/2020.01.26.919985 doi: 10.1101/2020.01.26.919985 id: cord-339720-d1stzy8w author: Zhao, Yuan title: Susceptibility of tree shrew to SARS-CoV-2 infection date: 2020-04-30 words: 2572.0 sentences: 180.0 pages: flesch: 58.0 cache: ./cache/cord-339720-d1stzy8w.txt txt: ./txt/cord-339720-d1stzy8w.txt summary: No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. In three young tree shrews (TS26, TS27 and TS28), we could detect viral RNA from only lungs in TS26 and TS27, but not in any tissue from TS28, although these animal had higher number of viral genomic copy numbers at the earlier stage of SARS-CoV-2 infection. Although SARS-CoV-2 infection didn''t cause severe disease in all three ages of tree shrews, viral replication and mild histopathological changes were still observed in this study. In conclusion, tree shrew is not as susceptible to SARS-CoV-2 infection as the reported animal models of COVID-19, though limited replication of SARS-CoV-2 and mild histopathology was detected and observed in some tissues. Young Old Adult 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Histopathological examination of affected tissues from SARS-CoV-2 infected tree shrews. abstract: Since SARS-CoV-2 became a pandemic event in the world, it has not only caused huge economic losses, but also a serious threat to global public health. Many scientific questions about SARS-CoV-2 and COVID-19 were raised and urgently need to be answered, including the susceptibility of animals to SARS-CoV-2 infection. Here we tested whether tree shrew, an emerging experimental animal domesticated from wild animal, is susceptible to SARS-CoV-2 infection. No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. Low levels of virus shedding and replication in tissues occurred in all three age groups, each of which showed his own characteristics. Histopathological examine revealed that pulmonary abnormalities were mild but the main changes although slight lesions were also observed in other tissues. In summary, tree shrew is not susceptible to SARS-CoV-2 infection and may not be a suitable animal for COVID-19 related researches. url: https://doi.org/10.1101/2020.04.30.029736 doi: 10.1101/2020.04.30.029736 id: cord-290802-761wqgbe author: Zhao, Zheng title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 words: 3890.0 sentences: 237.0 pages: flesch: 51.0 cache: ./cache/cord-290802-761wqgbe.txt txt: ./txt/cord-290802-761wqgbe.txt summary: title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. In sum, structurally, SARS-CoV-2 has high global/ core structural similarity to the RDRP catalytic domains of all other RNA viruses, which provides an opportunity for structure-based COVID-19 drug design and repurposing, noting that keys differences lie in the subtle details. According to the similarity of functionsite interaction fingerprints over all complexes, it was possible to divide the binding modes into four classes, where each class contains multiple PDB structures from different kinds of viruses (Table 1) . abstract: [Image: see text] The coronavirus disease of 2019 (COVID-19) pandemic speaks to the need for drugs that not only are effective but also remain effective given the mutation rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. We combined an RDRP structure data set, including 384 RDRP PDB structures and all corresponding RDRP–ligand interaction fingerprints, thereby revealing the structural characteristics of the active sites for application to RDRP-targeted drug discovery. Specifically, we revealed the intrinsic ligand-binding modes and associated RDRP structural characteristics. Four types of binding modes with corresponding binding pockets were determined, suggesting two major subpockets available for drug discovery. We screened a drug data set of 7894 compounds against these binding pockets and presented the top-10 small molecules as a starting point in further exploring the prevention of virus replication. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32946692/ doi: 10.1021/acs.jproteome.0c00623 id: cord-340028-6oicmeam author: Zhavoronkov, Alex title: Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date: 2020-03-31 words: 7228.0 sentences: 366.0 pages: flesch: 36.0 cache: ./cache/cord-340028-6oicmeam.txt txt: ./txt/cord-340028-6oicmeam.txt summary: Here we compare the expected benefit of treatments for elderly populations (60 years and older) that are currently in development, including standard preventative strategies such as vaccines and antivirals targeting SARS-CoV-2, and the potential added benefit of speculative geroprotective strategies such as rapalogs, NAD+ boosters, senolytics, and stem cell treatment. People >60 years of age with chronic medical conditions, such as type 2 diabetes or cardiovascular disease, direct immunosuppression from HIV, posttransplant or biologic treatment, pregnant individuals, or those with BMI>40, are believed to be at higher risk for influenza infection due to a weakened immune response [31] . As discussed in this paper, small clinical studies have shown that several geroprotective and senoremediative interventions, such as treatment with AGING sirolimus and rapalogs, can induce immunopotentiation, increase resistance to infection, and reduce disease severity in the elderly, without severe side effects. abstract: The recently identified SARS-CoV-2 betacoronavirus responsible for the COVID-19 pandemic has uncovered the age-associated vulnerability in the burden of disease and put aging research in the spotlight. The limited data available indicates that COVID-19 should be referred to as a gerolavic (from Greek, géros “old man” and epilavís, “harmful”) infection because the infection rates, severity, and lethality are substantially higher in the population aged 60 and older. This is primarily due to comorbidity but may be partially due to immunosenescence, decreased immune function in the elderly, and general loss of function, fitness, and increased frailty associated with aging. Immunosenescence is a major factor affecting vaccination response, as well as the severity and lethality of infectious diseases. While vaccination reduces infection rates, and therapeutic interventions reduce the severity and lethality of infections, these interventions have limitations. Previous studies showed that postulated geroprotectors, such as sirolimus (rapamycin) and its close derivative rapalog everolimus (RAD001), decreased infection rates in a small sample of elderly patients. This article presents a review of the limited literature available on geroprotective and senoremediative interventions that may be investigated to decrease the disease burden of gerolavic infections. This article also highlights a need for rigorous clinical validation of deep aging clocks as surrogate markers of biological age. These could be used to assess the need for, and efficacy of, geroprotective and senoremediative interventions and provide better protection for elderly populations from gerolavic infections. This article does not represent medical advice and the medications described are not yet licensed or recommended as immune system boosters, as they have not undergone clinical evaluation for this purpose. url: https://doi.org/10.18632/aging.102988 doi: 10.18632/aging.102988 id: cord-269488-7fy6exsd author: Zhen, Wei title: Development of a New Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection date: 2020-09-19 words: 1421.0 sentences: 73.0 pages: flesch: 56.0 cache: ./cache/cord-269488-7fy6exsd.txt txt: ./txt/cord-269488-7fy6exsd.txt summary: A LOD study with inactivated virus exhibited equal performance to the modified CDC assay with a final LOD of 1,301 ± 13 genome equivalents/ml for the Northwell Health Laboratories laboratory developed test (NWHL LDT) vs. The results demonstrate that the NWHL LDT multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and can be used as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2. The findings demonstrate that the NWHL LDT has comparable clinical performance for the specific detection of SARS-CoV-2 RNA in NP specimens and is more efficient and cost effective in comparison to the modified CDC assay. In summary, The NWHL LDT has comparable analytical sensitivity and accuracy for specific detection of SARS-CoV-2 RNA and also showed superior efficiency and cost-effectiveness when compared to the modified CDC assay. abstract: We describe the development of a new multiplex real time reverse transcription (RT)-PCR test for detection of SARS-CoV-2, with primers designed to amplify a 108 bp target on the spike surface glycoprotein (S gene) and a hydrolysis Taqman probe designed to specifically detect SARS-CoV-2. We then evaluated the limit of detection (LOD) and clinical performance of this new assay. A LOD study with inactivated virus exhibited equal performance to the modified CDC assay with a final LOD of 1,301 ± 13 genome equivalents/ml for the Northwell Health Laboratories laboratory developed test (NWHL LDT) vs. 1,249 ± 14 genome equivalents/ml for the modified CDC assay. Additionally, a clinical evaluation with 270 nasopharyngeal (NP) swab specimens exhibited 98.5% positive percent agreement and 99.3% negative percent agreement compared to the modified CDC assay. The NWHL LDT multiplex design allows testing of 91 patients per plate, versus a maximum of 29 patients per plate on the modified CDC assay, providing the benefit of testing significantly more patients per run and saving reagents, during a time when both of these parameters are critical. The results demonstrate that the NWHL LDT multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and can be used as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S1525157820304645 doi: 10.1016/j.jmoldx.2020.09.004 id: cord-332076-b0qtzzac author: Zhen, Wei title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-07-23 words: 4082.0 sentences: 216.0 pages: flesch: 50.0 cache: ./cache/cord-332076-b0qtzzac.txt txt: ./txt/cord-332076-b0qtzzac.txt summary: In the present study, we evaluated the analytical sensitivity and clinical performance of the following four SARS-CoV-2 molecular diagnostic assays granted emergency use authorization by the FDA using nasopharyngeal swabs from symptomatic patients: the New York SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel (modified CDC) assay, the Simplexa COVID-19 Direct (Diasorin Molecular) assay, GenMark ePlex SARS-CoV-2 (GenMark) assay, and the Hologic Panther Fusion SARS-CoV-2 (Hologic) assay. In this study, we evaluated the analytical and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted EUA by the FDA, including the modified CDC, DiaSorin Molecular, GenMark, and Hologic assays. For workflow, TAT, and ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, and GenMark) outperformed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, and separate areas for processing and performing the test. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel human coronavirus that causes coronavirus disease 2019 (COVID-19), was first discovered in December 2019 as the cause of an outbreak of pneumonia in the city of Wuhan, Hubei province, China. The clinical presentation of COVID-19 is fairly nonspecific, and symptoms overlap those of other seasonal respiratory infections concurrently circulating in the population. Furthermore, it is estimated that up to 80% of infected individuals experience mild symptoms or are asymptomatic, confounding efforts to reliably diagnose COVID-19 empirically. To support infection control measures, there is an urgent need for rapid and accurate molecular diagnostics to identify COVID-19-positive patients. In the present study, we evaluated the analytical sensitivity and clinical performance of the following four SARS-CoV-2 molecular diagnostic assays granted emergency use authorization by the FDA using nasopharyngeal swabs from symptomatic patients: the New York SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel (modified CDC) assay, the Simplexa COVID-19 Direct (Diasorin Molecular) assay, GenMark ePlex SARS-CoV-2 (GenMark) assay, and the Hologic Panther Fusion SARS-CoV-2 (Hologic) assay. This information is crucial for both laboratories and clinical teams as decisions on which testing platform to implement are made. url: https://www.ncbi.nlm.nih.gov/pubmed/32341143/ doi: 10.1128/jcm.00743-20 id: cord-336720-2bf3xzni author: Zhen, Wei title: Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date: 2020-04-22 words: 3045.0 sentences: 205.0 pages: flesch: 60.0 cache: ./cache/cord-336720-2bf3xzni.txt txt: ./txt/cord-336720-2bf3xzni.txt summary: In the present study, we have evaluated the analytical sensitivity and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted Emergency Use Authorization by the FDA using nasopharyngeal swabs from symptomatic patients. The LoD established by percent positive rate ranged from 1,000 copies/mL by both the GenMark and the 172 modified CDC assays to 50 copies/mL by the DiaSorin Molecular assay ( Table 2) . Overall turn-around time assessment, from sample to results, showed DiaSorin Molecular with the least 224 overall turn-around time to results, followed by GenMark, modified CDC assay and Hologic with the 225 greatest overall time ( Table 5) . DiaSorin 268 Molecular and GenMark showed 100% specificity, while Hologic and the CDC assay initially had two and 269 one discordant results, respectively. For workflow, TAT, and 298 ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, GenMark) out-299 performed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, 300 abstract: The novel human coronavirus SARS-CoV-2 was first discovered in the city of Wuhan, Hubei province, China, causing an outbreak of pneumonia in January 2020. As of April 10, 2020, the virus has rapidly disseminated to over 200 countries and territories, causing more than 1.6 million confirmed cases of COVID-19 and 97,000 deaths worldwide. The clinical presentation of COVID-19 is fairly non-specific, and symptoms overlap with other seasonal respiratory infections concurrently circulating in the population. Further, it is estimated that up to 80% of infected individuals experience mild symptoms or are asymptomatic, confounding efforts to reliably diagnose COVID-19 empirically. To support infection control measures, there is an urgent need for rapid and accurate molecular diagnostics to identify COVID-19 positive patients. In the present study, we have evaluated the analytical sensitivity and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted Emergency Use Authorization by the FDA using nasopharyngeal swabs from symptomatic patients. This information is crucial for both laboratories and clinical teams, as decisions on which testing platform to implement are made. url: https://doi.org/10.1101/2020.04.17.20069864 doi: 10.1101/2020.04.17.20069864 id: cord-336836-54o9vjdl author: Zhen, Wei title: Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 date: 2020-07-23 words: 3410.0 sentences: 165.0 pages: flesch: 54.0 cache: ./cache/cord-336836-54o9vjdl.txt txt: ./txt/cord-336836-54o9vjdl.txt summary: Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. In this study, our objective was to evaluate the analytical and clinical performance as well as the workflow of these three sample-to-answer platforms for SARS-CoV-2 detection in 108 nasopharyngeal (NP) swab specimens from symptomatic patients. We evaluated three sample-to-answer platforms currently in use in our health system for the detection of SARS-CoV-2, including Xpert Xpress and ID NOW, which are designed to be used in near-patient testing environments and outside the clinical laboratory environment. In summary, we evaluated three sample-to-answer platforms for the detection of SARS-CoV-2 using NP specimens, including two platforms that are designed to be used in the near-patient testing environment, Xpert Xpress and ID NOW. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the globe. As part of the worldwide response, many molecular diagnostic platforms have been granted emergency use authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 positive patients. Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. We found that Xpert Xpress had the lowest limit of detection (100% detection at 100 copies/ml), followed by ePlex (100% detection at 1,000 copies/ml), and ID NOW (20,000 copies/ml). Xpert Xpress also had highest positive percent agreement (PPA) compared to our reference standard (98.3%) followed by ePlex (91.4%) and ID NOW (87.7%). All three assays showed 100% negative percent agreement (NPA). In the workflow analysis, ID NOW produced the lowest time to result per specimen (∼17 min) compared to Xpert Xpress (∼46 min) and ePlex (∼1.5 h), but what ID NOW gained in rapid results, it lost in analytical and clinical performance. ePlex had the longest time to results and showed a slight improvement in PPA over ID NOW. Information about the clinical and analytical performance of these assays, as well as workflow, will be critical in making informed and timely decisions on testing platforms. url: https://doi.org/10.1128/jcm.00783-20 doi: 10.1128/jcm.00783-20 id: cord-341331-l24oe2pd author: Zheng, Baojia title: An increasing public health burden arising from children infected with SARS‐CoV2: a systematic review and meta‐analysis date: 2020-08-05 words: 3322.0 sentences: 214.0 pages: flesch: 52.0 cache: ./cache/cord-341331-l24oe2pd.txt txt: ./txt/cord-341331-l24oe2pd.txt summary: Therefore, it is valuable to perform a comprehensive analysis of the different published SARS-CoV2 pediatric cases recording clinical and epidemiological features, merging and This article is protected by copyright. The included studies were required to meet the following eligibility criteria: (1) studies focused on pediatric patients infected with SARS-CoV2 whose nucleic acid test or CT scan were positive; (2) retrospective observational studies, case reports or research articles describing the epidemiological, demographic, and clinical features of confirmed cases, which allowed stratification; and (3) a minimum size of patients (n>3) to conduct a meta-analysis. analysis, aiming to evaluate the features and situation of the children infected with SARS-CoV2 and their possibly increasing health burden on the public. In our study, we found that the proportion of asymptomatic infections in children was high; both males and females were susceptible to SARS-CoV2. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV2) is spreading all over the world and poses a great threat to humans. This study aimed to systematically review the current situation and public health burden associated with children infected with SARS‐CoV2. METHODS: We searched 4 electronic databases without language limitations. The pooled proportion or odds ratio (OR) and 95% CI confidence interval (CI) were calculated for each analysis to explore the prevalence of asymptomatic infection and coinfection, as well as to assess the sex of SARS‐CoV‐2‐infected children. RESULTS: We obtained data from 14 eligible studies with 410 patients for the meta‐analysis. The pooled proportion of asymptomatic infection was 40.45% (95%CI: 24.04‐56.85), while coinfection was 10.14% (95%CI: 3.97‐16.30), of which Mycoplasma pneumonia (50%, 95%CI: 28.24‐71.76) and influenza virus or parainfluenza virus (22.76%, 95%CI: 4.76‐40.77) were the most common pathogens. Both male and female children were susceptible to SARS‐CoV2 infection. And the pooled proportion of family clustering infection was 83.63% (95%CI: 77.54‐89.72). CONCLUSION: A high proportion of asymptomatic infections occurs in children infected with SARS‐CoV2, who are also susceptible to coinfection regardless of sex. These data affirm the increasing public health burden arising from infected children regarding the causation of asymptomatic infection or misdiagnosis and as a significant contributor to virus spread. The public should pay more attention to children during epidemics and conduct multimethod detection to further effectively identify infected children and control the source of infection. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/ppul.25008 doi: 10.1002/ppul.25008 id: cord-257265-lkzytud0 author: Zheng, Fang title: SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date: 2020-08-03 words: 4181.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-257265-lkzytud0.txt txt: ./txt/cord-257265-lkzytud0.txt summary: According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. abstract: BACKGROUND: The anti-viral effects of Novaferon, a potent antiviral protein drug on COVID-19 was evaluated in laboratory, and in a randomized, open-label, parallel group trial. METHODS: In laboratory, the inhibition of Novaferon on viral replication in cells infected with SARS-CoV-2, and on prevention of SARS-CoV-2 entry into healthy cells was determined. Antiviral effects of Novaferon in COVID-19 patients with treatment of Novaferon, Novaferon plus Lopinavir/Ritonavir, or Lopinavir/Ritonavir were evaluated. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to SARS-CoV-2 clearance. RESULTS: Novaferon inhibited the viral replication (EC(50) = 1.02 ng/ml), and prevented viral infection (EC(50) = 0.10 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher viral clearance rates on day 6than Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). Median time to viral clearance were 6 days, 6 days, and 9 days for three groups respectively, a 3-dayreductionin both Novaferon and Novaferon plus Lopinavir/Ritonavir groups compared with Lopinavir/Ritonavir group. CONCLUSIONS: Novaferon exhibited anti-SARS-CoV-2 effects in vitro and in COVID-19 patients. These data justified the further evaluation of Novaferon. TRIAL REGISTRATION NUMBER: number ChiCTR2000029496at the Chinese Clinical Trial Registry (http://www.chictr.org.cn/). url: https://www.ncbi.nlm.nih.gov/pubmed/32758689/ doi: 10.1016/j.ijid.2020.07.053 id: cord-322345-rq5gh710 author: Zheng, Fang title: A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19 date: 2020-04-29 words: 3617.0 sentences: 205.0 pages: flesch: 54.0 cache: ./cache/cord-322345-rq5gh710.txt txt: ./txt/cord-322345-rq5gh710.txt summary: We aimed to determine the anti-SARS-CoV-2 effects of Novaferon in vitro, and conducted a randomized, open-label, parallel group study to explore the antiviral effects of Novaferon for COVID-19. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to the SARS-CoV-2 clearance in COVID-19 patients Results Novaferon inhibited the viral replication in infected cells (EC50=1.02 ng/ml), and protected healthy cells from SARS-CoV-2 infection (EC50=0.1 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher SARS-CoV-2 clearance rates on day 6 than the Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). We first determined whether Novaferon was able to inhibit SARS-CoV-2 at cellular level, and then conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in patients with COVID-19 by observing the SARS-CoV-2 clearance rates at different times during the treatment period. abstract: Abstract Background Novaferon, a novel protein drug approved for the treatment of chronic hepatitis B in China, exhibits potent antiviral activities. We aimed to determine the anti-SARS-CoV-2 effects of Novaferon in vitro, and conducted a randomized, open-label, parallel group study to explore the antiviral effects of Novaferon for COVID-19. Methods In laboratory, the inhibition of Novaferon on viral replication in cells infected with SARS-CoV-2, and on SARS-CoV-2 entry into healthy cells was determined. Antiviral effects of Novaferon were evaluated in COVID-19 patients with treatment of Novaferon, Novaferon plus Lopinavir/Ritonavir, or Lopinavir/Ritonavir. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to the SARS-CoV-2 clearance in COVID-19 patients Results Novaferon inhibited the viral replication in infected cells (EC50=1.02 ng/ml), and protected healthy cells from SARS-CoV-2 infection (EC50=0.1 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher SARS-CoV-2 clearance rates on day 6 than the Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). Median time to SARS-CoV-2 clearance were 6 days, 6 days, and 9 days for three groups respectively, suggesting a 3-dayreduction of time to SARS-CoV-2 clearance in both Novaferon and Novaferon plus Lopinavir/Ritonavir groups compared with Lopinavir/Ritonavir group. Conclusions Novaferon exhibited anti-SARS-CoV-2 effects in vitro and in COVID-19 patients. These data justified the further evaluation of Novaferon. Key words: COVID-19, SARS-CoV-2, Novaferon, Antiviral drug, Lopinavir/Ritonavir url: https://doi.org/10.1101/2020.04.24.20077735 doi: 10.1101/2020.04.24.20077735 id: cord-291014-cfnoxhtd author: Zheng, Jian title: Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host date: 2018-02-28 words: 4394.0 sentences: 261.0 pages: flesch: 32.0 cache: ./cache/cord-291014-cfnoxhtd.txt txt: ./txt/cord-291014-cfnoxhtd.txt summary: In one example, our studies of mice infected with SARS-CoV showed that the severity of SARS correlated with the ability to develop a virus-specific immune response, while inhibitory alveolar macrophages and inefficient activation of dendritic cells (DCs) delayed this process and aggravated disease [1] . The CoV endonuclease, nsp15, efficiently prevented activation of host cell dsRNA sensors including melanoma differentiation-associated protein 5 (Mda5), 2 0 -5 0 oligoadenylate synthetase (OAS) and PKR [93, 94 ] , while coronavirus-encoded proteases countered innate immunity, including the IFN response, through diverse pathways [95] . Glycosylation of the HA protein not only mediated virus entry into host cells [115] [116] [117] , but also modulated IAV replication and transmission [118] , and the immune response against the virus [119] [120] [121] , thus representing a potential target for vaccine and drug development [122, 123 ] . abstract: Respiratory viruses, especially influenza A viruses and coronaviruses such as MERS-CoV, represent continuing global threats to human health. Despite significant advances, much needs to be learned. Recent studies in virology and immunology have improved our understanding of the role of the immune system in protection and in the pathogenesis of these infections and of co-evolution of viruses and their hosts. These findings, together with sophisticated molecular structure analyses, omics tools and computer-based models, have helped delineate the interaction between respiratory viruses and the host immune system, which will facilitate the development of novel treatment strategies and vaccines with enhanced efficacy. url: https://doi.org/10.1016/j.coviro.2017.11.002 doi: 10.1016/j.coviro.2017.11.002 id: cord-321358-plxz5mkg author: Zheng, Jun title: SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat date: 2020-03-15 words: 4759.0 sentences: 251.0 pages: flesch: 53.0 cache: ./cache/cord-321358-plxz5mkg.txt txt: ./txt/cord-321358-plxz5mkg.txt summary: An ongoing outbreak of pneumonia caused by a novel coronavirus, currently designated as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was reported recently. In this review, we summarize the key events occurred during the early stage of SARS-CoV-2 outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients as well as the possible transmission pathways of the virus. CoVs have been identified in both avian hosts and various mammals, including bat, camels, dogs and masked palm civets, and are previously regarded as pathogens that only cause mild diseases in the immunocompetent people until the emergence of the coronavirus causing severe acute respiratory syndrome (SARS-CoV) in late of 2002 [3] [4] [5] [6] . abstract: An ongoing outbreak of pneumonia caused by a novel coronavirus, currently designated as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was reported recently. However, as SARS-CoV-2 is an emerging virus, we know little about it. In this review, we summarize the key events occurred during the early stage of SARS-CoV-2 outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients as well as the possible transmission pathways of the virus. Furthermore, we also review the current knowledge on the origin and evolution of the SARS-CoV-2. We highlight bats as the potential natural reservoir and pangolins as the possible intermediate host of the virus, but their roles are waiting for further investigation. Finally, the advances in the development of chemotherapeutic options are also briefly summarized. url: https://www.ncbi.nlm.nih.gov/pubmed/32226285/ doi: 10.7150/ijbs.45053 id: cord-279172-d2algx16 author: Zheng, Kewen title: Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme date: 2006-11-02 words: 6381.0 sentences: 284.0 pages: flesch: 58.0 cache: ./cache/cord-279172-d2algx16.txt txt: ./txt/cord-279172-d2algx16.txt summary: During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 Å, which agrees well with the experimental observations made by X‐ray crystallography; (ii) His163 and Glu166 form the "tooth" conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate‐binding pocket formed by loop 140–146 and loop 184–197 is large enough to accommodate the substrate analog. In this research, by comparing the process of the MD simulation of monomer with dimer, our aim is to (i) find the structural variations and dynamics of the active site residues in SARS M pro monomer in contrast to the dimer, which result in an inactive monomer and provide useful information for receptor based drug design; (ii) investigate the detailed specific interactions involving the two monomers within the dimer and its functional roles in maintaining the activity of the dimer, which provides insights for the design of specific protease inhibitors using the interface of the dimer as a new target. abstract: The phenomenon that SARS coronavirus main protease (SARS M(pro)) dimer is the main functional form has been confirmed by experiment. However, because of the absence of structural information of the monomer, the reasons for this remain unknown. To investigate it, two molecular dynamics (MD) simulations in water for dimer and monomer models have been carried out, using the crystal structure of protomer A of the dimer as the starting structure for the monomer. During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 Å, which agrees well with the experimental observations made by X‐ray crystallography; (ii) His163 and Glu166 form the “tooth” conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate‐binding pocket formed by loop 140–146 and loop 184–197 is large enough to accommodate the substrate analog. However, during the MD simulation of the monomer complex, the three structural characteristics are all absent, which results directly in the inactivation of the monomer. Throughout the MD simulation of the dimer, the N‐terminus of protomer B forms stable hydrogen bonds with Phe140 and Glu166, through which His163, Glu166, and loop 140–146 are kept active form. Furthermore, a water‐bridge has been found between the N‐terminus of protomer B and Gly170, which stabilizes His172 and avoids it moving toward Tyr161 to disrupt the H‐bond between Tyr161 and His163, stabilizing the conformation of His163. The interactions between the N‐terminus and another monomer maintain the activity of dimer. Proteins 2007. © 2006 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17083088/ doi: 10.1002/prot.21160 id: cord-283912-ha2xwjzy author: Zheng, Meijuan title: Serum inflammatory factors are positively correlated with the production of specific antibodies in coronavirus disease 2019 patients date: 2020-09-22 words: 1523.0 sentences: 78.0 pages: flesch: 46.0 cache: ./cache/cord-283912-ha2xwjzy.txt txt: ./txt/cord-283912-ha2xwjzy.txt summary: 5 Thus, a detailed characterization of the associations between humoral immune responses and inflammatory factors could result in a better understanding of SARS-CoV-2-host interactions in COVID-19 patients. In the current study, the levels of RBD-specific IgG, RBD-specific IgA, and the frequencies of ASCs and ICOS+ T follicular helper (TFH) cells were found to be higher in severely affected COVID-19 patients than those in nonseverely affected patients. Collectively, these results indicated that severe COVID-19 illness induced strong humoral immune responses, which is consistent with previous studies showing higher IgG titers in severe patients than in nonsevere patients. Our study showed that the severely affected patients displayed higher levels of anti-RBD antibodies, increased frequencies of ASCs and ICOS + TFH cells, and elevated levels of CXCL13. Effective control of SARS-CoV-2 requires further investigation of the mechanism underlying the correlations between humoral immunity and inflammatory factors in severe COVID-19, and the results of such studies could be used to guide immunotherapy with passive antibodies while controlling hyperinflammation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32963357/ doi: 10.1038/s41423-020-00551-1 id: cord-288500-ko4eda9w author: Zheng, Ruijun title: Prevalence and associated factors of depression and anxiety among nurses during the outbreak of COVID-19 in China: A cross-sectional study date: 2020-10-23 words: 4678.0 sentences: 260.0 pages: flesch: 52.0 cache: ./cache/cord-288500-ko4eda9w.txt txt: ./txt/cord-288500-ko4eda9w.txt summary: The results indicated that COVID-19-related stress, relationship quality with family, and demographic characteristics were associated with depression, anxiety, and perceived health status. A study reported that health care workers at high risk of contracting SARS were more likely to have a higher prevalence of depression and anxiety, and develop post-traumatic stress during the SARS epidemic (McAlonan et al., 2007) . In this study, we hypothesize that COVID-19-related stress, relationship quality with family, and perceived health status are associated with the risk of depression and anxiety. The questionnaire contained ten main items: unknown origin of COVID-19, fear of infection, lack of effective treatment, poor patient compliance, nursing workload, poor social support, parent-child relationship quality, couple relationship quality, relationship quality with other family members, and perceived health status. The main findings indicated that nurses experiencing COVID-19-related stress and poor relationship quality with family were more likely to develop depression and anxiety symptoms and have health concerns. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a public health emergency of international concern and has caused traumatic experience for nurses worldwide. However, the prevalence of depression and anxiety symptoms in nurses, and how psychosocial factors influence nurses in this public crisis are unknown. OBJECTIVES: To determine the effect of COVID-19 on the mental health of nurses and the prevalence of anxiety and depression symptoms among nurses in China during the outbreak. DESIGN: A cross-sectional study. SETTINGS AND PARTICIPANTS: A total of 3,228 nurses in Sichuan Province and Wuhan City were selected by convenience sampling. All participants were invited to complete the questionnaire through WeChat from January 27 to February 3, 2020. METHODS: A self-reported questionnaire combining depression and anxiety scale was used to collect data anonymously. Binary and multivariate logistic regression was applied to measure the odds of psychosocial factors of anxiety and depression and perceived health, respectively. RESULTS: The total incidence of depression (34.3%) and anxiety (18.1%) during the COVID-19 outbreak was lower than that during the SARS outbreak; however, the rate of depression in our study (47.1%) was high and similar in a recent study (50.4%) about the health care workers exposed to COVID-19 in China. The results indicated that COVID-19-related stress, relationship quality with family, and demographic characteristics were associated with depression, anxiety, and perceived health status. Furthermore, the prevalence of depression was similar between nurses working in low-risk COVID-19 wards was as high as working in high-risk COVID-19 wards (OR, 1.078; 95% CI, 0.784–1.481). CONCLUSIONS: Our study revealed the high prevalence of depression and anxiety among nurses during the outbreak of COVID-19. COVID-19 factors and psychosocial factors were associated with mental health of nurses. The results suggest that hospitals should implement effective mental health promotion programs focused on occupational safety and family support to improve the well-being of nurses. url: https://api.elsevier.com/content/article/pii/S0020748920302959 doi: 10.1016/j.ijnurstu.2020.103809 id: cord-304871-gva617yp author: Zheng, Ting title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-06-08 words: 2576.0 sentences: 162.0 pages: flesch: 53.0 cache: ./cache/cord-304871-gva617yp.txt txt: ./txt/cord-304871-gva617yp.txt summary: title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China The objective of this study is to compare clinical characteristics and outcomes between patients with and without GI symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan. This retrospective study included 1320 patients with confirmed COVID-19 infection admitted to Jianghan Fangcang Shelter Hospital from February 5, 2020, to March 9, 2020. Multivariable logistic regression analysis showed Accepted Article that GI symptoms (p=0.045), male gender (p<0.001), and elevated CRP (p=0.008) were independent risk factors for patient transfer to a tertiary hospital ( Table 3) . Potential risk factors for developing GI symptoms, male gender, and increased CRP may help clinicians predict clinical worsening in COVID-19 patients. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms abstract: OBJECTIVE: Coronavirus disease 2019 (COVID‐19) is a health emergency worldwide, and gastrointestinal (GI) symptoms are increasingly reported in COVID‐19 patients. However, sample size was small and the incidence of GI symptoms in patients was variable across studies, and the correlation between these symptoms and clinical outcomes remains incompletely understood. The objective of this study is to compare clinical characteristics and outcomes between patients with and without GI symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan. METHODS: All patients admitted to Jianghan Fangcang Shelter Hospital were evaluated. Data on epidemiological and clinical characteristics, laboratory findings, treatment procedures, and clinical outcomes were retrieved from electronic medical records. RESULTS: This retrospective study recruited 1320 COVID‐19 patients admitted to hospital from February 5, 2020, to March 9, 2020. On the basis of the presence of GI symptoms, the sample was divided into a GI group (n=192) and a non‐GI group (n=1128). The most common GI symptoms were diarrhea (8.1%), anorexia (4.7%), and nausea and vomiting (4.3%). The risk of clinical deterioration was significantly higher in the GI group than in the non‐GI group (15.6% vs. 10.1%, p=0.032). GI symptoms (p=0.045), male gender (p<0.001), and increased C‐reactive protein (p=0.008) were independent risk factors for clinical worsening. CONCLUSION: The risk of clinical deterioration was significantly higher in the GI group. Furthermore, potential risk factors for developing GI symptoms, male gender, and increased C‐reactive protein can help clinicians predict clinical outcomes in COVID‐19 patients. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26146 doi: 10.1002/jmv.26146 id: cord-308833-ei1faruy author: Zheng, Xiaohong title: Experimental investigation of integrated air purifying technology for bioaerosol removal and inactivation in central air-conditioning system date: 2004 words: 2763.0 sentences: 158.0 pages: flesch: 54.0 cache: ./cache/cord-308833-ei1faruy.txt txt: ./txt/cord-308833-ei1faruy.txt summary: In this research, high voltage static electricity and ultraviolet technologies were integrated to an air purifying device which can be used to trap and kill airborne bacteria and viruses in central air-conditioning systems. This provides a basis for using this particular phage strain as a viral simulant in place of SARS CoV and other airborne viruses in the tests for evaluation of bioaerosol removal and inactivation by different types of air purifiers. Fig. 4(a) shows that the plaques formed on a GSM plate were used to sample the airflow containing phage aerosol generated with a source suspension with 10 5 pfu/mL when the integrated air purifier was turned off. In addition to particle removal test, airborne bacteria were also sampled in the experimental room with the integrated air purifier. Based upon the integrated technology of high voltage electric field, ultraviolet ray, composite silver material, and activated carbon fibers, an air purifying device has been developed to prevent airborne bacteria and virus spread through central air-conditioning system. abstract: In this research, high voltage static electricity and ultraviolet technologies were integrated to an air purifying device which can be used to trap and kill airborne bacteria and viruses in central air-conditioning systems. An experimental platform was built to mimic the central air system, in which the efficacy of the newly built device was examined. In addition to the standard physical and chemical tests, bacteriophages were used to simulate airborne viruses in the experimental system. The bacteriophage suspension was aerosolized into the air with ultrasonic wave atomization. The result showed that more than 86% removal efficiency of micro-particles (<10 micron in diameter) were removed after the device was in operation in a building and more than 95% of bacteriophages in the experimental system. It is concluded that the integrated air purifier is suitable for controlling air quality and preventing virus transmission through the central air system. url: https://www.ncbi.nlm.nih.gov/pubmed/32214716/ doi: 10.1007/bf03182817 id: cord-017108-vqbl0eov author: Zheng, Xiaolong title: Network-Based Analysis of Beijing SARS Data date: 2008 words: 2427.0 sentences: 158.0 pages: flesch: 56.0 cache: ./cache/cord-017108-vqbl0eov.txt txt: ./txt/cord-017108-vqbl0eov.txt summary: Instead, a strategy that focuses on nodes (e.g., patients, locations, or occupations) with high degree and strength may lead to more effective outbreak control and management. A public health implication of this finding is that the traditional disease control approach based on random immunization (which has been shown to be effective in many epidemic outbreaks [8] ) may not be effective (unless, of course, the entire population can be treated), because untreated hubs, albeit small in number, can still lead to rapid and large-scale infections [8] . In this section, we analyze the SARS transmission patterns based on the weighted occupation network (WON) as shown in Fig. 7 . To better understand the SARS epidemic transmission patterns and evolution, we have studied three networks derived from the patient survey data, including a patient contact network, a weighted district network, and a weighted occupation network. abstract: In this paper, we analyze Beijing SARS data using methods developed from the complex network analysis literature. Three kinds of SARS-related networks were constructed and analyzed, including the patient contact network, the weighted location (district) network, and the weighted occupation network. We demonstrate that a network-based data analysis framework can help evaluate various control strategies. For instance, in the case of SARS, a general randomized immunization control strategy may not be effective. Instead, a strategy that focuses on nodes (e.g., patients, locations, or occupations) with high degree and strength may lead to more effective outbreak control and management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121587/ doi: 10.1007/978-3-540-89746-0_7 id: cord-313639-qpt47sx2 author: Zheng, Yi title: Clinical characteristics of 34 COVID-19 patients admitted to intensive care unit in Hangzhou, China date: 2020-05-20 words: 3723.0 sentences: 191.0 pages: flesch: 49.0 cache: ./cache/cord-313639-qpt47sx2.txt txt: ./txt/cord-313639-qpt47sx2.txt summary: OBJECTIVE: This study summarizes and compares clinical and laboratory characteristics of 34 patients admitted to the intensive care unit (ICU) for complications from coronavirus disease 2019 (COVID-19) at the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China from Jan. 22 to Mar. 5, 2020. For this retrospective study, we analyzed data from patients admitted between Jan. 22 and Mar. 5, 2020, who had been diagnosed (according to the guidance of NHC (2020a)) with SARS-CoV-2 pneumonia in the ICU in the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. In this single-center case series of 34 ICU patients with SARS-CoV-2 infection in Hangzhou, China, 97.1% (33 cases) of patients had complications caused by ARDS, 44.1% (15) received IMV, 55.9% (19) only needed noninvasive respiratory support. abstract: OBJECTIVE: This study summarizes and compares clinical and laboratory characteristics of 34 patients admitted to the intensive care unit (ICU) for complications from coronavirus disease 2019 (COVID-19) at the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China from Jan. 22 to Mar. 5, 2020. METHODS: A total of 34 patients were divided into two groups, including those who required noninvasive ventilation (NIV) and invasive mechanical ventilation (IMV) with additional extracorporeal membrane oxygenation (ECMO) in 11 patients. Clinical features of COVID-19 patients were described and the parameters of clinical characteristics between the two groups were compared. RESULTS: The rates of the acute cardiac and kidney complications were higher in IMV cases than those in NIV cases. Most patients had lymphocytopenia on admission, with lymphocyte levels dropping progressively on the following days, and the more severe lymphopenia developed in the IMV group. In both groups, T lymphocyte counts were below typical lower limit norms compared to B lymphocytes. On admission, both groups had higher than expected amounts of plasma interleukin-6 (IL-6), which over time declined more in NIV patients. The prothrombin time was increased and the levels of platelet, hemoglobin, blood urea nitrogen (BUN), D-dimer, lactate dehydrogenase (LDH), and IL-6 were higher in IMV cases compared with NIV cases during hospitalization CONCLUSIONS: Data showed that the rates of complications, dynamics of lymphocytopenia, and changes in levels of platelet, hemoglobin, BUN, D-dimer, LDH and IL-6, and prothrombin time in these ICU patients were significantly different between IMV and NIV cases. url: https://doi.org/10.1631/jzus.b2000174 doi: 10.1631/jzus.b2000174 id: cord-282795-kje7rn57 author: Zheng, Yue title: Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date: 2020-09-21 words: 487.0 sentences: 36.0 pages: flesch: 58.0 cache: ./cache/cord-282795-kje7rn57.txt txt: ./txt/cord-282795-kje7rn57.txt summary: To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. Pseudotyped MLV viruses were tested on HEK293FT, HEK293T-ACE2, Huh7 and SupT1 cells. To test for specificity of neutralization, we asked whether neutralizing antibodies from SARSCoV-2 patients would exhibit cross-reactivity against a pseudotype expressing SARS-CoV-1 ( Figure 112 4). Characterization of 162 spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with 163 SARS-CoV Veesler D: Structure, Function, and 165 Antigenicity of the SARS-CoV-2 Spike Glycoprotein The 167 D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases 168 infectivity High-efficiency gene 170 transfer into CD34+ cells with a human immunodeficiency virus type 1-based retroviral 171 vector pseudotyped with vesicular stomatitis virus envelope glycoprotein G Pseudotyping Viral Vectors With Emerging Virus Envelope 177 Proteins abstract: Antibody neutralization is an important prognostic factor in many viral diseases. To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. These pseudovirions provide a practical means of assessing immune responses under laboratory conditions consistent with biocontainment level 2. url: https://www.ncbi.nlm.nih.gov/pubmed/32995778/ doi: 10.1101/2020.07.17.207563 id: cord-290904-ngvhk0qy author: Zheng, Zhiqiang title: Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date: 2020-07-16 words: 4471.0 sentences: 246.0 pages: flesch: 57.0 cache: ./cache/cord-290904-ngvhk0qy.txt txt: ./txt/cord-290904-ngvhk0qy.txt summary: In this study, we aim to verify if the sequence of the immunogen used to generate mAb 1A9, as well as three other mAbs, is conserved in different coronaviruses and if these mAbs bind to the S protein of SARS-CoV-2 expressed in mammalian cell lines. IF analysis performed on transiently transfected COS-7 cells showed binding of the four mAbs to this S protein fragment of SARS-CoV-2 ( Figure 2B ). Utility of monoclonal antibody 1A9 for detection of S protein in a sandwich ELISA format and in SARS-CoV-2 infected cells Based on indirect ELISA data, mAb 1A9 has the strongest binding to S protein when compared with the other three mAbs. Hence, a sandwich ELISA was performed to determine if it can be paired with the human mAb CR3022 which is known to bind to the S1 subunit of SARS-CoV-2. abstract: BACKGROUND: A novel coronavirus, SARS-CoV-2, which emerged at the end of 2019 and causes COVID-19, has resulted in worldwide human infections. While genetically distinct, SARS-CoV-1, the aetiological agent responsible for an outbreak of severe acute respiratory syndrome (SARS) in 2002–2003, utilises the same host cell receptor as SARS-CoV-2 for entry: angiotensin-converting enzyme 2 (ACE2). Parts of the SARS-CoV-1 spike glycoprotein (S protein), which interacts with ACE2, appear conserved in SARS-CoV-2. AIM: The cross-reactivity with SARS-CoV-2 of monoclonal antibodies (mAbs) previously generated against the S protein of SARS-CoV-1 was assessed. METHODS: The SARS-CoV-2 S protein sequence was aligned to those of SARS-CoV-1, Middle East respiratory syndrome (MERS) and common-cold coronaviruses. Abilities of mAbs generated against SARS-CoV-1 S protein to bind SARS-CoV-2 or its S protein were tested with SARS-CoV-2 infected cells as well as cells expressing either the full length protein or a fragment of its S2 subunit. Quantitative ELISA was also performed to compare binding of mAbs to recombinant S protein. RESULTS: An immunogenic domain in the S2 subunit of SARS-CoV-1 S protein is highly conserved in SARS-CoV-2 but not in MERS and human common-cold coronaviruses. Four murine mAbs raised against this immunogenic fragment could recognise SARS-CoV-2 S protein expressed in mammalian cell lines. In particular, mAb 1A9 was demonstrated to detect S protein in SARS-CoV-2-infected cells and is suitable for use in a sandwich ELISA format. CONCLUSION: The cross-reactive mAbs may serve as useful tools for SARS-CoV-2 research and for the development of diagnostic assays for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32700671/ doi: 10.2807/1560-7917.es.2020.25.28.2000291 id: cord-276034-a8pixbuc author: Zhi, Yan title: Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein date: 2005-04-25 words: 6210.0 sentences: 298.0 pages: flesch: 49.0 cache: ./cache/cord-276034-a8pixbuc.txt txt: ./txt/cord-276034-a8pixbuc.txt summary: Overlapping peptides were used to identify major histocompatibility complex class I-restricted epitopes in mice immunized with vectors encoding codon-optimized SARS-CoV spike protein. The optimized recombinant adenoviral vaccine vectors encoding spike can generate robust antigen-specific cellular immunity in mice and may potentially be useful for control of SARS-CoV infection. Therefore, several versions of replication-defective adenoviral vectors expressing spike protein were created to induce spike-specific T cell responses in mice and to screen for CD8 T-cell epitopes using an overlapping peptide library spanning the entire spike protein in IFN-g ELISPOT and intracellular IFN-g staining assays. More importantly, a single administration of the optimized SARS-CoV spike vaccine vectors based on replication-defective human and simian adenovirus can generate strong spikespecific CD8 T-cell responses in mice. More importantly, a single administration of an optimized SARS-CoV spike vaccine vector based on a replication-defective simian adenovirus can generate strong spike-specific CD8 T-cell responses in mice. abstract: The causative agent of severe acute respiratory syndrome (SARS) has been identified as a new type of coronavirus, SARS-associated coronavirus (SARS-CoV). CD8 T cells play an important role in controlling diseases caused by other coronaviruses and in mediating vaccine-induced protective immunity in corresponding animal models. The spike protein, a main surface antigen of SARS-CoV, is one of the most important antigen candidates for vaccine design. Overlapping peptides were used to identify major histocompatibility complex class I-restricted epitopes in mice immunized with vectors encoding codon-optimized SARS-CoV spike protein. CD8 T-cell responses were mapped to two H-2(b)-restricted epitopes (S436–443 and S525–532) and one H-2(d)-restricted epitope (S366–374). The identification of these epitopes will facilitate the evaluation of vaccine strategies in murine models of SARS-CoV infection. Furthermore, codon and promoter optimizations can greatly enhance the overall immunogenicity of spike protein in the context of replication-defective human and simian adenoviral vaccine carriers. The optimized recombinant adenoviral vaccine vectors encoding spike can generate robust antigen-specific cellular immunity in mice and may potentially be useful for control of SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15823604/ doi: 10.1016/j.virol.2005.01.050 id: cord-255774-ux3c3dzf author: Zhong, H. title: Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients date: 2020-07-05 words: 2900.0 sentences: 139.0 pages: flesch: 48.0 cache: ./cache/cord-255774-ux3c3dzf.txt txt: ./txt/cord-255774-ux3c3dzf.txt summary: Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Likewise, metatranscriptomics-detected bacterial or fungal respiratory co-infections were 6 3 defined if the respiratory specimens (at least one sample) of severe patients were mono-dominated (relative abundance >60%) by 6 4 pathogenic microbes known to cause nosocomial infections (appendix 2 p 9: TableS8). Sixty-seven serial 9 7 clinical specimens from the respiratory tract (RT) (n=47, sputum, nasal and throat swab) and gastrointestinal tract (GIT) (n=20, 9 8 anal swab and feces) of these patients were obtained during the same above period for comprehensive assessment of microbial non-rRNA transcripts) varied between different types of specimens, constituting a relatively high fraction of total high-quality 0 6 reads among RT specimens and a low fraction among GIT specimens (appendix 1 p 1: Supplementary figure 1 and appendix 2 0 7 p 4: TableS3). abstract: Summary Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics. url: http://medrxiv.org/cgi/content/short/2020.07.02.20143032v1?rss=1 doi: 10.1101/2020.07.02.20143032 id: cord-214854-ck61ja2t author: Zhong, Jing title: Rapid and sensitive detection of SARS-CoV-2 with functionalized magnetic nanoparticles date: 2020-10-08 words: 2059.0 sentences: 120.0 pages: flesch: 47.0 cache: ./cache/cord-214854-ck61ja2t.txt txt: ./txt/cord-214854-ck61ja2t.txt summary: Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and sensitive detection of specific biomolecules, e.g. protein, DNA/RNA and virus. demonstrated the feasibility of wash-free, sensitive and specific assays for the detection of different viruses, e.g. orchid and influenza viruses, with antibody-functionalized MNPs by measuring the reduction in the ac susceptibility in mixed-frequency ac magnetic fields [23] [24] [25] . All these approaches have demonstrated that MNP-based homogeneous biosensing is a wash-free and mix-and-measure approach for rapid and sensitive detection of specific biomolecules. abstract: The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies, and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important and urgent strategies throughout the whole world. As of October, 2020, there have not yet been any medicines or therapies to be effective against SARS-CoV-2. Thus, rapid and sensitive diagnostics is the most important measures to control the outbreak of SARS-CoV-2. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. Experimental results demonstrate that the proposed approach allows the rapid detection of mimic SARS-CoV-2 with a limit of detection of 0.084 nM (5.9 fmole). The proposed approach has great potential for designing a low-cost and point-of-care device for rapid and sensitive diagnostics of SARS-CoV-2. url: https://arxiv.org/pdf/2010.03886v1.pdf doi: nan id: cord-017715-99ri6x0y author: Zhou, Bo-Ping title: SARS date: 2015-07-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe acute respiratory syndrome (SARS) is an acute respiratory tract infectious disease induced by SARS-CoV and mainly transmitted through the short-distance air droplets and close contact. Its main clinical characteristics is abrupt onset of the disease and the initial symptom is fever accompanied with systematic symptoms of headache, soreness and fatigue, and respiratory tract symptoms such as cough, chest dullness, and dyspnea. A few cases may progress to acute respiratory distress syndrome (ARDS). Due to its self-limiting feature, the prognosis is predominantly good but may be poor in severe cases, with mortality about 9.3 %. Some patients may develop such complications such as lung fibrosis and necrosis of the head of femur. On April 8, 2003, SARS was defined as a legal infectious disease by the Ministry of Heath of China. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122356/ doi: 10.1007/978-94-017-7363-8_2 id: cord-327711-welf0eb1 author: Zhou, Daming title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date: 2020-06-13 words: 4847.0 sentences: 290.0 pages: flesch: 59.0 cache: ./cache/cord-327711-welf0eb1.txt txt: ./txt/cord-327711-welf0eb1.txt summary: Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. A neutralisation test for EY6A based on quantitative PCR detection of virus in the supernatant bathing infected Vero E6 cells after 5 days of culture, showed a ~1000-fold reduction in virus signal (Methods, Extended Data Fig. 3 ) indicating that it is highly neutralising. To elucidate the epitope of EY6A, we determined the crystal structures of the deglycosylated SARS-CoV-2 RBD in complex with EY6A Fab alone and in a ternary complex incorporating a nanobody (Nb) which has been shown to compete with ACE2 (for data on a closely related Nb see Huo 2020, submitted), as a crystallisation chaperone. abstract: The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6Å crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. url: https://doi.org/10.1101/2020.06.12.148387 doi: 10.1101/2020.06.12.148387 id: cord-278169-elhz77ek author: Zhou, Dapeng title: Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics date: 2020-06-10 words: 4216.0 sentences: 237.0 pages: flesch: 51.0 cache: ./cache/cord-278169-elhz77ek.txt txt: ./txt/cord-278169-elhz77ek.txt summary: In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1–4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1. The receptor-binding domain region of the SARS-CoV-1spike protein is densely covered by glycans except FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ, which overlaps with a previously identified "Achilles heel" (i.e., vulnerable spot) for antibody binding (Berry, et al. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on Severe Acute Respiratory Syndrome Coronavirus Neutralization Escape and Fitness abstract: Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins. The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown. Glycosylation by insect cells differs from the native form produced in human cells, but insect cell–derived influenza vaccines have been approved by the US Food and Drug Administration. In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1–4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites. We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1. All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans. MS/MS fragmentation clearly established the glycopeptide identities. Electron densities of glycans cover most of the spike receptor-binding domain of SARS-CoV-2, except YQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ, similar to a region FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ in SARS-CoV-1. Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain. Because the majority of antibody paratopes bind to the peptide portion with or without sugar modification, we propose a snake-catching model for predicted paratopes: a minimal length of peptide is first clamped by a paratope, and sugar modifications close to the peptide either strengthen or do not hinder the binding. url: https://www.ncbi.nlm.nih.gov/pubmed/32518941/ doi: 10.1093/glycob/cwaa052 id: cord-328687-clr1e9p6 author: Zhou, Fuling title: Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey date: 2020-09-15 words: 3719.0 sentences: 189.0 pages: flesch: 45.0 cache: ./cache/cord-328687-clr1e9p6.txt txt: ./txt/cord-328687-clr1e9p6.txt summary: BACKGROUND: Asymptomatic carriers were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without developing symptoms, which might be a potential source of infection outbreak. Recently, in order to avoid further nosocomial infection, all staff without clinical symptoms in our hospital participated in the physical examination before resumption of ordinary job, including chest CT, throat swab RT-PCR test and plasma COVID-19 IgM/IgG antibodies test. This study aims to analyze the examination results, understand the infection status of staff, track the infection related risk factors, as well as tracing of asymptomatic infection individual, so as to provide effective suggestions for other hospitals and non-medical institution in Wuhan, ensuring scientific and safe return to work. In our study, asymptomatic carrier refers to patients who have mild or non-symptoms but with positive test for viral nucleic acid of SARS-CoV-2 or with positive test for serum specific IgM antibody. abstract: BACKGROUND: Asymptomatic carriers were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without developing symptoms, which might be a potential source of infection outbreak. Here, we aim to clarify the epidemiologic and influencing factors of asymptomatic carriers in the general population. METHODS: In our hospital, all hospital staff have received throat swab RT-PCR test, plasma COVID-19 IgM/IgG antibodies test and chest CT examination. We analyzed the correlation between infection rates and gender, age, job position, work place and COVID-19 knowledge training of the staff. After that, all asymptomatic staff were re-examined weekly for 3 weeks. FINDINGS: A total of 3764 hospital staff were included in this single-center cross-sectional study. Among them, 126 hospital staff had abnormal findings, and the proportion of asymptomatic infection accounted for 0.76% (28/3674). There were 26 staff with IgM+, 73 with IgG+, and 40 with ground glass shadow of chest CT. Of all staff with abnormal findings, the older they are, the more likely they are to be the staff with abnormal results, regardless of their gender. Of 3674 hospital staff, the positive rate of labor staff is obviously higher than that of health care workers (HCWs) and administrative staff (P<0.05). In the course of participating in the treatment of COVID-19, there was no statistically significant difference in positive rates between high-risk departments and low-risk departments (P>0.05). The positive rate of HCWs who participated in the COVID-19 knowledge training was lower than those did not participate in early training (P <0.01). Importantly, it was found that there was no statistical difference between the titers of IgM antibody of asymptomatic infections and confirmed patients with COVID-19 in recovery period (P>0.05). During 3 weeks follow-up, all asymptomatic patients did not present the development of clinical symptoms or radiographic abnormalities after active intervention in isolation point. INTERPRETATION: To ensure the safety of resumption of work, institutions should conduct COVID-19 prevention training for staff and screening for asymptomatic patients, and take quarantine measures as soon as possible in areas with high density of population. FUNDING: The Key Project for Anti-2019 novel Coronavirus Pneumonia from the Ministry of Science and Technology, China; Wuhan Emergency Technology Project of COVID-19 epidemic, China. url: https://www.ncbi.nlm.nih.gov/pubmed/32954232/ doi: 10.1016/j.eclinm.2020.100510 id: cord-294363-bv6xa8v8 author: Zhou, Hong title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 words: 8902.0 sentences: 456.0 pages: flesch: 46.0 cache: ./cache/cord-294363-bv6xa8v8.txt txt: ./txt/cord-294363-bv6xa8v8.txt summary: Several studies demonstrated angiotensin converting enzyme 2 (ACE2) as an important therapeutic target of SARS-CoV-2 entry and infection, and many potential targets were subsequently proposed, such as the spike (S) protein and transmembrane serine protease 2 (TMPRSS2). Therefore, accelerating research for potential therapeutic target confirmation, promising drug discovery, and clinical verification development will speed up efforts to combat SARS-CoV-2. In addition to inhibiting the virus directly, ASOs are also expected to target the disease-related proteins involved in the inflammatory cytokine storm process, which could be considered a promising therapeutic strategy for combating SARS-CoV-2 . Although many strategies have been used to block the attachment, entry, replication and release processes to inhibit SARS-CoV-2 infection, how to prevent viral evasion from host immune responses and virus-induced cytopathic effects is considered one of the most urgent problems that need to be solved in SARS-CoV-2-induced pneumonia-associated respiratory syndrome (PARS) patients. abstract: As of April 9, 2020, a novel coronavirus (SARS‐CoV‐2) had caused 89,931 deaths and 1,503,900 confirmed cases worldwide, which indicates an increasingly severe and uncontrollable situation. Initially, little was known about the virus. As research continues, we have learned the genome structure, epidemiological and clinical characteristics and pathogenic mechanisms of SARS‐CoV‐2. Based on these discoveries, identifying potential targets involved in the processes of virus pathogenesis is urgently needed, and discovering or developing promising drugs based on potential targets is the most pressing need. Therefore, we summarize the potential therapeutic targets involved in virus pathogenesis and discuss the advancements, possibilities and significance of promising drugs based on these targets for treating SARS‐CoV‐2. This review will facilitate the identification of potential targets and provide promising clues for drug development that can be translated into clinical applications for combating SARS‐CoV‐2. url: https://www.ncbi.nlm.nih.gov/pubmed/32368792/ doi: 10.1111/bph.15092 id: cord-318126-gg68o52z author: Zhou, Juan title: Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection date: 2020-04-03 words: 972.0 sentences: 67.0 pages: flesch: 54.0 cache: ./cache/cord-318126-gg68o52z.txt txt: ./txt/cord-318126-gg68o52z.txt summary: We read with interest the article in this journal which revealed that CT scanning provides important bases for early diagnosis and treatment of COVID-19 (Corona Virus Infection Disease 2019) which is caused by SARS-COV2 (Severe Acute Respiratory Syndrome Coronavirus 2). We observed and analyzed the phenotypic characteristics of asymptomatic individuals originating from the active detection of high-risk individuals who had close contacts with COVID-19 patients during isolated observation with viral nucleic acid positive. A total of 26 cases of asymptomatic infection were detected as SARS-COV2 positive through swab specimen between January 20 to February 30. These data showed that people of different ages are generally susceptible to SARS-COV2, but the average age of asymptomatic patients is lower than the reported age of COVID-19 patients which was 40-70 years old (propinquity 73%). These cases proved that asymptomatic SARS-COV2 carriers can also spread the virus before the https://doi.org/10.1016/j.jinf.2020.03.028 0163-4453/© 2020 The British Infection Association. abstract: nan url: https://doi.org/10.1016/j.jinf.2020.03.028 doi: 10.1016/j.jinf.2020.03.028 id: cord-306598-xe0pq0ik author: Zhou, Mi title: Re-emergence of SARS-CoV2 in a discharged COVID-19 case date: 2020-04-02 words: 608.0 sentences: 50.0 pages: flesch: 72.0 cache: ./cache/cord-306598-xe0pq0ik.txt txt: ./txt/cord-306598-xe0pq0ik.txt summary: title: Re-emergence of SARS-CoV2 in a discharged COVID-19 case Re-emergence of SARS-CoV2 in a discharged COVID-19 case Dear Editor: Since December 2019, novel coronavirus (SARS-CoV2) infected disease (now nominated as COVID-19) has soon emerged as a global health concern. Here we report a case of COVID-19 who met the criteria for discharge but was tested positive for SARS-CoV2 again 10 days after discharge. There her nasal swab was obtained, and SARS-CoV2 was tested positive with real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) assay targeting ORF1ab and N gene of virus genome. RT-PCR examination for SARS-CoV-2 was performed on day 10, 11 and 14, and all 3 tests were negative. Her symptom was not relieved on day 25, so her nasal swab was obtained and the test for SARS-CoV-2 was positive again. Previous study on SARS-CoV showed that virus load could be detected for more than 10 weeks after disease onset. abstract: nan url: https://api.elsevier.com/content/article/pii/S1684118220300918 doi: 10.1016/j.jmii.2020.03.031 id: cord-287222-wojyisu0 author: Zhou, Min title: Coronavirus disease 2019 (COVID-19): a clinical update date: 2020-04-02 words: 5683.0 sentences: 276.0 pages: flesch: 35.0 cache: ./cache/cord-287222-wojyisu0.txt txt: ./txt/cord-287222-wojyisu0.txt summary: Of the first 99 laboratory-confirmed patients, 49 (49%) had been exposed to HSWM, which was reported to be the possible initial source of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [5] . New Coronavirus Infection Diagnosis and Treatment Scheme (Trial Version) published by Military Support Hubei Medical Team also put forward that for mild to moderate COVID-19 patients, corticosteroids should not be given principally and highdose corticosteroid pulse therapy was not recommended. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical pathology of critical patient with novel coronavirus pneumonia (COVID-19) abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a significant threat to global health. It caused a total of 80 868 confirmed cases and 3101 deaths in Chinese mainland until March 8, 2020. This novel virus spread mainly through respiratory droplets and close contact. As disease progressed, a series of complications tend to develop, especially in critically ill patients. Pathological findings showed representative features of acute respiratory distress syndrome and involvement of multiple organs. Apart from supportive care, no specific treatment has been established for COVID-19. The efficacy of some promising antivirals, convalescent plasma transfusion, and tocilizumab needs to be investigated by ongoing clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32240462/ doi: 10.1007/s11684-020-0767-8 id: cord-353012-rxhi8wd2 author: Zhou, Nan title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 words: 6412.0 sentences: 334.0 pages: flesch: 53.0 cache: ./cache/cord-353012-rxhi8wd2.txt txt: ./txt/cord-353012-rxhi8wd2.txt summary: Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Considering that the inhibitory dose of teicoplanin on the activity of cathepsin L is higher than that required for Ebola virus infection inhibition, a cell viability assay was performed to confirm that the inhibitory effect is not due to cytotoxicity (Fig. 6C) . Ebola trVLP system (28) , which can simulate the life cycle of wild-type Ebola viruses to a large extent, was applied to investigate whether teicoplanin and its glycopeptide antibiotic homologs dalbavancin, oritavancin, telavancin, and vancomycin can also inhibit the entry of Ebola trVLPs. Accordingly, the p4cis plasmid encoding Renilla luciferase, VP40, GP, and VP24 was transfected into HEK293T cells along with plasmids expressing T7 RNA polymerase, NP, VP35, VP30, and L viral proteins to produce Ebola trVLPs (Fig. 7A) . abstract: Ebola virus infection can cause severe hemorrhagic fever with a high mortality in humans. The outbreaks of Ebola viruses in 2014 represented the most serious Ebola epidemics in history and greatly threatened public health worldwide. The development of additional effective anti-Ebola therapeutic agents is therefore quite urgent. In this study, via high throughput screening of Food and Drug Administration-approved drugs, we identified that teicoplanin, a glycopeptide antibiotic, potently prevents the entry of Ebola envelope pseudotyped viruses into the cytoplasm. Furthermore, teicoplanin also has an inhibitory effect on transcription- and replication-competent virus-like particles, with an IC(50) as low as 330 nm. Comparative analysis further demonstrated that teicoplanin is able to block the entry of Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) envelope pseudotyped viruses as well. Teicoplanin derivatives such as dalbavancin, oritavancin, and telavancin can also inhibit the entry of Ebola, MERS, and SARS viruses. Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Notably, given that teicoplanin has routinely been used in the clinic with low toxicity, our work provides a promising prospect for the prophylaxis and treatment of Ebola, MERS, and SARS virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26953343/ doi: 10.1074/jbc.m116.716100 id: cord-258167-jqm3qyfm author: Zhou, Peng title: Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date: 2009-09-18 words: 2309.0 sentences: 118.0 pages: flesch: 57.0 cache: ./cache/cord-258167-jqm3qyfm.txt txt: ./txt/cord-258167-jqm3qyfm.txt summary: Studies using wild bat sera revealed that it is highly likely that the immunodominant epitopes overlap with the major neutralizing sites of the SL-CoV S protein. Our previous studies showed that the SL-CoV and SARS-CoV shared similar genomic organization and highly conserved gene products, with the exception of the spike protein (S protein), which had a low sequence identity, especially in the receptor binding domain (RBD) located at the N-terminal region of the S proteins. In this study, the immunogenicity and immunodominant region of S SL was determined using sera generated from DNA immunization and naturally infected bats. Hyperimmune mouse sera were generated by DNA immunizations with plasmids pcDNA 3.1(+) containing the codon-optimized fulllength S gene of SARS-CoV BJ01, SL-CoV Rp3, and two chimeric plasmids CS 310-518 and CS 259-518 (see Fig. 1 for diagrams). In this study, DNA constructs expressing four different S proteins, SARS-CoV BJ01, SL-CoV Rp3 S and two chimeras, were used to generate hyperimmune sera in mice via DNA immunization. abstract: Abstract SARS-like coronavirus (SL-CoV) in bats have a similar genomic organization to the human SARS-CoV. Their cognate gene products are highly conserved with the exception of the N-terminal region of the S proteins, which have only 63–64% sequence identity. The N-terminal region of coronavirus S protein is responsible for virus–receptor interaction. In this study, the immunogenicity of the SL-CoV S protein (SSL) was studied and compared with that of SARS-CoV (SSARS). DNA immunization in mice with SSL elicited a high titer of antibodies against HIV-pseudotyped SSL. The sera had low cross-reactivity, but no neutralization activity, for the HIV-pseudotyped SSARS. Studies using wild bat sera revealed that it is highly likely that the immunodominant epitopes overlap with the major neutralizing sites of the SL-CoV S protein. These results demonstrated that SL-CoV and SARS-CoV shared only a limited number of immunogenic epitopes in their S proteins and the major neutralization epitopes are substantially different. This work provides useful information for future development of differential serologic diagnosis and vaccines for coronaviruses with different S protein sequences. url: https://www.sciencedirect.com/science/article/pii/S0006291X09013527 doi: 10.1016/j.bbrc.2009.07.025 id: cord-316493-wszoi6p2 author: Zhou, Weimin title: First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood date: 2013-09-16 words: 4322.0 sentences: 237.0 pages: flesch: 55.0 cache: ./cache/cord-316493-wszoi6p2.txt txt: ./txt/cord-316493-wszoi6p2.txt summary: BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. To expand the epidemiological knowledge of four non-SARS-related endemic HCoVs in China, we expressed S proteins in a eukaryotic system and established an IFA for the detection of IgG or IgM antibodies against these four viruses. Our results showed that the S-based IFA enabled specific detection of IgG or IgM to four individual HCoVs. Using IFA, we investigated the natural seroprevalence of four non-SARS-related HCoVs in blood samples from a general population that comprised a variety of age groups. abstract: BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. However, the natural prevalence of antibodies against these viruses in serum among population is unknown. METHODS: To measure antibodies to the spike (S) protein of the four common non-SARS HCoVs, recombinant S proteins of the four HCoVs were expressed and characterised in 293 T cell. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. RESULTS: Of 794 blood samples tested, only 29 (3.65%) were negative for anti-S IgG. The seropositivity of the four anti-S IgG antibodies was >70% within the general population. The majority of seroconversions to four-HCoV positivity first occurred in children. Both S-IgG and S-IgM antibodies were detectable among children and increased with age, reaching a plateau at 6 years of age. However, no anti-S IgM was detected in healthy adults. CONCLUSION: Large proportions of children and adults in Beijing have evidence of anti-S IgG against four the HCoVs, and first infections by all four non-SARS HCoVs takes place during childhood. url: https://www.ncbi.nlm.nih.gov/pubmed/24040960/ doi: 10.1186/1471-2334-13-433 id: cord-347208-leo0x10l author: Zhou, Y. title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study date: 2020-06-10 words: 3429.0 sentences: 217.0 pages: flesch: 55.0 cache: ./cache/cord-347208-leo0x10l.txt txt: ./txt/cord-347208-leo0x10l.txt summary: title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study . https://doi.org/10.1101/2020.06.09.20076646 doi: medRxiv preprint 9 time from illness onset to arbidol or interferon treatment, elevated C-reactive protein (CRP), elevated interleukin-4 (IL-4) and interleukin-6 (IL-6), elevated D-dimer and more lobes lesion in lung CT images were significantly associated with the prolonged viral shedding of COVID-19. The results of univariable regression analysis demonstrated that age older than 65 years, illness onset before January 31, the time from illness onset to first medical visitation, hypertension, arbidol combination with interferon, lobe lesions in lung computed tomography (CT) images, and the time from illness onset to arbidol or interferon initiation were significantly associated with the duration of SARS-CoV-2 RNA shedding by univariable regression analysis. abstract: Abstract Objectives: Evaluate the risk factors of prolonged SARS-CoV-2 virus shedding and the impact of arbidol treatment on SARS-CoV-2 virus shedding. Methods: Data were retrospective collected from adults hospitalized with COVID-19 in Wuhan Union Hospital. We described the clinical features and SARS-CoV-2 RNA shedding of patients with COVID-19 and evaluated factors associated with prolonged virus shedding by multivariate regression analysis. Results: Among 238 patients, the median age was 55.5 years, 57.1% were female, 92.9% (221/238) used arbidol, 58.4% (139/238) used arbidol combination with interferon. The median time from illness onset to start arbidol was 8 days (IQR, 5-14 days) and the median duration of SARS-CoV-2 virus shedding was 23 days (IQR, 17.8-30 days). SARS-CoV-2 RNA clearance was significantly delayed in patients who received arbidol >7 days after illness onset, compared with those in whom arbidol treatment was started less than or equal to7 days after illness onset (HR, 1.738 [95% CI, 1.339-2.257], P < .001). Multivariate regression analysis revealed that prolonged viral shedding was significantly associated with initiation arbidol more than seven days after symptom onset (OR 2.078, 95% CI [1.114-3.876], P .004), more than 7 days from onset of symptoms to first medical visitation (OR 3.321, 95% CI[1.559-7.073], P .002), illness onset before Jan.31, 2020 (OR 3.223, 95% CI[1.450-7.163], P .021). Arbidol combination with interferon was also significantly associated with shorter virus shedding (OR .402, 95% CI[.206-.787], P .008). Conclusions: Early initiation of arbidol and arbidol combination with interferon as well as consulting doctor timely after illness onset were helpful for SARS-CoV-2 clearance. url: https://doi.org/10.1101/2020.06.09.20076646 doi: 10.1101/2020.06.09.20076646 id: cord-317435-4yuw7jo3 author: Zhou, Yadi title: Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 date: 2020-03-16 words: 7742.0 sentences: 388.0 pages: flesch: 39.0 cache: ./cache/cord-317435-4yuw7jo3.txt txt: ./txt/cord-317435-4yuw7jo3.txt summary: Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. The high druggability of HCoV-host interactome motivates us to develop a drug repurposing strategy by specifically targeting cellular proteins associated with HCoVs for potential treatment of 2019-nCoV/SARS-CoV-2. These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). abstract: Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV, also known as SARS-CoV-2), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV/SARS-CoV-2. Drug repurposing, representing as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV–host interactome and drug targets in the human protein–protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity with SARS-CoV (79.7%). Specifically, the envelope and nucleocapsid proteins of 2019-nCoV/SARS-CoV-2 are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. We further identify three potential drug combinations (e.g., sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations targeting 2019-nCoV/SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32194980/ doi: 10.1038/s41421-020-0153-3 id: cord-353572-b4mdiont author: Zhou, Yadi title: Network-based Drug Repurposing for Human Coronavirus date: 2020-02-05 words: 6871.0 sentences: 390.0 pages: flesch: 42.0 cache: ./cache/cord-353572-b4mdiont.txt txt: ./txt/cord-353572-b4mdiont.txt summary: Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs. Coronaviruses (CoVs) typically affect the respiratory tract of mammals, including humans, and lead to mild to severe respiratory tract infections [1] . These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). abstract: Human Coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle east respiratory syndrome coronavirus (MERS-CoV), and 2019 novel coronavirus (2019-nCoV), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV. Drug repurposing, represented as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV-host interactome and drug targets in the human protein-protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV has the highest nucleotide sequence identity with SARS-CoV (79.7%) among the six other known pathogenic HCoVs. Specifically, the envelope and nucleocapsid proteins of 2019-nCoV are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. Finally, we showcased three potential drug combinations (including sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) captured by the Complementary Exposure pattern: the targets of the drugs both hit the HCoV-host subnetwork, but target separate neighborhoods in the human protein-protein interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs. url: https://doi.org/10.1101/2020.02.03.20020263 doi: 10.1101/2020.02.03.20020263 id: cord-321131-f8qeytxc author: Zhou, Yanchen title: Protease inhibitors targeting coronavirus and filovirus entry date: 2015-04-30 words: 5517.0 sentences: 254.0 pages: flesch: 45.0 cache: ./cache/cord-321131-f8qeytxc.txt txt: ./txt/cord-321131-f8qeytxc.txt summary: Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. Cell culture studies demonstrated that endosomal cysteine proteases, in particular cathepsin B (CTSB) and/or L (CTSL), can activate the glycoproteins of filoviruses, SARS-CoV, other coronaviruses, and NiV and Hendra (HeV) viruses to facilitate entry into certain cell lines. The notion that coronaviruses, including SARS-CoV, use both a cathepsin-dependent endosomal pathway and a direct cell-surface serine protease-mediated pathway for entry (Simmons et al., 2013) is supported by our finding that the combination of K11777 and camostat was superior to either compound alone. abstract: Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. The respective enzymes are thus excellent targets for antiviral intervention. In cell culture, activation of Ebola virus, as well as SARS- and MERS-coronavirus can be accomplished by the endosomal cysteine proteases, cathepsin L (CTSL) and cathepsin B (CTSB). In addition, SARS- and MERS-coronavirus can use serine proteases localized at the cell surface, for their activation. However, it is currently unclear which protease(s) facilitate viral spread in the infected host. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl]amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. K11777 is already in advanced stages of development for a number of parasitic diseases, such as Chagas disease, and has proven to be safe and effective in a range of animal models. K11777 inhibition of SARS-CoV and Ebola virus entry was observed in the sub-nanomolar range. In order to assess whether cysteine or serine proteases promote viral spread in the host, we compared the antiviral activity of an optimized K11777-derivative with that of camostat, an inhibitor of TMPRSS2 and related serine proteases. Employing a pathogenic animal model of SARS-CoV infection, we demonstrated that viral spread and pathogenesis of SARS-CoV is driven by serine rather than cysteine proteases and can be effectively prevented by camostat. Camostat has been clinically used to treat chronic pancreatitis, and thus represents an exciting potential therapeutic for respiratory coronavirus infections. Our results indicate that camostat, or similar serine protease inhibitors, might be an effective option for treatment of SARS and potentially MERS, while vinyl sulfone-based inhibitors are excellent lead candidates for Ebola virus therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/25666761/ doi: 10.1016/j.antiviral.2015.01.011 id: cord-339951-how9cmw8 author: Zhou, Yaqing title: Clinical and Autoimmune Characteristics of Severe and Critical Cases of COVID‐19 date: 2020-05-14 words: 2580.0 sentences: 157.0 pages: flesch: 50.0 cache: ./cache/cord-339951-how9cmw8.txt txt: ./txt/cord-339951-how9cmw8.txt summary: The clinical, autoimmune, and laboratory characteristics of 21 patients who had laboratory‐confirmed severe and critical cases of coronavirus disease 2019 (COVID‐19) from the intensive care unit of the Huangshi Central Hospital, Hubei Province, China, were investigated. According to the sixth edition of Guidance for Corona Virus Disease 2019: Prevention, Control, Diagnosis and Management, issued by China''s National Health Commission, the diagnostic criteria for the clinical classification of COVID-19 are as follows: (i) mild-clinical symptoms are mild and no pneumonia manifestation can be found on imaging; (ii) ordinary-symptoms such as fever and respiratory tract symptoms and pneumonia manifestations can be seen on imaging; (iii) severe-any of the following: respiratory distress, respiratory rate (RR) ≥30 breaths/min, oxygen saturation <93% at rest, arterial partial pressure of oxygen (PaO 2 )/oxygen concentration (FIO 2 ) ≤300 mmHg (1 mmHg = 0.133 kPa), or >50% lesion progression within 24-48 hours on pulmonary imaging; and (iv) critical-any of the following: respiratory failure in which mechanical ventilation is required, shock occurs, or complications with another organ failure that require monitoring and treatment in the ICU. In this single-center and retrospective study, we have reported on the clinical and laboratory characteristics of 8 severe and 13 critical cases of SARS-CoV-2 in Huangshi, Hubei Province, China. abstract: In this study we report on the clinical and autoimmune characteristics of severe and critical novel coronavirus pneumonia caused by severe acute respiratory syndrome‒associated coronavirus 2 (SARS‐CoV‐2). The clinical, autoimmune, and laboratory characteristics of 21 patients who had laboratory‐confirmed severe and critical cases of coronavirus disease 2019 (COVID‐19) from the intensive care unit of the Huangshi Central Hospital, Hubei Province, China, were investigated. A total of 21 patients (13 men and 8 women), including 8 (38.1%) severe cases and 13 (61.9%) critical cases, were enrolled. Cough (90.5%) and fever (81.0%) were the dominant symptoms, and most patients (76.2%) had at least one coexisting disorder on admission. The most common characteristics on chest computed tomography were ground‐glass opacity (100%) and bilateral patchy shadowing (76.2%). The most common findings on laboratory measurement were lymphocytopenia (85.7%) and elevated levels of C‐reactive protein (94.7%) and interleukin‐6 (89.5%). The prevalence of anti‒52 kDa SSA/Ro antibody, anti‒60 kDa SSA/Ro antibody, and antinuclear antibody was 20%, 25%, and 50%, respectively. We also retrospectively analyzed the clinical and laboratory data from 21 severe and critical cases of COVID‐19. Autoimmune phenomena exist in COVID‐19 subjects, and the present results provide the rationale for a strategy of preventing immune dysfunction and optimal immunosuppressive therapy. url: https://doi.org/10.1111/cts.12805 doi: 10.1111/cts.12805 id: cord-266696-w9sb038q author: Zhou, Yi-Hua title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date: 2004-03-15 words: 1306.0 sentences: 67.0 pages: flesch: 56.0 cache: ./cache/cord-266696-w9sb038q.txt txt: ./txt/cord-266696-w9sb038q.txt summary: [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/14999642/ doi: 10.1086/382081 id: cord-313458-ka02rsla author: Zhou, Yitian title: Single-cell transcriptional profile of ACE2 in healthy and failing human hearts date: 2020-09-01 words: 1695.0 sentences: 86.0 pages: flesch: 46.0 cache: ./cache/cord-313458-ka02rsla.txt txt: ./txt/cord-313458-ka02rsla.txt summary: To explore the potential mechanisms contributing to this finding, we examined the expression of ACE2 in the different cells of the heart for heart samples from healthy individuals and heart failure patients and compared the results between these two groups. We found that the expression of ACE2 in cardiomyocytes was significantly increased compared to the other cells in the heart failure patients ( Figure 1L ). These results suggest that the cardiomyocytes of heart failure patients may be directly attacked by the virus and that this may contribute to the development of myocardial injury and severe conditions. We speculate that SARS-CoV-2 mainly attacks pericytes via ACE2, which leads to coronary microvascular disorder and myocardial injury in COVID-19 patients. This finding suggests that heart failure patients infected by the SARS-CoV-2 virus may suffer viral myocarditis and severe myocardial injury by direct attack on their cardiomyocytes. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32880862/ doi: 10.1007/s11427-020-1787-5 id: cord-300156-ags07bc5 author: Zhou, Yunyun title: Ocular Findings and Proportion with Conjunctival SARS-COV-2 in COVID-19 Patients date: 2020-04-21 words: 823.0 sentences: 50.0 pages: flesch: 52.0 cache: ./cache/cord-300156-ags07bc5.txt txt: ./txt/cord-300156-ags07bc5.txt summary: The 1 patient with ocular symptoms and positive SARS-CoV-2 conjunctival swab results was classified as a severe or critical case. Two patients without ocular symptoms showed positive results for conjunctival SARS-CoV-2, with one of them classified as a severe or critical case and another classified as a mild or moderate case. Of 3 patients who showed positive results for conjunctival SARS-CoV-2, 2 were severe or critical cases and 1 was a mild or moderate case. The finding of ocular symptoms was not associated significantly with the results of conjunctival SARS-CoV-2 detection (Table S2, Our study has several limitations. In conclusion, this study characterizes the ocular symptoms in COVID-19 patients, reports the proportion of samples with positive conjunctival and nasopharyngeal RT-PCR results from patients with COVID-19, and incorporates the duration of disease into the analysis. The appearance of symptoms and penlight findings or the results of positive conjunctival swab analysis were not correlated significantly with the duration of disease. abstract: nan url: https://doi.org/10.1016/j.ophtha.2020.04.028 doi: 10.1016/j.ophtha.2020.04.028 id: cord-309930-zlzuoeh2 author: Zhou, Zhiming title: Coronavirus disease 2019: initial chest CT findings date: 2020-03-24 words: 4232.0 sentences: 199.0 pages: flesch: 50.0 cache: ./cache/cord-309930-zlzuoeh2.txt txt: ./txt/cord-309930-zlzuoeh2.txt summary: METHODS: We retrospectively reviewed the initial chest CT data of 62 confirmed coronavirus disease 2019 patients (34 men, 28 women; age range 20–91 years old) who did not receive any antiviral treatment between January 21 and February 4, 2020, in Chongqing, China. Since December 2019, an increasing number of pneumonia cases caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei, China, and subsequently, an outbreak of coronavirus disease 2019 (COVID-19) swept the globe [1] [2] [3] [4] . Hence, it is very necessary to systematically analyze the chest CT findings associated with this disease systematically, for the timely isolation, COVID-19 RT-PCR and respiratory care of patients, and early implementation of infection prevention and control measures. To fully understand and early discriminate the CT features of this disease in its early stages, we collected initial chest CT data from confirmed COVID-19 patients who did not receive any antiviral treatment mainly from Chongqing Three Gorges Central Hospital for analysis. abstract: OBJECTIVES: To systematically analyze CT findings during the early and progressive stages of natural course of coronavirus disease 2019 and also to explore possible changes in pulmonary parenchymal abnormalities during these two stages. METHODS: We retrospectively reviewed the initial chest CT data of 62 confirmed coronavirus disease 2019 patients (34 men, 28 women; age range 20–91 years old) who did not receive any antiviral treatment between January 21 and February 4, 2020, in Chongqing, China. Patients were assigned to the early-stage group (onset of symptoms within 4 days) or progressive-stage group (onset of symptoms within 4–7 days) for analysis. CT characteristics and the distribution, size, and CT score of pulmonary parenchymal abnormalities were assessed. RESULTS: In our study, the major characteristic of coronavirus disease 2019 was ground-glass opacity (61.3%), followed by ground-glass opacity with consolidation (35.5%), rounded opacities (25.8%), a crazy-paving pattern (25.8%), and an air bronchogram (22.6%). No patient presented cavitation, a reticular pattern, or bronchial wall thickening. The CT scores of the progressive-stage group were significantly greater than those of the early-stage group (p = 0.004). CONCLUSIONS: Multiple ground-glass opacities with consolidations in the periphery of the lungs were the primary CT characteristic of coronavirus disease 2019. CT score can be used to evaluate the severity of the disease. If these typical alterations are found, then the differential diagnosis of coronavirus disease 2019 must be considered. KEY POINTS: • Multiple GGOs with consolidations in the periphery of the lungs were the primary CT characteristic of COVID-19. • The halo sign may be a special CT feature in the early-stage COVID-19 patients. • Significantly increased CT score may indicate the aggravation of COVID-19 in the progressive stage. url: https://www.ncbi.nlm.nih.gov/pubmed/32211963/ doi: 10.1007/s00330-020-06816-7 id: cord-308501-z3eiac25 author: Zhu, Chengliang title: nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk date: 2020-06-04 words: 847.0 sentences: 70.0 pages: flesch: 57.0 cache: ./cache/cord-308501-z3eiac25.txt txt: ./txt/cord-308501-z3eiac25.txt summary: An emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) pandemic, imposes a great threat to global public health 1 . The transmission and pathophysiology of SARS-CoV-2 gradually known among various populations, but public health effects of COVID-19 on women and their outcomes should not be ignored 1, 2 . In pregnant and perinatal women, vertical transmission of SARS-CoV-2 from infected mother to her newborn is a controversial issue [2] [3] [4] . Here, we represent clinical characteristics of COVID-19 pneumonia in puerperal women and evidence of SARS-CoV-2 shedding in her breastmilk. Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320303790?v=s5 doi: 10.1016/j.jinf.2020.06.001 id: cord-304088-xkg0ylz8 author: Zhu, Han title: Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date: 2020-04-21 words: 5532.0 sentences: 236.0 pages: flesch: 38.0 cache: ./cache/cord-304088-xkg0ylz8.txt txt: ./txt/cord-304088-xkg0ylz8.txt summary: While limited data exist, potential mechanisms of cardiac injury include direct viral entry through the angiotensin-converting enzyme 2 (ACE2) receptor and toxicity in host cells, hypoxia-related myocyte injury, and immune-mediated cytokine release syndrome. The increased incidence of cardiac injury among those with severe systemic inflammatory response syndromes (SIRS) and shock in the setting of COVID-19 also highlights an important relationship between the immune response to the virus and the cardiovascular system. Of note, SARS-CoV-2 also contains an RNA-dependent RNA polymerase which is the target of the anti-viral agent remdesivir, currently being studied randomized clinical trials for use against COVID-19 disease [26] . A recent retrospective, multi-center study of 150 patients confirmed that inflammatory markers, including elevated ferritin (mean 1297.6 ng/ml in non-survivors vs 614.0 ng/ml in survivors, p < 0.001) and IL-6 (p < 0.0001) were associated with more severe COVID-19 infection, suggesting that systemic inflammation may be a significant driver of multi-organ damage [18, 64] . abstract: PURPOSE OF REVIEW: Coronavirus disease of 2019 (COVID-19) is a cause of significant morbidity and mortality worldwide. While cardiac injury has been demonstrated in critically ill COVID-19 patients, the mechanism of injury remains unclear. Here, we review our current knowledge of the biology of SARS-CoV-2 and the potential mechanisms of myocardial injury due to viral toxicities and host immune responses. RECENT FINDINGS: A number of studies have reported an epidemiological association between history of cardiac disease and worsened outcome during COVID infection. Development of new onset myocardial injury during COVID-19 also increases mortality. While limited data exist, potential mechanisms of cardiac injury include direct viral entry through the angiotensin-converting enzyme 2 (ACE2) receptor and toxicity in host cells, hypoxia-related myocyte injury, and immune-mediated cytokine release syndrome. Potential treatments for reducing viral infection and excessive immune responses are also discussed. SUMMARY: COVID patients with cardiac disease history or acquire new cardiac injury are at an increased risk for in-hospital morbidity and mortality. More studies are needed to address the mechanism of cardiotoxicity and the treatments that can minimize permanent damage to the cardiovascular system. url: https://www.ncbi.nlm.nih.gov/pubmed/32318865/ doi: 10.1007/s11886-020-01292-3 id: cord-319876-psilbis0 author: Zhu, Jian title: COVID-19 Epidemic: Clinical Characteristics of Patients in Pediatric Isolation Ward date: 2020-07-09 words: 2424.0 sentences: 145.0 pages: flesch: 59.0 cache: ./cache/cord-319876-psilbis0.txt txt: ./txt/cord-319876-psilbis0.txt summary: It was found that 55 cases (83.3%) had fever and 48 cases (72.7%) coughed in the isolated area, 31 cases (47%) had a history of exposure, 26 cases (39.4%) had a decrease in lymphocytes (LYM), more than half had an increase in lactate dehydrogenase and creatine kinase isoenzyme, 14 cases (21.2%) had positive SARS-CoV-2 nucleic acid, 58 cases (87.9%) had abnormal chest computed tomography (CT), and 11 cases (16.7%) had sinus arrhythmia. Therefore, for some suspected children with COVID-19, we can make a comprehensive judgment through clinical symptoms, epidemiological history, LYM number, myocardial enzyme spectrum, chest CT, and electrocardiogram; put these children in an isolation ward for treatment; and then transfer them to a general ward for treatment after excluding COVID-19. At present, some of COVID-19 are asymptomatic infection, 10, 11 which suggests that it is not only from the clinical symptoms to judge whether the children should be admitted to the isolation ward. abstract: In order to accurately admit children with COVID-19 to an isolation ward, our study retrospectively analyzed the clinical characteristics of children in isolation wards during the COVID-19 epidemic. It was found that 55 cases (83.3%) had fever and 48 cases (72.7%) coughed in the isolated area, 31 cases (47%) had a history of exposure, 26 cases (39.4%) had a decrease in lymphocytes (LYM), more than half had an increase in lactate dehydrogenase and creatine kinase isoenzyme, 14 cases (21.2%) had positive SARS-CoV-2 nucleic acid, 58 cases (87.9%) had abnormal chest computed tomography (CT), and 11 cases (16.7%) had sinus arrhythmia. Therefore, for some suspected children with COVID-19, we can make a comprehensive judgment through clinical symptoms, epidemiological history, LYM number, myocardial enzyme spectrum, chest CT, and electrocardiogram; put these children in an isolation ward for treatment; and then transfer them to a general ward for treatment after excluding COVID-19. url: https://doi.org/10.1177/0009922820941228 doi: 10.1177/0009922820941228 id: cord-343455-v1648kng author: Zhu, Na title: Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells date: 2020-08-06 words: 4132.0 sentences: 237.0 pages: flesch: 49.0 cache: ./cache/cord-343455-v1648kng.txt txt: ./txt/cord-343455-v1648kng.txt summary: Here, we characterize the replication dynamics, cell tropism and morphogenesis of SARS-CoV-2 in organotypic human airway epithelial (HAE) cultures. SARS-CoV-2 replicates efficiently and infects both ciliated and secretory cells in HAE cultures. In this study, we compared the characteristics of the replication dynamics, cell tropism, and morphogenesis of SARS-CoV-2 and HCoV-NL63 in HAE cells, which express the shared receptor, to better understand the pathogenesis and transmission of SARS-CoV-2. As shown in Fig. 1a , HAE cells were highly susceptible to SARS-CoV-2 infection with peak virus production from apical wash at 48-72 h post infection (h pi) and remained at a high level from 3 to 6 days. As shown in Fig. 1c , virus particles were found on the apical surface of both ciliated cells and secretory cells; inclusion bodies formed by viral components were observed in the cytoplasm, which confirmed the infection of both cell types. abstract: SARS-CoV-2, a β-coronavirus, has rapidly spread across the world, highlighting its high transmissibility, but the underlying morphogenesis and pathogenesis remain poorly understood. Here, we characterize the replication dynamics, cell tropism and morphogenesis of SARS-CoV-2 in organotypic human airway epithelial (HAE) cultures. SARS-CoV-2 replicates efficiently and infects both ciliated and secretory cells in HAE cultures. In comparison, HCoV-NL63 replicates to lower titers and is only detected in ciliated cells. SARS-CoV-2 shows a similar morphogenetic process as other coronaviruses but causes plaque-like cytopathic effects in HAE cultures. Cell fusion, apoptosis, destruction of epithelium integrity, cilium shrinking and beaded changes are observed in the plaque regions. Taken together, our results provide important insights into SARS-CoV-2 cell tropism, replication and morphogenesis. url: https://doi.org/10.1038/s41467-020-17796-z doi: 10.1038/s41467-020-17796-z id: cord-301151-f6vya3qh author: Zhu, Xiaojuan title: Co-infection with respiratory pathogens among COVID-2019 cases date: 2020-05-11 words: 2599.0 sentences: 180.0 pages: flesch: 61.0 cache: ./cache/cord-301151-f6vya3qh.txt txt: ./txt/cord-301151-f6vya3qh.txt summary: In this study, the clinical features of COVID-19 patients were analyzed, then 39 respiratory pathogens in their throat swab were detected by specific real-time RT-PCR. 257 patients were diagnosed with the SARS-CoV-2 infection and their clinical severity was classified according to National Health Commission of the People''s Republic of China revised criteria for diagnosis and treatment of novel coronavirus infection pneumonia (trial version fifth, revised version). Below 15 years of age, a total of 11 (4.3 %) were diagnosed with the SARS-CoV-2 infection and there were no case in severe/critical category. In our study, 94.2 % of COVID-19 patients could be co-infected with one or more other pathogens, including 9 viruses, 11 bacteria and 4 fungi. Along with the course of disease, both the rates and pathogen species of co-infection among COVID-19 patients were decreased significantly, which may due to the treatment X. abstract: Accumulating evidence shows that microbial co-infection increases the risk of disease severity in humans. There have been few studies about SARS-CoV-2 co-infection with other pathogens. In this retrospective study, 257 laboratory-confirmed COVID-19 patients in Jiangsu Province were enrolled from January 22 to February 2, 2020. They were re-confirmed by real-time RT-PCR and tested for 39 respiratory pathogens. In total, 24 respiratory pathogens were found among the patients, and 242 (94.2 %) patients were co-infected with one or more pathogens. Bacterial co-infections were dominant in all COVID-19 patients, Streptococcus pneumoniae was the most common, followed by Klebsiella pneumoniae and Haemophilus influenzae. The highest and lowest rates of co-infections were found in patients aged 15–44 and below 15, respectively. Most co-infections occurred within 1–4 days of onset of COVID-19 disease. In addition, the proportion of viral co-infections, fungal co-infections and bacterial-fungal co-infections were the highest severe COVID-19 cases. These results will provide a helpful reference for diagnosis and clinical treatment of COVID-19 patients. url: https://doi.org/10.1016/j.virusres.2020.198005 doi: 10.1016/j.virusres.2020.198005 id: cord-333420-qqyg9um9 author: Zhu, Xun title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date: 2020-10-09 words: 460.0 sentences: 35.0 pages: flesch: 58.0 cache: ./cache/cord-333420-qqyg9um9.txt txt: ./txt/cord-333420-qqyg9um9.txt summary: title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. The on-going Coronavirus disease 2019 (Covid-19) pandemic has resulted in over 734,000 deaths, affect-20 ing more than 188 countries and territories (CSSE, 2020; Dong, et al., 2020) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV) 23 is the pathogenic cause of Covid-19 (Lescure, et al., 2020) . In order to quickly identify the clade of an isolate of SARS-Cov-2 given its sequencing FastQ files, 30 we have developed a bioinformatics pipeline and a user-friendly web interface. abstract: idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at https://github.com/xz-stjude/idcov. A documentation for installation can be found at https://github.com/xz-stjude/idcov/blob/master/README.md. url: https://doi.org/10.1101/2020.10.08.330456 doi: 10.1101/2020.10.08.330456 id: cord-302584-fwdpzv85 author: Zhu, Ying title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date: 2005-01-01 words: 3429.0 sentences: 170.0 pages: flesch: 54.0 cache: ./cache/cord-302584-fwdpzv85.txt txt: ./txt/cord-302584-fwdpzv85.txt summary: title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates Despite the fact that the SARS-CoV can cause an atypical and fatal form of pneumonia, the genome structure, gene expression pattern, and protein profiles of the virus are similar to those of other conventional coronaviruses [17] , which are only responsible for mild respiratory tract infections in a wide range of animals including humans, pigs, cows, mice, cats, and birds [10, 19] . In this report, we described the isolation of a new SARS-CoV strain (WHU) from a patient in Hubei Province, China during the late period of SARS outbreak. Comparative study of genetic characterization and nucleotide variation of all known SARS-CoV offers insights into understanding functions of the viral genes and revealing the evolution trends of the virus. abstract: Severe acute respiratory syndrome (SARS) caused by SARS-associated coronavirus (SARS-CoV) is a fatal disease. Prevention of future outbreaks is essential and requires understanding pathogenesis and evolution of the virus. We have isolated a SARS-CoV in China and analyzed 47 SARS-CoV genomes with the aims to reveal the evolution trends of the virus and provide insights into understanding pathogenesis and SARS epidemic. Specimen from a SARS patient was inoculated into cell culture. The presence of SARS-CoV was determined by RT-PCR and confirmed by electron microscopy. Virus was isolated followed by the determination of its genome sequences, which were then analyzed by comparing with other 46 SARS-CoV genomes. Genetic mutations with potential implications to pathogenesis and the epidemic were characterized. This viral genome consists of 29,728 nucleotides with overall organization in agreement with that of published isolates. A total of 348 positions were mutated on 47 viral genomes. Among them 22 had mutations in more than three genomes. Hot spots of nucleotide variations and unique trends of mutations were identified on the viral genomes. Mutation rates were different from gene to gene and were correlated well with periodical or geographic characteristics of the epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/15744567/ doi: 10.1007/s11262-004-4586-9 id: cord-307504-cogk5kig author: Zhu, Yuanmei title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date: 2020-03-28 words: 1946.0 sentences: 107.0 pages: flesch: 51.0 cache: ./cache/cord-307504-cogk5kig.txt txt: ./txt/cord-307504-cogk5kig.txt summary: title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. Taken together, these results suggested that 128 SARS-CoV-2 might evolve an increased interaction between the HR1 and HR2 domains in 129 the S2 fusion protein thus critically determining its high fusogenic activity. Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: 354 implications for virus fusogenic mechanism and identification of fusion inhibitors Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition 368 using spike protein heptad repeat-derived peptides Heptad repeat-derived peptides block protease-mediated direct entry from the cell surface of 371 severe acute respiratory syndrome coronavirus but not entry via the endosomal pathway abstract: The coronavirus disease COVID-19, caused by emerging SARS-CoV-2, has posed serious threats to global public health, economic and social stabilities, calling for the prompt development of therapeutics and prophylactics. In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Comparing to that of SARS-CoV, the heptad repeat 1 (HR1) sequence in the S2 fusion protein of SARS-CoV-2 possesses markedly increased α-helicity and thermostability, as well as a higher binding affinity with its corresponding heptad repeat 2 (HR1) site. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. IPB02 also inhibited the SARS-CoV pseudovirus efficiently. Moreover, the strcuture and activity relationship (SAR) of IPB02 were characterzized with a panel of truncated lipopeptides, revealing the amino acid motifs critical for its binding and antiviral capacities. Therefore, the presented results have provided important information for understanding the entry pathway of SARS-CoV-2 and the design of antivirals that target the membrane fusion step. url: https://doi.org/10.1101/2020.03.26.009233 doi: 10.1101/2020.03.26.009233 id: cord-327808-k3jec87p author: Zhu, Yunkai title: The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date: 2020-08-25 words: 2754.0 sentences: 155.0 pages: flesch: 61.0 cache: ./cache/cord-327808-k3jec87p.txt txt: ./txt/cord-327808-k3jec87p.txt summary: We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. The sequence at the S1/S2 boundary contains a cleavage site for the furin protease, 61 which could preactivate the S protein for membrane fusion and potentially reduce the 62 dependence of SARS-CoV-2 on plasma membrane proteases, such as transmembrane 63 serine protease 2 (TMPRSS2), to enable efficient cell entry (Shang et al., 2020) . Intriguingly, 188 these genes edited also significantly inhibited the infection by pseudovirus bearing the 189 spike protein of MERS-CoV in A549-ACE2-DPP4 cells ( Figure 3D ). Although no infectious virus was detected by focus-forming 299 assay (data not shown), viral RNA levels were higher in fecal samples for Sfull (20 and 300 40-fold) than Sdel at days 2 and 4, respectively ( Figure 5B ). abstract: The global spread of SARS-CoV-2 is posing major public health challenges. One unique feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the function of which remains uncertain. We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. A panel of host factors regulating the surface expression of ACE2 was identified for both viruses. Using a hamster model, animal-to-animal transmission with the Sdel virus was almost completely abrogated, unlike with Sfull. These findings highlight the critical role of the S1/S2 boundary of the SARS-CoV-2 spike protein in modulating virus entry and transmission. url: https://doi.org/10.1101/2020.08.25.266775 doi: 10.1101/2020.08.25.266775 id: cord-311123-swiewewq author: Zhuang, Shu-Fan title: Low-grade fever during COVID-19 convalescence: A report of 3 cases date: 2020-06-26 words: 2484.0 sentences: 141.0 pages: flesch: 53.0 cache: ./cache/cord-311123-swiewewq.txt txt: ./txt/cord-311123-swiewewq.txt summary: Reports of such cases are rare, and the mechanism and outcome of low-grade fever during COVID-19 convalescence are not completely clear. The patient''s condition did not improve, and COVID-19 was confirmed on February 7 by positive SARS-CoV-2 oropharyngeal swab test at our local Center for Disease Control (CDC). From disease onset on 4 February 2020, the patient had a fever with a maximum axillary temperature of 38.1°C, accompanied by a cough (details shown in Table 1 ) and multiple lesions on CT ( Figure 1 ). The patient''s condition did not improve, and COVID-19 was confirmed on February 5 by positive SARS-CoV-2 oropharyngeal swab test at our local CDC. During convalescence, the patient''s cough was completely relieved, and CT lesions resolved ( Figure 1 ), but her SARS-CoV-2 test remained positive. During the course of low-grade fever, the 3 patients had no other discomfort or comorbidities, and their temperature returned to normal without any treatment. abstract: BACKGROUND: Low-grade fever during convalescence is an atypical symptom of coronavirus disease 2019 (COVID-19). Reports of such cases are rare, and the mechanism and outcome of low-grade fever during COVID-19 convalescence are not completely clear. We report 3 cases with low-grade fever during COVID-19 convalescence and highlight the main clinical, radiographic, and laboratory characteristics, thereby increasing the level of expertise in the clinical management of COVID-19 during convalescence and facilitating individualized decision-making. CASE SUMMARY: We describe 3 patients with COVID-19, two females aged 62 and 66 years and a male 55 years, who had low-grade fever during COVID-19 convalescence. All 3 patients had no other discomfort or comorbidities during low-grade process. Lesions on computed tomography in all 3 patients had resolved during this period. Two patients tested negative on two consecutive severe acute respiratory syndrome coronavirus 2 tests with an interval of at least 24 h between tests. Body temperature in all 3 patients returned to normal after several days without treatment, and fever recurrence was not observed. CONCLUSION: Enhancing the knowledge of low-grade fever during COVID-19 convalescence may increase the expertise in the delivery of optimal healthcare services. url: https://doi.org/10.12998/wjcc.v8.i12.2655 doi: 10.12998/wjcc.v8.i12.2655 id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 words: 3947.0 sentences: 211.0 pages: flesch: 56.0 cache: ./cache/cord-346138-ip42zcld.txt txt: ./txt/cord-346138-ip42zcld.txt summary: The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. Several authors therefore suppose an infection of the gastrointestinal tract by the virus (11, 24) , with its continuous elimination with the feces which has been reported to last from 1 to 12 days (24) and in some cases, viral RNA were detected in feces or anal swabs even after the respiratory tests became negative (11, 22, 24) . The reference method for testing positivity to SARS-CoV-2 infection is represented by the pharyngeal swab that is taken from the patient''s nasopharynx or oropharynx and, through an RT-PCR analyzed for the presence of viral RNA (8) . abstract: Coronavirus disease 2019 quickly spread in China and has, since March 2020 become a pandemic, causing hundreds of thousands of deaths worldwide. The causative agent was promptly isolated and named SARS-CoV-2. Scientific efforts are related to identifying the best clinical management of these patients, but also in understanding their infectivity in order to limit the spread of the virus. Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out. However, the accuracy of such tests varies depending on the type of specimen used and the time of illness at which they are performed. This review of the literature aims to summarize the preliminary findings reported in studies on Covid-19 testing. The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. It highlights that most patients already reach the peak of the viral load in the upper airways within the first days of displaying symptoms, which thereafter tend to decrease. This suggests that many patients may already be infectious before symptoms start to appear. url: https://www.ncbi.nlm.nih.gov/pubmed/32974267/ doi: 10.3389/fpubh.2020.00487 id: cord-274231-2s7ki6g7 author: Ziebuhr, John title: SARS – Unprecedented global response to a newly emerging disease date: 2003-12-31 words: 1214.0 sentences: 57.0 pages: flesch: 51.0 cache: ./cache/cord-274231-2s7ki6g7.txt txt: ./txt/cord-274231-2s7ki6g7.txt summary: 293, 229 ± 231 (2003) ¹ Urban & Fischer Verlag http://www.urbanfischer.de/journals/ijmm Editorial SARS ± Unprecedented global response to a newly emerging disease Severe acute respiratory syndrome (SARS) is a life-threatening form of pneumonia that is characterized by fever, chills, myalgia, dry cough, and progressing lung infiltrates (Nicholls et al., 2003; Peiris et al., 2003a) . Only few weeks after the outbreak, the concerted global efforts have resulted in the identification of first coronavirus enzyme inhibitors (Anand et al., 2003; Xiong et al., 2003) that are hoped to be useful for the development of anti-SARS drugs. SARS Working Group: A novel coronavirus associated with severe acute respiratory syndrome SARS study group: Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome abstract: Abstract No Abstract url: https://www.ncbi.nlm.nih.gov/pubmed/14503787/ doi: 10.1078/1438-4221-00270 id: cord-349417-vn7q8wc4 author: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 words: 3379.0 sentences: 179.0 pages: flesch: 45.0 cache: ./cache/cord-349417-vn7q8wc4.txt txt: ./txt/cord-349417-vn7q8wc4.txt summary: Activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce 16 (in IBV: 15) mature products called nonstructural proteins (nsp) 1 to 16 (reviewed in Refs. The N-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups I, II, and III, are cleaved at two (in IBV) or three sites (in all other coronaviruses) by one (IBV and SARS-CoV) or two zinc-finger-containing papain-like cysteine proteases called PL1 pro and PL2 pro . The observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified RNA-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, NendoU, playing a central role. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037497/ doi: 10.1007/978-0-387-33012-9_1 id: cord-264916-c4n0kyog author: Zimmerman, Keith title: Natural protection of ocular surface from viral infections – a hypothesis date: 2020-07-09 words: 4671.0 sentences: 225.0 pages: flesch: 46.0 cache: ./cache/cord-264916-c4n0kyog.txt txt: ./txt/cord-264916-c4n0kyog.txt summary: A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. abstract: A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. One of the interesting aspects of the clinical manifestation of the infection is an accompanying ocular surface viral infection, viral conjunctivitis. Although occasional reports of viral conjunctivitis caused by this and the related SARS-CoV virus (causing the SARS outbreak in the early 2000s) are available, the prevalence of this complication among infected people appears low (∼1%). This is surprising, considering the recent discovery of the presence of viral receptors (ACE2 and TMPRSS2) in ocular surface tissue. The discrepancy between the theoretically expected high rate of concurrence of viral ocular surface inflammation and the observed relatively low occurrence can be explained by several factors. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32679424/ doi: 10.1016/j.mehy.2020.110082 id: cord-322102-4fi0y96f author: Zimmermann, Matthias title: Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic date: 2020-04-04 words: 4690.0 sentences: 252.0 pages: flesch: 47.0 cache: ./cache/cord-322102-4fi0y96f.txt txt: ./txt/cord-322102-4fi0y96f.txt summary: During the SARS-CoV-2 pandemic, the specialty must organize patient treatment in such a way that infection transmission is reduced to a minimum, while all relevant treatment options are at hand to provide adequate patient care. The search items used were "coronavirus disease 19, COVID-19, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, transmission, pandemic, oral surgical procedures, oral and maxillofacial surgery, dental, personal protective equipment, infection prevention and control." The last search was run on 29 March 2020. Healthcare workers who have been infected with SARS-CoV-2 and have recovered from COVID-19 should continue to follow infection control precautions, including use of the recommended personal protective equipment. Depending on the number of infected patients, there might come a time of risk of a scarcity of medical staff, ventilators, negative pressure rooms, and personal protective equipment. abstract: Oral and maxillofacial surgery is correlated with a high risk of SARS-CoV-2 transmission. Therefore, the aim of the review is to collect and discuss aspects of the management of patients in oral and maxillofacial surgery during the COVID-19 pandemic. In order to save resources and to avoid unnecessary exposure to infected patients, there is the need to schedule interventions depending on their priority. During the peak of the pandemic, no elective surgery should be performed. Even urgent procedures might be postponed if there is a view to recovery of a COVID-19 patient within a few days. Emergency procedures do not allow any delay. Specialties with overlap in therapies should have well defined arrangements among each other concerning the treatment spectra in order to avoid redundancy and loss of resources. Inpatient and outpatient units have to be organized in such a way that the risk of cross-infection among patients is reduced to a minimum. Especially, testing of patients for SARS-CoV-2 is important to detect the infected patients at an early stage. When surgery is performed on COVID-19 patients, adequate personal protective equipment is crucial. There must be negative pressure in the operating room, and aerosol formation must be reduced to a minimum. In order to address the COVID-19 challenge adequately, significant changes in the infrastructure of outpatient units, inpatient units, and operating rooms are needed. In addition, the demands concerning personal protective equipment increase significantly. The major aim is to protect patients as well as the medical staff from unnecessary infection, and to keep the healthcare system running effectively. Therefore, every effort should be taken to make the necessary investments. url: https://doi.org/10.1016/j.jcms.2020.03.011 doi: 10.1016/j.jcms.2020.03.011 id: cord-318478-fn0gcxbb author: Ziv, Omer title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 words: 5760.0 sentences: 343.0 pages: flesch: 56.0 cache: ./cache/cord-318478-fn0gcxbb.txt txt: ./txt/cord-318478-fn0gcxbb.txt summary: Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. abstract: The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies. url: https://doi.org/10.1101/2020.07.19.211110 doi: 10.1101/2020.07.19.211110 id: cord-353812-4oxbczqe author: Zoghi, Anahita title: A case of possible atypical demyelinating event of the central nervous system following COVID-19 date: 2020-06-24 words: 1543.0 sentences: 99.0 pages: flesch: 47.0 cache: ./cache/cord-353812-4oxbczqe.txt txt: ./txt/cord-353812-4oxbczqe.txt summary: Some COVID-19 patients, especially those suffering from a severe disease, are highly likely to have central nervous system (CNS) manifestations. It has been shown that severe infection with SARS-CoV-2 is associated with neurological manifestations such as headache, epilepsy, cerebrovascular events, and encephalitis (Bohmwald et al. Studies on SARS-CoV-1 revealed a delayed self-reactive T-cell suppression due to viral replication, which leads to neuroinflammation, demyelination or axonal damage of the CNS (Savarin et al., 2017 . Recent studies have shown that the novel coronavirus appears to cross the blood-brain barrier and cause acute or delayed CNS demyelination or axonal damage (Desforges et al., 2020) . Moreover, a recent report revealed that CNS delayed demyelinating events following COVID-19 . Severe COVID-19 may affect the CNS and have various acute or delayed neurological complications. During the COVID-19 pandemic, it is important to consider SARS-CoV-2 infection when seeing patients with neurological manifestations, especially those needing immune-modulator therapy, since the established recommendations are insufficient at this time. abstract: After the novel coronavirus disease outbreak first began in Wuhan, China, in December 2019, the viral epidemic has quickly spread across the world, and it is now a major public health concern. Here we present a 21-year-old male with encephalomyelitis following intermittent vomiting and malaise for 4 days. He reported upper respiratory signs and symptoms 2 weeks before this presentation. Two cerebrospinal fluid (CSF) analyses were notable for mononuclear pleocytosis, elevated protein (more than 100 mg/dl), and hypoglycorrhachia. Brain Magnetic Resonance Imaging (MRI) showed bilateral posterior internal capsule lesions extending to the ventral portion of the pons and a marbled splenium hyperintensity pattern. Cervical and thoracic MRI showed longitudinally extensive transverse myelitis (LETM), none of which were enhanced with gadolinium. Both the AQP4 and MOG antibodies were negative. Spiral chest computed tomography (CT) scan confirmed to COVID-19 as did the high IgG level against coronavirus, but the oropharyngeal swabs were negative. Neurological manifestations of COVID-19 have not been adequately studied. Some COVID-19 patients, especially those suffering from a severe disease, are highly likely to have central nervous system (CNS) manifestations. Our case is a post-COVID-19 demyelinating event in the CNS. url: https://api.elsevier.com/content/article/pii/S2211034820304004 doi: 10.1016/j.msard.2020.102324 id: cord-271978-j5enftje author: Zoltán, Köntös title: In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date: 2020-11-10 words: 2910.0 sentences: 153.0 pages: flesch: 52.0 cache: ./cache/cord-271978-j5enftje.txt txt: ./txt/cord-271978-j5enftje.txt summary: Conclusion Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients. Enthused by promising findings from a recent study by Pelletier and colleagues (12) , the present study was interested in Essential Iodine Drops (EID) for oral/nasal decontaminant in known or suspected cases of COVID-19 as a potentially better alternative to PVP-I. Briefly, the three dilutions of Essential Iodine Drops (EID) containing SARS-CoV-2 virus solution (1:1; 2:1 and 3:1) were tested in triplicates for virucidal activity as described by Pelletier and colleagues (12) . In vitro virucidal assay in the present study has indeed demonstrated that 75% and 50% of Essential Iodine Drops (EID) solution reduced SARS-CoV-2 virus titre after 60 seconds and 90 seconds of incubation by an LRV of 2.0 (99%). abstract: Background Aerosolization of respiratory droplets is considered the main route of coronavirus disease 2019 (COVID-19). Therefore, reducing the viral load of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) shed via respiratory droplets is potentially an ideal strategy to prevent the spread of the pandemic. The in vitro virucidal activity of intranasal Povidone-Iodine (PVP-I) has been demonstrated recently to reduce SARS-CoV-2 viral titres. This study evaluated the virucidal activity of the aqueous solution of Iodine-V (a clathrate complex formed by elemental iodine and fulvic acid) as in Essential Iodine Drops (EID) with 200 μg elemental iodine/ml content against SARS-CoV-2 to ascertain whether it is a better alternative to PVP-I. Methods SARS-CoV-2 (USAWA1/2020 strain) virus stock was prepared by infecting Vero 76 cells (ATCC CRL-1587) until cytopathic effect (CPE). The virucidal activity of EID against SARS-CoV-2 was tested in three dilutions (1:1; 2:1 and 3:1) in triplicates by incubating at room temperature (22 ± 2°C) for either 60 or 90 seconds. The surviving viruses from each sample were quantified by a standard end-point dilution assay. Results EID (200 μg iodine/ml) after exposure for 60 and 90 seconds was compared to controls. In both cases, the viral titre was reduced by 99% (LRV 2.0). The 1:1 dilution of EID with virus reduced SARS-CoV-2 virus from 31,623 cell culture infectious dose 50% (CCCID50) to 316 CCID50 within 90 seconds. Conclusion Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients. url: https://doi.org/10.1101/2020.11.07.370726 doi: 10.1101/2020.11.07.370726 id: cord-314933-wq1xo0z0 author: Zores, Florian title: COVID and the Renin-Angiotensin System: Are Hypertension or Its Treatments Deleterious? date: 2020-04-23 words: 3161.0 sentences: 172.0 pages: flesch: 49.0 cache: ./cache/cord-314933-wq1xo0z0.txt txt: ./txt/cord-314933-wq1xo0z0.txt summary: In this paper, we hypothesize that the reductions in Angiotensin-Converting Enzyme 2 (ACE-2) observed in hypertension and obesity can explain many abnormalities observed in SARS-CoV-2 and question the role of treatments interfering with ACE2. Like SARS-CoV, SARS-CoV-2 fuses with human cells after the receptor-binding domain of its S (Spike) protein binds with Angiotensin-Converting Enzyme 2 (ACE-2), an enzyme located on membrane of lung alveolar epithelial cells, renal tubular epithelial cells, enterocytes of the small intestine, and arterial and venous endothelial cells of the kidney (5-10). ACE2, Angiotensin Converting Enzyme 2; ACEi, Angiotensin Converting Enzyme Inhibitor; ang-(1-7), Angiotensin-(1-7); ANGII, angiotensin II; ANGIV, angiotensin IV; ARB, Angiotensin Receptor Blocker; ARDS, Acute Respiratory Distress Syndrome; AT1R, Angiotensin II Type 1 Receptor; AT4R, Angiotensin II Type 4 Receptor; SARS-CoV-2, Severe Acute Respiratory Syndrome CoronaVirus 2. Thus, decreased ACE2 expression promotes increased lung injury and ARB prevents it by limiting ANGII binding to AT1R (7, 8, 24, 25) (Figure 1C) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32391384/ doi: 10.3389/fcvm.2020.00071 id: cord-283861-kcv1bmyx author: Zou, J. title: Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents date: 2020-05-06 words: 3192.0 sentences: 175.0 pages: flesch: 63.0 cache: ./cache/cord-283861-kcv1bmyx.txt txt: ./txt/cord-283861-kcv1bmyx.txt summary: We quantitated anti-SARS/CoV-2 IgG and IgM by ELISA in self-collected blood samples (n=142) in arbitrarily-selected metro Atlanta residents, primarily acquaintances of the authors'' lab members from 4/17-4/27, 2020. While we do not claim this small immune survey is 49 broadly representative of metro Atlanta, and we have greater confidence in the IgG results, 50 which had only 2.4% positivity, it nonetheless demonstrates that persons with antibodies to 51 SARS/CoV-2, who''ve not suspected they''d been exposed to this virus, can readily be found in 52 various Atlanta area neighborhoods (9 positives were in 8 zip codes). Nonetheless, our quantitative approaches enabled seemingly readily and 74 reliable discernment that about 3 and 6 of 127 arbitrarily subjected Atlanta area residents 75 displayed SARs/CoV-2-specific IgG and IgM, respectively, which likely reflects that they have 76 been exposed to this virus. abstract: We quantitated anti-SARS/CoV-2 IgG and IgM by ELISA in self-collected blood samples (n=142) in arbitrarily-selected metro Atlanta residents, primarily acquaintances of the authors' lab members from 4/17-4/27, 2020. Archived serum (n=34), serum from nucleic acid test (NAT)-positive subjects (n=4), and samples collected from NAT-positive community members (n=4) served to validate the assay. The range of anti-SARS/CoV-2 antibodies in archived and NAT-positive sera indicated need to compromise sensitivity or specificity. Accordingly, we set a cutoff of 4 SD above the mean for IgG and 3 SD above the mean for IgM to indicate that an individual had been exposed, and developed some degree of immunity, to SARS/CoV-2. The IgG cutoff clearly compromised sensitivity but offered high specificity, both of which were harder to gauge for IgM. Based on these cutoffs, excluding subjects whose participation resulted from self-suspected SARS/CoV-2 infection, we found 7.1% positivity for anti-SARS/CoV-2 IgG (3 of 127 subjects) or IgM (6 of 127). While we do not claim this small immune survey is broadly representative of metro Atlanta, and we have greater confidence in the IgG results, which had only 2.4% positivity, it nonetheless demonstrates that persons with antibodies to SARS/CoV-2, who've not suspected they'd been exposed to this virus, can readily be found in various Atlanta area neighborhoods (9 positives were in 8 zip codes). Accordingly, these results support the notion that dissemination of the virus is more widespread than testing would indicate but also suggests that most persons in metro Atlanta remain vulnerable to this virus. More generally, these results support the general utility of sero-surveillance to guide public policy but also highlight the difficulty of discerning if individuals have immunity to SARS/CoV-2. url: http://medrxiv.org/cgi/content/short/2020.05.01.20087478v1?rss=1 doi: 10.1101/2020.05.01.20087478 id: cord-313627-g1iqhsdk author: Zou, Xiaojing title: Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection date: 2020-06-15 words: 1804.0 sentences: 126.0 pages: flesch: 55.0 cache: ./cache/cord-313627-g1iqhsdk.txt txt: ./txt/cord-313627-g1iqhsdk.txt summary: Conclusion Liver injury in patients with SARS-CoV-2 and chronic HBV co-infection was associated with severity and poor prognosis of disease. In this study, we aimed to describe the characteristics of liver function and its 3 relation with severity and prognosis in patients with SARS-CoV-2 and chronic HBV 4 co-infection, in order to provide evidence for the clinical treatment of these specific 5 patients and contribute to improving their prognosis. In the present study, we found that liver test abnormalities were relatively common 1 in patients with SARS-CoV-2 and chronic HBV co-infection, and the values of ALT, 2 AST, TBIL, ALP and γ-GT increased substantially during hospitalization. 6 The present study reported evidence of liver injury in patients with SARS-CoV-2 7 and chronic HBV co-infection. These findings 9 indicate that liver injury in patients with SARS-CoV-2 and chronic HBV co-infection 10 was associated with disease severity and worse prognosis. abstract: Summary Background and aims Coronavirus disease 2019 (COVID-19) is a major global health threat. We aimed to describe the characteristics of liver function in patients with SARS-CoV-2 and chronic hepatitis B virus (HBV) co-infection. Methods We enrolled all adult patients with SARS-CoV-2 and chronic HBV co-infection admitted to Tongji Hospital from February 1 to February 29, 2020. Data of demographic, clinical characteristics, laboratory tests, treatments, and clinical outcomes were collected. The characteristics of liver function and its relation with the severity and prognosis of disease were described. Results Of 105 SARS-CoV-2 and chronic HBV co-infected patients, elevated levels of liver test were seen in several patients at admission, including elevated levels of alanine aminotransferase (22,20.95%), aspartate aminotransferase (29, 27.62%), total bilirubin (7, 6.67%), gamma-glutamyl transferase (7, 6.67%) and alkaline phosphatase (1, 0.95%). The values of the indices mentioned above increased substantially during hospitalization (all P<0.05). 14 (13.33%) patients developed liver injury. Most of them (10, 71.43%) recovered after 8 (range 6-21) days. Notably, 4 (28.57%) patients rapidly progressed to acute-on-chronic liver failure. The proportion of severe COVID-19 was higher in patients with liver injury (P= 0.042). Complications including ACLF, acute cardiac injury and shock happened more frequently in patients with liver injury (all P<0.05). The mortality was higher in individuals with liver injury (28.57% vs 3.30%, P=0.004). Conclusion Liver injury in patients with SARS-CoV-2 and chronic HBV co-infection was associated with severity and poor prognosis of disease. During the treatment of COVID-19 in chronic HBV-infected patients, liver function should be taken seriously and evaluated frequently. url: https://www.ncbi.nlm.nih.gov/pubmed/32553907/ doi: 10.1016/j.cgh.2020.06.017 id: cord-319704-xzhoa03d author: Zuercher, S. J. title: Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence date: 2020-05-22 words: 6873.0 sentences: 370.0 pages: flesch: 47.0 cache: ./cache/cord-319704-xzhoa03d.txt txt: ./txt/cord-319704-xzhoa03d.txt summary: Results: Most original studies on MHP were conducted in China in the context of SARS-CoV-1, and reported on anxiety, depression, post-traumatic stress symptoms/disorder, general psychiatric morbidity, and psychological symptoms. While considerable efforts rely on protective and treatment measures such as virus transmission pathways, clinical presentations, and the development of vaccinations, attention is only recently given to short or long-term mental health problems (MHP, hereafter defined as psychiatric/psychological symptoms and mental illness/disorders) (Rajkumar, 2020) that may arise due to the different surrounding consequences of an epidemic in the general public, health care workers (HCW), and survivors of infectious diseases (survivors). In this rapid review of 74 original articles we found a wide range of MHP including anxiety, depression, PTSD and stress related symptoms or disorders, psychiatric morbidity, and many further MHP like paranoid ideation, hallucinations, and insomnia that may occur in the general public, HCW or survivors during and after epidemic outbreaks. abstract: Background: The swift spread of SARS-CoV-2 provides a challenge worldwide. As a consequence of restrictive public health measures like isolation, quarantine, and community containment, the provision of mental health services is a major challenge. Evidence from past virus epidemics and the current SARS-CoV-2 outbreak indicate high prevalence rates of mental health problems (MHP) as short- and long-term consequences. However, a broader picture of MHP among different populations is still lacking. Methods: We conducted a rapid review on MHP prevalence rates published since 2000, during and after epidemics, including the general public, health care workers, and survivors. Any quantitative articles reporting on MHP rates were included. Out of 2855 articles screened, a total of 74 were included in this review. Results: Most original studies on MHP were conducted in China in the context of SARS-CoV-1, and reported on anxiety, depression, post-traumatic stress symptoms/disorder, general psychiatric morbidity, and psychological symptoms. The MHP rates across studies, populations, and epidemics vary substantially. While some studies show high and persistent rates of MHP in populations directly affected by isolation, quarantine, threat of infection, infection, or life-threatening symptoms (e.g. health care workers), other studies report minor effects. Furthermore, even less affected populations (e.g. distant to epidemic epicenter, no contact history with suspected or confirmed cases) can show high rates of MHP. Discussion: MHP vary largely across countries and risk-groups in reviewed studies. The results call attention to potentially high MHP during epidemics. Individuals affected directly by an epidemic might be at a higher risk of short or even long-term mental health impairments. This study delivers insights stemming from a wide range of psychiatric instruments and questionnaires. The results call for the use of validated and standardized instruments, reference norms, and pre-post measurements to better understand the magnitude of the MHP during and after the epidemics. Nevertheless, emerging MHP should be considered during epidemics including the provision of access to mental health care to mitigate potential mental impairments. url: https://doi.org/10.1101/2020.05.19.20103788 doi: 10.1101/2020.05.19.20103788 id: cord-269001-m4mpcoab author: Zullo, Fabrizio title: COVID-19 Antibody Testing in Pregnancy date: 2020-05-18 words: 586.0 sentences: 38.0 pages: flesch: 54.0 cache: ./cache/cord-269001-m4mpcoab.txt txt: ./txt/cord-269001-m4mpcoab.txt summary: 1, 2 Almost all patients with COVID-19 infection test positive for 23 antiviral immunoglobulin-G (IgG) within about 10-20 days after symptom onset (Figure 1 ), but the 24 clinical value of antibody testing has not yet been completely elucidated, either in non-pregnant or 25 even more pregnant patients. Testing pregnant women for antibody response to COVID-19 may have different advantages, 33 including identifying: 1. Women still at risk for COVID-19 infection (e.g. IgM and IgG negative). Those tested positive to either IgM 69 or IgG at the rapid combined antibody test, have NP swab offered, and the outpatient appointment is 70 postponed, as shown in Figure 2B . In summary, we recommend testing for antibody response to SARS-CoV-2 for pregnant women Development and Clinical Application of A Rapid IgM-IgG Combined Antibody 111 Test for SARS-CoV-2 Infection Diagnosis abstract: nan url: https://doi.org/10.1016/j.ajogmf.2020.100142 doi: 10.1016/j.ajogmf.2020.100142 id: cord-275404-hv3y4x4g author: Zumla, Alimuddin title: Infection control and MERS-CoV in health-care workers date: 2014-05-20 words: 1527.0 sentences: 80.0 pages: flesch: 48.0 cache: ./cache/cord-275404-hv3y4x4g.txt txt: ./txt/cord-275404-hv3y4x4g.txt summary: 1 The WHO Emergency Committee concluded that the increase in cases reported among health-care workers from hospitals in Jeddah was amplifi ed due to overcrowding and inadequate infection control measures. 11 On the basis of analysis of data in a case-control study that involved 124 medical wards in 26 hospitals in Guangzhou, China, and Hong Kong, the risk factors for super-spreading events of SARS-CoV in the hospital setting were: close separation between beds of less than 1 m; performance of resuscitation; staff working while experiencing symptoms; and patients requiring oxygen or non-invasive ventilation therapy. A systematic review of fi ve case-control and fi ve retrospective cohort studies identifi ed tracheal intubation, tracheotomy, and manual ventilation before intubation as procedures associated with risk of transmission of SARS-CoV to health-care workers. Interim infection prevention and control recommendations for hospitalized patients with Middle East respiratory syndrome coronavirus (MERS-CoV) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/24857701/ doi: 10.1016/s0140-6736(14)60852-7 id: cord-292988-q1yz9y8k author: Zumla, Alimuddin title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 words: 3157.0 sentences: 174.0 pages: flesch: 39.0 cache: ./cache/cord-292988-q1yz9y8k.txt txt: ./txt/cord-292988-q1yz9y8k.txt summary: title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . abstract: Abstract As of May 11th 2020, the coronavirus disease 2019 (COVID-19) pandemic, caused by the novel, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused 274,361 deaths out of 3,917,366 (7% case fatality rate). As with the two other novel coronavirus zoonotic diseases of humans, SARS and MERS, no specific treatments for reducing mortality or morbidity are yet available. Deaths from COVID-19 will continue to rise globally until effective and appropriate treatments and vaccines are found. With no specific treatments being available for treating COVID-19 patients, the global medical, scientific, pharma and funding communities have rapidly initiated over 500 COVID-19 clinical on a range of antiviral drug regimens, biologics, repurposed drugs in various combinations. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. This is an area which has been eclipsed by the current emphasis the huge number of trials evaluating new anti-viral drugs, repurposed drugs and combinations thereof. MSCs should also be trialed for treatment of severe cases of MERS where mortality rates are upto 34% and MERS-CoV remains a WHO priority Blueprint pathogen. It’s about time funding agencies now invest more into development MSCs per se and other host-directed therapies in combination with other therapeutic interventions. MSC therapy could turn out to be an important contribution to bringing an end to the high COVID-19 and MERS death rates. url: https://doi.org/10.1016/j.ijid.2020.05.040 doi: 10.1016/j.ijid.2020.05.040 id: cord-320646-xk77u4g0 author: Zumla, Alimuddin title: The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security date: 2020-04-09 words: 2396.0 sentences: 132.0 pages: flesch: 48.0 cache: ./cache/cord-320646-xk77u4g0.txt txt: ./txt/cord-320646-xk77u4g0.txt summary: The emergence of new pathogens that cause lethal human respiratory illnesses with pandemic potential [2, 3] pose major challenges and rapidly focus the attention of global public health authorities and HCWs. Two zoonotic coronaviruses which cause lethal respiratory tract infections in humans feature on the WHO Blueprint list of priority pathogens for research and development [4] because of their pandemic potential. The World Health Organization International Health Regulations Emergency Committee declared COVID-19 outbreak a Global emergency [11] because SARS-CoV has spread rapidly within and outside China at an alarming pace and has caused considerable consternation and panic among the national, regional, and international public and political communities compounded by news media and social media hype [12] . Although the world awaits the development and evaluation of new vaccines, anti-SARS-CoV-2 specific drugs, antibody, and/or other host-directed interventions [32, 33] , public health infection control measures remain of prime importance in limiting human-to-human transmission, especially among close contacts and HCWs, and minimizing risk of international spread by identifying and isolating patients early. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32132379/ doi: 10.1097/mcp.0000000000000676 id: cord-329129-t84pu00z author: Zuo, J title: Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date: 2020-11-02 words: 3486.0 sentences: 175.0 pages: flesch: 50.0 cache: ./cache/cord-329129-t84pu00z.txt txt: ./txt/cord-329129-t84pu00z.txt summary: We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection. In this study we characterised SARS-CoV-2-specific T cell immune responses in a cohort of 100 donors at 6-months post-infection. Peptide pools from a range of viral proteins, including spike, nucleoprotein and membrane protein, were used to stimulate fresh PBMC and the magnitude of the global SARS-CoV-2-specific T-cell response was determined. Here we undertook, to our knowledge, the first assessment of the SARS-CoV-2-specific T cell immune response at six months following primary infection in a unique cohort of healthy adults with asymptomatic or mild-to-moderate COVID-19. abstract: The immune response to SARS-CoV-2 is critical in both controlling primary infection and preventing re-infection. However, there is concern that immune responses following natural infection may not be sustained and that this may predispose to recurrent infection. We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. T-cell immune responses to SARS-CoV-2 were present by ELISPOT and/or ICS analysis in all donors and are characterised by predominant CD4+ T cell responses with strong IL-2 cytokine expression. Median T-cell responses were 50% higher in donors who had experienced an initial symptomatic infection indicating that the severity of primary infection establishes a ‘setpoint’ for cellular immunity that lasts for at least 6 months. The T-cell responses to both spike and nucleoprotein/membrane proteins were strongly correlated with the peak antibody level against each protein. The rate of decline in antibody level varied between individuals and higher levels of nucleoprotein-specific T cells were associated with preservation of NP-specific antibody level although no such correlation was observed in relation to spike-specific responses. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection. url: https://doi.org/10.1101/2020.11.01.362319 doi: 10.1101/2020.11.01.362319 id: cord-023867-ti4b03lh author: Zuo, Wei title: SARS Coronavirus and Lung Fibrosis date: 2009-07-22 words: 4277.0 sentences: 244.0 pages: flesch: 51.0 cache: ./cache/cord-023867-ti4b03lh.txt txt: ./txt/cord-023867-ti4b03lh.txt summary: The mechanisms by which SARS-CoV infection causes lung fibrosis are not fully understood, but transforming growth factor-β (TGF-β) and angiotensin-converting enzyme 2 (ACE2)-mediated lung fibrosis are among the most documented ones. Therefore, SARS-CoV infection may lead to lung fibrosis through multiple signaling pathways and TGF-β activation is one of the major contributors. ACE2 proteins are expressed by alveolar epithelial cells, the primary targets of SARS-CoV in lung. Altogether, infection with SARS-CoV results in ACE2 downregulation through the binding of SARS-CoV spike protein to ACE2, and this spike protein-mediated ACE2 downregulation is responsible for the pathogenesis of lung fibrosis by upregulating ANG-II and activating TGF-b signaling. Both the TGF-b/Smad and the ACE2/ANG-II/CTGF pathways contribute to myofibroblast activation and ECM accumulation, collectively leading to the final lung fibrosis Role of extracellular signal-regulated kinase, p38 kinase, and activator protein-1 in transforming growth factor-beta 1-induced alpha smooth muscle actin expression in human fetal lung fibroblasts in vitro Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling abstract: Severe acute respiratory syndrome (SARS) is an acute infectious disease with significant mortality. A novel coronavirus (SARS-CoV) has been shown to be the causative agent of SARS. The typical clinical feature associated with SARS is diffuse alveolar damage in lung, and lung fibrosis is evident in patients who died from this disease. The mechanisms by which SARS-CoV infection causes lung fibrosis are not fully understood, but transforming growth factor-β (TGF-β) and angiotensin-converting enzyme 2 (ACE2)-mediated lung fibrosis are among the most documented ones. The activation of the TGF-β/Smad pathway is critical to lung fibrosis. SARS-CoV infection not only enhances the expression of TGF-β, but also facilitates its signaling activity. The SARS-CoV receptor ACE2 is a negative regulator of lung fibrosis, and SARS-CoV infection decreases ACE2 expression. Therefore, SARS-CoV infection may lead to lung fibrosis through multiple signaling pathways and TGF-β activation is one of the major contributors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176214/ doi: 10.1007/978-3-642-03683-5_15 id: cord-307942-t8165mdx author: Zwald, Marissa L. title: Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 date: 2020-04-10 words: 1619.0 sentences: 71.0 pages: flesch: 43.0 cache: ./cache/cord-307942-t8165mdx.txt txt: ./txt/cord-307942-t8165mdx.txt summary: On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). During the investigation period, 226 patients seen at one of the four urgent care centers met the inclusion criteria (i.e., Santa Clara County resident, respiratory symptoms, no recent travel, and no known close contact with a patient with confirmed COVID-19) and were tested for evidence of influenza virus infection; among those, 53 (23%) had positive test results for influenza. abstract: On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). At the time the investigation began, testing guidance recommended focusing on persons with clinical findings of lower respiratory illness and travel to an affected area or an epidemiologic link to a laboratory-confirmed COVID-19 case, or on persons hospitalized for severe respiratory disease and no alternative diagnosis (1). To rapidly understand the extent of COVID-19 in the community, SCCPHD, the California Department of Public Health (CDPH), and CDC began sentinel surveillance in Santa Clara County. During March 5-14, 2020, four urgent care centers in Santa Clara County participated as sentinel sites. For this investigation, county residents evaluated for respiratory symptoms (e.g., fever, cough, or shortness of breath) who had no known risk for COVID-19 were identified at participating urgent care centers. A convenience sample of specimens that tested negative for influenza virus was tested for SARS-CoV-2 RNA. Among 226 patients who met the inclusion criteria, 23% had positive test results for influenza. Among patients who had negative test results for influenza, 79 specimens were tested for SARS-CoV-2, and 11% had evidence of infection. This sentinel surveillance system helped confirm community transmission of SARS-CoV-2 in Santa Clara County. As a result of these data and an increasing number of cases with no known source of transmission, the county initiated a series of community mitigation strategies. Detection of community transmission is critical for informing response activities, including testing criteria, quarantine guidance, investigation protocols, and community mitigation measures (2). Sentinel surveillance in outpatient settings and emergency departments, implemented together with hospital-based surveillance, mortality surveillance, and serologic surveys, can provide a robust approach to monitor the epidemiology of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32271724/ doi: 10.15585/mmwr.mm6914e3 id: cord-337372-y43prnko author: bin‐Reza, Faisal title: The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence date: 2011-12-21 words: 4040.0 sentences: 226.0 pages: flesch: 45.0 cache: ./cache/cord-337372-y43prnko.txt txt: ./txt/cord-337372-y43prnko.txt summary: A limited effort was made to identify additional studies: reference lists of review articles were examined; the European Centre for Disease Prevention and Control''s (ECDC) Antimicrobial Resistance and Health Care Associated Infection Programme was consulted; and MEC''s and AN''s hardcopy literature files were hand-searched. [7] [8] [9] [10] [11] Two of these studies compared N95 respirators (designed to seal tightly to the wearer''s face and filter out very small particles or aerosols that may contain viruses) and surgical masks (used to block large droplets from coming into contact with the wearer''s mouth or nose) amongst healthcare workers; one trial found a lower rate of clinical respiratory illness associated with the use of non-fit-tested N95 respirators compared with medical masks, 6 whilst a non-inferiority trial found that masks and respirators offered similar protection to nurses against laboratory-confirmed influenza infection. abstract: Please cite this paper as: bin‐Reza et al. (2012) The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence. Influenza and Other Respiratory Viruses 6(4), 257–267. There are limited data on the use of masks and respirators to reduce transmission of influenza. A systematic review was undertaken to help inform pandemic influenza guidance in the United Kingdom. The initial review was performed in November 2009 and updated in June 2010 and January 2011. Inclusion criteria included randomised controlled trials and quasi‐experimental and observational studies of humans published in English with an outcome of laboratory‐confirmed or clinically‐diagnosed influenza and other viral respiratory infections. There were 17 eligible studies. Six of eight randomised controlled trials found no significant differences between control and intervention groups (masks with or without hand hygiene; N95/P2 respirators). One household trial found that mask wearing coupled with hand sanitiser use reduced secondary transmission of upper respiratory infection/influenza‐like illness/laboratory‐confirmed influenza compared with education; hand sanitiser alone resulted in no reduction. One hospital‐based trial found a lower rate of clinical respiratory illness associated with non‐fit‐tested N95 respirator use compared with medical masks. Eight of nine retrospective observational studies found that mask and/or respirator use was independently associated with a reduced risk of severe acute respiratory syndrome (SARS). Findings, however, may not be applicable to influenza and many studies were suboptimal. None of the studies established a conclusive relationship between mask/respirator use and protection against influenza infection. Some evidence suggests that mask use is best undertaken as part of a package of personal protection especially hand hygiene. The effectiveness of masks and respirators is likely linked to early, consistent and correct usage. url: https://www.ncbi.nlm.nih.gov/pubmed/22188875/ doi: 10.1111/j.1750-2659.2011.00307.x id: cord-306017-4wf4yhyz author: d''Aloja, Ernesto title: COVID-19 and medical liability: Italy denies the shield to its heroes date: 2020-07-24 words: 1005.0 sentences: 56.0 pages: flesch: 54.0 cache: ./cache/cord-306017-4wf4yhyz.txt txt: ./txt/cord-306017-4wf4yhyz.txt summary: As well known, Italy is one of the Countries in a worldwide context more severely affected by the SARS-CoV-2 pandemic and some of the northern regions paid the highest price in terms of deaths among health care workers (HCWs).The ''Istituto Nazionale Assicurazione Infortuni sul Lavoro'' (INAIL), the Italian public insurance body that protects workers in the event of accidents and occupational diseases, reported that 40% of the 236 filedfatal cases involved HCWs [1] . From a negligent pandemic point of view, this may mean that if the hospital À even a no-COVID one -does not provide for all these measures, and one or more cases of SARS-COV-2 positive patients are detected in the healthcare facility, a presumption of liability may be enough to pursuing a negligent pandemic crime (article 452, Italian penal code). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32734174/ doi: 10.1016/j.eclinm.2020.100470 id: cord-278923-u4gv2e7w author: da Silva, Joyce Kelly R. title: Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation date: 2020-05-12 words: 6372.0 sentences: 408.0 pages: flesch: 50.0 cache: ./cache/cord-278923-u4gv2e7w.txt txt: ./txt/cord-278923-u4gv2e7w.txt summary: A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 M(pro)), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). One study evaluated the in vitro antiviral effect against influenza type A (H1N1) of commercial essential oils that included cinnamon (Cinnamomum zeylanicum), bergamot (Citrus bergamia), lemongrass (Cymbopogon flexuosus), thyme (Thymus vulgaris), and lavender (Lavandula angustifolia). In this work, we carried out a molecular docking analysis of the major components of essential oils that exhibit antiviral activity (Tables 1 and 2 ) with known SARS-CoV-2 protein targets. Docking scores, normalized for molecular weight (DS norm , kJ/mol), of essential oil components with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular targets. abstract: Essential oils have shown promise as antiviral agents against several pathogenic viruses. In this work we hypothesized that essential oil components may interact with key protein targets of the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 M(pro)), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). The compound with the best normalized docking score to SARS-CoV-2 M(pro) was the sesquiterpene hydrocarbon (E)-β-farnesene. The best docking ligands for SARS−CoV Nsp15/NendoU were (E,E)-α-farnesene, (E)-β-farnesene, and (E,E)−farnesol. (E,E)−Farnesol showed the most exothermic docking to SARS-CoV-2 ADRP. Unfortunately, the docking energies of (E,E)−α-farnesene, (E)-β-farnesene, and (E,E)−farnesol with SARS-CoV-2 targets were relatively weak compared to docking energies with other proteins and are, therefore, unlikely to interact with the virus targets. However, essential oil components may act synergistically, essential oils may potentiate other antiviral agents, or they may provide some relief of COVID-19 symptoms. url: https://doi.org/10.3390/ijms21103426 doi: 10.3390/ijms21103426 id: cord-347613-tjeo62dv author: da Silva, Priscilla Gomes title: Corrigendum to “Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2”[Sci. Total Environ. 750 (2021) 141483] date: 2020-09-10 words: 445.0 sentences: 36.0 pages: flesch: 71.0 cache: ./cache/cord-347613-tjeo62dv.txt txt: ./txt/cord-347613-tjeo62dv.txt summary: In this study, HeLa cells that expressed or did not express ACE2 proteins from humans, Chinese horseshoe bats, civets, pigs and mice were used, and it was found that SARS-CoV-2 is able to use all ACE2 proteins (except for mouse ACE2) as an entry receptor to enter ACE2-expressing cells, but it could not enter cells that did not express ACE2, indicating that ACE2 is probably the cell receptor through which SARS-CoV-2 enters cells (Zhou et al., 2020) . This and other bat-coronaviruses share 88-92% nucleotide sequence homology with SARS-CoV-1 (Ye et al., 2020) , leading scientists to believe that SARS-CoV was transmitted directly to humans from wet market civets, with bats as the main reservoir hosts (Cui et al., 2019; Hu et al., 2017) ". Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus abstract: nan url: https://doi.org/10.1016/j.scitotenv.2020.142123 doi: 10.1016/j.scitotenv.2020.142123 id: cord-350925-1h6pbfwp author: da Silva, Priscilla Gomes title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 words: 5221.0 sentences: 279.0 pages: flesch: 49.0 cache: ./cache/cord-350925-1h6pbfwp.txt txt: ./txt/cord-350925-1h6pbfwp.txt summary: Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . abstract: Background Although an increasing body of data reports the detection of SARS-CoV-2 RNA in air, this does not correlate to the presence of infectious viruses, thus not evaluating the risk for airborne COVID-19. Hence there is a marked knowledge gap that requires urgent attention. Therefore, in this systematic review, viability/stability of airborne SARS-CoV-2, SARS-CoV and MERS-CoV viruses is discussed. Methods A systematic literature review was performed on PubMed/MEDLINE, Web of Science and Scopus to assess the stability and viability of SARS-CoV, MERS-CoV and SARS-CoV-2 on air samples. Results and discussion The initial search identified 27 articles. Following screening of titles and abstracts and removing duplicates, 11 articles were considered relevant. Temperatures ranging from 20 °C to 25 °C and relative humidity ranging from 40% to 50% were reported to have a protective effect on viral viability for airborne SARS-CoV and MERS-CoV. As no data is yet available on the conditions influencing viability for airborne SARS-CoV-2, and given the genetic similarity to SARS-CoV and MERS-CoV, one could extrapolate that the same conditions would apply. Nonetheless, the effect of these conditions seems to be residual considering the increasing number of cases in the south of USA, Brazil and India, where high temperatures and humidities have been observed. Conclusion Higher temperatures and high relative humidity can have a modest effect on SARS-CoV-2 viability in the environment, as reported in previous studies to this date. However, these studies are experimental, and do not support the fact that the virus has efficiently spread in the tropical regions of the globe, with other transmission routes such as the contact and droplet ones probably being responsible for the majority of cases reported in these regions, along with other factors such as human mobility patterns and contact rates. Further studies are needed to investigate the extent of aerosol transmission of SARS-CoV-2 as this would have important implications for public health and infection-control policies. url: https://www.sciencedirect.com/science/article/pii/S0048969720363312?v=s5 doi: 10.1016/j.scitotenv.2020.142802 id: cord-268561-vq1uhj5i author: da Silva, Severino Jefferson Ribeiro title: Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19 date: 2020-08-04 words: 9916.0 sentences: 594.0 pages: flesch: 47.0 cache: ./cache/cord-268561-vq1uhj5i.txt txt: ./txt/cord-268561-vq1uhj5i.txt summary: 11 The causative agent was identified as a novel CoV, eventually named SARS-CoV-2, and the respiratory syndrome associated with the infection was designated as coronavirus disease-2019 (COVID-19) by the World Health Organization (WHO). In direct tests, the clinical sample is examined directly for the presence of particles, virus antigens, or viral nucleic acids, whereas indirect methods detect the serological response against the infection (Figure 2 ). 11 Culture-based methods for SARS-CoV-2 detection have been used in research and public health laboratories in different parts of the world, but virus isolation is not recommended as a routine diagnostic procedure because it has low sensitivity, it is time-consuming, and it requires BSL-3 containment. 11 In addition to unequivocally confirming the diagnosis of a SARS-CoV-2 infection, regular sequencing of a percentage of patient samples from clinical cases can be used to monitor changes in the viral genome over time and trace transmission patterns. abstract: [Image: see text] In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis. url: https://doi.org/10.1021/acsinfecdis.0c00274 doi: 10.1021/acsinfecdis.0c00274 id: cord-307229-wjx90xki author: da Silveira, Matheus Pelinski title: Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date: 2020-07-29 words: 8418.0 sentences: 362.0 pages: flesch: 34.0 cache: ./cache/cord-307229-wjx90xki.txt txt: ./txt/cord-307229-wjx90xki.txt summary: Additionally, elevations of IL-1β, IFN-γ, IP10 and MCP1 in infections by the novel coronavirus were associated with the Th1 response; however, an increase in interleukins of the T helper type 2 (Th2) profile, such as IL-4, IL-5, IL10, which suppress the inflammation, was also associated with a greater severity of COVID-19, which may demonstrate an imbalance in immune regulation and an attempt to minimize tissue inflammatory damage [35, 40] . In addition, obesity is an important factor for the development of T2DM-especially when associated with low levels of physical activity and poor physical conditioning-and as mentioned, both diseases are related to higher expression of ACE2, increasing the risk of advanced infection by SARS-CoV-2 [43] . Similarly, regular exercise practices at moderate levels favor the function of the human body''s immune surveillance against pathogens, as they stimulate an exchange of white blood cells between the circulatory system and tissues, a fact that reduces morbidity and mortality from acute respiratory disease and infections viral. abstract: Acute viral respiratory infections are the main infectious disease in the world. In 2020, a new disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus disease 2019 (COVID-19), became a global pandemic. The immune response to the virus depends on factors such as genetics, age and physical state, and its main input receptor is the angiotensin-converting enzyme 2. The practice of physical exercises acts as a modulator of the immune system. During and after physical exercise, pro- and anti-inflammatory cytokines are released, lymphocyte circulation increases, as well as cell recruitment. Such practice has an effect on the lower incidence, intensity of symptoms and mortality in viral infections observed in people who practice physical activity regularly, and its correct execution must be considered to avoid damage. The initial response is given mainly by type I interferons (IFN-I), which drive the action macrophages and lymphocytes, followed by lymphocyte action. A suppression of the IFN-I response has been noted in COVID-19. Severe conditions have been associated with storms of pro-inflammatory cytokines and lymphopenia, as well as circulatory changes and virus dispersion to other organs. The practice of physical activities strengthens the immune system, suggesting a benefit in the response to viral communicable diseases. Thus, regular practice of adequate intensity is suggested as an auxiliary tool in strengthening and preparing the immune system for COVID-19. Further studies are needed to associate physical exercise with SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32728975/ doi: 10.1007/s10238-020-00650-3 id: cord-035067-ic843wr9 author: de Almeida, Joana Ferro Machado title: COVID-19 and the gastrointestinal tract: what do we already know? date: 2020-11-05 words: 5453.0 sentences: 336.0 pages: flesch: 56.0 cache: ./cache/cord-035067-ic843wr9.txt txt: ./txt/cord-035067-ic843wr9.txt summary: Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. Information on country of origin, mean age, different comorbidities, typical symptoms (fever, cough, and dyspnea, among others), gastrointestinal symptoms (diarrhea, nausea, vomiting, and abdominal pain), and the presence of viral RNA in feces, when cited, were included in this study for analysis. (19) According to the descriptive, cross-sectional, multicenter study (three hospitals in Hubei, China) by Pan et al., with 204 patients, in which 107 were male, mean age of 52.91±15.98 years, 103 (50.5%) reported some gastrointestinal symptom, such as lack of appetite (81; 78.6%), diarrhea (35; 34.0%), vomiting (4; 3.9%), and abdominal pain (2; 1.9%). (26) Cipriano et al., conducted a systematic review with six studies of patients from China, which points to the possibility of SARS-CoV-2 infection in the gastrointestinal tract and fecal-oral transmission. abstract: The new coronavirus disease pandemic is defining 2020, with almost 17.5 million infected individuals and 700 thousand deaths up to beginning of August. It is caused by SARS-CoV-2 and the transmission is through the respiratory tract. Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. The objective of this work was to review the literature related to the prevalence of gastrointestinal symptoms, and to check the possibility of fecal-oral transmission. We searched PubMed(®) database on COVID-19 and gastrointestinal tract and selected articles using the PRISMA method. We eliminated articles based on titles and abstracts, small number of patients and the mechanism of infection, leaving 14 studies. Comorbidities and laboratory alterations (elevation of hepatic aminotransferases and bilirubin) were related to worsening of the disease. The prevalence of gastrointestinal symptoms ranged from 6.8% to 61.3%, including diarrhea (8.14% to 33.7%), nausea/vomiting (1.53% to 26.4%), anorexia (12.1% to 40.0%) and abdominal pain (0% to 14.5%). The presence of viral RNA in stools was rarely tested, but positive in 0% to 48.1%. The gastrointestinal tract is affected by COVID-19, causing specific symptoms, laboratory alterations and viral presence in the feces. However, the results of prevalence and possibility of fecal-oral transmission were varied, requiring further studies for more assertive conclusions. It is important that healthcare professionals draw attention to this fact, since these changes can help make diagnosis and initiate early treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647386/ doi: 10.31744/einstein_journal/2020rw5909 id: cord-321049-9ozn6il7 author: de Almeida, Paula Rodrigues title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date: 2020-05-01 words: 1308.0 sentences: 73.0 pages: flesch: 49.0 cache: ./cache/cord-321049-9ozn6il7.txt txt: ./txt/cord-321049-9ozn6il7.txt summary: title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. Here, we present a fast, accurate and simple method of viral titration using QuantStudio 3D® microchip based RT-dPCR to titrate SARS-CoV2 genomic copies from controls to be used in RT-qPCR assays for diagnosis and research purposes. A dilution that results in approximately 200 to 2000 target copies in the final reaction usually presents better precision values. Results with precision values below 5% were selected to estimate quantity of SARS-CoV2 genomic copies based on RT-dPCR. RT-dPCR results of 10-fold serial dilution of SARS-CoV2 control using assays for three targets in the Nucleocapsid gene. These results indicate that these primer-probe assays are suitable for SARS-CoV2 quantification through RT-dPCR. abstract: In this study, serial dilutions of SARS-CoV 2 RNA extract were tested using RT-dPCR using three different primer-probe assays aiming SARS-CoV 2 nucleocapsid coding region. Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. High accuracy of this test allowed conclusions regarding the ability of this technique to evaluate precisely the amount of genomic copies present in a sample. We believe that this fast and safe method can assist other researchers in titration of SARS-CoV2 controls used in RT-qPCR without the need of virus isolation. url: https://doi.org/10.1101/2020.05.01.072728 doi: 10.1101/2020.05.01.072728 id: cord-275569-i5y23mmz author: de Bernardis, E. title: A putative role for the tobacco mosaic virus in smokers’ resistance to COVID-19 date: 2020-07-31 words: 1500.0 sentences: 69.0 pages: flesch: 41.0 cache: ./cache/cord-275569-i5y23mmz.txt txt: ./txt/cord-275569-i5y23mmz.txt summary: Though it is intuitively tempting, on the basis of physiopathological common knowledge, to predict a greater risk of contracting the SARS-CoV-2 infection in tobacco smokers, an analysis of studies from various countries shows that hospitalized COVID-19 patients have a lower, and apparently inversely proportional, rate of current tobacco smoking, in comparison with the respective general population, although once the disease has developed meta-analyses suggest that smoking is associated with a worse prognosis [1] . Incidentally, this behavior reminds the proposed effects of tobacco smoking, protective against initial SARS-CoV-2 infection and deleterious in the florid phase of the COVID-19 disease. Taken together, all these elements suggest that the oral use of tobacco, continuously exposing to non-pathogenic but immunogenic TMV particles, and chronically stimulating a natural antiviral response, may induce a state of resistance to the initial SARS-CoV-2 infection. abstract: Reports from various countries suggest that tobacco smoking might protect from SARS-CoV-2 infection, since the prevalence of smoking in COVID-19 hospitalized patients is lower than in the respective general population. Apart from nicotine or other chemicals contained in tobacco smoke, we propose that a single-stranded RNA virus that infects tobacco leaves, tobacco mosaic virus (TMV), might be implicated in this effect. TMV, though non-pathogenic, is found in smokers’ airways, and stimulates adaptive and innate immunity, with release of specific antibodies and interferons. The latter may have preventive and/or therapeutic effects against COVID-19. If confirmed by epidemiological and interventional studies, this might lead to the use of TMV as an immunological adjuvant against SARS-CoV-2 infection and COVID-19 disease. url: https://api.elsevier.com/content/article/pii/S0306987720322337 doi: 10.1016/j.mehy.2020.110153 id: cord-354510-jlg5je0s author: de Carvalho, A. F. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 words: 4112.0 sentences: 234.0 pages: flesch: 58.0 cache: ./cache/cord-354510-jlg5je0s.txt txt: ./txt/cord-354510-jlg5je0s.txt summary: Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. 13 Here we describe the use of a simple, virus-inactivating and denaturing solution as part of a swab collection kit, aiming to decrease the infectious potential of the clinical sample and, at the same time, to preserve highly frail RNA molecules during transportation and short-term storage before testing. In order to increase personnel safety, to avoid losing collaborators due to infections by SARS-CoV-2, and at the same time to increase preservation of the RNA contained in clinical samples, we introduced the use of the guanidinecontaining solution as collection and transport media instead of commonly used viral transport media (VTM). abstract: Background Since the emergence of the COVID-19, health officials have struggled to devise strategies to counteract the speed of the pandemic's spread across the globe. It became imperative to implement accurate diagnostic tests for the detection of SARS-CoV-2 RNA on respiratory samples. In many places, however, besides the limited availability of test reagents, laboratory personnel face the challenge of adapting their working routines to manipulate highly infective clinical samples. Here, we proposed the use of a virus-inactivating solution as part of a sample collection kit to decrease the infectious potential of the collected material without affecting the integrity of RNA samples used in diagnostic tests based on RT-qPCR. Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. RNA extracted from all samples was tested by RT-qPCR using probes for viral and human genes. Exposure of laboratory personnel to infective viruses was also accessed using ELISA tests. Findings The use of the DS did not interfere with the detection of viral genome or the endogenous human mRNA, since similar results were obtained from samples collected with VTM or DS. In addition, all tests of laboratory personnel for the presence of viral RNA and IgG antibodies against SARS-CoV-2 were negative. Interpretation The methodology described here provides a strategy that allow high diagnostic accuracy as well as safe manipulation of clinical samples by those involved with diagnostic procedures. Funding: CAPES, FAPEMIG, CNPq, MCTIC, FIOCRUZ and the UK Global Challenges Research Fund (GCRF). url: https://doi.org/10.1101/2020.06.18.20134304 doi: 10.1101/2020.06.18.20134304 id: cord-308597-ieju8gd8 author: de Carvalho, Renata Cristina title: The interference of COVID-19 in the male reproductive system: Important questions and the future of assisted reproduction techniques date: 2020-08-21 words: 1152.0 sentences: 58.0 pages: flesch: 49.0 cache: ./cache/cord-308597-ieju8gd8.txt txt: ./txt/cord-308597-ieju8gd8.txt summary: If the presence of SARS-Cov-2 in semen is confirmed, the methods of assisted human reproduction conduct should be modified, ensuring the timely safety of couples; however, current information about the virus raises other issues, such as: if seminal transmission exists, should a couple avoid sexual intercourse or use a barrier method if the male partner is known to be positive for the coronavirus disease 2019 (COVID-19)? If there is SARS-Cov-2 in an infected male''s semen, is double sperm washing effective in isolating the virus as it is for HIV and hepatitis C? In addition, even with the absence of the virus in the seminal sample, a study has reported the presence of orchialgia in men diagnosed with COVID-19 (16) , which is indicative of testicular damage. Absence of 2019 novel coronavirus in semen and testes of COVID-19 patients Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32876112/ doi: 10.6061/clinics/2020/e2183 id: cord-340015-x9frt0jh author: de Carvalho, Werther Brunow title: Expert recommendations for the care of newborns of mothers with COVID-19 date: 2020-05-11 words: 2822.0 sentences: 153.0 pages: flesch: 50.0 cache: ./cache/cord-340015-x9frt0jh.txt txt: ./txt/cord-340015-x9frt0jh.txt summary: Despite the lack of scientific evidence regarding the potential for viral transmission to their fetus in pregnant mothers diagnosed with or suspected of COVID-19, it is important to elaborate the lines of care by specialists from hospitals caring for suspected and confirmed COVID-19 cases to guide multidisciplinary teams and families diagnosed with the disease or involved in the care of pregnant women and newborns in this context. (10) proposed the presence of at least one of following clinical signs or symptoms as criteria for the neonatal diagnosis of COVID-2: thermal instability, hypoactivity, feeding difficulty, respiratory distress, chest X-ray with changes (including single or bilateral ground-glass patterns), COVID-19 diagnosis in family or caregiver of the newborn, intimate contact with people with suspected or confirmed COVID-19, or patients with unclear pneumonia. Despite the lack of scientific evidence regarding the potential viral transmission to their fetus by pregnant women with suspected or positive for COVID-19, multidisciplinary teams must be attentive to the disease signs and symptoms for guided and assertive decision making in the management of both mothers and newborns in the hospital environment and discharge. abstract: This article presents expert recommendations for assisting newborn children of mothers with suspected or diagnosed coronavirus disease 2019 (COVID-19). The consensus was developed by five experts with an average of 20 years of experience in neonatal intensive care working at a reference university hospital in Brazil for the care of pregnant women and newborns with suspected or confirmed COVID-19. Despite the lack of scientific evidence regarding the potential for viral transmission to their fetus in pregnant mothers diagnosed with or suspected of COVID-19, it is important to elaborate the lines of care by specialists from hospitals caring for suspected and confirmed COVID-19 cases to guide multidisciplinary teams and families diagnosed with the disease or involved in the care of pregnant women and newborns in this context. Multidisciplinary teams must be attentive to the signs and symptoms of COVID-19 so that decision-making is oriented and assertive for the management of the mother and newborn in both the hospital setting and at hospital discharge. url: https://doi.org/10.6061/clinics/2020/e1932 doi: 10.6061/clinics/2020/e1932 id: cord-290428-zrlqzbss author: de Faria Coelho-Ravagnani, Christianne title: Dietary recommendations during the COVID-19 pandemic date: 2020-07-12 words: 6419.0 sentences: 348.0 pages: flesch: 45.0 cache: ./cache/cord-290428-zrlqzbss.txt txt: ./txt/cord-290428-zrlqzbss.txt summary: Since to date there is no vaccine or evidence-based treatment for COVID-19, the optimization of nutrient intake through well-balanced meals and the use of good hygiene practices in food selection, preparation, and conservation is probably the most effective approach for managing the continuous risk of viral infection. There is no evidence that COVID-19 is spread through eating or touching raw fruits or vegetables; Prior to consumption, fresh fruits and vegetables should be washed or scrubbed under cold, running, potable tap water; While there are no special precautions for storing food, handwashing after putting away purchased food and before preparing food is recommended; Hands should be washed before and after food containers are washed EUFIC (2020) 19 Appropriate intakes of copper, folate, iron, selenium, zinc, and vitamins A, B 6 , B 12 , C, and D play an important role in the immune system; In general, these nutrients should be obtained through foods Supplements can be used to add nutrients to the diet in individuals who have specific challenges in meeting dietary requirements abstract: Optimal nutrition can improve well-being and might mitigate the risk and morbidity associated with coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review summarizes nutritional guidelines to support dietary counseling provided by dietitians and health-related professionals. The majority of documents encouraged the consumption of fruits, vegetables, and whole grain foods. Thirty-one percent of the guidelines highlighted the importance of minerals and vitamins such as zinc and vitamins C, A, and D to maintain a well-functioning immune system. Dietary supplementation has not been linked to COVID-19 prevention. However, supplementation with vitamins C and D, as well as with zinc and selenium, was highlighted as potentially beneficial for individuals with, or at risk of, respiratory viral infections or for those in whom nutrient deficiency is detected. There was no convincing evidence that food or food packaging is associated with the transmission of COVID-19, but good hygiene practices for handling and preparing foods were recommended. No changes to breastfeeding recommendations have been made, even in women diagnosed with COVID-19. url: https://doi.org/10.1093/nutrit/nuaa067 doi: 10.1093/nutrit/nuaa067 id: cord-321770-g5xcfhnh author: de Farias, Emmerson Carlos Franco title: MULTISYSTEM INFLAMMATORY SYNDROME IN A CHILD ASSOCIATED WITH CORONAVIRUS DISEASE 19 IN THE BRAZILIAN AMAZON: FATAL OUTCOME IN AN INFANT date: 2020-08-26 words: 2337.0 sentences: 117.0 pages: flesch: 42.0 cache: ./cache/cord-321770-g5xcfhnh.txt txt: ./txt/cord-321770-g5xcfhnh.txt summary: CASE DESCRIPTION: A seven-month-old infant, with SARS-CoV-2 infection and a history of extreme preterm birth and very low weight at birth, with an initial course of mild respiratory symptoms and abrupt progression to vasoplegic shock, myocarditis and hyperinflammation syndrome, shown by high levels of troponin I, ferritin, CRP, D-dimer and hypoalbuminemia. The diagnosis of MIS-C should be considered among children and adolescents aged from zero to 19 years, with characteristics of typical or atypical Kawasaki disease or shock syndrome, according to the case definition proposed by the World Health Organization (WHO) 8 , described in Chart 1. In this study, we describe a case of MIS-C in an infant infected with SARS-CoV-2, after parental authorization, which had a fatal outcome despite the support received in pediatric intensive care. This case report emphasizes the fatal clinical course of an infant admitted with infection by SARS-CoV-2, associated with significant comorbidity, presenting with hyperinflammatory and multiple organ dysfunction syndromes. abstract: OBJECTIVE: Recently, there have been reports of children with severe inflammatory syndrome and multiorgan dysfunction associated with elevated inflammatory markers. These cases are reported as presenting the Multisystem Inflammatory Syndrome in Children (MIS-C) associated with COVID-19. In this study, we describe with parental permission a case of MIS-C in an infant with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. CASE DESCRIPTION: A seven-month-old infant, with SARS-CoV-2 infection and a history of extreme preterm birth and very low weight at birth, with an initial course of mild respiratory symptoms and abrupt progression to vasoplegic shock, myocarditis and hyperinflammation syndrome, shown by high levels of troponin I, ferritin, CRP, D-dimer and hypoalbuminemia. Despite the intensive care provided, the child developed multiple organ dysfunction and died. COMMENTS: Patients with a history of extreme prematurity may present with MIS-C in the presence of COVID-19 and are a group of special concern. url: https://www.ncbi.nlm.nih.gov/pubmed/32876282/ doi: 10.1590/1984-0462/2020/38/2020165 id: cord-283705-ia65pade author: de Gabory, Ludovic title: Le virus influenza, le SARS-CoV2 et les voies aériennes : mise au point pour l’Otorhinolaryngologiste date: 2020-06-05 words: 3386.0 sentences: 319.0 pages: flesch: 69.0 cache: ./cache/cord-283705-ia65pade.txt txt: ./txt/cord-283705-ia65pade.txt summary: L''objectif de cet article est de faire une mise au point sur les mécanismes de production et de pénétration des gouttelettes de sécrétions, émises lors de tous les phénomènes expiratoires, susceptibles de transporter ces virus et venir au contact de la muqueuse respiratoire. Si ces ARNs sont détectables autour des patients, sur les surfaces et dans l''air ambiant à des distances variables selon les études (de 0,5 m jusqu''au-delà de la chambre du patient) cela ne préjuge pas du caractère infectieux (viabilité) du virus et de la dose minimale infectieuse. L''objectif de cette mise au point était d''analyser les données objectives de contagiosité des patients lors du transport des virus par le produit des sécrétions et leur possibilité de pénétration dans les voies aériennes. En pratique le pourcentage de VI infectieux dans les gouttelettes produites lors de la toux ou de l''expiration variaient de 5 à 42 % pour des particules de 0,3 à 8 µm de diamètres lorsque les patients ont les signes cliniques depuis 2 jours [47, 49, 54, 55] . abstract: Résumé Le virus influenza et le SARS-CoV2 provoquent des infections respiratoires hautes banales et basses sévères (Virus influenza 290 000 à 650 000 décès/an). Ces virus entrent en contact avec les voies aériennes soit par projection directe, soit par inhalation secondaire de gouttelettes en suspension dans l’air, soit par manuportage. L’objectif de cet article est de faire une mise au point sur les mécanismes de production et de pénétration des gouttelettes de sécrétions, émises lors de tous les phénomènes expiratoires, susceptibles de transporter ces virus et venir au contact de la muqueuse respiratoire. Les gouttelettes > 5 µm suivent les lois de la balistique, celles < 5 µm suivent le mouvement Brownien et restent en suspension dans l’air. Les aérosols de gouttelettes sont hétérogènes que le sujet soit sain ou malade. En période infectieuse, les gouttelettes ne contiennent pas toutes de l’ARN viral. Si ces ARNs sont détectables autour des patients, sur les surfaces et dans l’air ambiant à des distances variables selon les études (de 0,5 m jusqu’au-delà de la chambre du patient) cela ne préjuge pas du caractère infectieux (viabilité) du virus et de la dose minimale infectieuse. Il y a un décalage entre la période de contagiosité et celle de la détection de l’ARN. Enfin, si des gouttelettes sont inhalées, elles devront suivre les lois de la dynamique des fluides (filtration) pour se déposer dans l’arbre respiratoire. Tout ceci explique pour partie la contagiosité et l’expression clinique de ces virus de la fente olfactive aux alvéoles pulmonaires. url: https://api.elsevier.com/content/article/pii/S1879726120301522 doi: 10.1016/j.aforl.2020.05.010 id: cord-315465-u3zq9k5j author: de Jesus, Myrela Conceição Santos title: Family COVID-19 cluster analysis of an infant without respiratory symptoms date: 2020-08-26 words: 1854.0 sentences: 107.0 pages: flesch: 55.0 cache: ./cache/cord-315465-u3zq9k5j.txt txt: ./txt/cord-315465-u3zq9k5j.txt summary: Here, we report the case of a child with COVID-19 who attended an outpatient clinic in Aracaju, Northeast-Brazil, with gastrointestinal symptoms and no respiratory problems and the subsequent screening of his close family members. A 45-year-old asymptomatic uncle, who was unable to maintain social isolation due to work commitments had a positive nasopharyngeal/oropharyngeal RT-PCR assay result on 15th May 2020, but his IgM and IgG tests performed on the same day yielded negative results. This is a case report comprising a child with a chief complaint of diarrhea and the clinical history of his six contact family members during the 20 days prior to the onset of his symptoms. We also describe the clinical findings, molecular and serological assay results of the family members with whom he had been in contact up to 20 days before symptom onset. abstract: Diagnosing cases of coronavirus disease (COVID-19) with only non-respiratory symptoms has been challenging. We reported the diagnosis of a child who tested positive for COVID-19 with abdominal pain/diarrhea and tracked his family cluster. One member of the family tested positive for COVID-19 on real-time reverse-transcription polymerase chain reaction assay and three other family members had anti-SARS-CoV-2 antibodies. url: https://www.ncbi.nlm.nih.gov/pubmed/32876320/ doi: 10.1590/0037-8682-0494-2020 id: cord-260729-b12v3c8c author: de Lang, Anna title: Functional Genomics Highlights Differential Induction of Antiviral Pathways in the Lungs of SARS-CoV–Infected Macaques date: 2007-08-10 words: 6800.0 sentences: 335.0 pages: flesch: 51.0 cache: ./cache/cord-260729-b12v3c8c.txt txt: ./txt/cord-260729-b12v3c8c.txt summary: As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. In order to elucidate early host responses during the acute phase of SARS-CoV infection, we infected cynomolgus macaques with SARS-CoV and used macaque-specific microarrays and real-time (RT)-PCR techniques to study host gene expression profiles. In this study, we simultaneously examined virus replication and host-response gene expression profiles in macaque lungs during the acute phase of SARS to gain more insight into the early events that take place after SARS-CoV infection. In order to visualize the host response in the lungs of SARS-CoV-infected macaques, IFN-b production and translocation of phosphorylated STAT1 was studied using immunohistochemistry. The expression of IFN-b, which strongly correlated to the amount of virus present, continued throughout day 4 and was confirmed using immunohistochemistry; IFN-b-positive cells could be detected in the lungs of the SARS-CoV-infected macaques. abstract: The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs of adolescent cynomolgus macaques (Macaca fascicularis) that show lung pathology similar to that observed in human adults with SARS. Analysis of gene signatures revealed induction of a strong innate immune response characterized by the stimulation of various cytokine and chemokine genes, including interleukin (IL)-6, IL-8, and IP-10, which corresponds to the host response seen in acute respiratory distress syndrome. As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells. Our studies emphasize that the induction of early IFN signaling may be critical to confer protection against SARS-CoV infection and highlight the strength of combining functional genomics with immunohistochemistry to further unravel the pathogenesis of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/17696609/ doi: 10.1371/journal.ppat.0030112 id: cord-274252-h4occy7h author: de Lima Menezes, Gabriela title: Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) date: 2020-07-13 words: 4147.0 sentences: 262.0 pages: flesch: 56.0 cache: ./cache/cord-274252-h4occy7h.txt txt: ./txt/cord-274252-h4occy7h.txt summary: After main pocket validation using two control drugs and the main conformations of nsp1, molecular docking based on virtual screening were performed to identify novel potential inhibitors from DrugBank database. Three of them was ranked as the best compounds among them and showed better energy score than control molecules that have in vitro activity against nsp1 from SARS-CoV-2. Due to lack of active site information a blind docking using two cyclophilin inhibitors described as potential CoV suppressors (Carbajo-Lozoya et al., 2014; Kamitani et al., 2009; Pfefferle et al., 2011) were performed by AutoDock Vina (Morris et al., 2009 ) with nsp1 conformations in order to define the best pocket for virtual screening. After that, based on AutoDock Vina energy scores, it was possible to identify the main residues/regions involved in the interactions and thus define the target pockets to be used in the virtual screening simulations with DrugBank database. abstract: Non-structural protein 1 (nsp1) is found in all Betacoronavirus genus, an important viral group that causes severe respiratory human diseases. This protein has significant role in pathogenesis and it is considered a probably major virulence factor. As it is absent in humans, it becomes an interesting target of study, especially when it comes to the rational search for drugs, since it increases the specificity of the target and reduces possible adverse effects that may be caused to the patient. Using approaches in silico we seek to study the behavior of nsp1 in solution to obtain its most stable conformation and find possible drugs with affinity to all of them. For this purpose, complete model of nsp1 of SARS-CoV-2 were predicted and its stability analyzed by molecular dynamics simulations in five different replicas. After main pocket validation using two control drugs and the main conformations of nsp1, molecular docking based on virtual screening were performed to identify novel potential inhibitors from DrugBank database. It has been found 16 molecules in common to all five nsp1 replica conformations. Three of them was ranked as the best compounds among them and showed better energy score than control molecules that have in vitro activity against nsp1 from SARS-CoV-2. The results pointed out here suggest new potential drugs for therapy to aid the rational drug search against COVID-19. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1792992 doi: 10.1080/07391102.2020.1792992 id: cord-307406-59yh48tt author: de Loyola, Mariana Braccialli title: Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19 date: 2020-08-26 words: 5739.0 sentences: 408.0 pages: flesch: 47.0 cache: ./cache/cord-307406-59yh48tt.txt txt: ./txt/cord-307406-59yh48tt.txt summary: 2, 3 A1AT is an inhibitor of SARS-CoV-2 infection and two of the most important proteases in the pathophysiology of Covid-19: the transmembrane serine protease 2 (TMPRSS2) and the disintegrin and metalloproteinase 17 (ADAM17), as was well as an inhibitor of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. [4] [5] [6] Moreover, recent data indicate that lower IL-6:A1AT levels are related to worse prognosis in This review addresses the interplay between A1AT, TMPRSS2, ADAM17, and inflammatory molecules during SARS-CoV-2 infection with the aim of identifying new avenues for effective treatments against Covid-19. In order to achieve a more comprehensive understanding of A1AT in Covid-19, is important to address the following concerns: The evidence presented in this review highlights the relevance of the A1AT as a host protective factor, which can inhibit the TMPRSS2-mediated SARS-CoV-2 infection, modulate the deleterious effect of ADAM17 activation and the activity of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. abstract: Understanding Covid‐19 pathophysiology is crucial for a better understanding of the disease and development of more effective treatments. Alpha‐1‐antitrypsin (A1AT) is a constitutive tissue protector with antiviral and anti‐inflammatory properties. A1AT inhibits SARS‐CoV‐2 infection and two of the most important proteases in the pathophysiology of Covid‐19: the transmembrane serine protease 2 (TMPRSS2) and the disintegrin and metalloproteinase 17 (ADAM17). It also inhibits the activity of inflammatory molecules, such as IL‐8, TNF‐α, and neutrophil elastase (NE). TMPRSS2 is essential for SARS‐CoV‐2‐S protein priming and viral infection. ADAM17 mediates ACE2, IL‐6R, and TNF‐α shedding. ACE2 is the SARS‐CoV‐2 entry receptor and a key component for the balance of the renin‐angiotensin system, inflammation, vascular permeability, and pulmonary homeostasis. In addition, clinical findings indicate that A1AT levels might be important in defining Covid‐19 outcomes, potentially partially explaining associations with air pollution and with diabetes. In this review, we focused on the interplay between A1AT with TMPRSS2, ADAM17 and immune molecules, and the role of A1AT in the pathophysiology of Covid‐19, opening new avenues for investigating effective treatments. url: https://doi.org/10.1002/rmv.2157 doi: 10.1002/rmv.2157 id: cord-353217-gmc3qrci author: de Miranda Santos, Isabel Kinney Ferreira title: Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus date: 2020-08-04 words: 551.0 sentences: 34.0 pages: flesch: 36.0 cache: ./cache/cord-353217-gmc3qrci.txt txt: ./txt/cord-353217-gmc3qrci.txt summary: Recent large observational studies indicate that hydroxychloroquine (HY) does not affect outcomes of patients hospitalized with COVID-19 (1, 2) and may even be harmful (3) . In view of this situation and of the importance of correct interpretation of antibody profiles for planning preventive measures for COVID-19, we would like to bring the attention of readers to studies that raise concerns about the possible impact of HY upon antibody responses to SARS-CoV-2. To the best of our knowledge, there are no new facts in the scientific and medical literature that indicate that the same mechanism could not operate in HY-treated patients suffering from COVID-19 and negatively impact their SARS-CoV-2-specific antibody responses. As more needs to be learned about the role of antibodies in recovery from and protection against infection with SARS-CoV-2, the impact of HY and other treatment regimens on antibody responses requires systematic evaluation. abstract: nan url: https://doi.org/10.3389/fimmu.2020.01739 doi: 10.3389/fimmu.2020.01739 id: cord-346248-6wkyar57 author: de Moura, Diogo Turiani Hourneaux title: Diagnostic Characteristics of Serological-Based COVID-19 Testing: A Systematic Review and Meta-Analysis date: 2020-08-06 words: 3892.0 sentences: 214.0 pages: flesch: 42.0 cache: ./cache/cord-346248-6wkyar57.txt txt: ./txt/cord-346248-6wkyar57.txt summary: The aim of this study was to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based COVID-19 testing. This meta-analysis demonstrates suboptimal sensitivity and specificity of serologic-based diagnostic testing for SARS-CoV-2 and suggests that antibody testing alone, in its current form, is unlikely to be an adequate solution to the difficulties posed by COVID-19 and in guiding future policy decisions regarding social distancing and reopening of the economy worldwide. While this test is still the most effective method to date for the diagnosis of active COVID-19, serologic-based antibody testing to assist with known exposure to SARS-CoV-2 remains pivotal to accurately assessing the burden of disease. Therefore, we aim to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based testing (IgG and IgM) for COVID-19. abstract: Serologic testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) promises to assist in assessing exposure to and confirming the diagnosis of coronavirus disease 2019 (COVID-19), and to provide a roadmap for reopening countries worldwide. Considering this, a proper understanding of serologic-based diagnostic testing characteristics is critical. The aim of this study was to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based COVID-19 testing. Electronic searches were performed using Medline (PubMed), EMBASE, and Cochrane Library. Full-text observational studies that reported IgG or IgM diagnostic yield and used nucleic acid amplification tests (NAATs) of respiratory tract specimens, as a the reference standard in English language were included. A bivariate model was used to compute pooled sensitivity, specificity, positive/negative likelihood ratio (LR), diagnostic odds ratio (OR), and summary receiver operating characteristic curve (SROC) with corresponding 95% confidence intervals (CIs). Five studies (n=1,166 individual tests) met inclusion criteria. The pooled sensitivity, specificity, and diagnostic accuracy for IgG was 81% [(95% CI, 61-92);I(2)=95.28], 97% [(95% CI, 78-100);I(2)=97.80], and 93% (95% CI, 91-95), respectively. The sensitivity, specificity, and accuracy for IgM antibodies was 80% [(95% CI, 57-92);I(2)=94.63], 96% [(95% CI, 81-99);I(2)=92.96] and 95% (95% CI, 92-96). This meta-analysis demonstrates suboptimal sensitivity and specificity of serologic-based diagnostic testing for SARS-CoV-2 and suggests that antibody testing alone, in its current form, is unlikely to be an adequate solution to the difficulties posed by COVID-19 and in guiding future policy decisions regarding social distancing and reopening of the economy worldwide. url: https://www.ncbi.nlm.nih.gov/pubmed/32785570/ doi: 10.6061/clinics/2020/e2212 id: cord-306308-zjq6cscm author: de Moura, Ronald Rodrigues title: Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date: 2020-08-05 words: 2514.0 sentences: 175.0 pages: flesch: 54.0 cache: ./cache/cord-306308-zjq6cscm.txt txt: ./txt/cord-306308-zjq6cscm.txt summary: Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. abstract: AIMS: Brazil is nowadays one of the epicentres of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and new therapies are needed to face it. In the context of specific immune response against the virus, a correlation between Major Histocompatibility Complex Class I (MHC-I) and the severity of the disease in patients with COVID-19 has been suggested. Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. RESULTS: We identified 24 immunogenic epitopes in the SARS-CoV-2 protein S that could interact with 17 different MHC-I alleles (namely, HLA-A*01:01; HLA-A*02:01; HLA-A*11:01; HLA-A*24:02; HLA-A*68:01; HLA-A*23:01; HLA-A*26:01; HLA-A*30:02; HLA-A*31:01; HLA-B*07:02; HLA-B*51:01; HLA-B*35:01; HLA-B*44:02; HLA-B*35:03; HLA-C*05:01; HLA-C*07:01 and HLA-C*15:02) in the Brazilian population. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. url: https://doi.org/10.1136/jclinpath-2020-206946 doi: 10.1136/jclinpath-2020-206946 id: cord-323440-u3iz79kk author: de Niet, Annikki title: The role of children in the transmission of mild SARS‐CoV‐2 infection date: 2020-05-04 words: 506.0 sentences: 36.0 pages: flesch: 54.0 cache: ./cache/cord-323440-u3iz79kk.txt txt: ./txt/cord-323440-u3iz79kk.txt summary: We thank Dr Ludvigsson 1 on his effort to improve knowledge on SARS-CoV-2 infection in children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. 4 Furthermore, SARS-CoV-2 infection in children differs from adults in that they have a lower prevalence of increased C-reactive protein, signifying a milder immunological response and less immune damage. 1 The viral load in patients with mild disease showed to be lower compared with those having severe SARS-CoV-2 infection. 2 Reports from severe disease in infected healthcare workers further hint towards an association between higher viral load in critically ill patients and transmission of more severe SARS-CoV-2 infection. abstract: We thank dr. Ludvigsson (1) on his effort to improve knowledge on SARS-CoV-2 infection in children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. The huge age disparity in disease severity might be one of the most stringent fundamental knowledge gaps. url: https://www.ncbi.nlm.nih.gov/pubmed/32298494/ doi: 10.1111/apa.15310 id: cord-323824-74xvvwrw author: de Oliveira, Osmair Vital title: Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening date: 2020-06-02 words: 5373.0 sentences: 295.0 pages: flesch: 57.0 cache: ./cache/cord-323824-74xvvwrw.txt txt: ./txt/cord-323824-74xvvwrw.txt summary: Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below –8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. Our approach adopted here differs from those studies in the following way: the isolated S-protein receptor for docking calculations will be obtained from molecular dynamics (MD) simulation, and not directly from crystal structure or S-protein@ACE2 complex. (Muralidharan et al., 2020) obtained from docking calculations a binding energy of -4.1 kcal/mol using the SARS-CoV-2 protease and lopinavir drug, respectively, as receptor and ligand. In this way, our calculations indicate that the ivermectin drug may bind in the RBD region, inhibiting the coupling of the SARS-CoV-2 S-protein with the human ACE2 receptor. Therefore, herein we used molecular dynamics (MD) simulation and docking calculations to study the SARS-CoV-2 S-protein with the main goal to obtain possible drugs candidates for repurposing them against to COVID-19. abstract: Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from “up” to “down” conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below –8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak. url: https://doi.org/10.1080/07391102.2020.1772885 doi: 10.1080/07391102.2020.1772885 id: cord-103945-q3ry13vp author: de Oliveira, P. M. title: Evolution of spray and aerosol from respiratory releases: theoretical estimates for insight on viral transmission date: 2020-07-24 words: 9274.0 sentences: 485.0 pages: flesch: 59.0 cache: ./cache/cord-103945-q3ry13vp.txt txt: ./txt/cord-103945-q3ry13vp.txt summary: By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. The Lagrangian framework, given in Sec. 2(a), is considered in one (vertical) dimension and droplet clouds for two exhalation modes, speaking and coughing, are released at the height of the emitter''s mouth (1.5 m) and then let settle by gravity while evaporating in ambient air. abstract: By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. The settling times of a droplet cloud and its suspended viral dose are significantly affected by the droplet composition. The aerosol (defined as droplets smaller than 5 m resulting from 30 seconds of continued speech has o(1h) settling time and a viable viral dose an order-of-magnitude higher than in a short cough. The time-of-flight to reach 2m is only a few seconds resulting in a viral dose above the minimum required for infection, implying that physical distancing in the absence of ventilation is not sufficient to provide safety for long exposure times. The suspended aerosol emitted by continuous speaking for 1 hour in a poorly ventilated room gives 0.1-11% infection risk for initial viral loads of 10^8-10^10 copies/ml, respectively, decreasing to 0.03-3% for 10 air changes per hour by ventilation. The present results provide quantitative estimates useful for the development of physical-distancing and ventilation controls. url: http://medrxiv.org/cgi/content/short/2020.07.23.20160648v1?rss=1 doi: 10.1101/2020.07.23.20160648 id: cord-352911-9wbq9qo2 author: de Oliveira, Pedro Gonçalves title: Diacerein: a potential multi-target therapeutic drug for COVID-19 date: 2020-06-01 words: 2539.0 sentences: 135.0 pages: flesch: 45.0 cache: ./cache/cord-352911-9wbq9qo2.txt txt: ./txt/cord-352911-9wbq9qo2.txt summary: The mortality related to severe acute respiratory distress syndrome (ARDS) and multi-organ failure in COVID-19 patients has been suggested to be connected with cytokine storm syndrome (CSS), an excessive immune response that severely damages healthy lung tissue. Total extracts from monolayer cell cultures infected with SARS-CoV-2 and treated with rhein under the conditions described above will be analysed using commercially available protein arrays to determine the levels and activation state of proteins involved in the TLR-, Akt-, MAPK-, and NF-B-regulated signalling pathways. The mechanisms of action involved include the control of hyperinflammatory conditions by multi-faceted cytokine inhibition of IL-1, IL-2, IL-6, IL-8, IL-12, IL-18 and TNF-α; anti-platelet aggregation activity; and potential effects on viral infection and replication. Rhein suppresses lung inflammatory injury induced by human respiratory syncytial virus through inhibiting NLRP3 inflammasome activation via NF-κB pathway in mice abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 19 (COVID-19), was declared pandemic by the World Health Organization in March 2020. SARS-CoV-2 binds its host cell receptor, angiotensin-converting enzyme 2 (ACE2), through the viral spike (S) protein. The mortality related to severe acute respiratory distress syndrome (ARDS) and multi-organ failure in COVID-19 patients has been suggested to be connected with cytokine storm syndrome (CSS), an excessive immune response that severely damages healthy lung tissue. In addition, cardiac symptoms, including fulminant myocarditis, are frequent in patients in a severe state of illness. Diacerein (DAR) is an anthraquinone derivative drug whose active metabolite is rhein. Different studies have shown that this compound inhibits the IL-1, IL-2, IL-6, IL-8, IL-12, IL-18, TNF-α, NF-κB and NALP3 inflammasome pathways. The antiviral activity of rhein has also been documented. This metabolite prevents hepatitis B virus (HBV) replication and influenza A virus (IAV) adsorption and replication through mechanisms involving regulation of oxidative stress and alterations of the TLR4, Akt, MAPK, and NF-κB signalling pathways. Importantly, rhein inhibits the interaction between the SARS-CoV S protein and ACE2 in a dose-dependent manner, suggesting rhein as a potential therapeutic agent for the treatment of SARS-CoV infection. Based on these findings, we hypothesize that DAR is a multi-target drug useful for COVID-19 treatment. This anthraquinone may control hyperinflammatory conditions by multi-faceted cytokine inhibition and by reducing viral infection. url: https://www.sciencedirect.com/science/article/pii/S0306987720311828?v=s5 doi: 10.1016/j.mehy.2020.109920 id: cord-344829-adlp2rjy author: de Rivero Vaccari, Juan Carlos title: The Inflammasome in Times of COVID-19 date: 2020-10-08 words: 8722.0 sentences: 423.0 pages: flesch: 37.0 cache: ./cache/cord-344829-adlp2rjy.txt txt: ./txt/cord-344829-adlp2rjy.txt summary: Here we review the literature regarding the mechanism of inflammasome activation by CoV infection, the role of the inflammasome in ARDS, ventilator-induced lung injury (VILI), and Disseminated Intravascular Coagulation (DIC) as well as the potential mechanism by which the inflammasome may contribute to the damaging effects of inflammation in the cardiac, renal, digestive, and nervous systems in COVID-19 patients. Here we review the literature on the role of the inflammasome in CoV infections, which includes how CoVs activate inflammasomes upon infection, the role of the inflammasome in acute respiratory distress syndrome (ARDS), how ventilator-induced lung injury (VILI) activates the inflammasome, how the inflammasome plays a role in the systemic complications associated with COVID-19, and how the inflammasome is involved in the process of Disseminated Intravascular Coagulation (DIC). abstract: Coronaviruses (CoVs) are members of the genus Betacoronavirus and the Coronaviridiae family responsible for infections such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and more recently, coronavirus disease-2019 (COVID-19). CoV infections present mainly as respiratory infections that lead to acute respiratory distress syndrome (ARDS). However, CoVs, such as COVID-19, also present as a hyperactivation of the inflammatory response that results in increased production of inflammatory cytokines such as interleukin (IL)-1β and its downstream molecule IL-6. The inflammasome is a multiprotein complex involved in the activation of caspase-1 that leads to the activation of IL-1β in a variety of diseases and infections such as CoV infection and in different tissues such as lungs, brain, intestines and kidneys, all of which have been shown to be affected in COVID-19 patients. Here we review the literature regarding the mechanism of inflammasome activation by CoV infection, the role of the inflammasome in ARDS, ventilator-induced lung injury (VILI), and Disseminated Intravascular Coagulation (DIC) as well as the potential mechanism by which the inflammasome may contribute to the damaging effects of inflammation in the cardiac, renal, digestive, and nervous systems in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33149733/ doi: 10.3389/fimmu.2020.583373 id: cord-291729-4l4v9jxd author: de Salazar, Adolfo title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 words: 2641.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-291729-4l4v9jxd.txt txt: ./txt/cord-291729-4l4v9jxd.txt summary: CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. Our objective in this study has been to evaluate the efficacy of sample pooling in a multicentre way compared to the individual analysis for the detection of COVID-19 by using different commercial platforms available for genomic extraction and amplification by RT -PCR in real time. Here we report on the high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. In summary, we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. abstract: OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of COVID-19, by using different commercial platforms for nucleic acid extraction and amplification. METHODS: 3519 nasopharyngeal samples received at 9 Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of 10 samples and 11 pools of 9 samples) according to the existing methodology in each of the centres. RESULTS: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 22/29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.10% (CI95%; 94.11-98.82), 100%, 100% and 99.79% (CI95%; 99.56-99.90) respectively; accuracy was 99.80% (CI95%; 99.59-99.92) and kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted into a median loss of 2.87 (CI95%; 2.46-3.28) CTs for E gene, 3.36 (CI95%; 2.89-3.85) CTs for RdRP gene and 2.99 (CI95%; 2.56-3.43) CTs for N gene. CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. url: https://api.elsevier.com/content/article/pii/S1198743X20305371 doi: 10.1016/j.cmi.2020.09.008 id: cord-322087-gj5mfzxz author: de Sanctis, Vincenzo title: Coronavirus Disease 2019 (COVID-19) in adolescents: An update on current clinical and diagnostic characteristics date: 2020-05-11 words: 4581.0 sentences: 244.0 pages: flesch: 48.0 cache: ./cache/cord-322087-gj5mfzxz.txt txt: ./txt/cord-322087-gj5mfzxz.txt summary: This paper summarises the current findings (April 3,2020) from a systematic literature review on the current knowledge of COVID-19 in adolescents (10-19 years according to the WHO definition) and reports the preliminary epidemiological data stated by the Italian National Institute of Health. SARS-CoV-2 RNA was also detected in stool specimens but according to WHO-China report, fecal-oral transmission did not appear to be a significant factor in the spread of infection (Report of the WHO-China Joint Mission on Coronavirus Disease 2019,COVID-2019. Detailed epidemiological information based on a larger sample of COVID-19 patients is needed to determine the infectious period of SARS-CoV-2, as well as whether transmission can occur from asymptomatic individuals during the incubation period ("pre-symptomatic" period). In a small number of case reports and studies, a familial cluster of infection associated with SARS-CoV-2 has been reported, indicating possible personto-person transmission during the incubation period (18, 19) . abstract: The current outbreak of infections with SARS-CoV-2 is defined as Coronavirus Disease 2019 (COVID-19). The clinical symptoms of COVID-19 include fever, fatigue, cough, breathing difficulty that may lead to respiratory distress; a small population of patients may have diarrhea, nausea or vomiting. The highest infection rate occurs in adults; however, neonates, children, and adolescents can also be infected. As the outbreak continues to spread worldwide, attention has switched toward determinants of clinical manifestations and disease severity. The situation surrounding the outbreak is rapidly evolving and the information and recommendations are changing as new information becomes available. This paper summarises the current findings (April 3,2020) from a systematic literature review on the current knowledge of COVID-19 in adolescents (10-19 years according to the WHO definition) and reports the preliminary epidemiological data stated by the Italian National Institute of Health. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420943/ doi: 10.23750/abm.v91i2.9543 id: cord-349124-nhnl7zgi author: de Sandes‐Freitas, Tainá Veras title: Lessons from SARS‐CoV‐2 screening in a Brazilian organ transplant unit date: 2020-07-13 words: 1193.0 sentences: 85.0 pages: flesch: 47.0 cache: ./cache/cord-349124-nhnl7zgi.txt txt: ./txt/cord-349124-nhnl7zgi.txt summary: Evidence suggests that asymptomatic carriers might transmit the SARS‐CoV‐2, challenging the implementation of transmission preventive strategies. We report a single‐center experience using universal SARS‐CoV‐2 screening for all inpatients and newly admitted patients to an Organ Transplant Unit located in a region with significantly high community‐based transmission. We will describe the experience of a single center of screening all inpatients and newly admitted patients to the Organ Transplant Unit. On March 31, 2020, a 43-year-old man with alcoholic liver cirrhosis, hospitalized since March 23rd presented acute dyspnea and fever and was tested positive for SARS-CoV-2 (patient 1). We reported the COVID-19 screening strategy adopted by our center in a attempt to prevent nosocomial transmission and keep "clean" the Transplant Unit. Alert for non-respiratory symptoms of coronavirus disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Lessons from SARS-CoV-2 screening in a Brazilian organ transplant unit abstract: Protecting immunosuppressed patients during infectious disease outbreaks is crucial. During this novel coronavirus disease 2019 pandemic, preserving “clean areas” in hospitals assisting organ transplant recipients is key to protect them and to preserve transplantation activity. Evidence suggests that asymptomatic carriers might transmit the SARS‐CoV‐2, challenging the implementation of transmission preventive strategies. We report a single‐center experience using universal SARS‐CoV‐2 screening for all inpatients and newly admitted patients to an Organ Transplant Unit located in a region with significantly high community‐based transmission. url: https://doi.org/10.1111/tid.13376 doi: 10.1111/tid.13376 id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 words: 1791.0 sentences: 101.0 pages: flesch: 41.0 cache: ./cache/cord-334603-yt2pmxi3.txt txt: ./txt/cord-334603-yt2pmxi3.txt summary: title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. abstract: Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. Ethnicity has been the focus of attention after data from the United Kingdom showed a disproportionate number of deaths among healthcare workers from black, Asian and other ethnic minority backgrounds (1). In addition to ethnicity, socio-economic factors, prior vaccinations and exposure to other coronaviruses, other factors need to be considered to explain geographical and regional variations in susceptibility, severity of clinical expression of COVID-19 disease and outcomes. In the United States there have been disproportionate COVID-19 death rates among African Americans at around 2.6 times higher than that of other groups. Although these data could be due to multiple cultural and socioeconomic factors an underlying genetic susceptibility to SARS-CoV-2 infection may be a factor. url: https://doi.org/10.1016/j.ijid.2020.07.016 doi: 10.1016/j.ijid.2020.07.016 id: cord-299544-r3cqvf0c author: de Souza, T. H. title: Clinical Manifestations of Children with COVID-19: a Systematic Review date: 2020-04-03 words: 2582.0 sentences: 216.0 pages: flesch: 56.0 cache: ./cache/cord-299544-r3cqvf0c.txt txt: ./txt/cord-299544-r3cqvf0c.txt summary: Study Selection: Inclusion criteria were: (1) studied patients younger than 18 years old; (2) presented original data from cases of COVID-19 confirmed by reverse-transcription polymerase chain reaction; and (3) contained descriptions of clinical manifestations, laboratory tests or radiological examinations. https://doi.org/10.1101/2020.04.01.20049833 doi: medRxiv preprint children infected with SARS-CoV-2 may not meet all the criteria required in the suspected case definition. The following data were extracted, when available, from each elected article: first author, publication year, study design, number of cases, gender, age, clinical manifestations, laboratory tests, radiological examinations and outcomes (discharged, still hospitalized or death). In our study, we described the main clinical, laboratorial and radiological characteristics of children infected with SARS-CoV-2 reported in the literature. A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study abstract: Context: The coronavirus disease 2019 (COVID-19) outbreak is an unprecedented global public health challenge, leading to thousands of deaths every day worldwide. Despite the epidemiological importance, clinical patterns of children with COVID-19 remain unclear. Objective: To describe the clinical, laboratorial and radiological characteristics of children with COVID-19. Data Sources: The Medline database was searched between December 1st 2019 and March 30th 2020. Study Selection: Inclusion criteria were: (1) studied patients younger than 18 years old; (2) presented original data from cases of COVID-19 confirmed by reverse-transcription polymerase chain reaction; and (3) contained descriptions of clinical manifestations, laboratory tests or radiological examinations. Data Extraction: Number of cases, gender, age, clinical manifestations, laboratory tests, radiological examinations and outcomes. Results: A total of 34 studies (1,118 cases) were included. From all the cases, 1,111 had their severity classified: 14.3% were asymptomatic, 36.4% were mild, 46.0% were moderate, 2.2% were severe and 1.2% were critical. The most prevalent symptom was fever (16.3%), followed by cough (14.4%), nasal symptoms (3.6%), diarrhea (2.7%) and nausea/vomiting (2.5%). One hundred forty-five (12.9%) children were diagnosed with pneumonia and 43 (3.8%) upper airway infections were reported. Reduced lymphocyte count were reported in 13.1% of cases. Abnormalities on computed tomography was reported in 62.7% of cases. The most prevalent abnormalities reported were ground glass opacities, patchy shadows and consolidations. Only one death was reported. Conclusions: Clinical manifestations of children with COVID-19 differ widely from adults cases. Fever and respiratory symptoms should not be considered a hallmark of COVID-19 in children. url: http://medrxiv.org/cgi/content/short/2020.04.01.20049833v1?rss=1 doi: 10.1101/2020.04.01.20049833 id: cord-310333-70ldbw3r author: de Souza, Wanderley title: COVID-19 and parasitology date: 2020-05-30 words: 842.0 sentences: 43.0 pages: flesch: 52.0 cache: ./cache/cord-310333-70ldbw3r.txt txt: ./txt/cord-310333-70ldbw3r.txt summary: Emerging and reemerging diseases are a challenge for public health worldwide and particularly for Brazil, where the existence of the Amazon region provides a constant source of new pathogens that are transmitted from wild animals to man. Infectious diseases, such as severe acute respiratory syndrome (SARS), represent a major threat to public health. At present, the available data indicate the presence of 2.6 million infected people and 178 thousand dead (April 22), demonstrating the severity of COVID-19 due to the rapid spread of the virus and its high pathogenicity, which mainly, but not exclusively, affects the pulmonary system. Therefore, members of the parasitology community, especially those working with parasite-host cell interaction processes, can and shall contribute at this time. Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease Epidemiology and cause of severe acute respiratory syndrome (SARS) in 304 Guangdong, People''s Republic of China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32472383/ doi: 10.1007/s00436-020-06719-y id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 words: 9182.0 sentences: 433.0 pages: flesch: 39.0 cache: ./cache/cord-332992-8rmqg4rf.txt txt: ./txt/cord-332992-8rmqg4rf.txt summary: Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . abstract: In the late autumn of 2019, a new potentially lethal human coronavirus designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. The pandemic spread of this zoonotic virus has created a global health emergency and an unprecedented socioeconomic crisis. The severity of coronavirus disease 2019 (COVID-19), the illness caused by SARS-CoV‑2, is highly variable. Most patients (~85%) develop no or mild symptoms, while others become seriously ill, some succumbing to disease-related complications. In this review, the SARS-CoV‑2 life cycle, its transmission and the clinical and immunological features of COVID-19 are described. In addition, an overview is presented of the virological assays for detecting ongoing SARS-CoV‑2 infections and the serological tests for SARS-CoV-2-specific antibody detection. Also discussed are the different approaches to developing a COVID-19 vaccine and the perspectives of treating COVID-19 with antiviral drugs, immunomodulatory agents and anticoagulants/antithrombotics. Finally, the cardiovascular manifestations of COVID-19 are briefly touched upon. While there is still much to learn about SARS-CoV‑2, the tremendous recent advances in biomedical technology and knowledge and the huge amount of research into COVID-19 raise the hope that a remedy for this disease will soon be found. COVID-19 will nonetheless have a lasting impact on human society. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12471-020-01475-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12471-020-01475-1 doi: 10.1007/s12471-020-01475-1 id: cord-321598-ae241pmd author: de Vries, A.P.J. title: Immediate impact of COVID-19 on transplant activity in the Netherlands date: 2020-05-01 words: 2280.0 sentences: 132.0 pages: flesch: 49.0 cache: ./cache/cord-321598-ae241pmd.txt txt: ./txt/cord-321598-ae241pmd.txt summary: Worldwide, the delivery of transplant care is severely challenged by matters concerning but not limited to organ procurement, risk of SARS-CoV-2 transmission, screening strategies of donors and recipients, decisions to postpone or proceed with transplantation, the attributable risk of immunosuppression for COVID-19 and entrenched health care resources and capacity. In less than 60 days, despite increasingly stringent measures of the Dutch government to halt the spread of the infection, 28, 153 individuals have tested positive for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), 9,127 patients have been admitted to hospitals across the country (of which 2,508 in the Intensive Care Units (ICU) [4] ) and 3,134 have died, according to RIVM (National Institute for Public health and the Environment, April 15, 2020). To facilitate extra time needed for recipient test results to become available, allocation for liver, heart and lung transplantation is initiated before donor SARS-CoV-2 screening is known (Table 1A) . abstract: The rapid emergence of the COVID-19 pandemic is unprecedented and poses an unparalleled obstacle in the sixty-five year history of organ transplantation. Worldwide, the delivery of transplant care is severely challenged by matters concerning - but not limited to - organ procurement, risk of SARS-CoV-2 transmission, screening strategies of donors and recipients, decisions to postpone or proceed with transplantation, the attributable risk of immunosuppression for COVID-19 and entrenched health care resources and capacity. The transplant community is faced with choosing a lesser of two evils: initiating immunosuppression and potentially accepting detrimental outcome when transplant recipients develop COVID-19 versus postponing transplantation and accepting associated waitlist mortality. Notably, prioritization of health care services for COVID-19 care raises concerns about allocation of resources to deliver care for transplant patients who might otherwise have excellent 1-year and 10-year survival rates. Children and young adults with end-stage organ disease in particular seem more disadvantaged by withholding transplantation because of capacity issues than from medical consequences of SARS-CoV-2. This report details the nationwide response of the Dutch transplant community to these issues and the immediate consequences for transplant activity. Worrisome, there was a significant decrease in organ donation numbers affecting all organ transplant services. In addition, there was a detrimental effect on transplantation numbers in children with end-organ failure. Ongoing efforts focus on mitigation of not only primary but also secondary harm of the pandemic and to find right definitions and momentum to restore the transplant programs. url: https://doi.org/10.1016/j.trim.2020.101304 doi: 10.1016/j.trim.2020.101304 id: cord-286703-ipoj13va author: de Wilde, Adriaan H. title: Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date: 2017-01-15 words: 3343.0 sentences: 165.0 pages: flesch: 48.0 cache: ./cache/cord-286703-ipoj13va.txt txt: ./txt/cord-286703-ipoj13va.txt summary: Data from cell culture infection models (Chan et al., 2013a (Chan et al., , 2013b de Wilde et al., 2013b; Falzarano et al., 2013a; Kindler et al., 2013; Zielecki et al., 2013) and experiments in rhesus macaques (Falzarano et al., 2013b) and marmosets (Chan et al., 2015) suggested that interferons (IFNs) are potent inhibitors of MERS-CoV replication. As ribavirin has previously been reported to inhibit MERS-CoV replication (Falzarano et al., 2013a) and ALV and ribavirin have been used together during clinical trials for hepatitis C treatment (Pawlotsky et al., 2015) , this combination was tested in LLC-MK2 cells. (e, f) SARS-CoV-infected (e) Vero or (f) VeroE6 cells (MOI 0.01) were treated with various concentrations of ALV from 1 h p.i. onwards, and virus titers in the culture medium at 32 h p.i. were determined by plaque assay. abstract: Currently, there is no registered treatment for infections with emerging zoonotic coronaviruses like SARS- and MERS-coronavirus. We here report that in cultured cells low-micromolar concentrations of alisporivir, a non-immunosuppressive cyclosporin A-analog, inhibit the replication of four different coronaviruses, including MERS- and SARS-coronavirus. Ribavirin was found to further potentiate the antiviral effect of alisporivir in these cell culture-based infection models, but this combination treatment was unable to improve the outcome of SARS-CoV infection in a mouse model. Nevertheless, our data provide a basis to further explore the potential of Cyp inhibitors as host-directed, broad-spectrum inhibitors of coronavirus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/27840112/ doi: 10.1016/j.virusres.2016.11.011 id: cord-319877-izn315hb author: de Wit, Emmie title: SARS and MERS: recent insights into emerging coronaviruses date: 2016-06-27 words: 9387.0 sentences: 424.0 pages: flesch: 43.0 cache: ./cache/cord-319877-izn315hb.txt txt: ./txt/cord-319877-izn315hb.txt summary: Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters). abstract: The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 marked the second introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The continuing introductions of MERS-CoV from dromedary camels, the subsequent travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates highlight the need for prophylactic and therapeutic measures. Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. In this Review, we detail our present understanding of the transmission and pathogenesis of SARS-CoV and MERS-CoV, and discuss the current state of development of measures to combat emerging coronaviruses. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.81) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.81 doi: 10.1038/nrmicro.2016.81 id: cord-350104-b99y6n43 author: de Zwart, Onno title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey date: 2009-01-06 words: 5379.0 sentences: 255.0 pages: flesch: 52.0 cache: ./cache/cord-350104-b99y6n43.txt txt: ./txt/cord-350104-b99y6n43.txt summary: title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey PURPOSE: To study the levels of perceived threat, perceived severity, perceived vulnerability, response efficacy, and self-efficacy for severe acute respiratory syndrome (SARS) and eight other diseases in five European and three Asian countries. To explore if country differences were specific for SARS, perceived threat, risk perception, and efficacy beliefs related to avian influenza and other (infectious) diseases were also investigated. -To study levels of perceived threat, vulnerability (or risk perception), severity and comparative vulnerability for SARS in Denmark, The Netherlands, Poland, Spain, the UK, China, Hong Kong, and Singapore; -To compare perceived severity, vulnerability, and threat of SARS with other diseases and conditions, i.e., avian influenza, common cold, diabetes, HIV, high blood pressure, tuberculosis, food poisoning, and a heart attack; -To study differences and associations between these factors across the eight countries and between Europe and Asia. abstract: PURPOSE: To study the levels of perceived threat, perceived severity, perceived vulnerability, response efficacy, and self-efficacy for severe acute respiratory syndrome (SARS) and eight other diseases in five European and three Asian countries. METHOD: A computer-assisted phone survey was conducted among 3,436 respondents. The questionnaire focused on perceived threat, vulnerability, severity, response efficacy, and self-efficacy related to SARS and eight other diseases. RESULTS: Perceived threat of SARS in case of an outbreak in the country was higher than that of other diseases. Perceived vulnerability of SARS was at an intermediate level and perceived severity was high compared to other diseases. Perceived threat for SARS varied between countries in Europe and Asia with a higher perceived severity of SARS in Europe and a higher perceived vulnerability in Asia. Response efficacy and self-efficacy for SARS were higher in Asia compared to Europe. In multiple linear regression analyses, country was strongly associated with perceived threat. CONCLUSIONS: The relatively high perceived threat for SARS indicates that it is seen as a public health risk and offers a basis for communication in case of an outbreak. The strong association between perceived threat and country and different regional patterns require further research. url: https://www.ncbi.nlm.nih.gov/pubmed/19125335/ doi: 10.1007/s12529-008-9008-2 id: cord-332457-gan10za0 author: de Ángel Solá, David E. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 words: 2867.0 sentences: 168.0 pages: flesch: 39.0 cache: ./cache/cord-332457-gan10za0.txt txt: ./txt/cord-332457-gan10za0.txt summary: On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . abstract: The 2020 coronavirus pandemic is developing at different paces throughout the world. Some areas, like the Caribbean Basin, have yet to see the virus strike at full force. When it does, there is reasonable evidence to suggest the consequent COVID‐19 outbreaks will overwhelm healthcare systems and economies. This is particularly concerning in the Caribbean as pandemics can have disproportionately higher mortality impacts on lower and middle income countries. Preliminary observations from our team and others suggest that temperature and climatological factors could influence the spread of this novel coronavirus, making spatiotemporal predictions of its infectiousness possible. This review studies geographic and time‐based distribution of known respiratory viruses in the Caribbean Basin in an attempt to foresee how the pandemic will develop in this region. This review is meant to aid in planning short‐ and long‐term interventions to manage outbreaks at the international, national and sub‐national levels in the region. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25864 doi: 10.1002/jmv.25864 id: cord-321380-e5zq15hz author: del Campo, P. Lázaro title: No transmission of SARS-CoV-2 in a patient undergoing allogeneic Hematopoietic Cell Transplantation from a matched-related donor with unknown COVID-19 date: 2020-08-24 words: 1883.0 sentences: 122.0 pages: flesch: 53.0 cache: ./cache/cord-321380-e5zq15hz.txt txt: ./txt/cord-321380-e5zq15hz.txt summary: In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. Lastly, applied to our case, the low concentration of viral RNA in plasma of asymptomatic patients with COVID-19 [5] , and a theoretical inefficacy of SARS-CoV-2 J o u r n a l P r e -p r o o f to replicate inside lymphocytes could support the safety of blood products, including peripheral blood hematopoietic cells. abstract: The Hematology Department and its Hematopoietic Cell Transplantation (HCT) program implemented several measures during COVID-19 outbreak in order to keep clinical activities with the maximum security for both donors and recipients. Nevertheless, there was a lack of evidence whether blood products and specifically bone marrow can cause transfusion-transmitted infection. Initially, there were many uncertainties and did not exist formal recommendations. Before official statements were available, we performed an allogeneic HCT in a 57-year-old male from a related matched donor in the incubation period of COVID-19 where the patient did not develop the disease. Actual epidemiology data suggest that transmission may occur early in the course of infection, even from asymptomatic patients in the incubation period. In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. The low concentration of viral RNA in plasma of patients with COVID-19 could support the safety of blood products, including peripheral blood hematopoietic cells. In conclusion, blood products including hematopoietic stem cells are safe in the context of COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32928663/ doi: 10.1016/j.transci.2020.102921 id: cord-329392-fufattj8 author: den Hartog, Gerco title: SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date: 2020-08-08 words: 4326.0 sentences: 218.0 pages: flesch: 41.0 cache: ./cache/cord-329392-fufattj8.txt txt: ./txt/cord-329392-fufattj8.txt summary: Serum samples were obtained from the following cohorts: (1) a random selection of individuals (n = 224) from a national (Dutch) cohort representing all age groups and obtained 3 years prior to SARS-CoV-2 emergence (Pienter3 study, Netherlands trial register number NL5467); (2) individuals (Supplementary Table 2 ) with proven non-SARS-CoV-2 ILI caused by human coronaviruses (n = 110, HCoV ILI) or other viruses (n = 74, non-HCoV ILI) obtained from the National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands (trial register number NL4666) [18] , and from Erasmus Medical Center, Rotterdam, collected prior to the SARS-CoV-2 outbreak and at least 2 weeks after polymerase chain reaction (PCR) detection of the virus; and (3) The steps in assay validation were similar to recently developed bead-based multiplex immunoassays for CMV, EBV, and RSV, with minor modifications as described below [16, 17] . abstract: BACKGROUND: The COVID-19 pandemic necessitates better understanding of the kinetics of antibody production induced by infection with SARS-CoV-2. We aimed to develop a high-throughput multiplex assay to detect antibodies to SARS-CoV-2 to assess immunity to the virus in the general population. METHODS: Spike protein subunits S1 and receptor binding domain, and nucleoprotein were coupled to microspheres. Sera collected before emergence of SARS-CoV-2 (n = 224) and of non-SARS-CoV-2 influenza-like illness (n = 184), and laboratory-confirmed cases of SARS-CoV-2 infection (n = 115) with various severities of COVID-19 were tested for SARS-CoV-2–specific IgG concentrations. RESULTS: Our assay discriminated SARS-CoV-2–induced antibodies and those induced by other viruses. The assay specificity was 95.1%–99.0% with sensitivity 83.6%–95.7%. By merging the test results for all 3 antigens a specificity of 100% was achieved with a sensitivity of at least 90%. Hospitalized COVID-19 patients developed higher IgG concentrations and the rate of IgG production increased faster compared to nonhospitalized cases. CONCLUSIONS: The bead-based serological assay for quantitation of SARS-CoV-2–specific antibodies proved to be robust and can be conducted in many laboratories. We demonstrated that testing of antibodies against multiple antigens increases sensitivity and specificity compared to single-antigen–specific IgG determination. url: https://www.ncbi.nlm.nih.gov/pubmed/32766833/ doi: 10.1093/infdis/jiaa479 id: cord-296579-oa67njov author: d’Ettorre, Gabriella title: Analysis of type I IFN response and T cell activation in severe COVID-19/HIV-1 coinfection: A case report date: 2020-09-04 words: 2745.0 sentences: 155.0 pages: flesch: 51.0 cache: ./cache/cord-296579-oa67njov.txt txt: ./txt/cord-296579-oa67njov.txt summary: Hence, this study aims to compare type I IFN response and T cell activation levels between a SARS-CoV-2/HIV-1-coinfected female patient and age-matched HIV-1-positive or uninfected women. LESSONS: These results indicate that SARS-CoV-2 infection in HIV-1-positive female patient was associated with increased levels of IFNα/β-mRNAs and T cell activation compared to healthy individuals. [1] Despite high number of people living with human immunodeficiency virus (HIV)-1 globally (about 37 million) and higher severity impact for certain viral infections in this category, [2] severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)/HIV-1 coinfection has been described in few cases. This study reports a severe case of SARS-CoV-2 in a black female patient co-infected by HIV-1 under protease inhibitors (PI) regimen, who was treated with hydroxychloroquine. Because of the key role of chronic immune activation and persistent IFN-I response in driving HIV-1 disease, [8, 9] we evaluated IFNa and IFNb gene expression and T cell activation levels in patient with SARS-CoV-2/HIV-1 coinfection. abstract: RATIONALE: Complex immune dysregulation in interferon (IFN) and T cell response has been observed in human immunodeficiency virus (HIV-1)-infected patients as well as in coronavirus disease-2019 (COVID-19) patients. However, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)/HIV-1 coinfection has been described in only few cases worldwide and no data are available on immunological outcomes in HIV-1-patients infected with SARS-CoV-2. Hence, this study aims to compare type I IFN response and T cell activation levels between a SARS-CoV-2/HIV-1-coinfected female patient and age-matched HIV-1-positive or uninfected women. PATIENT CONCERNS: A 52-year-old woman diagnosed with SARS-CoV-2/HIV-1 coinfection, ten HIV-1-positive women and five age-matched-healthy individuals were enrolled in this study. DIAGNOSES: SARS-CoV-2 infection caused severe pneumonia in the second week of illness in HIV-1-positive patient under protease inhibitors. Chest high-resolution computed tomography images of the SARS-CoV-2/HIV-1-coinfected patient showed bilateral ground-glass opacities. INTERVENTIONS: SARS-CoV-2/HIV-1-coinfected female patient under darunavir/cobicistat regimen received a 7-days hydroxychloroquine therapy. Analysis of IFNα/β mRNA levels and CD4 and CD8 T cell (CD38, human leukocyte antigen-DR [HLA-DR], CD38 HLA-DR) frequencies were performed by RT/real-time PCR assays and flow cytometry, respectively. Median relative difference (MRD) was calculated for each immunological variable. For values greater than reference, MRD should be a positive number and for values that are smaller, MRD should be negative. OUTCOMES: The severe pneumonia observed in SARS-CoV-2/HIV-1-positive patient under protease inhibitors was reversed by a 7-days hydroxychloroquine therapy. At the end of treatment, on day 7, patient reported resolution of fever, normalization of respiratory rate (14 breaths/min), and improved oxygen arterial pressure with a F(i)O(2) of 30%. MRD values for IFNα/β and CD4 and CD8 T cells expressing CD38 and/or HLA-DR found in SARS-CoV-2-/HIV-1-coinfected woman were approximatively equal to 0 when refereed respectively to HIV-1-positive female patients [MRDs IFNα/β: median −0.2545 (range: −0.5/0.1); T cells: median −0.11 (range: −0.8/1.3)] and ≥ 6 when referred to healthy individuals [MRDs IFNα/β: median 28.45 (range: 15/41.9); T cells: median 10 (range 6/22)]. LESSONS: These results indicate that SARS-CoV-2 infection in HIV-1-positive female patient was associated with increased levels of IFNα/β-mRNAs and T cell activation compared to healthy individuals. url: https://www.ncbi.nlm.nih.gov/pubmed/32899009/ doi: 10.1097/md.0000000000021803 id: cord-102807-cxtzf5oe author: fiore, j. r. title: FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy date: 2020-06-19 words: 1686.0 sentences: 135.0 pages: flesch: 67.0 cache: ./cache/cord-102807-cxtzf5oe.txt txt: ./txt/cord-102807-cxtzf5oe.txt summary: title: FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint ABSTRACT 27 28 Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors 29 from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint Studies on blood donor cohorts are useful to evaluate the prevalence, incidence and natural course 63 of infectious diseases in the general population and may thus help to assess both the viral 64 circulation and the evolution of the COVID-19 outbreak. We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM 66 and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general 67 population three months after the local start of the epidemic. abstract: Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy). Among 904 subjects tested, only in 9 cases (0.99%) antibodies against SARS-CoV-2 were demonstrated. All the 9 seropositive patients were negative for the research of viral RNA by RT-PCR in nasopharyngeal swab. These data, along with those recently reported from other countries, clearly show that we are very far from herd immunity and that the containment measures are at the moment the only realistic instrument we have to slow the spread of the pandemic. url: http://medrxiv.org/cgi/content/short/2020.06.17.20133678v1?rss=1 doi: 10.1101/2020.06.17.20133678 id: cord-290598-wquwtovs author: li, s. title: Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients date: 2020-09-23 words: 1766.0 sentences: 126.0 pages: flesch: 51.0 cache: ./cache/cord-290598-wquwtovs.txt txt: ./txt/cord-290598-wquwtovs.txt summary: Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases. In this study, we assay the IgG and IgM antibodies in ocular disease patients undiagnosed COVID-19 (people have no symptom of COVID-19 and negative result for viral RNA testing) to estimate the seropositivity rate in different type of ocular disease. We enrolled 1331 individuals with different ocular diseases but negative to SARS-CoV-2 RNA testing in Eye and ENT Hospital of Fudan University from February 2020 to May 2020. We conducted a serological survey testing the IgG and IgM antibodies against SARS-CoV-2 antigens in each participant of different ocular disease. Our study evaluated the seroprevalence in patients with different ocular diseases, including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others. abstract: Using serological test to estimate the prevalence and infection potential of coronavirus disease 2019 in ocular diseases patients help understand the relationship between ocular diseases and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We conducted a cross-sectional study assaying the IgG and IgM antibodies in 1331 individuals with ocular diseases by using a magnetic chemiluminescence enzyme immunoassay kit, during the period from February 2020 to May 2020. In our study, the seroposivity in total ocular disease patients was 0.83% (11/1331). The patients with different ocular diseases including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others had seroposivity of 2.94%, 12.5%, 25%, 4.41%, 2.63%, 1.6%, 2.22% and 0%, respectively. Among that, two ocular surface disease groups (keratitis and conjunctival cyst) had higher seroprevalence compared with others. All the participants were reverse transcription polymerase chain reaction negative for SARS-CoV-2 from throat swabs. Our study evaluated the seroprevalence in patients with different ocular diseases, which will help us understand the relationship between ocular disease and SARS-CoV-2 infection. Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases. url: http://medrxiv.org/cgi/content/short/2020.09.22.20198465v1?rss=1 doi: 10.1101/2020.09.22.20198465 id: cord-015009-3o90pzw7 author: nan title: How and who does SARS kill? date: 2003-06-10 words: 911.0 sentences: 46.0 pages: flesch: 60.0 cache: ./cache/cord-015009-3o90pzw7.txt txt: ./txt/cord-015009-3o90pzw7.txt summary: Analysis of the complete genome sequence of the SARS virus, published in May 11 , suggests that it is not closely related to any of the three previously identified coronavirus subfamilies, nor does it seem to have arisen through a chance genetic recombination between known coronaviruses12. "Its unique sequence suggests that it has evolved independently from the other members of the family, in some animal host, for a long time," says Malik Peiris, a virologist at the University of Hong Kong. Recent investigations by researchers at the China Agricultural University in Beijing, for instance, have failed to find SARS-like coronaviruses in 732 animals from 54 wild and 11 domestic species in southern China, including palm civets. "The animals walk in and out of their houses," says Kenneth Shortridge, who led the University of Hong Kong''s efforts to monitor avian viruses in southern China until his retirement last year. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095033/ doi: 10.1038/nature.2003.2 id: cord-015516-hx7ktq8j author: nan title: In the Literature date: 2005-10-15 words: 1499.0 sentences: 80.0 pages: flesch: 46.0 cache: ./cache/cord-015516-hx7ktq8j.txt txt: ./txt/cord-015516-hx7ktq8j.txt summary: Experimental pulmonary infection with SARS coronavirus infection in mice reduced the expression of ACE2 in the lungs and, as also occurs in humans, caused diffuse lung injury. On the basis of these findings, the investigators proposed that the severe pulmonary alveolar injury seen in patients with SARS is the consequence of SARS coronavirus spike surface protein-associated down-regulation of ACE2. The authors suggest that recombinant ACE2 protein could be a potential therapeutic agent in this and related pulmonary infections and diffuse alveolar injuries. In patients with chronic infections involving the exit site or tunnel portion of peritoneal dialysis catheters, treatment with antibiotics and local care is often unsuccessful. This procedure was used by Crabtree and Burchette in 13 consecutive patients with chronic peritoneal dialysis catheter infections that had been present for a mean duration of 3.2 months, with successful results for all 13. Three patients subsequently had their catheters removed because of peritonitis without exit-site or tunnel infection at months 8-11. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107963/ doi: 10.1086/497097 id: cord-015619-msicix98 author: nan title: Virus Structure & Assembly date: 2009-02-24 words: 3302.0 sentences: 164.0 pages: flesch: 45.0 cache: ./cache/cord-015619-msicix98.txt txt: ./txt/cord-015619-msicix98.txt summary: The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111173/ doi: 10.1016/s0006-3495(08)79065-9 id: cord-015701-0m17unfx author: nan title: Neuartiges Coronavirus (SARS-CoV-2) date: 2020-02-24 words: 80.0 sentences: 15.0 pages: flesch: 80.0 cache: ./cache/cord-015701-0m17unfx.txt txt: ./txt/cord-015701-0m17unfx.txt summary: key: cord-015701-0m17unfx authors: nan title: Neuartiges Coronavirus (SARS-CoV-2) date: 2020-02-24 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1113-3096 sha: doc_id: 15701 cord_uid: 0m17unfx nan . Von der Gabe von Kortikosteroiden wird eher abgeraten. An einem Impfstoff gegen SARS-CoV-2 wird fieberhaft gearbeitet. Auch im Idealfall dürften entsprechende Zulassungsstudien aber nicht vor Ende 2020 zu erwarten sein. china World Health Organization. Novel Coronavirus (SARS-CoV-2) situation reports First Case of 2019 Novel Coronavirus in the United States abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117074/ doi: 10.1055/a-1113-3096 id: cord-025794-ckrclrwz author: nan title: Mitteilungen der ÖGKJ date: 2020-06-02 words: 911.0 sentences: 133.0 pages: flesch: 58.0 cache: ./cache/cord-025794-ckrclrwz.txt txt: ./txt/cord-025794-ckrclrwz.txt summary: Vom Roten Kreuz werden zusätzlich auch Kontaktpersonen von gesicherten SARS-CoV2 Fällen getestet, sodass diese gezielte Testung von Kindern als Kontaktpersonen die wahrscheinlichste Erklärung für die höheren Positivitätsraten in den behördlichen Angaben -verglichen mit den Daten allein aus den Kinderabteilungen -ist. Wenn eine Infektion ausgeschlossen werden kann, bedeutet dies für Mutter, Kind und auch das betreuende Personal eine enorme Erleichterung der Situation. Wenn die Mutter so krank ist, dass sie sich nicht selbst um das Kind kümmern kann, sollte das Neugeborene, nach Abwägung der individuellen Situation und den vorhandenen Optionen vor Ort, temporär von ihr getrennt und als Kontaktperson eines COVID-19-Falls eingestuft werden. Wenn eine Mutter (unabhängig von einem möglichen Verdacht auf SARS-CoV2-Infektion) sich entschieden hat, nicht zu stillen, ist es immer wünschenswert, dass das Neugeborene auf alle Fälle Kolostrum erhalten sollte. bei Einstufung als Verdachtsfall werden Mutter und Kind gemeinsam isoliert und wie jeder Isolationsfall den Richtlinien der Klinik entsprechend durch die Pflege betreut. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265657/ doi: 10.1007/s00112-020-00930-y id: cord-029332-yn603pvb author: nan title: Full Issue PDF date: 2020-07-15 words: 11306.0 sentences: 633.0 pages: flesch: 41.0 cache: ./cache/cord-029332-yn603pvb.txt txt: ./txt/cord-029332-yn603pvb.txt summary: Included are cases of Brugada type I pattern positivization (1) in the context of fever, one of the most common presenting symptoms of the disease (2); electrical ventricular storm (3); transient atrioventricular block in the absence of myocarditis (4); sinus node dysfunction requiring pacemaker implantation (5) ; and finally a provocative report on the use of amiodarone as a possible treatment for COVID-19 (6) . In addition to cases of direct myocardial injury, some with pathological evidence, we also present 2 cases of takotsubo cardiomyopathy (16, 17) Two cases highlight the special circumstances faced by patients with left ventricular assist devices (18, 19) , which include the inability to tolerate prone positioning to augment respiratory support because of the mechanical equipment and the hypothesis that mechanical circulatory support may provide a type of protection against the most serious hemodynamic consequences of severe acute respiratory syndrome coronavirus-2 infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363418/ doi: 10.1016/s2666-0849(20)30838-x id: cord-252550-yaosufpm author: nan title: Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission date: 2020-09-09 words: 508.0 sentences: 44.0 pages: flesch: 54.0 cache: ./cache/cord-252550-yaosufpm.txt txt: ./txt/cord-252550-yaosufpm.txt summary: authors: nan title: Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission SARS-CoV-2 infection down-regulates ACE2 expression and leads to the production of pro-inflammatory mediators, such as IL-6 [1] . As they lose ACE2-mediated protection, Ang-II signaling contributes to the pathological findings observed in COVID-19 patients, such as disseminated coagulopathy and acute tissue damage [4] . Toll-like receptors (TLRs) 3 and TLR 7/8 recognize SARS-CoV-2 RNA and initiate the inflammatory cascade via type I and type II IFN gene expression and NF-κB nuclear translocation [5, 6] . IL-6, an important player in COVID-19, binds IL-6R and gp130 receptors to activate JAK/STAT-3 pathway and then contribute to the CRS observed in COVID-19 patients [13] . Severe respiratory SARS-CoV2 infection: Does ACE2 receptor matter? Toll-like receptor 3 signaling via TRIF contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection abstract: nan url: https://doi.org/10.1042/cs-20200904_cor doi: 10.1042/cs-20200904_cor id: cord-281754-auqh3vtr author: nan title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date: 2017-09-12 words: 3626.0 sentences: 229.0 pages: flesch: 49.0 cache: ./cache/cord-281754-auqh3vtr.txt txt: ./txt/cord-281754-auqh3vtr.txt summary: As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/29737283/ doi: 10.1016/j.disamonth.2017.03.019 id: cord-324357-ys4tqy5x author: nan title: Hygiene at home: A bulwark against COVID-19 to be protect from SARS-CoV-2 date: 2020-05-15 words: 681.0 sentences: 51.0 pages: flesch: 67.0 cache: ./cache/cord-324357-ys4tqy5x.txt txt: ./txt/cord-324357-ys4tqy5x.txt summary: • by droplets emitted from the nose and mouth (splutering) when coughing, sneezing, but also when speaking, singing and screaming, • by direct contact between people: shaking hands, hugging, kissing, • secondarily through indirect contact: objects contaminated by an infected person. The National Academy of Medicine wishes to recall the fundamental rules of hygiene at home which it is essential to observe in the current epidemic context, especially in families with children. The respiratory hygiene rules are: • cover your mouth and nose if you cough or sneeze, preferably with a disposable tissue, throw away the tissue immediately and wash your hands immediately before touching anything. • avoid touching your face, nose, eyes and mouth, which can spread respiratory viruses through contaminated hands; • ventilate the housing by opening the windows for at least 20 min in the morning and evening and during houseworking. Hydro-alcoholic solutions disinfect but do not clean: so they cannot replace washing with soap and water when hands are dirty. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32427155/ doi: 10.1016/j.banm.2020.05.020 id: cord-332245-yfj1kkj7 author: nan title: SARS-CoV-2 Infektion bei Kindern und Jugendlichen: Ein Literaturüberblick der AG Infektiologie der ÖGKJ1 date: 2020-06-10 words: 2336.0 sentences: 334.0 pages: flesch: 55.0 cache: ./cache/cord-332245-yfj1kkj7.txt txt: ./txt/cord-332245-yfj1kkj7.txt summary: aktuell Infektiologie SARS-CoV-2 Infektion bei Kindern und Jugendlichen Ein Literaturüberblick der AG Infektiologie der ÖGKJ 1 F Im Dezember 2019 kam es in der chinesischen Region Hubei zum gehäuften Auftreten von Pneumoniefällen unbekannter Ätiologie [1] . Allerdings waren in dieser Altersgruppe knapp 80 % der Fälle lediglich Verdachtsfälle (ohne SARS-CoV-2-Laborbestätigung), sodass die Autoren davon ausgehen, dass ein nicht unbeträchtlicher Teil dieser schweren Verläufe durch andere Viren (v. Jedoch zeigten sich in einer diesen Kohorten vermehrte fetale Komplikationen wie Frühgeburtlichkeit oder respiratorischer Stress, wobei der direkte Zusammenhang mit SARS-CoV-2 nicht geklärt ist. So muss natürlich auf neonatalen Intensivstationen damit gerechnet werden, dass aufgrund einer SARS-CoV-2-Erkrankung der Mutter eine prämature Entbindung indiziert wird und die Frühgeborenen behandelt werden müssen. Bei den wenigen detaillierten Berichten über spezifische Symptome bei Kindern mit COVID-19 wird Fieber in 40-100 % und Husten in 40-100 % der symptomatischen Fälle beschrieben [7, 8, [15] [16] [17] [18] [19] . Bisher gibt es keine zugelassenen Medikamente zur Therapie von COVID-19 bei Erwachsenen und Kindern [32] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32536725/ doi: 10.1007/s00608-020-00794-1 id: cord-335597-anrzcsrt author: nan title: 44. Jahrestagung der Österreichischen Gesellschaft für Pneumologie date: 2020-10-26 words: 14629.0 sentences: 921.0 pages: flesch: 49.0 cache: ./cache/cord-335597-anrzcsrt.txt txt: ./txt/cord-335597-anrzcsrt.txt summary: Conclusions: In this study assessing the prognostic relevance of pulmonary exercise hemodynamics in patients with systemic sclerosis, PVR and TPR at peak exercise as well as mPAP/CO-slope and TPG/CO-slope turned out as age-independent predictors of all-cause mortality. Later-line treatment with lorlatinib in ALKand ROS1-rearrangement-positive NSCLC: a retrospective, multicenter analysis Background: Anti-fibrotic medication is effective in progressive fibrosing interstitial lung diseases (ILD), but a subgroup of fibrotic ILD patients also benefits from immunomodulatory therapies. Methods: HRCT of 127 subsequent single-center ILDboard patients (mean age 65 (standard deviation 14) years, 65 % male), were evaluated for radiological findings considered noninflammatory (reticulation including honeycombing (RET), traction bronchiectasis (TBR), emphysema (EMP)) or active inflammatory (consolidations (CON), ground glass opacities (GGO), noduli (NDL), mosaic attenuation (MOS)) in 6 distinct lung regions. abstract: nan url: https://doi.org/10.1007/s00508-020-01745-3 doi: 10.1007/s00508-020-01745-3 id: cord-337462-9mvk86q6 author: nan title: Humanity tested date: 2020-04-08 words: 1263.0 sentences: 59.0 pages: flesch: 50.0 cache: ./cache/cord-337462-9mvk86q6.txt txt: ./txt/cord-337462-9mvk86q6.txt summary: The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus'' RNA in selected populations. Singapore, Hong Kong and Taiwan have shown the world that, to contain the propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments need to quickly implement aggressive testing (by detecting the viral RNA through polymerase chain reaction (PCR)), the isolation of those infected and the tracing and quarantining of their contacts, while educating their citizens about the need for physical distancing and basic public health measures (in particular, frequent hand-washing and staying at home if feeling unwell). Medical-device companies and government and research laboratories around the world have rushed to adapt and scale up nucleic acid tests (mostly employing PCR, but also CRISPR-based detection and loop-mediated isothermal amplification) to detect the virus'' RNA, and government agencies are scrambling to assess them via emergency routes (such as the Emergency Use Authorization program 3 by the United States Food and Drug Administration (FDA)). abstract: The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus’ RNA in selected populations. url: https://doi.org/10.1038/s41551-020-0553-6 doi: 10.1038/s41551-020-0553-6 id: cord-337646-gkcm6ds0 author: nan title: The Federation’s Pages: WFPHA: World Federation of Public Health Associations www.wfpha.org Bettina Borisch and Marta Lomazzi, Federation’s Pages Editors date: 2020-09-17 words: 2529.0 sentences: 140.0 pages: flesch: 45.0 cache: ./cache/cord-337646-gkcm6ds0.txt txt: ./txt/cord-337646-gkcm6ds0.txt summary: The next coronavirus to generate a global public health crisis was the Middle East Respiratory Syndrome (MERS-CoV) that emerged in Saudi Arabia in 2012 among people working closely with camels. During the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV), held on 30 January 2020, the COVID-19 pandemic was underway. The association between Emerging Infectious Diseases (EIDs) and environmental destruction is widely recognized: deforestation destroys natural habitats, increases the density of remaining wild animal populations, increases their movements to look for food accompanied by the probability of human contact-all induce stress that impairs immune systems and increases viral shedding [16] . Environment preservation is urgent for many reasons: conservation of biodiversity, the fight against climate change, reduction of air, water and food pollution, and improvement of human health and quality of life [18] . abstract: nan url: https://doi.org/10.1057/s41271-020-00240-3 doi: 10.1057/s41271-020-00240-3 id: cord-338123-4pshh5ov author: nan title: SARS Alert Applicability date: 2004-08-17 words: 1461.0 sentences: 67.0 pages: flesch: 41.0 cache: ./cache/cord-338123-4pshh5ov.txt txt: ./txt/cord-338123-4pshh5ov.txt summary: If the illness is included in the list of notifiable infectious diseases, the case must be reported to the local public health authority so infection control measures can be implemented. To determine how the sickness certification system in other European Union countries operates and assesses the feasibility of the WHO alert surveillance, we interviewed specialists in infectious diseases or public health in France (seven imported cases of SARS, two in healthcare workers), Spain (one case), and Denmark (no cases) (2) by electronic mail. All hospitals that treated patients with suspected SARS either had their own committee to classify patients according to World Health Organization guidelines or followed the protocol for classification or reclassification of reported cases by the team members (3). From the first day that suspected cases were reported to the Taiwan Center for Disease Control, the patients were placed in negative-pressure isolation rooms when available. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15503403/ doi: 10.3201/eid1008.040221 id: cord-344454-hs3tthzi author: nan title: Les animaux contaminés par le SARS-CoV-2 représentent-ils un risque pour l’Homme ? date: 2020-09-15 words: 740.0 sentences: 76.0 pages: flesch: 70.0 cache: ./cache/cord-344454-hs3tthzi.txt txt: ./txt/cord-344454-hs3tthzi.txt summary: Bien que l''origine zoonotique de la COVID-19 soit bien établie (chauves-souris du genre Rhinolophus, hôtes intermédiaires possibles, dont le Pangolin asiatique), un seul cas de contamination animal-Homme par le SARS-CoV-2 ayant été documenté avec des visons d''élevage aux Pays-Bas, rien ne prouve à l''heure actuelle que les animaux participent à la propagation de la pandémie dans la population humaine. Bien que ces infections animales ne jouent pas de rôle dans l''évolution de la pandémie de COVID-19, l''Académie nationale de médecine et l''Académie vétérinaire de France recommandent, dans le cadre d''une stratégie globale « une seule santé » : • de mettre en oeuvre les mesures de biosécurité les plus strictes dans les élevages de visons encore indemnes afin d''éviter les contaminations humaines et tout risque de propagation ultérieure, voire la constitution d''un réservoir animal ; • d''éviter tout contact entre les personnes infectées par le SARS-CoV-2 ou suspectes de l''être, avec leurs animaux de compagnie, notamment s''il s''agit de furet ou de chat, et d''observer les mêmes mesures barrière que pour prévenir la contamination de leur entourage (lavage des mains, masques. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0001407920304842 doi: 10.1016/j.banm.2020.09.010 id: cord-353293-vjdwh19x author: nan title: Post-COVID-19 global health strategies: the need for an interdisciplinary approach date: 2020-06-11 words: 3856.0 sentences: 175.0 pages: flesch: 36.0 cache: ./cache/cord-353293-vjdwh19x.txt txt: ./txt/cord-353293-vjdwh19x.txt summary: Gemelli IRCSS (Rome, Italy) has set up a multidisciplinary healthcare service called "Post-COVID-19 Day Hospital." The specialist assessments offered to patients are outlined in the following sections. Furthermore, the important role of geriatrician acting as a care manager of patients who suffered COVID-19 disease is described. A respiratory follow-up is of pivotal importance to evaluate lung function, alveolar-arterial gas exchange, and exercise tolerance in recovered non-infective COVID-19 patients [5] . In this Post-COVID-19 Day Hospital, internal medicine and geriatric specialists are integrated with infectious disease physicians, pneumologists, immuno-rheumatologists, and other specialists into the management of the SARS-CoV-2 infection. As a whole, the post-acute care service at the Fondazione Policlinico Gemelli aims at expanding the knowledge of COVID-19 and its impact on health status and care needs as well as at promoting healthcare strategies to treat and prevent the clinical consequence of SARS-CoV-2 infection across different organs and systems. abstract: For survivors of severe COVID-19 disease, having defeated the virus is just the beginning of an uncharted recovery path. What follows after the acute phase of SARS-CoV-2 infection depends on the extension and severity of viral attacks in different cell types and organs. Despite the ridiculously large number of papers that have flooded scientific journals and preprint-hosting websites, a clear clinical picture of COVID-19 aftermath is vague at best. Without larger prospective observational studies that are only now being started, clinicians can retrieve information just from case reports and or small studies. This is the time to understand how COVID-19 goes forward and what consequences survivors may expect to experience. To this aim, a multidisciplinary post-acute care service involving several specialists has been established at the Fondazione Policlinico Universitario A. Gemelli IRCSS (Rome, Italy). Although COVID-19 is an infectious disease primarily affecting the lung, its multi-organ involvement requires an interdisciplinary approach encompassing virtually all branches of internal medicine and geriatrics. In particular, during the post-acute phase, the geriatrician may serve as the case manager of a multidisciplinary team. The aim of this article is to describe the importance of the interdisciplinary approach––coordinated by geriatrician––to cope the potential post-acute care needs of recovered COVID-19 patients. url: https://doi.org/10.1007/s40520-020-01616-x doi: 10.1007/s40520-020-01616-x id: cord-329221-miztel9l author: rudolf, f. title: Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population date: 2020-08-21 words: 3683.0 sentences: 249.0 pages: flesch: 54.0 cache: ./cache/cord-329221-miztel9l.txt txt: ./txt/cord-329221-miztel9l.txt summary: Conclusions and Relevance: This study emphasizes the need for large and diverse negative cohorts when determining specificities, and for diverse and representative positive samples when determining sensitivities of lateral flow assays for SARS-CoV-2 infections. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint On the other hand, the sensitivity needs to be assayed using a sufficiently large and representative sample of the antibody response in a population for time post infection, (but especially also in disease severity) i don''t know what you mean. To accurately calculate the specificity, we used the plasma of a blood donor cohort comWe characterised eleven different commercially available lateral flow assays (LFA) for detection of SARS-CoV-2 specific IgM and IgG with serum samples from the three cohorts (Table 1 ). abstract: Importance: Serological assays can help diagnose and determine the rate of SARS-CoV-2 infections in a population. Objective: We characterized and compared 11 different lateral flow assays for their performance in diagnostic or epidemiological settings. Design, Setting, Participants: We used two cohorts to determine the speci- ficity: (i) up to 350 blood donor samples from past influenza seasons and (ii) up to 110 samples which tested PCR negative for SARS-CoV-2 during the first wave of SARS-CoV-2 infections in Switzerland. The sensitivity was determined using up to 370 samples which tested PCR positive for SARS-CoV-2 during the same time and is representative for age distribution and severity. Main Outcome: We found a single test usable for epidemiological studies in the current low-prevalence setting, all other tests showed lacking sensitivity or specificity for a usage in either epidemiological or diagnostic setting. However, orthogonal testing by combining two tests without common cross-reactivities makes testing in a low-prevalence setting feasible. Results: Nine out of the eleven tests showed specificities below 99%, only five of eleven tests showed sensitivities comparable to established ELISAs, and only one ful- filled both criteria. Contrary to previous results from lab assays, five tests measured an IgM response in >80% of the samples. We found no common cross-reactivities, which allows orthogonal testing schemes for five tests of sufficient sensitivities. Conclusions and Relevance: This study emphasizes the need for large and diverse negative cohorts when determining specificities, and for diverse and repre- sentative positive samples when determining sensitivities of lateral flow assays for SARS-CoV-2 infections. Failure to adhere to statistically relevant sample sizes or cohorts exclusively made up of hospitalised patients fails to accurately capture the performance of these assays in epidemiological settings. Our results allow a rational choice between tests for different use cases. url: http://medrxiv.org/cgi/content/short/2020.08.18.20177204v1?rss=1 doi: 10.1101/2020.08.18.20177204 id: cord-339709-49q2xxkw author: sermet, i. title: Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children date: 2020-06-30 words: 4753.0 sentences: 317.0 pages: flesch: 58.0 cache: ./cache/cord-339709-49q2xxkw.txt txt: ./txt/cord-339709-49q2xxkw.txt summary: Despite a low frequency of respiratory symptoms, cases of Multisystem Inflammatory 108 Syndrome (MIS) have been reported in children that were infected by SARS-CoV-2 or were in contact 109 with COVID-19 patients 14, 15 . We also analysed SARS-CoV-2 and seasonal HCoVs humoral responses of patients with MIS 122 regarding antibody targets and functional neutralizing activity. Our study is the first to analyse in depth 123 the typology of humoral responses to SARS-CoV-2 in children, and provides evidence that prior 124 infections by seasonal coronaviruses has no significant impact on SARS-CoV-2 infection or related MIS 125 disease in children. We compared the prevalence of anti-N and -S antibodies against the four seasonal HCoVs in a 220 subpopulation of children among the HOS-P (n=54), MIS-P (n=15) and CTL (n=118) groups (Figure 1) . abstract: Background: Children have a lower rate of COVID-19, potentially related to cross-protective immunity conferred by seasonal coronaviruses (HCoVs). We tested if prior infections with seasonal coronaviruses impacted SARS-CoV-2 infections and related Multisystem Inflammatory Syndrome (MIS). Methods: This cross-sectional observational study in Paris hospitals enrolled 739 pauci or asymptomatic children (HOS group) plus 36 children with suspected MIS (MIS group). Prevalence, antigen specificity and neutralizing capability of SARS-CoV-2 antibodies were tested. Antibody frequency and titres against Nucleocapsid (N) and Spike (S) of the four seasonal coronaviruses (NL63, HKU1, 229E, OC43) were measured in a subset of seropositive patients (54 SARS-CoV-2 (HOS-P subgroup) and 15 MIS (MIS-P subgroup)), and in 118 matched SARS-CoV-2 seronegative patients (CTL subgroup). Findings: SARS-CoV-2 mean prevalence rate in HOSP children was 11.7% from April 1 to June 1. Neutralizing antibodies were found in 55.6% of seropositive children, and their relative frequency increased with time (up to 100 % by mid-May). A majority of MIS children (25/36) were SARS-CoV-2 seropositive, of which all tested (n=15) had neutralizing antibodies. On average, seropositive MIS children had higher N and S1 SARS-CoV-2 titres as compared to HOS children. Patients from HOS-P, MIS-P, and CTL subgroups had a similar prevalence of antibodies against the four seasonal HCoVs (66.9 -100%). The level of anti-SARS-CoV-2 antibodies was not significantly different in children who had prior seasonal coronavirus infection. Interpretation: Prior infection with HCoVs does not prevent SARS-CoV-2 infection and related MIS in children. Children develop neutralizing antibodies after SARS-CoV-2 infection. url: https://doi.org/10.1101/2020.06.29.20142596 doi: 10.1101/2020.06.29.20142596 id: cord-271701-tx0lqgff author: te Velthuis, Aartjan J.W. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 words: 7357.0 sentences: 367.0 pages: flesch: 56.0 cache: ./cache/cord-271701-tx0lqgff.txt txt: ./txt/cord-271701-tx0lqgff.txt summary: Commonly, its core subunit is a single RNA-dependent RNA polymerase (RdRp) that drives the production of template strands for replication, new genome molecules, and-in many RNA virus groupsalso subgenomic (sg) mRNAs. This canonical RdRp is structurally conserved among RNA viruses and widely accepted to drive catalysis of phosphodiester bond formation via a well-established reaction mechanism involving two metal ions that are coordinated by aspartate residues in its motifs A and C (3) (4) (5) . Interestingly, both nsp8 and nsp(7+8) are able to extend the RNA primers beyond template length in the presence of heparin ( Figure 4D and Supplementary Figure S2B ), suggesting that these extensions result from terminal transferase activity and not from template switching, as was previously observed for poliovirus 3D pol (20) . Subsequent alanine substitution of the N-terminal D/ ExD/E motif, composed of D50 and D52 in SARS-CoV, greatly affected primer extension activity on the CU 10 template as shown in Figure 5C . abstract: Uniquely among RNA viruses, replication of the ∼30-kb SARS-coronavirus genome is believed to involve two RNA-dependent RNA polymerase (RdRp) activities. The first is primer-dependent and associated with the 106-kDa non-structural protein 12 (nsp12), whereas the second is catalysed by the 22-kDa nsp8. This latter enzyme is capable of de novo initiation and has been proposed to operate as a primase. Interestingly, this protein has only been crystallized together with the 10-kDa nsp7, forming a hexadecameric, dsRNA-encircling ring structure [i.e. nsp(7+8), consisting of 8 copies of both nsps]. To better understand the implications of these structural characteristics for nsp8-driven RNA synthesis, we studied the prerequisites for the formation of the nsp(7+8) complex and its polymerase activity. We found that in particular the exposure of nsp8's natural N-terminal residue was paramount for both the protein's ability to associate with nsp7 and for boosting its RdRp activity. Moreover, this ‘improved’ recombinant nsp8 was capable of extending primed RNA templates, a property that had gone unnoticed thus far. The latter activity is, however, ∼20-fold weaker than that of the primer-dependent nsp12-RdRp at equal monomer concentrations. Finally, site-directed mutagenesis of conserved D/ExD/E motifs was employed to identify residues crucial for nsp(7+8) RdRp activity. url: https://www.ncbi.nlm.nih.gov/pubmed/22039154/ doi: 10.1093/nar/gkr893 id: cord-270994-1mmqfp7g author: ul Qamar, Muhammad Tahir title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants date: 2020-03-26 words: 2019.0 sentences: 139.0 pages: flesch: 55.0 cache: ./cache/cord-270994-1mmqfp7g.txt txt: ./txt/cord-270994-1mmqfp7g.txt summary: title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants Therefore, herein, we analysed the 3CL(pro) sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. On January 21, the first article related to 2019-nCoV was 27 published, which revealed that 2019-nCoV belongs to the beta-coronavirus group, sharing 28 ancestry with bat coronavirus HKU9-1, similar to SARS-coronaviruses, and despite sequence 29 diversity its spike protein interacts strongly with the human ACE2 receptor [1] . Structure-based activity analyses and high-57 throughput studies have identified potential inhibitors for SARS-CoV and MERS-CoV 3CL pro 58 Our analyses identified nine novel non-toxic, 171 druggable natural compounds that are predicted to bind with the receptor binding site and 172 catalytic dyad (Cys-145 and His-41) of SARS-CoV-2 3CL pro ( Table 2 ; Fig. S5 ). abstract: The recent outbreak of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 in December 2019 raised global health concerns. The viral 3-chymotrypsin-like cysteine protease (3CL(pro)) enzyme controls coronavirus replication and is essential for its life cycle. 3CL(pro) is a proven drug discovery target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV). Recent studies revealed that the genome sequence of SARS-CoV-2 is very similar to that of SARS-CoV. Therefore, herein, we analysed the 3CL(pro) sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. Our analyses revealed that the top nine hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimisation and drug development process to combat COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2095177920301271?v=s5 doi: 10.1016/j.jpha.2020.03.009 id: cord-295742-d11ty5ed author: van Dam, Peter A. title: High mortality of cancer patients in times of SARS-Cov-2: do not generalize! date: 2020-08-10 words: 1118.0 sentences: 59.0 pages: flesch: 51.0 cache: ./cache/cord-295742-d11ty5ed.txt txt: ./txt/cord-295742-d11ty5ed.txt summary: This is an important issue as in times limited of resources, the label "cancer with COVID-19" can compromise the access of intensive care (ICU) and outcome of patients dramatically in overwhelmed health care systems due to the outbreak of the SARS-CoV-2 pandemic. 4 The OpenSAFELY study, looking at factors associated with 5683 COVID-19-related hospital deaths in the linked electronic health records of 17 million adult NHS patients clearly showed that male gender (HR 1.99; 95% CI 1.80-2.10), age (with a very strong gradient), ethnicity (adjusted HR 1.71; 95% CI 1.44-2.02), uncontrolled diabetes (HR 2.26 95% CI: 2.18-2.56), obesity (with a very strong gradient) and various other medical conditions often had a higher impact on the probability to die of SARS-CoV-2 then cancer. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR abstract: nan url: https://api.elsevier.com/content/article/pii/S0959804920304214 doi: 10.1016/j.ejca.2020.07.021 id: cord-310507-5h6egve4 author: van Doorn, Amarylle S. title: Systematic review with meta‐analysis: SARS‐CoV‐2 stool testing and the potential for faecal‐oral transmission date: 2020-08-27 words: 3532.0 sentences: 238.0 pages: flesch: 49.0 cache: ./cache/cord-310507-5h6egve4.txt txt: ./txt/cord-310507-5h6egve4.txt summary: Since December 2019, the world has been dealing with the outbreak of the novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) leading to Corona Virus Disease 2019 (COVID-19) that emerged in Wuhan, China. However, there is a growing body of studies in which SARS-CoV-2 RNA was detected in stool samples (including anal swabs) from COVID-19 patients. 11, 15, 16 This study aims to (1) critically assess the clinical relevance of testing stool samples and anal swabs and (2) provide a critical overview of the available literature regarding the faecal-oral transmission of SARS-CoV-2. We collected the following data from the eligible original articles: study design, geographic location, study period, number of patients, age, types of tested specimens, number of tested specimens, methods of the performed tests, duration and prevalence of positive test results in different specimens, disease severity, gastrointestinal symptoms, endoscopic results, specific evidence supporting faecal-oral transmission and remarkable patient/population characteristics. abstract: BACKGROUND: Since the start of the COVID‐19 pandemic, there have been many scientific reports regarding gastrointestinal manifestations. Several reports indicate the possibility of viral shedding via faeces and the possibility of faecal‐oral transmission. AIMS: To critically assess the clinical relevance of testing stool samples and anal swabs and provide an overview of the potential faecal‐oral transmission of SARS‐CoV‐2. METHODS: A systematic literature search with MeSH terms was performed, scrutinising the Embase database, Google scholar, MEDLINE database through PubMed and The Cochrane Library, including articles from December 2019 until July 7 2020. Data were subsequently analysed with descriptive statistics. RESULTS: Ninety‐five studies were included in the qualitative analysis. 934/2149 (43%) patients tested positive for SARS‐CoV‐2 in stool samples or anal swabs, with positive test results up to 70 days after symptom onset. A meta‐analysis executed with studies of at least 10 patients revealed a pooled positive proportion of 51.8% (95% CI 43.8 ‐ 59.7%). Positive faecal samples of 282/443 patients (64%) remained positive for SARS‐CoV‐2 for a mean of 12.5 days, up to 33 days maximum, after respiratory samples became negative for SARS‐CoV‐2. Viable SARS‐CoV‐2 was found in 6/17 (35%) patients in whom this was specifically investigated. CONCLUSIONS: Viral shedding of SARS‐CoV‐2 in stool samples occurs in a substantial portion of patients, making faecal‐oral transmission plausible. Furthermore, detection in stool sample or anal swab can persist long after negative respiratory testing. Therefore, stool sample or anal swab testing should be (re)considered in relation to decisions for isolating or discharging a patient. url: https://doi.org/10.1111/apt.16036 doi: 10.1111/apt.16036 id: cord-265329-bsypo08l author: van Dorp, Lucy title: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 date: 2020-05-05 words: 4915.0 sentences: 270.0 pages: flesch: 49.0 cache: ./cache/cord-265329-bsypo08l.txt txt: ./txt/cord-265329-bsypo08l.txt summary: Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1 ) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk). In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. The genomic diversity of the global SARS-CoV-2 population being recapitulated in multiple countries points to extensive worldwide transmission of COVID-19, likely from extremely early on in the pandemic. abstract: SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 52,020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes. url: https://api.elsevier.com/content/article/pii/S1567134820301829 doi: 10.1016/j.meegid.2020.104351 id: cord-024786-f33eb1nf author: van Rensburg, V title: Current evidence for directed and supportive investigational therapies against COVID-19 date: 2020-04-24 words: 4411.0 sentences: 279.0 pages: flesch: 49.0 cache: ./cache/cord-024786-f33eb1nf.txt txt: ./txt/cord-024786-f33eb1nf.txt summary: Multiple trials across the globe are currently underway to assess the efficacy of CQ for the treatment and prevention of COVID-19, but no published, peer-reviewed results are available at the time of writing. [33] The rationale for the use of lopinavir/ritonavir (LPV/r) in COVID-19 stems from its in vitro activity against SARS-CoV-1, [34] as well as from a retrospective, multicentre cohort study evaluating LPV/r as early treatment in SARS-CoV-1, which demonstrated decreased mortality and intubation rates. [50] At the time of writing, there were no published peer-reviewed trials or case studies evaluating favipiravir in COVID-19, and its use is not currently recommended outside of clinical trials. A systematic review of treatment options in SARS-CoV-1 infection included corticosteroids'' effects on mortality, in vitro inhibition of SARS viral replication and acute respiratory distress syndrome. Drugs that purportedly inhibit SARS-CoV-2 replication (such as the investigational antivirals) or viral entry and replication (CQ and HCQ) may therefore be more effective when given earlier in the COVID-19 disease course. abstract: Coronavirus disease 2019 (COVID-19) is a global health crisis. There is currently a great need for effective and safe therapies directed at the disease, but no drugs are presently registered for use in COVID-19. Several directed therapies have been proposed, and most are still in clinical trials. Currently available published, peer-reviewed results mostly involve small sample sizes with study limitations restricting the interpretation of the findings. Many trials currently published also do not have a control group, limiting the interpretation of the effect of the intervention. Investigational directed therapies as well as investigational supportive therapies against COVID-19 are reviewed here. Chloroquine and hydroxychloroquine show promise as directed therapies, but current trial results are conflicting. Lopinavir/ritonavir also shows potential, but was started late in the disease course in most trials. No randomised controlled evidence is currently available for remdesivir and favipiravir. Corticosteroid use is not recommended for directed therapy against COVID-19, and the role of tocilizumab is currently unclear, based on limited evidence. Early initiation of investigational directed therapies may provide benefit in selected patients. The results from larger randomised controlled trials will clarify the place of these therapies in COVID-19 treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7221540/ doi: 10.7196/ajtccm.2020.v26i2.072 id: cord-323327-08p122lw author: van de Veerdonk, Frank L. title: Blocking IL-1 to prevent respiratory failure in COVID-19 date: 2020-07-18 words: 3019.0 sentences: 145.0 pages: flesch: 41.0 cache: ./cache/cord-323327-08p122lw.txt txt: ./txt/cord-323327-08p122lw.txt summary: These findings open new avenues for host-directed therapies in patients with symptomatic SARS-CoV-2 infection and might in addition to antiviral treatment be enough to curb the currently unacceptably high morbidity and mortality associated with COVID-19. Although ICU patients have been treated with glucocorticoids, some experts have even argued, based on studies in Middle-Eastern respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome (SARS), influenza, and respiratory syncytial virus (RSV), that they are likely to do more harm than good [1, 2] . The autoinflammatory loop can exacerbate from increase innate immune response into uncontrolled MAS a spectrum that associates with increasing ferritin levels van de Veerdonk and Netea Critical Care (2020) 24:445 patients in the early phase and reports that high dose intravenous anakinra started in patients outside of the ICU was safe and resulted in clinical benefit in 72% of patients [56] . abstract: COVID-19 is an emerging disease that can manifest itself as asymptomatic or mild respiratory tract infection in the majority of individuals, but in some, it can progress into severe pneumonia and acute respiratory distress syndrome (ARDS). Inflammation is known to play a crucial role in the pathogenesis of severe infections and ARDS and evidence is emerging that the IL-1/IL-6 pathway is highly upregulated in patients with severe disease. These findings open new avenues for host-directed therapies in patients with symptomatic SARS-CoV-2 infection and might in addition to antiviral treatment be enough to curb the currently unacceptably high morbidity and mortality associated with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32682440/ doi: 10.1186/s13054-020-03166-0 id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 words: 6706.0 sentences: 341.0 pages: flesch: 52.0 cache: ./cache/cord-309043-dlmx12vt.txt txt: ./txt/cord-309043-dlmx12vt.txt summary: The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. abstract: The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies. url: https://www.ncbi.nlm.nih.gov/pubmed/17520018/ doi: 10.1371/journal.pone.0000459 id: cord-297326-n0fpu8s3 author: ÁLVAREZ, E. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 words: 4995.0 sentences: 244.0 pages: flesch: 47.0 cache: ./cache/cord-297326-n0fpu8s3.txt txt: ./txt/cord-297326-n0fpu8s3.txt summary: Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. These equations involve three stocks (SUSCEPTIBLE, LATENT, INFECTED), three auxiliary variables (prevalence, contagion rate, recovery rate) and three parameters (incubation period, case fatality, disease duration). The simulation output for the variable ''sick per day'' fit the data reported by the Hong Kong authorities (Fig. 4a) , suggesting that the model was able to reproduce the epidemic curve. These results are consistent with a previous report showing the basic reproductive numbers for different SARS epidemic curves, which supports the notion that our model is able to largely replicate the disease outbreak in Hong Kong [31] . Under these conditions, the model output fits the epidemic curve observed in the Hong Kong SARS-CoV outbreak (Fig. 4) . abstract: System dynamics approach offers great potential for addressing how intervention policies can affect the spread of emerging infectious diseases in complex and highly networked systems. Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. The dynamic model developed with system dynamics methodology included 23 variables (five states, four flows, eight auxiliary variables, six parameters), five differential equations and 12 algebraic equations. The parameters were optimized following an iterative process of simulation to fit the real data from the epidemics. Univariate and multivariate sensitivity analyses were performed to determine the reliability of the model. In addition, we discuss how further testing using this model can inform community interventions to reduce the risk in current and future outbreaks, such as the recently Middle East respiratory syndrome coronavirus (MERS-CoV) epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/25591619/ doi: 10.1017/s095026881400377x id: cord-295792-hajvtzj9 author: Álvez, Fernando title: SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date: 2020-07-03 words: 4504.0 sentences: 196.0 pages: flesch: 46.0 cache: ./cache/cord-295792-hajvtzj9.txt txt: ./txt/cord-295792-hajvtzj9.txt summary: In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice abstract: Abstract The reasons for the relative resistance of children to certain infections such as that caused by coronavirus SARS- CoV2 are not yet fully clear. Deciphering these differences can provide important information about the pathogenesis of the disease. Regarding the SARS-CoV2 virus, children are at the same risk of infection as the general population of all ages, with the most serious cases being found in infants. However, it has been reported that the disease is much less frequent than in adults and that most cases are benign or moderate (even with high viral loads), provided there are no other risk factors or underlying diseases. It is not clear why they have lower morbidity and virtually no mortality. A series of findings, relationships and behavioral patterns between the infectious agent and the child host may account for the lower incidence and a greatly attenuated clinical presentation of the disease in children. url: https://www.sciencedirect.com/science/article/pii/S0301054620301075?v=s5 doi: 10.1016/j.aller.2020.05.003 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel